Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 170 of 226
Found at i:52286210 original size:90 final size:89
Alignment explanation
Indices: 52286079--52286390 Score: 247
Period size: 90 Copynumber: 3.5 Consensus size: 89
52286069 CAGCTCTATC
* * * * * * ** *
52286079 TCCGAGTTGGTGAAGAGGTGCAACCCCGTATCCTGAATGGTGTGATAATGCAGCCCCATATCCGG
1 TCCGGGTTGGTGTAGCGGTGCAGCCCCATATCCAGCTTGGTGTGATGATGCAGCCCCATATCCGG
*
52286144 CTTGGTGTGACGGTGTAACCACATA
66 CTTGGTGTGACGGTGCAACC-CATA
* * * * *
52286169 TCCGGGTTGGTGTAGCGGTGCAGCCCCATATCCAGCTTGGTGCGATGGTACAGCTCCA-AACTCG
1 TCCGGGTTGGTGTAGCGGTGCAGCCCCATATCCAGCTTGGTGTGATGATGCAGCCCCATATC-CG
*
52286233 GCTTGGTGTGACGGTGCGACTCCATA
65 GCTTGGTGTGACGGTGCAAC-CCATA
* * ** * * *
52286259 TCCGGCTTGGTG-CGACGGTGGGGCCCCATATCCAAG-GTGGTGTAATGATGCAGTCCCATATCC
1 TCCGGGTTGGTGTAG-CGGTGCAGCCCCATATCC-AGCTTGGTGTGATGATGCAGCCCCATATCC
* *
52286322 TGG-TTGGTGCTG-TGGTGCAGCCCCATA
64 -GGCTTGGTG-TGACGGTGCA-ACCCATA
* ** **
52286349 TCCTGGTTGGTGTAGTAGTGTTGCCCCATATCCAGCTTGGTG
1 TCCGGGTTGGTGTAGCGGTGCAGCCCCATATCCAGCTTGGTG
52286391 CATGGGTGCA
Statistics
Matches: 173, Mismatches: 39, Indels: 20
0.75 0.17 0.09
Matches are distributed among these distances:
89 5 0.03
90 157 0.91
91 11 0.06
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.26
Consensus pattern (89 bp):
TCCGGGTTGGTGTAGCGGTGCAGCCCCATATCCAGCTTGGTGTGATGATGCAGCCCCATATCCGG
CTTGGTGTGACGGTGCAACCCATA
Found at i:52288908 original size:82 final size:86
Alignment explanation
Indices: 52288816--52288988 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 86
52288806 TGATGTAAAT
52288816 TTAAAACTTCTAACTATTTGTTTTATG-TAAAAAAAA-TCAACCGTTG-A-ATATATATATTAAT
1 TTAAAACTTCTAACTATTTGTTTTATGATAAAAAAAATTCAACCGTTGAATATATATATATTAAT
*
52288877 ATATTGAGTGCTTTAGATTAA
66 ATATTGAGTACTTTAGATTAA
52288898 TTAAAACTTCTAACTATTTGTTTTATGTAATAAAAAAAATTCAACCGTTGAATATATATATATAT
1 TTAAAACTTCTAACTATTTGTTTTATG--ATAAAAAAAATTCAACCGTTG-A-ATATATATATAT
52288963 TAATATATTGAGTACTTTAGATTAA
62 TAATATATTGAGTACTTTAGATTAA
52288988 T
1 T
52288989 ATGAAAGAGA
Statistics
Matches: 82, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
82 27 0.33
85 9 0.11
86 10 0.12
89 1 0.01
90 35 0.43
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (86 bp):
TTAAAACTTCTAACTATTTGTTTTATGATAAAAAAAATTCAACCGTTGAATATATATATATTAAT
ATATTGAGTACTTTAGATTAA
Found at i:52295826 original size:48 final size:48
Alignment explanation
Indices: 52295774--52295872 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
52295764 GGAGGATCTT
* *
52295774 GAATAAATCTATTGAGAAATATAAATATGGAATAAATTGGTTAAAATA
1 GAATAAATCTATTGAGAAATATAAATATGAAATAAATTGGTCAAAATA
*
52295822 GAATAAATCTATTGAGAAATATAGATATGAAATAAATTGGTCAAAATA
1 GAATAAATCTATTGAGAAATATAAATATGAAATAAATTGGTCAAAATA
52295870 GAA
1 GAA
52295873 AGACGCAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.29
Consensus pattern (48 bp):
GAATAAATCTATTGAGAAATATAAATATGAAATAAATTGGTCAAAATA
Found at i:52295860 original size:25 final size:25
Alignment explanation
Indices: 52295784--52295860 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
52295774 GAATAAATCT
* *
52295784 ATTGAGAAATATAAATATGGAATAA
1 ATTGAGAAATATAGATATGAAATAA
**
52295809 ATTG-GTTAAA-ATAGA-AT-AAATCT
1 ATTGAG--AAATATAGATATGAAATAA
52295832 ATTGAGAAATATAGATATGAAATAA
1 ATTGAGAAATATAGATATGAAATAA
52295857 ATTG
1 ATTG
52295861 GTCAAAATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
22 3 0.08
23 12 0.30
24 6 0.15
25 16 0.40
26 3 0.08
ACGTcount: A:0.52, C:0.01, G:0.16, T:0.31
Consensus pattern (25 bp):
ATTGAGAAATATAGATATGAAATAA
Found at i:52295870 original size:25 final size:24
Alignment explanation
Indices: 52295798--52295871 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 24
52295788 AGAAATATAA
*
52295798 ATATGGAATAAATTGGTTAAAATAG
1 ATATGAAATAAATTGG-TAAAATAG
**
52295823 A-AT-AAATCTATTGAG-AAATATAG
1 ATATGAAATAAATTG-GTAAA-ATAG
52295846 ATATGAAATAAATTGGTCAAAATAG
1 ATATGAAATAAATTGGT-AAAATAG
52295871 A
1 A
52295872 AAGACGCAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
22 3 0.08
23 12 0.32
24 6 0.16
25 14 0.37
26 3 0.08
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.30
Consensus pattern (24 bp):
ATATGAAATAAATTGGTAAAATAG
Found at i:52302257 original size:30 final size:30
Alignment explanation
Indices: 52302180--52302258 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
52302170 AATGTGTATG
*
52302180 ATTGAATCAAAATTAAAGTTTTATGTATACA
1 ATTGAA-CCAAATTAAAGTTTTATGTATACA
*
52302211 TTTGAACCACAATTAAAGTTTCGTATGTA-A-A
1 ATTGAACCA-AATTAAAGTTT--TATGTATACA
*
52302242 ATTGCACCAAATTAAAG
1 ATTGAACCAAATTAAAG
52302259 CTCGTGTATC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
30 10 0.24
31 24 0.59
32 1 0.02
33 6 0.15
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (30 bp):
ATTGAACCAAATTAAAGTTTTATGTATACA
Found at i:52306699 original size:74 final size:75
Alignment explanation
Indices: 52306587--52306762 Score: 189
Period size: 74 Copynumber: 2.4 Consensus size: 75
52306577 TTTGTGGAAG
* * * *
52306587 TCAAATTGTTTAACTTGATTAAAAC-CCTTAAGAGATTTAACTTTA-CTGATTAAGTGCAAGCAA
1 TCAAATTGTTTAACTTGATTACATCTCCTAAAGAGATTTAACTTTATC-GATTAAATGCAAGCAA
*
52306650 ATCTCTGAAAC
65 ATCTATGAAAC
* ** *
52306661 TCAAATTGTTTAACTTGATTACATCTCCTAAAGA-ATTTAGCTTTATCGATTAAATGGGAGCAAT
1 TCAAATTGTTTAACTTGATTACATCTCCTAAAGAGATTTAACTTTATCGATTAAATGCAAGCAAA
* * *
52306725 TTTATGGAAG
66 TCTATGAAAC
* *
52306735 TTAAATTGTTTGACTTGATTACAT-TCCT
1 TCAAATTGTTTAACTTGATTACATCTCCT
52306763 GTTAGCTCAA
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
73 4 0.05
74 74 0.86
75 8 0.09
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (75 bp):
TCAAATTGTTTAACTTGATTACATCTCCTAAAGAGATTTAACTTTATCGATTAAATGCAAGCAAA
TCTATGAAAC
Found at i:52309972 original size:17 final size:17
Alignment explanation
Indices: 52309945--52309990 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
52309935 AAAGTTTAGG
52309945 GGGGAAATAAAAAGTTTT
1 GGGGAAAT-AAAAGTTTT
52309963 GGGG-AATAAAAG-TTT
1 GGGGAAATAAAAGTTTT
52309978 GAGGGAAAGTAAA
1 G-GGGAAA-TAAA
52309991 TAGAGGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 5 0.20
18 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.22
Consensus pattern (17 bp):
GGGGAAATAAAAGTTTT
Found at i:52310355 original size:9 final size:9
Alignment explanation
Indices: 52310341--52310377 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52310331 TATAGTTTGA
52310341 TATTCGAAT
1 TATTCGAAT
52310350 TATTCGAAT
1 TATTCGAAT
*
52310359 TATTCGAGT
1 TATTCGAAT
52310368 TATTCGAAT
1 TATTCGAAT
52310377 T
1 T
52310378 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:52311950 original size:28 final size:29
Alignment explanation
Indices: 52311913--52311974 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
52311903 GAAAAAAATA
*
52311913 AAAATTTATTCT-AAAA-GAGAATAAAAG
1 AAAATTTATTCTAAAAATAAGAATAAAAG
*
52311940 AAAATTCTATTCTAAAAATAAGAATAAAAT
1 AAAATT-TATTCTAAAAATAAGAATAAAAG
52311970 AAAAT
1 AAAAT
52311975 AAAATAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 6 0.20
28 6 0.20
29 4 0.13
30 14 0.47
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.27
Consensus pattern (29 bp):
AAAATTTATTCTAAAAATAAGAATAAAAG
Found at i:52311970 original size:5 final size:5
Alignment explanation
Indices: 52311954--52311983 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
52311944 TTCTATTCTA
52311954 AAAAT AAGAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAA
52311984 GAGAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:52313011 original size:23 final size:22
Alignment explanation
Indices: 52312962--52313018 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
52312952 AGGACATTGC
*
52312962 CTTTCTCCATCTTCCATCAAAT
1 CTTTTTCCATCTTCCATCAAAT
52312984 CTTTTTCCATCTCTCCAT-AATAT
1 CTTTTTCCATCT-TCCATCAA-AT
*
52313007 -TTTTTCTATCTT
1 CTTTTTCCATCTT
52313019 GATTATGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 23 0.74
23 7 0.23
ACGTcount: A:0.19, C:0.30, G:0.00, T:0.51
Consensus pattern (22 bp):
CTTTTTCCATCTTCCATCAAAT
Found at i:52319436 original size:24 final size:24
Alignment explanation
Indices: 52319382--52319441 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
52319372 TTAAAATATC
* *
52319382 ATTTAAAATCTATTTATCTGAATT
1 ATTTAAAATCTATTTAACTAAATT
* *
52319406 CTGTAAAATCTATTTAACTAAATT
1 ATTTAAAATCTATTTAACTAAATT
52319430 ATTTAAATATCT
1 ATTTAAA-ATCT
52319442 TATATAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (24 bp):
ATTTAAAATCTATTTAACTAAATT
Found at i:52322281 original size:21 final size:21
Alignment explanation
Indices: 52322245--52322298 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
52322235 ATCATATATT
52322245 CCAAGATTGC--ATATCATAC
1 CCAAGATTGCATATATCATAC
*
52322264 CCAAGATTGCATATATCATAT
1 CCAAGATTGCATATATCATAC
* *
52322285 CTAAGATTGTATAT
1 CCAAGATTGCATAT
52322299 CCTTGAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 10 0.33
21 20 0.67
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
CCAAGATTGCATATATCATAC
Found at i:52322725 original size:44 final size:44
Alignment explanation
Indices: 52322672--52323102 Score: 535
Period size: 44 Copynumber: 9.8 Consensus size: 44
52322662 ACCAGAATGG
* * * *
52322672 GAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGAA-AAAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC-AATACAT
* * *
52322716 GAAGACAAGATCTGTTTTCTTCGATCTACTT--CGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * * * * ***
52322758 GAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCA-CGCCAATACAT
