Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 93 of 208
Found at i:27605688 original size:7 final size:7
Alignment explanation
Indices: 27605676--27605707 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
27605666 CGGGCAATTG
27605676 TCTCCAC
1 TCTCCAC
27605683 TCTCCAC
1 TCTCCAC
27605690 TCTCCAC
1 TCTCCAC
*
27605697 TCTTCAC
1 TCTCCAC
27605704 TCTC
1 TCTC
27605708 ATCCAATCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.34
Consensus pattern (7 bp):
TCTCCAC
Found at i:27614585 original size:92 final size:92
Alignment explanation
Indices: 27614428--27614614 Score: 374
Period size: 92 Copynumber: 2.0 Consensus size: 92
27614418 GCACCACGTG
27614428 GCTATGAGTTAGTATACATTCTTTGATACATTATCTTTCTTAACCTGAATTGAGAAAGGGTAATG
1 GCTATGAGTTAGTATACATTCTTTGATACATTATCTTTCTTAACCTGAATTGAGAAAGGGTAATG
27614493 AAGACCTTGTTTTTCATATAGTGGGCA
66 AAGACCTTGTTTTTCATATAGTGGGCA
27614520 GCTATGAGTTAGTATACATTCTTTGATACATTATCTTTCTTAACCTGAATTGAGAAAGGGTAATG
1 GCTATGAGTTAGTATACATTCTTTGATACATTATCTTTCTTAACCTGAATTGAGAAAGGGTAATG
27614585 AAGACCTTGTTTTTCATATAGTGGGCA
66 AAGACCTTGTTTTTCATATAGTGGGCA
27614612 GCT
1 GCT
27614615 TGCTTATTTC
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 95 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (92 bp):
GCTATGAGTTAGTATACATTCTTTGATACATTATCTTTCTTAACCTGAATTGAGAAAGGGTAATG
AAGACCTTGTTTTTCATATAGTGGGCA
Found at i:27616332 original size:12 final size:12
Alignment explanation
Indices: 27616315--27616339 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27616305 CCAAGTTTCT
27616315 TTTATTTATTTG
1 TTTATTTATTTG
27616327 TTTATTTATTTG
1 TTTATTTATTTG
27616339 T
1 T
27616340 CACTTCAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTATTTATTTG
Found at i:27631487 original size:50 final size:50
Alignment explanation
Indices: 27631385--27631674 Score: 287
Period size: 50 Copynumber: 5.7 Consensus size: 50
27631375 TAAAGAGATT
* *
27631385 CCATGTAATACCATGTCTGGGACATGGCATTGGCATCAATGAGATTATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTC
* *
27631441 CCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGACGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* *
27631491 TCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
** * * **
27631541 CCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAATTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * * * * * * * * **
27631591 CCATATAATACCATATTTGGGATATGACATTGGCA--GTATAGGAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTC
*
27631640 CCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
27631675 TGTTATTATC
Statistics
Matches: 197, Mismatches: 36, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.01
49 36 0.18
50 123 0.62
53 3 0.02
55 1 0.01
56 33 0.17
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
Found at i:27632437 original size:24 final size:25
Alignment explanation
Indices: 27632410--27632461 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
27632400 AATGAAAGCT
27632410 TATTGA-TCTACTTTCATAGAAAAA
1 TATTGAGTCTACTTTCATAGAAAAA
27632434 TATTGAGTCTACTTTCATAGAAAAA
1 TATTGAGTCTACTTTCATAGAAAAA
27632459 TAT
1 TAT
27632462 CGGTCCAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (25 bp):
TATTGAGTCTACTTTCATAGAAAAA
Found at i:27638189 original size:32 final size:32
Alignment explanation
Indices: 27638145--27638210 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
27638135 AAAGAGATCC
*
27638145 CATGTAATACCATGTCTGGGACATGGCATTGG
1 CATGTAAGACCATGTCTGGGACATGGCATTGG
*
27638177 CATGTAAGACCATGTTTGGGACATGGCATTGG
1 CATGTAAGACCATGTCTGGGACATGGCATTGG
27638209 CA
1 CA
27638211 CCGAGAGGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (32 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGG
Found at i:27638252 original size:50 final size:50
Alignment explanation
Indices: 27638177--27638409 Score: 202
Period size: 50 Copynumber: 4.7 Consensus size: 50
27638167 ATGGCATTGG
*
27638177 CATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGAGGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAGGAGAGGTCC
* * *
27638227 CATGTAAGACCATGTCTGGGACATGGCGTTGGCAACGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAGGAGAGGTCC
*** * * * * ** **
27638277 CCCATAAGACTATGTCTGAGACATGACA-TGGACACCGATATAAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGG-CACCGAGAGGAGAGGTCC
* * * * ** * **
27638327 CATGTAAGAACATATCTGGGATATGACATTGGCA--GTACTGGAAACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGAGGAGAGGTCC
*
27638376 CATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
27638410 TGTTATTATC
Statistics
Matches: 144, Mismatches: 36, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
48 1 0.01
49 38 0.26
50 102 0.71
51 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAGGAGAGGTCC
Found at i:27642059 original size:34 final size:36
Alignment explanation
Indices: 27642021--27642105 Score: 115
Period size: 34 Copynumber: 2.5 Consensus size: 36
27642011 TTGACAAAGC
27642021 TAGCTCGCATATAAACACAAC-T-CATATATAAACA
1 TAGCTCGCATATAAACACAACTTGCATATATAAACA
* **
27642055 TAGCTCGCATGTAAACACAACTTGCATATATGCACA
1 TAGCTCGCATATAAACACAACTTGCATATATAAACA
27642091 -A-CTCGCATATAAACA
1 TAGCTCGCATATAAACA
27642106 TAGCTAACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
34 33 0.73
35 2 0.04
36 10 0.22
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.24
Consensus pattern (36 bp):
TAGCTCGCATATAAACACAACTTGCATATATAAACA
Found at i:27642069 original size:17 final size:17
Alignment explanation
Indices: 27642021--27642110 Score: 72
Period size: 17 Copynumber: 5.3 Consensus size: 17
27642011 TTGACAAAGC
27642021 TAGCTCGCATATAAACA
1 TAGCTCGCATATAAACA
* * **
27642038 CAACTCATATATAAACA
1 TAGCTCGCATATAAACA
*
27642055 TAGCTCGCATGTAAACA
1 TAGCTCGCATATAAACA
* * * **
27642072 CAACTTGCATATATGCA
1 TAGCTCGCATATAAACA
* *
27642089 CAACTCGCATATAAACA
1 TAGCTCGCATATAAACA
27642106 TAGCT
1 TAGCT
27642111 AACATAGAAA
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24
Consensus pattern (17 bp):
TAGCTCGCATATAAACA
Found at i:27642103 original size:51 final size:51
Alignment explanation
Indices: 27642027--27642127 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
27642017 AAGCTAGCTC
* **
27642027 GCATATAAACACAACTCATATATAAACATAGCTCGCAT-GTAAACACAACTT
1 GCATATAAACACAACTCACATATAAACATAGCTAACATAG-AAACACAACTT
** *
27642078 GCATATATGCACAACTCGCATATAAACATAGCTAACATAGAAACACAACT
1 GCATATAAACACAACTCACATATAAACATAGCTAACATAGAAACACAACT
27642128 CGCACATTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.22
Consensus pattern (51 bp):
GCATATAAACACAACTCACATATAAACATAGCTAACATAGAAACACAACTT
Found at i:27644900 original size:20 final size:21
Alignment explanation
Indices: 27644863--27644920 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 21
27644853 TAGGACATTA
27644863 TATGATTATGATAAGATATGC
1 TATGATTATGATAAGATATGC
** *
27644884 TATG-TTATGATTTGATATGA
1 TATGATTATGATAAGATATGC
* *
27644904 AATGATT-CGATAAGATA
1 TATGATTATGATAAGATA
27644921 CGTTAAGATA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (21 bp):
TATGATTATGATAAGATATGC
Found at i:27651000 original size:31 final size:31
Alignment explanation
Indices: 27650965--27651027 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
27650955 AATGAAGATA
27650965 ATTCCCACCTCAATCTCGTATAAGATGACTG
1 ATTCCCACCTCAATCTCGTATAAGATGACTG
*
27650996 ATTCCCACCTCAATCTCGTATAGGATGACTG
1 ATTCCCACCTCAATCTCGTATAAGATGACTG
27651027 A
1 A
27651028 AAAAGATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (31 bp):
ATTCCCACCTCAATCTCGTATAAGATGACTG
Found at i:27651610 original size:24 final size:25
Alignment explanation
Indices: 27651578--27651629 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
27651568 TCTAAAAGAG
* *
27651578 TTAGTATTTATTAATATAATATA-T
1 TTAGCATTTATTAACATAATATAGT
*
27651602 TTAGCATTTATTAGCATAATATAGT
1 TTAGCATTTATTAACATAATATAGT
27651627 TTA
1 TTA
27651630 CATAAATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (25 bp):
TTAGCATTTATTAACATAATATAGT
Found at i:27651638 original size:24 final size:24
Alignment explanation
Indices: 27651593--27651639 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
27651583 ATTTATTAAT
**
27651593 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATAAATTAGC
27651617 ATAATATAGTTTA-CATAAATTAG
1 ATAATATA-TTTAGCATAAATTAG
27651640 AATTAGGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (24 bp):
ATAATATATTTAGCATAAATTAGC
Found at i:27653879 original size:21 final size:22
Alignment explanation
Indices: 27653849--27653889 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
27653839 TTCGTGTAAC
* *
27653849 TTGAATTATAT-TCTTAGATGA
1 TTGAAATATATATATTAGATGA
27653870 TTGAAATATATATATTAGAT
1 TTGAAATATATATATTAGAT
27653890 TGAGAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.46
Consensus pattern (22 bp):
TTGAAATATATATATTAGATGA
Found at i:27655376 original size:7 final size:7
Alignment explanation
Indices: 27655364--27655397 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
27655354 TGGAAGAATC
27655364 AAATGAG
1 AAATGAG
27655371 AAATGAG
1 AAATGAG
27655378 AAATGAG
1 AAATGAG
27655385 AAATGAG
1 AAATGAG
27655392 AAATGA
