Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000581.1 Hibiscus syriacus cultivar Beakdansim tig00001134_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: 72504
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:533 original size:17 final size:19
Alignment explanation
Indices: 492--530 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
482 TATTCTCTTA
*
492 TTTT-TTTACTTTAATTGT
1 TTTTATTTACTTTAATCGT
510 TTTTATTTA-TTTAATCGT
1 TTTTATTTACTTTAATCGT
528 TTT
1 TTT
531 ATTACTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTTATTTACTTTAATCGT
Found at i:4235 original size:18 final size:18
Alignment explanation
Indices: 4212--4255 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4202 AATGTTGAAT
*
4212 AAAAAAACAGCAGTTCGA
1 AAAAAAAAAGCAGTTCGA
**
4230 AAAAAAAAAGTTGTTCGA
1 AAAAAAAAAGCAGTTCGA
4248 AAGAAAAA
1 AA-AAAAA
4256 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.61, C:0.09, G:0.16, T:0.14
Consensus pattern (18 bp):
AAAAAAAAAGCAGTTCGA
Found at i:5466 original size:16 final size:16
Alignment explanation
Indices: 5445--5476 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5435 CAATTCTAAC
5445 GGGAGAATTGAAACGG
1 GGGAGAATTGAAACGG
5461 GGGAGAATTGAAACGG
1 GGGAGAATTGAAACGG
5477 TCCTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.44, T:0.12
Consensus pattern (16 bp):
GGGAGAATTGAAACGG
Found at i:5970 original size:18 final size:19
Alignment explanation
Indices: 5940--5982 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
5930 TATTCTCTTA
*
5940 TTTT-TTTACTTTAATTGC
1 TTTTATTTACTTTAATCGC
*
5958 TTTTATTTA-TTTAATCGT
1 TTTTATTTACTTTAATCGC
5976 TTTTATT
1 TTTTATT
5983 ACTACTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTACTTTAATCGC
Found at i:7577 original size:18 final size:17
Alignment explanation
Indices: 7554--7602 Score: 80
Period size: 18 Copynumber: 2.8 Consensus size: 17
7544 AGAGTACAAT
7554 AAATAATTTAAAAATTAA
1 AAATAATTTAAAAATT-A
7572 AAATAATTTAAAAATTA
1 AAATAATTTAAAAATTA
*
7589 TAATAATTTAAAAA
1 AAATAATTTAAAAA
7603 ATATAATACT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATAATTTAAAAATTA
Found at i:7603 original size:18 final size:17
Alignment explanation
Indices: 7555--7610 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
7545 GAGTACAATA
*
7555 AATAATTTAAAAATTAAA
1 AATAATTTAAAAATT-AT
7573 AATAATTTAAAAATTAT
1 AATAATTTAAAAATTAT
*
7590 AATAATTTAAAAAATAT
1 AATAATTTAAAAATTAT
7607 AATA
1 AATA
7611 CTATAATAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 21 0.58
18 15 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATTTAAAAATTAT
Found at i:18388 original size:35 final size:38
Alignment explanation
Indices: 18304--18388 Score: 106
Period size: 36 Copynumber: 2.3 Consensus size: 38
18294 TTTATTAAAA
*
18304 AAATTATTAATTTACTAATAGATAATTAAAAAAATGAT
1 AAATTATTAATTTACTAATAAATAATTAAAAAAATGAT
* *
18342 AAATTAATAATTT-TTAATAAATAA-TAAAAAAAT-ATT
1 AAATTATTAATTTACTAATAAATAATTAAAAAAATGA-T
18378 AAA-TATTAATT
1 AAATTATTAATT
18389 AATATTTTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 8 0.19
36 13 0.31
37 9 0.21
38 12 0.29
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (38 bp):
AAATTATTAATTTACTAATAAATAATTAAAAAAATGAT
Found at i:18667 original size:23 final size:23
Alignment explanation
Indices: 18637--18687 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
18627 GAAGCGAACT
* **
18637 ACGAGCATCGAGCTTAATGAGCA
1 ACGAGCATCGAACTTAACAAGCA
18660 ACGAGCATCGAACTTAACAAGCA
1 ACGAGCATCGAACTTAACAAGCA
18683 ACGAG
1 ACGAG
18688 TCGAGCAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.14
Consensus pattern (23 bp):
ACGAGCATCGAACTTAACAAGCA
Found at i:29116 original size:31 final size:31
Alignment explanation
Indices: 29078--29171 Score: 136
Period size: 31 Copynumber: 3.0 Consensus size: 31
29068 CTCGAAGGAC
* * *
29078 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
29109 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
29140 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
29171 C
1 C
29172 CCTCGACCCT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 56 0.98
32 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:29977 original size:21 final size:21
