Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003295.1 Hibiscus syriacus cultivar Beakdansim tig00006930_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: 39668
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:42 original size:12 final size:12
Alignment explanation
Indices: 25--53 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
15 GGTCAATGAA
25 GATGAAGCTGAC
1 GATGAAGCTGAC
37 GATGAAGCTGAC
1 GATGAAGCTGAC
49 GATGA
1 GATGA
54 TGATGATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.17
Consensus pattern (12 bp):
GATGAAGCTGAC
Found at i:1613 original size:183 final size:183
Alignment explanation
Indices: 1264--2200 Score: 1581
Period size: 183 Copynumber: 5.1 Consensus size: 183
1254 CAAAGTTTTC
*
1264 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * * * *
1329 CAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTATAA
66 CAAAAAGTGTCGACATT---TACACATCGGAACTCAGAATTATAATGTAATAGATAATTTTGTAA
*
1392 TATAATCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
1448 ACACTTTTTAATATTGTGTCAGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
1513 CAAAAAGTGTCGACATTTACACATCGGAACTCATAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACTCAGAATTATAATGTAATAGATAATTTTGTAATAT
* * *
1578 AACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
1631 ACACTTTTTAATATTGTGTCGGTACTTTATGTACAGAATGGAAGAAAAATGTGTGGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * *
1696 CAAAAAGTGTCGACATTTACACTTCGGTACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACTCAGAATTATAATGTAATAGATAATTTTGTAATAT
** *
1761 AACCGGTATAAATATACATGTTTTATGAGCGAATAGGTATACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
1814 ACACTTTTTAATACTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
1879 CAAAAAGTGTCTACATTTACACATCGGAACTCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACTCAGAATTATAATGTAATAGATAATTTTGTAATAT
* * *
1944 AACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
1997 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGAAAGAAAAATGTATCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
2062 CAAAAAGTGTCGACATTTACACATCGAAACTCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACTCAGAATTATAATGTAATAGATAATTTTGTAATAT
2127 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
2180 ACACTTTTTAATATTGTGTCG
1 ACACTTTTTAATATTGTGTCG
2201 CTAATTTTAA
Statistics
Matches: 707, Mismatches: 44, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
183 629 0.89
184 75 0.11
186 3 0.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACTCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:5566 original size:23 final size:23
Alignment explanation
Indices: 5537--5584 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5527 AAACAGGTCA
*
5537 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCTAATATATT
*
5560 ATATAAGCGCTACCTAATATGTT
1 ATATAAGCGCTACCTAATATATT
5583 AT
1 AT
5585 TGTACTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:5635 original size:87 final size:87
Alignment explanation
Indices: 5537--5776 Score: 426
Period size: 87 Copynumber: 2.8 Consensus size: 87
5527 AAACAGGTCA
* *
5537 ATATAAGCGCTACCTATTATATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTATATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
5602 CCCGTTAAATACCTATTTTATT
66 CCCGTTAAATACCTATTTTATT
*
5624 ATATAAGCGCTATCTATTATATTATATAAGCGTTACCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGCTATCTATTATATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
5689 CCCGTTAAATACCTATTTTATT
66 CCCGTTAAATACCTATTTTATT
* * *
5711 ATATAAACACTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTATATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
5776 C
66 C
5777 TGGATAAATA
Statistics
Matches: 146, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 146 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTATCTATTATATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
CCCGTTAAATACCTATTTTATT
Found at i:5671 original size:23 final size:23
Alignment explanation
Indices: 5611--5671 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
5601 TCCCGTTAAA
* *
5611 TACCTATTTTATTATATAAGCGC
1 TACCTAATATATTATATAAGCGC
* * *
5634 TATCTATTATATTATATAAGCGT
1 TACCTAATATATTATATAAGCGC
*
5657 TACCTAATATGTTAT
1 TACCTAATATATTAT
