Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 35 of 190
Found at i:6118734 original size:1 final size:1
Alignment explanation
Indices: 6118728--6118779 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
6118718 ACCAATTCCC
* * * * **
6118728 TTTTTTTTTTTTTTTGTCTTTTTATTTTTGTTTTTTGATTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6118780 ACCCATCGAC
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.04, C:0.02, G:0.06, T:0.88
Consensus pattern (1 bp):
T
Found at i:6118755 original size:14 final size:13
Alignment explanation
Indices: 6118728--6118776 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
6118718 ACCAATTCCC
6118728 TTTT-TTTTTT-T
1 TTTTGTTTTTTAT
6118739 TTTTGTCTTTTTAT
1 TTTTGT-TTTTTAT
6118753 TTTTGTTTTTTGAT
1 TTTTGTTTTTT-AT
6118767 TTTT-TTTTTT
1 TTTTGTTTTTT
6118777 TTTACCCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.12
12 1 0.03
13 16 0.47
14 13 0.38
ACGTcount: A:0.04, C:0.02, G:0.06, T:0.88
Consensus pattern (13 bp):
TTTTGTTTTTTAT
Found at i:6118777 original size:14 final size:13
Alignment explanation
Indices: 6118728--6118777 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
6118718 ACCAATTCCC
6118728 TTTTTTTTTTT-T
1 TTTTTTTTTTTAT
* *
6118740 TTTGTCTTTTTAT
1 TTTTTTTTTTTAT
*
6118753 TTTTGTTTTTTGAT
1 TTTT-TTTTTTTAT
6118767 TTTTTTTTTTT
1 TTTTTTTTTTT
6118778 TTACCCATCG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 9 0.30
13 10 0.33
14 11 0.37
ACGTcount: A:0.04, C:0.02, G:0.06, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTAT
Found at i:6119193 original size:38 final size:37
Alignment explanation
Indices: 6119114--6119207 Score: 111
Period size: 37 Copynumber: 2.5 Consensus size: 37
6119104 AATTGAGGGA
* *
6119114 TTAAAACTTTAAATAAAATGTTCCATCATAATTAAGGT
1 TTAAAACTTTAAATAAAATGTTCCA-CATAATCAAGCT
*
6119152 TTAAAACTTTAAATAAAATGCTTTC-CATAATCAAGACT
1 TTAAAACTTTAAATAAAATG-TTCCACATAATCAAG-CT
*
6119190 TT-AAATTTTAAATAAAAT
1 TTAAAACTTTAAATAAAAT
6119208 ACTTCTTCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
37 24 0.48
38 23 0.46
39 3 0.06
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (37 bp):
TTAAAACTTTAAATAAAATGTTCCACATAATCAAGCT
Found at i:6121519 original size:22 final size:23
Alignment explanation
Indices: 6121473--6121515 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
6121463 TAAATGAAGA
*
6121473 AATTATGGTTAAATTTTTTATAT
1 AATTATGGTTAAATTTTTTAAAT
6121496 AATTAT-GTT-AATTTTTTAAA
1 AATTATGGTTAAATTTTTTAAA
6121516 ATAAACTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 3 0.16
23 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (23 bp):
AATTATGGTTAAATTTTTTAAAT
Found at i:6121591 original size:8 final size:9
Alignment explanation
Indices: 6121571--6121600 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
6121561 TTAAAGTAAT
*
6121571 AAAAAATGA
1 AAAAAAAGA
6121580 AAAAAAAGA
1 AAAAAAAGA
6121589 AAAAAAAGA
1 AAAAAAAGA
6121598 AAA
1 AAA
6121601 TTTTTATCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:6122395 original size:193 final size:193
Alignment explanation
Indices: 6122056--6122435 Score: 620
Period size: 193 Copynumber: 2.0 Consensus size: 193
6122046 ACATGACATA
*
6122056 ATTTTTTACGAAAAGTAAATTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCAAGTAGAGAT
1 ATTTTTTACGAAAAATAAATTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCAAGTAGAGAT
* * * *
6122121 GCTTTAGGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTATCGACGTACTGGAACATTTTAA
66 GCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTATCAAAGTACTGGAACATTTTAA
* * * *
6122186 GAATTATTTCAATAAAAAGGTTTTAATTTATTTTTTTCGAGAATAAA-TTTTTTTAACGTGAC
131 GAATTATTTAAATAAAAAAGTTTTAATTTATTTTTCTCAAGAATAAACTTTTTTTAACGTGAC
* *
6122248 ATTTTCTTACGAAAAATAAATTT-GAGCCTCCAAAGATGAGATTCTAAAAGTATTTCGAGTAGAG
1 ATTTT-TTACGAAAAATAAATTTAGA-CCTCCAAAGATGAGATTCTAAAAGTATTCCAAGTAGAG
*
6122312 ATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTATTAAAGTACTGGAACATTTT
64 ATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTATCAAAGTACTGGAACATTTT
6122377 AAGAATTATTTAAATAAAAAAGTTTTAATTTATTTTTCTCAAGAATAAACTTTTTTTAA
129 AAGAATTATTTAAATAAAAAAGTTTTAATTTATTTTTCTCAAGAATAAACTTTTTTTAA
6122436 TAAATAAAAA
Statistics
Matches: 173, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
192 7 0.04
193 157 0.91
194 9 0.05
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (193 bp):
ATTTTTTACGAAAAATAAATTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCAAGTAGAGAT
GCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTATCAAAGTACTGGAACATTTTAA
GAATTATTTAAATAAAAAAGTTTTAATTTATTTTTCTCAAGAATAAACTTTTTTTAACGTGAC
Found at i:6134021 original size:46 final size:47
Alignment explanation
Indices: 6133910--6134476 Score: 606
Period size: 46 Copynumber: 11.8 Consensus size: 47
6133900 GAAAACAGAT
* * *
6133910 GAGATTTTTAAAGTTGTTGAGCCTTTGCTGAGAGAAGCCCTTTTCAA
1 GAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
** *
6133957 GATATGAGATTTTAAAGTTGTTGAGCCTCTTTTGAGAGGAG-CATTTTCAA
1 G--A-GA-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
* * *
6134007 GAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAACCTTTTTCAA
1 GAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
* * * **
6134054 GAG-ATTTTAAAATTGTTGAGCTTCTACTGAGAAAAGCCCTTTTCAA
1 GAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
6134100 GAG-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
1 GAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
* * * *
6134146 GATGAGATTTTTAAAGTTGTTGAGTCTCTACTGAGATGAG-CTTTTTCAA
1 GA-GA-A-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
* * *
6134195 GAGATTTTTAAAGTTGTTGAGCTTCTGCTAAGAGGAGCCCTTTTCAA
1 GAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
** *
6134242 GATATGAGATTTTTAAAGTTGTTGAGCCTCTATTGAGAGGAGCCTTTTTCAA
1 G--A-GA-A-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
* * *
6134294 GATAAGAATTTTAAAGTTATTGAGCGTCTGTTGAGAGGAG-CCTTTTCAA
1 G---AGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
* * * * *
6134343 GAGAATTTTAAAGTTGTAGAGCCTTTGTTGAAAGGAGCCCTTTTTAA
1 GAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
*
6134390 AAG-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
1 GAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
* * *
6134436 GATAAAAATTTTAAAGTTGTTGAGCTTCTGTTGAGAGGAGC
1 G---AGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC
6134477 TTTTTTAGAT
Statistics
Matches: 438, Mismatches: 61, Indels: 39
0.81 0.11 0.07
Matches are distributed among these distances:
46 205 0.47
47 34 0.08
48 3 0.01
49 23 0.05
50 103 0.24
51 29 0.07
52 40 0.09
53 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (47 bp):
GAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAA
Found at i:6134213 original size:142 final size:142
Alignment explanation
Indices: 6133910--6134592 Score: 668
Period size: 142 Copynumber: 4.7 Consensus size: 142
6133900 GAAAACAGAT
*
6133910 GAGATTTTTAAAGTTGTTGAGCCTT-TGCTGAGAGAAGCCCTTTTCAAGATATGAGATTTTAAAG
1 GAGATTTTTAAAGTTGTTGAG-CTTCTGCTGAGAGGAGCCCTTTTC---A-A-GAGATTTTAAAG
** * * *
6133974 TTGTTGAGCCTCTTTTGAGAGGAG-CATTTTCAAG---AGAATTTTAAAGTTGTTGAGCCTCTGC
60 TTGTTGAGCCTCTACTGAGAGGAGCCCTTTTCAAGATAAGAATTTTAAAGTTGTTGAGTCTCTAC
*
6134035 TGAGA-GAAACCTTTTTCAA
125 TGAGATG--AGCTTTTTCAA
* * **
6134054 GAGA-TTTTAAAATTGTTGAGCTTCTACTGAGAAAAGCCCTTTTCAAGAGATTTTAAAGTTGTTG
1 GAGATTTTTAAAGTTGTTGAGCTTCTGCTGAGAGGAGCCCTTTTCAAGAGATTTTAAAGTTGTTG
* * *
6134118 AGCCTCTGCTGAGAGGAGCCCTTTTCAAGATGAGATTTTTAAAGTTGTTGAGTCTCTACTGAGAT
66 AGCCTCTACTGAGAGGAGCCCTTTTCAAGATAAGAATTTTAAAGTTGTTGAGTCTCTACTGAGAT
6134183 GAGCTTTTTCAA
131 GAGCTTTTTCAA
*
6134195 GAGATTTTTAAAGTTGTTGAGCTTCTGCTAAGAGGAGCCCTTTTCAAGATATGAGATTTTTAAAG
1 GAGATTTTTAAAGTTGTTGAGCTTCTGCTGAGAGGAGCCCTTTTC---A-A-GAGA-TTTTAAAG
* * * *
6134260 TTGTTGAGCCTCTATTGAGAGGAGCCTTTTTCAAGATAAGAATTTTAAAGTTATTGAG-CGTCTG
60 TTGTTGAGCCTCTACTGAGAGGAGCCCTTTTCAAGATAAGAATTTTAAAGTTGTTGAGTC-TCTA
* * *
6134324 TTGAGAGGAGCCTTTTCAA
124 CTGAGATGAGCTTTTTCAA
* * * * * *
6134343 GAGAATTTTAAAGTTGTAGAGCCTT-TGTTGAAAGGAGCCCTTTTTAAAAGATTTTAAAGTTGTT
1 GAGATTTTTAAAGTTGTTGAG-CTTCTGCTGAGAGGAGCCCTTTTCAAGAGATTTTAAAGTTGTT
* * *
6134407 GAGCCTCTGCTGAGAGGAGCCCTTTTCAAGATAAAAATTTTAAAGTTGTTGAGCTTCTGTTGAGA
65 GAGCCTCTACTGAGAGGAGCCCTTTTCAAGATAAGAATTTTAAAGTTGTTGAG--TCT-CT----
* *
6134472 GGAGCTTTTTTAGATGAG-ATTTTCAGA
123 --A-C----TGAGATGAGCTTTTTCA-A
* * *
6134499 TGAGATTTTTAAAGTTGTTGAGCTTCTGCTGAGAGGAG-CATTTCCAAGAGATTTTTAAAGTTAT
1 -GAGATTTTTAAAGTTGTTGAGCTTCTGCTGAGAGGAGCCCTTTTCAAGAGA-TTTTAAAGTTGT
6134563 TGAGCCTCTACTGAGAGGAGCCCTTTTCAA
64 TGAGCCTCTACTGAGAGGAGCCCTTTTCAA
6134593 AAAAAAAAAA
Statistics
Matches: 452, Mismatches: 53, Indels: 55
0.81 0.09 0.10
Matches are distributed among these distances:
138 34 0.08
139 10 0.02
140 1 0.00
141 14 0.03
142 128 0.28
143 37 0.08
144 6 0.01
145 4 0.01
146 1 0.00
147 5 0.01
148 114 0.25
149 3 0.01
155 6 0.01
156 20 0.04
157 69 0.15
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (142 bp):
GAGATTTTTAAAGTTGTTGAGCTTCTGCTGAGAGGAGCCCTTTTCAAGAGATTTTAAAGTTGTTG
AGCCTCTACTGAGAGGAGCCCTTTTCAAGATAAGAATTTTAAAGTTGTTGAGTCTCTACTGAGAT
GAGCTTTTTCAA
Found at i:6134425 original size:290 final size:285
Alignment explanation
Indices: 6133910--6134481 Score: 821
Period size: 290 Copynumber: 2.0 Consensus size: 285
6133900 GAAAACAGAT
*
6133910 GAGATTTTTAAAGTTGTTGAGCCTTTGCTGAGAGAAGCCCTTTTCAAGATATGAGATTTTAAAGT
1 GAGATTTTTAAAGTTGTTGAGCCTTTGCTAAGAGAAGCCCTTTTCAAGATATGAGATTTTAAAGT
* *
6133975 TGTTGAGCCTCTTTTGAGAGGAGCATTTTCAAGAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGA
66 TGTTGAGCCTCTATTGAGAGGAGCATTTTCAAGAGAATTTTAAAGTTATTGAGCCTCTGCTGAGA
* *
6134040 GAAACCTTTTTCAAGAGATTTTAAAATTGTTGAGCTTCTACTGAGAAAAGCCCTTTTCAAGAGAT
131 GAAACCTTTTTCAAGAGATTTTAAAATTGTAGAGCTTCTACTGAGAAAAGCCCTTTTCAAAAGAT
* * *
6134105 TTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAAGATGAGATTTTTAAAGTTGTTGAG
196 TTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAAGATAAAAATTTTAAAGTTGTTGAG
*
6134170 -TCTCTACTGAGATGAGCTTTTTCAA
261 CT-TCTACTGAGAGGAGCTTTTTCAA
*
6134195 GAGATTTTTAAAGTTGTTGAG-CTTCTGCTAAGAGGAGCCCTTTTCAAGATATGAGATTTTTAAA
1 GAGATTTTTAAAGTTGTTGAGCCTT-TGCTAAGAGAAGCCCTTTTCAAGATATGAGA-TTTTAAA
