Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold471
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1282308
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 143812 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:317820 original size:112 final size:112
Alignment explanation
Indices: 317623--317845 Score: 383
Period size: 112 Copynumber: 2.0 Consensus size: 112
317613 AACCCTGACG
* * *
317623 TGCACCTGGGCACACGACACACCTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGTTT
1 TGCACCTAGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
* * *
317688 TTTTTAAGTTTGACAAACAATAGACTTTAATTAGATATACATAAACC
66 TTCTTAAGTTTGACAAACAATAGACTCTAATTAGATATACACAAACC
317735 TGCACCTAGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTAGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
*
317800 TTCTTAAGTTTGACAAACAATAGACTCTATTTAGATATACACAAAC
66 TTCTTAAGTTTGACAAACAATAGACTCTAATTAGATATACACAAAC
317846 GAACAAAACT
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 104 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (112 bp):
TGCACCTAGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
TTCTTAAGTTTGACAAACAATAGACTCTAATTAGATATACACAAACC
Found at i:318056 original size:2 final size:2
Alignment explanation
Indices: 318049--318100 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
318039 CAGATGAACT
318049 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
318091 GA GA GA GA GA
1 GA GA GA GA GA
318101 TATTTCACCG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:318514 original size:21 final size:22
Alignment explanation
Indices: 318488--318539 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
318478 CTTAAAGGGA
318488 GCTTAAATGCCACTTAAAGAT-
1 GCTTAAATGCCACTTAAAGATG
* **
318509 GCTTAAAGGCGGCTTAAAGATG
1 GCTTAAATGCCACTTAAAGATG
318531 GCTTAAATG
1 GCTTAAATG
318540 TGACTTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (22 bp):
GCTTAAATGCCACTTAAAGATG
Found at i:318635 original size:11 final size:11
Alignment explanation
Indices: 318619--318659 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
318609 GATGGTATAT
318619 CCTTTAAGCCA
1 CCTTTAAGCCA
*
318630 CCTTTACGCCA
1 CCTTTAAGCCA
318641 CCTTTAAGCCA
1 CCTTTAAGCCA
318652 CCTTTAAG
1 CCTTTAAG
318660 GACTTGCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (11 bp):
CCTTTAAGCCA
Found at i:319543 original size:2 final size:2
Alignment explanation
Indices: 319536--319619 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
319526 TGTTAGTAAT
319536 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
319578 GA GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
319619 G
1 G
319620 GTGGTCAATA
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 80 0.99
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:320609 original size:5 final size:5
Alignment explanation
Indices: 320590--320716 Score: 116
Period size: 5 Copynumber: 25.4 Consensus size: 5
320580 CTGTAAAGTG
* * *
320590 CGAAA CGAAA TCGAAA CGAAA TCGAAA CGAAA CGAAA CCAAT CGAAA CAAAA
1 CGAAA CGAAA -CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA
* * * *
320642 CGAAA CCAAT CGAAA CGAAA TTG-AA CGAAA CGAAA CGAAA CGAAA CAAAA
1 CGAAA CGAAA CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA
* * *
320692 CCAAA --AAT CGACA CGAAA CGAAA CG
1 CGAAA CGAAA CGAAA CGAAA CGAAA CG
320717 GAAGGAATTT
Statistics
Matches: 98, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
3 2 0.02
4 1 0.01
5 84 0.86
6 11 0.11
ACGTcount: A:0.57, C:0.22, G:0.16, T:0.06
Consensus pattern (5 bp):
CGAAA
Found at i:320937 original size:2 final size:2
Alignment explanation
Indices: 320930--320973 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
320920 TTCAGACGTT
320930 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
320972 GA
1 GA
320974 TGCCTTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:321067 original size:3 final size:3
Alignment explanation
Indices: 321059--321084 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
321049 AGAGAGAGAT
321059 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
321085 ACTGAAGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:321777 original size:18 final size:18
Alignment explanation
Indices: 321754--321804 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
321744 TTTTAAAAAG
321754 TCCTATAGGAATTATATT
1 TCCTATAGGAATTATATT
* *
321772 TCCTATAGGAGAAATGTATT
1 TCCTATA-G-GAATTATATT
*
321792 TCCTGTAGGAATT
1 TCCTATAGGAATT
321805 TGATTCAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 11 0.41
19 2 0.07
20 14 0.52
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (18 bp):
TCCTATAGGAATTATATT
Found at i:322535 original size:12 final size:12
Alignment explanation
Indices: 322518--322544 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
322508 TCTATATCTC
322518 TCTTTCTCTCTT
1 TCTTTCTCTCTT
322530 TCTTTCTCTCTT
1 TCTTTCTCTCTT
322542 TCT
1 TCT
322545 CCCAAACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
TCTTTCTCTCTT
Found at i:322609 original size:2 final size:2
Alignment explanation
Indices: 322602--322683 Score: 146
Period size: 2 Copynumber: 41.0 Consensus size: 2
322592 TTTTAAGGCA
*
322602 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
322644 TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
322684 AACGTCTGAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
TC
Found at i:322930 original size:5 final size:5
Alignment explanation
Indices: 322920--323029 Score: 71
Period size: 5 Copynumber: 21.4 Consensus size: 5
322910 GTGTAAATTC
* * *
322920 CGTTT CGTTT CGTTT CGAATTTT GGTTT CGTTT CGTTT GGTTT TGTTT
1 CGTTT CGTTT CGTTT CG---TTT CGTTT CGTTT CGTTT CGTTT CGTTT
* * * * * *
322968 CGTTT CGATT GGTTT CTTTT CGTTT CGATTG GGTTT -GTTT TGTTT CG-TT
1 CGTTT CGTTT CGTTT CGTTT CGTTT CG-TTT CGTTT CGTTT CGTTT CGTTT
*
323017 CAATTT CGTTT CG
1 C-GTTT CGTTT CG
323030 CACTTTACAG
Statistics
Matches: 81, Mismatches: 17, Indels: 14
0.72 0.15 0.12
Matches are distributed among these distances:
4 7 0.09
5 64 0.79
6 6 0.07
8 4 0.05
ACGTcount: A:0.05, C:0.14, G:0.23, T:0.58
Consensus pattern (5 bp):
CGTTT
Found at i:322969 original size:20 final size:20
Alignment explanation
Indices: 322921--323016 Score: 104
Period size: 20 Copynumber: 4.7 Consensus size: 20
322911 TGTAAATTCC
*
322921 GTTTCGTTTCGTTTCGAATTTT
1 GTTTCGTTTCGTTT-G-GTTTT
322943 GGTTTCGTTTCGTTTGGTTTT
1 -GTTTCGTTTCGTTTGGTTTT
*
322964 GTTTCGTTTCGATTGGTTTCT
1 GTTTCGTTTCGTTTGGTTT-T
* *
322985 -TTTCGTTTCGATTGGGTTT
1 GTTTCGTTTCGTTTGGTTTT
*
323004 GTTTTGTTTCGTT
1 GTTTCGTTTCGTT
323017 CAATTTCGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
19 1 0.02
20 45 0.68
21 5 0.08
22 1 0.02
23 14 0.21
ACGTcount: A:0.04, C:0.11, G:0.24, T:0.60
Consensus pattern (20 bp):
GTTTCGTTTCGTTTGGTTTT
Found at i:323166 original size:8 final size:8
Alignment explanation
Indices: 323153--323191 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
323143 GCCGGGCGTC
323153 CGTCCGTG
1 CGTCCGTG
323161 CGTCCGTG
1 CGTCCGTG
323169 CGTCCGTG
1 CGTCCGTG
*
323177 TGTCCGTG
1 CGTCCGTG
323185 CGTCCGT
1 CGTCCGT
323192 ATGTCCGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.00, C:0.36, G:0.36, T:0.28
Consensus pattern (8 bp):
CGTCCGTG
Found at i:323196 original size:16 final size:16
Alignment explanation
Indices: 323162--323199 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
323152 CCGTCCGTGC
*
323162 GTCCGTGCGTCCGTGT
1 GTCCGTGCGTCCGTAT
323178 GTCCGTGCGTCCGTAT
1 GTCCGTGCGTCCGTAT
323194 GTCCGT
1 GTCCGT
323200 CTGTCACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.03, C:0.32, G:0.34, T:0.32
Consensus pattern (16 bp):
GTCCGTGCGTCCGTAT
Found at i:323197 original size:8 final size:8
Alignment explanation
Indices: 323154--323204 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
323144 CCGGGCGTCC
*
323154 GTCCGTGC
1 GTCCGTGT
*
323162 GTCCGTGC
1 GTCCGTGT
323170 GTCCGTGT
1 GTCCGTGT
*
323178 GTCCGTGC
1 GTCCGTGT
*
323186 GTCCGTAT
1 GTCCGTGT
*
323194 GTCCGTCT
1 GTCCGTGT
323202 GTC
1 GTC
323205 ACACTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.02, C:0.33, G:0.33, T:0.31
Consensus pattern (8 bp):
GTCCGTGT
Found at i:323197 original size:24 final size:24
Alignment explanation
Indices: 323149--323204 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
323139 AAATGCCGGG
* *
323149 CGTCCGTCCGTGCGTCCGTGCGTC
1 CGTCTGTCCGTGCGTCCGTACGTC
* *
323173 CGTGTGTCCGTGCGTCCGTATGTC
1 CGTCTGTCCGTGCGTCCGTACGTC
323197 CGTCTGTC
1 CGTCTGTC
323205 ACACTTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.02, C:0.36, G:0.32, T:0.30
Consensus pattern (24 bp):
CGTCTGTCCGTGCGTCCGTACGTC
Found at i:323539 original size:178 final size:172
Alignment explanation
Indices: 323213--323822 Score: 1004
Period size: 172 Copynumber: 3.5 Consensus size: 172
323203 TCACACTTTT
323213 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
* * *
323278 CTACTAATACTTTGGTCAACTTAGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
66 CCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
* *
323343 CTTTGACCACATTAATGACTCCGTTTTATCCAAAAATTGACC
131 CTTTGATCACAATAATGACTCCGTTTTATCCAAAAATTGACC
*
323385 TTGTAAGCGCTCTTATACATGTACCTACAAATTTTGACGGATTTTCATTAAATTTTTACCAAATG
1 TTGTAAGCGCTC---T-CATG--CCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATG
*
323450 TTGATACCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTT
60 TTTATACCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTT
*
323515 ATGGGACTTTGATCACAATAATGACACCGTTTTATCCAAAAATTGACC
125 ATGGGACTTTGATCACAATAATGACTCCGTTTTATCCAAAAATTGACC
***
323563 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATTTAAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
* * * *
323628 CCACTAATACTTTGGTCATGTTCGAAAATAAGCATTGGTTGATACTTTTTGCTGGAGTTATGGGA
66 CCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
323693 CTTTGATCACAATAATGACTCCGTTTTATCCAAAAATTGACC
131 CTTTGATCACAATAATGACTCCGTTTTATCCAAAAATTGACC
* *
323735 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAGTTTATACTAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
*
323800 CCACTCATACTTTGGTCAAGTTC
66 CCACTAATACTTTGGTCAAGTTC
323823 TTTAAGATTG
Statistics
Matches: 408, Mismatches: 24, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
172 239 0.59
174 4 0.01
175 2 0.00
176 4 0.01
178 159 0.39
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (172 bp):
TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
CCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
CTTTGATCACAATAATGACTCCGTTTTATCCAAAAATTGACC
Found at i:335351 original size:2 final size:2
Alignment explanation
Indices: 335344--335392 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
335334 TGTTTATTAT
* *
335344 GA GA GA GA TA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
335386 GA GA GA G
1 GA GA GA G
335393 TCAATTTCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
GA
Found at i:336194 original size:12 final size:12
Alignment explanation
Indices: 336145--336199 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
336135 ACTGTAGCTT
*
336145 TCCGTCCGTCAG
1 TCCGTCCGTCTG
336157 TCCGTCCGTCTG
1 TCCGTCCGTCTG
*
336169 TCTC-TCCGTATG
1 TC-CGTCCGTCTG
336181 TCCGTCCGTCTG
1 TCCGTCCGTCTG
*
336193 TCTGTCC
1 TCCGTCC
336200 CACTTCAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 1 0.03
12 35 0.95
13 1 0.03
ACGTcount: A:0.04, C:0.40, G:0.22, T:0.35
Consensus pattern (12 bp):
TCCGTCCGTCTG
Found at i:339981 original size:15 final size:15
