Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006331.1 Hibiscus syriacus cultivar Beakdansim tig00015132_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: 73480
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:2320 original size:18 final size:18
Alignment explanation
Indices: 2297--2351 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 18
2287 CTCAGTAATC
*
2297 TTATTCTCTGGTAATCTT
1 TTATTCACTGGTAATCTT
2315 TTATTCACACTGGTAATCTT
1 TTATT--CACTGGTAATCTT
2335 TTATTCACTGGT-ATCTT
1 TTATTCACTGGTAATCTT
2352 ACATTCCGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 5 0.15
18 12 0.35
20 17 0.50
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.51
Consensus pattern (18 bp):
TTATTCACTGGTAATCTT
Found at i:2329 original size:20 final size:20
Alignment explanation
Indices: 2304--2342 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2294 ATCTTATTCT
2304 CTGGTAATCTTTTATTCACA
1 CTGGTAATCTTTTATTCACA
2324 CTGGTAATCTTTTATTCAC
1 CTGGTAATCTTTTATTCAC
2343 TGGTATCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCACA
Found at i:2357 original size:17 final size:18
Alignment explanation
Indices: 2291--2357 Score: 50
Period size: 20 Copynumber: 3.8 Consensus size: 18
2281 TACATTCTCA
*
2291 GTAATCTT--ATTCTCTG
1 GTAATCTTACATTCACTG
**
2307 GTAATCTTTTATTCACACTG
1 GTAATCTTACATT--CACTG
**
2327 GTAATCTTTTATTCACTG
1 GTAATCTTACATTCACTG
2345 GT-ATCTTACATTC
1 GTAATCTTACATTC
2358 CGTGAACCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 8 0.18
17 9 0.20
18 10 0.23
20 17 0.39
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.48
Consensus pattern (18 bp):
GTAATCTTACATTCACTG
Found at i:13996 original size:17 final size:16
Alignment explanation
Indices: 13954--13996 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
13944 TTATCTTATG
*
13954 AAAAATAAAAGGAACA
1 AAAAATGAAAGGAACA
*
13970 ACAAATGAAAGGAACA
1 AAAAATGAAAGGAACA
13986 AAAAGATGAAA
1 AAAA-ATGAAA
13997 TCTTATGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.70, C:0.07, G:0.16, T:0.07
Consensus pattern (16 bp):
AAAAATGAAAGGAACA
Found at i:18928 original size:2 final size:2
Alignment explanation
Indices: 18879--18914 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18869 TTCAATGTGA
18879 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
18915 GAATATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27240 original size:16 final size:17
Alignment explanation
Indices: 27215--27248 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27205 TGGGTATTTT
27215 TTATTAGGG-TTTAAAA
1 TTATTAGGGTTTTAAAA
*
27231 TTATTTGGGTTTTAAAA
1 TTATTAGGGTTTTAAAA
27248 T
1 T
27249 ATTGATGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (17 bp):
TTATTAGGGTTTTAAAA
Found at i:32315 original size:29 final size:29
Alignment explanation
Indices: 32273--32331 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
32263 ATTTTCACCT
32273 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
32302 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
32331 A
1 A
32332 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:32700 original size:17 final size:18
Alignment explanation
Indices: 32662--32706 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
32652 TTTTATTAGG
32662 GTTTAAAATTATTTGAGT
1 GTTTAAAATTATTTGAGT
32680 -TTTAAAA-TA-TTGATGT
1 GTTTAAAATTATTTGA-GT
*
32696 GTTTAAGATTA
1 GTTTAAAATTA
32707 AAATTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 4 0.17
16 4 0.17
17 13 0.57
18 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (18 bp):
GTTTAAAATTATTTGAGT
Found at i:48056 original size:16 final size:17
Alignment explanation
Indices: 48035--48069 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
48025 TTACTATTCA
48035 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
48051 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
48068 CG
1 CG
48070 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:53024 original size:2 final size:2
Alignment explanation
Indices: 52982--53011 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52972 TATGCATCAA
52982 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
53012 GGTAAAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53277 original size:35 final size:35
Alignment explanation
Indices: 53235--53314 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
53225 AACACAATCA
* *
53235 TCAATTACATT-TAAAACCCCAAAATCTAAAATGCT
1 TCAATTACATTCT-AAACCCCAAAATCCAAAATACT
* * *
53270 TCAATTACATTCTAAACCTCAAATTCCAAAATATT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
53305 TCAATTACAT
1 TCAATTACAT
53315 GCCCAATCCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.44, C:0.23, G:0.01, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAATACT
Found at i:53771 original size:148 final size:149
Alignment explanation
Indices: 53496--53789 Score: 482
Period size: 148 Copynumber: 2.0 Consensus size: 149
53486 AAATACTCAA
** *
53496 TTCAGTTTATAAAATAGTTGACTCGATTTTTTTTCCGATTTGAGTTTATAAAATTTAAATCAAGT
1 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCCGATTTGAGATTATAAAATTTAAATCAAGT
* * * * *
53561 CGAATTGAATTGAATTTTTGAGTTTTTGTTTAAATTTAATTATAAATATTTATCATATTATAATA
66 CAAATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATCATACTATAATA
53626 TTATTTGATTCTAATTCAG
131 TTATTTGATTCTAATTCAG
*
53645 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTT-CGCTTTGAGATTATAAAATTTAAATCAAGT
1 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCCGATTTGAGATTATAAAATTTAAATCAAGT
* *
53709 CAAATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATATATATTTATTATACTATAATA
66 CAAATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATCATACTATAATA
53774 TTATTTGATTCTAATT
131 TTATTTGATTCTAATT
53790 TAAATAGTTT
Statistics
Matches: 134, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
148 102 0.76
149 32 0.24
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (149 bp):
TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCCGATTTGAGATTATAAAATTTAAATCAAGT
CAAATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATCATACTATAATA
TTATTTGATTCTAATTCAG
Found at i:54330 original size:35 final size:35
Alignment explanation
Indices: 54291--54370 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
54281 GGGTTTGGGC
*
54291 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAAA
* *
54326 ATGTAATTGAATTATTTTGGAATTTGGGGTTTAAA
1 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAAA
54361 ATGTAATTGA
1 ATGTAATTGA
54371 TGACTGTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAAA
Found at i:55354 original size:33 final size:32
Alignment explanation
Indices: 55286--55358 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 32
55276 CCCCGCCTCG
*
55286 ATTATATATATATATATAATTTTTTTATATAA
1 ATTATATATATATATATAATATTTTTATATAA
* * *
55318 ATTATATATATAATATTTTATATTTTTATATTA
1 ATTATATATAT-ATATATAATATTTTTATATAA
55351 ATTATATA
1 ATTATATA
55359 ATACAAACCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 11 0.31
33 25 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
ATTATATATATATATATAATATTTTTATATAA
Found at i:67848 original size:15 final size:15
Alignment explanation
Indices: 67828--67857 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
67818 TTATGCAGCT
*
67828 TGGAGCATTTCTGGC
1 TGGAGCATTACTGGC
67843 TGGAGCATTACTGGC
1 TGGAGCATTACTGGC
67858 AAACAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (15 bp):
TGGAGCATTACTGGC
Done.