Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001620.1 Corchorus olitorius cultivar O-4 contig01620, 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: 15122
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7741 original size:191 final size:186
Alignment explanation
Indices: 7394--7747 Score: 476
Period size: 191 Copynumber: 1.9 Consensus size: 186
7384 TTATTTATCT
* * * *
7394 AATGACCCTTATACTTTTAGCTTTATGTTATTTAATCCTTCACAAATTCTAGCTTGGTCGATTTA
1 AATGACCCTTATACTTTTAGCCTTATGATATTTAATCCTTCACAAATTCTAGCTTGGTCAATTCA
* *
7459 ACGCTTCGGCTTAAATTCTTTTATTTTTATTCTATTTGTCCGATTAAGGTGATTCAAATGTCTAT
66 ACGCTTCGGCTTAAATTCTTTTATTTTTATTCTATTTATCCAATTAAGGTGATTCAAATGTCTAT
7524 TAAAAGATAATTTCATGATCTACAACTTTCATGAAGAACTTGAAAGCTGAATAAAA
131 TAAAAGATAATTTCATGATCTACAACTTTCATGAAGAACTTGAAAGCTGAATAAAA
*
7580 AATGACCCTTATACTTTTCTA-CCTTATGATATTTAATCCTTTACAAATTCTAGCTTGGTCAATT
1 AATGACCCTTATAC-TTT-TAGCCTTATGATATTTAATCCTTCACAAATTCTAGCTTGGTCAATT
* * * * * * * * **
7644 CAACGCTTCGGTTTTAATTGTTTTTTTTCTTTTTTTGTAATTTATCTAATTTAGGTGATTCAGGT
64 CAACGCTTCGG-CTTAAAT-TCTTTTAT-TTTTATTCT-ATTTATCCAATTAAGGTGATTCAAAT
* *
7709 GTCTATTAAAAGGTAATTTCATGATTTACAACTTTCATG
125 GTCTATTAAAAGATAATTTCATGATCTACAACTTTCATG
7748 TAGGATTCAA
Statistics
Matches: 143, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
186 14 0.10
187 52 0.36
188 7 0.05
189 6 0.04
190 7 0.05
191 57 0.40
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (186 bp):
AATGACCCTTATACTTTTAGCCTTATGATATTTAATCCTTCACAAATTCTAGCTTGGTCAATTCA
ACGCTTCGGCTTAAATTCTTTTATTTTTATTCTATTTATCCAATTAAGGTGATTCAAATGTCTAT
TAAAAGATAATTTCATGATCTACAACTTTCATGAAGAACTTGAAAGCTGAATAAAA
Found at i:11513 original size:41 final size:41
Alignment explanation
Indices: 11453--11735 Score: 193
Period size: 41 Copynumber: 6.8 Consensus size: 41
11443 TAGAGAAAAT
* *
11453 TGCCCCTGTG-TA-ACATGTGTTTAGGGACTTAGATATAGG-
1 TGCCCCTGTGTTATAAATGTGCTT-GGGACTTAGATATAGGA
* * * * * *
11492 TGTCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGAGAGAGA
1 TGCCCCTGTGTTATAAATGTGCTTG-GGACTTAGATATAG-GA
* * *
11535 TGCCCCTGTGTTATAATTTTGCTTGGGGACTTTGATAT-GGA
1 TGCCCCTGTGTTATAAATGTGCTT-GGGACTTAGATATAGGA
** *
11576 TGCATCTGTGTTATAAATGTGCTTGAGGACTTTTAG-GA-AGGA
1 TGCCCCTGTGTTATAAATGTGCTTG-GGAC--TTAGATATAGGA
* *
11618 TTGCCCCTGTGTTATAATTGTGCTTGGGGACTTTGATATA-GA
1 -TGCCCCTGTGTTATAAATGTGCTT-GGGACTTAGATATAGGA
** * * *
11660 TGCCTTTGTGTTATAAATGTGCTTGAGGACTTTAGAAAGAGGGT
1 TGCCCCTGTGTTATAAATGTGCTTG-GGAC-TTAGATATA-GGA
* *
11704 TGTCCCTGTGTTATAAATGTGTTTGGGGACTT
1 TGCCCCTGTGTTATAAATGTGCTT-GGGACTT
11736 TGGTTATCAG
Statistics
Matches: 190, Mismatches: 35, Indels: 34
0.73 0.14 0.13
Matches are distributed among these distances:
39 8 0.04
40 5 0.03
41 74 0.39
42 15 0.08
43 60 0.32
44 27 0.14
45 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (41 bp):
TGCCCCTGTGTTATAAATGTGCTTGGGACTTAGATATAGGA
Found at i:11565 original size:43 final size:43
Alignment explanation
