Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 64 of 186
Found at i:20060097 original size:21 final size:22
Alignment explanation
Indices: 20060071--20060120 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
20060061 CGACCTGTAG
20060071 CACGGGCATT-TCCCAGGGT-CA
1 CACGGGC-TTATCCCAGGGTCCA
*
20060092 CACGGGCTTATCCCATGGTCCA
1 CACGGGCTTATCCCAGGGTCCA
*
20060114 CATGGGC
1 CACGGGC
20060121 GTGTGAGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 15 0.60
22 8 0.32
ACGTcount: A:0.18, C:0.34, G:0.28, T:0.20
Consensus pattern (22 bp):
CACGGGCTTATCCCAGGGTCCA
Found at i:20065801 original size:121 final size:121
Alignment explanation
Indices: 20065587--20065814 Score: 447
Period size: 121 Copynumber: 1.9 Consensus size: 121
20065577 TGAAATCGGG
*
20065587 ATAGCTTAATCTATCTATTTGGGGGATCAATTTGAAGATTATCAAAGTATTGAAATTAGGTCATG
1 ATAGCTTAATCTACCTATTTGGGGGATCAATTTGAAGATTATCAAAGTATTGAAATTAGGTCATG
20065652 GATGTATATGATGAAAATTATAAATTTATGGTATAAAATGAAAGGTTGTTGATGGT
66 GATGTATATGATGAAAATTATAAATTTATGGTATAAAATGAAAGGTTGTTGATGGT
20065708 ATAGCTTAATCTACCTATTTGGGGGATCAATTTGAAGATTATCAAAGTATTGAAATTAGGTCATG
1 ATAGCTTAATCTACCTATTTGGGGGATCAATTTGAAGATTATCAAAGTATTGAAATTAGGTCATG
20065773 GATGTATATGATGAAAATTATAAATTTATGGTATAAAATGAA
66 GATGTATATGATGAAAATTATAAATTTATGGTATAAAATGAA
20065815 GGGAAATTGA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 106 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (121 bp):
ATAGCTTAATCTACCTATTTGGGGGATCAATTTGAAGATTATCAAAGTATTGAAATTAGGTCATG
GATGTATATGATGAAAATTATAAATTTATGGTATAAAATGAAAGGTTGTTGATGGT
Found at i:20068586 original size:18 final size:17
Alignment explanation
Indices: 20068559--20068593 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20068549 TCTGGTGTTG
20068559 AATAGCAAGGGCGATGA
1 AATAGCAAGGGCGATGA
*
20068576 AATAGGCAAGGTCGATGA
1 AATA-GCAAGGGCGATGA
20068594 CGTGCCCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.11, G:0.34, T:0.14
Consensus pattern (17 bp):
AATAGCAAGGGCGATGA
Found at i:20076534 original size:40 final size:39
Alignment explanation
Indices: 20076479--20076557 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
20076469 AACACCTTAG
*
20076479 ACTACTTCGCTTAAATGGTGGATCTTTACCTTCCCTACA
1 ACTACTTCGCTTAAATGGCGGATCTTTACCTTCCCTACA
20076518 NACTACTTCGCTTAAATGGCGGATCTTTACCTTCCCTACA
1 -ACTACTTCGCTTAAATGGCGGATCTTTACCTTCCCTACA
20076558 CAACAGATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.34
Consensus pattern (39 bp):
ACTACTTCGCTTAAATGGCGGATCTTTACCTTCCCTACA
Found at i:20079608 original size:41 final size:41
Alignment explanation
Indices: 20079510--20079597 Score: 176
Period size: 41 Copynumber: 2.1 Consensus size: 41
20079500 GAACAATACA
20079510 TCACAATCTCATACATTTATGCATTCAATATTATAAACTAT
1 TCACAATCTCATACATTTATGCATTCAATATTATAAACTAT
20079551 TCACAATCTCATACATTTATGCATTCAATATTATAAACTAT
1 TCACAATCTCATACATTTATGCATTCAATATTATAAACTAT
20079592 TCACAA
1 TCACAA
20079598 CCATTCACAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (41 bp):
TCACAATCTCATACATTTATGCATTCAATATTATAAACTAT
Found at i:20094796 original size:16 final size:16
Alignment explanation
Indices: 20094775--20094816 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
20094765 TTTAATCACT
20094775 TTATTTTAAGTTCAAA
1 TTATTTTAAGTTCAAA
**
20094791 TTATTTTTAA-TTTGAA
1 TTA-TTTTAAGTTCAAA
20094807 TTATTTTAAG
1 TTATTTTAAG
20094817 ATCGTATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (16 bp):
TTATTTTAAGTTCAAA
Found at i:20095240 original size:20 final size:20
Alignment explanation
Indices: 20095215--20095262 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
20095205 ATACCAATTG
*
20095215 AATTAACAACTTTATAAAAT
1 AATTAAAAACTTTATAAAAT
20095235 AATTAAAAACTTTATAAAAT
1 AATTAAAAACTTTATAAAAT
20095255 AATATAAA
1 AAT-TAAA
20095263 TATAGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTAAAAACTTTATAAAAT
Found at i:20096997 original size:21 final size:20
Alignment explanation
Indices: 20096964--20097003 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
20096954 ATTGGGTAGG
20096964 TTTTACTTTAAGTTTTTATT
1 TTTTACTTTAAGTTTTTATT
*
20096984 TTTTATTTCTAAGTTTTTAT
1 TTTTACTT-TAAGTTTTTAT
20097004 CCATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTACTTTAAGTTTTTATT
Found at i:20097668 original size:29 final size:29
Alignment explanation
Indices: 20097636--20097693 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
20097626 AAAAAATGTG
* * * *
20097636 TGTGTTAGGTCGTGTGGGTCACACGAGCT
1 TGTGTTAGGCCATGTAGGCCACACGAGCT
20097665 TGTGTTAGGCCATGTAGGCCACACGAGCT
1 TGTGTTAGGCCATGTAGGCCACACGAGCT
20097694 GGGCTAGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (29 bp):
TGTGTTAGGCCATGTAGGCCACACGAGCT
Found at i:20100280 original size:27 final size:27
Alignment explanation
Indices: 20100250--20100401 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
20100240 ATATTAAGTC
* *
20100250 CGCACACTCAGTGCTATATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
20100277 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
20100305 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
20100332 CGCACACTTAGTGCAACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
20100359 CGCACACTTAGTGCTACATAGTCCAACT
1 CGCACACTTAGTGCTACATAGT-CAACT
20100387 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20100402 GTACAATTTA
Statistics
Matches: 115, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
27 70 0.61
28 45 0.39
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:20100311 original size:55 final size:54
Alignment explanation
Indices: 20100250--20100401 Score: 232
Period size: 55 Copynumber: 2.8 Consensus size: 54
20100240 ATATTAAGTC
* *
20100250 CGCACACTCAGTGCTATATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATC-AACT
* * * *
20100305 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCAACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAACT
20100359 CGCACACTTAGTGCTACATAGTCCAACTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGT-CAACTCGCACACTTAGTGCT
20100402 GTACAATTTA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 25 0.28
55 63 0.72
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAACT
Found at i:20100354 original size:82 final size:82
Alignment explanation
Indices: 20100250--20100401 Score: 250
Period size: 82 Copynumber: 1.9 Consensus size: 82
20100240 ATATTAAGTC
* *
20100250 CGCACACTCAGTGCTATATAGTCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
1 CGCACACTCAGTGCAACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
20100315 GTGCTACATAGTCAATT
66 GTGCTACATAGTCAATT
* * * *
20100332 CGCACACTTAGTGCAACATAGTCAATTCGCACACTTAGTGCTACATAGTCCAACTCGCACACTTA
1 CGCACACTCAGTGCAACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
20100397 GTGCT
66 GTGCT
20100402 GTACAATTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 64 1.00
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (82 bp):
CGCACACTCAGTGCAACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAATT
Found at i:20104310 original size:20 final size:20
Alignment explanation
Indices: 20104257--20104320 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
20104247 AGTTTTGCTC
* *
20104257 TGCTCTGTTCTATTATGTAT
1 TGCTCTGTTCTGTTATGTTT
* *
20104277 TGTTCTGTTTTGTTATGTTT
1 TGCTCTGTTCTGTTATGTTT
* * *
20104297 TGCTCTATTCTGTTCTGTTA
1 TGCTCTGTTCTGTTATGTTT
20104317 TGCT
1 TGCT
20104321 TTTGCTTTGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.09, C:0.14, G:0.17, T:0.59
Consensus pattern (20 bp):
TGCTCTGTTCTGTTATGTTT
Found at i:20104342 original size:31 final size:30
Alignment explanation
Indices: 20104277--20104342 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
20104267 TATTATGTAT
* * *
20104277 TGTTCTGTTTTGTTATGTTTTGCTCTATTC
1 TGTTCTGTTATGTTATGCTTTGCTCTATTA
* *
20104307 TGTTCTGTTATGCTTTTGCTTTGTTCTATTA
1 TGTTCTGTTATG-TTATGCTTTGCTCTATTA
20104338 TGTTC
1 TGTTC
20104343 CATTCTGCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.08, C:0.14, G:0.17, T:0.62
Consensus pattern (30 bp):
TGTTCTGTTATGTTATGCTTTGCTCTATTA
Found at i:20104501 original size:20 final size:20
Alignment explanation
Indices: 20104463--20104501 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20104453 TATTCTATTC
** *
20104463 TGCTCTGCTCTGTTTTGTTA
1 TGCTCTGCTCTACTATGTTA
20104483 TGCTCTGCTCTACTATGTT
1 TGCTCTGCTCTACTATGTT
20104502 CTGTTATGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.23, G:0.18, T:0.51
Consensus pattern (20 bp):
TGCTCTGCTCTACTATGTTA
Found at i:20104526 original size:25 final size:25
Alignment explanation
Indices: 20104460--20104529 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
20104450 ATCTATTCTA
*
20104460 TTCTGCTCTGCTCTGTTTTGTTATG
1 TTCTGCTCTGCTCTGTTCTGTTATG
* * *
20104485 CTCTGCTCTACTATGTTCTGTTATG
1 TTCTGCTCTGCTCTGTTCTGTTATG
20104510 TTCTGCTCTG-TCCTGTTCTG
1 TTCTGCTCTGCT-CTGTTCTG
20104530 GTTGGGTTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.06, C:0.24, G:0.19, T:0.51
Consensus pattern (25 bp):
TTCTGCTCTGCTCTGTTCTGTTATG
Found at i:20114103 original size:22 final size:22
Alignment explanation
Indices: 20114055--20114104 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
20114045 TTTGTTTATT
*
20114055 ATTAAATAATAAAGTTTAGTTAG
1 ATTAAAT-ATAAAGCTTAGTTAG
20114078 -TTAAAT-TAAAGCTTAGTTAG
1 ATTAAATATAAAGCTTAGTTAG
20114098 AATTAAA
1 -ATTAAA
20114105 CTAAGCTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (22 bp):
ATTAAATATAAAGCTTAGTTAG
Found at i:20115697 original size:416 final size:416
Alignment explanation
Indices: 20114911--20115706 Score: 1206
Period size: 416 Copynumber: 1.9 Consensus size: 416
20114901 TAGCCTCTAG
* *
20114911 TAGGGTAAATATATATTACAAATCGAATTGACATAACACAATTAAACATGCTACTGAGTGATTCT
1 TAGGGAAAATATATATTACAAATCGAATTGACATAACACAATTAAACATGCTACTGAATGATTCT
* *
20114976 AAATTAAGAGATATAAGGAGAGAATGTATATGAATTAAACAAAAACATCTTATATGAATTTGACT
66 AAATTAAGAGATATAAGGAGAGAATGTATATGAATGAAACAAAAACATCTTATATGAATCTGACT
* * * *
20115041 ATGAACTCTAGGTATGTGGTTGGCATGAAAATGGAATGTCTGAGTTATGTTGTATTGGCGTATAG
131 ATGAACTCTAAGTATGTGGCTAGCATGAAAATGGAATGTCTGAGTTATGTTGTATTGGCATATAG
* * *
20115106 TATTCCCCCATATAACATGCCATTGGCGTACTAAGTCTGTATAAGTTTTGTATACTTCATTGGGC
196 TATTCACCCATATAACATGCCATTGGCGTACTAAGTCTGTATAAGTTTTGTATACGTCATTAGGC
* *
20115171 GTACTCTGTCATGTTGAGTGATTCTTTTGAAAGATTAGATTTGGCTTTTAGTATTCTACTTAAGA
261 ATACTCTGTCATGTTGAGTAATTCTTTTGAAAGATTAGATTTGGCTTTTAGTATTCTACTTAAGA
* *
20115236 TCTCTATGGAACTCACTTAATTCTTTTGCACTTACCTTGTTACCCTCTTCCTTCTCAGGCTTTCT
326 TCTCTATGGAACTCACTTAATTCTTTTGAACTTACCCTGTTACCCTCTTCCTTCTCAGGCTTTCT
20115301 AAAGGACTATGCTAGAGGATATCTGT
391 AAAGGACTATGCTAGAGGATATCTGT
** *
20115327 TAGGGAAAATATATATTACAAA-CTGAATTGGTATAACACAATTAAACATGTTACTGAATGATTC
1 TAGGGAAAATATATATTACAAATC-GAATTGACATAACACAATTAAACATGCTACTGAATGATTC
* *
20115391 TAAA-TAAGGAGCTATAAGGAGAGAATGTATATGAATGAAACGAAAACATCTTATATGAATCTGA
