Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015951.1 Corchorus capsularis cultivar CVL-1 contig15972, 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: 70855
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:243 original size:37 final size:35
Alignment explanation
Indices: 202--277 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 35
192 ATGAAGAAGA
* **
202 TTTTCTTCAAAGTGTGATCTTTTCAAAAGAAAAAATG
1 TTTTCCTCAAAGTGCAATCTTTTC-AAAG-AAAAATG
*
239 TTTTCCTCGAAGTGCAATCTTTTCAAAGAAAAATG
1 TTTTCCTCAAAGTGCAATCTTTTCAAAGAAAAATG
274 TTTT
1 TTTT
278 TCAAAAAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 11 0.31
36 4 0.11
37 20 0.57
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (35 bp):
TTTTCCTCAAAGTGCAATCTTTTCAAAGAAAAATG
Found at i:1508 original size:35 final size:35
Alignment explanation
Indices: 1433--1969 Score: 588
Period size: 34 Copynumber: 15.5 Consensus size: 35
1423 TGCATTTTAA
*
1433 TTGACCCAGGGCGGTCTTGCTTCAGTTTA-TTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
*
1467 TTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
1502 TTGACCCAAGACGGTCTTTCTTCAGTTTATTT-AG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * *
1536 TTGACCCAAGGTGGTCTTTTTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
*
1571 TTGACCCAGGGCGGTCTTTCTTCAGTTTA-TTCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
1605 TTGACCCAGGGCGGTCCTTCTTTAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * *
1640 TTGACCCAGGACGGTCTTTCTTAAGTTTATTTCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * * * * * *
1675 TCGATCCAAGGTGATCATTCTTCAGTTTATTT-AA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
** * *
1709 TTGACCCAGGGCATTCTTGCTTCAGTTTATTTTAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * *
1744 TTGACCCATGGCGGTCTTTTTTTAGTTTA-TTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * * * *
1778 TTGACCCAGAGCGATCATTCTTAAGTTTATTTCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
1813 TTGA-CCAGGGCGGTCTTGCTTCAGTTTATTTCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* ** *
1847 TCGATTCAGGGCGATCATTT-TTCAGTTTATTT-AG
1 TTGACCCAGGGCGGTC-TTTCTTCAGTTTATTTCAG
* * * *
1881 TTGACCCACGGCGGTCTTGCTTAAGTTTATTTCTG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
1916 TTGACCCAGGGCAGTCATTTTTTTCAGTTTA-TTCAG
1 TTGACCCAGGGCGGTC--TTTCTTCAGTTTATTTCAG
1952 TTGACCCAGGGCGGTCTT
1 TTGACCCAGGGCGGTCTT
1970 GCATATAAAT
Statistics
Matches: 417, Mismatches: 75, Indels: 22
0.81 0.15 0.04
Matches are distributed among these distances:
33 2 0.00
34 195 0.47
35 189 0.45
36 21 0.05
37 10 0.02
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (35 bp):
TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
Found at i:1517 original size:69 final size:69
Alignment explanation
Indices: 1433--1969 Score: 578
Period size: 69 Copynumber: 7.8 Consensus size: 69
1423 TGCATTTTAA
* *
1433 TTGACCCAGGGCGGTCTTGCTTCAGTTTATTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
1498 TCAG
66 TCAG
* * * * * *
1502 TTGACCCAAGACGGTCTTTCTTCAGTTTATTTAGTTGACCCAAGGTGGTCTTTTTTCAGTTTATT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
1567 TCAG
66 TCAG
* * *
1571 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTCAATTGACCCAGGGCGGTCCTTCTTTAGTTTATT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
1636 TCAG
66 TCAG
* * * * * * * * *
1640 TTGACCCAGGACGGTCTTTCTTAAGTTTATTTCAATCGATCCAAGGTGATCATTCTTCAGTTTAT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTA-TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT
*
1705 TT-AA
65 TTCAG
