Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009642.1 Hibiscus syriacus cultivar Beakdansim tig00117054_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: 216009
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:200219 original size:20 final size:19
Alignment explanation
Indices: 200158--200220 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
200148 CGATTCTCTT
**
200158 GTTGCGATTTTCATTTCGT-
1 GTTGCGATAGTCATTTC-TC
*
200177 GTTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTT-CTC
200197 GTTGCGATAGTCATTCTCTC
1 GTTGCGATAGTCATT-TCTC
200217 GTTG
1 GTTG
200221 TGATTTTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 14 0.38
20 22 0.59
21 1 0.03
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.43
Consensus pattern (19 bp):
GTTGCGATAGTCATTTCTC
Found at i:202425 original size:94 final size:94
Alignment explanation
Indices: 201929--202402 Score: 826
Period size: 94 Copynumber: 5.1 Consensus size: 94
201919 TAGATTGCTT
* * *
201929 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
201994 ATTTGTCTTTTGTTCTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
202023 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
202088 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
202117 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
202182 ATTTGTCTTTGTTTTGTCTTTTGATTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
202211 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
202276 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * **
202305 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTGATACTCTGAAAATAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
202370 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
202398 AGTAA
1 AGTAA
202403 TGTAATCCAT
Statistics
Matches: 368, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 25 0.07
94 343 0.93
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:202987 original size:19 final size:19
Alignment explanation
Indices: 202965--203019 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
202955 AAAAATGACT
202965 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
202984 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
202998 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
203017 ATC
1 ATC
203020 ACAACGACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
14 9 0.32
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 13 0.46
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:203012 original size:33 final size:33
Alignment explanation
Indices: 202965--203044 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
202955 AAAAATGACT
* * *
202965 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
*
202998 ATCGTAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
*
203031 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
203045 CTAAATTCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGACAAA
Found at i:203192 original size:20 final size:19
Alignment explanation
Indices: 203089--203221 Score: 133
Period size: 20 Copynumber: 7.4 Consensus size: 19
203079 GATTCCCTCG
203089 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
203108 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
203122 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
203141 TTGCGATAGTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
203161 TTGCGATATTCATATTCGCA
1 TTGCGATTTTCAT-TTCGCA
203181 TTGCGATTTTCA---CG--
1 TTGCGATTTTCATTTCGCA
*
203195 TTGCGGTTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
203214 TTGCGATT
1 TTGCGATT
203222 CTCTCGTTGC
Statistics
Matches: 94, Mismatches: 8, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
14 17 0.18
16 9 0.10
17 9 0.10
19 26 0.28
20 31 0.33
21 2 0.02
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:203243 original size:33 final size:33
Alignment explanation
Indices: 203054--203234 Score: 218
Period size: 33 Copynumber: 5.3 Consensus size: 33
203044 ACTAAATTCG
* ** *
203054 CGTTGCGATTTTCATTTTGTTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
203087 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
203120 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTT
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC-TCT
* * *
203156 CCGCATTGCGATATTCATATTCGCATTGCGATTTTCA
1 -CG--TTGCGATTTTCAT-TTCGCATTGCGATTCTCT
*
203193 CGTTGCGGTTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
203226 CGTTGCGAT
1 CGTTGCGAT
203235 AGTAATTTCC
Statistics
Matches: 127, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
33 81 0.64
34 11 0.09
35 2 0.02
36 4 0.03
37 3 0.02
38 1 0.01
39 12 0.09
40 13 0.10
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:203300 original size:20 final size:20
Alignment explanation
