Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012794.1 Corchorus capsularis cultivar CVL-1 contig12815, 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: 73327
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:13790 original size:19 final size:19
Alignment explanation
Indices: 13766--13804 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
13756 AATGGAAGTT
13766 TCAGTTGTACCTCGTACGG
1 TCAGTTGTACCTCGTACGG
13785 TCAGTTGTACCTCGTACGG
1 TCAGTTGTACCTCGTACGG
13804 T
1 T
13805 AAGTCACTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.33
Consensus pattern (19 bp):
TCAGTTGTACCTCGTACGG
Found at i:18672 original size:21 final size:21
Alignment explanation
Indices: 18639--18682 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18629 AACTATAGCT
*
18639 TCATCTTGCTTAGGAAATGTC
1 TCATCTTGCTTAGGAAAGGTC
*
18660 TCATCTT-CTTTAGGCAAGGTC
1 TCATCTTGC-TTAGGAAAGGTC
18681 TC
1 TC
18683 GGCAGCAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (21 bp):
TCATCTTGCTTAGGAAAGGTC
Found at i:29187 original size:29 final size:29
Alignment explanation
Indices: 29145--29206 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
29135 TAAGAGCAAG
*
29145 ACTTTTTAATGTGTATTTATACACACACA
1 ACTTATTAATGTGTATTTATACACACACA
29174 ACTTATTAATGTGTATTTATACACACACA
1 ACTTATTAATGTGTATTTATACACACACA
29203 ACTT
1 ACTT
29207 TAATCTGCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.40
Consensus pattern (29 bp):
ACTTATTAATGTGTATTTATACACACACA
Found at i:37513 original size:30 final size:30
Alignment explanation
Indices: 37479--37535 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
37469 CATCAAAGAA
* * *
37479 AATGATGTGCCCAAGGCTTATCATGGAGGG
1 AATGATGCGCCAAAGACTTATCATGGAGGG
*
37509 AATGATGCGCCAAAGACTTATTATGGA
1 AATGATGCGCCAAAGACTTATCATGGA
37536 CTTGAAGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (30 bp):
AATGATGCGCCAAAGACTTATCATGGAGGG
Found at i:44475 original size:38 final size:38
Alignment explanation
Indices: 44432--44533 Score: 168
Period size: 38 Copynumber: 2.7 Consensus size: 38
44422 GGTTGTGCAT
* *
44432 AGTGGACCCGCGTCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
* *
44470 AGTGGACCCGTGCCTGAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
44508 AGTGGACCCGTGCCTCAGGGGGTTAA
1 AGTGGACCCGTGCCTCAGGGGGTTAA
44534 CTGTTGGCTA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 59 1.00
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.22
Consensus pattern (38 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
Found at i:44555 original size:6 final size:6
Alignment explanation
Indices: 44544--44574 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
44534 CTGTTGGCTA
44544 GATTGT GATTGT GATTGT GATTGT GATTGT G
1 GATTGT GATTGT GATTGT GATTGT GATTGT G
44575 GTGCAGCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.48
Consensus pattern (6 bp):
GATTGT
Found at i:47949 original size:38 final size:38
Alignment explanation
Indices: 47906--48044 Score: 235
Period size: 38 Copynumber: 3.7 Consensus size: 38
47896 GGTTGTGCAT
47906 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
*
47944 AGTGGACCCGCGCCTCAGGGGGTTAAATTGATGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
* *
47982 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
*
48020 AGTGGACCCGTGCCTCA-GGGGTTAA
1 AGTGGACCCGCGCCTCAGGGGGTTAA
48045 CTGTTGGCTA
Statistics
Matches: 97, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
37 8 0.08
38 89 0.92
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.21
Consensus pattern (38 bp):
AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
Found at i:48066 original size:6 final size:6
Alignment explanation
Indices: 48055--48079 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48045 CTGTTGGCTA
48055 GATTGT GATTGT GATTGT GATTGT G
1 GATTGT GATTGT GATTGT GATTGT G
48080 GTGCAGCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GATTGT
Found at i:48792 original size:21 final size:21
Alignment explanation
Indices: 48768--48808 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
48758 GAATTGTAGC
**
48768 TTCTTGGAAATGGCTCTTGCT
1 TTCTTGGAAATCCCTCTTGCT
*
48789 TTCTTTGAAATCCCTCTTGC
1 TTCTTGGAAATCCCTCTTGC
