Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 20 of 433
Found at i:5312048 original size:19 final size:19
Alignment explanation
Indices: 5312024--5312060 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5312014 AATCATATCT
5312024 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5312043 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
5312061 TGAAGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5312068 original size:17 final size:19
Alignment explanation
Indices: 5312027--5312068 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5312017 CATATCTTCT
*
5312027 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
5312046 AAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCG
5312063 AAGATT
1 AAGATT
5312069 ATATTTCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 1 0.05
19 15 0.68
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:5312460 original size:45 final size:45
Alignment explanation
Indices: 5312405--5312604 Score: 231
Period size: 45 Copynumber: 4.5 Consensus size: 45
5312395 GGAAGGCGAT
* * *
5312405 ATCTGCTATCTTTGATCTGCTCCCCATCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
5312450 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACTCTAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
** * ** * *
5312495 ATCTACT-TCTTCAATCTGCTCATCGTATAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * *
5312539 ATCTGTTATCTCCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * *
5312584 ATCTGTCATCTTGGATATGCT
1 ATCTGTTATCTTCGATCTGCT
5312605 TCGATGTAAA
Statistics
Matches: 128, Mismatches: 26, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
44 35 0.27
45 93 0.73
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.33
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:5312754 original size:78 final size:78
Alignment explanation
Indices: 5312621--5313041 Score: 614
Period size: 78 Copynumber: 5.4 Consensus size: 78
5312611 TAAACACATA
* * *
5312621 AAGGTCAAATCTGCTATGTCTTCGATCTGCT-TCTCGTCTAATATAGAGATGCCAAATCATCTTG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCT-GTCTAATACAGAGATGCCAAATCATCTTG
5312685 GATCTGCTTCAATG
65 GATCTGCTTCAATG
* * *
5312699 AAGGTCCA-ATCTGTTATGTCTTTGATCTGCTCCCTGTCTAATACAGAGATACCAAATCATCTTG
1 AAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATCTTG
5312763 GATCTGCTTCAATG
65 GATCTGCTTCAATG
* * * * *
5312777 AAGGTCAGATCTGCTGTGTCTTCTATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCTTAG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATCTTGG
*
5312842 ATCTGCTTCAATA
66 ATCTGCTTCAATG
* * **
5312855 AAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCC-GTCGAATATGGAGATGCCAAATCATCTTG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTC-CCTGTCTAATACAGAGATGCCAAATCATCTTG
5312919 GATCTGCTTCAATG
65 GATCTGCTTCAATG
* * * *
5312933 AAGGTCAGATCTGTTGTGTCTTTGATCTGCTCCCTGTCTAGTACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATCTTGG
5312998 ATCTGCTTCAATG
66 ATCTGCTTCAATG
5313011 AAGGTCAGATCTGCTATGTCTTCGATCTGCT
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCT
5313042 TTTCGTTGAA
Statistics
Matches: 304, Mismatches: 34, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
77 4 0.01
78 294 0.97
79 6 0.02
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (78 bp):
AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATCTTGG
ATCTGCTTCAATG
Found at i:5321997 original size:46 final size:46
Alignment explanation
Indices: 5321896--5321983 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
5321886 TATAACCCGC
* *
5321896 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCCCAT
* *
5321942 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTC
5321984 AACCATCCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCCCAT
Found at i:5333994 original size:3 final size:3
Alignment explanation
Indices: 5333986--5334012 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5333976 TCTTACTTTT
5333986 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
5334013 AGTAAACTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5334754 original size:2 final size:2
Alignment explanation
Indices: 5334747--5334778 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5334737 ACGTTTTTAG
5334747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5334779 CACATTATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5334938 original size:19 final size:19
Alignment explanation
Indices: 5334910--5334947 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5334900 TAGTCACACC
5334910 ACACAAAATAAAAAATTTA
1 ACACAAAATAAAAAATTTA
*
5334929 ACACACAATAAAAAATTTA
1 ACACAAAATAAAAAATTTA
5334948 TGTATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (19 bp):
ACACAAAATAAAAAATTTA
Found at i:5353347 original size:2 final size:2
Alignment explanation
Indices: 5353342--5353367 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5353332 TGTGTGTGTG
5353342 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5353368 ATTTAGCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5353664 original size:19 final size:19
Alignment explanation
Indices: 5353636--5353673 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5353626 TTGAGATTGC
*
5353636 CAACCGATTTGCTTGAAAT
1 CAACCGATTTGCCTGAAAT
*
5353655 CAACCTATTTGCCTGAAAT
1 CAACCGATTTGCCTGAAAT
5353674 TATTCATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (19 bp):
CAACCGATTTGCCTGAAAT
Found at i:5356201 original size:43 final size:44
Alignment explanation
Indices: 5356086--5357053 Score: 1178
Period size: 44 Copynumber: 22.4 Consensus size: 44
5356076 AAATCCAGAT
* * * * *
5356086 GATTTGGCGTCTTTGTAGCGGCAGAAAGCAGATCCAAGATAATA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
5356130 GATTTGGCATCTCTGTAGCGGTGAAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
5356174 GATTT-GCGTCTCTGTAGTGACGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
5356217 GATATTGGCGTCTCTGTAGCGGCGGAGAGCAAATCGAAGATAACA
1 GAT-TTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * * * *
5356262 GATTTGGCGTCTCTGTAGCAGCGGGGAACAGATCCAAGATAGCA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
5356306 GATTTGACGTCTCTGTAGCGGCAGAG-GCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
5356349 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCAAAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATC-GAAGATAACA
* *
5356394 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAACAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
5356434 GATTTGGCATCTCTGTA--GGCGGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGC-GGAGAGCAGATCGAAGATAACA
* * * * * *
5356477 GATTTGGTTTGGTTGTCACTATAGTGGCGAAGAGAAGATCGAAGAT----
1 GA-----TTTGG-CGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
5356523 GATTTGGCATCTCTGTAGCGGTGGAGAGTAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
5356567 AATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCG-ATATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
5356610 AATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCAAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
5356654 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAACAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
5356694 GATTTGGCATCTCTGTAGCCGCGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
5356738 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
5356782 GATTTGGCGTCT-TGTAACGGTGAAGAGCAGATCGAAGAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
5356821 GATTT-GCATCTCTGTAGCGGCGGAGAGTAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
5356864 GATTTGGCGTCTCTGTAGCGGC--AGTGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * * *
5356906 GATTTAGCGTCTCCGTAGCGGCAGAAAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
5356950 GATTTGGCGTCTCTGTA-CGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * * * *
5356993 GATTTGGCGTCTTTATAGCGACGGAGAGCAGATCGAAGATATCG
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
5357037 GATTTGGCGTCTCTGTA
1 GATTTGGCGTCTCTGTA
5357054 TTAGACGGAT
Statistics
Matches: 794, Mismatches: 95, Indels: 70
0.83 0.10 0.07
Matches are distributed among these distances:
38 8 0.01
39 44 0.06
40 78 0.10
41 5 0.01
42 38 0.05
43 185 0.23
44 324 0.41
45 80 0.10
46 2 0.00
48 5 0.01
49 6 0.01
50 16 0.02
51 3 0.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (44 bp):
GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
Found at i:5356203 original size:87 final size:87
Alignment explanation
Indices: 5356086--5357053 Score: 1131
Period size: 87 Copynumber: 11.2 Consensus size: 87
5356076 AAATCCAGAT
* * * * * *
5356086 GATTTGGCGTCTTTGTAGCGGCAGAAAGCAGATCCAAGATAATAGATTTGGCATCTCTGTAGCGG
1 GATTTGGCGTCTCTGTAGC-GCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
* *
5356151 TGAAGAGCAGATCGAAGATAACA
65 CGGAGAGCAGATCGAAGATAACA
*
5356174 GATTT-GCGTCTCTGTAGTGACGGAGAGCAGATCGAAGATAACAGATATTGGCGTCTCTGTAGCG
1 GATTTGGCGTCTCTGTAGCG-CGGAGAGCAGATCGAAGATAACAGAT-TTGGCGTCTCTGTAGCG
*
5356238 GCGGAGAGCAAATCGAAGATAACA
64 GCGGAGAGCAGATCGAAGATAACA
* * * * *
5356262 GATTTGGCGTCTCTGTAGCAGCGGGGAACAGATCCAAGATAGCAGATTTGACGTCTCTGTAGCGG
1 GATTTGGCGTCTCTGTAGC-GCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
*
5356327 CAGAG-GCAGATCGAAGATAACA
65 CGGAGAGCAGATCGAAGATAACA
*
5356349 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCAAAAGATAACAGATTTGGCGTCTCTGTAGCG
1 GATTTGGCGTCTCTGTAGC-GCGGAGAGCAGATC-GAAGATAACAGATTTGGCGTCTCTGTAGCG
* *
5356414 GCAGAGAGCAGATCGAACAT----
64 GCGGAGAGCAGATCGAAGATAACA
* * * *
5356434 GATTTGGCATCTCTGTAG-GCGGGAGAGCAGATCGAAGATAACAGATTTGGTTTGGTTGTCACTA
1 GATTTGGCGTCTCTGTAGCGC-GGAGAGCAGATCGAAGATAACAGA-----TTTGG-CGTCTCTG
* * *
5356498 TAGTGGCGAAGAGAAGATCGAAGAT----
59 TAGCGGCGGAGAGCAGATCGAAGATAACA
* * * *
