Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004831.1 Hibiscus syriacus cultivar Beakdansim tig00010883_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: 186144
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:1017 original size:3 final size:3
Alignment explanation
Indices: 1009--1043 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
999 ATCTATATTT
*
1009 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1044 TCAATATACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2277 original size:12 final size:11
Alignment explanation
Indices: 2253--2319 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 11
2243 GAAAAACATG
2253 AAATAAATGAAA
1 AAATAAAT-AAA
2265 AAATAGAAT-AA
1 AAATA-AATAAA
*
2276 AAATAAGAAAAA
1 AAATAA-ATAAA
*
2288 AAATAAA-AGA
1 AAATAAATAAA
2298 AAATAAATAAA
1 AAATAAATAAA
2309 TAAATGAAATA
1 -AAAT-AAATA
2320 TTAATATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
10 10 0.22
11 11 0.24
12 17 0.37
13 8 0.17
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.16
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:2279 original size:23 final size:21
Alignment explanation
Indices: 2253--2313 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 21
2243 GAAAAACATG
2253 AAATAAATGAAAAAATAGAATA-A
1 AAATAAAT-AAAAAATA-AA-AGA
*
2276 AAATAAGAAAAAAAATAAAAGA
1 AAATAA-ATAAAAAATAAAAGA
2298 AAATAAATAAATAAAT
1 AAATAAATAAA-AAAT
2314 GAAATATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 5 0.15
22 13 0.39
23 14 0.42
24 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (21 bp):
AAATAAATAAAAAATAAAAGA
Found at i:2413 original size:15 final size:17
Alignment explanation
Indices: 2343--2414 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 17
2333 ATATATATAT
*
2343 ATAATGAGTAAAATAGAAA
1 ATAAT-AGTAATATA-AAA
* *
2362 ATAATAATCATA-ACAATA
1 ATAATAGTAATATA-AA-A
2380 ATAATAGTAATATGAAAA
1 ATAATAGTAATAT-AAAA
2398 ATAATA-TAATATAAAA
1 ATAATAGTAATATAAAA
2414 A
1 A
2415 AAACCAAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
16 5 0.11
17 9 0.20
18 22 0.50
19 7 0.16
20 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (17 bp):
ATAATAGTAATATAAAA
Found at i:2649 original size:19 final size:19
Alignment explanation
Indices: 2627--2728 Score: 53
Period size: 23 Copynumber: 4.8 Consensus size: 19
2617 AAAAGTACAT
2627 ATATA-TATAAAAATAATAA
1 ATATAGTATAAAAA-AATAA
*
2646 ATATAGTATTAAAAAATAA
1 ATATAGTATAAAAAAATAA
* * *
2665 CCAAATGAATATAAACAAATAAAAA
1 --ATAT-AGTAT-AA-AAA-AATAA
2690 ATATACGTATAGATAAAAATAA
1 ATATA-GTATA-A-AAAAATAA
*
2712 TATATAGTGTAAAAAAA
1 -ATATAGTATAAAAAAA
2729 ATCAATTGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
19 10 0.16
20 12 0.19
21 4 0.06
22 14 0.22
23 16 0.25
24 3 0.05
25 4 0.06
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (19 bp):
ATATAGTATAAAAAAATAA
Found at i:2663 original size:22 final size:22
Alignment explanation
Indices: 2596--2664 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 22
2586 TAATACGCTT
*
2596 ATAAGTAAA-ATATTTTTAAAAA
1 ATAAGTAAATATA-TATTAAAAA
*
2618 A-AAGTACATATATA-TATAAAA
1 ATAAGTAAATATATATTA-AAAA
2639 ATAA-TAAATATAGTATTAAAAA
1 ATAAGTAAATATA-TATTAAAAA
2661 ATAA
1 ATAA
2665 CCAAATGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 2 0.05
21 19 0.49
22 16 0.41
23 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (22 bp):
ATAAGTAAATATATATTAAAAA
Found at i:3234 original size:37 final size:37
Alignment explanation
Indices: 3182--3279 Score: 117
Period size: 37 Copynumber: 2.6 Consensus size: 37
3172 GTGCTTGTGG
* * *
3182 ATCCTATCTTT-AGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAAGGAGTTTGAATCATAGCAAAACTCT
* * *
3219 ATCTTATTTTAAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTAAGGAGTTTGAATCATAGCAAAACTCT
*
3256 ATCCTATTTTTAGGAGTTTGAATC
1 ATCCTATTTTAAGGAGTTTGAATC
3280 TTAGAAGGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 3 0.06
37 49 0.94
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTAAGGAGTTTGAATCATAGCAAAACTCT
Found at i:4324 original size:106 final size:106
Alignment explanation
Indices: 4015--5279 Score: 1753
Period size: 106 Copynumber: 12.0 Consensus size: 106
4005 ATTGTTCTGA
* * ** * * *
4015 GTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGAGAAATTATTTGTTGACAAC
1 GTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* * * * *
4079 CAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGA
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * *
4121 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAATC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
* * * * * *
4180 AACCGCCCCTTCTTCGTGAAGTTGAGCTTGTGTTGTCTTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * * *
4221 GTCCAAGATCCTTCACTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
*
4286 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * * *
4327 GTCCAATATCCTACGCTGTGAAGTTTAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
*
4392 AGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * * *
4432 AGTCCGATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAAC
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
4497 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGA
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * *
4539 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGAAAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
* *
4604 AGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * *
4645 GTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
*
4710 AGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* *
4750 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
*
4815 CATCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * *
4856 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAAC
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
4921 CAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGA
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* *
4963 GTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
* *
5028 AGCGGTCCCTTCGTTGTGAAGTTGAGCTTGCGTTGTC-TGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * *
5068 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* * *
5133 CAGCGGTCCATTCGTCATAAAGTTGAACTTGCGTTGTC-TGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
* * *
5174 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAAC
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* * * *
5239 CAGCGGTCTCTTCGTTGTGAAATTGAACTTGTGTTGTCTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
5280 AGTGACACAA
Statistics
Matches: 1041, Mismatches: 105, Indels: 25
0.89 0.09 0.02
Matches are distributed among these distances:
100 79 0.08
101 3 0.00
102 4 0.00
104 3 0.00
105 9 0.01
106 937 0.90
107 6 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGG
Found at i:4633 original size:318 final size:318
Alignment explanation
Indices: 4012--5282 Score: 1973
Period size: 318 Copynumber: 4.0 Consensus size: 318
4002 AGCATTGTTC
* * ** *
4012 TGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGAGAAATTATTTGTTGAC
1 TGAGTCCAATATCCTACGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGAC
* * * * *
4076 AACCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTG
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
* * * * * *
4141 AAGTTGAAATTGACTCTG-AA-TGA-AA--T-TTTGTTGACAATCAACCGCCCCTTCTTCGTGAA
130 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
* * * * *
4200 GTTGAGCTTGTGTTGTCTTGG-GTCCAAGATCCTTCACTGAGAAGTTGAAATTGGCTCTGAAATT
195 GTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
4264 GGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
259 GGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
4324 TGAGTCCAATATCCTACGCTGTGAAGTTTAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* *
4389 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCGATATCCTTCGTTGTGA
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
*
4454 AGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
131 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
4519 TTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAG
196 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
* *
4584 GAAGTTGTTTATTGAAAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
261 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
4642 TGAGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 TGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
*
4707 ACCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
*
4772 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCATCGGTCCCTTCGTCGTGAAG
131 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
4837 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
196 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
* *
4902 GAAGTTATTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
261 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
4960 TGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* *
5025 ACCAGCGGTCCCTTCGTTGTGAAGTTGAGCTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * * * * *
5090 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCATTCGTCATAAAG
131 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * *
5155 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGA
196 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
