Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023228.1 Corchorus olitorius cultivar O-4 contig23261, 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: 7894
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Found at i:473 original size:30 final size:30
Alignment explanation
Indices: 412--881 Score: 405
Period size: 30 Copynumber: 15.6 Consensus size: 30
402 AATCCTAAAT
* * * *
412 CAGGATAAAAATATAGCGATGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCTTCAAC
* * *
442 CAAGATTAAAGTAAAGCAATGGTCTTCAAC
1 CAGGATTAAAATAAAGCAATGATCTTCAAC
* **
472 CATGATTAAAATAAAGCAACAATCCTT-AAC
1 CAGGATTAAAATAAAGCAATGAT-CTTCAAC
* * *
502 CAGGATTAAAATGAAGCAATGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCTTCAAC
* *
532 CGGGATTAAAATAAAGCAATGAT-TCTCAAA
1 CAGGATTAAAATAAAGCAATGATCT-TCAAC
* * * *
562 CAGGATTAAAATGACGCTATGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCTTCAAC
* * *
592 CATGATTAAACAT-AAGCAATGATCCTCAAA
1 CAGGATTAAA-ATAAAGCAATGATCTTCAAC
622 CAGGATTAAAATAAAGCAATGATCCTT-AAC
1 CAGGATTAAAATAAAGCAATGAT-CTTCAAC
652 CAGGATTAAAATAAAGCAATGATCCTT-AAC
1 CAGGATTAAAATAAAGCAATGAT-CTTCAAC
* *
682 CAGGATTAAACATAAAGCAATGATCCTCAAA
1 CAGGATTAAA-ATAAAGCAATGATCTTCAAC
* *
713 CAGGATTAAAATAAAGCAAAGATCCTTGAA-
1 CAGGATTAAAATAAAGCAATGAT-CTTCAAC
* * *
743 CAGGATTAACATAGAGCAGAT-ATCCTCAAC
1 CAGGATTAAAATAAAGCA-ATGATCTTCAAC
* * * * *
773 CAGGATAAAAATAAAGTAACGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCTTCAAC
* * * * *
803 CAGGATTAAAAATGAGGTAATGATCCTCAAA
1 CAGGATT-AAAATAAAGCAATGATCTTCAAC
* * * *
834 CAGGATTAATCATAAAGTAATGATCCTCAAA
1 CAGGATTAA-AATAAAGCAATGATCTTCAAC
*
865 CAGGATTCAAATAAAGC
1 CAGGATTAAAATAAAGC
882 TGATAAAGCA
Statistics
Matches: 365, Mismatches: 60, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
29 9 0.02
30 266 0.73
31 90 0.25
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.22
Consensus pattern (30 bp):
CAGGATTAAAATAAAGCAATGATCTTCAAC
Found at i:503 original size:60 final size:60
Alignment explanation
Indices: 394--881 Score: 505
Period size: 60 Copynumber: 8.1 Consensus size: 60
384 CAAATAAACC
* * * * * * * * *
394 AAAGTAATAATCCTAAATCAGGATAAAAATATAGCGATGATCCTCAACCAAGATTAAAGT
1 AAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAAT
* * * ** *
454 AAAGCAATGGTCTTCAACCATGATTAAAATAAAGCAACAATCCTTAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAAT
* * * * *
514 GAAGCAATGATCCTCAAACGGGATTAAAATAAAGCAATGATTCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAAT
* * * * *
574 GACGCTATGATCCTCAACCATGATTAAACAT-AAGCAATGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAACCAGGATTAAA-ATAAAGCAATGATCCTCAACCAGGATTAAAAT
* *
634 AAAGCAATGATCCTTAACCAGGATTAAAATAAAGCAATGATCCTTAACCAGGATTAAACAT
1 AAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAA-AT
* * * *
695 AAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAAAGATCCTTGAA-CAGGATTAACAT
