Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 178 of 205
Found at i:52823144 original size:17 final size:17
Alignment explanation
Indices: 52823124--52823157 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
52823114 TTTATTAACA
52823124 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
52823141 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
52823158 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:52823261 original size:17 final size:17
Alignment explanation
Indices: 52823241--52823274 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
52823231 TTTATTAAAA
52823241 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
52823258 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
52823275 TTTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:52823265 original size:117 final size:117
Alignment explanation
Indices: 52823059--52823294 Score: 427
Period size: 117 Copynumber: 2.0 Consensus size: 117
52823049 GTAGCAAATT
* *
52823059 AATTATATTTTAGTATTATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAACA
1 AATTATATTTTAGTATCATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAAAA
* *
52823124 ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATTTTA
66 ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAACAATTATGTTA
52823176 AATTATATTTTAGTATCATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAAAA
1 AATTATATTTTAGTATCATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAAAA
*
52823241 ATTTTATTAAATTATATATTTTATTAAATTATATTTTATAACAATTATGTTA
66 ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAACAATTATGTTA
52823293 AA
1 AA
52823295 ATATGATTAA
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
117 114 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (117 bp):
AATTATATTTTAGTATCATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAAAA
ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAACAATTATGTTA
Found at i:52823288 original size:16 final size:15
Alignment explanation
Indices: 52823241--52823288 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
52823231 TTTATTAAAA
*
52823241 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
52823258 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
52823273 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
52823289 GTTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:52823466 original size:39 final size:41
Alignment explanation
Indices: 52823422--52823526 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
52823412 TTCCTTATGT
*
52823422 TATTACACCTCTATTCCATTCAACCAAACACAAA-AA-TACC
1 TATTACGCCTCTATTCCATTCAACCAAACA-AAAGAATTACC
52823462 -ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTACC
1 TATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTACC
52823507 TATTACGCCTCTATTCCATT
1 TATTACGCCTCTATTCCATT
52823527 ACGCATCTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 15
0.78 0.01 0.21
Matches are distributed among these distances:
39 13 0.23
40 1 0.02
41 4 0.07
43 3 0.05
44 16 0.29
45 5 0.09
46 14 0.25
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (41 bp):
TATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTACC
Found at i:52823521 original size:46 final size:44
Alignment explanation
Indices: 52823438--52823528 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 44
52823428 ACCTCTATTC
52823438 CATTCAACCAAACACAAAAATACCATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAAAATACCATTACGCCTCTATTCCATTA
52823482 CATTCAACCAAACA-AAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAA-AA-TACC-ATTACGCCTCTATTCCATTA
52823528 C
1 C
52823529 GCATCTATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
43 3 0.07
44 16 0.36
45 4 0.09
46 21 0.48
ACGTcount: A:0.40, C:0.31, G:0.03, T:0.26
Consensus pattern (44 bp):
CATTCAACCAAACACAAAAATACCATTACGCCTCTATTCCATTA
Found at i:52823529 original size:16 final size:16
Alignment explanation
Indices: 52823508--52823576 Score: 120
Period size: 16 Copynumber: 4.3 Consensus size: 16
52823498 AGAATTACCT
52823508 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
52823524 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
52823540 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
52823556 ATTACGCCTCTATTCT
1 ATTACGCCTCTATTCC
52823572 ATTAC
1 ATTAC
52823577 AGCGAACCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.22, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:52832235 original size:188 final size:187
Alignment explanation
Indices: 52831906--52832255 Score: 531
Period size: 188 Copynumber: 1.9 Consensus size: 187
52831896 AACGCAGAGT
* *
52831906 TTGGTCTTAAGGTACACTAGCATTAGTGGCGCTTATACGAAAACGCCGCTAAAGTATAGTATTAG
1 TTGGTCTTAAGGTACACTAACATTAATGGCGCTTATACGAAAACGCCGCTAAAGTATAGTATTAG
* * *
52831971 CAGCGAGTAGTGAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTTGTCTTGAGGTATAT
66 CAGCGAGTAGTAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACAT
*
52832036 TAGGATTAGTGGCGCTTAT-TGGAAAACACCGCAAAATATTAACCAAAACACTGCGCA
131 TACGATTAGTGGCGCTTATAT-GAAAACACCGCAAAATATTAACCAAAACACTGCGCA
* * * * *
52832093 TTGGTCTTAATGTATAGTAACATTAATGGCGCTTATGCTAAAACGCCGCTAAAGTATAGTATTAG
1 TTGGTCTTAAGGTACACTAACATTAATGGCGCTTATACGAAAACGCCGCTAAAGTATAGTATTAG
* * * *
52832158 CGGCGAGTACTTAAAAGCGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACA
66 CAGCGAGTA-GTAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACA
*
52832223 TTACGATTAGTGGCGCTTATATGAAAACGCCGC
130 TTACGATTAGTGGCGCTTATATGAAAACACCGC
52832256 TAAAGCATAG
Statistics
Matches: 145, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
187 66 0.46
188 78 0.54
189 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (187 bp):
TTGGTCTTAAGGTACACTAACATTAATGGCGCTTATACGAAAACGCCGCTAAAGTATAGTATTAG
CAGCGAGTAGTAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACAT
TACGATTAGTGGCGCTTATATGAAAACACCGCAAAATATTAACCAAAACACTGCGCA
Found at i:52832361 original size:112 final size:113
Alignment explanation
Indices: 52832114--52832363 Score: 310
Period size: 112 Copynumber: 2.2 Consensus size: 113
52832104 GTATAGTAAC
* * *
52832114 ATTAATGGCGCTTA-TGCTAAAACGCCGCTAAAGTATAGTATTAGCGGCGAGTACTTAAAAGCGC
1 ATTAGTGGCGCTTATTG-GAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTACTTAAAAGCGC
* ** * *
52832178 CGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTACG
65 CACAA-CAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACG
* * *
52832228 ATTAGTGGCGCTTATAT-GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTA-TTGTAAAGTG
1 ATTAGTGGCGCTTAT-TGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTACTT-AAAAGCG
* * *
52832291 CCACAA-AATATTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGG
64 CCACAACAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACG
52832340 ATTAGTGGCGCTTATTGGAAAACG
1 ATTAGTGGCGCTTATTGGAAAACG
52832364 ACACAAAATA
Statistics
Matches: 118, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
111 1 0.01
112 58 0.49
113 2 0.02
114 56 0.47
116 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (113 bp):
ATTAGTGGCGCTTATTGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTACTTAAAAGCGCC
ACAACAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACG
Found at i:52832432 original size:300 final size:299
Alignment explanation
Indices: 52831871--52832664 Score: 1159
Period size: 300 Copynumber: 2.6 Consensus size: 299
52831861 GTTTACTACC
* * * *
52831871 AAGCGCCGCAATAC-ATCTTAACCAAAACGCAGAGTTTGGTCTTAAGGTACACTAGCATTAGTGG
1 AAGCGCCGCAAT-CTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTAG-ATTAGTGG
* * * * * *
52831935 CGCTTATACGAAAACGCCGCTAAAGTATAGTATTAGCAGCGAGTAGTGAAAGCGCCGCAATATTT
64 CGCTTATATGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTATTGAAAGCGCCGCAA-A-AT
* *
52832000 CTTAACCAAAACGCAGAGTTTTGTCTTGAGGTATATTAGGATTAGTGGCGCTTATTGGAAAAC-A
127 ATTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATTGGAAAACGA
*
52832064 CCGCAAAATATTAACCAAAACACTGCGCATTGGTCTTAATGTATAGTAACATTAATGGCGCTTAT
192 CCACAAAATATTAACCAAAACACTGCGCATTGGTCTTAATGTATAGTAACATTAATGGCGCTTAT
*
52832129 GCTAAAACGCCGCTAAAGTATAGTATTAGCGGCGAGTACT-TAA
257 GCTAAAACGCCGCTAAAGTATAGTATTAGCGGCAAGTACTGT-A
52832172 AAGCGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTACGATTAGTGGC
1 AAGCGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTA-GATTAGTGGC
* *
52832237 GCTTATATGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTATTGTAAAGTGCCACAAAATAT
65 GCTTATATGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTATTG-AAAGCGCCGCAAAATAT
*
52832302 TAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGGATTAGTGGCGCTTATTGGAAAACGA-C
129 TAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATTGGAAAACGACC
** * * * *
52832366 ACAAAATATTAACCAAAACGTTGCGCTTTGGTCTTGATGTATAGTAGCATTAGTGGCGCTTATGC
194 ACAAAATATTAACCAAAACACTGCGCATTGGTCTTAATGTATAGTAACATTAATGGCGCTTATGC
52832431 TAAAACGCCGCTAAAGTATAGTATTAGCGGCAAGTACTGTA
259 TAAAACGCCGCTAAAGTATAGTATTAGCGGCAAGTACTGTA
*
52832472 AAGCGCCGCAATCTTTCTTAACCAAAACGAAGAGTTTGGTGTTGAGGTACATTAGGATTAGTGGC
1 AAGCGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTA-GATTAGTGGC
* * *
52832537 GCTTATTTGAAAACGCCGCTAAAGGATAATATTAGCGGCGCGTATTGAAAAGCGCCGCAAAATAT
65 GCTTATATGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTATTG-AAAGCGCCGCAAAATAT
* * * *
52832602 TAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCAATT-GTGGCGCTTA-TGGTAAAACG
129 TAACCAAAACGCAGAG-TTTGGTCTTGAGGTATATTAG-GATTAGTGGCGCTTATTGG-AAAACG
52832665 CCGCTAAAAC
Statistics
Matches: 449, Mismatches: 36, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
300 299 0.67
301 136 0.30
302 14 0.03
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (299 bp):
AAGCGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTAGATTAGTGGCG
CTTATATGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTATTGAAAGCGCCGCAAAATATTA
ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATTGGAAAACGACCAC
AAAATATTAACCAAAACACTGCGCATTGGTCTTAATGTATAGTAACATTAATGGCGCTTATGCTA
AAACGCCGCTAAAGTATAGTATTAGCGGCAAGTACTGTA
Found at i:52832437 original size:74 final size:73
Alignment explanation
Indices: 52832292--52832428 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 73
52832282 TGTAAAGTGC
* * *
52832292 CACAAAATATTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGGATTAGTGGCGCTTATTG
1 CACAAAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTATAGTAGCATTAGTGGCGCTTATTG
52832357 GAAAACGA
66 GAAAACGA
** * *
52832365 CACAAAATATTAACCAAAACGTTGCGCTTTGGTCTTGATGTATAGTAGCATTAGTGGCGCTTAT
1 CACAAAATATTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATAGTAGCATTAGTGGCGCTTAT
52832429 GCTAAAACGC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
73 23 0.41
74 33 0.59
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (73 bp):
CACAAAATATTAACCAAAACGCAGAGTTTGGTCTTGAGGTATAGTAGCATTAGTGGCGCTTATTG
GAAAACGA
Found at i:52832683 original size:113 final size:113
Alignment explanation
Indices: 52832340--52832692 Score: 381
Period size: 114 Copynumber: 3.1 Consensus size: 113
52832330 GTATATTAGG
* * * * **
52832340 ATTAGTGGCGCTTATTGGAAAA-CGACACAAAATATTAACCAAAACGTTGCGCTTTGGTCTTGAT
1 ATTAGCGGCGCGTATT-GAAAAGCGCCGCAAAATATTAACCAAAACGAAGCGCTTTGGTCTTGAT
* * *
52832404 GTATAGTAGCATTAGTGGCGCTTATGCTAAAACGCCGCTAAAGTATAGT
65 GTATACTAGCATTAGTGGCGCTTATGCTAAAACGCCGCTAAAGCATAAT
** * * ** * * *
52832453 ATTAGCGGCAAGTACTGTAAAGCGCCGCAATCTTTCTTAACCAAAACGAAGAG-TTTGGTGTTGA
1 ATTAGCGGCGCGTATTGAAAAGCGCCGCAA--AATATTAACCAAAACGAAGCGCTTTGGTCTTGA
* * * * * *
52832517 GGTACATTAGGATTAGTGGCGCTTAT-TTGAAAACGCCGCTAAAGGATAAT
64 TGTATACTAGCATTAGTGGCGCTTATGCT-AAAACGCCGCTAAAGCATAAT
*
52832567 ATTAGCGGCGCGTATTGAAAAGCGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 ATTAGCGGCGCGTATTGAAAAGCGCCGCAAAATATTAACCAAAACGAAGCGCTTTGGTCTTGATG
