Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001559.1 Hibiscus syriacus cultivar Beakdansim tig00003081_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: 120951
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:10479 original size:10 final size:9
Alignment explanation
Indices: 10461--10490 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
10451 ATAAAAAATG
10461 AAAAACAAA
1 AAAAACAAA
*
10470 AAAAACCAA
1 AAAAACAAA
10479 AAAAACAAA
1 AAAAACAAA
10488 AAA
1 AAA
10491 GAAAAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAACAAA
Found at i:10506 original size:15 final size:15
Alignment explanation
Indices: 10453--10510 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
10443 GCCTGAAGAT
10453 AAAAAATGAAAAACAA-
1 AAAAAA-GAAAAA-AAC
*
10469 AAAAAACCAAAAAAAC
1 AAAAAA-GAAAAAAAC
*
10485 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAC
*
10500 AAGAAAGAAAA
1 AAAAAAGAAAA
10511 TAAGGGTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 19 0.53
16 17 0.47
ACGTcount: A:0.83, C:0.07, G:0.09, T:0.02
Consensus pattern (15 bp):
AAAAAAGAAAAAAAC
Found at i:11943 original size:51 final size:51
Alignment explanation
Indices: 11800--12985 Score: 1117
Period size: 51 Copynumber: 22.9 Consensus size: 51
11790 TGAAGCGGAA
* * * *
11800 GAAGATGTTCGAGTTC-ATACTCCCTAGAGAAAGAGTGAGTGAACCCGTTT
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * * * * *
11850 GAAGATGTCCGAGTTCCATACT-CCTAGAGAAAGAGGGAGCAAACCCATGT
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
11900 GAAGTTATTGGAGTTCTATACTTCCTAAAGAAAGAGGGAGCAAACCCGTTT
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* *
11951 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAG-ATAT-TC-GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * * *
12005 GAAGAT-GTCTGAGTTCCATACTCCATAGAGAAAGAGGGAGCGAACCCGTGT
1 GAAGATATTC-GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
12056 GAAGTTATTGGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* *
12107 GAAGAATATGTCCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTT
1 GAAG-ATAT-T-CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
12161 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTTT
1 ---GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * * * * *
12215 GAAAATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCATGT
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
12266 GAAGTTATT-GAAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAAACCGTTT
1 GAAGATATTCG-AGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * * *
12317 GAAGAAGATGTCCGAGTTCTATACTCCCTATAGAAAGAGGGAACAAACTCGTTT
1 GAAG-ATAT-T-CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * * * *
12371 GAAGAAGATGTACGAGTTCTATACTTCCTGAAGAAAGAGGAAGTGAACTCGTTT
1 GAAG-ATAT-T-CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
12425 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTT
1 ---GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * *
12479 GAAGATGTTCGAGTT-TCATACTCCTTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGATATTCGAGTTCT-ATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
12530 GAAGTTATTCGAGTTC-ATACTCCCTAGAGAAAGAGGGAGAGAACCCGTGT
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * *
12580 GAAGTTATTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCC----
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * ** *
12627 GATG-T-CT-GAGTTCCATACTCCCTAGGGAAAGAGGGAGCGAACCAGTTT
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
12675 GAAGAAAATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGACCGAACCTGTTT
1 GAAG---ATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * *
12729 GTTAAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAAGGAGCGAACCCGTTT
1 G---AAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
12783 GAAGATTTTCGAGTTCTATACTCCTTGAATAAAGAGGGAGCGAACCCGTTT
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * *
12834 AAAGATTTTCGAGTTCTATACTCCCTGAAA-AAAGAGGTAGCGAA-CCGTTT
1 GAAGATATTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTT
* * * *
12884 AAAGATTTTCGAGTTCTATACTCCCTGAAA-AAAGAGGTAGCGAACCCATTTT
1 GAAGATATTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCC-GTTT
* *
12936 CAGAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCC
1 --GAAGA-TATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCC
12986 ATTTCCAAAA
Statistics
Matches: 966, Mismatches: 127, Indels: 81
0.82 0.11 0.07
Matches are distributed among these distances:
44 31 0.03
45 1 0.00
46 1 0.00
47 3 0.00
48 3 0.00
50 153 0.16
51 379 0.39
52 14 0.01
53 5 0.01
54 321 0.33
55 39 0.04
56 5 0.01
57 11 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (51 bp):
GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
Found at i:11992 original size:54 final size:54
Alignment explanation
Indices: 11797--12985 Score: 992
Period size: 54 Copynumber: 22.9 Consensus size: 54
11787 TAGTGAAGCG
* *
11797 GAAGAAGATGT-TCGAGTTC-ATACTCCCTAGAGAAAGAGTGAGTGAACCCGTTT
1 GAAGAAGATGTCT-GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * * *
11850 ---GAAGATGTCCGAGTTCCATACT-CCTAGAGAAAGAGGGAGCAAACCCATGT
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
** * * * *
11900 GAAG-TTAT-T-GGAGTTCTATACTTCCTAAAGAAAGAGGGAGCAAACCCGTTT
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
11951 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
12005 ---GAAGATGTCTGAGTTCCATACTCCATAGAGAAAGAGGGAGCGAACCCGTGT
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
** * *
12056 GAAG-TTAT-T-GGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* * *
12107 GAAGAATATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* *
12161 GAAGAAGATGT-TCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCT-GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
12215 G-A-AA-ATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC--AT
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * * *
12264 G-TGAAGTTAT-TGAAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAAACCGTTT
1 GAAGAAGATGTCTG-AGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* * * * *
12317 GAAGAAGATGTCCGAGTTCTATACTCCCTATAGAAAGAGGGAACAAACTCGTTT
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * *
12371 GAAGAAGATGTAC-GAGTTCTATACTTCCT-GAAGAAAGAGGAAGTGAACTCGTTT
