Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000629.1 Hibiscus syriacus cultivar Beakdansim tig00001223_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: 64213
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:2244 original size:14 final size:16
Alignment explanation
Indices: 2214--2246 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2204 GCATAAGTAA
2214 AATGCATTCACCTAGT
1 AATGCATTCACCTAGT
2230 AATGC-TTCA-CTAGT
1 AATGCATTCACCTAGT
2244 AAT
1 AAT
2247 CTTACTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (16 bp):
AATGCATTCACCTAGT
Found at i:5219 original size:7 final size:7
Alignment explanation
Indices: 5207--5277 Score: 97
Period size: 7 Copynumber: 10.1 Consensus size: 7
5197 ACCTTTGTAA
*
5207 TAAACCT
1 TAAACCC
5214 TAAACCC
1 TAAACCC
5221 TAAACCC
1 TAAACCC
5228 TAAACCC
1 TAAACCC
5235 TAAACCC
1 TAAACCC
* *
5242 TAAATCA
1 TAAACCC
*
5249 TAAACTC
1 TAAACCC
5256 TAAACCC
1 TAAACCC
*
5263 TAAACCT
1 TAAACCC
5270 TAAACCC
1 TAAACCC
5277 T
1 T
5278 TAGCGCAACT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:12524 original size:48 final size:48
Alignment explanation
Indices: 12449--12576 Score: 159
Period size: 48 Copynumber: 2.7 Consensus size: 48
12439 GAGTACCAAC
* * ** *
12449 GCACCACTATCACACAGACGTCAGACTCGT-TCTTGTTATCATATAATG
1 GCACCACTGTCACACAGACGTCAGACTCGTGCCAAG-TATCATATAATA
* * *
12497 GCACCACTGTCACATAGACATCGGACTCGTGCCAAGTATCATATAATA
1 GCACCACTGTCACACAGACGTCAGACTCGTGCCAAGTATCATATAATA
*
12545 GCACCACCGTCACACAGACGTCAGACTCGTGC
1 GCACCACTGTCACACAGACGTCAGACTCGTGC
12577 TATAATCATA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
48 65 0.97
49 2 0.03
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (48 bp):
GCACCACTGTCACACAGACGTCAGACTCGTGCCAAGTATCATATAATA
Found at i:14983 original size:2 final size:2
Alignment explanation
Indices: 14976--15057 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
14966 GTTAATGCAA
14976 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
15018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15058 ATGGAAAGTA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17635 original size:37 final size:38
Alignment explanation
Indices: 17555--17638 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 38
17545 TAGGGAGACA
17555 ATCCTAAGAATGACTCAAACGACATTTTAGACAAACAG
1 ATCCTAAGAATGACTCAAACGACATTTTAGACAAACAG
* * * *
17593 A-CCTAAGAATTACTCAAATGA-ATTTCTAGAGAAA-TG
1 ATCCTAAGAATGACTCAAACGACATTT-TAGACAAACAG
17629 ATCCTAAGAA
1 ATCCTAAGAA
17639 GGAGAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 6 0.15
37 33 0.82
38 1 0.03
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (38 bp):
ATCCTAAGAATGACTCAAACGACATTTTAGACAAACAG
Found at i:17819 original size:18 final size:18
Alignment explanation
Indices: 17793--17830 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17783 TTGGGAATGG
*
17793 TTGCAAGAGCAGTCTTCA
1 TTGCAAGAGAAGTCTTCA
*
17811 TTGCTAGAGAAGTCTTCA
1 TTGCAAGAGAAGTCTTCA
17829 TT
1 TT
17831 CTTTTCCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (18 bp):
TTGCAAGAGAAGTCTTCA
Found at i:18599 original size:57 final size:57
Alignment explanation
Indices: 18538--18841 Score: 364
Period size: 57 Copynumber: 5.3 Consensus size: 57
18528 ATCAAACTTG
* *
18538 ACTTCTTCAAAAATTCATTTAGAGTTATCATCAAGAAGCCCCTAAAAATTAGGCTTT
1 ACTTCTTTAAAAATTCATTTAGAGTTATCATCAAGAAACCCCTAAAAATTAGGCTTT
* * * * * *
