Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 104 of 190
Found at i:31608010 original size:4 final size:4
Alignment explanation
Indices: 31607996--31608027 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
31607986 ATTTTTATGT
31607996 TTTA GTTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT
31608028 GTTTGTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:31608100 original size:15 final size:16
Alignment explanation
Indices: 31608077--31608107 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
31608067 TTTTTTTTAT
31608077 TATTCATTTTTGTTCA
1 TATTCATTTTTGTTCA
31608093 TATT-ATTTTTGTTCA
1 TATTCATTTTTGTTCA
31608108 CATTGTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (16 bp):
TATTCATTTTTGTTCA
Found at i:31608364 original size:109 final size:109
Alignment explanation
Indices: 31608168--31608489 Score: 445
Period size: 109 Copynumber: 3.0 Consensus size: 109
31608158 AAGGAAAATT
* * * *
31608168 TTTCAAAGTAAGGCAATATTTTGTGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGGGAAAACGTGCCCTAATGTGCTGGGTTT
* *
31608233 CAATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTTTAAAAA
* * *
31608277 TTTCAAAATAAGGTAATGTTTTGCGTTTGGGAATTCGGGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGGGAAAACGTGCCCTAATGTGCTGGGTTT
* *
31608342 CGATTTTTCTCGTTCGATCAAATAGCCAAATATCCTTTT-AAAA
66 CGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTTTAAAAA
* * * * *
31608385 TTTCGAAATAAGACAATATTTTGCATTTGGAAATTCGAGG-AAATGTACCCTAATGTGCTGGGTT
1 TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCG-GGAAAACGTGCCCTAATGTGCTGGGTT
* *
31608449 TCGA--TTTCTCGTTTAACCAAATAGCCAAATATCCTCTTAAA
65 TCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTTTAAA
31608490 TTTTAATCCA
Statistics
Matches: 188, Mismatches: 23, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
106 30 0.16
107 2 0.01
108 61 0.32
109 95 0.51
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGGGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTTTAAAAA
Found at i:31610172 original size:20 final size:20
Alignment explanation
Indices: 31610147--31610197 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
31610137 TTATGCTAAG
31610147 TAAATGGAATGAAAAGTAAA
1 TAAATGGAATGAAAAGTAAA
* * *
31610167 TAAAT-GAAGTGGAATGTAAG
1 TAAATGGAA-TGAAAAGTAAA
31610187 TAAATGGAATG
1 TAAATGGAATG
31610198 GTTCATCGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 20 0.77
21 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.24
Consensus pattern (20 bp):
TAAATGGAATGAAAAGTAAA
Found at i:31613214 original size:45 final size:44
Alignment explanation
Indices: 31613148--31613242 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
31613138 GGATTAGAAG
*
31613148 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
31613193 TGTAATGGAATAGAGGCGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
31613237 TGTAAT
1 TGTAAT
31613243 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.49
45 23 0.51
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:31613424 original size:18 final size:17
Alignment explanation
Indices: 31613403--31613437 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31613393 TTATTATTAA
*
31613403 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
31613421 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
31613438 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:31613501 original size:155 final size:157
Alignment explanation
Indices: 31613297--31613604 Score: 530
Period size: 155 Copynumber: 2.0 Consensus size: 157
31613287 CCCTTACCAT
*
31613297 AAATTTGTTTGGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTACCAA
1 AAATTTGTTTGGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATACCAA
*
31613362 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
31613427 TTTAATAAAATTCTTAATAATTAGAAG
131 TTTAATAAAATTCTTAATAATTAGAAG
* * * * *
31613454 AAATTTGTTTTGGTAAATTA-T-TTGTTATTGTTCTTTAAATTTTAATAAGATTATTAATATCAG
1 AAATTTGTTTGGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATACCAA
*
31613517 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAATTATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
31613582 TTTAATAAAATTCTTAATAATTA
131 TTTAATAAAATTCTTAATAATTA
31613605 ATATTCTTAC
Statistics
Matches: 143, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
155 124 0.87
156 1 0.01
157 18 0.13
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (157 bp):
AAATTTGTTTGGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATACCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTAGAAG
Found at i:31613571 original size:15 final size:15
Alignment explanation
Indices: 31613547--31613588 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31613537 TTTAAACATA
*
31613547 ATTATTATTAAATAT
1 ATTATAATTAAATAT
31613562 ATTATAATTAAAT-T
1 ATTATAATTAAATAT
*
31613576 A-TATAATTTAATA
1 ATTATAATTAAATA
31613589 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.42
14 2 0.08
15 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:31613671 original size:120 final size:121
Alignment explanation
Indices: 31613536--31613833 Score: 460
Period size: 120 Copynumber: 2.5 Consensus size: 121
31613526 ATTTAATCAT
* *
31613536 ATTTAAACATAATTATTATTAAATATATTATAATTAAATTATATAATTTAATAAAATTCTTAATA
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
31613601 ATTAATATTCTTACATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 ATTAATATTCTTACATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
31613658 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * * *
31613721 ATTACTATTCTTATATGAATTTATTCAAATCATAATATATGGTACTATAAAAGAAA
66 ATTAATATTCTTACATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* *
31613777 ATTTCAA-ATAATTAATATTAAATATATT-TAAATTAAAATATATGATTTAATAAAATT
1 ATTTCAACATAATTATTATTAAATATATTAT-AATTAAAATATATAATTTAATAAAATT
31613834 TAAAATAATT
Statistics
Matches: 164, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
119 4 0.02
120 155 0.95
121 4 0.02
122 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTACATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:31613706 original size:14 final size:15
Alignment explanation
Indices: 31613657--31613708 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31613647 GTAAAATATA
31613657 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
31613672 TATTAAATATATTAT
1 AATTAAATATATTAT
31613687 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
31613700 AATTTAATA
1 AATTAAATA
31613709 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:31613932 original size:47 final size:46
Alignment explanation
Indices: 31613881--31614024 Score: 127
Period size: 47 Copynumber: 3.1 Consensus size: 46
31613871 TTGTATAATT
*
31613881 TAAAATAATAAATATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTAATATTA-ATATAATTTAATAATAATATATAATTTCA
** * ** * *
31613928 TAAAATTCTTAATAATAA-ATTCTCTT-AT-ATGAATTTATACAATT--
1 TAAAATAATTAATATTAATATAAT-TTAATAAT-AATATATA-ATTTCA
*
31613972 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTAATATT-AATATAATTTAATAATAATATATAATTTCA
31614019 TAAAAT
1 TAAAAT
31614025 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
44 15 0.21
45 19 0.26
46 17 0.24
47 21 0.29
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (46 bp):
TAAAATAATTAATATTAATATAATTTAATAATAATATATAATTTCA
Found at i:31613944 original size:91 final size:91
Alignment explanation
Indices: 31613849--31614037 Score: 306
Period size: 91 Copynumber: 2.1 Consensus size: 91
31613839 TAATTATAAC
* * * *
31613849 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAATAAATATTACATATAATTTAATAAT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTTAATAAT
31613914 AATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
* * *
31613940 TAATAAATTCTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTTAATAAT
*
31614005 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
31614031 TAATAAA
1 TAATAAA
31614038 ATGTTCTTAT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:31614016 original size:44 final size:43
Alignment explanation
Indices: 31613830--31614016 Score: 128
Period size: 44 Copynumber: 4.1 Consensus size: 43
31613820 GATTTAATAA
* * * *
31613830 AATTTAAAATAATTATAACTAATAAAT-TATATTTTATGAATTTGTAT
1 AATTTAAAATAA-T-TAA-TATTAAATATA-ATTTAAT-AATATATAT
* *
31613877 AATTTAAAATAATAAATATTACATATAATTTAATAATAATATAT
1 AATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATATAT
** * * * *
31613921 AATTTCATAAAATTCTTAATAATAAAT-T-CTCTTATATGAATTTATAC
1 AA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATATAT
31613968 AATTTAAAATAATTAATATTAAATATAATTTAATAATGATATAT
1 AATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATATAT
31614012 AATTT
1 AATTT
31614017 CATAAAATTC
Statistics
Matches: 109, Mismatches: 20, Indels: 25
0.71 0.13 0.16
Matches are distributed among these distances:
43 6 0.06
44 46 0.42
45 11 0.10
46 8 0.07
47 35 0.32
48 3 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (43 bp):
AATTTAAAATAATTAATATTAAATATAATTTAATAATATATAT
Found at i:31614031 original size:47 final size:47
Alignment explanation
Indices: 31613899--31614037 Score: 146
Period size: 47 Copynumber: 3.0 Consensus size: 47
31613889 TAAATATTAC
*
31613899 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
31613946 AT-T-CTCTT-AT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAAT-TTAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
31613990 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
31614037 A
1 A
31614038 ATGTTCTTAT
Statistics
Matches: 70, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
44 19 0.27
45 15 0.21
46 15 0.21
47 21 0.30
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.43
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:31615462 original size:11 final size:11
Alignment explanation
Indices: 31615448--31615474 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
31615438 AAAAATTAAT
31615448 ACAAAAGTTTC
1 ACAAAAGTTTC
31615459 ACAAAAGTTTC
1 ACAAAAGTTTC
31615470 ACAAA
1 ACAAA
31615475 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:31617831 original size:12 final size:12
Alignment explanation
Indices: 31617814--31617838 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31617804 ATTTGCATAT
31617814 TATATTTTATAA
1 TATATTTTATAA
31617826 TATATTTTATAA
1 TATATTTTATAA
31617838 T
1 T
31617839 TTGCATATTA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATTTTATAA
Found at i:31623135 original size:32 final size:34
Alignment explanation
Indices: 31623099--31623175 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 34
31623089 TATAATTTAG
*
31623099 TAAAAATTATTTAGAAAATT-TTAATA-TTTA-TT
1 TAAAAATTATTTA-AAAATTGTTAAAATTTTATTT
31623131 TAAAAA-TATATTAAAAATTGTTAAAATTTTATTT
1 TAAAAATTAT-TTAAAAATTGTTAAAATTTTATTT
*
31623165 TTAAAATTATT
1 TAAAAATTATT
31623176 ATAATTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
31 9 0.24
32 14 0.37
33 4 0.11
34 8 0.21
35 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (34 bp):
TAAAAATTATTTAAAAATTGTTAAAATTTTATTT
Found at i:31623234 original size:28 final size:28
Alignment explanation
Indices: 31623160--31623234 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 28
31623150 GTTAAAATTT
*
31623160 TATTTTTAAAATTATTATAATTTATACAA
1 TATTTTTAAAATTATTAT-ATTTATAAAA
* *
31623189 T-TTTTTAAGAAAGTATTAT-TTTTTAAAA
1 TATTTTT-A-AAATTATTATATTTATAAAA
31623217 TATTTTTAATAATTATTA
1 TATTTTTAA-AATTATTA
