Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013898.1 Corchorus capsularis cultivar CVL-1 contig13919, 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: 6992
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Found at i:662 original size:6 final size:6
Alignment explanation
Indices: 651--695 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
641 ATTAATTTGC
*
651 TTTAGA TTTAGA TTCAGA TTTAGA TTTAGA TTTAGA TTTA-A TTTA
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTA
696 CTTTGCTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51
Consensus pattern (6 bp):
TTTAGA
Found at i:733 original size:15 final size:15
Alignment explanation
Indices: 713--742 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
703 TAGTATTTAG
*
713 TTTAATTGTTTTCTT
1 TTTAATTGCTTTCTT
728 TTTAATTGCTTTCTT
1 TTTAATTGCTTTCTT
743 AAAATCCCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTAATTGCTTTCTT
Found at i:4033 original size:333 final size:329
Alignment explanation
Indices: 2989--4744 Score: 1528
Period size: 334 Copynumber: 5.3 Consensus size: 329
2979 AGTAGTAAAA
* * * *
2989 ACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCAGCCACATTGGATTTAAAGATTTGATTT
1 ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTT
* * * *
3054 TACGAGCATCTAAATCTTGTTTTGATTTAATTAGAAATTAATTGGGAAAAAGTA-G-AAAATGAT
66 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT-TGAAAAA-TATGAAAAACGAT
* * * *
3117 ATTAGAAGCAT-AAAAATCTCTTCAATATTTTTGGCA-TTAAATTATATAT-TTTTATTAGTATT
129 ATTAAAAGCATGAAAAGTC-CTTCAATCTTTTTGG-AGTTAAATTATATATATTTTATGAGTATT
* * * * * *
3179 TTAGCCAAAAAATGAGGAAATATCATTT-GAGTCAATATTTGCAAAATGTTAGCC-GAAATCGTG
192 TTAGCCAAAAATTGA-GAAAAAT-TTTTCGGGTC-ATTTTTGCAAAATTTTA-CCTGAAATCGTG
* * * * * ** * * ** ***
3242 TAAAATAATCATCA-TGATTTTTGGAAAAAAAAAGTGTCCCAAAGCCCC-GAGTCAGTTTTGCAT
253 T--ACTAACCATCACGGTTTTTTTG-CTAAAAACGCGTTTCGGGGCCCCGGA-TCAGTTTTGCAT
* *
3305 GATTTATGGCGTCAAG
314 GATTTTTTGCGTCAAG
**
3321 ACTCCTTGAGGTAT-TCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTT
1 ACTCCTTGAAATATCT-ATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTT
* * * *
3385 TTACGAACATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTATGAAAAATATAAAAAATGAT
65 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT-TGAAAAATATGAAAAACGAT
* * * * *
3450 ATGAAAGGC-TCGAAAAGTCATTCAACCTTTTTGGAATTAAATTATATATATATTTCATGAGTAT
129 ATTAAAAGCAT-GAAAAGTCCTTCAATCTTTTTGGAGTTAAATTATATATAT-TTT-ATGAGTAT
* * *
3514 TTTAGCCAAAAATTGA-AGAAAATTTTTCGGGT-AGTTTTTTGCAAAATTTTTA-GTCAAAATCA
191 TTTAGCCAAAAATTGAGA-AAAATTTTTCGGGTCA--TTTTTGCAAAA-TTTTACCT-GAAATCG
* * * * *
3576 TGTACTAACCATGACTGTTTTTTTGCTAAAAACGAGTTTTGGGGCTCC-GACTCAGTTTTGCATG
251 TGTACTAACCATCACGGTTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGA-TCAGTTTTGCATG
* * *
3640 AGTTTTAGCGTCGAG
315 ATTTTTTGCGTCAAG
* * * * *
3655 ACTCCTT-AGAATATCTATATTCATCTAATTAAATTTCAACCACATTGCATTTAAGAAATTGTTT
1 ACTCCTTGA-AATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTT
*
3719 ATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAATATGAAAAACGAT
65 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT-TGAAAAATATGAAAAACGAT
* * *
3784 ATTAAAAGCGTGAAAAGGCCTCCAATCTTTTTGGAGTTAAATTATATATATTTTATGAGTATTTT
129 ATTAAAAGCATGAAAAGTCCTTCAATCTTTTTGGAGTTAAATTATATATATTTTATGAGTATTTT
* * *
3849 ATCCAAAAATTGAGTAAAAATTTTTCGGGTCATTATTTGCAAAATTTTACCTGGAATTGTGTACT
194 AGCCAAAAATTGAG-AAAAATTTTTCGGGTCATT-TTTGCAAAATTTTACCTGAAATCGTGTACT
* *
3914 AACCATTACGGTTTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGATCAGTTTTGCATTATTTTT
257 AACCATCACGG-TTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGATCAGTTTTGCATGATTTTT
*
3979 TGCGTCGAG
321 TGCGTCAAG
* * * * *
3988 ACTCCTTGAAATATCTATACTCATCTAAACAAATCTCAGCCACATTTGAATTTGATGATTTGTTT
