Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009509.1 Corchorus capsularis cultivar CVL-1 contig09530, 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: 19737
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:587 original size:110 final size:110
Alignment explanation
Indices: 352--648 Score: 454
Period size: 110 Copynumber: 2.6 Consensus size: 110
342 ACTATTATAG
* *
352 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
417 TATTTTTACC-AAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
466 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
531 TTACCAAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* **
576 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
640 TTTTTACCA
63 TTTTTACCA
649 TTTTAATTTA
Statistics
Matches: 173, Mismatches: 6, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
109 43 0.25
110 87 0.50
111 7 0.04
112 15 0.09
114 21 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (110 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:2747 original size:33 final size:32
Alignment explanation
Indices: 2700--2768 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
2690 CCAAGAGGGC
* *
2700 GGCTTACCGTGGCGAAGTCGCCCCACTTGGGA
1 GGCTTACCATGGCGAAGTCGCCCCACTGGGGA
*
2732 GGCTTAACCATGGCGAAGTCGCCCCAGTGGGGA
1 GGCTT-ACCATGGCGAAGTCGCCCCACTGGGGA
2765 GGCT
1 GGCT
2769 CCGCCGTGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 5 0.15
33 28 0.85
ACGTcount: A:0.17, C:0.29, G:0.36, T:0.17
Consensus pattern (32 bp):
GGCTTACCATGGCGAAGTCGCCCCACTGGGGA
Found at i:2870 original size:21 final size:21
Alignment explanation
Indices: 2846--2889 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2836 CAAAAGTGTA
*
2846 AAAAGTGGGGCGGTATTTAGC
1 AAAAGTAGGGCGGTATTTAGC
*
2867 AAAAGTAGGGTGGTATTTAGC
1 AAAAGTAGGGCGGTATTTAGC
2888 AA
1 AA
2890 CCCCCTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.34, T:0.25
Consensus pattern (21 bp):
AAAAGTAGGGCGGTATTTAGC
Found at i:4356 original size:30 final size:30
Alignment explanation
Indices: 4320--4379 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4310 AAGTTCGTGT
*
4320 TTGAAGATTTATTGAAG-ATAATTTCAAGAA
1 TTGAAGA-TCATTGAAGAATAATTTCAAGAA
*
4350 TTGAAGATCATTGAAGAATTATTTCAAGAA
1 TTGAAGATCATTGAAGAATAATTTCAAGAA
4380 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (30 bp):
TTGAAGATCATTGAAGAATAATTTCAAGAA
Found at i:10252 original size:30 final size:30
Alignment explanation
Indices: 10212--10270 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
10202 CAATGGGGAG
10212 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
* *
10242 GGAATTATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
10271 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.24
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:13894 original size:2 final size:2
Alignment explanation
Indices: 13887--13916 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13877 TCAAATGATC
13887 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
13917 TTTCATCATT
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:15129 original size:3 final size:3
Alignment explanation
Indices: 15121--15153 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
15111 ATGGTATGTC
15121 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
15154 TATATAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16672 original size:27 final size:27
Alignment explanation
Indices: 16635--16698 Score: 119
Period size: 27 Copynumber: 2.3 Consensus size: 27
16625 TAAAAACTAC
16635 TCCCTCTGTTCCTTTTTAATTGTCCCTT
1 TCCCT-TGTTCCTTTTTAATTGTCCCTT
16663 TCCCTTGTTCCTTTTTAATTGTCCCTT
1 TCCCTTGTTCCTTTTTAATTGTCCCTT
16690 TCCCTTGTT
1 TCCCTTGTT
16699 TTCCAGAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 31 0.86
28 5 0.14
ACGTcount: A:0.06, C:0.31, G:0.08, T:0.55
Consensus pattern (27 bp):
TCCCTTGTTCCTTTTTAATTGTCCCTT
Done.