31623235 AACATTTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
27 1 0.03
28 21 0.55
29 7 0.18
30 9 0.24
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (28 bp):
TATTTTTAAAATTATTATATTTATAAAA
Found at i:31623291 original size:10 final size:10
Alignment explanation
Indices: 31623208--31623295 Score: 52
Period size: 10 Copynumber: 8.5 Consensus size: 10
31623198 AAAGTATTAT
*
31623208 TTTTTAAAATA
1 TTTTTAATA-A
31623219 TTTTTAATAA
1 TTTTTAATAA
*
31623229 TTATTAA-ACA
1 TTTTTAATA-A
* *
31623239 TTTTTCTTACAA
1 -TTTT-TAATAA
* *
31623251 TTTTAAAGAA
1 TTTTTAATAA
*
31623261 TTTTTAAAAA
1 TTTTTAATAA
*
31623271 TTTTAAATAA
1 TTTTTAATAA
*
31623281 TTTTTACTAA
1 TTTTTAATAA
31623291 TTTTT
1 TTTTT
31623296 GTACAAAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
9 1 0.02
10 40 0.67
11 15 0.25
12 3 0.05
13 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.55
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:31623292 original size:20 final size:20
Alignment explanation
Indices: 31623209--31623294 Score: 70
Period size: 20 Copynumber: 4.2 Consensus size: 20
31623199 AAGTATTATT
31623209 TTTTAAAATATTTTTAATAA
1 TTTTAAAATATTTTTAATAA
* *
31623229 TTATTAAACAT-TTTTCTTACAA
1 TT-TTAAA-ATATTTT-TAATAA
*
31623251 TTTTAAAGA-ATTTTTAAAAA
1 TTTTAAA-ATATTTTTAATAA
*
31623271 TTTT-AAATAATTTTTACTAA
1 TTTTAAAAT-ATTTTTAATAA
31623291 TTTT
1 TTTT
31623295 TGTACAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 23 0.43
21 19 0.36
22 8 0.15
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (20 bp):
TTTTAAAATATTTTTAATAA
Found at i:31626378 original size:15 final size:15
Alignment explanation
Indices: 31626358--31626388 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31626348 TTTATTTTAT
31626358 TAATTAATAATGTAA
1 TAATTAATAATGTAA
*
31626373 TAATTAATAGTGTAA
1 TAATTAATAATGTAA
31626388 T
1 T
31626389 TATTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (15 bp):
TAATTAATAATGTAA
Found at i:31638442 original size:44 final size:44
Alignment explanation
Indices: 31638346--31638935 Score: 294
Period size: 44 Copynumber: 13.6 Consensus size: 44
31638336 AAGATGGCAA
* * * * **
31638346 ATCTTATCTCCCTGAAGTTGCAGCGGAGTAGATTAAAGTCGACA-
1 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA-ACCTCAG
* * **
31638390 ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCTCAG
1 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCTCAG
* * * * *
31638434 ATCTTATCTCACTGAAGTTGTAG-AGAGCAGA-TCACATCT-AG
1 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCTCAG
* * * *
31638475 -TCTTATCTCCCTAAAGTTGTAGTAGAGCAGACTAAGTAA--GCAG
1 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAA--AACCTCAG
* * *** *
31638518 GTCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTAAAGATGGCAA
1 ATCTTATCTC-CCTGAAGTTGTAGTGGA-GCAGATTAAA-ACCTCAG
** * * *
31638563 ATCTTATCTCCCTGAAGTTCCAGCGGAGCAGATTAAAGCCGACA-
1 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACC-TCAG
* * *
31638607 ATTTTATCTCCCTTAAGTTGTAGTGGAGC-GAATTGAAACCTCAG
1 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAG-ATTAAAACCTCAG
* * *** *
31638651 ATCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-TCGCATCT-AG
1 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCTCAG
* * *
31638692 -TCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTAAGTAA--GCAG
1 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAA--AACCTCAG
* * * *** *
31638735 GTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGCAA
1 ATCTTATCTC-CCTGAAGTTGTAGTGGA-GCAGATTAAA-ACCTCAG
* * *
31638780 ATCTTATCTCCCTGAAGTTGTAGCGGAGCAGATTAAAGCCGACA-
1 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACC-TCAG
* * * *
31638824 AT-TCTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAATCTCAG
1 ATCT-TATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCTCAG
** * * ***
31638868 ATCTTATCTTTCTGAAGTTGCAG-AGAGCAGATCGCAA-CT-AG
1 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCTCAG
*
31638909 -TCTTATCTCCCTGAAGTTGTAATGGAG
1 ATCTTATCTCCCTGAAGTTGTAGTGGAG
31638936 TAAGACTAAC
Statistics
Matches: 427, Mismatches: 83, Indels: 75
0.73 0.14 0.13
Matches are distributed among these distances:
40 58 0.14
41 24 0.06
42 16 0.04
43 41 0.10
44 216 0.51
45 66 0.15
46 6 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCTCAG
Found at i:31638995 original size:217 final size:217
Alignment explanation
Indices: 31638301--31638960 Score: 1086
Period size: 217 Copynumber: 3.0 Consensus size: 217
31638291 GACAGATCGA
*
31638301 GTCTTATCCTCCTGAAGTTGCAGTGAGACAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTG
1 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTG
* * * * *
31638366 CAGCGGAGTAGATTAAAGTCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCT
66 CAGCGGAGCAGATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAACCT
* *
31638431 CAGATCTTATCTCACTGAAGTTGTAGAGAGCAGATCACATCTAGTCTTATCTCCCTAAAGTTGTA
131 CAGATCTTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGTA
*
31638496 GTAGAGCAGACTAAGTAAGCAG
196 GTGGAGCAGACTAAGTAAGCAG
* *
31638518 GTCTTATCCTCCTGAAGTTGTAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTC
1 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTG
* * * *
31638583 CAGCGGAGCAGATTAAAGCCGACAATTTTATCTCCCTTAAGTTGTAGTGGAGCGAATTGAAACCT
66 CAGCGGAGCAGATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAACCT
31638648 CAGATCTTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGTA
131 CAGATCTTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGTA
31638713 GTGGAGCAGACTAAGTAAGCAG
196 GTGGAGCAGACTAAGTAAGCAG
31638735 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTG
1 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTG
* *
31638800 TAGCGGAGCAGATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAATCT
66 CAGCGGAGCAGATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAACCT
* * * *
31638865 CAGATCTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCAACTAGTCTTATCTCCCTGAAGTTGTA
131 CAGATCTTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGTA
* * *
31638930 ATGGAGTAAGACTAACTAAGCAG
196 GTGGAG-CAGACTAAGTAAGCAG
*
31638953 ATCTTATC
1 GTCTTATC
31638961 TCTCTAAGCA
Statistics
Matches: 411, Mismatches: 31, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
217 390 0.95
218 21 0.05
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (217 bp):
GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTG
CAGCGGAGCAGATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAACCT
CAGATCTTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGTA
GTGGAGCAGACTAAGTAAGCAG
Found at i:31639260 original size:44 final size:44
Alignment explanation
Indices: 31639182--31639265 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
31639172 GAAGATAGCA
* * * *
31639182 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTAAAGTTACAATGAAGCAGATTAAAGCCGAT
* *
31639226 AATCTTATCTCCCTAAAGTTACAATGAAGTAGATTGAAGC
1 AATCTTATCTCCCTAAAGTTACAATGAAGCAGATTAAAGC
31639266 ACTAATTCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTAAAGTTACAATGAAGCAGATTAAAGCCGAT
Found at i:31640696 original size:2 final size:2
Alignment explanation
Indices: 31640691--31640716 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31640681 ATATGTACCC
31640691 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
31640717 TAAAGAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31643618 original size:17 final size:17
Alignment explanation
Indices: 31643588--31643620 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31643578 TTACTATTTA
31643588 GATTTCTTTTTTTGGAT
1 GATTTCTTTTTTTGGAT
31643605 GATTT-TTTTATTTGGA
1 GATTTCTTTT-TTTGGA
31643621 GGTAAAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.15, C:0.03, G:0.18, T:0.64
Consensus pattern (17 bp):
GATTTCTTTTTTTGGAT
Found at i:31648317 original size:21 final size:21
Alignment explanation
Indices: 31648276--31648318 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
31648266 AATAAAGTAG
*
31648276 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
31648297 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
31648318 A
1 A
31648319 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:31648397 original size:58 final size:57
Alignment explanation
Indices: 31648301--31648461 Score: 175
Period size: 58 Copynumber: 2.8 Consensus size: 57
31648291 TATAGTATTA
* * * *
31648301 TATATTATGATTTTAGTAAATTCATA--TAATAATAATTATATTAAGAATTTTATTAAAT
1 TATA-TATTATTTTATTAAATT-ATATTTAATAATAATTATATTAA-AATATGATTAAAT
* *
31648359 TATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGGTTAAAT
1 TATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAAT
* * *
31648416 TATTTATTACTTTTATAAAATTATTTTTAATAATAATCT-TATTAAA
1 TATATATTA-TTTTATTAAATTATATTTAATAATAAT-TATATTAAA
31648462 TTTTAATAAC
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
56 3 0.03
57 33 0.37
58 52 0.58
59 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (57 bp):
TATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAAT
Found at i:31648649 original size:16 final size:16
Alignment explanation
Indices: 31648630--31648668 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
31648620 TTGAATTACT
31648630 AATTACAACTTTATTC
1 AATTACAACTTTATTC
*
31648646 AATTACATCTTTATTC
1 AATTACAACTTTATTC
*
31648662 AAATACA
1 AATTACA
31648669 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTACAACTTTATTC
Found at i:31654253 original size:16 final size:16
Alignment explanation
Indices: 31654232--31654262 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31654222 TTCACTGTTA
*
31654232 TGTCTTTTGTATTTTT
1 TGTCTTTTATATTTTT
31654248 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
31654263 GTATGCATAG
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:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:31655945 original size:25 final size:26
Alignment explanation
Indices: 31655916--31655973 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
31655906 TTTGATACTT
*
31655916 ATATTAATAGT-ATTTTATTAAT-TTA
1 ATATTAA-AGTGATTATATTAATATTA
*
31655941 ATATTAAAGTGATTATCTTAATATTA
1 ATATTAAAGTGATTATATTAATATTA
31655967 A-ATTAAA
1 ATATTAAA
31655974 TTTAATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 3 0.10
25 22 0.76
26 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (26 bp):
ATATTAAAGTGATTATATTAATATTA
Found at i:31655966 original size:31 final size:29
Alignment explanation
Indices: 31655931--31655989 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
31655921 AATAGTATTT
*
31655931 TATTAATTTAATATTAAAGTGATTATCTTAA
1 TATTAAATTAA-ATTAAA-TGATTATCTTAA
* *
31655962 TATTAAATTAAATTTAATGTTTATCTTA
1 TATTAAATTAAATTAAATGATTATCTTA
31655990 TAGATAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 5 0.20
31 10 0.40
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (29 bp):
TATTAAATTAAATTAAATGATTATCTTAA
Found at i:31665045 original size:25 final size:25
Alignment explanation
Indices: 31664990--31665054 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
31664980 TTTTAAGTGT
* * *
31664990 TTTCAGTATAAACTATCTATAGAAG
1 TTTCAATATATACTACCTATAGAAG
*
31665015 TCTCAATATATACTACCTATA-ACAG
1 TTTCAATATATACTACCTATAGA-AG
*
31665040 TTTCAAGATATACTA
1 TTTCAATATATACTA
31665055 TCAAAGACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (25 bp):
TTTCAATATATACTACCTATAGAAG
Found at i:31665430 original size:18 final size:17
Alignment explanation
Indices: 31665388--31665431 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