* *
6134259 GTTGTTGAGCCTCTATTGAGAGGAGCCTTTTTCAAGATAAGAATTTTAAAGTTATTGAGCGTCTG
64 GTTGTTGAGCCTCTATTGAGAGGAG-CATTTTCAAG---AGAATTTTAAAGTTATTGAGCCTCTG
* * * * ** *
6134324 TTGAGAGGAGCC-TTTTCAAGAGAATTTTAAAGTTGTAGAGCCTT-TGTTGA-AAGGAGCCCTTT
125 CTGAGAGAAACCTTTTTCAAGAG-ATTTTAAAATTGTAGAG-CTTCTACTGAGAA-AAGCCCTTT
*
6134386 TTAAAAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAAGATAAAAATTTTAAA
187 TCAAAAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAAGATAAAAATTTTAAA
**
6134451 GTTGTTGAGCTTCTGTTGAGAGGAGCTTTTT
252 GTTGTTGAGCTTCTACTGAGAGGAGCTTTTT
6134482 TAGATGAGAT
Statistics
Matches: 255, Mismatches: 22, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
284 3 0.01
285 50 0.20
286 31 0.12
287 9 0.04
289 12 0.05
290 146 0.57
291 4 0.02
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (285 bp):
GAGATTTTTAAAGTTGTTGAGCCTTTGCTAAGAGAAGCCCTTTTCAAGATATGAGATTTTAAAGT
TGTTGAGCCTCTATTGAGAGGAGCATTTTCAAGAGAATTTTAAAGTTATTGAGCCTCTGCTGAGA
GAAACCTTTTTCAAGAGATTTTAAAATTGTAGAGCTTCTACTGAGAAAAGCCCTTTTCAAAAGAT
TTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTCAAGATAAAAATTTTAAAGTTGTTGAG
CTTCTACTGAGAGGAGCTTTTTCAA
Found at i:6134499 original size:13 final size:13
Alignment explanation
Indices: 6134478--6134507 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6134468 GAGAGGAGCT
*
6134478 TTTTTAGATGAGA
1 TTTTCAGATGAGA
6134491 TTTTCAGATGAGA
1 TTTTCAGATGAGA
6134504 TTTT
1 TTTT
6134508 TAAAGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.20, T:0.50
Consensus pattern (13 bp):
TTTTCAGATGAGA
Found at i:6135072 original size:23 final size:23
Alignment explanation
Indices: 6135041--6135122 Score: 155
Period size: 23 Copynumber: 3.6 Consensus size: 23
6135031 TAAAAAATAA
*
6135041 GATTCGAATCCCAGAAGATCTGG
1 GATTTGAATCCCAGAAGATCTGG
6135064 GATTTGAATCCCAGAAGATCTGG
1 GATTTGAATCCCAGAAGATCTGG
6135087 GATTTGAATCCCAGAAGATCTGG
1 GATTTGAATCCCAGAAGATCTGG
6135110 GATTTGAATCCCA
1 GATTTGAATCCCA
6135123 ACAAGCTCTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (23 bp):
GATTTGAATCCCAGAAGATCTGG
Found at i:6136909 original size:193 final size:195
Alignment explanation
Indices: 6136545--6136934 Score: 664
Period size: 193 Copynumber: 2.0 Consensus size: 195
6136535 TGCATTGCAT
* *
6136545 ACATGACATAATTTTTTACAAAAAGTAAATTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCC
1 ACATGACAT-ATTTCTTACAAAAAGTAAATTGAGACCTCCAAAGATGAGATTCTAAAAGTATTCC
*
6136610 GAGTAGAGATGCTTTAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGG
65 GAGCAGAGATGCTTTAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGG
*
6136675 AACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAA-TTTTTTT
130 AACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCAAGAATAAACTTTTTTT
6136739 A
195 A
6136740 ACATGACAT-TTTCTTACGAAAAA-TAAATTCGAG-CCTCCAAAGATGAGATTCTAAAAGTATTC
1 ACATGACATATTTCTTAC-AAAAAGTAAATT-GAGACCTCCAAAGATGAGATTCTAAAAGTATTC
*
6136802 TGAGCAGAGATGCTTTAAGAAAT-TTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACT
64 CGAGCAGAGATGCTTTAAGAAATCTT-TAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACT
6136866 GGAACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCAAGAATAAACTTTTT
128 GGAACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCAAGAATAAACTTTTT
6136931 TTA
193 TTA
6136934 A
1 A
6136935 TAAATAAAAA
Statistics
Matches: 186, Mismatches: 5, Indels: 9
0.93 0.03 0.05
Matches are distributed among these distances:
192 2 0.01
193 159 0.85
194 16 0.09
195 9 0.05
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (195 bp):
ACATGACATATTTCTTACAAAAAGTAAATTGAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
AGCAGAGATGCTTTAAGAAATCTTTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGA
ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCAAGAATAAACTTTTTTTA
Found at i:6137791 original size:19 final size:18
Alignment explanation
Indices: 6137769--6137856 Score: 79
Period size: 18 Copynumber: 4.7 Consensus size: 18
6137759 AAATGAAAAG
6137769 AAAAAAGAAAAAAGAAGC
1 AAAAAAGAAAAAAGAAGC
* * *
6137787 CAAAAACAAAAAA-AAGG
1 AAAAAAGAAAAAAGAAGC
*
6137804 AAAAAAAATAAAAAGAAGAC
1 AAAAAAGA-AAAAAGAAG-C
* *
6137824 ATAAAATGAAAAAATGAAGA
1 A-AAAAAGAAAAAA-GAAGC
6137844 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
6137857 CAAATGAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
17 9 0.16
18 16 0.29
19 14 0.25
20 7 0.13
21 9 0.16
ACGTcount: A:0.78, C:0.05, G:0.12, T:0.05
Consensus pattern (18 bp):
AAAAAAGAAAAAAGAAGC
Found at i:6137837 original size:21 final size:19
Alignment explanation
Indices: 6137769--6137884 Score: 87
Period size: 19 Copynumber: 6.1 Consensus size: 19
6137759 AAATGAAAAG
*
6137769 AAAAAAG-AAAAAAGAAGC
1 AAAAAAGAAAAAAAGAAGA
* * *
6137787 CAAAAACAAAAAAA-AGGA
1 AAAAAAGAAAAAAAGAAGA
*
6137805 AAAAAA-ATAAAAAGAAGA
1 AAAAAAGAAAAAAAGAAGA
* *
6137823 CATAAAATGAAAAAATGAAGA
1 -A-AAAAAGAAAAAAAGAAGA
6137844 AAAAAAGAAAAAACA-AATGA
1 AAAAAAGAAAAAA-AGAA-GA
*
6137864 AAAAAGAGAAAAAATGAAGA
1 AAAAA-AGAAAAAAAGAAGA
6137884 A
1 A
6137885 GGACTTAGAT
Statistics
Matches: 76, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
17 6 0.08
18 15 0.20
19 20 0.26
20 15 0.20
21 20 0.26
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.05
Consensus pattern (19 bp):
AAAAAAGAAAAAAAGAAGA
Found at i:6137847 original size:11 final size:10
Alignment explanation
Indices: 6137769--6137884 Score: 54
Period size: 9 Copynumber: 12.0 Consensus size: 10
6137759 AAATGAAAAG
6137769 AAAA-AAGAA
1 AAAAGAAGAA
*
6137778 AAAAGAAGCCA
1 AAAAGAAG-AA
*
6137789 AAAACAA-AA
1 AAAAGAAGAA
6137798 AAAAG--GAA
1 AAAAGAAGAA
*
6137806 AAAA-AA-TA
1 AAAAGAAGAA
6137814 AAAAGAAGACA
1 AAAAGAAGA-A
* *
6137825 TAAA-ATGAA
1 AAAAGAAGAA
6137834 AAAATGAAGAAA
1 AAAA-GAAG-AA
6137846 AAAAGAA-AA
1 AAAAGAAGAA
*
6137855 AACAA-ATGAA
1 AA-AAGAAGAA
6137865 AAAAG-AGAA
1 AAAAGAAGAA
6137874 AAAATGAAGAA
1 AAAA-GAAGAA
6137885 GGACTTAGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 30
0.65 0.10 0.25
Matches are distributed among these distances:
8 11 0.14
9 29 0.37
10 13 0.16
11 20 0.25
12 6 0.08
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.05
Consensus pattern (10 bp):
AAAAGAAGAA
Found at i:6137848 original size:39 final size:34
Alignment explanation
Indices: 6137764--6137856 Score: 96
Period size: 39 Copynumber: 2.5 Consensus size: 34
6137754 AAGGTAAATG
* *
6137764 AAAAGAAAAAAGAAAAAAGAAGCCAAAAACAAAA
1 AAAAGAAAAAAAAAAAAAGAAGACAAAAACAAAA
*
6137798 AAAAGGAAAAAAAATAAAAAGAAGACATAAAATGAAAA
1 AAAA-GAAAAAAAA-AAAAAGAAGACA-AAAA-CAAAA
6137836 AATGAAGAAAAAAAGAAAAAA
1 AA--AAGAAAAAAA-AAAAAA
6137857 CAAATGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
34 4 0.08
35 8 0.16
36 11 0.22
37 4 0.08
38 6 0.12
39 13 0.27
40 3 0.06
ACGTcount: A:0.78, C:0.04, G:0.13, T:0.04
Consensus pattern (34 bp):
AAAAGAAAAAAAAAAAAAGAAGACAAAAACAAAA
Found at i:6138982 original size:100 final size:100
Alignment explanation
Indices: 6138878--6139071 Score: 248
Period size: 100 Copynumber: 1.9 Consensus size: 100
6138868 AAGCCTTTAT
* * * * *
6138878 TTTATGAAAAGATGTTTTTAGATA-AGATTTTTAAAATTTCAAAGCATCTGTTTATAATG-AGCT
1 TTTATGAAAAGATATTTTCA-AAAGAGATTTTTAAAATTTCAAAACATCTATTTATAA-GAAGCT
*
6138941 ATTTTCAAATAAAATTTTTAAAGTTTTAAAATCTCTG
64 ATTTTCAAATAAAATTTTTAAAGTTTCAAAATCTCTG
** * * * *
6138978 TTTATGAGGAGCTATTTTCAAAAGAGATTTTTAAAGTTTCAAAACCTCTATTTATGAGAAGCTAT
1 TTTATGAAAAGATATTTTCAAAAGAGATTTTTAAAATTTCAAAACATCTATTTATAAGAAGCTAT
6139043 TTTCAAATAAAATTTTTAAAGTTTCAAAA
66 TTTCAAATAAAATTTTTAAAGTTTCAAAA
6139072 CCTTAATTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
99 3 0.04
100 77 0.96
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (100 bp):
TTTATGAAAAGATATTTTCAAAAGAGATTTTTAAAATTTCAAAACATCTATTTATAAGAAGCTAT
TTTCAAATAAAATTTTTAAAGTTTCAAAATCTCTG
Found at i:6139073 original size:50 final size:49
Alignment explanation
Indices: 6138899--6139131 Score: 235
Period size: 50 Copynumber: 4.7 Consensus size: 49
6138889 ATGTTTTTAG
* * * * * *
6138899 ATAAGATTTTTAAAATTTCAAAGCATCTGTTTATAATGAGCTATTTTCAA
1 ATAAAATTTTTAAAGTTTCAAAACCTCTATTTATGA-GAGCTATTTTCAA
* * *
6138949 ATAAAATTTTTAAAGTTTTAAAATCTCTGTTTATGAGGAGCTATTTTCAA
1 ATAAAATTTTTAAAGTTTCAAAACCTCTATTTATGA-GAGCTATTTTCAA
*
6138999 A-AGAGATTTTTAAAGTTTCAAAACCTCTATTTATGAGAAGCTATTTTCAA
1 ATA-AAATTTTTAAAGTTTCAAAACCTCTATTTATGAG-AGCTATTTTCAA
* *
6139049 ATAAAATTTTTAAAGTTTCAAAACCT-TAATTTATGATG-GCCTATTTTTAG
1 ATAAAATTTTTAAAGTTTCAAAACCTCT-ATTTATGA-GAG-CTATTTTCAA
* *
6139099 AT---ACTTTTAAATTTTCAAAACCTCTATTTATGA
1 ATAAAATTTTTAAAGTTTCAAAACCTCTATTTATGA
6139132 AGAATCATTA
Statistics
Matches: 159, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
47 27 0.17
48 1 0.01
49 4 0.03
50 125 0.79
51 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (49 bp):
ATAAAATTTTTAAAGTTTCAAAACCTCTATTTATGAGAGCTATTTTCAA
Found at i:6139082 original size:100 final size:97
Alignment explanation
Indices: 6138902--6139131 Score: 268
Period size: 100 Copynumber: 2.3 Consensus size: 97
6138892 TTTTTAGATA
* * * *
6138902 AGATTTTTAAAATTTCAAAGCATCTGTTTATAATGAGCTATTTTCAAATAAAATTTTTAAAGTTT
1 AGATTTTTAAAATTTCAAAACCTCTATTTATGATGAGCTATTTTCAAATAAAATTTTTAAAGTTT
* * * *
6138967 TAAAATCTCTGTTTATGA-GGAGCTATTTTCAAAAG
66 CAAAACCTCTATTTATGATGG-CCTATTTT---AAG
*
6139002 AGATTTTTAAAGTTTCAAAACCTCTATTTATGA-GAAGCTATTTTCAAATAAAATTTTTAAAGTT
1 AGATTTTTAAAATTTCAAAACCTCTATTTATGATG-AGCTATTTTCAAATAAAATTTTTAAAGTT
*
6139066 TCAAAACCT-TAATTTATGATGGCCTATTTTTAG
65 TCAAAACCTCT-ATTTATGATGGCCTATTTTAAG
* * *
6139099 ATACTTTTAAATTTTCAAAACCTCTATTTATGA
1 AGATTTTTAAAATTTCAAAACCTCTATTTATGA
6139132 AGAATCATTA
Statistics
Matches: 114, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
97 32 0.28
99 2 0.02
100 78 0.68
101 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (97 bp):
AGATTTTTAAAATTTCAAAACCTCTATTTATGATGAGCTATTTTCAAATAAAATTTTTAAAGTTT
CAAAACCTCTATTTATGATGGCCTATTTTAAG
Found at i:6139082 original size:150 final size:150
Alignment explanation
Indices: 6138805--6139095 Score: 338
Period size: 150 Copynumber: 1.9 Consensus size: 150
6138795 TCAGATAAGT
* * * * *
6138805 TTTTTAAAGTTTTAAATCCTTTGTTTATGAAGAGCTATTTTTATACGAGATATTAAAGTTTTAAA
