Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014136.1 Corchorus capsularis cultivar CVL-1 contig14157, 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: 24759
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:109 original size:49 final size:48
Alignment explanation
Indices: 42--621 Score: 477
Period size: 49 Copynumber: 11.9 Consensus size: 48
32 CAATTTTCGG
* * * *
42 TTTTCACCTGCTACTTTCCAAAATGCCCTTCCCGGATGGAATGCATTTA
1 TTTT-ACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
*
91 TTGTTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCGCTGGT-
1 TT-TTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCACT--TA
* *
141 TTTTACCTG-T-TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCTC-TA
1 TTTTACCTGCTATTTTCC-AAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * * * *
187 GTTTTGCCCGCT-TTTTCTTAAAATGCCCTTCCCAGACGGAAGACATTTA
1 -TTTTACCTGCTATTTTC-CAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * **
236 TTTTTGCTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACCTGC
1 -TTTTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCA-CTTA
* *
286 TTTTATCTGCTA-TTCCCAAAATGCCCTTCCCGGACGGAAGGCACCTGT-
1 TTTTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCA-CT-TA
* * * * *
334 TTTTATCTGCTATTTCCCAAAATGCCCTTCCTGGACGGAAGGTACTTGT
1 TTTTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCACTT-A
* * * *
383 TTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGTACTTG
1 TTTTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * * *
431 TTTTCATCTGTTA-TTTCCCAAATGCCCTTCACGGACGGAAGCCACTTA
1 TTTT-ACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * *
479 TTTT-CGCTTG-TTTTTTCCTAAAATGCCCTTCCCGGACGGAAGGCAGTAA
1 TTTTAC-C-TGCTATTTTCC-AAAATGCCCTTCCCGGACGGAAGGCACTTA
* *
528 TCTTTACCTGCT-TTGTCTCAAAATGCCCTTCCCGGACGG-AGAGCACTAA
1 T-TTTACCTGCTATTTTC-CAAAATGCCCTTCCCGGACGGAAG-GCACTTA
* * * * *
577 TTTTTACCTG-T-TTTCCCTAAAACGCCTTTCCTGGATGGAAGGCAC
1 -TTTTACCTGCTATTTTCC-AAAATGCCCTTCCCGGACGGAAGGCAC
622 CATCCTCTTA
Statistics
Matches: 448, Mismatches: 55, Indels: 57
0.80 0.10 0.10
Matches are distributed among these distances:
45 1 0.00
47 17 0.04
48 172 0.38
49 240 0.54
50 16 0.04
51 2 0.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (48 bp):
TTTTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
Found at i:269 original size:97 final size:96
Alignment explanation
Indices: 50--621 Score: 436
Period size: 97 Copynumber: 5.9 Consensus size: 96
40 GGTTTTCACC
* * *
50 TGCTACTTT-CCAAAATGCCCTTCCCGGATGGAATGCATTTA-TTGTTACCTGCTATTTT-CCAA
1 TGCTA-TTTCCCAAAATGCCCTTCCCGGACGGAAGGC-TCTAGTT-TTACCTGCT-TTTTCCCAA
* ** *
112 AATGCCCTTCCCGGACGGAAGGCGCTGGTTTTTACC
62 AATGCCCTTCCCGGACGGAAGGCACTTATTTTT-CT
* * * * * **
148 TG-TTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCTCTAGTTTTGCCCGCTTTTTCTTAAAATG
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCTCTAGTTTTACCTGCTTTTTCCCAAAATG
* * *
212 CCCTTCCCAGACGGAAGACATTTATTTTTGCT
66 CCCTTCCCGGACGGAAGGCACTTATTTTT-CT
* * *
244 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACCT-GCTTTTATCTGC-TATTCCCAAAA