5356523 GATTTGGCATCTCTGTAGCGGTGGAGAGTAGATCGAAGATAACAAATTTGGCGTCTCTGTAGCGG
1 GATTTGGCGTCTCTGTAGC-GCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
*
5356588 CGGAGAGCAGATCG-ATATAACA
65 CGGAGAGCAGATCGAAGATAACA
* * *
5356610 AATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCTGTAGCGG
1 GATTTGGCGTCTCTGTAGC-GCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
*
5356675 CGGAGAGCAGATCGAACAT----
65 CGGAGAGCAGATCGAAGATAACA
*
5356694 GATTTGGCATCTCTGTAGCCGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
1 GATTTGGCGTCTCTGTAG-CGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
5356759 CGGAGAGCAGATCGAAGATAACA
65 CGGAGAGCAGATCGAAGATAACA
* *
5356782 GATTTGGCGTCT-TGTAACG-GTGAAGAGCAGATCGAAGAT----GATTT-GCATCTCTGTAGCG
1 GATTTGGCGTCTCTGTAGCGCG-G-AGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCG
*
5356840 GCGGAGAGTAGATCGAAGATAACA
64 GCGGAGAGCAGATCGAAGATAACA
* * * *
5356864 GATTTGGCGTCTCTGTAGCG-GCAGTGCAGATCGAAGATAACAGATTTAGCGTCTCCGTAGCGGC
1 GATTTGGCGTCTCTGTAGCGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGC
* *
5356928 AGAAAGCAGATCGAAGATAACA
66 GGAGAGCAGATCGAAGATAACA
* * * *
5356950 GATTTGGCGTCTCTGTA-CGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTTTATAGCGA
1 GATTTGGCGTCTCTGTAGC-GCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
* *
5357014 CGGAGAGCAGATCGAAGATATCG
65 CGGAGAGCAGATCGAAGATAACA
5357037 GATTTGGCGTCTCTGTA
1 GATTTGGCGTCTCTGTA
5357054 TTAGACGGAT
Statistics
Matches: 763, Mismatches: 82, Indels: 71
0.83 0.09 0.08
Matches are distributed among these distances:
81 15 0.02
82 48 0.06
83 28 0.04
84 111 0.15
85 30 0.04
86 55 0.07
87 243 0.32
88 120 0.16
89 89 0.12
90 23 0.03
91 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (87 bp):
GATTTGGCGTCTCTGTAGCGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGC
GGAGAGCAGATCGAAGATAACA
Found at i:5357361 original size:17 final size:17
Alignment explanation
Indices: 5357341--5357386 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 17
5357331 AATACAACCC
*
5357341 AAAATAAAAAATAAAAA
1 AAAAAAAAAAATAAAAA
5357358 AAAAAAAAAAATGAAGAAA
1 AAAAAAAAAAAT-AA-AAA
5357377 AAGAAAAAAA
1 AA-AAAAAAA
5357387 CCTAACCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 11 0.44
18 2 0.08
19 5 0.20
20 7 0.28
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (17 bp):
AAAAAAAAAAATAAAAA
Found at i:5357367 original size:18 final size:18
Alignment explanation
Indices: 5357341--5357386 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
5357331 AATACAACCC
*
5357341 AAAATAAAAAAT-AAAAA
1 AAAAAAAAAAATGAAAAA
5357358 AAAAAAAAAAATGAAGAAA
1 AAAAAAAAAAATGAA-AAA
*
5357377 AAGAAAAAAA
1 AAAAAAAAAA
5357387 CCTAACCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.44
18 2 0.08
19 12 0.48
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAAATGAAAAA
Found at i:5358210 original size:16 final size:16
Alignment explanation
Indices: 5358191--5358226 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5358181 CTTTATATAC
5358191 TTTATGTATTATTTAT
1 TTTATGTATTATTTAT
* *
5358207 TTTATTTTTTATTTAT
1 TTTATGTATTATTTAT
5358223 TTTA
1 TTTA
5358227 CGATCTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTATGTATTATTTAT
Found at i:5358274 original size:2 final size:2
Alignment explanation
Indices: 5358267--5358296 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5358257 TCTGTTTATG
5358267 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5358297 ATTTAGCTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5358587 original size:19 final size:19
Alignment explanation
Indices: 5358563--5358600 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5358553 TTGAGATTGC
*
5358563 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
5358582 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
5358601 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:5362519 original size:21 final size:22
Alignment explanation
Indices: 5362486--5362528 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
5362476 AATCAAATAT
*
5362486 TTTAGTAAATTAA-AACTCTTA
1 TTTAGTAAATTAACAAATCTTA
5362507 TTTA-TAAATTTAACAAATCTTA
1 TTTAGTAAA-TTAACAAATCTTA
5362529 CAAATATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (22 bp):
TTTAGTAAATTAACAAATCTTA
Found at i:5365166 original size:2 final size:2
Alignment explanation
Indices: 5365161--5365186 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5365151 CAAAAAAACA
5365161 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5365187 TAACATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5365791 original size:4 final size:4
Alignment explanation
Indices: 5365784--5365835 Score: 104
Period size: 4 Copynumber: 13.0 Consensus size: 4
5365774 TATATATATA
5365784 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5365832 TATG
1 TATG
5365836 GTTTCAGCCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:5368746 original size:6 final size:6
Alignment explanation
Indices: 5368735--5368774 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
5368725 GGGCTTCACT
5368735 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC -CATTCC TCTT
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TC-TTCC TCTT
5368775 GTTCTACTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 1 0.03
6 30 0.94
7 1 0.03
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCC
Found at i:5371781 original size:2 final size:2
Alignment explanation
Indices: 5371774--5371815 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5371764 AGTAAACAGC
*
5371774 GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5371816 ATGAGTGTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5375102 original size:64 final size:63
Alignment explanation
Indices: 5375001--5375130 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 63
5374991 AAAGATGGTC
5375001 TTATTCTTGTTCATCAACTCATCCTACCTAGATTGAAAATTGAAGTTGATGCTGAAAATTGTTG
1 TTATTCTTGTTCATCAACTCATCCTACCTAGATTGAAAATTGAAGTTGATGCTG-AAATTGTTG
5375065 TTATTCTTGTTCATCAACTCATCCTACCTAGATTGAAAATTGAAGTTGATGCTGAAATTGTTG
1 TTATTCTTGTTCATCAACTCATCCTACCTAGATTGAAAATTGAAGTTGATGCTGAAATTGTTG
5375128 TTA
1 TTA
5375131 AAATTATTAA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
63 12 0.18
64 54 0.82
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (63 bp):
TTATTCTTGTTCATCAACTCATCCTACCTAGATTGAAAATTGAAGTTGATGCTGAAATTGTTG
Found at i:5378955 original size:17 final size:18
Alignment explanation
Indices: 5378921--5378957 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5378911 TTTACTAAAA
5378921 AATAAAATATATTAATTT
1 AATAAAATATATTAATTT
*
5378939 AATAAAA-ATATTTATTT
1 AATAAAATATATTAATTT
5378956 AA
1 AA
5378958 ATTAGTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAAATATATTAATTT
Found at i:5383905 original size:22 final size:22
Alignment explanation
Indices: 5383854--5383905 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
5383844 AATGTGAACT
*
5383854 TCGATGAGGCAACTGTTAGTGA
1 TCGATGATGCAACTGTTAGTGA
*
5383876 TCGATGATGTAACTGTTAGTGA
1 TCGATGATGCAACTGTTAGTGA
5383898 TCGATGAT
1 TCGATGAT
5383906 ATAAGTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.33
Consensus pattern (22 bp):
TCGATGATGCAACTGTTAGTGA
Found at i:5384790 original size:38 final size:38
Alignment explanation
Indices: 5384739--5384940 Score: 271
Period size: 38 Copynumber: 5.3 Consensus size: 38
5384729 ATATTCGATG
* * *
5384739 TATATCTGGGTTAAATCCCACAAGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
5384777 TATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * *
5384815 TATATACGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAT
*
5384855 AATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* *
5384893 TATATCCGGGATAAATCCCGCAGGAC-TAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGG-CTTCGTGCTGGTAT
*
5384931 TATATTCGGG
1 TATATCCGGG
5384941 CCTTCGTACC
Statistics
Matches: 147, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
38 108 0.73
39 11 0.07
40 28 0.19
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:5384851 original size:78 final size:76
Alignment explanation
Indices: 5384762--5384940 Score: 252
Period size: 78 Copynumber: 2.3 Consensus size: 76
5384752 AATCCCACAA
*
5384762 GCTTCGTGCTGGTATTATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTATTATATACGGGCT
1 GCTTCGTGCTGGTATTATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTATTATATACGGG-A
5384827 TAAAGACCCGCAG
65 TAAA-ACCCGCAG
** * *
5384840 GCTTCGTGCTGGTAAAATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCGGGAT
1 GCTTCGTGCTGGTATTATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTATTATATACGGGAT
*
5384905 AAATCCCGCAG
66 AAAACCCGCAG
* *
5384916 GAC-TAGTGCTGGTATTATATTCGGG
1 G-CTTCGTGCTGGTATTATATCCGGG
5384941 CCTTCGTACC
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
76 26 0.29
77 5 0.06
78 59 0.66
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (76 bp):
GCTTCGTGCTGGTATTATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTATTATATACGGGAT
AAAACCCGCAG
Found at i:5385057 original size:43 final size:43
Alignment explanation
Indices: 5384933--5385044 Score: 170
Period size: 43 Copynumber: 2.6 Consensus size: 43
5384923 GCTGGTATTA
* *
5384933 TATTCGGGCCTTCGTACCTAGTAGGCTTCGTGTCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGTAGGCTTCGTGCCGGTGATGTG
* **
5384976 TATTCGGGCCTTCGTGCTTAACAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGTAGGCTTCGTGCCGGTGATGTG
*
5385019 TATTCGGGCCTTTGTGCCTAGTAGGC
1 TATTCGGGCCTTCGTGCCTAGTAGGC
5385045 GTAATGCCGG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.12, C:0.22, G:0.32, T:0.34
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGTAGGCTTCGTGCCGGTGATGTG
Found at i:5390709 original size:38 final size:38
Alignment explanation
Indices: 5390658--5390859 Score: 242