1 GAAGAAGATGT-CTGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* *
12425 GAAGAAGATGT-TCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTT
1 GAAGAAGATGTCT-GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
12479 GAAGATG-T-TC-GAGTT-TCATACTCCTTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCTGAGTTCT-ATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
** * *
12530 GAAG-TTAT-TC-GAGTTC-ATACTCCCTAGAGAAAGAGGGAGAGAACCCGTGT
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
** *
12580 GAAG-TTAT-TC-GAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCC----
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* * *
12627 ------GATGTCTGAGTTCCATACTCCCTAGGGAAAGAGGGAGCGAACCAGTTT
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
12675 GAAGAAAATGT-TCGAGTTCTATACTCCCTAGAGAAAGAGGGACCGAACCTGTTT
1 GAAGAAGATGTCT-GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
12729 GTTA-AAGAT-TTTCGAGTTCTATACTCCCT-GAAGAAAGAAGGAGCGAACCCGTTT
1 G-AAGAAGATGTCT-GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* * * *
12783 GAAG-A-TTTTC-GAGTTCTATACT-CCTTGAATAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCTGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* * *
12834 --A-AAGAT-TTTCGAGTTCTATACTCCCT-GAAAAAAGAGGTAGCGAA-CCGTTT
1 GAAGAAGATGTCT-GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* * * *
12884 --A-AAGAT-TTTCGAGTTCTATACTCCCT-GAAAAAAGAGGTAGCGAACCCATTT
1 GAAGAAGATGTCT-GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT
**
12935 TCAGAAGATTGT-TCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCC
1 GAAGAAGA-TGTCT-GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCC
12986 ATTTCCAAAA
Statistics
Matches: 962, Mismatches: 104, Indels: 138
0.80 0.09 0.11
Matches are distributed among these distances:
42 2 0.00
43 2 0.00
44 31 0.03
45 1 0.00
49 5 0.01
50 156 0.16
51 338 0.35
52 15 0.02
53 16 0.02
54 352 0.37
55 43 0.04
56 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (54 bp):
GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
Found at i:12187 original size:210 final size:212
Alignment explanation
Indices: 11800--13026 Score: 1281
Period size: 210 Copynumber: 5.9 Consensus size: 212
11790 TGAAGCGGAA
* * *
11800 GAAGATGT-TCGAGTT-CATACTCCCTAGAGAAAGAGTGAGTGAACCCGTTTGAAGATGTCCGAG
1 GAAGATGTCTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAG
* * * * ** * *
11863 TTCCATAC-TCCT-AGAGAAAGAGGGAGCAAACCCATGTGAAG-TTAT-TGGAGTTCTATACTTC
66 TTCTATACTTCCTGAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTCTATACTCC
* *
11924 CTAAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATG-TCTGAGTTCTATACTCCCTAG-AGAAA
131 CTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC-GAGTTCTATACTCCCTAGAAGAAA
11987 GAGGGAGCGAACCCGTTT
195 GAGGGAGCGAACCCGTTT
* * * * *
12005 GAAGATGTCT-GAGTTCCATACTCCATAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAG
1 GAAGATGTCTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAG
* *
12069 TTCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAATATGTCCGAGTTCTATACTT
66 TTCTATACTTCCTGAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGT-CGAGTTCTATACTC
*
12133 CCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAA
130 CCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTAGAAGAAA
*
12197 AAGGGAGCGAACCCGTTT
195 GAGGGAGCGAACCCGTTT
* * * * *
12215 GAAAATGTC-CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCATGTGAAGTTATT-GAA
1 GAAGATGTCTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCG-A
*
12278 GTTCTATACTTCCTGA-AGAAAGAGGGAGCGAAACCGTTTGAAGAAGATGTCCGAGTTCTATACT
65 GTTCTATACTTCCTGAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGT-CGAGTTCTATACT
* * * * *
12342 CCCT-ATAGAAAGAGGGAACAAACTCGTTTGAAGAAGATGTACGAGTTCTATACTTCCT-GAAGA
129 CCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTAGAAGA
* * *
12405 AAGAGGAAGTGAACTCGTTT
193 AAGAGGGAGCGAACCCGTTT
*
12425 GAAGAAGATGT-TCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTTC
1 ---GAAGATGTCTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* **
12489 GAGTT-TCATAC-TCCTTAGAGAAAGAGGGAGCGAACCCGTTTGAAG-TTAT-TCGAGTTC-ATA
63 GAGTTCT-ATACTTCCTGAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTCTATA
* * * * *
12549 CTCCCT-AGAGAAAGAGGGAGAGAACCCG--TG-TGAAGTTATTCGAGTTCTATACTTCCT-GAA
127 CTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTAGAA
12609 GAAAGAGGGAGCGAACCC----
191 GAAAGAGGGAGCGAACCCGTTT
* *
12627 ---GATGTCT-GAGTTCCATACTCCCTAGGGAAAGAGGGAGCGAACCAGTTTGAAGAAAATGTTC
1 GAAGATGTCTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG---ATGTTC
* * * * *
12688 GAGTTCTATACTCCCT-AGAGAAAGAGGGACCGAACCTGTTTGTTA-AAGATTTTCGAGTTCTAT
63 GAGTTCTATACTTCCTGAGAGAAAGAGGGAGCGAACCCGTTTG-AAGAAGA-TGTCGAGTTCTAT
* * *
12751 ACTCCCTGAAGAAAGAAGGAGCGAACCCGTTT---GAAGATTTTCGAGTTCTATACT-CCTTGAA
126 ACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTAGAA
*
12812 TAAAGAGGGAGCGAACCCGTTT
191 GAAAGAGGGAGCGAACCCGTTT
* * * * * * *
12834 AAAGAT-TTTCGAGTTCTATACTCCCT-GAAAAAAGAGGTAGCGAA-CCGTTTAAAGATTTTCGA
1 GAAGATGTCTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGA
* * * * **
12896 GTTCTATACTCCCTGA-AAAAAGAGGTAGCGAACCCATTTTCAGAAGATTGTTCGAGTTCTATAC
65 GTTCTATACTTCCTGAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TG-TCGAGTTCTATAC
* * *
12960 TCCCTGAAGAAAGAGGGAGCGAACCCATTTCCAA-AAGATTGTTCGAG-TCTCATACTCTCTA-A
128 TCCCTGAAGAAAGAGGGAGCGAACCCGTTT-GAAGAAGA-TGTTCGAGTTCT-ATACTCCCTAGA
13022 AGAAA
190 AGAAA
13027 TAGAGAGAAG
Statistics
Matches: 877, Mismatches: 92, Indels: 100
0.82 0.09 0.09
Matches are distributed among these distances:
196 47 0.05
197 1 0.00
199 39 0.04
200 6 0.01
201 1 0.00
202 11 0.01
203 67 0.08
204 1 0.00
205 15 0.02
206 134 0.15
207 72 0.08
208 4 0.00
209 41 0.05
210 320 0.36
211 20 0.02
212 10 0.01
213 87 0.10
214 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (212 bp):
GAAGATGTCTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAG
TTCTATACTTCCTGAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTCTATACTCC
CTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTAGAAGAAAG
AGGGAGCGAACCCGTTT
Found at i:13053 original size:55 final size:55
Alignment explanation
Indices: 12994--13180 Score: 236
Period size: 55 Copynumber: 3.4 Consensus size: 55
12984 CCATTTCCAA
* *
12994 AAGATTGTTCGAGTCTCATACTCTCTAAAGAAATAGAGAGAAGACACGATTATTG