* * *
52832632 TATACTAGCAATT-GTGGCGCTTATGGTAAAACGCCGCTAAAACATATT
66 TATACTAGC-ATTAGTGGCGCTTATGCTAAAACGCCGCTAAAGCATAAT
52832680 ATTAGCGGCGCGT
1 ATTAGCGGCGCGT
52832693 TGTGGGAAAC
Statistics
Matches: 193, Mismatches: 40, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
112 20 0.10
113 77 0.40
114 81 0.42
115 15 0.08
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (113 bp):
ATTAGCGGCGCGTATTGAAAAGCGCCGCAAAATATTAACCAAAACGAAGCGCTTTGGTCTTGATG
TATACTAGCATTAGTGGCGCTTATGCTAAAACGCCGCTAAAGCATAAT
Found at i:52832746 original size:16 final size:16
Alignment explanation
Indices: 52832712--52832769 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
52832702 CGCCACTAGA
52832712 TTATTATATAATGTAGT
1 TTATTATAT-ATGTAGT
*
52832729 TTATTATATATTTAGT
1 TTATTATATATGTAGT
52832745 TTATTATATATGTAGT
1 TTATTATATATGTAGT
52832761 TTATTATAT
1 TTATTATAT
52832770 TATATAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
16 30 0.77
17 9 0.23
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
TTATTATATATGTAGT
Found at i:52832781 original size:19 final size:19
Alignment explanation
Indices: 52832713--52832786 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 19
52832703 GCCACTAGAT
52832713 TATTATATAATG--TAGTT-
1 TATTATATAATGTTTA-TTA
*
52832730 TATTATATATTTAGTTTATTA
1 TATTATATA-AT-GTTTATTA
*
52832751 TA-TATGT-A-GTTTATTA
1 TATTATATAATGTTTATTA
52832767 TATTATATAATGTTTATTA
1 TATTATATAATGTTTATTA
52832786 T
1 T
52832787 TTTTGAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
16 10 0.22
17 13 0.29
18 2 0.04
19 10 0.22
20 6 0.13
21 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
TATTATATAATGTTTATTA
Found at i:52832782 original size:35 final size:33
Alignment explanation
Indices: 52832712--52832786 Score: 107
Period size: 32 Copynumber: 2.2 Consensus size: 33
52832702 CGCCACTAGA
*
52832712 TTATTATATAATGTAGTTTATTATATATTTAGT
1 TTATTATATAATGTAGTTTATTATATATTAAGT
52832745 TTATTATAT-ATGTAGTTTATTATATTATATAATGT
1 TTATTATATAATGTAGTTTATTATA-TAT-TAA-GT
52832780 TTATTAT
1 TTATTAT
52832787 TTTTGAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
32 15 0.39
33 12 0.32
34 2 0.05
35 9 0.24
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (33 bp):
TTATTATATAATGTAGTTTATTATATATTAAGT
Found at i:52841143 original size:21 final size:21
Alignment explanation
Indices: 52841117--52841187 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
52841107 CTACAACTTA
*
52841117 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
52841138 AAGCAGCGGTTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
52841159 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
52841180 AAGCAGAG
1 AAGCAGAG
52841188 TAGAGCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.32, C:0.18, G:0.45, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:52841718 original size:88 final size:85
Alignment explanation
Indices: 52841504--52841802 Score: 389
Period size: 83 Copynumber: 3.5 Consensus size: 85
52841494 GCGTTTTTGT
*
52841504 ATAAAAACAC-CGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA-AAAAAACGCCGCTAAAGACC
1 ATAAAAACGCTCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-ATAAAAAACGCCGCTAAAGACC
52841567 ATGTTCTTTAGCGGCGCTTAG
65 ATGTTCTTTAGCGGCGCTTAG
* * *
52841588 A-AAAAACGC-CGCTAAAG-TCCATGTTCTTTAGCAGCGCTTAATAAAAAACGCCTCTAAATACC
1 ATAAAAACGCTCGCTAAAGAT-CATGTTCTTTAGCGGCGCTTAATAAAAAACGCCGCTAAAGACC
*
52841650 ATGTTCTTTAGCGGCACTTA-
65 ATGTTCTTTAGCGGCGCTTAG
*
52841670 ATATTAAACGCCGCTCGCTAAAG-TCCATGTTCTTTAGCGGCGCTTAATAAAAAACGCCGCTAAA
1 ATA--AAA--ACGCTCGCTAAAGAT-CATGTTCTTTAGCGGCGCTTAATAAAAAACGCCGCTAAA
* *
52841734 GACCTTGTTCTTTAGAGGCGCTTAG
61 GACCATGTTCTTTAGCGGCGCTTAG
* *
52841759 ATAAAAACG-TCGTTAAAGATCATGTTCTTTAGCGGCGTTTAATA
1 ATAAAAACGCTCGCTAAAGATCATGTTCTTTAGCGGCGCTTAATA
52841803 TTAAGTGCCG
Statistics
Matches: 190, Mismatches: 15, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
82 3 0.02
83 73 0.38
84 32 0.17
85 6 0.03
87 6 0.03
88 67 0.35
89 3 0.02
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (85 bp):
ATAAAAACGCTCGCTAAAGATCATGTTCTTTAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCA
TGTTCTTTAGCGGCGCTTAG
Found at i:52841814 original size:130 final size:129
Alignment explanation
Indices: 52841506--52841806 Score: 366
Period size: 130 Copynumber: 2.4 Consensus size: 129
52841496 GTTTTTGTAT
* * * * **
52841506 AAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA-A--AAA-AACGC-CGCTAAAGAC
1 AAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCACTTA-ATATTAAACGCCGCTCGCTAAAGAC
*
52841566 CATGTTCTTTAGCGGCGCTTAGAAAAAACGCCGCTAAAGTCCATGTTCTTTAGCAGCGCTTAATA
65 CATGTTCTTTAGCGGCGCTTAGAAAAAACGCCGCTAAAGACCATGTTCTTTAGCAGCGCTTAATA
* *
52841631 AAAAACGCCTCTAAATACCATGTTCTTTAGCGGCACTTAATATTAAACGCCGCTCGCTAAAGTCC
1 AAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCACTTAATATTAAACGCCGCTCGCTAAAGACC
* *
52841696 ATGTTCTTTAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCTTGTTCTTTAG-AGGCGCTTAGA
66 ATGTTCTTTAGCGGCGCTT-AGAAAAAACGCCGCTAAAGACCATGTTCTTTAGCA-GCGCTTA-A
52841760 T-
128 TA
* * **
52841761 AAAAACGTCGT-TAAAGATCATGTTCTTTAGCGGCGTTTAATATTAA
1 AAAAACG-CCTCTAAAGACCATGTTCTTTAGCGGCACTTAATATTAA
52841807 GTGCCGCTAA
Statistics
Matches: 151, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
124 1 0.01
125 35 0.23
127 3 0.02
128 3 0.02
129 30 0.20
130 75 0.50
131 4 0.03
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (129 bp):
AAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCACTTAATATTAAACGCCGCTCGCTAAAGACC
ATGTTCTTTAGCGGCGCTTAGAAAAAACGCCGCTAAAGACCATGTTCTTTAGCAGCGCTTAATA
Found at i:52841819 original size:42 final size:42
Alignment explanation
Indices: 52841506--52841802 Score: 343
Period size: 42 Copynumber: 7.0 Consensus size: 42
52841496 GTTTTTGTAT
*
52841506 AAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA-A
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-ATA
* *
52841548 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT-AGA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAATA
*
52841589 AAAAACGCCGCTAAAG-TCCATGTTCTTTAGCAGCGCTTAATA
1 AAAAACGCCGCTAAAGAT-CATGTTCTTTAGCGGCGCTTAATA
* * * *
52841631 AAAAACGCCTCTAAATACCATGTTCTTTAGCGGCACTTAATA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAATA
**
52841673 TTAAACGCCGCTCGCTAAAG-TCCATGTTCTTTAGCGGCGCTTAATA
1 --AAA-AACGC-CGCTAAAGAT-CATGTTCTTTAGCGGCGCTTAATA
* * *
52841719 AAAAACGCCGCTAAAGACCTTGTTCTTTAGAGGCGCTTAGAT-
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-ATA
* * *
52841761 AAAAACGTCGTTAAAGATCATGTTCTTTAGCGGCGTTTAATA
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAATA
52841803 TTAAGTGCCG
Statistics
Matches: 216, Mismatches: 27, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
40 1 0.00
41 38 0.18
42 134 0.62
43 5 0.02
44 6 0.03
45 3 0.01
46 29 0.13
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAATA
Found at i:52841832 original size:42 final size:42
Alignment explanation
Indices: 52841513--52841882 Score: 138
Period size: 42 Copynumber: 8.7 Consensus size: 42
52841503 TATAAAAACA
* * * * ** *
52841513 CCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA-AAAAAACG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTA-ATATTAAGCG
* * * * * *
52841555 CCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGA-A-AAAACG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTA-ATATTAAGCG
** * * * * ** *
52841596 CCGCTAAAGTCCATGTTCTTTAGCAGCGCTTAATAAAAAACG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTAATATTAAGCG
* * * * * **
52841638 CCTCTAAATACCATGTTCTTTAGCGGCACTTAATATTAAACGCCG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTAATATT-AA-G-CG
** * * * ** *
52841683 CTCGCTAAAGTCCATGTTCTTTAGCGGCGCTTAATAAAAAACG
1 C-CGCTAAAGAACATGGTATTTAGCGGCGTTTAATATTAAGCG
* * * * * * * *
52841726 CCGCTAAAGACCTTGTTCTTTAGAGGCGCTTAGATA-AAAACG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTA-ATATTAAGCG
* * * * * *
52841768 TCGTTAAAGATCATGTTCTTTAGCGGCGTTTAATATTAAGTG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTAATATTAAGCG
* **
52841810 CCGCTAAAGAACATGGTATTTAGAGGCGTTTTTTATTAAGCG
1 CCGCTAAAGAACATGGTATTTAGCGGCGTTTAATATTAAGCG
*
52841852 CTGCTAAAGAACATGG-ACTTTAGCGGCGTTT
1 CCGCTAAAGAACATGGTA-TTTAGCGGCGTTT
52841883 TTTCTAAGCG
Statistics
Matches: 278, Mismatches: 41, Indels: 18
0.82 0.12 0.05
Matches are distributed among these distances:
40 1 0.00
41 41 0.15
42 193 0.69
43 8 0.03
45 5 0.02
46 30 0.11
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (42 bp):
CCGCTAAAGAACATGGTATTTAGCGGCGTTTAATATTAAGCG
Found at i:52841883 original size:42 final size:41
Alignment explanation
Indices: 52841785--52842022 Score: 183
Period size: 42 Copynumber: 5.4 Consensus size: 41
52841775 AGATCATGTT
* *
52841785 CTTTAGCGGCGTTTAATAT-TAAGTGCCGCTAAAGAACATGGTA
1 CTTTAGCGGCGTTT--TTTCTAAGCGCCGCTAAAGAACATGG-A
* * *
52841828 -TTTAGAGGCGTTTTTTATTAAGCGCTGCTAAAGAACATGGA
1 CTTTAGCGGCGTTTTTT-CTAAGCGCCGCTAAAGAACATGGA
* *
52841869 CTTTAGCGGCGTTTTTTCTAAGCGCTGCTACTAAGAGCCACTGAAGAACATGGC
1 CTTTAGCGGCGTTTTTTCTAA--GC-GC--C-----G---CTAAAGAACATGGA
* *
52841923 CTTTAGCGGCGCTTATTTCTAAGCGCCGCTAAAGAACATGGC
1 CTTTAGCGGCG-TTTTTTCTAAGCGCCGCTAAAGAACATGGA
* * *
52841965 CTTTAGCGGCGCTTATTTCTAAGCGCCGCTAAAGAATATGGT
1 CTTTAGCGGCG-TTTTTTCTAAGCGCCGCTAAAGAACATGGA
52842007 CTTTAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
52842023 GTTTGTAAAC
Statistics
Matches: 164, Mismatches: 14, Indels: 36
0.77 0.07 0.17
Matches are distributed among these distances:
40 2 0.01
41 8 0.05
42 111 0.68
43 2 0.01
44 2 0.01
45 1 0.01
50 1 0.01
51 1 0.01
52 2 0.01
53 2 0.01
54 23 0.14
55 9 0.05
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTTCTAAGCGCCGCTAAAGAACATGGA
Found at i:52845391 original size:40 final size:40
Alignment explanation
Indices: 52845347--52845576 Score: 318
Period size: 40 Copynumber: 5.8 Consensus size: 40
52845337 AGCATGATTA
* * * * *
52845347 CTCTTTGGGACCTAGCCTGGATATAACACCAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* * *
52845387 CTCTTCGAGG-TTTAGCACGGATATATTACTAGCACGAATG
1 CTCTTCG-GGACTTAGCCCGGATATATCACTAGCACGAATG
* * *
52845427 CTCTTCGGAACTTAGCCCAGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* *
52845467 CTCCTCGGGACTTAGCCCGGATATATCACTAGCACAAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
52845507 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
*
52845547 CTCCTCGGGACTTAGCCCGGATATATCACT
1 CTCTTCGGGACTTAGCCCGGATATATCACT
52845577 CTCAATTCTC
Statistics
Matches: 166, Mismatches: 22, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
39 1 0.01
40 163 0.98
41 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
Found at i:52846840 original size:37 final size:37
Alignment explanation
Indices: 52846790--52846868 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
52846780 TTATTACGAA
* * *
52846790 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
* *
52846827 GTCTTACCCGGACAAAATCCCCACGCGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
52846864 GTCTT
1 GTCTT
52846869 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:52847112 original size:49 final size:49
Alignment explanation
Indices: 52846987--52847496 Score: 865
Period size: 49 Copynumber: 10.6 Consensus size: 49
52846977 CCCTTTGGGA
* * * * *
52846987 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
52847034 CCTGT--CAGATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52847081 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52847130 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52847177 CTTATCATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52847226 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52847275 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52847324 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52847373 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52847422 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52847471 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