1 TTTTTAAAGTTTTAAATCCTCTGTTTATGAAGAGCTATTTTCAAAAGAGATATTAAAGTTTCAAA
* * * * * * * *
6138870 GCCTTTATTTTATGAAAAGATGTTTTTAGATAAGATTTTTAAAATTTCAAAGCATCTGTTTATAA
66 ACCTCTATTTTATGAAAAGATATTTTCAAATAAAATTTTTAAAATTTCAAAACATCTATTTATAA
6138935 TGAG-CTATTTTCAAATAAAA
131 TG-GCCTATTTTCAAATAAAA
* *
6138955 TTTTTAAAGTTTTAAAAT-CTCTGTTTATGAGGAGCTATTTTCAAAAGAGATTTTTAAAGTTTCA
1 TTTTTAAAGTTTT-AAATCCTCTGTTTATGAAGAGCTATTTTCAAAAGAGA-TATTAAAGTTTCA
* * * *
6139019 AAACCTCTA-TTTATGAGAAGCTATTTTCAAATAAAATTTTTAAAGTTTCAAAACCT-TAATTTA
64 AAACCTCTATTTTATGAAAAGATATTTTCAAATAAAATTTTTAAAATTTCAAAACATCT-ATTTA
*
6139082 TGATGGCCTATTTT
128 TAATGGCCTATTTT
6139096 TAGATACTTT
Statistics
Matches: 117, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
149 2 0.02
150 93 0.79
151 22 0.19
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (150 bp):
TTTTTAAAGTTTTAAATCCTCTGTTTATGAAGAGCTATTTTCAAAAGAGATATTAAAGTTTCAAA
ACCTCTATTTTATGAAAAGATATTTTCAAATAAAATTTTTAAAATTTCAAAACATCTATTTATAA
TGGCCTATTTTCAAATAAAA
Found at i:6139523 original size:19 final size:19
Alignment explanation
Indices: 6139499--6139544 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
6139489 GACCTAAAAG
*
6139499 CCCAAATTCAATGTTAAAC
1 CCCAAATTCAATATTAAAC
* *
6139518 CCCAAATTCAATATTGAAG
1 CCCAAATTCAATATTAAAC
6139537 CCCAAATT
1 CCCAAATT
6139545 TGGTTTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (19 bp):
CCCAAATTCAATATTAAAC
Found at i:6141686 original size:19 final size:19
Alignment explanation
Indices: 6141644--6141693 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
6141634 AAGAAAATTA
*
6141644 AAATAAAAC-AAT-TAGAT
1 AAATAAAACAAATATAGAG
*
6141661 AATTAAAACAAATATAGAG
1 AAATAAAACAAATATAGAG
*
6141680 AAATAAAATAAATA
1 AAATAAAACAAATA
6141694 ATGAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 8 0.30
18 3 0.11
19 16 0.59
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.22
Consensus pattern (19 bp):
AAATAAAACAAATATAGAG
Found at i:6142698 original size:10 final size:10
Alignment explanation
Indices: 6142683--6142708 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6142673 CTCAAATTAT
6142683 TTTTAATAAA
1 TTTTAATAAA
6142693 TTTTAATAAA
1 TTTTAATAAA
6142703 TTTTAA
1 TTTTAA
6142709 AATTTTATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:6144056 original size:10 final size:10
Alignment explanation
Indices: 6144041--6144071 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6144031 TATCAATTTC
6144041 AATGTAATAT
1 AATGTAATAT
6144051 AATGTAATAT
1 AATGTAATAT
*
6144061 AATATAATAT
1 AATGTAATAT
6144071 A
1 A
6144072 TTTCAACAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (10 bp):
AATGTAATAT
Found at i:6147613 original size:134 final size:134
Alignment explanation
Indices: 6147309--6147674 Score: 326
Period size: 134 Copynumber: 2.7 Consensus size: 134
6147299 GTGTTTTAAA
* * * * * *
6147309 AAAAAAGCCACCATTTTAGCAGCGTTTC-TATCTTTGAAATGCCGTTAAATTAGTTGCATTTTTA
1 AAAAATGCCTCCATATTAGCAGCG-TTCGTATCTTTGAGATGCCGCTAAATTAGTGGCATTTTTA
** * ** * * * ** *
6147373 TGAGAAAAACTCCATTGTTTTGGTGGTATTTGTAATTGAAAATATCGCTACTTTATTGGTGTTTG
65 TGAGAAAAAAACCATTGCTTTGGTGACATTTGTAAATGAAAAGATCACTACTTTAGAGGCGTTTG
6147438 TATAT
130 TATAT
* * * *
6147443 GAAAATGCCTCCATATTAGC-GACATTTGTATTTTTGAGATGCCGCT-AATTAAGTGGCATTTTT
1 AAAAATGCCTCCATATTAGCAG-CGTTCGTATCTTTGAGATGCCGCTAAATT-AGTGGCATTTTT
* *
6147506 ATGAGAAAAAAACCATTGCTTTGGTGACGTTTGTAAATGAAAACGCT-ACTACTTTAGAGGCGTT
64 ATGAGAAAAAAACCATTGCTTTGGTGACATTTGTAAATGAAAA-GATCACTACTTTAGAGGCGTT
*
6147570 TGTATCT
128 TGTATAT
* * *** * ***
6147577 AAAAATGCTTCCATATTAGCAGCGTTCGTGTCTTTGAGATATTGCTAATTTAGTGATGTTTTTAT
1 AAAAATGCCTCCATATTAGCAGCGTTCGTATCTTTGAGATGCCGCTAAATTAGTGGCATTTTTAT
* ** * *
6147642 AAGAAAAACGCCGTTGCTTTGGTGGCATTTGTA
66 GAGAAAAAAACCATTGCTTTGGTGACATTTGTA
6147675 TAAAAAACAC
Statistics
Matches: 183, Mismatches: 43, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
133 7 0.04
134 171 0.93
135 5 0.03
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (134 bp):
AAAAATGCCTCCATATTAGCAGCGTTCGTATCTTTGAGATGCCGCTAAATTAGTGGCATTTTTAT
GAGAAAAAAACCATTGCTTTGGTGACATTTGTAAATGAAAAGATCACTACTTTAGAGGCGTTTGT
ATAT
Found at i:6150263 original size:29 final size:28
Alignment explanation
Indices: 6150223--6150277 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
6150213 TTTTATCATT
*
6150223 ATACTCTAATTCTAAAATTAGAGTATATC
1 ATACTCTAATTC-AAAATTAAAGTATATC
*
6150252 ATAC-CTACATTCAAATTTAAAGTATA
1 ATACTCTA-ATTCAAAATTAAAGTATA
6150278 ATCAATTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (28 bp):
ATACTCTAATTCAAAATTAAAGTATATC
Found at i:6156365 original size:173 final size:174
Alignment explanation
Indices: 6156084--6156397 Score: 429
Period size: 173 Copynumber: 1.8 Consensus size: 174
6156074 TATATTGAAG
* * * * *
6156084 AAAAATGCCTTTAATAATTCTTTTTAAATTTTGTAGATAATTATTAAAGGCATTTTTAGATAACA
1 AAAAATGCCTTTAATAATTCTCTTTAAACTTAGTACATAATTACTAAAGGCATTTTTAGATAACA
* * * * * *
6156149 ACTGCCGTCAATAATTTTTTCTTAAAAAATTTTTAGGATTATTAAAGGCTTCTTTTACTGAAAAA
66 ACTGCCGTCAATAATTTTCTCTAAAAAAATTTTGAGAATTATTAAAGGCATCTTCTACTGAAAAA
6156214 TGCCTTCAATATACCACTATGGTTATAGAAGGCGTTTATTCCAT
131 TGCCTTCAATATACCACTATGGTTATAGAAGGCGTTTATTCCAT
* *
6156258 AAAAATGCTTTTAATAATTC-CTTTAAACTTAGTACATAATTACTGAAGGCATTTGTTA-ATAAC
1 AAAAATGCCTTTAATAATTCTCTTTAAACTTAGTACATAATTACTAAAGGCATTT-TTAGATAAC
* * *
6156321 ACAC-GCCTTCAATAATTTTCCTCTAAAAAAATTTTGA-AATTATTAAAGGCATCTTCTATTGAC
65 A-ACTGCCGTCAATAATTTT-CTCTAAAAAAATTTTGAGAATTATTAAAGGCATCTTCTACTGAA
6156384 AAATGCCTTCAATA
128 AAATGCCTTCAATA
6156398 AATAAATTTT
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
173 83 0.69
174 38 0.31
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (174 bp):
AAAAATGCCTTTAATAATTCTCTTTAAACTTAGTACATAATTACTAAAGGCATTTTTAGATAACA
ACTGCCGTCAATAATTTTCTCTAAAAAAATTTTGAGAATTATTAAAGGCATCTTCTACTGAAAAA
TGCCTTCAATATACCACTATGGTTATAGAAGGCGTTTATTCCAT
Found at i:6157821 original size:80 final size:80
Alignment explanation
Indices: 6157677--6157925 Score: 320
Period size: 80 Copynumber: 3.1 Consensus size: 80
6157667 AATATTATGG
* * *
6157677 TTTGCTGAACCTTGTTGTCTGAT-TTTTTTTATTGAATGATATTGTATGATATTAGGGGGGCTGA
1 TTTGCTGAACCTTGTTGTCTGATATTATTTTATTGAATGGTATTGTATGATATT-GGAGGGCTGA
6157741 ATCATATGCTGAATGA
65 ATCATATGCTGAATGA
* * * * * * *
6157757 TTTGCTAAACCTTGTTGTATGATATTGTATTACTGAATGGTATTGTATGATATTGAAGGCCTGAA
1 TTTGCTGAACCTTGTTGTCTGATATTATTTTATTGAATGGTATTGTATGATATTGGAGGGCTGAA
*
6157822 TCATATGCTGAATGG
66 TCATATGCTGAATGA
* * * * * *
6157837 TTTGCTGAACTTTGTTATCTAATATTATTTTGTTGAATGGTTTTGTATGATATTGGAGGGTTGAA
1 TTTGCTGAACCTTGTTGTCTGATATTATTTTATTGAATGGTATTGTATGATATTGGAGGGCTGAA
*
6157902 ACATATGCTGAATGA
66 TCATATGCTGAATGA
6157917 TTTGCTGAA
1 TTTGCTGAA
6157926 GGATGTTTCT
Statistics
Matches: 143, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
80 117 0.82
81 26 0.18
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (80 bp):
TTTGCTGAACCTTGTTGTCTGATATTATTTTATTGAATGGTATTGTATGATATTGGAGGGCTGAA
TCATATGCTGAATGA
Found at i:6162213 original size:293 final size:295
Alignment explanation
Indices: 6161352--6162267 Score: 1018
Period size: 304 Copynumber: 3.0 Consensus size: 295
6161342 AACCTAAACC
* * * * * * * * *
6161352 GCCTTCAATAATTACC-CCAAAAAATAATTGTGTAGAATATTAAAGGCATTTTGGGAAAAAAAAT
1 GCCTTCAATAA-TCCCACCAAAAATTTATTATGTGGAATATTAAAGGCGTTGTGGG-CAAAAAAC
* * * * * * *
6161416 GCCTTCAAGAATCCGTCGCGCCTTTTTTGTATGAAGTATTAAAGGCATTTTAAAAAAATACCTTC
64 GCCTTCAAAAATCCATCGAGTCTTTTTTATATAAATTATT--A-G-A-TTT--AAAAATACCTTC
* * *
6161481 AATAATACCAACTAAAAATTAATCAAATGGATTATGAAGGACGTTTTTCTATGGGTAGCGCCTTG
122 AATAATACCAACTAAAAATTAATCAAATGGATTATGAAGGACGTTTTCCTATAGGTAACGCCTTG
* * * * *
6161546 AATAATCCATAACAAAATGTTATTGAGGGCGTTTTTGGATATAATCGCCTTCAATAATCCGACCA
187 AATAATCCATAAGAAAATGTTATTGAAGGTGTTTTT-GATATAACCACCTTCAATAATCCGACCA
* * * *
6161611 TCAAAATTTATCGTATAGAATATTAATGGTATTTTTTACCAAAACT
251 TTAAAATTTATCGTATGGAATATTAATGGCA-TTTTTACCAAAAAT
* *
6161657 GCCTTCAATAATCCCACCAAAAATTTATTATGTGGAATATTAAAGGTGTTGTGGGCAAAAAATGC
1 GCCTTCAATAATCCCACCAAAAATTTATTATGTGGAATATTAAAGGCGTTGTGGGCAAAAAACGC
* * * *
6161722 TTTCAAGAATCCATTGAGTCTTTTTTATATAAATTATTGAAGGCATTTTAAAAAAACACCTTCAA
66 CTTCAAAAATCCATCGAGTCTTTTTTATATAAATTATT--A-G-A-TTT--AAAAATACCTTCAA
* * * * * *
6161787 TAATACCAACTAAAAACTAATCGAATGGATTATGAAGGGCGATTTCCTA-CGAGTAACGCCTTAA
124 TAATACCAACTAAAAATTAATCAAATGGATTATGAAGGACGTTTTCCTATAG-GTAACGCCTTGA
* * *
6161851 ATAATCCCTAATG-AAATGTTATTGAAGGTGTTTCTGGATATAACCACCTTCAATAATCCGATCA
188 ATAATCCATAA-GAAAATGTTATTGAAGGTGTTT-TTGATATAACCACCTTCAATAATCCGACCA
* * *
6161915 TTAAAATTTATCATCTGGAATATTAATGGCATTTTTACCAAAATT
251 TTAAAATTTATCGTATGGAATATTAATGGCATTTTTACCAAAAAT
* * *
6161960 GCCTTCAATAATCCCACCAAAAATTTATTGTGTGGAATATTGAAGGCGTTTTGGGCAAAAAACGC
1 GCCTTCAATAATCCCACCAAAAATTTATTATGTGGAATATTAAAGGCGTTGTGGGCAAAAAACGC
* *
6162025 CTTCAAAAATCCATCGAGTCTTTTTTGTATAAATTATT-G-TTT-AAAATGCCTTCAATAATACC
66 CTTCAAAAATCCATCGAGTCTTTTTTATATAAATTATTAGATTTAAAAATACCTTCAATAATACC
* * *
6162087 AACTATAAATTAATCAAATGGATTATGAAGGACGTTTTCCTATAGGTAATGCCTTGAATAATCTA
131 AACTAAAAATTAATCAAATGGATTATGAAGGACGTTTTCCTATAGGTAACGCCTTGAATAATCCA
* *
6162152 TAAGAAAAT-TGTATTGAAGGTGTTTATTAATATAACCACCTTCAATAATCCGACCATTAAAAGT
196 TAAGAAAATGT-TATTGAAGGTGTTT-TTGATATAACCACCTTCAATAATCCGACCATTAAAATT
* * * *
6162216 TATCGTTTGGAATATTAAAGGCATTTTGAGCCAAAAAC
259 TATCGTATGGAATATTAATGGCATTTTTA-CCAAAAAT
*
6162254 GCCTTCAATCATCC
1 GCCTTCAATAATCC
6162268 ATTCAAACTT
Statistics
Matches: 529, Mismatches: 74, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
292 2 0.00
293 151 0.29
294 20 0.04
296 3 0.01
299 1 0.00
303 108 0.20
304 200 0.38
305 44 0.08
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (295 bp):
GCCTTCAATAATCCCACCAAAAATTTATTATGTGGAATATTAAAGGCGTTGTGGGCAAAAAACGC
CTTCAAAAATCCATCGAGTCTTTTTTATATAAATTATTAGATTTAAAAATACCTTCAATAATACC
AACTAAAAATTAATCAAATGGATTATGAAGGACGTTTTCCTATAGGTAACGCCTTGAATAATCCA
TAAGAAAATGTTATTGAAGGTGTTTTTGATATAACCACCTTCAATAATCCGACCATTAAAATTTA
TCGTATGGAATATTAATGGCATTTTTACCAAAAAT
Found at i:6169875 original size:19 final size:19
Alignment explanation
Indices: 6169862--6169917 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
6169852 GAAAGGAGAA