Alignment explanation
Indices: 339961--339989 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
339951 GGCTTATTGA
339961 TATGGTATGCTATGC
1 TATGGTATGCTATGC
339976 TATGGTATGCTATG
1 TATGGTATGCTATG
339990 AGATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41
Consensus pattern (15 bp):
TATGGTATGCTATGC
Found at i:340185 original size:26 final size:26
Alignment explanation
Indices: 340156--340221 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
340146 TACGAGATTG
340156 TATGCTATGGTATGAGATTCCAATGC
1 TATGCTATGGTATGAGATTCCAATGC
**
340182 TATGCTATGGTATGAGATTTTAATGC
1 TATGCTATGGTATGAGATTCCAATGC
*
340208 TATGCTATGATATG
1 TATGCTATGGTATG
340222 GTGTATGTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (26 bp):
TATGCTATGGTATGAGATTCCAATGC
Found at i:341819 original size:2 final size:2
Alignment explanation
Indices: 341814--341868 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
341804 CAATATATAT
*
341814 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
341856 TC TC CC TC TC TC T
1 TC TC TC TC TC TC T
341869 AAAATAAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:360093 original size:2 final size:2
Alignment explanation
Indices: 360086--360125 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
360076 GTCATTTATT
* * *
360086 GA GA GA GA GA GA GA GA GA GA GA AA TA AA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
360126 TACTGTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (2 bp):
GA
Found at i:361114 original size:2 final size:2
Alignment explanation
Indices: 361107--361207 Score: 159
Period size: 2 Copynumber: 51.0 Consensus size: 2
361097 AATTTACAGT
361107 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
361149 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AA AA AG AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
361191 AG -G AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
361208 CATATGCGTG
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
1 1 0.01
2 91 0.99
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:361943 original size:92 final size:91
Alignment explanation
Indices: 361786--361969 Score: 359
Period size: 92 Copynumber: 2.0 Consensus size: 91
361776 TCTTTTCAAG
361786 TTCATTCCAAGACAACGTGTCAAGCTCAACAACTTTTATTTGAAGAGAATCCATGAATGTAGTAA
1 TTCATTCCAAGACAACGTGTCAAGCTCAACAACTTTTATTTGAAGAGAATCCATGAATGTAGTAA
361851 AAGACTGTTCCTTTGAAAGTGTGTGA
66 AAGACTGTTCCTTTGAAAGTGTGTGA
361877 NTTCATTCCAAGACAACGTGTCAAGCTCAACAACTTTTATTTGAAGAGAATCCATGAATGTAGTA
1 -TTCATTCCAAGACAACGTGTCAAGCTCAACAACTTTTATTTGAAGAGAATCCATGAATGTAGTA
361942 AAAGACTGTTCCTTTGAAAGTGTGTGA
65 AAAGACTGTTCCTTTGAAAGTGTGTGA
361969 T
1 T
361970 GTTTATTCAG
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 1 0.01
92 91 0.99
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (91 bp):
TTCATTCCAAGACAACGTGTCAAGCTCAACAACTTTTATTTGAAGAGAATCCATGAATGTAGTAA
AAGACTGTTCCTTTGAAAGTGTGTGA
Found at i:362409 original size:2 final size:2
Alignment explanation
Indices: 362404--362431 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
362394 GCAGTGTGTG
362404 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
362432 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:370580 original size:13 final size:13
Alignment explanation
Indices: 370562--370600 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
370552 TTGCCTCATT
370562 TTAATACATCTAC
1 TTAATACATCTAC
*
370575 TTAATAAATCTAC
1 TTAATACATCTAC
*
370588 TTATTACAGTCTA
1 TTAATACA-TCTA
370601 ATTGTATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (13 bp):
TTAATACATCTAC
Found at i:374116 original size:32 final size:32
Alignment explanation
Indices: 374048--374116 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
374038 GTACGAAAAC
374048 AATAAGGTCTTCCTTTGAAACGGAAAACCTTT
1 AATAAGGTCTTCCTTTGAAACGGAAAACCTTT
*
374080 -ATAAGGTCTTCCGTTTGAAACGGAAGA-CTTT
1 AATAAGGTCTTCC-TTTGAAACGGAAAACCTTT
374111 AATAAG
1 AATAAG
374117 AAACAGAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 16 0.47
32 18 0.53
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (32 bp):
AATAAGGTCTTCCTTTGAAACGGAAAACCTTT
Found at i:374141 original size:84 final size:87
Alignment explanation
Indices: 373993--374157 Score: 237
Period size: 84 Copynumber: 1.9 Consensus size: 87
373983 TACGAAAACA
* *
373993 ATAAGGTCTTCCGTTGGAAACAGAAGATCTTAATAATGAGAAACAGTACGAAAACAATAAGGTC-
1 ATAAGGTCTTCCGTTGGAAACAGAAGATCTT-ATAATAAGAAACAGAACGAAAACAATAAGGTCT
*
374057 TTCCTTTGAAACGGAAAACCTTT
65 TTCCTTGGAAACGGAAAACCTTT
* * *
374080 ATAAGGTCTTCCGTTTGAAACGGAAGA-CTT-TAATAAGAAACAGAACGAAATCAATAAGGTCTT
1 ATAAGGTCTTCCGTTGGAAACAGAAGATCTTATAATAAGAAACAGAACGAAAACAATAAGGTCTT
*
374143 TCGTTGGAAACGGAA
66 TCCTTGGAAACGGAA
374158 GACTTTAACT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 28 0.40
85 14 0.20
86 3 0.04
87 25 0.36
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (87 bp):
ATAAGGTCTTCCGTTGGAAACAGAAGATCTTATAATAAGAAACAGAACGAAAACAATAAGGTCTT
TCCTTGGAAACGGAAAACCTTT
Found at i:374616 original size:2 final size:2
Alignment explanation
Indices: 374609--374675 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
374599 CAAATTTGTC
*
374609 AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
374651 AG AG AG AG AC AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
374676 TTTTAGTGCT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.01, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:390407 original size:194 final size:195
Alignment explanation
Indices: 390068--390464 Score: 489
Period size: 194 Copynumber: 2.0 Consensus size: 195
390058 TTATTCCTTT
* * * *
390068 TAATATACAAATGATTGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGACATTG
1 TAAT-TACAAATGATTAAATATTTAAGGGGCAAGCCCTCTAGATCCTTAATGGGGACAGAAATTG
* * * *
390133 GTGCTTTGATTAATAGAATCGATTAAAATCATCAATGCTAACATTTTCTCTTCTACAATGCTTAT
65 GTGCTTTGATTAATAGAATAGATTAAAACCATCAATGCAAACATTTTCTCTTCTACAATGCTTAA
* * * * *
390198 CAAAATATGTCTCCTTTTCTAGATAAATTGCGTCAAAATTTAAGTAATTTGG-CCCTATAAATCC
130 CAAAATATATCTCCTTCTCTAGATAAATTACGTCAAAATTAAAGTAATTTGGCCCCTAAAAATCC
390262 C
195 C
*
390263 TAATTACAAATGATTAAATATTTAAGGGGCAAGCCCTGTAGATCCCTT-ATGGGGACAGAAATTG
1 TAATTACAAATGATTAAATATTTAAGGGGCAAGCCCTCTAGAT-CCTTAATGGGGACAGAAATTG
* * * * **
390327 GTG-TATTGA-TAAGTGGAATAGATTTAAACCATTAATGCAAACATTTTCTTTTCTATGATG-TC
65 GTGCT-TTGATTAA-TAGAATAGATTAAAACCATCAATGCAAACATTTTCTCTTCTACAATGCT-
* * * *
390389 TAACGAAATATATCTCCTTCTCTAGATATATTACGTCAAAGTTAAAGTACTTTGGCCCCTAAAAA
127 TAACAAAATATATCTCCTTCTCTAGATAAATTACGTCAAAATTAAAGTAATTTGGCCCCTAAAAA
390454 TCCC
192 TCCC
*
390458 TTATTAC
1 TAATTAC
390465 GTAATAAATG
Statistics
Matches: 172, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
193 5 0.03
194 141 0.82
195 26 0.15
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (195 bp):
TAATTACAAATGATTAAATATTTAAGGGGCAAGCCCTCTAGATCCTTAATGGGGACAGAAATTGG
TGCTTTGATTAATAGAATAGATTAAAACCATCAATGCAAACATTTTCTCTTCTACAATGCTTAAC
AAAATATATCTCCTTCTCTAGATAAATTACGTCAAAATTAAAGTAATTTGGCCCCTAAAAATCCC
Found at i:391571 original size:53 final size:53
Alignment explanation
Indices: 391495--391642 Score: 197
Period size: 53 Copynumber: 2.7 Consensus size: 53
391485 AAGAAATAAG
** * *
391495 AAGAAACAGTACGAAAACAATAAGGTGTTCCGTTTGAAACAGAATACCTAAAT
1 AAGAAACAGTACGAAAACAATAAGGTCCTCCGTTGGAAACAGAAGACCTAAAT
* *
391548 AAGAAACAGTACGAAAACAATAAGGTCCTCTGTTGGAAACAGAAGACCTTAAT
1 AAGAAACAGTACGAAAACAATAAGGTCCTCCGTTGGAAACAGAAGACCTAAAT
* *
391601 AAGAAACAGTACAAAAACAATTACTAGGTCTTCCGTTGGAAA
1 AAGAAACAGTACGAAAACAA-TA--AGGTCCTCCGTTGGAAA
391643 GTAAAACATT
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
53 66 0.80
54 2 0.02
56 15 0.18
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (53 bp):
AAGAAACAGTACGAAAACAATAAGGTCCTCCGTTGGAAACAGAAGACCTAAAT
Found at i:410319 original size:35 final size:35
Alignment explanation
Indices: 410273--410343 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
410263 CAATCAACTT
410273 AGATAGCTTTAATCCCTAATGATGACATGTGGTGC
1 AGATAGCTTTAATCCCTAATGATGACATGTGGTGC
*
410308 AGATAGCTTTAATCCCTGATGATGACATGTGGTGC
1 AGATAGCTTTAATCCCTAATGATGACATGTGGTGC
410343 A
1 A
410344 AATTATTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (35 bp):
AGATAGCTTTAATCCCTAATGATGACATGTGGTGC
Found at i:421457 original size:26 final size:26
Alignment explanation
Indices: 421417--421469 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
421407 ACAATGCTGT
* *
421417 TTGACACGACTACCCAAAGTCAAAGC
1 TTGACACAACAACCCAAAGTCAAAGC
*
421443 TTGACACAACAACCCAAAGTCCAAGC
1 TTGACACAACAACCCAAAGTCAAAGC
421469 T
1 T
421470 CCTGTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.32, G:0.13, T:0.15
Consensus pattern (26 bp):
TTGACACAACAACCCAAAGTCAAAGC
Found at i:423673 original size:33 final size:33
Alignment explanation
Indices: 423636--424148 Score: 305
Period size: 33 Copynumber: 16.0 Consensus size: 33
423626 TGATCATTTT
* *
423636 ACATAGGTAAATCCCTGTCCTTGTAACTGTTTG
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
** *
423669 ACATAGGTAACTCCCTGTCCCTGTCCCTGTTTC
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
* * * *
423702 ACATAGGTTAGGTAATTTCCTGTCCCTTTAAC----TA
1 AC--A---TAGGTAACTCCCTGTCCCTGTAACTGTTTG
*
423736 ACATAGGT-A---GC--TCCCTGTAACTGTTTG
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
* *
423763 ACATAAGTAACTCCCTGTCCCTGTAACTGTATG
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
* *
423796 ACATAGGTTAGGTAATTCCATGTCCCTGTAAC----TG
1 AC--A---TAGGTAACTCCCTGTCCCTGTAACTGTTTG
*
423830 ACATAGGTAACT-CCTGTCCCTGTAAATGTTTG
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
*** ** * *
423862 ACATACACAACTCCCTGTCTTTGTACCTGCTTG
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
*
423895 ACATAGGTAACTCCTTGTCCCTGTAACTGTTTG
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
* * *
423928 ACATATAGATAACTTCCAGT-CCTCGTAACTGTTTG
1 AC--ATAGGTAACTCCCTGTCCCT-GTAACTGTTTG
* * **
423963 ACATAAGTTAGAATTTCT-T-CCTGTAACTGTTTG
1 ACAT-AGGTA-ACTCCCTGTCCCTGTAACTGTTTG
* * * *
423996 ACCTAGGTAACTCCCTGTCCTTTTACCTGTTTG
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
*
424029 GCATAGGTAA---CC---CCCTGTAACTGTTTG
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
* *
424056 ACATAGATAACT-CCTGTCCCTGTACCTGTTTG
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
424088 ACATAGGTAA----C--TCCCTGTAACTGTTTG
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
* * * *
424115 ACTTAGGTAGCTCCCTTTCCCTGTTACTGTTTG
1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
424148 A
1 A
424149 TGTTAAATCA
Statistics
Matches: 369, Mismatches: 68, Indels: 86
0.71 0.13 0.16
Matches are distributed among these distances:
23 9 0.02
25 1 0.00
27 51 0.14
28 14 0.04
29 16 0.04
30 2 0.01
31 6 0.02
32 41 0.11
33 140 0.38
34 18 0.05
35 31 0.08
38 40 0.11
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (33 bp):
ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG
Found at i:423897 original size:99 final size:96
Alignment explanation
Indices: 423636--423902 Score: 301
Period size: 94 Copynumber: 2.7 Consensus size: 96
423626 TGATCATTTT
* * *
423636 ACATAGGTAAATCCCTGTCCTTGTAACTGTTTGACATAGGTAACTCCCTGTCCCTGTCCCTGTTT
1 ACATAGGT-AAT-CCTGTCCCTGTAACTGTTTGACATA-ATAACTCCCTGTCCCTGTACCTG-TT
* *
423701 CACATAGGTTAGGTAATTTCCTGTCCCTTTAACTA
62 GACATAGGTTAGGTAATTTCCTGTCCCTGTAACTA
* *
423736 ACATAGGT-A-GC--TCCCTGTAACTGTTTGACATAAGTAACTCCCTGTCCCTGTAACTGTATGA
1 ACATAGGTAATCCTGTCCCTGTAACTGTTTGACATAA-TAACTCCCTGTCCCTGTACCTGT-TGA