Period size: 38 Copynumber: 5.3 Consensus size: 38
5390648 ATATTCGATG
* **
5390658 TATATCCGGGTTAAATCCTGCAGGCTTCGTACTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGTTGGTAT
*
5390696 TATATCCGGGTTAAATCCCACAGGCTTCGTGTTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGTTGGTAT
* * * *
5390734 TATATCCAGGCTTAAAGACCCGCAGGCTTAGTGTTGGTAA
1 TATATCC-GGGTTAAA-TCCCGCAGGCTTCGTGTTGGTAT
* *
5390774 AATATCCGAGTTAAATCCCGCAGGCTTCGTGTTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGTTGGTAT
* * * * *
5390812 TATATCCGGGATAAATCCCGTAGGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGTTGGTAT
*
5390850 TATATTCGGG
1 TATATCCGGG
5390860 CCTTCGTGCC
Statistics
Matches: 139, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
38 101 0.73
39 13 0.09
40 25 0.18
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGTTGGTAT
Found at i:5390772 original size:78 final size:76
Alignment explanation
Indices: 5390689--5390859 Score: 225
Period size: 78 Copynumber: 2.2 Consensus size: 76
5390679 AGGCTTCGTA
*
5390689 CTGGTATTATATCCGGGTTAAATCCCACAGGCTTCGTGTTGGTATTATATCCAGGCTTAAAGACC
1 CTGGTATTATATCCGGGTTAAATCCCACAGGCTTCGTGTTGGTATTATATCC-GGCATAAA-ACC
*
5390754 CGCAGGCTTAGTG
64 CGCAGGCCTAGTG
* ** * * * *
5390767 TTGGTAAAATATCCGAGTTAAATCCCGCAGGCTTCGTGTTGGTATTATATCCGGGATAAATCCCG
1 CTGGTATTATATCCGGGTTAAATCCCACAGGCTTCGTGTTGGTATTATATCCGGCATAAAACCCG
*
5390832 TAGGCCTAGTG
66 CAGGCCTAGTG
*
5390843 CTGGTATTATATTCGGG
1 CTGGTATTATATCCGGG
5390860 CCTTCGTGCC
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
76 25 0.32
77 6 0.08
78 47 0.60
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (76 bp):
CTGGTATTATATCCGGGTTAAATCCCACAGGCTTCGTGTTGGTATTATATCCGGCATAAAACCCG
CAGGCCTAGTG
Found at i:5390900 original size:43 final size:43
Alignment explanation
Indices: 5390852--5390963 Score: 179
Period size: 43 Copynumber: 2.6 Consensus size: 43
5390842 GCTGGTATTA
*
5390852 TATTCGGGCCTTCGTGCCTAGTAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
5390895 TATTCGGGCCTTCGTGCCTAACAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* * *
5390938 TATTCAGGCCTTTGTACCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
5390964 GTAATGCCGG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.12, C:0.25, G:0.31, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:5390972 original size:43 final size:43
Alignment explanation
Indices: 5390882--5390976 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
5390872 GTAGGCTTCG
* * * **
5390882 TGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAACAGGCTTCG
1 TGCCGGTGATGTGTATTCAGGCCTTCGTACCTAACAGGCGTAA
* *
5390925 TGCCGGTGATGTGTATTCAGGCCTTTGTACCTAGCAGGCGTAA
1 TGCCGGTGATGTGTATTCAGGCCTTCGTACCTAACAGGCGTAA
5390968 TGCCGGTGA
1 TGCCGGTGA
5390977 AATGATATGT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (43 bp):
TGCCGGTGATGTGTATTCAGGCCTTCGTACCTAACAGGCGTAA
Found at i:5391359 original size:45 final size:42
Alignment explanation
Indices: 5391292--5391399 Score: 128
Period size: 45 Copynumber: 2.5 Consensus size: 42
5391282 TTGACTTGAT
* *
5391292 TATTCGGGCCTTTGAGCTTAGCAAACTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGT--GA-AC
**
5391337 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAC
1 TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAC
5391379 TGATATCGGGCC-TCGAGCCTA
1 T-AT-TCGGGCCTTCGAGCCTA
5391400 ACAGGCGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
42 3 0.05
43 13 0.23
44 7 0.12
45 34 0.60
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (42 bp):
TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAC
Found at i:5394664 original size:19 final size:19
Alignment explanation
Indices: 5394640--5394689 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
5394630 GGTATAGAGC
5394640 ACACACCCGTGTGCTAGGG
1 ACACACCCGTGTGCTAGGG
5394659 ACACACCCGTGTGCTAGGG
1 ACACACCCGTGTGCTAGGG
*
5394678 ACACGCCCGTGT
1 ACACACCCGTGT
5394690 CTCGAACCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.20, C:0.34, G:0.30, T:0.16
Consensus pattern (19 bp):
ACACACCCGTGTGCTAGGG
Found at i:5396370 original size:46 final size:46
Alignment explanation
Indices: 5396303--5396477 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
5396293 TGTAACCCGC
*
5396303 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
5396349 CCATAAGTGAACTCGGACTCAACTTAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
5396399 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
5396442 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG
5396478 ATGCCCAAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 61 0.58
47 24 0.23
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:5396422 original size:93 final size:93
Alignment explanation
Indices: 5396311--5396482 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
5396301 GCCCATAAGT
* ** * * *
5396311 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTTAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
5396376 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
5396404 GAACTCAGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
5396469 CGAGCTCGGATGCC
66 CGAGCTCGGATGCC
5396483 CAAATATTCC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:5402071 original size:46 final size:46
Alignment explanation
Indices: 5402004--5402178 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
5401994 TGTAACCTGC
*
5402004 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
5402050 CCATAAGTGAACTCGGACTCAACTTAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
5402100 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
5402143 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG
5402179 ATGCCCAAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 61 0.58
47 24 0.23
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:5402123 original size:93 final size:93
Alignment explanation
Indices: 5402012--5402183 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
5402002 GCCCATAAGT
* ** * * *
5402012 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTTAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
5402077 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
5402105 GAACTCAGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
5402170 CGAGCTCGGATGCC
66 CGAGCTCGGATGCC
5402184 CAAATATTCC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:5404122 original size:14 final size:14
Alignment explanation
Indices: 5404103--5404132 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5404093 TATTTTCAAG
5404103 ATAGATTAACGCAT
1 ATAGATTAACGCAT
*
5404117 ATAGATTCACGCAT
1 ATAGATTAACGCAT
5404131 AT
1 AT
5404133 TTATAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (14 bp):
ATAGATTAACGCAT
Found at i:5408808 original size:15 final size:15
Alignment explanation
Indices: 5408788--5408822 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
5408778 AATCGCCAGT
5408788 GAAGACTACACCGAA
1 GAAGACTACACCGAA
5408803 GAAGACTACACCGAA
1 GAAGACTACACCGAA
5408818 GAAGA
1 GAAGA
5408823 ATGGGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.23, G:0.23, T:0.06
Consensus pattern (15 bp):
GAAGACTACACCGAA
Found at i:5423748 original size:3 final size:3
Alignment explanation
Indices: 5423740--5423781 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
5423730 TATAAAAGCA
* *
5423740 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5423782 CGCACAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5433917 original size:45 final size:46
Alignment explanation
Indices: 5433827--5433918 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 46
5433817 TTTATTTGGC
*
5433827 TTTAAATAAATAAATTAAGAAGAGTCTATGTACAAAGAAGGCTTGAA
1 TTTAAATAAATAAATTAAAAAGAG-CTATGTACAAAGAAGGCTTGAA
5433874 TTTAAATAAATAAATTAAAAAGAG-TATGTACAAAGAAGGCTTGAA
1 TTTAAATAAATAAATTAAAAAGAGCTATGTACAAAGAAGGCTTGAA
5433919 AATTGGGTGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 21 0.48
47 23 0.52
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.27
Consensus pattern (46 bp):
TTTAAATAAATAAATTAAAAAGAGCTATGTACAAAGAAGGCTTGAA
Found at i:5434528 original size:26 final size:27
Alignment explanation
Indices: 5434495--5434546 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
5434485 CCTTGAAATC
5434495 TAAAAGT-A-GGACTAAATTCTTAAAAA
1 TAAAAGTAATGGACTAAATT-TTAAAAA
5434521 TAAAAGTAAATGGACTAAATTTTAAA
1 TAAAAGT-AATGGACTAAATTTTAAA
5434547 TTTATGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 7 0.30
28 6 0.26
29 10 0.43
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.29
Consensus pattern (27 bp):
TAAAAGTAATGGACTAAATTTTAAAAA
Found at i:5438406 original size:17 final size:17
Alignment explanation
Indices: 5438384--5438421 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5438374 CGAAATACAT
*
5438384 AATATACAATAATTTAA
1 AATATAAAATAATTTAA
*
5438401 AATATAAAATAATTTGA
1 AATATAAAATAATTTAA
5438418 AATA
1 AATA
5438422 AATATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
AATATAAAATAATTTAA
Found at i:5438453 original size:21 final size:20
Alignment explanation
Indices: 5438384--5438453 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 20
5438374 CGAAATACAT
5438384 AATATACAATAATTT-AAA-A
1 AATATA-AATAATTTGAAAGA
* *
5438403 TATA-AAATAATTTGAAATA
1 AATATAAATAATTTGAAAGA
*
5438422 AATATATAATAATTTTTAAAGA
1 AATATA-AATAA-TTTGAAAGA
*
5438444 ATTATAAATA
1 AATATAAATA
5438454 TATAAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 8 0.20
18 4 0.10
19 7 0.17
20 1 0.02
21 9 0.22
22 12 0.29
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (20 bp):
AATATAAATAATTTGAAAGA
Found at i:5445275 original size:185 final size:187
Alignment explanation
Indices: 5444924--5445321 Score: 560
Period size: 185 Copynumber: 2.2 Consensus size: 187
5444914 CCATACTACT
* ** *
