Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011976.1 Corchorus capsularis cultivar CVL-1 contig11997, 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: 39266
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:6167 original size:78 final size:77
Alignment explanation
Indices: 6085--6323 Score: 359
Period size: 78 Copynumber: 3.2 Consensus size: 77
6075 TTTTTTTAAC
*
6085 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
6150 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
6163 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
6228 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
6241 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
6299 TTTTTAGTTGAG
66 TTTTTAGTTGAG
6311 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
6324 ACCTAAACAA
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
70 56 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 88 0.57
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:6174 original size:70 final size:71
Alignment explanation
Indices: 6091--6323 Score: 310
Period size: 70 Copynumber: 3.2 Consensus size: 71
6081 TAACTAAAAT
* *
6091 AGTAAAA-TTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
6155 TAGTTG
66 TAGTTG
*
6161 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-ACT---A--GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
6226 GAGTTTTTAGTTG
59 GAGTTTTTAGTTG
* * * * *
6239 AGTAAAA-TAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
6303 TAGTTG
66 TAGTTG
6309 AGTAAAACTA-TAAAA
1 AGTAAAACTAGTAAAA
6324 ACCTAAACAA
Statistics
Matches: 147, Mismatches: 7, Indels: 18
0.85 0.04 0.10
Matches are distributed among these distances:
70 71 0.48
71 5 0.03
72 2 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 3 0.02
78 63 0.43
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (71 bp):
AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
TAGTTG
Found at i:7683 original size:21 final size:21
Alignment explanation
Indices: 7659--7703 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
7649 ACATCCCTTT
7659 AATTTGAGCC-CAATTGCATTG
1 AATTTGAGCCACAATTGCA-TG
* *
7680 AATTTGATCCACAATTTCATG
1 AATTTGAGCCACAATTGCATG
7701 AAT
1 AAT
7704 GTGGGAAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (21 bp):
AATTTGAGCCACAATTGCATG
Found at i:22102 original size:17 final size:16
Alignment explanation
Indices: 22050--22098 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
22040 CACCCCCCAA
*
22050 ATCACTGGTGATCTAAG
1 ATCACCGGTGATC-AAG
*
22067 ATCACCAGTGATGCAAG
1 ATCACCGGTGAT-CAAG
22084 ATCACCGGTGATCAA
1 ATCACCGGTGATCAA
22099 AGATTACATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 3 0.11
17 24 0.86
18 1 0.04
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
ATCACCGGTGATCAAG
Found at i:27597 original size:19 final size:18
Alignment explanation
Indices: 27573--27610 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
27563 AAGCCCTACA
27573 CAGCACAACCAGTCTGCAG
1 CAGCACAACCAG-CTGCAG
*
27592 CAGCACAGCCAGCTGCAG
1 CAGCACAACCAGCTGCAG
27610 C
1 C
27611 GCCTGCTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.29, C:0.39, G:0.24, T:0.08
Consensus pattern (18 bp):
CAGCACAACCAGCTGCAG
Found at i:35318 original size:10 final size:10
Alignment explanation
Indices: 35290--35319 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
35280 TAGTAGCAAA
35290 AAAAAAAAAG
1 AAAAAAAAAG
*
35300 AAAAGAAAAG
1 AAAAAAAAAG
35310 AAAAAAAAAG
1 AAAAAAAAAG
35320 CAGTCACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:37546 original size:5 final size:5
Alignment explanation
Indices: 37538--37572 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
37528 AGACCTTCCC
37538 TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA
1 TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA
37573 GTGATATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
TTCTA
Found at i:38484 original size:51 final size:49
Alignment explanation
Indices: 38420--38559 Score: 217
Period size: 51 Copynumber: 2.8 Consensus size: 49
38410 AACTAAGAAA
38420 ATAGTCTTACAAACCAACATAGCAACATTAAAACATAAACTAACAAATT
1 ATAGTCTTACAAACCAACATAGCAACATTAAAACATAAACTAACAAATT
* *
38469 ATGTAGTCTTCCAAACCAACATAGCAACATTAACACATAAACTAACAAATT
1 A--TAGTCTTACAAACCAACATAGCAACATTAAAACATAAACTAACAAATT
* * *
38520 ATAGTCTTACAAACCAACGTATCAACCTTAAAACATAAAC
1 ATAGTCTTACAAACCAACATAGCAACATTAAAACATAAAC
38560 ACTACAACAG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
49 35 0.43
51 47 0.57
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (49 bp):
ATAGTCTTACAAACCAACATAGCAACATTAAAACATAAACTAACAAATT
Done.