6169862 AAAGAAAAGGAAAGAAAAG
1 AAAGAAAAGGAAAGAAAAG
* *
6169881 AAAGAAAAGAAAAAGAAAAA
1 AAAGAAAAG-GAAAGAAAAG
**
6169901 AAAGATGAGGAAAGAAA
1 AAAGAAAAGGAAAGAAA
6169918 TCTTTAACGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (19 bp):
AAAGAAAAGGAAAGAAAAG
Found at i:6169881 original size:15 final size:16
Alignment explanation
Indices: 6169858--6169905 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 16
6169848 GTGGGAAAGG
*
6169858 AGAAAAAGAAAAGGAA
1 AGAAAAAGAAAAGAAA
6169874 AG-AAAAG-AAAGAAA
1 AGAAAAAGAAAAGAAA
6169888 AGAAAAAGAAAA-AAA
1 AGAAAAAGAAAAGAAA
6169903 AGA
1 AGA
6169906 TGAGGAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.28
15 16 0.55
16 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAAGAAA
Found at i:6169883 original size:9 final size:9
Alignment explanation
Indices: 6169862--6169892 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
6169852 GAAAGGAGAA
6169862 AAAGAAAAGG
1 AAAGAAAA-G
6169872 AAAGAAAAG
1 AAAGAAAAG
6169881 AAAGAAAAG
1 AAAGAAAAG
6169890 AAA
1 AAA
6169893 AAGAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:6169890 original size:5 final size:5
Alignment explanation
Indices: 6169861--6169905 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
6169851 GGAAAGGAGA
*
6169861 AAAAG AAAAG GAAAG AAAAG -AAAG AAAAG AAAAAG AAAA- AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG A
6169906 TGAGGAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 8 0.23
5 22 0.63
6 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:6170006 original size:19 final size:19
Alignment explanation
Indices: 6169982--6170020 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6169972 AAAATGGGTT
6169982 AGTTTTGTTCTTTAAAAAG
1 AGTTTTGTTCTTTAAAAAG
* * *
6170001 AGTTTTTTTTTTTTAAAAG
1 AGTTTTGTTCTTTAAAAAG
6170020 A
1 A
6170021 AAAGGAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (19 bp):
AGTTTTGTTCTTTAAAAAG
Found at i:6170625 original size:19 final size:20
Alignment explanation
Indices: 6170597--6170642 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
6170587 TATTTTTAAT
6170597 TAAA-AAATATATAAAAAAA
1 TAAATAAATATATAAAAAAA
**
6170616 T-AATAAATATATGTAAAAA
1 TAAATAAATATATAAAAAAA
6170635 TAAATAAA
1 TAAATAAA
6170643 AAAATGAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 15 0.65
20 6 0.26
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAATAAATATATAAAAAAA
Found at i:6173894 original size:11 final size:11
Alignment explanation
Indices: 6173850--6173896 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
6173840 TGATAAAATA
*
6173850 ATTTGATTTAAG
1 ATTT-ATTTATG
6173862 ATTTAATTTATG
1 ATTT-ATTTATG
6173874 ATTTATTTAT-
1 ATTTATTTATG
6173884 ATTTATATTATG
1 ATTTAT-TTATG
6173896 A
1 A
6173897 GTGGATTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 6 0.19
11 10 0.32
12 15 0.48
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (11 bp):
ATTTATTTATG
Found at i:6174392 original size:8 final size:8
Alignment explanation
Indices: 6174379--6174407 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
6174369 TAAATCAATT
6174379 TATATTTA
1 TATATTTA
6174387 TATATTTA
1 TATATTTA
6174395 TATATTTA
1 TATATTTA
6174403 -ATATT
1 TATATT
6174408 ATTTGTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTTA
Found at i:6179698 original size:6 final size:7
Alignment explanation
Indices: 6179679--6179709 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
6179669 TTTTATATTA
6179679 AAAATAT
1 AAAATAT
6179686 AAAATAT
1 AAAATAT
6179693 -AAATAT
1 AAAATAT
6179699 AAAATAT
1 AAAATAT
6179706 AAAA
1 AAAA
6179710 AATATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAATAT
Found at i:6179698 original size:13 final size:13
Alignment explanation
Indices: 6179680--6179708 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6179670 TTTATATTAA
6179680 AAATATAAAATAT
1 AAATATAAAATAT
6179693 AAATATAAAATAT
1 AAATATAAAATAT
6179706 AAA
1 AAA
6179709 AAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATATAAAATAT
Found at i:6180124 original size:16 final size:15
Alignment explanation
Indices: 6180100--6180133 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
6180090 ATATTATATA
6180100 ATAAAATTTTTTTATT
1 ATAAAA-TTTTTTATT
*
6180116 ATAATATTTTTTATT
1 ATAAAATTTTTTATT
6180131 ATA
1 ATA
6180134 TGTGAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATAAAATTTTTTATT
Found at i:6180695 original size:105 final size:106
Alignment explanation
Indices: 6180447--6180723 Score: 322
Period size: 105 Copynumber: 2.6 Consensus size: 106
6180437 GTGTTTGAAT
* * * * **
6180447 AATTATCAAAACGTTATATTTAACAAGTACGATTTTTTTTGTTTTATAAACACTGTAATATTAAA
1 AATTATCAAAAAGTTATATTTAACAAGTATGAGTGTTTTTGTTTTATAAATGCTGTAATATTAAA
* * * ** *
6180512 TAAGTACAATGTTTTGATAATTATAAACGTATTTTTTGATA
66 TAAGCACAACGTTTTGATAATTATAAACGCAGCTTTTGACA
* * *
6180553 AATTATCAAAAAGTTATATTTAACAAGTAT-AGCGTTTTTGTTATATAAATGTTGTAATATTAAA
1 AATTATCAAAAAGTTATATTTAACAAGTATGAGTGTTTTTGTTTTATAAATGCTGTAATATTAAA
* *
6180617 TAAGCACGACGTTTTGATCATTATAAACGCAGCTTTTGACA
66 TAAGCACAACGTTTTGATAATTATAAACGCAGCTTTTGACA
* * * ** * *
6180658 ATTTGTCAAAATGTTATATTTAACAAGCGTGATGTTTTTTTGTTTTATAAATGCCGTAATATTAA
1 AATTATCAAAAAGTTATATTTAACAAGTATGA-GTGTTTTTGTTTTATAAATGCTGTAATATTAA
6180723 A
65 A
6180724 CAAATATGAG
Statistics
Matches: 142, Mismatches: 27, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
105 85 0.60
106 29 0.20
107 28 0.20
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (106 bp):
AATTATCAAAAAGTTATATTTAACAAGTATGAGTGTTTTTGTTTTATAAATGCTGTAATATTAAA
TAAGCACAACGTTTTGATAATTATAAACGCAGCTTTTGACA
Found at i:6188381 original size:11 final size:11
Alignment explanation
Indices: 6188365--6188420 Score: 112
Period size: 11 Copynumber: 5.1 Consensus size: 11
6188355 CTTAAAAATG
6188365 ATAAAATCAAA
1 ATAAAATCAAA
6188376 ATAAAATCAAA
1 ATAAAATCAAA
6188387 ATAAAATCAAA
1 ATAAAATCAAA
6188398 ATAAAATCAAA
1 ATAAAATCAAA
6188409 ATAAAATCAAA
1 ATAAAATCAAA
6188420 A
1 A
6188421 AATAAAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 45 1.00
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
ATAAAATCAAA
Found at i:6188427 original size:6 final size:6
Alignment explanation
Indices: 6188322--6188445 Score: 64
Period size: 6 Copynumber: 20.5 Consensus size: 6
6188312 AAAACCAATC
*
6188322 AAAT-A AAATAA ATAATAA AAATGAA ATAA-AA AACTTAA AAATGATA
1 AAATAA AAATAA A-AATAA AAAT-AA A-AATAA AA-ATAA AAAT-A-A
* * * *
6188368 AAATCA AAAT-A AAATCA AAAT-A AAATCA AAAT-A AAATCA AAAT-A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* *
6188412 AAATCAAA AAATAA AAATAA ATAGAA AAA-AA AAA
1 AAAT--AA AAATAA AAATAA AAATAA AAATAA AAA
6188446 CTTGCGATCG
Statistics
Matches: 99, Mismatches: 6, Indels: 28
0.74 0.05 0.21
Matches are distributed among these distances:
5 30 0.30
6 43 0.43
7 14 0.14
8 12 0.12
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:6188433 original size:18 final size:19
Alignment explanation
Indices: 6188400--6188445 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
6188390 AAATCAAAAT
*
6188400 AAAATCAAAATAAAATCA-A
1 AAAATAAAAATAAAAT-AGA
6188419 AAAATAAAAAT-AAATAGA
1 AAAATAAAAATAAAATAGA
6188437 AAAA-AAAAA
1 AAAATAAAAA
6188446 CTTGCGATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 6 0.24
18 9 0.36
19 10 0.40
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (19 bp):
AAAATAAAAATAAAATAGA
Found at i:6188738 original size:31 final size:31
Alignment explanation
Indices: 6188697--6188772 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
6188687 TGAAATCTTG
* * *
6188697 TCAAAAAATTCAAAGTTTACTAGAAAACTCA
1 TCAAAAAATTCAAAGTTCACAAAAAAACTCA
**
6188728 TTGAAAAATTCAAAGTTCACAAAAAAACTCA
1 TCAAAAAATTCAAAGTTCACAAAAAAACTCA
6188759 TCAAAAAATTCAAA
1 TCAAAAAATTCAAA
6188773 CCTTCAACCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.24
Consensus pattern (31 bp):
TCAAAAAATTCAAAGTTCACAAAAAAACTCA
Found at i:6189286 original size:3 final size:3
Alignment explanation
Indices: 6189278--6189433 Score: 83
Period size: 3 Copynumber: 56.3 Consensus size: 3
6189268 AAATGATAGA
* *
6189278 AAT AAT AAT AAT AAT AAT AAT AGAGT AA- AAT -GT AAT AAA AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT AAT AAT
*
6189322 AAT -AT AAT -AT AAT -AT AAT -AT AAT -AT AAT -AC AAT -AT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** **
6189362 ACT -AT AAT -AT AAT AAT -AT GGT -AT GCT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
6189405 AAT AAT AAT AAT GAT AAAT AAT AAA AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT A
6189434 CTACGAAAAA
Statistics
Matches: 118, Mismatches: 16, Indels: 38
0.69 0.09 0.22
Matches are distributed among these distances:
2 27 0.23
3 85 0.72
4 4 0.03
5 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6189296 original size:15 final size:15
Alignment explanation
Indices: 6189278--6189433 Score: 83
Period size: 13 Copynumber: 11.3 Consensus size: 15
6189268 AAATGATAGA
6189278 AATAATAATAATAAT
1 AATAATAATAATAAT
6189293 AATAATAGAGTAA-AAT
1 AATAATA-A-TAATAAT
* *
6189309 -GTAATAAAAAT-AT
1 AATAATAATAATAAT
6189322 AAT-ATAAT-ATAAT
1 AATAATAATAATAAT
6189335 -ATAAT-ATAAT-AT
1 AATAATAATAATAAT
*
6189347 AAT-ACAAT-ATAAT
1 AATAATAATAATAAT
*
6189360 -ATACT-ATAAT-AT
1 AATAATAATAATAAT
**
6189372 AATAAT-ATGGT-AT
1 AATAATAATAATAAT
**
6189385 GCT-ATAATAATAAT
1 AATAATAATAATAAT
6189399 AATAATAATAATAAT
1 AATAATAATAATAAT
* *
6189414 AATGATAAATAATAAA
1 AATAAT-AATAATAAT
6189430 AATA
1 AATA
6189434 CTACGAAAAA
Statistics
Matches: 105, Mismatches: 19, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
12 19 0.18
13 35 0.33
14 5 0.05
15 28 0.27
16 15 0.14
17 3 0.03
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (15 bp):
AATAATAATAATAAT
Found at i:6189327 original size:5 final size:5
Alignment explanation
Indices: 6189317--6189427 Score: 102
Period size: 5 Copynumber: 21.8 Consensus size: 5
6189307 ATGTAATAAA
* *
6189317 AATAT AATAT AATAT AATAT AATAT AATAT AATAC AATAT AATAT ACTAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
** **
6189367 AATAT -A-AT AATAT GGTAT GCTAT AATAAT AATAAT AATAAT AATAAT
1 AATAT AATAT AATAT AATAT AATAT AAT-AT AAT-AT AAT-AT AAT-AT
6189414 AATGAT AA-AT AATA