** *
52322803 GAAGACAAGATCTATTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
52322847 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
*
52322891 GAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * * * * ***
52322935 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTC-ACGCCAATACAT
* *
52322980 GAAGACAATATCTGCTATCTTTGATCTACTTCATGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
52323024 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* *
52323068 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACG
52323103 ACAACCCAGG
Statistics
Matches: 334, Mismatches: 48, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.01
42 35 0.10
44 225 0.67
45 72 0.22
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
Found at i:52322978 original size:177 final size:177
Alignment explanation
Indices: 52322672--52323102 Score: 697
Period size: 177 Copynumber: 2.4 Consensus size: 177
52322662 ACCAGAATGG
* * * * *
52322672 GAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGAA-AAATGAAGACAAGATCTGTTTTCT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC-AATACATGAAGACAAGATCTGCTTTCT
52322736 TCGATCTACTT--CGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGT
65 TCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGT
*
52322799 ATGGGAAGACAAGATCTATTATCTTCGATCTACTTCACGCCAATACAT
130 ATGGGAAGACAAGATCTACTATCTTCGATCTACTTCACGCCAATACAT
* *
52322847 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATATT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
* * *
52322912 TGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTA
66 CGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTA
* * * *
52322977 TGGGAAGACAATATCTGCTATCTTTGATCTACTTCATGCCAATACAT
131 TGGGAAGACAAGATCTACTATCTTCGATCTACTTCACGCCAATACAT
52323024 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
52323089 CGATCTACTTCACG
66 CGATCTACTTCACG
52323103 ACAACCCAGG
Statistics
Matches: 235, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
174 2 0.01
175 64 0.27
177 169 0.72
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (177 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
CGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTA
TGGGAAGACAAGATCTACTATCTTCGATCTACTTCACGCCAATACAT
Found at i:52322984 original size:133 final size:132
Alignment explanation
Indices: 52322672--52323176 Score: 538
Period size: 133 Copynumber: 3.8 Consensus size: 132
52322662 ACCAGAATGG
** * * ** * * * *
52322672 GAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGAA-AAATGAAGACAAGATCTGTTTTCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACACC-AATACAGGAAGACAAGATCTGCTATCT
* * * * * *
52322736 TCGATCTACTT--CGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGT
65 TTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCA-CGCCAAT
***
52322799 ATGG
129 ACAT
* * *
52322803 GAAGACAAGATCT-ATTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCT
1 GAAGACAAGATCTGCTT-TCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATCT
*
52322867 TTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAATA
65 TTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATA
52322932 CAT
130 CAT
* * ** *
52322935 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTGCTATCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTC-ACACCAATACAGGAAGACAAGATCTGCTATCT
*
52323000 TTGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATA
65 TTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATA
52323065 CAT
130 CAT
** * * * *
52323068 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGA-CAACCCAGGGAGGCAAG-GCTGGTATCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCAC-ACCAATACAGGAAGACAAGATCTGCTATCT
* * ** *
52323131 TTGATCTGCTTCACTGTCGGTACAGGAA-AGCAAGATCTGCTATCTT
65 TTGATCTACTTCAC-GCCAATACATGAAGA-CAAGATCTGCTATCTT
52323177 CAACCTGCTC
Statistics
Matches: 319, Mismatches: 46, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
130 3 0.01
131 81 0.25
132 69 0.22
133 166 0.52
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (132 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATCTT
TGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATAC
AT
Found at i:52323165 original size:88 final size:88
Alignment explanation
Indices: 52323039--52323826 Score: 1030
Period size: 88 Copynumber: 9.0 Consensus size: 88
52323029 CAAGATCTGC
* * * * * * * * * * * *
52323039 TATCTTTGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACG
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
52323103 ACAACCCAGGGAGGCAAGGCTGG
66 ACAACCCAGGGAGGCAAGGCTGG
* * *
52323126 TATCTTTGATCTGCTTCACTGTCGGTACAGGAAAGCAAGATCTGCTATCTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
52323191 ACAACCCAGGGAGGCAAGGCTGA
66 ACAACCCAGGGAGGCAAGGCTGG
* * * *
52323214 TATTTTCGATTTGTTTCACTGTC-AGTACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
1 TATCTTCGATCTGCTTCACTGTCGA-TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
*
52323278 TACGACCCAGGGAGGCAAGGCTGG
65 TACAACCCAGGGAGGCAAGGCTGG
* * * *
52323302 TATCTTCGATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGTTATCTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
52323367 ACAACCTAGGGAGGCAAGGCTGG
66 ACAACCCAGGGAGGCAAGGCTGG
* *
52323390 TAT-TTCGATCTGCTTCACTGTCGATGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
52323454 ACAACCCAGGGAGACAAGGCTGG
66 ACAACCCAGGGAGGCAAGGCTGG
* * * * **
52323477 TATATTCGATCAGCTACGCTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
52323542 ACAACCCAGAGAGGCAAGGCTGG
66 ACAACCCAGGGAGGCAAGGCTGG
* * * * *
52323565 TATCTTCGATCTGCTTCGCTGTCGATGCAAGAAGGCAAGATTTGCTATTTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
52323630 ACAACCCAGAGAGGCAAGGCTGG
66 ACAACCCAGGGAGGCAAGGCTGG
* *
52323653 TATCTTCGATCTGCTTCGA-TGTCGATGCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCAC
1 TATCTTCGATCTGCTTC-ACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
* *
52323717 TACAACCCAGAGAGGCAAGGCTAG
65 TACAACCCAGGGAGGCAAGGCTGG
* * *
52323741 TATCTTCGATCTGCTTCA-TCGTC-AGTACAGGAAGGCAAGATCTGTTATTTTCAACCTGCTCCG
1 TATCTTCGATCTGCTTCACT-GTCGA-TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCA
* * *
52323804 CTGCAAACCAGGAAGGCAAGGCT
64 CTACAACCCAGGGAGGCAAGGCT
52323827 TTGTGATTTC
Statistics
Matches: 625, Mismatches: 69, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
87 100 0.16
88 524 0.84
89 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (88 bp):
TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
ACAACCCAGGGAGGCAAGGCTGG
Found at i:52323716 original size:351 final size:352
Alignment explanation
Indices: 52323039--52323826 Score: 1057
Period size: 351 Copynumber: 2.2 Consensus size: 352
52323029 CAAGATCTGC
* * * * * * * * * *
52323039 TATCTTTGATCTACTTCA-CGCCAATACATG-AAGACAAGATCTGCTTTCTTCGATCTACTTCAC
1 TATCTTCGATCTGCTTCATCGTCAGTACA-GAAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
* * * * * *
52323102 GACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTACAGGAAAGCAAGAT
65 TACAACCCAGGGAGGCAAGGCTGGTATATTCGATCAGCTACACTGTCGATACAGGAAAGCAAGAT
* * * *
52323167 CTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGATATTTTCGATTTGTTTCA
130 CTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAGGCTGATATCTTCGATCTGCTTCA
* *
52323232 CTGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAG
195 CTGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAG
* *
52323297 GCTGGTATCTTCGATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGTTATCTTCAACCTGCT
260 GCTGGTATCTTCGATCTGCTTCGATGTCAATACAGGAAGACAAGATCTGCTATCTTCAACCTGCT
* * *
52323362 CCACTACAACCTAGGGAGGCAAGGCTGG
325 CCACTACAACCCAGAGAGGCAAGGCTAG
*
52323390 TAT-TTCGATCTGCTTCA-CTGTC-GATGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCA
1 TATCTTCGATCTGCTTCATC-GTCAG-TACAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCA
* * ** *
52323452 CTACAACCCAGGGAGACAAGGCTGGTATATTCGATCAGCTACGCTGTCGATGTAGGAAGGCAAGA
64 CTACAACCCAGGGAGGCAAGGCTGGTATATTCGATCAGCTACACTGTCGATACAGGAAAGCAAGA
*
52323517 TCTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAGGCTGGTATCTTCGATCTGCTTC
129 TCTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAGGCTGATATCTTCGATCTGCTTC
* * * *
52323582 GCTGTC-GATGCAAGAAGGCAAGATTTGCTATTTTCAACCTGCTCCACTACAACCCAGAGAGGCA
194 ACTGTCAG-TACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCA
* * * *
52323646 AGGCTGGTATCTTCGATCTGCTTCGATGTCGATGCAGGAAGGCAAGATCTGCTATCTTTAACCTG
258 AGGCTGGTATCTTCGATCTGCTTCGATGTCAATACAGGAAGACAAGATCTGCTATCTTCAACCTG
52323711 CTCCACTACAACCCAGAGAGGCAAGGCTAG
323 CTCCACTACAACCCAGAGAGGCAAGGCTAG
* * * *
52323741 TATCTTCGATCTGCTTCATCGTCAGTACAGGAAGGCAAGATCTGTTATTTTCAACCTGCTCCGCT
1 TATCTTCGATCTGCTTCATCGTCAGTACAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
* * *
52323806 GCAAACCAGGAAGGCAAGGCT
66 ACAACCCAGGGAGGCAAGGCT
52323827 TTGTGATTTC
Statistics
Matches: 379, Mismatches: 51, Indels: 13
0.86 0.12 0.03
Matches are distributed among these distances:
350 15 0.04
351 293 0.77
352 69 0.18
353 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (352 bp):
TATCTTCGATCTGCTTCATCGTCAGTACAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
ACAACCCAGGGAGGCAAGGCTGGTATATTCGATCAGCTACACTGTCGATACAGGAAAGCAAGATC
TGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAGGCTGATATCTTCGATCTGCTTCAC
TGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAGG
CTGGTATCTTCGATCTGCTTCGATGTCAATACAGGAAGACAAGATCTGCTATCTTCAACCTGCTC
CACTACAACCCAGAGAGGCAAGGCTAG
Found at i:52325448 original size:10 final size:9
Alignment explanation
