Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009225.1 Corchorus capsularis cultivar CVL-1 contig09246, 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: 15891
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:165 original size:81 final size:78
Alignment explanation
Indices: 35--277 Score: 333
Period size: 81 Copynumber: 3.2 Consensus size: 78
25 TTTTTTTAAC
* *
35 TAAAATAGTAAAATTGTAAAAT-ATAATAGTTATAAGGATGTTAGATTTAATTATATAAAAATTG
1 TAAAATAGTAAAA-TGTAAAATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAG
99 AGTTTTTAGTTGAG
65 AGTTTTTAGTTGAG
113 TAAAATAGTAAAATGGTAAAATATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAAAT
1 TAAAATAGTAAAAT-GT-AAA-ATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAAAT
178 AGAGTTTTTAGTTGAG
63 AGAGTTTTTAGTTGAG
* *
194 TAAAATAGTAAAA--TAAAATAAT--TA--TA-AA-GATATTATATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGTAAAATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
251 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
264 TAAAACTATTAAAA
1 TAAAA-TAGTAAAA
278 CCTAAACAAT
Statistics
Matches: 155, Mismatches: 5, Indels: 17
0.88 0.03 0.10
Matches are distributed among these distances:
70 45 0.29
71 9 0.06
72 2 0.01
74 2 0.01
76 5 0.03
77 4 0.03
78 16 0.10
79 3 0.02
80 2 0.01
81 67 0.43
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (78 bp):
TAAAATAGTAAAATGTAAAATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:238 original size:70 final size:71
Alignment explanation
Indices: 119--277 Score: 230
Period size: 70 Copynumber: 2.2 Consensus size: 71
109 TGAGTAAAAT
* * * *
119 AGTAAAATGGTAAAATATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
1 AGTAAAATAGT-AAA-ATAATAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTT
184 TTTAGTTG
64 TTTAGTTG
*
192 AGTAAAATAGTAAAATAA-AATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAATAGTAAAATAATAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTT
256 TAGTTG
66 TAGTTG
*
262 AGTAAAACTATTAAAA
1 AGTAAAA-TAGTAAAA
278 CCTAAACAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
70 55 0.70
71 11 0.14
72 3 0.04
73 10 0.13
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (71 bp):
AGTAAAATAGTAAAATAATAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTT
TAGTTG
Found at i:356 original size:166 final size:166
Alignment explanation
Indices: 177--510 Score: 659
Period size: 166 Copynumber: 2.0 Consensus size: 166
167 TATATAAAAA
177 TAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAAT
1 TAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAAT
*
242 AAAAATAGAGTTTTTAGTTGAGTAAAACTATTAAAACCTAAACAATGGCAGTTTAGAAATATATT
66 AAAAACAGAGTTTTTAGTTGAGTAAAACTATTAAAACCTAAACAATGGCAGTTTAGAAATATATT
307 TGACAAATAAGGGTATAATAGGCGATTCAAAAGTTT
131 TGACAAATAAGGGTATAATAGGCGATTCAAAAGTTT
343 TAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAAT
1 TAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAAT
408 AAAAACAGAGTTTTTAGTTGAGTAAAACTATTAAAACCTAAACAATGGCAGTTTAGAAATATATT
66 AAAAACAGAGTTTTTAGTTGAGTAAAACTATTAAAACCTAAACAATGGCAGTTTAGAAATATATT
473 TGACAAATAAGGGTATAATAGGCGATTCAAAAGTTT
131 TGACAAATAAGGGTATAATAGGCGATTCAAAAGTTT
509 TA
1 TA
511 CAGCTGAACG
Statistics
Matches: 167, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 167 1.00
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.34
Consensus pattern (166 bp):
TAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAAT
AAAAACAGAGTTTTTAGTTGAGTAAAACTATTAAAACCTAAACAATGGCAGTTTAGAAATATATT
TGACAAATAAGGGTATAATAGGCGATTCAAAAGTTT
Found at i:547 original size:6 final size:6
Alignment explanation
Indices: 530--586 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
