Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 60 of 190
Found at i:17144639 original size:2 final size:2
Alignment explanation
Indices: 17144634--17144678 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
17144624 GAAAAAACAA
17144634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17144675 AT AT
1 AT AT
17144679 TAGTAACGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17144818 original size:2 final size:2
Alignment explanation
Indices: 17144811--17144848 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17144801 NNNNAAAATA
17144811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17144849 TAAAGATTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17152429 original size:5 final size:5
Alignment explanation
Indices: 17152419--17152450 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
17152409 TTTTTGGGAA
17152419 AAAAT AAAAT AAAAT AAAAT --AAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
17152451 GCATATATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.12
5 22 0.88
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:17152444 original size:13 final size:13
Alignment explanation
Indices: 17152426--17152450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17152416 GAAAAAATAA
17152426 AATAAAATAAAAT
1 AATAAAATAAAAT
17152439 AATAAAATAAAA
1 AATAAAATAAAA
17152451 GCATATATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:17152444 original size:18 final size:17
Alignment explanation
Indices: 17152417--17152450 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
17152407 AGTTTTTGGG
17152417 AAAAAATAAAATAAAAT
1 AAAAAATAAAATAAAAT
17152434 AAAATAATAAAATAAAA
1 AAAA-AATAAAATAAAA
17152451 GCATATATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAAATAAAATAAAAT
Found at i:17167496 original size:22 final size:22
Alignment explanation
Indices: 17167471--17167514 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17167461 ATCCCATCCT
*
17167471 TGCTCTTATTAGTTTTGTGTAA
1 TGCTCTCATTAGTTTTGTGTAA
17167493 TGCTCTCATTAGTTTTGTGTAA
1 TGCTCTCATTAGTTTTGTGTAA
17167515 AGTCACTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.52
Consensus pattern (22 bp):
TGCTCTCATTAGTTTTGTGTAA
Found at i:17168067 original size:14 final size:16
Alignment explanation
Indices: 17168039--17168070 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
17168029 AGAGTAGTTA
17168039 TTTTTATATATATGTT
1 TTTTTATATATATGTT
17168055 TTTTTA-ATA-ATGTT
1 TTTTTATATATATGTT
17168069 TT
1 TT
17168071 AATATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTTATATATATGTT
Found at i:17172757 original size:13 final size:13
Alignment explanation
Indices: 17172739--17172770 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17172729 TTTCCAGCAA
17172739 TTATGAATTTATT
1 TTATGAATTTATT
17172752 TTATGAATTTATT
1 TTATGAATTTATT
*
17172765 TGATGA
1 TTATGA
17172771 TGATCTAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:17172940 original size:50 final size:50
Alignment explanation
Indices: 17172865--17173107 Score: 378
Period size: 50 Copynumber: 4.8 Consensus size: 50
17172855 ATTTGGGTAA
17172865 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
17172915 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
17172965 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
17173015 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
17173065 AGAACATCTCATGTAAGACCATGTCTGGGACGTGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
17173108 TGTTATTATC
Statistics
Matches: 176, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 144 0.82
51 32 0.18
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:17178229 original size:141 final size:141
Alignment explanation
Indices: 17177991--17178258 Score: 335
Period size: 141 Copynumber: 1.9 Consensus size: 141
17177981 ACTTTTGCGT
** * * **
17177991 AATTACTTACTTAAAAGGTAATCCTTGGGGATTCTTACTTGCCGACTTATGGACGAAGACTTCTA
1 AATTACTTACTTAAAAGGTAATCCTTGCAGATTCTTACTTGCCGACTTATAGAAGAAGACCCCTA
* * *
17178056 GATAATTCCCAGATCACGTGACTTGCACCAACA-TATAGGATAGCTAAGTGAGGTG-GGTCTTAG
66 AATAATTCCCAGAGCACGTGACTTGCACCAACAGTATA-GATAGCCAAGTGA-GTGAGGTCTTAG
17178119 TGAAATCCTACAC
129 TGAAATCCTACAC
* * * * *
17178132 AATTACTTCCTTGAGAGGTAATCCTTGCAGATTCTTACTTGCGGATTTATAGAAGAAGACCCCTA
1 AATTACTTACTTAAAAGGTAATCCTTGCAGATTCTTACTTGCCGACTTATAGAAGAAGACCCCTA
* *
17178197 AATAATTCCCATG-GCACGTGACTTTCAGCAACAGGTATAGATAGCCAAGTGAGTGAGGTCTT
66 AATAATTCCCA-GAGCACGTGACTTGCACCAACA-GTATAGATAGCCAAGTGAGTGAGGTCTT
17178259 CATGAATAGT
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
141 84 0.79
142 19 0.18
143 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (141 bp):
AATTACTTACTTAAAAGGTAATCCTTGCAGATTCTTACTTGCCGACTTATAGAAGAAGACCCCTA
AATAATTCCCAGAGCACGTGACTTGCACCAACAGTATAGATAGCCAAGTGAGTGAGGTCTTAGTG
AAATCCTACAC
Found at i:17196708 original size:12 final size:12
Alignment explanation
Indices: 17196693--17196717 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17196683 ATCCTGTAAG
17196693 CCCATAAAGCAT
1 CCCATAAAGCAT
17196705 CCCATAAAGCAT
1 CCCATAAAGCAT
17196717 C
1 C
17196718 ATCCAGTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CCCATAAAGCAT
Found at i:17203747 original size:27 final size:27
Alignment explanation
Indices: 17203716--17203939 Score: 195
Period size: 27 Copynumber: 8.4 Consensus size: 27
17203706 CTCAATATTT
* *
17203716 GTAAAATAACCGTAATGCCCCTATAGG
1 GTAAAATGACCGTAATACCCCTATAGG
* *
17203743 GTAAAATGACCGTAATACCTCTGTAGG
1 GTAAAATGACCGTAATACCCCTATAGG
* * *
17203770 GTAAAATGACCGAAAAACCCTTATAGG
1 GTAAAATGACCGTAATACCCCTATAGG
* *
17203797 GT-AAATGACCGTAATGTCCCC-ATATG
1 GTAAAATGACCGTAAT-ACCCCTATAGG
* * * * *
17203823 ATAAAATGATCGTAATGCCCTTATAAG
1 GTAAAATGACCGTAATACCCCTATAGG
*
17203850 GTAAAATGACCGTAATACCCCCATAGG
1 GTAAAATGACCGTAATACCCCTATAGG
* * * * *
17203877 GCT-AAATGATCGAAATACCCTTGTAAG
1 G-TAAAATGACCGTAATACCCCTATAGG
* * *
17203904 GTAAAATGACCGTAATGCCTCTAGAGG
1 GTAAAATGACCGTAATACCCCTATAGG
17203931 GT-AAATGAC
1 GTAAAATGAC
17203940 TATTTTGCCC
Statistics
Matches: 153, Mismatches: 39, Indels: 11
0.75 0.19 0.05
Matches are distributed among these distances:
26 27 0.18
27 125 0.82
28 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTATAGG
Found at i:17203837 original size:80 final size:81
Alignment explanation
Indices: 17203719--17203919 Score: 203
Period size: 80 Copynumber: 2.5 Consensus size: 81
17203709 AATATTTGTA
* * * *
17203719 AAATAACCGTAATGCCCCTATAGGGTAAAATGACCGTAATA-CCTCTGTAGGGTAAAATGACCGA
1 AAATGACCGTAATGCCCCTATAGGATAAAATGACCGTAATACCCT-TATAAGGTAAAATGACCGA
**
17203783 AAAACCCTTATAGGG-T
65 AAAACCCCCATAGGGCT
* * * *
17203799 AAATGACCGTAATGTCCCC-ATATGATAAAATGATCGTAATGCCCTTATAAGGTAAAATGACCGT
1 AAATGACCGTAATG-CCCCTATAGGATAAAATGACCGTAATACCCTTATAAGGTAAAATGACCGA
*
17203863 AATACCCCCATAGGGCT
65 AAAACCCCCATAGGGCT
* * * * *
17203880 AAATGATCGAAATACCCTTGTAAGG-TAAAATGACCGTAAT
1 AAATGACCGTAATGCCCCTAT-AGGATAAAATGACCGTAAT
17203920 GCCTCTAGAG
Statistics
Matches: 98, Mismatches: 18, Indels: 9
0.78 0.14 0.07
Matches are distributed among these distances:
80 62 0.63
81 34 0.35
82 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (81 bp):
AAATGACCGTAATGCCCCTATAGGATAAAATGACCGTAATACCCTTATAAGGTAAAATGACCGAA
AAACCCCCATAGGGCT
Found at i:17203907 original size:107 final size:108
Alignment explanation
Indices: 17203717--17203920 Score: 286
Period size: 107 Copynumber: 1.9 Consensus size: 108
17203707 TCAATATTTG
* * **
17203717 TAAAATAACCGTAATGCCCCTATAGGGTAAAATGACCGTAATACCTCTGTAGGGTAAAATGACCG
1 TAAAATAACCGTAATGCCCCTATAAGGTAAAATGACCGTAATACCCCCATAGGGTAAAATGACCG
*
17203782 AAAAACCCTTATAGGGT-AAATGACCGTAATGTCCCCATATGA
66 AAAAACCCTTATAAGGTAAAATGACCGTAATGTCCCCATATGA
* * * *
17203824 TAAAATGATCGTAATGCCCTTATAAGGTAAAATGACCGTAATACCCCCATAGGGCT-AAATGATC
1 TAAAATAACCGTAATGCCCCTATAAGGTAAAATGACCGTAATACCCCCATAGGG-TAAAATGACC
* *
17203888 GAAATACCCTTGTAAGGTAAAATGACCGTAATG
65 GAAAAACCCTTATAAGGTAAAATGACCGTAATG
17203921 CCTCTAGAGG
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
107 69 0.82
108 15 0.18
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.24
Consensus pattern (108 bp):
TAAAATAACCGTAATGCCCCTATAAGGTAAAATGACCGTAATACCCCCATAGGGTAAAATGACCG
AAAAACCCTTATAAGGTAAAATGACCGTAATGTCCCCATATGA
Found at i:17204023 original size:24 final size:24
Alignment explanation
Indices: 17203958--17204054 Score: 104
Period size: 24 Copynumber: 4.0 Consensus size: 24
17203948 CCCACGAGTG
* * **
17203958 TAAATGATTGATTTGTCCGTGACG
1 TAAATGACTGATTTGTCTGTGATT
17203982 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
* *
17204006 TAAATGACTGATTTGTCTATAATT
1 TAAATGACTGATTTGTCTGTGATT
*** *
17204030 GGTATGACTGATTTGTCTGTTATT
1 TAAATGACTGATTTGTCTGTGATT
17204054 T
1 T
17204055 GTATAACTGA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATT
Found at i:17204058 original size:24 final size:24
Alignment explanation
Indices: 17203985--17204066 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
17203975 CGTGACGTAA
* **
17203985 ATGACTGATTTGTCTGTGATTTAA
