Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006290.1 Hibiscus syriacus cultivar Beakdansim tig00015016_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: 51998
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:188 original size:12 final size:12
Alignment explanation
Indices: 171--195 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
161 GTAGTTTGGA
171 GGTGGCTGCCAC
1 GGTGGCTGCCAC
183 GGTGGCTGCCAC
1 GGTGGCTGCCAC
195 G
1 G
196 ATCAGAGGAG
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:0.08, C:0.32, G:0.44, T:0.16
Consensus pattern (12 bp):
GGTGGCTGCCAC
Found at i:12318 original size:11 final size:11
Alignment explanation
Indices: 12246--12309 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
12236 ATTTTTCTTG
*
12246 AAGAATAAATAA
1 AAGAA-AAAGAA
12258 AAGAAGAAA-AA
1 AAGAA-AAAGAA
*
12269 AAGAAAATTGAA
1 AAGAAAA-AGAA
12281 AA-AAAAAGAA
1 AAGAAAAAGAA
*
12291 AAAAAAAAGAA
1 AAGAAAAAGAA
12302 AAGAAAAA
1 AAGAAAAA
12310 TAAATGAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
10 7 0.16
11 26 0.58
12 12 0.27
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:12318 original size:16 final size:16
Alignment explanation
Indices: 12256--12308 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
12246 AAGAATAAAT
*
12256 AAAAGAAGAAAAAAAG
1 AAAAGAAAAAAAAAAG
12272 AAAATTG-AAAAAAAAAG
1 AAAA--GAAAAAAAAAAG
12289 AAAA-AAAAAAGAAAAG
1 AAAAGAAAAAA-AAAAG
12305 AAAA
1 AAAA
12309 ATAAATGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 5 0.16
16 13 0.41
17 13 0.41
18 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAG
Found at i:13787 original size:82 final size:81
Alignment explanation
Indices: 13638--13900 Score: 305
Period size: 82 Copynumber: 3.2 Consensus size: 81
13628 AGATTTTTCT
* * * * * *
13638 AGTCTTATTTCCCCTGAATGAATAGTAGAGCATACACATCTCCCAAAATAGAT-ATGTCTACCCG
1 AGTCTGATTTCCCCTGAATGAATAGTGGAGCAGACACGTCT-TCAGAATAGATCA-GTCTACCCG
13702 AAAAAGAGGCACAGATCA
64 AAAAAGAGGCACAGATCA
* * * *
13720 AGTCTGATTTCCCCTGAATGAATAGTGGAGCAGATACGTCTTCTAGAATAAATCAGTATACCTGA
1 AGTCTGATTTCCCCTGAATGAATAGTGGAGCAGACACGTCTTC-AGAATAGATCAGTCTACCCGA
*
13785 AAAAGAGGCACGGATCA
65 AAAAGAGGCACAGATCA
* ** * * * *
13802 AGTCTGATTT-CCCTAAATGAATAGTGGAATAGACATGTCTTCCGAAATAGATCTGTCTACCCAA
1 AGTCTGATTTCCCCTGAATGAATAGTGGAGCAGACACGTCTTCAG-AATAGATCAGTCTACCCGA
13866 AAAAGAGGCACAGATCA
65 AAAAGAGGCACAGATCA
*
13883 AGTCTGATTTTCCCTGAA
1 AGTCTGATTTCCCCTGAA
13901 AGAAGAATGG
Statistics
Matches: 153, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 1 0.01
81 68 0.44
82 83 0.54
83 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (81 bp):
AGTCTGATTTCCCCTGAATGAATAGTGGAGCAGACACGTCTTCAGAATAGATCAGTCTACCCGAA
AAAGAGGCACAGATCA
Found at i:13950 original size:81 final size:81
Alignment explanation
Indices: 13680--13968 Score: 287
Period size: 82 Copynumber: 3.5 Consensus size: 81
13670 TACACATCTC
* * * * *
13680 CCAAAATAGATATGTCTACCCGAAAAAGAGGCACAGATCAAGTCTGATTTCCCCTGAATGAATAG
1 CCAAAATAGATCTGTATACCCAAAAAAGAGGCACAGATCAAGTCTGATTTTCCCTGAAAGAATAG
*
13745 TGGAGCAGA-TACGTCTT
66 TGGAG-AGACT-TGTCTT
* * * * ** *
13762 CTAGAATAAATCAGTATACCTGAAAAAGAGGCACGGATCAAGTCTGA-TTTCCCT-AAATGAATA
1 CCAAAATAGATCTGTATACCCAAAAAAGAGGCACAGATCAAGTCTGATTTTCCCTGAAA-GAATA
* *
13825 GTGGAATAGACATGTCTT
65 GTGG-AGAGACTTGTCTT
* * * *
13843 CCGAAATAGATCTGTCTACCCAAAAAAGAGGCACAGATCAAGTCTGATTTTCCCTGAAAGAAGAA
1 CCAAAATAGATCTGTATACCCAAAAAAGAGGCACAGATCAAGTCTGATTTTCCCTGAAAGAATAG
*
13908 TGGAGAGGACTTGTTTT
66 TGGAGA-GACTTGTCTT
* * * * *
13925 CCAAAATTGATCTGAATACCCAAAAACGAGGAATAGATCAAGTC
1 CCAAAATAGATCTGTATACCCAAAAAAGAGGCACAGATCAAGTC
13969 CGACCTACCC
Statistics
Matches: 167, Mismatches: 34, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
80 2 0.01
