Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002969.1 Hibiscus syriacus cultivar Beakdansim tig00006144_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: 66554
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5438 original size:20 final size:20
Alignment explanation
Indices: 5413--5450 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5403 ATCCTATTCT
5413 CTGATAATCTTACATTCCCA
1 CTGATAATCTTACATTCCCA
*
5433 CTGATAATCTTTCATTCC
1 CTGATAATCTTACATTCC
5451 ATGAACCAAA
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:0.26, C:0.29, G:0.05, T:0.39
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:6756 original size:20 final size:20
Alignment explanation
Indices: 6731--6850 Score: 87
Period size: 20 Copynumber: 5.6 Consensus size: 20
6721 AACACAAATG
* *
6731 AACGAACGTAAAGGAACACA
1 AACGAATGTAAAAGAACACA
** *
6751 AACGAATGTAAATTAACATA
1 AACGAATGTAAAAGAACACA
6771 AACGAATGAATGTAAAAGAACACA
1 AAC----GAATGTAAAAGAACACA
** *
6795 AACGAATGTAAATTAACATA
1 AACGAATGTAAAAGAACACA
6815 AACGAATGAATGTAAAAGAACACA
1 AAC----GAATGTAAAAGAACACA
*
6839 AACGAACGTAAA
1 AACGAATGTAAA
6851 TTAATTAGAT
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
20 44 0.56
24 34 0.44
ACGTcount: A:0.57, C:0.13, G:0.15, T:0.15
Consensus pattern (20 bp):
AACGAATGTAAAAGAACACA
Found at i:6786 original size:24 final size:24
Alignment explanation
Indices: 6721--6844 Score: 102
Period size: 24 Copynumber: 5.5 Consensus size: 24
6711 ATGATAAACA
* * * *
6721 AACACAAATGAACGAACGTAAAGG
1 AACACAAACGAATGAATGTAAAAG
**
6745 AACACAAAC----GAATGTAAATT
1 AACACAAACGAATGAATGTAAAAG
*
6765 AACATAAACGAATGAATGTAAAAG
1 AACACAAACGAATGAATGTAAAAG
**
6789 AACACAAAC----GAATGTAAATT
1 AACACAAACGAATGAATGTAAAAG
*
6809 AACATAAACGAATGAATGTAAAAG
1 AACACAAACGAATGAATGTAAAAG
6833 AACACAAACGAA
1 AACACAAACGAA
6845 CGTAAATTAA
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
20 33 0.42
24 45 0.58
ACGTcount: A:0.57, C:0.14, G:0.15, T:0.15
Consensus pattern (24 bp):
AACACAAACGAATGAATGTAAAAG
Found at i:6792 original size:44 final size:44
Alignment explanation
Indices: 6738--6854 Score: 216
Period size: 44 Copynumber: 2.7 Consensus size: 44
6728 ATGAACGAAC
*
6738 GTAAAGGAACACAAACGAATGTAAATTAACATAAACGAATGAAT
1 GTAAAAGAACACAAACGAATGTAAATTAACATAAACGAATGAAT
6782 GTAAAAGAACACAAACGAATGTAAATTAACATAAACGAATGAAT
1 GTAAAAGAACACAAACGAATGTAAATTAACATAAACGAATGAAT
*
6826 GTAAAAGAACACAAACGAACGTAAATTAA
1 GTAAAAGAACACAAACGAATGTAAATTAA
6855 TTAGATTTAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (44 bp):
GTAAAAGAACACAAACGAATGTAAATTAACATAAACGAATGAAT
Found at i:8617 original size:151 final size:151
Alignment explanation
Indices: 8343--8943 Score: 1156
Period size: 151 Copynumber: 4.0 Consensus size: 151
8333 CCTAAGAAGA
* *
8343 GTTATAGTGCATTCCTCCATAAAAGTTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
1 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
8408 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
8473 ATAAAAAGGTAGGAATCTAAC
131 ATAAAAAGGTAGGAATCTAAC
8494 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
1 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
8559 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
8624 ATAAAAAGGTAGGAATCTAAC
131 ATAAAAAGGTAGGAATCTAAC
8645 GTTATAATGCATTCCTCCAT-AAAATTCATCAAAACGACAC-AAAACAGGGTACCAAAATTTGTA
1 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
8708 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
8773 AT--AAAGGTAGGAATCTAAC
131 ATAAAAAGGTAGGAATCTAAC
8792 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
1 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
8857 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
8922 ATAAAAAGGTAGGAATCTAAC
