Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015976.1 Corchorus capsularis cultivar CVL-1 contig15997, 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: 37089
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:1159 original size:431 final size:430
Alignment explanation
Indices: 326--1298 Score: 1161
Period size: 431 Copynumber: 2.2 Consensus size: 430
316 GGTGATTCAA
** * * * *
326 GTGTCTATTAAAAGGTGGTTTCATGATCTACAACTTTCATGAAGGACCCACAAGCCATTTTTTAT
1 GTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATTAAGGACTCAAAAG-CAATTTTTAT
* * * * *
391 GATTCAATT-AAAAAAAGTGCTTCCGAAATTTTGTGGTTTCGATTGTCTGTCTATTTAATATCAT
65 GTTTCAATTCAAAAAAAGTGCCTCCGAAATTTGGTGGTTTCGACTGTCAGTCTATTTAATATCAT
*
455 AAAATTTTCGATCCACATGTCCGATTAAAGTTACTAAAGTGTCGGTTAGAAGATTATTGCATGAT
130 AAAATTTTCGATCCACATGTCCGATTAAAGTTACTAAAGTGTCGGTTAAAAGATTATTGCATGAT
* * *
520 CTACGTATTTCATGAAAGAGCCGAAAATTAAATTTGATTTACGAGTTTCATGAAGAGCTCAAAAG
195 ATACGTATTTCATGAAAGAGCCGAAAACTAAATTTGATCTACGAGTTTCATGAAGAGCTCAAAAG
* *
585 GGAATTTATGTTGCAAGATCTCCATCAACAAACATTTTCTTATTTGTATTATTTTCAAATGATCC
260 GGAATTTATGTTGCAAGATCTCCATCAACAAAAATTTTCTTATTTGAATTATTTTCAAATGATCC
* ** * *
650 TCATATTTAAGTACTTTATACTATTTAGTCATATACTGATTTTATCTTGATCGATTTAACACTTC
325 TCATATTTAAGTACCTTATACTATTTAGTCATATACAAATTCTATCTTGATAGATTTAACACTTC
* * *
715 AGATTTATTTTTTTATATTTTTTGTTATATTTGTCCGATTAA-G-
390 AGA--CATTTTTTT-T-TTCTTTGTTATATTTGTCCAATTAAGGT
* * *
758 GTGTCCATTAAAAGGTAATTTCATGATTTACAACTTTCATTAATGACTCAAAAGTCAATTTTTAT
1 GTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATTAAGGACTCAAAAG-CAATTTTTAT
*
823 GTTTCAATTCAAAAAAA-TGCCTCTC-AAA-TTGGTGGTTTCTACTGTCAGTCTATTTAATATCA
65 GTTTCAATTCAAAAAAAGTGCCTC-CGAAATTTGGTGGTTTCGACTGTCAGTCTATTTAATATCA
** * * * *
885 TATGATTTTGGATCCACATGTCTGATTAAAGTTATTCAAA-TGTTGGTTAAAAGATTATTGCATG
129 TAAAATTTTCGATCCACATGTCCGATTAAAGTTACT-AAAGTGTCGGTTAAAAGATTATTGCATG
* * * *
949 ATATACG-ATTTTCATGAAAGATCCGAAAGCTAAATTTGATCTACGTGTTTCATGAATG-GTTCA
193 ATATACGTA-TTTCATGAAAGAGCCGAAAACTAAATTTGATCTACGAGTTTCATGAA-GAGCTCA
*
1012 AAAGGGAATTTTTATGTTTCAAGATCTCCATCAACAAAAATTTTCTTATTTGAATTATTTATCAA
256 AAAGGGAA--TTTATGTTGCAAGATCTCCATCAACAAAAATTTTCTTATTTGAATTATTT-TCAA
** * *
1077 ATGA-CACTCATACTTT-TTTACCTTATACTATTTTA-TCCTTTACAAATTCTATCTT-ACTAGA
318 ATGATC-CTCATA-TTTAAGTACCTTATACTA-TTTAGTCATATACAAATTCTATCTTGA-TAGA
*
1138 TTTAACGCTTCAG-C-TTTTTTTTTTCTTTGTTATATTTGTCCAATTAAGGTAATTCAT
379 TTTAACACTTCAGACATTTTTTTTTTCTTTGTTATATTTGTCCAATTAAGG-------T
1195 GTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATTAAGGACTCAAAAGCTAATTTTTAT
1 GTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATTAAGGACTCAAAAGC-AATTTTTAT
* **
1260 GTTTCAATTCTAAAAAAG-GTATCCGACAATTT-GTGGTTT
65 GTTTCAATTCAAAAAAAGTGCCTCCGA-AATTTGGTGGTTT
1299 TGATTGTCTG