81 63 0.38
82 99 0.59
83 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24
Consensus pattern (81 bp):
CCAAAATAGATCTGTATACCCAAAAAAGAGGCACAGATCAAGTCTGATTTTCCCTGAAAGAATAG
TGGAGAGACTTGTCTT
Found at i:18390 original size:21 final size:21
Alignment explanation
Indices: 18365--18466 Score: 145
Period size: 21 Copynumber: 4.8 Consensus size: 21
18355 TCATACCAAG
*
18365 GACGAGAAGATCATTCATAAA
1 GACGAGAAGACCATTCATAAA
18386 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
18407 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
*
18428 GAC-ATGAAGACCCTTCATAAA
1 GACGA-GAAGACCATTCATAAA
18449 GAC-ATGAAGACCACTTCA
1 GACGA-GAAGACCA-TTCA
18467 CATTGGAGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
20 1 0.01
21 71 0.93
22 4 0.05
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.17
Consensus pattern (21 bp):
GACGAGAAGACCATTCATAAA
Found at i:22898 original size:25 final size:25
Alignment explanation
Indices: 22863--22945 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
22853 TCATGAAGAG
*
22863 AAAGAAGAGAAATGAAGAAAGAGAA
1 AAAGAAAAGAAATGAAGAAAGAGAA
* *
22888 AAAGAAAAGAAAAGAAGAAAGAAAGA
1 AAAGAAAAGAAATGAAGAAAGAGA-A
*
22914 AAAGAAAA-AAATTAA-AAAGGAGAA
1 AAAGAAAAGAAATGAAGAAA-GAGAA
*
22938 AAATAAAA
1 AAAGAAAA
22946 AAAAAGAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
24 11 0.22
25 29 0.59
26 9 0.18
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (25 bp):
AAAGAAAAGAAATGAAGAAAGAGAA
Found at i:22912 original size:16 final size:16
Alignment explanation
Indices: 22877--22922 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
22867 AAGAGAAATG
22877 AAGAAAGAGAAAAAGAA
1 AAGAAA-AGAAAAAGAA
22894 AAGAAAAGAAGAAAG-A
1 AAGAAAAGAA-AAAGAA
22910 AAGAAAAGAAAAA
1 AAGAAAAGAAAAA
22923 AATTAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.11
16 15 0.54
17 10 0.36
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAAAAGAA
Found at i:22912 original size:21 final size:20
Alignment explanation
Indices: 22861--22923 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 20
22851 CATCATGAAG
* *
22861 AGAAAGAAGAGAAATGAAGAA
1 AGAAAGAA-AGAAAAGAAAAA
22882 AGAGAA-AAAGAAAAGAAAAGA
1 AGA-AAGAAAGAAAAGAAAA-A
22903 AGAAAGAAAGAAAAGAAAAA
1 AGAAAGAAAGAAAAGAAAAA
22923 A
1 A
22924 ATTAAAAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 13 0.35
21 22 0.59
22 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
AGAAAGAAAGAAAAGAAAAA
Found at i:22953 original size:16 final size:16
Alignment explanation
Indices: 22884--22963 Score: 54
Period size: 16 Copynumber: 4.8 Consensus size: 16
22874 ATGAAGAAAG
* *
22884 AGAAAAAGAAAAGAAA
1 AGAAAAATAAAAAAAA
*
22900 AGAAGAAAGAAAGAAAAGA
1 AGAA-AAATAAA-AAAA-A
* **
22919 A-AAAAATTAAAAAGG
1 AGAAAAATAAAAAAAA
22934 AGAAAAATAAAAAAAA
1 AGAAAAATAAAAAAAA
22950 AGAATGAAATAAAA
1 AGAA--AAATAAAA
22964 TCGATCAAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
15 1 0.02
16 22 0.44
17 12 0.24
18 13 0.26
19 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
AGAAAAATAAAAAAAA
Found at i:25152 original size:36 final size:36
Alignment explanation
Indices: 25090--25195 Score: 133
Period size: 37 Copynumber: 2.9 Consensus size: 36
25080 GGGCAAATCT
* * *
25090 ATCTTAAGCCTTCATCGGAGAATAGTGAAGCAA-TCC
1 ATCTTAAGCCTTCA-CCGAGAGTAGTGAAGCAACTCA
*
25126 ATTTTAAGCCTTCACCTGAGAGTAGTGAAGCAACTCA
1 ATCTTAAGCCTTCACC-GAGAGTAGTGAAGCAACTCA
*
25163 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAA
1 ATCTTAAGCCTTCACCG-AGAGTAGTGAAGCAA
25196 ATCTATCCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
35 1 0.02
36 29 0.48
37 31 0.51
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCGAGAGTAGTGAAGCAACTCA
Found at i:25176 original size:37 final size:35
Alignment explanation