18595 ACTTCTTTAAAAATTAATTT-GAAGTAATCATCAAGAAACCCCTGAAAATCATGCTTA
1 ACTTCTTTAAAAATTCATTTAG-AGTTATCATCAAGAAACCCCTAAAAATTAGGCTTT
* * *
18652 ACTTCTTTAAAAATCCATTTATAGTTATCATCAAGAAACCTCTAAAAATTAGGC-TT
1 ACTTCTTTAAAAATTCATTTAGAGTTATCATCAAGAAACCCCTAAAAATTAGGCTTT
* * * * * *
18708 AGCTTCTTTAAAAAATCATTT-GAAGTAATCATAAAGAAACCCCTGAAAATCAGGCTTA
1 A-CTTCTTTAAAAATTCATTTAG-AGTTATCATCAAGAAACCCCTAAAAATTAGGCTTT
* *
18766 ACTTCTTTAAAAATCCATTTATAGTTATCATCAAGAAACCCCTAAAAATTAGGC-TT
1 ACTTCTTTAAAAATTCATTTAGAGTTATCATCAAGAAACCCCTAAAAATTAGGCTTT
*
18822 ATCTTCTTTAAAAAATCATT
1 A-CTTCTTTAAAAATTCATT
18842 AAGTACCCCT
Statistics
Matches: 204, Mismatches: 36, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
56 5 0.02
57 197 0.97
58 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (57 bp):
ACTTCTTTAAAAATTCATTTAGAGTTATCATCAAGAAACCCCTAAAAATTAGGCTTT
Found at i:18707 original size:114 final size:109
Alignment explanation
Indices: 18539--19811 Score: 1288
Period size: 114 Copynumber: 11.8 Consensus size: 109
18529 TCAAACTTGA
* * * *
18539 CTTCTTCAAAAATTCATTTAGAGTTATCATCAAGAAGCCCCTAAAAATTAGGCTTTA-CTTCTTT
1 CTTCTTTAAAAATTCATTT-GA--AAACATCAAGAAACCCCTAAAAATTAGGC-TTAGCTTCTTT
* * *
18603 AAAAATTAATTTGAAGTAATCATCAAGAAACCCCTGAAAATCATGCTTAA
62 AAAAATTCATTTGAAG-AA-CATCAAGAAACCCCTGAAAATCAGGCTTAG
* * *
18653 CTTCTTTAAAAATCCATTT-ATAGTTATCATCAAGAAACCTCTAAAAATTAGGCTTAGCTTCTTT
1 CTTCTTTAAAAATTCATTTGA-A---AACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTT
* * *
18717 AAAAAATCATTTGAAGTAATCATAAAGAAACCCCTGAAAATCAGGCTTAA
62 AAAAATTCATTTGAAG-AA-CATCAAGAAACCCCTGAAAATCAGGCTTAG
* * *
18767 CTTCTTTAAAAATCCATTT-ATAGTTATCATCAAGAAACCCCTAAAAATTAGGCTTATCTTCTTT
1 CTTCTTTAAAAATTCATTTGA-A---AACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTT
*
18831 AAAAAATCA-TT-AAG----T------ACCCCTGAAAATCAGGCTTAG
62 AAAAATTCATTTGAAGAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* *
18867 C-TCTTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAA
1 CTTC-TTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTT--A
* * * * * * *
18931 AAAATCCATTT-ATAGTTATCATTAAGAAACCCCTAAAAATTAGGTTTAAC
63 AAAATTCATTTGA-AG--AACATCAAGAAACCCCTGAAAATCAGGCTT-AG
* * *
18981 CTTTTTTTAAAATTCATTTGAAAACATCAAGAAACCCTTAAAAATTAGGCTTAG-TTCTTTAAAA
1 CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAA
* * *
19045 ATTCATTTGTA-AACATCAAGAAACCCCTGAAAACCATGCTTAG
66 ATTCATTTGAAGAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* * *
19088 CTTCTTTGAAAAA-TCATTTGTAAACATCAAGAAACCCCTAAAAATCAGGCTTAGC-TCTTTCAA
1 CTTCTTT-AAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAA
* **
19151 AATTCATTTGAA-AACATCAAGAAACCCTTGAAAATCAAACTTAG
65 AATTCATTTGAAGAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* * * * * * *
19195 CTCCTTTAAACATTCATTTGAAAACATAAAAAAAACCCAAAAAATTAGGCTTAGCTTCTTTCAAA
1 CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAA
* * *
19260 ATTCATTTGAA-AACATCATGAAACCCCTAAAAATTAGGCTTAG
66 ATTCATTTGAAGAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* * *
19303 CTTCTTTCAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAGTTAGGCTTAGCTTCTTTCAAA
1 CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAA
* * *
19368 ATTCATTTAAAG-ACATCAAGAAACCCCTAAAAATCAAGCTTAG
66 ATTCATTTGAAGAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* * * * ** *
19411 CTT-TTTTAAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAGACTTATTTTTTTTAAAA
1 CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTT--AA
