Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 6 of 333
Found at i:1569238 original size:21 final size:20
Alignment explanation
Indices: 1569212--1569258 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1569202 TAGCCTAACT
1569212 TATTATTATT-ATTTTGTAATA
1 TATTATTATTCATTTT-T-ATA
*
1569233 TATTATTTTTCATTTTTATA
1 TATTATTATTCATTTTTATA
1569253 TATTAT
1 TATTAT
1569259 GTAATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 10 0.42
22 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TATTATTATTCATTTTTATA
Found at i:1572630 original size:16 final size:17
Alignment explanation
Indices: 1572609--1572643 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1572599 GGCAGCCTCC
1572609 AAGTATATATAT-ATAT
1 AAGTATATATATAATAT
1572625 AAGTATATATATAATAT
1 AAGTATATATATAATAT
1572642 AA
1 AA
1572644 AGTCAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (17 bp):
AAGTATATATATAATAT
Found at i:1577223 original size:38 final size:38
Alignment explanation
Indices: 1577157--1577238 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 38
1577147 TCCCCTCTTC
*
1577157 TTTATTCCCTTTATAAACAATGACATTTATTTAAAGAT
1 TTTATTCCCTTTATAAACAACGACATTTATTTAAAGAT
** ** *
1577195 TTTATTCCCTTTATAAACTGCGGTATTTATTTAAGGAT
1 TTTATTCCCTTTATAAACAACGACATTTATTTAAAGAT
1577233 TTTATT
1 TTTATT
1577239 ATAGTGAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (38 bp):
TTTATTCCCTTTATAAACAACGACATTTATTTAAAGAT
Found at i:1585198 original size:12 final size:12
Alignment explanation
Indices: 1585176--1585210 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1585166 AATATAAATA
1585176 AATAGGTAATAAT
1 AATA-GTAATAAT
1585189 AATAGTAATAAT
1 AATAGTAATAAT
*
1585201 AATAATAATA
1 AATAGTAATA
1585211 GGACTAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (12 bp):
AATAGTAATAAT
Found at i:1586882 original size:44 final size:44
Alignment explanation
Indices: 1586820--1587329 Score: 207
Period size: 44 Copynumber: 11.8 Consensus size: 44
1586810 CCTTTATTTT
* * * *
1586820 AATCCGCTCCATTATAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
1586864 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-GCTTC
** * * * * * *
1586910 GGTCTGTTCCACTGTAATCTCAGGGAAATAGGA--CCT-GGTGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * * * * ***
1586951 GATCTACTCTACTGTAA-CTTCCGAGAGATAAGA-TCCTTTATTC
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTACTAGCTTC
* * *
1586994 TAATCCGCTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTC
1 -AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
1587039 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGA-TT-ACTA-GCTTC
** * * *
1587085 GGTCTGTTCCACTGTAATCTCAGGG-GAATAAGA--CCTAG-TGC
1 AATCTGCTCCACTGTAATCTCAGGGAG-ATAAGATTACTAGCTTC
* ** * * * * * *
1587126 GATCCACTCTACTGTAA-CTTCAGAGAGATAAGA-TCCTTGGTTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTAC-TAGCTTC
* * *
1587170 AATCCGCTCCACTGTAATCTCAGGGAGATAAGA--CCTAG-TGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * * * * * *
1587211 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGA-TCCTTGGTTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTAC-TAGCTTC
* * *
1587255 AATCCGCTCCACTGTAATCTCAGGGAGATAAGA--CCTAG-TGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
1587296 GATCTACTCCGCTGTAATCTCAGGGAGATAAGAT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
1587330 CTAAATTCTT
Statistics
Matches: 350, Mismatches: 89, Indels: 56
0.71 0.18 0.11
Matches are distributed among these distances:
40 3 0.01
41 107 0.31
42 12 0.03
43 11 0.03
44 138 0.39
45 15 0.04
46 64 0.18
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:1586991 original size:175 final size:175
Alignment explanation
Indices: 1586775--1587330 Score: 734
Period size: 175 Copynumber: 3.2 Consensus size: 175
1586765 AGATCTGAAA
* * * *
1586775 CGATCTACTCTACTGTAACCTCAGAGAAATAAGATCCTTTATTTTAATCCGCTCCATTATAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
1586840 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
66 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
* *
1586905 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAGGACCTGGTG
131 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTAGTG
* *
1586950 CGATCTACTCTACTGTAACTTCCGAGAGATAAGATCCTTTATTCTAATCCGCTCCACTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
* *
1587015 CAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTGAAAT
66 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
*
1587080 TCTTCGGTCTGTTCCACTGTAATCTCAGGGGAATAAGACCTAGTG
131 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTAGTG
* **
1587125 CGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTGGTTTTAATCCGCTCCACTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
* * * * * ** *
1587190 CAGGGAGATAAGA--CCTAG-TGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTG-
66 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC-TCAGGGAGATAAGAT-C-TGA
* ** * * *
1587250 -GTT-TT-AATCCGCTCCACTGTAATCTCAGGGAGATAAGACCTAGTG
128 AATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTAGTG
** *
1587295 CGATCTACTCCGCTGTAA-TCTCAGGGAGATAAGATC
1 CGATCTACTCTACTGTAACT-TCAGAGAGATAAGATC
1587331 TAAATTCTTC
Statistics
Matches: 340, Mismatches: 37, Indels: 13
0.87 0.09 0.03
Matches are distributed among these distances:
169 1 0.00
170 64 0.19
171 3 0.01
172 31 0.09
173 4 0.01
174 2 0.01
175 235 0.69
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (175 bp):
CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
TCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTAGTG
Found at i:1587027 original size:85 final size:85
Alignment explanation
Indices: 1586775--1587338 Score: 487
Period size: 85 Copynumber: 6.5 Consensus size: 85
1586765 AGATCTGAAA
* * * * * *
1586775 CGATCTACTCTACTGTAACCTCAGAGAAATAAGATCCTTTATTTTAATCCGCTCCATTATAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTAATTCTAATCCGCTCCACTGTAATCT
* * *
1586840 CAGGGAGATAGGATTACTAGCTT
66 CAGGGAGATAAGA--CCTAG-TG
* * ** * * ** * *
1586863 CAATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGAT-CTGAAATTCTTCGGTCTGTTCCACTGTA
1 CGATCTACTCTACTGTAACT-TCAGAGAGATAAGATCCT-TAATTC-T-AATCCGCTCCACTGTA
* * *
1586926 ATCTCAGGGAAATAGGACCTGGTG
62 ATCTCAGGGAGATAAGACCTAGTG
* *
1586950 CGATCTACTCTACTGTAACTTCCGAGAGATAAGATCCTTTATTCTAATCCGCTCCACTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTAATTCTAATCCGCTCCACTGTAATCT
* * * *
1587015 CAGAGAGATAGGATTACTAGCTT
66 CAGGGAGATAAGA--CCTAG-TG
* * ** * ** * *
1587038 CAATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGAT--TTGAAATTCTTCGGTCTGTTCCACTGT
1 CGATCTACTCTACTGTAACT-TCAGAGAGATAAGATCCTT--AATTC-T-AATCCGCTCCACTGT
1587100 AATCTCAGGG-GAATAAGACCTAGTG
61 AATCTCAGGGAG-ATAAGACCTAGTG
* ** *
1587125 CGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTGGTTTTAATCCGCTCCACTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTAATTCTAATCCGCTCCACTGTAATCT
1587190 CAGGGAGATAAGACCTAGTG
66 CAGGGAGATAAGACCTAGTG
** *
1587210 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGGTTTTAATCCGCTCCACTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTAATTCTAATCCGCTCCACTGTAATCT
1587275 CAGGGAGATAAGACCTAGTG
66 CAGGGAGATAAGACCTAGTG
** * *
1587295 CGATCTACTCCGCTGTAA-TCTCAGGGAGATAAGAT-CTAAATTCT
1 CGATCTACTCTACTGTAACT-TCAGAGAGATAAGATCCTTAATTCT
1587339 TCGATCTACT
Statistics
Matches: 383, Mismatches: 73, Indels: 44
0.77 0.15 0.09
Matches are distributed among these distances:
84 6 0.02
85 175 0.46
86 5 0.01
87 68 0.18
88 73 0.19
89 5 0.01
90 51 0.13
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (85 bp):
CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTAATTCTAATCCGCTCCACTGTAATCT
CAGGGAGATAAGACCTAGTG
Found at i:1587157 original size:41 final size:41
Alignment explanation
Indices: 1587092--1587328 Score: 219
Period size: 41 Copynumber: 5.6 Consensus size: 41
1587082 TTCGGTCTGT
1587092 TCCACTGTAATCTCAGGG-GAATAAGACCTAGTGCGATCCAC
1 TCCACTGTAATCTCAGGGAG-ATAAGACCTAGTGCGATCCAC
* * * *** *
1587133 TCTACTGTAA-CTTCAGAGAGATAAGATCCTTGGTTTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGA-CC-TAG-TGCGATCCAC
*
1587177 TCCACTGTAATCTCAGGGAGATAAGACCTAGTGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGACCTAGTGCGATCCAC
* * * *** *
1587218 TCTACTGTAA-CTTCAGAGAGATAAGATCCTTGGTTTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGA-CC-TAG-TGCGATCCAC
*
1587262 TCCACTGTAATCTCAGGGAGATAAGACCTAGTGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGACCTAGTGCGATCCAC
*
1587303 TCCGCTGTAATCTCAGGGAGATAAGA
1 TCCACTGTAATCTCAGGGAGATAAGA
1587329 TCTAAATTCT
Statistics
Matches: 153, Mismatches: 32, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
40 2 0.01
41 77 0.50
42 9 0.06
43 8 0.05
44 55 0.36
45 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (41 bp):
TCCACTGTAATCTCAGGGAGATAAGACCTAGTGCGATCCAC
Found at i:1602858 original size:30 final size:31
Alignment explanation
Indices: 1602824--1602925 Score: 113
Period size: 30 Copynumber: 3.4 Consensus size: 31
1602814 AAAAAAATAA
*
1602824 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
1602854 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
1602884 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
*
1602914 AGATTTCATTTT
1 AAATTTCATTTT
1602926 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
29 4 0.07
30 56 0.92
31 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:1603275 original size:3 final size:3
Alignment explanation
Indices: 1603267--1603309 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
1603257 CCAAGGCGTA
*
1603267 AAG AAG AAG AAG AAA AAG AAG AAGG AAG AAG AAAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG -AAG AAG AAG AA
1603310 AGAAAAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1603312 original size:7 final size:7
Alignment explanation
Indices: 1603266--1603351 Score: 67
Period size: 7 Copynumber: 12.9 Consensus size: 7
1603256 ACCAAGGCGT
1603266 AAAGAAG
1 AAAGAAG
1603273 -AAGAAG
1 AAAGAAG
1603279 AAA-AAG
1 AAAGAAG
1603285 -AAGAAG
1 AAAGAAG
*
1603291 GAAGAAG
1 AAAGAAG
1603298 AAAGAAG
1 AAAGAAG
1603305 -AAGAAAG
1 AAAG-AAG
*
1603312 AAAAAAG
1 AAAGAAG
1603319 AAA-AAG
1 AAAGAAG
* *
1603325 AGAAAAAA
1 A-AAGAAG
1603333 AAAGAA-
1 AAAGAAG
*
1603339 AAAGAAA
1 AAAGAAG
1603346 AAAGAA
1 AAAGAA
1603352 AAATAATAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
5 2 0.03
6 25 0.37
7 35 0.52
8 5 0.07
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:1603322 original size:6 final size:6
Alignment explanation
Indices: 1603270--1603354 Score: 82
Period size: 6 Copynumber: 13.3 Consensus size: 6
1603260 AGGCGTAAAG
* * *
1603270 AAGAAG AAGAAA AAGAAGA AGGAAG AAGAAA GAAGAAGA AAGAAAA AAGAAA
1 AAGAAA AAGAAA AAGAA-A AAGAAA AAGAAA -AAGAA-A AAG-AAA AAGAAA
1603322 AAGAGAA AA-AAA AAGAAA AAGAAAA AAGAAA AA
1 AAGA-AA AAGAAA AAGAAA AAG-AAA AAGAAA AA
1603355 TAATAAAACA
