Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008487.1 Hibiscus syriacus cultivar Beakdansim tig00111328_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: 82137
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:19625 original size:16 final size:16
Alignment explanation
Indices: 19604--19640 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
19594 TGTGTTCAAG
*
19604 AAATTGTTGACGGAAA
1 AAATTGTTAACGGAAA
*
19620 AAATTGTTAACGGAAG
1 AAATTGTTAACGGAAA
19636 AAATT
1 AAATT
19641 ATTATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.27
Consensus pattern (16 bp):
AAATTGTTAACGGAAA
Found at i:24548 original size:31 final size:31
Alignment explanation
Indices: 24513--24579 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
24503 TGTAATACAG
24513 TCCCCCAACATTTAGTTCGTTTGCAATATGA
1 TCCCCCAACATTTAGTTCGTTTGCAATATGA
*
24544 TCCCCCAACATTTAGTTCGTTTGCAATATGG
1 TCCCCCAACATTTAGTTCGTTTGCAATATGA
24575 TCCCC
1 TCCCC
24580 GACCGTTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.34
Consensus pattern (31 bp):
TCCCCCAACATTTAGTTCGTTTGCAATATGA
Found at i:26555 original size:30 final size:30
Alignment explanation
Indices: 26519--26595 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
26509 TCAAATGGTC
*
26519 GGGGACCATATTGTAAACAGATTAAATGTT
1 GGGGACCATATTGTAAACAGACTAAATGTT
** *
26549 GGGGACCATATTACAAATAGACTAAATGTT
1 GGGGACCATATTGTAAACAGACTAAATGTT
*
26579 GAGGGACTATATTGTAA
1 G-GGGACCATATTGTAA
26596 GTTTTAAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 27 0.69
31 12 0.31
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (30 bp):
GGGGACCATATTGTAAACAGACTAAATGTT
Found at i:28535 original size:2 final size:2
Alignment explanation
Indices: 28528--28558 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28518 TTTATTATCC
28528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28559 ACACCCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33133 original size:198 final size:198
Alignment explanation
Indices: 32784--33180 Score: 767
Period size: 198 Copynumber: 2.0 Consensus size: 198
32774 AAGGAACAAC
* *
32784 ATCATTTTTTTTACCACTGAGGTCACTTGGTTCGTGACTATCATAAGTAAAATATAACGGTGATC
1 ATCAATTTTTATACCACTGAGGTCACTTGGTTCGTGACTATCATAAGTAAAATATAACGGTGATC
*
32849 GACCAGTAATAGCCTGATGAGTGATAGCATGAACAATTGAGACAATGGTATACAAAAACGGATCA
66 GACCAGTAATAGCCTGATGAGTGATAACATGAACAATTGAGACAATGGTATACAAAAACGGATCA
32914 CACTAATGTCCCAGAGCACCAAACATAGAGGAGAAAAACTTGAAGAATATCCAAAGTGACCGAGT
131 CACTAATGTCCCAGAGCACCAAACATAGAGGAGAAAAACTTGAAGAATATCCAAAGTGACCGAGT
32979 GAA
196 GAA
32982 ATCAATTTTTATACCACTGAGGTCACTTGGTTCGTGACTATCATAAGTAAAATATAACGGTGATC
1 ATCAATTTTTATACCACTGAGGTCACTTGGTTCGTGACTATCATAAGTAAAATATAACGGTGATC
33047 GACCAGTAATAGCCTGATGAGTGATAACATGAACAATTGAGACAATGGTATACAAAAACGGATCA
66 GACCAGTAATAGCCTGATGAGTGATAACATGAACAATTGAGACAATGGTATACAAAAACGGATCA
33112 CACTAATGTCCCAGAGCACCAAACATAGAGGAGAAAAACTTGAAGAATATCCAAAGTGACCGAGT
131 CACTAATGTCCCAGAGCACCAAACATAGAGGAGAAAAACTTGAAGAATATCCAAAGTGACCGAGT
33177 GAA
196 GAA
33180 A
1 A
33181 AACCAAACTT
Statistics
Matches: 196, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
198 196 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (198 bp):