Indices: 25085--25195 Score: 132
Period size: 36 Copynumber: 3.1 Consensus size: 35
25075 GATTGGGGCA
* * *
25085 AATCTATCTTAAGCCTTCATCGGAGAATAGTGAAGC
1 AATCAATCTTAAGCCTTCA-CCGAGAGTAGTGAAGC
* *
25121 AATCCATTTTAAGCCTTCACCTGAGAGTAGTGAAGC
1 AATCAATCTTAAGCCTTCACC-GAGAGTAGTGAAGC
*
25157 AACTCAATCTTAAGCCTTCACCGAAGAGTAGTAAAGC
1 AA-TCAATCTTAAGCCTTCACCG-AGAGTAGTGAAGC
25194 AA
1 AA
25196 ATCTATCCAT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
35 1 0.02
36 33 0.51
37 31 0.48
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (35 bp):
AATCAATCTTAAGCCTTCACCGAGAGTAGTGAAGC
Found at i:25382 original size:42 final size:41
Alignment explanation
Indices: 25315--25416 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
25305 TTCACAATTT
* * ** * *
25315 ATAAGTCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCTGTAAGTCTTTAGAGCAAGATG
* *
25356 TTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCTGTAAGTCTTTAGAGCAAGATG
*
25398 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
25417 CATAAGACCT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCTGTAAGTCTTTAGAGCAAGATG
Found at i:25611 original size:201 final size:200
Alignment explanation
Indices: 25266--25670 Score: 675
Period size: 201 Copynumber: 2.0 Consensus size: 200
25256 GTTTTAAGAA
* * * *
25266 GATGAAATTTTTGAAAATGAAGAATGCGATTTTCAGAATTTCACAATTTATAAGTCCTTCAGGCC
1 GATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGTCCTTCAGGCC
* * *
25331 ATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGA
66 ATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
* *
25396 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGATATGATGTCTTCAAATGAATTCGAAAATG
131 TGATAAGTCCTTCGGGACATCCATAAGACCTTCGGATAGGATG-CTTCAAATGAATTCGAAAATG
25461 AAAAAT
195 AAAAAT
*
25467 GATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGTCCTTCGGGCC
1 GATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGTCCTTCAGGCC
*
25532 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
66 ATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
* * *
25597 TGATAAGTCCTTCGGGACATCCGTAAGACCTTCGGGTAGGATGCTTCAAATGAATTTGAAAATGA
131 TGATAAGTCCTTCGGGACATCCATAAGACCTTCGGATAGGATGCTTCAAATGAATTCGAAAATGA
25662 AAAAT
196 AAAAT
25667 GATG
1 GATG
25671 TTTTAAGAAG
Statistics
Matches: 190, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
200 30 0.16
201 160 0.84
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (200 bp):
GATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGTCCTTCAGGCC
ATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
TGATAAGTCCTTCGGGACATCCATAAGACCTTCGGATAGGATGCTTCAAATGAATTCGAAAATGA
AAAAT
Found at i:25847 original size:41 final size:42
Alignment explanation
Indices: 25729--25919 Score: 206
Period size: 42 Copynumber: 4.6 Consensus size: 42
25719 TTCACAATTT
** *
25729 ATAAGTCCTTCGGGTCATCAATAAGTCTTCCGAGCATGATGC
1 ATAAGTCCTTCGGGTCATCAATAAGTCTTTAGAGCAAGATGC
* * ** *
25771 TTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGTCATCAATAAGTCTTTAGAGCAAGATGC
* * * *
25812 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCGGGTCATCAATAAGTCTTTAGAGCAAGATGC
* * **
25854 TTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGTCATCAATAAGTCTTTAGAGCAAGATGC
* *
25895 ATAAGTCCTTCGGGCCATCCATAAG
1 ATAAGTCCTTCGGGTCATCAATAAG
25920 ACCTTCGGGT
Statistics
Matches: 118, Mismatches: 30, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
41 52 0.44
42 66 0.56
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (42 bp):
ATAAGTCCTTCGGGTCATCAATAAGTCTTTAGAGCAAGATGC
Found at i:25855 original size:213 final size:212
Alignment explanation
Indices: 25467--25859 Score: 642
Period size: 213 Copynumber: 1.8 Consensus size: 212
25457 AATGAAAAAT
*
