Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010681.1 Corchorus capsularis cultivar CVL-1 contig10702, 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: 23861
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:825 original size:3 final size:3
Alignment explanation
Indices: 817--846 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
807 ATTACTAGTT
817 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
847 GAGTTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3548 original size:30 final size:28
Alignment explanation
Indices: 3512--3576 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 28
3502 GATAACTTTA
3512 ATATATAGGTAATAGGTAATATATATATAT
1 ATATATAGGTAATA-GTAATATATA-ATAT
*
3542 ATATATAGGTAATATTAATATATAATAT
1 ATATATAGGTAATAGTAATATATAATAT
3570 ATATATA
1 ATATATA
3577 ACCCGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 11 0.32
29 9 0.26
30 14 0.41
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (28 bp):
ATATATAGGTAATAGTAATATATAATAT
Found at i:3552 original size:23 final size:26
Alignment explanation
Indices: 3523--3574 Score: 83
Period size: 23 Copynumber: 2.1 Consensus size: 26
3513 TATATAGGTA
3523 ATAGGTAATA-T-ATATAT-ATATAT
1 ATAGGTAATATTAATATATAATATAT
3546 ATAGGTAATATTAATATATAATATAT
1 ATAGGTAATATTAATATATAATATAT
3572 ATA
1 ATA
3575 TAACCCGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 10 0.38
24 1 0.04
25 6 0.23
26 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (26 bp):
ATAGGTAATATTAATATATAATATAT
Found at i:3945 original size:6 final size:6
Alignment explanation
Indices: 3934--3974 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
3924 TATATAGAAT
*
3934 ATATAA ATATAA ATATAA ATATAA A-ATAT AT-TAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA A
3975 AGAAATCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 8 0.26
6 23 0.74
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:3962 original size:7 final size:7
Alignment explanation
Indices: 3925--3975 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
3915 GACAAATATT
*
3925 ATATAGA
1 ATATAAA
3932 ATATATAA
1 ATATA-AA
3940 ATAT-AA
1 ATATAAA
3946 ATAT-AA
1 ATATAAA
3952 ATATAAA
1 ATATAAA
3959 ATATATTAA
1 ATATA--AA
3968 ATATAAA
1 ATATAAA
3975 A
1 A
3976 GAAATCTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
6 12 0.31
7 15 0.38
8 5 0.13
9 7 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (7 bp):
ATATAAA
Found at i:3980 original size:27 final size:27
Alignment explanation
Indices: 3925--3985 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
3915 GACAAATATT
* *
3925 ATATAGAATATATAAATATAAATATAA
1 ATATAAAATATATAAATATAAATAGAA
3952 ATATAAAATATATTAAATATAAA-AGAA
1 ATATAAAATATA-TAAATATAAATAGAA
*
3979 ATCTAAA
1 ATATAAA
3986 TGATTAAGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 20 0.67
28 10 0.33
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (27 bp):
ATATAAAATATATAAATATAAATAGAA
Found at i:4216 original size:2 final size:2
Alignment explanation
Indices: 4209--4238 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4199 ACTTTTGGCA
4209 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4239 GCACCGCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5432 original size:52 final size:50
Alignment explanation
Indices: 5365--5511 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 50
5355 TTAAAGATGT
* *
5365 TTAAGAATCCTTTATGAACAATGTTTAAAGATGGAAGAAAGTTTAATAATG
1 TTAAGAATCCTTTATGAATAATGTTTAAAGAT-GAAGAAACTTTAATAATG
* *
5416 CTTAATAATCCTTTATGAATAAGGTTTAAAGATTGAAGAAACTTTAATAATG
1 -TTAAGAATCCTTTATGAATAATGTTTAAAGA-TGAAGAAACTTTAATAATG
* *
5468 TGTAAGAATACTTAATGAATAATAAGCTTTAAAGATGAAGAAAC
1 T-TAAGAATCCTTTATGAATAAT--G-TTTAAAGATGAAGAAAC
5512 ATTTGGTTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
51 1 0.01
52 62 0.76
53 1 0.01
54 10 0.12
55 8 0.10
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.33
Consensus pattern (50 bp):
TTAAGAATCCTTTATGAATAATGTTTAAAGATGAAGAAACTTTAATAATG
Found at i:7387 original size:24 final size:23
Alignment explanation
Indices: 7359--7403 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
7349 ATTAGATGTT
7359 ATTTCATACTG-TTTGGACAAATAA
1 ATTTCAT-CTGATTTGG-CAAATAA
7383 ATTTCATCTGATTTGGCAAAT
1 ATTTCATCTGATTTGGCAAAT
7404 TTTTCTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (23 bp):
ATTTCATCTGATTTGGCAAATAA
Done.