Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012195.1 Corchorus capsularis cultivar CVL-1 contig12216, 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: 26212
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:509 original size:35 final size:36
Alignment explanation
Indices: 470--554 Score: 104
Period size: 35 Copynumber: 2.4 Consensus size: 36
460 TTAATAGAAG
* *
470 TTTCTGTATCCTTGTTGATTTCAAGTT-GTGGTGA-T
1 TTTCTGTATCCTTGTTGAATTC-ACTTGGTGGTGATT
**
505 TTTCTGTATCAAT-TTGAATTCACTTGGTGGTGATT
1 TTTCTGTATCCTTGTTGAATTCACTTGGTGGTGATT
540 TTTCTGTATCCTTGT
1 TTTCTGTATCCTTGT
555 GATCTTGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
33 3 0.07
34 14 0.34
35 23 0.56
36 1 0.02
ACGTcount: A:0.15, C:0.13, G:0.20, T:0.52
Consensus pattern (36 bp):
TTTCTGTATCCTTGTTGAATTCACTTGGTGGTGATT
Found at i:14344 original size:25 final size:27
Alignment explanation
Indices: 14292--14344 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
14282 TTACTCAACT
**
14292 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
14319 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
14344 A
1 A
14345 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:17811 original size:11 final size:11
Alignment explanation
Indices: 17797--17833 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
17787 TTTTACCATT
*
17797 AATTTTGTAAC
1 AATTTTGTCAC
17808 AATTTTGTCAC
1 AATTTTGTCAC
*
17819 AAATTTGTCAC
1 AATTTTGTCAC
17830 AATT
1 AATT
17834 GCAAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (11 bp):
AATTTTGTCAC
Found at i:20125 original size:19 final size:19
Alignment explanation
Indices: 20103--20146 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
20093 TAATTATTCC
* *
20103 ATTATTTTTTTAATCATAA
1 ATTATTTTTTAAATAATAA
20122 ATTATTTTTTAAATAATAA
1 ATTATTTTTTAAATAATAA
20141 ATTATT
1 ATTATT
20147 CCATTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTATTTTTTAAATAATAA
Found at i:20273 original size:38 final size:37
Alignment explanation
Indices: 20209--20304 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 37
20199 AATTTGCCTT
*
20209 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTATC
** *
20246 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTTTATC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCCTTTTATC
*
20284 TTTGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
20305 TGGCTTAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 19 0.37
38 32 0.63
ACGTcount: A:0.15, C:0.20, G:0.10, T:0.55
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTATC
Found at i:21500 original size:20 final size:19
Alignment explanation
Indices: 21475--21512 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
21465 TACTATTATT
21475 TTTTAAATTT-AATATTTTAC
1 TTTT-AATTTCAAT-TTTTAC
21495 TTTTAATTTCAATTTTTA
1 TTTTAATTTCAATTTTTA
21513 AATGCCAATA
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:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAATTTCAATTTTTAC
Found at i:21711 original size:22 final size:22
Alignment explanation
Indices: 21683--21866 Score: 106
Period size: 22 Copynumber: 8.3 Consensus size: 22
21673 TGTCTCTATG
*
21683 TGGTTATCAAAATTTTATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
21705 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
21728 -GGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
21749 TGGTTACCAAAATTTCATACGGA
1 TGGTTATCAAAATTTCATA-AGA
* *
21772 -AGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
21793 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
21815 TCAAGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
21839 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
21861 TGGTTA
1 TGGTTA
21867 ATTATCACAA
Statistics
Matches: 124, Mismatches: 28, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
20 2 0.02
22 100 0.81
23 4 0.03
24 18 0.15
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:21753 original size:44 final size:44
Alignment explanation
Indices: 21684--21811 Score: 170
Period size: 44 Copynumber: 2.9 Consensus size: 44
21674 GTCTCTATGT
* * ** *
21684 GGTTATCAAAATTTTATAAG-ATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAT-ACGGA
21728 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATACGGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATACGGA
*
21772 AGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA
21812 GGATCAAGTT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
43 3 0.04
44 73 0.96
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATACGGA
Found at i:21843 original size:46 final size:43
Alignment explanation
Indices: 21715--21859 Score: 175
Period size: 44 Copynumber: 3.3 Consensus size: 43
21705 TGGTTATTAT
*
21715 AATTTCATGAGGAGGTTATCAAAATTTCATAGTGTGGTTACCAA
1 AATTTCAT-AGGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
