Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014186.1 Corchorus capsularis cultivar CVL-1 contig14207, 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: 45133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4485 original size:2 final size:2
Alignment explanation
Indices: 4478--4510 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4468 AGTTATACAT
4478 AC AC AC AC AC AC 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 AC A
4511 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4515 original size:2 final size:2
Alignment explanation
Indices: 4510--4539 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4500 ACACACACAC
4510 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
4540 TAGAATGCCA
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
Found at i:5523 original size:32 final size:33
Alignment explanation
Indices: 5470--5537 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
5460 ATCGATTAAG
5470 GCGCAAAATGGGGGGCCAAAGTCAAAAAGCAGCA
1 GCGCAAAAT-GGGGGCCAAAGTCAAAAAGCAGCA
* * *
5504 GCGCAAAAT-GGGGCGAAAGTGAAAAAGTAGCA
1 GCGCAAAATGGGGGCCAAAGTCAAAAAGCAGCA
5536 GC
1 GC
5538 TGTAATCGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 22 0.71
34 9 0.29
ACGTcount: A:0.41, C:0.18, G:0.34, T:0.07
Consensus pattern (33 bp):
GCGCAAAATGGGGGCCAAAGTCAAAAAGCAGCA
Found at i:5862 original size:17 final size:17
Alignment explanation
Indices: 5840--5876 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5830 GGGTGATTTG
*
5840 ATTATTGTTAATGTATA
1 ATTATTGATAATGTATA
*
5857 ATTATTGATCATGTATA
1 ATTATTGATAATGTATA
5874 ATT
1 ATT
5877 TTTTTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (17 bp):
ATTATTGATAATGTATA
Found at i:6356 original size:21 final size:22
Alignment explanation
Indices: 6314--6359 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
6304 TAGGGTTATC
6314 TTTATTCATCTATATCTTAGGGT
1 TTTATTCATCTATA-CTTAGGGT
*
6337 TTTATTTATCTATA-TTAGGGT
1 TTTATTCATCTATACTTAGGGT
6358 TT
1 TT
6360 ATGTATGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
23 13 0.59
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.57
Consensus pattern (22 bp):
TTTATTCATCTATACTTAGGGT
Found at i:6611 original size:20 final size:19
Alignment explanation
Indices: 6586--6637 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
6576 ATTCAAATTG
6586 ACACGTAGCAAAACAATTCA
1 ACACGTAGCAAAA-AATTCA
*
6606 ACACGTAGCGAAAAGATTCA
1 ACACGTAGC-AAAAAATTCA
6626 ACACGTAGCAAA
1 ACACGTAGCAAA
6638 TTAAAAGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 3 0.10
20 23 0.77
21 4 0.13
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.13
Consensus pattern (19 bp):
ACACGTAGCAAAAAATTCA
Found at i:9790 original size:26 final size:27
Alignment explanation
Indices: 9747--9797 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
9737 AACCTGACTC
*
9747 GAACCCGAGAACCTGCCCAACCCGTCT
1 GAACCCGAGAACCCGCCCAACCCGTCT
9774 GAACCCGA-AACCCGCCCAACCCGT
1 GAACCCGAGAACCCGCCCAACCCGT
9798 TTTGACCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.27, C:0.47, G:0.18, T:0.08
Consensus pattern (27 bp):
GAACCCGAGAACCCGCCCAACCCGTCT
Found at i:9869 original size:16 final size:16
Alignment explanation
Indices: 9857--9927 Score: 74
Period size: 16 Copynumber: 4.4 Consensus size: 16
9847 CAAACCCGTG
*
9857 ACCCGAATGACCCGTA
1 ACCCGAATGACCCGAA
*
9873 ACCC-AGATAACCCGAA
