Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168067.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_316, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35514
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Found at i:482 original size:22 final size:22
Alignment explanation
Indices: 457--610 Score: 112
Period size: 22 Copynumber: 6.9 Consensus size: 22
447 AACTTAGTGG
*
457 TAAATCATTTATAATATAGTAA
1 TAAATCATTGATAATATAGTAA
* * *
479 TAAATATAATTTATAACATAGTAA
1 T-AA-ATCATTGATAATATAGTAA
* * * *
503 TAAATCAATGATAATTTAATAG
1 TAAATCATTGATAATATAGTAA
* *
525 CAAATCATTGATAATTTAGTAA
1 TAAATCATTGATAATATAGTAA
* * *
547 AAAATCATTGATAGCT-TAGTAG
1 TAAATCATTGATA-ATATAGTAA
* * *
569 TAAGTCACTGATAACATAGTAA
1 TAAATCATTGATAATATAGTAA
* *
591 TAAATCAGTGATAATGTAGT
1 TAAATCATTGATAATATAGT
611 TATCAATTAG
Statistics
Matches: 102, Mismatches: 26, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
22 79 0.77
23 5 0.05
24 18 0.18
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (22 bp):
TAAATCATTGATAATATAGTAA
Found at i:553 original size:44 final size:44
Alignment explanation
Indices: 491--605 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 44
481 AATATAATTT
*
491 ATAACATAGTAATAAATCAATGATAATTTAATAGCAAATCATTG
1 ATAACATAGTAATAAATCAATGATAATTTAATAGCAAATCACTG
** * * ** * * *
535 ATAATTTAGTAAAAAATCATTGATAGCTTAGTAGTAAGTCACTG
1 ATAACATAGTAATAAATCAATGATAATTTAATAGCAAATCACTG
*
579 ATAACATAGTAATAAATCAGTGATAAT
1 ATAACATAGTAATAAATCAATGATAAT
606 GTAGTTATCA
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (44 bp):
ATAACATAGTAATAAATCAATGATAATTTAATAGCAAATCACTG
Found at i:1406 original size:22 final size:22
Alignment explanation
Indices: 1381--1423 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1371 ATGATAGTAA
* *
1381 TAAATCATTGTTAACTTAGTGT
1 TAAATCATCGATAACTTAGTGT
*
1403 TAAATTATCGATAACTTAGTG
1 TAAATCATCGATAACTTAGTG
1424 CTAGATAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (22 bp):
TAAATCATCGATAACTTAGTGT
Found at i:1531 original size:22 final size:22
Alignment explanation
Indices: 1461--1521 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
1451 TTAGTGATGA
1461 CAATAAATCAATGATAATTTAG
1 CAATAAATCAATGATAATTTAG
1483 CAATAAATCAATGATAATTTAG
1 CAATAAATCAATGATAATTTAG
*
1505 CAATAAATCATTGATAA
1 CAATAAATCAATGATAA
1522 CTTTGGAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (22 bp):
CAATAAATCAATGATAATTTAG
Found at i:1619 original size:25 final size:25
Alignment explanation
Indices: 1575--1625 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1565 AACTAACCTT
*
1575 AATAGTAAATCAAATAATAAATTTA
1 AATAGTAAATCAAATAATAAACTTA
* * *
1600 AATAGTAAATGAATTGATAAACTTA
1 AATAGTAAATCAAATAATAAACTTA
1625 A
1 A
1626 TCATAAAGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (25 bp):
