Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016263.1 Corchorus capsularis cultivar CVL-1 contig16284, 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: 12035
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:691 original size:14 final size:15
Alignment explanation
Indices: 664--693 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
654 AAAAAAAATC
664 TAAAATACAAATAAA
1 TAAAATACAAATAAA
679 TAAAATA-AAATAAA
1 TAAAATACAAATAAA
693 T
1 T
694 CTATATCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAATACAAATAAA
Found at i:1039 original size:16 final size:16
Alignment explanation
Indices: 1007--1078 Score: 61
Period size: 12 Copynumber: 4.9 Consensus size: 16
997 TATATATATA
*
1007 TATATATAATTCATGTG
1 TATATAT-ATACATGTG
1024 TATATATATACATGTG
1 TATATATATACATGTG
1040 ----TATATACATGTG
1 TATATATATACATGTG
1052 --TATA-A-ACATGTG
1 TATATATATACATGTG
*
1064 TATATATACACATGT
1 TATATATATACATGT
1079 TGGCAAAAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
12 19 0.40
13 1 0.02
14 6 0.12
15 1 0.02
16 14 0.29
17 7 0.15
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (16 bp):
TATATATATACATGTG
Found at i:1045 original size:12 final size:12
Alignment explanation
Indices: 1028--1069 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
1018 CATGTGTATA
1028 TATATACATGTG
1 TATATACATGTG
1040 TATATACATGTG
1 TATATACATGTG
*
1052 TATAAACATGTG
1 TATATACATGTG
1064 TATATA
1 TATATA
1070 TACACATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.40
Consensus pattern (12 bp):
TATATACATGTG
Found at i:3185 original size:21 final size:21
Alignment explanation
Indices: 3161--3206 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
3151 TTAAAAAAAA
3161 AAAGGAAAAATAATGGTCTGC
1 AAAGGAAAAATAATGGTCTGC
3182 AAAGGAAAAATAATGGTCTGC
1 AAAGGAAAAATAATGGTCTGC
3203 AAAG
1 AAAG
3207 TTATCCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.09, G:0.24, T:0.17
Consensus pattern (21 bp):
AAAGGAAAAATAATGGTCTGC
Found at i:4501 original size:18 final size:19
Alignment explanation
Indices: 4463--4502 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
4453 AAAGGTTGAA
4463 CAACACATTTTGGCAAAAC
1 CAACACATTTTGGCAAAAC
4482 CAACACATTTTGGC-AAAC
1 CAACACATTTTGGCAAAAC
4500 CAA
1 CAA
4503 ATTTTTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (19 bp):
CAACACATTTTGGCAAAAC
Found at i:4596 original size:2 final size:2
Alignment explanation
Indices: 4589--4629 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4579 CAGAATCATG
4589 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4630 CTAGCTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5142 original size:23 final size:22
Alignment explanation
Indices: 4963--5392 Score: 147
Period size: 22 Copynumber: 19.7 Consensus size: 22
4953 AAGTTCTCAA
** *
4963 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCACAC
*
4985 AATG-AATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-ACAC
* * *
5007 TATTAGATGTTGATAACCAC-C
1 TATGAAATTTTGATAACCACAC
* * **