** * * * * *
1709 TTGACCCAGGGCATTCTTGCTTCAGTTTATTTTAGTTGACCCATGGCGGTCTTTTTTTAGTTTA-
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTA-TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT
1773 TTCAG
65 TTCAG
* * * * * *
1778 TTGACCCAGAGCGATCATTCTTAAGTTTATTTCAATTGA-CCAGGGCGGTCTTGCTTCAGTTTAT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTA-TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT
*
1842 TTCAA
65 TTCAG
* ** * * * * *
1847 TCGATTCAGGGCGATCATTT-TTCAGTTTATTTAGTTGACCCACGGCGGTCTTGCTTAAGTTTAT
1 TTGACCCAGGGCGGTC-TTTCTTCAGTTTATTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT
*
1911 TTCTG
65 TTCAG
* *
1916 TTGACCCAGGGCAGTCATTTTTTTCAGTTTATTCAGTTGACCCAGGGCGGTCTT
1 TTGACCCAGGGCGGTC--TTTCTTCAGTTTATTCAGTTGACCCAGGGCGGTCTT
1970 GCATATAAAT
Statistics
Matches: 387, Mismatches: 74, Indels: 12
0.82 0.16 0.03
Matches are distributed among these distances:
68 29 0.07
69 293 0.76
70 35 0.09
71 30 0.08
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (69 bp):
TTGACCCAGGGCGGTCTTTCTTCAGTTTATTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
TCAG
Found at i:2018 original size:35 final size:35
Alignment explanation
Indices: 1979--2599 Score: 930
Period size: 35 Copynumber: 17.6 Consensus size: 35
1969 TGCATATAAA
1979 TTTTCAGAGGTCAGAGTTGATCTCA-TTCTAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTC-AAGAAG
*
2014 TTTTCAGAGGTCAGAGTTGATCTCATTCCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
*
2049 TTTTCAAAGGTCAGAGTTGATCTCATTTCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
2084 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
*
2119 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGACG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
** * *
2154 TTTTC--ATTTCAAGAAGTT-TTCAAAGGTCATTCCAAGAAG
1 TTTTCAGAGGTC-AG-AGTTGATC-----TCATTTCAAGAAG
* *
2193 TTTTCAAAGGTCAGAGTTGATCTCATTCCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
2228 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
* *
2263 TTTTCAGAGGTCAGAGTTGATTTCATTGCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
2298 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
* * *
2333 TTTTCAAAGGTCAAAGTTGATCTCTTTTCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
*
2368 TTTTAAGAGGTCAGAGTTGATCTCATTTCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
*
2403 TTTTAAGAGGTCAGAGTTGATCTCATTTCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
*
2438 TTTTCAGAGGTCAGAGTTGATCGCATTTCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
* *
2473 TTTTCAGAGGTCAGAGTTGAACTCATTCCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
2508 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
2543 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAG-AG
1 TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
*
2577 ATTTTC-GATGATCAGAGTTGATC
1 -TTTTCAGA-GGTCAGAGTTGATC
2600 AAGTGCGGCT
Statistics
Matches: 539, Mismatches: 34, Indels: 26
0.90 0.06 0.04
Matches are distributed among these distances:
33 3 0.01
34 8 0.01
35 499 0.93
36 2 0.00
39 20 0.04
40 4 0.01
41 3 0.01
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (35 bp):
TTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAG
Found at i:2162 original size:16 final size:16
Alignment explanation
Indices: 2141--2175 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2131 AGAGTTGATC
*
2141 TCATTTCAAGACGTTT
1 TCATTTCAAGAAGTTT
2157 TCATTTCAAGAAGTTT
1 TCATTTCAAGAAGTTT
2173 TCA
1 TCA
2176 AAGGTCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (16 bp):
TCATTTCAAGAAGTTT
