Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 52 of 79
Found at i:17619312 original size:125 final size:124
Alignment explanation
Indices: 17619130--17619409 Score: 327
Period size: 125 Copynumber: 2.2 Consensus size: 124
17619120 GTTGTTCTGA
* *
17619130 ACAATTTTTAATACATTGTTGCGGCGTTTTTAGACAAAACGCCACTGATGCTTACCTTTTGCGGC
1 ACAATTTTTAATACATTGTTGCGGCGTTTTTAAACAAAACGCCACTGATGCATACCTTTTGCGGC
* * * * * *
17619195 GATTCT-GAG-AAAATGCTACTAAAAAGTTAAAATCTTGTAAGCAAAC-GACGCTGTTTTTGT
66 G-TTCTGGAGAAAAATGCCACTAAAAA-TCAAAATCCTGTAACCAAACAG-CGCCG-TATTGT
* * *
17619255 ACACTTTTTAATACATTGTTGCGGCGTTTTTATAAC-AAATGCCGCT-ATTGCATACCTTTTGCG
1 ACAATTTTTAATACATTGTTGCGGCGTTTTTA-AACAAAACGCCACTGA-TGCATACCTTTTGCG
* *
17619318 GCGTTGTGGAGAAAAATGCCACTAAAAATCAAATTCCTGTAACCAAACAGCGCCGTATTGT
64 GCGTTCTGGAGAAAAATGCCACTAAAAATCAAAATCCTGTAACCAAACAGCGCCGTATTGT
* * *
17619379 ACAATTTTTAAGACATTGTTGTGACGTTTTT
1 ACAATTTTTAATACATTGTTGCGGCGTTTTT
17619410 GGTCCAAACG
Statistics
Matches: 133, Mismatches: 17, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
124 36 0.27
125 79 0.59
126 18 0.14
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (124 bp):
ACAATTTTTAATACATTGTTGCGGCGTTTTTAAACAAAACGCCACTGATGCATACCTTTTGCGGC
GTTCTGGAGAAAAATGCCACTAAAAATCAAAATCCTGTAACCAAACAGCGCCGTATTGT
Found at i:17619779 original size:16 final size:15
Alignment explanation
Indices: 17619713--17619780 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 15
17619703 ATTAGACCAA
*
17619713 AAAAACCCTAAACCT
1 AAAACCCCTAAACCT
*
17619728 AAGA-CCCTAAACACCT
1 AAAACCCCT-AA-ACCT
*
17619744 GAAAACACCTAAATCCT
1 -AAAACCCCTAAA-CCT
17619761 AAAACCCCTAAACCAT
1 AAAACCCCTAAACC-T
17619777 AAAA
1 AAAA
17619781 TTTAAACCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
14 4 0.09
15 7 0.16
16 21 0.49
17 8 0.19
18 3 0.07
ACGTcount: A:0.51, C:0.32, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAACCCCTAAACCT
Found at i:17619846 original size:7 final size:7
Alignment explanation
Indices: 17619715--17619949 Score: 93
Period size: 7 Copynumber: 32.4 Consensus size: 7
17619705 TAGACCAAAA
17619715 AAACCCT
1 AAACCCT
17619722 AAA-CCT
1 AAACCCT
17619728 AAGACCCT
1 AA-ACCCT
17619736 AAACACCT
1 AAAC-CCT
17619744 GAAAACACCT
1 --AAAC-CCT
*
17619754 AAATCCT
1 AAACCCT
17619761 AAAACCCCT
1 -AAA-CCCT
*
17619770 AAACCAT
1 AAACCCT
***
17619777 AAAATTT
1 AAACCCT
17619784 AAACCCT
1 AAACCCT
* *
17619791 AATCTCT
1 AAACCCT
*
17619798 ATACCCT
1 AAACCCT
17619805 AAACCCTT
1 AAACCC-T
17619813 AAACCCT
1 AAACCCT
*
17619820 AATCCCT
1 AAACCCT
*
17619827 AAATTACCAT
1 -AA--ACCCT
17619837 AAACCCT
1 AAACCCT
*
17619844 AAACCTT
1 AAACCCT
**
17619851 AAACTAT
1 AAACCCT
17619858 AAA-CCT
1 AAACCCT
** *
17619864 CCACCAT
1 AAACCCT
17619871 ATTAA--CT
1 A--AACCCT
**
17619878 AAACGTT
1 AAACCCT
*
17619885 AAACCTT
1 AAACCCT
17619892 AAACCCT
1 AAACCCT
17619899 AAACCCT
1 AAACCCT
*
17619906 AAACCTT
1 AAACCCT
*
17619913 AAACCCC
1 AAACCCT
*
17619920 AAACCAT
1 AAACCCT
*
17619927 AAA-CAT
1 AAACCCT
* *
17619933 ACATCCT
1 AAACCCT
17619940 AAACCCT
1 AAACCCT
17619947 AAA
1 AAA
17619950 TATAGATATT
Statistics
Matches: 169, Mismatches: 42, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
5 2 0.01
6 12 0.07
7 112 0.66
8 26 0.15
9 6 0.04
10 11 0.07
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:17620101 original size:7 final size:7
Alignment explanation
Indices: 17620089--17620162 Score: 87
Period size: 7 Copynumber: 10.6 Consensus size: 7
17620079 CATTATATCA
17620089 TAAACCT
1 TAAACCT
17620096 TAAACCT
1 TAAACCT
*
17620103 TAAACCA
1 TAAACCT
*
17620110 TAAACGT
1 TAAACCT
17620117 TAAACCT
1 TAAACCT
*
17620124 TAAATAC-
1 TAAA-CCT
*
17620131 TAACCCT
1 TAAACCT
*
17620138 TAAACCC
1 TAAACCT
17620145 TAAACCT
1 TAAACCT
17620152 TAAACCT
1 TAAACCT
17620159 TAAA
1 TAAA
17620163 ACCATAAAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
6 1 0.02
7 53 0.96
8 1 0.02
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (7 bp):
TAAACCT
Found at i:17622547 original size:146 final size:146
Alignment explanation
Indices: 17622389--17622697 Score: 618
Period size: 146 Copynumber: 2.1 Consensus size: 146
17622379 TTTAAGTTTA
17622389 TTTTTTATTTTTAATTATCATTTTTTACACATAAACTCTTTTGGTTAGATGGTTAGATAATTGGG
1 TTTTTTATTTTTAATTATCATTTTTTACACATAAACTCTTTTGGTTAGATGGTTAGATAATTGGG
17622454 ATTTCATCATTGAGCTTTAAGTTTAATTCCTCTTATAAGCATTTTAATATGTATTTTTTATTTCA
66 ATTTCATCATTGAGCTTTAAGTTTAATTCCTCTTATAAGCATTTTAATATGTATTTTTTATTTCA
17622519 TGTTGTTTCAAACTTT
131 TGTTGTTTCAAACTTT
17622535 TTTTTTATTTTTAATTATCATTTTTTACACATAAACTCTTTTGGTTAGATGGTTAGATAATTGGG
1 TTTTTTATTTTTAATTATCATTTTTTACACATAAACTCTTTTGGTTAGATGGTTAGATAATTGGG
17622600 ATTTCATCATTGAGCTTTAAGTTTAATTCCTCTTATAAGCATTTTAATATGTATTTTTTATTTCA
66 ATTTCATCATTGAGCTTTAAGTTTAATTCCTCTTATAAGCATTTTAATATGTATTTTTTATTTCA
17622665 TGTTGTTTCAAACTTT
131 TGTTGTTTCAAACTTT
17622681 TTTTTTATTTTTAATTA
1 TTTTTTATTTTTAATTA
17622698 ATGTTTATAA
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 163 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (146 bp):
TTTTTTATTTTTAATTATCATTTTTTACACATAAACTCTTTTGGTTAGATGGTTAGATAATTGGG
ATTTCATCATTGAGCTTTAAGTTTAATTCCTCTTATAAGCATTTTAATATGTATTTTTTATTTCA
TGTTGTTTCAAACTTT
Found at i:17629262 original size:14 final size:15
Alignment explanation
Indices: 17629245--17629277 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
17629235 AAATTTTAAG
17629245 AAAAAAATAAAA-AT
1 AAAAAAATAAAACAT
*
17629259 AAAAATATAAAACAT
1 AAAAAAATAAAACAT
17629274 AAAA
1 AAAA
17629278 CTTTTATAAT
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:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAAAATAAAACAT
Found at i:17629803 original size:21 final size:22
Alignment explanation
Indices: 17629760--17629807 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
17629750 CCGTAAAAAT
* *
17629760 TATTAATTATTGTAAGTAGTAA
1 TATTAAATATTGTAAGCAGTAA
17629782 TATTAAATATTGTAA-CAGTAA
1 TATTAAATATTGTAAGCAGTAA
17629803 TATTA
1 TATTA
17629808 GTTACTATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (22 bp):
TATTAAATATTGTAAGCAGTAA
Found at i:17638055 original size:25 final size:26
Alignment explanation
Indices: 17638001--17638055 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
17637991 TACTGAATTT
*
17638001 TGTTTAATGATGCTTTATTTGATACA
1 TGTTTAATGATGCTTTATTAGATACA
17638027 -GTTTAATG-TGCTTT-TTAGATCACA
1 TGTTTAATGATGCTTTATTAGAT-ACA
17638051 TGTTT
1 TGTTT
17638056 CGGATGAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 5 0.19
24 9 0.35
25 12 0.46
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.51
Consensus pattern (26 bp):
TGTTTAATGATGCTTTATTAGATACA
Found at i:17639205 original size:46 final size:46
Alignment explanation
Indices: 17639124--17639442 Score: 233
Period size: 46 Copynumber: 7.1 Consensus size: 46
17639114 TTATTGCTGT
* * * * *
17639124 AATTGAGGTGTATAAATGTTGTTAATAG-AGATGTTAAAGTGCTGCA
1 AATTGAAGTGTTTAAATGCTGTAAATTGAAG-TGTTAAAGTGCTGCA
* * * *
17639170 AATTGAAGTGTTTAAATGCTATAAATTAAAGTGTTAAAATGTTGCA
1 AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGCTGCA
* *
17639216 AATTGAAGTATTTAAATGCTGTGAATTGAAGTGTTAAAGTGCTGCA
1 AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGCTGCA
* *
17639262 AATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTTAA--G-T---
1 AATTGAAGTGTTTAAATGCTGTAAATTGAAGTG-TTAAAGTGCTGCA
* * * * * * *
17639303 -ATTGAGGTGTATAAATGTTGTTAATTG-GGATGTTAAAGTGTTGTA
1 AATTGAAGTGTTTAAATGCTGTAAATTGAAG-TGTTAAAGTGCTGCA
* * * * * * * *
17639348 AGTTGAGGTGTTTAAATGCTATAAATTGAAGTATTTAATTGTTGTA
1 AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGCTGCA
* ** * * * *
17639394 AATTGAGGTACTGAAATGATGTAAATCGAAGTGTTTAAGTGCTGCA
1 AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGCTGCA
17639440 AAT
1 AAT
17639443 AATATATGAT
Statistics
Matches: 218, Mismatches: 44, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
39 5 0.02
40 26 0.12
41 1 0.00
42 1 0.00
44 1 0.00
45 1 0.00
46 176 0.81
47 7 0.03
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.38
Consensus pattern (46 bp):
AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGCTGCA
Found at i:17639297 original size:23 final size:23
Alignment explanation
Indices: 17639081--17639431 Score: 199
Period size: 23 Copynumber: 15.6 Consensus size: 23
17639071 GTATTGCAAT
* *
17639081 TTGAAGTGTTT-AGTAGTTGGAAA
1 TTGAAGTGTTTAAAT-GTTGTAAA
* * *
17639104 TTG-AGATGTTTTATTGCTGT-AA
1 TTGAAG-TGTTTAAATGTTGTAAA
* * *
17639126 TTGAGGTGTATAAATGTTGTTAA
1 TTGAAGTGTTTAAATGTTGTAAA
* * *
17639149 TAG-AGATG-TTAAAGTGCTGCAAA
1 TTGAAG-TGTTTAAA-TGTTGTAAA
* *
17639172 TTGAAGTGTTTAAATGCTATAAA
1 TTGAAGTGTTTAAATGTTGTAAA
* * *
17639195 TTAAAGTGTTAAAATGTTGCAAA
1 TTGAAGTGTTTAAATGTTGTAAA
* * *
17639218 TTGAAGTATTTAAATGCTGTGAA
1 TTGAAGTGTTTAAATGTTGTAAA
* *
17639241 TTGAAGTG-TTAAAGTGCTGCAAA
1 TTGAAGTGTTTAAA-TGTTGTAAA
17639264 TTGAAGTGTTTAAATGTTGTAAA
1 TTGAAGTGTTTAAATGTTGTAAA
*
17639287 TTGAAGTGTTTTAA----GT--A
1 TTGAAGTGTTTAAATGTTGTAAA
* * *
17639304 TTGAGGTGTATAAATGTTGTTAA
1 TTGAAGTGTTTAAATGTTGTAAA
* *
17639327 TTG-GGATG-TTAAAGTGTTGTAAG
1 TTGAAG-TGTTTAAA-TGTTGTAAA
* * *
17639350 TTGAGGTGTTTAAATGCTATAAA
1 TTGAAGTGTTTAAATGTTGTAAA
* *
17639373 TTGAAGTATTTAATTGTTGTAAA
1 TTGAAGTGTTTAAATGTTGTAAA
* ** * *
17639396 TTGAGGTACTGAAATGATGTAAA
1 TTGAAGTGTTTAAATGTTGTAAA
*
17639419 TCGAAGTGTTTAA
1 TTGAAGTGTTTAA
17639432 GTGCTGCAAA
Statistics
Matches: 250, Mismatches: 58, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
17 12 0.05
19 2 0.01
21 2 0.01
22 33 0.13
23 180 0.72
24 21 0.08
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (23 bp):
TTGAAGTGTTTAAATGTTGTAAA
Found at i:17639987 original size:5 final size:5
Alignment explanation
Indices: 17639977--17640003 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
17639967 CAAAAACACA
17639977 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
17640004 TTGGGTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:17641491 original size:26 final size:27
Alignment explanation
Indices: 17641354--17641604 Score: 272
Period size: 27 Copynumber: 9.3 Consensus size: 27
17641344 GGGTATAGCA
* *
17641354 GTCATTTTACCCTTTGGGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
17641381 GTCATTTTA-CCTTGCCAGGGTATTTCA
1 GTCATTTTACCCTT-CGAGGGTATTTCG
* * * **
17641408 GTAATTCTACCCTGCGAGGGTATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * * *
17641435 GTTATTTTACCATTTGGGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
17641462 GTCATTTTACCCTT-AAGGATATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
17641488 GTCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
17641515 GTTATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
17641542 ATCATTTTACCTTTTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