* * * * *
5220 GAAGTTGTTTGTTGACAACCAGCGGTCTCTTCGTTGTGAAATTGAACTTGTGTTGTCT
261 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
5278 TGAGT
1 TGAGT
5283 GACACAATAT
Statistics
Matches: 881, Mismatches: 70, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
312 128 0.15
313 3 0.00
314 3 0.00
315 2 0.00
317 3 0.00
318 742 0.84
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (318 bp):
TGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:6113 original size:22 final size:22
Alignment explanation
Indices: 6087--6204 Score: 200
Period size: 22 Copynumber: 5.4 Consensus size: 22
6077 ATGTTTGGTT
6087 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
6109 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
*
6131 AAAGGTTTGGCATTTGATGGTC
1 AAAGGTTTGGCATTTGATGCTC
6153 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
* *
6175 ATAGGTTTGGCATTTGATGTTC
1 AAAGGTTTGGCATTTGATGCTC
*
6197 AACGGTTT
1 AAAGGTTT
6205 AATGGGGTAG
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 90 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (22 bp):
AAAGGTTTGGCATTTGATGCTC
Found at i:6896 original size:172 final size:173
Alignment explanation
Indices: 6603--6949 Score: 583
Period size: 172 Copynumber: 2.0 Consensus size: 173
6593 AAAATAGGCC
*
6603 CAAACAAGTATTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTATTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTG
*
6668 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGGAATG
6733 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
* * *
6778 CAAACAAGTGTTTCAGGGTGTTGAACCAATGATCAATTCATTATGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTATTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
6840 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGGAATG
66 CAAAATG--TCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGGAATG
*
6905 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGTCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
6950 TTTAGGGAAT
Statistics
Matches: 164, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
170 14 0.09
172 100 0.61
174 1 0.01
175 49 0.30
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (173 bp):
CAAACAAGTATTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGGAATGAT
TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:7016 original size:31 final size:28
Alignment explanation
Indices: 6981--7054 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 28
6971 TTTTATGTCC
6981 CTTTTTCTTTTTGATTTTTGTTATTGTTT-CT
1 CTTTTTCTTTTT--TTTTTGTT-TT-TTTGCT
7012 CTTTTTTCTTTGTTTTTTTGTTTTTTTGCT
1 C-TTTTTCTTT-TTTTTTTGTTTTTTTGCT
7042 -TCTTTTCTTTTTT
1 CT-TTTTCTTTTTT
7055 GTTCTTGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
28 4 0.10
29 11 0.28
30 4 0.10
31 9 0.23
32 9 0.23
33 2 0.05
ACGTcount: A:0.03, C:0.11, G:0.08, T:0.78
Consensus pattern (28 bp):
CTTTTTCTTTTTTTTTTGTTTTTTTGCT
Found at i:9990 original size:31 final size:31
Alignment explanation
Indices: 9952--10107 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
9942 CCCGAAGGAC
* * *
9952 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
9983 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
10014 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
10045 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
10076 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
10107 C
1 C
10108 CCTCGACCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:10328 original size:24 final size:22
Alignment explanation
Indices: 10284--10329 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
10274 ATATACTTGT
*
10284 TTTCACATATATTTTCATATCA
1 TTTCACATATACTTTCATATCA
10306 TTTCACATATACACTTTCATATCA
1 TTTCACATAT--ACTTTCATATCA
10330 CATGCCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
24 11 0.52
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTCACATATACTTTCATATCA
Found at i:10967 original size:21 final size:21
Alignment explanation
Indices: 10943--10987 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
10933 TCTTGTTCGT
* *
10943 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
10964 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
10985 TTG
1 TTG
10988 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:14160 original size:31 final size:31
Alignment explanation
Indices: 14122--14277 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
14112 CCCGAAGGAC
* * *
14122 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
14153 CAGTCCATATGTCCCGAAGGACATATGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
14184 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
14215 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
14246 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
14277 C
1 C
14278 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:14481 original size:23 final size:24
Alignment explanation
Indices: 14455--14501 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
14445 ATATACTTGT
*
14455 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
14478 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
14502 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:15161 original size:21 final size:21
Alignment explanation
Indices: 15137--15181 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
15127 TCTTGTTCGT
* *
15137 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
15158 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
15179 TTG
1 TTG
15182 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:18288 original size:16 final size:16
Alignment explanation
Indices: 18251--18291 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
18241 AAAAATGAAG
*
18251 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
18267 AA-AAATAAAAGGAAA
1 AATAAATAAAAGGAAA
18282 AATAAATAAA
1 AATAAATAAA
18292 TAATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Found at i:18374 original size:18 final size:18
Alignment explanation
Indices: 18326--18379 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 18
18316 AAAATAGAAA
18326 AATAATAATCATAACAATAAT
1 AATAATAAT-ATAA-AAT-AT
18347 AATAATAATATGAAAATAT
1 AATAATAATAT-AAAATAT
18366 AAT-ATAATATAAAA
1 AATAATAATATAAAA
18380 AAAACCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.12
18 7 0.22
19 5 0.16
20 5 0.16
21 11 0.34
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
AATAATAATATAAAATAT
Found at i:18380 original size:18 final size:20
Alignment explanation
Indices: 18326--18380 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 20
18316 AAAATAGAAA
*
18326 AATAATAATCATAACAATAAT
1 AATAATAAT-ATAAAAATAAT
*
18347 AATAATAATATGAAAAT-AT
1 AATAATAATATAAAAATAAT
18366 AAT-ATAATATAAAAA
1 AATAATAATATAAAAA
18381 AAACCAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.35
19 5 0.16
20 6 0.19
21 9 0.29
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
AATAATAATATAAAAATAAT
Found at i:18589 original size:2 final size:2
Alignment explanation
Indices: 18582--18629 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
18572 ATATTTTAAA
*
18582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
18623 AA AT AT A
1 AT AT AT A
18630 GTATTAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:18637 original size:19 final size:19
Alignment explanation
Indices: 18579--18643 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
18569 AAAATATTTT
*
18579 AAAATATATATATATATATA
1 AAAATAAATATATATATA-A
* * *
18599 TATATATATATATATATAA
1 AAAATAAATATATATATAA
*
18618 ATAATAAATATAGTAT-TAA
1 AAAATAAATATA-TATATAA
18637 AAAATAA
1 AAAATAA
18644 CCAAATGAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 18 0.49
20 19 0.51
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATAAATATATATATAA
Found at i:18684 original size:23 final size:24
Alignment explanation
Indices: 18653--18701 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
18643 ACCAAATGAA
18653 TATAAATAAATAA-AAAATATA-TG
1 TATAAAT-AATAATAAAATATAGTG
* *
18676 TATAGATAATAATAATATATAGTG
1 TATAAATAATAATAAAATATAGTG
18700 TA
1 TA
18702 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
TATAAATAATAATAAAATATAGTG
Found at i:19218 original size:37 final size:38
Alignment explanation
Indices: 19177--19270 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 38
19167 TCTTATCTTT
19177 AGGAGTTTAAATCATAGTAGAACTCTATCCTA-TTTTA
1 AGGAGTTTAAATCATAGTAGAACTCTATCCTATTTTTA
* * * * * *
19214 AGGAGTTTTAATCTTAGCAAAATTCTATCTTATTTTTA
1 AGGAGTTTAAATCATAGTAGAACTCTATCCTATTTTTA
* *
19252 A-GAGTTTGAATCCTAGTAG
1 AGGAGTTTAAATCATAGTAG
19271 GACGAAAATG
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
37 40 0.87
38 6 0.13
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (38 bp):
AGGAGTTTAAATCATAGTAGAACTCTATCCTATTTTTA
Found at i:28794 original size:35 final size:35
Alignment explanation
Indices: 28750--28861 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
28740 AAAACATTCA
*
28750 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
28785 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
28820 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
28855 TCAATTT
1 TCAATTT
28862 AAGGAGGAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:29835 original size:30 final size:32
Alignment explanation
