Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022371.1 Corchorus olitorius cultivar O-4 contig22404, 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: 17650
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:1173 original size:76 final size:76
Alignment explanation
Indices: 1023--1173 Score: 178
Period size: 76 Copynumber: 2.0 Consensus size: 76
1013 ACAAGGGCCT
* * * * * *
1023 CGACTCCTCCTAGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTTAAGACCCAGCT
1 CGACTCCACCTAGGCGCACACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAGAT
*
1088 GGGCAGTGTCC
66 AGGCAGTGTCC
* * * *
1099 CGACTCCACCTAGGTGCACACATGGTTTGTC-TGAGGACCCATGTGATTTGCCTGATCACCCAGA
1 CGACTCCACCTAGGCGCACACATGG-TTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAGA
*
1163 TAGGCTGTGTC
65 TAGGCAGTGTC
1174 ATAGCTCGGT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
76 58 0.94
77 4 0.06
ACGTcount: A:0.18, C:0.31, G:0.26, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTAGGCGCACACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAGAT
AGGCAGTGTCC
Found at i:2460 original size:114 final size:113
Alignment explanation
Indices: 2215--2632 Score: 617
Period size: 114 Copynumber: 3.7 Consensus size: 113
2205 AAAATTTAAG
* * * * *
2215 ATAGCGGCGTTTCTGGCTAAAACGCCGCTAAATGAGGGCGTTTTAATTTTGTAAACGTCGCCATA
1 ATAGCGGCGTTTCTGGCCAAAACGCCGCTAAATGGGGGCGTTTGAA-TTTGCAAACGCCGCCATA
* ** *
2280 TTTAATTTTTTTCCGAAAAATGCAAATT-TGTAAAAATGAGACTAAAAT
65 TTTAAATTTTTTCCGGGAAATGCAAATTGAGTAAAAATGAGACTAAAAT
*
2328 ATAGCGGCGTTTCTGGCCAAAACGCCGCTAAATTGGGGCGTTTGAATTTGCAAACGCCGCCATAT
1 ATAGCGGCGTTTCTGGCCAAAACGCCGCTAAATGGGGGCGTTTGAATTTGCAAACGCCGCCATAT
*
2393 TTAAATTTTTTCCGGGGAAATACAAATTGAGTAAAAATGAGACTAAAAT
66 TTAAATTTTTTCC-GGGAAATGCAAATTGAGTAAAAATGAGACTAAAAT
* *
2442 ATAGCAGCGTTTCTGGCCAAAACGCTGCTAAATGGGGGCGTTTGAATTTGCAATACGCCGCCATA
1 ATAGCGGCGTTTCTGGCCAAAACGCCGCTAAATGGGGGCGTTTGAATTTGCAA-ACGCCGCCATA
*
2507 TTTAATTTTTTTTTCCGGGAAATGCAAATTGAGTAAAAATGAGACTAAAAT
65 TTTAA--ATTTTTTCCGGGAAATGCAAATTGAGTAAAAATGAGACTAAAAT
* * *
2558 ATAGCGGCGTTT-TGGCCAAACCGCCGCTAAATGGGGGCGTTTGAATTTGTAAATGCCGCCATAT
1 ATAGCGGCGTTTCTGGCCAAAACGCCGCTAAATGGGGGCGTTTGAATTTGCAAACGCCGCCATAT
2622 TT-AATTTTTTC
66 TTAAATTTTTTC
2633 TTAAGACTGA
Statistics
Matches: 278, Mismatches: 22, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
111 7 0.03
112 29 0.10
113 54 0.19
114 82 0.29
115 53 0.19
116 45 0.16
117 8 0.03
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (113 bp):
ATAGCGGCGTTTCTGGCCAAAACGCCGCTAAATGGGGGCGTTTGAATTTGCAAACGCCGCCATAT
