Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 48 of 135
Found at i:19379861 original size:20 final size:19
Alignment explanation
Indices: 19379780--19380066 Score: 243
Period size: 20 Copynumber: 14.4 Consensus size: 19
19379770 ATTTTATGAC
*
19379780 TTTACCAAAATATTTAAC-A
1 TTTACCAAAAT-TCTAACGA
* *
19379799 ATTACCAATAATTCTAAAGA
1 TTTACCAA-AATTCTAACGA
* * *
19379819 TTTATCAAAATATTTAACAA
1 TTTACCAAAAT-TCTAACGA
*
19379839 TTTACCAATAATTCTAAGGA
1 TTTACCAA-AATTCTAACGA
*
19379859 TTTACCAAAATATCTAATGA
1 TTTACCAAAAT-TCTAACGA
* *
19379879 TTTACCAATATTTCTAAGGA
1 TTTACCAA-AATTCTAACGA
* * *
19379899 TATACCAATATATCTAACAA
1 TTTACCAAAAT-TCTAACGA
* *
19379919 TTTGCCAAAATTTTTAACGA
1 TTTACCAAAA-TTCTAACGA
*
19379939 TTTACCAATAATTCTAACAA
1 TTTACCAA-AATTCTAACGA
19379959 TTTACCAAAATATCTAACGA
1 TTTACCAAAAT-TCTAACGA
* *
19379979 TTTACCAATAATTTTAAGGA
1 TTTACCAA-AATTCTAACGA
* *
19379999 TTTATCAAAATATCTAACGC
1 TTTACCAAAAT-TCTAACGA
*
19380019 TTTACCAAAATTTCTAATGA
1 TTTACCAAAA-TTCTAACGA
*
19380039 TTTATCAAAATATCTAACGA
1 TTTACCAAAAT-TCTAACGA
19380059 TTTACCAA
1 TTTACCAA
19380067 TATTTATGAG
Statistics
Matches: 213, Mismatches: 41, Indels: 27
0.76 0.15 0.10
Matches are distributed among these distances:
19 25 0.12
20 176 0.83
21 12 0.06
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (19 bp):
TTTACCAAAATTCTAACGA
Found at i:19380210 original size:20 final size:19
Alignment explanation
Indices: 19380185--19380269 Score: 64
Period size: 20 Copynumber: 4.3 Consensus size: 19
19380175 TATCTAAAAC
19380185 TTTACCAATAGTTTTATGGA
1 TTTACCAATA-TTTTATGGA
* * *
19380205 TTTACCAAAATATCTA-AGA
1 TTTACCAATAT-TTTATGGA
* *
19380224 CTTTGCCAATATTTTTATTGA
1 -TTTACCAATA-TTTTATGGA
*
19380245 TTTACCAGTATTTATATGGA
1 TTTACCAATATTT-TATGGA
19380265 TTTAC
1 TTTAC
19380270 TTTACTAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
19 6 0.12
20 41 0.82
21 3 0.06
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTACCAATATTTTATGGA
Found at i:19380214 original size:40 final size:40
Alignment explanation
Indices: 19380170--19380251 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
19380160 GCGAATTTGT
19380170 CAAAATATCTAAAACTTTACCAATAGTTTTATGGATTTAC
1 CAAAATATCTAAAACTTTACCAATAGTTTTATGGATTTAC
* * * *
19380210 CAAAATATCTAAGACTTTGCCAATATTTTTATTGATTTAC
1 CAAAATATCTAAAACTTTACCAATAGTTTTATGGATTTAC
19380250 CA
1 CA
19380252 GTATTTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (40 bp):
CAAAATATCTAAAACTTTACCAATAGTTTTATGGATTTAC
Found at i:19380429 original size:21 final size:20
Alignment explanation
Indices: 19380399--19380469 Score: 90
Period size: 21 Copynumber: 3.5 Consensus size: 20
19380389 AATTTATACA
19380399 TTTATCAAAATATCTAACATT
1 TTTATCAAAATATCTAACA-T
* *
19380420 TTTATTAAAATATATAACA-
1 TTTATCAAAATATCTAACAT
* *
19380439 ATTATCAAAATATCTAATAT
1 TTTATCAAAATATCTAACAT
19380459 TTTATCAAAAT
1 TTTATCAAAAT
19380470 TTTTAAAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 15 0.36
20 10 0.24
21 17 0.40
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTATCAAAATATCTAACAT
Found at i:19387789 original size:17 final size:16
Alignment explanation
Indices: 19387756--19387786 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19387746 TACTACTTTA
19387756 ATTTTATAATTTTAAT
1 ATTTTATAATTTTAAT
*
19387772 ATTTTTTAATTTTAA
1 ATTTTATAATTTTAA
19387787 ATAATAGTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTATAATTTTAAT
Found at i:19388671 original size:16 final size:15
Alignment explanation
Indices: 19388637--19388672 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19388627 AGTTTTGAAG
19388637 AAAAATGAATATTGT
1 AAAAATGAATATTGT
* *
19388652 AAAAATGTATGTTGT
1 AAAAATGAATATTGT
19388667 AAAAAT
1 AAAAAT
19388673 ATTGATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:19392667 original size:3 final size:3
Alignment explanation
Indices: 19392659--19392695 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
19392649 AGTATGAAAT
19392659 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19392696 CTTGATCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19409625 original size:29 final size:29
Alignment explanation
Indices: 19409583--19409641 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
19409573 GAGTTAAGTC
19409583 AGTCGTGAGCTTGAGAGGCGATGGAAGAA
1 AGTCGTGAGCTTGAGAGGCGATGGAAGAA
19409612 AGTCGTGAGCTTGAGAGGCGATGGAAGAA
1 AGTCGTGAGCTTGAGAGGCGATGGAAGAA
19409641 A
1 A
19409642 AGGACAAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.41, T:0.17
Consensus pattern (29 bp):
AGTCGTGAGCTTGAGAGGCGATGGAAGAA
Found at i:19415714 original size:3 final size:3
Alignment explanation
Indices: 19415700--19415729 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
19415690 TAATTTGGTC
*
19415700 ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19415730 TGATGGTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:19428548 original size:19 final size:18
Alignment explanation
Indices: 19428512--19428558 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
19428502 ATTTTTGTAG
*
19428512 TATAAATAATTTTAAGTA
1 TATAAAAAATTTTAAGTA
19428530 CTATAAAAAATTATT-AGTA
1 -TATAAAAAATT-TTAAGTA
19428549 TGATAAAAAA
1 T-ATAAAAAA
19428559 AATTCTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 22 0.88
20 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (18 bp):
TATAAAAAATTTTAAGTA
Found at i:19429349 original size:18 final size:20
Alignment explanation
Indices: 19429311--19429351 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
19429301 CTTCTTAGCC
19429311 ATAATATTTACAACATTTTT
1 ATAATATTTACAACATTTTT
*
19429331 ATAATATTT-CAA-TTTTTT
1 ATAATATTTACAACATTTTT
19429349 ATA
1 ATA
19429352 GTAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (20 bp):
ATAATATTTACAACATTTTT
Found at i:19437118 original size:27 final size:27
Alignment explanation
Indices: 19437088--19437164 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
19437078 TTTTTTTGAC
19437088 ATACATATTTTTAATTATAAAAACGAA
1 ATACATATTTTTAATTATAAAAACGAA
* * *
19437115 ATACACATTTTTAATTATAAAAATGTA
1 ATACATATTTTTAATTATAAAAACGAA
*
19437142 ATACATAATTTATAATTATAAAA
1 ATACAT-ATTTTTAATTATAAAA
19437165 GTGTAACAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 29 0.66
28 15 0.34
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (27 bp):
ATACATATTTTTAATTATAAAAACGAA
Found at i:19437152 original size:28 final size:28
Alignment explanation
Indices: 19437088--19437184 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
19437078 TTTTTTTGAC
* *
19437088 ATACAT-ATTTTTAATTATAAAAACGAA
1 ATACATAATTTTTAATTATAAAAATGTA
*
19437115 ATACA-CATTTTTAATTATAAAAATGTA
1 ATACATAATTTTTAATTATAAAAATGTA
* *
19437142 ATACATAATTTATAATTATAAAAGTGTA
1 ATACATAATTTTTAATTATAAAAATGTA
* * *
19437170 ACAAATACTTTTTAA
1 ATACATAATTTTTAA
19437185 ACATTAAATA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
27 29 0.49
28 30 0.51
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (28 bp):
ATACATAATTTTTAATTATAAAAATGTA
Found at i:19444453 original size:23 final size:23
Alignment explanation
Indices: 19444383--19444468 Score: 101
Period size: 21 Copynumber: 4.0 Consensus size: 23
19444373 CTTGATTAGT
19444383 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
19444404 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
19444424 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
*
19444447 ATACGACACATAAAGTGTCTGA
1 ATACGACACATAAAGTGCCTGA
19444469 TCAGCAAAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.17
21 23 0.43
23 22 0.41
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:19444469 original size:44 final size:41
Alignment explanation
Indices: 19444383--19444469 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 41
19444373 CTTGATTAGT
* *
