Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397275.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_34.0, 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: 2955990
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 53928 characters in sequence are not A, C, G, or T
File 6 of 8
Found at i:2063228 original size:12 final size:14
Alignment explanation
Indices: 2063186--2063348 Score: 57
Period size: 14 Copynumber: 11.2 Consensus size: 14
2063176 TTTATTTTTA
*
2063186 TTTATTATTATAATT
1 TTTA-TATTATATTT
* *
2063201 TATATATTATTTTAT
1 TTTATATTATATT-T
* *
2063216 TTTTTAATATATTT
1 TTTATATTATATTT
*
2063230 TTTATATTATATAT
1 TTTATATTATATTT
*
2063244 TTTATTTTA-ATTT
1 TTTATATTATATTT
** *
2063257 GTTTA-CCTATATTA
1 -TTTATATTATATTT
* *
2063271 TATAAATGT-TAATTT
1 TTTATAT-TAT-ATTT
*
2063286 TTTATATTTTATTT
1 TTTATATTATATTT
*
2063300 TATTTTAATT-T-TTAT
1 T-TTAT-ATTATATT-T
2063315 TCTTATATTATATTT
1 T-TTATATTATATTT
*
2063330 ATTTATTTTAATATTT
1 -TTTATATT-ATATTT
2063346 TTT
1 TTT
2063349 TTAATTATAA
Statistics
Matches: 109, Mismatches: 25, Indels: 28
0.67 0.15 0.17
Matches are distributed among these distances:
13 8 0.07
14 46 0.42
15 43 0.39
16 12 0.11
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (14 bp):
TTTATATTATATTT
Found at i:2063246 original size:112 final size:112
Alignment explanation
Indices: 2062769--2063229 Score: 774
Period size: 112 Copynumber: 4.1 Consensus size: 112
2062759 AAAATATAAG
2062769 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTT-AA-ATA-TTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
2062831 ATCATATATTTTATTTTATTTATTATTATAATATTTTATATTTTATT
66 ATCATATATTTTATTTTATTTATTATTATAATATTTTATATTTTATT
2062878 TTTAATATATTTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATA-TTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
*
2062943 TGTCATATATTTTATTTTATTTATTATTATAATATATTTATA-TTTATTT
65 TATCATATATTTTATTTTATTTATTATTATAATAT-TTTATATTTTA-TT
2062992 TTTAATATATTTATATTTTTATTATTAA-TTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
*
2063056 GTCATATATTTTATTTTATTTATTATTATAATATTTTATATTTTATT
66 ATCATATATTTTATTTTATTTATTATTATAATATTTTATATTTTATT
*
2063103 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATAT-TTTTAAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
2063167 ATCATATATTTTATTTTTATTTATTATTATAAT-TTATATATTATTTTATTT
66 ATCATATATTTTA-TTTTATTTATTATTATAATATT-T-TA-TATTTTA-TT
2063218 TTTAATATATTT
1 TTTAATATATTT
2063230 TTTATATTAT
Statistics
Matches: 336, Mismatches: 3, Indels: 20
0.94 0.01 0.06
Matches are distributed among these distances:
109 9 0.03
110 41 0.12
111 59 0.18
112 124 0.37
113 65 0.19
114 24 0.07
115 14 0.04
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (112 bp):
TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
ATCATATATTTTATTTTATTTATTATTATAATATTTTATATTTTATT
Found at i:2063272 original size:68 final size:68
Alignment explanation
Indices: 2063146--2063315 Score: 156
Period size: 68 Copynumber: 2.5 Consensus size: 68
2063136 ATATAATATC
* * * * * *
2063146 ATTTCTTAA-ATATTTTTAAATATCATATATTTTATTTTTATTTATTATTATAATTTATATATTA
1 ATTTTTTAATATATTTTT-TATATTATATATTTTATTTTAATTTATTACTATAATTTATATA-AA
*
2063210 T-TTT
64 TGTTA
*
2063214 ATTTTTTAATATATTTTTTATATTATATATTTTATTTTAATTTGTTTACCTAT-A-TTATATAAA
1 ATTTTTTAATATATTTTTTATATTATATATTTTATTTTAATTT-ATTA-CTATAATTTATATAAA
2063277 TGTTA
64 TGTTA
* *
2063282 ATTTTTT-ATATTTTATTTTATTTTA-AT-TTTTATT
1 ATTTTTTAATATATT-TTTTATATTATATATTTTATT
2063316 CTTATATTAT
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
66 7 0.08
67 10 0.11
68 55 0.63
69 12 0.14
70 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (68 bp):
ATTTTTTAATATATTTTTTATATTATATATTTTATTTTAATTTATTACTATAATTTATATAAATG
TTA
Found at i:2063305 original size:17 final size:17
Alignment explanation
Indices: 2063285--2063351 Score: 70
Period size: 17 Copynumber: 4.0 Consensus size: 17
2063275 AATGTTAATT
2063285 TTTTATATTTTATTTTA
1 TTTTATATTTTATTTTA
2063302 TTTTA-ATTTTTATTCTTA
1 TTTTATA-TTTTATT-TTA
*
2063320 TATTATA-TTTA-TTTA
1 TTTTATATTTTATTTTA
2063335 TTTTAATATTTT-TTTTA
1 TTTT-ATATTTTATTTTA
2063352 ATTATAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
15 6 0.14
16 5 0.12
17 23 0.55
18 7 0.17
19 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATATTTTATTTTA
Found at i:2063340 original size:33 final size:33
Alignment explanation
Indices: 2063287--2063357 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
2063277 TGTTAATTTT
2063287 TTATATTTTATTTTATTTTAAT-TTTTATTCTTATA
1 TTATATTTTATTTTATTTTAATATTTT-TT-TTA-A
2063322 TTATA-TTTA-TTTATTTTAATATTTTTTTTAA
1 TTATATTTTATTTTATTTTAATATTTTTTTTAA
2063353 TTATA
1 TTATA
2063358 ATATTATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
31 6 0.17
32 3 0.09
33 13 0.37
34 8 0.23
35 5 0.14
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (33 bp):
TTATATTTTATTTTATTTTAATATTTTTTTTAA
Found at i:2063344 original size:29 final size:29
Alignment explanation
Indices: 2063177--2063347 Score: 99
Period size: 29 Copynumber: 5.9 Consensus size: 29
2063167 ATCATATATT
* *
2063177 TTATTTTTATTTATTATT-ATAATTTATATA
1 TTATATTTATTTATT-TTAAT-ATTTTTATA
*
2063207 TTAT-TTTATTT-TTTAATATATTTTTTATA
1 TTATATTTATTTATTTTA-ATA-TTTTTATA
* *
2063236 TTATATAT-TTTATTTTAAT-TTGTTTA-C
1 TTATATTTATTTATTTTAATATT-TTTATA
* ** *
2063263 CTATATTATATAAATGTTAAT-TTTTTATA
1 TTATATT-TATTTATTTTAATATTTTTATA
* *
2063292 TTTTATTTTATTTTAATTTT--TATTCTTATA
1 TTATA-TTTA-TTT-ATTTTAATATTTTTATA
2063322 TTATATTTATTTATTTTAATATTTTT
1 TTATATTTATTTATTTTAATATTTTT
2063348 TTTAATTATA
Statistics
Matches: 107, Mismatches: 19, Indels: 31
0.68 0.12 0.20
Matches are distributed among these distances:
27 13 0.12
28 15 0.14
29 51 0.48
30 24 0.22
31 4 0.04
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (29 bp):
TTATATTTATTTATTTTAATATTTTTATA
Found at i:2063350 original size:12 final size:12
Alignment explanation
Indices: 2063290--2063353 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
2063280 TAATTTTTTA
2063290 TATTTT-AT-TT
1 TATTTTAATATT
*
2063300 TATTTTAATTTT
1 TATTTTAATATT
2063312 TATTCTT-ATA-T
1 TATT-TTAATATT
*
2063323 TATATT--TATT
1 TATTTTAATATT
2063333 TATTTTAATATT
1 TATTTTAATATT
*
2063345 TTTTTTAAT
1 TATTTTAAT
2063354 TATAATATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
9 2 0.05
10 14 0.32
11 6 0.14
12 20 0.45
13 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTTAATATT
Found at i:2063362 original size:34 final size:34
Alignment explanation
Indices: 2063293--2063362 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
2063283 TTTTTTATAT
*
2063293 TTTATTTTATTTTAATTTTTATTCTTATATTATA
1 TTTATTTTATTTTAATTTTTATTCTTATATAATA
2063327 TTTA-TTTATTTTAATATTTT-TT-TTAATTATAATA
1 TTTATTTTATTTTAAT-TTTTATTCTT-A-TATAATA
2063361 TT
1 TT
2063363 ATAAATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
32 2 0.06
33 14 0.44
34 16 0.50
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (34 bp):
TTTATTTTATTTTAATTTTTATTCTTATATAATA
Found at i:2073920 original size:168 final size:167
Alignment explanation
Indices: 2073638--2073980 Score: 474
Period size: 168 Copynumber: 2.0 Consensus size: 167
2073628 ATAGACCAAC
* * *
2073638 AATGAAAAGAGAAGAACCAATGGAAAAGGAATGAACGAAAAGATGGCAATTTGGGTGTGCTTTGA
1 AATG-AAAGAGAAGAACCAATGGAAAAGGAAAGAACGAAAAGATGGCAATTTGGGTATGCGTTGA
* *
2073703 TTTCCTCTGTTTCTTCCATGAAAGCCAACACAGAGTCAAAGGGCAGCAAAATAAGAATAAATCAA
65 TTTCCTCTGTTTCTTCCATCAAAGCCAACACAGAGTCAAAGGGCAGCAAAAGAAGAATAAATCAA
* * * *
2073768 TTAAAAAAGATTAATAATAAGAAATGATTTCATATA-A
130 TCAAAAAAGATTAATAAGAAGAAATAATTCCATATATA
* * * *
2073805 GAATGAAAGGGAAGAATCAATGGAAAAGGAAAAGAA-GAAAAAGATGTCAATTTTGGTATGCGTT
1 -AATGAAAGAGAAGAACCAATGGAAAAGG-AAAGAACG-AAAAGATGGCAATTTGGGTATGCGTT
* * *
2073869 GGTTTCCTCTGTTTCTTGCATCAAAGCCAACACAGAGTCAAAGGTCAGCAAAAGAAGAATAAATC
63 GATTTCCTCTGTTTCTTCCATCAAAGCCAACACAGAGTCAAAGGGCAGCAAAAGAAGAATAAATC
* *
2073934 ACTCAAAAAAGATTAATAAGAAGAGATAATTCCATATATA
128 AATCAAAAAAGATTAATAAGAAGAAATAATTCCATATATA
2073974 AATGAAA
1 AATGAAA
2073981 ATTTAATCAA
Statistics
Matches: 154, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
167 23 0.15
168 130 0.84
169 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.23
Consensus pattern (167 bp):
AATGAAAGAGAAGAACCAATGGAAAAGGAAAGAACGAAAAGATGGCAATTTGGGTATGCGTTGAT
TTCCTCTGTTTCTTCCATCAAAGCCAACACAGAGTCAAAGGGCAGCAAAAGAAGAATAAATCAAT
CAAAAAAGATTAATAAGAAGAAATAATTCCATATATA
Found at i:2074458 original size:26 final size:25
Alignment explanation
Indices: 2074423--2074506 Score: 66
Period size: 25 Copynumber: 3.4 Consensus size: 25
2074413 GAGTATGTAG
2074423 TTTTCCCCACGCTTTCCCTTACAAA
1 TTTTCCCCACGCTTTCCCTTACAAA
* *** * * *
2074448 TTTTCCTCCACCCAAGCGC--A-TAG
1 TTTTCC-CCACGCTTTCCCTTACAAA
2074471 TTTTCCCCACGCTTTCCCTTACAAA
1 TTTTCCCCACGCTTTCCCTTACAAA
2074496 TTTTCCTCCAC
1 TTTTCC-CCAC
2074507 CCAAGCGCAC
Statistics
Matches: 40, Mismatches: 14, Indels: 9
0.63 0.22 0.14
Matches are distributed among these distances:
22 7 0.17
23 7 0.17
24 2 0.05
25 13 0.32
26 11 0.28
ACGTcount: A:0.19, C:0.40, G:0.06, T:0.35
Consensus pattern (25 bp):
TTTTCCCCACGCTTTCCCTTACAAA
Found at i:2074476 original size:48 final size:48
Alignment explanation
Indices: 2074420--2074515 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2074410 GCAGAGTATG
2074420 TAGTTTTCCCCACGCTTTCCCTTACAAATTTTCCTCCACCCAAGCGCA
1 TAGTTTTCCCCACGCTTTCCCTTACAAATTTTCCTCCACCCAAGCGCA
2074468 TAGTTTTCCCCACGCTTTCCCTTACAAATTTTCCTCCACCCAAGCGCA
1 TAGTTTTCCCCACGCTTTCCCTTACAAATTTTCCTCCACCCAAGCGCA
2074516 CCTCACCACC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.21, C:0.40, G:0.08, T:0.31
Consensus pattern (48 bp):
TAGTTTTCCCCACGCTTTCCCTTACAAATTTTCCTCCACCCAAGCGCA
Found at i:2083877 original size:19 final size:19
Alignment explanation