Indices: 52325423--52325447 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52325413 CCTGGAAGAG
52325423 TTTTTTTCT
1 TTTTTTTCT
52325432 TTTTTTTCT
1 TTTTTTTCT
52325441 TTTTTTT
1 TTTTTTT
52325448 TGCACCATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:52330701 original size:21 final size:21
Alignment explanation
Indices: 52330675--52330726 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
52330665 CATATCTTCC
52330675 AAGATTGCATATATCATATCT
1 AAGATTGCATATATCATATCT
*
52330696 AAGATTGC--ATGTCATATCT
1 AAGATTGCATATATCATATCT
*
52330715 AAAATTGCATAT
1 AAGATTGCATAT
52330727 CTTTGAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 17 0.63
21 10 0.37
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (21 bp):
AAGATTGCATATATCATATCT
Found at i:52331856 original size:57 final size:57
Alignment explanation
Indices: 52331747--52331858 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 57
52331737 AAAAAAAAAG
* * *
52331747 AAAAAAAATTTGGGTGTTGGCCTATCAATGGCCGGCACCCAGTACGAAAAAAAGGAA
1 AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCGGCACCCAGCACGAAAAAAAGGAA
* * *
52331804 AAAAAAAATTTAGGTGCTGGCCTGTTAATGGTCGGCACCCAGCACAGTAAAAAAA
1 AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCGGCACCCAGCAC-G-AAAAAAA
52331859 TTTATTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 39 0.83
58 1 0.02
59 7 0.15
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (57 bp):
AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCGGCACCCAGCACGAAAAAAAGGAA
Found at i:52332146 original size:212 final size:211
Alignment explanation
Indices: 52331789--52332191 Score: 657
Period size: 212 Copynumber: 1.9 Consensus size: 211
52331779 CGGCACCCAG
* *
52331789 TACGAAAAAAAGGAAAAAAAAAATTTAGGTGCTGGCCTGTTAATGGTCGGCACCCAGCACAGTAA
1 TACGAAAAAAAGGAAAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAA
* * *
52331854 AAAAATTTATTTTTTTTCGTGTCAGTATCAGGTATCAGTATACGAAAAAAGTAATAAAAAAAAAT
66 AAAAATTTATCTTTTTTCATGTCAGTATCAAGTATCAGTATACGAAAAAAGTAATAAAAAAAAAT
*
52331919 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAAATTATTTTTTTCGTGTC
131 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT-AAAAAAAATTACTTTTTTCGTGTC
52331984 AGTATCAGGTATCAGTA
195 AGTATCAGGTATCAGTA
* *
52332001 TACGAAAAAAAGGAAGAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCATAGT
1 TACGAAAAAAAGGAA-AAAAAAAA-TTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
* *
52332066 AAAAAAATTTA-CTTTTTTCATGTCAGTATCAAGTATCAGTATACG-AAAAAGTAATAAAAATAT
64 AAAAAAATTTATCTTTTTTCATGTCAGTATCAAGTATCAGTATACGAAAAAAGTAATAAAAAAAA
* *
52332129 TTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAATTACTTTTTTCGT
129 ATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAATTACTTTTTTCGT
52332192 ATACTGATAC
Statistics
Matches: 177, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
211 20 0.11
212 71 0.40
213 39 0.22
214 47 0.27
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (211 bp):
TACGAAAAAAAGGAAAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAA
AAAAATTTATCTTTTTTCATGTCAGTATCAAGTATCAGTATACGAAAAAAGTAATAAAAAAAAAT
TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAATTACTTTTTTCGTGTCA
GTATCAGGTATCAGTA
Found at i:52332156 original size:105 final size:105
Alignment explanation
Indices: 52331789--52332191 Score: 587
Period size: 107 Copynumber: 3.8 Consensus size: 105
52331779 CGGCACCCAG
* * * *
52331789 TACGAAAAAAAGGAA-AAAAAAAA-TTTAGGTGCTGGCCTGTTAATGGTCGGCACCCAGCACAGT
1 TACG-AAAAAAGTAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
* *
52331852 AAAAAAATTTATTTTTTTTCGTGTCAGTATCAGGTATCAGTA
65 AAAAAAAATTA-CTTTTTTCGTGTCAGTATCAGGTATCAGTA
52331894 TACGAAAAAAGTAATAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
1 TACGAAAAAAGTAAT-AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
*
52331959 AAAAAAAAATTATTTTTTTCGTGTCAGTATCAGGTATCAGTA
65 -AAAAAAAATTACTTTTTTCGTGTCAGTATCAGGTATCAGTA
* * *
52332001 TACGAAAAAAAGGAAGAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCATAGT
1 TACG-AAAAAAGTAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
* * *
52332066 AAAAAAATTTACTTTTTTCATGTCAGTATCAAGTATCAGTA
65 AAAAAAAATTACTTTTTTCGTGTCAGTATCAGGTATCAGTA
** *
52332107 TACG-AAAAAGTAATAAAAATATTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
1 TACGAAAAAAGTAATAAAAA-AAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
52332171 AAAAAAAATTACTTTTTTCGT
65 AAAAAAAATTACTTTTTTCGT
52332192 ATACTGATAC
Statistics
Matches: 272, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
104 22 0.08
105 63 0.23
106 49 0.18
107 119 0.44
108 19 0.07
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (105 bp):
TACGAAAAAAGTAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTA
AAAAAAATTACTTTTTTCGTGTCAGTATCAGGTATCAGTA
Found at i:52336010 original size:3 final size:3
Alignment explanation
Indices: 52336002--52336040 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
52335992 TACTTCAAAA
*
52336002 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
52336041 GTTGGGGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:52346574 original size:13 final size:11
Alignment explanation
Indices: 52346543--52346571 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
52346533 CCATTGTACT
52346543 TTAAAAAGCAG
1 TTAAAAAGCAG
52346554 TTAAAAAGCAG
1 TTAAAAAGCAG
52346565 TTAAAAA
1 TTAAAAA
52346572 AAGTGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (11 bp):
TTAAAAAGCAG
Found at i:52347210 original size:15 final size:16
Alignment explanation
Indices: 52347183--52347213 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
52347173 AAACCAAATA
52347183 GGACAAGAAAAGAAAC
1 GGACAAGAAAAGAAAC
52347199 GGACAA-AAAAGAAAC
1 GGACAAGAAAAGAAAC
52347214 AGAAATAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.65, C:0.13, G:0.23, T:0.00
Consensus pattern (16 bp):
GGACAAGAAAAGAAAC
Found at i:52347534 original size:12 final size:12
Alignment explanation
Indices: 52347517--52347541 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52347507 TGCTGGTGAG
52347517 AAAGGAAGGAAA
1 AAAGGAAGGAAA
52347529 AAAGGAAGGAAA
1 AAAGGAAGGAAA
52347541 A
1 A
52347542 TACTGAAGAG
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
AAAGGAAGGAAA
Found at i:52348840 original size:51 final size:52
Alignment explanation
Indices: 52348765--52348866 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 52
52348755 AGAGCCAATG
* **
52348765 AATGAAAATGAATAAAAATGATAAAGTAAC-AAAAATAGATCACACAAATCC
1 AATGAAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATCC
*
52348816 AATGGAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATC
1 AATGAAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATC
52348867 ACTATCCACA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 26 0.57
52 20 0.43
ACGTcount: A:0.63, C:0.12, G:0.09, T:0.17
Consensus pattern (52 bp):
AATGAAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATCC
Found at i:52349056 original size:16 final size:18
Alignment explanation
Indices: 52349029--52349061 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52349019 TAGAATTTGG
52349029 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
52349046 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
52349062 GTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:52350292 original size:9 final size:9
Alignment explanation
Indices: 52350274--52350324 Score: 75
Period size: 9 Copynumber: 5.4 Consensus size: 9
52350264 TTTGGTTAAA
52350274 AATTACCCG
1 AATTACCCG
*
52350283 AATTAACCG
1 AATTACCCG
52350292 AATTACCCG
1 AATTACCCG
52350301 AAAATTACCCG
1 --AATTACCCG
52350312 AATTACCCG
1 AATTACCCG
52350321 AATT
1 AATT
52350325 GAATCACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
9 29 0.76
11 9 0.24
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:52350312 original size:20 final size:20
Alignment explanation
Indices: 52350274--52350322 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
52350264 TTTGGTTAAA
52350274 AATTACCCG--AATTAACCG
1 AATTACCCGAAAATTAACCG
*
52350292 AATTACCCGAAAATTACCCG
1 AATTACCCGAAAATTAACCG
52350312 AATTACCCGAA
1 AATTACCCGAA
52350323 TTGAATCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 9 0.32
20 19 0.68
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (20 bp):
AATTACCCGAAAATTAACCG
Found at i:52354535 original size:28 final size:25
Alignment explanation
Indices: 52354468--52354519 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
52354458 AAAATTGGTA
52354468 AGACATTTTCCATTCTTCTCTAAGC
1 AGACATTTTCCATTCTTCTCTAAGC
52354493 AGACATTTTCCATTC-TCTTCTAAGC
1 AGACATTTTCCATTCTTC-TCTAAGC
52354518 AG
1 AG
52354520 CAAACATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (25 bp):
AGACATTTTCCATTCTTCTCTAAGC
Found at i:52357011 original size:14 final size:14
Alignment explanation
Indices: 52356994--52357021 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52356984 AATATATATT
52356994 AATATATATTAATA
1 AATATATATTAATA
52357008 AATATATATTAATA
1 AATATATATTAATA
52357022 TATGTGAAAA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:52357024 original size:10 final size:10
Alignment explanation
Indices: 52356980--52357012 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
52356970 AAAAACAATT
52356980 TATTAATATA
1 TATTAATATA
52356990 TATTAATATA
1 TATTAATATA
*
52357000 TATTAATAAA
1 TATTAATATA
52357010 TAT
1 TAT
52357013 ATATTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TATTAATATA
Found at i:52357079 original size:32 final size:33
Alignment explanation