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGC-TCTAG-TTTTACCTGCTTTTTCCCAAAA
* * *
307 TGCCCTTCCCGGACGGAAGGCACCTGTTTTTAT
64 TGCCCTTCCCGGACGGAAGGCACTTATTTTTCT
* * * *
340 CTGCTATTTCCCAAAATGCCCTTCCTGGACGGAAGG-TACTTGTTTTTATCTGCTATTTCCCAAA
1 -TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCT-CTAG-TTTTACCTGCTTTTTCCCAAA
* *
404 ATGCCCTTCCCGGACGGAAGGTACTT-GTTTTCAT
63 ATGCCCTTCCCGGACGGAAGGCACTTATTTTTC-T
* * * * * *
438 CTGTTATTTCCC-AAATGCCCTTCACGGACGGAAGCCACTTA-TTTT-CGCTTGTTTTTTCCTAA
1 -TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCTC-TAGTTTTAC-C-TGCTTTTTCCCAA
* * * *
500 AATGCCCTTCCCGGACGGAAGGCAGTAATCTTTACC
62 AATGCCCTTCCCGGACGGAAGGCACTTAT-TTTTCT
* * *
536 TGCT-TTGTCTCAAAATGCCCTTCCCGGACGG-AGAGCACTAATTTTTACCTG--TTTTCCCTAA
1 TGCTATT-TCCCAAAATGCCCTTCCCGGACGGAAG-GCTCT-AGTTTTACCTGCTTTTTCCC-AA
* * * *
597 AACGCCTTTCCTGGATGGAAGGCAC
62 AATGCCCTTCCCGGACGGAAGGCAC
622 CATCCTCTTA
Statistics
Matches: 381, Mismatches: 69, Indels: 49
0.76 0.14 0.10
Matches are distributed among these distances:
95 4 0.01
96 61 0.16
97 226 0.59
98 80 0.21
99 9 0.02
100 1 0.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.33
Consensus pattern (96 bp):
TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCTCTAGTTTTACCTGCTTTTTCCCAAAATG
CCCTTCCCGGACGGAAGGCACTTATTTTTCT
Found at i:617 original size:146 final size:143
Alignment explanation
Indices: 56--621 Score: 570
Period size: 146 Copynumber: 3.9 Consensus size: 143
46 CACCTGCTAC
* * * *
56 TTTCC-AAAATGCCCTTCCCGGATGGAATGCATTTATTGTTACCTGCTATTTTCCAAAATGCCCT
1 TTTCCTAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGCTATTTCCCAAAATGCCCT
* * * *
120 TCCCGGACGGAAGGCGCTGGTTTTTACCTGTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCTC
66 TCCCGGACGGAAGGCACT-GTTTTTACCTGCTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCAC
*
185 -TAGTTTTGCCCGCTT
130 TTA-TTTTG-CTGCTT
* * * * *
200 TTTCTTAAAATGCCCTTCCCAGACGGAAGACATTTATTTTTGCTTGCTATTTCCCAAAATGCCCT
1 TTTCCTAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGCTATTTCCCAAAATGCCCT
* * * *
265 TCCCGGACGGAAGGCACCTGCTTTTATCTGCTATTCCCAAAATGCCCTTCCCGGACGGAAGGCAC
66 TCCCGGACGGAAGGCA-CTGTTTTTACCTGCTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCA-
* *
330 CTGT-TTTTATCTGCTA
129 CT-TATTTT-GCTGCTT
* * * * * *
346 TTTCCCAAAATGCCCTTCCTGGACGGAAGGTACTTGTTTTTATCTGCTATTTCCCAAAATGCCCT
1 TTTCCTAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGCTATTTCCCAAAATGCCCT
* * * * * * *
411 TCCCGGACGGAAGGTACTTGTTTTCATCTGTTATTTCCC-AAATGCCCTTCACGGACGGAAGCCA
66 TCCCGGACGGAAGGCAC-TGTTTTTACCTGCT-TTTCCCAAAACGCCCTTCCCGGACGGAAGGCA
*
475 CTTATTTTCGCTTGTTT
129 CTTATTTT-GC-TGCTT
* * * *
492 TTTCCTAAAATGCCCTTCCCGGACGGAAGGCAGTAATCTTTACCTGCT-TTGTCTCAAAATGCCC
1 TTTCCTAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGCTATT-TCCCAAAATGCCC
* * * *
556 TTCCCGGACGG-AGAGCACTAATTTTTACCTG-TTTTCCCTAAAACGCCTTTCCTGGATGGAAGG
65 TTCCCGGACGGAAG-GCACT-GTTTTTACCTGCTTTTCCC-AAAACGCCCTTCCCGGACGGAAGG
619 CAC
127 CAC
622 CATCCTCTTA
Statistics