*
423797 CATAGGTTAGGTAA-TTCCATGTCCCTGTAACTG
64 CATAGGTTAGGTAATTTCC-TGTCCCTGTAACTA
* * **
423830 ACATAGGTAACTCCTGTCCCTGTAAATGTTTGACATACACAACTCCCTGTCTTTGTACCTGCTTG
1 ACATAGGTAA-TCCTGTCCCTGTAACTGTTTGACATA-ATAACTCCCTGTCCCTGTACCTG-TTG
423895 ACATAGGT
63 ACATAGGT
423903 AACTCCTTGT
Statistics
Matches: 143, Mismatches: 14, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
93 5 0.03
94 76 0.53
95 1 0.01
96 1 0.01
97 1 0.01
98 1 0.01
99 48 0.34
100 10 0.07
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (96 bp):
ACATAGGTAATCCTGTCCCTGTAACTGTTTGACATAATAACTCCCTGTCCCTGTACCTGTTGACA
TAGGTTAGGTAATTTCCTGTCCCTGTAACTA
Found at i:424012 original size:27 final size:27
Alignment explanation
Indices: 423982--424130 Score: 127
Period size: 27 Copynumber: 5.1 Consensus size: 27
423972 AGAATTTCTT
*
423982 CCTGTAACTGTTTGACCTAGGTAACTC
1 CCTGTAACTGTTTGACATAGGTAACTC
* * *
424009 CCTGTCCTTTTACCTGTTTGGCATAGGTAACCC
1 CCTG------TAACTGTTTGACATAGGTAACTC
*
424042 CCTGTAACTGTTTGACATAGATAACTCCTGTC
1 CCTGTAACTGTTTGACATAGGTAA---C--TC
*
424074 CCTGTACCTGTTTGACATAGGTAACTC
1 CCTGTAACTGTTTGACATAGGTAACTC
* *
424101 CCTGTAACTGTTTGACTTAGGTAGCTC
1 CCTGTAACTGTTTGACATAGGTAACTC
424128 CCT
1 CCT
424131 TTCCCTGTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 22
0.74 0.10 0.17
Matches are distributed among these distances:
27 50 0.51
29 1 0.01
30 1 0.01
32 23 0.23
33 23 0.23
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (27 bp):
CCTGTAACTGTTTGACATAGGTAACTC
Found at i:427563 original size:169 final size:165
Alignment explanation
Indices: 427099--428104 Score: 1104
Period size: 166 Copynumber: 6.0 Consensus size: 165
427089 AATTAAAGGA
* *
427099 TTTTAAAGATTTACTCTA--TATATTCCTATGTATAAATTCGACCCCCATCGTGGCCCC-TACCA
1 TTTTAAAGATTTACTCTATGTATATT-CTATG-ATAAATTCAACCCCCATCGTGGCCCCAT-CCT
*
427161 ACCCCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGT
63 ACCCCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGACAAGT
* ** *
427226 TTCAGTTTTCCTGGCCTAACAGTTTCTGAGAAAAAGAT
128 TTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT
* * * * * * *
427264 TTTTAAAAATTTACTCCATGTATA-ACAATGTTAAAACTCAACCCACCATTGTGGCCCCATCCTA
1 TTTTAAAGATTTACTCTATGTATATTCTATGAT-AAATTCAACCC-CCATCGTGGCCCCATCCTA
** * * * * *
427328 ATCCCAAGGGTCATG-ATTTCAACAACTTTGAA-CTGACAATACCTGAAGATGCTTCCATACAAG
64 CCCCCAGGGGTCATGCTTTTC-ACAACTTTGAATCT-ACACTACCTGAGGATGCTTCCAGACAAG
* *
427391 TTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGAC
127 TTTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT
* * * *
427430 TATTAAAGCTTTACTCTTACTGTATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCC-TAC
1 TTTTAAAGATTTACTC-TA-TGTATATTC-TATG-ATAAATTCAACCCCCATCGTGGCCCCAT-C
* *
427494 CTACCCCCAGGGGTCATGCTTTTCACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAA
61 CTACCCCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGACAA
* * ** *
427559 GTTTCAGTTTTCCTGGCCCAACAGTTTCTGAGAAAAAGAT
126 GTTTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT
* * * * * * *
427599 TTTTAAAAATTTACTCCATGTATA-ACAATGTTAAAACTCAACCCACCATTGTGGCCCCATCCTA
1 TTTTAAAGATTTACTCTATGTATATTCTATGAT-AAATTCAACCC-CCATCGTGGCCCCATCCTA
** * * * * *
427663 ATCCCAAGGGTCATG-ATTTCAACAACTTTGAA-CTGACAATACCTGAAGATGCTTCCATACAAG
64 CCCCCAGGGGTCATGCTTTTC-ACAACTTTGAATCT-ACACTACCTGAGGATGCTTCCAGACAAG
* *
427726 TTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGAC
127 TTTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT
* * * *
427765 TATTAAAGCTTTACTCTTACTGTATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCC-TAC
1 TTTTAAAGATTTACTC-TA-TGTATATTC-TATG-ATAAATTCAACCCCCATCGTGGCCCCAT-C
* *
427829 CTACCCCCAGGGGTCATGCTTTTCACAAATTTGAATCTACACTACCTGAGGATGCTTCCA-CCTA
61 CTACCCCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGAC-A
427893 AGTTTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT
125 AGTTTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT
* *
427934 TTTTAAAGATTTACTCTAT-TATATTCCCATGTATAAATTCAACCCCCCCATTGTGGCCCCATCC
1 TTTTAAAGATTTACTCTATGTATATT-CTATG-ATAAATTCAA--CCCCCATCGTGGCCCCATCC
* * *
427998 TACCCCAAGGGGTCATGATTTTCACAATTTTGAATCTACACTACCTGAGGATGCTTCCAGACAAG
62 TACCCCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGACAAG
* *
428063 TTTCAGCTTTCCTTGCCTTATGG-TTCTTGAGAAGAAGAT
127 TTTCAGCTTTCCTGGCCTAATGGTTTC-TGAGAAGAAGAT
428102 TTT
1 TTT
428105 AGAAAAAAAA
Statistics
Matches: 697, Mismatches: 109, Indels: 67
0.80 0.12 0.08
Matches are distributed among these distances:
164 2 0.00
165 53 0.08
166 234 0.34
167 19 0.03
168 129 0.19
169 222 0.32
170 36 0.05
171 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (165 bp):
TTTTAAAGATTTACTCTATGTATATTCTATGATAAATTCAACCCCCATCGTGGCCCCATCCTACC
CCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGACAAGTTTC
AGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT
Found at i:427727 original size:335 final size:335
Alignment explanation
Indices: 427117--428100 Score: 1620
Period size: 335 Copynumber: 2.9 Consensus size: 335
427107 ATTTACTCTA
* * * *
427117 TATATTCCTATGTATAAATTCGACCCCCATCGTGGCCCCTACCAACCCCCAGGGGTCATGCTTTT
1 TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT
*
427182 CACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCTAACA
66 CACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCTAACA
427247 GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATAACAATGTTAAAACTCAACCCACCA
131 GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATAACAATGTTAAAACTCAACCCACCA
427312 TTGTGGCCCCATCCTAATCCCAAGGGTCATGATTTCAACAACTTTGAACTGACAATACCTGAAGA
196 TTGTGGCCCCATCCTAATCCCAAGGGTCATGATTTCAACAACTTTGAACTGACAATACCTGAAGA
427377 TGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGACTATTAAAGCTTT
261 TGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGACTATTAAAGCTTT
427442 ACTCTTACTG
326 ACTCTTACTG
427452 TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT
1 TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT
*
427517 CACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCCAACA
66 CACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCTAACA
427582 GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATAACAATGTTAAAACTCAACCCACCA
131 GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATAACAATGTTAAAACTCAACCCACCA
427647 TTGTGGCCCCATCCTAATCCCAAGGGTCATGATTTCAACAACTTTGAACTGACAATACCTGAAGA
196 TTGTGGCCCCATCCTAATCCCAAGGGTCATGATTTCAACAACTTTGAACTGACAATACCTGAAGA
427712 TGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGACTATTAAAGCTTT
261 TGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGACTATTAAAGCTTT
427777 ACTCTTACTG
326 ACTCTTACTG
427787 TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT
1 TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT
** * **
427852 CACAAATTTGAATCTACACTACCTGAGGATGCTTCCACCTAAGTTTCAGCTTTCCTGGCCTAATG
66 CACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCTAACA
* * * * * *
427917 GTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTAT-TATATTCCCATG-TATAAATTCAACCCC
131 GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATA--ACAATGTTA-AAACTCAA-CCC
* * * *
427980 CCCATTGTGGCCCCATCCT-ACCCCAAGGGGTCATGATTTTC-ACAATTTTGAATCT-ACACTAC
192 ACCATTGTGGCCCCATCCTAATCCCAA-GGGTCATGA-TTTCAACAACTTTGAA-CTGACAATAC
* * * **
428042 CTGAGGATGCTTCCAGACAAGTTTCAGCTTTCCTTGCCTTATGG-TTCTTGAGAAGAAGA
254 CTGAAGATGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTC-TGAGAAGAAGA
428101 TTTTAGAAAA
Statistics
Matches: 614, Mismatches: 27, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
334 4 0.01
335 488 0.79
336 20 0.03
337 96 0.16
338 6 0.01
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (335 bp):
TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT
CACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCTAACA
GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATAACAATGTTAAAACTCAACCCACCA
TTGTGGCCCCATCCTAATCCCAAGGGTCATGATTTCAACAACTTTGAACTGACAATACCTGAAGA
TGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGACTATTAAAGCTTT
ACTCTTACTG
Found at i:432830 original size:21 final size:21
Alignment explanation
Indices: 432804--432885 Score: 101
Period size: 21 Copynumber: 3.9 Consensus size: 21
432794 CACTTTGAAG
432804 TGTAAAATTCACAATTTAATC
1 TGTAAAATTCACAATTTAATC
*
432825 TGTAAAATTCACACTTTAATC
1 TGTAAAATTCACAATTTAATC
* ** *
432846 TATAAAATTTTCACTTTAATC
1 TGTAAAATTCACAATTTAATC
* *
432867 TGTAAAATTTACAAGTTAA
1 TGTAAAATTCACAATTTAA
432886 AGCGTAAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.40
Consensus pattern (21 bp):
TGTAAAATTCACAATTTAATC
Found at i:432906 original size:21 final size:21
Alignment explanation
Indices: 432867--433082 Score: 197
Period size: 21 Copynumber: 10.2 Consensus size: 21
432857 CACTTTAATC
*
432867 TGTAAAATTTACA-AGTTAAAG
1 TGTAAATTTTACAGA-TTAAAG
* * *
432888 CGTAAATTATACAGATTAAAT
1 TGTAAATTTTACAGATTAAAG
* *
432909 TGTGAATTTTACAAATT-AA-
1 TGTAAATTTTACAGATTAAAG
* *
432928 TGTGAATTTTACA-CTTCAAAG
1 TGTAAATTTTACAGATT-AAAG
*
432949 TGTCAATTTTACAGATTAAAG
1 TGTAAATTTTACAGATTAAAG
* **
432970 TGTGAATTTTACACTTTTTAAAAG
1 TGTAAATTTTACA--GATT-AAAG
*
432994 TGTAAATTTTACAGATTAAAA
1 TGTAAATTTTACAGATTAAAG
* *
433015 TGTAAAATTTACAGAATAAAG
1 TGTAAATTTTACAGATTAAAG
*
433036 TGTAAATTTTACAGATTAAAT
1 TGTAAATTTTACAGATTAAAG
* *
433057 TGTAAAATGTACAGATTAAAG
1 TGTAAATTTTACAGATTAAAG
433078 TGTAA
1 TGTAA
433083 TGTCTTTTGT
Statistics
Matches: 160, Mismatches: 27, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
18 2 0.01
19 13 0.08
20 4 0.03
21 118 0.74
22 5 0.03
23 2 0.01
24 16 0.10
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (21 bp):
TGTAAATTTTACAGATTAAAG
Found at i:442974 original size:42 final size:42
Alignment explanation
Indices: 442915--443651 Score: 909
Period size: 42 Copynumber: 17.7 Consensus size: 42
442905 TCTTAATCTC
*
442915 TGAAACTTT-AATATTTTCCTATGTCTTTATAACTTTAACCTA
1 TGAAA-TTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
* * *
442957 TGAAATTTGAATATTTTCCTATATCCTTAAAATTTTAACCTA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
* * *
442999 TGAAATTTGAATATTTTGCTCTTTTTTTTTTTATATAACTTTAACCTA
1 TGAAATTTGAATATTTT-C-C---TATATCTT-TATAACTTTAACCTA
* *
443047 TGAAATTTGAATATTTTCCTTTATTTTTATAACTTTAACCTA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
* * * * *
443089 T-AAAATTCAATTATTTTCTTATATCTTTATATCTTTAATCTA
1 TGAAATTTGAA-TATTTTCCTATATCTTTATAACTTTAACCTA
*
443131 TGAAATTTGAATATTTTCCTACATCTTTATAACTTTAACCTA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
*
443173 TGAAATTCGAATATTTTCCTATATCTTTATAACTTTAACCTA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
* * *
443215 TGAAATTTG-ATAATTTTCCTATCTTTTTATATCTTTAACCTA
1 TGAAATTTGAAT-ATTTTCCTATATCTTTATAACTTTAACCTA
*
443257 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACTTA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
*
443299 TGAAATTTGGATATTTTCC--TA----TAT--CTTTAACCTA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
*
443333 TGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
* * * *
443375 TGAAATTTGATTATTTTCCCATATCTTTATAACCTTAACATA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
443417 TGAAATTTGAATATTTTCC--TA----TAT--CTTTAACCTA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
*
443451 TGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
* * * * *
443493 TGAAATTTGATTATTTTGCTCTTTTTTTTTTTACAACTTTAACCTA
1 TGAAATTTGAATATTTT-C-C--TATATCTTTATAACTTTAACCTA
*
443539 TGAAATTTGAATATTGTCCTATATCTTTATAACTTTAACCTA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