AATAGTAAATCAAATAATAAACTTA
Found at i:2070 original size:29 final size:29
Alignment explanation
Indices: 2022--2098 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
2012 AACAATTATC
*
2022 CAAGTATCACATTAGTAAATAGATTTATAGTT
1 CAAGTATCACA-T--TAAATAGATTTAAAGTT
* **
2054 TAAGTATCACATTAAATATTTTTAAAGTT
1 CAAGTATCACATTAAATAGATTTAAAGTT
2083 CAAGTATCACATTAAA
1 CAAGTATCACATTAAA
2099 CAATTTAGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 29 0.73
31 1 0.03
32 10 0.25
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (29 bp):
CAAGTATCACATTAAATAGATTTAAAGTT
Found at i:5031 original size:20 final size:20
Alignment explanation
Indices: 4997--5037 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
4987 CTCCATTTTA
4997 ATTAAAAAGAGATTCA-AAT
1 ATTAAAAAGAGATTCACAAT
*
5016 ATTAAAAAGATTATTCACAAT
1 ATTAAAAAGA-GATTCACAAT
5037 A
1 A
5038 AATTTTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 5 0.26
21 4 0.21
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29
Consensus pattern (20 bp):
ATTAAAAAGAGATTCACAAT
Found at i:5489 original size:13 final size:13
Alignment explanation
Indices: 5471--5495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5461 ATGTATTTTT
5471 ATTACAAAATGAA
1 ATTACAAAATGAA
5484 ATTACAAAATGA
1 ATTACAAAATGA
5496 TTTATATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (13 bp):
ATTACAAAATGAA
Found at i:6711 original size:2 final size:2
Alignment explanation
Indices: 6704--6738 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6694 GTACTCTTTC
6704 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6739 TCCAAATATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8932 original size:39 final size:39
Alignment explanation
Indices: 8878--8952 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
8868 GGTATATATG
8878 TATATATATATATATATATGGCTTTCTATTGAAATTATA
1 TATATATATATATATATATGGCTTTCTATTGAAATTATA
*
8917 TATATATATATATATATTTGGCTTTCTATTGAAATT
1 TATATATATATATATATATGGCTTTCTATTGAAATT
8953 GTGCCTTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (39 bp):
TATATATATATATATATATGGCTTTCTATTGAAATTATA
Found at i:9286 original size:15 final size:15
Alignment explanation
Indices: 9246--9284 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
9236 TGGAACCATC
9246 TTTC-TTTC-TTTCT
1 TTTCTTTTCTTTTCT
9259 TTTCTTTTCTTTTCT
1 TTTCTTTTCTTTTCT
9274 TTT-TTTT-TTTT
1 TTTCTTTTCTTTT
9285 TTTGAAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 8 0.33
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTCTTTTCTTTTCT
Found at i:9287 original size:5 final size:5
Alignment explanation
Indices: 9246--9284 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
9236 TGGAACCATC
9246 TTTC- TTTC- TTTCT TTTCT TTTCT TTTCT TTT-T TTT-T TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