52847497 CACAATTATC
Statistics
Matches: 440, Mismatches: 17, Indels: 12
0.94 0.04 0.03
Matches are distributed among these distances:
45 2 0.00
46 1 0.00
47 89 0.20
49 348 0.79
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52850054 original size:40 final size:40
Alignment explanation
Indices: 52849997--52850095 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
52849987 GGGGTGTCAC
* *
52849997 ATATATGGCACTCAGTGTGCGATTCAAG-AAAACTTCGACT
1 ATATTTGGCACTTAGTGTGCGATTC-AGCAAAACTTCGACT
* * * *
52850037 ATATTTGGCACTTAGTGTGCGATTCGGCATAGCTTCGGCT
1 ATATTTGGCACTTAGTGTGCGATTCAGCAAAACTTCGACT
52850077 ATATTTGGCACTTAGTGTG
1 ATATTTGGCACTTAGTGTG
52850096 TGAGACTGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.02
40 51 0.98
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (40 bp):
ATATTTGGCACTTAGTGTGCGATTCAGCAAAACTTCGACT
Found at i:52850131 original size:41 final size:41
Alignment explanation
Indices: 52850065--52850163 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
52850055 GCGATTCGGC
* ** * * * *
52850065 ATAGCTTCGGCTATATTTGGCACTTAGTGTGTGAGACTGA-G
1 ATAGCTTCGGCTATGTAAGGAACTTAGTGTGAGA-AATGATA
*
52850106 ATAGCTTCGGCTATGTAAGGAACTTAGTGTGAGAAATTATA
1 ATAGCTTCGGCTATGTAAGGAACTTAGTGTGAGAAATGATA
52850147 ATAGCTTCGGCTATGTA
1 ATAGCTTCGGCTATGTA
52850164 TCGGCCTTAG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 3 0.06
41 46 0.94
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.33
Consensus pattern (41 bp):
ATAGCTTCGGCTATGTAAGGAACTTAGTGTGAGAAATGATA
Found at i:52852864 original size:40 final size:40
Alignment explanation
Indices: 52852820--52853047 Score: 366
Period size: 40 Copynumber: 5.7 Consensus size: 40
52852810 GCAAACACAT
* *
52852820 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
52852860 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
*
52852900 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
* * * *
52852940 TTGCCTTCGGGTCATAGCCCGGACATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
* * *
52852980 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
52853020 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
52853048 TCCAATGCTC
Statistics
Matches: 179, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 179 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
Found at i:52860381 original size:12 final size:12
Alignment explanation
Indices: 52860364--52860390 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52860354 GGGTACGGGT
52860364 AAGGGGTGTTAC
1 AAGGGGTGTTAC
52860376 AAGGGGTGTTAC
1 AAGGGGTGTTAC
52860388 AAG
1 AAG
52860391 CATTAACGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.41, T:0.22
Consensus pattern (12 bp):
AAGGGGTGTTAC
Found at i:52867063 original size:27 final size:28
Alignment explanation
Indices: 52867033--52867132 Score: 109
Period size: 27 Copynumber: 3.7 Consensus size: 28
52867023 TTTAGTTTAC
52867033 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
52867060 TAAAAATACTGAAATACCC-TCGATTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
52867087 TAAAATTACTGAAATA-CCTTCGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
52867114 TAAAATTACC-AAAGTACCC
1 TAAAATTACCGAAA-TACCC
52867133 CCGATTTACA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
26 7 0.11
27 54 0.86
28 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:52867115 original size:54 final size:54
Alignment explanation
Indices: 52867028--52867151 Score: 135
Period size: 54 Copynumber: 2.3 Consensus size: 54
52867018 AATACTTTAG
* * *
52867028 TTTACTAAAATTACCGAAATACCCTTAGTTTGTAAAAATACTGAAA-TACCCTCGA
1 TTTA-TAAAATTACCGAAATACCCTTAGCTTGTAAAAATAC-CAAAGTACCCCCGA
* * * *
52867083 TTTGTAAAATTACTGAAATA-CCTTCGACTTGTAAAATTACCAAAGTACCCCCGA
1 TTTATAAAATTACCGAAATACCCTTAG-CTTGTAAAAATACCAAAGTACCCCCGA
*
52867137 TTTACAAAATTACCG
1 TTTATAAAATTACCG
52867152 TTTTACCCCC
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
53 8 0.14
54 46 0.81
55 3 0.05
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (54 bp):
TTTATAAAATTACCGAAATACCCTTAGCTTGTAAAAATACCAAAGTACCCCCGA
Found at i:52867145 original size:27 final size:27
Alignment explanation
Indices: 52867115--52867177 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
52867105 TTCGACTTGT
52867115 AAAATTACCAAAGTACCCCCGATTTAC
1 AAAATTACCAAAGTACCCCCGATTTAC
****
52867142 AAAATTACCGTTTTACCCCCGATTTAC
1 AAAATTACCAAAGTACCCCCGATTTAC
*
52867169 ATAATTACC
1 AAAATTACC
52867178 GTTTTACCCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.29
Consensus pattern (27 bp):
AAAATTACCAAAGTACCCCCGATTTAC
Found at i:52867159 original size:81 final size:80
Alignment explanation
Indices: 52867074--52867473 Score: 230
Period size: 81 Copynumber: 4.9 Consensus size: 80
52867064 AATACTGAAA
* * * *
52867074 TACCCTCGATTTGTAAAATTACTGAAATACCTTCGACTTGTAAAATTACCAAAGTACCCCCGATT
1 TACCCTCGATTTATAAAATTACCGAAATACC-TCGATTTGTAAAATTACCAAAATACCCCCGATT
52867139 TACAAAATTACCGTTT
65 TACAAAATTACCGTTT
* * * *** * * * * **** * *
52867155 TACCCCCGATTTACATAATTACCGTTTTACCCCCAATT-TACATAATTATCGTTTTACCCTCGAC
1 TACCCTCGATTTATAAAATTACCGAAATACCTCGATTTGTA-A-AATTACCAAAATACCCCCGAT
52867219 TTACAAAATTACCGTTT
64 TTACAAAATTACCGTTT
* *** * * ***** **
52867236 TACCCTCGATTTACT-GAATTACCGTTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGAT
1 TACCCTCGATTTA-TAAAATTACCGAAATA-CCTCGATTTGTAAAATTACCAAAATACCCCCGAT
*
52867300 TTACAAAATTACTGTTT
64 TTACAAAATTACCGTTT
* ** * * *
52867317 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATA-CCCCTAGT
1 TACCCTCGATTTATAAAATTACCGAAATA-CCTCGATTTGTAAAATTACCAAAATACCCCCGA-T
** ****
52867381 TTGTAAAATTACCAAAA
64 TTACAAAATTACCGTTT
* * * * * *
52867398 TACCCTTGGTTTGTGAAATTACCGAAATACACTCAATTTGTAAAATTACCAAAATACCCCTGATT
1 TACCCTCGATTTATAAAATTACCGAAATAC-CTCGATTTGTAAAATTACCAAAATACCCCCGATT
*
52867463 TACAAAGTTAC
65 TACAAAATTAC
52867474 AGAAATACCC
Statistics
Matches: 239, Mismatches: 71, Indels: 18
0.73 0.22 0.05
Matches are distributed among these distances:
79 2 0.01
80 9 0.04
81 216 0.90
82 10 0.04
83 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (80 bp):
TACCCTCGATTTATAAAATTACCGAAATACCTCGATTTGTAAAATTACCAAAATACCCCCGATTT
ACAAAATTACCGTTT
Found at i:52867339 original size:27 final size:27
Alignment explanation
Indices: 52867128--52867338 Score: 287
Period size: 27 Copynumber: 7.8 Consensus size: 27
52867118 ATTACCAAAG
*
52867128 TACCCCCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
* *
52867155 TACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
* * * *
52867182 TACCCCCAATTTACATAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
*
52867209 TACCCTCGACTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
**
52867236 TACCCTCGATTTACTGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
* * *
52867263 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
* *
52867290 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
52867317 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAAAATTAC
52867339 TAAAATACCC
Statistics
Matches: 166, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 166 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCGTTT
Found at i:52867351 original size:54 final size:54
Alignment explanation
Indices: 52867074--52867338 Score: 226
Period size: 54 Copynumber: 4.9 Consensus size: 54
52867064 AATACTGAAA
** *** * * ** * *
52867074 TACCCTCGATTTGTAAAATTACTGAAATACCTTCGACTTGTAAAATTACCAAAG
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTACCGAAT
* * * * **
52867128 TACCCCCGATTTACAAAATTACCGTTTTACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTACCGAAT
* * * * **
52867182 TACCCCCAATTTACATAATTA-TCGTTTTACCCTCGACTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACT-GTTTTACCCTCGATTTACAAAATTACCGAAT
** * * * * **
52867236 TACCCTCGATTTACTGAATTACCGTTTTACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTACCGAAT
*
52867290 TACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTAC
52867339 TAAAATACCC
Statistics
Matches: 171, Mismatches: 38, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
54 171 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTACCGAAT
Found at i:52867362 original size:54 final size:54
Alignment explanation
Indices: 52867252--52867456 Score: 169
Period size: 54 Copynumber: 3.8 Consensus size: 54
52867242 CGATTTACTG
* **** * **
52867252 AATTACCGTTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAA
1 AATTACCGTTTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGTAA
* *
52867306 AATTACTGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAA
1 AATTACCGTTTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGTAA
**** * * * *
52867360 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTGA
1 AATTACCGTTTTACCCTCGA-TTTATAAAATTACTAAAATACCCTTGGTTTGTAA
*** * * * *
52867414 AATTACCGAAATACACTCAATTTGTAAAATTACCAAAATACCC
1 AATTACCGTTTTACCCTCGATTTATAAAATTACTAAAATACCC
52867457 CTGATTTACA
Statistics
Matches: 126, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
53 2 0.02
54 122 0.97
55 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (54 bp):
AATTACCGTTTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGTAA
Found at i:52867543 original size:27 final size:27
Alignment explanation
Indices: 52867290--52867546 Score: 154
Period size: 27 Copynumber: 9.4 Consensus size: 27
52867280 ATTACTGTTT
* * ***
52867290 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTTGGTTTACAAAATTACCGAAA
* * **
52867317 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGGTTTACAAAATTACCGAAA
** *
52867344 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCGAAA
* * ** *
52867371 TACCCCTAGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCGAAA
***
52867398 TACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCTTGGTTTACAAAATTACCGAAA
* *** ** *
52867425 TACACTCAATTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCGAAA
* * * *
52867452 TACCCCTGATTTACAAAGTTACAGAAA
1 TACCCTTGGTTTACAAAATTACCGAAA
* * **
52867479 TACCCTTGACTTTATAAAAATTATAGAAA
1 TACCCTTG-GTTTA-CAAAATTACCGAAA
* *
52867508 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGGTTTACAAAATTACCGAAA
*
52867535 TACCTTTGGTTT
1 TACCCTTGGTTT
52867547 GTAGATTTAC
Statistics
Matches: 186, Mismatches: 42, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
27 160 0.86
28 8 0.04
29 18 0.10
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (27 bp):
TACCCTTGGTTTACAAAATTACCGAAA
Found at i:52867638 original size:27 final size:26
Alignment explanation
Indices: 52867577--52867664 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 26
52867567 TTGTAGGATG
* * *
52867577 AAATGACTAAAATACCCCTATGAGGTT
1 AAATGACCATAATACCCCTAT-AGGGT
* *
52867604 AAAAGACCGTAA-AGCCCCTATAGGGT
1 AAATGACCATAATA-CCCCTATAGGGT
* *
52867630 AAAGTGACCATAATACCCCTGTATGGT
1 AAA-TGACCATAATACCCCTATAGGGT
52867657 AAAATGAC
1 -AAATGAC
52867665 GAATATGCCC
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
26 8 0.17
27 36 0.75
28 4 0.08
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (26 bp):
AAATGACCATAATACCCCTATAGGGT
Found at i:52868468 original size:26 final size:26
Alignment explanation
Indices: 52868439--52868588 Score: 230
Period size: 26 Copynumber: 5.8 Consensus size: 26
52868429 GATGAAGTGC
*
52868439 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
* *
52868465 AAAAGGGCTTATGCCGCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
52868491 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