19444383 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
* *
19444424 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGTCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
19444468 AT
1 AT
19444470 CAGCAAAGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 11 0.28
42 10 0.26
43 1 0.03
44 17 0.44
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:19445200 original size:16 final size:16
Alignment explanation
Indices: 19445179--19445230 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
19445169 TTTGGTTCGC
*
19445179 TGTATTGGTTTAGAGG
1 TGTATTGGATTAGAGG
19445195 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * * *
19445211 CGTAATGGAATAGAGA
1 TGTATTGGATTAGAGG
19445227 TGTA
1 TGTA
19445231 ATAGCAAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:19445277 original size:45 final size:44
Alignment explanation
Indices: 19445212--19445301 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 44
19445202 GATTAGAGGC
*
19445212 GTAATGGAATAGAGATGTAATAGCAAATCAACTGTTTGGTTGAAT
1 GTAATGGAATAGAGACGTAATAG-AAATCAACTGTTTGGTTGAAT
* * ***
19445257 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGACGTAATAGAAATCAACTGTTTGGTTGAAT
19445301 G
1 G
19445302 GAATAGCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (44 bp):
GTAATGGAATAGAGACGTAATAGAAATCAACTGTTTGGTTGAAT
Found at i:19449384 original size:6 final size:6
Alignment explanation
Indices: 19449370--19449411 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
19449360 TCCAAATTTG
* * *
19449370 AGCACA AGCAAA AGCAAA AGCAAA A-CAAA ATCAAA ATCAAA A
1 AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA A
19449412 TCGATTTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.67, C:0.19, G:0.10, T:0.05
Consensus pattern (6 bp):
AGCAAA
Found at i:19449404 original size:17 final size:17
Alignment explanation
Indices: 19449378--19449411 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19449368 TGAGCACAAG
19449378 CAAAAGCAAAAGCAAAA
1 CAAAAGCAAAAGCAAAA
* *
19449395 CAAAATCAAAATCAAAA
1 CAAAAGCAAAAGCAAAA
19449412 TCGATTTTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.18, G:0.06, T:0.06
Consensus pattern (17 bp):
CAAAAGCAAAAGCAAAA
Found at i:19449506 original size:19 final size:18
Alignment explanation
Indices: 19449482--19449524 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
19449472 AAATCTGGAG
19449482 AAAAGAAAATG-GAGAAAAT
1 AAAAGAAAATGTGAG--AAT
19449501 AAAAG-AAATGTGAGAAT
1 AAAAGAAAATGTGAGAAT
19449518 AAAAGAA
1 AAAAGAA
19449525 GCGTACCGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.36
18 6 0.27
19 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (18 bp):
AAAAGAAAATGTGAGAAT
Found at i:19450193 original size:22 final size:24
Alignment explanation
Indices: 19450151--19450194 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
19450141 TAACTAAGCT
19450151 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
19450175 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
19450195 TCTTGTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:19450593 original size:22 final size:21
Alignment explanation
Indices: 19450568--19450611 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
19450558 TCTCTTTCTC
19450568 TGTTTCTATTTT-TTTCTTCTTT
1 TGTTTCT-TTTTCTTT-TTCTTT
19450590 TGTTTCTTTTTCTTTTTCTTT
1 TGTTTCTTTTTCTTTTTCTTT
19450611 T
1 T
19450612 ACTTCCTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.80
Consensus pattern (21 bp):
TGTTTCTTTTTCTTTTTCTTT
Found at i:19451912 original size:18 final size:19
Alignment explanation
Indices: 19451889--19451928 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
19451879 CAAACCAAAA
19451889 AAACAACACATTTA-CAAT
1 AAACAACACATTTAGCAAT
*
19451907 AAACAACATATTTAGCAAT
1 AAACAACACATTTAGCAAT
19451926 AAA
1 AAA
19451929 GAAGAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (19 bp):
AAACAACACATTTAGCAAT
Found at i:19452735 original size:21 final size:22
Alignment explanation
Indices: 19452687--19452744 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
19452677 CTTTTAACAA
*
19452687 TTTATATTTATTTTAAGATTTAT
1 TTTA-ATTTATTTTAAGAATTAT
19452710 TTTAATTT-TTTT-AGAATTAT
1 TTTAATTTATTTTAAGAATTAT
*
19452730 TGTTAA-TAATTTTAA
1 T-TTAATTTATTTTAA
19452745 AAAAATCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 9 0.30
21 12 0.40
22 5 0.17
23 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTAATTTATTTTAAGAATTAT
Found at i:19456900 original size:14 final size:16
Alignment explanation
Indices: 19456863--19456897 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19456853 AAGAGATTTT
19456863 TTTTAAAAAATTATATA
1 TTTT-AAAAATTATATA
19456880 TTTTAAAAATTAT-TA
1 TTTTAAAAATTATATA
19456895 TTT
1 TTT
19456898 AAACTCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 9 0.50
17 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTAAAAATTATATA
Found at i:19460834 original size:18 final size:17
Alignment explanation
Indices: 19460808--19460842 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19460798 AATTATTTCT
19460808 AAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAGAAAAG
*
19460825 AAAAACAAAATAGAAAAG
1 AAAAA-AAAAAAGAAAAG
19460843 GAGATATGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAG
Found at i:19461663 original size:30 final size:31
Alignment explanation
Indices: 19461611--19461675 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
19461601 AACAACCTAG
**
19461611 TGACTTAAATAAAAACTTTTGAATTGTTCAA
1 TGACTTAAATAAAAACTTTTGAATAATTCAA
* *
19461642 TGACTTAAAT-GAAATTTTTGAATAATTCAA
1 TGACTTAAATAAAAACTTTTGAATAATTCAA
19461672 TGAC
1 TGAC
19461676 CACTTTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAATTCAA
Found at i:19462723 original size:19 final size:18
Alignment explanation
Indices: 19462699--19462736 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
19462689 TCTATTATGA
19462699 AATTATTCTATTAAAT-TAT
1 AATTATT-T-TTAAATGTAT
19462718 AATTATTTTTAAATGTAT
1 AATTATTTTTAAATGTAT
19462736 A
1 A
19462737 GTTACCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
AATTATTTTTAAATGTAT
Found at i:19510729 original size:21 final size:21
Alignment explanation
Indices: 19510699--19510751 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
19510689 CGTTGTTTCT
*
19510699 AATCTTACCGCTACAGTACCC
1 AATCTCACCGCTACAGTACCC
19510720 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTACCC
19510741 AATCTCACCGC
1 AATCTCACCGC
19510752 CACCGCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.42, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTACCC
Found at i:19529123 original size:27 final size:26
Alignment explanation
Indices: 19529063--19529124 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
19529053 TTATTTCTAA
19529063 AAAATAATTTGAAAGAATTTTAATATT
1 AAAA-AATTTGAAAGAATTTTAATATT
** *
19529090 ACTAAATTTGAAAAGAGTTTTAA-ATAT
1 AAAAAATTTG-AAAGAATTTTAATAT-T
19529117 AAAAAATT
1 AAAAAATT
19529125 AATCAAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (26 bp):
AAAAAATTTGAAAGAATTTTAATATT
Found at i:19530039 original size:26 final size:24
Alignment explanation
Indices: 19530010--19530058 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
19530000 TATATATTTA
19530010 TTATATAATATAAAATATAGATATAT
1 TTATATAATATAAAA-ATA-ATATAT
*
19530036 TTATATAATTTAAAAATAATATA
1 TTATATAATATAAAAATAATATA
19530059 AAATAAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 3 0.14
26 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTATATAATATAAAAATAATATAT
Found at i:19532723 original size:46 final size:46
Alignment explanation
Indices: 19532640--19532776 Score: 192
Period size: 46 Copynumber: 3.0 Consensus size: 46
19532630 CATGGAAAAA
* *
19532640 TTGTGAAAAGTAGG--TA-TGTTTCAGTGAAGAAAGCCATACTAAG