65 TAAATTAA-GAGATATAAGGAGAGAATGTATATGAATGAAACAAAAACATCTTATATGAATCTGA
* * *
20115455 CTCTGAACTTTAAGTATGTGGCTAGCATGAAAATGGAATGTCTGAGTTATGTTGTCTTGGCATAT
129 CTATGAACTCTAAGTATGTGGCTAGCATGAAAATGGAATGTCTGAGTTATGTTGTATTGGCATAT
* * * * *
20115520 AGTATTCACCCATGTGACATGCCATTGGCGTACTGAGTCTGTCTGAGTTTTGTATACGTCATTAG
194 AGTATTCACCCATATAACATGCCATTGGCGTACTAAGTCTGTATAAGTTTTGTATACGTCATTAG
* * * *
20115585 GCATACTCTTTCGTGTTGAGTAATTCTTTTGAAAGATTGGA-TTGTGCTTTTAGTATTCTGCTTA
259 GCATACTCTGTCATGTTGAGTAATTCTTTTGAAAGATTAGATTTG-GCTTTTAGTATTCTACTTA
* *
20115649 AGATCTCTATGGAACTCAC-TAAGTTCTTTTGAACTTGCCCCT-TTACCCTTTTCCTTCT
323 AGATCTCTATGGAACTCACTTAA-TTCTTTTGAACTT-ACCCTGTTACCCTCTTCCTTCT
20115707 GAAGCGTACT
Statistics
Matches: 341, Mismatches: 34, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
415 10 0.03
416 328 0.96
417 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (416 bp):
TAGGGAAAATATATATTACAAATCGAATTGACATAACACAATTAAACATGCTACTGAATGATTCT
AAATTAAGAGATATAAGGAGAGAATGTATATGAATGAAACAAAAACATCTTATATGAATCTGACT
ATGAACTCTAAGTATGTGGCTAGCATGAAAATGGAATGTCTGAGTTATGTTGTATTGGCATATAG
TATTCACCCATATAACATGCCATTGGCGTACTAAGTCTGTATAAGTTTTGTATACGTCATTAGGC
ATACTCTGTCATGTTGAGTAATTCTTTTGAAAGATTAGATTTGGCTTTTAGTATTCTACTTAAGA
TCTCTATGGAACTCACTTAATTCTTTTGAACTTACCCTGTTACCCTCTTCCTTCTCAGGCTTTCT
AAAGGACTATGCTAGAGGATATCTGT
Found at i:20121557 original size:13 final size:13
Alignment explanation
Indices: 20121539--20121564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20121529 AACCATTTTC
20121539 CTACACGACCCTT
1 CTACACGACCCTT
20121552 CTACACGACCCTT
1 CTACACGACCCTT
20121565 TGGCTAGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.46, G:0.08, T:0.23
Consensus pattern (13 bp):
CTACACGACCCTT
Found at i:20129422 original size:81 final size:81
Alignment explanation
Indices: 20129315--20129480 Score: 314
Period size: 81 Copynumber: 2.0 Consensus size: 81
20129305 TGAAAAATAA
*
20129315 AAGAAAACTTAATCTAATCCTACTCCTAAACTACAAGGGTTTTTGGATGCGTCGAAGATGACTTA
1 AAGAAAACTTAATCTAATCCTACTCCTAAACTACAAAGGTTTTTGGATGCGTCGAAGATGACTTA
20129380 GTTACATCAAACCCCT
66 GTTACATCAAACCCCT
*
20129396 AAGAAAACTTAATCTAATCCTACTCCTAAACTACAAAGGTTTTTGGATGCGTCTAAGATGACTTA
1 AAGAAAACTTAATCTAATCCTACTCCTAAACTACAAAGGTTTTTGGATGCGTCGAAGATGACTTA
20129461 GTTACATCAAACCCCT
66 GTTACATCAAACCCCT
20129477 AAGA
1 AAGA
20129481 TTGTATTTAT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (81 bp):
AAGAAAACTTAATCTAATCCTACTCCTAAACTACAAAGGTTTTTGGATGCGTCGAAGATGACTTA
GTTACATCAAACCCCT
Found at i:20132922 original size:9 final size:9
Alignment explanation
Indices: 20132910--20132981 Score: 65
Period size: 9 Copynumber: 7.7 Consensus size: 9
20132900 ACTCTTTAAT
20132910 ATTTTTATA
1 ATTTTTATA
20132919 ATTTTTATA
1 ATTTTTATA
*
20132928 ACTATTTAATA
1 A-T-TTTTATA
* *
20132939 AATTAT-TA
1 ATTTTTATA
*
20132947 AGTTTTATA
1 ATTTTTATA
20132956 ACTTTTTATA
1 A-TTTTTATA
20132966 ATTTTTTATA
1 A-TTTTTATA
20132976 ATTTTT
1 ATTTTT
20132982 GTTAAACTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
8 6 0.12
9 20 0.39
10 18 0.35
11 7 0.14
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:20132922 original size:28 final size:28
Alignment explanation
Indices: 20132890--20132980 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 28
20132880 AAAATAATAC
20132890 AATTTTATATACTCTTTAAT-ATTTTTAT
1 AATTTTATATACT-TTTAATAATTTTTAT
*
20132918 AATTTT-TATAACTATTTAATAAATTATTA-
1 AATTTTATAT-ACT-TTTAAT-AATTTTTAT
* *
20132947 AGTTTTATA-ACTTTTTATAATTTTTTAT
1 AATTTTATATACTTTTAATAA-TTTTTAT
20132975 AATTTT
1 AATTTT
20132981 TGTTAAACTA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
26 2 0.04
27 13 0.25
28 23 0.45
29 5 0.10
30 8 0.16
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (28 bp):
AATTTTATATACTTTTAATAATTTTTAT
Found at i:20138362 original size:174 final size:174
Alignment explanation
Indices: 20138072--20138397 Score: 492
Period size: 174 Copynumber: 1.9 Consensus size: 174
20138062 TGGAGTTGCT
* **
20138072 CTTAAATCCACCACAAATGAAGATAGTGAATCAACCAAAGATGTGGATGAAGAAAAAGAGATGTT
1 CTTAAATCCACCACAAATGAAGATAGTGAATCAACCAAAGAGGTGGATGAAGAAAAAGAGATGAC
* * **
20138137 CATGTTTGCTAGGAGATTCAAGAGATTCATGACCTTTAATAGAGGAAGAAGATTCCAAAAGAAGG
66 CATGTTTACTAGGAGATTCAAGAGATTCATGAACTCCAATAGAGGAAGAAGATTCCAAAAGAAGG
20138202 AGGGGTTAAAGCTTGAATCTACTAAGAAGAATGAGGGGTTAAAG
131 AGGGGTTAAAGCTTGAATCTACTAAGAAGAATGAGGGGTTAAAG
* * * *
20138246 CTTAAATCTACCACAAATGAAGATAGTTAATCAAGCGAAGAGGTGGATGAA-AACAAAGAGATGA
1 CTTAAATCCACCACAAATGAAGATAGTGAATCAACCAAAGAGGTGGATGAAGAA-AAAGAGATGA
* * * * *
20138310 CCATGTTTATTAGGAGATTGAAGAGATTCCTGAAGTCCAATAGAGGAAGAAGATTCCAAAAGAAT
65 CCATGTTTACTAGGAGATTCAAGAGATTCATGAACTCCAATAGAGGAAGAAGATTCCAAAAGAAG
20138375 GAGGGGTTAAAGCTTGAATCTAC
130 GAGGGGTTAAAGCTTGAATCTAC
20138398 CAAGGGGAAG
Statistics
Matches: 135, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
173 2 0.01
174 133 0.99
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.22
Consensus pattern (174 bp):
CTTAAATCCACCACAAATGAAGATAGTGAATCAACCAAAGAGGTGGATGAAGAAAAAGAGATGAC
CATGTTTACTAGGAGATTCAAGAGATTCATGAACTCCAATAGAGGAAGAAGATTCCAAAAGAAGG
AGGGGTTAAAGCTTGAATCTACTAAGAAGAATGAGGGGTTAAAG
Found at i:20151313 original size:21 final size:21
Alignment explanation
Indices: 20151289--20151332 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20151279 GGTCCTTACT
20151289 TATTTACCTATCAAAATTTTC
1 TATTTACCTATCAAAATTTTC
20151310 TATTTACCTATCAAAATTTTC
1 TATTTACCTATCAAAATTTTC
20151331 TA
1 TA
20151333 AGTCTCTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTTACCTATCAAAATTTTC
Found at i:20152564 original size:7 final size:7
Alignment explanation
Indices: 20152548--20152578 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
20152538 AATGCTACCT
*
20152548 CATATAA
1 CATATCA
20152555 CATATCA
1 CATATCA
20152562 CATATCA
1 CATATCA
20152569 CATATCA
1 CATATCA
20152576 CAT
1 CAT
20152579 GTTGCTCGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (7 bp):
CATATCA
Found at i:20156949 original size:25 final size:25
Alignment explanation
Indices: 20156869--20156965 Score: 71
Period size: 24 Copynumber: 4.1 Consensus size: 25
20156859 TTCCTGTTAC
*
20156869 ATGGCTC-TTGATGAGCTTCCCGA-T
1 ATGGCTCTTTG-TGAACTTCCCGATT
*
20156893 A-GGCTCTTCGTGAA-TTCCCGATT
1 ATGGCTCTTTGTGAACTTCCCGATT
** * *
20156916 AAAGTTCTTTGTGAACTTCCTGATT
1 ATGGCTCTTTGTGAACTTCCCGATT
* *
20156941 ATGGCTC-TTATGAGCTTCCCG-TT
1 ATGGCTCTTTGTGAACTTCCCGATT
20156964 AT
1 AT
20156966 ATAGCCCGGA
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
22 7 0.12
23 14 0.25
24 24 0.42
25 12 0.21
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (25 bp):
ATGGCTCTTTGTGAACTTCCCGATT
Found at i:20159490 original size:45 final size:45
Alignment explanation
Indices: 20159426--20159516 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
20159416 TTGAAGAGAT
20159426 AGAAGACTGAAAGGCTATTAGCCTGTCATTTGGTAGCTATGCTAC
1 AGAAGACTGAAAGGCTATTAGCCTGTCATTTGGTAGCTATGCTAC
20159471 AGAAGACTGAAAGGCTATTAGCCTGTCATTTGGTAGCTATGCTAC
1 AGAAGACTGAAAGGCTATTAGCCTGTCATTTGGTAGCTATGCTAC
20159516 A
1 A
20159517 TATATCTGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (45 bp):
AGAAGACTGAAAGGCTATTAGCCTGTCATTTGGTAGCTATGCTAC
Found at i:20187552 original size:94 final size:91
Alignment explanation
Indices: 20187428--20187639 Score: 239
Period size: 94 Copynumber: 2.3 Consensus size: 91
20187418 GTGTGTGTGC
* *
20187428 TAGTGTAAGACATGTCTTGGACATGCATCAGCCAC-ATTATGAGAGCCAGTGTAAGACCATGTCT
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCACGA-GAT--GAGCCAGTGTAAGA-CATGTCT
* *
20187492 GGGACATGGCATCGGCATTGAGA-CGAGAGA
62 AGGACAT-GCATCGGCATGGAGAGCGAGAGA
* * * *
20187522 TAGTGTAAGACATGTCTGGGACATGTATCAGCTACGAGATGTGCTAGTGTAAGACATGTCTAGGA
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAGATGAGCCAGTGTAAGACATGTCTAGGA
* * *
20187587 CATGCATCGGCATGGATATGTGAGAGC
66 CATGCATCGGCATGGAGA-GCGAGAGA
*
20187614 CAGTGTAAGACCATGTCTGGGACATG
1 TAGTGTAAGA-CATGTCTGGGACATG
20187640 GCATGTATAC
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
90 13 0.13
91 13 0.13
92 26 0.25
93 15 0.15
94 34 0.33
95 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (91 bp):
TAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAGATGAGCCAGTGTAAGACATGTCTAGGA
CATGCATCGGCATGGAGAGCGAGAGA
Found at i:20187608 original size:44 final size:45
Alignment explanation
Indices: 20187423--20187639 Score: 149
Period size: 44 Copynumber: 4.7 Consensus size: 45
20187413 GCGATGTGTG
* * * *
20187423 TGTGCTAGTGTAAGACATGTCTTGGACATGCATCAGCCACAT-TATGA
1 TGTGCTAGTGTAAGACATGTCTGGGACATGCATC-G--GCATGGACGA
* *
20187470 -GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGA
1 TGTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA-TG-GACGA
* * * * *
20187518 -GAGATAGTGTAAGACATGTCTGGGACATGTATCAGC-TACGA-GA
1 TGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCAT-GGACGA
* *
20187561 TGTGCTAGTGTAAGACATGTCTAGGACATGCATCGGCATGGA-TA
1 TGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATGGACGA
*
20187605 TGTGAGAGCCAGTGTAAGACCATGTCTGGGACATG
1 TGT----GCTAGTGTAAGA-CATGTCTGGGACATG
20187640 GCATGTATAC
Statistics
Matches: 137, Mismatches: 20, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
43 2 0.01
44 40 0.29
45 3 0.02
46 19 0.14
47 28 0.20
48 31 0.23
49 14 0.10
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (45 bp):
TGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATGGACGA
Found at i:20193025 original size:35 final size:35
Alignment explanation
Indices: 20192984--20193051 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
20192974 TGAATTGCAC
* *
20192984 ATCTGTATCTGTATCTGA-GATAGGCTTAGGCCCAT
1 ATCTGTATCTGCATCT-ATAATAGGCTTAGGCCCAT
*
20193019 ATCTGTATTTGCATCTATAATAGGCTTAGGCCC
1 ATCTGTATCTGCATCTATAATAGGCTTAGGCCC
20193052 TAATTTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 1 0.03
35 28 0.97
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (35 bp):
ATCTGTATCTGCATCTATAATAGGCTTAGGCCCAT
Found at i:20202647 original size:21 final size:21
Alignment explanation
Indices: 20202621--20202665 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
20202611 AAATAAATTT
20202621 GCACTTAGCAAAACAGAATAG
1 GCACTTAGCAAAACAGAATAG
* *
20202642 GCACTTAGCAAAATAGAATGG
1 GCACTTAGCAAAACAGAATAG
20202663 GCA
1 GCA
20202666 TTTGGTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (21 bp):
GCACTTAGCAAAACAGAATAG
Found at i:20202723 original size:19 final size:20
Alignment explanation
Indices: 20202686--20202730 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
20202676 ACACTGATAC
20202686 AAAAATATAGATACTTTAT-
1 AAAAATATAGATACTTTATG
*
20202705 AAAAAGTATTGATAC-TTATG
1 AAAAA-TATAGATACTTTATG
20202725 AAAAAT
1 AAAAAT
20202731 TGTCGATACC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.33
Consensus pattern (20 bp):
AAAAATATAGATACTTTATG
Found at i:20205210 original size:134 final size:134
