Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009884.1 Corchorus capsularis cultivar CVL-1 contig09905, 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: 80870
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1114 original size:589 final size:588
Alignment explanation
Indices: 1--2027 Score: 3100
Period size: 589 Copynumber: 3.4 Consensus size: 588
*
1 TATGCTGCAGCTATTCCTAATGTTGAAAGTACGGAAGCAAAATATATCCACCCAGTAATTAACAA
1 TATGCTGCAGCTATTCCCAATGTTGAAAGTACGGAAGCAAAATATATCCACCCAGTAATTAACAA
* * *
66 CACA-AACCTAGGAAACATATGAAGGCTAATGCATTATAAGAACTGTTCATCTCCTACACTAACG
66 CACACAACCTAGGAAACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTCCTACACTGACG
130 ACCCCTTTCTACGATATGTGGGTCGAATTACTTGTATAAG-AAAATTAATCCCCATGCCAAGAAA
131 ACCCCTTTCTACGATATGTGGGTCGAATTACTTGTATAAGAAAAATTAATCCCCATGCCAAGAAA
* * *
194 ACTACGGGTATATAATCTTTGATGAGCTGGATTAGGCCCTGGTTAAGCACAATTTCGGATTGAAT
196 ACTACGGGTATATAATCTGTGATGAGCTGTATCAGGCCCTGGTTAAGCACAATTTCGGATTGAAT
259 T-AAAAAAAACTAAAACAGAATCAAATATAAAATCTGATTATATTTATTTTACTAAACTTTAAAT
261 TAAAAAAAAACTAAAACAGAATCAAATATAAAATCTGATTATATTTATTTTACTAAACTTTAAAT
* *
323 GAAAAAACAACCTATATGTAAGCTCGGATGACATCTTGCATCTTGATATCATAAGTCTCAAATGT
326 G-AAAAACAACCTATATCTAAGCTCGGATGACATCTTGCATCTTGATATCAGAAGTCTCAAATGT
* * *
388 TTTCTCGCATCCTATCGGATTTAAACCAATCGCCATACCACCAACCTCATCAATTTTGATGGTAT
390 TTTCTTGCATCCTATCGGATCTGAACCAATCGCCATACCACCAACCTCATCAATTTTGATGGTAT
*
453 CTTA-ACCCAATATTCTCACATGTTGCACCCTGTATGATTCTCTCCCGAGTCGAATCACATCATT
455 C-TACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCCGAGTCGAATCACATCATT
* * * ** * ** *
517 TACTTGCACGAGATCTTCTGGAAAAATAGCCACCTGTAATTGACTGAACGAAGCAAAATTGGGTG
519 CACTTGCACGAGATATTTTACAAAAATGGCCACCTGGGATTGACTGAACGAAGCAAAACTGGGTG
582 AATAA
584 AATAA
*
587 TATGCTGCAGCTATTCCTAATGTTGAAAGTACGGAAGCAAAATATATCCACCCAGTAATTAACAA
1 TATGCTGCAGCTATTCCCAATGTTGAAAGTACGGAAGCAAAATATATCCACCCAGTAATTAACAA
*
652 CACA-AACCTAGGAAACATATGAAGGCTAATGCATTATAAAAACTGTTCATCTCCTACACTGACG
66 CACACAACCTAGGAAACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTCCTACACTGACG
716 ACCCCTTTCTACGATATGTGGGTCGAATTACTTGTATAAGAAAAATTAATCCCCATGCCAAGAAA
131 ACCCCTTTCTACGATATGTGGGTCGAATTACTTGTATAAGAAAAATTAATCCCCATGCCAAGAAA
781 ACTACGGGTATATAATCTGTGATGAGCTGTATCAGGCCCTGGTTAAGCACAATTTCGGATTGAAT
196 ACTACGGGTATATAATCTGTGATGAGCTGTATCAGGCCCTGGTTAAGCACAATTTCGGATTGAAT
846 TAAAAATAAAAACTAAAACAGAATCAAATATAAAATCTGATTATATTTATTTTACTAAACTTTAA
261 T-AAAA-AAAAACTAAAACAGAATCAAATATAAAATCTGATTATATTTATTTTACTAAACTTTAA
911 ATGAAAAACAACCTATATCTAAGCTCGGATGACATCTTGCATCTTGATATCAGAAGTCTCAAATG
324 ATGAAAAACAACCTATATCTAAGCTCGGATGACATCTTGCATCTTGATATCAGAAGTCTCAAATG
* *
976 TTTTCTTGCATCCTATCGGATCTGAACCAACCGCCATAACACCAACCTCATCAATTTTGATGGTA
389 TTTTCTTGCATCCTATCGGATCTGAACCAATCGCCATACCACCAACCTCATCAATTTTGATGGTA
* *
1041 TCTACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCCTAGTCTAATCACATCATT
454 TCTACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCCGAGTCGAATCACATCATT
* * *
1106 CACTTGCACGAGATTTTTTACAAAAATGGCCACCTGGGATTGACTGAACGAAGCGAAACCGGGTG
519 CACTTGCACGAGATATTTTACAAAAATGGCCACCTGGGATTGACTGAACGAAGCAAAACTGGGTG
*
1171 AATAC
584 AATAA
*
1176 TATGCTGCAGCTATTCCCAATGTTGAAAGTACGGAAGCAAAATATATCCACCCAGTAATTAATAA
1 TATGCTGCAGCTATTCCCAATGTTGAAAGTACGGAAGCAAAATATATCCACCCAGTAATTAACAA
* * * *
1241 CACACAACCCATGACACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTCCTGCACTGACG
66 CACACAACCTAGGAAACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTCCTACACTGACG
* * * * * **
1306 ACCCCTTTCTAGGATCTGTAGGTCGAATTACTTATATAAGAAAAGTTAATCATCATGCCAAGAAA
131 ACCCCTTTCTACGATATGTGGGTCGAATTACTTGTATAAGAAAAATTAATCCCCATGCCAAGAAA
* * * * * *
1371 ACTGCGAGTATATAATAC-GTGATGAGCTGTATCAAGCCCTTGTCAAGCACAATTTCGGATCGAA
196 ACTACGGGTATATAAT-CTGTGATGAGCTGTATCAGGCCCTGGTTAAGCACAATTTCGGATTGAA
* * *
1435 -TAAAAAAAAACTAAAACAAAATCAAATATAAAATCCGAATATATTTATTTTACTAAACTTTAAA
260 TTAAAAAAAAACTAAAACAGAATCAAATATAAAATCTGATTATATTTATTTTACTAAACTTTAAA
*
1499 TGATAAAACAATCTATATCTAAGCTCGGATGACATCTTGCATCTTGATATCAGAAGTCTCAAATG
325 TGA-AAAACAACCTATATCTAAGCTCGGATGACATCTTGCATCTTGATATCAGAAGTCTCAAATG
*
1564 TTTTCTTGCATCCTATCGGATCTGAACCAATCGCAATACCACCAACCTCATCAATTTTGATGGTA
389 TTTTCTTGCATCCTATCGGATCTGAACCAATCGCCATACCACCAACCTCATCAATTTTGATGGTA
* *
1629 TCTACACCCAATATTCTCACATCTTGCGCCCTGTATGATTCTCTCCCGAGTCGAATCACATTATT
454 TCTACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCCGAGTCGAATCACATCATT
* *
1694 CACTTGCACGTGATATTTTACAAAAATGGCCACCTGGGATTGACTGAACGAATCAAAACTGGGTG
519 CACTTGCACGAGATATTTTACAAAAATGGCCACCTGGGATTGACTGAACGAAGCAAAACTGGGTG
1759 AATAA
584 AATAA
* **
1764 TATGCTGCAGCTATTCCCAATGTTGAATGTACGGAAACAACAATAGCAAAATATATTTACCCAGT
1 TATGCTGCAGCTATTCCCAATGTTGAAAGTACGG--------A-AGCAAAATATATCCACCCAGT
* * * * * *
1829 AATTTATAACACACAACGC-AGGACACGTATGAAGGCTAATGCATTACAAAAAATGTTCATCTAC
57 AATTAACAACACACAAC-CTAGGAAACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTCC
* * * **
1893 TGCACTGACGACCCCTTTCTATGATCTGTGGGTCGAATTACTTGTATAAGAAAAATTAATCCTTA
121 TACACTGACGACCCCTTTCTACGATATGTGGGTCGAATTACTTGTATAAGAAAAATTAATCCCCA
* * ** * * * * *
1958 AGCCAA-ATAAACTGCGGGTATATAATCCATGATAAGCTGTATCTGCCCCTAGTTAGGCACAATT
186 TGCCAAGA-AAACTACGGGTATATAATCTGTGATGAGCTGTATCAGGCCCTGGTTAAGCACAATT
2022 TCGGAT
250 TCGGAT
2028 CGAAATATAT
Statistics
Matches: 1333, Mismatches: 88, Indels: 29
0.92 0.06 0.02
Matches are distributed among these distances:
586 167 0.13
587 146 0.11
588 286 0.21
589 308 0.23
590 230 0.17
591 1 0.00
596 3 0.00
597 191 0.14
598 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (588 bp):
TATGCTGCAGCTATTCCCAATGTTGAAAGTACGGAAGCAAAATATATCCACCCAGTAATTAACAA
CACACAACCTAGGAAACATATGAAGGCTAATGCATTATAAAAAATGTTCATCTCCTACACTGACG
ACCCCTTTCTACGATATGTGGGTCGAATTACTTGTATAAGAAAAATTAATCCCCATGCCAAGAAA
ACTACGGGTATATAATCTGTGATGAGCTGTATCAGGCCCTGGTTAAGCACAATTTCGGATTGAAT
