Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012494.1 Corchorus olitorius cultivar O-4 contig12527, 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: 40522
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:11459 original size:18 final size:17
Alignment explanation
Indices: 11424--11459 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11414 AGACTAAATG
*
11424 GATAAAAGCAAGATTTA
1 GATAAAAGCAACATTTA
11441 GATAAAAGCAACCATTTA
1 GATAAAAGCAA-CATTTA
11459 G
1 G
11460 TATTAATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (17 bp):
GATAAAAGCAACATTTA
Found at i:22815 original size:18 final size:18
Alignment explanation
Indices: 22781--22816 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
22771 TAAACAAAAC
22781 ATAATAAGTAAAGGAAAT
1 ATAATAAGTAAAGGAAAT
22799 ATAATAAGTCAAA-GAAAT
1 ATAATAAGT-AAAGGAAAT
22817 GATTTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.61, C:0.03, G:0.14, T:0.22
Consensus pattern (18 bp):
ATAATAAGTAAAGGAAAT
Found at i:26611 original size:42 final size:43
Alignment explanation
Indices: 26560--26653 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
26550 AGTGCATTAC
* *
26560 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
26601 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
26646 CTAATATT
1 CTAATATT
26654 AATTGTTTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:31803 original size:1 final size:1
Alignment explanation
Indices: 31797--31822 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
31787 CATTCTGCTC
31797 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
31823 CGAGCAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:36960 original size:20 final size:20
Alignment explanation
Indices: 36935--36978 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
36925 TTCATCAATT
*
36935 ATTAATTCTAATAATTCATA
1 ATTAATTCCAATAATTCATA
36955 ATTAATTCCAATAATTCATA
1 ATTAATTCCAATAATTCATA
36975 ATTA
1 ATTA
36979 GAATACATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTAATTCCAATAATTCATA
Found at i:38964 original size:31 final size:31
Alignment explanation
Indices: 38926--38987 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
38916 GAGTTTTGTA
*
38926 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
*
38957 AAACTTTTGAATCGCCTATCATATCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
38988 TTTCGAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATACCCTTATT
Found at i:39114 original size:79 final size:80
Alignment explanation
Indices: 39021--39191 Score: 236
Period size: 85 Copynumber: 2.1 Consensus size: 80
39011 CATTGTTTAA
* * *
39021 ATTTTTA-TAGTTTTAGACTTTTAGTCAACTAAAAATTCTATTTTTATTTAATTAAATCTAATAT
1 ATTTTTATTACTTTTAGACTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT
39085 CCTTATAACTATTTT
66 CCTTATAACTATTTT
* *
39100 ATTTTTATCATTTTACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCT
1 A-TTTT-T-A--TTACTTTTAGACTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCT
*
39165 AATATCCTTATACCTATTTT
61 AATATCCTTATAACTATTTT
39185 ATTTTTA
1 ATTTTTA
39192 CGATATTACT
Statistics
Matches: 80, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
79 1 0.01
80 4 0.05
81 1 0.01
82 2 0.03
83 1 0.01
84 4 0.05
85 67 0.84
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (80 bp):
ATTTTTATTACTTTTAGACTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT
CCTTATAACTATTTT
Found at i:39201 original size:85 final size:85
Alignment explanation
Indices: 39039--39201 Score: 274
Period size: 85 Copynumber: 1.9 Consensus size: 85
39029 AGTTTTAGAC
* *
39039 TTTTAGTCAACTAAAAATTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTT
*
39104 TTATCATTTTACTTTTATAG
66 TTATCATATTACTTTTATAG
*
39124 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTT
39189 TTA-CGATATTACT
66 TTATC-ATATTACT
39202 AATTTAATTA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
84 1 0.01
85 72 0.99
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52
Consensus pattern (85 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTT
TTATCATATTACTTTTATAG
Done.