Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008746.1 Corchorus capsularis cultivar CVL-1 contig08767, 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: 49697
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:476 original size:16 final size:16
Alignment explanation
Indices: 452--482 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
442 ATCAAAACCG
452 TTTTATTTATTTTTTA
1 TTTTATTTATTTTTTA
*
468 TTTTTTTTATTTTTT
1 TTTTATTTATTTTTT
483 TCTCTCCCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTATTTATTTTTTA
Found at i:9443 original size:16 final size:17
Alignment explanation
Indices: 9417--9528 Score: 94
Period size: 16 Copynumber: 7.0 Consensus size: 17
9407 AACCCGTCTG
9417 AACCT-GAATCCGAAAA
1 AACCTCGAATCCGAAAA
*
9433 AATC-CGAATCCGAAAA
1 AACCTCGAATCCGAAAA
* *
9449 AA-CACGAACCCG-AAA
1 AACCTCGAATCCGAAAA
* *
9464 AAGCTCAAATCCGAAAA
1 AACCTCGAATCCGAAAA
*
9481 AACC-CGAAGCCG-AAA
1 AACCTCGAATCCGAAAA
* * *
9496 AAGCTCAAACCCGAAAA
1 AACCTCGAATCCGAAAA
9513 AACC-CGAATCCGAAAA
1 AACCTCGAATCCGAAAA
9529 TTTATGAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
15 12 0.16
16 52 0.68
17 12 0.16
ACGTcount: A:0.51, C:0.29, G:0.13, T:0.07
Consensus pattern (17 bp):
AACCTCGAATCCGAAAA
Found at i:9475 original size:32 final size:32
Alignment explanation
Indices: 9439--9528 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
9429 AAAAAATCCG
*
9439 AATCCGAAAAAACACGAACCCGAAAAAGCTCA
1 AATCCGAAAAAACCCGAACCCGAAAAAGCTCA
*
9471 AATCCGAAAAAACCCGAAGCCGAAAAAGCTCA
1 AATCCGAAAAAACCCGAACCCGAAAAAGCTCA
* *
9503 AACCCGAAAAAACCCGAATCCGAAAA
1 AATCCGAAAAAACCCGAACCCGAAAA
9529 TTTATGAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.52, C:0.29, G:0.13, T:0.06
Consensus pattern (32 bp):
AATCCGAAAAAACCCGAACCCGAAAAAGCTCA
Found at i:9478 original size:48 final size:48
Alignment explanation
Indices: 9423--9528 Score: 140
Period size: 48 Copynumber: 2.2 Consensus size: 48
9413 TCTGAACCTG
* * * * *
9423 AATCCGAAAAAATCCGAATCCGAAAAAACACGAACCCGAAAAAGCTCA
1 AATCCGAAAAAACCCGAAGCCGAAAAAACACAAACCCGAAAAAACCCA
* * *
9471 AATCCGAAAAAACCCGAAGCCGAAAAAGCTCAAACCCGAAAAAACCCG
1 AATCCGAAAAAACCCGAAGCCGAAAAAACACAAACCCGAAAAAACCCA
9519 AATCCGAAAA
1 AATCCGAAAA
9529 TTTATGAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.52, C:0.28, G:0.13, T:0.07
Consensus pattern (48 bp):
AATCCGAAAAAACCCGAAGCCGAAAAAACACAAACCCGAAAAAACCCA
Found at i:9690 original size:26 final size:25
Alignment explanation
Indices: 9661--9719 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 25
9651 ACAGAACCCG
*
9661 AACCCGAATTAA-TCTGATCCAAATT
1 AACCCGAATTAACT-TGACCCAAATT
9686 CAACCCGAATTAACTTGACCCAAATT
1 -AACCCGAATTAACTTGACCCAAATT
9712 AACCCGAA
1 AACCCGAA
9720 CCCGAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 8 0.26
26 22 0.71
27 1 0.03
ACGTcount: A:0.41, C:0.29, G:0.08, T:0.22
Consensus pattern (25 bp):
AACCCGAATTAACTTGACCCAAATT
Found at i:9691 original size:32 final size:30