17641569 GTCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
17641596 ATTATTTTA
1 GTCATTTTA
17641605 GGCCCATTAC
Statistics
Matches: 185, Mismatches: 36, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
26 25 0.14
27 157 0.85
28 3 0.02
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCG
Found at i:17641526 original size:107 final size:107
Alignment explanation
Indices: 17641354--17641582 Score: 291
Period size: 107 Copynumber: 2.1 Consensus size: 107
17641344 GGGTATAGCA
** * *
17641354 GTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTACCTTGCCAGGGTATTTCAGTAATTCTACC
1 GTCATTTTACCC-TTAAGGATATTTCAGTCATTTTACCTTGCCAGGGTATTTCAGTAATTCTACC
* * *
17641419 CTGCGAGGGTATTTTAG-TTATTTTACCATTTGGGGGTATTTTG
65 CTGCGAGGGTA-TTTAGATCATTTTACCATTTGAGGGTATTTCG
* * * *
17641462 GTCATTTTACCCTTAAGGATATTTCAGTCATTTTACCCTT-CGAGGGTATTTCGGTTATTTTACC
1 GTCATTTTACCCTTAAGGATATTTCAGTCATTTTA-CCTTGCCAGGGTATTTCAGTAATTCTACC
* * *
17641526 CTTCGAGGGTATTTCGATCATTTTACCTTTTGAGGGTATTTCG
65 CTGCGAGGGTATTTAGATCATTTTACCATTTGAGGGTATTTCG
17641569 GTCATTTTACCCTT
1 GTCATTTTACCCTT
17641583 CGAGGGTATT
Statistics
Matches: 105, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
106 4 0.04
107 85 0.81
108 16 0.15
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.44
Consensus pattern (107 bp):
GTCATTTTACCCTTAAGGATATTTCAGTCATTTTACCTTGCCAGGGTATTTCAGTAATTCTACCC
TGCGAGGGTATTTAGATCATTTTACCATTTGAGGGTATTTCG
Found at i:17641592 original size:81 final size:81
Alignment explanation
Indices: 17641357--17641604 Score: 327
Period size: 81 Copynumber: 3.1 Consensus size: 81
17641347 TATAGCAGTC
*** * * *
17641357 ATTTTACCCTTTGGGGGTATTTCGGTCATTTTACCTTGCCAGGGTATTTCAGTAATTCTACCCTG
1 ATTTTACCCTTTGGGGGTATTTCGGTCATTTTACCTTTTAAGGGTATTTCAGTCATTTTACCCTT
**
17641422 CGAGGGTATTTTAGTT
66 CGAGGGTATTTCGGTT
* * * *
17641438 ATTTTACCATTTGGGGGTATTTTGGTCATTTTACC-CTTAAGGATATTTCAGTCATTTTACCCTT
1 ATTTTACCCTTTGGGGGTATTTCGGTCATTTTACCTTTTAAGGGTATTTCAGTCATTTTACCCTT
17641502 CGAGGGTATTTCGGTT
66 CGAGGGTATTTCGGTT
* * * * *
17641518 ATTTTACCCTTCGAGGGTATTTCGATCATTTTACCTTTTGAGGGTATTTCGGTCATTTTACCCTT
1 ATTTTACCCTTTGGGGGTATTTCGGTCATTTTACCTTTTAAGGGTATTTCAGTCATTTTACCCTT
*
17641583 CGAGGGTATTTCGATT
66 CGAGGGTATTTCGGTT
17641599 ATTTTA
1 ATTTTA
17641605 GGCCCATTAC
Statistics
Matches: 144, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
80 65 0.45
81 79 0.55
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.44
Consensus pattern (81 bp):
ATTTTACCCTTTGGGGGTATTTCGGTCATTTTACCTTTTAAGGGTATTTCAGTCATTTTACCCTT
CGAGGGTATTTCGGTT
Found at i:17642311 original size:34 final size:34
Alignment explanation
Indices: 17642243--17642311 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
17642233 GAAGAGGGAG
* *
17642243 AGAAAGGCAATATTCGGCCAAGAGAGAAGCAGGA
1 AGAAAGGCAATATTCGGCCAAAAGAGAAACAGGA
*
17642277 AGAAAGGCAATATTCGGCCACAAAGA-AAATAGGA
1 AGAAAGGCAATATTCGGCCA-AAAGAGAAACAGGA
17642311 A
1 A
17642312 AGAACCAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 27 0.87
35 4 0.13
ACGTcount: A:0.48, C:0.14, G:0.28, T:0.10
Consensus pattern (34 bp):
AGAAAGGCAATATTCGGCCAAAAGAGAAACAGGA
Found at i:17645998 original size:16 final size:16
Alignment explanation
Indices: 17645977--17646031 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
17645967 TGAATTACTT
17645977 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
17645993 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
17646009 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
17646025 ATTACAG
1 ATTACAG
17646032 TGAACCAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:17655509 original size:22 final size:23
Alignment explanation
Indices: 17655482--17655530 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
17655472 TATATTTTAT
*
17655482 TTCAAATGTTTCATATT-TACAC
1 TTCAAATGTTCCATATTATACAC
17655504 TTCAAATGTTCCATATTCATACAC
1 TTCAAATGTTCCATATT-ATACAC
17655528 TTC
1 TTC
17655531 TCGATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 16 0.67
24 8 0.33
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (23 bp):
TTCAAATGTTCCATATTATACAC
Found at i:17658102 original size:12 final size:12
Alignment explanation
Indices: 17658087--17658125 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
17658077 TTAAAACATA
17658087 ATTATAAATATC
1 ATTATAAATATC
* *
17658099 ATTA-AAACATA
1 ATTATAAATATC
17658110 ATTATAAATATC
1 ATTATAAATATC
17658122 ATTA
1 ATTA
17658126 ATAACATCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
ATTATAAATATC
Found at i:17658102 original size:23 final size:23
Alignment explanation
Indices: 17658076--17658132 Score: 105
Period size: 23 Copynumber: 2.4 Consensus size: 23
17658066 ATAGAAATAA
17658076 ATTAAAACATAATTATAAATATC
1 ATTAAAACATAATTATAAATATC
17658099 ATTAAAACATAATTATAAATATC
1 ATTAAAACATAATTATAAATATC
17658122 ATTAATAACAT
1 ATTAA-AACAT
17658133 CACAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 28 0.85
24 5 0.15
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (23 bp):
ATTAAAACATAATTATAAATATC
Found at i:17659007 original size:132 final size:132
Alignment explanation
Indices: 17658770--17659999 Score: 2194
Period size: 132 Copynumber: 9.3 Consensus size: 132
17658760 GATTCCTTGA
* * * * *
17658770 ACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA
1 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
*
17658835 GATTGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
66 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
17658900 GG
131 GG
17658902 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
1 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
17658967 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
66 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
17659032 GG
131 GG
17659034 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
1 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
17659099 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
66 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
17659164 GG
131 GG
17659166 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
1 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
17659231 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
66 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
17659296 GG
131 GG
17659298 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
1 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
17659363 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
66 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
17659428 GG
131 GG
17659430 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
1 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
17659495 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
66 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
17659560 GG
131 GG
17659562 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
1 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
17659627 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
66 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
17659692 GG
131 GG
17659694 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
1 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
* * *
17659759 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTATTTCTCT
66 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
17659824 AGG
131 -GG
* * * * * *
17659827 -CAACAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAAGCAATAGTGGAGTAGATCGAA
1 ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
* * * *
17659891 GATGGCAGATTTTACCTCCCTGTGGTTACAGTGCAGTACATTGAAGCCAGTAATTCTACTTCCCT
66 GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
17659956 GG
131 GG
* ** * * * *
17659958 GCAACGGTGGAATAGATTGAAGATTGCA-AGTCTTATCTCCCT
1 ACAACAATGAAATAAATTGAAAATTTCAGA-TCTTATCTCCCT
17660000 GCAGTTGCAG
Statistics
Matches: 1072, Mismatches: 23, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
131 3 0.00
132 1067 1.00
133 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (132 bp):
ACAACAATGAAATAAATTGAAAATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
GATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCCAGTAATTCTACTTCCCT
GG
Found at i:17659886 original size:44 final size:44
Alignment explanation
Indices: 17659720--17659911 Score: 152
Period size: 44 Copynumber: 4.4 Consensus size: 44
17659710 TTGAAAATTT
* * *
17659720 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGG
1 CAGATTTTATCTCCCTAAGCAATAGTGGAGTAGATTGAAGATGG
* * ** ** * ***
17659764 CGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAG
1 CAGATTTTATCTCCCT-AAGCAATAGTGGAGTAGATTGAAGATGG
* * * * * * * **
17659809 TA-ATTCTATTTCTCTAGGCAACAGTGGAATAGATTGAAGATTT
1 CAGATTTTATCTCCCTAAGCAATAGTGGAGTAGATTGAAGATGG
*
17659852 CAGATTTTATCTCCCTAAGCAATAGTGGAGTAGATCGAAGATGG
1 CAGATTTTATCTCCCTAAGCAATAGTGGAGTAGATTGAAGATGG
*
17659896 CAGATTTTACCTCCCT
1 CAGATTTTATCTCCCT
17659912 GTGGTTACAG
Statistics
Matches: 106, Mismatches: 40, Indels: 4
0.71 0.27 0.03
Matches are distributed among these distances:
43 19 0.18
44 69 0.65
45 18 0.17
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (44 bp):
CAGATTTTATCTCCCTAAGCAATAGTGGAGTAGATTGAAGATGG
Found at i:17660277 original size:21 final size:21
Alignment explanation
Indices: 17660229--17660304 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
17660219 ATTTTCAAGG
17660229 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
17660248 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
17660269 ATATTCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
17660290 TTATGCAATCTTAGA
1 ATATGCAATCTTAGA
17660305 AAATATGATT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 19 0.37
21 33 0.63
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:17660649 original size:3 final size:3
Alignment explanation
Indices: 17660641--17660682 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
17660631 TGTTATTAAG
* *
17660641 TTA TTA TTA TTG TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17660683 CTATATATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:17660840 original size:17 final size:17
Alignment explanation
Indices: 17660818--17660850 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17660808 ATAGACATAT
*
17660818 TATACATTTACATTTTA
1 TATACATATACATTTTA
17660835 TATACATATACATTTT
1 TATACATATACATTTT
17660851 TTATTTCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
TATACATATACATTTTA
Found at i:17662492 original size:15 final size:15
Alignment explanation
Indices: 17662469--17662498 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17662459 AAATAATAGT
17662469 TATAATGTTTTTATC
1 TATAATGTTTTTATC
*
17662484 TATATTGTTTTTATC
1 TATAATGTTTTTATC
17662499 CCTCAACAAA