TAAAAAAAAACTAAAACAGAATCAAATATAAAATCTGATTATATTTATTTTACTAAACTTTAAAT
GAAAAACAACCTATATCTAAGCTCGGATGACATCTTGCATCTTGATATCAGAAGTCTCAAATGTT
TTCTTGCATCCTATCGGATCTGAACCAATCGCCATACCACCAACCTCATCAATTTTGATGGTATC
TACACCCAATATTCTCACATCTTGCACCCTGTATGATTCTCTCCCGAGTCGAATCACATCATTCA
CTTGCACGAGATATTTTACAAAAATGGCCACCTGGGATTGACTGAACGAAGCAAAACTGGGTGAA
TAA
Found at i:3793 original size:22 final size:20
Alignment explanation
Indices: 3763--3805 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
3753 AAATAGATTC
*
3763 TATTCATCTATATTTTTCTTTT
1 TATTCATCT-TAGTTTT-TTTT
*
3785 TATTTATCTTAGTTTTTTTT
1 TATTCATCTTAGTTTTTTTT
3805 T
1 T
3806 GCAATAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTCATCTTAGTTTTTTTT
Found at i:5911 original size:2 final size:2
Alignment explanation
Indices: 5854--5896 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
5844 TGTTTAATTA
* *
5854 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5896 A
1 A
5897 AGCGAGTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9670 original size:25 final size:25
Alignment explanation
Indices: 9621--9671 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
9611 TTAGTTGAAT
*
9621 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
9646 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
9672 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Found at i:10608 original size:20 final size:21
Alignment explanation
Indices: 10566--10619 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
10556 GGTAAATGTT
10566 AATA-ATAAATATAAATAAAC
1 AATATATAAATATAAATAAAC
* *
10586 AATATATAAATCTAAAT-AGC
1 AATATATAAATATAAATAAAC
*
10606 AATATAGAAATATA
1 AATATATAAATATA
10620 TTTGACAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.28
Consensus pattern (21 bp):
AATATATAAATATAAATAAAC
Found at i:12372 original size:18 final size:18
Alignment explanation
Indices: 12349--12387 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
12339 ATCCAGAAGT
12349 CATGGAGTAGTTTATGAA
1 CATGGAGTAGTTTATGAA
12367 CATGGAGTAGTTTATGAA
1 CATGGAGTAGTTTATGAA
12385 CAT
1 CAT
12388 TAACAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (18 bp):
CATGGAGTAGTTTATGAA
Found at i:13006 original size:9 final size:9
Alignment explanation
Indices: 12994--13038 Score: 90
Period size: 9 Copynumber: 5.0 Consensus size: 9
12984 AACAGATGAA
12994 ATGGAAGAT
1 ATGGAAGAT
13003 ATGGAAGAT
1 ATGGAAGAT
13012 ATGGAAGAT
1 ATGGAAGAT
13021 ATGGAAGAT
1 ATGGAAGAT
13030 ATGGAAGAT
1 ATGGAAGAT
13039 GGTAATCAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (9 bp):
ATGGAAGAT
Found at i:13010 original size:27 final size:27
Alignment explanation
Indices: 12980--13037 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
12970 AAAGAAGAGC
*
12980 AAGAAACAGATGAAATGGAAGATATGG
1 AAGAAACAGAAGAAATGGAAGATATGG
* ** *
13007 AAGATATGGAAGATATGGAAGATATGG
1 AAGAAACAGAAGAAATGGAAGATATGG
13034 AAGA
1 AAGA
13038 TGGTAATCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.31, T:0.17
