Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008002.1 Hibiscus syriacus cultivar Beakdansim tig00110461_pilon, 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: 1031338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:995516 original size:3 final size:3
Alignment explanation
Indices: 995486--995533 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
995476 CAAAAACATT
995486 TTA TTA -TA TT- TTA TTTA TTTA TTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA
995532 TT
1 TT
995534 TATTTTTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.10
3 27 0.64
4 11 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:995627 original size:33 final size:33
Alignment explanation
Indices: 995590--995654 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
995580 GAAAATAAAT
*
995590 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGTATTAGAGTCCTATTAAAACACTAAAAC
*
995623 CAACGTATTAGAGTCCTATTGAAACACTAAAA
1 CAACGTATTAGAGTCCTATTAAAACACTAAAA
995655 TCGAAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (33 bp):
CAACGTATTAGAGTCCTATTAAAACACTAAAAC
Found at i:996042 original size:2 final size:2
Alignment explanation
Indices: 996035--996067 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
996025 TACATTGTTT
996035 TA TA TA TA 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 TA TA TA TA T
996068 TTTTCATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:996101 original size:33 final size:37
Alignment explanation
Indices: 996046--996114 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 37
996036 ATATATATAT
*
996046 ATATATATATATATATATATATTTTTCATTTTTATTA
1 ATATATATATATATATATATATTTTTCATTATTATTA
*
996083 ATAT-TAT-TATAT-TA-ATATTTTTTATTATTATT
1 ATATATATATATATATATATATTTTTCATTATTATT
996115 TTCTCATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 16 0.53
34 2 0.07
35 5 0.17
36 3 0.10
37 4 0.13
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (37 bp):
ATATATATATATATATATATATTTTTCATTATTATTA
Found at i:999786 original size:3 final size:3
Alignment explanation
Indices: 999778--999804 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
999768 CGTGTCTTAT
999778 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
999805 ACCGTAGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1007983 original size:15 final size:15
Alignment explanation
Indices: 1007963--1007999 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1007953 ATATTATTCT
1007963 TTCGAAAATGTATGC
1 TTCGAAAATGTATGC
1007978 TTCGAAAATGTATGC
1 TTCGAAAATGTATGC
*
1007993 TGCGAAA
1 TTCGAAA
1008000 GGCAATTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (15 bp):
TTCGAAAATGTATGC
Found at i:1014988 original size:33 final size:34
Alignment explanation
Indices: 1014937--1015002 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
1014927 CATTAATTAA
* *
1014937 TTAACAGTTTCTATCTAACT--GGAGTATTTTACT
1 TTAACAATTTCTAACTAACTAGGGA-TATTTTACT
*
1014970 TTAACAATTTTTAACTAACTAGGGATATTTTAC
1 TTAACAATTTCTAACTAACTAGGGATATTTTAC
1015003 CCCAAAGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 17 0.61
34 8 0.29
35 3 0.11
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (34 bp):
TTAACAATTTCTAACTAACTAGGGATATTTTACT
Found at i:1022660 original size:49 final size:49
Alignment explanation
Indices: 1022588--1022686 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
1022578 TTTTATTGAA
1022588 AAGTTATGTAAAATAGGGGTTATAAAACCCGAATGAAAATGTAAGAAGG
1 AAGTTATGTAAAATAGGGGTTATAAAACCCGAATGAAAATGTAAGAAGG
1022637 AAGTTATGTAAAATAGGGGTTATAAAACCCGAATGAAAATGTAAGAAGG
1 AAGTTATGTAAAATAGGGGTTATAAAACCCGAATGAAAATGTAAGAAGG
1022686 A
1 A
1022687 GGGGGGGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.22
Consensus pattern (49 bp):
AAGTTATGTAAAATAGGGGTTATAAAACCCGAATGAAAATGTAAGAAGG
Found at i:1023893 original size:7 final size:6
Alignment explanation
Indices: 1023862--1023892 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
1023852 TTATGATCGA
1023862 AATTTT AAATTTT AATTTT AATTTT AATTTT
1 AATTTT -AATTTT AATTTT AATTTT AATTTT
1023893 TGCAATTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
AATTTT
Done.