Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 168 of 325
Found at i:51911232 original size:11 final size:11
Alignment explanation
Indices: 51911203--51911271 Score: 93
Period size: 11 Copynumber: 5.8 Consensus size: 11
51911193 TGCACAAATC
51911203 ATTTTTTTTGAA
1 ATTTTTTTTG-A
51911215 ACTTTTTTTTTGA
1 A--TTTTTTTTGA
51911228 ATTTTTTTTGA
1 ATTTTTTTTGA
51911239 ATTTTTTTTCCGA
1 ATTTTTTTT--GA
51911252 ATTTTTTTTGA
1 ATTTTTTTTGA
51911263 ATTTTTTTT
1 ATTTTTTTT
51911272 ATACTTGTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
11 30 0.57
12 1 0.02
13 13 0.25
14 9 0.17
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.71
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:51911244 original size:24 final size:24
Alignment explanation
Indices: 51911203--51911271 Score: 104
Period size: 24 Copynumber: 2.8 Consensus size: 24
51911193 TGCACAAATC
*
51911203 ATTTTTTTTGAAACTTTTTTTT-TGA
1 ATTTTTTTTG-AA-TTTTTTTTCCGA
51911228 ATTTTTTTTGAATTTTTTTTCCGA
1 ATTTTTTTTGAATTTTTTTTCCGA
51911252 ATTTTTTTTGAATTTTTTTT
1 ATTTTTTTTGAATTTTTTTT
51911272 ATACTTGTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
23 8 0.19
24 24 0.57
25 10 0.24
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.71
Consensus pattern (24 bp):
ATTTTTTTTGAATTTTTTTTCCGA
Found at i:51912997 original size:30 final size:30
Alignment explanation
Indices: 51912912--51913008 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
51912902 TAAACTAAAA
* * *
51912912 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCCCGTGAGCTGAAGT
* * * *
51912942 TGAGCTGAGGTTAAACTCC-TAAGCTGAAGT
1 TGAGCTAAGGTTTAGC-CCGTGAGCTGAAGT
51912972 TGAGCTAAGGTTTAGCCCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCCCGTGAGCTGAAGT
51913001 ATGAGCTA
1 -TGAGCTA
51913009 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
29 3 0.06
30 49 0.92
31 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCCCGTGAGCTGAAGT
Found at i:51916458 original size:12 final size:12
Alignment explanation
Indices: 51916416--51916452 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
51916406 AAACTCTTTT
**
51916416 TCTTTTTCCTTC
1 TCTTTTTCAATC
51916428 TCTTTTTCAATC
1 TCTTTTTCAATC
51916440 TCTTTTTCAATC
1 TCTTTTTCAATC
51916452 T
1 T
51916453 TATTTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (12 bp):
TCTTTTTCAATC
Found at i:51917443 original size:49 final size:49
Alignment explanation
Indices: 51917326--51917468 Score: 207
Period size: 49 Copynumber: 2.9 Consensus size: 49
51917316 TCTATTGTGA
* *** *
51917326 GGTCACATGTGTAGTACTAAGTGCAGGATACTACGT-TATTGGATTATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
51917374 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
51917423 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
51917469 GCTTTGGCTA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
48 35 0.41
49 51 0.59
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:51918726 original size:14 final size:13
Alignment explanation
Indices: 51918702--51918740 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
51918692 TTTTGATCTC
51918702 CTTTTTGCTTTTCAT
1 CTTTTT-CTTTTC-T
51918717 CTTTTTCTTTTCT
1 CTTTTTCTTTTCT
*
51918730 CATTTTCTTTT
1 CTTTTTCTTTT
51918741 TACAAGAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 6 0.26
15 6 0.26
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.72
Consensus pattern (13 bp):
CTTTTTCTTTTCT
Found at i:51919692 original size:10 final size:10
Alignment explanation
Indices: 51919677--51919701 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
51919667 GTATACTTCT
51919677 TTTTTTTGAA
1 TTTTTTTGAA
51919687 TTTTTTTGAA
1 TTTTTTTGAA
51919697 TTTTT
1 TTTTT
51919702 CTAAAATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:51924301 original size:64 final size:62
Alignment explanation
Indices: 51924230--51924363 Score: 187
Period size: 64 Copynumber: 2.1 Consensus size: 62
51924220 GGGTAGGTTC
* * *
51924230 AAAAAAAAATTTACTTCATAAAATTCAAGTATTATATTGTATTTACCATTTTAGTAGTTTATA
1 AAAAAAAAAATTAATTCATAAAATTCAAGTATTATATTGTAATTACCATTTTAGTAG-TTATA
* * * *
51924293 AACAAAAAAAATTAATTCGTGAAATTCAAGTATTATATTGTAATTATCGTTTTAGTAGTTATA
1 AA-AAAAAAAATTAATTCATAAAATTCAAGTATTATATTGTAATTACCATTTTAGTAGTTATA
51924356 AAAAAAAA
1 AAAAAAAA
51924364 GAGTATAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
62 6 0.10
63 9 0.14
64 48 0.76
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (62 bp):
AAAAAAAAAATTAATTCATAAAATTCAAGTATTATATTGTAATTACCATTTTAGTAGTTATA
Found at i:51926547 original size:12 final size:12
Alignment explanation
Indices: 51926528--51926561 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
51926518 AGAAAGAAAA
51926528 GAGTGAAAAGGT
1 GAGTGAAAAGGT
* *
51926540 GTGTGAAAAAGT
1 GAGTGAAAAGGT
51926552 GAGTGAAAAG
1 GAGTGAAAAG
51926562 AAACGAGGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (12 bp):
GAGTGAAAAGGT
Found at i:51929858 original size:14 final size:14
Alignment explanation
Indices: 51929839--51929883 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
51929829 AACTCATCTT
*
51929839 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
51929853 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
51929866 AATTTAATTTAATG
1 AGTTTAATTTAATG
51929880 AGTT
1 AGTT
51929884 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:51930890 original size:29 final size:29
Alignment explanation
Indices: 51930858--51930917 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
51930848 ATAACCAAAC
* *
51930858 CTACAAAAACTTTATATCTATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
51930887 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
51930916 CT
1 CT
51930918 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:51932238 original size:18 final size:18
Alignment explanation
Indices: 51932215--51932264 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
51932205 GAAAGACAAA
*
51932215 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
51932233 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
51932251 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
51932265 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:51932241 original size:24 final size:24
Alignment explanation
Indices: 51932212--51932289 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
51932202 AATGAAAGAC
* *
51932212 AAAGAAAAAGAGATTGAGAGTGAA
1 AAAGAAAAAGAGATTGAGAGAGAG
* * *
51932236 AAAGAAAATGAGATTGAAAAAGAG
1 AAAGAAAAAGAGATTGAGAGAGAG
* *
51932260 AATGAAAAAGAGTTTGAGAGAGAG
1 AAAGAAAAAGAGATTGAGAGAGAG
51932284 AAAGAA
1 AAAGAA
51932290 TGTGAACAAG
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (24 bp):
AAAGAAAAAGAGATTGAGAGAGAG
Found at i:51934758 original size:14 final size:14
Alignment explanation
Indices: 51934739--51934783 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
51934729 AACTCATCTT
*
51934739 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
51934753 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
51934766 AATTTAATTTAATG
1 AGTTTAATTTAATG
51934780 AGTT
1 AGTT
51934784 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:51935801 original size:29 final size:29
Alignment explanation
Indices: 51935769--51935828 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
51935759 ATAACCAAAC
* *
51935769 CTACAAAAACTTTATATCTATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
51935798 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
51935827 CT
1 CT
51935829 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:51942949 original size:30 final size:30
Alignment explanation
Indices: 51942915--51943011 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
51942905 TAAACTAAAA
51942915 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
51942945 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
51942975 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
