Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008424.1 Hibiscus syriacus cultivar Beakdansim tig00111207_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: 4198033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 16
Found at i:4141246 original size:20 final size:18
Alignment explanation
Indices: 4141203--4141250 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
4141193 CACTTTTTCT
4141203 TTTCTTTC-TTTCTTTGA
1 TTTCTTTCTTTTCTTTGA
*
4141220 TTT-TTTCTTTTCTTTTTGC
1 TTTCTTTCTTTTC--TTTGA
4141239 TTTCTTTCTTTT
1 TTTCTTTCTTTT
4141251 TGCACGCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.27
19 7 0.27
20 8 0.31
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTCTTTCTTTTCTTTGA
Found at i:4145271 original size:12 final size:12
Alignment explanation
Indices: 4145232--4145281 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
4145222 TTGATTTCAC
4145232 TTTTTCTTTTCT
1 TTTTTCTTTTCT
**
4145244 TTCTTTCTTTGAT
1 TT-TTTCTTTTCT
4145257 TTTTTCTTTTCT
1 TTTTTCTTTTCT
*
4145269 TTTTGC-TTTCT
1 TTTTTCTTTTCT
4145280 TT
1 TT
4145282 CTTTTTGCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 7 0.22
12 15 0.47
13 10 0.31
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:4145278 original size:16 final size:15
Alignment explanation
Indices: 4145234--4145289 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
4145224 GATTTCACTT
4145234 TTTC-TTTT-CTTTC
1 TTTCTTTTTGCTTTC
*
4145247 TTTCTTTGATT-TTTTC
1 TTTCTTT--TTGCTTTC
4145263 TTTTCTTTTTGCTTTC
1 -TTTCTTTTTGCTTTC
4145279 TTTCTTTTTGC
1 TTTCTTTTTGC
4145290 ACGCTTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
13 4 0.11
14 2 0.06
15 13 0.36
16 10 0.28
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (15 bp):
TTTCTTTTTGCTTTC
Found at i:4145282 original size:20 final size:18
Alignment explanation
Indices: 4145239--4145286 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
4145229 CACTTTTTCT
4145239 TTTCTTTC-TTTCTTTGA
1 TTTCTTTCTTTTCTTTGA
*
4145256 TTT-TTTCTTTTCTTTTTGC
1 TTTCTTTCTTTTC--TTTGA
4145275 TTTCTTTCTTTT
1 TTTCTTTCTTTT
4145287 TGCACGCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.27
19 7 0.27
20 8 0.31
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTCTTTCTTTTCTTTGA
Found at i:4149308 original size:12 final size:12
Alignment explanation
Indices: 4149269--4149318 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
4149259 TTGATTTCAC
4149269 TTTTTCTTTTCT
1 TTTTTCTTTTCT
**
4149281 TTCTTTCTTTGAT
1 TT-TTTCTTTTCT
4149294 TTTTTCTTTTCT
1 TTTTTCTTTTCT
*
4149306 TTTTGC-TTTCT
1 TTTTTCTTTTCT
4149317 TT
1 TT
4149319 CTTTTTGCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 7 0.22
12 15 0.47
13 10 0.31
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:4149315 original size:16 final size:15
Alignment explanation
Indices: 4149271--4149326 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
4149261 GATTTCACTT
4149271 TTTC-TTTT-CTTTC
1 TTTCTTTTTGCTTTC
*
4149284 TTTCTTTGATT-TTTTC
1 TTTCTTT--TTGCTTTC
4149300 TTTTCTTTTTGCTTTC
1 -TTTCTTTTTGCTTTC
4149316 TTTCTTTTTGC
1 TTTCTTTTTGC
4149327 ACGCTTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
13 4 0.11
14 2 0.06
15 13 0.36
16 10 0.28
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (15 bp):
TTTCTTTTTGCTTTC
Found at i:4149319 original size:20 final size:18
Alignment explanation
Indices: 4149276--4149323 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
4149266 CACTTTTTCT
4149276 TTTCTTTC-TTTCTTTGA
1 TTTCTTTCTTTTCTTTGA
*
4149293 TTT-TTTCTTTTCTTTTTGC
1 TTTCTTTCTTTTC--TTTGA
4149312 TTTCTTTCTTTT
1 TTTCTTTCTTTT
4149324 TGCACGCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.27
19 7 0.27
20 8 0.31
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTCTTTCTTTTCTTTGA
Found at i:4150855 original size:19 final size:20
Alignment explanation
Indices: 4150814--4150856 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4150804 GAAGCCCCTT
*
4150814 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
4150834 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
4150853 TGAA
1 TGAA
4150857 GATAAATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4151205 original size:24 final size:24
Alignment explanation
Indices: 4151156--4151205 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
4151146 TTAAGGTAAG
* *
4151156 CTAGGTGAGTGTATTGGTAGATAA
1 CTAGGTGAGTGTATAGCTAGATAA
*
4151180 CTAGGTGAGT-TATAGCTTGATGAA
1 CTAGGTGAGTGTATAGCTAGAT-AA
4151204 CT
1 CT