Indices: 52357043--52357127 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
52357033 AACTTTTCTG
* * *
52357043 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
52357075 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
52357107 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
52357128 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:52357166 original size:34 final size:34
Alignment explanation
Indices: 52357108--52357173 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
52357098 CAAACACCAG
* *
52357108 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTACCAGTAAATCATTTTAC-GAAAAGT
*
52357143 AAAACATTTACCAG-AAATTATTTTACGAAAA
1 AAAACATTTACCAGTAAATCATTTTACGAAAA
52357174 ACATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 11 0.39
35 12 0.43
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTACCAGTAAATCATTTTACGAAAAGT
Found at i:52360366 original size:39 final size:39
Alignment explanation
Indices: 52360290--52360448 Score: 183
Period size: 39 Copynumber: 4.1 Consensus size: 39
52360280 ACTTCCAATA
* * * * **
52360290 CACCGACACACAGCATGTTAGGCACAAAGCCCAAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
** *
52360329 CATTGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
* * * * *
52360368 CACCAGCACAAAACCTGTTAGGCACTTAACCCGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
*
52360407 CACCGGCACAAAGCCTGCTAGGCGCTTAGCCCAAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
52360446 CAC
1 CAC
52360449 AGTATTTCTA
Statistics
Matches: 99, Mismatches: 21, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
39 99 1.00
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.16
Consensus pattern (39 bp):
CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
Found at i:52360435 original size:78 final size:78
Alignment explanation
Indices: 52360305--52360448 Score: 218
Period size: 78 Copynumber: 1.8 Consensus size: 78
52360295 ACACACAGCA
** *
52360305 TGTTAGGCACAAAGCCCAAATAATCATTGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCA
1 TGTTAGGCACAAAGCCCAAATAATCACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAATCA
52360370 CCAGCACAAAACC
66 CCAGCACAAAACC
* * *
52360383 TGTTAGGCACTTAA-CCCGAATAATCACCGGCACAAAGCCTGCTAGGCGCTTAGCCCAAATAATC
1 TGTTAGGCAC-AAAGCCCAAATAATCACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAATC
52360447 AC
65 AC
52360449 AGTATTTCTA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
78 57 0.97
79 2 0.03
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (78 bp):
TGTTAGGCACAAAGCCCAAATAATCACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAATCA
CCAGCACAAAACC
Found at i:52371693 original size:14 final size:15
Alignment explanation
Indices: 52371676--52371704 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52371666 ATTAGAAGTA
52371676 TTAAGAG-ATTTTAT
1 TTAAGAGTATTTTAT
52371690 TTAAGAGTATTTTAT
1 TTAAGAGTATTTTAT
52371705 GTCTTTAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
TTAAGAGTATTTTAT
Found at i:52375982 original size:30 final size:29
Alignment explanation
Indices: 52375956--52376035 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
52375946 TTGTTCTGGG
52375956 AAAAATAATTTTGACAAGATGGGTTCTGA
1 AAAAATAATTTTGACAAGATGGGTTCTGA
* * * *
52375985 AAAAATAAATTTAACATGATGTGTTCTGA
1 AAAAATAATTTTGACAAGATGGGTTCTGA
* *
52376014 AAAAATTATTTTGACGAGATGG
1 AAAAATAATTTTGACAAGATGG
52376036 ATTTTGTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (29 bp):
AAAAATAATTTTGACAAGATGGGTTCTGA
Found at i:52376034 original size:29 final size:28
Alignment explanation
Indices: 52375947--52376034 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 28
52375937 TGCTAAGTAT
*
52375947 TGTTCTGGGAAAAATAATTTTGACAAGATG
1 TGTTCT-GAAAAAATAATTTTGAC-AGATG
* * *
52375977 GGTTCTGAAAAAATAAATTTAACATGATG
1 TGTTCTGAAAAAATAATTTTGACA-GATG
*
52376006 TGTTCTGAAAAAATTATTTTGACGAGATG
1 TGTTCTGAAAAAATAATTTTGAC-AGATG
52376035 GATTTTGTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.02
29 41 0.85
30 6 0.12
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (28 bp):
TGTTCTGAAAAAATAATTTTGACAGATG
Found at i:52378492 original size:16 final size:16
Alignment explanation
Indices: 52378471--52378510 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
52378461 ACCATTGGTA
*
52378471 TTGTCTAAGGTACGTT
1 TTGTCTAAGGTACATT
52378487 TTGTCTAAGGTACATT
1 TTGTCTAAGGTACATT
52378503 TTGTCTAA
1 TTGTCTAA
52378511 CTACTACGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (16 bp):
TTGTCTAAGGTACATT
Found at i:52379575 original size:59 final size:59
Alignment explanation
Indices: 52379480--52379716 Score: 388
Period size: 59 Copynumber: 4.0 Consensus size: 59
52379470 CCACATCGAG
* *
52379480 AGAACTTCTAATTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
*
52379539 AGAACTTTTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
*
52379598 AGAATTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATT-AACA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAA-A
* *
52379657 ACAACTTCTATTTTATTAAATGAAACAAT-CTAAAATTAATTTGTACAAAAATATTCAAA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAA-TAATTTGTACAAAAATATTCAAA
52379716 A
1 A
52379717 ATAAATCACT
Statistics
Matches: 167, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
58 7 0.04
59 158 0.95
60 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (59 bp):
AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
Found at i:52380116 original size:18 final size:18
Alignment explanation
Indices: 52380093--52380136 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
52380083 GTGGAAAAAA
* *
52380093 GATACATATAAGGGTTAG
1 GATACACATAAGAGTTAG
52380111 GATACACATAAGAGTTAG
1 GATACACATAAGAGTTAG
52380129 GATACACA
1 GATACACA
52380137 CCTTGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (18 bp):
GATACACATAAGAGTTAG
Found at i:52384090 original size:3 final size:3
Alignment explanation
Indices: 52384069--52384131 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
52384059 TTTAAGATTT
* * * ** * * *
52384069 TTA TTA TTG TTA TTG TTA TTA TTA ATA CCA TCA TCA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52384117 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
52384132 AATTGTTTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:52388277 original size:6 final size:6
Alignment explanation
Indices: 52388266--52388292 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52388256 AGTGACTTTT
52388266 TTATAA TTATAA TTATAA TTATAA TTA
1 TTATAA TTATAA TTATAA TTATAA TTA
52388293 CTATGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:52402385 original size:14 final size:14
Alignment explanation
Indices: 52402366--52402392 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52402356 AAAATAATAC
52402366 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
52402380 AAAAAAATAAAAA
1 AAAAAAATAAAAA
52402393 AAGGTGCAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:52402526 original size:4 final size:4
Alignment explanation
Indices: 52402509--52402552 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
52402499 GAATGAGAGG
*
52402509 GAAA G-AA G-AA GAAA GAAA GAAA GAAA G-AA -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
52402553 ATGAAAGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 10 0.29
4 25 0.71
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:52402534 original size:22 final size:22
Alignment explanation
Indices: 52402509--52402588 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
52402499 GAATGAGAGG
52402509 GAAAGAAGAAGAAAGAAAGAAA
1 GAAAGAAGAAGAAAGAAAGAAA
* *
52402531 GAAAGAAAAAGAAGGAAAGAAAA
1 GAAAGAAGAAGAAAGAAAG-AAA
* * *
52402554 TGAAAGGAGAAGAGAAAAAAAAAA
1 -GAAAGAAGAAGA-AAGAAAGAAA
*
52402578 G-AAGTAGAAGA
1 GAAAGAAGAAGA
52402589 GGGGAGGAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 26 0.55
23 4 0.09
24 13 0.28
25 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (22 bp):
GAAAGAAGAAGAAAGAAAGAAA
Found at i:52402552 original size:18 final size:19
Alignment explanation
Indices: 52402508--52402552 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
52402498 AGAATGAGAG
52402508 GGAAAG-AAGAAGAAAGAA
1 GGAAAGAAAGAAGAAAGAA
*
52402526 AGAAAGAAAGAA-AAAGAA
1 GGAAAGAAAGAAGAAAGAA
52402544 GGAAAGAAA
1 GGAAAGAAA
52402553 ATGAAAGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (19 bp):
GGAAAGAAAGAAGAAAGAA
Found at i:52402553 original size:14 final size:14
Alignment explanation
Indices: 52402524--52402580 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
52402514 AAGAAGAAAG
52402524 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
*
52402538 AAAGAAGGAAAGAA
1 AAAGAAAGAAAGAA
*
52402552 AATGAAAGGAGAAGAGA
1 AAAGAAA-GA-AAGA-A
52402569 AAA-AAA-AAAGAA
1 AAAGAAAGAAAGAA
52402581 GTAGAAGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 1 0.03
13 4 0.11
14 19 0.53
15 2 0.06
16 7 0.19
17 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:52402559 original size:18 final size:17
Alignment explanation
Indices: 52402508--52402559 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
52402498 AGAATGAGAG
52402508 GGAAAGAAGAAGAAAGAA
1 GGAAAGAA-AAGAAAGAA
* *
52402526 AGAAAGAAAGAAAAAGAA
1 GGAAAGAAA-AGAAAGAA
52402544 GGAAAGAAAATGAAAG
1 GGAAAGAAAA-GAAAG
52402560 GAGAAGAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (17 bp):
GGAAAGAAAAGAAAGAA
Found at i:52403501 original size:284 final size:285
Alignment explanation
Indices: 52402988--52403654 Score: 1158
Period size: 284 Copynumber: 2.3 Consensus size: 285
52402978 AAAGTAAAAA
* *
