Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, 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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 68 of 77
Found at i:13629162 original size:41 final size:41
Alignment explanation
Indices: 13629078--13629231 Score: 157
Period size: 41 Copynumber: 3.7 Consensus size: 41
13629068 AAATGGGTTT
* * * *
13629078 CTCTGTTCAAAGGTTAAACAATTTTTAAGAAAAAAAATGGGCTC
1 CTCTATTCAAAGGCTAAACAACTTTT---AAAAAAAATAGGCTC
* **
13629122 CTCTATTCAGAGGCTAAACAACTTTTTTAAAAAATAGGCTC
1 CTCTATTCAAAGGCTAAACAACTTTTAAAAAAAATAGGCTC
* * * *
13629163 CTCTATTTATAGGGTAAACAACTTTAAAAAAAGAAATAGGCTC
1 CTCTATTCAAAGGCTAAACAACTTT-TAAAAA-AAATAGGCTC
13629206 CTCTATTCAAAGGCTAAACAA-TTTTA
1 CTCTATTCAAAGGCTAAACAACTTTTA
13629232 CAATAGCCTT
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
41 35 0.38
42 6 0.07
43 28 0.31
44 22 0.24
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (41 bp):
CTCTATTCAAAGGCTAAACAACTTTTAAAAAAAATAGGCTC
Found at i:13629210 original size:43 final size:42
Alignment explanation
Indices: 13629060--13629231 Score: 166
Period size: 43 Copynumber: 4.0 Consensus size: 42
13629050 ACTTTAAAAA
* * * * * *
13629060 AAAAAAGAAAATGGGTTTCTCTGTTCAAAGGTTAAACAATTTTT
1 AAAAAA-AAAATAGGCTCCTCTATTCAAAGGCTAAACAA-CTTT
* *
13629104 AAGAAAAAAAATGGGCTCCTCTATTCAGAGGCTAAACAACTTT
1 AA-AAAAAAAATAGGCTCCTCTATTCAAAGGCTAAACAACTTT
*** * * *
13629147 -TTTAAAAAATAGGCTCCTCTATTTATAGGGTAAACAACTTT
1 AAAAAAAAAATAGGCTCCTCTATTCAAAGGCTAAACAACTTT
*
13629188 AAAAAAAGAAATAGGCTCCTCTATTCAAAGGCTAAACAATTTT
1 AAAAAAA-AAATAGGCTCCTCTATTCAAAGGCTAAACAACTTT
13629231 A
1 A
13629232 CAATAGCCTT
Statistics
Matches: 105, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
41 34 0.32
42 3 0.03
43 35 0.33
44 29 0.28
45 4 0.04
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (42 bp):
AAAAAAAAAATAGGCTCCTCTATTCAAAGGCTAAACAACTTT
Found at i:13634138 original size:218 final size:218
Alignment explanation
Indices: 13633760--13634188 Score: 804
Period size: 218 Copynumber: 2.0 Consensus size: 218
13633750 AACATTTCTT
13633760 CCTTCTAGAATTTTTCTCCTACCATCTGGATGGACATTTTGACGAAAGCTTCTATTATGCTCAGT
1 CCTTCTAGAATTTTTCTCCTACCATCTGGATGGACATTTTGACGAAAGCTTCTATTATGCTCAGT
*
13633825 TTGTTTTTGACACTCCTTCCATCCTTGGATACATATATCCTCCTAGCCTAAAAGTCTCATAAGAT
66 TTGTTTTTGACACTCCTTCCATCCCTGGATACATATATCCTCCTAGCCTAAAAGTCTCATAAGAT
13633890 ATGGTACGATAATCGACATATTTCTTGCTATTATTCTACCTTTATTATCTCACATCCTCTACATT
131 ATGGTACGATAATCGACATATTTCTTGCTATTATTCTACCTTTATTATCTCACATCCTCTACATT
13633955 TCCCATTCTTCGAATTTATATCC
196 TCCCATTCTTCGAATTTATATCC
* *
13633978 CCTTCTAGAATTTTTCTCCTACCATCTGGATGGACATTTTGACGAAAGTTTTTATTATGCTCAGT
1 CCTTCTAGAATTTTTCTCCTACCATCTGGATGGACATTTTGACGAAAGCTTCTATTATGCTCAGT
*
13634043 TTGTTTTTGACACTCCTTCCATCCCTGGATACATATATCTTCCTAGCCTAAAAGTCTCATAAGAT
66 TTGTTTTTGACACTCCTTCCATCCCTGGATACATATATCCTCCTAGCCTAAAAGTCTCATAAGAT
* *
13634108 ATGGTACGATAATCGACATATTTCTTGCTATTATTCTGCCTTTATTATCTCACATCCTTTACATT
131 ATGGTACGATAATCGACATATTTCTTGCTATTATTCTACCTTTATTATCTCACATCCTCTACATT
13634173 TCCCATTCTTCGAATT
196 TCCCATTCTTCGAATT
13634189 ATCTTTCAGG
Statistics
Matches: 205, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
218 205 1.00
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (218 bp):
CCTTCTAGAATTTTTCTCCTACCATCTGGATGGACATTTTGACGAAAGCTTCTATTATGCTCAGT
TTGTTTTTGACACTCCTTCCATCCCTGGATACATATATCCTCCTAGCCTAAAAGTCTCATAAGAT
ATGGTACGATAATCGACATATTTCTTGCTATTATTCTACCTTTATTATCTCACATCCTCTACATT
TCCCATTCTTCGAATTTATATCC
Found at i:13639074 original size:19 final size:19
Alignment explanation
Indices: 13639047--13639091 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
13639037 TCTATTTCTT
*
13639047 TAGCTTTCATTTGTATGTA
1 TAGCCTTCATTTGTATGTA
13639066 TAGCCTTCATTTGTATGTA
1 TAGCCTTCATTTGTATGTA
13639085 TAGCCTT
1 TAGCCTT
13639092 TTGTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.49
Consensus pattern (19 bp):
TAGCCTTCATTTGTATGTA
Found at i:13641865 original size:19 final size:19
Alignment explanation
Indices: 13641819--13641867 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
13641809 ATCTACCTTT
*
13641819 AATTTTTTTAAATGAAAAC
1 AATTCTTTTAAATGAAAAC
* *
13641838 AAGTCTTTTAAATGAAAAG
1 AATTCTTTTAAATGAAAAC
*
13641857 AATTGTTTTAA
1 AATTCTTTTAA
13641868 TGTGCAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (19 bp):
AATTCTTTTAAATGAAAAC
Found at i:13644175 original size:28 final size:28
Alignment explanation
Indices: 13644107--13644177 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 28
13644097 TAGAAATCTC
13644107 TTAATTTATAATAATAAAATAAAATAAAA
1 TTAATTT-TAATAATAAAATAAAATAAAA
*
13644136 TTATTGTATTTAATAATGAAAATAAAAT-AAA
1 TTA--AT-TTTAATAAT-AAAATAAAATAAAA
13644167 TTAATTTTAAT
1 TTAATTTTAAT
13644178 TAAATCAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
28 6 0.17
29 4 0.11
31 14 0.39
32 12 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (28 bp):
TTAATTTTAATAATAAAATAAAATAAAA
Found at i:13645460 original size:7 final size:7
Alignment explanation
Indices: 13645445--13645486 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
13645435 CTTTAATTAA
13645445 TTTATAT
1 TTTATAT
*
13645452 TTTA-AA
1 TTTATAT
*
13645458 TTTAAAT
1 TTTATAT
13645465 TTTATAT
1 TTTATAT
13645472 TTTATAT
1 TTTATAT
13645479 TTTATAT
1 TTTATAT
13645486 T
1 T
13645487 AAAAAACAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTATAT
Found at i:13646790 original size:269 final size:269
Alignment explanation
Indices: 13646288--13646786 Score: 802
Period size: 269 Copynumber: 1.8 Consensus size: 269
13646278 TACTCAAATT
* * *
13646288 GATACTATATTTAATCAAATATAAATGTATCAAATAATTAATTAGAGAATGAACTATTTTATAAT
1 GATACTATATTTAATCAAATATAAATATATCAAATAATTAATAAGAGAATCAACTATTTTATAAT
*
13646353 TATAATTGTTGTATTTATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAAAT
66 TATAATTGTAGTATTTATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAAAT
*
13646418 TTTTTTAAAATTTTAATACTTTTAAAATGAATTGAATTAAGAGTGATTTAAAAATAATAATAAAA
131 TTTTTTAAAATTTTAATACTTTTAAAATGAATTGAATTAAGAATGATTTAAAAATAATAATAAAA
*
13646483 ACATAAATATAATTAATTTAGTTTTTTAATTATATTTTCTTTATATATTTATACATGAAATACAT
196 ACATAAATATAATTAATTTAGTTTTTGAATTATATTTTCTTTATATATTTATACATGAAATACAT
13646548 CAATTACTA
261 CAATTACTA
*
13646557 GATACTATATTTAATCAAATATAAATATATCAAATAATTGATAAGAGAATCAACTATTTTATAAT
1 GATACTATATTTAATCAAATATAAATATATCAAATAATTAATAAGAGAATCAACTATTTTATAAT
* * * *
13646622 TGTAATTGTAGTATTTGTTAATTTATTAATTATATATTGATTGATTTAATTTGTTAAATTAAATT
66 TATAATTGTAGTATTTATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAAAT
* * * * **
13646687 TTTTTTAAAATTTTAATGCTTTTAATATGAATTGAATTGAGAATTATTTAAAGTTAATAATAAAA
131 TTTTTTAAAATTTTAATACTTTTAAAATGAATTGAATTAAGAATGATTTAAAAATAATAATAAAA
*
13646752 ACGTAAATATAAATCT-ATTTAGTTATTTGAATTAT
196 ACATAAATAT-AAT-TAATTTAGTT-TTTGAATTAT
13646787 TTTCAAATTA
Statistics
Matches: 209, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
269 188 0.90
270 11 0.05
271 10 0.05
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (269 bp):
GATACTATATTTAATCAAATATAAATATATCAAATAATTAATAAGAGAATCAACTATTTTATAAT
TATAATTGTAGTATTTATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAAAT
TTTTTTAAAATTTTAATACTTTTAAAATGAATTGAATTAAGAATGATTTAAAAATAATAATAAAA
ACATAAATATAATTAATTTAGTTTTTGAATTATATTTTCTTTATATATTTATACATGAAATACAT
CAATTACTA
Found at i:13647363 original size:30 final size:30
Alignment explanation
Indices: 13647321--13647419 Score: 135
Period size: 30 Copynumber: 3.3 Consensus size: 30
13647311 AATAAAGAAA
* *
13647321 AATCTATTAGCTTGCAACAAGTAGTTGATG
1 AATCTATTAGCTTGCAAGAAGCAGTTGATG
* * **
13647351 AATTTGTTAGCTTGCAAGAAGCAACTGATG
1 AATCTATTAGCTTGCAAGAAGCAGTTGATG
*
13647381 AATCTATTAGCTTCCAAGAAGCAGTTGATG
1 AATCTATTAGCTTGCAAGAAGCAGTTGATG
13647411 AATCTATTA
1 AATCTATTA
13647420 AAAGAAATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (30 bp):
AATCTATTAGCTTGCAAGAAGCAGTTGATG
Found at i:13648660 original size:270 final size:271
Alignment explanation
Indices: 13648320--13648821 Score: 766
Period size: 270 Copynumber: 1.9 Consensus size: 271
13648310 ATTACTCAAA
** *
13648320 TGGATACTATATTTAATCAAATATAAATGTATCAAATAATTAATTTGAGAATCAATTATTTTATA
1 TGGATACTATATTTAATCAAATATAAATGTATCAAATAATTAATTAAAGAATCAACTATTTTATA
*
13648385 ATTGTAATTGT-TTTATTTATTAATTTATTAATTAT-TGATTGATTGATTTAATTTGTCAAATTG
66 ATTGTAATTGTAGTT-TTTATTAATTTATTAATTATAT-ATTGATTGATTTAATTTGTCAAATT-
*
13648448 AAAAA-TTTTT-AAATTTGTAATACTTTTAATATGAATTGAATTGA-AAGTGATTTAAAATCAAT
128 AAAAATTTTTTAAAATTT-TAATACTTTGAATATGAATTGAATTGAGAA-TGATTTAAAATCAAT
* *
13648510 AATAAAAACATAAATAT-AAT-TAATTTAGTTTTTTTAATTATATTTGTTTTATATATTTACACA
191 AATAAAAACATAAATATAAATCT-ATTTAGTTATTTGAATTATATTTGTTTTATATATTTACACA
13648573 TAAAATACATCAATTAT
255 TAAAATACATCAATTAT
*
13648590 TGGATATTATATTTAATCAAATATAAATGTATCAAATAATTAATTAAAGAATCAACTATTTTATA
1 TGGATACTATATTTAATCAAATATAAATGTATCAAATAATTAATTAAAGAATCAACTATTTTATA
* *
13648655 ATTGTAATTGTAGTTTTTGTTAATTTATTAATTATATATTGATTGATTTAATTTGTTAAATTAAA
66 ATTGTAATTGTAGTTTTTATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAA
* * * *
13648720 AATTTTTTAAAATTTTAATGCTTTGAATATGAATTGAATTGAGAATTATTTAAAGTTAATAATAA
131 AATTTTTTAAAATTTTAATACTTTGAATATGAATTGAATTGAGAATGATTTAAAATCAATAATAA
*
13648785 AAACGTAAATATAAATCTATTTAGTTATTTGAATTAT
196 AAACATAAATATAAATCTATTTAGTTATTTGAATTAT
13648822 TTTTAAATTA
Statistics
Matches: 210, Mismatches: 15, Indels: 13
0.88 0.06 0.05
Matches are distributed among these distances:
269 5 0.02
270 173 0.82
271 31 0.15
272 1 0.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (271 bp):
TGGATACTATATTTAATCAAATATAAATGTATCAAATAATTAATTAAAGAATCAACTATTTTATA
ATTGTAATTGTAGTTTTTATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAA
AATTTTTTAAAATTTTAATACTTTGAATATGAATTGAATTGAGAATGATTTAAAATCAATAATAA
AAACATAAATATAAATCTATTTAGTTATTTGAATTATATTTGTTTTATATATTTACACATAAAAT
ACATCAATTAT
Found at i:13648905 original size:24 final size:24
Alignment explanation
Indices: 13648878--13648923 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
13648868 TGTCAAGTGA
*
