Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 24
Found at i:4521138 original size:3 final size:3
Alignment explanation
Indices: 4521130--4521156 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4521120 GGATGAAGCC
4521130 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
4521157 CTTTGTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4526158 original size:21 final size:22
Alignment explanation
Indices: 4526115--4526167 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
4526105 ATTGACAATA
*
4526115 ATTAAATAGTTAAATGATCTAATTG
1 ATTAAA-A-TTAAAAGATCTAA-TG
4526140 A-TAAAATTAAAAGAT-TAATG
1 ATTAAAATTAAAAGATCTAATG
4526160 ATTAAAAT
1 ATTAAAAT
4526168 AGAATTTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.12
21 9 0.35
22 8 0.31
23 1 0.04
24 4 0.15
25 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (22 bp):
ATTAAAATTAAAAGATCTAATG
Found at i:4532435 original size:18 final size:18
Alignment explanation
Indices: 4532412--4532449 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4532402 TATTTGTTTT
4532412 TTAACAAGTTAGAAAATA
1 TTAACAAGTTAGAAAATA
*
4532430 TTAACAAGTTGGAAAATA
1 TTAACAAGTTAGAAAATA
4532448 TT
1 TT
4532450 TATATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (18 bp):
TTAACAAGTTAGAAAATA
Found at i:4533351 original size:18 final size:17
Alignment explanation
Indices: 4533303--4533356 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
4533293 AGGTTTACTT
*
4533303 AATTATTTTAAAAAATAA
1 AATTA-TTTAAAAAATTA
* *
4533321 AATTATTT-TAAATTTA
1 AATTATTTAAAAAATTA
4533337 AATTATTTAAAAAATTA
1 AATTATTTAAAAAATTA
4533354 AAT
1 AAT
4533357 GTAAAAATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 13 0.43
17 12 0.40
18 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTATTTAAAAAATTA
Found at i:4533372 original size:9 final size:9
Alignment explanation
Indices: 4533358--4533396 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
4533348 AAATTAAATG
4533358 TAAAAATAC
1 TAAAAATAC
4533367 TAAAAATAC
1 TAAAAATAC
* *
4533376 TAATATATAT
1 TAA-AAATAC
4533386 TAAAAATAC
1 TAAAAATAC
4533395 TA
1 TA
4533397 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAAATAC
Found at i:4533409 original size:19 final size:19
Alignment explanation
Indices: 4533358--4533410 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
4533348 AAATTAAATG
4533358 TAAAAATACTAAAAATACTAA
1 TAAAAATA--AAAAATACTAA
* * * *
4533379 TATATATTAAAAATACTAT
1 TAAAAATAAAAAATACTAA
4533398 TAAAAATAAAAAA
1 TAAAAATAAAAAA
4533411 ATAGATAATA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 20 0.80
21 5 0.20
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAATAAAAAATACTAA
Found at i:4536848 original size:14 final size:14
Alignment explanation
Indices: 4536829--4536855 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4536819 AACAGAATTC
4536829 ATATCATATATCAG
1 ATATCATATATCAG
4536843 ATATCATATATCA
1 ATATCATATATCA
4536856 TAACATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
ATATCATATATCAG
Found at i:4536879 original size:24 final size:24
Alignment explanation
Indices: 4536852--4536924 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
4536842 GATATCATAT
*
4536852 ATCATAACATAATTCAGATCAGAA
1 ATCATAACATAATTCAAATCAGAA
* *
4536876 ATCAGAACAGAATTCAAATCAGAA
1 ATCATAACATAATTCAAATCAGAA
*
4536900 ATCATAACATATTTCAAATCAGAA
1 ATCATAACATAATTCAAATCAGAA
4536924 A
1 A
4536925 CCAGATAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.23
Consensus pattern (24 bp):
ATCATAACATAATTCAAATCAGAA
Found at i:4536880 original size:12 final size:12
Alignment explanation
Indices: 4536865--4536903 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4536855 ATAACATAAT
4536865 TCAGATCAGAAA
1 TCAGATCAGAAA
* *
4536877 TCAGAACAGAAT
1 TCAGATCAGAAA
*
4536889 TCAAATCAGAAA
1 TCAGATCAGAAA
4536901 TCA
1 TCA
4536904 TAACATATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (12 bp):
TCAGATCAGAAA
Found at i:4537111 original size:16 final size:17
Alignment explanation
Indices: 4537080--4537112 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4537070 TATTAACTGA
4537080 CAGAATCATCAATTATT
1 CAGAATCATCAATTATT
*
4537097 CAGAAT-ATGAATTATT
1 CAGAATCATCAATTATT
4537113 AGGATCATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (17 bp):
CAGAATCATCAATTATT
Found at i:4538555 original size:23 final size:23
Alignment explanation
Indices: 4538537--4538596 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
4538527 CTCGTATAAA
4538537 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
4538560 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
