Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 14 of 344
Found at i:5083786 original size:11 final size:11
Alignment explanation
Indices: 5083772--5083816 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
5083762 AGATAAATAT
5083772 TATTTTATTAA
1 TATTTTATTAA
*
5083783 TATTTTAATAATA
1 TATTTT-ATTA-A
*
5083796 TATTTTATTAT
1 TATTTTATTAA
5083807 TATTTTATTA
1 TATTTTATTA
5083817 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:5083799 original size:24 final size:24
Alignment explanation
Indices: 5083767--5083822 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
5083757 TAATTAGATA
5083767 AATATTATTTTATTAATATTTTAAT
1 AATA-TATTTTATTAATATTTTAAT
* *
5083792 AATATATTTTATTATTATTTTATT
1 AATATATTTTATTAATATTTTAAT
*
5083816 AGTATAT
1 AATATAT
5083823 AAAGAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AATATATTTTATTAATATTTTAAT
Found at i:5086000 original size:46 final size:46
Alignment explanation
Indices: 5085948--5086175 Score: 305
Period size: 46 Copynumber: 5.0 Consensus size: 46
5085938 AGTGTGCTCT
**
5085948 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
5085994 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
*
5086040 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
5086086 GTGACATGAAAAGAATAAGACTATGGTTGAAAGATACTATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * * *
5086132 ATGACA-GAAAATGAGTAAGACCATAGCTGAAAGACACTATGGCA
1 CTGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
5086176 TCATGTCAAA
Statistics
Matches: 167, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.01
46 166 0.99
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:5087644 original size:35 final size:35
Alignment explanation
Indices: 5087582--5087719 Score: 129
Period size: 35 Copynumber: 3.9 Consensus size: 35
5087572 CACATATGGA
* * * * *
5087582 CGAATATGCATATTTAAGATAACTTCACATATATC
1 CGAATATACAAATTCAATATAACTTCACATGTATC
* * *
5087617 CGAGTATACAATTTCAATATAAGTTCACATGTAAT-
1 CGAATATACAAATTCAATATAACTTCACATGT-ATC
* *
5087652 CGAATACTA-AAATTCAATATAACCTCACATGTAGC
1 CGAATA-TACAAATTCAATATAACTTCACATGTATC
*
5087687 CGAATATACAAGTTCAATATAAGCTT-ACATGTA
1 CGAATATACAAATTCAATATAA-CTTCACATGTA
5087720 CTTACCTATG
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
34 3 0.04
35 74 0.89
36 6 0.07
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (35 bp):
CGAATATACAAATTCAATATAACTTCACATGTATC
Found at i:5094552 original size:36 final size:36
Alignment explanation
Indices: 5094511--5094583 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
5094501 TTCGAACAAG
5094511 TGCATCAAGGCTTCCCTTTGGAGGTAGAGAGGCTAA
1 TGCATCAAGGCTTCCCTTTGGAGGTAGAGAGGCTAA
5094547 TGCATCAAGGCTTCCCTTTGGAGGTAGAGAGGCTAA
1 TGCATCAAGGCTTCCCTTTGGAGGTAGAGAGGCTAA
5094583 T
1 T
5094584 CACGTTGAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (36 bp):
TGCATCAAGGCTTCCCTTTGGAGGTAGAGAGGCTAA
Found at i:5097816 original size:46 final size:44
Alignment explanation
Indices: 5097673--5097816 Score: 114
Period size: 46 Copynumber: 3.1 Consensus size: 44
5097663 CCCGCCCATA
* *
5097673 AGTGAACTCGGACTCAACTCAACGAGCTCAGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * * *
5097720 CA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCG--GATGC-CAACCATCT
5097766 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
5097812 AGTGA
1 AGTGA
5097817 CATGTCACTT
Statistics
Matches: 76, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.42
47 28 0.37
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:5103706 original size:30 final size:30
Alignment explanation
Indices: 5103672--5103749 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
5103662 AAAAAAAATG
5103672 ATAAAAAATAATAAAAATCATTAAAATTT-A
1 ATAAAAAAT-ATAAAAATCATTAAAATTTAA
* * *
5103702 ATAAATAATCTAAAAAATTATTAAAATTTAGA
1 ATAAAAAATAT-AAAAATCATTAAAATTTA-A
*
5103734 AAAAAAAATTATAAAA
1 ATAAAAAA-TATAAAA
5103750 TATATAGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 1 0.03
30 24 0.63
32 11 0.29
33 2 0.05
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (30 bp):
ATAAAAAATATAAAAATCATTAAAATTTAA
Found at i:5103726 original size:20 final size:20
Alignment explanation
Indices: 5103665--5103727 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
5103655 ATGTGACAAA
*
5103665 AAAAATGATAAAAAA-TAAT
1 AAAAATCATAAAAAATTAAT
* *
5103684 AAAAATCATTAAAATTTAAT
1 AAAAATCATAAAAAATTAAT