51943005 TGAGCTA
1 TGAGCTA
51943012 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:51946038 original size:41 final size:41
Alignment explanation
Indices: 51945990--51946074 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 41
51945980 CTAACATGAA
*
51945990 CTGGTGTAGAGTACTCTGAGCTATCTTGAGCTAAAGATAAG
1 CTGGTGTAGAGTACTCTGAGCTAACTTGAGCTAAAGATAAG
* *
51946031 CTGGTGTAGAGTACTCTGAGCTAACTTGAGCTGAAGATGAG
1 CTGGTGTAGAGTACTCTGAGCTAACTTGAGCTAAAGATAAG
51946072 CTG
1 CTG
51946075 CATATACACT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.28
Consensus pattern (41 bp):
CTGGTGTAGAGTACTCTGAGCTAACTTGAGCTAAAGATAAG
Found at i:51953924 original size:20 final size:20
Alignment explanation
Indices: 51953896--51953944 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
51953886 ATTGTTTGGG
51953896 TTTTGTTTTTTTTAACTTGT
1 TTTTGTTTTTTTTAACTTGT
* *
51953916 TTTTTTTTTTTTTTACTT-T
1 TTTTGTTTTTTTTAACTTGT
51953935 TGTTTGTTTT
1 T-TTTGTTTT
51953945 CTTGGTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.06, C:0.04, G:0.08, T:0.82
Consensus pattern (20 bp):
TTTTGTTTTTTTTAACTTGT
Found at i:51955253 original size:27 final size:27
Alignment explanation
Indices: 51955211--51955409 Score: 263
Period size: 27 Copynumber: 7.4 Consensus size: 27
51955201 TGGATAAGTT
* *
51955211 GTAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
**
51955238 GTAGAATTACCAAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
51955265 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* *
51955292 GTAGAATTACTGAAATGCCCCTATAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* * *
51955319 ATAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
51955346 GTAGAAATACTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* * *
51955373 GTAGAATTACTGAGATACCCTTGTGGG
1 GTAGAATTACTGAAATACCCCTGTAGG
*
51955400 GTAAAATTAC
1 GTAGAATTAC
51955410 AATTTTGCCC
Statistics
Matches: 150, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 150 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (27 bp):
GTAGAATTACTGAAATACCCCTGTAGG
Found at i:51955408 original size:81 final size:81
Alignment explanation
Indices: 51955211--51955409 Score: 290
Period size: 81 Copynumber: 2.5 Consensus size: 81
51955201 TGGATAAGTT
* * *
51955211 GTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTATT
1 GTAGAATTACTGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAAATACT
51955276 GAAATACCCCTGTAGG
66 GAAATACCCCTGTAGG
* * * * * *
51955292 GTAGAATTACTGAAATGCCCCTATAGGATAGAATTACCGAAATACCCTTGTAGGGTAGAAATACT
1 GTAGAATTACTGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAAATACT
51955357 GAAATACCCCTGTAGG
66 GAAATACCCCTGTAGG
* * *
51955373 GTAGAATTACTGAGATACCCTTGTGGGGTAAAATTAC
1 GTAGAATTACTGAAATACCCTTGTAGGGTAGAATTAC
51955410 AATTTTGCCC
Statistics
Matches: 102, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 102 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (81 bp):
GTAGAATTACTGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAAATACT
GAAATACCCCTGTAGG
Found at i:51956155 original size:2 final size:2
Alignment explanation
Indices: 51956148--51956183 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
51956138 GCTTCGCCAC
*
51956148 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51956184 CTGTTCTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51957530 original size:41 final size:41
Alignment explanation
Indices: 51957473--51957570 Score: 162
Period size: 41 Copynumber: 2.4 Consensus size: 41
51957463 ACAAGTGGAC
* *
51957473 TGAGCTG-ACATGAGCTGGCGTAGAGTACTCTGAGCTATCT
1 TGAGCTGAAGATGAGCTGGCGTAGAGTACTCTGAGCTAACT
*
51957513 TGAGCTGAAGATGAGCTGGTGTAGAGTACTCTGAGCTAACT
1 TGAGCTGAAGATGAGCTGGCGTAGAGTACTCTGAGCTAACT
51957554 TGAGCTGAAGATGAGCT
1 TGAGCTGAAGATGAGCT
51957571 ACTATACACT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 7 0.13
41 47 0.87
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.27
Consensus pattern (41 bp):
TGAGCTGAAGATGAGCTGGCGTAGAGTACTCTGAGCTAACT
Found at i:51960759 original size:20 final size:20
Alignment explanation
Indices: 51960725--51960782 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
51960715 TAGCTCACCT
* * *
51960725 AGCTCACAACTAGCTCAGCA
1 AGCTCACATCCAGCTCAACA
**
51960745 AGCTCAGTTCCAGCTCAACA
1 AGCTCACATCCAGCTCAACA
*
51960765 AGTTCACATCCAGCTCAA
1 AGCTCACATCCAGCTCAA
51960783 TTCCAGTTCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.34, G:0.14, T:0.19
Consensus pattern (20 bp):
AGCTCACATCCAGCTCAACA
Found at i:51971931 original size:14 final size:14
Alignment explanation
Indices: 51971897--51971931 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
51971887 GTAATTCGGT
* *
51971897 AAAAAAGTCGTACA
1 AAAAAATTCATACA
51971911 AAAAAATTCATACA
1 AAAAAATTCATACA
51971925 AAAAAAT
1 AAAAAAT
51971932 AATATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (14 bp):
AAAAAATTCATACA
Found at i:51974326 original size:46 final size:45
Alignment explanation
Indices: 51974260--51974346 Score: 156
Period size: 46 Copynumber: 1.9 Consensus size: 45
51974250 AAGTGTGGCA
51974260 TTCATTTATACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAGG
1 TTCATTTATACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAGG
*
51974305 TTCATCTTATACCAAGGTTCCTATCATTCTTGATAGTGGGTC
1 TTCAT-TTATACCAAGGTTCCTATCATCCTTGATAGTGGGTC
51974347 TCGTCTTTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 5 0.12
46 35 0.88
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (45 bp):
TTCATTTATACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAGG
Found at i:51975486 original size:18 final size:18
Alignment explanation
Indices: 51975465--51975500 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
51975455 ATAATAAACT
51975465 AAATGAAAATAAAACAAA
1 AAATGAAAATAAAACAAA
51975483 AAATGAAAATAAAACAAA
1 AAATGAAAATAAAACAAA
51975501 CATTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.11
Consensus pattern (18 bp):
AAATGAAAATAAAACAAA
Found at i:51982742 original size:15 final size:15
Alignment explanation
Indices: 51982722--51982775 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
51982712 GTATCTTGGG
51982722 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* * *
51982737 TCTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
51982752 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
51982767 TTTCTTTAT
1 TTTCTTTAT
51982776 TCGATTTTCT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.11, C:0.19, G:0.13, T:0.57
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:51982752 original size:30 final size:30
Alignment explanation
Indices: 51982718--51982777 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
51982708 TATCGTATCT
*
51982718 TGGGTTTCTTTATCCTGGATCTCTTTATTC
1 TGGGTTTCTCTATCCTGGATCTCTTTATTC
* *
51982748 TGGGTTTCTCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTCTATCCTGGATCTCTTTATTC
51982778 GATTTTCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.10, C:0.18, G:0.17, T:0.55
Consensus pattern (30 bp):
TGGGTTTCTCTATCCTGGATCTCTTTATTC
Found at i:51986810 original size:46 final size:46
Alignment explanation
Indices: 51986755--51986928 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 46
51986745 TTTGGGCATT
51986755 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* *** * *
51986801 CAAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA--TC
1 CGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATGTC
* *
51986848 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
*
51986894 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
51986929 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 66 0.62
47 31 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
Found at i:51986908 original size:93 final size:93
Alignment explanation
Indices: 51986749--51986920 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