Indices: 2083853--2083889 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2083843 ATTTATATTG
2083853 GTATGA-ATAAATATAAAAA
1 GTATGATAT-AATATAAAAA
2083872 GTATGATATAATATAAAA
1 GTATGATATAATATAAAA
2083890 TTATAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (19 bp):
GTATGATATAATATAAAAA
Found at i:2086229 original size:4 final size:4
Alignment explanation
Indices: 2086215--2086248 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
2086205 TTAATTTCCC
2086215 AATA TAATA AATA AATA AATA AATA AATA AATA A
1 AATA -AATA AATA AATA AATA AATA AATA AATA A
2086249 GGATTAGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:2091782 original size:31 final size:30
Alignment explanation
Indices: 2091740--2091802 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
2091730 ATCAAGCCTC
*
2091740 TATATTTTTATTTAAAGCCAAATAAACATT
1 TATATTTTTATTTAAAGCCAAATAAAAATT
** *
2091770 TATACTTTTTATTTTGAGTCAAATAAAAATT
1 TATA-TTTTTATTTAAAGCCAAATAAAAATT
2091801 TA
1 TA
2091803 AATGGCGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (30 bp):
TATATTTTTATTTAAAGCCAAATAAAAATT
Found at i:2097255 original size:16 final size:16
Alignment explanation
Indices: 2097216--2097255 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2097206 ACAAGTGAAA
2097216 AATTTTAAAATAAAAT
1 AATTTTAAAATAAAAT
*
2097232 AATATTAAAATATAAAT
1 AATTTTAAAATA-AAAT
2097249 -ATTTTAA
1 AATTTTAA
2097256 CTCTTGTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTTAAAATAAAAT
Found at i:2108873 original size:20 final size:21
Alignment explanation
Indices: 2108828--2108874 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
2108818 AGCTGGCCAG
*
2108828 TTTTTGTTCTTTCTTTTATTA
1 TTTTTGTTCTTTCTTTTATCA
*
2108849 ATTTT-TTCTTTCTTCTT-TCA
1 TTTTTGTTCTTTCTT-TTATCA
2108869 TTTTTG
1 TTTTTG
2108875 ATTTTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTTGTTCTTTCTTTTATCA
Found at i:2109525 original size:13 final size:13
Alignment explanation
Indices: 2109509--2109539 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2109499 AATCGCAATG
2109509 GAAAATCGAATAA
1 GAAAATCGAATAA
2109522 GAAAATCGAATAA
1 GAAAATCGAATAA
2109535 GAAAA
1 GAAAA
2109540 GAGCTGCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.16, T:0.13
Consensus pattern (13 bp):
GAAAATCGAATAA
Found at i:2115699 original size:18 final size:18
Alignment explanation
Indices: 2115676--2115710 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2115666 TAAATTTTTT
2115676 TAAAATATATATCATAAA
1 TAAAATATATATCATAAA
* *
2115694 TAAAATTTATATTATAA
1 TAAAATATATATCATAA
2115711 TTATGCTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATATATATCATAAA
Found at i:2122547 original size:19 final size:19
Alignment explanation
Indices: 2122523--2122563 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2122513 ATTTGCTATT
2122523 TTAGTGTAATATTTTGCAA
1 TTAGTGTAATATTTTGCAA
2122542 TTAGTGTAATATTTTGCAA
1 TTAGTGTAATATTTTGCAA
2122561 TTA
1 TTA
2122564 ATGTTCTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.49
Consensus pattern (19 bp):
TTAGTGTAATATTTTGCAA
Found at i:2127144 original size:14 final size:15
Alignment explanation
Indices: 2127125--2127153 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2127115 GTTTGTCAAA
2127125 CATG-AATTTGCTTC
1 CATGAAATTTGCTTC
2127139 CATGAAATTTGCTTC
1 CATGAAATTTGCTTC
2127154 TCAAATCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (15 bp):
CATGAAATTTGCTTC
Found at i:2133332 original size:36 final size:36
Alignment explanation
Indices: 2133287--2133383 Score: 113
Period size: 36 Copynumber: 2.7 Consensus size: 36
2133277 AAGTTAGTGT
* **
2133287 TTATTGCTTGATCTTGTTAAAAAACAAATGTAAGGG
1 TTATAGCTTGATCTCATTAAAAAACAAATGTAAGGG
* * *
2133323 TTATAGCTTGCTCTCATTAAAAAGCAAGTGTAAGGG
1 TTATAGCTTGATCTCATTAAAAAACAAATGTAAGGG
* * *
2133359 TTATCGCTTAATCTCATGAAAAAAC
1 TTATAGCTTGATCTCATTAAAAAAC
2133384 CGTTGTTAAG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (36 bp):
TTATAGCTTGATCTCATTAAAAAACAAATGTAAGGG
Found at i:2133965 original size:23 final size:24
Alignment explanation
Indices: 2133925--2133971 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2133915 CTAAAACCAG
* *
2133925 CACAAAAAGAAGTCGAAAGATTTC
1 CACAAAAAAAAATCGAAAGATTTC
*
2133949 CACAAAAAAAAAT-GAAAGCTTTC
1 CACAAAAAAAAATCGAAAGATTTC
2133972 ATTTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (24 bp):
CACAAAAAAAAATCGAAAGATTTC
Found at i:2148035 original size:35 final size:35
Alignment explanation
Indices: 2147983--2148064 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
2147973 GGAAAGCTAT
* * * *
2147983 TTGTTGAGGGTTGTGCTTGCTTTCGTGAAAAGGTA
1 TTGTTGAGGGTTATGCTTACTTCCGTGAAAAGGCA
*
2148018 TTGTT-AGTGGTTATGCTTACTTCCGTTAAAAGGCA
1 TTGTTGAG-GGTTATGCTTACTTCCGTGAAAAGGCA
2148053 TTGTTGAGGGTT
1 TTGTTGAGGGTT
2148065 TTGATTGAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 2 0.05
35 36 0.90
36 2 0.05
ACGTcount: A:0.18, C:0.10, G:0.30, T:0.41
Consensus pattern (35 bp):
TTGTTGAGGGTTATGCTTACTTCCGTGAAAAGGCA
Found at i:2149646 original size:19 final size:17
Alignment explanation
Indices: 2149622--2149667 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
2149612 GTAAATAAAC
*
2149622 ATAAAATTAAAATAACTT
1 ATAAAAATAAAATAA-TT
*
2149640 AATAAAAATAAACTAATT
1 -ATAAAAATAAAATAATT
2149658 ATAAAAATAA
1 ATAAAAATAA
2149668 CTAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 2 0.08
19 13 0.52
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAATAAAATAATT
Found at i:2149677 original size:16 final size:17
Alignment explanation
Indices: 2149640--2149677 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2149630 AAAATAACTT
*
2149640 AATAAAAATAAACTAAT
1 AATAAAAATAAACTAAA
*
2149657 TATAAAAAT-AACTAAA
1 AATAAAAATAAACTAAA
2149673 AATAA
1 AATAA
2149678 CAAAATTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAAAAATAAACTAAA
Found at i:2150914 original size:21 final size:19
Alignment explanation
Indices: 2150868--2150914 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
2150858 AAAGTGAGAA
*
2150868 AAATAG-AAAAAAGTAAAG
1 AAATAGAAAAAAAGAAAAG
*
2150886 AAAAAGAAGAAAAAGAAAAGG
1 AAATAGAA-AAAAAGAAAA-G
2150907 AAATAGAA
1 AAATAGAA
2150915 TTCTATGTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.22
19 1 0.04
20 9 0.39
21 8 0.35
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (19 bp):
AAATAGAAAAAAAGAAAAG
Found at i:2151088 original size:21 final size:22
Alignment explanation
Indices: 2151054--2151094 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2151044 TGTGATTAAT
* *
2151054 ATTAATTGATTAA-TTATTTTA
1 ATTAATTAACTAATTTATTTTA
2151075 ATTAATTAACTAATTTATTT
1 ATTAATTAACTAATTTATTT
2151095 ATAAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTAATTAACTAATTTATTTTA
Found at i:2151091 original size:17 final size:16
Alignment explanation
Indices: 2151075--2151125 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
2151065 AATTATTTTA
2151075 ATTAATTAACTAATTT
1 ATTAATTAACTAATTT
* * *
2151091 ATTTATAAAATAATTT
1 ATTAATTAACTAATTT
2151107 A--AATTAACTAATTT
1 ATTAATTAACTAATTT
2151121 ATTAA
1 ATTAA
2151126 AAGTAAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 11 0.41
16 16 0.59
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAATTAACTAATTT
Found at i:2157222 original size:36 final size:36
Alignment explanation
Indices: 2157180--2157313 Score: 205
Period size: 36 Copynumber: 3.7 Consensus size: 36
2157170 TAACCATTAA
2157180 AATGTCTTTCAAGGATCAAGCACAACTTTTCAATAC
1 AATGTCTTTCAAGGATCAAGCACAACTTTTCAATAC
2157216 AATGTCTTTCAAGGATCAAGCACAACTTTTCAATAC
1 AATGTCTTTCAAGGATCAAGCACAACTTTTCAATAC
* * *
2157252 AATGTCTTTCAAGAATCAAGCATAACCTTTCAATAC
1 AATGTCTTTCAAGGATCAAGCACAACTTTTCAATAC
* ***
2157288 AATGCCTTTTTTGGATCAAGCACAAC
1 AATGTCTTTCAAGGATCAAGCACAAC
2157314 CTTCCTAACT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 89 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (36 bp):
AATGTCTTTCAAGGATCAAGCACAACTTTTCAATAC
Found at i:2158638 original size:11 final size:11
Alignment explanation
Indices: 2158617--2158655 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2158607 TCTTTTCTGT
2158617 AAAGAGAAAAAA
1 AAAG-GAAAAAA
2158629 AAAGGAAAAACA
1 AAAGGAAAAA-A
2158641 AAA-GAAAAAA
1 AAAGGAAAAAA
2158651 AAAGG
1 AAAGG
2158656 TTCTTATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.16
11 13 0.52
12 8 0.32
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGGAAAAAA
Found at i:2161066 original size:42 final size:42
Alignment explanation
Indices: 2161018--2161099 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
2161008 ACTTCAATTA
* * *
2161018 AACTTAATTAAATGATTTAATTAAGTACAAGGACCAATTAAC
1 AACTTAACTAAATGATTCAATTAAGTACAAAGACCAATTAAC
* * * *
2161060 AACTTAACTGAATGGTTCAATTAAGTGCAAAGACGAATTA
1 AACTTAACTAAATGATTCAATTAAGTACAAAGACCAATTA
2161100 GCAAATTACA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.29
Consensus pattern (42 bp):
AACTTAACTAAATGATTCAATTAAGTACAAAGACCAATTAAC
Found at i:2163691 original size:28 final size:30
Alignment explanation
Indices: 2163660--2163735 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 30
2163650 TTTTAAAAAT
* *
2163660 TTTAAATAAGTTTTTAT-TTTTTATTTT-G
1 TTTAAATAAGTTTTTATATTTATATTTTAA
*
2163688 TTTAATTAAGTTTTTATATTTATATTTTAA
1 TTTAAATAAGTTTTTATATTTATATTTTAA
* *
2163718 ATTAAATAAATTTTTATA
1 TTTAAATAAGTTTTTATA
2163736 ATTAAAATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 16 0.40
29 9 0.22
30 15 0.38
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTAAATAAGTTTTTATATTTATATTTTAA
Found at i:2164839 original size:21 final size:22
Alignment explanation
Indices: 2164805--2164845 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2164795 AGTTTTTTTG
*
2164805 TCAAATATTAATTTTATTAATA
1 TCAAATATAAATTTTATTAATA
2164827 TCAAA-ATAAATTTTATTAA
1 TCAAATATAAATTTTATTAA
2164846 GTTTTAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (22 bp):
