Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002352.1 Hibiscus syriacus cultivar Beakdansim tig00004797_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: 2012169
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1985581 original size:11 final size:11
Alignment explanation
Indices: 1985559--1985608 Score: 59
Period size: 10 Copynumber: 4.7 Consensus size: 11
1985549 ATTTATTTTT
1985559 TAAAAATA-AA
1 TAAAAATACAA
1985569 TAAAAATACAA
1 TAAAAATACAA
*
1985580 TAAAAA-ATAA
1 TAAAAATACAA
* *
1985590 TTAAAATTCAA
1 TAAAAATACAA
1985601 TAAAAATA
1 TAAAAATA
1985609 GAATGTAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 16 0.50
11 16 0.50
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAAAATACAA
Found at i:1985585 original size:21 final size:22
Alignment explanation
Indices: 1985559--1985608 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
1985549 ATTTATTTTT
1985559 TAAAAATA-AATAAAAATACAA
1 TAAAAATATAATAAAAATACAA
* *
1985580 TAAAAA-ATAATTAAAATTCAA
1 TAAAAATATAATAAAAATACAA
1985601 TAAAAATA
1 TAAAAATA
1985609 GAATGTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAAATATAATAAAAATACAA
Found at i:1987155 original size:68 final size:68
Alignment explanation
Indices: 1987046--1987183 Score: 258
Period size: 68 Copynumber: 2.0 Consensus size: 68
1987036 TGACTATCAT
*
1987046 TACATTAGGTATCGACAATCAATTTTAGGATTAAATTTTATTTATATCTTAGTTAGTGTGTTAAC
1 TACATTAGGTATCAACAATCAATTTTAGGATTAAATTTTATTTATATCTTAGTTAGTGTGTTAAC
1987111 ATC
66 ATC
*
1987114 TACATTAGGTATTAACAATCAATTTTAGGATTAAATTTTATTTATATCTTAGTTAGTGTGTTAAC
1 TACATTAGGTATCAACAATCAATTTTAGGATTAAATTTTATTTATATCTTAGTTAGTGTGTTAAC
1987179 ATC
66 ATC
1987182 TA
1 TA
1987184 GTTTAGACGT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (68 bp):
TACATTAGGTATCAACAATCAATTTTAGGATTAAATTTTATTTATATCTTAGTTAGTGTGTTAAC
ATC
Found at i:1990898 original size:28 final size:28
Alignment explanation
Indices: 1990858--1990922 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
1990848 ATTTTAAAAT
*
1990858 ATCATCGAATTTATAAGAGCTACGTTAG
1 ATCATCGAATTTATAAGAACTACGTTAG
1990886 ATCATCGAATTTATAAGAACTACGTTAG
1 ATCATCGAATTTATAAGAACTACGTTAG
1990914 ATCATCGAA
1 ATCATCGAA
1990923 GTGACCTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (28 bp):
ATCATCGAATTTATAAGAACTACGTTAG
Found at i:1991172 original size:12 final size:11
Alignment explanation
Indices: 1991134--1991170 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1991124 TCGACCAAAC
*
1991134 AAATACAATTGA
1 AAATA-AATTAA
1991146 AAATAAATTAA
1 AAATAAATTAA
1991157 AAATAAATTAA
1 AAATAAATTAA
1991168 AAA
1 AAA
1991171 ATCGTTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (11 bp):
AAATAAATTAA
Found at i:1993043 original size:69 final size:69
Alignment explanation
Indices: 1992943--1993215 Score: 238
Period size: 69 Copynumber: 4.0 Consensus size: 69
1992933 TATTTATTCC
* *
1992943 GGGTGTCTCGCACGGGTA-CCCCGAAAGGTTAGAGTGACTCACACAG-GAGCACCTAATCATATT
1 GGGTGTCTCGCACGAG-AGCCCCGAAAGGTTAGAGTGACTCACA-AGAGAGCACCTAATCATAAT
1993006 TATTTT
64 TATTTT
* * * * * ** * *
1993012 GGGTGTCTCGTACGAGTGCCCCGGAGGGTTAGATTGACTTGCACGAGAGCACCTAATAATAATTA
1 GGGTGTCTCGCACGAGAGCCCCGAAAGGTTAGAGTGACTCACAAGAGAGCACCTAATCATAATTA
*
1993077 TTTC
66 TTTT
* * * * * * * *
1993081 GGGTGTCTCACA-AAGGAGCCCCGTAATG-TAGA--GACTCGCATGAGAGCACCTAATTATAAAT
1 GGGTGTCTCGCACGA-GAGCCCCGAAAGGTTAGAGTGACTCACAAGAGAGCACCTAATCATAATT
*
1993142 ATTCT
65 ATTTT
* *
1993147 AGGTGTCTCGCACGAGAGCCCCGAAGGGTTAGAGTGACATGCAC-A-AGAGCACCTAATCATAAT
1 GGGTGTCTCGCACGAGAGCCCCGAAAGGTTAGAGTGAC-T-CACAAGAGAGCACCTAATCATAAT
1993210 TATTTT
64 TATTTT
1993216 TAGTGTATCA
Statistics
Matches: 159, Mismatches: 36, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
66 48 0.30
67 5 0.03
68 6 0.04
69 97 0.61
70 1 0.01
71 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (69 bp):