51986739 ATGATGTTTG
* *
51986749 GGCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCAAACTCGTTGAG
51986814 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
51986842 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCAAACTCGTTGAG
51986907 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
51986921 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCAAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:51996029 original size:19 final size:19
Alignment explanation
Indices: 51996005--51996044 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
51995995 AGCTCCCATG
51996005 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
51996024 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
51996043 TA
1 TA
51996045 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:51997714 original size:11 final size:11
Alignment explanation
Indices: 51997698--51997734 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
51997688 TATACAAGTT
51997698 AAAAAAATTCG
1 AAAAAAATTCG
51997709 AAAAAAATT-G
1 AAAAAAATTCG
51997719 AAAAAAA-TC-
1 AAAAAAATTCG
51997728 AAAAAAA
1 AAAAAAA
51997735 AGTGATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 9 0.36
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:52000291 original size:51 final size:52
Alignment explanation
Indices: 52000215--52000316 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 52
52000205 TAATCCGAAG
52000215 AAATGAAGGAATTGCAAAAGCAAATTACTGAACTCCTAGACAAA-GATACAA
1 AAATGAAGGAATTGCAAAAGCAAATTACTGAACTCCTAGACAAAGGATACAA
52000266 AAATGAAGGAATTGCAAAAGCAAATTACTGAACTCCTAGACAAAGGATACA
1 AAATGAAGGAATTGCAAAAGCAAATTACTGAACTCCTAGACAAAGGATACA
52000317 TTTGAGAGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 44 0.88
52 6 0.12
ACGTcount: A:0.50, C:0.16, G:0.17, T:0.18
Consensus pattern (52 bp):
AAATGAAGGAATTGCAAAAGCAAATTACTGAACTCCTAGACAAAGGATACAA
Found at i:52003308 original size:438 final size:439
Alignment explanation
Indices: 52002492--52003366 Score: 1680
Period size: 438 Copynumber: 2.0 Consensus size: 439
52002482 CTAAATTCTA
*
52002492 TGATATTCGGCATCTATGATGTTCACACTAACTTAAATTCTGTTCACATTTGTATTTAACATGTT
1 TGATATTCGGCATCTATGATGTTCACACTAACTTAAATTCTATTCACATTTGTATTTAACATGTT
**
52002557 CACACAAAAGCATTAAAGTTTGGTTCATGCTTGAAGATGGTGCATGAATTGGCTGAACCATCATG
66 CACACAAAAGCATTAAAGTTTGGTTCATGCTTGAAGATGGTGCATGAATTGGCCAAACCATCATG
52002622 TTGCTTCACTTGATGCATTCATGCATATGTAGCCTAGAAGAAAAGCCATAATTCATGAATGTGCA
131 TTGCTTCACTTGATGCATTCATGCATATGTAGCCTAGAAGAAAAGCCATAATTCATGAATGTGCA
52002687 GCCCTTTAATACTCCTACATCTCCCTTGGTCAAATGAGGCTTGAATGTACCTTGAATACTTGAAT
196 GCCCTTTAATACTCCTACATCTCCCTTGGTCAAATGAGGCTTGAATGTACCTTGAATACTTGAAT
*
52002752 GGACATCTTGGATATGCATGATACATGCATGAAACATCCCAACGCATGTTCTTCCTTAATTACGG
261 GGACATCTTGGATATGCATGATACATACATGAAACATCCCAACGCATGTTCTTCCTTAATTACGG
*
52002817 TCCATGAATCTTCAAATACATGTACATAAAATAGCCCCCACTTGCATGAACGTCCCTAATACATG
326 TCCATGAATCTTCAAATACATGTACATAAAATAGCCCCCACTTGCATGAACGTCCCCAATACATG
52002882 AATTCCTTCAAATGCCATCCATTGAACACTAGTTGTGCATGTATCCTAT
391 AATTCCTTCAAATGCCATCCATTGAACACTAGTTGTGCATGTATCCTAT
52002931 TGATATTCGGCATCTATGATGTTCACACTAACTTAAATTCTATTCACATTTGTATTTAACATGTT
1 TGATATTCGGCATCTATGATGTTCACACTAACTTAAATTCTATTCACATTTGTATTTAACATGTT
*
52002996 CACACAAAAGTATTAAAGTTT-GTTCATGCTTGAAGATGGTGCATGAATTGGCCAAACCATCATG
66 CACACAAAAGCATTAAAGTTTGGTTCATGCTTGAAGATGGTGCATGAATTGGCCAAACCATCATG
52003060 TTGCTTCACTTGATGCATTCATGCATATGTAGCCTAGAAGAAAAGCCATAATTCATGAATGTGCA
131 TTGCTTCACTTGATGCATTCATGCATATGTAGCCTAGAAGAAAAGCCATAATTCATGAATGTGCA
52003125 GCCCTTTAATACTCCTACATCTCCCTTGGTCAAATGAGGCTTGAATGTACCTTGAATACTTGAAT
196 GCCCTTTAATACTCCTACATCTCCCTTGGTCAAATGAGGCTTGAATGTACCTTGAATACTTGAAT
*
52003190 GGACATCTTGGATATGCATGATACATACATGAAACGTCCCAACGCATGTTCTTCCTTAATTACGG
261 GGACATCTTGGATATGCATGATACATACATGAAACATCCCAACGCATGTTCTTCCTTAATTACGG
52003255 TCCATGAATCTTCAAATACATGTACATAAAATAGCCCCCACTTGCATGAACGTCCCCAATACATG
326 TCCATGAATCTTCAAATACATGTACATAAAATAGCCCCCACTTGCATGAACGTCCCCAATACATG
52003320 AATTCCTTCAAATGCCATCCATTGAACACTAGTTGTGCATGTATCCT
391 AATTCCTTCAAATGCCATCCATTGAACACTAGTTGTGCATGTATCCT
52003367 TCTATACGAT
Statistics
Matches: 429, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
438 345 0.80
439 84 0.20
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.32
Consensus pattern (439 bp):
TGATATTCGGCATCTATGATGTTCACACTAACTTAAATTCTATTCACATTTGTATTTAACATGTT
CACACAAAAGCATTAAAGTTTGGTTCATGCTTGAAGATGGTGCATGAATTGGCCAAACCATCATG
TTGCTTCACTTGATGCATTCATGCATATGTAGCCTAGAAGAAAAGCCATAATTCATGAATGTGCA
GCCCTTTAATACTCCTACATCTCCCTTGGTCAAATGAGGCTTGAATGTACCTTGAATACTTGAAT
GGACATCTTGGATATGCATGATACATACATGAAACATCCCAACGCATGTTCTTCCTTAATTACGG
TCCATGAATCTTCAAATACATGTACATAAAATAGCCCCCACTTGCATGAACGTCCCCAATACATG
AATTCCTTCAAATGCCATCCATTGAACACTAGTTGTGCATGTATCCTAT
Found at i:52003904 original size:20 final size:19
Alignment explanation
Indices: 52003851--52003905 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
52003841 AGCTAAAAGT
52003851 AAGCTCGATTGAGCTCAAAC
1 AAGCT-GATTGAGCTCAAAC
* *
52003871 AAGCTGATACGAGCTCAAAT
1 AAGCTGAT-TGAGCTCAAAC
*
52003891 GAGCTGAGTTGAGCT
1 AAGCTGA-TTGAGCT
52003906 GGACGGAGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.10
20 25 0.86
21 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (19 bp):
AAGCTGATTGAGCTCAAAC
Found at i:52005052 original size:14 final size:15
Alignment explanation
Indices: 52005023--52005055 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
52005013 AAAAGAGTGT
52005023 GAAAGAGAGCAAAAA
1 GAAAGAGAGCAAAAA
*
52005038 GAAAGTGAG-AAAAA
1 GAAAGAGAGCAAAAA
52005052 GAAA
1 GAAA
52005056 ACCGAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.67, C:0.03, G:0.27, T:0.03
Consensus pattern (15 bp):
GAAAGAGAGCAAAAA
Found at i:52005084 original size:18 final size:18
Alignment explanation
Indices: 52005046--52005108 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
52005036 AAGAAAGTGA
*
52005046 GAAAAAGAAAACCGAAATT
1 GAAAAAGAAAA-AGAAATT
*
52005065 GAAAAAGAAAAAGAATTT
1 GAAAAAGAAAAAGAAATT
**
52005083 GATTAAG-AAAAGAAAATT
1 GAAAAAGAAAAAG-AAATT
52005101 GAAAAAGA
1 GAAAAAGA
52005109 GAGTGAGTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
17 5 0.14
18 19 0.54
19 11 0.31
ACGTcount: A:0.65, C:0.03, G:0.17, T:0.14
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:52006797 original size:20 final size:20
Alignment explanation
Indices: 52006755--52006798 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
52006745 TCAGCTCCAA
***
52006755 TCAGCTTACTTGAGCTTGTT
1 TCAGCTTACTTGAGCTCAAT
*
52006775 TCAGCTTATTTGAGCTCAAT
1 TCAGCTTACTTGAGCTCAAT
52006795 TCAG
1 TCAG
52006799 TTTCTTTCAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.41
Consensus pattern (20 bp):
TCAGCTTACTTGAGCTCAAT
Found at i:52009322 original size:15 final size:15
Alignment explanation
Indices: 52009302--52009349 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
52009292 TCAAAGATGG
52009302 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
52009317 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
52009331 GTTTATGGATATAAA
1 GTTTATGGATATGAA
52009346 GTTT
1 GTTT
52009350 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:52009336 original size:14 final size:14
Alignment explanation
Indices: 52009296--52009339 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
52009286 AAGGATTCAA
52009296 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
52009310 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
52009325 AGATGGGTTTATGG
1 AGATGGGTTTATGG
52009339 A
1 A
52009340 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:52009365 original size:29 final size:29
Alignment explanation
Indices: 52009296--52009355 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
52009286 AAGGATTCAA
*
52009296 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
