Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011594.1 Corchorus capsularis cultivar CVL-1 contig11615, 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: 53120
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1625 original size:22 final size:22
Alignment explanation
Indices: 1595--1637 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1585 CCATCAAAAT
*
1595 TGCTGGGTAATGTTTTCTTTGC
1 TGCTAGGTAATGTTTTCTTTGC
1617 TGCTAGGTAATGTTTTCTTTG
1 TGCTAGGTAATGTTTTCTTTG
1638 TTGATCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.26, T:0.51
Consensus pattern (22 bp):
TGCTAGGTAATGTTTTCTTTGC
Found at i:4466 original size:25 final size:25
Alignment explanation
Indices: 4414--4464 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
4404 AATAAGTACT
4414 AAACATATAGGCAAACTTACTGGCA
1 AAACATATAGGCAAACTTACTGGCA
4439 AAACATATAGGCAAAC-T-CTGGCA
1 AAACATATAGGCAAACTTACTGGCA
4462 AAA
1 AAA
4465 AAAAAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 9 0.35
24 1 0.04
25 16 0.62
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.18
Consensus pattern (25 bp):
AAACATATAGGCAAACTTACTGGCA
Found at i:4658 original size:2 final size:2
Alignment explanation
Indices: 4651--4677 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4641 TAGAGGCAAG
4651 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 T
4678 GTTAGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15764 original size:33 final size:32
Alignment explanation
Indices: 15722--15794 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 32
15712 TACGTATCAG
15722 TTTTAGTTAACTTTGCAGCATTCACTTAACAA
1 TTTTAGTTAACTTTGCAGCATTCACTTAACAA
* *
15754 TTTTTAGTTAACTTTGTAGCATTCACTTATCAA
1 -TTTTAGTTAACTTTGCAGCATTCACTTAACAA
15787 TTTTAGTT
1 TTTTAGTT
15795 CAGCTTCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 8 0.21
33 30 0.79
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (32 bp):
TTTTAGTTAACTTTGCAGCATTCACTTAACAA
Found at i:17367 original size:12 final size:12
Alignment explanation
Indices: 17349--17383 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
17339 TGTTTAGTGT
17349 CATGGAAAATAC
1 CATGGAAAATAC
*
17361 TATGGAAAATAC
1 CATGGAAAATAC
*
17373 CAAGGAAAATA
1 CATGGAAAATA
17384 TTTTCTCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (12 bp):
CATGGAAAATAC
Found at i:20150 original size:12 final size:12
Alignment explanation
Indices: 20133--20165 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
20123 TTTGGTGTTG
*
20133 AGGAAAATACTA
1 AGGAAAATACCA
20145 AGGAAAATACCA
1 AGGAAAATACCA
20157 AGGAAAATA
1 AGGAAAATA
20166 TTTTCTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.61, C:0.09, G:0.18, T:0.12
Consensus pattern (12 bp):
AGGAAAATACCA
Found at i:23234 original size:21 final size:21
Alignment explanation
Indices: 23175--23234 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
23165 CACTGTTTAG
23175 GTACTGTACAGATGAGATT-A
1 GTACTGTACAGATGAGATTAA
* * * *
23195 -TATTGTATAGATCAAATTAA
1 GTACTGTACAGATGAGATTAA
23215 GTACTGTACAGATGAGATTA
1 GTACTGTACAGATGAGATTA
23235 TTAGAACAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
19 14 0.47