5444924 ACTGTAAAAGCTTTTGGCCTTTGAC---T--TTTAGAACTGGTAAACCTGTCTTTTATGGTCATC
1 ACTGTAAAAGCTTTTAGCCTTTGACTTTTAGTTTAGAACTGGTAAACCTACCTTTTATAGTCATC
* * * * *
5444984 ATCTCGTGATAGTATCAGATTTAGATTATCCTAGCAGTGTCATTGAACACCGCAAAAATCCCTAA
66 ATCTCATGATAATATCAGATTTAGATCATCCTACCAGTGACATTGAACACCGCAAAAATCCCTAA
* *
5445049 GCCTGTTATGCCACATTATTCATGTGCTATTAGGTCATCCTACCAGTGTCATTGAAC
131 GCCTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAAC
* * *
5445106 ACTGTAAAAGCTTTTAGTCTTTGACTTTTAGTTTAGAACTGGTAGACCTACCTTTTATATTCATC
1 ACTGTAAAAGCTTTTAGCCTTTGACTTTTAGTTTAGAACTGGTAAACCTACCTTTTATAGTCATC
* *
5445171 ATCTCATGATAATATCATATTTAGATCATCCTACCAGTGACATTG-A-A-CGCTAAAAATCCCTG
66 ATCTCATGATAATATCAGATTTAGATCATCCTACCAGTGACATTGAACACCGC-AAAAATCCCTA
* * *
5445233 ATCTTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAGC
130 AGCCTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAAC
5445291 ACTGTAAAAGCTTTTAGCCTTTGACTTTTAG
1 ACTGTAAAAGCTTTTAGCCTTTGACTTTTAG
5445322 AAATGGTAAA
Statistics
Matches: 190, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
182 23 0.12
184 3 0.02
185 95 0.50
186 1 0.01
187 68 0.36
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (187 bp):
ACTGTAAAAGCTTTTAGCCTTTGACTTTTAGTTTAGAACTGGTAAACCTACCTTTTATAGTCATC
ATCTCATGATAATATCAGATTTAGATCATCCTACCAGTGACATTGAACACCGCAAAAATCCCTAA
GCCTGTTATGCCACATTATTCACGCGCTATTAGGTCATCCTACCAGTGTCATTGAAC
Found at i:5451659 original size:50 final size:50
Alignment explanation
Indices: 5451584--5451709 Score: 225
Period size: 50 Copynumber: 2.5 Consensus size: 50
5451574 CCATGGCAAC
* *
5451584 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTACCTGATCAAGGACAAGTGA
5451634 AAGTGATAAGTGATAGCTTCGGCTACACTTACCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTACCTGATCAAGGACAAGTGA
*
5451684 AAGTGATAAGTGATAGCTTCGACTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
5451710 CTGATTAGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTACCTGATCAAGGACAAGTGA
Found at i:5451720 original size:31 final size:31
Alignment explanation
Indices: 5451685--5451745 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
5451675 GACAAGTGAA
*
5451685 AGTGATAAGTGATAGCTTCGACTACCTGATT
1 AGTGAAAAGTGATAGCTTCGACTACCTGATT
* *
5451716 AGTGAAAAGTGGTAGCTTCGGCTACCTGAT
1 AGTGAAAAGTGATAGCTTCGACTACCTGAT
5451746 CATCAGCTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (31 bp):
AGTGAAAAGTGATAGCTTCGACTACCTGATT
Found at i:5451769 original size:46 final size:46
Alignment explanation
Indices: 5451706--5451793 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
5451696 ATAGCTTCGA
* * *
5451706 CTACCTGATTAGTGAAAAGTGGTAGCT-TCGGCTACCTGATCATCAG
1 CTACCTGATCAGTGAAAAATGGTAGCTCT-GGCTACCTAATCATCAG
*
5451752 CTACTTGATCAGTGAAAAATGGTAGCTCTGGCTACCTAATCA
1 CTACCTGATCAGTGAAAAATGGTAGCTCTGGCTACCTAATCA
5451794 ATGAATAGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 36 0.97
47 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (46 bp):
CTACCTGATCAGTGAAAAATGGTAGCTCTGGCTACCTAATCATCAG
Found at i:5461057 original size:122 final size:122
Alignment explanation
Indices: 5460840--5461085 Score: 483
Period size: 122 Copynumber: 2.0 Consensus size: 122
5460830 AGATATATTG
5460840 AAAAGAATGACTAAATATTTGTATTCATTATCTACTTGTATCAATATAAAAATAGGACTTATACA
1 AAAAGAATGACTAAATATTTGTATTCATTATCTACTTGTATCAATATAAAAATAGGACTTATACA
5460905 TGAGTAAGTGTGACTAACTACTGCTAATTAATCCACTAACAATATACCAAACTTGAT
66 TGAGTAAGTGTGACTAACTACTGCTAATTAATCCACTAACAATATACCAAACTTGAT
*
5460962 AAAAGAATGACTGAATATTTGTATTCATTATCTACTTGTATCAATATAAAAATAGGACTTATACA
1 AAAAGAATGACTAAATATTTGTATTCATTATCTACTTGTATCAATATAAAAATAGGACTTATACA
5461027 TGAGTAAGTGTGACTAACTACTGCTAATTAATCCACTAACAATATACCAAACTTGAT
66 TGAGTAAGTGTGACTAACTACTGCTAATTAATCCACTAACAATATACCAAACTTGAT
5461084 AA
1 AA
5461086 CAGACTAACA
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 123 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (122 bp):
AAAAGAATGACTAAATATTTGTATTCATTATCTACTTGTATCAATATAAAAATAGGACTTATACA
TGAGTAAGTGTGACTAACTACTGCTAATTAATCCACTAACAATATACCAAACTTGAT
Found at i:5465679 original size:17 final size:17
Alignment explanation
Indices: 5465653--5465692 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5465643 GCATCAAGAT
*
5465653 TCAGAGTTAGAACACCA
1 TCAGAATTAGAACACCA
5465670 TCAGAATTAGAACACCA
1 TCAGAATTAGAACACCA
5465687 TCAGAA
1 TCAGAA
5465693 GAAGCGACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (17 bp):
TCAGAATTAGAACACCA
Found at i:5467196 original size:40 final size:39
Alignment explanation
Indices: 5467115--5467231 Score: 121
Period size: 39 Copynumber: 3.0 Consensus size: 39
5467105 CTTTAGGTGA
* * * * * **
5467115 TCAATTATTTTCTAGAAGTGAATTGTAAGGTTCATCAAT
1 TCAATCATTTTCCAGAACTGAATTGTAAAGTTGATTTAT
*
5467154 TCAATCATTGTT-TAGAACTGAATTAG-AAAGGTTGATTTAT
1 TCAATCATT-TTCCAGAACTGAATT-GTAAA-GTTGATTTAT
5467194 TCAATCATTTTCCAGAACTGAATTGTAAAGTTGATTTA
1 TCAATCATTTTCCAGAACTGAATTGTAAAGTTGATTTA
5467232 GAGTTGTTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
39 33 0.50
40 33 0.50
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.40
Consensus pattern (39 bp):
TCAATCATTTTCCAGAACTGAATTGTAAAGTTGATTTAT
Found at i:5468792 original size:21 final size:22
Alignment explanation
Indices: 5468749--5468793 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
5468739 TTCAATTAGT
* *
5468749 AAATATATTTTTAAAAGTTATAA
1 AAATATATTATTAAAAG-AATAA
5468772 AAATATATTATTAAAA-AATAA
1 AAATATATTATTAAAAGAATAA
5468793 A
1 A
5468794 CTAAAAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
23 15 0.75
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATATATTATTAAAAGAATAA
Found at i:5469268 original size:19 final size:20
Alignment explanation
Indices: 5469206--5469295 Score: 78
Period size: 19 Copynumber: 4.3 Consensus size: 20
5469196 ATATAATTTA
*
5469206 AATTTTTAAAAATTATTAT-
1 AATTTTTAAAAATTATTTTG
5469225 AATTTTTTAAAATATATAAACTTTTG
1 AA-TTTTTAAAA-AT-T--A-TTTTG
*
5469251 AATTTTTATAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
*
5469270 AA-ATTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
5469289 AATTTTT
1 AATTTTT
5469296 TTTTGTAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
18 7 0.12
19 18 0.32
20 13 0.23
21 2 0.04
22 2 0.04
24 2 0.04
25 11 0.19
26 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:5470602 original size:16 final size:16
Alignment explanation
Indices: 5470581--5470636 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
5470571 CGTTTGGTTC
5470581 ACTGTAATGGAATAGA
1 ACTGTAATGGAATAGA
*
5470597 ACTGTAATTGAATAGA
1 ACTGTAATGGAATAGA
**
5470613 GTTGTAATGGAATAGA
1 ACTGTAATGGAATAGA
*
5470629 GCTGTAAT
1 ACTGTAAT
5470637 AAGTAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.30
Consensus pattern (16 bp):
ACTGTAATGGAATAGA
Found at i:5470670 original size:46 final size:44
Alignment explanation
Indices: 5470618--5470711 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
5470608 ATAGAGTTGT
*
5470618 AATGGAATAGAGCTGTAATAAGTAATTCAACTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAT-AGT-ATTCAACTGTTTGGTTGAATGG
*** *
5470664 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATTG
1 AATGGAATAGAACTGTAATAGTATTCAACTGTTTGGTTGAATGG
5470708 AATG
1 AATG
5470712 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 22 0.51
45 3 0.07
46 18 0.42
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCAACTGTTTGGTTGAATGG
Found at i:5470876 original size:58 final size:58
Alignment explanation
Indices: 5470813--5470938 Score: 182
Period size: 58 Copynumber: 2.2 Consensus size: 58
5470803 TTTTAATAAG
* *
5470813 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAATAAAATTCTTAACATA
* * * *
5470871 ATTATTACTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAATAAAATTCTTAACATA
5470929 ATTATTATTA
1 ATTATTATTA
5470939 TATGAATTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 23 0.38
58 37 0.62
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAATAAAATTCTTAACATA
Found at i:5471907 original size:13 final size:14
Alignment explanation
Indices: 5471891--5471926 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5471881 CAATCTCATA
5471891 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
5471904 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
5471917 TCTC-ATTTCA
1 TCTCAATTTCA
5471927 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:5471916 original size:18 final size:19
Alignment explanation
Indices: 5471878--5471918 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
5471868 TGGTTCATGT
5471878 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
5471897 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
5471915 TTTC
1 TTTC
5471919 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:5472108 original size:39 final size:38
Alignment explanation
Indices: 5472041--5472175 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
5472031 ACCAATATGG
* * *
5472041 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
5472080 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
5472118 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
5472159 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
5472176 ACTCGAGGTT
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:5472441 original size:18 final size:19
Alignment explanation
Indices: 5472415--5472453 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5472405 TTTCAATTCA
5472415 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
5472434 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
5472452 AT
1 AT
5472454 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:5473805 original size:5 final size:5
Alignment explanation
Indices: 5473759--5473795 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
5473749 TTATGTTTAT
5473759 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