5028 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCACAC
* * * *
5051 TATGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCACAC
*
5072 ATAT-AAATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCACAC
* *
5095 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCACAC
* *
5117 TATGAAATTTGTGATAACCTCGC
1 TATGAAATTT-TGATAACCACAC
*
5140 TATGAAATTTTGATAA--ATCTTC
1 TATGAAATTTTGATAACCA-C-AC
* * *
5162 TTATAAAATTTTGATAAACATCCC
1 -TATGAAATTTTGATAACCA-CAC
* ** *
5186 TATAAAATTTTGATAACTTTC-T
1 TATGAAATTTTGATAAC-CACAC
*
5208 TATGAAATCTTGAT----A-AC
1 TATGAAATTTTGATAACCACAC
* * * *
5225 TA-CAAATTTTGATTACCTCCC
1 TATGAAATTTTGATAACCACAC
** * *
5246 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCACAC
* ** * *
5268 TATGAAATTTTGTTATTCTCCC
1 TATGAAATTTTGATAACCACAC
* *
5290 TATGAAATTTTGATTTA-CATAC
1 TATGAAATTTTGA-TAACCACAC
* *
5312 TATGAAATTTTGATAATCCTC-T
1 TATGAAATTTTGATAA-CCACAC
* * * *
5334 TGTGAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAACCACAC
**
5356 TATGAAATTTTGATAACCTTTA-
1 TATGAAATTTTGATAACC-ACAC
5378 TATGAAATTTTGATA
1 TATGAAATTTTGATA
5393 TCCTCCCTGA
Statistics
Matches: 301, Mismatches: 78, Indels: 58
0.69 0.18 0.13
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
21 25 0.08
22 189 0.63
23 72 0.24
24 1 0.00
25 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:5177 original size:45 final size:44
Alignment explanation
Indices: 5121--5224 Score: 127
Period size: 46 Copynumber: 2.3 Consensus size: 44
5111 TCACACTATG
* * *
5121 AAATTTGTGATAACCTCGCTATGAAATTTTGATAAATCTTCTTATA
1 AAATTT-TGATAACATCCCTATAAAATTTTGATAAAT-TTCTTATA
* *
5167 AAATTTTGATAAACATCCCTATAAAATTTTGATAACTTTCTTATG
1 AAATTTTGAT-AACATCCCTATAAAATTTTGATAAATTTCTTATA
*
5212 AAATCTTGATAAC
1 AAATTTTGATAAC
5225 TACAAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
44 3 0.06
45 20 0.39
46 28 0.55
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (44 bp):
AAATTTTGATAACATCCCTATAAAATTTTGATAAATTTCTTATA
Found at i:5340 original size:44 final size:43
Alignment explanation
Indices: 5097--5430 Score: 151
Period size: 44 Copynumber: 7.8 Consensus size: 43
5087 AATCACACTC
* * * *
5097 TGAAATTTTGATAATCACACTATGAAATTTGTGATA-ACCTCGCTA
1 TGAAATTTTGATAATC-CTCTTTGAAATTT-TGATATACAT-ACTA
* * * *
5142 TGAAATTTTGATAAATCTTCTTATAAAATTTTGATAAACATCCCTA
1 TGAAATTTTGAT-AATCCTCTT-TGAAATTTTGATATACAT-ACTA
* * *
5188 TAAAATTTTGATAA-CTTTCTTATGAAATCTTGATA-AC-TAC--
1 TGAAATTTTGATAATC-CTCTT-TGAAATTTTGATATACATACTA
* * ** * *
5228 --AAATTTTGATTA-CCTCCCTATGATTTTTTGATA-ACCTCATTA
1 TGAAATTTTGATAATCCT--CTTTGAAATTTTGATATACAT-ACTA
* * * * *
5270 TGAAATTTTGTTATTCTCCCTATGAAATTTTGATTTACATACTA
1 TGAAATTTTGATAATC-CTCTTTGAAATTTTGATATACATACTA
* *
5314 TGAAATTTTGATAATCCTCTTGTGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAATCCTCTT-TGAAATTTTGATATAC-ATACTA
* * **
5358 TGAAATTTTGATAA-CCTTTATATGAAATTTTGATAT-CCT-CCC
1 TGAAATTTTGATAATCCTCT-T-TGAAATTTTGATATACATACTA
*
5400 TG-AATTTTGAT-ATCCTCCTTGAAATTTTGAT
1 TGAAATTTTGATAATCCTCTTTGAAATTTTGAT
5431 TACTCCATAA
