Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003722.1 Hibiscus syriacus cultivar Beakdansim tig00007960_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: 49250
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5111 original size:20 final size:21
Alignment explanation
Indices: 5086--5125 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5076 AATTTCATAT
5086 TCTAACATCAATTT-CAACAC
1 TCTAACATCAATTTCCAACAC
*
5106 TCTAACATTAATTTCCAACA
1 TCTAACATCAATTTCCAACA
5126 TGGTACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.33
Consensus pattern (21 bp):
TCTAACATCAATTTCCAACAC
Found at i:8012 original size:31 final size:31
Alignment explanation
Indices: 7977--8046 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
7967 TAGGTTCTGC
* **
7977 GGCCCTGAGATCATTCTCGGGTAGGCCCTGT
1 GGCCCTGAGATCATTCTCAGGTAGGCCCCAT
* ** *
8008 GGCCCTGTGATTTTTCTTAGGTAGGCCCCAT
1 GGCCCTGAGATCATTCTCAGGTAGGCCCCAT
8039 GGCCCTGA
1 GGCCCTGA
8047 AAACTTTCTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.13, C:0.29, G:0.30, T:0.29
Consensus pattern (31 bp):
GGCCCTGAGATCATTCTCAGGTAGGCCCCAT
Found at i:14524 original size:19 final size:20
Alignment explanation
Indices: 14500--14545 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
14490 CAAAGTGGCC
* *
14500 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAAAAT
14519 CAATTTCAACACTCTAAAAT
1 CAATTTCAACACTCTAAAAT
*
14539 TAATTTC
1 CAATTTC
14546 TAGCATAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
CAATTTCAACACTCTAAAAT
Found at i:17938 original size:20 final size:20
Alignment explanation
Indices: 17913--17950 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17903 ATAGCGTGCA
*
17913 TGGTTAAAATAGGACAGATT
1 TGGTTAAAATAGAACAGATT
17933 TGGTTAAAATAGAACAGA
1 TGGTTAAAATAGAACAGA
17951 GTCAGCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (20 bp):
TGGTTAAAATAGAACAGATT
Found at i:21755 original size:2 final size:2
Alignment explanation
Indices: 21750--21779 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21740 TATAACACAC
21750 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
21780 TTAATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23344 original size:20 final size:20
Alignment explanation
Indices: 23319--23359 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
23309 ATAGCGTGCA
23319 TGGTTAAAATAGAACAGATT
1 TGGTTAAAATAGAACAGATT
*
23339 TGGTTAAAATAGAATAGATT
1 TGGTTAAAATAGAACAGATT
23359 T
1 T
23360 AGCTTATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (20 bp):
TGGTTAAAATAGAACAGATT
Found at i:23662 original size:27 final size:27
Alignment explanation
Indices: 23624--23676 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
23614 TTATCCATAG
* *
23624 ATCATCTTCGGACTCATCACTGAATAT
1 ATCATATTCGGAATCATCACTGAATAT
23651 ATCATATTCGGAATCATCACTGAATA
1 ATCATATTCGGAATCATCACTGAATA
23677 GATCTTAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (27 bp):
ATCATATTCGGAATCATCACTGAATAT
Found at i:40506 original size:12 final size:12
Alignment explanation
Indices: 40491--40540 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
40481 ACCTAAAAAG
*
40491 ACAAGGAAAATA
1 ACAAGTAAAATA