1 AAT-AT AATAT AATA
6189428 AAAATACTAC
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
3 2 0.02
4 6 0.07
5 57 0.62
6 27 0.29
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:6189409 original size:18 final size:17
Alignment explanation
Indices: 6189278--6189433 Score: 107
Period size: 15 Copynumber: 9.4 Consensus size: 17
6189268 AAATGATAGA
6189278 AATAATAATAATAATAAT
1 AATAATAATAAT-ATAAT
*
6189296 AATAGAGTAA-AATGTAAT
1 AATA-A-TAATAATATAAT
*
6189314 AAAAAT-ATAATATAAT
1 AATAATAATAATATAAT
6189330 -ATAAT-ATAATATAAT
1 AATAATAATAATATAAT
*
6189345 -ATAAT-ACAATATAAT
1 AATAATAATAATATAAT
*
6189360 -ATACT-ATAATATAAT
1 AATAATAATAATATAAT
* **
6189375 AAT-ATGGTATGCTATAAT
1 AATAAT--AATAATATAAT
6189393 AATAATAATAATAATAAT
1 AATAATAATAAT-ATAAT
*
6189411 AATAATGATAA-ATAAT
1 AATAATAATAATATAAT
*
6189427 AAAAATA
1 AATAATA
6189434 CTACGAAAAA
Statistics
Matches: 113, Mismatches: 16, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
15 43 0.38
16 20 0.18
17 4 0.04
18 37 0.33
19 6 0.05
20 3 0.03
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AATAATAATAATATAAT
Found at i:6192689 original size:59 final size:60
Alignment explanation
Indices: 6192567--6192696 Score: 190
Period size: 59 Copynumber: 2.2 Consensus size: 60
6192557 TTTTTTAGTC
* * **
6192567 AAAATGCCTTTAATAACCCCATTAATTTTTTTTTTGGGATTATTTAAGGCATTTTTGGTGA
1 AAAATGCCTTCAATAACCCCATTAA-TATTTTTTTGGGATTATTTAAGGCATTTTTGACGA
**
6192628 AAAATGCCTTCAATAACCCCATTAA-ATTTTTTTGGGATTATTTAAGGTGTTTTTGACGA
1 AAAATGCCTTCAATAACCCCATTAATATTTTTTTGGGATTATTTAAGGCATTTTTGACGA
6192687 AAAATGCCTT
1 AAAATGCCTT
6192697 GAGTAATCAC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 39 0.62
61 24 0.38
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (60 bp):
AAAATGCCTTCAATAACCCCATTAATATTTTTTTGGGATTATTTAAGGCATTTTTGACGA
Found at i:6192789 original size:35 final size:35
Alignment explanation
Indices: 6192750--6192816 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
6192740 ATTTTTCACC
6192750 AAAAACACCTTGAATAACCCCAAAAAAAATTTCAT
1 AAAAACACCTTGAATAACCCCAAAAAAAATTTCAT
* * **
6192785 AAAAACGCCTTGATTAACCCCATTAAAAATTT
1 AAAAACACCTTGAATAACCCCAAAAAAAATTT
6192817 TTTCGGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.24
Consensus pattern (35 bp):
AAAAACACCTTGAATAACCCCAAAAAAAATTTCAT
Found at i:6193027 original size:64 final size:64
Alignment explanation
Indices: 6192954--6193259 Score: 232
Period size: 64 Copynumber: 4.8 Consensus size: 64
6192944 GCAAAAAACA
* *
6192954 CCTTAAATAATCCCCTCATAAATTTTTATGATGTGATTACTCAAGGCGTTTTTGGAGAAAAATG
1 CCTTAAATAATCCCCTCATAAATTTTTATGACGTGATTACTCAAGGCGTTTTTGGAAAAAAATG
* * * * * * **
6193018 CCTTGAATAAT--CCTAAAAAAATTTTTAATG--G-GGTTATTGAAGGCGTTTTTGGCTAAAAAT
1 CCTTAAATAATCCCCT-CATAAATTTTT-ATGACGTGATTACTCAAGGCGTTTTTGGAAAAAAAT
6193078 G
64 G
* * * * * * *
6193079 CCTTCAATAATCCCCTCATAAATGTTTATGACATGATTAATCAAGGCGTTTTT-CACCAAAAACG
1 CCTTAAATAATCCCCTCATAAATTTTTATGACGTGATTACTCAAGGCGTTTTTGGA-AAAAAATG
**** * * * * * *
6193143 CCTTAAATAATCCTAAAAAAAATTTTTA--ACGAGGTTATTGAAGGTGTTTTTGGTAAAAAAAAT
1 CCTTAAATAATCCCCTCATAAATTTTTATGACGTGATTACTCAAGGCGTTTTTGG--AAAAAAAT
6193206 G
64 G
* * * *
6193207 CTTTTAATAATCCCCTCATAAATTTTTATGACATGATTACTCAAGGCATTTTT
1 CCTTAAATAATCCCCTCATAAATTTTTATGACGTGATTACTCAAGGCGTTTTT
6193260 TGTCAAAAAA
Statistics
Matches: 179, Mismatches: 50, Indels: 24
0.71 0.20 0.09
Matches are distributed among these distances:
61 38 0.21
62 29 0.16
63 12 0.07
64 83 0.46
65 1 0.01
66 16 0.09
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (64 bp):
CCTTAAATAATCCCCTCATAAATTTTTATGACGTGATTACTCAAGGCGTTTTTGGAAAAAAATG
Found at i:6193129 original size:125 final size:126
Alignment explanation
Indices: 6192906--6193259 Score: 435
Period size: 125 Copynumber: 2.8 Consensus size: 126
6192896 AGGCGTTTCC
* * * * * * * **
6192906 AAAAAAAGTTTTTAATAGGGTTGTTGAAAGTGTTTCTAGCAAAAAACACCTTAAATAATCCCCTC
1 AAAAAAAATTTTTAATGGGGTTATTGAAGGTGTTTTTGGCTAAAAATGCCTTAAATAATCCCCTC
** * * * *
6192971 ATAAATTTTTATGATGTGATTACTCAAGGCGTTTTTGGA-GAAAAATGCCTTGAATAATCCT
66 ATAAATTTTTATGACATGATTACTCAAGGCGTTTTT-CACCAAAAACGCCTTAAATAATCCT
* *
6193032 -AAAAAAATTTTTAATGGGGTTATTGAAGGCGTTTTTGGCTAAAAATGCCTTCAATAATCCCCTC
1 AAAAAAAATTTTTAATGGGGTTATTGAAGGTGTTTTTGGCTAAAAATGCCTTAAATAATCCCCTC
* *
6193096 ATAAATGTTTATGACATGATTAATCAAGGCGTTTTTCACCAAAAACGCCTTAAATAATCCT
66 ATAAATTTTTATGACATGATTACTCAAGGCGTTTTTCACCAAAAACGCCTTAAATAATCCT
* * * *
6193157 AAAAAAAATTTTTAACGAGGTTATTGAAGGTGTTTTTGG-TAAAAAAAATGCTTTTAATAATCCC
1 AAAAAAAATTTTTAATGGGGTTATTGAAGGTGTTTTTGGCT---AAAAATGCCTTAAATAATCCC
*
6193221 CTCATAAATTTTTATGACATGATTACTCAAGGCATTTTT
63 CTCATAAATTTTTATGACATGATTACTCAAGGCGTTTTT
6193260 TGTCAAAAAA
Statistics
Matches: 196, Mismatches: 27, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
124 1 0.01
125 105 0.54
126 35 0.18
128 55 0.28
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (126 bp):
AAAAAAAATTTTTAATGGGGTTATTGAAGGTGTTTTTGGCTAAAAATGCCTTAAATAATCCCCTC
ATAAATTTTTATGACATGATTACTCAAGGCGTTTTTCACCAAAAACGCCTTAAATAATCCT
Found at i:6196349 original size:19 final size:19
Alignment explanation
Indices: 6196325--6196362 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
6196315 TGCTATTGCA
*
6196325 TTGGTATTTTGATAACTTT
1 TTGGTAATTTGATAACTTT
6196344 TTGGTAATTTGATAACTTT
1 TTGGTAATTTGATAACTTT
6196363 AGAATGATGT
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:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (19 bp):
TTGGTAATTTGATAACTTT
Found at i:6202202 original size:17 final size:17
Alignment explanation
Indices: 6202182--6202242 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
6202172 AGTTGGCAAA
*
6202182 ATATTTGTTTTTAAAAG
1 ATATGTGTTTTTAAAAG
*
6202199 ATATGTGTTATTAGCAAA-
1 ATATGTGTTTTTA--AAAG
* *
6202217 ATATTTGTTTTTAAAGG
1 ATATGTGTTTTTAAAAG
6202234 ATATGTGTT
1 ATATGTGTT
6202243 ATTAGTTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 2 0.06
17 19 0.54
18 11 0.31
19 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (17 bp):
ATATGTGTTTTTAAAAG
Found at i:6202260 original size:35 final size:35
Alignment explanation
Indices: 6202177--6202247 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
6202167 TTTTGAGTTG
6202177 GCAAAATATTTGTTTTTAAAAGATATGTGTTATTA
1 GCAAAATATTTGTTTTTAAAAGATATGTGTTATTA
*
6202212 GCAAAATATTTGTTTTTAAAGGATATGTGTTATTA
1 GCAAAATATTTGTTTTTAAAAGATATGTGTTATTA
6202247 G
1 G
6202248 TTCATCTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (35 bp):
GCAAAATATTTGTTTTTAAAAGATATGTGTTATTA
Found at i:6203436 original size:23 final size:23
Alignment explanation
Indices: 6203410--6203454 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6203400 TGAAATATAT
6203410 GATTAAATAC-TTGCATATGTTTG
1 GATTAAATACATTGC-TATGTTTG
*
6203433 GATTAAGTACATTGCTATGTTT
1 GATTAAATACATTGCTATGTTT
6203455 TAAAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (23 bp):
GATTAAATACATTGCTATGTTTG
Found at i:6204716 original size:21 final size:22
Alignment explanation
Indices: 6204691--6204732 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6204681 AAAATGATTT
6204691 TTGAAAGC-A-TTGTCAAAACCA
1 TTGAAAGCTACTT-TCAAAACCA
6204712 TTGAAAGCTACTTTCAAAACC
1 TTGAAAGCTACTTTCAAAACC
6204733 CTAAAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 9 0.47
23 2 0.11
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (22 bp):
TTGAAAGCTACTTTCAAAACCA
Found at i:6207379 original size:24 final size:24
Alignment explanation
Indices: 6207318--6207380 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
6207308 CTACATTTTT
* * *
6207318 TTCAGTGGCAATATCCGAATTCTC
1 TTCAATGGCAATATTCGAATTCTA
**
6207342 TTCAATGGTGATATTCG-ATCTCTA
1 TTCAATGGCAATATTCGAAT-TCTA
6207366 TTCAATGGCAATATT
1 TTCAATGGCAATATT
6207381 TGAAGTCATC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 2 0.06
24 29 0.94
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (24 bp):
TTCAATGGCAATATTCGAATTCTA
Found at i:6207762 original size:24 final size:24
Alignment explanation
Indices: 6207735--6207798 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
6207725 CATTTGCATT
*
6207735 TTTTCGGTAGTAATATTTAAGTTC
1 TTTTCGATAGTAATATTTAAGTTC
* * *
6207759 TTTTTGATAGTGATATTTGAGTTC
1 TTTTCGATAGTAATATTTAAGTTC
* * *
6207783 TCTTCAATAGTGATAT
1 TTTTCGATAGTAATAT
6207799 CCAAAGTCGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (24 bp):
TTTTCGATAGTAATATTTAAGTTC
Found at i:6208473 original size:15 final size:14
Alignment explanation
Indices: 6208452--6208486 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
6208442 ATTCCAAAAA
6208452 AAAAATCAAAATTT
1 AAAAATCAAAATTT
6208466 AGAAAATCAAAATTT
1 A-AAAATCAAAATTT
6208481 AAAAAT
1 AAAAAT
6208487 TTAAACAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAAATCAAAATTT
Found at i:6208477 original size:23 final size:23
Alignment explanation
Indices: 6208451--6208507 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
6208441 AATTCCAAAA
6208451 AAAAAATCAAAATTTAGAA-AATC
1 AAAAAATCAAAATTTA-AACAATC
** *
6208474 AAAATTTAAAAATTTAAACAATC
1 AAAAAATCAAAATTTAAACAATC
*
6208497 TAAAAA-CAAAA
1 AAAAAATCAAAA
6208508 AATTAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAAAATCAAAATTTAAACAATC
Found at i:6211421 original size:11 final size:11
Alignment explanation
Indices: 6211402--6211440 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6211392 AAACTCATCA
6211402 GTTTATTATTC
1 GTTTATTATTC
*
6211413 GTTTGTTATTC
1 GTTTATTATTC
* *
6211424 TTTTATTGTTC
1 GTTTATTATTC
6211435 GTTTAT
1 GTTTAT
6211441 AATAATATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.67
Consensus pattern (11 bp):
GTTTATTATTC
Found at i:6219026 original size:21 final size:22
Alignment explanation
Indices: 6218987--6219028 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
6218977 AAGTTTTAGC
**
6218987 AGAGAGAAGAAAACGAAAGAAA
1 AGAGAGAAGAAAAAAAAAGAAA
6219009 AGAG-GAAGAAAAAAAAAGAA
1 AGAGAGAAGAAAAAAAAAGAA
6219029 GAAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.71, C:0.02, G:0.26, T:0.00
Consensus pattern (22 bp):
AGAGAGAAGAAAAAAAAAGAAA
Found at i:6219027 original size:16 final size:15
Alignment explanation
Indices: 6218991--6219043 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 15
