Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009538.1 Corchorus capsularis cultivar CVL-1 contig09559, 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: 91669
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5150 original size:14 final size:14
Alignment explanation
Indices: 5113--5163 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
5103 ACTTGACCAG
*
5113 GTAATTAATTGAAATA
1 GTAA-TAATT-AATTA
*
5129 GTATTAATTAATTA
1 GTAATAATTAATTA
5143 GTAATAA-TAATTGA
1 GTAATAATTAATT-A
5157 GTAATAA
1 GTAATAA
5164 GTTTGTAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 5 0.16
14 18 0.58
15 5 0.16
16 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (14 bp):
GTAATAATTAATTA
Found at i:7515 original size:2 final size:2
Alignment explanation
Indices: 7508--7532 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7498 TAATAATTTC
7508 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 T
7533 GGAAAAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11337 original size:3 final size:3
Alignment explanation
Indices: 11329--11363 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
11319 ATTCAAAAAT
11329 GAA GAA GAA GAA GAA GAA GAA GAA GAA G-A GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
11364 ATTCACCTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:14958 original size:3 final size:3
Alignment explanation
Indices: 14952--14994 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
14942 GAAGAAAATT
14952 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
14995 ATATATAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:22328 original size:72 final size:72
Alignment explanation
Indices: 22211--22355 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
22201 AAAATCGTGC
22211 CTAAATTTAAGGAGTTCATTGAACATGATAAATTTTTACTGGTTAGTTCCATGAATAACGTGGTG
1 CTAAATTTAAGGAGTTCATTGAACATGATAAATTTTTACTGGTTAGTTCCATGAATAACGTGGTG
22276 GGTCTGT
66 GGTCTGT
*
22283 CTAAATTTAAGGAGTTCATTTAACATGATAAATTTTTACTGGTTAGTTCCATGAATAACGTGGTG
1 CTAAATTTAAGGAGTTCATTGAACATGATAAATTTTTACTGGTTAGTTCCATGAATAACGTGGTG
22348 GGTCTGT
66 GGTCTGT
22355 C
1 C
22356 CCACCTAATA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (72 bp):
CTAAATTTAAGGAGTTCATTGAACATGATAAATTTTTACTGGTTAGTTCCATGAATAACGTGGTG
GGTCTGT
Found at i:42823 original size:11 final size:11
Alignment explanation
Indices: 42807--42833 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
42797 TTTTAATTTC
42807 TTCTTTTTTTT
1 TTCTTTTTTTT
42818 TTCTTTTTTTT
1 TTCTTTTTTTT
42829 TTCTT
1 TTCTT
42834 ATTAGAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:50834 original size:64 final size:64
Alignment explanation
Indices: 50733--50861 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
50723 TATTATTAAT
* *
50733 CAAATCATAAATCAGGGTTGGAGGAAGTCCACATTCACCATACTAAATTAACTATTCATCTTGC
1 CAAATCATAAATCAGGGTCGGAGGAAGTCCACATTCACCATACTAAATTAACAATTCATCTTGC
* *
50797 CAAATCCTAAATCAGGGTCGGAGGAAGTTCACATTCACCATACTAAATTAACAATTCATCTTGC
1 CAAATCATAAATCAGGGTCGGAGGAAGTCCACATTCACCATACTAAATTAACAATTCATCTTGC
50861 C
1 C
50862 CATGCGGGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (64 bp):
CAAATCATAAATCAGGGTCGGAGGAAGTCCACATTCACCATACTAAATTAACAATTCATCTTGC
Found at i:79857 original size:2 final size:2
Alignment explanation
Indices: 79781--79838 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
79771 AAAAAAATGC
* ** *
79781 AT AT AT AT AT AA AT AT GC AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79823 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
79839 GTGTGTGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Done.