Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020540.1 Corchorus olitorius cultivar O-4 contig20573, 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: 4323
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:455 original size:35 final size:35
Alignment explanation
Indices: 390--935 Score: 482
Period size: 35 Copynumber: 15.4 Consensus size: 35
380 ATTTGCGGTA
*
390 AACTGAAATAAACT-ACAGAAAAGATCGCCCTGGATC
1 AACTGAAATAAATTGA-AG-AAAGATCGCCCTGGATC
*
426 AACTGAAATAAATTGAAGAAAGACCGCCCTGGATC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
*
461 AACTGAAATAAATCGAAGAAAGATCGCCCTGGATC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
*
496 AACTGAAATAAACTGAAGAAAAGATCGCCCTGGATC
1 AACTGAAATAAATTGAAG-AAAGATCGCCCTGGATC
* *
532 AACTG-AATAGATTGTAGAAAAGATCGCCCTGGATC
1 AACTGAAATAAATTGAAG-AAAGATCGCCCTGGATC
* * * *
567 AACTGAAGTAAATTGAAGAAAGACCACCCTGGGTC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
* * * * *
602 AACTGAAATAGATTGAAGAGAGACCACCCTGGGTC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
* * *
637 AACTGACAT-ATTCTGAAGAAAGATCACCCTGGATC
1 AACTGAAATAAAT-TGAAGAAAGATCGCCCTGGATC
* * *
672 AACTAGATCAACTGAAATAAACTAAAGAAAGACCGCCCTGGGTC
1 AACT-GA--AA-T-AAAT----TGAAGAAAGATCGCCCTGGATC
**
716 AA--G---TAAGCTGAAGAAAAGATCGCCCTGGATC
1 AACTGAAATAAATTGAAG-AAAGATCGCCCTGGATC
* * * * * * *
747 CATTAAAATGAATTGAAGAAGGACCGCCCTGGGTC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
* * *
782 AACTGAAATAAACTGAAATAAAGATCGCCTTGGATC
1 AACTGAAATAAATTG-AAGAAAGATCGCCCTGGATC
* *
818 AACTGAAGT-AATTGAGGAAAGATCGCCCTGGATC
1 AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
* * * *
852 AA-TCAAAATGAACTGAAGAAAAATCGCCCTGGATC
1 AACT-GAAATAAATTGAAGAAAGATCGCCCTGGATC
* *
887 AGCTGAAATAAATGGAAGGAAAGATCGCCCTGGATC
1 AACTGAAATAAATTGAA-GAAAGATCGCCCTGGATC
*
923 AACTGAATTAAAT
1 AACTGAAATAAAT
936 CTTCAGCAAC
Statistics
Matches: 415, Mismatches: 71, Indels: 48
0.78 0.13 0.09
Matches are distributed among these distances:
30 4 0.01
31 16 0.04
33 1 0.00
34 25 0.06
35 235 0.57
36 107 0.26
37 1 0.00
38 1 0.00
39 1 0.00
41 3 0.01
44 21 0.05
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (35 bp):
AACTGAAATAAATTGAAGAAAGATCGCCCTGGATC
Found at i:471 original size:71 final size:69
Alignment explanation
Indices: 390--934 Score: 467
Period size: 71 Copynumber: 7.7 Consensus size: 69
380 ATTTGCGGTA
* *
390 AACTGAAATAAACT-ACAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAAGACCGCC
1 AACTGAAATAAA-TGA-AG-AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
454 CTGGATC
63 CTGGATC
461 AACTGAAATAAATCGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCCC
1 AACTGAAATAAAT-GAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAG-AAAGATCGCCC
526 TGGATC
64 TGGATC
* * * * * *
532 AACTG-AATAGATTGTAGAAAAGATCGCCCTGGATCAACTGAAGTAAATTGAAGAAAGACCACCC
