Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017521.1 Corchorus olitorius cultivar O-4 contig17554, 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: 20720
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1819 original size:16 final size:15
Alignment explanation
Indices: 1798--1839 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1788 TTACTCTGCT
1798 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
*
1814 TTGTTTTATGTTTAA
1 TTGTTTTCTGTTTAA
*
1829 TTGCTTTCTGT
1 TTGTTTTCTGT
1840 CAATCTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:2563 original size:14 final size:14
Alignment explanation
Indices: 2546--2585 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
2536 GCTTTTTCCG
2546 TTTTCTTTTTTTCT
1 TTTTCTTTTTTTCT
*
2560 TTTTC-TTTTTTGT
1 TTTTCTTTTTTTCT
2573 TTTTCATTTTTTT
1 TTTTC-TTTTTTT
2586 TTATCGGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 12 0.52
14 5 0.22
15 6 0.26
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (14 bp):
TTTTCTTTTTTTCT
Found at i:7443 original size:38 final size:39
Alignment explanation
Indices: 7345--7456 Score: 165
Period size: 39 Copynumber: 2.8 Consensus size: 39
7335 TTTTAATCAA
* *
7345 TTTTATTGATTTCCAAAATCTTCTTTTGGGA-TATCTTAAAC
1 TTTTATT--TTTCCAAAATCTTCTTTTGGAATTA-CCTAAAC
7386 TTTTATTTTTCCAAAATCTTCTTTTGGAATTACCTAAAC
1 TTTTATTTTTCCAAAATCTTCTTTTGGAATTACCTAAAC
7425 TTTTA-TTTTCCAAAATCTTCTTTTGGAATTAC
1 TTTTATTTTTCCAAAATCTTCTTTTGGAATTAC
7457 TTAATTAAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
38 27 0.40
39 32 0.47
40 2 0.03
41 7 0.10
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (39 bp):
TTTTATTTTTCCAAAATCTTCTTTTGGAATTACCTAAAC
Found at i:8090 original size:41 final size:41
Alignment explanation
Indices: 8045--8123 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
8035 TCGAATTGGA
8045 CAAATTACATCAAGAGGCAAACATAACCCTAAATCAGGAAT
1 CAAATTACATCAAGAGGCAAACATAACCCTAAATCAGGAAT
8086 CAAATTACATCAAGAGGCAAACATAACCCTAAATCAGG
1 CAAATTACATCAAGAGGCAAACATAACCCTAAATCAGG
8124 GGCCAAGGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.16
Consensus pattern (41 bp):
CAAATTACATCAAGAGGCAAACATAACCCTAAATCAGGAAT
Found at i:16075 original size:163 final size:163
Alignment explanation
Indices: 15805--16130 Score: 607
Period size: 163 Copynumber: 2.0 Consensus size: 163
15795 TCTATAAATG
15805 GAAAACTGGATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTTATATAATGTCT
1 GAAAACTGGATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTTATATAATGTCT
* *
15870 ACTGTTTAAAAACATACAATACCTAAATGATTAACCTATTTTTTATCTAGTATCACAAAAATTAA
66 ACTGTTTAAAAACATACAATACCTAAATGATTAACATATTTTTTATCTAATATCACAAAAATTAA
*
15935 AGTCTACGCCAATTGGAGAAAATAATTGCATGT
131 AATCTACGCCAATTGGAGAAAATAATTGCATGT
15968 GAAAACTGGATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTTATATAATGTCT
1 GAAAACTGGATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTTATATAATGTCT
*
16033 ACTGTTTAAGAACATACAATACCTAAATGATTAACATATTTTTTATCTAATATCACAAAAATTAA
66 ACTGTTTAAAAACATACAATACCTAAATGATTAACATATTTTTTATCTAATATCACAAAAATTAA
*
16098 AATCTACGCTAATTGGAGAAAATAATTGCATGT
131 AATCTACGCCAATTGGAGAAAATAATTGCATGT
16131 CTTAAGCCAT
Statistics
Matches: 158, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
163 158 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (163 bp):
GAAAACTGGATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTTATATAATGTCT
ACTGTTTAAAAACATACAATACCTAAATGATTAACATATTTTTTATCTAATATCACAAAAATTAA
AATCTACGCCAATTGGAGAAAATAATTGCATGT
Found at i:17098 original size:2 final size:2
Alignment explanation
Indices: 17091--17132 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
17081 GAAAGGTTTG
17091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17133 GCTGATAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18191 original size:26 final size:26
Alignment explanation
Indices: 18161--18213 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
18151 ACCGAATCAG
*
18161 CCAGTCAGATCGGTTGAACCGAGTAT
1 CCAGTCAGACCGGTTGAACCGAGTAT
18187 CCAGTCAGACCGGTTGAACCGAGTAT
1 CCAGTCAGACCGGTTGAACCGAGTAT
18213 C
1 C
18214 GGAGGCCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (26 bp):
CCAGTCAGACCGGTTGAACCGAGTAT
Found at i:20676 original size:2 final size:2
Alignment explanation
Indices: 20669--20712 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
20659 TGTTATATTT
20669 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20711 TA
1 TA
20713 GTAGTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.