Alignment explanation
Indices: 9655--9786 Score: 112
Period size: 32 Copynumber: 4.4 Consensus size: 30
9645 ATCCAAACAG
9655 AACCCGAACCCGAATTAATCTGATCCAAATT
1 AACCCGAACCCGAATTAA-CTGATCCAAATT
*
9686 ----C-AACCCGAATTAACTTGACCCAAATT
1 AACCCGAACCCGAATTAAC-TGATCCAAATT
* *
9712 AACCCGAACCCGAATTAACTTATCTTAAAATT
1 AACCCGAACCCGAATTAACTGATC--CAAATT
* * *
9744 AACCCGAAACTGAATTAACCTAATCCAAATT
1 AACCCGAACCCGAATTAA-CTGATCCAAATT
*
9775 CAATCCGAACCC
1 -AACCCGAACCC
9787 AAGTTAAACT
Statistics
Matches: 80, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
25 1 0.01
26 22 0.28
27 1 0.01
30 4 0.05
31 18 0.22
32 29 0.36
33 5 0.06
ACGTcount: A:0.40, C:0.30, G:0.08, T:0.23
Consensus pattern (30 bp):
AACCCGAACCCGAATTAACTGATCCAAATT
Found at i:21503 original size:17 final size:17
Alignment explanation
Indices: 21481--21514 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21471 CTCCACTAAC
21481 AGAACTAATATCATCAT
1 AGAACTAATATCATCAT
21498 AGAACTAATATCATCAT
1 AGAACTAATATCATCAT
21515 GCAACAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (17 bp):
AGAACTAATATCATCAT
Found at i:27270 original size:7 final size:7
Alignment explanation
Indices: 27258--27294 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
27248 GCATACCAGG
27258 GATGAGA
1 GATGAGA
27265 GATGAGA
1 GATGAGA
27272 GATGAGA
1 GATGAGA
27279 GATGAGA
1 GATGAGA
27286 GATGAGA
1 GATGAGA
27293 GA
1 GA
27295 GGCGGTGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (7 bp):
GATGAGA
Found at i:30131 original size:2 final size:2
Alignment explanation
Indices: 30124--30155 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30114 AAGATGATAC
30124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30156 CCTTACAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32230 original size:159 final size:159
Alignment explanation
Indices: 31941--32560 Score: 974
Period size: 159 Copynumber: 3.9 Consensus size: 159
31931 CACTGTTTAT
* * *
31941 AGCAACTGGCTCAAAGGAAACTTCTGGGTACTGTACAGCAAGAGGCTGATCACTACTAAGAGATT
1 AGCAATTGGCTCAAAGGAAACTTCTGGGTACTGTACAACAAGAGGCTGATCACCACTAAGAGATT
* *
32006 CACCAATCGGTTTCTTTCTAGATCTACCTTTTGGCCTCTTAA-GCTGATCTAGTTGAGATTCCTC
66 CACCAATTGGTTTCTTTCTAGGTCTACCTTTTGGCCTCTTAACG-TGATCTAGTTGAGATTCCTC
*
32070 AATTGGCTTATTTCCAGGAGCAGTGTCTAC
130 AATTGGCTTCTTTCCAGGAGCAGTGTCTAC
* * * **
32100 AGCAATTGGCTCAAGGGAAACTTCAGTGTACTGTACAACAAGAGGCTGATCACCACTAAGAGAAA
1 AGCAATTGGCTCAAAGGAAACTTCTGGGTACTGTACAACAAGAGGCTGATCACCACTAAGAGATT
* *
32165 CACCAATTGGTTTCTTTCTAGGTCTCCCTTTTGGCCTTTTAACGTGATCTAGTTGAGATTCCTCA
66 CACCAATTGGTTTCTTTCTAGGTCTACCTTTTGGCCTCTTAACGTGATCTAGTTGAGATTCCTCA
32230 ATTGGCTTCTTTCCAGGAGCAGTGTCTAC
131 ATTGGCTTCTTTCCAGGAGCAGTGTCTAC
* * * *
32259 AGCGATTGGCTCAACGGAAACTTCTGTGTAGTGTACAACAAGAGGCTGATCACCACTAAGAGATT
1 AGCAATTGGCTCAAAGGAAACTTCTGGGTACTGTACAACAAGAGGCTGATCACCACTAAGAGATT
*
32324 CACCAATTGGTTTCTTTCTAGGTCTACCTTTTGGCCTCTTAACGAGATCTAGTTGAGATTCCTCA
