Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009531.1 Corchorus olitorius cultivar O-4 contig09563, 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: 2732
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Found at i:90 original size:17 final size:17
Alignment explanation
Indices: 68--104 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
58 ATTGAAGAGG
68 AAAGAAGAAGCGAAAAA
1 AAAGAAGAAGCGAAAAA
*
85 AAAGAAGAGGCGAAAAA
1 AAAGAAGAAGCGAAAAA
102 AAA
1 AAA
105 AAACAGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.70, C:0.05, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAGCGAAAAA
Found at i:771 original size:19 final size:20
Alignment explanation
Indices: 731--767 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
721 CCTAACGTAC
*
731 AATTATTTTATTTGACTTAT
1 AATTAATTTATTTGACTTAT
751 AATTAATTT-TTTG-CTTA
1 AATTAATTTATTTGACTTA
768 ATAAATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 4 0.25
20 8 0.50
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
AATTAATTTATTTGACTTAT
Found at i:1808 original size:13 final size:13
Alignment explanation
Indices: 1790--1814 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1780 TTCAATGTTC
1790 TAAATATTATTTA
1 TAAATATTATTTA
1803 TAAATATTATTT
1 TAAATATTATTT
1815 GGAATTCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:2355 original size:75 final size:75
Alignment explanation
Indices: 2232--2381 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
2222 TCCTTTTAGA
2232 TCTACTTTTGTGAGGCATTTGCAATATTACAAAGGAGGTTGATGAGATCTAACCTAGCTTATAAG
1 TCTACTTTTGTGAGGCATTTGCAATATTACAAAGGAGGTTGATGAGATCTAACCTAGCTTATAAG
2297 ATTAATGGTT
66 ATTAATGGTT
2307 TCTACTTTTGTGAGGCATTTGCAATATTACAAAGGAGGTTGATGAGATCTAACCTAGCTTATAAG
1 TCTACTTTTGTGAGGCATTTGCAATATTACAAAGGAGGTTGATGAGATCTAACCTAGCTTATAAG
2372 ATTAATGGTT
66 ATTAATGGTT
2382 ACAAGTGGCC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (75 bp):
TCTACTTTTGTGAGGCATTTGCAATATTACAAAGGAGGTTGATGAGATCTAACCTAGCTTATAAG
ATTAATGGTT
Found at i:2600 original size:138 final size:142
Alignment explanation
Indices: 2399--2678 Score: 336
Period size: 138 Copynumber: 2.0 Consensus size: 142
2389 GCCATGAGTT
** * * * ** *
2399 TACACATGAATAAGTCCATTGAATCTGGGCTTATTAATAAGTACTGTTATAACTCTTAAATACAC
1 TACACATGAATAAACCCATTCAATCCGGACTTATTAATAAACACTATTATAACTCTTAAATACAC
* * * * * * *
2464 GGGGGGAAA-ACAAA-ATAGG-ATAGTTATTTCTACCCT-AAAAAAATTA-ATTAAAGCTTTTAG
66 AGGAGAAAAGACAAAGAT-GGTATAGTTATTTCAACCCTAAAAAAAAGTAGACTAAAGCTTTTAA
2524 TAATTTTGATGGG
130 TAATTTTGATGGG
* * *
2537 TACACATGAATAAACCCGTTCAATCCGGACTTATTAATAAACGCTATTATAACTCTTAAATACAT
1 TACACATGAATAAACCCATTCAATCCGGACTTATTAATAAACACTATTATAACTCTTAAATACAC
*
2602 AGGAGAAAAGACAAAGATGGTATAGTTATTTCAACCCTAAAAAAAAGTAGACTAGAGCTTTTAAT
66 AGGAGAAAAGACAAAGATGGTATAGTTATTTCAACCCTAAAAAAAAGTAGACTAAAGCTTTTAAT
*
2667 AATTTTGGTGGG
131 AATTTTGATGGG
2679 ATACGTACAA
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
138 60 0.51
139 7 0.06
140 18 0.15
141 9 0.08
142 23 0.20
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (142 bp):
TACACATGAATAAACCCATTCAATCCGGACTTATTAATAAACACTATTATAACTCTTAAATACAC
AGGAGAAAAGACAAAGATGGTATAGTTATTTCAACCCTAAAAAAAAGTAGACTAAAGCTTTTAAT
AATTTTGATGGG
Done.