Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001057.1 Hibiscus syriacus cultivar Beakdansim tig00002092_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: 94602
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5734 original size:21 final size:21
Alignment explanation
Indices: 5705--5753 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
5695 ATTGTCACTA
*
5705 CATGTTCTTGGATAAGTTGGT
1 CATGATCTTGGATAAGTTGGT
*
5726 CATGATCTTGGATAGGTTGGT
1 CATGATCTTGGATAAGTTGGT
5747 CATGATC
1 CATGATC
5754 ATACATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.12, G:0.29, T:0.39
Consensus pattern (21 bp):
CATGATCTTGGATAAGTTGGT
Found at i:13932 original size:18 final size:18
Alignment explanation
Indices: 13909--13997 Score: 151
Period size: 18 Copynumber: 4.9 Consensus size: 18
13899 ATATAACACA
*
13909 TATGTCTCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
13927 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
*
13945 TATGTCCCGAAAGACCAC
1 TATGTCCCGAAGGACCAC
*
13963 TATGTCCCGAAAGACCAC
1 TATGTCCCGAAGGACCAC
13981 TATGTCCCGAAGGACCA
1 TATGTCCCGAAGGACCA
13998 TATAGACCCT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.18
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:14835 original size:19 final size:19
Alignment explanation
Indices: 14811--14860 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
14801 CCTTGACGGG
14811 TGCATCGGTGCACTATCTA
1 TGCATCGGTGCACTATCTA
*
14830 TGCATCGGTGCGCTATCTA
1 TGCATCGGTGCACTATCTA
*
14849 TGCATCAGTGCA
1 TGCATCGGTGCA
14861 TAAATCTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (19 bp):
TGCATCGGTGCACTATCTA
Found at i:28757 original size:16 final size:17
Alignment explanation
Indices: 28736--28778 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
28726 CCTCAAACAG
28736 ACCCAAACCTAAATT-A
1 ACCCAAACCTAAATTAA
* *
28752 ACCCAACCCCAAATTAA
1 ACCCAAACCTAAATTAA
*
28769 ACCCAGACCT
1 ACCCAAACCT
28779 GAGGCCCAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.44, C:0.40, G:0.02, T:0.14
Consensus pattern (17 bp):
ACCCAAACCTAAATTAA
Found at i:31304 original size:18 final size:18
Alignment explanation
Indices: 31277--31316 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31267 AACTTGGTAT
*
31277 TTTTATAAAAATAAAATG
1 TTTTACAAAAATAAAATG
* *
31295 TTTTACAAAAATCACATG
1 TTTTACAAAAATAAAATG
31313 TTTT
1 TTTT
31317 TATGGTGTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (18 bp):
TTTTACAAAAATAAAATG
Found at i:41726 original size:6 final size:5
Alignment explanation
Indices: 41696--41725 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
41686 TTTTCGTTCT
41696 TTTTA TTTTA TTTTA TTTTA TTTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT
41726 TTCCCTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:45428 original size:20 final size:20
Alignment explanation
Indices: 45405--45443 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
45395 TTTACATCCG
45405 ATTCTTT-ATTTTTGCTAATT
1 ATTCTTTGATTTTT-CTAATT
45425 ATTCTTTGATTTTTCTAAT
1 ATTCTTTGATTTTTCTAAT
45444 GTTACTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.21, C:0.10, G:0.05, T:0.64
Consensus pattern (20 bp):
ATTCTTTGATTTTTCTAATT
Found at i:51933 original size:24 final size:24
Alignment explanation