1 ATGACTGATTTGTCTGTAATTTGT
* *
17204009 ATGACTGATTTGTCTATAATTGGT
1 ATGACTGATTTGTCTGTAATTTGT
*
17204033 ATGACTGATTTGTCTGTTATTTGT
1 ATGACTGATTTGTCTGTAATTTGT
*
17204057 ATAACTGATT
1 ATGACTGATT
17204067 CTGAGCATGG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.48
Consensus pattern (24 bp):
ATGACTGATTTGTCTGTAATTTGT
Found at i:17204191 original size:27 final size:27
Alignment explanation
Indices: 17204140--17204192 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
17204130 TATTATAATA
*
17204140 GTGGCTCTGCCACAATCACTGTTACTG
1 GTGGCTCTGCCACAATCACTATTACTG
17204167 GTGGCT-TGGCCACATAT-ACTATTACT
1 GTGGCTCT-GCCACA-ATCACTATTACT
17204193 AGTAGCTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.04
27 20 0.87
28 2 0.09
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (27 bp):
GTGGCTCTGCCACAATCACTATTACTG
Found at i:17204200 original size:27 final size:27
Alignment explanation
Indices: 17204148--17204200 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
17204138 TAGTGGCTCT
* * *
17204148 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTATTACTAGTAGCTTG
17204175 GCCACATAT-ACTATTACTAGTAGCTT
1 GCCACA-ATCACTATTACTAGTAGCTT
17204201 TGCTGCGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (27 bp):
GCCACAATCACTATTACTAGTAGCTTG
Found at i:17204309 original size:32 final size:32
Alignment explanation
Indices: 17204241--17204327 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
17204231 ACGATGCTAC
* ** **
17204241 TGATGGCTTTGTGCCGATCATATTACCGTTTC
1 TGATGGCTTTGTGCCGATCATATCACCACTAA
* *
17204273 TGATGGCTGTGTGCCGATCATATCACTACTAA
1 TGATGGCTTTGTGCCGATCATATCACCACTAA
*
17204305 TGATGGCTTTGTGCCAATCATAT
1 TGATGGCTTTGTGCCGATCATAT
17204328 TACTGTACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATATCACCACTAA
Found at i:17206105 original size:21 final size:20
Alignment explanation
Indices: 17206081--17206126 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
17206071 TGAAATGCAA
17206081 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
17206102 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
17206122 T-AACC
1 TCAACC
17206127 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:17206988 original size:22 final size:23
Alignment explanation
Indices: 17206962--17207005 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
17206952 GAAAATAACC
17206962 AAAATTAATCAAAATT-AATTAT
1 AAAATTAATCAAAATTCAATTAT
*
17206984 AAAATTAATTAAAATTCAATTA
1 AAAATTAATCAAAATTCAATTA
17207006 GTTCATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATTAATCAAAATTCAATTAT
Found at i:17209979 original size:28 final size:29
Alignment explanation
Indices: 17209937--17209998 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 29
17209927 GAATAAGAAG
* *
17209937 GAAAATAAAATAAAATC-TATTCTAAAAA
1 GAAAATAAAAGAAAACCATATTCTAAAAA
17209965 GAAAATAAAAGAAAACCATATTCTAAAAA
1 GAAAATAAAAGAAAACCATATTCTAAAAA
*
17209994 TAAAA
1 GAAAA
17209999 AGAAAAGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (29 bp):
GAAAATAAAAGAAAACCATATTCTAAAAA
Found at i:17210009 original size:12 final size:11
Alignment explanation
Indices: 17209990--17210031 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
17209980 CCATATTCTA
*
17209990 AAAATAAAAAG
1 AAAAGAAAAAG
*
17210001 AAAAG-TAAAG
1 AAAAGAAAAAG
17210011 AAAAGATAAAAG
1 AAAAGA-AAAAG
17210023 AAAAGAAAA
1 AAAAGAAAA
17210032 TTTGTCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.35
11 7 0.27
12 10 0.38
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:17210012 original size:10 final size:12
Alignment explanation
Indices: 17209996--17210028 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
17209986 TCTAAAAATA
17209996 AAAAGAAAAG-T
1 AAAAGAAAAGAT
17210007 -AAAGAAAAGAT
1 AAAAGAAAAGAT
17210018 AAAAGAAAAGA
1 AAAAGAAAAGA
17210029 AAATTTGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 1 0.05
12 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAAGAAAAGAT
Found at i:17214698 original size:15 final size:16
Alignment explanation
Indices: 17214674--17214711 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
17214664 GCATAATGGT
*
17214674 CACATGTCACA-TAAA
1 CACATATCACATTAAA
*
17214689 CACATATCACATTACA
1 CACATATCACATTAAA
17214705 CACATAT
1 CACATAT
17214712 TCATAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.45, C:0.29, G:0.03, T:0.24
Consensus pattern (16 bp):
CACATATCACATTAAA
Found at i:17218132 original size:41 final size:41
Alignment explanation
Indices: 17218029--17218138 Score: 107
Period size: 41 Copynumber: 2.7 Consensus size: 41
17218019 AAAAAATAAC
* *
17218029 AATCAAAT-AACCAAACCAAAATAATAAACAAATATAAGTAAT
1 AATCAAATAAACCATA--AAAATAATAAACAAATATAACTAAT
* * * *
17218071 CATTAAATAACCCATTAAAATAACT-AACAAATATAACTAAT
1 AATCAAATAAACCATAAAAATAA-TAAACAAATATAACTAAT
* *
17218112 AATCAAGTAAACCATAAAAATATTAAA
1 AATCAAATAAACCATAAAAATAATAAA
17218139 TGAAAACTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
40 1 0.02
41 41 0.77
42 7 0.13
43 4 0.08
ACGTcount: A:0.61, C:0.15, G:0.02, T:0.23
Consensus pattern (41 bp):
AATCAAATAAACCATAAAAATAATAAACAAATATAACTAAT
Found at i:17218590 original size:25 final size:25
Alignment explanation
Indices: 17218539--17218592 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
17218529 TTTATATTTA
* * *
17218539 AATAACACTAATATAATATTCAAAT
1 AATAACAATAAAATAATATCCAAAT
17218564 AATAACAATAAAATAATA-CCAATAT
1 AATAACAATAAAATAATATCCAA-AT
17218589 AATA
1 AATA
17218593 GCAAATGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (25 bp):
AATAACAATAAAATAATATCCAAAT
Found at i:17229059 original size:5 final size:5
Alignment explanation
Indices: 17229049--17229074 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17229039 AGAGCATTCG
17229049 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
17229075 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:17229834 original size:30 final size:31
Alignment explanation
Indices: 17229795--17229854 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
17229785 AGAGGTGGGA
*
17229795 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* *
17229826 TGGG-AGGGAGTAAAAATTTTGGGGAAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
17229855 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:17230021 original size:30 final size:30
Alignment explanation
Indices: 17229959--17230021 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
17229949 GGTTGGGAGG
* * * ***
17229959 GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTGAGAGAAAAGTAAAAA
17229989 GGAGTAAAAGTTTTGAGAGAAAAGTAAAAA
1 GGAGTAAAAGTTTTGAGAGAAAAGTAAAAA
17230019 GGA
1 GGA
17230022 TTGGGAGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.19
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGAGAAAAGTAAAAA
Found at i:17232595 original size:43 final size:43
Alignment explanation
Indices: 17232486--17232601 Score: 148
Period size: 43 Copynumber: 2.7 Consensus size: 43
17232476 GATTCTTTAA
*
17232486 ATGAAAGGGGTTGTTATGTGCTGATTCC-CCGTATCATTGATT
1 ATGAAAGGGGTTGCTATGTGCTGATTCCACCGTATCATTGATT
* * * *
17232528 AT--AAGGTGGTTGCTAAGTGTTGATTCCACTGTATCCTTGATT
1 ATGAAAGG-GGTTGCTATGTGCTGATTCCACCGTATCATTGATT
*
17232570 GTGAAAGGGGTTGCTATGTGCTGATTCCACCG
1 ATGAAAGGGGTTGCTATGTGCTGATTCCACCG
17232602 GGATCCTTTG
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
40 4 0.07
41 17 0.28
42 15 0.25
43 21 0.34
44 4 0.07
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.36
Consensus pattern (43 bp):
ATGAAAGGGGTTGCTATGTGCTGATTCCACCGTATCATTGATT
Found at i:17253645 original size:11 final size:12
Alignment explanation
Indices: 17253619--17253643 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17253609 ATTTTTAATA
17253619 TTATTTCATTTT
1 TTATTTCATTTT
17253631 TTATTTCATTTT
1 TTATTTCATTTT
17253643 T
1 T
17253644 ATAATTTAAT
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:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTTCATTTT
Found at i:17255677 original size:59 final size:59
Alignment explanation
Indices: 17255585--17255788 Score: 354
Period size: 59 Copynumber: 3.4 Consensus size: 59
17255575 ATTGATTTAT
*
17255585 TTTTGAATATTTTTGTACAAATTGTTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
*
17255644 TTTTGAATATTTTTGTACAAATTATTTTAATATTGTTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
* * *
17255703 TTTTGAATTTTTTTGTACAAGTTATTTTTATATTGTTTCATTTAATAAAATAGAAGCTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
17255762 TTTTGAATATTTTTGTACAAATATATT
1 TTTTGAATATTTTTGTACAAAT-TATT
17255789 ACTGACTGTG
Statistics
Matches: 136, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
59 132 0.97
60 4 0.03
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.52
Consensus pattern (59 bp):
TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
Found at i:17258364 original size:62 final size:62
Alignment explanation
Indices: 17258267--17258386 Score: 231
Period size: 62 Copynumber: 1.9 Consensus size: 62
17258257 TTAGTTAAGG
*
