Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3462
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: 47091
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:13663 original size:20 final size:20
Alignment explanation
Indices: 13635--13677 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
13625 TGGGTCTAAA
*
13635 ATTAGGTGGTGAAAATTAGG
1 ATTAAGTGGTGAAAATTAGG
13655 ATTAAGTGGTGAAAATTAGG
1 ATTAAGTGGTGAAAATTAGG
13675 ATT
1 ATT
13678 TGAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (20 bp):
ATTAAGTGGTGAAAATTAGG
Found at i:15881 original size:21 final size:21
Alignment explanation
Indices: 15847--15900 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
15837 CAATCAAAAT
*
15847 CAAACATA-TTGCCCCCTAAA
1 CAAACTTATTTGCCCCCTAAA
15867 CAAACTTATTTG-CCCCTAAA
1 CAAACTTATTTGCCCCCTAAA
15887 CAAACTTATTTGCC
1 CAAACTTATTTGCC
15901 TTGTATCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.35, C:0.31, G:0.06, T:0.28
Consensus pattern (21 bp):
CAAACTTATTTGCCCCCTAAA
Found at i:18078 original size:21 final size:20
Alignment explanation
Indices: 18054--18093 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
18044 TATGAGCATT
18054 AATGATTGATGATAGATTATG
1 AATGATTGATGATAG-TTATG
*
18075 AATGTTTGATGATAGTTAT
1 AATGATTGATGATAGTTAT
18094 ACAAGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (20 bp):
AATGATTGATGATAGTTATG
Found at i:18101 original size:20 final size:21
Alignment explanation
Indices: 18059--18101 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18049 GCATTAATGA
*
18059 TTGATGATAGATTATGAATGT
1 TTGATGATAGATTATGAAAGT
18080 TTGATGATAG-TTAT-ACAAGT
1 TTGATGATAGATTATGA-AAGT
18100 TT
1 TT
18102 TGTTAAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 9 0.45
21 10 0.50
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (21 bp):
TTGATGATAGATTATGAAAGT
Found at i:21537 original size:35 final size:35
Alignment explanation
Indices: 21483--21926 Score: 408
Period size: 35 Copynumber: 12.6 Consensus size: 35
21473 TCCTCATTGA
* *
21483 AATACCATACCTACGTTTCACAACTCGGTATGGAA
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* * ** * *
21518 AACACCATACCTACTTTTCA-TGCTCGGTATGGAA
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
** * *
21552 AATACCATACCTATATTTCATAACTCAGTATGGAC
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* * * * * * * *
21587 GATGCCATACCTATGTATCATAGCTCAATATGGAC
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* ** * * *
21622 GACGCCATACCTACGTTTCATAGCTCGGTATGGA-
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* * *
21656 AATACCATACCTACGTTTCATAGCTCGGTATGGA-
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* * *
21690 AATGCCATACCTACGTTTCACAGCTCAGTATGGTT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* * *
21725 AATACCATACCTATGTTTCACAACTCGGTATGGTT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
*
21760 AATACCATACCTATGTTTCACAACTCAGTATGGAT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* * * *
21795 GATACCATACCTACATTTCACAACTTAGTATGGTT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* *
21830 AATACCATACCTACATTTCACAACTCGGTATGGAT
1 AATACCATACCTACGTTTCACAACTCAGTATGGAT
* **
21865 GATACCATACCTACGTTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACGTTTCACAACTCAGTAT-G----GAT
*
21905 AATACCATACCTACATTTCACA
1 AATACCATACCTACGTTTCACA
21927 CTTTGCCATG
Statistics
Matches: 349, Mismatches: 53, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
34 90 0.26
35 237 0.68
36 1 0.00
40 21 0.06
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACGTTTCACAACTCAGTATGGAT
Found at i:21770 original size:173 final size:172
Alignment explanation
Indices: 21481--21926 Score: 498
Period size: 173 Copynumber: 2.5 Consensus size: 172
21471 TTTCCTCATT
* * * *
21481 GAAATACCATACCTACGTTTCACAACTCGGTATGGAAAACACCATACCTACTTTTCATGCTCGGT
1 GAAATACCATACCTACGTTTCACAACTCGGTATGG-AAATACCATACCTACGTTTCAAGCTCAGT
* * * * *
21546 ATGGAAAATACCATACCTATATTTCATAACTCAGTATGGACGATGCCATACCTATGTATCATAGC
65 ATGGAAAATACCATACCTATATTTCACAACTCAGTATGGACAATACCATACCTATGTATCACAAC
* * * * *
21611 TCAATATGGACGACGCCATACCTACGTTTCATAGCTCGGTATG
130 TCAATATGGACGACACCATACCTACATTTCACAACTCAGTATG
* * *