48809 ATTCCTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (21 bp):
TTCTTGGAAATCCCTCTTGCT
Found at i:49945 original size:5 final size:6
Alignment explanation
Indices: 49931--50015 Score: 73
Period size: 6 Copynumber: 13.7 Consensus size: 6
49921 AGCACCAAAG
* * * * *
49931 AAAATA AAAATA AAAAGA AAAAGA AAAAGA AAAAGA AAAATA AACAAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA-AATA
*
49980 CGAAAATTA AAAAGA AAAATA AAAA-A AAAATA AAAA
1 --AAAA-TA AAAATA AAAATA AAAATA AAAATA AAAA
50016 GATAAAGGGA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
5 5 0.07
6 51 0.75
7 7 0.10
8 2 0.03
9 3 0.04
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.08
Consensus pattern (6 bp):
AAAATA
Found at i:49951 original size:12 final size:12
Alignment explanation
Indices: 49927--50017 Score: 96
Period size: 12 Copynumber: 7.4 Consensus size: 12
49917 TAAAAGCACC
49927 AAAG-AAAATAA
1 AAAGAAAAATAA
* *
49938 AAATAAAAAGAA
1 AAAGAAAAATAA
*
49950 AAAGAAAAAGAA
1 AAAGAAAAATAA
49962 AAAGAAAAATAAACA
1 AAAGAAAAAT--A-A
*
49977 AAACGAAAATTAA
1 AAA-GAAAAATAA
49990 AAAGAAAAATAA
1 AAAGAAAAATAA
50002 AAA-AAAAATAA
1 AAAGAAAAATAA
50013 AAAGA
1 AAAGA
50018 TAAAGGGAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
11 14 0.21
12 38 0.56
13 4 0.06
14 2 0.03
15 4 0.06
16 6 0.09
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.08
Consensus pattern (12 bp):
AAAGAAAAATAA
Found at i:49992 original size:34 final size:34
Alignment explanation
Indices: 49936--50022 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
49926 CAAAGAAAAT
*
49936 AAAAATAAAAAGAAAAAGAAAAAGAAAAAGAAAA
1 AAAAACAAAAAGAAAAAGAAAAAGAAAAAGAAAA
* * ** *
49970 ATAAACAAAACGAAAATTAAAAAGAAAAATAAAAA
1 AAAAACAAAAAGAAAAAGAAAAAGAAAAA-GAAAA
* *
50005 AAAAATAAAAAGATAAAG
1 AAAAACAAAAAGAAAAAG
50023 GGAAGAAATC
Statistics
Matches: 40, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
34 24 0.60
35 16 0.40
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.08
Consensus pattern (34 bp):
AAAAACAAAAAGAAAAAGAAAAAGAAAAAGAAAA
Found at i:63059 original size:41 final size:41
Alignment explanation
Indices: 63012--63094 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
63002 CCATGCTTGT
63012 GACAACACCGAGCTGAACCCAAGCTCAAACAAGTGCTCCCC
1 GACAACACCGAGCTGAACCCAAGCTCAAACAAGTGCTCCCC
*
63053 GACAACACCGAGCTGAACCCAAGCTCGAACAAGTGCTCCCC
1 GACAACACCGAGCTGAACCCAAGCTCAAACAAGTGCTCCCC
63094 G
1 G
63095 CACTGATTAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.33, C:0.39, G:0.19, T:0.10
Consensus pattern (41 bp):
GACAACACCGAGCTGAACCCAAGCTCAAACAAGTGCTCCCC
Found at i:63797 original size:21 final size:21
Alignment explanation
Indices: 63773--63812 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
63763 GCTAAAGCTG
63773 AAAT-AAAGCCATCAGAGCTAT
1 AAATAAAAG-CATCAGAGCTAT
63794 AAATAAAAGCATCAGAGCT
1 AAATAAAAGCATCAGAGCT
63813 TTATGCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.17
Consensus pattern (21 bp):
AAATAAAAGCATCAGAGCTAT
Found at i:65117 original size:21 final size:21
Alignment explanation
Indices: 65093--65142 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
65083 AATCAGCAAC
* * *
65093 TTCTTCTTCCTCTTTTTCACA
1 TTCTTCTTCCCCGTTCTCACA
*
65114 TTCTTCTTCCCCGTTCTCACT
1 TTCTTCTTCCCCGTTCTCACA
65135 TTCTTCTT
1 TTCTTCTT
65143 TTTCTTCTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.36, G:0.02, T:0.56
Consensus pattern (21 bp):
TTCTTCTTCCCCGTTCTCACA
Found at i:66174 original size:11 final size:12
Alignment explanation
Indices: 66158--66189 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
66148 GAAGTTCGTG
66158 TTTGAAGATTA-
1 TTTGAAGATTAT
66169 TTTGAAGA-TAT
1 TTTGAAGATTAT
66180 TTTGAAGATT
1 TTTGAAGATT
66190 TGAAGACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 16 0.84
12 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (12 bp):
TTTGAAGATTAT
Found at i:66796 original size:18 final size:17
Alignment explanation
Indices: 66769--66804 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
66759 TTTCTCTTCA
66769 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
66786 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
66804 T
1 T
66805 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Done.