520 GTACTTTTTA
530 ATATAG -TATAG ATATAG ATATAG -TATAG ATATAG ATATAG ATATA-
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
575 A-ATAG -TATAG AT
1 ATATAG ATATAG AT
587 TATTATTATG
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
4 3 0.07
5 15 0.33
6 28 0.61
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:552 original size:17 final size:17
Alignment explanation
Indices: 530--574 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
520 GTACTTTTTA
530 ATATAGTATAGATATAG
1 ATATAGTATAGATATAG
547 ATATAGTATAGATATAG
1 ATATAGTATAGATATAG
564 ATATAGATATA
1 ATATAG-TATA
575 AATAGTATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.36
Consensus pattern (17 bp):
ATATAGTATAGATATAG
Found at i:563 original size:23 final size:21
Alignment explanation
Indices: 530--586 Score: 87
Period size: 23 Copynumber: 2.6 Consensus size: 21
520 GTACTTTTTA
530 ATATAGTATAGATATAGATAT
1 ATATAGTATAGATATAGATAT
551 AGTATAGATATAGATATAGATAT
1 A-TATAG-TATAGATATAGATAT
*
574 AAATAGTATAGAT
1 ATATAGTATAGAT
587 TATTATTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 8 0.24
22 9 0.27
23 16 0.48
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (21 bp):
ATATAGTATAGATATAGATAT
Found at i:1519 original size:17 final size:19
Alignment explanation
Indices: 1497--1531 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1487 TAATGACCTC
1497 TAAATTA-TATA-TTTCCT
1 TAAATTACTATACTTTCCT
1514 TAAATTACTATACTTTCC
1 TAAATTACTATACTTTCC
1532 AACATCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTACTATACTTTCCT
Found at i:2116 original size:53 final size:53
Alignment explanation
Indices: 2044--2150 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 53
2034 CGGTTGTTTT
* *
2044 ATTTTATAAATTCTTTTAAGATAATTCATTTAAGAAATCAAATTTTGTTGTGA
1 ATTTTATAAATTCTTTTAAGAAAATTCAATTAAGAAATCAAATTTTGTTGTGA
2097 ATTTTATAAATT-TTCTTAAGAAAATTCAATTAAGAAATCAAATTTTGTTGTGA
1 ATTTTATAAATTCTT-TTAAGAAAATTCAATTAAGAAATCAAATTTTGTTGTGA
2150 A
1 A
2151 ATGTTAACAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
52 2 0.04
53 49 0.96
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (53 bp):
ATTTTATAAATTCTTTTAAGAAAATTCAATTAAGAAATCAAATTTTGTTGTGA
Found at i:3171 original size:26 final size:25
Alignment explanation
Indices: 3142--3198 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
3132 ATTTCTACAT
*
3142 AAATTTAGTAAC-CTCACATTCTTAGA
1 AAATTTAGAAACACT-ACATTCTTA-A
3168 AAATTTAGAAACACTACATTCTTAA
1 AAATTTAGAAACACTACATTCTTAA
3193 AAATTT
1 AAATTT
3199 CAGGTTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 7 0.24
26 20 0.69
27 2 0.07
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (25 bp):
AAATTTAGAAACACTACATTCTTAA
Found at i:4524 original size:58 final size:58
Alignment explanation
Indices: 4406--4526 Score: 131
Period size: 58 Copynumber: 2.1 Consensus size: 58
4396 GCATTAATGT
* * * * *
4406 TAATTGATTGTAATTGATCAAAATATTCATTTAACAATTAATTAAATGGAATTATTAC
1 TAATTGATTGTAATTGATCAAAATAGTCAATCAACAATTAATTAAATGCAATTATAAC
* *
4464 TAATTGATTTTAATTGATCAAATTAGTCAAATCAACTAATTAATT-AAT-CAATCTA-AAC
1 TAATTGATTGTAATTGATCAAAATAGTC-AATCAAC-AATTAATTAAATGCAAT-TATAAC
4522 TAATT
1 TAATT
4527 AATATATTTC
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
58 35 0.66
59 10 0.19
60 8 0.15
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (58 bp):
TAATTGATTGTAATTGATCAAAATAGTCAATCAACAATTAATTAAATGCAATTATAAC
Found at i:4542 original size:30 final size:30
Alignment explanation
Indices: 4508--4568 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
4498 ACTAATTAAT
*
4508 TAATCAATCTAAACTAATTAATATATTTCC
1 TAATCAACCTAAACTAATTAATATATTTCC
* *
4538 TAATCAACCTAAAGTAATTAATTTATTTCC