21654 GAAATACCATACCTACGTTTCATAGCTCGGTATGGAAATGCCATACCTACGTTTCACAGCTCAGT
1 GAAATACCATACCTACGTTTCACAACTCGGTATGGAAATACCATACCTACGTTTCA-AGCTCAGT
** * * ** *
21719 ATGGTTAATACCATACCTATGTTTCACAACTCGGTATGGTTAATACCATACCTATGTTTCACAAC
65 ATGGAAAATACCATACCTATATTTCACAACTCAGTATGGACAATACCATACCTATGTATCACAAC
* * * *
21784 TCAGTATGGATGATACCATACCTACATTTCACAACTTAGTATG
130 TCAATATGGACGACACCATACCTACATTTCACAACTCAGTATG
* * *
21827 GTTAATACCATACCTACATTTCACAACTCGGTATGGATGATACCATACCTACGTTTCTTAA-CTC
1 G-AAATACCATACCTACGTTTCACAACTCGGTATGGA-AATACCATACCTACGTTTC--AAGCTC
*
21891 AGTATGGATTTGATAATACCATACCTACATTTCACA
62 AGTATGGA----A-AATACCATACCTATATTTCACA
21927 CTTTGCCATG
Statistics
Matches: 225, Mismatches: 38, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
172 18 0.08
173 127 0.56
174 31 0.14
175 27 0.12
176 1 0.00
177 1 0.00
180 20 0.09
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (172 bp):
GAAATACCATACCTACGTTTCACAACTCGGTATGGAAATACCATACCTACGTTTCAAGCTCAGTA
TGGAAAATACCATACCTATATTTCACAACTCAGTATGGACAATACCATACCTATGTATCACAACT
CAATATGGACGACACCATACCTACATTTCACAACTCAGTATG
Found at i:27121 original size:40 final size:40
Alignment explanation
Indices: 27047--27269 Score: 260
Period size: 39 Copynumber: 5.7 Consensus size: 40
27037 GCTACTCGTT
*
27047 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
27086 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
27126 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
27165 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
27204 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
27245 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27270 CATCATTCAA
Statistics
Matches: 161, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 81 0.50
40 65 0.40
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:27146 original size:79 final size:77
Alignment explanation
Indices: 27047--27269 Score: 259
Period size: 79 Copynumber: 2.8 Consensus size: 77
27037 GCTACTCGTT
* *
27047 CAAATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGACTTAGCCCGG-TATAGTAACTCGCACAA-TGCCTTCGGGACTTAGCCCGGA
*
27112 TTTAGTAACTCGCA
64 ATTAGTAACTCGCA
* * * *
27126 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGAA
1 CAAATGCCTTCGGACTTAGCCCGGTA-TAGTAACTCGCAC-AATGCCTTCGGGACTTAGCCCGGA
*
27190 ATTAGTATCTCGCA
64 ATTAGTAACTCGCA
* * * * *
27204 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGA-CTTAGCCCGG-TATAGTAAC-TCGCACAATGCCTTCGGGACTTAGCCCGG
27269 A
63 A
27270 CATCATTCAA
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
78 35 0.29
79 68 0.56
80 18 0.15
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGACTTAGCCCGGTATAGTAACTCGCACAATGCCTTCGGGACTTAGCCCGGAAT
TAGTAACTCGCA
Found at i:27229 original size:118 final size:119
Alignment explanation
Indices: 27047--27269 Score: 283
Period size: 118 Copynumber: 1.9 Consensus size: 119
27037 GCTACTCGTT
** *
27047 CAAATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
27112 TTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 TATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * * **
27165 CAAATGCCTTCGGGCTTAGCCCGAA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGACATAGCCCGAATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* *
27228 GATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
27270 CATCATTCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
117 4 0.04
118 66 0.74
119 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (119 bp):
CAAATGCCTTCGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:33216 original size:39 final size:39
Alignment explanation
Indices: 33141--33216 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
33131 ATTGCACATT
* *
33141 TTTTTTTTAACTTTTGTCCTTTCTTTCTTTTTTTTTAAG
1 TTTTTTTTAACTTTTGTCCTTTCATCCTTTTTTTTTAAG
33180 TTTTTTTTAACTTTTGT-CTTT-ATCCTTATTTATTTTA
1 TTTTTTTTAACTTTTGTCCTTTCATCCTT-TTT-TTTTA
33217 TTTATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 4 0.12
38 7 0.21
39 22 0.67
ACGTcount: A:0.13, C:0.12, G:0.04, T:0.71
Consensus pattern (39 bp):
TTTTTTTTAACTTTTGTCCTTTCATCCTTTTTTTTTAAG
Found at i:33225 original size:39 final size:39
Alignment explanation
