Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014277.1 Corchorus capsularis cultivar CVL-1 contig14298, 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: 39815
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:177 original size:20 final size:20
Alignment explanation
Indices: 152--190 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
142 TATAAAAAGG
152 GGGGGCGGTATTTAGCAAAA
1 GGGGGCGGTATTTAGCAAAA
*
172 GGGGGCGGTGTTTAGCAAA
1 GGGGGCGGTATTTAGCAAA
191 CCCCTATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.10, G:0.44, T:0.21
Consensus pattern (20 bp):
GGGGGCGGTATTTAGCAAAA
Found at i:21069 original size:13 final size:13
Alignment explanation
Indices: 21053--21079 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21043 TCAATTAGTG
21053 TAAGTATTTAGGA
1 TAAGTATTTAGGA
21066 TAAGTATTTAGGA
1 TAAGTATTTAGGA
21079 T
1 T
21080 GCTAATGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
TAAGTATTTAGGA
Found at i:22674 original size:2 final size:2
Alignment explanation
Indices: 22667--22693 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22657 AAGAAAAATC
22667 TA 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 TA T
22694 GTTGTAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23939 original size:15 final size:15
Alignment explanation
Indices: 23921--23961 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
23911 TCGATTATTA
23921 ATAAAAAATAAAATT
1 ATAAAAAATAAAATT
23936 ATAAAAAGA-AAAATT
1 ATAAAAA-ATAAAATT
23951 ATAAAAGAATA
1 ATAAAA-AATA
23962 TATTAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (15 bp):
ATAAAAAATAAAATT
Found at i:24542 original size:2 final size:2
Alignment explanation
Indices: 24530--24559 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
24520 CATCTATACT
24530 TA TA T- 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 TA TA TA T
24560 TTCTTTCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:31318 original size:17 final size:18
Alignment explanation
Indices: 31290--31326 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
31280 TATACATTAC
31290 ATTAGATGGAAAGGAAAG
1 ATTAGATGGAAAGGAAAG
31308 ATTAG-TGGAAAGGAAAG
1 ATTAGATGGAAAGGAAAG
31325 AT
1 AT
31327 GGAATCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.32, T:0.19
Consensus pattern (18 bp):
ATTAGATGGAAAGGAAAG
Found at i:31342 original size:24 final size:24
Alignment explanation
Indices: 31313--31359 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
31303 GAAAGATTAG
31313 TGGAAAGGAAAGATGGAATCATAA
1 TGGAAAGGAAAGATGGAATCATAA
* *
31337 TGGAAAGGTATGATGGAATCATA
1 TGGAAAGGAAAGATGGAATCATA
31360 GTTGAGTCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.04, G:0.30, T:0.21
Consensus pattern (24 bp):
TGGAAAGGAAAGATGGAATCATAA
Found at i:31929 original size:87 final size:85
Alignment explanation
Indices: 31819--31991 Score: 310
Period size: 87 Copynumber: 2.0 Consensus size: 85
31809 AAATCATATA
**
31819 ACCTGTAGCTGTAGGTCCAAGTGTGAGTGAAGAGTAACCGGGCAAACATAATTTTTTTTGAAAAG
1 ACCTGTAGCTGTAGGTCCAAGTGTGAGTGAAGAGTAACCGGGCAAACATAA--AATTTTGAAAAG
31884 AATGGCGAATTGAAAGCGCTTG
