Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013678.1 Corchorus olitorius cultivar O-4 contig13711, 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, 736
Length: 1227
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Found at i:346 original size:54 final size:54
Alignment explanation
Indices: 189--727 Score: 512
Period size: 54 Copynumber: 10.0 Consensus size: 54
179 TTCTTAATCA
* * *
189 ACCGCACTGGATC-ATTTAAGATTCAAC-CTTGATCA-CGAAAACCTTTCTTGGAATG
1 ACCGCACTGGATCAATTGAGGA-TCAACTC-TGATCATTGAAAA-C-TTCTTGGAATG
* ** * * *
244 ATCGCACTGGATCCAATTGAAAATCAACTCTGAT-AATCAAAACGTCTTGGAATG
1 ACCGCACTGGAT-CAATTGAGGATCAACTCTGATCATTGAAAACTTCTTGGAATG
* * * * *
298 ACTGCACTGTATCAATTGAAGATCAACTCTGATCATTGAAAATTTCTTGGAAAG
1 ACCGCACTGGATCAATTGAGGATCAACTCTGATCATTGAAAACTTCTTGGAATG
* * * *
352 ACCGCACTAGATC-ATCTG-GGATCAGCTCTGAT-TTCTAAAAACTTCTTGGAATG
1 ACCGCACTGGATCAAT-TGAGGATCAACTCTGATCAT-TGAAAACTTCTTGGAATG
* * *
405 ACCGCACTAGATC-ATCTGGGGATCAACTCTGATCATTGAAAACTTCTTGGATTG
1 ACCGCACTGGATCAAT-TGAGGATCAACTCTGATCATTGAAAACTTCTTGGAATG
* * * ** *
459 ACCACACAGGATCAATT-AGAGATCAACTCTAATCATCAAAAACTTCTTAGAATG
1 ACCGCACTGGATCAATTGAG-GATCAACTCTGATCATTGAAAACTTCTTGGAATG
* ** *
513 ACTGCACCAGATC-ATTTAGGATCAACTCTGATCATTGAAAACTTCTTGGAATG
1 ACCGCACTGGATCAATTGAGGATCAACTCTGATCATTGAAAACTTCTTGGAATG
* *
566 ACCACACTGGATCAATCTG-GGATCAACTCTGATCATTGAAAACTT-TTTGAATTG
1 ACCGCACTGGATCAAT-TGAGGATCAACTCTGATCATTGAAAACTTCTTGGAA-TG
* * ** *
620 ACCGCACAGGATCAATT-AGAGATCAACTCTAATCATCAAAAACTTCTTAGAATG
1 ACCGCACTGGATCAATTGAG-GATCAACTCTGATCATTGAAAACTTCTTGGAATG
* *
674 ACCGCACCGGATC-ATTTAGGATCAACTCTGATCATTGAAAACTTCTTGGAATG
1 ACCGCACTGGATCAATTGAGGATCAACTCTGATCATTGAAAACTTCTTGGAATG
727 A
1 A
728 GATCAACTCT
Statistics
Matches: 403, Mismatches: 62, Indels: 40
0.80 0.12 0.08
Matches are distributed among these distances:
52 1 0.00
53 151 0.37
54 208 0.52
55 22 0.05
56 14 0.03
57 7 0.02
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (54 bp):
ACCGCACTGGATCAATTGAGGATCAACTCTGATCATTGAAAACTTCTTGGAATG
Found at i:406 original size:107 final size:106
Alignment explanation
Indices: 266--727 Score: 463
Period size: 107 Copynumber: 4.3 Consensus size: 106
256 CCAATTGAAA
* * * * *
266 ATCAACTCTGAT-AATCAAAACGTCTTGGAATGACTGCACTGTATCAATTGAAGATCAACTCTGA
1 ATCAACTCTGATCATTAAAAACTTCTTGGAATGACCGCACAG-ATC-ATTGAAGATCAACTCTGA
* * *
330 TCATTGAAAATTTCTTGGAAAGACCGCACTAGATC-ATCTGGG
64 TCATTGAAAACTTCTTGGAATGACCACACTAGATCAATCTGGG
* * **
372 ATCAGCTCTGAT-TTCTAAAAACTTCTTGGAATGACCGCACTAGATCATCTGGGGATCAACTCTG
1 ATCAACTCTGATCAT-TAAAAACTTCTTGGAATGACCGCAC-AGATCAT-TGAAGATCAACTCTG
* *
436 ATCATTGAAAACTTCTTGGATTGACCACAC-AGGATCAAT-TAGAG
63 ATCATTGAAAACTTCTTGGAATGACCACACTA-GATCAATCT-GGG
* * * * * *
480 ATCAACTCTAATCATCAAAAACTTCTTAGAATGACTGCACCAGATCATTTAGGATCAACTCTGAT
