Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 30 of 32
Found at i:5539560 original size:39 final size:39
Alignment explanation
Indices: 5539487--5539563 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
5539477 AAAATTAAAA
*
5539487 ATATTTTTATATTTTTCACTTGAATATAAGTTATTTTAC
1 ATATTTTTATATTTTTCAATTGAATATAAGTTATTTTAC
* *
5539526 ATATTTTTATAATTTTTTAATT-AATTTATA-TTATTTTA
1 ATATTTTTAT-ATTTTTCAATTGAATATA-AGTTATTTTA
5539564 ATTTGATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 23 0.70
40 10 0.30
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (39 bp):
ATATTTTTATATTTTTCAATTGAATATAAGTTATTTTAC
Found at i:5539565 original size:27 final size:29
Alignment explanation
Indices: 5539526--5539586 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
5539516 GTTATTTTAC
**
5539526 ATATTTTTATAATTTTTTAATTA-A-TTT
1 ATATTTTTATAATTTGATAATTATATTTT
5539553 ATATTATTT-TAATTTGATAATTATATTTT
1 ATATT-TTTATAATTTGATAATTATATTTT
5539582 ATATT
1 ATATT
5539587 CTATTTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 17 0.59
28 4 0.14
29 8 0.28
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (29 bp):
ATATTTTTATAATTTGATAATTATATTTT
Found at i:5540969 original size:21 final size:21
Alignment explanation
Indices: 5540943--5540998 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 21
5540933 CTGTCAATTT
**
5540943 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
5540964 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
*
5540983 TATGTATCGATACAAT
1 CATGTATCGATACAAT
5540999 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 15 0.50
20 2 0.07
21 13 0.43
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:5541002 original size:13 final size:13
Alignment explanation
Indices: 5540984--5541010 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5540974 TACATTGAAT
5540984 ATGTATCGATACA
1 ATGTATCGATACA
5540997 ATGTATCGATACA
1 ATGTATCGATACA
5541010 A
1 A
5541011 GGTAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5543333 original size:2 final size:2
Alignment explanation
Indices: 5543326--5543351 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5543316 TATAAATTAC
5543326 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
5543352 CTTTATGCCA
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:5559849 original size:2 final size:2
Alignment explanation
Indices: 5559842--5559882 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5559832 GTCATTCATA
5559842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5559883 GTTGAGCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5561373 original size:22 final size:22
Alignment explanation
Indices: 5561294--5561373 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
5561284 GTCCGTCGGC
5561294 TTTAAATTTTAAATAATTTTT-T
1 TTTAAA-TTTAAATAATTTTTAT
* *
5561316 TATAAATTTAAATTAA-TTTAAT
1 TTTAAATTTAAA-TAATTTTTAT
* *
5561338 TTTAATAATAAAATAATTTTTAT
1 TTTAA-ATTTAAATAATTTTTAT
5561361 TTTAAATTTAAAT
1 TTTAAATTTAAAT
5561374 TTAATTATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
21 9 0.20
22 22 0.48
23 15 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAAATTTAAATAATTTTTAT
Found at i:5566172 original size:4 final size:4
Alignment explanation
Indices: 5566163--5566193 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
5566153 TTTAAAACAA
*
5566163 AAAT AAAT AAAT AAAT AAAT AAAT ATAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
5566194 GATATGCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:5567884 original size:2 final size:2
Alignment explanation
Indices: 5567871--5567925 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
5567861 AAAACCATCA
*
5567871 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5567913 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
5567926 ACAAAATGAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5569044 original size:13 final size:13
Alignment explanation
Indices: 5569026--5569050 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5569016 CTTTTTCCCA
5569026 GAAGAAAAAAAAG
1 GAAGAAAAAAAAG
5569039 GAAGAAAAAAAA
1 GAAGAAAAAAAA
5569051 AAACCCAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAG
Found at i:5569791 original size:2 final size:2
Alignment explanation
Indices: 5569786--5569825 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5569776 TGTGTGTCAC
*
5569786 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5569826 CTTTAAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5573478 original size:13 final size:13
Alignment explanation
Indices: 5573445--5573478 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5573435 TGAATCTAAT
5573445 TAAATATTAAATA
1 TAAATATTAAATA
* *
5573458 TGATTATTAAATA
1 TAAATATTAAATA
5573471 TAAATATT
1 TAAATATT
5573479 TAAAAAAATT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
TAAATATTAAATA
Found at i:5574124 original size:32 final size:33
Alignment explanation
Indices: 5574061--5574125 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
5574051 TTTGCAACAT
*
5574061 ATTTAATTTATTATAATAATTATTTTATTATAA
1 ATTTAATTTAATATAATAATTATTTTATTATAA
* *
5574094 ATTT-ATTTAATATATTAA-TATTTATTTTATAA
1 ATTTAATTTAATATAATAATTATTT-TATTATAA
5574126 CAATAGTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 5 0.18
32 19 0.68
33 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
ATTTAATTTAATATAATAATTATTTTATTATAA
Found at i:5574130 original size:17 final size:17
Alignment explanation
Indices: 5574059--5574130 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
5574049 TTTTTGCAAC
* *
5574059 ATATTTAATTTATTATA
1 ATATTTATTTTATAATA
* *
5574076 ATAATTATTTTATTATA
1 ATATTTATTTTATAATA
*
5574093 A-ATTTATTTAATATATTA
1 ATATTTATTT--TATAATA
*
5574111 ATATTTATTTTATAACA
1 ATATTTATTTTATAATA
5574128 ATA
1 ATA
5574131 GTCTATAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
16 7 0.16
17 24 0.53
18 6 0.13
19 8 0.18
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTTATTTTATAATA
Found at i:5577248 original size:2 final size:2
Alignment explanation
Indices: 5577241--5577277 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5577231 TAGCTTTCAT
5577241 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
5577278 TATTGTTTAT
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:5577522 original size:20 final size:21
Alignment explanation
Indices: 5577499--5577554 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 21
5577489 TTATTAAAAG
5577499 ATTAATTATTTATTATTTA-A
1 ATTAATTATTTATTATTTAGA
5577519 ATT-ATTATTTAATT-TTTAGA
1 ATTAATTATTT-ATTATTTAGA
*
5577539 A-TAAATATTT-TTATTT
1 ATTAATTATTTATTATTT
5577555 TAATAATTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
18 2 0.06
19 15 0.48
20 14 0.45
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTAATTATTTATTATTTAGA
Found at i:5582099 original size:2 final size:2
Alignment explanation
Indices: 5582092--5582123 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5582082 TAATTTCAGT
5582092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5582124 TTTTATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5585303 original size:2 final size:2
Alignment explanation
Indices: 5585292--5585327 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5585282 ATGTATAGCG
5585292 TA TA -A 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
5585328 GCAGCAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5585763 original size:2 final size:2
Alignment explanation
Indices: 5585756--5585783 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5585746 CAATTAAGAA
5585756 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
5585784 CTGTGTGTGT
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):
AT
Found at i:5587847 original size:2 final size:2
Alignment explanation
Indices: 5587842--5587876 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5587832 GTGTGTGTAT
5587842 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5587877 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5588216 original size:2 final size:2
Alignment explanation
Indices: 5588211--5588260 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