Alignment explanation
Indices: 29953--29997 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29943 TGTTGTTCGT
29953 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
29974 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
29995 TTG
1 TTG
29998 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:38884 original size:10 final size:9
Alignment explanation
Indices: 38869--38894 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
38859 CCGCAGCGAA
38869 TTTTTTTAT
1 TTTTTTTAT
38878 TTTTTTTAT
1 TTTTTTTAT
38887 TTTTTTTA
1 TTTTTTTA
38895 ATAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:43557 original size:26 final size:27
Alignment explanation
Indices: 43505--43558 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
43495 CTCGTATAAG
43505 ATATAGTGAAAATTATTTTTTTAAACT
1 ATATAGTGAAAATTATTTTTTTAAACT
*
43532 ATATATTGAAAATTA-TTTTTTAAACT
1 ATATAGTGAAAATTATTTTTTTAAACT
43558 A
1 A
43559 GGATCTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (27 bp):
ATATAGTGAAAATTATTTTTTTAAACT
Found at i:45005 original size:24 final size:25
Alignment explanation
Indices: 44967--45013 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
44957 TATCATTGTG
44967 ACACATTTTTCTATGCTCTTGTGTC
1 ACACATTTTTCTATGCTCTTGTGTC
44992 ACACA-TTTTCTATGCTCTTGTG
1 ACACATTTTTCTATGCTCTTGTG
45014 ACACGATCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (25 bp):
ACACATTTTTCTATGCTCTTGTGTC
Found at i:46103 original size:23 final size:23
Alignment explanation
Indices: 46085--46145 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
46075 CTCGTATAAA
46085 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
46108 TGCACCAAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
46131 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
46146 TATAAGATTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:46402 original size:30 final size:31
Alignment explanation
Indices: 46368--46426 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
46358 TATTGTATAG
46368 ACATATAAT-TTCCAT-ACCTTTATCACATGA
1 ACATATAATGTTCCATCA-CTTTATCACATGA
*
46398 ACATATCATGTTCCATCACTTTATCACAT
1 ACATATAATGTTCCATCACTTTATCACAT
46427 AGCTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (31 bp):
ACATATAATGTTCCATCACTTTATCACATGA
Found at i:48360 original size:99 final size:99
Alignment explanation
Indices: 48189--48425 Score: 341
Period size: 99 Copynumber: 2.4 Consensus size: 99
48179 AAATAACCAA
* * * *
48189 CAAATTCGCAACGCGATTCT-CAAATTCGCAATGTGAATTTTGTTTTAGCAACGCTAATTACCGA
1 CAAATTCGCAACGCGATTCTCCAAATTCGCAACGCGAATTTCGTTTTAGCAACGCTAACTACCGA
** *
48253 TATAGGTAAACACAACTATTCGTAAGTCAATTTT
66 TATAGGTAAACACAACTATTCACAACTCAATTTT
* * * *
48287 CAAATTTGCAACGCGATTCTCCAAAATCGCAGCGCGAATTTCGTTTTCGCAACGCTAACTACCGA
1 CAAATTCGCAACGCGATTCTCCAAATTCGCAACGCGAATTTCGTTTTAGCAACGCTAACTACCGA
* *
48352 TATTGGTAAACACAACTATTCACAACTCAGTTTT
66 TATAGGTAAACACAACTATTCACAACTCAATTTT
*
48386 CAAATTCGCAACGCGATTCTCCAAATTCGCAACGCTAATT
1 CAAATTCGCAACGCGATTCTCCAAATTCGCAACGCGAATT
48426 ACCGATATAG
Statistics
Matches: 121, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
98 19 0.16
99 102 0.84
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (99 bp):
CAAATTCGCAACGCGATTCTCCAAATTCGCAACGCGAATTTCGTTTTAGCAACGCTAACTACCGA
TATAGGTAAACACAACTATTCACAACTCAATTTT
Found at i:48700 original size:91 final size:91
Alignment explanation
Indices: 48589--48769 Score: 290
Period size: 91 Copynumber: 2.0 Consensus size: 91
48579 CGAATAGTTG
* * *
48589 TGTTTACCTATATCGGTAATTAGCGTTGTGAAAACGAAATTCACGTTACGATTTTGGAGAATCGT
1 TGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAATTCACATTACGATTTTGGAGAATCGC
48654 GTTGCGAATTTGAAAACTGAGTTGCA
66 GTTGCGAATTTGAAAACTGAGTTGCA
* * **
48680 TGTTTACCTATGTCGGTAATTAGCGTTGCGAAAACGAAATTCGCATTGTGATTTTGGAGAATCGC
1 TGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAATTCACATTACGATTTTGGAGAATCGC
*
48745 GTTGCGAATTTGAAAACTGTGTTGC
66 GTTGCGAATTTGAAAACTGAGTTGC
48770 GAAACTGGTG
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (91 bp):
TGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAATTCACATTACGATTTTGGAGAATCGC
GTTGCGAATTTGAAAACTGAGTTGCA
Done.