5473796 TAAAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:5476761 original size:2 final size:2
Alignment explanation
Indices: 5476754--5476784 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5476744 ACATGCGTAA
5476754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5476785 ATCATATTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5489071 original size:3 final size:3
Alignment explanation
Indices: 5489063--5489109 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5489053 GTTTATAGTG
5489063 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5489110 TATTCTATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5489421 original size:22 final size:22
Alignment explanation
Indices: 5489391--5489501 Score: 75
Period size: 23 Copynumber: 4.8 Consensus size: 22
5489381 ACATTATATG
* *
5489391 TTTTGAATTTGTTTATATGTTA
1 TTTTAAATTTGTTTATATATTA
*
5489413 TTTTAAA-TTGTTTTATAAATTA
1 TTTTAAATTTG-TTTATATATTA
5489435 TTTACTTAAATTTGCTTTATATATTA
1 -TT--TTAAATTTG-TTTATATATTA
* *
5489461 CTTTAAATTAAT-TTTATATTTTA
1 TTTTAAATT--TGTTTATATATTA
*
5489484 TTTTAGATTAT-TTTATAT
1 TTTTAAATT-TGTTTATAT
5489502 TACTTATTAC
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.04
22 24 0.33
23 26 0.36
25 7 0.10
26 13 0.18
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (22 bp):
TTTTAAATTTGTTTATATATTA
Found at i:5489460 original size:26 final size:24
Alignment explanation
Indices: 5489396--5489465 Score: 65
Period size: 26 Copynumber: 2.9 Consensus size: 24
5489386 ATATGTTTTG
*
5489396 AATTTGTTTATATGTTA-TT-TTA
1 AATTTGTTTATATATTATTTATTA
*
5489418 AA-TTGTTTTATAAATTATTTACTTA
1 AATTTG-TTTATATATTATTTA-TTA
5489443 AATTTGCTTTATATATTACTTTA
1 AATTTG-TTTATATATTA-TTTA
5489466 AATTAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 3 0.08
22 11 0.29
23 2 0.05
25 5 0.13
26 13 0.34
27 4 0.11
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (24 bp):
AATTTGTTTATATATTATTTATTA
Found at i:5490215 original size:23 final size:23
Alignment explanation
Indices: 5490188--5490244 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
5490178 AATAAATATT
5490188 AAATAAAAATAATTATATTTTTA
1 AAATAAAAATAATTATATTTTTA
5490211 AAATAAAAATAATTATATTTTTA
1 AAATAAAAATAATTATATTTTTA
5490234 AAATAAAAATA
1 AAATAAAAATA
5490245 TGAAGGAGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATAAAAATAATTATATTTTTA
Found at i:5499807 original size:26 final size:26
Alignment explanation
Indices: 5499770--5499853 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
5499760 TGATACAAAT
* *
5499770 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5499796 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
5499822 TGATAATGGGTTAGGTAAATGTTTTA
1 TGATAATGGGTTAGGTAAATGTTTCA
5499848 TGATAA
1 TGATAA
5499854 GAATTTTATA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:5501333 original size:28 final size:26
Alignment explanation
Indices: 5501291--5501365 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
5501281 AAAAGTAGCT
* * *
5501291 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGCA
** *
5501319 AAATTACTGTTATACCTTTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGCA
*
5501345 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
5501366 GGTTAATTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 21 0.55
27 1 0.03
28 16 0.42
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGCA
Found at i:5501510 original size:27 final size:27
Alignment explanation
Indices: 5501469--5501635 Score: 219
Period size: 27 Copynumber: 6.2 Consensus size: 27
5501459 GAGGAAGCGT
*
5501469 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
5501496 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
5501523 TCTGGTGGCTCTGCCACAAATATCTGG
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5501550 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
5501577 TCTGGTGGCTCTGCCACGACTATATGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
5501605 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
5501631 TCTGG
1 TCTGG
5501636 CAGCCATGTT
Statistics
Matches: 125, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
26 5 0.04
27 105 0.84
28 15 0.12
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:5501721 original size:19 final size:22
Alignment explanation
Indices: 5501697--5501736 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
5501687 CTCCCCACAC
5501697 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
5501716 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
5501737 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:5504620 original size:2 final size:2
Alignment explanation
Indices: 5504613--5504637 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5504603 AATTTTAGTT
5504613 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 T
5504638 TCACCTAGTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5506289 original size:20 final size:20
Alignment explanation
Indices: 5506264--5506309 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
5506254 TCTCTCGAAC
5506264 TCGGACTCAACTCAACGAGT
1 TCGGACTCAACTCAACGAGT
5506284 TCGGACTCAACTCAACGAGT
1 TCGGACTCAACTCAACGAGT
5506304 TCGGAC
1 TCGGAC
5506310 ATTCGCATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (20 bp):
TCGGACTCAACTCAACGAGT
Found at i:5521720 original size:17 final size:17
Alignment explanation
Indices: 5521683--5521731 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
5521673 AATAGAAGAC
**
5521683 AATAATAATAATATATT
1 AATAATAATAATATAAA
*
5521700 AATAAAAATAATATAAA
1 AATAATAATAATATAAA
*
5521717 AATAATACTAATATA
1 AATAATAATAATATA
5521732 GGGAAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATAATATAAA
Found at i:5521883 original size:3 final size:3
Alignment explanation
Indices: 5521875--5522016 Score: 80
Period size: 3 Copynumber: 47.3 Consensus size: 3
5521865 AAGTGCCATT
* * * * * * * *
5521875 ATA ATA ATA AAA ATA AAA ATA ACA AAA ATA ACA AT- ATG TTA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
5521922 ATA ATA ATA ATAA ATAA ATA ATG GTA ATA A-A TATA TATA A-A ATA ATA
1 ATA ATA ATA AT-A AT-A ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA
* *
5521969 GTA ACA GA-A ATA A-A ATAA ATA A-A ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA -ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
5522013 ATA A
1 ATA A
5522017 CACTCTCCCC
Statistics
Matches: 109, Mismatches: 20, Indels: 20
0.73 0.13 0.13
Matches are distributed among these distances:
2 10 0.09
3 83 0.76
4 16 0.15
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:5528074 original size:14 final size:15
Alignment explanation
Indices: 5528046--5528074 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5528036 ATGCTCACAC
5528046 ATAGAGCATGCAAGA
1 ATAGAGCATGCAAGA
5528061 ATAGAGCA-GCAAGA
1 ATAGAGCATGCAAGA
5528075 TACTCCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.14, G:0.28, T:0.10
Consensus pattern (15 bp):
ATAGAGCATGCAAGA
Found at i:5540830 original size:18 final size:18
Alignment explanation
Indices: 5540807--5540843 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5540797 TATTGCAGGG
5540807 AAGGTTAGATATTTATAA
1 AAGGTTAGATATTTATAA
5540825 AAGGTTAGATATTTATAA
1 AAGGTTAGATATTTATAA
5540843 A
1 A
5540844 GGGGCTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (18 bp):
AAGGTTAGATATTTATAA
Found at i:5544334 original size:13 final size:13
Alignment explanation
Indices: 5544281--5544341 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
5544271 ACACCTAAAA
* *
5544281 TTTTTAAAAGTAC
1 TTTTCAAAAGCAC
*
5544294 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
*
5544307 TTTTCCACAA-CAC
1 TTTT-CAAAAGCAC
* *
5544320 TTTTTAAAAGTAC
1 TTTTCAAAAGCAC
5544333 TTTTCAAAA
1 TTTTCAAAA
5544342 TCATTGCCAA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
12 3 0.08
13 30 0.81
14 4 0.11
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:5549113 original size:13 final size:13
Alignment explanation
Indices: 5549076--5549116 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
5549066 TATAGTGTTG
*
5549076 TTATTATTATTA-
1 TTATTACTATTAT
5549088 TTATTACTATTAT
1 TTATTACTATTAT
5549101 TTATT-CTATTTAT
1 TTATTACTA-TTAT
5549114 TTA
1 TTA
5549117 CTATTTTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 14 0.54
13 12 0.46
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTACTATTAT
Found at i:5550292 original size:54 final size:54
Alignment explanation
Indices: 5550233--5550345 Score: 174
Period size: 54 Copynumber: 2.1 Consensus size: 54
5550223 CATGGCTGCT
*
5550233 AGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCACC
1 AGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCACC
* * *
5550287 AGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCAGAGCCACC
1 AGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCACC
5550341 AGAAC
1 AGAAC
5550346 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.16
Consensus pattern (54 bp):
AGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCACC
Found at i:5550293 original size:27 final size:26
Alignment explanation
Indices: 5550233--5550345 Score: 154
Period size: 27 Copynumber: 4.2 Consensus size: 26
5550223 CATGGCTGCT
* *
5550233 AGAACAGATAATGTGACAGAGTCACC
1 AGAACAGATAATGTGGCAGAGCCACC
5550259 AGATACAGATAATCGTGGCAGAGCCACC
1 AGA-ACAGATAAT-GTGGCAGAGCCACC
5550287 AGAACAGATATATGTGGCAGAGCCACC
1 AGAACAGATA-ATGTGGCAGAGCCACC
* *
5550314 AGATCAGATATTTGTGGCAGAGCCACC
1 AGAACAGATA-ATGTGGCAGAGCCACC
5550341 AGAAC
1 AGAAC
5550346 GCTTCCTCCA
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 3 0.04
27 59 0.75
28 17 0.22
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.16
Consensus pattern (26 bp):
AGAACAGATAATGTGGCAGAGCCACC
Found at i:5551996 original size:26 final size:26
Alignment explanation
