Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014784.1 Corchorus capsularis cultivar CVL-1 contig14805, 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: 14140
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:505 original size:25 final size:26
Alignment explanation
Indices: 463--512 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
453 CAATGAATTA
* **
463 AAAATGACTAAAGTGCCCCT-GGTGC
1 AAAATGACCAAAACGCCCCTAGGTGC
488 AAAATGACCAAAACGCCCCTAGGTG
1 AAAATGACCAAAACGCCCCTAGGTG
513 ACTTCTAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (26 bp):
AAAATGACCAAAACGCCCCTAGGTGC
Found at i:4394 original size:25 final size:25
Alignment explanation
Indices: 4379--4469 Score: 155
Period size: 25 Copynumber: 3.6 Consensus size: 25
4369 CGCTCATGTT
* *
4379 CTTGCGTTTGGCAAACGAGCCTATG
1 CTTGCGTTTAGCAAACGAGCCTGTG
4404 CTTGCGTTTAGCAAACGAGCCTGTG
1 CTTGCGTTTAGCAAACGAGCCTGTG
4429 CTTGCGTTTAGCAAACGAGCCTGTG
1 CTTGCGTTTAGCAAACGAGCCTGTG
*
4454 CTTGCGTTTAGAAAAC
1 CTTGCGTTTAGCAAAC
4470 ACATAGGCTA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (25 bp):
CTTGCGTTTAGCAAACGAGCCTGTG
Found at i:5700 original size:31 final size:32
Alignment explanation
Indices: 5651--5719 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
5641 GGGAAATTTT
*
5651 ATATTTTCCGATTGTACCCTTATT-TTTAAAAC
1 ATATTTTCAGATTGTACCCTT-TTCTTTAAAAC
5683 ATATTTTCAG-TTGTACCCTTTTCTTTAAAAC
1 ATATTTTCAGATTGTACCCTTTTCTTTAAAAC
5714 ATATTT
1 ATATTT
5720 CTAAATTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 2 0.06
31 24 0.69
32 9 0.26
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (32 bp):
ATATTTTCAGATTGTACCCTTTTCTTTAAAAC
Found at i:5845 original size:37 final size:36
Alignment explanation
Indices: 5802--5873 Score: 92
Period size: 38 Copynumber: 2.0 Consensus size: 36
5792 ATTTGTCTTT
5802 TTGTTTCCAA-AGTCCTATTTAATTTTGCCTTTTGTCA
1 TTGTTTCCAATAGTCCTATTTAATTTTG--TTTTGTCA
* **
5839 TTGTTTCCAATCGTTGTATTTAATTTTGTTTTGTC
1 TTGTTTCCAATAGTCCTATTTAATTTTGTTTTGTC
5874 TTTTTGGTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 7 0.23
37 10 0.32
38 14 0.45
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (36 bp):
TTGTTTCCAATAGTCCTATTTAATTTTGTTTTGTCA
Found at i:6050 original size:18 final size:19
Alignment explanation
Indices: 6015--6051 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
6005 TACTATTATT
6015 TTTTGAATTTAATATTTTA
1 TTTTGAATTTAATATTTTA
6034 TTTT-AATTTCAAT-TTTTA
1 TTTTGAATTT-AATATTTTA
6052 AATGTCAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTGAATTTAATATTTTA
Found at i:6277 original size:22 final size:22
Alignment explanation
Indices: 6219--6359 Score: 88
Period size: 22 Copynumber: 6.3 Consensus size: 22
6209 TTTTCTCTAT
* * *
6219 ATGGTTAACAAAATTTTATAAG
1 ATGGTTATCAAAATTTCATAGG
* *
6241 ATGGTTATTACAATTTCATGAGG
1 ATGGTTATCAAAATTTCAT-AGG
* **
6264 A-GGTTATCAAAATTCCATACT
1 ATGGTTATCAAAATTTCATAGG
*
6285 ATGGTTACCAAAATTTCATAGG
1 ATGGTTATCAAAATTTCATAGG
* * *
6307 ATCAGGTTATTAAAATCTCTTAGG
1 AT--GGTTATCAAAATTTCATAGG
* **
6331 -TCGATTATTGAAATTTCATAGG
1 AT-GGTTATCAAAATTTCATAGG
*
6353 GTGGTTA
1 ATGGTTA
6360 ATTATCACAA
Statistics
Matches: 90, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
21 2 0.02
22 67 0.74
23 5 0.06
24 16 0.18
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (22 bp):
ATGGTTATCAAAATTTCATAGG
Found at i:6519 original size:22 final size:21
Alignment explanation
Indices: 6471--6777 Score: 101
Period size: 22 Copynumber: 13.8 Consensus size: 21
6461 TTTCATGGGG
* *