13648878 TAAT-TTTTAAGACTGTCCACATCT
1 TAATATTTTAA-ACCGTCCACATCT
13648902 TAATATTTTAAACCGTCCACAT
1 TAATATTTTAAACCGTCCACAT
13648924 AGAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.39
Consensus pattern (24 bp):
TAATATTTTAAACCGTCCACATCT
Found at i:13649397 original size:30 final size:30
Alignment explanation
Indices: 13649359--13649453 Score: 145
Period size: 30 Copynumber: 3.2 Consensus size: 30
13649349 AAGAAAAATC
*
13649359 TATTAGCTTGCAACAAGCAGTTGATGAATT
1 TATTAGCTTGCAAGAAGCAGTTGATGAATT
* * *
13649389 TGTTAGCTTGCAAGAAGCAGCTGATGAATC
1 TATTAGCTTGCAAGAAGCAGTTGATGAATT
*
13649419 TATTAGCTTGTAAGAAGCAGTTGATGAATT
1 TATTAGCTTGCAAGAAGCAGTTGATGAATT
13649449 TATTA
1 TATTA
13649454 AAAGAAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.34
Consensus pattern (30 bp):
TATTAGCTTGCAAGAAGCAGTTGATGAATT
Found at i:13651154 original size:53 final size:53
Alignment explanation
Indices: 13651074--13651177 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 53
13651064 TAAGAATTTT
* *
13651074 TTTTTTTTTTATGCTTACTCCTTTCTGCCAATTAATATTGTAGTTTGTCTTTC
1 TTTTTTTTTAATACTTACTCCTTTCTGCCAATTAATATTGTAGTTTGTCTTTC
* *
13651127 TTTTTTTTTAATATTTATTCCTTTCTGCCAATTAATATTGTAGTTTGTCTT
1 TTTTTTTTTAATACTTACTCCTTTCTGCCAATTAATATTGTAGTTTGTCTT
13651178 ATATTTTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (53 bp):
TTTTTTTTTAATACTTACTCCTTTCTGCCAATTAATATTGTAGTTTGTCTTTC
Found at i:13656533 original size:57 final size:58
Alignment explanation
Indices: 13656397--13656532 Score: 211
Period size: 58 Copynumber: 2.3 Consensus size: 58
13656387 ACAAAGGCTC
* * * *
13656397 AAGTTGAAGGTATCAATTTTTTTTGAAATTAAAAGTTTCAAAAAATATTTTTTGGGAA
1 AAGTTGAAAGTATCAATTTTTCTTAAAATTAAAAGTTTCAAAAAATATTTTTGGGGAA
*
13656455 AAGTTGAAAGTATCAATTTTTCTTAAAATT-AAAGTTTCAAAAAAATATTTTTGGGGAG
1 AAGTTGAAAGTATCAATTTTTCTTAAAATTAAAAGTTTC-AAAAAATATTTTTGGGGAA
13656513 AAGTTGAAAGTATCAATTTT
1 AAGTTGAAAGTATCAATTTT
13656533 CCTGCATAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
57 8 0.11
58 64 0.89
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.40
Consensus pattern (58 bp):
AAGTTGAAAGTATCAATTTTTCTTAAAATTAAAAGTTTCAAAAAATATTTTTGGGGAA
Found at i:13660578 original size:9 final size:8
Alignment explanation
Indices: 13660553--13660626 Score: 61
Period size: 7 Copynumber: 9.6 Consensus size: 8
13660543 TAAGATGATG
13660553 AAAAATG-
1 AAAAATGA
13660560 AAAAATGA
1 AAAAATGA
13660568 AAAAATGGA
1 AAAAAT-GA
13660577 AAAAA--A
1 AAAAATGA
13660583 AGAAAA--A
1 A-AAAATGA
13660590 AAAAATGAA
1 AAAAATG-A
*
13660599 AAAAAAGA
1 AAAAATGA
13660607 AAAAATG-
1 AAAAATGA
*
13660614 AGAAATGA
1 AAAAATGA
13660622 AAAAA
1 AAAAA
13660627 ATATATTCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
6 6 0.11
7 19 0.34
8 17 0.30
9 14 0.25
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (8 bp):
AAAAATGA
Found at i:13660582 original size:10 final size:9
Alignment explanation
Indices: 13660560--13660611 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
13660550 ATGAAAAATG
*
13660560 AAAAATGAA
1 AAAAAAGAA
**
13660569 AAAATGGAA
1 AAAAAAGAA
13660578 AAAAAAGAAAA
1 AAAAAAG--AA
13660589 AAAAAATGAA
1 AAAAAA-GAA
13660599 AAAAAAGAA
1 AAAAAAGAA
13660608 AAAA
1 AAAA
13660612 TGAGAAATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 19 0.53
10 8 0.22
11 8 0.22
12 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.06
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:13660593 original size:21 final size:21
Alignment explanation
Indices: 13660567--13660627 Score: 86
Period size: 21 Copynumber: 2.7 Consensus size: 21
13660557 ATGAAAAATG
13660567 AAAAAATGGAAAAAAAAGAAAA
1 AAAAAAT-GAAAAAAAAGAAAA
13660589 AAAAAATGAAAAAAAAGAAAA
1 AAAAAATGAAAAAAAAGAAAA
13660610 AATGAGAAATGAAAAAAA
1 AA--A-AAATGAAAAAAA
13660628 TATATTCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.44
22 7 0.19
23 1 0.03
24 12 0.33
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (21 bp):
AAAAAATGAAAAAAAAGAAAA
Found at i:13660611 original size:11 final size:12
Alignment explanation
Indices: 13660553--13660604 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 12
13660543 TAAGATGATG
13660553 AAAAATGAAAAATGA
1 AAAAATG-AAAA--A
*
13660568 AAAAATG-GAAA
1 AAAAATGAAAAA
13660579 AAAAA-GAAAAA
1 AAAAATGAAAAA
13660590 AAAAATGAAAAA
1 AAAAATGAAAAA
13660602 AAA
1 AAA
13660605 GAAAAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 1 0.03
11 14 0.42
12 9 0.27
13 2 0.06
15 7 0.21
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.08
Consensus pattern (12 bp):
AAAAATGAAAAA
Found at i:13661192 original size:13 final size:13
Alignment explanation
Indices: 13661174--13661199 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13661164 TTAGTTAAAG
13661174 AAAAATCAAAATA
1 AAAAATCAAAATA
13661187 AAAAATCAAAATA
1 AAAAATCAAAATA
13661200 GAAAGGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATCAAAATA
Found at i:13661338 original size:62 final size:59
Alignment explanation
Indices: 13661236--13661404 Score: 200
Period size: 62 Copynumber: 2.8 Consensus size: 59
13661226 TTTTGTAGGA
* *
13661236 AAAATTGATACTTTCAAC-TTTTCTCTAAAAATATTTTTTTTGGAAATTT-CGATTTTCAAAG
1 AAAATTGATACTTTCAACTTTTTCTC-AAAAATATTTTTTTTGAAAATTTAC--TTCT-AAAG
* *
13661297 AAAATTGATACTTTCAACTTTTTCTCAAAAATCCTTTTTTTTTTGAAAATTTACTTCTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAA---TATTTTTTTTGAAAATTTACTTCTAAAG
* *
13661359 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGAAAAT
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAAAT
13661405 GTATTTTATT
Statistics
Matches: 96, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
58 13 0.14
59 1 0.01
61 23 0.24
62 39 0.41
63 3 0.03
64 16 0.17
65 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.45
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAAATTTACTTCTAAAG
Found at i:13661596 original size:60 final size:60
Alignment explanation
Indices: 13661421--13661615 Score: 254
Period size: 60 Copynumber: 3.2 Consensus size: 60
13661411 TATTATTATT
* *
13661421 ATTTTTTTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--ATTTTTTGAAA
1 ATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTG-AA
* *
13661480 ATTTTGATCTTTAAGGAAAATTGATACTTTCAACTTTT-CCTCAAAACCT-TTTTTTTTTGAA
1 ATTTT-ATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCT-AAAA-ATATTTTTTTTTGAA
*
13661541 ATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAA
1 ATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTT-GAA
13661603 ATTTTTATTTTTA
1 A-TTTTATTTTTA
13661616 TTTAAAGAAA
Statistics
Matches: 119, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
59 9 0.08
60 68 0.57
61 20 0.17
62 11 0.09
63 11 0.09
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (60 bp):
ATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAA
Found at i:13661641 original size:5 final size:5
Alignment explanation
Indices: 13661633--13661704 Score: 62
Period size: 5 Copynumber: 14.4 Consensus size: 5
13661623 AAAATAGAAT
* *
13661633 AATAA AATAA AA-AA AATGAA AGTGAA AAT-A AATAA AA-AT AA-AA AATAA
1 AATAA AATAA AATAA AAT-AA AAT-AA AATAA AATAA AATAA AATAA AATAA
13661681 AATAAA AATAA AATAA AGATAA AA
1 AAT-AA AATAA AATAA A-ATAA AA
13661705 AGAATGTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
4 14 0.25
5 24 0.42
6 19 0.33
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:13661643 original size:22 final size:21
Alignment explanation
Indices: 13661618--13661688 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
13661608 TATTTTTATT
* *
13661618 TAAAGAAAATAGAATA-ATAAA
1 TAAAAAAAATAGAAAATA-AAA
*
13661639 ATAAAAAAAAT-GAAAGTGAAAA
1 -TAAAAAAAATAGAAAAT-AAAA
*
13661661 TAAATAAAAATAAAAAATAAAA
1 TAAA-AAAAATAGAAAATAAAA
13661683 TAAAAA
1 TAAAAA
13661689 TAAAATAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
21 9 0.22
22 26 0.65
23 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (21 bp):
TAAAAAAAATAGAAAATAAAA
Found at i:13661671 original size:6 final size:6
Alignment explanation
Indices: 13661662--13661705 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
13661652 AAGTGAAAAT
*
13661662 AAATAA AAATAA AAA-ATA AAATAA AAAT-A AAATAA AGATAA AAA
1 AAATAA AAATAA AAATA-A AAATAA AAATAA AAATAA AAATAA AAA
13661706 GAATGTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 6 0.18
6 26 0.79
7 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:13661678 original size:29 final size:29
Alignment explanation
Indices: 13661633--13661705 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
13661623 AAAATAGAAT
* * *
13661633 AATAAAATAAAAAAAATGAAAGTGAAAAT-A
1 AATAAAA-ATAAAAAAT-AAAATAAAAATAA
13661663 AATAAAAATAAAAAATAAAATAAAAATAA
1 AATAAAAATAAAAAATAAAATAAAAATAA
*
13661692 AATAAAGATAAAAA
1 AATAAAAATAAAAA
13661706 GAATGTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 9 0.24
29 22 0.58
30 7 0.18
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (29 bp):
AATAAAAATAAAAAATAAAATAAAAATAA
Found at i:13661679 original size:17 final size:18
Alignment explanation
Indices: 13661657--13661705 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
13661647 AATGAAAGTG
13661657 AAAAT-AAATAAAAATAA
1 AAAATAAAATAAAAATAA
13661674 AAAATAAAATAAAAAT--
1 AAAATAAAATAAAAATAA
13661690 AAAATAAAGATAAAAA
1 AAAATAAA-ATAAAAA
13661706 GAATGTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.27
17 12 0.40
18 10 0.33
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAATAAAATAAAAATAA
Found at i:13661702 original size:22 final size:22
Alignment explanation
Indices: 13661634--13661704 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
13661624 AAATAGAATA
*
13661634 ATAAAAT-AAAAAAAATGAAAG
1 ATAAAATAAAAAAAAATAAAAG
* *
13661655 -TGAAAATAAATAAAAATAAAAA
1 AT-AAAATAAAAAAAAATAAAAG
13661677 ATAAAATAAAAATAAAAT-AAAG
1 ATAAAATAAAAA-AAAATAAAAG
13661699 ATAAAA
1 ATAAAA
13661705 AGAATGTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
20 1 0.02
21 5 0.12
22 29 0.71
23 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (22 bp):
ATAAAATAAAAAAAAATAAAAG
Found at i:13661763 original size:25 final size:25