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
5 4 0.06
6 33 0.49
7 27 0.40
8 3 0.04
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:1603478 original size:13 final size:13
Alignment explanation
Indices: 1603460--1603507 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 13
1603450 AAGCAGCCCA
1603460 AAAAAAATAAAGC
1 AAAAAAATAAAGC
*
1603473 -AAAAAACAAAGC
1 AAAAAAATAAAGC
1603485 AAAAAAAATAAGCAGC
1 -AAAAAAATAA--AGC
1603501 AAAAAAA
1 AAAAAAA
1603508 AAGGGGGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 11 0.38
14 8 0.28
15 7 0.24
16 3 0.10
ACGTcount: A:0.77, C:0.10, G:0.08, T:0.04
Consensus pattern (13 bp):
AAAAAAATAAAGC
Found at i:1603487 original size:26 final size:26
Alignment explanation
Indices: 1603458--1603510 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
1603448 CAAAGCAGCC
1603458 CAAAAAAAATAA-AGCAAAAAACAAAG
1 CAAAAAAAATAACAGCAAAAAA-AAAG
1603484 CAAAAAAAATAAGCAGCAAAAAAAAAG
1 CAAAAAAAATAA-CAGCAAAAAAAAAG
1603511 GGGGCAGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 12 0.48
27 4 0.16
28 9 0.36
ACGTcount: A:0.75, C:0.11, G:0.09, T:0.04
Consensus pattern (26 bp):
CAAAAAAAATAACAGCAAAAAAAAAG
Found at i:1603570 original size:26 final size:26
Alignment explanation
Indices: 1603519--1603571 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1603509 AGGGGGCAGG
** *
1603519 CCAACAGCAGGCCCAATTCCAGCAGC
1 CCAACAGCAGGCCCAAGCCCAACAGC
*
1603545 CCAACAGCAGGCCCTAGCCCAACAGC
1 CCAACAGCAGGCCCAAGCCCAACAGC
1603571 C
1 C
1603572 AGCCTGTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.45, G:0.19, T:0.06
Consensus pattern (26 bp):
CCAACAGCAGGCCCAAGCCCAACAGC
Found at i:1603664 original size:5 final size:5
Alignment explanation
Indices: 1603654--1603712 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
1603644 GTCCAGCAGA
* *
1603654 AAAAG AAAAG AAAA- AAGAA- AAAAG AAAA- AAAGAA AAAAG AAGAG AAAAAG
1 AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAA-AG AAAAG AAAAG -AAAAG
1603704 AAAAG AAAA
1 AAAAG AAAA
1603713 ATTCAATTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 7 0.15
5 32 0.70
6 7 0.15
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1603667 original size:11 final size:11
Alignment explanation
Indices: 1603651--1603713 Score: 76
Period size: 11 Copynumber: 5.6 Consensus size: 11
1603641 GCAGTCCAGC
1603651 AGAAAAAGAAA
1 AGAAAAAGAAA
1603662 AGAAAAAAGAAA
1 AG-AAAAAGAAA
1603674 A-AAGAAA-AAA
1 AGAA-AAAGAAA
*
1603684 AGAAAAAAGAAG
1 AG-AAAAAGAAA
1603696 AGAAAAAGAAA
1 AGAAAAAGAAA
1603707 AGAAAAA
1 AGAAAAA
1603714 TTCAATTTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
10 6 0.13
11 23 0.51
12 16 0.36
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:1603671 original size:7 final size:7
Alignment explanation
Indices: 1603659--1603713 Score: 67
Period size: 7 Copynumber: 7.4 Consensus size: 7
1603649 GCAGAAAAAG
1603659 AAAAGAA
1 AAAAGAA
1603666 AAAAGAA
1 AAAAGAA
1603673 AAAAGAAA
1 AAAAG-AA
1603681 AAAAGAA
1 AAAAGAA
1603688 AAAAGAA
1 AAAAGAA
1603695 GAGAAA-AA
1 -A-AAAGAA
1603703 GAAAAGAA
1 -AAAAGAA
1603711 AAA
1 AAA
1603714 TTCAATTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
7 27 0.61
8 14 0.32
9 3 0.07
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:1603674 original size:18 final size:16
Alignment explanation
Indices: 1603654--1603712 Score: 66
Period size: 15 Copynumber: 3.5 Consensus size: 16
1603644 GTCCAGCAGA
1603654 AAAAGAAAAGAAAAAAG
1 AAAA-AAAAGAAAAAAG
*
1603671 AAAAAAGA-AAAAAAG
1 AAAAAAAAGAAAAAAG
1603686 AAAAAAGAAGAGAAAAAG
1 AAAAAA-AAGA-AAAAAG
1603704 AAAAGAAAA
1 AAAA-AAAA
1603713 ATTCAATTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
15 13 0.36
16 4 0.11
17 5 0.14
18 12 0.33
19 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:1603687 original size:22 final size:23
Alignment explanation
Indices: 1603651--1603713 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
1603641 GCAGTCCAGC
*
1603651 AGAAAAAGAAAAGAAAAAAGAA-
1 AGAAAAAAAAAAGAAAAAAGAAG
1603673 A-AAAGAAAAAAAGAAAAAAGAAG
1 AGAAA-AAAAAAAGAAAAAAGAAG
*
1603696 AGAAAAAGAAAAGAAAAA
1 AGAAAAAAAAAAGAAAAA
1603714 TTCAATTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 3 0.08
22 17 0.47
23 13 0.36
24 3 0.08
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AGAAAAAAAAAAGAAAAAAGAAG
Found at i:1604091 original size:20 final size:22
Alignment explanation
Indices: 1604066--1604108 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1604056 TCGGGTTTTG
1604066 AAATTT-TCGTG-TCTTCAAAA
1 AAATTTCTCGTGTTCTTCAAAA
*
1604086 AAATTTCTCGTGTTTTTCAAAA
1 AAATTTCTCGTGTTCTTCAAAA
1604108 A
1 A
1604109 TAAGGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
AAATTTCTCGTGTTCTTCAAAA
Found at i:1604265 original size:36 final size:35
Alignment explanation
Indices: 1604212--1604280 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
1604202 TAAAAATCGG
* * *
1604212 AAAATTTTTCGTGTTTTCAAAAGTTCCCGTGTTGC
1 AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
*
1604247 AAAAATTTTCATGTTTTTCAAAAATTCTCGTGTT
1 AAAAATTTTCATG-TTTTCAAAAATTCCCGTGTT
1604281 TTCAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 11 0.38
36 18 0.62
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (35 bp):
AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
Found at i:1604352 original size:17 final size:17
Alignment explanation
Indices: 1604212--1604565 Score: 173
Period size: 17 Copynumber: 19.9 Consensus size: 17
1604202 TAAAAATCGG
*
1604212 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* ** *
1604230 AAAAGTTCCCGTGTTGC
1 AAAAATTTTCGTGTTTC
*
1604247 AAAAATTTTCATGTTTTTC
1 AAAAATTTTC--GTGTTTC
*
1604266 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
** *
1604284 AAAAAAAATTC-TAATTTTC
1 -AAAAATTTTCGT--GTTTC
*
1604303 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* *
1604321 TGAAAA-CTTCTGTGTTTC
1 -AAAAATTTTC-GTGTTTC
1604339 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
1604356 TAAAATTTTCGTATTTC
1 AAAAATTTTCGTGTTTC
*
1604373 AAAAATTTTCTTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
1604391 -AAATTTTTCGTATTTA
1 AAAAATTTTCGTGTTTC
**
1604407 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
1604425 -AAAA-TTCCAGTGTTTC
1 AAAAATTTTC-GTGTTTC
*
1604441 AAAATTTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
**
1604458 AAAAAAAAAATTCCCGT-TTTCC
1 -----AAAAATTTTCGTGTTT-C
* *
1604480 AAAAACTTTCGTGTTTT
1 AAAAATTTTCGTGTTTC
**
1604497 AAGAAATTGACCGTGTTTC
1 AA-AAATT-TTCGTGTTTC
*
1604516 ATAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
1604533 AAAGAAATCTCGTGTTTC
1 AAA-AATTTTCGTGTTTC
1604551 -AAAATTTTCGTGTTT
1 AAAAATTTTCGTGTTT
1604566 TTTTAAAAAT
Statistics
Matches: 247, Mismatches: 62, Indels: 56
0.68 0.17 0.15
Matches are distributed among these distances:
16 19 0.08
17 105 0.43
18 70 0.28
19 40 0.16
21 3 0.01
22 10 0.04
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:1604584 original size:34 final size:34
Alignment explanation
Indices: 1604434--1604565 Score: 108
Period size: 36 Copynumber: 3.6 Consensus size: 34
1604424 CAAAATTCCA
* *
1604434 GTGTTTCAAAATTTTTCGTGTTTCAAAAAAAAAATTCCC
1 GTGTTTCAAAA-TTTTCGTGTTTC---AAAGAAA-TCTC
* *
1604473 GT-TTTCCAAAAACTTTCGTGTTT-TAAGAAAT-TGACC
1 GTGTTT-C-AAAATTTTCGTGTTTCAAAGAAATCT---C
1604509 GTGTTTCATAAATTTTCGTGTTTCAAAGAAATCTC
1 GTGTTTCA-AAATTTTCGTGTTTCAAAGAAATCTC
1604544 GTGTTTCAAAATTTTCGTGTTT
1 GTGTTTCAAAATTTTCGTGTTT
1604566 TTTTAAAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
34 15 0.19
35 15 0.19
36 17 0.22
37 10 0.13
38 4 0.05
39 13 0.17
40 4 0.05
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (34 bp):
GTGTTTCAAAATTTTCGTGTTTCAAAGAAATCTC
Found at i:1606588 original size:15 final size:15
Alignment explanation
Indices: 1606568--1606598 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1606558 AAACCGCTAC
1606568 CGAGGATCAAAATCT
1 CGAGGATCAAAATCT
1606583 CGAGGATCAAAATCT
1 CGAGGATCAAAATCT
1606598 C
1 C
1606599 TAAGATATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (15 bp):
CGAGGATCAAAATCT
Found at i:1611344 original size:32 final size:30
Alignment explanation
Indices: 1611308--1611367 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 30
1611298 TTTATATTTA
1611308 TTTTAAAAATTCAAAAAAAATTATAAAAATGT
1 TTTTAAAAA-T-AAAAAAAATTATAAAAATGT
*
1611340 TTTTAAGAATAAAAAAAATTATAAAAAT
1 TTTTAAAAATAAAAAAAATTATAAAAAT
1611368 TACAACAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 18 0.67
31 1 0.04
32 8 0.30
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (30 bp):
TTTTAAAAATAAAAAAAATTATAAAAATGT
Found at i:1618438 original size:23 final size:22
Alignment explanation
Indices: 1618387--1618438 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
1618377 CCTCGTCTTT
*
1618387 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
1618409 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
1618432 TTCTTTT
1 TTCTTTT
1618439 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:1618447 original size:12 final size:12
Alignment explanation
Indices: 1618396--1618450 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
1618386 TTTCTTTTGT
1618396 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
1618409 -TCATTTTC-TC
1 TTCTTTTTCAAC
1618419 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
1618432 TTCTTTTTCAAT
1 TTCTTTTTCAAC
1618444 TTCTTTT
1 TTCTTTT
1618451 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:1618457 original size:17 final size:18
Alignment explanation
Indices: 1618432--1618469 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1618422 TTTCTTCAAC
* *
1618432 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
1618449 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
1618467 TTC
1 TTC
1618470 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:1621590 original size:9 final size:9
Alignment explanation
Indices: 1621576--1621603 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1621566 TCTCAAACAT
1621576 AACCAATTC
1 AACCAATTC
1621585 AACCAATTC
1 AACCAATTC
1621594 AACCAATTC
1 AACCAATTC
1621603 A
1 A
1621604 TTTCACATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.21
Consensus pattern (9 bp):
AACCAATTC
Found at i:1622292 original size:35 final size:35
Alignment explanation
Indices: 1622247--1622316 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
1622237 AACGGTAGTA
1622247 GTAACAGTAACAATAACAGTATTCAACACACAAAG
1 GTAACAGTAACAATAACAGTATTCAACACACAAAG
* * *
1622282 GTAACGGTAACAGTAACAGTATTCGACACACAAAG
1 GTAACAGTAACAATAACAGTATTCAACACACAAAG
1622317 TGCCGAATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.17
Consensus pattern (35 bp):
GTAACAGTAACAATAACAGTATTCAACACACAAAG
Found at i:1622348 original size:6 final size:6
Alignment explanation
Indices: 1622327--1622360 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1622317 TGCCGAATCG
* *