31665378 TGTCGTTCGT
31665388 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
31665405 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
31665424 TTTCAAAA
1 TTTCAAAA
31665432 TGTTTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:31666987 original size:25 final size:25
Alignment explanation
Indices: 31666927--31666991 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
31666917 TTTTAAGTGT
* * *
31666927 TTTCAGTATAGACTATCTATAGTAG
1 TTTCAGTATATACTAGCTATAGCAG
**
31666952 TCCCAGTATATACTAGCTATAGCAG
1 TTTCAGTATATACTAGCTATAGCAG
*
31666977 TTTCAGGATATACTA
1 TTTCAGTATATACTA
31666992 TCAAAGACAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (25 bp):
TTTCAGTATATACTAGCTATAGCAG
Found at i:31667366 original size:18 final size:17
Alignment explanation
Indices: 31667324--31667367 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
31667314 TGTCGTTCGT
31667324 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
31667341 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
31667360 TTTCAAAA
1 TTTCAAAA
31667368 TGTTTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:31668344 original size:17 final size:18
Alignment explanation
Indices: 31668310--31668344 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31668300 CTATGATGTT
31668310 CGCCCGTGTGGACCCACA
1 CGCCCGTGTGGACCCACA
31668328 CGCCCGTGTGG-CCCACA
1 CGCCCGTGTGGACCCACA
31668345 TGAGCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.14, C:0.46, G:0.29, T:0.11
Consensus pattern (18 bp):
CGCCCGTGTGGACCCACA
Found at i:31673977 original size:18 final size:18
Alignment explanation
Indices: 31673954--31673999 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
31673944 GCCGTTCACC
31673954 CTCTTCCTTTCCTTTTTT
1 CTCTTCCTTTCCTTTTTT
* *
31673972 CTCTTCAATTTTCTTTTTT
1 CTCTTC-CTTTCCTTTTTT
31673991 -TCTTCCTTT
1 CTCTTCCTTT
31674000 GTGTGCTGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 11 0.46
19 10 0.42
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.67
Consensus pattern (18 bp):
CTCTTCCTTTCCTTTTTT
Found at i:31676711 original size:36 final size:35
Alignment explanation
Indices: 31676658--31676732 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
31676648 ATTCAAAAAA
* *
31676658 TAATTTTATTTTAATAGATTAATATT-TAATTTAATT
1 TAATTTTATCTTAATAGATAAATATTCT-A-TTAATT
31676694 TAATGTTTATCTT-ATAGATAAATATTCTATTAATT
1 TAAT-TTTATCTTAATAGATAAATATTCTATTAATT
31676729 TAAT
1 TAAT
31676733 AAGATTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 10 0.29
36 17 0.49
37 8 0.23
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.55
Consensus pattern (35 bp):
TAATTTTATCTTAATAGATAAATATTCTATTAATT
Found at i:31676742 original size:62 final size:58
Alignment explanation
Indices: 31676667--31676792 Score: 155
Period size: 62 Copynumber: 2.1 Consensus size: 58
31676657 ATAATTTTAT
** * * *
31676667 TTTAAT-AGATTAATATTTAATTTAATTTAATGTTTATCTTATAGATAAATATTCTATTAA
1 TTTAATAAGATTAATATGAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAA
*
31676727 TTTAATAAGATTTAATATGAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAA
1 TTTAATAAGA-TTAATATGAAATTTAATCTAATATTTATCTTGATAAATATTATATTAA
31676786 TTTAATA
1 TTTAATA
31676793 TTAAAGTGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 22 0.38
60 7 0.12
61 4 0.07
62 25 0.43
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (58 bp):
TTTAATAAGATTAATATGAAATTTAATCTAATATTTATCTTGATAAATATTATATTAA
Found at i:31678283 original size:73 final size:73
Alignment explanation
Indices: 31678148--31678323 Score: 248
Period size: 73 Copynumber: 2.4 Consensus size: 73
31678138 AAAATAAGAA
** * * *
31678148 TTAGCGGCGTTTTCCAGAAAGCGCCGC-GAAGAACCTTAGCCCAACGACGCCGTTTACCGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCTAAAAAACCTAAGCCCAACGACGCCGTTTACCGAGCTT
*
31678212 TTGAGGAT
66 TCGAGGAT
**
31678220 TTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAAAACCTAAGCCCAACGACGCCGTTT-CCTGAGCT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCTAAAAAACCTAAGCCCAACGACGCCGTTTACC-GAGCT
*
31678284 TTCGGGGAT
65 TTCGAGGAT
31678293 TTAGCGGCGTTTTTAAGAAAGCGCCGCTAAA
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCTAAA
31678324 GCTCAGGGAT
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
72 26 0.28
73 66 0.72
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.23
Consensus pattern (73 bp):
TTAGCGGCGTTTTTAAGAAAGCGCCGCTAAAAAACCTAAGCCCAACGACGCCGTTTACCGAGCTT
TCGAGGAT
Found at i:31678506 original size:101 final size:101
Alignment explanation
Indices: 31678326--31678507 Score: 231
Period size: 101 Copynumber: 1.8 Consensus size: 101
31678316 CCGCTAAAGC
* * * ** **
31678326 TCAGGGATTTATCGGCATTTTTGGGAAAGCGCCGGTAAAAAACCTAAGCACAACTACGTCGTTTT
1 TCAGGGATTTAGCGGCATTTTTGAGAAAGCACCGCAAAAAAACCTAAGCACAACTACACCGTTTT
*
31678391 CTCAGCTTTTGGGGATATAGCGGCGCTTTCTAATGT
66 CTCAGCTTTCGGGGATATAGCGGCGCTTTCTAATGT
* * * *
31678427 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAA-TGGCACCGTTT
1 TCAGGGATTTAGCGGCATTTTTGAGAAAGCACCGCAAAAAAACCTAAGCACAACT-ACACCGTTT
*
31678491 TCTGAGCTTTCGGGGAT
65 TCTCAGCTTTCGGGGAT
31678508 TTACTGGCGT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
100 1 0.01
101 66 0.99
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (101 bp):
TCAGGGATTTAGCGGCATTTTTGAGAAAGCACCGCAAAAAAACCTAAGCACAACTACACCGTTTT
CTCAGCTTTCGGGGATATAGCGGCGCTTTCTAATGT
Found at i:31678620 original size:113 final size:112
Alignment explanation
Indices: 31678420--31678760 Score: 425
Period size: 114 Copynumber: 3.0 Consensus size: 112
31678410 GCGGCGCTTT
* * *
31678420 CTAATGTTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAATGGCA
1 CTAATGCTCAGGGCTTTAGCGGCGTTTTTGA-AAAGCGCCGCAAAAAAACCTAAGCCCAACGGCA
*
31678485 CCGTTTTCTGAGCTTTCGGGGATTTA-CTGGCGTTTGTACAAAAGCGCCG
65 CCGTTTTCTGAGCTTTCGGGGATTTAGC-GGCGTTTTTA-AAAAGCGCCG
* * * * **
31678534 CTAATGCTCAGGTCTTTAGCGGCGTTCGTGGAAAAGCGCCACAAAAAAA-CTAAGCCCAACGGTG
1 CTAATGCTCAGGGCTTTAGCGGCGTT-TTTGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCA
* * *
31678598 TCGTTTTCTGAGCTTTCGGGGATTAAGCGGCGTTTTTAATAAAGCACCG
65 CCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAA-AAAGCGCCG
* * * *
31678647 CTAATGCTCGGGGCTTTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAAAACCTAATCTCAACGGCA
1 CTAATGCTCAGGGCTTTAGCGGCG-TTTTTGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCA
* * *
31678712 CCGTTTTCTAAGCTTTTGGGGATTTAGCGGCGTTTTTATGAAAGCGCCG
65 CCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTA-AAAAGCGCCG
31678761 TAAAAAAAAC
Statistics
Matches: 192, Mismatches: 29, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
112 1 0.01
113 93 0.48
114 95 0.49
115 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (112 bp):
CTAATGCTCAGGGCTTTAGCGGCGTTTTTGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCAC
CGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAAAAGCGCCG
Found at i:31678756 original size:114 final size:113
Alignment explanation
Indices: 31678420--31678756 Score: 426
Period size: 113 Copynumber: 3.0 Consensus size: 113
31678410 GCGGCGCTTT
* * * *
31678420 CTAATGTTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAATGGCA
1 CTAATGCTCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCA
* * *
31678485 CCGTTTTCTGAGCTTTCGGGGATTTA-CTGGCGTTTGTACAAAAGCGCCG
66 CCGTTTTCTGAGCTTTCGGGGATTTAGC-GGCGTTTTTA-TAAAGCACCG
* ** * * **
31678534 CTAATGCTCAGGTCTTTAGCGGCGTTCGTGGAAAAGCGCCACAAAAAAA-CTAAGCCCAACGGTG
1 CTAATGCTCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCA
* *
31678598 TCGTTTTCTGAGCTTTCGGGGATTAAGCGGCGTTTTTAATAAAGCACCG
66 CCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTT-ATAAAGCACCG
* * * *
31678647 CTAATGCTCGGGGCTTTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAAAACCTAATCTCAACGGCA
1 CTAATGCTCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCA
* *
31678712 CCGTTTTCTAAGCTTTTGGGGATTTAGCGGCGTTTTTATGAAAGC
66 CCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAT-AAAGC
31678757 GCCGTAAAAA
Statistics
Matches: 188, Mismatches: 31, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
113 96 0.51
114 92 0.49
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (113 bp):
CTAATGCTCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGGCA
CCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTATAAAGCACCG
Found at i:31678806 original size:73 final size:73
Alignment explanation
Indices: 31678654--31678834 Score: 188
Period size: 73 Copynumber: 2.5 Consensus size: 73
31678644 CCGCTAATGC
* * * * *
31678654 TCGGGGCTTTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAAAACCTAATCTCAACGGCACCGTTTT
1 TCGGGGATTTAGCGGCGTTTTTTAGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGCACCGTTTT
*
31678719 CTAAGCTT
66 CTAAGCCT
* * ** *
31678727 TTGGGGATTTAGCGGCG-TTTTTATGAAAGCGCCGTAAAAAAAACTAAGCCCAACGGTGCCTTTT
1 TCGGGGATTTAGCGGCGTTTTTTA-GAAAGCGCCGCAAAAAAAACTAAGCCCAACGGCACCGTTT
31678791 TCGGT-A-CCT
65 TC--TAAGCCT
* * *
31678800 TCGGGGATTTAACGACATTTTTTAGAAAGCGCCGC
1 TCGGGGATTTAGCGGCGTTTTTTAGAAAGCGCCGC
31678835 TAATGCTCAG
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
72 6 0.07
73 74 0.84
74 7 0.08
75 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (73 bp):
TCGGGGATTTAGCGGCGTTTTTTAGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGCACCGTTTT
CTAAGCCT
Found at i:31679237 original size:21 final size:21
Alignment explanation
Indices: 31679213--31679272 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
31679203 ATCGTTTTAT
*
31679213 TTTAGGTTTTAGGGTTTAAAA
1 TTTAGGATTTAGGGTTTAAAA
* ** **
31679234 TTTAAGATTTAATGTTTATGA
1 TTTAGGATTTAGGGTTTAAAA
*
31679255 TTTAGGGTTTAGGGTTTA
1 TTTAGGATTTAGGGTTTA
31679273 GGGTTTATGG
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (21 bp):
TTTAGGATTTAGGGTTTAAAA
Found at i:31679264 original size:14 final size:14
Alignment explanation
Indices: 31679247--31679281 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
31679237 AAGATTTAAT
31679247 GTTTATGATTTAGG
1 GTTTATGATTTAGG
* *
31679261 GTTTAGGGTTTAGG
1 GTTTATGATTTAGG
31679275 GTTTATG
1 GTTTATG
31679282 GTATAATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (14 bp):
GTTTATGATTTAGG
Found at i:31679265 original size:7 final size:7
Alignment explanation
Indices: 31679255--31679279 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31679245 ATGTTTATGA
31679255 TTTAGGG
1 TTTAGGG
31679262 TTTAGGG
1 TTTAGGG
31679269 TTTAGGG
1 TTTAGGG
31679276 TTTA
1 TTTA
31679280 TGGTATAATG
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:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:31679643 original size:15 final size:15
Alignment explanation
Indices: 31679625--31679688 Score: 78
Period size: 15 Copynumber: 4.3 Consensus size: 15
31679615 GTTGGTTGTT
31679625 GGTTTTAGGGTTTAG
1 GGTTTTAGGGTTTAG
31679640 GG-TTTAGGGTTTAAG
1 GGTTTTAGGGTTT-AG
*
31679655 GG-TTTAGTGGCTTAG
1 GGTTTTAG-GGTTTAG
*
31679670 GATTTTAGGGTTTAG
1 GGTTTTAGGGTTTAG
31679685 GGTT
1 GGTT
31679689 AGATTTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
14 10 0.24
15 23 0.55
16 9 0.21
ACGTcount: A:0.16, C:0.02, G:0.39, T:0.44
Consensus pattern (15 bp):
GGTTTTAGGGTTTAG
Found at i:31679656 original size:8 final size:7
Alignment explanation
Indices: 31679628--31679688 Score: 77
Period size: 7 Copynumber: 8.3 Consensus size: 7
31679618 GGTTGTTGGT
31679628 TTTAGGG
1 TTTAGGG
31679635 TTTAGGG
1 TTTAGGG
31679642 TTTAGGG
1 TTTAGGG
31679649 TTTAAGGG
1 TTT-AGGG
31679657 TTTAGTGG