52868517 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
52868543 AAAAGGGTTTATGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
52868569 AAAAGGG-TTTTGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
52868589 ACTAAAGAGG
Statistics
Matches: 113, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
25 12 0.11
26 101 0.89
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACTG
Found at i:52868517 original size:52 final size:52
Alignment explanation
Indices: 52868439--52868588 Score: 257
Period size: 52 Copynumber: 2.9 Consensus size: 52
52868429 GATGAAGTGC
*
52868439 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCGCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
52868491 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* * *
52868543 AAAAGGGTTTATGCCCCAGTTTACTGAAAAGGG-TTTTGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTT
52868589 ACTAAAGAGG
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 12 0.13
52 82 0.87
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:52868792 original size:42 final size:42
Alignment explanation
Indices: 52868733--52868824 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
52868723 TAGTCTCCCC
* ** *
52868733 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
*
52868775 AAATGGGTTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
52868817 AAATGGGC
1 AAATGGGC
52868825 CTATAGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:52868885 original size:31 final size:31
Alignment explanation
Indices: 52868847--52868925 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
52868837 CCGTTACAGT
*
52868847 AAAGGCTTCAGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
* *
52868878 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
52868909 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
52868926 AATCGTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATGATTTATGA
Found at i:52871118 original size:46 final size:46
Alignment explanation
Indices: 52871012--52871284 Score: 334
Period size: 46 Copynumber: 5.8 Consensus size: 46
52871002 TTTGACATGA
* * * *
52871012 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTC-T--T-ATTCA-TTTCATGTCACGT
*
52871062 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
*
52871108 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
** * *
52871154 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA-GATTAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATG-TCACGT
** * *
52871200 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
**
52871246 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
52871285 ATCAGAGAGC
Statistics
Matches: 206, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
45 4 0.02
46 177 0.86
47 1 0.00
49 1 0.00
50 23 0.11
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
Found at i:52871285 original size:46 final size:46
Alignment explanation
Indices: 52871060--52871289 Score: 370
Period size: 46 Copynumber: 5.0 Consensus size: 46
52871050 TTTCTGTCAT
** * * *
52871060 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
** *
52871106 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
* *
52871152 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAGATTAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
52871198 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
52871244 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
52871290 AGAGCACACT
Statistics
Matches: 175, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 175 1.00
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39
Consensus pattern (46 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
Found at i:52878601 original size:101 final size:101
Alignment explanation
Indices: 52878474--52878694 Score: 304
Period size: 101 Copynumber: 2.2 Consensus size: 101
52878464 AAACGGGGTT
* * * *
52878474 TTACTTGCACA-CATATATCGGAATCACAT-TTCGATGCCAACGTATAAAATGTGGACTTATTCA
1 TTACTCGCACATCATATATCAGAATCACATATT-GATGCCAACGTATAAAACGTGGACTTACTCA
*
52878537 CACACATATATCA-GAATCACATATCGATTCCATGGTC
65 CACACATATA-CAGGAATCACACATCGATTCCATGGTC
* * * *
52878574 TTACTCGCACATCACATATCAGAATCACATATTGATGCCAACGTATTAAACGTGGTCTTACTCGC
1 TTACTCGCACATCATATATCAGAATCACATATTGATGCCAACGTATAAAACGTGGACTTACTCAC
* *
52878639 GCACATGTACAGGAATCACACATCGATTCCATGGTC
66 ACACATATACAGGAATCACACATCGATTCCATGGTC
52878675 TTACTCGCACATCATATATC
1 TTACTCGCACATCATATATC
52878695 GAAATTCACA
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
100 12 0.11
101 92 0.87
102 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (101 bp):
TTACTCGCACATCATATATCAGAATCACATATTGATGCCAACGTATAAAACGTGGACTTACTCAC
ACACATATACAGGAATCACACATCGATTCCATGGTC
Found at i:52879259 original size:20 final size:20
Alignment explanation
Indices: 52879234--52879275 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
52879224 ATTTTCATTC
52879234 AACTTAGTCCAAAAACACAT
1 AACTTAGTCCAAAAACACAT
52879254 AACTTAGTCCAAAAACACAT
1 AACTTAGTCCAAAAACACAT
52879274 AA
1 AA
52879276 ATGGGCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.24, G:0.05, T:0.19
Consensus pattern (20 bp):
AACTTAGTCCAAAAACACAT
Found at i:52888280 original size:94 final size:94
Alignment explanation
Indices: 52888119--52888306 Score: 376
Period size: 94 Copynumber: 2.0 Consensus size: 94
52888109 CATACATATT
52888119 TAAGTATATTAAGAGTTTACTTCGGGTTATACGAACTTACCTGGTAATTGCTTCAATTTTGTATT
1 TAAGTATATTAAGAGTTTACTTCGGGTTATACGAACTTACCTGGTAATTGCTTCAATTTTGTATT
52888184 TCGGTTATTCCGAAACCTTTTGTTTTCCA
66 TCGGTTATTCCGAAACCTTTTGTTTTCCA
52888213 TAAGTATATTAAGAGTTTACTTCGGGTTATACGAACTTACCTGGTAATTGCTTCAATTTTGTATT
1 TAAGTATATTAAGAGTTTACTTCGGGTTATACGAACTTACCTGGTAATTGCTTCAATTTTGTATT
52888278 TCGGTTATTCCGAAACCTTTTGTTTTCCA
66 TCGGTTATTCCGAAACCTTTTGTTTTCCA
52888307 CGATCGACCT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (94 bp):
TAAGTATATTAAGAGTTTACTTCGGGTTATACGAACTTACCTGGTAATTGCTTCAATTTTGTATT
TCGGTTATTCCGAAACCTTTTGTTTTCCA
Found at i:52889571 original size:12 final size:12
Alignment explanation
Indices: 52889554--52889583 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
52889544 AAATATTGCA
52889554 AAATTATTTCAC
1 AAATTATTTCAC
52889566 AAATTATTTCAC
1 AAATTATTTCAC
52889578 AAATTA
1 AAATTA
52889584 AATGAGGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTATTTCAC
Found at i:52896652 original size:13 final size:13
Alignment explanation
Indices: 52896634--52896658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52896624 GGCGCATTCG
52896634 TAGTTAATTTAGC
1 TAGTTAATTTAGC
52896647 TAGTTAATTTAG
1 TAGTTAATTTAG
52896659 TTTTAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (13 bp):
TAGTTAATTTAGC
Found at i:52899938 original size:29 final size:28
Alignment explanation
Indices: 52899887--52899969 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 28
52899877 TTAATAAAAT
** *
52899887 AATTTTAAAAATTTAACATAAATTTTAA
1 AATTTTAAAAATAAAAAATAAATTTTAA
*
52899915 AATTTTAAAAATAAAAAATTAAATTCTTCA
1 AATTTTAAAAATAAAAAA-TAAATT-TTAA
52899945 AA--TTAAAAATATAAAAACTAAATTT
1 AATTTTAAAAATA-AAAAA-TAAATTT
52899970 CCAATCTCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
28 25 0.53
29 17 0.36
30 5 0.11
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (28 bp):
AATTTTAAAAATAAAAAATAAATTTTAA
Found at i:52900089 original size:22 final size:22
Alignment explanation
Indices: 52900064--52900110 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
52900054 AGATAGAAGC
*
52900064 TAGAAGTAGCATGAGAACAGCT
1 TAGAAGTAGCATGAGAACAACT
*
52900086 TAGAAGTAGCGTGAGAACAACT
1 TAGAAGTAGCATGAGAACAACT
52900108 TAG
1 TAG
52900111 CTCATAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (22 bp):
TAGAAGTAGCATGAGAACAACT
Found at i:52901518 original size:27 final size:27
Alignment explanation
Indices: 52901460--52901529 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 27
52901450 AGTAGAAGGC
*
52901460 TTATAAATA-AAAAATTAATAACTTTA
1 TTATAAATATAAAAATTAATAACTTAA
52901486 TT-TAAATATAATTAAA-TAATAA-TTAA
1 TTATAAATATAA--AAATTAATAACTTAA
*
52901512 TTATAAA-ATAAATATTAA
1 TTATAAATATAAAAATTAA
52901530 AGACCCTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
24 2 0.05
25 9 0.24
26 13 0.35
27 10 0.27
28 3 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (27 bp):
TTATAAATATAAAAATTAATAACTTAA
Found at i:52902646 original size:73 final size:73
Alignment explanation
Indices: 52902555--52902700 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
52902545 CAACAATGGG
52902555 CAAGTCTAGGAAGAATAAAAGTATTGGTAATTGGAGAATTTACAATATATACTATATAGACACAT
1 CAAGTCTAGGAAGAATAAAAGTATTGGTAATTGGAGAATTTACAATATATACTATATAGACACAT
52902620 GATTTTTT
66 GATTTTTT
52902628 CAAGTCTAGGAAGAATAAAAGTATTGGTAATTGGAGAATTTACAATATATACTATATAGACACAT
1 CAAGTCTAGGAAGAATAAAAGTATTGGTAATTGGAGAATTTACAATATATACTATATAGACACAT
52902693 GATTTTTT
66 GATTTTTT
52902701 TAAAATGTAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.34
Consensus pattern (73 bp):
CAAGTCTAGGAAGAATAAAAGTATTGGTAATTGGAGAATTTACAATATATACTATATAGACACAT
GATTTTTT
Found at i:52902801 original size:10 final size:10
Alignment explanation
Indices: 52902786--52902812 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
52902776 ATGCTTGTTC
52902786 AAGCTCGGTT
1 AAGCTCGGTT
52902796 AAGCTCGGTT
1 AAGCTCGGTT
52902806 AAGCTCG
1 AAGCTCG
52902813 TACTTTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (10 bp):
AAGCTCGGTT
Found at i:52907196 original size:40 final size:40
Alignment explanation
Indices: 52907141--52907241 Score: 166
Period size: 40 Copynumber: 2.5 Consensus size: 40
52907131 GTGGCTCGGA
* * *
52907141 TATAACAACCAGCACGAATGCCTTCAGGACTTAACCTGGT
1 TATAATAACCCGCACGAATGCCTTCAGGACTTAACCCGGT
*
52907181 TATAATAACCCGCACGAATGCCTTCGGGACTTAACCCGGT
1 TATAATAACCCGCACGAATGCCTTCAGGACTTAACCCGGT
52907221 TATAATAACCCGCACGAATGC
1 TATAATAACCCGCACGAATGC
52907242 TATGCACATA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (40 bp):
TATAATAACCCGCACGAATGCCTTCAGGACTTAACCCGGT
Found at i:52914539 original size:37 final size:37
Alignment explanation
Indices: 52914489--52914562 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
52914479 TGATCATTTC
52914489 TTGCATGGACCCTACCACGGAAGAATCAAAAAATGGG
1 TTGCATGGACCCTACCACGGAAGAATCAAAAAATGGG
*
52914526 TTGCATGGACCCTACCGCGGAAGAATCAAAAAATGGG
1 TTGCATGGACCCTACCACGGAAGAATCAAAAAATGGG
52914563 GTTCTCCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (37 bp):
TTGCATGGACCCTACCACGGAAGAATCAAAAAATGGG
Found at i:52918153 original size:38 final size:38
Alignment explanation
Indices: 52918075--52918166 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 38
52918065 CTCACTTCTA
* * * *
52918075 GTGAATTGTGATTTTCGTTTTAACCCATTACTACTGGG
1 GTGAATTGTGATTTTCGTTCTAACCCACTACCACTAGG
* * **
52918113 GTGAATTGTGATTTTTGTTCTGACCCACTACCGTTAGG
1 GTGAATTGTGATTTTCGTTCTAACCCACTACCACTAGG
*
52918151 GTGAATTGTGGTTTTC
1 GTGAATTGTGATTTTC
52918167 AACTTTTGCC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.42
Consensus pattern (38 bp):
GTGAATTGTGATTTTCGTTCTAACCCACTACCACTAGG
Found at i:52921139 original size:21 final size:20
Alignment explanation
Indices: 52921105--52921158 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
52921095 TGCATTTAAA
*
52921105 CTTTTTAAAGTTTAATCATT
1 CTTTTTAAATTTTAATCATT
* *
52921125 CTTTTTAAAATTTTAGTTATT
1 CTTTTT-AAATTTTAATCATT
52921146 C-TTTTAAATTTTA
1 CTTTTTAAATTTTA
52921159 TGTTAAACGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.27
20 10 0.33
21 12 0.40
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (20 bp):
CTTTTTAAATTTTAATCATT
Found at i:52921156 original size:19 final size:20
Alignment explanation
Indices: 52921105--52921163 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
52921095 TGCATTTAAA