52009325 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
52009354 AG
1 AG
52009356 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:52010373 original size:14 final size:14
Alignment explanation
Indices: 52010331--52010375 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
52010321 TTAAAGAAGC
52010331 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
52010345 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
52010358 AACTCATTTAATTA
1 AACTCATTAAATTA
52010372 AACT
1 AACT
52010376 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:52012861 original size:18 final size:18
Alignment explanation
Indices: 52012840--52012891 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
52012830 TCTTTCTCTC
*
52012840 TCTCAAACTCTTTTTCAA
1 TCTCAATCTCTTTTTCAA
* * *
52012858 TCTCATTTTCTTTTTCAC
1 TCTCAATCTCTTTTTCAA
52012876 TCTCAATCTCTTTTTC
1 TCTCAATCTCTTTTTC
52012892 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTCAATCTCTTTTTCAA
Found at i:52013961 original size:12 final size:12
Alignment explanation
Indices: 52013944--52013990 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
52013934 CAGATTTTGT
52013944 TTTTTTTTTGAA
1 TTTTTTTTTGAA
52013956 -TTTTTTTTGAA
1 TTTTTTTTTGAA
52013967 TTTTTTTTTCG-A
1 TTTTTTTTT-GAA
52013979 TTTTTTTTTGAA
1 TTTTTTTTTGAA
52013991 ACTTACTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 12 0.38
12 19 0.59
13 1 0.03
ACGTcount: A:0.15, C:0.02, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:52014197 original size:28 final size:29
Alignment explanation
Indices: 52014165--52014223 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
52014155 AAGGATTCAA
*
52014165 AGATGGGTTTATGG-TATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
52014193 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
52014222 AG
1 AG
52014224 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:52015241 original size:14 final size:14
Alignment explanation
Indices: 52015199--52015243 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
52015189 TTAAAGAAGC
52015199 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
52015213 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
52015226 AACTCATTTAATTA
1 AACTCATTAAATTA
52015240 AACT
1 AACT
52015244 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:52017872 original size:30 final size:30
Alignment explanation
Indices: 52017787--52017883 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
52017777 TAAACTAAAA
* *
52017787 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * *
52017817 TGAGCTAAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
52017847 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
52017876 ATGAGCTA
1 -TGAGCTA
52017884 GGAGTGAGCT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 1 0.02
30 54 0.98
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:52018180 original size:24 final size:24
Alignment explanation
Indices: 52018110--52018181 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
52018100 AGCATGCCTG
*
52018110 GACAGATTTAATGAGCTGCTAGTT
1 GACAGATTTAATGAGCTGCTGGTT
*
52018134 GACGGATTTAATGAGCTGCTGGTT
1 GACAGATTTAATGAGCTGCTGGTT
* * *
52018158 GACAAATTTAATGAGTTGTTGGTT
1 GACAGATTTAATGAGCTGCTGGTT
52018182 TCTTTTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (24 bp):
GACAGATTTAATGAGCTGCTGGTT
Found at i:52034574 original size:25 final size:29
Alignment explanation
Indices: 52034545--52034598 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 29
52034535 CATTGTCTCA
*
52034545 CTTTCTTC-TTTTT-TTTCA-TCT-TTTT
1 CTTTCCTCATTTTTCTTTCACTCTCTTTT
52034570 CTTTCCTCATTTTTCTTTCACTCTCTTTT
1 CTTTCCTCATTTTTCTTTCACTCTCTTTT
52034599 GCTAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.29
26 5 0.21
27 5 0.21
28 3 0.12
29 4 0.17
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.69
Consensus pattern (29 bp):
CTTTCCTCATTTTTCTTTCACTCTCTTTT
Found at i:52034584 original size:14 final size:13
Alignment explanation
Indices: 52034545--52034589 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
52034535 CATTGTCTCA
*
52034545 CTTTCTTCTTTTT
1 CTTTCATCTTTTT
52034558 -TTTCATCTTTTT
1 CTTTCATCTTTTT
*
52034570 CTTTCCTCATTTTT
1 CTTTCATC-TTTTT
52034584 CTTTCA
1 CTTTCA
52034590 CTCTCTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.41
13 6 0.22
14 10 0.37
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (13 bp):
CTTTCATCTTTTT
Found at i:52034598 original size:15 final size:14
Alignment explanation
Indices: 52034551--52034598 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
52034541 CTCACTTTCT
52034551 TCTTTTT-TTTCA-
1 TCTTTTTCTTTCAC
52034563 TCTTTTTCTTTC-C
1 TCTTTTTCTTTCAC
52034576 TCATTTTTCTTTCAC
1 TC-TTTTTCTTTCAC
52034591 TCTCTTTT
1 TCT-TTTT
52034599 GCTAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.23
13 6 0.19
14 11 0.35
15 7 0.23
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (14 bp):
TCTTTTTCTTTCAC
Found at i:52037649 original size:19 final size:19
Alignment explanation
Indices: 52037625--52037664 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
52037615 AGCTCCCATG
52037625 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
52037644 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
52037663 TA
1 TA
52037665 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:52038929 original size:14 final size:14
Alignment explanation
Indices: 52038907--52038954 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
52038897 ACCTAAACCG
* *
52038907 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
52038921 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
52038935 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
52038949 ACCATT
1 ACCATT
52038955 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:52040279 original size:21 final size:21
Alignment explanation
Indices: 52040253--52040302 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
52040243 ACATTCTTGT
52040253 AAAGAAAAAACAAAGAAAAG-A
1 AAAGAAAAAACAAA-AAAAGAA
* *
52040274 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAACAAAAAAAGAA
52040295 AAAGAAAA
1 AAAGAAAA
52040303 TGAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAACAAAAAAAGAA
Found at i:52040288 original size:6 final size:5
Alignment explanation
Indices: 52040253--52040320 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
52040243 ACATTCTTGT
* *
52040253 AAAGA AAAAA CAAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA
52040300 AAATGA AATA-A AAAGA AAAGA
1 AAA-GA AA-AGA AAAGA AAAGA
52040321 GAGGCAAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
4 4 0.08
5 29 0.56
6 18 0.35
7 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:52040293 original size:15 final size:14
Alignment explanation
Indices: 52040264--52040320 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
52040254 AAGAAAAAAC
52040264 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
52040280 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
52040295 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
52040311 AAAGAAAAGA
1 AAAGAAAAGA
52040321 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:52040399 original size:13 final size:12
Alignment explanation
Indices: 52040368--52040399 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
52040358 TTGAGAGAAC
52040368 TTGAAAAAGCCT
1 TTGAAAAAGCCT
52040380 TTGAAAAAGCCT
1 TTGAAAAAGCCT
52040392 TTGAAAAA
1 TTGAAAAA
52040400 CAAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:52040433 original size:24 final size:24
Alignment explanation
Indices: 52040406--52040468 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
52040396 AAAACAAAAA
*
52040406 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAAAGAGATT
* * *
52040430 GAAAAAGAGAATGAAAAAGAGTTT
1 GAAAAAGAAAAAGAAAAAGAGATT
* *
52040454 GAGAGAGAAAAAGAA