6471 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
6493 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
6515 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * * *
6540 AGGAGTACCAAAATTTGATATA
1 AGG-TTATCAAAATTTCATAGA
* *
6562 AGGTTATC-CAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
*
6581 AGTGATTATCGAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
6604 GATCGGATTATCAAAATTT-ATAGGA
1 -A--GG-TTATCAAAATTTCATA-GA
* *
6629 AGATTGTCAAAATTTCATAGCA
1 AGGTTATCAAAATTTCATAG-A
** * *
6651 TTGTTATCAAAATTTCAAAGCG
1 AGGTTATCAAAATTTCATAG-A
6673 AGGTTATCAAAATTAT-ATA-A
1 AGGTTATCAAAATT-TCATAGA
*
6693 TGTGATTAT-AAGAATTTCATA-A
1 AG-G-TTATCAA-AATTTCATAGA
* * *
6715 AGGGGTCAACAAAATTTTATA-A
1 A--GGTTATCAAAATTTCATAGA
*
6737 AGAAGTTATCAAAATTTCATAAA
1 AG--GTTATCAAAATTTCATAGA
*
6760 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
6778 AAATGTGATT
Statistics
Matches: 215, Mismatches: 40, Indels: 60
0.68 0.13 0.19
Matches are distributed among these distances:
19 2 0.01
20 10 0.05
21 28 0.13
22 128 0.60
23 8 0.04
24 8 0.04
25 21 0.10
26 6 0.03
27 4 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:6728 original size:44 final size:43
Alignment explanation
Indices: 6654--6801 Score: 113
Period size: 44 Copynumber: 3.3 Consensus size: 43
6644 CATAGCATTG
* * * *
6654 TTATCAAAATTTCA-AAGCGAGGTTATCAAAATTATATAATGTGA
1 TTAT-AAAATTTCATAA-AGAGGTCAACAAAATTTTATAATGTGA
* * *
6698 TTATAAGAATTTCATAAAGGGGTCAACAAAATTTTATAAAG-AA
1 TTATAA-AATTTCATAAAGAGGTCAACAAAATTTTATAATGTGA
* * *
6741 GTTATCAAAATTTCATAAAGAGGTTATC-AAATTTTCAAAATGTGA
1 -TTAT-AAAATTTCATAAAGAGGTCAACAAAATTTT-ATAATGTGA
*
6786 TTACAAAAATTTCATA
1 TTA-TAAAATTTCATA
6802 GTGGTATTTC
Statistics
Matches: 83, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
43 10 0.12
44 68 0.82
45 5 0.06
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (43 bp):
TTATAAAATTTCATAAAGAGGTCAACAAAATTTTATAATGTGA
Found at i:6728 original size:88 final size:87
Alignment explanation
Indices: 6636--6801 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 87
6626 GGAAGATTGT
* * *
6636 CAAAATTTCAT-AGCATTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTAT-ATAATGTGA
1 CAAAATTTCATAAG-A-AGTTATCAAAATTTCATAA-AGAGGTTATC-AAATTATCAAAATGTGA
* *
6698 TTATAAGAATTTCATAAAGGGGTCAA
62 TTACAAAAATTTCATAAAGGGGTCAA
* *
6724 CAAAATTTTATAAAGAAGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTCAT-AAGAAGTTATCAAAATTTCATAAAGAGGTTATCAAATTATCAAAATGTGATTA
6789 CAAAAATTTCATA
65 CAAAAATTTCATA
6802 GTGGTATTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
87 6 0.09
88 56 0.84
89 3 0.04
90 2 0.03
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.34
Consensus pattern (87 bp):
CAAAATTTCATAAGAAGTTATCAAAATTTCATAAAGAGGTTATCAAATTATCAAAATGTGATTAC
AAAAATTTCATAAAGGGGTCAA
Found at i:6908 original size:20 final size:20
Alignment explanation
Indices: 6883--6933 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
6873 TTATGGAGTA
6883 ATCAAAATTTCAAGGAGAAT
1 ATCAAAATTTCAAGGAGAAT
* *
6903 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGAAT
6922 ATCAAAATTTCA
1 ATCAAAATTTCA
6934 CGTGAAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGAAT
Found at i:7037 original size:22 final size:22
Alignment explanation
Indices: 6883--7369 Score: 259
Period size: 22 Copynumber: 22.5 Consensus size: 22
6873 TTATGGAGTA
**
6883 ATCAAAATTTCA-A-GGAGAAT
1 ATCAAAATTTCATAGGGAGGTT
*
6903 ATCAAAA-TTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* *
6922 ATCAAAATTTCA-CGTGAAGGTT
1 ATCAAAATTTCATAG-GGAGGTT