17258267 TTGGATTGTAAAAATGATTAACTTTGTATTAGACAATGGCAAGATTTTAAATTTGATTAACA
1 TTGGATTGTAAAAATGATTAACTTTGTATTAGACAATGGCAACATTTTAAATTTGATTAACA
17258329 TTGGATTGTAAAAATGATTAACTTTGTATTAGACAATGGCAACATTTTAAATTTGATT
1 TTGGATTGTAAAAATGATTAACTTTGTATTAGACAATGGCAACATTTTAAATTTGATT
17258387 GAGTTATAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (62 bp):
TTGGATTGTAAAAATGATTAACTTTGTATTAGACAATGGCAACATTTTAAATTTGATTAACA
Found at i:17266323 original size:40 final size:40
Alignment explanation
Indices: 17266251--17266470 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
17266241 TAATTATTGG
* *
17266251 TGATTGCACATACGTG-CCCTGTTTATATTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
17266290 TGGTTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * *
17266330 TGATTGTACATACGTGTCCTTTTTTATACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
17266370 TGATTGCACATACGTTCGCCTATTTGTACTTCGGTACTCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
*
17266410 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACACC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
17266450 TGAATGCACTTATGTGCCCCT
1 TGATTGCACATACGTGCCCCT
17266471 ATTTATACCC
Statistics
Matches: 154, Mismatches: 26, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 14 0.09
40 140 0.91
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:17266329 original size:20 final size:20
Alignment explanation
Indices: 17266267--17266451 Score: 81
Period size: 20 Copynumber: 9.2 Consensus size: 20
17266257 CACATACGTG
* *
17266267 CCCTGTTTATATTTCGGTAC
1 CCCTGTTTGTACTTCGGTAC
* * * ** *
17266287 CCCTGGTTGCACATATGTGC
1 CCCTGTTTGTACTTCGGTAC
17266307 CCCTGTTTGTACTTCGGTAC
1 CCCTGTTTGTACTTCGGTAC
* *
17266327 CCCTGATTGTACATACGTGT--
1 CCCTGTTTGTAC-TTCG-GTAC
* * *
17266347 CCTTTTTTATACTTCGGTAC
1 CCCTGTTTGTACTTCGGTAC
* * * *
17266367 CCCTGATTGCACATAC-GTTC
1 CCCTGTTTGTAC-TTCGGTAC
* *
17266387 GCCTATTTGTACTTCGGTAC
1 CCCTGTTTGTACTTCGGTAC
* * * * *
17266407 TCCTGATTGCACATAC-GTGC
1 CCCTGTTTGTAC-TTCGGTAC
17266427 CCCTGTTTGTACTTCGGTAC
1 CCCTGTTTGTACTTCGGTAC
*
17266447 ACCTG
1 CCCTG
17266452 AATGCACTTA
Statistics
Matches: 111, Mismatches: 46, Indels: 16
0.64 0.27 0.09
Matches are distributed among these distances:
18 2 0.02
19 7 0.06
20 93 0.84
21 7 0.06
22 2 0.02
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (20 bp):
CCCTGTTTGTACTTCGGTAC
Found at i:17281596 original size:58 final size:58
Alignment explanation
Indices: 17281506--17281623 Score: 209
Period size: 58 Copynumber: 2.0 Consensus size: 58
17281496 TGGTAGAAAA
* *
17281506 TTTGGAAAACCCACAAATTAGAGAGATTGTAAAATTGATGATGTTTTTAGTGTTTCTC
1 TTTGGAAAACCCACAAATTAGAGAGATGGTAAAATTGATGATGTTTTTAGTCTTTCTC
*
17281564 TTTGGAAAACCCACAAATTAGAGAGATGGTAAAATTGATGGTGTTTTTAGTCTTTCTC
1 TTTGGAAAACCCACAAATTAGAGAGATGGTAAAATTGATGATGTTTTTAGTCTTTCTC
17281622 TT
1 TT
17281624 GAAATTCTAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.38
Consensus pattern (58 bp):
TTTGGAAAACCCACAAATTAGAGAGATGGTAAAATTGATGATGTTTTTAGTCTTTCTC
Found at i:17289553 original size:26 final size:26
Alignment explanation
Indices: 17289524--17289574 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
17289514 TAAATACCTA
* *
17289524 TTTTGTAATCTATATATGTTTATAAAT
1 TTTTGT-ATATATATAAGTTTATAAAT
17289551 TTTTGTATATATATAAGTTTATAA
1 TTTTGTATATATATAAGTTTATAA
17289575 CCCAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (26 bp):
TTTTGTATATATATAAGTTTATAAAT
Found at i:17293304 original size:19 final size:20
Alignment explanation
Indices: 17293276--17293313 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
17293266 CTTTATTTGT
17293276 AATTTACTTTAT-GTAAAGA
1 AATTTACTTTATAGTAAAGA
*
17293295 AATTTGCTTTATAGTAAAG
1 AATTTACTTTATAGTAAAG
17293314 TTTTCTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (20 bp):
AATTTACTTTATAGTAAAGA
Found at i:17301833 original size:88 final size:88
Alignment explanation
Indices: 17301678--17301838 Score: 223
Period size: 88 Copynumber: 1.8 Consensus size: 88
17301668 GGTGATATTT
* * * * * * *
17301678 CAGCCTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAAATAACAGATCTTGTCTTCCTGTATTG
1 CAGCCTTATCTCCCTGAGCAGCAGTAGAATAGGTTGAAAATAACAAATCTTGCCTTCCTATACTG
17301743 GTAGTGAAGTAGATCGAAGATAC
66 GTAGTGAAGTAGATCGAAGATAC
* * * *
17301766 CAGCCTTATCTCCCTGAGCAGTAGTAGAATAGGTTGAAAATAGCAAATCTTGCCTTTCTATGCTG
1 CAGCCTTATCTCCCTGAGCAGCAGTAGAATAGGTTGAAAATAACAAATCTTGCCTTCCTATACTG
17301831 GTAGTGAA
66 GTAGTGAA
17301839 ACAGATTGAA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
88 62 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (88 bp):
CAGCCTTATCTCCCTGAGCAGCAGTAGAATAGGTTGAAAATAACAAATCTTGCCTTCCTATACTG
GTAGTGAAGTAGATCGAAGATAC
Found at i:17307230 original size:5 final size:5
Alignment explanation
Indices: 17307220--17307261 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
17307210 AAATTAGTTC
* *
17307220 TATTT TATTT TATTT TATTTT TGTTT TGTTT TA-TT TATTT TA
1 TATTT TATTT TATTT TA-TTT TATTT TATTT TATTT TATTT TA
17307262 GCAACAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.12
5 25 0.76
6 4 0.12
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:17307241 original size:16 final size:16
Alignment explanation
Indices: 17307222--17307255 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17307212 ATTAGTTCTA
17307222 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
* *
17307238 TTTTGTTTTGTTTTAT
1 TTTTATTTTATTTTAT
17307254 TT
1 TT
17307256 ATTTTAGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:17308737 original size:36 final size:36
Alignment explanation
Indices: 17308685--17308755 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
17308675 CCAATAAGTA
17308685 GGGAGAAAACATATGTTCTTTCTAGTATTATCACAT
1 GGGAGAAAACATATGTTCTTTCTAGTATTATCACAT
*
17308721 GGGATAAAACATATGTTCTTTCTAGTATTATCACA
1 GGGAGAAAACATATGTTCTTTCTAGTATTATCACA
17308756 CCCCCAAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (36 bp):
GGGAGAAAACATATGTTCTTTCTAGTATTATCACAT
Found at i:17310307 original size:11 final size:11
Alignment explanation
Indices: 17310291--17310318 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
17310281 AAGAGCTCCT
17310291 TCATAAATTTC
1 TCATAAATTTC
17310302 TCATAAATTTC
1 TCATAAATTTC
17310313 TCATAA
1 TCATAA
17310319 TTCTTGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (11 bp):
TCATAAATTTC
Found at i:17315134 original size:28 final size:28
Alignment explanation
Indices: 17315094--17315150 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
17315084 AACATACAAC
*
17315094 ATACAGTGACAGTCTCGGCCTGAGCCCA
1 ATACAGTAACAGTCTCGGCCTGAGCCCA
* *
17315122 ATACAGTAACAGTGTCGGCCTTAGCCCA
1 ATACAGTAACAGTCTCGGCCTGAGCCCA
17315150 A
1 A
17315151 AACAATAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (28 bp):
ATACAGTAACAGTCTCGGCCTGAGCCCA
Found at i:17315307 original size:26 final size:26
Alignment explanation
Indices: 17315276--17315371 Score: 120
Period size: 26 Copynumber: 3.7 Consensus size: 26
17315266 CATCAATATC
17315276 GCAGCAAAGCTGCCAATAATAGTAAA
1 GCAGCAAAGCTGCCAATAATAGTAAA
*
17315302 GTAGCAAAGCTGCCAATAATAGTAAA
1 GCAGCAAAGCTGCCAATAATAGTAAA
* * * *
17315328 GCAGCAAAGCTGTCAGTAACAGTAAC
1 GCAGCAAAGCTGCCAATAATAGTAAA
* * *
17315354 GCAACAGAGCTGCTAATA
1 GCAGCAAAGCTGCCAATA
17315372 TCAGTATCAC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAATAATAGTAAA
Found at i:17315668 original size:27 final size:27
Alignment explanation
Indices: 17315636--17315724 Score: 151
Period size: 27 Copynumber: 3.3 Consensus size: 27
17315626 TCCTCTTCAT
* *
17315636 GGGTATTTTGGTTATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
*
17315663 GGGTATTTCGATAATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
17315690 GGGTATTTCGGTAATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
17315717 GGGTATTT
1 GGGTATTT
17315725 TGAGCACGCT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.44
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACCCTTCGA
Found at i:17326833 original size:50 final size:50
Alignment explanation
Indices: 17326768--17327305 Score: 546
Period size: 50 Copynumber: 10.6 Consensus size: 50
17326758 TTTTGTACTA
* * * * ** *
17326768 CCAATGCCATATCCTAGATATGGTCTTAAATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * ** *
17326818 CCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCAGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
** * * *
17326868 CCAACACCATGTCCCAGACATGGTCTTACATAGGACCTCTCGTCTCAGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* *
17326918 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
17326968 CCAACT-CCATGTCCCATG-CATGGTCTTACATGGGACCTTTCATCTCGGTG
1 CCAA-TGCCATGTCCCA-GACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * *
17327018 CCAACGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCACCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * * *
17327068 CCAATGCCATGTCCTAGACATGGTCTTACATAGGACTTCTCATAATCTCAATGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGAC--CTC-TCATCTC---GGTG