52402988 TATAAAATTAGAAATTATGAAATTTTTTAAAGTAATAAAATACGGAGAAAAAAATACGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
* *
52403053 GGCCG-AGATAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTC
66 GGCCGAAG-TAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTC
* *
52403117 AAACAAAATGTACCGAAATAATATAAAATAATAAAATACAAAAATAATTTTTTTATTGAAAGTAA
130 AAACAAAATGTACCGAAATAATATAAAATAAAAAAATAAAAAAATAATTTTTTTATTGAAAGTAA
* *
52403182 TAAAATTCGGGAAAATAATACGAGCAAATGGCAGGAATAAGC-ATTTTTTTACACTAAATTAATT
195 TAAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGATTTTTTTACACTAAATTAATT
52403246 TAAAAAACACACTAAATTAATAAATT
260 TAAAAAACACACTAAATTAATAAATT
* *
52403272 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAACGCGGAGAAAAAAATAAGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
52403337 GGCCGAAGTAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCA
66 GGCCGAAGTAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCA
*
52403402 AACAAAATGTACTGAAATAATATAAAATAAAAAAATAAAAAAATAATTTTTTTATTGAAAGTAAT
131 AACAAAATGTACCGAAATAATATAAAATAAAAAAATAAAAAAATAATTTTTTTATTGAAAGTAAT
*
52403467 AAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGCTTTTTTTACACTAAATTAATTT
196 AAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGATTTTTTTACACTAAATTAATTT
52403532 AAAAAACACACTAAATTAATAAATT
261 AAAAAACACACTAAATTAATAAATT
* *
52403557 TATAAAATTAGAAATTATGATATTTTTTTAAGTAATAAAATGCGGAGAAAAGAATACGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
* *
52403622 GACTGAAGTAAGAGTGTTTTACTAACTATTTTT
66 GGCCGAAGTAAGAGTGTTTTACTAACT-TTTTT
52403655 TCAACATGCA
Statistics
Matches: 362, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
284 222 0.61
285 135 0.37
286 5 0.01
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (285 bp):
TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
GGCCGAAGTAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCA
AACAAAATGTACCGAAATAATATAAAATAAAAAAATAAAAAAATAATTTTTTTATTGAAAGTAAT
AAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGATTTTTTTACACTAAATTAATTT
AAAAAACACACTAAATTAATAAATT
Found at i:52408820 original size:9 final size:9
Alignment explanation
Indices: 52408806--52408831 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
52408796 ATGAAAACCA
52408806 TAATAATAT
1 TAATAATAT
52408815 TAATAATAT
1 TAATAATAT
52408824 TAATAATA
1 TAATAATA
52408832 ATTTTATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAATAATAT
Found at i:52408864 original size:16 final size:18
Alignment explanation
Indices: 52408843--52408889 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
52408833 TTTTATACTC
52408843 AAAATAATACTAA-C-TA
1 AAAATAATACTAACCATA
52408859 AAAATAATAACTAACCATA
1 AAAATAAT-ACTAACCATA
*
52408878 ATAATAATACTA
1 AAAATAATACTA
52408890 GTTTTTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 8 0.30
17 5 0.19
18 5 0.19
19 9 0.33
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAATACTAACCATA
Found at i:52409171 original size:10 final size:10
Alignment explanation
Indices: 52409143--52409180 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
52409133 AAAATACCAT
52409143 TTTTTCTCTTC
1 TTTTTCTC-TC
*
52409154 TCTTTCTCTC
1 TTTTTCTCTC
52409164 TTTTTCTCTC
1 TTTTTCTCTC
52409174 TTTTTCT
1 TTTTTCT
52409181 GCAACAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:52409289 original size:27 final size:27
Alignment explanation
Indices: 52409251--52409315 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
52409241 AACAAGACTA
*
52409251 GTGCCGCCCATGGGAAGGGCACCATTG
1 GTGCCGCCCATGGGAAGGGCACCATCG
*
52409278 GTGCCGCCCATGGGAATGGCACCATCG
1 GTGCCGCCCATGGGAAGGGCACCATCG
52409305 GTGCCGCCCAT
1 GTGCCGCCCAT
52409316 TAGTTAGGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.17, C:0.34, G:0.34, T:0.15
Consensus pattern (27 bp):
GTGCCGCCCATGGGAAGGGCACCATCG
Found at i:52409808 original size:20 final size:20
Alignment explanation
Indices: 52409780--52409818 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52409770 CAAAAAATGC
*
52409780 AAAAGTATAAAAAATATTAT
1 AAAAATATAAAAAATATTAT
* *
52409800 AAAAATATATAAGATATTA
1 AAAAATATAAAAAATATTA
52409819 AATTTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
AAAAATATAAAAAATATTAT
Found at i:52409826 original size:7 final size:7
Alignment explanation
Indices: 52409816--52409842 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
52409806 ATATAAGATA
52409816 TTAAATT
1 TTAAATT
52409823 TTAAATT
1 TTAAATT
52409830 TTAAATT
1 TTAAATT
52409837 TTAAAT
1 TTAAAT
52409843 ATATATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:52410838 original size:21 final size:20
Alignment explanation
Indices: 52410814--52410853 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
52410804 TGGTTATAAA
*
52410814 AAAATATTAATATTTAAATTT
1 AAAATAATAA-ATTTAAATTT
*
52410835 AAAATAATAAATTTTAATT
1 AAAATAATAAATTTAAATT
52410854 ATTTTTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATAATAAATTTAAATTT
Found at i:52410846 original size:28 final size:27
Alignment explanation
Indices: 52410788--52410857 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
52410778 TGTATAAATT
*
52410788 AATATTAATATTTAAATGGTTATAAAAA
1 AATATTAATATTTAAAT-GTTAAAAAAA
52410816 AATATTAATATTTAAAT-TTAAAATAATA
1 AATATTAATATTTAAATGTTAAAA-AA-A
*
52410844 AATTTTAATTATTT
1 AATATTAA-TATTT
52410858 TTTTGGTGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 5 0.14
27 2 0.05
28 25 0.68
29 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (27 bp):
AATATTAATATTTAAATGTTAAAAAAA
Found at i:52414661 original size:19 final size:18
Alignment explanation
Indices: 52414612--52414663 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
52414602 AAAATTTTGT
52414612 TTTTTAAATTAATTTTCA
1 TTTTTAAATTAATTTTCA
**
52414630 TTATTTATTTTAA-TTTCTA
1 TT-TTTAAATTAATTTTC-A
52414649 TATTTTAAATTAATT
1 T-TTTTAAATTAATT
52414664 CATATTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
18 6 0.23
19 18 0.69
20 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAAATTAATTTTCA
Found at i:52414785 original size:14 final size:15
Alignment explanation
Indices: 52414762--52414791 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52414752 ATGAATTAAA
52414762 TGTTT-TTTTTATTT
1 TGTTTATTTTTATTT
52414776 TGTTTATTTTTATTT
1 TGTTTATTTTTATTT
52414791 T
1 T
52414792 TTATAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (15 bp):
TGTTTATTTTTATTT
Found at i:52415045 original size:9 final size:9
Alignment explanation
Indices: 52415026--52415062 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
52415016 TGAGCTTTCG
*
52415026 AATTTGAAT
1 AATTCGAAT
*
52415035 AACTCGAAT
1 AATTCGAAT
52415044 AATTCGAAT
1 AATTCGAAT
52415053 AATTCGAAT
1 AATTCGAAT
52415062 A
1 A
52415063 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52422408 original size:102 final size:102
Alignment explanation
Indices: 52422290--52422489 Score: 319
Period size: 102 Copynumber: 2.0 Consensus size: 102
52422280 CCAGTGATTC
* * * *
52422290 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATTAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
*
52422355 CCAATGATTCAGGGAATCAACACTTAGCAACCCATCG
66 CCAATGAGTCAGGGAATCAACACTTAGCAACCCATCG
*
52422392 GGGGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
* * *
52422457 CCAATGAGTCGGGGAATTAGCACTTAGCAACCC
66 CCAATGAGTCAGGGAATCAACACTTAGCAACCC
52422490 CTTTCACAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 89 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
CCAATGAGTCAGGGAATCAACACTTAGCAACCCATCG
Found at i:52422453 original size:42 final size:40
Alignment explanation
Indices: 52422394--52422530 Score: 117
Period size: 42 Copynumber: 3.5 Consensus size: 40
52422384 ACCCATCGGG
*
52422394 GGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGAT
1 GGAATCAGCACTTAGCAACCCCCTTCACA-TTAAGATACG-T
* * *
52422436 GGAATCAGCACTTAGCAA-CCAC--CA-A-TGAG-T-CGG
1 GGAATCAGCACTTAGCAACCCCCTTCACATTAAGATACGT
* *
52422469 GGAATTAGCACTTAGCAACCCCTTTCACAATTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCAC-ATTAAGATAC-GT
* *
52422511 GGGATCAACACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
52422531 ACCAATGAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
33 17 0.23
34 4 0.05
35 1 0.01
36 5 0.07
38 2 0.03
39 5 0.07
40 1 0.01
41 4 0.05
42 35 0.47
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (40 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTAAGATACGT
Found at i:52422488 original size:75 final size:75
Alignment explanation
Indices: 52422392--52422564 Score: 265
Period size: 75 Copynumber: 2.3 Consensus size: 75
52422382 CAACCCATCG
* * *
52422392 GGGGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACAATTAAGATACGATGGAATCAACACTTAGCAACCA
* *
52422457 CCAATGAGTC
66 CCAATGAATA
* * * *
52422467 GGGGAATTAGCACTTAGCAACCCCTTTCACAATTAAGATACGGTGGGATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACAATTAAGATACGATGGAATCAACACTTAGCAACCA
52422532 CCAATGAATA
66 CCAATGAATA
52422542 GGGGAATCAGCACTTAGCAACCC
1 GGGGAATCAGCACTTAGCAACCC
52422565 TTTGGAGGAA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (75 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACAATTAAGATACGATGGAATCAACACTTAGCAACCA
CCAATGAATA
Found at i:52422559 original size:177 final size:177
Alignment explanation
Indices: 52422258--52422595 Score: 543
Period size: 177 Copynumber: 1.9 Consensus size: 177
52422248 CTGTTATCAG
* * * *
52422258 TGGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT
1 TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACAAT
* * *
