Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018338.1 Corchorus olitorius cultivar O-4 contig18371, 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: 41324
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4040 original size:5 final size:5
Alignment explanation
Indices: 4030--4068 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
4020 AGGTGTTCGT
* *
4030 GGGTC GGGTC GGGTC GGGCC GGGTC GGATTC GGGTC GGG
1 GGGTC GGGTC GGGTC GGGTC GGGTC GG-GTC GGGTC GGG
4069 CCAAGTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.03, C:0.21, G:0.59, T:0.18
Consensus pattern (5 bp):
GGGTC
Found at i:4064 original size:21 final size:20
Alignment explanation
Indices: 4030--4070 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
4020 AGGTGTTCGT
4030 GGGTCGGGTCGGGTCGGGCC
1 GGGTCGGGTCGGGTCGGGCC
*
4050 GGGTCGGATTCGGGTCGGGCC
1 GGGTCGG-GTCGGGTCGGGCC
4071 AAGTTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.02, C:0.24, G:0.56, T:0.17
Consensus pattern (20 bp):
GGGTCGGGTCGGGTCGGGCC
Found at i:8933 original size:72 final size:72
Alignment explanation
Indices: 8816--8958 Score: 286
Period size: 72 Copynumber: 2.0 Consensus size: 72
8806 GCGGCTTAGC
8816 GCGGGCAAAAAGACTAGTATTGTATAAAGTTTTCTTTCTTTTTTGCTAATTTCTCTCCTTTTTTT
1 GCGGGCAAAAAGACTAGTATTGTATAAAGTTTTCTTTCTTTTTTGCTAATTTCTCTCCTTTTTTT
8881 TTCCAAA
66 TTCCAAA
8888 GCGGGCAAAAAGACTAGTATTGTATAAAGTTTTCTTTCTTTTTTGCTAATTTCTCTCCTTTTTTT
1 GCGGGCAAAAAGACTAGTATTGTATAAAGTTTTCTTTCTTTTTTGCTAATTTCTCTCCTTTTTTT
8953 TTCCAA
66 TTCCAA
8959 GGTGAATAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.48
Consensus pattern (72 bp):
GCGGGCAAAAAGACTAGTATTGTATAAAGTTTTCTTTCTTTTTTGCTAATTTCTCTCCTTTTTTT
TTCCAAA
Found at i:16491 original size:30 final size:30
Alignment explanation
Indices: 16455--16748 Score: 426
Period size: 30 Copynumber: 9.7 Consensus size: 30
16445 ACTCTCTAAA
16455 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
16485 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
16515 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
16545 TGACACCAGAAGTTTTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
16575 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
16605 TGACACCAGAAGCTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
16635 TGACACCAGAAGATGTCGTGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
16665 TGACATCAGAAGTTATCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * * *
16695 TGACACCATAAGTTGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
*
16727 TGGCACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
16749 AAATTTCCAA
Statistics
Matches: 240, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
30 214 0.89
31 3 0.01
32 23 0.10
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:16734 original size:32 final size:32
Alignment explanation
Indices: 16455--16847 Score: 190
Period size: 30 Copynumber: 12.6 Consensus size: 32
16445 ACTCTCTAAA
* * *
16455 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAT
* * *
16485 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAT
** * *
16515 TGACACCAGAAGTTGTCAT-GGTCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAT
* ** * *
16545 TGACACCAGAAGTTTTCAT-GGTCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAT
** * *
16575 TGACACCAGAAGTTGTCAT-GGTCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAT
* ** * *
16605 TGACACCAGAAGCTGTCAT-GGTCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAT
* * * * *
