Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008354.1 Corchorus capsularis cultivar CVL-1 contig08375, 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: 22514
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:4502 original size:123 final size:123
Alignment explanation
Indices: 4282--4524 Score: 299
Period size: 123 Copynumber: 2.0 Consensus size: 123
4272 ACCAAATAAA
* *
4282 CCGAAAACTATTTTTTATAAAACGTTAACCGAACCGAAGTATCCTATTCCGAACATCAATCGAAC
1 CCGAAAACTAATTTTTATAAAACATTAACCGAACCGAAGTATCCTATTCCGAACATCAATCGAAC
* * * *
4347 CGAAATATTTCGGTTAACCAACCAGATGATATTTTAACATAAATTTTAAATTTATGAG
66 CAAAATATATCGGTCAACCAACCAGATGATATTTTAACATAAATTTAAAATTTATGAG
* * * * * * *
4405 CCGAACACTAATTTTTGTAAATCATTAACCGATCCGAAGTATCTTATTCCGAACATTAATCGAAT
1 CCGAAAACTAATTTTTATAAAACATTAACCGAACCGAAGTATCCTATTCCGAACATCAATCGAAC
* * * * * *
4470 CAAAATATATCGGTCAATCGATC-GAATTATATTTTAACTTCAATTTAAAATTTAT
66 CAAAATATATCGGTCAACCAACCAG-ATGATATTTTAACATAAATTTAAAATTTAT
4525 TAACCAAATT
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
122 1 0.01
123 99 0.99
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (123 bp):
CCGAAAACTAATTTTTATAAAACATTAACCGAACCGAAGTATCCTATTCCGAACATCAATCGAAC
CAAAATATATCGGTCAACCAACCAGATGATATTTTAACATAAATTTAAAATTTATGAG
Found at i:5297 original size:49 final size:49
Alignment explanation
Indices: 5225--5318 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
5215 GGTTATCATT
*
5225 ATATGTGTTTTAGATTTTAGATACTAAAAAACAATAACCGTCCTAACCA
1 ATATGTGTTTTAGATTTTAGATACTAAAAAACAACAACCGTCCTAACCA
* *
5274 ATATGTGTTTTAGATTTTAGATACTAAAAATCAACCACCGTCCTA
1 ATATGTGTTTTAGATTTTAGATACTAAAAAACAACAACCGTCCTA
5319 CCCAGCAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (49 bp):
ATATGTGTTTTAGATTTTAGATACTAAAAAACAACAACCGTCCTAACCA
Found at i:6289 original size:2 final size:2
Alignment explanation
Indices: 6282--6311 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6272 AAACCATTTA
*
6282 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6312 GTGAAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6703 original size:20 final size:20
Alignment explanation
Indices: 6678--6718 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
6668 GTTTTAGGAT
*
6678 GAATTTGATATTGGCAATAA
1 GAATTTGATATTGACAATAA
6698 GAATTTGATATTGACAATAA
1 GAATTTGATATTGACAATAA
6718 G
1 G
6719 GAGCAGGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (20 bp):
GAATTTGATATTGACAATAA
Found at i:8214 original size:17 final size:16
Alignment explanation
Indices: 8174--8217 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
8164 AGAACCTGAT
*
8174 GAACCCGAAACAACCC
1 GAACCCGAAAAAACCC
**
8190 GAGTCCGAAAGAAACCC
1 GAACCCGAAA-AAACCC
8207 GAACCCGAAAA
1 GAACCCGAAAA
8218 TACTAATACC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.45, C:0.34, G:0.18, T:0.02
Consensus pattern (16 bp):
GAACCCGAAAAAACCC
Found at i:8336 original size:16 final size:17
Alignment explanation
Indices: 8302--8348 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
8292 AATTAGACAA
*
8302 AAATAAAAATATTTGAT
1 AAATATAAATATTTGAT
8319 AAAT-TAAATAATTT-AT
1 AAATATAAAT-ATTTGAT
8335 AAATATAAAT-TTTG
1 AAATATAAATATTTG
8349 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (17 bp):
AAATATAAATATTTGAT
Found at i:9116 original size:17 final size:17
Alignment explanation
Indices: 9094--9146 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
9084 GAATAACCTG
9094 ACCTGAAATTGATCTGA
1 ACCTGAAATTGATCTGA
*
9111 ACCTGAAA--AATACATG-
1 ACCTGAAATTGAT-C-TGA
9127 ACCTGAAATTGATCTGA
1 ACCTGAAATTGATCTGA
9144 ACC
1 ACC
9147 CGAATTAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 2 0.07
16 11 0.38
17 14 0.48
18 2 0.07
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (17 bp):
ACCTGAAATTGATCTGA
Found at i:9726 original size:17 final size:17
Alignment explanation
Indices: 9704--9737 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9694 GTTTGGTTGA
*
9704 AGGGGTTGCAAGGGGTG
1 AGGGGTAGCAAGGGGTG
*
9721 AGGGGTAGGAAGGGGTG
1 AGGGGTAGCAAGGGGTG
9738 GCCATTACCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.62, T:0.15
Consensus pattern (17 bp):
AGGGGTAGCAAGGGGTG
Found at i:16564 original size:15 final size:15
Alignment explanation
Indices: 16546--16584 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
16536 CCAACTCCTC
16546 CCCCTCCCTACCCCA
1 CCCCTCCCTACCCCA
16561 CCCCTTCCC-ACCCCA
1 CCCC-TCCCTACCCCA
16576 CCCCTCCCT
1 CCCCTCCCT
16585 CATTTGAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.10, C:0.74, G:0.00, T:0.15
Consensus pattern (15 bp):
CCCCTCCCTACCCCA
Found at i:16564 original size:16 final size:16
Alignment explanation
Indices: 16530--16584 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
16520 TTTTCTAAAA
* * *
16530 CCCCTCCCAACTCCTC
1 CCCCTCCCTACCCCAC
16546 CCCCTCCCTACCCCAC
1 CCCCTCCCTACCCCAC
*
16562 CCCTTCCC-ACCCCA-
1 CCCCTCCCTACCCCAC
16576 CCCCTCCCT
1 CCCCTCCCT
16585 CATTTGAACC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 7 0.21
15 6 0.18
16 20 0.61
ACGTcount: A:0.11, C:0.73, G:0.00, T:0.16
Consensus pattern (16 bp):
CCCCTCCCTACCCCAC
Found at i:17524 original size:16 final size:16
Alignment explanation
Indices: 17503--17555 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
17493 GATTTTCGGA
17503 TTCGGATTCGAGTTTT
1 TTCGGATTCGAGTTTT
17519 TTCGGATTCTGA-TTTT
1 TTCGGATTC-GAGTTTT
*
17535 TTTGGATTCGAGTTTT
1 TTCGGATTCGAGTTTT
17551 TTCGG
1 TTCGG
17556 GTTTAGGTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 2 0.06
16 29 0.88
17 2 0.06
ACGTcount: A:0.11, C:0.11, G:0.25, T:0.53
Consensus pattern (16 bp):
TTCGGATTCGAGTTTT
Found at i:19566 original size:2 final size:2
Alignment explanation
Indices: 19559--19587 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19549 TAAATTAATT
19559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19588 TTTGAAGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.