Indices: 29801--29860 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
29791 CTTACTATTG
*
29801 AAAAATTTTC-ATGTCTTTAAAT-TAAAATTA
1 AAAAATTATCAATGTCTTTAAATATAAAATTA
*
29831 AAAAATTATCATATGTTTTTAAATATAAAA
1 AAAAATTATCA-ATGTCTTTAAATATAAAA
29861 AGTAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
32 11 0.44
33 5 0.20
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (32 bp):
AAAAATTATCAATGTCTTTAAATATAAAATTA
Found at i:29961 original size:35 final size:34
Alignment explanation
Indices: 29912--30024 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
29902 AAAAAAGACA
* *
29912 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
29947 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
* *
29982 AAAATTGAATTACTTTGGAATTTGAGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
30017 GAAATTGA
1 GAAATTGA
30025 GGATTGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 65 0.94
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:35378 original size:28 final size:27
Alignment explanation
Indices: 35337--35393 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
35327 ATGAATTATT
* * *
35337 ATTTAATATATAATGTATGAAATAAATA
1 ATTTAATAAATAATATATCAAA-AAATA
*
35365 ATTTTATAAATAATATATCAAAAAATA
1 ATTTAATAAATAATATATCAAAAAATA
35392 AT
1 AT
35394 CCTTCTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (27 bp):
ATTTAATAAATAATATATCAAAAAATA
Found at i:41489 original size:21 final size:21
Alignment explanation
Indices: 41464--41543 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 21
41454 CAGAACCCCA
* *
41464 GGGGGTATTGATTCCCCTTTG
1 GGGGGAATCGATTCCCCTTTG
* **
41485 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTT--TG
* *
41508 GGGGGAATCGGTT-CCCTCATG
1 GGGGGAATCGATTCCCCT-TTG
41529 GGGGG-ATCGATTCCC
1 GGGGGAATCGATTCCC
41544 TCTGCACCAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
20 6 0.13
21 23 0.50
22 4 0.09
23 13 0.28
ACGTcount: A:0.15, C:0.24, G:0.35, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTTTG
Found at i:41537 original size:20 final size:21
Alignment explanation
Indices: 41483--41545 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
41473 GATTCCCCTT
41483 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
41507 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
41527 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
41546 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:68686 original size:24 final size:24
Alignment explanation
Indices: 68659--68709 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
68649 TTCTCATTTT
*
68659 CTAATCCCT-CCTCTTTCAAAATCC
1 CTAA-CCCTGCCTCGTTCAAAATCC
*
68683 CTAACTCTGCCTCGTTCAAAATCC
1 CTAACCCTGCCTCGTTCAAAATCC
68707 CTA
1 CTA
68710 GCTGAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.25, C:0.39, G:0.04, T:0.31
Consensus pattern (24 bp):
CTAACCCTGCCTCGTTCAAAATCC
Found at i:74158 original size:17 final size:16
Alignment explanation
Indices: 74125--74155 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
74115 TATTTTTATT
*
74125 TTTCTTTTTTATTTTC
1 TTTCTTTTTCATTTTC
74141 TTTCTTTTTCATTTT
1 TTTCTTTTTCATTTT
74156 TCTCTCTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTCTTTTTCATTTTC
Found at i:74742 original size:20 final size:20
Alignment explanation
Indices: 74717--74773 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
74707 AACAAACTAA
74717 ATATTGTTGTGATTACCCAT
1 ATATTGTTGTGATTACCCAT
* * *
74737 ATATTGTTCCT-AATGCCCAT
1 ATATTGTT-GTGATTACCCAT
74757 ATATTGTTGTGATTACC
1 ATATTGTTGTGATTACC
74774 AAAACCAGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (20 bp):
ATATTGTTGTGATTACCCAT
Found at i:78318 original size:21 final size:22
Alignment explanation
Indices: 78280--78320 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
78270 AAAAATATTA
*
78280 ATATCAAAAATATTTATTTTAG
1 ATATCAAAAATATATATTTTAG
*
78302 ATATCAAAATTA-ATATTTT
1 ATATCAAAAATATATATTTT
78321 TGTTAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (22 bp):
ATATCAAAAATATATATTTTAG
Found at i:78343 original size:12 final size:12
Alignment explanation
Indices: 78328--78352 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
78318 TTTTGTTAAA
78328 AAACAATATTTT
1 AAACAATATTTT
78340 AAACAATATTTT
1 AAACAATATTTT
78352 A
1 A
78353 TTAAAAATAT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AAACAATATTTT
Found at i:78845 original size:23 final size:23
Alignment explanation
Indices: 78818--78861 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
78808 TTTTTAAATA
*
78818 TCTTAACTTAAATTATATTTTAT
1 TCTTAACTTAAAATATATTTTAT
*
78841 TCTTAAGTTAAAATATATTTT
1 TCTTAACTTAAAATATATTTT
78862 GAAGTTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (23 bp):
TCTTAACTTAAAATATATTTTAT
Found at i:78946 original size:36 final size:39
Alignment explanation
Indices: 78871--78960 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 39
78861 TGAAGTTAAG
* *
78871 ATATTTTAATATCTTTTAAAAGTTAAGATAATAAC-AAA-AT
1 ATATTTT-ATAT-TTTT-AAAGTGAAGATAAGAACAAAATAT
*
78911 ATATTTTATATTTTT-AAGTGAAGATAAGAATAAAATAT
1 ATATTTTATATTTTTAAAGTGAAGATAAGAACAAAATAT
78949 ATATTTTATATT
1 ATATTTTATATT
78961 AAATTAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
36 13 0.29
37 3 0.07
38 18 0.40
39 4 0.09
40 7 0.16
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (39 bp):
ATATTTTATATTTTTAAAGTGAAGATAAGAACAAAATAT
Found at i:79007 original size:81 final size:83
Alignment explanation
Indices: 78922--79091 Score: 258
Period size: 83 Copynumber: 2.1 Consensus size: 83
78912 TATTTTATAT
* *
78922 TTTTAAGTGA-AGAT-AAGAATAAAATATATA-TTTTATATTAAATTAATAATAAAA-TTTTAAA
1 TTTTAAGTGATA-ATAAAG-ATAAAATATACATTTTTATATTAAATTAATAATAAAACATTTAAA
*
78983 TATATTTCAAGTTAAGATAA
64 TATATTTCAAGTTAAAATAA
79003 TTTTAAGTGATAATAAAGATAAAATATACATTTTTATATTAAATTAATAATAAAACATTTAAATA
1 TTTTAAGTGATAATAAAGATAAAATATACATTTTTATATTAAATTAATAATAAAACATTTAAATA
*
79068 TATTTCAAGTTAAAATAT
66 TATTTCAAGTTAAAATAA
79086 TTTTAA
1 TTTTAA
79092 AAAAAATTAA
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
81 23 0.28
82 28 0.35
83 30 0.37
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (83 bp):
TTTTAAGTGATAATAAAGATAAAATATACATTTTTATATTAAATTAATAATAAAACATTTAAATA
TATTTCAAGTTAAAATAA
Found at i:79151 original size:16 final size:17
Alignment explanation
Indices: 79130--79190 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 17
79120 TATATATATT
79130 TATATTAAAA-TAAAAA
1 TATATTAAAATTAAAAA
79146 TATATTTAATAAGTTAAAAA
1 TATA-TTAA-AA-TTAAAAA
*
79166 -A-ATTAAAATTTAAAA
1 TATATTAAAATTAAAAA
79181 TATA-TAAAAT
1 TATATTAAAAT
79191 ATTATTAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
15 6 0.16
16 13 0.34
17 9 0.24
18 3 0.08
19 1 0.03
20 6 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TATATTAAAATTAAAAA
Found at i:85347 original size:21 final size:23
Alignment explanation
Indices: 85323--85370 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
85313 TTATTAAAAA
*
85323 ATTAATGATTTTTTAAT-TTA-T
1 ATTAATGATTATTTAATATTATT
*
85344 ATTAATTATTATTTAATATTATT
1 ATTAATGATTATTTAATATTATT
85367 ATTA
1 ATTA
85371 TGTAACTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
22 3 0.13
23 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTAATGATTATTTAATATTATT
Found at i:87774 original size:21 final size:20
Alignment explanation
Indices: 87743--87859 Score: 99
Period size: 20 Copynumber: 5.8 Consensus size: 20
87733 GATTCTGACT
*
87743 ATCGTATTGCGATTTCCCAA
1 ATCGCATTGCGATTTCCCAA
* *
87763 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTTCCCAA
* **
87785 ATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTCCCAA
* **
87805 ATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTCCCAA
* **
87825 ATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTCCCAA
*
87845 TTCGCATTGCGATTT
1 ATCGCATTGCGATTT
87860 AGTAAATCGC
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
20 60 0.69
21 19 0.22
22 8 0.09
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
ATCGCATTGCGATTTCCCAA
Found at i:87809 original size:20 final size:20
Alignment explanation
Indices: 87765--87870 Score: 151
Period size: 20 Copynumber: 5.2 Consensus size: 20
87755 TTTCCCAAAT
* * *
87765 TCGCGTTGCGATTTTCCTAAA
1 TCGCATTGCGATTTACGT-AA
87786 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
87806 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
*
87826 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAA
87846 TCGCATTGCGATTTA-GTAAA
1 TCGCATTGCGATTTACGT-AA
87866 TCGCA
1 TCGCA
87871 ACGAGATTCT
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 15 0.19
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:88759 original size:24 final size:24
Alignment explanation
Indices: 88732--88785 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
88722 GTATTCGAAA
88732 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
88756 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
88780 TTTGAT
1 TTTGAT
88786 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:91323 original size:20 final size:19
Alignment explanation
Indices: 91295--91349 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
91285 CAATCATCTT
*
91295 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
91315 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
91334 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
