Motif Alignment and Search Tool (MAST)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

If you use MAST in your research, please cite the following paper:
Timothy L. Bailey and Michael Gribskov, "Combining evidence using p-values: application to sequence homology searches", Bioinformatics, 14(1):48-54, 1998.

Inputs   |   Search Results   |   Program information   |   Documentation

Inputs

Top

Sequence Databases

The following sequence database was supplied to MAST.

Database Sequence Count Residue Count Last Modified
sample-dna-Klf1.fa 904 452000 Wed Jan 11 16:31:12 2012
Total 904 452000  

Motifs

The following motifs were supplied to MAST from "memechip_out/dreme_out/dreme.txt" last modified on Tue Jan 17 12:33:21 2012. It is recommended that motifs with a red name be removed because they have a similarity greater than 0.60 with another motif.

    Best possible match Similarity
Motif Width (+) (-) MCRCCCW TTATCW ARATA CCMCACCC ACAGMTG
MCRCCCW 7 ACACCCA TGGGTGT - 0.10 0.19 0.81 0.24
TTATCW 6 TTATCT AGATAA 0.10 - 0.32 0.08 0.17
ARATA 5 AGATA TATCT 0.19 0.32 - 0.11 0.59
CCMCACCC 8 CCACACCC GGGTGTGG 0.81 0.08 0.11 - 0.37
ACAGMTG 7 ACAGCTG CAGCTGT 0.24 0.17 0.59 0.37 -

Search Results

Top

Top Scoring Sequences

Each of the following 717 sequences has an E-value less than 8.2e+02.
The motif matches shown have a position p-value less than 0.0001.
Click on the arrow (↧) next to the E-value to view more information about a sequence.

Motif MCRCCCW
Motif TTATCW
Motif ARATA
Motif CCMCACCC
Motif ACAGMTG
Sequence E-value   Block Diagram
 