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGAAGACACGATTGTTG
* * * *
13049 AAGATTGTTCGAGTCTCATACTCTTTGAAGAAATAGGGAGCAGACACAATTGTTG
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGAAGACACGATTGTTG
* * * * *
13104 AAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGA-AAATAGACATGATTGTTG
1 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGA-AGACACGATTGTTG
13159 AAGA-TGTTCGAGT-TCTATACTC
1 AAGATTGTTCGAGTCTC-ATACTC
13181 CAAAAGGAGG
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 15 0.13
55 97 0.86
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (55 bp):
AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGAAGACACGATTGTTG
Found at i:13078 original size:110 final size:110
Alignment explanation
Indices: 12938--13181 Score: 289
Period size: 110 Copynumber: 2.2 Consensus size: 110
12928 CCCATTTTCA
* *
12938 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGC-GAACCCATTTCCAAAAGATTGT
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAG-ACACAATTCCAAAAGATTGT
* *
13002 TCGAGTCTCATACTCTCTAAAGAAATAGAGAGA-AGACACGATTATT
65 TCAAGTCTCATACTCTCTAAAGAAATAGA-AAATAGACACGATTATT
** * ****
13048 GAAGATTGTTCGAG-TCTCATACTCTTTGAAGAAATAGGGAGCAGACACAATTGTTGAAGATTGT
1 GAAGATTGTTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCAGACACAATTCCAAAAGATTGT
* * * * *
13112 TCAAGTCTTATACTCTCTGAAGGAATAGAAAATAGACATGATTGTT
65 TCAAGTCTCATACTCTCTAAAGAAATAGAAAATAGACACGATTATT
13158 GAAGA-TGTTCGAGTTCTATACTCC
1 GAAGATTGTTCGAGTTCTATACTCC
13182 AAAAGGAGGG
Statistics
Matches: 113, Mismatches: 17, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
109 19 0.17
110 93 0.82
111 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (110 bp):
GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGACACAATTCCAAAAGATTGTT
CAAGTCTCATACTCTCTAAAGAAATAGAAAATAGACACGATTATT
Found at i:15478 original size:20 final size:20
Alignment explanation
Indices: 15453--15493 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
15443 TCGTTTAAGT
15453 GGGTTGTCTTAACTATTAGA
1 GGGTTGTCTTAACTATTAGA
15473 GGGTTGTCTTAACTATTAGA
1 GGGTTGTCTTAACTATTAGA
15493 G
1 G
15494 CAATGACACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (20 bp):
GGGTTGTCTTAACTATTAGA
Found at i:20063 original size:2 final size:2
Alignment explanation
Indices: 20056--20083 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20046 TTTAGACCAA
20056 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
20084 TATGGGTAGA
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:27383 original size:15 final size:15
Alignment explanation
Indices: 27337--27383 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
27327 ATTTTTTTTC
27337 TATTTGTATACACTT
1 TATTTGTATACACTT
* *
27352 TCAGTTTTTCT-CACTT
1 T-A-TTTGTATACACTT
27368 TATTTGTATACACTT
1 TATTTGTATACACTT
27383 T
1 T
27384 CAATTTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 5 0.20
15 8 0.32
16 7 0.28
17 5 0.20
ACGTcount: A:0.21, C:0.17, G:0.06, T:0.55
Consensus pattern (15 bp):
TATTTGTATACACTT
Found at i:27391 original size:17 final size:17
Alignment explanation
Indices: 27333--27391 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
27323 CTTTATTTTT
*
27333 TTTCTATTTGTATACAC
1 TTTCAATTTGTATACAC
* * *
27350 TTTCAGTTTTTCT-CAC
1 TTTCAATTTGTATACAC
27366 TTT--ATTTGTATACAC
1 TTTCAATTTGTATACAC
27381 TTTCAATTTGT
1 TTTCAATTTGT
27392 TTTTCCCAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
14 5 0.16
15 6 0.19
16 6 0.19
17 15 0.47
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.56
Consensus pattern (17 bp):
TTTCAATTTGTATACAC
Found at i:28305 original size:29 final size:28
Alignment explanation
Indices: 28253--28332 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 28
28243 ATTTGAGTGT
*
28253 TTAAAGATT-TTTTTTAATCAAAATAAATAA
1 TTAAAG-TTATTTTTT-GTCAAAATAAAT-A
**
28283 TTAAAGTTATTTTTTGTCAAAATAGGTA
1 TTAAAGTTATTTTTTGTCAAAATAAATA
*
28311 TCTAAAG-TATTTTATGTCAAAA
1 T-TAAAGTTATTTTTTGTCAAAA
28333 CAGGTACATA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 16 0.36
29 16 0.36
30 12 0.27
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (28 bp):
TTAAAGTTATTTTTTGTCAAAATAAATA
Found at i:28322 original size:28 final size:29
Alignment explanation
Indices: 28284--28338 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
28274 AATAAATAAT
* *
28284 TAAAGTTATTTTTTGTCAAAATAGGTATC
1 TAAAGTTATTTTATGTCAAAACAGGTATC
28313 TAAAG-TATTTTATGTCAAAACAGGTA
1 TAAAGTTATTTTATGTCAAAACAGGTA
28339 CATAAACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (29 bp):
TAAAGTTATTTTATGTCAAAACAGGTATC
Found at i:28349 original size:28 final size:28
Alignment explanation
Indices: 28290--28349 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
28280 TAATTAAAGT
* * *
28290 TATTTTTTGTCAAAATAGGTATCTAAAG
1 TATTTTATGTCAAAACAGGTATCTAAAC
28318 TATTTTATGTCAAAACAGGTA-CATAAAC
1 TATTTTATGTCAAAACAGGTATC-TAAAC
28346 TATT
1 TATT
28350 CAAACTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (28 bp):
TATTTTATGTCAAAACAGGTATCTAAAC
Found at i:28495 original size:14 final size:14
Alignment explanation
Indices: 28476--28504 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28466 TACTTTAGGT
28476 ACCTATTTTGACTA
1 ACCTATTTTGACTA
28490 ACCTATTTTGACTA
1 ACCTATTTTGACTA
28504 A
1 A
28505 AAAGATAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (14 bp):
ACCTATTTTGACTA
Found at i:28498 original size:44 final size:44
Alignment explanation
Indices: 28436--28532 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 44
28426 AAGAATTGAA
* *
28436 TATTTTAACTACCTATTTTGACCCAAAAA-AT-ACTTTAGGTACC
1 TATTTTGACTACCTATTTTGA-CCAAAAAGATAACTTTAAGTACC
* * *
28479 TATTTTGACTAACCTATTTTGACTAAAAAGATAACTTTAATTATC
1 TATTTTGACT-ACCTATTTTGACCAAAAAGATAACTTTAAGTACC
28524 TATTTTGAC
1 TATTTTGAC
28533 CAAAAATTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 15 0.33
44 13 0.28
45 18 0.39
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (44 bp):
TATTTTGACTACCTATTTTGACCAAAAAGATAACTTTAAGTACC
Found at i:29290 original size:5 final size:5
Alignment explanation
Indices: 29254--29301 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
29244 ATTAACAAAC
* *
29254 AAATA AAAT- AAATA AGATA AGATA AAGA-A AAATA AAATA AAATA AAAT
1 AAATA AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA AAATA AAAT