1 TTGTGAAAAGTAGGTATAGTGTTTCAGTGAAGAAAACCATACTGAG
19532683 TTGTGAAAAGTAGGTATAGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATAGTGTTTCAGTGAAGAAAACCATACTGAG
* * *
19532729 TTGTGAAAAGTAGGTATGGTATTCCAGTGAATG-AAACCATACTGAG
1 TTGTGAAAAGTAGGTATAGTGTTTCAGTGAA-GAAAACCATACTGAG
19532775 TT
1 TT
19532777 ATAGCATTGT
Statistics
Matches: 85, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
43 14 0.16
45 2 0.02
46 68 0.80
47 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATAGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:19536943 original size:19 final size:19
Alignment explanation
Indices: 19536919--19536956 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19536909 ATTTACCAAT
19536919 ATATAATACGAAAATATAA
1 ATATAATACGAAAATATAA
* *
19536938 ATATAATATGAATATATAA
1 ATATAATACGAAAATATAA
19536957 TTTTTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
ATATAATACGAAAATATAA
Found at i:19537503 original size:303 final size:304
Alignment explanation
Indices: 19536945--19537551 Score: 1207
Period size: 303 Copynumber: 2.0 Consensus size: 304
19536935 TAAATATAAT
19536945 ATGAATATATAATTTTTTATTTAATTTAATATCTATAAATAATTTAATATATTTTAAATAAGTTA
1 ATGAATATATAATTTTTTATTTAATTTAATATCTATAAATAATTTAATATATTTTAAATAAGTTA
19537010 TATTATTTAATTTTTTTTTTTAAAATGATAAATATTGAGATTTTAACTAATTTACCCACTTAGAA
66 TATTATTTAATTTTTTTTTTTAAAATGATAAATATTGAGATTTTAACTAATTTACCCACTTAGAA
19537075 AATTGAGGTTCTAGAATGTAATTTCCATTTGACTATGAGTAGAGTTGATTTGACTGTTTTGACGC
131 AATTGAGGTTCTAGAATGTAATTTCCATTTGACTATGAGTAGAGTTGATTTGACTGTTTTGACGC
19537140 CTTGTTCCTGTGTTTTTATATTTTGGTCAATGATTCACAAAGCAAGTTGAAAAGAAAATTAATTG
196 CTTGTTCCTGTGTTTTTATATTTTGGTCAATGATTCACAAAGCAAGTTGAAAAGAAAATTAATTG
19537205 GGGGGATTATTCTCCTGAAAAGTAATATGAAGTTGGACCCACTG
261 GGGGGATTATTCTCCTGAAAAGTAATATGAAGTTGGACCCACTG
19537249 ATGAATATAT-ATTTTTTATTTAATTTAATATCTATAAATAATTTAATATATTTTAAATAAGTTA
1 ATGAATATATAATTTTTTATTTAATTTAATATCTATAAATAATTTAATATATTTTAAATAAGTTA
19537313 TATTATTTAATTTTTTTTTTTAAAATGATAAATATTGAGATTTTAACTAATTTACCCACTTAGAA
66 TATTATTTAATTTTTTTTTTTAAAATGATAAATATTGAGATTTTAACTAATTTACCCACTTAGAA
19537378 AATTGAGGTTCTAGAATGTAATTTCCATTTGACTATGAGTAGAGTTGATTTGACTGTTTTGACGC
131 AATTGAGGTTCTAGAATGTAATTTCCATTTGACTATGAGTAGAGTTGATTTGACTGTTTTGACGC
19537443 CTTGTTCCTGTGTTTTTATATTTTGGTCAATGATTCACAAAGCAAGTTGAAAAGAAAATTAATTG
196 CTTGTTCCTGTGTTTTTATATTTTGGTCAATGATTCACAAAGCAAGTTGAAAAGAAAATTAATTG
19537508 GGGGGATTATTCTCCTGAAAAGTAATATGAAGTTGGACCCACTG
261 GGGGGATTATTCTCCTGAAAAGTAATATGAAGTTGGACCCACTG
19537552 CTTTTAATTT
Statistics
Matches: 303, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
303 293 0.97
304 10 0.03
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (304 bp):
ATGAATATATAATTTTTTATTTAATTTAATATCTATAAATAATTTAATATATTTTAAATAAGTTA
TATTATTTAATTTTTTTTTTTAAAATGATAAATATTGAGATTTTAACTAATTTACCCACTTAGAA
AATTGAGGTTCTAGAATGTAATTTCCATTTGACTATGAGTAGAGTTGATTTGACTGTTTTGACGC
CTTGTTCCTGTGTTTTTATATTTTGGTCAATGATTCACAAAGCAAGTTGAAAAGAAAATTAATTG
GGGGGATTATTCTCCTGAAAAGTAATATGAAGTTGGACCCACTG
Found at i:19550075 original size:22 final size:22
Alignment explanation
Indices: 19550050--19550093 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19550040 ATAAAACTCG
*
19550050 TTTT-AAAAATCATTAAAATTAT
1 TTTTAAAAAAT-ATAAAAATTAT
19550072 TTTTAAAAAATATAAAAATTAT
1 TTTTAAAAAATATAAAAATTAT
19550094 ATAAAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAAAATATAAAAATTAT
Found at i:19558722 original size:40 final size:40
Alignment explanation
Indices: 19558678--19558753 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
19558668 CCCATCCATG
*
19558678 ACATGACACGGCATCAACCAAAGTTCCAAATTTTTTTAAT
1 ACATGACACGACATCAACCAAAGTTCCAAATTTTTTTAAT
19558718 ACATGACACGACATCAACCAAAGTTCCAAATTTTTT
1 ACATGACACGACATCAACCAAAGTTCCAAATTTTTT
19558754 AATCAGTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (40 bp):
ACATGACACGACATCAACCAAAGTTCCAAATTTTTTTAAT
Found at i:19561498 original size:4 final size:4
Alignment explanation
Indices: 19561489--19561514 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
19561479 ATGTCGACCC
19561489 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
19561515 CAAATTTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:19561800 original size:20 final size:22
Alignment explanation
Indices: 19561763--19561802 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
19561753 AATATTTAAT
19561763 TATTTATTAAATATTAAAAAAA
1 TATTTATTAAATATTAAAAAAA
19561785 TATTT-TTAAA-ATTAAAAA
1 TATTTATTAAATATTAAAAA
19561803 TTATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATTTATTAAATATTAAAAAAA
Found at i:19561847 original size:26 final size:26
Alignment explanation
Indices: 19561782--19561849 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
19561772 AATATTAAAA
* *
19561782 AAATATTTTTAAAATTAAAAATTATT
1 AAATATTTTTAAAATTAAAAATAAGT
* *
19561808 AAA-ATGTATGAAAATTATAAAA-AAGT
1 AAATAT-TTTTAAAATTA-AAAATAAGT
19561834 AAATATTTTTAAAATT
1 AAATATTTTTAAAATT
19561850 TTTAAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
25 2 0.06
26 25 0.76
27 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (26 bp):
AAATATTTTTAAAATTAAAAATAAGT
Found at i:19567683 original size:27 final size:28
Alignment explanation
Indices: 19567651--19567709 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
19567641 AAGAGAACCC
*
19567651 CGTGCCAAAA-ATGGCAGACTAAAGAGA
1 CGTGCCAAAATACGGCAGACTAAAGAGA
19567678 CGTGCCAAAATACGGCAGACTAAAGAGA
1 CGTGCCAAAATACGGCAGACTAAAGAGA
19567706 CGTG
1 CGTG
19567710 GCTTTCTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 10 0.33
28 20 0.67
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (28 bp):
CGTGCCAAAATACGGCAGACTAAAGAGA
Found at i:19574584 original size:49 final size:51
Alignment explanation
Indices: 19574519--19574614 Score: 151
Period size: 49 Copynumber: 1.9 Consensus size: 51
19574509 AATCCCATAG
*
19574519 TAATTCTCAACGATGAATTAACC-AA-ACTACACTCCTGGAGCTCCATATA
1 TAATTCTCAACAATGAATTAACCAAACACTACACTCCTGGAGCTCCATATA
* *
19574568 TAATTCTCAACAATGAATTAACCAAACACTACACTCTTTGAGCTCCA
1 TAATTCTCAACAATGAATTAACCAAACACTACACTCCTGGAGCTCCA
19574615 ACAGTAATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
49 22 0.52
50 2 0.05
51 18 0.43
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (51 bp):
TAATTCTCAACAATGAATTAACCAAACACTACACTCCTGGAGCTCCATATA
Found at i:19589628 original size:14 final size:14
Alignment explanation
Indices: 19589592--19589630 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
19589582 GCTTAATAAA
19589592 TTATGACATATGCT
1 TTATGACATATGCT
* * *
19589606 TAATAACATATGGT
1 TTATGACATATGCT
19589620 TTATGACATAT
1 TTATGACATAT
19589631 AAACTAATGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (14 bp):
TTATGACATATGCT
Found at i:19589951 original size:44 final size:45
Alignment explanation
Indices: 19589897--19590003 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
19589887 ATTACAACAT
* *
19589897 CATTCTATTCAACCAAACACA-AGAA-TACTGTTACAGCTCTATTC
1 CATTCCATTCAACCAAACA-ATAGAATTACTATTACAGCTCTATTC
*
19589941 CATTCCATTCAACCAAACAATTGAATTACTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACAATAGAATTACTATTACAGCTCTATTC
* * *
19589986 CATTACAGTGAACCAAAC
1 CATTCCATTCAACCAAAC
19590004 GTACCATTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 1 0.02
44 21 0.38
45 33 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (45 bp):
CATTCCATTCAACCAAACAATAGAATTACTATTACAGCTCTATTC
Found at i:19592076 original size:31 final size:32
Alignment explanation
Indices: 19592018--19592094 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
19592008 TTGATATTTA
* * * * *
19592018 ATTTTTTTAATTACAAATGGTATTTAAATTAT
1 ATTTTATTACTTACAAATAGTACTTAAACTAT
19592050 ATTTTATTACTTA-AAATAGTACTTAAACTAT
1 ATTTTATTACTTACAAATAGTACTTAAACTAT
*
