Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 202 of 204
Found at i:59403957 original size:21 final size:21
Alignment explanation
Indices: 59403931--59403971 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59403921 AGACGAGCAA
* *
59403931 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
59403952 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
59403972 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:59407037 original size:4 final size:4
Alignment explanation
Indices: 59407030--59407136 Score: 72
Period size: 4 Copynumber: 25.2 Consensus size: 4
59407020 TTATGCATGC
* * *
59407030 ATGT ATGT AGGGT ATGT AATGT ATGCC ATTGT ATGT A-GTT TTGT ATGT
1 ATGT ATGT A-TGT ATGT -ATGT ATG-T A-TGT ATGT ATG-T ATGT ATGT
* * * *
59407078 ATGT ATGT ATGT ATGC ATGC ATGT ATGT GTGT ATGT AGGGT ATGTT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-TGT ATG-T ATGT
*
59407128 ACGT ATGT A
1 ATGT ATGT A
59407137 AATAAGGTAA
Statistics
Matches: 81, Mismatches: 14, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
3 1 0.01
4 61 0.75
5 17 0.21
6 2 0.02
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.44
Consensus pattern (4 bp):
ATGT
Found at i:59411731 original size:33 final size:34
Alignment explanation
Indices: 59411649--59411739 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 34
59411639 ATTGACGGAT
* * *
59411649 AAGACCATAGCTGGACCATGGCAATATTTAAATGT
1 AAGACCATAGCTGGGCTATGGC-ATATTTAAATGA
*
59411684 AAGATCATAGCTGGGCTATGGCAT-TTT-AATGAA
1 AAGACCATAGCTGGGCTATGGCATATTTAAATG-A
* *
59411717 AAGACCATAACTGGGTTATGGCA
1 AAGACCATAGCTGGGCTATGGCA
59411740 CCTTGAATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 4 0.08
33 23 0.48
34 2 0.04
35 19 0.40
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26
Consensus pattern (34 bp):
AAGACCATAGCTGGGCTATGGCATATTTAAATGA
Found at i:59411754 original size:33 final size:32
Alignment explanation
Indices: 59411679--59411757 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
59411669 GCAATATTTA
* * * *
59411679 AATGTAAGATCATAGCTGGGCTATGGCATTTT
1 AATGTAAGACCATAACTGGGCTATGGCACTTG
* *
59411711 AATGAAAAGACCATAACTGGGTTATGGCACCTTG
1 AATG-TAAGACCATAACTGGGCTATGGCA-CTTG
59411745 AATGTAAGACCAT
1 AATGTAAGACCAT
59411758 GGTTGGTCCA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 4 0.11
33 28 0.74
34 6 0.16
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (32 bp):
AATGTAAGACCATAACTGGGCTATGGCACTTG
Found at i:59411876 original size:107 final size:107
Alignment explanation
Indices: 59411681--59411879 Score: 267
Period size: 107 Copynumber: 1.9 Consensus size: 107
59411671 AATATTTAAA
* * * **
59411681 TGTAAGATCATAGCTGGGCTATGGCATTTTAATGAAAAGACCATAACTGGGTTATGGCACCTTGA
1 TGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGAGTTATGGCACCTCAA
** *
59411746 ATGTAAGACCATGGTTGGTCCATGACAGTATATATATACATG
66 ATGTAAGACCATGGCAGGGCCATGACAGTATATATATACATG
* * *
59411788 TGTAAGACCATAGCTGGGCTATGGCATTCTGAT-AATAAGACCATAGCTGAGTTATTGCA-CTAC
1 TGTAAGACCATAGCTGGGCTATGGCATTCTAATGAA-AAGACCATAACTGAGTTATGGCACCT-C
59411851 AAATGTAAGACCATGGCAGGGCCATGACA
64 AAATGTAAGACCATGGCAGGGCCATGACA
59411880 ATGCATCTGT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
106 4 0.05
107 75 0.95
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (107 bp):
TGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGAGTTATGGCACCTCAA
ATGTAAGACCATGGCAGGGCCATGACAGTATATATATACATG
Found at i:59414670 original size:19 final size:19
Alignment explanation
Indices: 59414634--59414671 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
59414624 ATATGTTTCA
*
59414634 TTTTTTTTAATTTATGAAT
1 TTTTTTTTAAGTTATGAAT
59414653 TTTTTTTTGAAGTT-TGAAT
1 TTTTTTTT-AAGTTATGAAT
59414672 GGTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (19 bp):
TTTTTTTTAAGTTATGAAT
Found at i:59417053 original size:13 final size:13
Alignment explanation
Indices: 59417035--59417061 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59417025 CCTCCAGGCT
59417035 CTAAGCCCAAGAA
1 CTAAGCCCAAGAA
59417048 CTAAGCCCAAGAA
1 CTAAGCCCAAGAA
59417061 C
1 C
59417062 AATTCATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.33, G:0.15, T:0.07
Consensus pattern (13 bp):
CTAAGCCCAAGAA
Found at i:59417183 original size:33 final size:33
Alignment explanation
Indices: 59417143--59417227 Score: 170
Period size: 33 Copynumber: 2.6 Consensus size: 33
59417133 ATGTAAATAC
59417143 TACTGCATGTTTCATGTTTCATGTTTCATGCAA
1 TACTGCATGTTTCATGTTTCATGTTTCATGCAA
59417176 TACTGCATGTTTCATGTTTCATGTTTCATGCAA
1 TACTGCATGTTTCATGTTTCATGTTTCATGCAA
59417209 TACTGCATGTTTCATGTTT
1 TACTGCATGTTTCATGTTT
59417228 TTTTTCCCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.47
Consensus pattern (33 bp):
TACTGCATGTTTCATGTTTCATGTTTCATGCAA
Found at i:59417224 original size:7 final size:7
Alignment explanation
Indices: 59417148--59417205 Score: 62
Period size: 7 Copynumber: 7.6 Consensus size: 7
59417138 AATACTACTG
59417148 CATGTTT
1 CATGTTT
59417155 CATGTTT
1 CATGTTT
59417162 CATGTTT
1 CATGTTT
*
59417169 CATGCAATACTG
1 CATG---T--TT
59417181 CATGTTT
1 CATGTTT
59417188 CATGTTT
1 CATGTTT
59417195 CATGTTT
1 CATGTTT
59417202 CATG
1 CATG
59417206 CAATACTGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
7 37 0.84
9 1 0.02
10 1 0.02
12 5 0.11
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (7 bp):
CATGTTT
Found at i:59417402 original size:37 final size:37
Alignment explanation
Indices: 59417375--59417484 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
59417365 TTTATGTGTT
59417375 AAAGACTTATGTAATGTTTTTAATTATTTAGTGATTC
1 AAAGACTTATGTAATGTTTTTAATTATTTAGTGATTC
* * * *
59417412 AAAAATTTATGTAATGTTTTTAGTTATGTAGTGATTC
1 AAAGACTTATGTAATGTTTTTAATTATTTAGTGATTC
*
59417449 AAAGACTTATGTAAT-TTTTTAAATTATATAGTGATT
1 AAAGACTTATGTAATGTTTTT-AATTATTTAGTGATT
59417485 TAAATCGATT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 5 0.08
37 59 0.92
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.48
Consensus pattern (37 bp):
AAAGACTTATGTAATGTTTTTAATTATTTAGTGATTC
Found at i:59417505 original size:9 final size:9
Alignment explanation
Indices: 59417493--59417576 Score: 107
Period size: 9 Copynumber: 9.4 Consensus size: 9
59417483 TTTAAATCGA
*
59417493 TTAAGTTGG
1 TTAAGTCGG
*
59417502 TTAAATCGG
1 TTAAGTCGG
59417511 TTAAGTCGG
1 TTAAGTCGG
59417520 TTAAGTCGG
1 TTAAGTCGG
*
59417529 TTAAATCGG
1 TTAAGTCGG
59417538 TTAAGTCGG
1 TTAAGTCGG
59417547 TTAA-TCGG
1 TTAAGTCGG
* *
59417555 TTAAATAGG
1 TTAAGTCGG
*
59417564 TTAAATCGG
1 TTAAGTCGG
59417573 TTAA
1 TTAA
59417577 TTTTTAACCA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
8 8 0.12
9 59 0.88
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (9 bp):
TTAAGTCGG
Found at i:59417514 original size:27 final size:27
Alignment explanation
Indices: 59417484--59417576 Score: 134
Period size: 27 Copynumber: 3.5 Consensus size: 27
59417474 ATATAGTGAT
* *
59417484 TTAAATCGATTAAGTTGGTTAAATCGG
1 TTAAATCGGTTAAGTCGGTTAAATCGG
*
59417511 TTAAGTCGGTTAAGTCGGTTAAATCGG
1 TTAAATCGGTTAAGTCGGTTAAATCGG
* *
59417538 TTAAGTCGGTTAA-TCGGTTAAATAGG
1 TTAAATCGGTTAAGTCGGTTAAATCGG
59417564 TTAAATCGGTTAA
1 TTAAATCGGTTAA
59417577 TTTTTAACCA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
26 24 0.39
27 37 0.61
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.35
Consensus pattern (27 bp):
TTAAATCGGTTAAGTCGGTTAAATCGG
Found at i:59422556 original size:33 final size:35
Alignment explanation
Indices: 59422510--59422588 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 35
59422500 TAATAGATGT
* *
59422510 AAAACTTGAATTCTGATTC-ATATATATATATTT-G
1 AAAAATTGAATTCTGATTCAAT-TATATACATTTAG
*
59422544 AAAAATTG-ATTCTGATTTAATTATATACATTTAG
1 AAAAATTGAATTCTGATTCAATTATATACATTTAG
*
59422578 AAAAAATGAAT
1 AAAAATTGAAT
59422589 AGATATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 19 0.50
34 17 0.45
35 2 0.05
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (35 bp):
AAAAATTGAATTCTGATTCAATTATATACATTTAG
Found at i:59422583 original size:35 final size:34
Alignment explanation
Indices: 59422510--59422588 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 34
59422500 TAATAGATGT
* * *
59422510 AAAACTTGAATTCTGATTCATATATATATATTTG
1 AAAAATTGAATTCTGATTAATATATATACATTTG
59422544 AAAAATTG-ATTCTGATTTAAT-TATATACATTTAG
1 AAAAATTGAATTCTGA-TTAATATATATACATTT-G
*
59422578 AAAAAATGAAT
1 AAAAATTGAAT
59422589 AGATATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 17 0.45
34 19 0.50
35 2 0.05
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (34 bp):
AAAAATTGAATTCTGATTAATATATATACATTTG
Found at i:59426205 original size:17 final size:17
Alignment explanation
Indices: 59426183--59426216 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
59426173 ATCCACTAAT
*
59426183 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
59426200 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
59426217 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:59430843 original size:17 final size:17
Alignment explanation
Indices: 59430821--59430854 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
59430811 ATCCACTAAT
*
59430821 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
59430838 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
59430855 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:59431620 original size:14 final size:15
Alignment explanation
Indices: 59431594--59431622 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59431584 TTCTTTAAAA
59431594 GAAGTTAAGAGTGTC
1 GAAGTTAAGAGTGTC
59431609 GAAGTT-AGAGTGTC
1 GAAGTTAAGAGTGTC
59431623 ATCTACTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.07, G:0.34, T:0.28
Consensus pattern (15 bp):