* * *
52921105 CTTTTTAAAGTTTAATCATT
1 CTTTTTAAATTTTAGTTATT
52921125 CTTTTTAAAATTTTAGTTATT
1 CTTTTT-AAATTTTAGTTATT
52921146 C-TTTTAAATTTTATGTTA
1 CTTTTTAAATTTTA-GTTA
52921164 AACGTTATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.24
20 14 0.41
21 12 0.35
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (20 bp):
CTTTTTAAATTTTAGTTATT
Found at i:52923354 original size:23 final size:23
Alignment explanation
Indices: 52923334--52923375 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
52923324 CCATTAAACT
52923334 AAAAAT-AA-AATAAAATTTAAA
1 AAAAATCAACAATAAAATTTAAA
52923355 AAAAATCAACAATAAAATTTA
1 AAAAATCAACAATAAAATTTA
52923376 TATAAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAAATCAACAATAAAATTTAAA
Found at i:52931174 original size:11 final size:11
Alignment explanation
Indices: 52931147--52931176 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
52931137 AGATACGGTC
52931147 AACGGGTAAAA
1 AACGGGTAAAA
52931158 ATACGGGTAAAA
1 A-ACGGGTAAAA
52931170 AACGGGT
1 AACGGGT
52931177 CGCGTTTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.47, C:0.10, G:0.30, T:0.13
Consensus pattern (11 bp):
AACGGGTAAAA
Found at i:52931609 original size:7 final size:7
Alignment explanation
Indices: 52931597--52931622 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52931587 ATTTTTTTTG
52931597 TTATTAA
1 TTATTAA
52931604 TTATTAA
1 TTATTAA
52931611 TTATTAA
1 TTATTAA
52931618 TTATT
1 TTATT
52931623 TATGTTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTATTAA
Found at i:52949365 original size:33 final size:32
Alignment explanation
Indices: 52949317--52949380 Score: 119
Period size: 33 Copynumber: 2.0 Consensus size: 32
52949307 NNNNNNNNCT
52949317 AACCCTAACCTAATTTAATTAAAAACCCTAAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAAA
52949349 AACCCTAATCCTAATTTAATTAAAAACCCTAA
1 AACCCTAA-CCTAATTTAATTAAAAACCCTAA
52949381 CCTAAACCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.26
33 23 0.74
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (32 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAAA
Found at i:52949374 original size:24 final size:23
Alignment explanation
Indices: 52949345--52949467 Score: 93
Period size: 23 Copynumber: 5.0 Consensus size: 23
52949335 TTAAAAACCC
52949345 TAAAAACCCTAATCCTAATTTAAT
1 TAAAAACCCTAA-CCTAATTTAAT
**
52949369 TAAAAACCCTAACCTAAACCCTAAT
1 TAAAAACCCTAACCT-AA-TTTAAT
52949394 TAAATACCCTAACCCTAACCTAATTTAAT
1 T-AA-A----AACCCTAACCTAATTTAAT
* * * *
52949423 TCAAAACCTTAACCTAAATTATT
1 TAAAAACCCTAACCTAATTTAAT
* *
52949446 TAAAAACCCTAAACTAAGTTAA
1 TAAAAACCCTAACCTAATTTAA
52949468 CAATGTTACA
Statistics
Matches: 78, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
23 36 0.46
24 14 0.18
25 5 0.06
26 2 0.03
27 2 0.03
28 1 0.01
29 5 0.06
30 2 0.03
31 11 0.14
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.28
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:52949385 original size:38 final size:31
Alignment explanation
Indices: 52949317--52949430 Score: 111
Period size: 33 Copynumber: 3.9 Consensus size: 31
52949307 NNNNNNNNCT
52949317 AACCCTAA-CCTAATTTAATTAAAAACCCTAAA
1 AACCCTAATCCTAATTTAATTAAAAACCCT--A
52949349 AACCCTAATCCTAATTTAATTAAAAACCCT-
1 AACCCTAATCCTAATTTAATTAAAAACCCTA
* * *
52949379 AA-CCTAAACC----CTAATTAAATACCCT-
1 AACCCTAATCCTAATTTAATTAAAAACCCTA
*
52949404 AACCCTAA-CCTAATTTAATTCAAAACC
1 AACCCTAATCCTAATTTAATTAAAAACC
52949431 TTAACCTAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
25 17 0.24
26 5 0.07
29 17 0.24
30 2 0.03
32 8 0.11
33 21 0.30
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (31 bp):
AACCCTAATCCTAATTTAATTAAAAACCCTA
Found at i:52949413 original size:25 final size:24
Alignment explanation
Indices: 52949345--52949462 Score: 80
Period size: 24 Copynumber: 4.7 Consensus size: 24
52949335 TTAAAAACCC
**
52949345 TAAAAACCCTAATCCT-AATTTAAT
1 TAAAAACCCTAA-CCTAAACCTAAT
52949369 TAAAAACCCTAACCTAAACCCTAAT
1 TAAAAACCCTAACCTAAA-CCTAAT
*
52949394 TAAATACCCTAACCCT-AACCTAATT
1 TAAAAACCCTAA-CCTAAACCTAA-T
* * *
52949419 TAATTCAAAACCTTAACCTAAA-TTATT
1 T-A---AAAACCCTAACCTAAACCTAAT
*
52949446 TAAAAACCCTAAACTAA
1 TAAAAACCCTAACCTAA
52949463 GTTAACAATG
Statistics
Matches: 76, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
23 16 0.21
24 19 0.25
25 19 0.25
26 5 0.07
27 2 0.03
28 5 0.07
29 10 0.13
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (24 bp):
TAAAAACCCTAACCTAAACCTAAT
Found at i:52949620 original size:116 final size:116
Alignment explanation
Indices: 52949464--52949688 Score: 337
Period size: 116 Copynumber: 1.9 Consensus size: 116
52949454 CTAAACTAAG
**
52949464 TTAACAATGTTACATTCATGTAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAACAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
* *
52949529 T-AATTT-TACATAATTTGATAGTTTTACTAACCATTAACACAATTTGTTGAC
66 TAAATTTATAC-T-ATTTGATAATTTTACTAACAATTAACACAATTTGTTGAC
* * *
52949580 TTAATAATTTTACATTCACATAATGTTAGATTTGGTAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAACAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
* *
52949645 TAAATTTATACTATTTGATAATTTTAGTAACAATTAATACAATT
66 TAAATTTATACTATTTGATAATTTTACTAACAATTAACACAATT
52949689 ATCAATTAAT
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
116 89 0.91
117 6 0.06
118 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (116 bp):
TTAACAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
TAAATTTATACTATTTGATAATTTTACTAACAATTAACACAATTTGTTGAC
Found at i:52953011 original size:126 final size:125
Alignment explanation
Indices: 52952716--52953068 Score: 526
Period size: 126 Copynumber: 2.8 Consensus size: 125
52952706 CCCAAACATG
* * *
52952716 CTACTGTAGCAAAATCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTAC
* * * * *** *
52952781 TAGAAGTGATTTTACACTATTTGCTTAGAAACATCAACTCAAAATTATTTTTTCCGGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCGGGAC
* *
52952841 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATATCACAAATTTTTCTCAAATAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTAC
* * *
52952906 TACAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTCCGGGAC
* *
52952967 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGGGATTTCATAAATTCTTCTCAAATAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTAC
*
52953032 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
52953069 CTCGAAATTA
Statistics
Matches: 204, Mismatches: 23, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
125 93 0.46
126 111 0.54
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTAC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCGGGAC
Found at i:52955836 original size:39 final size:39
Alignment explanation
Indices: 52955782--52955861 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
52955772 GTATAATTTA
52955782 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
1 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
*
52955821 GAACTTTTGTTTGCATTCCTCATCCTTATCTTAGCTTTG
1 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
52955860 GA
1 GA
52955862 CTTCTCATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (39 bp):
GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
Found at i:52957351 original size:16 final size:16
Alignment explanation
Indices: 52957330--52957361 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52957320 GCGAGGAATG
52957330 GCTTAGTAGGAGCCTA
1 GCTTAGTAGGAGCCTA
*
52957346 GCTTAGTAGGTGCCTA
1 GCTTAGTAGGAGCCTA
52957362 AATAGGTACC
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:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (16 bp):
GCTTAGTAGGAGCCTA
Found at i:52957812 original size:22 final size:22
Alignment explanation
Indices: 52957787--52957833 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
52957777 TCAGCTCTAT
* *
52957787 CTTCCTTTCCATATCTCTTAAC
1 CTTCCTTTACATATCTCTCAAC
*
52957809 CTTCCTTTATATATCTCTCAAC
1 CTTCCTTTACATATCTCTCAAC
52957831 CTT
1 CTT
52957834 GGCTCTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.19, C:0.34, G:0.00, T:0.47
Consensus pattern (22 bp):
CTTCCTTTACATATCTCTCAAC
Found at i:52962085 original size:62 final size:62
Alignment explanation
Indices: 52961988--52962110 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
52961978 CAATCGAAAA
*
52961988 TTGGATGGTTGGGAAACAAGGGGTTTTCTCTTTCTTTCT-TTCTGCTATATTTGGAGGAATTC
1 TTGGATGGTTGGGAAACAAGGGGTCTTCTCTTTCTTTCTCTT-TGCTATATTTGGAGGAATTC
*
52962050 TTGGATGGTTGGGAAAGAAGGGGTCTTCTCTTTCTTTCTCTTTGCTATATTTGGAGGAATT
1 TTGGATGGTTGGGAAACAAGGGGTCTTCTCTTTCTTTCTCTTTGCTATATTTGGAGGAATT
52962111 TTTGTTTTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
62 56 0.97
63 2 0.03
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.43
Consensus pattern (62 bp):
TTGGATGGTTGGGAAACAAGGGGTCTTCTCTTTCTTTCTCTTTGCTATATTTGGAGGAATTC
Found at i:52964856 original size:12 final size:12
Alignment explanation
Indices: 52964839--52964863 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52964829 TTATATGTTC
52964839 TTTAAATTTTTT
1 TTTAAATTTTTT
52964851 TTTAAATTTTTT
1 TTTAAATTTTTT
52964863 T
1 T
52964864 AAAATTTTCT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTAAATTTTTT
Found at i:52967487 original size:10 final size:10
Alignment explanation
Indices: 52967472--52967530 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
52967462 TGCCCCTAAT
52967472 TTATAAAAAA
1 TTATAAAAAA
52967482 TTATAAAAAA
1 TTATAAAAAA
*
52967492 TTATAAAATA
1 TTATAAAAAA
*
52967502 -TATAGAAATA
1 TTATA-AAAAA
* *
52967512 TAGAAAAAAAA
1 T-TATAAAAAA
52967523 TTATAAAA
1 TTATAAAA
52967531 TTCTATAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
9 4 0.10
10 29 0.73
11 5 0.12
12 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:52967551 original size:21 final size:20
Alignment explanation
Indices: 52967527--52967599 Score: 55
Period size: 20 Copynumber: 3.7 Consensus size: 20
52967517 AAAAAATTAT
*
52967527 AAAATTCTATAAAGTCGTAA
1 AAAATTCTATAAAATCGTAA
* *
52967547 GAAAATTATAAAAAAT-GTAA
1 -AAAATTCTATAAAATCGTAA
*
52967567 AGAAA-TCTA-AAATTCGTAAA
1 A-AAATTCTATAAAATCGT-AA
52967587 AAAATT-TATAAAA
1 AAAATTCTATAAAA
52967600 GTTATCGTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
18 4 0.10
19 11 0.27
20 14 0.34
21 12 0.29
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.27
Consensus pattern (20 bp):
AAAATTCTATAAAATCGTAA
Found at i:52968130 original size:87 final size:84
Alignment explanation
Indices: 52968004--52968230 Score: 255
Period size: 87 Copynumber: 2.7 Consensus size: 84
52967994 TAACGGTTAA
* * * *
52968004 AGGGCATTTTTGATACATTTTGATAGTTTAAGTACCCAATTGAGTGTAAAAAAAAGCAGGGGCCT
1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAA--A-GGGCCT
* *
52968069 AATTACTTATGT-TGAAAAAGTTT
62 AATGACTT-TGTCTGAAAAAATTT
* *
52968092 -GGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAAGGGCTTTATG
1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGGGCCTAATG
* *
52968155 GCTTTTTCTGAAAAAATTT
66 ACTTTGTCTGAAAAAATTT
*
52968174 GAGGGCCTCTTTT-ATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAAAAAAA
1 -AGGGCCT-TTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAAA
52968231 ACTTAATTGT
Statistics
Matches: 122, Mismatches: 11, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
81 2 0.02
82 20 0.16
83 1 0.01
84 39 0.32
85 11 0.09
86 8 0.07
87 41 0.34
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (84 bp):
AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGGGCCTAATG
ACTTTGTCTGAAAAAATTT
Found at i:52968245 original size:84 final size:83
Alignment explanation
Indices: 52968004--52968259 Score: 241
Period size: 84 Copynumber: 3.0 Consensus size: 83
52967994 TAACGGTTAA
* * * * * *
52968004 AGGGCATTTTTGATACATTTTGATAGTTTAAGTACCCAATTGAGTGTAAAAAAAAGCAGGGGCCT
