Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009270.1 Hibiscus syriacus cultivar Beakdansim tig00112929_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: 41350
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Found at i:57 original size:13 final size:13
Alignment explanation
Indices: 35--70 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
25 ACGAGTCGGT
35 CGGG-CGGGTCAA
1 CGGGTCGGGTCAA
47 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
60 CGGGTCGGGTC
1 CGGGTCGGGTC
71 GGGTTGTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.11, C:0.25, G:0.50, T:0.14
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:63 original size:21 final size:20
Alignment explanation
Indices: 11--65 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1 CGCCGGTCAA
*
11 CGGTCAACGGGTTAACGAGT
1 CGGTCAACGGGTCAACGAGT
** *
31 CGGTCGGGCGGGTCAACGGGT
1 CGGTC-AACGGGTCAACGAGT
52 CGGGTCAACGGGTC
1 C-GGTCAACGGGTC
66 GGGTCGGGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 5 0.19
21 18 0.67
22 4 0.15
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (20 bp):
CGGTCAACGGGTCAACGAGT
Found at i:2123 original size:23 final size:24
Alignment explanation
Indices: 2097--2145 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
2087 ATCAAAACAT
*
2097 AAATCAGGTCAAGT-ATATATCAG
1 AAATCAGGTCAAGTAACATATCAG
2120 AAATCAGGTCAAGTAACATATCAG
1 AAATCAGGTCAAGTAACATATCAG
2144 AA
1 AA
2146 TCCAAGTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.22
Consensus pattern (24 bp):
AAATCAGGTCAAGTAACATATCAG
Found at i:2147 original size:23 final size:23
Alignment explanation
Indices: 2098--2171 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 23
2088 TCAAAACATA
*
2098 AATCAGGTCAAGT-ATATATCAG
1 AATCAGGTCAAGTAACATATCAG
2120 AAATCAGGTCAAGTAACATATCAG
1 -AATCAGGTCAAGTAACATATCAG
* * * *
2144 AATCCAAGTCATGTATCAGATCAG
1 AAT-CAGGTCAAGTAACATATCAG
2168 AATC
1 AATC
2172 CATGTCAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
23 17 0.39
24 27 0.61
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (23 bp):
AATCAGGTCAAGTAACATATCAG
Found at i:2154 original size:24 final size:24
Alignment explanation
Indices: 2127--2198 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
2117 CAGAAATCAG
*
2127 GTCAAGTAACATATCAGAATCCAA
1 GTCAAGTAACAGATCAGAATCCAA
* * *
2151 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTAACAGATCAGAATCCAA
*
2175 GTC-AGATATCAGATCAGAATCCAA
1 GTCAAG-TAACAGATCAGAATCCAA
2199 ATCGAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTAACAGATCAGAATCCAA
Found at i:4707 original size:12 final size:13
Alignment explanation
Indices: 4690--4724 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
4680 ACGAGTCGGT
4690 CGGGTCGGGTC-A
1 CGGGTCGGGTCAA
4702 CGGGTC-GGTCAA
1 CGGGTCGGGTCAA
4714 CGGGTCGGGTC
1 CGGGTCGGGTC
4725 GGGTTGTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 13 0.62
13 4 0.19
ACGTcount: A:0.09, C:0.26, G:0.49, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:6747 original size:24 final size:24
Alignment explanation
Indices: 6716--6788 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
6706 ATCAAAACAT
6716 AATCAGGTCAAGTATCATATCAGA
1 AATCAGGTCAAGTATCATATCAGA
* *
6740 AATCAGGTAAAGTAACATATCAG-
1 AATCAGGTCAAGTATCATATCAGA
* * *
6763 AATCCAAGTCATGTATCAGATCAGA
1 AAT-CAGGTCAAGTATCATATCAGA
6788 A
1 A
6789 TCCATGTCAG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 3 0.08
24 36 0.90
25 1 0.03
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (24 bp):
AATCAGGTCAAGTATCATATCAGA
Found at i:6790 original size:24 final size:24
Alignment explanation
Indices: 6758--6817 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
6748 AAAGTAACAT
6758 ATCAGAATCCAAGTCATG-TATCAG
1 ATCAGAATCCAAGTCA-GATATCAG
*
6782 ATCAGAATCCATGTCAGATATCAG
1 ATCAGAATCCAAGTCAGATATCAG
6806 ATCAGAATCCAA
1 ATCAGAATCCAA
6818 ATCGAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (24 bp):
ATCAGAATCCAAGTCAGATATCAG
Found at i:12670 original size:65 final size:65
Alignment explanation
Indices: 12566--12726 Score: 184
Period size: 65 Copynumber: 2.5 Consensus size: 65
12556 GAATTAAATT
* * * * *
12566 AAACATAGAATGCATTTCATGCATTGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTAT
1 AAACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATACACTCAGGATATTT-T
12629 G
65 G
* * * *
12630 AAAACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATACACTCTGGCTATTTT
1 -AAACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATACACTCAGGATATTTT
12694 G
65 G
**
12695 AAACATCGAATGCACATGATGCATCGATGCAC
1 AAACATCGAATGCATTTGATGCATCGATGCAC
12727 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 30 0.36
65 48 0.58
66 5 0.06
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (65 bp):
AAACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATACACTCAGGATATTTTG
Found at i:17126 original size:12 final size:12
Alignment explanation
Indices: 17109--17133 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17099 GTTCTTAAAT
17109 TGACAAAAGCGC
1 TGACAAAAGCGC
17121 TGACAAAAGCGC
1 TGACAAAAGCGC
17133 T
1 T
17134 TTATGGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (12 bp):
TGACAAAAGCGC
Found at i:18525 original size:24 final size:24
Alignment explanation
Indices: 18497--18576 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
18487 CACTTAACAA
18497 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
18521 TGCATCGATTCAT-CATGTTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
*
18542 TGCACCGATGCA-CGCC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
18565 TGCATCGATGCA
1 TGCATCGATGCA
18577 CAGGGTCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.25
22 1 0.02
23 14 0.32
24 15 0.34
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:24368 original size:11 final size:11
Alignment explanation
Indices: 24352--24383 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
24342 TTATTATACT
*
24352 ATTTTAATAAC
1 ATTTTAATAAA
24363 ATTTTAATAAA
1 ATTTTAATAAA
24374 ATTTTAATAA
1 ATTTTAATAA
24384 TTAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTTAATAAA
Found at i:24616 original size:17 final size:17
Alignment explanation
Indices: 24596--24630 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
24586 ATTTAAATAA
*
24596 TAAAGTTTTTAATATTT
1 TAAAATTTTTAATATTT
*
24613 TAAAATTTTTATTATTT
1 TAAAATTTTTAATATTT
24630 T
1 T
24631 CTAATCTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TAAAATTTTTAATATTT
Found at i:30249 original size:2 final size:2
Alignment explanation
Indices: 30244--30271 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30234 AGAAAAAATA
30244 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
30272 CAAGAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33473 original size:2 final size:2
Alignment explanation
Indices: 33466--33506 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
33456 CAGAAAAATA
33466 AT AT AT AT AT AT AT AT AT A- 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
33507 CAAGAATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33487 original size:19 final size:19
Alignment explanation
Indices: 33463--33503 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
33453 TTTCAGAAAA
33463 ATAATATATATATATATAT
1 ATAATATATATATATATAT
33482 ATAATATATATATATATAT
1 ATAATATATATATATATAT
33501 ATA
1 ATA
33504 TATCAAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAATATATATATATATAT
Done.