Indices: 33140--33227 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
33130 AATTGCACAT
* *
33140 TTTTTTTTTAACTTTTGTCCTTTCTTTCTTTTTTTTTAA
1 TTTTTTTTTAACTTTTGTCCTTTCATCCTTTTTTTTTAA
*
33179 GTTTTTTTTAACTTTTGT-CTTT-ATCCTTATTTATTTT-A
1 TTTTTTTTTAACTTTTGTCCTTTCATCCTT-TTT-TTTTAA
33217 TTTATTTTTTA
1 TTT-TTTTTTA
33228 TTGTTAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
37 4 0.10
38 10 0.24
39 28 0.67
ACGTcount: A:0.14, C:0.10, G:0.03, T:0.73
Consensus pattern (39 bp):
TTTTTTTTTAACTTTTGTCCTTTCATCCTTTTTTTTTAA
Found at i:33286 original size:24 final size:23
Alignment explanation
Indices: 33259--33328 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 23
33249 GAAATGTATA
*
33259 TTTAAAATGTTTTATAATA-TATTT
1 TTTAAAA-ATTTTA-AATATTATTT
33283 TTTATAAAATTTTAAATATTATTT
1 TTTA-AAAATTTTAAATATTATTT
*
33307 TTT--AAATATTAAATA-TATTT
1 TTTAAAAATTTTAAATATTATTT
33327 TT
1 TT
33329 AATAATATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.17
21 11 0.26
23 4 0.10
24 17 0.40
25 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (23 bp):
TTTAAAAATTTTAAATATTATTT
Found at i:33307 original size:23 final size:21
Alignment explanation
Indices: 33268--33428 Score: 81
Period size: 20 Copynumber: 7.7 Consensus size: 21
33258 ATTTAAAATG
33268 TTTTATAATATATTTTTTATAAAA
1 TTTTA-AATATA-TTTTTAT-AAA
33292 TTTTAAATATTATTTTT-TAAA
1 TTTTAAATA-TATTTTTATAAA
*
33313 TATTAAATATATTTTTA-ATAA
1 TTTTAAATATATTTTTATA-AA
* * *
33334 -TATAAAGA-A-TTTTA-ATA
1 TTTTAAATATATTTTTATAAA
*
33351 TTTTAAAGATATGATTTTT-CAAA
1 TTTT-AA-ATAT-ATTTTTATAAA
* *
33374 -TTT-ATTATTAGTTTTATAATA
1 TTTTAAATA-TATTTTTATAA-A
* *
33395 TTTTAAATGTATATTT-TAAA
1 TTTTAAATATATTTTTATAAA
33415 TTTTAAATATATTT
1 TTTTAAATATATTT
33429 AAAATTTGTT
Statistics
Matches: 105, Mismatches: 17, Indels: 34
0.67 0.11 0.22
Matches are distributed among these distances:
17 1 0.01
18 8 0.08
19 10 0.10
20 32 0.30
21 17 0.16
22 13 0.12
23 17 0.16
24 7 0.07
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTTAAATATATTTTTATAAA
Found at i:33339 original size:20 final size:21
Alignment explanation
Indices: 33277--33336 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
33267 GTTTTATAAT
*
33277 ATATT-TTTTATAAAATTTTAA
1 ATATTATTTT-TAAAATATTAA
*
33298 ATATTATTTTTTAAATATTAA
1 ATATTATTTTTAAAATATTAA
33319 ATA-TATTTTTAATAATAT
1 ATATTATTTTTAA-AATAT
33337 AAAGAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.24
21 22 0.65
22 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTATTTTTAAAATATTAA
Found at i:33419 original size:20 final size:18
Alignment explanation
Indices: 33394--33435 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
33384 GTTTTATAAT
*
33394 ATTTTAAATGTATATTTTAA
1 ATTTTAAA--TATATTTAAA
33414 ATTTTAAATATATTTAAA
1 ATTTTAAATATATTTAAA
33432 ATTT
1 ATTT
33436 GTTTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
20 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTTAAATATATTTAAA
Found at i:33429 original size:52 final size:54
Alignment explanation
Indices: 33380--33482 Score: 140
Period size: 52 Copynumber: 1.9 Consensus size: 54
33370 CAAATTTATT
* *
33380 ATTAGTTTTATAATATTTTAAATGTAT-ATTTTA-A-ATTTTAAATATATTTAAA
1 ATTAGTTTTATAATATTTAAAAT-TATGATTTTAGATATTTAAAATATATTTAAA
*
33432 ATTTGTTTTATAATATTTAAAATTATGATTTTAGATTATTTAAAATATATT
1 ATTAGTTTTATAATATTTAAAATTATGATTTTAGA-TATTTAAAATATATT
33483 ATTTTTAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
51 3 0.07
52 27 0.61
53 1 0.02
55 13 0.30
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (54 bp):
ATTAGTTTTATAATATTTAAAATTATGATTTTAGATATTTAAAATATATTTAAA
Found at i:33494 original size:27 final size:23
Alignment explanation
Indices: 33414--33487 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
33404 TATATTTTAA
*
33414 ATTTTAAATATATTTAAAATT-TG
1 ATTTTAGAT-TATTTAAAATTATG
* *
33437 -TTTTATAATATTTAAAATTATG
1 ATTTTAGATTATTTAAAATTATG
*
33459 ATTTTAGATTATTTAAAATATATT
1 ATTTTAGATTATTTAAAAT-TATG
33483 ATTTT
1 ATTTT
33488 TAAAGATATG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
21 11 0.26
22 8 0.19
23 16 0.37
24 8 0.19
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
ATTTTAGATTATTTAAAATTATG
Found at i:33563 original size:23 final size:26