Found at i:2189 original size:23 final size:23
Alignment explanation
Indices: 2157--2205 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
2147 CAAGACGTTT
*
2157 TCATTTCAAGAAGTTTTCAAAGG
1 TCATTCCAAGAAGTTTTCAAAGG
2180 TCATTCCAAGAAGTTTTCAAAGG
1 TCATTCCAAGAAGTTTTCAAAGG
2203 TCA
1 TCA
2206 GAGTTGATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (23 bp):
TCATTCCAAGAAGTTTTCAAAGG
Found at i:3995 original size:87 final size:86
Alignment explanation
Indices: 3886--4201 Score: 492
Period size: 87 Copynumber: 3.7 Consensus size: 86
3876 AAATTGTTAA
*
3886 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAGAA
3951 ATAAATAAATTATAAAGATTG
66 ATAAATAAATTATAAAGATTG
* *
3972 AGCTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAGT
1 A-ATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAGA
*
4037 AATAAATAAATAATAAA-ATTG
65 AATAAATAAATTATAAAGATTG
* * * * * * *
4058 AATAGTAATAAGAATATTTTCTAAATCTTGTCAAATTGTGGAAGGTTTAGGAGATATTTTAGGAA
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAG-A
4123 AATAAATAAATTATAAAGATAT-
65 AATAAATAAATTATAAAGAT-TG
4145 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATAT
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATAT
4202 AAAAAAGGAA
Statistics
Matches: 206, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
85 54 0.26
86 22 0.11
87 129 0.63
88 1 0.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (86 bp):
AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAGAA
ATAAATAAATTATAAAGATTG
Found at i:4084 original size:172 final size:172
Alignment explanation
Indices: 3886--4201 Score: 537
Period size: 172 Copynumber: 1.8 Consensus size: 172
3876 AAATTGTTAA
* *
3886 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAG-A
1 AATAATAATAAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAA
*
3950 AATAAATAAATTATAAAGAT-TGAGCTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGG
66 AATAAATAAATTATAAAGATAT-A-ATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGG
4014 GAGATTTAGAAGATATTTTAAGTAATAAATAAATAATAAAATTG
129 GAGATTTAGAAGATATTTTAAGTAATAAATAAATAATAAAATTG
* * * *
4058 AATAGTAATAAGAATATTTTCTAAATCTTGTCAAATTGTGGAAGGTTTAGGAGATATTTTAGGAA
1 AATAATAATAAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAA
4123 AATAAATAAATTATAAAGATATAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGA
66 AATAAATAAATTATAAAGATATAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGA
4188 GATTTAGAAGATAT
131 GATTTAGAAGATAT
4202 AAAAAAGGAA
Statistics
Matches: 135, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
172 112 0.83
173 22 0.16
174 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (172 bp):
AATAATAATAAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAA
AATAAATAAATTATAAAGATATAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGA
GATTTAGAAGATATTTTAAGTAATAAATAAATAATAAAATTG
Found at i:10232 original size:23 final size:23
Alignment explanation
Indices: 10200--10306 Score: 99
Period size: 23 Copynumber: 4.4 Consensus size: 23
10190 AACCCTAAAC
10200 ATAACATTAAGAATTTAATATAT
1 ATAACATTAAGAATTTAATATAT
* *
10223 ATAACCTTAAGAATTAAATATAACGTTAT
1 ATAACATTAAGAATT-TA-AT-A---TAT
10252 ATAACATTAAGAATTTAATATAT
1 ATAACATTAAGAATTTAATATAT
* * *
10275 ATAACGTT-AGAATTTAATTTAC
1 ATAACATTAAGAATTTAATATAT
*
10297 ATAACGTTAA
1 ATAACATTAA
10307 AAATAAATAA
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
22 20 0.29
23 25 0.36
24 1 0.01
25 2 0.03
26 2 0.03
27 2 0.03
28 1 0.01
29 17 0.24
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (23 bp):
ATAACATTAAGAATTTAATATAT
Found at i:10288 original size:22 final size:22