1622327 GTAACA GTAACG GTAATA GTAACA GTAACA GTAA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAA
1622361 TCGGCACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.21
Consensus pattern (6 bp):
GTAACA
Found at i:1622350 original size:18 final size:18
Alignment explanation
Indices: 1622327--1622361 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1622317 TGCCGAATCG
*
1622327 GTAACAGTAACGGTAATA
1 GTAACAGTAACAGTAATA
1622345 GTAACAGTAACAGTAAT
1 GTAACAGTAACAGTAAT
1622362 CGGCACATAA
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:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (18 bp):
GTAACAGTAACAGTAATA
Found at i:1623019 original size:22 final size:22
Alignment explanation
Indices: 1622977--1623022 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1622967 CTAACTAAAC
*
1622977 TCATATATTTTTCTTCTTCAAT
1 TCATATATTTTTATTCTTCAAT
*
1622999 TCATATCTTTTTATTAC-TCAAT
1 TCATATATTTTTATT-CTTCAAT
1623021 TC
1 TC
1623023 CCTACCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.57
Consensus pattern (22 bp):
TCATATATTTTTATTCTTCAAT
Found at i:1625007 original size:22 final size:22
Alignment explanation
Indices: 1624982--1625024 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1624972 TATCCAAACA
1624982 ATAACAACAAAATAGTAGCAAT
1 ATAACAACAAAATAGTAGCAAT
* **
1625004 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
1625025 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAT
Found at i:1625028 original size:11 final size:11
Alignment explanation
Indices: 1624989--1625029 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1624979 ACAATAACAA
1624989 CAAAATAGTAG
1 CAAAATAGTAG
* *
1625000 CAATATAATAG
1 CAAAATAGTAG
*
1625011 TAAAATAGTAG
1 CAAAATAGTAG
1625022 CAAAATAG
1 CAAAATAG
1625030 GGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:1627585 original size:38 final size:37
Alignment explanation
Indices: 1627526--1627630 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 37
1627516 CATTTTTAAG
**
1627526 AATAT-AAAGAATATATATAAGTATGTATATGATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAAAT-TAGA
* * *
1627563 AATATGCATAAATATATGTAAGTATATA-AAAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAAATTA-GA
*
1627601 AATATGAAAAATATATTTAAGTATGTATAA
1 AATATGAAAAATATATATAAGTATGTATAA
1627631 GTACGTATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
36 2 0.04
37 26 0.47
38 25 0.45
39 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.35
Consensus pattern (37 bp):
AATATGAAAAATATATATAAGTATGTATAAAATTAGA
Found at i:1628008 original size:19 final size:18
Alignment explanation
Indices: 1627984--1628044 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
1627974 AGTATATACA
1627984 ATATAATATTAGAAAATAT
1 ATATAATATT-GAAAATAT
*
1628003 ATATAATAGTGTAAAATAT
1 ATATAATATTG-AAAATAT
1628022 AACTAATAATATT-AAAATAT
1 -A-T-ATAATATTGAAAATAT
1628042 ATA
1 ATA
1628045 CAATGATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 1 0.03
18 2 0.06
19 17 0.47
20 8 0.22
21 1 0.03
22 7 0.19
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (18 bp):
ATATAATATTGAAAATAT
Found at i:1628326 original size:3 final size:3
Alignment explanation
Indices: 1628311--1628346 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1628301 AAACATAAAC
*
1628311 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1628347 CATTGGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1628464 original size:22 final size:23
Alignment explanation
Indices: 1628447--1628509 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 23
1628437 TGTATACACG
1628447 TACATAATAA-AATATATACTAA
1 TACATAATAATAATATATACTAA
1628469 TACATAATAATAATACTAATACTAA
1 TACATAATAATAATA-T-ATACTAA
*
1628494 TA-ATACTAATAATATA
1 TACATAATAATAATATA
1628510 AAAATAACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 11 0.30
23 5 0.14
24 12 0.32
25 9 0.24
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (23 bp):
TACATAATAATAATATATACTAA
Found at i:1628480 original size:3 final size:3
Alignment explanation
Indices: 1628450--1628516 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
1628440 ATACACGTAC
* * *
1628450 ATA ATA A-A ATA TATA CTA ATA CATA ATA ATA ATA CTA ATA CTA ATA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
1628496 ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
1628517 CAAGGATATT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1628993 original size:11 final size:12
Alignment explanation
Indices: 1628977--1629012 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
1628967 GAAAAAAAAA
1628977 GAAGAGAG-AGG
1 GAAGAGAGAAGG
1628988 GAAGAGAGAAGG
1 GAAGAGAGAAGG
1629000 G-AGAGAGAAGG
1 GAAGAGAGAAGG
1629011 GA
1 GA
1629013 GGGGGAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:1629135 original size:8 final size:8
Alignment explanation
Indices: 1629124--1629179 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
1629114 AAAAAATATT
1629124 TTTTTTTA
1 TTTTTTTA
1629132 TTTTTTTA
1 TTTTTTTA
1629140 -TTTTTTA
1 TTTTTTTA
1629147 TGTTTATATTA
1 T-TTT-T-TTA
* *
1629158 TATTGTTA
1 TTTTTTTA
*
1629166 TTTTTATA
1 TTTTTTTA
1629174 TTTTTT
1 TTTTTT
1629180 AGTATATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
7 7 0.18
8 21 0.55
9 3 0.08
10 3 0.08
11 4 0.11
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.79
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1629167 original size:34 final size:32
Alignment explanation
Indices: 1629129--1629192 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
1629119 ATATTTTTTT
* *
1629129 TTATTTTTTTATTTTTTATGTTTATATTATATTG
1 TTATTTTTATATTTTTTA-GTATATA-TATATTG
1629163 TTATTTTTATATTTTTTAGTATATATATAT
1 TTATTTTTATATTTTTTAGTATATATATAT
1629193 GGGAAAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.18
33 6 0.21
34 17 0.61
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (32 bp):
TTATTTTTATATTTTTTAGTATATATATATTG
Found at i:1629185 original size:26 final size:26
Alignment explanation
Indices: 1629119--1629186 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
1629109 AGGTAAAAAA
* * *
1629119 ATATTTTTTTTTATTTTTTTATTTTT
1 ATATTTTTTATTATATTGTTATTTTT
*
1629145 -TATGTTTATATTATATTGTTATTTTT
1 ATAT-TTTTTATTATATTGTTATTTTT
*
1629171 ATATTTTTTAGTATAT
1 ATATTTTTTATTATAT
1629187 ATATATGGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 3 0.09
26 28 0.82
27 3 0.09
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (26 bp):
ATATTTTTTATTATATTGTTATTTTT
Found at i:1630115 original size:44 final size:44
Alignment explanation
Indices: 1630068--1630663 Score: 381
Period size: 44 Copynumber: 13.6 Consensus size: 44
1630058 TTTTAATCCA
* * * *
1630068 CTCCACTGTAATCTCAGGCAGATAGGATTACTATCTTCAATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTCGATCTG
* * * *
1630112 CTCCGCTGTAATCTCAGGGAGATAAGATTTGA-AATTTTCGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGA-TT-ACTATCTTCGATCTG
* * *
1630157 TTCCACTGTAATCTCAGGGAGATAAGA-T-CTATCATTTTGATCCG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTATC--TTCGATCTG
* * *
1630201 CTCCACTGTAA-CTTCAGGGAGATAGGA-TAGTGTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTCGATCTG
* ** *
1630244 CTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTCGATCTG
* * * * *
1630288 CTCCACTGTAACCTCAGGGAGATAAGATCTGGAAT-TCTCCGGTCTA
1 CTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTATCTTCGATCTG
* * * * *
1630334 CTCCACTGTAACCTCAGGGAAATAAGA--CCTGAT-GT-GATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATTACT-ATCTTCGATCTG
* * * *
1630375 CTCTACTGTAA-CTTCAGAGAGATAAGA-T-CT-T-TT-AATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTCGATCTG
* * * *
1630414 CTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTCGATCTG
* * *
1630458 CTCCGCTGTAATCTCAGGGAGATAAGATCT-CTCAT-TTTGATCCG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-TACT-ATCTTCGATCTG
* * *
1630502 CTCCACTGTAA-CTTCAGGGAGATAGGA-TAGTGTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTCGATCTG
* ** *
1630545 CTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTCGATCTG
* * * * * * *
1630589 CTCCACTGTAACCTTAGGGAGATAAGATCTGAAATTTTTTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-T---ACTATCTTCGATCTG
*
1630637 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAATCTCAGGGAGATAAGA
1630664 CCTGTATAAT
Statistics
Matches: 433, Mismatches: 84, Indels: 66
0.74 0.14 0.11
Matches are distributed among these distances:
39 25 0.06
40 3 0.01
41 31 0.07
42 5 0.01
43 67 0.15
44 194 0.45
45 43 0.10
46 33 0.08
47 1 0.00
48 31 0.07
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTCGATCTG
Found at i:1630558 original size:87 final size:87
Alignment explanation
Indices: 1630068--1630616 Score: 399
Period size: 87 Copynumber: 6.3 Consensus size: 87
1630058 TTTTAATCCA
* * * * *
1630068 CTCCACTGTAATCTCAGGCAGATAGGATTACTATCTTCAATCTACTCCGCTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAAGA-TACTATCTTCGATCTGCTCCACTGTAATCTCAGGGAG
* ** *
1630133 ATAAGATTTGAAATTTTCGGTCTG
65 ATAAGATCTGTCATTTT-GATCTG
* * *
1630157 TTCCACTGTAATCTCAGGGAGATAAGAT-CTATCATTTTGATCCGCTCCACTGTAA-CTTCAGGG
1 CTCCACTGTAATCTCAGGGAGATAAGATACTATC--TTCGATCTGCTCCACTGTAATC-TCAGGG
* * *
1630220 AGATAGGATAGTGTC--TTCGATCTG
63 AGATAAGAT-CTGTCATTTTGATCTG
* * * *
1630244 CTCCGCTGTAATCTCAGGGAGATAAGAT-CTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
1 CTCCACTGTAATCTCAGGGAGATAAGATACTAT--CTTCGATCTGCTCCACTGTAATCTCAGGGA
** * * *
1630308 GATAAGATCTGGAATTCTCCGGTCTA
64 GATAAGATCTGTCATT-T-TGATCTG
* * * * * * *
1630334 CTCCACTGTAACCTCAGGGAAATAAGA-CCTGAT-GT-GATCTTCTCTACTGTAA-CTTCAGAGA
1 CTCCACTGTAATCTCAGGGAGATAAGATACT-ATCTTCGATCTGCTCCACTGTAATC-TCAGGGA
* *
1630395 GATAAGA----TC-TTTTAATCCG
64 GATAAGATCTGTCATTTTGATCTG
* * * * *
1630414 CTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAAGA-TACTATCTTCGATCTGCTCCACTGTAATCTCAGGGAG
* *
1630479 ATAAGATCTCTCATTTTGATCCG
65 ATAAGATCTGTCATTTTGATCTG
* * * *
1630502 CTCCACTGTAA-CTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAG
1 CTCCACTGTAATC-TCAGGGAGATAAGATACTATCTTCGATCTGCTCCACTGTAATCTCAGGGAG
* *** **
1630566 ATAAGATCTCTGGCTTCAATCTG
65 ATAAGATCTGTCATTTTGATCTG
* *
1630589 CTCCACTGTAACCTTAGGGAGATAAGAT
1 CTCCACTGTAATCTCAGGGAGATAAGAT
1630617 CTGAAATTTT
Statistics
Matches: 367, Mismatches: 67, Indels: 54
0.75 0.14 0.11
Matches are distributed among these distances:
80 24 0.07
81 3 0.01
82 5 0.01
83 27 0.07
84 1 0.00
86 3 0.01
87 175 0.48
88 40 0.11
89 55 0.15
90 33 0.09
91 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (87 bp):
CTCCACTGTAATCTCAGGGAGATAAGATACTATCTTCGATCTGCTCCACTGTAATCTCAGGGAGA
TAAGATCTGTCATTTTGATCTG
Found at i:1641740 original size:19 final size:21
Alignment explanation
Indices: 1641717--1641765 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 21
1641707 ATATGCATAA
1641717 ATATGTAAGTATAT-AAAAAT
1 ATATGTAAGTATATGAAAAAT
1641737 -TATG-AA--ATATGAAAAAT
1 ATATGTAAGTATATGAAAAAT
*
1641754 ATATTTAAGTAT
1 ATATGTAAGTAT
