Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 12 of 106
Found at i:5712959 original size:29 final size:27
Alignment explanation
Indices: 5712904--5712969 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 27
5712894 AGGTTCATCC
* *
5712904 TTGAAAACTATTGTTGGTTATTAGAATCT
1 TTGAAAACTATAGTTAGTTATTAGAA--T
* *
5712933 TTGAAAACTATAGTTAGTTGTTGGAAT
1 TTGAAAACTATAGTTAGTTATTAGAAT
5712960 TTGAAAACTA
1 TTGAAAACTA
5712970 CTCTCGGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 11 0.33
29 22 0.67
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (27 bp):
TTGAAAACTATAGTTAGTTATTAGAAT
Found at i:5719301 original size:24 final size:25
Alignment explanation
Indices: 5719268--5719314 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
5719258 TTATCCCATA
5719268 CATCATTTTTTT-TTTCTATTGACTG
1 CATCATTTTTTTCTTT-TATTGACTG
5719293 CATC-TTTTTTTCTTTTATTGAC
1 CATCATTTTTTTCTTTTATTGAC
5719315 CAAATGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.15, C:0.17, G:0.06, T:0.62
Consensus pattern (25 bp):
CATCATTTTTTTCTTTTATTGACTG
Found at i:5719302 original size:25 final size:24
Alignment explanation
Indices: 5719268--5719314 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
5719258 TTATCCCATA
*
5719268 CATCATTTTTTTTTTCTATTGACTG
1 CATCATTTTTTCTTT-TATTGACTG
*
5719293 CATCTTTTTTTCTTTTATTGAC
1 CATCATTTTTTCTTTTATTGAC
5719315 CAAATGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.15, C:0.17, G:0.06, T:0.62
Consensus pattern (24 bp):
CATCATTTTTTCTTTTATTGACTG
Found at i:5743040 original size:28 final size:28
Alignment explanation
Indices: 5743004--5743058 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
5742994 AAATTAAAAC
5743004 TTTACTTATATTT-GATATAATTTATTTA
1 TTTACTTATATTTAG-TATAATTTATTTA
* *
5743032 TTTATTTATATTTAGTGTAATTTATTT
1 TTTACTTATATTTAGTATAATTTATTT
5743059 TGTTGTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (28 bp):
TTTACTTATATTTAGTATAATTTATTTA
Found at i:5743720 original size:33 final size:33
Alignment explanation
Indices: 5743681--5743753 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
5743671 ATGTTAAATT
** *
5743681 AATATGTCATGTTATCATTAATTATAATATGTA
1 AATATGTCACATTATCATTAATTATAATATATA
* *
5743714 AATATGTCACATTATCATTAATTATGATATATT
1 AATATGTCACATTATCATTAATTATAATATATA
5743747 AATATGT
1 AATATGT
5743754 TACGTTATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (33 bp):
AATATGTCACATTATCATTAATTATAATATATA
Found at i:5743871 original size:29 final size:30
Alignment explanation
Indices: 5743814--5743916 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 30
5743804 ATCATTAATC
* * *
5743814 ATAAAAATTTATTTGACACAAAATAAAAAT
1 ATAAAAACTTATTTGACTCATAATAAAAAT
*
5743844 AAAAAAACTTATTTGACTCATAATAAAAAT
1 ATAAAAACTTATTTGACTCATAATAAAAAT
* * *
5743874 ATAATAACTTGA-TTGA-TCATAATAATAAC
1 ATAAAAACTT-ATTTGACTCATAATAAAAAT
*
5743903 ATAAAGACTTATTT
1 ATAAAAACTTATTT
5743917 AAATTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
28 1 0.02
29 21 0.34
30 38 0.62
31 1 0.02
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (30 bp):
ATAAAAACTTATTTGACTCATAATAAAAAT
Found at i:5746697 original size:16 final size:16
Alignment explanation
Indices: 5746652--5746698 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
5746642 TCTCAAAAAT
5746652 AAATATTCATAATTTTAA
1 AAATATT-A-AATTTTAA
* *
5746670 AAATATT-TATTTTGA
1 AAATATTAAATTTTAA
5746685 AAATATTAAATTTT
1 AAATATTAAATTTT
5746699 TATCATTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 13 0.52
16 5 0.20
18 7 0.28
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
AAATATTAAATTTTAA
Found at i:5751874 original size:20 final size:20
Alignment explanation
Indices: 5751837--5751874 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5751827 AGTGCTAAAA
*
5751837 AAACTATTAAGTACTTTATT
1 AAACTATTAAGTAATTTATT
5751857 AAACTA-TAAGTTAATTTA
1 AAACTATTAAG-TAATTTA
5751875 ATCCCTGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (20 bp):
AAACTATTAAGTAATTTATT
Found at i:5753455 original size:102 final size:102
Alignment explanation
Indices: 5753339--5753546 Score: 328
Period size: 102 Copynumber: 2.0 Consensus size: 102
5753329 AAAAAAACCG
*
5753339 AAACGGGTCACGGGTTATAGTTTCTTGGGCCTAAGTACGTCTTTATGGGCCAATTAAACCACCGC
1 AAACGGGTCACGGGTTATAGTTTATTGGGCCTAAGTACGTCTTTATGGGCCAATTAAACCACCG-
** * *
5753404 CT-CACGGGCAAGCAAGTTGGTATCCACCTAACAAGGA
65 CTGCACGGGCAAGCAAGTCCGTACCCAACTAACAAGGA
* *
5753441 AAACGGGTCACGGGTTGTAGTTTATTGGGCCTAAGTACTTCTTTATGGGCCAATTAAACCACCGC
1 AAACGGGTCACGGGTTATAGTTTATTGGGCCTAAGTACGTCTTTATGGGCCAATTAAACCACCGC
*
5753506 TGCTCGGGCAAGCAAGTCCGTACCCAACTAACAAGGA
66 TGCACGGGCAAGCAAGTCCGTACCCAACTAACAAGGA
5753543 AAAC
1 AAAC
5753547 TAGGGTTTTG
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 2 0.02
102 95 0.98
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (102 bp):
AAACGGGTCACGGGTTATAGTTTATTGGGCCTAAGTACGTCTTTATGGGCCAATTAAACCACCGC
TGCACGGGCAAGCAAGTCCGTACCCAACTAACAAGGA
Found at i:5759380 original size:2 final size:2
Alignment explanation
Indices: 5759373--5759398 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5759363 AACTTTACAA
5759373 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
5759399 TGCTACCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5771095 original size:2 final size:2
Alignment explanation
Indices: 5771090--5771153 Score: 87
Period size: 2 Copynumber: 32.0 Consensus size: 2
5771080 CAGAGAGGCC
*
5771090 AG AG AG AG AG AG AG AG AG AG AG AG -G ACG -G NAG AG AG CG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG -AG AG AG AG AG AG
5771132 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
5771154 GGCCAAAGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 2 0.04
2 52 0.93
3 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5777135 original size:12 final size:12
Alignment explanation
Indices: 5777118--5777144 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5777108 TCCTGGCCAC
5777118 TGAAGTAAAGCG
1 TGAAGTAAAGCG
5777130 TGAAGTAAAGCG
1 TGAAGTAAAGCG
5777142 TGA
1 TGA
5777145 TCATTGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.33, T:0.19
Consensus pattern (12 bp):
TGAAGTAAAGCG
Found at i:5786978 original size:15 final size:14
Alignment explanation
Indices: 5786958--5787000 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 14
5786948 GAACAAATAA
5786958 TTTTATTAATTATTT
1 TTTTA-TAATTATTT
5786973 TTTTATATATATATTT
1 TTTTATA-AT-TATTT
5786989 TTATTATAATTA
1 TT-TTATAATTA
5787001 ATTATATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.08
15 9 0.36
16 9 0.36
17 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATAATTATTT
Found at i:5794524 original size:3 final size:3
Alignment explanation
Indices: 5794516--5794545 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5794506 GCTACCACAC
*
5794516 TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
5794546 CCACCTTCGT
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:0.03, C:0.00, G:0.30, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:5796724 original size:2 final size:2
Alignment explanation
Indices: 5796719--5796749 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5796709 ATAACAAAAT
5796719 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
5796750 GACTCGATTA
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:5797323 original size:28 final size:27
Alignment explanation
Indices: 5797301--5797353 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
5797291 AAATATTGAT
5797301 AAATTATTT-TTTATTAATTAATATAA
1 AAATTATTTATTTATTAATTAATATAA
5797327 AAATTATTTAATTTATTAATTAA-ATAA
1 AAATTATTT-ATTTATTAATTAATATAA
5797354 TATCTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 9 0.36
27 4 0.16
28 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AAATTATTTATTTATTAATTAATATAA
Found at i:5797344 original size:24 final size:25
Alignment explanation
Indices: 5797313--5797371 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
5797303 ATTATTTTTT
5797313 ATTAATTAATATAAA-AATTAT-TTA
1 ATTAATTAATATAAATAA-TATCTTA
*
5797337 ATTTATTAAT-TAAATAATATCTTA
1 ATTAATTAATATAAATAATATCTTA
5797361 ATTAATTAATA
1 ATTAATTAATA
5797372 ATTTTTCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 7 0.23
24 23 0.77
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTAATTAATATAAATAATATCTTA
Found at i:5797365 original size:28 final size:28
Alignment explanation
Indices: 5797310--5797367 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
5797300 TAAATTATTT
*
5797310 TTTATTAATTAATATAAAAATTATTTAA
1 TTTATTAATTAATATAAAAATTAATTAA
**
5797338 TTTATTAATTAA-ATAATATCTTAATTAA
1 TTTATTAATTAATATAA-AAATTAATTAA
5797366 TT
1 TT
5797368 AATAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTATTAATTAATATAAAAATTAATTAA
Found at i:5805565 original size:2 final size:2
Alignment explanation
Indices: 5805560--5805591 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5805550 TTCATGTGTC
5805560 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5805592 ATTCTTACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5816711 original size:339 final size:335
Alignment explanation
Indices: 5815843--5816993 Score: 1269
Period size: 339 Copynumber: 3.4 Consensus size: 335
5815833 TATCTCAAAC
* * * *
5815843 ATAATTAATAAATTTATTAGTTATAATTTTTGTAATGTTAACACAAAATATAAAGTAAATATATT
1 ATAATTAATAAATTTATAAGTTATAATTTTTGTAATGTTAAAACAAAATAAAAAGTAAATAT-GT
* * *
5815908 TATATTCTATTTAAAGTGTATATATACTAAAAGTATTTTAATACATATATAATAGTAATT-TATT
65 T-TA---TATTTAAAGTATAT-TATACTAAAAATA-TTTAATATATATATAATAGTAATTATATT
* * *
5815972 TCTTATAAATTAACACAATATATAAAATATATATATTAAAAGACATTACAAGTCAATTAATAATC
