Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011912.1 Corchorus olitorius cultivar O-4 contig11945, 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: 63296
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Found at i:12216 original size:25 final size:25
Alignment explanation
Indices: 12187--12260 Score: 130
Period size: 25 Copynumber: 3.0 Consensus size: 25
12177 GAATGGTTTG
12187 TAGAGACCGAGCGAGAATGCTCAAA
1 TAGAGACCGAGCGAGAATGCTCAAA
*
12212 TAGAGACTGAGCGAGAATGCTCAAA
1 TAGAGACCGAGCGAGAATGCTCAAA
*
12237 TAGAGACCGAGCGAGACTGCTCAA
1 TAGAGACCGAGCGAGAATGCTCAA
12261 GATTGTTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAATGCTCAAA
Found at i:13045 original size:175 final size:176
Alignment explanation
Indices: 12776--13097 Score: 472
Period size: 175 Copynumber: 1.8 Consensus size: 176
12766 ACGAAGAAAC
*
12776 TTTGTGTTGATTATGCATTGGATATTGCAAGTAGCACTTCTCAGACGAATTACGAATTAGGAGGG
1 TTTGTGTTGATCATGCATTGGATATTGCAAGTAGCACTTCTCAGACGAATTACGAA-TAGGAGGG
*
12841 GATAATCTGAATTTTGGAGAAAATTTTCATCAAGAATATCACAATCCAATCCAC-T-CTGCATAT
65 GATAATCTGAATTTTGGAGAAAATTTTCATCAAGAATATCACAATCAAATCCACGTACTGCATAT
**
12904 ATTGGTGATGTTAATGGAGCTGGAATGTGGGCTATGAAGAAACTTAA
130 ATTAATGATGTTAATGGAGCTGGAATGTGGGCTATGAAGAAACTTAA
* * * *
12951 TTTGTGTTGATCGTGCGTTGGATATTGCAAGTAGCACTACTTGTCAGACGAATTATG-A-AGGAG
1 TTTGTGTTGATCATGCATTGGATATTGCAAGTAG--C-ACTTCTCAGACGAATTACGAATAGGAG
* * *
13014 GGGATAATCTGAATTTTGGAGGAATTTTTCATTAAGAATATCACAATCAAATCCACTGTACTGCA
63 GGGATAATCTGAATTTTGGAGAAAATTTTCATCAAGAATATCACAATCAAATCCAC-GTACTGCA
13079 TATATTAATGATGTTAATG
127 TATATTAATGATGTTAATG
13098 AAGTCCGGTG
Statistics
Matches: 130, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
175 88 0.68
177 3 0.02
178 39 0.30
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (176 bp):
TTTGTGTTGATCATGCATTGGATATTGCAAGTAGCACTTCTCAGACGAATTACGAATAGGAGGGG
ATAATCTGAATTTTGGAGAAAATTTTCATCAAGAATATCACAATCAAATCCACGTACTGCATATA
TTAATGATGTTAATGGAGCTGGAATGTGGGCTATGAAGAAACTTAA
Found at i:21537 original size:18 final size:17
Alignment explanation
Indices: 21513--21556 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
21503 GCTGTGGGGG
21513 TTTTATTTTATT-TTATT
1 TTTTATTTT-TTATTATT
21530 TATTTATTTTTTAATTATT
1 T-TTTATTTTTT-ATTATT
21549 TTTTATTT
1 TTTTATTT
21557 CAGAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 15 0.62
19 6 0.25
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTATTTTTTATTATT
Found at i:27839 original size:57 final size:56
Alignment explanation
Indices: 27731--27843 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 56
27721 AGACATCAAC
27731 AAATTTCAACCTACGTATTATCTGAATTATGGATGAAGAAGTTGCTTTCTTTCGTT
1 AAATTTCAACCTACGTATTATCTGAATTATGGATGAAGAAGTTGCTTTCTTTCGTT
27787 AAATTTCAACCTACGTATTATCTGAACTTATGGATGAAGAAGTTGCTTTCTTTCGTT
1 AAATTTCAACCTACGTATTATCTGAA-TTATGGATGAAGAAGTTGCTTTCTTTCGTT
27844 TATGGAATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 26 0.46
57 30 0.54
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (56 bp):
AAATTTCAACCTACGTATTATCTGAATTATGGATGAAGAAGTTGCTTTCTTTCGTT
Found at i:28479 original size:36 final size:36
Alignment explanation
Indices: 28432--28500 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
28422 GGTCTTGGGC
28432 TCTACTCTCACGAAATGTGAGTTTTCTTTGTAATTT
1 TCTACTCTCACGAAATGTGAGTTTTCTTTGTAATTT
*
28468 TCTACTCTCACGGAATGTGAGTTTTCTTTGTAA
1 TCTACTCTCACGAAATGTGAGTTTTCTTTGTAA
28501 ATAGGAAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (36 bp):
TCTACTCTCACGAAATGTGAGTTTTCTTTGTAATTT
Found at i:29052 original size:32 final size:32
Alignment explanation
Indices: 29002--29073 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
28992 TTCAAAGAAC
* * ** *
29002 ATTTTGTCCTATTTTATCAAAGTTTGAGGGTT
1 ATTTTGTCCTATTATATCAAAATTCAAGGGCT
29034 ATTTTGTCCT-TGTATATCAAAATTCAAGGGCT