Indices: 5551960--5552069 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5551950 CATGAAATTC
*
5551960 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
5551986 TTATCATGAAACATTTACCTAACCAA
1 TTATCATGAAACATTTACCTAACCTA
*
5552012 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
5552038 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5552064 TTATCA
1 TTATCA
5552070 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:5552506 original size:22 final size:23
Alignment explanation
Indices: 5552481--5552587 Score: 64
Period size: 23 Copynumber: 4.7 Consensus size: 23
5552471 TTTGAATTTG
* *
5552481 TTTATATGTTA-TTATAAATTGT
1 TTTATATATTACTTATAAATTAT
* *
5552503 TTTATAAATTATTTACTTAAATT-T
1 TTTATATATTACTTA--TAAATTAT
5552527 GCTTTATATATTACTT-TAAATTAAT
1 --TTTATATATTACTTATAAATT-AT
* * *
5552552 TTTATATTTTA-TTTTAGATTA-
1 TTTATATATTACTTATAAATTAT
5552573 TTT-TATATTACTTAT
1 TTTATATATTACTTAT
5552588 TACATTTTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
20 6 0.09
21 6 0.09
22 12 0.18
23 24 0.35
24 1 0.01
25 7 0.10
26 12 0.18
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTATATATTACTTATAAATTAT
Found at i:5552534 original size:26 final size:26
Alignment explanation
Indices: 5552495--5552544 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5552485 TATGTTATTA
*
5552495 TAAATTGTTTTATAAATTA-TTTACT
1 TAAATTGCTTTATAAATTACTTTACT
*
5552520 TAAATTTGCTTTATATATTACTTTA
1 TAAA-TTGCTTTATAAATTACTTTA
5552545 AATTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 13 0.62
27 4 0.19
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (26 bp):
TAAATTGCTTTATAAATTACTTTACT
Found at i:5552555 original size:23 final size:22
Alignment explanation
Indices: 5552529--5552580 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
5552519 TTAAATTTGC
5552529 TTTATATATTACTTTAAATTAAT
1 TTTATATATTACTTTAAATT-AT
* * *
5552552 TTTATATTTTATTTTAGATTAT
1 TTTATATATTACTTTAAATTAT
5552574 TTTATAT
1 TTTATAT
5552581 TACTTATTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTATATATTACTTTAAATTAT
Found at i:5556248 original size:23 final size:23
Alignment explanation
Indices: 5556222--5556265 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5556212 CATAACCATA
5556222 CAAAAAAAAAGT-AATAATAAAAT
1 CAAAAAAAAA-TAAATAATAAAAT
* *
5556245 CAAACAGAAATAAATAATAAA
1 CAAAAAAAAATAAATAATAAA
5556266 CCAAATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.16
Consensus pattern (23 bp):
CAAAAAAAAATAAATAATAAAAT
Found at i:5557305 original size:25 final size:26
Alignment explanation
Indices: 5557274--5557339 Score: 89
Period size: 25 Copynumber: 2.5 Consensus size: 26
5557264 GGCACTAACC
*
5557274 AATGGCCCAATTTTAAAACGAG-CCA
1 AATGGCCCAATTTTAAAACAAGCCCA
**
5557299 AATGGCCCAATCCTAAAACAAGCCCA
1 AATGGCCCAATTTTAAAACAAGCCCA
5557325 AATGGCCCAAATTTT
1 AATGGCCC-AATTTT
5557340 GATTTCAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 19 0.56
26 11 0.32
27 4 0.12
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (26 bp):
AATGGCCCAATTTTAAAACAAGCCCA
Found at i:5562472 original size:19 final size:19
Alignment explanation
Indices: 5562448--5562492 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5562438 TTTTTTTTTT
* *
5562448 TGCATT-CATTTCATGCATC
1 TGCATTACATTACAT-CATA
5562467 TGCATTACATTACATCATA
1 TGCATTACATTACATCATA
5562486 TGCATTA
1 TGCATTA
5562493 AAGTCCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (19 bp):
TGCATTACATTACATCATA
Found at i:5563261 original size:39 final size:39
Alignment explanation
Indices: 5563136--5563568 Score: 305
Period size: 39 Copynumber: 11.3 Consensus size: 39
5563126 AATCTTATTT
* * *
5563136 AGTATAATCAGTGGATAAT-GCTCG-TTTGAGCAAACATTC
1 AGTATAATCAGTAGAT--TCGCTCGCTTTGAACAAGCATTC
* * * *
5563175 AATATAATCAATAGATATGGCTCG--TTGAGCAA-CATTC
1 AGTATAATCAGTAGAT-TCGCTCGCTTTGAACAAGCATTC
* * * *
5563212 AGTAAAATTAGTGGATTCGCTTGCTTTGAACAAGCATTC
1 AGTATAATCAGTAGATTCGCTCGCTTTGAACAAGCATTC
* * * * *
5563251 AGGATAATTAGTAGATTTGCTCGC-TTGAGCAAGTATTC
1 AGTATAATCAGTAGATTCGCTCGCTTTGAACAAGCATTC
* * * *
5563289 AGTAAAATCAGTAGATTTGCTCGTTTTGAACAAGCATTT
1 AGTATAATCAGTAGATTCGCTCGCTTTGAACAAGCATTC
* * *
5563328 AATATAATCAGTAGATTCGTTCGC-TTGAGCAAGCATTC
1 AGTATAATCAGTAGATTCGCTCGCTTTGAACAAGCATTC
* * * * *
5563366 GGTA-AAGCTAGTGGATTTGCTCGTTTTGAACAAGCATTC
1 AGTATAATC-AGTAGATTCGCTCGCTTTGAACAAGCATTC
** * * *
5563405 AGTATAATTGGTATATTCGCTCGC-TTGAGA-AATCATTT
1 AGTATAATCAGTAGATTCGCTCGCTTTGA-ACAAGCATTC
* * ** *
5563443 ACTA-ACATCAGTGGATTCGCTCTTTTTAAACAAGCATTC
1 AGTATA-ATCAGTAGATTCGCTCGCTTTGAACAAGCATTC
* * ** *
5563482 AGTAAAATCAGTGGATTCGCTCTTTTTGAACAAGCATTT
1 AGTATAATCAGTAGATTCGCTCGCTTTGAACAAGCATTC
* * *
5563521 AGTATAATCAGTAGATTCGCTCG-TTTGAGCAAACTTTC
1 AGTATAATCAGTAGATTCGCTCGCTTTGAACAAGCATTC
*
5563559 AGTAAAATCA
1 AGTATAATCA
5563569 ATATTCTACT
Statistics
Matches: 310, Mismatches: 71, Indels: 27
0.76 0.17 0.07
Matches are distributed among these distances:
36 5 0.02
37 20 0.06
38 120 0.39
39 162 0.52
40 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (39 bp):
AGTATAATCAGTAGATTCGCTCGCTTTGAACAAGCATTC
Found at i:5563324 original size:77 final size:77
Alignment explanation
Indices: 5563136--5563568 Score: 392
Period size: 77 Copynumber: 5.6 Consensus size: 77
5563126 AATCTTATTT
* * * * * *
5563136 AGTATAATCAGTGGATAAT-GCTCG-TTTGAGCAAACATTCAATATAATCAATAGATATGGCTCG
1 AGTAAAATCAGTGGAT--TCGCTCGTTTTGAACAAGCATTCAGTATAATCAGTAGAT-TCGCTCG
5563199 -TTGAGCAA-CATTC
63 CTTGAGCAAGCATTC
* * * * * *
5563212 AGTAAAATTAGTGGATTCGCTTGCTTTGAACAAGCATTCAGGATAATTAGTAGATTTGCTCGCTT
1 AGTAAAATCAGTGGATTCGCTCGTTTTGAACAAGCATTCAGTATAATCAGTAGATTCGCTCGCTT
*
5563277 GAGCAAGTATTC
66 GAGCAAGCATTC
* * * * *
5563289 AGTAAAATCAGTAGATTTGCTCGTTTTGAACAAGCATTTAATATAATCAGTAGATTCGTTCGCTT
1 AGTAAAATCAGTGGATTCGCTCGTTTTGAACAAGCATTCAGTATAATCAGTAGATTCGCTCGCTT
5563354 GAGCAAGCATTC
66 GAGCAAGCATTC
* * * ** *
5563366 GGT-AAAGCTAGTGGATTTGCTCGTTTTGAACAAGCATTCAGTATAATTGGTATATTCGCTCGCT
1 AGTAAAATC-AGTGGATTCGCTCGTTTTGAACAAGCATTCAGTATAATCAGTAGATTCGCTCGCT
* * *
5563430 TGAGAAATCATTT
65 TGAGCAAGCATTC
* * * * * * **
5563443 ACTAACATCAGTGGATTCGCTCTTTTTAAACAAGCATTCAGTAAAATCAGTGGATTCGCTCTTTT
1 AGTAAAATCAGTGGATTCGCTCGTTTTGAACAAGCATTCAGTATAATCAGTAGATTCGCTC-GCT
* *
5563508 TGAACAAGCATTT
65 TGAGCAAGCATTC
* * * * * *
5563521 AGTATAATCAGTAGATTCGCTCG-TTTGAGCAAACTTTCAGTAAAATCA
1 AGTAAAATCAGTGGATTCGCTCGTTTTGAACAAGCATTCAGTATAATCA
5563569 ATATTCTACT
Statistics
Matches: 289, Mismatches: 61, Indels: 13
0.80 0.17 0.04
Matches are distributed among these distances:
74 1 0.00
75 10 0.03
76 51 0.18
77 195 0.67
78 32 0.11
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (77 bp):
AGTAAAATCAGTGGATTCGCTCGTTTTGAACAAGCATTCAGTATAATCAGTAGATTCGCTCGCTT
GAGCAAGCATTC
Found at i:5568640 original size:24 final size:24
Alignment explanation
Indices: 5568608--5568654 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
5568598 ACTTCCGTTT
5568608 TGCTAAATTTTGTGTCTGTTGCTC
1 TGCTAAATTTTGTGTCTGTTGCTC
5568632 TGCTAAATTTTGTGTCTGTTGCT
1 TGCTAAATTTTGTGTCTGTTGCT
5568655 TATTTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (24 bp):
TGCTAAATTTTGTGTCTGTTGCTC
Found at i:5570270 original size:29 final size:30
Alignment explanation
Indices: 5570211--5570278 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
5570201 AAATCTCAAA
5570211 ATATACATGAACTTTAATTTAATATGTAATT
1 ATATACATGAACTTTAATTTAATA-GTAATT
* **
5570242 ATATACATGAATTTTAATTTGGTA-TAATT
1 ATATACATGAACTTTAATTTAATAGTAATT
*
5570271 ATACACAT
1 ATATACAT
5570279 AAAACTCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 12 0.36
31 21 0.64
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (30 bp):
ATATACATGAACTTTAATTTAATAGTAATT
Found at i:5571856 original size:18 final size:19
Alignment explanation
Indices: 5571816--5571856 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
5571806 TATGTGGACT
5571816 ACCCATGTAGACCCACACG
1 ACCCATGTAGACCCACACG
* *
5571835 -CCCATGT-GGCCTACACG
1 ACCCATGTAGACCCACACG
5571852 ACCCA
1 ACCCA
5571857 AATTAGTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.27, C:0.44, G:0.17, T:0.12
Consensus pattern (19 bp):
ACCCATGTAGACCCACACG
Found at i:5576378 original size:27 final size:27
Alignment explanation
Indices: 5576348--5576409 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
5576338 GGGCAAAATG
5576348 GTAATTTTACCCCACAAGGGTATTTCA
1 GTAATTTTACCCCACAAGGGTATTTCA
* * *
5576375 GTAATTTTACCCTACAGGGGTATTTTA
1 GTAATTTTACCCCACAAGGGTATTTCA
5576402 GTAATTTT
1 GTAATTTT
5576410 TCAAACCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (27 bp):
GTAATTTTACCCCACAAGGGTATTTCA
Found at i:5576423 original size:54 final size:54
Alignment explanation
Indices: 5576365--5576515 Score: 151
Period size: 54 Copynumber: 2.8 Consensus size: 54
5576355 TACCCCACAA
** * * *
5576365 GGGTATTTCAGTAATTTTACCCTAC-AGGGGTATTTTAGTAATTTTTCAAACCAT
1 GGGTATTTCAGTAATTTTA-CAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
** * *
5576419 GGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAACTAG
1 GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
** * * * *
5576473 GGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTGGTAATT
1 GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATT
5576516 CTGTAAATTG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 2 0.02
54 82 0.98
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.42
Consensus pattern (54 bp):
GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
Found at i:5576481 original size:81 final size:81
Alignment explanation
Indices: 5576363--5576515 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
5576353 TTTACCCCAC
** *
5576363 AAGGGTATTTCAGTAATTTTACCCTACAGGGGTATTTTAGTAATTTT-TCAAACCATGGGTATTT
1 AAGGGTATTTCAGTAATTTTACCAAACAGGGGTATTTTAGTAATTTTAT-AAACCAAGGGTATTT