1 AAATGA
27655398 TTATGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (7 bp):
AAATGAG
Found at i:27667792 original size:42 final size:42
Alignment explanation
Indices: 27667746--27667830 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
27667736 ATAGAAGCAT
** *
27667746 ATAAGTGCTAAACAGAAACCCATGAGGGTTGAACGGAAGCTC
1 ATAAGTGCTAAACAGAAACCCACAAGGGTTAAACGGAAGCTC
* ** *
27667788 ATAAGTGCTGAATGGAAACCCACAAGGGTTAAACTGAAGCTC
1 ATAAGTGCTAAACAGAAACCCACAAGGGTTAAACGGAAGCTC
27667830 A
1 A
27667831 AAAGACTTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.18
Consensus pattern (42 bp):
ATAAGTGCTAAACAGAAACCCACAAGGGTTAAACGGAAGCTC
Found at i:27667847 original size:42 final size:42
Alignment explanation
Indices: 27667760--27667867 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 42
27667750 GTGCTAAACA
** * * * *
27667760 GAAACCCATGAGGGTTGAACGGAAGCTCATAAGTGCTGAATG
1 GAAACCCACAAGGGTTAAACGGAAGCTCAAAAGTACTGAACG
*
27667802 GAAACCCACAAGGGTTAAACTGAAGCTCAAAAG-ACTTGAACG
1 GAAACCCACAAGGGTTAAACGGAAGCTCAAAAGTAC-TGAACG
** *
27667844 GAAACCCATTACGGTTAAACGGAA
1 GAAACCCACAAGGGTTAAACGGAA
27667868 AACGGAAACT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 1 0.02
42 53 0.98
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (42 bp):
GAAACCCACAAGGGTTAAACGGAAGCTCAAAAGTACTGAACG
Found at i:27680554 original size:111 final size:109
Alignment explanation
Indices: 27680360--27680579 Score: 422
Period size: 111 Copynumber: 2.0 Consensus size: 109
27680350 CAATACCATG
27680360 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
1 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
27680425 GTTTATATGGTATACATATATCACTACTCTCTCTCTTAGACAACAA
66 GTTTATATGGTATACATATATCACTA--CTCTCTCTTAGACAACAA
27680471 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
1 CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
27680536 GTTTATATGGTATACATATATCACTACTCTCTCTTAGACAACAA
66 GTTTATATGGTATACATATATCACTACTCTCTCTTAGACAACAA
27680580 TACTTCATCA
Statistics
Matches: 109, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
109 18 0.17
111 91 0.83
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (109 bp):
CATGTAGTTGTATTGTTGTATTAAAGTTTGTTAATATGTACAGACATTTAGAAAAAGTAGTGTAT
GTTTATATGGTATACATATATCACTACTCTCTCTTAGACAACAA
Found at i:27685171 original size:29 final size:29
Alignment explanation
Indices: 27685124--27685192 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
27685114 GAAGATGTGG
* *
27685124 AGAACTTGTTTATTGAGAGTTCGTGATGA
1 AGAACTTGTTCATTAAGAGTTCGTGATGA
27685153 AGAACTTGTTCATTAAGAGTTCGTGATGA
1 AGAACTTGTTCATTAAGAGTTCGTGATGA
27685182 AGAACTTGTTC
1 AGAACTTGTTC
27685193 GTTGAGAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.36
Consensus pattern (29 bp):
AGAACTTGTTCATTAAGAGTTCGTGATGA
Found at i:27685324 original size:24 final size:24
Alignment explanation
Indices: 27685304--27685368 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
27685294 AAGATTTAGT
**
27685304 ACTTATTAGTGTAATATATTTAAC
1 ACTTATTAGCATAATATATTTAAC
* *
27685328 ATTTATTAGCATAATATATTTGAC
1 ACTTATTAGCATAATATATTTAAC
*
27685352 A-TTGATTAGAATAATAT
1 ACTT-ATTAGCATAATAT
27685369 TTTTCTACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (24 bp):
ACTTATTAGCATAATATATTTAAC
Found at i:27701864 original size:15 final size:15
Alignment explanation
Indices: 27701844--27701877 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
27701834 TTTATTGATT
27701844 ATTAATATTTTTTAG
1 ATTAATATTTTTTAG
27701859 ATTAATATTTTTTAG
1 ATTAATATTTTTTAG
27701874 ATTA
1 ATTA
27701878 TGACATCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
ATTAATATTTTTTAG
Found at i:27715580 original size:26 final size:25
Alignment explanation
Indices: 27715550--27715615 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 25
27715540 GCAACTCTTA
* *
27715550 TGAGCGTCCCGTTATATGGCTCTTCG
1 TGAGCTTCCCGTTA-AAGGCTCTTCG
*
27715576 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCG-TTAAAGGCTCTTCG
27715602 TGAGCTTCCCGTTA
1 TGAGCTTCCCGTTA
27715616 GTGCTCGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.08
26 30 0.83
27 3 0.08
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCCGTTAAAGGCTCTTCG
Found at i:27715687 original size:24 final size:24
Alignment explanation
Indices: 27715660--27715711 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
27715650 GGTGTTGCGT
*
27715660 GTTAATTGCTCTTCGGAGCTACCC
1 GTTAATTGCTCTTCGAAGCTACCC
*
27715684 GTTAATTGCTCTTTGAAGCTACCC
1 GTTAATTGCTCTTCGAAGCTACCC
27715708 GTTA
1 GTTA
27715712 TAGGCTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (24 bp):
GTTAATTGCTCTTCGAAGCTACCC
Found at i:27715718 original size:24 final size:24
Alignment explanation
Indices: 27715660--27715722 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
27715650 GGTGTTGCGT
* * *
27715660 GTTAATTGCTCTTCGGAGCTACCC
1 GTTAATGGCTCTTTGAAGCTACCC
*
27715684 GTTAATTGCTCTTTGAAGCTACCC
1 GTTAATGGCTCTTTGAAGCTACCC
27715708 GTT-ATAGGCTCTTTG
1 GTTAAT-GGCTCTTTG
27715723 TGAGCTTTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (24 bp):
GTTAATGGCTCTTTGAAGCTACCC
Found at i:27720389 original size:26 final size:26
Alignment explanation
Indices: 27720270--27720395 Score: 121
Period size: 26 Copynumber: 4.8 Consensus size: 26
27720260 AAGGCCTTAG
27720270 GAGTTTGAGTTGGTC-AGAGGACCCTT
1 GAGTTTGAGTTGGTCGA-AGGACCCTT
* ** *
27720296 GAATTTGAGTTGGTC-AGAGGATACTC
1 GAGTTTGAGTTGGTCGA-AGGACCCTT
* * * * * *
27720322 GAGTTTTAGTGGGTCGGAGAAGCCTA
1 GAGTTTGAGTTGGTCGAAGGACCCTT
*
27720348 AAGTTTGAGTTGGTCGAAGGACCCTT
1 GAGTTTGAGTTGGTCGAAGGACCCTT
27720374 GAGTTTGAGTTGGTCGAAGGAC
1 GAGTTTGAGTTGGTCGAAGGAC
27720396 TATGAACGGA
Statistics
Matches: 79, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.23, C:0.13, G:0.35, T:0.29
Consensus pattern (26 bp):
GAGTTTGAGTTGGTCGAAGGACCCTT
Found at i:27721949 original size:86 final size:86
Alignment explanation
Indices: 27721796--27721957 Score: 213
Period size: 86 Copynumber: 1.9 Consensus size: 86
27721786 TACATGCATA
* * * * *
27721796 AGGTTGAGTTCTCACTCTTAGTGAATTTATATCCCAGGATTTGGGTGGTCCTATTGCGACAATCT
1 AGGTTGAGTTCTCACTCTTAATGAATTCATATCCCAGGATTTAGCTGGTCCTATTGAGACAATCT
27721861 TGATGAATTCACTAACATATG
66 TGATGAATTCACTAACATATG
* *
27721882 AGGTTGAGTTCATTACTCTTAATGAGTTCATAT-CCA-GAGTTTAGCTGGTCCTATTGAGACCAA
1 AGGTTGAGTTC-TCACTCTTAATGAATTCATATCCCAGGA-TTTAGCTGGTCCTATTGAGA-CAA
27721945 -CTTGATGAATTCA
63 TCTTGATGAATTCA
27721958 TCAAATTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
85 2 0.03
86 44 0.67
87 20 0.30
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (86 bp):
AGGTTGAGTTCTCACTCTTAATGAATTCATATCCCAGGATTTAGCTGGTCCTATTGAGACAATCT
TGATGAATTCACTAACATATG
Found at i:27722464 original size:38 final size:38
Alignment explanation
Indices: 27722422--27722496 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
27722412 AAAAATATAT
* *
27722422 TTTTAAACGGTTACGATTTGAAAAAATTAGAATCTAGC
1 TTTTAAACGGTTACAATTTGAAAAAATCAGAATCTAGC
* *
27722460 TTTTAAACGGTTACAATTTGACAGAATCAGAATCTAG
1 TTTTAAACGGTTACAATTTGAAAAAATCAGAATCTAG
27722497 TGGTTGAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (38 bp):
TTTTAAACGGTTACAATTTGAAAAAATCAGAATCTAGC
Found at i:27723864 original size:21 final size:21
Alignment explanation
Indices: 27723825--27723864 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
27723815 GGCTTCTTTA
*
27723825 TTATTCATTAAAGACATTTCT
1 TTATTCATTAAAGAAATTTCT
27723846 TTATTCATTAATA-AAATTT
1 TTATTCATTAA-AGAAATTT
27723865 TCAACTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (21 bp):
TTATTCATTAAAGAAATTTCT
Found at i:27731564 original size:2 final size:2
Alignment explanation
Indices: 27731559--27731591 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27731549 TCTCTCTCTC
27731559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27731592 CATTGTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27734072 original size:14 final size:14
Alignment explanation
Indices: 27734053--27734092 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
27734043 TTGATTACCA
27734053 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
27734067 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
27734081 GAAAAATGTTTT
1 GTAAAATGTTTT
27734093 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:27734105 original size:34 final size:35
Alignment explanation
Indices: 27734061--27734127 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
27734051 CAGTAAAATG
* *
27734061 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
* *
27734095 TTTTCTGTAAAATAATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTT
27734128 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
Found at i:27734113 original size:20 final size:20
Alignment explanation
Indices: 27734076--27734115 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
27734066 CGTAAAATGA
**
27734076 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATAATTTACT
*
27734096 TTTCTGTAAAATAATTTACT
1 TTTCTGAAAAATAATTTACT
27734116 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATAATTTACT
Found at i:27736383 original size:20 final size:17
Alignment explanation
