Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004683.1 Hibiscus syriacus cultivar Beakdansim tig00010497_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: 72753
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6863 original size:25 final size:26
Alignment explanation
Indices: 6835--6884 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
6825 TAAAATAAAT
* *
6835 AATTA-TATTTAAAATGTTTTTATTA
1 AATTATTATTTAAAATATTTATATTA
6860 AATTATTATTTAAAATATTTATATT
1 AATTATTATTTAAAATATTTATATT
6885 TTTATGTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
AATTATTATTTAAAATATTTATATTA
Found at i:7843 original size:12 final size:12
Alignment explanation
Indices: 7791--7847 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
7781 GTTTGAAATA
7791 AAAATATATATTT
1 AAAA-ATATATTT
*
7804 AAAAATATTTTTT
1 AAAAATA-TATTT
* * *
7817 AATTATTAAATTT
1 AA-AAATATATTT
7830 AAAAATATATTT
1 AAAAATATATTT
7842 AAAAAT
1 AAAAAT
7848 GAGCTCTTCC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
12 16 0.47
13 15 0.44
14 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAAAATATATTT
Found at i:12953 original size:17 final size:17
Alignment explanation
Indices: 12931--12963 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12921 GAGCCCTTTT
12931 GCAAATA-AATTAAATTA
1 GCAAATACAA-TAAATTA
12948 GCAAATACAATAAATT
1 GCAAATACAATAAATT
12964 TTAAATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (17 bp):
GCAAATACAATAAATTA
Found at i:14708 original size:2 final size:2
Alignment explanation
Indices: 14703--14736 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
14693 AAAGCCCCCC
14703 CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
14737 GGAGTACGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:15343 original size:19 final size:20
Alignment explanation
Indices: 15314--15352 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
15304 AATGTAGTTT
15314 TTTTTATTTTA-AAAATAATA
1 TTTTTATTTTATAAAA-AATA
15334 TTTTTA-TTTATAAAAAATA
1 TTTTTATTTTATAAAAAATA
15353 AAAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTATTTTATAAAAAATA
Found at i:17546 original size:15 final size:15
Alignment explanation
Indices: 17528--17557 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17518 AAAAAAAAAG
17528 AAAATATAATAATAA
1 AAAATATAATAATAA
17543 AAAATATAATAATAA
1 AAAATATAATAATAA
17558 TAATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATATAATAATAA
Found at i:17566 original size:15 final size:13
Alignment explanation
Indices: 17528--17568 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
17518 AAAAAAAAAG
*
17528 AAAATATAATAAT
1 AAAAAATAATAAT
17541 AAAAAAT-ATAAT
1 AAAAAATAATAAT
*
17553 -AATAATAATAAT
1 AAAAAATAATAAT
17565 AAAA
1 AAAA
17569 GAAAATTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 5 0.22
12 10 0.43
13 8 0.35
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:17643 original size:22 final size:22
Alignment explanation
Indices: 17601--17644 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
17591 AATAATACGA
*
17601 AAAAATAGTTTAAAAATGAAAAG
1 AAAAATAG-TTAAAAAGGAAAAG
17624 AAAAATA-TTAAAATAGGAAAA
1 AAAAATAGTTAAAA-AGGAAAA
17645 CCAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAAATAGTTAAAAAGGAAAAG
Found at i:19781 original size:165 final size:164
Alignment explanation
Indices: 19370--20394 Score: 1550
Period size: 165 Copynumber: 6.2 Consensus size: 164
19360 TTATTGACAA
* * * * * * * **
19370 ATAACCCTTCTTGCCTTGAGCTATGTTGTAAACGATATGACCTCGAAGTTGAGTGTAATTAAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
* * * * * *
19435 CGGGGGTCTTTGGCAGATAACTCTTCTCGACTTAAGTTATACTGCCAATGATGTGCCTGAGAGCT
66 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCT-TGAGCT
* *
19500 GAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAG
130 GAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAG
* ** * * * *
19534 ATAACCCTTATAGCCTTGAGTTATATTGTGAATGATGTGCCCTCCAAGCTGAGAGTAATTGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
19599 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCT
66 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT-GAGCT
* * *
19664 AAGCGTAGTCGAACTCGAAGGTCTTTTAGTCACAG
130 GAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAG
19699 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
* * *
19764 CGAAGGTATTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
