Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009767.1 Corchorus capsularis cultivar CVL-1 contig09788, 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: 10670
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Found at i:2280 original size:35 final size:35
Alignment explanation
Indices: 2234--3318 Score: 1193
Period size: 35 Copynumber: 30.9 Consensus size: 35
2224 AACTCCTCTG
* * *
2234 GATCAACTCTGATCATC-GGAAATTTCTTGAAATGA
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
* * * * *
2269 GATCAACTCTGATCGT-TGGAAACTACTGGAAATGC
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
* * * *
2304 GATCAACTCTGATCGT-TGGAAACTAC-TGAAAATGC
1 GATCAACTCTGA-CCTCTGAAAACTTCTTG-AAATGA
* * * * * *
2339 GATCAACTTTGATCGT-TGGAAACTACTGGAAATGC
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
* * * * *
2374 GATCAACTCTGATCGT-TGGAAACTACTGGAAATGC
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
* * * * *
2409 GATCAACTCTGATCGT-TGGAAACTACTGGAAATGC
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
* * * *
2444 GATCAACTCTGATCGT-TGGAAACTAC-TGAAAATGC
1 GATCAACTCTGA-CCTCTGAAAACTTCTTG-AAATGA
* * * *
2479 GATCAACTCTGATCGT-TGGAGAA-TAC-TGAAAATGC
1 GATCAACTCTGA-CCTCT-GAAAACTTCTTG-AAATGA
* * * *
2514 GATCAACTCTGATCGT-TGGATAA-TAC-TGAAAATGC
1 GATCAACTCTGA-CCTCT-GAAAACTTCTTG-AAATGA
* * * *
2549 CATCAACTCTGATCATC-GGAAACTTCTTGGAATGA
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
*
2584 GATCAACTCTGACCTCTGAAAACGTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* * *
2619 GATCAACTCTAATCTCTGAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
2654 GATCAACTTTGACCTCTGAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
2689 GATCAACTCTGACCTCTGAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
2724 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
2759 GATCAACTCTGACCTCTGAAAACTTCTTTAAAATGA
1 GATCAACTCTGACCTCTGAAAACTTC-TTGAAATGA
** * *
2795 GATCAACTCTGATGAT-TGGAAACTTCTTGGAATGA
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
2830 GATCAACTCTGACCTCTTG-AAACTTCTT-AATATGA
1 GATCAACTCTGACCTC-TGAAAACTTCTTGAA-ATGA
* *
2865 GATCAACTCTGACCTCTGGAAACTTCTTGATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
2900 GATCAACTCTGACCTCTGAAAACTTGTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
2935 GATCAACTCTGACCTCTTAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
2970 GATTAATTCTGACCTC-GAAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTG-AAAACTTCTTGAAATGA
3005 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
3040 GATCAACTCTGACCTCTGAAAACATCCTCTGATATGA
1 GATCAACTCTGACCTCTGAAAAC-TTCT-TGAAATGA
3077 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
3112 GATCAACTCTGACCTCTGAAAACTTCTTGATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
3147 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
3182 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
3217 GATCAACTCTGACCTCTTAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
3252 GATCAACTCTGACCTCGGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
3287 GATCAACTCTGACCTCTGAAAACTTGTTGAAA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAA
3319 GACCGCACAG
Statistics
Matches: 961, Mismatches: 69, Indels: 40
0.90 0.06 0.04
Matches are distributed among these distances:
34 12 0.01
35 873 0.91
36 45 0.05
37 31 0.03
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (35 bp):
GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
Found at i:4427 original size:23 final size:22
Alignment explanation
Indices: 4396--4442 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
4386 AGCCTTATCA
*
4396 TTTCCCTTTTTTTCTGTTTTTTT
1 TTTCCCTTTTTTCCT-TTTTTTT
*
4419 TTTCTCTTTTTTCCTTTTTTTT
1 TTTCCCTTTTTTCCTTTTTTTT
4441 TT
1 TT
4443 GCCATGCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTCCCTTTTTTCCTTTTTTTT
Found at i:4541 original size:36 final size:37
Alignment explanation
Indices: 4500--4576 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
4490 ACTTTTTTAA
* *
4500 AAAACA-TTTTTCTTTTGAAAAGATTACACTTTGAGG
1 AAAACATTTTTTCTTTTGAAAAGATCACACTTTGAAG
*
4536 AAAACATTTTTTCTTTTGAAAATATCACACTTTGAAG
1 AAAACATTTTTTCTTTTGAAAAGATCACACTTTGAAG
4573 AAAA
1 AAAA
4577 TCTTCTTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 6 0.16
37 31 0.84
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (37 bp):
AAAACATTTTTTCTTTTGAAAAGATCACACTTTGAAG
Found at i:8917 original size:87 final size:86
Alignment explanation
Indices: 8703--9006 Score: 468
Period size: 87 Copynumber: 3.5 Consensus size: 86
8693 TTCCTTTTTT
* *
8703 ATATCTTCTAAAGCTCCCACAATTTGGCAAGATTTAGAAAATATTTTCATTATTATTAAATCTTT
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
8768 ATAATTTATT-TGTTTCTTAAA
66 ATAATTTATTAT-TTTCTTAAA
* * * * * *
8789 ATA-CTCCTAAACCTTCCACAACTTGACAAGATTTAGAAAATATTATCATCATTATTATATCTTT
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
8853 ATAATTTACTTATTTTCTTAAA
66 ATAATTTA-TTATTTTCTTAAA
*
8875 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTC
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
8940 ATAATTTATTTATTTTCTTAAA
66 ATAATTTA-TTATTTTCTTAAA
* *
8962 ATATCTTCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATT
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATT
9007 CTCTTTACAA
Statistics
Matches: 197, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
85 61 0.31
86 17 0.09
87 119 0.60
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (86 bp):
ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
ATAATTTATTATTTTCTTAAA
Found at i:9545 original size:2 final size:2
Alignment explanation
Indices: 9540--9568 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9530 GAAGAAAGAA
9540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9569 AATAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.