* * **
19475 AAATTCATTT-AAAAACATCAAGAAACCCTTGAAAATCAACCTTAG
64 AAATTCATTTGAAGAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* * *
19520 CTTCTTTAAAAATTCATTT-AAAACATCAAGAAACCCCT---AATT-TGCTTA-CTTTATTTCAA
1 CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGC-TTCTTTAAA
* * * *
19579 ATTTCATTTGAA-AACATTAAAAAACCCCTGAAAATCAGGCTCAG
65 AATTCATTTGAAGAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* * * *
19623 CTTCTTTAAAAATTCATTTGAAGACATCAAGAAACCCCT--GAATCAGGCTTAGCTTTTTTAAAA
1 CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAA
* *
19686 ATTCATTTGAAG-ACATCAAGAAACCCCTAAAAACCAGGCTTAG
66 ATTCATTTGAAGAACATCAAGAAACCCCTGAAAATCAGGCTTAG
* * * * * *
19729 TTTCTTTAAAAATTCGTTTGAAGACATCAAGAAACCCCTGAAAATCAGGCTTAACTTCTTTAAAA
1 CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAA
19794 ATTCATTTGAAG-ACATCA
66 ATTCATTTGAAGAACATCA
19812 TATTGTTGGG
Statistics
Matches: 998, Mismatches: 118, Indels: 92
0.83 0.10 0.08
Matches are distributed among these distances:
97 35 0.04
99 9 0.01
100 39 0.04
101 3 0.00
103 55 0.06
104 20 0.02
105 12 0.01
106 94 0.09
107 184 0.18
108 212 0.21
109 61 0.06
110 14 0.01
111 13 0.01
112 4 0.00
113 27 0.03
114 215 0.22
115 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (109 bp):
CTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAA
ATTCATTTGAAGAACATCAAGAAACCCCTGAAAATCAGGCTTAG
Found at i:18857 original size:43 final size:43
Alignment explanation
Indices: 18803--18884 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
18793 TCATCAAGAA
* *
18803 ACCCCTAAAAATTAGGCTTATCT-TCTTTAAAAAATCATTAAGT
1 ACCCCTAAAAATCAGGCTTAGCTCT-TTTAAAAAATCATTAAGT
* *
18846 ACCCCTGAAAATCAGGCTTAGCTCTTTTAAAAATTCATT
1 ACCCCTAAAAATCAGGCTTAGCTCTTTTAAAAAATCATT
18885 TGAAAACATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 33 0.97
44 1 0.03
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.34
Consensus pattern (43 bp):
ACCCCTAAAAATCAGGCTTAGCTCTTTTAAAAAATCATTAAGT
Found at i:18929 original size:54 final size:54
Alignment explanation
Indices: 18846--19811 Score: 1109
Period size: 54 Copynumber: 17.9 Consensus size: 54
18836 ATCATTAAGT
18846 ACCCCTGAAAATCAGGCTTAGC-TCTTTTAAAAATTCATTTGAAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTC-TTTAAAAATTCATTTGAAAACATCAAGAA
* * *
18900 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAAAATCCATTT-ATAGTTATCATTAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTT--AAAAATTCATTTGA-A---AACATCAAGAA
* * * * * *
18959 ACCCCTAAAAATTAGGTTTAACCTTTTTTTAAAATTCATTTGAAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTT-AGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * * *
19014 ACCCTTAAAAATTAGGCTTAG-TTCTTTAAAAATTCATTTGTAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * *
19067 ACCCCTGAAAACCATGCTTAGCTTCTTTGAAAAA-TCATTTGTAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTT-AAAAATTCATTTGAAAACATCAAGAA
* *
19121 ACCCCTAAAAATCAGGCTTAGC-TCTTTCAAAATTCATTTGAAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* ** * * * *
19174 ACCCTTGAAAATCAAACTTAGCTCCTTTAAACATTCATTTGAAAACATAAAAAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* ** * * *
19228 AACCCAAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAAACATCATGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * *
19282 ACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* *
19336 ACCCCT-AAAAGTTAGGCTTAGCTTCTTTCAAAATTCATTT-AAAGACATCAAGAA