1 AACTGAAATA-AATGAAG-AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGATCGCCC
*
596 TGGGTC
64 TGGATC
* * * * * * ** *
602 AACTGAAATAGATTGAAGAGAGACCACCCTGGGTCAACTGACATATTCTGAAGAAAGATCACCCT
1 AACTGAAATA-AATGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGATCGCCCT
667 GGATCAACTAGATC
65 -G--------GATC
* * * *
681 AACTGAAATAAACTAAAGAAAGACCGCCCTGGGTCAA--G---TAAGCTGAAGAAAAGATCGCCC
1 AACTGAAATAAA-TGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAG-AAAGATCGCCC
741 TGGATC
64 TGGATC
* * * * * * * * *
747 CATTAAAATGAATTGAAGAAGGACCGCCCTGGGTCAACTGAAATAAACTGAAATAAAGATCGCCT
1 AACTGAAAT-AAATGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTG-AAGAAAGATCGCCC
812 TGGATC
64 TGGATC
* * * * * *
818 AACTGAAGTAATTGAGGAAAGATCGCCCTGGATCAA-TCAAAATGAACTGAAGAAAAATCGCCCT
1 AACTGAAATAAATGAAGAAAGATCGCCCTGGATCAACT-GAAATAAACTGAAGAAAGATCGCCCT
882 GGATC
65 GGATC
* *
887 AGCTGAAATAAATGGAAGGAAAGATCGCCCTGGATCAACTGAATTAAA
1 AACTGAAATAAAT-GAA-GAAAGATCGCCCTGGATCAACTGAAATAAA
935 TCTTCAGCAA
Statistics
Matches: 389, Mismatches: 57, Indels: 56
0.77 0.11 0.11
Matches are distributed among these distances:
66 32 0.08
67 2 0.01
68 1 0.00
69 28 0.07
70 132 0.34
71 134 0.34
72 4 0.01
74 9 0.02
75 11 0.03
77 1 0.00
78 1 0.00
79 34 0.09
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (69 bp):
AACTGAAATAAATGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGATCGCCCTG
GATC
Found at i:840 original size:180 final size:184
Alignment explanation
Indices: 492--853 Score: 439
Period size: 180 Copynumber: 2.0 Consensus size: 184
482 GATCGCCCTG
* * * *
492 GATCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAATAGATTGTAGAAAAGATC
1 GATCAACTGAAATAAACTAAAGAAAAGACCGCCCTGGATCAAC-GAATAGACTGAAGAAAAGATC
* * * * *
557 GCCCTGGATCAACTGAAGTAAATTGAAGAAAGACCACCCTGGGTCAACTGAAATAGATTGAAGAG
65 GCCCTGGATCAACTAAAATAAATTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAA
* *
622 AGACCACCCTGGGTCAACTGACATATTCTGAAGAAAGATCACCCTGGATCAACTA
130 AGACCACCCTGGATCAACTGACATAATCTGAAGAAAGATCACCCTGGATCAACTA
* *
677 GATCAACTGAAATAAACTAAAG-AAAGACCGCCCTGGGTCAA-GTA-AG-CTGAAGAAAAGATCG
1 GATCAACTGAAATAAACTAAAGAAAAGACCGCCCTGGATCAACGAATAGACTGAAGAAAAGATCG
* * * * * *
738 CCCTGGATCCATTAAAATGAATTGAAGAAGGACCGCCCTGGGTCAACTGAAATAAACTGAAATAA
66 CCCTGGATCAACTAAAATAAATTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTG-AAGAA
* * * * *
803 AGATCGCCTTGGATCAACTGA-AGTAAT-TGAGGAAAGATCGCCCTGGATCAA
130 AGACCACCCTGGATCAACTGACA-TAATCTGAAGAAAGATCACCCTGGATCAA
854 TCAAAATGAA
Statistics
Matches: 151, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
180 86 0.57
181 25 0.17
182 2 0.01
184 17 0.11
185 21 0.14
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.19
Consensus pattern (184 bp):
GATCAACTGAAATAAACTAAAGAAAAGACCGCCCTGGATCAACGAATAGACTGAAGAAAAGATCG
CCCTGGATCAACTAAAATAAATTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAA
GACCACCCTGGATCAACTGACATAATCTGAAGAAAGATCACCCTGGATCAACTA
Found at i:870 original size:215 final size:217
Alignment explanation
Indices: 457--887 Score: 464
Period size: 215 Copynumber: 2.0 Consensus size: 217
447 GACCGCCCTG
* *
457 GATCAACTGAAATAAATCGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATC
1 GATCAACTGAAATAAATCAAAGAAAGACCGCCCTGGATCAAC-G--ATAAACTGAAGAAAAGATC
* * * * *
522 GCCCTGGATCAACTGAATAGATTGTAGAAAAGATCGCCCTGGATCAACTGAAGTAAATTGAAGAA
63 GCCCTGGATCAACTAAATAGATTGAAGAAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGAA
* * * * * *
587 AGACCACCCTGGGTCAACTGAAATAGATTGAAGAGAGACCACCCTGGGTCAACTGACATATTCTG
128 AGACCACCCTGGATCAACTGAAATAGATTGAAGAAAGACCACCCTGGATCAACTAAAATATACTG
*
652 AAGAAAGATCACCCTGGATCAACTA
193 AAGAAAAATCACCCTGGATCAACTA
* *
677 GATCAACTGAAATAAA-CTAAAGAAAGACCGCCCTGGGTCAA-G-TAAGCTGAAGAAAAGATCGC
1 GATCAACTGAAATAAATC-AAAGAAAGACCGCCCTGGATCAACGATAAACTGAAGAAAAGATCGC
* * * * *
739 CCTGGATCCATTAAA-ATGAATTGAAG-AAGGACCGCCCTGGGTCAACTGAAATAAACTGAAATA
65 CCTGGATCAACTAAATA-G-ATTGAAGAAAAGACCGCCCTGGATCAACTGAAATAAACTG-AAGA
* * * * * * *
802 AAGATCGCCTTGGATCAACTGAAGTA-ATTGAGGAAAGATCGCCCTGGATCAA-TCAAAATGA-A
127 AAGACCACCCTGGATCAACTGAAATAGATTGAAGAAAGACCACCCTGGATCAACT-AAAAT-ATA
*
864 CTGAAGAAAAATCGCCCTGGATCA
190 CTGAAGAAAAATCACCCTGGATCA
888 GCTGAAATAA
Statistics
Matches: 176, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
214 2 0.01
215 105 0.60
216 31 0.18
218 1 0.01
219 1 0.01
220 36 0.20
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (217 bp):
GATCAACTGAAATAAATCAAAGAAAGACCGCCCTGGATCAACGATAAACTGAAGAAAAGATCGCC
CTGGATCAACTAAATAGATTGAAGAAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGAAAGA
CCACCCTGGATCAACTGAAATAGATTGAAGAAAGACCACCCTGGATCAACTAAAATATACTGAAG
AAAAATCACCCTGGATCAACTA
Found at i:935 original size:36 final size:35
Alignment explanation
Indices: 724--935 Score: 189
Period size: 36 Copynumber: 6.0 Consensus size: 35
714 TCAAGTAAGC
* * * * *
724 TGAAGAAAAGATCGCCCTGGATCCATTAAAATGAAT
1 TGAAGGAAAGATCGCCCTGGATCAACTGAAAT-AAA
* * *
760 TGAA-GAAGGACCGCCCTGGGTCAACTGAAATAAA
1 TGAAGGAAAGATCGCCCTGGATCAACTGAAATAAA
** * * *
794 CTGAAATAAAGATCGCCTTGGATCAACTGAAGTAAT
1 -TGAAGGAAAGATCGCCCTGGATCAACTGAAATAAA
* *
830 TG-AGGAAAGATCGCCCTGGATCAA-TCAAAATGAAC
1 TGAAGGAAAGATCGCCCTGGATCAACT-GAAAT-AAA
* *
865 TGAA-GAAAAATCGCCCTGGATCAGCTGAAATAAA
1 TGAAGGAAAGATCGCCCTGGATCAACTGAAATAAA
*
899 TGGAAGGAAAGATCGCCCTGGATCAACTGAATTAAA
1 T-GAAGGAAAGATCGCCCTGGATCAACTGAAATAAA
935 T
1 T
936 CTTCAGCAAC
Statistics
Matches: 140, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
33 1 0.01
34 27 0.19
35 55 0.39
36 57 0.41
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (35 bp):
TGAAGGAAAGATCGCCCTGGATCAACTGAAATAAA
Done.