1 TAATCAACCTAAACTAATTAATATATTTCC
4568 T
1 T
4569 TTTATCCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (30 bp):
TAATCAACCTAAACTAATTAATATATTTCC
Found at i:5212 original size:139 final size:141
Alignment explanation
Indices: 4891--5220 Score: 540
Period size: 141 Copynumber: 2.4 Consensus size: 141
4881 TACAAATTTG
* * *
4891 ATTAGATAATCATCAATCAATTACAGCTTTGATTGGCAAAATTAACTAACAACATGTTCAATAAT
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACAACATGTTCAATAAT
*
4956 TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTGGCAAT
66 TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTAGCAAT
5021 TTTATGGTAAA
131 TTTATGGTAAA
*
5032 ATTATATAATCATCAATCAATTACAACTTTGATT-GACAAAATTAACTAACAACATGTTCAATAA
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGA-AAAATTAACTAACAACATGTTCAATAA
* * * *
5096 TTTATTTTTTTGGTAACGTAATTACTAATTGATTTATTTATTTATGTTAAT-TTTTTTGTAGCGA
65 TTTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTAGCAA
5160 -TTTATGGTAAA
130 TTTTATGGTAAA
*
5171 ATTAAATAATTATCAATCAATTACAACTTTGATTGGAAAAATTAACTAAC
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAAC
5221 GATCACTAAC
Statistics
Matches: 177, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
139 56 0.32
140 13 0.07
141 108 0.61
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (141 bp):
ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACAACATGTTCAATAAT
TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTAGCAAT
TTTATGGTAAA
Found at i:7977 original size:13 final size:14
Alignment explanation
Indices: 7954--7987 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
7944 ATAAAGCCAA
7954 TTTTTTCTTTTTCC
1 TTTTTTCTTTTTCC
*
7968 TTTTTT-TTTTTCG
1 TTTTTTCTTTTTCC
7981 TTTTTTC
1 TTTTTTC
7988 CAAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTTTCTTTTTCC
Found at i:8433 original size:60 final size:61
Alignment explanation
Indices: 8330--8444 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 61
8320 TAGTATGTAG
* *
8330 ATCAAAATTTCATAGGGAAATTAACAAAATTTCATAATGAGG-TTATCAAAATTTGTAGTT
1 ATCAAAATTTCATAGAGAAATTAACAAAATTTCATAAGGAGGTTTATCAAAATTTGTAGTT
* * *
8390 ATCAAGATTTCATA-AGAAAGTTATCAAAATTTTAT-AGGAAGGTTTATCAAAATTT
1 ATCAAAATTTCATAGAGAAA-TTAACAAAATTTCATAAGG-AGGTTTATCAAAATTT
8445 TATAGAAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
59 6 0.13
60 29 0.62
61 12 0.26
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (61 bp):
ATCAAAATTTCATAGAGAAATTAACAAAATTTCATAAGGAGGTTTATCAAAATTTGTAGTT
Found at i:8438 original size:23 final size:22
Alignment explanation
Indices: 8304--8513 Score: 127
Period size: 22 Copynumber: 9.7 Consensus size: 22
8294 TTAATAAGAG
*
8304 GGTTATCAAAATTTCATA-GTA
1 GGTTATCAAAATTTCATAGGAA
* *
8325 TGTAGATCAAAATTTCATAGGGAA
1 GGT-TATCAAAATTTCATA-GGAA
* * *
8349 -ATTAACAAAATTTCATAATG-A
1 GGTTATCAAAATTTCAT-AGGAA
*
8370 GGTTATCAAAA-TT--T--GTA
1 GGTTATCAAAATTTCATAGGAA
* *
8387 -GTTATCAAGATTTCATAAGAA
1 GGTTATCAAAATTTCATAGGAA
* *
8408 AGTTATCAAAATTTTATAGGAA
1 GGTTATCAAAATTTCATAGGAA
* *
8430 GGTTTATCAAAATTTTATAGAAA
1 GG-TTATCAAAATTTCATAGGAA
*
8453 GATTTATCAAAATTTCATA-GAGA
1 G-GTTATCAAAATTTCATAGGA-A
* *
8476 GGTTATCACAATTTCATAGTG-T
1 GGTTATCAAAATTTCATAG-GAA
*
8498 GATTATCAAAATTTCA
1 GGTTATCAAAATTTCA
8514 GTGTGTGATT
Statistics
Matches: 148, Mismatches: 24, Indels: 33
0.72 0.12 0.16
Matches are distributed among these distances:
16 10 0.07
17 3 0.02
19 2 0.01
21 7 0.05
22 84 0.57
23 39 0.26
24 3 0.02
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGAA
Found at i:8482 original size:45 final size:44
Alignment explanation
Indices: 8304--8513 Score: 145
Period size: 44 Copynumber: 4.9 Consensus size: 44
8294 TTAATAAGAG