GAAGTTAAGAGTGTC
Found at i:59441759 original size:18 final size:18
Alignment explanation
Indices: 59441736--59441774 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
59441726 CTAAATTTCA
59441736 TAATATAAATATTATTAT
1 TAATATAAATATTATTAT
* *
59441754 TAATATTAATATTTTTAT
1 TAATATAAATATTATTAT
59441772 TAA
1 TAA
59441775 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATATAAATATTATTAT
Found at i:59445614 original size:241 final size:238
Alignment explanation
Indices: 59445121--59445747 Score: 816
Period size: 241 Copynumber: 2.6 Consensus size: 238
59445111 CACCCATGTC
* *
59445121 GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCACCAAATACATGATTTTTTTTTAAAGAA
1 GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCTCCAAATACAT--TTTTTTTTAAAAGAA
* * * * * *
59445186 AAATGGAACATACCTGTGTCCTAAATAGACTTACATCTGCCACTTACGCTC-AGGTCCGATTAAC
64 AAATGGAACAAACCCGTGTCCTAAATAGACTTATATCTGACACTCACACTCGA-GTCCGATTAAC
* *
59445250 AAAAAAGTACTAACATG---C-AACTATATGAAAGAATGGTTGCAATTACAAGCTCCAACTCATC
128 AAAAAAGTACTAGCATGTAACTAACTATATGAAAGAACGGTTGCAATTACAAGCTCCAACTCATC
59445311 ATTTCAATTGAAGTACTCATGTCAGATACAACACATATTCATGCAA
193 ATTTCAATTGAAGTACTCATGTCAGATACAACACATATTCATGCAA
* * * * *
59445357 AGGAACAAGAGTATAGGAATATGATCTTTCAAAGACCTCCAAATACATTTTCTTTTTAAAAGGAA
1 GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCTCCAAATACATTTT-TTTTTAAAA-GAA
* * *
59445422 AAATGGAGCAAACCCGTGTCCTAAATAGGCTTATATTTGACACTCACACTCGAGTCCGATTAACA
64 AAATGGAACAAACCCGTGTCCTAAATAGACTTATATCTGACACTCACACTCGAGTCCGATTAACA
* * * *
59445487 GAAAAAGTACTAGCATGTAACTAACTATATGAAAGAACGGTTGCAATTACTAGCTCCGACTCGTT
129 -AAAAAGTACTAGCATGTAACTAACTATATGAAAGAACGGTTGCAATTACAAGCTCCAACTCATC
* * ** * *
59445552 GTTTCAATTTAAGTACTTGTGTCTGATACGACACATATTCATGCAA
193 ATTTCAATTGAAGTACTCATGTCAGATACAACACATATTCATGCAA
* *
59445598 GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCTCCAAATACA-TTTTTTTTAATAGTAAA
1 GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCTCCAAATACATTTTTTTTTAAAAGAAAA
* * * * * *
59445662 ATGGAACAAAACCCGTGTTCTAAAAAGCCTTATATCTAACATTCACACTCGAGTCTGATTAACAA
66 ATGGAAC-AAACCCGTGTCCTAAATAGACTTATATCTGACACTCACACTCGAGTCCGATTAACAA
*
59445727 AAATGTACTAGCATGTAACTA
130 AAAAGTACTAGCATGTAACTA
59445748 TATGAAAGAA
Statistics
Matches: 338, Mismatches: 44, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
234 3 0.01
235 8 0.02
236 99 0.29
237 16 0.05
238 31 0.09
239 57 0.17
240 4 0.01
241 120 0.36
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.28
Consensus pattern (238 bp):
GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCTCCAAATACATTTTTTTTTAAAAGAAAA
ATGGAACAAACCCGTGTCCTAAATAGACTTATATCTGACACTCACACTCGAGTCCGATTAACAAA
AAAGTACTAGCATGTAACTAACTATATGAAAGAACGGTTGCAATTACAAGCTCCAACTCATCATT
TCAATTGAAGTACTCATGTCAGATACAACACATATTCATGCAA
Found at i:59454105 original size:12 final size:12
Alignment explanation
Indices: 59454088--59454117 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
59454078 CTTTGAATTT
59454088 ATCATCATCGGA
1 ATCATCATCGGA
*
59454100 ATCATCATCGTA
1 ATCATCATCGGA
59454112 ATCATC
1 ATCATC
59454118 TTTCGACCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (12 bp):
ATCATCATCGGA
Found at i:59459831 original size:12 final size:12
Alignment explanation
Indices: 59459814--59459838 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59459804 TTCATGACAT
59459814 AATATGTTATAA
1 AATATGTTATAA
59459826 AATATGTTATAA
1 AATATGTTATAA
59459838 A
1 A
59459839 TTAAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AATATGTTATAA
Found at i:59461073 original size:4 final size:4
Alignment explanation
Indices: 59461064--59461091 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
59461054 ATACATGCAT
59461064 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
59461092 AAAGGTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:59470953 original size:26 final size:26
Alignment explanation
Indices: 59470919--59471003 Score: 84
Period size: 26 Copynumber: 3.2 Consensus size: 26
59470909 CCCCTTTGTA
59470919 TATTTAAAATTTAATCACTTTATTTT
1 TATTTAAAATTTAATCACTTTATTTT
* * * *
59470945 TATTTAAAATGGTCCTAA-CCCCTT-TGTA
1 TATTTAAAAT--T--TAATCACTTTATTTT
59470973 TATTTAAAATTTAATCACTTTATTTT
1 TATTTAAAATTTAATCACTTTATTTT
59470999 TATTT
1 TATTT
59471004 TTATTTTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
24 3 0.07
25 4 0.09
26 18 0.40
28 13 0.29
29 4 0.09
30 3 0.07
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.53
Consensus pattern (26 bp):
TATTTAAAATTTAATCACTTTATTTT
Found at i:59470974 original size:54 final size:54
Alignment explanation
Indices: 59470892--59471003 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
59470882 AAAAATTCCC
59470892 ATTTAAAATGGTCCTAACCCCTTTGTATATTTAAAATTTAATCACTTTATTTTT
1 ATTTAAAATGGTCCTAACCCCTTTGTATATTTAAAATTTAATCACTTTATTTTT
59470946 ATTTAAAATGGTCCTAACCCCTTTGTATATTTAAAATTTAATCACTTTATTTTT
1 ATTTAAAATGGTCCTAACCCCTTTGTATATTTAAAATTTAATCACTTTATTTTT
59471000 ATTT
1 ATTT
59471004 TTATTTTTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.49
Consensus pattern (54 bp):
ATTTAAAATGGTCCTAACCCCTTTGTATATTTAAAATTTAATCACTTTATTTTT
Found at i:59472331 original size:17 final size:17
Alignment explanation
Indices: 59472309--59472341 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
59472299 ATGGATTATT
59472309 AAAAAT-TTATAAAAATA
1 AAAAATATTA-AAAAATA
59472326 AAAAATATTAAAAAAT
1 AAAAATATTAAAAAAT
59472342 TAGTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATATTAAAAAATA
Found at i:59479620 original size:18 final size:18
Alignment explanation
Indices: 59479597--59479632 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
59479587 ATAGTTCAAG
59479597 GTGATAATAAGATCATAT
1 GTGATAATAAGATCATAT
59479615 GTGATAATAAGATCATAT
1 GTGATAATAAGATCATAT
59479633 TAGAAGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (18 bp):
GTGATAATAAGATCATAT
Found at i:59488532 original size:42 final size:42
Alignment explanation
Indices: 59488484--59488726 Score: 181
Period size: 42 Copynumber: 5.8 Consensus size: 42
59488474 TCACGTGACA
* * * *
59488484 TTCTATAGTACCGATCATCAGGTGAGTAAGAATGGTCCCGCC
1 TTCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCGCC
* * *
59488526 TTCTATAGTATCGATCCTCAGGAGAGGAAGAACGATCCCGTC
1 TTCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCGCC
* * * * * *
59488568 TGC-AGTGGTAACGATCATCGGGAGAGTAA-AACCTATCACGCC
1 TTCTA-TAGTATCGATCATCAGGAGAGTAAGAA-CGATCCCGCC
* * *
59488610 TTCTATAGTATCTATCATCAGGAGAGTAAGAACGGTCCCGTC
1 TTCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCGCC
* * * * * * *
59488652 TAT-GATAATAACAATCATAAGGAGAGT-AGGACTGATCACGCC
1 T-TCTATAGTATCGATCATCAGGAGAGTAAGAAC-GATCCCGCC
* *
59488694 TT-TGATAGTATCGATCTTCAGGAGAGTAGGAAC
1 TTCT-ATAGTATCGATCATCAGGAGAGTAAGAAC
59488727 AGTAACGATA
Statistics
Matches: 151, Mismatches: 42, Indels: 15
0.73 0.20 0.07
Matches are distributed among these distances:
41 8 0.05
42 136 0.90
43 7 0.05
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (42 bp):
TTCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCGCC
Found at i:59488669 original size:84 final size:84
Alignment explanation
Indices: 59488522--59488726 Score: 229
Period size: 84 Copynumber: 2.4 Consensus size: 84
59488512 AGAATGGTCC
* * ** * *
59488522 CGCCTTCTATAGTATCGATCCTCAGGAGAGGAAGAACGATCCCGTCTGCAGTGGTAACGATCATC
1 CGCCTTCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCGTCTGCAGTAATAACAATCATA
*
59488587 GGGAGAGTAAAACCT-ATCA
66 AGGAGAGTAAAA-CTGATCA
* *
59488606 CGCCTTCTATAGTATCTATCATCAGGAGAGTAAGAACGGTCCCGTCT--ATGATAATAACAATCA
1 CGCCTTCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCGTCTGCA-G-TAATAACAATCA
**
59488669 TAAGGAGAGTAGGACTGATCA
64 TAAGGAGAGTAAAACTGATCA
* *
59488690 CGCCTT-TGATAGTATCGATCTTCAGGAGAGTAGGAAC
1 CGCCTTCT-ATAGTATCGATCATCAGGAGAGTAAGAAC
59488727 AGTAACGATA
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
82 1 0.01
83 4 0.04
84 98 0.95
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (84 bp):
CGCCTTCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCGTCTGCAGTAATAACAATCATA
AGGAGAGTAAAACTGATCA
Found at i:59488836 original size:6 final size:6
Alignment explanation
Indices: 59488825--59488890 Score: 132
Period size: 6 Copynumber: 11.0 Consensus size: 6
59488815 GTAAGACCTG
59488825 CTCCTA CTCCTA CTCCTA CTCCTA CTCCTA CTCCTA CTCCTA CTCCTA
1 CTCCTA CTCCTA CTCCTA CTCCTA CTCCTA CTCCTA CTCCTA CTCCTA
59488873 CTCCTA CTCCTA CTCCTA
1 CTCCTA CTCCTA CTCCTA
59488891 TCAGATGAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCTA
Found at i:59492732 original size:19 final size:19
Alignment explanation
Indices: 59492707--59492769 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
59492697 CTTAACAAAA
* *
59492707 AAAAAATCAAAATCATTTTT
1 AAAAATTCAAAAT-ATTTAT
*
59492727 AAAAATTTAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
59492746 AAAAAAATCAAAAT-TTTA-
1 -AAAAATTCAAAATATTTAT
59492764 AAAAAT
1 AAAAAT
59492770 ATAAATAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
17 5 0.14
19 9 0.25
20 22 0.61
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:59492771 original size:30 final size:30
Alignment explanation
Indices: 59492735--59492793 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
59492725 TTAAAAATTT
**
59492735 AAAATATTTATAAAAAAATCAAAATTTTAA
1 AAAATATAAATAAAAAAATCAAAATTTTAA
* *
59492765 AAAATATAAATAAAAAATTTAAAATTTTA
1 AAAATATAAATAAAAAAATCAAAATTTTA
59492794 GAAATTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (30 bp):
AAAATATAAATAAAAAAATCAAAATTTTAA
Found at i:59513130 original size:13 final size:13
Alignment explanation
Indices: 59513112--59513136 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59513102 ACACTCAAAT