1641766 GTATAAGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 9
0.70 0.03 0.27
Matches are distributed among these distances:
16 4 0.17
17 6 0.26
18 5 0.22
19 6 0.26
21 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (21 bp):
ATATGTAAGTATATGAAAAAT
Found at i:1642140 original size:19 final size:20
Alignment explanation
Indices: 1642116--1642164 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1642106 TAATATTAGA
* *
1642116 AAAATATATA-TAATAGTGT
1 AAAATATATACTAATAATAT
1642135 AAAATATA-ACTAATAATAT
1 AAAATATATACTAATAATAT
1642154 AAAATATATAC
1 AAAATATATAC
1642165 AATGATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 23 0.88
20 2 0.08
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAATATATACTAATAATAT
Found at i:1642441 original size:3 final size:3
Alignment explanation
Indices: 1642426--1642461 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1642416 AAACATAAAC
*
1642426 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1642462 CATTGGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1642511 original size:12 final size:11
Alignment explanation
Indices: 1642494--1642532 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1642484 ACATAAGATT
1642494 AATAAAATATTA
1 AATAAAA-ATTA
*
1642506 AATAAAAATGA
1 AATAAAAATTA
1642517 AATAAAAATATA
1 AATAAAAAT-TA
1642529 AATA
1 AATA
1642533 TGAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 12 0.50
12 12 0.50
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAAAAATTA
Found at i:1642546 original size:19 final size:19
Alignment explanation
Indices: 1642497--1642547 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
1642487 TAAGATTAAT
*
1642497 AAAATATTAAATAAAAATGA
1 AAAATA-TATATAAAAATGA
* *
1642517 AATAA-AAATATAAATATGA
1 AA-AATATATATAAAAATGA
1642536 AAAATATATATA
1 AAAATATATATA
1642548 TATGTATACA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 2 0.08
19 18 0.72
20 3 0.12
21 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAATATATATAAAAATGA
Found at i:1642591 original size:15 final size:16
Alignment explanation
Indices: 1642570--1642615 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
1642560 TACATAATAA
1642570 AAAT-ATACTAATACAT
1 AAATAATACTAATAC-T
1642586 AATATAATACTAATACT
1 AA-ATAATACTAATACT
1642603 -AATAATACTAATA
1 AAATAATACTAATA
1642616 ATATAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 12 0.43
16 3 0.11
17 3 0.11
18 10 0.36
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAATACTAATACT
Found at i:1642615 original size:6 final size:6
Alignment explanation
Indices: 1642574--1642606 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1642564 TAATAAAAAT
1642574 ATACTA ATACATA ATA-TA ATACTA ATACTA ATA
1 ATACTA ATAC-TA ATACTA ATACTA ATACTA ATA
1642607 ATACTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 15 0.60
7 5 0.20
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACTA
Found at i:1643216 original size:8 final size:8
Alignment explanation
Indices: 1643203--1643261 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
1643193 GGTAAAAAAA
1643203 TATTTTTT
1 TATTTTTT
*
1643211 TTTTTTTT
1 TATTTTTT
1643219 TATTTTTT
1 TATTTTTT
1643227 TATTTTATAT
1 TATTTT-T-T
* *
1643237 TATATTGT
1 TATTTTTT
*
1643245 TATTTTTA
1 TATTTTTT
1643253 T-TTTTTT
1 TATTTTTT
1643260 TA
1 TA
1643262 GTATAATATA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
7 6 0.15
8 27 0.68
9 1 0.03
10 6 0.15
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (8 bp):
TATTTTTT
Found at i:1643255 original size:6 final size:6
Alignment explanation
Indices: 1643203--1643257 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
1643193 GGTAAAAAAA
* * *
1643203 TATTTT T-TTTT T-TTTT TATTTT TTTATTT TATATTA TATTGT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TAT-TTT TAT-TTT TATTTT TATTTT
1643251 TATTTT T
1 TATTTT T
1643258 TTTAGTATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 10 0.24
6 20 0.49
7 11 0.27
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:1656388 original size:38 final size:37
Alignment explanation
Indices: 1656329--1656433 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 37
1656319 CATTTTTAAG
**
1656329 AATAT-AAAGAATATATATAAGTATGTATATGATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAAAT-TAGA
* * *
1656366 AATATGCATAAATATATGTAAGTATATA-AAAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAAATTA-GA
*
1656404 AATATGAAAAATATATTTAAGTATGTATAA
1 AATATGAAAAATATATATAAGTATGTATAA
1656434 GTACGTATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
36 2 0.04
37 26 0.47
38 25 0.45
39 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.35
Consensus pattern (37 bp):
AATATGAAAAATATATATAAGTATGTATAAAATTAGA
Found at i:1656824 original size:19 final size:17
Alignment explanation
Indices: 1656800--1656848 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 17
1656790 TAATATTAGA
1656800 AAAATATATATAATAGTGT
1 AAAATATATATAATA-T-T
1656819 AAAATATAACTAATAATATT
1 AAAATAT-A-T-ATAATATT
1656839 AAAATATATA
1 AAAATATATA
1656849 CAATGATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 1 0.04
18 1 0.04
19 8 0.30
20 9 0.33
21 2 0.07
22 6 0.22
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
AAAATATATATAATATT
Found at i:1657262 original size:23 final size:23
Alignment explanation
Indices: 1657243--1657306 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
1657233 TGTATACACG
1657243 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATATATACTAA
*
1657266 TACATAATAATAATACTAATACTAA
1 TACATAATAAAAATA-T-ATACTAA
* *
1657291 TA-ATACTAATAATATA
1 TACATAATAAAAATATA
1657307 AAAATAACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 1 0.03
23 15 0.41
24 12 0.32
25 9 0.24
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (23 bp):
TACATAATAAAAATATATACTAA
Found at i:1657277 original size:3 final size:3
Alignment explanation
Indices: 1657246--1657313 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
1657236 ATACACGTAC
* * * *
1657246 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA CTA ATA CTA ATA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
1657293 ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
1657314 CAAGGATATT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1657942 original size:14 final size:14
Alignment explanation
Indices: 1657923--1657974 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
1657913 AAAAATATTT
1657923 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
1657937 TTTTTATGTTTATATTA
1 TTTTTAT-TTT-T-TTA
*
1657954 TATTGTTATTTTTATA
1 T-TT-TTATTTTTTTA
1657970 TTTTT
1 TTTTT
1657975 TAGTATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 9 0.28
15 5 0.16
16 4 0.12
17 5 0.16
18 5 0.16
19 4 0.12
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:1657962 original size:19 final size:19
Alignment explanation
Indices: 1657935--1657971 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1657925 TTTATTTTTT
*
1657935 TATTTTTATGTTTATATTA
1 TATTGTTATGTTTATATTA
*
1657954 TATTGTTATTTTTATATT
1 TATTGTTATGTTTATATT
1657972 TTTTAGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TATTGTTATGTTTATATTA
Found at i:1657984 original size:33 final size:32
Alignment explanation
Indices: 1657926--1657988 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
1657916 AATATTTTTT
* *
1657926 TTATTTTTTTATTTTTATGTTTATATTATATTG
1 TTATTTTTATATTTTTATGTATATA-TATATTG
1657959 TTATTTTTATATTTTT-TAGTATATATATAT
1 TTATTTTTATATTTTTAT-GTATATATATAT
1657989 GGGAAAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 6 0.22
33 21 0.78
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (32 bp):
TTATTTTTATATTTTTATGTATATATATATTG
Found at i:1658933 original size:44 final size:44
Alignment explanation
Indices: 1658886--1659434 Score: 379
Period size: 44 Copynumber: 12.6 Consensus size: 44
1658876 TTTTAATCCA
* * * *
1658886 CTCCACTGTAATCTCAGGCAGATAGGATTACTATCTTCAATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTCGATCTG
* * * *
1658930 CTCCGCTGTAATCTCAGGGAGATAAGATTTGA-AATTTTTCGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGA-TT-ACTA-TCTTCGATCTG
* * *
1658976 TTCCACTGTAATCTCAGGGAGATAAGA-T-CTATCATTTTGATCCG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTATC--TTCGATCTG
* * *
1659020 CTCCACTGTAA-CTTCAGGGAGATAGGA-TAGTGTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTCGATCTG
* ** *
1659063 CTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTCGATCTG
* * * * *
1659107 CTCCACTGTAACCTCAGGGAGATAAGATCTGGAAT-TCTCCGGTCTA
1 CTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTATCTTCGATCTG
* * * * *
1659153 CTCCACTGTAACCTCAGGGAAATAAGA--CCTGAT-GT-GATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATTACT-ATCTTCGATCTG
* * * *
1659194 CTCTACTGTAA-CTTCAGAGAGATAAGA-T-CT-T-TT-AATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTCGATCTG
* * * *
1659233 CTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTCGATCTG
* *
1659277 CTCCGCTGTAATCTCAGGGAGATAAGATCT-CTCAT-TT-GATCCG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-TACT-ATCTTCGATCTG
* * *
1659320 CTCCACTGTAA-CTTCAGGGAGATAGGA-TAGTGTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTCGATCTG
* ** *
1659363 CTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTCGATCTG
*
1659407 CTCCACTGTAACCTCAGGGAGATAAGAT
1 CTCCACTGTAATCTCAGGGAGATAAGAT
1659435 CTGAAATTTT
Statistics
Matches: 400, Mismatches: 72, Indels: 66
0.74 0.13 0.12
Matches are distributed among these distances:
39 25 0.06
40 3 0.01
41 33 0.08
42 6 0.01
43 91 0.23
44 165 0.41
45 11 0.03
46 65 0.16
47 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTCGATCTG
Found at i:1659089 original size:87 final size:87
Alignment explanation
Indices: 1658886--1659436 Score: 238
Period size: 87 Copynumber: 6.3 Consensus size: 87
1658876 TTTTAATCCA
* * ** * *
1658886 CTCCACTGTAATCTCAGGCAGATAGGAT-TA-CTATCTTCAATCTACTCCGCTGTAATCTCAGGG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTATC-A-CTTCAATCCGCTCCACTGTAACCTCAGGG
* * * *
1658949 AGATAAGAT-TTGAAATTTTTCGGTCTG
64 AGATAGGATAGTG----TCTTCGATCTG
* * ** *
1658976 TTCCACTGTAATCTCAGGGAGATAAGATCTATCATTTTGATCCGCTCCACTGTAACTTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTATCACTTCAATCCGCTCCACTGTAACCTCAGGGAG
1659041 ATAGGATAGTGTCTTCGATCTG
66 ATAGGATAGTGTCTTCGATCTG
* * ** *
1659063 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTATCACTTCAATCCGCTCCACTGTAACCTCAGGGAG
* * * * *
1659128 ATAAGAT-CTGGAATTCTCCGGTCTA
66 ATAGGATAGT-G---TCTTCGATCTG
* * * * * ** * * *
1659153 CTCCACTGTAACCTCAGGGAAATAAGACCTGAT---GT-GATCTTCTCTACTGTAACTTCAGAGA
1 CTCCACTGTAATCTCAGGGAGATAAGATCT-ATCACTTCAATCCGCTCCACTGTAACCTCAGGGA
* * * *
1659214 GATAAGAT-CT-T-TT-AATCCG
65 GATAGGATAGTGTCTTCGATCTG
* * * ** * * *
1659233 CTCCATTGTAATCTCAAGGAGATAGGAT-TA-CTATCTTTGATCTGCTCCGCTGTAATCTCAGGG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTATC-A-CTTCAATCCGCTCCACTGTAACCTCAGGG
