Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013718.1 Corchorus capsularis cultivar CVL-1 contig13739, 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: 37211
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--48 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1 CN
3 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
45 CT CT
1 CT CT
49 ATATATATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1341 original size:18 final size:18
Alignment explanation
Indices: 1288--1341 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
1278 TTATAAATCA
1288 TATATAATAAATAATGCT
1 TATATAATAAATAATGCT
*
1306 T-T-TAA-AAA-AAAG--
1 TATATAATAAATAATGCT
1318 TATATAATAAATAATGCT
1 TATATAATAAATAATGCT
1336 TATATA
1 TATATA
1342 GTCTATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 1 0.04
13 1 0.04
14 6 0.21
15 6 0.21
16 6 0.21
17 1 0.04
18 7 0.25
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (18 bp):
TATATAATAAATAATGCT
Found at i:5772 original size:21 final size:20
Alignment explanation
Indices: 5733--5772 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5723 CAATTTTCAC
* *
5733 ATTATAAGGTTATCGAGAAA
1 ATTATAAGGTTACCAAGAAA
5753 ATTATAAAGGTTACCAAGAA
1 ATTAT-AAGGTTACCAAGAA
5773 CGTTATACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.28
Consensus pattern (20 bp):
ATTATAAGGTTACCAAGAAA
Found at i:5914 original size:20 final size:20
Alignment explanation
Indices: 5885--5933 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
5875 CTTCAAAAGG
*
5885 TATAAAATTATTAA-AAATGT
1 TATAATATTATTAATAAAT-T
5905 TATAATATTATTAATAAATT
1 TATAATATTATTAATAAATT
5925 TAGTAATAT
1 TA-TAATAT
5934 CTTACATTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAATATTATTAATAAATT
Found at i:6196 original size:29 final size:29
Alignment explanation
Indices: 6104--6196 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 29
6094 TTACCTTTGT
* *
6104 TAGTTTGTTTATTTGGTCATTTCATTGGTTA
1 TAGTTTATTTATTTGGTCATTTC-TT-ATTA
*
6135 T-GTTTA-TTATTTGGTCATTGTTTATGTTTATTA
1 TAGTTTATTTATTTGGTCA----TT-T-CTTATTA
6168 TAGTTTATTTATTTGGTCATTTCTTATTA
1 TAGTTTATTTATTTGGTCATTTCTTATTA
6197 GGGGCATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
29 17 0.34
30 5 0.10
31 3 0.06
33 6 0.12
34 8 0.16
35 11 0.22
ACGTcount: A:0.18, C:0.05, G:0.15, T:0.61
Consensus pattern (29 bp):
TAGTTTATTTATTTGGTCATTTCTTATTA
Found at i:6410 original size:25 final size:25
Alignment explanation
Indices: 6371--6427 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
6361 TGGTCTGTCG
6371 CTTTTCTCTTCGATTATGCTATCTTC
1 CTTTT-TCTTCGATTATGCTATCTTC
* *
6397 CTTTTTCTTGGATTCTGCTATCTTC
1 CTTTTTCTTCGATTATGCTATCTTC
6422 CTTTTT
1 CTTTTT
6428 TCTGCTCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.09, C:0.25, G:0.09, T:0.58
Consensus pattern (25 bp):
CTTTTTCTTCGATTATGCTATCTTC
Found at i:7063 original size:6 final size:6
Alignment explanation
Indices: 7052--7080 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
7042 GTTTAGAATT
7052 ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATA
7081 TATGGTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:12424 original size:19 final size:20
Alignment explanation
Indices: 12397--12434 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12387 TACTATTATT
12397 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
12417 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
12435 AATGTCAATG
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:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:13240 original size:42 final size:42
Alignment explanation
Indices: 13181--13264 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
13171 GTTCCACCAC
* * *
13181 TATTTAAGTGGAGTTTTGCTACAAAACATGAGATTACTAGCA
1 TATTTAAATGGAGTTTTGCGACAAAACATGAGATGACTAGCA
*
13223 TATTTAAATGGAGTTTTGCGACAAAACATGTGATGACTAGCA
1 TATTTAAATGGAGTTTTGCGACAAAACATGAGATGACTAGCA
13265 ATGACACGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (42 bp):
TATTTAAATGGAGTTTTGCGACAAAACATGAGATGACTAGCA
Found at i:22511 original size:20 final size:20
Alignment explanation
Indices: 22486--22524 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22476 AATTATTTAT
22486 GAAATT-TTAATTAAAAAAAG
1 GAAATTATT-ATTAAAAAAAG
*
22506 GAAATTATTTTTAAAAAAA
1 GAAATTATTATTAAAAAAA
22525 TGGGGAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
GAAATTATTATTAAAAAAAG
Found at i:24040 original size:2 final size:2
Alignment explanation
Indices: 24033--24060 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24023 AGATATAAAA
24033 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24061 GAAAACACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25603 original size:27 final size:27
Alignment explanation
Indices: 25538--25609 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
25528 ATTAGGTTAA
* *
25538 TTTTGGATTTGCACTTGGGCATTTTAGC
1 TTTT-GATTTGCATTTGGACATTTTAGC
* *
25566 TTTTGACTTGCATTTGGACCTTTTAGC
1 TTTTGATTTGCATTTGGACATTTTAGC
*
25593 -TTTGAATTTGCTTTTGG
1 TTTTG-ATTTGCATTTGG
25610 GCCATAATGG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 4 0.11
27 29 0.78
28 4 0.11
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.50
Consensus pattern (27 bp):
TTTTGATTTGCATTTGGACATTTTAGC
Found at i:28705 original size:7 final size:7
Alignment explanation
Indices: 28693--28717 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28683 GTCTAGAGAC
28693 AATTAGG
1 AATTAGG
28700 AATTAGG
1 AATTAGG
28707 AATTAGG
1 AATTAGG
28714 AATT
1 AATT
28718 TAGCATATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (7 bp):
AATTAGG
Found at i:29162 original size:27 final size:26
Alignment explanation
Indices: 29093--29164 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 26
29083 TGAGTAAATT
*
29093 AGTAATCAGTAAAAAAGAGTAGAAAAC
1 AGTAATTAGT-AAAAAGAGTAGAAAAC
*
29120 AGT-ATTCAGTAAAAAGAGTGAGAAAAG
1 AGTAATT-AGTAAAAAGAGT-AGAAAAC
29147 AGTAATTAGTAAAAAGAG
1 AGTAATTAGTAAAAAGAG
29165 AAAAAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 11 0.28
27 26 0.65
28 3 0.08
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (26 bp):
AGTAATTAGTAAAAAGAGTAGAAAAC
Found at i:29294 original size:21 final size:22