**
6944 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * **
6966 TTCAAAATTTCACAAAGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
6988 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
7010 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
7032 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
7054 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
7076 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
7092 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
7114 ATCAAAATTTTATAGTGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
7137 ATCAAAATTTCATAGGAAGATTT
1 ATCAAAATTTCATAGGGAG-GTT
* *
7160 ATCAAAATTTTATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
7182 ATCAAAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
7204 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * *
7226 ACTGACAA-TTCATATGGAGGTT
1 A-TCAAAATTTCATAGGGAGGTT
* * * ** *
7248 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* ** *
7270 ATCAATATACCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
7292 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
7315 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
**
7337 ATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
7360 -TCAAAATTTC
1 ATCAAAATTTC
7370 GAGGTTAACT
Statistics
Matches: 354, Mismatches: 93, Indels: 38
0.73 0.19 0.08
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
18 1 0.00
19 18 0.05
20 10 0.03
21 11 0.03
22 237 0.67
23 64 0.18
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:7397 original size:21 final size:21
Alignment explanation
Indices: 7371--7417 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
7361 CAAAATTTCG
**
7371 AGGTTAACTAAATTTCAT-AAA
1 AGGTTAAAAAAATTT-ATAAAA
7392 AGGTTAAAAAAATTTATAAAA
1 AGGTTAAAAAAATTTATAAAA
7413 AGGTT
1 AGGTT
7418 CTCGAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (21 bp):
AGGTTAAAAAAATTTATAAAA
Found at i:7884 original size:16 final size:16
Alignment explanation
Indices: 7863--7933 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
7853 GACAGTTTCC
7863 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
7879 TCGGGTTATTTGGGTT
1 TCGGGTCATTCGGGTT
* *
7895 TCTGGTCATAT-GGGTC
1 TCGGGTCAT-TCGGGTT
* *
7911 TCGAGTCATTCGGATT
1 TCGGGTCATTCGGGTT
7927 TCGGGTC
1 TCGGGTC
7934 TACCGGGTCT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
15 1 0.02
16 41 0.95
17 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.34, T:0.39
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:8221 original size:42 final size:42
Alignment explanation
Indices: 8174--8255 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
8164 TAGATATTAA
*
8174 TTTTGAATATTAAATACATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
* *
8216 TTTTGAATATTAAATATATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
8256 TGTGTCAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.40
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:8402 original size:22 final size:22
Alignment explanation
Indices: 8375--8418 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
8365 TTTTTCATTA
8375 CTTCAATTATATAACTAGCCAT
1 CTTCAATTATATAACTAGCCAT
8397 CTTCAATTATATAACTAGCCAT
1 CTTCAATTATATAACTAGCCAT
8419 AAACAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (22 bp):
CTTCAATTATATAACTAGCCAT
Found at i:8425 original size:22 final size:22
Alignment explanation
Indices: 8378--8425 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
8368 TTCATTACTT
***
8378 CAATTATATAACTAGCCATCTT
1 CAATTATATAACTAGCCATAAA
