Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 114 of 240
Found at i:35479564 original size:44 final size:45
Alignment explanation
Indices: 35479364--35479615 Score: 231
Period size: 43 Copynumber: 5.8 Consensus size: 45
35479354 ATCACATACA
* * * **
35479364 ATGCC-ATATCACAGATATGGCCTTACATGTTATCAC--ATATCG
1 ATGCCAATATCCCAGATATGGTCTTACACGAAATCACATATATCG
* * *
35479406 ATGCCAATAGCCCAGCTATGGTCTTACATG-AAT--CATATATCG
1 ATGCCAATATCCCAGATATGGTCTTACACGAAATCACATATATCG
* *
35479448 ATGCCAAATGTCCCAGACATGGTCTTACACGAAATCACATA-A-CG
1 ATGCC-AATATCCCAGATATGGTCTTACACGAAATCACATATATCG
* * * *
35479492 ATGCCAATGTCCTAGACATGGTCTTACACGTAATCACATATATCG
1 ATGCCAATATCCCAGATATGGTCTTACACGAAATCACATATATCG
* *
35479537 ATGCC-ATATCCCATATATGGTCTTACAC-AAAGTCTCATATATCG
1 ATGCCAATATCCCAGATATGGTCTTACACGAAA-TCACATATATCG
* *
35479581 ATGCC-ATAGCCCA-ACTATGGTCTTATACGAAATCA
1 ATGCCAATATCCCAGA-TATGGTCTTACACGAAATCA
35479616 TGTAATGCCA
Statistics
Matches: 177, Mismatches: 21, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
40 1 0.01
42 18 0.10
43 76 0.43
44 67 0.38
45 11 0.06
46 4 0.02
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (45 bp):
ATGCCAATATCCCAGATATGGTCTTACACGAAATCACATATATCG
Found at i:35480535 original size:9 final size:9
Alignment explanation
Indices: 35480515--35480546 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
35480505 TTTACTTATT
35480515 TAACCTTTAA
1 TAACC-TTAA
35480525 TAACCTTAA
1 TAACCTTAA
35480534 TAACCTTAA
1 TAACCTTAA
35480543 TAAC
1 TAAC
35480547 TACACCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (9 bp):
TAACCTTAA
Found at i:35482303 original size:23 final size:23
Alignment explanation
Indices: 35482276--35482327 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
35482266 CAGAAAAGCG
*
35482276 CTGTAATATCCCGAAAATTACTA
1 CTGTAATACCCCGAAAATTACTA
*
35482299 CTGTAGTACCCCGAAAATTACTA
1 CTGTAATACCCCGAAAATTACTA
*
35482322 CAGTAA
1 CTGTAA
35482328 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (23 bp):
CTGTAATACCCCGAAAATTACTA
Found at i:35485085 original size:32 final size:32
Alignment explanation
Indices: 35485024--35485086 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
35485014 TTCAAAATTT
* *
35485024 TAATATTATTTAATATTTTTATTTCATTTTTG
1 TAATATTAATTAATATTTTTATTTAATTTTTG
*
35485056 TAAT-TTAATTAATATTTTTTTTATAATTTTT
1 TAATATTAATTAATATTTTTATT-TAATTTTT
35485087 TATAACAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (32 bp):
TAATATTAATTAATATTTTTATTTAATTTTTG
Found at i:35497273 original size:29 final size:30
Alignment explanation
Indices: 35497205--35497277 Score: 112
Period size: 29 Copynumber: 2.4 Consensus size: 30
35497195 AAAAAAATAG
* *
35497205 ACCCTAAACCCTAATTTATTTATTTTAAAAA
1 ACCCT-AACCCTAAATTATTTATTTCAAAAA
35497236 ACCCTAACCCTAAATTATTT-TTTCAAAAA
1 ACCCTAACCCTAAATTATTTATTTCAAAAA
35497265 ACCCTAACCCTAA
1 ACCCTAACCCTAA
35497278 CCCTAAGCCC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 21 0.52
30 14 0.35
31 5 0.12
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.33
Consensus pattern (30 bp):
ACCCTAACCCTAAATTATTTATTTCAAAAA
Found at i:35500250 original size:13 final size:12
Alignment explanation
Indices: 35500225--35500258 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
35500215 GGTTTCTATG
*
35500225 TCATTTTCAATT
1 TCATTTTCCATT
35500237 TCATCTTTCCATT
1 TCAT-TTTCCATT
35500250 TCATTTTCC
1 TCATTTTCC
35500259 CCTATTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (12 bp):
TCATTTTCCATT
Found at i:35504560 original size:102 final size:102
Alignment explanation
Indices: 35504382--35504588 Score: 387
Period size: 102 Copynumber: 2.0 Consensus size: 102
35504372 GTGCCTCTGA
35504382 TTGTTAATGTTTGAATTAAATTATCAAAGCCCGATTGAGAGTAGTAAATGGTTAGGATACAATTG
1 TTGTTAATGTTTGAATTAAATTATCAAAGCCCGATTGAGAGTAGTAAATGGTTAGGATACAATTG
*
35504447 GCATGCCAATAGAGTTTGTACGCGTGCTTGTACAAGT
66 GCATGCCAATAGAGTTTGTACGCATGCTTGTACAAGT
*
35504484 TTGTTAATGTTTGAATTAAATTATCAAAGCCCGATTGAGCGTAGTAAATGGTTAGGATACAATTG
1 TTGTTAATGTTTGAATTAAATTATCAAAGCCCGATTGAGAGTAGTAAATGGTTAGGATACAATTG
*
35504549 GCATGCTAATAGAGTTTGTACGCATGCTTGTACAAGT
66 GCATGCCAATAGAGTTTGTACGCATGCTTGTACAAGT
35504586 TTG
1 TTG
35504589 CACGTCGGTG
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (102 bp):
TTGTTAATGTTTGAATTAAATTATCAAAGCCCGATTGAGAGTAGTAAATGGTTAGGATACAATTG
GCATGCCAATAGAGTTTGTACGCATGCTTGTACAAGT
Found at i:35505064 original size:13 final size:13
Alignment explanation
Indices: 35505039--35505082 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
35505029 AAATGGTAAG
35505039 ATGAAATGATTAT
1 ATGAAATGATTAT
*
35505052 ATGAAATGCTTAT
1 ATGAAATGATTAT
35505065 ATGGAAAT-A-TAT
1 AT-GAAATGATTAT
35505077 ATGAAA
1 ATGAAA
35505083 CGGTTGTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.14
12 5 0.18
13 14 0.50
14 5 0.18
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (13 bp):
ATGAAATGATTAT
Found at i:35509170 original size:27 final size:27
Alignment explanation
Indices: 35509115--35509179 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
35509105 ATAAAAAATA
35509115 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAAC-TTTTTTTATTT
35509143 ACCAAAATATTATATA-TTTTTTTATTT
1 ACCAAAATATTATA-ACTTTTTTTATTT
35509170 ACCAAAATAT
1 ACCAAAATAT
35509180 ACCAAAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 21 0.58
28 14 0.39
29 1 0.03
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (27 bp):
ACCAAAATATTATAACTTTTTTTATTT
Found at i:35509627 original size:19 final size:19
Alignment explanation
Indices: 35509603--35509666 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
35509593 ATTAAAATAG
*
35509603 TTTAATTTAATAACTCTGT
1 TTTAATTTAATAACTCTAT
* *
35509622 TTTAATGTAATAAAT-TAT
1 TTTAATTTAATAACTCTAT
* *
35509640 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
35509659 TTTAATTT
1 TTTAATTT
35509667 TAAAAAATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 13 0.37
19 22 0.63
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:35509783 original size:78 final size:81
Alignment explanation
Indices: 35509680--35509899 Score: 264
Period size: 82 Copynumber: 2.8 Consensus size: 81
35509670 AAAATTAAAT
*
35509680 TAAACTATTTTA-AT-TTTATAAATTTAATATATTCCCTTAACTA-A--TATTAA-ATCAAA-A-
1 TAAACTATTTTATCTATTTATAAATTTAATATATT-CCTTAA-TAGACTTA-TAACAT-AAACAT
35509737 G-GAAAAAATAACGGAAACA
62 GTGAAAAAATAACGGAAACA
35509756 TAAACTATTTTATCTATTTATAAATTTAATATATT-CTTAATAGACTTATAACATAAACATGTTA
1 TAAACTATTTTATCTATTTATAAATTTAATATATTCCTTAATAGACTTATAACATAAACATG-T-
** * *
35509820 GACTAACTAATGGAAACA
64 GAAAAAATAACGGAAACA
35509838 TAAACTATTTTATCTATTTATAAATTTAATATATT-CTTAATAGACTTATAACATAAACATGT
1 TAAACTATTTTATCTATTTATAAATTTAATATATTCCTTAATAGACTTATAACATAAACATGT
35509900 TAGACTATTT
Statistics
Matches: 128, Mismatches: 5, Indels: 17
0.85 0.03 0.11
Matches are distributed among these distances:
75 2 0.02
76 18 0.14
77 7 0.05
78 24 0.19
79 1 0.01
81 1 0.01
82 75 0.59
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.39
Consensus pattern (81 bp):
TAAACTATTTTATCTATTTATAAATTTAATATATTCCTTAATAGACTTATAACATAAACATGTGA
AAAAATAACGGAAACA
Found at i:35509850 original size:82 final size:82
Alignment explanation
Indices: 35509749--35509906 Score: 316
Period size: 82 Copynumber: 1.9 Consensus size: 82
35509739 AAAAAATAAC
35509749 GGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAACATAAAC
1 GGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAACATAAAC
35509814 ATGTTAGACTAACTAAT
66 ATGTTAGACTAACTAAT
35509831 GGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAACATAAAC
1 GGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAACATAAAC
35509896 ATGTTAGACTA
66 ATGTTAGACTA
35509907 TTTTAATTAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (82 bp):
GGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAACATAAAC
ATGTTAGACTAACTAAT
Found at i:35510014 original size:18 final size:19
Alignment explanation
Indices: 35509975--35510070 Score: 124
Period size: 19 Copynumber: 5.2 Consensus size: 19
35509965 ATTTTATATT
35509975 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
35509994 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
35510012 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
35510031 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
35510049 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
35510068 TTA
1 TTA
35510071 CTTAATTAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 30 0.47
19 34 0.53
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:35510016 original size:37 final size:37
Alignment explanation
Indices: 35509975--35510070 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
35509965 ATTTTATATT
*
35509975 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
35510012 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
35510049 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
35510071 CTTAATTAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:35510802 original size:26 final size:27
Alignment explanation
Indices: 35510750--35510811 Score: 108
Period size: 28 Copynumber: 2.3 Consensus size: 27
35510740 TTTTTTTTGT
35510750 ATATTTTGATAAATAAAAAAATTTTATA
1 ATATTTTGATAAATAAAAAAA-TTTATA
35510778 ATATTTTGATAAATAAAAAAA-TTATA
1 ATATTTTGATAAATAAAAAAATTTATA
35510804 ATATTTTG
1 ATATTTTG
35510812 GTTATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 13 0.38
28 21 0.62
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (27 bp):
ATATTTTGATAAATAAAAAAATTTATA