Alignment explanation
Indices: 29188--29555 Score: 231
Period size: 22 Copynumber: 17.2 Consensus size: 22
29178 AATGGTAATC
*
29188 AGTAAAAGGTAATCAAT-AAG-
1 AGTAAAAGGTAATCAGTAAAGA
* *
29208 AGTAAAATAGTAGTCAGT-AAGA
1 AGTAAAA-GGTAATCAGTAAAGA
*
29230 AGT-AAAGGTAATTAGTAAAGAGA
1 AGTAAAAGGTAATCAGT-AA-AGA
29253 AGT-AAAGGTAATCAGTAAAAGA
1 AGTAAAAGGTAATCAGT-AAAGA
*
29275 A-TAAAAGGCAATCAGTAAAG-
1 AGTAAAAGGTAATCAGTAAAGA
* * *
29295 AGAAAAATGGTAATTAGGAAAGAA
1 AGTAAAA-GGTAATCAGTAAAG-A
**
29319 ACAAAAAGGTAATCAGT-AAG-
1 AGTAAAAGGTAATCAGTAAAGA
* **
29339 CG-AAATTGTAATCAGT-AAG-
1 AGTAAAAGGTAATCAGTAAAGA
* *
29358 AGTAAAAGAGTAATC-GGAAAAA
1 AGTAAAAG-GTAATCAGTAAAGA
29380 AGTAAAAGGTAATCAGT-AAGA
1 AGTAAAAGGTAATCAGTAAAGA
29401 AGTAAAA-GTAATCAGT-AAG-
1 AGTAAAAGGTAATCAGTAAAGA
* **
29420 AGTATATAGGTAATCAGCGAAG-
1 AGTA-AAAGGTAATCAGTAAAGA
** *
29442 AGTAAAAAACTAATCAAT-AAGA
1 AGT-AAAAGGTAATCAGTAAAGA
*
29464 AGTAAAAGGTAATCAGTAAAAA
1 AGTAAAAGGTAATCAGTAAAGA
**
29486 ACAAAAAGGTAATCAGTAAA-A
1 AGTAAAAGGTAATCAGTAAAGA
* *
29507 AGCAAAAAGGCAATCAGTAAA-A
1 AG-TAAAAGGTAATCAGTAAAGA
**
29529 AGTAAAAGAGTAAAAAGTAAAG-
1 AGTAAAAG-GTAATCAGTAAAGA
29551 AGTAA
1 AGTAA
29556 TCAGTAAAGA
Statistics
Matches: 279, Mismatches: 45, Indels: 46
0.75 0.12 0.12
Matches are distributed among these distances:
19 20 0.07
20 33 0.12
21 75 0.27
22 115 0.41
23 30 0.11
24 6 0.02
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.18
Consensus pattern (22 bp):
AGTAAAAGGTAATCAGTAAAGA
Found at i:29526 original size:29 final size:29
Alignment explanation
Indices: 29494--29563 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
29484 AAACAAAAAG
*
29494 GTAATCAGTAAAA-AGCAAAAAGGCAATCA
1 GTAATCAGTAAAAGAGCAAAAA-GCAAACA
** * * *
29523 GTAAAAAGTAAAAGAGTAAAAAGTAAAGA
1 GTAATCAGTAAAAGAGCAAAAAGCAAACA
29552 GTAATCAGTAAA
1 GTAATCAGTAAA
29564 GAAAAAAGGT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.59, C:0.07, G:0.19, T:0.16
Consensus pattern (29 bp):
GTAATCAGTAAAAGAGCAAAAAGCAAACA
Found at i:29532 original size:7 final size:7
Alignment explanation
Indices: 29463--29555 Score: 51
Period size: 7 Copynumber: 12.9 Consensus size: 7
29453 AATCAATAAG
29463 AAGTAAA
1 AAGTAAA
* *
29470 AGGTAAT
1 AAGTAAA
*
29477 CAGTAAA
1 AAGTAAA
**
29484 AAACAAA
1 AAGTAAA
*
29491 AAGGTAAT
1 AA-GTAAA
*
29499 CAGTAAA
1 AAGTAAA
*
29506 AAGCAAA
1 AAGTAAA
* *
29513 AAGGCAAT
1 AA-GTAAA
*
29521 CAGTAAA
1 AAGTAAA
29528 AAGTAAA
1 AAGTAAA
29535 AGAGTAAA
1 A-AGTAAA
29543 AAGTAAA
1 AAGTAAA
*
29550 GAGTAA
1 AAGTAA
29556 TCAGTAAAGA
Statistics
Matches: 62, Mismatches: 21, Indels: 6
0.70 0.24 0.07
Matches are distributed among these distances:
7 47 0.76
8 15 0.24
ACGTcount: A:0.61, C:0.06, G:0.18, T:0.14
Consensus pattern (7 bp):
AAGTAAA
Found at i:29543 original size:14 final size:14
Alignment explanation
Indices: 29522--29565 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
29512 AAAGGCAATC
29522 AGTAAAAAGTAAAAG
1 AGTAAAAAGT-AAAG
29537 AGTAAAAAGTAAAG
1 AGTAAAAAGTAAAG
**
29551 AGTAATCAGTAAAG
1 AGTAAAAAGTAAAG
29565 A
1 A
29566 AAAAAGGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.16