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:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (15 bp):
TATAATGTTTTTATC
Found at i:17670777 original size:2 final size:2
Alignment explanation
Indices: 17670770--17670799 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17670760 CTCATACTTT
17670770 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17670800 GATAGGTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:17673573 original size:46 final size:46
Alignment explanation
Indices: 17673521--17673661 Score: 230
Period size: 46 Copynumber: 3.1 Consensus size: 46
17673511 TTAATAGAGA
*
17673521 TGTTAAAGTGCTACAAATTGAAGTGTTTAAATGCTGTAAATTGAAG
1 TGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGAAG
* * *
17673567 TGTTAAAGTGTTGCAAATTGAAGTATTTAAATGCTGTGAATTGAAG
1 TGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGAAG
*
17673613 TGTTAAAGTGCTGCAAATTGAA-TGTTTAAATGTTGTAAATTGAAG
1 TGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGAAG
17673658 TGTT
1 TGTT
17673662 TTAAGTACTG
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 24 0.28
46 63 0.72
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (46 bp):
TGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGAAG
Found at i:17673662 original size:23 final size:23
Alignment explanation
Indices: 17673535--17673662 Score: 163
Period size: 23 Copynumber: 5.6 Consensus size: 23
17673525 AAAGTGCTAC
17673535 AAATTGAAGTGTTTAAATGCTGT
1 AAATTGAAGTGTTTAAATGCTGT
* *
17673558 AAATTGAAGTG-TTAAAGTGTTGC
1 AAATTGAAGTGTTTAAA-TGCTGT
*
17673581 AAATTGAAGTATTTAAATGCTGT
1 AAATTGAAGTGTTTAAATGCTGT
* *
17673604 GAATTGAAGTG-TTAAAGTGCTGC
1 AAATTGAAGTGTTTAAA-TGCTGT
*
17673627 AAATTGAA-TGTTTAAATGTTGT
1 AAATTGAAGTGTTTAAATGCTGT
17673649 AAATTGAAGTGTTT
1 AAATTGAAGTGTTT
17673663 TAAGTACTGA
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
22 24 0.27
23 60 0.67
24 5 0.06
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (23 bp):
AAATTGAAGTGTTTAAATGCTGT
Found at i:17675801 original size:46 final size:44
Alignment explanation
Indices: 17675711--17675803 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 44
17675701 TTACAACATT
17675711 ATTCCATTCAACCACACACAAGAATACTATTACAGTTCTATTCC
1 ATTCCATTCAACCACACACAAGAATACTATTACAGTTCTATTCC
17675755 ATTCCATTCAACCA-A-ACAATTGAATTACTAATTACAGCTT-TATTCC
1 ATTCCATTCAACCACACACAA--GAA-TACT-ATTACAG-TTCTATTCC
17675801 ATT
1 ATT
17675804 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
42 4 0.09
43 1 0.02
44 17 0.39
45 4 0.09
46 16 0.36
47 2 0.05
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
ATTCCATTCAACCACACACAAGAATACTATTACAGTTCTATTCC
Found at i:17675806 original size:16 final size:16
Alignment explanation
Indices: 17675784--17675855 Score: 99
Period size: 16 Copynumber: 4.5 Consensus size: 16
17675774 TTGAATTACT
*
17675784 AATTACAGCTTTATTC
1 AATTACAGCTCTATTC
*
17675800 CATTACAGCTCTATTC
1 AATTACAGCTCTATTC
*
17675816 AATAACAGCTCTATTC
1 AATTACAGCTCTATTC
*
17675832 AATAACAGCTCTATTC
1 AATTACAGCTCTATTC
*
17675848 CATTACAG
1 AATTACAG
17675856 TGAACTAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (16 bp):
AATTACAGCTCTATTC
Found at i:17680241 original size:29 final size:29
Alignment explanation
Indices: 17680199--17680271 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
17680189 CTACACTTGG
* *
17680199 AACAAAATGCAAGAAATCTATTTGCATTA
1 AACAAAATGTAAGAAATCTATGTGCATTA
*
17680228 AACAAAATGTAAGAAATCTATGTGTATTA
1 AACAAAATGTAAGAAATCTATGTGCATTA
17680257 AACAAAATGTAAGAA
1 AACAAAATGTAAGAA
17680272 CACATGTGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (29 bp):
AACAAAATGTAAGAAATCTATGTGCATTA
Found at i:17682752 original size:225 final size:225
Alignment explanation
Indices: 17682361--17682810 Score: 900
Period size: 225 Copynumber: 2.0 Consensus size: 225
17682351 TATTGTTAAT
17682361 GGAAACTTTCCGTATGTTGGATTACTGTTTGAGATATTTGTATGTGATTTGTAATGTATGCTATT
1 GGAAACTTTCCGTATGTTGGATTACTGTTTGAGATATTTGTATGTGATTTGTAATGTATGCTATT
17682426 TTGGAATATACGTTGTGTTACTCCGTCTTTTGCCTGTTGCCAGTTTCAGACTCACATTGAGCTCG
66 TTGGAATATACGTTGTGTTACTCCGTCTTTTGCCTGTTGCCAGTTTCAGACTCACATTGAGCTCG
17682491 CGTAGCTCACCCCCTCTTAGTTTTCTCTCTTTTAGGTAATTCTCGTGTTTGGCGTGGGACTCAGT
131 CGTAGCTCACCCCCTCTTAGTTTTCTCTCTTTTAGGTAATTCTCGTGTTTGGCGTGGGACTCAGT
17682556 GCGTCGGTGATCTTAGAACTTTTACTTGGG
196 GCGTCGGTGATCTTAGAACTTTTACTTGGG
17682586 GGAAACTTTCCGTATGTTGGATTACTGTTTGAGATATTTGTATGTGATTTGTAATGTATGCTATT
1 GGAAACTTTCCGTATGTTGGATTACTGTTTGAGATATTTGTATGTGATTTGTAATGTATGCTATT
17682651 TTGGAATATACGTTGTGTTACTCCGTCTTTTGCCTGTTGCCAGTTTCAGACTCACATTGAGCTCG
66 TTGGAATATACGTTGTGTTACTCCGTCTTTTGCCTGTTGCCAGTTTCAGACTCACATTGAGCTCG
17682716 CGTAGCTCACCCCCTCTTAGTTTTCTCTCTTTTAGGTAATTCTCGTGTTTGGCGTGGGACTCAGT
131 CGTAGCTCACCCCCTCTTAGTTTTCTCTCTTTTAGGTAATTCTCGTGTTTGGCGTGGGACTCAGT
17682781 GCGTCGGTGATCTTAGAACTTTTACTTGGG
196 GCGTCGGTGATCTTAGAACTTTTACTTGGG
17682811 TTTTTCTCAA
Statistics
Matches: 225, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
225 225 1.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (225 bp):
GGAAACTTTCCGTATGTTGGATTACTGTTTGAGATATTTGTATGTGATTTGTAATGTATGCTATT
TTGGAATATACGTTGTGTTACTCCGTCTTTTGCCTGTTGCCAGTTTCAGACTCACATTGAGCTCG
CGTAGCTCACCCCCTCTTAGTTTTCTCTCTTTTAGGTAATTCTCGTGTTTGGCGTGGGACTCAGT
GCGTCGGTGATCTTAGAACTTTTACTTGGG
Found at i:17685486 original size:319 final size:319
Alignment explanation
Indices: 17684902--17685544 Score: 1259
Period size: 319 Copynumber: 2.0 Consensus size: 319
17684892 AAAAAGTTTG
17684902 ACTCCAGCATGTTGAGTATTGATTTTTCTCGAAGTATAACAGTTGTGTTTATCTACAATGTCTTG
1 ACTCCAGCATGTTGAGTATTGATTTTTCTCGAAGTATAACAGTTGTGTTTATCTACAATGTCTTG
17684967 ATGATGGTTCTTTTATATATTTGCTACTTTATGTTGATGATATGTTAATTGCGGCTAAGAATCCA
66 ATGATGGTTCTTTTATATATTTGCTACTTTATGTTGATGATATGTTAATTGCGGCTAAGAATCCA
17685032 TTTGAAATTGATAATCTTAAAACCATGCTTAACTCTAAGTTTGAGATGAAGGATTTAGGTGTAGC
131 TTTGAAATTGATAATCTTAAAACCATGCTTAACTCTAAGTTTGAGATGAAGGATTTAGGTGTAGC
*
17685097 AAAGAAAATTTTGGGGATGAAAATTTTGAGAGAAAGACATTCTGAGAAATTATTTTTATTCCTAC
196 AAAGAAAATTTTGGGGATGAAAATTTTGAGAGAAAGACATTCCGAGAAATTATTTTTATTCCTAC
17685162 AAAGGTACATCAAGAAGATCCTTGAGAGATTTGAGATGCAAGATGCAAAACAAGTATAT
261 AAAGGTACATCAAGAAGATCCTTGAGAGATTTGAGATGCAAGATGCAAAACAAGTATAT
*
17685221 ACTCTAGCATGTTGAGTATTGATTTTTCTCGAAGTATAACAGTTGTGTTTATCTACAATGTCTTG
1 ACTCCAGCATGTTGAGTATTGATTTTTCTCGAAGTATAACAGTTGTGTTTATCTACAATGTCTTG
17685286 ATGATGGTTCTTTTATATATTTGCTACTTTATGTTGATGATATGTTAATTGCGGCTAAGAATCCA
66 ATGATGGTTCTTTTATATATTTGCTACTTTATGTTGATGATATGTTAATTGCGGCTAAGAATCCA
17685351 TTTGAAATTGATAATCTTAAAACCATGCTTAACTCTAAGTTTGAGATGAAGGATTTAGGTGTAGC
131 TTTGAAATTGATAATCTTAAAACCATGCTTAACTCTAAGTTTGAGATGAAGGATTTAGGTGTAGC
*
17685416 AAAGAAAATTTTGGGGATGAAAATTTTGAGAGATAGACATTCCGAGAAATTATTTTTATTCCTAC
196 AAAGAAAATTTTGGGGATGAAAATTTTGAGAGAAAGACATTCCGAGAAATTATTTTTATTCCTAC
17685481 AAAGGTACATCAAGAAGATCCTTGAGAGATTTGAGATGCAAGATGCAAAACAAGTATAT
261 AAAGGTACATCAAGAAGATCCTTGAGAGATTTGAGATGCAAGATGCAAAACAAGTATAT
17685540 ACTCC
1 ACTCC
17685545 TTTAATTGTA
Statistics
Matches: 320, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
319 320 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (319 bp):
ACTCCAGCATGTTGAGTATTGATTTTTCTCGAAGTATAACAGTTGTGTTTATCTACAATGTCTTG
ATGATGGTTCTTTTATATATTTGCTACTTTATGTTGATGATATGTTAATTGCGGCTAAGAATCCA
TTTGAAATTGATAATCTTAAAACCATGCTTAACTCTAAGTTTGAGATGAAGGATTTAGGTGTAGC
AAAGAAAATTTTGGGGATGAAAATTTTGAGAGAAAGACATTCCGAGAAATTATTTTTATTCCTAC
AAAGGTACATCAAGAAGATCCTTGAGAGATTTGAGATGCAAGATGCAAAACAAGTATAT
Found at i:17687429 original size:22 final size:23
Alignment explanation
Indices: 17687387--17687429 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
17687377 TTAAATAATA
*
17687387 AATTTTTATAATAAAAGTCTATT
1 AATTTTTATAATAAAAATCTATT
17687410 AATTTTTA-AA-AAATAATCTA
1 AATTTTTATAATAAA-AATCTA
17687430 GAGAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 3 0.17
22 7 0.39
23 8 0.44
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (23 bp):
AATTTTTATAATAAAAATCTATT
Found at i:17698994 original size:218 final size:219
Alignment explanation
Indices: 17698606--17699042 Score: 867
Period size: 218 Copynumber: 2.0 Consensus size: 219
17698596 AAAACAAATA
17698606 TTAGCAAATAATAATAAAAATCATATATATATTTTTGTGATAGAAACAAACTCTATCTAAAATTT
1 TTAGCAAATAATAATAAAAATCATATATATATTTTTGTGATAGAAACAAACTCTATCTAAAATTT
17698671 TTGTGATATATATATATATCCACACTACACTTACTGTGTTAAATATAAACACCGGTCATTTCTTT
66 TTGTGATATATATATATATCCACACTACACTTACTGTGTTAAATATAAACACCGGTCATTTCTTT
17698736 CTTTCTTTCTTTTTCTTTTTCTTTTGAGAATATTTTAATATTTTTTTGTTCAGTTTCAAAGATGA
131 CTTTCTTTCTTTTTCTTTTTCTTTTGAGAATATTTTAATATTTTTTTGTTCAGTTTCAAAGATGA
17698801 CATGTGATTTAGACATTTCAACAC
196 CATGTGATTTAGACATTTCAACAC
17698825 TTAGCAAAT-ATAATAAAAATCATATATATATTTTTGTGATAGAAACAAACTCTATCTAAAATTT
1 TTAGCAAATAATAATAAAAATCATATATATATTTTTGTGATAGAAACAAACTCTATCTAAAATTT
17698889 TTGTGATATATATATATATCCACACTACACTTACTGTGTTAAATATAAACACCGGTCATTTCTTT
66 TTGTGATATATATATATATCCACACTACACTTACTGTGTTAAATATAAACACCGGTCATTTCTTT
17698954 CTTTCTTTCTTTTTCTTTTTCTTTTGAGAATATTTTAATATTTTTTTGTTCAGTTTCAAAGATGA
131 CTTTCTTTCTTTTTCTTTTTCTTTTGAGAATATTTTAATATTTTTTTGTTCAGTTTCAAAGATGA
17699019 CATGTGATTTAGACATTTCAACAC
196 CATGTGATTTAGACATTTCAACAC
17699043 AACTTTAAAT
Statistics
Matches: 218, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
218 209 0.96
219 9 0.04
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (219 bp):
TTAGCAAATAATAATAAAAATCATATATATATTTTTGTGATAGAAACAAACTCTATCTAAAATTT
TTGTGATATATATATATATCCACACTACACTTACTGTGTTAAATATAAACACCGGTCATTTCTTT
CTTTCTTTCTTTTTCTTTTTCTTTTGAGAATATTTTAATATTTTTTTGTTCAGTTTCAAAGATGA
CATGTGATTTAGACATTTCAACAC
Found at i:17699636 original size:19 final size:20
Alignment explanation
Indices: 17699591--17699640 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
17699581 AAATAAAATA
**
17699591 TTTTTATTTATTTTGAAGAT
1 TTTTTATTTATTTACAAGAT
* *
17699611 GTCTTATTT-TTTACAAGAT
1 TTTTTATTTATTTACAAGAT
17699630 TTTTTATTTAT
1 TTTTTATTTAT
17699641 ATTTCTATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTTTATTTATTTACAAGAT
Found at i:17700447 original size:60 final size:61
Alignment explanation
Indices: 17700352--17700475 Score: 241
Period size: 60 Copynumber: 2.0 Consensus size: 61
17700342 TATGTTTGGA
17700352 TTAAAAATACTAAAGGAAAAGAAAAGAAAAGAGAGGAAAATTAAGAAAAGTAAATAATTAT
1 TTAAAAATACTAAAGGAAAAGAAAAGAAAAGAGAGGAAAATTAAGAAAAGTAAATAATTAT
17700413 TTAAAAATACTAAAGG-AAAGAAAAGAAAAGAGAGGAAAATTAAGAAAAGTAAATAATTAT
1 TTAAAAATACTAAAGGAAAAGAAAAGAAAAGAGAGGAAAATTAAGAAAAGTAAATAATTAT
17700473 TTA
1 TTA
17700476 TTATAGTTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 47 0.75
61 16 0.25
ACGTcount: A:0.63, C:0.02, G:0.16, T:0.19
Consensus pattern (61 bp):
TTAAAAATACTAAAGGAAAAGAAAAGAAAAGAGAGGAAAATTAAGAAAAGTAAATAATTAT
Found at i:17706438 original size:20 final size:20
Alignment explanation