29302 GAAGACAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 5 0.13
5 32 0.84
6 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:29298 original size:25 final size:25
Alignment explanation
Indices: 29258--29340 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
29248 ACAAACAAAT
* *
29258 AAAAT-AAATAAGATAAGATAAAGA
1 AAAATAAAATAAAATAAAATAAAGA
*
29282 AAAATAAAATAAAATAAAATGAAGA
1 AAAATAAAATAAAATAAAATAAAGA
* **
29307 CAAATAGGATAAAAATAATAAT-AAGA
1 AAAATAAAAT-AAAATAA-AATAAAGA
*
29333 AATATAAA
1 AAAATAAA
29341 GAAAAAAGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
24 5 0.11
25 23 0.50
26 15 0.33
27 3 0.07
ACGTcount: A:0.71, C:0.01, G:0.10, T:0.18
Consensus pattern (25 bp):
AAAATAAAATAAAATAAAATAAAGA
Found at i:29467 original size:79 final size:78
Alignment explanation
Indices: 29320--29467 Score: 192
Period size: 79 Copynumber: 1.9 Consensus size: 78
29310 ATAGGATAAA
* * * *
29320 AATAATAATAAGAAATATAAAGAAAAAAGAAACAAGGAAAAAATAAAAAATATAGATAAATAGGA
1 AATAATAATAAAAAATATAAAGAAAAAAGAAACAAGGAAAAAAT-AAAAATACACATAAATAGAA
29385 TAAATATAAAAAAT
65 TAAATATAAAAAAT
* *
29399 AATAATAATAAAAAATATAAAGAAAGAAGAAATAAGGGAACAAAAT-AAAATACACATTAAATA-
1 AATAATAATAAAAAATATAAAGAAAAAAGAAACAA-GGAA-AAAATAAAAATACACA-TAAATAG
29462 AATAAA
63 AATAAA
29468 AACTAGAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
79 45 0.75
80 10 0.17
81 5 0.08
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (78 bp):
AATAATAATAAAAAATATAAAGAAAAAAGAAACAAGGAAAAAATAAAAATACACATAAATAGAAT
AAATATAAAAAAT
Found at i:29756 original size:12 final size:11
Alignment explanation
Indices: 29712--29757 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 11
29702 TATCGCATAA
29712 AAAATAACAAAT
1 AAAATAA-AAAT
*
29724 AAAATAGAAAT
1 AAAATAAAAAT
29735 AAAATAAAAAAT
1 AAAAT-AAAAAT
29747 GAAAATAAAAA
1 -AAAATAAAAA
29758 AAGGATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 9 0.30
12 16 0.53
13 5 0.17
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:30842 original size:20 final size:19
Alignment explanation
Indices: 30809--30885 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 19
30799 GAGAAAAGGA
*
30809 AAAAGAAATTAATAATAAAT
1 AAAA-AAATAAATAATAAAT
30829 AAAAACAATAAATAATAAAT
1 AAAAA-AATAAATAATAAAT
*
30849 AAGATAAATAAATAATAAAAT
1 AA-AAAAATAAATAAT-AAAT
30870 GAAATAAAATAAATAA
1 -AAA-AAAATAAATAA
30886 ATAGATAAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.02
20 29 0.59
21 7 0.14
22 12 0.24
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (19 bp):
AAAAAAATAAATAATAAAT
Found at i:30858 original size:13 final size:12
Alignment explanation
Indices: 30822--30899 Score: 70
Period size: 13 Copynumber: 6.2 Consensus size: 12
30812 AGAAATTAAT
*
30822 AATAAATAAAAA
1 AATAAATAAATA
30834 CAATAAAT-AATA
1 -AATAAATAAATA
30846 AATAAGATAAATA
1 AATAA-ATAAATA
30859 AAT-AATAAAATGA
1 AATAAAT-AAAT-A
30872 AATAAAATAAATA
1 AAT-AAATAAATA
* *
30885 AATAGATAAGTA
1 AATAAATAAATA
30897 AAT
1 AAT
30900 GAAAAACATT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
11 7 0.12
12 20 0.36
13 22 0.39
14 4 0.07
15 3 0.05
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (12 bp):
AATAAATAAATA
Found at i:30874 original size:5 final size:4
Alignment explanation
Indices: 30822--30899 Score: 70
Period size: 4 Copynumber: 18.8 Consensus size: 4
30812 AGAAATTAAT
*
30822 AATA AATA AAAA CAATA AAT- AATA AATA AGATA AATA AAT- AATAA AATGA
1 AATA AATA AATA -AATA AATA AATA AATA A-ATA AATA AATA AAT-A AAT-A
* *
30872 AATAA AATA AATA AATA GATA AGTA AAT
1 AAT-A AATA AATA AATA AATA AATA AAT
30900 GAAAAACATT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
3 6 0.10
4 37 0.61
5 18 0.30
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:30877 original size:10 final size:9
Alignment explanation
Indices: 30822--30886 Score: 64
Period size: 9 Copynumber: 7.1 Consensus size: 9
30812 AGAAATTAAT
30822 AATAAATAA
1 AATAAATAA
30831 AA-ACAATAAA
1 AATA-AAT-AA
30841 TAATAAATAA
1 -AATAAATAA
*
30851 GATAAAT-A
1 AATAAATAA
30859 AAT-AATAA
1 AATAAATAA
30867 AATGAAATAA
1 AAT-AAATAA
30877 AATAAATAA
1 AATAAATAA
30886 A
1 A
30887 TAGATAAGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
7 3 0.06
8 8 0.17
9 18 0.38
10 12 0.26
11 5 0.11
12 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.22
Consensus pattern (9 bp):
AATAAATAA
Found at i:30900 original size:30 final size:31
Alignment explanation
Indices: 30822--30903 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 31
30812 AGAAATTAAT
*
30822 AATAAATAAAAACAAT-AAATAATAAATAAGATA
1 AATAAATAATAA-AATGAAAT-A-AAATAAGATA
30855 AATAAATAATAAAATGAAATAAAATAA-ATA
1 AATAAATAATAAAATGAAATAAAATAAGATA
*
30885 AATAGATAAGT-AAATGAAA
1 AATAAATAA-TAAAATGAAA
30904 AACATTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
30 19 0.42
31 7 0.16
32 4 0.09
33 15 0.33
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (31 bp):
AATAAATAATAAAATGAAATAAAATAAGATA
Found at i:31027 original size:13 final size:13
Alignment explanation
Indices: 31009--31107 Score: 59
Period size: 13 Copynumber: 7.9 Consensus size: 13
30999 ATATATATAT
31009 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
31022 TTTTAAAAA-TTA
1 TTTTAAAAACTAA
* *
31034 -TAT-AATA-TAGA
1 TTTTAAAAACTA-A
31045 TTTTTAAAAACTAA
1 -TTTTAAAAACTAA
*
31059 TTTTCAAAACT-A
1 TTTTAAAAACTAA
* *
31071 -TATAACATA-TAA
1 TTTTAA-AAACTAA
31083 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
31096 TTTTCAAAACTA
1 TTTTAAAAACTA
31108 TATACTATAT
Statistics
Matches: 64, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
10 4 0.06
11 7 0.11
12 8 0.12
13 39 0.61
14 4 0.06
15 2 0.03
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (13 bp):
TTTTAAAAACTAA
Found at i:31039 original size:39 final size:38
Alignment explanation
Indices: 30909--31245 Score: 270
Period size: 37 Copynumber: 8.9 Consensus size: 38
30899 TGAAAAACAT
* * * *
30909 TTTTTAAAACTAT-TCA-ATATATGTTTTAAAAAATAA
1 TTTTCAAAACTATATAATATATATATTTTTAAAAATAA
*
30945 TTTTCAAAA-TCATAT-A-GTATATATTTTTAACAGAATAA
1 TTTTCAAAACT-ATATAATATATATATTTTTAA-A-AATAA
*
30983 TTTTCAAAACTAGATAATATATATATTTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTTAAAAA-TAA
* * *
31022 TTTTAAAAATTATAT-A-ATATAGATTTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTTAAAAA-TAA
*