19592081 ATTCTATTATCTTA
1 ATTTTATTA-CTTA
19592095 GTTATTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 23 0.61
32 15 0.39
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (32 bp):
ATTTTATTACTTACAAATAGTACTTAAACTAT
Found at i:19593304 original size:61 final size:62
Alignment explanation
Indices: 19593226--19593348 Score: 151
Period size: 61 Copynumber: 2.0 Consensus size: 62
19593216 ATTTTTTAAC
* * ** * * * *
19593226 TTTTAGAGTTAGGACTAAATTGATAAATTTTGTAAA-ATTTGAGGGTTAAATTTATTA-ATTT
1 TTTTAGAATTAGAACTAAAAGGACAAATTTTATAAACA-TTAAGGGCTAAATTTATTATATTT
19593287 TTTTAGAATTAGAACTAAAAGGACAAATTTTATAAACATTAAGGGCTAAATTTATTATATTT
1 TTTTAGAATTAGAACTAAAAGGACAAATTTTATAAACATTAAGGGCTAAATTTATTATATTT
19593349 AGGATCAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
61 47 0.90
62 5 0.10
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (62 bp):
TTTTAGAATTAGAACTAAAAGGACAAATTTTATAAACATTAAGGGCTAAATTTATTATATTT
Found at i:19606183 original size:4 final size:4
Alignment explanation
Indices: 19606174--19606204 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
19606164 CATAATATTA
19606174 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
19606205 ATGTATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTC
Found at i:19608767 original size:2 final size:2
Alignment explanation
Indices: 19608760--19608788 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19608750 GGTAAGTGGT
19608760 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19608789 TCGTTTAGAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:19612877 original size:2 final size:2
Alignment explanation
Indices: 19612870--19612911 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19612860 ATTAATGAAA
19612870 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
19612912 TATACTGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:19617709 original size:20 final size:20
Alignment explanation
Indices: 19617650--19617710 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
19617640 AAAAATAAAA
* * *
19617650 TAAATAAATAATACATTAAAT
1 TAAAAAAATAACACA-TAATT
* *
19617671 TAAAAAAATAACTCCTAATT
1 TAAAAAAATAACACATAATT
19617691 TAAAGAAAATAA-ACATAATT
1 TAAA-AAAATAACACATAATT
19617711 ATCTAAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.30
Consensus pattern (20 bp):
TAAAAAAATAACACATAATT
Found at i:19630273 original size:23 final size:28
Alignment explanation
Indices: 19630241--19630292 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
19630231 TTGAATAAAT
19630241 TAATATTTTAA-AA-A-TA-TTTATATA
1 TAATATTTTAATAAGATTATTTTATATA
19630265 TAAT-TTTTAATAAGATTATTTTATATA
1 TAATATTTTAATAAGATTATTTTATATA
19630292 T
1 T
19630293 TCATAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.25
24 6 0.25
25 1 0.04
26 2 0.08
27 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TAATATTTTAATAAGATTATTTTATATA
Found at i:19631500 original size:61 final size:60
Alignment explanation
Indices: 19631428--19631545 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 60
19631418 AAGTTAGAAC
* * * *
19631428 TAAATTGATAAA-TTTCGTAAATATTGA-AGGTTAAGTTTATTGAATTTTTTAGAATTAAAAT
1 TAAAATGATAAAGTTT-GTAAACATTGAGA-GCTAAATTTATTGAATTTTTTAG-ATTAAAAT
*
19631489 TAAAATGATAAAGTTTGTAAACATTGAGAGCTAAATTTGTTGAATTTTTTAGATTAA
1 TAAAATGATAAAGTTTGTAAACATTGAGAGCTAAATTTATTGAATTTTTTAGATTAA
19631546 TACAATAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
60 5 0.10
61 41 0.82
62 4 0.08
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (60 bp):
TAAAATGATAAAGTTTGTAAACATTGAGAGCTAAATTTATTGAATTTTTTAGATTAAAAT
Found at i:19636740 original size:2 final size:2
Alignment explanation
Indices: 19636733--19636758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19636723 CTAATATCCC
19636733 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
19636759 ATGTGCCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:19639399 original size:10 final size:10
Alignment explanation
Indices: 19639384--19639408 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19639374 TCATAAAGTT
19639384 GGAGCGGGTC
1 GGAGCGGGTC
19639394 GGAGCGGGTC
1 GGAGCGGGTC
19639404 GGAGC
1 GGAGC
19639409 AAGATCACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.20, G:0.60, T:0.08
Consensus pattern (10 bp):
GGAGCGGGTC
Found at i:19644740 original size:2 final size:2
Alignment explanation
Indices: 19644727--19644769 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
19644717 TAATTACATC
*
19644727 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19644769 A
1 A
19644770 ACTTTTCATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19645253 original size:17 final size:18
Alignment explanation
Indices: 19645228--19645261 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19645218 TTGATATTTT
19645228 ATATATTTA-TATTTAAA
1 ATATATTTATTATTTAAA
*
19645245 ATATTTTTATTATTTAA
1 ATATATTTATTATTTAA
19645262 TTTAAATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATATTTATTATTTAAA
Found at i:19645656 original size:43 final size:43
Alignment explanation
Indices: 19645607--19645691 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
19645597 TAAAACCACT
19645607 TTTTTATAAAAGAAAACATGATAAGTACATGATAATTACCTAC
1 TTTTTATAAAAGAAAACATGATAAGTACATGATAATTACCTAC
*
19645650 TTTTTATAAAAGAAAACATGATAAGTGCATGATAATTACCTA
1 TTTTTATAAAAGAAAACATGATAAGTACATGATAATTACCTA
19645692 TTCTTCTCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (43 bp):
TTTTTATAAAAGAAAACATGATAAGTACATGATAATTACCTAC
Found at i:19646588 original size:130 final size:125
Alignment explanation
Indices: 19646301--19646640 Score: 484
Period size: 130 Copynumber: 2.7 Consensus size: 125
19646291 GATAAAATCA
* * * * *
19646301 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
** *
19646366 AGGTCCTTCAA-AAATAATTTCGAGTTGACGTTTCTGAGAAATAGTATAAAAAACGCTTC
66 AGGTCCTAGAAGAAATAATTTCGAGTTGACATTTCTGAGAAATAGTATAAAAAACGCTTC
*
19646425 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGTGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * * *
19646490 AGGTCCTGGAAGAAATAATTTCGATTTGACATTTCTGAGCAAATAGTATAAAACATGCTTC
66 AGGTCCTAGAAGAAATAATTTCGAGTTGACATTTCTGAG-AAATAGTATAAAAAACGCTTC
* *
19646551 AGGCAGGCAGGATGCTTTGTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTA
1 A---A-GCAGGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTA
*
19646616 CAGTAGGTTCTAGAAGAAATAATTT
62 CAGTAGGTCCTAGAAGAAATAATTT
19646641 GAAGAACGTA
Statistics
Matches: 193, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
124 68 0.35
125 25 0.13
126 20 0.10
129 1 0.01
130 79 0.41
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTAGAAGAAATAATTTCGAGTTGACATTTCTGAGAAATAGTATAAAAAACGCTTC
Found at i:19647327 original size:11 final size:11
Alignment explanation
Indices: 19647313--19647350 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
19647303 AAGAAATTTA
19647313 AGAGGAAATTG
1 AGAGGAAATTG
*
19647324 AGAGCAAATTG
1 AGAGGAAATTG
19647335 AGAGGAAATTTG
1 AGAGGAAA-TTG
19647347 AGAG
1 AGAG
19647351 AGGATTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 17 0.71
12 7 0.29
ACGTcount: A:0.45, C:0.03, G:0.34, T:0.18
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:19648819 original size:9 final size:9
Alignment explanation
Indices: 19648801--19648858 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
19648791 TTTGGTTAAA
19648801 AATTAACCG
1 AATTAACCG
*
19648810 AATTACCCG
1 AATTAACCG
19648819 AATTAACCG
1 AATTAACCG
* *
19648828 AATTACCCA
1 AATTAACCG
*
19648837 AATTAACCA
1 AATTAACCG
*
19648846 AATTAACCA
1 AATTAACCG
19648855 AATT
1 AATT
19648859 GAATCACTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:19648824 original size:18 final size:18
Alignment explanation
Indices: 19648800--19648858 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
