Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023159.1 Corchorus olitorius cultivar O-4 contig23192, 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: 6069
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:2621 original size:103 final size:105
Alignment explanation
Indices: 2367--2631 Score: 372
Period size: 110 Copynumber: 2.5 Consensus size: 105
2357 AGTTTAGCCT
* *
2367 TAATTTCACTAAGTTTAGCTCCAAATTATAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGC-CCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
2432 AATAATTTATTGTTATAGAGTTTTAGAAATAAAATACAAAAC
65 AATAA-TTATTGTTATAGAGTTTTAGAAATAAAATACAAAAC
* *
2474 TAATTTCACTAGCTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTGAATTCCATA
1 TAATTT--C-A-CTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAA
* * *
2539 ATTAATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAC
62 ATTAATAATTATTGTTATAGAGTTTTAGAAATAAAATACAAAAC
** *
2582 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
2632 TAGAAAAATT
Statistics
Matches: 144, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
103 40 0.28
104 1 0.01
105 1 0.01
107 8 0.06
108 35 0.24
109 1 0.01
110 47 0.33
111 11 0.08
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATTATTGTTATAGAGTTTTAGAAATAAAATACAAAAC
Found at i:4624 original size:21 final size:20
Alignment explanation
Indices: 4596--4663 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 20
4586 CATTGTACAT
4596 GTCAAATCATAAAATTTGATA
1 GTCAAATC-TAAAATTTGATA
* *
4617 GGCAAATCTCAAAGTTTGATA
1 GTCAAATCT-AAAATTTGATA
* * *
4638 ATCAAATCCAAAACTTGATA
1 GTCAAATCTAAAATTTGATA
4658 GTCAAA
1 GTCAAA
4664 CCACGTTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 15 0.39
21 23 0.61
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.28
Consensus pattern (20 bp):
GTCAAATCTAAAATTTGATA
Found at i:5040 original size:23 final size:21
Alignment explanation
Indices: 4989--5044 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 21
4979 CATACATGAT
*
4989 TAGGGGTTTGACCATTACAAT
1 TAGGGGTTTGACCATTACAAG
* * *
5010 TTGAGGTTTGATCCCATTACTAG
1 TAGGGGTTTGA--CCATTACAAG
5033 TAGGGGTTTGAC
1 TAGGGGTTTGAC
5045 TAATCATGCT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 10 0.37
23 17 0.63
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (21 bp):
TAGGGGTTTGACCATTACAAG
Found at i:5105 original size:87 final size:87
Alignment explanation
Indices: 4747--5102 Score: 444
Period size: 87 Copynumber: 4.1 Consensus size: 87
4737 CACCCACCTA
* ** * * *
4747 ATTTGGGGTTTTATCCCATTACTAGTAGAAGTTTGTCTAATCATGCTTTAATTTTCACTATACAT
1 ATTTGGGGTTTGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTAAATTTCACCATACAT
*
4812 GATTTGGGGTTTGACCATTATG
66 GATTTGGGGTTTGACCATTAAG
* * *
4834 ATTTGGGGTTTGATCCCATTACTAGTAGGGATTTGCCTAATCATTCTTTAAATTTCACTATACAT
1 ATTTGGGGTTTGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTAAATTTCACCATACAT
** * *
4899 GATTTATGGTTTGACTATTACG
66 GATTTGGGGTTTGACCATTAAG
* * * * *
4921 ATTTGGGGTTTGATCCTAATATTAGTAAGGGTTTGCCTAATCATGTTTTAAATTTCACCATACAT
1 ATTTGGGGTTTGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTAAATTTCACCATACAT
*
4986 GATTAGGGGTTTGACCATTACA-
66 GATTTGGGGTTTGACCATTA-AG
* * * *
5008 ATTTGAGGTTTGATCCCATTACTAGTAGGGGTTTGACTAATCATGCTTTACAGTTTGACCATACA
1 ATTTGGGGTTTGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTA-AATTTCACCATACA
** *
5073 TGATTTGTAGTTCGACCATTAAG
65 TGATTTGGGGTTTGACCATTAAG
5096 ATTTGGG
1 ATTTGGG
5103 TTTCACAACG
Statistics
Matches: 228, Mismatches: 38, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
87 193 0.85
88 35 0.15
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (87 bp):
ATTTGGGGTTTGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTAAATTTCACCATACAT
GATTTGGGGTTTGACCATTAAG
Found at i:5445 original size:2 final size:2
Alignment explanation
Indices: 5433--5482 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
5423 TTTAGTGTTT
5433 TA TA T- TA TA TA TA TA -A TA TA TA TA TA -A 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
*
5472 TA TA AA TA TA T
1 TA TA TA TA TA T
5483 CTTCTCATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5452 original size:11 final size:11
Alignment explanation
Indices: 5433--5481 Score: 71
Period size: 11 Copynumber: 4.4 Consensus size: 11
5423 TTTAGTGTTT
*
5433 TATATTATATA
1 TATAATATATA
5444 TATAATATATA
1 TATAATATATA
5455 TATAATATATA
1 TATAATATATA
*
5466 TATATATATAAA
1 TATA-ATATATA
5478 TATA
1 TATA
5482 TCTTCTCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATAATATATA
Done.