Consensus pattern (27 bp):
AAGAAACAGAAGAAATGGAAGATATGG
Found at i:13270 original size:14 final size:13
Alignment explanation
Indices: 13245--13269 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13235 TCTTTATTTA
13245 TTGCTTTTTTTTC
1 TTGCTTTTTTTTC
13258 TTGCTTTTTTTT
1 TTGCTTTTTTTT
13270 TAAAGAAAAA
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:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (13 bp):
TTGCTTTTTTTTC
Found at i:13731 original size:17 final size:19
Alignment explanation
Indices: 13691--13730 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
13681 CTTTTGTTGG
13691 GAGAATTTCGAAGAGATAA
1 GAGAATTTCGAAGAGATAA
13710 GAGAATTTCCG-AGAGATAA
1 GAGAATTT-CGAAGAGATAA
13729 GA
1 GA
13731 AGTCTGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.20
Consensus pattern (19 bp):
GAGAATTTCGAAGAGATAA
Found at i:13851 original size:19 final size:19
Alignment explanation
Indices: 13827--13871 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
13817 AAATTAAAGT
*
13827 AAATAAAATCCATGTGGCG
1 AAATAAAATCCACGTGGCG
13846 AAATAAAATCCACGTGGCG
1 AAATAAAATCCACGTGGCG
13865 AAATAAA
1 AAATAAA
13872 GAGGAGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (19 bp):
AAATAAAATCCACGTGGCG
Found at i:14544 original size:22 final size:22
Alignment explanation
Indices: 14519--14561 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
14509 TTTCTCTGCC
14519 TCTTCTCTTCTTCCTCTCTTTT
1 TCTTCTCTTCTTCCTCTCTTTT
* *
14541 TCTTCTCTTGTTGCTCTCTTT
1 TCTTCTCTTCTTCCTCTCTTT
14562 CTCCCTCCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.05, T:0.63
Consensus pattern (22 bp):
TCTTCTCTTCTTCCTCTCTTTT
Found at i:57574 original size:5 final size:6
Alignment explanation
Indices: 57556--57581 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
57546 TTTAGGTTTC
57556 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
57582 TTCTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:58992 original size:20 final size:20
Alignment explanation
Indices: 58967--59004 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58957 AAATTGTTCA
*
58967 GAAAAGATTCAACAGAGCAT
1 GAAAAGATTAAACAGAGCAT
58987 GAAAAGATTAAACAGAGC
1 GAAAAGATTAAACAGAGC
59005 TGTTTACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.13, G:0.21, T:0.13
Consensus pattern (20 bp):
GAAAAGATTAAACAGAGCAT
Found at i:59504 original size:6 final size:6
Alignment explanation
Indices: 59493--59522 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
59483 AAGATGATGT
59493 CGGTGA CGGTGA CGGTGA CGGTGA CGGTGA
1 CGGTGA CGGTGA CGGTGA CGGTGA CGGTGA
59523 TCTTCTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (6 bp):
CGGTGA
Found at i:62491 original size:1 final size:1
Alignment explanation
Indices: 62485--62518 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
62475 CGTGCTCAAG
* *
62485 TTTTTTTTTTTTTTTTTTTTTTTCTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