5588201 CTTTCAAAGA
5588211 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
5588253 AT AT AT AT
1 AT AT AT AT
5588261 CTTTTAACAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5601985 original size:2 final size:2
Alignment explanation
Indices: 5601978--5602007 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5601968 GTTTTTCCTT
*
5601978 TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5602008 CTTCTCTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:5606091 original size:18 final size:19
Alignment explanation
Indices: 5606047--5606091 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5606037 TTAATTTATT
*
5606047 CATCTGAAAAAAAATAATT
1 CATCTGAAAAAAAATAATA
*
5606066 CATCTGAAAAAAATTAA-A
1 CATCTGAAAAAAAATAATA
*
5606084 CATTTGAA
1 CATCTGAA
5606092 CTGTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (19 bp):
CATCTGAAAAAAAATAATA
Found at i:5610808 original size:14 final size:12
Alignment explanation
Indices: 5610781--5610815 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 12
5610771 TAATAAATAA
5610781 TAAATTTTTATT
1 TAAATTTTTATT
5610793 TAAATTTTAATATT
1 TAAATTTT--TATT
5610807 TAAATTTTT
1 TAAATTTTT
5610816 TTATATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.43
14 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TAAATTTTTATT
Found at i:5610835 original size:18 final size:16
Alignment explanation
Indices: 5610785--5610838 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
5610775 AAATAATAAA
5610785 TTTT-TATTTAAA--T
1 TTTTATATTTAAATTT
*
5610798 TTTAATATTTAAATTT
1 TTTTATATTTAAATTT
5610814 TTTTATATTTAAATCATT
1 TTTTATATTTAAAT--TT
5610832 TTTTATA
1 TTTTATA
5610839 ACATAAGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 3 0.09
14 8 0.24
16 14 0.41
18 9 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATATTTAAATTT
Found at i:5611513 original size:16 final size:16
Alignment explanation
Indices: 5611492--5611522 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5611482 ATAAAGTTGT
*
5611492 TATTAATTATTTTAAA
1 TATTAATAATTTTAAA
5611508 TATTAATAATTTTAA
1 TATTAATAATTTTAA
5611523 TTTTTATCAT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAATAATTTTAAA
Found at i:5612192 original size:3 final size:3
Alignment explanation
Indices: 5612184--5612212 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5612174 TAATCAAAGA
5612184 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5612213 CTTTTTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5614176 original size:2 final size:2
Alignment explanation
Indices: 5614171--5614196 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5614161 GAGATATATG
5614171 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
5614197 ATATATATAT
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:5614201 original size:2 final size:2
Alignment explanation
Indices: 5614196--5614227 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5614186 TCTCTCTCTC
5614196 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
5614228 AATTCTTGAA
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:5616376 original size:29 final size:29
Alignment explanation
Indices: 5616339--5616395 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
5616329 TTAATTTTAA
*
5616339 TTTTAAATATTATTATAAATTTTAAAATT
1 TTTTAAATATTATTATAAATATTAAAATT
* * *
5616368 TTTTTAATATTATTTTATATATTAAAAT
1 TTTTAAATATTATTATAAATATTAAAAT
5616396 GGATTTAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTAAATATTATTATAAATATTAAAATT
Found at i:5618306 original size:12 final size:12
Alignment explanation
Indices: 5618272--5618307 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5618262 ACACTCAACC
*
5618272 CTTATTATTACT
1 CTTATTATTATT
5618284 CTTATTATTATT
1 CTTATTATTATT
5618296 CTTATTATTATT
1 CTTATTATTATT
5618308 TAATCAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (12 bp):
CTTATTATTATT
Found at i:5619022 original size:110 final size:112
Alignment explanation
Indices: 5618866--5619073 Score: 311
Period size: 110 Copynumber: 1.9 Consensus size: 112
5618856 ATAATTAAAT
*
5618866 TAATACATATTATTACTGAATATATATAATCATAATTATACTAATTCATATTTTTA-GGTAATA-
1 TAATACATATTATTACTGAATATATATAATCATAATTATACTAATTCACATTTTTACGGTAATAT
5618929 ATAAATTACTAA-A-TTTATA-TTATTTTTATTTATCAATTATTATCTA
66 A-AAATT-CTAACATTTTATATTTATTTTTATTTATCAATTATTATCTA
* *
5618975 TAATAC-TATTCTTACTGGAATATATATTAATCATAATTATACTAATTCCCATTTTTACGGTAAT
1 TAATACATATTATTACT-GAATATATA-TAATCATAATTATACTAATTCACATTTTTACGGTAAT
5619039 ATAAAATTCTAACATTTTATATTTATTTTTATTTA
64 ATAAAATTCTAACATTTTATATTTATTTTTATTTA
5619074 CTAATAATTA
Statistics
Matches: 89, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
108 9 0.10
109 15 0.17
110 32 0.36
111 13 0.15
112 7 0.08
113 13 0.15
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (112 bp):
TAATACATATTATTACTGAATATATATAATCATAATTATACTAATTCACATTTTTACGGTAATAT
AAAATTCTAACATTTTATATTTATTTTTATTTATCAATTATTATCTA
Found at i:5619695 original size:22 final size:22
Alignment explanation
Indices: 5619665--5619727 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
5619655 TTTCAAACAT
* * *
5619665 TTTTCATTTAATTATTAATATA
1 TTTTAATTTAATTATTAAGAGA
*
5619687 TTTTAATTTTAA--ATAAGAGAGA
1 TTTTAA-TTTAATTATTA-AGAGA
5619709 TTTTAATTTAATTATTAAG
1 TTTTAATTTAATTATTAAG
5619728 TAAAAGAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
21 8 0.25
22 16 0.50
23 8 0.25
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (22 bp):
TTTTAATTTAATTATTAAGAGA
Found at i:5624581 original size:15 final size:15
Alignment explanation
Indices: 5624558--5624587 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5624548 TTAATATTTT
*
5624558 TATATATATAAAATA
1 TATAAATATAAAATA
5624573 TATAAATATAAAATA
1 TATAAATATAAAATA
5624588 CGATAAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAATATAAAATA
Found at i:5626026 original size:6 final size:7
Alignment explanation
Indices: 5626001--5626025 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5625991 AAAGCAACCA
5626001 TTTTTAT
1 TTTTTAT
5626008 TTTTTAT
1 TTTTTAT
5626015 TTTTTAT
1 TTTTTAT
5626022 TTTT
1 TTTT
5626026 ACTGCACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:5626309 original size:36 final size:36
Alignment explanation
Indices: 5626264--5626336 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
5626254 TATATATTCG
* *
5626264 TAATTTTAAACATA-ATATAAAAAAATAAT-TATAATA
1 TAATATTAAAAATATATAT-AAAAAATAATAT-TAATA
5626300 TAATATTAAAAATATATATAAAAAATAATATTAATA
1 TAATATTAAAAATATATATAAAAAATAATATTAATA
5626336 T
1 T
5626337 GACATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 28 0.85
37 5 0.15
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (36 bp):
TAATATTAAAAATATATATAAAAAATAATATTAATA
Found at i:5626316 original size:11 final size:12
Alignment explanation
Indices: 5626264--5626333 Score: 63
Period size: 13 Copynumber: 5.8 Consensus size: 12
5626254 TATATATTCG
* *
5626264 TAATTTTAAACA
1 TAATATTAAAAA
5626276 TAATA-TAAAAA
1 TAATATTAAAAA
*
5626287 -AATAATTATAATA
1 TAAT-ATTA-AAAA
5626300 TAATATTAAAAA
1 TAATATTAAAAA
*
5626312 TATATATAAAAAA
1 TA-ATATTAAAAA
5626325 TAATATTAA
1 TAATATTAA
5626334 TATGACATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
10 3 0.06
11 6 0.13
12 17 0.36
13 18 0.38
14 3 0.06
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATATTAAAAA
Found at i:5630173 original size:2 final size:2
Alignment explanation
Indices: 5630166--5630197 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5630156 CATTCTCTTA
5630166 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
5630198 TTAAAGGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5630299 original size:2 final size:2
Alignment explanation
Indices: 5630292--5630354 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
5630282 TAGCTTGTAG
5630292 TA TA 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 TA TA
5630334 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
5630355 GCTGCTTAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5630921 original size:12 final size:11
Alignment explanation
Indices: 5630904--5630941 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5630894 AATATATTAT