64 AATGGCGAATTGAAAGCGCTTG
31906 ACCTGTAGCTGTAGGTCCAAGTGTGAGTGAAGAGTAACCGGGCAAACATAAAATTTTGAAAAGAA
1 ACCTGTAGCTGTAGGTCCAAGTGTGAGTGAAGAGTAACCGGGCAAACATAAAATTTTGAAAAGAA
31971 TGGCGAATTGAAAGCGCTTG
66 TGGCGAATTGAAAGCGCTTG
31991 A
1 A
31992 TGGGTGGTGT
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
85 33 0.39
87 51 0.61
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (85 bp):
ACCTGTAGCTGTAGGTCCAAGTGTGAGTGAAGAGTAACCGGGCAAACATAAAATTTTGAAAAGAA
TGGCGAATTGAAAGCGCTTG
Found at i:33311 original size:132 final size:131
Alignment explanation
Indices: 33115--33381 Score: 363
Period size: 132 Copynumber: 2.0 Consensus size: 131
33105 GACTTCTATT
* * *
33115 AGTCGTTGCAAATTCATAGACTTTTCGCAACGACTTCTGCTAGTCATTGTTTAATATATTTTACA
1 AGTCGTTGCAAACTCATAAACTTTTCGCAACGACTTCTGCTAGTCATTGCTTAATATATTTTACA
* * * * *
33180 AATTGATTTTTGCAGCAACCTTGAATGTCGCTACAAAAAACATGATGACTTTTGAAACGACAGAT
66 AATTGATTTTCGCAGCAACCTTGAAAGTCACTACAAAAAACATAATGACTTTTGAAACCACA-AT
33245 TA
130 TA
* * * * * **
33247 AGTCGTTGCGAACTCTTAAACTTTTCGCAATGACTTTTGTTAGTGGTTGCTTAATATATTTTACA
1 AGTCGTTGCAAACTCATAAACTTTTCGCAACGACTTCTGCTAGTCATTGCTTAATATATTTTACA
* * *
33312 AATTGATTTTCGCAGCGACCTTGAAAGTCACTACAAAAAACATAATTACTTTTGAAGCCACAATT
66 AATTGATTTTCGCAGCAACCTTGAAAGTCACTACAAAAAACATAATGACTTTTGAAACCACAATT
33377 A
131 A
33378 AGTC
1 AGTC
33382 ACAACGACAA
Statistics
Matches: 117, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
131 8 0.07
132 109 0.93
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (131 bp):
AGTCGTTGCAAACTCATAAACTTTTCGCAACGACTTCTGCTAGTCATTGCTTAATATATTTTACA
AATTGATTTTCGCAGCAACCTTGAAAGTCACTACAAAAAACATAATGACTTTTGAAACCACAATT
A
Found at i:38552 original size:17 final size:17
Alignment explanation
Indices: 38530--38582 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
38520 TACTTTTGAC
38530 ATTTTTTGCATCTCAAT
1 ATTTTTTGCATCTCAAT
* ** *
38547 A-TTTTTGCATTTTGAC
1 ATTTTTTGCATCTCAAT
38563 ATTTTTTGCATCTCAAT
1 ATTTTTTGCATCTCAAT
38580 ATT
1 ATT
38583 CTTGCATTTC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.55
Consensus pattern (17 bp):
ATTTTTTGCATCTCAAT
Found at i:38553 original size:16 final size:16
Alignment explanation
Indices: 38532--38589 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
38522 CTTTTGACAT
38532 TTTTTGCATCTCAATA
1 TTTTTGCATCTCAATA
* *
38548 TTTTTGCATTTTGACAT-
1 TTTTTGCA-TCTCA-ATA
38565 TTTTTGCATCTCAATA
1 TTTTTGCATCTCAATA
*
38581 TTCTTGCAT
1 TTTTTGCAT
38590 TTCAGTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 2 0.06
16 19 0.56
17 11 0.32
18 2 0.06
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (16 bp):
TTTTTGCATCTCAATA
Found at i:38565 original size:33 final size:33
Alignment explanation
Indices: 38523--38591 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
38513 TGATGTGTAC
*
38523 TTTTGACATTTTTTGCATCTCAATATTTTTGCA
1 TTTTGACATTTTTTGCATCTCAATATTCTTGCA
38556 TTTTGACATTTTTTGCATCTCAATATTCTTGCA
1 TTTTGACATTTTTTGCATCTCAATATTCTTGCA
38589 TTT
1 TTT
38592 CAGTCACATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (33 bp):
TTTTGACATTTTTTGCATCTCAATATTCTTGCA
Done.