Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 36 of 335
Found at i:13218258 original size:102 final size:102
Alignment explanation
Indices: 13218082--13218286 Score: 410
Period size: 102 Copynumber: 2.0 Consensus size: 102
13218072 TGTAAGGAAT
13218082 AAGTTGTTAATATCCGTTCAGACACGTGGACCTATATCCTGTACATGCATTTGAAAAGAGCAGCT
1 AAGTTGTTAATATCCGTTCAGACACGTGGACCTATATCCTGTACATGCATTTGAAAAGAGCAGCT
13218147 TGCCGAAGAATGTCAAAAGATAAATTTGACACCACTA
66 TGCCGAAGAATGTCAAAAGATAAATTTGACACCACTA
13218184 AAGTTGTTAATATCCGTTCAGACACGTGGACCTATATCCTGTACATGCATTTGAAAAGAGCAGCT
1 AAGTTGTTAATATCCGTTCAGACACGTGGACCTATATCCTGTACATGCATTTGAAAAGAGCAGCT
13218249 TGCCGAAGAATGTCAAAAGATAAATTTGACACCACTA
66 TGCCGAAGAATGTCAAAAGATAAATTTGACACCACTA
13218286 A
1 A
13218287 TCGGTACAGG
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (102 bp):
AAGTTGTTAATATCCGTTCAGACACGTGGACCTATATCCTGTACATGCATTTGAAAAGAGCAGCT
TGCCGAAGAATGTCAAAAGATAAATTTGACACCACTA
Found at i:13227456 original size:40 final size:40
Alignment explanation
Indices: 13227401--13227477 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
13227391 GGCACTCTTT
13227401 CTAAGGCTTTATTTAGGTAAACAACAAACAAGTAATCATG
1 CTAAGGCTTTATTTAGGTAAACAACAAACAAGTAATCATG
13227441 CTAAGGCTTTATTTAGGTAAACAACAAACAAGTAATC
1 CTAAGGCTTTATTTAGGTAAACAACAAACAAGTAATC
13227478 TTGTTGAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (40 bp):
CTAAGGCTTTATTTAGGTAAACAACAAACAAGTAATCATG
Found at i:13229610 original size:24 final size:24
Alignment explanation
Indices: 13229583--13229643 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
13229573 AAATTTCAAT
*
13229583 TATTTCCAAATTTGAGA-ATTAAAA
1 TATTT-CAAATTTAAGATATTAAAA
* *
13229607 TATTTGAAATTTAAGATTTTAAAA
1 TATTTCAAATTTAAGATATTAAAA
*
13229631 TAATTCAAATTTA
1 TATTTCAAATTTA
13229644 TTGTTTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 9 0.29
24 22 0.71
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.43
Consensus pattern (24 bp):
TATTTCAAATTTAAGATATTAAAA
Found at i:13232658 original size:39 final size:38
Alignment explanation
Indices: 13232615--13232721 Score: 178
Period size: 39 Copynumber: 2.7 Consensus size: 38
13232605 TTTTATTGAT
13232615 TGGTTAACAGGAAGATGATGTCATAGATTTTAAAATTAA
1 TGGTTAAC-GGAAGATGATGTCATAGATTTTAAAATTAA
13232654 TGGTTAACGGAAAGATGATGTCATAGATTTTAAAATTAA
1 TGGTTAACGG-AAGATGATGTCATAGATTTTAAAATTAA
*
13232693 TGGTTAACGGGAAGATAATGTCATAGATT
1 TGGTTAAC-GGAAGATGATGTCATAGATT
13232722 ACATAATAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
38 2 0.03
39 61 0.94
40 2 0.03
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (38 bp):
TGGTTAACGGAAGATGATGTCATAGATTTTAAAATTAA
Found at i:13236238 original size:25 final size:25
Alignment explanation
Indices: 13236210--13236260 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
13236200 TCATCTTTTC
*
13236210 ATTAACTATATAATTGTTGGTGATA
1 ATTAACTATATAATTGTTGGAGATA
*
13236235 ATTAACTATTTAATTGTTGGAGATA
1 ATTAACTATATAATTGTTGGAGATA
13236260 A
1 A
13236261 AAATATAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.43
Consensus pattern (25 bp):
ATTAACTATATAATTGTTGGAGATA
Found at i:13239563 original size:3 final size:3
Alignment explanation
Indices: 13239555--13239599 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
13239545 AGATGCAAAT
13239555 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13239600 TCTGTTTGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13242140 original size:2 final size:2
Alignment explanation
Indices: 13242133--13242157 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13242123 TTAATTTAGA
13242133 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13242158 ATTTTCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13246966 original size:53 final size:53
Alignment explanation
Indices: 13246852--13246953 Score: 204
Period size: 53 Copynumber: 1.9 Consensus size: 53
13246842 AAAATCAGTT
13246852 AAAAAAAAAGAGCTTTTCAAAAAATTTATAAAATTTTAGTTTTAACTTTAAAA
1 AAAAAAAAAGAGCTTTTCAAAAAATTTATAAAATTTTAGTTTTAACTTTAAAA
13246905 AAAAAAAAAGAGCTTTTCAAAAAATTTATAAAATTTTAGTTTTAACTTT
1 AAAAAAAAAGAGCTTTTCAAAAAATTTATAAAATTTTAGTTTTAACTTT
13246954 CTTTTTAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (53 bp):
AAAAAAAAAGAGCTTTTCAAAAAATTTATAAAATTTTAGTTTTAACTTTAAAA
Found at i:13248486 original size:25 final size:25
Alignment explanation
Indices: 13248458--13248517 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
13248448 CAAATTTTGA
*
13248458 TATTTCGATCCGAACAAATCTTTAC
1 TATTTCAATCCGAACAAATCTTTAC
* **
13248483 TATTTTAATCTTAACAAATCTTTAC
1 TATTTCAATCCGAACAAATCTTTAC
*
13248508 TATTTTAATC
1 TATTTCAATC
13248518 TTAATCAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.45
Consensus pattern (25 bp):
TATTTCAATCCGAACAAATCTTTAC
Found at i:13248518 original size:25 final size:25
Alignment explanation
Indices: 13248470--13248521 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
13248460 TTTCGATCCG
13248470 AACAAATCTTTACTATTTTAATCTT
1 AACAAATCTTTACTATTTTAATCTT
13248495 AACAAATCTTTACTATTTTAATCTT
1 AACAAATCTTTACTATTTTAATCTT
13248520 AA
1 AA
13248522 TCAGTAATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (25 bp):
AACAAATCTTTACTATTTTAATCTT
Found at i:13255968 original size:331 final size:330
Alignment explanation
Indices: 13255343--13255975 Score: 908
Period size: 331 Copynumber: 1.9 Consensus size: 330
13255333 TTAAAAACTT
* *
13255343 TTATTTTAGACACCTAAAATAAATATTTACAATTTAAGCACCCACGTTACATAGTTTAATTATTT
1 TTATTTTAGACACCTAAAATAAAAATTTACAATTTAAGCACCCACATTACATAGTTTAATTATTT
*
13255408 TAGTCACTTCCATTAAAATCACAAATAACAAGTTGACGTAACTATTAAAGAAAATCAATATAATA
66 TAGTCACTTCCATTAAAATCACAAATAACAAGTTGACGTAACTATAAAAGAAAATCAATATAATA
* * * *
13255473 ATAAATATAGCTCTACACTTTTACATATTACATTAATTTAGTCGTAATTTTAAAAAATTAACTCT
131 ATAAATATAACTCTACACTTTTACATATTACATCAATTTAATCATAATTTTAAAAAATTAACTCT
13255538 CAAAATGTACAAATATTCTCAATCTAATCTTAATTCTAAAAACTAATATATATATATATATAAAT
196 CAAAATGTACAAATATTCTCAATCTAATCTTAATTCTAAAAACTAATATATATATATATATAAAT
13255603 AAATAAATATTAATATTAAATAATAATAAAAAACTTGCCATGCGTCACTAAATATATACCCGCTT
261 AAATAAATATTAATATT-AATAATAATAAAAAACTTGCCATGCGTCACTAAATATATACCCGCTT
13255668 GACTGA
325 GACTGA
* *
13255674 TTATTTTAGA-ATCCTAAAATAAAAATTTATAATTTAAGCACCCACATTATATAGTTTAATTATT
1 TTATTTTAGACA-CCTAAAATAAAAATTTACAATTTAAGCACCCACATTACATAGTTTAATTATT
* * * * * *
13255738 TT-GATCAGTTCTATTAAAATCACAAATGATAAGTTGATGTGACTATAAAAGAAAATCAATATAA
65 TTAG-TCACTTCCATTAAAATCACAAATAACAAGTTGACGTAACTATAAAAGAAAATCAATATAA
*
13255802 TAATAAATTTAAATTTAACTCT-CAACTTTTACATATTATATCAATTTAATCATAATTTTAAAAA
129 TAATAAA--T--A--TAACTCTAC-ACTTTTACATATTACATCAATTTAATCATAATTTTAAAAA
* * *
13255866 ATTAACTCTCAAAATTTATAAATATTCTCAATTTAATCTTAATTCTAAAAACTTCAA-A-A-A-A
187 ATTAACTCTCAAAATGTACAAATATTCTCAATCTAATCTTAATTCTAAAAAC-T-AATATATATA
*
13255927 TATATATAAATAAATAAATATTAATATT-A-AATAA-GAAAAACTTGCCATG
250 TATATATAAATAAATAAATATTAATATTAATAATAATAAAAAACTTGCCATG
13255976 AATATGTACC
Statistics
Matches: 271, Mismatches: 20, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
330 2 0.01
331 134 0.49
332 5 0.02
333 2 0.01
335 30 0.11
336 2 0.01
337 92 0.34
338 2 0.01
339 2 0.01
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (330 bp):
TTATTTTAGACACCTAAAATAAAAATTTACAATTTAAGCACCCACATTACATAGTTTAATTATTT
TAGTCACTTCCATTAAAATCACAAATAACAAGTTGACGTAACTATAAAAGAAAATCAATATAATA
ATAAATATAACTCTACACTTTTACATATTACATCAATTTAATCATAATTTTAAAAAATTAACTCT
CAAAATGTACAAATATTCTCAATCTAATCTTAATTCTAAAAACTAATATATATATATATATAAAT
AAATAAATATTAATATTAATAATAATAAAAAACTTGCCATGCGTCACTAAATATATACCCGCTTG
ACTGA
Found at i:13256590 original size:17 final size:17
Alignment explanation
Indices: 13256570--13256602 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13256560 TTGTTATGAG
*
13256570 TGGTATTTCAATTATTT
1 TGGTACTTCAATTATTT
13256587 TGGTACTTCAATTATT
1 TGGTACTTCAATTATT
13256603 CTTCCATTAT