4151206 CAAGCTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.28, C:0.08, G:0.30, T:0.34
Consensus pattern (24 bp):
CTAGGTGAGTGTATAGCTAGATAA
Found at i:4151813 original size:30 final size:31
Alignment explanation
Indices: 4151774--4151833 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
4151764 ACATGCTGCC
**
4151774 ATGATATCTAAATGATATGCAAACAAAATAA
1 ATGATATCTAAAACATATGCAAACAAAATAA
* *
4151805 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACAAAATA
4151834 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACAAAATAA
Found at i:4154998 original size:19 final size:20
Alignment explanation
Indices: 4154957--4155007 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
4154947 GAAACCCCTT
*
4154957 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
4154977 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
4154996 TGAAGATACATG
1 TGAAAATACATG
4155008 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4163878 original size:19 final size:19
Alignment explanation
Indices: 4163845--4163895 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
4163835 GCCATCTCTA
*
4163845 TCATTTCTT-TATTTCATT
1 TCATTACTTATATTTCATT
4163863 TCATT-CTTAATATTTCATT
1 TCATTACTT-ATATTTCATT
4163882 TCATTACTTATATT
1 TCATTACTTATATT
4163896 ATTATACCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
19 19 0.63
20 3 0.10
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.61
Consensus pattern (19 bp):
TCATTACTTATATTTCATT
Found at i:4166731 original size:9 final size:9
Alignment explanation
Indices: 4166717--4166755 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
4166707 ATCTCCATTG
4166717 CACCATCAA
1 CACCATCAA
4166726 CACCATCAA
1 CACCATCAA
*
4166735 TACCATCAA
1 CACCATCAA
*
4166744 CATCATCCAA
1 CACCAT-CAA
4166754 CA
1 CA
4166756 AGACCATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 21 0.81
10 5 0.19
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (9 bp):
CACCATCAA
Found at i:4171906 original size:14 final size:14
Alignment explanation
Indices: 4171884--4171920 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
4171874 TTCAAAAAAA
*
4171884 CAAACAAAAATAGG
1 CAAAAAAAAATAGG
4171898 CAAAAAAAAAATAGG
1 C-AAAAAAAAATAGG
4171913 CAAAAAAA
1 CAAAAAAA
4171921 CAAAAAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.73, C:0.11, G:0.11, T:0.05
Consensus pattern (14 bp):
CAAAAAAAAATAGG
Found at i:4171918 original size:16 final size:15
Alignment explanation
Indices: 4171889--4171920 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4171879 AAAAACAAAC
4171889 AAAAATAGGCAAAAA
1 AAAAATAGGCAAAAA
4171904 AAAAATAGGCAAAAA
1 AAAAATAGGCAAAAA
4171919 AA
1 AA
4171921 CAAAAAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.75, C:0.06, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAAATAGGCAAAAA
Found at i:4181689 original size:22 final size:22
Alignment explanation
Indices: 4181633--4181689 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
4181623 TTGGAGTGCA
*
4181633 AAAAGAAAGAAAATGACAAAAAG
1 AAAAG-AAGAAAATCACAAAAAG
* * *
4181656 AAGAA-AAAAAAATCAGAAAAGG
1 AA-AAGAAGAAAATCACAAAAAG
4181678 AAAAGAAGAAAA
1 AAAAGAAGAAAA
4181690 GAAGTTCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
21 2 0.07
22 21 0.78
23 2 0.07
24 2 0.07
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAAGAAGAAAATCACAAAAAG
Found at i:4181690 original size:14 final size:14
Alignment explanation
Indices: 4181650--4181692 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4181640 AGAAAATGAC
4181650 AAAAAGAAGAAAA-
1 AAAAAGAAGAAAAG
**
4181663 AAAAATCAGAAAAG
1 AAAAAGAAGAAAAG
*
4181677 GAAAAGAAGAAAAG
1 AAAAAGAAGAAAAG
4181691 AA
1 AA
4181693 GTTCAAAAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAAGAAGAAAAG
Found at i:4191891 original size:19 final size:19
Alignment explanation
Indices: 4191867--4191908 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
4191857 TCATTTTCTT
*
4191867 TATTTCATTTTATT-CTTAA
1 TATTTCATTTCATTACTT-A
4191886 TATTTCATTTCATTACTTA
1 TATTTCATTTCATTACTTA
4191905 TATT
1 TATT
4191909 ATTATACCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTCATTTCATTACTTA
Found at i:4195171 original size:20 final size:20
Alignment explanation
Indices: 4195129--4195171 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
4195119 GTGTTTCAAC
* *
4195129 TTTCTTTTTTTCTTTTTCTT
1 TTTCTTTTTTTCTTCTTCCT
4195149 TTTCTTTTATTT-TTCTTCCT
1 TTTCTTTT-TTTCTTCTTCCT
4195169 TTT
1 TTT
4195172 TGAGTGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTCTTTTTTTCTTCTTCCT
Done.