Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016237.1 Corchorus capsularis cultivar CVL-1 contig16258, 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: 15645
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Found at i:1693 original size:61 final size:62
Alignment explanation
Indices: 1622--1788 Score: 212
Period size: 61 Copynumber: 2.7 Consensus size: 62
1612 TCTTGTAACC
* * * *
1622 AAGGAGGACCTGTCCGAGGTCTGAAACTTG-AGAAGACCAGTCCGCGGTCGACTTT-AAAACT
1 AAGGAAGACCTATCAGAGGTCAGAAAC-TGAAGAAGACCAGTCCGCGGTCGACTTTAAAAACT
* * * *
1683 AAGGAAGACCTATCAGGGGTCAGAAACTGAAGAGGACCAGTCTGTGGTCGACTTTAAAAACT
1 AAGGAAGACCTATCAGAGGTCAGAAACTGAAGAAGACCAGTCCGCGGTCGACTTTAAAAACT
* * *
1745 AAGGAAGACCTATCTGAGGTCAGAAGCTGAAGAAGATCAGTCCG
1 AAGGAAGACCTATCAGAGGTCAGAAACTGAAGAAGACCAGTCCG
1789 TGATCCACTT
Statistics
Matches: 90, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
60 2 0.02
61 44 0.49
62 44 0.49
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.19
Consensus pattern (62 bp):
AAGGAAGACCTATCAGAGGTCAGAAACTGAAGAAGACCAGTCCGCGGTCGACTTTAAAAACT
Found at i:1799 original size:62 final size:61
Alignment explanation
Indices: 1604--1799 Score: 214
Period size: 62 Copynumber: 3.2 Consensus size: 61
1594 GACTAATCTC
** * * * * *
1604 TGGTCGACTCTTGTAACCAAGGAGGACCTGTCCGAGGTCTGAAACTTG-AGAAGACCAGTCCG
1 TGGTCGACT-TTAAAACTAAGGAAGACCTATCAGAGGTCAGAAAC-TGAAGAAGACCAGTCCG
* * * *
1666 CGGTCGACTTTAAAACTAAGGAAGACCTATCAGGGGTCAGAAACTGAAGAGGACCAGTCTG
1 TGGTCGACTTTAAAACTAAGGAAGACCTATCAGAGGTCAGAAACTGAAGAAGACCAGTCCG
* * *
1727 TGGTCGACTTTAAAAACTAAGGAAGACCTATCTGAGGTCAGAAGCTGAAGAAGATCAGTCCG
1 TGGTCGACTTT-AAAACTAAGGAAGACCTATCAGAGGTCAGAAACTGAAGAAGACCAGTCCG
* *
1789 TGATCCACTTT
1 TGGTCGACTTT
1800 GAATATTAGG
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
60 2 0.02
61 49 0.44
62 61 0.54
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (61 bp):
TGGTCGACTTTAAAACTAAGGAAGACCTATCAGAGGTCAGAAACTGAAGAAGACCAGTCCG
Found at i:1815 original size:62 final size:62
Alignment explanation
Indices: 1622--1847 Score: 199
Period size: 62 Copynumber: 3.7 Consensus size: 62
1612 TCTTGTAACC
* * * * * * *
1622 AAGGAGGACCTGTCCGAGGTCTGAAACTTG-AGAAGACCAGTCCGCGGTCGACTTT-AAAACT
1 AAGGAAGACCTATCTGAGGTCAGAAAC-TGAAGAAGACCAGTCCGTGATCCACTTTAAAAACT
* * * * * *
1683 AAGGAAGACCTATCAGGGGTCAGAAACTGAAGAGGACCAGTCTGTGGTCGACTTTAAAAACT
1 AAGGAAGACCTATCTGAGGTCAGAAACTGAAGAAGACCAGTCCGTGATCCACTTTAAAAACT
* * * *
1745 AAGGAAGACCTATCTGAGGTCAGAAGCTGAAGAAGATCAGTCCGTGATCCACTTTGAATA-T
1 AAGGAAGACCTATCTGAGGTCAGAAACTGAAGAAGACCAGTCCGTGATCCACTTTAAAAACT
* * * * *
1806 TAGGAAAGACCTGTTTGAGGTTTA-AAATTGAAGAAGACCAGT
1 AAGG-AAGACCTATCTGAGG-TCAGAAACTGAAGAAGACCAGT
1848 GTATGGTCGA
Statistics
Matches: 136, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
60 2 0.01
61 48 0.35
62 84 0.62
63 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22
Consensus pattern (62 bp):
AAGGAAGACCTATCTGAGGTCAGAAACTGAAGAAGACCAGTCCGTGATCCACTTTAAAAACT
Found at i:14560 original size:48 final size:46
Alignment explanation
Indices: 14486--14953 Score: 411
Period size: 48 Copynumber: 9.7 Consensus size: 46
14476 AAAGTGAACT
* * * * * *
14486 TGCCTTTCATCCGGAAAGGACATTTTAAGAAAAAGCGAGTAAAACTAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAA-C-AGTAAAAATAA
* * * *
14534 CGCCTTCCATCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAA-C-AGTAAAAA-TAA
* * *
14583 TGCCTTCCGTCCGGGAAGGGCACTTTGGGAAAAAGTAGGTAAAAATAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAA-CA-GTAAAAATAA
*
14631 -GCGTCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAAGT-AAAATAA
1 TGC--CTTCCGTCCGGGAAGGGCATTTTAGGAAAA-A-C-AGTAAAAATAA
* * *
14680 GTGCCTTCCGTCCGGGAAGGGCATTTT-GGTGAAAACAGGTAAAGATTAG
1 -TGCCTTCCGTCCGGGAAGGGCATTTTAGG-AAAAACA-GTAAA-AATAA
* *
14729 TGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAACAGGTAAAAATCAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAACA-GTAAAAAT-AA
* * * *
14777 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAAGTAAAGATTAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAAC-AGTAAA-AATAA
* * *
14825 TGCCTTCCGTTCGAGAAGGGCGTTTTAGGAAAAAACAGGTAAAAATAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTAGG-AAAAACA-GTAAAAATAA