5576427 TGGTAATTTTATAAACA
65 TGGTAATTTTATAAACA
* * *
5576444 AAGGGTATTTTAGTAATTTTA-CAAACTAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTT
1 AAGGGTATTTCAGTAATTTTACCAAAC-AGGGGTATTTTAGTAATTTTATAAACCAAGGGTATTT
5576508 TGGTAATT
65 TGGTAATT
5576516 CTGTAAATTG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
80 3 0.05
81 60 0.94
82 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (81 bp):
AAGGGTATTTCAGTAATTTTACCAAACAGGGGTATTTTAGTAATTTTATAAACCAAGGGTATTTT
GGTAATTTTATAAACA
Found at i:5576531 original size:27 final size:27
Alignment explanation
Indices: 5576392--5576515 Score: 160
Period size: 27 Copynumber: 4.6 Consensus size: 27
5576382 TACCCTACAG
* *
5576392 GGGTATTTTAGTAATTTT-TCAAACCAT
1 GGGTATTTTGGTAATTTTAT-AAACCAA
*
5576419 GGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTGGTAATTTTATAAACCAA
* * * *
5576446 GGGTATTTTAGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTATAAACCAA
*
5576473 GGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
5576500 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
5576516 CTGTAAATTG
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
27 82 0.99
28 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACCAA
Found at i:5576531 original size:54 final size:54
Alignment explanation
Indices: 5576392--5576517 Score: 180
Period size: 54 Copynumber: 2.3 Consensus size: 54
5576382 TACCCTACAG
* * * *
5576392 GGGTATTTTAGTAATTTTTCAAACCATGGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTAGTAATTCTACAAACTAGGGGTATTTTGGTAATTTTATAAACAAA
* * *
5576446 GGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTAGTAATTCTACAAACTAGGGGTATTTTGGTAATTTTATAAACAAA
*
5576500 GGGTATTTTGGTAATTCT
1 GGGTATTTTAGTAATTCT
5576518 GTAAATTGAG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (54 bp):
GGGTATTTTAGTAATTCTACAAACTAGGGGTATTTTGGTAATTTTATAAACAAA
Found at i:5580478 original size:27 final size:27
Alignment explanation
Indices: 5580448--5580509 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
5580438 GGGCAAAATG
5580448 GTAATTTTACCCCACAAGGGTATTTCA
1 GTAATTTTACCCCACAAGGGTATTTCA
* * *
5580475 GTAATTTTACCCTACAGGGGTATTTTA
1 GTAATTTTACCCCACAAGGGTATTTCA
5580502 GTAATTTT
1 GTAATTTT
5580510 TCAAACCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (27 bp):
GTAATTTTACCCCACAAGGGTATTTCA
Found at i:5580522 original size:27 final size:27
Alignment explanation
Indices: 5580492--5580614 Score: 160
Period size: 27 Copynumber: 4.6 Consensus size: 27
5580482 TACCCTACAG
* *
5580492 GGGTATTTTAGTAATTTT-TCAAACCAT
1 GGGTATTTTGGTAATTTTAT-AAACCAA
*
5580519 GGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTGGTAATTTTATAAACCAA
* * *
5580546 GGGTATTTTAGTAATTTTACAAA-CAG
1 GGGTATTTTGGTAATTTTATAAACCAA
*
5580572 GGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
5580599 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
5580615 CTGTAAATTG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 21 0.26
27 60 0.73
28 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACCAA
Found at i:5580523 original size:54 final size:53
Alignment explanation
Indices: 5580465--5580614 Score: 149
Period size: 53 Copynumber: 2.8 Consensus size: 53
5580455 TACCCCACAA
** * * *
5580465 GGGTATTTCAGTAATTTTACCCTAC-AGGGGTATTTTAGTAATTTTTCAAACCAT
1 GGGTATTTCAGTAATTTTA-CAAACAAAGGGTATTTTAGTAATTTTACAAA-CAG
** *
5580519 GGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAACAG
1 GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACAG
** * * * *
5580572 GGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTGGTAATT
1 GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATT
5580615 CTGTAAATTG
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 44 0.52
54 40 0.48
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (53 bp):
GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACAG
Found at i:5580595 original size:53 final size:54
Alignment explanation
Indices: 5580492--5580614 Score: 194
Period size: 53 Copynumber: 2.3 Consensus size: 54
5580482 TACCCTACAG
* *
5580492 GGGTATTTTAGTAATTTTTCAAACCATGGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAAA
* *
5580546 GGGTATTTTAGTAATTTTACAAA-CAGGGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAAA
*
5580599 GGGTATTTTGGTAATT
1 GGGTATTTTAGTAATT
5580615 CTGTAAATTG
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
53 42 0.66
54 22 0.34
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (54 bp):
GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAAA
Found at i:5580628 original size:27 final size:27
Alignment explanation
Indices: 5580598--5580668 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
5580588 TTATAAACCA
* *
5580598 AGGGTATTTTGGTAATTCTGTAAATTG
1 AGGGTAATTTGGTAATTCTGTAAATCG
***
5580625 AGGGTAAAACGGTAATTCTGTAAATCG
1 AGGGTAATTTGGTAATTCTGTAAATCG
*
5580652 -GGAGTACTTTGGTAATT
1 AGG-GTAATTTGGTAATT
5580669 TTACAAGTCG
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (27 bp):
AGGGTAATTTGGTAATTCTGTAAATCG
Found at i:5580640 original size:80 final size:80
Alignment explanation
Indices: 5580473--5580641 Score: 178
Period size: 80 Copynumber: 2.1 Consensus size: 80
5580463 AAGGGTATTT
** * *
5580473 CAGTAATTTTACCCTACAGGGGTATTTTAGTAATTTTTCAAACCATGGGTATTTTGGTAATTTTA
1 CAGTAATTTTA-CAAACAGGGGTATTTTAGTAATTTTTCAAACCAAGGGTATTTTGGTAATTCTA
***
5580538 TAAACAAAGGGTATTT
65 TAAACAAAGGGTAAAA
* * * *
5580554 TAGTAATTTTACAAACAGGGGTATTTTGGTGATTTTAT-AAACCAAGGGTATTTTGGTAATTCTG
1 CAGTAATTTTACAAACAGGGGTATTTTAGTAATTTT-TCAAACCAAGGGTATTTTGGTAATTCTA
***
5580618 TAAATTGAGGGTAAAA
65 TAAACAAAGGGTAAAA
*
5580634 CGGTAATT
1 CAGTAATT
5580642 CTGTAAATCG
Statistics
Matches: 71, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
80 60 0.85
81 11 0.15
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (80 bp):
CAGTAATTTTACAAACAGGGGTATTTTAGTAATTTTTCAAACCAAGGGTATTTTGGTAATTCTAT
AAACAAAGGGTAAAA
Found at i:5589438 original size:46 final size:46
Alignment explanation
Indices: 5588936--5589440 Score: 658
Period size: 46 Copynumber: 11.0 Consensus size: 46
5588926 ACAATACAAT
* * * * *
5588936 AACTCAATATGGTTTTCTTCATTGAAATACCATACCTACATTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
* * * *
5588982 ATCTC-GATATGCTTTTCTTTATTGAAATACCATACCTATGTTTCAC
1 AACTCAG-TATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
* *
5589028 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
* *
5589074 ATCTC-GATATAGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
1 AACTCAG-TATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
* * *
5589120 GAA-TCAGTATAGTTTTCTTTACTGAAATACCATACCTACATTCCAC
1 -AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
* ** * *
5589166 ATCTTGGTATAGTTTTCTTTA-TTATAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGA-AATACCATACCTACGTTTCAC
* * *
5589212 AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTATGTTTCAT
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
* *
5589258 AACTCAGTATGGATTTCTTTACTGAAATACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
* * *
5589304 ATCTCAGTATGGTTTTCTTTACTGAAATACCATACCTATGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
* *
5589350 ATCTCGGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
*
5589396 AACTCAATATGGTTTTCTTTACTGAAATACCATACCTACGTTTCA
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCA
5589441 TACTTTGCCA
Statistics
Matches: 406, Mismatches: 45, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
45 4 0.01
46 397 0.98
47 5 0.01
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
Found at i:5590660 original size:20 final size:20
Alignment explanation
Indices: 5590635--5590674 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5590625 CCTTATATAA
*
5590635 GAAAACTTTACTATAACATC
1 GAAAACTCTACTATAACATC
5590655 GAAAACTCTACTATAACATC
1 GAAAACTCTACTATAACATC
5590675 ATTTCCATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.28
Consensus pattern (20 bp):
GAAAACTCTACTATAACATC
Found at i:5591032 original size:11 final size:11
Alignment explanation
Indices: 5591016--5591043 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5591006 TATATTAAAC
5591016 AAAATAATAAT
1 AAAATAATAAT
5591027 AAAATAATAAT
1 AAAATAATAAT
5591038 AAAATA
1 AAAATA
5591044 TCTCATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:5593343 original size:17 final size:15
Alignment explanation
Indices: 5593321--5593367 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
5593311 TCTTCATAAA
5593321 CATATATCATTCATTT
1 CATATATCA-TCATTT
5593337 CATTATATCAAT-ATTT
1 CA-TATATC-ATCATTT
*
5593353 CATATACCATCATTT
1 CATATATCATCATTT
5593368 TCGTGAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 2 0.07
15 9 0.33
16 8 0.30
17 7 0.26
18 1 0.04
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (15 bp):
CATATATCATCATTT
Found at i:5594274 original size:46 final size:46
Alignment explanation
Indices: 5593726--5594271 Score: 723
Period size: 46 Copynumber: 11.9 Consensus size: 46
5593716 AATACTATAA
* * * * * *
5593726 CTCAATATAGTTTTCTTCATTGAAATACCATAGCTACATTCCACAA
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
* * *
5593772 CTCAGAATGGTTTTCTTCATTGAAATACCATACCTACATTCCACAT
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
* * * * *
5593818 CTCGGTATGGTTTTCTTTACTGAAATACCATATCTGCATTTCACAA
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
* *
5593864 CTCAGTATGGTTTTATTTACTAAAATACCATACCTACATTCCACAT
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
* * * * *
5593910 CTCAGTATGGTTGTCTTTAGTGAAATAACATACCTACATTTCACAA
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
* * *
5593956 CTCAGTCTGGTTTTATTTATTGAAATACCATACCTACATTCCACAT
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
* * * *
5594002 CACGGTATGATTTTCTTTACTGAAATACCATACCTACGTTCCACAT