5672 TGTACTTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (23 bp):
TACCTAATATATTATATAAGCGC
Found at i:6278 original size:17 final size:19
Alignment explanation
Indices: 6256--6298 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
6246 AATATAGTGA
6256 TTTTAAAAT-TTATTAT-T
1 TTTTAAAATATTATTATAT
6273 TTTT-AAATATTATTATAT
1 TTTTAAAATATTATTATAT
*
6291 TTATAAAA
1 TTTTAAAA
6299 AAAATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.18
17 11 0.50
18 4 0.18
19 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTAAAATATTATTATAT
Found at i:8976 original size:30 final size:29
Alignment explanation
Indices: 8883--8972 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 29
8873 AAACGGACTT
*
8883 AGTTTGGTGACCAAATTATAAGATTTTAAA
1 AGTTTGGTGACCAAAATATAA-ATTTTAAA
* *
8913 AGTTTGGTGACCAAAGTATAAACTTTGAAA
1 AGTTTGGTGACCAAAATATAAA-TTTTAAA
8943 AGTTTAGG-GACCAAAATAGT-AATTTTAAA
1 AGTTT-GGTGACCAAAATA-TAAATTTTAAA
8972 A
1 A
8973 AGTTACAGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.15
30 42 0.79
31 3 0.06
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (29 bp):
AGTTTGGTGACCAAAATATAAATTTTAAA
Found at i:11820 original size:28 final size:28
Alignment explanation
Indices: 11780--11845 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
11770 AATATATTAT
* *
11780 ATGATATGTTACAAATGTTAAGTACAAG
1 ATGACATGTTACAAAGGTTAAGTACAAG
11808 ATGACATGTTACAAAGGTTAAGTACAAG
1 ATGACATGTTACAAAGGTTAAGTACAAG
11836 ATGACATGTT
1 ATGACATGTT
11846 TTAAATGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (28 bp):
ATGACATGTTACAAAGGTTAAGTACAAG
Found at i:14831 original size:53 final size:49
Alignment explanation
Indices: 14745--14846 Score: 141
Period size: 53 Copynumber: 2.0 Consensus size: 49
14735 AGAACGATAA
*
14745 CAGTAATATATATCAATTATAGATGGATGTTTTGTTAAATGTGGATCTT
1 CAGTAATATATATCAATTATAGATGGATGTTTTGTTAAATGTGAATCTT
* *
14794 CAGTAATATATATCATGAAATTGTAGATGGATGTTTTGTTACATGTGAATCTT
1 CAGTAATATATATC----AATTATAGATGGATGTTTTGTTAAATGTGAATCTT
14847 ACTTTTAGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
49 14 0.30
53 32 0.70
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (49 bp):
CAGTAATATATATCAATTATAGATGGATGTTTTGTTAAATGTGAATCTT
Found at i:21238 original size:2 final size:2
Alignment explanation
Indices: 21231--21281 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
21221 ATGCTATTTA
21231 AT AT AT AT AT 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
21273 AT AT AT AT A
1 AT AT AT AT A
21282 CAACAAACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22213 original size:2 final size:2
Alignment explanation
Indices: 22208--22234 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22198 CTCTCTTTGT
22208 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 T
22235 GGATGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33629 original size:11 final size:11
Alignment explanation
Indices: 33613--33646 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
33603 AGGATGGACA
33613 TGGGTCGGGTT
1 TGGGTCGGGTT
33624 TGGGTCGGGTT
1 TGGGTCGGGTT
*
33635 TAGGTCGGGTT
1 TGGGTCGGGTT
33646 T
1 T
33647 TGGCCAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.03, C:0.09, G:0.50, T:0.38
Consensus pattern (11 bp):
TGGGTCGGGTT
Found at i:34822 original size:59 final size:59
Alignment explanation
Indices: 34726--34841 Score: 133
Period size: 59 Copynumber: 2.0 Consensus size: 59
34716 ACAGTTGGGT
* * * *
34726 GACTATTTTATAACTTTTAATAGCTGGGGAATCAACAAAGCAACATCCTATAATTGATG
1 GACTATTTTATAACTTTTAATAACTGAGGAATCAACAAAACAACATCATATAATTGATG
* * * * * * *
34785 GACTATTTTGTAATTTTTAATAATTGAGGATTTAACAAAATAATATCATATAATTGA
1 GACTATTTTATAACTTTTAATAACTGAGGAATCAACAAAACAACATCATATAATTGA
34842 GGGGACCATT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (59 bp):
GACTATTTTATAACTTTTAATAACTGAGGAATCAACAAAACAACATCATATAATTGATG
Found at i:35173 original size:11 final size:11
Alignment explanation
Indices: 35141--35175 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
35131 TTTATTTAGT
35141 TTTTAAAAATAA
1 TTTT-AAAATAA
35153 TTTGTAAAATAA
1 TTT-TAAAATAA
35165 TTTTAAAATAA
1 TTTTAAAATAA
35176 AAAAATAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.36
12 13 0.59
13 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (11 bp):
TTTTAAAATAA
Done.