52422323 TAAGATACGGTGGGATTAGCACTTAGCAACCACCAATGATTCAGGGAATCAACACTTAGCAACCC
66 TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAATCAGGGAATCAACACTTAGCAACCC
* *
52422388 ATCGGGGGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGA
131 ATCGGAGGAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGA
*
52422435 TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATTAGCACTTAGCAACCCCTTTCACAAT
1 TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACAAT
*
52422500 TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAAT-AGGGGAATCAGCACTTAGCAACC
66 TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAATCA-GGGAATCAACACTTAGCAACC
* *
52422564 CTTTGGAGGAATCAACACTTAGCAACCCCCTT
130 CATCGGAGGAATCAACACTTAGCAACCCCCTT
52422596 TATATTCAAT
Statistics
Matches: 147, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
176 1 0.01
177 146 0.99
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.22
Consensus pattern (177 bp):
TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACAAT
TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAATCAGGGAATCAACACTTAGCAACCC
ATCGGAGGAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGA
Found at i:52422561 original size:33 final size:33
Alignment explanation
Indices: 52422436--52422563 Score: 112
Period size: 33 Copynumber: 3.6 Consensus size: 33
52422426 AAGATACGAT
* *
52422436 GGAATCAGCACTTAGCAACCACCAATGAGTCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATAGG
* * *
52422469 GGAATTAGCACTTAGCAACCCCTTTCACAATTAAGATACGG
1 GGAATCAGCACTTAGCAA--CC--AC-CAA-TGA-ATA-GG
* *
52422510 TGGGATCAACACTTAGCAACCACCAATGAATAGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATAGG
52422544 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
52422564 CTTTGGAGGA
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
33 35 0.47
34 2 0.03
35 5 0.07
36 2 0.03
37 4 0.05
38 4 0.05
39 2 0.03
40 3 0.04
41 2 0.03
42 15 0.20
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATAGG
Found at i:52431120 original size:127 final size:127
Alignment explanation
Indices: 52430894--52431210 Score: 415
Period size: 127 Copynumber: 2.5 Consensus size: 127
52430884 TTTTATAACC
* * * *
52430894 AATTTTAGTATACCAAAATCATGTTATCCAAGACTTTACCAAGATTTCTAACGAAATACTAAAAA
1 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAACGAAATACTAAAAA
* * * * *
52430959 TTTTAAGTGCATATCTTAAGATATTTTGGTATATACCATAATTTTTATGGAATCTCGTTAAA
66 TTTTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * *
52431021 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAATGAAATTC-CAAAA
1 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAACGAAATACTAAAAA
52431085 TTTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
66 TTT-TAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * * * * *
52431148 AATTTTTGGCATACCAAAATCCA-GATT-TACAAGCCTATACCAATATTTTTAACAAAATGCTAA
1 AA-TTTTGGTATACCAAAAT-CATG-TTATCCAAGCCTTTACCAATATTTATAACGAAATACTAA
52431211 TTGTCTAATA
Statistics
Matches: 165, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
126 7 0.04
127 109 0.66
128 44 0.27
129 5 0.03
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.36
Consensus pattern (127 bp):
AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAACGAAATACTAAAAA
TTTTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
Found at i:52431218 original size:127 final size:127
Alignment explanation
Indices: 52430894--52431250 Score: 370
Period size: 127 Copynumber: 2.8 Consensus size: 127
52430884 TTTTATAACC
* * * * * * * * *
52430894 AATTTTAGTATACCAAAATCATGTTATCCAAGACTTTACCAAGATTTCTAA-CGAAATACTAAAA
1 AATTTTGGCATACCAAAATCATGTTATACAAGCCTATACCAATATTTATAATCAAAAT-C-CAAA
* * * * *
52430958 ATTT-TAAGTGCATATCTTAAGATATTTTGGTATATACCATAATTTTTATGGAATCTCGTTAAA
64 ATTTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * * * *
52431021 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAATGAAATTCCAAAAT
1 AATTTTGGCATACCAAAATCATGTTATACAAGCCTATACCAATATTTATAATCAAAATCCAAAAT
52431086 TTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
66 TTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * *
52431148 AATTTTTGGCATACCAAAATCCA-GATT-TACAAGCCTATACCAATATTTTTAA-CAAAATGC-T
1 AA-TTTTGGCATACCAAAAT-CATG-TTATACAAGCCTATACCAATATTTATAATCAAAATCCAA
* *
52431209 AATTGTCTAA-TAGCACATCCTCAA-ATATTTTGGTATATACCA
63 AATT-TCTAAGTA-CATAT-CTTAAGATATTTTGGTATATACCA
52431251 ACATTTACAA
Statistics
Matches: 199, Mismatches: 23, Indels: 16
0.84 0.10 0.07
Matches are distributed among these distances:
126 13 0.07
127 136 0.68
128 46 0.23
129 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (127 bp):
AATTTTGGCATACCAAAATCATGTTATACAAGCCTATACCAATATTTATAATCAAAATCCAAAAT
TTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
Found at i:52438856 original size:61 final size:63
Alignment explanation
Indices: 52438708--52438856 Score: 169
Period size: 63 Copynumber: 2.4 Consensus size: 63
52438698 AATATCCCTC
* * * * * *
52438708 ACACGGCCTGGACACACGCTCGTGTCTCTGGCCCTTGTGACTTTAAATCTAAAATAGTGAGTT
1 ACACGGCCTGGACACACGCTCGTGTCCCTGGCCCATGTGACTCTAAATCTAAAACAATGAGTA
* *
52438771 ACACGGCCTGGACACACGCCCGTGTCCCTGGCCCAT-TGACTCTAACT-TCAAAACAATGAGTA
1 ACACGGCCTGGACACACGCTCGTGTCCCTGGCCCATGTGACTCTAAATCT-AAAACAATGAGTA
* * *
52438833 ACATGG-CTTGACACACGGTCGTGT
1 ACACGGCCTGGACACACGCTCGTGT
52438857 GACCCACATG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
61 16 0.22
62 24 0.33
63 33 0.45
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (63 bp):
ACACGGCCTGGACACACGCTCGTGTCCCTGGCCCATGTGACTCTAAATCTAAAACAATGAGTA
Found at i:52439446 original size:22 final size:23
Alignment explanation
Indices: 52439401--52439451 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
52439391 AAAATATGAT
52439401 AGAAAGAAAAATGAACAAAAAAG
1 AGAAAGAAAAATGAACAAAAAAG
* *
52439424 AGAAGGAAGAATGAAC-AAAAAG
1 AGAAAGAAAAATGAACAAAAAAG
52439446 A-AAAGA
1 AGAAAGA
52439452 GGAGGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 4 0.16
22 7 0.28
23 14 0.56
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.04
Consensus pattern (23 bp):
AGAAAGAAAAATGAACAAAAAAG
Found at i:52443428 original size:28 final size:28
Alignment explanation
Indices: 52443349--52443428 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
52443339 AATTTTGGAC
* * *
52443349 AAAATTATAAAATATAAAAAATAAGGGA
1 AAAACTATAAAATCTAAAAAATAGGGGA
*
52443377 AAAACTATAAAATCTAAAAAATAGGGGC
1 AAAACTATAAAATCTAAAAAATAGGGGA
*
52443405 AAAACTGTAAAATCTAAAAAATAG
1 AAAACTATAAAATCTAAAAAATAG
52443429 TGGACATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.20
Consensus pattern (28 bp):
AAAACTATAAAATCTAAAAAATAGGGGA
Found at i:52446990 original size:16 final size:16
Alignment explanation
Indices: 52446964--52447003 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
52446954 TAACAGATCA
52446964 ACATCATACACATATAT
1 ACAT-ATACACATATAT
52446981 ACATATACACATATAT
1 ACATATACACATATAT
52446997 ATCATAT
1 A-CATAT
52447004 TAGAATTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (16 bp):
ACATATACACATATAT
Found at i:52448968 original size:3 final size:3
Alignment explanation
Indices: 52448954--52449008 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
52448944 AATTAAACAC
* * * *
52448954 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TGA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52449002 TAA TAA T
1 TAA TAA T
52449009 GAAATGTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52458397 original size:98 final size:98
Alignment explanation
Indices: 52458228--52458419 Score: 339
Period size: 98 Copynumber: 2.0 Consensus size: 98
52458218 ATACAATAAA
* *
52458228 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTTGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
52458293 CCTTTAGAATCCCAAACTCGGAATATTTCATTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCATTT
* *
52458326 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
52458391 CCTTTAGAATCTCAAACTCGGAATATTTC
66 CCTTTAGAATCCCAAACTCGGAATATTTC
52458420 CTTCATGATT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCATTT
Found at i:52458720 original size:15 final size:15
Alignment explanation
Indices: 52458702--52458734 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52458692 CAAATGCTAT
52458702 AATAATAAATACAAC
1 AATAATAAATACAAC
*
52458717 AATAATAAATACATC
1 AATAATAAATACAAC
52458732 AAT
1 AAT
52458735 GACATATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:52459222 original size:3 final size:3
Alignment explanation
Indices: 52459186--52459213 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
52459176 GCGCATGAAT
52459186 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
52459214 CGATAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:52459834 original size:6 final size:6
Alignment explanation
Indices: 52459823--52459857 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
52459813 TTTGTTTGTA
52459823 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAA
52459858 GCTGTAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:52460908 original size:19 final size:19
Alignment explanation
Indices: 52460884--52460934 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
52460874 TCTTGAAAAA
*
52460884 TAAAAAATTAAAT-ATTATT
1 TAAAAAATTAAATAACT-TT
*
52460903 TAAAAATTTAAATAACTTT
1 TAAAAAATTAAATAACTTT
*
52460922 TAAATAATTAAAT
1 TAAAAAATTAAAT
52460935 TATTTGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAAATTAAATAACTTT
Found at i:52460966 original size:30 final size:30
Alignment explanation