Statistics
Matches: 463, Mismatches: 52, Indels: 46
0.83 0.09 0.08
Matches are distributed among these distances:
428 23 0.05
429 2 0.00
430 8 0.02
431 143 0.31
432 75 0.16
433 57 0.12
434 55 0.12
435 7 0.02
436 2 0.00
437 80 0.17
438 9 0.02
439 2 0.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.41
Consensus pattern (430 bp):
GTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATTAAGGACTCAAAAGCAATTTTTATG
TTTCAATTCAAAAAAAGTGCCTCCGAAATTTGGTGGTTTCGACTGTCAGTCTATTTAATATCATA
AAATTTTCGATCCACATGTCCGATTAAAGTTACTAAAGTGTCGGTTAAAAGATTATTGCATGATA
TACGTATTTCATGAAAGAGCCGAAAACTAAATTTGATCTACGAGTTTCATGAAGAGCTCAAAAGG
GAATTTATGTTGCAAGATCTCCATCAACAAAAATTTTCTTATTTGAATTATTTTCAAATGATCCT
CATATTTAAGTACCTTATACTATTTAGTCATATACAAATTCTATCTTGATAGATTTAACACTTCA
GACATTTTTTTTTTCTTTGTTATATTTGTCCAATTAAGGT
Found at i:2804 original size:17 final size:15
Alignment explanation
Indices: 2768--2799 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2758 GTTTGTTATT
2768 TTTGTAGATATATGA
1 TTTGTAGATATATGA
2783 TTTGTAGATATATGA
1 TTTGTAGATATATGA
2798 TT
1 TT
2800 ATTGTGCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (15 bp):
TTTGTAGATATATGA
Found at i:3011 original size:120 final size:120
Alignment explanation
Indices: 2863--3102 Score: 408
Period size: 120 Copynumber: 2.0 Consensus size: 120
2853 CTCTAATTTC
2863 TTATTGTTGTTAGTTTTGCAATTGCAACTCTTTTTCTGCTTTTGTTCGATTTGTCTTGATCTTTT
1 TTATTGTTGTTAGTTTTGCAATTGCAACTCTTTTTCTGCTTTTGTTCGATTTGTCTTGATCTTTT
* * * *
2928 AGTTCAACTAGGTTTTTTTACCCGTGTTTCGCTGTGGATTTTAAAAAGTTGACAA
66 AGTTCAACTAGGTATTTTTACCCGCGCTTCGCTGCGGATTTTAAAAAGTTGACAA
*
2983 TTATTGTTGTTATTTTTGCAATTGCAACTCTTTTTCTGCTTTTGTTCGATTTGTCTTGATCTTTT
1 TTATTGTTGTTAGTTTTGCAATTGCAACTCTTTTTCTGCTTTTGTTCGATTTGTCTTGATCTTTT
* * *
3048 AGTTCAACTAGGTATTTTTACCTGCGCTTCGCTGCGTATTTTATAAAGTTGACAA
66 AGTTCAACTAGGTATTTTTACCCGCGCTTCGCTGCGGATTTTAAAAAGTTGACAA
3103 ATGATTTGTA
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 112 1.00
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.50
Consensus pattern (120 bp):
TTATTGTTGTTAGTTTTGCAATTGCAACTCTTTTTCTGCTTTTGTTCGATTTGTCTTGATCTTTT
AGTTCAACTAGGTATTTTTACCCGCGCTTCGCTGCGGATTTTAAAAAGTTGACAA
Found at i:3593 original size:21 final size:22
Alignment explanation
Indices: 3568--3612 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
3558 CACAACAATA
3568 ATTTAGTT-AAAAAATGAATTG
1 ATTTAGTTAAAAAAATGAATTG
3589 ATTTAGTTAAAAAAAATGAATTG
1 ATTTAGTT-AAAAAAATGAATTG
3612 A
1 A
3613 ATGACAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (22 bp):
ATTTAGTTAAAAAAATGAATTG
Found at i:4477 original size:445 final size:428
Alignment explanation
Indices: 3683--4583 Score: 994
Period size: 445 Copynumber: 2.1 Consensus size: 428
3673 AAGTGACCAT
3683 TTGATAAATAATCCAAATAAAAAATTATTTGTTGATGAGACGAAACATAAAAATTTCCTCTTAAA
