Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002556.1 Hibiscus syriacus cultivar Beakdansim tig00005187_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: 51973
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:5192 original size:14 final size:15
Alignment explanation
Indices: 5167--5195 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5157 TTTTATATAT
5167 AATAATATTTTAAAA
1 AATAATATTTTAAAA
5182 AATAA-ATTTTAAAA
1 AATAATATTTTAAAA
5196 TCATCATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATATTTTAAAA
Found at i:9111 original size:87 final size:87
Alignment explanation
Indices: 8965--9138 Score: 330
Period size: 87 Copynumber: 2.0 Consensus size: 87
8955 TACCAAGTCA
*
8965 ACATTTAGAAGTTTCAATTAAACATAAACAAAATATACCAAAACAGAACATCTGAGGAAATATAA
1 ACATTTAGAAGTTTCAATTAAACATAAACAAAATATACCAAAAAAGAACATCTGAGGAAATATAA
9030 TTGATGTGAACCTGAATAGCAT
66 TTGATGTGAACCTGAATAGCAT
*
9052 ACATTTATAAGTTTCAATTAAACATAAACAAAATATACCAAAAAAGAACATCTGAGGAAATATAA
1 ACATTTAGAAGTTTCAATTAAACATAAACAAAATATACCAAAAAAGAACATCTGAGGAAATATAA
9117 TTGATGTGAACCTGAATAGCAT
66 TTGATGTGAACCTGAATAGCAT
9139 GCCCTGTATG
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.26
Consensus pattern (87 bp):
ACATTTAGAAGTTTCAATTAAACATAAACAAAATATACCAAAAAAGAACATCTGAGGAAATATAA
TTGATGTGAACCTGAATAGCAT
Found at i:17318 original size:51 final size:49
Alignment explanation
Indices: 17203--17333 Score: 131
Period size: 51 Copynumber: 2.6 Consensus size: 49
17193 CATGCCAAGA
* * ** * *
17203 TGACGAGTTTCAATAAAAAATATTTTTATTCTAACTTTTTATCTTGATG
1 TGACGAGATTCAATAAAAAATATTTTTATTCAAACTCGTCATCTTGACG
* *
17252 TGA-TAGATTTTAATAAAATAATATATTTTATTCAAACTCGTCATCTTGACG
1 TGACGAGA-TTCAATAAAA-AATAT-TTTTATTCAAACTCGTCATCTTGACG
17303 TGACGAG-TTCGAATAAAAAAATATTTTTATT
1 TGACGAGATTC-AAT-AAAAAATATTTTTATT
17334 AGAACTCATC
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
48 2 0.03
49 12 0.18
50 14 0.21
51 32 0.48
52 6 0.09
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (49 bp):
TGACGAGATTCAATAAAAAATATTTTTATTCAAACTCGTCATCTTGACG
Found at i:17368 original size:50 final size:51
Alignment explanation
Indices: 17203--17368 Score: 119
Period size: 50 Copynumber: 3.3 Consensus size: 51
17193 CATGCCAAGA
* * * ** * *
17203 TGACGAGTTTCAAT-AAAAAATAT-TTTTATTCTAACTTTTTATCTTGATG
1 TGACGAATTCCAATAAAAAAATATATTTTATTCAAACTCATCATCTTGACG
* ** * *
17252 TGA-TAGATTTTAATAAAATAATATATTTTATTCAAACTCGTCATCTTGACG
1 TGACGA-ATTCCAATAAAAAAATATATTTTATTCAAACTCATCATCTTGACG
* * *
17303 TGACGAGTTCGAATAAAAAAATAT-TTTTATT-AGAACTCATCA-CTTTGAGG
1 TGACGAATTCCAATAAAAAAATATATTTTATTCA-AACTCATCATC-TTGACG
*
17353 TGATGAATTCCAATAA
1 TGACGAATTCCAATAA
17369 CACTGTAAAA
Statistics
Matches: 92, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
48 1 0.01
49 11 0.12
50 41 0.45
51 38 0.41
52 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (51 bp):
TGACGAATTCCAATAAAAAAATATATTTTATTCAAACTCATCATCTTGACG
Found at i:17470 original size:6 final size:7
Alignment explanation
Indices: 17451--17477 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
17441 ATTATACTTA
17451 AATTTTT
1 AATTTTT
17458 AATTTTT
1 AATTTTT
17465 AATTTTT
1 AATTTTT
17472 AATTTT
1 AATTTT
17478 GACTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
AATTTTT
Found at i:18557 original size:21 final size:23
Alignment explanation
Indices: 18531--18575 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
18521 TAAGTATTTT
*
18531 TTTATA-TTTTAA-ATTAAAAAA
1 TTTATAGTTTTAATAATAAAAAA
18552 TTTATAGGTTTTAATAATAAAAAA
1 TTTATA-GTTTTAATAATAAAAAA
18576 ATTAAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TTTATAGTTTTAATAATAAAAAA
Found at i:18833 original size:30 final size:27
Alignment explanation