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:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (17 bp):
TGGTACTTCAATTATTT
Found at i:13262669 original size:5 final size:5
Alignment explanation
Indices: 13262659--13262685 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
13262649 ATTCTGTGAG
13262659 GCACA GCACA GCACA GCACA GCACA GC
1 GCACA GCACA GCACA GCACA GCACA GC
13262686 CAAGGCATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.41, G:0.22, T:0.00
Consensus pattern (5 bp):
GCACA
Found at i:13276614 original size:21 final size:21
Alignment explanation
Indices: 13276594--13276644 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
13276584 AATTCTAATA
*
13276594 AATTTAAAATATATATA-AAT
1 AATTTAAAAAATATATAGAAT
*
13276614 ATTTTCAAAAAATATATAGTAAT
1 AATTT-AAAAAATATATAG-AAT
13276637 AATTTAAA
1 AATTTAAA
13276645 TTTTATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 3 0.12
23 7 0.28
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTTAAAAAATATATAGAAT
Found at i:13276694 original size:25 final size:24
Alignment explanation
Indices: 13276659--13276707 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
13276649 ATATTAAAAT
*
13276659 TTATATAAATATTAAATAAATATAA
1 TTATATAAATATTAAAGAAA-ATAA
*
13276684 TTATATTAATATTAAAGAAAATAA
1 TTATATAAATATTAAAGAAAATAA
13276708 GAATCCCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
TTATATAAATATTAAAGAAAATAA
Found at i:13280010 original size:12 final size:12
Alignment explanation
Indices: 13279993--13280017 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13279983 TCTTTCTCCC
13279993 ACCCTAAGTTTG
1 ACCCTAAGTTTG
13280005 ACCCTAAGTTTG
1 ACCCTAAGTTTG
13280017 A
1 A
13280018 TTAAAATAGA
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:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (12 bp):
ACCCTAAGTTTG
Found at i:13281665 original size:47 final size:47
Alignment explanation
Indices: 13281558--13281748 Score: 186
Period size: 47 Copynumber: 3.9 Consensus size: 47
13281548 AATGTGATTT
* * * *
13281558 CCGTATAAGACCATAGCTGGGCTATGGCTTCGGACAAATGTGATATGTGCTT
1 CCGTATAAGACCATATCTGGGATATGGCATCGG-----TGTGATATGTGCTA
*
13281610 CCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTA
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* * * *
13281657 CTGTATAAGACCATATTTGGGATATGGCATCAGTGTGATATGTGAT-
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* ** * *
13281703 CCGTGTAAGACCATGGCTGGGTTATGGCCTCGGTATGTGATATGTG
1 CCGTATAAGACCATATCTGGGATATGGCATCGG--TGTGATATGTG
13281749 ACTATGTGCA
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 25 0.21
47 54 0.45
48 11 0.09
52 29 0.24
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (47 bp):
CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
Found at i:13281781 original size:95 final size:93
Alignment explanation
Indices: 13281596--13281766 Score: 211
Period size: 93 Copynumber: 1.8 Consensus size: 93
13281586 TTCGGACAAA
* *
13281596 TGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
1 TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
*
13281661 ATAAGACCATATTTGGGATATGGCATCAG
66 ACAAGACCATATTT-GGATATGGCATCAG
* * * * *
13281690 TGTGATATGTG-ATCCGTGTAAGACCATGGCTGGGTTATGGCCTCGGTATGTGATATGTGACTA-
1 TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGG--TGTGATATGTG-CTAC
*
13281753 TGTGCAAGACCATA
63 TGTACAAGACCATA
13281767 GTTTTACTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
93 28 0.43
94 11 0.17
95 23 0.35
96 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (93 bp):
TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
ACAAGACCATATTTGGATATGGCATCAG
Found at i:13291441 original size:21 final size:21
Alignment explanation
Indices: 13291407--13291458 Score: 95
Period size: 21 Copynumber: 2.4 Consensus size: 21
13291397 GAAGAAAAAA
13291407 AAATCAATACCCAACATCAATC
1 AAATCAA-ACCCAACATCAATC
13291429 AAATCAAACCCAACATCAATC
1 AAATCAAACCCAACATCAATC
13291450 AAATCAAAC
1 AAATCAAAC
13291459 AAAAGAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (21 bp):
AAATCAAACCCAACATCAATC
Found at i:13294971 original size:53 final size:53
Alignment explanation
Indices: 13294890--13295040 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
13294880 CTTACACGGT
* *
13294890 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
13294945 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
13294998 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
13295041 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:13301963 original size:53 final size:53
Alignment explanation
Indices: 13301882--13302032 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
13301872 CTTACACGGT
* *
13301882 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
13301937 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
13301990 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
13302033 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:13306892 original size:26 final size:26
Alignment explanation
Indices: 13306862--13306920 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
13306852 AGGTGGAAAA
*
13306862 TGTAATTAAATCCATAGTCTAAATTT
1 TGTAATTAAATCCATAGTATAAATTT
13306888 TGTAATTAAATCCATAGTATAAATTT
1 TGTAATTAAATCCATAGTATAAATTT
*
13306914 TGGAATT
1 TGTAATT
13306921 TGTTAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (26 bp):
TGTAATTAAATCCATAGTATAAATTT
Found at i:13314808 original size:16 final size:17
Alignment explanation
Indices: 13314777--13314810 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13314767 TCATTAACAA
*
13314777 AATATACTTAAATAAAT
1 AATAGACTTAAATAAAT
13314794 AATAGACTT-AATAAAT
1 AATAGACTTAAATAAAT
13314810 A
1 A
13314811 GTGATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (17 bp):
AATAGACTTAAATAAAT
Found at i:13315171 original size:2 final size:2
Alignment explanation
Indices: 13315164--13315196 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13315154 GATAGGCTGC
13315164 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
13315197 TGCTATTATT
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:13316480 original size:2 final size:2
Alignment explanation
Indices: 13316473--13316498 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13316463 TGAACCAACT
13316473 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
13316499 GCAAAACAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13330907 original size:6 final size:6
Alignment explanation
Indices: 13330898--13330928 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
13330888 AGCACCAGAA
*
13330898 GCTGAT GCTGAT GCTGAT GCTGAT GCCGAT G
1 GCTGAT GCTGAT GCTGAT GCTGAT GCTGAT G
13330929 AACCCTCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.19, G:0.35, T:0.29
Consensus pattern (6 bp):
GCTGAT
Found at i:13337465 original size:27 final size:29
Alignment explanation
Indices: 13337435--13337496 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
13337425 AGTTTTAGAT
*
13337435 TTTTTTTTTATGAATT-G-AAATTTTTAA
1 TTTTTTTATATGAATTGGTAAATTTTTAA
* * *
13337462 TTTTTTTATATTATTTGGTAAGTTTTTAA
1 TTTTTTTATATGAATTGGTAAATTTTTAA
13337491 TTTTTT
1 TTTTTT
13337497 AAAATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 13 0.45
28 1 0.03
29 15 0.52
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (29 bp):
TTTTTTTATATGAATTGGTAAATTTTTAA
Found at i:13339260 original size:17 final size:18
Alignment explanation
Indices: 13339219--13339260 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
13339209 AAAAGAGGAA
13339219 AAAAT-AAAGAGAAAAAT
1 AAAATAAAAGAGAAAAAT
**
13339236 AACGTAAAAGA-AAAAAT
1 AAAATAAAAGAGAAAAAT
13339253 AAAATAAA
1 AAAATAAA
13339261 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (18 bp):
AAAATAAAAGAGAAAAAT
Found at i:13349440 original size:32 final size:32
Alignment explanation
Indices: 13349404--13349467 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
13349394 TTCAAGGGGA