1 TTGATAAATAATCCAAATAAAAAATTATTTGTTGATGAGACGAAACATAAAAATTTCCTCTTAAA
* * * * * *
3748 CCTTTCATGAAACTCATCGATCAAATTCAGCATCGGGTCCTTCATGAAAGTCGTAGATCATGCAA
66 CCCTTCATGAAACTCATCAATCAAACTCAGAATAGGATCCTTCATGAAAGTCGTAGATCATGCAA
*** * * * *
3813 TAACCTTTTAATTGAACTTGAATAACTTCAATCGGATATGTGGATCGAAAGTTATATGATATTAA
131 TAACCTTTTAACCAAACTTGAATAACTTAAATAGGATATGTGGATCGAAAATTATATGAAATTAA
*
3878 ATAGACCGACAATCGAAACCACCAAATTTCAGAAGCATTTTTTAGAGTTGAAACATAAAAATTGG
196 ATAGACCGACAATCGAAACCACCAAATTTCAGAAGCATTTTTTAGAGTTGAAACATAAAAATTAG
* * *
3943 ATTGTGAGTCCTTAATGAAAGTTGTAGTCTTGTAGATCATGAAAATACCTTTTAATAGACAATAT
261 ATTGTGAGCCCTTAA-GAAA----TAG-CTAGTAGATCATGAAAATACCTTTTAATAGAC-A-AC
* * * *
4008 TTGAATCACCTTAAACGGAAAAATATAACCAAAAAAAAAAAAAAGCTGAAGCGTTTAATCGATTA
318 TTGAATCACATTAAA-AG-AAAA-A-AA--TAAAAAAAAAAAAA-CTGAAGCGTTAAATCGATTA
* * * * **
4073 AGATAGAATTAA-TAAAGGACTAAGTAGTATGAAATAGAAAAGTATGAGGGTCAA
376 AGACAGAA-TAAGTAAAGGACTAAATAGCAT-AAAGAGAAAAGTATGAGAATCAA
* * *
4127 TTGATAAATAATCCAAATAAAAAA-TGTTTGTTGATGGAGATGAAACAT-AAAATTTCCTCTTGA
1 TTGATAAATAATCCAAATAAAAAATTATTTGTTGAT-GAGACGAAACATAAAAATTTCCTCTTAA
* * * *
4190 GCCCTTCATGAAACTCGTCAATCAAGCTCA-AATTTAGGATCCTTCATGAAAGTCGTAGATTATG
65 ACCCTTCATGAAACTCATCAATCAAACTCAGAA--TAGGATCCTTCATGAAAGTCGTAGATCATG
*
4254 CAATAACCTTTTAACCAACACTTTAATAACTTAAATAGGATATGTGGATCGAAAATTATATGAAA
128 CAATAACCTTTTAACCAA-ACTTGAATAACTTAAATAGGATATGTGGATCGAAAATTATATGAAA
* * *
4319 TTAAATAGACC-AGTAATCGAAACCACCAAATTTCGGTAGCATTTTTTAGAGTTGAAACATAAAA
192 TTAAATAGACCGA-CAATCGAAACCACCAAATTTCAGAAGCATTTTTTAGAGTTGAAACATAAAA
* * * *
4383 ATTAGCTTTTGAGCCCTTCAA-AAA-AG-TAGTAGATCATGAAATTACCTTTTAATGGAC-ACTT
256 ATTAGATTGTGAGCCCTT-AAGAAATAGCTAGTAGATCATGAAAATACCTTTTAATAGACAACTT
* ** *
4444 GAATCACTTTAATTGGAAAAATAGAAAAAAAATAAAACAATTAAAATTGAAGCGTTAAATCGATT
320 GAATCAC----ATT----AAA-AG-AAAAAAATAAAAAAAAAAAAACTGAAGCGTTAAATCGATT
* *
4509 AAGACAGAATAAGTAAAGGATTAAATAGCATAAAGAGAAAAGTATGAGAATCAT
375 AAGACAGAATAAGTAAAGGACTAAATAGCATAAAGAGAAAAGTATGAGAATCAA
*
4563 TTGATAAATAATCTAAA-AAAA
1 TTGATAAATAATCCAAATAAAA
4584 TTAGTTGTTG
Statistics
Matches: 392, Mismatches: 50, Indels: 39
0.81 0.10 0.08
Matches are distributed among these distances:
434 10 0.03
435 4 0.01
436 38 0.10
437 68 0.17
438 12 0.03
439 2 0.01
440 2 0.01
441 1 0.00
442 10 0.03
443 48 0.12
444 81 0.21
445 114 0.29
446 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (428 bp):
TTGATAAATAATCCAAATAAAAAATTATTTGTTGATGAGACGAAACATAAAAATTTCCTCTTAAA
CCCTTCATGAAACTCATCAATCAAACTCAGAATAGGATCCTTCATGAAAGTCGTAGATCATGCAA
TAACCTTTTAACCAAACTTGAATAACTTAAATAGGATATGTGGATCGAAAATTATATGAAATTAA
ATAGACCGACAATCGAAACCACCAAATTTCAGAAGCATTTTTTAGAGTTGAAACATAAAAATTAG
ATTGTGAGCCCTTAAGAAATAGCTAGTAGATCATGAAAATACCTTTTAATAGACAACTTGAATCA