Alignment explanation
Indices: 20205016--20205275 Score: 295
Period size: 134 Copynumber: 1.9 Consensus size: 134
20205006 ATATTCACAA
* * * ** ** *
20205016 ATTTATTGATACCTTTTTTGATATCGATACAAAAATGGCATTCTGTTTTTTAAAATATTTACCAA
1 ATTTATCGATACCTTCTTTAATATCGATACAAAAATGGCATTCTGACTTCCAAAAGATTTACCAA
* * * * *
20205081 GTTTCAATATGGTATCAATACGTTTTGCTTGGTATTGATAAAATTATTTAAGTATCGATAGAAGT
66 GTATCAATATAGTATCAATACCTTTTGCTTGATATCGATAAAATTATTTAAGTATCGATAGAAGT
20205146 ACAC
131 ACAC
* * * **
20205150 ATTTATCGATACCTTCTTTAATATCGATACCAAATTGGCATTCTGACTTCCAAAGGATTTATTAA
1 ATTTATCGATACCTTCTTTAATATCGATACAAAAATGGCATTCTGACTTCCAAAAGATTTACCAA
* * * * * **
20205215 GTATCGATATAGTATCGATACCTTTTGTTTGATATCGATAAATTTCTTTTGGTATCGATAG
66 GTATCAATATAGTATCAATACCTTTTGCTTGATATCGATAAAATTATTTAAGTATCGATAG
20205276 TTTTAGTTCC
Statistics
Matches: 101, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
134 101 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.42
Consensus pattern (134 bp):
ATTTATCGATACCTTCTTTAATATCGATACAAAAATGGCATTCTGACTTCCAAAAGATTTACCAA
GTATCAATATAGTATCAATACCTTTTGCTTGATATCGATAAAATTATTTAAGTATCGATAGAAGT
ACAC
Found at i:20205898 original size:13 final size:13
Alignment explanation
Indices: 20205846--20205898 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
20205836 AGTTTGGCAA
20205846 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
20205859 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
20205872 TG-TTTTTAAGAAG
1 TGCTTTTGAA-AAG
20205885 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
20205898 T
1 T
20205899 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 5 0.16
13 21 0.66
14 6 0.19
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:20206697 original size:20 final size:20
Alignment explanation
Indices: 20206674--20206713 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20206664 TTTTCTATCA
20206674 TTTCTAAATTTTT-ATAATAT
1 TTTC-AAATTTTTCATAATAT
*
20206694 TTTCATATTTTTCATAATAT
1 TTTCAAATTTTTCATAATAT
20206714 ACTAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCAAATTTTTCATAATAT
Found at i:20206768 original size:28 final size:27
Alignment explanation
Indices: 20206737--20206791 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
20206727 ATATATTCAA
*
20206737 CCAT-TTTTAATAATATTTTATAATTTTT
1 CCATGTTTTAAT-ATATTTCA-AATTTTT
*
20206765 CCATGTTTTTATATATTTCAAATTTTT
1 CCATGTTTTAATATATTTCAAATTTTT
20206792 TATAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 11 0.46
29 6 0.25
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (27 bp):
CCATGTTTTAATATATTTCAAATTTTT
Found at i:20206783 original size:18 final size:19
Alignment explanation
Indices: 20206752--20206801 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
20206742 TTTAATAATA
* *
20206752 TTTTATAATTTTTC-CATGT
1 TTTTATAATATTTCAAAT-T
20206771 TTTTAT-ATATTTCAAATT
1 TTTTATAATATTTCAAATT
20206789 TTTTATAATATTT
1 TTTTATAATATTT
20206802 TTATATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTATAATATTTCAAATT
Found at i:20206810 original size:19 final size:19
Alignment explanation
Indices: 20206788--20206830 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
20206778 TATTTCAAAT
*
20206788 TTTTTATAATATTTTTA-TA
1 TTTTCATAA-ATTTTTATTA
*
20206807 TTTTCATTAATTTTTATTA
1 TTTTCATAAATTTTTATTA
20206826 TTTTC
1 TTTTC
20206831 CTAAGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTCATAAATTTTTATTA
Found at i:20206839 original size:19 final size:18
Alignment explanation
Indices: 20206798--20206847 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
20206788 TTTTTATAAT
*
20206798 ATTTTTATATTTTCATTA
1 ATTTTTATATTTTCACTA
20206816 ATTTTTATTATTTTC-CTA
1 ATTTTTA-TATTTTCACTA
*
20206834 AGTTTTATAGTTTT
1 ATTTTTATA-TTTT
20206848 ATAAACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 19 0.68
19 7 0.25
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.66
Consensus pattern (18 bp):
ATTTTTATATTTTCACTA
Found at i:20207552 original size:10 final size:10
Alignment explanation
Indices: 20207537--20207620 Score: 50
Period size: 9 Copynumber: 8.4 Consensus size: 10
20207527 AAATTATGAA
20207537 AAAAATATAT
1 AAAAATATAT
*
20207547 AAAAATGT-T
1 AAAAATATAT
** *
20207556 AAAGTTATGAA
1 AAAAATAT-AT
*
20207567 AAATAATATTT
1 AAA-AATATAT
20207578 AAAAATATA-
1 AAAAATATAT
20207587 AAAAATAT-T
1 AAAAATATAT
*
20207596 ACAAAATCATAA
1 A-AAAAT-ATAT
20207608 AAAAAT-TAT
1 AAAAATATAT
20207617 AAAA
1 AAAA
20207621 CAAATTTAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 15
0.67 0.15 0.18
Matches are distributed among these distances:
9 21 0.38
10 17 0.31
11 13 0.24
12 4 0.07
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (10 bp):
AAAAATATAT
Found at i:20207566 original size:30 final size:30
Alignment explanation
Indices: 20207526--20207583 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
20207516 TTAAATTATA
20207526 TAAATTATGAAAAA-AATATATAAAAATGT
1 TAAATTATGAAAAATAATATATAAAAATGT
*
20207555 TAAAGTTATGAAAAATAATATTTAAAAAT
1 TAAA-TTATGAAAAATAATATATAAAAAT
20207584 ATAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 10 0.38
31 12 0.46
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTATGAAAAATAATATATAAAAATGT
Found at i:20207595 original size:19 final size:20
Alignment explanation
Indices: 20207566--20207620 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
20207556 AAAGTTATGA
20207566 AAAATAATATTTAAAAAT-AT
1 AAAA-AATATTTAAAAATCAT
20207586 AAAAAATA-TTACAAAATCAT
1 AAAAAATATTTA-AAAATCAT
20207606 AAAAAA-ATTATAAAA
1 AAAAAATATT-TAAAA
20207621 CAAATTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 16 0.52
21 2 0.06
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAAAATATTTAAAAATCAT
Found at i:20208296 original size:19 final size:20
Alignment explanation
Indices: 20208262--20208303 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
20208252 TTTTTCAATT
*
20208262 TTTATAATATATTTTTGTAA
1 TTTATAATATATTTTTATAA
20208282 TTTATAATA-ATTTTTATAA
1 TTTATAATATATTTTTATAA
20208301 TTT
1 TTT
20208304 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTATAATATATTTTTATAA
Found at i:20213782 original size:24 final size:25
Alignment explanation
Indices: 20213737--20213784 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
20213727 TATAAAAAAA
*
20213737 TTAAAAATATAATAAACCAAATATAT
1 TTAAAAATAT-ATAAAACAAATATAT
*
20213763 TTAAAAATAT-TAAAATAAATAT
1 TTAAAAATATATAAAACAAATAT
20213785 TAAAACAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
26 10 0.50
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
TTAAAAATATATAAAACAAATATAT
Found at i:20215168 original size:20 final size:20
Alignment explanation
Indices: 20215143--20215187 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20215133 AGGGACTAAA
* *
20215143 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
20215163 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
20215183 ATGAA
1 ATGAA
20215188 TACATATGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:20222310 original size:48 final size:48
Alignment explanation
Indices: 20222198--20222360 Score: 206
Period size: 48 Copynumber: 3.4 Consensus size: 48
20222188 TATGTGTGCT
* * * * * *
20222198 AGTGTAAGACATGTCTGAGACATGCATTAGCCAC-AG-CA-TGAGAGAC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTA-AGCC
*
20222244 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTAAGCC
* *
20222292 AGTGTAAGACATGCCTGGGACATGCATCGGCCTCGAGATATTTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTAAGCC
*
20222340 AATGTAAGACATGTCTGGGAC
1 AGTGTAAGACATGTCTGGGAC
20222361 GTGGATCAAT
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
46 31 0.30
47 2 0.02
48 67 0.66
49 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTAAGCC
Found at i:20222440 original size:48 final size:48
Alignment explanation
Indices: 20222244--20222457 Score: 189
Period size: 48 Copynumber: 4.5 Consensus size: 48
20222234 CATGAGAGAC
* **
20222244 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCT
* ** *
20222292 AGTGTAAGACATGCCTGGGACATGCATCGGCCTCGAGATATTTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCT
* * * **** ** ** *
20222340 AATGTAAGACATGTCTGGGACGTGGATCAATATTAAGA-CGA-GAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCT
* * *
20222386 AGTGTAAGATATGTCTAGGACATGCATCGGCCTCGTGATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCT
* * *
20222434 AGTGTAAGACCTGGCTAGGACATG
1 AGTGTAAGACATGTCTGGGACATG
20222458 GCGTCAGCTT
Statistics
Matches: 128, Mismatches: 36, Indels: 4
0.76 0.21 0.02
Matches are distributed among these distances:
46 29 0.23
47 1 0.01
48 98 0.77
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCT
Found at i:20225767 original size:69 final size:68
Alignment explanation
Indices: 20225609--20225775 Score: 212
Period size: 69 Copynumber: 2.5 Consensus size: 68
20225599 GTTACACAAC
* * *
20225609 CTTTT-TCAGCTTGTCTGACTAGTGTTGGGCAAACAATTTTGGTCAATCTAATTAGCATTGGGCG
1 CTTTTGTCAGCTTGTCTGACTAGTGCTGGGCAAACAATTTAGGTCAATCTAATTAGCACTGGGCG
*
20225673 CAG
66 CAA
* * * * *
20225676 CCTTTGTCAGCTTGTCTGACTAGTGCTGGGCACACAATTGTCAGTTCATTC-GATTAGCACTGGG
1 CTTTTGTCAGCTTGTCTGACTAGTGCTGGGCAAACAATT-T-AGGTCAATCTAATTAGCACTGGG
20225740 CGCAA
64 CGCAA
*
20225745 CTTTTGTCAGCTTGTCTAACTAGTGCTGGGC
1 CTTTTGTCAGCTTGTCTGACTAGTGCTGGGC
20225776 GCAGAATCAT
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
67 4 0.05
68 31 0.36
69 45 0.52
70 6 0.07
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.34
Consensus pattern (68 bp):
CTTTTGTCAGCTTGTCTGACTAGTGCTGGGCAAACAATTTAGGTCAATCTAATTAGCACTGGGCG
CAA
Found at i:20234242 original size:69 final size:69
Alignment explanation
Indices: 20234130--20234291 Score: 243
Period size: 69 Copynumber: 2.3 Consensus size: 69
20234120 ACAACATTCG
* * * * *
20234130 TGTCATATTAAGGCTCGTAGGTGAAAATCCGTAATCTCTAACACTGTTAGTGAGAGCAAAGCTCC
1 TGTCATATTAAGGCTAGTAGGCGAAAATCCATAATCTCCAACACAGTTAGTGAGAGCAAAGCTCC
* *
20234195 TAGT
66 CAGC
* *
20234199 TGTCATATTAAGGCTTGTAGGCGAAAATCTATAATCTCCAACACAGTTAGTGAGAGCAAAGCTCC
1 TGTCATATTAAGGCTAGTAGGCGAAAATCCATAATCTCCAACACAGTTAGTGAGAGCAAAGCTCC
20234264 CAGC
66 CAGC
20234268 TGTCATATTAAGGCTAGTAGGCGA
1 TGTCATATTAAGGCTAGTAGGCGA
20234292 GGAGCCGCAG
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 84 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (69 bp):
TGTCATATTAAGGCTAGTAGGCGAAAATCCATAATCTCCAACACAGTTAGTGAGAGCAAAGCTCC
CAGC
Found at i:20234479 original size:137 final size:136
Alignment explanation
Indices: 20234169--20234515 Score: 322
Period size: 137 Copynumber: 2.5 Consensus size: 136
20234159 CGTAATCTCT
* * * * * * **
20234169 AACACTGTTAGTGAGAGCAAAGCTCCTAGTTGTCATATTAAGGCTTGTAGGCGAAAATCTATAAT
1 AACACAGTTAGCGAGAGCAAAGCTCCTAGCTGTCATATTAAGGCTCGTAGGCGAAAGTC-ACAGC
* * * * * *
20234234 CTCCAACACAGTTAGTGAGAGCAAAGCTCCCAGCTGTCATATTAAGGCTAGTAGGCGAGGAGCCG