** * *
17327124 TTAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTTATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* *
17327174 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GGTG
* * * * *
17327230 CCAATGCCATGTCTCAGACATGGTCTTACACT---AGCTCACATATCGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCGGTG
* *
17327278 TCGATGCCATGTCCCAGACATGGTCTTA
1 CCAATGCCATGTCCCAGACATGGTCTTA
17327306 TACGAGATCG
Statistics
Matches: 413, Mismatches: 58, Indels: 36
0.81 0.11 0.07
Matches are distributed among these distances:
48 29 0.07
49 1 0.00
50 285 0.69
51 5 0.01
52 3 0.01
53 16 0.04
54 8 0.02
56 65 0.16
57 1 0.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:17327325 original size:48 final size:48
Alignment explanation
Indices: 17327233--17327325 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 48
17327223 AATGATGCCA
* * * * *
17327233 ATGCCATGTCTCAGACATGGTCTTACACTAGCTCACATATCGATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACGAGATCACACACCGATGTCG
* * *
17327281 ATGCCATGTCCCAGACATGGTCTTATACGAGATCGCACGCCGATG
1 ATGCCATGTCCCAGACATGGTCTTACACGAGATCACACACCGATG
17327326 CCATATCTCA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACGAGATCACACACCGATGTCG
Found at i:17330179 original size:30 final size:31
Alignment explanation
Indices: 17330111--17330169 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
17330101 CACCCTTAAA
* **
17330111 ATATTTACACTATTGATCTGTCAAATTTTTC
1 ATATTTACACTATTAATCCCTCAAATTTTTC
17330142 ATATTTACACT-TTAATCCCTCAAATTTT
1 ATATTTACACTATTAATCCCTCAAATTTT
17330170 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (31 bp):
ATATTTACACTATTAATCCCTCAAATTTTTC
Found at i:17332420 original size:16 final size:15
Alignment explanation
Indices: 17332395--17332428 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
17332385 AAAGTTGATA
*
17332395 ATAATTAATATATATT
1 ATAATAAATATA-ATT
17332411 ATAATAAATATAATT
1 ATAATAAATATAATT
17332426 ATA
1 ATA
17332429 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:17332549 original size:30 final size:30
Alignment explanation
Indices: 17332492--17332550 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
17332482 TGCCTTTAAA
* *
17332492 AATATTTATAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACAACTAATTTTT
* *
17332522 AATATTTACAAAAGGAG-CAACTAAATTTT
1 AATATTTACAAAAAGAGACAACTAATTTTT
17332551 GCAAATAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAACTAATTTTT
Found at i:17338934 original size:59 final size:59
Alignment explanation
Indices: 17338842--17338959 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
17338832 AATTGATTAA
17338842 AAAAATTTAATAAGCAAATGCATTAATGCACATACATACTTATGAAATTAAAAATAATC
1 AAAAATTTAATAAGCAAATGCATTAATGCACATACATACTTATGAAATTAAAAATAATC
17338901 AAAAATTTAATAAGCAAATGCATTAATGCACATACATACTTATGAAATTAAAAATAATC
1 AAAAATTTAATAAGCAAATGCATTAATGCACATACATACTTATGAAATTAAAAATAATC
17338960 TCTTGTACGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.29
Consensus pattern (59 bp):
AAAAATTTAATAAGCAAATGCATTAATGCACATACATACTTATGAAATTAAAAATAATC
Found at i:17344241 original size:50 final size:49
Alignment explanation
Indices: 17344187--17344377 Score: 159
Period size: 50 Copynumber: 3.9 Consensus size: 49
17344177 GGCTGTTACA
* *
17344187 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCAGGGAGATG
1 AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGGCA-GGACATG
* * * * *
17344237 AGAGGTCCCCCATAAGACAATGTCTAGGACATGGCATGGGCACCGG-TATG
1 AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGGCA--GGACATG
** * * * * * * *
17344287 AGAACTCCTATGTAAGACCATATCTGGGATATGGCATTGGCAGTACACG
1 AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGGCAGGACATG
* ** * *
17344336 AAACATCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGGCA
17344378 TGTTATTATC
Statistics
Matches: 110, Mismatches: 29, Indels: 5
0.76 0.20 0.03
Matches are distributed among these distances:
48 1 0.01
49 36 0.33
50 71 0.65
51 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (49 bp):
AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGGCAGGACATG
Found at i:17344604 original size:20 final size:20
Alignment explanation
Indices: 17344579--17344627 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
17344569 TGAGTTAATT
17344579 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
17344599 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
17344619 AAG-AAGCAA
1 AAGTAAGCAA
17344628 AGACCTTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:17346905 original size:27 final size:27
Alignment explanation
Indices: 17346867--17346920 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
17346857 TATTACTTTG
17346867 ATTGATCCGGGTTCGACCCATTCCTAT
1 ATTGATCCGGGTTCGACCCATTCCTAT
17346894 ATTGATCCGGGTTCGACCCATTCCTAT
1 ATTGATCCGGGTTCGACCCATTCCTAT
17346921 GTTTGCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.33
Consensus pattern (27 bp):
ATTGATCCGGGTTCGACCCATTCCTAT
Found at i:17354120 original size:33 final size:32
Alignment explanation
Indices: 17354080--17354155 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 32
17354070 CACGGTTTAG
*
17354080 GCCATTTTGGGCCATGTAGA-CCACATAGGCAA
1 GCCATTTTGGGCCATGT-GACCCACACAGGCAA
*
17354112 TGCTATTTTGGGCCATGTGACCCACACAGGCAA
1 -GCCATTTTGGGCCATGTGACCCACACAGGCAA
17354145 GCCATTTTGGG
1 GCCATTTTGGG
17354156 TCGTGTGGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 12 0.31
33 27 0.69
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (32 bp):
GCCATTTTGGGCCATGTGACCCACACAGGCAA
Found at i:17367038 original size:19 final size:19
Alignment explanation
Indices: 17367014--17367063 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
17367004 TTCAAAGATG
17367014 TGCAATCTTAGATATGATA
1 TGCAATCTTAGATATGATA
17367033 TGCAATCTTAGATATGATA
1 TGCAATCTTAGATATGATA
*
17367052 TACAATCTTAGA
1 TGCAATCTTAGA
17367064 AGATATGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (19 bp):
TGCAATCTTAGATATGATA
Found at i:17367408 original size:3 final size:3
Alignment explanation
Indices: 17367400--17367435 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
17367390 TGTTATTAAG
17367400 TTA TTA TTA -TA GTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
17367436 CTATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:17367434 original size:12 final size:13
Alignment explanation
Indices: 17367392--17367435 Score: 65
Period size: 12 Copynumber: 3.5 Consensus size: 13
17367382 GATTTTCTTG
17367392 TTATTAAGTTATTA
1 TTATT-AGTTATTA
17367406 TTA-TAGTTATTA
1 TTATTAGTTATTA
17367418 TTATTA-TTATTA
1 TTATTAGTTATTA
17367430 TTATTA
1 TTATTA
17367436 CTATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 23 0.79
13 3 0.10
14 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (13 bp):
TTATTAGTTATTA
Found at i:17367594 original size:17 final size:17
Alignment explanation
Indices: 17367563--17367606 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
17367553 CATAACTTTT
*
17367563 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
17367579 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
17367596 ATATACATTTT
1 ATATACATTTT
17367607 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:17367783 original size:30 final size:31
Alignment explanation
Indices: 17367749--17367827 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
17367739 ATTTCAATAG
* * *
17367749 ATGTAATTATTATTATTTGT-TTTTATATAT
1 ATGTAATTATTATTATTTATAATCTATATAT
17367779 ATGTAATTATCT-TT-TTTATAATCTATATAT
1 ATGTAATTAT-TATTATTTATAATCTATATAT
*
17367809 ATGTAGATAATTATTATTT
1 ATGTA-ATTATTATTATTT
17367828 TTATATATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
29 4 0.10
30 26 0.65
31 7 0.17
32 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (31 bp):
ATGTAATTATTATTATTTATAATCTATATAT
Found at i:17372651 original size:14 final size:15
Alignment explanation
Indices: 17372625--17372657 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
17372615 TCCTAAGCTG
*
17372625 GGAAGGACCTTATGT
1 GGAAGGACCTTATCT
17372640 GGAAGG-CCTTATCT
1 GGAAGGACCTTATCT
17372654 GGAA
1 GGAA
17372658 AAGTATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.24
Consensus pattern (15 bp):
GGAAGGACCTTATCT
Found at i:17374122 original size:88 final size:88
Alignment explanation
Indices: 17373984--17374288 Score: 296
Period size: 88 Copynumber: 3.5 Consensus size: 88
17373974 AAGATAGCAT
* ** *
17373984 ATCTTGCCTTCCTGTACCGGTAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGATTACA
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGATTACA
*
17374049 GCGGAGTAGGTTGAAAATAGTAG
66 GTGGAGTAGGTTGAAAATAGTAG
* * * * * *
17374072 ATCTTGCCTTCCTGTACTGACAGTGAAGCAGATTGAAGGCGCCAGTCTTGCCTCCCTAGG-TTGC
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT-GGATTAC
* ** ** *
17374136 AGTGGAGCAGACTGAGGATAGCAG
65 AGTGGAGTAGGTTGAAAATAGTAG
* * * * * * **
17374160 ATCTTGCCTTCCTATACAGGCAGCGAAGCAGATCGAAAACTCCGGCCTTGTCC-CCCT-GAACAG
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTG-CCTCCCTGGATTA-
17374223 CAGTGGAGTAGGTT-AGAAATAGTAG