Statistics
Matches: 227, Mismatches: 42, Indels: 46
0.72 0.13 0.15
Matches are distributed among these distances:
37 1 0.00
38 24 0.11
39 15 0.07
40 3 0.01
41 12 0.05
42 4 0.02
43 10 0.04
44 85 0.37
45 43 0.19
46 30 0.13
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (43 bp):
TGAAATTTTGATAATCCTCTTTGAAATTTTGATATACATACTA
Found at i:5436 original size:19 final size:20
Alignment explanation
Indices: 5380--5430 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
5370 AACCTTTATA
5380 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
5400 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
5419 TGAAATTTTGAT
1 TGAAATTTTGAT
5431 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:5561 original size:22 final size:22
Alignment explanation
Indices: 5536--5761 Score: 156
Period size: 22 Copynumber: 10.3 Consensus size: 22
5526 AATTACATTT
*
5536 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
5558 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
5580 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
5602 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
5624 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
5646 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
* *
5668 TGAAATTTTGATAATCAGATCTCTA
1 TGAAATTTTGATAA-C--CTCTTTA
* * *
5693 TGAAATTTCGATAATCACTTTA
1 TGAAATTTTGATAACCTCTTTA
* *
5715 TGAGATTTT-ATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
5735 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
5755 TGAAATT
1 TGAAATT
5762 GAGACTTTTA
Statistics
Matches: 157, Mismatches: 40, Indels: 16
0.74 0.19 0.08
Matches are distributed among these distances:
19 2 0.01
20 19 0.12
21 7 0.04
22 108 0.69
23 3 0.02
25 18 0.11
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:5625 original size:66 final size:66
Alignment explanation
Indices: 5536--5684 Score: 174
Period size: 66 Copynumber: 2.3 Consensus size: 66
5526 AATTACATTT
* * * * * * * ** *
5536 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC-TTTATAAAATTTTGTTGACCCCTC
1 TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCGCTT-TAAAATTTTGATAACAACAC
5600 TA
65 TA
* *
5602 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACT
1 TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCGCTTTAAAATTTTGATAACAACACT
5667 A
66 A
5668 TGAAATTTTGATAATCA
1 TGAAATTTTGATAATCA
5685 GATCTCTATG
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
66 68 0.97
67 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (66 bp):
TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCGCTTTAAAATTTTGATAACAACACT
A
Found at i:5796 original size:22 final size:22
Alignment explanation
Indices: 5536--5821 Score: 96
Period size: 22 Copynumber: 12.8 Consensus size: 22
5526 AATTACATTT
* *
5536 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
*
5558 TGAAATTTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
* * * *
5580 TAAAATTTTGTTGACCCCTC-TA
1 TGAAATTTTGAT-AACCTTCATA
* *
5602 TGAAATTTTGATAATC-ACATTA
1 TGAAATTTTGATAACCTTCA-TA