Indices: 51905--51951 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
51895 TTATCTTAAT
51905 GGCCTTTTCTAGTATTTAGAAATG
1 GGCCTTTTCTAGTATTTAGAAATG
* * *
51929 GGCCTTTTTTATTATTTGGAAAT
1 GGCCTTTTCTAGTATTTAGAAAT
51952 TGTTAGTAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (24 bp):
GGCCTTTTCTAGTATTTAGAAATG
Found at i:52428 original size:31 final size:31
Alignment explanation
Indices: 52386--52473 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
52376 ATTCGAGGAC
52386 TAAATTAATATTTTATCTAAAGTTTAAAGGT
1 TAAATTAATATTTTATCTAAAGTTTAAAGGT
* **
52417 TAATTTAATATTTTATCTAACA-TTTAGGGGT
1 TAAATTAATATTTTATCTAA-AGTTTAAAGGT
* *
52448 TAAATTAGTATTTTTTTCTAAAGTTT
1 TAAATTAATA-TTTTATCTAAAGTTT
52474 GAAGACAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
31 35 0.73
32 13 0.27
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (31 bp):
TAAATTAATATTTTATCTAAAGTTTAAAGGT
Found at i:57185 original size:6 final size:6
Alignment explanation
Indices: 57174--57202 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
57164 CCCTACGGCC
57174 TTTCCT TTTCCT TTTCCT TTTCCT TTTCC
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCC
57203 CTCTATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTCCT
Found at i:87576 original size:123 final size:123
Alignment explanation
Indices: 87398--87666 Score: 420
Period size: 123 Copynumber: 2.2 Consensus size: 123
87388 TAATTAGAAT
*
87398 CTAAATTTTCAA-TTTTTCAAAACCATGTTAACATTTAATTTTTGTTTTATTTTAGTACTTACTG
1 CTAAATTTT-AATTTTTTCAAAACCATGTTAACATTTAATTTTTGTTTTATTTTAGTACTTACCG
*
87462 TTAAAAACTTAATGCATGTATTTAATACCTT-AATTATTAGTTTTAGCCTGTTTTAGTAC
65 TTAAAAACTTAATGCATGTATTTAATA-CTTAAACTATTAGTTTTAGCCTGTTTTAGTAC
87521 CTAAATTTTAATTTTTTCAAAACCATGCTTAACATTTAATTTTTGTTTTA-TTTAGTACTTACCG
1 CTAAATTTTAATTTTTTCAAAACCATG-TTAACATTTAATTTTTGTTTTATTTTAGTACTTACCG
* **
87585 TTTAAAACTTAATGCATGTATTTAATACTTAAACTATTAGTTTTAGTTTGTTTTAGTAC
65 TTAAAAACTTAATGCATGTATTTAATACTTAAACTATTAGTTTTAGCCTGTTTTAGTAC
*
87644 CTAAACTTTCAATTTTTT-AAAAC
1 CTAAA-TTTTAATTTTTTCAAAAC
87667 TTAATGTTAA
Statistics
Matches: 136, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
122 5 0.04
123 98 0.72
124 33 0.24
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (123 bp):
CTAAATTTTAATTTTTTCAAAACCATGTTAACATTTAATTTTTGTTTTATTTTAGTACTTACCGT
TAAAAACTTAATGCATGTATTTAATACTTAAACTATTAGTTTTAGCCTGTTTTAGTAC
Found at i:89782 original size:13 final size:13
Alignment explanation
Indices: 89764--89816 Score: 88
Period size: 13 Copynumber: 4.1 Consensus size: 13
89754 TAAAAAATTA
* *
89764 CCCCTTAACAGAC
1 CCCCTTAGCAGCC
89777 CCCCTTAGCAGCC
1 CCCCTTAGCAGCC
89790 CCCCTTAGCAGCC
1 CCCCTTAGCAGCC
89803 CCCCTTAGCAGCC
1 CCCCTTAGCAGCC
89816 C
1 C
89817 ATGTGTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.19, C:0.53, G:0.13, T:0.15
Consensus pattern (13 bp):
CCCCTTAGCAGCC
Found at i:94274 original size:14 final size:14
Alignment explanation
Indices: 94255--94294 Score: 66
Period size: 12 Copynumber: 3.0 Consensus size: 14
94245 AAAAAAATTA
94255 CCCCTTAGCAGCCC
1 CCCCTTAGCAGCCC
94269 CCCCTTAGCAG--C
1 CCCCTTAGCAGCCC
94281 CCCCTTAGCAGCCC
1 CCCCTTAGCAGCCC
94295 ATGTGCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.50
14 12 0.50
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (14 bp):
CCCCTTAGCAGCCC
Done.