25467 GATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGTCCTTCGGGCC
1 GATGAAATTTTTAAAAACGAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGTCCTTCGGGCC
* *
25532 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
66 ATCAATAAGTCTTCCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
* ** * *
25597 TGATAAGTCCTTCGGGACATCCGTAAGACCTTCGGGTAGGATGCTTCAAATGAATTTGAAAATGA
131 TGATAAGTCATTCGGGACATCAATAAGACCTTCGAGCAGGATGCTT-AAATGAATTTGAAAATGA
25662 AAAATGATGTTTTAAGAA
195 AAAATGATGTTTTAAGAA
* *
25680 GATGAAATTTTTAAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGTC
1 GATGAAATTTTTAAAAACGAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGTCCTTCGGGCC
*
25745 ATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
66 ATCAATAAGTCTTCCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
* * * *
25810 TGATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAAT
131 TGATAAGTCATTCGGGACATCAATAAGACCTTCGAGCAGGATGCTTAAAT
25860 CCTTCGGGTC
Statistics
Matches: 165, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
212 4 0.02
213 161 0.98
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (212 bp):
GATGAAATTTTTAAAAACGAAGAATGCGAGTTTCAAAATTTCACAATGTATAAGTCCTTCGGGCC
ATCAATAAGTCTTCCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
TGATAAGTCATTCGGGACATCAATAAGACCTTCGAGCAGGATGCTTAAATGAATTTGAAAATGAA
AAATGATGTTTTAAGAA
Found at i:25868 original size:83 final size:83
Alignment explanation
Indices: 25729--25919 Score: 337
Period size: 83 Copynumber: 2.3 Consensus size: 83
25719 TTCACAATTT
*
25729 ATAAGTCCTTCGGGTCATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCCTTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
25794 AGCCTTTAGAGCAAGATG
66 AGCCTTTAGAGCAAGATG
* *
25812 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCCTTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
*
25877 AGTCTTTAGAGCAAGATG
66 AGCCTTTAGAGCAAGATG
*
25895 ATAAGTCCTTCGGGCCATCCATAAG
1 ATAAGTCCTTCGGGCCATCAATAAG
25920 ACCTTCGGGT
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 102 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (83 bp):
ATAAGTCCTTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
AGCCTTTAGAGCAAGATG
Found at i:26052 original size:296 final size:296
Alignment explanation
Indices: 25516--26126 Score: 1078
Period size: 296 Copynumber: 2.1 Consensus size: 296
25506 TTCACAATGT
*
25516 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTA
1 ATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTA
* *
25581 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGACATCCGTAAGACCTTCGGGTAGGATGCTTCAA
66 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGATTCAA
25646 ATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGAAATTTTTAAAAACGAAGAATGCGAGT
131 ATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGAAATTTTTAAAAACGAAGAATGCGAGT
* * *
25711 TTCAAAATTTCACAATTTATAAGTCCTTCGGGTCATCAATAAGTCTTCCGAGCATGATGCTTAAA
196 TTCAAAATTTCACAATGTATAAGTCATTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAA
25776 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
261 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
* *
25812 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTA
* *
25877 AGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGATTCAA
66 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGATTCAA
* * *
25942 ATGAATTTGAAAATGAAAAATGATGTTTTAAGATGATGAAATTTTTTAAAACGAAGAATGTGAGT
131 ATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGAAATTTTTAAAAACGAAGAATGCGAGT
* * *
26007 TTCAAAATTTCACAATGTATAAGTCATTCGGGCCATCATTAAGTCTTTCGAGCATGGTGCTTAAA
196 TTCAAAATTTCACAATGTATAAGTCATTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAA
26072 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