Indices: 17706413--17706450 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17706403 TTTTTTAAAA
17706413 AAAATCT-ATATAATAATTGT
1 AAAATCTAATATAA-AATTGT
17706433 AAAATCTAATATAAAATT
1 AAAATCTAATATAAAATT
17706451 TACCTCGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATCTAATATAAAATTGT
Found at i:17707440 original size:51 final size:51
Alignment explanation
Indices: 17707385--17707484 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
17707375 AAATTATTTA
*
17707385 AAATAGGGATTTACGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* *
17707436 AAATATGGATTTAAGAGAAATTTAGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
17707485 GAAAATTTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.25, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:17707458 original size:11 final size:10
Alignment explanation
Indices: 17707444--17707520 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 10
17707434 TTAAATATGG
17707444 ATTTAAGAGAA
1 ATTT-AGAGAA
*
17707455 ATTTAGAAGGA
1 ATTTAG-AGAA
17707466 ATTTGAGAGCAA
1 ATTT-AGAG-AA
*
17707478 ATTGAGAGAAA
1 ATTTAGAG-AA
17707489 ATTTAGAGGAA
1 ATTTAGA-GAA
*
17707500 ATTGAGAGGAA
1 ATTTAGA-GAA
17707511 ATTT-GAGAA
1 ATTTAGAGAA
17707520 A
1 A
17707521 GGATTAGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 40 0.73
12 7 0.13
ACGTcount: A:0.48, C:0.01, G:0.26, T:0.25
Consensus pattern (10 bp):
ATTTAGAGAA
Found at i:17707499 original size:33 final size:34
Alignment explanation
Indices: 17707444--17707518 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 34
17707434 TTAAATATGG
* *
17707444 ATTTAAGAGAAATTTAGAAGGAATTTGAGAGCAA
1 ATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAA
*
17707478 A-TTGAGAGAAAATTTAG-AGGAAATTGAGAGGAA
1 ATTTGAGAG-AAATTTAGAAGGAAATTGAGAGCAA
17707511 ATTTGAGA
1 ATTTGAGA
17707519 AAGGATTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 21 0.58
34 15 0.42
ACGTcount: A:0.47, C:0.01, G:0.27, T:0.25
Consensus pattern (34 bp):
ATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAA
Found at i:17707501 original size:22 final size:23
Alignment explanation
Indices: 17707465--17707518 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
17707455 ATTTAGAAGG
17707465 AATTTGAGAGCAAATTGAGAGAA
1 AATTTGAGAGCAAATTGAGAGAA
* *
17707488 AATTT-AGAGGAAATTGAGAGGA
1 AATTTGAGAGCAAATTGAGAGAA
17707510 AATTTGAGA
1 AATTTGAGA
17707519 AAGGATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (23 bp):
AATTTGAGAGCAAATTGAGAGAA
Found at i:17710996 original size:39 final size:39
Alignment explanation
Indices: 17710951--17711028 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
17710941 ATGACATTAA
17710951 GAATTAAATTGAATAAAGTGAAAGCTATTGGAAATTTGG
1 GAATTAAATTGAATAAAGTGAAAGCTATTGGAAATTTGG
17710990 GAATTAAATTGAATAAAGTGAAAGCTATTGGAAATTTGG
1 GAATTAAATTGAATAAAGTGAAAGCTATTGGAAATTTGG
17711029 TTATAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.31
Consensus pattern (39 bp):
GAATTAAATTGAATAAAGTGAAAGCTATTGGAAATTTGG
Found at i:17713966 original size:32 final size:31
Alignment explanation
Indices: 17713930--17713994 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
17713920 AAAATTTCAA
17713930 AATTCAAAAAAGTAGAAG-GACTAAAATTGATC
1 AATTCAAAAAA-TA-AAGAGACTAAAATTGATC
* *
17713962 AATTCAAAAAATACAGATACTAAAATTGATC
1 AATTCAAAAAATAAAGAGACTAAAATTGATC
17713993 AA
1 AA
17713995 ATTAAAGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 2 0.07
31 17 0.57
32 11 0.37
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (31 bp):
AATTCAAAAAATAAAGAGACTAAAATTGATC
Found at i:17714035 original size:30 final size:30
Alignment explanation
Indices: 17714001--17714065 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
17713991 TCAAATTAAA
17714001 GTACATAGACTAATCCTTAACTTTTGCATT
1 GTACATAGACTAATCCTTAACTTTTGCATT
17714031 GTACATAGACTAATCCTTAACTTTTGCATT
1 GTACATAGACTAATCCTTAACTTTTGCATT
17714061 GTACA
1 GTACA
17714066 AGAATTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (30 bp):
GTACATAGACTAATCCTTAACTTTTGCATT
Found at i:17717017 original size:21 final size:21
Alignment explanation
Indices: 17716993--17717033 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17716983 GTCAATAACC
17716993 AAATGTTCACACAAACAGACA
1 AAATGTTCACACAAACAGACA
**
17717014 AAATGTTCTGACAAACAGAC
1 AAATGTTCACACAAACAGAC
17717034 GTATATTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.12, T:0.17
Consensus pattern (21 bp):
AAATGTTCACACAAACAGACA
Found at i:17726908 original size:18 final size:18
Alignment explanation
Indices: 17726885--17726924 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17726875 GTTTTAAAAT
*
17726885 TGAATAACGATTTGTAAA
1 TGAATAACGATTTGGAAA
* *
17726903 TGAATAATGTTTTGGAAA
1 TGAATAACGATTTGGAAA
17726921 TGAA
1 TGAA
17726925 CGACACAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (18 bp):
TGAATAACGATTTGGAAA
Found at i:17731299 original size:46 final size:46
Alignment explanation
Indices: 17731247--17731343 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 46
17731237 AATTTGTCTT
* *
17731247 TATAGGAAGAGATGTCAACTATCTTATATGAAGATAATACAGCATG
1 TATAGGAAGAGAAGTCAACTATCTTATATGAAGATAATACAACATG
* *
17731293 TATAGGAAGAGAAGTCAACTATCTTATCTGAAGATAATGCAACATG
1 TATAGGAAGAGAAGTCAACTATCTTATATGAAGATAATACAACATG
17731339 TATAG
1 TATAG
17731344 CTCAATTGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (46 bp):
TATAGGAAGAGAAGTCAACTATCTTATATGAAGATAATACAACATG
Found at i:17732889 original size:21 final size:21
Alignment explanation
Indices: 17732865--17732908 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17732855 ATATTTTTAA
*
17732865 ATTTGTTTAGATT-TATAATTT
1 ATTT-TTTAGATTATACAATTT
*
17732886 ATTTTTTATATTATACAATTT
1 ATTTTTTAGATTATACAATTT
17732907 AT
1 AT
17732909 ATAATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (21 bp):
ATTTTTTAGATTATACAATTT
Found at i:17733232 original size:3 final size:3
Alignment explanation
Indices: 17733224--17733264 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
17733214 GCAAAAACAA
17733224 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17733265 GGTTAAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17734662 original size:28 final size:27
Alignment explanation
Indices: 17734623--17734688 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 27
17734613 TTTTTGCCCG
17734623 TTTATTATTATTGTCGTTATTATTTTATT-
1 TTTATT-TTATT-TC-TTATTATTTTATTA
*
17734652 TTTATTTTA-TTCTTGTTATTTTATTA
1 TTTATTTTATTTCTTATTATTTTATTA
*
17734678 TTTCTTTTATT
1 TTTATTTTATT
17734689 ATTCTCACGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 12 0.36
26 10 0.30
27 2 0.06
28 3 0.09
29 6 0.18
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (27 bp):
TTTATTTTATTTCTTATTATTTTATTA
Found at i:17746970 original size:8 final size:8
Alignment explanation
Indices: 17746947--17747039 Score: 89
Period size: 8 Copynumber: 11.4 Consensus size: 8
17746937 AATAAATAAG
17746947 TATTATAT
1 TATTATAT
17746955 TAATTATAT
1 T-ATTATAT
*
17746964 TATTATAA
1 TATTATAT
17746972 TATTA-AT
1 TATTATAT
*
17746979 TATAATAT
1 TATTATAT
*
17746987 TATAATAT
1 TATTATAT
**
17746995 TACAATAT
1 TATTATAT
*
17747003 TAATTATAA
1 T-ATTATAT
*
17747012 TATTATAA
1 TATTATAT
17747020 TATTATAT
1 TATTATAT
17747028 TAATTATAT
1 T-ATTATAT
17747037 TAT
1 TAT
17747040 AGAGAATTGA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
7 5 0.07
8 47 0.64
9 21 0.29
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (8 bp):
TATTATAT
Found at i:17746976 original size:20 final size:20
Alignment explanation
Indices: 17746951--17747025 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
17746941 AATAAGTATT
17746951 ATATTAATTATATTATTATA
1 ATATTAATTATATTATTATA
*
17746971 ATATTAATTATAATATTATA
1 ATATTAATTATATTATTATA
17746991 ATATTACA--ATATTAATTATA
1 ATATTA-ATTATATT-ATTATA
*
17747011 ATATT-ATAATATTAT
1 ATATTAATTATATTAT
17747026 ATTAATTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.02
19 6 0.12
20 41 0.84
21 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTAATTATATTATTATA
Found at i:17746995 original size:28 final size:28
Alignment explanation
Indices: 17746948--17747040 Score: 123
Period size: 28 Copynumber: 3.2 Consensus size: 28
17746938 ATAAATAAGT
* *
17746948 ATTATATTAATTATATTATTATAATATTA
1 ATTATAAT-ATTATAATATTATAATATTA
*
17746977 ATTATAATATTATAATATTACAATATTA
1 ATTATAATATTATAATATTATAATATTA
*
17747005 ATTATAATATTATAATATTATATTAATTA
1 ATTATAATATTATAATATTATAAT-ATTA
17747034 TATTATA
1 -ATTATA
17747041 GAGAATTGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
28 40 0.70
29 11 0.19
30 6 0.11
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (28 bp):
ATTATAATATTATAATATTATAATATTA
Found at i:17748195 original size:25 final size:24
Alignment explanation
Indices: 17748134--17748193 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
17748124 AAGTGGAAAG
17748134 TGAATTTGAATTGAAATGTGATTAT
1 TGAA-TTGAATTGAAATGTGATTAT
*
17748159 TGAATAGAAATTGAAATG-G--T-T
1 TGAATTG-AATTGAAATGTGATTAT
17748180 TGAATTGAATTGAA
1 TGAATTGAATTGAA
17748194 TTATTGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 7 0.22
21 7 0.22
22 1 0.03
24 3 0.09
25 14 0.44
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (24 bp):
TGAATTGAATTGAAATGTGATTAT
Found at i:17748202 original size:18 final size:19
Alignment explanation
Indices: 17748139--17748219 Score: 71
Period size: 19 Copynumber: 4.3 Consensus size: 19
17748129 GAAAGTGAAT
17748139 TTGAATTGAAATGTG-ATTA
1 TTGAATTGAAAT-TGAATTA
*
17748158 TTGAATAGAAATTGAAATGGT-
1 TTGAATTGAAATTG-AAT--TA
17748179 TTGAATTG-AATTGAATTA
1 TTGAATTGAAATTGAATTA
* *
17748197 TTGAATTGAACTGGAA-TA
1 TTGAATTGAAATTGAATTA
17748215 TTGAA
1 TTGAA
17748220 ATTGGTGATT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.02
18 17 0.33
19 19 0.37
20 7 0.13
21 7 0.13
22 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.38
Consensus pattern (19 bp):
TTGAATTGAAATTGAATTA
Found at i:17748625 original size:45 final size:45
Alignment explanation
Indices: 17748556--17748655 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
17748546 GCTGACTACT
* *
17748556 GTTACTGTTACTGATTCAATACTTTGTGTG-TCGAATACTGTTACC
1 GTTACTGTTACAGATTCAATACTTTGTGTGCT-GAATAATGTTACC
* *
17748601 GTTATTGTTACAGATTC-ATCACTTTGTGTGCTGAATAATGTTACT
1 GTTACTGTTACAGATTCAAT-ACTTTGTGTGCTGAATAATGTTACC
*
17748646 GCTACTGTTA
1 GTTACTGTTA
17748656 TTGTTTACTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 2 0.04
45 44 0.94
46 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (45 bp):
GTTACTGTTACAGATTCAATACTTTGTGTGCTGAATAATGTTACC
Found at i:17755532 original size:21 final size:21
Alignment explanation
Indices: 17755508--17755585 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
17755498 AAACTGTTGC
*
17755508 TTTCCAAAAGAAAACGGAGGA
1 TTTCCAAAAGAAAACAGAGGA
* *