Indices: 11497--11737 Score: 224
Period size: 41 Copynumber: 5.7 Consensus size: 43
11487 ATAGGTGTCT
*
11497 CTGTGTTATAAATGTGTTTGAGGACTTTGAGAGAGAGATGCCC
1 CTGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGAGATGCCC
* * * * * **
11540 CTGTGTTATAATTTTGCTTGGGGACTTTGATA-TG-GATGCAT
1 CTGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGAGATGCCC
*
11581 CTGTGTTATAAATGTGCTTGAGGACTTTTAG-GA-AGGATTGCCC
1 CTGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGA-GA-TGCCC
* * * * *
11624 CTGTGTTATAATTGTGCTTGGGGACTTT--GATATAGATGCCT
1 CTGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGAGATGCCC
* * * * *
11665 TTGTGTTATAAATGTGCTTGAGGACTTTAGAAAGAGGGTTGTCC
1 CTGTGTTATAAATGTGCTTGAGGACTTT-GAGAGAGAGATGCCC
* *
11709 CTGTGTTATAAATGTGTTTGGGGACTTTG
1 CTGTGTTATAAATGTGCTTGAGGACTTTG
11738 GTTATCAGGT
Statistics
Matches: 156, Mismatches: 33, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
41 61 0.39
42 6 0.04
43 58 0.37
44 31 0.20
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.39
Consensus pattern (43 bp):
CTGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGAGATGCCC
Found at i:11572 original size:84 final size:83
Alignment explanation
Indices: 11476--11737 Score: 332
Period size: 84 Copynumber: 3.1 Consensus size: 83
11466 CATGTGTTTA
* *
11476 GGGACTTAGATATAGGTGTCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGAGAGAGATGCCCC
1 GGGACTTTGATATAGGTG-CTCTGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGAGATGCCCC
*
11541 TGTGTTATAATTTTGCTTG
65 TGTGTTATAATTGTGCTTG
*
11560 GGGACTTTGATAT-GGATGCATCTGTGTTATAAATGTGCTTGAGGACTTTTAG-GA-AGGATTGC
1 GGGACTTTGATATAGG-TGC-TCTGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGA-GA-TGC
11622 CCCTGTGTTATAATTGTGCTTG
62 CCCTGTGTTATAATTGTGCTTG
* * * * * *
11644 GGGACTTTGATATAGATGCCTTTGTGTTATAAATGTGCTTGAGGACTTTAGAAAGAGGGTTGTCC
1 GGGACTTTGATATAGGTG-CTCTGTGTTATAAATGTGCTTGAGGACTTT-GAGAGAGAGATGCCC
* *
11709 CTGTGTTATAAATGTGTTTG
64 CTGTGTTATAATTGTGCTTG
11729 GGGACTTTG
1 GGGACTTTG
11738 GTTATCAGGT
Statistics
Matches: 156, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
82 1 0.01
83 7 0.04
84 111 0.71
85 34 0.22
86 3 0.02
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (83 bp):
GGGACTTTGATATAGGTGCTCTGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGAGATGCCCCT
GTGTTATAATTGTGCTTG
Found at i:13735 original size:12 final size:12
Alignment explanation
Indices: 13718--13745 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13708 ATTAATTAAC
13718 ATAAAATAAAAA
1 ATAAAATAAAAA
13730 ATAAAATAAAAA
1 ATAAAATAAAAA
13742 ATAA
1 ATAA
13746 CTTTTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:14544 original size:2 final size:2
Alignment explanation
Indices: 14537--14561 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14527 GTATAGATAC
14537 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
14562 TATTTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.