Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007708.1 Corchorus capsularis cultivar CVL-1 contig07729, 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: 83585
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:8377 original size:129 final size:129
Alignment explanation
Indices: 8136--8416 Score: 312
Period size: 129 Copynumber: 2.2 Consensus size: 129
8126 TGAGCCCATT
* * * *
8136 TCACCACTATGATGCTCACCATCTTGCTTTATACTCTGCTTAAGTCTAGTAGAAGATTCCTCTGC
1 TCACTACTATGTTGCTCACCATCTTGCTTCATACTCTGCTTAAGTCTAGTAGAAGATACCTCTGC
* ** * * * * * * * * **
8201 GATGTCTTTGCTAACATTAAACTTGAGTGACTGGTTCTTTTCTTCTGATTCATCTTTCTTTGAC
66 AATGTCCCTGCCAACATCAAACTCGAGTAACTGGTTCTCTTCCTCTGAATCATCCTTCTCCGAC
* * * *
8265 TCAGTACTATGTTGCTCACCATCTTGCTTCATGCTCTGCTTCAGTCCT-GTAGAAGATACTTCTG
1 TCACTACTATGTTGCTCACCATCTTGCTTCATACTCTGCTTAAGT-CTAGTAGAAGATACCTCTG
* *
8329 CAATGTCCCTGCCAACGTCAAACTCGGGTAACTGGTTCTCTTCCTCTGAATCATCCTTCTCCGAC
65 CAATGTCCCTGCCAACATCAAACTCGAGTAACTGGTTCTCTTCCTCTGAATCATCCTTCTCCGAC
* * *
8394 TCACTAATATGTGGCTCAGCATC
1 TCACTACTATGTTGCTCACCATC
8417 CTCTGAACTG
Statistics
Matches: 124, Mismatches: 27, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
129 122 0.98
130 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.37
Consensus pattern (129 bp):
TCACTACTATGTTGCTCACCATCTTGCTTCATACTCTGCTTAAGTCTAGTAGAAGATACCTCTGC
AATGTCCCTGCCAACATCAAACTCGAGTAACTGGTTCTCTTCCTCTGAATCATCCTTCTCCGAC
Found at i:8566 original size:96 final size:93
Alignment explanation
Indices: 8357--8585 Score: 253
Period size: 96 Copynumber: 2.4 Consensus size: 93
8347 CAAACTCGGG
* ** *
8357 TAACTGGTTCTCTTCCTCTGAATCATCCTTCTCCGACTCACTAATATGTGGCTCAGCATCCTCTG
1 TAACTGGTTCTCTTCCTCTGATTCATCCTTCTCCGACTCACTAATATGCAGCTCACCATCCTCTG
*
8422 AACTGTCCCCGCTCACATCACGCTTGAA
66 AACTGTCACCGCTCACATCACGCTTGAA
* * * * * * * *
8450 TAACAGGATCACTTCATCTGATTCATCCTCCTCCTCTGACTCGCTACTATGCATCTCACCATCCT
1 TAACTGGTTCTCTTCCTCTGATTCATCCT--T-CTCCGACTCACTAATATGCAGCTCACCATCCT
*
8515 CTGAACTGTCACCGCTCACATCA-GACTTGAC
63 CTGAACTGTCACCGCTCACATCACG-CTTGAA
* * * *
8546 TGATTGGTTCTCTTCCTCTGATTCATCTTTCTCTGACTCA
1 TAACTGGTTCTCTTCCTCTGATTCATCCTTCTCCGACTCA
8586 TCAGAGCTAG
Statistics
Matches: 110, Mismatches: 22, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
93 33 0.30
94 1 0.01
95 2 0.02
96 74 0.67
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (93 bp):
TAACTGGTTCTCTTCCTCTGATTCATCCTTCTCCGACTCACTAATATGCAGCTCACCATCCTCTG
AACTGTCACCGCTCACATCACGCTTGAA
Found at i:10962 original size:16 final size:16
Alignment explanation
Indices: 10943--10977 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
10933 TGTGCTAAAG
10943 AAAAA-AAAACTAAATT
1 AAAAACAAAAC-AAATT
10959 AAAAACAAAACAAATT
1 AAAAACAAAACAAATT
10975 AAA
1 AAA
10978 GAGACAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAACAAAACAAATT
Found at i:19724 original size:1 final size:1
Alignment explanation
Indices: 19720--19744 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
19710 ATAAAAAAAA
19720 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
19745 CACATTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:32393 original size:24 final size:24
Alignment explanation
Indices: 32364--32542 Score: 288
Period size: 24 Copynumber: 7.5 Consensus size: 24
32354 TCAACTCAGT
32364 CTGCCTTTGGTGCCACAAGCACCC
1 CTGCCTTTGGTGCCACAAGCACCC
32388 CTGCCTTTGGTAG-CACAAGCACCC
1 CTGCCTTTGGT-GCCACAAGCACCC
32412 CTGCCTTTGGTGCCACAAGCACCC
1 CTGCCTTTGGTGCCACAAGCACCC
*
32436 CTGCCTTTGGTGCCACGAGCACCC
1 CTGCCTTTGGTGCCACAAGCACCC
*
32460 CTGCCTTTGGTTCCACAAGCACCC