Matches: 346, Mismatches: 61, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
144 11 0.03
145 118 0.34
146 211 0.61
147 5 0.01
148 1 0.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.33
Consensus pattern (143 bp):
TTTCCTAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGCTATTTCCCAAAATGCCCT
TCCCGGACGGAAGGCACTGTTTTTACCTGCTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACT
TATTTTGCTGCTT
Found at i:5382 original size:21 final size:21
Alignment explanation
Indices: 5358--5411 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5348 GAATTGAGTC
5358 AATTACTTAATTTAATTACCA
1 AATTACTTAATTTAATTACCA
* *
5379 AATTACTTAACTTAATTACTA
1 AATTACTTAATTTAATTACCA
* *
5400 ATTTTCTTAATT
1 AATTACTTAATT
5412 GCATCGAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTACTTAATTTAATTACCA
Found at i:5385 original size:65 final size:68
Alignment explanation
Indices: 5306--5432 Score: 170
Period size: 69 Copynumber: 1.9 Consensus size: 68
5296 GAGTTAAGTC
* *
5306 AATTACCAAGTTACTTAA-TT-TGA-TAATTTACTTAATTGCAACGAATTGAGTCAATTACTTAA
1 AATTACCAAATTACTTAACTTATGACTAATTTACTTAATTGCAACGAATTAAGTCAATTACTTAA
5368 TTT
66 TTT
* * * *
5371 AATTACCAAATTACTTAACTTAATTACTAATTTTCTTAATTGCATCGAATTAAGTTAATTAC
1 AATTACCAAATTACTTAACTT-ATGACTAATTTACTTAATTGCAACGAATTAAGTCAATTAC
5433 CAAATTACTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 17 0.33
66 2 0.04
68 2 0.04
69 31 0.60
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (68 bp):
AATTACCAAATTACTTAACTTATGACTAATTTACTTAATTGCAACGAATTAAGTCAATTACTTAA
TTT
Found at i:5435 original size:56 final size:54
Alignment explanation
Indices: 5364--5552 Score: 182
Period size: 56 Copynumber: 3.4 Consensus size: 54
5354 AGTCAATTAC
* * *
5364 TTAATTTAATTACCAAATTACTTAACTTAATTACTAATTTTCTTAATTGCATCGAA
1 TTAAGTTAATTACCAAATTACTTAA-TTAATTACTAATTTACTTAATTACA-CGAA
* * * *
5420 TTAAGTTAATTACCAAATTACTTTATCTAACTA-TCAAATTGCTTAATTACACTGAA
1 TTAAGTTAATTACCAAATTACTTAAT-TAATTACT-AATTTACTTAATTACAC-GAA
** * **
5476 TTAAGTGGATTACCAAATTACTTAATTTAATCACCGATTTACTTAATTACACCGAA
1 TTAAGTTAATTACCAAATTACTTAA-TTAATTACTAATTTACTTAATTACA-CGAA
**
5532 TTAAGTTGTTTACCAAATTAC
1 TTAAGTTAATTACCAAATTAC
5553 CAATTTACTT
Statistics
Matches: 110, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
55 3 0.03
56 105 0.95
57 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (54 bp):
TTAAGTTAATTACCAAATTACTTAATTAATTACTAATTTACTTAATTACACGAA
Found at i:5560 original size:43 final size:43
Alignment explanation
Indices: 5512--5595 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
5502 TTAATCACCG
5512 ATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCA
5555 ATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTAC
1 ATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTAC
5596 TAAATTTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (43 bp):
ATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCA
Found at i:7536 original size:35 final size:35
Alignment explanation
Indices: 7497--7593 Score: 104
Period size: 44 Copynumber: 2.5 Consensus size: 35
7487 AATTACCAAA
7497 TTACCAATTTACTTAATTACACCGAATTAAGTTGT