91350 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:91337 original size:19 final size:17
Alignment explanation
Indices: 91302--91452 Score: 77
Period size: 19 Copynumber: 8.8 Consensus size: 17
91292 CTTAATGTCT
*
91302 ATCGCAACGCGGAAATGA
1 ATCGCAATGC-GAAATGA
91320 CTATCGCAATGCGAAATGAAA
1 --ATCGCAATGCGAAATG--A
*
91341 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
91355 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
91374 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
91388 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
**
91407 ATCGCAA--CG-AGGGA
1 ATCGCAATGCGAAATGA
*
91421 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
91440 ATCGCAACGCGAA
1 ATCGCAATGCGAA
91453 TTTAGTTTCG
Statistics
Matches: 104, Mismatches: 10, Indels: 35
0.70 0.07 0.23
Matches are distributed among these distances:
14 24 0.23
16 14 0.13
17 14 0.13
19 42 0.40
20 9 0.09
21 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.12
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:91359 original size:14 final size:14
Alignment explanation
Indices: 91340--91427 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
91330 GCGAAATGAA
91340 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
91354 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
91373 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
91387 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
91406 AATCGCAACGAGGG
1 AATCGCAACGAGAG
91420 AATCGCAA
1 AATCGCAA
91428 AGCGAAATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 27 0.46
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.34
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:91364 original size:33 final size:33
Alignment explanation
Indices: 91322--91448 Score: 236
Period size: 33 Copynumber: 3.8 Consensus size: 33
91312 GGAAATGACT
91322 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
91355 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
91388 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
91421 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
91449 CGAATTTAGT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 92 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:91500 original size:33 final size:33
Alignment explanation
Indices: 91458--91537 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
91448 GCGAATTTAG
* * *
91458 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
91491 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
91524 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
91538 AGTCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:91505 original size:19 final size:19
Alignment explanation
Indices: 91477--91537 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
91467 GCGATTTTGT
*
91477 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
91496 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
91510 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
91529 CATTGCGAT
1 CGTTGCGAT
91538 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 10 0.30
16 3 0.09
17 3 0.09
19 17 0.52
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:91663 original size:14 final size:14
Alignment explanation
Indices: 91644--91677 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
91634 CATCAATTAA
91644 ACAAATAAACTTTT
1 ACAAATAAACTTTT
* *
91658 ACAAATCATCTTTT
1 ACAAATAAACTTTT
91672 ACAAAT
1 ACAAAT
91678 CAATTAAACA
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:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATAAACTTTT
Found at i:91678 original size:14 final size:14
Alignment explanation
Indices: 91653--91679 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
91643 AACAAATAAA
91653 CTTTTACAAATCAT
1 CTTTTACAAATCAT
91667 CTTTTACAAATCA
1 CTTTTACAAATCA
91680 ATTAAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTTTACAAATCAT
Found at i:93093 original size:21 final size:21
Alignment explanation
Indices: 93027--93093 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
93017 GTGAATCGGG
*
93027 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
93047 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
93069 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
93090 CTCT
1 CTCT
93094 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:93112 original size:42 final size:41
Alignment explanation
Indices: 93027--93149 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
93017 GTGAATCGGG
* * * *
93027 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
93069 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
93111 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
93150 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:93586 original size:19 final size:19
Alignment explanation
Indices: 93546--93727 Score: 151
Period size: 19 Copynumber: 10.2 Consensus size: 19
93536 TATGGAACTT
*
93546 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
93567 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
93586 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
*
93606 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAATG
93625 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
93639 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
93658 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
93672 AGAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
93691 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
93705 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
93724 AAAA
1 AAAA
93728 ACTATATATT
Statistics
Matches: 133, Mismatches: 12, Indels: 34
0.74 0.07 0.19
Matches are distributed among these distances:
14 31 0.23
15 3 0.02
16 6 0.05
17 6 0.05
18 3 0.02
19 55 0.41
20 18 0.14
21 11 0.08
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:93650 original size:33 final size:33
Alignment explanation
Indices: 93570--93727 Score: 226
Period size: 33 Copynumber: 4.6 Consensus size: 33
93560 AAAAATGACT
93570 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAAC--GAG-A-G--A
*
93609 ATCGCAACGCGAAACGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
93642 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
93675 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
93708 ATCGCAATGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
93728 ACTATATATT
Statistics
Matches: 115, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
33 84 0.73
35 1 0.01
36 1 0.01
37 3 0.03
39 26 0.23
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:93721 original size:14 final size:14
Alignment explanation
Indices: 93624--93714 Score: 74
Period size: 14 Copynumber: 5.8 Consensus size: 14
93614 AACGCGAAAC
93624 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
93638 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
93656 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
*
93671 GAGAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
93689 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
93704 GAAAATCGCAA
1 GAAAATCGCAA
93715 TGCGAAATGA
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 31 0.49
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:93795 original size:37 final size:33
Alignment explanation
Indices: 93724--93847 Score: 108
Period size: 35 Copynumber: 3.5 Consensus size: 33
93714 ATGCGAAATG
* *
93724 AAAAACTATATATTATA-TTGTCAAAACCGTT-TTAA
1 AAAAACTATATATTATAGTTTTCAAAA---TTCTT-T
93759 AAAAACTATATATTATACGTTTTCAAAATTACTTT
1 AAAAACTATATATTATA-GTTTTCAAAATT-CTTT
* *
93794 AAAAACTATATACTATATGTTTTTCAAAATTGTTT
1 AAAAACTATATATTATA-G-TTTTCAAAATTCTTT
93829 CAAAAACTATATATATATA
1 -AAAAACTATATAT-TATA
93848 TATATATATA
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
34 2 0.03
35 37 0.49
36 25 0.33
37 12 0.16
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.40
Consensus pattern (33 bp):
AAAAACTATATATTATAGTTTTCAAAATTCTTT
Found at i:93798 original size:35 final size:36
Alignment explanation
Indices: 93759--93847 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
93749 ACCGTTTTAA
93759 AAAAACTATATATTATACG-TTTTCAAAATTACTTT-
1 AAAAACTATATATTATACGTTTTTCAAAATT-CTTTC
* * *
93794 AAAAACTATATACTATATGTTTTTCAAAATTGTTTC
1 AAAAACTATATATTATACGTTTTTCAAAATTCTTTC
93830 AAAAACTATATATATATA
1 AAAAACTATATAT-TATA
93848 TATATATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
35 20 0.43
36 23 0.49
37 4 0.09
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (36 bp):
AAAAACTATATATTATACGTTTTTCAAAATTCTTTC
Found at i:93818 original size:36 final size:34
Alignment explanation
Indices: 93759--93846 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 34
93749 ACCGTTTTAA
*
93759 AAAAACTATATATTATACGTTTTCAAAATTACTTT-
1 AAAAACTATATA-TATATGTTTTCAAAATT-CTTTC
*
93794 AAAAACTATATACTATATGTTTTTCAAAATTGTTTC
1 AAAAACTATATA-TATATG-TTTTCAAAATTCTTTC
93830 AAAAACTATATATATAT
1 AAAAACTATATATATAT
93847 ATATATATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
35 25 0.52
36 23 0.48
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.42
Consensus pattern (34 bp):
AAAAACTATATATATATGTTTTCAAAATTCTTTC
Found at i:93843 original size:2 final size:2
Alignment explanation
Indices: 93836--93888 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
93826 TTTCAAAAAC