TCAAATATAAATTTTATTAATA
Found at i:2172505 original size:25 final size:22
Alignment explanation
Indices: 2172462--2172511 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 22
2172452 GTAGTCTTCA
2172462 ATAATTAATTAATTAATATTTT
1 ATAATTAATTAATTAATATTTT
2172484 ATAATTATATATAATTTAATATTTT
1 ATAATTA-AT-TAA-TTAATATTTT
2172509 ATA
1 ATA
2172512 TAATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 7 0.28
23 2 0.08
24 3 0.12
25 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATTAATTAATTAATATTTT
Found at i:2172707 original size:25 final size:25
Alignment explanation
Indices: 2172676--2172726 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2172666 CGTTTGGTAC
2172676 ATTACAATGTAATGTGATTACAGGT
1 ATTACAATGTAATGTGATTACAGGT
2172701 ATTACAATGTAATGTGATTACAGGT
1 ATTACAATGTAATGTGATTACAGGT
2172726 A
1 A
2172727 ATGTGATTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (25 bp):
ATTACAATGTAATGTGATTACAGGT
Found at i:2172729 original size:15 final size:15
Alignment explanation
Indices: 2172709--2172754 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
2172699 GTATTACAAT
2172709 GTAATGTGATTACAG
1 GTAATGTGATTACAG
* *
2172724 GTAATGTGATTGCAA
1 GTAATGTGATTACAG
*
2172739 GTAATGCGATTACAG
1 GTAATGTGATTACAG
2172754 G
1 G
2172755 GAAAATAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (15 bp):
GTAATGTGATTACAG
Found at i:2172933 original size:27 final size:25
Alignment explanation
Indices: 2172903--2172999 Score: 76
Period size: 25 Copynumber: 3.8 Consensus size: 25
2172893 TATAAATTTA
2172903 ATATATTATTAATTTTTATATAATATC
1 ATATATT-TTAATTTTTAT-TAATATC
*
2172930 ATAT-TTTAAATATATTT-TTAATATC
1 ATATATTTTAAT-T-TTTATTAATATC
* *
2172955 ATATATTTT-ATTTTTATTTATTATT
1 ATATATTTTAATTTTTA-TTAATATC
2172980 ATA-ATTTTATATATTTTATT
1 ATATATTTTA-AT-TTTTATT
2173000 TTCATTTCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
23 3 0.05
24 6 0.10
25 26 0.45
26 11 0.19
27 12 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
ATATATTTTAATTTTTATTAATATC
Found at i:2172992 original size:33 final size:33
Alignment explanation
Indices: 2172955--2173040 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
2172945 TTTTAATATC
*
2172955 ATATATTTTATTTTTATTTA-TTATTATAATTTT
1 ATATATTTTATTTTTATTTATTTAATAT-ATTTT
* *
2172988 ATATATTTTATTTTCATTTCTTTAATATATTTT
1 ATATATTTTATTTTTATTTATTTAATATATTTT
* *
2173021 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
2173041 TAATTTGTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 32 0.71
34 13 0.29
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTTAATATATTTT
Found at i:2173127 original size:26 final size:27
Alignment explanation
Indices: 2173091--2173143 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
2173081 TATTTTATTT
* * *
2173091 TATTTTAATTTTTATTCTTATATTATA
1 TATTTTAATTTTAATTATAATATTATA
2173118 TATTTT-ATTTTAATTATAATATTATA
1 TATTTTAATTTTAATTATAATATTATA
2173144 AAATATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTTTAATTTTAATTATAATATTATA
Found at i:2175135 original size:21 final size:20
Alignment explanation
Indices: 2175106--2175156 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
2175096 GGAAACAGAG
* *
2175106 AAAATAAAAGAAAACGGAAGA
1 AAAAGAAAAGAAAACAGAA-A
*
2175127 AAAAGAAAATAAAACAGAAA
1 AAAAGAAAAGAAAACAGAAA
2175147 AACAAGAAAA
1 AA-AAGAAAA
2175157 CATGTTACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (20 bp):
AAAAGAAAAGAAAACAGAAA
Found at i:2177067 original size:87 final size:88
Alignment explanation
Indices: 2176920--2177193 Score: 329
Period size: 96 Copynumber: 3.0 Consensus size: 88
2176910 AAAATAAAAG
* * *
2176920 AAAAGGGAA-AACAAAGAAAATAAAACAG-AAAAACAAGAAAATATGAACCGGAAAAAGAAAGG-
1 AAAAGGGAAGAA-AAAGAAAATAAAACAGAAAAAACAAGAAAACATGAACTGGAAAATGAAAGGA
* * *
2176982 GAATGCAAAATGGGTTCTCCAGAG
65 AAATGCGAAATGGGTTCTCCAGAA
**
2177006 AAAAGGGAAGAAAAAGAAAGCAAAACAGAAAAAACAAGAAAACATGAACTGGAAAATGAAAGGAA
1 AAAAGGGAAGAAAAAGAAAATAAAACAGAAAAAACAAGAAAACATGAACTGGAAAATGAAAGGAA
2177071 AATGCGAAATGGGTTCTCCAGAAAAA
66 AATGCGAAATGGGTTCTCCAG---AA
** * *
2177097 ATACAAGAAAATGAAATAATAAAAATAAAACAGAAAAAACAAGAAAACATGAACTTGAAAATGAA
1 A-A-AAGGGAA-GAAA-AA-GAAAATAAAACAGAAAAAACAAGAAAACATGAACTGGAAAATGAA
*
2177162 AGGAAAATGCGAAATGCGTTCTCCAGAA
61 AGGAAAATGCGAAATGGGTTCTCCAGAA
2177190 AAAA
1 AAAA
2177194 AAAAAAGAAA
Statistics
Matches: 162, Mismatches: 15, Indels: 17
0.84 0.08 0.09
Matches are distributed among these distances:
86 23 0.14
87 33 0.20
88 20 0.12
91 4 0.02
92 2 0.01
93 8 0.05
94 4 0.02
95 2 0.01
96 66 0.41
ACGTcount: A:0.59, C:0.10, G:0.19, T:0.11
Consensus pattern (88 bp):
AAAAGGGAAGAAAAAGAAAATAAAACAGAAAAAACAAGAAAACATGAACTGGAAAATGAAAGGAA
AATGCGAAATGGGTTCTCCAGAA
Found at i:2177381 original size:2 final size:2
Alignment explanation
Indices: 2177374--2177456 Score: 113
Period size: 2 Copynumber: 44.0 Consensus size: 2
2177364 TCTGATATTC
2177374 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT AT
* *
2177415 AA AT -T TT AT -T AT -T AT AT A- 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
2177453 AT AT
1 AT AT
2177457 CGGCATTGAA
Statistics
Matches: 74, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
1 5 0.07
2 69 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2182062 original size:22 final size:22
Alignment explanation
Indices: 2182020--2182062 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2182010 GGTGGTCCAA
*
2182020 TAAGAAACTAAAGAAACAAAAC
1 TAAGAAACTAAAAAAACAAAAC
*
2182042 TAAGAAA-TAACAAAAAGAAAA
1 TAAGAAACTAA-AAAAACAAAA
2182063 GCGAAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.72, C:0.09, G:0.09, T:0.09
Consensus pattern (22 bp):
TAAGAAACTAAAAAAACAAAAC
Found at i:2192670 original size:20 final size:21
Alignment explanation
Indices: 2192647--2192685 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2192637 AAGTTAATTT
2192647 TATTTTAGGT-TTATTTATCA
1 TATTTTAGGTGTTATTTATCA
*
2192667 TATTTTAGTTGTTATTTAT
1 TATTTTAGGTGTTATTTAT
2192686 TAGTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (21 bp):
TATTTTAGGTGTTATTTATCA
Found at i:2195467 original size:21 final size:21
Alignment explanation
Indices: 2195443--2195485 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2195433 CTCCATCATT
*
2195443 TCCAGT-AGCTTCAAATGGGCC
1 TCCAGTAAG-TTCAAATAGGCC
2195464 TCCAGTAAGTTCAAATAGGCC
1 TCCAGTAAGTTCAAATAGGCC
2195485 T
1 T
2195486 ACAGCTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
TCCAGTAAGTTCAAATAGGCC
Found at i:2197095 original size:80 final size:83
Alignment explanation
Indices: 2196997--2197154 Score: 191
Period size: 83 Copynumber: 1.9 Consensus size: 83
2196987 TGTCTTATAT
* * *
2196997 AATACATCATCAATAATAACAAAAT-A-AAAAAACAAAGCC-AA-ATC-AACATACATTAAAAAA
1 AATACATCAGCAACAATAA-AAAATGAGAAAAAACAAAACCTAATATCGAACAT-CATTAAAAAA
*
2197057 ACAACCTAATACTATAAACA
64 ACAAACTAATACTATAAACA
* * * *
2197077 AATACATCAGGAACAATAAAAAATGAGAAAAAACAAAACCTAATATCGATCATCATTAAAAATAG
1 AATACATCAGCAACAATAAAAAATGAGAAAAAACAAAACCTAATATCGAACATCATTAAAAAAAC
2197142 AAACTAATACTAT
66 AAACTAATACTAT
2197155 TCACCAACAA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
79 5 0.08
80 17 0.26
81 12 0.18
82 2 0.03
83 25 0.38
84 4 0.06
ACGTcount: A:0.60, C:0.16, G:0.04, T:0.19
Consensus pattern (83 bp):
AATACATCAGCAACAATAAAAAATGAGAAAAAACAAAACCTAATATCGAACATCATTAAAAAAAC
AAACTAATACTATAAACA
Found at i:2197382 original size:22 final size:22
Alignment explanation
Indices: 2197342--2197383 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2197332 CTTGAAAACT
*
2197342 TTCAAGGTTTGTAGCTTTCAGG
1 TTCAAGGTTTGTAGATTTCAGG
*
2197364 TTCAAGGTTTGTTGATTTCA
1 TTCAAGGTTTGTAGATTTCA
2197384 AGTTGAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (22 bp):
TTCAAGGTTTGTAGATTTCAGG
Found at i:2197490 original size:30 final size:30
Alignment explanation
Indices: 2197422--2197495 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
2197412 TGTTGATTTG
*
2197422 TCACTCTCAATTTAGTATTTAGACTGGATT
1 TCACTCTCGATTTAGTATTTAGACTGGATT
* * ** *
2197452 GCAATCTCGATTTAGTATTTAGGTTGGGTT
1 TCACTCTCGATTTAGTATTTAGACTGGATT
2197482 TCACTCTCGATTTA
1 TCACTCTCGATTTA
2197496 TCGTTATCTC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (30 bp):
TCACTCTCGATTTAGTATTTAGACTGGATT
Found at i:2200429 original size:21 final size:20
Alignment explanation
Indices: 2200376--2200434 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
2200366 CATAAAAACT
2200376 AATAAAT-AATAGCAAAATTAA
1 AATAAATAAATA--AAAATTAA
*
2200397 AGTAAATAAATATAAAATTAA
1 AATAAATAAATA-AAAATTAA
* *
2200418 AATAACTTAATAAAAAT
1 AATAAATAAATAAAAAT
2200435 AAACTAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 5 0.16
21 23 0.72
22 4 0.12
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (20 bp):
AATAAATAAATAAAAATTAA
Found at i:2200432 original size:19 final size:18
Alignment explanation
Indices: 2200408--2200450 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
2200398 GTAAATAAAT
*
2200408 ATAAAATTAAAATAACTTA
1 ATAAAAATAAAATAA-TTA
*
2200427 ATAAAAATAAACTAATTA
1 ATAAAAATAAAATAATTA
2200445 A-AAAAA
1 ATAAAAA
2200451 CACTAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 13 0.59
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAAAATAAAATAATTA
Found at i:2203255 original size:21 final size:20
Alignment explanation
Indices: 2203231--2203275 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
2203221 TTAAAGTAAT
2203231 TTAAAATAAAATAACATAAAA
1 TTAAAATAAAATAAC-TAAAA
* *
2203252 TTAAAGTAAAATAACTTAAA
1 TTAAAATAAAATAACTAAAA
2203272 TTAA
1 TTAA
2203276 CTACTCGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
TTAAAATAAAATAACTAAAA
Found at i:2209287 original size:31 final size:31
Alignment explanation
Indices: 2209249--2209319 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
2209239 TTCAACTATT
2209249 ATGTTGATAATGAACTTGGTTATGTAAACAA