Indices: 203227--203300 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
203217 CGATTCTCTC
* *
203227 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* **
203247 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
203267 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
203288 GTTGCGATAGTCA
1 GTTGCGATAGTCA
203301 AATGAATTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:206696 original size:20 final size:19
Alignment explanation
Indices: 206675--206954 Score: 86
Period size: 20 Copynumber: 13.9 Consensus size: 19
206665 GCGATAGTCA
206675 GAATCTCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
* * *
206694 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
*
206714 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
*
206734 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
* * *
206754 GTAT-TCGCATTGTGATTTAT
1 GAATCTCG--TTGCGATTTAC
* *
206774 GTAT-TCGCATTACGATTTAC
1 GAATCTCG--TTGCGATTTAC
*
206794 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* *
206814 -AGATACGCGTTGCGAATTAC
1 GA-AT-CTCGTTGCGATTTAC
*
206834 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* * *
206854 GGATACGCATTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* * * *
206875 GTATTGTCGTTGCAATTTAT
1 G-AATCTCGTTGCGATTTAC
* *
206895 GGATACGCGTTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* * *
206916 GGATACTCGTTGAGATAGT-C
1 GAAT-CTCGTTGCGAT-TTAC
*
206936 AGAATCGCGTTGCGATTTA
1 -GAATCTCGTTGCGATTTA
206955 TATGTTCGCG
Statistics
Matches: 199, Mismatches: 45, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
18 2 0.01
19 6 0.03
20 151 0.76
21 35 0.18
22 5 0.03
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (19 bp):
GAATCTCGTTGCGATTTAC
Found at i:206747 original size:60 final size:60
Alignment explanation
Indices: 206683--206871 Score: 254
Period size: 60 Copynumber: 3.1 Consensus size: 60
206673 CAGAATCTCG
206683 TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
* * * * *
206743 TTGCGATTTAC-GTATTCGCATTGTGATTTATGTATTCGCATTACGATTTACGTATTCTCG
1 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
* * * * * * *
206803 TTGCGATTTACAGATACGCGTTGCGAATTACGTATTCTCGTTGCGATTTACGGATACGCA
1 TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
206863 TTGCGATTT
1 TTGCGATTT
206872 TACGTATTGT
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.01
60 108 0.98
61 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (60 bp):
TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
Found at i:206926 original size:41 final size:41
Alignment explanation
Indices: 206678--206927 Score: 256
Period size: 40 Copynumber: 6.2 Consensus size: 41
206668 ATAGTCAGAA
* * *
206678 TCTCGTTGCGATTTACAGATTCGCATTGCGA-TTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
* * * * *
206718 TCGCATTGCGATTTACGTATTCGCATTGCGA-TTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
* * * * * * * *
206758 TCGCATTGTGATTTATGTATTCGCATTACGA-TTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
* *
206798 TCTCGTTGCGATTTACAGATACGCGTTGCGA-ATTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
*
206838 TCTCGTTGCGATTTACGGATACGCATTGCGATTTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
* * * *
206879 TGTCGTTGCAATTTATGGATACGCGTTGCGATTTTACGGAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
*
206920 ACTCGTTG
1 TCTCGTTG
206928 AGATAGTCAG
Statistics
Matches: 182, Mismatches: 27, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
40 132 0.73
41 50 0.27
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (41 bp):
TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
Found at i:206963 original size:20 final size:20
Alignment explanation
Indices: 206940--206992 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
206930 ATAGTCAGAA
*
206940 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
206960 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
206980 TCGCGTTGTGATT
1 TCGCGTTGCGATT
206993 CTGGAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:207091 original size:20 final size:20
Alignment explanation
Indices: 207044--207095 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
207034 TCTTCATAAT
207044 CGCGTTGCGATTCTGGGAAC
1 CGCGTTGCGATTCTGGGAAC
* **
207064 TGATTTGCGATTCT-GGAGAC
1 CGCGTTGCGATTCTGGGA-AC
207084 CGCGTTGCGATT
1 CGCGTTGCGATT
207096 TTTATTTCGC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.31
Consensus pattern (20 bp):
CGCGTTGCGATTCTGGGAAC
Found at i:210735 original size:19 final size:19
Alignment explanation
Indices: 210711--210750 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
210701 TTTGATGTTT
*
210711 TGCTACAGCTAGAACTAGA
1 TGCTACAGCCAGAACTAGA
210730 TGCTACAGCCAGAACTAGA
1 TGCTACAGCCAGAACTAGA
210749 TG
1 TG
210751 TCACGAGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (19 bp):
TGCTACAGCCAGAACTAGA
Done.