Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010422.1 Corchorus capsularis cultivar CVL-1 contig10443, 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: 34058
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:396 original size:23 final size:23
Alignment explanation
Indices: 366--412 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
356 GATCCGTTGA
366 GCGGTGGTAATAGCAACGGCGGC
1 GCGGTGGTAATAGCAACGGCGGC
* *
389 GCGGTGGTGATAGCAACGGTGGC
1 GCGGTGGTAATAGCAACGGCGGC
412 G
1 G
413 ATGGCAAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.47, T:0.15
Consensus pattern (23 bp):
GCGGTGGTAATAGCAACGGCGGC
Found at i:11407 original size:432 final size:426
Alignment explanation
Indices: 10577--11437 Score: 1537
Period size: 432 Copynumber: 2.0 Consensus size: 426
10567 CCCATAGCAA
*
10577 AGTAGCGATCTAGAGTAGTCTGATCATCAGTAGTCTTCTAGCTGACTCGAAGTTCACACACATCC
1 AGTAGCGATCTAGAGTAGTCTGATCATCAGTAGTCTTCCAGCTGACTCGAAGTTCACACACATCC
*
10642 TCATTAAGGCATGAATATCGTCAGAAGTGAAGAAACTTGTATATATTCGATAAATGTTTGCTTTT
66 TCATTAAGGCATGAATATCGTCAGAAGTGAAGAAACTTGTATATATTCGATAAATGTTTGCATTT
10707 TTATGGACCCAAATTTGAACTCATTCAGCCAAACTATGATCCAAGCCTAAAGTCAATTAAAATAA
131 TTATGGACCCAAATTTGAACTCATTCAGCCAAACTATGATCCAAGCCTAAAGTCAATTAAAATAA
*
10772 AGAGAAAGACTAATCGGGCTACTAAAATGTGTTAATGAATATTAATTGATTGGTTTAAGTCGTTT
196 AGAGAAAGACTAATCAGGCTACTAAAATGTGTTAATGAATATTAA-T-ATTGGTTTAAGTCGTTT
*
10837 GTCGCTTGTTTTCATTAAGCAATGGTTTGGGTTTAAGTATTACGAATAAGGAAATTATTGTTGAG
259 GTCGCTTGTTTTCATTAAGCAATGGTTTGAGTTTAAGTATTACGAATAAGGAAATTATTGTTGAG
* * *
10902 AGAGAGAGGGGGAGAGCTTTAATCTGTAGTGGGTCCAATACAAGTGTTAGACATTCAGTGTTAGA
324 AGAAAGAGAGGGAGAGCTTTAATCTGCAGTGGGTCCAATACAAGTGTTAGACATTCAGTGTTAGA
10967 CTAAATTTAATTTAGCTGAGAAATTAGCTTTCGAGGAG
389 CTAAATTTAATTTAGCTGAGAAATTAGCTTTCGAGGAG
11005 AGTAGCGATCTAGAGTAGTCTGATCATCAGTAGTCTTCCAGCTGACTCGAAGTTCACACACATCC
1 AGTAGCGATCTAGAGTAGTCTGATCATCAGTAGTCTTCCAGCTGACTCGAAGTTCACACACATCC
11070 TCATTAAGGCATGAATATCGTCAGAAGTGAAGAAACTTGTATATATTCGATAAATGTTTGCATTT
66 TCATTAAGGCATGAATATCGTCAGAAGTGAAGAAACTTGTATATATTCGATAAATGTTTGCATTT
*
11135 TTATGGACCCAAATTTGAAATGCAGGGCTCATTGAGCCAAACTATGATCCAAGCCTAAAGTCAAT
131 TTATGGACCCAAATTTG--A---A---CTCATTCAGCCAAACTATGATCCAAGCCTAAAGTCAAT
11200 TAAAATAAAGAGAAAGACTAATCAGGCTACTAAAATGTGTTAATGAATATT-A-ATTGGTTTAAG
188 TAAAATAAAGAGAAAGACTAATCAGGCTACTAAAATGTGTTAATGAATATTAATATTGGTTTAAG
*
11263 TGGTTTGTCGCTTGTTTTCATTAAGCAATGGTTTGAGTTTAAGTATTACGAATAAGGAAATTATT
253 TCGTTTGTCGCTTGTTTTCATTAAGCAATGGTTTGAGTTTAAGTATTACGAATAAGGAAATTATT
11328 GTTGAGAGAAAGAGAGGGAGAGCTTTAATCTGCAGTGGGTCCAATACAAGTGTTAGACATTCAGT
318 GTTGAGAGAAAGAGAGGGAGAGCTTTAATCTGCAGTGGGTCCAATACAAGTGTTAGACATTCAGT
11393 GTTAGACTAAATTTAATTTAGCTGAGAAATTAGCTTTCGAGGAG
383 GTTAGACTAAATTTAATTTAGCTGAGAAATTAGCTTTCGAGGAG
11437 A
1 A
11438 AGAAAACTGA
Statistics
Matches: 416, Mismatches: 9, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
428 145 0.35
430 1 0.00
432 181 0.44
433 1 0.00
435 1 0.00
436 87 0.21
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (426 bp):
AGTAGCGATCTAGAGTAGTCTGATCATCAGTAGTCTTCCAGCTGACTCGAAGTTCACACACATCC
TCATTAAGGCATGAATATCGTCAGAAGTGAAGAAACTTGTATATATTCGATAAATGTTTGCATTT
TTATGGACCCAAATTTGAACTCATTCAGCCAAACTATGATCCAAGCCTAAAGTCAATTAAAATAA
AGAGAAAGACTAATCAGGCTACTAAAATGTGTTAATGAATATTAATATTGGTTTAAGTCGTTTGT
CGCTTGTTTTCATTAAGCAATGGTTTGAGTTTAAGTATTACGAATAAGGAAATTATTGTTGAGAG
AAAGAGAGGGAGAGCTTTAATCTGCAGTGGGTCCAATACAAGTGTTAGACATTCAGTGTTAGACT
AAATTTAATTTAGCTGAGAAATTAGCTTTCGAGGAG
Found at i:14037 original size:30 final size:30
Alignment explanation
Indices: 14003--14064 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
13993 GATTGACTCT
*
14003 AAAAACTTACTCAACGTACTAAAAAACCCA
1 AAAAACTGACTCAACGTACTAAAAAACCCA
* *
14033 AAAAACTGACTCAACTTACTAAAAAATCCA
1 AAAAACTGACTCAACGTACTAAAAAACCCA
14063 AA
1 AA
14065 GGGGACTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.55, C:0.24, G:0.03, T:0.18
Consensus pattern (30 bp):
AAAAACTGACTCAACGTACTAAAAAACCCA
Found at i:14359 original size:2 final size:2
Alignment explanation
Indices: 14352--14384 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
14342 GACGGAAAGG
14352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
14385 GATAATGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16515 original size:6 final size:6
Alignment explanation
Indices: 16497--16534 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
16487 TCACAAGATG
*
16497 AGCTGA AGTTGA AGCTGA AGCTGA AGCTGA AGCTGA AG
1 AGCTGA AGCTGA AGCTGA AGCTGA AGCTGA AGCTGA AG
16535 AAGTTGGAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.18
Consensus pattern (6 bp):
AGCTGA
Done.