Indices: 52460921--52460997 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
52460911 TAAATAACTT
* *
52460921 TTAAATAATTAAATTATTTGTTAAATCTTAAA
1 TTAAAT-A-TAAATTACTTGTGAAATCTTAAA
*
52460953 TTAAATATAAATTACTTGTGAAATTTTAAA
1 TTAAATATAAATTACTTGTGAAATCTTAAA
*
52460983 TTAAA-ATAATTTACT
1 TTAAATATAAATTACT
52460998 AATTAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 9 0.22
30 25 0.61
31 1 0.02
32 6 0.15
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (30 bp):
TTAAATATAAATTACTTGTGAAATCTTAAA
Found at i:52461005 original size:29 final size:30
Alignment explanation
Indices: 52460941--52461007 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
52460931 AAATTATTTG
* **
52460941 TTAAATCTTAAATTAAATATAAATTACTTG
1 TTAAATTTTAAATTAAATATAAATTACTAA
* *
52460971 TGAAATTTTAAATTAAA-ATAATTTACTAA
1 TTAAATTTTAAATTAAATATAAATTACTAA
52461000 TTAAATTT
1 TTAAATTT
52461008 AATAAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (30 bp):
TTAAATTTTAAATTAAATATAAATTACTAA
Found at i:52461623 original size:24 final size:25
Alignment explanation
Indices: 52461574--52461627 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
52461564 TTAAATTTTA
*
52461574 TATTTAATGTATCATTACATTAAAT
1 TATTTAATATATCATTACATTAAAT
*
52461599 TATTTAA-ATATCATATA-ATTTAAT
1 TATTTAATATATCAT-TACATTAAAT
52461623 TATTT
1 TATTT
52461628 TTAGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (25 bp):
TATTTAATATATCATTACATTAAAT
Found at i:52464253 original size:46 final size:46
Alignment explanation
Indices: 52464186--52464278 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
52464176 GAGTTTGCCC
* ** *
52464186 AGGTTCCAAGCTCTTGCATATGTAGTGGACTCTAGAATACATGAAT
1 AGGTTCCAAGCTCCTGCATATGTAGCAGACTCAAGAATACATGAAT
* *
52464232 AGGTTCCGAGCTCCTGCATATGTTGCAGACTCAAGAATACATGAAT
1 AGGTTCCAAGCTCCTGCATATGTAGCAGACTCAAGAATACATGAAT
52464278 A
1 A
52464279 TTAAGCCCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (46 bp):
AGGTTCCAAGCTCCTGCATATGTAGCAGACTCAAGAATACATGAAT
Found at i:52469786 original size:15 final size:17
Alignment explanation
Indices: 52469755--52469788 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
52469745 TTAAAGTGTA
52469755 AATTTACTTTAATTTAT
1 AATTTACTTTAATTTAT
52469772 AATTT-CTTT-ATTTAT
1 AATTTACTTTAATTTAT
52469787 AA
1 AA
52469789 GAGATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTACTTTAATTTAT
Found at i:52477672 original size:20 final size:20
Alignment explanation
Indices: 52477647--52477692 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
52477637 CATTGGATGG
*
52477647 AAAATGAATGTATGAAATGA
1 AAAATGAATATATGAAATGA
**
52477667 AAAATGGTTATATGAAATGA
1 AAAATGAATATATGAAATGA
52477687 AAAATG
1 AAAATG
52477693 GTTGGAGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (20 bp):
AAAATGAATATATGAAATGA
Found at i:52477693 original size:20 final size:20
Alignment explanation
Indices: 52477657--52477695 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
52477647 AAAATGAATG
52477657 TATGAAATGAAAAATGGTTA
1 TATGAAATGAAAAATGGTTA
52477677 TATGAAATGAAAAATGGTT
1 TATGAAATGAAAAATGGTT
52477696 GGAGATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.31
Consensus pattern (20 bp):
TATGAAATGAAAAATGGTTA
Found at i:52481733 original size:28 final size:28
Alignment explanation
Indices: 52481668--52481756 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
52481658 ATACAATTCT
*
52481668 GGGTAAAATTATAAAAATTTAAAAAATAG
1 GGGTAAAATTAT-AAAATTTAAAAAATAA
* * *
52481697 GGGTAAAAACTATAAAATCTAAAAACTAA
1 GGGT-AAAATTATAAAATTTAAAAAATAA
* *
52481726 TGGTAAAATTGTAAAATTTAAAAAATAA
1 GGGTAAAATTATAAAATTTAAAAAATAA
52481754 GGG
1 GGG
52481757 ACACACGGCC
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
28 22 0.45
29 20 0.41
30 7 0.14
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (28 bp):
GGGTAAAATTATAAAATTTAAAAAATAA
Found at i:52485549 original size:50 final size:50
Alignment explanation
Indices: 52485423--52485720 Score: 262
Period size: 50 Copynumber: 5.9 Consensus size: 50
52485413 CATTTGGGTA
* *
52485423 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA-T
* * * *
52485477 ATGACAGGTCCCATGTAAGACCATGTTTAGGACATGGCGTTGGCACCGAGAT
1 A--AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
*
52485529 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * * *
52485579 GAGAGGTCCCCCGTAGGACCATGTCTGGGACATGGCATGGGCACCAATAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * * * *
52485629 GAGAACTCCCATGTAAGGCCATATATGGGATATGGCATTGGCAGTAC-AGGA-
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCGA-GAT
* * *
52485680 AACA--TCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
52485721 TGTTATTATC
Statistics
Matches: 202, Mismatches: 37, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
49 31 0.15
50 121 0.60
51 3 0.01
52 4 0.02
53 4 0.02
54 1 0.00
55 1 0.00
56 37 0.18
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:52491562 original size:16 final size:16
Alignment explanation
Indices: 52491543--52491573 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52491533 AAGCTATTTT
*
52491543 ATTATTTATTTTTAAA
1 ATTATTAATTTTTAAA
52491559 ATTATTAATTTTTAA
1 ATTATTAATTTTTAA
52491574 TGTCACATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATTAATTTTTAAA
Found at i:52491653 original size:6 final size:6
Alignment explanation
Indices: 52491642--52491706 Score: 62
Period size: 6 Copynumber: 10.5 Consensus size: 6
52491632 ATTTTTAATT
* *
52491642 ATTATA ATTATA ATTATA ATTATA ATTTATT ATTCA-A ATTATTA AATATA
1 ATTATA ATTATA ATTATA ATTATA A-TTATA ATT-ATA ATTA-TA ATTATA
52491692 ATT-TA ATTAATA ATT
1 ATTATA ATT-ATA ATT
52491707 CAAATATAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
5 6 0.12
6 28 0.57
7 15 0.31
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTATA
Found at i:52491682 original size:31 final size:30
Alignment explanation
Indices: 52491636--52491716 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
52491626 GAATATATTT
52491636 TTAATTATT-ATAATTATAATTATAATTATAA
1 TTAATTATTCA-AATTATAATTATAATT-TAA
* *
52491667 TTTATTATTCAAATTATTAAATATAATTTAA
1 TTAATTATTCAAATTA-TAATTATAATTTAA
*
52491698 TTAATAATTCAAA-TATAAT
1 TTAATTATTCAAATTATAAT
52491717 AAGACGAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 3 0.07
30 2 0.05
31 27 0.63
32 11 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAATTATTCAAATTATAATTATAATTTAA
Found at i:52510238 original size:18 final size:18
Alignment explanation
Indices: 52510198--52510240 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
52510188 AATTAGAATG
*
52510198 TAAAAATTAAACTAAAAA
1 TAAAAATTAAAATAAAAA
*
52510216 CAAAAATATAAAAT-AAAA
1 TAAAAAT-TAAAATAAAAA
52510234 TAAAAAT
1 TAAAAAT
52510241 GGATAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (18 bp):
TAAAAATTAAAATAAAAA
Found at i:52528986 original size:26 final size:26
Alignment explanation
Indices: 52528950--52529001 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
52528940 GTTGCACAAA
52528950 CCTACGTGTTACACATATCATCCATT
1 CCTACGTGTTACACATATCATCCATT
52528976 CCTACGTGTTACACATATCATCCATT
1 CCTACGTGTTACACATATCATCCATT
52529002 ATATGTTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.35
Consensus pattern (26 bp):
CCTACGTGTTACACATATCATCCATT
Found at i:52529315 original size:33 final size:35
Alignment explanation
Indices: 52529278--52529345 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
52529268 CCATTTTTGA
* *
52529278 CACTG-TACTGAGAAGGGCTAAGGCTCAA-ACTGT
1 CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
*
52529311 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
52529346 TCAACTGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (35 bp):
CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:52530949 original size:5 final size:5
Alignment explanation
Indices: 52530939--52530967 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
52530929 TCATATGTAC
52530939 ACATA ACATA ACATA ACATA ACATA ACAT
1 ACATA ACATA ACATA ACATA ACATA ACAT
52530968 TATAAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (5 bp):
ACATA
Found at i:52531665 original size:12 final size:12
Alignment explanation
Indices: 52531648--52531677 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
52531638 CCTCACACGC
52531648 CCGTGTGCTAGG
1 CCGTGTGCTAGG
52531660 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
52531672 CTGTGT
1 CCGTGT
52531678 AGCTTCTTGA
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:0.23, G:0.40, T:0.30
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:52537407 original size:18 final size:18
Alignment explanation
Indices: 52537384--52537438 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
52537374 TAATTTGGAG
52537384 AAAGAATTATGCTAGGTT
1 AAAGAATTATGCTAGGTT
52537402 AAAGAATTATGCTAGGTT
1 AAAGAATTATGCTAGGTT
52537420 AAAGAATTATGCTAGGTT
1 AAAGAATTATGCTAGGTT
52537438 A
1 A
52537439 TAACTTATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (18 bp):
AAAGAATTATGCTAGGTT
Found at i:52552703 original size:18 final size:18
Alignment explanation
Indices: 52552680--52552769 Score: 126
Period size: 18 Copynumber: 5.0 Consensus size: 18
52552670 CCCAACTACT
*
52552680 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
52552698 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* * *
52552716 ATATATGTGAATAGTATC
1 GTATACGTGAATAGTACC
*
52552734 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
52552752 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
52552770 ATAAACGGTC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:52552737 original size:36 final size:36