0
100
200
300
400
500
chr4:32996229-32996728 6.2
+
-
chr5:30289969-30290468 6.2
+
-
chr5:64826642-64827141 6.2
+
-
chr6:34857296-34857795 6.2
+
-
chr7:138568415-138568914 6.2
+
-
chr7:151917814-151918313 6.2
+
-
chr10:57527585-57528084 6.2
+
-
chr12:114386594-114387093 6.2
+
-
chr8:97257705-97258204 9
+
-
chr17:25039619-25040118 9
+
-
chr5:123643388-123643887 9.3
+
-
chr11:58166514-58167013 9.3
+
-
chr3:145253492-145253991 9.8
+
-
chr5:27985060-27985559 9.8
+
-
chr11:53839888-53840387 9.8
+
-
chr1:135846957-135847456 10
+
-
chr17:43466518-43467017 10
+
-
chr17:84179515-84180014 10
+
-
chr9:57618594-57619093 14
+
-
chr4:111175599-111176098 14
+
-
chr4:135730666-135731165 14
+
-
chr5:35503672-35504171 14
+
-
chr11:57590460-57590959 14
+
-
chr4:109112541-109113040 15
+
-
chr17:29575284-29575783 16
+
-
chr1:169314208-169314707 16
+
-
chr2:28462972-28463471 16
+
-
chr3:51492458-51492957 16
+
-
chr5:65203207-65203706 16
+
-
chr7:148318028-148318527 16
+
-
chr8:71137139-71137638 16
+
-
chr10:110604369-110604868 16
+
-
chr17:24289205-24289704 16
+
-
chr4:128724869-128725368 16
+
-
chr13:3866266-3866765 16
+
-
chr15:91082416-91082915 16
+
-
chr19:55941582-55942081 16
+
-
chr11:86427476-86427975 18
+
-
chr11:102226517-102227016 18
+
-
chr12:102194283-102194782 18
+
-
chr14:119195312-119195811 18
+
-
chr19:6300361-6300860 18
+
-
chr15:58719281-58719780 20
+
-
chr7:111009340-111009839 21
+
-
chr11:69759803-69760302 22
+
-
chr11:95666703-95667202 22
+
-
chr14:122643097-122643596 22
+
-
chr7:99891353-99891852 23
+
-
chr16:49777000-49777499 23
+
-
chr11:32155991-32156490 24
+
-
chr9:120025371-120025870 24
+
-
chr9:42909938-42910437 24
+
-
chr11:60988820-60989319 24
+
-
chr2:131039492-131039991 24
+
-
chr17:26651347-26651846 24
+
-
chr4:135733850-135734349 24
+
-
chr2:93306457-93306956 25
+
-
chr8:24254796-24255295 27
+
-
chr16:8686809-8687308 29
+
-
chr16:14166506-14167005 29
+
-
chr3:96108390-96108889 29
+
-
chr1:134264178-134264677 30
+
-
chr2:103797834-103798333 30
+
-
chr16:32509880-32510379 30
+
-
chr7:25940386-25940885 30
+
-
chr1:169322898-169323397 35
+
-
chr17:12397643-12398142 35
+
-
chr1:36977019-36977518 35
+
-
chr1:196501891-196502390 35
+
-
chr3:79383670-79384169 35
+
-
chr4:43977111-43977610 35
+
-
chr4:118241267-118241766 35
+
-
chr5:96888622-96889121 35
+
-
chr5:109105616-109106115 35
+
-
chr5:139858102-139858601 35
+
-
chr7:139969684-139970183 35
+
-
chr8:108344711-108345210 35
+
-
chr9:21940049-21940548 35
+
-
chr10:40924608-40925107 35
+
-
chr11:69186641-69187140 35
+
-
chr11:115367840-115368339 35
+
-
chr12:112796794-112797293 35
+
-
chr14:41760574-41761073 35
+
-
chr15:81700367-81700866 35
+
-
chr17:12229956-12230455 35
+
-
chr18:60666681-60667180 35
+
-
chr19:53259937-53260436 35
+
-
chr5:118933401-118933900 37
+
-
chr15:56455064-56455563 37
+
-
chr12:70394726-70395225 40
+
-
chr19:5922116-5922615 40
+
-
chr1:92185726-92186225 42
+
-
chr2:25742741-25743240 42
+
-
chr2:25869096-25869595 42
+
-
chr3:33209988-33210487 42
+
-
chr4:124283413-124283912 42
+
-
chr5:45951565-45952064 42
+
-
chr7:71081138-71081637 42
+
-
chr9:42938268-42938767 42
+
-
chr11:90524332-90524831 42
+
-
chr4:122963965-122964464 44
+
-
chr5:89056517-89057016 45
+
-
chr19:56465963-56466462 45
+
-
chr8:125244309-125244808 45
+
-
chr16:10384212-10384711 45
+
-
chr17:47672783-47673282 46
