Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003804.1 Hibiscus syriacus cultivar Beakdansim tig00008142_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: 64751
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:4161 original size:21 final size:22
Alignment explanation
Indices: 4106--4162 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
4096 TAACAAAATT
4106 CAATGTAACACATTATTTTAAA
1 CAATGTAACACATTATTTTAAA
*
4128 CAATGCAACACATTA-TTTAAA
1 CAATGTAACACATTATTTTAAA
*
4149 GAA-GTAACAACATT
1 CAATGTAAC-ACATT
4163 CAATGTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 13 0.42
22 14 0.45
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (22 bp):
CAATGTAACACATTATTTTAAA
Found at i:4182 original size:126 final size:126
Alignment explanation
Indices: 4000--4230 Score: 462
Period size: 126 Copynumber: 1.8 Consensus size: 126
3990 TCCAATATTT
4000 AACAATGCAACACATTATTTAAAGAAGTAACAACATTCAATGTAATATTATCACTTTACCTGTAT
1 AACAATGCAACACATTATTTAAAGAAGTAACAACATTCAATGTAATATTATCACTTTACCTGTAT
4065 ACCATCCATGTTACTATAAAACAACATGATATAACAAAATTCAATGTAACACATTATTTTA
66 ACCATCCATGTTACTATAAAACAACATGATATAACAAAATTCAATGTAACACATTATTTTA
4126 AACAATGCAACACATTATTTAAAGAAGTAACAACATTCAATGTAATATTATCACTTTACCTGTAT
1 AACAATGCAACACATTATTTAAAGAAGTAACAACATTCAATGTAATATTATCACTTTACCTGTAT
4191 ACCATCCATGTTACTATAAAACAACATGATATAACAAAAT
66 ACCATCCATGTTACTATAAAACAACATGATATAACAAAAT
4231 ATAAAATTTC
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 105 1.00
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (126 bp):
AACAATGCAACACATTATTTAAAGAAGTAACAACATTCAATGTAATATTATCACTTTACCTGTAT
ACCATCCATGTTACTATAAAACAACATGATATAACAAAATTCAATGTAACACATTATTTTA
Found at i:7488 original size:15 final size:15
Alignment explanation
Indices: 7468--7582 Score: 167
Period size: 15 Copynumber: 7.7 Consensus size: 15
7458 ATGTTGTTAG
*
7468 TATGTGAATATGTTA
1 TATGTGAATATGTTC
*
7483 TATGTGAATATATTC
1 TATGTGAATATGTTC
* *
7498 TACGTGAAAATGTTC
1 TATGTGAATATGTTC
7513 TATGTGAATATGTTC
1 TATGTGAATATGTTC
* *
7528 TACGTGAAAATGTTC
1 TATGTGAATATGTTC
7543 TATGTGAATATGTTC
1 TATGTGAATATGTTC
*
7558 TATGTGAATGTGTTC
1 TATGTGAATATGTTC
7573 TATGTGAATA
1 TATGTGAATA
7583 AATGATACTT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 87 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (15 bp):
TATGTGAATATGTTC
Found at i:13133 original size:15 final size:15
Alignment explanation
Indices: 13113--13196 Score: 114
Period size: 15 Copynumber: 5.6 Consensus size: 15
13103 TTTTATTAGG
* *
13113 ATGTGAAAATGTTTT
1 ATGTGAATATGTTCT
13128 ATGTGAATATGTTCT
1 ATGTGAATATGTTCT
* *
13143 ACGTGAAAATGTTCT
1 ATGTGAATATGTTCT
*
13158 ATGTGAATATGTTTT
1 ATGTGAATATGTTCT
*
13173 ATGTGAATGTGTTCT
1 ATGTGAATATGTTCT
13188 ATGTGAATA
1 ATGTGAATA
13197 AATGATACTT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (15 bp):
ATGTGAATATGTTCT
Found at i:13338 original size:23 final size:23
Alignment explanation
Indices: 13312--13373 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
13302 TACGCAGTCC
*
13312 TTCGGGACAATTCTATGTGGTCA
1 TTCGGGACAATTCTATGCGGTCA
* * *
13335 TTCGGGACTATTCTACGCGGTCC
1 TTCGGGACAATTCTATGCGGTCA
* *
13358 TTTGGGACAAATCTAT
1 TTCGGGACAATTCTAT
13374 ATGGCACTTC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (23 bp):
TTCGGGACAATTCTATGCGGTCA
Found at i:13366 original size:46 final size:47
Alignment explanation
Indices: 13299--13398 Score: 125
Period size: 46 Copynumber: 2.1 Consensus size: 47
13289 GAGTCGAGGG
* *
13299 TTCTACGCAGTCCTTCGGGACAATTCTATGTGGTCA-TTCGG-G-ACTA
1 TTCTACGCAGTCCTTCGGGACAAATCTATATGG-CACTTCGGTGCA-TA
* *
13345 TTCTACGCGGTCCTTTGGGACAAATCTATATGGCACTTCGGTGCATA
1 TTCTACGCAGTCCTTCGGGACAAATCTATATGGCACTTCGGTGCATA
13392 TTCTACG
1 TTCTACG
13399 TGGCAATTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
45 2 0.04
46 34 0.72
47 10 0.21
48 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (47 bp):
TTCTACGCAGTCCTTCGGGACAAATCTATATGGCACTTCGGTGCATA
Found at i:13402 original size:24 final size:24
Alignment explanation
Indices: 13375--13427 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
13365 CAAATCTATA
* *
13375 TGGCACTTCGGTGCATATTCTACG
1 TGGCAATTCGGTGCAAATTCTACG
13399 TGGCAATTCGGTGCAAATTCTACG