124 TCTTATAAATTAACACAATATATAAAATATATATATTAAAAGATATTACAAGTTAATTAATAATA
* * ** * *
5816037 ATATTTTCATTAATTAATTTAATTAGTTATATAAGTTTGTCCTTAATTACAAGAAATT-AAAAAA
189 ATAATTTCATGAATTAATTTAATTAACTATAGAA-TTTGTCCTTAATTACATGAAATTAAAAAAA
* ** * * *
5816101 AA-AACTAAGTTT-TTAAACTATTATAATCTTGCAACTTCTCTTAAGATTTATATGTTATACGTT
253 AATAACTAA-TTTCAT-AACTATTATAATCTCACAACTTCTCTTTAGGTTTATA---TATAAGTT
*
5816164 TATATAAACAAGAGTATATATATT
313 TATATAAATAA-AGTATATATATT
* * * * *
5816188 GTAATTGATAATTTTATGAGTTGTAATTTTTGTAATGTTAAAACAAAATAAAAAGTAAATATGTT
1 ATAATTAATAAATTTATAAGTTATAATTTTTGTAATGTTAAAACAAAATAAAAAGTAAATATGTT
* * * * * * *
5816253 TAAATTTAAAGTATA-TATAC-ACACACA-CTCATTTATATATAATAGTAATTATATTAT-TTAT
66 TATATTTAAAGTATATTATACTAAAAATATTTAATATATATATAATAGTAATTATATT-TCTTAT
* * * *
5816314 AAA-TGACATTAATATATATAAAGTATATATATTAAAAGATATTACAAGTTAGTTAATAATTATA
130 AAATTAACA-CAATATATA-AAA-TATATATATTAAAAGATATTACAAGTTAATTAATAATAATA
*
5816378 ATTTCATGAATTAATTTAATTAACTATACGAATTTGTTCTTAATTACATGAAATTAAAAAAAAAT
192 ATTTCATGAATTAATTTAATTAACTATA-GAATTTGTCCTTAATTACATGAAATTAAAAAAAAAT
*
5816443 AACTACATTTCATAACTATTATAAACTCACAACTTCTCTTTAGGTTTATATATAAGTTTATATAA
256 AACTA-ATTTCATAACTATTATAATCTCACAACTTCTCTTTAGGTTTATATATAAGTTTATATAA
5816508 ATAAAGTTATATATATT
320 ATAAAG-TATATATATT
* *
5816525 ATAATTAATAATTTTATAAGTTATAA-TTTTGTAATGTTAACACAAAATAAAAAGTAAATATGTT
1 ATAATTAATAAATTTATAAGTTATAATTTTTGTAATGTTAAAACAAAATAAAAAGTAAATATGTT
5816589 TATATTTAAAGTATATGTATACTAAAAATATTTAAGTATATATATAATAGTAATTATATTTCTTA
66 TATATTTAAAGTATAT-TATACTAAAAATATTTAA-TATATATATAATAGTAATTATATTTCTTA
* *
5816654 TAAATTAACACAATATATAAACTATATATATTGAAAA-ATATTACAAGTTAATTAATAATAATAG
129 TAAATTAACACAATATATAAAATATATATATT-AAAAGATATTACAAGTTAATTAATAATAATAA
*
5816718 TTTCATGAATTAATTTAATTAACTATATGGATTTGTCCTTAATTTA-ATGAAATTAAAAAAAAAT
193 TTTCATGAATTAATTTAATTAACTATA-GAATTTGTCCTTAA-TTACATGAAATTAAAAAAAAAT
** * * * * * * *
5816782 AGTTAGGTTTCAAAACTATTCTAATCTCAAAAGTTCTCTTTAAGTATATATGTTATAAGTTTATA
256 AACTA-ATTTCATAACTATTATAATCTCACAACTTCTCTTTAGGT-T-TAT-ATATAAGTTTATA
*
5816847 TAAATAATGGTATATATATT
317 TAAATAA-AGTATATATATT
* * *
5816867 ATAATTAATAAATTTATAAGTCATAATTTTTGTAATATTAAAAAACAAAATAGAAAGTAAATA--
1 ATAATTAATAAATTTATAAGTTATAATTTTTGTAATGTT--AAAACAAAATAAAAAGTAAATATG
* * * ** * *
5816930 TATATATATATA-TAT-TTATGTTAAAAGTA--T-ATATATATATATTAGTAATTATATTTCTTT
64 TTTATATTTAAAGTATATTATACTAAAAATATTTAATATATATATAATAGTAATTATATTTC-TT
5816990 ATAA
128 ATAA
5816994 TATGATATGA
Statistics
Matches: 694, Mismatches: 84, Indels: 64
0.82 0.10 0.08
Matches are distributed among these distances:
335 23 0.03
336 97 0.14
337 63 0.09
338 93 0.13
339 140 0.20
340 74 0.11
341 44 0.06
342 60 0.09
343 23 0.03
344 2 0.00
345 75 0.11
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (335 bp):
ATAATTAATAAATTTATAAGTTATAATTTTTGTAATGTTAAAACAAAATAAAAAGTAAATATGTT
TATATTTAAAGTATATTATACTAAAAATATTTAATATATATATAATAGTAATTATATTTCTTATA
AATTAACACAATATATAAAATATATATATTAAAAGATATTACAAGTTAATTAATAATAATAATTT
CATGAATTAATTTAATTAACTATAGAATTTGTCCTTAATTACATGAAATTAAAAAAAAATAACTA
ATTTCATAACTATTATAATCTCACAACTTCTCTTTAGGTTTATATATAAGTTTATATAAATAAAG
TATATATATT
Found at i:5817391 original size:15 final size:15
Alignment explanation
Indices: 5817365--5817415 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
5817355 CAATTCAATG
*
5817365 TGATTACAAGTAATA
1 TGATTGCAAGTAATA
5817380 T-ACTTGCAAGTAATA
1 TGA-TTGCAAGTAATA
*
5817395 TGATTGCAAGCAATA
1 TGATTGCAAGTAATA
5817410 TGATTG
1 TGATTG
5817416 TAGATAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 1 0.03
15 30 0.94
16 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (15 bp):
TGATTGCAAGTAATA
Found at i:5817728 original size:29 final size:28
Alignment explanation
Indices: 5817683--5817761 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
5817673 TTTAATATAG
5817683 TTTTTTATA-T-TA-TATATTTTATTAA
1 TTTTTTATACTATATTATATTTTATTAA
5817708 TTTCTTT-TACCTATATTATATAATTT-TTAA
1 TTT-TTTATA-CTATATTATAT--TTTATTAA
*
5817738 TTTTTTATATTATATTATATTTTA
1 TTTTTTATACTATATTATATTTTA
5817762 ATTTCTAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
25 5 0.11
26 3 0.07
27 4 0.09
28 2 0.05
29 18 0.41
30 9 0.20
31 3 0.07
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTTTATACTATATTATATTTTATTAA
Found at i:5817746 original size:24 final size:24
Alignment explanation
Indices: 5817683--5817765 Score: 76
Period size: 31 Copynumber: 3.1 Consensus size: 24
5817673 TTTAATATAG
*
5817683 TTTTTTATATTATATATTTTATTAA
1 TTTTTTATATTATATAATTT-TTAA
5817708 TTTCTTTTACCTATATTATATAATTTTTAA
1 --T-TTTT---TATATTATATAATTTTTAA
*
5817738 TTTTTTATATTATATTATATTTTAA
1 TTTTTTATATTATATAAT-TTTTAA
5817763 TTT
1 TTT
5817766 CTAATTCTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
24 12 0.24
25 9 0.18
27 5 0.10
28 5 0.10
30 4 0.08
31 14 0.29
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTTTATATTATATAATTTTTAA
Found at i:5817749 original size:55 final size:54
Alignment explanation
Indices: 5817683--5817788 Score: 144
Period size: 55 Copynumber: 1.9 Consensus size: 54
5817673 TTTAATATAG
* *
5817683 TTTTTTATATTATA-TATTTTATTAATTTCT-TTTACCTATATTATATAATTTTTAA
1 TTTTTTATATTATATTATATT-TTAATTTCTAATT-CCTATATTATAT-ATTTTTAA
*
5817738 TTTTTTATATTATATTATATTTTAATTTCTAATTCTTATATTATATATTTT
1 TTTTTTATATTATATTATATTTTAATTTCTAATTCCTATATTATATATTTT
5817789 ATTTTAATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 5 0.11
55 34 0.74
56 7 0.15
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (54 bp):
TTTTTTATATTATATTATATTTTAATTTCTAATTCCTATATTATATATTTTTAA
Found at i:5817776 original size:26 final size:26
Alignment explanation
Indices: 5817747--5817796 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
5817737 ATTTTTTATA
5817747 TTATATTATAT-TTTAATTTCTAATTC
1 TTATATTATATATTTAATTT-TAATTC
*
5817773 TTATATTATATATTTTATTTTAAT
1 TTATATTATATATTTAATTTTAAT
5817797 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATATTATATATTTAATTTTAATTC
Found at i:5817807 original size:15 final size:15
Alignment explanation
Indices: 5817780--5817811 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5817770 TTCTTATATT
5817780 ATATATTTTATTTTA
1 ATATATTTTATTTTA
*
5817795 ATATTTTTTATTTTA
1 ATATATTTTATTTTA
5817810 AT
1 AT
5817812 TATAACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:5821306 original size:12 final size:12
Alignment explanation
Indices: 5821260--5821303 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
5821250 GATGTTGGTA
5821260 GATAGATAGATT
1 GATAGATAGATT
5821272 GATAGATAGATTT
1 GATAGATAGA-TT
* *
5821285 GAGA-ATATATT
1 GATAGATAGATT
5821296 GATAGATA
1 GATAGATA
5821304 TATATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (12 bp):
GATAGATAGATT
Found at i:5825795 original size:37 final size:37
Alignment explanation
Indices: 5825754--5825832 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
5825744 ATTTAGATGG
*
5825754 TTACGATGACATATTGACGTACATACTAGAGATAGTA
1 TTACGATGACATATTGACATACATACTAGAGATAGTA
5825791 TTACGATGACATATTGACATACATACTAGAGATAGTA
1 TTACGATGACATATTGACATACATACTAGAGATAGTA
5825828 TTACG
1 TTACG
5825833 TGTGAGACCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (37 bp):
TTACGATGACATATTGACATACATACTAGAGATAGTA
Found at i:5843229 original size:108 final size:108
Alignment explanation
Indices: 5843051--5843248 Score: 290
Period size: 108 Copynumber: 1.8 Consensus size: 108
5843041 GCATGTAAGC
* * *
5843051 TATCATCTACACATATTTAGCTCTCTCCTGAGTCCATGTTTAAGAGGTCCTTTTTAGGGCCAGAA
1 TATCATCTACACATATTTAACTCTCTCCTGAGTCCATGTTTAAGAGGTCATTATTAGGGCCAGAA
5843116 GCCCAGAACGAAAATGTAAA-AGTTTATTGAGCAGCGAGTGAGG
66 GCCCAGAACGAAAATG-AAAGAGTTTATTGAGCAGCGAGTGAGG
* * * * *
5843159 TATCATTTACATATATTTAACTTTCTTCTGAGTCCATGTTTAATAGGTCATTATTAGGGCCAGAA
1 TATCATCTACACATATTTAACTCTCTCCTGAGTCCATGTTTAAGAGGTCATTATTAGGGCCAGAA
* *
5843224 TCCCAGAACGTAAATGAAAGAGTTT
66 GCCCAGAACGAAAATGAAAGAGTTT
5843249 GTCACTATTA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
107 3 0.04
108 76 0.96
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (108 bp):
TATCATCTACACATATTTAACTCTCTCCTGAGTCCATGTTTAAGAGGTCATTATTAGGGCCAGAA
GCCCAGAACGAAAATGAAAGAGTTTATTGAGCAGCGAGTGAGG
Found at i:5859294 original size:21 final size:23
Alignment explanation
Indices: 5859218--5859303 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
5859208 TAACAATATG
*
5859218 TTATTATT-AAATAATAATTTAATTT
1 TTATTATTAAAATATTAA--TAA-TT
*
5859243 TTATTATTTAAATATTAATAATT
1 TTATTATTAAAATATTAATAATT
*
5859266 TTATTATTAAAATATTAA-GA-T
1 TTATTATTAAAATATTAATAATT
*
5859287 TTAGTATTAAAATATTA
1 TTATTATTAAAATATTA
5859304 TTTATTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
21 17 0.30
22 1 0.02
23 19 0.34
24 3 0.05
25 8 0.14
26 8 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATTATTAAAATATTAATAATT
Found at i:5859384 original size:27 final size:26
Alignment explanation
Indices: 5859325--5859394 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 26
5859315 ACTTAATTTC
* *
5859325 TTTTTTTATTTTTATTTTCATTTTTAA
1 TTTTTTTATTTATAATTTCATTTTT-A
* *
5859352 TCTTTTAATTTATAATTTCATTTTT-
1 TTTTTTTATTTATAATTTCATTTTTA
* *
5859377 TTTTTTTTTTTAGAATTT
1 TTTTTTTATTTATAATTT
5859395 GGAGAAGGAG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 14 0.40
27 21 0.60
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.74
Consensus pattern (26 bp):
TTTTTTTATTTATAATTTCATTTTTA
Found at i:5859528 original size:22 final size:22
Alignment explanation
Indices: 5859495--5859554 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
5859485 ATTAAAATTA
*
5859495 AAATTTTAATAATTTATTAGT-
1 AAATATTAATAATTTATTAGTG
** *
5859516 ACAATATTAATAATGAATTATTG
1 A-AATATTAATAATTTATTAGTG