31059 TTTTCAAAACTATATAACATATA-A-TTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATATTTTTAAAAA-TAA
* * **
31096 TTTTCAAAACTATATACTATATATGTTTTTCAAAAATGT
1 TTTTCAAAACTATATAATATATATATTTTT-AAAAATAA
* * *
31135 TTTTAAAAACTATATATTATATATATTTTTTTAAAAAAATA
1 TTTTCAAAACTATATA--ATATATATATTTTTAAAAATA-A
* * *
31176 TTTTTAAAACTATAT-A-ATATATGTTTTCAAAAA-AA
1 TTTTCAAAACTATATAATATATATATTTTTAAAAATAA
*
31211 TGTTTTCAAAAGCTATAT-AT-TATATATTTTCAAAA
1 --TTTTCAAAA-CTATATAATATATATATTTTTAAAA
31246 TATTTAAAAA
Statistics
Matches: 253, Mismatches: 28, Indels: 38
0.79 0.09 0.12
Matches are distributed among these distances:
35 2 0.01
36 23 0.09
37 92 0.36
38 44 0.17
39 43 0.17
40 23 0.09
41 26 0.10
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.44
Consensus pattern (38 bp):
TTTTCAAAACTATATAATATATATATTTTTAAAAATAA
Found at i:34025 original size:3 final size:3
Alignment explanation
Indices: 34017--34069 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
34007 AAATACATGT
34017 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
34065 ATA AT
1 ATA AT
34070 TGGTTCTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:37953 original size:3 final size:3
Alignment explanation
Indices: 37945--37969 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
37935 TTAATTTGAA
37945 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
37970 GTATAGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:39690 original size:30 final size:31
Alignment explanation
Indices: 39654--39713 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
39644 AAATTTTATA
39654 GGGTAAAATTAT-GGAAAATATAAAAAAAAG
1 GGGTAAAATTATGGGAAAATATAAAAAAAAG
*
39684 GGGTAAAATTATGGGAAAATATTAAAAAAA
1 GGGTAAAATTATGGGAAAATATAAAAAAAA
39714 TGGAAGATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.58, C:0.00, G:0.20, T:0.22
Consensus pattern (31 bp):
GGGTAAAATTATGGGAAAATATAAAAAAAAG
Found at i:41760 original size:2 final size:2
Alignment explanation
Indices: 41753--41777 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41743 ATAACTTATC
41753 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41778 CATTATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53526 original size:43 final size:43
Alignment explanation
Indices: 53465--53620 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 43
53455 CAGAGCCAAT
53465 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
53508 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
53559 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
53602 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
53621 GACCGCTGGT
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
43 38 0.45
44 3 0.04
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 3 0.04
51 20 0.24
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:53526 original size:98 final size:98
Alignment explanation
Indices: 53252--53811 Score: 741
Period size: 106 Copynumber: 5.5 Consensus size: 98
53242 AGGTTTTACC
53252 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
53317 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTT
*
53357 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
53422 ATGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
53455 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
53520 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
53553 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
53614 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCGATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAAC-A-------ATTT
* * * *
53655 CAGAGCCAATTTCAACTTCACAACGAAGGAGATTGGCCTCCAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
53720 ACGAAGAGACCGCTGGTTGTCAACAAGTAATTTCCCAGTTT
66 ACGAAGGGACCGCTGGTTGT---CAA-TAA----ACAATTT
* * * * *
53761 TAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGCCTCGAAACAACGCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
53812 TCTTGCATTG
Statistics
Matches: 416, Mismatches: 19, Indels: 39
0.88 0.04 0.08
Matches are distributed among these distances:
94 88 0.21
95 1 0.00
98 102 0.25
102 5 0.01
103 1 0.00
104 2 0.00
105 86 0.21
106 123 0.30
109 3 0.01
110 3 0.01
113 1 0.00
114 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (98 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
Found at i:53618 original size:94 final size:95
Alignment explanation
Indices: 53257--53742 Score: 668
Period size: 98 Copynumber: 4.9 Consensus size: 95
53247 TTACCCAGAG
53257 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
53322 GGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGA
66 GGGACCGCTGGTTGTCAA-TAA-A-----CAATTTC--A
* *
53361 GCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGA
1 -CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
53426 AGGGACCGCTGGTTGTCAATAAACAATTTCAGA
65 AGGGACCGCTGGTTGTCAATAAACAATTTC--A
53459 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 -CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
53524 AGGGACCGCTGGTTGTCAATAAACAATTTC-
65 AGGGACCGCTGGTTGTCAATAAACAATTTCA
53554 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
53619 GGGACCGCTGGTTGTCAATAAACAACTTCCCGATTTCAGA
66 GGGACCGCTGGTTGTCAATAAAC-A-------ATTTC--A
* * * *
53659 GCCAATTTCAACTTCACAACGAAGGAGATTGGCCTCCAGACAACACAAGTTCAACTTCACAACGA
1 -CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
53724 AGAGACCGCTGGTTGTCAA
65 AGGGACCGCTGGTTGTCAA
53743 CAAGTAATTT
Statistics
Matches: 358, Mismatches: 11, Indels: 23
0.91 0.03 0.06
Matches are distributed among these distances:
94 88 0.25
95 1 0.00
98 102 0.28
102 5 0.01
103 1 0.00
104 2 0.01
105 81 0.23
106 78 0.22
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (95 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTCA
Found at i:56424 original size:29 final size:29
Alignment explanation
Indices: 56392--56516 Score: 99
Period size: 29 Copynumber: 4.3 Consensus size: 29
56382 CATTTTACAC
*
56392 AAATAGCACCATTTTCGAATTAATTCCCA
1 AAATAGCACCAATTTCGAATTAATTCCCA
** **** * * *
56421 AAATATTATTTTTTTCGAA-AAATTACTA
1 AAATAGCACCAATTTCGAATTAATTCCCA
*
56449 AAATAGTACCAATTTCGAATTAATTCCCA
1 AAATAGCACCAATTTCGAATTAATTCCCA
* ***
56478 GAATAGCACCAAAACCGAATTAATTCCCA
1 AAATAGCACCAATTTCGAATTAATTCCCA
*
56507 GAATAGCACC
1 AAATAGCACC
56517 GGTCAACGGT
Statistics
Matches: 74, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
