Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020635.1 Corchorus olitorius cultivar O-4 contig20668, 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: 3581
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.29
Found at i:668 original size:54 final size:53
Alignment explanation
Indices: 600--1128 Score: 395
Period size: 54 Copynumber: 9.9 Consensus size: 53
590 TTCTTGGAGT
* *
600 GACCATACTGGATCAAAT-TGGAGATCAACTCTGATCATCGGAAACTTCTTGAAC
1 GACCACACTGGATC--ATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGAAC
*
654 GACCACACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAAC
1 GACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTG-AAC
* * * * * *
708 GACCATACCGGATCATCTGAAGATCAACTCTGATCTTCAAAAATTTCTTGAAAC
1 GACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTG-AAC
*** * * * * * * *
762 GTTAACACCGGGTCATCTGGAGATCAATTTTGATCTTTGAAAACTTCTAGGAA-
1 GACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCT-TGAAC
* * * * * *
815 GAACCGCACTGGATCATCTGGACATCAACTCTGAACTTCGAAAACTTTTTGGAAG
1 G-ACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTT-GAAC
* * * *
870 GACCACACTGGATCATTTGGAGATAAACTCTGATCATCAAAAACTTCTTGGAAT
1 GACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTT-GAAC
* * * *
924 GACCGCACGGGATTATCT-GAGGATCAACTCTGATCAT--AAAACTTCTTGGAAT
1 GACCACACTGGATCATCTGGA-GATCAACTCTGATCATCGAAAACTTCTT-GAAC
* * * * * *
976 GACCACACTGGATC-TTTGGCGATCAACTCTGACCATTGACAACTTCTTGGAAT
1 GACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTT-GAAC
* * * * * * * * * *
1029 GACCGCACTTGACCTTTTGGGGATCAACTCTGACCATTGAAAACTTCCTGGAAT
1 GACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTT-CTTGAAC
** * * * * * *
1083 GACTGCACTGGATCTTTTGGGGATCAACACTGACCATTGAAAACTT
1 GACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTT
1129 ATTGGAATGA
Statistics
Matches: 399, Mismatches: 64, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
51 17 0.04
52 29 0.07
53 59 0.15
54 290 0.73
55 4 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (53 bp):
GACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAAAACTTCTTGAAC
Found at i:1202 original size:35 final size:35
Alignment explanation
Indices: 1104--1552 Score: 544
Period size: 35 Copynumber: 12.6 Consensus size: 35
1094 ATCTTTTGGG
* * ** * * *
1104 GATCAACACTGACCATTGAAAACTTATTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
*
1139 GATCAACTCTGATCATAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT-AAAAAACTTCTTGAAACGA
*
1175 GATCAACTCTGATAATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
* * *
1210 GATCAAGTTTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
** * *
1245 GATCAACTCTGATCATCGAAAATTTCTT-AGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGA-AACGA
** *
1280 GATCAACTCTGATCATTGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
* *
1315 GATCAACTCTGATCA-ACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATA-AAAAACTTCTTGAAACGA
* * *
1350 GATCAACTCTGATCATAAAATACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
*
1385 GATCAACTCTGATCATAAAAAAAAACTTCTTGAAACAA
1 GATCAACTCTGATCAT---AAAAAACTTCTTGAAACGA
1423 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAACGA
* *
1460 GATCAACTCTGATCATAAAAAAAACTTCTTAAAAGGA
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAACGA
1497 GATCAACTCTGATCATAAAAAAC-TCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
1531 GATCAACTCTGATCATAAAAAA
1 GATCAACTCTGATCATAAAAAA
1553 AAAAAAGACT
Statistics
Matches: 372, Mismatches: 34, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
34 32 0.09
35 206 0.55
36 32 0.09
37 71 0.19
38 31 0.08
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
Found at i:1772 original size:92 final size:93
Alignment explanation
Indices: 1603--1783 Score: 258
Period size: 92 Copynumber: 2.0 Consensus size: 93
1593 GATCAACTCT
** * *
1603 GATCTCTAAAAACTTCTATGAAAGACCGCACAAGGTCATCTTAAAATCAACTTAGATCTCTGAAA
1 GATCTCTAAAAACTTCTATGAAAGACAACACAAGGTCATCTTAAAATCAACTTAAATCTCTCAAA
*
1668 ACTTCTATGAAAGACCGCCCAGGGCTTA
66 ACTTCTATGAAAGACCGCACAGGGCTTA
* * * *
1696 GATCTCTGAAAACTTCTATGAAAGACAACA-AAGGGTC-TCTTCAGATCAACTTAAATTTCTCAA
1 GATCTCTAAAAACTTCTATGAAAGACAACACAA-GGTCATCTTAAAATCAACTTAAATCTCTCAA
1759 AACTTCTATGAAAGACCGCACAGGG
65 AACTTCTATGAAAGACCGCACAGGG
1784 TGCTTGAAGG
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
92 47 0.60
93 31 0.40
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (93 bp):
GATCTCTAAAAACTTCTATGAAAGACAACACAAGGTCATCTTAAAATCAACTTAAATCTCTCAAA
ACTTCTATGAAAGACCGCACAGGGCTTA
Done.