64 CAGTGGAGTAGGTTGA-AAATAGTAG
*
17374248 ATCTTGCCTTCCTGTACT-AGCAGTGAAGCAGATCGAAGACA
1 ATCTTGCCTTCCTGTACTGA-CAGCGAAGCAGATCGAAGACA
17374289 TTAGTCTTAT
Statistics
Matches: 169, Mismatches: 42, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
86 1 0.01
87 1 0.01
88 163 0.96
89 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.23
Consensus pattern (88 bp):
ATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGATTACA
GTGGAGTAGGTTGAAAATAGTAG
Found at i:17374593 original size:44 final size:45
Alignment explanation
Indices: 17374543--17374658 Score: 155
Period size: 44 Copynumber: 2.6 Consensus size: 45
17374533 ATCACATCGG
* * *
17374543 GTCTTATCTCCCTAAAGTTACAGTGGAGCAGACTGAGT-AAGAAA
1 GTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAATGAACAAA
* *
17374587 GTCTTATCCCCCTAAAATTGCAGTGGAGCAGACTGAATGAACAAA
1 GTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAATGAACAAA
* *
17374632 -TCCTATCTCCCTAAAGTTGTAGTGGAG
1 GTCTTATCTCCCTAAAGTTGCAGTGGAG
17374659 TGGATTAGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 57 0.92
45 5 0.08
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (45 bp):
GTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAATGAACAAA
Found at i:17375129 original size:19 final size:19
Alignment explanation
Indices: 17375101--17375169 Score: 102
Period size: 19 Copynumber: 3.5 Consensus size: 19
17375091 CAAGGATGTG
17375101 CAATCTTAGATATGATATA
1 CAATCTTAGATATGATATA
* *
17375120 CAATCCTAGATAAGATATA
1 CAATCTTAGATATGATATA
17375139 TGCAATCTTAGATATGATATA
1 --CAATCTTAGATATGATATA
17375160 CAATCTTAGA
1 CAATCTTAGA
17375170 AGATATGATT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 27 0.61
21 17 0.39
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (19 bp):
CAATCTTAGATATGATATA
Found at i:17375515 original size:3 final size:3
Alignment explanation
Indices: 17375507--17375554 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
17375497 TGTTATTAAG
17375507 TTA TTA TTA TTA -TA GTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17375552 TTA
1 TTA
17375555 CTATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17375525 original size:15 final size:15
Alignment explanation
Indices: 17375499--17375549 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
17375489 GATTTTCTTG
17375499 TTATTA-AGTTATTA
1 TTATTATAGTTATTA
17375513 TTATTATAGTTATTA
1 TTATTATAGTTATTA
17375528 TTATTATTA-TTATTA
1 TTATTA-TAGTTATTA
17375543 TTATTAT
1 TTATTAT
17375550 TATTACTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.20
15 26 0.74
16 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
TTATTATAGTTATTA
Found at i:17375715 original size:17 final size:17
Alignment explanation
Indices: 17375684--17375727 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
17375674 CATAACTTTT
*
17375684 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
17375700 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
17375717 ATATACATTTT
1 ATATACATTTT
17375728 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:17376012 original size:17 final size:18
Alignment explanation
Indices: 17375966--17376014 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
17375956 TGTACATGTA
17375966 TATATTTATATATTTTTT
1 TATATTTATATATTTTTT
* * *
17375984 TCTAATGA-ATATTTTTTT
1 TATATTTATATA-TTTTTT
17376002 TATATTTATATAT
1 TATATTTATATAT
17376015 ATACATATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
17 3 0.13
18 17 0.74
19 3 0.13
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TATATTTATATATTTTTT
Found at i:17398059 original size:11 final size:11
Alignment explanation
Indices: 17398043--17398068 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17398033 ATCAATGACT
17398043 ACTTATGTTAA
1 ACTTATGTTAA
17398054 ACTTATGTTAA
1 ACTTATGTTAA
17398065 ACTT
1 ACTT
17398069 TCCCTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (11 bp):
ACTTATGTTAA
Found at i:17398111 original size:56 final size:49
Alignment explanation
Indices: 17398005--17398121 Score: 144
Period size: 56 Copynumber: 2.2 Consensus size: 49
17397995 TTGAATGACT
*
17398005 ACTTATGTTAAACTTTCCCTGTTTAGTTATCAATGACTACTTATGTTAA
1 ACTTATGTTAAACTTTCCCTGTTTAGTTATCAATGACTACGTATGTTAA
* *
17398054 ACTTATGTTAAACTTTCCCTGTTTTTATTTAGTTAATGACTAAATACGTATGTTAA
1 ACTTATGTTAAACTTTCCCTG--TTTAGTTA-TCAATGAC----TACGTATGTTAA
17398110 ACTTATGTTAAA
1 ACTTATGTTAAA
17398122 TTTAGTTATC
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
49 21 0.36
51 7 0.12
52 7 0.12
56 23 0.40
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (49 bp):
ACTTATGTTAAACTTTCCCTGTTTAGTTATCAATGACTACGTATGTTAA
Found at i:17401490 original size:49 final size:49
Alignment explanation
Indices: 17401435--17401538 Score: 147
Period size: 49 Copynumber: 2.1 Consensus size: 49
17401425 TCATGTGTTA
* * *
17401435 TAATTTTATAAAGCGTTGAGC-TTTTAATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAACGTTCA-CATTTTAATTCATGATATTAAACTTAATTT
* *
17401484 TAATTTTATAAAATGTTCACATTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAACGTTCACATTTTAATTCATGATATTAAACTTAATTT
17401533 TAATTT
1 TAATTT
17401539 GTTTTTTTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
48 1 0.02
49 48 0.98
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.49
Consensus pattern (49 bp):
TAATTTTATAAAACGTTCACATTTTAATTCATGATATTAAACTTAATTT
Found at i:17403084 original size:222 final size:222
Alignment explanation
Indices: 17402698--17403153 Score: 822
Period size: 222 Copynumber: 2.0 Consensus size: 222
17402688 GATTATGACA
*
17402698 TAGAATTTCATGAATTTCATGTAACCTACTGTTAATATATGAATATTATGTTTGTGCAAAATATA
1 TAGAATTTCATGAATTTCATGTAACCTACTGTTAATATATGAATATTATGTTTATGCAAAATATA
* *
17402763 ATTCTTAAGTTATTTATTACTGCTAATATTTTTTTATTGTAGAATAATTAAATTATTTGTTTCAC
66 ATTCTCAAATTATTTATTACTGCTAATATTTTTTTATTGTAGAATAATTAAATTATTTGTTTCAC
*
17402828 TAATGATATTTTAGCACATTAAATATGAATTGCAGTTTAAAAATAATAAAGTAGATTATATATAA
131 TAATGATATTTTAGCACATTAAATATGAATTGCAGTTTAAAAATAATAAAGTAGAATATATATAA
*
17402893 TTTTTATAGTATTATATATTATGATTT
196 TTTTTATAGTATTATATATGATGATTT
**
17402920 TAGAATTTCATGAATTTCATGTAACCTTTTGTTAATATATGAATATTATGTTTATGCAAAATATA
1 TAGAATTTCATGAATTTCATGTAACCTACTGTTAATATATGAATATTATGTTTATGCAAAATATA
17402985 ATTCTCAAATTATTTATTACTGCTAATATTTTTTTATTGTAGAATAATTAAATTATTTGTTTCAC
66 ATTCTCAAATTATTTATTACTGCTAATATTTTTTTATTGTAGAATAATTAAATTATTTGTTTCAC
*
17403050 TAATGATATTTTAGCACATTAAATATGTATTGCAGTTTAAAAATAATAAAGTAGAATATATATAA
131 TAATGATATTTTAGCACATTAAATATGAATTGCAGTTTAAAAATAATAAAGTAGAATATATATAA
17403115 TTTTTATAGTATTATATATGATGATTT
196 TTTTTATAGTATTATATATGATGATTT
*
17403142 TAGTAAATTCAT
1 TAG-AATTTCAT
17403154 ATAAGAATAA
Statistics
Matches: 224, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
222 217 0.97
223 7 0.03
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (222 bp):
TAGAATTTCATGAATTTCATGTAACCTACTGTTAATATATGAATATTATGTTTATGCAAAATATA
ATTCTCAAATTATTTATTACTGCTAATATTTTTTTATTGTAGAATAATTAAATTATTTGTTTCAC
TAATGATATTTTAGCACATTAAATATGAATTGCAGTTTAAAAATAATAAAGTAGAATATATATAA
TTTTTATAGTATTATATATGATGATTT
Found at i:17403458 original size:45 final size:44
Alignment explanation
Indices: 17403368--17403460 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
17403358 ATTACAACAT
*
17403368 CATTCCATTCAACCAAACACAAGAATACTGTTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
*
17403412 CATTCTATTCAACCAAA-A-AATTGAATTACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAA--GAA-TACTATTACAGTTCTATTC
17403457 CATT
1 CATT
17403461 ACAACTCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
42 2 0.05
43 1 0.02
44 19 0.43
45 22 0.50
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:17403463 original size:16 final size:16
Alignment explanation
Indices: 17403442--17403481 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
17403432 TTGAATTACT
*
17403442 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
17403458 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
17403474 ATTACAGC
1 ATTACAGC
17403482 GAACCAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:17416925 original size:22 final size:23
Alignment explanation
Indices: 17416878--17416932 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
17416868 AAATTATGCT
*
17416878 AGTAAAAATTCAGACAAGCTACC
1 AGTAAAAATGCAGACAAGCTACC
*
17416901 AGTAAAAATGCAGACAAGCT-GC
1 AGTAAAAATGCAGACAAGCTACC
17416923 AGTAAAAATG
1 AGTAAAAATG
17416933 TGATAAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.16
Consensus pattern (23 bp):
AGTAAAAATGCAGACAAGCTACC
Found at i:17426046 original size:18 final size:17
Alignment explanation
Indices: 17426007--17426171 Score: 87
Period size: 18 Copynumber: 9.7 Consensus size: 17
17425997 GGTTGTAAAA
17426007 TAAAATTAAATATTGCTT-
1 TAAAATTAAATA-TG-TTG
17426025 TAAAATTAAATATCGTTG
1 TAAAATTAAATAT-GTTG
** * *
17426043 TAAAA-TATTTA-ATAG
1 TAAAATTAAATATGTTG
17426058 TAAAATTAAATATGATTG
1 TAAAATTAAATATG-TTG
*
17426076 TAAAATTAAATATGGTTT
1 TAAAATTAAATAT-GTTG
**
17426094 TAAAA-TATTTAAT-TT-
1 TAAAATTAAAT-ATGTTG