4538583 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
4538597 ATATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:4539321 original size:66 final size:66
Alignment explanation
Indices: 4539208--4539357 Score: 223
Period size: 66 Copynumber: 2.3 Consensus size: 66
4539198 TTTTTCTCAT
* * *
4539208 GGGGGAATCGGTTCCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTCATA-TCTGT
1 GGGGGTATCGGTT-CCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTC-GT
4539272 TGA
64 TGA
*
4539275 -GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGTT
4539339 GA
65 GA
4539341 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
4539358 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
65 7 0.09
66 51 0.67
67 18 0.24
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGTTG
A
Found at i:4545425 original size:23 final size:22
Alignment explanation
Indices: 4545399--4545466 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 22
4545389 CACCACAGCT
4545399 CGTATAAATGCACCGAAGTGCCC
1 CGTA-AAATGCACCGAAGTGCCC
*
4545422 CGTAGAATTGCACCGAAGTGCCC
1 CGTA-AAATGCACCGAAGTGCCC
*
4545445 CGTAAAATTGCACCGTAGTGCC
1 CGTAAAA-TGCACCGAAGTGCC
4545467 ATATAATGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 2 0.05
23 38 0.95
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (22 bp):
CGTAAAATGCACCGAAGTGCCC
Found at i:4546190 original size:64 final size:64
Alignment explanation
Indices: 4546080--4546226 Score: 206
Period size: 64 Copynumber: 2.2 Consensus size: 64
4546070 TTTTCTCATG
* * *
4546080 GGGGAATCGGTTCCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTCATATCCGTTG
1 GGGGTATCGGTT--CCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTG
4546145 A
64 A
* *
4546146 -GGGTATCGGTTCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTTGA
1 GGGGTATCGGTTCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTGA
4546210 GGGGGTATCGGTTCCCC
1 -GGGGTATCGGTTCCCC
4546227 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
63 6 0.08
64 42 0.58
65 10 0.14
66 15 0.21
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (64 bp):
GGGGTATCGGTTCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTGA
Found at i:4550139 original size:14 final size:13
Alignment explanation
Indices: 4550120--4550165 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
4550110 TTTTTATTTA
4550120 TATTAATTTGAATT
1 TATTAATTT-AATT
4550134 TATTAATTTAATT
1 TATTAATTTAATT
*
4550147 TATTTAGATTTAAAT
1 TA-TTA-ATTTAATT
4550162 TATT
1 TATT
4550166 TTATATTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 6 0.21
14 14 0.48
15 9 0.31
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (13 bp):
TATTAATTTAATT
Found at i:4550168 original size:16 final size:16
Alignment explanation
Indices: 4550138--4550224 Score: 99
Period size: 16 Copynumber: 5.6 Consensus size: 16
4550128 TGAATTTATT
*
4550138 AATTTAATTTA-TTTA
1 AATTTAAATTATTTTA
*
4550153 GATTTAAATTATTTTA
1 AATTTAAATTATTTTA
* *
4550169 TA-TTAACATCATTTTA
1 AATTTAA-ATTATTTTA
*
4550185 AATTTAAATTA-TTTG
1 AATTTAAATTATTTTA
4550200 AATTTAAATTATTTTA
1 AATTTAAATTATTTTA
4550216 AATTTAAAT
1 AATTTAAAT
4550225 GAATTTGAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
15 27 0.45
16 29 0.48
17 4 0.07
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
AATTTAAATTATTTTA
Found at i:4550174 original size:15 final size:15
Alignment explanation
Indices: 4550117--4550224 Score: 96
Period size: 15 Copynumber: 7.1 Consensus size: 15
4550107 TATTTTTTAT
* *
4550117 TTATATTAATTTGAA
1 TTATTTTAATTTAAA
* *
4550132 TT-TATTAATTTAAT
1 TTATTTTAATTTAAA
4550146 TTA-TTTAGATTTAAA
1 TTATTTTA-ATTTAAA
4550161 TTATTTT-ATATTAACA
1 TTATTTTAAT-TTAA-A
*
4550177 TCATTTTAAATTTAAA
1 TTATTTT-AATTTAAA
*
4550193 TTATTTGAATTTAAA
1 TTATTTTAATTTAAA
4550208 TTATTTTAAATTTAAA
1 TTATTTT-AATTTAAA
4550224 T
1 T
4550225 GAATTTGAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
14 17 0.22
15 29 0.38
16 25 0.32
17 4 0.05
18 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (15 bp):
TTATTTTAATTTAAA
Found at i:4550191 original size:32 final size:31
Alignment explanation
Indices: 4550149--4550233 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 31
4550139 ATTTAATTTA
* *
4550149 TTTAGATTTAAATTATTT-TATATTAACATCAT
1 TTTAAATTTAAATTATTTGAAT-TTAA-ATCAT
*
4550181 TTTAAATTTAAATTATTTGAATTTAAATTAT
1 TTTAAATTTAAATTATTTGAATTTAAATCAT
*
4550212 TTTAAATTTAAATGAATTTGAA
1 TTTAAATTTAAAT-TATTTGAA
4550234 GAATTTAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
31 17 0.36
32 28 0.60
33 2 0.04
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTAAATTTAAATTATTTGAATTTAAATCAT
Done.