+
-
chr14:71023666-71024165 46
+
-
chr15:98860006-98860505 48
+
-
chr1:136638482-136638981 50
+
-
chr2:103962052-103962551 50
+
-
chr2:150491523-150492022 50
+
-
chr6:8295406-8295905 50
+
-
chr11:68709695-68710194 50
+
-
chr13:112863645-112864144 50
+
-
chr18:61379741-61380240 50
+
-
chr4:151334552-151335051 50
+
-
chr10:59256089-59256588 50
+
-
chr10:126642277-126642776 50
+
-
chr13:107890789-107891288 50
+
-
chr9:98389943-98390442 51
+
-
chr12:70884547-70885046 51
+
-
chr8:107823858-107824357 52
+
-
chr9:90156773-90157272 52
+
-
chr5:118929927-118930426 53
+
-
chr1:88208803-88209302 54
+
-
chr2:103324308-103324807 54
+
-
chr4:44084689-44085188 54
+
-
chr6:86027772-86028271 54
+
-
chr7:28233711-28234210 54
+
-
chr7:110976195-110976694 54
+
-
chr9:118957547-118958046 54
+
-
chr10:60612190-60612689 54
+
-
chr11:94858859-94859358 54
+
-
chr13:110473134-110473633 54
+
-
chr14:79702844-79703343 54
+
-
chr16:91352914-91353413 54
+
-
chr17:5112057-5112556 54
+
-
chr19:10736425-10736924 54
+
-
chr7:149571622-149572121 54
+
-
chr2:122090760-122091259 56
+
-
chr12:77577208-77577707 58
+
-
chr15:38999170-38999669 58
+
-
chr6:146178951-146179450 58
+
-
chr13:25281583-25282082 58
+
-
chr2:72858951-72859450 60
+
-
chr15:34829705-34830204 60
+
-
chr7:19832207-19832706 61
+
-
chr9:107206718-107207217 61
+
-
chr17:28960252-28960751 61
+
-
chr15:83139085-83139584 62
+
-
chr8:97323995-97324494 62
+
-
chr1:133343883-133344382 63
+
-
chr5:143814329-143814828 63
+
-
chr8:97963970-97964469 63
+
-
chr9:21069279-21069778 63
+
-
chr4:129140945-129141444 64
+
-
chr13:112833730-112834229 64
+
-
chr1:135693776-135694275 64
+
-
chr4:62177553-62178052 65
+
-
chr5:144579744-144580243 66
+
-
chr14:63796627-63797126 66
+
-
chr6:38866493-38866992 66
+
-
chr9:20561645-20562144 66
+
-
chr19:5845899-5846398 68
+
-
chr1:183187347-183187846 70
+
-
chr16:8655671-8656170 71
+
-
chr9:108243080-108243579 71
+
-
chr7:105490727-105491226 72
+
-
chr9:7790421-7790920 72
+
-
chr2:77015535-77016034 74
+
-
chr4:128532893-128533392 74
+
-
chr18:23868477-23868976 74
+
-
chr9:75406569-75407068 75
+
-
chr10:93585404-93585903 75
+
-
chr11:84636993-84637492 75
+
-
chr14:56154883-56155382 75
+
-
chr16:91804489-91804988 75
+
-
chr1:137838164-137838663 75
+
-
chr2:5220411-5220910 75
+
-
chr2:156710230-156710729 75
+
-
chr3:95468979-95469478 75
+
-
chr3:104843905-104844404 75
+
-
chr4:154862420-154862919 75
+
-
chr9:113850421-113850920 75
+
-
chr11:117187372-117187871 75
+
-
chr3:84162553-84163052 76
+
-
chr4:118863136-118863635 77
+
-
chr17:47735006-47735505 77
+
-
chr19:55293251-55293750 77
+
-
chr11:97307230-97307729 77
+
-
chr13:73612725-73613224 77
+
-
chr1:134941435-134941934 79
+
-
chr18:62325792-62326291 79
+
-
chr3:138480016-138480515 79
+
-
chr11:32150818-32151317 79
+
-
chr14:61272713-61273212 79
+
-
chr18:57137388-57137887 79
+
-
chr8:73222228-73222727 82
+
-
chr4:111173963-111174462 83
+
-
chr9:66197482-66197981 83
+
-
chr15:58828420-58828919 86
+
-
chr5:33616214-33616713 87
+
-
chr10:111261811-111262310 87
+
-
chr1:186481027-186481526 87
+
-
chr17:45884716-45885215 87
+
-
chr4:149892777-149893276 88
+
-
chr4:154303237-154303736 88
+
-
chr7:91033422-91033921 88
+
-
chr11:62363716-62364215 88
+
-
chr17:85277579-85278078 88
+
-
chr7:148956813-148957312 89
+
-
chr7:128112657-128113156 89
