Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010244.1 Corchorus capsularis cultivar CVL-1 contig10265, 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: 13413
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:439 original size:12 final size:10
Alignment explanation
Indices: 408--450 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
398 TGTTCATGAA
408 TATGTTCGATT
1 TATGTTCG-TT
*
419 AATGTTCGTT
1 TATGTTCGTT
429 TGATAGTTCGTT
1 T-AT-GTTCGTT
441 TATGTTCGTT
1 TATGTTCGTT
451 AAATAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 9 0.32
11 11 0.39
12 8 0.29
ACGTcount: A:0.16, C:0.09, G:0.21, T:0.53
Consensus pattern (10 bp):
TATGTTCGTT
Found at i:3278 original size:4 final size:4
Alignment explanation
Indices: 3269--3294 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3259 GTTAAGCCAA
3269 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
3295 TTTTTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:3572 original size:7 final size:7
Alignment explanation
Indices: 3560--3584 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3550 CAAGTGTCTA
3560 TTTTCTC
1 TTTTCTC
3567 TTTTCTC
1 TTTTCTC
3574 TTTTCTC
1 TTTTCTC
3581 TTTT
1 TTTT
3585 GTTGGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCTC
Found at i:7763 original size:3 final size:3
Alignment explanation
Indices: 7755--7786 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
7745 TGCACCTTAT
7755 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
7787 CTATATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:7799 original size:2 final size:2
Alignment explanation
Indices: 7788--7819 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
7778 ATTATTATTC
7788 TA TA TA -A TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7820 GTTGTGCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:8004 original size:23 final size:25
Alignment explanation
Indices: 7963--8011 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
7953 ATCAATTAGT
7963 ACTATAAATAGGTAGGGTATG-ACA
1 ACTATAAATAGGTAGGGTATGTACA
7987 ACTATAAATA-GTAGGGTATGTACA
1 ACTATAAATAGGTAGGGTATGTACA
8011 A
1 A
8012 AATGCAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (25 bp):
ACTATAAATAGGTAGGGTATGTACA
Found at i:9009 original size:12 final size:12
Alignment explanation
Indices: 8976--9010 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
8966 CATATATAAT
8976 AACTAAATTTTA
1 AACTAAATTTTA
8988 AA-TAAATTTTA
1 AACTAAATTTTA
*
8999 AACTTAATTTTA
1 AACTAAATTTTA
9011 CATTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (12 bp):
AACTAAATTTTA
Found at i:9972 original size:242 final size:242
Alignment explanation
Indices: 9541--9995 Score: 611
Period size: 242 Copynumber: 1.9 Consensus size: 242
9531 ACAAAGTTCC
* *
9541 CCTCTTCATATGGTCCCAATAAGTAGATAGAAATAATAACTAAATGAATGTTTTTGATCATCCAT
1 CCTCTTCATATAGTCCCAATAAGTAGATAGAAATAATAACTAAATGAATGTTTTTGAGCA--CAT
** * *
9606 GTGTTAATAATGGCCTTATTCTTTTCGACTAATGTATTGAATGCTGCACAGCAAACGGCCCCATC
64 GTGTTAATAATGGCAGTATTCTTTTCGACTAATGTATTGAATGCTGCAAAACAAACGGCCCCATC
* *
9671 TTCATATAATTCCAATAAGTAGATAGGAAATGAATGTTATTGATCAATGTGATAATGATGCCTAG
129 TTCATATAATCCCAATAAGTAGATAGGAAATGAATATTATTGATCAATGTGATAATGATGCCTAG
9736 TTTCTTCTT-GACTTTGTAATGTTGCATAACAAATTGTTATATATGGTCA
194 TTTCTT-TTGGACTTTGTAATGTTGCATAACAAATTGTTATATATGGTCA
* *
9785 CCTCTTCTTATAGTCGCAATAAGTAGATATG-AATAATAACT-AATGAATGTTATTT-AGCA-AT
1 CCTCTTCATATAGTCCCAATAAGTAGATA-GAAATAATAACTAAATGAATGTT-TTTGAGCACAT
* * * *
9846 GTGTTAATAAT-GCAAAGT-TTCTTTTGGACTGATGTATTGAATAAGTTGCAAAACAAACGG-CT
64 GTGTTAATAATGGC--AGTATTCTTTTCGACTAATGTATTGAAT--GCTGCAAAACAAACGGCCC
* * *
9908 CATCTTCATATAGTCCCAATAGGTAGATGGGAAATGAAATATTATTGATCAATGTGATAATGATG
125 CATCTTCATATAATCCCAATAAGTAGATAGGAAATG-AATATTATTGATCAATGTGATAATGATG
9973 CCTAGTTTCTTTTGGACTTTGTA
189 CCTAGTTTCTTTTGGACTTTGTA
9996 TGGAACGTTG
Statistics
Matches: 186, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
239 2 0.01
240 35 0.19
241 36 0.19
242 60 0.32
243 13 0.07
244 39 0.21
245 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (242 bp):
CCTCTTCATATAGTCCCAATAAGTAGATAGAAATAATAACTAAATGAATGTTTTTGAGCACATGT
GTTAATAATGGCAGTATTCTTTTCGACTAATGTATTGAATGCTGCAAAACAAACGGCCCCATCTT
CATATAATCCCAATAAGTAGATAGGAAATGAATATTATTGATCAATGTGATAATGATGCCTAGTT
TCTTTTGGACTTTGTAATGTTGCATAACAAATTGTTATATATGGTCA
Found at i:10087 original size:45 final size:45
Alignment explanation
Indices: 10022--10111 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
10012 AAATGTTCAC
* ** *
10022 CTCTTCTTATAGTCTGAATAATTAGATAT-TATGTAATAATAACTA
1 CTCTTCGTATAGTCCCAATAAGTAGATATATATG-AATAATAACTA
10067 CTCTTCGTATAGTCCCAATAAGTAGATATATATGAATAATAACTA
1 CTCTTCGTATAGTCCCAATAAGTAGATATATATGAATAATAACTA
10112 AACAGATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 36 0.90
46 4 0.10
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (45 bp):
CTCTTCGTATAGTCCCAATAAGTAGATATATATGAATAATAACTA
Done.