* * * * *
1659296 AGATAAGAT-CTCTCATTTGATCCG
64 AGATAGGATAGTGTC-TTCGATCTG
* ** * * * *
1659320 CTCCACTGTAA-CTTCAGGGAGATAGGA--TAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTA-TCACTTCAATCCGCTCCACTGTAACCTCAGGG
* ** * *
1659382 AGATAAGATCTCTGGCTTCAATCTG
64 AGATAGGAT-AGTGTCTTCGATCTG
*
1659407 CTCCACTGTAACCTCAGGGAGATAAGATCT
1 CTCCACTGTAATCTCAGGGAGATAAGATCT
1659437 GAAATTTTTT
Statistics
Matches: 364, Mismatches: 71, Indels: 53
0.75 0.15 0.11
Matches are distributed among these distances:
78 1 0.00
79 1 0.00
80 24 0.07
81 1 0.00
82 2 0.01
83 30 0.08
84 1 0.00
86 43 0.12
87 160 0.44
88 5 0.01
89 1 0.00
90 88 0.24
91 6 0.02
92 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (87 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTATCACTTCAATCCGCTCCACTGTAACCTCAGGGAG
ATAGGATAGTGTCTTCGATCTG
Found at i:1659103 original size:177 final size:170
Alignment explanation
Indices: 1658876--1659306 Score: 495
Period size: 177 Copynumber: 2.5 Consensus size: 170
1658866 AGATCCTTTA
* * *
1658876 TTTTAATCCACTCCACTGTAATCTCAGGCAGATAGGATTACTATCTTCAATCTACTCCGCTGTAA
1 TTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAA
* * * ** * *
1658941 TCTCAGGGAGATAAGATTTGAAATTTTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGATCT
66 TCTCAGGGAGATAAGATCTGAAATTCTCCGGTCTACTCCACTGTAACCTCAGGGAAATAAGA-C-
* * * *
1659006 ATCATTTTGATCCGCTCCACTGTAACTTCAGGGAGATAGGATAG
129 ATCA-TGTGATCCGCTCCACTGTAACTTCAGAGAGATAAGAT-C
* * * * ** *
1659050 TGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACT
1 T-T-TT-AATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-TACTATCTTCAATCTGCTCCGCT
* *
1659114 GTAACCTCAGGGAGATAAGATCTGGAATTCTCCGGTCTACTCCACTGTAACCTCAGGGAAATAAG
62 GTAATCTCAGGGAGATAAGATCTGAAATTCTCCGGTCTACTCCACTGTAACCTCAGGGAAATAAG
* * ** *
1659179 ACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATC
127 ACATCATGTGATCCGCTCCACTGTAACTTCAGAGAGATAAGATC
* * **
1659223 TTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAA
1 TTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAA
1659288 TCTCAGGGAGATAAGATCT
66 TCTCAGGGAGATAAGATCT
1659307 CTCATTTGAT
Statistics
Matches: 212, Mismatches: 40, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
169 1 0.00
170 66 0.31
171 2 0.01
172 1 0.00
173 1 0.00
174 32 0.15
175 3 0.01
176 3 0.01
177 102 0.48
178 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (170 bp):
TTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAA
TCTCAGGGAGATAAGATCTGAAATTCTCCGGTCTACTCCACTGTAACCTCAGGGAAATAAGACAT
CATGTGATCCGCTCCACTGTAACTTCAGAGAGATAAGATC
Found at i:1670566 original size:38 final size:37
Alignment explanation
Indices: 1670507--1670611 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 37
1670497 CATTTTTAAG
**
1670507 AATAT-AAAGAATATATATAAGTATGTATATGATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAAAT-TAGA
* * *
1670544 AATATGCATAAATATATGTAAGTATATA-AAAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAAATTA-GA
*
1670582 AATATGAAAAATATATTTAAGTATGTATAA
1 AATATGAAAAATATATATAAGTATGTATAA
1670612 GTACGTATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
36 2 0.04
37 26 0.47
38 25 0.45
39 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.35
Consensus pattern (37 bp):
AATATGAAAAATATATATAAGTATGTATAAAATTAGA
Found at i:1671001 original size:19 final size:17
Alignment explanation
Indices: 1670977--1671025 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 17
1670967 TAATATTAGA
1670977 AAAATATATATAATAGTGT
1 AAAATATATATAATA-T-T
1670996 AAAATATAACTAATAATATT
1 AAAATAT-A-T-ATAATATT
1671016 AAAATATATA
1 AAAATATATA
1671026 CAATGATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 1 0.04
18 1 0.04
19 8 0.30
20 9 0.33
21 2 0.07
22 6 0.22
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
AAAATATATATAATATT
Found at i:1671306 original size:3 final size:3
Alignment explanation
Indices: 1671292--1671323 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1671282 AAACATAAAC
1671292 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1671324 CATTGGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1671442 original size:23 final size:23
Alignment explanation
Indices: 1671423--1671486 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
1671413 TGTATACACG
1671423 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATATATACTAA
*
1671446 TACATAATAATAATACTAATACTAA
1 TACATAATAAAAATA-T-ATACTAA
* *
1671471 TA-ATACTAATAATATA
1 TACATAATAAAAATATA
1671487 AAAATAACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 1 0.03
23 15 0.41
24 12 0.32
25 9 0.24
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (23 bp):
TACATAATAAAAATATATACTAA
Found at i:1671457 original size:3 final size:3
Alignment explanation
Indices: 1671426--1671493 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
1671416 ATACACGTAC
* * * *
1671426 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA CTA ATA CTA ATA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
1671473 ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
1671494 CAAGGATATT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1671971 original size:11 final size:12
Alignment explanation
Indices: 1671955--1671990 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
1671945 GAAAAAAAAA
1671955 GAAGAGAG-AGG
1 GAAGAGAGAAGG
1671966 GAAGAGAGAAGG
1 GAAGAGAGAAGG
1671978 G-AGAGAGAAGG
1 GAAGAGAGAAGG
1671989 GA
1 GA
1671991 GGGGGAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:1672109 original size:8 final size:8
Alignment explanation
Indices: 1672098--1672158 Score: 52
Period size: 8 Copynumber: 7.2 Consensus size: 8
1672088 GTAAAAAAAA
1672098 TATTTTTT
1 TATTTTTT
1672106 TATTTTTT
1 TATTTTTT
1672114 T-TATTTTT
1 TAT-TTTTT
1672122 TATGTTTATAT
1 TAT-TTT-T-T
* *
1672133 TATATTGT
1 TATTTTTT
*
1672141 TATTTTTA
1 TATTTTTT
1672149 TATTTTTT
1 TATTTTTT
1672157 TA
1 TA
1672159 GTATATATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
7 1 0.02
8 30 0.71
9 4 0.10
10 3 0.07
11 4 0.10
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (8 bp):
TATTTTTT
Found at i:1672148 original size:19 final size:18
Alignment explanation
Indices: 1672097--1672152 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 18
1672087 GGTAAAAAAA
1672097 ATATT-TTT-TTATTTTT
1 ATATTATTTGTTATTTTT
* *
1672113 -T-TTATTTTTTATGTTT
1 ATATTATTTGTTATTTTT
1672129 ATATTATATTGTTATTTTT
1 ATATTAT-TTGTTATTTTT
1672148 ATATT
1 ATATT
1672153 TTTTTAGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 7 0.22
17 1 0.03
18 4 0.12
19 14 0.44
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (18 bp):
ATATTATTTGTTATTTTT
Found at i:1676388 original size:19 final size:20
Alignment explanation
Indices: 1676366--1676403 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1676356 TTTTTTTTGT
1676366 AAAATT-TAATTTAAATATA
1 AAAATTATAATTTAAATATA
*
1676385 AAAATTATATTTTAAATAT
1 AAAATTATAATTTAAATAT
1676404 TGAAATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTATAATTTAAATATA
Found at i:1676652 original size:6 final size:6
Alignment explanation
Indices: 1676641--1676674 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1676631 GGCAACGGGC
1676641 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1676675 GTAAAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:1683087 original size:215 final size:215
Alignment explanation
Indices: 1682716--1683146 Score: 704
Period size: 215 Copynumber: 2.0 Consensus size: 215
1682706 CTAGCCCAAC
* * *
1682716 TTGAGAGGAGACAAACCCTAGTTCGACTACTTTCCATTTGTTGTCGTAAGCTGCAATGGGATGAT
1 TTGAGAGGAGACAAACCCTAGTTCGACCACTTTCCATTTGTTGTCATAAACTGCAATGGGATGAT
* *
1682781 GAGAGAAAACAAGAACCACAATCCCAAGTTGTTGTACTCACGACCTACAAGCCTGTTATCAAGGA
66 GAGAGAAAACAAGAACCACAATCCCAAGTTATTGTACTCACAACCTACAAGCCTGTTATCAAGGA
* * * * *
1682846 GAAGTCAAGATCGAAGGGTCCAAAA-GGTTTGCCATTTACATCGTGGAGCATGTCGAGG-CCATC
131 GAACTCAAGACCGAAGGGTCCAAAAGGGCTT-CCATTTACATCGTAGAGCATGTCG-GGACCACC
1682909 GACCGCCATAAATCTCGAGTTT
194 GACCGCCATAAATCTCGAGTTT
* *
1682931 TTGAGAGGAGACAAACCCTAGTTTGACCACTTTCCATTTGTTGTCATAAACTGCAGTGGGATGAT
1 TTGAGAGGAGACAAACCCTAGTTCGACCACTTTCCATTTGTTGTCATAAACTGCAATGGGATGAT
*
1682996 GAGAGAAAACGAGAACCACAATCCCAAGTTATTGTACTCACAACCTACAAGCCTGTTATCAAGGA
66 GAGAGAAAACAAGAACCACAATCCCAAGTTATTGTACTCACAACCTACAAGCCTGTTATCAAGGA
1683061 GAACTCAAGACCGAAGGGTCCAAAAGGGCTTCCATTTACATCGTAGAGCATGTCGGGACCACCGA
131 GAACTCAAGACCGAAGGGTCCAAAAGGGCTTCCATTTACATCGTAGAGCATGTCGGGACCACCGA
*
1683126 CCGCCGTAAATCTCGAGTTT
196 CCGCCATAAATCTCGAGTTT
1683146 T
1 T
1683147 CAAGAAGGCA
Statistics
Matches: 200, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
214 2 0.01
215 194 0.97
216 4 0.02
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (215 bp):
TTGAGAGGAGACAAACCCTAGTTCGACCACTTTCCATTTGTTGTCATAAACTGCAATGGGATGAT
GAGAGAAAACAAGAACCACAATCCCAAGTTATTGTACTCACAACCTACAAGCCTGTTATCAAGGA
GAACTCAAGACCGAAGGGTCCAAAAGGGCTTCCATTTACATCGTAGAGCATGTCGGGACCACCGA
CCGCCATAAATCTCGAGTTT
Found at i:1684159 original size:238 final size:238
Alignment explanation
Indices: 1683741--1684457 Score: 1427
Period size: 238 Copynumber: 3.0 Consensus size: 238
1683731 CTTTCTTGCT
1683741 TAAACATACATTCCTCTAATTAACTAAATTCATTTTTTTCTTATTATCTAGTCCTCCCTAAAAGT
1 TAAACATACATTCCTCTAATTAACTAAATTCATTTTTTTCTTATTATCTAGTCCTCCCTAAAAGT
1683806 GTGTCTGGTATGAACTTATTGGGTGTACTTGTCGAAGCAAGCTATGGTGACAAACAAAAAAAAAA
66 GTGTCTGGTATGAACTTATTGGGTGTACTTGTCGAAGCAAGCTATGGTGACAAACAAAAAAAAAA
1683871 GAAAAAGGAAAGAACACTAACAAATTTTTATGTAGTTTGGTGTAAACCTACGTCTATTGGTTTAC
131 GAAAAAGGAAAGAACACTAACAAATTTTTATGTAGTTTGGTGTAAACCTACGTCTATTGGTTTAC
1683936 TGGGCCTTCACAAGAGATAAATCCATTGCTAAATCACAAGAGA
196 TGGGCCTTCACAAGAGATAAATCCATTGCTAAATCACAAGAGA
1683979 TAAACATACATTCCTCTAATTAACTAAATTCATTTTTTTCTTATTATCTAGTCCTCCCTAAAAGT
1 TAAACATACATTCCTCTAATTAACTAAATTCATTTTTTTCTTATTATCTAGTCCTCCCTAAAAGT
1684044 GTGTCTGGTATGAACTTATTGGGTGTACTTGTCGAAGCAAGCTATGGTGACAAACAAAAAAAAAA
66 GTGTCTGGTATGAACTTATTGGGTGTACTTGTCGAAGCAAGCTATGGTGACAAACAAAAAAAAAA
1684109 GAAAAAGGAAAGAACACTAACAAATTTTTATGTAGTTTGGTGTAAACCTACGTCTATTGGTTTAC
131 GAAAAAGGAAAGAACACTAACAAATTTTTATGTAGTTTGGTGTAAACCTACGTCTATTGGTTTAC
1684174 TGGGCCTTCACAAGAGATAAATCCATTGCTAAATCACAAGAGA
196 TGGGCCTTCACAAGAGATAAATCCATTGCTAAATCACAAGAGA
1684217 TAAACATACATTCCTCTAATTAACTAAATTCATTTTTTTCTTATTATCTAGTCCTCCCTAAAAGT
1 TAAACATACATTCCTCTAATTAACTAAATTCATTTTTTTCTTATTATCTAGTCCTCCCTAAAAGT
1684282 GTGTCTGGTATGAACTTATTGGGTGTACTTGTCGAAGCAAGCTATGGTGACAAACAAAAAAAAAA
66 GTGTCTGGTATGAACTTATTGGGTGTACTTGTCGAAGCAAGCTATGGTGACAAACAAAAAAAAAA
1684347 G-AAAAGGAAAGAACACTAACAAATTTTTATGTAGTTTGGTGTAAACCTACGTCTATTGGTTTAC
131 GAAAAAGGAAAGAACACTAACAAATTTTTATGTAGTTTGGTGTAAACCTACGTCTATTGGTTTAC
1684411 TGGGCCTTCACAAGAGATAAATCCATTGCTAAATCACAAGAGA
196 TGGGCCTTCACAAGAGATAAATCCATTGCTAAATCACAAGAGA
1684454 TAAA
1 TAAA
1684458 TCCATTGCTA
Statistics
Matches: 479, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
