Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009203.1 Corchorus capsularis cultivar CVL-1 contig09224, 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: 77759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:322 original size:2 final size:2
Alignment explanation
Indices: 310--370 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
300 TCTTGCCCAA
310 CT CT C- 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
351 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
371 ATATATATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2058 original size:1 final size:1
Alignment explanation
Indices: 2052--2081 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2042 AAGGAAAGAG
2052 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2082 CCATCATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10081 original size:21 final size:21
Alignment explanation
Indices: 10036--10081 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
10026 TTCAACGGAG
* *
10036 TTTTGCTAAATACCGTCCTAA
1 TTTTGCTAAATACCGCCCCAA
*
10057 TTTTGCTAAATACCGCCCCAC
1 TTTTGCTAAATACCGCCCCAA
10078 TTTT
1 TTTT
10082 TACACTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.28, G:0.09, T:0.39
Consensus pattern (21 bp):
TTTTGCTAAATACCGCCCCAA
Found at i:10384 original size:32 final size:32
Alignment explanation
Indices: 10304--10389 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 32
10294 AAAATAGCCG
* * *
10304 AGCCGCCCCACCGGCGCGGCCTGCCGTGGCTA
1 AGCCGCCCCACCGGGGCGGCCTGCCCTGGCGA
*
10336 AGCCGCCCCACCGGGGCAGCCTGCCCTGGCGA
1 AGCCGCCCCACCGGGGCGGCCTGCCCTGGCGA
**
10368 AGCCGCCCCAATGGGGCGGCCT
1 AGCCGCCCCACCGGGGCGGCCT
10390 ATTCATAGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.12, C:0.45, G:0.35, T:0.08
Consensus pattern (32 bp):
AGCCGCCCCACCGGGGCGGCCTGCCCTGGCGA
Found at i:10441 original size:32 final size:33
Alignment explanation
Indices: 10304--10440 Score: 111
Period size: 32 Copynumber: 4.2 Consensus size: 33
10294 AAAATAGCCG
** * *
10304 AGCCGCCCCACCGGCGCGGCCTG-CCGTGGCTA
1 AGCCGCCCCAATGGGGCGGCCTGCCCATGGCTA
** * *
10336 AGCCGCCCCACCGGGGCAGCCTGCCC-TGGCGA
1 AGCCGCCCCAATGGGGCGGCCTGCCCATGGCTA
*** *
10368 AGCCGCCCCAATGGGGCGGCCTATTCATAG-TGA
1 AGCCGCCCCAATGGGGCGGCCTGCCCATGGCT-A
* *
10401 AGCCGCCCTAGTGGGGCGGCCTGCCCATGG-TA
1 AGCCGCCCCAATGGGGCGGCCTGCCCATGGCTA
10433 AGCCGCCC
1 AGCCGCCC
10441 TCTTGGGGCG
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
32 55 0.65
33 30 0.35
ACGTcount: A:0.14, C:0.41, G:0.34, T:0.12
Consensus pattern (33 bp):
AGCCGCCCCAATGGGGCGGCCTGCCCATGGCTA
Found at i:34351 original size:1 final size:1
Alignment explanation
Indices: 34347--34381 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
34337 CTTTTTTATC
34347 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34382 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:47603 original size:2 final size:2
Alignment explanation
Indices: 47596--47626 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
47586 ACTCTTAAAT
*
47596 AC AC AC AC GC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
47627 AAAGAACACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:51414 original size:16 final size:16
Alignment explanation
Indices: 51390--51424 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
51380 ACTACAATAC
*
51390 CCTATTAATTAAAGTA
1 CCTAATAATTAAAGTA
51406 CCTAATAATTAAAGTA
1 CCTAATAATTAAAGTA
51422 CCT
1 CCT
51425 TACTTAGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (16 bp):
CCTAATAATTAAAGTA
Found at i:52297 original size:61 final size:60
Alignment explanation
Indices: 52193--52309 Score: 198
Period size: 61 Copynumber: 1.9 Consensus size: 60
52183 CTATAGTGGG
* *
52193 TAGCAATTTATCGAATAATTTTCACAAGCATGGAGGATATCAGCTCCAAGCAAAAGCGGA
1 TAGCAATTTATCAAATAATCTTCACAAGCATGGAGGATATCAGCTCCAAGCAAAAGCGGA
*
52253 TAGCAATTTATCAAATAATCTTCGACAAGCATGGAGGATTTCAGCTCCAAGCAAAAG
1 TAGCAATTTATCAAATAATCTTC-ACAAGCATGGAGGATATCAGCTCCAAGCAAAAG