65 CTCCAACACAGTTAATGAGAGAAAAGCTCCCAGCTGTCACATTAAGGCTAGCAGACGAAGAGCCG
*
20234299 CAGCCCT
130 CAGCCCC
* * * * *
20234306 AGCATAGTTAGCAAGAGTAAAGCTTCC-AACTGTCATATTAAGGCTCGTAGGCGAAGAGTCACAG
1 AACACAGTTAGCGAGAGCAAAGC-TCCTAGCTGTCATATTAAGGCTCGTAGGCGAA-AGTCACAG
* * * * *
20234370 CCTCAAACACAGTTAATGAGAGAAAAGCTCCTAGTTGTCACATTAAGGTTCA-CA-ATGAAGAGC
64 CCTCCAACACAGTTAATGAGAGAAAAGCTCCCAGCTGTCACATTAAGGCT-AGCAGACGAAGAGC
*
20234433 CGTAGCCTCC
128 CGCAGCC-CC
* * ** * * *
20234443 AACACAGTTAGCGAGAGCAGAGCTCCTAGCTATCATACCAAGGCTCGCAGGCGAAAAGCCACTGC
1 AACACAGTTAGCGAGAGCAAAGCTCCTAGCTGTCATATTAAGGCTCGTAGGCG-AAAGTCACAGC
20234508 CTCCAACA
65 CTCCAACA
20234516 TAGTAGAGCA
Statistics
Matches: 165, Mismatches: 39, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
136 15 0.09
137 141 0.85
138 9 0.05
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.21
Consensus pattern (136 bp):
AACACAGTTAGCGAGAGCAAAGCTCCTAGCTGTCATATTAAGGCTCGTAGGCGAAAGTCACAGCC
TCCAACACAGTTAATGAGAGAAAAGCTCCCAGCTGTCACATTAAGGCTAGCAGACGAAGAGCCGC
AGCCCC
Found at i:20236608 original size:21 final size:21
Alignment explanation
Indices: 20236584--20236651 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
20236574 AACCCAAACC
20236584 CATTGGTGAACCTACATTTCA
1 CATTGGTGAACCTACATTTCA
* * **
20236605 CATTGAT-ATACTTAC-TCAACA
1 CATTGGTGA-ACCTACAT-TTCA
20236626 CATTGGTGAACCTACATTTCA
1 CATTGGTGAACCTACATTTCA
20236647 CATTG
1 CATTG
20236652 ATATACTTAC
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
20 2 0.06
21 31 0.89
22 2 0.06
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (21 bp):
CATTGGTGAACCTACATTTCA
Found at i:20236643 original size:42 final size:42
Alignment explanation
Indices: 20236584--20236663 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
20236574 AACCCAAACC
20236584 CATTGGTGAACCTACATTTCACATTGATATACTTACTCAACA
1 CATTGGTGAACCTACATTTCACATTGATATACTTACTCAACA
20236626 CATTGGTGAACCTACATTTCACATTGATATACTTACTC
1 CATTGGTGAACCTACATTTCACATTGATATACTTACTC
20236664 TAGTTCAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (42 bp):
CATTGGTGAACCTACATTTCACATTGATATACTTACTCAACA
Found at i:20241263 original size:5 final size:5
Alignment explanation
Indices: 20241237--20241294 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
20241227 ATGTGTTAAA
* *
20241237 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
20241286 ATATT ATAT
1 ATATT ATAT
20241295 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:20241273 original size:10 final size:9
Alignment explanation
Indices: 20241238--20241295 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
20241228 TGTGTTAAAA
20241238 TATATATAT
1 TATATATAT
*
20241247 TAAAT-TAT
1 TATATATAT
20241255 TAT-TATAT
1 TATATATAT
20241263 TATAGTATAT
1 TATA-TATAT
20241273 TATAT-TA-
1 TATATATAT
20241280 TATATTATAT
1 TATA-TATAT
20241290 TATATA
1 TATATA
20241296 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:20241285 original size:12 final size:12
Alignment explanation
Indices: 20241240--20241295 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
20241230 TGTTAAAATA
*
20241240 TATATATTAAAT
1 TATATATTATAT
20241252 TAT-TATTATATT
1 TATATATTATA-T
20241264 ATAGTATATTATAT
1 -TA-TATATTATAT
20241278 TATATATTATAT
1 TATATATTATAT
20241290 TATATA
1 TATATA
20241296 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:20242583 original size:15 final size:15
Alignment explanation
Indices: 20242563--20242619 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
20242553 CGATGAATTT
20242563 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
20242578 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
20242593 ATTGAATTTATATTG
1 ATTGAATTTATATTG
20242608 ATTGAA-TTATAT
1 ATTGAATTTATAT
20242620 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:20243021 original size:23 final size:23
Alignment explanation
Indices: 20242991--20243077 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
20242981 GCTTTATCGA
* *
20242991 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
20243014 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
20243035 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
20243057 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
20243078 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:20244493 original size:166 final size:166
Alignment explanation
Indices: 20244219--20244550 Score: 664
Period size: 166 Copynumber: 2.0 Consensus size: 166
20244209 AGTATAATTG
20244219 AAACACATGTTAAAGTAAACCAGAAGTTTACTGATACAAATACATTTACTACTTAGTGTGACCAG
1 AAACACATGTTAAAGTAAACCAGAAGTTTACTGATACAAATACATTTACTACTTAGTGTGACCAG
20244284 TTAGACCATCTTGGATCATATATGATGCGAAAATTAATTAAGAATTCATATGGACATTCATTAAA
66 TTAGACCATCTTGGATCATATATGATGCGAAAATTAATTAAGAATTCATATGGACATTCATTAAA
20244349 GAACCAGAAGATTCTTTAATTTAAATGAATTCTCAT
131 GAACCAGAAGATTCTTTAATTTAAATGAATTCTCAT
20244385 AAACACATGTTAAAGTAAACCAGAAGTTTACTGATACAAATACATTTACTACTTAGTGTGACCAG
1 AAACACATGTTAAAGTAAACCAGAAGTTTACTGATACAAATACATTTACTACTTAGTGTGACCAG
20244450 TTAGACCATCTTGGATCATATATGATGCGAAAATTAATTAAGAATTCATATGGACATTCATTAAA
66 TTAGACCATCTTGGATCATATATGATGCGAAAATTAATTAAGAATTCATATGGACATTCATTAAA
20244515 GAACCAGAAGATTCTTTAATTTAAATGAATTCTCAT
131 GAACCAGAAGATTCTTTAATTTAAATGAATTCTCAT
20244551 TGTTGCTTGT
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 166 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Consensus pattern (166 bp):
AAACACATGTTAAAGTAAACCAGAAGTTTACTGATACAAATACATTTACTACTTAGTGTGACCAG
TTAGACCATCTTGGATCATATATGATGCGAAAATTAATTAAGAATTCATATGGACATTCATTAAA
GAACCAGAAGATTCTTTAATTTAAATGAATTCTCAT
Found at i:20245442 original size:18 final size:18
Alignment explanation
Indices: 20245419--20245454 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20245409 ATCTAATGTT
20245419 TTAATTTGAATCAAAGTC
1 TTAATTTGAATCAAAGTC
20245437 TTAATTTGAATCAAAGTC
1 TTAATTTGAATCAAAGTC
20245455 CCAGTAGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (18 bp):
TTAATTTGAATCAAAGTC
Found at i:20250693 original size:19 final size:20
Alignment explanation
Indices: 20250644--20250695 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
20250634 TTATAAAAAA
*
20250644 ATTTATATTAAA-ATATTTT
1 ATTTATATTAAATATATATT
*
20250663 ATATTAGA-TAAATATA-ATT
1 AT-TTATATTAAATATATATT
20250682 ATTTATATTAAATA
1 ATTTATATTAAATA
20250696 AATGCAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 4 0.15
19 16 0.59
20 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTTATATTAAATATATATT
Found at i:20255496 original size:26 final size:26
Alignment explanation
Indices: 20255467--20255519 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
20255457 CATTGCAGCA
20255467 ACTTGCTATGAAATTCTTAGAACGTG
1 ACTTGCTATGAAATTCTTAGAACGTG
*
20255493 ACTTGGTATGAAATTCTTAGAACGTG
1 ACTTGCTATGAAATTCTTAGAACGTG
20255519 A
1 A
20255520 GGAGATCGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (26 bp):
ACTTGCTATGAAATTCTTAGAACGTG
Found at i:20256447 original size:21 final size:21
Alignment explanation
Indices: 20256421--20256469 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
20256411 AGATTATGGC
20256421 TATATATTATT-TT-TCTAATAT
1 TATATATTATTATTGT-TAA-AT
20256442 TATATATTATTATTGTTAAAT
1 TATATATTATTATTGTTAAAT
20256463 TATATAT
1 TATATAT
20256470 AATAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 20 0.77
22 5 0.19
23 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TATATATTATTATTGTTAAAT
Found at i:20256521 original size:59 final size:58
Alignment explanation
Indices: 20256438--20256548 Score: 159
Period size: 59 Copynumber: 1.9 Consensus size: 58
20256428 TATTTTTCTA
* *
20256438 ATATTATATATTATTATTGTTAAATTATATATAATAATAATTTTATAAAAATATGATT
1 ATATTATATATTATTATTATTAAATTATATATAATAATAATGTTATAAAAATATGATT
* * * *
20256496 ATATTATTTATTATATTTTATTAAATTATATTTAATAATAATGTTATTAAAAT
1 ATATTATATATTAT-TATTATTAAATTATATATAATAATAATGTTATAAAAAT
20256549 TTAATAACAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 13 0.28
59 33 0.72
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (58 bp):
ATATTATATATTATTATTATTAAATTATATATAATAATAATGTTATAAAAATATGATT
Found at i:20262686 original size:21 final size:19
Alignment explanation
Indices: 20262660--20262732 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 19
20262650 ATCTAATTAC
20262660 AAATATTTAATTATTATATTT
1 AAATATTTAATTA-TAT-TTT
*
20262681 AAATATTTAAATATATTTT
1 AAATATTTAATTATATTTT
* *
20262700 ATATATTCTAATTAAATTTAAT
1 AAATATT-TAATTATATTT--T
*
20262722 AAATAATTAAT
1 AAATATTTAAT
20262733 ATTAATTACT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 9 0.21
20 12 0.28
21 16 0.37
22 6 0.14
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTTAATTATATTTT
Found at i:20262975 original size:13 final size:13
Alignment explanation
Indices: 20262954--20263024 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
20262944 AAATTTTTCT
20262954 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
20262967 AAAGTACTTCTCA
1 AAAGCACTTCTCA
20262980 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
20262993 AAAGTACTTCTCA
1 AAAGCACTTCTCA
* *
20263006 AAAACACTTTTCA
1 AAAGCACTTCTCA
20263019 AAAGCA
1 AAAGCA
20263025 TTGCCAAACT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.25
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:20262984 original size:26 final size:26
Alignment explanation
Indices: 20262954--20263022 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
20262944 AAATTTTTCT
20262954 AAAGCACTTCTCAAAAGTACTTCTCA
1 AAAGCACTTCTCAAAAGTACTTCTCA
20262980 AAAGCACTTCTCAAAAGTACTTCTCA
1 AAAGCACTTCTCAAAAGTACTTCTCA
* *
20263006 AAAACACTTTTCAAAAG
1 AAAGCACTTCTCAAAAG
20263023 CATTGCCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (26 bp):
AAAGCACTTCTCAAAAGTACTTCTCA
Found at i:20263366 original size:51 final size:51
Alignment explanation
Indices: 20263288--20263386 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
20263278 TTTGAATGCA
* * *
20263288 CACTCATTTTCTTAGGAGACTAGATAAATTAAAGTTTTAAGTGGACTTGCC
1 CACTCACTTTCTTAGGAGACTAGATAAAATAAAGTTTCAAGTGGACTTGCC
* *
20263339 CACTCACTTTCTTTGGAGACTATATAAAATAAAGTTTCAAGTGGACTT
1 CACTCACTTTCTTAGGAGACTAGATAAAATAAAGTTTCAAGTGGACTT
20263387 AGACATGCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (51 bp):
CACTCACTTTCTTAGGAGACTAGATAAAATAAAGTTTCAAGTGGACTTGCC
Found at i:20275725 original size:30 final size:30
Alignment explanation
Indices: 20275691--20275750 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
20275681 ACTTAACAAG
20275691 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAATAAAATTAA
* *
20275721 CAAATTCCTTTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAATAAAATTAA
20275751 TAATAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAATAAAATTAA
Found at i:20279046 original size:127 final size:126
Alignment explanation
Indices: 20278779--20279220 Score: 607
Period size: 127 Copynumber: 3.5 Consensus size: 126