Found at i:35515077 original size:28 final size:28
Alignment explanation
Indices: 35515023--35515077 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
35515013 TATTAAACTA
* * *
35515023 ATTATAGTTTGAATATTAATATCAATAT
1 ATTATAATTTAAATAATAATATCAATAT
* *
35515051 ATTATAATTTAAATAATATTATTAATA
1 ATTATAATTTAAATAATAATATCAATA
35515078 ATTTCTTATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (28 bp):
ATTATAATTTAAATAATAATATCAATAT
Found at i:35521610 original size:3 final size:3
Alignment explanation
Indices: 35521602--35521641 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
35521592 GTACTTACGC
* *
35521602 TAA TAA TAA TAGA CAA TAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
35521642 ATTAATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 30 0.94
4 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:35522342 original size:13 final size:13
Alignment explanation
Indices: 35522324--35522350 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35522314 TTTTTCTGTA
35522324 TCAAATCAGTGTT
1 TCAAATCAGTGTT
35522337 TCAAATCAGTGTT
1 TCAAATCAGTGTT
35522350 T
1 T
35522351 TTTTTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TCAAATCAGTGTT
Found at i:35522869 original size:23 final size:23
Alignment explanation
Indices: 35522843--35522886 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
35522833 TGTAAATTTT
35522843 CAAAATTCCACCATATTGAATTC
1 CAAAATTCCACCATATTGAATTC
35522866 CAAAATTCCACCATATTGAAT
1 CAAAATTCCACCATATTGAAT
35522887 GCCTATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.30
Consensus pattern (23 bp):
CAAAATTCCACCATATTGAATTC
Found at i:35523256 original size:22 final size:22
Alignment explanation
Indices: 35523223--35523286 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
35523213 TATCTAATAT
* *
35523223 TTTAAATATAAATATTTATTTTA
1 TTTATATATAAATATTT-GTTTA
35523246 TTT-TATATAAATATTTGTTTA
1 TTTATATATAAATATTTGTTTA
* *
35523267 TTTATATTTATATATTTGTT
1 TTTATATATAAATATTTGTT
35523287 CGCTAACGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 7 0.19
22 26 0.72
23 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (22 bp):
TTTATATATAAATATTTGTTTA
Found at i:35528484 original size:13 final size:13
Alignment explanation
Indices: 35528466--35528490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35528456 GAATTAATAT
35528466 GTGTGAAAATTTC
1 GTGTGAAAATTTC
35528479 GTGTGAAAATTT
1 GTGTGAAAATTT
35528491 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:35529602 original size:42 final size:43
Alignment explanation
Indices: 35529488--35529650 Score: 156
Period size: 43 Copynumber: 3.8 Consensus size: 43
35529478 ATAGGATTCT
* * *
35529488 GATATGTGATTTCGTGTAAGACCAC-GTCTGGGACGTTGGCATC
1 GATATGAGATTTCGTGTAAGACC-CTGTCTGGGACATCGGCATC
* *
35529531 GATTTGAGATTTACGTGTAAGACCGTGTCTGGGACATCGGCATC
1 GATATGAGATTT-CGTGTAAGACCCTGTCTGGGACATCGGCATC
*
35529575 G-TAT-ACGATTTCGTGTAAGACCCTGTCTGGGACAGT-GGTATC
1 GATATGA-GATTTCGTGTAAGACCCTGTCTGGGACA-TCGGCATC
** * *
35529617 GATATTTGATTAT-ATGTAAGACCATGTCTGGGAC
1 GATATGAGATT-TCGTGTAAGACCCTGTCTGGGAC
35529651 GTTGGCATTG
Statistics
Matches: 102, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
42 29 0.28
43 44 0.43
44 29 0.28
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (43 bp):
GATATGAGATTTCGTGTAAGACCCTGTCTGGGACATCGGCATC
Found at i:35535408 original size:40 final size:40
Alignment explanation
Indices: 35535360--35535560 Score: 287
Period size: 40 Copynumber: 5.0 Consensus size: 40
35535350 AACACACTAG
* * * *
35535360 ACAGAAGCTCATAAAAGCT-AGTCCAACCGAAACACACCAG
1 ACAGAAGCTCATAAGAGTTGA-TCCAACCGAAACACGCCAA
* *
35535400 ACAAAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAA
1 ACAGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAA
* * *
35535440 GCAGAAGCTCATAAGATTTGATCCAATCGAAACACGCCAA
1 ACAGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAA
* *
35535480 ATAGAAGCTCATAAGAGTTGATCCAACAGAAACACGCCAA
1 ACAGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAA
35535520 ACAGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAA
1 ACAGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAA
35535560 A
1 A
35535561 TAGATAATAT
Statistics
Matches: 144, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 143 0.99
41 1 0.01
ACGTcount: A:0.44, C:0.27, G:0.16, T:0.13
Consensus pattern (40 bp):
ACAGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAA
Found at i:35536007 original size:19 final size:20
Alignment explanation
Indices: 35535952--35536018 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
35535942 CAGTAAAATG
35535952 TTTTCTGGAAAATGATTTAC
1 TTTTCTGGAAAATGATTTAC
*
35535972 TTTTTTGGAAAATGATTTAC
1 TTTTCTGGAAAATGATTTAC
*
35535992 TTTTCTGG-AAACGATTTAC
1 TTTTCTGGAAAATGATTTAC
35536011 TTTTCTGG
1 TTTTCTGG
35536019 TGTTTGGATG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 18 0.41
20 26 0.59
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.48
Consensus pattern (20 bp):
TTTTCTGGAAAATGATTTAC
Found at i:35538336 original size:24 final size:24
Alignment explanation
Indices: 35538304--35538350 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
35538294 TAAAACATAC
35538304 AGGAGCAAAAACAACAGAGAAATG
1 AGGAGCAAAAACAACAGAGAAATG
*
35538328 AGGAGCAAAAATAACAGAGAAAT
1 AGGAGCAAAAACAACAGAGAAAT
35538351 TAACAAGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.60, C:0.11, G:0.23, T:0.06
Consensus pattern (24 bp):
AGGAGCAAAAACAACAGAGAAATG
Found at i:35539664 original size:28 final size:28
Alignment explanation
Indices: 35539632--35539714 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
35539622 TTTTAAAACC
35539632 ATATTTGACTCGTAGATATTAAATAATA
1 ATATTTGACTCGTAGATATTAAATAATA
* **
35539660 ATATTT-A--C--A-A-ACTTTAA-AACC
1 ATATTTGACTCGTAGATA-TTAAATAATA
35539681 ATATTTGACTCGTAGATATTAAATAATA
1 ATATTTGACTCGTAGATATTAAATAATA
35539709 ATATTT
1 ATATTT
35539715 ACAAACTTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
21 9 0.22
22 6 0.15
23 1 0.03
24 1 0.03
25 1 0.03
26 1 0.03
27 6 0.15
28 15 0.38
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (28 bp):
ATATTTGACTCGTAGATATTAAATAATA
Found at i:35539680 original size:49 final size:49
Alignment explanation
Indices: 35539623--35539722 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
35539613 CAAAAACCTT
35539623 TTTAAAACCATATTTGACTCGTAGATATTAAATAATAATATTTACAAAC
1 TTTAAAACCATATTTGACTCGTAGATATTAAATAATAATATTTACAAAC
35539672 TTTAAAACCATATTTGACTCGTAGATATTAAATAATAATATTTACAAAC
1 TTTAAAACCATATTTGACTCGTAGATATTAAATAATAATATTTACAAAC
35539721 TT
1 TT
35539723 ACTCGTCAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (49 bp):
TTTAAAACCATATTTGACTCGTAGATATTAAATAATAATATTTACAAAC
Found at i:35542594 original size:28 final size:29
Alignment explanation
Indices: 35542562--35542660 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
35542552 ATAATAAGCC
*
35542562 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
35542590 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
35542618 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
35542647 CGCACACTTAGTGC
1 CGCACACTTAGTGC
35542661 CAATCTCATG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:35548567 original size:14 final size:15
Alignment explanation
Indices: 35548527--35548576 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
35548517 AATTTGAATT
*
35548527 TAAAATTTGAAAA-C
1 TAAATTTTGAAAAGC
* *
35548541 TTAA-TTTGAAAAGT
1 TAAATTTTGAAAAGC
35548555 TAAATTTTG-AAAGC
1 TAAATTTTGAAAAGC
35548569 TAAATTTT
1 TAAATTTT
35548577 AGATAAACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 8 0.27
14 18 0.60
15 4 0.13
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (15 bp):
TAAATTTTGAAAAGC
Found at i:35553889 original size:25 final size:24
Alignment explanation
Indices: 35553843--35553889 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
35553833 TGATGAGACT
35553843 AAAGGGTCTTTTTTTTTCTTATTC
1 AAAGGGTCTTTTTTTTTCTTATTC
* *
35553867 AAAGGGATTTTTTTTTTTTTTAT
1 AAAGGG-TCTTTTTTTTTCTTAT
35553890 AAATTCTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.62
Consensus pattern (24 bp):
AAAGGGTCTTTTTTTTTCTTATTC
Found at i:35556268 original size:19 final size:19
Alignment explanation
Indices: 35556244--35556280 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35556234 TATTTTATTA
35556244 TTTTATTAAATAAATAAAT
1 TTTTATTAAATAAATAAAT
**
35556263 TTTTATTATTTAAATAAA
1 TTTTATTAAATAAATAAA
35556281 ATAACTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTATTAAATAAATAAAT
Found at i:35556791 original size:29 final size:28
Alignment explanation
Indices: 35556757--35556813 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
35556747 TTATTTGAAC
* *
35556757 TAATTAATTATATTATAAAAATATTAAAT
1 TAATTAATAACATTATAAAAATA-TAAAT
*
35556786 TAATTAATAACATTATAAGAATATAAAT
1 TAATTAATAACATTATAAAAATATAAAT
35556814 ACAAAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
TAATTAATAACATTATAAAAATATAAAT
Found at i:35559919 original size:13 final size:13
Alignment explanation
Indices: 35559874--35559919 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
35559864 TTAGTAATTT
35559874 TATTATTGATGGAA
1 TATTATT-ATGGAA
35559888 TATTATTATAGG-A
1 TATTATTAT-GGAA
35559901 TATTATTATGGAA
1 TATTATTATGGAA
*
35559914 TGTTAT
1 TATTAT
35559920 CTTTTAGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.07
13 18 0.62
14 9 0.31
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (13 bp):
TATTATTATGGAA