1 GAAAAAGAAAAAGAA
52040469 TGTGAACAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.25, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAGAGATT
Found at i:52040435 original size:13 final size:12
Alignment explanation
Indices: 52040406--52040450 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
52040396 AAAACAAAAA
* *
52040406 GAAAAAGAAAAA
1 GAAAAAGAGAAT
* *
52040418 GAAAATGAGATT
1 GAAAAAGAGAAT
52040430 GAAAAAGAGAAT
1 GAAAAAGAGAAT
52040442 GAAAAAGAG
1 GAAAAAGAG
52040451 TTTGAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (12 bp):
GAAAAAGAGAAT
Found at i:52043518 original size:19 final size:19
Alignment explanation
Indices: 52043494--52043533 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
52043484 AGCTCCCATG
52043494 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
52043513 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
52043532 TA
1 TA
52043534 TCAGCTCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:52044798 original size:14 final size:14
Alignment explanation
Indices: 52044776--52044822 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
52044766 ACCTAAACCG
* *
52044776 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
52044790 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
*
52044804 ACC-TTTCGTTCCT
1 ACCATTTTGTTCCT
52044817 ACCATT
1 ACCATT
52044823 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 12 0.41
14 17 0.59
ACGTcount: A:0.19, C:0.30, G:0.06, T:0.45
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:52044814 original size:13 final size:14
Alignment explanation
Indices: 52044780--52044822 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
52044770 AAACCGACCA
*
52044780 ATTT-GTTCATACC
1 ATTTCGTTCCTACC
*
52044793 ATTTTGTTCCTACC
1 ATTTCGTTCCTACC
52044807 -TTTCGTTCCTACC
1 ATTTCGTTCCTACC
52044820 ATT
1 ATT
52044823 CCATTCGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.16, C:0.28, G:0.07, T:0.49
Consensus pattern (14 bp):
ATTTCGTTCCTACC
Found at i:52049790 original size:30 final size:30
Alignment explanation
Indices: 52049754--52049850 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
52049744 ACATCACTCC
*
52049754 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
52049784 TAGCTCAACTTTAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
*
52049814 CAGCTCAACTTTAGCTCACGAGCTAAACCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
52049844 TAGCTCA
1 TAGCTCA
52049851 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 48 0.91
31 5 0.09
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:52051547 original size:12 final size:12
Alignment explanation
Indices: 52051530--52051554 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52051520 GTTATACAAG
52051530 TCAAAAAAAAAT
1 TCAAAAAAAAAT
52051542 TCAAAAAAAAAT
1 TCAAAAAAAAAT
52051554 T
1 T
52051555 TCGAAAAGAA
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:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (12 bp):
TCAAAAAAAAAT
Found at i:52051580 original size:19 final size:19
Alignment explanation
Indices: 52051544--52051583 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
52051534 AAAAAAATTC
*
52051544 AAAAAAAAATTTCGAAAAG
1 AAAAAAAAATCTCGAAAAG
52051563 AAAAAAAAATCT-GAAAA-
1 AAAAAAAAATCTCGAAAAG
52051580 AAAA
1 AAAA
52051584 GTGTTTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 5 0.25
19 11 0.55
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAAAAAATCTCGAAAAG
Found at i:52052500 original size:9 final size:10
Alignment explanation
Indices: 52052493--52052549 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
52052483 AAGAGAAAAT
52052493 AAAGAAAAGA
1 AAAGAAAAGA
52052503 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
52052515 AAAGAAGA-A
1 AAAGAAAAGA
52052524 AAAGAAAATGA
1 AAAGAAAA-GA
52052535 AATA-AAAAGA
1 AA-AGAAAAGA
52052545 AAAGA
1 AAAGA
52052550 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:52052517 original size:6 final size:5
Alignment explanation
Indices: 52052493--52052549 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
52052483 AAGAGAAAAT
*
52052493 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
52052540 AAAGA AAAGA
1 AAAGA AAAGA
52052550 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:52052524 original size:15 final size:14
Alignment explanation
Indices: 52052493--52052549 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
52052483 AAGAGAAAAT
52052493 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
52052509 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
52052524 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
52052540 AAAGAAAAGA
1 AAAGAAAAGA
52052550 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:52052626 original size:12 final size:12
Alignment explanation
Indices: 52052618--52052642 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52052608 TTTGAAAAGC
52052618 AAAAAGAAAATG
1 AAAAAGAAAATG
52052630 AAAAAGAAAATG
1 AAAAAGAAAATG
52052642 A
1 A
52052643 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:52052639 original size:18 final size:18
Alignment explanation
Indices: 52052612--52052667 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
52052602 AAAGCCTTTG
52052612 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
52052631 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
52052649 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
52052666 AA
1 AA
52052668 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:52052699 original size:30 final size:30
Alignment explanation
Indices: 52052618--52052699 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
52052608 TTTGAAAAGC
* *
52052618 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAG-AAATGAAAAAGAAATTTGAGAGTG
*
52052648 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGA-AATGAAAAAGAAATTTGAGAGTG
52052678 AAAAAGAAATGAAAAAGAAATT
1 AAAAAGAAATGAAAAAGAAATT
52052700 GAAACAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 12 0.27
30 33 0.73
ACGTcount: A:0.65, C:0.01, G:0.21, T:0.13
Consensus pattern (30 bp):
AAAAAGAAATGAAAAAGAAATTTGAGAGTG
Found at i:52058618 original size:20 final size:20
Alignment explanation
Indices: 52058595--52058638 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
52058585 AGCTCCAATC
*
52058595 AGCTCACTTGAGCTCGTTTT
1 AGCTCACTTGAGCTCGATTT
***
52058615 AGCTTGTTTGAGCTCGATTT
1 AGCTCACTTGAGCTCGATTT
52058635 AGCT
1 AGCT
52058639 TCTTTCCAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
AGCTCACTTGAGCTCGATTT
Found at i:52058639 original size:20 final size:20
Alignment explanation
Indices: 52058602--52058639 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
52058592 ATCAGCTCAC
*
52058602 TTGAGCTCGTTTTAGCTTGT
1 TTGAGCTCGATTTAGCTTGT
52058622 TTGAGCTCGATTTAGCTT
1 TTGAGCTCGATTTAGCTT
52058640 CTTTCCAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTTGT
Found at i:52058654 original size:20 final size:20
Alignment explanation
Indices: 52058605--52058654 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
52058595 AGCTCACTTG
* * *
52058605 AGCTCGTTTTAGCTTGTTTG
1 AGCTCGATTTAGCTTCTTTC
52058625 AGCTCGATTTAGCTTCTTTCC
1 AGCTCGATTTAGCTTCTTT-C
52058646 AGCTC-ATTT
1 AGCTCGATTT
52058655 CTTTTTCCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (20 bp):
AGCTCGATTTAGCTTCTTTC
Found at i:52065214 original size:27 final size:26
Alignment explanation
Indices: 52065183--52065241 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
52065173 AATATCTAGC
*
52065183 TTTAATGTGTCTAGTTTA-GGACATCAA
1 TTTAATGTGTCTAGCTTAGGGACA--AA
52065210 TTTAATGTGTCTAGCTTAGGGACAAA
1 TTTAATGTGTCTAGCTTAGGGACAAA
52065236 TTTAAT
1 TTTAAT
52065242 TGTTGCTGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 8 0.27
27 17 0.57
28 5 0.17
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.41
Consensus pattern (26 bp):