Indices: 27736368--27736402 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27736358 TTATTATTAC
27736368 AAATATTTTATAATTATT
1 AAATATTTTA-AATTATT
*
27736386 AAGTATTTTAAATTATT
1 AAATATTTTAAATTATT
27736403 TAGGAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AAATATTTTAAATTATT
Found at i:27736412 original size:18 final size:18
Alignment explanation
Indices: 27736372--27736414 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
27736362 TATTACAAAT
*
27736372 ATTTTATAATTATTAAGT
1 ATTTTATAATTATTAAGG
*
27736390 ATTTTA-AATTATTTAGG
1 ATTTTATAATTATTAAGG
27736407 AGTTTTAT
1 A-TTTTAT
27736415 GTTAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (18 bp):
ATTTTATAATTATTAAGG
Found at i:27736730 original size:41 final size:44
Alignment explanation
Indices: 27736640--27736730 Score: 107
Period size: 47 Copynumber: 2.1 Consensus size: 44
27736630 AATATTGTTG
* *
27736640 TTGTTGTTTAAATGAAAAACCAACTTATGTGATAGCTGATATTGTTA
1 TTGTTGTTGAAATGAAAAACCAACTTATGTGA-AGCTG--ATTGGTA
*
27736687 TTGTTGTTGAAATGGAAAACCAACTTATGTG-A-CTG-TTGGTA
1 TTGTTGTTGAAATGAAAAACCAACTTATGTGAAGCTGATTGGTA
27736728 TTG
1 TTG
27736731 GGAGATTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 8 0.20
44 3 0.07
45 1 0.02
47 29 0.71
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (44 bp):
TTGTTGTTGAAATGAAAAACCAACTTATGTGAAGCTGATTGGTA
Found at i:27742072 original size:206 final size:206
Alignment explanation
Indices: 27741718--27742212 Score: 698
Period size: 206 Copynumber: 2.4 Consensus size: 206
27741708 TGATACTGTT
* * *
27741718 AGTCATAAAGATAGGAATTGATTTGTCTTTTTCCTAAGGCTATTAGTAGGCACATGGCAAACAAT
1 AGTCATAAAAATAGGAATTGATTTGTCTATTTCCTAAGGCTATTAGTATGCACATGGCAAACAAT
* *
27741783 AACTTTATAAAAATCCAAACCTGCAATTCAATTTGATACAAACAATGATCATATTTGAATCAACA
66 AACTTTAGAAAAATCCAAACCTACAATTCAATTTGATACAAACAATGATCATATTTGAATCAACA
* *
27741848 TTTAAAAAAGGTTTTGAATCATATTTGAATAATTCAATGACATACACA-TATTCGAATAATTCAA
131 TTTAAAAAAGGTTTTGAATCATATTTGAATAATTCAATGACAGACACAGT-TTCAAATAATTCAA
*
27741912 TAAAGACTGATA
195 TAAAAACTGATA
* * * *
27741924 AGTCATAAAAATAAGAATTGATTTGTCTCTTTCCTAAGGATATTAGTATGCACATGGCAGACAAT
1 AGTCATAAAAATAGGAATTGATTTGTCTATTTCCTAAGGCTATTAGTATGCACATGGCAAACAAT
* * *
27741989 ACCTTTAGAAAAATCCAAACCTACAATTCACTTTGATACAAACAATGATCATATTTGGATCAACA
66 AACTTTAGAAAAATCCAAACCTACAATTCAATTTGATACAAACAATGATCATATTTGAATCAACA
* *
27742054 TTTGAAAAATGTTTTGAATCATATTTGAATAATTCAATGACAGACACAGTTTCAAATAATTCAAT
131 TTTAAAAAAGGTTTTGAATCATATTTGAATAATTCAATGACAGACACAGTTTCAAATAATTCAAT
* *
27742119 AAAAATTGATT
196 AAAAACTGATA
* * * *
27742130 TGTC----AAATAGGAACTT-ATTTGTCTATTTCCTAAGGCTA-TATGTATGCATATGACAAACC
1 AGTCATAAAAATAGGAA-TTGATTTGTCTATTTCCTAAGGCTATTA-GTATGCACATGGCAAACA
*
27742189 ATAACTTTGGAAAAATCCAAACCT
64 ATAACTTTAGAAAAATCCAAACCT
27742213 GCCATACACT
Statistics
Matches: 258, Mismatches: 28, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
201 2 0.01
202 64 0.25
203 2 0.01
206 189 0.73
207 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (206 bp):
AGTCATAAAAATAGGAATTGATTTGTCTATTTCCTAAGGCTATTAGTATGCACATGGCAAACAAT
AACTTTAGAAAAATCCAAACCTACAATTCAATTTGATACAAACAATGATCATATTTGAATCAACA
TTTAAAAAAGGTTTTGAATCATATTTGAATAATTCAATGACAGACACAGTTTCAAATAATTCAAT
AAAAACTGATA
Found at i:27745380 original size:27 final size:27
Alignment explanation
Indices: 27745345--27745417 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
27745335 CTTTCCACAT
* *
27745345 GATATTCTTGATGGACTTTTCACGTTA
1 GATACTCTTGATGGACTTCTCACGTTA
* *
27745372 GATACTCTTGACGGACTTCTCATGTTA
1 GATACTCTTGATGGACTTCTCACGTTA
*
27745399 GATAGTCTTGATGGACTTC
1 GATACTCTTGATGGACTTC
27745418 CTACATATAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (27 bp):
GATACTCTTGATGGACTTCTCACGTTA
Found at i:27745905 original size:50 final size:50
Alignment explanation
Indices: 27745830--27745931 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
27745820 TCAACATAAC
27745830 TAGTTTACAACCATCTATATATTTAGATACCATATTGCTTGCAACCACTA
1 TAGTTTACAACCATCTATATATTTAGATACCATATTGCTTGCAACCACTA
*
27745880 TAGTTTACAACCATCTATATATTTAGGTACCATATTGCTTGCAACCACTA
1 TAGTTTACAACCATCTATATATTTAGATACCATATTGCTTGCAACCACTA
27745930 TA
1 TA
27745932 CACCGTTACT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (50 bp):
TAGTTTACAACCATCTATATATTTAGATACCATATTGCTTGCAACCACTA
Found at i:27747987 original size:84 final size:84
Alignment explanation
Indices: 27747883--27748081 Score: 226
Period size: 84 Copynumber: 2.3 Consensus size: 84
27747873 GATTCTTTGA
* *
27747883 ATGAAAGGGGTTGTTATGTGCTGATTCCCCGTATCA-TTGATTAT-AAGGTGGTTGCTAAGTGCT
1 ATGAAAGGGGTTGCTATGTGCTGATTCCCCATATCACTTGATTATAAAGG-GGTTGCTAAGTGCT
* *
27747946 GATTCCACCGTATCCTTGATT
65 GATTCC-CCGTATCATTAATT
* * * *
27747967 CTGAAAGGGGTTGCTATGTGCTGATTCCCCATATCATTCCTTGTTTGTGAAAGGGGTTGCTATGT
1 ATGAAAGGGGTTGCTATGTGCTGATTCCCCATATCA---CTTGATTAT-AAAGGGGTTGCTAAGT
27748032 GCTGATTCCCCGTATCATTAATT
62 GCTGATTCCCCGTATCATTAATT
*
27748055 AT--AAGGTGGTTGCTAAGTGCTGATTCC
1 ATGAAAGG-GGTTGCTATGTGCTGATTCC
27748082 ATCGTGTAAC
Statistics
Matches: 98, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
84 33 0.34
86 4 0.04
87 19 0.19
88 19 0.19
89 19 0.19
90 4 0.04
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (84 bp):
ATGAAAGGGGTTGCTATGTGCTGATTCCCCATATCACTTGATTATAAAGGGGTTGCTAAGTGCTG
ATTCCCCGTATCATTAATT
Found at i:27748025 original size:46 final size:45
Alignment explanation
Indices: 27747883--27748081 Score: 199
Period size: 46 Copynumber: 4.6 Consensus size: 45
27747873 GATTCTTTGA
*
27747883 ATGAAAGGGGTTGTTATGTGCTGATTCCCCGTATCA---TTGATT
1 ATGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCATCCTTGATT
*
27747925 AT--AAGGTGGTTGCTAAGTGCTGATTCCACCG--T-ATCCTTGATT
1 ATGAAAGG-GGTTGCTATGTGCTGATTCC-CCGTATCATCCTTGATT
* * *
27747967 CTGAAAGGGGTTGCTATGTGCTGATTCCCCATATCATTCCTTGTTT
1 ATGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCA-TCCTTGATT
* *
27748013 GTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCA---TTAATT
1 ATGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCATCCTTGATT
*
27748055 AT--AAGGTGGTTGCTAAGTGCTGATTCC
1 ATGAAAGG-GGTTGCTATGTGCTGATTCC
27748082 ATCGTGTAAC
Statistics
Matches: 133, Mismatches: 12, Indels: 25
0.78 0.07 0.15
Matches are distributed among these distances:
39 1 0.01
40 9 0.07
41 37 0.28
42 19 0.14
43 19 0.14
44 5 0.04
45 1 0.01
46 42 0.32
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (45 bp):
ATGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCATCCTTGATT
Found at i:27753065 original size:22 final size:21
Alignment explanation
Indices: 27753040--27753088 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
27753030 GTTGGTTTAA
*
27753040 TAATAAAAATAATGTTATATAT
1 TAATAAAAATAATATTAT-TAT
*
27753062 TAATAACAATAATATTATTAT
1 TAATAAAAATAATATTATTAT
27753083 TAATAA
1 TAATAA
27753089 TAAAACCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TAATAAAAATAATATTATTAT
Found at i:27753082 original size:25 final size:24
Alignment explanation
Indices: 27753036--27753093 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 24
27753026 CTATGTTGGT
* *
27753036 TTAATAATAAAAATAATGTTATATA
1 TTAATAACAAAAATAATATTAT-TA
27753061 TTAATAAC---AATAATATTATTA
1 TTAATAACAAAAATAATATTATTA
*
27753082 TTAATAATAAAA
1 TTAATAACAAAA
27753094 CCCACTGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
21 9 0.33
22 10 0.37
24 1 0.04
25 7 0.26
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
TTAATAACAAAAATAATATTATTA
Found at i:27766716 original size:2 final size:2
Alignment explanation
Indices: 27766709--27766745 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
27766699 TTACTATTAT
27766709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27766746 AATTTTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27767417 original size:10 final size:10
Alignment explanation
Indices: 27767402--27767431 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
27767392 ATAAATGTTT
27767402 ATTTATTTTA
1 ATTTATTTTA
27767412 ATTTATTTTA
1 ATTTATTTTA
27767422 ATTTAGTTTT
1 ATTTA-TTTT
27767432 TTTTATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (10 bp):
ATTTATTTTA
Found at i:27770250 original size:19 final size:19
Alignment explanation
Indices: 27770228--27770279 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
27770218 TTTCTATAAA
27770228 TATTTTGAATCTTAAAAAT
1 TATTTTGAATCTTAAAAAT
* *
27770247 TATTTTGAATTTTTGAAAAT
1 TATTTTGAA-TCTTAAAAAT
27770267 TATTTTGAATCTT
1 TATTTTGAATCTT
27770280 TTTTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (19 bp):
TATTTTGAATCTTAAAAAT
Found at i:27770254 original size:39 final size:39
Alignment explanation
Indices: 27770202--27770279 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
27770192 ATTATAATTA
27770202 AAAAATAAATTTGAAATTTCT-ATAAA-TATTTTGAATCTT
1 AAAAATAAATTTG-AATTTCTGA-AAATTATTTTGAATCTT
* * *
27770241 AAAAATTATTTTGAATTTTTGAAAATTATTTTGAATCTT
1 AAAAATAAATTTGAATTTCTGAAAATTATTTTGAATCTT
27770280 TTTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 9 0.26
39 25 0.74
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (39 bp):
AAAAATAAATTTGAATTTCTGAAAATTATTTTGAATCTT