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
* * * * * *
5594048 CTCGGTATGGTTTTCTTTTCTGAAATATCATACCTACGTTTCACAA
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
* *
5594094 CTCTGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCACAT
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
*
5594140 CTCAGTATGGTTTCCTTTACTGAAATACCATACCTACATTCCACAT
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
* * * *
5594186 CTCAGTATGGTTTTCTTTACGGAAATACCATAACTACGTTTCACAT
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
5594232 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATT
1 CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATT
5594272 TCATACTTTG
Statistics
Matches: 437, Mismatches: 63, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 437 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (46 bp):
CTCAGTATGGTTTTCTTTACTGAAATACCATACCTACATTCCACAT
Found at i:5603646 original size:2 final size:2
Alignment explanation
Indices: 5603639--5603663 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5603629 TTTCTTGATC
5603639 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 T
5603664 TCAAAATTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5604361 original size:13 final size:13
Alignment explanation
Indices: 5604343--5604378 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
5604333 TGGTTTATTT
5604343 ACCATTTAAGACC
1 ACCATTTAAGACC
5604356 ACCATTTAAGACC
1 ACCATTTAAGACC
*
5604369 CCCATATTAA
1 ACCAT-TTAA
5604379 AAATCCAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.39, C:0.31, G:0.06, T:0.25
Consensus pattern (13 bp):
ACCATTTAAGACC
Found at i:5611611 original size:13 final size:13
Alignment explanation
Indices: 5611593--5611620 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5611583 CGAATAGAAG
5611593 AAGGGAAATTGAT
1 AAGGGAAATTGAT
5611606 AAGGGAAATTGAT
1 AAGGGAAATTGAT
5611619 AA
1 AA
5611621 AAGAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (13 bp):
AAGGGAAATTGAT
Found at i:5612873 original size:42 final size:42
Alignment explanation
Indices: 5612826--5612932 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
5612816 TATTGGTCTC
*
5612826 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGATGACAAGATT
5612868 GGCACTAAGTGTGCGGGTATAAATGGACACGATGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGATGACAAGATT
*
5612910 GGCACTAAGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
5612933 ATTTGTACAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGATGACAAGATT
Found at i:5612998 original size:27 final size:28
Alignment explanation
Indices: 5612941--5613009 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 28
5612931 AAATTTGTAC
**
5612941 AGCACTAAGTGTGCAAATTTGATTATAT
1 AGCACTAAGTGTGCAAAGCTGATTATAT
* *
5612969 AGCACTATGTGTGC-AAGCTGATTTTAT
1 AGCACTAAGTGTGCAAAGCTGATTATAT
5612996 AGCACTAAGTGTGC
1 AGCACTAAGTGTGC
5613010 GGACTCACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.64
28 13 0.36
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCAAAGCTGATTATAT
Found at i:5625042 original size:23 final size:23
Alignment explanation
Indices: 5625016--5625069 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5625006 CGAGCCGAAA
5625016 CGGTAAGCTCCGTAGAACTAAAT
1 CGGTAAGCTCCGTAGAACTAAAT
** *
5625039 CGGTAAGCTTTGTAGAGCTAAAT
1 CGGTAAGCTCCGTAGAACTAAAT
*
5625062 CTGTAAGC
1 CGGTAAGC
5625070 CCGAAGGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (23 bp):
CGGTAAGCTCCGTAGAACTAAAT
Found at i:5633097 original size:39 final size:38
Alignment explanation
Indices: 5633036--5633378 Score: 146
Period size: 37 Copynumber: 9.1 Consensus size: 38
5633026 CTCATTTCGC
* * *
5633036 ATAATCAATGGATAAT-ATTCGTTTAAGCATGCATTCCA-T
1 ATAATCAGTGGAT-ATCACTCGTTTAAGCA-CCATT-CAGT
5633075 ATAATCAGTGGATATCACTCGTTTGAA-C-CCATTCAGT
1 ATAATCAGTGGATATCACTCGTTT-AAGCACCATTCAGT
* * * * *
5633112 ATAATCAGTGGATATCGCTCGTTTGAGCAACTTTTAGT
1 ATAATCAGTGGATATCACTCGTTTAAGCACCATTCAGT
* * * ** * * *
5633150 ATAATTAGTAGACATTGCTCTTTTGAGCA-CGTTCAGT
1 ATAATCAGTGGATATCACTCGTTTAAGCACCATTCAGT
* * * ** *
5633187 ATATTTAGTAGATATTGCTCGTTTGAGC-CCATTCAGT
1 ATAATCAGTGGATATCACTCGTTTAAGCACCATTCAGT
** * * * *
5633224 ATAATCAGTGGATATTGCTCGTTTGAGGAACTTTCAGT
1 ATAATCAGTGGATATCACTCGTTTAAGCACCATTCAGT
** * ** * *
5633262 ATAATCAGTAAACATTGCTCTTTTGAGCA-CATTCAGT
1 ATAATCAGTGGATATCACTCGTTTAAGCACCATTCAGT
* * ** * *
5633299 A-AATTTAGTAGATATTGCTCGTTTGAGCA-CATTCATT
1 ATAA-TCAGTGGATATCACTCGTTTAAGCACCATTCAGT
* ** * * * *
5633336 ATAATCAGTAGATATTGCTCATTTGAGCAACTTTCAGT
1 ATAATCAGTGGATATCACTCGTTTAAGCACCATTCAGT
5633374 ATAAT
1 ATAAT
5633379 TAGTAGACAT
Statistics
Matches: 254, Mismatches: 40, Indels: 21
0.81 0.13 0.07
Matches are distributed among these distances:
36 5 0.02
37 151 0.59
38 76 0.30
39 20 0.08
40 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (38 bp):
ATAATCAGTGGATATCACTCGTTTAAGCACCATTCAGT
Found at i:5633188 original size:75 final size:74
Alignment explanation
Indices: 5633106--5633475 Score: 429
Period size: 75 Copynumber: 5.0 Consensus size: 74
5633096 TTTGAACCCA
* * * *
5633106 TTCAGTATAATCAGTGGATATCGCTCGTTTGAGCAACTTTTAGTATAATTAGTAGACATTGCTCT
1 TTCAGTATAATCAGTAGATATTGCTCGTTTGAGC-ACATTCAGTATAATTAGTAGACATTGCTCT
5633171 TTTGAGCACG
65 TTTGAGCACG
* * * * * * *
5633181 TTCAGTATATTTAGTAGATATTGCTCGTTTGAGCCCATTCAGTATAATCAGTGGATATTGCTCGT
1 TTCAGTATAATCAGTAGATATTGCTCGTTTGAGCACATTCAGTATAATTAGTAGACATTGCTCTT
* *
5633246 TTGAGGAACT
66 TTGA-GCACG
* * * * *
5633256 TTCAGTATAATCAGTAAACATTGCTCTTTTGAGCACATTCAGTA-AATTTAGTAGATATTGCTCG
1 TTCAGTATAATCAGTAGATATTGCTCGTTTGAGCACATTCAGTATAA-TTAGTAGACATTGCTCT
*
5633320 TTTGAGCACA
65 TTTGAGCACG
* * * *
5633330 TTCATTATAATCAGTAGATATTGCTCATTTGAGCAACTTTCAGTATAATTAGTAGACATTTCTCT
1 TTCAGTATAATCAGTAGATATTGCTCGTTTGAGC-ACATTCAGTATAATTAGTAGACATTGCTCT
*
5633395 TTTGAGTACG
65 TTTGAGCACG
* * * *
5633405 TTCAGTAGATTCAGTAGATATTGCTCGTTTGAACACATTCAGTATAATGAGTAGACATTGCT-TG
1 TTCAGTATAATCAGTAGATATTGCTCGTTTGAGCACATTCAGTATAATTAGTAGACATTGCTCT-
5633469 TTTGAGC
65 TTTGAGC
5633476 CTATTCAATA
Statistics
Matches: 248, Mismatches: 42, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
73 1 0.00
74 94 0.38
75 151 0.61
76 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (74 bp):
TTCAGTATAATCAGTAGATATTGCTCGTTTGAGCACATTCAGTATAATTAGTAGACATTGCTCTT
TTGAGCACG
Found at i:5633282 original size:112 final size:112
Alignment explanation
Indices: 5633092--5633475 Score: 570
Period size: 112 Copynumber: 3.4 Consensus size: 112
5633082 GTGGATATCA
* * * *
5633092 CTCGTTTGAACCCATTCAGTATAATCAGTGGATATCGCTCGTTTGAGCAACTTTTAGTATAATTA
1 CTCGTTTGAACACATTCAGTATAATCAGTAGATATTGCTCGTTTGAGCAACTTTCAGTATAATTA
*
5633157 GTAGACATTGCTCTTTTGAGCACGTTCAGTATATTTAGTAGATATTG
66 GTAGACATTGCTCTTTTGAGCACGTTCAGTAAATTTAGTAGATATTG
* * * * *
5633204 CTCGTTTGAGCCCATTCAGTATAATCAGTGGATATTGCTCGTTTGAGGAACTTTCAGTATAATCA
1 CTCGTTTGAACACATTCAGTATAATCAGTAGATATTGCTCGTTTGAGCAACTTTCAGTATAATTA
* *
5633269 GTAAACATTGCTCTTTTGAGCACATTCAGTAAATTTAGTAGATATTG
66 GTAGACATTGCTCTTTTGAGCACGTTCAGTAAATTTAGTAGATATTG
* * *
5633316 CTCGTTTGAGCACATTCATTATAATCAGTAGATATTGCTCATTTGAGCAACTTTCAGTATAATTA
1 CTCGTTTGAACACATTCAGTATAATCAGTAGATATTGCTCGTTTGAGCAACTTTCAGTATAATTA
* * * *
5633381 GTAGACATTTCTCTTTTGAGTACGTTCAGTAGATTCAGTAGATATTG
66 GTAGACATTGCTCTTTTGAGCACGTTCAGTAAATTTAGTAGATATTG
* * *
5633428 CTCGTTTGAACACATTCAGTATAATGAGTAGACATTGCTTGTTTGAGC
1 CTCGTTTGAACACATTCAGTATAATCAGTAGATATTGCTCGTTTGAGC
5633476 CTATTCAATA
Statistics
Matches: 246, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 246 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (112 bp):
CTCGTTTGAACACATTCAGTATAATCAGTAGATATTGCTCGTTTGAGCAACTTTCAGTATAATTA
GTAGACATTGCTCTTTTGAGCACGTTCAGTAAATTTAGTAGATATTG
Found at i:5633482 original size:37 final size:38
Alignment explanation
Indices: 5633074--5633482 Score: 383
Period size: 37 Copynumber: 11.0 Consensus size: 38
5633064 ATGCATTCCA
* ** * *
5633074 TATAATCAGTGGATATCACTCGTTTGAAC-CCATTCAG
1 TATAATCAGTAGATATTGCTCGTTTGAGCACTATTCAG
* * *
5633111 TATAATCAGTGGATATCGCTCGTTTGAGCAACT-TTTAG
1 TATAATCAGTAGATATTGCTCGTTTGAGC-ACTATTCAG
* * * *
5633149 TATAATTAGTAGACATTGCTCTTTTGAGCAC-GTTCAG
1 TATAATCAGTAGATATTGCTCGTTTGAGCACTATTCAG
* * *
5633186 TATATTTAGTAGATATTGCTCGTTTGAGC-CCATTCAG
1 TATAATCAGTAGATATTGCTCGTTTGAGCACTATTCAG
* *
5633223 TATAATCAGTGGATATTGCTCGTTTGAGGAACT-TTCAG
1 TATAATCAGTAGATATTGCTCGTTTGA-GCACTATTCAG
* * *
5633261 TATAATCAGTAAACATTGCTCTTTTGAGCAC-ATTCAG
1 TATAATCAGTAGATATTGCTCGTTTGAGCACTATTCAG
* *
5633298 TA-AATTTAGTAGATATTGCTCGTTTGAGCAC-ATTCAT
1 TATAA-TCAGTAGATATTGCTCGTTTGAGCACTATTCAG
*
5633335 TATAATCAGTAGATATTGCTCATTTGAGCAACT-TTCAG
1 TATAATCAGTAGATATTGCTCGTTTGAGC-ACTATTCAG
* * * * * *
5633373 TATAATTAGTAGACATTTCTCTTTTGAGTAC-GTTCAG
1 TATAATCAGTAGATATTGCTCGTTTGAGCACTATTCAG
* * *
5633410 TAGATTCAGTAGATATTGCTCGTTTGAACAC-ATTCAG
1 TATAATCAGTAGATATTGCTCGTTTGAGCACTATTCAG
* * *
5633447 TATAATGAGTAGACATTGCTTGTTTGAGC-CTATTCA
1 TATAATCAGTAGATATTGCTCGTTTGAGCACTATTCA
5633483 ATATTCCATT
Statistics
Matches: 307, Mismatches: 52, Indels: 26
0.80 0.14 0.07
Matches are distributed among these distances:
36 4 0.01
37 212 0.69
38 89 0.29
39 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (38 bp):
TATAATCAGTAGATATTGCTCGTTTGAGCACTATTCAG
Found at i:5635845 original size:93 final size:93
Alignment explanation
Indices: 5635733--5635905 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
5635723 CGCCCATAAG
*** *
5635733 CGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
5635798 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
*
5635826 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
5635891 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
5635906 CAAATATCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Done.