20278769 AACATAAGGA
** * * *
20278779 AATATTTCGTGTTTGGGAGTTTGAGAGATCGTGCCCAATTGTGCTGGGTTTCGATTTTTCATTTG
1 AATATTTCGAATTTGGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTCG
* * * * *
20278844 ACTAAAATACAAAATA-TCCTTTTGGAATTTTGTCTATGTTTTCTTAAATTAAAACGAGGC
66 ACTAAAGTGCAGAATATTCCTTTTGAAATTTTGTCCATGTTTTCTTAAATTAAAACGAGGC
*
20278904 AATATTTCGAATTTGGGGAGCTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTC
1 AATATTTCGAATTT-GGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTC
* **
20278969 GACTAAAGTGCGGAATATTCCTTTTGAAATTTCATCCATGTTTTCTTAAATTAAAACGAGGC
65 GACTAAAGTGCAGAATATTCCTTTTGAAATTTTGTCCATGTTTTCTTAAATTAAAACGAGGC
* * *
20279031 AATATTTCGAATTTGGGGAGTTTGAGAGATCATGCCCAATCGTGCTGGGTTTCAATTTTTCATTC
1 AATATTTCGAATTT-GGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTC
* **
20279096 GACTAAAGTGCAGAATATTCCTTTTGAAATTTTGTCCATGTTTTCTTAAATTAACATAAGGC
65 GACTAAAGTGCAGAATATTCCTTTTGAAATTTTGTCCATGTTTTCTTAAATTAAAACGAGGC
* * * * * * * *
20279158 AATATTTCGTATTTGGAAATTTGATAAATCGTGTCCAATCGTGCTAGGTTTCGATTTACCATT
1 AATATTTCGAATTTGGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATT
20279221 TGGCAAAATA
Statistics
Matches: 280, Mismatches: 35, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
125 12 0.04
126 98 0.35
127 170 0.61
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (126 bp):
AATATTTCGAATTTGGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTCG
ACTAAAGTGCAGAATATTCCTTTTGAAATTTTGTCCATGTTTTCTTAAATTAAAACGAGGC
Found at i:20279765 original size:40 final size:40
Alignment explanation
Indices: 20279710--20279789 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
20279700 TCCGCTGGGG
20279710 ACAATAAGAGAGTCAAGCCGTAAAATTGATTATTTTCTAT
1 ACAATAAGAGAGTCAAGCCGTAAAATTGATTATTTTCTAT
20279750 ACAATAAGAGAGTCAAGCCGTAAAATTGATTATTTTCTAT
1 ACAATAAGAGAGTCAAGCCGTAAAATTGATTATTTTCTAT
20279790 CCTTTTTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (40 bp):
ACAATAAGAGAGTCAAGCCGTAAAATTGATTATTTTCTAT
Found at i:20290500 original size:64 final size:64
Alignment explanation
Indices: 20290431--20290552 Score: 208
Period size: 64 Copynumber: 1.9 Consensus size: 64
20290421 AATTCATAGT
* * *
20290431 ACATCTAGTTAGGAGCATTTGATTCATTTTGATTATAGCATCCTAATTATTTGACATATATATC
1 ACATCTAGCTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATATATATC
*
20290495 ACATCTAGCTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGGCATA
1 ACATCTAGCTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATA
20290553 AGCATAGATA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (64 bp):
ACATCTAGCTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATATATATC
Found at i:20290924 original size:177 final size:177
Alignment explanation
Indices: 20290628--20291382 Score: 1151
Period size: 177 Copynumber: 4.3 Consensus size: 177
20290618 GAAGTCACGT
* * * *
20290628 GCCTTAACCCCTTAAACAGTAGGGTAACAGACTAAAAATTACAGATCTTATCTCCATGTATCGAC
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCGAC
* * *
20290693 TATAGAGTAGATAAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGTAGATTTTAGCCA
66 TATGGAGTAGATCAAAGATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGTAGATTTTAGCCA
* *
20290758 CC-AGCCTTATCTCTCTGAGGTAGTAAGAGAGCAGGTTAAAGATACGA
131 CCGA-CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
* *
20290805 GCCTTAACCCCCTAAGCAGTATGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGC
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCGAC
*
20290870 TATGGAGTAGATCGAAA-ATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGTAGATTTAAGCC
66 TATGGAGTAGATC-AAAGATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGTAGATTTTAGCC
* * * *
20290934 ACCGGCCTTATCTCTCTGAGATAACAAGAGAGCAGATTGAAGATACGA
130 ACCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
* * *
20290982 GCCTTAACCCCCTAAGCAGTAGGGTAACAAGCTAAAAATTACAGATCTTATCTCCATGTATCGGC
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCGAC
* * *
20291047 TATGGA-TCAGATCAAAGATGGCGAGTCTTATCCCCATGTATCGACTATGGAGCAGATTTTAGCC
66 TATGGAGT-AGATCAAAGATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGTAGATTTTAGCC
*
20291111 ACCGACCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATACGA
130 ACCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
* * * *
20291159 GTCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAAATCTTATCTTCATGTATCGAT
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCGAC
* *
20291224 TATGGAGCAGATCAAAGATGGCGAG-CTTATCTCCATGTATCGGCTATGGAGAAGATTTTAGCCA
66 TATGGAGTAGATCAAAGATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGTAGATTTTAGCCA
* *
20291288 CTGACCTTATCTCTCTGAGGTAGTAAGAGAGCAGGTTGAAGATACGA
131 CCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
*
20291335 GCCTTAACTCCCTAAGCAGTAGGGTAACAGGCTAGAAAA-TACAGATCT
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCT-GAAAATTACAGATCT
20291383 CCTCTAAACA
Statistics
Matches: 528, Mismatches: 44, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
176 123 0.23
177 402 0.76
178 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (177 bp):
GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCGAC
TATGGAGTAGATCAAAGATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGTAGATTTTAGCCA
CCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
Found at i:20291605 original size:84 final size:84
Alignment explanation
Indices: 20291334--20291612 Score: 387
Period size: 84 Copynumber: 3.3 Consensus size: 84
20291324 TGAAGATACG
* * *
20291334 AGCCTTAACTCCCTAAGCAGTAGGGTAACAGGCTAGAAAATACAGATCTCCTCTAAACAGTAGTG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAAATACAGATCTCCCCTAAACAGTAGTG
* *
20291399 GAGCAGAACAAAGACAGTA
66 GAGCAGATCGAAGACAGTA
* * * * * * * *
20291418 AGCCTTAACCTCTTAAGTAATAGGGTAATAGGTTGGAAAATACAGATCTCTCCTAAATAGTAGTG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAAATACAGATCTCCCCTAAACAGTAGTG
20291483 GAGCAGATCGAAGACAGTA
66 GAGCAGATCGAAGACAGTA
* * *
20291502 AGCCTTAACCCCTTAAGCAGTAGGGTAACATGCTGGAAAATACAAATCTCCCCTAAACAGTAGTG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAAATACAGATCTCCCCTAAACAGTAGTG
* *
20291567 GAACAGATCGAAGACAGCA
66 GAGCAGATCGAAGACAGTA
*
20291586 AGCCTTAACCCCCTAAGCAGCAGGGTA
1 AGCCTTAACCCCCTAAGCAGTAGGGTA
20291613 TTAGGCTTCT
Statistics
Matches: 169, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 169 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (84 bp):
AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAAATACAGATCTCCCCTAAACAGTAGTG
GAGCAGATCGAAGACAGTA
Found at i:20294101 original size:127 final size:127
Alignment explanation
Indices: 20293842--20294277 Score: 599
Period size: 127 Copynumber: 3.5 Consensus size: 127
20293832 AACATAAGGA
** * * * *
20293842 AATATTTCGTGTTTGGG-AGTTTGAGAGATCATGCTCAATCGTGCTGGGTTTTGATTTTTCATTT
1 AATATTTCGAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTC
* * ** * * *
20293906 GACTAAAATACAAAATA-TCCTTTTGGAATTTCGTCTATGTTTCCTTAAATTAAAATGAGGC
66 GACTAAAGTGCGGAATATTCCTTTTGAAATTTCGTCTATGTTTTCTTAAATTAAAACGAGGC
* *
20293967 AATATTTCGAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTTGATTTTCCATTC
1 AATATTTCGAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTC
*
20294032 GACTAAAGTGCGGAATATTCCTTTTGAAATTTCGTCCATGTTTTCTTAAATTAAAACGAGGC
66 GACTAAAGTGCGGAATATTCCTTTTGAAATTTCGTCTATGTTTTCTTAAATTAAAACGAGGC
* * *
20294094 AATATTTCAAATTTGGGGAGTTTGAGAGATCGTGCCTAATCGTGCTGGGTTTCGATTTTTCATTC
1 AATATTTCGAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTC
* *
20294159 GACTAAAGTGCGGAATATTCCTTTTGAAATTTCGTCTATGTTTTCTTAAATTAACAGGAGGC
66 GACTAAAGTGCGGAATATTCCTTTTGAAATTTCGTCTATGTTTTCTTAAATTAAAACGAGGC
* * * * * * *
20294221 AATATTTCGTATTT-GGAAATTCGATAAATTGTGCCCAATCGTGCTAGGTTTCGATTT
1 AATATTTCGAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTT
20294278 ACCGTTTGGC
Statistics
Matches: 277, Mismatches: 32, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
125 15 0.05
126 91 0.33
127 171 0.62
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (127 bp):
AATATTTCGAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTC
GACTAAAGTGCGGAATATTCCTTTTGAAATTTCGTCTATGTTTTCTTAAATTAAAACGAGGC
Found at i:20295816 original size:46 final size:46
Alignment explanation
Indices: 20295749--20295872 Score: 221
Period size: 46 Copynumber: 2.7 Consensus size: 46
20295739 CAATGCCACG
20295749 TTTCGCATTAGCCATTCGGCTTTACCTCATATCCATCTCATACACA
1 TTTCGCATTAGCCATTCGGCTTTACCTCATATCCATCTCATACACA
*
20295795 TTTCGCATTAGCCATTCGGCTTTACCTCATATCCATCTCATACATA
1 TTTCGCATTAGCCATTCGGCTTTACCTCATATCCATCTCATACACA
* *
20295841 TTTCGCATTAGCCATTCGACTTTACCACATAT
1 TTTCGCATTAGCCATTCGGCTTTACCTCATAT
20295873 ATACTCTTCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 75 1.00
ACGTcount: A:0.24, C:0.31, G:0.09, T:0.36
Consensus pattern (46 bp):
TTTCGCATTAGCCATTCGGCTTTACCTCATATCCATCTCATACACA
Found at i:20299502 original size:15 final size:15
Alignment explanation
Indices: 20299484--20299524 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
20299474 TCTATTTGAT
20299484 TTTATTCTATATGTG
1 TTTATTCTATATGTG
*
20299499 TTTATGCTATATGTG
1 TTTATTCTATATGTG
20299514 TTTATT-TATAT
1 TTTATTCTATAT
20299525 TTAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.22, C:0.05, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTATTCTATATGTG
Found at i:20300008 original size:89 final size:88
Alignment explanation
Indices: 20299815--20300073 Score: 308
Period size: 88 Copynumber: 3.0 Consensus size: 88
20299805 TTTTGTTTCC
* * * **
20299815 AAATTAAAAGTAAATAAAATATGTTTCAAGATCTATTCCCGCTGTTCAATGGATTTTATTCCATT
1 AAATTAAAAGTAAATAAAATCTGTTTCGAGATTTATTCCCGCCATTCAA-GGATTTTATTCCATT
*
20299880 ATTTTTA-TTTATTTCCAAACGAG
65 ATTTTGATTTTATTTCCAAACGAG
* ** * *
20299903 AAATTAAAAGTAAATAAGATCCATTTCGAGATTTATTCCCGCCCTACAACGGATTTTATTCCATT
1 AAATTAAAAGTAAATAAAATCTGTTTCGAGATTTATTCCCGCCATTCAA-GGATTTTATTCCATT
* *
20299968 ATTTTGATTTTATTTCCAAATGGG
65 ATTTTGATTTTATTTCCAAACGAG
* * * * * *
20299992 AAATTAAAGGTAAATAAAATCTGTTTCGAGATTGATTCCCGTCATTCAATGAATTTATTCCA-AA
1 AAATTAAAAGTAAATAAAATCTGTTTCGAGATTTATTCCCGCCATTCAAGGATTTTATTCCATTA
20300056 TTTTG-TTTTATTTCCAAA
66 TTTTGATTTTATTTCCAAA
20300074 AACGAGTAAA
Statistics
Matches: 146, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
86 13 0.09
87 6 0.04
88 72 0.49
89 55 0.38
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (88 bp):
AAATTAAAAGTAAATAAAATCTGTTTCGAGATTTATTCCCGCCATTCAAGGATTTTATTCCATTA
TTTTGATTTTATTTCCAAACGAG
Found at i:20300098 original size:79 final size:79
Alignment explanation
Indices: 20300003--20300239 Score: 305
Period size: 79 Copynumber: 3.0 Consensus size: 79
20299993 AATTAAAGGT
** * *
20300003 AAATAAAATCTGTTTCGAGATTGATTCCCGTCATTCAATGAATTTATTCCAAATTTTGTTTTATT
1 AAATAAAATCCATTTCGGGATTGATTCCCGTCATTCAATGATTTTATTCCAAATTTTGTTTTATT
20300068 TCCAAAAACGAGTA
66 TCCAAAAACGAGTA
* * * *