1 TGGCAATTCGGTGCAAATTCTACG
13423 TGGCA
1 TGGCA
13428 GTTTTGACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (24 bp):
TGGCAATTCGGTGCAAATTCTACG
Found at i:15610 original size:24 final size:23
Alignment explanation
Indices: 15554--15610 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
15544 CTTTAATCTG
15554 AATTAT-AT-TTTATAAATACAT
1 AATTATAATATTTATAAATACAT
* * *
15575 -ATTAAAAGATTTATAATTACAAT
1 AATTATAATATTTATAAATAC-AT
15598 AATTATAATATTT
1 AATTATAATATTT
15611 TTTGATATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
20 4 0.15
21 1 0.04
22 10 0.37
23 2 0.07
24 10 0.37
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTATAATATTTATAAATACAT
Found at i:24249 original size:17 final size:18
Alignment explanation
Indices: 24222--24260 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
24212 TGTAGGACCA
24222 AAGTAGAAAGTGAAAGCC
1 AAGTAGAAAGTGAAAGCC
24240 AAGT-GAAAGTGAAAGCC
1 AAGTAGAAAGTGAAAGCC
24257 AAGT
1 AAGT
24261 TGATTCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.49, C:0.10, G:0.28, T:0.13
Consensus pattern (18 bp):
AAGTAGAAAGTGAAAGCC
Found at i:43343 original size:44 final size:45
Alignment explanation
Indices: 43252--43349 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
43242 ATACTTTGGG
* *
43252 AATAAGTT-GGTAATGCTGGTAATAGCTCCAATATAGACATAGGA
1 AATAAGTTGGGTAATGCTGGTAATAGCTCCAACATAGACAGAGGA
* ** *
43296 AATAAGTTGGGTAATGCTGGTAATAGCTCCACCATAGTGAGA-TA
1 AATAAGTTGGGTAATGCTGGTAATAGCTCCAACATAGACAGAGGA
43340 AATAAGTTGG
1 AATAAGTTGG
43350 ATTTCCAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 19 0.40
45 28 0.60
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (45 bp):
AATAAGTTGGGTAATGCTGGTAATAGCTCCAACATAGACAGAGGA
Found at i:52888 original size:15 final size:15
Alignment explanation
Indices: 52868--52897 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52858 TGAAAGTTAT
*
52868 GAAAAGAATCTGAAA
1 GAAAAGAATATGAAA
52883 GAAAAGAATATGAAA
1 GAAAAGAATATGAAA
52898 ATGAAAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.03, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAAAGAATATGAAA
Found at i:54891 original size:25 final size:25
Alignment explanation
Indices: 54836--54898 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
54826 ATAAGTCTAG
*
54836 ATTCAATATTTTGATACATGATCACA
1 ATTC-ATATTATGATACATGATCACA
* *
54862 TTTCATATTATGATACATGA-CATGA
1 ATTCATATTATGATACATGATCA-CA
54887 ATTCATATTATG
1 ATTCATATTATG
54899 CATTAAGTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 2 0.06
25 27 0.84
26 3 0.09
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCACA
Found at i:54976 original size:31 final size:30
Alignment explanation
Indices: 54938--54997 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
54928 TTATATAAGA
54938 TATGTGATAAA-GTGATGGAACATGATATGTT
1 TATGTGATAAAGGT-ATGGAA-ATGATATGTT
*
54969 TATGTGATAAAGGTATGGAAATTATATGT
1 TATGTGATAAAGGTATGGAAATGATATGT
54998 CTATACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 17 0.63
32 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATGATATGTT
Found at i:55251 original size:23 final size:23
Alignment explanation
Indices: 55225--55276 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
55215 TTATATGGCA
*
55225 CGGTGCAATTCTACGCGGTACTT
1 CGGTGCAATTCTACGCGGCACTT
*
55248 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTT
55271 CGGTGC
1 CGGTGC
55277 GTTTATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTT
Found at i:61040 original size:19 final size:19
Alignment explanation
Indices: 61016--61062 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
61006 ATGCCATCAA
61016 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
61035 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
61054 TGCATCGAT
1 TGCATCGAT
61063 ACACCCCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:61789 original size:23 final size:23
Alignment explanation
Indices: 61757--61802 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
61747 TATGGTACTA
*
61757 TGGTATAATTCTACGCGGCACTT
1 TGGTACAATTCTACGCGGCACTT
*
61780 TGGTACAATTCTACGTGGCACTT
1 TGGTACAATTCTACGCGGCACTT
61803 CGGTGCGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (23 bp):
TGGTACAATTCTACGCGGCACTT
Done.