Found at i:35563971 original size:12 final size:11
Alignment explanation
Indices: 35563951--35563983 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
35563941 TCTTTTTCAG
35563951 TTTTATTTTAA
1 TTTTATTTTAA
35563962 TTTTAGTTTTAA
1 TTTTA-TTTTAA
35563974 TTTT-TTTTAA
1 TTTTATTTTAA
35563984 AAGTTATGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 5 0.24
12 10 0.48
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (11 bp):
TTTTATTTTAA
Found at i:35583196 original size:45 final size:44
Alignment explanation
Indices: 35583120--35583306 Score: 173
Period size: 44 Copynumber: 4.3 Consensus size: 44
35583110 ATATGTGGTT
* *
35583120 GAAGCCACCAA-ATTCGTAGACAAGCTACCATGTAGGCTGTGGA
1 GAAGCCACCAATATTCGCAGACAAGCTACCATGTAGGTTGTGGA
* * * *
35583163 CGAAGCCACAAATATTCGCAGACAAGTTGCCATGTAAGTTGTGGA
1 -GAAGCCACCAATATTCGCAGACAAGCTACCATGTAGGTTGTGGA
* * * * * *
35583208 TAAACCACCAATATTTGAAGACAATCTACCATGTAGGTTGCGGA
1 GAAGCCACCAATATTCGCAGACAAGCTACCATGTAGGTTGTGGA
* * * * * *
35583252 TAAACCACCAAT-TTTGCAAACAAGCTGCCATG-AGGTAGTGGA
1 GAAGCCACCAATATTCGCAGACAAGCTACCATGTAGGTTGTGGA
35583294 CGAAGCCACCAAT
1 -GAAGCCACCAAT
35583307 TCTTCCTCCT
Statistics
Matches: 117, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
42 8 0.07
43 26 0.22
44 56 0.48
45 27 0.23
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (44 bp):
GAAGCCACCAATATTCGCAGACAAGCTACCATGTAGGTTGTGGA
Found at i:35585437 original size:101 final size:101
Alignment explanation
Indices: 35585262--35585448 Score: 374
Period size: 101 Copynumber: 1.9 Consensus size: 101
35585252 ACTAGCACAG
35585262 TGCTTAGAAAAACTAGGTGTACTACACATTTGGCGATATCCCTTACCAGACTTAATCTTTGCTTA
1 TGCTTAGAAAAACTAGGTGTACTACACATTTGGCGATATCCCTTACCAGACTTAATCTTTGCTTA
35585327 TAATATACTTTCTTAACTAATCTTTTTGTTAATCTT
66 TAATATACTTTCTTAACTAATCTTTTTGTTAATCTT
35585363 TGCTTAGAAAAACTAGGTGTACTACACATTTGGCGATATCCCTTACCAGACTTAATCTTTGCTTA
1 TGCTTAGAAAAACTAGGTGTACTACACATTTGGCGATATCCCTTACCAGACTTAATCTTTGCTTA
35585428 TAATATACTTTCTTAACTAAT
66 TAATATACTTTCTTAACTAAT
35585449 AGAATAACTT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 86 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (101 bp):
TGCTTAGAAAAACTAGGTGTACTACACATTTGGCGATATCCCTTACCAGACTTAATCTTTGCTTA
TAATATACTTTCTTAACTAATCTTTTTGTTAATCTT
Found at i:35585607 original size:28 final size:28
Alignment explanation
Indices: 35585567--35585623 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
35585557 ATGCCTTTAA
*
35585567 ATCAGATTCGCCAGATCTGGGGTGTGAC
1 ATCAGATCCGCCAGATCTGGGGTGTGAC
35585595 ATCAGATCCGCCAGATCTGGGGTGTGAC
1 ATCAGATCCGCCAGATCTGGGGTGTGAC
35585623 A
1 A
35585624 GCATAAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.23
Consensus pattern (28 bp):
ATCAGATCCGCCAGATCTGGGGTGTGAC
Found at i:35590476 original size:40 final size:40
Alignment explanation
Indices: 35590416--35590494 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
35590406 ACTAAAATAG
* *
35590416 GGGTGCCGAAGTAAAAATAGGGGCACGTATGTGCATTCAA
1 GGGTACCGAAGTAAAAATAGGGGCACGAATGTGCATTCAA
*
35590456 GGGTACCGAAGTATAAATAGGGGCACGAATGTGCATTCA
1 GGGTACCGAAGTAAAAATAGGGGCACGAATGTGCATTCA
35590495 TACATTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.33, C:0.15, G:0.32, T:0.20
Consensus pattern (40 bp):
GGGTACCGAAGTAAAAATAGGGGCACGAATGTGCATTCAA
Found at i:35593111 original size:7 final size:7
Alignment explanation
Indices: 35593099--35593173 Score: 105
Period size: 7 Copynumber: 10.1 Consensus size: 7
35593089 ACAAAAAATG
35593099 AAATGCA
1 AAATGCA
35593106 AAATGCA
1 AAATGCA
35593113 TGAAATGCA
1 --AAATGCA
*
35593122 AAATGAA
1 AAATGCA
35593129 AAATGCA
1 AAATGCA
35593136 AAATGCA
1 AAATGCA
35593143 TGAAATGCA
1 --AAATGCA
35593152 AAATGCA
1 AAATGCA
35593159 AAATGCA
1 AAATGCA
35593166 AAATGCA
1 AAATGCA
35593173 A
1 A
35593174 TCCGTGTGGC
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
7 48 0.77
9 14 0.23
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (7 bp):
AAATGCA
Found at i:35593115 original size:30 final size:29
Alignment explanation
Indices: 35593093--35593172 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 29
35593083 TGACAAACAA
*
35593093 AAAATG-AAATGCAAAATGCATGAAATGC
1 AAAATGAAAATGCAAAATGCATGAAATAC
*
35593121 AAAATGAAAAATGCAAAATGCATGAAATGC
1 AAAATG-AAAATGCAAAATGCATGAAATAC
35593151 AAAATGCAAAATGCAAAATGCA
1 AAAATG-AAAATGCAAAATGCA
35593173 ATCCGTGTGG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 6 0.12
30 43 0.88
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.16
Consensus pattern (29 bp):
AAAATGAAAATGCAAAATGCATGAAATAC
Found at i:35593126 original size:23 final size:21
Alignment explanation
Indices: 35593099--35593173 Score: 105
Period size: 23 Copynumber: 3.4 Consensus size: 21
35593089 ACAAAAAATG
35593099 AAATGCAAAATGCATGAAATGCA
1 AAATGCAAAATGCA--AAATGCA
*
35593122 AAATGAAAAATGCAAAATGCA
1 AAATGCAAAATGCAAAATGCA
35593143 TGAAATGCAAAATGCAAAATGCA
1 --AAATGCAAAATGCAAAATGCA
35593166 AAATGCAA
1 AAATGCAA
35593174 TCCGTGTGGC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
21 15 0.31
23 33 0.69
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (21 bp):
AAATGCAAAATGCAAAATGCA
Found at i:35597909 original size:20 final size:20
Alignment explanation
Indices: 35597884--35597922 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35597874 TACTTTCTTC
35597884 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
35597904 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
35597923 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:35605065 original size:60 final size:59
Alignment explanation
Indices: 35604956--35605079 Score: 135
Period size: 60 Copynumber: 2.1 Consensus size: 59
35604946 CCCGGTCATC
* * * *
35604956 TATCACCCTACAGACATGAGGATTAGCGCCCTGACCATTCAACCTATCATTCATACCAGG
1 TATCACCCTACAAACAGGAGGATTAGCACCCTGACCATTCAA-CTATCATTCAGACCAGG
* * * *
35605016 TATCACCCTACAAATAGGAGGATTAGCATCTTGACCATTCAGA-TAATCATTGAGACCAGG
1 TATCACCCTACAAACAGGAGGATTAGCACCCTGACCATTCA-ACT-ATCATTCAGACCAGG
35605076 -ATCA
1 TATCA
35605080 TTCCTATTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 5 0.09
60 48 0.89
61 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (59 bp):
TATCACCCTACAAACAGGAGGATTAGCACCCTGACCATTCAACTATCATTCAGACCAGG
Found at i:35611103 original size:24 final size:24
Alignment explanation
Indices: 35611053--35611116 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
35611043 AATGTTGCAG
* * **
35611053 ACAAACCGCCAGAACAATATGTGA
1 ACAAATCGCCAGAACAATACGCAA
*
35611077 ACAAATCTCCAGAACAATACGCAA
1 ACAAATCGCCAGAACAATACGCAA
*
35611101 ACAAATCGCGAGAACA
1 ACAAATCGCCAGAACA
35611117 CCAAATAGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.48, C:0.27, G:0.14, T:0.11
Consensus pattern (24 bp):
ACAAATCGCCAGAACAATACGCAA
Found at i:35612281 original size:22 final size:22
Alignment explanation
Indices: 35612256--35612297 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
35612246 CAACAATGGT
35612256 GAAAAAAAGAAGAAAAATGAGA
1 GAAAAAAAGAAGAAAAATGAGA
* * *
35612278 GAAAAAGAGAGGGAAAATGA
1 GAAAAAAAGAAGAAAAATGA
35612298 AAGCGAAGGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.05
Consensus pattern (22 bp):
GAAAAAAAGAAGAAAAATGAGA
Found at i:35626486 original size:6 final size:6
Alignment explanation
Indices: 35626475--35626520 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
35626465 ATTGTGTATG
35626475 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATA
35626521 TACCTTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TATACA
Found at i:35627755 original size:3 final size:3
Alignment explanation
Indices: 35627747--35627774 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
35627737 TTGTAGTGAG
35627747 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
35627775 AGATGCACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:35638606 original size:22 final size:23
Alignment explanation
Indices: 35638580--35638622 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35638570 GCAATCGTAA
35638580 ATATGA-CATGTAATCTTAGAAT
1 ATATGATCATGTAATCTTAGAAT
**
35638602 ATATGATTTTGTAATCTTAGA
1 ATATGATCATGTAATCTTAGA
35638623 GATTTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (23 bp):
ATATGATCATGTAATCTTAGAAT
Found at i:35642584 original size:50 final size:51
Alignment explanation
Indices: 35642524--35642656 Score: 155
Period size: 50 Copynumber: 2.6 Consensus size: 51
35642514 TATCATTCGA
* * *
35642524 TACACGTAGTAACCTTCACATAGCACTACACACGTGATCAAA-CTTTCCGGT
1 TACACGTAGTAACCTTCACATAGTACTACACACGTGACCAAATCCTTCC-GT
* *
35642575 T-CACGTAGT-AGCTTGCACATAGTACTACATACGTGACCAAATCCTTCCGT
1 TACACGTAGTAACCTT-CACATAGTACTACACACGTGACCAAATCCTTCCGT
* * *
35642625 TACACATAGTAGCCTGCACATAGTACTACACA
1 TACACGTAGTAACCTTCACATAGTACTACACA
35642657 TGTGGCCATT
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
49 4 0.06
50 34 0.50
51 28 0.41
52 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.26
Consensus pattern (51 bp):
TACACGTAGTAACCTTCACATAGTACTACACACGTGACCAAATCCTTCCGT
Found at i:35642644 original size:51 final size:51
Alignment explanation
Indices: 35642524--35642711 Score: 177
Period size: 51 Copynumber: 3.7 Consensus size: 51
35642514 TATCATTCGA
* * * * * *
35642524 TACACGTAGTAACCTTCACATAGCACTACACACGTGATCAAA-CTTTCCGGT
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAATCCTTCC-GT
* * *
35642575 T-CACGTAGTAGCTTGCACATAGTACTACATACGTGACCAAATCCTTCCGT
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAATCCTTCCGT
* * * * *
35642625 TACACATAGTAGCCTGCACATAGTACTACACATGTGGCCATTAT-CTAT-TGA