6218981 TTTAGCAGAG
6218991 AGAAGAAAACGAAAGAAA
1 AGAAGAAAA--AAA-AAA
*
6219009 AGAGGAAGAAAAAAAA
1 AGAAGAA-AAAAAAAA
6219025 AGAAG-AAAAAAAAA
1 AGAAGAAAAAAAAAA
6219039 AGAAG
1 AGAAG
6219044 TTTAGATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 13 0.41
15 1 0.03
16 7 0.22
17 3 0.09
18 6 0.19
19 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (15 bp):
AGAAGAAAAAAAAAA
Found at i:6221050 original size:24 final size:24
Alignment explanation
Indices: 6221009--6221055 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
6220999 ATTTGCATTT
*
6221009 TTGTTTATTTATGTCATTCTTTAC
1 TTGTTTAATTATGTCATTCTTTAC
*
6221033 TTGTGTTAATTATG-CATTTTTTA
1 TTGT-TTAATTATGTCATTCTTTA
6221056 TCCAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.19, C:0.09, G:0.11, T:0.62
Consensus pattern (24 bp):
TTGTTTAATTATGTCATTCTTTAC
Found at i:6224861 original size:18 final size:18
Alignment explanation
Indices: 6224838--6224897 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
6224828 AAAAAACATC
*
6224838 TTTAAAATTTTAAAATTT
1 TTTAAAATTTTAAAATAT
* *
6224856 TTTAAAAATTAAAAATAT
1 TTTAAAATTTTAAAATAT
* *
6224874 TCT-AAATTTTGAAATAT
1 TTTAAAATTTTAAAATAT
6224891 TTTAAAA
1 TTTAAAA
6224898 AATTATAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
17 13 0.39
18 20 0.61
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
TTTAAAATTTTAAAATAT
Found at i:6225052 original size:20 final size:20
Alignment explanation
Indices: 6225014--6225052 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6225004 ATTTTTAAAA
* * *
6225014 AATATTTTATAATATATTTT
1 AATATTTTAAAAAAAATTTT
6225034 AATATTTTAAAAAAAATTT
1 AATATTTTAAAAAAAATTT
6225053 AGATTTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATTTTAAAAAAAATTTT
Found at i:6225094 original size:20 final size:21
Alignment explanation
Indices: 6225071--6225118 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
6225061 TTATTTTCAA
*
6225071 TTTTTTAAGTTT-AGGAAATT
1 TTTTTTAAGTTTAAGAAAATT
* *
6225091 TTTTTGAATTTTAAGAAAATT
1 TTTTTTAAGTTTAAGAAAATT
6225112 TTATTTT
1 TT-TTTT
6225119 TATTAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 10 0.45
21 9 0.41
22 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.58
Consensus pattern (21 bp):
TTTTTTAAGTTTAAGAAAATT
Found at i:6225188 original size:20 final size:19
Alignment explanation
Indices: 6225113--6225188 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 19
6225103 AAGAAAATTT
* *
6225113 TATTTTTATTAAACTATT-
1 TATTTTTATTAAATTTTTA
* *
6225131 TATTTTTAATGAATTTTTCA
1 TATTTTTATTAAATTTTT-A
* *
6225151 TATTCTTTTTTAATTTTTTA
1 TATT-TTTATTAAATTTTTA
*
6225171 TATTTTTATTAAAATTTT
1 TATTTTTATTAAATTTTT
6225189 GAAGGTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
18 14 0.32
19 11 0.25
20 9 0.20
21 10 0.23
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (19 bp):
TATTTTTATTAAATTTTTA
Found at i:6225215 original size:19 final size:19
Alignment explanation
Indices: 6225156--6225216 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
6225146 TTTCATATTC
*
6225156 TTTTTTAATTTTTTATA-TT
1 TTTTTTAA-TTTTTAAAGTT
* * *
6225175 TTTATTAAAATTTTGAAGGTT
1 TTT-TT-TAATTTTTAAAGTT
6225196 TTTTTTAATTTTTAAAGTT
1 TTTTTTAATTTTTAAAGTT
6225215 TT
1 TT
6225217 CATAATTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 16 0.50
20 9 0.28
21 7 0.22
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTTTTAATTTTTAAAGTT
Found at i:6225234 original size:8 final size:8
Alignment explanation
Indices: 6225196--6225262 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
6225186 TTTGAAGGTT
6225196 TTTTTTAA
1 TTTTTTAA
*
6225204 TTTTTAAA
1 TTTTTTAA
*
6225212 GTTTTCATAA
1 -TTTT-TTAA
6225222 TTTTTTTAA
1 -TTTTTTAA
6225231 TTTTTTAAA
1 TTTTTT-AA
*
6225240 TATTTTAGA
1 TTTTTTA-A
6225249 -TTTTTAA
1 TTTTTTAA
6225256 TTTTTTA
1 TTTTTTA
6225263 TAATATTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
7 1 0.02
8 25 0.53
9 15 0.32
10 6 0.13
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.67
Consensus pattern (8 bp):
TTTTTTAA
Found at i:6225251 original size:27 final size:26
Alignment explanation
Indices: 6225158--6225273 Score: 89
Period size: 28 Copynumber: 4.2 Consensus size: 26
6225148 TCATATTCTT
*
6225158 TTTTAATTTTTTATATTTTTATTAAA-A
1 TTTTAATTTTTT-TAATTTT-TTAAATA
6225185 TTTTGAAGGTTTTTTTTAA-TTTTTAAAGT-
1 TTTT-AA---TTTTTTTAATTTTTTAAA-TA
6225214 TTTCATAATTTTTTTAATTTTTTAAATA
1 TTT--TAATTTTTTTAATTTTTTAAATA
6225242 TTTTAGA--TTTTTAATTTTTTATAATA
1 TTTTA-ATTTTTTTAATTTTTTA-AATA
6225268 TTTTAA
1 TTTTAA
6225274 AATATTTCAT
Statistics
Matches: 76, Mismatches: 1, Indels: 26
0.74 0.01 0.25
Matches are distributed among these distances:
25 15 0.20
26 11 0.14
27 15 0.20
28 18 0.24
29 6 0.08
30 4 0.05
31 7 0.09
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTAATTTTTTTAATTTTTTAAATA
Found at i:6225261 original size:25 final size:26
Alignment explanation
Indices: 6225224--6225272 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
6225214 TTTCATAATT
6225224 TTTTTAATTTTTTA-AATATTTTAGA
1 TTTTTAATTTTTTATAATATTTTAGA
6225249 TTTTTAATTTTTTATAATATTTTA
1 TTTTTAATTTTTTATAATATTTTA
6225273 AAATATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTTTAATTTTTTATAATATTTTAGA
Found at i:6225290 original size:35 final size:34
Alignment explanation
Indices: 6225219--6225288 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 34
6225209 AAAGTTTTCA
* *
6225219 TAATTTTTTTAATTTTTTAAATATTTTAGATTTT
1 TAATTTTTTTAATTTTTAAAATATTTCAGATTTT
*
6225253 TAATTTTTTATAATATTTTAAAATATTTCATATTTT
1 TAATTTTTT-TAAT-TTTTAAAATATTTCAGATTTT
6225289 AAAATGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 9 0.29
35 4 0.13
36 18 0.58
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (34 bp):
TAATTTTTTTAATTTTTAAAATATTTCAGATTTT
Found at i:6225298 original size:27 final size:26
Alignment explanation
Indices: 6225230--6225334 Score: 77
Period size: 26 Copynumber: 4.0 Consensus size: 26
6225220 AATTTTTTTA
* * * *
6225230 ATTTTTTAAATATTTT-AGATTTTTA
1 ATTTTTAAAATATTTTAAAATATTTC
*
6225255 ATTTTTTATAATATTTTAAAATATTTC
1 A-TTTTTAAAATATTTTAAAATATTTC
* * * *
6225282 ATATTTTAAAATGTTTTTCAATTATTTG
1 AT-TTTTAAAAT-ATTTTAAAATATTTC
* *
6225310 ATTTTTAAAATTTTTTAAAAAATTT
1 ATTTTTAAAATATTTTAAAATATTT
6225335 TTTTAATACT
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
25 1 0.02
26 25 0.40
27 24 0.38
28 13 0.21
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (26 bp):
ATTTTTAAAATATTTTAAAATATTTC
Found at i:6235643 original size:30 final size:31
Alignment explanation
Indices: 6235604--6235669 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
6235594 TTTAAATCAT
* *
6235604 ATTTTGTTATTGC-T-TTTTCAATTGATTTTA
1 ATTTAGTTATTGCATATTTACAATT-ATTTTA
*
6235634 ATTTAGTTATTGCATATTTACAGTTATTTTA
1 ATTTAGTTATTGCATATTTACAATTATTTTA
6235665 ATTTA
1 ATTTA
6235670 ATTTAGGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 12 0.39
31 12 0.39
32 7 0.23
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (31 bp):
ATTTAGTTATTGCATATTTACAATTATTTTA
Found at i:6236154 original size:15 final size:15
Alignment explanation
Indices: 6236116--6236167 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
6236106 TTTTGGATAG
6236116 ATTTTAG-TTA-TTT
1 ATTTTAGTTTAGTTT
*
6236129 GATTCTAGTTTAGTTT
1 -ATTTTAGTTTAGTTT
*
6236145 ATTTTAGTTTGGTTT
1 ATTTTAGTTTAGTTT
*
6236160 ATATTAGT
1 ATTTTAGT
6236168 ATTGTATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 6 0.19
15 23 0.72
16 3 0.09
ACGTcount: A:0.21, C:0.02, G:0.15, T:0.62
Consensus pattern (15 bp):
ATTTTAGTTTAGTTT
Found at i:6243855 original size:13 final size:13
Alignment explanation
Indices: 6243837--6243861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6243827 TTTCCATGCA
6243837 TGTTTCATTATTT
1 TGTTTCATTATTT
6243850 TGTTTCATTATT
1 TGTTTCATTATT
6243862 GTTATATTTA
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (13 bp):
TGTTTCATTATTT
Found at i:6244043 original size:20 final size:20
Alignment explanation
Indices: 6244010--6244048 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
6244000 TTACTTTTAT
6244010 TTCTTTTTATATTTATATTTC
1 TTCTTTTTATATTTA-ATTTC
6244031 TTCTTTTTA-ATTTAATTT
1 TTCTTTTTATATTTAATTT
6244049 AGTTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (20 bp):
TTCTTTTTATATTTAATTTC
Found at i:6245957 original size:10 final size:10
Alignment explanation
Indices: 6245944--6245973 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6245934 TTTTAAAAAG
6245944 AAAAAAC-AA
1 AAAAAACAAA
6245953 AAAAAACAAA
1 AAAAAACAAA
6245963 AAAAAACAAA
1 AAAAAACAAA
6245973 A
1 A
6245974 TTTCAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.35
10 13 0.65
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:6245993 original size:8 final size:9
Alignment explanation
Indices: 6245944--6245973 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
6245934 TTTTAAAAAG
6245944 AAAAAACAA
1 AAAAAACAA
6245953 AAAAAACAAA
1 AAAAAAC-AA
6245963 AAAAAACAA
1 AAAAAACAA
6245972 AA
1 AA
6245974 TTTCAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:6247041 original size:26 final size:29
Alignment explanation
Indices: 6247011--6247075 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 29
6247001 AAATAAATAA
6247011 ATAAAA-ACAACAAAAA-A-AAAATATAG
1 ATAAAATACAACAAAAATATAAAATATAG
* *
6247037 ATAAAATA-AACAAAAATATAAAATTTTG
1 ATAAAATACAACAAAAATATAAAATATAG
6247065 ATAAAATACAA
1 ATAAAATACAA
6247076 ACTTCAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 14 0.42
27 2 0.06
28 15 0.45
29 2 0.06
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (29 bp):
ATAAAATACAACAAAAATATAAAATATAG
Found at i:6248242 original size:23 final size:22
Alignment explanation
Indices: 6248207--6248269 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
6248197 AAAACTATTG
* *
6248207 AAAAAAATTAAAAACAAAAATA
1 AAAAAAATCAAAAAAAAAAATA
6248229 AAAAGAAATCAAAAAAAAAAA-A
1 AAAA-AAATCAAAAAAAAAAATA
**
6248251 ACAAAATTTCAAAAAAAAA
1 A-AAAAAATCAAAAAAAAA
6248270 TTATAGAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.81, C:0.06, G:0.02, T:0.11
Consensus pattern (22 bp):
AAAAAAATCAAAAAAAAAAATA
Found at i:6248245 original size:14 final size:14