5859539 AAATATTAATAATTTA
1 AAATATTAATAATTTA
5859555 ATAATATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
AAATATTAATAATTTATTAGTG
Found at i:5866499 original size:2 final size:2
Alignment explanation
Indices: 5866492--5866526 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5866482 AATTGCTTTC
*
5866492 AT AT AT AT TT AT AT -T 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
5866527 TTGAAATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:5870681 original size:3 final size:3
Alignment explanation
Indices: 5870673--5870704 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5870663 AAACAGTTTA
*
5870673 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5870705 GGATGGTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5872703 original size:10 final size:10
Alignment explanation
Indices: 5872688--5872717 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5872678 TTGAAAACTC
5872688 AATTGAAACA
1 AATTGAAACA
*
5872698 AATTGAAAGA
1 AATTGAAACA
5872708 AATTGAAACA
1 AATTGAAACA
5872718 TCTTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (10 bp):
AATTGAAACA
Found at i:5872799 original size:213 final size:214
Alignment explanation
Indices: 5872517--5872920 Score: 609
Period size: 215 Copynumber: 1.9 Consensus size: 214
5872507 TGCTTTAAAG
*
5872517 TTTTTTTATTAAAATAAGTAAAACAAAAAAAAACAAAAAAAACCTTCAAATATAAAAAACAACTT
1 TTTTTTTATTAAAATAAATAAAACAAAAAAAAACAAAAAAAACCTTCAAATATAAAAAACAACTT
* * * * * *
5872582 ATTTTTTACATAAGGTGT-AAA-AAAAATTAATTCAATGGAATACGAAATATCAAAAAAATAAAA
66 ATTTTTGACATAAGATGTAAAAGAAAAAATAATTCAATAGAAAACGAAAGATCAAAAAAATAAAA
*
5872645 AGGAGTTCTAATTGAATTACACTTGTCATTCAATTGAAA-ACTCAATTGAAACAAATTGAAAGAA
131 AGGAGTTCTAATTGAATGACACTTGTCATTCAATT-AAAGACTCAATTGAAACAAATTGAAAGAA
5872709 ATTGAAACATCTTATTTTTA
195 ATTGAAACATCTTATTTTTA
* * * * *
5872729 TTTTTTTATTAAAATAAATAAAAGTAAAAAAATAA-AAAAAAAACCTTTAAATGTCAAGAACAAC
1 TTTTTTTATTAAAATAAATAAAA-CAAAAAAA-AACAAAAAAAACCTTCAAATATAAAAAACAAC
*
5872793 TTATTTTTGACATAAGATGTAAAAGAAAAAATAATTCAATAGAAAACGAAAGGTCAAAAAAATAA
64 TTATTTTTGACATAAGATGTAAAAGAAAAAATAATTCAATAGAAAACGAAAGATCAAAAAAATAA
* *
5872858 AAAGGGGTTCTAATTGAATGACACTTGTCATTCAATTAAAGATTCAATTGAAACAAATTGAAA
129 AAAGGAGTTCTAATTGAATGACACTTGTCATTCAATTAAAGACTCAATTGAAACAAATTGAAA
5872921 TATCTTACTT
Statistics
Matches: 171, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
212 22 0.13
213 50 0.29
214 8 0.05
215 91 0.53
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.29
Consensus pattern (214 bp):
TTTTTTTATTAAAATAAATAAAACAAAAAAAAACAAAAAAAACCTTCAAATATAAAAAACAACTT
ATTTTTGACATAAGATGTAAAAGAAAAAATAATTCAATAGAAAACGAAAGATCAAAAAAATAAAA
AGGAGTTCTAATTGAATGACACTTGTCATTCAATTAAAGACTCAATTGAAACAAATTGAAAGAAA
TTGAAACATCTTATTTTTA
Found at i:5874051 original size:108 final size:109
Alignment explanation
Indices: 5873910--5874116 Score: 344
Period size: 108 Copynumber: 1.9 Consensus size: 109
5873900 ATAAATTTTG
* * *
5873910 AGTAAATTTAAATAAAAAGGTAAATTGGGTAAGAGTTGAATAATTACAAAAGAATGTGTATTTGT
1 AGTAAATTTAAATAAAAAGGTAAATTGGATAAGAGTTGAATAATTACAAAAGAACGTGTATTTAT
* *
5873975 AATTTGTGAAAGTTGTAACTAAATCAATATATTTTGCTAATTTA
66 AAATTGTGAAAGTTGTAACTAAATCAACATATTTTGCTAATTTA
**
5874019 AGTAAATTTAAAT-AAAAGGTAAATTGGATAAGAGTTGAATAATTTTAAAAGAACGTGTATTTAT
1 AGTAAATTTAAATAAAAAGGTAAATTGGATAAGAGTTGAATAATTACAAAAGAACGTGTATTTAT
5874083 AAATTGTGAAAGTTGTAACTAAATCAACATATTT
66 AAATTGTGAAAGTTGTAACTAAATCAACATATTT
5874117 AGTCATTTTA
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 78 0.86
109 13 0.14
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (109 bp):
AGTAAATTTAAATAAAAAGGTAAATTGGATAAGAGTTGAATAATTACAAAAGAACGTGTATTTAT
AAATTGTGAAAGTTGTAACTAAATCAACATATTTTGCTAATTTA
Found at i:5874855 original size:17 final size:17
Alignment explanation
Indices: 5874833--5874900 Score: 61
Period size: 18 Copynumber: 4.1 Consensus size: 17
5874823 ATTAGTAACT
5874833 AAATTATTAATTTTATA
1 AAATTATTAATTTTATA
*
5874850 AAATTA--AA-TATATA
1 AAATTATTAATTTTATA
* *
5874864 AAATTATTAAATTAATTA
1 AAATTATTAATTTTA-TA
* *
5874882 AAATTATGAATTTTTTA
1 AAATTATTAATTTTATA
5874899 AA
1 AA
5874901 CCCATATGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
14 11 0.28
15 2 0.05
16 2 0.05
17 12 0.30
18 13 0.32
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (17 bp):
AAATTATTAATTTTATA
Found at i:5875693 original size:2 final size:2
Alignment explanation
Indices: 5875686--5875712 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5875676 TGAACAGTTC
5875686 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 T
5875713 CACACATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5893914 original size:25 final size:25
Alignment explanation
Indices: 5893880--5893930 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
5893870 TTATGAGGAC
5893880 TTATGTTCTATCATCTAGTAAACTA
1 TTATGTTCTATCATCTAGTAAACTA
*
5893905 TTATGTTCTATCATCTAGTTAACTA
1 TTATGTTCTATCATCTAGTAAACTA
5893930 T
1 T
5893931 GTTCAACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (25 bp):
TTATGTTCTATCATCTAGTAAACTA
Found at i:5893934 original size:22 final size:23
Alignment explanation
Indices: 5893878--5893934 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 23
5893868 ATTTATGAGG
5893878 ACTTATGTTCTATCATCTAGTAA
1 ACTTATGTTCTATCATCTAGTAA
*
5893901 ACTATTATGTTCTATCATCTAGTTA
1 AC--TTATGTTCTATCATCTAGTAA
5893926 AC-TATGTTC
1 ACTTATGTTC
5893935 AACTAAAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 7 0.23
23 2 0.06
25 22 0.71
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.46
Consensus pattern (23 bp):
ACTTATGTTCTATCATCTAGTAA
Found at i:5902010 original size:898 final size:892
Alignment explanation
Indices: 5899866--5903973 Score: 4180
Period size: 882 Copynumber: 4.6 Consensus size: 892
5899856 TGTAATTGCA
* * * * * *
5899866 TTGGTTGAAGGCATATTGGTGCAAGACAAGAGTCTAAATTGAGGATGCCCATAGCGCAGAGTGTG
1 TTGGTTGAAGGCATATTGGTGCAAGAGAAGAGGCTAAATTGAGGAGGGCCATACCACA-AGTGTG
* ** ** * *
5899931 GACTGGTGATTGGTCAGAATAATAAATAGGTGTAGGTCTCACTCAGAGAAAGCAAAAGGCACATT
65 GACTGGTGATTGGTCAGAATGATAAATAGGCATACATCTCACTCAGAGGAAGAAAAAGGCACA-T
* *
5899996 TCTTTTCTGTTGGCCCTTTTTTTTTTTTGCTAGGA-AGGTTGTTGTGGATTAACTGCTTTGTTCC
129 TCTTTTCTGTTGG-CCTTTTTTTTTTTTGCTA-AATAGGTTGTTGTGGATTAACTGCTTTATTCC
* *
5900060 TCTATTTCACAGTGCTAAGTCAGATTTCCAATTTTTAATGACTGTGATTCCAGGTATGAGG-TGA
192 TCTATTTCACAGTGCTAAGGCAGATTTCCATTTTTTAATGACTGTGATTCCAGGTATGAGGCT-A
* *
5900124 GCTTGCCCACATGCAAATACAGTACATACTGCCTAATTTAATTAATTATTTATTTTGCCACTTAT
256 GCTTGCCCACATGCAAATATAGTACATACAGCCTAATTT-A-T--TTATTTATTTTGCCACTTAT
* * *
5900189 TTCTAAGGACTTGTTAGAAAACAGATAAATCTAAGTCCATAAAGTTCTGTATTTTGCTCTTAATG
317 TTCTGAGGACTTGTTAGAAAACAGATCAATCTAAGTCCATAAAGTTCTGTATTATGCTCTTAATG
5900254 TTGACTTCAGATCAGATTCCTCTGATCAAATATTTCAGGATATAATATAGGGAACCAAGAAGAAA
382 TTGACTTCAGATCAGATTCCTCTGATCAAATATTTCAGGATATAATATAGGGAACCAA-AAGAAA
* * * * * *
5900319 AACGCTAGGCATTGGGGCATTCCAAGAATCAAACTTGGGACCT-TTGCAGCCAAAGCGAGAATCA
446 AAAGCTAGGCATTGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATCA
* *
5900383 TACCACTAGACCAAATGCCCAATTTTGTTGTCTATAATGTTTTGTTATTATTATAACATCTATAG
511 TACCACTAGACCAAATGCCCGATTTTGTTGTCTATAAGGTTTTGTTATTATTATAACATCTATAG
* * * *
5900448 GTGGTAAATATTCAAAAAATGATGCTTACTTTTCTTTCTTTATTTGTTGATGAACTCTCTGAGAA
576 GTGGTAAAT-TTCAAAAAATGGTGCATACTTTT-TTTCTTTATTTATTGATGAAGTCTCTGAGAA
* * * * *
5900513 CTAGAATGTTGGTGAGCTTTCTTGCTATTGGAATACCTAGTAAAGTGATTCAAAACTGTTCAAAG
639 CTAGATTGTTTGTGAGCTTTTTTGCTATTGGAATACATAGTAAAGTGATTCAAAATTGTTCAAAG
* * *
5900578 ATGAGGGTATAT--GCAATTAGCAGTTATGCGGGTATTGTTTACAAAATGACATGTCGTAGTAAA
704 ATGAGGGTATATGGGCAATTAGCAGTTATGCAGG-ATTGTTCACAAAATGACATGTCGTAATAAA
** * * * ** * *
5900641 TTTTTCTCTGCTGGGCTCTGAAGGATGAATACTAAAGTCTGCTAATCGGACAACGGATGCTAAAC
768 TTTTTCTCTGCAAGACTCTGAAGGATGAATACTAAAATCTGTTAATCACACAAGGGATGCTAAAT
* * * *
5900706 ATTTTAGCTGTAAAGTCATCCTGCAATTGCATTGAGCTAGCTTCAGATCCTGTTTAGACCT
833 ACTTTAGCTGTAAAGTCATTCTGTAATTGCATTGAGCTAG-TTCAAATCCTGTTTAGACCT
* * * *
5900767 TTGGTTGAAGGCATATTGGTGCAAGAGGAGAGGCTAAGTTGAGGAGGCCCATACCGC-AGAT-TG
1 TTGGTTGAAGGCATATTGGTGCAAGAGAAGAGGCTAAATTGAGGAGGGCCATACCACAAG-TGTG
* * * * *
5900830 AACTGGTGATAGGTTAGAATGATAAATAGACATACGTCTCACTCAGAGGAAGAAAAAGGCACATT
65 GACTGGTGATTGGTCAGAATGATAAATAGGCATACATCTCACTCAGAGGAAGAAAAAGGCACA-T
* *
5900895 TCTTTTCCGTTGGCCTTCTGTTTTTTTATTTTTTATTTTTTGCTAGATAGGTTGTTGTGGATTAA
129 TCTTTTCTGTTGG-C--C----------TTTTTT-TTTTTTGCTAAATAGGTTGTTGTGGATTAA
* *
5900960 CTGCTTTATTCCTCTATCTCACAGTGCTAAGGCAGATTTCCATTTTCTAATGACTGTGATTCCAG
180 CTGCTTTATTCCTCTATTTCACAGTGCTAAGGCAGATTTCCATTTTTTAATGACTGTGATTCCAG
*
5901025 GTATGAGGCTAGCTTGCCCACATACAAATATAGTACATACAGCCTAATTTATTTATTTATTTTGC
245 GTATGAGGCTAGCTTGCCCACATGCAAATATAGTACATACAGCCTAATTTATTTATTTATTTTGC
* * *
5901090 TACTTATTTCTGATGACTTGTTAGAAAACAGATCAATCTAAGTCCATAAAGTTCTGTACTAAAT-
310 CACTTATTTCTGAGGACTTGTTAGAAAACAGATCAATCTAAGTCCATAAAGTTCTGTA-T-TATG
* * * * *
5901154 CTCTTAATGTTGACTTAAGATCAGATTCCTCTGGTTAAATACTTCTGGATATAATATAGGGAACC
373 CTCTTAATGTTGACTTCAGATCAGATTCCTCTGATCAAATATTTCAGGATATAATATAGGGAACC
5901219 AAAAGGAAAAAAGCTAGGCATTGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAG
438 AAAA-GAAAAAAGCTAGGCATTGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAG
*
5901284 CGAGAATCATACCACTAGACCAAATGCCCGATTTTGTTGTCTGTAAGGTTTTGTTATTATTATAA
502 CGAGAATCATACCACTAGACCAAATGCCCGATTTTGTTGTCTATAAGGTTTTGTTATTATTATAA
* *
5901349 CATCTATTGGTGGTAAATTTTAAAAAATGGTGCATAC-TTTTTT-TTT-TTTATTGATGAAGTCT
567 CATCTATAGGTGGTAAATTTCAAAAAATGGTGCATACTTTTTTTCTTTATTTATTGATGAAGTCT
* * * *
5901411 CTAAGAACTAGATTGTTTGCGAGCTTTTTTTTCTATTGGAATACATAGTAAAGTGCTTCAAAATT