1 TTTAG-GG
* *
31679665 CTTAGGAT
1 TTTAGG-G
31679673 TTTAGGG
1 TTTAGGG
31679680 TTTAGGG
1 TTTAGGG
31679687 TT
1 TT
31679689 AGATTTTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
7 29 0.62
8 18 0.38
ACGTcount: A:0.16, C:0.02, G:0.38, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:31679744 original size:15 final size:16
Alignment explanation
Indices: 31679726--31679758 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31679716 AGATAAATAT
*
31679726 AAAATA-TTATTTCAA
1 AAAATATTTATATCAA
31679741 AAAATATTTATATCAA
1 AAAATATTTATATCAA
31679757 AA
1 AA
31679759 TGGGTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATATTTATATCAA
Found at i:31680351 original size:114 final size:114
Alignment explanation
Indices: 31680088--31680555 Score: 812
Period size: 114 Copynumber: 4.1 Consensus size: 114
31680078 GCGCTTCAGC
*
31680088 AAAAACGCCGCTAAAGGTGATGTATTACTGGCGTTTTATGAAGAAACGCCGCAAATTTCCTTTAA
1 AAAAACGCCGCTAAAGGTGATGTATTACCGGCGTTTTATGAAGAAACGCCGCAAATTTCCTTTAA
*
31680153 GTGTAACAGAGACGGTGCC-TTTTTTGTTTTCTTTTAGTGGTGCATTTT
66 GTGTAACAGAGACGGTGCCGTTTTTTGTTTTCTTTTAGTGGCGCATTTT
* *
31680201 AAAAACGCCGCTAAAGGTGATGTATTACCGGTGTTTTATGAAGAAACGCCGTAAATTTCCTTTAA
1 AAAAACGCCGCTAAAGGTGATGTATTACCGGCGTTTTATGAAGAAACGCCGCAAATTTCCTTTAA
* *
31680266 GTGTAACAGAGACGGTGTCGTTTTTTGTTTTCTTTTAGTGGCGTATTTT
66 GTGTAACAGAGACGGTGCCGTTTTTTGTTTTCTTTTAGTGGCGCATTTT
* *
31680315 AAAAATGCCGTTAAAGGTGATGTATTACCGGCGTTTTATGAAGAAACGCCGCAAATTTCCTTTAA
1 AAAAACGCCGCTAAAGGTGATGTATTACCGGCGTTTTATGAAGAAACGCCGCAAATTTCCTTTAA
*
31680380 GTGTAACAGAAACGGTGCCGTTTTTTGTTTTCTTTTAGTGGCGCATTTT
66 GTGTAACAGAGACGGTGCCGTTTTTTGTTTTCTTTTAGTGGCGCATTTT
* * *
31680429 AAAAATGCCGCTAAAGGTGATGTATTACCAGCGCTTTATGAAGAAACGCCGCAAATTTCCTTTAA
1 AAAAACGCCGCTAAAGGTGATGTATTACCGGCGTTTTATGAAGAAACGCCGCAAATTTCCTTTAA
31680494 GTGTAACAGAGACGGTGCCGTTTTTATGTTTTCTTTTAGTGGCGCATTTT
66 GTGTAACAGAGACGGTGCCGTTTTT-TGTTTTCTTTTAGTGGCGCATTTT
31680544 AAAAACGCCGCT
1 AAAAACGCCGCT
31680556 GCGTTTTACG
Statistics
Matches: 335, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
113 80 0.24
114 220 0.66
115 35 0.10
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (114 bp):
AAAAACGCCGCTAAAGGTGATGTATTACCGGCGTTTTATGAAGAAACGCCGCAAATTTCCTTTAA
GTGTAACAGAGACGGTGCCGTTTTTTGTTTTCTTTTAGTGGCGCATTTT
Found at i:31680638 original size:97 final size:97
Alignment explanation
Indices: 31680463--31680651 Score: 306
Period size: 97 Copynumber: 1.9 Consensus size: 97
31680453 TTACCAGCGC
* * * *
31680463 TTTATGAAGAAACGCCGCAAATTTCCTTTAAGTGTAACAGAGACGGTGCCGTTTTTATGTTTTCT
1 TTTACGAAGAAACGCCGCAAATTTCCTTTAAGTGTAACAAAGACGGTGACATTTTTATGTTTTCT
*
31680528 TTTAGTGGCGCATTTTAAAAACGCCGCTGCGT
66 TTTAGTGGCGCATTTAAAAAACGCCGCTGCGT
* *
31680560 TTTACGAAGAAGCGCCGCAAATTTCCTTTAAGTGTAACAAAGACGGTGACATTTTTTTGTTTTCT
1 TTTACGAAGAAACGCCGCAAATTTCCTTTAAGTGTAACAAAGACGGTGACATTTTTATGTTTTCT
*
31680625 TTTAGTGGTGCATTTAAAAAACGCCGC
66 TTTAGTGGCGCATTTAAAAAACGCCGC
31680652 AAATATTTAT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (97 bp):
TTTACGAAGAAACGCCGCAAATTTCCTTTAAGTGTAACAAAGACGGTGACATTTTTATGTTTTCT
TTTAGTGGCGCATTTAAAAAACGCCGCTGCGT
Found at i:31681134 original size:173 final size:175
Alignment explanation
Indices: 31680839--31681187 Score: 594
Period size: 173 Copynumber: 2.0 Consensus size: 175
31680829 TCGTTTTTTT
*
31680839 CCCATACATTATACCGAAACTTAAACGCCAACTTAAACGTGACTTATCCCCCAAAATCCCATCCT
1 CCCATACATTATACCGAAACTTAAACCCCAACTTAAACGTGACTTATCCCCCAAAATCCCATCCT
*
31680904 CCCCCAAATCCCTAAAATTTCCTCTAATCCACATTTCCCCAAACCCGACCCCTTGCAACGTTGCC
66 CCCCCAAATCCCTAAAATTTCCCCTAATCCACATTTCCCCAAACCCGACCCCTTGCAACGTTGCC
*
31680969 GTTTCCTCTGGAGCATCACCGTCTCCGTCCGTCGGTCTCCTCTGC
131 GTTTCCTCTGGAGCATCACCGTCTCCATCCGTCGGTCTCCTCTGC
* * *
31681014 CCCATACATTTTACCGAAACTTAAACCCCAAC-T-ATCGTGACTTATCCCCCAAAATCCCATTCT
1 CCCATACATTATACCGAAACTTAAACCCCAACTTAAACGTGACTTATCCCCCAAAATCCCATCCT
* * *
31681077 CCCCCAAGTCCCTAAAATTTCCCCTAATCCATATTTCCCCAAACCCGACCTCTTGCAACGTTGCC
66 CCCCCAAATCCCTAAAATTTCCCCTAATCCACATTTCCCCAAACCCGACCCCTTGCAACGTTGCC
*
31681142 GTTTCCTCTGGCGCATCACCGTCTCCATCCGTCGGTCTCCTCTGC
131 GTTTCCTCTGGAGCATCACCGTCTCCATCCGTCGGTCTCCTCTGC
31681187 C
1 C
31681188 GTAACAATCG
Statistics
Matches: 164, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
173 133 0.81
174 1 0.01
175 30 0.18
ACGTcount: A:0.23, C:0.40, G:0.10, T:0.26
Consensus pattern (175 bp):
CCCATACATTATACCGAAACTTAAACCCCAACTTAAACGTGACTTATCCCCCAAAATCCCATCCT
CCCCCAAATCCCTAAAATTTCCCCTAATCCACATTTCCCCAAACCCGACCCCTTGCAACGTTGCC
GTTTCCTCTGGAGCATCACCGTCTCCATCCGTCGGTCTCCTCTGC
Found at i:31682246 original size:9 final size:9
Alignment explanation
Indices: 31682232--31682290 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
31682222 CTTAATTTAA
*
31682232 TACATAATT
1 TACATAACT
31682241 TACATAACT
1 TACATAACT
*
31682250 CACATAACT
1 TACATAACT
* *
31682259 TACAAAAGT
1 TACATAACT
* *
31682268 CACAT-ACA
1 TACATAACT
31682276 TACATAACT
1 TACATAACT
31682285 TA-ATAA
1 TACATAA
31682291 ATGGTACATA
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
8 9 0.24
9 29 0.76
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (9 bp):
TACATAACT
Found at i:31682354 original size:19 final size:17
Alignment explanation
Indices: 31682330--31682380 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 17
31682320 ACATAACTTA
31682330 TTAATATTTATATATAGTT
1 TTAATATTTATATATA--T
* *
31682349 TTAATATATGTATATAT
1 TTAATATTTATATATAT
*
31682366 TTAAAATTTATATAT
1 TTAATATTTATATAT
31682381 TAATGTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 13 0.48
19 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
TTAATATTTATATATAT
Found at i:31682417 original size:9 final size:9
Alignment explanation
Indices: 31682403--31682753 Score: 238
Period size: 9 Copynumber: 39.7 Consensus size: 9
31682393 TATTGACACA
31682403 TTACATAAC
1 TTACATAAC
31682412 TTACATAAC
1 TTACATAAC
* *
31682421 CTATATAA-
1 TTACATAAC
31682429 -TACATAAC
1 TTACATAAC
*
31682437 CTACATAAC
1 TTACATAAC
31682446 TTACATAA-
1 TTACATAAC
31682454 -TACATAAC
1 TTACATAAC
*
31682462 TTAAATAA-
1 TTACATAAC
*
31682470 ATACATAAC
1 TTACATAAC
31682479 TTACATAA-
1 TTACATAAC
31682487 -TACATAAC
1 TTACATAAC
*
31682495 TTATATAA-
1 TTACATAAC
31682503 -TACATAAC
1 TTACATAAC
31682511 TTACATAATAAC
1 TTAC---ATAAC
*
31682523 TTACATAGC
1 TTACATAAC
*
31682532 TTATATAAC
1 TTACATAAC
31682541 TTACATAAC
1 TTACATAAC
*
31682550 TTACATATC
1 TTACATAAC
**
31682559 TTTTATAA-
1 TTACATAAC
31682567 TATATGCATAAC
1 T-TA--CATAAC
*
31682579 TTACATAAT
1 TTACATAAC
*
31682588 TTACTTAA-
1 TTACATAAC
31682596 -TACATAAC
1 TTACATAAC
*
31682604 TTACATATAT
1 TTACATA-AC
*
31682614 TATATCTTAAC
1 T-TA-CATAAC
31682625 TTACATAATAAC
1 TTAC---ATAAC
*
31682637 TTACATAGC
1 TTACATAAC
*
31682646 TTATATAAC
1 TTACATAAC
31682655 TTACATAAC
1 TTACATAAC
*
31682664 TTATATAAC
1 TTACATAAC
31682673 TTACATAA-
1 TTACATAAC
31682681 -TACATAAC
1 TTACATAAC
*
31682689 TTACATAAT
1 TTACATAAC
*
31682698 TTACTTAA-
1 TTACATAAC
31682706 -TACATAA-
1 TTACATAAC
*
31682713 TCAACATATA-
1 T-TACATA-AC
*
31682723 TTATATAAC
1 TTACATAAC
31682732 TTACATAA-
1 TTACATAAC
31682740 -TACATAAC
1 TTACATAAC
31682748 TTACAT
1 TTACAT
31682754 TGAGAAAAAT
Statistics
Matches: 270, Mismatches: 40, Indels: 64
0.72 0.11 0.17
Matches are distributed among these distances:
7 52 0.19
8 8 0.03
9 173 0.64
10 6 0.02
11 10 0.04
12 21 0.08
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.37
Consensus pattern (9 bp):
TTACATAAC
Found at i:31682434 original size:16 final size:16
Alignment explanation
Indices: 31682404--31682753 Score: 191
Period size: 16 Copynumber: 21.9 Consensus size: 16
31682394 ATTGACACAT
31682404 TACATAACTTACATAA
1 TACATAACTTACATAA
*
31682420 CCTATATAA--TACATAA
1 --TACATAACTTACATAA
31682436 CCTACATAACTTACATAA
1 --TACATAACTTACATAA
*
31682454 TACATAACTTAAATAAA
1 TACATAACTTACAT-AA
31682471 TACATAACTTACATAA
1 TACATAACTTACATAA
*
31682487 TACATAACTTATATAA
1 TACATAACTTACATAA
31682503 TACATAACTTAC---A
1 TACATAACTTACATAA
*
31682516 TA-ATAACTTACATAGCT
1 TACATAACTTACATA--A
*
31682533 TATATAACTTACATAA
1 TACATAACTTACATAA
* **
31682549 CTTACATATCTTTTATAA
1 --TACATAACTTACATAA
*
31682567 T--AT-A--TGCATAA
1 TACATAACTTACATAA
* *
31682578 CTTACATAATTTACTTAA
1 --TACATAACTTACATAA
31682596 TACATAACTTACAT-A
1 TACATAACTTACATAA
* * *
31682611 TATTATATCTTAACTTACA
1 TA-CATAACTT-ACATA-A
*
31682630 TA-ATAACTTACATAGCT
1 TACATAACTTACATA--A
*
31682647 TATATAACTTACATAA
1 TACATAACTTACATAA
*
31682663 CTTATATAACTTACATAA
1 --TACATAACTTACATAA
31682681 TACATAACTTACATAA
1 TACATAACTTACATAA
*
31682697 T---TTACTTA-ATACA
1 TACATAACTTACATA-A
* *
31682710 TA-ATCAAC--ATATAT
1 TACAT-AACTTACATAA
*
31682724 TATATAACTTACATAA
1 TACATAACTTACATAA
31682740 TACATAACTTACAT
1 TACATAACTTACAT
31682754 TGAGAAAAAT
Statistics
Matches: 265, Mismatches: 33, Indels: 70
0.72 0.09 0.19
Matches are distributed among these distances:
11 5 0.02
12 12 0.05
13 12 0.05
14 8 0.03
15 11 0.04
16 115 0.43
17 29 0.11
18 70 0.26
19 3 0.01
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.37
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:31682441 original size:25 final size:25
Alignment explanation
Indices: 31682404--31682753 Score: 203
Period size: 25 Copynumber: 14.6 Consensus size: 25
31682394 ATTGACACAT
* *
31682404 TACATAACTTACATAACCTATATAA
1 TACATAACTTACATAACTTACATAA
*
31682429 TACATAACCTACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
31682454 TACATAACTTAAATAA-ATACATAA
1 TACATAACTTACATAACTTACATAA
*
31682478 CTTACATAA--TACATAACTTATATAA
1 --TACATAACTTACATAACTTACATAA
*
31682503 TACATAACTTACATAA-TAAC-T--
1 TACATAACTTACATAACTTACATAA
* *
31682524 TACATAGCTTATATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* **
31682549 CTTACATATCTTTTATAA--T--AT-A
1 --TACATAACTTACATAACTTACATAA
* * *
31682571 TGCATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACATAA
31682596 TACATAACTTACATATA-TT--AT-A
1 TACATAACTTACATA-ACTTACATAA
* *
31682618 T-CTTAACTTACATAA-TAAC-T--
1 TACATAACTTACATAACTTACATAA
* *
31682638 TACATAGCTTATATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
*
31682663 CTTATATAACTTACATAA--TACATAA
1 --TACATAACTTACATAACTTACATAA
* *
31682688 CTTACATAATTTACTTAA--TACATAA
1 --TACATAACTTACATAACTTACATAA
*
31682713 TCAACATATA-TTATATAACTTACATAA
1 T--ACATA-ACTTACATAACTTACATAA
31682740 TACATAACTTACAT
1 TACATAACTTACAT
31682754 TGAGAAAAAT
Statistics
Matches: 255, Mismatches: 38, Indels: 64
0.71 0.11 0.18
Matches are distributed among these distances:
20 15 0.06
21 38 0.15
22 10 0.04
23 14 0.05
24 17 0.07
25 117 0.46
26 9 0.04
27 35 0.14
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.37
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:31682638 original size:12 final size:12
Alignment explanation
Indices: 31682574--31682643 Score: 58
Period size: 12 Copynumber: 6.0 Consensus size: 12
31682564 TAATATATGC
31682574 ATAACTTACATA
1 ATAACTTACATA
*
31682586 ATTTACTTA-ATA
1 A-TAACTTACATA
31682598 CATAACTTACAT-
1 -ATAACTTACATA
* *
31682610 AT-A-TTATATC
1 ATAACTTACATA
*
31682620 TTAACTTACATA
1 ATAACTTACATA
31682632 ATAACTTACATA
1 ATAACTTACATA
31682644 GCTTATATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
9 5 0.11
10 2 0.04
11 3 0.07
12 26 0.58
13 9 0.20
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:31682650 original size:33 final size:30
Alignment explanation
Indices: 31682490--31682662 Score: 120
Period size: 30 Copynumber: 6.0 Consensus size: 30