1 AAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCC-TCAACCAGGATTAAAAT
* * * * *
755 AGAGCAGAT-ATCCTCAACCAGGATAAAAATAAAGTAACGATCCTCAAACAGGATTAAAAAT
1 AAAGCA-ATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATT-AAAAT
* * * * * * * *
816 GAGGTAATGATCCTCAAACAGGATTAATCATAAAGTAATGATCCTCAAACAGGATTCAAAT
1 AAAGCAATGATCCTCAACCAGGATTAA-AATAAAGCAATGATCCTCAACCAGGATTAAAAT
877 AAAGC
1 AAAGC
882 TGATAAAGCA
Statistics
Matches: 356, Mismatches: 63, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
59 5 0.01
60 239 0.67
61 83 0.23
62 29 0.08
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.22
Consensus pattern (60 bp):
AAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAAT
Found at i:548 original size:90 final size:90
Alignment explanation
Indices: 394--878 Score: 505
Period size: 90 Copynumber: 5.4 Consensus size: 90
384 CAAATAAACC
* * * * * * * *
394 AAAGTAATAATCCTAAATCAGGATAAAAATATAGCGATGATCCTCAACCAAGATTAAAGTAAAGC
1 AAAGCAATAATCCTCAACCAGGATTAAAATA-AGCAATGATCCTCAAACAGGATTAAAATAAAGC
* *
459 AATGGT-CTTCAACCATGATTAAAAT
65 AATGATCCTTCAACCAGGATTAAAAT
* * *
484 AAAGCAACAATCCTTAACCAGGATTAAAATGAAGCAATGATCCTCAAACGGGATTAAAATAAAGC
1 AAAGCAATAATCCTCAACCAGGATTAAAAT-AAGCAATGATCCTCAAACAGGATTAAAATAAAGC
* *
549 AATGATTC-TCAAACAGGATTAAAAT
65 AATGATCCTTCAACCAGGATTAAAAT
* * * * *
574 GACGCTATGATCCTCAACCATGATTAAACATAAGCAATGATCCTCAAACAGGATTAAAATAAAGC
1 AAAGCAATAATCCTCAACCAGGATTAAA-ATAAGCAATGATCCTCAAACAGGATTAAAATAAAGC
639 AATGATCCTT-AACCAGGATTAAAAT
65 AATGATCCTTCAACCAGGATTAAAAT
* *
664 AAAGCAATGATCCTTAACCAGGATTAAACATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
1 AAAGCAATAATCCTCAACCAGGATTAAA-AT-AAGCAATGATCCTCAAACAGGATTAAAATAAAG
* * *
729 CAAAGATCCTTGAA-CAGGATTAACAT
64 CAATGATCCTTCAACCAGGATTAAAAT
* * * * * *
755 AGAGCAGAT-ATCCTCAACCAGGATAAAAATAAAGTAACGATCCTCAAACAGGATTAAAAATGAG
1 AAAGCA-ATAATCCTCAACCAGGATTAAAAT-AAGCAATGATCCTCAAACAGGATT-AAAATAAA
* * *
819 GTAATGATCC-TCAAACAGGATTAATCAT
63 GCAATGATCCTTCAACCAGGATTAA-AAT
* * * *
847 AAAGTAATGATCCTCAAACAGGATTCAAATAA
1 AAAGCAATAATCCTCAACCAGGATTAAAATAA
879 AGCTGATAAA
Statistics
Matches: 339, Mismatches: 45, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
90 202 0.60
91 108 0.32
92 29 0.09
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.22
Consensus pattern (90 bp):
AAAGCAATAATCCTCAACCAGGATTAAAATAAGCAATGATCCTCAAACAGGATTAAAATAAAGCA
ATGATCCTTCAACCAGGATTAAAAT
Found at i:1223 original size:71 final size:71
Alignment explanation
Indices: 1143--1553 Score: 434
Period size: 71 Copynumber: 5.8 Consensus size: 71
1133 CATTTTGCAG
* * * * * * * * *
1143 TCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGATCTACTGAAGTAAATTGAGGAAAGATTGT
1 TCAATTGAAATAAACTGAAGAAAAGATCACCCTGGATCAACTGAAATAAACTGAAGAAAGATCGC
1208 CCTGGA
66 CCTGGA
* *
1214 TCAATTGAAATAAACTGAAGAAAAGATCACCCTGGATCAAGTGAAATAAACTGAAGAAAAGATCA
1 TCAATTGAAATAAACTGAAGAAAAGATCACCCTGGATCAACTGAAATAAACTGAAG-AAAGATCG