632 CTGAGAACTAGATTGTTTGTGAGC-TTTTTTGCTATTGGAATACATAGTAAAGTGATTCAAAATT
* *
5901476 GTTCAAAGATGA-GGTATATAGGGCAATTAGCAGTTATGCAGGAATT-TTCACACAATGATATGT
696 GTTCAAAGATGAGGGTATAT-GGGCAATTAGCAGTTATGCAGG-ATTGTTCACAAAATGACATGT
* * *
5901539 CGTAATAAAATTTTCTCTGCAAGACTCTGAAGGATGAATGCTAAAATCT-TTATTCACACAAGGG
759 CGTAATAAATTTTTCTCTGCAAGACTCTGAAGGATGAATACTAAAATCTGTTAATCACACAAGGG
*
5901603 ATGCTAAATACTTTAGCTGTAAAGTCATTCTGTAATTGCATTGAGCTAGCTTCAAATCTTGTTTA
824 ATGCTAAATACTTTAGCTGTAAAGTCATTCTGTAATTGCATTGAGCTAG-TTCAAATCCTGTTTA
5901668 GACCT
888 GACCT
*
5901673 TTGGTTGAAGGCATATTGGTGCAAGAGAAGAGGCTAAATTGAGAAGGGCCATACCACCAAGTGTG
1 TTGGTTGAAGGCATATTGGTGCAAGAGAAGAGGCTAAATTGAGGAGGGCCATACCA-CAAGTGTG
5901738 GACT-G-G-TTGGTCAGAATGATAAATAGGCATACATCTCACTCAGAGGAAGAAAAAGGCACATC
65 GACTGGTGATTGGTCAGAATGATAAATAGGCATACATCTCACTCAGAGGAAGAAAAAGGCACAT-
* *
5901800 TCTTTTCTGTTGGCATTCTTTTTTTTTTTTTTTTGATATATAGGTTGTTGTGGATTAACTGCTTT
129 TCTTTTCTGTTGGC---C----TTTTTTTTTTTTGCTAAATAGGTTGTTGTGGATTAACTGCTTT
* *
5901865 ATTCCTCTATTTCACAGCGCCAAGGCAGATTTCCATTTTTTAATGACTGTGATTCCAGGTATGAG
187 ATTCCTCTATTTCACAGTGCTAAGGCAGATTTCCATTTTTTAATGACTGTGATTCCAGGTATGAG
* * * *
5901930 GCTAGCTTGCCCACATGCAAATATAGTACATAAAGCCTAATTTATTTGTTTATTTTGCTACTTGT
252 GCTAGCTTGCCCACATGCAAATATAGTACATACAGCCTAATTTATTTATTTATTTTGCCACTTAT
* *
5901995 TTCTGAGGGCTTGTTAGAAAACAGATCAATCTAAGTACATAAAGTTCTGTATTATGCTCTTAATG
317 TTCTGAGGACTTGTTAGAAAACAGATCAATCTAAGTCCATAAAGTTCTGTATTATGCTCTTAATG
* * * *
5902060 TTGACTTCAGATCAGATTCCTCTGTTAAAATATTTCA-CATTATAA-ATAGGGAACGAAATAGAA
382 TTGACTTCAGATCAGATTCCTCTGATCAAATATTTCAGGA-TATAATATAGGGAACCAAA-AGAA
*
5902123 AAAAGCTAGGCCTTGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATC
445 AAAAGCTAGGCATTGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATC
* * *
5902188 ATACCACTAGACCAAATGCCCGATTTTGTAGTCTGT-AGTGTTTTGTTATTGTTATAACATCTAT
510 ATACCACTAGACCAAATGCCCGATTTTGTTGTCTATAAG-GTTTTGTTATTATTATAACATCTAT
** * *
5902252 AGGTGGTAAATTTTCACCAAATAGTGC-TAACTTTTCATTCTTTATTTATTGATGAAGTCTCTGA
574 AGGTGGTAAA-TTTCAAAAAATGGTGCAT-ACTTTT-TTTCTTTATTTATTGATGAAGTCTCTGA
* **** * ** * ** *
5902316 GAACTAGATT-TTT-T----TTTTTT-TTA-T--AAT-TGGGGGAGGGGGGATTCGAACCCTTCT
636 GAACTAGATTGTTTGTGAGCTTTTTTGCTATTGGAATACATAGTA-AAGTGATTC-AA-AATTGT
*** * * * ** * * * * ** *
5902370 TTTTAGGTAAGGGGATCATGCACCAACTAATG-AGCTAAATGCTCGG-GTGCTCTCTGAGAACTA
698 TCAAAGATGAGGGTAT-ATG-GGCAA-TTA-GCAG-T-TATGC-AGGATTG-T-TCACA-AAAT-
* * * **** * * * * * *
5902433 GATTAT-TTGTGAGCTTTTTTTGCTATTGAAATACTCAGTAAAG-TG-CT-C-AAAAT-TGTTCA
752 GA-CATGTCGTAATAAATTTTT-CT-CTGCAAGACTCTG-AAGGATGAATACTAAAATCTGTT-A
* ** * * * * * ** *** *
5902492 A--AGATGAGTGTATAGGGC-AATTAGCAGTTATGCAG-GAA-TTGTTCACAAAATGACA---AG
812 ATCACACAAG-GGAT---GCTAAATA-C-TTTA-GCTGTAAAGTCATTCTGTAATTG-CATTGAG
* * ** *
5902549 -TA-ATAAAATGTTCTCTG-CAAG-GCT
869 CTAGTTCAAA---TC-CTGTTTAGACCT
* * *
5902573 CTGGTTGAAGGCATATTGGTGCAAGAGAAGAGGCTATATTGAGGA-GGCTCATACCA-GAGTGTG
1 TTGGTTGAAGGCATATTGGTGCAAGAGAAGAGGCTAAATTGAGGAGGGC-CATACCACAAGTGTG
* * * *
5902636 GACTGGTGATTGGTCAGAATGCTAGATAGGCATACATCAT-ACTCAGAGGAAGACAATGGCAACA
65 GACTGGTGATTGGTCAGAATGATAAATAGGCATACATC-TCACTCAGAGGAAGAAAAAGGC-ACA
* * * * *
5902700 GTT-TTTTCTGTTGGCC--TTTTTCTTTAGCCAAATAGGTTGTTGTGGATTGACTACTTTATTCC
128 -TTCTTTTCTGTTGGCCTTTTTTTTTTTTGCTAAATAGGTTGTTGTGGATTAACTGCTTTATTCC
* * * *
5902762 TTTATTTCACAGTGCTGAGGCAGGTTTCCATTTTTTTATGACTGTGATTCCAGGTATGATGG-TA
192 TCTATTTCACAGTGCTAAGGCAGATTTCCATTTTTTAATGACTGTGATTCCAGGTATGA-GGCTA
* *
5902826 GCTTGCCCACATGCAAATATTGTACATACAGCCTAATTTATATATTTATTTTGCCACTTATTTCT
256 GCTTGCCCACATGCAAATATAGTACATACAGCCTAATTTATTTATTTATTTTGCCACTTATTTCT
*
5902891 ---GA---G---G-AAACAGATCAATCTAAGTCCATAAAGCTCTGTATTATGCTCTTAATGTTGA
321 GAGGACTTGTTAGAAAACAGATCAATCTAAGTCCATAAAGTTCTGTATTATGCTCTTAATGTTGA
* * * * *
5902946 CTTCAGATCAGATTCCTCTAATAAAATATTTTAGGATATAATATAGGGATCCAAAAAGAAAAAAT
386 CTTCAGATCAGATTCCTCTGATCAAATATTTCAGGATATAATATAGGGAACC-AAAAGAAAAAAG
* *
5903011 CCAGGGATTGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATCATACC
450 CTAGGCATTGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATCATACC
* * * * *
5903076 ACTAGACCAAATGCCCG-TTTTGGTTGTCTATAATGTTTTTTTATTATTGTAACATCTATGGGTA
515 ACTAGACCAAATGCCCGATTTT-GTTGTCTATAAGGTTTTGTTATTATTATAACATCTATAGGTG
* *
5903140 GTAAAGTTGCAAAAAATGGTGCATACTTTTCTTTTTTTATTTATTGATGAAGTCT-TGGGTCAGA
579 GTAAA-TTTCAAAAAATGGTGCATACTTTT-TTTCTTTATTTATTGATGAAGTCTCT--G--AGA
* * * *
5903204 ACTAGATTGTTTGTGAGCTTTTTAGCTATTGTAATACTTAGTAAAGTGCTTCAAAATTGTTCAAA
638 ACTAGATTGTTTGTGAGCTTTTTTGCTATTGGAATACATAGTAAAGTGATTCAAAATTGTTCAAA
** * ** * * *
5903269 GATGAGCTTACA-GGAG-AATTAGCAGTTAAACTGGATTGTTCACAAAATGACATGTCGAAATGA
703 GATGAGGGTATATGG-GCAATTAGCAGTTATGCAGGATTGTTCACAAAATGACATGTCGTAATAA
** * * * * * * *
5903332 CCTTTTGTTTGCAAGGCTCTGAAGGATGAATACTAAAGTCTGCTAAAT-GCACAATGGATGCTAA
767 ATTTTTCTCTGCAAGACTCTGAAGGATGAATACTAAAATCTG-TTAATCACACAAGGGATGCTAA
* * * * * *
5903396 ATAC-ATAGCTGTAAAGCCATTCTGTAATTGCATTGAGCTAGGTCTGATTCCTGTTTTGACCT
831 ATACTTTAGCTGTAAAGTCATTCTGTAATTGCATTGAGCTAGTTC-AAATCCTGTTTAGACCT
* * *
5903458 TTGGTTGAAGGCGTATTGGTGCAAGAGGATA-AGGCTAAATGGAGGAGGGCCATACCACAGATTG
1 TTGGTTGAAGGCATATTGGTGCAAGA-GA-AGAGGCTAAATTGAGGAGGGCCATACCACA-AGTG
* ** * * *
5903522 TAGG-CTGGTGATTGGTCAGAA-GCTAAATAGAAACACTTCTCACTGAGAGGAAGAAAAAGGCAC
63 T-GGACTGGTGATTGGTCAGAATGATAAATAGGCATACATCTCACTCAGAGGAAGAAAAAGGCAC
*
5903585 ATTCCTTTCCTGTTGGCC-TTTTTTTTTTTGCTAAATAGGTTGTTGT---TT--C--C-----T-
127 ATT-CTTTTCTGTTGGCCTTTTTTTTTTTTGCTAAATAGGTTGTTGTGGATTAACTGCTTTATTC
* * * *
5903636 -T-TATTTCACAGGGTTAAGGCAGATTTCCATTTTCTAATGACTATCG-TTCCAGGTATGAGGCT
191 CTCTATTTCACAGTGCTAAGGCAGATTTCCATTTTTTAATGACTGT-GATTCCAGGTATGAGGCT
* ** * ** *
5903698 AGCTTGCCCACATGCGAAGT-TAGTATGTAGAGCCTAATTTATTTATTTCCTTTGCCACATATTT
255 AGCTTGCCCACATGC-AAATATAGTACATACAGCCTAATTTATTTATTTATTTTGCCACTTATTT
* * * * * * * *
5903762 CCGAAGACTCGTTAGGAAACAGATCAATATAAGTCCGTAAAGTTCTGTATTATG-TTTTAAAGTT
319 CTGAGGACTTGTTAGAAAACAGATCAATCTAAGTCCATAAAGTTCTGTATTATGCTCTTAATGTT
* * *
5903826 GACTTCAAATCAGATTCCTCTGATCAAATATTTCAGGATAGAATATAGGGAACCAAAAAGAGAAA
384 GACTTCAGATCAGATTCCTCTGATCAAATATTTCAGGATATAATATAGGGAACC-AAAAGAAAAA
* *
5903891 AGCAAGGCATTGGGGCATTCCGAGAATCGAACTCGGGACCCCTCGCACCCAAAGCGAGAATCATA
448 AGCTAGGCATTGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATCATA
5903956 CCACTAGACCAAATGCCC
513 CCACTAGACCAAATGCCC
5903974 ACCTTTTTAT
Statistics
Matches: 2687, Mismatches: 373, Indels: 313
0.80 0.11 0.09
Matches are distributed among these distances:
872 2 0.00
873 101 0.04
874 5 0.00
876 3 0.00
879 1 0.00
880 3 0.00
881 10 0.00
882 253 0.09
883 221 0.08
884 25 0.01
885 39 0.01
886 49 0.02
887 56 0.02
888 50 0.02
889 7 0.00
890 12 0.00
891 4 0.00
892 168 0.06
893 12 0.00
894 22 0.01
895 8 0.00
896 162 0.06
897 68 0.03
898 226 0.08
899 96 0.04
900 73 0.03
901 156 0.06
902 17 0.01
903 23 0.01
904 12 0.00
905 109 0.04
906 176 0.07
907 62 0.02
908 101 0.04
909 122 0.05
910 91 0.03
911 9 0.00
912 132 0.05
913 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (892 bp):
TTGGTTGAAGGCATATTGGTGCAAGAGAAGAGGCTAAATTGAGGAGGGCCATACCACAAGTGTGG
ACTGGTGATTGGTCAGAATGATAAATAGGCATACATCTCACTCAGAGGAAGAAAAAGGCACATTC
TTTTCTGTTGGCCTTTTTTTTTTTTGCTAAATAGGTTGTTGTGGATTAACTGCTTTATTCCTCTA
TTTCACAGTGCTAAGGCAGATTTCCATTTTTTAATGACTGTGATTCCAGGTATGAGGCTAGCTTG
CCCACATGCAAATATAGTACATACAGCCTAATTTATTTATTTATTTTGCCACTTATTTCTGAGGA
CTTGTTAGAAAACAGATCAATCTAAGTCCATAAAGTTCTGTATTATGCTCTTAATGTTGACTTCA
GATCAGATTCCTCTGATCAAATATTTCAGGATATAATATAGGGAACCAAAAGAAAAAAGCTAGGC
ATTGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCACCCAAAGCGAGAATCATACCACTAGA
CCAAATGCCCGATTTTGTTGTCTATAAGGTTTTGTTATTATTATAACATCTATAGGTGGTAAATT
TCAAAAAATGGTGCATACTTTTTTTCTTTATTTATTGATGAAGTCTCTGAGAACTAGATTGTTTG
TGAGCTTTTTTGCTATTGGAATACATAGTAAAGTGATTCAAAATTGTTCAAAGATGAGGGTATAT
GGGCAATTAGCAGTTATGCAGGATTGTTCACAAAATGACATGTCGTAATAAATTTTTCTCTGCAA
GACTCTGAAGGATGAATACTAAAATCTGTTAATCACACAAGGGATGCTAAATACTTTAGCTGTAA
AGTCATTCTGTAATTGCATTGAGCTAGTTCAAATCCTGTTTAGACCT
Found at i:5923611 original size:15 final size:15
Alignment explanation
Indices: 5923593--5923644 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
5923583 GGGGCGTAAG
5923593 GAGGAGGATATCCCT
1 GAGGAGGATATCCCT
*
5923608 GAGGAGGATAACCCT
1 GAGGAGGATATCCCT
*
5923623 G-GG-GG-TATCCTT
1 GAGGAGGATATCCCT
*
5923635 GAGGGGGATA
1 GAGGAGGATA
5923645 ACCCGGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 6 0.19
13 4 0.13
14 4 0.13
15 17 0.55
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.19
Consensus pattern (15 bp):
GAGGAGGATATCCCT
Found at i:5928055 original size:157 final size:155
Alignment explanation
Indices: 5927759--5928076 Score: 516
Period size: 157 Copynumber: 2.0 Consensus size: 155
5927749 AAGAGTGGCA
5927759 TGCAATGACAGTATAAAATGATGGTATCTACATGCACGCGTTTATTGATTATTTAAAAATTTTTG
1 TGCAATGACAGTATAAAATGATGGTATCTACATGCACGCGTTTATTGATTATTTAAAAATTTTTG
5927824 ATTATTTGCTTATTTATTATTTTTATTTATATAATTATTAATTTTGGTTTTCTATTTAAATCCAT
66 ATTATTTGCTTATTTATTATTTTTATTTATATAATTATTAATTTTGGTTTTCTATTTAAATCCAT
5927889 GTTTGTTGTTGATCAATTTTTTTACT
131 G-TTGTTGTTGATCAATTTTTTTACT
5927915 NTGCAATGACAGTATAAAATGATGGTATCTACATGCACGCGTTTATTGATTATTTAAAAA-TTTT
1 -TGCAATGACAGTATAAAATGATGGTATCTACATGCACGCGTTTATTGATTATTTAAAAATTTTT
*
5927979 GATTATTTG-TTATTTATTATTTTTTTATTTATAT-ATATACTTTATTTTTTGGTTTTCTATTTA
65 GATTATTTGCTTATTTATTA--TTTTTATTTATATAAT-TA--TTA-ATTTTGGTTTTCTATTTA
*
5928042 AATCCATGTTTGTTGTTGGTCAATTTTTTTACT
124 AATCCATG-TTGTTGTTGATCAATTTTTTTACT
5928075 TG
1 TG
5928077 ATTACAAAGC
Statistics
Matches: 153, Mismatches: 2, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
155 10 0.07
156 15 0.10
