Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002006.1 Hibiscus syriacus cultivar Beakdansim tig00004103_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: 62592
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2479 original size:6 final size:6
Alignment explanation
Indices: 2428--2535 Score: 117
Period size: 6 Copynumber: 18.0 Consensus size: 6
2418 ATCAATTTCT
* * * * * * * *
2428 CAACCT CAACCT CAACCT CAACCT CAACCT CAACCT CAACCT CAGCCC
1 CAACCC CAACCC CAACCC CAACCC CAACCC CAACCC CAACCC CAACCC
* * *
2476 CAGCCC CAGCCC CAGCCC CAACCC CAACCC CAACCC CAACCC CAACCC
1 CAACCC CAACCC CAACCC CAACCC CAACCC CAACCC CAACCC CAACCC
2524 CAACCC CAACCC
1 CAACCC CAACCC
2536 ATGCAATAAT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 99 1.00
ACGTcount: A:0.30, C:0.60, G:0.04, T:0.06
Consensus pattern (6 bp):
CAACCC
Found at i:3167 original size:149 final size:149
Alignment explanation
Indices: 2975--3279 Score: 456
Period size: 151 Copynumber: 2.0 Consensus size: 149
2965 GTTTTTTTAG
* **
2975 TAAT-TAGAGGTTCTATAATACTAATTTTGTAAAACTTTATATTTTATT-TT-ATTTTAAAATAA
1 TAATATAGAGGTTCTATAATAATAATTTCATAAAACTTTATATTTT-TTATTCATTTTAAAATAA
* * *
3037 TTAGAAATATTAAACTCATCTATCTCAATAG-TAAAAGAAAAATTATTTTTCTTATAAGTTTTAA
65 TTAGAAATATTAAACCCATCTATCTCAA-AGATAAAAGAAAAATTATTTTTCTTACAAGTCTTAA
*
3101 AATCAATCAGTTACATCTATA
129 AATCAATAAGTTACATCTATA
* *
3122 TAGTATAGAGGTTGTTATAATAATAATTTCATAAAACTTTATATTTTTTATTGCATTTTAAAATA
1 TAATATAGAGGTT-CTATAATAATAATTTCATAAAACTTTATATTTTTTATT-CATTTTAAAATA
3187 ATTAGAAATATTAAACCCATCTATCTCAAAGATAAAAGAAAAATTATTTTTCTTACAAGTCTTAA
64 ATTAGAAATATTAAACCCATCTATCTCAAAGATAAAAGAAAAATTATTTTTCTTACAAGTCTTAA
*
3252 AATCAATAAGTTTCATCTATA
129 AATCAATAAGTTACATCTATA
3273 TAATATA
1 TAATATA
3280 TATGCGACTA
Statistics
Matches: 141, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
147 3 0.02
148 10 0.07
149 31 0.22
150 2 0.01
151 95 0.67
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (149 bp):
TAATATAGAGGTTCTATAATAATAATTTCATAAAACTTTATATTTTTTATTCATTTTAAAATAAT
TAGAAATATTAAACCCATCTATCTCAAAGATAAAAGAAAAATTATTTTTCTTACAAGTCTTAAAA
TCAATAAGTTACATCTATA
Found at i:6745 original size:55 final size:55
Alignment explanation
Indices: 6527--6948 Score: 396
Period size: 55 Copynumber: 7.8 Consensus size: 55
6517 CCACTGGGTT
* * * **
6527 TGCTCCCT-TTTGCTTCAGGGAGTATAAAACTCAAACAATCTTCATA-AAACAAGTC
1 TGCTCCCTATTT-CTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAAACGTGTC
* * * * *
6582 TGTTCTCTATTCCTTCAGAGAGTATAGGACT---A-AATCTTCAACAAATGTGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* * * *
6633 CGCTCCCCATTCCTTCAGAGAGTATAGGACT----CAATCTTCAATCAAACGTGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-CAAACGTGTC
* * * * *
6685 CGCTCCCTATTTTTTCAGAGAGTATATGACTTGAACAACCTTCAACAAACGTGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* * * * * **
6740 TGCTCCCTATTCCTTCAAAGAGTATAAGACTCAAATAATTTTCAACATTCGTGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* * * ** *
6795 TGCTCCCTATTTCTTCAGAGAGTATTAGACTCGAACAATTTTCAATATTCATGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* * * * *
6850 TGCTCCCTATTGCTTAAGAGAGTATGAGACTTGAACAATCTTCAACAATCGTGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* *
6905 TGCTCTCTATTTGTTCAGAGAGTATAAGACTCGAACAATCTTCA
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCA
6949 TTTGCTTCAC
Statistics
Matches: 307, Mismatches: 52, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
50 1 0.00
51 50 0.16
52 37 0.12
55 208 0.68
56 11 0.04
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (55 bp):
TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
Found at i:28200 original size:9 final size:10
Alignment explanation
Indices: 28171--28200 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28161 ACTTTCTCAT