* * *
5624 TGTAATTTTGATAACC-TCGCTT
1 TGAAATTTTGATAACCTTC-ATA
**
5646 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
*
5668 TGAAATTTTGATAATCAGATCTC-TA
1 TGAAATTTTGATAA-C--CT-TCATA
*
5693 TGAAATTTCGATAATCACTT--TA
1 TGAAATTTTGATAA-C-CTTCATA
*
5715 TGAGATTTT-ATAACCTTC-TA
1 TGAAATTTTGATAACCTTCATA
* * *
5735 TCAAATTTTGGTACTCCTT-ATGAAA
1 TGAAATTTTGATA-ACCTTCAT---A
*
5760 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTCATA
*
5783 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
*
5805 TAAAATTTTGATAACCT
1 TGAAATTTTGATAACCT
5822 CCTCATGAAA
Statistics
Matches: 202, Mismatches: 37, Indels: 49
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.01
20 11 0.05
21 16 0.08
22 130 0.64
23 5 0.02
24 3 0.01
25 22 0.11
26 6 0.03
27 6 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:5830 original size:44 final size:43
Alignment explanation
Indices: 5511--5832 Score: 181
Period size: 44 Copynumber: 7.2 Consensus size: 43
5501 AGAAATACCA
** *
5511 CTATGAAATTTTTG-TAATTACATTTTGAAAA-TTTGATAACCTC
1 CTATGAAA-TTTTGATAACCACATTAT-AAAATTTTGATAACCTC
* * * * * *
5554 TTTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCC
1 -CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTC
* **
5598 TCTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTC
1 -CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTC
* * * * *
5642 GCTTTGAAATTTTGATAACAACACTATGAAATTTTGATAATCAGATC
1 -CTATGAAATTTTGATAACCACATTATAAAATTTTGATAA-C--CTC
* * * * * *
5689 TCTATGAAATTTCGATAATCACTTTATGAGATTTT-ATAACCTT
1 -CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTC
* *
5732 CTATCAAATTTTGGT-ACTC-C-TTATGAAATTGAGACTTTT-ATAACCTTC
1 CTATGAAATTTTGATAAC-CACATTAT--AA---A-A-TTTTGATAACC-TC
* *
5780 ATATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTC
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTC
5823 CTCATGAAAT
1 CT-ATGAAAT
5833 ATTTAATGAA
Statistics
Matches: 212, Mismatches: 47, Indels: 38
0.71 0.16 0.13
Matches are distributed among these distances:
40 4 0.02
41 2 0.01
42 14 0.07
43 17 0.08
44 106 0.50
45 3 0.01
46 5 0.02
47 39 0.18
48 16 0.08
49 3 0.01
50 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTC
Found at i:5883 original size:22 final size:22
Alignment explanation
Indices: 5858--5900 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5848 GTTAACAACA
5858 CTATGAAATTCTT-ATAATCTCG
1 CTATGAAATT-TTGATAATCTCG
*
5880 CTATGACATTTTGATAATCTC
1 CTATGAAATTTTGATAATCTC
5901 TTTGATAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCTCG
Found at i:5964 original size:22 final size:22
Alignment explanation
Indices: 5932--5995 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
5922 TTGTGATAAT
* *
5932 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTAAA
* *
5954 TAACCAACCTAAGAGATTTAAA
1 TAACCAACCTATGAAATTTAAA
*
5976 TAACCTGATCCTATGAAATT
1 TAACC--AACCTATGAAATT
5996 ATGGTAACCA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
22 23 0.70
24 10 0.30
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTAAA
Found at i:6012 original size:22 final size:22
Alignment explanation
Indices: 5986--6063 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
5976 TAACCTGATC
5986 CTATGAAATTATGGTAACCACA
1 CTATGAAATTATGGTAACCACA
* *
6008 CTATGAAATTTTGGTAAGCACA
1 CTATGAAATTATGGTAACCACA
* * * *
6030 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTATGGTAACCACA
6051 CTCATGAAATTAT
1 CT-ATGAAATTAT
6064 AATAGCCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 2 0.04
22 45 0.96
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (22 bp):
CTATGAAATTATGGTAACCACA
Found at i:6294 original size:19 final size:20
Alignment explanation
Indices: 6263--6300 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6253 TATTGAAATT
6263 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
6282 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
6301 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:6648 original size:31 final size:31
Alignment explanation
Indices: 6613--6678 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
6603 TGCCAATTTA
* * *
6613 GAAATATGTTTTAAAGGA-AAGGGTACAATTG
1 GAAATATATTTTAAA-AATAAGGGTACAATCG
6644 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
6675 GAAA
1 GAAA
6679 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:6714 original size:2 final size:2
Alignment explanation
Indices: 6707--6754 Score: 78
Period size: 2 Copynumber: 23.5 Consensus size: 2
6697 TTCATACTTT
*
6707 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6750 TA TA T
1 TA TA T
6755 GAACCTTCAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7347 original size:31 final size:31
Alignment explanation
Indices: 7312--7402 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
7302 CACTTTTAAT
* **
7312 AGGGTCAATGCT-ATAAATCTTTTATTTTAGG
1 AGGGTCAATG-TGATAAAACTTCAATTTTAGG
* *
7343 AGGGTCAAAGTGATAAAACTTCAATTTTAGT
1 AGGGTCAATGTGATAAAACTTCAATTTTAGG
* *
7374 AGGGTCAATATGATAAAACATCAATTTTA
1 AGGGTCAATGTGATAAAACTTCAATTTTA
7403 ATGGAGTCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 1 0.02
31 50 0.98
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (31 bp):
AGGGTCAATGTGATAAAACTTCAATTTTAGG
Found at i:7412 original size:31 final size:30
Alignment explanation
Indices: 7343--7419 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
7333 TTATTTTAGG
* * *
7343 AGGGTCAAAGTGATAAAACTTCAATTTTAGT
1 AGGGTC-AATTGATAAAACATCAATTTTAAT
7374 AGGGTCAATATGATAAAACATCAATTTTAAT
1 AGGGTCAAT-TGATAAAACATCAATTTTAAT
7405 -GGAGTCAATTGATAA
1 AGG-GTCAATTGATAA
7420 TTTCTCTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.24
31 31 0.76
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (30 bp):
AGGGTCAATTGATAAAACATCAATTTTAAT
Found at i:8665 original size:32 final size:32
Alignment explanation
Indices: 8629--8724 Score: 111
Period size: 32 Copynumber: 2.9 Consensus size: 32
8619 ATTTGGTGAC
* **
8629 CTCACCAGGTGAGTATTGTACTGGGTGAGTAT
1 CTCACCAGGTGAGTATTGCACCAGGTGAGTAT
8661 CTCACCAGGTGAGTATTGCACCAGGTGAGTAT
