Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015239.1 Corchorus capsularis cultivar CVL-1 contig15260, 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: 19240
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:597 original size:11 final size:11
Alignment explanation
Indices: 554--591 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
544 TTCCTATATA
*
554 AAATAAATTAT
1 AAATTAATTAT
565 CAAA-TAATTAT
1 -AAATTAATTAT
576 AAATTAATTAT
1 AAATTAATTAT
587 AAATT
1 AAATT
592 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:2026 original size:29 final size:29
Alignment explanation
Indices: 1976--2051 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
1966 AGTGAAAATG
*
1976 TAATAAAATTATTCAATTCTAACTAAGGTTC
1 TAATAAAA--ATTTAATTCTAACTAAGGTTC
2007 TAATAAAAATTTAATTCTAACTAAGGTTC
1 TAATAAAAATTTAATTCTAACTAAGGTTC
2036 TAATAAAAATTTAATT
1 TAATAAAAATTTAATT
2052 AGGTGTGGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 36 0.82
31 8 0.18
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.39
Consensus pattern (29 bp):
TAATAAAAATTTAATTCTAACTAAGGTTC
Found at i:2665 original size:54 final size:54
Alignment explanation
Indices: 2600--2758 Score: 221
Period size: 54 Copynumber: 2.9 Consensus size: 54
2590 GCGGTTGTGG
* *
2600 CTGTGGCCGCCCTCGTGTAGAAGAAGTTGAACGATCTGTCTTTGGATTAGGAGGT
1 CTGTGGCCGCCCTCGTGTAGCAGAAGTTGAACGATCTGTCTTTAGATTAGGA-GT
* * *
2655 -TGTGGCCGCCCTCGTGTAGCAGAAGTTGATCGATCTGTTTTTAGATTTGGAGT
1 CTGTGGCCGCCCTCGTGTAGCAGAAGTTGAACGATCTGTCTTTAGATTAGGAGT
* * * *
2708 CTGTGGCCGCCCCCGGGTAGCCGAAGTTGAGCGATCTGTCTTTAGATTAGG
1 CTGTGGCCGCCCTCGTGTAGCAGAAGTTGAACGATCTGTCTTTAGATTAGG
2759 CGGCGTTTCA
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
53 2 0.02
54 90 0.98
ACGTcount: A:0.18, C:0.20, G:0.32, T:0.30
Consensus pattern (54 bp):
CTGTGGCCGCCCTCGTGTAGCAGAAGTTGAACGATCTGTCTTTAGATTAGGAGT
Found at i:12974 original size:19 final size:18
Alignment explanation
Indices: 12941--12977 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12931 TTGAAATAAT
12941 TCTTCAATAATCTTCAAG
1 TCTTCAATAATCTTCAAG
*
12959 TCTTCAAATTATCTTCAAG
1 TCTTC-AATAATCTTCAAG
12978 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAG
Found at i:14322 original size:31 final size:30
Alignment explanation
Indices: 14250--14361 Score: 143
Period size: 30 Copynumber: 3.7 Consensus size: 30
14240 AGGTCGATTC
* *
14250 GGATTCCGAGGAGGATTTTGACACGGATGA
1 GGATCCCGAGGAGGATTTTGACCCGGATGA
* **
14280 CGATCCCGAGGAGGATTTTGACCCGGACAA
1 GGATCCCGAGGAGGATTTTGACCCGGATGA
*
14310 GGATCCCCGAGGACGATTTTGACCCGGATGA
1 GGAT-CCCGAGGAGGATTTTGACCCGGATGA
* *
14341 GGATCCCGAGGAAGAATTTGA
1 GGATCCCGAGGAGGATTTTGA
14362 GGTGTCAGCC
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
30 43 0.61
31 27 0.39
ACGTcount: A:0.27, C:0.21, G:0.33, T:0.20
Consensus pattern (30 bp):
GGATCCCGAGGAGGATTTTGACCCGGATGA
Found at i:19154 original size:45 final size:46
Alignment explanation
Indices: 19105--19240 Score: 130
Period size: 49 Copynumber: 2.8 Consensus size: 46
19095 CAGTCTTTAC
* * *
19105 TTACTT-TTCCCCAAAATGTCCTTCCCAGACATAAGCCATTCATTT
1 TTACTTATTCCCCAAAACGCCCTTCCCAGACAGAAGCCATTCATTT
* * *
19150 TTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATTT
1 TTAC-T--TATTCCCCAAAACGCCCTTCCCAGACAGAAGCCATTCATTT
* * *
19199 TTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA
1 TTAC-T--TATTCCCCAAAACGCCCTTCCCAGACAGAAGCCA
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
45 4 0.05
46 1 0.01
48 1 0.01
49 75 0.93
ACGTcount: A:0.24, C:0.33, G:0.12, T:0.30
Consensus pattern (46 bp):
TTACTTATTCCCCAAAACGCCCTTCCCAGACAGAAGCCATTCATTT
Found at i:19167 original size:49 final size:49
Alignment explanation
Indices: 19124--19240 Score: 207
Period size: 49 Copynumber: 2.4 Consensus size: 49
19114 CCCAAAATGT
*
19124 CCTTCCCAGACATAAGCCATTCATTTTTACTTGCTATTTCCCAAAGCGC
1 CCTTCCCAGACAGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGCGC
*
19173 CCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGCGC
1 CCTTCCCAGACAGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGCGC
*
19222 CCTTCCCAGACGGAAGCCA
1 CCTTCCCAGACAGAAGCCA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 66 1.00
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (49 bp):
CCTTCCCAGACAGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGCGC
Done.