ATCAATTTTTATACCACTGAGGTCACTTGGTTCGTGACTATCATAAGTAAAATATAACGGTGATC
GACCAGTAATAGCCTGATGAGTGATAACATGAACAATTGAGACAATGGTATACAAAAACGGATCA
CACTAATGTCCCAGAGCACCAAACATAGAGGAGAAAAACTTGAAGAATATCCAAAGTGACCGAGT
GAA
Found at i:44177 original size:3 final size:3
Alignment explanation
Indices: 44169--44208 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
44159 GTACTTTACT
44169 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44209 AATGATTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51094 original size:31 final size:32
Alignment explanation
Indices: 51059--51122 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
51049 GCTGAAACTC
*
51059 AACTCGAAAGCTACTTGATA-CTGACTCGAAA
1 AACTCGAAAGATACTTGATACCTGACTCGAAA
** *
51090 AACTCGCGAGATACTTGATACCTGACTTGAAA
1 AACTCGAAAGATACTTGATACCTGACTCGAAA
51122 A
1 A
51123 GTTCACAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (32 bp):
AACTCGAAAGATACTTGATACCTGACTCGAAA
Found at i:59567 original size:2 final size:2
Alignment explanation
Indices: 59560--59591 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
59550 CCAAAATCTC
59560 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
59592 TACACCTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63056 original size:51 final size:53
Alignment explanation
Indices: 62929--63068 Score: 230
Period size: 51 Copynumber: 2.7 Consensus size: 53
62919 GATATTAAAC
* * *
62929 AGAACACTCATTCAGTGTGAAAATTTGTTGTGTATATAGTCTATTTTTGGTGAT
1 AGAACAC-CAATCAGTATGAAGATTTGTTGTGTATATAGTCTATTTTTGGTGAT
62983 AGAACACCAATCAGTATGAAGATTTGTTGTGTATATAGTCTATTTTT-G-GAT
1 AGAACACCAATCAGTATGAAGATTTGTTGTGTATATAGTCTATTTTTGGTGAT
63034 AGAACACCAATCAGTATGAAGATTTGTTGTGTATA
1 AGAACACCAATCAGTATGAAGATTTGTTGTGTATA
63069 AAACCTGTTT
Statistics
Matches: 83, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
51 38 0.46
52 1 0.01
53 37 0.45
54 7 0.08
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (53 bp):
AGAACACCAATCAGTATGAAGATTTGTTGTGTATATAGTCTATTTTTGGTGAT
Found at i:63247 original size:25 final size:25
Alignment explanation
Indices: 63219--63269 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
63209 ATTCAATATT
*
63219 TTCTCTCTGA-TATGAAATATAGAAA
1 TTCTCTCT-ACTATGAAACATAGAAA
*
63244 TTCTGTCTACTATGAAACATAGAAA
1 TTCTCTCTACTATGAAACATAGAAA
63269 T
1 T
63270 AGCAGCTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (25 bp):
TTCTCTCTACTATGAAACATAGAAA
Found at i:73343 original size:79 final size:79
Alignment explanation
Indices: 73212--73377 Score: 314
Period size: 79 Copynumber: 2.1 Consensus size: 79
73202 TTTTCCCTGT
*
73212 GCACCACCCAAACTTACATCCATCAACCAAAACAATGGTAATTAATTGAAAACTATCGTCACCCA
1 GCACCACCCAAACTTACACCCATCAACCAAAACAATGGTAATTAATTGAAAACTATCGTCACCCA
73277 TCATTATTATACCA
66 TCATTATTATACCA
73291 GCACCACCCAAACTTACACCCATCAACCAAAACAATGGTAATTAATTGAAAACTATCGTCACCCA
1 GCACCACCCAAACTTACACCCATCAACCAAAACAATGGTAATTAATTGAAAACTATCGTCACCCA
*
73356 TCTTTATTATACCA
66 TCATTATTATACCA
73370 GCACCACC
1 GCACCACC
73378 TTGTCTATGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 85 1.00
ACGTcount: A:0.39, C:0.31, G:0.07, T:0.23
Consensus pattern (79 bp):
GCACCACCCAAACTTACACCCATCAACCAAAACAATGGTAATTAATTGAAAACTATCGTCACCCA
TCATTATTATACCA
Done.