261 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
26108 ATAAGTCCTTCGGGCCATC
1 ATAAGTCCTTCGGGCCATC
26127 CGTAAGACCT
Statistics
Matches: 298, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
296 298 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (296 bp):
ATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTA
AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGATTCAA
ATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGAAATTTTTAAAAACGAAGAATGCGAGT
TTCAAAATTTCACAATGTATAAGTCATTCGGGCCATCAATAAGTCTTCCGAGCATGATGCTTAAA
TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
Found at i:26132 original size:41 final size:42
Alignment explanation
Indices: 26025--26137 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
26015 TTCACAATGT
* * * * * *
26025 ATAAGTCATTCGGGCCATCATTAAGTCTTTCGAGCATGGTGC
1 ATAAGTCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGC
* * * *
26067 TTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGC
*
26108 ATAAGTCCTTCGGGCCATCCGTAAGACCTT
1 ATAAGTCCTTCGGGCCATCAGTAAG-CCTT
26138 CGGGTAGGAC
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 21 0.38
42 35 0.62
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (42 bp):
ATAAGTCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGC
Found at i:26185 original size:213 final size:213
Alignment explanation
Indices: 25812--26235 Score: 740
Period size: 213 Copynumber: 2.0 Consensus size: 213
25802 GAGCAAGATG
25812 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
* *
25877 AGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGATTCAA
66 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGACGATTCAA
* * * *
25942 ATGAATTTGAAAATGAAAAATGATGTTTTAAGATGATGAAATTTTTTAAAACGAAGAATGTGAGT
131 ATGAATTTGAAAATGAAAAATGAAGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGAGT
26007 TTCAAAATTTCACAATGT
196 TTCAAAATTTCACAATGT
* *
26025 ATAAGTCATTCGGGCCATCATTAAGTCTTTCGAGCATGGTGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
* * *
26090 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGACGTTTTAA
66 AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGACGATTCAA
*
26155 ATGAATTTGAAAATGGAAAATGAAGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGAGT
131 ATGAATTTGAAAATGAAAAATGAAGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGAGT
26220 TTCAAAATTTCACAAT
196 TTCAAAATTTCACAAT
26236 TTTTAAAATC
Statistics
Matches: 199, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
213 199 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (213 bp):
ATAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
AGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGACGATTCAA
ATGAATTTGAAAATGAAAAATGAAGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGAGT
TTCAAAATTTCACAATGT
Found at i:32274 original size:31 final size:31
Alignment explanation
Indices: 32232--32335 Score: 190
Period size: 31 Copynumber: 3.4 Consensus size: 31
32222 ATAACTTTTA
* *
32232 ATAGTCAAGAGACACAACAAAGCAACTCTTT
1 ATAGTCGAGAGACACAACAAAGCAACTCTCT
32263 ATAGTCGAGAGACACAACAAAGCAACTCTCT
1 ATAGTCGAGAGACACAACAAAGCAACTCTCT
32294 ATAGTCGAGAGACACAACAAAGCAACTCTCT
1 ATAGTCGAGAGACACAACAAAGCAACTCTCT
32325 ATAGTCGAGAG
1 ATAGTCGAGAG
32336 GTCATTTCGT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (31 bp):
ATAGTCGAGAGACACAACAAAGCAACTCTCT
Found at i:37577 original size:194 final size:194
Alignment explanation
Indices: 37377--37745 Score: 451
Period size: 194 Copynumber: 1.9 Consensus size: 194
37367 AAATGTCTCG
* * * * * * *
37377 AAAGTATCGATATCTTACATACATGTATCGATACATAATAATAT-AACATGTTGAAGTTTGACAA
1 AAAGTATCGATACCTTACACAAATGTATCGATACATAACAAT-TGAACAGGTTAAAATTTGACAA
* * * * * *
37441 AATCAGTTTCAGTTTGACAAAACATGTAGAG-A-TACC-AGAT-TGTTGAAATTTGTATCGATAT