1 ATGTTGATAATGAACTTGGTTATGTAAACAA
2209280 ATGTTGATAATGAACTTGGTTATGTAAACAA
1 ATGTTGATAATGAACTTGGTTATGTAAACAA
2209311 ATGTTGATA
1 ATGTTGATA
2209320 TTCTCATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.37
Consensus pattern (31 bp):
ATGTTGATAATGAACTTGGTTATGTAAACAA
Found at i:2210997 original size:37 final size:36
Alignment explanation
Indices: 2210941--2211077 Score: 141
Period size: 37 Copynumber: 3.7 Consensus size: 36
2210931 CAAAAGTCAC
* * *
2210941 TGCCTTTTGAGTATCAAGCACAACCTTTACAAGCCAC
1 TGCCTTTTAAGGATCAAGCACAACCTTTACAA-CCAA
* * * *
2210978 TACCTTTTAAGGATTAAGCACAACCTCTACAATCAAA
1 TGCCTTTTAAGGATCAAGCACAACCTTTACAA-CCAA
*
2211015 TGCCTTTTAAGGATCAAACACAA-CTTCTACAACCAAA
1 TGCCTTTTAAGGATCAAGCACAACCTT-TACAACC-AA
* *
2211052 TTCCTTTTAAGGATCAAGCATAACCT
1 TGCCTTTTAAGGATCAAGCACAACCT
2211078 CTCTACCTTT
Statistics
Matches: 81, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
36 3 0.04
37 76 0.94
38 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (36 bp):
TGCCTTTTAAGGATCAAGCACAACCTTTACAACCAA
Found at i:2211037 original size:74 final size:74
Alignment explanation
Indices: 2210941--2211079 Score: 183
Period size: 74 Copynumber: 1.9 Consensus size: 74
2210931 CAAAAGTCAC
* * * * *
2210941 TGCCTTTTGAGTATCAAGCACAACCTT-TACAAGCC-ACTACCTTTTAAGGATTAAGCACAACCT
1 TGCCTTTTAAGGATCAAACACAA-CTTCTACAA-CCAAATACCTTTTAAGGATCAAGCACAACCT
2211004 CTACAATCAAA
64 CTACAATCAAA
* *
2211015 TGCCTTTTAAGGATCAAACACAACTTCTACAACCAAATTCCTTTTAAGGATCAAGCATAACCTCT
1 TGCCTTTTAAGGATCAAACACAACTTCTACAACCAAATACCTTTTAAGGATCAAGCACAACCTCT
2211080 CTACCTTTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
73 5 0.09
74 51 0.91
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (74 bp):
TGCCTTTTAAGGATCAAACACAACTTCTACAACCAAATACCTTTTAAGGATCAAGCACAACCTCT
ACAATCAAA
Found at i:2211163 original size:31 final size:30
Alignment explanation
Indices: 2211080--2211163 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
2211070 CATAACCTCT
*
2211080 CTACCTTTTGCTTGGAGGTATAACCTTAACA
1 CTACCTTTT-CATGGAGGTATAACCTTAACA
* * * *
2211111 CTACCTTTTTAAGGAGTTATAACCTTAATA
1 CTACCTTTTCATGGAGGTATAACCTTAACA
* *
2211141 TTGCCCTTTTCATGGAGGTATAA
1 CT-ACCTTTTCATGGAGGTATAA
2211164 ACAACAACAA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
30 17 0.40
31 25 0.60
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (30 bp):
CTACCTTTTCATGGAGGTATAACCTTAACA
Found at i:2214397 original size:20 final size:21
Alignment explanation
Indices: 2214369--2214412 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2214359 TGGGTTTGCC
* *
2214369 TTTCTTTTCTTTTCTT-TTTT
1 TTTCCTTTCTTCTCTTCTTTT
2214389 TTTCCTTTCTTCTCTTCTTTT
1 TTTCCTTTCTTCTCTTCTTTT
2214410 TTT
1 TTT
2214413 GTTCCTCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTCCTTTCTTCTCTTCTTTT
Found at i:2222876 original size:2 final size:2
Alignment explanation
Indices: 2222869--2222900 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2222859 AATACATTGA
2222869 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
2222901 TACATTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2232098 original size:6 final size:6
Alignment explanation
Indices: 2232087--2232117 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2232077 TGTGGTGAGA
2232087 TGGGTT TGGGTT TGGGTT TGGGTT TGGGTT T
1 TGGGTT TGGGTT TGGGTT TGGGTT TGGGTT T
2232118 TCGATGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TGGGTT
Found at i:2235247 original size:2 final size:2
Alignment explanation
Indices: 2235240--2235267 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2235230 AATTTATAGC
2235240 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
2235268 GTTAATCTCT
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:2236105 original size:21 final size:21
Alignment explanation
Indices: 2236080--2236121 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2236070 TTTTTTATTG
2236080 TTAATTTTTATATAATATCAT
1 TTAATTTTTATATAATATCAT
*
2236101 TTAATTTTTGTATAATATCAT
1 TTAATTTTTATATAATATCAT
2236122 CTCTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAATTTTTATATAATATCAT
Found at i:2236158 original size:20 final size:19
Alignment explanation
Indices: 2236148--2236265 Score: 64
Period size: 20 Copynumber: 6.1 Consensus size: 19
2236138 TAATATCTTA
* *
2236148 TATTTT-ATTTTTATTTTT
1 TATTTTAATATTTATATTT
*
2236166 TATTATAATATTATATATTT
1 TATTTTAATATT-TATATTT
* **
2236186 TATTTTAAT-TTCTCTAACAT
1 TATTTTAATATT-TAT-ATTT
* *
2236206 AATTTTAATTTTTTATATTT
1 TATTTTAA-TATTTATATTT
*
2236226 TATTTTAAT-TTTAAATTTT
1 TATTTTAATATTTATA-TTT
*
2236245 TATATTATATATTT-TATTT
1 TATTTTA-ATATTTATATTT
2236264 TA
1 TA
2236266 ATTATAACAT
Statistics
Matches: 76, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
18 10 0.13
19 23 0.30
20 35 0.46
21 6 0.08
22 2 0.03
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTTAATATTTATATTT
Found at i:2236166 original size:13 final size:13
Alignment explanation
Indices: 2236145--2236265 Score: 52
Period size: 13 Copynumber: 8.8 Consensus size: 13
2236135 TTTTAATATC
2236145 TTATATTTTATTT
1 TTATATTTTATTT
* *
2236158 TTATTTTTTATTA
1 TTATATTTTATTT
* *
2236171 TAATATTATATATT
1 TTATATTTTAT-TT
*
2236185 TTAT-TTTAATTT
1 TTATATTTTATTT
2236197 CTCTAACATAATTTTAATTTT
1 -T-T---AT-ATTTT-A-TTT
2236218 TTATATTTTA-TT
1 TTATATTTTATTT
2236230 TTA-ATTTTAAATTT
1 TTATATTTT--ATTT
* *
2236244 TTATATTATATAT
1 TTATATTTTATTT
2236257 TT-TATTTTA
1 TTATATTTTA
2236266 ATTATAACAT
Statistics
Matches: 81, Mismatches: 13, Indels: 29
0.66 0.11 0.24
Matches are distributed among these distances:
11 5 0.06
12 13 0.16
13 30 0.37
14 11 0.14
15 9 0.11
16 2 0.02
17 2 0.02
19 4 0.05
20 2 0.02
21 3 0.04
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATATTTTATTT
Found at i:2236243 original size:33 final size:33
Alignment explanation
Indices: 2236206--2236268 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2236196 TCTCTAACAT
* *
2236206 AATTTTAATTTTTTATATTTTATTTTAATTTTA
1 AATTTTAATATTATATATTTTATTTTAATTTTA
*
2236239 AATTTTTATATTATATATTTTATTTTAATT
1 AATTTTAATATTATATATTTTATTTTAATT
2236269 ATAACATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (33 bp):
AATTTTAATATTATATATTTTATTTTAATTTTA
Found at i:2239207 original size:11 final size:12
Alignment explanation
Indices: 2239179--2239218 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2239169 ATTTTTATTA
2239179 AACATGGTGTGT
1 AACATGGTGTGT
*
2239191 AACATGTTGTG-
1 AACATGGTGTGT
*
2239202 AACATGGCGTGT
1 AACATGGTGTGT
2239214 AACAT
1 AACAT
2239219 TTTTTGAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (12 bp):
AACATGGTGTGT
Found at i:2239213 original size:23 final size:23
Alignment explanation
Indices: 2239163--2239263 Score: 121
Period size: 23 Copynumber: 4.3 Consensus size: 23
2239153 GCAAATGGCA
*
2239163 TGTAACATTTTTATTAAACATGGTG
1 TGTAACA-TTTT-TTGAACATGGTG
* * *
2239188 TGTAACATGTTGTGAACATGGCG
1 TGTAACATTTTTTGAACATGGTG
2239211 TGTAACATTTTTTGAACATGGTG
1 TGTAACATTTTTTGAACATGGTG
* * *
2239234 TATAATATTTTTTGAACATGGAG
1 TGTAACATTTTTTGAACATGGTG
2239257 TGTAACA
1 TGTAACA
2239264 ACATGACTGA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 54 0.84
24 3 0.05
25 7 0.11
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (23 bp):
TGTAACATTTTTTGAACATGGTG
Found at i:2239250 original size:46 final size:48
Alignment explanation
Indices: 2239157--2239263 Score: 137
Period size: 46 Copynumber: 2.3 Consensus size: 48
2239147 GTGTTAGCAA
* *
2239157 ATGGCATGTAACATTTTTATTAAACATGGTGTGTAACATGTTGTGAAC
1 ATGGCGTGTAACATTTTTATTAAACATGGTGTATAACATGTTGTGAAC
* * * *
2239205 ATGGCGTGTAACA-TTTT-TTGAACATGGTGTATAATATTTTTTGAAC
1 ATGGCGTGTAACATTTTTATTAAACATGGTGTATAACATGTTGTGAAC
*
2239251 ATGGAGTGTAACA
1 ATGGCGTGTAACA
2239264 ACATGACTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
46 36 0.69
47 4 0.08
48 12 0.23
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.38
Consensus pattern (48 bp):
ATGGCGTGTAACATTTTTATTAAACATGGTGTATAACATGTTGTGAAC
Found at i:2245753 original size:76 final size:76
Alignment explanation
Indices: 2245543--2245842 Score: 334
Period size: 76 Copynumber: 4.0 Consensus size: 76
2245533 TTGGTACACA
* * * * *
2245543 CTCCAATTGTTAGATGTCGATGATATCTAGTGCTGACACGCTAAGTCATTGTAGTATTATGGGAT
1 CTCCAATTGTTAGATGTCGATGACATCTTGTGGTGACACGTTAAGTCGTTGTAGTATTATGGGAT
* * *
2245608 GATATGTCACG
66 GACATGCCATG
* * * * **
2245619 C-CCTACTTGTTAAATGTCGATG-CATCTTGTGGTGAGATGTTAAGTCGTTGTAGTATTATGAAA
1 CTCC-AATTGTTAGATGTCGATGACATCTTGTGGTGACACGTTAAGTCGTTGTAGTATTATGGGA
2245682 TGACATGCCATG
65 TGACATGCCATG
* * * * *
2245694 CTCCAATTGTTAGATGTCGATGACATCTTGTGGTGACACATTGAGTTGTTATAGTATTATGGGGT
1 CTCCAATTGTTAGATGTCGATGACATCTTGTGGTGACACGTTAAGTCGTTGTAGTATTATGGGAT
* **
2245759 GGCACACCATG
66 GACATGCCATG
* * * * *
2245770 CTCCACTTGTTAGATGTCGATGACATCTTGTGGTGACACCTTGAGTCGTTGCAGTATTATGGGGT
1 CTCCAATTGTTAGATGTCGATGACATCTTGTGGTGACACGTTAAGTCGTTGTAGTATTATGGGAT
2245835 GACATGCC
66 GACATGCC
2245843 GCACTGGCTG
Statistics
Matches: 185, Mismatches: 36, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
75 60 0.32
76 125 0.68
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (76 bp):
CTCCAATTGTTAGATGTCGATGACATCTTGTGGTGACACGTTAAGTCGTTGTAGTATTATGGGAT
GACATGCCATG
Found at i:2245938 original size:76 final size:76
Alignment explanation
Indices: 2245851--2246176 Score: 373
Period size: 76 Copynumber: 4.3 Consensus size: 76
2245841 CCGCACTGGC
* * * *
2245851 TGAGTCGTTGCAATATTATAGGGTGACACACCATGCTCCAATTATTAGATGTCGATGACATCTTG
1 TGAGTCGTTGCAGTATTATGGGGTGACACACCATGCTCCACTTGTTAGATGTCGATGACATCTTG
2245916 TGGTAACACAT
66 TGGTAACACAT
* * * * * *
2245927 TGAGTCATTGCATTATTATGGGGTGACACATCACGCTCTACTTGTTAGATGTCGATGATATCTTG
1 TGAGTCGTTGCAGTATTATGGGGTGACACACCATGCTCCACTTGTTAGATGTCGATGACATCTTG
* * **
2245992 TGGCAAAACGC
66 TGGTAACACAT