13349404 ATACTTGTATCTTCATTTGATTTGAGAGGTTT
1 ATACTTGTATCTTCATTTGATTTGAGAGGTTT
13349436 ATACTTGTATCTTCATTTGATTTGAGAGGTTT
1 ATACTTGTATCTTCATTTGATTTGAGAGGTTT
13349468 TCATTTAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.09, G:0.19, T:0.50
Consensus pattern (32 bp):
ATACTTGTATCTTCATTTGATTTGAGAGGTTT
Found at i:13353116 original size:20 final size:21
Alignment explanation
Indices: 13353091--13353134 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
13353081 TTTTGATAAA
13353091 ATCGAAA-AATAAAATTCTCC
1 ATCGAAATAATAAAATTCTCC
13353111 ATCGAAATAATAAAATTCTCC
1 ATCGAAATAATAAAATTCTCC
13353132 ATC
1 ATC
13353135 TGATATGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.48, C:0.20, G:0.05, T:0.27
Consensus pattern (21 bp):
ATCGAAATAATAAAATTCTCC
Found at i:13357616 original size:21 final size:22
Alignment explanation
Indices: 13357586--13357634 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
13357576 TTTTTAATTG
*
13357586 TTTAATGTCATT-TTA-ATAAT
1 TTTAATGTCATTAATACATAAT
13357606 TTTATATGTCATTAATACATAAT
1 TTTA-ATGTCATTAATACATAAT
13357629 TTTAAT
1 TTTAAT
13357635 AAATTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 4 0.16
21 8 0.32
22 4 0.16
23 9 0.36
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTAATGTCATTAATACATAAT
Found at i:13363071 original size:2 final size:2
Alignment explanation
Indices: 13363064--13363088 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13363054 ATATTTTGTC
13363064 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13363089 AACAACCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13368057 original size:32 final size:32
Alignment explanation
Indices: 13368021--13368089 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
13368011 GGATATATGT
13368021 TGTTAAACTAGTGATTTAATAAGTTCTAATAG
1 TGTTAAACTAGTGATTTAATAAGTTCTAATAG
13368053 TGTTAAACTAGTGATTTAATAAGTTCTAATAG
1 TGTTAAACTAGTGATTTAATAAGTTCTAATAG
13368085 TGTTA
1 TGTTA
13368090 TCCCGAACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (32 bp):
TGTTAAACTAGTGATTTAATAAGTTCTAATAG
Found at i:13368412 original size:2 final size:2
Alignment explanation
Indices: 13368407--13368439 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13368397 TTTTTATGGT
13368407 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
13368440 TGCTTTTATG
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:13371734 original size:47 final size:47
Alignment explanation
Indices: 13371627--13371817 Score: 186
Period size: 47 Copynumber: 3.9 Consensus size: 47
13371617 AATGTGATTT
* * * *
13371627 CCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGCTT
1 CCGTATAAGACCATATCTGGGATATGGCATC-G-G---TGTGATATGTGCTA
*
13371679 CCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTA
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* * * *
13371726 CTGTATAAGACCATATATGGGATATGGCATCAGTGTGATATGTGAT-
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* ** * *
13371772 CCGTGTAAGACCATGGCTGGGCTATGGCCTCGGTATGTGATATGTG
1 CCGTATAAGACCATATCTGGGATATGGCATCGG--TGTGATATGTG
13371818 ACTATGTGCA
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 25 0.21
47 54 0.45
48 11 0.09
50 1 0.01
51 1 0.01
52 27 0.23
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (47 bp):
CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
Found at i:13373702 original size:13 final size:13
Alignment explanation
Indices: 13373684--13373709 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13373674 CGGTCTCGGG
13373684 TAAGGGGGCGTTA
1 TAAGGGGGCGTTA
13373697 TAAGGGGGCGTTA
1 TAAGGGGGCGTTA
13373710 CAGTTAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.46, T:0.23
Consensus pattern (13 bp):
TAAGGGGGCGTTA
Found at i:13381133 original size:12 final size:12
Alignment explanation
Indices: 13381105--13381134 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13381095 AACAAAAAGA
*
13381105 ACAACAAACTGT
1 ACAATAAACTGT
13381117 ACAATAAACTGT
1 ACAATAAACTGT
13381129 ACAATA
1 ACAATA
13381135 CGATTGCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (12 bp):
ACAATAAACTGT
Found at i:13382827 original size:18 final size:18
Alignment explanation
Indices: 13382806--13382845 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
13382796 TTACTCTCTC
*
13382806 TTTT-TTTTTATTTTGCTA
1 TTTTCTTTTT-TTTTACTA
13382824 TTTTCTTTTTTTTTACTA
1 TTTTCTTTTTTTTTACTA
13382842 TTTT
1 TTTT
13382846 ACTACCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTTTTTACTA
Found at i:13384610 original size:53 final size:53
Alignment explanation
Indices: 13384529--13384679 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
13384519 CTTACACGGT
* *
13384529 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
13384584 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
13384637 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
13384680 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:13391788 original size:35 final size:35
Alignment explanation
Indices: 13391761--13391927 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
13391751 CATGGCAAAG
13391761 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
13391796 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
*
13391831 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGC
** * * *
13391871 TAAGAAATGTAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGC
** *
13391906 TGAAAAATATAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
13391928 TCAATGAGGA
Statistics
Matches: 117, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
34 1 0.01
35 83 0.71
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
Found at i:13391851 original size:40 final size:40
Alignment explanation
Indices: 13391772--13391888 Score: 131
Period size: 40 Copynumber: 3.0 Consensus size: 40
13391762 GTGAAATGTA
13391772 GGTATGGTATTATCCATACTGAGCTGTGAAA--T--GTA-
1 GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
13391807 GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
1 GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
* * **
13391847 GGTAT--TATCAAATCCATACTGAGTTAAGAAATGTAGGTAT
1 GGTATGGTAT--TATCCATACTGAGCTGTGAAATGTAGGTAT
13391887 GG
1 GG
13391889 CATTTCCCAT
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
35 31 0.44
37 1 0.01
38 3 0.04
39 3 0.04
40 33 0.46
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (40 bp):
GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT
Found at i:13391899 original size:75 final size:74
Alignment explanation
Indices: 13391761--13391931 Score: 208
Period size: 75 Copynumber: 2.4 Consensus size: 74
13391751 CATGGCAAAG
** *
13391761 TGTGAAATGTAGGTATGGTA-TT---ATCCATACTGAGCTGTGAAATGTAGGTATGGTATTATCC
1 TGTGAAATGTAGGTATGGTATTTCAAATCCATACTGAGCTAAGAAATGTAGGTATGGCATTATCC
*
13391822 ATACTGAGC
66 ATACCGAGC
*
13391831 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
1 TGTGAAATGTAGGTATGGTATT-TCAAATCCATACTGAGCTAAGAAATGTAGGTATGGCATTAT-
*
13391895 CCATACCGAGT
64 CCATACCGAGC
** *
13391906 TGAAAAATATAGGTATGGTATTTCAA
1 TGTGAAATGTAGGTATGGTATTTCAA
13391932 TGAGGAAAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
70 20 0.23
71 1 0.01
72 1 0.01
74 5 0.06
75 59 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (74 bp):
TGTGAAATGTAGGTATGGTATTTCAAATCCATACTGAGCTAAGAAATGTAGGTATGGCATTATCC
ATACCGAGC
Found at i:13394762 original size:75 final size:72
Alignment explanation
Indices: 13394675--13394845 Score: 215
Period size: 75 Copynumber: 2.4 Consensus size: 72
13394665 GTTTTCCTCA
** * * *
13394675 TTGA-AATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 TTGATAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCATAAC
13394738 TCAGTATGG
65 TCAGTAT-G
* *
13394747 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCATAG
1 --TTGATAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCATAA
13394812 CTCAGTATG
64 CTCAGTATG
13394821 --GATAATACCATACCTACATTTCACA