*
5103704 AAATAATC-TAAAAAATTATT
1 AAA-AATCATAAAAAATTAAT
5103724 AAAA
1 AAAA
5103728 TTTAGAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 13 0.36
20 19 0.53
21 4 0.11
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATCATAAAAAATTAAT
Found at i:5103748 original size:22 final size:25
Alignment explanation
Indices: 5103713--5103759 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
5103703 TAAATAATCT
5103713 AAAAAATTATTAAAAT-T-TAGAAA
1 AAAAAATTATTAAAATATATAGAAA
5103736 AAAAAATTA-TAAAATATATAGAAA
1 AAAAAATTATTAAAATATATAGAAA
5103760 TATAGGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 10 0.45
24 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (25 bp):
AAAAAATTATTAAAATATATAGAAA
Found at i:5104046 original size:19 final size:17
Alignment explanation
Indices: 5104015--5104063 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
5104005 ATTTCTTAAA
*
5104015 TAATTATTTATTT-TTT
1 TAATTATTTATTTGTGT
5104031 TCAATTATTTCAATTTGTGT
1 T-AATTATTT--ATTTGTGT
5104051 TAATTATTTATTT
1 TAATTATTTATTT
5104064 AGCCATGTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 1 0.04
17 12 0.43
19 12 0.43
20 3 0.11
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (17 bp):
TAATTATTTATTTGTGT
Found at i:5109415 original size:14 final size:14
Alignment explanation
Indices: 5109396--5109436 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
5109386 TAAACCAAAC
*
5109396 TTTTCAAAAATATT
1 TTTTCAAAAGTATT
*
5109410 TTTTCAAAAGTA-C
1 TTTTCAAAAGTATT
5109423 TTTTCAAAAGTATT
1 TTTTCAAAAGTATT
5109437 ATCAAACTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (14 bp):
TTTTCAAAAGTATT
Found at i:5110809 original size:3 final size:3
Alignment explanation
Indices: 5110742--5110800 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
5110732 TTTGTTAACT
*
5110742 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* *
5110787 CTA TTA TTA GTA TT
1 TTA TTA TTA TTA TT
5110801 GGTATTATTG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 1 0.02
3 47 0.98
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5115843 original size:16 final size:17
Alignment explanation
Indices: 5115824--5115857 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5115814 CAAAAGGCTT
*
5115824 AAGAATAAAAAA-CAAA
1 AAGAAGAAAAAATCAAA
5115840 AAGAAGAAAAAATCAAA
1 AAGAAGAAAAAATCAAA
5115857 A
1 A
5115858 TCAAGATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (17 bp):
AAGAAGAAAAAATCAAA
Found at i:5118132 original size:44 final size:44
Alignment explanation
Indices: 5118083--5118221 Score: 120
Period size: 44 Copynumber: 3.2 Consensus size: 44
5118073 AGTTACAGAT
* *
5118083 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
* * * ** ** * * * * *
5118127 CTTGCC-TCTTTCGGTTGTGATAG-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTAC-ATTGACAGCGAAGCAGATCGAAGACACAA-AC
5118171 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
5118215 CTTGCCT
1 CTTGCCT
5118222 CTTTCGGTTG
Statistics
Matches: 66, Mismatches: 25, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
43 18 0.27
44 30 0.45
45 18 0.27
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (44 bp):
CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
Found at i:5118164 original size:43 final size:43
Alignment explanation
Indices: 5118115--5118252 Score: 134
Period size: 43 Copynumber: 3.2 Consensus size: 43
5118105 GAAGCAGATC
5118115 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
* * * * * ** ** * * *
5118158 GAAGACAAAAGATCTTGCCTTCCTAC-ATTGACAGCGAAGCAGATC
1 GAAGACACAA-ACCTTGCC-TCTTTCGGTTGTGATAG-AGCTGGTT
5118203 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
5118246 GAAGACA
1 GAAGACA
5118253 AAAGATCTTG
Statistics
Matches: 67, Mismatches: 24, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
43 25 0.37
44 24 0.36
45 18 0.27
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (43 bp):
GAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
Found at i:5118228 original size:88 final size:88
Alignment explanation
Indices: 5118079--5118376 Score: 415
Period size: 88 Copynumber: 3.4 Consensus size: 88
5118069 ATGAAGTTAC
*
5118079 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
5118144 TGATAGAGCTGGTTGAAGACAAA
66 TGATAGAGCTGGTTGAAGACAAA
*
5118167 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
5118232 TGATAGAGCTGGTTGAAGACAAA
