Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014356.1 Corchorus capsularis cultivar CVL-1 contig14377, 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: 18708
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:3447 original size:22 final size:22
Alignment explanation
Indices: 3422--3464 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3412 AAGCCACATA
3422 GTGGCCGTGAAATTCGGCCATG
1 GTGGCCGTGAAATTCGGCCATG
*
3444 GTGGCCGTGAGATTCGGCCAT
1 GTGGCCGTGAAATTCGGCCAT
3465 CCTTCAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.37, T:0.23
Consensus pattern (22 bp):
GTGGCCGTGAAATTCGGCCATG
Found at i:6377 original size:11 final size:11
Alignment explanation
Indices: 6353--6387 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6343 TTGACAACGC
6353 AACAAAAACAA
1 AACAAAAACAA
* *
6364 AACGAAAACGA
1 AACAAAAACAA
6375 AACAAAAACAA
1 AACAAAAACAA
6386 AA
1 AA
6388 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:14079 original size:26 final size:26
Alignment explanation
Indices: 14043--14096 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
14033 CCTCCCTGAC
14043 TGTTTTTATAGGCAAATAAATGAATG
1 TGTTTTTATAGGCAAATAAATGAATG
14069 TGTTTTTATAGGCAAATAAATGAATG
1 TGTTTTTATAGGCAAATAAATGAATG
14095 TG
1 TG
14097 CATATTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (26 bp):
TGTTTTTATAGGCAAATAAATGAATG
Found at i:14772 original size:19 final size:21
Alignment explanation
Indices: 14726--14773 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
14716 TGTGGCACGC
*
14726 CACATGTACCAAAAAATCGTGC
1 CACATGTACCAAAAAA-CGTGA
14748 CACATGTACC-AAAAA-GTGA
1 CACATGTACCAAAAAACGTGA
14767 CACATGT
1 CACATGT
14774 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
21 5 0.20
22 10 0.40
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (21 bp):
CACATGTACCAAAAAACGTGA
Found at i:14778 original size:53 final size:53
Alignment explanation
Indices: 14693--14793 Score: 166
Period size: 53 Copynumber: 1.9 Consensus size: 53
14683 GATGTGGCAC
**
14693 GCCACATGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAATCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAATCGT
* *
14746 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAA
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAA
14794 GTGACACGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.39, C:0.28, G:0.18, T:0.16
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAATCGT
Found at i:14812 original size:31 final size:31
Alignment explanation
Indices: 14745--14842 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
14735 CAAAAAATCG
* *
14745 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* *
14776 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** *
14807 TGCCACATGTTTCAAAAA-TGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
14837 TGCCAC
1 TGCCAC
14843 GTGCACAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
30 17 0.29
31 41 0.71
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:15658 original size:73 final size:73
Alignment explanation
Indices: 15570--15717 Score: 269
Period size: 73 Copynumber: 2.0 Consensus size: 73
15560 GAGTTAATCT
* *
15570 TTGATTCTCCATCTTTGAAGTATCTACTCTTAATTTGATAGAATAAGTCCTTATTTTATACCGTA
1 TTGATTCTCCATCTTTGAAGTATCTACTCTTAATTTGATACAATAAATCCTTATTTTATACCGTA
15635 TAAGTTCA
66 TAAGTTCA
*
15643 TTGATTCTCCTTCTTTGAAGTATCTACTCTTAATTTGATACAATAAATCCTTATTTTATACCGTA
1 TTGATTCTCCATCTTTGAAGTATCTACTCTTAATTTGATACAATAAATCCTTATTTTATACCGTA
15708 TAAGTTCA
66 TAAGTTCA
15716 TT
1 TT
15718 CTTTTTGTAC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.45
Consensus pattern (73 bp):
TTGATTCTCCATCTTTGAAGTATCTACTCTTAATTTGATACAATAAATCCTTATTTTATACCGTA
TAAGTTCA
Found at i:16658 original size:12 final size:14
Alignment explanation
Indices: 16643--16674 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16633 TTGAAAGAAT
16643 AAAAGAA-AAA-AA
1 AAAAGAAGAAACAA
16655 AAAAGAAGAAACAA
1 AAAAGAAGAAACAA
16669 AAAAGA
1 AAAAGA
16675 CAGATGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAACAA
Done.