65 AATCAGTTTCAATATGACAAAACAGGTAAAGCACT-CCTAGATATGTTG-AA--GGTATCGATAC
* *
37502 TTTTCTAAGTATATGCACCAAAGTATCGGTACTTTAGGAATTTAAAAGAATTGCAATAATAGCGC
126 TTTTATAAGTATATGCACCAAAGTATCGGTACTTTAGGAATTGAAAAGAATTGCAATAATAGCGC
37567 CTAT
191 CTAT
* *
37571 AAAGTATCGATACCTTAGACAAATGTATCGATACATGACAATTGAACAGGTTAAAATTTGACAAA
1 AAAGTATCGATACCTTACACAAATGTATCGATACATAACAATTGAACAGGTTAAAATTTGACAAA
** *
37636 ATTGGTTTCAATATGACAAAACCGGTAAAGCACTCCTAGATATGTTGAAGGTATCGATACTTTTA
66 ATCAGTTTCAATATGACAAAACAGGTAAAGCACTCCTAGATATGTTGAAGGTATCGATACTTTTA
* * *
37701 TAAGTATATGTATCATAGTATCGGTACTTTAGGAATTGAAAAGAA
131 TAAGTATATGCACCAAAGTATCGGTACTTTAGGAATTGAAAAGAA
37746 ATGAAAAAAA
Statistics
Matches: 147, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
193 1 0.01
194 131 0.89
195 3 0.02
196 7 0.05
197 5 0.03
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.32
Consensus pattern (194 bp):
AAAGTATCGATACCTTACACAAATGTATCGATACATAACAATTGAACAGGTTAAAATTTGACAAA
ATCAGTTTCAATATGACAAAACAGGTAAAGCACTCCTAGATATGTTGAAGGTATCGATACTTTTA
TAAGTATATGCACCAAAGTATCGGTACTTTAGGAATTGAAAAGAATTGCAATAATAGCGCCTAT
Found at i:39468 original size:159 final size:156
Alignment explanation
Indices: 39191--39497 Score: 474
Period size: 159 Copynumber: 1.9 Consensus size: 156
39181 ACCTAATATG
* * *
39191 TTGATAATACTAATAACAAATTAAGTAATTAACCTTTTTTTTATCGTTGGATTTCTAAGGCCACA
1 TTGATAATACTAATAACAAATTAAGTAATTAACCTTTTTATTATCGTCGAATTTCTAAGGCCACA
*
39256 TCAACTTAAAAGGAGCTATCTATTACATTATATAAACGCTACCTAATATGTTATTATGGTTGATA
66 TCAACTTAAAAGGAGCTATCTATTACATTACATAAACGCTACCTAATATGTTATTATGGTTGATA
39321 ACAAATCAAATAATTAACCGATTATA
131 ACAAATCAAATAATTAACCGATTATA
*
39347 TTGATAATACTAATAACATATTAAGTAATTAACCTATTTTATTATCGTCGAATTTCTAAGG-CAC
1 TTGATAATACTAATAACAAATTAAGTAATTAACCT-TTTTATTATCGTCGAATTTCTAAGGCCA-
* ** *
39411 CATCAGCTTTAAAAAGGCA-CTATCTATTATGTTACATAAGCGCTACCTAATATGTTATTATGGT
64 CATCAAC-TT-AAAAGG-AGCTATCTATTACATTACATAAACGCTACCTAATATGTTATTATGGT
39475 TGATAACAAATCAAATAATTAAC
126 TGATAACAAATCAAATAATTAAC
39498 TAATTATGTA
Statistics
Matches: 137, Mismatches: 9, Indels: 7
0.90 0.06 0.05
Matches are distributed among these distances:
156 36 0.26
157 28 0.20
158 2 0.01
159 70 0.51
160 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (156 bp):
TTGATAATACTAATAACAAATTAAGTAATTAACCTTTTTATTATCGTCGAATTTCTAAGGCCACA
TCAACTTAAAAGGAGCTATCTATTACATTACATAAACGCTACCTAATATGTTATTATGGTTGATA
ACAAATCAAATAATTAACCGATTATA
Found at i:39764 original size:224 final size:225
Alignment explanation
Indices: 39347--40154 Score: 915
Period size: 225 Copynumber: 3.6 Consensus size: 225
39337 ACCGATTATA
*
39347 TTGATAATACT-AATAACATATTAAGTAATTAACCTATTTTATTATCGTCGAATTTCTAAGG-CA
1 TTGATAATACTGAA-AACAAATTAAGTAATTAACCTATTTTATTATCGTCG-ATTTCTAAGGCCA
* *
39410 CCATCAGCTTTAAAAAGGCACTATCTATTATGTTACATAAGCGCTACCTAATATGTTATTATGGT
64 -CATCAGCTTTAAAAAGGCGCTATCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGGT
* * ** * * *
39475 TGATAACAAATCAAATAATTAACTAATTATG-TATCGTCAGATTTCTAAGATTATATCAACTTAA
128 TGATAACAAATTAAGTAATTAACTGGTTATGTTATCGTCGGATTTCTAAGACTCTATCAACTTAA
39539 ACTTTGGTAATATTTTTGACGTTACCTAATATG
193 ACTTTGGTAATATTTTTGACGTTACCTAATATG
* * * * **
39572 ATGATAATATTGAAAACAAATTAAATAATTAACCTATTTTGTTATCGTCAGATCGCTAAGGCCAC
1 TTGATAATACTGAAAACAAATTAAGTAATTAACCTATTTTATTATCGTC-GATTTCTAAGGCCAC
* * * *
39637 ATCA-ATTTAAAAAGGCGTTATCTATTACATTACATAAGCGCTACCTAATATGTTATTTTGGTTG
65 ATCAGCTTTAAAAAGGCGCTATCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGGTTG
* **
39701 ATAACAAATTAAGTAATTAACTGGTTATGTTTTCGTCGGATTTCTAAGACTCTA-CCGCTTAAAC
130 ATAACAAATTAAGTAATTAACTGGTTATGTTATCGTCGGATTTCTAAGACTCTATCAACTTAAAC
* * ** *
39765 TTTAGT-ATCATTTTAGGTGTTATCTAATATG
195 TTTGGTAAT-ATTTTTGACGTTACCTAATATG
* *
