Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004670.1 Hibiscus syriacus cultivar Beakdansim tig00010473_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: 61602
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:11001 original size:19 final size:19
Alignment explanation
Indices: 10979--11020 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
10969 TACTGTAAAG
10979 TATACAAAT-ATATTCCGAC
1 TATA-AAATGATATTCCGAC
* *
10998 TATAAAATGATTTTCCGAT
1 TATAAAATGATATTCCGAC
11017 TATA
1 TATA
11021 GAATATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (19 bp):
TATAAAATGATATTCCGAC
Found at i:11860 original size:60 final size:60
Alignment explanation
Indices: 11723--11860 Score: 134
Period size: 60 Copynumber: 2.3 Consensus size: 60
11713 AACGTAATAA
** * * *
11723 ATAGTCGGGTGATCATTTTTTAACTTTTAATAGTAGAGGGACATAATAAAGCAACATTCT
1 ATAGTCGGAAGATCATTTTGTAACTTTTAATAGTAGAGAGACATAATAAAACAACATTCT
* * * * * ** * *
11783 ATAATTGGAGGACCATTTTGTAACTTTTAATTA-TTGAGAGATTTAATAAAATAATATTCT
1 ATAGTCGGAAGATCATTTTGTAACTTTTAA-TAGTAGAGAGACATAATAAAACAACATTCT
11843 ATAGTCGGAAGATCATTT
1 ATAGTCGGAAGATCATTT
11861 ATATTTTACC
Statistics
Matches: 60, Mismatches: 17, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
60 58 0.97
61 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (60 bp):
ATAGTCGGAAGATCATTTTGTAACTTTTAATAGTAGAGAGACATAATAAAACAACATTCT
Found at i:15079 original size:2 final size:2
Alignment explanation
Indices: 15072--15155 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
15062 CGCATTTTTC
15072 AT AT AT AT AT 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 AT AT AT AT AT
15114 AT AT AT AT AT 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 AT AT AT AT AT
15156 TTATTTATTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17986 original size:105 final size:105
Alignment explanation
Indices: 17786--18456 Score: 1155
Period size: 105 Copynumber: 6.4 Consensus size: 105
17776 TTATTGTTCC
* * * * * *
17786 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGG-GAAATTGTTTGTTGATA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAATTGGAGAAA-TGTTTGGTGACA
* * *
17850 GCCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
17892 GAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
17957 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
17997 GGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATTTGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
18062 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
18102 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
18167 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
18207 GGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATTTGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
18272 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
18312 GAGTCCAATATCCTTCGTTGTAAAGTTGAATTTGGCTCTGAATTGGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
*
18377 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
18417 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
18457 GGTAAAACCT
Statistics
Matches: 539, Mismatches: 25, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
105 500 0.93
106 39 0.07
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:28726 original size:20 final size:20
Alignment explanation
Indices: 28687--28730 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28677 ATGGTTAGTA
*
28687 AAATAAAAATAAATGAAAAT
1 AAATAAAAATAAAAGAAAAT
28707 AAATAAAAATAACAAG-AAAT
1 AAATAAAAATAA-AAGAAAAT
28727 AAAT
1 AAAT
28731 GGCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAAAGAAAAT
Found at i:29793 original size:4 final size:4
Alignment explanation
Indices: 29784--29814 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
29774 TGCAAAGAAA
*
29784 AAAT AAAT AAAT AAAT AAAT AAAC AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
29815 CAACGGGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:33290 original size:59 final size:59
Alignment explanation
Indices: 33195--33307 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
33185 ATAGTCGACG
* *
33195 AACTTAATAAAATAATATTATACAATATGATGACCATTTTATAACTTTTAATAGTTAAA
1 AACTTAATAAAATAATATTATACAATAGGATAACCATTTTATAACTTTTAATAGTTAAA
* * * *
33254 AACTTAATAAAATAATATTTTATAGTCGGATAACCATTTTATAACTTTTAATAG