157 74 0.48
159 5 0.03
160 49 0.32
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.53
Consensus pattern (155 bp):
TGCAATGACAGTATAAAATGATGGTATCTACATGCACGCGTTTATTGATTATTTAAAAATTTTTG
ATTATTTGCTTATTTATTATTTTTATTTATATAATTATTAATTTTGGTTTTCTATTTAAATCCAT
GTTGTTGTTGATCAATTTTTTTACT
Found at i:5928419 original size:15 final size:17
Alignment explanation
Indices: 5928356--5928439 Score: 61
Period size: 17 Copynumber: 4.9 Consensus size: 17
5928346 CTTTTATTTG
*
5928356 TTATTATTTATTTATTT
1 TTATTATTTATTTATTA
*
5928373 TTCACTCA-TTA-TTATTA
1 TT-A-TTATTTATTTATTA
5928390 TTATTATTTACTTTATTA
1 TTATTATTTA-TTTATTA
5928408 TT-TTATTT-TTTATCT-
1 TTATTATTTATTTAT-TA
*
5928423 TTCATTATTTTTTTATT
1 TT-ATTATTTATTTATT
5928440 TTCTAAAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
15 9 0.16
16 5 0.09
17 22 0.40
18 17 0.31
19 2 0.04
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTATTTATTTATTA
Found at i:5929254 original size:11 final size:12
Alignment explanation
Indices: 5929226--5929261 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
5929216 CGATCGGATT
5929226 TTTTTCTTTTTGA
1 TTTTT-TTTTTGA
5929239 TTTTTTTTTTGA
1 TTTTTTTTTTGA
5929251 TTTTTTCTTTT
1 TTTTTT-TTTT
5929262 TGTTTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTTGA
Found at i:5929259 original size:26 final size:27
Alignment explanation
Indices: 5929225--5929276 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
5929215 CCGATCGGAT
5929225 TTTTTTCTTTTTGATTT-T-TTTTTTGA
1 TTTTTTCTTTTTG-TTTCTCTTTTTTGA
5929251 TTTTTTCTTTTTGTTTCTCTTTTTTG
1 TTTTTTCTTTTTGTTTCTCTTTTTTG
5929277 TGGCTAACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 3 0.12
26 14 0.58
27 7 0.29
ACGTcount: A:0.04, C:0.08, G:0.08, T:0.81
Consensus pattern (27 bp):
TTTTTTCTTTTTGTTTCTCTTTTTTGA
Found at i:5943223 original size:2 final size:2
Alignment explanation
Indices: 5943216--5943248 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5943206 TGATTGTGTT
*
5943216 TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5943249 TTTTAGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5953440 original size:2 final size:2
Alignment explanation
Indices: 5953433--5953460 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5953423 TGCCATTCAA
5953433 CT 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 CT
5953461 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5953465 original size:2 final size:2
Alignment explanation
Indices: 5953460--5953489 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5953450 TCTCTCTCTC
5953460 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5953490 NCTACTACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5953502 original size:2 final size:2
Alignment explanation
Indices: 5953497--5953522 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5953487 ATANCTACTA
5953497 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
5953523 TATATATATA
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:5953528 original size:2 final size:2
Alignment explanation
Indices: 5953523--5953552 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5953513 CTCTCTCTCT
5953523 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5953553 AACCAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5960042 original size:2 final size:2
Alignment explanation
Indices: 5960035--5960072 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5960025 CAAAACAATT
* *
5960035 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5960073 AAACTGATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5962631 original size:15 final size:15
Alignment explanation
Indices: 5962611--5962643 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
5962601 TTTTATTTAT
5962611 ATTTAAATA-AATTAA
1 ATTTAAATATAA-TAA
5962626 ATTTAAATATAATAA
1 ATTTAAATATAATAA
5962641 ATT
1 ATT
5962644 ATTACATGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTTAAATATAATAA
Found at i:5967992 original size:21 final size:24
Alignment explanation
Indices: 5967967--5968015 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 24
5967957 AATGTAAGTA
5967967 ATTTTTAAAT-TTATTT-A-TTTT
1 ATTTTTAAATATTATTTAATTTTT
5967988 A-TTTTAAATATTATTTAATTTTT
1 ATTTTTAAATATTATTTAATTTTT
5968011 ATTTT
1 ATTTT
5968016 ATTTTTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.33
21 7 0.29
22 1 0.04
23 5 0.21
24 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
ATTTTTAAATATTATTTAATTTTT
Found at i:5968028 original size:23 final size:23
Alignment explanation
Indices: 5967969--5968016 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
5967959 TGTAAGTAAT
5967969 TTTTAAAT-TTATTT-A-TTTTA
1 TTTTAAATATTATTTAATTTTTA
5967989 TTTTAAATATTATTTAATTTTTA
1 TTTTAAATATTATTTAATTTTTA
5968012 TTTTA
1 TTTTA
5968017 TTTTTATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.32
21 6 0.24
22 1 0.04
23 10 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTAAATATTATTTAATTTTTA
Found at i:5968498 original size:24 final size:24
Alignment explanation
Indices: 5968451--5968499 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5968441 TTACGTTAAC
* * *
5968451 GCTTTTCAATGCCTTGCAACGGAT
1 GCTTTCCAATGCCCTACAACGGAT
*
5968475 GCTTTCCAATGCCCTACAATGGAT
1 GCTTTCCAATGCCCTACAACGGAT
5968499 G
1 G
5968500 TGGTGAGAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (24 bp):
GCTTTCCAATGCCCTACAACGGAT
Found at i:5968808 original size:32 final size:33
Alignment explanation
Indices: 5968772--5968842 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
5968762 AAAATTTAAT
* * *
5968772 ATTTTTTGTTGTTTGGATAAAT-TATTAAAAAC
1 ATTTTTTATCGTTTGGATAAATGTATGAAAAAC
* * *
5968804 ATTTTCTATCGTTTGGATAATTGTATGAAAAAT
1 ATTTTTTATCGTTTGGATAAATGTATGAAAAAC
5968837 ATTTTT
1 ATTTTT
5968843 CATTATCACT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (33 bp):
ATTTTTTATCGTTTGGATAAATGTATGAAAAAC
Found at i:5969751 original size:15 final size:16
Alignment explanation
Indices: 5969721--5969754 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5969711 TAATTTTAAT
5969721 AATATTGAATAATTTA
1 AATATTGAATAATTTA
*
5969737 AATATT-AATATTTTA
1 AATATTGAATAATTTA
5969752 AAT
1 AAT
5969755 TAAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AATATTGAATAATTTA
Found at i:5973039 original size:6 final size:6
Alignment explanation
Indices: 5973030--5973252 Score: 142
Period size: 6 Copynumber: 37.3 Consensus size: 6
5973020 TCTGAACACC
* * * * *
5973030 TATATA TATATA TATACA TATACA TATATA TATATG TATATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * *
5973078 TATATA TATATA TATGTA TATGTA TATGTA TGTATA TATATA CACATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * * * * *
5973126 TGTATA TGTATG TATATG TATACA TATACA TATGTG CATATA TACATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * *
5973174 TACA-A TACATA TATATG TATATA TATATA TATATG TGTACA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * *
5973221 TATATG TATACA TATTTG TATATG TATATA TA
1 TATATA TATATA TATATA TATATA TATATA TA
5973253 CACGTCCGGT
Statistics
Matches: 172, Mismatches: 44, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
5 4 0.02
6 168 0.98
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:5973070 original size:28 final size:28
Alignment explanation
Indices: 5973031--5973252 Score: 158
Period size: 28 Copynumber: 8.0 Consensus size: 28
5973021 CTGAACACCT
* * *
5973031 ATATATATATATATACATATACATATAT
1 ATATATATATATGTATATATATATATAT
* *
5973059 ATATATGTATATGTATATGTATATATAT
1 ATATATATATATGTATATATATATATAT
* * *
5973087 ATATATGTATATGTATATGTATGTATAT
1 ATATATATATATGTATATATATATATAT
* * * *
5973115 ATATACACATATGTATATGTATGTATAT
1 ATATATATATATGTATATATATATATAT
* * ** * ** *
5973143 GTATACATATACATATGTGCATATATAC
1 ATATATATATATGTATATATATATATAT
* * ** *
5973171 ATGTACA-ATACATATATATGTATATAT
1 ATATATATATATGTATATATATATATAT
* *
5973198 ATATATATATGTGTACATATATATATAT
1 ATATATATATATGTATATATATATATAT
* * * *
5973226 GTATACATATTTGTATATGTATATATA
1 ATATATATATATGTATATATATATATA
5973253 CACGTCCGGT
Statistics
Matches: 157, Mismatches: 36, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
27 20 0.13
28 137 0.87
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (28 bp):
ATATATATATATGTATATATATATATAT
Found at i:5973075 original size:16 final size:16
Alignment explanation
Indices: 5973053--5973252 Score: 129
Period size: 16 Copynumber: 12.3 Consensus size: 16
5973043 ATACATATAC
*
5973053 ATATATATATATGTAT
1 ATATATGTATATGTAT
*
5973069 ATGTATATGTATATATAT
1 A--TATATGTATATGTAT
5973087 ATATATGTATATGTAT
1 ATATATGTATATGTAT
* *
5973103 ATGTATGTATATATAT
1 ATATATGTATATGTAT
*
5973119 ACACATATGTATATGTAT
1 --ATATATGTATATGTAT
* **
5973137 GTATATGTATACATAT
1 ATATATGTATATGTAT
* **
5973153 ACATATGTGCA--TAT
1 ATATATGTATATGTAT
* * **
5973167 ATACATGTACAATACAT
1 ATATATGTA-TATGTAT
5973184 ATATATGTATA--TAT
1 ATATATGTATATGTAT
* * *
5973198 ATATATATATGTGTAC
1 ATATATGTATATGTAT
*
5973214 ATATATATATATGTAT
1 ATATATGTATATGTAT
*
5973230 ACATATTTGTATATGTAT
1 --ATATATGTATATGTAT
5973248 ATATA
1 ATATA
5973253 CACGTCCGGT
Statistics
Matches: 141, Mismatches: 32, Indels: 22
0.72 0.16 0.11
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 69 0.49
17 10 0.07
18 41 0.29
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (16 bp):
ATATATGTATATGTAT
Found at i:5975550 original size:51 final size:51
Alignment explanation
Indices: 5975473--5975572 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
5975463 AAGCTTTCAC
*
5975473 GGGCTTTGACATGTAGTGCTTCAACTTACTTTGTAACTCTGCCTTGCTCAT
1 GGGCTTTGACATGTACTGCTTCAACTTACTTTGTAACTCTGCCTTGCTCAT
*
5975524 GGGCTTTGACATGTACTGCTTGAACTTACTTTGTAACTCTGCCTTGCTC