1 ACCCGA-ATGACCCGAA
*
9889 ACCCGAATGACCCGAG
1 ACCCGAATGACCCGAA
*
9905 ACCC-ATATGACCTGAA
1 ACCCGA-ATGACCCGAA
9921 ACCCGAA
1 ACCCGAA
9928 AAACCTGAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
15 2 0.04
16 41 0.91
17 2 0.04
ACGTcount: A:0.37, C:0.37, G:0.17, T:0.10
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:9869 original size:32 final size:32
Alignment explanation
Indices: 9833--9906 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
9823 GAACCCGCCC
**
9833 GACCCGAGACAC-GACAAACCCGTGACCCGAAT
1 GACCCGAGACACAGA-AAACCCGAAACCCGAAT
* *
9865 GACCCGTA-ACCCAGATAACCCGAAACCCGAAT
1 GACCCG-AGACACAGAAAACCCGAAACCCGAAT
9897 GACCCGAGAC
1 GACCCGAGAC
9907 CCATATGACC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
31 1 0.03
32 31 0.89
33 3 0.09
ACGTcount: A:0.35, C:0.38, G:0.20, T:0.07
Consensus pattern (32 bp):
GACCCGAGACACAGAAAACCCGAAACCCGAAT
Found at i:9909 original size:32 final size:32
Alignment explanation
Indices: 9857--9927 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
9847 CAAACCCGTG
9857 ACCCGAATGACCCGTAACCCAGATAACCCGAA
1 ACCCGAATGACCCGTAACCCAGATAACCCGAA
* * *
9889 ACCCGAATGACCCG-AGACCCATATGACCTGAA
1 ACCCGAATGACCCGTA-ACCCAGATAACCCGAA
9921 ACCCGAA
1 ACCCGAA
9928 AAACCTGAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 1 0.03
32 34 0.97
ACGTcount: A:0.37, C:0.37, G:0.17, T:0.10
Consensus pattern (32 bp):
ACCCGAATGACCCGTAACCCAGATAACCCGAA
Found at i:10752 original size:16 final size:16
Alignment explanation
Indices: 10733--10884 Score: 202
Period size: 16 Copynumber: 9.6 Consensus size: 16
10723 CCCAACCCGA
10733 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
10749 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
10765 GACCCG-GAACCCGAAT
1 GACCCGAG-ACCCGAAT
10781 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
* *
10797 GACCCGAAACCCGACT
1 GACCCGAGACCCGAAT
*
10813 GACCCGAGACCCGACT
1 GACCCGAGACCCGAAT
10829 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
*
10845 AACCCGA-ACCC-AGAT
1 GACCCGAGACCCGA-AT
* *
10860 GACCTGAAACCCGAAT
1 GACCCGAGACCCGAAT
*
10876 GACCGGAGA
1 GACCCGAGA
10885 AAACTACTTG
Statistics
Matches: 122, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
14 1 0.01
15 12 0.10
16 107 0.88
17 2 0.02
ACGTcount: A:0.32, C:0.38, G:0.24, T:0.07
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:11289 original size:33 final size:33
Alignment explanation
Indices: 11252--11314 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
11242 AAGTGAAGCC
11252 AATGAAGTTCCCGCATTAGGAATGATAAAAAAA
1 AATGAAGTTCCCGCATTAGGAATGATAAAAAAA
*
11285 AATGAAGTTCTCGCATTAGGAATGATAAAA
1 AATGAAGTTCCCGCATTAGGAATGATAAAA
11315 GGTTTTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (33 bp):
AATGAAGTTCCCGCATTAGGAATGATAAAAAAA
Found at i:25480 original size:38 final size:38
Alignment explanation
Indices: 25438--25630 Score: 278
Period size: 38 Copynumber: 5.0 Consensus size: 38
25428 GGCTGTGCAT
*
25438 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
*
25476 AGTGGACCCGTGTCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
*
25514 AGTGGACACGTGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
* * * * *
25552 AATGGACCCGCGCCTCGGGGGGTTAAGCTGTTGGGTAAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGAT-GGT-AAG
* *
25592 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGCAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