* *
443581 TAAAATTTGAATATTTTCCTATATCTTTATATCTTTAACCTA
1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
443623 TGAAATTTGAATATTTTCCTATATCTTTA
1 TGAAATTTGAATATTTTCCTATATCTTTA
443652 CACCGAGCTC
Statistics
Matches: 601, Mismatches: 63, Indels: 62
0.83 0.09 0.09
Matches are distributed among these distances:
34 54 0.09
36 10 0.02
40 10 0.02
41 12 0.02
42 424 0.71
43 18 0.03
44 3 0.00
45 1 0.00
46 34 0.06
47 5 0.01
48 30 0.05
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (42 bp):
TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
Found at i:442977 original size:21 final size:22
Alignment explanation
Indices: 442952--443015 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
442942 TATAACTTTA
442952 ACCTATGAAATTTGAATATTTT
1 ACCTATGAAATTTGAATATTTT
*** *
442974 -CCTAT-ATCCTT-AAAATTTT
1 ACCTATGAAATTTGAATATTTT
442993 AACCTATGAAATTTGAATATTTT
1 -ACCTATGAAATTTGAATATTTT
443016 GCTCTTTTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 7
0.67 0.18 0.16
Matches are distributed among these distances:
19 7 0.23
20 3 0.10
21 10 0.33
22 3 0.10
23 7 0.23
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (22 bp):
ACCTATGAAATTTGAATATTTT
Found at i:443334 original size:76 final size:76
Alignment explanation
Indices: 443242--443651 Score: 398
Period size: 76 Copynumber: 5.1 Consensus size: 76
443232 CCTATCTTTT
*
443242 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACTTATGAAATTT
1 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTATGAAATTT
*
443307 GGATATTTTCC
66 GAATATTTTCC
*
443318 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT
1 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTATGAAATTT
*
443383 GATTATTTTCC
66 GAATATTTTCC
* * ** * *
443394 CATATCTTTATAACCT-T-AACATATGAA-A-TTT-GAATATTTTCCTATATCTTTAACCTATGA
1 TATATC-TT-TAACCTATGAA-ATTTGAATATTTTCCTATATCTT--TATAACTTTAACCTATGA
443454 AATTTGAATATTTTCC
61 AATTTGAATATTTTCC
* * * * *
443470 TATATCTTTATAACTTAAACCTATGAAATTTGATTATTTTGCTCTTTTTTTTTTTACAACTTTAA
1 TATATC----T---TT-AACCTATGAAATTTGAATATTTT-C-C--TATATCTTTATAACTTTAA
*
443535 CCTATGAAATTTGAATATTGTCC
54 CCTATGAAATTTGAATATTTTCC
* *
443558 TATATCTTTATAACTTTAACCTATAAAATTTGAATATTTTCCTATATCTTTATATCTTTAACCTA
1 --TA----TAT--CTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA
443623 TGAAATTTGAATATTTTCC
58 TGAAATTTGAATATTTTCC
443642 TATATCTTTA
1 TATATCTTTA
443652 CACCGAGCTC
Statistics
Matches: 274, Mismatches: 31, Indels: 58
0.75 0.09 0.16
Matches are distributed among these distances:
74 6 0.02
75 3 0.01
76 121 0.44
77 9 0.03
78 9 0.03
79 1 0.00
81 1 0.00
82 8 0.03
83 6 0.02
84 39 0.14
85 3 0.01
86 1 0.00
87 1 0.00
88 52 0.19
89 2 0.01
90 7 0.03
92 1 0.00
94 3 0.01
96 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.48
Consensus pattern (76 bp):
TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTATGAAATTT
GAATATTTTCC
Found at i:443373 original size:118 final size:118
Alignment explanation
Indices: 443200--443651 Score: 600
Period size: 118 Copynumber: 3.7 Consensus size: 118
443190 CCTATATCTT
* * * * *
443200 TATAACTTTAACCTATGAAATTTG-ATAATTTTCCTATCTTTTTATATCTTTAACCTATGAAATT
1 TATATCTTTAACCTATGAAATTTGAAT-ATTTTCCTATATCTTTATAACTTAAACCTATGAAATT
* *
443264 TGAATATTTTCCTATATCTTTATAACTTTAACTTATGAAATTTGGATATTTTCC
65 TGAATATTTTCCTATATCTTTATAACTTTAACATATGAAATTTGAATATTTTCC
443318 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT
1 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT
* * *
443383 GATTATTTTCCCATATCTTTATAACCTTAACATATGAAATTTGAATATTTTCC
66 GAATATTTTCCTATATCTTTATAACTTTAACATATGAAATTTGAATATTTTCC
443436 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT
1 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT
* * * * * * *
443501 GATTATTTTGCTCTTTTTTTTTTTACAACTTTAACCTATGAAATTTGAATATTGTCC
66 GAATATTTT-C-C--TATATCTTTATAACTTTAACATATGAAATTTGAATATTTTCC
* * *
443558 TATATCTTTATAACTTTAACCTATAAAATTTGAATATTTTCCTATATCTTTATATCTTTAACCTA
1 --TA----TAT--CTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTA
443623 TGAAATTTGAATATTTTCCTATATCTTTA
58 TGAAATTTGAATATTTTCCTATATCTTTA
443652 CACCGAGCTC
Statistics
Matches: 296, Mismatches: 25, Indels: 18
0.87 0.07 0.05
Matches are distributed among these distances:
118 179 0.60
119 3 0.01
120 1 0.00
122 34 0.11
124 2 0.01
126 7 0.02
128 4 0.01
129 1 0.00
130 65 0.22
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.48
Consensus pattern (118 bp):
TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT
GAATATTTTCCTATATCTTTATAACTTTAACATATGAAATTTGAATATTTTCC
Found at i:443601 original size:21 final size:21
Alignment explanation
Indices: 443577--443645 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
443567 ATAACTTTAA
443577 CCTATAAAATTTGAATATTTT
1 CCTATAAAATTTGAATATTTT
**
443598 CCTAT-ATCTTT--ATATCTTT
1 CCTATAAAATTTGAATAT-TTT
*
443617 AACCTATGAAATTTGAATATTTT
1 --CCTATAAAATTTGAATATTTT
443640 CCTATA
1 CCTATA
443646 TCTTTACACC
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
18 4 0.11
19 3 0.08
20 4 0.11
21 15 0.41
22 4 0.11
23 3 0.08
24 4 0.11
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.48
Consensus pattern (21 bp):
CCTATAAAATTTGAATATTTT
Found at i:445410 original size:17 final size:17
Alignment explanation
Indices: 445377--445410 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
445367 CTGTGGTTTC
*
445377 ACCAATTTTCGTTGAAT
1 ACCAATTTTCGTGGAAT
*
445394 ACCAATTTTTGTGGAAT
1 ACCAATTTTCGTGGAAT
445411 TCTTTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (17 bp):
ACCAATTTTCGTGGAAT
Found at i:455524 original size:30 final size:30
Alignment explanation
Indices: 455490--455548 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
455480 AATTTCATCA
* *
455490 TGCGATAAATGCTAAAAATGCAAATTGTCT
1 TGCGATAAATGATAAAAATGCAAACTGTCT
455520 TGCGATAAATGATAAAAATGCAAACTGTC
1 TGCGATAAATGATAAAAATGCAAACTGTC
455549 ATGCTCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (30 bp):
TGCGATAAATGATAAAAATGCAAACTGTCT
Found at i:458291 original size:21 final size:20
Alignment explanation
Indices: 458265--458340 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 20
458255 ATTTGTAACT
458265 TGCATGTAGACATAATTATCC
1 TGCATGTAGACATAATTAT-C
* *
458286 TGCATGTAGACAGAATTATAT
1 TGCATGTAGACATAATTAT-C
*
458307 TGCATGTAGACACAATTATC
1 TGCATGTAGACATAATTATC
*
458327 TAGCATGTTGACAT
1 T-GCATGTAGACAT
458341 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 1 0.02
21 46 0.98
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (20 bp):
TGCATGTAGACATAATTATC
Found at i:462409 original size:161 final size:160
Alignment explanation
Indices: 462129--462630 Score: 686
Period size: 161 Copynumber: 3.1 Consensus size: 160
462119 AACATCCACA
* * ** * * *
462129 AAGAAAATGAACGTAAACTGCAAATATTTGGAATTTTTCTAAGTCCAAGGGGCATAACTATG-CG
1 AAGAAAATGAGCGGAAACTGCAAATAACTCGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG
* * * * *
462193 GAAATTGCTC-TATCATACCCAAAATCAAACTTGACCTAGATATTATT-TAGATAAACCTGCATA
66 AAAATTGCTCGT-TCGTACCCAATATCGAACTTGACCTAGATATTATTAT-GATAAACCTGTATA
* * *
462256 CCAAATTTCATATTAATGTGTGCACCCTTTGCG
129 CCAAATTTCAT-TTAATATGTTCATCCTTTGCG
* *
462289 AAGAAAATGAGCGGAAGCTGCAAGTAACTCGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG
1 AAGAAAATGAGCGGAAACTGCAAATAACTCGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG
* *
462354 AAAATTGCCCGTTCGTACCCAATATCGAACTTGACCTAGATATTATTATGATAAACCTGTATACT
66 AAAATTGCTCGTTCGTACCCAATATCGAACTTGACCTAGATATTATTATGATAAACCTGTATACC
*
462419 AAATTTCATTTTAATATGTTCATCCTCTGCG
131 AAATTTCA-TTTAATATGTTCATCCTTTGCG
* *
462450 AAAAAAATGAGCGGAAACTGCAAATAACTCGAATTTGTCTAAGTCCAAGGGCCATAACTCTGTCG
1 AAGAAAATGAGCGGAAACTGCAAATAACTCGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG
* * *
462515 AAAATTGCTCGATCGTACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCAGTATACC
66 AAAATTGCTCGTTCGTACCCAATATCGAACTTGACCTAGATATTATTATGATAAACCTGTATACC
* *
462580 AAATTTCATTTCAATATGTTTATCCTTTGCA
131 AAATTTCATTT-AATATGTTCATCCTTTGCG
*
462611 AAGAAAATGAACGGAAACTG
1 AAGAAAATGAGCGGAAACTG
462631 TTGGTGGACC
Statistics
Matches: 303, Mismatches: 34, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
160 56 0.18
161 244 0.81
162 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (160 bp):
AAGAAAATGAGCGGAAACTGCAAATAACTCGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG
AAAATTGCTCGTTCGTACCCAATATCGAACTTGACCTAGATATTATTATGATAAACCTGTATACC
AAATTTCATTTAATATGTTCATCCTTTGCG
Found at i:464825 original size:53 final size:53
Alignment explanation
Indices: 464743--464907 Score: 278
Period size: 53 Copynumber: 3.1 Consensus size: 53
464733 TAAGCAGCAC
*
464743 CAAACCTTTGATACGACCATTCGTGTGACAATGTACGAACTGAATCGCAATGAA
1 CAAA-CTTTGATACGACCATTCGTTTGACAATGTACGAACTGAATCGCAATGAA
*
464797 CAAACTTTGATACGACCATTCGTTTGACAATTGT-CGAGCTGAATCGCAATGAA
1 CAAACTTTGATACGACCATTCGTTTGACAA-TGTACGAACTGAATCGCAATGAA
*
464850 CAAACTTTGATACGACCATTTGTTTGACAATGTACGAACTGAATCGCAATGAA
1 CAAACTTTGATACGACCATTCGTTTGACAATGTACGAACTGAATCGCAATGAA
464903 CAAAC
1 CAAAC
464908 ATAGTTTTAA
Statistics
Matches: 105, Mismatches: 4, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
52 3 0.03
53 95 0.90
54 7 0.07
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (53 bp):
CAAACTTTGATACGACCATTCGTTTGACAATGTACGAACTGAATCGCAATGAA
Found at i:469065 original size:9 final size:9
Alignment explanation
Indices: 469051--469079 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
469041 TCAATATGAG
469051 AAAAGGTAA
1 AAAAGGTAA
469060 AAAAGGT-A
1 AAAAGGTAA
469068 AAAAGGTAA
1 AAAAGGTAA
469077 AAA
1 AAA
469080 CTTGTTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (9 bp):
AAAAGGTAA
Found at i:476671 original size:6 final size:6
Alignment explanation
Indices: 476660--476697 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
476650 TGCTATACCC
476660 TCGGCG TCGGCGG T-GGCG TCGGCG TCGGCG TCGGCG TC
1 TCGGCG TCGGC-G TCGGCG TCGGCG TCGGCG TCGGCG TC
476698 CGGACCTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.07
6 26 0.87
7 2 0.07
ACGTcount: A:0.00, C:0.32, G:0.50, T:0.18
Consensus pattern (6 bp):
TCGGCG
Found at i:477044 original size:19 final size:19
Alignment explanation
Indices: 477022--477061 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
477012 TTTCGGATGC
* *
477022 TGGAGGAGGTTAAGGTTTT
1 TGGAGCAGGTTAAAGTTTT
477041 TGGAGCAGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
477060 TG
1 TG
477062 TTGTGGGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:477053 original size:177 final size:176
Alignment explanation
Indices: 476835--477714 Score: 1253
Period size: 177 Copynumber: 4.9 Consensus size: 176
476825 GGGTCCTAAA
* * ** * * *
476835 TTTCAGATGCTGGAGGAGGTTAAGGTTGTGGGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * * * * * *
476900 GATAGCA-ATATCTTAGTTACTGCTGGTCCGTACATCACCAAATTTGCATGGATGGTGTGCCTTA
66 GAT-G-ATATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTTA
* * * *
476964 TGATACTGATGCACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGG
129 TGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG
* * **
477012 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGTGGGTGCCCAT-
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCC-TC
* * *
477076 TGATAGCA-ATATCTAAGTTACTACTGGTCCTAACTTCACCAAACTTGTATGGATGATGCGTCTT
65 TGAT-G-ATATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTT
477140 ATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG
128 ATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG
*
477189 TTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
477254 GATGATTATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTTAT
66 GATGA-TATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTTAT
*
477319 GATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGA
130 GATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG
* *
477366 TTTCGGATGCTGGAAGAGGTTAAGGTTTTTATAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
*
477431 GATGATTATATCTTAGTTACTACTGGTCCTTACTTCACAAAACTTGTATGGATGGTGCGTCTTAT
66 GATGA-TATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTTAT
477496 GATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG
130 GATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG
* ***
477543 TTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTAAATAAAGTTTTTGAAACAGGTGCC
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG-T---TAAAGTTTTTGTTGCAGGTGCC
* * * ** *
477608 CTCTGATGATGATATCTTAGTTATTACTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTC
62 CTCTGATGAT-ATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTC
* *
477673 TTATGATACTGATGCACCTGACAGGCTTGAATGCTGAGTCTG
126 TTATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTG
477715 GTTTCGGATG
Statistics
Matches: 647, Mismatches: 47, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
175 1 0.00
176 2 0.00
177 526 0.81
178 2 0.00
180 1 0.00
181 115 0.18
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (176 bp):
TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
GATGATATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTTATG
ATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG
Found at i:478396 original size:20 final size:20
Alignment explanation
Indices: 478373--478415 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
478363 TATGATATAG
478373 TATTGTATGATATGAAACAA
1 TATTGTATGATATGAAACAA
* *
478393 TATTGTTTGATATGATACAA
1 TATTGTATGATATGAAACAA
478413 TAT
1 TAT
478416 GATATCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (20 bp):
TATTGTATGATATGAAACAA
Found at i:478691 original size:15 final size:15
Alignment explanation
Indices: 478658--478804 Score: 73
Period size: 15 Copynumber: 9.3 Consensus size: 15
478648 ATATTCTATA
* **
478658 ATATTGTATCATACA
1 ATATTGTATAATATG
478673 ATATTGTATAATATG
1 ATATTGTATAATATG
478688 ATATTGGTTTCAGTAATATAG
1 ATATT-G--T-A-TAATAT-G
* * *
478709 A-ATTATATCACATG
1 ATATTGTATAATATG
* *
478723 AAATTGTATTATATG
1 ATATTGTATAATATG
*
478738 ATATTGTAATATTATATA
1 ATATTGT-ATA--ATATG
* *
478756 ATATTGTATCATACG
1 ATATTGTATAATATG
*
478771 ATATTGTATGATATG
1 ATATTGTATAATATG
*
478786 ATATTGGT-TTATATG
1 ATATT-GTATAATATG
478801 ATAT
1 ATAT
478805 ATTATCTTAT
Statistics
Matches: 103, Mismatches: 18, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
14 2 0.02
15 68 0.66
16 6 0.06
17 3 0.03
18 12 0.12
19 1 0.01
20 9 0.09
21 2 0.02
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (15 bp):
ATATTGTATAATATG
Found at i:478737 original size:50 final size:46
Alignment explanation
Indices: 478675--478841 Score: 147
Period size: 50 Copynumber: 3.4 Consensus size: 46
478665 ATCATACAAT
*
478675 ATTGTATAATATGATATTGGTTTCAGTAATATAGAATTATATCACATGAA
1 ATTGTATTATATGATATTGGTTT-A-TAATATA-AATT-TATCACATGAA
* * * * *
478725 ATTGTATTATATGATATT-GTAATATTATATAATATTGTATCATACGAT
1 ATTGTATTATATGATATTGGT-TTATAATATAA-ATT-TATCACATGAA
* *
478773 ATTGTATGATATGATATTGGTTTATATGATATATTATCTTATCACATGAA
1 ATTGTATTATATGATATTGGTTTATA--ATATA-AAT-TTATCACATGAA
*
478823 GTTGTATTATATGATATTG
1 ATTGTATTATATGATATTG
478842 TAATATATAT
Statistics
Matches: 94, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
47 1 0.01
48 37 0.39
49 5 0.05
50 50 0.53
51 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.46
Consensus pattern (46 bp):
ATTGTATTATATGATATTGGTTTATAATATAAATTTATCACATGAA
Found at i:478752 original size:18 final size:18
Alignment explanation
Indices: 478729--478763 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
478719 CATGAAATTG
*
478729 TATTATATGATATTGTAA
1 TATTATATAATATTGTAA
478747 TATTATATAATATTGTA
1 TATTATATAATATTGTA
478764 TCATACGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
TATTATATAATATTGTAA
Found at i:478760 original size:98 final size:97
Alignment explanation
Indices: 478641--478863 Score: 305
Period size: 98 Copynumber: 2.3 Consensus size: 97
478631 CTATGATACA
*
478641 ATATTGT-ATATTCTATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTCAGTA-A
1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTT-A-TAGA
478704 TATAGAAT-TATATCACATGAAATTGTATTATATG
64 TATAGAATCT-TATCACATGAAATTGTATTATATG
* *
478738 ATATTGTAATATTATATAATATTGTATCATACGATATTGTATGATATGATATTGGTTTATATGAT
1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTATA-GAT
** *
478803 ATATTATCTTATCACATGAAGTTGTATTATATG
65 ATAGAATCTTATCACATGAAATTGTATTATATG
*
478836 ATATTGTAATA-TATAT--TATTGTGTCATA
1 ATATTGTAATATTATATAATATTGTATCATA
478864 TGATACAATA
Statistics
Matches: 115, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
95 11 0.10
96 2 0.02
97 13 0.11
98 88 0.77
99 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.46
Consensus pattern (97 bp):
ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTATAGATA
TAGAATCTTATCACATGAAATTGTATTATATG
Found at i:478842 original size:15 final size:15
Alignment explanation
Indices: 478720--478868 Score: 90
Period size: 15 Copynumber: 9.4 Consensus size: 15
478710 ATTATATCAC
*
478720 ATGAAATTGTATTAT
1 ATGATATTGTATTAT
478735 ATGATATTGTAATATTAT
1 ATGATATTG---TATTAT
* *
478753 ATAATATTGTATCAT
1 ATGATATTGTATTAT
* *
478768 ACGATATTGTATGAT
1 ATGATATTGTATTAT
478783 ATGATATTGGT-TTAT
1 ATGATATT-GTATTAT
478798 ATGATATAT-TATCTTAT
1 ATGATAT-TGTA--TTAT
478815 CACATGA-AGTTGTATTAT
1 ---ATGATA-TTGTATTAT
*
478833 ATGATATTGTAATAT
1 ATGATATTGTATTAT
* *
478848 AT-ATTATTGTGTCAT
1 ATGA-TATTGTATTAT
478863 ATGATA
1 ATGATA
478869 CAATATGTAT
Statistics
Matches: 106, Mismatches: 12, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
14 2 0.02
15 68 0.64
16 5 0.05
17 4 0.04
18 18 0.17
19 2 0.02
20 7 0.07
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (15 bp):
ATGATATTGTATTAT
Found at i:478893 original size:15 final size:15
Alignment explanation
Indices: 478873--478902 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
478863 ATGATACAAT
478873 ATGTATAATATAATA
1 ATGTATAATATAATA
*
478888 ATGTATTATATAATA
1 ATGTATAATATAATA
478903 TTTTGCTTTA
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:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
ATGTATAATATAATA
Found at i:485836 original size:23 final size:24
Alignment explanation
Indices: 485809--485856 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
485799 CCTTGCTACA
*
485809 ATGATACATTTAAAAGTTG-TATG
1 ATGATACATTCAAAAGTTGTTATG
485832 ATGATACATTCAAAAGTTGTTATG
1 ATGATACATTCAAAAGTTGTTATG
485856 A
1 A
485857 CGAAACGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (24 bp):
ATGATACATTCAAAAGTTGTTATG
Found at i:488866 original size:17 final size:18
Alignment explanation
Indices: 488827--488867 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
488817 TCAGGTTAGC
488827 TCAAATTTTCAGGTCCAT
1 TCAAATTTTCAGGTCCAT
* *
488845 ACAAATTTTCA-GTCCTT
1 TCAAATTTTCAGGTCCAT
488862 TCAAAT
1 TCAAAT
488868 GTTTGCGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (18 bp):
TCAAATTTTCAGGTCCAT
Found at i:489034 original size:16 final size:16
Alignment explanation
Indices: 489013--489043 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
489003 GTTCATGTCA
489013 TTCAGGTCTGTAGTAT
1 TTCAGGTCTGTAGTAT
*
489029 TTCAGGTCTTTAGTA
1 TTCAGGTCTGTAGTA
489044 CATGTATGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (16 bp):
TTCAGGTCTGTAGTAT
Found at i:494337 original size:2 final size:2
Alignment explanation
Indices: 494330--494379 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
494320 AAAGAAAAAC
*
494330 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
494372 GA GA GA GA
1 GA GA GA GA
494380 TTTATTTCTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:498437 original size:21 final size:21
Alignment explanation
Indices: 498430--498502 Score: 146
Period size: 21 Copynumber: 3.5 Consensus size: 21
498420 CAATAGTAAT
498430 ATCATTATATGCAGTGCTAAC
1 ATCATTATATGCAGTGCTAAC
498451 ATCATTATATGCAGTGCTAAC
1 ATCATTATATGCAGTGCTAAC
498472 ATCATTATATGCAGTGCTAAC
1 ATCATTATATGCAGTGCTAAC
498493 ATCATTATAT
1 ATCATTATAT
498503 ACTATTATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (21 bp):
ATCATTATATGCAGTGCTAAC
Found at i:498460 original size:42 final size:42
Alignment explanation
Indices: 498413--498502 Score: 146
Period size: 42 Copynumber: 2.1 Consensus size: 42
498403 GGTAAATTTT
*
498413 TTATATGCAATAG-TAATATCATTATATGCAGTGCTAACATCA
1 TTATATGCAAT-GCTAACATCATTATATGCAGTGCTAACATCA
*
498455 TTATATGCAGTGCTAACATCATTATATGCAGTGCTAACATCA
1 TTATATGCAATGCTAACATCATTATATGCAGTGCTAACATCA
498497 TTATAT
1 TTATAT
498503 ACTATTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 44 0.98
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (42 bp):
TTATATGCAATGCTAACATCATTATATGCAGTGCTAACATCA
Found at i:499651 original size:4 final size:4
Alignment explanation
Indices: 499644--499783 Score: 77
Period size: 4 Copynumber: 34.5 Consensus size: 4
499634 CAGTCAATAA
* * * *
499644 TCAG TCAG ACTG TCAG TCAG TCAG TCAG TCAA TCAG TCAAT TACATG T-AG
1 TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TC-AG T-CA-G TCAG
* * * * *
499694 -CTAG TCAG TCAG TCAA TCAG TCAG ACTG TCAG TCAA TCAG TCAG TTAG
1 TC-AG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG
* ** * * * * *
499742 ACTT TCAG TCAG TTAG ACTG TCAG TCAG ACAG TCCG TCAG TC
1 TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TC
499784 CTGGGGTTTT
Statistics
Matches: 96, Mismatches: 34, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
3 1 0.01
4 89 0.93
5 4 0.04
6 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (4 bp):
TCAG
Found at i:500644 original size:21 final size:22
Alignment explanation
Indices: 500618--500702 Score: 149
Period size: 21 Copynumber: 4.0 Consensus size: 22
500608 TGCGTCTTTT
500618 TACCCCAATGA-ACCCCAATGA
1 TACCCCAATGATACCCCAATGA
500639 TACCCCAATGA-ACCCCAATGA
1 TACCCCAATGATACCCCAATGA
500660 TACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA
500682 -ACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA
500703 ACTTTGAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
21 53 0.84
22 10 0.16
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (22 bp):
TACCCCAATGATACCCCAATGA
Found at i:500645 original size:11 final size:11
Alignment explanation
Indices: 500618--500702 Score: 149
Period size: 11 Copynumber: 8.0 Consensus size: 11
500608 TGCGTCTTTT
500618 TACCCCAATGA
1 TACCCCAATGA
500629 -ACCCCAATGA
1 TACCCCAATGA
500639 TACCCCAATGA
1 TACCCCAATGA
500650 -ACCCCAATGA
1 TACCCCAATGA
500660 TACCCCAATGA
1 TACCCCAATGA
500671 TACCCCAATGA
1 TACCCCAATGA
500682 -ACCCCAATGA
1 TACCCCAATGA
500692 TACCCCAATGA
1 TACCCCAATGA
500703 ACTTTGAAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
10 30 0.42
11 41 0.58
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (11 bp):
TACCCCAATGA
Found at i:500670 original size:32 final size:32
Alignment explanation
Indices: 500618--500704 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
500608 TGCGTCTTTT
500618 TACCCCAATGA-ACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA-ACCCCAATGA