93836 TA TA TA TA TA 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 TA TA
93878 TA TA TA TA TA T
1 TA TA TA TA TA T
93889 GTTTTCAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:94704 original size:13 final size:13
Alignment explanation
Indices: 94686--94710 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
94676 TTTATATAAT
94686 TTAATATTTTTTA
1 TTAATATTTTTTA
94699 TTAATATTTTTT
1 TTAATATTTTTT
94711 GTTACATCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTAATATTTTTTA
Found at i:96128 original size:14 final size:14
Alignment explanation
Indices: 96109--96147 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
96099 TAATGGGGAG
96109 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
96123 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
96137 GAATCTCTGCA
1 TAATCCCTGCA
96148 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:101048 original size:45 final size:45
Alignment explanation
Indices: 100992--101083 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
100982 TCTTTGGAAA
* *
100992 TATTACATGAATGGCATTTCTTTCTTGTATTTCAAACACTTCGTG
1 TATTACATGAATGGCATTTCTTTCTTATATTTCAAACACTCCGTG
* * *
101037 TATTACTTGAATGGTATTTCTTTCTTATATTTCAAATACTCCGTG
1 TATTACATGAATGGCATTTCTTTCTTATATTTCAAACACTCCGTG
101082 TA
1 TA
101084 GTACCTAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (45 bp):
TATTACATGAATGGCATTTCTTTCTTATATTTCAAACACTCCGTG
Found at i:114525 original size:11 final size:11
Alignment explanation
Indices: 114509--114540 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
114499 CCAAACCTGA
114509 AAGGGTCAACG
1 AAGGGTCAACG
114520 AAGGGTCAACG
1 AAGGGTCAACG
114531 AAGGGTCAAC
1 AAGGGTCAAC
114541 TAAACAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.34, T:0.09
Consensus pattern (11 bp):
AAGGGTCAACG
Found at i:115583 original size:26 final size:26
Alignment explanation
Indices: 115561--115611 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
115551 AGAGGTAATT
115561 GAAGTGTAAAACTAGATTAGGTAACA
1 GAAGTGTAAAACTAGATTAGGTAACA
*
115587 GAATTGTAAAACTAGATTAGGTAAC
1 GAAGTGTAAAACTAGATTAGGTAAC
115612 TTTGTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.25
Consensus pattern (26 bp):
GAAGTGTAAAACTAGATTAGGTAACA
Found at i:119372 original size:15 final size:15
Alignment explanation
Indices: 119352--119381 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
119342 GATTAGTCTC
119352 TTTCCTAATTTAGAG
1 TTTCCTAATTTAGAG
119367 TTTCCTAATTTAGAG
1 TTTCCTAATTTAGAG
119382 AAATATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
TTTCCTAATTTAGAG
Found at i:129787 original size:15 final size:15
Alignment explanation
Indices: 129767--129801 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
129757 ACCATGAAAT
129767 TAATTTATAAAATAC
1 TAATTTATAAAATAC
*
129782 TAATTTATAAAATAT
1 TAATTTATAAAATAC
129797 TAATT
1 TAATT
129802 AGAAATTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATTTATAAAATAC
Found at i:131502 original size:15 final size:15
Alignment explanation
Indices: 131476--131512 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
131466 TAATTTATAA
131476 TTATACATTTAATATT
1 TTATA-ATTTAATATT
*
131492 TTATAATTTAATGTT
1 TTATAATTTAATATT
131507 TTATAA
1 TTATAA
131513 AGTAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (15 bp):
TTATAATTTAATATT
Found at i:131961 original size:22 final size:22
Alignment explanation
Indices: 131933--131984 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
131923 TGAGTACCAG
*
131933 GAATGTCATGGGTATAAACGT-T
1 GAATGTCATGAGTATAAAC-TAT
131955 GAATGTCATGAGTATAAACTAT
1 GAATGTCATGAGTATAAACTAT
131977 GAATGTCA
1 GAATGTCA
131985 AATGATTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31
Consensus pattern (22 bp):
GAATGTCATGAGTATAAACTAT
Found at i:134282 original size:38 final size:37
Alignment explanation
Indices: 134226--134328 Score: 127
Period size: 38 Copynumber: 2.8 Consensus size: 37
134216 TTTTGTATAT
* *
134226 ACATATATATATAATATAGTTTTGAAAACATATTTGAA
1 ACATATATATATTATATAGTTTTTAAAACA-ATTTGAA
* * *
134264 ACATCTATATATTTTATAGTTTTTAAAACACTTTGAA
1 ACATATATATATTATATAGTTTTTAAAACAATTTGAA
* *
134301 A-ATAAATATAATATATAGTTTTTAAAAC
1 ACATATATATATTATATAGTTTTTAAAAC
134329 GTTTTTAAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 23 0.41
37 7 0.12
38 26 0.46
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (37 bp):
ACATATATATATTATATAGTTTTTAAAACAATTTGAA
Found at i:134406 original size:19 final size:18
Alignment explanation
Indices: 134358--134407 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
134348 ATACGGTTTT
134358 AAAAAAACA-TTTTTAAA
1 AAAAAAACATTTTTTAAA
*
134375 ATAAATATA-ATTTTTTAAA
1 A-AAA-AAACATTTTTTAAA
134394 AAAAGAAACATTTT
1 AAAA-AAACATTTT
134408 GAAAACATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 1 0.04
18 9 0.35
19 16 0.62
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAAAAACATTTTTTAAA
Found at i:134469 original size:110 final size:110
Alignment explanation
Indices: 134289--134499 Score: 248
Period size: 110 Copynumber: 1.9 Consensus size: 110
134279 ATAGTTTTTA
* * * * * *
134289 AAACACTTTGAAAATAAATATAATATATAGTTTTTAAAACGTTTTTAAGAAAATATATTATACGG
1 AAACACTTTGAAAACAAATATAATATATAGTTTTGAAAACGATTTTAAAAAAATATAATATACAG
*
134354 TTTT-AAAAAAACATTTTTAAAA-TAAATATAATTTTTTAAAAAAAG
66 TTTTAAAAAAAACATTTTGAAAACT--ATATAATTTTTTAAAAAAAG
* * * * *
134399 AAACATTTTGAAAACATATATATTATATAGTTTTGAAATC-ATTTTAAAAAAACTTATAATATAT
1 AAACACTTTGAAAACAAATATAATATATAGTTTTGAAAACGATTTTAAAAAAA--TATAATATAC
*
134463 AGTTTAAAAAAAAACATTTTGAAAACTATATAATTTT
64 AGTTTTAAAAAAAACATTTTGAAAACTATATAATTTT
134500 GAAAACGTTT
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
109 10 0.12
110 34 0.40
111 22 0.26
112 17 0.20
113 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (110 bp):
AAACACTTTGAAAACAAATATAATATATAGTTTTGAAAACGATTTTAAAAAAATATAATATACAG
TTTTAAAAAAAACATTTTGAAAACTATATAATTTTTTAAAAAAAG
Found at i:134630 original size:14 final size:15
Alignment explanation
Indices: 134611--134652 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
134601 ATCGTTGTTG
134611 TTTATTTTTATTTA-
1 TTTATTTTTATTTAT
*
134625 TTTATTTTTATTAAT
1 TTTATTTTTATTTAT
*
134640 TTTATTTTCATTT
1 TTTATTTTTATTT
134653 TAATTGTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTTATTTAT
Found at i:137647 original size:19 final size:19
Alignment explanation
Indices: 137613--137657 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
137603 ATTTAGACAT
137613 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
137631 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
137650 TTTGCATT
1 TTTGCATT
137658 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:141533 original size:165 final size:166
Alignment explanation
Indices: 141021--141668 Score: 991
Period size: 165 Copynumber: 3.9 Consensus size: 166
141011 ACCTGCCACC
*
141021 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAAGTCAA
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAAGTCAA
*
141086 GAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
66 GAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
141151 GCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
131 GCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
* *
141187 AAGACCTTTGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAAGTCAA
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAAGTCAA
*
141252 GAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
66 GAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
141317 GCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
131 GCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
* * * * *
141353 AAGACCTTTGAGTTCGATTACACTCAGCTCCAAGGCATATCATTTGCAGCATAGCTT-AAGTCGA
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAAGTCAA
* * *
141417 GAAGGGCTATCTGCCAAAGAACCC-CAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
66 GAAGGGCTATCTGCCAAAG-ACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTAC
141481 AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
130 AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
* * * * *
141518 AGGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATATGCAGCATAGCTT-AAGTCGA
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAAGTCAA
* * * * *
141582 GAAGGGCTATCTGCCAAAGACTCC-CGAGTTCGATTACACTCAACTGC-GGGGTCATATCATTTA
66 GAAGGGCTATCTGCCAAAGAC-CCTCAAGTTCGATTACACTCAGCTTCAAGGG-CATAACATTTA
* * * *
141645 CAACATAGCTCATGGCAAGAAGGG
129 CAGCATAACTCAAGGCTAGAAGGG
141669 CTATTTGTCA
Statistics
Matches: 454, Mismatches: 25, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
164 5 0.01
165 227 0.50
166 222 0.49
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (166 bp):
AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAAGTCAA
GAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
GCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
Found at i:142291 original size:38 final size:37
Alignment explanation
Indices: 142235--142335 Score: 118
Period size: 38 Copynumber: 2.8 Consensus size: 37
142225 TTTTGTATAT
142235 ACATATATATATAATATAGTTTTGAAAACATATTTGAA
1 ACATATATATATAATATAGTTTTGAAAACA-ATTTGAA
* ** * *
142273 ACATCTATATATTTTATAGTTTTTAAAACACTTTGAA
1 ACATATATATATAATATAGTTTTGAAAACAATTTGAA
*
142310 A-ATA-A-ATATAATATAGTTTTTAAAAC
1 ACATATATATATAATATAGTTTTGAAAAC