66 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT-GAGCT
***
19829 GAGCGTAGTCGAACTCAAAGGTC-TTTGGTTGGTAG
130 GAGCGTAGTCGAACTCAAAGGTCTTTTGG-TCACAG
* * * * *
19864 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGGAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
* * *
19929 CGAAGGTCTTTGGCAGATAGCCCTTCTCGGCTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
66 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT-GAGCT
19994 GAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAG
130 GAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAG
20029 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
* *
20094 CGGGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCT
66 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGAGCT
20159 GAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAG
130 GAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAG
20194 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
* *
20259 CGGGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCT
66 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGAGCT
*
20324 GAGCGCAGTCGAACTCAAAGGTCTTTTGGTCACAG
130 GAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAG
*
20359 ATAACCCTTCTAGCCTTGAGTTATGCTCTAAATGAT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
20395 TTGTTTTTTT
Statistics
Matches: 796, Mismatches: 60, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
164 137 0.17
165 652 0.82
166 7 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (164 bp):
ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGAGCTG
AGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAG
Found at i:23805 original size:18 final size:19
Alignment explanation
Indices: 23764--23808 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
23754 AGTTAATGTG
23764 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
23783 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
23801 AATGCAAA
1 AATGCAAA
23809 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:25669 original size:18 final size:18
Alignment explanation
Indices: 25648--25685 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
25638 AAACAAAAAA
25648 AAAAGAAAAT-ATAATAAT
1 AAAA-AAAATAATAATAAT
*
25666 AAAAAATATAATAATAAT
1 AAAAAAAATAATAATAAT
25684 AA
1 AA
25686 TAATAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (18 bp):
AAAAAAAATAATAATAAT
Found at i:25673 original size:15 final size:15
Alignment explanation
Indices: 25653--25682 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
25643 AAAAAAAAAG
25653 AAAATATAATAATAA
1 AAAATATAATAATAA
25668 AAAATATAATAATAA
1 AAAATATAATAATAA
25683 TAATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATATAATAATAA
Found at i:25691 original size:15 final size:13
Alignment explanation
Indices: 25653--25693 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
25643 AAAAAAAAAG
*
25653 AAAATATAATAAT
1 AAAAAATAATAAT
25666 AAAAAAT-ATAAT
1 AAAAAATAATAAT
*
25678 -AATAATAATAAT
1 AAAAAATAATAAT
25690 AAAA
1 AAAA
25694 GAAAATTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 5 0.22
12 10 0.43
13 8 0.35
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:25768 original size:22 final size:22
Alignment explanation
Indices: 25726--25769 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
25716 AATAATACGA
*
25726 AAAAATAGTTTAAAAATGAAAAG
1 AAAAATAG-TTAAAAAGGAAAAG
25749 AAAAATA-TTAAAATAGGAAAA
1 AAAAATAGTTAAAA-AGGAAAA
25770 CCAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAAATAGTTAAAAAGGAAAAG
Found at i:26824 original size:24 final size:24
Alignment explanation
Indices: 26791--26838 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
26781 GATGTTATAT
* *
26791 ATATTTTTTATTTTTTAAAATAAA
1 ATATTATTTAATTTTTAAAATAAA
26815 ATATTATTTAATTTTTAAAATAAA
1 ATATTATTTAATTTTTAAAATAAA
26839 TTGTACGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATATTATTTAATTTTTAAAATAAA
Found at i:31770 original size:23 final size:23
Alignment explanation
Indices: 31739--31783 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31729 ACCCTCACAG
*
31739 TCATAAACGGAAGTAAGATTTTT
1 TCATAAACGGAACTAAGATTTTT
* *
31762 TCATGAACGGGACTAAGATTTT
1 TCATAAACGGAACTAAGATTTT
31784 ATGATAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (23 bp):
TCATAAACGGAACTAAGATTTTT
Found at i:38033 original size:2 final size:2
Alignment explanation
