Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011496.1 Corchorus capsularis cultivar CVL-1 contig11517, 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: 29060
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3369 original size:13 final size:13
Alignment explanation
Indices: 3348--3377 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3338 GGTGAGTACG
*
3348 GCATGGCATGGGT
1 GCATAGCATGGGT
3361 GCATAGCATGGGT
1 GCATAGCATGGGT
3374 GCAT
1 GCAT
3378 GGGTGTTGGC
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:0.20, C:0.17, G:0.40, T:0.23
Consensus pattern (13 bp):
GCATAGCATGGGT
Found at i:8600 original size:21 final size:21
Alignment explanation
Indices: 8576--8624 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
8566 CAGCTGGGGG
* * *
8576 CCCATGTGGTATGCTTCTCGC
1 CCCATGTGGTATGCCTCGCGA
*
8597 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
8618 CCCATGT
1 CCCATGT
8625 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.35, G:0.24, T:0.31
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:9680 original size:14 final size:15
Alignment explanation
Indices: 9639--9673 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
9629 AGAAATTTCC
*
9639 AAGTACAAAACTTGG
1 AAGTACAAAATTTGG
9654 AAGTACAAAATTTGG
1 AAGTACAAAATTTGG
9669 AAGTA
1 AAGTA
9674 TAAATTTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.23
Consensus pattern (15 bp):
AAGTACAAAATTTGG
Found at i:10345 original size:33 final size:33
Alignment explanation
Indices: 10303--10370 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
10293 CTGACTATTC
*
10303 GTGCCTGGAGGTTGCGAAAGAAGCGCACAGCAA
1 GTGCCTGGAGGTTGCGAAAGAAGCGCACAACAA
10336 GTGCCTGGAGGTTGCGAAAGAAGCGCACAACAA
1 GTGCCTGGAGGTTGCGAAAGAAGCGCACAACAA
10369 GT
1 GT
10371 CTTCAGATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.21, G:0.35, T:0.13
Consensus pattern (33 bp):
GTGCCTGGAGGTTGCGAAAGAAGCGCACAACAA
Found at i:11284 original size:84 final size:84
Alignment explanation
Indices: 11128--11303 Score: 208
Period size: 84 Copynumber: 2.1 Consensus size: 84
11118 ATTTAAACTT
* *** ** *
11128 GGAAATTTCTACTTCCAAATTCCATCTAATTTCCTTTCGATGTCACACACAAGGTCATAAGGACG
1 GGAAATTTCTACTTCCAAATTCCATCTAACTTCCGCCCGATGTCACACACAAAATCATAAGGACA
* *
11193 TAAGGACATAAGGACATTG
66 CAAGGACATAAGGAAATTG
* * *
11212 GGAAATTTCTACTTCCAAATTTCATCTAACTTCCGCCCTATGTCACACATAAAATCATAAGGACA
1 GGAAATTTCTACTTCCAAATTCCATCTAACTTCCGCCCGATGTCACACACAAAATCATAAGGACA
** *
11277 CCGGGACATAGGGAAATTG
66 CAAGGACATAAGGAAATTG
*
11296 GGGAATTT
1 GGAAATTT
11304 ATATTTGGAG
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (84 bp):
GGAAATTTCTACTTCCAAATTCCATCTAACTTCCGCCCGATGTCACACACAAAATCATAAGGACA
CAAGGACATAAGGAAATTG
Found at i:11398 original size:98 final size:98
Alignment explanation
Indices: 11209--11504 Score: 391
Period size: 99 Copynumber: 3.0 Consensus size: 98
11199 CATAAGGACA
* *
11209 TTGGGAAATTTCTACTTCCAAATTTCATCTAACTTCCGCCCTATGTCACACATAAAATCATAAGG
1 TTGGG-AATTTATACTT-CAAATTTCATCTAACTTCCTCCCTATGTCACACATAAAATCATAAGG
*
11274 ACACCGGGACATAGGGAAATTGGGG-AATTTATAT
64 ACATCGGGACATAGGGAAATTGGGGAAATTTATAT
11308 TT-GGAGATTTATACTTCGAAATTTCATCTAACTTCCTCCCTATGTCACACATAAAAATCATAAG
1 TTGGGA-ATTTATACTTC-AAATTTCATCTAACTTCCTCCCTATGTCACACAT-AAAATCATAAG
11372 GACATCGGGACATAGGGAAATT-GGGAAATTTATAT
63 GACATCGGGACATAGGGAAATTGGGGAAATTTATAT
* * * * * ** **
11407 TTGGGAATTTATATTTACAAATTTAATCTAATTTCTTCCCTATGTCGCACGCAAGGTCATAAGGA
1 TTGGGAATTTATACTT-CAAATTTCATCTAACTTCCTCCCTATGTCACACATAAAATCATAAGGA
**
11472 CATAAGGACATAGGGAAATTGGGGAAATTTATA
65 CATCGGGACATAGGGAAATTGGGGAAATTTATA
11505 CTTCCAAATT
Statistics
Matches: 176, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
97 2 0.01
98 76 0.43
99 94 0.53
100 4 0.02
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (98 bp):
TTGGGAATTTATACTTCAAATTTCATCTAACTTCCTCCCTATGTCACACATAAAATCATAAGGAC
ATCGGGACATAGGGAAATTGGGGAAATTTATAT
Found at i:11417 original size:14 final size:15
Alignment explanation
Indices: 11392--11422 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
11382 CATAGGGAAA
11392 TTGGGAAATTTATAT
1 TTGGGAAATTTATAT
11407 TTGGG-AATTTATAT
1 TTGGGAAATTTATAT
11421 TT
1 TT
11423 ACAAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (15 bp):
TTGGGAAATTTATAT
