Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006531.1 Hibiscus syriacus cultivar Beakdansim tig00015920_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: 74261
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:190 original size:6 final size:6
Alignment explanation
Indices: 179--209 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
169 GTCCCCCACA
*
179 CAGTGC CAGTGC CAGTGC CAGTGC CACTGC C
1 CAGTGC CAGTGC CAGTGC CAGTGC CAGTGC C
210 CCTGCCCCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.39, G:0.29, T:0.16
Consensus pattern (6 bp):
CAGTGC
Found at i:6173 original size:2 final size:2
Alignment explanation
Indices: 6166--6194 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6156 CTATAAGAAT
6166 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6195 GCTCTTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10298 original size:60 final size:60
Alignment explanation
Indices: 10219--10331 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
10209 AAATAGTCCC
10219 CTGACTATAGGATGCTACTTTATTAAGTCCCTCAACTATTAAAAGCTACAAAACGATCCT
1 CTGACTATAGGATGCTACTTTATTAAGTCCCTCAACTATTAAAAGCTACAAAACGATCCT
* * * * *
10279 CTGACTATA-GAGTGCTACTTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAA
1 CTGACTATAGGA-TGCTACTTTATTAAGTCCCTCAACTATTAAAAGCTACAAAA
10332 TGGTCACACA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (60 bp):
CTGACTATAGGATGCTACTTTATTAAGTCCCTCAACTATTAAAAGCTACAAAACGATCCT
Found at i:10654 original size:60 final size:60
Alignment explanation
Indices: 10542--10679 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
10532 AATATAATGA
* * * *
10542 ATAGTCAAAGGACCATTTCGTAACTTTTAATAGTCAATGGACTTAACGAAGCAACATTCT
1 ATAGTCAAAGGACCATTTCATAACTTTTAATAATCAAAGGACTTAACAAAGCAACATTCT
** * * * * *
10602 ATAGTCAAAGGACTGTTTTATAACTTTTAATAATTAAAGGACTTAATAAAGCAATA-CCAT
1 ATAGTCAAAGGACCATTTCATAACTTTTAATAATCAAAGGACTTAACAAAGCAACATTC-T
*
10662 ATAGTCAGAGGACCATTT
1 ATAGTCAAAGGACCATTT
10680 GTGTACTTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
59 1 0.02
60 62 0.98
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (60 bp):
ATAGTCAAAGGACCATTTCATAACTTTTAATAATCAAAGGACTTAACAAAGCAACATTCT
Found at i:12070 original size:23 final size:23
Alignment explanation
Indices: 12044--12090 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
12034 CTTCAAAAAA
12044 AAAAACTAACCAAATTCAAATTC
1 AAAAACTAACCAAATTCAAATTC
*
12067 AAAATCTAACCAAATTCAAATTC
1 AAAAACTAACCAAATTCAAATTC
12090 A
1 A
12091 GTCTTTTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.23
Consensus pattern (23 bp):
AAAAACTAACCAAATTCAAATTC
Found at i:12258 original size:20 final size:16
Alignment explanation
Indices: 12220--12253 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12210 TTAATCTTTG
12220 TATTTAATAAAATATA
1 TATTTAATAAAATATA
*
12236 TATTTAATTAAATATA
1 TATTTAATAAAATATA
12252 TA
1 TA
12254 GATATAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTAATAAAATATA
Found at i:17284 original size:17 final size:18
Alignment explanation
Indices: 17264--17298 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17254 AATATAATTT
*
17264 ATTAATTTGATA-CTTAA
1 ATTAATTTAATATCTTAA
17281 ATTAATTTAATATCTTAA
1 ATTAATTTAATATCTTAA
17299 TATAAGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTAATTTAATATCTTAA
Found at i:20001 original size:2 final size:2
Alignment explanation
Indices: 19994--20029 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19984 ATTTTCAACT
19994 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20030 GTTAAGTATA
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):
TA
Found at i:24870 original size:16 final size:17
Alignment explanation
Indices: 24838--24870 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
24828 TCCAGCTACA
*
24838 CCATTTTGATCCGAAAC
1 CCATTTTGATCCAAAAC
24855 CCATTTT-ATCCAAAAC
1 CCATTTTGATCCAAAAC
24871 TTTAAAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (17 bp):
CCATTTTGATCCAAAAC
Found at i:29946 original size:37 final size:37
Alignment explanation
Indices: 29891--29965 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
29881 ACATACAGAT
29891 AGTTGAACCACACAATTTCAACTAACAAATATGTAAA
1 AGTTGAACCACACAATTTCAACTAACAAATATGTAAA
*
29928 AGTTGAACCACACGATTTCAACTAACAAATATGTAAA
1 AGTTGAACCACACAATTTCAACTAACAAATATGTAAA
29965 A
1 A
29966 ACTGAATTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.24
Consensus pattern (37 bp):
AGTTGAACCACACAATTTCAACTAACAAATATGTAAA
Found at i:32604 original size:13 final size:12
Alignment explanation
Indices: 32585--32622 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
32575 GATATACCCT
32585 TTTTTATTAATA
