Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006689.1 Corchorus capsularis cultivar CVL-1 contig06710, 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: 27422
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:1666 original size:14 final size:14
Alignment explanation
Indices: 1647--1675 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1637 TCTTGTGAGG
1647 AAACAAGTTTGAAA
1 AAACAAGTTTGAAA
1661 AAACAAGTTTGAAA
1 AAACAAGTTTGAAA
1675 A
1 A
1676 GTTAGGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
AAACAAGTTTGAAA
Found at i:3290 original size:16 final size:17
Alignment explanation
Indices: 3261--3298 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
3251 CTGGCAAAAT
3261 GAACCCGAAACCCGCCC
1 GAACCCGAAACCCGCCC
3278 GAACCCG-AACCCGCCC
1 GAACCCGAAACCCGCCC
*
3294 AAACC
1 GAACC
3299 AAAGTTGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (17 bp):
GAACCCGAAACCCGCCC
Found at i:14053 original size:143 final size:143
Alignment explanation
Indices: 13795--14078 Score: 541
Period size: 143 Copynumber: 2.0 Consensus size: 143
13785 GGCCATGTCT
*
13795 TTGACGATGTTGAAGCCGCAGATCTAGGAGAACTAGGTTGAAAACTTGAATTGGATGACTCGTCT
1 TTGACGATGTTGAAGCCGCAGATCTAGGAGAACTAGGTTGAAAACTTGAATTGGATGACTCCTCT
*
13860 TCTTGTTGTCGGCTTTGTGTCTCCTTCCTTAATTGAAATAGTGTTCTTTCAGGCTCAGGATTGAA
66 TCTTGTTGTCGGCTTTGTGTCTCCTTCCTTAATTGAAACAGTGTTCTTTCAGGCTCAGGATTGAA
13925 TTCTAAATCTTAA
131 TTCTAAATCTTAA
*
13938 TTGACGATGTTGAAGCCGCAGATCTAGGAGAACTAGGTTGAGAACTTGAATTGGATGACTCCTCT
1 TTGACGATGTTGAAGCCGCAGATCTAGGAGAACTAGGTTGAAAACTTGAATTGGATGACTCCTCT
14003 TCTTGTTGTCGGCTTTGTGTCTCCTTCCTTAATTGAAACAGTGTTCTTTCAGGCTCAGGATTGAA
66 TCTTGTTGTCGGCTTTGTGTCTCCTTCCTTAATTGAAACAGTGTTCTTTCAGGCTCAGGATTGAA
14068 TTCTAAATCTT
131 TTCTAAATCTT
14079 CAATACCACT
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
143 138 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.36
Consensus pattern (143 bp):
TTGACGATGTTGAAGCCGCAGATCTAGGAGAACTAGGTTGAAAACTTGAATTGGATGACTCCTCT
TCTTGTTGTCGGCTTTGTGTCTCCTTCCTTAATTGAAACAGTGTTCTTTCAGGCTCAGGATTGAA
TTCTAAATCTTAA
Found at i:19661 original size:18 final size:17
Alignment explanation
Indices: 19638--19673 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
19628 CTAGACCTAA
19638 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
19656 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
19673 A
1 A
19674 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:20310 original size:18 final size:19
Alignment explanation
Indices: 20265--20322 Score: 84
Period size: 18 Copynumber: 3.2 Consensus size: 19
20255 TTCTTGAAAT
**
20265 AATTCTTC-AATGGTCTTC
1 AATTCTTCAAATTATCTTC
20283 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATTATCTTC
20302 AATTC-TCAAATTATCTTC
1 AATTCTTCAAATTATCTTC
20320 AAT
1 AAT
20323 AAATCTTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 24 0.65
19 13 0.35
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATTATCTTC
Found at i:20808 original size:31 final size:31
Alignment explanation
Indices: 20734--20819 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 31
20724 GGCATGCCAC
* * * *
20734 GTGTCACTTGTTGGAACACGTGCCGTGACAT
1 GTGTCACTTTTTTGTACACGTGGCGTGACAT
* *
20765 GTGTCACATTTTTGTACACGTGGCGTGGCAT
1 GTGTCACTTTTTTGTACACGTGGCGTGACAT
20796 GTGTCACTTTTTTGTACACGTGGC
1 GTGTCACTTTTTTGTACACGTGGC
20820 ATGCCACGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (31 bp):
GTGTCACTTTTTTGTACACGTGGCGTGACAT
Found at i:22840 original size:18 final size:17
Alignment explanation
Indices: 22817--22852 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
22807 CTAGACCTAA
22817 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
22835 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
22852 A
1 A
22853 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:23489 original size:18 final size:19
Alignment explanation
Indices: 23444--23501 Score: 84
Period size: 18 Copynumber: 3.2 Consensus size: 19
23434 TTCTTGAAAT
**
23444 AATTCTTC-AATGGTCTTC
1 AATTCTTCAAATTATCTTC
23462 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATTATCTTC
23481 AATTC-TCAAATTATCTTC
1 AATTCTTCAAATTATCTTC
23499 AAT
1 AAT
23502 AAATCTTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 24 0.65
19 13 0.35
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATTATCTTC
Found at i:23908 original size:31 final size:31
Alignment explanation
Indices: 23873--23973 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 31
23863 GTGCACATGA
*
23873 CATGCCACATGTCACATTTTGAAACATGTGG
1 CATGCCACATGTCACATTTTGAAACACGTGG
* * *
23904 CATGCCACGTGTCACTTTTTGGAACACGTGG
1 CATGCCACATGTCACATTTTGAAACACGTGG
* * ** * *
23935 CGTGACATGTGTCACTTTTTTG-TACACGTGG
1 CATGCCACATGTCAC-ATTTTGAAACACGTGG
23966 CATGCCAC
1 CATGCCAC
23974 GTCGGACACC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 52 0.90
32 6 0.10
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.31
Consensus pattern (31 bp):
CATGCCACATGTCACATTTTGAAACACGTGG
Found at i:26109 original size:31 final size:31
Alignment explanation
Indices: 26071--26173 Score: 188
Period size: 31 Copynumber: 3.3 Consensus size: 31
26061 AGAAAAGTGA
26071 GGTTACTAACCTCGAAGTGCTCATGATTAGG
1 GGTTACTAACCTCGAAGTGCTCATGATTAGG
26102 GGTTACTAACCTCGAAGTGCTCATGATTAGG
1 GGTTACTAACCTCGAAGTGCTCATGATTAGG
* *
26133 GGTTACTAACCTTGAAGTGCTCATGATTAGT
1 GGTTACTAACCTCGAAGTGCTCATGATTAGG
26164 GGTTACTAAC
1 GGTTACTAAC
26174 ACCCTTTATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (31 bp):
GGTTACTAACCTCGAAGTGCTCATGATTAGG
Found at i:26702 original size:21 final size:22
Alignment explanation
Indices: 26678--26721 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
26668 TGAAAAATTC
26678 AAAATTTT-GCAAAATTTT-TGA
1 AAAATTTTCG-AAAATTTTATGA
26699 AAAATTTTCGAAAATTTTATGA
1 AAAATTTTCGAAAATTTTATGA
26721 A
1 A
26722 TTTCTATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (22 bp):
AAAATTTTCGAAAATTTTATGA
Done.