237 110 0.23
238 369 0.77
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (238 bp):
TAAACATACATTCCTCTAATTAACTAAATTCATTTTTTTCTTATTATCTAGTCCTCCCTAAAAGT
GTGTCTGGTATGAACTTATTGGGTGTACTTGTCGAAGCAAGCTATGGTGACAAACAAAAAAAAAA
GAAAAAGGAAAGAACACTAACAAATTTTTATGTAGTTTGGTGTAAACCTACGTCTATTGGTTTAC
TGGGCCTTCACAAGAGATAAATCCATTGCTAAATCACAAGAGA
Found at i:1684454 original size:26 final size:26
Alignment explanation
Indices: 1684418--1684483 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
1684408 TACTGGGCCT
1684418 TCACAAGAGATAAATCCATTGCTAAA
1 TCACAAGAGATAAATCCATTGCTAAA
1684444 TCACAAGAGATAAATCCATTGCTAAA
1 TCACAAGAGATAAATCCATTGCTAAA
1684470 TCACAAGAGATAAA
1 TCACAAGAGATAAA
1684484 CATACATTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21
Consensus pattern (26 bp):
TCACAAGAGATAAATCCATTGCTAAA
Found at i:1684704 original size:264 final size:263
Alignment explanation
Indices: 1684181--1684712 Score: 1012
Period size: 264 Copynumber: 2.0 Consensus size: 263
1684171 TACTGGGCCT
1684181 TCACAAGAGATAAATCCATTGCTAAATCACAAGAGATAAACATACATTCCTCTAATTAACTAAAT
1 TCACAAGAGATAAATCCATTGCTAAATCACAAGAGATAAACATACATTCCTCTAATTAACTAAAT
1684246 TCATTTTTTTCTTATTATCTAGTCCTCCCTAAAAGTGTGTCTGGTATGAACTTATTGGGTGTACT
66 TCATTTTTTTCTTATTATCTAGTCCTCCCTAAAAGTGTGTCTGGTATGAACTTATTGGGTGTACT
*
1684311 TGTCGAAGCAAGCTATGGTGACAAACAAAAAAAAAAGAAAAGGAAAGAACACTAACAAATTTTTA
131 TGTCGAAGCAAGCTATGGTGACAAACAAAAAAAAAAAAAAAGGAAAGAACACTAACAAATTTTTA
1684376 TGTAGTTTGGTGTAAACCTACGTCTATTGGTTTACTGGGCCTTCACAAGAGATAAATCCATTGCT
196 TGTAGTTTGGTGTAAACCTACGTCTATTGGTTTACTGGGCCTTCACAAGAGATAAATCCATTGCT
1684441 AAA
261 AAA
1684444 TCACAAGAGATAAATCCATTGCTAAATCACAAGAGATAAACATACATTCCTCTAATTAACTAAAT
1 TCACAAGAGATAAATCCATTGCTAAATCACAAGAGATAAACATACATTCCTCTAATTAACTAAAT
1684509 TCA-TTTTTTCTTATTATCTAGTCCTCCCTAAAAGTGTGTCTGGTATGAACTTATTGGGTGTACT
66 TCATTTTTTTCTTATTATCTAGTCCTCCCTAAAAGTGTGTCTGGTATGAACTTATTGGGTGTACT
1684573 TGTCGAAGCAAGCTATGGTGACAAACAAAAAAAAAAAAAAAAGGGAAAGAACACTAACAAATTTT
131 TGTCGAAGCAAGCTATGGTGACAAAC-AAAAAAAAAAAAAAA-GGAAAGAACACTAACAAATTTT
* *
1684638 TATGTAGTTTGGTGTAAACCTACGTCTATTTGTTTACTTGGCCTTCACAAGAGATAAATCCATTG
194 TATGTAGTTTGGTGTAAACCTACGTCTATTGGTTTACTGGGCCTTCACAAGAGATAAATCCATTG
1684703 CTAAA
259 CTAAA
1684708 TCACA
1 TCACA
1684713 GTACAAATAA
Statistics
Matches: 264, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
262 87 0.33
263 82 0.31
264 95 0.36
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (263 bp):
TCACAAGAGATAAATCCATTGCTAAATCACAAGAGATAAACATACATTCCTCTAATTAACTAAAT
TCATTTTTTTCTTATTATCTAGTCCTCCCTAAAAGTGTGTCTGGTATGAACTTATTGGGTGTACT
TGTCGAAGCAAGCTATGGTGACAAACAAAAAAAAAAAAAAAGGAAAGAACACTAACAAATTTTTA
TGTAGTTTGGTGTAAACCTACGTCTATTGGTTTACTGGGCCTTCACAAGAGATAAATCCATTGCT
AAA
Found at i:1685131 original size:12 final size:12
Alignment explanation
Indices: 1685114--1685141 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1685104 TTTATTTAAC
1685114 TAAAATTCAAAA
1 TAAAATTCAAAA
1685126 TAAAATTCAAAA
1 TAAAATTCAAAA
1685138 TAAA
1 TAAA
1685142 TAAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAAATTCAAAA
Found at i:1686462 original size:22 final size:22
Alignment explanation
Indices: 1686437--1686480 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1686427 TAGTCATATA
1686437 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
1686459 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
1686481 TATTTAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:1686540 original size:16 final size:17
Alignment explanation
Indices: 1686504--1686540 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1686494 AATTTTATTT
*
1686504 TAATAATAAATTTTAAA
1 TAATAATAAATTCTAAA
1686521 -AATAAT-AATTCTAAA
1 TAATAATAAATTCTAAA
1686536 TAATA
1 TAATA
1686541 TTATTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTCTAAA
Found at i:1686593 original size:15 final size:15
Alignment explanation
Indices: 1686573--1686630 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
1686563 ATTCAATATT
1686573 AATATTTTAATAATA
1 AATATTTTAATAATA
*
1686588 AATATTTAGTACAATTATA
1 AATATTT--T--AATAATA
*
1686607 AATATATTAATAATA
1 AATATTTTAATAATA
*
1686622 AATGTTTTA
1 AATATTTTA
1686631 TAGTATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 20 0.59
17 2 0.06
19 12 0.35
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:1688818 original size:6 final size:6
Alignment explanation
Indices: 1688809--1688834 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1688799 TTGTTGTTGT
1688809 TGATGC TGATGC TGATGC TGATGC TG
1 TGATGC TGATGC TGATGC TGATGC TG
1688835 CTGGTGGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (6 bp):
TGATGC
Found at i:1694713 original size:16 final size:15
Alignment explanation
Indices: 1694692--1694739 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
1694682 GATGTGAATA
1694692 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
1694708 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
1694723 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
1694739 A
1 A
1694740 ATAATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:1694715 original size:24 final size:24
Alignment explanation
Indices: 1694688--1694743 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1694678 TAATGATGTG
*
1694688 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
1694712 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
1694736 AATAATAA
1 AATAATAA
1694744 TTAATATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:1694722 original size:8 final size:8
Alignment explanation
Indices: 1694688--1694739 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
1694678 TAATGATGTG
*
1694688 AATAATAA
1 AATATTAA
1694696 AATATATAA
1 AATAT-TAA
1694705 AATA-TAA
1 AATATTAA
1694712 AATATTAA
1 AATATTAA
*
1694720 AATATCAA
1 AATATTAA
*
1694728 AATATTAG
1 AATATTAA
1694736 AATA
1 AATA
1694740 ATAATTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:1694929 original size:24 final size:22
Alignment explanation
Indices: 1694902--1694954 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
1694892 TAAAAATATG
1694902 TACATAATATAGTGTTAAAATACA
1 TACATAATATA--GTTAAAATACA
* *
1694926 TACATAATATAGTTAAGATATA
1 TACATAATATAGTTAAAATACA
1694948 TACATAA
1 TACATAA
1694955 GATAACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 16 0.59
24 11 0.41
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (22 bp):
TACATAATATAGTTAAAATACA
Found at i:1694950 original size:22 final size:23
Alignment explanation
Indices: 1694894--1694954 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 23
1694884 GATAATATTA
*
1694894 AAAATATGTACATAATATAGTGTT
1 AAAATATATACATAATATAG-GTT
*
1694918 AAAATACATACATAATATA-GTT
1 AAAATATATACATAATATAGGTT
*
1694940 AAGATATATACATAA
1 AAAATATATACATAA
1694955 GATAACATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 16 0.48
24 17 0.52
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (23 bp):
AAAATATATACATAATATAGGTT
Found at i:1694979 original size:30 final size:29
Alignment explanation
Indices: 1694943--1695010 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
1694933 TATAGTTAAG
*
1694943 ATATATACATAAGATAACATGTAAAAATAT
1 ATATATAAATAAGATAACAT-TAAAAATAT
* * *
1694973 ATATATAAATAATATAATATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAAATAT
*
1695002 ATACATAAA
1 ATATATAAA
1695011 ATAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAAATAT
Found at i:1695001 original size:25 final size:25
Alignment explanation
Indices: 1694973--1695029 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
1694963 GTAAAAATAT
* *
1694973 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAAAATAATATAAAAG
* * *
1694998 ATATATACATAAAATAGTATAAAAT
1 ATATATAAATAAAATAATATAAAAG
1695023 ATATATA
1 ATATATA
1695030 TACACGTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAAATAAAATAATATAAAAG
Found at i:1695506 original size:30 final size:30
Alignment explanation
Indices: 1695470--1695572 Score: 179
Period size: 30 Copynumber: 3.4 Consensus size: 30
1695460 TAGGTACAAG
*
1695470 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
1695500 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1695530 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1695560 TGGTGGTGGAAAA
1 TGGTGGTGGAAAA
1695573 AGAGTGGAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.22, C:0.03, G:0.50, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:1695581 original size:11 final size:11
Alignment explanation
Indices: 1695565--1695590 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1695555 GGAGTTGGTG
1695565 GTGGAAAAAGA
1 GTGGAAAAAGA
1695576 GTGGAAAAAGA
1 GTGGAAAAAGA
1695587 GTGG
1 GTGG
1695591 CTAGTGGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.42, T:0.12
Consensus pattern (11 bp):
GTGGAAAAAGA
Found at i:1695581 original size:41 final size:41
Alignment explanation
Indices: 1695535--1695613 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
1695525 GGAGTTGGTG
* *
1695535 GTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGA
1 GTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAGA
1695576 GTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAA
1 GTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAA
1695614 GGTGTGGCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.30, C:0.03, G:0.46, T:0.22
Consensus pattern (41 bp):
GTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAGA
Found at i:1695612 original size:30 final size:30
Alignment explanation
Indices: 1695575--1695655 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
1695565 GTGGAAAAAG
*
1695575 AGTGGAAAAAGAGTGGCTAGTGGAGTTGGT
1 AGTGGAAAAGGAGTGGCTAGTGGAGTTGGT
* *
1695605 GGTGGAAAAGGTGTGGCTAGTGGAGTTGGT
1 AGTGGAAAAGGAGTGGCTAGTGGAGTTGGT
1695635 AGTGGAAAAGGAGTGGCTAGT
1 AGTGGAAAAGGAGTGGCTAGT
1695656 TGAGAAAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.27, C:0.04, G:0.46, T:0.23
Consensus pattern (30 bp):
AGTGGAAAAGGAGTGGCTAGTGGAGTTGGT
Found at i:1695621 original size:71 final size:71
Alignment explanation
Indices: 1695505--1695650 Score: 274
Period size: 71 Copynumber: 2.1 Consensus size: 71
1695495 GGAGTTGGTG
*
1695505 GTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGA
1 GTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTAGTGGA
1695570 AAAAGA
66 AAAAGA
1695576 GTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTAGTGGA
1 GTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTAGTGGA
*
1695641 AAAGGA
66 AAAAGA
1695647 GTGG
1 GTGG
1695651 CTAGTTGAGA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.27, C:0.03, G:0.47, T:0.23
Consensus pattern (71 bp):
GTGGAAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTAGTGGA
AAAAGA
Found at i:1696421 original size:14 final size:14
Alignment explanation
Indices: 1696402--1696451 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
