Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023756.1 Corchorus olitorius cultivar O-4 contig23789, 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: 23687
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:6240 original size:15 final size:16
Alignment explanation
Indices: 6220--6256 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
6210 AGAGGTTGAA
6220 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
*
6235 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
6251 AGAAAA
1 AGAAAA
6257 TAAAACAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.65, C:0.11, G:0.08, T:0.16
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:9597 original size:21 final size:21
Alignment explanation
Indices: 9549--9598 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
9539 GGAATGGCGA
*
9549 TGGCACAGGCATAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
9570 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
9591 TGGCACGG
1 TGGCACGG
9599 TGAATGGCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Found at i:12890 original size:19 final size:19
Alignment explanation
Indices: 12866--12904 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12856 ACGCGGAAAC
12866 AATTTTTTTTTTCGACGCA
1 AATTTTTTTTTTCGACGCA
*
12885 AATTTTTTTTTTTGACGCA
1 AATTTTTTTTTTCGACGCA
12904 A
1 A
12905 GACTCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (19 bp):
AATTTTTTTTTTCGACGCA
Found at i:13325 original size:15 final size:16
Alignment explanation
Indices: 13305--13344 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
13295 AGAGGTTGAA
13305 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
*
13320 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
13336 AGAAAACAA
1 AGAAAACAA
13345 AACAAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:14753 original size:17 final size:18
Alignment explanation
Indices: 14731--14769 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
14721 CTCTTGAAAT
14731 AAATCTTC-TAAGTCTTC
1 AAATCTTCATAAGTCTTC
14748 AAATCTTCAAATAAGTCTTC
1 AAATCTTC--ATAAGTCTTC
14768 AA
1 AA
14770 TGAGTCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
20 11 0.58
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (18 bp):
AAATCTTCATAAGTCTTC
Found at i:14754 original size:29 final size:30
Alignment explanation
Indices: 14722--14781 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
14712 CAATTCTTCC
*
14722 TCTTGAAATAAATCTTC-TAAGTCTTCAAA
1 TCTTCAAATAAATCTTCATAAGTCTTCAAA
* *
14751 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAATCTTC-ATAAGTCTTCAAA
14782 CACGAACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.58
31 11 0.42
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (30 bp):
TCTTCAAATAAATCTTCATAAGTCTTCAAA
Found at i:16470 original size:31 final size:31
Alignment explanation
Indices: 16434--16511 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
16424 AGGGCTAAAT
*
16434 GCTCAATTTGGTCCTAAATCTTTGAGCGAG-C
1 GCTCAATTTGGTCCTAAATCTTTGAACG-GTC
16465 GCTCAATTTGGTCCTAAATCTTTGAACGGTC
1 GCTCAATTTGGTCCTAAATCTTTGAACGGTC
*
16496 GCTCAATTTAGTCCTA
1 GCTCAATTTGGTCCTA
16512 TTTCTGACGG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 1 0.02
31 43 0.98
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (31 bp):
GCTCAATTTGGTCCTAAATCTTTGAACGGTC
Found at i:19522 original size:42 final size:43
Alignment explanation
Indices: 19476--19563 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
19466 GATTTATCAT
19476 TATCCATGTGGC-TTTTTTTCACTTTAGAAATAGCCACGTGGC
1 TATCCATGTGGCTTTTTTTTCACTTTAGAAATAGCCACGTGGC
*
19518 TATCCATGTGGCTTTTTTTTTACTTTAGAAATAGCCACGTGGC
1 TATCCATGTGGCTTTTTTTTCACTTTAGAAATAGCCACGTGGC
19561 TAT
1 TAT
19564 TTTATTGAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 12 0.27
43 32 0.73
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (43 bp):
TATCCATGTGGCTTTTTTTTCACTTTAGAAATAGCCACGTGGC
Found at i:19725 original size:31 final size:30
Alignment explanation
Indices: 19644--19742 Score: 137
Period size: 31 Copynumber: 3.3 Consensus size: 30
19634 AATAGGATTG
*
19644 AATTGAGCGACCACTCAAAGGTTTAGGACCA
1 AATTGAGCG-CCGCTCAAAGGTTTAGGACCA
* * *
19675 AATTAAGC-ACGTTCAAAGGTTTAGGACCA
1 AATTGAGCGCCGCTCAAAGGTTTAGGACCA
19704 AATTGAGCGCTCGCTCAAAGGTTTAGGACCA
1 AATTGAGCGC-CGCTCAAAGGTTTAGGACCA
19735 AATTGAGC
1 AATTGAGC
19743 ATTTAGCCCT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
29 25 0.42
31 34 0.58
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.22
Consensus pattern (30 bp):
AATTGAGCGCCGCTCAAAGGTTTAGGACCA
Found at i:21993 original size:13 final size:13
Alignment explanation
Indices: 21975--22000 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21965 AAGGTAACAA
21975 CAAAAATCATCAC
1 CAAAAATCATCAC
21988 CAAAAATCATCAC
1 CAAAAATCATCAC
22001 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Done.