1 TTGATAATACCATACCTACATTTCACA
13394846 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 25 0.28
74 8 0.09
75 55 0.62
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.32
Consensus pattern (72 bp):
TTGATAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCATAACT
CAGTATG
Found at i:13394842 original size:35 final size:36
Alignment explanation
Indices: 13394679--13394843 Score: 196
Period size: 35 Copynumber: 4.6 Consensus size: 36
13394669 TCCTCATTGA
*
13394679 AATACCATACCTACATTTTTCA-A-CTCGGTATGGGA-
1 AATACCATACCTACA--TTTCATAGCTCAGTATGGGAT
* * *
13394714 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCATAGCTCAGTATGG----GAT
*
13394754 AATACCATACCTACATTTCACAGCTCAGTAT-GGAT
1 AATACCATACCTACATTTCATAGCTCAGTATGGGAT
13394789 AATACCATACCTACATTTCATAGCTCAGTAT-GGAT
1 AATACCATACCTACATTTCATAGCTCAGTATGGGAT
13394824 AATACCATACCTACATTTCA
1 AATACCATACCTACATTTCA
13394844 CACTTTGCCA
Statistics
Matches: 115, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
33 4 0.03
34 1 0.01
35 80 0.70
39 3 0.03
40 27 0.23
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (36 bp):
AATACCATACCTACATTTCATAGCTCAGTATGGGAT
Found at i:13396026 original size:53 final size:53
Alignment explanation
Indices: 13395945--13396095 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
13395935 CTTACACGGT
* *
13395945 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAACCCAG-CTATGGTCTTATACGGAATCACATTA
* *
13396000 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACATTA
** *
13396053 TCACATTGCACCGATGCCATAACCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGG
13396096 GCGCACTTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:13397864 original size:8 final size:8
Alignment explanation
Indices: 13397851--13397879 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
13397841 TTATGTTTAG
13397851 TATATTAT
1 TATATTAT
13397859 TATATTAT
1 TATATTAT
13397867 TATATTAT
1 TATATTAT
13397875 TATAT
1 TATAT
13397880 AATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:13399218 original size:15 final size:15
Alignment explanation
Indices: 13399198--13399254 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
13399188 CGATGAATTT
13399198 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
13399213 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
13399228 ATTGAATTTATATTG
1 ATTGAATTTATATTG
13399243 ATTGAA-TTATAT
1 ATTGAATTTATAT
13399255 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:13399659 original size:23 final size:23
Alignment explanation
Indices: 13399629--13399715 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
13399619 GCTTTATCGA
* *
13399629 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
13399652 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
13399673 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
13399695 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
13399716 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:13402928 original size:19 final size:19
Alignment explanation
Indices: 13402904--13402941 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13402894 AGTTCAATGA
13402904 CTTAAAATAAAAACTTTCG
1 CTTAAAATAAAAACTTTCG
*
13402923 CTTAAAATGAAAACTTTCG
1 CTTAAAATAAAAACTTTCG
13402942 AATAGTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (19 bp):
CTTAAAATAAAAACTTTCG
Found at i:13409256 original size:15 final size:16
Alignment explanation
Indices: 13409236--13409268 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
13409226 TATATATATT
13409236 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
13409251 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
13409268 T
1 T
13409269 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:13409371 original size:20 final size:22
Alignment explanation
Indices: 13409317--13409372 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
13409307 TTAAGAATTA
* *
13409317 TTTTAGTAT-TATTTTTATTTG
1 TTTTAATATATATTTTTATGTG
*
13409338 TTTTAATATTTATTTTTATGT-
1 TTTTAATATATATTTTTATGTG
13409359 TTTTAA-ATATATTT
1 TTTTAATATATATTT
13409373 GATTTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 14 0.45
22 10 0.32
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTTAATATATATTTTTATGTG
Found at i:13409392 original size:26 final size:24
Alignment explanation
Indices: 13409343--13409402 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
13409333 ATTTGTTTTA
* *
13409343 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTAAAAT
13409367 ATATTTGATTTATTATATTTTAAAAT
1 ATATTT-ATTT-TTATATTTTAAAAT
* *
13409393 TTTTTTATTT
1 ATATTTATTT
13409403 AATGAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 6 0.20
25 8 0.27
26 16 0.53
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTAAAAT
Found at i:13409402 original size:25 final size:26
Alignment explanation
Indices: 13409346--13409403 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
13409336 TGTTTTAATA
* *
13409346 TTTATTT-TTATGTTTTTAAATATAT
1 TTTATTTATTATATTTTAAAATATAT
* *
13409371 TTGATTTATTATATTTTAAAAT-TTT
1 TTTATTTATTATATTTTAAAATATAT
13409396 TTTATTTA
1 TTTATTTA
13409404 ATGAAATAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTATTTATTATATTTTAAAATATAT
Found at i:13411418 original size:50 final size:50
Alignment explanation
Indices: 13411363--13411504 Score: 185
Period size: 51 Copynumber: 2.8 Consensus size: 50
13411353 TCTGGTACGT
*
13411363 ATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGCTACAC
1 ATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCGGCTACAC
* * * * ** * *
13411413 GTAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTATCGGGTACGC
1 ATAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CAATCGGCTACAC
*
13411464 ATAGTAGCCTGCACTTAGTACTACACACGTGACCTCACAAT
1 ATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAAT
13411505 AGATCATTCG
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
50 35 0.47
51 40 0.53
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
ATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCGGCTACAC
Found at i:13411490 original size:51 final size:50
Alignment explanation
Indices: 13411350--13411497 Score: 197
Period size: 50 Copynumber: 2.9 Consensus size: 50
13411340 GTAGCCAAAG
* *
13411350 CTATCTGGTACGTATAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCGAA
* * * * * *
13411400 CAATCTGCTACACGTAGTAGCCTGCACTTAGTACTACACATGTGATCGAA
1 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCGAA
* *
13411450 GTTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACC
1 -CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACC
13411498 TCACAATAGA
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 42 0.52
51 39 0.48
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (50 bp):
CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCGAA
Found at i:13425346 original size:22 final size:22
Alignment explanation
Indices: 13425305--13425347 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
13425295 CTATATATAC
* *
13425305 CTATAAGTGAAAAACGGTGCTA
1 CTATAAGGGAAAAACAGTGCTA
*
13425327 CTATAAGGGAAAAATAGTGCT
1 CTATAAGGGAAAAACAGTGCT
13425348 TGTGCTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (22 bp):
CTATAAGGGAAAAACAGTGCTA
Found at i:13426323 original size:31 final size:31
Alignment explanation
Indices: 13426265--13426323 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
13426255 CTTAATAGCC
* *
13426265 CAGTGAATTAAATAAAATTTTTTGAATAGTA
1 CAGTGAATTAAATAAAATCTTTCGAATAGTA
*
13426296 CAGTGACTTAAATGAAAA-CTTTCGAATA
1 CAGTGAATTAAAT-AAAATCTTTCGAATA
13426324 AATTAGTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (31 bp):
CAGTGAATTAAATAAAATCTTTCGAATAGTA
Found at i:13439462 original size:3 final size:3
Alignment explanation
Indices: 13439454--13439483 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
13439444 TTAAAATCAC