1 TTTTTATTAATA
32597 TCTTTTATATAAT-
1 T-TTTTAT-TAATA
32610 TTTTTATTAATA
1 TTTTTATTAATA
32622 T
1 T
32623 ACTCATATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 4 0.17
12 8 0.35
13 7 0.30
14 4 0.17
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTATTAATA
Found at i:41999 original size:30 final size:29
Alignment explanation
Indices: 41935--42000 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
41925 ATTTTATGTT
* *
41935 AGGGGATGAACTTGAATTTTTAAAATTCTA
1 AGGGGATGAACTTGAATTATAAAAATTC-A
*
41965 AGGGGATGAACTTTTAACTTATAAAAATTCA
1 AGGGGATGAAC-TTGAA-TTATAAAAATTCA
*
41996 GGGGG
1 AGGGG
42001 CGAAAACAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 11 0.37
31 9 0.30
32 10 0.33
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (29 bp):
AGGGGATGAACTTGAATTATAAAAATTCA
Found at i:42424 original size:23 final size:22
Alignment explanation
Indices: 42396--42476 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 22
42386 ACGAACAGAT
42396 GTAAACGAACACAATAAACGAAC
1 GTAAACGAACACAA-AAACGAAC
*
42419 GTAAACGAACACAAACGAACGAAT
1 GTAAACGAACACAAA--AACGAAC
**
42443 GTAAACGAACACAACAAATAAAC
1 GTAAACGAACACAA-AAACGAAC
*
42466 ATAAACGAACA
1 GTAAACGAACA
42477 TAAATGAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.02
23 28 0.56
24 20 0.40
25 1 0.02
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (22 bp):
GTAAACGAACACAAAAACGAAC
Found at i:42435 original size:47 final size:47
Alignment explanation
Indices: 42377--42476 Score: 139
Period size: 47 Copynumber: 2.1 Consensus size: 47
42367 CACAAATGAG
* * * *
42377 CGAACATAAACGAAC-AGATGTAAACGAACACAATAAACGAACGTAAA
1 CGAACACAAACGAACGA-ATGTAAACGAACACAACAAACAAACATAAA
*
42424 CGAACACAAACGAACGAATGTAAACGAACACAACAAATAAACATAAA
1 CGAACACAAACGAACGAATGTAAACGAACACAACAAACAAACATAAA
42471 CGAACA
1 CGAACA
42477 TAAATGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 46 0.98
48 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.13, T:0.09
Consensus pattern (47 bp):
CGAACACAAACGAACGAATGTAAACGAACACAACAAACAAACATAAA
Found at i:42454 original size:24 final size:24
Alignment explanation
Indices: 42377--42456 Score: 103
Period size: 24 Copynumber: 3.4 Consensus size: 24
42367 CACAAATGAG
*
42377 CGAACATAAACGAAC-AGATGTAAA
1 CGAACACAAACGAACGA-ATGTAAA
*
42401 CGAACACAATA--AACGAACGTAAA
1 CGAACACAA-ACGAACGAATGTAAA
42424 CGAACACAAACGAACGAATGTAAA
1 CGAACACAAACGAACGAATGTAAA
42448 CGAACACAA
1 CGAACACAA
42457 CAAATAAACA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
22 1 0.02
23 18 0.37
24 29 0.59
25 1 0.02
ACGTcount: A:0.55, C:0.21, G:0.15, T:0.09
Consensus pattern (24 bp):
CGAACACAAACGAACGAATGTAAA
Found at i:42683 original size:14 final size:14
Alignment explanation
Indices: 42666--42716 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
42656 ATAAACGCAT
42666 ATAAACGAATAAAC
1 ATAAACGAATAAAC
42680 ATAAACGAATAAAC
1 ATAAACGAATAAAC
** *
42694 ATAAATAAATGAAC
1 ATAAACGAATAAAC
42708 ATAAACGAA
1 ATAAACGAA
42717 CATATTACCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.65, C:0.12, G:0.08, T:0.16
Consensus pattern (14 bp):
ATAAACGAATAAAC
Found at i:49853 original size:37 final size:36
Alignment explanation
Indices: 49782--49853 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
49772 TATATTTTTT
*
49782 ATTTTATAAAAAAATTATATAAATATTATGAATTTA
1 ATTTTATAAAAAAATTATATAAATATTATCAATTTA
* *
49818 ATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTATAAA-AAAATTATATAAATATTAT-CAATTT
49854 GTAATATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 22 0.71
37 9 0.29
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (36 bp):
ATTTTATAAAAAAATTATATAAATATTATCAATTTA
Found at i:50773 original size:65 final size:65
Alignment explanation
Indices: 50669--50796 Score: 229
Period size: 65 Copynumber: 2.0 Consensus size: 65
50659 CACCACTCTC
50669 GATCACCCTCAAACAACGACGAAAAGTAAAGCAATATCCTTTGCTATTTTCATTAGTAATTTAGT
1 GATCACCCTCAAACAACGACGAAAAGTAAAGCAATATCCTTTGCTATTTTCATTAGTAATTTAGT
** *
50734 GATCACCCTCAAACCGCGACGAGAAGTAAAGCAATATCCTTTGCTATTTTCATTAGTAATTTA
1 GATCACCCTCAAACAACGACGAAAAGTAAAGCAATATCCTTTGCTATTTTCATTAGTAATTTA
50797 CTGTGCGACA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.30
Consensus pattern (65 bp):
GATCACCCTCAAACAACGACGAAAAGTAAAGCAATATCCTTTGCTATTTTCATTAGTAATTTAGT
Found at i:69951 original size:20 final size:19
Alignment explanation
Indices: 69922--69960 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
69912 TTACATTCTG
69922 TCTTAGGGGTTTCAAAACC
1 TCTTAGGGGTTTCAAAACC
*
69941 TCTTGAGGGGTTTCGAAACC
1 TCTT-AGGGGTTTCAAAACC
69961 ATACCCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (19 bp):
TCTTAGGGGTTTCAAAACC
Done.