142336 GTTTTTAAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
34 19 0.35
35 1 0.02
36 2 0.04
37 7 0.13
38 26 0.47
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (37 bp):
ACATATATATATAATATAGTTTTGAAAACAATTTGAA
Found at i:142330 original size:34 final size:37
Alignment explanation
Indices: 142243--142335 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 37
142233 ATACATATAT
* *
142243 ATATAATATAGTTTTGAAAACATATTTGAAACATCTAT
1 ATATAATATAGTTTTTAAAACATATTTGAAACA-CTAA
** *
142281 ATATTTTATAGTTTTTAAAACA-CTTTGAAA-A-TAA
1 ATATAATATAGTTTTTAAAACATATTTGAAACACTAA
142315 ATATAATATAGTTTTTAAAAC
1 ATATAATATAGTTTTTAAAAC
142336 GTTTTTAAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
34 21 0.44
36 1 0.02
37 7 0.15
38 19 0.40
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (37 bp):
ATATAATATAGTTTTTAAAACATATTTGAAACACTAA
Found at i:142411 original size:18 final size:17
Alignment explanation
Indices: 142364--142417 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
142354 ATACGGTTTT
142364 AAAAAAACATTTTTAAA
1 AAAAAAACATTTTTAAA
*
142381 ATAAATATA-ATTTTTAAA
1 A-AAA-AAACATTTTTAAA
*
142399 AAAAGAAACATTTTGAAA
1 AAAA-AAACATTTTTAAA
142417 A
1 A
142418 CATATATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 6 0.20
18 22 0.73
19 2 0.07
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (17 bp):
AAAAAAACATTTTTAAA
Found at i:142447 original size:36 final size:35
Alignment explanation
Indices: 142403--142472 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
142393 TTTAAAAAAA
* * *
142403 GAAACATTTTGAAAACA-TATATATTATATAGTTTT
1 GAAACATTTTAAAAAAACT-TATAATATATAGTTTT
142438 GAAATCATTTTAAAAAAACTTATAATATATAGTTT
1 GAAA-CATTTTAAAAAAACTTATAATATATAGTTT
142473 AAAAAAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 4 0.13
36 25 0.83
37 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (35 bp):
GAAACATTTTAAAAAAACTTATAATATATAGTTTT
Found at i:142536 original size:37 final size:39
Alignment explanation
Indices: 142494--142568 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 39
142484 TTTTGAAAAC
* *
142494 TATATAATTTTGAAA-ACGTTTTTAAAA-ATA-TATATAA
1 TATATAATTTTAAAATAC-TTTTGAAAATATATTATATAA
142531 TATATAATTTTAAAATACTTTTGAAAATATATTATATA
1 TATATAATTTTAAAATACTTTTGAAAATATATTATATA
142569 GTTTGTAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 22 0.67
38 5 0.15
39 6 0.18
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (39 bp):
TATATAATTTTAAAATACTTTTGAAAATATATTATATAA
Found at i:142630 original size:14 final size:15
Alignment explanation
Indices: 142611--142652 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
142601 ATCGTTGTTG
142611 TTTATTTTTATTTA-
1 TTTATTTTTATTTAT
*
142625 TTTATTTTTATTAAT
1 TTTATTTTTATTTAT
*
142640 TTTATTTTCATTT
1 TTTATTTTTATTT
142653 TAATTGTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTTATTTAT
Found at i:153780 original size:19 final size:19
Alignment explanation
Indices: 153745--153790 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
153735 TTATAACTTT
153745 TATAATATTTGAATTTAAGAA
1 TATAA-ATTTGAATTTAA-AA
153766 TATAAATTT-AATTTAAAA
1 TATAAATTTGAATTTAAAA
153784 T-TAAATT
1 TATAAATT
153791 ATAAATCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.24
18 3 0.12
19 7 0.28
20 4 0.16
21 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (19 bp):
TATAAATTTGAATTTAAAA
Found at i:156633 original size:16 final size:16
Alignment explanation
Indices: 156612--156718 Score: 160
Period size: 16 Copynumber: 6.7 Consensus size: 16
156602 ACCCGACCTG
*
156612 TTCAACCTGACCTGTT
1 TTCAACCTGACATGTT
*
156628 TTCAACTTGACATGTT
1 TTCAACCTGACATGTT
*
156644 TTCAACCTGACCTGTT
1 TTCAACCTGACATGTT
*
156660 TTTAACCTGACATGTT
1 TTCAACCTGACATGTT
*
156676 TTTAACCTGACATGTT
1 TTCAACCTGACATGTT
156692 TTCAACCTGACATGTT
1 TTCAACCTGACATGTT
*
156708 TTTAACCTGAC
1 TTCAACCTGAC
156719 CTGTAAATGA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 83 1.00
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.40
Consensus pattern (16 bp):
TTCAACCTGACATGTT
Found at i:156653 original size:32 final size:32
Alignment explanation
Indices: 156612--156722 Score: 177
Period size: 32 Copynumber: 3.5 Consensus size: 32
156602 ACCCGACCTG
*
156612 TTCAACCTGACCTGTTTTCAACTTGACATGTT
1 TTCAACCTGACCTGTTTTCAACCTGACATGTT
*
156644 TTCAACCTGACCTGTTTTTAACCTGACATGTT
1 TTCAACCTGACCTGTTTTCAACCTGACATGTT
* *
156676 TTTAACCTGACATGTTTTCAACCTGACATGTT
1 TTCAACCTGACCTGTTTTCAACCTGACATGTT
*
156708 TTTAACCTGACCTGT
1 TTCAACCTGACCTGT
156723 AAATGATTCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 73 1.00
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.41
Consensus pattern (32 bp):
TTCAACCTGACCTGTTTTCAACCTGACATGTT
Found at i:157004 original size:23 final size:24
Alignment explanation
Indices: 156970--157019 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
156960 ATGCAATGGA
*
156970 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGATTAATTTATAT
156994 AAATT-ATATAGATTAATTTATAT
1 AAATTAATATAGATTAATTTATAT
157017 AAA
1 AAA
157020 AATAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATTAATATAGATTAATTTATAT
Found at i:157027 original size:25 final size:25
Alignment explanation
Indices: 156969--157027 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
156959 AATGCAATGG
* *
156969 AAAATTAATATAGTTTAATTTATAT
1 AAAAATAATATAGATTAATTTATAT
*
156994 --AAATTATATAGATTAATTTATAT
1 AAAAATAATATAGATTAATTTATAT
157017 AAAAATAATAT
1 AAAAATAATAT
157028 TATATAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 20 0.71
25 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (25 bp):
AAAAATAATATAGATTAATTTATAT
Found at i:157030 original size:16 final size:15
Alignment explanation
Indices: 157007--157036 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
156997 TTATATAGAT
157007 TAATTTATATAAAAA
1 TAATTTATATAAAAA
157022 TAATATTATATAAAA
1 TAAT-TTATATAAAA
157037 TAACTTGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATTTATATAAAAA
Found at i:158860 original size:2 final size:2
Alignment explanation
Indices: 158842--158885 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
158832 TGGTGGGTGT
* *
158842 GA GA AA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
158884 GA
1 GA
158886 AACCTGAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
GA
Found at i:160353 original size:24 final size:24
Alignment explanation
Indices: 160319--160375 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
160309 TTTACCGAAA
*
160319 ATAAAAAAAGTACAATATCA-AAGG
1 ATAAAACAAGTACAATATCAGAA-G
*
160343 ATAAAACAAGTACAATTTCAGAAG
1 ATAAAACAAGTACAATATCAGAAG
*
160367 ATAATACAA
1 ATAAAACAA
160376 TAAGGAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.19
Consensus pattern (24 bp):
ATAAAACAAGTACAATATCAGAAG
Found at i:161399 original size:288 final size:288
Alignment explanation
Indices: 160883--161458 Score: 1125
Period size: 288 Copynumber: 2.0 Consensus size: 288
160873 TCAGACAAGG
160883 ACTGTTTCCAAACACCACCAAATGCAACACGGACCTCAAGACCATCTAAGAAGCTGCAACCTTCT
1 ACTGTTTCCAAACACCACCAAATGCAACACGGACCTCAAGACCATCTAAGAAGCTGCAACCTTCT
*
160948 GGTGGTTCAAGCTTTGCCATGGTTCCCGGCAACAGGGTAGAAAAGATGGACCCAAAGTCACTGAA
66 GCTGGTTCAAGCTTTGCCATGGTTCCCGGCAACAGGGTAGAAAAGATGGACCCAAAGTCACTGAA
161013 GGAAAGTGCATTATAAGGACAGTGCGACACAAATCTTTTAGAAACCCCAAAACCAAAAGAATCAG
131 GGAAAGTGCATTATAAGGACAGTGCGACACAAATCTTTTAGAAACCCCAAAACCAAAAGAATCAG
161078 CATAGAGATGTAACATACCATTTGAAAAATAAGATTCAAACAAGTAAAATGCAGAAAAATCGACA
196 CATAGAGATGTAACATACCATTTGAAAAATAAGATTCAAACAAGTAAAATGCAGAAAAATCGACA
161143 TTTCAGATGCTTACTGGTTAACTTTGAC
261 TTTCAGATGCTTACTGGTTAACTTTGAC
161171 ACTGTTTCCAAACACCACCAAATGCAACACGGACCTCAAGACCATCTAAGAAGCTGCAACCTTCT
1 ACTGTTTCCAAACACCACCAAATGCAACACGGACCTCAAGACCATCTAAGAAGCTGCAACCTTCT
* *
161236 GCTGGTTCAAGCTTTGCCATGGTTCCCGGCATCAGGGTAGAAAGGATGGACCCAAAGTCACTGAA
66 GCTGGTTCAAGCTTTGCCATGGTTCCCGGCAACAGGGTAGAAAAGATGGACCCAAAGTCACTGAA
161301 GGAAAGTGCATTATAAGGACAGTGCGACACAAATCTTTTAGAAACCCCAAAACCAAAAGAATCAG
131 GGAAAGTGCATTATAAGGACAGTGCGACACAAATCTTTTAGAAACCCCAAAACCAAAAGAATCAG
161366 CATAGAGATGTAACATACCATTTGAAAAATAAGATTCAAACAAGTAAAATGCAGAAAAATCGACA
196 CATAGAGATGTAACATACCATTTGAAAAATAAGATTCAAACAAGTAAAATGCAGAAAAATCGACA
161431 TTTCAGATGCTTACTGGTTAACTTTGAC
261 TTTCAGATGCTTACTGGTTAACTTTGAC
161459 CCAAGTGACC
Statistics
Matches: 285, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
288 285 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (288 bp):
ACTGTTTCCAAACACCACCAAATGCAACACGGACCTCAAGACCATCTAAGAAGCTGCAACCTTCT
GCTGGTTCAAGCTTTGCCATGGTTCCCGGCAACAGGGTAGAAAAGATGGACCCAAAGTCACTGAA
GGAAAGTGCATTATAAGGACAGTGCGACACAAATCTTTTAGAAACCCCAAAACCAAAAGAATCAG
CATAGAGATGTAACATACCATTTGAAAAATAAGATTCAAACAAGTAAAATGCAGAAAAATCGACA
TTTCAGATGCTTACTGGTTAACTTTGAC
Found at i:161983 original size:61 final size:60
Alignment explanation
Indices: 161918--162060 Score: 162
Period size: 61 Copynumber: 2.3 Consensus size: 60
161908 GTTGTCTATT
* *
161918 AATTTTAAATTTATTTAATTTAGTCTAAATTTAATGATT-TAATATATTAATTTAAGCTTCA
1 AATTTAAAATTT-TTTAATTTAATCTAAATTTAATG-TTATAATATATTAATTTAAGCTTCA
* * * * *
161979 AATTTCAACTTTTTTCAATTTAATCTAATTTTAATGTTATAATTTTTTAATTTAAGCTTCA
1 AATTTAAAATTTTTT-AATTTAATCTAAATTTAATGTTATAATATATTAATTTAAGCTTCA
* *
162040 TATTTAAAATTTGTTCAATTT
1 AATTTAAAATTT-TTTAATTT
162061 GATCCTTATA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
60 5 0.07