13439454 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13439484 ACATTTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:13441349 original size:6 final size:6
Alignment explanation
Indices: 13441338--13441362 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13441328 AATTAATTAA
13441338 TTATGG TTATGG TTATGG TTATGG T
1 TTATGG TTATGG TTATGG TTATGG T
13441363 GGAGGGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TTATGG
Found at i:13441536 original size:2 final size:2
Alignment explanation
Indices: 13441529--13441558 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13441519 CCGTTAGATC
13441529 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13441559 GGTGGAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13443123 original size:1 final size:1
Alignment explanation
Indices: 13443117--13443146 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
13443107 AGAATAACTC
13443117 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13443147 AATGCAGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13443392 original size:3 final size:3
Alignment explanation
Indices: 13443384--13443426 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
13443374 GCATACTTCC
* * * *
13443384 TAA TAA TAA TGA TAA TGA TGA TAA TAA TAG TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
13443427 GTGTTCCTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:13446777 original size:12 final size:12
Alignment explanation
Indices: 13446762--13446802 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
13446752 TAATTTGATA
13446762 TTTAAATTTATT
1 TTTAAATTTATT
* *
13446774 TTTAAATTTGTA
1 TTTAAATTTATT
*
13446786 TTTAAATTTAAT
1 TTTAAATTTATT
13446798 TTTAA
1 TTTAA
13446803 TGTTTAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (12 bp):
TTTAAATTTATT
Found at i:13446812 original size:24 final size:24
Alignment explanation
Indices: 13446753--13446802 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
13446743 TTCAACGTTT
*
13446753 AATTTGATATTTAAATTTATTTTTA
1 AATTTG-TATTTAAATTTAATTTTA
13446778 AATTTGTATTTAAATTTAATTTTA
1 AATTTGTATTTAAATTTAATTTTA
13446802 A
1 A
13446803 TGTTTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (24 bp):
AATTTGTATTTAAATTTAATTTTA
Found at i:13447337 original size:16 final size:16
Alignment explanation
Indices: 13447326--13447361 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
13447316 AAATTAAATC
13447326 AATAAAAAATTATAAA
1 AATAAAAAATTATAAA
13447342 AATAAAAAATATATATAA
1 AATAAAAAAT-TATA-AA
13447360 AA
1 AA
13447362 AATTCAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 4 0.22
18 4 0.22
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AATAAAAAATTATAAA
Found at i:13451438 original size:95 final size:95
Alignment explanation
Indices: 13451275--13451452 Score: 268
Period size: 95 Copynumber: 1.9 Consensus size: 95
13451265 CTTTTTTATA
* * ** *
13451275 AACACACTCGGTGCCATTCACGACTACAACAAAGAATGAATTATTCTTCTTTTTAAATTCAATGC
1 AACACACTCGGTCCCATTCACGACTACAACAAAGAACGAATTATTCTTCAATATAAATTCAATGC
13451340 AAACGCAACGCATCTTCAGGAGATTCATAG
66 AAACGCAACGCATCTTCAGGAGATTCATAG
* * *
13451370 AACACATTCGGTCCCATTCACGAGTACGACAAAAGAACGAATTATTCTT-AATATAAATTCAATG
1 AACACACTCGGTCCCATTCACGACTACAAC-AAAGAACGAATTATTCTTCAATATAAATTCAATG
13451434 CAAACGCAACGCATCTTCA
65 CAAACGCAACGCATCTTCA
13451453 TCAGATATAT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 57 0.77
96 17 0.23
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (95 bp):
AACACACTCGGTCCCATTCACGACTACAACAAAGAACGAATTATTCTTCAATATAAATTCAATGC
AAACGCAACGCATCTTCAGGAGATTCATAG
Found at i:13453447 original size:17 final size:16
Alignment explanation
Indices: 13453421--13453452 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
13453411 TACCATTAGT
13453421 AATTTAAAATTTTATA
1 AATTTAAAATTTTATA
13453437 AATTATAAAATTTTAT
1 AATT-TAAAATTTTAT
13453453 CATTTTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTAAAATTTTATA
Found at i:13465701 original size:21 final size:21
Alignment explanation
Indices: 13465662--13465702 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13465652 CCACAAGAAA
* * *
13465662 CCTCTTTATAAATATATTTCT
1 CCTCTTTACAAAGAGATTTCT
13465683 CCTCTTTACAAAGAGATTTC
1 CCTCTTTACAAAGAGATTTC
13465703 ATAGGGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (21 bp):
CCTCTTTACAAAGAGATTTCT
Found at i:13475321 original size:2 final size:2
Alignment explanation
Indices: 13475314--13475339 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13475304 GGCCAACAGG
13475314 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13475340 TCATATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13477812 original size:13 final size:14
Alignment explanation
Indices: 13477796--13477831 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
13477786 CAATCTCATA
13477796 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
13477809 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
13477822 TCTC-ATTTCA
1 TCTCAATTTCA
13477832 TTCCAATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:13477821 original size:18 final size:19
Alignment explanation
Indices: 13477783--13477823 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
13477773 TGGCTCATGT
13477783 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
13477802 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
13477820 TTTC
1 TTTC
13477824 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:13478483 original size:15 final size:15
Alignment explanation
Indices: 13478463--13478509 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
13478453 TAATATATAT
13478463 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
13478478 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
13478493 TTCAATCAATATAAA
1 TTCAATCAATATAAA
13478508 TT
1 TT
13478510 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:13479283 original size:21 final size:21
Alignment explanation
Indices: 13479257--13479300 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
13479247 AGACTACTGT
13479257 TGCTGTTCAAAATAGTCTTAG
1 TGCTGTTCAAAATAGTCTTAG
13479278 TGCTGTTCAAAATAGTCTTAG
1 TGCTGTTCAAAATAGTCTTAG
13479299 TG
1 TG
13479301 TAAAATGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (21 bp):
TGCTGTTCAAAATAGTCTTAG
Found at i:13482100 original size:53 final size:53
Alignment explanation
Indices: 13482035--13482176 Score: 187
Period size: 53 Copynumber: 2.7 Consensus size: 53
13482025 TAAGCATCAC
* * *
13482035 ACACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCATATT
1 ACACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATT
* * * *
13482088 ATACCGATGCCATAGCCCAGCTATGGTCTTATATGGAGTCATATTATCACATT
1 ACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATT
* *
13482141 GCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 ACACCGATGCCATAGCCCAGCTATGGTCTTATACGG
13482177 GCGCACTTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 1 0.01
53 76 0.99
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (53 bp):
ACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATT
Found at i:13483492 original size:18 final size:18
Alignment explanation
Indices: 13483469--13483512 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
13483459 CCTAACCGTA
*
13483469 AAACTTTCTTCCACGGAG
1 AAACTTTCTTCCACAGAG
13483487 AAACTTTCTTCCACAGAG
1 AAACTTTCTTCCACAGAG
13483505 AAACTTTC
1 AAACTTTC
13483513 AAGAACACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (18 bp):
AAACTTTCTTCCACAGAG
Found at i:13485384 original size:13 final size:13
Alignment explanation
Indices: 13485354--13485401 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
13485344 GTTCATGTTT
*
13485354 TCAATCTCAATATC
1 TCAATTTCAAT-TC
13485368 TCAATTTCAATTC
1 TCAATTTCAATTC
13485381 TCAA-TTCAATTTC
1 TCAATTTCAA-TTC
13485394 TC-ATTTCA
1 TCAATTTCA
13485402 TTCCAATAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 6 0.19
13 15 0.48
14 10 0.32
