Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005108.1 Hibiscus syriacus cultivar Beakdansim tig00011481_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: 74155
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:10971 original size:20 final size:20
Alignment explanation
Indices: 10946--10995 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
10936 GTGCCAAAGA
10946 ACTTTAACCAGTGATTTGAC
1 ACTTTAACCAGTGATTTGAC
* *
10966 ACTTTAACCAGTGGTTTGTC
1 ACTTTAACCAGTGATTTGAC
10986 ACTTTAACCA
1 ACTTTAACCA
10996 ATAGAATCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (20 bp):
ACTTTAACCAGTGATTTGAC
Found at i:22229 original size:23 final size:26
Alignment explanation
Indices: 22174--22223 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
22164 CATTTAAATG
*
22174 ATAAACGAACACAAACGAACGAACATA
1 ATAAATGAACACAAACGAAC-AACATA
*
22201 ATAAATGAACATAAACGAA-AACA
1 ATAAATGAACACAAACGAACAACA
22224 AAAAATAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
27 17 0.81
ACGTcount: A:0.62, C:0.18, G:0.10, T:0.10
Consensus pattern (26 bp):
ATAAATGAACACAAACGAACAACATA
Found at i:22512 original size:14 final size:15
Alignment explanation
Indices: 22481--22521 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
22471 CTGTTCGAAT
*
22481 ATAAATAAACA-AAC
1 ATAAATGAACATAAC
22495 ATAAATGAACATAA-
1 ATAAATGAACATAAC
*
22509 ATAAACGAACATA
1 ATAAATGAACATA
22522 TAATCGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.66, C:0.12, G:0.05, T:0.17
Consensus pattern (15 bp):
ATAAATGAACATAAC
Found at i:22633 original size:43 final size:40
Alignment explanation
Indices: 22562--22641 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 40
22552 AACGAGCCCT
* *
22562 TTGTTCGTGTTCGTTCATTTAATTAAACGAACGTAAAATC
1 TTGTTCATGTTCGTTCATTTAATTAAACGAACATAAAATC
22602 TTGTTCATGTTCGTTCATTTAATAAATAAACGAACATAAA
1 TTGTTCATGTTCGTTCATTTAAT---TAAACGAACATAAA
22642 CGAACTTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 22 0.63
43 13 0.37
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (40 bp):
TTGTTCATGTTCGTTCATTTAATTAAACGAACATAAAATC
Found at i:37817 original size:212 final size:212
Alignment explanation
Indices: 37450--37876 Score: 845
Period size: 212 Copynumber: 2.0 Consensus size: 212
37440 AATGACGGGA
37450 CTTCATCTTTATTTAGCTAAAAGCAAACTTTTTGGCATCAATGTGGAGGATGATATCATGGGAGA
1 CTTCATCTTTATTTAGCTAAAAGCAAACTTTTTGGCATCAATGTGGAGGATGATATCATGGGAGA
37515 TAGGGCTGCGGCTATTGGATGCTCTGTAGGTTCATTTCCGACCGTTTACTTGGGACTTCCGTTAG
66 TAGGGCTGCGGCTATTGGATGCTCTGTAGGTTCATTTCCGACCGTTTACTTGGGACTTCCGTTAG
*
37580 GGGCAAAAAGAAATTGTGAGAAATTGTGGGAGTCGGTTCTTGATAATTTCCACAAGAAACTAGCG
131 GGGCAAAAAGAAATTGTGAGAAATTGTGGGAGCCGGTTCTTGATAATTTCCACAAGAAACTAGCG
37645 GGGTGGAAAGCCTCTTC
196 GGGTGGAAAGCCTCTTC
37662 CTTCATCTTTATTTAGCTAAAAGCAAACTTTTTGGCATCAATGTGGAGGATGATATCATGGGAGA
1 CTTCATCTTTATTTAGCTAAAAGCAAACTTTTTGGCATCAATGTGGAGGATGATATCATGGGAGA
37727 TAGGGCTGCGGCTATTGGATGCTCTGTAGGTTCATTTCCGACCGTTTACTTGGGACTTCCGTTAG
66 TAGGGCTGCGGCTATTGGATGCTCTGTAGGTTCATTTCCGACCGTTTACTTGGGACTTCCGTTAG
37792 GGGCAAAAAGAAATTGTGAGAAATTGTGGGAGCCGGTTCTTGATAATTTCCACAAGAAACTAGCG
131 GGGCAAAAAGAAATTGTGAGAAATTGTGGGAGCCGGTTCTTGATAATTTCCACAAGAAACTAGCG
37857 GGGTGGAAAGCCTCTTC
196 GGGTGGAAAGCCTCTTC
37874 CTT
1 CTT
37877 GTCATTGGCA
Statistics