20 1 0.03
21 15 0.50
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.33
Consensus pattern (21 bp):
GTACTGTACAGATGAGATTAA
Found at i:28496 original size:3 final size:3
Alignment explanation
Indices: 28471--28541 Score: 108
Period size: 3 Copynumber: 24.0 Consensus size: 3
28461 TACTATATAC
* * *
28471 TAT TA- TAT TAT TGT TGT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28518 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
28542 CTCAAAATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:30322 original size:15 final size:17
Alignment explanation
Indices: 30292--30326 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
30282 ATTAATTGAT
30292 TTTCATTTATAAATTGC
1 TTTCATTTATAAATTGC
30309 TTTCA-TTA-AAATTGC
1 TTTCATTTATAAATTGC
30324 TTT
1 TTT
30327 TGAGTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 3 0.17
17 5 0.28
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTCATTTATAAATTGC
Found at i:31565 original size:16 final size:16
Alignment explanation
Indices: 31544--31579 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
31534 TAGGTGTCAT
31544 CACTCATCACATGCCA
1 CACTCATCACATGCCA
* *
31560 CACTCATCATATGCTA
1 CACTCATCACATGCCA
31576 CACT
1 CACT
31580 TTCAGATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.39, G:0.06, T:0.25
Consensus pattern (16 bp):
CACTCATCACATGCCA
Found at i:32724 original size:17 final size:16
Alignment explanation
Indices: 32682--32724 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
32672 CCATTTTCAT
*
32682 TTTCTCATTAATCATA
1 TTTCTCATTAATCACA
*
32698 TTTTTACATTAATCACCA
1 TTTCT-CATTAATCA-CA
32716 TTTCTCATT
1 TTTCTCATT
32725 GGTCCATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 13 0.59
18 5 0.23
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTCTCATTAATCACA
Found at i:36135 original size:20 final size:22
Alignment explanation
Indices: 36110--36188 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 22
36100 GTAAAACGGT
36110 AATCAGTAAAG-AGTAATAG-A
1 AATCAGTAAAGAAGTAATAGTA
36130 AATCAGT-AAGAAGTAATAGTA
1 AATCAGTAAAGAAGTAATAGTA
* * **
36151 AA-CAGTAAAAAAGTAAAAAGGC
1 AATCAGTAAAGAAGT-AATAGTA
36173 AATCAGTAAA-AAGTAA
1 AATCAGTAAAGAAGTAA
36189 AAAGGTATCT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
19 3 0.06
20 19 0.38
21 11 0.22
22 10 0.20
23 7 0.14
ACGTcount: A:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (22 bp):
AATCAGTAAAGAAGTAATAGTA
Found at i:36239 original size:22 final size:22
Alignment explanation
Indices: 36096--36244 Score: 71
Period size: 22 Copynumber: 7.0 Consensus size: 22
36086 GCAATCAGAA
* *
36096 AAAG-GTAAAACGGTAATCAGT
1 AAAGAGTAAAATGATAATCAGT
*
36117 AAAGAGTAATA-GA-AATCAGT
1 AAAGAGTAAAATGATAATCAGT
* *
36137 -AAGAAGTAATA-G-TAAACAGT
1 AAAG-AGTAAAATGATAATCAGT
* * **
36157 AAAAAAGTAAAAAGGCAATCAGT
1 -AAAGAGTAAAATGATAATCAGT
* * * *
36180 AAAAAGTAAAAAGGT-ATCTG-
1 AAAGAGTAAAATGATAATCAGT
* * *
36200 AAAGGGTAAAATGGTAATTAGT
1 AAAGAGTAAAATGATAATCAGT
*
36222 AAAGAGTAAAGTGATAATCAGT
1 AAAGAGTAAAATGATAATCAGT
36244 A
1 A
36245 GAGTAATGGT
Statistics
Matches: 101, Mismatches: 18, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