CATTAAAAGAAAAAAATAAAAAAAAAAAAACTGAAGCGTTAAATCGATTAAGACAGAATAAGTAA
AGGACTAAATAGCATAAAGAGAAAAGTATGAGAATCAA
Found at i:6514 original size:30 final size:31
Alignment explanation
Indices: 6450--6515 Score: 91
Period size: 32 Copynumber: 2.2 Consensus size: 31
6440 AAAAAATTAT
*
6450 TGAAAACCATATTTACCCTTACCAATTTACA
1 TGAAAACCATATTTACCCTTACCAATTCACA
*
6481 TGAAACACCATATTTACCCTT-GCAA-TCACA
1 TGAAA-ACCATATTTACCCTTACCAATTCACA
6511 TGAAA
1 TGAAA
6516 TTACACCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 9 0.28
31 8 0.25
32 15 0.47
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (31 bp):
TGAAAACCATATTTACCCTTACCAATTCACA
Found at i:10454 original size:17 final size:18
Alignment explanation
Indices: 10426--10459 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
10416 AAATAAAAAA
10426 AAAAAGTCTAAAAGACTT
1 AAAAAGTCTAAAAGACTT
10444 AAAAAGT-TAAAAGACT
1 AAAAAGTCTAAAAGACT
10460 AAATAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (18 bp):
AAAAAGTCTAAAAGACTT
Found at i:10868 original size:68 final size:68
Alignment explanation
Indices: 10759--10896 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
10749 AAGAAATTAG
10759 TCTACTTTGATCTTTTATGACCTTCAGGACCCTTTTGGTTCATGGGTATCTTGGAATATACCTGG
1 TCTACTTTGATCTTTTATGACCTTCAGGACCCTTTTGGTTCATGGGTATCTTGGAATATACCTGG
10824 GTA
66 GTA
10827 TCTACTTTGATCTTTTATGACCTTCAGGACCCTTTTGGTTCATGGGTATCTTGGAATATACCTGG
1 TCTACTTTGATCTTTTATGACCTTCAGGACCCTTTTGGTTCATGGGTATCTTGGAATATACCTGG
10892 GTA
66 GTA
10895 TC
1 TC
10897 CTGTGAGATG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (68 bp):
TCTACTTTGATCTTTTATGACCTTCAGGACCCTTTTGGTTCATGGGTATCTTGGAATATACCTGG
GTA
Found at i:12519 original size:27 final size:27
Alignment explanation
Indices: 12477--12540 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
12467 TAAGTAAAAA
12477 AGCTTTTA-T-ATTTTACGATTAGTTC
1 AGCTTTTATTAATTTTACGATTAGTTC
*
12502 ATCTTTTATTAATTTTACGATTAGTTC
1 AGCTTTTATTAATTTTACGATTAGTTC
12529 AGCTTTTATTAA
1 AGCTTTTATTAA
12541 CTTCTTATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 7 0.20
26 1 0.03
27 27 0.77
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (27 bp):
AGCTTTTATTAATTTTACGATTAGTTC
Found at i:13811 original size:29 final size:29
Alignment explanation
Indices: 13775--13861 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
13765 CTTTTTTTGA
*
13775 CTCCTGAACTTTAATTTTGGACGTTTTGTC
1 CTCCTGAACTTTAATTTTGGACGTTTT-AC
*
13805 C-CCTGAACTTTAATTTTAGACGTTTTAC
1 CTCCTGAACTTTAATTTTGGACGTTTTAC
* *
13833 CTCCTAAACTCTCAATTTTGGACGTTTTA
1 CTCCTGAACT-TTAATTTTGGACGTTTTA
13862 ATCCCTCTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
28 2 0.04
29 31 0.62
30 17 0.34
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (29 bp):
CTCCTGAACTTTAATTTTGGACGTTTTAC