5630904 TATTTTGTGTTA
1 TATTTT-TGTTA
5630916 TA-TTTTGTTA
1 TATTTTTGTTA
*
5630926 TATTTTTATTA
1 TATTTTTGTTA
5630937 TATTT
1 TATTT
5630942 ATATAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 7 0.29
11 15 0.62
12 2 0.08
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (11 bp):
TATTTTTGTTA
Found at i:5637291 original size:16 final size:16
Alignment explanation
Indices: 5637270--5637301 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5637260 ATACATCTTG
5637270 TCAACTTCTTTAAAAC
1 TCAACTTCTTTAAAAC
5637286 TCAACTTCTTTAAAAC
1 TCAACTTCTTTAAAAC
5637302 GCTTGATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.38
Consensus pattern (16 bp):
TCAACTTCTTTAAAAC
Found at i:5641502 original size:45 final size:45
Alignment explanation
Indices: 5641438--5641533 Score: 192
Period size: 45 Copynumber: 2.1 Consensus size: 45
5641428 CAGAGTAACG
5641438 ATATATATATATATATGTATGTGTGTGTGTGTGTAAGAAAGGAAA
1 ATATATATATATATATGTATGTGTGTGTGTGTGTAAGAAAGGAAA
5641483 ATATATATATATATATGTATGTGTGTGTGTGTGTAAGAAAGGAAA
1 ATATATATATATATATGTATGTGTGTGTGTGTGTAAGAAAGGAAA
5641528 ATATAT
1 ATATAT
5641534 TCTAAGTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (45 bp):
ATATATATATATATATGTATGTGTGTGTGTGTGTAAGAAAGGAAA
Found at i:5644469 original size:13 final size:13
Alignment explanation
Indices: 5644445--5644484 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
5644435 TTTAAATAAA
5644445 TTAATA-TTTACT
1 TTAATATTTTACT
5644457 TTAATATTTTACT
1 TTAATATTTTACT
*
5644470 TTAAAATTTTTACT
1 TTAATA-TTTTACT
5644484 T
1 T
5644485 AATTAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 6 0.24
13 11 0.44
14 8 0.32
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATATTTTACT
Found at i:5644947 original size:19 final size:19
Alignment explanation
Indices: 5644911--5644949 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5644901 CATCATTTAA
*
5644911 TTTATTTTTAAATTAATTT
1 TTTATTTTTAAATAAATTT
5644930 TTTA-TTTTAAATAAAATTT
1 TTTATTTTTAAAT-AAATTT
5644949 T
1 T
5644950 AATAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTTTAAATAAATTT
Found at i:5644949 original size:18 final size:19
Alignment explanation
Indices: 5644911--5644949 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5644901 CATCATTTAA
* *
5644911 TTTATTTTTAAATTAATTT
1 TTTATTTTTAAATAAAATT
5644930 TTTA-TTTTAAATAAAATT
1 TTTATTTTTAAATAAAATT
5644948 TT
1 TT
5644950 AATAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTTTAAATAAAATT
Found at i:5645221 original size:29 final size:29
Alignment explanation
Indices: 5645189--5645244 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
5645179 ATTACATCTA
*
5645189 AAATAAAATTTTATTTTTAATTTATATTT
1 AAATAAAATTTAATTTTTAATTTATATTT
**
5645218 AAATAATGTTTAATTTTTAATTTATAT
1 AAATAAAATTTAATTTTTAATTTATAT
5645245 CGTAATATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (29 bp):
AAATAAAATTTAATTTTTAATTTATATTT
Found at i:5645347 original size:16 final size:16
Alignment explanation
Indices: 5645326--5645364 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5645316 AAATATATTT
5645326 AAATAAATTA-ATAAA
1 AAATAAATTACATAAA
*
5645341 AATATAACTTACATAAA
1 AA-ATAAATTACATAAA
5645358 AAATAAA
1 AAATAAA
5645365 ATAGGCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 11 0.55
17 7 0.35
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAAATTACATAAA
Found at i:5645362 original size:24 final size:23
Alignment explanation
Indices: 5645306--5645365 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
5645296 AATCAATTAT
*
5645306 TAAAAAATAAAAATATATTTAAA
1 TAAAAAATAAAAATATACTTAAA
* *
5645329 TAAATTAATAAAAATATAACTTACA
1 TAAA-AAATAAAAATAT-ACTTAAA
5645354 TAAAAAATAAAA
1 TAAAAAATAAAA
5645366 TAGGCTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 4 0.13
24 18 0.58
25 9 0.29
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAAAATAAAAATATACTTAAA
Found at i:5646465 original size:14 final size:15
Alignment explanation
Indices: 5646434--5646475 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
5646424 ATAATATTGT
5646434 AATAATTATTTTTAA
1 AATAATTATTTTTAA
5646449 AATAA-TATTTATTAA
1 AATAATTATTT-TTAA
* *
5646464 ATTTATTATTTT
1 AATAATTATTTT
5646476 ATTTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 5 0.22
15 13 0.57
16 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATAATTATTTTTAA
Found at i:5651685 original size:2 final size:2
Alignment explanation
Indices: 5651678--5651706 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5651668 AAAAGTTATT
5651678 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
5651707 TCATATAAGA
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:5664631 original size:2 final size:2
Alignment explanation
Indices: 5664624--5664653 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5664614 TTCCCATGAA
5664624 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
5664654 TCTTCTAAGA
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):
AT
Found at i:5667272 original size:25 final size:25
Alignment explanation
Indices: 5667234--5667291 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
5667224 AAAGTTTTTA
*
5667234 TATTA-TTATTAATATAATTTTAAT
1 TATTATTTATCAATATAATTTTAAT
5667258 TATTATTTATCAATATAATTTTAAT
1 TATTATTTATCAATATAATTTTAAT
*
5667283 AATTTATTT
1 TA-TTATTT
5667292 GTTGTTTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 5 0.17
25 19 0.63
26 6 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TATTATTTATCAATATAATTTTAAT
Found at i:5678428 original size:20 final size:19
Alignment explanation
Indices: 5678382--5678425 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
5678372 TTTCCCCCAA
5678382 GCAAAATGCATTTTTCTTT
1 GCAAAATGCATTTTTCTTT
5678401 GCAAAATGCATTTTTCTTT
1 GCAAAATGCATTTTTCTTT
5678420 GCAAAA
1 GCAAAA
5678426 ATGGACATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (19 bp):
GCAAAATGCATTTTTCTTT
Found at i:5681606 original size:36 final size:36
Alignment explanation
Indices: 5681284--5681686 Score: 404
Period size: 36 Copynumber: 11.3 Consensus size: 36
5681274 TAAGCATCCT
* **
5681284 CACGTGCTCAGAACTACTCAAACTGTTAATTGTTAA
1 CACGTGCTCAGAACTACTCAATCTGTTAATTACTAA
* * * * *
5681320 CATGTACTCAGAAGTAATCAATCTGTTAATTCCTAA
1 CACGTGCTCAGAACTACTCAATCTGTTAATTACTAA
* * *
5681356 CACATGCTCAGAAATACTCAATCTGTTAATTACCAA
1 CACGTGCTCAGAACTACTCAATCTGTTAATTACTAA
* * *
5681392 CACGTGCTCAGAGCTACTCAAGCAGTTAATTACTAA
1 CACGTGCTCAGAACTACTCAATCTGTTAATTACTAA
* ** *
5681428 CACGTGCTCACATGTACTCAATCGGTTAATTACTAA
1 CACGTGCTCAGAACTACTCAATCTGTTAATTACTAA
* * * * *
5681464 CACGTGCTCAGAACTAATTAGTCTGTCAATTACTAC
1 CACGTGCTCAGAACTACTCAATCTGTTAATTACTAA
* * *
5681500 CACGTGCTCAGAACTACTCAAACTGTTAAGTGCTAA
1 CACGTGCTCAGAACTACTCAATCTGTTAATTACTAA
*
5681536 CA-GTGCTCA-AACTACTCAATCTGTTAATTTCTAA
1 CACGTGCTCAGAACTACTCAATCTGTTAATTACTAA
* * *
5681570 C-CAATGCTCAGAACTACTCAATCTGTCAATGACTAA
1 CAC-GTGCTCAGAACTACTCAATCTGTTAATTACTAA
* * *
5681606 CA--TGCATCAGAGCCACTCAATCGGTTAATTACTAA
1 CACGTGC-TCAGAACTACTCAATCTGTTAATTACTAA
* * * *
5681641 CAGGTGTTCACATCTACTCAAT-TGTTTAATTACTAA
1 CACGTGCTCAGAACTACTCAATCTG-TTAATTACTAA
5681677 CACGTGCTCA
1 CACGTGCTCA
5681687 AGCATGCTCG
Statistics
Matches: 298, Mismatches: 61, Indels: 16
0.79 0.16 0.04
Matches are distributed among these distances:
34 26 0.09
35 40 0.13
36 230 0.77
37 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (36 bp):
CACGTGCTCAGAACTACTCAATCTGTTAATTACTAA
Found at i:5681857 original size:198 final size:197
Alignment explanation
Indices: 5681577--5682280 Score: 551
Period size: 198 Copynumber: 3.6 Consensus size: 197
5681567 TAACCAATGC
* * * * *
5681577 TCAGAACTACTCAATCTGTCAATGACTAACA--TGCATCAGAGCCACTCAATCGGTTAATTACTA
1 TCAGAACTACGCAATCTGTTAATTACTAACATGTGC-TCAGAGCTACTCAATCAGTTAATTACTA
* * * * *
5681640 ACAGGTGTTCACATCTACTCAATTGTTTAATTACTAACACGTGCTCAAGCATGCTCGCGCGCTCA
65 ACACGTGCTCATATCTACTCAATTG-TTAATTACTAACACGTGCTCAAGCATGCTCACACGCTCA
** * ** * **
5681705 GAGCTACTCAACCCGTTAATTTTTAACACGTGCTCAGAACAACTCAATCCATTAATT-TCGAGCA
129 GAAATACTCAACCCGTCAATTACTAACACGTGCTCAGAACAACTCAAACCATTAATTGT-GAAAA
5681769 CATGA
193 CATGA