8400 CAATTATATAACTAGCCATAAA
1 CAATTATATAACTAGCCATAAA
8422 CAAT
1 CAAT
8426 GAAAATAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (22 bp):
CAATTATATAACTAGCCATAAA
Found at i:8840 original size:16 final size:16
Alignment explanation
Indices: 8821--8857 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
8811 TCATACGGGT
8821 CTCGGGTTACAGGTCA
1 CTCGGGTTACAGGTCA
*
8837 CTCGGGTTACGGGTCA
1 CTCGGGTTACAGGTCA
*
8853 TTCGG
1 CTCGG
8858 ATTTCGGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.35, T:0.27
Consensus pattern (16 bp):
CTCGGGTTACAGGTCA
Found at i:8857 original size:48 final size:48
Alignment explanation
Indices: 8805--8901 Score: 110
Period size: 48 Copynumber: 2.0 Consensus size: 48
8795 TTATTCAGGT
*
8805 TTCGGATCATACGGGTC-TC-GGGTTACAGGTCACTCGGGT-TACGGGTCA
1 TTCGGAT--TACGGGTCATCTGGGTTACAGATCACTCGGGTCT-CGGGTCA
* * *
8853 TTCGGATTTCGGGTCATCTGGGTTACCGATCATTCGGGTCTCGGGTCA
1 TTCGGATTACGGGTCATCTGGGTTACAGATCACTCGGGTCTCGGGTCA
8901 T
1 T
8902 CTAGGTTGCG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
46 7 0.17
47 2 0.05
48 32 0.76
49 1 0.02
ACGTcount: A:0.14, C:0.23, G:0.32, T:0.31
Consensus pattern (48 bp):
TTCGGATTACGGGTCATCTGGGTTACAGATCACTCGGGTCTCGGGTCA
Found at i:8865 original size:16 final size:16
Alignment explanation
Indices: 8814--8921 Score: 55
Period size: 16 Copynumber: 6.9 Consensus size: 16
8804 TTTCGGATCA
*
8814 TACGGGTC--TCGGGT
1 TACGGGTCATTCGGAT
* * *
8828 TACAGGTCACTCGGGT
1 TACGGGTCATTCGGAT
8844 TACGGGTCATTCGGAT
1 TACGGGTCATTCGGAT
* *
8860 TTCGGGTCA-TCTGGGT
1 TACGGGTCATTC-GGAT
* * *
8876 TACCGATCATTCGGGT
1 TACGGGTCATTCGGAT
*
8892 CT-CGGGTCATCTAGG-T
1 -TACGGGTCAT-TCGGAT
*
8908 TGCGGGTCATTCGG
1 TACGGGTCATTCGG
8922 GTCTTGGGTC
Statistics
Matches: 74, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
14 7 0.09
15 6 0.08
16 55 0.74
17 6 0.08
ACGTcount: A:0.13, C:0.22, G:0.34, T:0.31
Consensus pattern (16 bp):
TACGGGTCATTCGGAT
Found at i:8876 original size:32 final size:32
Alignment explanation
Indices: 8832--8931 Score: 112
Period size: 32 Copynumber: 3.1 Consensus size: 32
8822 TCGGGTTACA
*
8832 GGTCA-CTCGGGTTACGGGTCATTCGGATTTCG
1 GGTCATCT-GGGTTACGGGTCATTCGGATCTCG
* * *
8864 GGTCATCTGGGTTACCGATCATTCGGGTCTCG
1 GGTCATCTGGGTTACGGGTCATTCGGATCTCG
* * * *
8896 GGTCATCTAGGTTGCGGGTCATTCGGGTCTTG
1 GGTCATCTGGGTTACGGGTCATTCGGATCTCG
8928 GGTC
1 GGTC
8932 GGGCAGGTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 56 0.97
33 2 0.03
ACGTcount: A:0.11, C:0.22, G:0.35, T:0.32
Consensus pattern (32 bp):
GGTCATCTGGGTTACGGGTCATTCGGATCTCG
Found at i:8914 original size:48 final size:47
Alignment explanation
Indices: 8816--8923 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 47
8806 TCGGATCATA
* * *
8816 CGGGTC-TCGGGTTACAGGTCACTCGGGTTACGGGTCATTCGGATTT
1 CGGGTCATCGGGTTACAGATCACTCGGGTTACGGGTCATTAGGATTG
* *
8862 CGGGTCATCTGGGTTACCGATCATTCGGGTCT-CGGGTCATCTAGG-TTG
1 CGGGTCATC-GGGTTACAGATCACTCGGGT-TACGGGTCAT-TAGGATTG
8910 CGGGTCATTCGGGT
1 CGGGTCA-TCGGGT
8924 CTTGGGTCGG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
46 6 0.12
47 2 0.04
48 38 0.73
49 6 0.12
ACGTcount: A:0.12, C:0.22, G:0.35, T:0.31
Consensus pattern (47 bp):
CGGGTCATCGGGTTACAGATCACTCGGGTTACGGGTCATTAGGATTG
Found at i:9997 original size:3 final size:3
Alignment explanation
Indices: 9989--10022 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
9979 CTTATCAATT
9989 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
10023 GAGCAAGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Done.