Found at i:27770380 original size:9 final size:9
Alignment explanation
Indices: 27770366--27770394 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
27770356 GACCAATCTG
27770366 TTATTCGAA
1 TTATTCGAA
27770375 TTATTCGAA
1 TTATTCGAA
27770384 TTATTCGAA
1 TTATTCGAA
27770393 TT
1 TT
27770395 GTAAAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTATTCGAA
Found at i:27772751 original size:42 final size:43
Alignment explanation
Indices: 27772695--27772804 Score: 118
Period size: 44 Copynumber: 2.6 Consensus size: 43
27772685 GATGCCACTA
* * *
27772695 TCCCAAACAGGGTCTTACAAG-AAATCAT-ATAA-GACGCCAATG
1 TCCCAGACATGGTCTTACAAGTAAATC-TCA-AACGACGCCAACG
* *
27772737 TCCCAGACATGGTCTTACACGTAAATCTCAAATCGATGCCAACG
1 TCCCAGACATGGTCTTACAAGTAAATCTCAAA-CGACGCCAACG
*
27772781 TCCCAGACATGGTCTTACACGTAA
1 TCCCAGACATGGTCTTACAAGTAA
27772805 TCACATACCG
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
42 21 0.36
43 6 0.10
44 32 0.54
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACAAGTAAATCTCAAACGACGCCAACG
Found at i:27783703 original size:26 final size:22
Alignment explanation
Indices: 27783675--27783720 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
27783665 AGTGTAACAA
27783675 GAAAGAAAAATTGATTTAATAT
1 GAAAGAAAAATTGATTTAATAT
27783697 GAAAGAAAAATTGATTTAATAT
1 GAAAGAAAAATTGATTTAATAT
27783719 GA
1 GA
27783721 TTAATTAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.30
Consensus pattern (22 bp):
GAAAGAAAAATTGATTTAATAT
Found at i:27784241 original size:22 final size:22
Alignment explanation
Indices: 27784213--27784294 Score: 119
Period size: 22 Copynumber: 3.7 Consensus size: 22
27784203 AAAGTAAATA
* *
27784213 GTACTAAACCCTCATGGCTAAC
1 GTACTAAGCTCTCATGGCTAAC
27784235 GTACTAAGCTCTCATGGCTAAC
1 GTACTAAGCTCTCATGGCTAAC
** *
27784257 GTACTAAGCTCTCATGTTTCAC
1 GTACTAAGCTCTCATGGCTAAC
27784279 GTACTAAGCTCTCATG
1 GTACTAAGCTCTCATG
27784295 TTTGAACAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (22 bp):
GTACTAAGCTCTCATGGCTAAC
Found at i:27789199 original size:13 final size:13
Alignment explanation
Indices: 27789181--27789210 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
27789171 TCCGTAGGCT
27789181 AACATCCCTCCAA
1 AACATCCCTCCAA
27789194 AACATCCCTCCAA
1 AACATCCCTCCAA
27789207 AACA
1 AACA
27789211 CACCTTGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.13
Consensus pattern (13 bp):
AACATCCCTCCAA
Found at i:27815329 original size:16 final size:17
Alignment explanation
Indices: 27815304--27815338 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
27815294 ACTTTTTCAA
27815304 TCATCCCTCATCC-CTC
1 TCATCCCTCATCCTCTC
*
27815320 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
27815337 TC
1 TC
27815339 TCAACTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:27817062 original size:25 final size:25
Alignment explanation
Indices: 27817033--27817084 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
27817023 AAACAAACAG
*
27817033 AAAAAAAATGGAATT-AAAATTTAAC
1 AAAAAAAATAGAATTCAAAA-TTAAC
27817058 AAAAAAAATAGAATTCAAAATTAAC
1 AAAAAAAATAGAATTCAAAATTAAC
27817083 AA
1 AA
27817085 TTTCACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (25 bp):
AAAAAAAATAGAATTCAAAATTAAC
Found at i:27818838 original size:28 final size:26
Alignment explanation
Indices: 27818797--27818851 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
27818787 TATTATAAAA
*
27818797 TTAATTAAAATTAAAAATTTTAATAAT
1 TTAAGTAAAATTAAAAATTTT-ATAAT
**
27818824 TTAAGTAAAATTTAATTATTTTATAAT
1 TTAAGTAAAA-TTAAAAATTTTATAAT
27818851 T
1 T
27818852 ATTATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
TTAAGTAAAATTAAAAATTTTATAAT
Found at i:27823332 original size:27 final size:27
Alignment explanation
Indices: 27823302--27823418 Score: 182
Period size: 27 Copynumber: 4.3 Consensus size: 27
27823292 TTAAACTATT
27823302 GAAATACCCTCGAAGGGTAAAATTATC
1 GAAATACCCTCGAAGGGTAAAATTATC
27823329 GAAATACCCTCGAAGGGTAAAATTATC
1 GAAATACCCTCGAAGGGTAAAATTATC
*
27823356 GAAATACCCACGAAGGGTAAAATTATC
1 GAAATACCCTCGAAGGGTAAAATTATC
* * *
27823383 AAAATACCCCCGAAAGGG-AAAATGATC
1 GAAATACCCTCG-AAGGGTAAAATTATC
27823410 GAAATACCC
1 GAAATACCC
27823419 CATGGGGTAA
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
27 79 0.94
28 5 0.06
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (27 bp):
GAAATACCCTCGAAGGGTAAAATTATC
Found at i:27824097 original size:259 final size:259
Alignment explanation
Indices: 27823631--27824148 Score: 991
Period size: 259 Copynumber: 2.0 Consensus size: 259
27823621 GTTCAAGGCT
27823631 TACTGTCTTTCTGCTTATGGCTTTTAGCCGTTCTATCTATGGTGTCGAGTCGTTCTATTGACTTA
1 TACTGTCTTTCTGCTTATGGCTTTTAGCCGTTCTATCTATGGTGTCGAGTCGTTCTATTGACTTA
*
27823696 GTGCTACAACTGGTGCTAAGCTTGGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGT
66 GTGCTACAACTGGTGCTAAGCTTAGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGT
27823761 GTTGGTTGGTACGGGTGGTGTATTGGTTGGATTGGGCAGAATTTCTGTCTGCATAGCTGCATCTG
131 GTTGGTTGGTACGGGTGGTGTATTGGTTGGATTGGGCAGAATTTCTGTCTGCATAGCTGCATCTG
27823826 ATACTGATTCTGTAATGGGCTTAGGTCCACCTGGTTTTGTTAATAGGCTAAGGCACACCTGATA
196 ATACTGATTCTGTAATGGGCTTAGGTCCACCTGGTTTTGTTAATAGGCTAAGGCACACCTGATA
27823890 TACTGTCTTTCTGCTTATGGCTTTTAGCCGTTCTATCTATGGTGTCGAGTCGTTCTATTGACTTA
1 TACTGTCTTTCTGCTTATGGCTTTTAGCCGTTCTATCTATGGTGTCGAGTCGTTCTATTGACTTA
* *
27823955 GTGCTGCAACTGGTGCTAAGCTTAGTGTGTTGGCTGGGTGGGTCAATTTTATTCCCACATGGTGT
66 GTGCTACAACTGGTGCTAAGCTTAGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGT
27824020 GTTGGTTGGTACGGGTGGTGTATTGGTTGGATTGGGCAGAATTTCTGTCTGCATAGCTGCATCTG
131 GTTGGTTGGTACGGGTGGTGTATTGGTTGGATTGGGCAGAATTTCTGTCTGCATAGCTGCATCTG
* *
27824085 ATACTTATTCTGTAATGGGTTTAGGTCCACCTGGTTTTGTTAATAGGCTAAGGCACACCTGATA
196 ATACTGATTCTGTAATGGGCTTAGGTCCACCTGGTTTTGTTAATAGGCTAAGGCACACCTGATA
27824149 CTATGCCTGG
Statistics
Matches: 254, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
259 254 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (259 bp):
TACTGTCTTTCTGCTTATGGCTTTTAGCCGTTCTATCTATGGTGTCGAGTCGTTCTATTGACTTA
GTGCTACAACTGGTGCTAAGCTTAGTGTGTTGGCTGGGTGGGTCAATTTTATCCCCACATGGTGT
GTTGGTTGGTACGGGTGGTGTATTGGTTGGATTGGGCAGAATTTCTGTCTGCATAGCTGCATCTG
ATACTGATTCTGTAATGGGCTTAGGTCCACCTGGTTTTGTTAATAGGCTAAGGCACACCTGATA
Found at i:27840374 original size:40 final size:41
Alignment explanation
Indices: 27840330--27840477 Score: 144
Period size: 40 Copynumber: 3.7 Consensus size: 41
27840320 TTGCACAAAT
* * *
27840330 GTGCCCCTGTTTGTACTTCGGTACCCCTT-ATAGCACATGC
1 GTGCCCCTATTTGTACTTCGATACCCCTTGATAGCACATAC
* * *
27840370 GTGCCCTTATTTG-ACTTCGATA-CCCTTGGTTGCACATAC
1 GTGCCCCTATTTGTACTTCGATACCCCTTGATAGCACATAC
* *
27840409 GTGACCCTACTTGTACTTCGATACCCC-TGATTA-CACATAC
1 GTGCCCCTATTTGTACTTCGATACCCCTTGA-TAGCACATAC
* * * *
27840449 ATCCCCCTATTTGCACTTTGATACCCCTT
1 GTGCCCCTATTTGTACTTCGATACCCCTT
27840478 ATTGCAAATG
Statistics
Matches: 86, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
38 5 0.06
39 26 0.30
40 50 0.58
41 5 0.06
ACGTcount: A:0.19, C:0.32, G:0.15, T:0.34
Consensus pattern (41 bp):
GTGCCCCTATTTGTACTTCGATACCCCTTGATAGCACATAC
Found at i:27861742 original size:78 final size:77
Alignment explanation
Indices: 27861637--27861788 Score: 277
Period size: 78 Copynumber: 2.0 Consensus size: 77
27861627 GTAATTAGGC
27861637 CTTAGGATAGAAATTAATAAAAATAAGTGTTTTTAACACATTTCATAAGTGTTATGACCCAATAG
1 CTTAGGATAGAAATTAATAAAAATAAGTGTTTTTAACACATTTCATAAGTGTTATGACCCAATAG
27861702 GCTAACACGGGA
66 GCTAACACGGGA
* *
27861714 CTTAGGATAGAAAATTAATAAAAATAAGTGTTTTTAACACATTTCGTAGGTGTTATGACCCAATA
1 CTTAGGATAG-AAATTAATAAAAATAAGTGTTTTTAACACATTTCATAAGTGTTATGACCCAATA
27861779 GGCTAACACG
65 GGCTAACACG
27861789 AGCCTTATAT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 10 0.14
78 62 0.86
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (77 bp):
CTTAGGATAGAAATTAATAAAAATAAGTGTTTTTAACACATTTCATAAGTGTTATGACCCAATAG
GCTAACACGGGA
Found at i:27862831 original size:8 final size:8
Alignment explanation
Indices: 27862786--27862816 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
27862776 ATTGATTTAT
27862786 TTTATTTG
1 TTTATTTG
27862794 TTTATTTG
1 TTTATTTG
27862802 TTTATTTG
1 TTTATTTG
27862810 TTTATTT
1 TTTATTT
27862817 TCATTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (8 bp):
TTTATTTG
Found at i:27865644 original size:11 final size:10
Alignment explanation
Indices: 27865624--27865661 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
27865614 GGGGGTTACA
27865624 TAAATTTTTT
1 TAAATTTTTT
*
27865634 TAAGTTTTTT
1 TAAATTTTTT
27865644 TAAA-TTTTT
1 TAAATTTTTT
27865653 TAAATTTTT
1 TAAATTTTT
27865662 AATTACTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (10 bp):
TAAATTTTTT
Found at i:27868582 original size:10 final size:10
Alignment explanation
Indices: 27868567--27868597 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
27868557 GTTATGCATA
27868567 AAATGGATTG
1 AAATGGATTG
27868577 AAATGGATTG
1 AAATGGATTG
*
27868587 AAATGGTTTG
1 AAATGGATTG
27868597 A
1 A
27868598 TTTTAGGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
AAATGGATTG
Found at i:27870037 original size:19 final size:19
Alignment explanation