Alignment explanation
Indices: 33533--33581 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 26
33523 ATAATATTTT
33533 AAATATATATT-T-AAA-ATTTTAAA
1 AAATATATATTATAAAACATTTTAAA
33556 AAATATATATTATAAAACATTTTAAA
1 AAATATATATTATAAAACATTTTAAA
33582 TATACATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 3 0.13
26 8 0.35
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATATATATTATAAAACATTTTAAA
Found at i:33582 original size:23 final size:20
Alignment explanation
Indices: 33528--33590 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 20
33518 GTTTTATAAT
33528 ATTTTAAATATATATTTAAA
1 ATTTTAAATATATATTTAAA
33548 ATTTTAAAAAATATATATTATAAAA
1 ATTTT---AAATATATATT-T-AAA
*
33573 CATTTTAAATATACATTT
1 -ATTTTAAATATATATTT
33591 TAATTTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
20 5 0.14
22 1 0.03
23 21 0.58
24 1 0.03
25 3 0.08
26 5 0.14
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTTAAATATATATTTAAA
Found at i:33719 original size:12 final size:10
Alignment explanation
Indices: 33691--33715 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
33681 AAAGAAGGAT
33691 AAAAAGTTAA
1 AAAAAGTTAA
33701 AAAAAGTTAA
1 AAAAAGTTAA
33711 AAAAA
1 AAAAA
33716 AAGTGTCAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (10 bp):
AAAAAGTTAA
Found at i:34506 original size:43 final size:44
Alignment explanation
Indices: 34445--34541 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 44
34435 TCCTAATTGG
*
34445 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
34488 GAAAATAGTTTCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
34532 -AAAATA-TTTC
1 GAAAATAGTTTC
34542 TAGAATATGA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
42 4 0.08
43 45 0.90
44 1 0.02
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.31
Consensus pattern (44 bp):
GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:38068 original size:37 final size:39
Alignment explanation
Indices: 37936--38157 Score: 258
Period size: 40 Copynumber: 5.7 Consensus size: 39
37926 TTGAATGATG
* *
37936 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTA-A
*
37976 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAA
38015 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAA
*
38054 T-CGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACT-AA
* * *
38092 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTA-A
* *
38132 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
38158 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 11, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
37 33 0.20
38 4 0.02
39 36 0.22
40 78 0.48
41 10 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAA
Found at i:46092 original size:36 final size:37
Alignment explanation
Indices: 46052--46178 Score: 157
Period size: 39 Copynumber: 3.3 Consensus size: 37
46042 GGACTAAGAT
*
46052 CGAAGGCATTTGTGCGAGATACTAATGGGCTAAG-CC
1 CGAAGGCATTTGTGCGAGTTACTAATGGGCTAAGTCC
*
46088 CGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACT-AAT--GGGCTAAGTCC
* * *
46128 CGAAGGCAATTGTGCGAGTTACTTAACCGGGCTATGTCC
1 CGAAGGCATTTGTGCGAGTTAC-TAA-TGGGCTAAGTCC
46167 CGAAGGCATTTG
1 CGAAGGCATTTG
46179 AACGAGTAGC
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
36 22 0.28
37 3 0.04
39 27 0.35
40 25 0.32
41 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (37 bp):
CGAAGGCATTTGTGCGAGTTACTAATGGGCTAAGTCC
Found at i:46141 original size:40 final size:39
Alignment explanation
Indices: 45999--46178 Score: 194
Period size: 40 Copynumber: 4.7 Consensus size: 39
45989 TTGAATGATG
* * *
45999 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-A
* *
46039 TCCGGACTAAGAT--CGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
46077 T--GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AA
* *
46114 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTTAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC-TAA
*
46154 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
46179 AACGAGTAGC
Statistics
Matches: 119, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
36 29 0.24
37 3 0.03
38 2 0.02
39 41 0.34
40 42 0.35
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Done.