+
-
chr8:109927244-109927743 89
+
-
chr3:89612431-89612930 90
+
-
chr18:62120158-62120657 90
+
-
chr5:107138559-107139058 90
+
-
chr5:65255865-65256364 91
+
-
chr5:139672808-139673307 91
+
-
chr6:72223026-72223525 91
+
-
chr7:149565910-149566409 91
+
-
chr2:121963844-121964343 92
+
-
chr4:153400588-153401087 92
+
-
chr5:77087237-77087736 92
+
-
chr5:116395144-116395643 92
+
-
chr7:111007530-111008029 92
+
-
chr7:111019148-111019647 92
+
-
chr8:87494750-87495249 92
+
-
chr9:44096486-44096985 92
+
-
chr11:104890315-104890814 92
+
-
chr17:24339802-24340301 92
+
-
chr15:98886719-98887218 94
+
-
chr19:6236070-6236569 95
+
-
chr16:33115731-33116230 96
+
-
chr9:65063485-65063984 97
+
-
chr18:54151151-54151650 1e+02
+
-
chr13:3862103-3862602 1e+02
+
-
chr3:19087307-19087806 1e+02
+
-
chr7:35754127-35754626 1e+02
+
-
chr11:102236405-102236904 1e+02
+
-
chr12:112505815-112506314 1e+02
+
-
chr4:154285745-154286244 1e+02
+
-
chr10:76673549-76674048 1.1e+02
+
-
chr2:84681996-84682495 1.1e+02
+
-
chr5:121049618-121050117 1.1e+02
+
-
chr12:27135944-27136443 1.1e+02
+
-
chr17:28946040-28946539 1.1e+02
+
-
chr18:85054319-85054818 1.1e+02
+
-
chr1:156887119-156887618 1.1e+02
+
-
chr15:76083900-76084399 1.1e+02
+
-
chr15:85935655-85936154 1.1e+02
+
-
chr14:70506762-70507261 1.1e+02
+
-
chr15:78243390-78243889 1.1e+02
+
-
chr16:6504644-6505143 1.1e+02
+
-
chr11:90547830-90548329 1.1e+02
+
-
chr5:108943418-108943917 1.1e+02
+
-
chr17:26079525-26080024 1.1e+02
+
-
chr19:4558365-4558864 1.1e+02
+
-
chr1:55087778-55088277 1.1e+02
+
-
chr4:109725663-109726162 1.1e+02
+
-
chr11:61433608-61434107 1.1e+02
+
-
chr12:33905458-33905957 1.1e+02
+
-
chr2:167169233-167169732 1.1e+02
+
-
chr4:44016940-44017439 1.1e+02
+
-
chr5:137730860-137731359 1.1e+02
+
-
chr5:143681950-143682449 1.1e+02
+
-
chr12:110018192-110018691 1.1e+02
+
-
chr14:69922788-69923287 1.1e+02
+
-
chr2:180447046-180447545 1.2e+02
+
-
chr17:35879925-35880424 1.2e+02
+
-
chr2:152650541-152651040 1.2e+02
+
-
chr4:9588078-9588577 1.2e+02
+
-
chr1:82633924-82634423 1.2e+02
+
-
chr7:148354574-148355073 1.2e+02
+
-
chr9:44773667-44774166 1.2e+02
+
-
chr4:153535135-153535634 1.2e+02
+
-
chr5:64979148-64979647 1.2e+02
+
-
chr9:122282103-122282602 1.2e+02
+
-
chrX:68727377-68727876 1.2e+02
+
-
chr11:30901439-30901938 1.2e+02
+
-
chr7:26004857-26005356 1.2e+02
+
-
chr8:74937710-74938209 1.2e+02
+
-
chr11:99087548-99088047 1.3e+02
+
-
chr17:29067183-29067682 1.3e+02
+
-
chr10:107550274-107550773 1.3e+02
+
-
chr5:138127197-138127696 1.3e+02
+
-
chr6:72324694-72325193 1.3e+02
+
-
chr6:144850420-144850919 1.3e+02
+
-
chr7:25993969-25994468 1.3e+02
+
-
chr19:5841547-5842046 1.3e+02
+
-
chr7:16987195-16987694 1.3e+02
+
-
chr15:83253024-83253523 1.3e+02
+
-
chr1:157198531-157199030 1.3e+02
+
-
chr9:121335573-121336072 1.3e+02
+
-
chr1:77295122-77295621 1.3e+02
+
-
chr3:154291294-154291793 1.3e+02
+
-
chr4:151104036-151104535 1.3e+02
+
-
chr5:118932602-118933101 1.3e+02
+
-
chr11:96817330-96817829 1.3e+02
+
-
chr13:56459266-56459765 1.3e+02
+
-
chr14:41775477-41775976 1.3e+02
+
-
chr6:121187425-121187924 1.3e+02
+
-
chr12:3795439-3795938 1.3e+02
+
-
chr15:79757891-79758390 1.3e+02
+
-
chr3:121365445-121365944 1.4e+02
+
-
chr9:107982359-107982858 1.4e+02
+
-
chr8:85946912-85947411 1.4e+02
+
-
chr12:82044358-82044857 1.4e+02
+
-