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCA-AATCCT-TCCGT
* *
35642676 TACACATAGTAGCCTACACTTAGTACTACACACGTG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTG
35642712 TTTATAGGCA
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
50 37 0.32
51 75 0.65
52 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (51 bp):
TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAATCCTTCCGT
Found at i:35642655 original size:26 final size:24
Alignment explanation
Indices: 35642625--35642707 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 24
35642615 ATCCTTCCGT
35642625 TACACATAGTAGCCTGCACATAGTAC
1 TACACATAGTAGCCT-CAC-TAGTAC
* * *
35642651 TACACAT-GTGGCCATTATCTATTGA-
1 TACACATAGTAGCC-TCA-CTAGT-AC
35642676 TACACATAGTAGCCTACACTTAGTAC
1 TACACATAGTAGCCT-CAC-TAGTAC
35642702 TACACA
1 TACACA
35642708 CGTGTTTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
25 19 0.43
26 25 0.57
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (24 bp):
TACACATAGTAGCCTCACTAGTAC
Found at i:35645859 original size:44 final size:46
Alignment explanation
Indices: 35645809--35645904 Score: 126
Period size: 44 Copynumber: 2.1 Consensus size: 46
35645799 TATTACAACA
*
35645809 TCCATTCCATTCAACCAAAC-ATAAGAA-TACT-ATTACAGCTCTAT
1 TCCATTCCATTCAACCAAACAAT-AGAATTACTGATTACAACTCTAT
* *
35645853 TCCATTCCATTGAACCAAACAATTGAATTACTGATTACAACTCTAT
1 TCCATTCCATTCAACCAAACAATAGAATTACTGATTACAACTCTAT
*
35645899 TTCATT
1 TCCATT
35645905 ATAGTTATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
44 22 0.49
45 6 0.13
46 17 0.38
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (46 bp):
TCCATTCCATTCAACCAAACAATAGAATTACTGATTACAACTCTAT
Found at i:35646999 original size:46 final size:46
Alignment explanation
Indices: 35646943--35647071 Score: 195
Period size: 46 Copynumber: 2.8 Consensus size: 46
35646933 TGTAGGAATA
* *
35646943 AAATTGCTAAAAGATCATATCTAATAATAATATCCTATTAAAAATC
1 AAATTACTAAAAGATAATATCTAATAATAATATCCTATTAAAAATC
* * * *
35646989 AAATTTCTAAAAGATAATATCTAATAAAAATATCTTATTAGAAATC
1 AAATTACTAAAAGATAATATCTAATAATAATATCCTATTAAAAATC
*
35647035 AAATTACTAAAAGATAATATCTAATAATAATCTCCTA
1 AAATTACTAAAAGATAATATCTAATAATAATATCCTA
35647072 ACACCCCTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (46 bp):
AAATTACTAAAAGATAATATCTAATAATAATATCCTATTAAAAATC
Found at i:35652183 original size:47 final size:47
Alignment explanation
Indices: 35652120--35652592 Score: 768
Period size: 47 Copynumber: 10.1 Consensus size: 47
35652110 GAAATGATAG
* *
35652120 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
35652167 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
35652214 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
35652261 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
35652308 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
35652355 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
35652402 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
35652449 TAAGGCCTAATGGCCGATGCGATAAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
35652496 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * * *
35652542 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
35652589 TAAG
1 TAAG
35652593 TCCCGAAGGG
Statistics
Matches: 405, Mismatches: 20, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
46 39 0.10
47 366 0.90
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:35652767 original size:37 final size:37
Alignment explanation
Indices: 35652711--35652789 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
35652701 CCGAGCTCTA
* * *
35652711 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
35652748 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
35652785 AAGAC
1 AAGAC
35652790 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:35655284 original size:100 final size:100
Alignment explanation
Indices: 35655173--35655357 Score: 273
Period size: 100 Copynumber: 1.9 Consensus size: 100
35655163 ATTTCATTTC
* * * * * *
35655173 TTCTTCTTCTTTTTTTAATTTCTCGAGCTTTTACAGTTCAAAAATGGTGGACAAAGCTAAAA-CT
1 TTCTTCTTCTTTTTTAAATTTCTCAAGCTTTTACAATTCAAAAATGGCGAACAAAGCTAAAACCG
35655237 GAGAACCCATCTTTACTCCATAGGTATCAGTTTCTT
66 GA-AACCCATCTTTACTCCATAGGTATCAGTTTCTT
* * *
35655273 TTCTTTTTCTTTTTTAAATTTCTTAAGCTTTTACAATTTAAAAATGGCGAACAAAGCTAAAACCG
1 TTCTTCTTCTTTTTTAAATTTCTCAAGCTTTTACAATTCAAAAATGGCGAACAAAGCTAAAACCG
35655338 GAAACCCATCTTTACTCCAT
66 GAAACCCATCTTTACTCCAT
35655358 GGAAAATATG
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
100 72 0.96
101 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (100 bp):
TTCTTCTTCTTTTTTAAATTTCTCAAGCTTTTACAATTCAAAAATGGCGAACAAAGCTAAAACCG
GAAACCCATCTTTACTCCATAGGTATCAGTTTCTT
Found at i:35656754 original size:16 final size:16
Alignment explanation
Indices: 35656733--35656770 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
35656723 TTTGGTTCAC
*
35656733 TGTAATGGAATAAAGT
1 TGTAATAGAATAAAGT
35656749 TGTAATAGAATAAAGT
1 TGTAATAGAATAAAGT
35656765 TGTAAT
1 TGTAAT
35656771 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (16 bp):
TGTAATAGAATAAAGT
Found at i:35669950 original size:33 final size:33
Alignment explanation
Indices: 35669911--35670026 Score: 171
Period size: 33 Copynumber: 3.5 Consensus size: 33
35669901 ATTATAAAGC
35669911 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
*
35669944 ATGTATAATTGACCTAAAATTAATTGTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* * *
35669977 AT-TTTTATTTACCCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGA-CCTAAAATTAATTGTTGGTGT
*
35670010 ATGTATAATTGATCTAA
1 ATGTATAATTGACCTAA
35670027 GTATACATTG
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
32 6 0.08
33 60 0.83
34 6 0.08
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:35670169 original size:37 final size:37
Alignment explanation
Indices: 35670084--35670170 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
35670074 GTATAAATAT
* * *
35670084 ATTGATTAGTTCATTAAAGCATGTTCAAAGTCCTCAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTCCTAAC
*
35670121 ATTGATTAGTTTAATAAAGCATGTTCAAAGT-TTGAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTCCT-AAC
35670158 ATTGATTAGTTTA
1 ATTGATTAGTTTA
35670171 TTTATTTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 1 0.02
37 44 0.98
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (37 bp):
ATTGATTAGTTTAATAAAGCATGTTCAAAGTCCTAAC
Found at i:35673101 original size:17 final size:17
Alignment explanation
Indices: 35673079--35673116 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
35673069 CGATTGCATG
35673079 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
35673096 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
35673113 TTTC
1 TTTC
35673117 CTTTGAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.13, G:0.11, T:0.66
Consensus pattern (17 bp):
TTTCTATTGCTGTTTAT
Found at i:35673883 original size:22 final size:22
Alignment explanation
Indices: 35673842--35673917 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
35673832 GAAGATGAAA
35673842 CTGGAAATTG--TTGCATTTGTT
1 CTGGAAATTGTTTTG-ATTTGTT
* *
35673863 -TTGATATTGTTCTTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
35673885 CTGGAAATTGTTTTGA-TTGTCT
1 CTGGAAATTGTTTTGATTTGT-T
35673907 GCTGGAAATTG
1 -CTGGAAATTG
35673918 AATTTGTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
20 7 0.16
21 4 0.09
22 12 0.27
23 22 0.49
ACGTcount: A:0.18, C:0.08, G:0.24, T:0.50
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:35675148 original size:25 final size:25
Alignment explanation
Indices: 35675114--35675241 Score: 153
Period size: 25 Copynumber: 5.3 Consensus size: 25
35675104 TACATCAATA
35675114 ATTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
*
35675139 ATTAAAATAAGGACTCATCAATA----
1 ATTAAAATAAGGACT--TTAATATTTT
35675162 ATTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
* *
35675187 ATTAAAATAAGGAC--TAATCA-ATA
1 ATTAAAATAAGGACTTTAAT-ATTTT
35675210 ATTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
35675235 ATTAAAA
1 ATTAAAA
35675242 ATCTTATTTA
Statistics
Matches: 87, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
21 5 0.06
23 34 0.39
24 2 0.02
25 41 0.47
27 5 0.06
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (25 bp):
ATTAAAATAAGGACTTTAATATTTT
Found at i:35675163 original size:48 final size:48
Alignment explanation
Indices: 35675106--35675241 Score: 263
Period size: 48 Copynumber: 2.8 Consensus size: 48
35675096 TAAAAAATTA
35675106 CATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACT
1 CATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACT
35675154 CATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACT
1 CATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACT
*
35675202 AATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAA
1 CATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAA
35675242 ATCTTATTTA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 87 1.00
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.36
Consensus pattern (48 bp):
CATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACT
Found at i:35675169 original size:23 final size:22
Alignment explanation
Indices: 35675107--35675224 Score: 114
Period size: 23 Copynumber: 5.0 Consensus size: 22
35675097 AAAAAATTAC
35675107 ATCAATAATTAAAATAAGGACT
1 ATCAATAATTAAAATAAGGACT
*
35675129 -TTAATATTTTATTAAAATAAGGACT
1 ATCAATA----ATTAAAATAAGGACT