19648790 TTTTGGTTAA
19648800 AAATTAACCGAATTACCC
1 AAATTAACCGAATTACCC
*
19648818 GAATTAACCGAATTACCC
1 AAATTAACCGAATTACCC
* *
19648836 AAATTAACCAAATTAACC
1 AAATTAACCGAATTACCC
19648854 AAATT
1 AAATT
19648859 GAATCACTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATTAACCGAATTACCC
Found at i:19649004 original size:18 final size:18
Alignment explanation
Indices: 19648962--19649008 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
19648952 ATTTAATTTT
*
19648962 ATGATTGGGTTGGGTTGG
1 ATGATTGGGTTGGGTTGA
* *
19648980 GTAATTGGGTTGGGTTGA
1 ATGATTGGGTTGGGTTGA
19648998 ATGATTGGGTT
1 ATGATTGGGTT
19649009 TAGATTGGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.40
Consensus pattern (18 bp):
ATGATTGGGTTGGGTTGA
Found at i:19650379 original size:15 final size:15
Alignment explanation
Indices: 19650355--19650410 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
19650345 CTTCCCTCCT
*
19650355 TTTTTTATTTTAAAA
1 TTTTTAATTTTAAAA
* *
19650370 TTTTTAATTTTTATA
1 TTTTTAATTTTAAAA
**
19650385 TTTCAAATTTTAAAA
1 TTTTTAATTTTAAAA
19650400 --TTTAATTTTAA
1 TTTTTAATTTTAA
19650411 TTATTAGTAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 9 0.28
15 23 0.72
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAATTTTAAAA
Found at i:19650382 original size:21 final size:21
Alignment explanation
Indices: 19650356--19650410 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
19650346 TTCCCTCCTT
*
19650356 TTTTTATTTTAAAATTTTTAA
1 TTTTTATTTTAAAATTTTAAA
*
19650377 TTTTTATATTTCAAATTTTAAA
1 TTTTTAT-TTTAAAATTTTAAA
* *
19650399 ATTTAATTTTAA
1 TTTTTATTTTAA
19650411 TTATTAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTATTTTAAAATTTTAAA
Found at i:19661294 original size:14 final size:14
Alignment explanation
Indices: 19661277--19661310 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
19661267 GAGAGATTTT
19661277 AGAAAAGAGAAAAA
1 AGAAAAGAGAAAAA
*
19661291 AGAAGAGAGAAAAA
1 AGAAAAGAGAAAAA
19661305 A-AAAAG
1 AGAAAAG
19661311 CGAGAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AGAAAAGAGAAAAA
Found at i:19662605 original size:27 final size:29
Alignment explanation
Indices: 19662575--19662629 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
19662565 TAAAATAGAT
19662575 AATA-AAATTACATTTT-A-ACTCTAAAAA
1 AATATAAATTA-ATTTTGACACTCTAAAAA
*
19662602 AATATAATTTAATTTTGACACTCTAAAA
1 AATATAAATTAATTTTGACACTCTAAAA
19662630 TAGTTTCACC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 9 0.38
28 6 0.25
29 9 0.38
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (29 bp):
AATATAAATTAATTTTGACACTCTAAAAA
Found at i:19668572 original size:33 final size:33
Alignment explanation
Indices: 19668527--19668594 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
19668517 CAGATTTCAT
19668527 TGTTACCATTATTCATTCGGTTGAAAAATGTGG
1 TGTTACCATTATTCATTCGGTTGAAAAATGTGG
*
19668560 TGTTACCGTTATTCATTCGGTTGAAAAATGTGG
1 TGTTACCATTATTCATTCGGTTGAAAAATGTGG
19668593 TG
1 TG
19668595 AAGAAATGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.40
Consensus pattern (33 bp):
TGTTACCATTATTCATTCGGTTGAAAAATGTGG
Found at i:19668767 original size:20 final size:22
Alignment explanation
Indices: 19668721--19668769 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
19668711 TGTAGCATAA
*
19668721 AATATATGTATTTAATTATTAT
1 AATATATGTAGTTAATTATTAT
*
19668743 -TTATAT-TAGTTAA-TATTAT
1 AATATATGTAGTTAATTATTAT
19668762 AATATATG
1 AATATATG
19668770 AGATATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
19 6 0.27
20 11 0.50
21 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (22 bp):
AATATATGTAGTTAATTATTAT
Found at i:19670951 original size:50 final size:50
Alignment explanation
Indices: 19670867--19671107 Score: 274
Period size: 50 Copynumber: 4.8 Consensus size: 50
19670857 ATTTGGGTAA
** *
19670867 AGAGATCCCATGTAAGACCATGTCTGGGGTATGGCATTGGCACCGAGACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
19670917 AGAGGTCCCACGTAAGACCATGTTTGGGACATGGCATTGGCATCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
19670967 AGAGGTCCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGATCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
19671017 AGA-ACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA--GTACATG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
19671066 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
19671108 TGTTATTATC
Statistics
Matches: 163, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 122 0.75
51 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:19672239 original size:9 final size:9
Alignment explanation
Indices: 19672225--19672273 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
19672215 ATTGGTTAAA
*
19672225 AATTAACTG
1 AATTAACCG
*
19672234 AATTAACTG
1 AATTAACCG
*
19672243 AATTACCCG
1 AATTAACCG
19672252 AATTAACCG
1 AATTAACCG
19672261 AATTAACCG
1 AATTAACCG
19672270 AATT
1 AATT
19672274 GAATCACTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:19672416 original size:18 final size:18
Alignment explanation
Indices: 19672376--19672419 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
19672366 AATTTTTATG
**
19672376 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
19672394 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
19672412 TTTGGGTT
1 ATTGGGTT
19672420 TGTTAGGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:19675290 original size:30 final size:30
Alignment explanation
Indices: 19675254--19675316 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
19675244 ATTTATTTTA
19675254 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
19675284 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
19675314 TTG
1 TTG
19675317 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:19675420 original size:18 final size:18
Alignment explanation
Indices: 19675399--19675438 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
19675389 GAAATATTTA
*
19675399 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
19675417 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
19675435 TTTT
1 TTTT
19675439 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:19675461 original size:12 final size:12
Alignment explanation
Indices: 19675440--19675473 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19675430 TATATTTTTT
*
19675440 AAAATTATATAA
1 AAAATAATATAA
19675452 AAAATAATATAA
1 AAAATAATATAA
*
19675464 AAATTAATAT
1 AAAATAATAT
19675474 GGACAGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:19677776 original size:70 final size:70
Alignment explanation
Indices: 19677700--19677840 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
19677690 CATGTAAGTG
19677700 TGATGGGTTGTGGATCAAAGCCCATGACAAATGCACACATAACGTTCTATGAAGATGTGAATTGA
1 TGATGGGTTGTGGATCAAAGCCCATGACAAATGCACACATAACGTTCTATGAAGATGTGAATTGA
19677765 CCCGA
66 CCCGA
19677770 TGATGGGTTGTGGATCAAAGCCCATGACAAATGCACACATAACGTTCTATGAAGATGTGAATTGA
1 TGATGGGTTGTGGATCAAAGCCCATGACAAATGCACACATAACGTTCTATGAAGATGTGAATTGA
19677835 CCCGA
66 CCCGA
19677840 T
1 T
19677841 TCGTAGAACA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (70 bp):
TGATGGGTTGTGGATCAAAGCCCATGACAAATGCACACATAACGTTCTATGAAGATGTGAATTGA
CCCGA
Found at i:19679105 original size:20 final size:20
Alignment explanation
Indices: 19679082--19679123 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
19679072 TTTTTTGGAA
19679082 TTTTCTAATATTTTT-AGATT
1 TTTTCTAAT-TTTTTAAGATT
* *
19679102 TTTTTTCATTTTTTAAGATT
1 TTTTCTAATTTTTTAAGATT
19679122 TT
1 TT
19679124 AACAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTCTAATTTTTTAAGATT
Found at i:19679112 original size:28 final size:27
Alignment explanation
Indices: 19679062--19679123 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
19679052 AGATATTTTT