1 ACCCCTGAAAA-TCAGGCTTAGCTTCTTTAAAAATTCATTTGAAA-ACATCAAGAA
* * *
19390 ACCCCTAAAAATCAAGCTTAGCTT-TTTTAAAATTCATTTGAAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* ** * *
19443 ACCCCTGAAAATCAGACTTATTTTTTTTAAAAAAATTCATTTAAAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTT--AAAAATTCATTTGAAAACATCAAGAA
* **
19499 ACCCTTGAAAATCAACCTTAGCTTCTTTAAAAATTCATTT-AAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
** * * * * *
19552 ACCCCT---AAT-TTGCTTA-CTTTATTTCAAATTTCATTTGAAAACATTAAAAA
1 ACCCCTGAAAATCAGGCTTAGC-TTCTTTAAAAATTCATTTGAAAACATCAAGAA
* *
19602 ACCCCTGAAAATCAGGCTCAGCTTCTTTAAAAATTCATTTGAAGACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* *
19656 ACCCCTG--AATCAGGCTTAGCTTTTTTAAAAATTCATTTGAAGACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * * * *
19708 ACCCCTAAAAACCAGGCTTAGTTTCTTTAAAAATTCGTTTGAAGACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* *
19762 ACCCCTGAAAATCAGGCTTAACTTCTTTAAAAATTCATTTGAAGACATCA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCA
19812 TATTGTTGGG
Statistics
Matches: 784, Mismatches: 99, Indels: 58
0.83 0.11 0.06
Matches are distributed among these distances:
48 1 0.00
49 19 0.02
50 20 0.03
52 53 0.07
53 158 0.20
54 392 0.50
55 39 0.05
56 58 0.07
58 11 0.01
59 26 0.03
60 7 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (54 bp):
ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
Found at i:26484 original size:6 final size:6
Alignment explanation
Indices: 26473--26559 Score: 156
Period size: 6 Copynumber: 14.5 Consensus size: 6
26463 ATGCTTGTCG
26473 AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA
1 AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA
* *
26521 AAACAA AAACCA AAACAA AAACAA AAGCAA AAACAA AAA
1 AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA AAA
26560 TATAGCAGAA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.82, C:0.17, G:0.01, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:37744 original size:23 final size:23
Alignment explanation
Indices: 37718--37763 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
37708 CACCACAGCT
*
37718 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
37741 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
37764 TATAATAATG
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:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:41171 original size:18 final size:19
Alignment explanation
Indices: 41148--41185 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41138 TTTTTAAGTG
41148 ATAAAAG-AAATTAAATAA
1 ATAAAAGCAAATTAAATAA
*
41166 ATAAAAGCAATTTAAATAA
1 ATAAAAGCAAATTAAATAA
41185 A
1 A
41186 AATAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (19 bp):
ATAAAAGCAAATTAAATAA
Found at i:41686 original size:45 final size:45
Alignment explanation
Indices: 41630--41717 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
41620 TCATCAAGAA
* *
41630 ACCCCTAAAAATTAGGCTTATCT-TCTTTAAAAAATCATTTGAAGT
1 ACCCCTAAAAATCAGGCTTAGCTCT-TTTAAAAAATCATTTGAAGT
* *
41675 ACCCCTGAAAATCAGGCTTAGCTCTTTTAAAAATTCATTTGAA
1 ACCCCTAAAAATCAGGCTTAGCTCTTTTAAAAAATCATTTGAA
41718 AATATCAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 37 0.97
46 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (45 bp):
ACCCCTAAAAATCAGGCTTAGCTCTTTTAAAAAATCATTTGAAGT
Found at i:41744 original size:54 final size:54
Alignment explanation
Indices: 41675--42639 Score: 1105