Alignment explanation
Indices: 10249--10305 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
10239 AATATAACGT
*
10249 TATATAACATTAAGAATTTAATA
1 TATATAACGTT-AGAATTTAATA
*
10272 TATATAACGTTAGAATTTAATT
1 TATATAACGTTAGAATTTAATA
*
10294 TACATAACGTTA
1 TATATAACGTTA
10306 AAAATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 21 0.68
23 10 0.32
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (22 bp):
TATATAACGTTAGAATTTAATA
Found at i:10340 original size:53 final size:53
Alignment explanation
Indices: 10266--10378 Score: 190
Period size: 53 Copynumber: 2.1 Consensus size: 53
10256 CATTAAGAAT
10266 TTAATATATATAACGTTAGAATTTAATTTACATAACGTTAAAAATAAATAACAA
1 TTAA-ATATATAACGTTAGAATTTAATTTACATAACGTTAAAAATAAATAACAA
* *
10320 TTAAATATATAACGTTAGAATTTAATTTGCATAACGTTAAAAATAAATGACAA
1 TTAAATATATAACGTTAGAATTTAATTTACATAACGTTAAAAATAAATAACAA
*
10373 CTAAAT
1 TTAAAT
10379 TTGTGATCTA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 52 0.93
54 4 0.07
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.35
Consensus pattern (53 bp):
TTAAATATATAACGTTAGAATTTAATTTACATAACGTTAAAAATAAATAACAA
Found at i:10513 original size:2 final size:2
Alignment explanation
Indices: 10506--10534 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10496 GCCAAAATAC
10506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10535 AGCTTCTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20915 original size:24 final size:24
Alignment explanation
Indices: 20888--20933 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
20878 CATTTTTGCA
20888 TATTTTC-CTTAGGTAATTTAGTTG
1 TATTTTCGCTTA-GTAATTTAGTTG
*
20912 TATTTTCGTTTAGTAATTTAGT
1 TATTTTCGCTTAGTAATTTAGT
20934 ATTGTTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.57
Consensus pattern (24 bp):
TATTTTCGCTTAGTAATTTAGTTG
Found at i:21108 original size:22 final size:22
Alignment explanation
Indices: 21080--21141 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
21070 CTTGGCATGC
21080 ATATTCATTGTCATTTCTATTT
1 ATATTCATTGTCATTTCTATTT
*
21102 ATATTCATT-TACTTTTC-A-TT
1 ATATTCATTGT-CATTTCTATTT
21122 A-A-TCA-TGTCATTTCTATTT
1 ATATTCATTGTCATTTCTATTT
21141 A
1 A
21142 GATTGAACGC
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 4 0.12
20 3 0.09
21 2 0.06
22 14 0.41
ACGTcount: A:0.26, C:0.15, G:0.03, T:0.56
Consensus pattern (22 bp):
ATATTCATTGTCATTTCTATTT
Found at i:21615 original size:33 final size:32
Alignment explanation
Indices: 21575--21714 Score: 136
Period size: 33 Copynumber: 4.2 Consensus size: 32
21565 AGCACTTGTG
21575 ACCGGCCACGCGACTTGGAGATGCCCGCGCAAC
1 ACCGGCCACGCGACTTGGAGATGCCCG-GCAAC
* *
21608 ACCGGCCATGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGG-CAAC
* ** *
21641 ACCGGCCACGCGACATGGCCATGCCCGGCCAC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCAAC
** * ** *
21673 AACCGGCCACATGACTCGGCCATGCCCGGCCAC
1 -ACCGGCCACGCGACTTGGAGATGCCCGGCAAC
21706 AACCGGCCA
1 -ACCGGCCA
21715 TATGATCCTT
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
32 3 0.03
33 90 0.97
ACGTcount: A:0.21, C:0.42, G:0.28, T:0.09
Consensus pattern (32 bp):
ACCGGCCACGCGACTTGGAGATGCCCGGCAAC
Found at i:21698 original size:66 final size:66
Alignment explanation
Indices: 21575--21714 Score: 158
Period size: 66 Copynumber: 2.1 Consensus size: 66
21565 AGCACTTGTG
* * ** * *
21575 ACCGGCCACGCGACTTGGAGATGCCCGCGCAACACCGGCCATGCGACTTGGAGATGCCCGGCCAT
1 ACCGGCCACGCGACATGGACATGCCCGCGCAACACCGGCCACACGACTCGGACATGCCCGGCCA-
21640 C-
65 CA
* * * *
21641 ACCGGCCACGCGACATGGCCATGCCCG-GCCACAACCGGCCACATGACTCGGCCATGCCCGGCCA
