Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001873.1 Hibiscus syriacus cultivar Beakdansim tig00003797_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: 80098
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1860 original size:7 final size:7
Alignment explanation
Indices: 1848--1872 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1838 TTAATCTGAA
1848 TTTAAGG
1 TTTAAGG
1855 TTTAAGG
1 TTTAAGG
1862 TTTAAGG
1 TTTAAGG
1869 TTTA
1 TTTA
1873 GAGTATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (7 bp):
TTTAAGG
Found at i:8307 original size:2 final size:2
Alignment explanation
Indices: 8300--8349 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
8290 ACATGTAAGA
8300 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
8342 AT AT AT AT
1 AT AT AT AT
8350 TTGAAAGAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29135 original size:62 final size:62
Alignment explanation
Indices: 29024--29145 Score: 145
Period size: 62 Copynumber: 2.0 Consensus size: 62
29014 AACATAATAA
* ** * * * *
29024 ATAGTTGGGTAATCATTTTGTAACTTTTAATAATTGAGAGACTCGACAAAGTAACTTTTTTT
1 ATAGTCGGGTAATCATTTTGTAACTTTTAATAATAAAAAAACTCAACAAAATAACTTTTTTT
* * * *
29086 ATAGTCGGGTGATTATTTTGTAACTTTTAATAGTAAAAAAATTCAACAAAATAACTTTTT
1 ATAGTCGGGTAATCATTTTGTAACTTTTAATAATAAAAAAACTCAACAAAATAACTTTTT
29146 ATAATATGAA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (62 bp):
ATAGTCGGGTAATCATTTTGTAACTTTTAATAATAAAAAAACTCAACAAAATAACTTTTTTT
Found at i:30325 original size:19 final size:19
Alignment explanation
Indices: 30301--30339 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
30291 TTAGTTCTTT
30301 GCCAAGCTTTGTTTTAAAG
1 GCCAAGCTTTGTTTTAAAG
30320 GCCAAGCTTTGTTTTAAAG
1 GCCAAGCTTTGTTTTAAAG
30339 G
1 G
30340 TTTTACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (19 bp):
GCCAAGCTTTGTTTTAAAG
Found at i:41244 original size:6 final size:6
Alignment explanation
Indices: 41230--41265 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
41220 ACCAAGACAC
* *
41230 ACATAT ACATGT ACATAT ACATGT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
41266 GTATGTATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:41247 original size:12 final size:12
Alignment explanation
Indices: 41230--41263 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
41220 ACCAAGACAC
41230 ACATATACATGT
1 ACATATACATGT
41242 ACATATACATGT
1 ACATATACATGT
41254 ACATATACAT
1 ACATATACAT
41264 ATGTATGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (12 bp):
ACATATACATGT
Found at i:43271 original size:18 final size:18
Alignment explanation
Indices: 43248--43282 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43238 CTAGGAGATT
43248 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
43266 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
43283 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:43368 original size:21 final size:22
Alignment explanation
Indices: 43339--43382 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
43329 GTTGTATGAT
43339 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
43360 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
43382 A
1 A
43383 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:44722 original size:149 final size:149
Alignment explanation
Indices: 44260--44712 Score: 879
Period size: 149 Copynumber: 3.0 Consensus size: 149
44250 GAGTCGAGGG
44260 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
44325 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
44390 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
44409 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
44474 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
44539 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
