Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010203.1 Corchorus capsularis cultivar CVL-1 contig10224, 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: 72817
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:542 original size:3 final size:3
Alignment explanation
Indices: 536--566 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
526 TTTAGGGTGT
536 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
567 ATTTTGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11978 original size:16 final size:18
Alignment explanation
Indices: 11943--11979 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
11933 AAAAATTTGT
*
11943 TTGGCCAAAAAAAATGAA
1 TTGGCCAAAAAAAATAAA
11961 TTGG-CAAAAAAAA-AAA
1 TTGGCCAAAAAAAATAAA
11977 TTG
1 TTG
11980 TTTGCAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.19
Consensus pattern (18 bp):
TTGGCCAAAAAAAATAAA
Found at i:11986 original size:19 final size:19
Alignment explanation
Indices: 11913--11986 Score: 55
Period size: 22 Copynumber: 3.7 Consensus size: 19
11903 TCCTAGTCTT
11913 AAAATTGTTTTGCAACCAAAAA
1 AAAATTG-TTTGCAA--AAAAA
*
11935 AAATTTGTTTGGCCAAAAAAA
1 AAAATTGTTT-G-CAAAAAAA
*
11956 ATGAATTG---GCAAAAAAA
1 A-AAATTGTTTGCAAAAAAA
11973 AAAATTGTTTGCAA
1 AAAATTGTTTGCAA
11987 TCAAATAGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 15
0.69 0.07 0.25
Matches are distributed among these distances:
16 5 0.12
17 9 0.21
18 1 0.02
19 4 0.10
21 9 0.21
22 11 0.26
23 3 0.07
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (19 bp):
AAAATTGTTTGCAAAAAAA
Found at i:16215 original size:30 final size:30
Alignment explanation
Indices: 16152--16215 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
16142 TATAATAAAA
* * *
16152 ATATATAATCAATGTTTTTTTTTTGCTACT
1 ATATATAATCAATGTTTTATATATGCTACT
*
16182 ATATATAATCAATGTTTATATATATGTTA-T
1 ATATATAATCAATGTTT-TATATATGCTACT
16212 ATAT
1 ATAT
16216 GTATAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (30 bp):
ATATATAATCAATGTTTTATATATGCTACT
Found at i:16760 original size:17 final size:17
Alignment explanation
Indices: 16730--16768 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
16720 TACAAAAATT
16730 AAAAAGAAAATAAAATAA
1 AAAAAGAAAATAAAA-AA
*
16748 AAAAAG-AATTAAAAAA
1 AAAAAGAAAATAAAAAA
16764 AAAAA
1 AAAAA
16769 ACAAAAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 7 0.35
18 6 0.30
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (17 bp):
AAAAAGAAAATAAAAAA
Found at i:16761 original size:22 final size:22
Alignment explanation
Indices: 16736--16779 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16726 AATTAAAAAG
*
16736 AAAATAAAATAAA-AAAAGAATT
1 AAAA-AAAAAAAACAAAAGAATT
16758 AAAAAAAAAAAACAAAAGAATT
1 AAAAAAAAAAAACAAAAGAATT
16780 GTCGACGCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (22 bp):
AAAAAAAAAAAACAAAAGAATT
Found at i:16769 original size:17 final size:18
Alignment explanation
Indices: 16730--16774 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
16720 TACAAAAATT
*
16730 AAAAAGAAAATAAAATAA
1 AAAAAGAAAATAAAAAAA
*
16748 AAAAAG-AATTAAAAAAA
1 AAAAAGAAAATAAAAAAA
*
16765 AAAAACAAAA
1 AAAAAGAAAA
16775 GAATTGTCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.84, C:0.02, G:0.04, T:0.09
Consensus pattern (18 bp):
AAAAAGAAAATAAAAAAA
Found at i:34547 original size:12 final size:12
Alignment explanation
Indices: 34530--34557 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
34520 AATGGAATTC
34530 CTTAAACCAGCA
1 CTTAAACCAGCA
34542 CTTAAACCAGCA
1 CTTAAACCAGCA
34554 CTTA
1 CTTA
34558 CGCTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.21
Consensus pattern (12 bp):
CTTAAACCAGCA
Found at i:36717 original size:64 final size:64
Alignment explanation
Indices: 36596--36717 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
36586 GGGCAATTGG
* * * * *
36596 TATTTGTGGAAAGCTCGAGTTTACAACAAGTGATAGTAGAATCAGATATGTGGTCAATGGACTT
1 TATTGGTGGAAAACTCGAGTTTACAACAAGTGACAATAGAATCAGATATGTGATCAATGGACTT
* * *
36660 TATTGGTGGAAAACTCGGGTTTACAACAAGTGACAATA-AAGTTAGATGTGTGATCAAT
1 TATTGGTGGAAAACTCGAGTTTACAACAAGTGACAATAGAA-TCAGATATGTGATCAAT
36718 TTTGTGCAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 2 0.04
64 47 0.96
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (64 bp):
TATTGGTGGAAAACTCGAGTTTACAACAAGTGACAATAGAATCAGATATGTGATCAATGGACTT
Found at i:51215 original size:27 final size:28
Alignment explanation
Indices: 51162--51215 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
51152 CAAGGCACCT
* * *
51162 ATTGATTATGTCGATTTGTAAGATTAGG
1 ATTGACTAAGTCGATTTGTAAAATTAGG
51190 ATTGACTAAGTCGA-TTGTAAAATTAG
1 ATTGACTAAGTCGATTTGTAAAATTAG
51216 TAATCAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (28 bp):
ATTGACTAAGTCGATTTGTAAAATTAGG
Found at i:55352 original size:32 final size:31
Alignment explanation
Indices: 55281--55352 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
55271 ACTGACATGG
* * *
55281 CAATGCCACGTCGGACCAAAATGCTACGTGG
1 CAATGCCACGTCAGACCAAAACGCTACGTGA
* *
55312 CAAGGCCACGTCAGACCAAGACGCTGACGTGA
1 CAATGCCACGTCAGACCAAAACGCT-ACGTGA
*
55344 CATTGCCAC
1 CAATGCCAC
55353 ATATGTAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 21 0.64
32 12 0.36
ACGTcount: A:0.29, C:0.32, G:0.25, T:0.14
Consensus pattern (31 bp):
CAATGCCACGTCAGACCAAAACGCTACGTGA
Found at i:61783 original size:2 final size:2
Alignment explanation
Indices: 61776--61803 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
61766 CCCAGTCTAG
61776 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
61804 GCTTGTTAAA
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):
TA
Found at i:67945 original size:6 final size:6
Alignment explanation
Indices: 67934--67965 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
67924 CTTTAAATAT
67934 TATCTA TATCTA TATCTA TATCTA TAT-TA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA TAT
67966 TAAAAAGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (6 bp):
TATCTA
Found at i:70987 original size:21 final size:21
Alignment explanation
Indices: 70961--71025 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 21
70951 TTGGTTTCAC
70961 TTGTTTGATGGAATATTACAA
1 TTGTTTGATGGAATATTACAA
*
70982 TTGTTTGATGAAATTGTGTATTACAA
1 TTGTTTGATGGAA-----TATTACAA
*
71008 TTGTTTCATGGAATATTA
1 TTGTTTGATGGAATATTA
71026 TATCATCTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
21 17 0.47
26 19 0.53
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (21 bp):
TTGTTTGATGGAATATTACAA
Done.