1 ACCGGCCACGCGACATGGACATGCCCGCGCAAC-ACCGGCCACACGACTCGGACATGCCCGGCCA
21705 CA
65 CA
21707 ACCGGCCA
1 ACCGGCCA
21715 TATGATCCTT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
65 5 0.08
66 57 0.92
ACGTcount: A:0.21, C:0.42, G:0.28, T:0.09
Consensus pattern (66 bp):
ACCGGCCACGCGACATGGACATGCCCGCGCAACACCGGCCACACGACTCGGACATGCCCGGCCAC
A
Found at i:23292 original size:16 final size:17
Alignment explanation
Indices: 23271--23303 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23261 CAATTTTGGC
23271 AGTTAC-AGAGAGAGAA
1 AGTTACAAGAGAGAGAA
*
23287 AGTTACAAGAGGGAGAA
1 AGTTACAAGAGAGAGAA
23304 TGAAGATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.06, G:0.33, T:0.12
Consensus pattern (17 bp):
AGTTACAAGAGAGAGAA
Found at i:25557 original size:13 final size:14
Alignment explanation
Indices: 25539--25568 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
25529 ATAATCGGAC
25539 TTTGCATCCAT-CA
1 TTTGCATCCATGCA
25552 TTTGCATCCATGCA
1 TTTGCATCCATGCA
25566 TTT
1 TTT
25569 AGTAGAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.20, C:0.27, G:0.10, T:0.43
Consensus pattern (14 bp):
TTTGCATCCATGCA
Found at i:32229 original size:20 final size:20
Alignment explanation
Indices: 32203--32248 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
32193 ATGCATCAAG
32203 AACTAATATGAAAATACCAC
1 AACTAATATGAAAATACCAC
*
32223 GACTAATATGAAAATACCAC
1 AACTAATATGAAAATACCAC
32243 AACTAA
1 AACTAA
32249 AAGAAACAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.54, C:0.20, G:0.07, T:0.20
Consensus pattern (20 bp):
AACTAATATGAAAATACCAC
Found at i:36458 original size:15 final size:15
Alignment explanation
Indices: 36438--36470 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
36428 ACGTAAGGTG
36438 GCACAAAACCCACAT
1 GCACAAAACCCACAT
*
36453 GCACAAAACTCACAT
1 GCACAAAACCCACAT
36468 GCA
1 GCA
36471 GTGGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.36, G:0.09, T:0.09
Consensus pattern (15 bp):
GCACAAAACCCACAT
Found at i:44065 original size:2 final size:2
Alignment explanation
Indices: 44058--44085 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44048 GAACAACTTG
44058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44086 CTGAACAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47979 original size:11 final size:10
Alignment explanation
Indices: 47960--48000 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
47950 ATAACAATGC
47960 TTTTTATTTT
1 TTTTTATTTT
*
47970 TTTTTA-ATT
1 TTTTTATTTT
47979 TTTTTATTTT
1 TTTTTATTTT
47989 TATTTT-TTTT
1 T-TTTTATTTT
47999 TT
1 TT
48001 CAAATGAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 9 0.33
10 14 0.52
11 4 0.15
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:47990 original size:15 final size:13
Alignment explanation
Indices: 47966--48000 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
47956 ATGCTTTTTA
*
47966 TTTTTTTTTAATT
1 TTTTTTTTTTATT
47979 TTTTTATTTTTATT
1 TTTTT-TTTTTATT
47993 TTTTTTTT
1 TTTTTTTT
48001 CAAATGAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTATT
Found at i:51339 original size:31 final size:30
Alignment explanation
Indices: 51301--51394 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 30
51291 GCTCAAAAAG
*
51301 GCCCCTGAACTTACATAA-AACTGCCAAATAA
1 GCCCCTGAACTT-C-TAATAACAGCCAAATAA
**
51332 GCCCCTGAAC-TCTAATTGCAGCCAAATAA
1 GCCCCTGAACTTCTAATAACAGCCAAATAA
*
51361 GCCCCTGAACTCTTTAA-AA-AGGCCAAATAA
1 GCCCCTGAACT-TCTAATAACA-GCCAAATAA
51391 GCCC
1 GCCC
51395 TTTTCTGATG
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
28 3 0.06
