Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024742.1 Corchorus olitorius cultivar O-4 contig24775, 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: 13624
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Found at i:2525 original size:31 final size:30
Alignment explanation
Indices: 2490--2547 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2480 CTAACCCTAG
*
2490 ACCCAGCA-GACCCGAGACCCGGATGACCTGA
1 ACCCAG-ATGACCCGA-ACCCGAATGACCTGA
*
2521 ACCCAGATGAGCCGAACCCGAATGACC
1 ACCCAGATGACCCGAACCCGAATGACC
2548 CGAGAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.31, C:0.38, G:0.24, T:0.07
Consensus pattern (30 bp):
ACCCAGATGACCCGAACCCGAATGACCTGA
Found at i:2550 original size:15 final size:15
Alignment explanation
Indices: 2498--2550 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
2488 AGACCCAGCA
*
2498 GACCCGAGACCCGGAT
1 GACCCGA-ACCCGAAT
*
2514 GACCTGAACCC-AGAT
1 GACCCGAACCCGA-AT
*
2529 GAGCCGAACCCGAAT
1 GACCCGAACCCGAAT
2544 GACCCGA
1 GACCCGA
2551 GAAAATTACC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 23 0.77
16 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.26, T:0.08
Consensus pattern (15 bp):
GACCCGAACCCGAAT
Found at i:3607 original size:75 final size:74
Alignment explanation
Indices: 3475--3699 Score: 274
Period size: 75 Copynumber: 3.0 Consensus size: 74
3465 TTTGAATGCC
* * *
3475 CTTTGGAAATTACTAA-AGGCTCTCATCAACTTTTAACATGGGAGAATCATTTTGCCCCGTTTTG
1 CTTTGGAATTTACTAATA-GCTCTCATCAACTTTTAACGTTGGAG-ATCATTTTGCCCCGTTTTG
3539 GTCTTTTCTCA
64 GTCTTTTCTCA
* * * *
3550 CTTTGGAATTTACCAATAGCTCTCTTCAACTTTTAACGTTGGAGAGCCTTTTCGCCCCGTTTTGG
1 CTTTGGAATTTACTAATAGCTCTCATCAACTTTTAACGTTGGAGATCATTTT-GCCCCGTTTTGG
3615 TCTTTTCTCA
65 TCTTTTCTCA
* * * ** *
3625 CTCTGGAATTTACTGATAGCTC-CAATCAACTTTTAATGTTGGAGATTTTTTTTGCCCTGTTTTG
1 CTTTGGAATTTACTAATAGCTCTC-ATCAACTTTTAACGTTGGAGA-TCATTTTGCCCCGTTTTG
3689 GTCTTTTCTCA
64 GTCTTTTCTCA
3700 ATTTATTAGT
Statistics
Matches: 130, Mismatches: 16, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
74 7 0.05
75 118 0.91
76 5 0.04
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (74 bp):
CTTTGGAATTTACTAATAGCTCTCATCAACTTTTAACGTTGGAGATCATTTTGCCCCGTTTTGGT
CTTTTCTCA
Found at i:3977 original size:2 final size:2
Alignment explanation
Indices: 3970--4017 Score: 57
Period size: 2 Copynumber: 24.5 Consensus size: 2
3960 CATAATGCCT
3970 TA TA TA TA TA TA CT- TA TA TA TA -A TA TA -A GTA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
4011 TA TA TA T
1 TA TA TA T
4018 TAATTAATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 3 0.07
2 36 0.88
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5289 original size:131 final size:133
Alignment explanation
Indices: 5072--5310 Score: 367
Period size: 131 Copynumber: 1.8 Consensus size: 133
5062 AATATTTTTT
* *
5072 AAAATTCTAATATATCTAAGTTTTTTTTAATTAAATTGGTAAAACGGTAAAAATAAAAATAGGTA
1 AAAATTCTAATATATCTAAG-TTTTTTTAATTAAAATAGTAAAACGGTAAAAATAAAAATAGGTA
*
5137 TAAGGATATTGGATTAAATTAAATAAAAATAGAGTTTTTAGTTAATTAAAACTTTAAAAGTATGT
65 TAAGGATATTAGATTAAATTAAATAAAAATAGAGTTTTTAGTTAATTAAAACTTTAAAAGTATGT
5202 TTAA
130 TTAA
* * * *
5206 AAAATTCTAATATATAC-AAG-TTTTTTAATTAAAATAGTATAATGGTAAAAAT-TAAATAGTTA
1 AAAATTCTAATATAT-CTAAGTTTTTTTAATTAAAATAGTAAAACGGTAAAAATAAAAATAGGTA
*
5268 TAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTT
65 TAAGGATATTAGATTAAATTAAATAAAAATAGAGTTTTTAGTT
5311 GAGTAAAATT
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
131 49 0.51
132 28 0.29
134 18 0.19
135 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (133 bp):
AAAATTCTAATATATCTAAGTTTTTTTAATTAAAATAGTAAAACGGTAAAAATAAAAATAGGTAT
AAGGATATTAGATTAAATTAAATAAAAATAGAGTTTTTAGTTAATTAAAACTTTAAAAGTATGTT
TAA
Found at i:5422 original size:15 final size:15
Alignment explanation
Indices: 5402--5431 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5392 CGTACTTTTT
5402 AATATAGTATAGATA
1 AATATAGTATAGATA
5417 AATATAGTATAGATA
1 AATATAGTATAGATA
5432 TAGATATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (15 bp):
AATATAGTATAGATA
Found at i:6405 original size:2 final size:2
Alignment explanation
Indices: 6400--6426 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6390 ACTATATAAA
6400 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
6427 ATGTACAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.