40503 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
40516 TACAA--AAAATGA
1 -ACAAGTAAAAT-A
40528 ACAAGTAAAATA
1 ACAAGTAAAATA
40540 A
1 A
40541 AAACACTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
13 7 0.22
14 4 0.12
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.14
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:47027 original size:20 final size:20
Alignment explanation
Indices: 46998--47057 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
46988 TAATCAAGTC
*
46998 GTTATAGTGTAGTGGTAAGG
1 GTTATCGTGTAGTGGTAAGG
*
47018 GTTATCGTGTAATGGTAAGG
1 GTTATCGTGTAGTGGTAAGG
47038 GTTATCGTGTAGTGGTAAGG
1 GTTATCGTGTAGTGGTAAGG
47058 ATTCTCACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.35
Consensus pattern (20 bp):
GTTATCGTGTAGTGGTAAGG
Found at i:47318 original size:31 final size:31
Alignment explanation
Indices: 47277--47338 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
47267 CACGAAACCT
47277 ATTGACGTAATTCTTTATGAGCGAGCTTCAA
1 ATTGACGTAATTCTTTATGAGCGAGCTTCAA
* * * *
47308 ATTGATGTAATTCTTTTTGTGCTAGCTTCAA
1 ATTGACGTAATTCTTTATGAGCGAGCTTCAA
47339 TCATGTGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.42
Consensus pattern (31 bp):
ATTGACGTAATTCTTTATGAGCGAGCTTCAA
Found at i:49009 original size:260 final size:253
Alignment explanation
Indices: 48505--49023 Score: 662
Period size: 252 Copynumber: 2.0 Consensus size: 253
48495 TTTTTTTATT
*
48505 TCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGTCGG
1 TCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGTCGG
* * *
48570 TCAGTTTTTTTAAATGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAATACTCAACC
66 TCAGATTTTTTAAATGTGATATTCGGGTCGGGTCGAGTTCGGGTGTAGGGTGAAAATACCCAACC
* * *
48635 TGAAAATATATATTTTACCTTATATTTTGGAATAATTACAATAATACCCCTCTATATATAATTTT
131 AGAAAATATATATTTTACCTTATATTTTAGAATAATTACAATAATACCACTCTATATATAATTTT
*
48700 TTCAATTAAGTCACTGATTTTTATTGAATAAAAATAATTTTTTTTATTTCGGGTCGGG
196 TTCAATTAAGTCACTGATTTTTATTGAATAAAAATAATTTTTTTTATTTCGGGTCAGG
*
48758 TCGGGTC-GATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAAC-TTATTTTGGTTGGGTCA
1 TCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGG-TCGGTC-
* * *
48821 GGTCA-ATTTTTTAAGTGTGAT-TTC-GGTCGGGTCGGGTTCGGGTGTAGGGTGAAAAATACCCG
64 GGTCAGATTTTTTAAATGTGATATTCGGGTCGGGTCGAGTTCGGGTGTAGGGTG-AAAATACCCA
*
48883 ACCAGACCCACCCAAATATATAAATTTTACCTTATATTTTTAGAAT-ATTACAATAA-ACTACTC
128 ACCAG----A---AAATATAT--ATTTTACCTTATA-TTTTAGAATAATTACAATAATACCACTC
** *
48946 TATATATTTTTTTTTCCAATTAAGTCACT-ATTTTTA-TGAATAAAACA-ATTTTTTTTATTATT
183 TATATATAATTTTTT-CAATTAAGTCACTGATTTTTATTGAATAAAA-ATA-ATTTTTT-TTATT
49008 TCGGGTCAGG
244 TCGGGTCAGG
*
49018 TTGGGT
1 TCGGGT
49024 GAAACTTTAT
Statistics
Matches: 232, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
250 25 0.11
251 24 0.10
252 57 0.25
253 12 0.05
255 1 0.00
258 18 0.08
259 32 0.14
260 55 0.24
261 8 0.03
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (253 bp):
TCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGTCGG
TCAGATTTTTTAAATGTGATATTCGGGTCGGGTCGAGTTCGGGTGTAGGGTGAAAATACCCAACC
AGAAAATATATATTTTACCTTATATTTTAGAATAATTACAATAATACCACTCTATATATAATTTT
TTCAATTAAGTCACTGATTTTTATTGAATAAAAATAATTTTTTTTATTTCGGGTCAGG
Done.