* ** * * *
5681774 TCAGATCTACTTAATC-GATTAGTTACTAACATGTGCTCAGAGCTAC-CGAATCGGTTAACTT-T
1 TCAGAACTACGCAATCTG-TTAATTACTAACATGTGCTCAGAGCTACTC-AATCAGTTAA-TTAC
* * * *
5681836 TAGCACGTGCTCATATCTACTCAATCAGTTAATTACTAACACGTGCTCAAGCATCCTCACATGCT
63 TAACACGTGCTCATATCTACTCAAT-TGTTAATTACTAACACGTGCTCAAGCATGCTCACACGCT
* * * * * * * *
5681901 CAGAAATACTTAATCTGTCAATTACTACCACGTGCTCAGAACTACTTAAACCGTTAATTGTTAAA
127 CAGAAATACTCAACCCGTCAATTACTAACACGTGCTCAGAACAACTCAAACCATTAATTGTGAAA
*
5681966 ACATGC
192 ACATGA
5681972 TCAGAACTACGCAATCTGTTAATTACTAACATGTGCTCAGAGCTACTCAATCAGTTAATTACTAA
1 TCAGAACTACGCAATCTGTTAATTACTAACATGTGCTCAGAGCTACTCAATCAGTTAATTACTAA
* * * * * ***
5682037 CACGTGTTCATATCTACTC-ATTCAGTTAATTACTTACATGTTCTCAAGCATGCTTATGTGCTCA
66 CACGTGCTCATATCTACTCAATT--GTTAATTACTAACACGTGCTCAAGCATGCTCACACGCTCA
* * * * * * ** * ** * * * ** * *
5682101 GAACTACTTAATCCATTAATTATTGCCACGTGATTGGAACTACTCAATCCGTTACCTGTTAACAC
129 GAAATACTCAACCCGTCAATTACTAACACGTGCTCAGAACAACTCAAACCATTAATTGTGAAAAC
* *
5682166 GTAA
194 ATGA
* * ** ** * * *
5682170 TCAGAACTACTCAATCAGTTAATTTGTAACACATG-TACAGAACTAATCAATCTGTTAATTACTA
1 TCAGAACTACGCAATCTGTTAATTACTAACATGTGCT-CAGAGCTACTCAATCAGTTAATTACTA
* * * *
5682234 ACATGTGCTCAGAGCTACTCAATCGGTTAATTACTAACACGTGCTCA
65 ACACGTGCTCATATCTACTCAAT-TGTTAATTACTAACACGTGCTCA
5682281 TATGTCCTCA
Statistics
Matches: 409, Mismatches: 83, Indels: 29
0.79 0.16 0.06
Matches are distributed among these distances:
196 1 0.00
197 30 0.07
198 367 0.90
199 11 0.03
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (197 bp):
TCAGAACTACGCAATCTGTTAATTACTAACATGTGCTCAGAGCTACTCAATCAGTTAATTACTAA
CACGTGCTCATATCTACTCAATTGTTAATTACTAACACGTGCTCAAGCATGCTCACACGCTCAGA
AATACTCAACCCGTCAATTACTAACACGTGCTCAGAACAACTCAAACCATTAATTGTGAAAACAT
GA
Found at i:5681947 original size:36 final size:36
Alignment explanation
Indices: 5681897--5682070 Score: 168
Period size: 36 Copynumber: 4.8 Consensus size: 36
5681887 CATCCTCACA
* * * *
5681897 TGCTCAGAAATACTTAATCTGTCAATTACTACCACG
1 TGCTCAGAACTACTCAATCTGTTAATTACTAACACG
* * * ** * *
5681933 TGCTCAGAACTACTTAAACCGTTAATTGTTAAAACA
1 TGCTCAGAACTACTCAATCTGTTAATTACTAACACG
* *
5681969 TGCTCAGAACTACGCAATCTGTTAATTACTAACATG
1 TGCTCAGAACTACTCAATCTGTTAATTACTAACACG
* *
5682005 TGCTCAGAGCTACTCAATCAGTTAATTACTAACACG
1 TGCTCAGAACTACTCAATCTGTTAATTACTAACACG
* * * * *
5682041 TGTTCATATCTACTCATTCAGTTAATTACT
1 TGCTCAGAACTACTCAATCTGTTAATTACT
5682071 TACATGTTCT
Statistics
Matches: 112, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 112 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (36 bp):
TGCTCAGAACTACTCAATCTGTTAATTACTAACACG
Found at i:5682065 original size:72 final size:71
Alignment explanation
Indices: 5681893--5682530 Score: 309
Period size: 72 Copynumber: 8.6 Consensus size: 71
5681883 CAAGCATCCT
* * * * * * * * *
5681893 CACATGCTCAGAAATACTTAATCTGTCAATTACTACCACGTGCTCAGAACTACTTAAACCGTTAA
1 CACATGCTCATAACTACTCAATC-GTTAATTACTAACACGTGCTCAGAGCTACTCAATCAGTTAA
**
5681958 TTGTTAA
65 TTACTAA
* * * *
5681965 AACATGCTCAGAACTACGCAATCTGTTAATTACTAACATGTGCTCAGAGCTACTCAATCAGTTAA
1 CACATGCTCATAACTACTCAATC-GTTAATTACTAACACGTGCTCAGAGCTACTCAATCAGTTAA
5682030 TTACTAA
65 TTACTAA
* * * * * * *
5682037 CACGTGTTCATATCTACTCATTCAGTTAATTACTTACATGTTCTCAAGCATGCTTATGTGCTCAG
1 CACATGCTCATAACTACTCAATC-GTTAATTACTAACACGTGCTC-AG-A-GC-TA----CTCA-
* * * *
5682102 AACTACTTAATCCATTAA
56 ATC-AGTTAAT-TACTAA
* * * ** ** ** *
5682120 TTA-TTGCCACGTGATTGGAACTACTCAATCCGTTACCTGTTAACACGTAATCAGAACTACTCAA
1 -CACATG---C-TCA-T--AACTACTCAAT-CGTTAATTACTAACACGTGCTCAGAGCTACTCAA
**
5682184 TCAGTTAATTTGTAA
57 TCAGTTAATTACTAA
* * * *
5682199 CACATG-TACAGAACTAATCAATCTGTTAATTACTAACATGTGCTCAGAGCTACTCAATCGGTTA
1 CACATGCT-CATAACTACTCAATC-GTTAATTACTAACACGTGCTCAGAGCTACTCAATCAGTTA
5682263 ATTACTAA
64 ATTACTAA
* ** * * * * * * * *
5682271 CACGTGCTCATATGTCCTCACTCGCTTAATTACTAAAACATGCTCAAAACTACTTAATCCA-TCA
1 CACATGCTCATAACTACTCAATCG-TTAATTACTAACACGTGCTCAGAGCTACTCAAT-CAGTTA
*
5682335 ATTACTAG
64 ATTACTAA
* * * ** *
5682343 CACATGCTCAAAACTACTCAAAACCGTTACTTGTTAACACGTGCTCAGAACTACTCAATCCA-TT
1 CACATGCTCATAACTACTC--AATCGTTAATTACTAACACGTGCTCAGAGCTACTCAAT-CAGTT
*
5682407 AATTTCTAA
63 AATTACTAA
* * * *
5682416 CA-ATTGCTCAGAACTACTCAATCTGTTAGTTACTAACACATGCTCAGAGCTACTTAATCAGTTA
1 CACA-TGCTCATAACTACTCAATC-GTTAATTACTAACACGTGCTCAGAGCTACTCAATCAGTTA
5682480 ATTAC-AA
64 ATTACTAA
* * *
5682487 GCACATGGTCATATCTACT-AGATCGTTAATTACCAACACGTGCT
1 -CACATGCTCATAACTACTCA-ATCGTTAATTACTAACACGTGCT
5682531 TATATCTACT
Statistics
Matches: 421, Mismatches: 111, Indels: 69
0.70 0.18 0.11
Matches are distributed among these distances:
71 27 0.06
72 257 0.61
73 58 0.14
74 5 0.01
75 3 0.01
76 2 0.00
78 1 0.00
79 5 0.01
80 10 0.02
81 4 0.01
82 10 0.02
83 6 0.01
84 1 0.00
86 2 0.00
87 3 0.01
88 2 0.00
89 2 0.00
90 22 0.05
91 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (71 bp):
CACATGCTCATAACTACTCAATCGTTAATTACTAACACGTGCTCAGAGCTACTCAATCAGTTAAT
TACTAA
Found at i:5682200 original size:36 final size:35
Alignment explanation
Indices: 5682137--5682484 Score: 137
Period size: 36 Copynumber: 9.7 Consensus size: 35
5682127 CACGTGATTG
* ** **
5682137 GAACTACTCAATCCGTTACCTGTTAACACGTAATCA
1 GAACTACTCAATCAGTTAATTACTAACACGT-ATCA
**
5682173 GAACTACTCAATCAGTTAATTTGTAACACATGTA-CA
1 GAACTACTCAATCAGTTAATTACTAACAC--GTATCA
* * * *
5682209 GAACTAATCAATCTGTTAATTACTAACATGTGCTCA
1 GAACTACTCAATCAGTTAATTACTAACACGT-ATCA
* * *
5682245 GAGCTACTCAATCGGTTAATTACTAACACGTGCTCA
1 GAACTACTCAATCAGTTAATTACTAACACGT-ATCA
* ** * * * * *
5682281 TATGTCCTCACTC-GCTTAATTACTAAAACATGCTCA
1 GAACTACTCAATCAG-TTAATTACTAACACGT-ATCA
* * * * * *
5682317 AAACTACTTAATCCA-TCAATTACTAGCACATGCTCA
1 GAACTACTCAAT-CAGTTAATTACTAACACGT-ATCA
* * * * ** *
5682353 AAACTACTCAAAACCGTTACTTGTTAACACGTGCTCA
1 GAACTACTC-AATCAGTTAATTACTAACACGT-ATCA
* ** *
5682390 GAACTACTCAATCCA-TTAATTTCTAACAATTGCTCA
1 GAACTACTCAAT-CAGTTAATTACTAACACGT-ATCA
* * * *
5682426 GAACTACTCAATCTGTTAGTTACTAACACATGCTCA
1 GAACTACTCAATCAGTTAATTACTAACACGT-ATCA
* *
5682462 GAGCTACTTAATCAGTTAATTAC
1 GAACTACTCAATCAGTTAATTAC
5682485 AAGCACATGG
Statistics
Matches: 244, Mismatches: 57, Indels: 22
0.76 0.18 0.07
Matches are distributed among these distances:
34 2 0.01
35 2 0.01
36 210 0.86
37 28 0.11
38 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.30
Consensus pattern (35 bp):
GAACTACTCAATCAGTTAATTACTAACACGTATCA
Found at i:5682252 original size:234 final size:217
Alignment explanation
Indices: 5681936--5682505 Score: 589
Period size: 217 Copynumber: 2.5 Consensus size: 217
5681926 TACCACGTGC
* * * * *
5681936 TCAGAACTACTTAAACCGTTAA-TTGTTAAAACATGCTCAGAACTACGCAATCTGTTAATTACTA
1 TCAGAACTACTCAATCAGTTAATTTG-TAACACATGCTCAGAACTACTCAATCTGTTAATTACTA
* *
5682000 ACATGTGCTCAGAGCTACTCAATCAGTTAATTACTAACACGTGTTCATATCTACTCATTCAG-TT
65 ACATGTGCTCAGAGCTACTCAATCAGTTAATTACTAACACGTGCTCATATCTACTCACTC-GCTT
* * *
5682064 AATTACTTACATGTTCTCAAGCATGCTTATGTGCTCAGAACTACTTAATCCATTAATTA-TTGCC
129 AATTAC-T--A-------AA--A--C--A--TGCTCAAAACTACTTAATCCATCAATTACTAG-C
* *** *
5682128 ACGTGATTGGAACTACTC-AATCCGTTACCTGTTAACACGTAA
175 ACATGATCAAAACTACTCAAAACCGTTACCTGTTAACACGTAA
*
5682170 TCAGAACTACTCAATCAGTTAATTTGTAACACATG-TACAGAACTAATCAATCTGTTAATTACTA
1 TCAGAACTACTCAATCAGTTAATTTGTAACACATGCT-CAGAACTACTCAATCTGTTAATTACTA
* * *
5682234 ACATGTGCTCAGAGCTACTCAATCGGTTAATTACTAACACGTGCTCATATGTCCTCACTCGCTTA
65 ACATGTGCTCAGAGCTACTCAATCAGTTAATTACTAACACGTGCTCATATCTACTCACTCGCTTA
*
5682299 ATTACTAAAACATGCTCAAAACTACTTAATCCATCAATTACTAGCACATGCTCAAAACTACTCAA
130 ATTACTAAAACATGCTCAAAACTACTTAATCCATCAATTACTAGCACATGATCAAAACTACTCAA
* **
5682364 AACCGTTACTTGTTAACACGTGC
195 AACCGTTACCTGTTAACACGTAA
* *
5682387 TCAGAACTACTCAATCCA-TTAATTTCTAACA-ATTGCTCAGAACTACTCAATCTGTTAGTTACT
1 TCAGAACTACTCAAT-CAGTTAATTTGTAACACA-TGCTCAGAACTACTCAATCTGTTAATTACT
** * * *
5682450 AACACATGCTCAGAGCTACTTAATCAGTTAATTAC-AAGCACATGGTCATATCTACT
64 AACATGTGCTCAGAGCTACTCAATCAGTTAATTACTAA-CACGTGCTCATATCTACT
5682506 AGATCGTTAA
Statistics
Matches: 293, Mismatches: 34, Indels: 35
0.81 0.09 0.10
Matches are distributed among these distances:
216 43 0.15
217 120 0.41
218 4 0.01
220 1 0.00