59513112 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
59513125 TTCTCAAAAGCA
1 TTCTCAAAAGCA
59513137 ACGAAGAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:59518874 original size:15 final size:15
Alignment explanation
Indices: 59518855--59518886 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
59518845 ATGTGATAAT
59518855 TTTTTATGTTTTATTA
1 TTTTTAT-TTTTATTA
59518871 TTTTTATTTTTATTA
1 TTTTTATTTTTATTA
59518886 T
1 T
59518887 ATATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTTTATTTTTATTA
Found at i:59519651 original size:2 final size:2
Alignment explanation
Indices: 59519644--59519668 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59519634 ATGCCTTTGA
59519644 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
59519669 AATTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59524571 original size:30 final size:31
Alignment explanation
Indices: 59524519--59524581 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 31
59524509 GGCTCGGCCT
59524519 ATTCATCATAATTCATGCAATATCAAAGAAC
1 ATTCATCATAATTCATGCAATATCAAAGAAC
59524550 ATTCATCATAATTCA-GCAATATCAAAGAAC
1 ATTCATCATAATTCATGCAATATCAAAGAAC
59524580 AT
1 AT
59524582 CTTCAACTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (31 bp):
ATTCATCATAATTCATGCAATATCAAAGAAC
Found at i:59528051 original size:4 final size:4
Alignment explanation
Indices: 59528032--59528067 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
59528022 GTTGTAAAGT
59528032 TTTA TTT- TTATA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA
59528068 CTTAGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.07
4 26 0.87
5 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:59529153 original size:18 final size:20
Alignment explanation
Indices: 59529122--59529163 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
59529112 AAAATCAGTC
*
59529122 AAAAAAGTCAAAA-T-AATA
1 AAAAAAGACAAAATTCAATA
*
59529140 AAAAAAGACGAAATTCAATA
1 AAAAAAGACAAAATTCAATA
59529160 AAAA
1 AAAA
59529164 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
19 1 0.05
20 8 0.40
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAAAAGACAAAATTCAATA
Found at i:59541152 original size:22 final size:22
Alignment explanation
Indices: 59541127--59541172 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
59541117 GAATTCAATG
* *
59541127 TTCACTTTGGTAATTGAGTTTT
1 TTCAATTTGATAATTGAGTTTT
*
59541149 TTCAATTTGATACTTGAGTTTT
1 TTCAATTTGATAATTGAGTTTT
59541171 TT
1 TT
59541173 TTTTGTCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.15, T:0.57
Consensus pattern (22 bp):
TTCAATTTGATAATTGAGTTTT
Found at i:59542571 original size:25 final size:23
Alignment explanation
Indices: 59542543--59542589 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
59542533 ATTTTAAAAT
59542543 CTAAAAAAATAAAGAGACTAAATTC
1 CTAAAAAAAT-AA-AGACTAAATTC
**
59542568 CTAAAAGTATAAAGACTAAATT
1 CTAAAAAAATAAAGACTAAATT
59542590 TCAAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 2 0.10
25 8 0.40
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (23 bp):
CTAAAAAAATAAAGACTAAATTC
Found at i:59545214 original size:30 final size:31
Alignment explanation
Indices: 59545180--59545247 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
59545170 ACTTAACAGC
* *
59545180 CAATGGCTTAAATAAAAAC-TTCCGATAGTT
1 CAATGACTTAAATAAAAACTTTCCAATAGTT
* * *
59545210 CAATGATTTAAATGAAAACTTTCTAATAGTT
1 CAATGACTTAAATAAAAACTTTCCAATAGTT
59545241 CAATGAC
1 CAATGAC
59545248 CATTTTGTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (31 bp):
CAATGACTTAAATAAAAACTTTCCAATAGTT
Found at i:59545242 original size:31 final size:30
Alignment explanation
Indices: 59545187--59545246 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
59545177 AGCCAATGGC
*
59545187 TTAAATAAAAACTTCCGATAGTTCAATGAT
1 TTAAATAAAAACTTCCAATAGTTCAATGAT
* *
59545217 TTAAATGAAAACTTTCTAATAGTTCAATGA
1 TTAAATAAAAAC-TTCCAATAGTTCAATGA
59545247 CCATTTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (30 bp):
TTAAATAAAAACTTCCAATAGTTCAATGAT
Found at i:59548843 original size:30 final size:30
Alignment explanation
Indices: 59548807--59548871 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
59548797 CAAAAAAAAC
59548807 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
*
59548837 CTCTCAAATTTCTCCTTAAATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
59548867 CTCTC
1 CTCTC
59548872 TTTAATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.28, C:0.31, G:0.03, T:0.38
Consensus pattern (30 bp):
CTCTCAAATTTCTCCCTAAATTTCTCAAAG
Found at i:59549085 original size:26 final size:28
Alignment explanation
Indices: 59549025--59549086 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 28
59549015 GGGTTAATTT
*
59549025 TAATTTTTTAATATTTTTTTCTTCTATA
1 TAATTTTTTAATATATTTTTCTTCTATA
59549053 TAA--TTTTAAT-TAATTTTTCTT-T-TA
1 TAATTTTTTAATAT-ATTTTTCTTCTATA
59549077 TAATTTTTTA
1 TAATTTTTTA
59549087 TAACAGTCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
24 5 0.17
25 2 0.07
26 20 0.67
28 3 0.10
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (28 bp):
TAATTTTTTAATATATTTTTCTTCTATA
Found at i:59550600 original size:18 final size:18
Alignment explanation
Indices: 59550577--59550614 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
59550567 TGCCAGGTGC
*
59550577 GTATCTTAGCCCTTATAT
1 GTATCTTAACCCTTATAT
59550595 GTATCTTAACCCTTATAT
1 GTATCTTAACCCTTATAT
59550613 GT
1 GT
59550615 TTCCTTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.45
Consensus pattern (18 bp):
GTATCTTAACCCTTATAT
Found at i:59551102 original size:57 final size:57
Alignment explanation
Indices: 59550989--59551106 Score: 132
Period size: 57 Copynumber: 2.1 Consensus size: 57
59550979 TATTTGTGTA
* * ****
59550989 AAATTTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTTAATATTTTAATAG
1 AAATTTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAG
* *
59551046 TAAATTATTTT-TA-TGTTTTATTTAATAAAATATAAGTTCTTTTGAATAAGGCAATAG
1 -AAATT-TTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAG
59551103 AAAT
1 AAAT
59551107 AATGCAACAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
56 4 0.08
57 36 0.71
58 7 0.14
59 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (57 bp):
AAATTTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAG
Found at i:59555735 original size:44 final size:44
Alignment explanation
Indices: 59555636--59555752 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 44
59555626 GGCTCGTACA
* * * *
59555636 ATGCCAACGTCCCAGACGTGGTTTTACA-TTTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCACAAATCG
*
59555679 ATACC-ACTGTCCCAGACAG-GGTCTTACACGTAAATCACAAATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAATCACAAATCG
*
59555723 ATGCCAACGTCCCAGACGTGATCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
59555753 ATAACACACA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
42 2 0.03
43 22 0.35
44 36 0.58
45 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCACAAATCG
Found at i:59556200 original size:28 final size:25
Alignment explanation
Indices: 59556169--59556222 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 25
59556159 TTATATTTGG
59556169 TTTATTATAATAACTTTATAATATATTA
1 TTTATTAT-A-AACTTTATAAT-TATTA
*
59556197 TTTATTATAACCTTTATAATTATTA
1 TTTATTATAAACTTTATAATTATTA
59556222 T
1 T
59556223 AAAAACTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 6 0.24
26 10 0.40
27 1 0.04
28 8 0.32
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTATTATAAACTTTATAATTATTA
Found at i:59556201 original size:25 final size:25
Alignment explanation
Indices: 59556173--59556222 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
59556163 ATTTGGTTTA
59556173 TTATAATAA-CTTTATAATATATTAT
1 TTATAATAACCTTTATAAT-TATTAT
*
59556198 TTATTATAACCTTTATAATTATTAT
1 TTATAATAACCTTTATAATTATTAT
59556223 AAAAACTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATAATAACCTTTATAATTATTAT
Found at i:59557083 original size:124 final size:125
Alignment explanation
Indices: 59556860--59557131 Score: 395
Period size: 124 Copynumber: 2.2 Consensus size: 125
59556850 TAAGGCCAAA
*
59556860 CAGGAACTACTGTA-AAAAAAGAGCATCCACGTGGAAGATTTTTTCATCAATTTTGCTGACAATG
1 CAGGAACTACTGTAGAAAAAA-AGCATCCACGTGGAAGATTTTTTCATCAA-TTAGCTGACAATG
*
59556924 CATCCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTATCAAAATTATTTTTT
64 CATCCTACTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTATCAAAATTATTTTTT
* * ** * * * *
59556986 TAGGAACTACTGTAGAAAAAAAGCGTTTACGTGGGAGCTTTTTTCATCAA-TAGCTGACAGTGTA
1 CAGGAACTACTGTAGAAAAAAAGCATCCACGTGGAAGATTTTTTCATCAATTAGCTGACAATGCA
* * *
59557050 TCCTGCTTGAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTCAAAATTATTTTTT
66 TCCTACTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTATCAAAATTATTTTTT
59557110 CAGGAACTACTGTAGAAAAAAA
1 CAGGAACTACTGTAGAAAAAAA
59557132 ATCCTTATTG
Statistics
Matches: 131, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
124 88 0.67
126 37 0.28
127 6 0.05
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (125 bp):
CAGGAACTACTGTAGAAAAAAAGCATCCACGTGGAAGATTTTTTCATCAATTAGCTGACAATGCA
TCCTACTTGAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTATCAAAATTATTTTTT
Found at i:59557229 original size:33 final size:34
Alignment explanation
Indices: 59557186--59557264 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 34
59557176 CTAAACACAA
* *
59557186 AATTATTTAAAAAAAGCTAAA-CCTAATTTAACT
1 AATTTTTTAAAAAAAGCTAAACCCTAAGTTAACT
** *
59557219 AATTTTTT-AAAAACTCTAAACCCTAAGTTAATT
1 AATTTTTTAAAAAAAGCTAAACCCTAAGTTAACT
59557252 AATTTATTTAAAA
1 AATTT-TTTAAAA
59557265 CCCCTAAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