9285 TTTGAAAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 16 0.47
5 18 0.53
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTCT
Found at i:18423 original size:353 final size:358
Alignment explanation
Indices: 17719--18550 Score: 1089
Period size: 353 Copynumber: 2.3 Consensus size: 358
17709 GAATATATCA
* * * *
17719 CCACACAAATTCTAACACTATTATTGAAGGCGTATATTCCAAGA-AATACACCTTTAATAATTTC
1 CCACACAAATTCTAACACTGTTATTGAAGGCATATATT-TAAGATAA-ACACCTTTAATAATTCC
* * *
17783 TATCATAGTTTGTAGT-TAATTACTGAAGGCGGTTGCAGAAAACAACGCCTTCAATAA-AATCCA
64 TATCACAGTTTGTA-TATAATTACTGAAGGCGGTTACAG-AAACAATGCCTTCAATAATAATCCA
* * * * *
17846 ATACAAAAACTTTTCTCGAATTATTAAAGGCGTCTTTTATTATTACACACCTTCAATATACCACA
127 ATACAAAAACATTTCTAGAATTATTAAAGACGCCTTTTATTATAACACACCTTCAATATACCACA
* *
17911 ATGGTAATAGAAGGCGTTTATTAAAAAGGACATTCAATATATCTTTAAACTTAGTAATCCATTAC
192 ATGGTAATAGAAGGCATTTATTAAAAAAGACATTCAATATATCTTTAAACTTAGTAATCCATTAC
* * * * * *
17976 TGAATGCGTTTGTTAATTAACAGACGCCTTCAAAATTTTTTCACTTAATATTTTGAGAATTATTA
257 TAAAGGCGTTTGTTAATTAACAGACACCTTCAAAATTTTTCCACTAAATATGTTGAGAATTATTA
*
18041 AAGGCGTCTCCTATTATAAAATGCTTTCTATATACTG
322 AAGGCGTCTCCTACTATAAAATGCTTTCTATATACTG
*
18078 CCACACAAATTCTAACACTGTTATTGAAGGCATATATTTAAGATAGACACCTTTAATAATTCCTA
1 CCACACAAATTCTAACACTGTTATTGAAGGCATATATTTAAGATAAACACCTTTAATAATTCCTA
* * * ** * *
18143 TCACAGTTTCTATATAATTACTGAAGGCGATTTCAG-AA-AATGCCTTCAATAATTTTTC-TTA-
66 TCACAGTTTGTATATAATTACTGAAGGCGGTTACAGAAACAATGCCTTCAATAATAATCCAATAC
* *
18204 AAAAA-ATTTCGTAG-ATTATTAAAGACGCCTTTTATTATAA-ACCGCCTTCAATATACCACGAT
131 AAAAACATTTC-TAGAATTATTAAAGACGCCTTTTATTATAACA-CACCTTCAATATACCACAAT
*
18266 GGTAATAGAAGGCATTTATTAGAAAAAGAGCCTTCAATATA-CATTTAAACTTAGTAATCCATTA
194 GGTAATAGAAGGCATTTATTA-AAAAAGA-CATTCAATATATC-TTTAAACTTAGTAATCCATTA
18330 CTAAAGGCGTTTGTTAA-TAACAGACACCTTCAAAATTTTTCCACTAAATATGTTGAGAATTATT
256 CTAAAGGCGTTTGTTAATTAACAGACACCTTCAAAATTTTTCCACTAAATATGTTGAGAATTATT
* **
18394 AAAGGTGTCTTTTACTATAAAAT-CTTTCTATATACTG
321 AAAGGCGTCTCCTACTATAAAATGCTTTCTATATACTG
* * ** *
18431 CCACACAAATTATAACACTG-TATTGAAGGCATATATTTAAAATAAATGCCTTTAATAATTCTTA
1 CCACACAAATTCTAACACTGTTATTGAAGGCATATATTTAAGATAAACACCTTTAATAATTCCTA
* * *
18495 TCACAGTTTGTATATAATTAATGAATGCGGTTACAGATAATAATGCCTTCAATAAT
66 TCACAGTTTGTATATAATTACTGAAGGCGGTTACAGA-AACAATGCCTTCAATAAT
18551 CTTCCAAAAA
Statistics
Matches: 417, Mismatches: 45, Indels: 26
0.85 0.09 0.05
Matches are distributed among these distances:
352 71 0.17
353 98 0.24
354 78 0.19
355 76 0.18
356 4 0.01
357 1 0.00
358 52 0.12
359 37 0.09
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (358 bp):
CCACACAAATTCTAACACTGTTATTGAAGGCATATATTTAAGATAAACACCTTTAATAATTCCTA
TCACAGTTTGTATATAATTACTGAAGGCGGTTACAGAAACAATGCCTTCAATAATAATCCAATAC