Alignment explanation
Indices: 13661728--13661775 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
13661718 AACCTAATCT
*
13661728 AATAAATAAATAAAAT-AAAAAAACA
1 AATAAACAAAT-AAATGAAAAAAACA
13661753 AATAAACAAATAAATGAAAAAAA
1 AATAAACAAATAAATGAAAAAAA
13661776 AAAACCTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (25 bp):
AATAAACAAATAAATGAAAAAAACA
Found at i:13662748 original size:14 final size:14
Alignment explanation
Indices: 13662738--13662767 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13662728 GAAAAAAAAT
13662738 TAATAATAAAATAA
1 TAATAATAAAATAA
*
13662752 TAATAATATAATAA
1 TAATAATAAAATAA
13662766 TA
1 TA
13662768 TATATAACTA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATAATAAAATAA
Found at i:13662750 original size:8 final size:7
Alignment explanation
Indices: 13662739--13662870 Score: 55
Period size: 8 Copynumber: 18.3 Consensus size: 7
13662729 AAAAAAAATT
13662739 AATAATAA
1 AATAAT-A
13662747 AATAAT-
1 AATAATA
13662753 AATAATA
1 AATAATA
13662760 TAATAATA
1 -AATAATA
*
13662768 TAT-ATA
1 AATAATA
*
13662774 ACTATATA
1 AATA-ATA
13662782 AATACAATA
1 AAT--AATA
*
13662791 CAT-ATA
1 AATAATA
*
13662797 AAT-ATT
1 AATAATA
13662803 AATAGA-A
1 AATA-ATA
13662810 AATAAATA
1 AAT-AATA
13662818 AATAAATA
1 AAT-AATA
13662826 AATAA-A
1 AATAATA
13662832 GATATACATA
1 -A-ATA-ATA
*
13662842 TATTAATA
1 -AATAATA
13662850 AATAAT-
1 AATAATA
13662856 AATAAT-
1 AATAATA
13662862 AATAATA
1 AATAATA
13662869 AA
1 AA
13662871 ATACATAAAA
Statistics
Matches: 98, Mismatches: 11, Indels: 31
0.70 0.08 0.22
Matches are distributed among these distances:
6 33 0.34
7 16 0.16
8 38 0.39
9 8 0.08
10 3 0.03
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (7 bp):
AATAATA
Found at i:13662873 original size:56 final size:55
Alignment explanation
Indices: 13662736--13662879 Score: 129
Period size: 53 Copynumber: 2.7 Consensus size: 55
13662726 GAGAAAAAAA
* * * * *
13662736 ATTAAT-AATAA-AATAATAATAATATAATAATATATATAACTATATAAATACAAT
1 ATTAATAAATAATAATAATAATAATAAAATAA-ATAAATAAATAAAGAAATACAAT
* * * *
13662790 A-CATATAAATATTAAT-AGAA-AAT-AAATAAATAAATAAATAAAGATATACATAT
1 ATTA-ATAAATAATAATAATAATAATAAAATAAATAAATAAATAAAGAAATACA-AT
*
13662843 ATTAATAAATAATAATAATAATAATAAAATACATAAA
1 ATTAATAAATAATAATAATAATAATAAAATAAATAAA
13662880 ATACAAAAGA
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
52 16 0.23
53 20 0.29
54 10 0.14
55 10 0.14
56 13 0.19
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (55 bp):
ATTAATAAATAATAATAATAATAATAAAATAAATAAATAAATAAAGAAATACAAT
Found at i:13663063 original size:1 final size:1
Alignment explanation
Indices: 13663053--13663162 Score: 94
Period size: 1 Copynumber: 110.0 Consensus size: 1
13663043 ACGTTGTCAC
* * * * * * * * *
13663053 TTTTTGTTTTTTTTGTTTTTTTTGTTTTGTTTTTTTATTATTTTTTGTTTTTTTTTATTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
13663118 TTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13663163 GACCAAAGCT
Statistics
Matches: 81, Mismatches: 28, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (1 bp):
T
Found at i:13663071 original size:8 final size:8
Alignment explanation
Indices: 13663053--13663162 Score: 141
Period size: 8 Copynumber: 13.4 Consensus size: 8
13663043 ACGTTGTCAC
13663053 TTTTTGTTT
1 TTTTTG-TT
13663062 TTTTTGTTT
1 TTTTTG-TT
13663071 TTTTTGTT
1 TTTTTGTT
13663079 TTGTTT-TT
1 TT-TTTGTT
* *
13663087 TTATTATT
1 TTTTTGTT
*
13663095 TTTTGTTTT
1 TTTT-TGTT
*
13663104 TTTTTATT
1 TTTTTGTT
13663112 TTTTTGTT
1 TTTTTGTT
13663120 TTTTTGTT
1 TTTTTGTT
13663128 TTTTTGTT
1 TTTTTGTT
13663136 TTTTTGTT
1 TTTTTGTT
13663144 TTTTTGTT
1 TTTTTGTT
13663152 TTTTTGTT
1 TTTTTGTT
13663160 TTT
1 TTT
13663163 GACCAAAGCT
Statistics
Matches: 93, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
7 2 0.02
8 66 0.71
9 25 0.27
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (8 bp):
TTTTTGTT
Found at i:13663262 original size:41 final size:41
Alignment explanation
Indices: 13663170--13663334 Score: 217
Period size: 41 Copynumber: 4.0 Consensus size: 41
13663160 TTTGACCAAA
* * * *
13663170 GCTCCTTTAAACAAAGGCTCAACGACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-ATAAATT
13663213 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
*
13663254 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGAAAAATAAATT
* *
13663295 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAAT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAAT
13663335 ACTCCTAGAC
Statistics
Matches: 112, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
39 2 0.02
40 1 0.01
41 76 0.68
42 4 0.04
43 29 0.26
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
Found at i:13664596 original size:9 final size:9
Alignment explanation
Indices: 13664584--13664616 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
13664574 ATTTTTTCCC
13664584 CTTTTTTTT
1 CTTTTTTTT
13664593 CTTTTTTTTT
1 C-TTTTTTTT
13664603 CTTTTTTTT
1 CTTTTTTTT
13664612 CTTTT
1 CTTTT
13664617 CTCATTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:13664597 original size:19 final size:19
Alignment explanation
Indices: 13664575--13664616 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13664565 CATTTTCTCA
13664575 TTTTTTCCCCTTTTTTTTC
1 TTTTTTCCCCTTTTTTTTC
***
13664594 TTTTTTTTTCTTTTTTTTC
1 TTTTTTCCCCTTTTTTTTC
13664613 TTTT
1 TTTT
13664617 CTCATTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTCCCCTTTTTTTTC
Found at i:13664598 original size:10 final size:10
Alignment explanation
Indices: 13664585--13664616 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
13664575 TTTTTTCCCC
13664585 TTTTTTTTCT
1 TTTTTTTTCT
13664595 TTTTTTTTC-
1 TTTTTTTTCT
13664604 TTTTTTTTCT
1 TTTTTTTTCT
13664614 TTT
1 TTT
13664617 CTCATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:13668412 original size:13 final size:13
Alignment explanation
Indices: 13668394--13668419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13668384 TTAGTTAAAG
13668394 AAAAATCAAAATA
1 AAAAATCAAAATA
13668407 AAAAATCAAAATA
1 AAAAATCAAAATA
13668420 GAAAGGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATCAAAATA
Found at i:13668589 original size:131 final size:118
Alignment explanation
Indices: 13668438--13668801 Score: 425
Period size: 130 Copynumber: 3.0 Consensus size: 118
13668428 TGAAAGAATG
* * * *
13668438 ATTTTTTTTTGTGTAGGAAAAATTGATACTTTTAACTTTTCCCCAAAAATATTTTTTTTGGAAAT
1 ATTTTTTTTTTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAAT
13668503 TTCGATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCCAAAACTATTTTTTTGAAAA
64 TT-GATTTT-AAGGAAAATTGATACTTTCAACTTTTCCCCAAAACTATTTTTTTG--AA
* *
13668562 TGTATTTTTTTTTTTTTTTTTAAGAAAAATTGATACTTTCAACTTTTTCCTAAAAATAATTTTTT
1 ---A----TTTTTTTTTTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTT
*
13668627 GGAAATTTTGATCTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAACCT-TTTTTTCTGAA
58 GGAAA-TTTGAT-TTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAA-CTATTTTTT-TGAA
* *
13668691 A---TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCC-AAAATATTTTTTGAAAATTT
1 ATTTTTTTTTTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTT
*
13668752 -ATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
66 GA-TTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAACTATTTTTTT
13668802 TTTGGAAATT
Statistics
Matches: 213, Mismatches: 13, Indels: 35
0.82 0.05 0.13
Matches are distributed among these distances:
114 2 0.01
115 43 0.20
116 4 0.02
117 11 0.05
118 5 0.02
119 37 0.17
126 1 0.00
127 1 0.00
129 2 0.01
130 53 0.25
131 53 0.25
132 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (118 bp):
ATTTTTTTTTTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTT
GATTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAACTATTTTTTTGAA
Found at i:13668652 original size:60 final size:58
Alignment explanation
Indices: 13668573--13668821 Score: 290
Period size: 59 Copynumber: 4.2 Consensus size: 58
13668563 GTATTTTTTT
* *
13668573 TTTTTTTTTTAAGAAAAATTGATACTTTCAACTTTTTCCTAAAAATAATTTTTTGGAAA
1 TTTTATTTTTAAGAAAAATTGATACTTTCAAC-TTTTCCCAAAAATAATTTTTTGGAAA
* * * *
13668632 TTTTGATCTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAACCT--TTTTTTCTGAAA
1 TTTT-ATTTTTAAGAAAAATTGATACTTTCAACTTTTCC-CAAAA-ATAATTTTTT-GGAAA
*
13668692 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAT-ATTTTTT-GAAA
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCAAAAATAATTTTTTGGAAA
* * *
13668748 ATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTGGAAA
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTT-CCCAAAAATA---ATTTTTTGGAAA
13668810 TTTTGATTTTTA
1 TTTT-ATTTTTA
13668822 TTTAAAGAAA
Statistics
Matches: 163, Mismatches: 15, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
56 38 0.23
57 9 0.06
58 10 0.06
59 48 0.29
60 37 0.23
61 7 0.04
62 7 0.04
63 7 0.04
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (58 bp):
TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCAAAAATAATTTTTTGGAAA
Found at i:13668664 original size:130 final size:120
Alignment explanation
Indices: 13668570--13668801 Score: 318
Period size: 115 Copynumber: 2.0 Consensus size: 120
13668560 AATGTATTTT
*
13668570 TTTTTTTTTTTTTAAGAAAAATTGATACTTTCAACTTTTTCCTAAAAATAATTTTTTGGAAATTT
1 TTTTTTTTTTTTTAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATAATTTTTTGGAAATTT
*
13668635 TGATCTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAACCT-TTTTTTCTGAAA
66 TGAT-TTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAA-CTATTTTTT-TGAAA
* * *
13668692 ---TTTTATTTTTAAGAAAAATTGATACTTTCAAC-TTTTCCCCAAAAT-ATTTTTT-GAAAATT
1 TTTTTTTTTTTTTAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATAATTTTTTGGAAATTT
*
13668751 T-ATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
66 TGA-TTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAACTATTTTTTT
13668802 TTTGGAAATT
Statistics
Matches: 102, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
114 2 0.02
115 43 0.42
116 8 0.08
117 7 0.07
118 11 0.11
119 31 0.30
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (120 bp):
TTTTTTTTTTTTTAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATAATTTTTTGGAAATTT
TGATTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAACTATTTTTTTGAAA
Found at i:13668872 original size:29 final size:30
Alignment explanation
Indices: 13668839--13668925 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 30
13668829 AAAATAGAAT
* *
13668839 AATAAAATAAAAAAATGAAACTGAAAAT-A
1 AATAAAATAAAAAAATGAAAATAAAAATAA
*
13668868 AATAAAAATAAAAAAA-CAAAATAAAAATAA
1 AAT-AAAATAAAAAAATGAAAATAAAAATAA
*
13668898 AATAAAGATAAAAAGAATGTTAAATAAA
1 AATAAA-ATAAAAA-AATG-AAAATAAA
13668926 CCTAATCTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
29 15 0.32
30 23 0.49
31 2 0.04
33 7 0.15
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (30 bp):
AATAAAATAAAAAAATGAAAATAAAAATAA
Found at i:13668876 original size:6 final size:6
Alignment explanation
Indices: 13668867--13668911 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
13668857 AACTGAAAAT
* *
13668867 AAATAA AAATAA AAAAACA AAATAA AAAT-A AAATAA AGATAA AAA
1 AAATAA AAATAA AAATA-A AAATAA AAATAA AAATAA AAATAA AAA
13668912 GAATGTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 5 0.15
6 23 0.70
7 5 0.15
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.13
Consensus pattern (6 bp):
AAATAA
Found at i:13668878 original size:30 final size:30
Alignment explanation
Indices: 13668828--13668916 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 30
13668818 TTTATTTAAA
*
13668828 GAAAATAGAATAATAAAATAAAAAAATGAAACT
1 GAAAATA-AAT-A-AAAATAAAAAAATGAAAAT
*
13668861 GAAAATAAATAAAAATAAAAAAA-CAAAAT
1 GAAAATAAATAAAAATAAAAAAATGAAAAT
* *
13668890 AAAAATAAAATAAAGATAAAAAGAATG
1 GAAAAT-AAATAAAAATAAAAA-AATG
13668917 TTAAATAAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 9 0.19
30 26 0.54
31 3 0.06
32 3 0.06
33 7 0.15
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (30 bp):
GAAAATAAATAAAAATAAAAAAATGAAAAT
Found at i:13668963 original size:26 final size:26
Alignment explanation
Indices: 13668934--13668983 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
13668924 AACCTAATCT
*
13668934 AATAAATAAATAAAAT-AAAAAAAACA
1 AATAAACAAAT-AAATGAAAAAAAACA
13668960 AATAAACAAATAAATGAAAAAAAA
1 AATAAACAAATAAATGAAAAAAAA
13668984 AAAACCTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.14
Consensus pattern (26 bp):
AATAAACAAATAAATGAAAAAAAACA
Found at i:13669989 original size:53 final size:52
Alignment explanation
Indices: 13669921--13670063 Score: 125
Period size: 53 Copynumber: 2.7 Consensus size: 52
13669911 AAAAAAAAAT
* * * *
13669921 TAATAAT-AATATAATAATAATATAATAATATATATAACTATATAAATACA-A
1 TAATAATAAATATAATAATAATATAATAA-ATAAATAAATAAAGAAATACATA
* *
13669972 TACAT-ATAAATATTAATAGAAAATA-AATAAATAAATAAATAAAGATATACATA
1 TA-ATAATAAATA-TAATA-ATAATATAATAAATAAATAAATAAAGAAATACATA
* *
13670025 TATTAATAAATAATAATAATAA-ATAATAAAATACATAAA
1 TAATAATAAAT-ATAATAATAATATAAT-AAATAAATAAA
13670064 ATACAAAAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
51 5 0.07
52 29 0.39
53 34 0.46
54 6 0.08
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (52 bp):
TAATAATAAATATAATAATAATATAATAAATAAATAAATAAAGAAATACATA
Found at i:13670001 original size:4 final size:4
Alignment explanation
Indices: 13669992--13670054 Score: 53
Period size: 4 Copynumber: 16.8 Consensus size: 4
13669982 TATTAATAGA
* * * * *
13669992 AAAT AAAT AAAT AAAT AAAT AAAG ATAT ACAT ATAT TAAT AAAT -AAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
13670039 -AAT -AAT AAAT -AAT AAA
1 AAAT AAAT AAAT AAAT AAA
13670055 ATACATAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 12 0.24
4 37 0.76
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:13671773 original size:41 final size:41
Alignment explanation
Indices: 13671715--13672142 Score: 383
Period size: 41 Copynumber: 10.1 Consensus size: 41
13671705 ATGATTGTCA
* * * *
13671715 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAG
* * * *
13671756 AGGAGCAATTTATTTTTCAAAATTGTGGTGCCTCTATTTAG
1 AGGAGCAATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAG
* * * *
13671797 AGGAGAAATTTACTTTTCAAAGTTG-TGTTGCCTCTATTTAG
1 AGGAGCAATTTATTTTTCAAAGTTGTTG-AGCCTCTGTTTAG
* * * * *
13671838 AGGAGCAATTTACTTTCCAAAAGTTGTGGTGCCTCTATTTAG
1 AGGAGCAATTTATTTTTC-AAAGTTGTTGAGCCTCTGTTTAG
* * * *
13671880 AGGAGCCATTTACTTTTCAAAGTTGTTAAGCCTCTGATTAG
1 AGGAGCAATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAG
* * *
13671921 AGGAGCCATTTATTTTTCTAAAGTCGTTGAGTCTCTGTTTAG
1 AGGAGCAATTTATTTTTC-AAAGTTGTTGAGCCTCTGTTTAG
* *
13671963 AGGAGCCATTTATTTTTCCAAAGTTGTTGAGCCTCTGATTAG
1 AGGAGCAATTTATTTTT-CAAAGTTGTTGAGCCTCTGTTTAG
* * *
13672005 AGGAGTC-ATTTATTTTTTTCAAAATTGTTTAGCCTCTGATTAG
1 AGGAG-CAATTTA--TTTTTCAAAGTTGTTGAGCCTCTGTTTAG
** *
13672048 AGGAGCCTTGTTTATTTTTCAAAAGTTGTTGAGCCTCTGATTAG
1 AGGAG-C-AATTTATTTTTC-AAAGTTGTTGAGCCTCTGTTTAG
** * * *
13672092 AGGAGCTTTGTTTATGTTTATTAAAGTCGTTAAGCCTCTGTTTAG
1 AGGAGC--AATTTAT-TTT-TCAAAGTTGTTGAGCCTCTGTTTAG
13672137 AGGAGC
1 AGGAGC
13672143 TTTGATCAAA
Statistics
Matches: 337, Mismatches: 36, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
40 1 0.00
41 123 0.36
42 102 0.30
43 38 0.11
44 39 0.12
45 33 0.10
46 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (41 bp):
AGGAGCAATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAG
Found at i:13672087 original size:87 final size:83
Alignment explanation
Indices: 13671715--13672142 Score: 366
Period size: 83 Copynumber: 5.1 Consensus size: 83
13671705 ATGATTGTCA
* * * * * * *
13671715 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTC-AAAAT
1 AGGAGCCATTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCTAAAAT
* * *
13671779 TGTGGTGCCTCT-ATTTAG
66 CGTTGAGCCTCTGA-TTAG
** * * * * *
13671797 AGGAGAAATTTACTTTTCAAAGTTG-TGTTGCCTCT-ATTTAGAGGAGCAATTTA-CTTTCCAAA
1 AGGAGCCATTTATTTTTCAAAGTTGTTG-AGCCTCTGA-TTAGAGGAGCCATTTATTTTTCTAAA
* * *
13671859 AGTTGTGGTGCCTCT-ATTTAG
64 A-TCGTTGAGCCTCTGA-TTAG
* * *
13671880 AGGAGCCATTTACTTTTCAAAGTTGTTAAGCCTCTGATTAGAGGAGCCATTTATTTTTCTAAAGT
1 AGGAGCCATTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCTAAAAT
* *
13671945 CGTTGAGTCTCTGTTTAG
66 CGTTGAGCCTCTGATTAG
* *
13671963 AGGAGCCATTTATTTTTCCAAAGTTGTTGAGCCTCTGATTAGAGGAGTCATTTATTTTTTTCAAA
1 AGGAGCCATTTATTTTT-CAAAGTTGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCT-AAA
* *
13672028 ATTGTTTAGCCTCTGATTAG
64 ATCGTTGAGCCTCTGATTAG
* **
13672048 AGGAGCCTTGTTTATTTTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTGTTTATGTTTAT
1 AGGAGCC--ATTTATTTTTC-AAAGTTGTTGAGCCTCTGATTAGAGGAGC--CATTTAT-TTT-T
* * *
13672113 -TAAAGTCGTTAAGCCTCTGTTTAG
59 CTAAAATCGTTGAGCCTCTGATTAG
13672137 AGGAGC
1 AGGAGC
13672143 TTTGATCAAA
Statistics
Matches: 294, Mismatches: 35, Indels: 27
0.83 0.10 0.08
Matches are distributed among these distances:
81 5 0.02
82 50 0.17
83 92 0.31
84 49 0.17
85 25 0.09
86 1 0.00
87 37 0.13
89 30 0.10
90 4 0.01
91 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (83 bp):
AGGAGCCATTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCTAAAAT
CGTTGAGCCTCTGATTAG
Found at i:13672413 original size:6 final size:6
Alignment explanation
Indices: 13672402--13672490 Score: 70
Period size: 6 Copynumber: 14.0 Consensus size: 6
13672392 CCCAATGGGC
* * * **
13672402 TTTTAT TTTTAT TTTCAT TGTTAT TTTTAT TATTTGT CTATTTAT TAATAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T-TTTAT -T-TTTAT TTTTAT
* *
13672453 ATTTAT TTTTAT TTTTAT TATCTAT TTTTAT TATTTAT
1 TTTTAT TTTTAT TTTTAT T-TTTAT TTTTAT T-TTTAT
13672491 CTACTTTTAT
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
6 44 0.68
7 15 0.23
8 6 0.09
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (6 bp):
TTTTAT
Found at i:13672459 original size:4 final size:4
Alignment explanation
Indices: 13672427--13672599 Score: 51
Period size: 4 Copynumber: 43.5 Consensus size: 4
13672417 CATTGTTATT
* * * * *
13672427 TTTA -TTA TTTG TCTA TTTA TTAA TATA TTTA -TT- TTTA TTTT TATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
* * * * *
13672473 TCTA TTTT TATTA TTTA TCTA CTTTTA TTT- TTTT TATTA TTTA TCTA
1 TTTA TTTA T-TTA TTTA TTTA --TTTA TTTA TTTA T-TTA TTTA TTTA
* * * * *
13672520 TTTCT TTTA TTTA TCTA ATT- TTT- TTTA TTT- TTT- GTTA TTTA TTAA
1 TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
13672565 TATA TTTA TCTT- TTTA TTTTGA TTTA TTT- TTTA TT
1 TTTA TTTA T-TTA TTTA -TTT-A TTTA TTTA TTTA TT
13672600 AAGATTAGGA
Statistics
Matches: 121, Mismatches: 31, Indels: 34
0.65 0.17 0.18
Matches are distributed among these distances:
3 25 0.21
4 72 0.60
5 20 0.17
6 4 0.03
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:13672499 original size:36 final size:36
Alignment explanation
Indices: 13672422--13672514 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 36
13672412 ATTTTCATTG
* * *
13672422 TTATTTTTATTATTTGTCTATTTATTAATATATTTATTT
1 TTATTTTTATTA-TTAT-T-TTTATTAATATATCTACTT
*
13672461 TTATTTTTATTATCTATTTTTATT-ATTTATCTACTT
1 TTATTTTTATTAT-TATTTTTATTAATATATCTACTT
*
13672497 TTATTTTTTTTATTATTT
1 TTATTTTTATTATTATTT
13672515 ATCTATTTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
35 5 0.10
36 21 0.44
37 6 0.12
38 2 0.04
39 14 0.29
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (36 bp):
TTATTTTTATTATTATTTTTATTAATATATCTACTT
Found at i:13672516 original size:52 final size:51
Alignment explanation
Indices: 13672402--13672516 Score: 142
Period size: 51 Copynumber: 2.2 Consensus size: 51
13672392 CCCAATGGGC
* * *
13672402 TTTTATTTTTATTTTCATTGTTATTTTTATTATTTGTCTATTTATTAATAT
1 TTTTATTTTTATTTTCATTATTATTTTTATTATTTATCTACTTATTAATAT
* * * *
13672453 ATTTATTTTTATTTTTATTATCTATTTTTATTATTTATCTACTT-TTATTTT
1 TTTTATTTTTATTTTCATTAT-TATTTTTATTATTTATCTACTTATTAATAT
13672504 TTTTATTATTTAT
1 TTTTATT-TTTAT
13672517 CTATTTCTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 29 0.54
52 25 0.46
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (51 bp):
TTTTATTTTTATTTTCATTATTATTTTTATTATTTATCTACTTATTAATAT
Found at i:13672517 original size:43 final size:43