1 GGGCTTTGACATGTACTGCTTCAACTTACTTTGTAACTCTGCCTTGCTC
5975573 CTCCTCATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (51 bp):
GGGCTTTGACATGTACTGCTTCAACTTACTTTGTAACTCTGCCTTGCTCAT
Found at i:5976971 original size:21 final size:21
Alignment explanation
Indices: 5976947--5977000 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
5976937 GGAGAGCCCG
5976947 ATCGAGGCTCCCAAAGGGAGC
1 ATCGAGGCTCCCAAAGGGAGC
* *
5976968 ATCGA-GTTCCCCAAGGGGAGC
1 ATCGAGGCT-CCCAAAGGGAGC
5976989 ATC-AGTGCTCCC
1 ATCGAG-GCTCCC
5977001 TTTCTTTGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 3 0.11
21 22 0.81
22 2 0.07
ACGTcount: A:0.24, C:0.31, G:0.30, T:0.15
Consensus pattern (21 bp):
ATCGAGGCTCCCAAAGGGAGC
Found at i:5978188 original size:13 final size:14
Alignment explanation
Indices: 5978159--5978191 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
5978149 CAAAAATGAG
*
5978159 AAGCAAAGGACGCA
1 AAGCAAAGGAAGCA
5978173 AAGCAAA-GAAGCA
1 AAGCAAAGGAAGCA
5978186 AAGCAA
1 AAGCAA
5978192 GTTAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.58, C:0.18, G:0.24, T:0.00
Consensus pattern (14 bp):
AAGCAAAGGAAGCA
Found at i:5983464 original size:30 final size:30
Alignment explanation
Indices: 5983429--5983492 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
5983419 GAGGGAAACC
5983429 TTTTTCCGCCCGACAACTTCACTTATATAT
1 TTTTTCCGCCCGACAACTTCACTTATATAT
5983459 TTTTTCCGCCCGACAACTTCACTTATATAT
1 TTTTTCCGCCCGACAACTTCACTTATATAT
5983489 TTTT
1 TTTT
5983493 CTTTCTGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.22, C:0.28, G:0.06, T:0.44
Consensus pattern (30 bp):
TTTTTCCGCCCGACAACTTCACTTATATAT
Found at i:5985345 original size:9 final size:8
Alignment explanation
Indices: 5985290--5985344 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
5985280 AAATAGAATT
5985290 AAAATAAA
1 AAAATAAA
5985298 AAAATAAA
1 AAAATAAA
5985306 AAAAT-AA
1 AAAATAAA
5985313 AAAATAAA
1 AAAATAAA
*
5985321 ATTAATAATA
1 A-AAATAA-A
*
5985331 TAAATTAAA
1 -AAAATAAA
5985340 AAAAT
1 AAAAT
5985345 TTAAAATTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 7 0.18
8 20 0.51
9 6 0.15
10 5 0.13
11 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAATAAA
Found at i:5985351 original size:34 final size:34
Alignment explanation
Indices: 5985280--5985344 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
5985270 ACATATGAAC
*
5985280 AAATAGAATTAAAATAAAAAAATAAAAAAATAAA
1 AAATAAAATTAAAATAAAAAAATAAAAAAATAAA
* *
5985314 AAATAAAATTAATAAT-ATAAATTAAAAAAAT
1 AAATAAAATTAA-AATAAAAAAATAAAAAAAT
5985345 TTAAAATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 24 0.89
35 3 0.11
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (34 bp):
AAATAAAATTAAAATAAAAAAATAAAAAAATAAA
Found at i:5994710 original size:15 final size:15
Alignment explanation
Indices: 5994690--5994721 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5994680 ATTACATGGA
5994690 TTTTACATTTCATTT
1 TTTTACATTTCATTT
*
5994705 TTTTACTTTTCATTT
1 TTTTACATTTCATTT
5994720 TT
1 TT
5994722 ATTTTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTACATTTCATTT
Found at i:5995513 original size:1 final size:1
Alignment explanation
Indices: 5995507--5995533 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5995497 GTGATTTATT
5995507 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
5995534 TGTGGCAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6018961 original size:9 final size:9
Alignment explanation
Indices: 6018947--6018981 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
6018937 ATCTTGTTTA
6018947 TTTTTAATT
1 TTTTTAATT
6018956 TTTTTAATT
1 TTTTTAATT
*
6018965 TTGTTTATTT
1 TT-TTTAATT
6018975 TTTTTAA
1 TTTTTAA
6018982 AATTATGTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (9 bp):
TTTTTAATT
Found at i:6019035 original size:14 final size:14
Alignment explanation
Indices: 6019016--6019045 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6019006 TGCACTCTCA
*
6019016 AAAACTTTAATTAT
1 AAAACTCTAATTAT
6019030 AAAACTCTAATTAT
1 AAAACTCTAATTAT
6019044 AA
1 AA
6019046 GAGAGAGAAA
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:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAACTCTAATTAT
Found at i:6020490 original size:30 final size:30
Alignment explanation
Indices: 6020449--6020536 Score: 124
Period size: 30 Copynumber: 2.9 Consensus size: 30
6020439 CAACACAAAT
*
6020449 GTCATGCCATCTTATAAATTGAAGTAAAG-
1 GTCATGTCATCTTATAAATTGAAGTAAAGA
6020478 GATCATGTCATCTTATAAATTGAAGTAAAGA
1 G-TCATGTCATCTTATAAATTGAAGTAAAGA
* * *
6020509 GTTATGTCATCCTATAAATTAAAGTAAA
1 GTCATGTCATCTTATAAATTGAAGTAAA
6020537 AATATTAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
29 1 0.02
30 51 0.96
31 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (30 bp):
GTCATGTCATCTTATAAATTGAAGTAAAGA
Found at i:6024531 original size:12 final size:12
Alignment explanation
Indices: 6024514--6024559 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
6024504 ATCAAGAAGG
*
6024514 AGACGAGGATGA
1 AGACGAAGATGA
*
6024526 AGACGAAGACGA
1 AGACGAAGATGA
6024538 AGACGAAGATGA
1 AGACGAAGATGA
6024550 AGACGAAGAT
1 AGACGAAGAT
6024560 CGGAGTTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.48, C:0.11, G:0.35, T:0.07
Consensus pattern (12 bp):
AGACGAAGATGA
Found at i:6024535 original size:6 final size:6
Alignment explanation
Indices: 6024514--6024558 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
6024504 ATCAAGAAGG
* * *
6024514 AGACGA GGATGA AGACGA AGACGA AGACGA AGATGA AGACGA AGA
1 AGACGA AGACGA AGACGA AGACGA AGACGA AGACGA AGACGA AGA
6024559 TCGGAGTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.11, G:0.36, T:0.04
Consensus pattern (6 bp):
AGACGA
Found at i:6039381 original size:3 final size:3
Alignment explanation
Indices: 6039373--6039397 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6039363 ATTCCATTCC
6039373 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
6039398 TTTCCTTTGG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6050687 original size:2 final size:2
Alignment explanation
Indices: 6050680--6050711 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6050670 TGTGTACATG
6050680 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6050712 AATAAAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6065280 original size:18 final size:20
Alignment explanation
Indices: 6065257--6065300 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
6065247 GATTTTAAAT
6065257 TTTAATAATAAA-A-TTTTA
1 TTTAATAATAAATAGTTTTA
**
6065275 TTTAATTGTAAATAGTTTTA
1 TTTAATAATAAATAGTTTTA
6065295 TTTAAT
1 TTTAAT
6065301 CGTGTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 1 0.05
20 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTAATAATAAATAGTTTTA
Found at i:6065395 original size:39 final size:41
Alignment explanation
Indices: 6065317--6065398 Score: 105
Period size: 39 Copynumber: 2.0 Consensus size: 41
6065307 AAATGTGTTA
*
6065317 TTAATCGTGTCGTGTCGTATATTGACACGTTTAATAAACGTG
1 TTAATCGTGTCGTGTCG-ATATTGACACGTGTAATAAACGTG
* * *
6065359 TTAATCGTTTCGTGTCG-TGTT-ACACGTGTATTAAACGTG
1 TTAATCGTGTCGTGTCGATATTGACACGTGTAATAAACGTG
6065398 T
1 T
6065399 ACATATACGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 17 0.47
40 3 0.08
42 16 0.44
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (41 bp):
TTAATCGTGTCGTGTCGATATTGACACGTGTAATAAACGTG
Found at i:6078029 original size:48 final size:48
Alignment explanation
Indices: 6077969--6078067 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
6077959 AAAAGCATAG
*
6077969 CTGTTTCAGCACATGCTCATGGTTGCTATCAAGATTAGAACCCCAGAA
1 CTGTTTCAGCACATGCTCATGCTTGCTATCAAGATTAGAACCCCAGAA
6078017 CTGTTTCAGCACATGCTCATGCTTGCTATCAAGATTAGAACCCCAGAA
1 CTGTTTCAGCACATGCTCATGCTTGCTATCAAGATTAGAACCCCAGAA
6078065 CTG
1 CTG
6078068 ACTTACATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (48 bp):
CTGTTTCAGCACATGCTCATGCTTGCTATCAAGATTAGAACCCCAGAA
Found at i:6086833 original size:153 final size:156
Alignment explanation
Indices: 6086551--6086858 Score: 347
Period size: 153 Copynumber: 2.0 Consensus size: 156
6086541 GACCTCAACA
** *
6086551 TTCTTCTGCTTCAAACCAATCTGTGGAGTTGACTCATCATCGTCCATGACTACACTTTTTACATC
1 TTCTTCTGCTTCAAACCAATCTCCGGAGTTGACTCATCATCGTCCATGACTACACTTTTAACATC
* ** * * * * *
6086616 AGCGAATGTCACCTTCTTCTGATTCACACTAATCACTGGAGTTGATTGATTATCTGCCATGATTA
66 AGAGAATGAAACCCTCTTCTGATTCAAACTAATCACCGGAGTTGACTCATTATCTGCCATGATTA
* *
6086681 TGCTTTTAACATCAGAGAATGAAACC
131 GGCTTTTAACATCAGAGAAGGAAACC
* * * * *
6086707 TTCTTCTGGTTCAAACCAATCTCCGGTGTTG-C-C-TCATCTTCCATGATTACGCTTTTAACATC
1 TTCTTCTGCTTCAAACCAATCTCCGGAGTTGACTCATCATCGTCCATGACTACACTTTTAACATC
* * * * *
6086769 AGAGGATGAAACCCTCTTCTGCTTCAAAGC-AATCTCCGGTGTTGACTCATTATCTTCC-TCGAT
66 AGAGAATGAAACCCTCTTCTGATTCAAA-CTAATCACCGGAGTTGACTCATTATCTGCCAT-GAT
*
6086832 TAGGCTTTTTACATCAGAGAAGGAAAC
129 TAGGCTTTTAACATCAGAGAAGGAAAC
6086859 AGAAGATCGA
Statistics
Matches: 126, Mismatches: 24, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
152 1 0.01
153 95 0.75
154 2 0.02
155 1 0.01
156 27 0.21
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (156 bp):
TTCTTCTGCTTCAAACCAATCTCCGGAGTTGACTCATCATCGTCCATGACTACACTTTTAACATC
AGAGAATGAAACCCTCTTCTGATTCAAACTAATCACCGGAGTTGACTCATTATCTGCCATGATTA
GGCTTTTAACATCAGAGAAGGAAACC
Found at i:6086846 original size:78 final size:78
Alignment explanation
Indices: 6086551--6086858 Score: 318
Period size: 78 Copynumber: 4.0 Consensus size: 78
6086541 GACCTCAACA
** * * * *
6086551 TTCTTCTGCTTCAAACCAATCTGTGGAGTTGACTCATCATCGTCCATGACTACACTTTTTACATC
1 TTCTTCTGCTTCAAACCAATCTCCGGAGTTGACTCATCATCTTCCATGATTACGCTTTTAACATC
* **
