Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007658.1 Corchorus olitorius cultivar O-4 contig07684, 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, 846
Length: 1410
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Found at i:183 original size:71 final size:70
Alignment explanation
Indices: 92--686 Score: 566
Period size: 71 Copynumber: 8.6 Consensus size: 70
82 TTGCTGAAGA
*
92 TTTATTTCAGTTGATCCAGGGCGATCTTTCCTTCCATTTATTTCAGCTGATCCAGGGCGAT-TTT
1 TTTATTTCAGTTGATCCAGGGCGATCTTT-CTT-CATTTATTTCAGTTGATCCAGGGCGATCTTT
156 TCTTCAG
64 TCTTCAG
* * * * * *
163 TTCATTT-TGATTGATCCAGGGCGATCTTTCCTCAATTACTTCAGTTGATCCAAGGCGATCTTTA
1 TTTATTTCAG-TTGATCCAGGGCGATCTTTCTTCATTTATTTCAGTTGATCCAGGGCGATCTTT-
227 T-TTCAG
64 TCTTCAG
* * * * * * * *
233 TTTATTTCAGTTGACCCAGGGCGGTCCTTCTTCAATTCATTTTAATGGATCCAAGGCGATCTTTT
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTC-ATTTATTTCAGTTGATCCAGGGCGATCTTTT
298 CTTCAG
65 CTTCAG
* * * * *
304 CTTA---C--TTGACCCAGGGCGATCTTTCTTTAGTTTATTTCAGTTGACCCAGGGCGGTC-TTT
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA-TTTATTTCAGTTGATCCAGGGCGATCTTTT
*
363 CTTCAA
65 CTTCAG
* * * * * *
369 TTCACTCCAGTTGATCCAGGGCGATCCTTTCTTTAGTTTATTTCAGTTGACCCAGGGCGGTC-TT
1 TTTATTTCAGTTGATCCAGGGCGAT-CTTTCTTCA-TTTATTTCAGTTGATCCAGGGCGATCTTT
433 TCTTCAG
64 TCTTCAG
* *
440 TTTATTTCAGTTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTT
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA-TTTATTTCAGTTGATCCAGGGCGATCTTTT
505 CTTCAG
65 CTTCAG
* * * * * *
511 TTTATTCCAGTTGACCCAGGGCGGTCTTTCTTTAATTTATTTCAGTTGATCTAGGGCGATCTTTC
1 TTTATTTCAGTTGATCCAGGGCGATCTTTC-TTCATTTATTTCAGTTGATCCAGGGCGATCTTTT
576 CTT-AG
65 CTTCAG
* *
581 TTTATTTCAGTTGATCGAGGGCGATC-TT-TTC-TTTA----A-TTGATCCAAGGCGATC-TTTC
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCATTTATTTCAGTTGATCCAGGGCGATCTTTTC
*
637 TTCAA
66 TTCAG
* *
642 TTTACTTT-AGTAGATCCAGGGCGATCTTCTCTGCAGTTTATTTCA
1 TTTA-TTTCAGTTGATCCAGGGCGATCTT-TCTTCA-TTTATTTCA
687 ATCGATTGTA
Statistics
Matches: 438, Mismatches: 60, Indels: 53
0.79 0.11 0.10
Matches are distributed among these distances:
60 5 0.01
61 35 0.08
62 5 0.01
63 1 0.00
64 2 0.00
65 11 0.03
66 47 0.11
67 2 0.00
68 2 0.00
69 25 0.06
70 109 0.25
71 191 0.44
72 3 0.01
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (70 bp):
TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCATTTATTTCAGTTGATCCAGGGCGATCTTTTC
TTCAG
Found at i:185 original size:35 final size:35
Alignment explanation
Indices: 92--686 Score: 589
Period size: 35 Copynumber: 17.3 Consensus size: 35
82 TTGCTGAAGA
92 TTTATTTCAGTTGATCCAGGGCGATCTTTCCTTCCA-
1 TTTATTTCAGTTGATCCAGGGCGATCTTT-CTT-CAG
* *
128 TTTATTTCAGCTGATCCAGGGCGATTTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * *
163 TTCATTT-TGATTGATCCAGGGCGATCTTTCCTCA-
1 TTTATTTCAG-TTGATCCAGGGCGATCTTTCTTCAG
* * * *
197 ATTACTTCAGTTGATCCAAGGCGATCTTTATTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTT-CTTCAG
* * * *
233 TTTATTTCAGTTGACCCAGGGCGGTCCTTCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * * * *
268 TTCATTTTAATGGATCCAAGGCGATCTTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAG
* * *
304 CTTA---C--TTGACCCAGGGCGATCTTTCTTTAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * *
334 TTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * * *
369 TTCACTCCAGTTGATCCAGGGCGATCCTTTCTTTAG
1 TTTATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAG
* *
405 TTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
*
440 TTTATTTCAGTTGATCCAGGGCGGTCTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
475 TTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAG
1 TTTATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAG
* * * * *
511 TTTATTCCAGTTGACCCAGGGCGGTCTTTCTTTAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
*
546 TTTATTTCAGTTGATCTAGGGCGATCTTTCCTT-AG
1 TTTATTTCAGTTGATCCAGGGCGATCTTT-CTTCAG
*
581 TTTATTTCAGTTGATCGAGGGCGATC-TT-TTC--
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* *
612 TTTA----A-TTGATCCAAGGCGATCTTTCTTCAA
1 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* *
642 TTTACTTT-AGTAGATCCAGGGCGATCTTCTCTGCAG
1 TTTA-TTTCAGTTGATCCAGGGCGATCTT-TCTTCAG
678 TTTATTTCA
1 TTTATTTCA
687 ATCGATTGTA
Statistics
Matches: 459, Mismatches: 74, Indels: 52
0.78 0.13 0.09
Matches are distributed among these distances:
26 14 0.03
27 3 0.01
28 3 0.01
30 15 0.03
31 17 0.04
32 2 0.00
33 1 0.00
34 28 0.06
35 244 0.53
36 132 0.29
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (35 bp):
TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAG
Found at i:460 original size:106 final size:106
Alignment explanation
Indices: 92--613 Score: 596
Period size: 106 Copynumber: 5.0 Consensus size: 106
82 TTGCTGAAGA
* * * *
92 TTTATTTCAGTTGATCCAGGGCGATCTTTCCTTCCA-TTTATTTCAGCTGATCCAGGGCGATTTT
1 TTTATTTCAGTTGACCCAGGGCGATCTTT-CTT-CAGTTTATTTCAGTTGATCCAGGGCGGTCTT
* *
156 TCTTCAGTTCATTT-TGATTGATCCAGGGCGAT-CTTTCCTCA-
64 TCTTCAGTTCATTTCAG-TTGATCCAGGGCGATCCTTTCTTCAG
* * * * * * *
197 ATTACTTCAGTTGATCCAAGGCGATCTTTATTTCAGTTTATTTCAGTTGACCCAGGGCGGTCCTT
1 TTTATTTCAGTTGACCCAGGGCGATCTTT-CTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTT
* * * * * *
262 CTTCAATTCATTTTAATGGATCCAAGGCGATCTTTTCTTCAG
65 CTTCAGTTCATTTCAGTTGATCCAGGGCGATCCTTTCTTCAG
* * *
304 CTTA---C--TTGACCCAGGGCGATCTTTCTTTAGTTTATTTCAGTTGACCCAGGGCGGTCTTTC
1 TTTATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTTC
* * * *
364 TTCAATTCACTCCAGTTGATCCAGGGCGATCCTTTCTTTAG
66 TTCAGTTCATTTCAGTTGATCCAGGGCGATCCTTTCTTCAG
*
405 TTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTTC
1 TTTATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTTC
*
470 TTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAG
66 TTCAGTTCATTTCAGTTGATCCAGGGCGATCCTTTCTTCAG
* * * * * *
511 TTTATTCCAGTTGACCCAGGGCGGTCTTTCTTTAATTTATTTCAGTTGATCTAGGGCGATCTTTC
1 TTTATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTT-
* * *
576 CTT-AGTTTATTTCAGTTGATCGAGGGCGATCTTTTCTT
65 CTTCAGTTCATTTCAGTTGATCCAGGGCGATCCTTTCTT
614 TAATTGATCC
Statistics
Matches: 360, Mismatches: 47, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
101 69 0.19
102 17 0.05
104 4 0.01
105 77 0.21
106 187 0.52
107 6 0.02
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (106 bp):
TTTATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGGTCTTTC
TTCAGTTCATTTCAGTTGATCCAGGGCGATCCTTTCTTCAG
Found at i:643 original size:25 final size:26
Alignment explanation
Indices: 586--643 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
576 CTTAGTTTAT
* * *
586 TTCAGTTGATCGAGGGCGATCTTTTC
1 TTCAATTGATCCAAGGCGATCTTTTC
*
612 TTTAATTGATCCAAGGCGATC-TTTC
1 TTCAATTGATCCAAGGCGATCTTTTC
637 TTCAATT
1 TTCAATT
644 TACTTTAGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (26 bp):
TTCAATTGATCCAAGGCGATCTTTTC
Found at i:1278 original size:27 final size:27
Alignment explanation
Indices: 1240--1340 Score: 157
Period size: 27 Copynumber: 3.7 Consensus size: 27
1230 GTTTCCTTTA
1240 TGGATCCCGATGGTCATGAGACAAAAC
1 TGGATCCCGATGGTCATGAGACAAAAC
1267 TGGATCCCGATGGTCATGAGACAAAAC
1 TGGATCCCGATGGTCATGAGACAAAAC
* ** *
1294 TGGATCCCGATGGTCGTGAGATGAAAT
1 TGGATCCCGATGGTCATGAGACAAAAC
*
1321 TAGATCCCGATGGTCATGAG
1 TGGATCCCGATGGTCATGAG
1341 CAATTTGGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.22
Consensus pattern (27 bp):
TGGATCCCGATGGTCATGAGACAAAAC
Done.