*
1279 CCCTGTA
65 CCCTGGA
* * *
1286 TCAATTGAAATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGC
1 TCAATTGAAATAAACTGAAGAAAAGATCACCCTGGATCAACTGAAATAAACTGAAGAAAGATCGC
*
1351 CCTGGG
66 CCTGGA
** * * * *
1357 TCAA-CAAAATAAACTGAAGAAAGGATCACCCTGGATCAACTGAAGTAAAATGAAGAAAAGATCA
1 TCAATTGAAATAAACTGAAGAAAAGATCACCCTGGATCAACTGAAATAAACTGAAG-AAAGATCG
*
1421 CCCTAGA
65 CCCTGGA
* * * * * * * *
1428 TCAAACTGAAATAAACTGAA-ATAGGACCACCCTAGG-TCAACTGAAATGAATTGAATAAGGATC
1 TC-AATTGAAATAAACTGAAGAAAAGATCACCCT-GGATCAACTGAAATAAACTGAAGAAAGATC
1491 GCCCTGGA
64 GCCCTGGA
* * * *
1499 TCAACTGAAGTGAATTGAAG-AAAGATCACCCTGGATCAAACTGAAATAAACTGAA
1 TCAATTGAAATAAACTGAAGAAAAGATCACCCTGGATC-AACTGAAATAAACTGAA
1554 ATAGGACCAT
Statistics
Matches: 283, Mismatches: 49, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
69 2 0.01
70 69 0.24
71 105 0.37
72 93 0.33
73 14 0.05
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (71 bp):
TCAATTGAAATAAACTGAAGAAAAGATCACCCTGGATCAACTGAAATAAACTGAAGAAAGATCGC
CCTGGA
Found at i:1248 original size:36 final size:36
Alignment explanation
Indices: 1143--1580 Score: 424
Period size: 36 Copynumber: 12.3 Consensus size: 36
1133 CATTTTGCAG
* * * *
1143 TCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
* * * * ***
1179 TCTACTGAAGTAAATTG-AGGAAAGATTGTCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
*
1214 TCAATTGAAATAAACTGAAGAAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
* *
1250 TCAAGTGAAATAAACTGAAGAAAAGATCACCCTGTA
1 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
* * *
1286 TCAATTGAAATAAATTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
* * *
1322 TCAACTGAAATAAACTGAAG-AAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
* *
1357 TCAAC-AAAATAAACTGAAGAAAGGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
* * *
1392 TCAACTGAAGTAAAATGAAGAAAAGATCACCCTAGA
1 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
* * *
1428 TCAAACTGAAATAAACTGAA-ATAGGACCACCCTAGG-
1 TC-AACTGAAATAAACTGAAGAAAAGATCACCCT-GGA
* * * * *
1464 TCAACTGAAATGAATTGAA-TAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
* * *
1499 TCAACTGAAGTGAATTGAAG-AAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
* * * * *
1534 TCAAACTGAAATAAACTGAA-ATAGGACCATCCTGGG
1 TC-AACTGAAATAAACTGAAGAAAAGATCACCCTGGA
1570 TCAACTGAAAT
1 TCAACTGAAAT
1581 GAATTTAAGC
Statistics
Matches: 334, Mismatches: 59, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
34 15 0.04
35 127 0.38
36 176 0.53
37 16 0.05
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.20
Consensus pattern (36 bp):
TCAACTGAAATAAACTGAAGAAAAGATCACCCTGGA
Found at i:1421 original size:142 final size:141
Alignment explanation
Indices: 1143--1553 Score: 486
Period size: 142 Copynumber: 2.9 Consensus size: 141
1133 CATTTTGCAG
* * * * * * *
1143 TCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGATCTACTGAAGTAAATTGAGGAAAGATTGT