20300082 AAATAAAATTCATTTCGGGATTGATTCCCTTCGTTCAACGATTTTATTCCAAATTTTGTTTTATT
1 AAATAAAATCCATTTCGGGATTGATTCCCGTCATTCAATGATTTTATTCCAAATTTTGTTTTATT
*
20300147 TCCAAAAACAAGTA
66 TCCAAAAACGAGTA
* * * * * *
20300161 AAATAAAATCCATTTCGGGATTGATACTCGCCATTCAATGATTTTATTTC-AGTTTCGATTTTAT
1 AAATAAAATCCATTTCGGGATTGATTCCCGTCATTCAATGATTTTATTCCAAATTTTG-TTTTAT
* *
20300225 TTTCAAAACCGAGTA
65 TTCCAAAAACGAGTA
20300240 TTAAAGCTAA
Statistics
Matches: 135, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
78 5 0.04
79 130 0.96
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (79 bp):
AAATAAAATCCATTTCGGGATTGATTCCCGTCATTCAATGATTTTATTCCAAATTTTGTTTTATT
TCCAAAAACGAGTA
Found at i:20303041 original size:23 final size:23
Alignment explanation
Indices: 20303015--20303061 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
20303005 AATTCATAGC
20303015 CATTTCTCAGAGTTGTTCATAAA
1 CATTTCTCAGAGTTGTTCATAAA
20303038 CATTTCTCAGAGTTGTTCATAAA
1 CATTTCTCAGAGTTGTTCATAAA
20303061 C
1 C
20303062 TTAACCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (23 bp):
CATTTCTCAGAGTTGTTCATAAA
Found at i:20314597 original size:180 final size:179
Alignment explanation
Indices: 20314327--20314679 Score: 562
Period size: 180 Copynumber: 2.0 Consensus size: 179
20314317 GAGCTACGGA
** *
20314327 ACTCCAAATTAAGATCGTTAATTTTCCCAGAAACTAGACTCATATATATTCTTACCATAAAATTT
1 ACTCCAAATTAAGATCACTAATTTTCCCAGAAACTAGACTAATATATATTCTTACCATAAAATTT
* *
20314392 TTAGAATTTTTGGTTTAGCCAATTAGTACAGTTTATTCATTAAAGTTACCCCTATTTCACTGTCC
66 TTAGAATTTTTGATTTAGCCAATTAGTACAGTTTATTCATTAAAGATACCCCTATTTCACTGTCC
20314457 AATAATTCCGACCTCTCTTCACTAAAAATTAGTTATCTCATGGAAAGCG
131 AATAATTCCGACCTCTCTTCACTAAAAATTAGTTATCTCATGGAAAGCG
* *
20314506 ACTCCAAATTAAGAATCACTAATTTTCTCAGAAACTAGACTAATATATTTTCTTACCATAAAATT
1 ACTCCAAATTAAG-ATCACTAATTTTCCCAGAAACTAGACTAATATATATTCTTACCATAAAATT
* *
20314571 TTTAGAATTTTTGATTTAGCCAATTAGTACAGTTTATTCATTAAAGATACTCCTGTTTCACTGTC
65 TTTAGAATTTTTGATTTAGCCAATTAGTACAGTTTATTCATTAAAGATACCCCTATTTCACTGTC
* * * * * *
20314636 CGATAGTTCTGATCTTTCTTCACTAAAAATTATTTATCTCATGG
130 CAATAATTCCGACCTCTCTTCACTAAAAATTAGTTATCTCATGG
20314680 TATAGATCTC
Statistics
Matches: 158, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
179 13 0.08
180 145 0.92
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.39
Consensus pattern (179 bp):
ACTCCAAATTAAGATCACTAATTTTCCCAGAAACTAGACTAATATATATTCTTACCATAAAATTT
TTAGAATTTTTGATTTAGCCAATTAGTACAGTTTATTCATTAAAGATACCCCTATTTCACTGTCC
AATAATTCCGACCTCTCTTCACTAAAAATTAGTTATCTCATGGAAAGCG
Found at i:20315029 original size:16 final size:16
Alignment explanation
Indices: 20315010--20315041 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20315000 AACTGTTTTA
20315010 TTACAAAATTTCATTT
1 TTACAAAATTTCATTT
*
20315026 TTACATAATTTCATTT
1 TTACAAAATTTCATTT
20315042 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (16 bp):
TTACAAAATTTCATTT
Found at i:20315306 original size:50 final size:50
Alignment explanation
Indices: 20315252--20315534 Score: 329
Period size: 50 Copynumber: 5.6 Consensus size: 50
20315242 CTAGTACGCA
* *
20315252 TAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGATACACG
* * * * * * * *
20315302 TAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAA-CGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAA--CAATCTGATACACG
*
20315353 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATTTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGATACACG
* *
20315403 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATCCACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGATACACG
* * * *
20315453 TAGTAGCCTGCACTTAGTACTACATACGTGACCTAA-AA-CTGTCTTAAACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTG--ATACACG
*
20315503 CATAGTAGCCTGCACATAGTACTACACATGTG
1 --TAGTAGCCTGCACTTAGTACTACACATGTG
20315535 TTCTCACAAT
Statistics
Matches: 197, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
48 3 0.02
49 4 0.02
50 121 0.61
51 40 0.20
52 29 0.15
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGATACACG
Found at i:20315363 original size:101 final size:101
Alignment explanation
Indices: 20315245--20315428 Score: 341
Period size: 101 Copynumber: 1.8 Consensus size: 101
20315235 AAGCTCTCTA
* *
20315245 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCC
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCC
20315310 TGCACTTAGTACTACACACGTGATCAAAGTTAACGG
66 TGCACTTAGTACTACACACGTGATCAAAGTTAACGG
*
20315346 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATTTGATACACGTAGTAGCC
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCC
20315411 TGCACTTAGTACTACACA
66 TGCACTTAGTACTACACA
20315429 TGCGACCTAA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 80 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (101 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGATACACGTAGTAGCC
TGCACTTAGTACTACACACGTGATCAAAGTTAACGG
Found at i:20315482 original size:151 final size:152
Alignment explanation
Indices: 20315252--20315534 Score: 424
Period size: 151 Copynumber: 1.9 Consensus size: 152
20315242 CTAGTACGCA
* * *
20315252 TAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATACACGTAGTAGCCTGCACTT
* ** ** *
20315317 AGTACTACACACGTGATC-AAAGTTAACGGGTACGCATAGTAGCCTGCACTTAGTACTACACATG
66 AGTACTACACACGTGACCTAAAACTAACGGAAACGCATAGTAGCCTGCACATAGTACTACACATG
20315381 TGACCTAACAATTTGATACACG
131 TGACCTAACAATTTGATACACG
*
20315403 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATCCACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATACACGTAGTAGCCTGCACTT
* ** **
20315468 AGTACTACATACGTGACCTAAAACTGTCTTAAACGCATAGTAGCCTGCACATAGTACTACACATG
66 AGTACTACACACGTGACCTAAAACTAACGGAAACGCATAGTAGCCTGCACATAGTACTACACATG
20315533 TG
131 TG
20315535 TTCTCACAAT
Statistics
Matches: 116, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
151 77 0.66
152 39 0.34
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (152 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATACACGTAGTAGCCTGCACTT
AGTACTACACACGTGACCTAAAACTAACGGAAACGCATAGTAGCCTGCACATAGTACTACACATG
TGACCTAACAATTTGATACACG
Found at i:20319925 original size:48 final size:47
Alignment explanation
Indices: 20319859--20320073 Score: 165
Period size: 46 Copynumber: 4.6 Consensus size: 47
20319849 AAGCTGACGC
*
20319859 CATGTCCCAGACAGGTCTTACACTAGCTT-GTTCATCACGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTAG-TCATCA-GAGGCTGATG
* * * *
20319907 CATGTCCCAGTCATGTCTTACACTAGCTCTCGTC-TCA-ACGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCT-TAGTCATCAGAGGCTGATG
* * *
20319953 CATGTCCCAAACATGTCTTACACTGGCTTAAAT-ATCAAGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTT-AGTCATC-AGAGGCTGATG
* * * * * * * *
20320001 CATGTTCCTGACATGTCTTGCACTGGC-T-CTCATAATGTGG-TCGGTG
1 CATGTCCCAGACATGTCTTACACTAGCTTAGTCATCA-GAGGCT-GATG
*
20320047 CATGTCCCAGACATGTTTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
20320074 ACACATACCA
Statistics
Matches: 134, Mismatches: 24, Indels: 20
0.75 0.13 0.11
Matches are distributed among these distances:
45 4 0.03
46 65 0.49
47 2 0.01
48 59 0.44
49 3 0.02
50 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTTAGTCATCAGAGGCTGATG
Found at i:20319960 original size:94 final size:94
Alignment explanation
Indices: 20319859--20320031 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 94
20319849 AAGCTGACGC
* ** * *
20319859 CATGTCCCAGACAGGTCTTACACTAGCTT-GTTCATCACGAGGCTGATGCATGTCCCAGTCATGT
1 CATGTCCCAAACAGGTCTTACACTAGCTTAAAT-ATCAAGAGGCTGATGCATGTCCCAGACATGT
20319923 CTTACACTAGCTCTCGTCTCAACGCCGATG
65 CTTACACTAGCTCTCGTCTCAACGCCGATG
* * * *
20319953 CATGTCCCAAACATGTCTTACACTGGCTTAAATATCAAGAGGCTGATGCATGTTCCTGACATGTC
1 CATGTCCCAAACAGGTCTTACACTAGCTTAAATATCAAGAGGCTGATGCATGTCCCAGACATGTC
* *
20320018 TTGCACTGGCTCTC
66 TTACACTAGCTCTC
20320032 ATAATGTGGT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
94 66 0.99
95 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (94 bp):
CATGTCCCAAACAGGTCTTACACTAGCTTAAATATCAAGAGGCTGATGCATGTCCCAGACATGTC
TTACACTAGCTCTCGTCTCAACGCCGATG
Found at i:20324792 original size:93 final size:93
Alignment explanation
Indices: 20324665--20324837 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 93
20324655 CGCCCATAAG
* *
20324665 CGAACTCGGACTCAACTCAAAGAGCTTGAGCGTTCGCATCCATAAATGAACTCTGACTCAACTCA
1 CGAACTCGGACTCAACTCAAAGAGCTTGAACGTTCGCATCCATAAATGAACTCGGACTCAACTCA
*
20324730 ACGAGCTCGGATGCCTAGTTATATCTCA
66 ACGAGCTCAGATGCCTAGTTATATCTCA
* *
20324758 CGAACTCGGACTCAACTCAACGAG-TTCGAACGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAAAGAGCTT-GAACGTTCGCATCCATAAATGAACTCGGACTCAACTC
*
20324822 AACGAGTTCAGATGCC
65 AACGAGCTCAGATGCC
20324838 CAAATATCCG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAAAGAGCTTGAACGTTCGCATCCATAAATGAACTCGGACTCAACTCA
ACGAGCTCAGATGCCTAGTTATATCTCA
Found at i:20324820 original size:46 final size:46
Alignment explanation
Indices: 20324658--20324830 Score: 163
Period size: 46 Copynumber: 3.7 Consensus size: 46
20324648 TGTAACCCGC
* *
20324658 CCATAAGCGAACTCGGACTCAACTCAAAGAGCTT-GAGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAG-TTCGAACGTTCGCAT
** * * * * * * *
20324704 CCATAAATGAACTCTGACTCAACTCAACGAGCTCGGATGCCTAGTTAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGAACG-TTCG-CAT
* *
20324752 ATC-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACGTTCGCAT
1 -CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGAACGTTCGCAT
*
20324797 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC
20324831 AGATGCCCAA
Statistics
Matches: 97, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
44 1 0.01
45 5 0.05
46 57 0.59
47 29 0.30
48 4 0.04
49 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGAACGTTCGCAT
Found at i:20338079 original size:30 final size:30
Alignment explanation
Indices: 20338043--20338102 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
20338033 TTCCCGAGCC
*
20338043 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
20338073 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
20338103 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:20340796 original size:5 final size:5
Alignment explanation
Indices: 20340786--20340817 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
20340776 CTATCTGTAA
20340786 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
20340818 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:20340811 original size:9 final size:9
Alignment explanation
Indices: 20340787--20340817 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
20340777 TATCTGTAAA
20340787 AAATAAAAT
1 AAATAAAAT
20340796 AAAATAAAAT
1 -AAATAAAAT
20340806 AAATAAAAT
1 AAATAAAAT
20340815 AAA
1 AAA
20340818 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:20350631 original size:26 final size:25
Alignment explanation
Indices: 20350589--20350659 Score: 106
Period size: 26 Copynumber: 2.8 Consensus size: 25