Alignment explanation
Indices: 52552681--52552769 Score: 142
Period size: 36 Copynumber: 2.5 Consensus size: 36
52552671 CCAACTACTG
*
52552681 TATACGTGAACAGTACCGTATACGTGAATAGTGCCA
1 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
* * *
52552717 TATATGTGAATAGTATCGTATACGTGAATAGTGCCG
1 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
52552753 TATACGTGAATAGTACC
1 TATACGTGAATAGTACC
52552770 ATAAACGGTC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (36 bp):
TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
Found at i:52555530 original size:22 final size:22
Alignment explanation
Indices: 52555482--52555578 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 22
52555472 TTTATGAAAG
* *
52555482 GATAAATAA-ATTTAAATATTAA
1 GATAAATAATATTTATAT-TTAT
* *
52555504 AATAAATAATATTTATTTTTAT
1 GATAAATAATATTTATATTTAT
*
52555526 GATAATTAAATGATATT-TATTTAT
1 GATAAAT-AAT-AT-TTATATTTAT
* *
52555550 TAT-AATAATATTTATCTTTAT
1 GATAAATAATATTTATATTTAT
*
52555571 GAAAAATA
1 GATAAATA
52555579 TTAAAAATAA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
20 2 0.04
21 9 0.16
22 23 0.40
23 11 0.19
24 10 0.18
25 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (22 bp):
GATAAATAATATTTATATTTAT
Found at i:52555535 original size:26 final size:27
Alignment explanation
Indices: 52555506--52555558 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
52555496 AATATTAAAA
*
52555506 TAAATAATATTTATTT-TTATGATAAT
1 TAAATAATATTTATTTATTATAATAAT
*
52555532 TAAATGATATTTATTTATTATAATAAT
1 TAAATAATATTTATTTATTATAATAAT
52555559 ATTTATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (27 bp):
TAAATAATATTTATTTATTATAATAAT
Found at i:52555578 original size:19 final size:19
Alignment explanation
Indices: 52555538--52555580 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
52555528 TAATTAAATG
* *
52555538 ATATTTATTTATTATAATA
1 ATATTTATCTATTATAAAA
52555557 ATATTTATCT-TTATGAAAA
1 ATATTTATCTATTAT-AAAA
52555576 ATATT
1 ATATT
52555581 AAAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
ATATTTATCTATTATAAAA
Found at i:52557642 original size:13 final size:13
Alignment explanation
Indices: 52557624--52557695 Score: 58
Period size: 13 Copynumber: 5.3 Consensus size: 13
52557614 AACATGAAAG
52557624 TAAAAATAAAAAA
1 TAAAAATAAAAAA
52557637 TAAAAAGTAAAAATA
1 TAAAAA-TAAAAA-A
* *
52557652 AAGAAAATAAATAA
1 TA-AAAATAAAAAA
52557666 T-AAAATAAAGAAA
1 TAAAAATAAA-AAA
*
52557679 -ATAAATAAATAAA
1 TAAAAATAAA-AAA
52557692 TAAA
1 TAAA
52557696 TAAAACTTGG
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
12 8 0.17
13 18 0.39
14 9 0.20
15 7 0.15
16 4 0.09
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:52557645 original size:20 final size:20
Alignment explanation
Indices: 52557620--52557674 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
52557610 TATTAACATG
52557620 AAAGTAAAAATAAAAAATAA
1 AAAGTAAAAATAAAAAATAA
52557640 AAAGTAAAAATAAAGAAAATAA
1 AAAGTAAAAAT-AA-AAAATAA
52557662 ATAA-T-AAAATAAA
1 A-AAGTAAAAATAAA
52557675 GAAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
21 7 0.22
22 9 0.28
23 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (20 bp):
AAAGTAAAAATAAAAAATAA
Found at i:52557658 original size:29 final size:29
Alignment explanation
Indices: 52557625--52557700 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
52557615 ACATGAAAGT
*
52557625 AAAAATAAAAAATAAAA-AGTA-AAAATAA
1 AAAAATAAAAAATAAAATA-AAGAAAATAA
*
52557653 AGAAAATAAATAATAAAATAAAGAAAATAA
1 A-AAAATAAAAAATAAAATAAAGAAAATAA
*
52557683 ATAAATAAATAAATAAAA
1 AAAAATAAA-AAATAAAA
52557701 CTTGGGTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.03
29 23 0.57
30 16 0.40
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (29 bp):
AAAAATAAAAAATAAAATAAAGAAAATAA
Found at i:52557665 original size:4 final size:4
Alignment explanation
Indices: 52557627--52557699 Score: 57
Period size: 4 Copynumber: 18.8 Consensus size: 4
52557617 ATGAAAGTAA
* *
52557627 AAAT AAA- AAAT AAA- AAGT -AA- AAAT AAAGA AAAT AAAT -AAT AAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT -AAAT
*
52557672 AAAGA AAAT AAAT AAAT AAAT AAAT AAA
1 AAA-T AAAT AAAT AAAT AAAT AAAT AAA
52557700 ACTTGGGTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
3 11 0.20
4 35 0.64
5 9 0.16
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:52559610 original size:25 final size:25
Alignment explanation
Indices: 52559562--52559610 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
52559552 CATAATTGAA
* * *
52559562 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
52559587 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
52559611 GTGTATTGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:52562411 original size:39 final size:39
Alignment explanation
Indices: 52562349--52562427 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
52562339 TAGGAAACTC
* ** *
52562349 ATCCCTTATAAGAGTGTTGTCATAGGGTGTTTTTAACCT
1 ATCCCTTATAAGAGAGTCATCATAGGGTGTTTGTAACCT
*
52562388 ATCCTTTATAAGAGAGTCATCATAGGGTGTTTGTAACCT
1 ATCCCTTATAAGAGAGTCATCATAGGGTGTTTGTAACCT
52562427 A
1 A
52562428 CTCAAGTGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (39 bp):
ATCCCTTATAAGAGAGTCATCATAGGGTGTTTGTAACCT
Found at i:52572149 original size:12 final size:12
Alignment explanation
Indices: 52572132--52572156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52572122 ATCATTTCTA
52572132 TTCATTTAGTTC
1 TTCATTTAGTTC
52572144 TTCATTTAGTTC
1 TTCATTTAGTTC
52572156 T
1 T
52572157 GCATGCAATT
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:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TTCATTTAGTTC
Found at i:52577974 original size:17 final size:16
Alignment explanation
Indices: 52577940--52577984 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
52577930 TTGGCAACTT
*
52577940 GTAAGCTCTCAAGTTTG
1 GTAAGCTCGC-AGTTTG
52577957 GTAAGCTCGCAGTCTTG
1 GTAAGCTCGCAGT-TTG
*
52577974 GTGAGCTCGCA
1 GTAAGCTCGCA
52577985 CAATTTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (16 bp):
GTAAGCTCGCAGTTTG
Found at i:52583959 original size:12 final size:12
Alignment explanation
Indices: 52583925--52583972 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
52583915 GGCCTCTCAT
52583925 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
52583937 -GTTCTTCTTTTC
1 TTTTCTT-TTTTC
52583949 TTTTCTTTTTTC
1 TTTTCTTTTTTC
52583961 TTTTCATTTTTT
1 TTTTC-TTTTTT
52583973 TCAAGTGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 5 0.16
12 15 0.48
13 11 0.35
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:52584433 original size:25 final size:23
Alignment explanation
Indices: 52584400--52584446 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
52584390 CGGTAGAGGG
*
52584400 TTTTTTTTATTTTTTTGTTTTTTA
1 TTTTTTTTA-TTTTGTGTTTTTTA
52584424 TTTTCTTTTATTTTGTGTTTTTT
1 TTTT-TTTTATTTTGTGTTTTTT
52584447 TGTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.06, C:0.02, G:0.06, T:0.85
Consensus pattern (23 bp):
TTTTTTTTATTTTGTGTTTTTTA
Found at i:52584447 original size:25 final size:24
Alignment explanation
Indices: 52584400--52584457 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
52584390 CGGTAGAGGG
*
52584400 TTTTTTTTATTTTTTTGTTTTTTA
1 TTTTTTTTATTTTTGTGTTTTTTA
*
52584424 TTTTCTTTTATTTTGTGTTTTTTTGTA
1 TTTT-TTTTATTTT-TGTGTTTTT-TA
52584451 TTTTTTT
1 TTTTTTT
52584458 ACTATACTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.14
25 9 0.31
26 10 0.34
27 6 0.21
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.84
Consensus pattern (24 bp):
TTTTTTTTATTTTTGTGTTTTTTA
Found at i:52584458 original size:25 final size:24
Alignment explanation
Indices: 52584400--52584457 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 24
52584390 CGGTAGAGGG
52584400 TTTTTTTTATTTTTTTGTTTTTTA
1 TTTTTTTTATTTTTTTGTTTTTTA
52584424 TTTTCTTTTATTTTGTGTT-TTTTTGTA
1 TTTT-TTTTATTTT-T-TTGTTTTT-TA
52584451 TTTTTTT
1 TTTTTTT
52584458 ACTATACTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 4 0.13
25 9 0.30
26 9 0.30
27 8 0.27
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.84
Consensus pattern (24 bp):
TTTTTTTTATTTTTTTGTTTTTTA
Found at i:52588895 original size:14 final size:15
Alignment explanation
Indices: 52588876--52588904 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52588866 AAATACGATC
52588876 CTTGTATAAA-AAAA
1 CTTGTATAAATAAAA
52588890 CTTGTATAAATAAAA
1 CTTGTATAAATAAAA
52588905 TTAGTCGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (15 bp):
CTTGTATAAATAAAA
Found at i:52589525 original size:3 final size:3
Alignment explanation
Indices: 52589510--52589589 Score: 54
Period size: 3 Copynumber: 25.7 Consensus size: 3
52589500 TGAATGAGTA
* * *
52589510 AAT AAT TAT AAT AAT AAGGT AAGT AAT AAT AAG AA- ATAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AA--T AA-T AAT AAT AAT AAT A-AT AAT AAT AAT
* * * *
52589558 AAT AAA AAT AAT AAT AGT AAA AAT AAT GAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52589590 CACTATTAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
2 1 0.02
3 52 0.85
4 5 0.08
5 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:52589567 original size:15 final size:15
Alignment explanation
Indices: 52589549--52589589 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
52589539 TAAGAAATAC
52589549 AATAATAATAATAAA
1 AATAATAATAATAAA
*
52589564 AATAATAATAGTAAA
1 AATAATAATAATAAA
*
52589579 AATAATGATAA
1 AATAATAATAA
52589590 CACTATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (15 bp):
AATAATAATAATAAA
Done.