*
17426109 TAAAATTCAATATGGTTG
1 TAAAATTAAATAT-GTTG
**
17426127 TAAAA-TATTTAAT-TT-
1 TAAAATTAAAT-ATGTTG
*
17426142 TAAAATTAAATATGGCTG
1 TAAAATTAAATAT-GTTG
17426160 TAAAATTAAATA
1 TAAAATTAAATA
17426172 GATTAAAACG
Statistics
Matches: 111, Mismatches: 20, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
15 21 0.19
16 13 0.12
17 15 0.14
18 61 0.55
19 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.42
Consensus pattern (17 bp):
TAAAATTAAATATGTTG
Found at i:17426080 original size:51 final size:51
Alignment explanation
Indices: 17426007--17426132 Score: 173
Period size: 51 Copynumber: 2.5 Consensus size: 51
17425997 GGTTGTAAAA
*
17426007 TAAAATTAAATATTGCTT-TAAAATTAAATATCGTTGTAAAATATTTAATAG
1 TAAAATTAAATA-TGATTGTAAAATTAAATATCGTTGTAAAATATTTAATAG
* * **
17426058 TAAAATTAAATATGATTGTAAAATTAAATATGGTTTTAAAATATTTAATTT
1 TAAAATTAAATATGATTGTAAAATTAAATATCGTTGTAAAATATTTAATAG
* *
17426109 TAAAATTCAATATGGTTGTAAAAT
1 TAAAATTAAATATGATTGTAAAAT
17426133 ATTTAATTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 4 0.06
51 63 0.94
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (51 bp):
TAAAATTAAATATGATTGTAAAATTAAATATCGTTGTAAAATATTTAATAG
Found at i:17426111 original size:15 final size:15
Alignment explanation
Indices: 17426091--17426147 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
17426081 TTAAATATGG
17426091 TTTTAAAATATTTAA
1 TTTTAAAATATTTAA
**
17426106 TTTTAAAAT-TCAATA
1 TTTTAAAATATTTA-A
17426121 TGGTTGTAAAATATTTAA
1 T--TT-TAAAATATTTAA
17426139 TTTTAAAAT
1 TTTTAAAAT
17426148 TAAATATGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 2 0.06
15 17 0.52
16 2 0.06
17 2 0.06
18 8 0.24
19 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (15 bp):
TTTTAAAATATTTAA
Found at i:17426113 original size:33 final size:33
Alignment explanation
Indices: 17426076--17426165 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
17426066 AATATGATTG
*
17426076 TAAAATTAAATATGGTTTTAAAATATTTAATTT
1 TAAAATTAAATATGGTTGTAAAATATTTAATTT
*
17426109 TAAAATTCAATATGGTTGTAAAATATTTAATTT
1 TAAAATTAAATATGGTTGTAAAATATTTAATTT
*
17426142 TAAAATTAAATATGGCTGTAAAAT
1 TAAAATTAAATATGGTTGTAAAAT
17426166 TAAATAGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (33 bp):
TAAAATTAAATATGGTTGTAAAATATTTAATTT
Found at i:17426198 original size:84 final size:83
Alignment explanation
Indices: 17426023--17426196 Score: 226
Period size: 84 Copynumber: 2.1 Consensus size: 83
17426013 TAAATATTGC
*
17426023 TTTAAAATTAAATATCGTTGTAAAATATTTAATAGTAAAATTAAATATGATTGTAAAATTAAATA
1 TTTAAAATTAAATATCGTTGTAAAATATTTAATAGTAAAATTAAATATGACTGTAAAATTAAATA
* * *
17426088 TGGTTTTAAAATATTTAAT
66 -GGTATTAAAAAAATTAAT
* * ** *
17426107 TTTAAAATTCAATATGGTTGTAAAATATTTAATTTTAAAATTAAATATGGCTGTAAAATTAAATA
1 TTTAAAATTAAATATCGTTGTAAAATATTTAATAGTAAAATTAAATATGACTGTAAAATTAAATA
17426172 -G-ATTAAAACGAAATTAAT
66 GGTATTAAAA--AAATTAAT
17426190 TTTAAAA
1 TTTAAAA
17426197 ATCAAAATTA
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
81 6 0.08
82 1 0.01
83 13 0.16
84 59 0.75
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (83 bp):
TTTAAAATTAAATATCGTTGTAAAATATTTAATAGTAAAATTAAATATGACTGTAAAATTAAATA
GGTATTAAAAAAATTAAT
Found at i:17426206 original size:19 final size:19
Alignment explanation
Indices: 17426182--17426278 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
17426172 GATTAAAACG
17426182 AAATTAATTTTAAAAATCA
1 AAATTAATTTTAAAAATCA
** *
17426201 AAATTAA-TAAAAGAAATAA
1 AAATTAATTTTAA-AAATCA
*
17426220 ATTAATT-ATTGTTTAAAAT-A
1 A--AATTAATT-TTAAAAATCA
* *
17426240 AATTTATTTTTAAAAATCA
1 AAATTAATTTTAAAAATCA
*
17426259 AAATTAAATTTAAAAATCA
1 AAATTAATTTTAAAAATCA
17426278 A
1 A
17426279 GAAAAAAGTT
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
18 13 0.22
19 33 0.56
20 3 0.05
21 9 0.15
22 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATTAATTTTAAAAATCA
Found at i:17426290 original size:19 final size:19
Alignment explanation
Indices: 17426249--17426290 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
17426239 AAATTTATTT
* *
17426249 TTAAAAATCAAAATTAAAT
1 TTAAAAATCAAAATAAAAG
17426268 TTAAAAATCAAGAA-AAAAG
1 TTAAAAATCAA-AATAAAAG
17426287 TTAA
1 TTAA
17426291 TTAAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
TTAAAAATCAAAATAAAAG
Found at i:17426291 original size:66 final size:63
Alignment explanation
Indices: 17426211--17426336 Score: 155
Period size: 66 Copynumber: 2.0 Consensus size: 63
17426201 AAATTAATAA
*** * * *
17426211 AAGAAATAAATTAATTATTGTTTAAAATAAATTTATTTTTAAAAATCAAAATTAAATTTAAAAAT
1 AAGAAATAAATTAATTAAAATTTAAAATAAATTT-TATATAAAAAACAAAA-T-AATTTAAAAAT
17426276 C
63 C
17426277 AAGAAA-AAAGTTAATTAAAATTTAAAATAAATTTTATATAAAAAACAAAATAATTTAAAA
1 AAGAAATAAA-TTAATTAAAATTTAAAATAAATTTTATATAAAAAACAAAATAATTTAAAA
17426337 TAATAGCGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
63 9 0.17
64 1 0.02
65 16 0.30
66 27 0.51
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (63 bp):
AAGAAATAAATTAATTAAAATTTAAAATAAATTTTATATAAAAAACAAAATAATTTAAAAATC
Found at i:17428162 original size:20 final size:20
Alignment explanation
Indices: 17428117--17428165 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
17428107 ATCATGGTCT
17428117 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTCTTTACTTAC
* *
17428136 TCT-CTTACTTGTTTACTTCC
1 T-TGCTTACTTCTTTACTTAC
17428156 TTGCTTACTT
1 TTGCTTACTT
17428166 AAATAACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.10, C:0.27, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTCTTTACTTAC
Found at i:17428483 original size:50 final size:50
Alignment explanation
Indices: 17428416--17428557 Score: 169
Period size: 50 Copynumber: 2.8 Consensus size: 50
17428406 TTTCTTGTAC
* * * **
17428416 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
17428466 TGCCCATGCCATGTCCCAGACATGGTCTTA-TTGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATATCGG
* *
17428516 TGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
17428558 TATAACCTCA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.01
50 76 0.97
51 1 0.01
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:17435824 original size:21 final size:21
Alignment explanation
Indices: 17435799--17435841 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
17435789 GGTTCATATT
* *
17435799 ATTTTGGTGTTCCTTTCACTA
1 ATTTTGGTCTACCTTTCACTA
17435820 ATTTTGGTCTACCTTTCACTA
1 ATTTTGGTCTACCTTTCACTA
17435841 A
1 A
17435842 CCCCCATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.49
Consensus pattern (21 bp):
ATTTTGGTCTACCTTTCACTA
Found at i:17449204 original size:14 final size:15
Alignment explanation
Indices: 17449170--17449198 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17449160 TGGCTTTACT
17449170 AAAG-TACTAAAGTA
1 AAAGTTACTAAAGTA
17449184 AAAGTTACTAAAGTA
1 AAAGTTACTAAAGTA
17449199 CAGTTAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (15 bp):
AAAGTTACTAAAGTA
Found at i:17449709 original size:5 final size:5
Alignment explanation
Indices: 17449701--17449744 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
17449691 CAAAGCAATG
*
17449701 CAAAA CAAAA CAAAA CAAAA CCAAAA CCAAAA CCAAAA CCAAA C
1 CAAAA CAAAA CAAAA CAAAA -CAAAA -CAAAA -CAAAA CAAAA C
17449745 CCAAAAATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
5 20 0.54
6 17 0.46
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:17449727 original size:6 final size:6
Alignment explanation
Indices: 17449701--17449750 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
17449691 CAAAGCAATG
*
17449701 CAAAA- CAAAA- CAAAA- CAAAAC CAAAAC CAAAAC CAAAAC CAAACC
1 CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC
17449746 CAAAA
1 CAAAA
17449751 ATGGATTACA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
5 15 0.36
6 27 0.64
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAC
Found at i:17455329 original size:1 final size:1
Alignment explanation
Indices: 17455323--17455354 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
17455313 TTTTGTTTCG
17455323 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17455355 GCTTTTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17455508 original size:21 final size:22
Alignment explanation
Indices: 17455484--17455541 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
17455474 TTATTTTTTT
17455484 TTTCTCCTTTCTCCTTTCTCC-
1 TTTCTCCTTTCTCCTTTCTCCG
17455505 TTTCTCCTTTCTCCTTTCTCCG
1 TTTCTCCTTTCTCCTTTCTCCG
*
17455527 TTT-TCGTTT-TCCTTT
1 TTTCTCCTTTCTCCTTT
17455542 TTTTGTGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 6 0.17
21 26 0.74
22 3 0.09
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.60
Consensus pattern (22 bp):
TTTCTCCTTTCTCCTTTCTCCG
Found at i:17455543 original size:7 final size:7
Alignment explanation
Indices: 17455484--17455525 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
17455474 TTATTTTTTT
17455484 TTTCTCC
1 TTTCTCC
17455491 TTTCTCC
1 TTTCTCC
17455498 TTTCTCC
1 TTTCTCC
17455505 TTTCTCC
1 TTTCTCC
17455512 TTTCTCC
1 TTTCTCC