500650 -ACCCCAATGATACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA-ACCCCAATGA
500682 -ACCCCAATGATACCCCAATGAAC
1 TACCCCAATGATACCCCAATGAAC
500705 TTTGAAATAC
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
31 12 0.22
32 42 0.78
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (32 bp):
TACCCCAATGATACCCCAATGAACCCCAATGA
Found at i:501459 original size:11 final size:11
Alignment explanation
Indices: 501436--501593 Score: 161
Period size: 11 Copynumber: 15.0 Consensus size: 11
501426 ATTTCAAAGT
*
501436 TCATTAGGGTA
1 TCATTGGGGTA
*
501447 TCATTGGGATA
1 TCATTGGGGTA
*
501458 TCATT-TGGTA
1 TCATTGGGGTA
*
501468 TCATAGGGGTA
1 TCATTGGGGTA
* *
501479 TAATTAGGTGT-
1 TCATT-GGGGTA
*
501490 T--TTTGGGTA
1 TCATTGGGGTA
501499 TCATTGGGGTA
1 TCATTGGGGTA
*
501510 ACATTGGGGT-
1 TCATTGGGGTA
501520 TCATTGGGGTA
1 TCATTGGGGTA
501531 TCATTGGGGT-
1 TCATTGGGGTA
501541 TCATTGGGGTA
1 TCATTGGGGTA
501552 TCATTGGGGT-
1 TCATTGGGGTA
*
501562 TCATTGGAGTA
1 TCATTGGGGTA
501573 TCATTGGGGT-
1 TCATTGGGGTA
*
501583 TCATTTGGGTA
1 TCATTGGGGTA
501594 AAAAGACGCA
Statistics
Matches: 121, Mismatches: 17, Indels: 18
0.78 0.11 0.12
Matches are distributed among these distances:
8 3 0.02
9 3 0.02
10 44 0.36
11 67 0.55
12 4 0.03
ACGTcount: A:0.20, C:0.08, G:0.33, T:0.39
Consensus pattern (11 bp):
TCATTGGGGTA
Found at i:501468 original size:21 final size:20
Alignment explanation
Indices: 501434--501593 Score: 151
Period size: 21 Copynumber: 7.6 Consensus size: 20
501424 ATATTTCAAA
501434 GTTCATTAGGGTATCATTGGG
1 GTTCATT-GGGTATCATTGGG
* * *
501455 ATATCATTTGGTATCATAGGG
1 GT-TCATTGGGTATCATTGGG
* * * * *
501476 GTATAATTAGGTGT-TTTTGG
1 GT-TCATTGGGTATCATTGGG
*
501496 GTATCATTGGGGTAACATTGGG
1 GT-TCATT-GGGTATCATTGGG
501518 GTTCATTGGGGTATCATTGGG
1 GTTCATT-GGGTATCATTGGG
501539 GTTCATTGGGGTATCATTGGG
1 GTTCATT-GGGTATCATTGGG
501560 GTTCATTGGAGTATCATTGGG
1 GTTCATTGG-GTATCATTGGG
501581 GTTCATTTGGGTA
1 GTTCA-TTGGGTA
501594 AAAAGACGCA
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
20 12 0.10
21 90 0.77
22 15 0.13
ACGTcount: A:0.19, C:0.08, G:0.33, T:0.39
Consensus pattern (20 bp):
GTTCATTGGGTATCATTGGG
Found at i:502378 original size:7 final size:7
Alignment explanation
Indices: 502366--502405 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
502356 ATCTGCTACC
502366 AATAAAA
1 AATAAAA
502373 AATAAAA
1 AATAAAA
*
502380 ATTAAAA
1 AATAAAA
502387 AATAAAA
1 AATAAAA
*
502394 AGTAAAA
1 AATAAAA
502401 AATAA
1 AATAA
502406 CAAACCACCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (7 bp):
AATAAAA
Found at i:503995 original size:10 final size:10
Alignment explanation
Indices: 503977--504031 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
503967 GATTCTGATA
503977 CACGAACGAT
1 CACGAACGAT
*
503987 CACGCACGAT
1 CACGAACGAT
503997 ACACGAACGAT
1 -CACGAACGAT
*
504008 CACGCACGAT
1 CACGAACGAT
*
504018 ACACGGACGAT
1 -CACGAACGAT
504029 CAC
1 CAC
504032 TAACTTACTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 21 0.54
11 18 0.46
ACGTcount: A:0.36, C:0.35, G:0.20, T:0.09
Consensus pattern (10 bp):
CACGAACGAT
Found at i:503997 original size:21 final size:21
Alignment explanation
Indices: 503973--504031 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
503963 GCACGATTCT
503973 GATACACGAACGATCACGCAC
1 GATACACGAACGATCACGCAC
503994 GATACACGAACGATCACGCAC
1 GATACACGAACGATCACGCAC
*
504015 GATACACGGACGATCAC
1 GATACACGAACGATCAC
504032 TAACTTACTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.32, G:0.20, T:0.10
Consensus pattern (21 bp):
GATACACGAACGATCACGCAC
Found at i:504006 original size:11 final size:11
Alignment explanation
Indices: 503973--504028 Score: 71
Period size: 11 Copynumber: 5.3 Consensus size: 11
503963 GCACGATTCT
503973 GATACACGAAC
1 GATACACGAAC
*
503984 GAT-CACGCAC
1 GATACACGAAC
503994 GATACACGAAC
1 GATACACGAAC
*
504005 GAT-CACGCAC
1 GATACACGAAC
*
504015 GATACACGGAC
1 GATACACGAAC
504026 GAT
1 GAT
504029 CACTAACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 18 0.46
11 21 0.54
ACGTcount: A:0.38, C:0.30, G:0.21, T:0.11
Consensus pattern (11 bp):
GATACACGAAC
Found at i:505068 original size:21 final size:21
Alignment explanation
Indices: 505043--505096 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
505033 ATTTTCCTGA
*
505043 TACACGCACGATC-CCGCACGT
1 TACACGAACGATCACC-CACGT
505064 TACACGAACGATCACCCACGT
1 TACACGAACGATCACCCACGT
505085 TACACGAACGAT
1 TACACGAACGAT
505097 TTAACACGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.31, C:0.37, G:0.17, T:0.15
Consensus pattern (21 bp):
TACACGAACGATCACCCACGT
Found at i:508193 original size:32 final size:32
Alignment explanation
Indices: 508147--508378 Score: 337
Period size: 32 Copynumber: 7.3 Consensus size: 32
508137 TGCATGTTAA
*
508147 TTTAACAGTTATGCCCCAACCATTTAGGGGAC
1 TTTAACAGTCATGCCCCAACCATTTAGGGGAC
* *
508179 TTTAATAGCCATGCCCCAACCATTTAGGGGAC
1 TTTAACAGTCATGCCCCAACCATTTAGGGGAC
*
508211 TTAAACAGTCATGCCCCAACCATTTA-GGGACC
1 TTTAACAGTCATGCCCCAACCATTTAGGGGA-C
508243 TTTAACAGTCATGCCCCAACCATTTAGGGGAC
1 TTTAACAGTCATGCCCCAACCATTTAGGGGAC
* * *
508275 TTTAACAATAATGCCCCAACCATTAAGGGGAC
1 TTTAACAGTCATGCCCCAACCATTTAGGGGAC
* *
508307 TTTAACAATCATGCCTCAACCATTTAGGGGAC
1 TTTAACAGTCATGCCCCAACCATTTAGGGGAC
508339 TTTAAGC-GTCATGCCCCAACCATTTAGGGGAC
1 TTTAA-CAGTCATGCCCCAACCATTTAGGGGAC
508371 --TAACAGTC
1 TTTAACAGTC
508379 TTGGTTAAAC
Statistics
Matches: 181, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
29 1 0.01
30 6 0.03
31 4 0.02
32 165 0.91
33 5 0.03
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (32 bp):
TTTAACAGTCATGCCCCAACCATTTAGGGGAC
Found at i:526299 original size:1 final size:1
Alignment explanation
Indices: 526293--526317 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
526283 TGTTTCCGGA
526293 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
526318 AAAGACCCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:527970 original size:42 final size:42
Alignment explanation
Indices: 527907--527992 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
527897 TCTAATGTAG
* * * * *
527907 TGGAACCAAGATTTTTTTTTCTTGATGTTGTTCTGTTTAGTC
1 TGGAACCAAGAGTTATCTTTCTTGATATTGTTCTGTATAGTC
*
527949 TGGAACCAAGAGTTATCTTTCTTGATATTGTTTTGTATAGTC
1 TGGAACCAAGAGTTATCTTTCTTGATATTGTTCTGTATAGTC
527991 TG
1 TG
527993 AGAGTTATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49
Consensus pattern (42 bp):
TGGAACCAAGAGTTATCTTTCTTGATATTGTTCTGTATAGTC
Found at i:572903 original size:2 final size:2
Alignment explanation
Indices: 572896--572920 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
572886 NNNNNNNNNN
572896 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
572921 AACAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:576423 original size:11 final size:11
Alignment explanation
Indices: 576415--576445 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
576405 ACTGGAGTGG
576415 ACCCAGAGTAA
1 ACCCAGAGTAA
*
576426 ACCCAAAGTAA
1 ACCCAGAGTAA
576437 ACCCAGAGT
1 ACCCAGAGT
576446 GGACACAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.29, G:0.16, T:0.10
Consensus pattern (11 bp):
ACCCAGAGTAA
Found at i:579100 original size:20 final size:21
Alignment explanation
Indices: 579060--579101 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
579050 AAGCGACGAA
579060 AATCGACTCCCCCATGCGTTAG
1 AATCGACTCCCCCA-GCGTTAG
579082 AATCGACTCCCCC-GCGTTAG
1 AATCGACTCCCCCAGCGTTAG
579102 GGGTTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (21 bp):
AATCGACTCCCCCAGCGTTAG
Found at i:583271 original size:18 final size:17
Alignment explanation
Indices: 583224--583271 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
583214 TCTCTCGACA
*
583224 GTTTTTTTTTTGCTTTT
1 GTTTTTTTTTTGTTTTT
583241 GTTTTTTTTTTGTTTTT
1 GTTTTTTTTTTGTTTTT
583258 GTTTTTTGTTTTGT
1 GTTTTTT-TTTTGT
583272 CAATTGCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 23 0.79
18 6 0.21
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (17 bp):
GTTTTTTTTTTGTTTTT
Found at i:586480 original size:4 final size:4
Alignment explanation
Indices: 586471--586517 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
586461 TTACATAACT
586471 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
586518 TATATATANT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:589209 original size:15 final size:15
Alignment explanation
Indices: 589189--589220 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
589179 GCCAAAGCTA
589189 TATGAGGCGCCGTTT
1 TATGAGGCGCCGTTT
589204 TATGAGGCGCCGTTT
1 TATGAGGCGCCGTTT
589219 TA
1 TA
589221 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.31, T:0.34
Consensus pattern (15 bp):
TATGAGGCGCCGTTT
Found at i:589305 original size:20 final size:20
Alignment explanation
Indices: 589277--589464 Score: 155
Period size: 20 Copynumber: 9.0 Consensus size: 20
589267 CAATAATTCG
* *
589277 AATTATTGATACCAGAAAAT
1 AATTCTTGATATCAGAAAAT
*
589297 AATTCTTGATATCAAAAAAT
1 AATTCTTGATATCAGAAAAT
589317 AATTCTTGATATCCA-AAAATCT
1 AATTCTTGATAT-CAGAAAA--T
* *
589339 ATTTTTTGTGATATCAGAAAAT
1 A-ATTCT-TGATATCAGAAAAT
* *
589361 AATTCTTGATTTCAAAAAAAT
1 AATTCTTGATATC-AGAAAAT
589382 AATTCTTGATATCA-AAAAT
1 AATTCTTGATATCAGAAAAT
* *
589401 CTATTTTGTGATATCAGAAAAT
1 -AATTCT-TGATATCAGAAAAT
* * *
589423 AATTTTTGATATCACAAATT
1 AATTCTTGATATCAGAAAAT
*
589443 CGAATTCTTGATATCAAAAAAT
1 --AATTCTTGATATCAGAAAAT
589465 GTGATTTTCT
Statistics
Matches: 138, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
19 5 0.04
20 56 0.41
21 36 0.26
22 26 0.19
23 5 0.04
24 10 0.07
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.38
Consensus pattern (20 bp):
AATTCTTGATATCAGAAAAT
Found at i:589358 original size:64 final size:62
Alignment explanation
Indices: 589240--589487 Score: 270
Period size: 62 Copynumber: 3.9 Consensus size: 62
589230 AAGTATTTTC
* * * *
589240 TGATATCAAAAAATAAATAT-TTGATAT-CAATAATTCGAATTAT-TGATACCAGAAAATAATTC
1 TGATATCAAAAAAT-AAT-TCTTGATATCCAA-AAATC-TATTTTGTGATATCAGAAAATAATTC
589302 T
62 T
589303 TGATATCAAAAAATAATTCTTGATATCCAAAAATCTATTTTTTGTGATATCAGAAAATAATTCT
1 TGATATCAAAAAATAATTCTTGATATCCAAAAATCTA--TTTTGTGATATCAGAAAATAATTCT
* *
589367 TGATTTCAAAAAAATAATTCTTGATAT-CAAAAATCTATTTTGTGATATCAGAAAATAATTTT
1 TGATATC-AAAAAATAATTCTTGATATCCAAAAATCTATTTTGTGATATCAGAAAATAATTCT
* * * * * *
589429 TGATATCACAAATTCGAATTCTTGATATCAAAAAATGTGATTTTCTGATATCACAAAAT
1 TGATATCAAAAAAT--AATTCTTGATATCCAAAAATCT-ATTTTGTGATATCAGAAAAT
589488 GGATTTTTTG
Statistics
Matches: 162, Mismatches: 13, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
61 7 0.04
62 44 0.27
63 32 0.20
64 42 0.26
65 37 0.23
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (62 bp):
TGATATCAAAAAATAATTCTTGATATCCAAAAATCTATTTTGTGATATCAGAAAATAATTCT
Found at i:589448 original size:22 final size:21
Alignment explanation
Indices: 589234--589503 Score: 83
Period size: 20 Copynumber: 12.6 Consensus size: 21
589224 TTTTTAAAGT
* * *
589234 ATTTTCTGATATCAAAAAATAA
1 ATTTT-TGATATCACAAATTGA
*
589256 ATATTTGATATCA-ATAATTCGA
1 ATTTTTGATATCACA-AATT-GA
* * * *
589278 ATTATTGATACCAGAAAAT-A
1 ATTTTTGATATCACAAATTGA
* * *
589298 ATTCTTGATATCAAAAAAT-A
1 ATTTTTGATATCACAAATTGA
* *
589318 ATTCTTGATATCCAAAAATCT-A
1 ATTTTTGATAT-CACAAAT-TGA
* * *
589340 TTTTTTGTGATATCAGAAAAT-A
1 -ATTTT-TGATATCACAAATTGA
* * * *
589362 ATTCTTGATTTCAAAAAAAT-A
1 ATTTTTGATATC-ACAAATTGA
* *
589383 ATTCTTGATATCAAAAATCT--
1 ATTTTTGATATCACAAAT-TGA
* *
589403 ATTTTGTGATATCAGAAAAT-A