TTAAATTTTTTCCGGGAAATGCAAATTGAGTAAAAATGAGACTAAAAT
Found at i:2620 original size:229 final size:226
Alignment explanation
Indices: 2215--2632 Score: 651
Period size: 229 Copynumber: 1.8 Consensus size: 226
2205 AAAATTTAAG
* * * * *
2215 ATAGCGGCGTTTCTGGCTAAAACGCCGCTAAATGAGGGCGTTTTAATTTTGTAAACGTCGCCATA
1 ATAGCAGCGTTTCTGGCCAAAACGCCGCTAAATGAGGGCGTTTGAATTTTGCAAACGCCGCCATA
*
2280 TTTAATTTTTTTCCGAAAAATGCAAATTTGTAAAAATGAGACTAAAATATAGCGGCGTTTCTGGC
66 TTTAATTTTTTTCCGAAAAATGCAAATTAGTAAAAATGAGACTAAAATATAGCGGCGTTTCTGGC
*
2345 CAAAACGCCGCTAAATTGGGGCGTTTGAATTTGCAAACGCCGCCATATTTAAATTTTTTCCGGGG
131 CAAAACGCCGCTAAATGGGGGCGTTTGAATTTGCAAACGCCGCCATATTT-AATTTTTTCCGGGG
2410 AAATACAAATTGAGTAAAAATGAGACTAAAAT
195 AAATACAAATTGAGTAAAAATGAGACTAAAAT
* *
2442 ATAGCAGCGTTTCTGGCCAAAACGCTGCTAAATGGGGGCGTTTGAA-TTTGCAATACGCCGCCAT
1 ATAGCAGCGTTTCTGGCCAAAACGCCGCTAAATGAGGGCGTTTGAATTTTGCAA-ACGCCGCCAT
**
2506 ATTTAATTTTTTTTTCCGGGAAATGCAAATTGAGTAAAAATGAGACTAAAATATAGCGGCGTTT-
65 ATTTAA--TTTTTTTCCGAAAAATGCAAATT-AGTAAAAATGAGACTAAAATATAGCGGCGTTTC
* * *
2570 TGGCCAAACCGCCGCTAAATGGGGGCGTTTGAATTTGTAAATGCCGCCATATTTAATTTTTTC
127 TGGCCAAAACGCCGCTAAATGGGGGCGTTTGAATTTGCAAACGCCGCCATATTTAATTTTTTC
2633 TTAAGACTGA
Statistics
Matches: 173, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
226 6 0.03
227 56 0.32
228 9 0.05
229 71 0.41
230 31 0.18
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (226 bp):
ATAGCAGCGTTTCTGGCCAAAACGCCGCTAAATGAGGGCGTTTGAATTTTGCAAACGCCGCCATA
TTTAATTTTTTTCCGAAAAATGCAAATTAGTAAAAATGAGACTAAAATATAGCGGCGTTTCTGGC
CAAAACGCCGCTAAATGGGGGCGTTTGAATTTGCAAACGCCGCCATATTTAATTTTTTCCGGGGA
AATACAAATTGAGTAAAAATGAGACTAAAAT
Found at i:2770 original size:14 final size:14
Alignment explanation
Indices: 2751--2779 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2741 ATTTTCTAAG
2751 TCTCCTTTCTCCCT
1 TCTCCTTTCTCCCT
2765 TCTCCTTTCTCCCT
1 TCTCCTTTCTCCCT
2779 T
1 T
2780 GGTTCTCTTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (14 bp):
TCTCCTTTCTCCCT
Found at i:5443 original size:32 final size:30
Alignment explanation
Indices: 5338--5449 Score: 125
Period size: 32 Copynumber: 3.5 Consensus size: 30
5328 ACAAAAGTCA
*
5338 AAATAGCGGCGTTTTATACAAGAACGCCGCT
1 AAATAGCGGCGTTTT-TACAGGAACGCCGCT
*
5369 AAATAGCGGCATTTTTTTACAGGAACGCCGCT
1 AAATAGCGGC--GTTTTTACAGGAACGCCGCT
* * *
5401 GAATAGCGGCGCTTGTTTACAGGAAAGCAGCT
1 AAATAGCGGCG-TT-TTTACAGGAACGCCGCT
5433 AAATAGCGGCGTATTTT
1 AAATAGCGGCGT-TTTT
5450 GTACGAAAAC
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