1 CTCACCAGGTGAGTATTGCACCAGGTGAGTAT
* * * *
8693 TTGTACCAGGTGAGTGTTTGTACCAGGTGAGT
1 CT-CACCAGGTGAGT-ATTGCACCAGGTGAGT
8725 GTTTGTACCA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 30 0.55
33 11 0.20
34 14 0.25
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (32 bp):
CTCACCAGGTGAGTATTGCACCAGGTGAGTAT
Found at i:8671 original size:16 final size:16
Alignment explanation
Indices: 8631--8724 Score: 100
Period size: 16 Copynumber: 5.8 Consensus size: 16
8621 TTGGTGACCT
8631 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
* **
8647 TACTGGGTGAGTATCT-
1 CACCAGGTGAGTAT-TG
8663 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
8679 CACCAGGTGAGTATTTG
1 CACCAGGTGAGTA-TTG
* *
8696 TACCAGGTGAGTGTTTG
1 CACCAGGTGAGT-ATTG
*
8713 TACCAGGTGAGT
1 CACCAGGTGAGT
8725 GTTTGTACCA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
15 1 0.02
16 35 0.53
17 30 0.45
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (16 bp):
CACCAGGTGAGTATTG
Found at i:8702 original size:17 final size:17
Alignment explanation
Indices: 8632--8742 Score: 129
Period size: 17 Copynumber: 6.7 Consensus size: 17
8622 TGGTGACCTC
8632 ACCAGGTGAGTA-TTGT
1 ACCAGGTGAGTATTTGT
** * *
8648 ACTGGGTGAGTATCT-C
1 ACCAGGTGAGTATTTGT
*
8664 ACCAGGTGAGTA-TTGC
1 ACCAGGTGAGTATTTGT
8680 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
*
8697 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
*
8714 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
*
8731 ACCAAGTGAGTA
1 ACCAGGTGAGTA
8743 GGGTAGGAAC
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
15 1 0.01
16 33 0.41
17 47 0.58
ACGTcount: A:0.23, C:0.14, G:0.32, T:0.31
Consensus pattern (17 bp):
ACCAGGTGAGTATTTGT
Found at i:9706 original size:30 final size:27
Alignment explanation
Indices: 9667--9851 Score: 74
Period size: 27 Copynumber: 6.5 Consensus size: 27
9657 GAATTGGTTC
9667 TCCCCTGGTGCGTGGCACTAGGGGAGTCCT
1 TCCCCTGGTGC---GCACTAGGGGAGTCCT
* *
9697 TCCCTTGGTGCGCACTAGGGGAGT-GT
1 TCCCCTGGTGCGCACTAGGGGAGTCCT
* * *
9723 CTCCCCTAGTGCCACGCACTTGGGGGAGT-GT
1 -TCCCCTGGTG---CGCAC-TAGGGGAGTCCT
* * *
9754 CTCCCCTTGTGCGCACTTGGGGAGT-GT
1 -TCCCCTGGTGCGCACTAGGGGAGTCCT
* * * *
9781 CTCCCCTTGTGCGCCCTGGGGGAG-CAT
1 -TCCCCTGGTGCGCACTAGGGGAGTCCT
* *
9808 CTCCCCTGGTGGTGCGCACTTGGGGAGT-GT
1 -TCCCC---TGGTGCGCACTAGGGGAGTCCT
9838 CTCCCCTGGTGCGC
1 -TCCCCTGGTGCGC
9852 CTCACCTGGG
Statistics
Matches: 131, Mismatches: 14, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.01
27 68 0.52
28 5 0.04
30 37 0.28
31 20 0.15
ACGTcount: A:0.09, C:0.31, G:0.35, T:0.25
Consensus pattern (27 bp):
TCCCCTGGTGCGCACTAGGGGAGTCCT
Found at i:9727 original size:27 final size:27
Alignment explanation
Indices: 9697--9905 Score: 145
Period size: 27 Copynumber: 7.4 Consensus size: 27
9687 GGGGAGTCCT
*
9697 TCCCTTGGTGCGCACTAGGGGAGTGTC
1 TCCCTTGGTGCGCACTGGGGGAGTGTC
* *
9724 TCCCCTAGTGCCACGCACTTGGGGGAGTGTC
1 TCCCTTGGTG---CGCAC-TGGGGGAGTGTC
*
9755 TCCCCTT-GTGCGCACTTGGGGAGTGTC
1 T-CCCTTGGTGCGCACTGGGGGAGTGTC
* **