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAAGATCGC
* *
1208 CCTGGATCAATTGAAATAAACTGAAGAAAAGATCACCCTGGATCAAGTGAAATAAACTGAAGAAA
66 CCTGGATCAA-CGAAATAAACTGAAG-AAAGATCACCCTGGATCAACTGAAATAAACTGAAGAAA
1273 AGATCACCCT-GTA
129 AGATCACCCTAG-A
* * *
1286 TCAATTGAAATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGC
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAAGATCGC
* * * *
1351 CCTGGGTCAACAAAATAAACTGAAGAAAGGATCACCCTGGATCAACTGAAGTAAAATGAAGAAAA
66 CCTGGATCAACGAAATAAACTGAAGAAA-GATCACCCTGGATCAACTGAAATAAACTGAAGAAAA
1416 GATCACCCTAGA
130 GATCACCCTAGA
* * * * * * * *
1428 TCAAACTGAAATAAACTGAA-ATAGGACCACCCTAGG-TCAACTGAAATGAATTGAATAAGGATC
1 TC-AATTGAAATAAACTGAAGAAAAGATCGCCCT-GGATCAACTGAAATAAATTGAAGAAAGATC
* * *
1491 GCCCTGGATCAACTGAAGTGAATTGAAGAAAGATCACCCTGGATCAAACTGAAATAAACTGAA
64 GCCCTGGATCAAC-GAAATAAACTGAAGAAAGATCACCCTGGATC-AACTGAAATAAACTGAA
1554 ATAGGACCAT
Statistics
Matches: 228, Mismatches: 34, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
141 3 0.01
142 115 0.50
143 110 0.48
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (141 bp):
TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAAGATCGC
CCTGGATCAACGAAATAAACTGAAGAAAGATCACCCTGGATCAACTGAAATAAACTGAAGAAAAG
ATCACCCTAGA
Found at i:1585 original size:106 final size:108
Alignment explanation
Indices: 1142--1580 Score: 516
Period size: 107 Copynumber: 4.1 Consensus size: 108
1132 CCATTTTGCA
* * * * *
1142 GTCAATTGAAATAAACTGCAGAGAA-GATCGCCCTGGATCTACTGAAGTAAATTG-AGGAAAGAT
1 GTCAACTGAAATAAACTGAAGA-AAGGATCACCCTGGATCAACTGAAGTAAATTGAAGAAAAGAT
*** * * *
1205 TGTCCTGGATCAATTGAAATAAACTGAAGAAAAGATCACCCTGG
65 CACCCTGGATCAACTGAAATAAACTGAAGATAAGACCACCCTGG
* * * * * *
1249 ATCAAGTGAAATAAACTGAAGAAAAGATCACCCTGTATCAATTGAAATAAATTGAAGAAAAGATC
1 GTCAACTGAAATAAACTGAAGAAAGGATCACCCTGGATCAACTGAAGTAAATTGAAGAAAAGATC
* *
1314 GCCCTGGATCAACTGAAATAAACTGAAGA-AAGACCGCCCTGG
66 ACCCTGGATCAACTGAAATAAACTGAAGATAAGACCACCCTGG
* *
1356 GTCAAC-AAAATAAACTGAAGAAAGGATCACCCTGGATCAACTGAAGTAAAATGAAGAAAAGATC
1 GTCAACTGAAATAAACTGAAGAAAGGATCACCCTGGATCAACTGAAGTAAATTGAAGAAAAGATC
* * *
1420 ACCCTAGATCAAACTGAAATAAACTGAA-ATAGGACCACCCTAG
66 ACCCTGGATC-AACTGAAATAAACTGAAGATAAGACCACCCTGG
* * * * *
1463 GTCAACTGAAATGAATTGAA-TAAGGATCGCCCTGGATCAACTGAAGTGAATTGAAG-AAAGATC
1 GTCAACTGAAATAAACTGAAGAAAGGATCACCCTGGATCAACTGAAGTAAATTGAAGAAAAGATC
* *
1526 ACCCTGGATCAAACTGAAATAAACTGAA-ATAGGACCATCCTGG
66 ACCCTGGATC-AACTGAAATAAACTGAAGATAAGACCACCCTGG
1569 GTCAACTGAAAT
1 GTCAACTGAAAT
1581 GAATTTAAGC
Statistics
Matches: 290, Mismatches: 37, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
106 122 0.42
107 123 0.42
108 45 0.16
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.20
Consensus pattern (108 bp):
GTCAACTGAAATAAACTGAAGAAAGGATCACCCTGGATCAACTGAAGTAAATTGAAGAAAAGATC
ACCCTGGATCAACTGAAATAAACTGAAGATAAGACCACCCTGG
Done.