Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014897.1 Corchorus olitorius cultivar O-4 contig14930, 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: 56347
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:215 original size:39 final size:40
Alignment explanation
Indices: 159--238 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
149 TTTTATTCCT
159 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
199 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
238 A
1 A
239 GTCTTAGGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:591 original size:204 final size:201
Alignment explanation
Indices: 349--758 Score: 723
Period size: 204 Copynumber: 2.0 Consensus size: 201
339 TTCCTTAATA
349 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
* *
414 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGGATAGTTCTATATATATAATAG
66 ATTTAATAAATCAACCACTAATGTTCAACT-ACTTTTTTTTGGGATAGTT-T-TATATATAATAA
* *
479 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCATAGACT-TAAAAATTAATAACAT
128 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAATAATCATAGACTAAAAAAATTAATAACAT
543 TCACCATTG
193 TCACCATTG
552 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
617 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAATA
65 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGGATAGTTTTATATATAATAATA
*
682 ATGTGTTGTATCTTATTCACTACAACTTTGTTAATAATCTTAGACTAAAAAAATTAATAACATTC
130 ATGTGTTGTATCTTATTCACTACAACTTTGTTAATAATCATAGACTAAAAAAATTAATAACATTC
747 ACCATTG
195 ACCATTG
754 ATAAA
1 ATAAA
759 GTTATTAAGC
Statistics
Matches: 199, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
201 57 0.29
202 30 0.15
203 33 0.17
204 79 0.40
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (201 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGGATAGTTTTATATATAATAATAA
TGTGTTGTATCTTATTCACTACAACTTTGTTAATAATCATAGACTAAAAAAATTAATAACATTCA
CCATTG
Found at i:2678 original size:58 final size:57
Alignment explanation
Indices: 2587--2695 Score: 173
Period size: 58 Copynumber: 1.9 Consensus size: 57
2577 ATCATGCCTC
*
2587 GGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGTCTT
1 GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGTCTT
* * *
2644 GGTCCGAAAACGTCTTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
2696 TTTGATTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 13 0.28
58 34 0.72
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (57 bp):
GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGTCTT
Found at i:13336 original size:20 final size:21
Alignment explanation
Indices: 13280--13338 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
13270 TTCGTATCAT
* *
13280 CGTGTTAATCAGGTAATTAAAG
1 CGTGTTAATCATGT-CTTAAAG
* * *
13302 CGTGTCACTCGTGTCTTAAA-
1 CGTGTTAATCATGTCTTAAAG
13322 CGTGTTAATCATGTCTT
1 CGTGTTAATCATGTCTT
13339 TGACACAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 14 0.48
21 5 0.17
22 10 0.34
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (21 bp):
CGTGTTAATCATGTCTTAAAG
Found at i:13949 original size:23 final size:24
Alignment explanation
Indices: 13913--13960 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
13903 AGGGCCTTAC
* *
13913 AAAAAATGTAATAAGTTATAACAA
1 AAAAAAGGTAATAAGGTATAACAA
*
13937 AAAAAAGGT-ATAAGGTATTACAA
1 AAAAAAGGTAATAAGGTATAACAA
13960 A
1 A
13961 TCTCCAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.23
Consensus pattern (24 bp):
AAAAAAGGTAATAAGGTATAACAA
Found at i:15128 original size:23 final size:23
Alignment explanation
Indices: 15098--15141 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
15088 TGGAGGAAGA
