Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018439.1 Corchorus olitorius cultivar O-4 contig18472, 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: 49871
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:2473 original size:9 final size:9
Alignment explanation
Indices: 2461--2491 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
2451 GATTAATGCT
2461 TTGAATTGC
1 TTGAATTGC
2470 TTGAATTGC
1 TTGAATTGC
2479 TTGAATTGC
1 TTGAATTGC
2488 TTGA
1 TTGA
2492 TTGGGTCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (9 bp):
TTGAATTGC
Found at i:6697 original size:27 final size:26
Alignment explanation
Indices: 6667--6726 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
6657 CTGAACTTTA
*
6667 TTAAAAGCACTTATAAAATAAATTTTC
1 TTAAAAGCACATATAAAATAAA-TTTC
* * **
6694 TTAAAATCACATCTAAAATCGATTTC
1 TTAAAAGCACATATAAAATAAATTTC
6720 TTAAAAG
1 TTAAAAG
6727 TGATTTCTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (26 bp):
TTAAAAGCACATATAAAATAAATTTC
Found at i:14118 original size:19 final size:21
Alignment explanation
Indices: 14087--14150 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
14077 TTGATACTGT
*
14087 TTAGCAACTGTACAGATGAGA
1 TTAGCTACTGTACAGATGAGA
*
14108 TTA-CT-CTGTACAGATTAGA
1 TTAGCTACTGTACAGATGAGA
* *
14127 TTAGGTACTGTACATATGAGA
1 TTAGCTACTGTACAGATGAGA
14148 TTA
1 TTA
14151 TTAGAACAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.44
20 2 0.06
21 18 0.50
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (21 bp):
TTAGCTACTGTACAGATGAGA
Found at i:14139 original size:21 final size:20
Alignment explanation
Indices: 14093--14150 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
14083 CTGTTTAGCA
14093 ACTGTACAGATGAGATTACT
1 ACTGTACAGATGAGATTACT
* *
14113 -CTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA-CT
*
14133 ACTGTACATATGAGATTA
1 ACTGTACAGATGAGATTA
14151 TTAGAACAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 16 0.50
20 1 0.03
21 15 0.47
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACTGTACAGATGAGATTACT
Found at i:20785 original size:4 final size:4
Alignment explanation
Indices: 20778--20812 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
20768 AAAAAAAAAA
* *
20778 AAAG AAAG AGAG AGAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
20813 ATACAGTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:25687 original size:22 final size:22
Alignment explanation
Indices: 25626--25693 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
25616 TGGTGTCATT
*
25626 AACAATGAAAAATAATAAATAA
1 AACAATGAAAAACAATAAATAA
* * * *
25648 AAAAATGAACATCTATAAA-AA
1 AACAATGAAAAACAATAAATAA
25669 AACAATGAAAAACAAATAAATAA
1 AACAATGAAAAAC-AATAAATAA
25692 AA
1 AA
25694 TGAAAGCATT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
21 12 0.34
22 19 0.54
23 4 0.11
ACGTcount: A:0.72, C:0.07, G:0.04, T:0.16
Consensus pattern (22 bp):
AACAATGAAAAACAATAAATAA
Found at i:31306 original size:21 final size:21
Alignment explanation
Indices: 31282--31328 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
31272 ATACGTGATA
31282 TAAGGAAAATGATATTACATT
1 TAAGGAAAATGATATTACATT
31303 TAAGGAAAATGATATTACATT
1 TAAGGAAAATGATATTACATT
*
31324 CAAGG
1 TAAGG
31329 GTCATCCCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (21 bp):
TAAGGAAAATGATATTACATT
Found at i:32714 original size:30 final size:30
Alignment explanation
Indices: 32678--32737 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
32668 CCCAGAATCC
*
32678 CCCATGCGGCCCCCGCACTGCCATTTTGCG
1 CCCATGCGGCCCCCACACTGCCATTTTGCG
*
32708 CCCATGCGGCCCCCACGCTGCCATTTTGCG
1 CCCATGCGGCCCCCACACTGCCATTTTGCG
32738 ACACCGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.10, C:0.47, G:0.23, T:0.20
Consensus pattern (30 bp):
CCCATGCGGCCCCCACACTGCCATTTTGCG
Found at i:39170 original size:68 final size:68
Alignment explanation
Indices: 39061--39197 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
39051 TGAACCCTCC
*
39061 ACGAAACTCGTAGATTAAGTTTAGCTTTCGGATCCTTATGAAAGTCGTAAATCATGCAATAACCA
1 ACGAAACTCGTAGATCAAGTTTAGCTTTCGGATCCTTATGAAAGTCGTAAATCATGCAATAACCA
39126 TTT
66 TTT
39129 ACGAAACTCGTAGATCAAGTTTAGCTTTCGGATCCTTATGAAAGTCGTAAATCATGCAATAACCA
1 ACGAAACTCGTAGATCAAGTTTAGCTTTCGGATCCTTATGAAAGTCGTAAATCATGCAATAACCA
39194 TTT
66 TTT
39197 A
1 A
39198 ACTGACACTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (68 bp):
ACGAAACTCGTAGATCAAGTTTAGCTTTCGGATCCTTATGAAAGTCGTAAATCATGCAATAACCA
TTT
Found at i:46386 original size:38 final size:37
Alignment explanation
Indices: 46344--46424 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 37
46334 TCTTCAACGT
*
46344 TTTTTCTCTTTCTCGTTGTAGT-AGCTCTTTCCAAAGCA
1 TTTTTC-CTTT-TCCTTGTAGTGAGCTCTTTCCAAAGCA
* *
46382 TTTTTCCTTTTCCTTTTAGTGGGAGCTTTTTCCAAAGCA
1 TTTTTCCTTTTCCTTGTAGT--GAGCTCTTTCCAAAGCA
46421 TTTT
1 TTTT
46425 CCAGCCGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 8 0.22
37 4 0.11
38 6 0.16
39 19 0.51
ACGTcount: A:0.15, C:0.21, G:0.14, T:0.51
Consensus pattern (37 bp):
TTTTTCCTTTTCCTTGTAGTGAGCTCTTTCCAAAGCA
Done.