17755529 TTTCCAGAAGAAAACAAAGGA
1 TTTCCAAAAGAAAACAGAGGA
* *
17755550 TTTCCAAAAGAAGACAGAAGA
1 TTTCCAAAAGAAAACAGAGGA
* *
17755571 TTTTCAACAGAAAAC
1 TTTCCAAAAGAAAAC
17755586 TAAGGTGTCT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (21 bp):
TTTCCAAAAGAAAACAGAGGA
Found at i:17755573 original size:42 final size:42
Alignment explanation
Indices: 17755508--17755590 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
17755498 AAACTGTTGC
* *
17755508 TTTCCAAAAGAAAACGGAGGATTTCCAGA-AGAAAACAAAGGA
1 TTTCCAAAAGAAAACAGAAGATTTCCA-ACAGAAAACAAAGGA
* * *
17755550 TTTCCAAAAGAAGACAGAAGATTTTCAACAGAAAACTAAGG
1 TTTCCAAAAGAAAACAGAAGATTTCCAACAGAAAACAAAGG
17755591 TGTCTATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.17
Consensus pattern (42 bp):
TTTCCAAAAGAAAACAGAAGATTTCCAACAGAAAACAAAGGA
Found at i:17759643 original size:19 final size:19
Alignment explanation
Indices: 17759619--17759665 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
17759609 CTCTTTTTTT
17759619 TTTGCATT-CATTCCATGCA
1 TTTGCATTACATTCCAT-CA
*
17759638 TTTGCATTACATTGCATCA
1 TTTGCATTACATTCCATCA
*
17759657 TATGCATTA
1 TTTGCATTA
17759666 GATTTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43
Consensus pattern (19 bp):
TTTGCATTACATTCCATCA
Found at i:17763915 original size:44 final size:44
Alignment explanation
Indices: 17763867--17764150 Score: 129
Period size: 44 Copynumber: 6.5 Consensus size: 44
17763857 CTTGAACAGC
*
17763867 AGTGGAGTAGGTTGAAGATTACAGATCCTATCTCCCTAAGTAGT
1 AGTGGAGTAGGTTGAAGATCACAGATCCTATCTCCCTAAGTAGT
* * * *** * *
17763911 AGTGGAGCAGATCGAAGA-CGGTGAATCTTATCTTCCC-AAGGCAGT
1 AGTGGAGTAGGTTGAAGATCACAG-ATCCTATC-TCCCTAA-GTAGT
* * * * * * * * **
17763956 AGAGAAGTAGATTTAAG-CCACTGGTCCTATCTCCCTGAGCGGT
1 AGTGGAGTAGGTTGAAGATCACAGATCCTATCTCCCTAAGTAGT
* ** * *
17763999 AATGGAGTAGGTTGAAGATTGCAGATCCTGTATCCCTAAGTAGT
1 AGTGGAGTAGGTTGAAGATCACAGATCCTATCTCCCTAAGTAGT
* ** * *
17764043 AGTGGAGCAAATCGAAGA-CAGC-GAATCATATCTTCCC-AAGGTAGT
1 AGTGGAGTAGGTTGAAGATCA-CAG-ATCCTATC-TCCCTAA-GTAGT
* *
17764088 AG-GGAAGT-GGATTTAAG-TCACTAG-TCCTATCTCCCTGAGTAGT
1 AGTGG-AGTAGG-TTGAAGATCAC-AGATCCTATCTCCCTAAGTAGT
17764131 AGTGGAGTAGGTTGAAGATC
1 AGTGGAGTAGGTTGAAGATC
17764151 GTAGATCTTG
Statistics
Matches: 168, Mismatches: 53, Indels: 38
0.65 0.20 0.15
Matches are distributed among these distances:
43 41 0.24
44 84 0.50
45 42 0.25
46 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (44 bp):
AGTGGAGTAGGTTGAAGATCACAGATCCTATCTCCCTAAGTAGT
Found at i:17764024 original size:132 final size:132
Alignment explanation
Indices: 17763843--17764149 Score: 452
Period size: 132 Copynumber: 2.3 Consensus size: 132
17763833 CAGATCAAAA
* * * *
17763843 ACTGGTCCTATCTCCTTGAACAGCAGTGGAGTAGGTTGAAGATTACAGATCCTATCTCCCTAAGT
1 ACTGGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTACAGATCCTATATCCCTAAGT
* * * *
17763908 AGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGCAGTAGAGAAGTAGATTTAAG
66 AGTAGTGGAGCAAATCGAAGACAGCGAATCATATCTTCCCAAGGCAGTAGAGAAGTAGATTTAAG
17763973 CC
131 CC
* * * *
17763975 ACTGGTCCTATCTCCCTGAGCGGTAATGGAGTAGGTTGAAGATTGCAGATCCTGTATCCCTAAGT
1 ACTGGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTACAGATCCTATATCCCTAAGT
* * *
17764040 AGTAGTGGAGCAAATCGAAGACAGCGAATCATATCTTCCCAAGGTAGTAGGGAAGTGGATTTAAG
66 AGTAGTGGAGCAAATCGAAGACAGCGAATCATATCTTCCCAAGGCAGTAGAGAAGTAGATTTAAG
*
17764105 TC
131 CC
* *
17764107 ACTAGTCCTATCTCCCTGAGTAGTAGTGGAGTAGGTTGAAGAT
1 ACTGGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGAT
17764150 CGTAGATCTT
Statistics
Matches: 155, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
132 155 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (132 bp):
ACTGGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTACAGATCCTATATCCCTAAGT
AGTAGTGGAGCAAATCGAAGACAGCGAATCATATCTTCCCAAGGCAGTAGAGAAGTAGATTTAAG
CC
Found at i:17764271 original size:44 final size:44
Alignment explanation
Indices: 17764217--17764322 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
17764207 CTTGAAATTA
*
17764217 CAGTGGAGCAGATTGAAAATAC-AAGTCTTATCTCCCTGAAGTTG
1 CAGTGGAGCAGATTGAAAATACTAA-TCCTATCTCCCTGAAGTTG
* ** *
17764261 CAGTGGAGCAGACTGAAGCTACTAATCCTATCTCCTTGAAGTTG
1 CAGTGGAGCAGATTGAAAATACTAATCCTATCTCCCTGAAGTTG
*
17764305 CAGTGGAGCGGATT-AAAA
1 CAGTGGAGCAGATTGAAAA
17764323 CAATGAATCT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
43 2 0.04
44 48 0.92
45 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (44 bp):
CAGTGGAGCAGATTGAAAATACTAATCCTATCTCCCTGAAGTTG
Found at i:17765935 original size:3 final size:3
Alignment explanation
Indices: 17765927--17765972 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
17765917 TTTAACCTTG
*
17765927 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17765973 TACTCATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:17767107 original size:211 final size:212
Alignment explanation
Indices: 17766848--17767271 Score: 841
Period size: 211 Copynumber: 2.0 Consensus size: 212
17766838 CCGGTCTTCT
17766848 GGATTTTATAAGACCAAAAATTATCATTTTAATAAATTTAAATTTTTATTAAAATGATTTAATTA
1 GGATTTTATAAGACCAAAAATTATCATTTTAATAAATTTAAATTTTTATTAAAATGATTTAATTA
17766913 TAAGGTAATCGATCACACATAAGTAAAAAAAATTGGTGGCAACTCCCATTTTCGTTTTATTTTCA
66 TAAGGTAATCGATCACACATAAGTAAAAAAAATTGGTGGCAACTCCCATTTTCGTTTTATTTTCA
17766978 AAATCCAAGTCGACCCCGTTTTATCAAAAAAATTGTGTCAACACTCACGATGGAGTTTGACGAGG
131 AAATCCAAGTCGACCCCGTTTTATCAAAAAAATTGTGTCAACACTCACGATGGAGTTTGACGAGG
17767043 AGATCGTGAAGTTTAAC
196 AGATCGTGAAGTTTAAC
17767060 GGATTTTATAA-ACCAAAAATTATCATTTTAATAAATTTAAATTTTTATTAAAATGATTTAATTA
1 GGATTTTATAAGACCAAAAATTATCATTTTAATAAATTTAAATTTTTATTAAAATGATTTAATTA
17767124 TAAGGTAATCGATCACACATAAGTAAAAAAAATTGGTGGCAACTCCCATTTTCGTTTTATTTTCA
66 TAAGGTAATCGATCACACATAAGTAAAAAAAATTGGTGGCAACTCCCATTTTCGTTTTATTTTCA
17767189 AAATCCAAGTCGACCCCGTTTTATCAAAAAAATTGTGTCAACACTCACGATGGAGTTTGACGAGG
131 AAATCCAAGTCGACCCCGTTTTATCAAAAAAATTGTGTCAACACTCACGATGGAGTTTGACGAGG
17767254 AGATCGTGAAGTTTAAC
196 AGATCGTGAAGTTTAAC
17767271 G
1 G
17767272 TTTACGACAC
Statistics
Matches: 212, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
211 201 0.95
212 11 0.05
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (212 bp):
GGATTTTATAAGACCAAAAATTATCATTTTAATAAATTTAAATTTTTATTAAAATGATTTAATTA
TAAGGTAATCGATCACACATAAGTAAAAAAAATTGGTGGCAACTCCCATTTTCGTTTTATTTTCA
AAATCCAAGTCGACCCCGTTTTATCAAAAAAATTGTGTCAACACTCACGATGGAGTTTGACGAGG
AGATCGTGAAGTTTAAC
Found at i:17767796 original size:5 final size:6
Alignment explanation
Indices: 17767780--17767837 Score: 55
Period size: 6 Copynumber: 8.8 Consensus size: 6
17767770 GAGGCAACCC
17767780 ATTTTT ATTTTT ATTTTT ATTTGTTT ATATACTTT ATTTTT ATTTTCT
1 ATTTTT ATTTTT ATTTTT A-TT-TTT AT-T--TTT ATTTTT ATTTT-T
17767828 A-TTTT ATTTT
1 ATTTTT ATTTT
17767838 CTCGCATGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
5 2 0.04
6 27 0.60
7 5 0.11
8 6 0.13
9 5 0.11
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:17774018 original size:16 final size:16
Alignment explanation
Indices: 17773999--17774038 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
17773989 ATTATTTTAA
*
17773999 TTTA-ATATTTAATATT
1 TTTATATATTGAA-ATT
17774015 TTTATATATTGAAATT
1 TTTATATATTGAAATT
17774031 TTTATATA
1 TTTATATA
17774039 GTCATCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTATATATTGAAATT
Found at i:17782726 original size:17 final size:17
Alignment explanation
Indices: 17782704--17782737 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17782694 TGAAGAAGCC
17782704 CCTTGAATGTAAGAGCT
1 CCTTGAATGTAAGAGCT
17782721 CCTTGAATGTAAGAGCT
1 CCTTGAATGTAAGAGCT
17782738 TAGCCAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (17 bp):
CCTTGAATGTAAGAGCT
Found at i:17797055 original size:20 final size:20
Alignment explanation
Indices: 17797014--17797050 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17797004 ACAGAAATAA
17797014 TGTCAAGTATATAATATTAT
1 TGTCAAGTATATAATATTAT
17797034 TGTCAAGTA-ATAA-ATTA
1 TGTCAAGTATATAATATTA
17797051 CATTGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (20 bp):
TGTCAAGTATATAATATTAT
Found at i:17799651 original size:57 final size:58
Alignment explanation
Indices: 17799583--17799701 Score: 177
Period size: 57 Copynumber: 2.1 Consensus size: 58
17799573 TTTTTATTGA
* *
17799583 AATAGAATTAATATTAAATTAAATTTAATACTTATCTTAAT-AGTATTTTATTAATTT
1 AATAGAATTAATATTAAATTAAATCTAATACTTATCTTAATAAGTATTATATTAATTT
* * * *
17799640 AATAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTT
1 AATAGAATTAATATTAAATTAAATCTAATACTTATCTTAATAAGTATTATATTAATTT
17799698 AATA
1 AATA
17799702 TTAAAGTGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
57 36 0.65
58 19 0.35
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (58 bp):
AATAGAATTAATATTAAATTAAATCTAATACTTATCTTAATAAGTATTATATTAATTT
Found at i:17799714 original size:58 final size:56
Alignment explanation
Indices: 17799588--17799721 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 56
17799578 ATTGAAATAG
* * *
17799588 AATT-AATATTAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAAT
1 AATTAAATATTAAATTTAATCTAATACTTATCTTAATAGTATTATATTAATTTAAT
* * *
17799643 AGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAAT
1 A-ATTAAATATTAAATTTAATCTAATACTTATCTTAAT-AGTATTATATTAATTTAAT
*
17799701 -ATTAAAGTGATTAAGTTTAAT
1 AATTAAA-T-ATTAAATTTAAT
17799722 TATAGTTGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
55 1 0.01
56 8 0.12
57 29 0.43
58 29 0.43
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (56 bp):
AATTAAATATTAAATTTAATCTAATACTTATCTTAATAGTATTATATTAATTTAAT
Found at i:17805545 original size:15 final size:16
Alignment explanation
Indices: 17805520--17805549 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17805510 TTTATTATGG
17805520 TTTCAATTTAATCTTT
1 TTTCAATTTAATCTTT
17805536 TTTC-ATTTAATCTT
1 TTTCAATTTAATCTT
17805550 GCCTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTCAATTTAATCTTT
Found at i:17805693 original size:14 final size:14
Alignment explanation
Indices: 17805666--17805699 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17805656 TTTTAGTTCA
* *
17805666 TTTTTGTTTTTATT
1 TTTTTATTTATATT
17805680 TTTTTATTTATATT
1 TTTTTATTTATATT
17805694 TTTTTA
1 TTTTTA
17805700 ATGTTGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTTATTTATATT
Found at i:17809720 original size:17 final size:17
Alignment explanation
Indices: 17809682--17809737 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
17809672 GCAAAAAAAA
17809682 AAAAAAGGAG-AAGAAG
1 AAAAAAGGAGAAAGAAG
17809698 AGAGAAAAGAAGAGAAAGAAG
1 A-A-AAAAG--GAGAAAGAAG
*
17809719 AAAAAAGGAGGAAGAAG
1 AAAAAAGGAGAAAGAAG
17809736 AA
1 AA
17809738 TAGGGAGCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
16 1 0.03
17 12 0.35
18 5 0.15
19 5 0.15
20 4 0.12
21 7 0.21