Matches: 214, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 214 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (212 bp):
CTTCATCTTTATTTAGCTAAAAGCAAACTTTTTGGCATCAATGTGGAGGATGATATCATGGGAGA
TAGGGCTGCGGCTATTGGATGCTCTGTAGGTTCATTTCCGACCGTTTACTTGGGACTTCCGTTAG
GGGCAAAAAGAAATTGTGAGAAATTGTGGGAGCCGGTTCTTGATAATTTCCACAAGAAACTAGCG
GGGTGGAAAGCCTCTTC
Found at i:46916 original size:43 final size:42
Alignment explanation
Indices: 46844--46927 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 42
46834 TTAATCATGA
*
46844 AGGGGGTTTTTAAAGAGGCCTACCTTTCCTATCAAAAAAAAG
1 AGGGGGTTTTTAAAGAGACCTACCTTTCCTATCAAAAAAAAG
*
46886 AGGGAGGTTTTTAATGAGACCT-CCTATTCCTATCAAAAAAAA
1 AGGG-GGTTTTTAAAGAGACCTACCT-TTCCTATCAAAAAAAA
46928 AAACCGATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 7 0.18
43 31 0.82
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (42 bp):
AGGGGGTTTTTAAAGAGACCTACCTTTCCTATCAAAAAAAAG
Found at i:53846 original size:22 final size:22
Alignment explanation
Indices: 53821--53867 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
53811 CTGTTAGCGC
53821 CCGACGATGGAAGCTGTGACTG
1 CCGACGATGGAAGCTGTGACTG
*
53843 CCGACGATGGAGGCTGTGACTG
1 CCGACGATGGAAGCTGTGACTG
53865 CCG
1 CCG
53868 GCGAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.26, G:0.38, T:0.17
Consensus pattern (22 bp):
CCGACGATGGAAGCTGTGACTG
Found at i:58373 original size:24 final size:24
Alignment explanation
Indices: 58346--58400 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
58336 CTGATATCCA
58346 TTTTATGTAAT-TATACATTATTAG
1 TTTTAT-TAATCTATACATTATTAG
* *
58370 TTTTATTCATCTATATATTATTAG
1 TTTTATTAATCTATACATTATTAG
*
58394 TTATATT
1 TTTTATT
58401 TTATAAGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.58
Consensus pattern (24 bp):
TTTTATTAATCTATACATTATTAG
Found at i:62569 original size:29 final size:29
Alignment explanation
Indices: 62527--62612 Score: 156
Period size: 29 Copynumber: 3.0 Consensus size: 29
62517 CACAGTGGCC
62527 GTAGGTCGCCATGC-CTTCCGGGCGACCTT
1 GTAGGTCGCCATGCAC-TCCGGGCGACCTT
62556 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
62585 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
62613 ACCCTTGCTC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 55 0.98
30 1 0.02
ACGTcount: A:0.13, C:0.35, G:0.31, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:62704 original size:29 final size:29
Alignment explanation
Indices: 62671--62726 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
62661 TCCCAACACA
*
62671 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
62700 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
62727 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.38, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:62771 original size:33 final size:33
Alignment explanation
Indices: 62730--62818 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 33
62720 GCGACCTACC
* *
62730 CTCGCTCGGCTGCCCTCAGATTCCCTAGCATAG
1 CTCGCTCGGCTGCCCTCAGATGCCATAGCATAG
* * *
62763 CTCGCTCGGTTGCCCTCGGATGCCATCGCATAG
1 CTCGCTCGGCTGCCCTCAGATGCCATAGCATAG
* * * *
62796 CTCGTTCGGATGGCCTCGGATGC
1 CTCGCTCGGCTGCCCTCAGATGC
62819 TCTCGGATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.12, C:0.36, G:0.27, T:0.25
Consensus pattern (33 bp):
CTCGCTCGGCTGCCCTCAGATGCCATAGCATAG
Found at i:62786 original size:10 final size:10