31682480 TACATAATAC
* *
31682490 ATAACTTATATA-A-TACATAACTTACATA
1 ATAACTTACATAGATTATATAACTTACATA
*
31682518 ATAACTTACATAGCTTATATAACTTAC---
1 ATAACTTACATAGATTATATAACTTACATA
** * * *
31682545 ATAACTTACATATCTTTTATAA--TATATGC
1 ATAACTTACATAGATTATATAACTTACAT-A
31682574 ATAACTTACATA-A-T-T-T-ACTTA-ATA
1 ATAACTTACATAGATTATATAACTTACATA
*
31682598 CATAACTTACATATATTATATCTTAACTTACATA
1 -ATAACTTACATAGATTATA---TAACTTACATA
*
31682632 ATAACTTACATAGCTTATATAACTTACATA
1 ATAACTTACATAGATTATATAACTTACATA
31682662 A
1 A
31682663 CTTATATAAC
Statistics
Matches: 117, Mismatches: 10, Indels: 34
0.73 0.06 0.21
Matches are distributed among these distances:
24 1 0.01
25 17 0.15
26 4 0.03
27 22 0.19
28 12 0.10
29 12 0.10
30 23 0.20
32 1 0.01
33 22 0.19
34 3 0.03
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (30 bp):
ATAACTTACATAGATTATATAACTTACATA
Found at i:31682650 original size:114 final size:108
Alignment explanation
Indices: 31682432--31682741 Score: 368
Period size: 114 Copynumber: 2.9 Consensus size: 108
31682422 TATATAATAC
* * * * * *
31682432 ATAACCTACATAACTTACATAA--TACATAACTTAAATAA-ATACATAACTTACATAATACATAA
1 ATAACTTACATAACTTACATAACTTAAATAA--TACATAACTTACATAATTTACTTAATACATAA
31682494 CTT--ATATA--ATACATAACTTACATAATAACTTACATAGCTTAT
64 CTTACATATATTATAC-TAACTTACATAATAACTTACATAGCTTAT
* *
31682536 ATAACTTACATAACTTACATATCTTTTATAATATATGCATAACTTACATAATTTACTTAATACAT
1 ATAACTTACATAACTTACATAAC--TTA-AATA-ATACATAACTTACATAATTTACTTAATACAT
31682601 AACTTACATATATTATATCTTAACTTACATAATAACTTACATAGCTTAT
62 AACTTACATATATTATA-C-TAACTTACATAATAACTTACATAGCTTAT
* *
31682650 ATAACTTACATAACTTATATAACTTACATAATACATAACTTACATAATTTACTTAATACATAA-T
1 ATAACTTACATAACTTACATAACTTAAATAATACATAACTTACATAATTTACTTAATACATAACT
*
31682714 CAACATATATTATA-TAACTTACATAATA
66 -TACATATATTATACTAACTTACATAATA
31682742 CATAACTTAC
Statistics
Matches: 179, Mismatches: 14, Indels: 23
0.83 0.06 0.11
Matches are distributed among these distances:
104 20 0.11
107 14 0.08
108 7 0.04
109 28 0.16
110 45 0.25
111 8 0.04
112 3 0.02
113 3 0.02
114 51 0.28
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (108 bp):
ATAACTTACATAACTTACATAACTTAAATAATACATAACTTACATAATTTACTTAATACATAACT
TACATATATTATACTAACTTACATAATAACTTACATAGCTTAT
Found at i:31682744 original size:114 final size:110
Alignment explanation
Indices: 31682429--31682746 Score: 312
Period size: 110 Copynumber: 2.9 Consensus size: 110
31682419 ACCTATATAA
* * * * * *
31682429 TACATAACCTACATAACTTACATAATACATAACTTAAATAA-ATACATAACTTACATAATACATA
1 TACATAACTTACATAACTTATATAATACATAA--TACATAACTTACATAATTTACTTAATACATA
** * * * * *
31682493 ACTTATATAATACATAACTTACATAATAACTTACATAGCTTATATAACT
64 ACACATATATTATATAACTTACATAAT-ACATA-ATAACTTACATAACT
* * *
31682542 TACATAACTTACATATCTTTTATAAT--AT-ATGCATAACTTACATAATTTACTTAATACATAAC
1 TACATAACTTACATAACTTATATAATACATAATACATAACTTACATAATTTACTTAATACATAAC
*
31682604 TTACATATATTATAT--CTTA-ACT--TACATAATAACTTACATAGCT
66 --ACATATATTATATAACTTACA-TAATACATAATAACTTACATAACT
*
31682647 TATATAACTTACATAACTTATATAACTTACATAATACATAACTTACATAATTTACTTAATACATA
1 TACATAACTTACATAACTTATATAA--TACATAATACATAACTTACATAATTTACTTAATACATA
31682712 ATCAACATATATTATATAACTTACATAATACATAA
64 A-C-ACATATATTATATAACTTACATAATACATAA
31682747 CTTACATTGA
Statistics
Matches: 168, Mismatches: 22, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
105 34 0.20
106 4 0.02
107 2 0.01
108 6 0.04
109 29 0.17
110 46 0.27
111 12 0.07
112 5 0.03
113 23 0.14
114 7 0.04
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (110 bp):
TACATAACTTACATAACTTATATAATACATAATACATAACTTACATAATTTACTTAATACATAAC
ACATATATTATATAACTTACATAATACATAATAACTTACATAACT
Found at i:31684576 original size:21 final size:21
Alignment explanation
Indices: 31684551--31684601 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
31684541 CTACAACTTA
31684551 AAGCAGAGGC-GACAACGAGAG
1 AAGCAGAGGCTG-CAACGAGAG
*
31684572 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAACGAGAG
31684593 AAGCAGAGG
1 AAGCAGAGG
31684602 TTCAAAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.39, C:0.18, G:0.41, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCTGCAACGAGAG
Found at i:31685095 original size:43 final size:44
Alignment explanation
Indices: 31685048--31685168 Score: 176
Period size: 42 Copynumber: 2.8 Consensus size: 44
31685038 TGAAGAAAGT
* *
31685048 GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTAC-TCAAGC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACTTCAAGC
*
31685091 GCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTT-CTTCTAGC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACTTCAAGC
* *
31685133 GCCGCTAAAAAACATGATCTTTAGCTGCGTTTTTTA
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTA
31685169 AGCGCCGCTA
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
41 1 0.01
42 37 0.53
43 32 0.46
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (44 bp):
GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTACTTCAAGC
Found at i:31686090 original size:29 final size:27
Alignment explanation
Indices: 31686024--31686090 Score: 62
Period size: 29 Copynumber: 2.3 Consensus size: 27
31686014 AAATTTTATT
* *
31686024 TATATAATTACATAATATTAAAATTTA
1 TATATAATTACATAATATCAAAATTAA
* *
31686051 TATATCAAATTACATATTGAATCAAAGTTAA
1 TATAT--AATTACATAAT--ATCAAAATTAA
31686082 TATATAATT
1 TATATAATT
31686091 TTAATATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.16
29 14 0.44
31 13 0.41
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (27 bp):
TATATAATTACATAATATCAAAATTAA
Found at i:31687938 original size:9 final size:9
Alignment explanation
Indices: 31687917--31688085 Score: 63
Period size: 9 Copynumber: 17.3 Consensus size: 9
31687907 AATTTAGTAC
31687917 AATTATAAAA
1 AATTAT-AAA
31687927 AATTATAAA
1 AATTATAAA
31687936 AATATATAAA
1 AAT-TATAAA
*
31687946 AATAAATAAATA
1 AAT-TAT-AA-A
31687958 AAGCTTATAAA
1 AA--TTATAAA
**
31687969 AATCCTAAA
1 AATTATAAA
**
31687978 AATCCTAAA
1 AATTATAAA
31687987 ATATT-T-AA
1 A-ATTATAAA
31687995 AATTATATAA
1 AATTATA-AA
*
31688005 ACTTATAAA
1 AATTATAAA
* *
31688014 AAATAGAAA
1 AATTATAAA
*
31688023 AATTAGGAAAAA
1 AATT---ATAAA
*
31688035 AATCATAAA
1 AATTATAAA
31688044 AACTTATAAA
1 AA-TTATAAA
*
31688054 TATTATCAAA
1 AATTAT-AAA
*
31688064 ACTTATAATA
1 AATTATAA-A
**
31688074 AAAAATAAA
1 AATTATAAA
31688083 AAT
1 AAT
31688086 ATTTAAATTA
Statistics
Matches: 123, Mismatches: 21, Indels: 31
0.70 0.12 0.18
Matches are distributed among these distances:
7 3 0.02
8 4 0.03
9 48 0.39
10 48 0.39
11 5 0.04
12 12 0.10
13 2 0.02
14 1 0.01
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.28
Consensus pattern (9 bp):
AATTATAAA
Found at i:31687946 original size:19 final size:19
Alignment explanation
Indices: 31687920--31688085 Score: 60
Period size: 19 Copynumber: 8.6 Consensus size: 19
31687910 TTAGTACAAT
31687920 TATA-AAAAATTATAAAAA
1 TATATAAAAATTATAAAAA
*
31687938 TATATAAAAATAAATAAATAA
1 TATATAAAAAT-TATAAA-AA
**
31687959 -AGCTTATAAAAATCCTAAAAA
1 TA---TATAAAAATTATAAAAA
* * *
31687980 TCCTA-AAATATT-TAAAAT
1 T-ATATAAAAATTATAAAAA
*
31687998 TATAT-AAACTTATAAAAA
1 TATATAAAAATTATAAAAA
* *
31688016 -ATAGAAAAATTAGGAAAAA
1 TATATAAAAATTA-TAAAAA
* *
31688035 AATCATAAAAACTTATAAATA
1 TAT-ATAAAAA-TTATAAAAA
*
31688056 T-TATCAAAACTTATAATAAA
1 TATAT-AAAAATTATAA-AAA
*
31688076 -AAATAAAAAT
1 TATATAAAAAT
31688086 ATTTAAATTA
Statistics
Matches: 108, Mismatches: 22, Indels: 35
0.65 0.13 0.21
Matches are distributed among these distances:
17 9 0.08
18 21 0.19
19 29 0.27
20 19 0.18
21 14 0.13
22 7 0.06
23 9 0.08
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.28
Consensus pattern (19 bp):
TATATAAAAATTATAAAAA
Found at i:31693222 original size:44 final size:44
Alignment explanation
Indices: 31693174--31693263 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
31693164 ATATCTCAAG
* *
31693174 GTCCATGTTTATAACATGGCAATTAAGGAAGAATTGACGGGAAA
1 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
31693218 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
1 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
31693262 GT
1 GT
31693264 ACCTTGGTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (44 bp):
GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
Found at i:31693365 original size:50 final size:50
Alignment explanation
Indices: 31693287--31693533 Score: 323
Period size: 50 Copynumber: 4.9 Consensus size: 50
31693277 CATGTCAACA
* *
31693287 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC
* * * *
31693337 CGAGATGAGAGGTCCCGTGTAAGTCCATGTCTTGGACATGCCATTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC
* *
31693387 CGAGATGAGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC
** * * *
31693437 CGAGATGAGAGGTCCCCCGTAAGACCATGCCTGGGACATGGCATGGGCAT
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC
* ** * * *
31693487 CGATATGAGAACTCCCATGTAAGACCATATCTGGGATATTGCATTGG
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
31693534 TAGTACAGGA
Statistics
Matches: 168, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 168 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (50 bp):
CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC
Found at i:31699132 original size:44 final size:44
Alignment explanation
Indices: 31699083--31699172 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 44
31699073 ATATCTCAAG
31699083 GTCCATGTTTATAACATGGCAATGAAGGAA-GAATTGACGGAAAA
1 GTCCATGTTTATAACATGGCAATGAA-GAAGGAATTGACGGAAAA
* *
31699127 GTCCATGTTTATAACATGGTAATTAAGAAGGAATTGACGGAAAA
1 GTCCATGTTTATAACATGGCAATGAAGAAGGAATTGACGGAAAA
31699171 GT
1 GT
31699173 ACCTTGGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 3 0.07
44 40 0.93
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (44 bp):
GTCCATGTTTATAACATGGCAATGAAGAAGGAATTGACGGAAAA
Found at i:31699334 original size:50 final size:50
Alignment explanation
Indices: 31699196--31699334 Score: 208
Period size: 49 Copynumber: 2.8 Consensus size: 50
31699186 CATGTCAACA
* *
31699196 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGAGTTGGAAC
* * *
31699246 CGAGATGAGAGGT-TCATGTAAGACCATGTCTAGCACATGGAGTTGGAAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGAGTTGGAAC
* *
31699295 TGAGATGAGAGGTCCCCTGTAAGACCATGTCTGGGACATG
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATG
31699335 AAATGTGCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 43 0.55
50 35 0.45
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (50 bp):
CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGAGTTGGAAC
Found at i:31699353 original size:50 final size:49
Alignment explanation
Indices: 31699195--31699379 Score: 201
Period size: 50 Copynumber: 3.7 Consensus size: 49
31699185 CCATGTCAAC
*
31699195 ACGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
1 ACGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGAGTT-GCA
* * * * *
31699245 CCGAGATGAGAGGT-TCATGTAAGACCATGTCTAGCACATGGAGTTGGA
1 ACGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGAGTTGCA
* * *
31699293 ACTGAGATGAGAGGTCCCCTGTAAGACCATGTCTGGGACATGAAATGTGCA
1 AC-GAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGAGT-TGCA
* * * ** *
31699344 TCAATATGAGAACTCCCATGTAAGACCATTTCTGGG
1 ACGAGATGAGAGGTCCCATGTAAGACCATGTCTGGG
31699380 TTATGACATT
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
48 3 0.03
49 39 0.35
50 65 0.59
51 4 0.04
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (49 bp):
ACGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGAGTTGCA
Found at i:31704870 original size:39 final size:39
Alignment explanation
Indices: 31704816--31704894 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
31704806 ACATGTTAGT
31704816 TGCTAACTAGAATGGAAGATGTGATAGATGTAACACCCC
1 TGCTAACTAGAATGGAAGATGTGATAGATGTAACACCCC
*
31704855 TGCTAACTAGAATGGAATATGTGATAGATGTAACACCCC
1 TGCTAACTAGAATGGAAGATGTGATAGATGTAACACCCC
31704894 T
1 T
31704895 TAGCCGGTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (39 bp):
TGCTAACTAGAATGGAAGATGTGATAGATGTAACACCCC
Found at i:31706117 original size:21 final size:21
Alignment explanation
Indices: 31706092--31706148 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
31706082 TGAGATATGC
*
31706092 CACATGACCATGTGAATGGGT
1 CACATGGCCATGTGAATGGGT
* * *
31706113 CACATGGCCCTATGGATGGGT
1 CACATGGCCATGTGAATGGGT
31706134 CACATGGCCATGTGA
1 CACATGGCCATGTGA
31706149 TCAAACCGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (21 bp):
CACATGGCCATGTGAATGGGT
Found at i:31708292 original size:20 final size:20
Alignment explanation
Indices: 31708264--31708314 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
31708254 ATAGTATTTT
31708264 ATTAATTTAATATTAAATTG
1 ATTAATTTAATATTAAATTG
*
31708284 ATTATTTTAATATTAAA-T-
1 ATTAATTTAATATTAAATTG
31708302 -TTAATTTAATATT
1 ATTAATTTAATATT
31708315 TAACTTGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 12 0.41
19 1 0.03
20 16 0.55
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTAATTTAATATTAAATTG
Found at i:31708304 original size:12 final size:12
Alignment explanation
Indices: 31708265--31708317 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
31708255 TAGTATTTTA
31708265 TTAATTTAATAT
1 TTAATTTAATAT
* * *
31708277 TAAATTGATTATT
1 TTAATTTAATA-T
31708290 TTAATATTAA-AT
1 TTAAT-TTAATAT
31708302 TTAATTTAATAT
1 TTAATTTAATAT
31708314 TTAA
1 TTAA
31708318 CTTGTAGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
11 4 0.12
12 20 0.62
13 6 0.19
14 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TTAATTTAATAT
Found at i:31709071 original size:22 final size:22
Alignment explanation
Indices: 31709043--31709101 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
31709033 GTAGGAAATA
*
31709043 GAGAGCTTAGTACGTTAAACAT
1 GAGAGCTTAGTACGTGAAACAT
31709065 GAGAGCTTAGTACGTGAAACAT
1 GAGAGCTTAGTACGTGAAACAT
31709087 GAGAGCTTAGTACGT
1 GAGAGCTTAGTACGT
31709102 ACTATCAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (22 bp):
GAGAGCTTAGTACGTGAAACAT
Found at i:31711785 original size:33 final size:33
Alignment explanation
Indices: 31711718--31711785 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
31711708 TTAAAAGAGC
* * *
31711718 TTTAATGCGAAAGGTAAAATGACTAAGAGGCCT
1 TTTAATGCGAAAGGTAAAATGACCAACAGACCT
31711751 TTTAATGCGAAAGGTAAAA-GATCCAACCA-ACCT
1 TTTAATGCGAAAGGTAAAATGA-CCAA-CAGACCT
31711784 TT
1 TT
31711786 AGAACTTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 2 0.07
33 27 0.90
34 1 0.03
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (33 bp):
TTTAATGCGAAAGGTAAAATGACCAACAGACCT
Found at i:31712391 original size:15 final size:15
Alignment explanation
Indices: 31712371--31712402 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31712361 CATTTCACTA
*
31712371 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
31712386 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
31712401 TT
1 TT
31712403 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:31713800 original size:13 final size:15
Alignment explanation
Indices: 31713770--31713802 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
31713760 ATTGATTTTG
31713770 ATTAAGTAAAATTTA
1 ATTAAGTAAAATTTA
31713785 ATTAA-TAAAA-TTA
1 ATTAAGTAAAATTTA
31713798 ATTAA
1 ATTAA
31713803 AATTAATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 5 0.28
15 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
ATTAAGTAAAATTTA
Found at i:31714388 original size:59 final size:61
Alignment explanation
Indices: 31714280--31714396 Score: 157
Period size: 59 Copynumber: 1.9 Consensus size: 61
31714270 AGTGAGTATC
* * * * *
31714280 TTAATATTAAATTTAATTTCATGTTTATCATGTTGATAAATATTCTATTAATTAAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTAT-ATCTTGATAAATATTATATTAATTAAATAAGAT
*
31714342 TTAATATTAAATTTAATCTAATATTT-T-TCTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATATCTTGATAAATATTATATTAATTAAATA
31714397 TTAAAGTGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 25 0.51
61 1 0.02
62 23 0.47
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (61 bp):
TTAATATTAAATTTAATCTAATATTTATATCTTGATAAATATTATATTAATTAAATAAGAT
Found at i:31715361 original size:12 final size:12
Alignment explanation
Indices: 31715346--31715370 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31715336 AGAAAGAAAG
31715346 AAAAAGAATTAA
1 AAAAAGAATTAA
31715358 AAAAAGAATTAA
1 AAAAAGAATTAA
31715370 A
1 A
31715371 GTAAAATAGT
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAGAATTAA
Found at i:31716291 original size:30 final size:30
Alignment explanation
Indices: 31716221--31716309 Score: 109
Period size: 25 Copynumber: 3.1 Consensus size: 30
31716211 TCCATATTTA
31716221 TGGAAAGTCAAAGATATGGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
31716248 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
31716276 TGGAAAG-CTAAAGATATGGGTATCGAGATAT
1 TGGAAAGTC-AAAGATATGGGTATC-AAATAT
31716307 TGG
1 TGG
31716310 CATAAGAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
25 21 0.39
26 2 0.04
27 2 0.04
28 1 0.02
29 1 0.02
30 19 0.35
31 8 0.15
ACGTcount: A:0.42, C:0.07, G:0.26, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:31720945 original size:30 final size:30
Alignment explanation
Indices: 31720881--31720969 Score: 116
Period size: 25 Copynumber: 3.1 Consensus size: 30
31720871 TTTATATTTA
31720881 TGGAAAGTCAAAGATATGGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
31720908 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
* *
31720936 TGGAAAGTCAAAGATATGCGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
31720967 TGG
1 TGG
31720970 CATAATAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
25 21 0.39
26 2 0.04
27 2 0.04
28 1 0.02
30 20 0.37
31 8 0.15
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:31738811 original size:25 final size:25
Alignment explanation
Indices: 31738761--31738811 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
31738751 ACTCTTCTCA
* *
31738761 TCTCTTCACTTCTCTCTCATTTTTC
1 TCTCTTCACTTCCCTCTCATTATTC
*
31738786 TCTCTTCATTTCCCT-TCAATTATTC
1 TCTCTTCACTTCCCTCTC-ATTATTC
31738811 T
1 T
31738812 TCATTTCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (25 bp):
TCTCTTCACTTCCCTCTCATTATTC
Found at i:31744132 original size:24 final size:24
Alignment explanation
Indices: 31744100--31744149 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
31744090 ATTTTTAAAG
* *
31744100 AAAAAATATTTTAGTATACATTGT
1 AAAAAATATATTAATATACATTGT
31744124 AAAAAATATATTAATATACATTGT
1 AAAAAATATATTAATATACATTGT
31744148 AA
1 AA
31744150 GTTCTATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (24 bp):
AAAAAATATATTAATATACATTGT
Found at i:31746005 original size:25 final size:25
Alignment explanation
Indices: 31745976--31746033 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
31745966 TATTTTCTCA
* *
31745976 AAAATTTAATAATTCAGT-AATTTG
1 AAAATTTAATAATTAAATAAATTTG
*
31746000 ATAAATTAAATAATTAAATAAATTTG
1 A-AAATTTAATAATTAAATAAATTTG
31746026 AAAATTTA
1 AAAATTTA
31746034 GGAGAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 1 0.04
25 20 0.71
26 7 0.25
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (25 bp):
AAAATTTAATAATTAAATAAATTTG
Found at i:31747762 original size:16 final size:17
Alignment explanation
Indices: 31747731--31747763 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31747721 CATATTCTAG
31747731 CATATATCAAAACATAT
1 CATATATCAAAACATAT
*
31747748 CATATA-CAGAACATAT
1 CATATATCAAAACATAT
31747764 AACAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.27
Consensus pattern (17 bp):
CATATATCAAAACATAT
Found at i:31749260 original size:42 final size:43
Alignment explanation
Indices: 31749160--31749319 Score: 116
Period size: 42 Copynumber: 3.7 Consensus size: 43
31749150 ATAAAGCTCG
* * *
31749160 TACAAGGCCAACGTCCCAGAC-GTGGTCTTACTTGGAAACAAA
1 TACAATGCCAATGTCCCAGACAGTGGTCTTACTAGGAAACAAA
* ** *
31749202 TATCGATGCCGCTGTCCCAGACAG-GGTCTTA-TAGGAAATCATA
1 TA-CAATGCCAATGTCCCAGACAGTGGTCTTACTAGGAAA-CAAA
* * ***
31749245 TACAATGCCAATGTCCCAGACA-TGATCTTACATGTATGTCTCAAA
1 TACAATGCCAATGTCCCAGACAGTGGTCTTAC---TAGGAAACAAA
*
31749290 T-CAATGCCAATGTCCCAGAC-GTGGTGTTAC
1 TACAATGCCAATGTCCCAGACAGTGGTCTTAC
31749320 ACAAAATTTA
Statistics
Matches: 91, Mismatches: 18, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
42 31 0.34
43 26 0.29
44 27 0.30
45 4 0.04
46 3 0.03
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (43 bp):
TACAATGCCAATGTCCCAGACAGTGGTCTTACTAGGAAACAAA
Found at i:31755577 original size:16 final size:17
Alignment explanation
Indices: 31755546--31755578 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31755536 CATATTCTAG
31755546 CATATATCAAAACATAT
1 CATATATCAAAACATAT
*
31755563 CATATA-CAGAACATAT
1 CATATATCAAAACATAT
31755579 AACAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.27
Consensus pattern (17 bp):
CATATATCAAAACATAT
Found at i:31784245 original size:21 final size:21
Alignment explanation
Indices: 31784216--31784329 Score: 79
Period size: 21 Copynumber: 5.4 Consensus size: 21
31784206 ACTTAACTCA
*
31784216 TATGAGTTTCAGTTTAACCCT
1 TATGGGTTTCAGTTTAACCCT
* * * *
31784237 TCTGGGTTTCAGTTCAGCTCT
1 TATGGGTTTCAGTTTAACCCT
* * *
31784258 TTTGAGCTTT-AGTTTAACCTT
1 TATG-GGTTTCAGTTTAACCCT
* *
31784279 TATGGGTTTCCA-TTTAGCACT
1 TATGGGTTT-CAGTTTAACCCT
* * *
31784300 TATGAGCTTCCGTTTAACCCT
1 TATGGGTTTCAGTTTAACCCT
31784321 TATGGGTTT
1 TATGGGTTT
31784330 TCGTTTAGCA
Statistics
Matches: 66, Mismatches: 23, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
20 5 0.08
21 56 0.85
22 5 0.08
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.45
Consensus pattern (21 bp):
TATGGGTTTCAGTTTAACCCT
Found at i:31784334 original size:21 final size:21
Alignment explanation
Indices: 31784269--31784345 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
31784259 TTGAGCTTTA
31784269 GTTTAAC-CTTTATGGGTTTCC
1 GTTTAACAC-TTATGGGTTTCC
* * * *
31784290 ATTTAGCACTTATGAGCTTCC
1 GTTTAACACTTATGGGTTTCC
* *
31784311 GTTTAACCCTTATGGGTTTTC
1 GTTTAACACTTATGGGTTTCC
*
31784332 GTTTAGCACTTATG
1 GTTTAACACTTATG
31784346 TGCTTCTGTG
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.44
Consensus pattern (21 bp):
GTTTAACACTTATGGGTTTCC
Found at i:31784351 original size:42 final size:42
Alignment explanation
Indices: 31784216--31784351 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 42
31784206 ACTTAACTCA
* * * *
31784216 TATGAGTTTCAGTTTAACCCTTCTGGG-TTTCAGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTTC-GTTTAGCACT
* * * * *
31784258 TTTGAGCTTTAGTTTAACCTTTATGGGTTTCCATTTAGCACT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTTCGTTTAGCACT
*
31784300 TATGAGCTTCCGTTTAACCCTTATGGGTTTTCGTTTAGCACT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTTCGTTTAGCACT
*
31784342 TATGTGCTTC
1 TATGAGCTTC
31784352 TGTGCAGCCT
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 74 0.96
43 3 0.04
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTTCGTTTAGCACT
Found at i:31796558 original size:27 final size:26
Alignment explanation
Indices: 31796468--31796579 Score: 104
Period size: 27 Copynumber: 4.2 Consensus size: 26
31796458 AAAGGTTGTT
** *
31796468 AAATGA-CAGTAATACCCCATAAGGTA
1 AAATGATC-GTAATACCCTGTAGGGTA
*
31796494 AAATGA-CTGAAATACTCCTGTAGGGT-
1 AAATGATC-GTAATAC-CCTGTAGGGTA
31796520 AAATGATCGTAATACCCTTGTAGGGTA
1 AAATGATCGTAATACCC-TGTAGGGTA
* *
31796547 AAATGATCGTAATACCCCAGTAAGGTA
1 AAATGATCGTAATA-CCCTGTAGGGTA
31796574 AAATGA
1 AAATGA
31796580 CCATAATGCC
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
25 2 0.03
26 33 0.45
27 35 0.48
28 3 0.04
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (26 bp):
AAATGATCGTAATACCCTGTAGGGTA
Found at i:31797007 original size:21 final size:21
Alignment explanation
Indices: 31796966--31797007 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
31796956 TATCCCCACA
* *
31796966 TGGTGTGTTGGTTGGTATGGG
1 TGGTGTATTGGTTGATATGGG
31796987 TGGTGTATTGGTTTGAT-TGGG
1 TGGTGTATTGG-TTGATATGGG
31797008 CTGGGTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.07, C:0.00, G:0.48, T:0.45
Consensus pattern (21 bp):
TGGTGTATTGGTTGATATGGG
Found at i:31801162 original size:14 final size:14
Alignment explanation
Indices: 31801139--31801177 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
31801129 CTAGAAAAAG
31801139 AAACCATTTTCCAA
1 AAACCATTTTCCAA
* *
31801153 AAATCATTTTTCAA
1 AAACCATTTTCCAA
31801167 AAACCATTTTC
1 AAACCATTTTC
31801178 GGTCAAACAA
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:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (14 bp):
AAACCATTTTCCAA
Found at i:31809725 original size:16 final size:16
Alignment explanation
Indices: 31809704--31809735 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31809694 AAATTGGTTG
*
31809704 ATTTTTAGTTTAATTA
1 ATTTTTAGGTTAATTA
31809720 ATTTTTAGGTTAATTA
1 ATTTTTAGGTTAATTA
31809736 GATTAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
ATTTTTAGGTTAATTA
Found at i:31815288 original size:27 final size:27
Alignment explanation
Indices: 31815176--31815303 Score: 105
Period size: 27 Copynumber: 4.7 Consensus size: 27
31815166 AATCCATTGG
** * *
31815176 GACAGTAAATGTGGGGTAGTCCACTAG
1 GACAGTAAACATGGGGTAGTTCACTAA
* *
31815203 GACAGTAAACATGGGGTAGCTCA-TCGA
1 GACAGTAAACATGGGGTAGTTCACT-AA
* * * * *
31815230 TACAATAAACACGGGGTAATTCACTGA
1 GACAGTAAACATGGGGTAGTTCACTAA
*
31815257 TACAGTAAACATGGGGTAGTTCACTAA
1 GACAGTAAACATGGGGTAGTTCACTAA
* * *
31815284 GACAGAAAACACGAGGTAGT
1 GACAGTAAACATGGGGTAGT
31815304 CTGTCGGGAC
Statistics
Matches: 80, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
26 1 0.01
27 78 0.98
28 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (27 bp):
GACAGTAAACATGGGGTAGTTCACTAA
Found at i:31818737 original size:6 final size:6
Alignment explanation
Indices: 31818717--31818753 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
31818707 GTGATGATGT
* *
31818717 AAAGGA AAATGA AAAGAA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA A
31818754 TGGTTTCGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (6 bp):
AAAGGA
Found at i:31839582 original size:50 final size:50
Alignment explanation
Indices: 31839484--31839917 Score: 446
Period size: 50 Copynumber: 8.6 Consensus size: 50
31839474 CCATCTCATA
* *
31839484 TAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTACCATG
1 TAAGACCATGTCTGGGACATGGCGTTGGCA-CA--GAG---ATGAGAGGTCCCATG
*
31839540 TACGACCATGTCTGGGACATGGCGTTGGCACAGAGATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCGTTGGCACAGAGATGAGAGGTCCCATG
31839590 TAAGACCATG-CTTGGGACATGGCGTTGGCATC-GAGATGAGAGGTCCCATG
1 TAAGACCATGTC-TGGGACATGGCGTTGGCA-CAGAGATGAGAGGTCCCATG
* * *
31839640 TAAGACCATCTCTGGGACATGGCATTGGCACCA-AGATGAGAGGTCCCACG
1 TAAGACCATGTCTGGGACATGGCGTTGGCA-CAGAGATGAGAGGTCCCATG
* * ** *
31839690 TAAGACCATCTCTTGGACATGGCGTTGGCACCTAGATGAGAGGTCCCACG
1 TAAGACCATGTCTGGGACATGGCGTTGGCACAGAGATGAGAGGTCCCATG
* * * **
31839740 TAAGACCATGTCTGGGACATGGCGTTGGCACTGGGATGACAGGTCCCCCG
1 TAAGACCATGTCTGGGACATGGCGTTGGCACAGAGATGAGAGGTCCCATG
* * * * * **
31839790 TAAGACCATGTCTGGGACATAGCATGGGCACCGATATGAGATCTCCCATG
1 TAAGACCATGTCTGGGACATGGCGTTGGCACAGAGATGAGAGGTCCCATG
* * * * * * ** *
31839840 TAAGACCATATCTGGGATATGGCATT-G-ACAGTACAGGAAACATCTCATG
1 TAAGACCATGTCTGGGACATGGCGTTGGCACAG-AGATGAGAGGTCCCATG
*
31839889 TAAGACCATGTCTGGGACATGGCTTTGGC
1 TAAGACCATGTCTGGGACATGGCGTTGGC
31839918 TTGTTATTAT
Statistics
Matches: 327, Mismatches: 43, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
48 3 0.01
49 37 0.11
50 252 0.77
51 2 0.01
53 3 0.01
55 2 0.01
56 28 0.09
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCGTTGGCACAGAGATGAGAGGTCCCATG
Found at i:31840126 original size:13 final size:13
Alignment explanation
Indices: 31840110--31840135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31840100 GTTATAATCA
31840110 AGAGTTGTTTAAG
1 AGAGTTGTTTAAG
31840123 AGAGTTGTTTAAG
1 AGAGTTGTTTAAG
31840136 CAAGCAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (13 bp):
AGAGTTGTTTAAG
Found at i:31841491 original size:23 final size:23
Alignment explanation
Indices: 31841453--31841503 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
31841443 GGGAGAGAAA
*
31841453 TGTAATATCCCAAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
31841476 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
31841499 AGTAA
1 TGTAA
31841504 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCAAAAATTACTAC
Found at i:31845660 original size:47 final size:46
Alignment explanation
Indices: 31845608--31845899 Score: 209
Period size: 49 Copynumber: 6.2 Consensus size: 46
31845598 TGGTTAGACC
* *
31845608 ATGGCATCATGTGATATGTGATTTCCGTATAAGACCATAGGTGGGCT
1 ATGGCATCATGTGATATGTGA-TTCCGTGTAAGACCATAGCTGGGCT
* * * * * *
31845655 ATGGCATCGGTGTGATGTGATTATGAGTTCCGTATAAAACCATATCTGGGAT
1 ATGGCATC-ATGTGA--T-A-TGTGA-TTCCGTGTAAGACCATAGCTGGGCT
* * * * * *
31845707 ATGGCATCGGTGTGATATGTGCTACTGTGTAAGACCATATCTGGGAT
1 ATGGCATC-ATGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCT
31845754 ATGGCATCA---G---TGTGATTCCGTGTAAGACCATAGCTGGGCT
1 ATGGCATCATGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCT
* *
31845794 ATGGCATCAGTAAGTGATACGTGATTCCGTGTAAGACCATAGCTGGACT
1 ATGGCATCA-T--GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCT
* * * * ** *
31845843 ATGTCATTGGTATGTGTTATGTGATTACGTGTAAGACCATAATTGGACT
1 ATGGCA-T--CATGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCT
31845892 ATGGCATC
1 ATGGCATC
31845900 GAGAAAACGA
Statistics
Matches: 198, Mismatches: 30, Indels: 35
0.75 0.11 0.13
Matches are distributed among these distances:
40 34 0.17
43 1 0.01
46 1 0.01
47 37 0.19
48 9 0.05
49 70 0.35
50 3 0.02
51 2 0.01
52 41 0.21
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (46 bp):
ATGGCATCATGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCT
Found at i:31845697 original size:52 final size:53
Alignment explanation
Indices: 31845616--31845722 Score: 153
Period size: 52 Copynumber: 2.0 Consensus size: 53
31845606 CCATGGCATC
* * * * *
31845616 ATGTGATATGTGATTTCCGTATAAGACCATAGGTGGGCTATGGCATCGGTGTG
1 ATGTGATATATGAGTTCCGTATAAAACCATAGCTGGGATATGGCATCGGTGTG
*
31845669 ATGTGAT-TATGAGTTCCGTATAAAACCATATCTGGGATATGGCATCGGTGTG
1 ATGTGATATATGAGTTCCGTATAAAACCATAGCTGGGATATGGCATCGGTGTG
31845721 AT
1 AT
31845723 ATGTGCTACT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
52 41 0.85
53 7 0.15
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (53 bp):
ATGTGATATATGAGTTCCGTATAAAACCATAGCTGGGATATGGCATCGGTGTG
Found at i:31851538 original size:15 final size:15
Alignment explanation
Indices: 31851518--31851547 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31851508 TGAATGTAAT
31851518 TCACTCATGAAGCTA
1 TCACTCATGAAGCTA
31851533 TCACTCATGAAGCTA
1 TCACTCATGAAGCTA
31851548 AGGCTTTTGA
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:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (15 bp):
TCACTCATGAAGCTA
Found at i:31852057 original size:113 final size:114
Alignment explanation
Indices: 31851855--31852297 Score: 626
Period size: 114 Copynumber: 3.9 Consensus size: 114
31851845 AAAATAAGCA
* * * * *
31851855 TTAGCGGCGTTTTT-GAGAAAGCGCTGC-AAAAAACCTAAGCCCAACGATGTCGTTTCCCGAGCT
1 TTAGCGGCGTTTTTGGA-AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
31851918 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCATTTATAAGAAAGCGCCGCTAATGCTCAGGGAT
31851968 TTAGCGGCGTTTTTCGG-AAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTAGCGGCGTTTTT-GGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
31852031 TTCGGGGATTTAGCGGCATTTATAAGAAAGCGCCGCTAATGCTTAGGGAT
65 TTCGGGGATTTAGCGGCATTTATAAGAAAGCGCCGCTAATGCTCAGGGAT
* ** *
31852081 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGACCAACGAAACCATTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
31852146 TCGGGGATTTAGCGGCATTTATAAGAAAGCGTCGCTAATGCTCAGGGAT
66 TCGGGGATTTAGCGGCATTTATAAGAAAGCGCCGCTAATGCTCAGGGAT
* * * * *
31852195 TTAGCGACATTTTTGGAAAAGCGCCACAAAAAAACCTAAGTCCAACGACGCCGTTTTCTGAGGTT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* **
31852260 TCGGGGATTTAGCGGCGTTT-TTGGAAAAGCGCCGCTAA
66 TCGGGGATTTAGCGGCATTTATAAG-AAAGCGCCGCTAA
31852298 AAATATTTTA
Statistics
Matches: 298, Mismatches: 27, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
112 2 0.01
113 127 0.43
114 168 0.56
115 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCATTTATAAGAAAGCGCCGCTAATGCTCAGGGAT
Found at i:31852565 original size:15 final size:15
Alignment explanation
Indices: 31852545--31852575 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31852535 CATATTTTAA
31852545 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
31852560 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
31852575 G
1 G
31852576 ATTAGGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:31852890 original size:8 final size:8
Alignment explanation
Indices: 31852877--31852904 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
31852867 TGGGATTTAA
31852877 GGTTTAGG
1 GGTTTAGG
31852885 GGTTTAGG
1 GGTTTAGG
31852893 GGTTTAGG
1 GGTTTAGG
31852901 GGTT
1 GGTT
31852905 AGATGTTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.50, T:0.39
Consensus pattern (8 bp):
GGTTTAGG
Found at i:31852915 original size:14 final size:14
Alignment explanation
Indices: 31852896--31852928 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31852886 GTTTAGGGGT
31852896 TTAGGGGTT-AGATG
1 TTAGGGGTTAAGA-G
31852910 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
31852924 TTAGG
1 TTAGG
31852929 AATTTAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.33
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:31853662 original size:49 final size:49
Alignment explanation
Indices: 31853588--31853685 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 49
31853578 TTTTTTATAA
* *
31853588 AAACGCCGAAAAAAATAAACTAATTTATAAAAAACA-AAATGAAAAATTT
1 AAACGCCGAAAAAAATAAACCAATTTATAAAAAA-ATAAATAAAAAATTT
*
31853637 AAACGCCGCAAAAAATAAACCAATTTATAAAAAAATAAATAAAAAATTT
1 AAACGCCGAAAAAAATAAACCAATTTATAAAAAAATAAATAAAAAATTT
31853686 TTCGACTAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 1 0.02
49 44 0.98
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.20
Consensus pattern (49 bp):
AAACGCCGAAAAAAATAAACCAATTTATAAAAAAATAAATAAAAAATTT
Found at i:31853829 original size:56 final size:56
Alignment explanation
Indices: 31853769--31853878 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 56