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
AAAAAAGGAGAAAGAAG
Found at i:17809827 original size:17 final size:16
Alignment explanation
Indices: 17809801--17809890 Score: 78
Period size: 17 Copynumber: 5.5 Consensus size: 16
17809791 CGGCCCGAAG
*
17809801 AAGAAGAAGAGAAAGGA
1 AAGAAAAAGA-AAAGGA
17809818 AAGAAAAAGAAGAA-GA
1 AAGAAAAAGAA-AAGGA
*
17809834 AAGGAAAA-AAAA-GA
1 AAGAAAAAGAAAAGGA
* *
17809848 AAAAAAAAGAAAAAGAAA
1 AAGAAAAAG-AAAAG-GA
17809866 AAGAAAAAGAAAAAGGA
1 AAGAAAAAG-AAAAGGA
17809883 AAGAAAAA
1 AAGAAAAA
17809891 ACAGTCAGGT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
14 10 0.16
15 2 0.03
16 14 0.23
17 20 0.33
18 15 0.25
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAAAGGA
Found at i:17809827 original size:20 final size:20
Alignment explanation
Indices: 17809798--17809864 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
17809788 GTTCGGCCCG
*
17809798 AAGAAGAAGAAGAGAAAGGA
1 AAGAAAAAGAAGAGAAAGGA
17809818 AAGAAAAAGAAGAAGAAAGGA
1 AAGAAAAAGAAG-AGAAAGGA
17809839 AA-AAAAAGAA-A-AAA--A
1 AAGAAAAAGAAGAGAAAGGA
17809854 AAGAAAAAGAA
1 AAGAAAAAGAA
17809865 AAAGAAAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
15 3 0.07
16 8 0.18
17 3 0.07
18 1 0.02
20 19 0.43
21 10 0.23
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AAGAAAAAGAAGAGAAAGGA
Found at i:17809834 original size:26 final size:26
Alignment explanation
Indices: 17809798--17809880 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 26
17809788 GTTCGGCCCG
*
17809798 AAGAAGAAGAAGAGAAAGGAAAGAAA
1 AAGAAGAAGAAGAGAAAGAAAAGAAA
*
17809824 AAGAAGAAGAA-AGGAAAAAAAAGAAAA
1 AAGAAGAAGAAGA-GAAAGAAAAG-AAA
* * *
17809851 AAAAAGAAAAAGAAAAAGAAAAAGAAA
1 AAGAAGAAGAAGAGAAAG-AAAAGAAA
17809878 AAG
1 AAG
17809881 GAAAGAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
25 1 0.02
26 19 0.41
27 20 0.43
28 6 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (26 bp):
AAGAAGAAGAAGAGAAAGAAAAGAAA
Found at i:17809850 original size:6 final size:6
Alignment explanation
Indices: 17809817--17809890 Score: 82
Period size: 6 Copynumber: 12.5 Consensus size: 6
17809807 AAGAGAAAGG
* *
17809817 AAAGAA AAAGAA GAAGAA AGGAAAAA AAAG-A AAA-AA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA A--AAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
17809865 AAAGAA AAAGAA AAAG-G AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA
17809891 ACAGTCAGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
5 12 0.21
6 40 0.70
8 5 0.09
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:17809858 original size:36 final size:38
Alignment explanation
Indices: 17809817--17809891 Score: 109
Period size: 36 Copynumber: 2.0 Consensus size: 38
17809807 AAGAGAAAGG
* *
17809817 AAAGAAAAAGAAGAAG-AAAGGAAAAA-AAAGAAAAAA
1 AAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAGAAAAAA
17809853 AAAGAAAAAGAAAAAGAAAAAGAAAAAGGAAAGAAAAAA
1 AAAGAAAAAGAAAAAGAAAAAGAAAAA-GAAAGAAAAAA
17809892 CAGTCAGGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 15 0.44
37 9 0.26
39 10 0.29
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (38 bp):
AAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAGAAAAAA
Found at i:17809891 original size:12 final size:10
Alignment explanation
Indices: 17809816--17809891 Score: 66
Period size: 10 Copynumber: 7.7 Consensus size: 10
17809806 GAAGAGAAAG
*
17809816 GAAAGAAAAA
1 GAAAAAAAAA
* *
17809826 GAAGAAGAAA
1 GAAAAAAAAA
*
17809836 GGAAAAAAAA
1 GAAAAAAAAA
17809846 GAAAAAAAAA
1 GAAAAAAAAA
*
17809856 G-AAAAAGAA
1 GAAAAAAAAA
*
17809865 -AAAGAAAAA
1 GAAAAAAAAA
*
17809874 GAAAAAGGAAA
1 GAAAAA-AAAA
17809885 GAAAAAA
1 GAAAAAA
17809892 CAGTCAGGTC
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
9 13 0.26
10 28 0.56
11 9 0.18
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:17809982 original size:19 final size:20
Alignment explanation
Indices: 17809958--17810011 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
17809948 GTATCAGCCA
17809958 ACCCAGCAGGCCA-GCCAG-C
1 ACCCAGCAGG-CAGGCCAGAC
*
17809977 ACCCAGCAAGCAGGCCAGAC
1 ACCCAGCAGGCAGGCCAGAC
17809997 AGCCCAGCA-GCAGGC
1 A-CCCAGCAGGCAGGC
17810012 AGCCAAACAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 2 0.06
19 14 0.45
20 8 0.26
21 7 0.23
ACGTcount: A:0.30, C:0.43, G:0.28, T:0.00
Consensus pattern (20 bp):
ACCCAGCAGGCAGGCCAGAC
Found at i:17809988 original size:23 final size:20
Alignment explanation
Indices: 17809961--17810016 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 20
17809951 TCAGCCAACC
17809961 CAGCAGGCCAGCCAGCACCCAG
1 CAGCAGGCCAGCCAG--CCCAG
*
17809983 CAAGCAGGCCAGACAGCCCAG
1 C-AGCAGGCCAGCCAGCCCAG
17810004 CAGCAGG-CAGCCA
1 CAGCAGGCCAGCCA
17810017 AACAGCAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 5 0.16
20 6 0.19
21 6 0.19
22 1 0.03
23 13 0.42
ACGTcount: A:0.30, C:0.41, G:0.29, T:0.00
Consensus pattern (20 bp):
CAGCAGGCCAGCCAGCCCAG
Found at i:17818144 original size:5 final size:6
Alignment explanation
Indices: 17818119--17818158 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
17818109 ACAACTGTAT
*
17818119 AAATAA AAGAT-A AAGTAA AAATAA AAATAA AAATAA AAAT
1 AAATAA AA-ATAA AAATAA AAATAA AAATAA AAATAA AAAT
17818159 TCTATTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 1 0.03
6 27 0.90
7 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:17820379 original size:54 final size:54
Alignment explanation
Indices: 17820316--17820428 Score: 208
Period size: 54 Copynumber: 2.1 Consensus size: 54
17820306 CTAATATGAG
17820316 TTTATAAATATTTAGGTCATGCAAGATGCTTCTTTAAATTTTTGGGCTCTTTCA
1 TTTATAAATATTTAGGTCATGCAAGATGCTTCTTTAAATTTTTGGGCTCTTTCA
* *
17820370 TTTATAAATATTTGGGTCATGCAAGATTCTTCTTTAAATTTTTGGGCTCTTTCA
1 TTTATAAATATTTAGGTCATGCAAGATGCTTCTTTAAATTTTTGGGCTCTTTCA
17820424 TTTAT
1 TTTAT
17820429 TGTTTCTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (54 bp):
TTTATAAATATTTAGGTCATGCAAGATGCTTCTTTAAATTTTTGGGCTCTTTCA
Found at i:17820414 original size:30 final size:30
Alignment explanation
Indices: 17820320--17820415 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 30
17820310 TATGAGTTTA
* *
17820320 TAAATATTTAGGTCATGCAAGATGCTTCTT
1 TAAATATTTGGGTCATGCAAGATTCTTCTT
* * *
17820350 TAAATTTTTGGG-C-T-C---TTTCATT-TA
1 TAAATATTTGGGTCATGCAAGATTC-TTCTT
17820374 TAAATATTTGGGTCATGCAAGATTCTTCTT
1 TAAATATTTGGGTCATGCAAGATTCTTCTT
*
17820404 TAAATTTTTGGG
1 TAAATATTTGGG
17820416 CTCTTTCATT
Statistics
Matches: 49, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
24 14 0.29
25 3 0.06
26 1 0.02
27 2 0.04
28 1 0.02
29 3 0.06
30 25 0.51
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (30 bp):
TAAATATTTGGGTCATGCAAGATTCTTCTT
Found at i:17822759 original size:19 final size:19
Alignment explanation
Indices: 17822722--17822759 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
17822712 AAATGATTAT
*
17822722 ATAAGTAGAATGATAAATA
1 ATAAGTAGAATGAAAAATA
17822741 ATAAGTA-AATGAAAGAATA
1 ATAAGTAGAATGAAA-AATA
17822760 TTATTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.24
Consensus pattern (19 bp):
ATAAGTAGAATGAAAAATA
Found at i:17822782 original size:15 final size:15
Alignment explanation
Indices: 17822762--17822805 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
17822752 AAAGAATATT
17822762 ATTATAATAATCATC
1 ATTATAATAATCATC
*
17822777 ATTATAATAA-CATT
1 ATTATAATAATCATC
*
17822791 AATATTAATAATCAT
1 ATTA-TAATAATCAT
17822806 ATCATGGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 16 0.64
16 3 0.12
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTATAATAATCATC
Found at i:17822931 original size:15 final size:17
Alignment explanation
Indices: 17822894--17822935 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
17822884 TGAAAATATC
*
17822894 AAAAATAATAAGAAATA
1 AAAAATAACAAGAAATA
17822911 ATAAAATAACAAG-AATA
1 A-AAAATAACAAGAAATA
17822928 AAAAATAA
1 AAAAATAA
17822936 TAACGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 6 0.26
18 10 0.43
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAATAACAAGAAATA
Found at i:17822933 original size:24 final size:23
Alignment explanation
Indices: 17822895--17822955 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
17822885 GAAAATATCA
*
17822895 AAAATAATAAGAAATAATAA-AAT
1 AAAA-AATAAAAAATAATAACAAT
*
17822918 AACAAGAATAAAAAATAATAACGAT
1 AA-AA-AATAAAAAATAATAACAAT
17822943 AAAAAATAAAAAA
1 AAAAAATAAAAAA
17822956 AATTGTGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 11 0.33
24 18 0.55
25 4 0.12
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAAAATAAAAAATAATAACAAT
Found at i:17822934 original size:16 final size:16
Alignment explanation
Indices: 17822894--17822951 Score: 73
Period size: 16 Copynumber: 3.5 Consensus size: 16
17822884 TGAAAATATC
17822894 AAAAATAATAAGAAATA
1 AAAAATAATAAG-AATA
*
17822911 ATAAAATAACAAGAATA
1 A-AAAATAATAAGAATA
17822928 AAAAATAATAACG-ATA
1 AAAAATAATAA-GAATA
17822944 AAAAATAA
1 AAAAATAA
17822952 AAAAAATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
16 20 0.54
17 7 0.19
18 10 0.27
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.17
Consensus pattern (16 bp):
AAAAATAATAAGAATA
Found at i:17822951 original size:7 final size:7
Alignment explanation
Indices: 17822895--17822955 Score: 50
Period size: 7 Copynumber: 7.9 Consensus size: 7
17822885 GAAAATATCA
17822895 AAAATAAT
1 AAAA-AAT
*
17822903 AAGAAAT
1 AAAAAAT
17822910 AATAAAAT
1 AA-AAAAT
17822918 AACAAGAAT
1 AA-AA-AAT
17822927 AAAAAAT
1 AAAAAAT
*
17822934 AATAACGAT
1 AA-AA-AAT
17822943 AAAAAAT
1 AAAAAAT
17822950 AAAAAA
1 AAAAAA
17822956 AATTGTGCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
7 18 0.41
8 17 0.39
9 9 0.20
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (7 bp):
AAAAAAT
Found at i:17823190 original size:14 final size:14
Alignment explanation
Indices: 17823171--17823202 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
17823161 GTAAATAAAT
17823171 AAAATAATACATAA
1 AAAATAATACATAA
*
17823185 AAAATAATATATAA
1 AAAATAATACATAA
17823199 AAAA
1 AAAA
17823203 ATCAATACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAATACATAA
Found at i:17826868 original size:100 final size:101
Alignment explanation
Indices: 17826694--17826894 Score: 395
Period size: 100 Copynumber: 2.0 Consensus size: 101
17826684 GTTGTTTTAA
17826694 TAAAATCAAATTGTTTATTAAAAACAACCATTTTACGAGGTGACCCGATCACATCTCATCAAAAA
1 TAAAATCAAATTGTTTATTAAAAACAACCATTTTACGAGGTGACCCGATCACATCTCATCAAAAA
17826759 AGATTGGTGGCGACTCCCATTTTCGTTTTCGTTTTC
66 AGATTGGTGGCGACTCCCATTTTCGTTTTCGTTTTC
17826795 TAAAATCAAA-TGTTTATTAAAAACAACCATTTTACGAGGTGACCCGATCACATCTCATCAAAAA
1 TAAAATCAAATTGTTTATTAAAAACAACCATTTTACGAGGTGACCCGATCACATCTCATCAAAAA
17826859 AGATTGGTGGCGACTCCCATTTTCGTTTTCGTTTTC
66 AGATTGGTGGCGACTCCCATTTTCGTTTTCGTTTTC
17826895 GTTTTCAAAA
