Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007571.1 Corchorus capsularis cultivar CVL-1 contig07592, 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: 33949
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:583 original size:20 final size:19
Alignment explanation
Indices: 560--608 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
550 AAAATAAAAC
560 AAAATCAATTTCCTTTAAA
1 AAAATCAATTTCCTTTAAA
* **
579 TAAAATCTATCGCCTTTAAA
1 -AAAATCAATTTCCTTTAAA
599 AAAA-CAATTT
1 AAAATCAATTT
609 TATTATTAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATCAATTTCCTTTAAA
Found at i:778 original size:29 final size:30
Alignment explanation
Indices: 719--797 Score: 106
Period size: 29 Copynumber: 2.6 Consensus size: 30
709 TAAATACCCA
* *
719 AAAAAAATCCCTTATGTTTTACTTTTGGGAC
1 AAAATAATCCCTTATGTTTTA-TTTGGGGAC
750 AAAATAATCCCTTATGTTTT-TTTGGGGAC
1 AAAATAATCCCTTATGTTTTATTTGGGGAC
* *
779 AAATTAATCCCTTACGTTT
1 AAAATAATCCCTTATGTTT
798 CAAAAATAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.57
31 19 0.43
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (30 bp):
AAAATAATCCCTTATGTTTTATTTGGGGAC
Found at i:982 original size:31 final size:31
Alignment explanation
Indices: 930--1039 Score: 152
Period size: 31 Copynumber: 3.6 Consensus size: 31
920 AAGGGACTAA
930 TTTGTCCC-AAA-AAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
*
959 TTTGTCCCAAAAGAAAAATATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
* * * * *
990 TTTGGCACAAAAGAATAACATAAGGCATTAT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1021 TTTGTCCCAAAAGAAAAAC
1 TTTGTCCCAAAAGAAAAAC
1040 TACAATTTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
29 8 0.12
30 3 0.04
31 58 0.84
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.28
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Found at i:2033 original size:23 final size:23
Alignment explanation
Indices: 2005--2050 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1995 TTCATAAAAA
*
2005 GCATTCATTGGTACATTCATCCC
1 GCATTCATTGGTACATTAATCCC
2028 GCATTCATTGGTACATTAATCCC
1 GCATTCATTGGTACATTAATCCC
2051 ACTTTGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (23 bp):
GCATTCATTGGTACATTAATCCC
Found at i:4367 original size:29 final size:29
Alignment explanation
Indices: 4319--4391 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 29
4309 CTCATTTTTG
*
4319 AAACATAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGA-TAATTTGTCCCAAAACA
*
4348 AAACATAAGGGATAATTTTGTTCCAAAAGCA
1 AAACATAAGGGATAA-TTTGTCCCAAAA-CA
4379 AAACATAAGGGAT
1 AAACATAAGGGAT
4392 TTTTTGGGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 3 0.08
29 22 0.56
31 14 0.36
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (29 bp):
AAACATAAGGGATAATTTGTCCCAAAACA
Found at i:10188 original size:17 final size:18
Alignment explanation
Indices: 10155--10190 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10145 CTTCTCTTGC
10155 ATGAAAACACTTCTTTTT
1 ATGAAAACACTTCTTTTT
*
10173 ATGAAAACA-TTTTTTTT
1 ATGAAAACACTTCTTTTT
10190 A
1 A
10191 AAACTACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (18 bp):
ATGAAAACACTTCTTTTT
Found at i:11618 original size:23 final size:23
Alignment explanation
Indices: 11585--11631 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
11575 CAACCGGCCA
*
11585 CAACCGGCCATCGCATGGGGCAT
1 CAACCGCCCATCGCATGGGGCAT
11608 CAACCGCCCATCGCATGGGGCAT
1 CAACCGCCCATCGCATGGGGCAT
11631 C
1 C
11632 CGCGTACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.38, G:0.28, T:0.13
Consensus pattern (23 bp):
CAACCGCCCATCGCATGGGGCAT
Found at i:30170 original size:25 final size:28
Alignment explanation
Indices: 30122--30174 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 28
30112 TAGATTTAGA
*
30122 TTTAGATTTAATTTTCTTTGCTTTATTT
1 TTTAGATTTAATTGTCTTTGCTTTATTT
30150 TTTAG-TTTAATTGT-TTT-CTTTATTT
1 TTTAGATTTAATTGTCTTTGCTTTATTT
30175 GTTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 8 0.33
26 3 0.12
27 8 0.33
28 5 0.21
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.70
Consensus pattern (28 bp):
TTTAGATTTAATTGTCTTTGCTTTATTT
Found at i:30218 original size:34 final size:34
Alignment explanation
Indices: 30148--30218 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
30138 TTTGCTTTAT
*** **
30148 TTTTTAGTTTAATTGTTTTCTTTATTTGTTTTTA
1 TTTTTAGTTTAATTGTTTTCTTTATAAATTGATA
30182 TTTTTAGTTTAATTGTTTTCTTTATAAATTGATA
1 TTTTTAGTTTAATTGTTTTCTTTATAAATTGATA
30216 TTT
1 TTT
30219 ACAATCCCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.20, C:0.03, G:0.08, T:0.69
Consensus pattern (34 bp):
TTTTTAGTTTAATTGTTTTCTTTATAAATTGATA
Found at i:32670 original size:25 final size:25
Alignment explanation
Indices: 32622--32669 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
32612 TTTTAGATAT
32622 AATATATATTAATAAATAAATAATA
1 AATATATATTAATAAATAAATAATA
*
32647 AATATAT-TT--TAAATAAGTAATA
1 AATATATATTAATAAATAAATAATA
32669 A
1 A
32670 TGAGTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 13 0.59
24 2 0.09
25 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AATATATATTAATAAATAAATAATA
Done.