20350579 CTCTTTTAAT
*
20350589 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
20350614 AACTGGGGAAAAAGCCCTTTTCGGTA
1 AACTGGGG-CAAAGCCCTTTTCGATA
20350640 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
20350660 GCACTTCCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 19 0.46
26 22 0.54
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:20350818 original size:25 final size:25
Alignment explanation
Indices: 20350790--20350837 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
20350780 ATAATTAAAC
* *
20350790 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
20350815 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
20350838 CACATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:20357988 original size:31 final size:31
Alignment explanation
Indices: 20357945--20358030 Score: 156
Period size: 31 Copynumber: 2.8 Consensus size: 31
20357935 TCAAGTTCAG
20357945 CATAT-ACTGGGCCGAAGCCTTTACATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
*
20357975 CATATCACTGGGCCGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
20358006 CATATCACTGGGCCGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
20358031 TGTAACAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
30 5 0.09
31 48 0.91
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:20358293 original size:26 final size:25
Alignment explanation
Indices: 20358248--20358318 Score: 106
Period size: 26 Copynumber: 2.8 Consensus size: 25
20358238 CTCTTTTAAT
*
20358248 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
20358273 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGC-AAAGCCCTTTTCGATA
*
20358299 AACTGGAGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
20358319 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
25 20 0.48
26 22 0.52
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:20358390 original size:20 final size:21
Alignment explanation
Indices: 20358365--20358412 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
20358355 AAATGAATAC
*
20358365 ATCATGTGCATATCATA-CAT
1 ATCATGTGCATATCATATCAA
*
20358385 ATCATGTGCATATCGTATCAA
1 ATCATGTGCATATCATATCAA
20358406 ATCATGT
1 ATCATGT
20358413 ATATCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (21 bp):
ATCATGTGCATATCATATCAA
Found at i:20358477 original size:25 final size:25
Alignment explanation
Indices: 20358449--20358496 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
20358439 ATAATTAAAC
* *
20358449 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
20358474 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
20358497 CACATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:20359626 original size:13 final size:13
Alignment explanation
Indices: 20359608--20359632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20359598 GTTCAGCTAG
20359608 AGAAGAAGAAAAA
1 AGAAGAAGAAAAA
20359621 AGAAGAAGAAAA
1 AGAAGAAGAAAA
20359633 GAATAAAACT
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGAAGAAGAAAAA
Found at i:20360896 original size:46 final size:44
Alignment explanation
Indices: 20360752--20360972 Score: 162
Period size: 46 Copynumber: 4.8 Consensus size: 44
20360742 GGATAGGATG
* *
20360752 CCGATGCCATGTCCCGGACATGGTCTTACACTAGCT-TAAC-TCGTA-G
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT--CGTC-TATA
* * * * *
20360798 CAGATGCATGTCCCAGACATGTTTTACACTGGCT-TACATCTAGA
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CGTCTATA
* *
20360842 GGCTGATGCATGTCCCAGACATGTTTTACACTAGCTCTCGTCTCACTA
1 --CCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCT-A-TA
* * * * *
20360890 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCGTAATGTGG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGT-CTAT-A
20360938 CCGATGCATGTCCCAGACATGTCTTACACTAGCTC
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCTC
20360973 ACAATAGTCC
Statistics
Matches: 146, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
43 4 0.03
44 15 0.10
45 13 0.09
46 60 0.41
47 29 0.20
48 24 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (44 bp):
CCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTATA
Found at i:20373254 original size:6 final size:6
Alignment explanation
Indices: 20373238--20373336 Score: 85
Period size: 6 Copynumber: 16.3 Consensus size: 6
20373228 CTTTTTTTTA
* * *
20373238 TTTATT CTTATT TTTA-T TTTATT TTTATT TTTATT TTTCTT TTGATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* ** * *
20373285 TTTATT TTCATT TCAATTT TATTATT TTATTTT TTTATT ATTA-T TTTATT
1 TTTATT TTTATT TTTA-TT T-TTATT TT-TATT TTTATT TTTATT TTTATT
20373335 TT
1 TT
20373337 GAAAGACATA
Statistics
Matches: 73, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
5 9 0.12
6 52 0.71
7 11 0.15
8 1 0.01
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:20373258 original size:17 final size:16
Alignment explanation
Indices: 20373232--20373336 Score: 90
Period size: 17 Copynumber: 6.2 Consensus size: 16
20373222 TGACTCCTTT
20373232 TTTTTA-TTTATTCTTA
1 TTTTTATTTTATT-TTA
20373248 TTTTTATTTTATTTTTA
1 TTTTTATTTTA-TTTTA
*
20373265 TTTTTATTTTTCTTTTGA
1 TTTTTA-TTTTATTTT-A
*
20373283 TTTTTATTTTCATTTCA
1 TTTTTATTTT-ATTTTA
*
20373300 ATTTTA--TTATTTTA
1 TTTTTATTTTATTTTA
20373314 TTTTTTTATTATTATTTTA
1 --TTTTTATT-TTATTTTA
20373333 TTTT
1 TTTT
20373337 GAAAGACATA
Statistics
Matches: 73, Mismatches: 6, Indels: 19
0.74 0.06 0.19
Matches are distributed among these distances:
14 5 0.07
15 2 0.03
16 11 0.15
17 31 0.42
18 16 0.22
19 8 0.11
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTATTTTA
Found at i:20377188 original size:46 final size:46
Alignment explanation
Indices: 20377055--20377276 Score: 170
Period size: 46 Copynumber: 4.8 Consensus size: 46
20377045 GGGATAGGAT
* * *
20377055 GCCGATGCCATGTCCCGGACATGGTCTTACACTAGCT-T-AACTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTAG-AG
* *
20377101 GCCGATGCATGTCCTAGACATGTCTTACACTGGCT-TACATCTAGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATCTAGAG
* **
20377147 GCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCA-CT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCT-AGAG
* * * * * *
20377193 GCCGATACCATGTCCC-GAACATGGTTTTACACTGGCTCTCGT-AATGTG
1 GCCGAT-GCATGTCCCAG-ACAT-GTCTTACACTAGCTCTCATCTA-GAG
* *
20377241 GCCGATGCATGTTCCAGACATGTCTTACATTAGCTC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTC
20377277 ACAATAGTCC
Statistics
Matches: 142, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
44 14 0.10
45 13 0.09
46 67 0.47
47 25 0.18
48 23 0.16
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTAGAG
Found at i:20395416 original size:213 final size:215
Alignment explanation
Indices: 20395007--20395437 Score: 803
Period size: 214 Copynumber: 2.0 Consensus size: 215
20394997 CTTCAACCCC
20395007 TTGTCAAAATCACTATTGGAGACCTAGGAAGCTTCAGTTTCAACTTCCTTGTGCATGTGAGCTCA
1 TTGTCAAAATCACTATTGGAGACCTAGGAAGCTTCAGTTTCAACTTCCTTGTGCATGTGAGCTCA
* *
20395072 ATTCTCACCTAATTTTTGTAATTTTTATATTTTTTTTAGATCGTTGAAACTAGGTCCAACTAGTC
66 ATTCTCACCTAATTTTTGTAATTTTTATAGTTTTTTTAGATCGTTGAAACTAGGTCCAACTAGCC
*
20395137 CATACCTTTGTTTTTGAATTTGTTAAAAATTTTAGAAGTTTCAATTGATGAATCTTGAATG-TTT
131 CATACCTTCGTTTTTGAATTTGTTAAAAATTTTAGAAGTTTCAATTGATGAATCTTGAATGTTTT
20395201 TTTTTATGATAATTATGTGT
196 TTTTTATGATAATTATGTGT
*
20395221 TTGTCAAAATCACTATTGGAGACCTAGGAAGCTTCGGTTTCAACTTCCTTGTGCATGTGAGCTCA
1 TTGTCAAAATCACTATTGGAGACCTAGGAAGCTTCAGTTTCAACTTCCTTGTGCATGTGAGCTCA
*
20395286 ATTCTCACCTAATTTTTGTAATTTTTAT-GTTTTTTTAGATTGTTGAAACTAGGTCCAACTAGCC
66 ATTCTCACCTAATTTTTGTAATTTTTATAGTTTTTTTAGATCGTTGAAACTAGGTCCAACTAGCC
20395350 CATACCTTCGTTTTTGAATTTGTTAAAAATTTTAGAAGTTTCAATTGATGAATCTTGAATGTTTT
131 CATACCTTCGTTTTTGAATTTGTTAAAAATTTTAGAAGTTTCAATTGATGAATCTTGAATGTTTT
20395415 TTTTTATGATAATTATGTGT
196 TTTTTATGATAATTATGTGT
20395435 TTG
1 TTG
20395438 AAACTTTGAT
Statistics
Matches: 211, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
213 93 0.44
214 118 0.56
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (215 bp):
TTGTCAAAATCACTATTGGAGACCTAGGAAGCTTCAGTTTCAACTTCCTTGTGCATGTGAGCTCA
ATTCTCACCTAATTTTTGTAATTTTTATAGTTTTTTTAGATCGTTGAAACTAGGTCCAACTAGCC
CATACCTTCGTTTTTGAATTTGTTAAAAATTTTAGAAGTTTCAATTGATGAATCTTGAATGTTTT
TTTTTATGATAATTATGTGT
Found at i:20400657 original size:29 final size:29
Alignment explanation
Indices: 20400617--20400693 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
20400607 CACGATAACG
20400617 TAAGTGACTAAAACGTAACATTTCAAATA
1 TAAGTGACTAAAACGTAACATTTCAAATA
* *
20400646 TAAGTGATTAAAACATAACATTTCAAATA
1 TAAGTGACTAAAACGTAACATTTCAAATA
* *
20400675 TAAGTTACTAAAATGTAAC
1 TAAGTGACTAAAACGTAAC
20400694 TTGAGACAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (29 bp):
TAAGTGACTAAAACGTAACATTTCAAATA
Found at i:20401329 original size:23 final size:22
Alignment explanation
Indices: 20401295--20401337 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
20401285 ATCAACATTT
20401295 TAAATATATAAATACCACATTTGA
1 TAAATATATAAA-ACC-CATTTGA
20401319 TAAA-ATATAAAACCCATTT
1 TAAATATATAAAACCCATTT
20401338 ATACCATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 7 0.37
24 4 0.21
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAATATATAAAACCCATTTGA
Found at i:20413122 original size:26 final size:26
Alignment explanation
Indices: 20413093--20413145 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
20413083 TAATCTAAAA
* *
20413093 ATTTTAATTAATTACATAAATGATCT
1 ATTTTAATAAAATACATAAATGATCT
* *
20413119 ATTTTTATAAAATACGTAAATGATCT
1 ATTTTAATAAAATACATAAATGATCT
20413145 A
1 A
20413146 AAATTTATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (26 bp):
ATTTTAATAAAATACATAAATGATCT
Found at i:20413412 original size:11 final size:11
Alignment explanation
Indices: 20413394--20413423 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
20413384 TATTTTTCTG
20413394 TTTA-TTATTA
1 TTTATTTATTA
20413404 TTTATTTATTA
1 TTTATTTATTA
20413415 TTTATTTAT
1 TTTATTTAT
20413424 AATATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:20413531 original size:14 final size:13
Alignment explanation
Indices: 20413488--20413519 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
20413478 TATTTAAATC
20413488 TTTTTTATTTATT
1 TTTTTTATTTATT
20413501 TATTTTTATTTATT
1 T-TTTTTATTTATT
20413515 TTTTT
1 TTTTT
20413520 ATATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTATTTATT
Found at i:20418528 original size:20 final size:20
Alignment explanation
Indices: 20418489--20418529 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20418479 TGCATATGGC
20418489 TTATGTTATGTGATTAAGGT
1 TTATGTTATGTGATTAAGGT
20418509 TTATGTTATGTGATTAAGGT
1 TTATGTTATGTGATTAAGGT
20418529 T
1 T
20418530 GGATTCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (20 bp):
TTATGTTATGTGATTAAGGT
Found at i:20420587 original size:39 final size:39
Alignment explanation