* * * ** *
2246003 TGAGCCGTTGTAGTATTATGAGGTGACATGCCATGCTCCATTTGTTAGATGTCGATGACATCTTG
1 TGAGTCGTTGCAGTATTATGGGGTGACACACCATGCTCCACTTGTTAGATGTCGATGACATCTTG
*
2246068 TGGTGACACAT
66 TGGTAACACAT
* * * * * *
2246079 TGAGTCATTGCAGTATTATGGGGTGACACACTAAGCTCCACTTCTTAAATGTCGATGACATCGTG
1 TGAGTCGTTGCAGTATTATGGGGTGACACACCATGCTCCACTTGTTAGATGTCGATGACATCTTG
* * **
2246144 TGATGACATGT
66 TGGTAACACAT
2246155 TGAGTCGTTGCAGTATTATGGG
1 TGAGTCGTTGCAGTATTATGGG
2246177 CAAACCCAAG
Statistics
Matches: 204, Mismatches: 46, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
76 204 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (76 bp):
TGAGTCGTTGCAGTATTATGGGGTGACACACCATGCTCCACTTGTTAGATGTCGATGACATCTTG
TGGTAACACAT
Found at i:2245992 original size:192 final size:192
Alignment explanation
Indices: 2245689--2246034 Score: 514
Period size: 192 Copynumber: 1.8 Consensus size: 192
2245679 AAATGACATG
* * ** *
2245689 CCATGCTCCAATTGTTAGATGTCGATGACATCTTGTGGTGACACATTGAGTTGTTATAGTATTAT
1 CCATGCTCCAATTATTAGATGTCGATGACATCTTGTGGTAACACATTGAGTCATTACAGTATTAT
* * ** * *
2245754 GGGGTGGCACACCATGCTCCACTTGTTAGATGTCGATGACATCTTGTGGTGACAC-CTTGAGTCG
66 GGGGTGACACACCACGCTCCACTTGTTAGATGTCGATGACATCTTGTGGCAAAACGC-TGAGCCG
*
2245818 TTGCAGTATTATGGGGTGACATGCCGCACTGGCTGAGTCGTTGCAATATTATAGGGTGACACA
130 TTGCAGTATTATGAGGTGACATGCCGCACTGGCTGAGTCGTTGCAATATTATAGGGTGACACA
* *
2245881 CCATGCTCCAATTATTAGATGTCGATGACATCTTGTGGTAACACATTGAGTCATTGCATTATTAT
1 CCATGCTCCAATTATTAGATGTCGATGACATCTTGTGGTAACACATTGAGTCATTACAGTATTAT
* * *
2245946 GGGGTGACACATCACGCTCTACTTGTTAGATGTCGATGATATCTTGTGGCAAAACGCTGAGCCGT
66 GGGGTGACACACCACGCTCCACTTGTTAGATGTCGATGACATCTTGTGGCAAAACGCTGAGCCGT
*
2246011 TGTAGTATTATGAGGTGACATGCC
131 TGCAGTATTATGAGGTGACATGCC
2246035 ATGCTCCATT
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
192 134 0.99
193 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (192 bp):
CCATGCTCCAATTATTAGATGTCGATGACATCTTGTGGTAACACATTGAGTCATTACAGTATTAT
GGGGTGACACACCACGCTCCACTTGTTAGATGTCGATGACATCTTGTGGCAAAACGCTGAGCCGT
TGCAGTATTATGAGGTGACATGCCGCACTGGCTGAGTCGTTGCAATATTATAGGGTGACACA
Found at i:2246164 original size:152 final size:153
Alignment explanation
Indices: 2245849--2246174 Score: 433
Period size: 152 Copynumber: 2.1 Consensus size: 153
2245839 TGCCGCACTG
*
2245849 GCTGAGTCGTTGCAATATTAT-AGGGTGACACACCATGCTCCAATTATTAGATGTCGATGACATC
1 GCTGAGTCGTTGCAGTATTATGAGGGTGACACACCATGCTCCAATTATTAGATGTCGATGACATC
* * * * *
2245913 TTGTGGTAACACATTGAGTCATTGCATTATTATGGGGTGACACATCACGCTCTACTTGTTAGATG
66 TTGTGGTAACACATTGAGTCATTGCAGTATTATGGGGTGACACATCAAGCTCCACTTCTTAAATG
* * *
2245978 TCGATGATATCTTGTGGCAAAAC
131 TCGATGACATCGTGTGACAAAAC
* * ** * *
2246001 GCTGAGCCGTTGTAGTATTATGA-GGTGACATGCCATGCTCCATTTGTTAGATGTCGATGACATC
1 GCTGAGTCGTTGCAGTATTATGAGGGTGACACACCATGCTCCAATTATTAGATGTCGATGACATC
*
2246065 TTGTGGTGACACATTGAGTCATTGCAGTATTATGGGGTGACACA-CTAAGCTCCACTTCTTAAAT
66 TTGTGGTAACACATTGAGTCATTGCAGTATTATGGGGTGACACATC-AAGCTCCACTTCTTAAAT
** * *
2246129 GTCGATGACATCGTGTGATGACAT
130 GTCGATGACATCGTGTGACAAAAC
*
2246153 GTTGAGTCGTTGCAGTATTATG
1 GCTGAGTCGTTGCAGTATTATG
2246175 GGCAAACCCA
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
151 1 0.01
152 147 0.99
153 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (153 bp):
GCTGAGTCGTTGCAGTATTATGAGGGTGACACACCATGCTCCAATTATTAGATGTCGATGACATC
TTGTGGTAACACATTGAGTCATTGCAGTATTATGGGGTGACACATCAAGCTCCACTTCTTAAATG
TCGATGACATCGTGTGACAAAAC
Found at i:2246169 original size:344 final size:343
Alignment explanation
Indices: 2245543--2246176 Score: 899
Period size: 344 Copynumber: 1.8 Consensus size: 343
2245533 TTGGTACACA
* * * * *
2245543 CTCCAATTGTTAGATGTCGATGATATCTAGTGCTGACACGCTAAGTCATTGTAGTATTATGGGAT
1 CTCCAATTATTAGATGTCGATGACATCTAGTGCTAACACACTAAGTCATTGCAGTATTATGGGAT
* ** ** * * * *
2245608 GATATGTCACGCCCTACTTGTTAAATGTCGATGCATCTTGTGGTGAGATGTTAAGTCGTTGTAGT
66 GACACATCACGCCCTACTTGTTAAATGTCGATGCATCTTGTGGCAAAACGCTAAGCCGTTGTAGT
2245673 ATTATGAAATGACATGCCATGCTCCAATTGTTAGATGTCGATGACATCTTGTGGTGACACATTGA
131 ATTATGAAATGACATGCCATGCTCCAATTGTTAGATGTCGATGACATCTTGTGGTGACACATTGA
** * * * * * * *
2245738 GTTGTTATAGTATTATGGGGTGGCACACCATGCTCCACTTGTTAGATGTCGATGACATCTTGTGG
196 GTCATTACAGTATTATGGGGTGACACACCAAGCTCCACTTCTTAAATGTCGATGACATCGTGTGA
2245803 TGACACCTTGAGTCGTTGCAGTATTATGGGGTGACATGCCGCACTGGCTGAGTCGTTGCAATATT
261 TGACACCTTGAGTCGTTGCAGTATTATGGGGTGACATGCCGCACTGGCTGAGTCGTTGCAATATT
2245868 ATAGGGTGACACACCATG
326 ATAGGGTGACACACCATG
* * * * * *
2245886 CTCCAATTATTAGATGTCGATGACATCTTGTGGTAACACATTGAGTCATTGCATTATTATGGGGT
1 CTCCAATTATTAGATGTCGATGACATCTAGTGCTAACACACTAAGTCATTGCAGTATTATGGGAT
* * * *
2245951 GACACATCACGCTCTACTTGTTAGATGTCGATGATATCTTGTGGCAAAACGCTGAGCCGTTGTAG
66 GACACATCACGCCCTACTTGTTAAATGTCGATG-CATCTTGTGGCAAAACGCTAAGCCGTTGTAG
** *
2246016 TATTATGAGGTGACATGCCATGCTCCATTTGTTAGATGTCGATGACATCTTGTGGTGACACATTG
130 TATTATGAAATGACATGCCATGCTCCAATTGTTAGATGTCGATGACATCTTGTGGTGACACATTG
* *
2246081 AGTCATTGCAGTATTATGGGGTGACACACTAAGCTCCACTTCTTAAATGTCGATGACATCGTGTG
195 AGTCATTACAGTATTATGGGGTGACACACCAAGCTCCACTTCTTAAATGTCGATGACATCGTGTG
**
2246146 ATGACATGTTGAGTCGTTGCAGTATTATGGG
260 ATGACACCTTGAGTCGTTGCAGTATTATGGG
2246177 CAAACCCAAG
Statistics
Matches: 250, Mismatches: 40, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
343 82 0.33
344 168 0.67
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (343 bp):
CTCCAATTATTAGATGTCGATGACATCTAGTGCTAACACACTAAGTCATTGCAGTATTATGGGAT
GACACATCACGCCCTACTTGTTAAATGTCGATGCATCTTGTGGCAAAACGCTAAGCCGTTGTAGT
ATTATGAAATGACATGCCATGCTCCAATTGTTAGATGTCGATGACATCTTGTGGTGACACATTGA
GTCATTACAGTATTATGGGGTGACACACCAAGCTCCACTTCTTAAATGTCGATGACATCGTGTGA
TGACACCTTGAGTCGTTGCAGTATTATGGGGTGACATGCCGCACTGGCTGAGTCGTTGCAATATT
ATAGGGTGACACACCATG
Found at i:2247519 original size:35 final size:35
Alignment explanation
Indices: 2247461--2247620 Score: 148
Period size: 35 Copynumber: 4.7 Consensus size: 35
2247451 CTTAAGAAGT
*** *
2247461 CCAATTAACTTAATTATTTAATTTAATCAATGAGGC
1 CCAA-TAACTTAATTAAACAATTTAATCAATTAGGC
* * * *
2247497 CTAATAATTTAATTAAACAATTTGATCAATTAAGC
1 CCAATAACTTAATTAAACAATTTAATCAATTAGGC
* * *
2247532 CCAATAACTTGATTAAACAA-ATAATCAATTAGAC
1 CCAATAACTTAATTAAACAATTTAATCAATTAGGC
* * *
2247566 CCAATAACTTAATAAAATAATTTAATGAATTAGG-
1 CCAATAACTTAATTAAACAATTTAATCAATTAGGC
*
2247600 -C-ACAACTTAATTAAACAATTT
1 CCAATAACTTAATTAAACAATTT
2247621 TAATTAAGTG
Statistics
Matches: 99, Mismatches: 24, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
32 17 0.17
33 1 0.01
34 27 0.27
35 51 0.52
36 3 0.03
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (35 bp):
CCAATAACTTAATTAAACAATTTAATCAATTAGGC
Found at i:2249407 original size:23 final size:23
Alignment explanation
Indices: 2249381--2249441 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
2249371 AACACAACTA
* * * *
2249381 TTGAAATATAATAGACACATTTG
1 TTGAAATATAACAAAAACATATG
2249404 TTGAAATATAACAAAAACATATG
1 TTGAAATATAACAAAAACATATG
* *
2249427 TTGAAACACAACAAA
1 TTGAAATATAACAAA
2249442 TACTACTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.26
Consensus pattern (23 bp):
TTGAAATATAACAAAAACATATG
Found at i:2255204 original size:37 final size:37
Alignment explanation
Indices: 2255154--2255226 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
2255144 GCGTACTGAA
* *
2255154 TGATTTTTTATTTGCTGTAAACCTAGGCTAAAAGTAT
1 TGATTTTTGATTTGCTGTAAACCTAGGCCAAAAGTAT
*
2255191 TGATTTTTGATTTGTTGTAAACCTAGGCCAAAAGTA
1 TGATTTTTGATTTGCTGTAAACCTAGGCCAAAAGTA
2255227 GTATTTTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (37 bp):
TGATTTTTGATTTGCTGTAAACCTAGGCCAAAAGTAT
Found at i:2255629 original size:15 final size:15
Alignment explanation
Indices: 2255609--2255658 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2255599 TTATTTATAC
2255609 TTATTTATGTTAAAA
1 TTATTTATGTTAAAA
2255624 TTATTT-T-TTAAAAAA
1 TTATTTATGTT--AAAA
**
2255639 ACATTTATGTTAAAA
1 TTATTTATGTTAAAA
2255654 TTATT
1 TTATT
2255659 AACAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 2 0.07
14 1 0.04
15 21 0.78
16 1 0.04
17 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (15 bp):
TTATTTATGTTAAAA
Found at i:2259818 original size:27 final size:27
Alignment explanation
Indices: 2259787--2259844 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
2259777 TATCAATAAT
*
2259787 TAAATCATCAATTATTAATATTTTAAA
1 TAAATCACCAATTATTAATATTTTAAA
*
2259814 TAAATTACCAATTATTAATATTTTAAA
1 TAAATCACCAATTATTAATATTTTAAA
2259841 -AAAT
1 TAAAT
2259845 AAAATAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAATCACCAATTATTAATATTTTAAA
Found at i:2259902 original size:21 final size:20
Alignment explanation
Indices: 2259878--2259940 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
2259868 ATATTTAAAT
*
2259878 TAAATAAAATATTAACATTTC
1 TAAATAAAATATTAA-ATTTA
*
2259899 TAAATATTAATGATTAAA-TTA
1 TAAATA-AAAT-ATTAAATTTA
*
2259920 TAAATAAAATGTTAATATTTA
1 TAAATAAAATATTAA-ATTTA
2259941 AATTATCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 17 0.50
22 4 0.12
23 5 0.15
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
TAAATAAAATATTAAATTTA
Found at i:2259966 original size:42 final size:42
Alignment explanation
Indices: 2259877--2259970 Score: 104
Period size: 42 Copynumber: 2.2 Consensus size: 42
2259867 AATATTTAAA
2259877 TTAAATAAAATATTAACATTTCTAAATATTAATGATTAAATT
1 TTAAATAAAATATTAACATTTCTAAATATTAATGATTAAATT
* * * *
2259919 ATAAATAAAATGTTAATA-TT-TAAATTATCT-ATTATTAATATT
1 TTAAATAAAATATTAACATTTCTAAA-TAT-TAATGATTAA-ATT
2259961 TTAAATAAAA
1 TTAAATAAAA
2259971 ATCAATTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
40 4 0.09
41 12 0.27
42 28 0.64
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (42 bp):
TTAAATAAAATATTAACATTTCTAAATATTAATGATTAAATT
Found at i:2259993 original size:23 final size:23
Alignment explanation
Indices: 2259931--2259995 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 23