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
100 90 0.90
101 10 0.10
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (101 bp):
TAAAATCAAATTGTTTATTAAAAACAACCATTTTACGAGGTGACCCGATCACATCTCATCAAAAA
AGATTGGTGGCGACTCCCATTTTCGTTTTCGTTTTC
Found at i:17830231 original size:4 final size:4
Alignment explanation
Indices: 17830222--17830256 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
17830212 TATTTTATCT
* *
17830222 TTTA TTTA TTTA TTTA TTTG TTCA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
17830257 GCTTATCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:17838251 original size:101 final size:99
Alignment explanation
Indices: 17838081--17838378 Score: 478
Period size: 101 Copynumber: 3.0 Consensus size: 99
17838071 CAACCACATA
17838081 GTTAATAGATGATGAAGTAGGCAACT-GC--GACACCTATCATTTCGAATATTGTGTGGTCAAAA
1 GTTAATAGATGATGAAGTAGGCAACTCGCATGACACCTATCATTTCGAATATTGTGTGGTCAAAA
17838143 ATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
66 ATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
17838177 GTTAATAGATGATGAAGTAGG-ATACTGCGACATGACACCTATCATTTCGAATATTGTGTGGTCA
1 GTTAATAGATGATGAAGTAGGCA-ACT-CG-CATGACACCTATCATTTCGAATATTGTGTGGTCA
17838241 AAAATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
63 AAAATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
* * * *
17838278 GTTAATAGATGATGAAGTAGGCAACTACGGCATGATACCTACCATTTTGAATATTGTATGGTCAA
1 GTTAATAGATGATGAAGTAGGCAACT-C-GCATGACACCTATCATTTCGAATATTGTGTGGTCAA
*
17838343 AAATGAAAGGTTAGGTGTGATAGAACATGAGGGCAT
64 AAATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
17838379 ATATAGTTTT
Statistics
Matches: 188, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
95 1 0.01
96 24 0.13
98 1 0.01
99 1 0.01
101 159 0.85
102 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.27
Consensus pattern (99 bp):
GTTAATAGATGATGAAGTAGGCAACTCGCATGACACCTATCATTTCGAATATTGTGTGGTCAAAA
ATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
Found at i:17840180 original size:19 final size:19
Alignment explanation
Indices: 17840156--17840198 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17840146 TTTTATTTTT
*
17840156 TTATTA-ATTGATAATGTAA
1 TTATTATATTCAT-ATGTAA
*
17840175 TTATTATTTTCATATGTAA
1 TTATTATATTCATATGTAA
17840194 TTATT
1 TTATT
17840199 TTTTCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (19 bp):
TTATTATATTCATATGTAA
Found at i:17840233 original size:18 final size:18
Alignment explanation
Indices: 17840206--17840264 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
17840196 ATTTTTTCTT
*
17840206 TTTATATATATATGTATA
1 TTTATGTATATATGTATA
17840224 TTTATGTATATAT-T-TA
1 TTTATGTATATATGTATA
17840240 TTTCCATGTATATATACGTATA
1 TTT--ATGTATATAT--GTATA
17840262 TTT
1 TTT
17840265 TTCAATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 5 0.15
17 1 0.03
18 22 0.65
21 1 0.03
22 5 0.15
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (18 bp):
TTTATGTATATATGTATA
Found at i:17842196 original size:25 final size:28
Alignment explanation
Indices: 17842145--17842197 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
17842135 GGGTTCTGAT
* *
17842145 TTTCTTCTTTAAATCTAACAATCAAGAA
1 TTTCTTCTTTAAATCAAAAAATCAAGAA
17842173 TTTC-TCTTT-AATCAAAAAAT-AAGAA
1 TTTCTTCTTTAAATCAAAAAATCAAGAA
17842198 CTAATTATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 5 0.22
26 9 0.39
27 5 0.22
28 4 0.17
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (28 bp):
TTTCTTCTTTAAATCAAAAAATCAAGAA
Found at i:17847703 original size:88 final size:88
Alignment explanation
Indices: 17847554--17847966 Score: 664
Period size: 88 Copynumber: 4.7 Consensus size: 88
17847544 AGCAGATCAG
*
17847554 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
17847619 CCTTGGGATACAGCGGAGCAGGT
66 CCCTGGGTTACAGCGGAGCAGGT
* * *
17847642 TAAAAATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGTAGATCGAAGGCACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
17847707 CCCTGGGTTACAGCGGAGCAGGT
66 CCCTGGGTTACAGCGGAGCAGGT
** * *
17847730 TAAAAGCAGCAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* **
17847795 CCCTAGGTTGTAGCGGAGCAGGT
66 CCCTGGGTTACAGCGGAGCAGGT
** *
17847818 TAAAAATAATAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
17847883 CCCTGGGTTGCAGCGGAGTAGGT
66 CCCTGGGTTACAGCGGAGCAGGT
17847906 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTT
17847967 ATCTCCTTGA
Statistics
Matches: 298, Mismatches: 27, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 298 1.00
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTACAGCGGAGCAGGT
Found at i:17847704 original size:44 final size:44
Alignment explanation
Indices: 17847568--17847794 Score: 129
Period size: 43 Copynumber: 5.2 Consensus size: 44
17847558 AATAGCAGAT
* * *
17847568 CTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGGCACCAGC
* * * ** *** * *
17847612 CTTGCC-TCCTTGGGAT--ACAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCC-T-GCATCGACAGCGAAGCAGATCGAAGGCACCAG-C
*
17847656 CTTGCCTTCCTGCATCGACAGCGAAGTAGATCGAAGGCACCAGC
1 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGGCACCAGC
* ** * * * ** * * *
17847700 CTTGCCTCCCTGGGT-TACAGCGGAGCAGGTTAAAAGCAGCAGAT
1 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGGCACCAG-C
* * * *
17847744 CTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACTAGC
1 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGGCACCAGC
17847788 CTTGCCT
1 CTTGCCT
17847795 CCCTAGGTTG
Statistics
Matches: 126, Mismatches: 49, Indels: 16
0.66 0.26 0.08
Matches are distributed among these distances:
43 43 0.34
44 43 0.34
45 40 0.32
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (44 bp):
CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGGCACCAGC
Found at i:17847772 original size:45 final size:44
Alignment explanation
Indices: 17847628--17847772 Score: 103
Period size: 45 Copynumber: 3.3 Consensus size: 44
17847618 TCCTTGGGAT
* ** *
17847628 ACAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCATCG
1 ACAGCGAAGCAGGTTAAAAGCAGCAGATCTTGCCTTCCT-CACCG
* * ** * * * * *****
17847673 ACAGCGAAGTAGATCGAAGGCACCAG-CCTTGCCTCCCTGGGTT
1 ACAGCGAAGCAGGTTAAAAGCAGCAGATCTTGCCTTCCTCACCG
*
17847716 ACAGCGGAGCAGGTTAAAAGCAGCAGATCTTGCCTTCCTACACCG
1 ACAGCGAAGCAGGTTAAAAGCAGCAGATCTTGCCTTCCT-CACCG
17847761 ACAGCGAAGCAG
1 ACAGCGAAGCAG
17847773 ATCGAAGACA
Statistics
Matches: 67, Mismatches: 31, Indels: 4
0.66 0.30 0.04
Matches are distributed among these distances:
43 19 0.28
44 20 0.30
45 28 0.42
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (44 bp):
ACAGCGAAGCAGGTTAAAAGCAGCAGATCTTGCCTTCCTCACCG
Found at i:17848030 original size:44 final size:44
Alignment explanation
Indices: 17847964--17848293 Score: 229
Period size: 44 Copynumber: 7.6 Consensus size: 44
17847954 AGACACCAGC
* * *
17847964 CTTATCTCCTTGAGCAACAGTGGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
* * * * * *** *
17848008 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAG-C
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
* * *
17848051 CTTGTCTCTCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
* * * * * * ** *
17848095 CTTATCTCCTTAAGCAACAGTGGAGCAGATCG-AAGTCCCCAGCT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
* ** *
17848139 -TTGTCTCCCTGGGCAGCAGTTGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
* * * * * ** *
17848182 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGTCCCCAG-C
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
* ** *
17848225 CTTGTCTCCCTAAATAGCAATGGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
* *
17848269 TTTATCTCCCTAAGCAGTAGTGGAG
1 CTTATCTCCCTAAGCAGCAGTGGAG
17848294 CAGATCGAGG
Statistics
Matches: 200, Mismatches: 79, Indels: 14
0.68 0.27 0.05
Matches are distributed among these distances:
43 90 0.45
44 110 0.55
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
Found at i:17848065 original size:87 final size:87
Alignment explanation
Indices: 17847856--17848301 Score: 556
Period size: 87 Copynumber: 5.1 Consensus size: 87
17847846 CCGACAGCGA
* * * ** * *
17847856 AGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGTAGGTT-AAAAATAGCAGAT
1 AGCAGATCGAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTA-CAGAT
** * * * *
17847920 CTTGCCTTCCT--GCACCGACAGCGA
65 CTTATCTCCCTAAGCA--G-TAGTGG
* * * *
17847944 AGCAGATCGAAGACACCAGCCTTATCTCCTTGAGCAACAGTGGAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
17848009 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
*
17848031 AGCAGATCGAAGACCCCAGCCTTGTCTCTCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
* **
17848096 TTATCTCCTTAAGCAACAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* * * *
17848118 AGCAGATCGAAGTCCCCAGCTTTGTCTCCCTGGGCAGCAGTTGAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
17848183 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* * ** * *
17848205 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTAAATAGCAATGGAGTAGGTTGAAAATTACAGATT
1 AGCAGATCGAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
17848270 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
17848292 AGCAGATCGA
1 AGCAGATCGA
17848302 GGATGGTAAA
Statistics
Matches: 316, Mismatches: 39, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
87 250 0.79
88 57 0.18
89 6 0.02
90 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (87 bp):
AGCAGATCGAAGACCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
TTATCTCCCTAAGCAGTAGTGG
Found at i:17848235 original size:43 final size:43
Alignment explanation
Indices: 17848012--17848237 Score: 159
Period size: 43 Copynumber: 5.2 Consensus size: 43
17848002 ACAGATCTTA
* *
17848012 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAGCCTTG
1 TCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCCCCAGCCTTG
* * * * * * ** * *
17848055 TCTCTCTGAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGATCTTA
1 TCTCCCTAAGCAGCAGTGGAGCAGATCG-AAGTCCCCAG-CCTTG
* * *
17848099 TCTCCTTAAGCAACAGTGGAGCAGATCGAAGTCCCCAGCTTTG
1 TCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCCCCAGCCTTG
** * * * * * ** * *
17848142 TCTCCCTGGGCAGCAGTTGAGTAGGTTGAAAAT-TACAGATCTTA
1 TCTCCCTAAGCAGCAGTGGAGCAGATCG-AAGTCCCCAG-CCTTG
*
17848186 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTG
1 TCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCCCCAGCCTTG
17848229 TCTCCCTAA
1 TCTCCCTAA
17848238 ATAGCAATGG
Statistics
Matches: 126, Mismatches: 51, Indels: 12
0.67 0.27 0.06
Matches are distributed among these distances:
43 68 0.54
44 58 0.46
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (43 bp):
TCTCCCTAAGCAGCAGTGGAGCAGATCGAAGTCCCCAGCCTTG
Found at i:17848407 original size:44 final size:44
Alignment explanation
Indices: 17848310--17848413 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 44