1 ATTTTGTCCTAT-TATATCAAAATTCAAGGGCT
29066 ATTTTGTC
1 ATTTTGTC
29074 TATCAATTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 1 0.03
32 33 0.97
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (32 bp):
ATTTTGTCCTATTATATCAAAATTCAAGGGCT
Found at i:30631 original size:2 final size:2
Alignment explanation
Indices: 30624--30656 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30614 ACCGAGTTAA
30624 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
30657 CAGTCATCTT
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:31631 original size:10 final size:10
Alignment explanation
Indices: 31618--31650 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
31608 TGAAAAAAGA
31618 CCAAAAGGAG
1 CCAAAAGGAG
31628 CCAAAAGGAG
1 CCAAAAGGAG
31638 CCAAAAGGAG
1 CCAAAAGGAG
31648 CCA
1 CCA
31651 CCACATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.48, C:0.24, G:0.27, T:0.00
Consensus pattern (10 bp):
CCAAAAGGAG
Found at i:39202 original size:20 final size:21
Alignment explanation
Indices: 39174--39213 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
39164 TTATTATGTG
39174 AAAGAATAGGAC-ATTTGAAGA
1 AAAGAATA-GACAATTTGAAGA
39195 AAAG-ATAGACAATTTGAAG
1 AAAGAATAGACAATTTGAAG
39214 GTTAAGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 11 0.61
21 4 0.22
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.20
Consensus pattern (21 bp):
AAAGAATAGACAATTTGAAGA
Found at i:44148 original size:45 final size:45
Alignment explanation
Indices: 44071--44165 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
44061 AGTAAAACAA
* *
44071 AAAAGCAGACACTCATGGGGGTTCTCTTTTTGTTGTTTAAGCAGT
1 AAAAGCAGAAACTCATGGAGGTTCTCTTTTTGTTGTTTAAGCAGT
*
44116 GAAAAGCAGAAACTGATGGAGGTT-TCTTTTTGTTGTTTAAGCAGT
1 -AAAAGCAGAAACTCATGGAGGTTCTCTTTTTGTTGTTTAAGCAGT
44161 AAAAG
1 AAAAG
44166 GCATTAGATT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 5 0.11
45 21 0.46
46 20 0.43
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (45 bp):
AAAAGCAGAAACTCATGGAGGTTCTCTTTTTGTTGTTTAAGCAGT
Found at i:46199 original size:18 final size:18
Alignment explanation
Indices: 46176--46210 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
46166 TTGACTCGCC
46176 CCACTCACCTCTCCGATT
1 CCACTCACCTCTCCGATT
*
46194 CCACTCCCCTCTCCGAT
1 CCACTCACCTCTCCGAT
46211 CCGACCAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.54, G:0.06, T:0.26
Consensus pattern (18 bp):
CCACTCACCTCTCCGATT
Found at i:54466 original size:174 final size:175
Alignment explanation
Indices: 54176--54526 Score: 668
Period size: 174 Copynumber: 2.0 Consensus size: 175
54166 GAGAAAGTGA
*
54176 CAAGGATGAGTTTCCCCCATGCCCTCATTGCAAAAAGATCAACCATTTGCCTAAATATTGTTGGT
1 CAAGGATGAGTTTCCCCCATGCCCTCATTGCAAAAAGACCAACCATTTGCCTAAATATTGTTGGT
54241 ATAGACCAGATGCCATCTGCAAAACTTGTAAACAACTTGGCCATGTAGCAAAGGTGTGTAAAAGC
66 ATAGACCAGATGCCATCTGCAAAACTTGTAAACAACTTGGCCATGTAGCAAAGGTGTGTAAAAGC
54306 AAAAAGAAGAAG-AAGCAAGCAAACCAGGCTCAAGTGGAAGAAAG
131 AAAAAGAAGAAGCAAGCAAGCAAACCAGGCTCAAGTGGAAGAAAG
54350 CAAGGATGAGTTTCCCCCATGCCCTCATTGCAAAAAGACCAACCATTTGCCTAAATATTGTTGGT
1 CAAGGATGAGTTTCCCCCATGCCCTCATTGCAAAAAGACCAACCATTTGCCTAAATATTGTTGGT
*
54415 ATAGACCAGATGCCATCTGCAAGACTTGTAAACAACTTGGCCATGTAGCAAAGGTGTGTAAAAGC
66 ATAGACCAGATGCCATCTGCAAAACTTGTAAACAACTTGGCCATGTAGCAAAGGTGTGTAAAAGC
*
54480 AAGAAGAAGAAGCAAGCAAGCAAACCAGGCTCAAGTGGAAGAAAG
131 AAAAAGAAGAAGCAAGCAAGCAAACCAGGCTCAAGTGGAAGAAAG
54525 CA
1 CA
54527 GCAGCAATGG
Statistics
Matches: 173, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
174 139 0.80
175 34 0.20
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.20
Consensus pattern (175 bp):
CAAGGATGAGTTTCCCCCATGCCCTCATTGCAAAAAGACCAACCATTTGCCTAAATATTGTTGGT
ATAGACCAGATGCCATCTGCAAAACTTGTAAACAACTTGGCCATGTAGCAAAGGTGTGTAAAAGC
AAAAAGAAGAAGCAAGCAAGCAAACCAGGCTCAAGTGGAAGAAAG
Done.