19679062 AGATTTTTAGTTTTTTGGAATTTTCTA
1 AGATTTTTAGTTTTTTGGAATTTTCTA
* *** *
19679089 ATATTTTTAGATTTTTTTTCATTTTTTA
1 AGATTTTTAG-TTTTTTGGAATTTTCTA
19679117 AGATTTT
1 AGATTTT
19679124 AACAATTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (27 bp):
AGATTTTTAGTTTTTTGGAATTTTCTA
Found at i:19680012 original size:88 final size:89
Alignment explanation
Indices: 19679891--19680068 Score: 349
Period size: 88 Copynumber: 2.0 Consensus size: 89
19679881 TAAAAAACAA
19679891 TTTTGTTTAAATATGAAAAAAAGAATCATTAAAAATTTAATATTATTTTAAATAATAAAATTGAA
1 TTTTGTTTAAATATGAAAAAAAGAATCATTAAAAATTTAATATTATTTTAAATAATAAAATTGAA
19679956 CTTTCGTCTAGAAAAAAGATGTTC
66 CTTTCGTCTAGAAAAAAGATGTTC
19679980 TTTTGTTTAAA-ATGAAAAAAAGAATCATTAAAAATTTAATATTATTTTAAATAATAAAATTGAA
1 TTTTGTTTAAATATGAAAAAAAGAATCATTAAAAATTTAATATTATTTTAAATAATAAAATTGAA
19680044 CTTTCGTCTAGAAAAAAGATGTTC
66 CTTTCGTCTAGAAAAAAGATGTTC
19680068 T
1 T
19680069 GATTTATGAC
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 78 0.88
89 11 0.12
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (89 bp):
TTTTGTTTAAATATGAAAAAAAGAATCATTAAAAATTTAATATTATTTTAAATAATAAAATTGAA
CTTTCGTCTAGAAAAAAGATGTTC
Found at i:19720925 original size:15 final size:15
Alignment explanation
Indices: 19720907--19720936 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19720897 CCACCAACAC
19720907 CAACAACAACAATAA
1 CAACAACAACAATAA
19720922 CAACAACAACAATAA
1 CAACAACAACAATAA
19720937 TAATAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.27, G:0.00, T:0.07
Consensus pattern (15 bp):
CAACAACAACAATAA
Found at i:19726052 original size:3 final size:3
Alignment explanation
Indices: 19726038--19726087 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
19726028 AAATGACATT
* * *
19726038 TTA TTA TT- TTA TTA TTA TTG TTA TTA TTA ATA TTA TTG TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19726084 TTA T
1 TTA T
19726088 GAAATAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:19726073 original size:18 final size:18
Alignment explanation
Indices: 19726041--19726082 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
19726031 TGACATTTTA
*
19726041 TTATT-TTATTATTATTG
1 TTATTATTAATATTATTG
19726058 TTATTATTAATATTATTG
1 TTATTATTAATATTATTG
19726076 TTATTAT
1 TTATTAT
19726083 ATTATGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTATTATTAATATTATTG
Found at i:19728284 original size:25 final size:25
Alignment explanation
Indices: 19728255--19728302 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
19728245 AAACTCCAAA
19728255 CCAACCACATACTACTACATTTTTC
1 CCAACCACATACTACTACATTTTTC
19728280 CCAACCACATACTACTACATTTT
1 CCAACCACATACTACTACATTTT
19728303 CCTCAAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.31
Consensus pattern (25 bp):
CCAACCACATACTACTACATTTTTC
Found at i:19739084 original size:23 final size:23
Alignment explanation
Indices: 19739056--19739119 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 23
19739046 ATAACATATG
19739056 AAATATGTTATTATTAATAGT-AT
1 AAATATGTTATTATTAAT-GTAAT
* * *
19739079 AAATATATGATTGATGAATGTAAT
1 AAATATGTTATT-ATTAATGTAAT
19739103 AAATATG-TATATATTAA
1 AAATATGTTAT-TATTAA
19739120 AACAGAAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (23 bp):
AAATATGTTATTATTAATGTAAT
Found at i:19739938 original size:27 final size:26
Alignment explanation
Indices: 19739908--19739992 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
19739898 TCTCAAATTT
*
19739908 TATATTTTTATAAATGATCTAAGTTTA
1 TATATTTTTATAAAT-TTCTAAGTTTA
* *
19739935 TATATTTTTGA-AAATTTTTAAGGTTTT
1 TATATTTTT-ATAAATTTCTAA-GTTTA
* *
19739962 TAAATTTTTATAAATTTCTAAATTTA
1 TATATTTTTATAAATTTCTAAGTTTA
19739988 TATAT
1 TATAT
19739993 ATTTGAAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
26 12 0.26
27 34 0.72
28 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (26 bp):
TATATTTTTATAAATTTCTAAGTTTA
Found at i:19739983 original size:18 final size:18
Alignment explanation
Indices: 19739962--19739996 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19739952 TTAAGGTTTT
*
19739962 TAAATTTTTATAAATTTC
1 TAAATTTATATAAATTTC
*
19739980 TAAATTTATATATATTT
1 TAAATTTATATAAATTT
19739997 GAAATATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TAAATTTATATAAATTTC
Found at i:19739998 original size:53 final size:53
Alignment explanation
Indices: 19739905--19740014 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 53
19739895 AAATCTCAAA
* * *
19739905 TTTTATATTTTTATAAATGATCTAAGTTTATATATTTTTGAAA-ATTTTTAAGGT
1 TTTTAAATTTTTATAAATGATCTAAATTTATATATATTTGAAATA-TTTTAA-GT
*
19739959 TTTTAAATTTTTATAAAT-TTCTAAATTTATATATATTTGAAATATTTTAAGT
1 TTTTAAATTTTTATAAATGATCTAAATTTATATATATTTGAAATATTTTAAGT
19740011 TTTT
1 TTTT
19740015 CTTTATAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
52 6 0.12
53 27 0.53
54 18 0.35
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (53 bp):
TTTTAAATTTTTATAAATGATCTAAATTTATATATATTTGAAATATTTTAAGT
Found at i:19744488 original size:3 final size:3
Alignment explanation
Indices: 19744482--19744507 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19744472 AATAATAATA
19744482 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
19744508 AAAAGGAGGA
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:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:19749622 original size:18 final size:19
Alignment explanation
Indices: 19749599--19749639 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
19749589 GTTTATGTGC
* *
19749599 TATAAATTATATAATAT-A
1 TATAAATAACATAATATGA
19749617 TATAAATAACATAATATGA
1 TATAAATAACATAATATGA
19749636 TATA
1 TATA
19749640 TTAAAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
TATAAATAACATAATATGA
Found at i:19749633 original size:23 final size:21
Alignment explanation
Indices: 19749607--19749651 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
19749597 GCTATAAATT
19749607 ATATAATATATATAAATAACATA
1 ATATAATATAT-TAAA-AACATA
*
19749630 ATATGATATATTAAAAACATA
1 ATATAATATATTAAAAACATA
19749651 A
1 A
19749652 AAAATGAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 4 0.19
23 10 0.48
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATAATATATTAAAAACATA
Found at i:19750829 original size:13 final size:13
Alignment explanation
Indices: 19750797--19750839 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
19750787 TTAAATGTTA
*
19750797 AAATAATATAAAG
1 AAATAATAAAAAG
19750810 TAAATAATAAAAAG
1 -AAATAATAAAAAG
19750824 AAATAA-AACAAAG
1 AAATAATAA-AAAG
19750837 AAA
1 AAA
19750840 GAACAGAGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 2 0.07
13 13 0.48
14 12 0.44
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (13 bp):
AAATAATAAAAAG
Found at i:19751911 original size:23 final size:23
Alignment explanation
Indices: 19751880--19751967 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
19751870 GCTTTGCCGA
*
19751880 TCAGACACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
19751903 TCAGGCACTTTATGTGTCATATT
1 TCAGGCACTTTATGTGTCGTATT
* ** *
19751926 TCAGGCACCTCGTGTGT--TGTT
1 TCAGGCACTTTATGTGTCGTATT
*
19751947 TCAGGCAC-TTATTTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
19751968 ACTGATCAGG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.09
21 11 0.21
22 2 0.04
23 35 0.66
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:19753716 original size:27 final size:27
Alignment explanation
Indices: 19753664--19753716 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
19753654 ATGCTTTTCA
* *
19753664 ATTTTTTAAAAATATAAAATATAAATT
1 ATTTTCTAAAAATATAAAATAAAAATT
19753691 ATTTTCTAAAAATA-AAAATGAAAAAT
1 ATTTTCTAAAAATATAAAAT-AAAAAT
19753717 AATAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
ATTTTCTAAAAATATAAAATAAAAATT
Found at i:19760925 original size:3 final size:3