Indices: 27869991--27870037 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
27869981 ATTTGTCTTA
*
27869991 GTTAATTTTATTAATTTAT
1 GTTAATTTGATTAATTTAT
*
27870010 GTTATTTTGATTAATTTAAT
1 GTTAATTTGATTAATTT-AT
27870030 -TTAATTTG
1 GTTAATTTG
27870038 GTTTTTCGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.62
Consensus pattern (19 bp):
GTTAATTTGATTAATTTAT
Found at i:27875175 original size:2 final size:2
Alignment explanation
Indices: 27875168--27875208 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
27875158 AATGCTACTT
27875168 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27875209 CTTCCACATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27881504 original size:41 final size:41
Alignment explanation
Indices: 27881437--27881518 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
27881427 ATGCAATAAC
* * *
27881437 AAAAATTAAAAATGAAAGCAAGAAATATTTTTGGATTTTTT
1 AAAAATTAAAAATAAAAACAAGAAATATTTTTGGAATTTTT
27881478 AAAAATTAAAAATAAAAACGAA-AAATATTTTTGGAATTTTT
1 AAAAATTAAAAATAAAAAC-AAGAAATATTTTTGGAATTTTT
27881519 GATTTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 35 0.95
42 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.35
Consensus pattern (41 bp):
AAAAATTAAAAATAAAAACAAGAAATATTTTTGGAATTTTT
Found at i:27881576 original size:18 final size:18
Alignment explanation
Indices: 27881545--27881581 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27881535 TGTATAAAAA
* *
27881545 ATAAACACACAAATAAAC
1 ATAAAAACAAAAATAAAC
27881563 ATAAAAACAAAAATAAAC
1 ATAAAAACAAAAATAAAC
27881581 A
1 A
27881582 CACATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.16, G:0.00, T:0.11
Consensus pattern (18 bp):
ATAAAAACAAAAATAAAC
Found at i:27883494 original size:32 final size:32
Alignment explanation
Indices: 27883453--27883517 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
27883443 TATAGGGACT
27883453 AGAAATGTAAATAAACCTTAGCTACAATATTA
1 AGAAATGTAAATAAACCTTAGCTACAATATTA
*
27883485 AGAAATGTAAATACACCTTAGCTACAATATTA
1 AGAAATGTAAATAAACCTTAGCTACAATATTA
27883517 A
1 A
27883518 CTAACTTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (32 bp):
AGAAATGTAAATAAACCTTAGCTACAATATTA
Found at i:27885759 original size:22 final size:22
Alignment explanation
Indices: 27885734--27885776 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
27885724 AAAAATTATA
*
27885734 AAATAGACTAATA-AAATAAATT
1 AAATA-ACTAAAATAAATAAATT
27885756 AAATAACTAAAATAAATAAAT
1 AAATAACTAAAATAAATAAAT
27885777 AAGAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (22 bp):
AAATAACTAAAATAAATAAATT
Found at i:27885777 original size:17 final size:18
Alignment explanation
Indices: 27885745--27885788 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
27885735 AATAGACTAA
27885745 TAAAATAAATTAAATAAC
1 TAAAATAAATTAAATAAC
*
27885763 TAAAATAAA-TAAATAAG
1 TAAAATAAATTAAATAAC
*
27885780 AAAAATAAA
1 TAAAATAAA
27885789 CAACCGACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
TAAAATAAATTAAATAAC
Found at i:27885788 original size:13 final size:13
Alignment explanation
Indices: 27885747--27885788 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
27885737 TAGACTAATA
*
27885747 AAATAAATTAAAT
1 AAATAAAATAAAT
*
27885760 AACTAAAATAAAT
1 AAATAAAATAAAT
27885773 AAATAAGAA-AAAT
1 AAATAA-AATAAAT
27885786 AAA
1 AAA
27885789 CAACCGACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 23 0.92
14 2 0.08
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:27888684 original size:61 final size:59
Alignment explanation
Indices: 27888573--27888688 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 59
27888563 ATCACTTTAA
* *
27888573 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATAT
1 TATTAAATTAATATAATACTTATCAAGATAAACATTAGATTAAATCTAATATTAAATAT
27888632 TATTAAATTAAT-TGAATA-TTATCTACAAGATAAACATTA-AGTTAAATCTAATATTAA
1 TATTAAATTAATAT-AATACTTA--T-CAAGATAAACATTAGA-TTAAATCTAATATTAA
27888689 GATAATCACT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
58 4 0.08
59 16 0.32
60 2 0.04
61 28 0.56
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (59 bp):
TATTAAATTAATATAATACTTATCAAGATAAACATTAGATTAAATCTAATATTAAATAT
Found at i:27888772 original size:68 final size:70
Alignment explanation
Indices: 27888621--27888775 Score: 156
Period size: 68 Copynumber: 2.2 Consensus size: 70
27888611 ATTAAATTTA
* **
27888621 ATATTAAATATTATTAAATTAATTGAATATTATCTACAAGATAAACATTAAGTTAAATCTAATAT
1 ATATTAAATAATATTAAATTAATAAAATATTATCTA-AAGATAAACATTAAGTTAAATCTAATAT
27888686 TAAGAT
65 TAAGAT
* ** ** * * *
27888692 A-ATCACTTTAATATTAAATTAATAAAATATTAT-T-AAGATAAGTATTAATTTTAATTTAATAT
1 ATATTA-AATAATATTAAATTAATAAAATATTATCTAAAGATAAACATTAAGTTAAATCTAATAT
27888754 TAA-AT
65 TAAGAT
27888759 ATATTAGAATAATATTA
1 ATATTA-AATAATATTA
27888776 TTTTTGAAAT
Statistics
Matches: 67, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
67 3 0.04
68 37 0.55
70 4 0.06
71 23 0.34
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.42
Consensus pattern (70 bp):
ATATTAAATAATATTAAATTAATAAAATATTATCTAAAGATAAACATTAAGTTAAATCTAATATT
AAGAT
Found at i:27888775 original size:37 final size:37
Alignment explanation
Indices: 27888699--27888785 Score: 90
Period size: 37 Copynumber: 2.3 Consensus size: 37
27888689 GATAATCACT
*
27888699 TTAATATTAAATTAATAAAATATTATTAAGATAAGTA
1 TTAATTTTAAATTAATAAAATATTATTAAGATAAGTA
*
27888736 TTAATTTTAATTTAATATTAAATA-TATT-AGAATAA-TA
1 TTAATTTTAAATTAATA--AAATATTATTAAG-ATAAGTA
*
27888773 TTATTTTTGAAAT
1 TTAATTTT-AAAT
27888786 AGTCAATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
37 26 0.62
38 11 0.26
39 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (37 bp):
TTAATTTTAAATTAATAAAATATTATTAAGATAAGTA
Found at i:27891078 original size:243 final size:240
Alignment explanation
Indices: 27890650--27891137 Score: 859
Period size: 243 Copynumber: 2.0 Consensus size: 240
27890640 TGTAGGGTAC
*
27890650 AACAAGTATGTAAGTGGTAAAAGTACTAGGGAAGGCCTTGTTCTTAGAGGAGGATCGCATTTCGG
1 AACAAGTATGTAAGTGGTAAAAGTACCAGGGAAGGCCTTGTTCTTAGAGGAGGATCGCATTTCGG
* *
27890715 CCCCTCTACTGAAAAAATGGGCAAATTAGCCGTTATACATTTCAAAACGTGCAAATTAGCATCTC
66 CCCCTCTACTGAAAAAATGGGCAAATTAGCCCTTATACATTTCAAAACGTGCAAATTAGCATATC
* *
27890780 TGTTAAATTTTATTTGTTAAATGATGGCGTGGAAGGTTAATTTAAATGATTAATTACTAATTTAG
131 TGTTAAATTTTATTTGTTAAATGATGGCGTGAAAGATTAATTTAAATGATTAATTACTAATTTAG
27890845 TCCCTGAACTATAATTAAAATATCATTTTGATTTTTTTTTAAATTATT
196 TCCCTGAACTATAATTAAAATATCATTTTGA---TTTTTTAAATTATT
* * *
27890893 AACAAGTATGTAAGTGGTAAAAGTACCAGGGAAGGCCTTGTTCTTAGAGGCGGATTGCATTTTGG
1 AACAAGTATGTAAGTGGTAAAAGTACCAGGGAAGGCCTTGTTCTTAGAGGAGGATCGCATTTCGG
*
27890958 CCCCTCTACTGAAAAAATGGGCAAATTAGCCCTTATACATTTCAAAACGTGCAAATTAGTATATC
66 CCCCTCTACTGAAAAAATGGGCAAATTAGCCCTTATACATTTCAAAACGTGCAAATTAGCATATC
*
27891023 TGTTAAATTTTATTTGTTAAATGATGGCGTGAAAGATTAATTTAAATGATTAATTACTAATTTAT
131 TGTTAAATTTTATTTGTTAAATGATGGCGTGAAAGATTAATTTAAATGATTAATTACTAATTTAG
27891088 TCCCTGAACTATAATTAAAATATCATTTTGATTTTTTAAATTATT
196 TCCCTGAACTATAATTAAAATATCATTTTGATTTTTTAAATTATT
27891133 AACAA
1 AACAA
27891138 TAATTCTAAA
Statistics
Matches: 235, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
240 19 0.08
243 216 0.92
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (240 bp):
AACAAGTATGTAAGTGGTAAAAGTACCAGGGAAGGCCTTGTTCTTAGAGGAGGATCGCATTTCGG
CCCCTCTACTGAAAAAATGGGCAAATTAGCCCTTATACATTTCAAAACGTGCAAATTAGCATATC
TGTTAAATTTTATTTGTTAAATGATGGCGTGAAAGATTAATTTAAATGATTAATTACTAATTTAG
TCCCTGAACTATAATTAAAATATCATTTTGATTTTTTAAATTATT
Found at i:27891194 original size:9 final size:9
Alignment explanation
Indices: 27891146--27891235 Score: 56
Period size: 9 Copynumber: 9.4 Consensus size: 9
27891136 AATAATTCTA
*
27891146 AAAAATTTT
1 AAAAATATT
*
27891155 AAAAATCTT
1 AAAAATATT
*
27891164 AAAAATAAAT
1 AAAAAT-ATT
*
27891174 ATAAATTATT
1 A-AAAATATT
27891184 AAAAATATT
1 AAAAATATT
*
27891193 AAGAATATT
1 AAAAATATT
*
27891202 AGAAATTATGTT
1 A-AAA--ATATT
27891214 AAAATATATT
1 AAAA-ATATT
*
27891224 TAAAA-ATT
1 AAAAATATT
27891232 AAAA
1 AAAA
27891236 TTATAAATGA
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
8 6 0.09
9 31 0.48
10 15 0.23
11 7 0.11
12 5 0.08
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (9 bp):
AAAAATATT
Found at i:27891194 original size:29 final size:28
Alignment explanation
Indices: 27891148--27891230 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
27891138 TAATTCTAAA
* *
27891148 AAATT-TTAAAAATCTTAAAAATAAATAT
1 AAATTATTAAAAATATTAAAAAT-AATAG
* *
27891176 AAATTATTAAAAATATTAAGAATATTAG
1 AAATTATTAAAAATATTAAAAATAATAG
27891204 AAATTATGTTAAAATATATTTAAAAAT
1 AAATTA--TTAAAA-ATA-TTAAAAAT
27891231 TAAAATTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 14 0.31
29 15 0.33
30 6 0.13
31 3 0.07
32 7 0.16
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (28 bp):
AAATTATTAAAAATATTAAAAATAATAG
Found at i:27891236 original size:29 final size:30
Alignment explanation
Indices: 27891182--27891239 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
27891172 ATATAAATTA
27891182 TTAAAAATATTAAGAATATTAGAAATTATG
1 TTAAAAATATTAAGAATATTAGAAATTATG
27891212 TTAAAATATATTTAA-AA-ATTA-AAATTAT
1 TTAAAA-ATA-TTAAGAATATTAGAAATTAT