44558 TCAACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
44623 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
44688 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
44707 TCTACG
1 TCTACG
44713 GGGCACTTCG
Statistics
Matches: 300, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 300 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:44735 original size:23 final size:23
Alignment explanation
Indices: 44691--44735 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
44681 ATCATTATAT
*
44691 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* * *
44714 GGCACTTCGGTGTATTTATACG
1 GGCACTACGGTGCAATTATACG
44736 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:45851 original size:2 final size:2
Alignment explanation
Indices: 45844--45876 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
45834 ATGAAATAAT
45844 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 T
45877 GAAAAACACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47256 original size:31 final size:32
Alignment explanation
Indices: 47199--47258 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
47189 TAAAATTTTT
*
47199 AAAAATTTAGAGATTTAAATTAAAATTTTGAA
1 AAAAATTAAGAGATTTAAATTAAAATTTTGAA
*
47231 AAAAATTGAAGAG-TTT-AATTGAAATTTT
1 AAAAATT-AAGAGATTTAAATTAAAATTTT
47259 TTGTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 11 0.44
32 10 0.40
33 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (32 bp):
AAAAATTAAGAGATTTAAATTAAAATTTTGAA
Found at i:48908 original size:35 final size:35
Alignment explanation
Indices: 48863--48982 Score: 107
Period size: 35 Copynumber: 3.4 Consensus size: 35
48853 TTAAGCCTGC
* * *
48863 TGCTCATTAAGTTCGATGCTCGTTG-CTCGCCTCAT
1 TGCTCATTAAGCTCAATGCTCATTGTC-CGCCTCAT
*
48898 TGCTCCTTAAGCTCAATGCTCATTGTCCGCCTCAT
1 TGCTCATTAAGCTCAATGCTCATTGTCCGCCTCAT
* ** * ** **
48933 TGCACATTAAGGACAATGCTCGTTGTTTGCCTTGT
1 TGCTCATTAAGCTCAATGCTCATTGTCCGCCTCAT
*
48968 TGCTCGTTAAGCTCA
1 TGCTCATTAAGCTCA
48983 TTGAAATTTT
Statistics
Matches: 67, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
35 66 0.99
36 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (35 bp):
TGCTCATTAAGCTCAATGCTCATTGTCCGCCTCAT
Found at i:49240 original size:45 final size:45
Alignment explanation
Indices: 49184--49269 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
49174 TAAAATATTA
* * * *
49184 ATTAATAATTTAGT-ATTTTTTTGTTGTTTATTAGAAAATTAATAG
1 ATTAACAATTTA-TCATTTTTTTATTATATATTAGAAAATTAATAG
*
49229 ATTAACAATTTATCATTTTTTTATTATATATTAGTAAATTA
1 ATTAACAATTTATCATTTTTTTATTATATATTAGAAAATTA
49270 GTAATTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (45 bp):
ATTAACAATTTATCATTTTTTTATTATATATTAGAAAATTAATAG
Found at i:49719 original size:21 final size:23
Alignment explanation
Indices: 49676--49728 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
49666 AATTTTGTAC
* *
49676 TCTCTAAAATTTTATTATTTATA
1 TCTCTAAAATTTTATAATATATA
49699 TCTCT-AAA-TTTATAATATATA
1 TCTCTAAAATTTTATAATATATA
49720 T-TCTTAAAA
1 TCTC-TAAAA
49729 AAACAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.08
21 13 0.50
22 6 0.23
23 5 0.19
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (23 bp):
TCTCTAAAATTTTATAATATATA
Found at i:50927 original size:31 final size:31
Alignment explanation
Indices: 50870--50928 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
50860 AAATAGGGTA
* * *
50870 AATTTTTTATTTGGTCATTCATCTATTACTT
1 AATTTTTTATTTGGTAACTCAACTATTACTT
50901 AATTTTTTATTTGGTAACTCAACTATTA
1 AATTTTTTATTTGGTAACTCAACTATTA
50929 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (31 bp):
AATTTTTTATTTGGTAACTCAACTATTACTT
Found at i:50947 original size:25 final size:26
Alignment explanation
Indices: 50919--50986 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
50909 ATTTGGTAAC
* *
50919 TCAACTATT-ATTTTTTTAAATCATA