1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAAG-A---ACTT
** * *
52968069 AATTACTTATGTTGAAAAAGT-T-
61 AATGGCTT-TTTTGAAAAAATATG
* ** *
52968091 TGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAGGGCTTTATGG
1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAGAACTTAATGG
*
52968156 CTTTTTCTGAAAAAATTTG
66 CTTTTT-TGAAAAAATATG
*
52968175 AGGGCCTCTTTT-ATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAAAAAA-AACTTAAT
1 AGGGCCT-TTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAAGAACTTAAT
* *
52968238 TGTTTTTTTGAAAAAATATG
64 GGCTTTTTTGAAAAAATATG
52968258 AG
1 AG
52968260 AACTTTTTAC
Statistics
Matches: 144, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
81 2 0.01
82 16 0.11
83 14 0.10
84 50 0.35
85 12 0.08
86 9 0.06
87 41 0.28
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (83 bp):
AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAGAACTTAATGG
CTTTTTTGAAAAAATATG
Found at i:52970159 original size:247 final size:247
Alignment explanation
Indices: 52969366--52970244 Score: 1286
Period size: 247 Copynumber: 3.6 Consensus size: 247
52969356 AAATAATAAT
* * *
52969366 AATAACATACAATAGATAATGAACTTATGGTTTGAAACTAGTTAACAATAACACATGAAATATGT
1 AATAACATACAATAGATAATGAAATTATGGTTTGAAACTAATTAATAATAACACATGAAATATGT
*** * * * * *
52969431 ACGATGTTAAAATTGAAAATTTTAGGTTAAAAATGGTTATCATGGCGTTGGCATCAATCTTGAGT
66 ACGATGTTAAAA-TGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT
*
52969496 GGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATCCCTATC
130 GGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTCCTATC
*
52969561 ACATGTGTATGCGTGT--AAAAACAAAAATTTGTGAACACAAATGTGTGTTTAAA
195 ACATGCGTATGCGTGTGGAAAAA-AAAAATTT-TGAACACAAATGTGTGTTTAAA
* *
52969614 AATAGCATACAATAGATAATGAAACTTATGGTTTGAAAATAATTAATAATAACACATGAAATATG
1 AATAACATACAATAGATAATGAAA-TTATGGTTTGAAACTAATTAATAATAACACATGAAATATG
52969679 TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT
65 TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT
*
52969744 GGATGTCGAGTTAAGTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATT--TATC
130 GGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTCCTATC
* * * *
52969807 ACATGCGTATGTGGGTGGAAACAACAAATTTTGAACACAAATGTGTGTTTAAA
195 ACATGCGTATGCGTGTGGAAAAAAAAAATTTTGAACACAAATGTGTGTTTAAA
52969860 AATAACATACAATAGATAATGAAATGTATGGTTTGAAACTAATTAATAATAACACATGAAATATG
1 AATAACATACAATAGATAATGAAAT-TATGGTTTGAAACTAATTAATAATAACACATGAAATATG
* * *
52969925 TATGATGTTAAAATGAAAAAAA-A-ATTAAAATTTTTTTATCATGATGTTGTCATCAATCTTGAG
65 TACGATGTTAAAATGAAAAAAATAGATTAAAA-TTGTTTATCATGGTGTTGTCATCAATCTTGAG
* ** *
52969988 TTGATGTCGAGTTAACTTATGTTACCAACTCAATCAAACACATTAATATATACTAGAATTCCTAT
129 TGGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTCCTAT
* * * * * *
52970053 CACACGCATATGCGTGTGGATATAAAAAATTTTGAACACAAATCTGTGTTCAAA
194 CACATGCGTATGCGTGTGGAAAAAAAAAATTTTGAACACAAATGTGTGTTTAAA
* *
52970107 TATAACATACAATAGATAACGAAATATATGGTTTGAAACTAATTAATAATAACACATGAAATATG
1 AATAACATACAATAGATAATGAAAT-TATGGTTTGAAACTAATTAATAATAACACATGAAATATG
* * * *
52970172 TACAATGTTAAAAT-AAAAAAATAGATTAAAATTGTTTAACATGGTTTTGTCATCAATCTTAAGT
65 TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT
*
52970236 TGATGTCGA
130 GGATGTCGA
52970245 TTATACACAC
Statistics
Matches: 573, Mismatches: 49, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
244 7 0.01
245 87 0.15
246 128 0.22
247 167 0.29
248 134 0.23
249 50 0.09
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (247 bp):
AATAACATACAATAGATAATGAAATTATGGTTTGAAACTAATTAATAATAACACATGAAATATGT
ACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGTG
GATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTCCTATCA
CATGCGTATGCGTGTGGAAAAAAAAAATTTTGAACACAAATGTGTGTTTAAA
Found at i:52973213 original size:25 final size:26
Alignment explanation
Indices: 52973159--52973213 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
52973149 GAGCTATTAA
*
52973159 CGGGAAGCTCGTAAGAACCATATAAT
1 CGGGAAGCTCGTAAGAACCAAATAAT
* *
52973185 -GGGAAGCTGGTGAGAACCAAAT-AT
1 CGGGAAGCTCGTAAGAACCAAATAAT
52973209 CGGGA
1 CGGGA
52973214 TACTTATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.16
Consensus pattern (26 bp):
CGGGAAGCTCGTAAGAACCAAATAAT
Found at i:52981894 original size:49 final size:50
Alignment explanation
Indices: 52981833--52981997 Score: 142
Period size: 49 Copynumber: 3.3 Consensus size: 50
52981823 AAGCTGATCT
*
52981833 GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAACGGGTAGCTCCAAA
1 GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAACGGGAAGCTCCAAA
* * * * * * *
52981883 GAGCAAT-TAACGGGAAGCAC-CAGATAGCCATATAACAGGCAG-TTCAAGC
1 GAGCAATATAACGGGAAGCTCACAAAGAGCCA-ATAACGGGAAGCTCCAA-A
* ** *
52981932 GAGC-A-CTAACGGGAAGCTCACAAAGAGCCTTTAATCGGGAAGCTCACGAA
1 GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAA-CGGGAAGCTC-CAAA
*
52981982 GAGCCATATAACGGGA
1 GAGCAATATAACGGGA
52981998 CGCTTATAAG
Statistics
Matches: 88, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
48 28 0.32
49 37 0.42
50 12 0.14
51 3 0.03
52 8 0.09
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.13
Consensus pattern (50 bp):
GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAACGGGAAGCTCCAAA
Found at i:52981996 original size:26 final size:26
Alignment explanation
Indices: 52981833--52981997 Score: 139
Period size: 24 Copynumber: 6.6 Consensus size: 26
52981823 AAGCTGATCT
*
52981833 GAGCAATATAACGGGAAGCTCACAAA
1 GAGCCATATAACGGGAAGCTCACAAA
*
52981859 GAGCCA-ATAACGGGTAGCTC-CAAA
1 GAGCCATATAACGGGAAGCTCACAAA
* * *
52981883 GAGCAAT-TAACGGGAAGCAC-CAGA
1 GAGCCATATAACGGGAAGCTCACAAA
* * * * **
52981907 TAGCCATATAACAGGCAGTTCA-AGC
1 GAGCCATATAACGGGAAGCTCACAAA
*
52981932 GAG-CA-CTAACGGGAAGCTCACAAA
1 GAGCCATATAACGGGAAGCTCACAAA
* *
52981956 GAGCC-TTTAATCGGGAAGCTCACGAA
1 GAGCCATATAA-CGGGAAGCTCACAAA
52981982 GAGCCATATAACGGGA
1 GAGCCATATAACGGGA
52981998 CGCTTATAAG
Statistics
Matches: 108, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
23 11 0.10
24 34 0.31
25 30 0.28
26 29 0.27
27 4 0.04
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.13
Consensus pattern (26 bp):
GAGCCATATAACGGGAAGCTCACAAA
Found at i:52985965 original size:19 final size:20
Alignment explanation
Indices: 52985933--52985976 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
52985923 TATTTTTATC
* *
52985933 ATAAAAAATCATTAAAAATT
1 ATAAAAAATAATTAAAAATA
52985953 ATAAAAAA-AATTAAAAATA
1 ATAAAAAATAATTAAAAATA
52985972 ATAAA
1 ATAAA
52985977 TTTGATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
ATAAAAAATAATTAAAAATA
Found at i:52986111 original size:10 final size:10
Alignment explanation
Indices: 52986098--52986172 Score: 66
Period size: 10 Copynumber: 7.7 Consensus size: 10
52986088 ATTTAAAGTT
52986098 TTATAAAAAA
1 TTATAAAAAA
*
52986108 TTATAAAAAC
1 TTATAAAAAA
52986118 TTAT-AAAAA
1 TTATAAAAAA
52986127 -TATAAAAAA
1 TTATAAAAAA
* **
52986136 TT-CAAAATT
1 TTATAAAAAA
*
52986145 TTCTAAAAAA
1 TTATAAAAAA
*
52986155 ATATAAAAAAA
1 TTAT-AAAAAA
52986166 TTATAAA
1 TTATAAA
52986173 TCACAAAACA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
8 3 0.06
9 15 0.30
10 23 0.46
11 9 0.18
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:52986121 original size:20 final size:18
Alignment explanation
Indices: 52986098--52986134 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
52986088 ATTTAAAGTT
52986098 TTATAAAAAATTATAAAAAC
1 TTAT-AAAAA-TATAAAAAC
52986118 TTATAAAAATATAAAAA
1 TTATAAAAATATAAAAA
52986135 ATTCAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
TTATAAAAATATAAAAAC
Found at i:52986130 original size:49 final size:47
Alignment explanation
Indices: 52986003--52986172 Score: 159
Period size: 49 Copynumber: 3.5 Consensus size: 47
52985993 CGAACTTACA
* *
52986003 AAAAAATTATAAAAATTATTAAAACATCAT-CAAAATTTATAGTTATTAT
1 AAAAAATTATAAAAATTA-TAAAACAT-ATAAAAAATTTAAAGTT-TTAT
52986052 AAAAAAATTAT-AAAATTA-ACAAAGCATATAAAACATATTTAAAGTTTTAT
1 -AAAAAATTATAAAAATTATA-AAA-CATATAAAA-A-ATTTAAAGTTTTAT
* * *
52986102 AAAAAATTATAAAAACTTATAAAA-ATATAAAAAATTCAAAATTTTCT
1 AAAAAATTATAAAAA-TTATAAAACATATAAAAAATTTAAAGTTTTAT
*
52986149 AAAAAAATATAAAAAAATTATAAA
1 -AAAAAAT-TATAAAAATTATAAA
52986173 TCACAAAACA
Statistics
Matches: 104, Mismatches: 6, Indels: 22
0.79 0.05 0.17
Matches are distributed among these distances:
47 12 0.12
48 20 0.19
49 37 0.36
50 19 0.18
51 15 0.14
52 1 0.01
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (47 bp):
AAAAAATTATAAAAATTATAAAACATATAAAAAATTTAAAGTTTTAT
Found at i:52988684 original size:19 final size:21
Alignment explanation
Indices: 52988655--52988695 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
52988645 GTCCCTTGGA
52988655 ACCCAAAAATTATA-GTTTTG
1 ACCCAAAAATTATATGTTTTG
*
52988675 ACCC-AAAATTTTATGTTTTG
1 ACCCAAAAATTATATGTTTTG
52988695 A
1 A
52988696 TCAATTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
ACCCAAAAATTATATGTTTTG
Found at i:52990968 original size:52 final size:52
Alignment explanation
Indices: 52990862--52991033 Score: 214
Period size: 50 Copynumber: 3.4 Consensus size: 52
52990852 ATGATGCTTA
* * *
52990862 AATGCATGATTTAA-TTAA-GATGCAAAC-TAAA-TGAACA-AATGAGTTACTT
1 AATGCATGACTTAATTTAATGATGCAAACTTAAACT-AACATGA-GAGTTACAT
52990911 AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
* *
52990963 AATGCATGTCATAATTT-ATGATGCAAACTT-AACTAACATGAGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
* *
52991013 AATGCATGACTTTATTAAATG
1 AATGCATGACTTAATTTAATG
52991034 CAGAACACAT
Statistics
Matches: 108, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
49 13 0.12
50 37 0.34
51 25 0.23
52 31 0.29
53 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (52 bp):
AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
Found at i:52993259 original size:19 final size:18
Alignment explanation
Indices: 52993222--52993257 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52993212 AAAAATTGTC
*
52993222 TTGTGTCGTTTTCATATA
1 TTGTGTCCTTTTCATATA
52993240 TTGTGTCCTTTT-ATATA
1 TTGTGTCCTTTTCATATA
52993257 T
1 T
52993258 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.17, C:0.11, G:0.14, T:0.58
Consensus pattern (18 bp):
TTGTGTCCTTTTCATATA
Found at i:52995894 original size:40 final size:40
Alignment explanation
Indices: 52995839--52995920 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
52995829 TGTTGAGGAG
52995839 ATTGCTTCAAACCGTACAAAGACTTTTGTAAGAGACAAAC
1 ATTGCTTCAAACCGTACAAAGACTTTTGTAAGAGACAAAC
*
52995879 ATTGCTTCAAACCGTATAAAGACTTTTGTAAGAGACAAAC
1 ATTGCTTCAAACCGTACAAAGACTTTTGTAAGAGACAAAC
52995919 AT
1 AT
52995921 AATATTCTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (40 bp):
ATTGCTTCAAACCGTACAAAGACTTTTGTAAGAGACAAAC
Found at i:52999311 original size:25 final size:25
Alignment explanation
Indices: 52999263--52999311 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
52999253 CTAGGTTAAT
* *
52999263 TAGAGTTTAAGTGGGAAAGTAAAAA
1 TAGAGTTTAACTAGGAAAGTAAAAA
52999288 TAGAGTTTAACTAGGAGAAG-AAAA
1 TAGAGTTTAACTAGGA-AAGTAAAA
52999312 GCCAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.49, C:0.02, G:0.27, T:0.22
Consensus pattern (25 bp):
TAGAGTTTAACTAGGAAAGTAAAAA
Found at i:52999771 original size:19 final size:19
Alignment explanation
Indices: 52999746--52999818 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 19
52999736 GAACAAATGC
52999746 AAAATTATTAAAAAAT-TT
1 AAAATTATTAAAAAATATT
*
52999764 AGAAATTA-TAAAGAATATT
1 A-AAATTATTAAAAAATATT
52999783 AATAATTATTGAAAAAATATTT
1 AA-AATTATT-AAAAAATA-TT
52999805 AAAA-TATATAAAAA
1 AAAATTAT-TAAAAA
52999819 CTAAAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
18 9 0.20
19 14 0.30
20 9 0.20
21 10 0.22
22 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (19 bp):