Alignment explanation
Indices: 13672454--13672561 Score: 132
Period size: 43 Copynumber: 2.5 Consensus size: 43
13672444 TATTAATATA
13672454 TTTATTTTTATTTTTA-TTATCTATTT-TTATTATTTATCT-ACT
1 TTTATTTTT-TTTTTATTTATCTATTTCTT-TTATTTATCTAACT
*
13672496 TTTATTTTTTTTATTATTTATCTATTTCTTTTATTTATCTAATT
1 TTTATTTTTTTT-TTATTTATCTATTTCTTTTATTTATCTAACT
*
13672540 TTTTTTATTTTTTGTTATTTAT
1 TTTATT-TTTTTT-TTATTTAT
13672562 TAATATATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
41 3 0.05
42 12 0.21
43 20 0.34
44 9 0.16
45 14 0.24
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (43 bp):
TTTATTTTTTTTTTATTTATCTATTTCTTTTATTTATCTAACT
Found at i:13672531 original size:17 final size:18
Alignment explanation
Indices: 13672509--13672549 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
13672499 ATTTTTTTTA
13672509 TTATTTATCT-ATTTCTT
1 TTATTTATCTAATTTCTT
*
13672526 TTATTTATCTAATTTTTT
1 TTATTTATCTAATTTCTT
13672544 TTATTT
1 TTATTT
13672550 TTTGTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATTTATCTAATTTCTT
Found at i:13672545 original size:18 final size:17
Alignment explanation
Indices: 13672423--13672549 Score: 69
Period size: 17 Copynumber: 7.8 Consensus size: 17
13672413 TTTTCATTGT
* *
13672423 TATTTTTATTATTTGTC
1 TATTTTTTTTATTTATC
*
13672440 TATTTATTAATATATTTAT-
1 TATTT-TT--TTTATTTATC
13672459 T-TTTATTTTTA-TTATC
1 TATTT-TTTTTATTTATC
*
13672475 TATTTTTATTATTTATC
1 TATTTTTTTTATTTATC
*
13672492 TA---CTTTTA--T-T-
1 TATTTTTTTTATTTATC
*
13672502 T-TTTTTATTATTTATC
1 TATTTTTTTTATTTATC
*
13672518 TATTTCTTTTATTTATC
1 TATTTTTTTTATTTATC
13672535 TAATTTTTTTTATTT
1 T-ATTTTTTTTATTT
13672550 TTTGTTATTT
Statistics
Matches: 83, Mismatches: 12, Indels: 29
0.67 0.10 0.23
Matches are distributed among these distances:
10 1 0.01
11 1 0.01
12 5 0.06
14 5 0.06
15 5 0.06
16 10 0.12
17 29 0.35
18 20 0.24
19 1 0.01
20 6 0.07
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.72
Consensus pattern (17 bp):
TATTTTTTTTATTTATC
Found at i:13672557 original size:10 final size:9
Alignment explanation
Indices: 13672495--13672559 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
13672485 ATTTATCTAC
13672495 TTTTATTTT
1 TTTTATTTT
13672504 TTTTATTATT
1 TTTTATT-TT
* *
13672514 TATCTATTTC
1 T-TTTATTTT
*
13672524 TTTTATTTA
1 TTTTATTTT
* *
13672533 TCTAATTTT
1 TTTTATTTT
13672542 TTTTATTTT
1 TTTTATTTT
13672551 TTGTTATTT
1 TT-TTATTT
13672560 ATTAATATAT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
9 28 0.64
10 11 0.25
11 5 0.11
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTTATTTT
Found at i:13672605 original size:17 final size:18
Alignment explanation
Indices: 13672568--13672605 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
13672558 TTATTAATAT
**
13672568 ATTTATCTTTTTATTTTG
1 ATTTATCTTTTTATTAAG
13672586 ATTTAT-TTTTTATTAAG
1 ATTTATCTTTTTATTAAG
13672603 ATT
1 ATT
13672606 AGGATAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (18 bp):
ATTTATCTTTTTATTAAG
Found at i:13672932 original size:32 final size:31
Alignment explanation
Indices: 13672896--13672964 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
13672886 AATTTTCAGA
* *
13672896 TTTCGATTGAATTTTTCAACGAGGTTTGAATT
1 TTTCGA-TGAATTTTCCAACGAAGTTTGAATT
* * *
13672928 TTTCGATGACTTTTCCGACTAAGTTTGAATT
1 TTTCGATGAATTTTCCAACGAAGTTTGAATT
13672959 TTTCGA
1 TTTCGA
13672965 CCAACTTCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.46
Consensus pattern (31 bp):
TTTCGATGAATTTTCCAACGAAGTTTGAATT
Found at i:13673420 original size:17 final size:17
Alignment explanation
Indices: 13673394--13673508 Score: 51
Period size: 17 Copynumber: 6.5 Consensus size: 17
13673384 CGTTCTCAAG
13673394 TTTT-TTTATTT-TTTT
1 TTTTATTTATTTATTTT
*
13673409 TATTTATTTATTTATTAT
1 T-TTTATTTATTTATTTT
* * *
13673427 TATTATTAGATTAGAATTGTT
1 TTTTATT-TATT--TATT-TT
**
13673448 TAATATTT-TTTATTTT
1 TTTTATTTATTTATTTT
13673464 ATTTTATTT-TATTATTTT
1 -TTTTATTTAT-TTATTTT
13673482 TTTTACTTT-TTTATTTT
1 TTTTA-TTTATTTATTTT
*
13673499 ATTTTCTTTA
1 -TTTTATTTA
13673509 AATAAATTTA
Statistics
Matches: 77, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
15 1 0.01
16 5 0.06
17 37 0.48
18 22 0.29
19 2 0.03
20 3 0.04
21 7 0.09
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTATTTATTTATTTT
Found at i:13673465 original size:5 final size:5
Alignment explanation
Indices: 13673455--13673503 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
13673445 GTTTAATATT
*
13673455 TTTTA TTTTA TTTTA TTTTA --TTA TTTT- TTTTA -CTT- TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
13673500 TTTT
1 TTTT
13673504 CTTTAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.08
4 8 0.22
5 26 0.70
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:13673468 original size:10 final size:10
Alignment explanation
Indices: 13673455--13673503 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 10
13673445 GTTTAATATT
13673455 TTTTATTTTA
1 TTTTATTTTA
13673465 TTTTATTTTA
1 TTTTATTTTA
13673475 --TTATTTT-
1 TTTTATTTTA
*
13673482 TTTTA-CTT-
1 TTTTATTTTA
13673490 TTTTATTTTA
1 TTTTATTTTA
13673500 TTTT
1 TTTT
13673504 CTTTAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
8 14 0.42
9 5 0.15
10 14 0.42
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:13673479 original size:25 final size:24
Alignment explanation
Indices: 13673446--13673501 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
13673436 ATTAGAATTG
*
13673446 TTTAATATTTTTTATT-TTATTTTAT
1 TTTATTATTTTTT-TTATT-TTTTAT
13673471 TTTATTATTTTTTTTACTTTTTTAT
1 TTTATTATTTTTTTTA-TTTTTTAT
13673496 TTTATT
1 TTTATT
13673502 TTCTTTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 2 0.07
25 24 0.86
26 2 0.07
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTATTATTTTTTTTATTTTTTAT
Found at i:13673589 original size:58 final size:58
Alignment explanation
Indices: 13673526--13673790 Score: 331
Period size: 58 Copynumber: 4.6 Consensus size: 58
13673516 TTAAAAAATT
13673526 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAATGG
1 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAATGG
* * * * * * *
13673584 ATTTTTAAGAAAAAGTTGAAATTATCAATTTTTCTTAGAAACAAGTTTTCAAAAGTGA
1 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAATGG
* * *
13673642 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAA-AAG-TTTCAAAAAAT--
1 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCT-TAAA--AATAAGTTTTC-AAAAATGG
* *
13673700 ATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAGTTTTCAAAAATGG
1 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAATGG
* * *
13673758 ATTCTTGAGGAAAAGTTGAAAGTACCAATTTTC
1 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTC
13673791 TCTGCACAAA
Statistics
Matches: 177, Mismatches: 22, Indels: 16
0.82 0.10 0.07
Matches are distributed among these distances:
55 2 0.01
56 9 0.05
57 7 0.04
58 143 0.81
59 6 0.03
60 8 0.05
61 2 0.01
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.37
Consensus pattern (58 bp):
ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAATGG
Found at i:13674940 original size:21 final size:21
Alignment explanation
Indices: 13674914--13674963 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
13674904 GAGTTTGAGC
*
13674914 TTAGCTTACTCCCTCAGTGAA
1 TTAGCTAACTCCCTCAGTGAA
*
13674935 TTAGCTAACTCCCTCAGTGAG
1 TTAGCTAACTCCCTCAGTGAA
13674956 TTAGCTAA
1 TTAGCTAA
13674964 GGCTTTGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (21 bp):
TTAGCTAACTCCCTCAGTGAA
Found at i:13679314 original size:13 final size:13
Alignment explanation
Indices: 13679286--13679318 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
13679276 CACGATTTAA
13679286 ATTT-TATTTTTT
1 ATTTATATTTTTT
13679298 -TTTATATTTTTT
1 ATTTATATTTTTT
13679310 ATTTATATT
1 ATTTATATT
13679319 AAATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.16
12 8 0.42
13 8 0.42
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
ATTTATATTTTTT
Found at i:13685257 original size:2 final size:2
Alignment explanation
Indices: 13685250--13685277 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13685240 TCATTTTGGT
13685250 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
13685278 AAAGATCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13688946 original size:2 final size:2
Alignment explanation
Indices: 13688939--13688969 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13688929 ATCATTCCTT
13688939 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13688970 TTATTTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13692309 original size:27 final size:27
Alignment explanation
Indices: 13692271--13692325 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
13692261 GCCATCTGTC
13692271 AATGGTCCATGGCATAAATGATTCATT
1 AATGGTCCATGGCATAAATGATTCATT
* *
13692298 AATGGTTCATGGCATAAATGATTTATT
1 AATGGTCCATGGCATAAATGATTCATT
13692325 A
1 A
13692326 TAAAATAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (27 bp):
AATGGTCCATGGCATAAATGATTCATT
Found at i:13693034 original size:3 final size:3
Alignment explanation
Indices: 13693021--13693059 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
13693011 ATGTATATAG
13693021 TTA TATA TTA TTA -TA TTA TTA TTA TTA TTTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
13693060 TTTTTAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 25 0.76
4 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13693060 original size:10 final size:9
Alignment explanation
Indices: 13693021--13693059 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
13693011 ATGTATATAG
13693021 TTATATATTA
1 TTAT-TATTA
13693031 TTA-TATTA
1 TTATTATTA
13693039 TTATTATTA
1 TTATTATTA
13693048 TTTATTATTA
1 -TTATTATTA
13693058 TT
1 TT
13693060 TTTTTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.30
9 7 0.26
10 12 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTATTATTA
Found at i:13693492 original size:26 final size:26
Alignment explanation
Indices: 13693461--13693513 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
13693451 GGGAGTGAGG
*