AAAAACATTTCTAGAATTATTAAAGACGCCTTTTATTATAACACACCTTCAATATACCACAATGG
TAATAGAAGGCATTTATTAAAAAAGACATTCAATATATCTTTAAACTTAGTAATCCATTACTAAA
GGCGTTTGTTAATTAACAGACACCTTCAAAATTTTTCCACTAAATATGTTGAGAATTATTAAAGG
CGTCTCCTACTATAAAATGCTTTCTATATACTG
Found at i:25003 original size:21 final size:20
Alignment explanation
Indices: 24970--25015 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
24960 ATAATTTTGG
24970 TTTTGATAACTTTTG-ATAAA
1 TTTTGATAACTTTTGTAT-AA
*
24990 TTTTTATAACCTTTTGTATAA
1 TTTTGATAA-CTTTTGTATAA
25011 TTTTG
1 TTTTG
25016 GTAATTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 8 0.36
21 12 0.55
22 2 0.09
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTTGATAACTTTTGTATAA
Found at i:25030 original size:21 final size:22
Alignment explanation
Indices: 25006--25099 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 22
24996 TAACCTTTTG
25006 TATAATTTTGGTAATTTA-TGA
1 TATAATTTTGGTAATTTATTGA
* * * *
25027 TATAAGTTTAGT-AGTCATTGA
1 TATAATTTTGGTAATTTATTGA
* *
25048 TATAATTTTGATAATTT-TTTA
1 TATAATTTTGGTAATTTATTGA
* * **
25069 TAAAATTTTTGTAACCTATTGA
1 TATAATTTTGGTAATTTATTGA
25091 TATAATTTT
1 TATAATTTT
25100 AATAATCTTT
Statistics
Matches: 53, Mismatches: 17, Indels: 5
0.71 0.23 0.07
Matches are distributed among these distances:
20 3 0.06
21 37 0.70
22 13 0.25
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (22 bp):
TATAATTTTGGTAATTTATTGA
Found at i:25076 original size:63 final size:63
Alignment explanation
Indices: 24982--25100 Score: 141
Period size: 63 Copynumber: 1.9 Consensus size: 63
24972 TTGATAACTT
* * * **
24982 TTGATAAATTTTTATAACCTTTTGTATAATTTTGGTAATTTA-TGATATAAGTTTAGTAGTCA
1 TTGATAAATTTTGATAACCTTTTATAAAATTTTGGTAACCTATTGATATAAGTTTAGTAGTCA
** * *
25044 TTGATATAATTTTGATAATTTTTTATAAAATTTTTGTAACCTATTGATATAATTTTA
1 TTGATA-AATTTTGATAACCTTTTATAAAATTTTGGTAACCTATTGATATAAGTTTA
25101 ATAATCTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
62 6 0.13
63 28 0.61
64 12 0.26
ACGTcount: A:0.34, C:0.04, G:0.10, T:0.52
Consensus pattern (63 bp):
TTGATAAATTTTGATAACCTTTTATAAAATTTTGGTAACCTATTGATATAAGTTTAGTAGTCA
Found at i:25091 original size:32 final size:34
Alignment explanation
Indices: 25055--25134 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 34
25045 TGATATAATT
25055 TTGATAATTTTTTATAAAAT-TTTTG-TAACCTA
1 TTGATAATTTTTTATAAAATCTTTTGATAACCTA
* * *
25087 TTGAT-ATAATTTTA-ATAATCTTTTGATAACTTA
1 TTGATAAT-TTTTTATAAAATCTTTTGATAACCTA
25120 -TGATATATTTTTTAT
1 TTGATA-ATTTTTTAT
25135 GATTATTGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
31 6 0.16
32 19 0.50
33 11 0.29
34 2 0.05
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (34 bp):
TTGATAATTTTTTATAAAATCTTTTGATAACCTA
Found at i:25415 original size:22 final size:22