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (13 bp):
TCAATTTCAATTC
Found at i:13485583 original size:39 final size:38
Alignment explanation
Indices: 13485516--13485650 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
13485506 ACCAATATGG
* * *
13485516 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
13485555 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
13485593 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
13485634 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
13485651 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:13485915 original size:18 final size:19
Alignment explanation
Indices: 13485889--13485927 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
13485879 TTTCAATTCA
13485889 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
13485908 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
13485926 AT
1 AT
13485928 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:13487255 original size:5 final size:5
Alignment explanation
Indices: 13487245--13487297 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
13487235 TTACTTATTT
* *
13487245 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
13487293 ATATA
1 ATATA
13487298 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:13487261 original size:12 final size:12
Alignment explanation
Indices: 13487244--13487299 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
13487234 TTTACTTATT
13487244 TATATAATATAA
1 TATATAATATAA
13487256 TATATAATATAATA
1 TATATAATAT-A-A
13487270 TACTATAATATAA
1 TA-TATAATATAA
*
13487283 TA-ATAATTTAA
1 TATATAATATAA
13487294 TATATA
1 TATATA
13487300 TTTTAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:13491839 original size:13 final size:14
Alignment explanation
Indices: 13491823--13491858 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
13491813 CAATCTCATA
13491823 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
13491836 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
13491849 TCTC-ATTTCA
1 TCTCAATTTCA
13491859 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:13491848 original size:18 final size:19
Alignment explanation
Indices: 13491810--13491850 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
13491800 TGGTTCATGT
13491810 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
13491829 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
13491847 TTTC
1 TTTC
13491851 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:13492040 original size:39 final size:38
Alignment explanation
Indices: 13491973--13492107 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
13491963 ACCAATATGG
* * *
13491973 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
13492012 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
13492050 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
13492091 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
13492108 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:13492373 original size:18 final size:19
Alignment explanation
Indices: 13492347--13492385 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
13492337 TTTCAATTCA
13492347 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
13492366 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
13492384 AT
1 AT
13492386 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:13493713 original size:5 final size:5
Alignment explanation
Indices: 13493703--13493755 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
13493693 TTACTTATTT
* *
13493703 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
13493751 ATATA
1 ATATA
13493756 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:13493719 original size:12 final size:12
Alignment explanation
Indices: 13493702--13493757 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
13493692 TTTACTTATT
13493702 TATATAATATAA
1 TATATAATATAA
13493714 TATATAATATAATA
1 TATATAATAT-A-A
13493728 TACTATAATATAA
1 TA-TATAATATAA
*
13493741 TA-ATAATTTAA
1 TATATAATATAA
13493752 TATATA
1 TATATA
13493758 TTTTAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:13497590 original size:53 final size:53
Alignment explanation
Indices: 13497525--13497666 Score: 205
Period size: 53 Copynumber: 2.7 Consensus size: 53
13497515 TACGCATCAC
* *
13497525 ACACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCACATT
1 ACACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATT
* * *
13497578 ATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCATATTATCACATT
1 ACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATT
* *
13497631 GCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 ACACCGATGCCATAGCCCAGCTATGGTCTTATACGG
13497667 GCGCACTTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 1 0.01
53 79 0.99
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (53 bp):
ACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATT
Found at i:13501462 original size:51 final size:51
Alignment explanation
Indices: 13501357--13501472 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
13501347 TACTACCAAA
* * * **
13501357 TATAATATCATATCTTCTAAGATTACATATCTTAGATAAGATATGTAATCT
1 TATAATATCATATCTTATAAGATTACATATCATAGATAAGATATCTAAGAT
* * * ** *
13501408 TATAAAATAATATCTTATAAGATTCCATATCATATCTAAGATCTCTAAGAT
1 TATAATATCATATCTTATAAGATTACATATCATAGATAAGATATCTAAGAT
13501459 TATAATATCATATC
1 TATAATATCATATC
13501473 ATGTTTCCAT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (51 bp):
TATAATATCATATCTTATAAGATTACATATCATAGATAAGATATCTAAGAT
Found at i:13504265 original size:51 final size:51
Alignment explanation
Indices: 13504160--13504275 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
13504150 TACTACCAAA
* * * **
13504160 TATAATATCATATCTTCTAAGATTACATATCTTAGATAAGATATGTAATCT
1 TATAATATCATATCTTATAAGATTACATATCATAGATAAGATATCTAAGAT
* * * ** *
13504211 TATAAAATAATATCTTATAAGATTCCATATCATATCTAAGATCTCTAAGAT
1 TATAATATCATATCTTATAAGATTACATATCATAGATAAGATATCTAAGAT
13504262 TATAATATCATATC
1 TATAATATCATATC
13504276 ATGTTTCCAT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (51 bp):
TATAATATCATATCTTATAAGATTACATATCATAGATAAGATATCTAAGAT
Found at i:13505729 original size:7 final size:7
Alignment explanation
Indices: 13505717--13505741 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13505707 CTTATATTTA
13505717 TATTTTT
1 TATTTTT
13505724 TATTTTT
1 TATTTTT
13505731 TATTTTT
1 TATTTTT
13505738 TATT
1 TATT
13505742 ACACCCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TATTTTT
Found at i:13510971 original size:19 final size:19
Alignment explanation
Indices: 13510943--13510995 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
13510933 ATAGGAAGGG
13510943 ATAT-ATTTTAAAATT-AT
1 ATATAATTTTAAAATTAAT
*
13510960 ATATAAATTTT-AATTTAAT
1 ATAT-AATTTTAAAATTAAT
13510979 ATATAA-TTTAAAATTAA
1 ATATAATTTTAAAATTAA
13510996 ATCAATTCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 7 0.23
18 12 0.40
19 11 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATAATTTTAAAATTAAT
Found at i:13515985 original size:22 final size:22
Alignment explanation
Indices: 13515959--13516006 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
13515949 AATCGTGGGC
13515959 TTTTAAAGTTTCCATTATTGTT
1 TTTTAAAGTTTCCATTATTGTT
13515981 TTTTAAAGTTTCCATTATTGTT
1 TTTTAAAGTTTCCATTATTGTT
13516003 TTTT
1 TTTT
13516007 TATATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.62
Consensus pattern (22 bp):
TTTTAAAGTTTCCATTATTGTT
Found at i:13537580 original size:2 final size:2
Alignment explanation
Indices: 13537573--13537598 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13537563 GAATGAAATC
13537573 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13537599 TTAATATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13537889 original size:21 final size:22
Alignment explanation