1696392 GAGTTGATTT
1696402 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
1696416 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
1696431 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
1696445 TT-AAAAA
1 TTGAAAAA
1696452 GACCTCAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 4 0.12
14 15 0.45
15 14 0.42
ACGTcount: A:0.64, C:0.06, G:0.14, T:0.16
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:1696564 original size:73 final size:73
Alignment explanation
Indices: 1696431--1696673 Score: 290
Period size: 76 Copynumber: 3.3 Consensus size: 73
1696421 AAAACAGAAA
* * ** *
1696431 TTGA-AAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCGCAATA
1 TTGACAAA-CAGAAATTGAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATA
1696495 TGAGTTAATTT
63 TGAGTTAATTT
* * *
1696506 TTGACAAACAGAAATTGAAATTACCTCGGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGA
1 TTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
*
1696571 GTTGATTTTT
66 GTT-A-ATTT
* * *
1696581 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGACAAACAGAAA-TTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
*
1696646 AGTTGATTT
65 AGTTAATTT
* *
1696655 TTTACGAACAGAAATTGAA
1 TTGACAAACAGAAATTGAA
1696674 GAACAGAAAT
Statistics
Matches: 143, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
73 38 0.27
74 15 0.10
75 38 0.27
76 52 0.36
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (73 bp):
TTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTAATTT
Found at i:1696679 original size:14 final size:14
Alignment explanation
Indices: 1696660--1696687 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1696650 GATTTTTTAC
1696660 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1696674 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1696688 AAAACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:1696731 original size:89 final size:88
Alignment explanation
Indices: 1696581--1696763 Score: 271
Period size: 89 Copynumber: 2.1 Consensus size: 88
1696571 GTTGATTTTT
* *
1696581 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAATACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
* * *
1696646 AGTTGATTTTTTACGAACAGAAA
66 AGTTAATTTTTGACAAACAGAAA
*
1696669 TTGAAGAACAGAAATTGAAAAA-ACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACAGAAATTGAAAAATACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTCGCAAT
1696732 ATGAGTTAATTTTTGACAAACAGAAA
63 ATGAGTTAATTTTTGACAAACAGAAA
1696758 TTGAAA
1 TTGAAA
1696764 TTACCTCAGC
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
87 8 0.09
88 20 0.24
89 55 0.65
90 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (88 bp):
TTGAAAAACAGAAATTGAAAAATACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTAATTTTTGACAAACAGAAA
Found at i:1696884 original size:74 final size:73
Alignment explanation
Indices: 1696669--1697689 Score: 672
Period size: 73 Copynumber: 13.3 Consensus size: 73
1696659 CGAACAGAAA
* * *
1696669 TTGAAGAACAGAAATTGAAAAA-ACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTTAAAAATACCTCAGC--GTG-TCCGAGGCTCAACTCACCTCTCGCAATA
*
1696733 TGAGTTAATTT
63 TGAGTTGATTT
* * *
1696744 TTGACAAACAGAAA-TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGT-CCGAGGCTCAACTCACCTCTCGCAATATG
1696808 AGTTGATTT
65 AGTTGATTT
*
1696817 TTGAAAAACAAAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATG
1696882 AGTTGATTTTTT
65 AGTTGA---TTT
* ** * * ** * * * * *
1696894 TTTACGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAG-CATGTGAGC-CGAGGCTCAAC
1 TTGAAAAACAGAAATTTAA-AA-A-TACCT---CAG-CGT--GTC-CGAG-GCTC-A-ACTC---
*
1696957 TCACCTCTCGCAATATGAGTTAATTT
50 --ACCTCTCGCAATATGAGTTGATTT
* * * *
1696983 TTGACAAACAGAAA-TTGAAATTACCTCAGCATGTCTCGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTC-CGAGGCTCAACTCACCTCTCGCAATATG
*
1697047 AGTCGATTT
65 AGTTGATTT
1697056 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATG
1697121 AGTTGATTTTTT
65 AGTTGA---TTT
* ** * * ** * * * * *
1697133 TTTACGAACAGAAATTGAAGAACAGAAATTGAAAAGACCT-TAGCATGTGAGC-CGAGGCTCAAC
1 TTGAAAAACAGAAATTTAA-AA-A-TACCT---CAG-CGTGT--C-CGAG-GCTC-A-ACTC---
1697196 TCACCTCTCGCAATATGAGTTGATTTTTT
50 --ACCTCTCGCAATATGAGTTGA---TTT
* ** * * *
1697225 TTTACGAACAGAAA-TTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTTAAAAATACCTCAGC--GTG-TCCGAGGCTCAACTCACCTCTCGCAATA
1697289 TGAGTTGATTT
63 TGAGTTGATTT
* * * *
1697300 TTGACAAACAGAAA-TTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTC-CGAGGCTCAACTCACCTCTCGCAATATG
1697364 AGTTGATTT
65 AGTTGATTT
* * *
1697373 TTGACAAACAGAAA-TTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATG
1697437 AGTTGA-TT
65 AGTTGATTT
* * * **
1697445 TT-AAAAACA-AAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTACAATA
1 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGT---CCGAGGCTCAACTCACCTCTCGCAATA
* *
1697508 TGAGCTAATTT
63 TGAGTTGATTT
* ** * **
1697519 TTTATGAACATAAA-TTAAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATG
1697583 AGTTGATTTTTT
65 AGTTGA---TTT
* ** * *
1697595 TTTACGAACA-AAATTTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTTAAAAATACCTCAGC--GTG-TCCGAGGCTCAACTCACCTCTCGCAATA
*
1697659 TGAGCTGA-TT
63 TGAGTTGATTT
*
1697669 TTGAAAAAGTAGAAA-TTAAAA
1 TTGAAAAA-CAGAAATTTAAAA
1697690 GGTTCAACCC
Statistics
Matches: 768, Mismatches: 104, Indels: 148
0.75 0.10 0.15
Matches are distributed among these distances:
70 3 0.00
71 25 0.03
72 7 0.01
73 253 0.33
74 118 0.15
75 80 0.10
76 31 0.04
77 35 0.05
78 63 0.08
79 8 0.01
80 8 0.01
81 2 0.00
82 2 0.00
83 8 0.01
84 8 0.01
85 15 0.02
86 9 0.01
87 8 0.01
88 4 0.01
89 16 0.02
90 2 0.00
91 2 0.00
92 61 0.08
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (73 bp):
TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:1696918 original size:14 final size:14
Alignment explanation
Indices: 1696899--1696926 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1696889 TTTTTTTTAC
1696899 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1696913 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1696927 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:1696996 original size:239 final size:239
Alignment explanation
Indices: 1696423--1697609 Score: 1712
Period size: 239 Copynumber: 5.0 Consensus size: 239
1696413 AAATTGAAAA
* *
1696423 AACAGAAATTGAA-AAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTC
1 AACAGAAATTGAAGAA-CAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTC
*
1696487 TCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCGGCGTGTCCCGAGGCTCAA
65 TCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAA
*
1696552 CTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTC
130 CTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTC
1696617 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTACG
193 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
*
1696661 AACAGAAATTGAAGAACAGAAATTGAAAAAACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
1 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
1696726 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
66 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
*
1696791 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTTAAAAATACCTCAGCGTGTCCTG
131 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTG
1696856 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
196 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
1696900 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
1 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
* *
1696965 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCATGTCTCGAGGCTCAAC
66 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
*
1697030 TCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTG
131 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTG
1697095 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
196 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
*
1697139 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTTAGCATGTGAGCCGAGGCTCAACTCACCTCT
1 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
* * * ** **
1697204 CGCAATATGAGTTGATTTTTTTTTACGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGC
66 CGCAATATGAGTT-A--ATTTTTGACAAACAGAAATTGAAATTACCTCAGC--GTGTCCCGAGGC
* * *
1697269 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAA-TTGAAATTACCTCAGCGTG
126 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTG
*
1697333 TCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTT--G
191 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
** *
1697376 -AC---------A-AACAGAAATTGAAATTACCTCAGC--GTG-TCCTGAGGCTCAACTCACCTC
1 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTC
* * * * * *
1697427 TCGCAATATGAGTTGA-TTTT-AAAAACAAAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTC
65 TCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGT--CCCGAGGCTC
** * * * ** * **
1697490 AACTCACCTCTTACAATATGAGCTAATTTTTTATGAACATAAA-TTAAAACCACCTCAGCGTGTC
128 AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTC
1697554 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
193 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
1697601 AACA-AAATT
1 AACAGAAATT
1697610 TGAAAATACC
Statistics
Matches: 874, Mismatches: 50, Indels: 56
0.89 0.05 0.06
Matches are distributed among these distances:
217 3 0.00
219 119 0.14
220 4 0.00
223 7 0.01
224 34 0.04
225 1 0.00
226 23 0.03
227 1 0.00
236 75 0.09
237 1 0.00
238 145 0.17
239 327 0.37
240 1 0.00
242 29 0.03
243 53 0.06
244 51 0.06
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (239 bp):
AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTG
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
Found at i:1697044 original size:73 final size:72
Alignment explanation
Indices: 1696908--1697131 Score: 322
Period size: 74 Copynumber: 3.0 Consensus size: 72
1696898 CGAACAGAAA
* *
1696908 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGT---CCGAGGCTCAACTCACCTCTCGCAATAT
*
1696973 GAGTTAATTT
63 GAGTTGATTT
* *
1696983 TTGACAAACAGAAATTGAAATTACCTCAGCATGTCTCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTC-CGAGGCTCAACTCACCTCTCGCAATATGA
*
1697048 GTCGATTT
65 GTTGATTT
* *
1697056 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAA-TTGAAAATACCTCAGCATGTCC-GAGGCTCAACTCACCTCTCGCAATATG
1697121 AGTTGATTT
64 AGTTGATTT
1697130 TT
1 TT
1697132 TTTTACGAAC
Statistics
Matches: 135, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
72 1 0.01
73 49 0.36
74 55 0.41
75 30 0.22
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (72 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTT
Found at i:1697157 original size:14 final size:14
Alignment explanation
Indices: 1697138--1697165 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1697128 TTTTTTTTAC
