Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014414.1 Corchorus capsularis cultivar CVL-1 contig14435, 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: 45531
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:10657 original size:22 final size:22
Alignment explanation
Indices: 10625--10667 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10615 AAAATCCTAA
10625 AATAGAGTTCCT-TTAACCCATC
1 AATAGAGTTCCTATT-ACCCATC
*
10647 AATAGATTTCCTATTACCCAT
1 AATAGAGTTCCTATTACCCAT
10668 AAAACCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.35
Consensus pattern (22 bp):
AATAGAGTTCCTATTACCCATC
Found at i:15773 original size:34 final size:34
Alignment explanation
Indices: 15725--15793 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
15715 AATCCATTCA
*
15725 GTTTGAGAACTATAGCGAACATTGCTGAGAAATC
1 GTTTGACAACTATAGCGAACATTGCTGAGAAATC
*
15759 GTTTGACAATTATAGCGAACATTGCTGAGAAATC
1 GTTTGACAACTATAGCGAACATTGCTGAGAAATC
15793 G
1 G
15794 AGTAGAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (34 bp):
GTTTGACAACTATAGCGAACATTGCTGAGAAATC
Found at i:21391 original size:64 final size:66
Alignment explanation
Indices: 21312--21441 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 66
21302 CGTAACATCC
21312 CAGCTTGGAGACTT-AAATAAAGGAAGCAAACTTCATGAGTACAA-TGAAACTGATTCCATTTTG
1 CAGCTTGGAGACTTAAAATAAAGGAAGCAAACTTCATGAGTACAATTGAAACTGATTCCATTTTG
21375 T
66 T
21376 CAGCTTGGAGACTTAAAATAAAGGAAGCAAACTTCATGAGTACAATTGAAACTGATTCCATTTTG
1 CAGCTTGGAGACTTAAAATAAAGGAAGCAAACTTCATGAGTACAATTGAAACTGATTCCATTTTG
21441 T
66 T
21442 ATGAAAATTT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
64 14 0.22
65 30 0.47
66 20 0.31
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (66 bp):
CAGCTTGGAGACTTAAAATAAAGGAAGCAAACTTCATGAGTACAATTGAAACTGATTCCATTTTG
T
Found at i:27653 original size:23 final size:23
Alignment explanation
Indices: 27623--27671 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
27613 AAAACAACCC
27623 TTATGAATTTGGGACTATGAAAT
1 TTATGAATTTGGGACTATGAAAT
27646 TTATGAATTTGGGACTATGAAAT
1 TTATGAATTTGGGACTATGAAAT
27669 TTA
1 TTA
27672 ACCCTTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (23 bp):
TTATGAATTTGGGACTATGAAAT
Found at i:28876 original size:25 final size:25
Alignment explanation
Indices: 28822--28888 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
28812 GCAGCCTATG
*
28822 TGTTTTCTAAACGCAAGCACAGACT
1 TGTTTGCTAAACGCAAGCACAGACT
* ** *
28847 CGTTTGCTAAACGCAAGCGTAGTCT
1 TGTTTGCTAAACGCAAGCACAGACT
*
28872 TGTTTGCCAAACGCAAG
1 TGTTTGCTAAACGCAAG
28889 AACATGAGCG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (25 bp):
TGTTTGCTAAACGCAAGCACAGACT
Found at i:29917 original size:2 final size:2
Alignment explanation
Indices: 29910--29942 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29900 GCGCAAAAAG
29910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29943 ATAAAGATTG
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31187 original size:32 final size:32
Alignment explanation
Indices: 31153--31301 Score: 140
Period size: 32 Copynumber: 4.6 Consensus size: 32
31143 CCGTGGTGAA
* * *
31153 GCCGCCCCACTTGGGAGGCTTCGCCACGGCAA
1 GCCGCCCCACTGGGGCGGCTTCGCCACGGCAG
* *
31185 GCCGCCCTCA-TGGGGCGGCTTCACCATGGGCAG
1 GCCGCCC-CACTGGGGCGGCTTCGCCA-CGGCAG
* * *
31218 GCCGCCCAACTAGGGCGGCTTAGCCA-GAGCAG
1 GCCGCCCCACTGGGGCGGCTTCGCCACG-GCAG
* **
31250 GCCGTCCCGGTGGGGCGGCTTCGCCACGGCAG
1 GCCGCCCCACTGGGGCGGCTTCGCCACGGCAG
**
31282 GCCGCCCCGGTGGGGCGGCT
1 GCCGCCCCACTGGGGCGGCT
31302 CGGCTATTTT
Statistics
Matches: 96, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
31 1 0.01
32 68 0.71
33 27 0.28
ACGTcount: A:0.12, C:0.38, G:0.38, T:0.12
Consensus pattern (32 bp):
GCCGCCCCACTGGGGCGGCTTCGCCACGGCAG
Found at i:31481 original size:32 final size:32