Indices: 18776--18833 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
18766 CTCAAAACAT
**
18776 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATAAAAATA
18803 TATTATTTTAGTATCATTTTAATAAAAATA
1 TATTATTTTA-TAT-A-TTTAATAAAAATA
18833 T
1 T
18834 TAATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 3 0.12
29 1 0.04
30 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTATTTTATATATTTAATAAAAATA
Found at i:20047 original size:29 final size:29
Alignment explanation
Indices: 19945--20048 Score: 72
Period size: 29 Copynumber: 3.5 Consensus size: 29
19935 TAAAAGATAT
* *
19945 ATTTATAAT-ATTATAAAAATATTTATTTAT
1 ATTTA-AATAATT-TAAAATTATTTATTTAA
* *
19975 TTTTAAA-AATTTAATTAATTATTTGTTTGAA
1 ATTTAAATAATTTAA--AATTATTTATTT-AA
**
20006 A--TAATATTTTTTAAAATTATTTATTTAA
1 ATTTAA-ATAATTTAAAATTATTTATTTAA
20034 ATTTAAATAATTTAA
1 ATTTAAATAATTTAA
20049 GTTTAGAATA
Statistics
Matches: 56, Mismatches: 10, Indels: 17
0.67 0.12 0.20
Matches are distributed among these distances:
28 6 0.11
29 26 0.46
30 18 0.32
31 6 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
ATTTAAATAATTTAAAATTATTTATTTAA
Found at i:20243 original size:78 final size:78
Alignment explanation
Indices: 20186--20336 Score: 275
Period size: 78 Copynumber: 1.9 Consensus size: 78
20176 AAATGAAGTT
* **
20186 TTAGAATAATTTATTATAAATTTTATAAATACATAAAAGTAATTATTTTTTTATTTTCAAATAAA
1 TTAGAATAATTTAATATAAATTTTATAAATACATAAAAGTAATTATTTAATTATTTTCAAATAAA
20251 ATGAAAAAAAAAA
66 ATGAAAAAAAAAA
20264 TTAGAATAATTTAATATAAATTTTATAAATACATAAAAGTAATTATTTAATTATTTTCAAATAAA
1 TTAGAATAATTTAATATAAATTTTATAAATACATAAAAGTAATTATTTAATTATTTTCAAATAAA
20329 ATGAAAAA
66 ATGAAAAA
20337 TTATTCTTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (78 bp):
TTAGAATAATTTAATATAAATTTTATAAATACATAAAAGTAATTATTTAATTATTTTCAAATAAA
ATGAAAAAAAAAA
Found at i:20328 original size:36 final size:36
Alignment explanation
Indices: 20210--20328 Score: 82
Period size: 36 Copynumber: 3.1 Consensus size: 36
20200 TATAAATTTT
**
20210 ATAAATACATAAAAGTAATTATTTTTTTATTTTCAA
1 ATAAATACATAAAAGTAATTATTTAATTATTTTCAA
* * * *
20246 ATAAAATGAAAAAAAAAATTAGAATAATTTAATATAAATTTT---
1 AT-AAAT---ACATAAAAGT--AATTATTTAAT-T--ATTTTCAA
20288 ATAAATACATAAAAGTAATTATTTAATTATTTTCAA
1 ATAAATACATAAAAGTAATTATTTAATTATTTTCAA
20324 ATAAA
1 ATAAA
20329 ATGAAAAATT
Statistics
Matches: 61, Mismatches: 10, Indels: 24
0.64 0.11 0.25
Matches are distributed among these distances:
33 5 0.08
35 1 0.02
36 17 0.28
37 4 0.07
38 7 0.11
40 7 0.11
41 4 0.07
42 10 0.16
43 1 0.02
45 5 0.08
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (36 bp):
ATAAATACATAAAAGTAATTATTTAATTATTTTCAA
Found at i:21009 original size:41 final size:42
Alignment explanation
Indices: 20964--21045 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 42
20954 AATTCTTACA
20964 TGTACAATATAATAATATTAATTAATA-TTATATTTATAGAG
1 TGTACAATATAATAATATTAATTAATATTTATATTTATAGAG
* *
21005 TGTACAATATATTAATGTTAATTAATATTTATATTTATAGA
1 TGTACAATATAATAATATTAATTAATATTTATATTTATAGA
21046 TTTTGATGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 25 0.66
42 13 0.34
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (42 bp):
TGTACAATATAATAATATTAATTAATATTTATATTTATAGAG
Found at i:21182 original size:29 final size:29
Alignment explanation
Indices: 21148--21232 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
21138 AAGGCTTAGC
21148 ACTTTTATCATAGTATATCGACTTAATTT
1 ACTTTTATCATAGTATATCGACTTAATTT
*
21177 ACTTTTATCAAAGTATATCGACTTAATTT
1 ACTTTTATCATAGTATATCGACTTAATTT
* *
21206 TCTTTTATCATAGTATATCAACTTAAT
1 ACTTTTATCATAGTATATCGACTTAAT
21233 AAAAAATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (29 bp):
ACTTTTATCATAGTATATCGACTTAATTT
Found at i:26903 original size:105 final size:105