Alignment explanation
Indices: 25387--25441 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
25377 AGTATAATAA
*
25387 AAGTTATCAATTATTGACAATT
1 AAGTTATCAATTATTGACAACT
* * *
25409 AAGTTATCAGTTATTTACTACT
1 AAGTTATCAATTATTGACAACT
25431 AAGTTATCAAT
1 AAGTTATCAAT
25442 AATATACTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (22 bp):
AAGTTATCAATTATTGACAACT
Found at i:25449 original size:22 final size:22
Alignment explanation
Indices: 25408--25459 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
25398 TATTGACAAT
* * *
25408 TAAGTTATCAGTTATTTACTAC
1 TAAGTTATCAATAATATACTAC
25430 TAAGTTATCAATAATATACTAC
1 TAAGTTATCAATAATATACTAC
*
25452 TAAATTAT
1 TAAGTTAT
25460 GAAGGATTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (22 bp):
TAAGTTATCAATAATATACTAC
Found at i:25498 original size:22 final size:22
Alignment explanation
Indices: 25456--25512 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
25446 TACTACTAAA
* * *
25456 TTATGAAGGATTTGCTATTAAT
1 TTATGAAAGATTTGCCATTAAG
*
25478 TTATGAAAGATTTGCCGTTAAG
1 TTATGAAAGATTTGCCATTAAG
25500 TTAT-AAATGATTT
1 TTATGAAA-GATTT
25513 ACCAATCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (22 bp):
TTATGAAAGATTTGCCATTAAG
Found at i:25801 original size:22 final size:23
Alignment explanation
Indices: 25776--25835 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
25766 TTTACTATTT
25776 AATTTTTAATT-ATTTATCACAA
1 AATTTTTAATTGATTTATCACAA
** *
25798 AATTACT-ATTGATTTATCACTA
1 AATTTTTAATTGATTTATCACAA
25820 AATTATTT-A-TGATTTA
1 AATT-TTTAATTGATTTA
25836 CTACCAAGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 3 0.10
22 26 0.84
23 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.50
Consensus pattern (23 bp):
AATTTTTAATTGATTTATCACAA
Found at i:26262 original size:11 final size:11
Alignment explanation
Indices: 26246--26280 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
26236 ATTTATTTAC
26246 TATTAAGTTAT
1 TATTAAGTTAT
*
26257 TATTAATTTAT
1 TATTAAGTTAT
26268 TATTAAGTTAT
1 TATTAAGTTAT
26279 TA
1 TA
26281 GTAATTACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (11 bp):
TATTAAGTTAT
Found at i:26265 original size:22 final size:22
Alignment explanation
Indices: 26222--26286 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
26212 TCGACTATTA
* * * *
26222 ACTACTAAATTATCATTTATTT
1 ACTATTAAGTTATTATTAATTT
26244 ACTATTAAGTTATTATTAATTT
1 ACTATTAAGTTATTATTAATTT
* *
26266 ATTATTAAGTTATTAGTAATT
1 ACTATTAAGTTATTATTAATT
26287 ACCACTAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (22 bp):
ACTATTAAGTTATTATTAATTT
Found at i:27025 original size:68 final size:68
Alignment explanation
Indices: 26947--27085 Score: 251
Period size: 68 Copynumber: 2.0 Consensus size: 68
26937 TTTACTAAAC
* *