61 62 0.90
62 2 0.03
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (60 bp):
AATTTAAAATTTTTTAATTTAATCTAAATTTAATGTTATAATATATTAATTTAAGCTTCA
Found at i:162112 original size:18 final size:19
Alignment explanation
Indices: 162089--162127 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
162079 AATTCTTTCA
*
162089 ATTAATATATA-TTTTTAT
1 ATTAATATATAGTTTATAT
162107 ATTAATATATAGTTTATAT
1 ATTAATATATAGTTTATAT
162126 AT
1 AT
162128 ACTAATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
ATTAATATATAGTTTATAT
Found at i:162151 original size:33 final size:33
Alignment explanation
Indices: 162104--162246 Score: 176
Period size: 33 Copynumber: 4.5 Consensus size: 33
162094 TATATATTTT
162104 TATATTAATATATAGTTTATATATACTAATGAAC
1 TATA-TAATATATAGTTTATATATACTAATGAAC
*
162138 TATATAATATATAG-TT-TGTATA-T-AT--A-
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
162164 -ATATACTATATAGGTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
162196 TATATAATATATAGTTTATATATACTAATAAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
162229 TATATAATGTATAGTTTA
1 TATATAATATATAGTTTA
162247 GGGTTTAGGG
Statistics
Matches: 94, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
25 12 0.13
26 2 0.02
27 6 0.06
28 1 0.01
29 4 0.04
30 1 0.01
31 6 0.06
32 2 0.02
33 56 0.60
34 4 0.04
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATGAAC
Found at i:162161 original size:18 final size:18
Alignment explanation
Indices: 162091--162168 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 18
162081 TTCTTTCAAT
*
162091 TAATATATA-TTTTTATA
1 TAATATATAGTTTATATA
162108 TTAATATATAGTTTATATA
1 -TAATATATAGTTTATATA
* *
162127 TACTA-AT-G--AACTATA
1 TAATATATAGTTTA-TATA
162142 TAATATATAGTTTGTATATA
1 TAATATATAG-TT-TATATA
162162 TAATATA
1 TAATATA
162169 CTATATAGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
14 1 0.02
15 8 0.17
16 3 0.06
17 3 0.06
18 13 0.28
19 7 0.15
20 11 0.23
21 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (18 bp):
TAATATATAGTTTATATA
Found at i:162173 original size:25 final size:26
Alignment explanation
Indices: 162139--162201 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
162129 CTAATGAACT
* * *
162139 ATATAATATATAGTTTGTATATA-TA
1 ATATACTATATAGGTTATATATACTA
162164 ATATACTATATAGGTTATATATACTA
1 ATATACTATATAGGTTATATATACTA
162190 ATGA-ACTATATA
1 AT-ATACTATATA
162202 ATATATAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.61
26 12 0.36
27 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (26 bp):
ATATACTATATAGGTTATATATACTA
Found at i:162182 original size:58 final size:59
Alignment explanation
Indices: 162112--162234 Score: 212
Period size: 58 Copynumber: 2.1 Consensus size: 59
162102 TTTATATTAA
* * *
162112 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATATA-TAATATAC
1 TATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATAAAC
162170 TATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATAAAC
1 TATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATAAAC
162229 TATATA
1 TATATA
162235 ATGTATAGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 48 0.79
59 13 0.21
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.43
Consensus pattern (59 bp):
TATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATAAAC
Found at i:162265 original size:91 final size:92
Alignment explanation
Indices: 162104--162335 Score: 224
Period size: 91 Copynumber: 2.5 Consensus size: 92
162094 TATATATTTT
* * *
162104 TATATTAATATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATATATAATATA
1 TATA-TAATATATAGTTTATATATACTAATAAACTATATAATATATAGTTTGGATATAGAATATA
*
162169 CTATATA-GGTT-ATATATACTAATGA-AC
65 CTATATATAGTTCATATATA--AATGATAC
* * * ** *
162196 TATATAATATATAGTTTATATATACTAATAAACTATATAATGTATAGTTTAGGGTTTAGGGT-TT
1 TATATAATATATAGTTTATATATACTAATAAACTATATAATATATAGTTT-GGATATAGAATATA
* * *
162260 TTATATATAGTTCATATGTAAATTATAC
65 CTATATATAGTTCATATATAAATGATAC
*
162288 TATATAGTATATATAGTTTATATATA-TAATATATAGTATATAA-ATATA
1 TATATA--ATATATAGTTTATATATACTAATA-A-ACTATATAATATATA
162336 AACTATAGTA
Statistics
Matches: 117, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
91 55 0.47
92 20 0.17
93 11 0.09
94 23 0.20
95 8 0.07
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (92 bp):
TATATAATATATAGTTTATATATACTAATAAACTATATAATATATAGTTTGGATATAGAATATAC
TATATATAGTTCATATATAAATGATAC
Found at i:162299 original size:34 final size:36
Alignment explanation
Indices: 162261--162329 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
162251 TTAGGGTTTT
*
162261 TATATATAGTTCATATGTA-AAT-TATACTATATAG
1 TATATATAGTTCATATATATAATATATACTATATAG
* *
162295 TATATATAGTTTATATATATAATATATAGTATATA
1 TATATATAGTTCATATATATAATATATACTATATA
162330 AATATAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 17 0.57
35 3 0.10
36 10 0.33
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (36 bp):
TATATATAGTTCATATATATAATATATACTATATAG
Found at i:162300 original size:2 final size:2
Alignment explanation
Indices: 162283--162361 Score: 70
Period size: 2 Copynumber: 37.0 Consensus size: 2
162273 ATATGTAAAT
*
162283 TA TA CTA TA TA GTA TA TA TA GTT TA TA TA TA TA -A TA TA TA GTA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* *
162326 TA TA AA TA TA AA CTA TA GTA 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
162362 GGTCATATGT
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
1 1 0.02
2 53 0.83
3 10 0.16
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:162313 original size:20 final size:19
Alignment explanation
Indices: 162283--162414 Score: 99
Period size: 20 Copynumber: 6.6 Consensus size: 19
162273 ATATGTAAAT
162283 TATACTATATAGTATATATAG
1 TATA-TATATA-TATATATAG
*
162304 TTTATATATATAATATATAG
1 TATATATATAT-ATATATAG
* *
162324 TATATAAATATAAACTATAG
1 TATATATATATATA-TATAG
162344 TATATATATATATATATAGG
1 TATATATATATATATATA-G
* *
162364 TCATATGTA-A-ACTATATAT
1 T-ATATATATATA-TATATAG
* *
162383 TATATAAATATCA-ACTCTAG
1 TATATATATAT-ATA-TATAG
162403 TATATATATATA
1 TATATATATATA
162415 GGTCATATGT
Statistics
Matches: 89, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
18 5 0.06
19 12 0.13
20 62 0.70
21 10 0.11
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (19 bp):
TATATATATATATATATAG
Found at i:162389 original size:53 final size:52
Alignment explanation
Indices: 162331--162458 Score: 156
Period size: 53 Copynumber: 2.4 Consensus size: 52
162321 TAGTATATAA
162331 ATATAAACTATAGTATATATATATATATATAGGTCATATGTAAACTATATATT
1 ATATAAA-TATAGTATATATATATATATATAGGTCATATGTAAACTATATATT
*
162384 ATATAAATATCA--ACTCTAGTATATATATATAGGTCATATGTAAACTATATAGTT
1 ATATAAATAT-AGTA-TATA-TATATATATATAGGTCATATGTAAACTATATA-TT
*
162438 -TATATATATAGT-TCATATATA
1 ATATAAATATAGTAT-ATATATA
162459 AACTATAGTT
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
51 1 0.02
52 12 0.18
53 50 0.77
54 2 0.03
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (52 bp):
ATATAAATATAGTATATATATATATATATAGGTCATATGTAAACTATATATT
Found at i:162447 original size:13 final size:13
Alignment explanation
Indices: 162429--162458 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
162419 ATATGTAAAC
*
162429 TATATAGTTTATA
1 TATATAGTTCATA
162442 TATATAGTTCATA
1 TATATAGTTCATA
162455 TATA
1 TATA
162459 AACTATAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (13 bp):
TATATAGTTCATA
Found at i:162498 original size:22 final size:21
Alignment explanation
Indices: 162472--162546 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 21
162462 TATAGTTCAT
162472 ATATATGGTATATAAATATAA
1 ATATATGGTATATAAATATAA
*
162493 ACTATA-GTTTATATAAATAGTATA
1 A-TATATG-GTATATAAATA-TA-A
*
162517 A-ATATAGTATATAAATATAA
1 ATATATGGTATATAAATATAA
*
162537 AT-TATAGTAT
1 ATATATGGTAT
162547 GTAGTTTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
20 10 0.22
21 4 0.09
22 27 0.60
23 2 0.04
24 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (21 bp):
ATATATGGTATATAAATATAA
Found at i:162516 original size:33 final size:31
Alignment explanation
Indices: 162282--162522 Score: 133
Period size: 33 Copynumber: 7.7 Consensus size: 31
162272 CATATGTAAA
**
162282 TTATACTATATAGTATATATAGTTTA-TATA-T
1 TTATA-TATATAGTATATATA-TAAACTATAGT
*
162313 ATA-ATATATAGTATATAAATATAAACTATAGT
1 TTATATATATAGTATAT--ATATAAACTATAGT
* ** *
162345 ATATATATATA-TATATAGGT-CA-TAT-GT
1 TTATATATATAGTATATATATAAACTATAGT
** * * *
162372 AAACTATATATTA-TATAAATATCAACTCTAGT
1 TTA-TATATA-TAGTATATATATAAACTATAGT
* * *
162404 ATATATATATAGGT-CATATGTAAACTATATAGT
1 TTATATATATA-GTATATATATAAAC--TATAGT
162437 TTATATATATAGT-TCATATATAAACTATAGT
1 TTATATATATAGTAT-ATATATAAACTATAGT
* *
162468 TCATATATATGGTATATAAATATAAACTATAGT
1 TTATATATATAGTATAT--ATATAAACTATAGT
* *
162501 TTATATAAATAGTATAAATATA
1 TTATATATATAGTATATATATA
162523 GTATATAAAT
Statistics
Matches: 165, Mismatches: 27, Indels: 36
0.72 0.12 0.16
Matches are distributed among these distances:
27 4 0.02
28 9 0.05
29 21 0.13
30 8 0.05
31 48 0.29
32 17 0.10
33 58 0.35
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (31 bp):
TTATATATATAGTATATATATAAACTATAGT
Found at i:162529 original size:13 final size:13
Alignment explanation
Indices: 162487--162535 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
162477 TGGTATATAA
162487 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
162501 TTATATAA-ATAG-