1 ATTTT-TGATATCACAAATTGA
589424 ATTTTTGATATCACAAATTCGA
1 ATTTTTGATATCACAAATT-GA
* *
589446 ATTCTTGATATCAAAAAATGTG-
1 ATTTTTGATATC-ACAAAT-TGA
*
589468 ATTTTCTGATATCACAAAATGGA
1 ATTTT-TGATATCAC-AAATTGA
*
589491 TTTTTTGATATCA
1 ATTTTTGATATCA
589504 AGAATTAAAG
Statistics
Matches: 198, Mismatches: 32, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
20 58 0.29
21 55 0.28
22 48 0.24
23 30 0.15
24 7 0.04
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (21 bp):
ATTTTTGATATCACAAATTGA
Found at i:589477 original size:23 final size:22
Alignment explanation
Indices: 589388--589504 Score: 89
Period size: 22 Copynumber: 5.4 Consensus size: 22
589378 AAATAATTCT
** *
589388 TGATATC-AAAAATCTATTTTG
1 TGATATCAAAAAATGGATTTTC
* *
589409 TGATATCAGAAAAT-AATTTT-
1 TGATATCAAAAAATGGATTTTC
* * * *
589429 TGATATCACAAATTCGA-ATTC
1 TGATATCAAAAAATGGATTTTC
589450 TTGATATCAAAAAATGTGATTTTC
1 -TGATATCAAAAAATG-GATTTTC
* *
589474 TGATATCACAAAATGGATTTTT
1 TGATATCAAAAAATGGATTTTC
589496 TGATATCAA
1 TGATATCAA
589505 GAATTAAAGT
Statistics
Matches: 77, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
20 14 0.18
21 13 0.17
22 31 0.40
23 16 0.21
24 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (22 bp):
TGATATCAAAAAATGGATTTTC
Found at i:589499 original size:45 final size:42
Alignment explanation
Indices: 589234--589504 Score: 176
Period size: 42 Copynumber: 6.4 Consensus size: 42
589224 TTTTTAAAGT
* * *
589234 ATTTTCTGATATCAAAAAATAAATATTTGATATCA-ATAATTCG
1 ATTTTTTGATATCAAAAAAT-AATTTTTGATATCACA-AAATCG
* * * * * *
589277 AATTATTGATACCAGAAAATAATTCTTGATATCAAAAAAT--
1 ATTTTTTGATATCAAAAAATAATTTTTGATATCACAAAATCG
* * * * *
589317 AATTCTTGATATCCAAAAATCTATTTTTTGTGATATCAGAAAAT--
1 ATTTTTTGATAT-CAAAAA-ATA-ATTTT-TGATATCACAAAATCG
* * * * *
589361 AATTCTTGATTTCAAAAAAATAATTCTTGATATCA-AAAATCT
1 ATTTTTTGATATC-AAAAAATAATTTTTGATATCACAAAATCG
* * *
589403 ATTTTGTGATATCAGAAAATAATTTTTGATATCACAAATTCG
1 ATTTTTTGATATCAAAAAATAATTTTTGATATCACAAAATCG
* * * *
589445 AATTCTTGATATCAAAAAATGTGATTTTCTGATATCACAAAATGG
1 ATTTTTTGATATCAAAAAA--TAATTTT-TGATATCACAAAATCG
589490 ATTTTTTGATATCAA
1 ATTTTTTGATATCAA
589505 GAATTAAAGT
Statistics
Matches: 180, Mismatches: 36, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
40 15 0.08
41 32 0.18
42 49 0.27
43 22 0.12
44 35 0.19
45 27 0.15
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (42 bp):
ATTTTTTGATATCAAAAAATAATTTTTGATATCACAAAATCG
Found at i:589580 original size:21 final size:22
Alignment explanation
Indices: 589527--589580 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
589517 GGGTTTTTTA
* *
589527 ATATCAAAAAATGATTTTCTTG
1 ATATCAAAAAATCATTCTCTTG
** *
589549 ATATCCGAAAATCCTTCT-TTG
1 ATATCAAAAAATCATTCTCTTG
589570 ATATCAAAAAA
1 ATATCAAAAAA
589581 ATCGTCAGAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (22 bp):
ATATCAAAAAATCATTCTCTTG
Found at i:589657 original size:22 final size:22
Alignment explanation
Indices: 589622--589665 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
589612 AATCATTTGT
*
589622 ATTTTCTGAAATCAGAAGATAA
1 ATTTTCTGAAATCAGAAAATAA
* *
589644 ATTTTTTGATATCAGAAAATAA
1 ATTTTCTGAAATCAGAAAATAA
589666 GACCTACAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (22 bp):
ATTTTCTGAAATCAGAAAATAA
Found at i:599503 original size:32 final size:32
Alignment explanation
Indices: 599465--599539 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
599455 GCCATCTTTT
599465 CCCCCGGAAAAATGGCTATATAGCAGTTCTTC
1 CCCCCGGAAAAATGGCTATATAGCAGTTCTTC
*
599497 CCCCCGGAAAAATGGCTATATAGCAGTTTTTC
1 CCCCCGGAAAAATGGCTATATAGCAGTTCTTC
599529 CCCCACGGAAA
1 CCCC-CGGAAA
599540 GCTGACTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 35 0.85
33 6 0.15
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (32 bp):
CCCCCGGAAAAATGGCTATATAGCAGTTCTTC
Found at i:599549 original size:33 final size:32
Alignment explanation
Indices: 599465--599552 Score: 122
Period size: 32 Copynumber: 2.7 Consensus size: 32
599455 GCCATCTTTT
*
599465 CCCCCGGAAAAATGGCTATATAGCAGTTCTTC
1 CCCCCGGAAAAATGACTATATAGCAGTTCTTC
* *
599497 CCCCCGGAAAAATGGCTATATAGCAGTTTTTC
1 CCCCCGGAAAAATGACTATATAGCAGTTCTTC
**
599529 CCCCACGGAAAGCTGACTATATAG
1 CCCC-CGGAAAAATGACTATATAG
599553 TGGGCTTTCC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 35 0.69
33 16 0.31
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (32 bp):
CCCCCGGAAAAATGACTATATAGCAGTTCTTC
Found at i:600406 original size:4 final size:4
Alignment explanation
Indices: 600397--600442 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
600387 AAACGTGACA
*
600397 GACG GACG GACG GACG GACG GACA GACG GACG GACG GACG GACG GA
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GA
600443 ACAGGGTAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.48, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:617396 original size:56 final size:56
Alignment explanation
Indices: 617285--617397 Score: 127
Period size: 56 Copynumber: 2.0 Consensus size: 56
617275 CTGATATATT
* * ** * * *
617285 CTCCCTCCTCTTGATTTCACTGAGCAAATATAATGGCGGTGTAATGTTCACATAAA
1 CTCCCTCCTCTTGATTTCACTCAGCAAATACAATAACGATGAAATATTCACATAAA
* * * *
617341 CTCCCTCCTCTTGATTTCACTCAGCAGATGCAATAATGATGAAATATTCATATAAA
1 CTCCCTCCTCTTGATTTCACTCAGCAAATACAATAACGATGAAATATTCACATAAA
617397 C
1 C
617398 ATATAATCTA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (56 bp):
CTCCCTCCTCTTGATTTCACTCAGCAAATACAATAACGATGAAATATTCACATAAA
Found at i:618605 original size:36 final size:38
Alignment explanation
Indices: 618558--618652 Score: 140
Period size: 36 Copynumber: 2.5 Consensus size: 38
618548 CCAGGTAATC
618558 AGTGTGTTCGAATTGTATGAGAATTCACA-TT-TAGAT
1 AGTGTGTTCGAATTGTATGAGAATTCACATTTATAGAT
* *
618594 AGTGTGTTCGAATTGTATAAGAATTTACATTTACTAGAT
1 AGTGTGTTCGAATTGTATGAGAATTCACATTTA-TAGAT
*
618633 AGTGTGTTCGAACTGTATGA
1 AGTGTGTTCGAATTGTATGA
618653 AAAGTGGAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
36 27 0.52
37 2 0.04
39 23 0.44
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (38 bp):
AGTGTGTTCGAATTGTATGAGAATTCACATTTATAGAT
Found at i:627985 original size:91 final size:91
Alignment explanation
Indices: 627825--627993 Score: 241
Period size: 91 Copynumber: 1.9 Consensus size: 91
627815 ATATCGAACA
* * * * *
627825 TGACCTAGATATTATCATAATGAATCTGTATACCAAATTTCATTTCAATATCCTCAACTCCTGCA
1 TGACCTAGATATTATCATAATAAATCTGAACACAAAATTTCATTTCAATATACTCAACTCCTGCA
627890 AAGAAAATGAACGAAAACTGCACACT
66 AAGAAAATGAACGAAAACTGCACACT
* * *
627916 TGACCTAGATATTATCATGATAAATCTGAACACAAAATTTCATTTCAATATATTCATC-CTCTGC
1 TGACCTAGATATTATCATAATAAATCTGAACACAAAATTTCATTTCAATATACTCAACTC-CTGC
*
627980 GAAGAAAATGAACG
65 AAAGAAAATGAACG
627994 GAAGCTGTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
90 1 0.01
91 67 0.99
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.30
Consensus pattern (91 bp):
TGACCTAGATATTATCATAATAAATCTGAACACAAAATTTCATTTCAATATACTCAACTCCTGCA
AAGAAAATGAACGAAAACTGCACACT
Found at i:629613 original size:159 final size:159
Alignment explanation
Indices: 629324--629642 Score: 478
Period size: 159 Copynumber: 2.0 Consensus size: 159
629314 ATATTTTTTG
*
629324 TCTGCTTTAATCTGCACTGAATGTTGTCTAAAAGAAAAACTGCCTGAAAGCCGTTTTATGCTAAA
1 TCTGCTTTAACCTGCACTGAATGTTGTCTAAAAGAAAAACTGCCTGAAAGCCGTTTTATGCTAAA
* * *
629389 AATAACAGGAAGGATTTCACTTCACGATGTTATATTTCTTGATTAATTTATAACATTTTGTATCG
66 AATAACAGGAAGGAGTTCACTTCACGATGTTATATTTCTTGATTAATTTATAACATATTATATCG
* * *
629454 TTAAGTCTAAAAAAACTACAGTATACCGA
131 TTAAGCCTAAAAAAACTACAATACACCGA
* *
629483 TCTGCTTTAACCTGCACTGAATGTTGTCTAAAAGAAAAATTGCTTGAAAGCCGTTTTATGCTAAA
1 TCTGCTTTAACCTGCACTGAATGTTGTCTAAAAGAAAAACTGCCTGAAAGCCGTTTTATGCTAAA
* * * * * *
629548 AATAGCGGGAGGGAGTTCACTTTATGATGTTATATTTCTTGATTAATTT-TCAGCATATTATATC
66 AATAACAGGAAGGAGTTCACTTCACGATGTTATATTTCTTGATTAATTTAT-AACATATTATATC
*
629612 GTTAAGCCTCAAAAAACTACAATACACCGA
130 GTTAAGCCTAAAAAAACTACAATACACCGA
629642 T
1 T
629643 AACAAATATT
Statistics
Matches: 143, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
158 1 0.01
159 142 0.99
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (159 bp):
TCTGCTTTAACCTGCACTGAATGTTGTCTAAAAGAAAAACTGCCTGAAAGCCGTTTTATGCTAAA
AATAACAGGAAGGAGTTCACTTCACGATGTTATATTTCTTGATTAATTTATAACATATTATATCG
TTAAGCCTAAAAAAACTACAATACACCGA
Found at i:639471 original size:18 final size:18
Alignment explanation
Indices: 639448--639483 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
639438 CATTTTTTCA
*
639448 TACAGTTATAGACCACAG
1 TACAGTTAAAGACCACAG
639466 TACAGTTAAAGACCACAG
1 TACAGTTAAAGACCACAG
639484 CCCGCATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (18 bp):
TACAGTTAAAGACCACAG
Found at i:652201 original size:2 final size:2
Alignment explanation
Indices: 652196--652245 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
652186 ATTCTTCTTG
* *
652196 AT AT AT AA AT AT AT AT AT AT AT AT NT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
652238 AT AT AT AT
1 AT AT AT AT
652246 CAATATAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:652251 original size:12 final size:11
Alignment explanation
Indices: 652196--652257 Score: 67
Period size: 10 Copynumber: 5.7 Consensus size: 11
652186 ATTCTTCTTG
652196 ATATATA-AAT
1 ATATATATAAT
652206 ATATATAT-AT
1 ATATATATAAT
*
652216 ATATNTAT-AT
1 ATATATATAAT
652226 ATATATATATAT
1 ATATATATA-AT
652238 ATATATATCAAT
1 ATATATAT-AAT
*
652250 ATAAATAT
1 ATATATAT
652258 TTACAAAGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
10 25 0.56
12 19 0.42
13 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATATATAAT
Found at i:661502 original size:12 final size:12
Alignment explanation
Indices: 661485--661511 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
661475 ATAACATGAG
661485 TTTAATACAAAC
1 TTTAATACAAAC
661497 TTTAATACAAAC
1 TTTAATACAAAC
661509 TTT
1 TTT
661512 TTTGTCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (12 bp):
TTTAATACAAAC
Found at i:665604 original size:2 final size:2
Alignment explanation
Indices: 665597--665621 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
665587 ACACCTCACG
665597 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
665622 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:666386 original size:2 final size:2
Alignment explanation
Indices: 666379--666421 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
666369 NNNNNNNNNN
666379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
666418 AT AT
1 AT AT
666422 CACATAGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:668219 original size:202 final size:202
Alignment explanation
Indices: 667860--668266 Score: 769
Period size: 202 Copynumber: 2.0 Consensus size: 202
667850 GCAGAAAATA
667860 TATAAGCGAGGTTAAACCGGATGCTATGGGGAAAATTCAGCCTGCGCATGAGCTAGCCTGGTTCC
1 TATAAGCGAGGTTAAACCGGATGCTATGGGGAAAATTCAGCCTGCGCATGAGCTAGCCTGGTTCC
*
667925 TGTGCGTCATGGGTAGCTCAGGGAACCAGGCTAGCACACGTTTATCTGAATCGGTATCGGGATTC
66 TGTGCGTAATGGGTAGCTCAGGGAACCAGGCTAGCACACGTTTATCTGAATCGGTATCGGGATTC
* *
667990 CGTGCCATATGCACGCATAAGTTCAAAGGCATTTTAATTGTAAAGTTGTCAGTAAACAGTACAAA
131 CGTGCCATATGCACACATAAGTTCAAAGGCATTGTAATTGTAAAGTTGTCAGTAAACAGTACAAA
668055 AACAAAG
196 AACAAAG
668062 TATAAGCGAGGTTAAACCGGATGCTATGGGGAAAATTCAGCCTGCGCATGAGCTAGCCTGGTTCC
1 TATAAGCGAGGTTAAACCGGATGCTATGGGGAAAATTCAGCCTGCGCATGAGCTAGCCTGGTTCC
668127 TGTGCGTAATGGGTAGCTCAGGGAACCAGGCTAGCACACGTTTATCTGAATCGGTATCGGGATTC
66 TGTGCGTAATGGGTAGCTCAGGGAACCAGGCTAGCACACGTTTATCTGAATCGGTATCGGGATTC
* *
668192 CGTGCCATATGCACACATAATTTCAAAGGCATTGTAATTGTAAAGTTGTCAGTAAACAGTACAGA
