Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020249.1 Corchorus olitorius cultivar O-4 contig20282, 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: 34280
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:12462 original size:25 final size:25
Alignment explanation
Indices: 12433--12480 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
12423 CTACTATTTG
* *
12433 TTGGCAGGTTTCTAGTGTTTGGTTT
1 TTGGCAGGTCTCTAGTGGTTGGTTT
* *
12458 TTGGCTGGTCTCTGGTGGTTGGT
1 TTGGCAGGTCTCTAGTGGTTGGT
12481 GACTGCTTCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.04, C:0.10, G:0.38, T:0.48
Consensus pattern (25 bp):
TTGGCAGGTCTCTAGTGGTTGGTTT
Found at i:17679 original size:20 final size:20
Alignment explanation
Indices: 17656--17701 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
17646 GGTGGATCTT
17656 AAACCAAAGAGATATTGTAC
1 AAACCAAAGAGATATTGTAC
**
17676 AAACCATCGAGATATTGTAC
1 AAACCAAAGAGATATTGTAC
17696 AAACCA
1 AAACCA
17702 TCCTACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.20
Consensus pattern (20 bp):
AAACCAAAGAGATATTGTAC
Found at i:17702 original size:20 final size:20
Alignment explanation
Indices: 17664--17703 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
17654 TTAAACCAAA
17664 GAGATATTGTACAAACCATC
1 GAGATATTGTACAAACCATC
17684 GAGATATTGTACAAACCATC
1 GAGATATTGTACAAACCATC
17704 CTACAAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (20 bp):
GAGATATTGTACAAACCATC
Found at i:19479 original size:47 final size:47
Alignment explanation
Indices: 19410--19500 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
19400 AAATTTTATC
*
19410 TTAAGTTTGTTTACAGTGAAATTAGAATATATATATATATATATATA
1 TTAAGTTTGTTTACAGTGAAATTAAAATATATATATATATATATATA
19457 TTAAGTTTGTTTACAGTGAAATTAAAATATATATATATATATAT
1 TTAAGTTTGTTTACAGTGAAATTAAAATATATATATATATATAT
19501 TTCTTCAAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (47 bp):
TTAAGTTTGTTTACAGTGAAATTAAAATATATATATATATATATATA
Found at i:21452 original size:29 final size:31
Alignment explanation
Indices: 21379--21456 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 31
21369 CAGTAATACC
* *
21379 GTTTGAGAGGGACTAAAATGTCCTCATATTGCAA
1 GTTT-AGAGGG-C-AAAATGTCCTCAAATTGAAA
*
21413 GTTTAGGGGGCAAAATGTCC-CAAATT-AAA
1 GTTTAGAGGGCAAAATGTCCTCAAATTGAAA
21442 GTTTAGAGGGCAAAA
1 GTTTAGAGGGCAAAA
21457 AGTCAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 16 0.40
30 5 0.12
31 9 0.22
32 1 0.03
33 5 0.12
34 4 0.10
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.26
Consensus pattern (31 bp):
GTTTAGAGGGCAAAATGTCCTCAAATTGAAA
Found at i:25550 original size:6 final size:6
Alignment explanation
Indices: 25545--25584 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
25535 AACAGTCAAC
* *
25545 TCCAAC TCCAAT TCCAAC TCCAAT TCCAAT TCCAAT TCCA
1 TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TCCA
25585 TAATAGAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.28
Consensus pattern (6 bp):
TCCAAT
Found at i:25562 original size:12 final size:12
Alignment explanation
Indices: 25545--25584 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
25535 AACAGTCAAC
25545 TCCAACTCCAAT
1 TCCAACTCCAAT
25557 TCCAACTCCAAT
1 TCCAACTCCAAT
*
25569 TCCAATTCCAAT
1 TCCAACTCCAAT
25581 TCCA
1 TCCA
25585 TAATAGAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.28
Consensus pattern (12 bp):
TCCAACTCCAAT
Found at i:25564 original size:18 final size:18
Alignment explanation
Indices: 25541--25584 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
25531 AAAAAACAGT
25541 CAACTCCAACTCCAATTC
1 CAACTCCAACTCCAATTC
*
25559 CAACTCCAATTCCAATTC
1 CAACTCCAACTCCAATTC
*
25577 CAATTCCA
1 CAACTCCA
25585 TAATAGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (18 bp):
CAACTCCAACTCCAATTC
Found at i:25979 original size:50 final size:52
Alignment explanation
Indices: 25917--26022 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 52
25907 AAAAAAGAGG
*
25917 AAATATTAAAATCCTAAAAAATAC-AAA-A-AAAAATGAAGATTAACAATGAT
1 AAATATTAAAATCAT-AAAAATACAAAACACAAAAATGAAGATTAACAATGAT
*
25967 AAATATTCAAATCATAAAAATACTAAAACAGCAAAAATGAAGATTAACAATGAT
1 AAATATTAAAATCATAAAAATAC-AAAACA-CAAAAATGAAGATTAACAATGAT
26021 AA
1 AA
26023 GGACGTACCG
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
49 8 0.16
50 13 0.27
51 3 0.06
52 1 0.02
54 24 0.49
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (52 bp):
AAATATTAAAATCATAAAAATACAAAACACAAAAATGAAGATTAACAATGAT
Found at i:27298 original size:57 final size:57
Alignment explanation
Indices: 27206--27316 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
27196 TTTGTGTTTT
* * * * *
27206 GACAAATCTTGTGTATTGCAAAATTTGTTCCTCTTCATATCCAACCTGTCTTTCGAA
1 GACAAACCTTGTCTATTGCAAAATTCGTTCATCTTCATATCCAACCAGTCTTTCGAA
27263 GACAAACCTTGTCTATTGCAAAATTCGTTCATCTTCATATCCAACCAGTCTTTC
1 GACAAACCTTGTCTATTGCAAAATTCGTTCATCTTCATATCCAACCAGTCTTTC
27317 CAAGTAAACA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (57 bp):
GACAAACCTTGTCTATTGCAAAATTCGTTCATCTTCATATCCAACCAGTCTTTCGAA
Found at i:32370 original size:18 final size:18
Alignment explanation
Indices: 32347--32385 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
32337 TTGATCAAAC
32347 AATATATCTTAGTCTTAA
1 AATATATCTTAGTCTTAA
32365 AATATATCTTAGTCTTAA
1 AATATATCTTAGTCTTAA
32383 AAT
1 AAT
32386 GTACTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (18 bp):
AATATATCTTAGTCTTAA
Done.