Alignment explanation
Indices: 19760917--19760943 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19760907 GAACATTCAC
19760917 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
19760944 AGGCATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19761205 original size:4 final size:4
Alignment explanation
Indices: 19761198--19761242 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
19761188 TTACTTTAGG
* * * *
19761198 ATTA ATTA TTTA ATTA TTTA ATTA TTTA ATTA TTTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
19761243 CTTGGATTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (4 bp):
ATTA
Found at i:19761212 original size:8 final size:8
Alignment explanation
Indices: 19761199--19761242 Score: 79
Period size: 8 Copynumber: 5.5 Consensus size: 8
19761189 TACTTTAGGA
19761199 TTAATTAT
1 TTAATTAT
19761207 TTAATTAT
1 TTAATTAT
19761215 TTAATTAT
1 TTAATTAT
19761223 TTAATTAT
1 TTAATTAT
*
19761231 TTAATTAA
1 TTAATTAT
19761239 TTAA
1 TTAA
19761243 CTTGGATTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TTAATTAT
Found at i:19768908 original size:31 final size:31
Alignment explanation
Indices: 19768873--19768937 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
19768863 AATAGGTATC
*
19768873 TAAACTTGACACTTTTTCCTAATTTGGTACT
1 TAAACTTGACACTTTTTCCTAAGTTGGTACT
*
19768904 TAAACTTGACACTTTTTCTTAAGTTGGTACT
1 TAAACTTGACACTTTTTCCTAAGTTGGTACT
19768935 TAA
1 TAA
19768938 TCTCTTTGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.45
Consensus pattern (31 bp):
TAAACTTGACACTTTTTCCTAAGTTGGTACT
Found at i:19773410 original size:7 final size:7
Alignment explanation
Indices: 19773398--19773428 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
19773388 ATGAAAACTT
19773398 TCTTATA
1 TCTTATA
19773405 TCTTATA
1 TCTTATA
19773412 TCTTATA
1 TCTTATA
19773419 TCTTATA
1 TCTTATA
19773426 TCT
1 TCT
19773429 ACCGTAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (7 bp):
TCTTATA
Found at i:19783177 original size:23 final size:23
Alignment explanation
Indices: 19783133--19783195 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
19783123 TTGTGTGACG
* *
19783133 AATAAAATTT-ATATAAATAAATT
1 AATAAAATTTCAAATATATAAA-T
19783156 AATAAAATTTCAAATATA-AAAT
1 AATAAAATTTCAAATATATAAAT
* *
19783178 AGTAAAATATACAAATAT
1 AATAAAAT-TTCAAATAT
19783196 GAGACACACG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 8 0.24
23 21 0.62
24 5 0.15
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAAAATTTCAAATATATAAAT
Found at i:19783183 original size:22 final size:23
Alignment explanation
Indices: 19783149--19783195 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
19783139 ATTTATATAA
* *
19783149 ATAAATTAATAAAAT-TTCAAAT
1 ATAAAATAATAAAATATACAAAT
*
19783171 ATAAAATAGTAAAATATACAAAT
1 ATAAAATAATAAAATATACAAAT
19783194 AT
1 AT
19783196 GAGACACACG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAAATAATAAAATATACAAAT
Found at i:19784272 original size:15 final size:15
Alignment explanation
Indices: 19784237--19784278 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
19784227 ATTTTTACGG
19784237 TTTAAAA-AATTTTT
1 TTTAAAATAATTTTT
**
19784251 TAAAAAATAATTTTT
1 TTTAAAATAATTTTT
*
19784266 TTTAAAATTATTT
1 TTTAAAATAATTT
19784279 AAAAATAGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAAAATAATTTTT
Found at i:19784356 original size:22 final size:22
Alignment explanation
Indices: 19784329--19784383 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
19784319 TTAAATATGG
19784329 ATTTGAGAGAAATTTG-GAAGGAA
1 ATTTGAGAGAAA-TTGAG-AGGAA
19784352 A-TTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
19784374 ATTTGAGAGA
1 ATTTGAGAGA
19784384 GGATTAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.24
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:19784381 original size:12 final size:12
Alignment explanation
Indices: 19784329--19784382 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
19784319 TTAAATATGG
19784329 ATTTGAGA-GAA
1 ATTTGAGAGGAA
19784340 ATTTG-GAAGGAA
1 ATTTGAG-AGGAA
*
19784352 A-TTGAGAGCAA
1 ATTTGAGAGGAA
19784363 A-TTGAGAGGAA
1 ATTTGAGAGGAA
19784374 ATTTGAGAG
1 ATTTGAGAG
19784383 AGGATTAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 1 0.03
11 24 0.65
12 12 0.32
ACGTcount: A:0.43, C:0.02, G:0.31, T:0.24
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:19785893 original size:20 final size:20
Alignment explanation
Indices: 19785843--19785893 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
19785833 CTATTTCTTT
*
19785843 TAAATTGAAAATTACATTTA
1 TAAAATGAAAATTACATTTA
* * *
19785863 TAAAATAAAAATT-TATTTT
1 TAAAATGAAAATTACATTTA
19785882 TAATAATGAAAA
1 TAA-AATGAAAA
19785894 ATGTGAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (20 bp):
TAAAATGAAAATTACATTTA
Found at i:19794364 original size:9 final size:9
Alignment explanation
Indices: 19794350--19794389 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
19794340 TCTTCATATC
19794350 TTTATTATT
1 TTTATTATT
19794359 TTTATTATT
1 TTTATTATT
*
19794368 TTTATCATTT
1 TTTATTA-TT
*
19794378 TTTATTCTT
1 TTTATTATT
19794387 TTT
1 TTT
19794390 GGGTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 20 0.74
10 7 0.26
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTATT
Found at i:19798322 original size:14 final size:13
Alignment explanation
Indices: 19798290--19798323 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
19798280 TTGATTCTAG
19798290 AAAAT-GAAACAA
1 AAAATAGAAACAA
19798302 AAAATAGAAACAA
1 AAAATAGAAACAA
19798315 ACAAATAGA
1 A-AAATAGA
19798324 GCCGAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 8 0.40
14 7 0.35
ACGTcount: A:0.74, C:0.09, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAATAGAAACAA
Found at i:19798783 original size:14 final size:14
Alignment explanation
Indices: 19798766--19798795 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19798756 AGGTGAACTA
19798766 GCAGAGAAGATGAG
1 GCAGAGAAGATGAG
*
19798780 GCAGAGATGATGAG
1 GCAGAGAAGATGAG
19798794 GC
1 GC
19798796 TGCAATCTTT
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:0.37, C:0.10, G:0.43, T:0.10
Consensus pattern (14 bp):
GCAGAGAAGATGAG
Found at i:19798844 original size:33 final size:33
Alignment explanation
Indices: 19798807--19798871 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
19798797 GCAATCTTTA
19798807 GGTGAAGAGAGTGAAAAGA-GAAGCTGTGGAAAG
1 GGTGAAGAGAGTGAAAAGATG-AGCTGTGGAAAG
*
19798840 GGTGAAGAGAGTGAAGAGATGAGCTGTGGAAA
1 GGTGAAGAGAGTGAAAAGATGAGCTGTGGAAA
19798872 ATGTCTTACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.43, T:0.14
Consensus pattern (33 bp):
GGTGAAGAGAGTGAAAAGATGAGCTGTGGAAAG
Found at i:19800815 original size:114 final size:113
Alignment explanation
Indices: 19800627--19800834 Score: 312
Period size: 114 Copynumber: 1.8 Consensus size: 113
19800617 ATCAGTTTAG
* * * * *
19800627 GATATTTTGATTTTTATTCTATATGATTTTAATTTCAAAAATAAAAAATTGAATAAAAGGATTTG
1 GATATTTAGATTTTTATTCTATACGATTTTAATTTCAAAAATAAAAAATCGAATAAAACGAATTG
*
19800692 ATTCATTTTTTAATCTAAAAATCAAATTAAAATCGTATTATTAATTTCA
66 ATTCATTTTTT-ATCCAAAAATCAAATTAAAATCGTATTATTAATTTCA
*
19800741 GATATTTAGATTTTTATTCTATACCG-TTTTAATTTCAAAAAT-GAAAATCGAATAAAACGAATT
1 GATATTTAGATTTTTATTCTATA-CGATTTTAATTTCAAAAATAAAAAATCGAATAAAACGAATT
*
19800804 GATTCATTTTTTATCCAAAATTCAAATTAAA
65 GATTCATTTTTTATCCAAAAATCAAATTAAA
19800835 CTAAACCAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
112 17 0.20
113 29 0.34
114 38 0.45
115 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (113 bp):
GATATTTAGATTTTTATTCTATACGATTTTAATTTCAAAAATAAAAAATCGAATAAAACGAATTG
ATTCATTTTTTATCCAAAAATCAAATTAAAATCGTATTATTAATTTCA
Found at i:19801870 original size:31 final size:31
Alignment explanation