17848300 GAGGATGGTA
* * *
17848310 AATCTTATCTCCCTGAGGTTACAGTGAAGCAGATTAAAACCGAT
1 AATCTTATCTCCCTGAGGTTACAGCGAAGCAGATTAAAACCAAC
* * * * *
17848354 AATCCTATCTCCCTGAGGTTATAGCGGAGCGGATTAAAA-TAAC
1 AATCTTATCTCCCTGAGGTTACAGCGAAGCAGATTAAAACCAAC
*
17848397 AGATCTTATCTCTCTGA
1 A-ATCTTATCTCCCTGA
17848414 AATTACGGTA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
43 2 0.04
44 47 0.96
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGGTTACAGCGAAGCAGATTAAAACCAAC
Found at i:17849728 original size:23 final size:24
Alignment explanation
Indices: 17849692--17849736 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
17849682 TACAATTAAG
*
17849692 TTTATTTTATTTTTAAATTTCATC
1 TTTAATTTATTTTTAAATTTCATC
17849716 TTTAATTTATTTTT-AATTTCA
1 TTTAATTTATTTTTAAATTTCA
17849737 ATTTGGCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTAATTTATTTTTAAATTTCATC
Found at i:17849732 original size:11 final size:11
Alignment explanation
Indices: 17849692--17849734 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
17849682 TACAATTAAG
*
17849692 TTTATTTTATT
1 TTTAATTTATT
*
17849703 TTTAAATTTCATC
1 TTT-AATTT-ATT
17849716 TTTAATTTATT
1 TTTAATTTATT
17849727 TTTAATTT
1 TTTAATTT
17849735 CAATTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 13 0.48
12 9 0.33
13 5 0.19
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTAATTTATT
Found at i:17849923 original size:19 final size:19
Alignment explanation
Indices: 17849899--17849941 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17849889 TTTTATTTTT
*
17849899 TTATTA-ATTGATAATGTAA
1 TTATTATATTCAT-ATGTAA
*
17849918 TTATTATTTTCATATGTAA
1 TTATTATATTCATATGTAA
17849937 TTATT
1 TTATT
17849942 TTTTCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (19 bp):
TTATTATATTCATATGTAA
Found at i:17850006 original size:18 final size:18
Alignment explanation
Indices: 17849964--17850009 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
17849954 CTTTCTATAT
* **
17849964 ATATGTATATTTATTTTT
1 ATATATATATTTATTTCC
*
17849982 ATGTATATATTTATTTCC
1 ATATATATATTTATTTCC
17850000 ATATATATAT
1 ATATATATAT
17850010 ACGCATATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (18 bp):
ATATATATATTTATTTCC
Found at i:17855267 original size:7 final size:7
Alignment explanation
Indices: 17855255--17855628 Score: 137
Period size: 7 Copynumber: 53.7 Consensus size: 7
17855245 ATATTACTGT
17855255 CTAAACC
1 CTAAACC
17855262 CTAAACC
1 CTAAACC
*
17855269 CTAAACT
1 CTAAACC
* *
17855276 ATAAACT
1 CTAAACC
* *
17855283 TTAAGCCC
1 CTAA-ACC
*
17855291 CTAACCC
1 CTAAACC
17855298 CTAAAACC
1 CT-AAACC
17855306 CT-AACC
1 CTAAACC
17855312 CT-AACC
1 CTAAACC
*
17855318 CTTAAACA
1 C-TAAACC
17855326 C-ACAACC
1 CTA-AACC
*
17855333 ATAAACC
1 CTAAACC
*
17855340 ATAAACC
1 CTAAACC
17855347 CTAAACC
1 CTAAACC
17855354 CTAAA-C
1 CTAAACC
*
17855360 CTACACC
1 CTAAACC
17855367 CTAAA--
1 CTAAACC
*
17855372 TTATAACC
1 CTA-AACC
* *
17855380 ATTAAACT
1 -CTAAACC
* *
17855388 CTTAACA
1 CTAAACC
17855395 CTAAACC
1 CTAAACC
17855402 CTAAACC
1 CTAAACC
*
17855409 TTAAACC
1 CTAAACC
*
17855416 CTAACCCC
1 CTAA-ACC
*
17855424 CTAAATC
1 CTAAACC
17855431 CTAAACC
1 CTAAACC
* *
17855438 TTAAA-A
1 CTAAACC
17855444 CTAAACC
1 CTAAACC
* **
17855451 ATAAAAT
1 CTAAACC
*
17855458 CTAAATC
1 CTAAACC
*
17855465 CTAAACT
1 CTAAACC
17855472 CT-AACC
1 CTAAACC
17855478 CTTAAACCC
1 C-TAAA-CC
17855487 CT-AACAC
1 CTAAAC-C
17855494 CTAAACC
1 CTAAACC
*
17855501 TTAAA-C
1 CTAAACC
*
17855507 ATAAAACC
1 CT-AAACC
17855515 CTAAACC
1 CTAAACC
*
17855522 ATAAA-C
1 CTAAACC
*
17855528 ATAAACC
1 CTAAACC
*
17855535 ATAAACC
1 CTAAACC
*
17855542 ATAAA-C
1 CTAAACC
* *
17855548 ATACACC
1 CTAAACC
*
17855555 CTAAATC
1 CTAAACC
*
17855562 GT-AACC
1 CTAAACC
* *
17855568 ATTAAACT
1 -CTAAACC
* *
17855576 CTTAACA
1 CTAAACC
*
17855583 CTAAATC
1 CTAAACC
17855590 CTAAACC
1 CTAAACC
*
17855597 TTAAACC
1 CTAAACC
*
17855604 CCAAACC
1 CTAAACC
* *
17855611 ATATA-C
1 CTAAACC
*
17855617 CTACACC
1 CTAAACC
17855624 CTAAA
1 CTAAA
17855629 TATATATATT
Statistics
Matches: 275, Mismatches: 67, Indels: 50
0.70 0.17 0.13
Matches are distributed among these distances:
5 2 0.01
6 48 0.17
7 184 0.67
8 35 0.13
9 6 0.02
ACGTcount: A:0.45, C:0.34, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:17855360 original size:21 final size:21
Alignment explanation
Indices: 17855256--17855628 Score: 155
Period size: 21 Copynumber: 17.9 Consensus size: 21
17855246 TATTACTGTC
*
17855256 TAAACCCTAAACCCTAAACTA
1 TAAACCCTAAACCCTAAACCA
** * * *
17855277 TAAACTTTAAGCCCCTAACCCC
1 TAAACCCTAA-ACCCTAAACCA
* *
17855299 TAAAACCCT-AACCCTAACCCT
1 T-AAACCCTAAACCCTAAACCA
* *
17855320 TAAACAC-ACAACCATAAACCA
1 TAAACCCTA-AACCCTAAACCA
17855341 TAAACCCTAAACCCTAAACC-
1 TAAACCCTAAACCCTAAACCA
* *
17855361 TACACCCTAAA--TTATAACCA
1 TAAACCCTAAACCCTA-AACCA
* * * *
17855381 TTAAACTCTTAACACTAAACCC
1 -TAAACCCTAAACCCTAAACCA
* * *
17855403 TAAACCTTAAACCCTAACCCCC
1 TAAACCCTAAACCCTAA-ACCA
* * *
17855425 TAAATCCTAAACCTTAAAAC-
1 TAAACCCTAAACCCTAAACCA
* **
17855445 TAAACCATAAAATCTAAATCC-
1 TAAACCCTAAACCCTAAA-CCA
* *
17855466 TAAACTCT-AACCCTTAAACCCC
1 TAAACCCTAAACCC-TAAA-CCA
*
17855488 T-AACACCTAAACCTTAAA-CA
1 TAAAC-CCTAAACCCTAAACCA
*
17855508 TAAAACCCTAAACCATAAA-CA
1 T-AAACCCTAAACCCTAAACCA
* *
17855529 TAAACCATAAACCATAAA-CA
1 TAAACCCTAAACCCTAAACCA
* * *
17855549 TACACCCTAAATCGT-AACCA
1 TAAACCCTAAACCCTAAACCA
* * *
17855569 TTAAACTCTTAACACTAAATCC-
1 -TAAACCCTAAACCCTAAA-CCA
* *
17855591 TAAACCTTAAACCCCAAACCA
1 TAAACCCTAAACCCTAAACCA
* *
17855612 TATA-CCTACACCCTAAA
1 TAAACCCTAAACCCTAAA
17855629 TATATATATT
Statistics
Matches: 261, Mismatches: 68, Indels: 47
0.69 0.18 0.12
Matches are distributed among these distances:
18 2 0.01
19 6 0.02
20 76 0.29
21 121 0.46
22 43 0.16
23 13 0.05
ACGTcount: A:0.45, C:0.34, G:0.01, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAACCA
Found at i:17855497 original size:22 final size:22
Alignment explanation
Indices: 17855382--17855506 Score: 63
Period size: 22 Copynumber: 5.9 Consensus size: 22
17855372 TTATAACCAT
*
17855382 TAAACTCTTAACAC-TAAA-CCC
1 TAAACTCTAAAC-CTTAAACCCC
* *
17855403 TAAAC-CTTAAACCCTAACCCCC
1 TAAACTC-TAAACCTTAAACCCC
*
17855425 TAAA-TCCTAAACCTTAAA--AC
1 TAAACT-CTAAACCTTAAACCCC
* *
17855445 TAAAC-CATAAA-ATCTAAA-TCC
1 TAAACTC-TAAACCT-TAAACCCC
*
17855466 TAAACTCTAACCCTTAAACCCC
1 TAAACTCTAAACCTTAAACCCC
17855488 TAACAC-CTAAACCTTAAAC
1 TAA-ACTCTAAACCTTAAAC
17855507 ATAAAACCCT
Statistics
Matches: 80, Mismatches: 11, Indels: 25
0.69 0.09 0.22
Matches are distributed among these distances:
19 2 0.03
20 15 0.19
21 25 0.31
22 35 0.44
23 3 0.04
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAACTCTAAACCTTAAACCCC
Found at i:17855559 original size:20 final size:20
Alignment explanation
Indices: 17855493--17855559 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
17855483 ACCCCTAACA
*
17855493 CCTAAACCTTAAACATAAAAC
1 CCTAAACCATAAACAT-AAAC
17855514 CCTAAACCATAAACATAAAC
1 CCTAAACCATAAACATAAAC
* *
17855534 CATAAACCATAAACATACAC
1 CCTAAACCATAAACATAAAC
17855554 CCTAAA
1 CCTAAA
17855560 TCGTAACCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.16
Consensus pattern (20 bp):
CCTAAACCATAAACATAAAC
Found at i:17855825 original size:21 final size:21
Alignment explanation
Indices: 17855793--17855834 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
17855783 TATAAAATAA
17855793 TAAACCTCAAA-CCTCAAACTC
1 TAAACCTCAAACCCT-AAACTC
17855814 TAAACCAT-AAACCCTAAACTC
1 TAAACC-TCAAACCCTAAACTC
17855835 ACAGATACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACCTCAAACCCTAAACTC
Found at i:17857953 original size:37 final size:37
Alignment explanation
Indices: 17857912--17857985 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
17857902 TAAAAATTAA
17857912 CTTAGTAATTTACTAAATAAATATTCGCATATATTGT
1 CTTAGTAATTTACTAAATAAATATTCGCATATATTGT
17857949 CTTAGTAATTTACTAAATAAATATTCGCATATATTGT
1 CTTAGTAATTTACTAAATAAATATTCGCATATATTGT
17857986 TTAAATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (37 bp):
CTTAGTAATTTACTAAATAAATATTCGCATATATTGT
Found at i:17858665 original size:39 final size:37
Alignment explanation
Indices: 17858598--17858690 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
17858588 TCCAGTATGG
* *
17858598 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
17858637 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
17858674 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
17858691 AATCTGTAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:17858817 original size:12 final size:13
Alignment explanation
Indices: 17858802--17858830 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17858792 GTGTCAATTT
17858802 ATTT-GTGTGAAA
1 ATTTCGTGTGAAA
17858814 ATTTCGTGTGAAA
1 ATTTCGTGTGAAA
17858827 ATTT
1 ATTT
17858831 TATCGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.45
Consensus pattern (13 bp):
ATTTCGTGTGAAA
Found at i:17860284 original size:19 final size:19
Alignment explanation
Indices: 17860233--17860284 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
17860223 GTTAGCCGAA
*
17860233 TGTATATATATGTTTTGAAT
1 TGTATATATATG-TATGAAT
* *
17860253 TTTAT-TAAAATGTATGAAT
1 TGTATAT-ATATGTATGAAT
17860272 TGTATATATATGT
1 TGTATATATATGT
17860285 GTGTGTGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (19 bp):
TGTATATATATGTATGAAT
Found at i:17860816 original size:41 final size:41
Alignment explanation
Indices: 17860759--17860903 Score: 213
Period size: 41 Copynumber: 3.5 Consensus size: 41
17860749 GGCTCGATGC
17860759 CTAGCAGGCTTAATGCCGGTGAATTATTTTAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTTAGACTTTATGT
*
17860800 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTTAGACTTTATGT
* * * *
17860841 CTAGCAGGCTTAAGGCCGGTGAAATGA-TTTGGACTTTAAGT
1 CTAGCAGGCTTAATGCCGGTG-AATTATTTTAGACTTTATGT
17860882 CTAGCAGGC-TAAGTGCCGGTGA
1 CTAGCAGGCTTAA-TGCCGGTGA
17860904 TCTGAATCAG
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
40 4 0.04
41 87 0.92
42 4 0.04
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAATTATTTTAGACTTTATGT
Found at i:17860927 original size:41 final size:42
Alignment explanation
Indices: 17860882--17860985 Score: 167
Period size: 41 Copynumber: 2.5 Consensus size: 42
17860872 GACTTTAAGT
*
17860882 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA-AC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGAC
*
17860923 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGAC
*
17860965 CTAGCAGG-TAAGTGCTGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
17860986 ATATGTTAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 50 0.85
42 9 0.15
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (42 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGAC
Done.