* * *
8304 GGTTATCAAAATTTCATAGTATG-TAGATCAAAATTTCATAGGGAA
1 GGTTATCAAAATTTCATAGAAAGAT-TATCAAAATTTCATA-GGAA
* * * * *
8349 -ATTAACAAAATTTCATA-ATGAGGTTATCAAAA-TT--T--GTA
1 GGTTATCAAAATTTCATAGA-AAGATTATCAAAATTTCATAGGAA
* *
8387 -GTTATCAAGATTTCATAAGAAAG-TTATCAAAATTTTATAGGAA
1 GGTTATCAAAATTTCAT-AGAAAGATTATCAAAATTTCATAGGAA
*
8430 GGTTTATCAAAATTTTATAGAAAGATTTATCAAAATTTCATA-GAGA
1 GG-TTATCAAAATTTCATAGAAAGA-TTATCAAAATTTCATAGGA-A
* ***
8476 GGTTATCACAATTTCATAGTGTGATTATCAAAATTTCA
1 GGTTATCAAAATTTCATAGAAAGATTATCAAAATTTCA
8514 GTGTGTGATT
Statistics
Matches: 131, Mismatches: 20, Indels: 29
0.73 0.11 0.16
Matches are distributed among these distances:
38 24 0.18
39 5 0.04
40 1 0.01
41 2 0.02
43 4 0.03
44 44 0.34
45 33 0.25
46 18 0.14
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGAAAGATTATCAAAATTTCATAGGAA
Found at i:8535 original size:22 final size:22
Alignment explanation
Indices: 8456--8524 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
8446 ATAGAAAGAT
* * *
8456 TTATCAAAATTTCA-TAGAGAGG
1 TTATCAAAATTTCAGT-GTGTGA
*
8478 TTATCACAATTTCA-TAGTGTGA
1 TTATCAAAATTTCAGT-GTGTGA
8500 TTATCAAAATTTCAGTGTGTGA
1 TTATCAAAATTTCAGTGTGTGA
8522 TTA
1 TTA
8525 CTAACAATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
22 40 0.98
23 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCAGTGTGTGA
Found at i:10142 original size:14 final size:14
Alignment explanation
Indices: 10123--10165 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
10113 CAGAAAAATG
10123 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
**
10137 AAAGAAAGGGAAAA
1 AAAGAAAAAGAAAA
10151 TAAAG-AAAAGAAAA
1 -AAAGAAAAAGAAAA
10165 A
1 A
10166 GGATGAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 1 0.04
14 19 0.79
15 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAGAAAAAGAAAA
Found at i:10977 original size:28 final size:28
Alignment explanation
Indices: 10946--11004 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
10936 ACCGTAATAG
* * *
10946 CCCTAGTATATTAAAATTACCGTTTTAC
1 CCCTAGTAGACTAAAATTACAGTTTTAC
* *
10974 CCCTATTAGGCTAAAATTACAGTTTTAC
1 CCCTAGTAGACTAAAATTACAGTTTTAC
11002 CCC
1 CCC
11005 CAGAGGCCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (28 bp):
CCCTAGTAGACTAAAATTACAGTTTTAC
Found at i:11017 original size:28 final size:28
Alignment explanation
Indices: 10958--11018 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
10948 CTAGTATATT
* * * *
10958 AAAATTACCGTTTTACCCCTATTAGGCT
1 AAAATTACAGTTTTACCCCCATGAGGCA
10986 AAAATTACAGTTTTACCCCCA-GAGGCCA
1 AAAATTACAGTTTTACCCCCATGAGG-CA
11014 AAAAT
1 AAAAT
11019 GATTAAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 3 0.11
28 25 0.89
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (28 bp):
AAAATTACAGTTTTACCCCCATGAGGCA
Found at i:11409 original size:14 final size:14
Alignment explanation
Indices: 11390--11434 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
11380 TTTATTACTA
11390 TTTTTAATAAATTG
1 TTTTTAATAAATTG
*
11404 TTTTT-ATAAATGG
1 TTTTTAATAAATTG
* *
11417 TTTTTATTAAAATG
1 TTTTTAATAAATTG
11431 TTTT
1 TTTT
11435 GGGTGCATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTTTAATAAATTG
Found at i:11898 original size:14 final size:15
Alignment explanation
Indices: 11853--11898 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
11843 ATTGGATTTA
11853 TTATTACTAA-TTGTT
1 TTATTA-TAACTTGTT
11868 TTATTATAACTTGTT
1 TTATTATAACTTGTT
*
11883 TTTTTATAAC-TGTT
1 TTATTATAACTTGTT
11897 TT
1 TT
11899 GGTTGTGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 9 0.31
15 20 0.69
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.63
Consensus pattern (15 bp):
TTATTATAACTTGTT
Done.