Indices: 13537847--13537890 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
13537837 ATAATAATTT
*
13537847 TATTTATATTTTAAATTGTAAA
1 TATTTATATTTTAAAGTGTAAA
13537869 TATTTA-ATTTTTAAAGT-TAAA
1 TATTTATA-TTTTAAAGTGTAAA
13537890 T
1 T
13537891 TTATGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TATTTATATTTTAAAGTGTAAA
Found at i:13553276 original size:32 final size:32
Alignment explanation
Indices: 13553240--13553305 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
13553230 AATTATTACC
13553240 TTAGTATAGCGTAAAAAAACAATGTTGAGTAG
1 TTAGTATAGCGTAAAAAAACAATGTTGAGTAG
13553272 TTAGTATAGCGTAAAAAAACAATGTTGAGTAG
1 TTAGTATAGCGTAAAAAAACAATGTTGAGTAG
13553304 TT
1 TT
13553306 CTAACATGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (32 bp):
TTAGTATAGCGTAAAAAAACAATGTTGAGTAG
Found at i:13554646 original size:2 final size:2
Alignment explanation
Indices: 13554639--13554664 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13554629 GGGCAATTAA
13554639 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13554665 GTTAAGCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13556416 original size:19 final size:20
Alignment explanation
Indices: 13556376--13556417 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
13556366 AATTATATTT
*
13556376 ATTTAAAATAAAAATATTAA
1 ATTTAAAATAAAAATATAAA
*
13556396 ATTTAAATTAAAAA-ATAAA
1 ATTTAAAATAAAAATATAAA
13556415 ATT
1 ATT
13556418 ACAATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTTAAAATAAAAATATAAA
Found at i:13556430 original size:7 final size:7
Alignment explanation
Indices: 13556387--13556451 Score: 57
Period size: 7 Copynumber: 9.4 Consensus size: 7
13556377 TTTAAAATAA
13556387 AAATATT
1 AAATATT
13556394 AAAT-TT
1 AAATATT
13556400 -AA-ATT
1 AAATATT
* *
13556405 AAAAAAT
1 AAATATT
13556412 AAA-ATT
1 AAATATT
13556418 ACAATATT
1 A-AATATT
13556426 AAATATTT
1 AAATA-TT
13556434 AAATATTT
1 AAATA-TT
13556442 AAATATT
1 AAATATT
13556449 AAA
1 AAA
13556452 AAATATTGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
5 4 0.08
6 7 0.14
7 20 0.40
8 19 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:13556440 original size:15 final size:14
Alignment explanation
Indices: 13556387--13556451 Score: 57
Period size: 15 Copynumber: 4.7 Consensus size: 14
13556377 TTTAAAATAA
13556387 AAATATTAAAT-TT
1 AAATATTAAATATT
* *
13556400 -AA-ATTAAAAAAT
1 AAATATTAAATATT
13556412 AAA-ATTACAATATT
1 AAATATTA-AATATT
13556426 AAATATTTAAATATTT
1 AAATA-TTAAATA-TT
13556442 AAATATTAAA
1 AAATATTAAA
13556452 AAATATTGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 6 0.14
12 3 0.07
13 6 0.14
14 7 0.17
15 10 0.24
16 10 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATTAAATATT
Found at i:13556532 original size:21 final size:21
Alignment explanation
Indices: 13556475--13556534 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
13556465 TTTGATCGGC
* *
13556475 CATTAATCGACGTTGACCAAT
1 CATTAATTGGCGTTGACCAAT
*
13556496 CATTAATTGGCATTGACCAA-
1 CATTAATTGGCGTTGACCAAT
* *
13556516 CATTGATTGTGTGTTGACC
1 CATTAATTG-GCGTTGACC
13556535 TACCATGTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 8 0.25
21 24 0.75
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (21 bp):
CATTAATTGGCGTTGACCAAT
Found at i:13559970 original size:9 final size:9
Alignment explanation
Indices: 13559932--13559988 Score: 55
Period size: 10 Copynumber: 6.2 Consensus size: 9
13559922 TGAAATGTGG
13559932 TAAAAATTAA
1 TAAAAATT-A
13559942 TAAAAA--A
1 TAAAAATTA
*
13559949 TAAAAATCAA
1 TAAAAAT-TA
*
13559959 TAAAATTTA
1 TAAAAATTA
13559968 TAAAAAATTA
1 T-AAAAATTA
13559978 TAAAAATTA
1 TAAAAATTA
13559987 TA
1 TA
13559989 TTTTTATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
7 7 0.17
9 12 0.30
10 21 0.52
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:13560071 original size:29 final size:29
Alignment explanation
Indices: 13560038--13560106 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
13560028 TCTTTACATT
*
13560038 TTTTATACTCTTCTTACG-CCTTTATAAAA
1 TTTTATAAT-TTCTTACGACCTTTATAAAA
**
13560067 TTTTATAATTTCTTACGATTTTTATAAAA
1 TTTTATAATTTCTTACGACCTTTATAAAA
*
13560096 TTTTACAATTT
1 TTTTATAATTT
13560107 TTATAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 8 0.23
29 27 0.77
ACGTcount: A:0.30, C:0.13, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTTATAATTTCTTACGACCTTTATAAAA
Found at i:13560091 original size:19 final size:18
Alignment explanation
Indices: 13560067--13560119 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
13560057 CTTTATAAAA
* *
13560067 TTTTATAATTTCTTACGAT
1 TTTTATAAATT-TTACAAT
13560086 TTTTATAAAATTTTACAAT
1 TTTTAT-AAATTTTACAAT
13560105 TTTTATAAAATTTTA
1 TTTTAT-AAATTTTA
13560120 TGATTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 27 0.87
20 4 0.13
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTATAAATTTTACAAT
Found at i:13560118 original size:29 final size:29
Alignment explanation
Indices: 13560058--13560120 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
13560048 TTCTTACGCC
* ** *
13560058 TTTATAAAATTTTATAATTTCTTACGATT
1 TTTATAAAATTTTACAATTTCTTAAAAAT
13560087 TTTATAAAATTTTACAATTT-TTATAAAAT
1 TTTATAAAATTTTACAATTTCTTA-AAAAT
13560116 TTTAT
1 TTTAT
13560121 GATTTTTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (29 bp):
TTTATAAAATTTTACAATTTCTTAAAAAT
Found at i:13560125 original size:19 final size:19
Alignment explanation
Indices: 13560079--13560127 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
13560069 TTATAATTTC
13560079 TTACGATTTTTATAAAATT
1 TTACGATTTTTATAAAATT
*
13560098 TTACAATTTTTATAAAATT
1 TTACGATTTTTATAAAATT
*
13560117 TTATGATTTTT
1 TTACGATTTTT
13560128 GTATTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (19 bp):
TTACGATTTTTATAAAATT
Found at i:13560142 original size:29 final size:28
Alignment explanation
Indices: 13560096--13560190 Score: 90
Period size: 29 Copynumber: 3.5 Consensus size: 28
13560086 TTTTATAAAA
* *
13560096 TTTTACAATTTTTA-TAAAATTTTATGAT
1 TTTTATAATTTTTATTAAAATTTAAT-AT
*
13560124 TTTTGT-ATTTTTAATTAAAATTTAATAT
1 TTTTATAATTTTT-ATTAAAATTTAATAT
* *
13560152 TTTTATAATTTTTATT-AATTTTTAT-T
1 TTTTATAATTTTTATTAAAATTTAATAT
*
13560178 TTTTATTATTTTT
1 TTTTATAATTTTT
13560191 TGCCACATGT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
26 13 0.23
27 13 0.23
28 15 0.26
29 16 0.28
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (28 bp):
TTTTATAATTTTTATTAAAATTTAATAT
Found at i:13560147 original size:28 final size:29
Alignment explanation
Indices: 13560122--13560190 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 29
13560112 AAATTTTATG
*
13560122 ATTTTTGT-ATTTTTAATTAAAA-TTTAAT
1 ATTTTTATAATTTTT-ATTAAAATTTTAAT
*
13560150 ATTTTTATAATTTTTATT--AATTTTTAT
1 ATTTTTATAATTTTTATTAAAATTTTAAT
*
13560177 -TTTTTATTATTTTT
1 ATTTTTATAATTTTT
13560191 TGCCACATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 15 0.42
27 5 0.14
28 10 0.28
29 6 0.17
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (29 bp):
ATTTTTATAATTTTTATTAAAATTTTAAT
Found at i:13560172 original size:19 final size:18
Alignment explanation
Indices: 13560144--13560190 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
13560134 TTAATTAAAA
*
13560144 TTTAATATTTTTATAATT
1 TTTATTATTTTTATAATT
13560162 TTTATTAATTTTTAT--TT
1 TTTATT-ATTTTTATAATT
13560179 TTTATTATTTTT
1 TTTATTATTTTT
13560191 TGCCACATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 6 0.22
17 8 0.30
18 5 0.19
19 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTATTTTTATAATT
Found at i:13564176 original size:47 final size:47
Alignment explanation
Indices: 13564046--13564217 Score: 161
Period size: 47 Copynumber: 3.6 Consensus size: 47
13564036 ATAGTAAAAC
* * * *
13564046 TATGGTCTTGCACA-TAGTCACATATCACATATCGAGGCCATAGCCCAGC
1 TATGGTCTTACACAGTAG-CACATATCAC--ATCGATGCCATATCCCAGA
* * * *
13564095 CATGGTCTTACAC-GGATCACATATCACA-CTGATGCCATATCCCATA
1 TATGGTCTTACACAGTAGCACATATCACATC-GATGCCATATCCCAGA