Found at i:14230 original size:29 final size:30
Alignment explanation
Indices: 14197--14271 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
14187 GAAGATTGAG
*
14197 AGTTTAGGGGATAAAATATCCAAA-ATTA-A
1 AGTTTAGGGG-TAAAACATCCAAACATTACA
* *
14226 AGTTTATGTGGCAAAACATCCAAACATTACA
1 AGTTTA-GGGGTAAAACATCCAAACATTACA
14257 AGTTTAGGGGTAAAA
1 AGTTTAGGGGTAAAA
14272 GGGGCATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
29 17 0.45
30 14 0.37
31 7 0.18
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.27
Consensus pattern (30 bp):
AGTTTAGGGGTAAAACATCCAAACATTACA
Found at i:15782 original size:15 final size:14
Alignment explanation
Indices: 15759--15788 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
15749 ATAAAAATTA
15759 AATATTTTTATTTT
1 AATATTTTTATTTT
15773 AATATATTTTATTTT
1 AATAT-TTTTATTTT
15788 A
1 A
15789 TTGAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:19264 original size:45 final size:44
Alignment explanation
Indices: 19195--19283 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 44
19185 AGATTACTTC
*
19195 TCCAACTCATCATTAATCCGGGGTAGGGATATTTTCGTAATTCCA
1 TCCAACTCATCATTAATCCGGGGTA-GGATATTTTAGTAATTCCA
* * *
19240 TCCAGCTCATCATTAATTCGGGGTAGGATCTTTTAGTAATTCCA
1 TCCAACTCATCATTAATCCGGGGTAGGATATTTTAGTAATTCCA
19284 CTACTCTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 17 0.43
45 23 0.57
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (44 bp):
TCCAACTCATCATTAATCCGGGGTAGGATATTTTAGTAATTCCA
Found at i:20549 original size:167 final size:166
Alignment explanation
Indices: 20206--20613 Score: 554
Period size: 167 Copynumber: 2.5 Consensus size: 166
20196 AAACGAGCTC
* * *
20206 TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTATGACATTTAAGTAATCTGCCAAGTAGGTAAA
1 TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGGCAAATAGG-AAA
* * ** * * *
20271 A-ACGAAAAAGATTAGTTCTCTAACTCATCATCAATCCTTGATGGGGATCTTTTATTAATTCCAC
65 AGACGAAAAAAATAAGTTCTCTAACTCAAAAGCAATCCTTGATAGGGATCTTTTAGTAATTCCAC
* * *
20335 TACTCTATTCAAGTCCATTGAGAAATGACCAAAAAGA
130 TACTCTATTAAAGTCAACTGAGAAATGACCAAAAAGA
* *
20372 TTACTTATTTAATCCCCTCAAAAATCAAAAGTTAGGACATTTAAGTAATCTGGCAAATAGGAAAA
1 TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGGCAAATAGGAAAA
* * *
20437 GACGAAAAAAATAAGTTTTCTAATTCCAAAAGCAAGT-CTTGGTAGGGATCTTTTAGTAATTCCA
66 GACGAAAAAAATAAGTTCTCTAACT-CAAAAGCAA-TCCTTGATAGGGATCTTTTAGTAATTCCA
20501 CTACTCTATTAAAGTCAACTGAGAAATGACCAAAAAG-
129 CTACTCTATTAAAGTCAACTGAGAAATGACCAAAAAGA
* * *
20538 TCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGGCATTTAAGTAATC-GGTCAAATGGGAA
1 T-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGG-CAAATAGGAA
20602 AAGACGAAAAAA
64 AAGACGAAAAAA
20614 TTGGTTCTCT
Statistics
Matches: 214, Mismatches: 23, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
