Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012648.1 Corchorus capsularis cultivar CVL-1 contig12669, 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: 21681
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:4470 original size:5 final size:5
Alignment explanation
Indices: 4460--4493 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
4450 ATGTTACTGA
4460 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
4494 TTTGCCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (5 bp):
TTTTG
Found at i:5321 original size:44 final size:43
Alignment explanation
Indices: 5235--5321 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
5225 TGATTTGCCT
* * *
5235 TCACACCGCCTTGGTCAAATTGAAAAGCCAACATGGCTTTTTA
1 TCACACCACCTTGGTCAAATTGAAAAGCCAACATAGCCTTTTA
*
5278 TCACAGCCACCTTGGTCAAATTG-AAAGCCCGACATAGCCTTTTA
1 TCACA-CCACCTTGGTCAAATTGAAAAG-CCAACATAGCCTTTTA
5322 AAATTCTCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 9 0.24
44 29 0.76
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (43 bp):
TCACACCACCTTGGTCAAATTGAAAAGCCAACATAGCCTTTTA
Found at i:5594 original size:22 final size:22
Alignment explanation
Indices: 5509--5592 Score: 132
Period size: 22 Copynumber: 3.7 Consensus size: 22
5499 CTTTTGAAGG
5509 ATGGCCGAATCTCACGACCACC
1 ATGGCCGAATCTCACGACCACC
*
5531 ATGTGGCCGAATCTCATGACCACC
1 A--TGGCCGAATCTCACGACCACC
*
5555 ATGGCCGAATCTCACGGCCACC
1 ATGGCCGAATCTCACGACCACC
5577 ATGGCCGAATCTCACG
1 ATGGCCGAATCTCACG
5593 GCAACATACT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
22 36 0.63
24 21 0.37
ACGTcount: A:0.25, C:0.37, G:0.21, T:0.17
Consensus pattern (22 bp):
ATGGCCGAATCTCACGACCACC
Found at i:5789 original size:22 final size:22
Alignment explanation
Indices: 5748--5789 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5738 TACCATTATG
*
5748 TGGCCGAATCTCATGACCACTA
1 TGGCCGAATCTCACGACCACTA
*
5770 TGGCCGAATCTCACGGCCAC
1 TGGCCGAATCTCACGACCAC
5790 AGTCTTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (22 bp):
TGGCCGAATCTCACGACCACTA
Found at i:9487 original size:44 final size:43
Alignment explanation
Indices: 9401--9487 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
9391 TGATTTGCCT
* * *
9401 TCACACCGCCTTGGTCAAATTGAAAAGCCAACATGGCTTTTTA
1 TCACACCACCTTGGTCAAATTGAAAAGCCAACATAGCCTTTTA
*
9444 TCACAGCCACCTTGGTCAAATTG-AAAGCCCGACATAGCCTTTTA
1 TCACA-CCACCTTGGTCAAATTGAAAAG-CCAACATAGCCTTTTA
9488 AAATTCTCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 9 0.24
44 29 0.76
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (43 bp):
TCACACCACCTTGGTCAAATTGAAAAGCCAACATAGCCTTTTA
Found at i:9728 original size:22 final size:22
Alignment explanation
Indices: 9675--9763 Score: 133
Period size: 22 Copynumber: 4.0 Consensus size: 22
9665 CTTTTGAAGG
9675 ATGGCCGAATCTCACGACCACC
1 ATGGCCGAATCTCACGACCACC
*
9697 ATGTGGCCGAATCTCATGACCACC
1 A--TGGCCGAATCTCACGACCACC
*
9721 ATGGCCGAATCTCACGGCCACC
1 ATGGCCGAATCTCACGACCACC
*
9743 ATGGCCGAATCTCACGGCCAC
1 ATGGCCGAATCTCACGACCAC
9764 ATACTAACCC
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
22 41 0.66
24 21 0.34
ACGTcount: A:0.25, C:0.38, G:0.21, T:0.16
Consensus pattern (22 bp):
ATGGCCGAATCTCACGACCACC
Found at i:9955 original size:22 final size:22
Alignment explanation
Indices: 9914--9955 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9904 TACCATTATG
*
9914 TGGCCGAATCTCATGACCACTA
1 TGGCCGAATCTCACGACCACTA
*
9936 TGGCCGAATCTCACGGCCAC
1 TGGCCGAATCTCACGACCAC
9956 AGTCTTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (22 bp):
TGGCCGAATCTCACGACCACTA
Found at i:16617 original size:7 final size:8
Alignment explanation
Indices: 16605--16645 Score: 52
Period size: 7 Copynumber: 5.5 Consensus size: 8
16595 TCTCCAGATC
16605 TTTGGAT-
1 TTTGGATG
16612 TTTGGATG
1 TTTGGATG
*
16620 TTT-GATC
1 TTTGGATG
16627 TTTGGAT-
1 TTTGGATG
16634 TTTGGATG
1 TTTGGATG
16642 TTTG
1 TTTG
16646 AATCAATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
7 20 0.67
8 10 0.33
ACGTcount: A:0.12, C:0.02, G:0.29, T:0.56
Consensus pattern (8 bp):
TTTGGATG
Found at i:16629 original size:22 final size:22
Alignment explanation
Indices: 16601--16646 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
16591 TAAGTCTCCA
16601 GATCTTTGGATTTTGGATGTTT
1 GATCTTTGGATTTTGGATGTTT
16623 GATCTTTGGATTTTGGATGTTT
1 GATCTTTGGATTTTGGATGTTT
16645 GA
1 GA
16647 ATCAATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.04, G:0.28, T:0.52
Consensus pattern (22 bp):
GATCTTTGGATTTTGGATGTTT
Found at i:16645 original size:15 final size:15
Alignment explanation
Indices: 16605--16645 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
16595 TCTCCAGATC
16605 TTTGGAT-TTTGGAT
1 TTTGGATCTTTGGAT
16619 GTTT-GATCTTTGGAT
1 -TTTGGATCTTTGGAT
*
16634 TTTGGATGTTTG
1 TTTGGATCTTTG
16646 AATCAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.12, C:0.02, G:0.29, T:0.56
Consensus pattern (15 bp):
TTTGGATCTTTGGAT
Found at i:16797 original size:13 final size:13
Alignment explanation
Indices: 16779--16804 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16769 TAGAAGGAAA
16779 AGTGTTGCACATG
1 AGTGTTGCACATG
16792 AGTGTTGCACATG
1 AGTGTTGCACATG
16805 CTAGAGACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
AGTGTTGCACATG
Found at i:16853 original size:31 final size:31
Alignment explanation
Indices: 16815--16877 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
16805 CTAGAGACTC
*
16815 ATAGGGGAGGTTCGAAACTCCAACTCATTCA
1 ATAGGGGAGGTTCGAAACTCCAACCCATTCA
16846 ATAGGGGAGGTTCGAAACTCCAACCCATTCA
1 ATAGGGGAGGTTCGAAACTCCAACCCATTCA
16877 A
1 A
16878 ATGATTCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (31 bp):
ATAGGGGAGGTTCGAAACTCCAACCCATTCA
Done.