26947 AAAAAGATAGTATATTTTTAATTATTGTTTTATTGTTGTTACCATCATTCACAATGACTTTTTTT
1 AAAAAAATAGTATATTTTTAATTATTGTTTTATTGTTGTTACCATCATTCAAAATGACTTTTTTT
27012 TAT
66 TAT
*
27015 AAAAAAATAGTATATTTTTAATTATTGTTTTATTGTTGTTATCATCATTCAAAATGACTTTTTTT
1 AAAAAAATAGTATATTTTTAATTATTGTTTTATTGTTGTTACCATCATTCAAAATGACTTTTTTT
27080 TAT
66 TAT
27083 AAA
1 AAA
27086 TTTTAATGCC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (68 bp):
AAAAAAATAGTATATTTTTAATTATTGTTTTATTGTTGTTACCATCATTCAAAATGACTTTTTTT
TAT
Found at i:29884 original size:18 final size:19
Alignment explanation
Indices: 29850--29885 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29840 GTACTTTTTT
*
29850 AGTCTAATTATTAAAAAAA
1 AGTCTAATTAATAAAAAAA
29869 AGTCTAA-TAATAAAAAA
1 AGTCTAATTAATAAAAAA
29886 TTCATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (19 bp):
AGTCTAATTAATAAAAAAA
Found at i:30526 original size:690 final size:679
Alignment explanation
Indices: 29449--31499 Score: 2287
Period size: 652 Copynumber: 3.0 Consensus size: 679
29439 TCATAAAACA
29449 TATAA-ATATATATAGTTAATATATTAAAACAAAAAATTGAAAGGCAAAAAATAGAGAAAAAAAA
1 TATAATATATATATAGTTAATATATTAAAACAAAAAATTGAAAGGC-AAAAA-A-A-AAAAAAAA
* * *
29513 ATATATATATATACTTAAATGACTTAATTATGATTATTTTTAATAAATTTATTTATTAACATAAA
62 A-ACA-A-ATATGCTTAAATGACTTAATTA--ATTATTTTTAATAAATTTATTTATCAACAT-AA
29578 TTGCATATATAATTATTTTTACAACAACTAAAGAAACAAACTTCATATAATTGTTTTATTCCTAT
121 TTGCATATATAATTATTTTTACAACAACTAAAGAAACAAACTTCATATAATTGTTTTATTCCTAT
* * * * * * *
29643 GCACATTAAGCTTTTATATAATTCTATTTGTATTTTCATTCGATAT-TAAAATCATTTTACTTAT
186 GCATATTAAGTTTTTATATTATTCTATTTGTATTTTCATTTGATGTGAAAAATTATTTTACTTAT
* *
29707 GAAATAGAGTTTAATAATAAAATAAAATCATTTAAATTAAAGTTTATAAAAAAATTACTAATGAT
251 GAAAAAGAGTTTAATAATAAAATAAAATCATTTAAATTAAAATTTAT-AAAAAATTACTAATG-T
* * *
29772 ATTTTAATTAATCACTTCTAATATTTTCGAAATTAAAATTTTATTAAGTGTTTAGTCAATCACTT
314 ATTTTAATCAATCACTT-TAATATTTTTGAAATTAAAATTTTATTAAGGGTTTAGTCAATCACTT
*
29837 TTAGTACTTTTTTAGTCTAATTATTAAAAAAAAGTCTAATAATAAAAAATTCATTTAAATTAAAA
378 TTAGTACTTTTTTAGTTTAATTATT-AAAAAAAGTCTAATAAT-AAAAATTCATTTAAATTAAAA
29902 TTTATAAAAAAAATTTACTAAAGATATTTTAGTCAATTACTGTTAATACTTAAAATTAAAATTTT
441 TTTATAAAAAAAA-TTA-TAAAGATATTTTAGTCAATTACTGTTAATACTTAAAATTAAAATTTT
* *
29967 ATGTAGTTTTATTTCTAAAAAAATTTATTTTTAATTATATTTTATTTAAATTAAATTTAAATAAA
504 AT-TAGTTTTATTTCTAATAAAATTTATTTTTAATTATATTTAATTTAAATTAAATTTAAATAAA
*
30032 TTAATAAAATTATATATTTAAGAATGAATTTGTTAATTTTAAAATTTTAT-GTGGTATTTAAATC
568 TTAATAAAATTATATATTTAAG-ATGAATTTGTTAATTTTAAAATTTTATAG-GGTATTTAAGTC
*
30096 AATCACTATTAATAGTTTTGGAGTTTACATTTTTATATATAGAT-A-AT
631 GATCACTATTAATAGTTTTGGAGTTTACATTTTTATATATAGATGATAT
*
30143 TATAATACATATATAGTTAATATATTAAAACAAAAAATTGAAAGGCAAAAAAAAAAAAAAAAACA
1 TATAATATATATATAGTTAATATATTAAAACAAAAAATTGAAAGGCAAAAAAAAAAAAAAAAACA