chr5:129513006-129513505 1.4e+02
+
-
chr6:35303481-35303980 1.5e+02
+
-
chr11:107308644-107309143 1.5e+02
+
-
chr14:69939827-69940326 1.5e+02
+
-
chr10:40726424-40726923 1.5e+02
+
-
chr16:91086848-91087347 1.5e+02
+
-
chr12:58298570-58299069 1.5e+02
+
-
chr6:81915769-81916268 1.5e+02
+
-
chr2:167454295-167454794 1.5e+02
+
-
chr18:74156786-74157285 1.5e+02
+
-
chr11:57767826-57768325 1.5e+02
+
-
chr12:80012617-80013116 1.5e+02
+
-
chr1:170140427-170140926 1.5e+02
+
-
chr11:104842983-104843482 1.5e+02
+
-
chr3:153454530-153455029 1.6e+02
+
-
chr5:37112216-37112715 1.6e+02
+
-
chr4:46419779-46420278 1.6e+02
+
-
chr15:82060183-82060682 1.6e+02
+
-
chr14:70865967-70866466 1.6e+02
+
-
chr2:31940725-31941224 1.6e+02
+
-
chr7:148976466-148976965 1.6e+02
+
-
chr13:20241988-20242487 1.7e+02
+
-
chr11:115626400-115626899 1.7e+02
+
-
chr4:41334759-41335258 1.7e+02
+
-
chr13:57679178-57679677 1.7e+02
+
-
chr16:34031622-34032121 1.7e+02
+
-
chr1:183146440-183146939 1.7e+02
+
-
chr8:4656602-4657101 1.7e+02
+
-
chr14:51490140-51490639 1.7e+02
+
-
chr9:31059932-31060431 1.7e+02
+
-
chr19:24348713-24349212 1.7e+02
+
-
chr12:85791925-85792424 1.7e+02
+
-
chr5:144685597-144686096 1.8e+02
+
-
chr6:41654153-41654652 1.8e+02
+
-
chr3:60589030-60589529 1.8e+02
+
-
chr1:134979850-134980349 1.8e+02
+
-
chr11:89087923-89088422 1.8e+02
+
-
chr11:101309433-101309932 1.8e+02
+
-
chr9:114375902-114376401 1.8e+02
+
-
chr11:87563495-87563994 1.9e+02
+
-
chr11:121294775-121295274 1.9e+02
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chr1:33631214-33631713 7.5e+02
+
-
chr3:88305500-88305999 7.5e+02
+
-
chr1:181078666-181079165 7.5e+02
+
-
chr6:70740091-70740590 7.6e+02
+
-
chr9:118353189-118353688 7.6e+02
+
-
chr1:22562531-22563030 7.7e+02
+
-
chr9:107198663-107199162 7.7e+02
+
-
chr15:22324758-22325257 7.7e+02
+
-
chr15:78888127-78888626 7.7e+02
+
-
chr15:36250679-36251178 7.8e+02
+
-
chr19:7017107-7017606 7.8e+02
+
-
chr13:104819583-104820082 7.8e+02
+
-
chr1:157123773-157124272 7.8e+02
+
-
chr11:115373883-115374382 7.8e+02
+
-
chr12:70465144-70465643 7.8e+02
+
-
chr5:22924217-22924716 7.8e+02
+
-
chr6:97129434-97129933 7.8e+02
+
-
chr8:98213265-98213764 7.8e+02
+
-
chr12:32828022-32828521 7.9e+02
+
-
chr2:25148316-25148815 7.9e+02
+
-
chr10:126640072-126640571 7.9e+02
+
-
chr11:115372413-115372912 7.9e+02
+
-
chr18:65586915-65587414 8e+02
+
-
chr4:76585120-76585619 8e+02
+
-
chr5:148390438-148390937 8e+02
+
-
chr9:104996246-104996745 8e+02
+
-
chr16:30565674-30566173 8e+02
+
-
chr5:129723300-129723799 8e+02
+
-
chr7:134369102-134369601 8e+02
+
-
chr4:3153985-3154484 8e+02
+
-
chr19:5896488-5896987 8.1e+02
+
-
chr14:63729029-63729528 8.1e+02
+
-
chr4:44262429-44262928 8.1e+02
+
-
chr7:106951865-106952364 8.1e+02
+
-
chr11:32145485-32145984 8.1e+02
+
-
chr13:112837038-112837537 8.1e+02
+
-
chr15:96173312-96173811 8.2e+02
+
-
chr1:37000448-37000947 8.2e+02
+
-
chr4:56610205-56610704 8.2e+02
+
-
chr10:20961510-20962009 8.2e+02
+
-
chr13:45499434-45499933 8.2e+02
+
-
Motif MCRCCCW
Motif TTATCW
Motif ARATA
Motif CCMCACCC
Motif ACAGMTG
Top
MAST version
4.8.0 (Release date: Tue Jan 17 11:51:47 EST 2012)
Reference
Timothy L. Bailey and Michael Gribskov, "Combining evidence using p-values: application to sequence homology searches", Bioinformatics, 14(1):48-54, 1998.
Command line summary