17455519 TTTCTCC
1 TTTCTCC
17455526 GTTTTCGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (7 bp):
TTTCTCC
Found at i:17471191 original size:15 final size:15
Alignment explanation
Indices: 17471171--17471222 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
17471161 TAATAGGCAT
17471171 GTTTTAGTAGTCATC
1 GTTTTAGTAGTCATC
17471186 GTTTTAGTAATATGTACAT-
1 GTTTTAG---TA-GT-CATC
17471205 GTTTTAGTAGTCATC
1 GTTTTAGTAGTCATC
17471220 GTT
1 GTT
17471223 GCCAGATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
14 3 0.10
15 12 0.39
16 2 0.06
18 2 0.06
19 9 0.29
20 3 0.10
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (15 bp):
GTTTTAGTAGTCATC
Found at i:17480509 original size:42 final size:42
Alignment explanation
Indices: 17480462--17480563 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
17480452 TTGATTCATC
*
17480462 CGATGATGCACTTATGT-TCTAATATATTTGCTTAGGTTC-TT
1 CGATGATGCACTTATGTGTC-AATATATTTGATTAGGTTCGTT
* *
17480503 CTGATGATGCACTTATGTGTCATTATATTTGATTTGGTTCGTT
1 C-GATGATGCACTTATGTGTCAATATATTTGATTAGGTTCGTT
*
17480546 CGATGGTGCAC-TATGTGT
1 CGATGATGCACTTATGTGT
17480564 GTTGGTATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
41 8 0.15
42 41 0.76
43 5 0.09
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.45
Consensus pattern (42 bp):
CGATGATGCACTTATGTGTCAATATATTTGATTAGGTTCGTT
Found at i:17483230 original size:28 final size:28
Alignment explanation
Indices: 17483186--17483242 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
17483176 GTAGCGTAAG
17483186 ACCTTCATGGTCCCAACACCAACACGAT
1 ACCTTCATGGTCCCAACACCAACACGAT
*
17483214 ACCTTCATGGTCTCAACACCAACACGAT
1 ACCTTCATGGTCCCAACACCAACACGAT
17483242 A
1 A
17483243 TACTTTGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.37, G:0.11, T:0.19
Consensus pattern (28 bp):
ACCTTCATGGTCCCAACACCAACACGAT
Found at i:17486910 original size:39 final size:39
Alignment explanation
Indices: 17486867--17486968 Score: 150
Period size: 39 Copynumber: 2.6 Consensus size: 39
17486857 AACATGTTTT
*
17486867 TGAGTATTGTGATATATGCTTGAATGTTATGTGAATATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGAATATA
* * *
17486906 TGAGTATTGTTATATATGCTTAAATTTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGAATATA
* *
17486945 TGTGTAATGTGATATATGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
17486969 AGTGAACGTG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGAATATA
Found at i:17489586 original size:27 final size:26
Alignment explanation
Indices: 17489546--17489877 Score: 341
Period size: 27 Copynumber: 12.3 Consensus size: 26
17489536 GTACTAGGCC
* * *
17489546 TAAAATAACCGAAATACCCTTAATGGG
1 TAAAATGACTGAAATACCCTGAA-GGG
17489573 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCT-GAAGGG
*
17489600 TAAAATGACCGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCT-GAAGGG
* *
17489627 TAAAATGACTAAAATACCCTCGAAGGT
1 TAAAATGACTGAAATACCCT-GAAGGG
17489654 TAAAATGA-TCGAAATACCCCTGAAGGG
1 TAAAATGACT-GAAATA-CCCTGAAGGG
*
17489681 TAAAATGACTAAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCT-GAAGGG
17489708 TAAAATGA-TCGAAATACCCCTGAAGGG
1 TAAAATGACT-GAAATA-CCCTGAAGGG
* ** *
17489735 TAAAATAACCAAAATACCCCCGAAGGG
1 TAAAATGACTGAAATA-CCCTGAAGGG
17489762 TAAAATGA-TCGAAATACCCCTGAAGGG
1 TAAAATGACT-GAAATA-CCCTGAAGGG
17489789 TAAAATGA-TCGAAATACCCTTGAAGGG
1 TAAAATGACT-GAAATACCC-TGAAGGG
17489816 TAAAATGACTGAAATACCTTCT-AAGGG
1 TAAAATGACTGAAATACC--CTGAAGGG
** **
17489843 TAAAATGACCAAAATACATTCGAAGGG
1 TAAAATGACTGAAATACCCT-GAAGGG
17489870 TAAAATGA
1 TAAAATGA
17489878 TTGTTATACC
Statistics
Matches: 267, Mismatches: 23, Indels: 30
0.83 0.07 0.09
Matches are distributed among these distances:
25 1 0.00
26 9 0.03
27 243 0.91
28 13 0.05
29 1 0.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (26 bp):
TAAAATGACTGAAATACCCTGAAGGG
Found at i:17489887 original size:54 final size:54
Alignment explanation
Indices: 17489546--17489878 Score: 449
Period size: 54 Copynumber: 6.2 Consensus size: 54
17489536 GTACTAGGCC
* * * **
17489546 TAAAATAACCGAAATA-CCCTTAATGGGTAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCCTGAA-GGGTAAAATGACCAAAATACCCTCGAAGGG
* * *
17489600 TAAAATGACCGAAATA-CCCTCGAAGGGTAAAATGACTAAAATACCCTCGAAGGT
1 TAAAATGATCGAAATACCCCT-GAAGGGTAAAATGACCAAAATACCCTCGAAGGG
*
17489654 TAAAATGATCGAAATACCCCTGAAGGGTAAAATGACTAAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCCTGAAGGGTAAAATGACCAAAATACCCTCGAAGGG
* *
17489708 TAAAATGATCGAAATACCCCTGAAGGGTAAAATAACCAAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCCTGAAGGGTAAAATGACCAAAATACCCTCGAAGGG
* * *
17489762 TAAAATGATCGAAATACCCCTGAAGGGTAAAATGATCGAAATACCCTTGAAGGG
1 TAAAATGATCGAAATACCCCTGAAGGGTAAAATGACCAAAATACCCTCGAAGGG
* **
17489816 TAAAATGA-CTGAAATACCTTCT-AAGGGTAAAATGACCAAAATACATTCGAAGGG
1 TAAAATGATC-GAAATACC-CCTGAAGGGTAAAATGACCAAAATACCCTCGAAGGG
17489870 TAAAATGAT
1 TAAAATGAT
17489879 TGTTATACCC
Statistics
Matches: 254, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
53 1 0.00
54 245 0.96
55 8 0.03
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (54 bp):
TAAAATGATCGAAATACCCCTGAAGGGTAAAATGACCAAAATACCCTCGAAGGG
Found at i:17489888 original size:81 final size:81
Alignment explanation
Indices: 17489546--17489878 Score: 422
Period size: 81 Copynumber: 4.1 Consensus size: 81
17489536 GTACTAGGCC
* * *
17489546 TAAAATAACCGAAATACCCTT-AATGGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGACC
1 TAAAATGATCGAAATACCCTTGAA-GGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATGACC
*
17489610 GAAATACCCTCGAAGGG
65 AAAATACCCTCGAAGGG
* * * *
17489627 TAAAATGA-CTAAAATACCCTCGAAGGTTAAAATGA-TCGAAATACCCCTGAAGGGTAAAATGAC
1 TAAAATGATC-GAAATACCCTTGAAGGGTAAAATGACT-GAAATACCCCCGAAGGGTAAAATGAC
*
17489690 TAAAATACCCTCGAAGGG
64 CAAAATACCCTCGAAGGG
* * ** * *
17489708 TAAAATGATCGAAATACCCCTGAAGGGTAAAATAACCAAAATACCCCCGAAGGGTAAAATGATCG
1 TAAAATGATCGAAATACCCTTGAAGGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATGACCA
17489773 AAATACCC-CTGAAGGG
66 AAATACCCTC-GAAGGG
** *
17489789 TAAAATGATCGAAATACCCTTGAAGGGTAAAATGACTGAAATACCTTCTAAGGGTAAAATGACCA
1 TAAAATGATCGAAATACCCTTGAAGGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATGACCA
**
17489854 AAATACATTCGAAGGG
66 AAATACCCTCGAAGGG
17489870 TAAAATGAT
1 TAAAATGAT
17489879 TGTTATACCC
Statistics
Matches: 215, Mismatches: 30, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
80 3 0.01
81 208 0.97
82 4 0.02
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (81 bp):
TAAAATGATCGAAATACCCTTGAAGGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATGACCA
AAATACCCTCGAAGGG
Found at i:17517242 original size:17 final size:17
Alignment explanation
Indices: 17517220--17517269 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
17517210 ATAGAAAGTC
17517220 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
*
17517237 AAAGATATAGGTATCAG
1 AAAGATATGGGTATCAG
17517254 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
17517270 AAATTTGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:17521861 original size:17 final size:17
Alignment explanation
Indices: 17521839--17521871 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
17521829 ATAGAAAGTC
17521839 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
17521856 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
17521872 AAATCTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:17527448 original size:29 final size:28
Alignment explanation
Indices: 17527383--17527477 Score: 86
Period size: 29 Copynumber: 3.4 Consensus size: 28
17527373 CCTTTTAGAC
* *
17527383 ATAGCCACAAAGACTTCTTTTAACATAT
1 ATAGCCACAAAGACTTCTTTTAACAGAG
* * * *
17527411 ATAGTCACATAGACTTTTTTTTCACAGAG
1 ATAGCCACAAAGAC-TTCTTTTAACAGAG
* * *
17527440 ATAGCCACAAAGGCGTCCTTT--CAGAG
1 ATAGCCACAAAGACTTCTTTTAACAGAG
17527466 ATAGCCACAAAG
1 ATAGCCACAAAG
17527478 GCTCACTTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
26 17 0.31
28 16 0.30
29 21 0.39
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (28 bp):
ATAGCCACAAAGACTTCTTTTAACAGAG
Found at i:17534455 original size:15 final size:15
Alignment explanation
Indices: 17534437--17534466 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17534427 ATTAATAAAG
*
17534437 TCTTAATTTTTATGA
1 TCTTAATTTTAATGA
17534452 TCTTAATTTTAATGA
1 TCTTAATTTTAATGA
17534467 ATAATGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (15 bp):
TCTTAATTTTAATGA
Found at i:17536481 original size:38 final size:38
Alignment explanation
Indices: 17536430--17536506 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
17536420 TTCGAGACTT
17536430 AATTTAATTTTGGTTGTAATTGGACTTGAACATTGGAC
1 AATTTAATTTTGGTTGTAATTGGACTTGAACATTGGAC
*
17536468 AATTTAATTTTGGTTGTAATTGGACTTGGACATTGGAC
1 AATTTAATTTTGGTTGTAATTGGACTTGAACATTGGAC
17536506 A
1 A
17536507 TTTTTTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.42
Consensus pattern (38 bp):
AATTTAATTTTGGTTGTAATTGGACTTGAACATTGGAC
Found at i:17542542 original size:21 final size:18
Alignment explanation
