Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016414.1 Corchorus capsularis cultivar CVL-1 contig16435, 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: 17968
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Found at i:582 original size:56 final size:57
Alignment explanation
Indices: 495--609 Score: 178
Period size: 56 Copynumber: 2.0 Consensus size: 57
485 ATCAAACCTC
495 CAAAAGGTGCACAATAAGAAGCAGGCAAAAAAATGAGATGC-TGCAAGAGACCCAAG
1 CAAAAGGTGCACAATAAGAAGCAGGCAAAAAAATGAGATGCATGCAAGAGACCCAAG
**
551 CAAAAGGTGCACAATAAGAAGCAGGGTAAAAAATGAGATGCATAATGCAAGAGACCCAA
1 CAAAAGGTGCACAATAAGAAGCAGGCAAAAAAATGAGATGC---ATGCAAGAGACCCAA
610 CCTGAAATCT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
56 39 0.74
60 14 0.26
ACGTcount: A:0.49, C:0.17, G:0.24, T:0.10
Consensus pattern (57 bp):
CAAAAGGTGCACAATAAGAAGCAGGCAAAAAAATGAGATGCATGCAAGAGACCCAAG
Found at i:10006 original size:21 final size:21
Alignment explanation
Indices: 9972--10028 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
9962 CTCGACTCCA
*
9972 GCTTGG-GGCCCATGTGGTAT
1 GCTTGGCGACCCATGTGGTAT
* *
9992 GCTTGGCGCCCCATGTGGTTT
1 GCTTGGCGACCCATGTGGTAT
* *
10013 GCCTCGCGACCCATGT
1 GCTTGGCGACCCATGT
10029 CCTCCAGTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.09, C:0.30, G:0.33, T:0.28
Consensus pattern (21 bp):
GCTTGGCGACCCATGTGGTAT
Found at i:16127 original size:54 final size:54
Alignment explanation
Indices: 16048--16150 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
16038 AAATAATTTA
* *
16048 AAGTGGATAGTATGACAGCTTCGGGTGTCAAACTTTGGCAACAAGTAAAGTTTT
1 AAGTGGATACTATGACAACTTCGGGTGTCAAACTTTGGCAACAAGTAAAGTTTT
* *
16102 AAGTGGATACTTTGACAACTTCGGGTGTCAAACTTTGGCAACAATTAAA
1 AAGTGGATACTATGACAACTTCGGGTGTCAAACTTTGGCAACAAGTAAA
16151 CAAATAGTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (54 bp):
AAGTGGATACTATGACAACTTCGGGTGTCAAACTTTGGCAACAAGTAAAGTTTT
Found at i:16280 original size:33 final size:33
Alignment explanation
Indices: 16238--16364 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
16228 TATATTTTTT
16238 ATGTGACAACTTCAGGTGCCACTAATATGCTTG
1 ATGTGACAACTTCAGGTGCCACTAATATGCTTG
* *
16271 ATGTGACAACTTCAAGTGCCACTGATATGCTTG
1 ATGTGACAACTTCAGGTGCCACTAATATGCTTG
* * **
16304 ATGTGACAACTTCATGTGCCCCTAATATATTTG
1 ATGTGACAACTTCAGGTGCCACTAATATGCTTG
16337 ATGTGACAACTTCAGGTGCCACTAATAT
1 ATGTGACAACTTCAGGTGCCACTAATAT
16365 TCAAGAGTAA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (33 bp):
ATGTGACAACTTCAGGTGCCACTAATATGCTTG
Found at i:16462 original size:32 final size:33
Alignment explanation
Indices: 16396--16469 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
16386 ATAATTTTTA
* * *
16396 ATGATAAAAGAAAGGTAGTAGGAGGAGATTATGC
1 ATGAT-AAAGAAAGGTAGTAAGAAGAGATCATGC
16430 ATGATAAAGAAAGGTAG-AAGAAGAGATCATGC
1 ATGATAAAGAAAGGTAGTAAGAAGAGATCATGC
*
16462 ATGTTAAA
1 ATGATAAA
16470 TAAATTTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 19 0.53
33 12 0.33
34 5 0.14
ACGTcount: A:0.47, C:0.04, G:0.28, T:0.20
Consensus pattern (33 bp):
ATGATAAAGAAAGGTAGTAAGAAGAGATCATGC
Found at i:16698 original size:17 final size:17
Alignment explanation
Indices: 16665--16716 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
16655 TATGGAAAAG
16665 ACAAGAGAAT-TGAGAGA
1 ACAAGAGAATATG-GAGA
16682 ACAAGAGAATATGGAGA
1 ACAAGAGAATATGGAGA
* *
16699 AGAAAAGAATATGGAGA
1 ACAAGAGAATATGGAGA
16716 A
1 A
16717 TGGGAGAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 30 0.94
18 2 0.06
ACGTcount: A:0.56, C:0.04, G:0.29, T:0.12
Consensus pattern (17 bp):
ACAAGAGAATATGGAGA
Found at i:16706 original size:19 final size:19
Alignment explanation
Indices: 16655--16716 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 19
16645 AGAATTGAAG
* *
16655 TATGGAAAAGACAAGAGAA
1 TATGGAGAAGAAAAGAGAA
16674 T-T-GAG-AGAACAAGAGAA
1 TATGGAGAAGAA-AAGAGAA
16691 TATGGAGAAG-AAA-AGAA
1 TATGGAGAAGAAAAGAGAA
16708 TATGGAGAA
1 TATGGAGAA
16717 TGGGAGAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 3 0.08
17 23 0.62
18 4 0.11
19 5 0.14
20 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.29, T:0.13
Consensus pattern (19 bp):
TATGGAGAAGAAAAGAGAA
Found at i:17014 original size:6 final size:6
Alignment explanation
Indices: 17003--17029 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16993 AAAGCAAAGC
17003 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
17030 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Done.