32 10 0.26
33 22 0.58
34 3 0.08
35 3 0.08
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (34 bp):
AATTTTTTAAAAAAAGCTAAACCCTAAGTTAACT
Found at i:59557272 original size:34 final size:34
Alignment explanation
Indices: 59557204--59557392 Score: 157
Period size: 34 Copynumber: 5.5 Consensus size: 34
59557194 AAAAAAAGCT
* *
59557204 AAACCTAATTTAACTAATTT-TTTAAAAACTCTA
1 AAACCTAATTTAATTAATTTATTTAAAAACCCTA
* * *
59557237 AACCCTAAGTTAATTAATTTATTTAAAACCCCTA
1 AAACCTAATTTAATTAATTTATTTAAAAACCCTA
** ** * * ***
59557271 AAACCTAAACCTAAACACAAAGTTATTAAAAAAAAATA
1 AAACCT-AA--TTTA-ATTAATTTATTTAAAAACCCTA
*
59557309 AAACCTAATTTAATTAATTT-TATTAAAAACTCTA
1 AAACCTAATTTAATTAATTTAT-TTAAAAACCCTA
* * *
59557343 AACCCTAAGTTAATTAATTTATTTAAAACCCCTA
1 AAACCTAATTTAATTAATTTATTTAAAAACCCTA
59557377 AAACCTAATTTAATTA
1 AAACCTAATTTAATTA
59557393 TTAAAAAAAT
Statistics
Matches: 117, Mismatches: 32, Indels: 13
0.72 0.20 0.08
Matches are distributed among these distances:
33 18 0.15
34 71 0.61
35 5 0.04
37 3 0.03
38 20 0.17
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (34 bp):
AAACCTAATTTAATTAATTTATTTAAAAACCCTA
Found at i:59557297 original size:105 final size:106
Alignment explanation
Indices: 59557162--59557384 Score: 371
Period size: 106 Copynumber: 2.1 Consensus size: 106
59557152 TTTCCCTAAA
* **
59557162 CCCT-AAACCTAGACCTAAACACAAAATTATTTAAAAAAAGCT-AAACCTAATTTAACTAATTTT
1 CCCTAAAACCTAAACCTAAACACAAAATTA-TTAAAAAAAAATAAAACCTAATTTAACTAATTTT
59557225 -TTAAAAACTCTAAACCCTAAGTTAATTAATTTATTTAAAAC
65 ATTAAAAACTCTAAACCCTAAGTTAATTAATTTATTTAAAAC
* *
59557266 CCCTAAAACCTAAACCTAAACACAAAGTTATTAAAAAAAAATAAAACCTAATTTAATTAATTTTA
1 CCCTAAAACCTAAACCTAAACACAAAATTATTAAAAAAAAATAAAACCTAATTTAACTAATTTTA
59557331 TTAAAAACTCTAAACCCTAAGTTAATTAATTTATTTAAAAC
66 TTAAAAACTCTAAACCCTAAGTTAATTAATTTATTTAAAAC
59557372 CCCTAAAACCTAA
1 CCCTAAAACCTAA
59557385 TTTAATTATT
Statistics
Matches: 111, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
104 14 0.13
105 43 0.39
106 54 0.49
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.30
Consensus pattern (106 bp):
CCCTAAAACCTAAACCTAAACACAAAATTATTAAAAAAAAATAAAACCTAATTTAACTAATTTTA
TTAAAAACTCTAAACCCTAAGTTAATTAATTTATTTAAAAC
Found at i:59567498 original size:31 final size:29
Alignment explanation
Indices: 59567441--59567498 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
59567431 ATAAATTTAA
*
59567441 AATTTAGTCTCTATATTTTTATTTTTAGT
1 AATTTAGTCTCTATATTTTTAATTTTAGT
59567470 AATTTAGTCACTCTA-ATTTTTAGATTTTA
1 AATTTAGT--CTCTATATTTTTA-ATTTTA
59567499 AAATTTAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 8 0.32
30 7 0.28
31 10 0.40
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.57
Consensus pattern (29 bp):
AATTTAGTCTCTATATTTTTAATTTTAGT
Found at i:59567504 original size:30 final size:28
Alignment explanation
Indices: 59567436--59567505 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
59567426 TCTTTATAAA
*
59567436 TTTAAAATTTAGTCTCTATATTTTTATT
1 TTTAAAATTTAGTCTCTATATTTTTAAT
*
59567464 TTTAGTAATTTAGTCACTCTA-ATTTTTAGAT
1 TTTA-AAATTTAGT--CTCTATATTTTTA-AT
59567495 TTTAAAATTTA
1 TTTAAAATTTA
59567506 AGCCCAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 4 0.11
29 8 0.23
30 13 0.37
31 10 0.29
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.56
Consensus pattern (28 bp):
TTTAAAATTTAGTCTCTATATTTTTAAT
Found at i:59568775 original size:31 final size:31
Alignment explanation
Indices: 59568735--59568807 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
59568725 AACTTTTCGA
*
59568735 AATTGAGTGACCAAAACGTAAACTTACTAAT
1 AATTTAGTGACCAAAACGTAAACTTACTAAT
59568766 AATTTAGTGACCAAAACGTAAACTTACTAAT
1 AATTTAGTGACCAAAACGTAAACTTACTAAT
59568797 AATTTAGTGAC
1 AATTTAGTGAC
59568808 ATTAGGTGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (31 bp):
AATTTAGTGACCAAAACGTAAACTTACTAAT
Found at i:59572884 original size:21 final size:21
Alignment explanation
Indices: 59572860--59572906 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
59572850 CTTATGGCAT
59572860 ATTTTAACCTTTATTTATTT-A
1 ATTTTAACCTTTATTT-TTTGA
*
59572881 ATTTAAACCTTTATTTTTTGA
1 ATTTTAACCTTTATTTTTTGA
59572902 ATTTT
1 ATTTT
59572907 GCCCCAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTTTAACCTTTATTTTTTGA
Found at i:59578595 original size:31 final size:31
Alignment explanation
Indices: 59578537--59578597 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
59578527 TTATTAGCCC
*
59578537 AGTGACTTAAATAAAAACTTTTGAATAGTTT
1 AGTGACTTAAATAAAAACTTTTAAATAGTTT
* *
59578568 AGTGACTTAAATGAAGA-TTTTCAAATAGTT
1 AGTGACTTAAATAAAAACTTTT-AAATAGTT
59578598 CAATGACCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.38
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTTAAATAGTTT
Found at i:59580194 original size:19 final size:19
Alignment explanation
Indices: 59580172--59580215 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
59580162 AATAAACATT
59580172 AAAAATTATTTTAAAAATA
1 AAAAATTATTTTAAAAATA
*
59580191 AAAAATTATTTTAAAATTA
1 AAAAATTATTTTAAAAATA
59580210 AAAAAT
1 AAAAAT
59580216 AAAAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATTATTTTAAAAATA
Found at i:59583205 original size:27 final size:27
Alignment explanation
Indices: 59583175--59583231 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
59583165 GGAATAAAAA
59583175 GGCGGCACCAATGGTGCC-TTTCTCATT
1 GGCGGCACCAATGGTGCCATTTC-CATT
59583202 GGCGGCACCAATGGTGCCATTTCCATT
1 GGCGGCACCAATGGTGCCATTTCCATT
59583229 GGC
1 GGC
59583232 AGAATAGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (27 bp):
GGCGGCACCAATGGTGCCATTTCCATT
Found at i:59585137 original size:17 final size:17
Alignment explanation
Indices: 59585115--59585162 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
59585105 GTAATTTTAC
59585115 TATTTTAATAACTTATA
1 TATTTTAATAACTTATA
* *
59585132 TATTTTTATAA-TTA-C
1 TATTTTAATAACTTATA
*
59585147 CATTTTAATAACTTAT
1 TATTTTAATAACTTAT
59585163 TTTTATAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 9 0.36
16 6 0.24
17 10 0.40
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTTTAATAACTTATA
Found at i:59585981 original size:20 final size:20
Alignment explanation
Indices: 59585952--59585989 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
59585942 GTTAAAAAAA
*
59585952 TAGAGGGACTAATTTAATAG
1 TAGAGAGACTAATTTAATAG
59585972 TAGAGAGACTAATTTAAT
1 TAGAGAGACTAATTTAAT
59585990 CATGTTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (20 bp):
TAGAGAGACTAATTTAATAG
Found at i:59587820 original size:20 final size:21
Alignment explanation
Indices: 59587781--59587826 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
59587771 AAAAATATAA
59587781 ATTTTGAATTGTTTATAAA-T
1 ATTTTGAATTGTTTATAAATT
*
59587801 ATTTTGAATTTTTTGA-AAATT
1 ATTTTGAATTGTTT-ATAAATT
59587822 ATTTT
1 ATTTT
59587827 AAAATACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (21 bp):
ATTTTGAATTGTTTATAAATT
Found at i:59590395 original size:21 final size:21
Alignment explanation
Indices: 59590371--59590410 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
59590361 ACTCTCTCTT
59590371 TAACTAAAATTAAA-TCAATGG
1 TAACTAAAA-TAAATTCAATGG
*
59590392 TAACTTAAATAAATTCAAT
1 TAACTAAAATAAATTCAAT
59590411 AATTTATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (21 bp):
TAACTAAAATAAATTCAATGG
Found at i:59590744 original size:33 final size:35
Alignment explanation
Indices: 59590681--59590760 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 35
59590671 AAATTACAAA
*
59590681 AAAAATTATAATTCAAAAATTTTATAAAAAATTC-
1 AAAAATTATAATTCAAAAAATTTATAAAAAATTCT
* * *
59590715 AAAATTTATATTTTAAAAAATTTAT-AAAAATTCT
1 AAAAATTATAATTCAAAAAATTTATAAAAAATTCT
59590749 AAAAATATATAA
1 AAAAAT-TATAA
59590761 AAAAAATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 8 0.21
34 26 0.68
35 4 0.11
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (35 bp):
AAAAATTATAATTCAAAAAATTTATAAAAAATTCT
Found at i:59590887 original size:16 final size:16
Alignment explanation
Indices: 59590868--59590898 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59590858 TTTGAAAATT
59590868 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
59590884 TTTCAAATTTATATG
1 TTTCAAATATATATG
59590899 CTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:59602068 original size:14 final size:16
Alignment explanation
Indices: 59602029--59602068 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
59602019 TAAATTTTAA
*
59602029 AAATATAATATACAAT
1 AAATTTAATATACAAT
59602045 AAATTT-ATATA-AAT
1 AAATTTAATATACAAT
59602059 -AATTTAATAT
1 AAATTTAATAT
59602069 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 5 0.23
14 7 0.32
15 5 0.23
16 5 0.23
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTTAATATACAAT
Found at i:59604816 original size:29 final size:28
Alignment explanation
Indices: 59604773--59604828 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
59604763 CCAAACATTT
*
59604773 TTTCAAACTTAATATTTTTATTCAAACCC
1 TTTCAAACTTAATATATTT-TTCAAACCC
* *
59604802 TTTCAAATTTCATATATTTTTCAAACC
1 TTTCAAACTTAATATATTTTTCAAACC
59604829 TAGAAAGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (28 bp):
TTTCAAACTTAATATATTTTTCAAACCC
Found at i:59605656 original size:14 final size:14
Alignment explanation
Indices: 59605637--59605664 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59605627 GCAGTCATGC
59605637 CTTGAAGACTCCAT
1 CTTGAAGACTCCAT
59605651 CTTGAAGACTCCAT
1 CTTGAAGACTCCAT
59605665 TTTGCTAAAA
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:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (14 bp):
CTTGAAGACTCCAT
Found at i:59605712 original size:2 final size:2
Alignment explanation
