Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012448.1 Corchorus olitorius cultivar O-4 contig12481, 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: 15164
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:51 original size:33 final size:32
Alignment explanation
Indices: 5--84 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 32
1 CACA
* * *
5 AAATTT-GCGGCGTTTAAGTTAA-TAAATGCTGC
1 AAATTTAGTGGCGTTT-A-TTAACTAAACGCCGC
37 AAATTTAGTGGCGTTTATTAACTTAAACGCCGC
1 AAATTTAGTGGCGTTTATTAAC-TAAACGCCGC
70 AAATTTAGTGGCGTT
1 AAATTTAGTGGCGTT
85 GTTGGTCTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 4 0.10
32 7 0.17
33 31 0.74
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (32 bp):
AAATTTAGTGGCGTTTATTAACTAAACGCCGC
Found at i:631 original size:159 final size:158
Alignment explanation
Indices: 343--643 Score: 385
Period size: 159 Copynumber: 1.9 Consensus size: 158
333 CGCCGCTATA
* *
343 TATTATAAGCGTAGAGTTGGAAAATTTTTTTGTTTTAGGAGGAGGGAATTTTTCCCTCCAAAAAA
1 TATTATAAGCGTAGAGTTGGAAAATTTCTTTGTTTGAGGAGGAGGGAATTTTTCCCTCCAAAAAA
* *
408 AGGGAAAAAAAATCTATCCCTCCATATATTAGAATAGCAGCGTTTCCTTTTCTAGATGCCACTAA
66 AGGGAAAAAAAATCTATCCCTCCATATATTAGAATAGCAGCGTTTCCTTTTCTAAACGCCACTAA
*
473 TTAGCGGCGTCTGATGTCCAAACGCTGC
131 ATAGCGGCGTCTGATGTCCAAACGCTGC
* * * * *
501 TATTATAGGTGTAGAGTTGTAAACTTTCTTTGTTTGAGTGGGGAGGGAATTTTTCCCTCCAAAAA
1 TATTATAAGCGTAGAGTTGGAAAATTTCTTTGTTTGAG-GAGGAGGGAATTTTTCCCTCCAAAAA
* * * * *
566 AA-GGAGAAAAAAATCTCTCCCTCTATATATTA-ATATGGCGGCGTCTTTC-TTTC-AAACCGCC
65 AAGGGA-AAAAAAATCTATCCCTCCATATATTAGA-ATAGCAGCGT-TTCCTTTTCTAAA-CGCC
*
627 ACTAAATGGCGGCGTCT
126 ACTAAATAGCGGCGTCT
644 TCTTCTCAAC
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
158 38 0.31
159 81 0.66
160 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (158 bp):
TATTATAAGCGTAGAGTTGGAAAATTTCTTTGTTTGAGGAGGAGGGAATTTTTCCCTCCAAAAAA
AGGGAAAAAAAATCTATCCCTCCATATATTAGAATAGCAGCGTTTCCTTTTCTAAACGCCACTAA
ATAGCGGCGTCTGATGTCCAAACGCTGC
Found at i:7888 original size:13 final size:13
Alignment explanation
Indices: 7870--7905 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
7860 GAAATCGTTA
*
7870 AAATCAATGTCAT
1 AAATCAAAGTCAT
7883 AAATCAAAGTCAT
1 AAATCAAAGTCAT
*
7896 AAACCAAAGT
1 AAATCAAAGT
7906 AAAACCAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.22
Consensus pattern (13 bp):
AAATCAAAGTCAT
Found at i:9127 original size:13 final size:12
Alignment explanation
Indices: 9108--9142 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
9098 ATATTTTTTT
*
9108 TTTCTTTTTCCT
1 TTTCTTTTTCCC
9120 TATTCTTTTTCCC
1 T-TTCTTTTTCCC
9133 TTTCTTTTTC
1 TTTCTTTTTC
9143 TTCCTTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTCTTTTTCCC
Found at i:9305 original size:25 final size:26
Alignment explanation
Indices: 9250--9306 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
9240 GGCCTGCTAG
*
9250 GCAGG-CCAAGCGGCCTGGGCTGCGC
1 GCAGGCCCAAGCGGCCTGGGCTGCCC
9275 GCCAGGCCCAAGC-G-CTGGGCTGCCC
1 G-CAGGCCCAAGCGGCCTGGGCTGCCC
9300 AGCAGGC
1 -GCAGGC
9307 AGCGCAGCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
25 16 0.57
26 6 0.21
27 6 0.21
ACGTcount: A:0.14, C:0.39, G:0.40, T:0.07
Consensus pattern (26 bp):
GCAGGCCCAAGCGGCCTGGGCTGCCC
Found at i:11131 original size:54 final size:54
Alignment explanation
Indices: 11072--11179 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
11062 TACAAGTATT
11072 ACTTTTATTTATTTATTTATTTTTGAAAAAAGTTTAAGAACATTATAGGTCATC
1 ACTTTTATTTATTTATTTATTTTTGAAAAAAGTTTAAGAACATTATAGGTCATC
11126 ACTTTTATTTATTTATTTATTTTTGAAAAAAGTTTAAGAACATTATAGGTCATC
1 ACTTTTATTTATTTATTTATTTTTGAAAAAAGTTTAAGAACATTATAGGTCATC
11180 TCATCTCTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.48
Consensus pattern (54 bp):
ACTTTTATTTATTTATTTATTTTTGAAAAAAGTTTAAGAACATTATAGGTCATC
Found at i:14945 original size:50 final size:50
Alignment explanation
Indices: 14881--15031 Score: 293
Period size: 50 Copynumber: 3.0 Consensus size: 50
14871 CCCAATGGAA
*
14881 ATGGACTTGGACTTGTAATGGACCAAATGCCCTGACTTGGAGTTGGACTT
1 ATGGACTTGGACTTGTACTGGACCAAATGCCCTGACTTGGAGTTGGACTT
14931 ATGGACTTGGACTTGTACTGGACCAAATGCCCTGACTTGGAGTTGGACTT
1 ATGGACTTGGACTTGTACTGGACCAAATGCCCTGACTTGGAGTTGGACTT
14981 ATGGACTTGGACTTGTACTGGACCAAATGCCCTGACTTGGAGTTGGACTT
1 ATGGACTTGGACTTGTACTGGACCAAATGCCCTGACTTGGAGTTGGACTT
15031 A
1 A
15032 GATCCCAACC
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 100 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (50 bp):
ATGGACTTGGACTTGTACTGGACCAAATGCCCTGACTTGGAGTTGGACTT
Done.