1 CTGCCTTTGGTGCCACAAGCACCC
* * *
32484 CTGGCTTTGGTGCCACGAGCACTC
1 CTGCCTTTGGTGCCACAAGCACCC
*
32508 CTGCCTTTGGTGCTACAAGCACCC
1 CTGCCTTTGGTGCCACAAGCACCC
32532 CTGCCTTTGGT
1 CTGCCTTTGGT
32543 TCAACTGGAA
Statistics
Matches: 142, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
23 1 0.01
24 140 0.99
25 1 0.01
ACGTcount: A:0.15, C:0.39, G:0.22, T:0.24
Consensus pattern (24 bp):
CTGCCTTTGGTGCCACAAGCACCC
Found at i:32682 original size:24 final size:22
Alignment explanation
Indices: 32642--32705 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
32632 ATCAAGCACA
* *
32642 CCTGCATTTGGCGCTTCCAGCTCT
1 CCTGCTTTTGGCGCTT-CAAC-CT
32666 CCTGCTTTTGG-GACTTCAACCT
1 CCTGCTTTTGGCG-CTTCAACCT
*
32688 -CTGCTTTTGGTGCTTCAA
1 CCTGCTTTTGGCGCTTCAA
32706 GTACCCCTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 16 0.44
22 3 0.08
23 4 0.11
24 13 0.36
ACGTcount: A:0.11, C:0.31, G:0.20, T:0.38
Consensus pattern (22 bp):
CCTGCTTTTGGCGCTTCAACCT
Found at i:32718 original size:24 final size:23
Alignment explanation
Indices: 32620--32721 Score: 68
Period size: 24 Copynumber: 4.4 Consensus size: 23
32610 GAACAGGAAG
* * *
32620 TGCTTTTGGAGCATCAAGCACACC
1 TGCTTTTGG-GCTTCAAGTACCCC
* * *
32644 TGCATTTGGCGCTTCCAGCT-CTCC
1 TGCTTTTGG-GCTTCAAG-TACCCC
*
32668 TGCTTTTGGGACTTC-A--ACCTC
1 TGCTTTTGGG-CTTCAAGTACCCC
32689 TGCTTTTGGTGCTTCAAGTACCCC
1 TGCTTTTGG-GCTTCAAGTACCCC
32713 TGCTTTTGG
1 TGCTTTTGG
32722 AGCATCTTCT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
21 15 0.25
22 2 0.03
23 2 0.03
24 42 0.69
ACGTcount: A:0.14, C:0.29, G:0.22, T:0.35
Consensus pattern (23 bp):
TGCTTTTGGGCTTCAAGTACCCC
Found at i:36777 original size:6 final size:6
Alignment explanation
Indices: 36766--36801 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
36756 ATACAAGCTG
* *
36766 GAAGAT GAAGAT GAAGAT GAAGAG GAAGAG GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
36802 TACTCAGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.39, T:0.11
Consensus pattern (6 bp):
GAAGAT
Found at i:40960 original size:21 final size:21
Alignment explanation
Indices: 40936--40978 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40926 TTCCTCATTC
40936 TTTTACAACTTGTTATTGATA
1 TTTTACAACTTGTTATTGATA
40957 TTTTACAACTTGTTATTGATA
1 TTTTACAACTTGTTATTGATA
40978 T
1 T
40979 GGTTTGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (21 bp):
TTTTACAACTTGTTATTGATA
Found at i:60771 original size:55 final size:55
Alignment explanation
Indices: 60687--60794 Score: 216
Period size: 55 Copynumber: 2.0 Consensus size: 55
60677 TATCAGTAAC
60687 TTTAAAATCCAATTTCTATTGTCGTGAATTCTGGGTAATTAATGAGCTTTGATAA
1 TTTAAAATCCAATTTCTATTGTCGTGAATTCTGGGTAATTAATGAGCTTTGATAA
60742 TTTAAAATCCAATTTCTATTGTCGTGAATTCTGGGTAATTAATGAGCTTTGAT
1 TTTAAAATCCAATTTCTATTGTCGTGAATTCTGGGTAATTAATGAGCTTTGAT
60795 TATCATTTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (55 bp):
TTTAAAATCCAATTTCTATTGTCGTGAATTCTGGGTAATTAATGAGCTTTGATAA
Found at i:63340 original size:2 final size:2
Alignment explanation
Indices: 63333--63362 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
63323 AGAGTATTAT
63333 TA 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 TA
63363 GTAATGACAA
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):
TA
Found at i:66545 original size:3 final size:3
Alignment explanation
Indices: 66537--66561 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
66527 TCTCTCTCTC
66537 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
66562 TTTTCTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Done.