27891240 AAATGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 7 0.27
30 10 0.38
31 5 0.19
32 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (30 bp):
TTAAAAATATTAAGAATATTAGAAATTATG
Found at i:27899499 original size:24 final size:24
Alignment explanation
Indices: 27899472--27899555 Score: 64
Period size: 24 Copynumber: 3.4 Consensus size: 24
27899462 TGAATAAAAA
27899472 TATTAAAATATATAATATTATATT
1 TATTAAAATATATAATATTATATT
**
27899496 TATTTTAATAT-TAATATTATTATTAT
1 TATTAAAATATATAATATTA-TA-T-T
* * *
27899522 TATTAAATTGTATAATTTTAATATT
1 TATTAAAATATATAATATT-ATATT
*
27899547 GA-TAAAATA
1 TATTAAAATA
27899556 AAATTATATA
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
23 8 0.18
24 16 0.36
25 3 0.07
26 9 0.20
27 8 0.18
28 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTAAAATATATAATATTATATT
Found at i:27900503 original size:20 final size:20
Alignment explanation
Indices: 27900465--27900504 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
27900455 AATTTTAAAA
***
27900465 TATTTTTAAAATGCTTTTTT
1 TATTTTTAAAATAAGTTTTT
27900485 TATTTTTAAAATAAGTTTTT
1 TATTTTTAAAATAAGTTTTT
27900505 GGTGTTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
TATTTTTAAAATAAGTTTTT
Found at i:27914106 original size:14 final size:15
Alignment explanation
Indices: 27914067--27914109 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
27914057 TATTTAACAC
27914067 ATATATATATA-TAT
1 ATATATATATATTAT
*
27914081 ATAAATAT-TATTAT
1 ATATATATATATTAT
27914095 ATAT-TATATATTAT
1 ATATATATATATTAT
27914109 A
1 A
27914110 AGCTCAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATATATATTAT
Found at i:27918293 original size:17 final size:17
Alignment explanation
Indices: 27918253--27918295 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
27918243 ATGGAATTAG
*
27918253 AATTGAATTGAAAAAATG
1 AATT-AATTGAAAAAATA
* *
27918271 ATTTAATTGAATAAATA
1 AATTAATTGAAAAAATA
27918288 AATTAATT
1 AATTAATT
27918296 TAAATAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (17 bp):
AATTAATTGAAAAAATA
Found at i:27926835 original size:36 final size:37
Alignment explanation
Indices: 27926788--27926865 Score: 140
Period size: 36 Copynumber: 2.1 Consensus size: 37
27926778 CTTTATTTTT
*
27926788 AAAATTAAAAAATATTTATTTGAAAATTATGTAAATA
1 AAAATTAAAAAATATTTATTTGAAAATTATATAAATA
27926825 AAAATT-AAAAATATTTATTTGAAAATTATATAAATA
1 AAAATTAAAAAATATTTATTTGAAAATTATATAAATA
27926861 AAAAT
1 AAAAT
27926866 GAATTTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 34 0.85
37 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (37 bp):
AAAATTAAAAAATATTTATTTGAAAATTATATAAATA
Found at i:27932763 original size:29 final size:29
Alignment explanation
Indices: 27932713--27932774 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
27932703 TTTTTTAAAG
* *
27932713 TTTTTTTAATATTGATCTTTTTATTATTC
1 TTTTTTTAATATTGATCTTTTTAGTATTA
27932742 TTTTTTTAAATATTG-T-TGTTTTAGTATTA
1 TTTTTTT-AATATTGATCT-TTTTAGTATTA
27932771 TTTT
1 TTTT
27932775 CTTGAATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 21 0.72
30 7 0.24
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.69
Consensus pattern (29 bp):
TTTTTTTAATATTGATCTTTTTAGTATTA
Found at i:27936210 original size:13 final size:11
Alignment explanation
Indices: 27936178--27936220 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
27936168 CTATTTTCTA
*
27936178 AATAAAATAAT
1 AATAAAATATT
27936189 AAT-AAATATTT
1 AATAAAATA-TT
27936200 AAGTAAAATATT
1 AA-TAAAATATT
27936212 AATAAAATA
1 AATAAAATA
27936221 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:27948580 original size:28 final size:28
Alignment explanation
Indices: 27948544--27948610 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
27948534 TTTCGTCTTC
* *
27948544 AAGATAGTCCTTGGCAAACTTTCCTCAT
1 AAGACAGTCCTTGGCAAACTTTCCACAT
*
27948572 AAGACAGTCCTTGGCAGACTTTCCACAT
1 AAGACAGTCCTTGGCAAACTTTCCACAT
27948600 AAGACAGTCCT
1 AAGACAGTCCT
27948611 CAGCGGACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (28 bp):
AAGACAGTCCTTGGCAAACTTTCCACAT
Found at i:27948619 original size:28 final size:28
Alignment explanation
Indices: 27948561--27948623 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
27948551 TCCTTGGCAA
* **
27948561 ACTTTCCTCATAAGACAGTCCTTGGCAG
1 ACTTTCCACATAAGACAGTCCTCAGCAG
*
27948589 ACTTTCCACATAAGACAGTCCTCAGCGG
1 ACTTTCCACATAAGACAGTCCTCAGCAG
27948617 ACTTTCC
1 ACTTTCC
27948624 CTGATTCTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ACTTTCCACATAAGACAGTCCTCAGCAG
Found at i:27957274 original size:54 final size:54
Alignment explanation
Indices: 27957163--27957354 Score: 277
Period size: 57 Copynumber: 3.6 Consensus size: 54
27957153 AGAAAATATG
* *
27957163 CTGCAAGAAAAGACAAGTGAACAGGAAATATTCGCTG---AC-G-AAATATTCC
1 CTGCAAGAAAAGACGAGTGAACAGGAAATATTCTCTGAAAACAGTAAATATTCC
*
27957212 CTGCAAGAAAAGACGAGTGAACAAGAAATATTCTCTGAAAACAGTAAATATTCC
1 CTGCAAGAAAAGACGAGTGAACAGGAAATATTCTCTGAAAACAGTAAATATTCC
* *
27957266 CTGGAAGAAAAGACGAGTGAACAGGAAATATTCTCTGATTAAAACAGTAAAAATTCC
1 CTGCAAGAAAAGACGAGTGAACAGGAAATATTCTCTG---AAAACAGTAAATATTCC
27957323 CTGCAAGAAAAGACGAGTGAACAGGAAATATT
1 CTGCAAGAAAAGACGAGTGAACAGGAAATATT
27957355 TTGTGTAATT
Statistics
Matches: 128, Mismatches: 7, Indels: 8
0.90 0.05 0.06
Matches are distributed among these distances:
49 34 0.27
52 2 0.02
53 1 0.01
54 44 0.34
57 47 0.37
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.19
Consensus pattern (54 bp):
CTGCAAGAAAAGACGAGTGAACAGGAAATATTCTCTGAAAACAGTAAATATTCC
Found at i:27959946 original size:13 final size:13
Alignment explanation
Indices: 27959928--27959968 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
27959918 AATACAACTT
27959928 AGAAAGAAAAGAA
1 AGAAAGAAAAGAA
*
27959941 AGAAAGAAAAATAA
1 AGAAAG-AAAAGAA
27959955 AG-AAGAAAAGAA
1 AGAAAGAAAAGAA
27959967 AG
1 AG
27959969 TCACGCTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.32
13 9 0.36
14 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (13 bp):
AGAAAGAAAAGAA
Found at i:27962066 original size:13 final size:13
Alignment explanation
Indices: 27962048--27962076 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27962038 GACACACGGG
27962048 CGTGTGACTTAGT
1 CGTGTGACTTAGT
27962061 CGTGTGACTTAGT
1 CGTGTGACTTAGT
27962074 CGT
1 CGT
27962077 ATAAGACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.17, G:0.31, T:0.38
Consensus pattern (13 bp):
CGTGTGACTTAGT
Found at i:27967578 original size:24 final size:26
Alignment explanation
Indices: 27967531--27967588 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 26
27967521 TGTAGCTACA
*
27967531 ATGTATTATTAGCATTATAAATTTCTC
1 ATGTATTATTAGCA-TATAAATTTATC
* *
27967558 ATGTATTATTAGC-T-TAGATTTATT
1 ATGTATTATTAGCATATAAATTTATC
27967582 ATGTATT
1 ATGTATT
27967589 TGTTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.50
25 1 0.04
27 13 0.46
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (26 bp):
ATGTATTATTAGCATATAAATTTATC
Found at i:27973619 original size:9 final size:9
Alignment explanation
Indices: 27973605--27973635 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
27973595 TAAGAACGAA
27973605 TCGAGTTAT
1 TCGAGTTAT
*
27973614 TCGAGTTAA
1 TCGAGTTAT
27973623 TCGAGTTAT
1 TCGAGTTAT
27973632 TCGA
1 TCGA
27973636 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:27973963 original size:30 final size:31
Alignment explanation
Indices: 27973929--27973988 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
27973919 AAACCTTTTA
*
27973929 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
27973959 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
27973989 TCCCACCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:27975632 original size:22 final size:22
Alignment explanation
Indices: 27975587--27975642 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
27975577 GACGGAAAGC
* * *
27975587 AAAAACAAGATAAAAACTTTAA
1 AAAAACAAGAGAAAAACCTAAA
*
27975609 AAAAACAAGAGAAAACCCTAAA
1 AAAAACAAGAGAAAAACCTAAA
**
27975631 AACTACAAGAGA
1 AAAAACAAGAGA
27975643 GCGTAGACAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.66, C:0.14, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAAACAAGAGAAAAACCTAAA
Found at i:27992997 original size:11 final size:12
Alignment explanation
Indices: 27992976--27993000 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27992966 TATAACTCTA
27992976 TTTCTTTTTTTT
1 TTTCTTTTTTTT
27992988 TTTCTTTTTTTT
1 TTTCTTTTTTTT
27993000 T
1 T
27993001 CTGTATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:27994774 original size:12 final size:12
Alignment explanation
Indices: 27994757--27994784 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
27994747 TATATGATCT
27994757 TCATACTTGAGA
1 TCATACTTGAGA
27994769 TCATACTTGAGA
1 TCATACTTGAGA
27994781 TCAT
1 TCAT
27994785 CATTGTCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (12 bp):
TCATACTTGAGA
Found at i:27995600 original size:138 final size:139
Alignment explanation
Indices: 27995434--27995718 Score: 491
Period size: 139 Copynumber: 2.1 Consensus size: 139
27995424 GAGAACATAG
*