35675154 CATCAATAATTAAAATAAGGACT
1 -ATCAATAATTAAAATAAGGACT
*
35675177 -TTAATATTTTATTAAAATAAGGACT
1 ATCAATA----ATTAAAATAAGGACT
35675202 AATCAATAATTAAAATAAGGACT
1 -ATCAATAATTAAAATAAGGACT
35675225 TTAATATTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 23
0.75 0.04 0.21
Matches are distributed among these distances:
21 10 0.12
23 30 0.38
25 30 0.38
27 10 0.12
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (22 bp):
ATCAATAATTAAAATAAGGACT
Found at i:35678948 original size:47 final size:45
Alignment explanation
Indices: 35678897--35679064 Score: 132
Period size: 47 Copynumber: 3.6 Consensus size: 45
35678887 TATTTAATAT
*
35678897 TAATTATTTTAAATTGTATAAATTCATATAAGAAAAATTATTATCAA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTAT-AA
* * **
35678944 TAATT-TTATGAAA-TTATATATT-AT-T-ATTAAATTATATGTAATAA
1 TAATTATT-TTAAATTTATAAATTCATATAAGAAAATT-TAT-T-ATAA
* * *
35678988 TAATTATTTTAAATTATACAAATTCATATAAGATAATTTATTAGTTA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTA-TAA
35679035 TAATTATTTTAAATTTTATTAAA-TCATATA
1 TAATTATTTTAAA-TTTA-TAAATTCATATA
35679065 TTTTAATTAA
Statistics
Matches: 95, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
42 5 0.05
43 4 0.04
44 14 0.15
45 12 0.13
46 10 0.11
47 36 0.38
48 9 0.09
49 5 0.05
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (45 bp):
TAATTATTTTAAATTTATAAATTCATATAAGAAAATTTATTATAA
Found at i:35678970 original size:91 final size:91
Alignment explanation
Indices: 35678823--35679030 Score: 308
Period size: 91 Copynumber: 2.3 Consensus size: 91
35678813 TTGATTTTAG
* * *
35678823 TAAATTTATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
35678888 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* * *
35678915 TAAATTCATATAAGAAAAATTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
35678980 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
35679006 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
35679031 GTTATAATTA
Statistics
Matches: 104, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 89 0.86
92 15 0.14
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:35678991 original size:44 final size:43
Alignment explanation
Indices: 35678844--35679005 Score: 116
Period size: 44 Copynumber: 3.6 Consensus size: 43
35678834 AAGAACATTT
* * *
35678844 TATTATTAAGAATT-TTATGAAATTATATATCATTATTAAATTA
1 TATTAATAATAATTATT-TGAAATTATATATAATTATTAAATTA
* * * *
35678887 TATTTAATATTAATTATTTTAAATTGTATA-AATTCATATAAGA-AA
1 TA-TTAATAATAATTATTTGAAATTATATATAATT-AT-TAA-ATTA
* *
35678932 AATTATTATCAATAATT-TTATGAAATTATATATTATTATTAAATTA
1 TATTA--AT-AATAATTATT-TGAAATTATATATAATTATTAAATTA
*
35678978 TATGTAATAATAATTATTTTAAATTATA
1 TAT-TAATAATAATTATTTGAAATTATA
35679006 CAAATTCATA
Statistics
Matches: 91, Mismatches: 15, Indels: 25
0.69 0.11 0.19
Matches are distributed among these distances:
43 5 0.05
44 40 0.44
45 12 0.13
46 11 0.12
47 20 0.22
48 3 0.03
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (43 bp):
TATTAATAATAATTATTTGAAATTATATATAATTATTAAATTA
Found at i:35679005 original size:26 final size:28
Alignment explanation
Indices: 35678843--35678919 Score: 52
Period size: 28 Copynumber: 2.8 Consensus size: 28
35678833 TAAGAACATT
* *
35678843 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATAATATA
* ** *
35678873 TCATTATTAAATTATATTTAATATTA-A
1 TTATTATTAAATTATATGAAATAATATA
*
35678900 TTATT-TTAAATTGTAT-AAAT
1 TTATTATTAAATTATATGAAAT
35678920 TCATATAAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
25 3 0.08
26 10 0.26
27 5 0.13
28 12 0.32
29 1 0.03
30 7 0.18
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATAATATA
Found at i:35679212 original size:25 final size:26
Alignment explanation
Indices: 35679180--35679234 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
35679170 TTATTAAATT
*
35679180 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
35679205 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
35679230 A-ATAT
1 ATATAT
35679235 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:35679432 original size:44 final size:45
Alignment explanation
Indices: 35679369--35679466 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
35679359 CTATTACACC
* *
35679369 TCTATTCCATTCAACCAAACACAAGA-TTACTATTACGCCTCTAT
1 TCTATTACATTCAACCAAACACAAGATTTACTATTACACCTCTAT
*** *
35679413 TCTATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTAT
1 TCTATTACATTCAACCAAACACAAGATTTACTATTACACCTCTAT
*
35679458 TCCATTACA
1 TCTATTACA
35679467 CCTCTATTCC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 22 0.48
45 24 0.52
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.35
Consensus pattern (45 bp):
TCTATTACATTCAACCAAACACAAGATTTACTATTACACCTCTAT
Found at i:35679465 original size:45 final size:44
Alignment explanation
Indices: 35679357--35679466 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 44
35679347 TTTTCCATTA
35679357 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * * ***
35679396 TACTATTACGCCTCTATTCTATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
35679441 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
35679467 CCTCTATTCC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
39 16 0.29
44 16 0.29
45 24 0.43
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:35679466 original size:16 final size:16
Alignment explanation
Indices: 35679445--35679498 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
35679435 TTGATTTGCT
35679445 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
35679461 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
35679477 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
35679493 AATACA
1 ATTACA
35679499 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:35689342 original size:16 final size:16
Alignment explanation
Indices: 35689323--35689356 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35689313 GTAAATGGGT
* *
35689323 AAATAAATTATAAATA
1 AAATAAAATAAAAATA
35689339 AAATAAAATAAAAATA
1 AAATAAAATAAAAATA
35689355 AA
1 AA
35689357 TCGTCATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAAATAAAAATA
Found at i:35690326 original size:27 final size:25
Alignment explanation
Indices: 35690287--35690355 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 25
35690277 CGTTTCGACC
* *
35690287 CACATCTCATGTGAGCAGACCTATTTT
1 CACAGCTCATGTGAGCAGACCGA--TT
* *
35690314 CACAGCTCGTGTGAGCATACCGATT
1 CACAGCTCATGTGAGCAGACCGATT
35690339 CACAGCTCATGTGAGCA
1 CACAGCTCATGTGAGCA
35690356 TACATGTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 18 0.49
27 19 0.51
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (25 bp):
CACAGCTCATGTGAGCAGACCGATT
Found at i:35695525 original size:20 final size:20
Alignment explanation
Indices: 35695475--35695525 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 20
35695465 AATAGTTCTG
*
35695475 TCTCTTGATGAACAGTTGTA
1 TCTCTTGATGAACAATTGTA
*
35695495 T-T-TT-TTGAACAATTGTA
1 TCTCTTGATGAACAATTGTA
*
35695512 TCTCTTGGTGAACA
1 TCTCTTGATGAACA
35695526 GATTCCTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
17 12 0.48
18 3 0.12
19 3 0.12
20 7 0.28
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (20 bp):
TCTCTTGATGAACAATTGTA
Found at i:35696844 original size:23 final size:23
Alignment explanation
Indices: 35696818--35696861 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
35696808 AATCTAATTC
*
35696818 ATTTGATATATTTAATATTTAAT
1 ATTTGATATATTAAATATTTAAT
*
35696841 ATTTTATATATTAAATATTTA
1 ATTTGATATATTAAATATTTA
35696862 TCAAAAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTTGATATATTAAATATTTAAT
Found at i:35702011 original size:43 final size:43
Alignment explanation
Indices: 35701950--35702132 Score: 244
Period size: 43 Copynumber: 4.3 Consensus size: 43
35701940 TTATTTTTAT
*
35701950 AAACGCCGCTAAAGGTCATGTTCTTTAGTGGCAC-TTTTCCTAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCACTTTTTCC-AC
**
35701993 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGTGCTTTTTCCAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCACTTTTTCCAC
* **
35702036 AAACGTCGCTAAAGGTCATGTTCTTTAGCGGTGCTTTTTCCAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCACTTTTTCCAC
* * * *
35702079 AAACACCGTTAAAGGTCATGTTCTTTTAGCGACA-TTTTTACAC
1 AAACGCCGCTAAAGGTCATGTTC-TTTAGCGGCACTTTTTCCAC
35702122 AAACGCCGCTA
1 AAACGCCGCTA
35702133 TTTGTTTGGT
Statistics
Matches: 125, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
43 112 0.90
44 13 0.10
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCACTTTTTCCAC
Found at i:35702602 original size:87 final size:87
Alignment explanation
Indices: 35702481--35702657 Score: 273
Period size: 87 Copynumber: 2.0 Consensus size: 87
35702471 TTCTGCTCTG
*
35702481 CTCTGCTTCCCTCACTGCAGCCTCTGCTTCTCTCGATGCCGTATCTGCTTTAAGTTGTAGCTGGA
1 CTCTGCTTCCCTCACTGCAGCCTCTGCTTCTCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGA
*
35702546 GTTCTTCATATTTCTTTTGAAC
66 GTTCTTCATATTTCCTTTGAAC
* * * * * * *
35702568 CTCTTCTTCTCTCGCTGCAGCCTTTGCTTCTCTCGCTGTCGCCTCTGCTTTAAGTTGTAGCTGGA
1 CTCTGCTTCCCTCACTGCAGCCTCTGCTTCTCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGA
35702633 GTTCTTCATATTTCCTTTGAAC
66 GTTCTTCATATTTCCTTTGAAC
35702655 CTC
1 CTC
35702658 AACTGTGGTC
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.12, C:0.30, G:0.17, T:0.41
Consensus pattern (87 bp):
CTCTGCTTCCCTCACTGCAGCCTCTGCTTCTCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGA
GTTCTTCATATTTCCTTTGAAC
Found at i:35702611 original size:21 final size:21