Consensus pattern (14 bp):
AGTAAAAAGTAAAG
Found at i:29615 original size:47 final size:48
Alignment explanation
Indices: 29523--29648 Score: 139
Period size: 47 Copynumber: 2.6 Consensus size: 48
29513 AAGGCAATCA
* *
29523 GTAAAAAGTAAAAGAGTAAAAAGTAAAGAGTAATCAGTAAAGAAAAAAG
1 GTAAAAAGTAAAAGAGT-AAAAGTAAAGAATAATCAATAAAGAAAAAAG
* * *
29572 GTAAAATAG-AAAAGAGT-AAAGTACAGAATAATCAATAAGGAAAAATG
1 GTAAAA-AGTAAAAGAGTAAAAGTAAAGAATAATCAATAAAGAAAAAAG
** *
29619 CCAAAAAGTAAAAGAGTAATCAGTAAAGAA
1 GTAAAAAGTAAAAGAGTAA-AAGTAAAGAA
29649 AAAATGATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
46 2 0.03
47 37 0.58
48 1 0.02
49 22 0.34
50 2 0.03
ACGTcount: A:0.61, C:0.05, G:0.19, T:0.15
Consensus pattern (48 bp):
GTAAAAAGTAAAAGAGTAAAAGTAAAGAATAATCAATAAAGAAAAAAG
Found at i:29642 original size:82 final size:81
Alignment explanation
Indices: 29540--29731 Score: 233
Period size: 82 Copynumber: 2.4 Consensus size: 81
29530 GTAAAAGAGT
* ** *
29540 AAAAAGTAAAGAGTAATCAGTAAAGAAAAAAGG-TAAAATAGAAAAGAGTAAAGTACAGAATAAT
1 AAAAAGTAAAGAGTAATCAGTAAAGAAAAAAGGAT-AAAGAGAAAAGAGTAAACAAAAGAATAAT
* *
29604 CAATAAGGAAAAATGCC
65 CAATAAAGAAAAATGAC
* * *
29621 AAAAAGTAAAAGAGTAATCAGTAAAGAAAAAATGATAAAGAGTAAAGAGTAAACAAAAGAGTAAT
1 AAAAAGT-AAAGAGTAATCAGTAAAGAAAAAAGGATAAAGAGAAAAGAGTAAACAAAAGAATAAT
* *
29686 CAGTAAAGAAAAATGAT
65 CAATAAAGAAAAATGAC
* **
29703 AAAGAGTAAAGAGTAAAGAGTAAAGAAAA
1 AAAAAGTAAAGAGTAATCAGTAAAGAAAA
29732 GAGTAATCGC
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
81 27 0.28
82 67 0.71
83 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.19, T:0.15
Consensus pattern (81 bp):
AAAAAGTAAAGAGTAATCAGTAAAGAAAAAAGGATAAAGAGAAAAGAGTAAACAAAAGAATAATC
AATAAAGAAAAATGAC
Found at i:29668 original size:7 final size:7
Alignment explanation
Indices: 29629--29737 Score: 79
Period size: 7 Copynumber: 16.3 Consensus size: 7
29619 CCAAAAAGTA
29629 AAAGAGT
1 AAAGAGT
**
29636 AATCAGT
1 AAAGAGT
**
29643 AAAGAAA
1 AAAGAGT
29650 AAATGA-T
1 AAA-GAGT
29657 AAAGAGT
1 AAAGAGT
29664 AAAGAGT
1 AAAGAGT
*
29671 AAACA--
1 AAAGAGT
29676 AAAGAGT
1 AAAGAGT
**
29683 AATCAGT
1 AAAGAGT
*
29690 AAAGA-A
1 AAAGAGT
29696 AAATGA-T
1 AAA-GAGT
29703 AAAGAGT
1 AAAGAGT
29710 AAAGAGT
1 AAAGAGT
29717 AAAGAGT
1 AAAGAGT
29724 AAAGA--
1 AAAGAGT
29729 AAAGAGT
1 AAAGAGT
29736 AA
1 AA
29738 TCGCTAAGAA
Statistics
Matches: 79, Mismatches: 15, Indels: 16
0.72 0.14 0.15
Matches are distributed among these distances:
5 9 0.11
6 7 0.09
7 61 0.77
8 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.21, T:0.15
Consensus pattern (7 bp):
AAAGAGT
Found at i:29726 original size:53 final size:47
Alignment explanation
Indices: 29628--29719 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 47
29618 GCCAAAAAGT
29628 AAAAGAGTAATCAGTAAAGAAAAAATGATAAAGAGTAAAGAGTAAAC
1 AAAAGAGTAATCAGTAAAGAAAAAATGATAAAGAGTAAAGAGTAAAC
29675 AAAAGAGTAATCAGTAAAG-AAAAATGATAAAGAGTAAAGAGTAAA
1 AAAAGAGTAATCAGTAAAGAAAAAATGATAAAGAGTAAAGAGTAAA
29720 GAGTAAAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 26 0.58
47 19 0.42
ACGTcount: A:0.62, C:0.03, G:0.20, T:0.15