66 CACCAATTGGTTTCTTTCTAGGTCTACCTTTTGGCCTCTTAACGTGATCTAGTTGAGATTCCTCA
* *
32389 GTTGGCTTCTTTCCAGGAGCACTGTCTAC
131 ATTGGCTTCTTTCCAGGAGCAGTGTCTAC
* * * *
32418 AG-AGAGTGGCTCAAAGGAAACTTCTGGGTACTGTATAGCAAGAGGCTGATCGCCACTAAGAGAT
1 AGCA-ATTGGCTCAAAGGAAACTTCTGGGTACTGTACAACAAGAGGCTGATCACCACTAAGAGAT
* *
32482 TCACCAATTGGTTTCTTTCTAGGTCTACCTTTGGGCCTCTTAACCTGATCTAGTTGAGATTCCTC
65 TCACCAATTGGTTTCTTTCTAGGTCTACCTTTTGGCCTCTTAACGTGATCTAGTTGAGATTCCTC
32547 AATTGGCTTCTTTC
130 AATTGGCTTCTTTC
32561 TAGGTCTTCC
Statistics
Matches: 423, Mismatches: 36, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
159 422 1.00
160 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (159 bp):
AGCAATTGGCTCAAAGGAAACTTCTGGGTACTGTACAACAAGAGGCTGATCACCACTAAGAGATT
CACCAATTGGTTTCTTTCTAGGTCTACCTTTTGGCCTCTTAACGTGATCTAGTTGAGATTCCTCA
ATTGGCTTCTTTCCAGGAGCAGTGTCTAC
Found at i:36354 original size:21 final size:21
Alignment explanation
Indices: 36330--36373 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
36320 ATAAGGGCCC
36330 TAAAACACA-ATTTGAATAAAT
1 TAAAACACATATTT-AATAAAT
* *
36351 TAAAATACATATTTAGTAAAT
1 TAAAACACATATTTAATAAAT
36372 TA
1 TA
36374 TGACATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.34
Consensus pattern (21 bp):
TAAAACACATATTTAATAAAT
Found at i:36548 original size:20 final size:21
Alignment explanation
Indices: 36523--36564 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
36513 TCTTGGGTTC
36523 TACTCTCACG-GAATGTGAGT
1 TACTCTCACGCGAATGTGAGT
* *
36543 TACTCTCATGCGATTGTGAGT
1 TACTCTCACGCGAATGTGAGT
36564 T
1 T
36565 TTCTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TACTCTCACGCGAATGTGAGT
Found at i:37431 original size:14 final size:14
Alignment explanation
Indices: 37412--37441 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
37402 GGTGATTCAA
37412 GTGTTTATTAAAAG
1 GTGTTTATTAAAAG
37426 GTGTTTATTAAAAG
1 GTGTTTATTAAAAG
37440 GT
1 GT
37442 AATTTCATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (14 bp):
GTGTTTATTAAAAG
Found at i:38375 original size:20 final size:20
Alignment explanation
Indices: 38350--38389 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
38340 AAATTGGTCC
38350 TTCAAGTAAAAAAATATGTA
1 TTCAAGTAAAAAAATATGTA
38370 TTCAAGTAAAAAAATATGTA
1 TTCAAGTAAAAAAATATGTA
38390 ATTTAGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (20 bp):
TTCAAGTAAAAAAATATGTA
Found at i:48461 original size:27 final size:27
Alignment explanation
Indices: 48425--48490 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
48415 CTATTTTTTC
*
48425 AAATATATTTTTAAAT-TGTCATTATTA
1 AAATATA-TTTTAAATATGCCATTATTA
*
48452 AAATATATTTTAACTATGCCATTATTA
1 AAATATATTTTAAATATGCCATTATTA
48479 AAATATAATTTT
1 AAATAT-ATTTT
48491 GTGTGCGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 7 0.20
27 23 0.66
28 5 0.14
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (27 bp):
AAATATATTTTAAATATGCCATTATTA
Done.