Alignment explanation
Indices: 35702567--35702617 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
35702557 TTCTTTTGAA
*
35702567 CCTCTTCTTCTCTCGCTGCAG
1 CCTCTGCTTCTCTCGCTGCAG
*
35702588 CCTTTGCTTCTCTCGCTGTC-G
1 CCTCTGCTTCTCTCGCTG-CAG
35702609 CCTCTGCTT
1 CCTCTGCTT
35702618 TAAGTTGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.02, C:0.41, G:0.16, T:0.41
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCAG
Found at i:35704277 original size:12 final size:12
Alignment explanation
Indices: 35704260--35704304 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
35704250 AGGTTATGTA
35704260 TTATTATGTAAG
1 TTATTATGTAAG
*
35704272 TTATTATGTAGG
1 TTATTATGTAAG
35704284 TTATTATGTAAG
1 TTATTATGTAAG
*
35704296 TCATTATGT
1 TTATTATGT
35704305 TGGTTATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:35704290 original size:24 final size:24
Alignment explanation
Indices: 35704253--35704311 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
35704243 TTTATGTAGG
*
35704253 TTATGTA--TTATTATGTAAGTTA
1 TTATGTAGGTTATTATGTAAGTCA
35704275 TTATGTAGGTTATTATGTAAGTCA
1 TTATGTAGGTTATTATGTAAGTCA
*
35704299 TTATGTTGGTTAT
1 TTATGTAGGTTAT
35704312 GTAAGTTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 7 0.21
24 26 0.79
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.53
Consensus pattern (24 bp):
TTATGTAGGTTATTATGTAAGTCA
Found at i:35704313 original size:21 final size:22
Alignment explanation
Indices: 35704263--35704317 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
35704253 TTATGTATTA
*
35704263 TTATGTAAGTTATTATGTAGGTT
1 TTATGTAAGTCATTATGTAGG-T
*
35704286 ATTATGTAAGTCATTATGTTGG-
1 -TTATGTAAGTCATTATGTAGGT
35704308 TTATGTAAGT
1 TTATGTAAGT
35704318 TGTGATATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
24 19 0.66
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (22 bp):
TTATGTAAGTCATTATGTAGGT
Found at i:35704476 original size:21 final size:20
Alignment explanation
Indices: 35704437--35704475 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
35704427 GTAATGTATC
*
35704437 AATTTTTAAAAATATATATA
1 AATTTTAAAAAATATATATA
35704457 AATTTT-AAAAATATATATA
1 AATTTTAAAAAATATATATA
35704476 TTAAAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTTAAAAAATATATATA
Found at i:35704513 original size:9 final size:9
Alignment explanation
Indices: 35704499--35704579 Score: 69
Period size: 9 Copynumber: 9.0 Consensus size: 9
35704489 TAAATATTAA
35704499 TAAGTTATG
1 TAAGTTATG
35704508 TAAGTTATG
1 TAAGTTATG
* *
35704517 TATTA-TAAATT
1 TA--AGT-TATG
*
35704528 TAAATTATG
1 TAAGTTATG
35704537 TAAGTTATG
1 TAAGTTATG
35704546 -AA-TTATG
1 TAAGTTATG
35704553 TAAGTTATG
1 TAAGTTATG
* *
35704562 TAAATTACG
1 TAAGTTATG
35704571 TAAGTTATG
1 TAAGTTATG
35704580 AAATTTGAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.09
8 4 0.07
9 41 0.72
10 2 0.04
11 5 0.09
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:35704551 original size:16 final size:16
Alignment explanation
Indices: 35704503--35704581 Score: 83
Period size: 16 Copynumber: 5.0 Consensus size: 16
35704493 TATTAATAAG
*
35704503 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGAA
* *
35704519 TTA--TAAATT-TAAA
1 TTATGTAAGTTATGAA
35704532 TTATGTAAGTTATGAA
1 TTATGTAAGTTATGAA
35704548 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATG--AA
*
35704566 TTACGTAAGTTATGAA
1 TTATGTAAGTTATGAA
35704582 ATTTGAACTT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 5 0.10
16 22 0.42
18 15 0.29
ACGTcount: A:0.39, C:0.01, G:0.15, T:0.44
Consensus pattern (16 bp):
TTATGTAAGTTATGAA
Found at i:35712344 original size:28 final size:28
Alignment explanation
Indices: 35712281--35712434 Score: 220
Period size: 28 Copynumber: 5.5 Consensus size: 28
35712271 ATATTAAGTC
*
35712281 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
35712308 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
35712336 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
*
35712364 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
35712392 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
35712421 CGCACACTTAGTGC
1 CGCACACTTAGTGC
35712435 CAATCTCATG
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 75 0.65
29 19 0.16
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:35716906 original size:23 final size:24
Alignment explanation
Indices: 35716865--35716915 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
35716855 TCCCTAACTT
* *
35716865 TAAACCCCTAGCACGTCTAACCCC
1 TAAACCCCTAACACCTCTAACCCC
*
35716889 TAAACCCCTAAC-CCTCTAGCCCC
1 TAAACCCCTAACACCTCTAACCCC
35716912 TAAA
1 TAAA
35716916 TCTTAAATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.31, C:0.45, G:0.06, T:0.18
Consensus pattern (24 bp):
TAAACCCCTAACACCTCTAACCCC
Found at i:35717288 original size:41 final size:40
Alignment explanation
Indices: 35717212--35717294 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
35717202 TAAAATATTT
* * *
35717212 TTAGCGGCGCTTTTCAAAAAAGTCGCTAAATCCCCCAGCA
1 TTAGCGGCGCTTTTCAAAAAAGCCGCCAAAGCCCCCAGCA
*
35717252 TTAGCGGCGCTTTTTCAAAAACGCCGCCAAAGCCCCCAGCA
1 TTAGCGGCGC-TTTTCAAAAAAGCCGCCAAAGCCCCCAGCA
35717293 TT
1 TT
35717295 TTTGGCCGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
40 10 0.26
41 28 0.74
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGCTTTTCAAAAAAGCCGCCAAAGCCCCCAGCA
Found at i:35718003 original size:113 final size:113
Alignment explanation
Indices: 35717299--35718161 Score: 1081
Period size: 114 Copynumber: 7.6 Consensus size: 113
35717289 AGCATTTTTG
* *
35717299 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTG
1 GCCGCTAAAT-CCCGAAAGCTCACAAAACGACGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTC
* * *
35717364 TCAAAAACGCCGATAAAACCCTGAGCATTAGCGGCGCTTCCTTAAAAAC
65 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * *
35717413 GCCGCTAAATCACCGAAAGTTCACAAAACGACGTCGTTGGGCCTATGTTTTTTTGGGGCGCTTTC
1 GCCGCTAAATC-CCGAAAGCTCACAAAACGACGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTC
* * **
35717478 CCAAAAACGCCACTAAAGCCCTGAGCATTAGTAGCGCTTTCTTAAAAAC
65 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * * *
35717527 GACGCTAAATCCTCGAAAGCTCACAAAACGGCGACGTTGGGCTTATGTTTTTTTTTGCGGTGCTT
1 GCCGCTAAATCC-CGAAAGCTCACAAAACGACGTCGTTGGGCTTATG--TTTTTTTGCGGCGCTT
* * *
35717592 TCTCAAAAACGCCGCTAAAACCCTGAGCATTAGCAGCGCTTCCTTAAAAAC
63 TCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * * * *
35717643 GCCACTAAATCCCCGAAAGCTCACAAAACAACATCGTTGGGCTTTTGTTTTTTTGCGGTGCTTTG
1 GCCGCTAAAT-CCCGAAAGCTCACAAAACGACGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTT-
* *
35717708 C-CAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAT
64 CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * * * *
35717757 GCCACTAAATCCCTGAAAACTCACAAAAC-AGCGTCATTGGGATTATGTTTTTTTGCGGCGATTT
1 GCCGCTAAATCCC-GAAAGCTCACAAAACGA-CGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTT
* *
35717821 CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGTGGCACTTTCTTAAAAAC
64 CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * * * *
35717871 GCCGTTAAATCCCCGAAAGCTCAGAAAACGACATCGTTGTGCTTA-GATTTTTTGCGGCGCTTTC
1 GCCGCTAAAT-CCCGAAAGCTCACAAAACGACGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTC
* *
35717935 TCAAAAATGCCGCTAAAACCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
65 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * * * * *
35717984 GCCGTTAAATCCTCGAAAGCTCACAAAACGGCGTCTTTGGGCTTATTTTTTTTTGCAGTGCTTTG
1 GCCGCTAAATCC-CGAAAGCTCACAAAACGACGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTT-
* *
35718049 C-CAAAAAC-TCACTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
64 CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * * * * *
35718097 GCCGCAAAATCCCCAGAAGTTCACAAAACGGCGTCGTTGTGCTTA-GGTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCGA-AAGCTCACAAAACGACGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTC
35718161 T
65 T
35718162 GGAAACGCCG
Statistics
Matches: 649, Mismatches: 84, Indels: 34
0.85 0.11 0.04
Matches are distributed among these distances:
111 1 0.00
112 18 0.03
113 179 0.28
114 346 0.53
115 6 0.01
116 97 0.15
117 2 0.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (113 bp):
GCCGCTAAATCCCGAAAGCTCACAAAACGACGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTCT
CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
Found at i:35722186 original size:25 final size:25
Alignment explanation
Indices: 35722158--35722215 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
35722148 GCGAGCCATT
*
35722158 TATCGGGAAGCTCAAGAGAGCCAAA
1 TATCGGGAAACTCAAGAGAGCCAAA
** * *
35722183 TATCGAAAAACTCATGATAGCCAAA
1 TATCGGGAAACTCAAGAGAGCCAAA
35722208 TATCGGGA
1 TATCGGGA
35722216 TTCTCATAAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.17
Consensus pattern (25 bp):
TATCGGGAAACTCAAGAGAGCCAAA
Found at i:35722690 original size:26 final size:28
Alignment explanation
Indices: 35722661--35722728 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
35722651 AATCCTTATT
*
35722661 TCAAGACTAA-CC-GATTTTCATACATA
1 TCAAGACAAACCCAGATTTTCATACATA
* * *
35722687 TCAATAGAAACCCATATTTTCATACATA
1 TCAAGACAAACCCAGATTTTCATACATA
* *
35722715 TCAATAGAAACCCA
1 TCAAGACAAACCCA
35722729 TATCAATAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 7 0.19
27 2 0.06
28 27 0.75
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.28
Consensus pattern (28 bp):
TCAAGACAAACCCAGATTTTCATACATA
