Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023386.1 Corchorus olitorius cultivar O-4 contig23419, 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: 24032
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:396 original size:21 final size:22
Alignment explanation
Indices: 358--404 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
348 AATTTTGTGT
358 TTTGCGTCAAAGAAAAAAAAAA
1 TTTGCGTCAAAGAAAAAAAAAA
* *
380 TTTGCGTTAAA-AAAAAAAAAT
1 TTTGCGTCAAAGAAAAAAAAAA
401 TTTG
1 TTTG
405 TTCCTGCGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28
Consensus pattern (22 bp):
TTTGCGTCAAAGAAAAAAAAAA
Found at i:1467 original size:21 final size:21
Alignment explanation
Indices: 1443--1555 Score: 133
Period size: 21 Copynumber: 5.4 Consensus size: 21
1433 CTTAGGCAAT
*
1443 TCCAATGAGCTTGAAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
*
1464 TCCAATGAGCGTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
**
1485 TTTAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
*
1506 TCCAATAAGCTTGGAA-TTCGC
1 TCCAATGAGCTTGGAACTT-GC
1527 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
1548 TCCAATGA
1 TCCAATGA
1556 ACTCCTAGCA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
20 5 0.06
21 73 0.91
22 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:4086 original size:33 final size:33
Alignment explanation
Indices: 4040--4120 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 33
4030 GTGTTTTAGA
** *
4040 TGTTGTTACTGATGATACTAAACCTAATTTAAG
1 TGTTGTTTGTGATGACACTAAACCTAATTTAAG
* ** *
4073 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
1 TGTTGTTTGTGATGACACTAAACCTAATTTAAG
4106 TGTTGTTTGTGATGA
1 TGTTGTTTGTGATGA
4121 AAAAAATTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGTGATGACACTAAACCTAATTTAAG
Found at i:4135 original size:33 final size:32
Alignment explanation
Indices: 4067--4168 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 32
4057 CTAAACCTAA
* **
4067 TTTAAGTGTTGTTTGTGATGACACTAAATCTGT
1 TTTAGGTGTTGTTTGTGATGA-AAAAAATCTGT
*
4100 TTTAGGTGTTGTTTGTGATGAAAAAAATTCAGT
1 TTTAGGTGTTGTTTGTGATGAAAAAAA-TCTGT
* **
4133 TTT-GGATGCTAATTGTGATGAAAAAAAATCTGT
1 TTTAGG-TGTTGTTTGTGATG-AAAAAAATCTGT
4166 TTT
1 TTT
4169 GGTTGATCAT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 6 0.10
33 45 0.78
34 7 0.12
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (32 bp):
TTTAGGTGTTGTTTGTGATGAAAAAAATCTGT
Found at i:6261 original size:52 final size:52
Alignment explanation
Indices: 6198--6302 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
6188 AACAAGAATT
* *
6198 GCAGGACAACTTCGGCCCAGAACTTGTTCAGCTTCGGGGCAGAAGTTGTTGC
1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
6250 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
6302 G
1 G
6303 GAAAGAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (52 bp):
GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
Found at i:6292 original size:22 final size:22
Alignment explanation
Indices: 6256--6299 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6246 TTGCGCAGGA
*
6256 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCACAGAACTTGTT
* *
6278 CAACTTCGGGACAGAAGTTGTT
1 CAACTTCGGCACAGAACTTGTT
6300 GCGGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTGTT
Found at i:12819 original size:21 final size:21
Alignment explanation
Indices: 12795--12849 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
12785 GAGCAAGTTC
12795 CAAGCTCATTGGAGAAGGTGT
1 CAAGCTCATTGGAGAAGGTGT
* *
12816 CAAGCTCATTCGAGAAGGTTT
1 CAAGCTCATTGGAGAAGGTGT
12837 CAAGCTCATTGGA
1 CAAGCTCATTGGA
12850 ATTGCCTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (21 bp):
CAAGCTCATTGGAGAAGGTGT
Found at i:14524 original size:21 final size:21
Alignment explanation
Indices: 14500--14591 Score: 141
Period size: 21 Copynumber: 4.4 Consensus size: 21
14490 CTTAGGCAAT
14500 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGAAACCTTC
*
14521 TCCAATGAGCTTGACACCTTC
1 TCCAATGAGCTTGAAACCTTC
*
14542 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGAAACCTTC
*
14563 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGAAACCTT-C
14584 TCCAATGA
1 TCCAATGA
14592 TCTCCTAGCA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 3 0.04
21 64 0.96
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGAAACCTTC
Found at i:15696 original size:21 final size:21
Alignment explanation
Indices: 15670--15710 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
15660 TTGAAGCCCT
15670 ATTGGATAAAAGTGGTACTAA
1 ATTGGATAAAAGTGGTACTAA
**
15691 ATTGGATCTAAGTGGTACTA
1 ATTGGATAAAAGTGGTACTA
15711 GGGTTTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (21 bp):
ATTGGATAAAAGTGGTACTAA
Found at i:17272 original size:16 final size:15
Alignment explanation
Indices: 17234--17275 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
17224 ACAGAGGTTG
*
17234 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
17249 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
17264 ACTAGAAAACAA
1 AC-AGAAAACAA
17276 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:22484 original size:11 final size:11
Alignment explanation
Indices: 22470--22499 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
22460 AAAGGAAAAG
22470 GCTAGGAAGGA
1 GCTAGGAAGGA
22481 GCTAGGAAGGA
1 GCTAGGAAGGA
22492 GCTAGGAA
1 GCTAGGAA
22500 AGATCCTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.43, T:0.10
Consensus pattern (11 bp):
GCTAGGAAGGA
Found at i:22907 original size:21 final size:21
Alignment explanation
Indices: 22883--22953 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
22873 CTTAGGCAAT
*
22883 TCCAATGGGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
22904 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
22925 TCCAATGAGCTTGGAACCTGC
1 TCCAATGAGCTTGGAACCTTC
22946 TCCAATGA
1 TCCAATGA
22954 TCTCCTAGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Done.