Consensus pattern (47 bp):
AAAAGAGTAATCAGTAAAGAAAAAATGATAAAGAGTAAAGAGTAAAC
Found at i:29765 original size:53 final size:53
Alignment explanation
Indices: 29623--29739 Score: 156
Period size: 53 Copynumber: 2.3 Consensus size: 53
29613 AAAATGCCAA
*
29623 AAAGTAAAAGAGTAATCAGTAAAGAAAAA--AT---GA-TAAAGAGTAAAGAGT
1 AAAG-AAAAGAGTAATCAGTAAAGAAAAATGATAAACAGTAAAGAGTAAAGAGT
* *
29671 AAACAAAAGAGTAATCAGTAAAGAAAAATGATAAAGAGTAAAGAGTAAAGAGT
1 AAAGAAAAGAGTAATCAGTAAAGAAAAATGATAAACAGTAAAGAGTAAAGAGT
29724 AAAGAAAAGAGTAATC
1 AAAGAAAAGAGTAATC
29740 GCTAAGAAGT
Statistics
Matches: 61, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
47 24 0.39
48 3 0.05
49 2 0.03
52 2 0.03
53 30 0.49
ACGTcount: A:0.61, C:0.03, G:0.21, T:0.15
Consensus pattern (53 bp):
AAAGAAAAGAGTAATCAGTAAAGAAAAATGATAAACAGTAAAGAGTAAAGAGT
Found at i:29800 original size:27 final size:28
Alignment explanation
Indices: 29758--29812 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
29748 GTAATGGTTG
29758 TCAGTAAAAAAGAGTAAGAAAAGAGTAA
1 TCAGTAAAAAAGAGTAAGAAAAGAGTAA
*
29786 TCAGT-AAAAAGAGTAAGAAATGAGTAA
1 TCAGTAAAAAAGAGTAAGAAAAGAGTAA
29813 AAAATGGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.58, C:0.04, G:0.22, T:0.16
Consensus pattern (28 bp):
TCAGTAAAAAAGAGTAAGAAAAGAGTAA
Found at i:29812 original size:38 final size:37
Alignment explanation
Indices: 29760--29849 Score: 112
Period size: 37 Copynumber: 2.4 Consensus size: 37
29750 AATGGTTGTC
29760 AGTAAAAAAGAGTAAGAAAA-GAGTAATCAGT-AAAAAG
1 AGTAAAAAAGAGTAA-AAAATG-GTAATCAGTAAAAAAG
* *
29797 AGTAAGAAATGAGTAAAAAATGGTGATCAGTAAAAAAG
1 AGTAA-AAAAGAGTAAAAAATGGTAATCAGTAAAAAAG
*
29835 AGTAAAAGAGAGTAA
1 AGTAAAAAAGAGTAA
29850 TTAGTGATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 25 0.54
38 21 0.46
ACGTcount: A:0.59, C:0.02, G:0.23, T:0.16
Consensus pattern (37 bp):
AGTAAAAAAGAGTAAAAAATGGTAATCAGTAAAAAAG
Found at i:29831 original size:65 final size:65
Alignment explanation
Indices: 29750--29872 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 65
29740 GCTAAGAAGT
29750 AATGGTTGTCAGTAAAAAAGAGTAAGAAAAGAGTAATCAGT-AAAAAGAGTAAGAAATGAGTAAA
1 AATGGTTGTCAGTAAAAAAGAGTAA-AAAAGAGTAATCAGTGAAAAAGAGTAAGAAATGAGTAAA
29814 A
65 A
* * *
29815 AATGG-TGATCAGTAAAAAAGAGTAAAAGAGAGTAATTAGTGATAAAGAGTAAGAAATG
1 AATGGTTG-TCAGTAAAAAAGAGTAAAAAAGAGTAATCAGTGAAAAAGAGTAAGAAATG
29873 GTGATCAGTA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
64 15 0.28
65 38 0.72
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.20
Consensus pattern (65 bp):
AATGGTTGTCAGTAAAAAAGAGTAAAAAAGAGTAATCAGTGAAAAAGAGTAAGAAATGAGTAAAA
Found at i:29837 original size:27 final size:27
Alignment explanation
Indices: 29797--29895 Score: 110
Period size: 27 Copynumber: 3.6 Consensus size: 27
29787 CAGTAAAAAG
*
29797 AGTAAGAAATGAGTAAAAAATGGTGATC
1 AGTAA-AAAAGAGTAAAAAATGGTGATC
* * *
29825 AGTAAAAAAGAGTAAAAGA-GAGTAATT
1 AGTAAAAAAGAGTAAAAAATG-GTGATC
* * *
29852 AGTGATAAAGAGTAAGAAATGGTGATC
1 AGTAAAAAAGAGTAAAAAATGGTGATC
29879 AGTAAAAAAGAGTAAAA
1 AGTAAAAAAGAGTAAAA
29896 TGTGGTATTC
