Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007810.1 Corchorus capsularis cultivar CVL-1 contig07831, 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: 8506
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Found at i:1515 original size:25 final size:22
Alignment explanation
Indices: 1466--1523 Score: 57
Period size: 25 Copynumber: 2.5 Consensus size: 22
1456 TCAATTTCAA
1466 ATAACCAAATCAATTCAACAAC
1 ATAACCAAATCAATTCAACAAC
1488 ATAACCCAATATCAAATATCAA-AAC
1 ATAA-CCAA-ATC-AAT-TCAACAAC
*
1513 AT-ATCAAATCA
1 ATAACCAAATCA
1524 TGCAATAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
21 1 0.03
22 7 0.23
23 7 0.23
24 4 0.13
25 8 0.26
26 4 0.13
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (22 bp):
ATAACCAAATCAATTCAACAAC
Found at i:3305 original size:21 final size:21
Alignment explanation
Indices: 3262--3304 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3252 ATAAACTGGA
3262 TTGCTAAACACCGTCCCCCTT
1 TTGCTAAACACCGTCCCCCTT
*
3283 TTGCTAAATACCG-CCCCCTT
1 TTGCTAAACACCGTCCCCCTT
3303 TT
1 TT
3305 TACACTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.19, C:0.40, G:0.09, T:0.33
Consensus pattern (21 bp):
TTGCTAAACACCGTCCCCCTT
Found at i:3435 original size:24 final size:24
Alignment explanation
Indices: 3376--3433 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 24
3366 TCAAACCCTA
*
3376 AAATTCATTTCTAACAACTTCTTC
1 AAATTCATTTCTAACAACATCTTC
3400 AAACTTCATTTCTAACAA-ATCTTC
1 AAA-TTCATTTCTAACAACATCTTC
3424 AAATTCATTT
1 AAATTCATTT
3434 TCCTTCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 7 0.22
24 11 0.34
25 14 0.44
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATTCATTTCTAACAACATCTTC
Found at i:3472 original size:26 final size:26
Alignment explanation
Indices: 3443--3510 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
3433 TTCCTTCATT
3443 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
3469 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
3495 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
3511 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:3577 original size:10 final size:10
Alignment explanation
Indices: 3562--3592 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3552 ACTAATTAAT
3562 ATTAAAAAAA
1 ATTAAAAAAA
3572 ATTAAAAAAA
1 ATTAAAAAAA
*
3582 TTTAAAAAAA
1 ATTAAAAAAA
3592 A
1 A
3593 AGAAAATGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
ATTAAAAAAA
Found at i:3882 original size:49 final size:49
Alignment explanation
Indices: 3810--3955 Score: 249
Period size: 49 Copynumber: 3.0 Consensus size: 49
3800 CACAGCCCAA
*
3810 ATTTAGTGATGGTATGGAATCTCTTTTGTGAACTCTTAACAATCATTGT
1 ATTTAGTGATGGTATAGAATCTCTTTTGTGAACTCTTAACAATCATTGT
3859 ATTTAGTGATGGTATAGAATCTCTTTTGTGAACTCTTAACAATCATTGT
1 ATTTAGTGATGGTATAGAATCTCTTTTGTGAACTCTTAACAATCATTGT
** *
3908 ATTTAGTGATAAT-TTGAATCTCTTTTGTGAACTCTTAACAATCATTGT
1 ATTTAGTGATGGTATAGAATCTCTTTTGTGAACTCTTAACAATCATTGT
3956 TATTGTGTTC
Statistics
Matches: 93, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
48 34 0.37
49 59 0.63
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (49 bp):
ATTTAGTGATGGTATAGAATCTCTTTTGTGAACTCTTAACAATCATTGT
Found at i:4191 original size:73 final size:73
Alignment explanation
Indices: 4059--4324 Score: 374
Period size: 73 Copynumber: 3.7 Consensus size: 73
4049 GAAGAAAAGG
* * * * * * *
4059 ACCCTGAGCAAGTCATGCGCATGACC-AGAGTAGGTCATGCCCATGCCCTCCATATGCGTTTTAG
1 ACCC-GAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACCTCTATAGGCGTTTTAG
4123 CCTTCTTGC
65 CCTTCTTGC
* *
4132 ACCCGAGGAAGTCATGCACATGATCAACAGAAGGTCATGCCCATGACCTCTATAGGCGTTTTAGC
1 ACCCGAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACCTCTATAGGCGTTTTAGC
4197 CTTCTTGC
66 CTTCTTGC
* *
4205 ACCTGAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACCTCTAAAGGCGTTTTAGC
1 ACCCGAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACCTCTATAGGCGTTTTAGC
4270 CTTCTTGC
66 CTTCTTGC
* * **
4278 ACCTGAGTAAGTCATGCACATGACCAACACAA-GTCATGTGCATGACC
1 ACCCGAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACC
4325 AGGACGGACA
Statistics
Matches: 177, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
72 31 0.18
73 146 0.82
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (73 bp):
ACCCGAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACCTCTATAGGCGTTTTAGC
CTTCTTGC
Done.