1697138 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1697152 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1697166 AAGACCTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:1697282 original size:317 final size:294
Alignment explanation
Indices: 1696675--1697689 Score: 1064
Period size: 317 Copynumber: 3.3 Consensus size: 294
1696665 GAAATTGAAG
** *
1696675 AACAGAAATTGAAAAAACCTCAGCATGTGAGC-CGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AACAGAAATTGAAATTACCTCAGCATGT---CTCGAGGCTCAACTCACCTCTCGCAATATGAGTC
* * * * *
1696739 AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAA
63 GATTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
* * * *
1696804 TATGAGTTGATTTTTGAAAAACAAAAATTTAAAAATACCTCAGC--GTG-TCCTGAGGCTCAACT
128 TATGAGTTGA-TTTT-AAAAACAAAAA-TTGAAAAGACCTCAGCATGTGAGCC-AAGGCTCAACT
* * *
1696866 CACCTCTCGCAATATGAGTTGATTTTTTTTTACGAACAGAAATTGAAGAACAGAAATTGAAAAGA
189 CACCTCTCACAATATGAGCT-A--ATTTTTT----AC----------GAACAGAAATTGAAAAGA
1696931 CCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACA
237 CCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACA
1696989 AACAGAAATTGAAATTACCTCAGCATGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
1 AACAGAAATTGAAATTACCTCAGCATGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
1697054 TTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
66 TTTTGAAAAACAGAAA-TTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
* *
1697119 TGAGTTGATTTTTTTTTACGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTTAGCATGTGAG
130 TGAGTTGA-----TTTT----------A---AA-AACAAAAATTGAAAAGACCTCAGCATGTGAG
* * * *
1697184 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACGAACAGAAATTGAAAAGAC
176 CCAAGGCTCAACTCACCTCTCACAATATGAGCT-A--ATTTTTTACGAACAGAAATTGAAAAGAC
*
1697249 CTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA
238 CTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACA
* * *
1697306 AACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCATGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
* * *
1697371 TTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
66 TTTTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
* *
1697436 GAGTTGATTTTAAAAACAAAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCT
131 GAGTTGATTTTAAAAACAAAAATTGAAAAGACCTCAGCATGTGAGCCAAGGCTCAACTCACCTCT
* * * * *
1697501 TACAATATGAGCTAATTTTTTATGAACATAAATT-AAAACCACCTCAGC--GTG-TCCTGAGGCT
196 CACAATATGAGCTAATTTTTTACGAACAGAAATTGAAAA-GACCTCAGCATGTGAGCC-GAGGCT
* * *
1697562 CAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
259 CAACTCACCTCTCGCAATATGAGTT-A--ATTTTTGACA
*
1697601 AACA-AAATTTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATGAG-
1 AACAGAAA-TTGAAATTACCTCAGCATGT---CTCGAGGCTCAACTCACCTCTCGCAATATGAGT
*
1697663 CTGA-TTTTGAAAAAGTAGAAATTAAAA
62 C-GATTTTTGAAAAA-CAGAAATTAAAA
1697690 GGTTCAACCC
Statistics
Matches: 623, Mismatches: 45, Indels: 83
0.83 0.06 0.11
Matches are distributed among these distances:
291 2 0.00
292 34 0.05
293 4 0.01
294 28 0.04
295 29 0.05
296 10 0.02
297 97 0.16
298 3 0.00
301 1 0.00
311 5 0.01
312 48 0.08
313 53 0.09
314 26 0.04
316 54 0.09
317 157 0.25
326 1 0.00
327 2 0.00
329 15 0.02
330 7 0.01
331 45 0.07
332 2 0.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (294 bp):
AACAGAAATTGAAATTACCTCAGCATGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
TTTTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTAAAAACAAAAATTGAAAAGACCTCAGCATGTGAGCCAAGGCTCAACTCACCTCT
CACAATATGAGCTAATTTTTTACGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCA
ACTCACCTCTCGCAATATGAGTTAATTTTTGACA
Found at i:1697739 original size:54 final size:54
Alignment explanation
Indices: 1697639--1697744 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
1697629 GAACCGAGGC
*
1697639 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* * *
1697693 TCAACCCACTTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
1697745 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 32 0.71
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:1697976 original size:122 final size:123
Alignment explanation
Indices: 1697781--1698021 Score: 369
Period size: 122 Copynumber: 2.0 Consensus size: 123
1697771 CCTGAAGCTC
* * *
1697781 AACTCACCTCTCGCAATATGAGTTGAAATTAAACCAAAAAAATTGAAAATACCTCAGCGTGCCCC
1 AACTCACCTCTCGCAATATGAGTTCAAATTAAA-CAAAAAAACTAAAAATACCTCAGCGTGCCCC
1697846 GAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTT
65 GAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAAGGCTT
* * * *
1697906 AACTCACCTCTCGCAATATGAG-TCAATTTAAA-ACATAAACTAAAAATACTTCAGCGTGCCCCG
1 AACTCACCTCTCGCAATATGAGTTCAAATTAAACAAAAAAACTAAAAATACCTCAGCGTGCCCCG
* *
1697969 AGGCTCAACTCACTTCTTGCAATATGAGTTGATTTTGAAAACAAAAATTAAAA
66 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAAA
1698022 ATACCTCAAC
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
121 16 0.15
122 61 0.57
124 8 0.07
125 22 0.21
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (123 bp):
AACTCACCTCTCGCAATATGAGTTCAAATTAAACAAAAAAACTAAAAATACCTCAGCGTGCCCCG
AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAGGCTT
Found at i:1698043 original size:71 final size:70
Alignment explanation
Indices: 1697900--1698074 Score: 210
Period size: 71 Copynumber: 2.5 Consensus size: 70
1697890 AAAAATTAAA
* * * * * * *
1697900 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACTTCAGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
1697964 CCCCG
66 CCCCG
* *
1697969 AGGCTCAACTCACTTCTTGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACGT
* **
1698034 GTCTTG
65 GCCCCG
1698040 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTT
1698075 CCCTTGAAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
69 25 0.28
70 6 0.07
71 59 0.66
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:1707303 original size:40 final size:40
Alignment explanation
Indices: 1707220--1707482 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
1707210 TTGAATGTTG
* * * * * *
1707220 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
1707260 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
1707300 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1707340 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
1707380 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
1707420 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
1707459 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
1707483 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:1707502 original size:79 final size:80
Alignment explanation
Indices: 1707259--1707517 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
1707249 AAGTGAATAT
* * * * * *
1707259 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
1707323 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
1707339 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
1707404 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
1707419 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
1707483 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
1707498 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
1707518 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:1709569 original size:30 final size:31
Alignment explanation
Indices: 1709535--1709603 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 31
1709525 GCAATGTATG
*
1709535 AATGAATGCATGAATGAATGCATGAATG-TC
1 AATGAATGCATGAATGAATGCATGAATGTTA
*
1709565 AATGAATGCATGAATGAATGGATGAATGTTA
1 AATGAATGCATGAATGAATGCATGAATGTTA
1709596 AATGAATG
1 AATGAATG
1709604 TCAGTCATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 27 0.75
31 9 0.25
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (31 bp):
AATGAATGCATGAATGAATGCATGAATGTTA
Found at i:1709603 original size:4 final size:4
Alignment explanation
Indices: 1709527--1709592 Score: 69
Period size: 4 Copynumber: 16.0 Consensus size: 4
1709517 TGGGATATGC
* * * *
1709527 AATG TATG AATG AATG CATG AATG AATG CATG AATG TCAATG AATG CATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG --AATG AATG AATG
*
1709577 AATG AATG GATG AATG
1 AATG AATG AATG AATG
1709593 TTAAATGAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
4 46 0.92
6 4 0.08
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.27
Consensus pattern (4 bp):
AATG
Found at i:1711143 original size:16 final size:15
Alignment explanation
Indices: 1711122--1711169 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
1711112 GATGTGAATA
1711122 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
1711138 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
1711153 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
1711169 A
1 A
1711170 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:1711145 original size:24 final size:24
Alignment explanation
Indices: 1711118--1711173 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1711108 TAATGATGTG
*
1711118 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
1711142 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
1711166 AATAATAA
1 AATAATAA
1711174 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:1711152 original size:8 final size:8
Alignment explanation
Indices: 1711118--1711169 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
1711108 TAATGATGTG
*
1711118 AATAATAA
1 AATATTAA
1711126 AATATATAA
1 AATAT-TAA
1711135 AATA-TAA
1 AATATTAA
1711142 AATATTAA
1 AATATTAA
*
1711150 AATATCAA
1 AATATTAA
*
1711158 AATATTAG
1 AATATTAA
1711166 AATA
1 AATA
1711170 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:1711389 original size:22 final size:24
Alignment explanation
Indices: 1711326--1711390 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
1711316 CGTGATAATA
*
1711326 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
1711351 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
1711374 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
1711391 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:1711415 original size:30 final size:29
Alignment explanation
Indices: 1711379--1711446 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
1711369 TATAGTTAAG
*
1711379 ATATATACATAAGATAACATGTAAAAATAT
1 ATATATAAATAAGATAACAT-TAAAAATAT
* * *
1711409 ATATATAAATAATATAATATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAAATAT
*
1711438 ATACATAAA
1 ATATATAAA
1711447 ATAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAAATAT
Found at i:1711437 original size:25 final size:25
Alignment explanation
Indices: 1711409--1711465 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
1711399 GTAAAAATAT
* *
1711409 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAAAATAATATAAAAG
* * *
1711434 ATATATACATAAAATAGTATAAAAT
1 ATATATAAATAAAATAATATAAAAG
1711459 ATATATA
1 ATATATA
1711466 TACACGTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAAATAAAATAATATAAAAG
Done.