222 1 0.00
224 2 0.01
231 1 0.00
233 3 0.01
234 115 0.39
235 3 0.01
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (217 bp):
TCAGAACTACTCAATCAGTTAATTTGTAACACATGCTCAGAACTACTCAATCTGTTAATTACTAA
CATGTGCTCAGAGCTACTCAATCAGTTAATTACTAACACGTGCTCATATCTACTCACTCGCTTAA
TTACTAAAACATGCTCAAAACTACTTAATCCATCAATTACTAGCACATGATCAAAACTACTCAAA
ACCGTTACCTGTTAACACGTAA
Found at i:5682492 original size:36 final size:34
Alignment explanation
Indices: 5682218--5682545 Score: 129
Period size: 36 Copynumber: 9.1 Consensus size: 34
5682208 AGAACTAATC
** * *
5682218 AATCTGTTAATTACTAACATGTGCTCAGAGCTACTC
1 AATC-GTTAATTAC-AACACATGCTCAGATCTACTT
* * * * *
5682254 AATCGGTTAATTACTAACACGTGCTCATATGTCCTC
1 AATC-GTTAATTAC-AACACATGCTCAGATCTACTT
* * * *
5682290 ACTCGCTTAATTACTAAAACATGCTCAAAACTACTT
1 AATCG-TTAATTAC-AACACATGCTCAGATCTACTT
* * * * * *
5682326 AATCCATCAATTACTAGCACATGCTCAAAACTACTCAA
1 AAT-CGTTAATTAC-AACACATGCTCAGATCTACT--T
* * ** * * *
5682364 AACCGTTACTTGTTAACACGTGCTCAGAACTACTC
1 AATCGTTAATT-ACAACACATGCTCAGATCTACTT
* * * *
5682399 AATCCATTAATTTCTAACA-ATTGCTCAGAACTACTC
1 AAT-CGTTAATTAC-AACACA-TGCTCAGATCTACTT
* *
5682435 AATCTGTTAGTTACTAACACATGCTCAGAGCTACTT
1 AATC-GTTAATTAC-AACACATGCTCAGATCTACTT
* *
5682471 AATCAGTTAATTACAAGCACATGGTCATATCTAC-T
1 AATC-GTTAATTACAA-CACATGCTCAGATCTACTT
* * *
5682506 AGATCGTTAATTACCAACACGTGCTTATATCTACTT
1 A-ATCGTTAATTA-CAACACATGCTCAGATCTACTT
5682542 AATC
1 AATC
5682546 TGCTCATAGC
Statistics
Matches: 230, Mismatches: 48, Indels: 29
0.75 0.16 0.09
Matches are distributed among these distances:
35 34 0.15
36 170 0.74
37 24 0.10
38 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (34 bp):
AATCGTTAATTACAACACATGCTCAGATCTACTT
Found at i:5682505 original size:145 final size:145
Alignment explanation
Indices: 5682232--5682493 Score: 330
Period size: 145 Copynumber: 1.8 Consensus size: 145
5682222 TGTTAATTAC
* * ** * * ** * *
5682232 TAACATGTGCTCAGAGCTACTCAATCGGTTAATTACTAACACGTGCTCATATGTCCTCACTCGCT
1 TAACACGTGCTCAGAACTACTCAATCCATTAATTACTAACAAGTGCTCAGAACTACTCAATCGCT
*
5682297 TAATTACTAAAACATGCTCAAAACTACTTAATCCATCAATTACTAGCACATGCTCAAAACTACTC
66 TAATTACTAAAACATGCTCAAAACTACTTAATCCATCAATTACAAGCACATGCTCAAAACTACTC
5682362 AAAACCGTTACTTGT
131 AAAACCGTTACTTGT
* *
5682377 TAACACGTGCTCAGAACTACTCAATCCATTAATTTCTAACAATTGCTCAGAACTACTCAATCTG-
1 TAACACGTGCTCAGAACTACTCAATCCATTAATTACTAACAAGTGCTCAGAACTACTCAATC-GC
* * * * *
5682441 TTAGTTACTAACACATGCTCAGAGCTACTTAAT-CAGTTAATTACAAGCACATG
65 TTAATTACTAAAACATGCTCAAAACTACTTAATCCA-TCAATTACAAGCACATG
5682494 GTCATATCTA
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
144 2 0.02
145 94 0.97
146 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (145 bp):
TAACACGTGCTCAGAACTACTCAATCCATTAATTACTAACAAGTGCTCAGAACTACTCAATCGCT
TAATTACTAAAACATGCTCAAAACTACTTAATCCATCAATTACAAGCACATGCTCAAAACTACTC
AAAACCGTTACTTGT
Found at i:5684173 original size:18 final size:19
Alignment explanation
Indices: 5684150--5684187 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5684140 ATGAAATGAA
5684150 AGTGAA-GAAAGACAAAAG
1 AGTGAATGAAAGACAAAAG
*
5684168 AGTGAATTGGAAGACAAAAG
1 AGTGAA-TGAAAGACAAAAG
5684188 TGAAGGGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.05, G:0.29, T:0.11
Consensus pattern (19 bp):
AGTGAATGAAAGACAAAAG
Found at i:5684474 original size:18 final size:18
Alignment explanation
Indices: 5684448--5684504 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
5684438 TAATATATAT
*
5684448 ATATGATAAAAAATTAAA
1 ATATAATAAAAAATTAAA
*
5684466 ATATAATAAAATA-TAAA
1 ATATAATAAAAAATTAAA
* *
5684483 A-ATAATATAAATTTATAA
1 ATATAATAAAAAATTA-AA
5684501 ATAT
1 ATAT
5684505 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 8 0.26
17 7 0.23
18 14 0.45
19 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
ATATAATAAAAAATTAAA
Found at i:5684487 original size:16 final size:16
Alignment explanation
Indices: 5684453--5684495 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
5684443 TATATATATG
5684453 ATAA-AAAATTAAAAT
1 ATAATAAAATTAAAAT
5684468 ATAATAAAATATAAAA-
1 ATAATAAAAT-TAAAAT
5684484 ATAATATAAATT
1 ATAATA-AAATT
5684496 TATAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.16
16 12 0.48
17 9 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAATAAAATTAAAAT
Found at i:5685290 original size:11 final size:11
Alignment explanation
Indices: 5685276--5685334 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
5685266 GATTCAATTT
5685276 TTATATTTATA
1 TTATATTTATA
*
5685287 TTAT-GTTATA
1 TTATATTTATA
* *
5685297 TTTTAATTATA
1 TTATATTTATA
5685308 -T-T-TTTATA
1 TTATATTTATA
*
5685316 TTATATTCATA
1 TTATATTTATA
5685327 TTATATTT
1 TTATATTT
5685335 TAAATTATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
8 5 0.13
9 2 0.05
10 10 0.26
11 21 0.55
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (11 bp):
TTATATTTATA
Found at i:5685295 original size:5 final size:5
Alignment explanation
Indices: 5685276--5685333 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
5685266 GATTCAATTT
* *
5685276 TTATA TTTATA TTATG TTATA TTTTAA TTATA TT-T- TTATA TTATA TTCATA
1 TTATA -TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TT-ATA
5685327 TTATA TT
1 TTATA TT
5685334 TTAAATTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 26 0.59
6 14 0.32
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:5685300 original size:35 final size:35
Alignment explanation
Indices: 5685272--5685342 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
5685262 TTTTGATTCA
*
5685272 ATTTTTATATTTATATT-ATGTTATATTTTAATTAT
1 ATTTTTATA-TTATATTCATATTATATTTTAATTAT
5685307 ATTTTTATATTATATTCATATTATATTTTAAATTAT
1 ATTTTTATATTATATTCATATTATATTTT-AATTAT
5685343 CAATTTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 7 0.21
35 20 0.61
36 6 0.18
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (35 bp):
ATTTTTATATTATATTCATATTATATTTTAATTAT
Found at i:5687698 original size:3 final size:3
Alignment explanation
Indices: 5687690--5687715 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5687680 TGACATTCTT
5687690 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
5687716 TAAATATAAT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5688994 original size:20 final size:20
Alignment explanation
Indices: 5688962--5689001 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
5688952 TCAAATCAAG
5688962 TTAATTTTAAAAATTTATTT
1 TTAATTTTAAAAATTTATTT
5688982 TTAATATTTAAAAATTTATT
1 TTAAT-TTTAAAAATTTATT
5689002 AATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATTTTAAAAATTTATTT
Found at i:5689005 original size:18 final size:19
Alignment explanation
Indices: 5688962--5689009 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
5688952 TCAAATCAAG
5688962 TTAAT-TTTAAAAATTTATTT
1 TTAATATTTAAAAATTTA--T
5688982 TTAATATTTAAAAATTTA-
1 TTAATATTTAAAAATTTAT
5689000 TTAATATTTA
1 TTAATATTTA
5689010 TTTGTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.37
20 5 0.19
21 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAATATTTAAAAATTTAT
Found at i:5692532 original size:30 final size:30
Alignment explanation
Indices: 5692491--5692551 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
5692481 ATTTGGTTAG
5692491 AAATGTATTTAACAATTAACACAAAGAAAC
1 AAATGTATTTAACAATTAACACAAAGAAAC
*
5692521 AAATTTATTTAACAATTAACACAAAGAAAC
1 AAATGTATTTAACAATTAACACAAAGAAAC
5692551 A
1 A
5692552 TTCTCTGACG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.13, G:0.05, T:0.25
Consensus pattern (30 bp):
AAATGTATTTAACAATTAACACAAAGAAAC
Found at i:5693666 original size:6 final size:6
Alignment explanation
Indices: 5693619--5693663 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
5693609 ATCATGTTAA
* *
5693619 CCATAG CCATAG CCATAG CCATAG CCATAG CCACAG CCACAG CCA
1 CCATAG CCATAG CCATAG CCATAG CCATAG CCATAG CCATAG CCA
5693664 CAGGCTATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.33, C:0.40, G:0.16, T:0.11
Consensus pattern (6 bp):
CCATAG
Found at i:5704659 original size:6 final size:6
Alignment explanation
Indices: 5704650--5704713 Score: 56
Period size: 6 Copynumber: 9.8 Consensus size: 6
5704640 GTTTAAATTT
* * *