39796 TTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTATTATCGTCTGATTTCTAATGTCC-
1 TTGATAATACTGAAAACAAATTAAGTAATTAACCTATTTTATTATCGTC-GATTTCTAA-GGCCA
* *
39860 CATTAGCTTTAAAAAGGCGCTA-CTTATTACGTTACATAAGCGCTACCTAATATGTTATTATAGT
64 CATCAGCTTTAAAAAGGCGCTATC-TATTACGTTACATAAGCGCTACCTAATATGTTATTATGGT
* * * *
39924 TGATAACAAATTAAGTAATTAAGC-GGTTATATTATCGTTGGATTTCTAAGGCTCCATCAACTTA
128 TGATAACAAATTAAGTAATTAA-CTGGTTATGTTATCGTCGGATTTCTAAGACTCTATCAACTTA
* ** *
39988 AAATTTGACAACATTTTT-ATTCGTTACCTAATATG
192 AACTTTGGTAATATTTTTGA--CGTTACCTAATATG
* * * * **
40023 TTGATAATACTGATAACAAATTAAGTAATTAACTTATTTTGTTATCGTCGGATTTCTGA-GCTTC
1 TTGATAATACTGAAAACAAATTAAGTAATTAACCTATTTTATTATCGTC-GATTTCTAAGGCCAC
* * * ** *
40087 ATTAGC-TTAAAAATGAGCTA-CTTATTACGTTTTATAAGTGCTACCTAATAAT-TTATTATGGT
65 ATCAGCTTTAAAAAGGCGCTATC-TATTACGTTACATAAGCGCTACCTAAT-ATGTTATTATGGT
*
40149 TAATAA
128 TGATAA
40155 TATTTCCGGT
Statistics
Matches: 496, Mismatches: 72, Indels: 30
0.83 0.12 0.05
Matches are distributed among these distances:
223 2 0.00
224 166 0.33
225 230 0.46
226 30 0.06
227 68 0.14
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (225 bp):
TTGATAATACTGAAAACAAATTAAGTAATTAACCTATTTTATTATCGTCGATTTCTAAGGCCACA
TCAGCTTTAAAAAGGCGCTATCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGGTTGA
TAACAAATTAAGTAATTAACTGGTTATGTTATCGTCGGATTTCTAAGACTCTATCAACTTAAACT
TTGGTAATATTTTTGACGTTACCTAATATG
Found at i:40100 original size:109 final size:111
Alignment explanation
Indices: 39783--40101 Score: 292
Period size: 118 Copynumber: 2.8 Consensus size: 111
39773 CATTTTAGGT
* *
39783 GTTATCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTATTATCGTCTGA
1 GTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAA-CTATTTTATTATCGTCGGA
* * *
39848 TTTCTAATG-TCCCATTAGCTTTAAAAAGGCGCTACTTATTACGTTACATAAGC
65 TTTCTAAGGCT-CCATTAGC-TTAAAAATGCGCAAC-TATTA--TT--ATAAGC
* * * ** * *
39901 GCTACCTAATATGTT-ATTATAGTTGATAACAAATTAAGTAATTAAGCGGTTATATTATCGTTGG
1 GTTACCTAATATGTTGATAATA-CTGATAACAAATTAAGTAATTAA-CTATTTTATTATCGTCGG
* * * * **
39965 ATTTCTAAGGCTCCATCAACTTAAAATTTG-ACAAC-ATT-TT-TATTC
64 ATTTCTAAGGCTCCATTAGCTTAAAA-ATGCGCAACTATTATTATAAGC
*
40010 GTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACTTATTTTGTTATCGTCGGA
1 GTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAAC-TATTTTATTATCGTCGGA
* *
40075 TTTCTGA-GCTTCATTAGCTTAAAAATG
65 TTTCTAAGGCTCCATTAGCTTAAAAATG
40102 AGCTACTTAT
Statistics
Matches: 164, Mismatches: 32, Indels: 21
0.76 0.15 0.10
Matches are distributed among these distances:
107 2 0.01
108 15 0.09
109 58 0.35
110 5 0.03
112 2 0.01
115 3 0.02
117 14 0.09
118 64 0.39
119 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (111 bp):
GTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACTATTTTATTATCGTCGGAT
TTCTAAGGCTCCATTAGCTTAAAAATGCGCAACTATTATTATAAGC
Found at i:40304 original size:16 final size:17
Alignment explanation
Indices: 40283--40318 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
40273 CGTTATCAAT
40283 TTTAACCAACTAC-CTA
1 TTTAACCAACTACACTA
*
40299 TTTAACCAATTACACTA
1 TTTAACCAACTACACTA
40316 TTT
1 TTT
40319 TTTAATAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTAACCAACTACACTA
Found at i:41822 original size:52 final size:55
Alignment explanation
Indices: 41762--41883 Score: 157
Period size: 52 Copynumber: 2.3 Consensus size: 55
41752 TAATCGGGAC
*
41762 ACTCAACAAAACAACG-CTC-TATAGTTGGAGACCATTTTATAACTT-TACGGGG
1 ACTCAACAAAACAACGTCTCGTATAGTTGGAGACCATCTTATAACTTGTACGGGG
** *
41814 ACTCAAC-AAAGTA-GTTTCGTATAGTTGGAGACCATCTTATAACTTGTACGGGG
1 ACTCAACAAAACAACGTCTCGTATAGTTGGAGACCATCTTATAACTTGTACGGGG
*
41867 -CTCAACAAAGCAACGTC
1 ACTCAACAAAACAACGTC
41884 ATGGAGGACC
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
50 1 0.02
51 6 0.11