29 22 0.42
30 14 0.26
31 14 0.26
ACGTcount: A:0.37, C:0.31, G:0.13, T:0.19
Consensus pattern (30 bp):
GCCCCTGAACTTCTAATAACAGCCAAATAA
Found at i:52646 original size:168 final size:165
Alignment explanation
Indices: 52264--52708 Score: 536
Period size: 168 Copynumber: 2.7 Consensus size: 165
52254 TGAGTCATTT
* *
52264 GTCAATTGAGAAATGACAAAAAAGTTTAGTTATTTAAT--TTCCTCAAGAATCAGAAGTTAGGAC
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCTT--TCAAGAATCAAAAGTTAGGAC
* * * * ** ** * *
52327 ATCTAAGTAATCTGTCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAACTCATCATCAATCCT
63 ATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAAAAGTTCTCTAACTCAAAAGCAAGCCT
* * *
52392 TGATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
128 TGATGGGGATCTTTTAGTAATTCCAATACTCTATTAAA
* * * **
52430 GTCCATTGAGAAATGACCGAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCTTTCAAGAATCAAAAGTTAGGACAT
* *
52495 TTATGTAATCTGCCAAGTAGGAAAATACGAAAAAAAAAAAGTTCTCTAACTCCAAAAGCAAGCCT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACG-AAAAAAAAAAGTTCTCTAACT-CAAAAGCAAGCCT
*
52560 TGA-GAGGGGTCTTTTAGTAATTCCAATACTCTATTAAA
128 TGATG-GGGATCTTTTAGTAATTCCAATACTCTATTAAA
* *
52598 GTCAATTGAGAAATGACCAAAAAGTCTAGTCATTTAATCCTTTCAAGAATTAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCTTTCAAGAATCAAAAGTTAGGACAT
* * **
52663 TTAAGTAATCTGCCAAGTGGGAAAAGACGTAAAAAATTAGTTCTCT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAAAAGTTCTCT
52709 CGCTCCTCAT
Statistics
Matches: 236, Mismatches: 37, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
166 79 0.33
167 34 0.14
168 123 0.52
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCTTTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAAAAGTTCTCTAACTCAAAAGCAAGCCTTGA
TGGGGATCTTTTAGTAATTCCAATACTCTATTAAA
Found at i:60890 original size:30 final size:30
Alignment explanation
Indices: 60854--60912 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
60844 GACTACTTAA
*
60854 TTGGTAATTACTCGACTTTATCCCAAACAT
1 TTGGTAATTACACGACTTTATCCCAAACAT
60884 TTGGTAATTACACGACTTTATCCCAAACA
1 TTGGTAATTACACGACTTTATCCCAAACA
60913 CATACAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (30 bp):
TTGGTAATTACACGACTTTATCCCAAACAT
Found at i:60923 original size:30 final size:30
Alignment explanation
Indices: 60859--60923 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
60849 CTTAATTGGT
* ** ***
60859 AATTACTCGACTTTATCCCAAACATTTGGT
1 AATTACACGACTTTATCCCAAACACATACA
60889 AATTACACGACTTTATCCCAAACACATACA
1 AATTACACGACTTTATCCCAAACACATACA
60919 AATTA
1 AATTA
60924 AGGGATTCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (30 bp):
AATTACACGACTTTATCCCAAACACATACA
Found at i:63976 original size:25 final size:24
Alignment explanation
Indices: 63948--64015 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 24
63938 CGTTTAGTAA
63948 TTAAATATATAATATTTATTTATTT
1 TTAAATATAT-ATATTTATTTATTT
63973 TT-AAT-TCAT-TATTTA-TTA-TT
1 TTAAATAT-ATATATTTATTTATTT
*
63993 TTAAATATATTTA-TTATTTATTT
1 TTAAATATATATATTTATTTATTT
64016 ATTTGTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
20 4 0.11
21 11 0.30
22 12 0.32
23 3 0.08
24 5 0.14
25 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (24 bp):
TTAAATATATATATTTATTTATTT
Found at i:63985 original size:22 final size:22
Alignment explanation
Indices: 63948--64015 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 22
63938 CGTTTAGTAA
63948 TTAAATATATAATATTTATTTATT
1 TTAAATATAT--TATTTATTTATT
*
63972 TTTAAT-TCATTATTTA-TTATT
1 TTAAATAT-ATTATTTATTTATT
63993 TTAAATATATT-TATTATTTATT
1 TTAAATATATTAT-TTATTTATT