1 AACTTAATAAAATAATATTATACAATAGGATAACCATTTTATAACTTTTAATAG
33308 CTGAAGTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (59 bp):
AACTTAATAAAATAATATTATACAATAGGATAACCATTTTATAACTTTTAATAGTTAAA
Found at i:33415 original size:8 final size:8
Alignment explanation
Indices: 33402--33436 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
33392 TTATTCATGC
33402 AATTATGA
1 AATTATGA
33410 AATTATGA
1 AATTATGA
33418 AATTATGA
1 AATTATGA
*
33426 AATTATAA
1 AATTATGA
33434 AAT
1 AAT
33437 AAAAGAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (8 bp):
AATTATGA
Found at i:36005 original size:17 final size:17
Alignment explanation
Indices: 35963--36018 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
35953 TAAAAATATA
**
35963 ATTTATATATCTTATTAT
1 ATTTATATATAAT-TTAT
*
35981 ATAT-TATATAATTTAT
1 ATTTATATATAATTTAT
*
35997 ATTTATATATTATTTAT
1 ATTTATATATAATTTAT
*
36014 TTTTA
1 ATTTA
36019 AAAACAACGC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 7 0.23
17 21 0.68
18 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTATATATAATTTAT
Found at i:44737 original size:24 final size:25
Alignment explanation
Indices: 44703--44751 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
44693 CCGTTCGTTT
44703 AAATGATAAATAAACACAAATGAAC
1 AAATGATAAATAAACACAAATGAAC
*
44728 AAATG-TAAATAAACATAAATGAAC
1 AAATGATAAATAAACACAAATGAAC
44752 GAACATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.18
Consensus pattern (25 bp):
AAATGATAAATAAACACAAATGAAC
Found at i:44760 original size:24 final size:24
Alignment explanation
Indices: 44708--44760 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
44698 CGTTTAAATG
*
44708 ATAAATAAACACAAATGAACAAAT
1 ATAAATAAACACAAATGAACAAAC
* * *
44732 GTAAATAAACATAAATGAACGAAC
1 ATAAATAAACACAAATGAACAAAC
44756 ATAAA
1 ATAAA
44761 ATTATTTGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.64, C:0.11, G:0.08, T:0.17
Consensus pattern (24 bp):
ATAAATAAACACAAATGAACAAAC
Found at i:45939 original size:25 final size:25
Alignment explanation
Indices: 45910--45991 Score: 92
Period size: 25 Copynumber: 3.1 Consensus size: 25
45900 TTATGAGAGT
45910 TTATAATTTTGAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
*
45935 TTATAATTTTAGAAATATTTTTTATTTAA
1 TTATAATTTT-G-AA-A-TTTTAATTTAA
* * *
45964 ATATACTTTTAAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
45989 TTA
1 TTA
45992 ATATTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 22 0.47
26 2 0.04
27 4 0.09
28 1 0.02
29 18 0.38
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATAATTTTGAAATTTTAATTTAA
Found at i:45992 original size:29 final size:28
Alignment explanation
Indices: 45915--46002 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
45905 AGAGTTTATA
*
45915 ATTTTGAAATTTTAATTTAATT--ATA-
1 ATTTTAAAATTTTAATTTAATTAAATAT
*
45940 ATTTTAGAAATATTT--TTTATTTAAATAT
1 ATTTTA-AAAT-TTTAATTTAATTAAATAT
45968 ACTTTTAAAATTTTAATTTAATT-AATATT
1 A-TTTTAAAATTTTAATTTAATTAAATA-T
45997 ATTTTA
1 ATTTTA
46003 TTTTTATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
25 11 0.22
26 4 0.08
27 9 0.18
28 14 0.27
29 13 0.25
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (28 bp):
ATTTTAAAATTTTAATTTAATTAAATAT
Found at i:52435 original size:22 final size:22
Alignment explanation
Indices: 52407--52451 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
52397 GCAATGAAAC
52407 ATTGAATAATAACTATCATGTT
1 ATTGAATAATAACTATCATGTT
52429 ATTGAATAATAACTATCATGTT
1 ATTGAATAATAACTATCATGTT
52451 A
1 A
52452 ATGTTGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (22 bp):
ATTGAATAATAACTATCATGTT
Found at i:57537 original size:70 final size:71
Alignment explanation
Indices: 57458--57590 Score: 223
Period size: 71 Copynumber: 1.9 Consensus size: 71
57448 TAGCACCTAT
* *
57458 ACTTTTAATTTTTT-AAAATCATACTTAAATTTTAATTTTTGTTTTATTTTAGTACCCACCGTGT
1 ACTTTTAATTTTTTCAAAATCATACTTAAAGTTTAATTTTTGTTTCATTTTAGTACCCACCGTGT
57522 ACATAA
66 ACATAA
* *
57528 ACTTTTAATTTTTTCAAGATCATACTTAAAGTTTAGTTTTTGTTTCATTTTAGTACCCACCGT
1 ACTTTTAATTTTTTCAAAATCATACTTAAAGTTTAATTTTTGTTTCATTTTAGTACCCACCGT
57591 TAAAAGCTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
70 14 0.24
71 44 0.76
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.50
Consensus pattern (71 bp):
ACTTTTAATTTTTTCAAAATCATACTTAAAGTTTAATTTTTGTTTCATTTTAGTACCCACCGTGT
ACATAA
Done.