19 3 0.03
20 33 0.33
21 18 0.18
22 41 0.41
23 6 0.06
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.20
Consensus pattern (22 bp):
AAAGAGTAAAATGATAATCAGT
Found at i:36390 original size:22 final size:21
Alignment explanation
Indices: 36326--36403 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 21
36316 AAAGTAATGG
36326 TAATCAGTAAGAGTAAAATAA
1 TAATCAGTAAGAGTAAAATAA
* *
36347 TAATCAATAAAAAAGTAAAAAATAA
1 TAATCAGT--AAGAGT--AAAATAA
*
36372 TAATCAGTAACGAGTAAAATGA
1 TAATCAGTAA-GAGTAAAATAA
*
36394 TAGTCAGTAA
1 TAATCAGTAA
36404 TTAAATTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 7 0.15
22 15 0.33
23 7 0.15
24 3 0.07
25 14 0.30
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (21 bp):
TAATCAGTAAGAGTAAAATAA
Found at i:36485 original size:28 final size:30
Alignment explanation
Indices: 36444--36598 Score: 83
Period size: 29 Copynumber: 5.2 Consensus size: 30
36434 AAAAGAGAAA
*
36444 AAAAAGAAGAGT-A-AAAAGTGGTAATCAGT
1 AAAAAGAAGAGTAAGAAAAG-AGTAATCAGT
*
36473 AAAAA-AATAGTAAGAAAAGAGTAATCAGT
1 AAAAAGAAGAGTAAGAAAAGAGTAATCAGT
* * * *
36502 AAAAAGATTAAGAAATGAGTAAAAAATGGTGATCAGT
1 AAAAAG---AAG-AGTAAG-AAAAGA--GTAATCAGT
* *
36539 AAAAA-AAGAGTAA-AAGAGAGTAATTAGT
1 AAAAAGAAGAGTAAGAAAAGAGTAATCAGT
* * *
36567 -AATA-AAGAGTAAGAAATG-GTGATCAGT
1 AAAAAGAAGAGTAAGAAAAGAGTAATCAGT
36594 AAAAA
1 AAAAA
36599 CAAATAGTAA
Statistics
Matches: 95, Mismatches: 19, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
27 18 0.19
28 18 0.19
29 20 0.21
30 9 0.09
32 3 0.03
33 5 0.05
34 4 0.04
35 5 0.05
37 13 0.14
ACGTcount: A:0.57, C:0.03, G:0.21, T:0.19
Consensus pattern (30 bp):
AAAAAGAAGAGTAAGAAAAGAGTAATCAGT
Found at i:36513 original size:27 final size:28
Alignment explanation
Indices: 36464--36523 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
36454 GTAAAAAGTG
36464 GTAATCAGTAAAAAAATAGTAAGAAAAGA
1 GTAATCAGTAAAAAAATA-TAAGAAAAGA
* *
36493 GTAATCAGTAAAAAGAT-TAAGAAATGA
1 GTAATCAGTAAAAAAATATAAGAAAAGA
36520 GTAA
1 GTAA
36524 AAAATGGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 13 0.45
29 16 0.55
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.20
Consensus pattern (28 bp):
GTAATCAGTAAAAAAATATAAGAAAAGA
Found at i:36537 original size:66 final size:66
Alignment explanation
Indices: 36452--36584 Score: 196
Period size: 66 Copynumber: 2.0 Consensus size: 66
36442 AAAAAAAGAA
* * *
36452 GAGTAAAAAGTGGTAATCAGTAAAAAAATAGTAAGAAAAGAGTAATCAGTAA-AAAGATTAAGAA
1 GAGTAAAAAATGGTAATCAGTAAAAAAAGAGTAA-AAAAGAGTAATCAGTAATAAAGAGTAAGAA
36516 AT
65 AT
* * *
36518 GAGTAAAAAATGGTGATCAGTAAAAAAAGAGTAAAAGAGAGTAATTAGTAATAAAGAGTAAGAAA
1 GAGTAAAAAATGGTAATCAGTAAAAAAAGAGTAAAAAAGAGTAATCAGTAATAAAGAGTAAGAAA
36583 T
66 T
36584 G
1 G
36585 GTGATCAGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 15 0.25
66 45 0.75
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (66 bp):
GAGTAAAAAATGGTAATCAGTAAAAAAAGAGTAAAAAAGAGTAATCAGTAATAAAGAGTAAGAAA
T
Found at i:36594 original size:27 final size:26
Alignment explanation
Indices: 36518--36598 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 26
36508 ATTAAGAAAT