28 20 0.27
29 54 0.73
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (29 bp):
AAATAGCACCAATTTCGAATTAATTCCCA
Found at i:56561 original size:7 final size:7
Alignment explanation
Indices: 56516--56546 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
56506 AGAATAGCAC
56516 CGGTCAA
1 CGGTCAA
56523 CGGTCAA
1 CGGTCAA
56530 CGGTCAA
1 CGGTCAA
*
56537 CGATCAA
1 CGGTCAA
56544 CGG
1 CGG
56547 GTCGGGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:56563 original size:12 final size:13
Alignment explanation
Indices: 56540--56579 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
56530 CGGTCAACGA
56540 TCAACGGGTCGGG
1 TCAACGGGTCGGG
56553 TCAAC-GGTCGGG
1 TCAACGGGTCGGG
*
56565 TAAACGGGTCGGG
1 TCAACGGGTCGGG
56578 TC
1 TC
56580 GGGTAAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.17, C:0.23, G:0.42, T:0.17
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:56591 original size:13 final size:13
Alignment explanation
Indices: 56542--56578 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
56532 GTCAACGATC
*
56542 AACGGGTCGGGTC
1 AACGGGTCGGGTA
56555 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
56567 AACGGGTCGGGT
1 AACGGGTCGGGT
56579 CGGGTAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:56634 original size:11 final size:10
Alignment explanation
Indices: 56604--56655 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
56594 ACGGGTCGTG
56604 ACCGGTC-AA
1 ACCGGTCAAA
56613 ACCGGTCAAA
1 ACCGGTCAAA
56623 ACCGGTTCAAA
1 ACCGG-TCAAA
*
56634 ACCGGT-TAA
1 ACCGGTCAAA
56643 ACCGGTCAAA
1 ACCGGTCAAA
56653 ACC
1 ACC
56656 AGTTTCCAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:63723 original size:29 final size:29
Alignment explanation
Indices: 63691--63817 Score: 87
Period size: 29 Copynumber: 4.3 Consensus size: 29
63681 CATTTTACAC
63691 AAATAGCACCATTTTCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
** *** * * *
63720 AAATATTATTTTTTTTTCGAA-AAATTACTA
1 AAATAGCA--CCATTTTCGAATTAATTCCCA
63750 AAATAGCACCCA-TTTCGAATTAATTCCCA
1 AAATAGCA-CCATTTTCGAATTAATTCCCA
* ****
63779 GAATAGCACCAAAACCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
*
63808 GAATAGCACC
1 AAATAGCACC
63818 GGTCAACGGT
Statistics
Matches: 73, Mismatches: 21, Indels: 8
0.72 0.21 0.08
Matches are distributed among these distances:
28 10 0.14
29 43 0.59
30 12 0.16
31 8 0.11
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (29 bp):
AAATAGCACCATTTTCGAATTAATTCCCA
Found at i:63850 original size:13 final size:13
Alignment explanation
Indices: 63832--63873 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
63822 AACGGTCAAC
63832 GGTCAACGGGTCG
1 GGTCAACGGGTCG
63845 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
63857 GGTAAACGGGTCG
1 GGTCAACGGGTCG
63870 GGTC
1 GGTC
63874 GGGTAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:63875 original size:18 final size:18
Alignment explanation
Indices: 63852--63903 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
63842 TCGGGTCAAC
63852 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
63870 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
*
63888 AGTCGGGTAAACGGGT
1 GGTCGGGTAAACGGGT
63904 AAACGGGTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.19, C:0.15, G:0.46, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:63946 original size:11 final size:10
Alignment explanation
Indices: 63916--63967 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
63906 ACGGGTCGTG
63916 ACCGGTC-AA
1 ACCGGTCAAA
63925 ACCGGTCAAA
1 ACCGGTCAAA
63935 ACCGGTTCAAA
1 ACCGG-TCAAA
*
63946 ACCGGT-TAA
1 ACCGGTCAAA
63955 ACCGGTCAAA
1 ACCGGTCAAA
63965 ACC
1 ACC
63968 AGTTTCCAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:66455 original size:5 final size:5
Alignment explanation
Indices: 66445--66473 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
66435 GTAACTTTTA
66445 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
66474 GGTTGAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:79270 original size:19 final size:19
Alignment explanation
Indices: 79242--79279 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
79232 TAAGATCATA
79242 AAAATGTTATATAAAAATT
1 AAAATGTTATATAAAAATT
* *
79261 AAAATTTTATTTAAAAATT
1 AAAATGTTATATAAAAATT
79280 CAAACAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AAAATGTTATATAAAAATT
Found at i:82064 original size:449 final size:449
Alignment explanation
Indices: 81226--82125 Score: 1701
Period size: 449 Copynumber: 2.0 Consensus size: 449
81216 TACTTTTGTT
81226 CGAGTTTTATAAAATTTTTCTCATTGAATTCAAAAAACATAGGTCACTTTTGTTTCGTTCAATTT
1 CGAGTTTTATAAAATTTTTCTCATTGAATTCAAAAAACATAGGTCACTTTTGTTTCGTTCAATTT
81291 AAGATGTGATCACTGAAGATTAATGACCGTTAAACCTTTAATGGTTTGCTGATGTGACACGATAA
66 AAGATGTGATCACTGAAGATTAATGACCGTTAAACCTTTAATGGTTTGCTGATGTGACACGATAA
81356 ATATATAAAATTAAAATTACATTATTTCCACTTAGATACTACGCGGATTAAATTTTGGTCAATTT
131 ATATATAAAATTAAAATTACATTATTTCCACTTAGATACTACGCGGATTAAATTTTGGTCAATTT
81421 TCTTTCATATTTGTACACTTTTGCTTACTAAATTAAAAAAAATAAAGTTTTGGTCACTTACATTA
196 TCTTTCATATTTGTACACTTTTGCTTACTAAATTAAAAAAAATAAAGTTTTGGTCACTTACATTA
*
81486 TCGTTTTATTAAGTTTTGGTCATTTGGACGTTGAATGTCGTTAGTTTGATGACACGGCTTGTTAT
261 TCGTTTTATTAAGTTTTGGTCATTTGGACGTTGAATGTCGTTAGTTTGATGACACGACTTGTTAT
*
81551 TAAAATGGTTTAATTTTCATTTTAACCCCCAAACTTTAGACAAAATACTGATTATGAGTCTTATT
326 TAAAATGGCTTAATTTTCATTTTAACCCCCAAACTTTAGACAAAATACTGATTATGAGTCTTATT
* *
81616 GTAAATTCAAATTAGTTTAGTGGATGAATTCACGGATCCAACAATCGGGTGGTTTTCAC
391 GTAAATTCAAATTAGTTTAGTGGATGAATTCACGGATCCAACAATCGGGTCGTCTTCAC
* **
81675 CGAGTTTTATAAATTTTTTCTCATTGAATTCAAAATCCATAGGTCACTTTTGTTTCGTTCAATTT
1 CGAGTTTTATAAAATTTTTCTCATTGAATTCAAAAAACATAGGTCACTTTTGTTTCGTTCAATTT
81740 AAGATGTGATCACTGAAGATTAATGACCGTTAAACCTTTAATGGTTTGCTGATGTGACACGATAA
66 AAGATGTGATCACTGAAGATTAATGACCGTTAAACCTTTAATGGTTTGCTGATGTGACACGATAA
* *
81805 ATATATAAAATTAAAATTACATTATTTCCACTTAGATACTATGTGGATTAAATTTTGGTCAATTT
131 ATATATAAAATTAAAATTACATTATTTCCACTTAGATACTACGCGGATTAAATTTTGGTCAATTT
81870 TCTTTCATATTTGTACACTTTTGCTTACTAAATTAAAAAAAATAAAGTTTTGGTCACTTACATTA
196 TCTTTCATATTTGTACACTTTTGCTTACTAAATTAAAAAAAATAAAGTTTTGGTCACTTACATTA
*
81935 TCGTTTTATTAAGTTTTGGTCATTTGGACGTTGAATGTCGTTAGTTTGATGACATGACTTGTTAT
261 TCGTTTTATTAAGTTTTGGTCATTTGGACGTTGAATGTCGTTAGTTTGATGACACGACTTGTTAT