131 ATAAAAAGGTAGGAATCTAAC
8943 G
1 G
8944 ATGGAACTTG
Statistics
Matches: 444, Mismatches: 2, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
147 37 0.08
148 20 0.05
149 180 0.41
150 20 0.05
151 187 0.42
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (151 bp):
GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
ATAAAAAGGTAGGAATCTAAC
Found at i:8923 original size:298 final size:301
Alignment explanation
Indices: 8343--8943 Score: 1163
Period size: 298 Copynumber: 2.0 Consensus size: 301
8333 CCTAAGAAGA
*
8343 GTTATAGTGCATTCCTCCATAAAAGTTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
1 GTTATAATGCATTCCTCCATAAAAGTTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
8408 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
8473 ATAAAAAGGTAGGAATCTAACGTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAA
131 AT-AAAAGGTAGGAATCTAACGTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAA
8538 AACAGGGTACCAAAATTTGTAAATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAA
195 AACAGGGTACCAAAATTTGTAAATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAA
8603 GAACAAACGCATTTAATAATAATAAAAAGGTAGGAATCTAAC
260 GAACAAACGCATTTAATAATAATAAAAAGGTAGGAATCTAAC
8645 GTTATAATGCATTCCTCCATAAAA-TTCATCAAAACGACAC-AAAACAGGGTACCAAAATTTGTA
1 GTTATAATGCATTCCTCCATAAAAGTTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
8708 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
8773 AT-AAAGGTAGGAATCTAACGTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAA
131 ATAAAAGGTAGGAATCTAACGTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAA
8837 ACAGGGTACCAAAATTTGTAAATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAG
196 ACAGGGTACCAAAATTTGTAAATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAG
8902 AACAAACGCATTTAATAATAATAAAAAGGTAGGAATCTAAC
261 AACAAACGCATTTAATAATAATAAAAAGGTAGGAATCTAAC
8943 G
1 G
8944 ATGGAACTTG
Statistics
Matches: 298, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
298 169 0.57
300 90 0.30
301 16 0.05
302 23 0.08
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (301 bp):
GTTATAATGCATTCCTCCATAAAAGTTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
ATAAAAGGTAGGAATCTAACGTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAA
ACAGGGTACCAAAATTTGTAAATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAG
AACAAACGCATTTAATAATAATAAAAAGGTAGGAATCTAAC
Found at i:25569 original size:23 final size:23
Alignment explanation
Indices: 25530--25589 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
25520 ACAACGCTAA
*
25530 ATGAACATATAAATGAATATGTTC
1 ATGAACAT-TAAATGAACATGTTC
25554 ATGAACATTAAATGAACATGTTC
1 ATGAACATTAAATGAACATGTTC
* *
25577 GTGAACAATAAAT
1 ATGAACATTAAAT
25590 AAACGAATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 25 0.76
24 8 0.24
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (23 bp):
ATGAACATTAAATGAACATGTTC
Found at i:25635 original size:30 final size:30
Alignment explanation
Indices: 25583--25688 Score: 106
Period size: 30 Copynumber: 3.5 Consensus size: 30
25573 GTTCGTGAAC
* **
25583 AATAAATAAACGAATACAAACACCTTCAAA
1 AATAAATAAACGAACATGAACACCTTCAAA
** **
25613 AATAAATAAACGAACATGAACACGAT-ATTG
1 AATAAATAAACGAACATGAACACCTTCA-AA
** *
25643 AATATTTAAATGAACATGAACACCTTCAAA
1 AATAAATAAACGAACATGAACACCTTCAAA
25673 AATAAATAAACGAACA
1 AATAAATAAACGAACA
25689 CAAACATAAC
Statistics
Matches: 57, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
29 1 0.02
30 55 0.96
31 1 0.02
ACGTcount: A:0.57, C:0.16, G:0.08, T:0.20
Consensus pattern (30 bp):
AATAAATAAACGAACATGAACACCTTCAAA
Found at i:25876 original size:14 final size:15
Alignment explanation
Indices: 25848--25883 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