Indices: 19801835--19801894 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
19801825 ATTAACAACC
19801835 CAATGAATTAAATAAAAACTTTCAAATAGCT
1 CAATGAATTAAATAAAAACTTTCAAATAGCT
* * *
19801866 CAATGACTTACATAAAAACTTTCGAATAG
1 CAATGAATTAAATAAAAACTTTCAAATAG
19801895 TTTAGTGACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.28
Consensus pattern (31 bp):
CAATGAATTAAATAAAAACTTTCAAATAGCT
Found at i:19811648 original size:18 final size:16
Alignment explanation
Indices: 19811617--19811652 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
19811607 ATTAGTTAGA
19811617 ATTTTTTATTAATTTG
1 ATTTTTTATTAATTTG
19811633 ATTTTTTAGTTAAATTTG
1 ATTTTTTA-TT-AATTTG
19811651 AT
1 AT
19811653 ATTCAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (16 bp):
ATTTTTTATTAATTTG
Found at i:19811703 original size:24 final size:22
Alignment explanation
Indices: 19811675--19811720 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19811665 TAAAAAAGTT
*
19811675 AAATTTGATTATAATTTTTTTTAA
1 AAATTT-ATT-TAATATTTTTTAA
*
19811699 AAATTTATTTACTATTTTTTAA
1 AAATTTATTTAATATTTTTTAA
19811721 TAAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 3 0.15
24 6 0.30
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
AAATTTATTTAATATTTTTTAA
Found at i:19811730 original size:23 final size:22
Alignment explanation
Indices: 19811691--19811735 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
19811681 GATTATAATT
** *
19811691 TTTTTTAAAAATTTATTTACTA
1 TTTTTTAAAAAAATATTGACTA
19811713 TTTTTTAATAAAAATATTGACTA
1 TTTTTTAA-AAAAATATTGACTA
19811736 AAAAGTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTTAAAAAAATATTGACTA
Found at i:19811823 original size:17 final size:17
Alignment explanation
Indices: 19811796--19811838 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
19811786 TTTATGCTAT
*
19811796 TTTTTTAATTTGTATAAA
1 TTTTTT-ATTTATATAAA
*
19811814 TTTTTTATTTATTTAAA
1 TTTTTTATTTATATAAA
*
19811831 TATTTTAT
1 TTTTTTAT
19811839 AATCTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTTTATTTATATAAA
Found at i:19812030 original size:18 final size:18
Alignment explanation
Indices: 19812009--19812050 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
19811999 AATTTTACTA
19812009 AAAAATATT-CACAACATT
1 AAAAATATTGCA-AACATT
* *
19812027 AAAAAAATTGTAAACATT
1 AAAAATATTGCAAACATT
19812045 AAAAAT
1 AAAAAT
19812051 TAAATTTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAATATTGCAAACATT
Found at i:19819038 original size:97 final size:98
Alignment explanation
Indices: 19818913--19819102 Score: 373
Period size: 97 Copynumber: 1.9 Consensus size: 98
19818903 ATCTGCATGT
19818913 TCAACCTACTAAAACAACCTAATCTTAAATAAAAAATATAATATCAATTTATTACAAGTCATTTC
1 TCAACCTACTAAAACAACCTAATCTTAAATAAAAAATATAATATCAATTTATTACAAGTCATTTC
19818978 ATATCATGTATCGAACATATTTGTAAACATATA
66 ATATCATGTATCGAACATATTTGTAAACATATA
19819011 TCAACCTACT-AAACAACCTAATCTTAAATAAAAAATATAATATCAATTTATTACAAGTCATTTC
1 TCAACCTACTAAAACAACCTAATCTTAAATAAAAAATATAATATCAATTTATTACAAGTCATTTC
19819075 ATATCATGTATCGAACATATTTGTAAAC
66 ATATCATGTATCGAACATATTTGTAAAC
19819103 CAATAATTAA
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 82 0.89
98 10 0.11
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (98 bp):
TCAACCTACTAAAACAACCTAATCTTAAATAAAAAATATAATATCAATTTATTACAAGTCATTTC
ATATCATGTATCGAACATATTTGTAAACATATA
Found at i:19823757 original size:42 final size:42
Alignment explanation
Indices: 19823679--19823776 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
19823669 GCTCTCAGTA
* *
19823679 TCGCACACTTAGTGCCCGTTATTCAACATCTCCATTTTAATT
1 TCGCACACTTAGTGCCCGTTATCCAACATCTCCATTTTAATC
* * *
19823721 TCGCACACTTAGTGCCCTTTATCCAACCTCGT-CATTTTAGTC
1 TCGCACACTTAGTGCCCGTTATCCAACATC-TCCATTTTAATC
19823763 TCGCACACTTAGTG
1 TCGCACACTTAGTG
19823777 TTGTTCATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
42 49 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.36
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCGTTATCCAACATCTCCATTTTAATC
Found at i:19839274 original size:11 final size:11
Alignment explanation
Indices: 19839258--19839282 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19839248 GGGGTGTTAC
19839258 AAGTTTTGGCT
1 AAGTTTTGGCT
19839269 AAGTTTTGGCT
1 AAGTTTTGGCT
19839280 AAG
1 AAG
19839283 CAATATTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (11 bp):
AAGTTTTGGCT
Found at i:19849110 original size:21 final size:21
Alignment explanation
Indices: 19849084--19849187 Score: 64
Period size: 21 Copynumber: 5.0 Consensus size: 21
19849074 ATGAGAGCTA
19849084 AACGGAAACCCATAAGGGTTG
1 AACGGAAACCCATAAGGGTTG
* *** * *
19849105 AACGGAAGCTTGTAAGAGCTG
1 AACGGAAACCCATAAGGGTTG
* *
19849126 AACGGAAACCTATAAGGGTTA
1 AACGGAAACCCATAAGGGTTG
** * * * * *
19849147 AATTGAAGCTCAAAAGAGCTG
1 AACGGAAACCCATAAGGGTTG
*
19849168 AACAGAAACCCATAAGGGTT
1 AACGGAAACCCATAAGGGTT
19849188 AAACTAAAGC
Statistics
Matches: 55, Mismatches: 28, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.17
Consensus pattern (21 bp):
AACGGAAACCCATAAGGGTTG
Found at i:19849198 original size:42 final size:42
Alignment explanation
Indices: 19849067--19849198 Score: 165
Period size: 42 Copynumber: 3.1 Consensus size: 42
19849057 AGGCTTAACA
* * * *
19849067 GAAGCTCATGAGAGCTAAACGGAAACCCATAAGGGTTGAACG
1 GAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
** * *
19849109 GAAGCTTGTAAGAGCTGAACGGAAACCTATAAGGGTTAAATT
1 GAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
* *
19849151 GAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACT
1 GAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
*
19849193 AAAGCT
1 GAAGCT
19849199 NNNNNNNNNN
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
Found at i:19854334 original size:21 final size:21
Alignment explanation
Indices: 19854308--19854510 Score: 113
Period size: 21 Copynumber: 9.7 Consensus size: 21
19854298 ATGAGAGCTA
*
19854308 AACGGAAACCCATAAGGGTTG
1 AACGGAAACTCATAAGGGTTG
* ** * *
19854329 AACGGAAGCTTGTAAGAGCTG
1 AACGGAAACTCATAAGGGTTG
*
19854350 AACGGAAAC-CTATAAGGGTTA
1 AACGGAAACTC-ATAAGGGTTG
** * * * *
19854371 AATTGAAGCTCAAAAGAGCTG
1 AACGGAAACTCATAAGGGTTG
* * *
19854392 AACAGAAACCCATAAGGGTTA
1 AACGGAAACTCATAAGGGTTG
* * * * *
19854413 AACTGAAGCTCAAAAGAGCTG
1 AACGGAAACTCATAAGGGTTG
* * *
19854434 AACAGAAACCCATAAGGGTTA
1 AACGGAAACTCATAAGGGTTG
* * * *
19854455 AAC-TAAAGCTCAAAAGAGCTG
1 AACGGAAA-CTCATAAGGGTTG
*
19854476 AACGGAAACTCATTAGGGTTG
1 AACGGAAACTCATAAGGGTTG
19854497 AACGGAAACTCATA
1 AACGGAAACTCATA
19854511 TGAGTTAACA
Statistics
Matches: 125, Mismatches: 53, Indels: 8
0.67 0.28 0.04
Matches are distributed among these distances:
20 3 0.02
21 118 0.94
22 4 0.03
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
AACGGAAACTCATAAGGGTTG
Found at i:19854354 original size:42 final size:42
Alignment explanation
Indices: 19854291--19854495 Score: 275
Period size: 42 Copynumber: 4.9 Consensus size: 42
19854281 AGGCTTAACA
** * * *
19854291 GAAGCTCATGAGAGCTAAACGGAAACCCATAAGGGTTGAACG
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
*** * *
19854333 GAAGCTTGTAAGAGCTGAACGGAAACCTATAAGGGTTAAATT
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
*
19854375 GAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACT
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
*
19854417 GAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACT
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
* * *
19854459 AAAGCTCAAAAGAGCTGAACGGAAACTCATTAGGGTT
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTT
19854496 GAACGGAAAC
Statistics
Matches: 145, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 145 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (42 bp):
GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
Done.