Alignment explanation
Indices: 6248216--6248256 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 14
6248206 GAAAAAAATT
6248216 AAAAACAAAAATAAA
1 AAAAACAAAAA-AAA
6248231 AAGAAATCAAAAAAAA
1 AA-AAA-CAAAAAAAA
6248247 AAAAACAAAA
1 AAAAACAAAA
6248257 TTTCAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.21
15 5 0.21
16 8 0.33
17 6 0.25
ACGTcount: A:0.85, C:0.07, G:0.02, T:0.05
Consensus pattern (14 bp):
AAAAACAAAAAAAA
Found at i:6254441 original size:59 final size:58
Alignment explanation
Indices: 6254378--6254776 Score: 387
Period size: 59 Copynumber: 6.8 Consensus size: 58
6254368 TTGTACAAGA
* * **
6254378 AAAAATTGATACTTTTAACTTTTTTTCAAAATATTTATTTTTGAAATTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTTTTCAAAATATTT-TTTTTGAAAATTTAATTTTAAG
* * * * *
6254437 AAAAATTAATACTTTCAACTTTTCTTCAAAAAATTTTTTCTTGAGAATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTTTCAAAATATTTTTT-TTGAAAATTTAATTTTAAG
* * *
6254496 AAAAATTGATACTTTCAA-TTTTTTTAAAAAAATATTTTTTTGGAAAACTTTAATTTTGAG
1 AAAAATTGATACTTTCAACTTTTTTT--CAAAATATTTTTTTTGAAAA-TTTAATTTTAAG
* ** * *
6254556 AAAAATTGATGCTTTCAA-TTTTTACTAAAAAAAAAAATTTTTTTGAAAATTT-ATTTCTAAG
1 AAAAATTGATACTTTCAACTTTTT--T--TCAAAATATTTTTTTTGAAAATTTAATTT-TAAG
* * * * * * *
6254617 GAAAATTGATACTTTTAACTTTTTCTCAAAAAAATTTCTCTTGAAAATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTTTC-AAAATATTTTTTTTGAAAATTTAATTTTAAG
* **
6254676 AAAAATTGATAATTTCAA-TTTTTTCTCAAAAT-TTTTTTTT-AAAATTTACCTTTAAG
1 AAAAATTGATACTTTCAACTTTTTT-TCAAAATATTTTTTTTGAAAATTTAATTTTAAG
*
6254732 AAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTTTGAA
1 AAAAATTGATACTTTCAACTTTTTTTC-AAAATATTTTTTTTGAA
6254777 TTATTTTAAA
Statistics
Matches: 279, Mismatches: 44, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
56 33 0.12
57 16 0.06
58 26 0.09
59 110 0.39
60 50 0.18
61 21 0.08
62 23 0.08
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTTTTCAAAATATTTTTTTTGAAAATTTAATTTTAAG
Found at i:6255172 original size:21 final size:22
Alignment explanation
Indices: 6255135--6255178 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
6255125 TTCAGCAGAA
6255135 CCCTTCTTCTCTTCTCTCTTTT
1 CCCTTCTTCTCTTCTCTCTTTT
*
6255157 CCCTTCTT-TTTTCTCTCTTTT
1 CCCTTCTTCTCTTCTCTCTTTT
6255178 C
1 C
6255179 TCTTTAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (22 bp):
CCCTTCTTCTCTTCTCTCTTTT
Found at i:6255793 original size:16 final size:14
Alignment explanation
Indices: 6255764--6255803 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
6255754 ATAAATTAAC
6255764 AATAATAATAGATA
1 AATAATAATAGATA
6255778 AATATATAACTAGATA
1 AATA-ATAA-TAGATA
*
6255794 AATAAAAATA
1 AATAATAATA
6255804 TATATATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 6 0.26
15 7 0.30
16 10 0.43
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (14 bp):
AATAATAATAGATA
Found at i:6255853 original size:15 final size:14
Alignment explanation
Indices: 6255833--6255864 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
6255823 AAAAGAAAGA
6255833 AAAAAAATAACAAAT
1 AAAAAAATAA-AAAT
6255848 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
6255862 AAA
1 AAA
6255865 GATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:6255925 original size:15 final size:15
Alignment explanation
Indices: 6255837--6255917 Score: 56
Period size: 15 Copynumber: 5.1 Consensus size: 15
6255827 GAAAGAAAAA
*
6255837 AAATAACAAATAAAA
1 AAATAACAAATAAAT
6255852 AAATAA-AAATAAAGAT
1 AAATAACAAAT-AA-AT
* **
6255868 ATATATATTAATAAAT
1 AAATA-ACAAATAAAT
*
6255884 AGTAATAATAAATAAAT
1 A--AATAACAAATAAAT
*
6255901 AAATAACAAATACAT
1 AAATAACAAATAAAT
6255916 AA
1 AA
6255918 GATACAAAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
14 4 0.08
15 22 0.42
16 8 0.15
17 13 0.25
18 6 0.11
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (15 bp):
AAATAACAAATAAAT
Found at i:6255948 original size:7 final size:7
Alignment explanation
Indices: 6255936--6255973 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
6255926 AGGAAAATAT
6255936 ATATAAA
1 ATATAAA
6255943 ATATAAA
1 ATATAAA
*
6255950 ATA-ATA
1 ATATAAA
6255956 ATAATAAA
1 AT-ATAAA
6255964 ATATAAA
1 ATATAAA
6255971 ATA
1 ATA
6255974 CAACATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 4 0.15
7 19 0.70
8 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATATAAA
Found at i:6256268 original size:42 final size:42
Alignment explanation
Indices: 6256169--6256374 Score: 229
Period size: 42 Copynumber: 4.8 Consensus size: 42
6256159 TTTGATCAAG
* * *
6256169 GCTCCTCTAAGCAGAGGCTCAACAACTTTGAAAAACATAAACAAT
1 GCTCCTCTAATCAGAGGCTCAACGACTTT-AAAAACA-ATA-AAT
*
6256214 GCTCCTCTAATCAGATGCTCAACGACTTTAAAAACGAATAAA-
1 GCTCCTCTAATCAGAGGCTCAACGACTTTAAAAAC-AATAAAT
* * * *
6256256 GCTCCTCTAATCAGAGGTTCAATGACTTTGAAAAATAA-ATAAG
1 GCTCCTCTAATCAGAGGCTCAACGACTTT-AAAAACAATA-AAT
* *
6256299 GCTCTTCTAATCAGAGGCTCAACGACTTTTAAAA-AATAAAT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTAAAAACAATAAAT
*
6256340 GGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAA
1 -GCTCCTCTAATCAGAGGCTCAACGACTTTAAAAA
6256375 GTAAATGGCT
Statistics
Matches: 140, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
41 5 0.04
42 67 0.48
43 33 0.24
44 8 0.06
45 27 0.19
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.25
Consensus pattern (42 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTAAAAACAATAAAT
Found at i:6256326 original size:85 final size:84
Alignment explanation
Indices: 6256166--6256380 Score: 288
Period size: 85 Copynumber: 2.5 Consensus size: 84
6256156 AGATTTGATC
* * * * *
6256166 AAGGCTCCTCTAAGCAGAGGCTCAACAACTTTGAAAAACATAAACAATGCTCCTCTAATCAGATG
1 AAGGCTCCTCTAATCAGAGGCTCAACGACTTTG-AAAA-ATAAATAAGGCTCCTCTAATCAGAGG
6256231 CTCAACGACTTTAAAAACGAATA
64 CTCAACGACTTTAAAAA--AATA
* * *
6256254 AA-GCTCCTCTAATCAGAGGTTCAATGACTTTGAAAAATAAATAAGGCTCTTCTAATCAGAGGCT
1 AAGGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAGGCTCCTCTAATCAGAGGCT
*
6256318 CAACGACTTTTAAAAAATA
66 CAACGACTTTAAAAAAATA
*
6256337 AATGGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAAT
1 AA-GGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAAT
6256381 GGCTCATTGA
Statistics
Matches: 113, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
83 6 0.05
85 75 0.66
86 4 0.04
87 26 0.23
88 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (84 bp):
AAGGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAGGCTCCTCTAATCAGAGGCT
CAACGACTTTAAAAAAATA
Found at i:6257376 original size:11 final size:11
Alignment explanation
Indices: 6257362--6257417 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
6257352 TTTTCATTCA
6257362 TTTTTTTTCTT
1 TTTTTTTTCTT
*
6257373 TTTTTTTTCAT
1 TTTTTTTTCTT
**
6257384 TTTCATTTCTT
1 TTTTTTTTCTT
*
6257395 TTTTCTTT-TT
1 TTTTTTTTCTT
* *
6257405 TTTCTTTTATT
1 TTTTTTTTCTT
6257416 TT
1 TT
6257418 AAGCATAGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
10 8 0.22
11 28 0.78
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:6257416 original size:25 final size:25
Alignment explanation
Indices: 6257351--6257417 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
6257341 TGAGTCCTCC
* * *
6257351 TTTTTCATTCATTTTTTTTCTTTTT
1 TTTTTCTTTTATTTTTTTTCTCTTT
6257376 TTTTTCATTTTCATTTCTTTTT-TCTTT
1 TTTTTC-TTTT-ATTT-TTTTTCTCTTT
6257403 TTTTTCTTTTATTTT
1 TTTTTCTTTTATTTT
6257418 AAGCATAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
24 1 0.03
25 10 0.28
26 6 0.17
27 14 0.39
28 5 0.14
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTTCTTTTATTTTTTTTCTCTTT
Found at i:6265233 original size:19 final size:19
Alignment explanation
Indices: 6265194--6265229 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6265184 GAATGACATA
6265194 ATTAATAAAGTAAATAAAC
1 ATTAATAAAGTAAATAAAC
*
6265213 ATTAATGAA-TAAATAAA
1 ATTAATAAAGTAAATAAA
6265230 ACATATACAA
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:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (19 bp):
ATTAATAAAGTAAATAAAC
Found at i:6265961 original size:61 final size:61
Alignment explanation
Indices: 6265799--6265965 Score: 223
Period size: 60 Copynumber: 2.8 Consensus size: 61
6265789 TGTACAAGGG
** * *** *
6265799 AAAATTGATACTTTCAACTTTTCTTAAAAAAAAAACTTTTTTTGAAAATTTATTTCTAAGA
1 AAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTTTTTGAAAATTTACTTCTAAGA
*
6265860 AAAATTGATACTTTCAACTTTTCCTC--AAAATTTTTTTTTTTTGAAAATTTACCTT-TAAGA
1 AAAATTGATACTTTCAACTTTTCC-CAAAAAATATTTTTTTTTTGAAAATTTA-CTTCTAAGA
6265920 AAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTTTTTGAA
1 AAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTTTTTGAA
6265966 TTTTTTTAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
59 1 0.01
60 49 0.53
61 43 0.46
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.46
Consensus pattern (61 bp):
AAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTTTTTGAAAATTTACTTCTAAGA
Found at i:6265991 original size:16 final size:17
Alignment explanation
Indices: 6265972--6266040 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 17
6265962 TGAATTTTTT
6265972 TAAAA-AAATAATAAAA
1 TAAAATAAATAATAAAA
*
6265988 TAAAATAAACAAAGTAAAAA
1 TAAAATAAA-TAA-T-AAAA
6266008 TGAAAATAAATAA-AAAGA
1 T-AAAATAAATAATAAA-A
6266026 T-AAATAAA-AATAAAA
1 TAAAATAAATAATAAAA
6266041 ATATTAAACA
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
15 3 0.07
16 15 0.34
17 6 0.14
18 4 0.09
19 1 0.02
20 7 0.16
21 8 0.18
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.17
Consensus pattern (17 bp):
TAAAATAAATAATAAAA
Found at i:6266392 original size:21 final size:22
Alignment explanation
Indices: 6266357--6266400 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
6266347 TTCAGCAGAA
*
6266357 CCCTTCTTCTCTTCTCTCTCTT
1 CCCTTCTTCTCTTCTCTCCCTT
6266379 CCCTTCTT-TCTTCTCTCCCTT
1 CCCTTCTTCTCTTCTCTCCCTT
6266400 C
1 C
6266401 TCTCTAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (22 bp):
CCCTTCTTCTCTTCTCTCCCTT
Found at i:6266594 original size:31 final size:31
Alignment explanation
Indices: 6266536--6266594 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
6266526 TGGGCAGCTA
*
6266536 ACCAAAAAATTCAAACTTGGTCAAAAAAGTC