TTTAATGTGTCTAGCTTAGGGACAAA
Found at i:52066874 original size:22 final size:20
Alignment explanation
Indices: 52066842--52066890 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
52066832 GCCAAATTTA
52066842 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
52066865 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
52066885 TGAACA
1 TGAACA
52066891 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:52067661 original size:10 final size:11
Alignment explanation
Indices: 52067645--52067680 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
52067635 TTATACAAGT
*
52067645 AAAAAAAATCG
1 AAAAAAATTCG
52067656 AAAAAAATTC-
1 AAAAAAATTCG
52067666 AAAAAAATTCG
1 AAAAAAATTCG
52067677 AAAA
1 AAAA
52067681 GAAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.72, C:0.08, G:0.06, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:52068711 original size:11 final size:12
Alignment explanation
Indices: 52068679--52068709 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
52068669 TTGAGAGAAC
52068679 TTGAAAAAGCCT
1 TTGAAAAAGCCT
52068691 TTGAAAAAGCCT
1 TTGAAAAAGCCT
52068703 TTGAAAA
1 TTGAAAA
52068710 GCAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:52077096 original size:18 final size:18
Alignment explanation
Indices: 52077056--52077104 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
52077046 GTTCATTTTT
*
52077056 CTTTCTTTCTTCACTCTCA
1 CTTTCTTT-TTCAATCTCA
* *
52077075 CTTTCTTTTTCAATTTCG
1 CTTTCTTTTTCAATCTCA
52077093 CTTTCCTTTTTC
1 CTTT-CTTTTTC
52077105 TCATTCTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.08, C:0.31, G:0.02, T:0.59
Consensus pattern (18 bp):
CTTTCTTTTTCAATCTCA
Found at i:52080323 original size:17 final size:19
Alignment explanation
Indices: 52080301--52080340 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
52080291 GCACACACAA
52080301 AATTAA-TTTAG-CAAATT
1 AATTAATTTTAGACAAATT
*
52080318 AATTAATTTTAGACACATT
1 AATTAATTTTAGACAAATT
52080337 AATT
1 AATT
52080341 TTCGGCTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 9 0.45
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (19 bp):
AATTAATTTTAGACAAATT
Found at i:52082858 original size:15 final size:15
Alignment explanation
Indices: 52082838--52082885 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
52082828 TCAAAGATGG
52082838 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
52082853 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
52082867 GTTTATGGATATAAA
1 GTTTATGGATATGAA
52082882 GTTT
1 GTTT
52082886 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:52082872 original size:14 final size:14
Alignment explanation
Indices: 52082832--52082875 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
52082822 AAGGATTCAA
52082832 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
52082846 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
52082861 AGATGGGTTTATGG
1 AGATGGGTTTATGG
52082875 A
1 A
52082876 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:52082901 original size:29 final size:29
Alignment explanation
Indices: 52082832--52082891 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
52082822 AAGGATTCAA
*
52082832 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
52082861 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
52082890 AG
1 AG
52082892 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:52083909 original size:14 final size:14
Alignment explanation
Indices: 52083867--52083911 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
52083857 TTAAAGAAGT
52083867 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
52083881 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
52083894 AACTCATTTAATTA
1 AACTCATTAAATTA
52083908 AACT
1 AACT
52083912 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:52086646 original size:16 final size:16
Alignment explanation
Indices: 52086625--52086670 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
52086615 ATGTATCGAC
*
52086625 AAAAGCCGAAATGCCA
1 AAAAGCCGAAAAGCCA
*
52086641 AAAAGCCGAAAAGCTA
1 AAAAGCCGAAAAGCCA
*
52086657 AAATGCCGAAAAGC
1 AAAAGCCGAAAAGC
52086671 TGAAAGTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.52, C:0.22, G:0.20, T:0.07
Consensus pattern (16 bp):
AAAAGCCGAAAAGCCA
Found at i:52086654 original size:8 final size:8
Alignment explanation
Indices: 52086625--52086675 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
52086615 ATGTATCGAC
52086625 AAAAGCCG
1 AAAAGCCG
* *
52086633 AAATGCCA
1 AAAAGCCG
52086641 AAAAGCCG
1 AAAAGCCG
*
52086649 AAAAG-CT
1 AAAAGCCG
52086656 AAAATGCCG
1 AAAA-GCCG
*
52086665 AAAAGCTG
1 AAAAGCCG
52086673 AAA
1 AAA
52086676 GTTTGGCTAC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
7 5 0.15
8 24 0.71
9 5 0.15
ACGTcount: A:0.53, C:0.20, G:0.20, T:0.08
Consensus pattern (8 bp):
AAAAGCCG
Found at i:52086671 original size:16 final size:15
Alignment explanation
Indices: 52086625--52086676 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
52086615 ATGTATCGAC
* *
52086625 AAAAGCCGAAATGCCA
1 AAAAGCCGAAAAG-CT
52086641 AAAAGCCGAAAAGCT
1 AAAAGCCGAAAAGCT
52086656 AAAATGCCGAAAAGCT
1 AAAA-GCCGAAAAGCT
*
52086672 GAAAG
1 AAAAG
52086677 TTTGGCTACG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 6 0.19
16 26 0.81
ACGTcount: A:0.52, C:0.19, G:0.21, T:0.08
Consensus pattern (15 bp):
AAAAGCCGAAAAGCT
Found at i:52086939 original size:29 final size:29
Alignment explanation
Indices: 52086897--52086998 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
52086887 TGAATATGAC
* *
52086897 TGGGCCTAACGGGCCACATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
52086926 TGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
52086955 TGGGCCTAATGGGCCATATAAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
52086983 TGGGCTTAATGGGCCA
1 TGGGCCTAATGGGCCA
52086999 GATACAGGTA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 16 0.25
29 49 0.75
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:52086969 original size:58 final size:57
Alignment explanation
Indices: 52086897--52087007 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
52086887 TGAATATGAC
* *
52086897 TGGGCCTAACGGGCCACATAAATGTGATTTGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAACGGGCCACATAAATATGA-TTGGGCCTAATGGGCCAGATACAGGTGATT
* * *
52086955 TGGGCCTAATGGGCCATATAAATATGATTGGGCTTAATGGGCCAGATACAGGT
1 TGGGCCTAACGGGCCACATAAATATGATTGGGCCTAATGGGCCAGATACAGGT
52087008 ATGTGAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 24 0.50
58 24 0.50
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (57 bp):
TGGGCCTAACGGGCCACATAAATATGATTGGGCCTAATGGGCCAGATACAGGTGATT
Found at i:52092952 original size:29 final size:28
Alignment explanation
Indices: 52092897--52093011 Score: 131
Period size: 29 Copynumber: 4.0 Consensus size: 28
52092887 GTGAGCATGA
* * *
52092897 ATATGAATGTGAATGGGCCTAACGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
52092925 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* *
52092954 ATATACAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * * *
52092983 ATATCAATATGATTGGGCTTAATAGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
52093011 A
1 A
52093012 GATACAAGTA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
28 26 0.35
29 49 0.65
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:52093945 original size:30 final size:30
Alignment explanation
Indices: 52093909--52094005 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
52093899 AGCTCACTCC
52093909 TAGCTCATA-TTTAGCTCACGAGATAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGATAAACCT
* * * * * *
52093939 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGATAAACCT
* * *
52093969 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGATAAACCT
52093999 TAGCTCA
1 TAGCTCA
52094006 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGATAAACCT
Found at i:52095661 original size:78 final size:78
Alignment explanation
Indices: 52095510--52095654 Score: 177
Period size: 78 Copynumber: 1.9 Consensus size: 78
52095500 AAAAAATTGT
* * *
52095510 TTCGTGAAATTCAAGTATTATACTATATTTACCTTTTTAGTAGTTTATAAACAAAAAAATATATA
1 TTCGTGAAATTCAAGTATTATACTATAATTACCATTTTAGTAGTTTATAAACAAAAAAATATAAA
*
52095575 CAAAAAAAACTAC
66 AAAAAAAAACTAC
* * ** * **
52095588 TTCGTGAGATTCAAGTATTGTGTTATAATTATCATTTTAGTAG-TTATAAA-AAAAGTATATAAA
1 TTCGTGAAATTCAAGTATTATACTATAATTACCATTTTAGTAGTTTATAAACAAAAAAATATAAA
52095651 AAAA
66 AAAA
52095655 TCAAAAAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
76 13 0.23
77 7 0.12
78 36 0.64
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (78 bp):
TTCGTGAAATTCAAGTATTATACTATAATTACCATTTTAGTAGTTTATAAACAAAAAAATATAAA
AAAAAAAAACTAC
Found at i:52095662 original size:21 final size:22
Alignment explanation
Indices: 52095635--52095685 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
52095625 TAGTAGTTAT
*
52095635 AAAAAAAGTATATAAAAAAATC-
1 AAAAAAAATATA-AAAAAAATCG
*
52095657 AAAAAAAATTTAAAAAAAATCG
1 AAAAAAAATATAAAAAAAATCG
52095679 AAAAAAA
1 AAAAAAA
52095686 GAGAGGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (22 bp):
AAAAAAAATATAAAAAAAATCG
Found at i:52096618 original size:5 final size:5
Alignment explanation
Indices: 52096597--52096664 Score: 50
Period size: 5 Copynumber: 13.0 Consensus size: 5
52096587 ACATTCTTGT
* * *
52096597 AAAGA AAAAA TAAAGA AAAGA AATGAA AAAGCA AAAGA AGA-A AAAGA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA
52096644 AAATGA AATA-A AAAGA AAAGA
1 AAA-GA AA-AGA AAAGA AAAGA
52096665 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
4 4 0.08
5 28 0.56
6 17 0.34
7 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.06
Consensus pattern (5 bp):
AAAGA
Found at i:52096618 original size:16 final size:15
Alignment explanation
Indices: 52096597--52096664 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 15
52096587 ACATTCTTGT
*
52096597 AAAGAAAAAATAAAGA
1 AAAGAAAGAA-AAAGA
52096613 AAAGAAATGAAAAAGCA
1 AAAGAAA-GAAAAAG-A
52096630 AAAG-AAGAAAAAGA
1 AAAGAAAGAAAAAGA
*
52096644 AAATGAAATAAAAAGA
1 AAA-GAAAGAAAAAGA
52096660 AAAGA
1 AAAGA
52096665 GAGGCAAGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
14 4 0.09
15 10 0.22
16 25 0.54
17 7 0.15
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.06
Consensus pattern (15 bp):
AAAGAAAGAAAAAGA
Found at i:52096657 original size:25 final size:25
Alignment explanation
Indices: 52096612--52096660 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
52096602 AAAAATAAAG
52096612 AAAAGAAATGAAAAAGCAAAAGAAGA
1 AAAAGAAATGAAAAA-CAAAAGAAGA
*
52096638 AAAAGAAAATGAAATA-AAAAGAA
1 AAAAG-AAATGAAAAACAAAAGAA
52096661 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 5 0.24
27 9 0.43
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (25 bp):
AAAAGAAATGAAAAACAAAAGAAGA
Found at i:52096764 original size:12 final size:12
Alignment explanation
Indices: 52096725--52096782 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
52096715 AAAAAGCCTT
*
52096725 TGAAAAAGAAAA
1 TGAAAAAGAGAA
* *
52096737 AGAAAAAGAAAA
1 TGAAAAAGAGAA
* *
52096749 TGAAAATGAGAT
1 TGAAAAAGAGAA
52096761 TGAAAAAGAGAA
1 TGAAAAAGAGAA
52096773 TGAAAAAGAG
1 TGAAAAAGAG
52096783 TTTGAGAGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.10
Consensus pattern (12 bp):
TGAAAAAGAGAA
Found at i:52096787 original size:24 final size:24
Alignment explanation
Indices: 52096738--52096796 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
52096728 AAAAGAAAAA
*
52096738 GAAAAAGAAAATGAAAATGAGATT
1 GAAAAAGAAAATGAAAAAGAGATT
* *
52096762 GAAAAAGAGAATGAAAAAGAGTTT
1 GAAAAAGAAAATGAAAAAGAGATT
* *
52096786 GAGAGAGAAAA
1 GAAAAAGAAAA
52096797 AGAATGTGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (24 bp):
GAAAAAGAAAATGAAAAAGAGATT
Found at i:52096814 original size:17 final size:18
Alignment explanation
Indices: 52096791--52096831 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
52096781 AGTTTGAGAG
*
52096791 AGAAAAAGAA-TGTGAAAA
1 AGAAAAAAAAGTG-GAAAA
52096809 AGAAAAAAAAGTGGAAAA
1 AGAAAAAAAAGTGGAAAA
52096827 AGAAA
1 AGAAA
52096832 TTGAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (18 bp):
AGAAAAAAAAGTGGAAAA
Found at i:52097991 original size:30 final size:30
Alignment explanation
Indices: 52097957--52098053 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
52097947 AGCTCACTCC
*
52097957 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
52097987 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
52098017 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
52098047 TAGCTCA
1 TAGCTCA
52098054 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:52100820 original size:30 final size:30
Alignment explanation
Indices: 52100784--52100880 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
52100774 AGCTCACTCC
52100784 TAGCTC-ACTTTCAACACACAAGCTAAACCT
1 TAGCTCAACTTT-AACACACAAGCTAAACCT
* * * *
52100814 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAACACACAAGCTAAACCT
* * * * *
52100844 TAGCTCAACTTTAGCTCACGAGCTATAGCT
1 TAGCTCAACTTTAACACACAAGCTAAACCT
52100874 TAGCTCA
1 TAGCTCA
52100881 TTTTAGTTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
30 56 0.92
31 5 0.08
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (30 bp):
TAGCTCAACTTTAACACACAAGCTAAACCT
Found at i:52102453 original size:93 final size:93
Alignment explanation
Indices: 52102341--52102511 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
52102331 GCCCATAAGT
* *
52102341 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52102406 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
52102434 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52102499 CGAGTTCGGATGC
66 CGAGTTCGGATGC
52102512 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:52102508 original size:46 final size:46
Alignment explanation
Indices: 52102333--52102508 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
52102323 TGTAACCCGC
* * *
52102333 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
52102379 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
52102429 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
52102472 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52102509 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:52104931 original size:29 final size:29
Alignment explanation
Indices: 52104892--52104979 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
52104882 CAAAGATAAC
*
52104892 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
52104921 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
52104950 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
52104980 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:52104950 original size:15 final size:15
Alignment explanation
Indices: 52104892--52104970 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
52104882 CAAAGATAAC
*
52104892 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
52104906 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
52104921 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
52104935 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
52104950 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
52104965 AAGAAA
1 AAGAAA
52104971 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:52104979 original size:15 final size:15
Alignment explanation
Indices: 52104903--52104979 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
52104893 AGAAAACCGA
52104903 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
52104918 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
52104932 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
52104946 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