Background letter frequencies (from non-redundant database):
A: 0.274   C: 0.225   G: 0.225   T: 0.274

Result calculation took 0.252 seconds
show model parameters...

Explanation of MAST Results

Top

The MAST results consist of

Inputs

MAST received the following inputs.

Sequence Databases

This table summarises the sequence databases specified to MAST.

Database
The name of the database file.
Sequence Count
The number of sequences in the database.
Residue Count
The number of residues in the database.
Motifs

Summary of the motifs specified to MAST.

Name
The name of the motif. If the motif has been removed or removal is recommended to avoid highly similar motifs then it will be displayed in red text.
Width
The width of the motif. No gaps are allowed in motifs supplied to MAST as it only works for motifs of a fixed width.
Best possible match
The sequence that would achieve the best possible match score and its reverse complement for nucleotide motifs.
Similarity
MAST computes the pairwise correlations between each pair of motifs. The correlation between two motifs is the maximum sum of Pearson's correlation coefficients for aligned columns divided by the width of the shorter motif. The maximum is found by trying all alignments of the two motifs. Motifs with correlations below 0.60 have little effect on the accuracy of the combined scores. Pairs of motifs with higher correlations should be removed from the query. Correlations above the supplied threshold are shown in red text.
Nominal Order and Spacing

This diagram shows the normal spacing of the motifs specified to MAST.

Search Results

MAST provides the following motif search results.

Top Scoring Sequences

This table summarises the top scoring sequences with a Sequence E-value better than the threshold (default 10). The sequences are sorted by the Sequence E-value from most to least significant.

Sequence
The name of the sequence. This maybe be linked to search a sequence database for the sequence name.
E-value
The E-value of the sequence. For DNA only; if strands were scored seperately then there will be two E-values for the sequence seperated by a "/". The score for the provided sequence will be first and the score for the reverse-complement will be second.
Click on this to show additional information about the sequence such as a description, combined p-value and the annotated sequence.
Block Diagram
The block diagram shows the best non-overlapping tiling of motif matches on the sequence.
  • The length of the line shows the length of a sequence relative to all the other sequences.
  • A block is shown where the positional p-value of a motif is less (more significant) than the significance threshold which is 0.0001 by default.
  • If a significant motif match (as specified above) overlaps other significant motif matches then it is only displayed as a block if its positional p-value is less (more significant) then the product of the positional p-values of the significant matches that it overlaps.
  • The position of a block shows where a motif has matched the sequence.
  • The width of a block shows the width of the motif relative to the length of the sequence.
  • The colour and border of a block identifies the matching motif as in the legend.
  • The height of a block gives an indication of the significance of the match as taller blocks are more significant. The height is calculated to be proportional to the negative logarithm of the positional p-value, truncated at the height for a p-value of 1e-10.
  • Hovering the mouse cursor over the block causes the display of the motif name and other details in the hovering text.
  • DNA only; blocks displayed above the line are a match on the given DNA, whereas blocks displayed below the line are matches to the reverse-complement of the given DNA.
  • DNA only; when strands are scored separately then blocks may overlap on opposing strands.
Additional Sequence Information

Clicking on the ↧ link expands a box below the sequence with additional information and adds two dragable buttons below the block diagram.

Description
The description appearing after the identifier in the fasta file used to specify the sequence.
Combined p-value
The combined p-value of the sequence. DNA only; if strands were scored seperately then there will be two p-values for the sequence seperated by a "/". The score for the provided sequence will be first and the score for the reverse-complement will be second.
Annotated Sequence
The annotated sequence shows a portion of the sequence with the matching motif sequences displayed above. The displayed portion of the sequence can be modified by sliding the two buttons below the sequence block diagram so that the portion you want to see is between the two needles attached to the buttons. By default the two buttons move together but you can drag one individually by holding shift before you start the drag. If the strands were scored seperately then they can't be both displayed at once due to overlaps and so a radio button offers the choice of strand to display.

Scoring

MAST scores sequences using the following measures.

Position score calculation

The score for the match of a position in a sequence to a motif is computed by by summing the appropriate entry from each column of the position-dependent scoring matrix that represents the motif. Sequences shorter than one or more of the motifs are skipped.

Position p-value

The position p-value of a match is the probability of a single random subsequence of the length of the motif scoring at least as well as the observed match.

Sequence p-value

The sequence p-value of a score is defined as the probability of a random sequence of the same length containing some match with as good or better a score.

Combined p-value

The combined p-value of a sequence measures the strength of the match of the sequence to all the motifs and is calculated by

  1. finding the score of the single best match of each motif to the sequence (best matches may overlap),
  2. calculating the sequence p-value of each score,
  3. forming the product of the p-values,
  4. taking the p-value of the product.
Sequence E-value

The E-value of a sequence is the expected number of sequences in a random database of the same size that would match the motifs as well as the sequence does and is equal to the combined p-value of the sequence times the number of sequences in the database.