AAAATTATTAAAAAATATT
Found at i:52999842 original size:14 final size:15
Alignment explanation
Indices: 52999823--52999851 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52999813 TAAAAACTAA
52999823 AAAAAT-ATATTATG
1 AAAAATAATATTATG
52999837 AAAAATAATATTATG
1 AAAAATAATATTATG
52999852 TGGTTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (15 bp):
AAAAATAATATTATG
Found at i:53001073 original size:2 final size:2
Alignment explanation
Indices: 53001066--53001094 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53001056 ACTCCGCCAT
53001066 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53001095 CCAGAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53001737 original size:19 final size:18
Alignment explanation
Indices: 53001695--53001740 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
53001685 ATATAATTGT
*
53001695 AATAATTTTTAATTATTT
1 AATAATTTTTAATTATTA
* *
53001713 ATTAATTTTGTAATTGTTA
1 AATAATTTT-TAATTATTA
53001732 AATAATTTT
1 AATAATTTT
53001741 AAAAACTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (18 bp):
AATAATTTTTAATTATTA
Found at i:53010300 original size:20 final size:20
Alignment explanation
Indices: 53010262--53010306 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
53010252 AAACTAAACA
53010262 AAAATTCAGATATAATTA-T
1 AAAATTCAGATATAATTATT
53010281 AAAATTCA-ATATAAACTTATT
1 AAAATTCAGATAT-AA-TTATT
53010302 AAAAT
1 AAAAT
53010307 GAAATTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.17
19 10 0.43
20 3 0.13
21 6 0.26
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAATTCAGATATAATTATT
Found at i:53013880 original size:14 final size:14
Alignment explanation
Indices: 53013861--53013900 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
53013851 TTGATTGGCA
53013861 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
53013875 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
53013889 GGAAAATGTTTT
1 GTAAAATGTTTT
53013901 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:53013913 original size:34 final size:35
Alignment explanation
Indices: 53013869--53013935 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
53013859 CAGTAAAATG
* *
53013869 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
53013903 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
53013936 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:53013922 original size:20 final size:20
Alignment explanation
Indices: 53013884--53013923 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
53013874 CGTAAAATGA
**
53013884 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
53013904 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
53013924 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:53016092 original size:59 final size:58
Alignment explanation
Indices: 53016029--53016168 Score: 226
Period size: 59 Copynumber: 2.4 Consensus size: 58
53016019 ATAAACAAAA
****
53016029 AAATTTGACAATGTTATAAATTTTTTTTATTTCTATTTTTTATAATTTTTTTAAATTAT
1 AAATTTGACAATGTTATAAATAAAATTTATTTCTATTTTTTATAA-TTTTTTAAATTAT
*
53016088 AAATTTGACAATGTTATAAAAAAAATTTATTTCTATTTTTTATAATTTTTTAAATTAT
1 AAATTTGACAATGTTATAAATAAAATTTATTTCTATTTTTTATAATTTTTTAAATTAT
53016146 AAATTTGACAATGTTATAAATAA
1 AAATTTGACAATGTTATAAATAA
53016169 TGTTTAACTG
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
58 35 0.47
59 40 0.53
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (58 bp):
AAATTTGACAATGTTATAAATAAAATTTATTTCTATTTTTTATAATTTTTTAAATTAT
Found at i:53016942 original size:14 final size:14
Alignment explanation
Indices: 53016923--53016950 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53016913 TCTTTAAAAA
53016923 GAATTAACTTATTT
1 GAATTAACTTATTT
53016937 GAATTAACTTATTT
1 GAATTAACTTATTT
53016951 TTAAAGGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
GAATTAACTTATTT
Found at i:53033698 original size:21 final size:21
Alignment explanation
Indices: 53033672--53033713 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53033662 CAAACAATCA
*
53033672 CAAAAAATATTAATACCTTTT
1 CAAAAAATATCAATACCTTTT
* *
53033693 CAAAAAGTATCGATACCTTTT
1 CAAAAAATATCAATACCTTTT
53033714 ACTAGGTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
CAAAAAATATCAATACCTTTT
Found at i:53038652 original size:51 final size:50
Alignment explanation
Indices: 53038527--53038714 Score: 198
Period size: 51 Copynumber: 3.7 Consensus size: 50
53038517 TATCATTCGA
* * * *
53038527 TACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAAATTTTCGG
1 TACACATAGTAGCCTACACATAGTACTACACACGTGACCAAAACTTCCGG
* ** * *
53038577 TTCATGTAGTAGCCTACACATAGTACCACACACGTGACCAAAGCCTTCCGG
1 TACACATAGTAGCCTACACATAGTACTACACACGTGACCAAA-ACTTCCGG
* * * *
53038628 TACACATAGTAGCCTACACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACATAGTAGCCTACACATAGTACTACACACGTGACCA-AAACT-TCCGG
* * *
53038679 TACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 TACACATAGTAGCCTACACATAGTACTACACACGTG
53038715 TTTATAGGCA
Statistics
Matches: 114, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
50 36 0.32
51 76 0.67
52 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (50 bp):
TACACATAGTAGCCTACACATAGTACTACACACGTGACCAAAACTTCCGG
Found at i:53038658 original size:12 final size:13
Alignment explanation
Indices: 53038628--53038660 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
53038618 AGCCTTCCGG
53038628 TACACATAGTAGCC
1 TACACATAGTA-CC
53038642 TACACATAGTA-C
1 TACACATAGTACC
53038654 TACACAT
1 TACACAT
53038661 GTGACCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (13 bp):
TACACATAGTACC
Found at i:53052374 original size:74 final size:75
Alignment explanation
Indices: 53052250--53052398 Score: 237
Period size: 74 Copynumber: 2.0 Consensus size: 75
53052240 GTTGTCCCAT
53052250 AATTTTTTGATGTCATGGGAAACAGGTTGACAACATGTTTGCAACGTGTTGACTACTTCTATTAG
1 AATTTTTTGATGTCATGGGAAACAGGTTGACAACATGTTTGCAACGTGTTGACTACTTCTATTAG
53052315 GATTTGTATA
66 GATTTGTATA
* * * * *
53052325 AATTTTTT-ATGTCATGTGAAATAGGTTGATAACATGTTTGCAACTTGTTGACTGCTTCTATTAG
1 AATTTTTTGATGTCATGGGAAACAGGTTGACAACATGTTTGCAACGTGTTGACTACTTCTATTAG
*
53052389 GATTTTTATA
66 GATTTGTATA
53052399 TAAATTACTA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
74 60 0.88
75 8 0.12
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (75 bp):
AATTTTTTGATGTCATGGGAAACAGGTTGACAACATGTTTGCAACGTGTTGACTACTTCTATTAG
GATTTGTATA
Found at i:53052691 original size:73 final size:75
Alignment explanation
Indices: 53052498--53053158 Score: 497
Period size: 73 Copynumber: 9.1 Consensus size: 75
53052488 TTTTTACCCT
* ** * * * *
53052498 AACC-TTTTT-AAGGTTGCCTTAGAC-GGGTTTATCCCAA-CTTTTTTTAA-GTTGCCTTGGAAA
1 AACCTTTTTTAAAAGTTGCCTTAGACAATGTCTATCCCAATC-TTTTTAAAGGTTGCCTTAGACA
53052558 AGGTCTATCCC
65 AGGTCTATCCC
* * * * * *
53052569 AACC-TTTTT-AAGGTTGCTTTAAACGA-GTCTATCCC-AGCATTTTT-AAGGTTGTCTTAGAC-
1 AACCTTTTTTAAAAGTTGCCTTAGACAATGTCTATCCCAATC-TTTTTAAAGGTTGCCTTAGACA
* *
53052628 AGGTCAATCCT
65 AGGTCTATCCC
* * * *
53052639 AACCTTTTTTAAAAGTTGCCTTAGACAATGCCTATCCTAATCTTTTT-CAGGTTACCTTAGACGA
1 AACCTTTTTTAAAAGTTGCCTTAGACAATGTCTATCCCAATCTTTTTAAAGGTTGCCTTAGAC-A
53052703 A--TCTATCCC
65 AGGTCTATCCC
* * * *
53052712 AACC-TTTTT-AAGGTTGCCTTAGACGA-GTCTATCCCAACCTTTTTTTAAGGTTGCCTTAGAC-
1 AACCTTTTTTAAAAGTTGCCTTAGACAATGTCTATCCCAATC-TTTTTAAAGGTTGCCTTAGACA
*
53052773 TGGTCTA-CCC
65 AGGTCTATCCC
* * * *
53052783 TAA-CATTTTTAAAAGGTTGCCTTAGACAA-GTCTATCTCAACCTTTTTAAAAAGTTGCCTTAGA
1 -AACCTTTTTTAAAA-GTTGCCTTAGACAATGTCTATCCCAATCTTTTT-AAAGGTTGCCTTAGA
53052846 CAAGGTCTATCCC
63 CAAGGTCTATCCC
* * *
53052859 AA-ATTTTTTAAAAGGTTGCCTTCGAC--TGGTCTATCCCAACCTTTTTTAAAGGTTGCCTTAGA
1 AACCTTTTTTAAAA-GTTGCCTTAGACAAT-GTCTATCCCAATC-TTTTTAAAGGTTGCCTTAGA
*
53052921 CAAGGTCTATACC
63 CAAGGTCTATCCC
* * *
53052934 AACC-TTTTT-AAGGTTACCTTAGACGAT-TCTATCCCAATCTTTTTTAAAGGTTGCCTTAGACA
1 AACCTTTTTTAAAAGTTGCCTTAGACAATGTCTATCCCAATC-TTTTTAAAGGTTGCCTTAGACA
53052996 AGGTCTATCCC
65 AGGTCTATCCC
* * * ** * **
53053007 AACTTTTTTTAAAGGTTTCCTTAGACAAAATCTATCCCAA-CTTTTTTAAAAGTTTATCTTAGAC
1 AACCTTTTTTAAAAGTTGCCTTAGACAATGTCTATCCCAATC-TTTTT-AAAGGTTGCCTTAGAC
*
53053071 -TGGTCTATCCC
64 AAGGTCTATCCC
* * * * *
53053082 AACC-TTTTT-AAGGTTGCCTTAAACGA-GCCTATCCCAACCTTTTTCAAAGGTTGGCCTT-GAC
1 AACCTTTTTTAAAAGTTGCCTTAGACAATGTCTATCCCAATCTTTTT-AAAGGTT-GCCTTAGAC
* *
53053143 TAGGTCTTTCCC
64 AAGGTCTATCCC
53053155 AACC
1 AACC
53053159 CTTTAATAAG
Statistics
Matches: 489, Mismatches: 68, Indels: 64
0.79 0.11 0.10
Matches are distributed among these distances:
70 26 0.05
71 74 0.15
72 65 0.13
73 129 0.26
74 53 0.11
75 111 0.23
76 31 0.06
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (75 bp):
AACCTTTTTTAAAAGTTGCCTTAGACAATGTCTATCCCAATCTTTTTAAAGGTTGCCTTAGACAA
GGTCTATCCC
Found at i:53052691 original size:108 final size:106
Alignment explanation
Indices: 53052502--53053125 Score: 492
Period size: 108 Copynumber: 5.7 Consensus size: 106
53052492 TACCCTAACC
* * * * *
53052502 TTTTTAAGGTTGCCTTAGACGGGTTTATCCCAA-CTTTTTTTAAGTTGCCTTGGAAAAGGTCTAT
1 TTTTTAAGGTTGCCTTAGAC-GGTCTATCCCAACCTTTTTTAAAGTTGCCTTAGACAAGGCCTAT
* * * *
53052566 CCCAACCTTTTTAAGGTTGCTTTAAACGAGTCTATCCCAGCA
65 CCCAACCTTTTTAAGGTTACCTTAAACGAATCTATCCCAACA
* * * *
53052608 TTTTTAAGGTTGTCTTAGACAGGTCAATCCTAACCTTTTTTAAAAGTTGCCTTAGACAATGCCTA
1 TTTTTAAGGTTGCCTTAGAC-GGTCTATCCCAACCTTTTTT-AAAGTTGCCTTAGACAAGGCCTA
* * * * *
53052673 TCCTAATCTTTTTCAGGTTACCTTAGACGAATCTATCCCAACC
64 TCCCAACCTTTTTAAGGTTACCTTAAACGAATCTATCCCAACA
* * *
53052716 TTTTTAAGGTTGCCTTAGACGAGTCTATCCCAACCTTTTTTTAAGGTTGCCTTAGAC-TGGTCTA
1 TTTTTAAGGTTGCCTTAGACG-GTCTATCCCAACC-TTTTTTAAAGTTGCCTTAGACAAGGCCTA
* * * * *
53052780 -CCCTAACATTTTTAAAAGGTTGCCTTAGAC-AAGTCTATCTCAACC
64 TCCC-AACCTTTTT--AAGGTTACCTTAAACGAA-TCTATCCCAACA
* * * *
53052825 TTTTTAAAAAGTTGCCTTAGACAAGGTCTATCCCAA-ATTTTTTAAAAGGTTGCCTTCGAC-TGG
1 TTTTT--AAGGTTGCCTTAGAC--GGTCTATCCCAACCTTTTTT-AAA-GTTGCCTTAGACAAGG
* * * * *
53052888 TCTATCCCAACCTTTTTTAAAGGTTGCCTTAGAC-AAGGTCTATACCAACC
60 CCTATCCCAACC-TTTTT-AAGGTTACCTTAAACGAA--TCTATCCCAACA
* * * *
53052938 TTTTTAAGGTTACCTTAGACGATTCTATCCCAATCTTTTTTAAAGGTTGCCTTAGACAAGGTCTA
1 TTTTTAAGGTTGCCTTAGACG-GTCTATCCCAACCTTTTTTAAA-GTTGCCTTAGACAAGGCCTA
* * * * *
53053003 TCCCAACTTTTTTTAAAGGTTTCCTTAGACAAAATCTATCCCAACT
64 TCCCAAC-CTTTTT-AAGGTTACCTTAAAC-GAATCTATCCCAACA
* ** * * *
53053049 TTTTTAAAAGTTTATCTTAGACTGGTCTATCCCAACC-TTTTTAAGGTTGCCTTAAACGA-GCCT
1 TTTTT--AAGGTTGCCTTAGAC-GGTCTATCCCAACCTTTTTTAAAGTTGCCTTAGACAAGGCCT
53053112 ATCCCAACCTTTTT
63 ATCCCAACCTTTTT
53053126 CAAAGGTTGG
Statistics
Matches: 434, Mismatches: 58, Indels: 49
0.80 0.11 0.09
Matches are distributed among these distances:
106 30 0.07
107 19 0.04
108 98 0.23
109 41 0.09
110 42 0.10
111 95 0.22
112 57 0.13
113 51 0.12
114 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.37
Consensus pattern (106 bp):
TTTTTAAGGTTGCCTTAGACGGTCTATCCCAACCTTTTTTAAAGTTGCCTTAGACAAGGCCTATC
CCAACCTTTTTAAGGTTACCTTAAACGAATCTATCCCAACA
Found at i:53053001 original size:148 final size:146
Alignment explanation
Indices: 53052494--53053158 Score: 669
Period size: 148 Copynumber: 4.6 Consensus size: 146
53052484 AAACTTTTTA
* * *
53052494 CCCTAACCTTTTTAAGGTTGCCTTAGACGGGTT-TATCCCAA-CTTTTTTTAA-GTTGCCTTGGA
1 CCCTAACCTTTTTAAGGTTGCCTTAGAC-GATTCTATCCCAACCTTTTTTAAAGGTTGCCTTAGA
* * * * *
53052556 AAAGGTCTATCCCAACCTTTTTAAGGTTGCTTTAAACGAGTCTATCCC-AGCATTTTT-AAGGTT
65 CAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCCAACCTTTTTTAAAGGTT
* *
53052619 GTCTTAGACAGGTCAAT
130 GCCTTAGACAGGTCTAT
* * * * * * *
53052636 -CCTAACCTTTTTTAAAAGTTGCCTTAGACAATGCCTATCCTAATC-TTTTT-CAGGTTACCTTA
1 CCCTAACC-TTTTT-AAGGTTGCCTTAGACGAT-TCTATCCCAACCTTTTTTAAAGGTTGCCTTA
*
53052698 GACGAA--TCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCCAACCTTTTTTTAAG
63 GAC-AAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCCAACCTTTTTTAAAG
*
53052761 GTTGCCTTAGACTGGTCTA-
127 GTTGCCTTAGACAGGTCTAT
* * * * * *
53052780 CCCTAACATTTTTAAAAGGTTGCCTTAGACAAGTCTATCTCAACCTTTTTAAAAAGTTGCCTTAG
1 CCCTAACCTTTTT--AAGGTTGCCTTAGACGATTCTATCCCAACCTTTTTTAAAGGTTGCCTTAG
** *
53052845 ACAAGGTCTATCCCAAATTTTTTAAAAGGTTGCCTTCGACTG-GTCTATCCCAACCTTTTTTAAA
64 ACAAGGTCTATCCCAACCTTTTT--AAGGTTGCCTTAGAC-GAGTCTATCCCAACCTTTTTTAAA
53052909 GGTTGCCTTAGACAAGGTCTAT
126 GGTTGCCTTAGAC-AGGTCTAT
* * *
53052931 ACC-AACCTTTTTAAGGTTACCTTAGACGATTCTATCCCAATCTTTTTTAAAGGTTGCCTTAGAC
1 CCCTAACCTTTTTAAGGTTGCCTTAGACGATTCTATCCCAACCTTTTTTAAAGGTTGCCTTAGAC
* * * *
53052995 AAGGTCTATCCCAACTTTTTTTAAAGGTTTCCTTAGACAAAATCTATCCCAA-CTTTTTTAAAAG
66 AAGGTCTATCCCAAC-CTTTTT-AAGGTTGCCTTAGAC-GAGTCTATCCCAACCTTTTTT-AAAG
* ** *
53053059 TTTATCTTAGACTGGTCTAT
127 GTTGCCTTAGACAGGTCTAT
* ** *
53053079 CCC-AACCTTTTTAAGGTTGCCTTAAACGAGCCTATCCCAACCTTTTTCAAAGGTTGGCCTT-GA
1 CCCTAACCTTTTTAAGGTTGCCTTAGACGATTCTATCCCAACCTTTTTTAAAGGTT-GCCTTAGA
* *
53053142 CTAGGTCTTTCCCAACC
65 CAAGGTCTATCCCAACC
53053159 CTTTAATAAG
Statistics
Matches: 438, Mismatches: 61, Indels: 43
0.81 0.11 0.08
Matches are distributed among these distances:
141 7 0.02
142 6 0.01
143 56 0.13
144 41 0.09
145 51 0.12
146 12 0.03
147 15 0.03
148 151 0.34
149 82 0.19
150 15 0.03
151 2 0.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (146 bp):
CCCTAACCTTTTTAAGGTTGCCTTAGACGATTCTATCCCAACCTTTTTTAAAGGTTGCCTTAGAC
AAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCCAACCTTTTTTAAAGGTTG
CCTTAGACAGGTCTAT
Found at i:53053158 original size:38 final size:38
Alignment explanation
Indices: 53052498--53053158 Score: 603
Period size: 37 Copynumber: 18.1 Consensus size: 38
53052488 TTTTTACCCT
* *
53052498 AACC-TTTTT-AAGGTTGCCTTAGAC-GGGTTTATCCC
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* * *
53052533 AA-CTTTTTTTAA-GTTGCCTTGGAAAAGGTCTATCCC
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* * *
53052569 AACC-TTTTT-AAGGTTGCTTTAAACGA-GTCTATCCC
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* * * * *
53052604 -AGCATTTTT-AAGGTTGTCTTAGAC-AGGTCAATCCT
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* * * *
53052639 AACCTTTTTTAAAAGTTGCCTTAGACAATGCCTATCCT
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* * *
53052677 AATC-TTTTT-CAGGTTACCTTAGACGAA--TCTATCCC
1 AACCTTTTTTAAAGGTTGCCTTAGAC-AAGGTCTATCCC
*
53052712 AACC-TTTTT-AAGGTTGCCTTAGACGA-GTCTATCCC
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* *
53052747 AACCTTTTTTTAAGGTTGCCTTAGAC-TGGTCTA-CCC
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* * *
53052783 TAACATTTTTAAAAGGTTGCCTTAGACAA-GTCTATCTC
1 -AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* *
53052821 AACCTTTTTAAAAAGTTGCCTTAGACAAGGTCTATCCC
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* * *
53052859 AA-ATTTTTTAAAAGGTTGCCTTCGAC-TGGTCTATCCC
1 AACCTTTTTT-AAAGGTTGCCTTAGACAAGGTCTATCCC
*
53052896 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATACC
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* * *
53052934 AACC-TTTTT-AAGGTTACCTTAGACGA-TTCTATCCC
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
*
53052969 AATCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* * **
53053007 AACTTTTTTTAAAGGTTTCCTTAGACAAAATCTATCCC
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* ** *
53053045 AA-CTTTTTTAAAAGTTTATCTTAGAC-TGGTCTATCCC
1 AACCTTTTTT-AAAGGTTGCCTTAGACAAGGTCTATCCC
* * *
53053082 AACC-TTTTT-AAGGTTGCCTTAAACGA-GCCTATCCC
1 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
* * *
53053117 AACCTTTTTCAAAGGTTGGCCTT-GACTAGGTCTTTCCC
1 AACCTTTTTTAAAGGTT-GCCTTAGACAAGGTCTATCCC
53053155 AACC
1 AACC
53053159 CTTTAATAAG
Statistics
Matches: 513, Mismatches: 81, Indels: 61
0.78 0.12 0.09
Matches are distributed among these distances:
34 5 0.01
35 124 0.24
36 78 0.15
37 177 0.35
38 129 0.25
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (38 bp):
AACCTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCC
Found at i:53055760 original size:15 final size:15
Alignment explanation
Indices: 53055742--53055783 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
53055732 TTCTCAGTTG
53055742 TCTTCTTCTTCG-CTT
1 TCTTCTTCTTCGTC-T
*
53055757 TCTTCGTCTTCGTCT
1 TCTTCTTCTTCGTCT
53055772 TCTTCTTCTTCG
1 TCTTCTTCTTCG
53055784 GTGATTGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 23 0.96
16 1 0.04
ACGTcount: A:0.00, C:0.33, G:0.10, T:0.57
Consensus pattern (15 bp):
TCTTCTTCTTCGTCT
Found at i:53061323 original size:24 final size:23
Alignment explanation
Indices: 53061288--53061341 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
53061278 TAGTTGCATG
*
53061288 TTTTATAAGTAATAAATATTTTTA
1 TTTT-TAAGTAATAAATAATTTTA
*
53061312 TTTTTAATGTAATAATTAATTTTA
1 TTTTTAA-GTAATAAATAATTTTA
*
53061336 CTTTTA
1 TTTTTA
53061342 TATAATGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTTAAGTAATAAATAATTTTA
Found at i:53063130 original size:23 final size:23
Alignment explanation
Indices: 53063104--53063153 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
53063094 AGCATTATGT
*
53063104 CATTTTAGTGCAATTCATTTTGC
1 CATTATAGTGCAATTCATTTTGC
*
53063127 CATTATAGTGCAATTCATTTTGG
1 CATTATAGTGCAATTCATTTTGC
53063150 CATT
1 CATT
53063154 CGATACATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (23 bp):
CATTATAGTGCAATTCATTTTGC
Found at i:53063375 original size:21 final size:23
Alignment explanation
Indices: 53063331--53063377 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
53063321 TGAAAAGGAT
53063331 ACGTCATTCTAAATTGTGGATAA
1 ACGTCATTCTAAATTGTGGATAA
*
53063354 ACGTCATTCTCAA-TGT-GATAA
1 ACGTCATTCTAAATTGTGGATAA
53063375 ACG
1 ACG
53063378 AGCATCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 3 0.13
23 12 0.52
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (23 bp):
ACGTCATTCTAAATTGTGGATAA
Found at i:53067773 original size:12 final size:12
Alignment explanation
Indices: 53067756--53067785 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53067746 CCTCACACCC
53067756 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
53067768 CCGTGTGCTAGG
1 CCGTGTGCCAGG
53067780 CCGTGT
1 CCGTGT
53067786 AACTTTCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:53075625 original size:51 final size:52
Alignment explanation
Indices: 53075570--53075677 Score: 166
Period size: 51 Copynumber: 2.1 Consensus size: 52
53075560 TTTCATTTTT
53075570 CATTTTTATTTTGGAGAAAACCA-AATTCATTTCCAAATGATTCC-ATTTCTC
1 CATTTTTATTTTGGAGAAAACCATAA-TCATTTCCAAATGATTCCTATTTCTC
* * *
53075621 CATTTTTATTTTGGAGAAAACCATAATCATTTGCAAATGTTTCCTATTTTTC
1 CATTTTTATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCTATTTCTC
53075673 CATTT
1 CATTT
53075678 CACCATTTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
51 39 0.75
52 13 0.25
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.44
Consensus pattern (52 bp):
CATTTTTATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCTATTTCTC
Found at i:53085186 original size:20 final size:20
Alignment explanation
Indices: 53085152--53085193 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53085142 AACTATTTAA
** *
53085152 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
53085172 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
53085192 AT
1 AT
53085194 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:53085568 original size:17 final size:18
Alignment explanation
Indices: 53085548--53085584 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
53085538 TTTTCCAAAA
53085548 TTGAGTCAAGGACT-TTT
1 TTGAGTCAAGGACTGTTT
53085565 TTGAGTCAAGGACTGTTT
1 TTGAGTCAAGGACTGTTT
53085583 TT
1 TT
53085585 ATGAATGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (18 bp):
TTGAGTCAAGGACTGTTT
Found at i:53086042 original size:49 final size:49
Alignment explanation
Indices: 53085909--53086043 Score: 139
Period size: 49 Copynumber: 2.7 Consensus size: 49
53085899 GTAAAGAGAT
* * * * *
53085909 CCCATGTAAGACCATGTCTGAGACATGGCATGGGCACCGATATGAGAACT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGAAAAGAGAACC
* * * *
53085959 CCCATGTAAGACTATATCTGGGATATGACATTGGCA-GTAAAAGA-AACAC
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACG-AAAAGAGAAC-C
*
53086008 CCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
53086044 TGTTATTATC
Statistics
Matches: 69, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
48 4 0.06
49 35 0.51
50 30 0.43
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (49 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAAAAGAGAACC
Found at i:53089758 original size:26 final size:26
Alignment explanation
Indices: 53089729--53089781 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
53089719 CTTTCCGAAC
53089729 TAGGTATGGTCACTATGAGTTTCTTG
1 TAGGTATGGTCACTATGAGTTTCTTG
53089755 TAGGTATGGTCACTATGAGTTTCTTG
1 TAGGTATGGTCACTATGAGTTTCTTG
53089781 T
1 T
53089782 GATTCCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.43
Consensus pattern (26 bp):
TAGGTATGGTCACTATGAGTTTCTTG
Found at i:53093503 original size:56 final size:50
Alignment explanation
Indices: 53093407--53093653 Score: 205
Period size: 50 Copynumber: 4.8 Consensus size: 50
53093397 ATTTGGGTAA
* * *
53093407 AGAGATCCCATGTAAGACCATGTCTGGGACTTGACATTGGCATCATTAAAGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C---AAAG--ATG
* **
53093463 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAAAGATG
* * ** *
53093513 AGAGGTCTCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACAAAGATG
** * * *
53093563 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGA--
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CA-AAGATG
** * *
53093613 A-ACATCCCATGTAAGACCATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
53093654 TGTTATTATC
Statistics
Matches: 161, Mismatches: 26, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
49 36 0.22
50 80 0.50
51 2 0.01
52 4 0.02
55 1 0.01
56 38 0.24
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAAAGATG
Found at i:53093515 original size:50 final size:50
Alignment explanation
Indices: 53093460--53093653 Score: 214
Period size: 50 Copynumber: 3.9 Consensus size: 50
53093450 CATTAAAGTT
* *
53093460 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
* * *
53093510 ATGAGAGGTCTCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
** * *
53093560 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* * ** * *
53093609 AAGAAACATCCCATGTAAGACCATGTCTGGGACATAGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
53093654 TGTTATTATC
Statistics
Matches: 122, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
48 1 0.01
49 40 0.33
50 79 0.65
51 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:53095444 original size:56 final size:50
Alignment explanation
Indices: 53095348--53095594 Score: 205
Period size: 50 Copynumber: 4.8 Consensus size: 50
53095338 ATTTGGGTAA
* * *
53095348 AGAGATCCCATGTAAGACCATGTCTGGGACTTGACATTGGCATCATTAAAGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C---AAAG--ATG
* **
53095404 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAAAGATG
* * ** *
53095454 AGAGGTCTCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACAAAGATG
** * * *
53095504 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGA--
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CA-AAGATG
** * *
53095554 A-ACATCCCATGTAAGACCATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
53095595 TGTTATTATC
Statistics
Matches: 161, Mismatches: 26, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
49 36 0.22
50 80 0.50
51 2 0.01
52 4 0.02
55 1 0.01
56 38 0.24
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAAAGATG
Done.