1 ACCAAAAAATTCAAACTTCGTCAAAAAAGTC
* *
6266567 ACCAAAAAATT-TAACTTTCGTCGAAAAA
1 ACCAAAAAATTCAAAC-TTCGTCAAAAAA
6266595 TTCAACCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.22
Consensus pattern (31 bp):
ACCAAAAAATTCAAACTTCGTCAAAAAAGTC
Found at i:6267041 original size:21 final size:20
Alignment explanation
Indices: 6266937--6267045 Score: 69
Period size: 21 Copynumber: 5.2 Consensus size: 20
6266927 AACCGAAAAA
* * *
6266937 AAATCAAAAAAATAAAAAATT
1 AAATTAAAAAAATAATAGA-T
*
6266958 AAA-TAAAAAATATTAATATAT
1 AAATTAAAAAA-A-TAATAGAT
*
6266979 -AATTAAATGAAGATAATCAGAT
1 AAATTAAA--AAAATAAT-AGAT
* * *
6267001 AAACTAAAAAATTAACAGAT
1 AAATTAAAAAAATAATAGAT
6267021 AAATTAACAAAAATAATAGAT
1 AAATTAA-AAAAATAATAGAT
6267042 AAAT
1 AAAT
6267046 ATATAACTAG
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
20 18 0.26
21 33 0.49
22 9 0.13
23 8 0.12
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (20 bp):
AAATTAAAAAAATAATAGAT
Found at i:6267058 original size:16 final size:15
Alignment explanation
Indices: 6267033--6267062 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6267023 ATTAACAAAA
6267033 ATAATAGATAAATAT
1 ATAATAGATAAATAT
6267048 ATAACTAGATAAATA
1 ATAA-TAGATAAATA
6267063 AAAATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (15 bp):
ATAATAGATAAATAT
Found at i:6267114 original size:6 final size:6
Alignment explanation
Indices: 6267098--6267252 Score: 64
Period size: 7 Copynumber: 24.0 Consensus size: 6
6267088 AAGAAAGAAA
* * **
6267098 AAAAAT AAAAAAT AAAAAAT AAAAAT AAAAAT ATATATT AATAAAT AGTAAT
1 AAAAAT -AAAAAT -AAAAAT AAAAAT AAAAAT A-AAAAT AA-AAAT AAAAAT
* * * *
6267150 AATAAAT AAATAAAT AACAAAT ACATAAGAT ACAAAG AAAAAT ATATAT
1 AA-AAAT -AA-AAAT AA-AAAT A-A-AA-AT AAAAAT AAAAAT AAAAAT
* * *
6267199 -AAAAT ATAAAAT AATAAT -AAAA- AAAAAT ATAAAAT ACAACAT AAAAGT
1 AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT A-AAAAT A-AAAAT AAAAAT
6267247 AAAAAT
1 AAAAAT
6267253 TAGGCATACT
Statistics
Matches: 112, Mismatches: 25, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
5 10 0.09
6 40 0.36
7 49 0.44
8 10 0.09
9 3 0.03
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:6267185 original size:15 final size:15
Alignment explanation
Indices: 6267100--6267177 Score: 54
Period size: 15 Copynumber: 5.1 Consensus size: 15
6267090 GAAAGAAAAA
*
6267100 AAATAAAAAATAAA-
1 AAATAACAAATAAAT
6267114 AAATAA-AAATAAA-
1 AAATAACAAATAAAT
**
6267127 AATATATATTAATAAAT
1 AA-ATA-ACAAATAAAT
*
6267144 AGTAATAATAAATAAAT
1 A--AATAACAAATAAAT
*
6267161 AAATAACAAATACAT
1 AAATAACAAATAAAT
6267176 AA
1 AA
6267178 GATACAAAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
13 9 0.17
14 9 0.17
15 15 0.28
16 6 0.11
17 11 0.20
18 3 0.06
19 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (15 bp):
AAATAACAAATAAAT
Found at i:6267211 original size:18 final size:17
Alignment explanation
Indices: 6267187--6267234 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
6267177 AGATACAAAG
6267187 AAAAATATAT-ATAAAA
1 AAAAATATATAATAAAA
6267203 TATAAAATA-ATAATAAAA
1 -A-AAAATATATAATAAAA
*
6267221 AAAAATATAAAATA
1 AAAAATATATAATA
6267235 CAACATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 6 0.22
17 9 0.33
18 12 0.44
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAATATATAATAAAA
Found at i:6267366 original size:15 final size:14
Alignment explanation
Indices: 6267338--6267388 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
6267328 AATTGTTAGT
*
6267338 ATTTTGGCTCTTTTA
1 ATTTTGGGT-TTTTA
6267353 ATTTCTGGGTTTTTA
1 ATTT-TGGGTTTTTA
*
6267368 ATTGTTGGGTTTTGA
1 ATT-TTGGGTTTTTA
6267383 ATTTTG
1 ATTTTG
6267389 ATAAAGAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 3 0.09
15 24 0.75
16 5 0.16
ACGTcount: A:0.14, C:0.06, G:0.22, T:0.59
Consensus pattern (14 bp):
ATTTTGGGTTTTTA
Found at i:6268022 original size:3 final size:3
Alignment explanation
Indices: 6268014--6268072 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
6268004 AGAAAAGTCC
*
6268014 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GTA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
6268062 GAA GTA GAA GA
1 GAA GAA GAA GA
6268073 GTTTGTTAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:6277260 original size:15 final size:16
Alignment explanation
Indices: 6277232--6277281 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
6277222 TTTTGGGGTA
6277232 GTTTTGGAATTATGAG
1 GTTTTGGAATTATGAG
6277248 GTTTTGG-ATTATGA-
1 GTTTTGGAATTATGAG
* *
6277262 TTTTTGGAATTTTG-G
1 GTTTTGGAATTATGAG
6277277 GTTTT
1 GTTTT
6277282 TTTTTAGGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 6 0.21
15 16 0.55
16 7 0.24
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (16 bp):
GTTTTGGAATTATGAG
Found at i:6277746 original size:13 final size:12
Alignment explanation
Indices: 6277716--6277815 Score: 67
Period size: 13 Copynumber: 7.9 Consensus size: 12
6277706 ATTTTGCTTT
6277716 TTTTTTTTTTGGTA
1 TTTTTTTTTT--TA
*
6277730 TTTTTTTTTTGA
1 TTTTTTTTTTTA
**
6277742 TTTTTACTTTTA
1 TTTTTTTTTTTA
* *
6277754 TTTTTATTCTCTA
1 TTTTT-TTTTTTA
6277767 TTTTTTATTTTTA
1 TTTTTT-TTTTTA
*
6277780 -TTATTTTTTTA
1 TTTTTTTTTTTA
**
6277791 TCTTTTTTAATTA
1 T-TTTTTTTTTTA
6277804 TTTTTGTTTTTT
1 TTTTT-TTTTTT
6277816 TGTTGTGTGA
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
11 6 0.09
12 24 0.37
13 25 0.38
14 10 0.15
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:6277819 original size:8 final size:8
Alignment explanation
Indices: 6277767--6277816 Score: 55
Period size: 9 Copynumber: 5.8 Consensus size: 8
6277757 TTATTCTCTA
6277767 TTTTTTAT
1 TTTTTTAT
6277775 TTTTATTAT
1 TTTT-TTAT
6277784 TTTTTTAT
1 TTTTTTAT
6277792 CTTTTTTAAT
1 -TTTTTT-AT
*
6277802 TATTTTTGT
1 T-TTTTTAT
6277811 TTTTTT
1 TTTTTT
6277817 GTTGTGTGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
8 13 0.35
9 17 0.46
10 7 0.19
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTTAT
Found at i:6277980 original size:17 final size:18
Alignment explanation
Indices: 6277934--6277980 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
6277924 TACATGATTT
*
6277934 ATTATATATTTTTGCATG
1 ATTATTTATTTTTGCATG
*
6277952 ATTATTTGTTTTTGCATG
1 ATTATTTATTTTTGCATG
*
6277970 A-TGTTTATTTT
1 ATTATTTATTTT
6277981 CATGGTTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.21, C:0.04, G:0.13, T:0.62
Consensus pattern (18 bp):
ATTATTTATTTTTGCATG
Found at i:6278231 original size:26 final size:26
Alignment explanation
Indices: 6278196--6278260 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
6278186 ATTTGTTATG
6278196 ATATTGCATGATTGCATGTTTTGATA
1 ATATTGCATGATTGCATGTTTTGATA
* *
6278222 ATATTACATGATTGTATGTTTTGATA
1 ATATTGCATGATTGCATGTTTTGATA
6278248 ATATTGCATGATT
1 ATATTGCATGATT
6278261 TGATCATGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.48
Consensus pattern (26 bp):
ATATTGCATGATTGCATGTTTTGATA
Found at i:6282258 original size:3 final size:3
Alignment explanation
Indices: 6282250--6282275 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6282240 GTTTATTTAT
6282250 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
6282276 TGTAAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6282379 original size:23 final size:23
Alignment explanation
Indices: 6282352--6282419 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
6282342 CAATGACAAT
6282352 AAGAT-AATAAATAAAATAAGAAC
1 AAGATAAATAAATAAAATAA-AAC
6282375 AAGATAAATAAAT-AAATAAAAC
1 AAGATAAATAAATAAAATAAAAC
* *
6282397 AAGGTAAATAAAATAAGATAAAA
1 AAGATAAAT-AAATAAAATAAAA
6282420 AACTTAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.28
23 15 0.38
24 14 0.35
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.18
Consensus pattern (23 bp):
AAGATAAATAAATAAAATAAAAC
Found at i:6282841 original size:17 final size:17
Alignment explanation
Indices: 6282800--6282848 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
6282790 TTCAAATTTG
* *
6282800 CAAGAATTTTAGATTCG
1 CAAGAATTTTAAATTCA
* *
6282817 TAAAAATTTTAAATTCA
1 CAAGAATTTTAAATTCA
*
6282834 CAAGAATTTTCAATT
1 CAAGAATTTTAAATT
6282849 TTCGCAAGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (17 bp):
CAAGAATTTTAAATTCA
Found at i:6282896 original size:19 final size:18
Alignment explanation
Indices: 6282834--6282892 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
6282824 TTTAAATTCA
* *
6282834 CAAGAATTTTCAATTTTCG
1 CAAGATTTTTC-AGTTTCG
6282853 CAAGATTTTTCAGTTTCG
1 CAAGATTTTTCAGTTTCG
*
6282871 TAAGATTTTTCAGCTTT-G
1 CAAGATTTTTCAG-TTTCG
6282889 CAAG
1 CAAG
6282893 GATTAAAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 22 0.63
19 13 0.37
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (18 bp):
CAAGATTTTTCAGTTTCG
Found at i:6283000 original size:32 final size:31
Alignment explanation
Indices: 6282917--6283033 Score: 146
Period size: 32 Copynumber: 3.7 Consensus size: 31
6282907 AAGGTTTTAG
* * * *
6282917 TTTCGCAAAAAATTTAATTCTCAAACTTTCAA
1 TTTCGC-AAGAATTTGATTATCAAAATTTCAA
*
6282949 TTTCACAAG-ATTTGATTATCAAAATTTCAA
1 TTTCGCAAGAATTTGATTATCAAAATTTCAA
*
6282979 TTTTGCAAGAATTTTGATTATCAAAATTTCAA
1 TTTCGCAAGAA-TTTGATTATCAAAATTTCAA
*
6283011 TTTCGCAAGAATTTAATTATCAA
1 TTTCGCAAGAATTTGATTATCAA
6283034 GAACTTAGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.34
31 14 0.19
32 35 0.47
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (31 bp):
TTTCGCAAGAATTTGATTATCAAAATTTCAA
Found at i:6283051 original size:16 final size:15
Alignment explanation
Indices: 6283016--6283054 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
6283006 TTCAATTTCG
*
6283016 CAAGAATTTAATTAT
1 CAAGAACTTAATTAT
*
6283031 CAAGAACTTAGATTCT
1 CAAGAACTTA-ATTAT
6283047 CAAGAACT
1 CAAGAACT
6283055 CAAATTCGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (15 bp):
CAAGAACTTAATTAT
Found at i:6283356 original size:20 final size:20
Alignment explanation
Indices: 6283333--6283371 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6283323 TATCCAGAAT
* *
6283333 TTCAAAGCTTCTTATTCAAG
1 TTCAAAGATTCATATTCAAG
6283353 TTCAAAGATTCATATTCAA
1 TTCAAAGATTCATATTCAA
6283372 TAAATTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (20 bp):
TTCAAAGATTCATATTCAAG
Done.