Period size: 54 Copynumber: 17.9 Consensus size: 54
41665 CATTTGAAGT
*
41675 ACCCCTGAAAATCAGGCTTAGC-TCTTTTAAAAATTCATTTGAAAATATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTC-TTTAAAAATTCATTTGAAAACATCAAGAA
* * * *
41729 ACCCCTTAAAATCAGGCTTAGCTTCTTTAAAAAAATCCATTT-ATAGTTATCATTAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTT--AAAAATTCATTTGA-A---AACATCAAGAA
* * * *
41788 ACCCCTAAAAATTAGGTTTAGCTTTTTTTAAAAATTCATTTGAAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGC-TTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * * *
41843 ACCCTTAAAAATTAGGCTTAG-TTCTTTAAAAATTCATTTGTAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * *
41896 ACCCCTGAAAACCATGCTTAGCTTCTTTGAAAAA-TCATTTGTAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTT-AAAAATTCATTTGAAAACATCAAGAA
*
41950 ACCCCTGAAAATCAGGCTTAGC-TCTTTCAAAATTCATTTGAAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* ** * * * * *
42003 ACCCTTGAAAATCAAACTTAGCTCCTTTAAACATTCATTTGGAAACATAAAAAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* ** * * *
42057 AACCCAAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAAACATCATGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * * *
42111 ACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTAAAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* *
42165 ACCCCT-AAAAGTTAGGCTTAGCTTCTTTCAAAATTCATTT-AAAGACATCAAGAA
1 ACCCCTGAAAA-TCAGGCTTAGCTTCTTTAAAAATTCATTTGAAA-ACATCAAGAA
* *
42219 ACCCCTAAAAATCAAGCTTAGCTTCTTT-AAAATTCATTTGAAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * ** * * *
42272 ACCCCTGAAATTCAGACTTATTTTTTTTAAAAATTTATTTAAAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* **
42326 ACCCTTGAAAATCAACCTTAGCTTCTTTAAAAATTCATTT-AAAACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
** * * * * * *
42379 ACCCCT---AAT-TTGCTTAGTTTATTTCAAATTTCATTTGAAAACATTAAAAAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACA-TCAAGAA
* * *
42430 ACCCCTGAAAATCAGGCTCAGCTTGTTTAAAAATTCATTTGAAGACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * *
42484 ACCCCT--AAATCATGCTTAGCTTTTTTAAAAATTCATTTGAAGACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * *
42536 ACCCCTGAAAACCAGGCTTAGTTTCTTTAAAAATTCATTTGAAGACATCAAGAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* *
42590 ACCCCTGAAAATCAGGCTTAACTTCTTTAAAAATTCATTTGAAGACATCA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCA
42640 TATTGTTGGG
Statistics
Matches: 784, Mismatches: 101, Indels: 52
0.84 0.11 0.06
Matches are distributed among these distances:
49 20 0.03
50 9 0.01
51 11 0.01
52 53 0.07
53 156 0.20
54 412 0.53
55 66 0.08
56 12 0.02
58 12 0.02
59 28 0.04
60 5 0.01
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (54 bp):
ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
Found at i:41961 original size:107 final size:107
Alignment explanation
Indices: 41675--42639 Score: 1099
Period size: 107 Copynumber: 9.0 Consensus size: 107
41665 CATTTGAAGT
*
41675 ACCCCTGAAAATCAGGCTTAGC-TCTTTTAAAAATTCATTTGAAAATATCAAGAAACCCCTTAAA
1 ACCCCTGAAAATCAGGCTTAGCTTC-TTTAAAAATTCATTTGAAAACATCAAGAAACCCC-TAAA
* * * *
41739 ATCAGGCTTAGCTTCTTTAAAAAAATCCATTT-ATAGTTATCATTAAGAA
64 ATTAGGCTTAGCTTCTTT--AAAAATTCATTTGA-A---AACATCAAGAA
* * * * *
41788 ACCCCTAAAAATTAGGTTTAGCTTTTTTTAAAAATTCATTTGAAAACATCAAGAAACCCTTAAAA
1 ACCCCTGAAAATCAGGCTTAGC-TTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCT-AAA
*