*
82000 TAAAATGGCTTAATTTTTATTTTAACCCCCAAACTTTAGACAAAATACTGATTATGAGTCTTATT
326 TAAAATGGCTTAATTTTCATTTTAACCCCCAAACTTTAGACAAAATACTGATTATGAGTCTTATT
82065 GTAAATTCAAATTAGTTTAGTGGATGAATTCACGGATCCAACAATCGGGTCGTCTTCAC
391 GTAAATTCAAATTAGTTTAGTGGATGAATTCACGGATCCAACAATCGGGTCGTCTTCAC
82124 CG
1 CG
82126 GAGGTACTTT
Statistics
Matches: 440, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
449 440 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (449 bp):
CGAGTTTTATAAAATTTTTCTCATTGAATTCAAAAAACATAGGTCACTTTTGTTTCGTTCAATTT
AAGATGTGATCACTGAAGATTAATGACCGTTAAACCTTTAATGGTTTGCTGATGTGACACGATAA
ATATATAAAATTAAAATTACATTATTTCCACTTAGATACTACGCGGATTAAATTTTGGTCAATTT
TCTTTCATATTTGTACACTTTTGCTTACTAAATTAAAAAAAATAAAGTTTTGGTCACTTACATTA
TCGTTTTATTAAGTTTTGGTCATTTGGACGTTGAATGTCGTTAGTTTGATGACACGACTTGTTAT
TAAAATGGCTTAATTTTCATTTTAACCCCCAAACTTTAGACAAAATACTGATTATGAGTCTTATT
GTAAATTCAAATTAGTTTAGTGGATGAATTCACGGATCCAACAATCGGGTCGTCTTCAC
Found at i:83018 original size:31 final size:31
Alignment explanation
Indices: 82980--83040 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
82970 ACCTTTAGTG
* *
82980 ACCACATCTTAATTAAAACGAAACAAAAGTA
1 ACCACATCTTAACTAAAACAAAACAAAAGTA
83011 ACCACATCTTAACTAAAACAAAACAAAAGT
1 ACCACATCTTAACTAAAACAAAACAAAAGT
83041 GAACAAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.18
Consensus pattern (31 bp):
ACCACATCTTAACTAAAACAAAACAAAAGTA
Found at i:83051 original size:31 final size:31
Alignment explanation
Indices: 82976--83052 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
82966 ATTAACCTTT
* * *
82976 AGTGACCACATCTTAATTAAAACGAAACAAA
1 AGTGAACACATCTTAACTAAAACAAAACAAA
83007 AGT-AACCACATCTTAACTAAAACAAAACAAA
1 AGTGAA-CACATCTTAACTAAAACAAAACAAA
*
83038 AGTGAACAAATCTTA
1 AGTGAACACATCTTA
83053 TGTTTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 37 0.93
32 2 0.05
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.19
Consensus pattern (31 bp):
AGTGAACACATCTTAACTAAAACAAAACAAA
Found at i:87063 original size:70 final size:72
Alignment explanation
Indices: 86982--87126 Score: 240
Period size: 70 Copynumber: 2.0 Consensus size: 72
86972 AGGACTACTG
* *
86982 CCAGAAGAGGTTGTATTTGTTTCAGCTTCTTATCTTCCTTC-A-ATTAGCTCTACGTGCATTAGA
1 CCAGAACAGGTTGTATTTGTTTCAGCTTCTTATCCTCCTTCAATATTAGCTCTACGTGCATTAGA
87045 ATGACTT
66 ATGACTT
* *
87052 CCAGAACAGGTTGTATTTGTTTCAGCTTCTTGTCCTCCTTCAATATTAGCTCTACGTGCATTGGA
1 CCAGAACAGGTTGTATTTGTTTCAGCTTCTTATCCTCCTTCAATATTAGCTCTACGTGCATTAGA
87117 ATGACTT
66 ATGACTT
87124 CCA
1 CCA
87127 CGCTGACTAG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
70 38 0.55
71 1 0.01
72 30 0.43
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (72 bp):
CCAGAACAGGTTGTATTTGTTTCAGCTTCTTATCCTCCTTCAATATTAGCTCTACGTGCATTAGA
ATGACTT
Found at i:95704 original size:65 final size:65
Alignment explanation
Indices: 95600--95837 Score: 350
Period size: 65 Copynumber: 3.7 Consensus size: 65
95590 TACGTCACAT
* * * * *
95600 ATCACTCATATGACTCATGTATCTTTGTGGTGTATGAGGTGGAGTGATAATTGAATAATGTACAA
1 ATCACTCATATTACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATTGTACAG
* * *
95665 ATCACTAATATAACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATTGTATAG
1 ATCACTCATATTACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATTGTACAG
* * * *
95730 ACCACTCATATTACTTATGTATCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATTGTACTG
1 ATCACTCATATTACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATTGTACAG
* *
95795 ATCACTCATATTACTCGTGTACCTTTGTAGTGCATGAGGTGGA
1 ATCACTCATATTACTCATGTACCTTTGTGGTGCATGAGGTGGA
95838 ATCTATGATG
Statistics
Matches: 154, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 154 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (65 bp):
ATCACTCATATTACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATTGTACAG
Found at i:96655 original size:2 final size:2
Alignment explanation
Indices: 96650--96699 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
96640 ACACACATGC
*
96650 AT AT AT AT AC 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
96692 AT AT AT AT
1 AT AT AT AT
96700 CTCATTTTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:98887 original size:54 final size:54
Alignment explanation
Indices: 98407--98886 Score: 626
Period size: 54 Copynumber: 8.9 Consensus size: 54
98397 CTATGTGTAT
* * * **
98407 TATCGGCACTAAGTGTGTAACCCACTGAATTCATAAT-ATGTTAATGAATAACCG
1 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATGA-GTTTATGAACGACCG
* * * **
98461 TATCGTCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAGTGACCG
1 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATGAGTTTATGAACGACCG
* * * * *
98515 TATAGGTACTAAGTGTGCAACCAACAGAATTCATAAT-ATGTTTATGAACCACCG
1 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATGA-GTTTATGAACGACCG
* *
98569 TATCGGCACTAAGTGTGAAACCCACGGAATTCATAATGAGTTTATGAACGATCG
1 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATGAGTTTATGAACGACCG
* *
98623 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAAT-ATGTTTATGAACGACTG
1 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATGA-GTTTATGAACGACCG
98677 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATGAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATGAGTTTATGAACGACCG
98731 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATGAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATGAGTTTATGAACGACCG
* * * * *
98785 TATCGGCACTAAGTGTGCAACCTACGAAATTCACAATGAGTTTGTGAATGACCG
1 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATGAGTTTATGAACGACCG
* * * * * *
98839 TATCGGCCCTATA-TGTGCACCCCAAGGATTTCAAAATGAGTTTGTGAA
1 TATCGGCACTA-AGTGTGCAACCCACGGAATTCATAATGAGTTTATGAA
98887 TTTCCATATT
Statistics
Matches: 382, Mismatches: 38, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
53 2 0.01
54 376 0.98
55 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATGAGTTTATGAACGACCG
Found at i:99440 original size:2 final size:2
Alignment explanation
Indices: 99433--99470 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
99423 GACGTGTTTA
99433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
99471 ATAATGTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:100304 original size:24 final size:23
Alignment explanation
Indices: 100249--100303 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
