Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005569.1 Corchorus capsularis cultivar CVL-1 contig05587, 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: 18916
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:4950 original size:50 final size:50
Alignment explanation
Indices: 4886--4982 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
4876 CTCGCCTAAA
*
4886 TTGCAATTCCGCTCAAGGACTATACTTACAACGAACCCAACAAAAGATCC
1 TTGCAATTCCGCTCAAGGACTATACTTAAAACGAACCCAACAAAAGATCC
* * *
4936 TTGCAATTCTGCTCAAGGACTATACTTAAAACGAAGCCAGCAAAAGA
1 TTGCAATTCCGCTCAAGGACTATACTTAAAACGAACCCAACAAAAGA
4983 AGGGCGAACG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.21
Consensus pattern (50 bp):
TTGCAATTCCGCTCAAGGACTATACTTAAAACGAACCCAACAAAAGATCC
Found at i:6764 original size:20 final size:20
Alignment explanation
Indices: 6724--6765 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6714 TCTTACAAGA
* *
6724 TTCTAGCCGTTGGAGCTCTT
1 TTCTAGCCGTTAGAGCACTT
*
6744 TTCTAGCCGTTATAGCACTT
1 TTCTAGCCGTTAGAGCACTT
6764 TT
1 TT
6766 TTCACCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
TTCTAGCCGTTAGAGCACTT
Found at i:7059 original size:104 final size:105
Alignment explanation
Indices: 6824--7059 Score: 314
Period size: 104 Copynumber: 2.3 Consensus size: 105
6814 CTGTCAGAAA
* * * ** *
6824 AGTATTAGTCGATGAAAACTTC-AGTTTTAATTCCAGTATTAATCGACTATAACTCCAAGTCTTC
1 AGTATTAATCGATGAAAAC-TCAAGTTTGAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTC
* * *
6888 TCTTTTAAAAAAGTGGCAGTGTTGACAGCGAATCCAGAGGC
65 ACTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCAGAGCC
*
6929 AGTATTAATCGATGAAAACTCCAGTTTGAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
1 AGTATTAATCGATGAAAACTCAAGTTTGAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
* *
6994 C-TTTGAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCAGAGCC
* * *
7033 AGTATTAATTGATGAATACTTAAGTTT
1 AGTATTAATCGATGAAAACTCAAGTTT
7060 CATGTTTCAA
Statistics
Matches: 115, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
104 59 0.51
105 56 0.49
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (105 bp):
AGTATTAATCGATGAAAACTCAAGTTTGAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCAGAGCC
Found at i:7687 original size:50 final size:52
Alignment explanation
Indices: 7603--7704 Score: 181
Period size: 50 Copynumber: 2.0 Consensus size: 52
7593 AAACATATAA
7603 GTTCATTTGAAATAATACAAAAGAAATTATTGCATTGCACCTTTAGTTACAC
1 GTTCATTTGAAATAATACAAAAGAAATTATTGCATTGCACCTTTAGTTACAC
*
7655 GTTCATTTGAAAT-A-ACACAAGAAATTATTGCATTGCACCTTTAGTTACAC
1 GTTCATTTGAAATAATACAAAAGAAATTATTGCATTGCACCTTTAGTTACAC
7705 TCCCCCTATA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 35 0.71
51 1 0.02
52 13 0.27
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (52 bp):
GTTCATTTGAAATAATACAAAAGAAATTATTGCATTGCACCTTTAGTTACAC
Found at i:12511 original size:20 final size:20
Alignment explanation
Indices: 12471--12512 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12461 TCTTACAAGA
* *
12471 TTCTAGCCGTTGGAGCTCTT
1 TTCTAGCCGTTAGAGCACTT
*
12491 TTCTAGCCGTTATAGCACTT
1 TTCTAGCCGTTAGAGCACTT
12511 TT
1 TT
12513 TTCACCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
TTCTAGCCGTTAGAGCACTT
Found at i:12807 original size:104 final size:105
Alignment explanation
Indices: 12572--12807 Score: 339
Period size: 104 Copynumber: 2.3 Consensus size: 105
12562 CTGTCAGAAA
* ** * * ** *
12572 AGTATTAGTCGATGAAAACTTTAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAGTCTTCT
1 AGTATTAATCGATGAAAACTCAAGTTTGAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
*
12637 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGGC
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
*
12677 AGTATTAATCGATGAAAACTCCAGTTTGAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
1 AGTATTAATCGATGAAAACTCAAGTTTGAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
*
12742 C-TTTGAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * *
12781 AGTATTAATTGATGAATACTTAAGTTT
1 AGTATTAATCGATGAAAACTCAAGTTT
12808 CATGTTTCAA
Statistics
Matches: 117, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
104 59 0.50
105 58 0.50
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (105 bp):
AGTATTAATCGATGAAAACTCAAGTTTGAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
Found at i:12835 original size:105 final size:105
Alignment explanation
Indices: 12572--12827 Score: 316
Period size: 105 Copynumber: 2.4 Consensus size: 105
12562 CTGTCAGAAA
* ** * * * ** *
12572 AGTATTAGTCGATGAAAACTTTAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAGTCTTCT
1 AGTATTAATCGATGAAAACTCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTTCA
*
12637 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGGC
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * * **
12677 AGTATTAATCGATGAAAACTCCAGTTTGAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
1 AGTATTAATCGATGAAAACTCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTTCA
*
12742 C-TTTGAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * * *
12781 AGTATTAATTGATGAATACTTAAGTTTCATGTTTCAACATTCATCGA
1 AGTATTAATCGATGAAAACTCAAGTTTCA-GTTTCAACATTAATCGA
12828 TTGAAACTTT
Statistics
Matches: 131, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
104 60 0.46
105 71 0.54
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (105 bp):
AGTATTAATCGATGAAAACTCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTTCA
CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
Found at i:14213 original size:36 final size:36
Alignment explanation
Indices: 14158--14249 Score: 130
Period size: 36 Copynumber: 2.6 Consensus size: 36
14148 CCCGAGTTTG
* * * *
14158 TCAAAAAGCATCAGCCGAAATTCACCTTCCCCTCTT
1 TCAAGAAGCGTCAGTCGAAATGCACCTTCCCCTCTT
14194 TCAAGAAGCGTCAGTCGAAATGCACCTTCCCCTCTT
1 TCAAGAAGCGTCAGTCGAAATGCACCTTCCCCTCTT
* *
14230 TCAAGAAGCGTAAGTAGAAA
1 TCAAGAAGCGTCAGTCGAAA
14250 CTGCTCATCA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (36 bp):
TCAAGAAGCGTCAGTCGAAATGCACCTTCCCCTCTT
Found at i:15992 original size:11 final size:11
Alignment explanation
Indices: 15976--16019 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
15966 TATACTATAT
15976 CTAATTAATAA
1 CTAATTAATAA
*
15987 CTAATTAATAT
1 CTAATTAATAA
*
15998 CTAATTAATAG
1 CTAATTAATAA
*
16009 TTAATTAATAA
1 CTAATTAATAA
16020 TGAATAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (11 bp):
CTAATTAATAA
Found at i:15997 original size:22 final size:22
Alignment explanation
Indices: 15972--16018 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
15962 CCATTATACT
15972 ATATCTAATTAATAACTAATTA
1 ATATCTAATTAATAACTAATTA
**
15994 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAACTAATTA
16016 ATA
1 ATA
16019 ATGAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAACTAATTA
Done.