41853 ATTAGGCTTAG-TTCTTTAAAAATTCATTTGTAAACATCAAGAA
64 ATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * *
41896 ACCCCTGAAAACCATGCTTAGCTTCTTTGAAAAA-TCATTTGTAAACATCAAGAAACCCCTGAAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTT-AAAAATTCATTTGAAAACATCAAGAAACCCCT-AAA
* *
41960 ATCAGGCTTAGC-TCTTTCAAAATTCATTTGAAAACATCAAGAA
64 ATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* ** * * * * * **
42003 ACCCTTGAAAATCAAACTTAGCTCCTTTAAACATTCATTTGGAAACATAAAAAAAACCCAAAAAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACAT-CAAGAAACCCCTAAAA
* *
42068 TTAGGCTTAGCTTCTTTCAAAATTCATTTGAAAACATCATGAA
65 TTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * * *
42111 ACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTAAAAACATCAAGAAACCCCTAAAAG
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAA-
*
42176 TTAGGCTTAGCTTCTTTCAAAATTCATTT-AAAGACATCAAGAA
65 TTAGGCTTAGCTTCTTTAAAAATTCATTTGAAA-ACATCAAGAA
* * *
42219 ACCCCTAAAAATCAAGCTTAGCTTCTTT-AAAATTCATTTGAAAACATCAAGAAACCCCTGAAAT
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAT
* ** * * *
42283 TCAGACTTATTTTTTTTAAAAATTTATTTAAAAACATCAAGAA
66 T-AGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* **
42326 ACCCTTGAAAATCAACCTTAGCTTCTTTAAAAATTCATTT-AAAACATCAAGAAACCCCT--AAT
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAT
* * * * * * *
42388 T-TGCTTAGTTTATTTCAAATTTCATTTGAAAACATTAAAAAA
66 TAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACA-TCAAGAA
* * *
42430 ACCCCTGAAAATCAGGCTCAGCTTGTTTAAAAATTCATTTGAAGACATCAAGAAACCCCT-AAAT
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAT
* * * *
42494 CATGCTTAGCTTTTTTAAAAATTCATTTGAAGACATCAAGAA
66 TAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
* * *
42536 ACCCCTGAAAACCAGGCTTAGTTTCTTTAAAAATTCATTTGAAGACATCAAGAAACCCCTGAAAA
1 ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCT-AAAA
* * *
42601 TCAGGCTTAACTTCTTTAAAAATTCATTTGAAGACATCA
65 TTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCA
42640 TATTGTTGGG
Statistics
Matches: 737, Mismatches: 95, Indels: 45
0.84 0.11 0.05
Matches are distributed among these distances:
103 25 0.03
104 40 0.05
105 22 0.03
106 70 0.09
107 272 0.37
108 224 0.30
111 12 0.02
113 26 0.04
114 45 0.06
115 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (107 bp):
ACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAT
TAGGCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAA
Found at i:53600 original size:12 final size:12
Alignment explanation
Indices: 53568--53621 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
53558 TATACAAATA
*
53568 CCTAACTC-TCA
1 CCTAACTCTTCT
53579 CCTAACTCTTCT
1 CCTAACTCTTCT
* *
53591 CCTAATTCTTCA
1 CCTAACTCTTCT
* *
53603 CATAACTCTTCA
1 CCTAACTCTTCT
53615 CCTAACT
1 CCTAACT
53622 ATATTAATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
11 8 0.22
12 28 0.78
ACGTcount: A:0.26, C:0.39, G:0.00, T:0.35
Consensus pattern (12 bp):
CCTAACTCTTCT
Found at i:53608 original size:24 final size:23
Alignment explanation
Indices: 53567--53621 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
53557 ATATACAAAT
*
53567 ACCTAACTCTCACCTAACTCTTC
1 ACCTAACTCTCACATAACTCTTC
* *
53590 TCCTAATTCTTCACATAACTCTTC
1 ACCTAACTC-TCACATAACTCTTC
53614 ACCTAACT
1 ACCTAACT
53622 ATATTAATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.27, C:0.38, G:0.00, T:0.35
Consensus pattern (23 bp):
ACCTAACTCTCACATAACTCTTC
Done.