28171 GTTTGTTCAA
1 GTTTGTTCAA
28181 GTTTGTTCAA
1 GTTTGTTCAA
28191 GTTT-TTCAA
1 GTTTGTTCAA
28200 G
1 G
28201 GGAATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (10 bp):
GTTTGTTCAA
Found at i:29303 original size:17 final size:17
Alignment explanation
Indices: 29281--29343 Score: 90
Period size: 17 Copynumber: 3.6 Consensus size: 17
29271 TATGGAATTT
29281 GATTCCAATTCTTGATA
1 GATTCCAATTCTTGATA
*
29298 GATTCCAATTCCTGATA
1 GATTCCAATTCTTGATA
* *
29315 GATTCCAATTCCTTCACA
1 GATTCCAATT-CTTGATA
29333 GATTCCAATTC
1 GATTCCAATTC
29344 CCTCATAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 27 0.66
18 14 0.34
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.37
Consensus pattern (17 bp):
GATTCCAATTCTTGATA
Found at i:35294 original size:2 final size:2
Alignment explanation
Indices: 35282--35319 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
35272 TATGATGAAG
35282 TA TA T- TA TA 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 TA TA TA TA TA T
35320 TAATAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:42490 original size:23 final size:24
Alignment explanation
Indices: 42446--42490 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
42436 TGGTATTAAT
*
42446 TTTCTAAAAGTAAAAAATAAAAAA
1 TTTCTAAAAGTAAAAAAAAAAAAA
*
42470 TTTCT-AAATTAAAAAAAAAAA
1 TTTCTAAAAGTAAAAAAAAAAA
42491 CTTAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (24 bp):
TTTCTAAAAGTAAAAAAAAAAAAA
Found at i:44320 original size:2 final size:2
Alignment explanation
Indices: 44315--44375 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
44305 ATATAATAAC
44315 TA TA TA 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 TA TA TA
44357 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
44376 TAAATTGTAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49691 original size:21 final size:22
Alignment explanation
Indices: 49650--49693 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
49640 CTCTTTAACA
*
49650 TTTTAATACATAATGTTTCAAT
1 TTTTAATACATAATGTCTCAAT
49672 TTTTAAT-CA-AATAGTCTCAAT
1 TTTTAATACATAAT-GTCTCAAT
49693 T
1 T
49694 GGATGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 10 0.50
22 7 0.35
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (22 bp):
TTTTAATACATAATGTCTCAAT
Found at i:53014 original size:60 final size:59
Alignment explanation
Indices: 52881--53015 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 59
52871 ATCCTTATAC
* * * ** *
52881 TTTAAATATTTTAA-TACATCATCAAATGATGTCTCTCATTTAAATTAGTCTTTAAATT
1 TTTAAATATTTTAATTTCATCATCAAATGAAGACTCTCATTTAAATTAGTCAATAAAGT
* * * *
52939 TTTAAACATTCTAATTTCATGC-TCAAATTAAGACTCTCATTCTAAATTGGTCAATAAAGT
1 TTTAAATATTTTAATTTCAT-CATCAAATGAAGACTCTCATT-TAAATTAGTCAATAAAGT
52999 TTTAAATATTTTAATTT
1 TTTAAATATTTTAATTT
53016 TATTTCCAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
58 12 0.19
59 20 0.32
60 30 0.48
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (59 bp):
TTTAAATATTTTAATTTCATCATCAAATGAAGACTCTCATTTAAATTAGTCAATAAAGT
Found at i:53275 original size:59 final size:60
Alignment explanation
Indices: 53140--53275 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 60
53130 GATCGAAACG
* * * * * * *
53140 TTAAAAAATTTAAAAAATAATTTAGAATGAAAGTCCTAATTTAAAGATGAAATTAAAATA
1 TTAAAAAATTTAAGAATTAATTTAGAATGAAAATCATAATCTAAAAATAAAATTAAAATA
* * *
53200 TTAAAAAATATGAGAATTAATTTATAAT-AAAATCATAATCTAAAAATAAAATTAAAATA
1 TTAAAAAATTTAAGAATTAATTTAGAATGAAAATCATAATCTAAAAATAAAATTAAAATA
*
53259 TTTAAAAATTTAAGAAT
1 TTAAAAAATTTAAGAAT
53276 AAGAGTTAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 40 0.63
60 23 0.37
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (60 bp):
TTAAAAAATTTAAGAATTAATTTAGAATGAAAATCATAATCTAAAAATAAAATTAAAATA
Done.