13693461 AAAAATTTT-TAGAAATTTTTGGCGAA
1 AAAAATTTTCTAGAAATTTCTGG-GAA
*
13693487 AAAAATTTTCTGGAAATTTCTGGGAA
1 AAAAATTTTCTAGAAATTTCTGGGAA
13693513 A
1 A
13693514 TTTCCAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (26 bp):
AAAAATTTTCTAGAAATTTCTGGGAA
Found at i:13693990 original size:12 final size:11
Alignment explanation
Indices: 13693959--13694112 Score: 50
Period size: 12 Copynumber: 13.2 Consensus size: 11
13693949 GCTTCAGGTT
*
13693959 TTTTTTCTTT-
1 TTTTTTATTTA
*
13693969 TTTTTAATTTA
1 TTTTTTATTTA
*
13693980 TTTGTTTATTTG
1 TTT-TTTATTTA
13693992 TTTTATTA-TT-
1 TTTT-TTATTTA
*
13694002 TTATTTATTTA
1 TTTTTTATTTA
* *
13694013 TTTTTAGATTAGA
1 TTTTT-TATT-TA
*
13694026 TTTATTTA-ATA
1 TTT-TTTATTTA
13694037 TTTTTTATCTTTA
1 TTTTTTA--TTTA
*
13694050 TCTTATT-TTTA
1 T-TTTTTATTTA
13694061 TTTTTGT-TTTA
1 TTTTT-TATTTA
*
13694072 CCTTTCTTTATATTT
1 --TTT-TTTAT-TTA
13694087 TATTTTTATTTA
1 T-TTTTTATTTA
13694099 TTTTTTTATTTA
1 -TTTTTTATTTA
13694111 TT
1 TT
13694113 CTATTTTCTT
Statistics
Matches: 108, Mismatches: 16, Indels: 39
0.66 0.10 0.24
Matches are distributed among these distances:
9 3 0.03
10 20 0.19
11 26 0.24
12 27 0.25
13 19 0.18
14 11 0.10
15 2 0.02
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:13693995 original size:25 final size:25
Alignment explanation
Indices: 13693967--13694033 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
13693957 TTTTTTTTCT
* *
13693967 TTTTTTTAATTTATTTGTTTATTTG
1 TTTTATTAATTTATTTATTTATTTG
*
13693992 TTTTATTATTTTATTTATTTATTT-
1 TTTTATTAATTTATTTATTTATTTG
**
13694016 TTAGATTAGATTTATTTA
1 TTTTATTA-ATTTATTTA
13694034 ATATTTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 6 0.17
25 29 0.83
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (25 bp):
TTTTATTAATTTATTTATTTATTTG
Found at i:13694098 original size:17 final size:17
Alignment explanation
Indices: 13694038--13694112 Score: 57
Period size: 17 Copynumber: 4.5 Consensus size: 17
13694028 TATTTAATAT
*
13694038 TTTTTATCTT-TATCTTA
1 TTTTTAT-TTATATTTTA
* *
13694055 TTTTTATTTTTGTTTTA
1 TTTTTATTTATATTTTA
** *
13694072 CCTTTCTTTATATTTTA
1 TTTTTATTTATATTTTA
13694089 TTTTTATTTAT-TTTT-
1 TTTTTATTTATATTTTA
13694104 TTATTTATT
1 TT-TTTATT
13694113 CTATTTTCTT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
15 2 0.04
16 12 0.26
17 32 0.70
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTTTATTTATATTTTA
Found at i:13694298 original size:58 final size:59
Alignment explanation
Indices: 13694138--13694545 Score: 472
Period size: 58 Copynumber: 6.8 Consensus size: 59
13694128 AAAAAAATCA
* * *
13694138 AAATTTCCAAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATC
1 AAATTTTCAAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATT
* *
13694198 AAAATTTCAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATT
1 AAATTTTC-AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATT
* * *
13694258 AAAGTTTC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAAT
1 AAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATT
* * * * *
13694315 AAAATTTCAAAAAAAAGGATTTATTTTTTAGGAAGAGTTGAAAGTATCAATTTTCCTTAAAAATA
1 AAATTTTC--AAAAAA--A--TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATT
* * * *
13694380 AAATTTTC-AAAAAATATTTTTGGGGAAAAGTTGAAACTATCAATTTTTCTT---AATA
1 AAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATT
* *
13694435 AAATTTTCAAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATTAATTTTCCTCG-AAATT
1 AAATTTTCAAAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATT
*
13694495 AAAATTTTCAAAAAAATA-TTTTCAGGGAAAAGTTGAAAGTATCAATTTTCC
1 -AAATTTTCAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCC
13694546 CTACACAAGA
Statistics
Matches: 303, Mismatches: 29, Indels: 33
0.83 0.08 0.09
Matches are distributed among these distances:
55 12 0.04
56 7 0.02
57 12 0.04
58 109 0.36
59 26 0.09
60 64 0.21
61 22 0.07
62 6 0.02
64 34 0.11
65 11 0.04
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (59 bp):
AAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATT
Found at i:13694459 original size:180 final size:176
Alignment explanation
Indices: 13694130--13694545 Score: 506
Period size: 180 Copynumber: 2.3 Consensus size: 176
13694120 CTTTAAATAA
* * *
13694130 AAAAATCAAAATTTC-CAAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAA
1 AAAAAT-AAAATTTCAAAAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAA
* *
13694194 AATCAAAATTTCAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATTA
65 AATCAAAATTTC-AAAAAAAGATTTTTGAGGAAAAGTTGAAACTATCAATTTTCCTT--AAATAA
* *
13694259 AAGTTTCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT
127 AAGTTTCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTC
* *
13694309 AAAAATAAAATTTCAAAAAAAAGGATTTATTTTTTAGGAAGAGTTGAAAGTATCAATTTTCCTTA
1 AAAAATAAAATTTCAAAAAAAA-GA--TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTA
* * *
13694374 AAAAT-AAAATTTTC-AAAAAATATTTTTGGGGAAAAGTTGAAACTATCAATTTTTCTT-AATAA
63 AAAATCAAAA-TTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAACTATCAATTTTCCTTAAATAA
* *
13694436 AATTTTCAAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATTAATTTTCCTC
127 AAGTTTC-AAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTC
* * *
13694489 GAAATTAAAATTTTC--AAAAAA-ATA-TTTTCAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAATAAAA-TTTCAAAAAAAAGATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCC
13694546 CTACACAAGA
Statistics
Matches: 209, Mismatches: 18, Indels: 24
0.83 0.07 0.10
Matches are distributed among these distances:
174 5 0.02
175 27 0.13
177 11 0.05
178 15 0.07
179 18 0.09
180 82 0.39
181 8 0.04
182 43 0.21
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (176 bp):
AAAAATAAAATTTCAAAAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA
ATCAAAATTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAACTATCAATTTTCCTTAAATAAAAGT
TTCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTC
Found at i:13704131 original size:35 final size:32
Alignment explanation
Indices: 13704092--13704156 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 32
13704082 TATGATATTT
13704092 TAAATTTTAAAATCTCTAATATGATATTTAAATTA
1 TAAATTTTAAAA--T-TAATATGATATTTAAATTA
**
13704127 TAAATTTTTTAATTAATATGATATTTAAAT
1 TAAATTTTAAAATTAATATGATATTTAAAT
13704157 GATTGTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 17 0.61
33 1 0.04
35 10 0.36
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
TAAATTTTAAAATTAATATGATATTTAAATTA
Found at i:13704139 original size:28 final size:29
Alignment explanation
Indices: 13704072--13704139 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 29
13704062 AATTATGATG
* *
13704072 AAATATTTAATATGATATTTTAAATTTTA
1 AAATCTTTAATATGATATTTTAAATTATA
*
13704101 AAATCTCTAATATGATA-TTTAAATTATA
1 AAATCTTTAATATGATATTTTAAATTATA
* *
13704129 AATTTTTTAAT
1 AAATCTTTAAT
13704140 TAATATGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 18 0.55
29 15 0.45
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (29 bp):
AAATCTTTAATATGATATTTTAAATTATA
Found at i:13728757 original size:16 final size:15
Alignment explanation
Indices: 13728731--13728761 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
13728721 AGCATGATTA
13728731 CATGAGATAATATTT
1 CATGAGATAATATTT
13728746 CATGACGATAATATTT
1 CATGA-GATAATATTT
13728762 TATTGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (15 bp):
CATGAGATAATATTT
Found at i:13730401 original size:120 final size:122
Alignment explanation
Indices: 13730260--13730481 Score: 340
Period size: 122 Copynumber: 1.8 Consensus size: 122
13730250 TATATGAATA
* * *
13730260 TTAATAAAATCATCACTTGTGACATTA-TTTTTTATTAATAATTTTTTTATGCTT-ACAAAAGTT
1 TTAATAAAATCACCACATGTGACATTATTTTTTTATTAATAATTTTTTTATGCTTGAAAAAAGTT
*
13730323 ATAAAATATTTCTAACATTTTTAGAATATTTTAGAAAGTTCCTTTGTATAAATATTT
66 ATAAAATATTTCTAACACTTTTAGAATATTTTAGAAAGTTCCTTTGTATAAATATTT
** * *
13730380 TTAATAAAATCACCACATGTGATTTTATTTTTTTATTAATAATTTTTTTATGTTTGAAAAAATTT
1 TTAATAAAATCACCACATGTGACATTATTTTTTTATTAATAATTTTTTTATGCTTGAAAAAAGTT
* *
13730445 TTAAAATATTTTTAACACTTTTAGAATATTTTAGAAA
66 ATAAAATATTTCTAACACTTTTAGAATATTTTAGAAA
13730482 ATTTTTTATG
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
120 23 0.26
121 26 0.29
122 41 0.46
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.49
Consensus pattern (122 bp):
TTAATAAAATCACCACATGTGACATTATTTTTTTATTAATAATTTTTTTATGCTTGAAAAAAGTT
ATAAAATATTTCTAACACTTTTAGAATATTTTAGAAAGTTCCTTTGTATAAATATTT
Found at i:13730582 original size:18 final size:19
Alignment explanation
Indices: 13730556--13730593 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
13730546 TAAAAAATTC
13730556 TAAAATTTTTAT-AATATT
1 TAAAATTTTTATAAATATT
* *
13730574 TAAATTTTTTGTAAATATT
1 TAAAATTTTTATAAATATT
13730593 T
1 T
13730594 TTTAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TAAAATTTTTATAAATATT
Found at i:13730658 original size:24 final size:24
Alignment explanation
Indices: 13730628--13730702 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
13730618 TTTATAGTTA
*
13730628 TTTTATTTATTTTTTATTATTTAT
1 TTTTATTTATTTATTATTATTTAT
* * **
13730652 TTTTATTCATTCATTATTATAAAT
1 TTTTATTTATTTATTATTATTTAT
13730676 TTTATATTT-TATTATTA-TATTTAT
1 TTT-TATTTAT-TTATTATTATTTAT
13730700 TTT
1 TTT
13730703 AACATATCGT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
24 31 0.77
25 9 0.22
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTATTTATTTATTATTATTTAT
Found at i:13730783 original size:16 final size:16
Alignment explanation
Indices: 13730759--13730789 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13730749 TAGAATAAAT
*
13730759 AGAATAAATAAAAAAG
1 AGAAAAAATAAAAAAG
13730775 AGAAAAAATAAAAAA
1 AGAAAAAATAAAAAA
13730790 TACCAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AGAAAAAATAAAAAAG
Found at i:13730894 original size:11 final size:11
Alignment explanation
Indices: 13730874--13730917 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
13730864 CTGGAGTGAT
*
13730874 TTGGAGCGGTC
1 TTGGACCGGTC
13730885 TTGGACCGGT-
1 TTGGACCGGTC
*