GGGTGTCTCGCACGAGAGCCCCGAAAGGTTAGAGTGACTCACAAGAGAGCACCTAATCATAATTA
TTTT
Found at i:1996290 original size:21 final size:21
Alignment explanation
Indices: 1996264--1996304 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1996254 AACACTTTCG
*
1996264 TATTGTACTTCAGACCCTTCA
1 TATTGTACTTCAGAACCTTCA
1996285 TATTGTACTTCAGAACCTTC
1 TATTGTACTTCAGAACCTTC
1996305 GAGAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (21 bp):
TATTGTACTTCAGAACCTTCA
Found at i:1997356 original size:15 final size:15
Alignment explanation
Indices: 1997338--1997368 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1997328 AAAATTGATA
1997338 AATTTAATAAAAAAT
1 AATTTAATAAAAAAT
*
1997353 AATTTTATAAAAAAT
1 AATTTAATAAAAAAT
1997368 A
1 A
1997369 CCATATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATTTAATAAAAAAT
Found at i:1997852 original size:24 final size:24
Alignment explanation
Indices: 1997783--1997852 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
1997773 TTGTTATCTG
1997783 CCAATCCATACACGTAATTGGATC
1 CCAATCCATACACGTAATTGGATC
* * * *
1997807 CCAAGCGATAC-C-CAA-T--CT-
1 CCAATCCATACACGTAATTGGATC
1997825 CCAATCCATACACGTAATTGGATC
1 CCAATCCATACACGTAATTGGATC
1997849 CCAA
1 CCAA
1997853 GCAATTCCTA
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 9 0.28
19 2 0.06
20 2 0.06
21 2 0.06
22 2 0.06
23 2 0.06
24 13 0.41
ACGTcount: A:0.34, C:0.33, G:0.11, T:0.21
Consensus pattern (24 bp):
CCAATCCATACACGTAATTGGATC
Found at i:1997866 original size:42 final size:43
Alignment explanation
Indices: 1997778--1997866 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 43
1997768 ACTTGTTGTT
*
1997778 ATCTGCCAATCCATACACGTAATTGGATCCCAAGCGATACCCA
1 ATCTGCCAATCCATACACGTAATTGGATCCCAAGCAATACCCA
* *
1997821 ATCT-CCAATCCATACACGTAATTGGATCCCAAGCAATTCCTA
1 ATCTGCCAATCCATACACGTAATTGGATCCCAAGCAATACCCA
1997863 ATCT
1 ATCT
1997867 TACTCATTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
42 39 0.91
43 4 0.09
ACGTcount: A:0.33, C:0.31, G:0.11, T:0.25
Consensus pattern (43 bp):
ATCTGCCAATCCATACACGTAATTGGATCCCAAGCAATACCCA
Found at i:2003118 original size:69 final size:67
Alignment explanation
Indices: 2003028--2003256 Score: 242
Period size: 69 Copynumber: 3.3 Consensus size: 67
2003018 TGACTCAAAT
*
2003028 GGAGCACCTAATCATATTTATTCTGGGTGTCTCGCACGGGAGCCTCGAATGGTTAGAGTGACTCG
1 GGAGCACCTAATCATAATTATT-TGGGTGTCTCGCACGGGAGCCTC-AATGGTTAGAGTGACTCG
*
2003093 TATT
64 TATG
* ** ** * * * *
2003097 GGAGTACCTAATTGTAATTATTTCGATTGTCTCGCACGAGAGCTTCTATGGGTTAGAGTGGCTCG
1 GGAGCACCTAATCATAATTATTT-GGGTGTCTCGCACGGGAGCCTCAAT-GGTTAGAGTGACTCG
*
2003162 TACG
64 TATG
* * * *
2003166 GGAGCACCTAATCATAAATATTATGGGTGTCTCGCACTGGAGCCTCAAAGGGTTAGTGTGACTCG
1 GGAGCACCTAATCATAATTATT-TGGGTGTCTCGCACGGGAGCCTC-AATGGTTAGAGTGACTCG
*
2003231 CATG
64 TATG
*
2003235 GGAGCACCTAATCAAAATTATT
1 GGAGCACCTAATCATAATTATT
2003257 CCCAATGTCT
Statistics
Matches: 127, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
68 3 0.02
69 122 0.96
70 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (67 bp):
GGAGCACCTAATCATAATTATTTGGGTGTCTCGCACGGGAGCCTCAATGGTTAGAGTGACTCGTA
TG
Found at i:2003276 original size:138 final size:138
Alignment explanation
Indices: 2003028--2003276 Score: 345
Period size: 138 Copynumber: 1.8 Consensus size: 138
2003018 TGACTCAAAT
** * * *
2003028 GGAGCACCTAATCATATTTATTCTGGGTGTCTCGCACGGGAGCCTCGAATGGTTAGAGTGACTCG
1 GGAGCACCTAATCATAAATATTATGGGTGTCTCGCACGGGAGCCTCAAAGGGTTAGAGTGACTCG
* * * *** * * *
2003093 TATTGGAGTACCTAATTGTAATTATTTCGATTGTCTCGCACGAGAGCTTCTATGGGTTAGAGTGG
66 CATGGGAGCACCTAATCAAAATTATTCCCAATGTCTCGCACGAGAGCTTCTATGGGTTAGAGTGG
2003158 CTCGTACG
131 CTCGTACG
* *
2003166 GGAGCACCTAATCATAAATATTATGGGTGTCTCGCACTGGAGCCTCAAAGGGTTAGTGTGACTCG
1 GGAGCACCTAATCATAAATATTATGGGTGTCTCGCACGGGAGCCTCAAAGGGTTAGAGTGACTCG
*
2003231 CATGGGAGCACCTAATCAAAATTATTCCCAATGTCTCTCACGAGAG
