Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000591.1 Hibiscus syriacus cultivar Beakdansim tig00001147_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: 60970
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:5393 original size:2 final size:2
Alignment explanation
Indices: 5386--5417 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5376 CATCCAGGAA
5386 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5418 TTATTAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16951 original size:14 final size:14
Alignment explanation
Indices: 16920--16962 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
16910 CTAAAACCCT
* *
16920 CTCTCTCTCTCCCG
1 CTCTCTCTCTCACA
*
16934 CTCTCTCTCTGACA
1 CTCTCTCTCTCACA
16948 CTCTCTCTCATCACA
1 CTCTCTCTC-TCACA
16963 GGTGAATAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.12, C:0.49, G:0.05, T:0.35
Consensus pattern (14 bp):
CTCTCTCTCTCACA
Found at i:17034 original size:12 final size:12
Alignment explanation
Indices: 17017--17075 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
17007 ATTTTTCTCC
17017 CTTTCTTCTTTT
1 CTTTCTTCTTTT
17029 CTTTCTT-TATTT
1 CTTTCTTCT-TTT
*
17041 CTTCCTTCTTTT
1 CTTTCTTCTTTT
*
17053 -TTTCTT-TTCT
1 CTTTCTTCTTTT
*
17063 -TTTCTACTTTT
1 CTTTCTTCTTTT
17074 CT
1 CT
17076 CTACCAACTC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
10 8 0.21
11 9 0.24
12 20 0.53
13 1 0.03
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTCTTCTTTT
Found at i:17215 original size:16 final size:16
Alignment explanation
Indices: 17196--17227 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17186 TCAAGTAAGA
17196 AATGTTCCTCAAATGC
1 AATGTTCCTCAAATGC
17212 AATGTTCCTCAAATGC
1 AATGTTCCTCAAATGC
17228 TCATTTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (16 bp):
AATGTTCCTCAAATGC
Found at i:22730 original size:26 final size:25
Alignment explanation
Indices: 22683--22735 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
22673 TTCCAACTTG
22683 TTTGGTATAAATAGATATTTTATATT
1 TTTGGTATAAATAGATATTTTA-ATT
*
22709 TTTGGATATAATTAGATA-TTTAATT
1 TTTGG-TATAAATAGATATTTTAATT
22734 TT
1 TT
22736 AAAATGCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 5 0.20
26 9 0.36
27 11 0.44
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (25 bp):
TTTGGTATAAATAGATATTTTAATT
Found at i:32074 original size:16 final size:18
Alignment explanation
Indices: 32055--32089 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
32045 ATATTTAGAT
32055 TAATTT-AAAT-TTAATA
1 TAATTTCAAATATTAATA
32071 TAATTTCAAATATTAATA
1 TAATTTCAAATATTAATA
32089 T
1 T
32090 TAAATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 4 0.24
18 7 0.41
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTTCAAATATTAATA
Found at i:40411 original size:11 final size:11
Alignment explanation
Indices: 40395--40423 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
40385 TAATATTAAA
40395 ATACAAAACGG
1 ATACAAAACGG
40406 ATACAAAACGG
1 ATACAAAACGG
40417 ATACAAA
1 ATACAAA
40424 CAATAACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.17, G:0.14, T:0.10
Consensus pattern (11 bp):
ATACAAAACGG
Found at i:45155 original size:29 final size:29
Alignment explanation
Indices: 45110--45167 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
45100 GTGTTGGTCG
*
45110 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
45139 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
45168 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:45231 original size:13 final size:14
Alignment explanation
Indices: 45213--45250 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
45203 TGGGCATCCG
45213 AGGCCATCCGACC-
1 AGGCCATCCGACCA
45226 AGGCCATCCGACCA
1 AGGCCATCCGACCA
*
45240 AGGCAATCCGA
1 AGGCCATCCGA
45251 GAGCATCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.29, C:0.39, G:0.24, T:0.08
Consensus pattern (14 bp):
AGGCCATCCGACCA
Found at i:45363 original size:29 final size:29
Alignment explanation
Indices: 45325--45381 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
45315 GAGCGAGGGT
* *
45325 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCCCCCGGAAGGCATGGCGACCTACA
45354 AGGTCCCCCGGAAGGCATGGCGACCTAC
1 AGGTCCCCCGGAAGGCATGGCGACCTAC
45382 GACCAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.33, G:0.35, T:0.11
Consensus pattern (29 bp):
AGGTCCCCCGGAAGGCATGGCGACCTACA
Found at i:47136 original size:150 final size:149
Alignment explanation
Indices: 46948--47253 Score: 540
Period size: 150 Copynumber: 2.0 Consensus size: 149
46938 CCGAAGTGCA
*
46948 GCGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATATAATTCCTTAAGAA
1 GCGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAA
* *
47013 TCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGTTCCACAGAATA
66 TCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGTTCCAAAGAATA
*
47078 TATATATATCCCGAAGGACC
130 TACATATATCCCGAAGGACC
*
47098 GCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAA
1 GCGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAA
*
47163 TCATATACATATACTAAGGATCAAGTATGTGTCTTTTAAGACTTCACACATGTTCCAAAGAATAT
66 TCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATAT
*
47228 ACATATGTCCCGAAGGACC
131 ACATATATCCCGAAGGACC
47247 GCGTAGA
1 GCGTAGA
47254 CCCTCTACCC
Statistics
Matches: 149, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
149 51 0.34
150 98 0.66
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
GCGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAA
TCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATAT
ACATATATCCCGAAGGACC
Found at i:56924 original size:2 final size:2
Alignment explanation
Indices: 56917--56964 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
56907 GTGATTTAAT
56917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56958 TA TA TA T
1 TA TA TA T
56965 CCTAATAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.