Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01005161.1 Corchorus olitorius cultivar O-4 contig05182, 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, 621
Length: 1036
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Found at i:325 original size:36 final size:36
Alignment explanation
Indices: 278--346 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
268 CGTCTCTATC
278 GTTTTCTGTATTATTAGAAATTTGTGATTCTTTTTT
1 GTTTTCTGTATTATTAGAAATTTGTGATTCTTTTTT
314 GTTTTCTGTATTATTAGAAATTTGTGATTCTTT
1 GTTTTCTGTATTATTAGAAATTTGTGATTCTTT
347 CTTTTTACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.59
Consensus pattern (36 bp):
GTTTTCTGTATTATTAGAAATTTGTGATTCTTTTTT
Found at i:637 original size:21 final size:21
Alignment explanation
Indices: 611--659 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
601 TGTCATCATC
* *
611 ATTATCTTTAGGATTCTTGGT
1 ATTATCATTAGGATTATTGGT
632 ATTATCATTAGGATTATTGGT
1 ATTATCATTAGGATTATTGGT
653 ATTATCA
1 ATTATCA
660 GTATCATCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (21 bp):
ATTATCATTAGGATTATTGGT
Found at i:638 original size:27 final size:27
Alignment explanation
Indices: 579--641 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
569 TTCCTCTAGT
579 TTATCATTATCATTAGGATTCTTGTCA
1 TTATCATTATCATTAGGATTCTTGTCA
* *
606 TCATCATTATCTTTAGGATTCTTGGT-A
1 TTATCATTATCATTAGGATTCTT-GTCA
633 TTATCATTA
1 TTATCATTA
642 GGATTATTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 30 0.94
28 2 0.06
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (27 bp):
TTATCATTATCATTAGGATTCTTGTCA
Found at i:855 original size:109 final size:108
Alignment explanation
Indices: 660--912 Score: 427
Period size: 109 Copynumber: 2.3 Consensus size: 108
650 GGTATTATCA
* *
660 GTATCATCGGTATTAATAAAAGTATTGGTATCATCGGTATTAGTAAGAGTATTGGTATCATCGGT
1 GTATCATCGGTATTAGTAAAAGTATTGGTATCATCGGTATTAGTAAGAGTATCGGTATCATCGGT
* *
725 ATTAGTAAAAGTATTGGTATCATCGGTATTAGTAAAAGTATTG
66 ATTAGTAAAAGTATCGGTATCATCGGTATTAATAAAAGTATTG
768 GTATCATCGGTATTAGTAAAAGTATTGGTATCATCGGTAATTAGTATA-AGTATCGGTATCATCG
1 GTATCATCGGTATTAGTAAAAGTATTGGTATCATCGGT-ATTAGTA-AGAGTATCGGTATCATCG
*
832 GTATTAGTATAAGTATCGGTATCATCGGTATTAATAAAAGTATTG
64 GTATTAGTAAAAGTATCGGTATCATCGGTATTAATAAAAGTATTG
*
877 GTATCATCGGTATTAGTAAGAGTATTGGTATCATCG
1 GTATCATCGGTATTAGTAAAAGTATTGGTATCATCG
913 CTTTTTTTAA
Statistics
Matches: 137, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
108 37 0.27
109 99 0.72
110 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (108 bp):
GTATCATCGGTATTAGTAAAAGTATTGGTATCATCGGTATTAGTAAGAGTATCGGTATCATCGGT
ATTAGTAAAAGTATCGGTATCATCGGTATTAATAAAAGTATTG
Found at i:927 original size:27 final size:27
Alignment explanation
Indices: 660--912 Score: 425
Period size: 27 Copynumber: 9.3 Consensus size: 27
650 GGTATTATCA
*
660 GTATCATCGGTATTAATAAAAGTATTG
1 GTATCATCGGTATTAGTAAAAGTATTG
*
687 GTATCATCGGTATTAGTAAGAGTATTG
1 GTATCATCGGTATTAGTAAAAGTATTG
714 GTATCATCGGTATTAGTAAAAGTATTG
1 GTATCATCGGTATTAGTAAAAGTATTG
741 GTATCATCGGTATTAGTAAAAGTATTG
1 GTATCATCGGTATTAGTAAAAGTATTG
768 GTATCATCGGTATTAGTAAAAGTATTG
1 GTATCATCGGTATTAGTAAAAGTATTG
* *
795 GTATCATCGGTAATTAGTATAAGTATCG
1 GTATCATCGGT-ATTAGTAAAAGTATTG
* *
823 GTATCATCGGTATTAGTATAAGTATCG
1 GTATCATCGGTATTAGTAAAAGTATTG
*
850 GTATCATCGGTATTAATAAAAGTATTG
1 GTATCATCGGTATTAGTAAAAGTATTG
*
877 GTATCATCGGTATTAGTAAGAGTATTG
1 GTATCATCGGTATTAGTAAAAGTATTG
904 GTATCATCG
1 GTATCATCG
913 CTTTTTTTAA
Statistics
Matches: 215, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
27 190 0.88
28 25 0.12
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (27 bp):
GTATCATCGGTATTAGTAAAAGTATTG
Found at i:927 original size:136 final size:135
Alignment explanation
Indices: 660--914 Score: 422
Period size: 136 Copynumber: 1.9 Consensus size: 135
650 GGTATTATCA
* *
660 GTATCATCGGTATTAATAAAAGTATTGGTATCATCGGTATTAGTAAGAGTATTGGTATCATCGGT
1 GTATCATCGGTATTAATAAAAGTATCGGTATCATCGGTATTAGTAAGAGTATCGGTATCATCGGT
* *
725 ATTAGTAAAAGTATTGGTATCATCGGTATTAGTAAAAGTATTGGTATCATCGGTATTAGTAAAAG
66 ATTAATAAAAGTATTGGTATCATCGGTATTAGTAAAAGTATTGGTATCATCGCTATTAGTAAAAG
790 TATTG
131 TATTG
* *
795 GTATCATCGGTAATTAGTATAAGTATCGGTATCATCGGTATTAGTATA-AGTATCGGTATCATCG
1 GTATCATCGGT-ATTAATAAAAGTATCGGTATCATCGGTATTAGTA-AGAGTATCGGTATCATCG
*
859 GTATTAATAAAAGTATTGGTATCATCGGTATTAGTAAGAGTATTGGTATCATCGCT
64 GTATTAATAAAAGTATTGGTATCATCGGTATTAGTAAAAGTATTGGTATCATCGCT
915 TTTTTTAAAA
Statistics
Matches: 111, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
135 11 0.10
136 99 0.89
137 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (135 bp):
GTATCATCGGTATTAATAAAAGTATCGGTATCATCGGTATTAGTAAGAGTATCGGTATCATCGGT
ATTAATAAAAGTATTGGTATCATCGGTATTAGTAAAAGTATTGGTATCATCGCTATTAGTAAAAG
TATTG
Done.