15098 GGGTTAGTGGTAACTGTTTTGAT
1 GGGTTAGTGGTAACTGTTTTGAT
*
15121 GGGTTAGTGGTGACTGTTTTG
1 GGGTTAGTGGTAACTGTTTTG
15142 GTGCATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.14, C:0.05, G:0.39, T:0.43
Consensus pattern (23 bp):
GGGTTAGTGGTAACTGTTTTGAT
Found at i:23418 original size:17 final size:17
Alignment explanation
Indices: 23396--23429 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
23386 AATAAAATAA
*
23396 TAAAAATTATTAAAAAT
1 TAAAAATAATTAAAAAT
23413 TAAAAATAATTAAAAAT
1 TAAAAATAATTAAAAAT
23430 GAATTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAATAATTAAAAAT
Found at i:24654 original size:16 final size:16
Alignment explanation
Indices: 24615--24645 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24605 AAAAGAATTC
*
24615 AATTTTAATTATTTTT
1 AATTTTTATTATTTTT
24631 AATTTTTATTATTTT
1 AATTTTTATTATTTT
24646 ATTTATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
AATTTTTATTATTTTT
Found at i:24979 original size:17 final size:18
Alignment explanation
Indices: 24957--24990 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
24947 AAAATGAAAA
24957 TTTTCAATGC-TTTGATT
1 TTTTCAATGCGTTTGATT
24974 TTTTCAATGCGTTTGAT
1 TTTTCAATGCGTTTGAT
24991 AATTAAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.18, C:0.12, G:0.15, T:0.56
Consensus pattern (18 bp):
TTTTCAATGCGTTTGATT
Found at i:25658 original size:2 final size:2
Alignment explanation
Indices: 25651--25687 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
25641 ATCAGTATCC
*
25651 AT AT AT AT AT TT 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 AT AT AT AT A
25688 ACAGAAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:27156 original size:21 final size:21
Alignment explanation
Indices: 27130--27172 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
27120 TTCGTTGTAA
27130 GTTTTCCACCTCTCATGGATT
1 GTTTTCCACCTCTCATGGATT
27151 GTTTTCCACCTCTCATGGATT
1 GTTTTCCACCTCTCATGGATT
27172 G
1 G
27173 GAAACAATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.16, T:0.42
Consensus pattern (21 bp):
GTTTTCCACCTCTCATGGATT
Found at i:28162 original size:19 final size:19
Alignment explanation
Indices: 28142--28178 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28132 AATTAATTAT
28142 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
28160 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
28179 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:31600 original size:33 final size:33
Alignment explanation
Indices: 31558--31624 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
31548 AGGGCATGGA
31558 GTCAATTCAATTGAAAGGACTCAACGGTGGTAT
1 GTCAATTCAATTGAAAGGACTCAACGGTGGTAT
31591 GTCAATTCAATTGAAAGGACTCAACGGTGGTAT
1 GTCAATTCAATTGAAAGGACTCAACGGTGGTAT
31624 G
1 G
31625 AACGAAAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (33 bp):
GTCAATTCAATTGAAAGGACTCAACGGTGGTAT
Found at i:32975 original size:20 final size:21
Alignment explanation
Indices: 32936--32986 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
32926 TTTTCCTTTC
32936 CTTTGATTTGATTGATTATTG
1 CTTTGATTTGATTGATTATTG
32957 CTTTGA-TTGATTG-TCTATT-
1 CTTTGATTTGATTGAT-TATTG
*
32976 CCTTGATTTGA
1 CTTTGATTTGA
32987 ATTAGTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.22
20 15 0.56
21 6 0.22
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.55
Consensus pattern (21 bp):
CTTTGATTTGATTGATTATTG
Found at i:34004 original size:26 final size:25
Alignment explanation
Indices: 33962--34018 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 25
33952 AACAATCCAA
*
33962 AGAAAATAATAAGTTCGGTCTAACC
1 AGAAAATAACAAGTTCGGTCTAACC
*
33987 AGAAAATTAACAAGTTCGGTCTAGCC