25630 A
1 A
25631 TTGTGATTGT
Statistics
Matches: 138, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
38 102 0.74
39 5 0.04
40 31 0.22
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (38 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
Found at i:25640 original size:6 final size:6
Alignment explanation
Indices: 25629--25665 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
25619 CTGTTGGCAA
* *
25629 GATTGT GATTGT AATTGT GATTGT GATTGC GATTGT G
1 GATTGT GATTGT GATTGT GATTGT GATTGT GATTGT G
25666 GTGCAGCCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (6 bp):
GATTGT
Found at i:30076 original size:77 final size:77
Alignment explanation
Indices: 29983--30138 Score: 285
Period size: 77 Copynumber: 2.0 Consensus size: 77
29973 ACCATGTGTA
*
29983 CTTATTGCAGAAGTCCTTGTATGATTTGAAACAGTCTCCTAGACAGTGGTATAATAGGTTTGACT
1 CTTATTGCAGAAGTCCTTGTATGATTTGAAACAGTCTCCTAGACAGTGGTATAAGAGGTTTGACT
30048 CATGTATGGCTT
66 CATGTATGGCTT
*
30060 CTTATTGCAGAAGTCCTTGTATGATTTGAAACAGTCTCCTAGACTGTGGTATAAGAGGTTTGACT
1 CTTATTGCAGAAGTCCTTGTATGATTTGAAACAGTCTCCTAGACAGTGGTATAAGAGGTTTGACT
*
30125 CATGTATGGTTT
66 CATGTATGGCTT
30137 CT
1 CT
30139 CATGATTTTG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (77 bp):
CTTATTGCAGAAGTCCTTGTATGATTTGAAACAGTCTCCTAGACAGTGGTATAAGAGGTTTGACT
CATGTATGGCTT
Found at i:34596 original size:6 final size:6
Alignment explanation
Indices: 34585--34612 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
34575 CAATGCAATC
34585 ATCCCA ATCCCA ATCCCA ATCCCA ATCC
1 ATCCCA ATCCCA ATCCCA ATCCCA ATCC
34613 ACCTACCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
ATCCCA
Found at i:36482 original size:24 final size:25
Alignment explanation
Indices: 36422--36480 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
36412 TTCAAACTCT
*
36422 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
36447 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
36471 AAAC-TCATTT
1 AAACTTCATTT
36481 TCCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 6 0.18
24 9 0.27
25 18 0.55
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:37629 original size:29 final size:30
Alignment explanation
Indices: 37513--37632 Score: 116
Period size: 31 Copynumber: 4.0 Consensus size: 30
37503 ACGTGGCATG
* * * *
37513 CCACGTGTACAAAAAAGTGACACATGTCATA
1 CCACGTATAC-AAAAAGTGACACGTGACACA
* * * *
37544 TCATGTGTACAAAAAGTGACACGTGTCACA
1 CCACGTATACAAAAAGTGACACGTGACACA
**
37574 CCACGTATACCAAAAAGTGACACGTGACATG
1 CCACGTATA-CAAAAAGTGACACGTGACACA
*
37605 CCACGTATACAAAAAG-GACATGTGACAC
1 CCACGTATACAAAAAGTGACACGTGACAC
37633 GTGTCACTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 10 0.13
30 31 0.41
31 35 0.46
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.18
Consensus pattern (30 bp):
CCACGTATACAAAAAGTGACACGTGACACA
Found at i:38198 original size:44 final size:44
Alignment explanation
Indices: 38135--38224 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
38125 ATAGGATAGT
38135 TTACTAATAATAACTACAAATCCAATTATCCAACACAATTTAGA
1 TTACTAATAATAACTACAAATCCAATTATCCAACACAATTTAGA
38179 TTACTAATAATAACTACAAATCCAATTATCCAACACAATTTAGA
1 TTACTAATAATAACTACAAATCCAATTATCCAACACAATTTAGA
38223 TT
1 TT
38225 TCGGCAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (44 bp):
TTACTAATAATAACTACAAATCCAATTATCCAACACAATTTAGA
Done.