Found at i:11646 original size:76 final size:76
Alignment explanation
Indices: 11510--11717 Score: 267
Period size: 76 Copynumber: 2.7 Consensus size: 76
11500 TTATACTTCC
* *
11510 AAATTTAACACTTGGAAATTCCTACTTCCAAATTTCTTTAATTTCCTCCCTATGAGATTCATCCG
1 AAATTT-ACACTTGGAAATTTCTACTTCCAAATTTCTTTAATTTCCTCCCTATGACATTCATCCG
11575 CACATAGGG--T
65 CACATAGGGACT
* * *
11585 GATAATTTACACTTGGAAATTTCTACTTCCAAATTTCTTTTATTTGCTCCCTATGTCATTCATCC
1 -A-AATTTACACTTGGAAATTTCTACTTCCAAATTTCTTTAATTTCCTCCCTATGACATTCATCC
*
11650 GGACATAGGGACT
64 GCACATAGGGACT
** * * *
11663 AAATTTTGACTTGGAAATTTATACTTCCAAATTTCGTCTAATTTCTTCCCTATGA
1 AAATTTACACTTGGAAATTTCTACTTCCAAATTTC-TTTAATTTCCTCCCTATGA
11718 AACTCATCGG
Statistics
Matches: 114, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
76 93 0.82
77 20 0.18
78 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (76 bp):
AAATTTACACTTGGAAATTTCTACTTCCAAATTTCTTTAATTTCCTCCCTATGACATTCATCCGC
ACATAGGGACT
Found at i:11834 original size:15 final size:15
Alignment explanation
Indices: 11814--11845 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11804 AAATTTATAA
11814 TTCCAAATTTTGTAC
1 TTCCAAATTTTGTAC
*
11829 TTCCAAGTTTTGTAC
1 TTCCAAATTTTGTAC
11844 TT
1 TT
11846 GGAAATTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.50
Consensus pattern (15 bp):
TTCCAAATTTTGTAC
Found at i:12064 original size:76 final size:76
Alignment explanation
Indices: 11919--12109 Score: 274
Period size: 76 Copynumber: 2.5 Consensus size: 76
11909 GAGCGCACTC
* * * * *
11919 TTTAATTTGCTCTCTATGTCACTTATCCGGACATCGGGACTAATTTTACACTTGGAAATTCCTAT
1 TTTAATTTCCTCCCTATGTCACTCATCCGGACATCGGGACTAATTTTACACTTGGAAATTCATAC
11984 TTCCAAATTTA
66 TTCCAAATTTA
* *
11995 TTTTATTTCCTCCCTATGTCACTCATCCGGACATCGGGACTAATTTTACACTTGGAAATTTATAC
1 TTTAATTTCCTCCCTATGTCACTCATCCGGACATCGGGACTAATTTTACACTTGGAAATTCATAC
*
12060 TTCCAAATTTC
66 TTCCAAATTTA
* * * *
12071 TTTAATTTCCTCCATATGTCATTCATCTGGACATAGGGA
1 TTTAATTTCCTCCCTATGTCACTCATCCGGACATCGGGA
12110 TTAAATTTGG
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 102 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.40
Consensus pattern (76 bp):
TTTAATTTCCTCCCTATGTCACTCATCCGGACATCGGGACTAATTTTACACTTGGAAATTCATAC
TTCCAAATTTA
Found at i:21885 original size:31 final size:29
Alignment explanation
Indices: 21785--21888 Score: 79
Period size: 31 Copynumber: 3.4 Consensus size: 29
21775 GAAGGCTAAT
* *
21785 TGCTCAAATGAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGCCCTAACGTTTG-C-AAA
* * *
21816 TGCTCAAATAAGAGCCCCATC-TTTG-AATT
1 TGCTCAAATAAG-GCCCTAACGTTTGCAA-A
21845 TGGC-CAAATAAGGCCCTAACGTTTGCCAGAA
1 T-GCTCAAATAAGGCCCTAACGTTTG-CA-AA
21876 TGCTCAAATAAGG
1 TGCTCAAATAAGG
21889 GTCTGTCTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
28 8 0.14
29 13 0.23
30 4 0.07
31 26 0.46
32 6 0.11
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (29 bp):
TGCTCAAATAAGGCCCTAACGTTTGCAAA
Found at i:21962 original size:31 final size:31
Alignment explanation
Indices: 21920--21994 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
21910 AACTGACACC
*
21920 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTCCGATAACGTT
*
21951 AGGTCCTTATTTGAGCATTTCCGATAACGTT
1 AGGCCCTTATTTGAGCATTTCCGATAACGTT
21982 AGGCCCTTATTTG
1 AGGCCCTTATTTG
21995 GCCAAATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTCCGATAACGTT
Found at i:22023 original size:29 final size:29
Alignment explanation
Indices: 21982--22052 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
21972 CGATAACGTT
21982 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
* * *
22011 GGGTCCTTATTTGGTCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
22040 AGGCCCTTATTTG
1 AGGCCCTTATTTG
22053 AACATTTTCG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:28105 original size:31 final size:31
Alignment explanation
Indices: 28067--28135 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
28057 AGTTTTGAGA
*
28067 AACTTTTGAAACGCCTATTATACCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
* *
28098 AACTTTTGAAATACCTATTATATCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
28129 AACTTTT
1 AACTTTT
28136 ACAGTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.46
Consensus pattern (31 bp):
AACTTTTGAAACACCTATTATACCCTTATTT
Done.