Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012703.1 Corchorus olitorius cultivar O-4 contig12736, 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: 10992
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:733 original size:2 final size:2
Alignment explanation
Indices: 726--755 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
716 CTTTAACTAG
726 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
756 GGAATACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:796 original size:67 final size:66
Alignment explanation
Indices: 688--822 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 66
678 TACGCATGTG
*
688 TGGAATATATGATTTATCAATTATTATGCTTTAACTAGTATATATATATATATATTATATATATA
1 TGGAATACATGATTTATCAATTATTATGCTTTAACTAGTATATATATATATATA-TATATATATA
753 TA
65 TA
*
755 TGGAATACATGATTTATCAATTATTATGCTTTAATTAGTATATATATATATATATATATATATAT
1 TGGAATACATGATTTATCAATTATTATGCTTTAACTAGTATATATATATATATATATATATATAT
820 A
66 A
821 TG
1 TG
823 AGAGAGGATC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 14 0.21
67 52 0.79
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.47
Consensus pattern (66 bp):
TGGAATACATGATTTATCAATTATTATGCTTTAACTAGTATATATATATATATATATATATATAT
A
Found at i:800 original size:2 final size:2
Alignment explanation
Indices: 793--821 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
783 CTTTAATTAG
793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
822 GAGAGAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3788 original size:25 final size:23
Alignment explanation
Indices: 3760--3806 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3750 TACATTTTTT
*
3760 TAACTTGATTTATTATTTTTTTCTC
1 TAACTT-ATTTATT-TTTTATTCTC
*
3785 TAACTTTTTTATTTTTTATTCT
1 TAACTTATTTATTTTTTATTCT
3807 TTTCTTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.19, C:0.11, G:0.02, T:0.68
Consensus pattern (23 bp):
TAACTTATTTATTTTTTATTCTC
Found at i:3965 original size:69 final size:69
Alignment explanation
Indices: 3854--4114 Score: 413
Period size: 69 Copynumber: 3.8 Consensus size: 69
3844 TGTGGGATAT
* * *
3854 CAAAAGGGAAACAAATTACTACCTAGCTATGGAGGATAGGACATACGCCGTATATCTTTTCTGGG
1 CAAAAGGGAAAAAAATTACTACCTAGCAATGGAGGACAGGACATACGCCGTATATCTTTTCTGGG
3919 GAAA
66 GAAA
* * *
3923 CAAAAGGGAAAAAAATTACTACCTAACCATGGAGGATAGGACATACGCCGTATATCTTTTCTGGG
1 CAAAAGGGAAAAAAATTACTACCTAGCAATGGAGGACAGGACATACGCCGTATATCTTTTCTGGG
3988 GAAA
66 GAAA
3992 CAAAAGGGAAAAAAATTACTACCTAGCAATGGAGGACAGGACATACGCCGTATATCTTTTCTGGG
1 CAAAAGGGAAAAAAATTACTACCTAGCAATGGAGGACAGGACATACGCCGTATATCTTTTCTGGG
4057 GAAA
66 GAAA
*
4061 CAAAAGGG--GAAAA--ACTACCTAGCAATGGAGGACACAGGACATACGCCGTATATC
1 CAAAAGGGAAAAAAATTACTACCTAGCAATGGAGG--ACAGGACATACGCCGTATATC
4115 AGAATACATA
Statistics
Matches: 183, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
65 18 0.10
67 25 0.14
69 140 0.77
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (69 bp):
CAAAAGGGAAAAAAATTACTACCTAGCAATGGAGGACAGGACATACGCCGTATATCTTTTCTGGG
GAAA
Found at i:6663 original size:215 final size:214
Alignment explanation
Indices: 6034--7643 Score: 1834
Period size: 215 Copynumber: 7.5 Consensus size: 214
6024 ACGTTTACCC
* * * * **