27995434 ATATAATTAATATATGATTTTGATTCATACAAAATATTAATTGTATATATTTTACCGAA-TTTAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTTAT
* * *
27995498 TAATATAAAAAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAGTATTCTT
66 TAATATAAAAAGTTATATTAATTAATCTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTT
27995563 TTGAAAAGA
131 TTGAAAAGA
*
27995572 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTTGT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTTAT
* *
27995637 TAATATAAATAGTTATATTAATTAATCTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
66 TAATATAAAAAGTTATATTAATTAATCTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTT
*
27995702 TTGGAAAGA
131 TTGAAAAGA
27995711 ATATAATT
1 ATATAATT
27995719 TCTTTTTCTA
Statistics
Matches: 138, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
138 58 0.42
139 80 0.58
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (139 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTTAT
TAATATAAAAAGTTATATTAATTAATCTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTT
TTGAAAAGA
Found at i:27995787 original size:75 final size:75
Alignment explanation
Indices: 27995694--27995843 Score: 250
Period size: 75 Copynumber: 2.0 Consensus size: 75
27995684 ATGGAAATTA
* *
27995694 ATATTCTTTTGGAAAGAATATAATT-TCTTTTTCTA-ACTTTCCATTTGTCTTCTTTATTAATAA
1 ATATTCTTTTGGAAAGAATATAATTCT-TTTTTC-AGACTTTCCATTTGCCTTCTCTATTAATAA
27995757 GGGAATAATCCT
64 GGGAATAATCCT
27995769 ATATTCTTTTGGAAAGAATATAATTCTTTTTTCAGACTTTCCATTTGCCTTCTCTATTAATAAGG
1 ATATTCTTTTGGAAAGAATATAATTCTTTTTTCAGACTTTCCATTTGCCTTCTCTATTAATAAGG
27995834 GAATAATCCT
66 GAATAATCCT
27995844 GGTTTTCCTT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
74 1 0.01
75 69 0.97
76 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATATAATTCTTTTTTCAGACTTTCCATTTGCCTTCTCTATTAATAAGG
GAATAATCCT
Found at i:28000576 original size:2 final size:2
Alignment explanation
Indices: 28000565--28000603 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
28000555 TAAATATTAT
28000565 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28000604 ATAAGAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28000666 original size:7 final size:7
Alignment explanation
Indices: 28000654--28000680 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28000644 CCTTACTTAC
28000654 TTTACCT
1 TTTACCT
28000661 TTTACCT
1 TTTACCT
28000668 TTTACCT
1 TTTACCT
28000675 TTTACC
1 TTTACC
28000681 GTTNNNNNNN
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTACCT
Found at i:28001190 original size:17 final size:17
Alignment explanation
Indices: 28001168--28001201 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28001158 ATATATGATT
28001168 AATTGAAGATGA-AATGA
1 AATTGAA-ATGAGAATGA
28001185 AATTGAAATGAGAATGA
1 AATTGAAATGAGAATGA
28001202 TATGAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
AATTGAAATGAGAATGA
Found at i:28003080 original size:16 final size:16
Alignment explanation
Indices: 28003059--28003091 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28003049 GAGGGCTGAT
28003059 TAAGGATGGAAATGAA
1 TAAGGATGGAAATGAA
28003075 TAAGGATGGAAATGAA
1 TAAGGATGGAAATGAA
28003091 T
1 T
28003092 TTGACACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.21
Consensus pattern (16 bp):
TAAGGATGGAAATGAA
Found at i:28004743 original size:10 final size:10
Alignment explanation
Indices: 28004725--28004754 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28004715 ATCTAGGCAA
28004725 TGGTATGTTT
1 TGGTATGTTT
*
28004735 TGTTATGTTT
1 TGGTATGTTT
28004745 TGGTATGTTT
1 TGGTATGTTT
28004755 GAGTAAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.27, T:0.63
Consensus pattern (10 bp):
TGGTATGTTT
Found at i:28015018 original size:10 final size:10
Alignment explanation
Indices: 28015000--28015029 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28014990 ATCTAGGAAA
28015000 TGGTATGTTT
1 TGGTATGTTT
*
28015010 TGTTATGTTT
1 TGGTATGTTT
28015020 TGGTATGTTT
1 TGGTATGTTT
28015030 GAGCAAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.27, T:0.63
Consensus pattern (10 bp):
TGGTATGTTT
Found at i:28018112 original size:27 final size:26
Alignment explanation
Indices: 28018032--28018256 Score: 256
Period size: 27 Copynumber: 8.5 Consensus size: 26
28018022 TATAACAGTT
*
28018032 ATTTTACCCTATGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGTATTTCGATC
* *
28018058 ATTTTACCCTATGGGGTATTTTGGTC
1 ATTTTACCCTATGGGGTATTTCGATC
*
28018084 ATTTTACCTTATGGGGGTATTTCGATC
1 ATTTTACCCTAT-GGGGTATTTCGATC
* * *
28018111 ATTTTACCCTATAAGAGTATTT-TAGTC
1 ATTTTACCCTAT-GGGGTATTTCGA-TC
28018138 ATTTTACCCTATGGGGGTATTTC-AGTC
1 ATTTTACCCTAT-GGGGTATTTCGA-TC
** * *
28018165 ATTTTACCCTATAAAGATATTTCAATC
1 ATTTTACCCTAT-GGGGTATTTCGATC
28018192 ATTTTACCCTATTGGGGTATTTCGATC
1 ATTTTACCCTA-TGGGGTATTTCGATC
* *
28018219 ATTTTATCCTACGGGGTATTTCGATC
1 ATTTTACCCTATGGGGTATTTCGATC
28018245 ATTTTACCCTAT
1 ATTTTACCCTAT
28018257 TTTAGGGTCT
Statistics
Matches: 170, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
26 61 0.36
27 107 0.63
28 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.44
Consensus pattern (26 bp):
ATTTTACCCTATGGGGTATTTCGATC
Found at i:28022096 original size:17 final size:18
Alignment explanation
Indices: 28022066--28022106 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
28022056 TAAATTAAAT
28022066 ATAATATTAAATTTATTA-A
1 ATAATATT-AATTT-TTAGA
28022085 ATAATATT-ATTTTTAGA
1 ATAATATTAATTTTTAGA
28022102 ATAAT
1 ATAAT
28022107 TAACTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.14
17 10 0.48
19 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATAATATTAATTTTTAGA
Found at i:28024664 original size:12 final size:13
Alignment explanation
Indices: 28024640--28024668 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28024630 GGGCTATAAC
28024640 TATTGCATTTATT
1 TATTGCATTTATT
28024653 TATTGC-TTTATT
1 TATTGCATTTATT
28024665 TATT
1 TATT
28024669 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:28030648 original size:23 final size:23
Alignment explanation
Indices: 28030618--28030664 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
28030608 TCCGTTTATT
28030618 GTCAACTGGGTGGATTGTGTAGA
1 GTCAACTGGGTGGATTGTGTAGA
28030641 GTCAACTGGGTGGATTGTGTAGA
1 GTCAACTGGGTGGATTGTGTAGA
28030664 G
1 G
28030665 GCCGGAGTCA
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:0.21, C:0.09, G:0.40, T:0.30
Consensus pattern (23 bp):
GTCAACTGGGTGGATTGTGTAGA
Found at i:28033231 original size:42 final size:43
Alignment explanation
Indices: 28033124--28033239 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 43
28033114 CTCATACAAT
* * * *
28033124 GCCAACGTCCTAGACGTGGTCTTACATGTAATCAAATAACGAT
1 GCCAATGTCCTAGACATGGTCTTACACGTAATCAAATAACGAA
* * * *
28033167 GTCACTGTCCTAGACAGGGTCTTACACGTAATCATAT-ACGAA
1 GCCAATGTCCTAGACATGGTCTTACACGTAATCAAATAACGAA
*
28033209 GCCAATGTCCCAGACATGGTCTTACACGTAA
1 GCCAATGTCCTAGACATGGTCTTACACGTAA
28033240 ATCTCAAATC
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
42 31 0.51
43 30 0.49
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (43 bp):
GCCAATGTCCTAGACATGGTCTTACACGTAATCAAATAACGAA
Found at i:28039097 original size:43 final size:42
Alignment explanation
Indices: 28039047--28039168 Score: 147
Period size: 43 Copynumber: 2.9 Consensus size: 42
28039037 GAGGTGTGGT
*
28039047 TTCGTGTAAGACCATGTCTGGAACATTGGCATCGATATAAGA
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATAAGA
* * *
28039089 TTGCGTGTAAGACCATGTTTGGGACATTGGCACCG-TATATGA
1 TT-CGTGTAAGACCATGTCTGGGACATTGGCATCGATATAAGA
* * * **
28039131 TTCATGTAAGACCCTATCTGGGACAGAGGCATCGATAT
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGATAT
28039169 GTGATAACAT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 25 0.37
42 13 0.19
43 29 0.43
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (42 bp):
TTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATAAGA
Found at i:28039153 original size:41 final size:42
Alignment explanation
Indices: 28039051--28039204 Score: 141
Period size: 43 Copynumber: 3.7 Consensus size: 42
28039041 TGTGGTTTCG
* * * * *
28039051 TGTAAGACCATGTCTGGAACATTGGCATCGATATAAGATTGCG
1 TGTAAGACCATATCTGGGACATTGGCACCGATATATGATT-CA
* *
28039094 TGTAAGACCATGTTTGGGACATTGGCACCG-TATATGATTCA
1 TGTAAGACCATATCTGGGACATTGGCACCGATATATGATTCA
* ** * * *
28039135 TGTAAGACCCTATCTGGGACAGAGGCATCGATATGTGATAACA
1 TGTAAGACCATATCTGGGACATTGGCACCGATATATGAT-TCA
* *
28039178 TGTAAGACCATATATGGGATA-TGGCAC
1 TGTAAGACCATATCTGGGACATTGGCAC
28039205 TGTATGTGAT
Statistics
Matches: 91, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
41 25 0.27
42 19 0.21
43 47 0.52
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGACATTGGCACCGATATATGATTCA
Found at i:28040799 original size:27 final size:27
Alignment explanation
Indices: 28040761--28040817 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
28040751 TTTATTTATC
28040761 GTTCAAGTACATAGAAAACAATTACAT
1 GTTCAAGTACATAGAAAACAATTACAT
28040788 GTTCAAGTACATAGAAAACAATTACAT
1 GTTCAAGTACATAGAAAACAATTACAT
28040815 GTT
1 GTT
28040818 TACTATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (27 bp):
GTTCAAGTACATAGAAAACAATTACAT