1 ATATA-AATATAGT
162513 -TATAAATATAGT
1 ATATAAATATAGT
162525 ATATAAATATA
1 ATATAAATATA
162536 AATTATAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
10 2 0.07
11 8 0.27
13 14 0.47
14 4 0.13
15 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:162542 original size:13 final size:14
Alignment explanation
Indices: 162480--162570 Score: 60
Period size: 15 Copynumber: 6.3 Consensus size: 14
162470 ATATATATGG
162480 TATATAAATATAAA
1 TATATAAATATAAA
**
162494 CTATAGTTTATATAAA
1 -TATA-TAAATATAAA
*
162510 TAGTATAAATAT-AG
1 TA-TATAAATATAAA
162524 TATATAAATATAAA
1 TATATAAATATAAA
* * **
162538 T-TATAGTATGTAGTT
1 TATATA-AATATA-AA
162553 TATATAAATATAAA
1 TATATAAATATAAA
162567 TATA
1 TATA
162571 AACCCTAAAT
Statistics
Matches: 56, Mismatches: 14, Indels: 13
0.67 0.17 0.16
Matches are distributed among these distances:
13 13 0.23
14 13 0.23
15 16 0.29
16 14 0.25
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.41
Consensus pattern (14 bp):
TATATAAATATAAA
Found at i:162584 original size:14 final size:13
Alignment explanation
Indices: 162563--162593 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
162553 TATATAAATA
162563 TAAATATAAACCC
1 TAAATATAAACCC
162576 TAAATTATAAACCC
1 TAAA-TATAAACCC
162590 TAAA
1 TAAA
162594 CCATATATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAATATAAACCC
Found at i:162623 original size:24 final size:22
Alignment explanation
Indices: 162597--162653 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
162587 CCCTAAACCA
*
162597 TATATACTATATA-TATATAAAC
1 TATATAATATATATTA-ATAAAC
*
162619 TATATAATTTATATTAATAAAC
1 TATATAATATATATTAATAAAC
*
162641 TATATAATTTATA
1 TATATAATATATA
162654 CGATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 30 0.94
23 2 0.06
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (22 bp):
TATATAATATATATTAATAAAC
Found at i:162735 original size:13 final size:11
Alignment explanation
Indices: 162706--162737 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
162696 ATTGTATAGC
162706 TTATATATAAT
1 TTATATATAAT
*
162717 TCATATATAAT
1 TTATATATAAT
162728 TTATATATAA
1 TTATATATAA
162738 ACTATGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TTATATATAAT
Found at i:162825 original size:27 final size:28
Alignment explanation
Indices: 162779--162839 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
162769 ATATATAAAC
* **
162779 TATATAGTATTATAGTTTATACATGGTA
1 TATATAGTATTATACTTTATACATAATA
162807 TATATAGT-TTATACTTTATACATAATA
1 TATATAGTATTATACTTTATACATAATA
162834 TATATA
1 TATATA
162840 AACTATATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (28 bp):
TATATAGTATTATACTTTATACATAATA
Found at i:162838 original size:2 final size:2
Alignment explanation
Indices: 162831--162917 Score: 63
Period size: 2 Copynumber: 43.0 Consensus size: 2
162821 TTTATACATA
* * *
162831 AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT A- AT AC AT AT ACT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
* * *
162873 TT AT AT AT AA ACT AT AT AT -T TT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
162914 AT AT
1 AT AT
162918 GTAACATCCC
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
1 3 0.04
2 60 0.90
3 4 0.06
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:162846 original size:27 final size:27
Alignment explanation
Indices: 162789--162846 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
162779 TATATAGTAT
* ** ***
162789 TATAGTTTATACATGGTATATATAGTT
1 TATACTTTATACATAATATATATAAAC
162816 TATACTTTATACATAATATATATAAAC
1 TATACTTTATACATAATATATATAAAC
162843 TATA
1 TATA
162847 TAGTTTATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (27 bp):
TATACTTTATACATAATATATATAAAC
Found at i:162856 original size:22 final size:21
Alignment explanation
Indices: 162831--162917 Score: 94
Period size: 20 Copynumber: 4.3 Consensus size: 21
162821 TTTATACATA
162831 ATATATATAAACTATATAGTTT
1 ATATATATAAACTATATA-TTT
*
162853 ATATATATAATAC-ATATACTT
1 ATATATATAA-ACTATATATTT
162874 -TATATATAAACTATATATTT
1 ATATATATAAACTATATATTT
* *
162894 -TATAT-TATA-TATATATAT
1 ATATATATAAACTATATATTT
162912 ATATAT
1 ATATAT
162918 GTAACATCCC
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
18 8 0.14
19 10 0.17
20 21 0.36
21 2 0.03
22 15 0.26
23 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (21 bp):
ATATATATAAACTATATATTT
Found at i:165398 original size:23 final size:23
Alignment explanation
Indices: 165370--165414 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
165360 ATTATTATAT
165370 GGCACTACGGTGCAATTATACGC
1 GGCACTACGGTGCAATTATACGC
*
165393 GGCACTCCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
165415 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:170747 original size:23 final size:23
Alignment explanation
Indices: 170711--170756 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
170701 CATTATTATA
*
170711 TGGCACTACAGTGCAATTCTACG
1 TGGCACTACAGTGCAATTATACG
* *
170734 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACAGTGCAATTATACG
170757 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
TGGCACTACAGTGCAATTATACG
Found at i:171890 original size:209 final size:209
Alignment explanation
Indices: 171528--172334 Score: 1150
Period size: 209 Copynumber: 3.8 Consensus size: 209
171518 TTTTTTCTCA
**
171528 ACTTATTACTTATTTATATTTATTAATTGGCCCATAACTTTTTAAATGAATATAATTTAGTACAT
1 ACTTATTACTTATTTATATTT-TTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACAT
* *
171593 TTTTGTATTAATTTCAACCTCAAAAATTTAAAATTATTTCGATTTGTTCCCT-TTTGTGTTGTAT
65 TTTTGTATTAATTTCAACCTC-AAAATTTAAAATTATTTCGATTTGATCCCTATTTGTGTTGTTT
* *
171657 AATATATTTTAATTTTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTTATTTGC
129 AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
*
171722 ACCTGAAATTGACACAT
194 ATCTGAAATTGAC-CAT
*
171739 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATAGGTATAATTTAGTAC-T
1 ACTTATTACTTATTTATATTTTT-AATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACAT
* *
171803 TTTTGTATTAATTTTAACCTTAAAATTTAAAATTATTTCGATTTGATCCCT-TTTGTGTTGTTTA
65 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTATTTGTGTTGTTTA
*
171867 ATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATATAGTCCTCCAAATTTTATTTGCA
130 ATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCA
171932 TCTGAAATTGACCTAT
195 TCTGAAATTGACC-AT
* *
171948 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTATATTTTT-AATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACAT
* * *
172013 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCATCATCAATGTGTGTT
65 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCC--C-T--ATTTGTGTT
* *
172078 GTTTAATTTATTT-AA--TTT-TTT-TAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTTAT
125 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
*
172138 TTGCATATGAAATTGATCCAT
190 TTGCATCTGAAATTGA-CCAT
* **
172159 ACTTATTACTTGA-TT-T-TTTTTAATTGGCCCATAATTTTTTAAATGGGTATAATTTAGTATTT
1 ACTTATTACTT-ATTTATATTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACAT
* *
172221 TTTTGTATTAATTCCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
65 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT-AT---T-TGTGTT
*
172286 GTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
125 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
172335 ATTCTTAAAT
Statistics
Matches: 548, Mismatches: 28, Indels: 38
0.89 0.05 0.06
Matches are distributed among these distances:
204 2 0.00
205 1 0.00
206 1 0.00
208 106 0.19
209 184 0.34
210 69 0.13
211 127 0.23
212 10 0.02
213 27 0.05
215 2 0.00
216 19 0.03
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.51
Consensus pattern (209 bp):
ACTTATTACTTATTTATATTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACATT
TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTATTTGTGTTGTTTAA
TATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCAT
CTGAAATTGACCAT
Found at i:179863 original size:24 final size:24
Alignment explanation
Indices: 179836--179889 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
179826 CGTTCATTTA
179836 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
179860 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
179884 CGTTCG
1 CGTTCG
179890 ATTATGTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:179865 original size:14 final size:14
Alignment explanation
Indices: 179846--179897 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
179836 CGTTCGTGAA
179846 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
179860 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
179874 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
179884 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
179898 TGTTTATGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 23 0.68
ACGTcount: A:0.10, C:0.13, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:179894 original size:24 final size:24
Alignment explanation
Indices: 179847--179921 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
179837 GTTCGTGAAC
* *
179847 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
179871 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
* *
179895 GTTTGTTTATGTTCTTTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
179919 GTT
1 GTT
179922 TAACCCAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Done.