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
26 1 0.02
27 49 0.88
28 6 0.11
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (27 bp):
AGTAAAAAAGAGTAAAAAATGGTGATC
Found at i:29839 original size:54 final size:53
Alignment explanation
Indices: 29793--29895 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 53
29783 TAATCAGTAA
29793 AAAGAGTAAGAAATGAGTAAAAAATGGTGATCAGTAAAAAAGAGTAAAAGAGAG
1 AAAGAGTAAGAAA-GAGTAAAAAATGGTGATCAGTAAAAAAGAGTAAAAGAGAG
** * * *
29847 TAATTAGTGATAAAGAGTAAGAAATGGTGATCAGTAAAAAAGAGTAAAA
1 -AAAGAGTAAGAAAGAGTAAAAAATGGTGATCAGTAAAAAAGAGTAAAA
29896 TGTGGTATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 34 0.79
55 9 0.21
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.18
Consensus pattern (53 bp):
AAAGAGTAAGAAAGAGTAAAAAATGGTGATCAGTAAAAAAGAGTAAAAGAGAG
Found at i:29926 original size:19 final size:19
Alignment explanation
Indices: 29899--29980 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 19
29889 AGTAAAATGT
*
29899 GGTATTCAGTAAGAAAAGG
1 GGTAATCAGTAAGAAAAGG
*
29918 GGTAATCAGTAAAAAAGAGTAAAATGT
1 GGTAATCAGT-----A-AG-AAAA-GG
*
29945 GGTATTCAGTAAGAAAAGG
1 GGTAATCAGTAAGAAAAGG
29964 GGTAATCAGTAA-AAAAG
1 GGTAATCAGTAAGAAAAG
29981 AGTAAAAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
18 5 0.10
19 21 0.42
20 4 0.08
21 2 0.04
22 1 0.02
24 1 0.02
25 2 0.04
26 4 0.08
27 10 0.20
ACGTcount: A:0.48, C:0.05, G:0.27, T:0.21
Consensus pattern (19 bp):
GGTAATCAGTAAGAAAAGG
Found at i:29927 original size:46 final size:46
Alignment explanation
Indices: 29876--30002 Score: 227
Period size: 46 Copynumber: 2.7 Consensus size: 46
29866 AGAAATGGTG
29876 ATCAGTAAAAAAGAGTAAAATGTGGTATTCAGTAAGAAAAGGGGTA
1 ATCAGTAAAAAAGAGTAAAATGTGGTATTCAGTAAGAAAAGGGGTA
29922 ATCAGTAAAAAAGAGTAAAATGTGGTATTCAGTAAGAAAAGGGGTA
1 ATCAGTAAAAAAGAGTAAAATGTGGTATTCAGTAAGAAAAGGGGTA
* *
29968 ATCAGTAAAAAAGAGTAAAAATATGGTAATCAGTA
1 ATCAGTAAAAAAGAGT-AAAATGTGGTATTCAGTA
30003 CAAAGAGTAA
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
46 62 0.79
47 16 0.21
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.22
Consensus pattern (46 bp):
ATCAGTAAAAAAGAGTAAAATGTGGTATTCAGTAAGAAAAGGGGTA
Found at i:30021 original size:26 final size:27
Alignment explanation
Indices: 29964--30029 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
29954 TAAGAAAAGG
29964 GGTAATCAGTAAAAAAGAGTAAAAATAT
1 GGTAATCAGT-AAAAAGAGTAAAAATAT
*
29992 GGTAATCAGTACAAAGAGTAAAAA-AT
1 GGTAATCAGTAAAAAGAGTAAAAATAT
*
30018 GGTAATTAGTAA
1 GGTAATCAGTAA
30030 TCAAGAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
26 12 0.34
27 13 0.37
28 10 0.29
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.23
Consensus pattern (27 bp):
GGTAATCAGTAAAAAGAGTAAAAATAT
Found at i:34347 original size:23 final size:24
Alignment explanation
Indices: 34304--34348 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
34294 TGTGGATTTC
34304 GGAATATAAAGTATCTTTACAATT
1 GGAATATAAAGTATCTTTACAATT
34328 GGAATATAAAGT-TCTTTACAA
1 GGAATATAAAGTATCTTTACAA
34349 CGTCTGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (24 bp):
GGAATATAAAGTATCTTTACAATT
Done.