Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013291.1 Corchorus olitorius cultivar O-4 contig13324, 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: 30009
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1646 original size:3 final size:3
Alignment explanation
Indices: 1638--1668 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1628 GCTTTCTTTG
1638 CTT CTT CTT CTT CTT CTT CTT CTT CTT -TT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1669 CTTTTCCAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:14571 original size:109 final size:109
Alignment explanation
Indices: 14287--14648 Score: 523
Period size: 109 Copynumber: 3.3 Consensus size: 109
14277 CGTTGAATGC
** *
14287 AAGAATTTTT-ATTATTATTTTTCTTTTGTGAGATAAAAAGTTGTGAAA-TCAGTTTGGACCGTT
1 AAGAATTTTTAATT-TT-TTTTTCTTTTGTGAGATAAAAAGTTGTGAAAGAAAGTTTGGGCCGTT
* *
14350 GTAATTTTTGGACCGTGGGCCCTTAAATGCAAGAAAATTGTATAGAG
64 GTAA-TTTTGGACCGTGGGCCCTTGAATGCAAGAAAATTGTATGGAG
* *
14397 AAGAGTTTTTGAAATTTTTTTTCTTTTGTGAGATAAAAAGTTGTGAAAGAAAGTTTGGGCCGTTG
1 AAGAATTTTT-AATTTTTTTTTCTTTTGTGAGATAAAAAGTTGTGAAAGAAAGTTTGGGCCGTTG
* * *
14462 TAATTTTGTACCGTGAGCCGTTGAATGCAAGAAAATTGTATGGAG
65 TAATTTTGGACCGTGGGCCCTTGAATGCAAGAAAATTGTATGGAG
* * * *
14507 AAGAATTTTTAATTTTTTTTTCTTTTGTGAGATAGAAAGTCGTGAAAGAAATTTTGGGTCGTTGT
1 AAGAATTTTTAATTTTTTTTTCTTTTGTGAGATAAAAAGTTGTGAAAGAAAGTTTGGGCCGTTGT
**
14572 AATTTTGGACCGTGGGCCCTTGAATGCAAGAAAATTGTATGCTG
66 AATTTTGGACCGTGGGCCCTTGAATGCAAGAAAATTGTATGGAG
14616 AAGAATTTTTAA-TTTTTTTTCTTTTGTGAGATA
1 AAGAATTTTTAATTTTTTTTTCTTTTGTGAGATA
14649 TAATATCGAA
Statistics
Matches: 228, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
108 21 0.09
109 101 0.44
110 86 0.38
111 18 0.08
112 2 0.01
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.40
Consensus pattern (109 bp):
AAGAATTTTTAATTTTTTTTTCTTTTGTGAGATAAAAAGTTGTGAAAGAAAGTTTGGGCCGTTGT
AATTTTGGACCGTGGGCCCTTGAATGCAAGAAAATTGTATGGAG
Found at i:21259 original size:31 final size:30
Alignment explanation
Indices: 21224--21300 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
21214 ATACCGTACA
21224 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTACTTACAAAAAAGG-TCAATTT
* * **
21255 GGTCCCCCTAC-TATAAAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAAAAGGTCAATTT
21284 GGTCCCTCTACTTACAA
1 GGTCCCTCTACTTACAA
21301 TTTGGTGTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 17 0.44
30 12 0.31
31 10 0.26
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAAAGGTCAATTT
Found at i:21642 original size:29 final size:31
Alignment explanation
Indices: 21593--21669 Score: 104
Period size: 30 Copynumber: 2.5 Consensus size: 31
21583 TGTCACCAAA
* *
21593 TTGTAAGTAGAGGGACTAAATTGA-CAGTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
* *
21623 TTGTAA-TAGGGGGACCAAATTGATCCCTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
21653 TTGTAAGTAGAGGGACC
1 TTGTAAGTAGAGGGACC
21670 TGCACGGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 15 0.38
30 16 0.40
31 9 0.22
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (31 bp):
TTGTAAGTAGAGGGACCAAATTGATCACTTT
Found at i:23085 original size:19 final size:19
Alignment explanation
Indices: 23061--23102 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
23051 TATGCCCCTA
23061 CTAAGATATATAAATATAT
1 CTAAGATATATAAATATAT
23080 CTAAGATATATAAATATAT
1 CTAAGATATATAAATATAT
23099 CTAA
1 CTAA
23103 AATTTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (19 bp):
CTAAGATATATAAATATAT
Found at i:23578 original size:57 final size:58
Alignment explanation
Indices: 23484--23607 Score: 196
Period size: 57 Copynumber: 2.2 Consensus size: 58
23474 ATCAGGATCA
* * *
23484 CAGTGGACTGATCAGACAGAGGAGGAAGGATCGCGTTCAATCAACAATTGCGAGCAAT
1 CAGTGGACAGATCAGACAAAGGAGGAAGGATCACGTTCAATCAACAATTGCGAGCAAT
* *
23542 CAGTGGACAG-TCCGACAAAGGAGGAAGGATCACGTTCAATCAACAATTGGGAGCAAT
1 CAGTGGACAGATCAGACAAAGGAGGAAGGATCACGTTCAATCAACAATTGCGAGCAAT
23599 CAGTGGACA
1 CAGTGGACA
23608 ACATTGTAGT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
57 52 0.85
58 9 0.15
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.16
Consensus pattern (58 bp):
CAGTGGACAGATCAGACAAAGGAGGAAGGATCACGTTCAATCAACAATTGCGAGCAAT
Found at i:26247 original size:15 final size:14
Alignment explanation
Indices: 26215--26258 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
26205 TATATATATA
**
26215 TATTATAATATTAA
1 TATTATAATATTTT
26229 TATTAATAATATTTT
1 TATT-ATAATATTTT
26244 TATTATATATATTTT
1 TATTATA-ATATTTT
26259 AAAATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTATAATATTTT
Done.