Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020026.1 Corchorus olitorius cultivar O-4 contig20059, 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: 8597
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1806 original size:6 final size:6
Alignment explanation
Indices: 1797--1848 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
1787 AATCAATAAA
*
1797 AAAATC AAAATC AAAATC ATAATC AAAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
1845 AAAA
1 AAAA
1849 AGGGAATTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:3542 original size:69 final size:69
Alignment explanation
Indices: 3454--3620 Score: 307
Period size: 69 Copynumber: 2.4 Consensus size: 69
3444 TGCTTTGGGC
3454 TTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCATAT
1 TTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCATAT
3519 AGGT
66 AGGT
3523 TTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCATAT
1 TTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCATAT
3588 AGGT
66 AGGT
* **
3592 TTTTCCACAAGCCGATTTCGTTTCCATAC
1 TTTTCCACAAGCCAAACTCGTTTCCATAC
3621 AAATCAAGCC
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 95 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (69 bp):
TTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCATAT
AGGT
Found at i:6054 original size:169 final size:169
Alignment explanation
Indices: 5770--6407 Score: 1050
Period size: 169 Copynumber: 3.8 Consensus size: 169
5760 TTGGCGCATC
5770 AAGTCCTCCGGGCAATTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCATCAAAA
1 AAGTCCTCCGGGCAATTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCATCAAAA
* *
5835 GTTTATGTTTAAGTTTAAAATCCTTGTTTAAGGTCTCTTTTCAAAGTTTACATTGGTAAGTCCTC
66 GTTCATGTTTAAGTTTAAAATCCTTGTTTAAGGTCTCTTTTCAGAGTTTACATTGGTAAGTCCTC
5900 CGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGAT
131 CGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGAT
*
5939 AAGTCCTCCGGGCAATTGATAAAACCTTCGGGTATCATTTCATTTTATCAAGTTTTTCATCAAAA
1 AAGTCCTCCGGGCAATTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCATCAAAA
6004 GTTCATGTTTAAGTTTAAAATCCTTGTTTAAGGTCTCTTTTCAGAGTTTACATTGGTAAGTCCTC
66 GTTCATGTTTAAGTTTAAAATCCTTGTTTAAGGTCTCTTTTCAGAGTTTACATTGGTAAGTCCTC
*
6069 CGAGCACGATTTCAGAAACCTCCGGGTATTAATTCTGAT
131 CGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGAT
* *
6108 AAGTCCTCCAGGCAATTGATAAAACCTCCGGGTATCATTTTATTTTATCAAGTTTTTCATCAAAA
1 AAGTCCTCCGGGCAATTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCATCAAAA
* * * *
6173 ATTCATGTTTAAGTTTAAAATCCTTGTTTAAGGTCTCTATTCAGAGTTTGCGTTGGTAAGTCCTC
66 GTTCATGTTTAAGTTTAAAATCCTTGTTTAAGGTCTCTTTTCAGAGTTTACATTGGTAAGTCCTC
6238 CGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGAT
131 CGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGAT
* * * * * *
6277 AAGTCCTCCGGTCAATTGGTAAAGCCTCCGGGTACCATTTCATTTCACCAAG-TTTT--TCAAAA
1 AAGTCCTCCGGGCAATTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCATCAAAA
* * * * *
6339 GTTCATGTTTAAG-TTAGAATCTTTGTTTAAGGTCTCATTTCAGAGTTTACATTTGATAAGACCT
66 GTTCATGTTTAAGTTTAAAATCCTTGTTTAAGGTCTCTTTTCAGAGTTTACA-TTGGTAAGTCCT
6403 CCGGG
130 CCGGG
6408 TTTCTCATAT
Statistics
Matches: 439, Mismatches: 29, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
165 32 0.07
166 33 0.08
168 4 0.01
169 370 0.84
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (169 bp):
AAGTCCTCCGGGCAATTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCATCAAAA
GTTCATGTTTAAGTTTAAAATCCTTGTTTAAGGTCTCTTTTCAGAGTTTACATTGGTAAGTCCTC
CGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGAT
Found at i:6512 original size:30 final size:30
Alignment explanation
Indices: 6478--6709 Score: 237
Period size: 30 Copynumber: 8.0 Consensus size: 30