31853759 GCAATAGTGG
* * *
31853769 TGTTTTTTATAAAAACGCCGCAAAAATAAATCAATTTATAAAAAATAAAATAAATT
1 TGTTTTTTATAAAAACGCCGCAAAAAAAAACCAATTTATAAAAAACAAAATAAATT
* *
31853825 TGTTTTTTATAAAAACGCTGCAAAAAAAAACCAATTTATACAAAACAAAATAAA
1 TGTTTTTTATAAAAACGCCGCAAAAAAAAACCAATTTATAAAAAACAAAATAAA
31853879 AAATTTTTAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (56 bp):
TGTTTTTTATAAAAACGCCGCAAAAAAAAACCAATTTATAAAAAACAAAATAAATT
Found at i:31853880 original size:199 final size:200
Alignment explanation
Indices: 31853637--31854021 Score: 523
Period size: 199 Copynumber: 1.9 Consensus size: 200
31853627 TGAAAAATTT
* *
31853637 AAACGCCGCAAAAAATAAACCAATTTATAAAAAAATAAATAAAAAATTTTTCGACTAGCAAAACG
1 AAACGCCGCAAAAAATAAACCAATTTATAAAAAAATAAATAAAAAATTTTTAGAATAGCAAAACG
* *
31853702 GCGTCGTTTTTGTTCAAAATGAAAAAAATTTTGC-G-ATAAAAACGCCGCTAAAGGTAAGCAATA
66 GCGTCG-TTTCGTTCAAAATGAAAAAAATTTTGCGGCATAAAAA---CGCTAAAGGTAAGCAACA
* *
31853765 GT-GGTG-TTTTTTATAAAAACGCCGC-AAAAATAAATCAATTTATAAAAAATAAAATAAATTTG
127 -TCGGCGTTTTTTTATAAAAACGCCACAAAAAATAAATCAATTTATAAAAAATAAAATAAATTTG
31853827 TTTTTTATAA
191 TTTTTTATAA
* *
31853837 AAACGCTGCAAAAAA-AAACCAATTTATACAAAACA-AAATAAAAAATTTTTAGAATAGCAAAAC
1 AAACGCCGCAAAAAATAAACCAATTTATA-AAAAAATAAATAAAAAATTTTTAGAATAGCAAAAC
* * **** *
31853900 GGCGTCGTTTCGTTCAAAATGAAAAAAGTTTTGCGGCGTTTTTATGCTAAAGGTAAGCAACATCG
65 GGCGTCGTTTCGTTCAAAATGAAAAAAATTTTGCGGCATAAAAACGCTAAAGGTAAGCAACATCG
*
31853965 GCGTTTTTTTATAAAAATGCCACAAAAAATAAATCAATTTATAAAAAATAAAATAAA
130 GCGTTTTTTTATAAAAACGCCACAAAAAATAAATCAATTTATAAAAAATAAAATAAA
31854022 AAAATTTTTA
Statistics
Matches: 163, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
196 1 0.01
197 19 0.12
198 42 0.26
199 80 0.49
200 21 0.13
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (200 bp):
AAACGCCGCAAAAAATAAACCAATTTATAAAAAAATAAATAAAAAATTTTTAGAATAGCAAAACG
GCGTCGTTTCGTTCAAAATGAAAAAAATTTTGCGGCATAAAAACGCTAAAGGTAAGCAACATCGG
CGTTTTTTTATAAAAACGCCACAAAAAATAAATCAATTTATAAAAAATAAAATAAATTTGTTTTT
TATAA
Found at i:31855305 original size:106 final size:106
Alignment explanation
Indices: 31855120--31855315 Score: 320
Period size: 106 Copynumber: 1.8 Consensus size: 106
31855110 CATTTTGTTC
* * *
31855120 AAAAACGCCGCAAAAAATAAACTAATTCATAAAAAACAAAATAAAAAATTTTTAGCATAGTAAAA
1 AAAAACGCCGCAAAAAATAAACTAATTCATAAAAAACAAAATAAAAAAATTTTAGAATAGCAAAA
* *
31855185 CAGTGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTTAT
66 CAGCGACATTTTGTTCAAAATGAAATAGCGGCGTTTTTTAT
* *
31855226 AAAAACGCCGCAAAAAATAAACTACTTTATAAAAAACAAAATAAAAAAATTTTAGAATAGCAAAA
1 AAAAACGCCGCAAAAAATAAACTAATTCATAAAAAACAAAATAAAAAAATTTTAGAATAGCAAAA
*
31855291 CGGCGACATTTTGTTCAAAATGAAA
66 CAGCGACATTTTGTTCAAAATGAAA
31855316 AAAAATTTGC
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 82 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.25
Consensus pattern (106 bp):
AAAAACGCCGCAAAAAATAAACTAATTCATAAAAAACAAAATAAAAAAATTTTAGAATAGCAAAA
CAGCGACATTTTGTTCAAAATGAAATAGCGGCGTTTTTTAT
Found at i:31855532 original size:21 final size:20
Alignment explanation
Indices: 31855495--31855534 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
31855485 AAAACGCCGC
**
31855495 AAAAAAATAAACTAATTTAT
1 AAAAAAATAAAAAAATTTAT
31855515 AAAAAAATAAAAAAAATTTA
1 AAAAAAAT-AAAAAAATTTA
31855535 GACTAGCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAAAATAAAAAAATTTAT
Found at i:31855747 original size:107 final size:107
Alignment explanation
Indices: 31855615--31855830 Score: 317
Period size: 107 Copynumber: 2.0 Consensus size: 107
31855605 AAAGGTAAGC
* * * *
31855615 AATAGCGGCGTTTTTTTTATAAAAACGCCTCAAAAATTAAATCAATTTATAAAAAATAAAATAAA
1 AATAGCGGAGTTTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAA
* * * *
31855680 AAATATTTAGCATATCAAAATGGTGTCATTTTGTTCAAAATGA
66 AAATATTTAGAATAGC-AAACGGCGTCATTTTGTTCAAAATGA
31855723 AATAGCGGAG-TTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAA
1 AATAGCGGAGTTTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAA
* * *
31855787 AAATTTTTAGAATAGCAAACGGCGTCGTTTTGTTCGAAATGA
66 AAATATTTAGAATAGCAAACGGCGTCATTTTGTTCAAAATGA
31855829 AA
1 AA
31855831 AAAGTTTTGC
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
106 24 0.25
107 64 0.66
108 9 0.09
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.31
Consensus pattern (107 bp):
AATAGCGGAGTTTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAA
AAATATTTAGAATAGCAAACGGCGTCATTTTGTTCAAAATGA
Found at i:31855759 original size:257 final size:253
Alignment explanation
Indices: 31855120--31855852 Score: 1001
Period size: 258 Copynumber: 2.8 Consensus size: 253
31855110 CATTTTGTTC
* * * *
31855120 AAAAACGCCGCAAAAAATAAA-CTAATTCATAAAAAACAAAATAAAAAATTTTTAGCATAGT-AA
1 AAAAACGCCTCAAAAATTAAATC-AATTTATAAAAAATAAAATAAAAAATTTTTAGCATA-TCAA
31855183 AACAGTGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAAC
64 AACAGTGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAAC
* * *
31855248 TACTTTATAAAAAACAAAATAAAAAAATTTTAGAATAGCAAAACGGCGA-CATTTTGTTCAAAAT
129 TAATTTAT---AAA-AAAATAAAAAAAATTTAGAATAGCAAAACGGC-ATCGTTTTGTTCAAAAT
*
31855312 GAAAAAAAATTTGCGGCGTTGTTAATGAAAACGCTGCTAAAGGTAAGCAATAGCGGTGTTTTTTA
189 GAAAAAAAATTTGCGGCGTTGTT-ATGAAAACGCCGCTAAAGGTAAGCAATAGCGGTGTTTTTTA
31855377 T
253 T
* * *
31855378 AAAATCG-CTGCAAAAATTAAATCAATTTATAAAAAATAAAATAAAAATTTTTTAGCATAGCAAA
1 AAAAACGCCT-CAAAAATTAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATATCAAA
* * *
31855442 ACAGTGTCATTTGGCTCAAAATGAAATAGCGGCGGTTTTTATAAAAACGCCGCAAAAAAATAAAC
65 ACAGTGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTTATAAAAACGCCGC-AAAAAATAAAC
* * *
31855507 TAATTTATAAAAAAATAAAAAAAATTTAGACTAGCAAAACGACATTGTTTTGTTCAAAATGAAAA
129 TAATTTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCATCGTTTTGTTCAAAATGAAAA
*
31855572 AAAATTTGCGGCGTTGTTATGAACAACGCCGCTAAAGGTAAGCAATAGCGGCGTTTTTTTTAT
194 AAAATTTGCGGCGTTGTTATGAA-AACGCCGCTAAAGGTAAGCAATAGC-G-GTGTTTTTTAT
*
31855635 AAAAACGCCTCAAAAATTAAATCAATTTATAAAAAATAAAATAAAAAATATTTAGCATATCAAAA
1 AAAAACGCCTCAAAAATTAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATATCAAAA
** *
31855700 TGGTGTCATTTTGTTCAAAATGAAATAGCGGAGTTTTTTTATAAAAACGCCGCAAAAAATAAA-T
66 CAGTGTCATTTTGTTCAAAATGAAATAGCGGCG-TTTTTTATAAAAACGCCGCAAAAAATAAACT
* * *
31855764 CAATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGC-AAACGGCGTCGTTTTGTTCGAAATG
130 -AATTTATAAAAAA-ATAA-AAAAAA--TTTAGAATAGCAAAACGGCATCGTTTTGTTCAAAATG
** *
31855828 AAAAAAGTTTTGCGGCGTTTTTATG
190 AAAAAAAATTTGCGGCGTTGTTATG
31855853 CTAAAGGTAA
Statistics
Matches: 423, Mismatches: 37, Indels: 28
0.87 0.08 0.06
Matches are distributed among these distances:
254 6 0.01
255 89 0.21
256 5 0.01
257 120 0.28
258 125 0.30
259 25 0.06
260 43 0.10
261 10 0.02
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (253 bp):
AAAAACGCCTCAAAAATTAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATATCAAAA
CAGTGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAAATAAACTA
ATTTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCATCGTTTTGTTCAAAATGAAAAAA
AATTTGCGGCGTTGTTATGAAAACGCCGCTAAAGGTAAGCAATAGCGGTGTTTTTTAT
Found at i:31856026 original size:317 final size:316
Alignment explanation
Indices: 31855570--31856169 Score: 997
Period size: 316 Copynumber: 1.9 Consensus size: 316
31855560 TCAAAATGAA
** *
31855570 AAAAAATTTGCGGCGTTGTTATGAACAACGCCGCTAAAGGTAAGCAATAGCGGCGTTTTTTTTAT
1 AAAAAATTTGCGAAGTTGTTATGAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTTTTTTTAT
* * * *
31855635 AAAAACGCCTCAAAAATTAAATCAATTTATAAAAAATAAAATAAAAAATATTTAGCATATCAAAA
66 AAAAACGCCACAAAAAATAAATCAAATTATAAAAAATAAAATAAAAAATATTTAGCATAGCAAAA
* * * *
31855700 TGGTGTCATTTTGTTCAAAATGAAATAGCGGAGTTTTTTTATAAAAACGCCGCAAAAAATAAATC
131 CGGTGTCATTTTATTCAAAATGAAATAGCGGAG-TTTTTTATAAAAACGCCACAAAAAATAAACC
*
31855765 AATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCA-AACGGCGTCGTTTTGTTCGAAATGA
195 AATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAGAACGGCGTCGTTTTGTTCAAAATGA
*
31855829 AAAAAGTTTTGCGGCGTTTTTATGCTAAAGGTAAGCAATAGCGGCGTTTTTTTTTTT
260 AAAAAATTTTGCGGCGTTTTTATGCTAAAGGTAAGCAATAGCGGCGTTTTTTTTTTT
*
31855886 AAAAATTTTGCGAAGTTGTTCAT-AAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTTTTTTTA
1 AAAAAATTTGCGAAGTTGTT-ATGAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTTTTTTTA
* *
31855950 TAAAAACGCCACAAAAAAATAAATTAAATTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAA
65 TAAAAACGCCAC-AAAAAATAAATCAAATTATAAAAAATAAAATAAAAAATATTTAGCATAGCAA
*
31856015 AACGGTGTCATTTTATTCAAAATGAAATAGCGGCGTTTTTTATAAAAACGCCACAAAAAATAAAC
129 AACGGTGTCATTTTATTCAAAATGAAATAGCGGAGTTTTTTATAAAAACGCCACAAAAAATAAAC
31856080 CAATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAGAACGGCGTCGTTTTGTTCAAAATG
194 CAATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAGAACGGCGTCGTTTTGTTCAAAATG
*
31856145 AAAAAAATTTTGTGGCGTTTTTATG
259 AAAAAAATTTTGCGGCGTTTTTATG
31856170 AAAGAACGCC
Statistics
Matches: 263, Mismatches: 18, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
316 136 0.52
317 127 0.48
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (316 bp):
AAAAAATTTGCGAAGTTGTTATGAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTTTTTTTAT
AAAAACGCCACAAAAAATAAATCAAATTATAAAAAATAAAATAAAAAATATTTAGCATAGCAAAA
CGGTGTCATTTTATTCAAAATGAAATAGCGGAGTTTTTTATAAAAACGCCACAAAAAATAAACCA
ATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAGAACGGCGTCGTTTTGTTCAAAATGAA
AAAAATTTTGCGGCGTTTTTATGCTAAAGGTAAGCAATAGCGGCGTTTTTTTTTTT
Found at i:31856093 original size:106 final size:108
Alignment explanation
Indices: 31855931--31856147 Score: 330
Period size: 106 Copynumber: 2.0 Consensus size: 108
31855921 AAAGGTAAGC
** *
31855931 AATAGCGGCGTTTTTTTTATAAAAACGCCACAAAAAAATAAATTAAATTATAAAAAATAAAATAA
1 AATAGCGGCG-TTTTTTTATAAAAACGCCACAAAAAAATAAACCAAATTATAAAAAACAAAATAA
* *
31855996 AAAATTTTTAGCATAGCAAAACGGTGTCATTTTATTCAAAATGA
65 AAAATTTTTAGAATAGCAAAACGGCGTCATTTTATTCAAAATGA
*
31856040 AATAGCGGCG-TTTTTTATAAAAACGCCAC-AAAAAATAAACCAATTTATAAAAAACAAAATAAA
1 AATAGCGGCGTTTTTTTATAAAAACGCCACAAAAAAATAAACCAAATTATAAAAAACAAAATAAA
* * *
31856103 AAATTTTTAGAATAGCAGAACGGCGTCGTTTTGTTCAAAATGA
66 AAATTTTTAGAATAGCAAAACGGCGTCATTTTATTCAAAATGA
31856146 AA
1 AA
31856148 AAAATTTTGT
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
106 70 0.71
107 19 0.19
109 10 0.10
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.28
Consensus pattern (108 bp):
AATAGCGGCGTTTTTTTATAAAAACGCCACAAAAAAATAAACCAAATTATAAAAAACAAAATAAA
AAATTTTTAGAATAGCAAAACGGCGTCATTTTATTCAAAATGA
Found at i:31856331 original size:107 final size:107
Alignment explanation
Indices: 31856206--31856405 Score: 330
Period size: 107 Copynumber: 1.9 Consensus size: 107
31856196 CACAAATGCA
* * *
31856206 TATAAAATCGCCGCAAAAAATAAACCAATTTATAAAAAATAAAATAAAAATTTTTTAGCATAGCA
1 TATAAAATCGCCGCAAAAAATAAACCAATTTATAAAAAAGAAAATAAAAAATTTTTAGAATAGCA
*
31856271 AAACGGTGTCATTTTGTTCAAAACGAAATACCGGCGTTTTTT
66 AAACGGAGTCATTTTGTTCAAAACGAAATACCGGCGTTTTTT
31856313 TATAGAAA-CGCCGCAAAAAATAAACCAATTTATAAAAAAGAAAATAAAAAATTTTTAGAATAGC
1 TATA-AAATCGCCGCAAAAAATAAACCAATTTATAAAAAAGAAAATAAAAAATTTTTAGAATAGC
* *
31856377 AAAACGGAGTCGTTTTGTTCAAAATGAAA
65 AAAACGGAGTCATTTTGTTCAAAACGAAA
31856406 AAAATTTTGC
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
107 83 0.97
108 3 0.03
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (107 bp):
TATAAAATCGCCGCAAAAAATAAACCAATTTATAAAAAAGAAAATAAAAAATTTTTAGAATAGCA
AAACGGAGTCATTTTGTTCAAAACGAAATACCGGCGTTTTTT
Done.