62519 CTTTCTCGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:64185 original size:19 final size:20
Alignment explanation
Indices: 64139--64186 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
64129 TGTGGCACGC
*
64139 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
64161 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
64180 CACATGT
1 CACATGT
64187 CACGTCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:64200 original size:53 final size:53
Alignment explanation
Indices: 64106--64208 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
64096 GACGTGGCAC
* **
64106 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* * **
64159 GCCACATGTACCAAAAAGTGACACATGTCACGTCATGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
64209 GACACGTGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:69141 original size:27 final size:28
Alignment explanation
Indices: 69110--69162 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
69100 AACTTGTACG
* *
69110 ATTTT-GACGTTTTGTCCATAAACTTTA
1 ATTTTGGACATTTTGCCCATAAACTTTA
*
69137 ATTTTGGACATTTTGCCCTTAAACTT
1 ATTTTGGACATTTTGCCCATAAACTT
69163 GCAATTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (28 bp):
ATTTTGGACATTTTGCCCATAAACTTTA
Found at i:73676 original size:38 final size:38
Alignment explanation
Indices: 73625--73703 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
73615 TTGAACCCCT
73625 GCCCGTTTGGGTTAGCTTGGTGCACCTAACCAAAATAG
1 GCCCGTTTGGGTTAGCTTGGTGCACCTAACCAAAATAG
73663 GCCCGTTTGGGTTAGCTTGGTGCACCTAACCAAAATAG
1 GCCCGTTTGGGTTAGCTTGGTGCACCTAACCAAAATAG
73701 GCC
1 GCC
73704 AGAATCCCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (38 bp):
GCCCGTTTGGGTTAGCTTGGTGCACCTAACCAAAATAG
Found at i:75665 original size:80 final size:80
Alignment explanation
Indices: 75526--75688 Score: 274
Period size: 80 Copynumber: 2.0 Consensus size: 80
75516 TATCCTACCA
**
75526 CTTTCAAGGCTAGTTTTGGAAATAACTTTTAAATATGTATTGGGTTTAGAAACGGGACTTATATT
1 CTTTCAAGGCTAGTTTTGGAAATAACTTTTAAATATACATTGGGTTTAGAAACGGGACTTATATT
75591 TTGAGACAAAAAAAG
66 TTGAGACAAAAAAAG
75606 CTTTCAAGGCTAGTTTTGGAAATAACTTTTAAATATACATTGGGTTTAGAAA-GGAGACTTATAT
1 CTTTCAAGGCTAGTTTTGGAAATAACTTTTAAATATACATTGGGTTTAGAAACGG-GACTTATAT
* *
75670 TTTGGGACAAGAAAAG
65 TTTGAGACAAAAAAAG
75686 CTT
1 CTT
75689 CTAGAAGGGA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
79 2 0.03
80 76 0.97
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (80 bp):
CTTTCAAGGCTAGTTTTGGAAATAACTTTTAAATATACATTGGGTTTAGAAACGGGACTTATATT
TTGAGACAAAAAAAG
Found at i:77652 original size:10 final size:10
Alignment explanation
Indices: 77637--77667 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
77627 TTAAACAGTG
77637 TAGGTTGAAA
1 TAGGTTGAAA
77647 TAGGTTGAAA
1 TAGGTTGAAA
77657 TAGGTTGAAA
1 TAGGTTGAAA
77667 T
1 T
77668 TTCAAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
TAGGTTGAAA
Done.