Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005303.1 Hibiscus syriacus cultivar Beakdansim tig00012005_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: 71287
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:8735 original size:18 final size:19
Alignment explanation
Indices: 8712--8748 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
8702 CCAGTAATCC
8712 TATTCCC-TGGTAATCTTT
1 TATTCCCATGGTAATCTTT
8730 TATTCCCATTGGTAATCTT
1 TATTCCCA-TGGTAATCTT
8749 ACATTTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCCATGGTAATCTTT
Found at i:26184 original size:35 final size:36
Alignment explanation
Indices: 26117--26191 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
26107 AAAACAGTCC
* *
26117 TCAATTTCATTCTAAATCCCAAATTTCAAAAATAAT
1 TCAATTACATTCTAAATCCCAAAATTCAAAAATAAT
* *
26153 TCAATTACATTCTAAA-CCCAAAATTCTAAAATACT
1 TCAATTACATTCTAAATCCCAAAATTCAAAAATAAT
26188 TCAA
1 TCAA
26192 AATAATTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
35 20 0.57
36 15 0.43
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (36 bp):
TCAATTACATTCTAAATCCCAAAATTCAAAAATAAT
Found at i:28739 original size:50 final size:50
Alignment explanation
Indices: 28682--28859 Score: 338
Period size: 50 Copynumber: 3.6 Consensus size: 50
28672 TGTTTGGTTT
*
28682 GTTTATGTTCACGAACAAGCTCGTTTACAAGCTTGTTTATTGAGTCATTC
1 GTTTATGTTCACGAACAAGCTCGTTTATAAGCTTGTTTATTGAGTCATTC
28732 GTTTATGTTCACGAACAAGCTCGTTTATAAGCTTGTTTATTGAGTCATTC
1 GTTTATGTTCACGAACAAGCTCGTTTATAAGCTTGTTTATTGAGTCATTC
*
28782 GTTTATGTTCACGAACAAGCTCGTTTATAAGCTTGTTTATTGAGTCTTTC
1 GTTTATGTTCACGAACAAGCTCGTTTATAAGCTTGTTTATTGAGTCATTC
28832 GTTTATGTTCACGAACAAGCTCGTTTAT
1 GTTTATGTTCACGAACAAGCTCGTTTAT
28860 CTAGTTCTCA
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 126 1.00
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.42
Consensus pattern (50 bp):
GTTTATGTTCACGAACAAGCTCGTTTATAAGCTTGTTTATTGAGTCATTC
Found at i:35237 original size:60 final size:59
Alignment explanation
Indices: 35113--35226 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 59
35103 CAATCCCCCA
** * * *
35113 ACTATAGGGTATTACTTTATTGAGTCCCTCAACTATTAAATGTTATAAAATAGTATTCCG
1 ACTATAGGACATTACTTTATTGAATCCCTCAACTATTAAAAGTTATAAAATAATATT-CG
* *
35173 ACTATAGGACATTACTTTGTTGAATCTCC-CTACTATTAAAAGTTATAAAATAAT
1 ACTATAGGACATTACTTTATTGAATC-CCTCAACTATTAAAAGTTATAAAATAAT
35227 CACTTGACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 44 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (59 bp):
ACTATAGGACATTACTTTATTGAATCCCTCAACTATTAAAAGTTATAAAATAATATTCG
Found at i:40439 original size:27 final size:27
Alignment explanation
Indices: 40404--40457 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
40394 CAAATTTTTG
40404 GGAATTTTGTCATTGAACAATCAGTTT
1 GGAATTTTGTCATTGAACAATCAGTTT
40431 GGAATTTTGTCATTGAACAATCAGTTT
1 GGAATTTTGTCATTGAACAATCAGTTT
40458 TAAGATTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (27 bp):
GGAATTTTGTCATTGAACAATCAGTTT
Found at i:46031 original size:40 final size:40
Alignment explanation
Indices: 45976--46064 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
45966 GAGAACAAAC
45976 CAACTCGAATATCAAACATCACACTAATCACAGACAGAAA
1 CAACTCGAATATCAAACATCACACTAATCACAGACAGAAA
* *
46016 CAACTCGAATATCAAACATCGCATTAATCACAGACAGAAA
1 CAACTCGAATATCAAACATCACACTAATCACAGACAGAAA
**
46056 GGACTCGAA
1 CAACTCGAA
46065 CCAAAACCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (40 bp):
CAACTCGAATATCAAACATCACACTAATCACAGACAGAAA
Found at i:48306 original size:21 final size:21
Alignment explanation
Indices: 48282--48324 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
48272 AATTGCGTTT
48282 AGATAATGTTATCGTATTTGA
1 AGATAATGTTATCGTATTTGA
48303 AGATAATGTTATCGTATTTGA
1 AGATAATGTTATCGTATTTGA
48324 A
1 A
48325 CACAATAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.42
Consensus pattern (21 bp):