* * * *
14873 GTGCCTTCCGTCAGGGAAGGGCGTTTTGGGAAAAACTGGTAAAAATAAA
1 -TGCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAAC-AGTAAAAAT-AA
*
14922 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTAGGAAA
14954 TAGCAAGTGA
Statistics
Matches: 360, Mismatches: 39, Indels: 42
0.82 0.09 0.10
Matches are distributed among these distances:
46 1 0.00
47 7 0.02
48 199 0.55
49 146 0.41
50 4 0.01
51 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (46 bp):
TGCCTTCCGTCCGGGAAGGGCATTTTAGGAAAAACAGTAAAAATAA
Found at i:14614 original size:49 final size:48
Alignment explanation
Indices: 14535--14953 Score: 527
Period size: 48 Copynumber: 8.6 Consensus size: 48
14525 TAAAACTAAC
* * * *
14535 GCCTTCCATCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAA-CAGGTAAAAATAAGT
** * *
14584 GCCTTCCGTCCGGGAAGGGCACTTTGGGAAAAAGTAGGTAAAAATAAGC
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAA-CAGGTAAAAATAAGT
* * * *
14633 GTCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAAGT-AAAATAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAA-A-CAGGTAAAAATAAGT
* * *
14682 GCCTTCCGTCCGGGAAGGGCATTTTGGTG-AAAACAGGTAAAGATTAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGG-GAAAAACAGGTAAAAATAAGT
* *
14730 GCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAACAGGTAAAAATCAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTAAAAATAAGT
* * *
14778 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAAGTAAAGATTAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTAAAAATAAGT
* * *
14826 GCCTTCCGTTCGAGAAGGGCGTTTTAGGAAAAAACAGGTAAAAATAAGT
1 GCCTTCCGTCCGGGAAGGGCGTTTT-GGGAAAAACAGGTAAAAATAAGT
* * *
14875 GCCTTCCGTCAGGGAAGGGCGTTTTGGGAAAAACTGGTAAAAATAAAT
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTAAAAATAAGT
*
14923 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAA
14954 TAGCAAGTGA
Statistics
Matches: 324, Mismatches: 41, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
47 5 0.02
48 166 0.51
49 147 0.45
50 6 0.02
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (48 bp):
GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTAAAAATAAGT
Found at i:14903 original size:97 final size:97
Alignment explanation
Indices: 14535--14953 Score: 547
Period size: 97 Copynumber: 4.3 Consensus size: 97
14525 TAAAACTAAC
* * *
14535 GCCTTCCATCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGGAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAACAAGTAAAAATAAGTGCCTTCCGTCCGGGAA
* * *
14600 GGGCACTTTGGGAAAAAGTAGGTAAAAATAAGC
66 GGGCATTTTGGGAAAAA-CAGGTAAAAATAAGT
* * * *
14633 GTCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAAGT-AAAATAAGTGCCTTCCGTCCGGGA
1 GCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAA-AACAAGTAAAAATAAGTGCCTTCCGTCCGGGA
* *
14697 AGGGCATTTTGGTG-AAAACAGGTAAAGATTAGT
65 AGGGCATTTTGG-GAAAAACAGGTAAAAATAAGT
* *
14730 GCCTTCCGTCCGGGAAGGGCGTTTTAGG-AAAAACAGGTAAAAATCAGTGCCTTCCGTCCGGGAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAACAAGTAAAAATAAGTGCCTTCCGTCCGGGAA
* * * *
14794 GGGCGTTTTGGGAAAAACAAGTAAAGATTAGT
66 GGGCATTTTGGGAAAAACAGGTAAAAATAAGT
* * * *
14826 GCCTTCCGTTCGAGAAGGGCGTTTTAGGAAAAAACAGGTAAAAATAAGTGCCTTCCGTCAGGGAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAACAAGTAAAAATAAGTGCCTTCCGTCCGGGAA
* * *
14891 GGGCGTTTTGGGAAAAACTGGTAAAAATAAAT
66 GGGCATTTTGGGAAAAACAGGTAAAAATAAGT
* *
14923 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTAGGAAA
14954 TAGCAAGTGA
Statistics
Matches: 285, Mismatches: 31, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
95 6 0.02
96 81 0.28
97 124 0.44
98 66 0.23
99 8 0.03
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (97 bp):
GCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAACAAGTAAAAATAAGTGCCTTCCGTCCGGGAA
GGGCATTTTGGGAAAAACAGGTAAAAATAAGT
Found at i:15405 original size:19 final size:20
Alignment explanation
Indices: 15374--15411 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
15364 TTAAATTAAT
15374 TTAAATTATTTCTT-TAAAG
1 TTAAATTATTTCTTCTAAAG
15393 TTAAACTTA-TTCTTCTAAA
1 TTAAA-TTATTTCTTCTAAA
15412 AAACTAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.50
Consensus pattern (20 bp):
TTAAATTATTTCTTCTAAAG
Done.