1 ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACA-TTGCATTTAAGGATTTGTTT
* * * * *
4053 TTATGAGCATCTGAATCTTGTTTTGATTTAATTAGAAACTAATTTAGAGAAATATGGAAAACGAT
65 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTT-GAAAAATATGAAAAACGAT
* * * * * **
4118 ATAAAAAGCGTGAAAAGTCCTCCAATATTTTTGGAGTTGAATTATATATA--TTATGAGTATAGT
129 ATTAAAAGCATGAAAAGTCCTTCAATCTTTTTGGAGTTAAATTATATATATTTTATGAGTATTTT
* * * * * ** *
4181 GGCTAAAAATTGAGAAAATATATTTCGTGTTTATTTTTGCAAAATTTTAGTTGAAATCGTGTACC
194 AGCCAAAAATTGAGAAAA-ATTTTTCG-GGTCATTTTTGCAAAATTTTACCTGAAATCGTGTACT
** * * * * * *
4246 ATGCATCAAGGTTTTTTTTGGCTAAAAACACGTTCCGGGGTCTCGGGTCAGTTTTGCATGATTTT
257 AACCATCACGG-TTTTTTT-GCTAAAAACGCGTTTCGGGGCCCCGGATCAGTTTTGCATGATTTT
* * *
4311 TTGTGGCAAA
320 TTGCGTCAAG
* * * * *
4321 ACTCCTTGAAATATCTATAGTCATCTAACCTAATCTTAGCCACATTGGATTTAAGGATTTGTTTT
1 ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTT
* * * * * *
4386 TACGAGCATTTGAATCATGTACTT-AATGTGATTAGAAATTAATTTGAAAAAGAAAATAAGAAAA
66 TACGAGCATCTGAATCTTGT--TTCGATTTAATTAGAAATTAATTTG----A-AAAATATGAAAA
* * * *
4450 ACGATATTAGAAGCATGAGAAA-TCCTTCAATCTTTTTGGCGTTGAATTATATGT-TTTTATGAG
124 ACGATATTAAAAGCATGA-AAAGTCCTTCAATCTTTTTGGAGTTAAATTATATATATTTTATGAG
* * * * * *
4513 TATTGTGGCTAAAAATTGAGAAAAATATTTT-GGTTCAATTTTTGTAAAACTTTAGCC-GAAATC
188 TATTTTAGCCAAAAATTGAGAAAAAT-TTTTCGGGTC-ATTTTTGCAAAATTTTA-CCTGAAATC
* * * * *
4576 GTG---T-ACCATTACGGTTTTTTGGCTAAATTAAAACGCGTTTCGGGGGCCCGGAACAATTTT-
250 GTGTACTAACCATCACGGTTTTTTTGCT--A--AAAACGCGTTTCGGGGCCCCGGATCAGTTTTG
* *
4636 CCTGA-TTTTTGACGCCAAG
311 CATGATTTTTTG-CGTCAAG
* * * * *
4655 ACTCCTTAAAATATATCTTTATTCATGTAACCAAATCTCAG---C--TGTATTTAAGGATTTGTT
1 ACTCCTT-GAA-ATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTT
* *
4715 TTTACGAGCATCTAAATCTTATTTCGATTT
64 TTTACGAGCATCTGAATCTTGTTTCGATTT
4745 GTTGGGGGTC
Statistics
Matches: 1177, Mismatches: 193, Indels: 110
0.80 0.13 0.07
Matches are distributed among these distances:
329 2 0.00
330 3 0.00
331 45 0.04
332 263 0.22
333 280 0.24
334 351 0.30
335 56 0.05
336 62 0.05
337 79 0.07
338 36 0.03
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (329 bp):
ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTT
TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAATATGAAAAACGATAT
TAAAAGCATGAAAAGTCCTTCAATCTTTTTGGAGTTAAATTATATATATTTTATGAGTATTTTAG
CCAAAAATTGAGAAAAATTTTTCGGGTCATTTTTGCAAAATTTTACCTGAAATCGTGTACTAACC
ATCACGGTTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGATCAGTTTTGCATGATTTTTTGCGT
CAAG
Found at i:5556 original size:3 final size:3
Alignment explanation
Indices: 5548--5572 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5538 TATGTTGCTC
5548 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
5573 ATTGTCGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:6432 original size:16 final size:16
Alignment explanation
Indices: 6413--6480 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
6403 ATTTTTGGGT
6413 ACCCGAACCCGAAATG
1 ACCCGAACCCGAAATG
* *
6429 ACCCGAATCC-AAACG
1 ACCCGAACCCGAAATG
6444 ACCCGAACCCGAAATG
1 ACCCGAACCCGAAATG
* *
6460 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
6476 ACCCG
1 ACCCG
6481 CCCCCGATCA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
15 13 0.30
16 31 0.70
ACGTcount: A:0.40, C:0.40, G:0.15, T:0.06
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:6451 original size:31 final size:31
Alignment explanation
Indices: 6413--6472 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
6403 ATTTTTGGGT
* *
6413 ACCCGAACCCGAAATGACCCGAATCCAAACG
1 ACCCGAACCCGAAATGACCCAAACCCAAACG
6444 ACCCGAACCCGAAATGACCCAAACCCAAA
1 ACCCGAACCCGAAATGACCCAAACCCAAA
6473 ATGACCCGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.40, G:0.13, T:0.05
Consensus pattern (31 bp):
ACCCGAACCCGAAATGACCCAAACCCAAACG
Done.