Alignment explanation
Indices: 62767--62884 Score: 83
Period size: 10 Copynumber: 11.1 Consensus size: 10
62757 GCATAGCTCG
*
62767 CTCGGTTGCC
1 CTCGGATGCC
62777 CTCGGATGCC
1 CTCGGATGCC
* *
62787 ATCGCATAGCTC
1 CTCGGAT-GC-C
* *
62799 GTTCGGATGGC
1 -CTCGGATGCC
*
62810 CTCGGATGCT
1 CTCGGATGCC
*
62820 CTCGGATGCT
1 CTCGGATGCC
*
62830 CTCGGATGGC
1 CTCGGATGCC
*
62840 CTCGGATGCT
1 CTCGGATGCC
62850 CTCGGATAGCC
1 CTCGGAT-GCC
*
62861 TCGGTCGGATGGC
1 -C--TCGGATGCC
62874 CTCGGATGCC
1 CTCGGATGCC
62884 C
1 C
62885 AGCGTGTTGG
Statistics
Matches: 85, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
10 63 0.74
11 5 0.06
12 4 0.05
13 7 0.08
14 6 0.07
ACGTcount: A:0.11, C:0.32, G:0.32, T:0.25
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:62837 original size:30 final size:33
Alignment explanation
Indices: 62759--62882 Score: 143
Period size: 33 Copynumber: 3.8 Consensus size: 33
62749 ATTCCCTAGC
* * *
62759 ATAG-CTCGCTCGGTTGCCCTCGGATGC-CATCGC
1 ATAGCCTCG-TCGGATGGCCTCGGATGCTC-TCGG
62792 ATAG-CTCGTTCGGATGGCCTCGGATGCTCTCGG
1 ATAGCCTCG-TCGGATGGCCTCGGATGCTCTCGG
62825 AT-G-CTC-TCGGATGGCCTCGGATGCTCTCGG
1 ATAGCCTCGTCGGATGGCCTCGGATGCTCTCGG
62855 ATAGCCTCGGTCGGATGGCCTCGGATGC
1 ATAGCCTC-GTCGGATGGCCTCGGATGC
62883 CCAGCGTGTT
Statistics
Matches: 82, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
30 26 0.32
31 1 0.01
32 7 0.09
33 29 0.35
34 19 0.23
ACGTcount: A:0.12, C:0.31, G:0.32, T:0.25
Consensus pattern (33 bp):
ATAGCCTCGTCGGATGGCCTCGGATGCTCTCGG
Found at i:63199 original size:24 final size:25
Alignment explanation
Indices: 63172--63235 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 25
63162 TAAAAAATCA
63172 TAAGATATAGT-GTTTCTATTTAAT
1 TAAGATATAGTCGTTTCTATTTAAT
*
63196 TAAGATATTACTTCCGTTTCTATTTAAT
1 TAAGATA-TA-GT-CGTTTCTATTTAAT
*
63224 TAAGATGTAGTC
1 TAAGATATAGTC
63236 AGCCCGAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 7 0.21
25 3 0.09
26 2 0.06
27 2 0.06
28 19 0.58
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (25 bp):
TAAGATATAGTCGTTTCTATTTAAT
Found at i:64062 original size:13 final size:13
Alignment explanation
Indices: 64044--64069 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64034 GAAATAAAAA
64044 TTATTTCTTTAAT
1 TTATTTCTTTAAT
64057 TTATTTCTTTAAT
1 TTATTTCTTTAAT
64070 CACTGAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTCTTTAAT
Found at i:72402 original size:80 final size:86
Alignment explanation
Indices: 72236--72410 Score: 272
Period size: 80 Copynumber: 2.1 Consensus size: 86
72226 TGTTAAAGTC
* *
72236 TACCAAATTGTTATTTCAATAGAACAACCCCATATCATTTTCCATTTCTCATGAGAGAGAGACAG
1 TACCAAATTGTTATTTCAATAGAACAACACCACAT-ATTTTCCATTTCTCATGAGAGAGAGACAG
72301 TTAATTCTGCTCAGTTCTACAA
65 TTAATTCTGCTCAGTTCTACAA
*
72323 TACCAAATTGTTA-TTCAATAG-A-AACACCACGT-TTTTCCATTTCTCATGAGAGAG-GACAGT
1 TACCAAATTGTTATTTCAATAGAACAACACCACATATTTTCCATTTCTCATGAGAGAGAGACAGT
72383 T-ATTCTGCTCAGTTCTACAA
66 TAATTCTGCTCAGTTCTACAA
72403 TACCAAAT
1 TACCAAAT
72411 GTTGGTTATG
Statistics
Matches: 85, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
80 27 0.32
81 7 0.08
82 22 0.26
84 7 0.08
85 1 0.01
86 8 0.09
87 13 0.15
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (86 bp):
TACCAAATTGTTATTTCAATAGAACAACACCACATATTTTCCATTTCTCATGAGAGAGAGACAGT
TAATTCTGCTCAGTTCTACAA
Done.