30208 AATATGCTTAAATGACTTAATTACAATTATTTTTAATAAATTTATTTATCAACATAAGTTGCATA
66 AATATGCTTAAATGACTTAATT--AATTATTTTTAATAAATTTATTTATCAACATAA-TTGCATA
* * * **
30273 TACAATTCTTTTTAGCAACAACTAAAGAAACAAACTTCATATAATTGCTTTATTAATATGCATAT
128 TATAATTATTTTTA-CAACAACTAAAGAAACAAACTTCATATAATTGTTTTATTCCTATGCATAT
* * *
30338 TAAGTTTTTATATTGTTCTATTTGTATTTTCATTTTATGTGAAAAATTATTTTACTTTTGAAAAA
192 TAAGTTTTTATATTATTCTATTTGTATTTTCATTTGATGTGAAAAATTATTTTACTTATGAAAAA
* *
30403 GAGTTTAATAAATAAAATAAAATCATTTAAAAGTAAAATTTATAAAAAATTTCTAATAGTATTTT
257 GAGTTTAAT-AATAAAATAAAATCATTT-AAATTAAAATTTATAAAAAATTACTAAT-GTATTTT
30468 AATCAATCACTTTAATATTTTTGAAATTAAAATTTTATTAAGGGTTTAGTCAATCACTTTTAGTA
319 AATCAATCACTTTAATATTTTTGAAATTAAAATTTTATTAAGGGTTTAGTCAATCACTTTTAGTA
30533 C-TTTTTAGTTTAATTATTAAAAAAA-TC---TAAT----A---ATTTAAATTAAAATTTAT-AA
384 CTTTTTTAGTTTAATTATTAAAAAAAGTCTAATAATAAAAATTCATTTAAATTAAAATTTATAAA
* * * * * * * * * *
30585 AAAAACTAT-TA-A-CTCTTA--AAATTAAATTTTAAGTAGTT----TT---ATTTCTCATAACT
449 AAAAATTATAAAGATATTTTAGTCAATT-ACTGTTAA-TACTTAAAATTAAAATTT-T-ATTAGT
* * * *
30638 TTAATTT-TAATCATATTTGA---TTAA--A-ATTAAATTTAAA-TAAAT-T-AATAAAAGTT-A
510 TTTATTTCTAATAAAATTT-ATTTTTAATTATATTTAATTTAAATTAAATTTAAAT-AAA-TTAA
* * * * *
30692 T-AAATTA-AG-------ATGAATTTGTTAA-TTTAAAATTTTATAGGATACTTAGGTTGATCCA
572 TAAAATTATATATTTAAGATGAATTTGTTAATTTTAAAATTTTATAGGGTATTTAAGTCGAT-CA
* * * *
30747 CTATTAACAGTTTTAGAATTCACACTTTTATATATAAGAGATAGATAGATTGAT
636 CTATTAATAGTTTTGGAGTTTACA-TTTT-TATAT-----ATAGAT-GA-T-AT
* * * * *
30801 TATTACATATATATATAGTTAATTATATTAAAAGAAAAAAATGAAA-GC----AAAAAATAGAGA
1 TA-TA-ATATATATATAGTTAA-TATATTAAAACAAAAAATTGAAAGGCAAAAAAAAAAAAAAAA
* *
30861 ACAAA-ATGCTTAAATGACTTAATT-ATTGATTTTTTAATAAATTTATTTCTC-ACATCATTGTC
63 ACAAATATGCTTAAATGACTTAATTAATT-A-TTTTTAATAAATTTATTTATCAACATAATTG-C
* * *
30923 -TATATAATTATTTTTACAACAGCTAAA-AGAACAAATTTCATAAAATTGTTTTTTATTCCCTAT
125 ATATATAATTATTTTTACAACAACTAAAGA-AACAAACTTCATATAATTG--TTTTATT-CCTAT
*
30986 GCATCATTAAGCTTTTTATATTATTCTATTTGTATTTT-ATATGATGTGAAAAATTATTTTACTT
186 GCAT-ATTAAG-TTTTTATATTATTCTATTTGTATTTTCATTTGATGTGAAAAATTATTTTACTT
31050 ATG-AAAAGAGTTTAATAATAAAAATAAAATCATTTAAATTAAAATTTAT-AAAAATTACTAATG
249 ATGAAAAAGAGTTTAATAAT-AAAATAAAATCATTTAAATTAAAATTTATAAAAAATTACTAAT-
*
31113 GTATTTTAATCAATCACTTTAAATATTTTT-AAATTAAAATTTTATTAAGGATTTAGTCAATCAC
312 GTATTTTAATCAATCACTTT-AATATTTTTGAAATTAAAATTTTATTAAGGGTTTAGTCAATCAC
*
31177 TTTTAGTACTGTTTTAGTTTAATTA-T-AAAAAAGTCTAATAATAAAAATTCATTTAAATTAAAA
376 TTTTAGTACTTTTTTAGTTTAATTATTAAAAAAAGTCTAATAATAAAAATTCATTTAAATTAAAA
* *
31240 TTTATAAAAAAAATTATTAAAGATATTTTAGTCAATTACTGTTCACACTTAAAATTAAAATTTTA
441 TTTATAAAAAAAATTA-TAAAGATATTTTAGTCAATTACTGTTAATACTTAAAATTAAAATTTT-
* * * *
31305 AATAGTTTTATTTCTCATAAATTTTATTTTTAATTAT-TTGTGATTTAAATTAAATTTAAAT-AA