Indices: 20420503--20420659 Score: 210
Period size: 39 Copynumber: 4.0 Consensus size: 39
20420493 CAAATCCAAT
* *
20420503 CACCACCAC-AAAGCATGCGGGACTTTAAGCCCGGATATAA
1 CACCAGCACGAAAGCCTGCGGGAC-TT-AGCCCGGATATAA
*
20420543 TACCAGCAC-AAAGCCTGCGGGACTTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTGCGGGAC-TTAGCCCGGATATAA
* *
20420582 CACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTGCGGGACTTAGCCCGGATATAA
* *
20420621 CACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTGCGGGACTTAGCCCGGATATAA
20420660 TTCTCCATTA
Statistics
Matches: 110, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 75 0.68
40 35 0.32
ACGTcount: A:0.31, C:0.30, G:0.22, T:0.17
Consensus pattern (39 bp):
CACCAGCACGAAAGCCTGCGGGACTTAGCCCGGATATAA
Found at i:20426868 original size:39 final size:39
Alignment explanation
Indices: 20426801--20427095 Score: 486
Period size: 39 Copynumber: 7.5 Consensus size: 39
20426791 ACAAAGCATG
* * *
20426801 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTA
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
20426841 CGGAACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
*
20426881 CGGGACTTAGCTCGGATAT-ACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
20426919 CGGGAGTTAGCCCAGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
20426958 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
20426997 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
20427036 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
20427075 CGGGACTTAGCCCGGATATAA
1 CGGGACTTAGCCCGGATATAA
20427096 TACTCCATTA
Statistics
Matches: 242, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
38 35 0.14
39 188 0.78
40 19 0.08
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:20431927 original size:241 final size:241
Alignment explanation
Indices: 20431499--20431989 Score: 820
Period size: 241 Copynumber: 2.0 Consensus size: 241
20431489 AATGAGAAAA
** * *
20431499 TATGATAAAAATTGATTTTCGGACCTAGAGGTAAAATGGTCATTTTGTCAAAGTCTAGGGGCAAA
1 TATG-TAAAAATTGATTTTCGGACCTAGAGGTAAAATGACCAATTTGTCAAAGTCTAGAGGCAAA
* *
20431564 ATGGTCAATTTGCCCAATTATGAATTTTTGAGTGTTTAGGTTAATATGATGATGAAATGAATAAA
65 ATGGTCAATTTACCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGATGATGAAATGAATAAA
* * * *
20431629 TTTCTATCATTTTAGATCAAGAATTACAAAATTCGGGTTTAGACCGGGGAAAAGCAAAACAAGTG
130 TTTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACCGGGGAAAAGCAAAACAAGTA
* * *
20431694 GACTAAGTTGAACTAGTCGTCTACATTTTGTATACCGAGGTAAGTTC
195 GACTAAGTCGAACTAGTCGTCTACATTTTGTATACAGAAGTAAGTTC
*
20431741 TATGTAAAAATTGATTTTCGGACCTAGAGGTAAAATGACCAATTTGTGAAAGTCTAGAGGCAAAA
1 TATGTAAAAATTGATTTTCGGACCTAGAGGTAAAATGACCAATTTGTCAAAGTCTAGAGGCAAAA
* *
20431806 TGGTCAATTTATCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGCTGATGAAATGAATAAAT
66 TGGTCAATTTACCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGATGATGAAATGAATAAAT
*
20431871 TTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACTGGGGAAAAGCAAAACAAGTAG
131 TTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACCGGGGAAAAGCAAAACAAGTAG
20431936 ACTAAGTCGAACTAGTCGTCTACATTTTGTATACAGAAGTAAGTTC
196 ACTAAGTCGAACTAGTCGTCTACATTTTGTATACAGAAGTAAGTTC
20431982 TATGTAAA
1 TATGTAAA
20431990 TAATACAACT
Statistics
Matches: 232, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
241 228 0.98
242 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (241 bp):
TATGTAAAAATTGATTTTCGGACCTAGAGGTAAAATGACCAATTTGTCAAAGTCTAGAGGCAAAA
TGGTCAATTTACCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGATGATGAAATGAATAAAT
TTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACCGGGGAAAAGCAAAACAAGTAG
ACTAAGTCGAACTAGTCGTCTACATTTTGTATACAGAAGTAAGTTC
Found at i:20432220 original size:47 final size:44
Alignment explanation
Indices: 20432155--20432276 Score: 147
Period size: 47 Copynumber: 2.6 Consensus size: 44
20432145 TTTGTGTGCT
* *
20432155 AGTGTAAGAAATGTCTGGGACATGCATCGGCCACATT-ATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG---CATTGACGAGAGCC
*
20432201 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCATTGAGACGAGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATT--GACGAGAGCC
20432249 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
20432277 TGCTACGAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
45 4 0.06
46 13 0.19
47 27 0.40
48 23 0.34
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATTGACGAGAGCC
Found at i:20432346 original size:48 final size:45
Alignment explanation
Indices: 20432248--20432419 Score: 127
Period size: 48 Copynumber: 3.7 Consensus size: 45
20432238 AGACGAGAGC
* *
20432248 CAGTGTAAGACATGTCTGGGACATGCATCTGCTACG---AGATGTGT
1 CAGTGTAAGACATGTCAGGGACATGCATC-GC-ACGTATAGAGGTGT
*
20432292 CAGTGTAAGACTATATCAGGGACATAGCATCAGCACGTATAGAGGTGT
1 CAGTGTAAGAC-ATGTCAGGGACAT-GCATC-GCACGTATAGAGGTGT
* *
20432340 CAGTGTAAAACCATGTCTA-GGACATGGCATCGACACGTATAAAGGTGT
1 CAGTGTAAGA-CATGTC-AGGGACAT-GCATCG-CACGTATAGAGGTGT
* * * **
20432388 AAATGCAAGACCATGTTTGGGACATGGCATCG
1 CAGTGTAAGA-CATGTCAGGGACAT-GCATCG
20432420 GTACGGATAT
Statistics
Matches: 105, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
44 11 0.10
45 14 0.13
46 7 0.07
47 1 0.01
48 70 0.67
49 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (45 bp):
CAGTGTAAGACATGTCAGGGACATGCATCGCACGTATAGAGGTGT
Found at i:20432558 original size:47 final size:47
Alignment explanation
Indices: 20432440--20432565 Score: 164
Period size: 47 Copynumber: 2.6 Consensus size: 47
20432430 GTGAGAGCTC
* * *
20432440 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTTGATTTCAATAGTCA
1 GTGTAAGACCATGTCTGGGACATGGCATC-GACTTGA-TTCAATAGCCA
*
20432489 GTGTAAGACCATGTCTGGGACATGGCATCGACTTGA-TGAATGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACTTGATTCAAT-AGCCA
* *
20432536 GTGTAAGACCGTGTCTGCGACATGGCATCG
1 GTGTAAGACCATGTCTGGGACATGGCATCG
20432566 GCATCATACC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
46 4 0.06
47 32 0.46
48 6 0.09
49 28 0.40
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (47 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGACTTGATTCAATAGCCA
Found at i:20433591 original size:28 final size:28
Alignment explanation
Indices: 20433560--20433641 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
20433550 AAGACATGGG
20433560 CGTGTCATGGCCGTGTGAGAGACACGAA
1 CGTGTCATGGCCGTGTGAGAGACACGAA
*
20433588 CGTGTCATGGCCGTGTGAGAGACACGAG
1 CGTGTCATGGCCGTGTGAGAGACACGAA
* * *
20433616 CATGTCATAGTCGTGTGAGAGACACG
1 CGTGTCATGGCCGTGTGAGAGACACG
20433642 GGCAATGGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.20
Consensus pattern (28 bp):
CGTGTCATGGCCGTGTGAGAGACACGAA
Found at i:20434122 original size:241 final size:241
Alignment explanation
Indices: 20433690--20434131 Score: 767
Period size: 241 Copynumber: 1.8 Consensus size: 241
20433680 CCCTGTAGTC
* * *
20433690 AAAGTCTAGGGGCAAAATGGTCAATTTGCCCAATTATGAATTTTTGAGTGTTTAGGTTAATATGA
1 AAAGTCTAGAGGCAAAATGGTCAATTTACCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGA
* * *
20433755 TGATGAAATGAATAAATTTCTATCATTTTAGATCAAGAATTACAAAATTCGGGTTTAGACCGGGG
66 TGATGAAATGAATAAATTTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACCGGGG
* * * *
20433820 AAAAGCAAAACAAGTGGACTAAGTTGAACTAGTCGTCTACATTTTGTATACCGAGGTAAGTTCTA
131 AAAAGCAAAACAAGTAGACTAAGTCGAACTAGTCGTCTACATTTTGTATACAGAAGTAAGTTCTA
20433885 TGTAAAAATTGATTTTCGGACCTAGAGGTAAAATGACCAATTTGTG
196 TGTAAAAATTGATTTTCGGACCTAGAGGTAAAATGACCAATTTGTG
* *
20433931 AAAGTCTAGAGGCAAAATGGTCAATTTATCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGC
1 AAAGTCTAGAGGCAAAATGGTCAATTTACCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGA
*
20433996 TGATGAAATGAATAAATTTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACTGGGG
66 TGATGAAATGAATAAATTTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACCGGGG
20434061 AAAAGCAAAACAAGTAGACTAAGTCGAACTAGTCGTCTACATTTTGTATACAGAAGTAAGTTCTA
131 AAAAGCAAAACAAGTAGACTAAGTCGAACTAGTCGTCTACATTTTGTATACAGAAGTAAGTTCTA
20434126 TGTAAA
196 TGTAAA
20434132 TAATACAACT
Statistics
Matches: 188, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
241 188 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (241 bp):
AAAGTCTAGAGGCAAAATGGTCAATTTACCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGA
TGATGAAATGAATAAATTTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACCGGGG
AAAAGCAAAACAAGTAGACTAAGTCGAACTAGTCGTCTACATTTTGTATACAGAAGTAAGTTCTA
TGTAAAAATTGATTTTCGGACCTAGAGGTAAAATGACCAATTTGTG
Found at i:20434362 original size:47 final size:44
Alignment explanation
Indices: 20434297--20434418 Score: 147
Period size: 47 Copynumber: 2.6 Consensus size: 44
20434287 TTTGTGTGCT
* *
20434297 AGTGTAAGAAATGTCTGGGACATGCATCGGCCACATT-ATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG---CATTGACGAGAGCC
*
20434343 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCATTGAGACGAGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATT--GACGAGAGCC
20434391 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
20434419 TGCTACGAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
45 4 0.06
46 13 0.19
47 27 0.40
48 23 0.34
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATTGACGAGAGCC
Found at i:20434488 original size:48 final size:45
Alignment explanation
Indices: 20434390--20434561 Score: 127
Period size: 48 Copynumber: 3.7 Consensus size: 45
20434380 AGACGAGAGC
* *
20434390 CAGTGTAAGACATGTCTGGGACATGCATCTGCTACG---AGATGTGT
1 CAGTGTAAGACATGTCAGGGACATGCATC-GC-ACGTATAGAGGTGT
*
20434434 CAGTGTAAGACTATATCAGGGACATAGCATCAGCACGTATAGAGGTGT
1 CAGTGTAAGAC-ATGTCAGGGACAT-GCATC-GCACGTATAGAGGTGT
* *
20434482 CAGTGTAAAACCATGTCTA-GGACATGGCATCGACACGTATAAAGGTGT
1 CAGTGTAAGA-CATGTC-AGGGACAT-GCATCG-CACGTATAGAGGTGT
* * * **
20434530 AAATGCAAGACCATGTTTGGGACATGGCATCG
1 CAGTGTAAGA-CATGTCAGGGACAT-GCATCG
20434562 GTACGGATAT
Statistics
Matches: 105, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
44 11 0.10
45 14 0.13
46 7 0.07
47 1 0.01
48 70 0.67
49 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (45 bp):
CAGTGTAAGACATGTCAGGGACATGCATCGCACGTATAGAGGTGT
Found at i:20434700 original size:47 final size:47
Alignment explanation
Indices: 20434582--20434707 Score: 164
Period size: 47 Copynumber: 2.6 Consensus size: 47
20434572 GTGAGAGCTC
* * *
20434582 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTTGATTTCAATAGTCA
1 GTGTAAGACCATGTCTGGGACATGGCATC-GACTTGA-TTCAATAGCCA
*
20434631 GTGTAAGACCATGTCTGGGACATGGCATCGACTTGA-TGAATGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACTTGATTCAAT-AGCCA
* *
20434678 GTGTAAGACCGTGTCTGCGACATGGCATCG
1 GTGTAAGACCATGTCTGGGACATGGCATCG
20434708 GCATCATACC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
46 4 0.06
47 32 0.46
48 6 0.09
49 28 0.40
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (47 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGACTTGATTCAATAGCCA
Done.