6086616 AGCGAATGTCACC
66 AGAGAATGAAACC
* * * * * * * * * *
6086629 TTCTTCTGATTCACACTAATCACTGGAGTTGATTGATTATCTGCCATGATTATGCTTTTAACATC
1 TTCTTCTGCTTCAAACCAATCTCCGGAGTTGACTCATCATCTTCCATGATTACGCTTTTAACATC
6086694 AGAGAATGAAACC
66 AGAGAATGAAACC
* *
6086707 TTCTTCTGGTTCAAACCAATCTCCGGTGTTG-C-C-TCATCTTCCATGATTACGCTTTTAACATC
1 TTCTTCTGCTTCAAACCAATCTCCGGAGTTGACTCATCATCTTCCATGATTACGCTTTTAACATC
*
6086769 AGAGGATGAAACC
66 AGAGAATGAAACC
* * * * * *
6086782 CTCTTCTGCTTCAAAGCAATCTCCGGTGTTGACTCATTATCTTCC-TCGATTAGGCTTTTTACAT
1 TTCTTCTGCTTCAAACCAATCTCCGGAGTTGACTCATCATCTTCCAT-GATTACGCTTTTAACAT
*
6086846 CAGAGAAGGAAAC
65 CAGAGAATGAAAC
6086859 AGAAGATCGA
Statistics
Matches: 189, Mismatches: 37, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
75 66 0.35
76 1 0.01
77 2 0.01
78 120 0.63
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (78 bp):
TTCTTCTGCTTCAAACCAATCTCCGGAGTTGACTCATCATCTTCCATGATTACGCTTTTAACATC
AGAGAATGAAACC
Found at i:6088918 original size:105 final size:105
Alignment explanation
Indices: 6088782--6089003 Score: 302
Period size: 105 Copynumber: 2.1 Consensus size: 105
6088772 CTTTGGACCC
* * * * * * *
6088782 CATTTGGACCCTCTTGCGCTTTAATGTTTTTTTATTGGAAACTTCAAATGTTTTAGTGTTTTCCT
1 CATTTGGACCCTCTAGCGCTTTAAAGTTTTTTTAATGGAAACTTCAAACGTTTGAATGGTTTCCT
* * *
6088847 TCTAGCAAGTTGTTCCTGTTTTCCTTGTTTCAATGTTTTT
66 TCTAACAAGTCGCTCCTGTTTTCCTTGTTTCAATGTTTTT
* *
6088887 CATTTGGACCGTCTAGCGTTTTAACAG-TTTTTTAATGGAAACTTCAAACGTTTGAATGGTTTCC
1 CATTTGGACCCTCTAGCGCTTTAA-AGTTTTTTTAATGGAAACTTCAAACGTTTGAATGGTTTCC
* *
6088951 TTCTAACAAGTCGCTCTTGTTTTCCTTGTTTTAATGTTTTT
65 TTCTAACAAGTCGCTCCTGTTTTCCTTGTTTCAATGTTTTT
6088992 CATTTGGACCCT
1 CATTTGGACCCT
6089004 AACAAGTTGT
Statistics
Matches: 101, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
105 100 0.99
106 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (105 bp):
CATTTGGACCCTCTAGCGCTTTAAAGTTTTTTTAATGGAAACTTCAAACGTTTGAATGGTTTCCT
TCTAACAAGTCGCTCCTGTTTTCCTTGTTTCAATGTTTTT
Found at i:6093981 original size:14 final size:14
Alignment explanation
Indices: 6093964--6094005 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
6093954 AGAAAAGCAA
*
6093964 AGAAGGAAACCAGG
1 AGAAGAAAACCAGG
6093978 AGAAGAAAACCAGG
1 AGAAGAAAACCAGG
6093992 AGAAGAAAACCAGG
1 AGAAGAAAACCAGG
6094006 GAAACTCACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.55, C:0.14, G:0.31, T:0.00
Consensus pattern (14 bp):
AGAAGAAAACCAGG
Found at i:6093983 original size:27 final size:28
Alignment explanation
Indices: 6093953--6094005 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
6093943 TACTTAAACA
* *
6093953 AAGAAAAGCA-AAGAAGGAAACCAGGAG
1 AAGAAAACCAGAAGAAGAAAACCAGGAG
*
6093980 AAGAAAACCAGGAGAAGAAAACCAGG
1 AAGAAAACCAGAAGAAGAAAACCAGG
6094006 GAAACTCACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.58, C:0.13, G:0.28, T:0.00
Consensus pattern (28 bp):
AAGAAAACCAGAAGAAGAAAACCAGGAG
Found at i:6127750 original size:28 final size:28
Alignment explanation
Indices: 6127718--6127775 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
6127708 TTCGGAGTAT
*
6127718 AGGGGCAAAATC-ATAATTTTTTCGTCCC
1 AGGGGC-AAATCGATAAATTTTTCGTCCC
*
6127746 AGGGGCAAATCGGTAAATTTTTCGTCCC
1 AGGGGCAAATCGATAAATTTTTCGTCCC
6127774 AG
1 AG
6127776 CACTTGTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (28 bp):
AGGGGCAAATCGATAAATTTTTCGTCCC
Found at i:6128961 original size:2 final size:2
Alignment explanation
Indices: 6128956--6128996 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
6128946 TATATATATA
6128956 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
6128997 CATGATGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:6129149 original size:37 final size:39
Alignment explanation
Indices: 6129108--6129209 Score: 136
Period size: 37 Copynumber: 2.6 Consensus size: 39
6129098 ATAGTGTCCG
* *
6129108 TGTGCACAATGTGGGGGGATGTACACGATGG-GACTG-A
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGACGGCA
** *
6129145 TGTGCACGATGTGGGGGGATACACACGATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGACGGC-A
6129185 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
6129210 TGAGCCGGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
37 28 0.51
38 3 0.05
40 24 0.44
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.22
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTGACGGCA
Found at i:6135049 original size:24 final size:24
Alignment explanation
Indices: 6135014--6135060 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
6135004 TGGTTTATTT
*
6135014 GTTGGTGTATGATCCCCTTGCTTG
1 GTTGGTGCATGATCCCCTTGCTTG
* *
6135038 GTTGGTGCATGATCTCTTTGCTT
1 GTTGGTGCATGATCCCCTTGCTT
6135061 AAAAGAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.45
Consensus pattern (24 bp):
GTTGGTGCATGATCCCCTTGCTTG
Found at i:6142470 original size:16 final size:16
Alignment explanation
Indices: 6142446--6142479 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6142436 AAGTAATAAC
6142446 TATTATATTATATTTT
1 TATTATATTATATTTT
* *
6142462 TATTTTATTTTATTTT
1 TATTATATTATATTTT
6142478 TA
1 TA
6142480 CAAAATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTATATTATATTTT
Found at i:6149204 original size:2 final size:2
Alignment explanation
Indices: 6149199--6149228 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6149189 AAAAAAATAA
6149199 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6149229 CAGCAAACCG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6162399 original size:2 final size:2
Alignment explanation
Indices: 6162392--6162419 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6162382 TTTTATTTCT
6162392 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
6162420 ACTACTTTCT
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:6185671 original size:2 final size:2
Alignment explanation
Indices: 6185664--6185700 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6185654 AGATATTATT
6185664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6185701 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6185787 original size:2 final size:2
Alignment explanation
Indices: 6185780--6185808 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6185770 NNNNNNNNNN
6185780 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 T
6185809 TGTATTAGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6186502 original size:20 final size:21
Alignment explanation
Indices: 6186479--6186517 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6186469 TAGTTATAAA
6186479 ACAAT-AT-TTATCCAAAGAAG
1 ACAATAATCTTAT-CAAAGAAG
6186499 ACAATAATCTTATCAAAGA
1 ACAATAATCTTATCAAAGA
6186518 TTGTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (21 bp):
ACAATAATCTTATCAAAGAAG
Found at i:6188370 original size:15 final size:14
Alignment explanation
Indices: 6188350--6188393 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
6188340 AGTGTATTTA
6188350 TTATAATTAATAATT
1 TTATAATT-ATAATT
6188365 TTATAAATTATAATT
1 TTAT-AATTATAATT
*
6188380 TTATAATNATAATT
1 TTATAATTATAATT
6188394 AGATTTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 14 0.52
16 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTATAATTATAATT
Found at i:6188472 original size:119 final size:122
Alignment explanation
Indices: 6188266--6188505 Score: 416
Period size: 119 Copynumber: 2.0 Consensus size: 122
6188256 TTAAAAAAAA
6188266 ATAATTAGATTTCAAAACTATTCTAATCTCATAATTTCTTTTAAGTATATATTTTATAAGTTTAT
1 ATAATTAGATTTCAAAACTATTCTAATCTCATAATTTCTTTTAAGTATATATTTTATAAGTTTAT
* *
6188331 ACAAACAAAAGTGTATTTATTATAATTAATAATTTTATAAATTATAA-TTTTATAAT
66 ACAAACAAAAGTATATATATTATAATTAATAATTTTATAAATTATAATTTTTATAAT
6188387 NATAATTAGATTTCAAAACTATTCTAATCTCATAATTT-TTTT-A-TATATATTTTATAAGTTTA
1 -ATAATTAGATTTCAAAACTATTCTAATCTCATAATTTCTTTTAAGTATATATTTTATAAGTTTA
*
6188449 TACAAATAAAAGTATATATATTATAATTAATAATTTTATAAATTATAATTTTTATAA
65 TACAAACAAAAGTATATATATTATAATTAATAATTTTATAAATTATAATTTTTATAA
6188506 CGATAATATA
Statistics
Matches: 114, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
119 64 0.56
120 9 0.08
121 4 0.04
122 37 0.32
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (122 bp):
ATAATTAGATTTCAAAACTATTCTAATCTCATAATTTCTTTTAAGTATATATTTTATAAGTTTAT
ACAAACAAAAGTATATATATTATAATTAATAATTTTATAAATTATAATTTTTATAAT
Found at i:6188495 original size:53 final size:53
Alignment explanation
Indices: 6188319--6188496 Score: 133
Period size: 53 Copynumber: 3.1 Consensus size: 53
6188309 AGTATATATT
* * *
6188319 TTATAAGTTTATACAAACAAAAGTGTATTTATTATAATTAATAATTTTATAAA
1 TTATAAGTTTATACAAATAAAAGTATATATATTATAATTAATAATTTTATAAA
* * * * * * *
6188372 TTATAATTTTATA-ATNATAATTAGATTTCAAAACTATTCTAATCTCATAATTTTTTTATATATA
1 TTATAAGTTTATACA-AATAA-AAG-TAT--ATA-TATTATAAT-TAATAA---TTTTATA-A-A
6188436 TTTTATAAGTTTATACAAATAAAAGTATATATATTATAATTAATAATTTTATAAA
1 --TTATAAGTTTATACAAATAAAAGTATATATATTATAATTAATAATTTTATAAA
6188491 TTATAA
1 TTATAA
6188497 TTTTTATAAC
Statistics
Matches: 94, Mismatches: 16, Indels: 30
0.67 0.11 0.21
Matches are distributed among these distances:
52 1 0.01
53 21 0.22
54 2 0.02
55 3 0.03
56 1 0.01
57 8 0.09
58 8 0.09
59 5 0.05
60 5 0.05
61 8 0.09
62 9 0.10
63 1 0.01
64 3 0.03
65 2 0.02
66 16 0.17
67 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (53 bp):
TTATAAGTTTATACAAATAAAAGTATATATATTATAATTAATAATTTTATAAA
Found at i:6188501 original size:16 final size:16
Alignment explanation
Indices: 6188469--6188505 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6188459 AGTATATATA
6188469 TTAT-AATTAATAATT
1 TTATAAATTAATAATT
6188484 TTATAAATT-ATAATTT
1 TTATAAATTAATAA-TT
6188500 TTATAA
1 TTATAA