1 TCAAATATTAATTTTTTTAAATAATA
*
50944 TCAAATGTTACATTTTTTTAAATAATA
1 TCAAATATTA-ATTTTTTTAAATAATA
*
50971 TCAAATGTTACATTTT
1 TCAAATATTA-ATTTT
50987 GGTTATGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 7 0.18
27 31 0.82
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (26 bp):
TCAAATATTAATTTTTTTAAATAATA
Found at i:50959 original size:26 final size:27
Alignment explanation
Indices: 50928--50986 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
50918 CTCAACTATT
*
50928 ATTTTTTTAAATCATATCAAATGTTAC
1 ATTTTTTTAAATAATATCAAATGTTAC
50955 ATTTTTTTAAATAATATCAAATGTTAC
1 ATTTTTTTAAATAATATCAAATGTTAC
50982 ATTTT
1 ATTTT
50987 GGTTATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.51
Consensus pattern (27 bp):
ATTTTTTTAAATAATATCAAATGTTAC
Found at i:52938 original size:29 final size:29
Alignment explanation
Indices: 52883--52938 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
52873 CCAAAATTTA
** *
52883 TTCGGTTCGGTTAATATTTTTAAAAAATG
1 TTCGGTTCGGTTAATAGGTTAAAAAAATG
52912 TTCGGTTCGGTTAAT-GGTTAAAGAAAA
1 TTCGGTTCGGTTAATAGGTTAAA-AAAA
52939 AAAAGTTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (29 bp):
TTCGGTTCGGTTAATAGGTTAAAAAAATG
Found at i:56830 original size:177 final size:177
Alignment explanation
Indices: 56534--56884 Score: 621
Period size: 177 Copynumber: 2.0 Consensus size: 177
56524 TTTTTAAATT
** *
56534 TTACATAGATTTAAGACCGTTAAATTAGTAAAATATAAAATTGAGATTAACAGTAGAAAATTATA
1 TTACATAGATTTAAGACCACTAAATTAGTAAAATATAAAATTAAGATTAACAGTAGAAAATTATA
* *
56599 AGATATTCAGTGAAAAAATGACTTAATCTTAACTTTCTATTTTCACTCATCCAACTGTCTTAAAT
66 AGATATTCAATGAAAAAATGACTTAATCTTAACTTTATATTTTCACTCATCCAACTGTCTTAAAT
*
56664 CTATGTAAACTGAAAACTATTTTACACTGTATAAATGAATCTTATAA
131 CTATGTAAACTGAAAACTATTTTACACAGTATAAATGAATCTTATAA
*
56711 TTACATAGATTTAAGACCACTAAATTAGTAAAATATAAAATTAAGATTAACCGTAGAAAATTATA
1 TTACATAGATTTAAGACCACTAAATTAGTAAAATATAAAATTAAGATTAACAGTAGAAAATTATA
*
56776 AGATATTCAATGAAAAAATGACTTAATCTTAGCTTTATATTTTCACTCATCCAACTGTCTTAAAT
66 AGATATTCAATGAAAAAATGACTTAATCTTAACTTTATATTTTCACTCATCCAACTGTCTTAAAT
*
56841 CTATGTAAACTGAAAATTATTTTACACAGTATAAATGAATCTTA
131 CTATGTAAACTGAAAACTATTTTACACAGTATAAATGAATCTTA
56885 ACCCATATAT
Statistics
Matches: 165, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
177 165 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (177 bp):
TTACATAGATTTAAGACCACTAAATTAGTAAAATATAAAATTAAGATTAACAGTAGAAAATTATA
AGATATTCAATGAAAAAATGACTTAATCTTAACTTTATATTTTCACTCATCCAACTGTCTTAAAT
CTATGTAAACTGAAAACTATTTTACACAGTATAAATGAATCTTATAA
Found at i:56896 original size:2 final size:2
Alignment explanation
Indices: 56889--56915 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56879 ATCTTAACCC
56889 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
56916 GGGATATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67236 original size:25 final size:25
Alignment explanation
Indices: 67205--67262 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
67195 AAATGTGATT
*
67205 TTTAATTTGATAA-AAAACAGAACTAA
1 TTTAATTAGA-AAGAAAA-AGAACTAA
*
67231 -TTAATTAGAAAGAAAAAGAATTAA
1 TTTAATTAGAAAGAAAAAGAACTAA
67255 TTTAATTA
1 TTTAATTA
67263 ATTACAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (25 bp):
TTTAATTAGAAAGAAAAAGAACTAA
Found at i:77540 original size:49 final size:49
Alignment explanation
Indices: 77467--77560 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
77457 TTTTGTTGAA
** *
77467 TAATGCTAAGGTGCAGGCGTGCCTAGGTGAACGCCTTGACAACACTGGT
1 TAATGCTAAGGTGCAGGCACGCCTAGGTGAACACCTTGACAACACTGGT
*
77516 TAATGCTAAGGTGCAGGCACGCCTAGGTGCACACCTTGACAACAC
1 TAATGCTAAGGTGCAGGCACGCCTAGGTGAACACCTTGACAACAC
77561 AGATTACAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.20
Consensus pattern (49 bp):
TAATGCTAAGGTGCAGGCACGCCTAGGTGAACACCTTGACAACACTGGT
Done.