52310 GAGGAGCATC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 21 0.40
61 32 0.60
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (60 bp):
TAGCAATTTATCAAATAATCTTCACAAGCATGGAGGATATCAGCTCCAAGCAAAAGCGGA
Found at i:57896 original size:13 final size:13
Alignment explanation
Indices: 57878--57905 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
57868 ATTTTAGACT
57878 TTTAGTAGATATA
1 TTTAGTAGATATA
57891 TTTAGTAGATATA
1 TTTAGTAGATATA
57904 TT
1 TT
57906 GCATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TTTAGTAGATATA
Found at i:63346 original size:13 final size:13
Alignment explanation
Indices: 63317--63346 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
63307 ATCAAATCAG
*
63317 AAAAGAGAAACAA
1 AAAAGAGAAAAAA
63330 AAAAGAGAAAAAA
1 AAAAGAGAAAAAA
63343 AAAA
1 AAAA
63347 TAAAAGGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAA
Found at i:66635 original size:2 final size:2
Alignment explanation
Indices: 66630--66655 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
66620 ACACACACAT
66630 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
66656 GTTTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66825 original size:25 final size:25
Alignment explanation
Indices: 66797--66881 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
66787 GGATTTAGGT
66797 GAGGAAGGGAAATGGAAGGAAAAGG
1 GAGGAAGGGAAATGGAAGGAAAAGG
* * * *
66822 GAGGGAGGGGGAA-GTAA-AAGAAAGG
1 GA-GGAAGGGAAATGGAAGGA-AAAGG
66847 TGAGGAAGGGAAATGGAAGGAAAAGG
1 -GAGGAAGGGAAATGGAAGGAAAAGG
*
66873 GAGGGAGGG
1 GAGGAAGGG
66882 GGAAGTAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
24 1 0.02
25 26 0.57
26 18 0.39
27 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.52, T:0.05
Consensus pattern (25 bp):
GAGGAAGGGAAATGGAAGGAAAAGG
Found at i:66834 original size:21 final size:21
Alignment explanation
Indices: 66810--66892 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
66800 GAAGGGAAAT
66810 GGAAGGAAAAGGGAGGGAGGG
1 GGAAGGAAAAGGGAGGGAGGG
* *
66831 GGAAGTAAAAGAAAGGTGAGGAAGGG
1 GGAAG---GA-AAAGG-GAGGGAGGG
66857 AAATGGAAGGAAAAGGGAGGGAGGG
1 ----GGAAGGAAAAGGGAGGGAGGG
*
66882 GGAAGTAAAAG
1 GGAAGGAAAAG
66893 AAAGGGAATG
Statistics
Matches: 48, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
21 15 0.31
24 1 0.02
25 13 0.27
26 13 0.27
27 1 0.02
30 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.51, T:0.05
Consensus pattern (21 bp):
GGAAGGAAAAGGGAGGGAGGG
Found at i:66869 original size:51 final size:51
Alignment explanation
Indices: 66793--66897 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
66783 GTTTGGATTT
66793 AGGTGAGGAAGGGAAATGGAAGGAAAAGGGAGGGAGGGGGAAGTAAAAGAA
1 AGGTGAGGAAGGGAAATGGAAGGAAAAGGGAGGGAGGGGGAAGTAAAAGAA
66844 AGGTGAGGAAGGGAAATGGAAGGAAAAGGGAGGGAGGGGGAAGTAAAAGAA
1 AGGTGAGGAAGGGAAATGGAAGGAAAAGGGAGGGAGGGGGAAGTAAAAGAA
66895 AGG
1 AGG
66898 GAATGATGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.45, C:0.00, G:0.50, T:0.06
Consensus pattern (51 bp):
AGGTGAGGAAGGGAAATGGAAGGAAAAGGGAGGGAGGGGGAAGTAAAAGAA
Found at i:66896 original size:25 final size:25
Alignment explanation
Indices: 66817--66899 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
66807 AATGGAAGGA
66817 AAAGGGAGGGAGGGGGAAGTAAAAG
1 AAAGGGAGGGAGGGGGAAGTAAAAG
* * * *
66842 AAAGGTGA-GGA-AGGGAAATGGAAGG
1 AAAGG-GAGGGAGGGGGAAGT-AAAAG
66867 AAAAGGGAGGGAGGGGGAAGTAAAAG
1 -AAAGGGAGGGAGGGGGAAGTAAAAG
66893 AAAGGGA
1 AAAGGGA
66900 ATGATGATCA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
24 6 0.13
25 20 0.44
26 13 0.29
27 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.49, T:0.05
Consensus pattern (25 bp):
AAAGGGAGGGAGGGGGAAGTAAAAG
Found at i:70620 original size:2 final size:2
Alignment explanation
Indices: 70615--70644 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
70605 TATATAAGCA
70615 AT 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 AT
70645 TGATGATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.