Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007564.1 Corchorus capsularis cultivar CVL-1 contig07585, 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: 22525
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:14029 original size:2 final size:2
Alignment explanation
Indices: 14024--14054 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14014 ATCAAATCAA
14024 AT 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 AT A
14055 GTTTAAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20644 original size:2 final size:2
Alignment explanation
Indices: 20639--20691 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
20629 AAAAAAAATA
* * *
20639 AT AT AT AT -T A- AT AA AT AT AT AT AT AT AT AT AT AT AC AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20679 AGT AT AT AT AT AT
1 A-T AT AT AT AT AT
20692 TATGTATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:21581 original size:31 final size:31
Alignment explanation
Indices: 21546--21607 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
21536 ATACTTTGAG
*
21546 GCCCATGACCAATGGGATAGAATTGGGCTAT
1 GCCCATGACCAATAGGATAGAATTGGGCTAT
21577 GCCCATGACCAATAGGATAGAATTGGGCTAT
1 GCCCATGACCAATAGGATAGAATTGGGCTAT
21608 TGGAAAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (31 bp):
GCCCATGACCAATAGGATAGAATTGGGCTAT
Found at i:22376 original size:33 final size:33
Alignment explanation
Indices: 22334--22454 Score: 190
Period size: 33 Copynumber: 3.7 Consensus size: 33
22324 CTTTTACACT
*
22334 GAGCCTCCCCACTAGGACGGCTCAGCCACGGTA
1 GAGCCTCCCCACTAGGACGGCTCAGCCACGGTG
22367 GAGCCTCCCCACTAGGACGGCTCAGCCACGGTG
1 GAGCCTCCCCACTAGGACGGCTCAGCCACGGTG
* *
22400 GAGCCTCCCCACTAGGGA-GGCTCAACCACGGCG
1 GAGCCTCCCCACTA-GGACGGCTCAGCCACGGTG
*
22433 GAGCCTCCCCACTAGGGCGGCT
1 GAGCCTCCCCACTAGGACGGCT
22455 TCACCATGGG
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
32 2 0.02
33 77 0.94
34 3 0.04
ACGTcount: A:0.19, C:0.40, G:0.30, T:0.12
Consensus pattern (33 bp):
GAGCCTCCCCACTAGGACGGCTCAGCCACGGTG
Found at i:22418 original size:16 final size:16
Alignment explanation
Indices: 22399--22449 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
22389 CAGCCACGGT
22399 GGAGCCTCCCCACTAG
1 GGAGCCTCCCCACTAG
* * *
22415 GGAGGCTCAACCAC-GG
1 GGAGCCTC-CCCACTAG
22431 CGGAGCCTCCCCACTAG
1 -GGAGCCTCCCCACTAG
22448 GG
1 GG
22450 CGGCTTCACC
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.20, C:0.39, G:0.31, T:0.10
Consensus pattern (16 bp):
GGAGCCTCCCCACTAG
Found at i:22476 original size:33 final size:32
Alignment explanation
Indices: 22340--22503 Score: 127
Period size: 33 Copynumber: 5.0 Consensus size: 32
22330 CACTGAGCCT
* * *
22340 CCCCACTAGGACGGC-TCAGCCACGGTAGAGCCT
1 CCCCACTAGGGCGGCTTCA-CCACGGCAG-GCCG
* ** *
22373 CCCCACTAGGACGGC-TCAGCCACGGTGGAGCCT
1 CCCCACTAGGGCGGCTTCA-CCACGGCAG-GCCG
* * *
22406 CCCCACTAGGGAGGC-TCAACCACGGCGGAGCCT
1 CCCCACTAGGGCGGCTTC-ACCACGGCAG-GCCG
*
22439 CCCCACTAGGGCGGCTTCACCATGGGCAGGCCG
1 CCCCACTAGGGCGGCTTCACCA-CGGCAGGCCG
* *
22472 CCCCACTGGGGCGGCTTCGCCACGGCAGGCCG
1 CCCCACTAGGGCGGCTTCACCACGGCAGGCCG
22504 TCCCGGTGGG
Statistics
Matches: 117, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
32 9 0.08
33 101 0.86
34 7 0.06
ACGTcount: A:0.17, C:0.40, G:0.32, T:0.11
Consensus pattern (32 bp):
CCCCACTAGGGCGGCTTCACCACGGCAGGCCG
Found at i:22495 original size:66 final size:66
Alignment explanation
Indices: 22335--22507 Score: 183
Period size: 66 Copynumber: 2.6 Consensus size: 66
22325 TTTTACACTG
* * *
22335 AGCCTCCCCACTAGGACGGCTCAGCCACGGTAGAGCCTCCCCACTAGGACGGCTCAGCCACGGTG
1 AGCCGCCCCACTAGGGCGGCTCAGCCACGGCAGAGCCTCCCCACTAGGACGGCTCAGCCACGGTG
*
22400 G
66 C
* * * * * *
22401 AGCCTCCCCACTAGGGAGGCTCAACCACGGCGGAGCCTCCCCACTAGGGCGGCTTCA-CCATGG-
1 AGCCGCCCCACTAGGGCGGCTCAGCCACGGCAGAGCCTCCCCACTAGGACGGC-TCAGCCACGGT
22464 GC
65 GC
*
22466 AGGCCGCCCCACTGGGGCGGCTTC-GCCACGGCAG-GCCGTCCC
1 A-GCCGCCCCACTAGGGCGGC-TCAGCCACGGCAGAGCC-TCCC
22508 GGTGGGGCGG
Statistics
Matches: 90, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
65 5 0.06
66 80 0.89
67 5 0.06
ACGTcount: A:0.17, C:0.41, G:0.31, T:0.12
Consensus pattern (66 bp):
AGCCGCCCCACTAGGGCGGCTCAGCCACGGCAGAGCCTCCCCACTAGGACGGCTCAGCCACGGTG
C
Found at i:22514 original size:32 final size:33
Alignment explanation
Indices: 22439--22519 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
22429 GGCGGAGCCT
* *
22439 CCCCACTAGGGCGGCTTCACCATGGGCAGGCCG
1 CCCCACTGGGGCGGCTTCACCATCGGCAGGCCG
*
22472 CCCCACTGGGGCGGCTTCGCCA-CGGCAGGCCG
1 CCCCACTGGGGCGGCTTCACCATCGGCAGGCCG
* **
22504 TCCCGGTGGGGCGGCT
1 CCCCACTGGGGCGGCT
22520 AGACCA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 22 0.52
33 20 0.48
ACGTcount: A:0.10, C:0.40, G:0.38, T:0.12
Consensus pattern (33 bp):
CCCCACTGGGGCGGCTTCACCATCGGCAGGCCG
Done.