36518 GAGTAAAAAATGGTGATCAGTAAAAAAA
1 GAGT-AAAAATGGTGATCAGT-AAAAAA
* * *
36546 GAGTAAAAGA-GAGTAATTAGTAATAAA
1 GAGTAAAA-ATG-GTGATCAGTAAAAAA
36573 GAGTAAGAAATGGTGATCAGTAAAAA
1 GAGTAA-AAATGGTGATCAGTAAAAA
36599 CAAATAGTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
27 28 0.65
28 15 0.35
ACGTcount: A:0.54, C:0.02, G:0.23, T:0.20
Consensus pattern (26 bp):
GAGTAAAAATGGTGATCAGTAAAAAA
Found at i:36663 original size:26 final size:26
Alignment explanation
Indices: 36633--36696 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
36623 TAAGAAAAGG
*
36633 GGTAATCAGTAAAAAGAGTAAAATAT
1 GGTAATCAGTAAAAAGAGTAAAAAAT
*
36659 GGTAATCAGTACAAAGAGTAAAAAAT
1 GGTAATCAGTAAAAAGAGTAAAAAAT
*
36685 GGTAATTAGTAA
1 GGTAATCAGTAA
36697 TCAAGAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (26 bp):
GGTAATCAGTAAAAAGAGTAAAAAAT
Found at i:40314 original size:63 final size:63
Alignment explanation
Indices: 40240--40359 Score: 186
Period size: 63 Copynumber: 1.9 Consensus size: 63
40230 ATTCAGTACT
* * *
40240 TGTATTCGGAGTTTATGGTATTATTCAGCAGTGGATGGTATTTTCAGACTATGTGTTTAATTA
1 TGTACTCGGAGTTTATGGTATTATTCAGCAGTGGATGATATTTCCAGACTATGTGTTTAATTA
* * *
40303 TGTACTCGGAGTTTATGGTATTATTTAGCAGTGGGTGATGTTTCCAGACTATGTGTT
1 TGTACTCGGAGTTTATGGTATTATTCAGCAGTGGATGATATTTCCAGACTATGTGTT
40360 CAAACATGGA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (63 bp):
TGTACTCGGAGTTTATGGTATTATTCAGCAGTGGATGATATTTCCAGACTATGTGTTTAATTA
Found at i:44041 original size:12 final size:12
Alignment explanation
Indices: 44026--44067 Score: 56
Period size: 10 Copynumber: 3.8 Consensus size: 12
44016 AAATTATGCA
44026 TATTTTTATAGC
1 TATTTTTATAGC
44038 TATTTTTATA--
1 TATTTTTATAGC
44048 TATTTTT-T-GC
1 TATTTTTATAGC
44058 TATTTTTATA
1 TATTTTTATA
44068 TGTGTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
9 1 0.04
10 14 0.54
11 1 0.04
12 10 0.38
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (12 bp):
TATTTTTATAGC
Found at i:44059 original size:20 final size:22
Alignment explanation
Indices: 44025--44068 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
44015 CAAATTATGC
44025 ATATTTTTATAGCTATTTTTAT
1 ATATTTTTATAGCTATTTTTAT
44047 ATATTTTT-T-GCTATTTTTAT
1 ATATTTTTATAGCTATTTTTAT
44067 AT
1 AT
44069 GTGTTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.59
21 1 0.05
22 8 0.36
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (22 bp):
ATATTTTTATAGCTATTTTTAT
Found at i:44075 original size:20 final size:20
Alignment explanation
Indices: 44036--44075 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
44026 TATTTTTATA
*
44036 GCTATTTTTATATATTTTTT
1 GCTATTTTTATATATGTTTT
*
44056 GCTATTTTTATATGTGTTTT
1 GCTATTTTTATATATGTTTT
44076 TACCCTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (20 bp):
GCTATTTTTATATATGTTTT
Found at i:45619 original size:6 final size:6
Alignment explanation
Indices: 45605--45642 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
45595 ATTAATTTGC
* *
45605 TTTAGA TTTATA TTTAGA TTTAGA TTTATA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
45643 GCTTTGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (6 bp):
TTTAGA