25838 TGTTTCTTTG
25848 TTATTTTATAATATT
1 TTATTTTATAATATT
25863 TTATTTTA-AATATT
1 TTATTTTATAATATT
25877 TATATTT
1 T-TATTT
25884 ATTGTATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTTATAATATT
Found at i:29033 original size:2 final size:2
Alignment explanation
Indices: 29026--29051 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29016 TCAAATCGAA
29026 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
29052 TTTAGAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38512 original size:21 final size:21
Alignment explanation
Indices: 38473--38512 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38463 TCATTTTCAT
* * *
38473 TGTATTTTATTTTATTTTTTA
1 TGTATTTGATATTAATTTTTA
38494 TGTATTTGATATTAATTTT
1 TGTATTTGATATTAATTTT
38513 AGGGTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (21 bp):
TGTATTTGATATTAATTTTTA
Found at i:43941 original size:22 final size:20
Alignment explanation
Indices: 43898--43941 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
43888 ATCACATGAA
* *
43898 ATTTTATCTAAAATAGATTT
1 ATTTTATATAAAATAGACTT
43918 ATTTATATATAAATATAGACTT
1 ATTT-TATATAAA-ATAGACTT
43940 AT
1 AT
43942 AAACAAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 7 0.35
22 9 0.45
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (20 bp):
ATTTTATATAAAATAGACTT
Found at i:47754 original size:66 final size:66
Alignment explanation
Indices: 47648--47775 Score: 238
Period size: 66 Copynumber: 1.9 Consensus size: 66
47638 TCTAACAGTT
*
47648 TTAATATAAAATATTTTACAATACAAAACTACCTAAAAGTGTTATTTGAATTGAATTTAGATACT
1 TTAATATAAAATATCTTACAATACAAAACTACCTAAAAGTGTTATTTGAATTGAATTTAGATACT
47713 G
66 G
*
47714 TTAATATAAAATATCTTACAATACAAAACTGCCTAAAAGTGTTATTTGAATTGAATTTAGAT
1 TTAATATAAAATATCTTACAATACAAAACTACCTAAAAGTGTTATTTGAATTGAATTTAGAT
47776 TTTAGTATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (66 bp):
TTAATATAAAATATCTTACAATACAAAACTACCTAAAAGTGTTATTTGAATTGAATTTAGATACT
G
Found at i:47936 original size:2 final size:2
Alignment explanation
Indices: 47931--47967 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
47921 CGAGTGTGTG
47931 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47968 GATAGATCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57249 original size:20 final size:20
Alignment explanation
Indices: 57219--57275 Score: 98
Period size: 19 Copynumber: 2.9 Consensus size: 20
57209 ACCTTTAAAG
57219 CATGTCAAAAAGACATAAAAA
1 CATGTC-AAAAGACATAAAAA
57240 CATGTCAAAAGACAT-AAAA
1 CATGTCAAAAGACATAAAAA
57259 CATGTCAAAAGACATAA
1 CATGTCAAAAGACATAA
57276 TTATTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.54
20 10 0.29
21 6 0.17
ACGTcount: A:0.58, C:0.16, G:0.11, T:0.16
Consensus pattern (20 bp):
CATGTCAAAAGACATAAAAA
Found at i:61766 original size:40 final size:40
Alignment explanation
Indices: 61726--61803 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
61716 ATATGTATTA
61726 TATATCAT--TATAAAATAATATTTA-AATTAAAATTAAAT
1 TATATCATAGTATAAAA-AATATTTATAATTAAAATTAAAT
* * *
61764 TATATCATAGTATTATAAATATTTATAATTAAATTTAAAT
1 TATATCATAGTATAAAAAATATTTATAATTAAAATTAAAT
61804 AAACTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 8 0.24
39 8 0.24
40 18 0.53
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (40 bp):
TATATCATAGTATAAAAAATATTTATAATTAAAATTAAAT
Found at i:62302 original size:12 final size:11
Alignment explanation
Indices: 62277--62301 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
62267 GAAACTTTGG
62277 TTTCTGGGGGT
1 TTTCTGGGGGT
62288 TTTCTGGGGGT
1 TTTCTGGGGGT
62299 TTT
1 TTT
62302 TTCCCTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.40, T:0.52
Consensus pattern (11 bp):
TTTCTGGGGGT
Done.