131 CGTGCCATATGCACACATAAGTTCAAAGGCATTGTAATTGTAAAGTTGTCAGTAAACAGTACAAA
668257 AACAAAG
196 AACAAAG
668264 TAT
1 TAT
668267 TCCTTTTTAA
Statistics
Matches: 200, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
202 200 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (202 bp):
TATAAGCGAGGTTAAACCGGATGCTATGGGGAAAATTCAGCCTGCGCATGAGCTAGCCTGGTTCC
TGTGCGTAATGGGTAGCTCAGGGAACCAGGCTAGCACACGTTTATCTGAATCGGTATCGGGATTC
CGTGCCATATGCACACATAAGTTCAAAGGCATTGTAATTGTAAAGTTGTCAGTAAACAGTACAAA
AACAAAG
Found at i:672103 original size:168 final size:168
Alignment explanation
Indices: 671623--672445 Score: 1352
Period size: 168 Copynumber: 4.9 Consensus size: 168
671613 CATGTGTTGG
* * *
671623 AGTAGAGAAGAAGATTTTTTAAGATTTAA-ATCATTTTTACTATATGGCCATATTGGCCCCACCC
1 AGTAGAGAAGAAGATTTTCTAAGATTTAATA-CATTTTTACTATTTGGCCATATTGGCCCCTCCC
* * * * * *
671687 CAGAGCATGAA-CACCTTACCCAGGGGTCATGAATTTCACAATTTTA-GTAGAGAGCCTCATGGA
65 TAGAGCCTGAATC-CCTGACCCAGGGGTCATGAATTTCACAA-TTTAGGAAGAGGGCTTCATGGA
*
671750 CATCATAATCATGCATTTAGTTTTTAACAAATATATATGGG
128 CATCATAATCATGCATTTAGTTTTTAACAAATATATATGGT
*
671791 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCC-TGA-CGGCCCCATCC
1 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCAT-ATTGGCCCC-TCC
* *
671854 C-AGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGATGAGGGCTTCATGGAC
64 CTAGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGAC
* * *
671918 ATCATTATCATGCATTTAGGTTTTAACAAATATATATGAT
129 ATCATAATCATGCATTTAGTTTTTAACAAATATATATGGT
671958 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT
1 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT
672023 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT
66 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT
672088 CATAATCATGCATTTAGTTTTTAACAAATATATATGGT
131 CATAATCATGCATTTAGTTTTTAACAAATATATATGGT
672126 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT
1 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT
672191 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT
66 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT
672256 CATAATCATGCATTTAGTTTTTAACAAATATATATGGT
131 CATAATCATGCATTTAGTTTTTAACAAATATATATGGT
*
672294 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCACCCT
1 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT
* * *
672359 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACAT
66 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT
* * *
672424 TATAACCATGCATTCAGTTTTT
131 CATAATCATGCATTTAGTTTTT
672446 TCCTCACATG
Statistics
Matches: 620, Mismatches: 27, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
166 4 0.01
167 147 0.24
168 468 0.75
169 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (168 bp):
AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT
AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT
CATAATCATGCATTTAGTTTTTAACAAATATATATGGT
Found at i:672660 original size:7 final size:7
Alignment explanation
Indices: 672650--672695 Score: 74
Period size: 7 Copynumber: 6.4 Consensus size: 7
672640 AAAATTGTTA
672650 ACGCACG
1 ACGCACG
672657 ACGCACAG
1 ACGCAC-G
672665 ACGCACG
1 ACGCACG
672672 ACGCACG
1 ACGCACG
*
672679 ACGCACA
1 ACGCACG
672686 ACGCACG
1 ACGCACG
672693 ACG
1 ACG
672696 ACGGACGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 29 0.81
8 7 0.19
ACGTcount: A:0.33, C:0.41, G:0.26, T:0.00
Consensus pattern (7 bp):
ACGCACG
Found at i:672702 original size:21 final size:22
Alignment explanation
Indices: 672650--672695 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
672640 AAAATTGTTA
672650 ACGCACGACGCACAGACGCACG
1 ACGCACGACGCACAGACGCACG
672672 ACGCACGACGCACA-ACGCACG
1 ACGCACGACGCACAGACGCACG
672693 ACG
1 ACG
672696 ACGGACGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.33, C:0.41, G:0.26, T:0.00
Consensus pattern (22 bp):
ACGCACGACGCACAGACGCACG
Found at i:682857 original size:172 final size:172
Alignment explanation
Indices: 682560--683356 Score: 1452
Period size: 172 Copynumber: 4.6 Consensus size: 172
682550 GTATCGAGTC
* *
682560 TATCGACCAAGGCTGATTTTCGAACTTGACCAACGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
* *
682625 TAATGAATATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGAT-AAACT
66 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAAC-
* * *
682689 GGGGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
130 GGAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG
*
682732 TATTGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
682797 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
682862 GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG
682904 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
*
682969 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGAATAAAACG
66 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
*
683034 GAGTCGTTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG
683076 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
683141 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
683206 GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG
* *
683248 TATCGACCAATGCTGATTTTCGAACTTGACCAAGATAATAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
* *
683313 TAATGAAAATCCGTCAAAATTTGTAGGCATGAAAGCGCTTACAA
66 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAA
683357 AAAAGTGTGA
Statistics
Matches: 607, Mismatches: 17, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
172 603 0.99
173 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (172 bp):
TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG
Found at i:683381 original size:8 final size:8
Alignment explanation
Indices: 683370--683463 Score: 116
Period size: 8 Copynumber: 11.8 Consensus size: 8
683360 AGTGTGACGG
*
683370 ACGGACGC
1 ACGGACCC
*
683378 ACGGACAC
1 ACGGACCC
* *
683386 ATGGACGC
1 ACGGACCC
683394 ACGGACCC
1 ACGGACCC
*
683402 ACAGACCC
1 ACGGACCC
*
683410 ACGGACAC
1 ACGGACCC
683418 ACGGACCC
1 ACGGACCC
683426 ACGGACCC
1 ACGGACCC
*
683434 ACGGACAC
1 ACGGACCC
683442 ACGGACCC
1 ACGGACCC
*
683450 ACGGACAC
1 ACGGACCC
683458 ACGGAC
1 ACGGAC
683464 GGACGCCCGG
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 74 1.00
ACGTcount: A:0.31, C:0.41, G:0.27, T:0.01
Consensus pattern (8 bp):
ACGGACCC
Found at i:683397 original size:24 final size:24
Alignment explanation
Indices: 683365--683464 Score: 128
Period size: 24 Copynumber: 4.2 Consensus size: 24
683355 AAAAAAGTGT
* * *
683365 GACGGACGGACGCACGGACACATG
1 GACGCACGGACCCACGGACACACG
* *
683389 GACGCACGGACCCACAGACCCACG
1 GACGCACGGACCCACGGACACACG
* *
683413 GACACACGGACCCACGGACCCACG
1 GACGCACGGACCCACGGACACACG
*
683437 GACACACGGACCCACGGACACACG
1 GACGCACGGACCCACGGACACACG
683461 GACG
1 GACG
683465 GACGCCCGGC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.30, C:0.40, G:0.29, T:0.01
Consensus pattern (24 bp):
GACGCACGGACCCACGGACACACG
Found at i:684455 original size:2 final size:2
Alignment explanation
Indices: 684450--684475 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
684440 TCAGTGTGTT
684450 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
684476 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:685827 original size:16 final size:16
Alignment explanation
Indices: 685806--685840 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
685796 AAAATACCCG
685806 GTAATTTGTGAAACTA
1 GTAATTTGTGAAACTA
685822 GTAATTTGTGAAACTA
1 GTAATTTGTGAAACTA
685838 GTA
1 GTA
685841 TTTTTAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (16 bp):
GTAATTTGTGAAACTA
Found at i:686484 original size:16 final size:17
Alignment explanation
Indices: 686463--686495 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
686453 AGATAAGATT
686463 TTCCGTTTTCC-TTCCG
1 TTCCGTTTTCCGTTCCG
686479 TTCCGTTTTCCGTTCCG
1 TTCCGTTTTCCGTTCCG
686496 CGTTTTAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.00, C:0.36, G:0.15, T:0.48
Consensus pattern (17 bp):
TTCCGTTTTCCGTTCCG
Found at i:687289 original size:166 final size:166
Alignment explanation
Indices: 686748--687864 Score: 1460
Period size: 166 Copynumber: 6.7 Consensus size: 166
686738 TATCTCAACC
* * *
686748 ACTATTTTTCGCAGATGCTTGAAATTTTTACACAGT-GTTGTGA-AGGCATGCCATATTGTGGGA
1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGT-ATAGGCATGCCATATCGTGGGA
* * *
686811 TATATTTTTGTACCAATCGGACGTCAACTTCCTGTAAAATGACGACTTTGCTTATTTTTTAACCA
65 TATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTTTTAGCCA
* *
686876 AAATTTTCAAACAAATTTTCGTCAAA-AATTTATTAGCA
129 AAATTTTCAAACAAATTTTCGTCAAAGAA-TTCTCAGCA
* *
686914 ACTATTTATCGCAGATGCTTGAAATTTCTACACAATATTTGTATAGGCATGCCATATCGTGGGAT
1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT
* * * * * * *
686979 AAAATTTTGTACCAATCAGACGTCAACTTCCTGTAAAATGACGACTTTGCTTATTTTTTAACCCA
66 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTTTTAGCCAA
*
687044 AATTTTCAAACAAATTTTTGTCAAAGAATTCTCAGCA
130 AATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA
* *
687081 ACTGTTTATCGCAGATGCTTGAAATTTTTACACAGAATTTGTATAGGCATGCCATATCGTGGGAT
1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT
* * *
687146 ATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATAACGACTTTGTTTATTTTTAGCAAAA
66 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAA
*
687211 ATTTTCAAACAAATTTTTGTCAAAGAATTCTCAGCA
131 ATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA
* * *
687247 ACTGTTTATCGCAGATGTTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATATCGTGGGAT
1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT
* ** * * **
687312 GTATTTTTGTACCAATCAAACGTCAACTTCCTGTTTAATGA-GTACTTTGTTAATTTTTTTCCAA
66 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTTTTAGCCAA
* * * *
687376 AATTTTCAAACAAATTTTTGTTAAAGATTTCTCAGTA
130 AATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA
* * * * * * * *
687413 ACTATTCATCGCATAAGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCATATTGTGGGAT
1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT
* * *
687478 TTATTTTTGTATCAATCGGACGTCAACTCCCTGTTAAAT-ACTGACTTTGTTTA-TTTTAGCCAA
66 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAC-GACTTTGTTTATTTTTAGCCAA
* *
687541 AATTTTCAAACAAATTTTCCTCAAAGATTTCTCAGCA
130 AATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA
* * *
687578 GCTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGT-TAAGGCATGCCATATTGTGGGA
1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTAT-AGGCATGCCATATCGTGGGA
* *
687642 TATATTTTTGTACCCATCGGACGTCAACTTCCTGTTCAATGA-GTACTTTGTTTA-TTTTAGCCA
65 TATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTTTTAGCCA
* *
687705 AAATTTTCAAACAAATTTTCCTCAAAGATTTCTCAGCA
129 AAATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA
* * * * *
687743 GCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATATCCTGGGAT
1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT
* * * * * * * *
687808 ATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAAAGTCGACTTTGCTTATTTT
66 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
687865 GCATATTCAC
Statistics
Matches: 849, Mismatches: 90, Indels: 24
0.88 0.09 0.02
Matches are distributed among these distances:
164 2 0.00
165 288 0.34
166 331 0.39
167 226 0.27
168 2 0.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (166 bp):
ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT
ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAA
ATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA
Done.