2259921 AAATAAAATG
** *
2259931 TTAATA-TTTAAATTATCTATTA
1 TTAATATTTTAAAAAATCAATTA
2259953 TTAATATTTTAAATAAAAATCAATTA
1 TTAATATTTT--A-AAAAATCAATTA
2259979 TTAATATTTTAAAAAAT
1 TTAATATTTTAAAAAAT
2259996 AAAATAATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 6 0.17
23 9 0.25
24 1 0.03
25 1 0.03
26 19 0.53
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAATATTTTAAAAAATCAATTA
Found at i:2260075 original size:147 final size:147
Alignment explanation
Indices: 2259760--2260260 Score: 628
Period size: 147 Copynumber: 3.3 Consensus size: 147
2259750 GAAATAACAT
* * * * *
2259760 TTAAATTATATATAAAATATCAATAATTAAATCATCAATTATTAATATTTTAAATAAATTACCAA
1 TTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTATCAA
2259825 TTATTAATATTTTAAAAAATAAAATAACAAATTAATCATAATAATATTTAAATTAAATAAAATAT
66 TTATTAATATTTTAAAAAATAAAAT----AATTAATCATAATAATATTTAAATTAAATAAAATAT
* *
2259890 TAACATTTCTAAATATTAATGA
127 TAATATTT-TAAATATTAATTA
* * *
2259912 TTAAATTATAAATAAAATGTTAATATTTAAATTATCTATTATTAATATTTTAAATAAA-AATCAA
1 TTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTATCAA
* * * *
2259976 TTATTAATATTTTAAAAAATAAAATAATTGATCAAAATAATATTTAAATTAAACAAAATAGTAAT
66 TTATTAATATTTTAAAAAATAAAATAATTAATCATAATAATATTTAAATTAAATAAAATATTAAT
2260041 ATTTTAAAATATTAATTA
131 ATTTT-AAATATTAATTA
* ** * *
2260059 TAAAATTATAAATAAAATATTAATATTTAAATGGTCAAGTATTAATATTTTAAATAAATTATTAA
1 TTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTATCAA
* * * * *
2260124 TTATTAAAATTGAAAAATAAAATAAAAAAATAGTTAATCATAATAATATTTAAATTAAATAAATT
66 TTATTAATATT-----TTAAAA-AATAAAATAATTAATCATAATAATATTTAAATTAAATAAAAT
*
2260189 ATTAATATTTTAAATATCAATTA
125 ATTAATATTTTAAATATTAATTA
* * *
2260212 TTCAATTATAAATAAAATATTCATATTTAAATTA-CAGTTATTAATATTT
1 TTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTT
2260261 AAAAATGCAC
Statistics
Matches: 302, Mismatches: 39, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
146 1 0.00
147 102 0.34
148 14 0.05
151 29 0.10
152 65 0.22
153 45 0.15
154 46 0.15
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (147 bp):
TTAAATTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTATCAA
TTATTAATATTTTAAAAAATAAAATAATTAATCATAATAATATTTAAATTAAATAAAATATTAAT
ATTTTAAATATTAATTA
Found at i:2260363 original size:42 final size:42
Alignment explanation
Indices: 2260305--2260548 Score: 249
Period size: 42 Copynumber: 5.9 Consensus size: 42
2260295 ATATTTAAAG
*
2260305 TAAATAAAATATTAATATTTTAAAATATTAATTACTAATAT-A
1 TAAATAAAATATTAATATTTTAAAATATTAATTATTAA-ATCA
* *
2260347 TAAATAAAATATTAATA-TTT-AAATGATCAATTATTAATATTTAA
1 TAAATAAAATATTAATATTTTAAAAT-ATTAATTATTAA-A--TCA
* * * *
2260391 CAAATAAAATA--AAAATTATT--CATAATAA-TATTTAAAT--
1 TAAATAAAATATTAATATT-TTAAAATATTAATTA-TTAAATCA
*
2260428 TAAATAAAATATTAATATTTTAAAATATTAATGATTAAATCA
1 TAAATAAAATATTAATATTTTAAAATATTAATTATTAAATCA
*
2260470 TAAATAAAATATTAATATTTTAAAATATTAATGATTAAATCA
1 TAAATAAAATATTAATATTTTAAAATATTAATTATTAAATCA
* *
2260512 TAAATAAAATATTAATA-TTTGAATTATTAATTATTAA
1 TAAATAAAATATTAATATTTTAAAATATTAATTATTAA
2260549 TATTTGAATT
Statistics
Matches: 173, Mismatches: 15, Indels: 29
0.80 0.07 0.13
Matches are distributed among these distances:
37 10 0.06
38 2 0.01
39 6 0.03
40 16 0.09
41 36 0.21
42 86 0.50
43 4 0.02
44 13 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (42 bp):
TAAATAAAATATTAATATTTTAAAATATTAATTATTAAATCA
Found at i:2260381 original size:22 final size:20
Alignment explanation
Indices: 2260305--2260575 Score: 105
Period size: 22 Copynumber: 13.1 Consensus size: 20
2260295 ATATTTAAAG
*
2260305 TAAATA-AAATATTAATATTT
1 TAAATATAATTATTAATA-TT
* *
2260325 TAAAATATTAATTACTAATATA
1 T-AAATA-TAATTATTAATATT
*
2260347 TAAATA-AAATATTAATATT
1 TAAATATAATTATTAATATT
2260366 TAAATGATCAATTATTAATATT
1 TAAAT-AT-AATTATTAATATT
* * * *
2260388 TAACAAATAA-AATAAAAATT
1 TAA-ATATAATTATTAATATT
**
2260408 ATTCATAATAA-TATTTAA-A-T
1 -TAAAT-ATAATTA-TTAATATT
*
2260428 TAAATA-AAATATTAATATTT
1 TAAATATAATTATTAATA-TT
* *
2260448 TAAAATATTAATGATTAA-ATCA
1 T-AAATA-TAATTATTAATAT-T
*
2260470 TAAATA-AAATATTAATATTT
1 TAAATATAATTATTAATA-TT
* *
2260490 TAAAATATTAATGATTAA-ATCA
1 T-AAATA-TAATTATTAATAT-T
*
2260512 TAAATA-AAATATTAATATT
1 TAAATATAATTATTAATATT
*
2260531 TGAATTATTAATTATTAATATT
1 T-AAATA-TAATTATTAATATT
*
2260553 TGAATTATTAATTATTAATATT
1 T-AAATA-TAATTATTAATATT
2260575 T
1 T
2260576 TAATTAAATT
Statistics
Matches: 191, Mismatches: 32, Indels: 54
0.69 0.12 0.19
Matches are distributed among these distances:
17 6 0.03
18 4 0.02
19 33 0.17
20 21 0.11
21 42 0.22
22 61 0.32
23 24 0.13
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAATATAATTATTAATATT
Found at i:2260448 original size:123 final size:122
Alignment explanation
Indices: 2260142--2260489 Score: 454
Period size: 123 Copynumber: 2.8 Consensus size: 122
2260132 ATTGAAAAAT
* *
2260142 AAAATAAAA-AAATAGTTAATCATAATAATATTTAAATTAAATAAATTATTAATATTTT-AAATA
1 AAAATAAAATAAATAATT-ATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATA
* * * *
2260205 TCAATTATTCAAT-TATAAATAAAATATTCATATTTAAATTACAGTTATTAATATTTAA
65 TTAATTATT-AATATATAAATAAAATATTAATATTTAAATGACAATTATTAATATTTAA
* * * *
2260263 AAATGCACTAAAATAAATAATTGATCGTGACAATATTTAAAGTAAATAAAATATTAATATTTTAA
1 AAA---A-TAAAATAAATAATT-ATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAA
*
2260328 AATATTAATTACTAATATATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTAA
61 AATATTAATTATTAATATATAAATAAAATATTAATATTTAAATGA-CAATTATTAATATTTAA
*
2260391 CAAATAAAATAAA-AATTATTCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATA
1 AAAATAAAATAAATAATTA-TCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATA
*
2260455 TTAATGATTAA-ATCATAAATAAAATATTAATATTT
65 TTAATTATTAATAT-ATAAATAAAATATTAATATTT
2260490 TAAAATATTA
Statistics
Matches: 198, Mismatches: 19, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
121 3 0.02
122 3 0.02
123 75 0.38
124 10 0.05
125 6 0.03
126 45 0.23
127 38 0.19
128 18 0.09
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.40
Consensus pattern (122 bp):
AAAATAAAATAAATAATTATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATAT
TAATTATTAATATATAAATAAAATATTAATATTTAAATGACAATTATTAATATTTAA
Found at i:2260451 original size:16 final size:14
Alignment explanation
Indices: 2260432--2260574 Score: 72
Period size: 15 Copynumber: 10.1 Consensus size: 14
2260422 TTAAATTAAA
2260432 TAAAATATTAATATTT
1 TAAAATATTAATA--T
2260448 TAAAATATTAATGAT
1 TAAAATATTAAT-AT
2260463 T-AAATCA-TAA-A-
1 TAAAAT-ATTAATAT
2260474 TAAAATATTAATATTT
1 TAAAATATTAATA--T
2260490 TAAAATATTAATGAT
1 TAAAATATTAAT-AT
2260505 T-AAATCA-TAA-A-
1 TAAAAT-ATTAATAT
2260516 TAAAATATTAATATT
1 TAAAATATTAATA-T
* *
2260531 TGAATTATTAATTAT
1 TAAAATATTAA-TAT
*
2260546 TAATAT-TTGAATTAT
1 TAAAATATT-AA-TAT
*
2260561 T-AATTATTAATAT
1 TAAAATATTAATAT
2260574 T
1 T
2260575 TTAATTAAAT
Statistics
Matches: 102, Mismatches: 7, Indels: 39
0.69 0.05 0.26
Matches are distributed among these distances:
11 4 0.04
12 16 0.16
13 6 0.06
14 20 0.20
15 28 0.27
16 26 0.25
17 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.45
Consensus pattern (14 bp):
TAAAATATTAATAT
Found at i:2260545 original size:7 final size:7
Alignment explanation
Indices: 2260533--2260598 Score: 59
Period size: 7 Copynumber: 9.4 Consensus size: 7
2260523 TTAATATTTG
2260533 AATTATT
1 AATTATT
2260540 AATTATT
1 AATTATT
2260547 AA-TATTT
1 AATTA-TT
2260554 GAATTATT
1 -AATTATT
2260562 AATTATT
1 AATTATT
*
2260569 AATATTTT
1 AAT-TATT
2260577 AATTA--
1 AATTATT
2260582 AATTA-T
1 AATTATT
2260588 AAGTTATT
1 AA-TTATT
2260596 AAT
1 AAT
2260599 ATTTAAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
5 5 0.10
6 4 0.08
7 26 0.52
8 13 0.26
9 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (7 bp):
AATTATT
Found at i:2260578 original size:15 final size:14
Alignment explanation
Indices: 2260533--2260598 Score: 59
Period size: 15 Copynumber: 4.7 Consensus size: 14
2260523 TTAATATTTG
2260533 AATTATTAATTATT
1 AATTATTAATTATT
2260547 AA-TATTTGAATTATT
1 AATTA-TT-AATTATT
*
2260562 AATTATTAATATTTT
1 AATTATTAAT-TATT
2260577 AATTA--AATTA-T
1 AATTATTAATTATT
2260588 AAGTTATTAAT
1 AA-TTATTAAT
2260599 ATTTAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
11 3 0.07
12 4 0.09
13 5 0.12
14 10 0.23
15 19 0.44
16 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
AATTATTAATTATT
Found at i:2260616 original size:27 final size:27
Alignment explanation
Indices: 2260555--2260609 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2260545 TTAATATTTG
*
2260555 AATTATTAA-TTATTAATATTTTAATTA
1 AATTA-TAAGTTATTAATATTTTAATAA
2260582 AATTATAAGTTATTAATA-TTTAA-AA
1 AATTATAAGTTATTAATATTTTAATAA
2260607 AAT
1 AAT
2260610 CTAATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 4 0.15
26 8 0.31
27 14 0.54
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
AATTATAAGTTATTAATATTTTAATAA
Found at i:2271724 original size:15 final size:15
Alignment explanation
Indices: 2271706--2271755 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2271696 TTATTTATAT
2271706 TTATTTATGTTAAAA
1 TTATTTATGTTAAAA
*
2271721 TTATTT-TTTTAAAA
1 TTATTTATGTTAAAA
*
2271735 -GACGTTTATGTTAAAA
1 TTA--TTTATGTTAAAA
2271751 TTATT
1 TTATT
2271756 AACAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 1 0.04
14 7 0.26
15 11 0.41
16 7 0.26
17 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (15 bp):
TTATTTATGTTAAAA
Found at i:2273755 original size:30 final size:28
Alignment explanation
Indices: 2273721--2273781 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 28
2273711 ATTATGCATT
2273721 GAATATTTTATATTAAATAATCTCATTCTA
1 GAATA-TTTAT-TTAAATAATCTCATTCTA
2273751 G-A-A--TATTTAAATAATCTCATTCTA
1 GAATATTTATTTAAATAATCTCATTCTA
2273775 GAATATT
1 GAATATT
2273782 CAATGCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