52104962 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
52104977 ATA
1 ATA
52104980 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:52108038 original size:93 final size:93
Alignment explanation
Indices: 52107926--52108097 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
52107916 GCCCATAAGT
* *
52107926 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52107991 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
52108019 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52108084 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
52108098 AACCATCCTA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:52108093 original size:46 final size:46
Alignment explanation
Indices: 52107918--52108093 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
52107908 TGTAACCCGC
* * *
52107918 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
52107964 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
52108014 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
52108057 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52108094 TGCCAACCAT
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:52112723 original size:39 final size:39
Alignment explanation
Indices: 52112669--52112831 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
52112659 TGTGAATGAA
52112669 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
52112708 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
** *
52112747 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
52112786 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
52112826 TGTGCG
1 TGTGCG
52112832 GGTTACCATA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52112847 original size:40 final size:39
Alignment explanation
Indices: 52112669--52112861 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
52112659 TGTGAATGAA
* *
52112669 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* *
52112708 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
52112747 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
52112786 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
52112826 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGG
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGG
52112862 TGTTTTGAAC
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52120686 original size:39 final size:39
Alignment explanation
Indices: 52120632--52120794 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
52120622 TGTGAATGAA
52120632 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
52120671 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
** *
52120710 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
52120749 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
52120789 TGTGCG
1 TGTGCG
52120795 GGTTACCATA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52120810 original size:40 final size:39
Alignment explanation
Indices: 52120632--52120824 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
52120622 TGTGAATGAA
* *
52120632 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* *
52120671 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
52120710 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
52120749 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
52120789 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGG
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGG
52120825 TGTTTTGAAC
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52129569 original size:26 final size:26
Alignment explanation
Indices: 52129540--52129625 Score: 108
Period size: 24 Copynumber: 3.4 Consensus size: 26
52129530 ATAAGACATC
52129540 ATGTGAACACACATAAATTCAGCACA
1 ATGTGAACACACATAAATTCAGCACA
** *
52129566 ATGTGAACACATTTAAGTT-A-CATC-
1 ATGTGAACACACATAAATTCAGCA-CA
52129590 ATGTGAACACACAT-AATTCAGCACA
1 ATGTGAACACACATAAATTCAGCACA
52129615 ATGTGAACACA
1 ATGTGAACACA
52129626 TTTAAGTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
23 3 0.06
24 16 0.32
25 15 0.30
26 16 0.32
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (26 bp):
ATGTGAACACACATAAATTCAGCACA
Found at i:52129624 original size:49 final size:50
Alignment explanation
Indices: 52129535--52129634 Score: 193
Period size: 49 Copynumber: 2.0 Consensus size: 50
52129525 AATTCATAAG
52129535 ACATCATGTGAACACACATAAATTCAGCACAATGTGAACACATTTAAGTT
1 ACATCATGTGAACACACATAAATTCAGCACAATGTGAACACATTTAAGTT
52129585 ACATCATGTGAACACACAT-AATTCAGCACAATGTGAACACATTTAAGTT
1 ACATCATGTGAACACACATAAATTCAGCACAATGTGAACACATTTAAGTT
52129634 A
1 A
52129635 TGTGATATCT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 31 0.62
50 19 0.38
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (50 bp):
ACATCATGTGAACACACATAAATTCAGCACAATGTGAACACATTTAAGTT
Found at i:52129846 original size:30 final size:30
Alignment explanation
Indices: 52129744--52129846 Score: 77
Period size: 30 Copynumber: 3.4 Consensus size: 30
52129734 TCGAGTTAAA
*
52129744 TGAAAATGAGCT-AGGCTTTAGCTCGTGAGC
1 TGAATATGAGCTAAGG-TTTAGCTCGTGAGC
* * * * * * *
52129774 TAAAGT-TGAGCTGAGATTAAACTCCTAAGC
1 TGAA-TATGAGCTAAGGTTTAGCTCGTGAGC
*
52129804 TGAA-ACTAAGCTAAGGTTTAGCTCGTGAGC
1 TGAATA-TGAGCTAAGGTTTAGCTCGTGAGC
52129834 TGAATATGAGCTA
1 TGAATATGAGCTA
52129847 GGGGTGAGCT
Statistics
Matches: 52, Mismatches: 16, Indels: 10
0.67 0.21 0.13
Matches are distributed among these distances:
30 49 0.94
31 3 0.06
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (30 bp):
TGAATATGAGCTAAGGTTTAGCTCGTGAGC
Found at i:52133208 original size:10 final size:11
Alignment explanation
Indices: 52133155--52133208 Score: 60
Period size: 10 Copynumber: 5.1 Consensus size: 11
52133145 ATGCATACTC
52133155 CTTCAAGCTCAA
1 CTTC-AGCTCAA
*
52133167 -ATCAGCTCAA
1 CTTCAGCTCAA
52133177 -TTCAGCTCAA
1 CTTCAGCTCAA
*
52133187 CTTCAACTCAA
1 CTTCAGCTCAA
52133198 CTT-AGCTCAA
1 CTTCAGCTCAA
52133208 C
1 C
52133209 GAGCTCGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 23 0.62
11 14 0.38
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.26
Consensus pattern (11 bp):
CTTCAGCTCAA
Found at i:52138279 original size:30 final size:30
Alignment explanation
Indices: 52138245--52138341 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
52138235 AGCTCACTCC
52138245 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
52138275 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
52138305 CAGCTCAACTTTAGCTCATGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
52138335 TAGCTCA
1 TAGCTCA
52138342 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:52140493 original size:15 final size:14
Alignment explanation
Indices: 52140458--52140497 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
52140448 AGAAACGACA
*
52140458 AAAGAAAAAGAGTG
1 AAAGAAAAAGAATG
*
52140472 AGAGAAAAAGAATG
1 AAAGAAAAAGAATG
*
52140486 AAAGGAAAAGAA
1 AAAGAAAAAGAA
52140498 AAAAAGTGGA
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:0.68, C:0.00, G:0.28, T:0.05
Consensus pattern (14 bp):
AAAGAAAAAGAATG
Found at i:52142745 original size:13 final size:13
Alignment explanation
Indices: 52142727--52142761 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
52142717 CGGCTAACCT
52142727 ACATAATTAAATA
1 ACATAATTAAATA
52142740 ACATAATTAAATA
1 ACATAATTAAATA
*
52142753 AAATAATTA
1 ACATAATTA
52142762 TTCATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:52148239 original size:71 final size:71
Alignment explanation
Indices: 52148155--52148318 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
52148145 CGATTTGTCT
52148155 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
52148220 CTTTCA
66 CTTTCA
52148226 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
52148291 CTTTCA
66 CTTTCA
52148297 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
52148319 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Done.