5704650 ATATAA ATATATA ATATTTAA ATATAA ATATAA CATAAAA ATAAAA AAATACA
1 ATATAA ATATA-A ATA--TAA ATATAA ATATAA -ATATAA ATATAA ATATA-A
5704703 ATATAA ATATA
1 ATATAA ATATA
5704714 CACATTGTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
6 29 0.59
7 14 0.29
8 4 0.08
9 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (6 bp):
ATATAA
Found at i:5720962 original size:158 final size:158
Alignment explanation
Indices: 5720668--5720985 Score: 559
Period size: 158 Copynumber: 2.0 Consensus size: 158
5720658 GCTTAGTGCT
5720668 TAGTTCTATTCTAATCAACGACTTTAATCCACGCATCTTTTTGAGTTATACTATTGTGAAAACAT
1 TAGTTCTATTCTAATCAACGACTTTAATCCACGCATCTTTTTGAGTTATACTATTGTGAAAACAT
5720733 ATGAAACCCTTTTTCTTCATTACACAAAAGAAATCTAAGAGATCAACTGAAAACTGTCAATATTA
66 ATGAAACCCTTTTTCTTCATTACACAAAAGAAATCTAAGAGATCAACTGAAAACTGTCAATATTA
5720798 CTTGAATCAAGTGTACTGTTCAATCAAC
131 CTTGAATCAAGTGTACTGTTCAATCAAC
* * *
5720826 TAGTTCTATTCTAATCAACGACTTTAATCCACGTATCTTTTTTAGTTATTGC-ATTGTGAAAACA
1 TAGTTCTATTCTAATCAACGACTTTAATCCACGCATCTTTTTGAGTTA-TACTATTGTGAAAACA
* *
5720890 TATGAAACCCTTTTTCTTTATTACACAAAAGAAATCTAAGATATCAACTGAAAACTGTCAATATT
65 TATGAAACCCTTTTTCTTCATTACACAAAAGAAATCTAAGAGATCAACTGAAAACTGTCAATATT
5720955 AAC-TGAATCAAGTGTACTGTTCAATCAAC
130 -ACTTGAATCAAGTGTACTGTTCAATCAAC
5720984 TA
1 TA
5720986 ACATCCATCT
Statistics
Matches: 153, Mismatches: 5, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
158 149 0.97
159 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.35
Consensus pattern (158 bp):
TAGTTCTATTCTAATCAACGACTTTAATCCACGCATCTTTTTGAGTTATACTATTGTGAAAACAT
ATGAAACCCTTTTTCTTCATTACACAAAAGAAATCTAAGAGATCAACTGAAAACTGTCAATATTA
CTTGAATCAAGTGTACTGTTCAATCAAC
Found at i:5723987 original size:2 final size:2
Alignment explanation
Indices: 5723980--5724029 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
5723970 AATTGGGTAC
* *
5723980 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT 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
5724022 AT AT AT AT
1 AT AT AT AT
5724030 TAAAAATAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5727557 original size:13 final size:13
Alignment explanation
Indices: 5727539--5727563 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5727529 CATAAAGTGT
5727539 TGTATCGATACAA
1 TGTATCGATACAA
5727552 TGTATCGATACA
1 TGTATCGATACA
5727564 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5727561 original size:33 final size:33
Alignment explanation
Indices: 5727519--5727585 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5727509 TTCAACGATT
5727519 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
5727552 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
5727585 T
1 T
5727586 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:5734155 original size:21 final size:24
Alignment explanation
Indices: 5734111--5734155 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5734101 TTCCCCTCGC
*
5734111 TTTTTATTTTATATATTTATATAA
1 TTTTTATTTAATATATTTATATAA
5734135 TTTTTA-TTAATAT-TTTA-ATAA
1 TTTTTATTTAATATATTTATATAA
5734156 ATTACGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 4 0.20
23 6 0.30
24 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTTATTTAATATATTTATATAA
Found at i:5737600 original size:2 final size:2
Alignment explanation
Indices: 5737593--5737626 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5737583 GGATGGCAGG
*
5737593 TA TA TA TA TA AA 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
5737627 ACTTGCCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5745618 original size:68 final size:68
Alignment explanation
Indices: 5745509--5745645 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
5745499 GCTATGGCTC
5745509 AGGGCATATGTGAGCTGTTATGGGTAAAAATACTCCTAGTAGACTTGAAAATTTCAAGAGGTGAA
1 AGGGCATATGTGAGCTGTTATGGGTAAAAATACTCCTAGTAGACTTGAAAATTTCAAGAGGTGAA
5745574 CCT
66 CCT
5745577 AGGGCATATGTGAGCTGTTATGGGTAAAAATACTCCTAGTAGACTTGAAAATTTCAAGAGGTGAA
1 AGGGCATATGTGAGCTGTTATGGGTAAAAATACTCCTAGTAGACTTGAAAATTTCAAGAGGTGAA
5745642 CCT
66 CCT
5745645 A
1 A
5745646 TGAAGCTCTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (68 bp):
AGGGCATATGTGAGCTGTTATGGGTAAAAATACTCCTAGTAGACTTGAAAATTTCAAGAGGTGAA
CCT
Found at i:5746189 original size:35 final size:36
Alignment explanation
Indices: 5746122--5746189 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
5746112 GAAATAAACA
** *
5746122 TTTTTCTGGTTCAAATTTATCATTTCATTTATCAAT
1 TTTTTCTGGTTCAAATTTATCACATCACTTATCAAT
*
5746158 TTTTTCTGGTTCAATTTTATCACATC-CTTATC
1 TTTTTCTGGTTCAAATTTATCACATCACTTATC
5746190 TTCAAGGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 5 0.18
36 23 0.82
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.54
Consensus pattern (36 bp):
TTTTTCTGGTTCAAATTTATCACATCACTTATCAAT
Found at i:5748282 original size:42 final size:42
Alignment explanation
Indices: 5748223--5748310 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
5748213 CGATGATATA
5748223 GATGCGCTGACATGGCTCGTCACCTTGTATACACTAAAGTAG
1 GATGCGCTGACATGGCTCGTCACCTTGTATACACTAAAGTAG
*
5748265 GATGCGCTGACATGGCTCGTCACCTTGTATACACTCAAGTAG
1 GATGCGCTGACATGGCTCGTCACCTTGTATACACTAAAGTAG
5748307 GATG
1 GATG
5748311 TGCATCCACG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (42 bp):
GATGCGCTGACATGGCTCGTCACCTTGTATACACTAAAGTAG
Found at i:5749969 original size:158 final size:159
Alignment explanation
Indices: 5749654--5749972 Score: 554
Period size: 159 Copynumber: 2.0 Consensus size: 159
5749644 GCTTAGTGCT
5749654 TAGTTCTATTCTAATCAACGACTTTAATCCACGCATCTTTTTGAGTATTACTATTGTGAAAACAT
1 TAGTTCTATTCTAATCAACGACTTTAATCCACGCATCTTTTTGAGTATTACTATTGTGAAAACAT
*
5749719 ATGAAACCCCTTTTTCTTCATTACACAAAAGAAATCTAAGAGATCAACTGAAAACTGTCAATATT
66 ATGAAAACCCTTTTTCTTCATTACACAAAAGAAATCTAAGAGATCAACTGAAAACTGTCAATATT
5749784 ACTTGAATCAAGTGTACTGTTCAATCAAC
131 ACTTGAATCAAGTGTACTGTTCAATCAAC
* * *
5749813 TAGTTCTATTCTAATCAACGACTTTAATCCACGTATCTTTTTTAGTTATTGC-ATTGTGAAAACA
1 TAGTTCTATTCTAATCAACGACTTTAATCCACGCATCTTTTTGAG-TATTACTATTGTGAAAACA
*
5749877 TATGAAAACCCTTTTTCTT-ATTACACAAAAGAAATCTAAGATATCAACTGAAAACTGTCAATAT
65 TATGAAAACCCTTTTTCTTCATTACACAAAAGAAATCTAAGAGATCAACTGAAAACTGTCAATAT
5749941 TAAC-TGAATCAAGTGTACTGTTCAATCAAC
130 T-ACTTGAATCAAGTGTACTGTTCAATCAAC
5749971 TA
1 TA
5749973 ACATCCATCT
Statistics
Matches: 153, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
158 73 0.48
159 75 0.49
160 5 0.03
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.35
Consensus pattern (159 bp):
TAGTTCTATTCTAATCAACGACTTTAATCCACGCATCTTTTTGAGTATTACTATTGTGAAAACAT
ATGAAAACCCTTTTTCTTCATTACACAAAAGAAATCTAAGAGATCAACTGAAAACTGTCAATATT
ACTTGAATCAAGTGTACTGTTCAATCAAC
Found at i:5752962 original size:2 final size:2
Alignment explanation
Indices: 5752955--5753006 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
5752945 AATTGGGTAC
* *
5752955 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT 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
5752997 AT AT AT AT AT
1 AT AT AT AT AT
5753007 TAAAAATAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5756536 original size:13 final size:13
Alignment explanation
Indices: 5756518--5756542 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5756508 CATAAAGTGT
5756518 TGTATCGATACAA
1 TGTATCGATACAA
5756531 TGTATCGATACA
1 TGTATCGATACA
5756543 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5756540 original size:33 final size:33
Alignment explanation
Indices: 5756498--5756564 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5756488 TTCAACGATT
5756498 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
5756531 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
5756564 T
1 T
5756565 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:5763137 original size:22 final size:25
Alignment explanation
Indices: 5763092--5763137 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5763082 TTCCCCTCGC
*
5763092 TTTTTATTTTATATATTTATATAAT
1 TTTTTATTTAATATATTTATATAAT
5763117 TTTTTA-TTAATAT-TTTA-ATAA
1 TTTTTATTTAATATATTTATATAA
5763138 ATTACGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 6 0.30
25 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTTATTTAATATATTTATATAAT
Found at i:5766583 original size:2 final size:2
Alignment explanation
Indices: 5766576--5766611 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5766566 GGATGGCAGG
*
5766576 TA TA TA TA TA AA 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
5766612 ACTTGCCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5778699 original size:12 final size:12
Alignment explanation
Indices: 5778682--5778707 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5778672 ACTCACATAG
5778682 AATATTTTTGTT
1 AATATTTTTGTT
5778694 AATATTTTTGTT
1 AATATTTTTGTT
5778706 AA
1 AA
5778708 GTGTGTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (12 bp):
AATATTTTTGTT
Found at i:5778752 original size:22 final size:22
Alignment explanation
Indices: 5778720--5778774 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
5778710 GTGTTAGGTA
*
5778720 GTATATTAGGTAAAAATATTAG
1 GTATGTTAGGTAAAAATATTAG
* * **
5778742 GTGTGTTAGGTGAGCATATTAG
1 GTATGTTAGGTAAAAATATTAG
5778764 GTATGTTAGGT
1 GTATGTTAGGT
5778775 GGTGTGTTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (22 bp):
GTATGTTAGGTAAAAATATTAG
Found at i:5778779 original size:34 final size:34
Alignment explanation
Indices: 5778741--5778806 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
5778731 AAAAATATTA
*
5778741 GGTGTGTTAGGTGAGCATATTAGGTATGTTAGGT
1 GGTGTGTTAGGTAAGCATATTAGGTATGTTAGGT
*
5778775 GGTGTGTTAGGTAAGCATATTAGGTGTGTTAG
1 GGTGTGTTAGGTAAGCATATTAGGTATGTTAG
5778807 ATAAGTAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.21, C:0.03, G:0.38, T:0.38
Consensus pattern (34 bp):
GGTGTGTTAGGTAAGCATATTAGGTATGTTAGGT
Found at i:5780097 original size:24 final size:24
Alignment explanation
Indices: 5780052--5780104 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5780042 TTGGCTGTAC
* * * * *
5780052 ATTAGCTGTATAATGTTGTGATGT
1 ATTAGCTGCACAATATTATGATAT
5780076 ATTAGCTGCACAATATTATGATAT
1 ATTAGCTGCACAATATTATGATAT
5780100 ATTAG
1 ATTAG
5780105 TTGTACATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (24 bp):
ATTAGCTGCACAATATTATGATAT
Found at i:5782735 original size:34 final size:35
Alignment explanation
Indices: 5782684--5782767 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 35
5782674 TCTTTGTTAA
*
5782684 GTGTGTTAGGT-AGTATATTAGGTAAACATATTAG
1 GTGTGTTAGGTGAGTATATTAGGTAAACAAATTAG
*
5782718 GTTTGTTAGGTGA-TATATTAGGTAAACAAATTAG
1 GTGTGTTAGGTGAGTATATTAGGTAAACAAATTAG
5782752 GTGTGTTAGGTGAGTA
1 GTGTGTTAGGTGAGTA
5782768 AGACAATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 42 0.93
35 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (35 bp):
GTGTGTTAGGTGAGTATATTAGGTAAACAAATTAG
Found at i:5782888 original size:12 final size:12
Alignment explanation
Indices: 5782871--5782896 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5782861 ACACACACAG
5782871 AATATCTTTGTT
1 AATATCTTTGTT
5782883 AATATCTTTGTT
1 AATATCTTTGTT
5782895 AA
1 AA
5782897 GTGTGTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (12 bp):
AATATCTTTGTT
Found at i:5785085 original size:205 final size:202
Alignment explanation
Indices: 5784736--5785114 Score: 650
Period size: 205 Copynumber: 1.9 Consensus size: 202
5784726 CTAATACTTT
* *
5784736 TAGTTTTCATAGAATTAATTGAAGGACCGAATCTTTGATTCTGGATGTTCCGATCATATGACAGG
1 TAGTTTTCATAAAATTAATTGAAGAACCGAATCTTTGATTCTGGATGTTCCGATCATATGACAGG
* *
5784801 AGATATGTATAAACTCTGTAATGTCTCAGAGTACAAAGGCAGACGAGTTGTGGTGACTGCAAATG
66 AGATATGGATAAACTCTGTAATGTCTCAGAGTACAAAGGCAAACGAGTTGTGGTGACTGCAAATG
5784866 ACTCGCGGCTACCAATCACTCATGTTGGTGGTATAGTGATTGATAAAGAAGATAAGAGACTTCTA
131 ACTCGCGGCTACCAATCACTCATGTTGGTGGTATAGTGATTGATAAAGAAGATAAGAGACTTCTA
5784931 GTGCTTA
196 GTGCTTA
* *
5784938 TAGTTTTCATAAAATTAATTGTAGAAGAACTGAATCTTTGATTCTGGATGTTCCGGTCATATGAC
1 TAGTTTTCATAAAATTAA-T-T-GAAGAACCGAATCTTTGATTCTGGATGTTCCGATCATATGAC
*
5785003 AGGAGATATGGATAAACTCTGTAATGTCTCAGAGTATAAAGGCAAACGAGTTGTGGTGACTGCAA
63 AGGAGATATGGATAAACTCTGTAATGTCTCAGAGTACAAAGGCAAACGAGTTGTGGTGACTGCAA
* *
5785068 ATGATTTGCGGCTACCAATCACTCATGTTGGTGGTATAGTGATTGAT
128 ATGACTCGCGGCTACCAATCACTCATGTTGGTGGTATAGTGATTGAT
5785115 TCCTGTCTGA
Statistics
Matches: 165, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
202 17 0.10
203 1 0.01
204 1 0.01
205 146 0.88
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (202 bp):
TAGTTTTCATAAAATTAATTGAAGAACCGAATCTTTGATTCTGGATGTTCCGATCATATGACAGG
AGATATGGATAAACTCTGTAATGTCTCAGAGTACAAAGGCAAACGAGTTGTGGTGACTGCAAATG
ACTCGCGGCTACCAATCACTCATGTTGGTGGTATAGTGATTGATAAAGAAGATAAGAGACTTCTA
GTGCTTA
Found at i:5785856 original size:150 final size:150
Alignment explanation
Indices: 5785585--5785888 Score: 581
Period size: 150 Copynumber: 2.0 Consensus size: 150
5785575 TTGGAAAGGT
5785585 GAAGCAATCTTCAGTCAATGGTATGCGATATATGGTGACTTTTATTGATAATCATTCAAGATATG
1 GAAGCAATCTTCAGTCAATGGTATGCGATATATGGTGACTTTTATTGATAATCATTCAAGATATG
5785650 TCTGGGTGTACTTTATTAAAAAAAAATCTGAGTCCTTGGAAAAATTCAAAGAATTCAAGTTAATG
66 TCTGGGTGTACTTTATTAAAAAAAAATCTGAGTCCTTGGAAAAATTCAAAGAATTCAAGTTAATG
5785715 GTCGAAGGAGAAGTTGAAAA
131 GTCGAAGGAGAAGTTGAAAA
* * *
5785735 GAAGCAGTCTTCAGTCAATGGTATGCGGTATATGGTGACTTTTATTGATAATCATTTAAGATATG
1 GAAGCAATCTTCAGTCAATGGTATGCGATATATGGTGACTTTTATTGATAATCATTCAAGATATG
5785800 TCTGGGTGTACTTTATTAAAAAAAAATCTGAGTCCTTGGAAAAATTCAAAGAATTCAAGTTAATG
66 TCTGGGTGTACTTTATTAAAAAAAAATCTGAGTCCTTGGAAAAATTCAAAGAATTCAAGTTAATG
5785865 GTCGAAGGAGAAGTTGAAAA
131 GTCGAAGGAGAAGTTGAAAA
5785885 GAAG
1 GAAG
5785889 ATTGATGCCT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 151 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (150 bp):
GAAGCAATCTTCAGTCAATGGTATGCGATATATGGTGACTTTTATTGATAATCATTCAAGATATG
TCTGGGTGTACTTTATTAAAAAAAAATCTGAGTCCTTGGAAAAATTCAAAGAATTCAAGTTAATG
GTCGAAGGAGAAGTTGAAAA
Found at i:5786423 original size:13 final size:13
Alignment explanation
Indices: 5786407--5786434 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5786397 AACATATTTC
5786407 ACTTCTTTATTCA
1 ACTTCTTTATTCA
5786420 ACTTCTTTATTCA
1 ACTTCTTTATTCA
5786433 AC
1 AC
5786435 AGAAGAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (13 bp):
ACTTCTTTATTCA
Found at i:5786520 original size:39 final size:39
Alignment explanation
Indices: 5786477--5786555 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
5786467 AGTTAGAAGA
*
5786477 AATTCAACAAACTTCAAAAACTGTTGCAAAGTCTTTATC
1 AATTCAACAAACTCCAAAAACTGTTGCAAAGTCTTTATC
** *
5786516 AATTCAGTAAACTCCAAAAACTGTTGCAAAGTTTTTATC
1 AATTCAACAAACTCCAAAAACTGTTGCAAAGTCTTTATC
5786555 A
1 A
5786556 CAAGAAAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.32
Consensus pattern (39 bp):
AATTCAACAAACTCCAAAAACTGTTGCAAAGTCTTTATC
Found at i:5788357 original size:24 final size:24
Alignment explanation
Indices: 5788330--5788385 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
5788320 CTGTACGTTT
* *
5788330 GCTGTATAATGTTATGATATATTA
1 GCTGTACAATATTATGATATATTA
*
5788354 GCTGTGCAATATTATGATATATTA
1 GCTGTACAATATTATGATATATTA
5788378 GCTGTACA
1 GCTGTACA
5788386 TTAGCTATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (24 bp):
GCTGTACAATATTATGATATATTA
Found at i:5791731 original size:5 final size:5
Alignment explanation
Indices: 5791721--5791748 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5791711 AAGGTTCTTT
5791721 CACAG CACAG CACAG CACAG CACAG CAC
1 CACAG CACAG CACAG CACAG CACAG CAC
5791749 CAAGTCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.43, G:0.18, T:0.00
Consensus pattern (5 bp):
CACAG
Found at i:5792729 original size:3 final size:3
Alignment explanation
Indices: 5792721--5792752 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5792711 CTGTTTTTAT
*
5792721 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5792753 TTTGCTGTTT
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):
TTA
Found at i:5804008 original size:2 final size:2
Alignment explanation
Indices: 5804001--5804033 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5803991 TGGGGGCAAC
*
5804001 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5804034 TGGGGGACCC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5804129 original size:2 final size:2
Alignment explanation