24 19 0.70
25 4 0.15
26 1 0.04
28 1 0.04
29 1 0.04
30 1 0.04
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (28 bp):
GAATATTTATTTAAATAATCTCATTCTA
Found at i:2273761 original size:24 final size:24
Alignment explanation
Indices: 2273733--2273781 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2273723 ATATTTTATA
2273733 TTAAATAATCTCATTCTAGAATAT
1 TTAAATAATCTCATTCTAGAATAT
2273757 TTAAATAATCTCATTCTAGAATAT
1 TTAAATAATCTCATTCTAGAATAT
2273781 T
1 T
2273782 CAATGCAACT
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:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAAATAATCTCATTCTAGAATAT
Found at i:2275362 original size:21 final size:21
Alignment explanation
Indices: 2275312--2275362 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2275302 CTTTGTGAAA
2275312 TTTTGCAACTCAAGTTTCCAT
1 TTTTGCAACTCAAGTTTCCAT
* * * *
2275333 TATTACAACTCACGTTTGCAT
1 TTTTGCAACTCAAGTTTCCAT
2275354 TTTTGCAAC
1 TTTTGCAAC
2275363 CTATTGTTCG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.24, G:0.10, T:0.41
Consensus pattern (21 bp):
TTTTGCAACTCAAGTTTCCAT
Found at i:2290304 original size:7 final size:7
Alignment explanation
Indices: 2290292--2290316 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2290282 CCAAACTTGA
2290292 TCAACCT
1 TCAACCT
2290299 TCAACCT
1 TCAACCT
2290306 TCAACCT
1 TCAACCT
2290313 TCAA
1 TCAA
2290317 AAACCAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.40, G:0.00, T:0.28
Consensus pattern (7 bp):
TCAACCT
Found at i:2291633 original size:19 final size:20
Alignment explanation
Indices: 2291606--2291643 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2291596 TAGATATCGA
*
2291606 AAACTAACTAGTC-TTTAAT
1 AAACAAACTAGTCGTTTAAT
*
2291625 AAACAAACTGGTCGTTTAA
1 AAACAAACTAGTCGTTTAA
2291644 CAAATTTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (20 bp):
AAACAAACTAGTCGTTTAAT
Found at i:2296635 original size:253 final size:253
Alignment explanation
Indices: 2296181--2296683 Score: 898
Period size: 253 Copynumber: 2.0 Consensus size: 253
2296171 ATCCAATTAT
** * * *
2296181 AAAAAAATTAATAATAGTACTCAAAGTTAGGCACTATTTTTCATCCTTTCAAATTAAGGGGCTTA
1 AAAAAAAAAAATAATAGTACTCAAAGCTAGGCACTATTTTCCATCCTTTCAAATTAAGGAGCTTA
2296246 AGACTTAAAAGCTTATCATATAATTTTTATTGGACTTTAATCATCCTTCTTCTTAATTCTCATTT
66 AGACTTAAAAGCTTATCATATAATTTTTATTGGACTTTAATCATCCTTCTTCTTAATTCTCATTT
* *
2296311 AAGGAATCAAATAGTATACAGTTGAATATATTATCTTTAACTTGATGGATACAACATATAATATA
131 AAAGAATCAAATAGTATACAGTTGAATATATTATCTTTAACTTAATGGATACAACATATAATATA
2296376 ATCCTGAATGATCATATATAATTGTGTTTCAATAGTTATTTTATATTATACTTGTCGC
196 ATCCTGAATGATCATATATAATTGTGTTTCAATAGTTATTTTATATTATACTTGTCGC
2296434 AAAAAAAAAAATAATAGTACTCAAAGCTAGGCACTATTTTCCATCCTTTCAAATTAAGGAGCTTA
1 AAAAAAAAAAATAATAGTACTCAAAGCTAGGCACTATTTTCCATCCTTTCAAATTAAGGAGCTTA
2296499 AGACTTAAAAGCTTATCATATAATTTTTATTGGACTTTAATCATCCTTCTTCTTAATTCTCATTT
66 AGACTTAAAAGCTTATCATATAATTTTTATTGGACTTTAATCATCCTTCTTCTTAATTCTCATTT
* * * *
2296564 AAAGAATCAAATAGTATATAGTTGAATATATTATCTTTAACTTAATGGATACAACATATGATCTT
131 AAAGAATCAAATAGTATACAGTTGAATATATTATCTTTAACTTAATGGATACAACATATAATATA
*
2296629 ATCCTGAATGATCATATATAATTGTGTTTCAATAGTTATTTTATCTTATACTTGT
196 ATCCTGAATGATCATATATAATTGTGTTTCAATAGTTATTTTATATTATACTTGT
2296684 TGTGTAACAT
Statistics
Matches: 238, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
253 238 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (253 bp):
AAAAAAAAAAATAATAGTACTCAAAGCTAGGCACTATTTTCCATCCTTTCAAATTAAGGAGCTTA
AGACTTAAAAGCTTATCATATAATTTTTATTGGACTTTAATCATCCTTCTTCTTAATTCTCATTT
AAAGAATCAAATAGTATACAGTTGAATATATTATCTTTAACTTAATGGATACAACATATAATATA
ATCCTGAATGATCATATATAATTGTGTTTCAATAGTTATTTTATATTATACTTGTCGC
Found at i:2297102 original size:8 final size:8
Alignment explanation
Indices: 2297078--2297135 Score: 59
Period size: 8 Copynumber: 7.4 Consensus size: 8
2297068 GTCAAAAAAA
2297078 TTAATAAT
1 TTAATAAT
2297086 TTAATTAAT
1 TTAA-TAAT
2297095 TTAATAAT
1 TTAATAAT
2297103 TT-ATACAT
1 TTAATA-AT
*
2297111 TTAATTAT
1 TTAATAAT
*
2297119 GTAA-AA-
1 TTAATAAT
2297125 TTAATAAT
1 TTAATAAT
2297133 TTA
1 TTA
2297136 GTTACCAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 3 0.07
7 6 0.15
8 22 0.54
9 10 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (8 bp):
TTAATAAT
Found at i:2297442 original size:19 final size:20
Alignment explanation
Indices: 2297420--2297462 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2297410 TATGTTAAAT
2297420 ATTTAACTT-TATTT-ATGTA
1 ATTT-ACTTATATTTGATGTA
*
2297439 ATTTATTTATATTTGATGTA
1 ATTTACTTATATTTGATGTA
2297459 ATTT
1 ATTT
2297463 TTTTAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 9 0.43
20 9 0.43
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (20 bp):
ATTTACTTATATTTGATGTA
Found at i:2297459 original size:20 final size:19
Alignment explanation
Indices: 2297429--2297467 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2297419 TATTTAACTT
2297429 TATTTATGTAATTTATTTA
1 TATTTATGTAATTTATTTA
*
2297448 TATTTGATGTAATTTTTTTA
1 TATTT-ATGTAATTTATTTA
2297468 GTTTATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (19 bp):
TATTTATGTAATTTATTTA
Found at i:2298766 original size:21 final size:22
Alignment explanation
Indices: 2298741--2298782 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2298731 TATAAAATAA
*
2298741 TTAAAATATT-TTTTTATTAAT
1 TTAAAAAATTATTTTTATTAAT
*
2298762 TTAAAAAATTATTTTTTTTAA
1 TTAAAAAATTATTTTTATTAA
2298783 AAAAAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTAAAAAATTATTTTTATTAAT
Found at i:2298907 original size:11 final size:11
Alignment explanation
Indices: 2298891--2298948 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
2298881 CTTTTTTTTT
2298891 AATTAATAAAA
1 AATTAATAAAA
2298902 AATTAAT-AAA
1 AATTAATAAAA
2298912 AATTATATAATAA
1 AATTA-ATAA-AA
**
2298925 TAATT--TTTAA
1 -AATTAATAAAA
2298935 AATTAATAAAA
1 AATTAATAAAA
2298946 AAT
1 AAT
2298949 AAAATTATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
9 4 0.11
10 10 0.27
11 16 0.43
12 1 0.03
13 2 0.05
14 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTAATAAAA
Found at i:2299235 original size:21 final size:23
Alignment explanation
Indices: 2299211--2299264 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
2299201 AATTTAACTT
*
2299211 ATGAAAATTATAATA-TTT-TTC
1 ATGAAAATTATAATACTTTGTCC
*
2299232 ATGAATATTA-AATACTTTGTCC
1 ATGAAAATTATAATACTTTGTCC
*
2299254 ATCAAAATTAT
1 ATGAAAATTAT
2299265 TTAGAGGAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.15
21 12 0.46
22 10 0.38
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (23 bp):
ATGAAAATTATAATACTTTGTCC
Found at i:2299864 original size:19 final size:20
Alignment explanation
Indices: 2299840--2299877 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2299830 AAAGACTTAA
2299840 TTTTTTAAT-ATTTTTAACC
1 TTTTTTAATCATTTTTAACC
*
2299859 TTTTTTAATCCTTTTTAAC
1 TTTTTTAATCATTTTTAAC
2299878 AAGGTAGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTTAATCATTTTTAACC
Found at i:2303099 original size:30 final size:30
Alignment explanation
Indices: 2303058--2303118 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2303048 ATTTTCATAT
* *
2303058 TACAAGCAATGGGATCAATACTTTTATTAG
1 TACAAGAAATGGGATCAACACTTTTATTAG
2303088 TACAAGAAATGGGATCAACACTTTTATTAG
1 TACAAGAAATGGGATCAACACTTTTATTAG
2303118 T
1 T
2303119 TTTGTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (30 bp):
TACAAGAAATGGGATCAACACTTTTATTAG
Found at i:2303352 original size:22 final size:22
Alignment explanation
Indices: 2303327--2303368 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2303317 GTTTTGTTTA
*
2303327 CTTTTTTTTTCACATTACAATG
1 CTTTCTTTTTCACATTACAATG
*
2303349 CTTTCTTTTTCATATTACAA
1 CTTTCTTTTTCACATTACAA
2303369 GAAATCTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.02, T:0.55
Consensus pattern (22 bp):
CTTTCTTTTTCACATTACAATG
Found at i:2303454 original size:41 final size:40
Alignment explanation
Indices: 2303355--2303456 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 40
2303345 AATGCTTTCT
* * *
2303355 TTTTCATATTACAAGAAATCTGTTATTACTTTTTAAATTTT
1 TTTTCATATTACAAGAAATCTGTTATTAATTTTT-AATATA
* * *
2303396 TTTTACATATTATAAGAAATCTTTTTTTGAATTATTT-ATATA
1 TTTT-CATATTACAAGAAATCTGTTATT-AATT-TTTAATATA
2303438 TTTTCATATTACAAGAAAT
1 TTTTCATATTACAAGAAAT
2303457 GGGATGAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
41 18 0.35
42 27 0.53
43 3 0.06
44 3 0.06
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (40 bp):
TTTTCATATTACAAGAAATCTGTTATTAATTTTTAATATA
Found at i:2303721 original size:110 final size:108
Alignment explanation
Indices: 2303495--2303713 Score: 291
Period size: 110 Copynumber: 2.0 Consensus size: 108
2303485 GCTTTATTTT
* * *
2303495 ATTATTTTTGAAAGTGTTAATAAAATTTTTTTATTCAAATCTTTTTTTTTCATATTACAAGAAAT
1 ATTATTTTTGAAAGTGCTAATAAAAGTTTTTTATTCAAATCTTTTTTTTTCACATTACAAGAAAT
* * * *
2303560 CTTTTGGTACTTTTTTTAATTTTTTTATCGAATTTATTTTAAA
66 CCTTTAGTACTTTTTTAAATTTTTATATCGAATTTATTTTAAA
* **
2303603 ATTATTTTTGAAAGTGCTAATAAAGGGTTTTTTATTCAAATCTTTTTTTTTTCACATTACTTGAA
1 ATTATTTTTGAAAGTGCTAATAAA-AGTTTTTTATTCAAATC-TTTTTTTTTCACATTACAAGAA
*
2303668 ATCCTTTATTACTTTTTTAAATTTTCTAT-TC-AATTT-TTTTAAA
64 ATCCTTTAGTACTTTTTTAAATTTT-TATATCGAATTTATTTTAAA
2303711 ATT
1 ATT
2303714 CAATTTTTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
108 33 0.34
109 20 0.21
110 42 0.43
111 2 0.02
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.56
Consensus pattern (108 bp):
ATTATTTTTGAAAGTGCTAATAAAAGTTTTTTATTCAAATCTTTTTTTTTCACATTACAAGAAAT
CCTTTAGTACTTTTTTAAATTTTTATATCGAATTTATTTTAAA
Found at i:2303723 original size:17 final size:16
Alignment explanation
Indices: 2303695--2303729 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2303685 TAAATTTTCT
2303695 ATTCAATTTTTTTAAA
1 ATTCAATTTTTTTAAA
2303711 ATTCAATTTTTTTAAA
1 ATTCAATTTTTTTAAA
