Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015804.1 Corchorus olitorius cultivar O-4 contig15837, 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: 18645
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:2506 original size:20 final size:20
Alignment explanation
Indices: 2465--2508 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2455 AATCAACCTC
* *
2465 TTTTAATGACCTTATTATGT
1 TTTTAATGACCTTATAAAGT
*
2485 TTTTAGTGACCTTATAAAGT
1 TTTTAATGACCTTATAAAGT
2505 TTTT
1 TTTT
2509 TTTAGTAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTAATGACCTTATAAAGT
Found at i:3843 original size:17 final size:16
Alignment explanation
Indices: 3803--3853 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
3793 CATGTAATCT
**
3803 TTGATCACCGGTGATC
1 TTGATCACTAGTGATC
3819 TTGCATCACTAGTGATC
1 TTG-ATCACTAGTGATC
3836 TTAGATCACTAGTGATC
1 TT-GATCACTAGTGATC
3853 T
1 T
3854 GGGGGGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (16 bp):
TTGATCACTAGTGATC
Found at i:5662 original size:25 final size:26
Alignment explanation
Indices: 5628--5683 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
5618 GATCAGTTTC
* *
5628 CTTTCCTCAAAA-TGAAGGAATTAGA
1 CTTTCATCAAAAGTAAAGGAATTAGA
5653 CTTTCATCAAAAGTAAAGGAATTAGA
1 CTTTCATCAAAAGTAAAGGAATTAGA
*
5679 GTTTC
1 CTTTC
5684 CTTGAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (26 bp):
CTTTCATCAAAAGTAAAGGAATTAGA
Found at i:12531 original size:31 final size:31
Alignment explanation
Indices: 12460--12531 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
12450 GTCTATCAGC
* *
12460 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
* *
12491 TAATT-ATTTGTTTAATTTAATAC-TTAATTT
1 T-TTTAATTTGTTTAATTTAAGACTTTAATTT
12521 GTTTTAATTTG
1 -TTTTAATTTG
12532 CAATAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
30 8 0.24
31 23 0.70
32 2 0.06
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:12950 original size:12 final size:12
Alignment explanation
Indices: 12916--12953 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12906 CGGAATCAAA
*
12916 CCCGAGTCCGAA
1 CCCGAGTCCGAG
12928 CCCGA-TCCGAG
1 CCCGAGTCCGAG
*
12939 CCCGAGCCCGAG
1 CCCGAGTCCGAG
12951 CCC
1 CCC
12954 TACCTGAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.18, C:0.50, G:0.26, T:0.05
Consensus pattern (12 bp):
CCCGAGTCCGAG
Found at i:13396 original size:20 final size:20
Alignment explanation
Indices: 13373--13419 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
13363 TTTTTAAAAT
13373 GAAAATTACATTTTCTTCAA
1 GAAAATTACATTTTCTTCAA
13393 GAAAATTACATTTTCTTCAA
1 GAAAATTACATTTTCTTCAA
*
13413 AAAAATT
1 GAAAATT
13420 TAATGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (20 bp):
GAAAATTACATTTTCTTCAA
Found at i:15468 original size:13 final size:13
Alignment explanation
Indices: 15446--15480 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
15436 GATAATTCTT
*
15446 TTTGATCCTTCAA
1 TTTGACCCTTCAA
15459 TTTGACCCTTCAA
1 TTTGACCCTTCAA
*
15472 CTTGACCCT
1 TTTGACCCT
15481 CCTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.40
Consensus pattern (13 bp):
TTTGACCCTTCAA
Found at i:17386 original size:152 final size:151
Alignment explanation
Indices: 17213--17487 Score: 487
Period size: 152 Copynumber: 1.8 Consensus size: 151
17203 TCACAAGAAC
*
17213 CTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTCAATGAAAATA
1 CTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATA
*
17278 AAGTTTTTAGTAGAATAAAACTGTATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAA
66 AAGTTTTTAGTAGAATAAAAATGTATATT-AAAAATTTTAATATATCCAAGTTTTTAATGAAAAA
17343 TAGTAAAAATGGTAAAAATAAA
130 TAGTAAAAATGGTAAAAATAAA
*
17365 CTTTTAAATTATAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATA
1 CTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATA
* * *
17430 GAGTTTTTAGTAGAATAAAAATTTATATTAAAAATTTTCATATATCCAAGTTTTTAAT
66 AAGTTTTTAGTAGAATAAAAATGTATATTAAAAATTTTAATATATCCAAGTTTTTAAT
17488 AGAGTTTTTA
Statistics
Matches: 117, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
151 28 0.24
152 89 0.76
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.37
Consensus pattern (151 bp):
CTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATA
AAGTTTTTAGTAGAATAAAAATGTATATTAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAT
AGTAAAAATGGTAAAAATAAA
Found at i:18434 original size:34 final size:35
Alignment explanation
Indices: 18377--18443 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
18367 AGAATAACTG
*
18377 TAAAAAATTTTATTTCTAAAAATA-ATTGTAAAATT
1 TAAAAAATTTCATTTCTAAAAATATATT-TAAAATT
18412 TAAAAAATTTCA-TT-TAAGAAATATATTTAAAA
1 TAAAAAATTTCATTTCTAA-AAATATATTTAAAA
18444 GATTCTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 3 0.10
34 12 0.41
35 14 0.48
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (35 bp):
TAAAAAATTTCATTTCTAAAAATATATTTAAAATT
Done.