Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023618.1 Corchorus olitorius cultivar O-4 contig23651, 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: 16888
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:5548 original size:13 final size:13
Alignment explanation
Indices: 5530--5555 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5520 TAAAGGAAAA
5530 AGAAGAAGAAGTT
1 AGAAGAAGAAGTT
5543 AGAAGAAGAAGTT
1 AGAAGAAGAAGTT
5556 CGACTAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (13 bp):
AGAAGAAGAAGTT
Found at i:8693 original size:44 final size:43
Alignment explanation
Indices: 8617--8702 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 43
8607 ATCTCCGTTG
* * *
8617 ATATTTGTTATACATCCTTCATGCATGGTCCATGT-CTTTGTAT
1 ATATATGTTATACATCCATCATGCATGATCCAT-TCCTTTGTAT
* *
8660 ATATATGTTCATACATTCATCATGCATTATCCATTCCTTTGTA
1 ATATATGTT-ATACATCCATCATGCATGATCCATTCCTTTGTA
8703 CATAGGTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 9 0.25
44 27 0.75
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.45
Consensus pattern (43 bp):
ATATATGTTATACATCCATCATGCATGATCCATTCCTTTGTAT
Found at i:10798 original size:149 final size:150
Alignment explanation
Indices: 10612--10917 Score: 605
Period size: 149 Copynumber: 2.0 Consensus size: 150
10602 GAAATGAAAA
10612 AATGATGAAAAAAAGAGAAATACGAACGAGCTCTAGGGAGAAAACCCGAGAAAGGGCAGTCTAGA
1 AATGATGAAAAAAAGAGAAATACGAACGAGCTCTAGGGAGAAAACCCGAGAAAGGGCAGTCTAGA
10677 GCAAGGATCGGAATTCTTGGAGCCTCCTAAACAATCAGAGAAAACAGGACCTCTTTTGTAGTAAC
66 GCAAGGATCGGAATTCTTGGAGCCTCCTAAACAATCAGAGAAAACAGGACCTCTTTTGTAGTAAC
10742 AAGTATTGGCTCAGGCGAAT
131 AAGTATTGGCTCAGGCGAAT
10762 AATGATG-AAAAAAGAGAAATACGAACGAGCTCTAGGGAGAAAACCCGAGAAAGGGCAGTCTAGA
1 AATGATGAAAAAAAGAGAAATACGAACGAGCTCTAGGGAGAAAACCCGAGAAAGGGCAGTCTAGA
10826 GCAAGGATCGGAATTCTTGGAGCCTCCTAAACAATCAGAGAAAACAGGACCTCTTTTGTAGTAAC
66 GCAAGGATCGGAATTCTTGGAGCCTCCTAAACAATCAGAGAAAACAGGACCTCTTTTGTAGTAAC
10891 AAGTATTGGCTCAGGCGAAT
131 AAGTATTGGCTCAGGCGAAT
10911 AATGATG
1 AATGATG
10918 GACGAAGTTA
Statistics
Matches: 156, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
149 149 0.96
150 7 0.04
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.18
Consensus pattern (150 bp):
AATGATGAAAAAAAGAGAAATACGAACGAGCTCTAGGGAGAAAACCCGAGAAAGGGCAGTCTAGA
GCAAGGATCGGAATTCTTGGAGCCTCCTAAACAATCAGAGAAAACAGGACCTCTTTTGTAGTAAC
AAGTATTGGCTCAGGCGAAT
Found at i:11870 original size:35 final size:35
Alignment explanation
Indices: 11824--12512 Score: 807
Period size: 35 Copynumber: 19.8 Consensus size: 35
11814 ATTACCATCT
*
11824 TCCAGATGACTCAGTGTAGCATCTTCAAAATTGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
*
11859 TCCAGATGACTCGGTGCAGCATCTTCAAAATTGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
*
11894 TCCAGATGACTCGGTGCAGCATCTTCAAAATTGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
*
11929 TCCAGATGACTCGGTGCAGCATCTTCAAAATT-AA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
* * *
11963 ACTCAGATGACTCGGTGTAGCTTCTTCAAAGTTG--
1 TC-CAGATGACTCGGTGTAGCATCTTCAAAATTGAA
11997 TCCAAAGATGACTCGGTGTAGCATCTTCAAAATTGAA
1 TCC--AGATGACTCGGTGTAGCATCTTCAAAATTGAA
* *
12034 TCCAGATGACTCGGTGCAACATCTTCAAAATTGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
* * *
12069 TCAAGATGACTCGGTGCAACATCTTCAAAATTGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
* *
12104 TCCAGATGACTCAGTCTAGCATCTTCAAAGA-TGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAA-ATTGAA
*
12139 -CTCAGATGACTGGGTGTAGCATCTTCAAAATTGAA
1 TC-CAGATGACTCGGTGTAGCATCTTCAAAATTGAA
12174 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
*
12209 -CTCAGATGACTCGGTGCAGCATCTTCAAAATTGAA
1 TC-CAGATGACTCGGTGTAGCATCTTCAAAATTGAA
*
12244 -CTCAGATGACTCGGTGCAGCATCTTCAAAATTGAA
1 TC-CAGATGACTCGGTGTAGCATCTTCAAAATTGAA
* * *
12279 -CTCAGATGACTCGGTGTAGCATCCTCAAAGTTTAA
1 TC-CAGATGACTCGGTGTAGCATCTTCAAAATTGAA
* * *
12314 TCTAGATGACTCGATGTAGCATCTTCAATA-TGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
** *
12348 -CTTGGATGACTCGGTGTAGCATCTTCAAAGA-TGGA
1 TC-CAGATGACTCGGTGTAGCATCTTCAAA-ATTGAA
*** *
12383 TTTGGATGACTCGGTGTAGCATCTTCAATA-TGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
* * * *
12417 -CTCGGATGACTCAGTGTAGCATCTTCAAGA-TGGA
1 TC-CAGATGACTCGGTGTAGCATCTTCAAAATTGAA
* * * *
12451 TTCAGATGACTCAGTGCAGCATCTTCAATA-TGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
*
12485 -CTAGGATGACTCGGTGTAGCATCTTCAA
1 TCCA-GATGACTCGGTGTAGCATCTTCAA
12513 TATGGACTCA
Statistics
Matches: 583, Mismatches: 53, Indels: 37
0.87 0.08 0.05
Matches are distributed among these distances:
33 3 0.01
34 116 0.20
35 458 0.79
36 3 0.01
37 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (35 bp):
TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
Found at i:14591 original size:15 final size:15
Alignment explanation
Indices: 14561--14602 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
14551 TTACTTTGTT
14561 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
14577 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
14592 TTGCTTTCTGT
1 TTGTTTTCTGT
14603 GAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.