Indices: 59605705--59605729 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59605695 GCTTACATTC
59605705 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
59605730 AAAGGTGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59610026 original size:48 final size:48
Alignment explanation
Indices: 59609969--59610072 Score: 190
Period size: 48 Copynumber: 2.2 Consensus size: 48
59609959 TCGGATGGGT
* *
59609969 GAACGAGATCTACGGTGCACAGGTGTAGGTGACCTGCGCCGATAAGGA
1 GAACGAGATCTACGGCGCACAGGTGTAGGTGACCCGCGCCGATAAGGA
59610017 GAACGAGATCTACGGCGCACAGGTGTAGGTGACCCGCGCCGATAAGGA
1 GAACGAGATCTACGGCGCACAGGTGTAGGTGACCCGCGCCGATAAGGA
59610065 GAACGAGA
1 GAACGAGA
59610073 CTGAGATCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.29, C:0.22, G:0.36, T:0.13
Consensus pattern (48 bp):
GAACGAGATCTACGGCGCACAGGTGTAGGTGACCCGCGCCGATAAGGA
Found at i:59614495 original size:29 final size:30
Alignment explanation
Indices: 59614457--59614527 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
59614447 TCTTCACAAA
**
59614457 TTTAAAATTTAGTCCCTGTA-TTTTT-AAT
1 TTTAAAATTTAGTCCCTACACTTTTTAAAT
*
59614485 TTTAGAAATTTAGTCTCTACACTTTTTAAAT
1 TTTA-AAATTTAGTCCCTACACTTTTTAAAT
59614516 TTTAAAATTTAG
1 TTTAAAATTTAG
59614528 GTTCAACAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 4 0.11
29 13 0.35
30 13 0.35
31 7 0.19
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (30 bp):
TTTAAAATTTAGTCCCTACACTTTTTAAAT
Found at i:59619118 original size:209 final size:207
Alignment explanation
Indices: 59618712--59619630 Score: 916
Period size: 209 Copynumber: 4.5 Consensus size: 207
59618702 ATGCATTAGT
* * * * *
59618712 TATGGGTACTTAAAGAAAAATGAGGAGTCCAAGCAATATAGCTTGTTGGTAATTTCTAATCTATG
1 TATGGATACTTAAAGAAAAATGAGGAGTTCAAGCAATATAGCTAGTCGGTAATTTCTAAGCTATG
* * * * *
59618777 AGAATCTAATGGAAAACCACATTGTGTATTTTGACATTTGAATTTATACTTCTTGGCCTTCATTG
66 AGAAACTAAT-GAAAACCACATTGTGCATTTTGATATTTGAATTTATAGTT-TTGACCTTCATTG
* * * * *
59618842 CTAGTTAGCGGTGTTACTGGGACTTGGGTGTGAGCTTTGGATAGCCTATATGTCTGATGTACATT
129 CTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAG-TTTGGATAGCCTATATGTCTAATATGCATT
59618907 AGATATGGGTGCTAGA
193 AGATAT-GGTGCTAGA
* * * *
59618923 TATGGATACTTCAAGAAAAAT-AGGAGTTCAAGCAGTATAGCTAGTCAGTGATTTCTAAGCTATG
1 TATGGATACTTAAAGAAAAATGAGGAGTTCAAGCAATATAGCTAGTCGGTAATTTCTAAGCTATG
* * * *
59618987 AGAAAGTAATGAAAACCACATTGTGCATTTTGATACTTGACTTTATAGGTTTTGACCTTCAATGC
66 AGAAACTAATGAAAACCACATTGTGCATTTTGATATTTGAATTTATA-GTTTTGACCTTCATTGC
* *
59619052 TAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGTGTTGCG-TAGCCTACATGTCCAATATGCATT
130 TAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGT-TTG-GATAGCCTATATGTCTAATATGCATT
*
59619116 AGATATTGGTGTTAG-
193 AGATA-TGGTGCTAGA
* * * *
59619131 TAAGGATACGTAAAGAAAAATGAGGAG-TCTGAGCAATATAGCTAGTCGGTAATTTCGAAGCTAT
1 TATGGATACTTAAAGAAAAATGAGGAGTTC-AAGCAATATAGCTAGTCGGTAATTTCTAAGCTAT
* * * * *
59619195 GAGAAACTAATG--AACCACATTGTGCATTTTGATATTTGAATCTATAGTTTTCAGTCTTTAGTG
65 GAGAAACTAATGAAAACCACATTGTGCATTTTGATATTTGAATTTATAGTTTTGA-CCTTCATTG
* *
59619258 CTAGTTAACTGTGTTACCGGGACTTGGGTGTGAGCATTGGATAGCCTATATGTCTAATATGC---
129 CTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAG-TTTGGATAGCCTATATGTCTAATATGCATT
59619320 ----A---T-C-AGA
193 AGATATGGTGCTAGA
* *** *
59619326 TATGGGTACTTAAAGAAAAATGAGGAGTTTGCGCAATATAGCTAGTCGGTAATCTCTAAGCTATG
1 TATGGATACTTAAAGAAAAATGAGGAGTTCAAGCAATATAGCTAGTCGGTAATTTCTAAGCTATG
* *
59619391 AAAAACTAATGAAGAACCACATTGTGCATTTTGGTATTTGAATTTATAGTTTTTGACCTTCATTG
66 AGAAACTAATGAA-AACCACATTGTGCATTTTGATATTTGAATTTATAG-TTTTGACCTTCATTG
* * * **
59619456 CTATTTAG-TCATGTTACCGGGACTTGGGTGTGACG-TTGGATACCCCGTATGTCTAATATGCAT
129 CTAGTTAGCT-GTGTTACCGGGACTTGGGTGTGA-GTTTGGATAGCCTATATGTCTAATATGCAT
59619519 TAG--A---TG-T---
192 TAGATATGGTGCTAGA
* * * *
59619526 T-T-G-TACTTCAAGAAAAATGAGGAGTCCAA--ATATAATAGCAAGTTGGTAATTTCTAAGCTA
1 TATGGATACTTAAAGAAAAATGAGGAGTTCAAGCA-AT-ATAGCTAGTCGGTAATTTCTAAGCTA
* * * * *
59619586 TGGGAAACTAATGAATAACCACATTTTGCACTCTGCTATTTGAAT
64 TGAGAAACTAATGAA-AACCACATTGTGCATTTTGATATTTGAAT
59619631 GACATTCAAT
Statistics
Matches: 600, Mismatches: 82, Indels: 66
0.80 0.11 0.09
Matches are distributed among these distances:
194 2 0.00
195 67 0.11
196 4 0.01
197 106 0.18
198 68 0.11
199 7 0.01
200 2 0.00
202 2 0.00
206 7 0.01
207 92 0.15
208 21 0.04
209 155 0.26
210 48 0.08
211 19 0.03
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (207 bp):
TATGGATACTTAAAGAAAAATGAGGAGTTCAAGCAATATAGCTAGTCGGTAATTTCTAAGCTATG
AGAAACTAATGAAAACCACATTGTGCATTTTGATATTTGAATTTATAGTTTTGACCTTCATTGCT
AGTTAGCTGTGTTACCGGGACTTGGGTGTGAGTTTGGATAGCCTATATGTCTAATATGCATTAGA
TATGGTGCTAGA
Found at i:59619487 original size:198 final size:197
Alignment explanation
Indices: 59618573--59619630 Score: 1042
Period size: 197 Copynumber: 5.3 Consensus size: 197
59618563 GTAGTTTTTC
* * *
59618573 AGCTATGAGAAGCTAATGTAGAACCACATTGTGCATTTTGATATTTGACTTTATAGTTTTTGACC
1 AGCTATGAGAAACTAATGAAGAACCACATTGTGCATTTTGATATTTGAATTTATAG-TTTTGACC
* * * * *
59618638 TTCATTGCTGGTTAGCTGTG-TACAGGGACTTGGGTGTGAGCGTTGAATAGCCTATATGTCCAAT
65 TTCAATGCTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCTATATGTCTAAT
* *** * *
59618702 ATGCATTAGTTATGGGTACTTAAAGAAAAATGAGGAGTCCAAGCAATATAGCTTGTTGGTAATTT
130 ATGCATTAGATATGGGTACTTAAAGAAAAATGAGGAGTTTGAGCAATATAGCTAGTCGGTAATTT
59618767 CTA
195 CTA
* * * * * *
59618770 ATCTATGAGAATCTAATGGAA-AACCACATTGTGTATTTTGACATTTGAATTTATACTTCTTGGC
1 AGCTATGAGAAACTAAT-GAAGAACCACATTGTGCATTTTGATATTTGAATTTATAGTT-TTGAC
* * * *
59618834 CTTCATTGCTAGTTAGCGGTGTTACTGGGACTTGGGTGTGAGCTTTGGATAGCCTATATGTCTGA
64 CTTCAATGCTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCC--TA----T-A
** * * ** *
59618899 TGTACATTAGATATGGGTGCTAGATATGGATACTTCAAGAAAAAT-AGGAGTTCAAGCAGTATAG
122 TGT-C--TA-ATATGCAT--TAGATATGGGTACTTAAAGAAAAATGAGGAGTTTGAGCAATATAG
* *
59618963 CTAGTCAGTGATTTCTA
181 CTAGTCGGTAATTTCTA
* * *
59618980 AGCTATGAGAAAGTAATGAA-AACCACATTGTGCATTTTGATACTTGACTTTATAGGTTTTGACC
1 AGCTATGAGAAACTAATGAAGAACCACATTGTGCATTTTGATATTTGAATTTATA-GTTTTGACC
* * *
59619044 TTCAATGCTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGTGTTGCG-TAGCCTACATGTCCAA
65 TTCAATGCTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGCGTTG-GATAGCCTATATGTCTAA
* *
59619108 TATGCATTAGATATTGGTGTTAGTAAGGATACGTAAAGAAAAATGAGGAGTCTGAGCAATATAGC
129 TATGCATTAGATA-------T-G---GG-TACTTAAAGAAAAATGAGGAGTTTGAGCAATATAGC
*
59619173 TAGTCGGTAATTTCGA
182 TAGTCGGTAATTTCTA
* * *
59619189 AGCTATGAGAAACTAAT---GAACCACATTGTGCATTTTGATATTTGAATCTATAGTTTTCAGTC
1 AGCTATGAGAAACTAATGAAGAACCACATTGTGCATTTTGATATTTGAATTTATAGTTTTGA-CC
* * * *
59619251 TTTAGTGCTAGTTAACTGTGTTACCGGGACTTGGGTGTGAGCATTGGATAGCCTATATGTCTAAT
65 TTCAATGCTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCTATATGTCTAAT
* * *
59619316 ATGCATCAGATATGGGTACTTAAAGAAAAATGAGGAGTTTGCGCAATATAGCTAGTCGGTAATCT
130 ATGCATTAGATATGGGTACTTAAAGAAAAATGAGGAGTTTGAGCAATATAGCTAGTCGGTAATTT
59619381 CTA
195 CTA
* *
59619384 AGCTATGAAAAACTAATGAAGAACCACATTGTGCATTTTGGTATTTGAATTTATAGTTTTTGACC
1 AGCTATGAGAAACTAATGAAGAACCACATTGTGCATTTTGATATTTGAATTTATAG-TTTTGACC
* * * * **
59619449 TTCATTGCTATTTAG-TCATGTTACCGGGACTTGGGTGTGA-CGTTGGATACCCCGTATGTCTAA
65 TTCAATGCTAGTTAGCT-GTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCTATATGTCTAA
* ** * ** * * *
59619512 TATGCATTAGATGTTTGTACTTCAAGAAAAATGAGGAG-TCCA-AATATAATAGCAAGTTGGTAA
129 TATGCATTAGATATGGGTACTTAAAGAAAAATGAGGAGTTTGAGCA-AT-ATAGCTAGTCGGTAA
59619575 TTTCTA
192 TTTCTA
* * * * * *
59619581 AGCTATGGGAAACTAATGAATAACCACATTTTGCACTCTGCTATTTGAAT
1 AGCTATGAGAAACTAATGAAGAACCACATTGTGCATTTTGATATTTGAAT
59619631 GACATTCAAT
Statistics
Matches: 715, Mismatches: 105, Indels: 82
0.79 0.12 0.09
Matches are distributed among these distances:
195 64 0.09
196 13 0.02
197 183 0.26
198 105 0.15
199 7 0.01
200 3 0.00
201 1 0.00
202 4 0.01
203 1 0.00
204 2 0.00
205 4 0.01
206 8 0.01
207 102 0.14
208 14 0.02
209 135 0.19
210 47 0.07
211 22 0.03
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (197 bp):
AGCTATGAGAAACTAATGAAGAACCACATTGTGCATTTTGATATTTGAATTTATAGTTTTGACCT
TCAATGCTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCTATATGTCTAATA
TGCATTAGATATGGGTACTTAAAGAAAAATGAGGAGTTTGAGCAATATAGCTAGTCGGTAATTTC
TA
Found at i:59626391 original size:62 final size:62
Alignment explanation
Indices: 59626294--59626420 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
59626284 AAGTAATTTT
59626294 TTTAGGAACTGAGAAATAGATAAATATGGTGGTTCTAAGCTACAAACAAACTTTCTATTGGA
1 TTTAGGAACTGAGAAATAGATAAATATGGTGGTTCTAAGCTACAAACAAACTTTCTATTGGA
*
59626356 TTTAGGAACTGAGAAATAGATAAATATGGTGGTTCTAAGCTATAAACAAACTTTCTATTGGA
1 TTTAGGAACTGAGAAATAGATAAATATGGTGGTTCTAAGCTACAAACAAACTTTCTATTGGA
59626418 TTT
1 TTT
59626421 GTTAAGCTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (62 bp):
TTTAGGAACTGAGAAATAGATAAATATGGTGGTTCTAAGCTACAAACAAACTTTCTATTGGA
Found at i:59630048 original size:8 final size:7
Alignment explanation
Indices: 59630016--59630048 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
59630006 ATCTTCATAT
59630016 TTTTGAA
1 TTTTGAA
59630023 TTTTGAA
1 TTTTGAA
59630030 TTTTGAA
1 TTTTGAA
59630037 TTTTGAAA
1 TTTTG-AA
59630045 TTTT
1 TTTT
59630049 AATGGGAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (7 bp):
TTTTGAA
Found at i:59633123 original size:2 final size:2
Alignment explanation
Indices: 59633116--59633151 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
59633106 AATCAACCAA
59633116 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
59633152 TACATACATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:59635667 original size:20 final size:20
Alignment explanation
Indices: 59635637--59635684 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