504 ATTAGTTTTATTTCTAATAAAATTTATTTTTAATTATATT-TAATTTAAATTAAATTTAAATAAA
* * * *
31368 TTAATAACAAGTTATATATTTAAGGATGAATTTATTAATTTAAAAAATTTATAGGAGTATTTCAG
568 TTAATAA-AA-TTATATATTTAA-GATGAATTTGTTAATTTTAAAATTTTATAGG-GTATTTAAG
* * *
31433 TCGATTACTATTAATAATTTTGGAGTTTACACTTTTATATATAGATGATAT
629 TCGATCACTATTAATAGTTTTGGAGTTTACATTTTTATATATAGATGATAT
31484 ATATAATATATATATA
1 -TATAATATATATATA
31500 TATGCTAACG
Statistics
Matches: 1144, Mismatches: 116, Indels: 206
0.78 0.08 0.14
Matches are distributed among these distances:
645 22 0.02
646 36 0.03
647 4 0.00
648 5 0.00
650 1 0.00
651 33 0.03
652 97 0.08
653 58 0.05
654 56 0.05
655 65 0.06
656 45 0.04
657 7 0.01
658 14 0.01
659 4 0.00
660 17 0.01
661 25 0.02
662 18 0.02
663 21 0.02
664 11 0.01
665 3 0.00
666 3 0.00
667 7 0.01
668 9 0.01
669 10 0.01
670 8 0.01
671 3 0.00
672 1 0.00
673 12 0.01
674 13 0.01
675 7 0.01
676 22 0.02
678 3 0.00
679 10 0.01
680 9 0.01
681 2 0.00
682 16 0.01
683 7 0.01
684 8 0.01
685 2 0.00
686 6 0.01
687 4 0.00
688 75 0.07
689 97 0.08
690 84 0.07
691 62 0.05
692 29 0.03
693 35 0.03
694 19 0.02
695 39 0.03
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (679 bp):
TATAATATATATATAGTTAATATATTAAAACAAAAAATTGAAAGGCAAAAAAAAAAAAAAAAACA
AATATGCTTAAATGACTTAATTAATTATTTTTAATAAATTTATTTATCAACATAATTGCATATAT
AATTATTTTTACAACAACTAAAGAAACAAACTTCATATAATTGTTTTATTCCTATGCATATTAAG
TTTTTATATTATTCTATTTGTATTTTCATTTGATGTGAAAAATTATTTTACTTATGAAAAAGAGT
TTAATAATAAAATAAAATCATTTAAATTAAAATTTATAAAAAATTACTAATGTATTTTAATCAAT
CACTTTAATATTTTTGAAATTAAAATTTTATTAAGGGTTTAGTCAATCACTTTTAGTACTTTTTT
AGTTTAATTATTAAAAAAAGTCTAATAATAAAAATTCATTTAAATTAAAATTTATAAAAAAAATT
ATAAAGATATTTTAGTCAATTACTGTTAATACTTAAAATTAAAATTTTATTAGTTTTATTTCTAA
TAAAATTTATTTTTAATTATATTTAATTTAAATTAAATTTAAATAAATTAATAAAATTATATATT
TAAGATGAATTTGTTAATTTTAAAATTTTATAGGGTATTTAAGTCGATCACTATTAATAGTTTTG
GAGTTTACATTTTTATATATAGATGATAT
Found at i:30604 original size:33 final size:33
Alignment explanation
Indices: 30550--30615 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
30540 GTTTAATTAT
30550 TAAAAAAATCTAATAATTT-AAATTAAAATTTA
1 TAAAAAAATCTAATAATTTAAAATTAAAATTTA
* *
30582 TAAAAAAA-CTATTAACTCTTAAAATTAAATTTTA
1 TAAAAAAATCTAATAA-T-TTAAAATTAAAATTTA
30616 AGTAGTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 6 0.21
32 9 0.31
33 2 0.07
34 12 0.41
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAAAATCTAATAATTTAAAATTAAAATTTA
Found at i:31494 original size:11 final size:13
Alignment explanation
Indices: 31468--31499 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
31458 TTTACACTTT
31468 TATATATAGATGA
1 TATATATAGATGA
31481 TATATATA-AT-A
1 TATATATAGATGA
31492 TATATATA
1 TATATATA
31500 TATGCTAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (13 bp):
TATATATAGATGA
Done.