1 ATCAACTCTGATCATTAAAAACTTCTTGGAATGACCGCA-CAGATCATTGAAGATCAACTCTGAT
*
545 CATTGAAAACTTCTTGGAATGACCACACTGGATCAATCTGGG
65 CATTGAAAACTTCTTGGAATGACCACACTAGATCAATCTGGG
* *
587 ATCAACTCTGATCATTGAAAACTT-TTTGAATTGACCGCACAGGATCAATT-AGAGATCAACTCT
1 ATCAACTCTGATCATTAAAAACTTCTTGGAA-TGACCGCACA-GATC-ATTGA-AGATCAACTCT
* ** * * ** * *
650 AATCATCAAAAACTTCTTAGAATGACCGCACCGGATC-ATTTAGG
62 GATCATTGAAAACTTCTTGGAATGACCACACTAGATCAATCTGGG
*
694 ATCAACTCTGATCATTGAAAACTTCTTGGAATGA
1 ATCAACTCTGATCATTAAAAACTTCTTGGAATGA
728 GATCAACTCT
Statistics
Matches: 301, Mismatches: 40, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
106 21 0.07
107 185 0.61
108 93 0.31
109 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (106 bp):
ATCAACTCTGATCATTAAAAACTTCTTGGAATGACCGCACAGATCATTGAAGATCAACTCTGATC
ATTGAAAACTTCTTGGAATGACCACACTAGATCAATCTGGG
Found at i:527 original size:161 final size:161
Alignment explanation
Indices: 266--727 Score: 635
Period size: 161 Copynumber: 2.9 Consensus size: 161
256 CCAATTGAAA
* * * * * * * *
266 ATCAACTCTGAT-AATCAAAACGTCTTGGAATGACTGCACTGTATCAATT-GAAGATCAACTCTG
1 ATCAACTCTGATCATTGAAAACTTCTTGGATTGACCGCACAGGATCAATTAG-AGATCAACTCTA
** * * * * * * * * *
329 ATCATTGAAAATTTCTTGGAAAGACCGCACTAGATCATCTGGGATCAGCTCTGAT-TTCTAAAAA
65 ATCATCAAAAACTTCTTAGAATGACCGCACCAGATCATTTAGGATCAACTCTGATCAT-TGAAAA
*
393 CTTCTTGGAATGACCGCACTAGATC-ATCTGGGG
129 CTTCTTGGAATGACCACACTAGATCAATCT-GGG
*
426 ATCAACTCTGATCATTGAAAACTTCTTGGATTGACCACACAGGATCAATTAGAGATCAACTCTAA
1 ATCAACTCTGATCATTGAAAACTTCTTGGATTGACCGCACAGGATCAATTAGAGATCAACTCTAA
*
491 TCATCAAAAACTTCTTAGAATGACTGCACCAGATCATTTAGGATCAACTCTGATCATTGAAAACT
66 TCATCAAAAACTTCTTAGAATGACCGCACCAGATCATTTAGGATCAACTCTGATCATTGAAAACT
*
556 TCTTGGAATGACCACACTGGATCAATCTGGG
131 TCTTGGAATGACCACACTAGATCAATCTGGG
* *
587 ATCAACTCTGATCATTGAAAACTTTTTGAATTGACCGCACAGGATCAATTAGAGATCAACTCTAA
1 ATCAACTCTGATCATTGAAAACTTCTTGGATTGACCGCACAGGATCAATTAGAGATCAACTCTAA
*
652 TCATCAAAAACTTCTTAGAATGACCGCACCGGATCATTTAGGATCAACTCTGATCATTGAAAACT
66 TCATCAAAAACTTCTTAGAATGACCGCACCAGATCATTTAGGATCAACTCTGATCATTGAAAACT
717 TCTTGGAATGA
131 TCTTGGAATGA
728 GATCAACTCT
Statistics
Matches: 270, Mismatches: 28, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
160 12 0.04
161 252 0.93
162 6 0.02
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (161 bp):
ATCAACTCTGATCATTGAAAACTTCTTGGATTGACCGCACAGGATCAATTAGAGATCAACTCTAA
TCATCAAAAACTTCTTAGAATGACCGCACCAGATCATTTAGGATCAACTCTGATCATTGAAAACT
TCTTGGAATGACCACACTAGATCAATCTGGG
Found at i:942 original size:35 final size:35
Alignment explanation
Indices: 693--939 Score: 289
Period size: 35 Copynumber: 6.8 Consensus size: 35
683 GATCATTTAG
** *
693 GATCAACTCTGATCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
728 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAATGA
*
765 GATCAACTCTGATCATAAAAAAAAAAATCTTCTTGAAACGA
1 GATCAACTCTGATCAT-----AAAAAA-CTTCTTGAAATGA
*
806 GATCAACTCTGATCAT-AAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
840 GATCAACTTTGATCATAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT-AAAAAACTTCTTGAAATGA
* ** *
876 GAACAACTCTGATCATCGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
**
911 GATCAACTCTGATCATCGAAAACTTCTTG
1 GATCAACTCTGATCATAAAAAACTTCTTG
940 GAACAACCAC
Statistics
Matches: 191, Mismatches: 13, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
34 27 0.14
35 65 0.34
36 31 0.16
37 31 0.16
40 8 0.04
41 29 0.15
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (35 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
Found at i:1016 original size:54 final size:54
Alignment explanation
Indices: 910--1168 Score: 197
Period size: 54 Copynumber: 4.8 Consensus size: 54
900 TCTTGGAATG
* * *
910 AGATCAACTCTGATCATC-GAAAACTTCTTGGAACA-ACCACACCGGATTATCTGG
1 AGATCAACTCTGATC-TCTGAAAACTTCTTTGAA-AGACCACACCGGATCATCTGA
* * * *
964 GGATCAACTCTGATCTCTAAAAACTTCTTTGAAAGACCGCA-CGAGGTCATCTGA
1 AGATCAACTCTGATCTCTGAAAACTTCTTTGAAAGACCACACCG-GATCATCTGA
* * * * * *
1018 AGATCAACT-TAGATTTTCTGAAAACTTCTATGAAAGACCATATCGGGTCATCTTA
1 AGATCAACTCT-GA-TCTCTGAAAACTTCTTTGAAAGACCACACCGGATCATCTGA
* ** * * * * *
1073 AAATC-TGTTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTA
1 AGATCAACTCT-GATCTCTGAAAACTTCTTTGAAAGACCACACCGGATCATCTGA
* * *
1127 AGATCTA-TTTAGATCTCTGAAAACTTCTATGAAAGACCACAC
1 AGATCAACTCT-GATCTCTGAAAACTTCTTTGAAAGACCACAC
1169 TAGGTCATTT
Statistics
Matches: 174, Mismatches: 23, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
53 6 0.03
54 126 0.72
55 40 0.23
56 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (54 bp):
AGATCAACTCTGATCTCTGAAAACTTCTTTGAAAGACCACACCGGATCATCTGA
Found at i:1169 original size:54 final size:54
Alignment explanation
Indices: 975--1181 Score: 265
Period size: 54 Copynumber: 3.8 Consensus size: 54
965 GATCAACTCT
* * * * * *
975 GATCTCTAAAAACTTCTTTGAAAGACCGCAC-GAGGTCATCTGAAGATCAACTTA
1 GATCTCTGAAAACTTCTATGAAAGACCACACTG-GGTCATCTTAAGATCTATTTA
* * * *
1029 GATTTTCTGAAAACTTCTATGAAAGACCATA-TCGGGTCATCTTAAAATCTGTTTA
1 GA-TCTCTGAAAACTTCTATGAAAGACCACACT-GGGTCATCTTAAGATCTATTTA
1084 GATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTATTTA
1 GATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTATTTA
* *
1138 GATCTCTGAAAACTTCTATGAAAGACCACACTAGGTCATTTTAA
1 GATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
1182 ACACTTGTAC
Statistics
Matches: 133, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
54 90 0.68
55 42 0.32
56 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (54 bp):
GATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTATTTA
Done.