59635627 TCATTTAAAT
59635637 TTAATTATAAAATATTTTATA
1 TTAA-TATAAAATATTTTATA
* *
59635658 TTAATATAAACTTTTTTATA
1 TTAATATAAAATATTTTATA
*
59635678 TTTATAT
1 TTAATAT
59635685 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATATAAAATATTTTATA
Found at i:59639279 original size:9 final size:10
Alignment explanation
Indices: 59639257--59639288 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
59639247 GAGGATAGTC
59639257 AAATTTTCAA
1 AAATTTTCAA
59639267 AAATTTT-AA
1 AAATTTTCAA
59639276 AAATTTTCAA
1 AAATTTTCAA
59639286 AAA
1 AAA
59639289 AAAAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (10 bp):
AAATTTTCAA
Found at i:59644278 original size:31 final size:31
Alignment explanation
Indices: 59644230--59644316 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
59644220 ATGAACTTTG
* * *
59644230 AACTTTGATT-TGGTTCAATTATATATATGA
1 AACTTTGATTGTGGTTCAAATATACACATGA
*
59644260 AACTTTGATTGTGGTTCAAATGTACACATGA
1 AACTTTGATTGTGGTTCAAATATACACATGA
* * * *
59644291 AAATTTCATTGTGATTCAACTATACA
1 AACTTTGATTGTGGTTCAAATATACA
59644317 ATATATATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 10 0.21
31 37 0.79
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (31 bp):
AACTTTGATTGTGGTTCAAATATACACATGA
Found at i:59646053 original size:22 final size:21
Alignment explanation
Indices: 59646006--59646054 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
59645996 GATCATTTTT
59646006 AATTTTTTAATTTTCTTTATA
1 AATTTTTTAATTTTCTTTATA
* *
59646027 TATTTTTTAGATTTT-TTTTTA
1 AATTTTTTA-ATTTTCTTTATA
*
59646048 AAATTTT
1 AATTTTT
59646055 AGGATTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
AATTTTTTAATTTTCTTTATA
Found at i:59646085 original size:24 final size:25
Alignment explanation
Indices: 59646046--59646095 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
59646036 GATTTTTTTT
*
59646046 TAAAATTTTAGGATTTTTAAAAATA
1 TAAAATTTTAGAATTTTTAAAAATA
*
59646071 TAAAA-TTTAGAATTTTTATAAATA
1 TAAAATTTTAGAATTTTTAAAAATA
59646095 T
1 T
59646096 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (25 bp):
TAAAATTTTAGAATTTTTAAAAATA
Found at i:59646103 original size:19 final size:20
Alignment explanation
Indices: 59646076--59646123 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
59646066 AAATATAAAA
*
59646076 TTTAGAATTTTTATAAA-TAT
1 TTTA-AATTTTTAAAAATTAT
59646096 TTTAAA-TTTTAAAAATTAT
1 TTTAAATTTTTAAAAATTAT
*
59646115 TTTGAATTT
1 TTTAAATTT
59646124 ATTTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 8 0.33
19 10 0.42
20 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTAAATTTTTAAAAATTAT
Found at i:59646532 original size:2 final size:2
Alignment explanation
Indices: 59646525--59646565 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
59646515 AATAATCTTT
59646525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59646566 TAGTTTAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59646846 original size:13 final size:13
Alignment explanation
Indices: 59646828--59646852 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59646818 CATTTCAATA
59646828 AAAAAATAAAAAT
1 AAAAAATAAAAAT
59646841 AAAAAATAAAAA
1 AAAAAATAAAAA
59646853 CTTATGAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:59653652 original size:30 final size:31
Alignment explanation
Indices: 59653610--59653721 Score: 86
Period size: 31 Copynumber: 3.6 Consensus size: 31
59653600 TGGAAGAGCC
*
59653610 TAATTGAAATATTTAAAAATTTTCA-AAGGTT
1 TAATTAAAATATTTAAAAATTTT-AGAAGGTT
* * *
59653641 TAA-TAATATATTTCAAAAACTTTAGAGGGTT
1 TAATTAAAATATTT-AAAAATTTTAGAAGGTT
* * * *
59653672 TAATTAAAATCTTCAAAAATTTT-GAGGGTA
1 TAATTAAAATATTTAAAAATTTTAGAAGGTT
* *
59653702 TAACTAAAAATTTTTAAAAA
1 TAA-TTAAAATATTTAAAAA
59653722 AAATTTGGGA
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
30 18 0.28
31 40 0.62
32 7 0.11
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38
Consensus pattern (31 bp):
TAATTAAAATATTTAAAAATTTTAGAAGGTT
Found at i:59653672 original size:31 final size:30
Alignment explanation
Indices: 59653652--59653710 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
59653642 AATAATATAT
59653652 TTCAAAAACTTTAGAGGGTTTAATTAAAATC
1 TTCAAAAA-TTTAGAGGGTTTAATTAAAATC
* * *
59653683 TTCAAAAATTTTGAGGGTATAACTAAAA
1 TTCAAAAATTTAGAGGGTTTAATTAAAA
59653711 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (30 bp):
TTCAAAAATTTAGAGGGTTTAATTAAAATC
Found at i:59654980 original size:31 final size:31
Alignment explanation
Indices: 59654945--59655003 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
59654935 ATTTAGTACT
59654945 TGAACTTGACATATTTTT-CTAACTTGGTCTC
1 TGAACTTGAC-TATTTTTCCTAACTTGGTCTC
* *
59654976 TGAACTTGACTCTTTTTCCTAATTTGGT
1 TGAACTTGACTATTTTTCCTAACTTGGT
59655004 ACCTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (31 bp):
TGAACTTGACTATTTTTCCTAACTTGGTCTC
Found at i:59655491 original size:29 final size:29
Alignment explanation
Indices: 59655459--59655551 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
59655449 AAACTGGGCC
59655459 AAAAAAAAGTTTAGGTACCAAATTAGAAA
1 AAAAAAAAGTTTAGGTACCAAATTAGAAA
** * * **
59655488 AAAATGTCAAGTTCAGGTACC-AATTTGAGCC
1 AAAA--AAAAGTTTAGGTACCAAATTAGA-AA
*
59655519 CAAAAAAAGTTTAGGTACCAAATTA-AAA
1 AAAAAAAAGTTTAGGTACCAAATTAGAAA
59655547 AAAAA
1 AAAAA
59655552 TGTCAAGTTC
Statistics
Matches: 46, Mismatches: 14, Indels: 9
0.67 0.20 0.13
Matches are distributed among these distances:
28 4 0.09
29 17 0.37
30 10 0.22
31 15 0.33
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.22
Consensus pattern (29 bp):
AAAAAAAAGTTTAGGTACCAAATTAGAAA
Found at i:59655506 original size:31 final size:31
Alignment explanation
Indices: 59655465--59655569 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
59655455 GGCCAAAAAA
*
59655465 AAGTTTAGGTACCAAATTAGAAAAAAATGTC
1 AAGTTCAGGTACCAAATTAGAAAAAAATGTC
* **
59655496 AAGTTCAGGTACCAATTTGAGCCCAAAAA----
1 AAGTTCAGGTACCAAATT-AG-AAAAAAATGTC
* *
59655525 AAGTTTAGGTACCAAATTAAAAAAAAATGTC
1 AAGTTCAGGTACCAAATTAGAAAAAAATGTC
*
59655556 AAGTTCAAGTACCA
1 AAGTTCAGGTACCA
59655570 GATATTATAT
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
27 5 0.09
28 1 0.02
29 16 0.28
31 28 0.49
32 2 0.04
33 5 0.09
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (31 bp):
AAGTTCAGGTACCAAATTAGAAAAAAATGTC
Found at i:59655568 original size:60 final size:60
Alignment explanation
Indices: 59655402--59655569 Score: 230
Period size: 60 Copynumber: 2.8 Consensus size: 60
59655392 TAAACCTCTG
* * * * *
59655402 AAAAAGCTTAGGTAACAAATTAAGAAAAAATGGCAAGTTC-AGATACCAAACTGGGCCAAA
1 AAAAAGTTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAG-TACCAAACTGAGCCAAA
* * ** *
59655462 AAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAGGTACCAATTTGAGCCCAA
1 AAAAAGTTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTACCAAACTGAGCCAAA
59655522 AAAAAGTTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTACCA
1 AAAAAGTTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTACCA
59655570 GATATTATAT
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (60 bp):
AAAAAGTTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTACCAAACTGAGCCAAA
Found at i:59657732 original size:29 final size:29
Alignment explanation
Indices: 59657698--59657766 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
59657688 GATTTTTTTT
*
59657698 AAAATTTTAATTAATCTCTCAAAAACTTA
1 AAAATTTTAATTAATCTCACAAAAACTTA
* * *
59657727 AAAATTCTT-ATTAATCTCACAAGAATTTT
1 AAAATT-TTAATTAATCTCACAAAAACTTA
59657756 AAAATTTTAAT
1 AAAATTTTAAT
59657767 CAGACCCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 2 0.06
29 30 0.88
30 2 0.06
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (29 bp):
AAAATTTTAATTAATCTCACAAAAACTTA
Found at i:59666956 original size:39 final size:38
Alignment explanation
Indices: 59666911--59666988 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 38
59666901 TTAAATTTTG
**
59666911 ATTTGGTATTTAAACTTGACATA-TTTTTTTAATTTGATA
1 ATTTGGTATCCAAA-TTGA-ATACTTTTTTTAATTTGATA
*
59666950 ATTTGGTATCCAAATTTAATACTTTTTTTTAATTTGATA
1 ATTTGGTATCCAAATTGAATAC-TTTTTTTAATTTGATA
59666989 CCTAAATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 3 0.09
38 3 0.09
39 28 0.82
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (38 bp):
ATTTGGTATCCAAATTGAATACTTTTTTTAATTTGATA
Found at i:59666996 original size:31 final size:31
Alignment explanation
Indices: 59666948--59667015 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
59666938 TTTAATTTGA
* *
59666948 TAATTTGGTATCCAAATTT-AATACTTTTTTT
1 TAATTTGATATCCAAATTTGAAT-CTTTTTCT
*
59666979 TAATTTGATA-CCTAAATTTGACTCTTTTTCT
1 TAATTTGATATCC-AAATTTGAATCTTTTTCT
59667010 TAATTT
1 TAATTT
59667016 AGTATCTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 2 0.06
31 28 0.88
32 2 0.06
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (31 bp):
TAATTTGATATCCAAATTTGAATCTTTTTCT
Found at i:59672315 original size:91 final size:90
Alignment explanation
Indices: 59672215--59672396 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 90
59672205 TCTGAATTAA
* *
59672215 ATTTAATTTATTTAGCCCAACAAATTGAAA-ATTTAGATTCATTTTGAAGCTCGATTTTAAAAAA
1 ATTTAATTTACTTAGCCCAACAAATT-AAAGATTTAGACTCATTTTGAAGCTCGA-TTTAAAAAA
*
59672279 AATCAATGGTATTAAATTAATAGGTCG
64 AATCAATCGTATTAAATTAATAGGTCG
* *
59672306 ATTTAATTTACTTAGCCCAATAAATTAAAGATTTAGGCTCATTTTGAAGCTCGATTTAAAAAAAA
1 ATTTAATTTACTTAGCCCAACAAATTAAAGATTTAGACTCATTTTGAAGCTCGATTTAAAAAAAA
59672371 TCAATCGTATTAAATTAATAGGTCG
66 TCAATCGTATTAAATTAATAGGTCG
59672396 A
1 A
59672397 AACTCGTTGA
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
90 39 0.46
91 46 0.54
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (90 bp):