Found at i:45628 original size:18 final size:17
Alignment explanation
Indices: 45605--45642 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
45595 ATTAATTTGC
45605 TTTAGATTTATATTTAGA
1 TTTAGATTTATATTTA-A
45623 TTTAGATTTATATTTAA
1 TTTAGATTTATATTTAA
45640 TTT
1 TTT
45643 GCTTTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTAGATTTATATTTAA
Found at i:49208 original size:62 final size:62
Alignment explanation
Indices: 49115--49271 Score: 190
Period size: 62 Copynumber: 2.5 Consensus size: 62
49105 GTGTGACTGG
* * * * **
49115 ACTGACCCTTTATCCGAAAGGGTATTCTGGGAAATTGAAACTATA-TCTGAGGATGTGGCAAA
1 ACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAATAGAAACTATACACT-AGGATGTAACAAA
** * *
49177 GTTGACTCTTTGTCCAAAAGGGTATTTTGGGAAATAGAAACTATACACTAGGATGTAACAAA
1 ACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAATAGAAACTATACACTAGGATGTAACAAA
* *
49239 ACTGGCCCTTTGTCTGAAAGGGTATTTTGGGAA
1 ACTGACCCTTTGTCCGAAAGGGTATTTTGGGAA
49272 TACAAAACTT
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
62 76 0.97
63 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (62 bp):
ACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAATAGAAACTATACACTAGGATGTAACAAA
Found at i:49330 original size:63 final size:64
Alignment explanation
Indices: 49184--49361 Score: 157
Period size: 63 Copynumber: 2.8 Consensus size: 64
49174 AAAGTTGACT
* * * * * * ** *
49184 CTTTGTCCAAAAGGGTATTTTGGG-AAA-TAGAAA-CTATACACTAGGATGTAACAAAACTGGCC
1 CTTTGTCCAAAAGGGCATTTTGGGAAAACTA-AAACCTAAATACAAGAATGTGATGAAACTAGCC
** * * * * *
49246 CTTTGTCTGAAAGGGTATTTTGGGAATAC-AAAACTTAAATGCAGGAATGTGATGAAACTAGCC
1 CTTTGTCCAAAAGGGCATTTTGGGAAAACTAAAACCTAAATACAAGAATGTGATGAAACTAGCC
* *
49309 CTTTGTCCAAAAGGGCGTTTTGGGAAAACTAGAACCTAAATACAAGAATGTGA
1 CTTTGTCCAAAAGGGCATTTTGGGAAAACTAAAACCTAAATACAAGAATGTGA
49362 CAAAAATCGA
Statistics
Matches: 89, Mismatches: 23, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
62 25 0.28
63 45 0.51
64 19 0.21
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (64 bp):
CTTTGTCCAAAAGGGCATTTTGGGAAAACTAAAACCTAAATACAAGAATGTGATGAAACTAGCC
Found at i:49479 original size:49 final size:48
Alignment explanation
Indices: 49422--49546 Score: 160
Period size: 49 Copynumber: 2.5 Consensus size: 48
49412 CTTTGTCTGA
*
49422 AAGGGCGTTTTGGGAAAAAGCAGGTAAAAACAAGTGCCTTCCATCTGGG
1 AAGGGCGTTTTGGG-AAAAGCAGGTAAAAACAAGTGCCTTCCATCCGGG
* ** *
49471 AAGGGCGTTTTAGGGAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGG
1 AAGGGCGTTTT-GGGAAAAGCAGGTAAAAACAAGTGCCTTCCATCCGGG
* *
49520 AAGGGCATTTTGGGGGAAAGCAGGTAA
1 AAGGGCGTTTT-GGGAAAAGCAGGTAA
49547 CAACTGAAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
49 63 0.95
50 3 0.05
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (48 bp):
AAGGGCGTTTTGGGAAAAGCAGGTAAAAACAAGTGCCTTCCATCCGGG
Found at i:52410 original size:13 final size:13
Alignment explanation
Indices: 52390--52421 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
52380 ATGATTATGC
52390 ATAA-TGCAATTT
1 ATAAGTGCAATTT
52402 ATAAGTGCAATTT
1 ATAAGTGCAATTT
52415 ATAAGTG
1 ATAAGTG
52422 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (13 bp):
ATAAGTGCAATTT
Done.