6188506 CGATAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATAAATTAATAATT
Found at i:6188556 original size:15 final size:16
Alignment explanation
Indices: 6188536--6188572 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
6188526 TAAATATATT
6188536 TATATATTTAAAA-AA
1 TATATATTTAAAAGAA
*
6188551 TATATA-TTAAAAGTA
1 TATATATTTAAAAGAA
6188566 TATATAT
1 TATATAT
6188573 AATAGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TATATATTTAAAAGAA
Found at i:6188815 original size:29 final size:29
Alignment explanation
Indices: 6188782--6188838 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
6188772 TGGTAAAATT
* *
6188782 ACTACCCGAATTCGATAATAGAATACCTC
1 ACTACCCGAACTAGATAATAGAATACCTC
*
6188811 ACTACCCGAACTAGATTATAGAATACCT
1 ACTACCCGAACTAGATAATAGAATACCT
6188839 TAACTCTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.25
Consensus pattern (29 bp):
ACTACCCGAACTAGATAATAGAATACCTC
Found at i:6193479 original size:2 final size:2
Alignment explanation
Indices: 6193472--6193514 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
6193462 ACCACCATAG
6193472 AT AT AT AT 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
6193514 A
1 A
6193515 GAGAGAGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6193519 original size:2 final size:2
Alignment explanation
Indices: 6193514--6193546 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6193504 ATATATATAT
6193514 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6193547 NATATTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6193560 original size:2 final size:2
Alignment explanation
Indices: 6193555--6193592 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6193545 GANATATTAT
6193555 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6193593 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6193597 original size:2 final size:2
Alignment explanation
Indices: 6193592--6193632 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
6193582 ATATATATAT
6193592 AG AG AG AG AG AG AG AG ATG AG A- AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG A
6193633 AATCTAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.02
Consensus pattern (2 bp):
AG
Found at i:6235797 original size:22 final size:24
Alignment explanation
Indices: 6235745--6235811 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 24
6235735 TTAAAGATTA
6235745 TTTTAATTTTATATAAATAATTTT
1 TTTTAATTTTATATAAATAATTTT
*** *
6235769 AAATAATTTT-T-TTAATAATTTT
1 TTTTAATTTTATATAAATAATTTT
6235791 TTTTAATTTTATA-AAAGTAAT
1 TTTTAATTTTATATAAA-TAAT
6235812 AATGTAATTA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 17 0.53
23 4 0.12
24 11 0.34
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (24 bp):
TTTTAATTTTATATAAATAATTTT
Found at i:6236985 original size:28 final size:28
Alignment explanation
Indices: 6236924--6236986 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
6236914 AACTTATAAC
* *
6236924 ATATGAACAAATAGAATAAAAATAAAAA
1 ATATAAACAAATAAAATAAAAATAAAAA
* *
6236952 AAATAAACAAATATAAATAAAAAT-AATA
1 ATATAAACAAATA-AAATAAAAATAAAAA
6236980 ATATAAA
1 ATATAAA
6236987 TTTAAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (28 bp):
ATATAAACAAATAAAATAAAAATAAAAA
Found at i:6239383 original size:18 final size:18
Alignment explanation
Indices: 6239327--6239386 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
6239317 GTTATTATCA
*
6239327 ATTATGATATATTTGCAT
1 ATTATGATATATCTGCAT
* *
6239345 GTTA-CAT-TATCAT-CA-
1 ATTATGATATATC-TGCAT
6239360 ATTATGATATATCTGCAT
1 ATTATGATATATCTGCAT
6239378 ATTATGATA
1 ATTATGATA
6239387 CGTTAACATG
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
15 3 0.09
16 8 0.25
17 9 0.28
18 12 0.38
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (18 bp):
ATTATGATATATCTGCAT
Found at i:6239999 original size:33 final size:34
Alignment explanation
Indices: 6239962--6240027 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
6239952 ATTATAAAGG
6239962 AATATAATTACTATTATA-TATAT-TTTTAACATA
1 AATATAATTACT-TTATATTATATGTTTTAACATA
* *
6239995 AATATATTTACTTTATATTTTATGTTTTAACAT
1 AATATAATTACTTTATATTATATGTTTTAACAT
6240028 TACAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 5 0.17
33 15 0.52
34 9 0.31
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (34 bp):
AATATAATTACTTTATATTATATGTTTTAACATA
Found at i:6240480 original size:2 final size:2
Alignment explanation
Indices: 6240473--6240504 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6240463 ATTTATGCTT
6240473 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6240505 GATTCATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6253877 original size:2 final size:2
Alignment explanation
Indices: 6253870--6253903 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6253860 CGTAATTCAT
6253870 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6253904 AAGGGGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6254548 original size:30 final size:30
Alignment explanation
Indices: 6254476--6254564 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
6254466 TAAAAAATTA
* * *
6254476 AAATAAATTTTTATATTTTTATTATG-TTT
1 AAATAAATTTTTATATTTTTATTTTGAATC
* *
6254505 AATTAAATTTTTATGTTTTTATTTTGAATC
1 AAATAAATTTTTATATTTTTATTTTGAATC
*
6254535 AAATAAGTTTTTATATTTTTATTTTGAATC
1 AAATAAATTTTTATATTTTTATTTTGAATC
6254565 GAACAAGTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 23 0.45
30 28 0.55
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.60
Consensus pattern (30 bp):
AAATAAATTTTTATATTTTTATTTTGAATC
Found at i:6254573 original size:30 final size:30
Alignment explanation
Indices: 6254512--6254573 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
6254502 TTTAATTAAA
* *
6254512 TTTTTATGTTTTTATTTTGAATCAAATAAG
1 TTTTTATATTTTTATTTTGAATCAAACAAG
*
6254542 TTTTTATATTTTTATTTTGAATCGAACAAG
1 TTTTTATATTTTTATTTTGAATCAAACAAG
6254572 TT
1 TT
6254574 CTCATGATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (30 bp):
TTTTTATATTTTTATTTTGAATCAAACAAG
Found at i:6256153 original size:19 final size:20
Alignment explanation
Indices: 6256117--6256155 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
6256107 CTGAGAGAGC
**
6256117 AGAGAGAAGAGGTGGAGGGA
1 AGAGAGAAGAGGAAGAGGGA
6256137 AGAG-GAAGAGGAAGAGGGA
1 AGAGAGAAGAGGAAGAGGGA
6256156 CGGTCGGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.54, T:0.03
Consensus pattern (20 bp):
AGAGAGAAGAGGAAGAGGGA
Found at i:6279629 original size:18 final size:17
Alignment explanation
Indices: 6279608--6279659 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
6279598 ATATTACAAG
6279608 TTAATTAATAATTATAAT
1 TTAATTAATAA-TATAAT
6279626 TTAA-T-A-AAT-TAAT
1 TTAATTAATAATATAAT
6279639 TTAATTAATAATATAAAT
1 TTAATTAATAATAT-AAT
6279657 TTA
1 TTA
6279660 TTTTTGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 8 0.28
14 2 0.07
15 3 0.10
16 4 0.14
17 2 0.07
18 10 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATTAATAATATAAT
Found at i:6290904 original size:22 final size:23
Alignment explanation
Indices: 6290858--6290904 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
6290848 AACTAAGTCA
6290858 GATAAATGTTGGAACAAAACCAG
1 GATAAATGTTGGAACAAAACCAG
* *
6290881 GATAAATGTT-GAGCAAAACTAG
1 GATAAATGTTGGAACAAAACCAG
6290903 GA
1 GA
6290905 GAACCAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (23 bp):
GATAAATGTTGGAACAAAACCAG
Found at i:6295694 original size:18 final size:18
Alignment explanation
Indices: 6295668--6295702 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6295658 GTGGTGGCAG
*
6295668 TAGGGACAGAGGCAGCAT
1 TAGGAACAGAGGCAGCAT
*
6295686 TAGGAACAGTGGCAGCA
1 TAGGAACAGAGGCAGCA
6295703 GCATTATCAA
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:0.34, C:0.17, G:0.37, T:0.11
Consensus pattern (18 bp):
TAGGAACAGAGGCAGCAT
Found at i:6296197 original size:22 final size:23
Alignment explanation
Indices: 6296159--6296204 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
6296149 ACTAAGTCAA
6296159 ATAAACGTTGGAGCAAAACCAGG
1 ATAAACGTTGGAGCAAAACCAGG
*
6296182 ATAAACGTT-GAGCAAAACTAGG
1 ATAAACGTTGGAGCAAAACCAGG
6296204 A
1 A
6296205 GAACCAGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.46, C:0.15, G:0.24, T:0.15
Consensus pattern (23 bp):
ATAAACGTTGGAGCAAAACCAGG
Found at i:6299320 original size:23 final size:23
Alignment explanation
Indices: 6299294--6299342 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
6299284 CCATGACGGC
6299294 ACGAGCTGTGACCCTCAGCCGGG
1 ACGAGCTGTGACCCTCAGCCGGG
6299317 ACGAGCTGTGACCCTCAGCCGGG
1 ACGAGCTGTGACCCTCAGCCGGG
6299340 ACG
1 ACG
6299343 GCGATACCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.18, C:0.35, G:0.35, T:0.12
Consensus pattern (23 bp):
ACGAGCTGTGACCCTCAGCCGGG
Found at i:6301730 original size:27 final size:27
Alignment explanation
Indices: 6301641--6301820 Score: 155
Period size: 28 Copynumber: 6.5 Consensus size: 27
6301631 CATAGCTTGA
*
6301641 AACAATTAAATTTTTCAACATGGCA-AGT
1 AACAACTAAATTTTT-AACATGGCATA-T
* * *
6301669 AAAAACTACATTTTTTAACATGGCATGT
1 AACAACTA-AATTTTTAACATGGCATAT
* *
6301697 AACAACTAAATTTTTAACACGACATAT
1 AACAACTAAATTTTTAACATGGCATAT
* * * *
6301724 AATAACTACAGTTTTCAACATGGCGTAT
1 AACAACTA-AATTTTTAACATGGCATAT
* * ** *
6301752 AACAACTAAATCTTTAACATAGTGTGT
1 AACAACTAAATTTTTAACATGGCATAT
* *
6301779 AACAACTATATTTTTTAACATGGCATGT
1 AACAACTA-AATTTTTAACATGGCATAT
6301807 AACAACTAAATTTT
1 AACAACTAAATTTT
6301821 CAATATAATG
Statistics
Matches: 120, Mismatches: 28, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
27 48 0.40
28 66 0.55
29 6 0.05
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (27 bp):
AACAACTAAATTTTTAACATGGCATAT
Done.