1 AGAAAA-TAACAAGTTCGGTCTAACC
34013 AGAAAA
1 AGAAAA
34019 CACCTAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.21
Consensus pattern (25 bp):
AGAAAATAACAAGTTCGGTCTAACC
Found at i:38037 original size:35 final size:35
Alignment explanation
Indices: 38000--38602 Score: 714
Period size: 35 Copynumber: 17.2 Consensus size: 35
37990 TTCAATCAAC
* * * * *
38000 CCAGGGCGGTCTATCTTCAGTTAATTTCGGTTGAC
1 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
* * * **
38035 CCAGGGCGGTCTTTTTTTAGTTTATTTCAACTGA-
1 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
* * * *
38069 CCTAGGGTGGTCTTTATTCGGTTTATTTCAGTTGA-
1 CC-AGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
*
38104 CCCGGG-GTAGTCTTTCTTCAGTTTATTTCAGTTGAT
1 CCAGGGCG-A-TCTTTCTTCAGTTTATTTCAGTTGAT
* *
38140 CCAGGGCGATCTTTCTTCAATTAATTTCAGTTGAT
1 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
*
38175 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAC
1 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
* * *
38210 CCAGGGCGGTCTTTCTTCAGTTAATTTCAATTGAT
1 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
*
38245 CCAGGGCGATCTTTCTTCAGTTTAATTCAGTTGAT
1 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
* *
38280 CCAGGGTGATCTTTTCTTCAATTTATTTCAGTTGAT
1 CCAGGGCGATC-TTTCTTCAGTTTATTTCAGTTGAT
*
38316 CCAGGGCGATCTTTTCTT-AGTTTATTTCAGTTGAC
1 CCAGGGCGATC-TTTCTTCAGTTTATTTCAGTTGAT
* * *
38351 CCAGGG-TAGTCTTTCATCAATTTATTTCAGTTGAT
1 CCAGGGCGA-TCTTTCTTCAGTTTATTTCAGTTGAT
* * * *
38386 CTAGGGCGATCTTTCTTCAATTAATTTCAATTGAT
1 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
38421 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
1 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
38456 CCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGAT
1 CCAGGGCGATC-TTTCTTCAGTTTATTTCAGTTGAT
* *
38492 CCAGGGCGGTCTTTCTTCAGTTTATTGT-AATTGAT
1 CCAGGGCGATCTTTCTTCAGTTTATT-TCAGTTGAT
* * *
38527 CCAAGGTGATCTTTCTTCAGTTTATTTCAGTTGAC
1 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
* * ** *
38562 CCAGGGTGGTCTTTCTAGAGTTTATTTCAGTTGAC
1 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
38597 CCAGGG
1 CCAGGG
38603 AGGACCAAAG
Statistics
Matches: 495, Mismatches: 61, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
33 1 0.00
34 12 0.02
35 400 0.81
36 81 0.16
37 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (35 bp):
CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAT
Found at i:38377 original size:176 final size:176
Alignment explanation
Indices: 38013--38602 Score: 787
Period size: 176 Copynumber: 3.4 Consensus size: 176
38003 GGGCGGTCTA
* * * * * * *
38013 TCTTCAGTTAATTTCGGTTGACCCAGGGCGGTCTTTTTTTAGTTTATTTCAACTGA-CCTAGGGT
1 TCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTAATTTCAATTGATCC-AGGGC
* * * * *
38077 GGTCTTTATTCGGTTTATTTCAGTTGACCCGGGGT-AGTC-TTTCTTCAGTTTATTTCAGTTGAT
65 GATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGA-TCTTTTCTTCAGTTTATTTCAGTTGAT
* * *
38140 CCAGGGCGATCTTTCTTCAATTAATTTCAGTTGATCCAGGGCGATCTT
129 CCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTT
38188 TCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTAATTTCAATTGATCCAGGGCG
1 TCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTAATTTCAATTGATCCAGGGCG
* *
38253 ATCTTTCTTCAGTTTAATTCAGTTGATCCAGGGTGATCTTTTCTTCAATTTATTTCAGTTGATCC
66 ATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCC
*
38318 AGGGCGATCTTTTCTT-AGTTTATTTCAGTTGACCCAGGGT-AGTCTT
131 AGGGCGATC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGTGA-TCTT
* * * * * *
38364 TCATCAATTTATTTCAGTTGATCTAGGGCGATCTTTCTTCAATTAATTTCAATTGATCCAGGGCG
