Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024404.1 Corchorus olitorius cultivar O-4 contig24437, 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: 22458
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:4689 original size:31 final size:28
Alignment explanation
Indices: 4619--4692 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 28
4609 CCAAATTGCG
*
4619 AGTTCAGGGGGC-AAACATCCAAATTAA
1 AGTTCAGGGGGCAAAACATCAAAATTAA
* * *
4646 AGTTTAGAGGGCAAAACGTCAAAATCGTAAA
1 AGTTCAGGGGGCAAAACATCAAAAT--T-AA
4677 AGTTCAGGGGGCAAAA
1 AGTTCAGGGGGCAAAA
4693 AGGGCATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
27 10 0.27
28 10 0.27
30 1 0.03
31 16 0.43
ACGTcount: A:0.42, C:0.15, G:0.26, T:0.18
Consensus pattern (28 bp):
AGTTCAGGGGGCAAAACATCAAAATTAA
Found at i:12230 original size:14 final size:14
Alignment explanation
Indices: 12207--12236 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12197 CCAATTTAGG
*
12207 TTTAGTTTTAAGTT
1 TTTAGATTTAAGTT
12221 TTTAGATTTAAGTT
1 TTTAGATTTAAGTT
12235 TT
1 TT
12237 ATTTTTATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.63
Consensus pattern (14 bp):
TTTAGATTTAAGTT
Found at i:12306 original size:30 final size:29
Alignment explanation
Indices: 12260--12316 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
12250 TTTGGATTAG
12260 TTATTTATGCTATAATTTTCAA-TTTCCT
1 TTATTTATGCTATAATTTTCAAGTTTCCT
*
12288 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTAT-TTATG-CTATAATTTTCAAGTTTC
12317 ATTAATAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 5 0.20
30 12 0.48
31 4 0.16
ACGTcount: A:0.23, C:0.14, G:0.05, T:0.58
Consensus pattern (29 bp):
TTATTTATGCTATAATTTTCAAGTTTCCT
Found at i:13681 original size:43 final size:42
Alignment explanation
Indices: 13614--13707 Score: 161
Period size: 43 Copynumber: 2.2 Consensus size: 42
13604 CTCGATGAAA
*
13614 TGGATTTGAGAGGAATGGCCGAAGGCTTGTTATTCCTCGTTG
1 TGGATTTGAGAGAAATGGCCGAAGGCTTGTTATTCCTCGTTG
13656 TGGATTTGAGAGAAAATGGCCGAAGGCTTGTTATTCCTCGTTG
1 TGGATTTGAGAG-AAATGGCCGAAGGCTTGTTATTCCTCGTTG
13699 TCGGATTTG
1 T-GGATTTG
13708 CTAGATTTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 12 0.24
43 30 0.61
44 7 0.14
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (42 bp):
TGGATTTGAGAGAAATGGCCGAAGGCTTGTTATTCCTCGTTG
Found at i:13983 original size:102 final size:102
Alignment explanation
Indices: 13864--14064 Score: 357
Period size: 102 Copynumber: 2.0 Consensus size: 102
13854 GCTTTGTTGT
* *
13864 TGCTTTATTGATGGAGAAGAACTTTGCTTTAGATTTGGTTTGCTTGAGAAGAACTTTGCCTTGCC
1 TGCTTTATTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCC
*
13929 TTGCCTTGAATTTGGAGAGATCGCTGGTGGCTTGGAA
66 TTGCCTTGAATTTAGAGAGATCGCTGGTGGCTTGGAA
*
13966 TGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCC
1 TGCTTTATTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCC
*
14031 TTGCCTTGAATTTAGAGAGATTGCTGGTGGCTTG
66 TTGCCTTGAATTTAGAGAGATCGCTGGTGGCTTG
14065 TAATCTCTGA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 94 1.00
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.38
Consensus pattern (102 bp):
TGCTTTATTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCC
TTGCCTTGAATTTAGAGAGATCGCTGGTGGCTTGGAA
Found at i:16559 original size:46 final size:45
Alignment explanation
Indices: 16451--16620 Score: 216
Period size: 46 Copynumber: 3.7 Consensus size: 45
16441 CCTTTCAACA
*
16451 TTGGCGGGGTTGATTATTTATTACCCTCTACCTCTGCATCGA-TT
1 TTGGCGGGGTTGATTATTTATTGCCCTCTACCTCTGCATCGACTT
* * * *
16495 TTGGCGGGGTCGATTATTTATCGCCATCCACCTCTGCATCGACTT
1 TTGGCGGGGTTGATTATTTATTGCCCTCTACCTCTGCATCGACTT
* *
16540 ATTAGCGGGGTTGATTATTTATTGCCCTCTACCTCTGCATCGGCTT
1 -TTGGCGGGGTTGATTATTTATTGCCCTCTACCTCTGCATCGACTT
* **
16586 CTTGGCGGGGTTGATTTTTTTATCACCCTCTACCT
1 -TTGGCGGGGTTGA-TTATTTATTGCCCTCTACCT
16621 TTTGCTTCAA
Statistics
Matches: 107, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
44 37 0.35
45 2 0.02
46 51 0.48
47 17 0.16
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (45 bp):
TTGGCGGGGTTGATTATTTATTGCCCTCTACCTCTGCATCGACTT
Found at i:17305 original size:22 final size:22
Alignment explanation
Indices: 17277--17319 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
17267 GCAATGCTTT
17277 GGTGGTTGAATCTTTTGAAGAA
1 GGTGGTTGAATCTTTTGAAGAA
17299 GGTGGTTGAATCTTTTGAAGA
1 GGTGGTTGAATCTTTTGAAGA
17320 TGACAACCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.37
Consensus pattern (22 bp):
GGTGGTTGAATCTTTTGAAGAA
Found at i:19834 original size:43 final size:43
Alignment explanation
Indices: 19770--19863 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 43
19760 CTTGATGAAA
*
19770 TGGATTTGAAAGGAATGGCCGAAGGCTTGTTATTCCTCGTTG-
1 TGGATTTGAAAGAAATGGCCGAAGGCTTGTTATTCCTCGTTGC
* *
19812 TGGATTTGAGAGAAAATGGCCGAAGGCTTGTTATTTCTCGTTGC
1 TGGATTTGAAAG-AAATGGCCGAAGGCTTGTTATTCCTCGTTGC
*
19856 CGGATTTG
1 TGGATTTG
19864 CTAGATTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 11 0.24
43 28 0.61
44 7 0.15
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (43 bp):
TGGATTTGAAAGAAATGGCCGAAGGCTTGTTATTCCTCGTTGC
Found at i:20205 original size:102 final size:102
Alignment explanation
Indices: 20022--20220 Score: 353
Period size: 102 Copynumber: 2.0 Consensus size: 102
20012 ATTGTTGTTA
* *
20022 CTTTATTGATGGAGAAGAACTTTGTTTCAGATTTGGTTTGCTTGAGAAGAACTTTGCCTTGCCTT
1 CTTTATTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCCTT
*
20087 GCCTTGAATTTGGAGAGATCGCTGGTGGCTTGGAATG
66 GCCTTGAATTTAGAGAGATCGCTGGTGGCTTGGAATG
*
20124 CTTTGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCCTT
1 CTTTATTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCCTT
*
20189 GCCTTGAATTTAGAGAGATTGCTGGTGGCTTG
66 GCCTTGAATTTAGAGAGATCGCTGGTGGCTTG
20221 TAATCTCTGA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.38
Consensus pattern (102 bp):
CTTTATTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCCTT
GCCTTGAATTTAGAGAGATCGCTGGTGGCTTGGAATG
Done.