6468 TCATTGTTTT
6478 ATTGCTTTATTTTAATCCTGATTGAGGATC
1 ATTGCTTTATTTTAATCCTGATTGAGGATC
* *
6508 ATTGCTTTGTTTTAATCCTGTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGATTGAGGATC
** *
6538 GCTGCTTTATTTTAATCCTGGTTGAGGATC
1 ATTGCTTTATTTTAATCCTGATTGAGGATC
* * *
6568 ATTGCTTTATTTTAATCCTGGTTTATGATC
1 ATTGCTTTATTTTAATCCTGATTGAGGATC
* *
6598 ATCG-TTTATTTTAATCCTGGTT----A--
1 ATTGCTTTATTTTAATCCTGATTGAGGATC
* *
6621 ATTGCTTCATTTTAATCCTGTTTGAGGATC
1 ATTGCTTTATTTTAATCCTGATTGAGGATC
** *
6651 GCTGCTTTATTTTAATCCT-AGTTGAGGAAC
1 ATTGCTTTATTTTAATCCTGA-TTGAGGATC
* * *
6681 AGTGCTTTATTTCAATCCTGATTTAGGAT
1 ATTGCTTTATTTTAATCCTGATTGAGGAT
6710 TATCACTCTA
Statistics
Matches: 169, Mismatches: 24, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
23 3 0.02
24 16 0.09
25 1 0.01
28 1 0.01
29 18 0.11
30 129 0.76
31 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.47
Consensus pattern (30 bp):
ATTGCTTTATTTTAATCCTGATTGAGGATC
Found at i:6573 original size:60 final size:59
Alignment explanation
Indices: 6480--6709 Score: 278
Period size: 60 Copynumber: 3.9 Consensus size: 59
6470 ATTGTTTTAT
* *
6480 TGCTTTATTTTAATCCTGATTGAGGATCATTGCTTTGTTTTAATCCTGTTTGAGGATCGC
1 TGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTT-AGGATCGC
* *
6540 TGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTTATGATC-A
1 TGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCT-GTTTAGGATCGC
*
6599 T-CGTTTATTTTAATCCTGGTT----A--ATTGCTTCATTTTAATCCTGTTTGAGGATCGC
1 TGC-TTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTT-AGGATCGC
* * * *
6653 TGCTTTATTTTAATCCTAGTTGAGGAACAGTGCTTTATTTCAATCCTGATTTAGGAT
1 TGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTG-TTTAGGAT
6710 TATCACTCTA
Statistics
Matches: 147, Mismatches: 11, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
52 4 0.03
53 23 0.16
54 18 0.12
55 2 0.01
58 2 0.01
59 19 0.13
60 72 0.49
61 7 0.05
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (59 bp):
TGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTAGGATCGC
Found at i:7187 original size:26 final size:27
Alignment explanation
Indices: 7158--7261 Score: 117
Period size: 26 Copynumber: 4.0 Consensus size: 27
7148 AGGATCACCT
7158 AGGGGCATTTTGGTCATTTTA-AGTTC
1 AGGGGCATTTTGGTCATTTTACAGTTC
* **
7184 AGGGGCATTTTGATCATTTTACACCT-
1 AGGGGCATTTTGGTCATTTTACAGTTC
* *
7210 AGGGGAATTTTGGTCA-TTTACATATTC
1 AGGGGCATTTTGGTCATTTTACA-GTTC
*
7237 AGGGGTATTTTGGTCATTTTA-AGTT
1 AGGGGCATTTTGGTCATTTTACAGTT
7262 AGATTAGCTA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
25 6 0.09
26 37 0.57
27 18 0.28
28 4 0.06
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.42
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTACAGTTC
Found at i:7220 original size:52 final size:53
Alignment explanation
Indices: 7153--7257 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 53
7143 GCATTAGGAT
* *
7153 CACCTAGGGGCATTTTGGTCATTTTA-A-GTTCAGGGGCATTTTGATCATTTTA
1 CACCTAGGGGAATTTTGGTCA-TTTACATATTCAGGGGCATTTTGATCATTTTA
* *
7205 CACCTAGGGGAATTTTGGTCATTTACATATTCAGGGGTATTTTGGTCATTTTA
1 CACCTAGGGGAATTTTGGTCATTTACATATTCAGGGGCATTTTGATCATTTTA
7258 AGTTAGATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
51 4 0.09
52 21 0.45
53 22 0.47
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.41
Consensus pattern (53 bp):
CACCTAGGGGAATTTTGGTCATTTACATATTCAGGGGCATTTTGATCATTTTA
Found at i:7442 original size:20 final size:21
Alignment explanation
Indices: 7417--7456 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
7407 GGATATTTAC
7417 ACTT-GGTCATTTGTCTTAAA
1 ACTTGGGTCATTTGTCTTAAA
*
7437 ACTTGGGTCATTTGTTTTAA
1 ACTTGGGTCATTTGTCTTAA
7457 TGAATTTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (21 bp):
ACTTGGGTCATTTGTCTTAAA
Done.