1 TCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTAATTTCAATTGATCCAGGGCG
*
38429 ATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCC
66 ATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCC
* * *
38494 AGGGCGGTCTTTCTTCAGTTTATTGT-AATTGATCCAAGGTGATCTT
131 AGGGCGATCTTTCTTCAGTTTATT-TCAGTTGATCCAGGGTGATCTT
* ** * * *
38540 TCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTAGAGTTTATTTCAGTTGACCCAGGG
1 TCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTAATTTCAATTGATCCAGGG
38603 AGGACCAAAG
Statistics
Matches: 364, Mismatches: 43, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
175 92 0.25
176 264 0.73
177 8 0.02
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (176 bp):
TCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTAATTTCAATTGATCCAGGGCG
ATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCC
AGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTT
Found at i:47186 original size:66 final size:66
Alignment explanation
Indices: 47116--47250 Score: 261
Period size: 66 Copynumber: 2.0 Consensus size: 66
47106 CGAAAAGTAC
47116 CTAAAACTAAAACATAGCATTTCAAGTTTGTTACATTTTTTTCAAAAAAAAAATACTAATGAAGA
1 CTAAAACTAAAACATAGCATTTCAAGTTTGTTACATTTTTTTCAAAAAAAAAATACTAATGAAGA
47181 A
66 A
*
47182 CTAAAACTAAAACATAGCATTTCAAGTTTGTTACATTTTTTTCAAGAAAAAAATACTAATGAAGA
1 CTAAAACTAAAACATAGCATTTCAAGTTTGTTACATTTTTTTCAAAAAAAAAATACTAATGAAGA
47247 A
66 A
47248 CTA
1 CTA
47251 CAATAACTAC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (66 bp):
CTAAAACTAAAACATAGCATTTCAAGTTTGTTACATTTTTTTCAAAAAAAAAATACTAATGAAGA
A
Found at i:48156 original size:27 final size:27
Alignment explanation
Indices: 48124--48197 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
48114 AGGGTCACCT
* *
48124 AGGGGGATTTTGGGTCATTTGCACATTC
1 AGGGGCATTTT-GGTCATTTGCACATCC
*
48152 AGGGGCATTTTAGTCATTTGCACATCC
1 AGGGGCATTTTGGTCATTTGCACATCC
48179 AGGGGCATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
48198 TAAGCTCACT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 32 0.76
28 10 0.24
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.36
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACATCC
Found at i:51252 original size:40 final size:41
Alignment explanation
Indices: 51167--51252 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 41
51157 TTTAGCCTTT
* * * *
51167 GATTTAGGACTTTATTTACTATTTGGTGTAATTTAGTCCCT
1 GATTTAGGACTTTAATTACTATTTGGTGCAATTTAGCCCCA
* *
51208 GATTTAGGATTTTAATTATTA-TTGGTGCAATTT-GACCCCA
1 GATTTAGGACTTTAATTACTATTTGGTGCAATTTAG-CCCCA
51248 GATTT
1 GATTT
51253 TAGAAATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
39 1 0.03
40 19 0.50
41 18 0.47
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (41 bp):
GATTTAGGACTTTAATTACTATTTGGTGCAATTTAGCCCCA
Found at i:53035 original size:28 final size:28
Alignment explanation
Indices: 53003--53063 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
52993 TTACGAAAGT
*
53003 CGTTTCGACAGGGTCTCCCGGACCCGAA
1 CGTTTCGACAGGATCTCCCGGACCCGAA
53031 CGTTTCGACAGGATCTCCCGGACCCGAA
1 CGTTTCGACAGGATCTCCCGGACCCGAA
53059 CGTTT
1 CGTTT
53064 ATAGCAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.18, C:0.34, G:0.26, T:0.21
Consensus pattern (28 bp):
CGTTTCGACAGGATCTCCCGGACCCGAA
Found at i:55885 original size:17 final size:17
Alignment explanation
Indices: 55862--55907 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
55852 ACTCCTGGCC
55862 AAAGACCAATTATATGT
1 AAAGACCAATTATATGT
*
55879 GAAGACCCAATTATATGT
1 AAAGA-CCAATTATATGT
*
55897 AAAGTCCAATT
1 AAAGACCAATT
55908 TAAATTGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (17 bp):
AAAGACCAATTATATGT
Done.