13730895 TTGGAACGGTC
1 TTGGACCGGTC
13730906 TTGGACCGGTC
1 TTGGACCGGTC
13730917 T
1 T
13730918 CTCTCTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.11, C:0.20, G:0.39, T:0.30
Consensus pattern (11 bp):
TTGGACCGGTC
Found at i:13730897 original size:21 final size:21
Alignment explanation
Indices: 13730873--13730915 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
13730863 TCTGGAGTGA
*
13730873 TTTGGAGCGGTCTTGGACCGG
1 TTTGGAACGGTCTTGGACCGG
13730894 TTTGGAACGGTCTTGGACCGG
1 TTTGGAACGGTCTTGGACCGG
13730915 T
1 T
13730916 CTCTCTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.12, C:0.19, G:0.40, T:0.30
Consensus pattern (21 bp):
TTTGGAACGGTCTTGGACCGG
Found at i:13731594 original size:40 final size:40
Alignment explanation
Indices: 13731514--13731629 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 40
13731504 AGATCATAAA
* ***
13731514 CTGGCAAGCTTGAATTCAATGCAAAAGATGCACAGAGTCAT
1 CTGGTAAGCTTGAATTTGGTGC-AAAGATGCACAGAGTCAT
* *
13731555 CT-GTCATGTTTGAATTTGGTGCAAAGATGCACA-ATGTCAT
1 CTGGT-AAGCTTGAATTTGGTGCAAAGATGCACAGA-GTCAT
* * *
13731595 CTGGTAAGCTTGAATTTGGTGAAAAAATACACAGA
1 CTGGTAAGCTTGAATTTGGTGCAAAGATGCACAGA
13731630 CAATTGACAA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
39 1 0.02
40 42 0.70
41 17 0.28
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (40 bp):
CTGGTAAGCTTGAATTTGGTGCAAAGATGCACAGAGTCAT
Found at i:13733120 original size:2 final size:2
Alignment explanation
Indices: 13733113--13733147 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
13733103 ACATGCATAC
*
13733113 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13733148 ACCCCTCTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:13739321 original size:32 final size:33
Alignment explanation
Indices: 13739281--13739346 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
13739271 ATTTCATTTT
* *
13739281 TTTTAAATTTAAATTAAATAAAT-TATTTAATA
1 TTTTAAATTAAAATAAAATAAATCTATTTAATA
*
13739313 TTTTAAATTAAAATAAAATATATCGTATTTAATA
1 TTTTAAATTAAAATAAAATAAATC-TATTTAATA
13739347 ATATAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 20 0.69
34 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (33 bp):
TTTTAAATTAAAATAAAATAAATCTATTTAATA
Found at i:13739343 original size:26 final size:26
Alignment explanation
Indices: 13739287--13739361 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 26
13739277 TTTTTTTTAA
* *
13739287 ATTTAAATT-AAATAAATTATTTAAT
1 ATTTAAATTAAAATAAAATATATAAT
**
13739312 ATTTTAAATTAAAATAAAATATATCGT
1 A-TTTAAATTAAAATAAAATATATAAT
*
13739339 ATTT-AA-TAATATAAAATAT-TAAT
1 ATTTAAATTAAAATAAAATATATAAT
13739362 TTTTTTATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 2 0.05
24 12 0.29
25 3 0.07
26 11 0.27
27 13 0.32
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
ATTTAAATTAAAATAAAATATATAAT
Found at i:13745686 original size:17 final size:18
Alignment explanation
Indices: 13745653--13745694 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
13745643 TTTATAATAT
*
13745653 TTTATTTATTTTTCATTC
1 TTTATTTATTATTCATTC
13745671 TTTATTT-TTATTCATTC
1 TTTATTTATTATTCATTC
*
13745688 ATTATTT
1 TTTATTT
13745695 CAATAGGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTATTATTCATTC
Found at i:13746683 original size:14 final size:14
Alignment explanation
Indices: 13746666--13746699 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13746656 AGATGAAAGG
*
13746666 ATAAAATAATAATA
1 ATAAAATAAAAATA
13746680 ATAAAATAAAAATA
1 ATAAAATAAAAATA
*
13746694 GTAAAA
1 ATAAAA
13746700 ATTTTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (14 bp):
ATAAAATAAAAATA
Found at i:13748022 original size:119 final size:119
Alignment explanation
Indices: 13747806--13748044 Score: 460
Period size: 119 Copynumber: 2.0 Consensus size: 119
13747796 TGCAATTAGT
13747806 TTTAAATGTTTTGTGTGATTAATAAAATAAACAACAGAATTAAATGGATAGTGACTCATGAAAAT
1 TTTAAATGTTTTGTGTGATTAATAAAATAAACAACAGAATTAAATGGATAGTGACTCATGAAAAT
13747871 CAGCACTAATGACTATAATTTGATGTTTAATTTGTTTGTTTCTAGATCTAATTA
66 CAGCACTAATGACTATAATTTGATGTTTAATTTGTTTGTTTCTAGATCTAATTA
* *
13747925 TTTACATGTTTTGTGTGATTAATAAAATAAACAACAGATTTAAATGGATAGTGACTCATGAAAAT
1 TTTAAATGTTTTGTGTGATTAATAAAATAAACAACAGAATTAAATGGATAGTGACTCATGAAAAT
13747990 CAGCACTAATGACTATAATTTGATGTTTAATTTGTTTGTTTCTAGATCTAATTA
66 CAGCACTAATGACTATAATTTGATGTTTAATTTGTTTGTTTCTAGATCTAATTA
13748044 T
1 T
13748045 ATGGTCACGA
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 118 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (119 bp):
TTTAAATGTTTTGTGTGATTAATAAAATAAACAACAGAATTAAATGGATAGTGACTCATGAAAAT
CAGCACTAATGACTATAATTTGATGTTTAATTTGTTTGTTTCTAGATCTAATTA
Found at i:13748248 original size:3 final size:3
Alignment explanation
Indices: 13748240--13748266 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
13748230 CATAAAAATA
13748240 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
13748267 GATCTTAACA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:13751717 original size:3 final size:3
Alignment explanation
Indices: 13751709--13751733 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13751699 CTTTTAAAAG
13751709 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
13751734 TAATTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:13751739 original size:4 final size:4
Alignment explanation
Indices: 13751730--13751756 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
13751720 ATAATAATAA
13751730 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
13751757 AAAAAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:13752934 original size:4 final size:4
Alignment explanation
Indices: 13752920--13752955 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
13752910 TTTCTATTAT
*
13752920 TTTA TTTTA TTTA TTTA TCTA TTTA TTTA TTTA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
13752956 TTACCAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:13752940 original size:25 final size:24
Alignment explanation
Indices: 13752903--13752955 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
13752893 GGTCTGGTTA
* *
13752903 ATTTTTTTTTCTA-TTATTTTATTTT
1 ATTTATTTATCTATTTA-TTTA-TTT
13752928 ATTTATTTATCTATTTATTTATTT
1 ATTTATTTATCTATTTATTTATTT
13752952 ATTT
1 ATTT
13752956 TTACCAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 15 0.60
26 3 0.12
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (24 bp):
ATTTATTTATCTATTTATTTATTT
Found at i:13753062 original size:12 final size:12
Alignment explanation
Indices: 13753045--13753070 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13753035 GTTCTGTTAA
13753045 AATAATACTAAT
1 AATAATACTAAT
13753057 AATAATACTAAT
1 AATAATACTAAT
13753069 AA
1 AA
13753071 ATAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAATACTAAT
Found at i:13758361 original size:145 final size:144
Alignment explanation
Indices: 13758131--13758393 Score: 365
Period size: 145 Copynumber: 1.8 Consensus size: 144
13758121 CTTAATTTCA
* *
13758131 TATTTTTTTGGTGCATTTGAAATCATAGCAGTACCCTGGGATGTGTGAAATTACTAAAATACCCA
1 TATTTTTTTGGTGCATTTGAAATCATAGCAATACCCTGGGAGGTGTGAAATTACTAAAATACCCA
*
13758196 TTTAGGGATATTTTCATAATTTTA-CTTTCTCGAGCTC-AGATTTTCATGAAAATATCCAAATCT
66 TTTAGGGATATTTTCATAATTTGACCTTT-TCGAGCTCGA-ATTTTCATGAAAATATCCAAATCT
13758259 TAATGTCATAATATTT
129 TAATGTCATAATATTT
*
13758275 TATTATTTTTGGTGCATTTGAAATCATAGCAATACCCCT-GGAGGTGTGAAATTACTAAAATA-T
1 TATT-TTTTTGGTGCATTTGAAATCATAGCAATA-CCCTGGGAGGTGTGAAATTACTAAAATACC
* ** *
13758338 CTTTTA-GGATTATTTTTTGTAATTTGACCTTTTCGAGCTCGAATTTTTATGAAAAT
64 CATTTAGGGA-TA-TTTTCATAATTTGACCTTTTCGAGCTCGAATTTTCATGAAAAT
13758394 TTTTAAAAGT
Statistics
Matches: 105, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
143 3 0.03
144 11 0.10
145 82 0.78
146 9 0.09
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (144 bp):
TATTTTTTTGGTGCATTTGAAATCATAGCAATACCCTGGGAGGTGTGAAATTACTAAAATACCCA
TTTAGGGATATTTTCATAATTTGACCTTTTCGAGCTCGAATTTTCATGAAAATATCCAAATCTTA
ATGTCATAATATTT
Found at i:13758415 original size:145 final size:145
Alignment explanation
Indices: 13758131--13758429 Score: 358
Period size: 145 Copynumber: 2.1 Consensus size: 145
13758121 CTTAATTTCA
* *
13758131 TATT-TTTTTGGTGCATTTGAAATCATAGCAGTACCCTGGGATGTGTGAAATTACTAAAATACCC
1 TATTATTTTTGGTGCATTTGAAATCATAGCAATACCCTGGGAGGTGTGAAATTACTAAAATACCC
* * *
13758195 ATTTAGGGATATTTTCATAATTTTACTTTCTCGAGCTCAGATTTTCATGAAAATATCCAAATCTT
66 ATTTAGGGATATTTTCATAATTTGACTTTCTCGAGCTCAGATTTTCATGAAAATATCCAAAACTC
13758260 AATGTCATAATATTT
131 AATGTCATAATATTT
*
13758275 TATTATTTTTGGTGCATTTGAAATCATAGCAATACCCCT-GGAGGTGTGAAATTACTAAAATA-T
1 TATTATTTTTGGTGCATTTGAAATCATAGCAATA-CCCTGGGAGGTGTGAAATTACTAAAATACC
* ** * * **
13758338 CTTTTA-GGATTATTTTTTGTAATTTGACCTTT-TCGAGCTC-GAATTTTTATGAAAATTTTTAA
65 CATTTAGGGA-TA-TTTTCATAATTTGA-CTTTCTCGAGCTCAG-ATTTTCATGAAAATATCCAA
* * *
13758400 AAGTCAATTTTATAATATTT
126 AACTCAATGTCATAATATTT
*
13758420 TATGATTTTT
1 TATTATTTTT
13758430 ATTGTTTTAA
Statistics
Matches: 132, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
143 3 0.02
144 12 0.09
145 109 0.83
146 8 0.06
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (145 bp):
TATTATTTTTGGTGCATTTGAAATCATAGCAATACCCTGGGAGGTGTGAAATTACTAAAATACCC
ATTTAGGGATATTTTCATAATTTGACTTTCTCGAGCTCAGATTTTCATGAAAATATCCAAAACTC
AATGTCATAATATTT
Found at i:13759750 original size:3 final size:3
Alignment explanation
Indices: 13759742--13759781 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
13759732 TGTCATAAAC
13759742 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
13759782 TTGGATGCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13759867 original size:3 final size:3
Alignment explanation
Indices: 13759845--13759880 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
13759835 CAAAAAAAAG
* *
13759845 AAT AAT TAT AAT AGT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13759881 GACGATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:13764060 original size:185 final size:184
Alignment explanation
Indices: 13763713--13764061 Score: 438