9782 TCCCCTT-GTGCGCCCTGGGGGAGCATC
1 T-CCCTTGGTGCGCACTGGGGGAGTGTC
*
9809 TCCCCTGGTGGTGCGCACTTGGGGAGTGTC
1 T-CCCT--TGGTGCGCACTGGGGGAGTGTC
* * **
9839 TCCCCTGGTGCGCCTCACCTGGGGGATTAAC
1 TCCCTTGGTGCG---CA-CTGGGGGAGTGTC
* *
9870 TCCCTTGGTGCGC-CTTGGGGACTGTC
1 TCCCTTGGTGCGCACTGGGGGAGTGTC
*
9896 TCCCCTGGTG
1 TCCCTTGGTG
9906 ACTAACTTTT
Statistics
Matches: 146, Mismatches: 24, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
26 18 0.12
27 55 0.38
28 6 0.04
29 4 0.03
30 24 0.16
31 35 0.24
32 4 0.03
ACGTcount: A:0.09, C:0.32, G:0.34, T:0.26
Consensus pattern (27 bp):
TCCCTTGGTGCGCACTGGGGGAGTGTC
Found at i:9811 original size:85 final size:84
Alignment explanation
Indices: 9665--9851 Score: 214
Period size: 85 Copynumber: 2.2 Consensus size: 84
9655 GGGAATTGGT
* **
9665 TCTCCCCTGGTGCGTGGCACTAGGGGAGTCCTTCCCTTGGTGCGCACTAGGGGAGTGTCTCCCCT
1 TCTCCCCTGGTGC---GCACTAGGGGAGTCCTCCCCTTGGTGCGCACTAGGGGAGCATCTCCCCT
9730 AGTGCCACGCACTTGGGGGAGTG
63 AGTGCCACGCACTT-GGGGAGTG
* * * * * *
9753 TCTCCCCTTGTGCGCACTTGGGGAGTGTCTCCCCTT-GTGCGCCCTGGGGGAGCATCTCCCCTGG
1 TCTCCCCTGGTGCGCACTAGGGGAGT-CCTCCCCTTGGTGCGCACTAGGGGAGCATCTCCCCTAG
***
9817 TGGTGCGCACTTGGGGAGTG
65 TGCCACGCACTTGGGGAGTG
9837 TCTCCCCTGGTGCGC
1 TCTCCCCTGGTGCGC
9852 CTCACCTGGG
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
84 22 0.26
85 44 0.52
86 7 0.08
88 12 0.14
ACGTcount: A:0.09, C:0.32, G:0.35, T:0.25
Consensus pattern (84 bp):
TCTCCCCTGGTGCGCACTAGGGGAGTCCTCCCCTTGGTGCGCACTAGGGGAGCATCTCCCCTAGT
GCCACGCACTTGGGGAGTG
Found at i:9902 original size:57 final size:58
Alignment explanation
Indices: 9698--9905 Score: 241
Period size: 57 Copynumber: 3.6 Consensus size: 58
9688 GGGAGTCCTT
* * * *
9698 CCCTTGGTGCGCACTAGGGGAGTGTCTCCCCTAGTGC-CACGCACTTGGGGGAGTGTCTC
1 CCCTTGGTGCGCACTTGGGGAGTGTCTCCCCTGGTGCGC-C-CACCTGGGGGAGTATCTC
* *
9757 CCCTT-GTGCGCACTTGGGGAGTGTCTCCCCTTGTGCG--C-CCTGGGGGAGCATCTC
1 CCCTTGGTGCGCACTTGGGGAGTGTCTCCCCTGGTGCGCCCACCTGGGGGAGTATCTC
* *
9811 CCCTGGTGGTGCGCACTTGGGGAGTGTCTCCCCTGGTGCGCCTCACCTGGGGGATTAACT-
1 CCCT--TGGTGCGCACTTGGGGAGTGTCTCCCCTGGTGCGCC-CACCTGGGGGAGTATCTC
*
9871 CCCTTGGTGCGC-CTTGGGGACTGTCTCCCCTGGTG
1 CCCTTGGTGCGCACTTGGGGAGTGTCTCCCCTGGTG
9906 ACTAACTTTT
Statistics
Matches: 131, Mismatches: 10, Indels: 18
0.82 0.06 0.11
Matches are distributed among these distances:
54 17 0.13
55 1 0.01
56 1 0.01
57 53 0.40
58 37 0.28
59 5 0.04
60 5 0.04
61 12 0.09
ACGTcount: A:0.09, C:0.32, G:0.34, T:0.25
Consensus pattern (58 bp):
CCCTTGGTGCGCACTTGGGGAGTGTCTCCCCTGGTGCGCCCACCTGGGGGAGTATCTC
Found at i:11832 original size:12 final size:12
Alignment explanation
Indices: 11815--11861 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
11805 AAAGTGACCA
11815 CCCAAGAGAAAT
1 CCCAAGAGAAAT
11827 CCCAAGAGAAAT
1 CCCAAGAGAAAT
11839 CCC-AGAAGAAAT
1 CCCAAG-AGAAAT
*
11851 CCTAAGAGAAA
1 CCCAAGAGAAA
11862 CAGCAAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 2 0.06
12 28 0.88
13 2 0.06
ACGTcount: A:0.51, C:0.23, G:0.17, T:0.09
Consensus pattern (12 bp):
CCCAAGAGAAAT
Done.