Alignment explanation
Indices: 31372--31485 Score: 108
Period size: 33 Copynumber: 3.5 Consensus size: 32
31362 CCGGTGCCGT
*
31372 CCCCCTGGGGCGG--CTGAGCCATGGCCA-AGCCG
1 CCCCCTGGGGCGGCACT-A-CCATGGACAGA-CCG
* *
31404 CCCTCCTGGGGCGGCACTACCATGGCCAGGCCG
1 CCC-CCTGGGGCGGCACTACCATGGACAGACCG
* * *
31437 CCTCCCTGGGGCGGCCCTACCATGGATAGATCG
1 CC-CCCTGGGGCGGCACTACCATGGACAGACCG
31470 CCCCCTGGGGCGGCAC
1 CCCCCTGGGGCGGCAC
31486 CGGTACTAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
32 16 0.23
33 50 0.71
34 2 0.03
35 2 0.03
ACGTcount: A:0.12, C:0.41, G:0.34, T:0.12
Consensus pattern (32 bp):
CCCCCTGGGGCGGCACTACCATGGACAGACCG
Found at i:31645 original size:33 final size:32
Alignment explanation
Indices: 31555--31666 Score: 170
Period size: 32 Copynumber: 3.5 Consensus size: 32
31545 GCCTAGCCGC
* *
31555 CCTAGTGGGGCGGCTAGCCGTGGCAGAGCCGT
1 CCTAGTGGGGAGGCTAGCCGTGGCAGAGCCAT
*
31587 CCTAGTGGGGTGGCTAGCCGTGGCAGAGCCAT
1 CCTAGTGGGGAGGCTAGCCGTGGCAGAGCCAT
*
31619 CCTAGTGGGGAGGCTCCGCCGTGGCAGAGCCAT
1 CCTAGTGGGGAGGCT-AGCCGTGGCAGAGCCAT
*
31652 CCTAGTGGAGAGGCT
1 CCTAGTGGGGAGGCT
31667 CCGCGTGGCT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 44 0.59
33 30 0.41
ACGTcount: A:0.15, C:0.27, G:0.41, T:0.17
Consensus pattern (32 bp):
CCTAGTGGGGAGGCTAGCCGTGGCAGAGCCAT
Found at i:32031 original size:13 final size:13
Alignment explanation
Indices: 32013--32039 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32003 TCACCACGTC
32013 ATCTATGAAACCA
1 ATCTATGAAACCA
32026 ATCTATGAAACCA
1 ATCTATGAAACCA
32039 A
1 A
32040 CCAATAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (13 bp):
ATCTATGAAACCA
Found at i:33704 original size:14 final size:14
Alignment explanation
Indices: 33685--33713 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
33675 TATTTCCTAT
33685 ATATAACTATTAAA
1 ATATAACTATTAAA
33699 ATATAACTATTAAA
1 ATATAACTATTAAA
33713 A
1 A
33714 GACTAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
ATATAACTATTAAA
Found at i:35353 original size:87 final size:87
Alignment explanation
Indices: 35207--35383 Score: 327
Period size: 87 Copynumber: 2.0 Consensus size: 87
35197 CTGCAACAAT
**
35207 AAACCCAAATTACTCGAGCTGCACTTCAATATCAAAACCTCTGAAAACTAACAGTTAAATGTATA
1 AAACCCAAATTACTCGAGCTGCACTTCAATATCAAAACCTCTGAAAACTAACAAATAAATGTATA
35272 ATAACGAGAAAAATACAAAAGG
66 ATAACGAGAAAAATACAAAAGG
*
35294 AAACCCAAATTACTCGAGCTGCACTTCGATATCAAAACCTCTGAAAACTAACAAATAAATGTATA
1 AAACCCAAATTACTCGAGCTGCACTTCAATATCAAAACCTCTGAAAACTAACAAATAAATGTATA
35359 ATAACGAGAAAAATACAAAAGG
66 ATAACGAGAAAAATACAAAAGG
35381 AAA
1 AAA
35384 AATTTTCCTT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.50, C:0.19, G:0.11, T:0.20
Consensus pattern (87 bp):
AAACCCAAATTACTCGAGCTGCACTTCAATATCAAAACCTCTGAAAACTAACAAATAAATGTATA
ATAACGAGAAAAATACAAAAGG
Found at i:37797 original size:1 final size:1
Alignment explanation
Indices: 37791--37820 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
37781 AAACAGAATT
37791 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
37821 CTAACTGTAC
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39762 original size:24 final size:24
Alignment explanation
Indices: 39735--39815 Score: 126
Period size: 24 Copynumber: 3.4 Consensus size: 24
39725 AAGCCCAGCT
* *
39735 ATGCATTGGGGTTCTCATCCCATC
1 ATGCATTGGAGTTCTCATGCCATC
*
39759 ATGCATTGGCGTTCTCATGCCATC
1 ATGCATTGGAGTTCTCATGCCATC
39783 ATGCATTGGAGTTCTCATGCCATC
1 ATGCATTGGAGTTCTCATGCCATC
*
39807 ATGGATTGG
1 ATGCATTGG
39816 TGTGGCTGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (24 bp):
ATGCATTGGAGTTCTCATGCCATC
Found at i:45504 original size:2 final size:2
Alignment explanation
Indices: 45497--45531 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
45487 CTTGTGTTCC
45497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.