Period size: 185 Copynumber: 1.9 Consensus size: 184
13763703 TTGAACATAT
*** *
13763713 CGCCACATAAATTTTAACACTATTATTGAATGCGTATATCCAACAAAGATGGCTTTAATAATTTA
1 CGCCACATAAATTTTAACACTATTATTGAATGCGTATATCCAACAAAGACACCTTTAATAATTCA
* * *
13763778 TATAACAGTTTGTAGTTAATTACTGAATACGGTTGCAGAAAACAATGCCTTCAAAATTTTTTCAC
66 TATAACAGTTTGTAGATAATAACTGAATACGGTTGCAGAAAACAACGCCTTCAAAA-TTTTTCAC
* **
13763843 TAAATATTTTGAGAATTATTAAAGGTGTCTTTTACTGTTAAATGCTTCTATATAC
130 TAAAAATTTTGAGAATTATTAAAGACGTCTTTTACTGTTAAATGCTTCTATATAC
* ** *
13763898 CGCCACATAAATTTTAACACTGTTATTGAATGCGTATATTTAAGATAA-ACACCTTTAATAATTC
1 CGCCACATAAATTTTAACACTATTATTGAATGCGTATATCCAACA-AAGACACCTTTAATAATTC
* *
13763962 CTATCACAGTTTGTAGATAATAACTGAA-AGCGGTTGCAGAAAACAACGCCTTCAATAA-TTTTC
65 ATATAACAGTTTGTAGATAATAACTGAATA-CGGTTGCAGAAAACAACGCCTTCAA-AATTTTTC
* *
13764025 -CTAAAAAATTTTTTACG-ATTTTTAAAGACGTCTTTTA
128 ACT-AAAAA-TTTTGA-GAATTATTAAAGACGTCTTTTA
13764062 TTATAAACTG
Statistics
Matches: 140, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
183 2 0.01
184 10 0.07
185 123 0.88
186 5 0.04
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (184 bp):
CGCCACATAAATTTTAACACTATTATTGAATGCGTATATCCAACAAAGACACCTTTAATAATTCA
TATAACAGTTTGTAGATAATAACTGAATACGGTTGCAGAAAACAACGCCTTCAAAATTTTTCACT
AAAAATTTTGAGAATTATTAAAGACGTCTTTTACTGTTAAATGCTTCTATATAC
Found at i:13764640 original size:296 final size:299
Alignment explanation
Indices: 13764073--13764640 Score: 824
Period size: 296 Copynumber: 1.9 Consensus size: 299
13764063 TATAAACTGC
*
13764073 CTTCAATATACCACGATGGTAATGGAAAGCGTTTATTAGAAAAGACGGCCTTCAATATACCTTTA
1 CTTCAATATACCACGATGGTAATGGAAAGCGTTTATTAGAAAAGACGGCATTCAATATACCTTTA
* *
13764138 AACTTAGTAATCAATTATTGAAAGCGTTTGTTAATAATAGACGCCTTCAAAATATTTTCACTAAA
66 AACTTAGTAATCAATTACTGAAAGCGTTTGTTAATAATAGACGCCATCAAAATATTTTCACTAAA
* *** * ** *
13764203 TATTTTAAGAATTATTAAAGGTTTCTTCTACTGTCAAATGCCTTCTATATATCGGCCACATAAAT
131 TATTTTAAAAATTATTAAAGACGTCTTCTACTGTAAAACACCTTCTATATATCCGCCACATAAAT
* * *
13764268 TCTAACATTGTTATTGAAGGTGTACATCCAAGAAAGATGCCTTTAATAATTCTTATCACAATTTG
196 TCTAACACTGTTATTGAAGGCGTACATCCAAGAAAGATGCCTTTAATAATTCTTATCACAATTTA
13764333 TAGATAATAACTGAAGGTGGTTACGGAAAACAAAGCCTT
261 TAGATAATAACTGAAGGTGGTTACGGAAAACAAAGCCTT
* *
13764372 CTTCAATATACCACGATGGTAATGGAAGGCGTTTATTAGAAAAGA-TGCATTCAATATACCTTTA
1 CTTCAATATACCACGATGGTAATGGAAAGCGTTTATTAGAAAAGACGGCATTCAATATACCTTTA
* * ** *
13764436 AACTTAGTAATCTATTACTG-AAG-ATGTTGTTAATAATAGACGCCATCAAAAT-TTATTCTTTT
66 AACTTAGTAATCAATTACTGAAAGCGT-TTGTTAATAATAGACGCCATCAAAATATT-TTCACTA
* * *
13764498 AATATTTTAAAAATTATTAAAGACGTCTTCTACTGTAAAACATCTTCTATATA-CCGTCTCATAA
129 AATATTTTAAAAATTATTAAAGACGTCTTCTACTGTAAAACACCTTCTATATATCCGCCACATAA
* * *
13764562 ATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAATATGCCTTTAATAATT-TCTATCATAGT
194 ATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAAGATGCCTTTAATAATTCT-TATCACAAT
13764626 TTATAGATAATAACT
258 TTATAGATAATAACT
13764641 TAGGGCGGTT
Statistics
Matches: 239, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
295 1 0.00
296 82 0.34
297 77 0.32
298 35 0.15
299 44 0.18
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (299 bp):
CTTCAATATACCACGATGGTAATGGAAAGCGTTTATTAGAAAAGACGGCATTCAATATACCTTTA
AACTTAGTAATCAATTACTGAAAGCGTTTGTTAATAATAGACGCCATCAAAATATTTTCACTAAA
TATTTTAAAAATTATTAAAGACGTCTTCTACTGTAAAACACCTTCTATATATCCGCCACATAAAT
TCTAACACTGTTATTGAAGGCGTACATCCAAGAAAGATGCCTTTAATAATTCTTATCACAATTTA
TAGATAATAACTGAAGGTGGTTACGGAAAACAAAGCCTT
Found at i:13766973 original size:21 final size:21
Alignment explanation
Indices: 13766924--13766974 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
13766914 AATTGAGCAA
*
13766924 CAACAGCAACAAATTAATGAC
1 CAACAGCAACAAATCAATGAC
**
13766945 CATA-AGCAACACCTCAATGAC
1 CA-ACAGCAACAAATCAATGAC
13766966 CAACAGCAA
1 CAACAGCAA
13766975 AGACTCACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.49, C:0.29, G:0.10, T:0.12
Consensus pattern (21 bp):
CAACAGCAACAAATCAATGAC
Found at i:13768717 original size:36 final size:34
Alignment explanation
Indices: 13768651--13768718 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 34
13768641 ATATATAAAC
* * *
13768651 CAAATATTTTCTGGTATAAATATACCACTGACAG
1 CAAATATTTTCTGGCATAAACATACAACTGACAG
*
13768685 CAAATATTTTTCTAGGCATAAACCTACAACTGAC
1 CAAATA-TTTTCT-GGCATAAACATACAACTGAC
13768719 TTCACATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 6 0.21
35 6 0.21
36 16 0.57
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (34 bp):
CAAATATTTTCTGGCATAAACATACAACTGACAG
Found at i:13772812 original size:21 final size:21
Alignment explanation
Indices: 13772786--13772829 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
13772776 CTATTCCTTC
13772786 AAGGAACATCCAAGCTTGACT
1 AAGGAACATCCAAGCTTGACT
13772807 AAGGAACATCCAAGCTTGACT
1 AAGGAACATCCAAGCTTGACT
13772828 AA
1 AA
13772830 AGTTCGGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (21 bp):
AAGGAACATCCAAGCTTGACT
Found at i:13773545 original size:3 final size:3
Alignment explanation
Indices: 13773526--13773592 Score: 109
Period size: 3 Copynumber: 22.0 Consensus size: 3
13773516 AATTATACTC
13773526 TAA TCAA TAA CTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13773573 TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
13773593 ATATATAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.03
3 53 0.87
4 6 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:13774942 original size:4 final size:4
Alignment explanation
Indices: 13774929--13774963 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
13774919 TAGACACCAT
13774929 TTTA -TTA TTTA TTTA TTTA TTTCA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTT
13774964 TCTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 22 0.76
5 4 0.14
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:13775872 original size:27 final size:26
Alignment explanation
Indices: 13775835--13775886 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
13775825 AGGTAAAAAA
*
13775835 TTTTTTTTTTAATTTTTTATATATTAT
1 TTTTTTTTTTAAATTTTTAT-TATTAT
13775862 TTTTTTTTTTAAATTTTTATTATTA
1 TTTTTTTTTTAAATTTTTATTATTA
13775887 ATATTTATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTTTTTTTAAATTTTTATTATTAT
Found at i:13779335 original size:12 final size:13
Alignment explanation
Indices: 13779320--13779379 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 13
13779310 AATATTATTT
13779320 TAAATA-TAAATA
1 TAAATATTAAATA
13779332 TAAA-ATTAAATA
1 TAAATATTAAATA
* *
13779344 TATATA-AAAATA
1 TAAATATTAAATA
*
13779356 TATATAATTAAATA
1 TAAAT-ATTAAATA
13779370 TAAA-ATTAAA
1 TAAATATTAAA
13779380 AAATAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 1 0.03
12 29 0.73
13 2 0.05
14 8 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAATATTAAATA
Found at i:13779360 original size:16 final size:16
Alignment explanation
Indices: 13779323--13779361 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
13779313 ATTATTTTAA
* *
13779323 ATATAAATATAAAATT
1 ATATATATATAAAAAT
*
13779339 AAATATATATAAAAAT
1 ATATATATATAAAAAT
13779355 ATATATA
1 ATATATA
13779362 ATTAAATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATATATATAAAAAT
Found at i:13779372 original size:22 final size:22
Alignment explanation
Indices: 13779319--13779380 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
13779309 AAATATTATT
*
13779319 TTAAATATAAATATAAAATTAA
1 TTAAATATAAAAATAAAATTAA
* * *
13779341 ATATATATAAAAAT-ATATATAA
1 TTAAATATAAAAATAAAAT-TAA
*
13779363 TTAAATATAAAATTAAAA
1 TTAAATATAAAAATAAAA
13779381 AATAATTTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
21 3 0.10
22 25 0.83
23 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TTAAATATAAAAATAAAATTAA
Found at i:13780479 original size:2 final size:2
Alignment explanation
Indices: 13780472--13780500 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13780462 AAGTTAAAGG
13780472 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 A
13780501 CAAAAATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13780724 original size:40 final size:39
Alignment explanation
Indices: 13780678--13780766 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
13780668 GTTCATAATA
* *
13780678 TATTTATTTAA-TTAATGAATATTAAAATATTATTTATG-AT
1 TATTTA-TTAAGTTAATAAAAATT-AAAT-TTATTTATGAAT
*
13780718 TATTTATTAAGTTAATAAAAATTAAATTTGTTTATGAAT
1 TATTTATTAAGTTAATAAAAATTAAATTTATTTATGAAT
*
13780757 TATTCATTAA
1 TATTTATTAA
13780767 ATATTTTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
38 8 0.19
39 19 0.44
40 16 0.37
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.51
Consensus pattern (39 bp):
TATTTATTAAGTTAATAAAAATTAAATTTATTTATGAAT
Found at i:13789775 original size:17 final size:19
Alignment explanation
Indices: 13789740--13789775 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
13789730 TTGCTTCCCC
13789740 CACTGTAGATCCACTAAGA
1 CACTGTAGATCCACTAAGA
13789759 CACTG-AGATCC-CTAAGA
1 CACTGTAGATCCACTAAGA
13789776 TTTTGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (19 bp):
CACTGTAGATCCACTAAGA
Found at i:13801753 original size:5 final size:5
Alignment explanation
Indices: 13801745--13801769 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13801735 ATTTTCTTTT
13801745 AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA
13801770 TTAAAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:13804262 original size:3 final size:3
Alignment explanation
Indices: 13804254--13804300 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
13804244 ATGCATAAAC
13804254 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
13804301 GGTGGTGGTG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13808835 original size:13 final size:13
Alignment explanation
Indices: 13808817--13808843 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13808807 TGTTCCAATA
13808817 TAAGACCTGCAAC
1 TAAGACCTGCAAC
13808830 TAAGACCTGCAAC
1 TAAGACCTGCAAC
13808843 T
1 T
13808844 GGCCTACCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.19
Consensus pattern (13 bp):
TAAGACCTGCAAC
Done.