Indices: 5804122--5804157 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5804112 GACGTTCCCC
*
5804122 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5804158 TACGCCATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5804832 original size:13 final size:13
Alignment explanation
Indices: 5804814--5804845 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5804804 TAAATATCAT
5804814 ATTAATCAAATTA
1 ATTAATCAAATTA
*
5804827 ATTAATTAAATTA
1 ATTAATCAAATTA
5804840 ATTAAT
1 ATTAAT
5804846 ATACATTCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAATCAAATTA
Found at i:5816590 original size:19 final size:19
Alignment explanation
Indices: 5816548--5816591 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5816538 TTTTTTAAAG
* *
5816548 AAAAAAAATATTATATTTT
1 AAAAAAAATATTACATGTT
5816567 AAAAAAAATATTACA-GTT
1 AAAAAAAATATTACATGTT
5816585 AGAAAAA
1 A-AAAAA
5816592 TAAGAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAAAAATATTACATGTT
Found at i:5822756 original size:31 final size:30
Alignment explanation
Indices: 5822713--5822773 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
5822703 ATATTGATAT
5822713 ATTTTATAATTAAATT-TAAATTAAAATAAA
1 ATTTTATAATTAAATTAT-AATTAAAATAAA
5822743 ATTTTATTAATTAAATTATAATTAAAATAAA
1 ATTTTA-TAATTAAATTATAATTAAAATAAA
5822774 TGAATTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 6 0.21
31 22 0.76
32 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
ATTTTATAATTAAATTATAATTAAAATAAA
Found at i:5822812 original size:15 final size:15
Alignment explanation
Indices: 5822724--5822817 Score: 52
Period size: 14 Copynumber: 6.1 Consensus size: 15
5822714 TTTTATAATT
5822724 AAATTTAAATTAAAATA
1 AAATTT-AATT-AAATA
* *
5822741 AAATTTTATT-AATT
1 AAATTTAATTAAATA
5822755 AAATTATAATTAAA-A
1 AAATT-TAATTAAATA
* *
5822770 TAAA-TGAATTTAA-A
1 -AAATTTAATTAAATA
* *
5822784 ATATTATATTTTAAATA
1 AAATT-TA-ATTAAATA
5822801 AAATTTAATTAAATA
1 AAATTTAATTAAATA
5822816 AA
1 AA
5822818 TTTGTCTTAT
Statistics
Matches: 58, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
13 2 0.03
14 16 0.28
15 15 0.26
16 14 0.24
17 11 0.19
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (15 bp):
AAATTTAATTAAATA
Found at i:5823425 original size:21 final size:21
Alignment explanation
Indices: 5823374--5823425 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
5823364 ATTAAAAAGT
* *
5823374 TAAAAAAATTAAAATTTTACA
1 TAAAATAATTAAAATTTTAAA
* *
5823395 -AAATTAAATTAAATTTTTAAA
1 TAAAAT-AATTAAAATTTTAAA
5823416 TAAAATAATT
1 TAAAATAATT
5823426 TTATTATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAATAATTAAAATTTTAAA
Found at i:5823438 original size:9 final size:9
Alignment explanation
Indices: 5823424--5823452 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5823414 AATAAAATAA
5823424 TTTTATTAT
1 TTTTATTAT
5823433 TTTTATTAT
1 TTTTATTAT
5823442 TTTTATT-T
1 TTTTATTAT
5823450 TTT
1 TTT
5823453 AAACTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTATTAT
Found at i:5823529 original size:10 final size:10
Alignment explanation
Indices: 5823503--5823539 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5823493 TTTTTTGAAT
5823503 AATAATGTT-A
1 AATAAT-TTAA
5823513 AAT-ATTTAA
1 AATAATTTAA
5823522 AATAATTTAA
1 AATAATTTAA
5823532 AATAATTT
1 AATAATTT
5823540 TTTTAACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 2 0.08
9 6 0.24
10 17 0.68
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (10 bp):
AATAATTTAA
Found at i:5826347 original size:41 final size:40
Alignment explanation
Indices: 5826293--5826383 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 40
5826283 AAGTAAAATG
** *
5826293 ATAATTTTATATTAATATTTATATTCAA-TAATTAAATTAAA
1 ATAATTTTATATTAA-ATAAATATT-AATTAATTAAATAAAA
* *
5826334 ATAATTTTTTATTAAATAAATATTAATTTATTTAAATAAAA
1 ATAATTTTATATTAAATAAATATTAA-TTAATTAAATAAAA
5826375 ATAATTTTA
1 ATAATTTTA
5826384 AACTCGAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
39 2 0.05
40 7 0.17
41 33 0.79
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (40 bp):
ATAATTTTATATTAAATAAATATTAATTAATTAAATAAAA
Found at i:5826383 original size:20 final size:21
Alignment explanation
Indices: 5826323--5826383 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
5826313 ATATTCAATA
* *
5826323 ATTAAATTAAAATAATTTTTT
1 ATTAAATAAAAATAATTTTAT
*
5826344 ATTAAATAAATATTAA-TTTAT
1 ATTAAATAAA-AATAATTTTAT
5826365 -TTAAATAAAAATAATTTTA
1 ATTAAATAAAAATAATTTTA
5826384 AACTCGAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.12
20 13 0.38
21 13 0.38
22 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAAATAAAAATAATTTTAT
Found at i:5827124 original size:11 final size:11
Alignment explanation
Indices: 5827110--5827163 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
5827100 ATTAGATACG
5827110 ATATAAATATA
1 ATATAAATATA
*
5827121 ATATAAAAATTA
1 ATATAAATA-TA
5827133 AT-TAAAATATA
1 ATAT-AAATATA
5827144 ATAT-AATATA
1 ATATAAATATA
5827154 A-A-AAATATA
1 ATATAAATATA
5827163 A
1 A
5827164 ACATGATACC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 8 0.22
10 7 0.19
11 13 0.35
12 9 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAATATA
Found at i:5827229 original size:32 final size:32
Alignment explanation
Indices: 5827182--5827244 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
5827172 CCAATATATG
*
5827182 ATGTATAAAATTTATAT-AATATAAATTATTA
1 ATGTATAAAATTTATATAAATATAAAATATTA
5827213 ATGTATAAAAATTTATATAAATATAAAATATT
1 ATGTAT-AAAATTTATATAAATATAAAATATT
5827245 TTAAATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 6 0.21
32 11 0.38
33 12 0.41
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (32 bp):
ATGTATAAAATTTATATAAATATAAAATATTA
Found at i:5827237 original size:18 final size:18
Alignment explanation
Indices: 5827188--5827245 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
5827178 TATGATGTAT
5827188 AAAATTTATAT-AATAT-
1 AAAATTTATATAAATATA
*
5827204 -AAA-TTAT-TAATGTATA
1 AAAATTTATATAA-ATATA
5827220 AAAATTTATATAAATATA
1 AAAATTTATATAAATATA
5827238 AAATATTT
1 AAA-ATTT
5827246 TAAATAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 6 0.18
17 3 0.09
18 11 0.33
19 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAAATTTATATAAATATA
Found at i:5827252 original size:20 final size:18
Alignment explanation
Indices: 5827216--5827254 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
5827206 ATTATTAATG
*
5827216 TATAAAAATTTATATAAA
1 TATAAAAATTTAAATAAA
5827234 TATAAAATATTTTAAATAAA
1 TATAAAA-A-TTTAAATAAA
5827254 T
1 T
5827255 TATGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAAAATTTAAATAAA
Found at i:5827253 original size:32 final size:32
Alignment explanation
Indices: 5827188--5827253 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
5827178 TATGATGTAT
* **
5827188 AAAATTTATATAATATAAATTATTAATGTATA
1 AAAATTTATATAATATAAAATATTAATAAATA
*
5827220 AAAATTTATATAAATATAAAATATT-TTAAATA
1 AAAATTTATAT-AATATAAAATATTAATAAATA
5827252 AA
1 AA
5827254 TTATGAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (32 bp):
AAAATTTATATAATATAAAATATTAATAAATA
Found at i:5827776 original size:20 final size:19
Alignment explanation
Indices: 5827735--5827773 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
5827725 TATATGAAAC
*
5827735 TATTTAAATAATTAATTAA
1 TATTTAAATAATTAAATAA
5827754 TATTTAATATAATTAGAATA
1 TATTTAA-ATAATTA-AATA
5827774 TATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 7 0.41
21 3 0.18
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTTAAATAATTAAATAA
Found at i:5828221 original size:4 final size:4
Alignment explanation
Indices: 5828212--5828237 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5828202 ATAACTCGAA
5828212 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
5828238 TTGTAAAAGA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:5828291 original size:2 final size:2
Alignment explanation
Indices: 5828284--5828317 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5828274 GAAAGGATAG
5828284 CT CT CT 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 CT CT CT
5828318 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.