31 16 0.23
32 49 0.71
33 4 0.06
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (30 bp):
AAATAGCGGCGTTTTTACAGGAACGCCGCT
Found at i:5759 original size:152 final size:152
Alignment explanation
Indices: 5483--5786 Score: 563
Period size: 152 Copynumber: 2.0 Consensus size: 152
5473 AATCAAAATT
5483 TTGTTCTGAAAAATAATTCCCCGGCGTTTATGGTTTAGAAACGCCGCTATTTAGCTTTGTTTTGT
1 TTGTTCTGAAAAATAATTCCCCGGCGTTTATGGTTTAGAAACGCCGCTATTTAGCTTTGTTTTGT
* *
5548 ATTCAAAACGCCGCTATTTGAAATAGTGGCGTCTTGCTTTAAAACGCCGCAAAATAACGGCAGTT
66 ATTCAAAACGCCGCTATTTGAAATAGCGGCGTCTTGCTTTAAAACGCCGCAAAACAACGGCAGTT
5613 TTTATAACGGCACTTCTGACGG
131 TTTATAACGGCACTTCTGACGG
*
5635 TTGTTCTGAAATATAATTCCCCGGCGTTTATGGTTTAGAAACGCCGCTATTTAGCTTTGTTTTGT
1 TTGTTCTGAAAAATAATTCCCCGGCGTTTATGGTTTAGAAACGCCGCTATTTAGCTTTGTTTTGT
* *
5700 ATTCAAAACGCCGCTATTTGAAATAGCGGCGTCTTGCTTTAAAATGCCGCAAAACAACGGCGGTT
66 ATTCAAAACGCCGCTATTTGAAATAGCGGCGTCTTGCTTTAAAACGCCGCAAAACAACGGCAGTT
5765 TTTATAACGGCACTTCTGACGG
131 TTTATAACGGCACTTCTGACGG
5787 CGTTGTGTTA
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
152 147 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (152 bp):
TTGTTCTGAAAAATAATTCCCCGGCGTTTATGGTTTAGAAACGCCGCTATTTAGCTTTGTTTTGT
ATTCAAAACGCCGCTATTTGAAATAGCGGCGTCTTGCTTTAAAACGCCGCAAAACAACGGCAGTT
TTTATAACGGCACTTCTGACGG
Found at i:9347 original size:12 final size:12
Alignment explanation
Indices: 9330--9360 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
9320 TACATGCATG
9330 AAATTTTTTCGA
1 AAATTTTTTCGA
9342 AAA-TTTTTCGA
1 AAATTTTTTCGA
9353 AAATTTTT
1 AAATTTTT
9361 GAATTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (12 bp):
AAATTTTTTCGA
Found at i:10294 original size:27 final size:28
Alignment explanation
Indices: 10264--10317 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
10254 TCATTACTCC
10264 CCTTTGTT-TTCACCTT-CACATTTCTTT
1 CCTTT-TTCTTCACCTTCCACATTTCTTT
* *
10291 CCTTTTTCTTCTCCTTCCCCATTTCTT
1 CCTTTTTCTTCACCTTCCACATTTCTT
10318 CACCATGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 2 0.09
27 12 0.52
28 9 0.39
ACGTcount: A:0.07, C:0.35, G:0.02, T:0.56
Consensus pattern (28 bp):
CCTTTTTCTTCACCTTCCACATTTCTTT
Found at i:11938 original size:19 final size:19
Alignment explanation
Indices: 11914--11954 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
11904 GAACGTTTGT
11914 AATCCTGATATTTGAATGA
1 AATCCTGATATTTGAATGA
11933 AATCCTGATATTTGAATGA
1 AATCCTGATATTTGAATGA
11952 AAT
1 AAT
11955 GAAATCAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
AATCCTGATATTTGAATGA
Done.