6034 AAAACGTTGTCATAAATGTCGGAGAAGTCTGTTTTAAAAAGACGTTTGTT-AAAAATGTCGCATG
1 AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATG
* * *
6098 ATTGAACAACGTTTGAGATAAACGTCTCAACAAACGTCGCAAAAGCATAAACAAAAGCGACGTTA
66 ATTGAACGACGTTTGAGA-AAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTA
* *
6163 TTAAAAAAACGTCACTCAGTTTAAAAAAGAGTCGCAATG-TATTGCGACATTTATTAAAATGTCA
130 TT-AAAAAACGTCACTCAATTTAAAAAAGAGTCGCAA-GATATTACGACATTTATTAAAATGTCA
* *
6227 TATTTTAAAACGACATTTTATA
193 TATTTTAAAACGACGTTTTACA
* * * ** *
6249 ACAACGTTTTTATAAATGTTGGAAAAGTCTATCTTAAAGCGACGTTCCTTGACAAATGTCGCATG
1 AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATG
* * * *
6314 ATTGAACGACATTTTGAGAAACACGTCGCTACAAACGTCGCAAAAGCATAAACAATAGCGACATT
66 ATTGAACGAC-GTTTGAGAAA-ACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTT
* * * * *
6379 ATTAGAAAACGTCACTCAGTTTAAAAAAGAGTCGCAATATACTACGACATTTATTAAAATGTTAT
129 ATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCAT
* * **
6444 ATTTTAAAATGACATTTTATT
194 ATTTTAAAACGACGTTTTACA
* * * * * ** * *
6465 ACAACATTCTTATAAATGTTGGAGAAGTCTATCTTAAAGCGACGTTTGTTGATTAATGTCACTTG
1 AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATG
* * * * * * *
6530 ATTGAATGACATTTGAGAAACACATCGCTACAAACATTGCAAAAGCATAAACTAGAGCGACGTTA
66 ATTGAACGACGTTTGAGAAA-ACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTA
* * * * *
6595 TTAAAAAACATCACTCAAATTAAAAAAGAGTCGCAAGGTATTGCGACATTTATCAAAATGTCATA
130 TTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCATA
6660 TTTTAAAACGACGTTTT-C-
195 TTTTAAAACGACGTTTTACA
* * * * * * * *
6678 TAAACGTTGTTATAAATATCGGAGAAGTATGTCTTAAAGCGACATTTGTTAAAAAACGTCGCATG
1 AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATG
* * * *
6743 ATTGAACGGCGTTTGAGAAAAATGTCGT-TACAAACGTCGCACAAA-CATAAACTAGAGCGACAT
66 ATTGAACGACGTTTGAG-AAAACGTC-TCTACAAACGTCGCA-AAAGCATAAACAAGAGCGACGT
* * * * *
6806 TATT-AAAAACGTCACTCAATTTAAAAAAGTGCCGCAAGGTGA-TGCGATATTTATTAAAATGTC
128 TATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGAT-ATTACGACATTTATTAAAATGTC
***
6869 ATATTTTAAAACGACGTTTCGGA
192 ATATTTTAAAACGACGTTTTACA
*
6892 AAAACGTT-TCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTATGTTGAAAAATGTCGCAT
1 AAAACGTTGT-TATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCAT
* **
6956 GATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGTATAAACAAGAGCGACGCAA
65 GATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTA
* * *
7021 TTAAAAAACGTCACTCAATTTTAAAAACGAGTCGCAAGATTTTACGACGTTTATTAAAATGTCAT
130 TTAAAAAACGTCACTCAA-TTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCAT
* *
7086 -TTATT-AAATGACGTTTCT-GA
194 ATT-TTAAAACGACGTTT-TACA
* * * *
7106 AAAACGTTGTTATAAATGTCGGAAAAGACTATCTTAAAGCGACGTTTTTTCAAAAATGTTGCATG
1 AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATG
* * **
7171 ATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGTATAAACAAGAGTGACGCAAT
66 ATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTAT
* * * * **
7236 TAAAAAACGCCACTCAATTTTAAAAAGGAGTCGCAAGATTTTATGATGTTTATTAAAATGTCAT-
131 TAAAAAACGTCACTCAA-TTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCATA
*
7300 TTATT-AAACGACG-TTTCCGA
195 TT-TTAAAACGACGTTTTAC-A