Found at i:35722709 original size:28 final size:28
Alignment explanation
Indices: 35722674--35722731 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
35722664 AGACTAACCG
35722674 ATTTTCATACATATCAATAGAAACCCAT
1 ATTTTCATACATATCAATAGAAACCCAT
35722702 ATTTTCATACATATCAATAGAAACCCAT
1 ATTTTCATACATATCAATAGAAACCCAT
35722730 AT
1 AT
35722732 CAATAGAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (28 bp):
ATTTTCATACATATCAATAGAAACCCAT
Found at i:35722732 original size:16 final size:16
Alignment explanation
Indices: 35722711--35722741 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35722701 TATTTTCATA
35722711 CATATCAATAGAAACC
1 CATATCAATAGAAACC
35722727 CATATCAATAGAAAC
1 CATATCAATAGAAAC
35722742 TCTATTGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.23, G:0.06, T:0.19
Consensus pattern (16 bp):
CATATCAATAGAAACC
Found at i:35726901 original size:13 final size:11
Alignment explanation
Indices: 35726847--35726895 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 11
35726837 TTCAGATCCG
35726847 ATCAAAAAAAT
1 ATCAAAAAAAT
35726858 ATTTCAAAAAAAT
1 A--TCAAAAAAAT
35726871 ATCAAAATCAAA-
1 ATCAAAA--AAAT
35726883 ATCAAAAAAAT
1 ATCAAAAAAAT
35726894 AT
1 AT
35726896 TTCAAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 3 0.09
11 9 0.27
12 7 0.21
13 14 0.42
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.22
Consensus pattern (11 bp):
ATCAAAAAAAT
Found at i:35726943 original size:6 final size:6
Alignment explanation
Indices: 35726934--35726973 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
35726924 TGAAAATGAT
*
35726934 GAAAAA G-AAAA GAAAAA G-AGAA GAAAAA G-AAAA GAAAAA G
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G
35726974 GAGAGACCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
5 14 0.48
6 15 0.52
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:35726950 original size:11 final size:11
Alignment explanation
Indices: 35726934--35726973 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
35726924 TGAAAATGAT
35726934 GAAAAAGAAAA
1 GAAAAAGAAAA
*
35726945 GAAAAAGAGAA
1 GAAAAAGAAAA
35726956 GAAAAAGAAAA
1 GAAAAAGAAAA
35726967 GAAAAAG
1 GAAAAAG
35726974 GAGAGACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:35727931 original size:13 final size:12
Alignment explanation
Indices: 35727913--35727960 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
35727903 CTTTGAGTCA
*
35727913 AAAAAATAAAAAT
1 AAAAAA-AAAAAG
*
35727926 AAAAAAATAAAG
1 AAAAAAAAAAAG
35727938 AAAAAAGAAAAAG
1 AAAAAA-AAAAAG
35727951 AAAAAGAAAA
1 AAAAA-AAAA
35727961 TGGAGAGGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 10 0.33
13 19 0.63
14 1 0.03
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:35727948 original size:6 final size:6
Alignment explanation
Indices: 35727914--35727960 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
35727904 TTTGAGTCAA
* *
35727914 AAAAAT AAAAAT AAAAA- AATAAAG AAAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AA-AAAG -AAAAAG AAAAAG AAAAAG AAAA
35727961 TGGAGAGGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.05
6 30 0.79
7 4 0.11
8 2 0.05
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (6 bp):
AAAAAG
Found at i:35727948 original size:19 final size:19
Alignment explanation
Indices: 35727920--35727960 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
35727910 TCAAAAAAAT
*
35727920 AAAAATAAAAA-AATAAAGA
1 AAAAAGAAAAAGAA-AAAGA
35727939 AAAAAGAAAAAGAAAAAGA
1 AAAAAGAAAAAGAAAAAGA
35727958 AAA
1 AAA
35727961 TGGAGAGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAAAGA
Found at i:35729338 original size:50 final size:50
Alignment explanation
Indices: 35729216--35729855 Score: 725
Period size: 50 Copynumber: 12.8 Consensus size: 50
35729206 CTGGCATTGT
* *
35729216 AGTGGAACAGATTAAAGCTACAACAGTGAATCTTACTT-CCCGGCGTGGC
1 AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
* * * ** * *
35729265 ATTGAAATAGATTAAAGCTACAACAATGAATCTTACTTCCCTGGCGGTGC
1 AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
*
35729315 AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTAC
1 AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
* * * *
35729365 GGTGAAACAGATTAAAGCTACAACAGTGAATCTTACTTCCCAGGCGTTGC
1 AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
* * * ** *
35729415 AGTGAAACAGATTAAGGCTACAACAGCAAATCTTACTTCCTTGGCGGTGC
1 AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
* * * *
35729465 AGTGGAACAGATTAAAGCTACAATAGCAAATCTTACTT-CCCAGTGTTGC
1 AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
* * * *
35729514 AATGAAACAAATTAAAGCTACAATAGCGAATCTTACTTCCCCGGCGTTGC
1 AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
* * * * *** *
35729564 AATAGAACAGATTGAAGCTACAATAGCGAATCTTACTTCTATGGCATTGC
1 AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
* * *
35729614 AGTGAAACAGATTAAAGCTACAACAGTGAATCTTACTTCCCCGGCGTGGC
1 AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
* * *
35729664 AGT-GAAGCAGATTAAAGCTACAACAGTGAATCTTACTTCCCCGACATTGC
1 AGTGGAA-CAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
* * **
35729714 AGT-GAAGTAGGTTAAAGCTACAACAATGAATCTTACTTCCCCGGCGTTGC
1 AGTGGAA-CAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
* * *
35729764 GGT-GAGACAGATTAAAGCTACAACAGC-AGATCTTACTTCCCCAGCGTTAC
1 AGTGGA-ACAGATTAAAGCTACAACAGCGA-ATCTTACTTCCCCGGCGTTGC
* * * *
35729814 AATGAAACAGATTAAAGCTACAACAACGAATCTTATTTCCCC
1 AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCC
35729856 TGTAATATCC
Statistics
Matches: 503, Mismatches: 81, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
49 77 0.15
50 423 0.84
51 3 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (50 bp):
AGTGGAACAGATTAAAGCTACAACAGCGAATCTTACTTCCCCGGCGTTGC
Found at i:35729654 original size:249 final size:248
Alignment explanation
Indices: 35729216--35729853 Score: 812
Period size: 249 Copynumber: 2.6 Consensus size: 248
35729206 CTGGCATTGT
* * *
35729216 AGTGGAACAGATTAAAGCTACAACAGTGAATCTTACTTCCCGGCGTGGCATTGAAATAGATTAAA
1 AGTGGAACAGATTAAAGCTACAACAGTGAATCTTACTTCCCGGCGTTGCAATGAAACAGATTAAA
** * * *
35729281 GCTACAACAATGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCTACAACAGCGAAT
66 GCTACAACAGCGAATCTTACTTCCCCGGCGTTGCAAT-GAACAGATTAAAGCTACAACAGCGAAT
* * *
35729346 CTTACTTCCCCGGCGTTACGGTGAAACAGATTAAAGCTACAACAGTGAATCTTACTTCCCAGGCG
130 CTTACTTCCACGGCATTACAGTGAAACAGATTAAAGCTACAACAGTGAATCTTACTTCCCAGGCG
* * ** * *
35729411 TTGCAGTGAAACAGATTAAGGCTACAACAGCAAATCTTACTTCCTTGGCGGTGC
195 TGGCAGTGAAACAGATTAAAGCTACAACAGCAAATCTTACTTCCCCGACAGTGC
* ** * * *
35729465 AGTGGAACAGATTAAAGCTACAATAGCAAATCTTACTTCCCAGTGTTGCAATGAAACAAATTAAA
1 AGTGGAACAGATTAAAGCTACAACAGTGAATCTTACTTCCCGGCGTTGCAATGAAACAGATTAAA
* * *
35729530 GCTACAATAGCGAATCTTACTTCCCCGGCGTTGCAATAGAACAGATTGAAGCTACAATAGCGAAT
66 GCTACAACAGCGAATCTTACTTCCCCGGCGTTGCAAT-GAACAGATTAAAGCTACAACAGCGAAT
* * * *
35729595 CTTACTTCTATGGCATTGCAGTGAAACAGATTAAAGCTACAACAGTGAATCTTACTTCCCCGGCG
130 CTTACTTCCACGGCATTACAGTGAAACAGATTAAAGCTACAACAGTGAATCTTACTTCCCAGGCG
* ** *
35729660 TGGCAGTGAAGCAGATTAAAGCTACAACAGTGAATCTTACTTCCCCGACATTGC
195 TGGCAGTGAAACAGATTAAAGCTACAACAGCAAATCTTACTTCCCCGACAGTGC
* * * ** *
35729714 AGT-GAAGTAGGTTAAAGCTACAACAATGAATCTTACTTCCCCGGCGTTGCGGTGAGACAGATTA
1 AGTGGAA-CAGATTAAAGCTACAACAGTGAATCTTACTT-CCCGGCGTTGCAATGAAACAGATTA
* * *
35729778 AAGCTACAACAGC-AGATCTTACTTCCCCAGCGTTACAATGAAACAGATTAAAGCTACAACAACG
64 AAGCTACAACAGCGA-ATCTTACTTCCCCGGCGTTGCAATG-AACAGATTAAAGCTACAACAGCG
*
35729842 AATCTTATTTCC
127 AATCTTACTTCC
35729854 CCTGTAATAT
Statistics
Matches: 330, Mismatches: 55, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
248 3 0.01
249 244 0.74
250 83 0.25
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (248 bp):
AGTGGAACAGATTAAAGCTACAACAGTGAATCTTACTTCCCGGCGTTGCAATGAAACAGATTAAA
GCTACAACAGCGAATCTTACTTCCCCGGCGTTGCAATGAACAGATTAAAGCTACAACAGCGAATC
TTACTTCCACGGCATTACAGTGAAACAGATTAAAGCTACAACAGTGAATCTTACTTCCCAGGCGT
GGCAGTGAAACAGATTAAAGCTACAACAGCAAATCTTACTTCCCCGACAGTGC
Found at i:35729885 original size:23 final size:23
Alignment explanation
Indices: 35729855--35729906 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
35729845 CTTATTTCCC
* *
35729855 CTGTAATATCCTAAAAATTACTA
1 CTGTAATACCCCAAAAATTACTA
*
35729878 CTGTAATACCCCGAAAATTACTA
1 CTGTAATACCCCAAAAATTACTA
*
35729901 CAGTAA
1 CTGTAA
35729907 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (23 bp):
CTGTAATACCCCAAAAATTACTA
Found at i:35730402 original size:8 final size:8
Alignment explanation
Indices: 35730389--35730426 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
35730379 TTTTAGATAA
35730389 TATTTTAT
1 TATTTTAT
35730397 TATTTTAT
1 TATTTTAT
35730405 TATTTTAT
1 TATTTTAT
*
35730413 TATTATTTT
1 TATT-TTAT
35730422 TATTT
1 TATTT
35730427 AGTATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:35738700 original size:50 final size:50
Alignment explanation
Indices: 35738641--35738750 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
35738631 TTCATATTCC
* *
35738641 GGAATGCTCATACGAGC-ATGTAAACAGGAAGCTCTTTCGAGCCATATAACG
1 GGAA-GCTCATACGAGCGAAGT-AACAGGAAGCTCTTGCGAGCCATATAACG
** * * * *
35738692 GGAAGCTCATGTGAGCGAAGTAACGGGAAGCTCTTGCGAGCCATTTATCT
1 GGAAGCTCATACGAGCGAAGTAACAGGAAGCTCTTGCGAGCCATATAACG
35738742 GGAAGCTCA
1 GGAAGCTCA
35738751 ATAGAGCCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
50 43 0.86
51 7 0.14
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (50 bp):
GGAAGCTCATACGAGCGAAGTAACAGGAAGCTCTTGCGAGCCATATAACG