1 TTACCAATTTACTTAATTACACCGAATTAAGTTGT
7532 TTACCAAATTACTTAATTTACTTAATTACACCGAATTAAGTTGT
1 TTA-C------C--AATTTACTTAATTACACCGAATTAAGTTGT
*
7576 TTACCAAATTACTTAATT
1 TTACCAATTTACTTAATT
7594 TAATCACCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
35 15 0.29
36 1 0.02
37 1 0.02
42 1 0.02
43 1 0.02
44 33 0.63
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.41
Consensus pattern (35 bp):
TTACCAATTTACTTAATTACACCGAATTAAGTTGT
Found at i:7536 original size:43 final size:43
Alignment explanation
Indices: 7473--7716 Score: 317
Period size: 43 Copynumber: 5.3 Consensus size: 43
7463 ACACGATCAG
**
7473 CACCGAATTAAGTTAATTACCAAATTACCAATTTACTTAATTA
1 CACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTA
*
7516 CACCGAATTAAGTTGTTTACCAAATTACTTAATTTACTTAATTA
1 CACCGAATTAAGTTGTTTACCAAATTAC-CAATTTACTTAATTA
7560 CACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATCACCAATTTACTTAATTA
1 CACCGAATTAAGTTGTTTACC-----A---AA--T--T-ACCAATTTACTTAATTA
**
7616 CACCGAATTAAGTTAATTACCAAATTACCAATTTACTTAATTA
1 CACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTA
7659 CACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTA
1 CACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTA
7702 CACCGAATTAAGTTG
1 CACCGAATTAAGTTG
7717 ACTAATTTGC
Statistics
Matches: 179, Mismatches: 8, Indels: 28
0.83 0.04 0.13
Matches are distributed among these distances:
43 99 0.55
44 36 0.20
46 1 0.01
48 2 0.01
49 1 0.01
51 1 0.01
52 2 0.01
54 1 0.01
56 34 0.19
57 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.37
Consensus pattern (43 bp):
CACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATTA
Found at i:9561 original size:9 final size:10
Alignment explanation
Indices: 9538--9564 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9528 GAAACTGAAA
9538 TTTTTGGTTG
1 TTTTTGGTTG
9548 TTTTTGGTTG
1 TTTTTGGTTG
9558 TTTTTGG
1 TTTTTGG
9565 GGAATGGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (10 bp):
TTTTTGGTTG
Found at i:11668 original size:8 final size:7
Alignment explanation
Indices: 11645--11681 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
11635 GGCAACCCAA
11645 TTTT-AT
1 TTTTAAT
11651 TTTTAAT
1 TTTTAAT
11658 TTTTAAT
1 TTTTAAT
11665 TTTT-AT
1 TTTTAAT
11671 TTTTAGAT
1 TTTTA-AT
11679 TTT
1 TTT
11682 ATGAATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 10 0.36
7 13 0.46
8 5 0.18
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:17792 original size:2 final size:2
Alignment explanation
Indices: 17785--17823 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17775 CGACTTCCAT
17785 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
17824 TACTAAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18468 original size:12 final size:14
Alignment explanation
Indices: 18440--18471 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
18430 ACATAAATTC
18440 AATGTTATAACATA
1 AATGTTATAACATA
18454 AATGTTAT-A-ATA
1 AATGTTATAACATA
18466 AATGTT
1 AATGTT
18472 CTAAAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (14 bp):
AATGTTATAACATA
Done.