Indices: 17542498--17542543 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 18
17542488 ATTCGAAACT
17542498 AAATTGAGAACATTTGAA
1 AAATTGAGAACATTTGAA
*
17542516 AGATTGAGAAAACATTTAGAA
1 AAATTGAG--AACATTT-GAA
17542537 AAATTGA
1 AAATTGA
17542544 ACTGCAGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 7 0.30
20 7 0.30
21 9 0.39
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.26
Consensus pattern (18 bp):
AAATTGAGAACATTTGAA
Found at i:17542708 original size:12 final size:12
Alignment explanation
Indices: 17542691--17542717 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17542681 CACACGCCCG
17542691 TGTGCTAGGCCA
1 TGTGCTAGGCCA
17542703 TGTGCTAGGCCA
1 TGTGCTAGGCCA
17542715 TGT
1 TGT
17542718 AACTGCCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30
Consensus pattern (12 bp):
TGTGCTAGGCCA
Found at i:17545244 original size:149 final size:149
Alignment explanation
Indices: 17544957--17545259 Score: 444
Period size: 149 Copynumber: 2.0 Consensus size: 149
17544947 CCCCTTTTAC
* * * * * *
17544957 GATTTAGTCCTTTTCACTTAATTAAGCATGCAAACGTCAAACTTTTTTAACGAATTTTTTATACG
1 GATTTAGTCATTTTCACTTAATTAAGCATGCAAACGTCAAAATTTCTTAACAAAATTATTATACG
* * * * *
17545022 ACTCTAAAAACATACCTTGGAAATTAAAATAATAATAAAATAAATATTTACTCATCAGATTTGTT
66 ACCCTAAAAACATACCATGGAAATTAAAATAATAATAAAATAAATATTTACTCATCAAATTTATG
**
17545087 GTTTCAAAACCACTATTCT
131 GTCCCAAAACCACTATTCT
17545106 GATTTAGTCATTTTCACTTAATTAAGCATGCAAACGTCAAAATTTCTTAACAAAATTATTATACG
1 GATTTAGTCATTTTCACTTAATTAAGCATGCAAACGTCAAAATTTCTTAACAAAATTATTATACG
* **
17545171 ACCCTAAAAACATACCATGGGAATTAAAATAATAATAAAATAAATATTTACTTGTCAAATTTATG
66 ACCCTAAAAACATACCATGGAAATTAAAATAATAATAAAATAAATATTTACTCATCAAATTTATG
*
17545236 GTCCCAAAACCACTGTTCT
131 GTCCCAAAACCACTATTCT
*
17545255 AATTT
1 GATTT
17545260 CACTAAAAAC
Statistics
Matches: 136, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
149 136 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (149 bp):
GATTTAGTCATTTTCACTTAATTAAGCATGCAAACGTCAAAATTTCTTAACAAAATTATTATACG
ACCCTAAAAACATACCATGGAAATTAAAATAATAATAAAATAAATATTTACTCATCAAATTTATG
GTCCCAAAACCACTATTCT
Found at i:17546126 original size:25 final size:25
Alignment explanation
Indices: 17546080--17546128 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
17546070 TTATTCTACC
**
17546080 CCTAGTAAAATTTTGATGATTTTAA
1 CCTAGTAAAATTTTGACAATTTTAA
17546105 CCTAGTAAAATTTTGACAATTTTA
1 CCTAGTAAAATTTTGACAATTTTA
17546129 CTCTTGGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (25 bp):
CCTAGTAAAATTTTGACAATTTTAA
Found at i:17548998 original size:27 final size:25
Alignment explanation
Indices: 17548967--17549038 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 25
17548957 ATTAATATCC
*
17548967 AAATAAGTAAAATAAAATAAAATAAA
1 AAATAA-TAAAATAAAAAAAAATAAA
* *
17548993 GTAATAAATAAAGTAAATAAAAAATAAA
1 -AAAT-AATAAAATAAA-AAAAAATAAA
17549021 AAATAATAAAAATAAAAA
1 AAATAAT-AAAATAAAAA
17549039 TTGGGTTGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 5 0.14
27 21 0.57
28 11 0.30
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.19
Consensus pattern (25 bp):
AAATAATAAAATAAAAAAAAATAAA
Found at i:17549000 original size:13 final size:14
Alignment explanation
Indices: 17548981--17549014 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
17548971 AAGTAAAATA
17548981 AAATAAAATAAAGT
1 AAATAAAATAAAGT
17548995 -AAT-AAATAAAGT
1 AAATAAAATAAAGT
17549007 AAATAAAA
1 AAATAAAA
17549015 AATAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 9 0.50
13 6 0.33
14 3 0.17
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (14 bp):
AAATAAAATAAAGT
Found at i:17549003 original size:12 final size:12
Alignment explanation
Indices: 17548986--17549026 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
17548976 AAATAAAATA
17548986 AAATAAAGTAAT
1 AAATAAAGTAAT
17548998 AAATAAAGTAAAT
1 AAATAAAGT-AAT
*
17549011 AAA-AAA-TAAA
1 AAATAAAGTAAT
17549021 AAATAA
1 AAATAA
17549027 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 5 0.19
11 3 0.12
12 12 0.46
13 6 0.23
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (12 bp):
AAATAAAGTAAT
Found at i:17549028 original size:17 final size:17
Alignment explanation
Indices: 17548975--17549038 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 17
17548965 CCAAATAAGT
17548975 AAAATAAAATAA-AATAA
1 AAAATAAAA-AATAATAA
*
17548992 AGTAATAAATAAAGTAAATAA
1 A-AAATAAA-AAA-T-AATAA
17549013 AAAATAAAAAATAAT-A
1 AAAATAAAAAATAATAA
17549029 AAAATAAAAA
1 AAAATAAAAA
17549039 TTGGGTTGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 11 0.28
17 4 0.10
18 9 0.22
19 4 0.10
20 6 0.15
21 6 0.15
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (17 bp):
AAAATAAAAAATAATAA
Found at i:17561316 original size:24 final size:24
Alignment explanation
Indices: 17561289--17561344 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
17561279 AACTATATGG
17561289 CATGCTTTTCTCATATGTGCAAGA
1 CATGCTTTTCTCATATGTGCAAGA
* *
17561313 CATGCTTATCTCATATGTGCATGA
1 CATGCTTTTCTCATATGTGCAAGA
17561337 CATGCTTT
1 CATGCTTT
17561345 GCCAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (24 bp):
CATGCTTTTCTCATATGTGCAAGA
Found at i:17565773 original size:24 final size:25
Alignment explanation
Indices: 17565700--17565805 Score: 92
Period size: 25 Copynumber: 4.3 Consensus size: 25
17565690 TACATGTATA
* *
17565700 CTCATACGAGCTATGAATCGGTATA-
1 CTCATACGAGCTGTAAATCGGTA-AG
* *
17565725 CTCTTACGAGCTGTAAATCGATAAG
1 CTCATACGAGCTGTAAATCGGTAAG
*
17565750 CTCATATGAGCTG-AAATCGGTAAG
1 CTCATACGAGCTGTAAATCGGTAAG
* * * *
17565774 CTC-TCACAAGATGAAAATCAGTAAG
1 CTCAT-ACGAGCTGTAAATCGGTAAG
17565799 CTCATAC
1 CTCATAC
17565806 AAGATGTGGT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
23 1 0.02
24 19 0.29
25 45 0.68
26 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (25 bp):
CTCATACGAGCTGTAAATCGGTAAG
Found at i:17568876 original size:25 final size:26
Alignment explanation
Indices: 17568839--17568893 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
17568829 AATATTCTAT
*
17568839 ATTTAGACGATTTTACCCCTAGTAAA
1 ATTTAGACAATTTTACCCCTAGTAAA
*
17568865 ATTT-GACAATTTTACCCCTAGTCAA
1 ATTTAGACAATTTTACCCCTAGTAAA
17568890 ATTT
1 ATTT
17568894 TGAGAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (26 bp):
ATTTAGACAATTTTACCCCTAGTAAA
Found at i:17569062 original size:6 final size:6
Alignment explanation
Indices: 17569043--17569079 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
17569033 AAATTAATCC
*
17569043 TTTCCA TTT-C- TTTCCA TTTCCA TTTCAA TTTCCA TTT
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTT
17569080 TGGAAACCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
4 3 0.11
5 2 0.07
6 22 0.81
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTCCA
Found at i:17570927 original size:55 final size:55
Alignment explanation
Indices: 17570843--17570946 Score: 199
Period size: 55 Copynumber: 1.9 Consensus size: 55
17570833 ACTCGTGATA
*
17570843 TGGTATCGTTACCAAATTGAGTTACTGACTTCTTACACATTCAAAATATGCAATT
1 TGGTATCGATACCAAATTGAGTTACTGACTTCTTACACATTCAAAATATGCAATT
17570898 TGGTATCGATACCAAATTGAGTTACTGACTTCTTACACATTCAAAATAT
1 TGGTATCGATACCAAATTGAGTTACTGACTTCTTACACATTCAAAATAT
17570947 TAAAGAGGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (55 bp):
TGGTATCGATACCAAATTGAGTTACTGACTTCTTACACATTCAAAATATGCAATT
Found at i:17586531 original size:27 final size:27
Alignment explanation
Indices: 17586490--17586926 Score: 435
Period size: 27 Copynumber: 16.3 Consensus size: 27
17586480 TGAGAGGTGA
* * *
17586490 AAAATGATTGAATTACCCCCGAAGGGT
1 AAAATGATCGAAATACCCTCGAAGGGT
* * * *
17586517 AAAATGACCGTATTACCC-CGGAGGGT
1 AAAATGATCGAAATACCCTCGAAGGGT
*
17586543 AAAATGACCGAAATACCCTC-ATAGGGT
1 AAAATGATCGAAATACCCTCGA-AGGGT
*
17586570 AAAATGAAT-GAAATACCCTTGAAGGGT
1 AAAATG-ATCGAAATACCCTCGAAGGGT
* *
17586597 AAAATGACCGAAATACCCTCGAAAGGT
1 AAAATGATCGAAATACCCTCGAAGGGT
* * *
17586624 AAAATGA-CTAAAATACCCTTG-AGTGT
1 AAAATGATC-GAAATACCCTCGAAGGGT
* ** *
17586650 AAAATGATCAAAATACCCTTTATGGGT
1 AAAATGATCGAAATACCCTCGAAGGGT
* * *
17586677 AAAATGATTGAATTACCC-CTAAAGGGT
1 AAAATGATCGAAATACCCTC-GAAGGGT
* *
17586704 AAAATGATCGAAACACCCTCAAAGGGT
1 AAAATGATCGAAATACCCTCGAAGGGT
*
17586731 AAAATGATCGAAATA-CCTCCATAGGGT
1 AAAATGATCGAAATACCCTCGA-AGGGT
* *
17586758 AAAAGGATTGAAATACCC-CTGAAGGGT
1 AAAATGATCGAAATACCCTC-GAAGGGT
*
17586785 AAAATGATTGAAATACCCTCGAAGGGT
1 AAAATGATCGAAATACCCTCGAAGGGT
* *
17586812 AAAATGACCGAAATACCCTCGAAAGGT
1 AAAATGATCGAAATACCCTCGAAGGGT
**
17586839 AAAATGATCGAAATACCCTTAAAGGGT
1 AAAATGATCGAAATACCCTCGAAGGGT
*
17586866 AAAATGATCAAAATACCCTCGAAGGGT
1 AAAATGATCGAAATACCCTCGAAGGGT
*
17586893 AAAATGA-CTGAAATACCCTC-ATAGTGT
1 AAAATGATC-GAAATACCCTCGA-AGGGT
17586920 AAAATGA
1 AAAATGA
17586927 CTTTTATACC
Statistics
Matches: 348, Mismatches: 46, Indels: 32
0.82 0.11 0.08
Matches are distributed among these distances:
26 53 0.15
27 288 0.83
28 7 0.02
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (27 bp):
AAAATGATCGAAATACCCTCGAAGGGT
Done.