* * * * *
7320 AAAACGTTGATATAAATGTCAGAAAAGTCTATCTTAAAGCAACGTTTGTTAAAAAAATATCGCAT
1 AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTT-GAAAAATGTCGCAT
* * * **
7385 GATTGAACGACGTTTGAGAAAACATCTCTACAAACGTCGCAAAAGTATAAACAATAGCGACGCAA
65 GATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTA
* *
7450 TTAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATTTTACGACGTTTATTAAAATGTCAT
130 TTAAAAAACGTCACTCAA-TTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCAT
* ** *
7515 -TTATT-AAATGACGTTTCCCT
194 ATT-TTAAAACGACGTTTTACA
*
7535 AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGAGGTTTGTT-AAAAATGTCGCATG
1 AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATG
* * * * *
7599 ATTGAACGACGTTAGACAAAAATGTCTCTACAAATGTCGTAAAAG
66 ATTGAACGACGTTTGA-GAAAACGTCTCTACAAACGTCGCAAAAG
7644 TGTGAGCAAT
Statistics
Matches: 1217, Mismatches: 154, Indels: 49
0.86 0.11 0.03
Matches are distributed among these distances:
212 75 0.06
213 168 0.14
214 368 0.30
215 389 0.32
216 168 0.14
217 49 0.04
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (214 bp):
AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTGTTGAAAAATGTCGCATG
ATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTAT
TAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCATAT
TTTAAAACGACGTTTTACA
Found at i:7484 original size:429 final size:426
Alignment explanation
Indices: 6034--7643 Score: 1845
Period size: 429 Copynumber: 3.8 Consensus size: 426
6024 ACGTTTACCC
* * * *
6034 AAAACGTTGTCATAAATGTCGGAGAAGTCTGTTTTAAA-AAGACGTTTGTT-AAAAATGTCGCAT
1 AAAACGTTGT-ATAAATGTCGGAAAAGTCTATCTTAAAGCA-ACGTTTGTTGAAAAATGTCGCAT
* * * * **
6097 GATTGAACAACGTTTGAGATAAACGTCTCAACAAACGTCGCAAAAGCATAAACAAAAGCGACGTT
64 GATTGAACGACGTTTGAGA-AAACATCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGCA
* *
6162 ATTAAAAAAACGTCACTC-AGTTTAAAAAAGAGTCGCAATG-TATTGCGACATTTATTAAAATGT
128 ATT-AAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAA-GATATTACGACATTTATTAAAATGT
* * * *
6225 CATATTTTAAAACGACATTT-TATAACAACGTTTTTATAAATGTTGGAAAAGTCTATCTTAAAGC
191 CATATTTTAAAACGACGTTTCTA-AA-AACGTTGTTATAAATGTCGGAAAAGACTATCTTAAAGC
** * * *
6289 GACGTTCCTTGACAAATGTCGCATGATTGAACGACATTTTGAGAAACACGTCGCTACAAACGTCG
254 GACGTTTGTT-AAAAATGTCGCATGATTGAACGAC-GTTTGAGAAA-ACGTCTCTACAAACGTCG
* * * *
6354 CAAAAGCATAAACAATAGCGACATTATTAGAAAACGTCACTCAGTTTAAAAAAGAGTCGCAATAT
316 CAAAAGCATAAACAAGAGCGACATTATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGAT
* * * * * ****
6419 ACTACGACATTTATTAAAATGTTATATTTTAAAATGACATTTTATT
381 AATACGATATTTATTAAAATGTCATATTTTAAAACGACGTTTCCGA
* * * * * * ** * *
6465 ACAACATTCTTATAAATGTTGGAGAAGTCTATCTTAAAGCGACGTTTGTTGATTAATGTCACTTG
1 AAAACGTT-GTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATG
* * * * * * **
6530 ATTGAATGACATTTGAGAAACACATCGCTACAAACATTGCAAAAGCATAAACTAGAGCGACGTTA
65 ATTGAACGACGTTTGAGAAA-ACATCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGCAA
* * * * *
6595 TTAAAAAACATCACTCAA-ATTAAAAAAGAGTCGCAAGGTATTGCGACATTTATCAAAATGTCAT
129 TTAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCAT
* * *
6659 ATTTTAAAACGACGTTTTCT--AAACGTTGTTATAAATATCGGAGAAGTA-TGTCTTAAAGCGAC