64015 T
1 T
64016 ATTTGTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 1 0.03
21 16 0.42
22 13 0.34
23 1 0.03
24 7 0.18
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (22 bp):
TTAAATATATTATTTATTTATT
Found at i:64003 original size:18 final size:19
Alignment explanation
Indices: 63959--64011 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
63949 TAAATATATA
*
63959 ATATTTATTTATTTTTAATTC
1 ATATTTA-TTA-TTTTAAATC
63980 ATTATTTATTATTTTAAAT-
1 A-TATTTATTATTTTAAATC
63999 ATATTTATTATTT
1 ATATTTATTATTT
64012 ATTTATTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 12 0.40
19 1 0.03
20 7 0.23
21 4 0.13
22 6 0.20
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
ATATTTATTATTTTAAATC
Found at i:64026 original size:25 final size:24
Alignment explanation
Indices: 63960--64032 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
63950 AAATATATAA
*
63960 TATTTATTTA-TTTTTA-ATTCAT
1 TATTTATTTATTTTTTATATTTAT
*
63982 TATTTA-TTATTTTAAATATATTTAT
1 TATTTATTTATTTT--TTATATTTAT
64007 TATTTATTTATTTGTTTATATATTAT
1 TATTTATTTATTT-TTTATAT-TTAT
64033 ATCTAAGATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
21 3 0.07
22 9 0.22
24 2 0.05
25 16 0.39
26 10 0.24
27 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (24 bp):
TATTTATTTATTTTTTATATTTAT
Found at i:65300 original size:21 final size:21
Alignment explanation
Indices: 65276--65327 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
65266 AGAAGGAAAA
65276 TTATTTTTAATCAATTGTAA-T
1 TTATTTTTAATC-ATTGTAATT
* *
65297 TTATGATATAATCATTGTAATT
1 TTAT-TTTTAATCATTGTAATT
65319 TTATTTTTA
1 TTATTTTTA
65328 TGAATGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (21 bp):
TTATTTTTAATCATTGTAATT
Found at i:65362 original size:3 final size:3
Alignment explanation
Indices: 65356--65400 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
65346 TTTTTTTAAA
65356 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
65401 TTGCAATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:65532 original size:12 final size:12
Alignment explanation
Indices: 65515--65557 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
65505 TTAATACAGG
65515 TATCGACGGATA
1 TATCGACGGATA
*
65527 TATCGAATGGATA
1 TATCG-ACGGATA
65540 TATCGACGGATA
1 TATCGACGGATA
65552 TATCGA
1 TATCGA
65558 GGTATCGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:68096 original size:10 final size:10
Alignment explanation
Indices: 68081--68106 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
68071 AATTTAATAT
68081 GGATATTTAC
1 GGATATTTAC
68091 GGATATTTAC
1 GGATATTTAC
68101 GGATAT
1 GGATAT
68107 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:68234 original size:12 final size:12
Alignment explanation
Indices: 68217--68255 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
68207 GTACAGATAT
68217 CGGATATATCGA
1 CGGATATATCGA
68229 CGGATATATCGA
1 CGGATATATCGA
68241 --GATATA--GA
1 CGGATATATCGA
68249 CGGATAT
1 CGGATAT
68256 TTAATTCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 2 0.08
10 11 0.44
12 12 0.48
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:68250 original size:20 final size:20
Alignment explanation
Indices: 68213--68255 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
68203 AGGGGTACAG
68213 ATATCGGATATATCGACGGAT
1 ATATCGGATATA-CGACGGAT
68234 ATATCGAGATATA-GACGGAT
1 ATATCG-GATATACGACGGAT
68254 AT
1 AT
68256 TTAATTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 6 0.29
22 6 0.29
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (20 bp):
ATATCGGATATACGACGGAT
Done.