Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016074.1 Corchorus olitorius cultivar O-4 contig16107, 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: 30958
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3652 original size:16 final size:15
Alignment explanation
Indices: 3614--3655 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
3604 ACAGAGATTG
3614 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
3629 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
3644 ACTAGAAAACAA
1 AC-AGAAAACAA
3656 AGCAGAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:4431 original size:11 final size:11
Alignment explanation
Indices: 4415--4440 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4405 CCTTTGCCTA
4415 AAAACTAGAAG
1 AAAACTAGAAG
4426 AAAACTAGAAG
1 AAAACTAGAAG
4437 AAAA
1 AAAA
4441 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:19049 original size:19 final size:18
Alignment explanation
Indices: 19012--19051 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
19002 TTCTTGAGAT
*
19012 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
19030 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
19049 AAT
1 AAT
19052 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:24201 original size:26 final size:26
Alignment explanation
Indices: 24171--24230 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
24161 GTGGATTGTA
*
24171 AAATAAATTCGAAT-AATTAAGACATT
1 AAATAAATTCAAATGAATTAA-ACATT
*
24197 AAATAAATTTAAATGAATTAAACATT
1 AAATAAATTCAAATGAATTAAACATT
24223 AAA-AAATT
1 AAATAAATT
24231 TCAAGACTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 5 0.16
26 20 0.65
27 6 0.19
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (26 bp):
AAATAAATTCAAATGAATTAAACATT
Found at i:25269 original size:2 final size:2
Alignment explanation
Indices: 25262--25286 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25252 CTCGTACTTT
25262 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
25287 TGCGGATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25727 original size:144 final size:143
Alignment explanation
Indices: 25457--25735 Score: 454
Period size: 144 Copynumber: 1.9 Consensus size: 143
25447 TTAAATTATA
* *
25457 TTTATCAGTATATTTATATCAAAAGTTTTTATCATCACTTTTAATCCAAAATTTAAATGTATTTA
1 TTTATCAATATATTTAAATCAAAAGTTTTTATCATCACTTTTAATCCAAAATTTAAATGTATTTA
* *
25522 TCAAGTTAAATAAAATTTCAAATTATAAATTTAAGATTATAGCAAACCTTACTATAAATACAATA
66 TCAAGTTAAATAAAATTTCAAATTATAAATTTAAGATTATAACAAACCTTAATATAAATACAATA
25587 GTTACTCCTACCC
131 GTTACTCCTACCC
*
25600 TTTATCAATATATTTAAATCAAAAG-TTTTATCA-CTACTTTTAATCCAGAATTTAAAATGTATT
1 TTTATCAATATATTTAAATCAAAAGTTTTTATCATC-ACTTTTAATCCAAAATTT-AAATGTATT
* *
25663 TATCAAGTTAAAATAAAATTTCAAATTATCAATTTAAGATTATAACAAACCTTAATATGAATACA
64 TATCAAGTT-AAATAAAATTTCAAATTATAAATTTAAGATTATAACAAACCTTAATATAAATACA
25728 ATAGTTAC
128 ATAGTTAC
25736 GTACTCTACG
Statistics
Matches: 126, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
141 1 0.01
142 25 0.20
143 41 0.33
144 59 0.47
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.39
Consensus pattern (143 bp):
TTTATCAATATATTTAAATCAAAAGTTTTTATCATCACTTTTAATCCAAAATTTAAATGTATTTA
TCAAGTTAAATAAAATTTCAAATTATAAATTTAAGATTATAACAAACCTTAATATAAATACAATA
GTTACTCCTACCC
Found at i:25908 original size:34 final size:34
Alignment explanation
Indices: 25865--25939 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
25855 CAATACAATG
** *
25865 GTATTCAAGTTCGTTGGAGTTTGTTGGAGTGCAA
1 GTATTCAAGTTCGTCAGAGTTCGTTGGAGTGCAA
25899 GTATTCAAGTTCGTCAGAGTTCGTTGGAGTGCAA
1 GTATTCAAGTTCGTCAGAGTTCGTTGGAGTGCAA
25933 GTATTCA
1 GTATTCA
25940 TGCCACATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.23, C:0.12, G:0.29, T:0.36
Consensus pattern (34 bp):
GTATTCAAGTTCGTCAGAGTTCGTTGGAGTGCAA
Found at i:30489 original size:21 final size:21
Alignment explanation
Indices: 30465--30537 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
30455 GGCATGGAAT
30465 GGTGATGGCACGGGCATGGCC
1 GGTGATGGCACGGGCATGGCC
30486 GGTGATGGCACGGGCATGGCC
1 GGTGATGGCACGGGCATGGCC
* * *
30507 GGTGGTGGCACGGTGAATGGGC
1 GGTGATGGCACGG-GCATGGCC
*
30529 GGTAATGGC
1 GGTGATGGC
30538 TTAGTAGTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 33 0.72
22 13 0.28
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.16
Consensus pattern (21 bp):
GGTGATGGCACGGGCATGGCC
Found at i:30520 original size:11 final size:10
Alignment explanation
Indices: 30465--30537 Score: 51
Period size: 11 Copynumber: 6.9 Consensus size: 10
30455 GGCATGGAAT
30465 GGTGATGGCAC
1 GGTGATGGC-C
30476 GG-GCATGGCC
1 GGTG-ATGGCC
30486 GGTGATGGCAC
1 GGTGATGGC-C
30497 GG-GCATGGCC
1 GGTG-ATGGCC
*
30507 GGTGGTGGCAC
1 GGTGATGGC-C
*
30518 GGTGAATGGGC
1 GGTG-ATGGCC
*
30529 GGTAATGGC
1 GGTGATGGC
30538 TTAGTAGTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
10 21 0.42
11 26 0.52
12 3 0.06
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.16
Consensus pattern (10 bp):
GGTGATGGCC
Done.