AGATAATGTTATCGTATTTGA
Found at i:50278 original size:20 final size:21
Alignment explanation
Indices: 50253--50305 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
50243 AAAATGGACC
50253 TCTTAAATTTCAC-TTTGTAA
1 TCTTAAATTTCACATTTGTAA
*
50273 TCTTAACATTT-ACATTTTTAA
1 TCTTAA-ATTTCACATTTGTAA
*
50294 T-TTAATTTTCAC
1 TCTTAAATTTCAC
50306 GAATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
20 14 0.50
21 11 0.39
ACGTcount: A:0.30, C:0.15, G:0.02, T:0.53
Consensus pattern (21 bp):
TCTTAAATTTCACATTTGTAA
Found at i:50610 original size:2 final size:2
Alignment explanation
Indices: 50513--50593 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
50503 AAATAGAGAA
*
50513 AT AT AT AT TT 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 AT AT AT
50555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50594 AAATGAGACA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:50830 original size:30 final size:31
Alignment explanation
Indices: 50764--50837 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 31
50754 ATTATCAATC
*
50764 ATATAATAGTTTTATAATATAAAAAAATTTGGT
1 ATAT-ATA-TTTTATAATATAAAAAAATTAGGT
* *
50797 ATATAT-TTTTAT-ATTTAAAAAAATTAGTTT
1 ATATATATTTTATAATATAAAAAAATTAG-GT
50827 ATATATATTTT
1 ATATATATTTT
50838 TTTGAAAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 13 0.36
30 13 0.36
31 4 0.11
32 2 0.06
33 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (31 bp):
ATATATATTTTATAATATAAAAAAATTAGGT
Found at i:56209 original size:58 final size:58
Alignment explanation
Indices: 56119--56228 Score: 211
Period size: 58 Copynumber: 1.9 Consensus size: 58
56109 TATTTAATAT
56119 GAGAGCTGCAGGTATAATTGGCATACCAAGAGTCGAGGGATTATCAGTGGTCCTTTGG
1 GAGAGCTGCAGGTATAATTGGCATACCAAGAGTCGAGGGATTATCAGTGGTCCTTTGG
*
56177 GAGAGCTGCATGTATAATTGGCATACCAAGAGTCGAGGGATTATCAGTGGTC
1 GAGAGCTGCAGGTATAATTGGCATACCAAGAGTCGAGGGATTATCAGTGGTC
56229 ATTCGGGACA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.25
Consensus pattern (58 bp):
GAGAGCTGCAGGTATAATTGGCATACCAAGAGTCGAGGGATTATCAGTGGTCCTTTGG
Found at i:63151 original size:23 final size:23
Alignment explanation
Indices: 63124--63191 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
63114 CATTTTATAT
63124 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* * **
63147 GGCACTTCGGTGCAATTCTACAT
1 GGCACTACGGTGCATTTCTACGC
* *
63170 GGCACTCCGGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
63192 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:66524 original size:23 final size:23
Alignment explanation
Indices: 66493--66558 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
66483 CCTTATATGG
*
66493 CACTTCGGTGCATTTCTACGCAA
1 CACTACGGTGCATTTCTACGCAA
* ***
66516 CACTACGGTGCAATTCTACGTGG
1 CACTACGGTGCATTTCTACGCAA
* *
66539 CACTACGATGCATTTATACG
1 CACTACGGTGCATTTCTACG
66559 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (23 bp):
CACTACGGTGCATTTCTACGCAA
Found at i:67637 original size:18 final size:18
Alignment explanation
Indices: 67614--67684 Score: 124
Period size: 18 Copynumber: 3.9 Consensus size: 18
67604 AGGGATTATC
*
67614 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
67632 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
67650 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
67668 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
67685 AATATTCAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.20, C:0.21, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:70887 original size:22 final size:22
Alignment explanation
Indices: 70861--70903 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
70851 TAAAATTATA
*
70861 ATTAATTTTTATAATAAATAAT
1 ATTAATTATTATAATAAATAAT
*
70883 ATTAATTATTATATTAAATAA
1 ATTAATTATTATAATAAATAA
70904 ATATCATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAATTATTATAATAAATAAT
Done.