16635 TGACACCAGAAGATGTCGTGA-TGT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAT
* * * * *
16665 TGACATCAGAAGTTATCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAT
*
16695 TGACACCATAAGTTGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAT
* ** *
16727 TGGCACCAGAAGTTGTCATGATAAATT-TCCAAT
1 TGACACCAGAAGTTGTCAT-A-ATTTTATTCAAT
* * ** *
16760 AGATACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAT
* *
16792 TGACACCAGAAGTTGTCATGATTTTACCTTTCAAAA
1 TGACACCAGAAGTTGTCATAATTTTA---TTC-AAT
*
16828 TGACACAAGAAGTTGTCATA
1 TGACACCAGAAGTTGTCATA
16848 TGCACTATTA
Statistics
Matches: 310, Mismatches: 42, Indels: 16
0.84 0.11 0.04
Matches are distributed among these distances:
30 212 0.68
31 5 0.02
32 48 0.15
33 19 0.06
34 3 0.01
35 3 0.01
36 20 0.06
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (32 bp):
TGACACCAGAAGTTGTCATAATTTTATTCAAT
Found at i:18923 original size:33 final size:33
Alignment explanation
Indices: 18860--18923 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
18850 ATACTGAATA
**
18860 ATATTGCCCCTGAAGAGGCATAAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
* *
18893 ATATTGCCCCTGTAGTGGCATAAACCCATGA
1 ATATTGCCCCTGAAGAGGCATAAACCCATGA
18924 AAAGATCACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
Found at i:35008 original size:99 final size:99
Alignment explanation
Indices: 34872--35071 Score: 400
Period size: 99 Copynumber: 2.0 Consensus size: 99
34862 TGATACAATT
34872 AATTGCACAAAAATGCATGAACAAAATTAAAGAAAACAATTAAATATGCTAATGCAAAATAAGAA
1 AATTGCACAAAAATGCATGAACAAAATTAAAGAAAACAATTAAATATGCTAATGCAAAATAAGAA
34937 TGCCAATTAGGATGACAAGAACTAATTTAACAAG
66 TGCCAATTAGGATGACAAGAACTAATTTAACAAG
34971 AATTGCACAAAAATGCATGAACAAAATTAAAGAAAACAATTAAATATGCTAATGCAAAATAAGAA
1 AATTGCACAAAAATGCATGAACAAAATTAAAGAAAACAATTAAATATGCTAATGCAAAATAAGAA
35036 TGCCAATTAGGATGACAAGAACTAATTTAACAAG
66 TGCCAATTAGGATGACAAGAACTAATTTAACAAG
35070 AA
1 AA
35072 CTAAAATTCA
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.54, C:0.12, G:0.13, T:0.21
Consensus pattern (99 bp):
AATTGCACAAAAATGCATGAACAAAATTAAAGAAAACAATTAAATATGCTAATGCAAAATAAGAA
TGCCAATTAGGATGACAAGAACTAATTTAACAAG
Found at i:35029 original size:47 final size:47
Alignment explanation
Indices: 34879--35029 Score: 114
Period size: 48 Copynumber: 3.1 Consensus size: 47
34869 ATTAATTGCA
34879 CAAAAATGCATGAACAAAATTAAAGAAAACAATTAAATATGCTAATG
1 CAAAAATGCATGAACAAAATTAAAGAAAACAATTAAATATGCTAATG
* * * * * * *
34926 CAAAATAAGAATG--C-CAATTAGGATGACAAGAACTAATTTAACAAG--AATTG
1 CAAAA-ATGCATGAACAAAATTA--A--AGAA-AAC-AATTAAATATGCTAA-TG
34976 CACAAAAATGCATGAACAAAATTAAAGAAAACAATTAAATATGCTAATG
1 --CAAAAATGCATGAACAAAATTAAAGAAAACAATTAAATATGCTAATG
35025 CAAAA
1 CAAAA
35030 TAAGAATGCC
Statistics
Matches: 75, Mismatches: 14, Indels: 30
0.63 0.12 0.25
Matches are distributed among these distances:
45 5 0.07
46 1 0.01
47 11 0.15
48 13 0.17
49 10 0.13
50 10 0.13
51 13 0.17
52 6 0.08
53 1 0.01
54 5 0.07
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.21
Consensus pattern (47 bp):
CAAAAATGCATGAACAAAATTAAAGAAAACAATTAAATATGCTAATG
Found at i:37372 original size:14 final size:14
Alignment explanation
Indices: 37353--37379 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
37343 AGCGATCTCT
37353 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
37367 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
37380 TTTGAACCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (14 bp):
TTTTTGTTTTTTTG
Done.