ATTTAATTTACTTAGCCCAACAAATTAAAGATTTAGACTCATTTTGAAGCTCGATTTAAAAAAAA
TCAATCGTATTAAATTAATAGGTCG
Found at i:59675755 original size:205 final size:203
Alignment explanation
Indices: 59675401--59676218 Score: 1048
Period size: 205 Copynumber: 4.0 Consensus size: 203
59675391 TGTTTCATAG
* *
59675401 GTTTCTATAACTCTCTAAAGCAAAATACTAGTCGCCGGACAACGAAACATTCTCTCGAGTCAAAT
1 GTTTCTATAACTCTCTAAAGCAAAATACTAGTCGCCGGACAACAAAACATTCTCTAGAGTCAAAT
* ** * * *
59675466 CCAATCTTATGGACCAACTTTTACTAAGACATTCATTCACCGGACTGTCGCAATACATCTCGTTT
66 CCAATTTTATGGACCAACTTTTACCGAGACATTCATTC-CCCGACTTTCGCAATGCATCTCGTTT
* * * *
59675531 CCACAATAGAACGAAGATGAAAGCTCGTACATGTGTTTATGCAAACTGAGTTTTAGCTTCTCAAG
130 CCACGATAGAACAAAGATGAAAGCTCGT-CATGTGTTTATGCAAACCGAGTTTTAGCTTCTCAAT
59675596 ATGCAGCAAT
194 ATGCAGCAAT
* * * *
59675606 GTTTCTATAACTCTCTAAATCAAAATACTAGTTGCCGGACTACAAAACATTCTCAAGAGTCAAAT
1 GTTTCTATAACTCTCTAAAGCAAAATACTAGTCGCCGGACAACAAAACATTCTCTAGAGTCAAAT
* ** * *
59675671 CCAATTTTATGGACCAGCTTCAACTGAGACATTCATACCCCGCACTTTCGCAATGCATCTCGTTT
66 CCAATTTTATGGACCAACTTTTACCGAGACATTCATTCCCCG-ACTTTCGCAATGCATCTCGTTT
** * * *
59675736 CCGTGATAGAACAAAGATGAAAGCTCGTACATGTGTTAATGAAAACCAAGTTTTAGCTTCTCAAT
130 CCACGATAGAACAAAGATGAAAGCTCGT-CATGTGTTTATGCAAACCGAGTTTTAGCTTCTCAAT
59675801 ATGCAGCAAT
194 ATGCAGCAAT
*
59675811 GTTTCTATAACTCTCTAAAGCAAAATACTAGTCGCCAGACAACAAAACATTCTCTCA-AGTC-AA
1 GTTTCTATAACTCTCTAAAGCAAAATACTAGTCGCCGGACAACAAAACATTCTCT-AGAGTCAAA
* * * ** *
59675874 TTCGATTTTATGGACCAACTTTGACCGAGACATTCATTCGCCATACTTTCGCAATGCATCTTGTT
65 TCCAATTTTATGGACCAACTTTTACCGAGACATTCATTC-CCCGACTTTCGCAATGCATCTCGTT
* * * *
59675939 TCCACGATAGAACAGAGATGAAAGCTAGGTCTTGTGTTTATGCAGACCCGAGTTTTAGCTTCTCA
129 TCCACGATAGAACAAAGATGAAAGCT-CGTCATGTGTTTATGCA-AACCGAGTTTTAGCTTCTCA
59676004 ATATGCAGCAAT
192 ATATGCAGCAAT
* * *
59676016 GTTTCTACAACTCTCTAAAGCAAAATACTAGTTGCCGGACAACAAAACTTTCTCTAGAGTCAAAT
1 GTTTCTATAACTCTCTAAAGCAAAATACTAGTCGCCGGACAACAAAACATTCTCTAGAGTCAAAT
** * * *
59676081 CTGATTTTATGGACCAACTTGTACCGAGACATTCATTCACCAGACTTTCGCAATGCATCTCGTAT
66 CCAATTTTATGGACCAACTTTTACCGAGACATTCATTC-CCCGACTTTCGCAATGCATCTCGTTT
* ** * * *
59676146 -CAGAGATAGAACGGAGATGAAAGCTCGGTCGTGTGTCTACGCAAACCCGAGTTTTAGCTTCTCA
130 CCA-CGATAGAACAAAGATGAAAGCTC-GTCATGTGTTTATGCAAA-CCGAGTTTTAGCTTCTCA
59676210 ATATGCAGC
192 ATATGCAGC
59676219 CAGGATTAAA
Statistics
Matches: 536, Mismatches: 67, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
204 92 0.17
205 323 0.60
206 121 0.23
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (203 bp):
GTTTCTATAACTCTCTAAAGCAAAATACTAGTCGCCGGACAACAAAACATTCTCTAGAGTCAAAT
CCAATTTTATGGACCAACTTTTACCGAGACATTCATTCCCCGACTTTCGCAATGCATCTCGTTTC
CACGATAGAACAAAGATGAAAGCTCGTCATGTGTTTATGCAAACCGAGTTTTAGCTTCTCAATAT
GCAGCAAT
Found at i:59684585 original size:18 final size:18
Alignment explanation
Indices: 59684538--59684588 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
59684528 GGTCCGACAT
* *
59684538 CAGCTCCAACGACGGCCA
1 CAGCTCCATCGGCGGCCA
59684556 CAGCTCCATCGGCGGCCA
1 CAGCTCCATCGGCGGCCA
* *
59684574 CGGCTCCGTCGGCGG
1 CAGCTCCATCGGCGG
59684589 GAAAGGCGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.16, C:0.43, G:0.31, T:0.10
Consensus pattern (18 bp):
CAGCTCCATCGGCGGCCA
Found at i:59698537 original size:176 final size:174
Alignment explanation
Indices: 59698179--59698861 Score: 790
Period size: 176 Copynumber: 3.9 Consensus size: 174
59698169 CCAAACAGTG
** * *
59698179 ATTAAACTGAGAGTGAATACATACAATTCCTACAAGATTATCACAATGCTAGGCAAAATCAGATC
1 ATTAAACTGAGAGACAATACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATCAGATC
* ** * *
59698244 GAAAATCATCAATTCAT-A--CTATATAATAAAACGTCG-ATCTGAAATTTTAATCTATTGTCTT
66 GAAAATCATCAATT-ATGATGTTATATAATAAAAC-AAGAATCTGAAATTTTCATCTATAGTCTT
* *
59698305 CTTGTTTCATATATATTCTCAGAAACCAAACAGTAGCTAAACGATCA
129 CTTTTTTC-TATATATTCTCAGGAACCAAACAGTAGCTAAACGATCA
*
59698352 ATTAAACTGAGAGACAATACATACAATT-CTGACAAAAGTATCACAATGCTAAGCAAAATCAGAT
1 ATTAAACTGAGAGACAATACATACAATTCCT-ACAAAATTATCACAATGCTAAGCAAAATCAGAT
* * *** * *
59698416 ACGAAGATCATCGAACTATGATGTTATATAATAAAATGTGAATCTGAAATTTCCATCTATTGTCC
65 -CGAAAATCATC-AATTATGATGTTATATAATAAAACAAGAATCTGAAATTTTCATCTATAGT-C
**
59698481 TT-TTTTTTCTATATATTCTCAGGAACCAAACAGTAGCTAAAATATCA
127 TTCTTTTTTCTATATATTCTCAGGAACCAAACAGTAGCTAAACGATCA
* ** * * * * *
59698528 GTTAAACTGACCG--GATACATACAATTCCAACAAAATTATCACAATGCCAAACAAAAGCAGATC
1 ATTAAACTGAGAGACAATACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATCAGATC
** * *
59698591 GAAAAGAATCAATGTATGTTGTTATATAATAAAACAAGAATCTGAAATTTTCATATATAGTCTTC
66 GAAAATCATCAAT-TATGATGTTATATAATAAAACAAGAATCTGAAATTTTCATCTATAGTCTTC
* *
59698656 TTTTTTCCAGTATACTCTCAGGAACCAAACAGTAGCTAAACGATCA
130 TTTTTTCTA-TATATTCTCAGGAACCAAACAGTAGCTAAACGATCA
* * * * * *
59698702 ATTAAACTGAGA-ACGGAGACGTACATTTCCTACAAACTTATCGCAATGCTAAGCAAAATCAGAT
1 ATTAAACTGAGAGAC-AATACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATCAGAT
* * *
59698766 CAAAAATCATCAATTTATGACGTTATAAAATAAAACAAGAATCTGAAATTTTCATCTATAGTCTT
65 CGAAAATCATCAA-TTATGATGTTATATAATAAAACAAGAATCTGAAATTTTCATCTATAGTCTT
*
59698831 CTTTTTTCCAATATATTCTCAGGAACCAAAC
129 CTTTTTT-CTATATATTCTCAGGAACCAAAC
59698862 GATCAATTAA
Statistics
Matches: 431, Mismatches: 62, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
172 7 0.02
173 112 0.26
174 95 0.22
175 5 0.01
176 168 0.39
177 41 0.10
178 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (174 bp):
ATTAAACTGAGAGACAATACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATCAGATC
GAAAATCATCAATTATGATGTTATATAATAAAACAAGAATCTGAAATTTTCATCTATAGTCTTCT
TTTTTCTATATATTCTCAGGAACCAAACAGTAGCTAAACGATCA
Found at i:59698691 original size:350 final size:335
Alignment explanation
Indices: 59698009--59698861 Score: 910
Period size: 350 Copynumber: 2.5 Consensus size: 335
59697999 CAACCATTAA
* * * * * * *
59698009 ATCAATTAAACAGATAACGGATACATACAATCCCCTACAAAATTATCACAATGCTTAGCAAAACC
1 ATCAATTAAACTGAGAACGAAGACATACAAT-TCCTACAAAATTATCACAATGCTAAGCAAAATC
* * * * *
59698074 ATATCGAAAACCAACAATTTATGACGTTATATAATAAAAATGGAATATGAAGTTTTCATCTATTG
65 AGATCGAAAATCATCAATTTATGACGTTATATAAT-AAAATGGAATCTGAAATTTTCATCTATTG
* * * * *
59698139 TCATATTTGTTTCTTATATATTCTCAGGAACCAAACAGTGATTAAACTGAGAGTGAATACATACA
129 TCCT-TTTTTTTC-TATATATTCTCAGGAACCAAACAGTGATAAAACTGAAACTGAATACATACA
* * * ** * **
59698204 ATTCCTACAAGATTATCACAATGCTAGGCAAAATCAGATCGAAAATCATCAATTCATACTATATA
192 ATTCCAACAAAATTATCACAATGCCAAACAAAAGCAGATCGAAAAGAATCAATTCATACTATATA
** * * *
59698269 ATAAAACGTCGATCTGAAATTTTAATCTATTGTCTTCTTGTTTCATATATATTCTCAGAAACCAA
257 ATAAAACGAAGATCTGAAATTTTAATATATAGTCTTCTTGTTTCATATATACTCTCAGAAACCAA
59698334 ACAGTAGCTAAACG
322 ACAGTAGCTAAACG
* *
59698348 ATCAATTAAACTGAGAGAC-AATACATACAATT-CTGACAAAAGTATCACAATGCTAAGCAAAAT
1 ATCAATTAAACTGAGA-ACGAAGACATACAATTCCT-ACAAAATTATCACAATGCTAAGCAAAAT
* * * *
59698411 CAGATACGAAGATCATCGAA-CTATGATGTTATATAATAAAATGTGAATCTGAAATTTCCATCTA
64 CAGAT-CGAAAATCATC-AATTTATGACGTTATATAATAAAATG-GAATCTGAAATTTTCATCTA
* *
59698475 TTGTCCTTTTTTTTCTATATATTCTCAGGAACCAAACAGTAGCTAAAATATCAGTTAAACTGACC
126 TTGTCCTTTTTTTTCTATATATTCTCAGGAACCAAACAGT-GAT-AAA-A-C--TGAAACTGA--
59698540 GGATACATACAATTCCAACAAAATTATCACAATGCCAAACAAAAGCAGATCGAAAAGAATCAATG
183 --ATACATACAATTCCAACAAAATTATCACAATGCCAAACAAAAGCAGATCGAAAAGAATCAAT-
** * * *
59698605 T-ATGTTGTTATATAATAAAAC-AAGAATCTGAAATTTTCATATATAGTCTTCTTTTTTCCA-GT
245 TCA---TACTATATAATAAAACGAAG-ATCTGAAATTTTAATATATAGTCTTCTTGTTT-CATAT
*
59698667 ATACTCTCAGGAACCAAACAGTAGCTAAACG
305 ATACTCTCAGAAACCAAACAGTAGCTAAACG
* * * * *
59698698 ATCAATTAAACTGAGAACGGAGACGTACATTTCCTACAAACTTATCGCAATGCTAAGCAAAATCA
1 ATCAATTAAACTGAGAACGAAGACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATCA
* * ** *
59698763 GATCAAAAATCATCAATTTATGACGTTATAAAATAAAACAAGAATCTGAAATTTTCATCTATAGT
66 GATCGAAAATCATCAATTTATGACGTTATATAATAAAA-TGGAATCTGAAATTTTCATCTATTGT
*
59698828 -CTTCTTTTTTCCAATATATTCTCAGGAACCAAAC
130 CCTT-TTTTTT-CTATATATTCTCAGGAACCAAAC
59698862 GATCAATTAA
Statistics
Matches: 428, Mismatches: 59, Indels: 43
0.81 0.11 0.08
Matches are distributed among these distances:
337 27 0.06
338 44 0.10
339 73 0.17
340 5 0.01
341 1 0.00
343 6 0.01
347 55 0.13
348 6 0.01
349 58 0.14
350 149 0.35
351 4 0.01
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (335 bp):
ATCAATTAAACTGAGAACGAAGACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATCA
GATCGAAAATCATCAATTTATGACGTTATATAATAAAATGGAATCTGAAATTTTCATCTATTGTC
CTTTTTTTTCTATATATTCTCAGGAACCAAACAGTGATAAAACTGAAACTGAATACATACAATTC
CAACAAAATTATCACAATGCCAAACAAAAGCAGATCGAAAAGAATCAATTCATACTATATAATAA
AACGAAGATCTGAAATTTTAATATATAGTCTTCTTGTTTCATATATACTCTCAGAAACCAAACAG
TAGCTAAACG
Found at i:59699724 original size:16 final size:16
Alignment explanation
Indices: 59699687--59699726 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
59699677 TTAATAAAAT
* *
59699687 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
59699703 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
59699719 TAAAATTA
1 TAAAATTA
59699727 CCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:59699759 original size:59 final size:67
Alignment explanation
Indices: 59699715--59699907 Score: 213
Period size: 59 Copynumber: 3.1 Consensus size: 67
59699705 AAATTAATTG
59699715 TTAGTAAAATTACCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTACCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
59699779 GA
66 GA
* * *
59699781 TTAGT-AAATT----TATCA--AATT-ATTAATTGTATTAATTGTTGTAATAAAACCTAACATTT
1 TTAGTAAAATTACCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
59699838 GA
66 GA
* * *
59699840 TTAGT-AAATT----TATCA--AATT-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
1 TTAGTAAAATTACCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