194 ATTTTAAAACGACG-TTTCTAAAAACGTTGTTATAAATGTCGGAAAAG-ACTATCTTAAAGCGAC
* * * *
6721 ATTTGTTAAAAAACGTCGCATGATTGAACGGCGTTTGAGAAAAATGTCGT-TACAAACGTCGCAC
257 GTTTGTT-AAAAATGTCGCATGATTGAACGACGTTTGAG-AAAACGTC-TCTACAAACGTCGCA-
* * * * *
6785 AAA-CATAAACTAGAGCGACATTATT-AAAAACGTCACTCAATTTAAAAAAGTGCCGCAAGGTGA
318 AAAGCATAAACAAGAGCGACATTATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGATAA
* *
6848 TGCGATATTTATTAAAATGTCATATTTTAAAACGACGTTTCGGA
383 TACGATATTTATTAAAATGTCATATTTTAAAACGACGTTTCCGA
* * *
6892 AAAACGTTTCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTATGTTGAAAAATGTCGCATG
1 AAAACG-TTGTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATG
* *
6957 ATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGTATAAACAAGAGCGACGCAAT
65 ATTGAACGACGTTTGAGAAAACATCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGCAAT
* * *
7022 TAAAAAACGTCACTCAATTTTAAAAACGAGTCGCAAGATTTTACGACGTTTATTAAAATGTCAT-
130 TAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCATA
*
7086 TTATT-AAATGACGTTTCTGAAAAACGTTGTTATAAATGTCGGAAAAGACTATCTTAAAGCGACG
195 TT-TTAAAACGACGTTTCT-AAAAACGTTGTTATAAATGTCGGAAAAGACTATCTTAAAGCGACG
* *
7150 TTTTTTCAAAAATGTTGCATGATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAG
258 TTTGTT-AAAAATGTCGCATGATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAG
* * *** * * ** *
7215 TATAAACAAGAGTGACGCAATTAAAAAACGCCACTCAATTTTAAAAAGGAGTCGCAAGATTTTAT
322 CATAAACAAGAGCGACATTATTAAAAAACGTCACTCAA-TTTAAAAAAGAGTCGCAAGATAATAC
*
7280 GATGTTTATTAAAATGTCAT-TTATT-AAACGACGTTTCCGA
386 GATATTTATTAAAATGTCATATT-TTAAAACGACGTTTCCGA
* * *
7320 AAAACGTTGATATAAATGTCAGAAAAGTCTATCTTAAAGCAACGTTTGTTAAAAAAATATCGCAT
1 AAAACGTTG-TATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTT-GAAAAATGTCGCAT
* *
7385 GATTGAACGACGTTTGAGAAAACATCTCTACAAACGTCGCAAAAGTATAAACAATAGCGACGCAA
64 GATTGAACGACGTTTGAGAAAACATCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGCAA
* *
7450 TTAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATTTTACGACGTTTATTAAAATGTCAT
129 TTAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCAT
* *
7515 -TTATT-AAATGACGTTTCCCT-AAAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGA
194 ATT-TTAAAACGACGTTT--CTAAAAACGTTGTTATAAATGTCGGAAAAGACTATCTTAAAGCGA
* * * * * *
7577 GGTTTGTTAAAAATGTCGCATGATTGAACGACGTTAGACAAAAATGTCTCTACAAATGTCGTAAA
256 CGTTTGTTAAAAATGTCGCATGATTGAACGACGTTTGA-GAAAACGTCTCTACAAACGTCGCAAA
7642 AG
320 AG
7644 TGTGAGCAAT
Statistics
Matches: 1015, Mismatches: 135, Indels: 60
0.84 0.11 0.05
Matches are distributed among these distances:
425 5 0.00
426 66 0.07
427 215 0.21
428 216 0.21
429 330 0.33
430 2 0.00
431 111 0.11
432 69 0.07
433 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (426 bp):
AAAACGTTGTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGA
TTGAACGACGTTTGAGAAAACATCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGCAATT
AAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCATAT
TTTAAAACGACGTTTCTAAAAACGTTGTTATAAATGTCGGAAAAGACTATCTTAAAGCGACGTTT
GTTAAAAATGTCGCATGATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATA
AACAAGAGCGACATTATTAAAAAACGTCACTCAATTTAAAAAAGAGTCGCAAGATAATACGATAT
TTATTAAAATGTCATATTTTAAAACGACGTTTCCGA
Done.