Alignment explanation
Indices: 26754--26950 Score: 270
Period size: 105 Copynumber: 1.9 Consensus size: 105
26744 TCAAAAGGCT
* * *
26754 GCTTACTCTCCTCTTTAGAAGGTGGTTCCTGACCACCATCTGCCTCAAAACTCTCAACTTTACCC
1 GCTTACTCTCCTCTTTAGAAAGTGGTTCATGACCACCATATGCCTCAAAACTCTCAACTTTACCC
* * *
26819 AAGTCACCATCAGTAGTCTCATGATTACCTGTAAATTGTG
66 AACTCACCATCACTAGCCTCATGATTACCTGTAAATTGTG
* **
26859 GCTTACTCTCGTCTTTA-ATAAGTGGTTCATGACCATTATATGCCTCAAAACTCTCAACTTTACC
1 GCTTACTCTCCTCTTTAGA-AAGTGGTTCATGACCACCATATGCCTCAAAACTCTCAACTTTACC
* **
26923 TAACTCGGCATCACTAGCCTCATGATTA
65 CAACTCACCATCACTAGCCTCATGATTA
26951 TCTATAGATT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 1 0.01
105 78 0.99
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.32
Consensus pattern (105 bp):
GCTTACTCTCCTCTTTAGAAAGTGGTTCATGACCACCATATGCCTCAAAACTCTCAACTTTACCC
AACTCACCATCACTAGCCTCATGATTACCTGTAAATTGTG
Found at i:29652 original size:67 final size:67
Alignment explanation
Indices: 29544--29679 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
29534 TAAATTATAA
29544 TTATTTATTTCCTTAGAAAATAATCGTAGAAAACAACTATTTTTCTCTCTCGATAGCAAGACTAT
1 TTATTTATTTCCTTAGAAAATAATCGTAGAAAACAACTATTTTTCTCTCTCGATAGCAAGACTAT
29609 TG
66 TG
29611 TTATTTATTTCCTTAGAAAATAATCGTAGAAAACAACTATTTTTCTCTCTCGATAGCAAGACTAT
1 TTATTTATTTCCTTAGAAAATAATCGTAGAAAACAACTATTTTTCTCTCTCGATAGCAAGACTAT
29676 TG
66 TG
29678 TT
1 TT
29680 CTTGGGGATT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (67 bp):
TTATTTATTTCCTTAGAAAATAATCGTAGAAAACAACTATTTTTCTCTCTCGATAGCAAGACTAT
TG
Found at i:47030 original size:21 final size:22
Alignment explanation
Indices: 47004--47046 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
46994 AGTCGAGGGT
*
47004 TACATAGGTCCTT-GGGACATA
1 TACATAGGTCATTCGGGACATA
47025 TACATAGGTCATTCGGGACATA
1 TACATAGGTCATTCGGGACATA
47047 CATAAGGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (22 bp):
TACATAGGTCATTCGGGACATA
Found at i:47063 original size:21 final size:21
Alignment explanation
Indices: 47004--47063 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
46994 AGTCGAGGGT
*
47004 TACATAGGTC-CTTGGGACATA
1 TACATAGGTCATTTGGGACA-A
*
47025 TACATAGGTCATTCGGGAC-A
1 TACATAGGTCATTTGGGACAA
*
47045 TACATAAGGTCTTTTGGGA
1 TACAT-AGGTCATTTGGGA
47064 TAAATTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.18
21 21 0.64
22 6 0.18
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (21 bp):
TACATAGGTCATTTGGGACAA
Found at i:50428 original size:18 final size:19
Alignment explanation
Indices: 50396--50431 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
50386 CATTCAAGGG
50396 TATCGATACCTAAGGGTAA
1 TATCGATACCTAAGGGTAA
50415 TATCGATA-CTAAGGGTA
1 TATCGATACCTAAGGGTA
50432 CCGATACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (19 bp):
TATCGATACCTAAGGGTAA
Found at i:51297 original size:22 final size:22
Alignment explanation
Indices: 51269--51312 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
51259 AGTGGAGGGT
*
51269 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGAGACATA
*
51291 TACATAGGTCTTTCGAGACATA
1 TACATAGGTCCTTCGAGACATA
51313 CATGAGGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (22 bp):
TACATAGGTCCTTCGAGACATA
Found at i:51315 original size:20 final size:21
Alignment explanation
Indices: 51269--51324 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
51259 AGTGGAGGGT
* *
51269 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCTTTCGAGACA-A
51291 TACATAGGTCTTTCGAGAC-A
1 TACATAGGTCTTTCGAGACAA
51311 TACATGAGGTCTTT
1 TACAT-AGGTCTTT
51325 TGGGACAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 6 0.19
21 8 0.26
22 17 0.55
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (21 bp):
TACATAGGTCTTTCGAGACAA
Done.