21759 AATTTCATACGGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
1 AATTTCATA-GGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
* * ***
21803 AATTTCATAGGATCAAGTTATTAAAATTTCTTAG-GTTGGTTATTGA
1 AATTTCATAGG---AAGTTATCAAAATTTCATAGTG-TGGTTACCAA
21849 AATTTCATAGG
1 AATTTCATAGG
21860 GTGGTTAATT
Statistics
Matches: 90, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
43 3 0.03
44 50 0.56
45 1 0.01
46 36 0.40
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.37
Consensus pattern (43 bp):
AATTTCATAGGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
Found at i:21927 original size:22 final size:22
Alignment explanation
Indices: 21902--22295 Score: 129
Period size: 22 Copynumber: 17.7 Consensus size: 22
21892 ATCAAAGAGA
* *
21902 TTATCAAAATCTCATAACGAGG
1 TTATCAAAATTTCATAATGAGG
* *
21924 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAATGAGG
*
21946 TTAACAAAATTTCATTAA-GAGG
1 TTATCAAAATTTCA-TAATGAGG
* * * *
21968 TTA-CTAATATTTTATGAGGAGG
1 TTATC-AAAATTTCATAATGAGG
21990 TTATCAAAATTTCAT-ATGAAGG
1 TTATCAAAATTTCATAATG-AGG
* * * *
22012 TTATAAAAATCTCAATTTCATAAGG
1 TTATCAAAATTTC-A--TAATGAGG
* * *
22037 AGTAACAAAATTTGAT-A-GAAGG
1 -TTATCAAAATTTCATAATG-AGG
*
22059 TTATC-AAATCTCAT-A-GAGTG
1 TTATCAAAATTTCATAATGAG-G
* *
22079 ATTAT-AGAAATTTCATAGAGATCAGA
1 -TTATCA-AAATTTCAT--A-ATGAGG
* *
22105 TTATCAAAATTTC-TAGA-AAGA
1 TTATCAAAATTTCATA-ATGAGG
* **
22126 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAATGAGG
*
22148 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATAA-TGAGG
* * *
22170 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAATGAGG
*
22192 TTATCAGAATTTCAT-A-GAGGG
1 TTATCAAAATTTCATAATGA-GG
* * * *
22213 ATCAACAAAAATTT-ATAAAGAGT
1 -TTATC-AAAATTTCATAATGAGG
* *
22236 TTATCAAAATTTCATAAAGAGC
1 TTATCAAAATTTCATAATGAGG
* * * *
22258 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAATGAGG
22280 TTA-CAAAAATTTCATA
1 TTATC-AAAATTTCATA
22296 GTGGTATTTC
Statistics
Matches: 277, Mismatches: 61, Indels: 68
0.68 0.15 0.17
Matches are distributed among these distances:
19 2 0.01
20 11 0.04
21 41 0.15
22 173 0.62
23 17 0.06
24 3 0.01
25 16 0.06
26 12 0.04
27 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGAGG
Found at i:22512 original size:22 final size:22
Alignment explanation
Indices: 22377--22691 Score: 150
Period size: 22 Copynumber: 14.5 Consensus size: 22
22367 TTATTGAGTA
*
22377 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
22397 ATCAAAATTTCGTATGAATGTT
1 ATCAAAATTTCATAGGGAGGTT
***
22419 ATCAAAATTTCATAATTTA-GTT
1 ATCAAAATTTCAT-AGGGAGGTT
* * *
22441 TTCAAAATTTCATA-AGAGGGTC
1 ATCAAAATTTCATAGGGA-GGTT
* * * *
22463 ATCAAAATTTCTTA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
22485 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
22507 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
22529 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
22551 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
22567 A-CTAAGATTTCATAAGAAAGTT
1 ATC-AAAATTTCATAGGGAGGTT
*
22589 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* * *
22612 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGGAG-GTT
* *
22635 ATTAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
22657 ATCACAATTTTGATAGTGTGATT
1 ATCA-AAATTTCATAGGGAGGTT
22680 ATCAAAATTTCA
1 ATCAAAATTTCA
22692 GCGTGTGATT
Statistics
Matches: 222, Mismatches: 55, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
15 1 0.00
16 7 0.03
17 4 0.02
19 2 0.01
20 12 0.05
21 6 0.03
22 129 0.58
23 61 0.27
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:22613 original size:23 final size:23
Alignment explanation
Indices: 22587--22689 Score: 102
Period size: 23 Copynumber: 4.5 Consensus size: 23
22577 CATAAGAAAG
22587 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
22610 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* * *
22633 TTATTAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
* * * *
22655 TTATCACAATTTTGATAGTG-TGA
1 TTATCAAAATTTT-ATAGGGAGGT
22678 TTATCAAAATTT
1 TTATCAAAATTT
22690 CAGCGTGTGA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
22 11 0.17
23 54 0.83
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:22687 original size:45 final size:46
Alignment explanation
Indices: 22587--22691 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 46
22577 CATAAGAAAG
* *
22587 TTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGCGAGGTTTATCAAAATTTTATAGGAAGAT
* * *
22633 TTATTAAAATTTCATAGCGAGG-TTATCACAATTTTGATAGTG-TGA-
1 TTATCAAAATTTCATAGCGAGGTTTATCAAAATTTT-ATAG-GAAGAT
22678 TTATCAAAATTTCA
1 TTATCAAAATTTCA
22692 GCGTGTGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
45 25 0.49
46 25 0.49
47 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (46 bp):
TTATCAAAATTTCATAGCGAGGTTTATCAAAATTTTATAGGAAGAT
Done.