100239 TATAAAGTTC
*
100249 TTTATTTTCTTTTCTTTTCAAGT
1 TTTATTTTCTTTTATTTTCAAGT
100272 TTTCATTTTCATTTTATTTT-AAGT
1 TTT-ATTTTC-TTTTATTTTCAAGT
100296 TTTATTTT
1 TTTATTTT
100304 TAAACATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.28
24 13 0.45
25 8 0.28
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTATTTTCTTTTATTTTCAAGT
Found at i:100671 original size:14 final size:14
Alignment explanation
Indices: 100652--100683 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
100642 ACGAACTTAA
100652 ACGATTATTGATTT
1 ACGATTATTGATTT
100666 ACGATTATTGATTT
1 ACGATTATTGATTT
100680 ACGA
1 ACGA
100684 CAATTGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (14 bp):
ACGATTATTGATTT
Found at i:100689 original size:14 final size:14
Alignment explanation
Indices: 100658--100691 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
100648 TTAAACGATT
**
100658 ATTGATTTACGATT
1 ATTGATTTACGACA
100672 ATTGATTTACGACA
1 ATTGATTTACGACA
100686 ATTGAT
1 ATTGAT
100692 GTTGATGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (14 bp):
ATTGATTTACGACA
Found at i:101341 original size:24 final size:24
Alignment explanation
Indices: 101314--101362 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
101304 TTATAGAATA
101314 ATTATCAACTTCATATATTATTTT
1 ATTATCAACTTCATATATTATTTT
101338 ATTATCAACTTCATATATTATTTT
1 ATTATCAACTTCATATATTATTTT
101362 A
1 A
101363 ATATATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTATCAACTTCATATATTATTTT
Found at i:106569 original size:88 final size:89
Alignment explanation
Indices: 106465--106633 Score: 234
Period size: 88 Copynumber: 1.9 Consensus size: 89
106455 CAGACCATGC
* * * * *
106465 GGGTAAAAAAATTGGCCTATTAAG-TCATCTCCATAATTAATTTGAGATCTGC-ACATTTGTTGC
1 GGGTAAAAAAATTGGCCTA-TAAGATCATCTCAAAAATTAATTTGAGATCTACGACATTTATTAC
*
106528 ATTAACTTAAAACTCATCATATCGT
65 AGTAACTTAAAACTCATCATATCGT
* *
106553 GGGTAAAAAAATTGGCCTATAAGATCATCTTAAAAATTAATTTGAGATTTACGACATTTATTACA
1 GGGTAAAAAAATTGGCCTATAAGATCATCTCAAAAATTAATTTGAGATCTACGACATTTATTACA
*
106618 GTAACTTGAAACTCAT
66 GTAACTTAAAACTCAT
106634 TACATCGACA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
87 4 0.06
88 42 0.60
89 24 0.34
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (89 bp):
GGGTAAAAAAATTGGCCTATAAGATCATCTCAAAAATTAATTTGAGATCTACGACATTTATTACA
GTAACTTAAAACTCATCATATCGT
Found at i:108613 original size:2 final size:2
Alignment explanation
Indices: 108601--108638 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
108591 CAAATACTTT
*
108601 TA TA AA TA 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 TA TA TA TA
108639 ATTTATACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:110184 original size:4 final size:4
Alignment explanation
Indices: 110169--110205 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
110159 GAATAGGGGG
*
110169 AGAA ATAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
110206 AATCAGAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.03
Consensus pattern (4 bp):
AGAA
Found at i:111595 original size:23 final size:23
Alignment explanation
Indices: 111569--111617 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
111559 CAGTCTTTCG
*
111569 GGATAATTT-TACGTGGTCCTTCA
1 GGAT-ATTTCTACATGGTCCTTCA
111592 GGATATTTCTACATGGTCCTTCA
1 GGATATTTCTACATGGTCCTTCA
111615 GGA
1 GGA
111618 CATCTATGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (23 bp):
GGATATTTCTACATGGTCCTTCA
Found at i:111686 original size:22 final size:22
Alignment explanation
Indices: 111631--111686 Score: 87
Period size: 21 Copynumber: 2.5 Consensus size: 22
111621 CTATGTGCAT
*
111631 GACATTTCTACGTGGTCCTTCGG
1 GACA-TTCTATGTGGTCCTTCGG
111654 GACA-TCTATGTGGTCCTTCGG
1 GACATTCTATGTGGTCCTTCGG
111675 GACATTCTATGT
1 GACATTCTATGT
111687 AGCAATTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 20 0.65
22 7 0.23
23 4 0.13
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (22 bp):
GACATTCTATGTGGTCCTTCGG
Found at i:113148 original size:60 final size:58
Alignment explanation
Indices: 113084--113212 Score: 141
Period size: 59 Copynumber: 2.2 Consensus size: 58
113074 GTCCAAGGAC
** * * *
113084 TAATTTAAAAAGTGAGTCATAGTTTAAGGATGAAACTAAAATGTTCAAAAGTTTAAGTAA
1 TAATTTAAAAAGAAAGT-ATAGTTTAAGGATAAAACTAAAATATTCAAAAGTTTAA-AAA
* * * * *
113144 TAATTTAGAATGAAAGTATAGTTTGAGGATAAAATTAAAATATTCCAAAGTTTAAAAA
1 TAATTTAAAAAGAAAGTATAGTTTAAGGATAAAACTAAAATATTCAAAAGTTTAAAAA
113202 TCAATTTAAAA
1 T-AATTTAAAA
113213 TCAGGGTTAT
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
58 3 0.05
59 41 0.72
60 13 0.23
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.33
Consensus pattern (58 bp):
TAATTTAAAAAGAAAGTATAGTTTAAGGATAAAACTAAAATATTCAAAAGTTTAAAAA
Found at i:118343 original size:25 final size:25
Alignment explanation
Indices: 118312--118374 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
118302 ATATATTAAG
*
118312 TTCAAACATTCAATCATCCAACAAA
1 TTCAAACATCCAATCATCCAACAAA
118337 TTCAAACATCCAATCATCCAACAAA
1 TTCAAACATCCAATCATCCAACAAA
118362 TTCAAACATCCAA
1 TTCAAACATCCAA
118375 AATAAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (25 bp):
TTCAAACATCCAATCATCCAACAAA
Found at i:120308 original size:23 final size:22
Alignment explanation
Indices: 120258--120354 Score: 85
Period size: 23 Copynumber: 4.5 Consensus size: 22
120248 AAACCGGACT
*
120258 GGTGTATCGATGCACA-T--AG
1 GGTGCATCGATGCACATTCAAG
*
120277 AGTGCATCGATGCACATTCAAG
1 GGTGCATCGATGCACATTCAAG
* * * *
120299 GCGTGCATCGGTGTACCTTC-AT
1 G-GTGCATCGATGCACATTCAAG
*
120321 GGTGAATCGATGCACATTCAAG
1 GGTGCATCGATGCACATTCAAG
120343 GGATGCATCGAT
1 GG-TGCATCGAT
120355 ACACTAACTA
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
19 14 0.24
20 1 0.02
21 14 0.24
22 7 0.12
23 23 0.39
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (22 bp):
GGTGCATCGATGCACATTCAAG
Found at i:120674 original size:36 final size:36
Alignment explanation
Indices: 120634--120712 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
120624 AATTTAAACA
*
120634 CTAAGTGAAGATAGGTCAGTTAAACCTAATTCTCTC
1 CTAAGTGAAGATAGGTCAGCTAAACCTAATTCTCTC
120670 CTAAGTGAAGATAGGTCAGCTAAACCTAATTCTCTC
1 CTAAGTGAAGATAGGTCAGCTAAACCTAATTCTCTC
120706 CTAAGTG
1 CTAAGTG
120713 TCCAAAAATC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (36 bp):
CTAAGTGAAGATAGGTCAGCTAAACCTAATTCTCTC
Done.