2303727 ATT
1 ATT
2303730 ATTTGTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTCAATTTTTTTAAA
Found at i:2304652 original size:54 final size:54
Alignment explanation
Indices: 2304587--2304730 Score: 162
Period size: 60 Copynumber: 2.6 Consensus size: 54
2304577 TGTGCTACAC
* * * *
2304587 AATGTACAAAATCTAAAACTATATATTAAAATCTAAAACAAAAATTGATTATAT
1 AATGTACAAAATCTAAAACTATATGTTAAAATCCAAAACAAAAATTAACTATAT
* *
2304641 AATGTGCAAAATCTAAATTTAAAACTATATGTTAAAATCCAAAATAAAAATTAACTATAT
1 AATGTACAAAATC------TAAAACTATATGTTAAAATCCAAAACAAAAATTAACTATAT
* *
2304701 AATATACAAAATCTAAAATTATATGTTAAA
1 AATGTACAAAATCTAAAACTATATGTTAAA
2304731 TTTCCCGTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
54 28 0.37
60 47 0.63
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (54 bp):
AATGTACAAAATCTAAAACTATATGTTAAAATCCAAAACAAAAATTAACTATAT
Found at i:2304670 original size:60 final size:60
Alignment explanation
Indices: 2304595--2304717 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
2304585 ACAATGTACA
* * * * *
2304595 AAATCTAAAACTATATATTAAAATCTAAAACAAAAATTGATTATATAATGTGCAAAATCT
1 AAATCTAAAACTATATATTAAAATCCAAAACAAAAATTAACTATATAATATACAAAATCT
* * *
2304655 AAATTTAAAACTATATGTTAAAATCCAAAATAAAAATTAACTATATAATATACAAAATCT
1 AAATCTAAAACTATATATTAAAATCCAAAACAAAAATTAACTATATAATATACAAAATCT
2304715 AAA
1 AAA
2304718 ATTATATGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (60 bp):
AAATCTAAAACTATATATTAAAATCCAAAACAAAAATTAACTATATAATATACAAAATCT
Found at i:2305009 original size:54 final size:55
Alignment explanation
Indices: 2304901--2305010 Score: 177
Period size: 54 Copynumber: 2.0 Consensus size: 55
2304891 TGTACAAAAT
* *
2304901 TTGTACAAAATTTAAAACTATATATGTTAAAATCTAAAACAAAAATTAGCTATATA
1 TTGTACAAAATCTAAAAC-ATATATGTTAAAATCTAAAACAAAAATTAACTATATA
*
2304957 TTGTACAAAATCTAAAAC-TATATGTTAAAATCTAAAACAAAAATTAATTATATA
1 TTGTACAAAATCTAAAACATATATGTTAAAATCTAAAACAAAAATTAACTATATA
2305011 CAATTGGTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 34 0.67
56 17 0.33
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.34
Consensus pattern (55 bp):
TTGTACAAAATCTAAAACATATATGTTAAAATCTAAAACAAAAATTAACTATATA
Found at i:2305345 original size:44 final size:45
Alignment explanation
Indices: 2305282--2305385 Score: 174
Period size: 44 Copynumber: 2.3 Consensus size: 45
2305272 ACCTTCGACT
*
2305282 TTATTATTAAAAACTATATGCTTTAATCAACTGAGCTACACTAG-
1 TTATTATTAAAAATTATATGCTTTAATCAACTGAGCTACACTAGC
2305326 TTATTATTAAAAATTATATGCTTTAATCAACTGAGCTACACTAGC
1 TTATTATTAAAAATTATATGCTTTAATCAACTGAGCTACACTAGC
*
2305371 TATATTAATAAAAAT
1 T-TATTATTAAAAAT
2305386 AATTTTATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
44 43 0.77
45 1 0.02
46 12 0.21
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (45 bp):
TTATTATTAAAAATTATATGCTTTAATCAACTGAGCTACACTAGC
Found at i:2305518 original size:32 final size:32
Alignment explanation
Indices: 2305417--2305531 Score: 78
Period size: 32 Copynumber: 3.6 Consensus size: 32
2305407 TAAAATTTGT
** *
2305417 ACAAAATCTAAACCTATATATTAAAATTTAAA
1 ACAAAATCTAAAATTATATGTTAAAATTTAAA
* ** **
2305449 ACAAAAAT-TAATTATGTA-ATGCACAAAATTT-GT
1 AC-AAAATCTAA-AAT-TATATG-TTAAAATTTAAA
2305482 ACAAAATCTAAAATTATATGTTAAAATTTAAA
1 ACAAAATCTAAAATTATATGTTAAAATTTAAA
*
2305514 ACAAAAACT--AATTATATG
1 ACAAAATCTAAAATTATATG
2305532 AAATTGGTTG
Statistics
Matches: 62, Mismatches: 14, Indels: 16
0.67 0.15 0.17
Matches are distributed among these distances:
30 9 0.15
31 9 0.15
32 23 0.37
33 12 0.19
34 9 0.15
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (32 bp):
ACAAAATCTAAAATTATATGTTAAAATTTAAA
Found at i:2305939 original size:95 final size:96
Alignment explanation
Indices: 2305817--2306010 Score: 336
Period size: 95 Copynumber: 2.0 Consensus size: 96
2305807 TAACTAAGAT
* *
2305817 ATTCTAATTATATTTATAAAATTAATCTTGTTCTTTATAATGTACAAAATTTGTATAAAATATAA
1 ATTCTAATTATATTTATAAAATTAATCTTGTTCTATATAATGTACAAAATCTGTATAAAATATAA
*
2305882 AACTTATTAATTTGGTAGAATATATTCTAAA
66 AACTTATTAATTTGATAGAATATATTCTAAA
*
2305913 ATTC-AATTATATTTATAAAATTAATCTTGTTCTATATAATGTACAAAATCTGTATAAAATATAG
1 ATTCTAATTATATTTATAAAATTAATCTTGTTCTATATAATGTACAAAATCTGTATAAAATATAA
*
2305977 AACTTATTAATTTGATAGAATATGTTCTAAA
66 AACTTATTAATTTGATAGAATATATTCTAAA
2306008 ATT
1 ATT
2306011 TTTTATTTAT
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
95 89 0.96
96 4 0.04
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.44
Consensus pattern (96 bp):
ATTCTAATTATATTTATAAAATTAATCTTGTTCTATATAATGTACAAAATCTGTATAAAATATAA
AACTTATTAATTTGATAGAATATATTCTAAA
Found at i:2305986 original size:50 final size:49
Alignment explanation
Indices: 2305837--2305987 Score: 118
Period size: 50 Copynumber: 3.1 Consensus size: 49
2305827 TATTTATAAA
* *
2305837 ATTAATCTTGTTCTTTATAATGTACAAAATTTGTATAAAATATAAAACTT
1 ATTAATCTTGTTCTATATAATGTACAAAATCTGTATAAAATAT-AAACTT
*** * * * **
2305887 ATTAAT-TTGGTAGAATATATTCTA-AAATTCAAT-TAT-ATTTATAAA---
1 ATTAATCTT-GTTCTATATAATGTACAAAATC--TGTATAAAATATAAACTT
2305932 ATTAATCTTGTTCTATATAATGTACAAAATCTGTATAAAATATAGAACTT
1 ATTAATCTTGTTCTATATAATGTACAAAATCTGTATAAAATATA-AACTT
2305982 ATTAAT
1 ATTAAT
2305988 TTGATAGAAT
Statistics
Matches: 72, Mismatches: 18, Indels: 22
0.64 0.16 0.20
Matches are distributed among these distances:
44 1 0.01
45 19 0.26
46 12 0.17
47 2 0.03
48 3 0.04
49 10 0.14
50 24 0.33
51 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (49 bp):
ATTAATCTTGTTCTATATAATGTACAAAATCTGTATAAAATATAAACTT
Found at i:2309372 original size:27 final size:28
Alignment explanation
Indices: 2309303--2309356 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
2309293 AAATCAAGTT
*
2309303 ACACACTATGTTTAAAAATAATATTGTC
1 ACACACCATGTTTAAAAATAATATTGTC
*
2309331 ACACACCATATTTAAAAA-AATATTGT
1 ACACACCATGTTTAAAAATAATATTGT
2309357 TACATGTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (28 bp):
ACACACCATGTTTAAAAATAATATTGTC
Found at i:2309482 original size:27 final size:28
Alignment explanation
Indices: 2309442--2309514 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
2309432 CGTCATATTT
2309442 AAAAAATAATTTTGTTACACACCATGATC
1 AAAAAAT-ATTTTGTTACACACCATGATC
* * * *
2309471 AAAAAAT-TTTTGTTATATACCATGTTT
1 AAAAAATATTTTGTTACACACCATGATC
*
2309498 AAAAAATAATATTGTTA
1 AAAAAAT-ATTTTGTTA
2309515 TACATCATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 23 0.62
29 14 0.38
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (28 bp):
AAAAAATATTTTGTTACACACCATGATC
Found at i:2309528 original size:29 final size:29
Alignment explanation
Indices: 2309435--2309528 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
2309425 AAATGCACGT
*
2309435 CATATTTAAAAAATAATTTTGTTACACAC
1 CATATTTAAAAAATAATTTTGTTATACAC
* *
2309464 CATGA-TCAAAAAAT--TTTTGTTATATAC
1 CAT-ATTTAAAAAATAATTTTGTTATACAC
* * *
2309491 CATGTTTAAAAAATAATATTGTTATACAT
1 CATATTTAAAAAATAATTTTGTTATACAC
*
2309520 CATACTTAA
1 CATATTTAA
2309529 GGTGTTTCAT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
27 22 0.43
29 28 0.55
30 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (29 bp):
CATATTTAAAAAATAATTTTGTTATACAC
Found at i:2309637 original size:30 final size:29
Alignment explanation
Indices: 2309580--2309658 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
2309570 TAAAGACTAA
* *
2309580 GTTACACGTCATGTTTAAAAAATAATATT
1 GTTACACGTCATGTTAAAAAAAAAATATT
*
2309609 GTTATACGTCATGTTGAAAAAAAAAATATT
1 GTTACACGTCATGTT-AAAAAAAAAATATT
* * * *
2309639 ATTGCACGTAATTTTAAAAA
1 GTTACACGTCATGTTAAAAA
2309659 TGCTTAATTC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 19 0.46
30 22 0.54
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (29 bp):
GTTACACGTCATGTTAAAAAAAAAATATT
Found at i:2309854 original size:29 final size:28
Alignment explanation
Indices: 2309812--2309915 Score: 122
Period size: 29 Copynumber: 3.7 Consensus size: 28
2309802 TAGAGACCAA
2309812 GTTACACA-TCATGTTTAAAACATAATATT
1 GTTACACACT-ATGTTTAAAA-ATAATATT
* *
2309841 GTTACACACAATGTTCAAAAAATAATATT
1 GTTACACACTATGTT-TAAAAATAATATT
*
2309870 GTTACACACTATGTTTAAAAA-AATGTT
1 GTTACACACTATGTTTAAAAATAATATT
* *
2309897 GTTATACATTATGTTTAAA
1 GTTACACACTATGTTTAAA
2309916 GTTTTTAACT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
27 22 0.33
28 5 0.08
29 35 0.53
30 4 0.06
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (28 bp):
GTTACACACTATGTTTAAAAATAATATT
Found at i:2309856 original size:102 final size:102
Alignment explanation
Indices: 2309673--2309861 Score: 236
Period size: 102 Copynumber: 1.9 Consensus size: 102
2309663 TAATTCCAAA
* *
2309673 AGTTTATGATCTAGTGAAATACAAAAATAGAAACCAAGATACACGTCATGTCTAAAAAATAATGT
1 AGTTTATGATCTAGTGAAATACAAAAATAGAAACCAAGATACACATCATGTCTAAAAAATAATAT
* *****
2309738 CGTTATATGTTGTGTTCAAAAAGATGTTAAATTTAAG
66 CGTTACACACAATGTTCAAAAAGATGTTAAATTTAAG
* * * * *
2309775 AGTTTAT-ATCGTAGTGAAATACAAAGATAGAGACCAAGTTACACATCATGTTTAAAACATAATA
1 AGTTTATGATC-TAGTGAAATACAAAAATAGAAACCAAGATACACATCATGTCTAAAAAATAATA
*
2309839 TTGTTACACACAATGTTCAAAAA
65 TCGTTACACACAATGTTCAAAAA
2309862 ATAATATTGT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
101 3 0.04
102 69 0.96
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (102 bp):
AGTTTATGATCTAGTGAAATACAAAAATAGAAACCAAGATACACATCATGTCTAAAAAATAATAT
CGTTACACACAATGTTCAAAAAGATGTTAAATTTAAG
Found at i:2310136 original size:29 final size:29
Alignment explanation
Indices: 2310103--2310169 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
2310093 AGTTATATAC
**
2310103 CATGTTTAAAAAATAATGTTATTACACAT
1 CATGTTTAAAAAATAAAATTATTACACAT
* *
2310132 CATG-TTAAAAAATAAAATTGTTACACGT
1 CATGTTTAAAAAATAAAATTATTACACAT
2310160 CATGTTTAAA
1 CATGTTTAAA
2310170 GCATTTAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 24 0.73
29 9 0.27
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (29 bp):
CATGTTTAAAAAATAAAATTATTACACAT
Done.