* *
13564141 TATGGTCTTATACAGTAGCACATATCACATCGATGCCATATCCCGGA
1 TATGGTCTTACACAGTAGCACATATCACATCGATGCCATATCCCAGA
* * * *
13564188 TATGCTCTTATACGGAAGCACATATCACAT
1 TATGGTCTTACACAGTAGCACATATCACAT
13564218 TTCTCCGAAG
Statistics
Matches: 102, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
45 1 0.01
46 24 0.24
47 54 0.53
48 11 0.11
49 12 0.12
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (47 bp):
TATGGTCTTACACAGTAGCACATATCACATCGATGCCATATCCCAGA
Found at i:13564252 original size:52 final size:48
Alignment explanation
Indices: 13564064--13564256 Score: 185
Period size: 47 Copynumber: 4.0 Consensus size: 48
13564054 TGCACATAGT
* * ** * *
13564064 CACATATCACATATCGAGGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATATCACA-CTCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* * * *
13564112 CACATATCACACT-GATGCCATATCCCATATATGGTCTTATACAGTAG
1 CACATATCACACTCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* * *
13564159 CACATATCACA-TCGATGCCATATCCCGGATATGCTCTTATACGGAAG
1 CACATATCACACTCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
13564206 CACATATCACATTTCTCCGAAGCCATAGCCCAGCTATGGTCTTATACGGAA
1 CACATATCACA---CT-CGATGCCATAGCCCAGATATGGTCTTATACGGAA
13564257 ATCAAATTTC
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
46 25 0.21
47 53 0.45
48 11 0.09
51 1 0.01
52 29 0.24
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (48 bp):
CACATATCACACTCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
Found at i:13567891 original size:53 final size:53
Alignment explanation
Indices: 13567827--13567960 Score: 207
Period size: 53 Copynumber: 2.5 Consensus size: 53
13567817 TCATGCCAAA
* *
13567827 GCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCACATTATACCGAT
1 GCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
* *
13567880 GCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGCACCGAT
1 GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
*
13567933 GCCATAGCCCAGCTATGGTCTTAAACGG
1 GCCATAGCCCAGCTATGGTCTTATACGG
13567961 GCGCACTTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
52 1 0.01
53 74 0.99
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (53 bp):
GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
Found at i:13570143 original size:3 final size:3
Alignment explanation
Indices: 13570129--13570182 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
13570119 GACAATAAAG
*
13570129 AAT AAT AGT AAT AAT AAT AAT -AT AGAT AAT AAT -AT ATAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT
13570173 AAT AAT AAT A
1 AAT AAT AAT A
13570183 GTTAGAGATA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.14
3 32 0.73
4 6 0.14
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:13570392 original size:3 final size:3
Alignment explanation
Indices: 13570384--13570495 Score: 63
Period size: 3 Copynumber: 37.3 Consensus size: 3
13570374 TATAAATATG
* * * *
13570384 ATA ATA ATA ATA ATG ATA ATG ATA ATA ATA ATA AT- ATA GTA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
13570431 ATA A-A AGTA A-A ATTA ATA GTA A-A TTG ATA ATA ATA AT- GTA CATTA
1 ATA ATA A-TA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA
*
13570476 ATA ACA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA -ATA A
13570496 AGGATAGGAA
Statistics
Matches: 83, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
2 8 0.10
3 65 0.78
4 8 0.10
5 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13570806 original size:35 final size:31
Alignment explanation
Indices: 13570764--13570849 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 31
13570754 TATGCATAAC
13570764 AATAAAAATACAATATTAAAATATATATACGAGT
1 AATAAAAATACAATATTAAAA-ATATATAC-A-T
**
13570798 AATAAAAAATGTATCCGTATTAAAAATATATACAT
1 AAT-AAAAA--TA-CAATATTAAAAATATATACAT
13570833 AATAAAAATACAATATT
1 AATAAAAATACAATATT
13570850 TAAAGCATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
31 5 0.11
32 2 0.05
34 8 0.18
35 9 0.20
36 1 0.02
37 10 0.23
38 9 0.20
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (31 bp):
AATAAAAATACAATATTAAAAATATATACAT
Found at i:13570838 original size:17 final size:17
Alignment explanation
Indices: 13570780--13570842 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
13570770 AATACAATAT
13570780 TAAAATATATATACGAGTAA
1 TAAAA-ATATATAC-A-TAA
* * * *
13570800 TAAAAAATGTATCCGTAT
1 T-AAAAATATATACATAA
13570818 TAAAAATATATACATAA
1 TAAAAATATATACATAA
13570835 TAAAAATA
1 TAAAAATA
13570843 CAATATTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 20 0.59
18 3 0.09
20 7 0.21
21 4 0.12
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (17 bp):
TAAAAATATATACATAA
Found at i:13575324 original size:39 final size:39
Alignment explanation
Indices: 13575276--13575397 Score: 172
Period size: 39 Copynumber: 3.1 Consensus size: 39
13575266 AAGTCTAATA
* *
13575276 GAAGTACATAAGTGCTAAACGGAAGACCGAAGGCTAACT
1 GAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACT
* * **
13575315 GAAGCACATACGTGCTAAACGGGAGCCCGAACACTAACT
1 GAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACT
*
13575354 GAAGCACATAAGTGCTGAACGGAAGCCCGAAGGCTAACT
1 GAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACT
*
13575393 AAAGC
1 GAAGC
13575398 TCACCAGAGC
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 71 1.00
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (39 bp):
GAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACT
Found at i:13576550 original size:75 final size:72
Alignment explanation
Indices: 13576463--13576633 Score: 206
Period size: 75 Copynumber: 2.4 Consensus size: 72
13576453 GTTTTCCTCA
** * * **
13576463 TTGA-AATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 TTGATAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
13576526 TCAGTATGG
65 TCAGTAT-G
* *
13576535 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAG
1 --TTGATAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
13576600 CTCAGTATG
64 CTCAGTATG
13576609 --GATAATACCATACCTACATTTCACA
1 TTGATAATACCATACCTACATTTCACA
13576634 CTTTGCCATG
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 25 0.29
74 8 0.09
75 54 0.62
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (72 bp):
TTGATAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATG
Found at i:13576645 original size:35 final size:35
Alignment explanation
Indices: 13576467--13576633 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
13576457 TCCTCATTGA
** * *
13576467 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAGCTCAGTAT-GGAT
* ** *
13576502 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAGCTCAGTAT-G----GAT
13576542 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAGCTCAGTATGGAT
13576577 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAGCTCAGTATGGAT
13576612 AATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
13576634 CTTTGCCATG
Statistics
Matches: 119, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
35 89 0.75
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAGCTCAGTATGGAT
Found at i:13583747 original size:2 final size:2
Alignment explanation
Indices: 13583740--13583766 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13583730 GAAGCTTCTT
13583740 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13583767 CTATGTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13591085 original size:24 final size:24
Alignment explanation
Indices: 13591031--13591085 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
13591021 TTAATCTTTA
13591031 TACTATTAAAAAAATTAAACAAAGT
1 TACTATTAAAAAAATTAAAC-AAGT
* *
13591056 TA-TATTAAAATAAATTTAAC-ATT
1 TACTATTAAAA-AAATTAAACAAGT
13591079 TACTATT
1 TACTATT
13591086 TTAAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 4 0.15
24 12 0.46
25 10 0.38
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (24 bp):
TACTATTAAAAAAATTAAACAAGT
Done.