Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012319.1 Corchorus olitorius cultivar O-4 contig12352, 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: 24017
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:549 original size:13 final size:12
Alignment explanation
Indices: 528--560 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
518 TAATTCAATG
528 TTTTAAATATTA
1 TTTTAAATATTA
540 TTTATAAATATTA
1 TTT-TAAATATTA
553 TTTTAAAT
1 TTTTAAAT
561 TCCAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTAAATATTA
Found at i:2706 original size:53 final size:53
Alignment explanation
Indices: 2644--2749 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
2634 AGAGGTCTTG
2644 GTCTGATTTGAAATTGTAACAATGATGCATCAATTCTTAGATACTATGTCAAC
1 GTCTGATTTGAAATTGTAACAATGATGCATCAATTCTTAGATACTATGTCAAC
2697 GTCTGATTTGAAATTGTAACAATGATGCATCAATTCTTAGATACTATGTCAAC
1 GTCTGATTTGAAATTGTAACAATGATGCATCAATTCTTAGATACTATGTCAAC
2750 AACACGTTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (53 bp):
GTCTGATTTGAAATTGTAACAATGATGCATCAATTCTTAGATACTATGTCAAC
Found at i:4763 original size:155 final size:156
Alignment explanation
Indices: 4478--4789 Score: 432
Period size: 155 Copynumber: 2.0 Consensus size: 156
4468 CTTTTTGGTC
* * * * * **
4478 ATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTATCAAGGCTTGCTTTTG
1 ATTTCTCAATGGACTTTAATAGAGTAGTGAAATTACTAAAAGATCCCCATCAAGGATTGATGATG
* * * * * * *
4543 GAGTTAGAGAACTAATATTTTTCGTCTTTTTCTACTTGGCGGATTACTTGAATGTTCTAACTTTT
66 GAGCTAGAGAACTAATATTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATATCCAAACTTTT
*
4608 GATTCTT-AAGGGGATTAAATAAGTAA
131 GATTCTTGAA-GGGATTAAATAACTAA
4634 ATTTCTCAATGGA-TTTGAATAGAGTAGTGAAATTACTAAAAGATCCCCATCAAGGATTGATGAT
1 ATTTCTCAATGGACTTT-AATAGAGTAGTGAAATTACTAAAAGATCCCCATCAAGGATTGATGAT
* *
4698 -GAGCTAGGGAACTAATCTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATATCCAAACTTT
65 GGAGCTAGAGAACTAATATTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATATCCAAACTTT
4762 TGATTCTTGAAGGGATTAAATAACTAA
130 TGATTCTTGAAGGGATTAAATAACTAA
4789 A
1 A
4790 CTTTTTGGTC
Statistics
Matches: 137, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
155 82 0.60
156 55 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (156 bp):
ATTTCTCAATGGACTTTAATAGAGTAGTGAAATTACTAAAAGATCCCCATCAAGGATTGATGATG
GAGCTAGAGAACTAATATTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATATCCAAACTTTT
GATTCTTGAAGGGATTAAATAACTAA
Found at i:6036 original size:38 final size:38
Alignment explanation
Indices: 5994--6070 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
5984 GATAACTTGG
*
5994 ATTTTTTTCTGTACTAAACCCTATCTAATTAATGTGCT
1 ATTTTTTTCCGTACTAAACCCTATCTAATTAATGTGCT
6032 ATTTTTTTCCGTACTAAACCCTATCTAATTAATGTGCT
1 ATTTTTTTCCGTACTAAACCCTATCTAATTAATGTGCT
6070 A
1 A
6071 AATTTACCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.45
Consensus pattern (38 bp):
ATTTTTTTCCGTACTAAACCCTATCTAATTAATGTGCT
Found at i:6736 original size:19 final size:19
Alignment explanation
Indices: 6714--6765 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
6704 GGGCTGAAAT
6714 TAATTAATTATTAAATAAA
1 TAATTAATTATTAAATAAA
* *
6733 TAA-TAATTATTTTATTAAA
1 TAATTAATTA-TTAAATAAA
6752 TAATT-ATTATTAAA
1 TAATTAATTATTAAA
6766 AATCCTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATTAATTATTAAATAAA
Found at i:8198 original size:51 final size:50
Alignment explanation
Indices: 8097--8198 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
8087 GTTCTTCATA
* **
8097 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
*
8147 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACT-GTACACGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT
8198 T
1 T
8199 CTTTATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 8 0.18
51 35 0.80
52 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Found at i:10070 original size:14 final size:14
Alignment explanation
Indices: 10053--10105 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
10043 TTATTGTTGT
10053 TATTGATATTGATA
1 TATTGATATTGATA
** * *
10067 TATTTTTTTTGGTACA
1 TATTGATATT-G-ATA
10083 TATTGATATTGATA
1 TATTGATATTGATA
10097 TATTGATAT
1 TATTGATAT
10106 ATTTTCCTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
14 18 0.62
15 2 0.07
16 9 0.31
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (14 bp):
TATTGATATTGATA
Found at i:10924 original size:24 final size:24
Alignment explanation
Indices: 10896--10941 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
10886 CCGACTATAA
*
10896 TATATAATATGATT-TTAAAAATAT
1 TATAT-ATATCATTATTAAAAATAT
10920 TATATATATCATTATTAAAAAT
1 TATATATATCATTATTAAAAAT
10942 TCAGAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TATATATATCATTATTAAAAATAT
Found at i:14727 original size:30 final size:31
Alignment explanation
Indices: 14683--14859 Score: 198
Period size: 31 Copynumber: 5.8 Consensus size: 31
14673 GGCATGCCAC
* *
14683 GTGTCACTTTTTGGTATACGTGGGGTTACAT
1 GTGTCACTTTTTGGTACACGTGGCGTTACAT
*
14714 GTGTCAC-TTTTGGTACACGTGGGGTTACAT
1 GTGTCACTTTTTGGTACACGTGGCGTTACAT
* *
14744 GTGTCAC-TTTTGGTACACGTGGCGTGACAC
1 GTGTCACTTTTTGGTACACGTGGCGTTACAT
* * * * *
14774 ATGTCACTTTTTAGTGCACGTGGCGTGACAC
1 GTGTCACTTTTTGGTACACGTGGCGTTACAT
* *
14805 GTATCACTTTTTGGTAAACGTGGCGTGT-CAT
1 GTGTCACTTTTTGGTACACGTGGCGT-TACAT
* *
14836 GTGTCACTTTTTAGTACACATGGC
1 GTGTCACTTTTTGGTACACGTGGC
14860 ATGCCACGTC
Statistics
Matches: 126, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
30 55 0.44
31 71 0.56
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (31 bp):
GTGTCACTTTTTGGTACACGTGGCGTTACAT
Done.