165 4 0.02
166 79 0.37
167 130 0.61
168 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (166 bp):
TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGGCAAATAGGAAAA
GACGAAAAAAATAAGTTCTCTAACTCAAAAGCAATCCTTGATAGGGATCTTTTAGTAATTCCACT
ACTCTATTAAAGTCAACTGAGAAATGACCAAAAAGA
Found at i:21033 original size:13 final size:13
Alignment explanation
Indices: 21015--21039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21005 TTTCCTTCTT
21015 CAGTCCATTTTTC
1 CAGTCCATTTTTC
21028 CAGTCCATTTTT
1 CAGTCCATTTTT
21040 GTTGGGTCCG
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:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (13 bp):
CAGTCCATTTTTC
Found at i:22066 original size:17 final size:17
Alignment explanation
Indices: 22044--22077 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22034 ATGAAAAGAC
22044 AAGAGAATATGGAGAAT
1 AAGAGAATATGGAGAAT
22061 AAGAGAATATGGAGAAT
1 AAGAGAATATGGAGAAT
22078 CAGAAAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.29, T:0.18
Consensus pattern (17 bp):
AAGAGAATATGGAGAAT
Found at i:27352 original size:36 final size:36
Alignment explanation
Indices: 27299--27398 Score: 173
Period size: 36 Copynumber: 2.8 Consensus size: 36
27289 TATTTCTTTG
* *
27299 ATGTGACAACTTTAGGTGTCACTAATATTCTTGATC
1 ATGTGACAACTTCAGGTGCCACTAATATTCTTGATC
*
27335 ATGTGACAGCTTCAGGTGCCACTAATATTCTTGATC
1 ATGTGACAACTTCAGGTGCCACTAATATTCTTGATC
27371 ATGTGACAACTTCAGGTGCCACTAATAT
1 ATGTGACAACTTCAGGTGCCACTAATAT
27399 ATAAGGTAGT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (36 bp):
ATGTGACAACTTCAGGTGCCACTAATATTCTTGATC
Found at i:29586 original size:19 final size:19
Alignment explanation
Indices: 29562--29601 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
29552 GATAATTGGA
*
29562 AAAGGAACCTTCTGTGGTC
1 AAAGGAAACTTCTGTGGTC
*
29581 AAAGGAAACTTTTGTGGTC
1 AAAGGAAACTTCTGTGGTC
29600 AA
1 AA
29602 GTCCAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (19 bp):
AAAGGAAACTTCTGTGGTC
Found at i:30265 original size:17 final size:17
Alignment explanation
Indices: 30221--30272 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
30211 TTCGGGTCTT
* *
30221 GGGTAATACGAGTCGC-
1 GGGTCATACGAGTCTCG
* *
30237 GAGTCATACGAGTGTCG
1 GGGTCATACGAGTCTCG
*
30254 GGGTCATTCGAGTCTCG
1 GGGTCATACGAGTCTCG
30271 GG
1 GG
30273 TTGTGTGGGT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.23
Consensus pattern (17 bp):
GGGTCATACGAGTCTCG
Found at i:36359 original size:14 final size:14
Alignment explanation
Indices: 36340--36366 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36330 TTGCATATTC
36340 ATGTATTGTCATTA
1 ATGTATTGTCATTA
36354 ATGTATTGTCATT
1 ATGTATTGTCATT
36367 TTGCCTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (14 bp):
ATGTATTGTCATTA
Done.