Found at i:35738707 original size:25 final size:25
Alignment explanation
Indices: 35738641--35738750 Score: 80
Period size: 25 Copynumber: 4.4 Consensus size: 25
35738631 TTCATATTCC
* * *
35738641 GGAATGCTCATACGAG-CATGTAAACA
1 GGAA-GCTCATGCGAGCCATAT-AACG
* *
35738667 GGAAGCTCTTTCGAGCCATATAACG
1 GGAAGCTCATGCGAGCCATATAACG
* *
35738692 GGAAGCTCATGTGAGCGA-AGTAACG
1 GGAAGCTCATGCGAGCCATA-TAACG
* * * *
35738717 GGAAGCTCTTGCGAGCCATTTATCT
1 GGAAGCTCATGCGAGCCATATAACG
35738742 GGAAGCTCA
1 GGAAGCTCA
35738751 ATAGAGCCAA
Statistics
Matches: 66, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
24 1 0.02
25 57 0.86
26 8 0.12
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (25 bp):
GGAAGCTCATGCGAGCCATATAACG
Found at i:35741132 original size:23 final size:23
Alignment explanation
Indices: 35741106--35741215 Score: 73
Period size: 23 Copynumber: 4.9 Consensus size: 23
35741096 TGCACCACAA
*
35741106 AGGCCAAACAGAGTATGCCATAT
1 AGGCCAAACAGAATATGCCATAT
** * * *
35741129 AGGCTTAGCA-AATTATGCCACAA
1 AGGCCAAACAGAA-TATGCCATAT
*
35741152 AGGCCAAACAGAATACGCCATAT
1 AGGCCAAACAGAATATGCCATAT
** * * *
35741175 AGGCTTAGCAAAATATGCCATAA
1 AGGCCAAACAGAATATGCCATAT
*
35741198 AGCCCAAACA-AA-ATGCCA
1 AGGCCAAACAGAATATGCCA
35741216 CCCAGGCATT
Statistics
Matches: 63, Mismatches: 22, Indels: 6
0.69 0.24 0.07
Matches are distributed among these distances:
21 6 0.10
22 3 0.05
23 52 0.83
24 2 0.03
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (23 bp):
AGGCCAAACAGAATATGCCATAT
Found at i:35741157 original size:46 final size:46
Alignment explanation
Indices: 35741100--35741207 Score: 171
Period size: 46 Copynumber: 2.3 Consensus size: 46
35741090 ACATAATGCA
* * *
35741100 CCACAAAGGCCAAACAGAGTATGCCATATAGGCTTAGCAAATTATG
1 CCACAAAGGCCAAACAGAATACGCCATATAGGCTTAGCAAAATATG
35741146 CCACAAAGGCCAAACAGAATACGCCATATAGGCTTAGCAAAATATG
1 CCACAAAGGCCAAACAGAATACGCCATATAGGCTTAGCAAAATATG
* *
35741192 CCATAAAGCCCAAACA
1 CCACAAAGGCCAAACA
35741208 AAATGCCACC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.16
Consensus pattern (46 bp):
CCACAAAGGCCAAACAGAATACGCCATATAGGCTTAGCAAAATATG
Found at i:35741726 original size:25 final size:25
Alignment explanation
Indices: 35741698--35741781 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 25
35741688 ACAGTTGGTA
35741698 AGAGCATACCGATTTATAGCTTGTG
1 AGAGCATACCGATTTATAGCTTGTG
* * * *
35741723 AGAGTATATCAATTTATAGCTCGTG
1 AGAGCATACCGATTTATAGCTTGTG
*
35741748 AGAGCATACCGATTCATAGCTTGT-
1 AGAGCATACCGATTTATAGCTTGTG
35741772 ATGAGCATAC
1 A-GAGCATAC
35741782 ATGTACGTGA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 1 0.02
25 48 0.98
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (25 bp):
AGAGCATACCGATTTATAGCTTGTG
Found at i:35743539 original size:17 final size:17
Alignment explanation
Indices: 35743517--35743554 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
35743507 CACTTGCCCA
35743517 TGTGTGGCAAACGACCG
1 TGTGTGGCAAACGACCG
* *
35743534 TGTGTGGCACATGACCG
1 TGTGTGGCAAACGACCG
35743551 TGTG
1 TGTG
35743555 AGCAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (17 bp):
TGTGTGGCAAACGACCG
Found at i:35755971 original size:19 final size:21
Alignment explanation
Indices: 35755947--35755991 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
35755937 CAACCCAATT
35755947 TTTATTTTTA-TTT-TTTTAC
1 TTTATTTTTATTTTATTTTAC
35755966 TTTA-TTTTATTTTATTTTAC
1 TTTATTTTTATTTTATTTTAC
35755986 -TTATTT
1 TTTATTT
35755992 GGATATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.22
19 10 0.43
20 8 0.35
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATTTTTATTTTATTTTAC
Found at i:35760145 original size:7 final size:6
Alignment explanation
Indices: 35760131--35760191 Score: 50
Period size: 6 Copynumber: 9.3 Consensus size: 6
35760121 TTATTTTCTA
* * *
35760131 TTTATT TTTATT TTTATT CTTATTT TTTACTT TTTACT TTTAGTTGT TTTCTT
1 TTTATT TTTATT TTTATT TTTA-TT TTTA-TT TTTATT TTTA--T-T TTTATT
35760184 TTTATT TT
1 TTTATT TT
35760192 CTTAGCCTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
6 28 0.64
7 12 0.27
9 4 0.09
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:35760191 original size:20 final size:18
Alignment explanation
Indices: 35760131--35760191 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 18
35760121 TTATTTTCTA
*
35760131 TTTA-TTTTTATTTTTAT
1 TTTATTTTTTCTTTTTAT
35760148 TCTTATTTTTTACTTTTTACT
1 T-TTATTTTTT-CTTTTTA-T
35760169 TTTAGTTGTTTTCTTTTTAT
1 TTTA-TT-TTTTCTTTTTAT
35760189 TTT
1 TTT
35760192 CTTAGCCTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 1 0.03
18 3 0.08
19 5 0.14
20 13 0.35
21 11 0.30
22 4 0.11
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTATTTTTTCTTTTTAT
Found at i:35763073 original size:22 final size:22
Alignment explanation
Indices: 35763048--35763090 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35763038 GATAAATGTT
*
35763048 ATTTAATTATTATTTTATTAAG
1 ATTTAAGTATTATTTTATTAAG
*
35763070 ATTTTAGTATTATTTTATTAA
1 ATTTAAGTATTATTTTATTAA
35763091 TAAATGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTTAAGTATTATTTTATTAAG
Found at i:35774972 original size:7 final size:7
Alignment explanation
Indices: 35774962--35775002 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
35774952 CTTTTAATCA
35774962 ATTTACC
1 ATTTACC
35774969 ATTTGACC
1 ATTT-ACC
35774977 ATTTACC
1 ATTTACC
*
35774984 ATTTAGC
1 ATTTACC
35774991 ATTTGACC
1 ATTT-ACC
35774999 ATTT
1 ATTT
35775003 TACACTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
7 17 0.57
8 13 0.43
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (7 bp):
ATTTACC
Found at i:35774982 original size:15 final size:14
Alignment explanation
Indices: 35774962--35775002 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
35774952 CTTTTAATCA
35774962 ATTTACCATTTGACC
1 ATTTACCATTT-ACC
*
35774977 ATTTACCATTTAGC
1 ATTTACCATTTACC
35774991 ATTTGACCATTT
1 ATTT-ACCATTT
35775003 TACACTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (14 bp):
ATTTACCATTTACC
Found at i:35775030 original size:19 final size:19
Alignment explanation
Indices: 35774969--35775030 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
35774959 TCAATTTACC
*
35774969 ATTTGACCATTTACCATTT
1 ATTTGACCATTTTCCATTT
* *
35774988 AGCATTTGACCATTTTACACTT
1 ---ATTTGACCATTTTCCATTT
35775010 ATTTGACCATTTTCCATTT
1 ATTTGACCATTTTCCATTT
35775029 AT
1 AT
35775031 CAATATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 19 0.54
22 16 0.46
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (19 bp):
ATTTGACCATTTTCCATTT
Found at i:35779581 original size:23 final size:23
Alignment explanation
Indices: 35779553--35779596 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
35779543 GAATAATATG
35779553 ATTATTCTTAAAAGATCCTTATT
1 ATTATTCTTAAAAGATCCTTATT
35779576 ATTATTCTTAAAAGATCCTTA
1 ATTATTCTTAAAAGATCCTTA
35779597 ATCAAGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (23 bp):
ATTATTCTTAAAAGATCCTTATT
Found at i:35781620 original size:27 final size:26
Alignment explanation
Indices: 35781579--35781725 Score: 95
Period size: 27 Copynumber: 5.5 Consensus size: 26
35781569 GGCCTTCAGA
* **
35781579 AAGGTAAAATTACTAAAATATGCTCG
1 AAGGTAAAATGACTAAAATACCCTCG
*
35781605 AAGGATAAAATGACTAGAATACCCTCG
1 AAGG-TAAAATGACTAAAATACCCTCG
* * *
35781632 AAGGGTAAAATGA-TCGAAATACCCCCA
1 AA-GGTAAAATGACT-AAAATACCCTCG
* *
35781659 AAGGGTAAAATTGTC-GAAATATCCC-CG
1 AA-GGTAAAA-TGACTAAAATA-CCCTCG
*
35781686 AAGGGTAAAATGACTGAAATACCCT-G
1 AA-GGTAAAATGACTAAAATACCCTCG
*
35781712 TAGGATAAAATGAC
1 AAGG-TAAAATGAC
35781726 CGTAATGCCC
Statistics
Matches: 100, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
25 2 0.02
26 22 0.22
27 69 0.69
28 7 0.07
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (26 bp):
AAGGTAAAATGACTAAAATACCCTCG
Found at i:35781747 original size:27 final size:27
Alignment explanation
Indices: 35781687--35781803 Score: 155
Period size: 27 Copynumber: 4.4 Consensus size: 27
35781677 ATATCCCCGA
* * * *
35781687 AGGGTAAAATGACTGAAAT-ACCCTGT
1 AGGGTAAAATGACCGTAATGCCCCTAT
*
35781713 AGGATAAAATGACCGTAATGCCCCTAT
1 AGGGTAAAATGACCGTAATGCCCCTAT
35781740 AGGGTAAAATGACCGTAATGCCCCTAT
1 AGGGTAAAATGACCGTAATGCCCCTAT
* * *
35781767 AGGGTAAATTGACCGTAATACCCCTGT
1 AGGGTAAAATGACCGTAATGCCCCTAT
35781794 AGGGTAAAAT
1 AGGGTAAAAT
35781804 AACTATTTTG
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 16 0.20
27 64 0.80
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (27 bp):
AGGGTAAAATGACCGTAATGCCCCTAT
Found at i:35781749 original size:53 final size:54
Alignment explanation
Indices: 35781606--35781803 Score: 156
Period size: 54 Copynumber: 3.7 Consensus size: 54
35781596 ATATGCTCGA
* * * * *
35781606 AGGATAAAATGACTAG-AATACCCTCGA-AGGGTAAAATGATCGAAAT-ACCCCCAA
1 AGGATAAAATGAC-CGTAATACCC-CTATAGGGTAAAATGACCGAAATGA-CCCTAT
* * * * * *
35781660 AGGGTAAAATTG-TCGAAATATCCCCGA-AGGGTAAAATGACTGAAAT-ACCCTGT
1 AGGATAAAA-TGACCGTAATA-CCCCTATAGGGTAAAATGACCGAAATGACCCTAT
* * *
35781713 AGGATAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGTAATGCCCCTAT
1 AGGATAAAATGACCGTAATACCCCTATAGGGTAAAATGACCGAAATGACCCTAT
* * *
35781767 AGGGTAAATTGACCGTAATACCCCTGTAGGGTAAAAT
1 AGGATAAAATGACCGTAATACCCCTATAGGGTAAAAT
35781804 AACTATTTTG
Statistics
Matches: 117, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
52 7 0.06
53 34 0.29
54 71 0.61
55 5 0.04
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (54 bp):
AGGATAAAATGACCGTAATACCCCTATAGGGTAAAATGACCGAAATGACCCTAT
Done.