Found at i:28044495 original size:17 final size:17
Alignment explanation
Indices: 28044470--28044502 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28044460 GCAATGGTAA
*
28044470 TTCGTTATTTTTAATTT
1 TTCGATATTTTTAATTT
28044487 TTCGATATTTTTAATT
1 TTCGATATTTTTAATT
28044503 ATGTTACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TTCGATATTTTTAATTT
Found at i:28049064 original size:22 final size:24
Alignment explanation
Indices: 28049039--28049088 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
28049029 CACCTATTGG
28049039 ATAATTTA-C-AAT-TAATATACAA
1 ATAATTTATCAAATATAATATA-AA
28049061 ATAA-TTATCAAATATAATATAAA
1 ATAATTTATCAAATATAATATAAA
28049084 ATAAT
1 ATAAT
28049089 CTTAAAGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 9 0.38
24 7 0.29
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAATTTATCAAATATAATATAAA
Found at i:28050498 original size:31 final size:31
Alignment explanation
Indices: 28050444--28050801 Score: 530
Period size: 31 Copynumber: 11.7 Consensus size: 31
28050434 ATCTAATGCT
*
28050444 CAAATC-AATTCGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
28050474 CGAATCAAATTTGACAATGTATAT-C-TATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
28050503 CAAATC-AATTCGGCAATGAATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
28050533 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
28050564 CAAATC-AACTCGGCAATGTATATTCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
28050594 CAAATCAAATTCGGCAATGTATATTCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
28050625 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
28050656 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
28050686 CAAATCAAATTCGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
28050717 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
28050748 CAAATCAAATTCGGCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
28050779 CAATTCAAATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
28050802 GAACATATAC
Statistics
Matches: 298, Mismatches: 24, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
28 14 0.05
29 10 0.03
30 72 0.24
31 202 0.68
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.29
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATATA
Found at i:28050592 original size:61 final size:62
Alignment explanation
Indices: 28050444--28050812 Score: 525
Period size: 61 Copynumber: 6.0 Consensus size: 62
28050434 ATCTAATGCT
* * * * *
28050444 CAAATC-AATTCGGCAATATATATCCATATACGAATCAAATTTGACAATGTAT-ATC-TATA
1 CAAATCAAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
*
28050503 CAAATC-AATTCGGCAATGAATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* * **
28050564 CAAATC-AACTCGGCAATGTATATTCATATACAAATCAAATTCGGCAATGTATATTCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* *
28050625 CAAATCAAATTCGGCAATGTATAACCATATACAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* *
28050686 CAAATCAAATTCGACAATGTATAACCATATACAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* * * *
28050748 CAAATCAAATTCGGCAATGTATATCTATAAACAATTCAAATTCGGCAATGTATAGAACATATA
1 CAAATCAAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATA-ACCATATA
28050811 CA
1 CA
28050813 TTTAAATTCA
Statistics
Matches: 282, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
59 47 0.17
60 2 0.01
61 125 0.44
62 99 0.35
63 9 0.03
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.28
Consensus pattern (62 bp):
CAAATCAAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
Found at i:28050631 original size:92 final size:92
Alignment explanation
Indices: 28050444--28050801 Score: 546
Period size: 92 Copynumber: 3.9 Consensus size: 92
28050434 ATCTAATGCT
* * * * *
28050444 CAAATC-AATTCGGCAATATATATCCATATACGAATCAAATTTGACAATGTATATC-TATACAAA
1 CAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCATATACAAA
*
28050507 TC-AATTCGGCAATGAATATCCATATA
66 TCAAATTCGGCAATGTATATCCATATA
*
28050533 CAAATCAAATTCGGCAATGTATAACCATATACAAATC-AACTCGGCAATGTATATTCATATACAA
1 CAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATA-TCATATACAA
*
28050597 ATCAAATTCGGCAATGTATATTCATATA
65 ATCAAATTCGGCAATGTATATCCATATA
28050625 CAAATCAAATTCGGCAATGTATAACCATATACAAATC-AATTCGGCAATGTATATCCATATACAA
1 CAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATAT-CATATACAA
* *
28050689 ATCAAATTCGACAATGTATAACCATATA
65 ATCAAATTCGGCAATGTATATCCATATA
*
28050717 CAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATAAACAA
1 CAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATC-ATATACAA
*
28050782 TTCAAATTCGGCAATGTATA
65 ATCAAATTCGGCAATGTATA
28050802 GAACATATAC
Statistics
Matches: 247, Mismatches: 15, Indels: 10
0.91 0.06 0.04
Matches are distributed among these distances:
89 19 0.08
90 29 0.12
91 11 0.04
92 146 0.59
93 42 0.17
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.29
Consensus pattern (92 bp):
CAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCATATACAAA
TCAAATTCGGCAATGTATATCCATATA
Found at i:28058115 original size:31 final size:31
Alignment explanation
Indices: 28058073--28058493 Score: 593
Period size: 31 Copynumber: 13.7 Consensus size: 31
28058063 ATACAATGCT
*
28058073 CAAATC-AATTCGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
28058103 CGAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
28058134 CAAATC-AATTCAGCAATGAATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
28058164 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
28058195 TAAATC-AATTCTGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
28058225 CAAATAAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
28058256 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
28058286 CAAATCAAATTCAGCAATTTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
28058317 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
28058347 CAAATCAAATTCGGCAATGTATAACCATAAA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
28058378 CAAATCAAATTAGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
** *
28058409 CAAATCAAATTCAACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
28058440 CAAATCAAATTCGGCAATGTATATCTATA-A
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
28058470 AAAATTCAAATTCGGCAATGTATA
1 CAAA-TCAAATTCGGCAATGTATA
28058494 AAACATATAC
Statistics
Matches: 348, Mismatches: 37, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
30 118 0.34
31 230 0.66
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.29
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATATA
Found at i:28058170 original size:61 final size:61
Alignment explanation
Indices: 28058073--28058504 Score: 650
Period size: 61 Copynumber: 7.0 Consensus size: 61
28058063 ATACAATGCT
* * * *
28058073 CAAATCAATTCGGCAATATATATCCATATACGAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* *
28058134 CAAATCAATTCAGCAATGAATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* * *
28058195 TAAATCAATTCTGCAATGTATATCCATATACAAATAAAATTCGGCAATGTATAACCATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* *
28058256 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCAGCAATTTATAACCATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
*
28058317 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATAAA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* * **
28058378 CAAATCAAATTAGGCAATGTATAACCATATACAAATCAAATTCAACAATGTATAACCATATA
1 CAAATC-AATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* * *
28058440 CAAATCAAATTCGGCAATGTATATCTATA-AAAAATTCAAATTCGGCAATGTATAAAACATATA
1 CAAATC-AATTCGGCAATGTATATCCATATACAAA-TCAAATTCGGCAATGTAT-AACCATATA
28058503 CA
1 CA
28058505 TTTAAATTCA
Statistics
Matches: 338, Mismatches: 30, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
61 236 0.70
62 92 0.27
63 10 0.03
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.28
Consensus pattern (61 bp):
CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
Found at i:28060842 original size:41 final size:42
Alignment explanation
Indices: 28060735--28060897 Score: 130
Period size: 42 Copynumber: 3.8 Consensus size: 42
28060725 AATGTGATAT
** * * * * *
28060735 CGTGTAAGACCACCTCTGAGACGTTGGCATCGATTTAAGATTTA
1 CGTGTAAGACCATGTCTGGGACATTGGCGTCG-TATATGA-TTA
* *
28060779 TGTGTAAGACCATGTCTTGGACATTGGCGTCGTATATGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCGTCGTATATGATTA
* ** *
28060821 CGTGTAAGACC-TGTCTGGGACAATGGTATCGTTATTTGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCGTCG-TATATGATTA
* * * * *
28060863 CATGTAAGACCACGTCTGAGACGTTGGCGTTGTAT
1 CGTGTAAGACCATGTCTGGGACATTGGCGTCGTAT
28060898 GAGCTTTTGA
Statistics
Matches: 94, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
41 16 0.17
42 35 0.37
43 18 0.19
44 25 0.27
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACATTGGCGTCGTATATGATTA
Found at i:28065300 original size:2 final size:2
Alignment explanation
Indices: 28065293--28065340 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
28065283 TTATTTAGCC
28065293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28065335 TA TA TA
1 TA TA TA
28065341 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.