66 CATGGGAGCACCTAATCAAAATTATTCCCAATGTCTCGCACGAGAG
2003277 GCCCAAAAGA
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
138 94 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (138 bp):
GGAGCACCTAATCATAAATATTATGGGTGTCTCGCACGGGAGCCTCAAAGGGTTAGAGTGACTCG
CATGGGAGCACCTAATCAAAATTATTCCCAATGTCTCGCACGAGAGCTTCTATGGGTTAGAGTGG
CTCGTACG
Found at i:2006807 original size:31 final size:31
Alignment explanation
Indices: 2006761--2006840 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
2006751 TTCGATAATA
* *
2006761 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAATAATTTTATAATCATTTA-ATAAATT
* *
2006792 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAATAATTTTATAATCATTTAATAAATT
**
2006823 TAATAAGCATTTTATAAT
1 TAATAATAATTTTATAAT
2006841 TTTTTAAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 37 0.90
32 4 0.10
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (31 bp):
TAATAATAATTTTATAATCATTTAATAAATT
Found at i:2006818 original size:19 final size:20
Alignment explanation
Indices: 2006794--2006843 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2006784 GATAAATTTA
*
2006794 TTAATAATTTTATAATC-TT
1 TTAATAATTTTATAAGCATT
*
2006813 TTAATAAATTTAATAAGCATT
1 TTAAT-AATTTTATAAGCATT
2006834 TT-ATAATTTT
1 TTAATAATTTT
2006844 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (20 bp):
TTAATAATTTTATAAGCATT
Found at i:2006846 original size:31 final size:31
Alignment explanation
Indices: 2006780--2006847 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
2006770 TTTTATAGTA
* *
2006780 TTTAGATAAATTTATTAATAATTTTATAATCT
1 TTTA-ATAAATTTAATAAGAATTTTATAATCT
* *
2006812 TTTAATAAATTTAATAAGCATTTTATAATTT
1 TTTAATAAATTTAATAAGAATTTTATAATCT
2006843 TTTAA
1 TTTAA
2006848 ACTTTATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTAATAAATTTAATAAGAATTTTATAATCT
Found at i:2007601 original size:31 final size:30
Alignment explanation
Indices: 2007566--2007652 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
2007556 TCAATAAAGT
2007566 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
2007597 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
2007628 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
2007653 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:2007628 original size:20 final size:20
Alignment explanation
Indices: 2007561--2007628 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
2007551 TTTCGTCAAT
*
2007561 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
2007579 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
2007600 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
2007619 ATAA-ATTTAT
1 A-AAGATTTAT
2007629 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:2011823 original size:20 final size:21
Alignment explanation
Indices: 2011785--2011823 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2011775 TTTATTAATA
* *
2011785 TTAAAAATCATATTTAACATT
1 TTAAAAATCATAGTAAACATT
2011806 TTAAAAATCAT-GTAAACA
1 TTAAAAATCATAGTAAACA
2011824 CCTAATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (21 bp):
TTAAAAATCATAGTAAACATT
Found at i:2012019 original size:3 final size:3
Alignment explanation
Indices: 2012011--2012169 Score: 268
Period size: 3 Copynumber: 52.3 Consensus size: 3
2012001 TTTCACATGT
2012011 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2012059 TTC TTC TTC TT- TTC TTC TTC TTC TTC TTTC TTC TTTC TTC TTC TTCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC -TTC TTC TTC TT-C
2012106 TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2012152 TTC -TC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC T
Statistics
Matches: 150, Mismatches: 0, Indels: 12
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.03
3 134 0.89
4 12 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Done.