52 38 0.67
53 10 0.18
54 2 0.04
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (55 bp):
ACTCAACAAAACAACGTCTCGTATAGTTGGAGACCATCTTATAACTTGTACGGGG
Found at i:43879 original size:31 final size:30
Alignment explanation
Indices: 43844--44019 Score: 140
Period size: 31 Copynumber: 5.7 Consensus size: 30
43834 GGAGCATCTT
*
43844 GGGCCTAAGAGCCTACCCAAGAAAGTTCTCA
1 GGGCC-AAGAGCCTACCCAAGAAAGATCTCA
*
43875 GGGCCACAGGGCCTACCCAAGAAAGATCTCA
1 GGGCCA-AGAGCCTACCCAAGAAAGATCTCA
* * * *
43906 GGGCCGTAGGGCCTACCCAAGAATGATCTTA
1 GGGCC-AAGAGCCTACCCAAGAAAGATCTCA
* *
43937 GGGCCATGAGACCTACCCAAGAAAAATGCT-A
1 GGGCCAAGAG-CCTACCCAAGAAAGAT-CTCA
* * * **
43968 GGGCCGCAG-GGCTACCCAAGAATGATCTTG
1 GGGCC-AAGAGCCTACCCAAGAAAGATCTCA
* *
43998 GGGCCGCATAGCCTACCCAAGA
1 GGGCC-AAGAGCCTACCCAAGA
44020 GTCATTAGGT
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
29 2 0.02
30 24 0.20
31 91 0.76
32 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.27, T:0.14
Consensus pattern (30 bp):
GGGCCAAGAGCCTACCCAAGAAAGATCTCA
Found at i:44012 original size:92 final size:92
Alignment explanation
Indices: 43839--44019 Score: 224
Period size: 92 Copynumber: 2.0 Consensus size: 92
43829 CTAAGGGAGC
* *
43839 ATCTTGGGCCTAAGAGCCTACCCAAGAAAGTTCTCAGGGCCACAGGGCCTACCCAAGAAAGATCT
1 ATCTTGGGCCTAAGAGCCTACCCAAGAAAATGCTCAGGGCCACAGGGCCTACCCAAGAAAGATCT
* *
43904 CAGGGCCGTAGGGCCTACCCAAGAATG
66 CAGGGCCGCAGAGCCTACCCAAGAATG
* * *
43931 ATCTTAGGGCC-ATGAGACCTACCCAAGAAAAATGCT-AGGGCCGCAGGG-CTACCCAAGAATGA
1 ATCTT-GGGCCTAAGAG-CCTACCCAAG-AAAATGCTCAGGGCCACAGGGCCTACCCAAGAAAGA
** *
43993 TCTTGGGGCCGCATAGCCTACCCAAGA
63 TCTCAGGGCCGCAGAGCCTACCCAAGA
44020 GTCATTAGGT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
92 44 0.58
93 26 0.34
94 6 0.08
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.15
Consensus pattern (92 bp):
ATCTTGGGCCTAAGAGCCTACCCAAGAAAATGCTCAGGGCCACAGGGCCTACCCAAGAAAGATCT
CAGGGCCGCAGAGCCTACCCAAGAATG
Found at i:44013 original size:61 final size:61
Alignment explanation
Indices: 43854--44019 Score: 194
Period size: 62 Copynumber: 2.7 Consensus size: 61
43844 GGGCCTAAGA
* * * * * * *
43854 GCCTACCCAAGAAAGTTCTCAGGGCCACAGGGCCTACCCAAGAAAGATCTCAGGGCCGTAGG
1 GCCTACCCAAGAATGATCTTAGGGCCA-TGAGCCTACCCAAGAAAAATCTCAGGGCCGCAGG
43916 GCCTACCCAAGAATGATCTTAGGGCCATGAGACCTACCCAAGAAAAATGCT-AGGGCCGCAGG
1 GCCTACCCAAGAATGATCTTAGGGCCATGAG-CCTACCCAAGAAAAAT-CTCAGGGCCGCAGG
*
43978 G-CTACCCAAGAATGATCTTGGGGCCGCAT-AGCCTACCCAAGA
1 GCCTACCCAAGAATGATCTTAGGG-C-CATGAGCCTACCCAAGA
44020 GTCATTAGGT
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
61 34 0.37
62 53 0.58
63 5 0.05
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (61 bp):
GCCTACCCAAGAATGATCTTAGGGCCATGAGCCTACCCAAGAAAAATCTCAGGGCCGCAGG
Found at i:46086 original size:39 final size:39
Alignment explanation
Indices: 46042--46118 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
46032 CTTGGCTCAG
* * * *
46042 CGACTCGGCTCAGTGGCTCAACTCGGTGGCTCTGCTCGA
1 CGACTCGGCTCAGTGACTCAACGCGGCGGCTCGGCTCGA
*
46081 CGACTCGGCTCAGTGACTCGACGCGGCGGCTCGGCTCG
1 CGACTCGGCTCAGTGACTCAACGCGGCGGCTCGGCTCG
46119 GTGGCTCAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.35, G:0.34, T:0.19
Consensus pattern (39 bp):
CGACTCGGCTCAGTGACTCAACGCGGCGGCTCGGCTCGA
Found at i:50418 original size:17 final size:17
Alignment explanation
Indices: 50386--50434 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
50376 CTTCCCCTTG
*
50386 TTGAGTCATCATCTTTGC
1 TTGAGTC-TTATCTTTGC
50404 TTGAGTCTTATCTTTGC
1 TTGAGTCTTATCTTTGC
*
50421 TTAAGTCTTCATCT
1 TTGAGTCTT-ATCT
50435 CATGACAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 17 0.61
18 11 0.39
ACGTcount: A:0.16, C:0.20, G:0.14, T:0.49
Consensus pattern (17 bp):
TTGAGTCTTATCTTTGC
Done.