59699897 GA
66 GA
59699899 TTAGTAAAA
1 TTAGTAAAA
59699908 CAAACTTGAT
Statistics
Matches: 120, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
59 104 0.87
60 3 0.03
61 3 0.03
65 5 0.04
66 5 0.04
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (67 bp):
TTAGTAAAATTACCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
GA
Found at i:59702318 original size:18 final size:17
Alignment explanation
Indices: 59702291--59702324 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
59702281 TGTCAATGGT
59702291 AAAATAATAATAAATTG
1 AAAATAATAATAAATTG
59702308 AAAATTAATAATAAATT
1 AAAA-TAATAATAAATT
59702325 TTTTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AAAATAATAATAAATTG
Found at i:59704858 original size:6 final size:6
Alignment explanation
Indices: 59704844--59704878 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
59704834 TGAATTCCCT
* *
59704844 CCACCG CCGCCG CCGCCG CCACCG CCACCG CCACC
1 CCACCG CCACCG CCACCG CCACCG CCACCG CCACC
59704879 TTCCATTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.11, C:0.69, G:0.20, T:0.00
Consensus pattern (6 bp):
CCACCG
Found at i:59709239 original size:21 final size:21
Alignment explanation
Indices: 59709215--59709255 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
59709205 TTATTGTTTT
59709215 TAGACATACTATTACTGCTTC
1 TAGACATACTATTACTGCTTC
* * *
59709236 TAGATATATTATTATTGCTT
1 TAGACATACTATTACTGCTT
59709256 AGAAAACCCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (21 bp):
TAGACATACTATTACTGCTTC
Found at i:59717377 original size:18 final size:18
Alignment explanation
Indices: 59717339--59717374 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
59717329 TTATTATTTT
*
59717339 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
59717357 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
59717375 TAACTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:59719356 original size:7 final size:7
Alignment explanation
Indices: 59719344--59719377 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
59719334 TCAATTCAAT
59719344 ATAAAAA
1 ATAAAAA
59719351 ATAAAAA
1 ATAAAAA
59719358 ATAAAAA
1 ATAAAAA
59719365 ATAAAAA
1 ATAAAAA
59719372 ATAAAA
1 ATAAAA
59719378 CTATCTTCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:59731800 original size:33 final size:32
Alignment explanation
Indices: 59731705--59731804 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 32
59731695 TTAATATTTT
*
59731705 AATATATGAAATATAAATTTTAAATATGATTAAATA
1 AATATAT-AAAT-TATATTTTAAATAT--TTAAATA
* * * *
59731741 ATTAATATTAATTAT-TTCTAAA-ATTTAATTA
1 AAT-ATATAAATTATATTTTAAATATTTAAATA
59731772 GAATATATAAATTATATTTTAAATATTTAAATA
1 -AATATATAAATTATATTTTAAATATTTAAATA
59731805 TAACCATTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
31 16 0.31
32 8 0.16
33 10 0.20
34 6 0.12
35 2 0.04
36 5 0.10
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (32 bp):
AATATATAAATTATATTTTAAATATTTAAATA
Found at i:59749679 original size:15 final size:16
Alignment explanation
Indices: 59749659--59749700 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
59749649 ATTTACATTT
*
59749659 TTAAACTTAAAAAT-C
1 TTAAACTTAAAAATAA
59749674 TTAAAC-TAAAAATAA
1 TTAAACTTAAAAATAA
*
59749689 TTAAATTTAAAA
1 TTAAACTTAAAA
59749701 GGCATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 11 0.48
16 5 0.22
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAACTTAAAAATAA
Found at i:59755312 original size:21 final size:22
Alignment explanation
Indices: 59755286--59755332 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
59755276 CTCTGCTCAA
*
59755286 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
59755307 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
59755329 ACTC
1 ACTC
59755333 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:59763413 original size:91 final size:90
Alignment explanation
Indices: 59763303--59763474 Score: 265
Period size: 91 Copynumber: 1.9 Consensus size: 90
59763293 CTTAAATAGG
59763303 GTGGGTCAAAATCTAATAATAAAAATATACAATACAATAACCG-GTATATATAAAATAACTTATC
1 GTGGGTCAAAATCTAATAATAAAAATATACAATACAATAA-CGTGTATATATAAAATAACTTATC
59763367 AAATCAAACCCTTATATATACATATGT
65 AAATC-AACCCTTATATATACATATGT
* * * * *
59763394 GTGGGTCAAGATGTAATAATAAAAATATATAATACAATAATGTGTATATATAAAATAGCTTATCA
1 GTGGGTCAAAATCTAATAATAAAAATATACAATACAATAACGTGTATATATAAAATAACTTATCA
*
59763459 AATCTACCCTTATATA
66 AATCAACCCTTATATA
59763475 CAGAGAAATT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
90 12 0.16
91 62 0.84
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (90 bp):
GTGGGTCAAAATCTAATAATAAAAATATACAATACAATAACGTGTATATATAAAATAACTTATCA
AATCAACCCTTATATATACATATGT
Found at i:59769489 original size:3 final size:3
Alignment explanation
Indices: 59769481--59769512 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
59769471 GTGGAAGATG
*
59769481 GAT GAT GAT GAT GAT GAT GAT GAT GAC GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
59769513 AGAAGAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:59771050 original size:6 final size:6
Alignment explanation
Indices: 59771039--59771065 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
59771029 ACAAATTTAT
59771039 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
59771066 GTACTCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:59781204 original size:22 final size:23
Alignment explanation
Indices: 59781162--59781204 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
59781152 CAAAATGGTG
* *
59781162 AAATTACATTTTTATTATCGTAA
1 AAATTACAGTTTAATTATCGTAA
59781185 AAATTACAGTTTAATT-TCGT
1 AAATTACAGTTTAATTATCGT
59781205 CCCCCCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (23 bp):
AAATTACAGTTTAATTATCGTAA
Found at i:59784166 original size:16 final size:16
Alignment explanation
Indices: 59784141--59784172 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
59784131 TGCTTTGCAC
59784141 TAAAACATTTTTTTTG
1 TAAAACATTTTTTTTG
*
59784157 TAAAATATTTTTTTTG
1 TAAAACATTTTTTTTG
59784173 GTCCCAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.59
Consensus pattern (16 bp):
TAAAACATTTTTTTTG
Found at i:59784250 original size:20 final size:20
Alignment explanation
Indices: 59784221--59784263 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
59784211 TTTAACATTA
59784221 TTTTTATCTCAAAAGTATTT
1 TTTTTATCTCAAAAGTATTT
* * *
59784241 TTTTTGTCTCAGAAGTGTTT
1 TTTTTATCTCAAAAGTATTT
59784261 TTT
1 TTT
59784264 AGAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (20 bp):
TTTTTATCTCAAAAGTATTT
Found at i:59791517 original size:20 final size:21
Alignment explanation
Indices: 59791480--59791522 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
59791470 TTTTAAATAT
*
59791480 TATTTAAATAATTCAAAAAAA
1 TATTTAAATAATTAAAAAAAA
* *
59791501 TATTT-AATATTTAAAAATAA
1 TATTTAAATAATTAAAAAAAA
59791521 TA
1 TA
59791523 ATCTTGTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTTAAATAATTAAAAAAAA
Found at i:59792560 original size:14 final size:15
Alignment explanation
Indices: 59792543--59792571 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59792533 ATTGATGACA
59792543 TTTATGAA-TATAAT
1 TTTATGAATTATAAT
59792557 TTTATGAATTATAAT
1 TTTATGAATTATAAT
59792572 CTAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (15 bp):
TTTATGAATTATAAT
Found at i:59797816 original size:17 final size:18
Alignment explanation
Indices: 59797788--59797824 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
59797778 GTTTGATTAA
59797788 TAATTAATTACTTAAAAT
1 TAATTAATTACTTAAAAT
59797806 TAATT-ATTACTTAAAAT
1 TAATTAATTACTTAAAAT
59797823 TA
1 TA
59797825 TCTGGTTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTAATTACTTAAAAT
Found at i:59799453 original size:21 final size:20
Alignment explanation
Indices: 59799414--59799453 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
59799404 ATGTTGGGGA
*
59799414 TTTTGAAGGTGCTTTGAAGG
1 TTTTGAAGGTGATTTGAAGG
*
59799434 TTTTGAATGTGATGTTGAAG
1 TTTTGAAGGTGAT-TTGAAG
59799454 AGTCGGCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.03, G:0.33, T:0.42
Consensus pattern (20 bp):
TTTTGAAGGTGATTTGAAGG
Found at i:59800344 original size:17 final size:17
Alignment explanation
Indices: 59800324--59800356 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
59800314 ATATCTTTCG
*
59800324 AATATGAATATGTATCC
1 AATATGAATATATATCC
59800341 AATATGAATATATATC
1 AATATGAATATATATC
59800357 AGACATAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (17 bp):
AATATGAATATATATCC
Found at i:59807907 original size:135 final size:135
Alignment explanation
Indices: 59807665--59807935 Score: 506
Period size: 135 Copynumber: 2.0 Consensus size: 135
59807655 CCTTCTTTTC
59807665 TCACAAACTTTCAATTGTATCAAATTACTCAGAAAATAGTTAATGATTAAGGATTGCTAATGTAG
1 TCACAAACTTTCAATTGTATCAAATTACTCAGAAAATAGTTAATGATTAAGGATTGCTAATGTAG
*
59807730 ATAGATAGAAGATACCAATGACATAATGATCCGTAGGTAGGTTTGAATAAGCAGTACATTTACTT
66 ATAGACAGAAGATACCAATGACATAATGATCCGTAGGTAGGTTTGAATAAGCAGTACATTTACTT
*
59807795 GCGAT
131 ACGAT
*
59807800 TCACAAACTTTCAATTGTATCAAATTGCTCAGAAAATAGTTAATGATTAAGGATTGCTAATGTAG
1 TCACAAACTTTCAATTGTATCAAATTACTCAGAAAATAGTTAATGATTAAGGATTGCTAATGTAG
*
59807865 ATAGACAGAAGATACCAATGATATAATGATCCGTAGGTAGGTTTGAATAAGCAGTACATTTACTT
66 ATAGACAGAAGATACCAATGACATAATGATCCGTAGGTAGGTTTGAATAAGCAGTACATTTACTT
59807930 ACGAT
131 ACGAT
59807935 T
1 T
59807936 AGTATAAAAA
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
135 132 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (135 bp):
TCACAAACTTTCAATTGTATCAAATTACTCAGAAAATAGTTAATGATTAAGGATTGCTAATGTAG
ATAGACAGAAGATACCAATGACATAATGATCCGTAGGTAGGTTTGAATAAGCAGTACATTTACTT
ACGAT
Done.