Indices: 38028--38057 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38018 TGTGCGTGTG
38028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38058 ATTTTTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40161 original size:20 final size:21
Alignment explanation
Indices: 40132--40170 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40122 CATGAAATAT
*
40132 AAAGGCAAAGTGTAGCATGTA
1 AAAGGCAAAGTGAAGCATGTA
40153 AAAGG-AAAGTGAAGCATG
1 AAAGGCAAAGTGAAGCATG
40171 GATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.46, C:0.08, G:0.31, T:0.15
Consensus pattern (21 bp):
AAAGGCAAAGTGAAGCATGTA
Found at i:44789 original size:2 final size:2
Alignment explanation
Indices: 44782--44820 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
44772 TAACAAACAT
*
44782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44821 TTAAGTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46158 original size:16 final size:16
Alignment explanation
Indices: 46137--46169 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
46127 TAAAAAATAA
46137 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
46153 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
46169 A
1 A
46170 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:46246 original size:16 final size:16
Alignment explanation
Indices: 46225--46279 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
46215 CATGTTCGTT
46225 ACGAACACGAACATAA
1 ACGAACACGAACATAA
46241 ACGAACACGAACATAA
1 ACGAACACGAACATAA
*
46257 ATGAACACGAACATAA
1 ACGAACACGAACATAA
46273 ACGAACA
1 ACGAACA
46280 TAAACGTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.56, C:0.24, G:0.13, T:0.07
Consensus pattern (16 bp):
ACGAACACGAACATAA
Found at i:47050 original size:24 final size:24
Alignment explanation
Indices: 47009--47078 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
46999 AGATTGTGTT
*
47009 AAACATAAAT-GAATGAACATAAAC
1 AAACAT-AATCGAACGAACATAAAC
47033 AAACATAATCGAACGAACATAAAC
1 AAACATAATCGAACGAACATAAAC
* * *
47057 GAACATAACCAAACGAACATAA
1 AAACATAATCGAACGAACATAA
47079 CCGAACGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 3 0.07
24 38 0.93
ACGTcount: A:0.60, C:0.19, G:0.09, T:0.13
Consensus pattern (24 bp):
AAACATAATCGAACGAACATAAAC
Found at i:47053 original size:14 final size:14
Alignment explanation
Indices: 47034--47085 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
47024 AACATAAACA
*
47034 AACATAATCGAACG
1 AACATAACCGAACG
47048 AACAT-A---AACG
1 AACATAACCGAACG
*
47058 AACATAACCAAACG
1 AACATAACCGAACG
47072 AACATAACCGAACG
1 AACATAACCGAACG
47086 TTCACGAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.27
11 1 0.03
13 1 0.03
14 22 0.67
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.10
Consensus pattern (14 bp):
AACATAACCGAACG
Found at i:59114 original size:23 final size:24
Alignment explanation
Indices: 59088--59147 Score: 104
Period size: 23 Copynumber: 2.5 Consensus size: 24
59078 AGGATAAAGA
59088 TAAAAGAGATTTATTTATTTTA-T
1 TAAAAGAGATTTATTTATTTTATT
*
59111 TAAAAGAGATTGATTTATTTTATT
1 TAAAAGAGATTTATTTATTTTATT
59135 TAAAAGAGATTTA
1 TAAAAGAGATTTA
59148 ATAGCTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (24 bp):
TAAAAGAGATTTATTTATTTTATT
Found at i:63100 original size:17 final size:17
Alignment explanation
Indices: 63043--63100 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
63033 AACATGAACC
*
63043 AGATAAGGAAGCTGATTT
1 AGAT-AGGAAGCTGAATT
*
63061 AGATAGGAA-AT-AATT
1 AGATAGGAAGCTGAATT
*
63076 -GAATAGGAAGCTGACTT
1 AG-ATAGGAAGCTGAATT
63093 AGATAGGA
1 AGATAGGA
63101 CATAAGACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
14 1 0.03
15 10 0.31
16 2 0.06
17 14 0.44
18 5 0.16
ACGTcount: A:0.43, C:0.05, G:0.28, T:0.24
Consensus pattern (17 bp):
AGATAGGAAGCTGAATT
Found at i:72519 original size:27 final size:28
Alignment explanation
Indices: 72451--72521 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
72441 AAATTATAAA
* *
72451 TTAATCACTGAACTTTACTTTTCTTTAT
1 TTAATCACTGAACTTTACATTTCTTAAT
* *
72479 TTCACTCACT--ACTTTA-ATTTGTTAAT
1 TT-AATCACTGAACTTTACATTTCTTAAT
72505 TTAATCACTGAACTTTA
1 TTAATCACTGAACTTTA
72522 TGTATTAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
25 6 0.17
26 9 0.26
27 12 0.34
28 2 0.06
29 6 0.17
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.49
Consensus pattern (28 bp):
TTAATCACTGAACTTTACATTTCTTAAT
Done.