66 TGATAGAGCTGGTTGAAGACAAA
* * ** *
5118255 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATTGAA-A-ACAAAGCCTTGCGTCCATCGATT
1 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGGTT
* * * * **
5118318 G-CAGTGGAGCTAGTTAAAGA-AGC
65 GTGA-TAGAGCTGGTTGAAGACAAA
* *
5118341 AGATCTTGCCTTCCTGCATTAACAGCAAAGCAGATC
1 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATC
5118377 AAAAAAAAAA
Statistics
Matches: 191, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
86 40 0.21
87 28 0.15
88 123 0.64
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (88 bp):
AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
TGATAGAGCTGGTTGAAGACAAA
Found at i:5118263 original size:44 final size:44
Alignment explanation
Indices: 5118127--5118265 Score: 138
Period size: 44 Copynumber: 3.2 Consensus size: 44
5118117 AGACACAAAC
5118127 CTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGAT
* * * ** ** * * * * *
5118171 CTTGCCTTCCTAC-ATTGACAGCGAAGCAGATCGAAGACACAA-AC
1 CTTGCC-TCTTTCGGTTGTGATAG-AGCTGGTTGAAGACAAAAGAT
5118215 CTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGAT
5118259 CTTGCCT
1 CTTGCCT
5118266 TCCTACATTA
Statistics
Matches: 67, Mismatches: 24, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
43 18 0.27
44 31 0.46
45 18 0.27
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (44 bp):
CTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGAT
Found at i:5118658 original size:44 final size:44
Alignment explanation
Indices: 5118610--5118759 Score: 135
Period size: 44 Copynumber: 3.4 Consensus size: 44
5118600 CCAGAAATCC
*
5118610 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATGAGGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATGAAGGATCT
* * * ** ** *
5118654 TATCTTCCTG-AGATTACAGCGGAGCAGA-TCGAA-GACACTATCC
1 TATCTCCCTGAAG-TTACAGTGGAGCGGATTAAAATGA-AGGATCT
* * *
5118697 TATCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATGAAGGATCT
* *
5118741 TATCTCTCTGAGGTTACAG
1 TATCTCCCTGAAGTTACAG
5118760 CAGAGTAGGT
Statistics
Matches: 79, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
42 2 0.03
43 28 0.35
44 48 0.61
45 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATGAAGGATCT
Found at i:5120241 original size:3 final size:3
Alignment explanation
Indices: 5120171--5120232 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
5120161 TTTGTTAACT
*
5120171 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
5120216 TTA CTA TTA TTA GTA TT
1 TTA TTA TTA TTA TTA TT
5120233 GGTATTATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
2 1 0.02
3 50 0.98
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5124845 original size:18 final size:17
Alignment explanation
Indices: 5124822--5124857 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5124812 TAAGTTGAGA
*
5124822 CCCAAATATTAATTTAAC
1 CCCAAAT-TTAATGTAAC
5124840 CCCAAATTTAATGTAAC
1 CCCAAATTTAATGTAAC
5124857 C
1 C
5124858 ATGGACTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.31
Consensus pattern (17 bp):
CCCAAATTTAATGTAAC
Found at i:5132215 original size:59 final size:61
Alignment explanation
Indices: 5132140--5132285 Score: 158
Period size: 59 Copynumber: 2.4 Consensus size: 61
5132130 TTATTGTTAT
*
5132140 TGTTATTAA-ATTTTAATAGGATTATTATCAAAAATAATTTAATAAAAAATAA-AA-A-ATAA
1 TGTTA-TAATATTTTAATAGAATTATTATCAAAAATAATTTAAT-AAAAATAATAATATATAA
* * * * *
5132199 TGTTATCATATTTTAATATAATTATTATTAAATATAATTTAGTAAAAATAATAATATATAA
1 TGTTATAATATTTTAATAGAATTATTATCAAAAATAATTTAATAAAAATAATAATATATAA
**
5132260 T-TTAATAATATTTTAATTCAATTATT
1 TGTT-ATAATATTTTAATAGAATTATT
5132286 TTTGTATTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
58 10 0.14
59 36 0.49
60 3 0.04
61 24 0.33
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (61 bp):
TGTTATAATATTTTAATAGAATTATTATCAAAAATAATTTAATAAAAATAATAATATATAA
Found at i:5138285 original size:10 final size:10
Alignment explanation
Indices: 5138270--5138294 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5138260 TTATTTTTTT
5138270 ATTGAAAAAA
1 ATTGAAAAAA
5138280 ATTGAAAAAA
1 ATTGAAAAAA
5138290 ATTGA
1 ATTGA
5138295 TTTTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (10 bp):
ATTGAAAAAA
Found at i:5141463 original size:18 final size:18
Alignment explanation
Indices: 5141440--5141484 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
5141430 AGTCTAGATT
5141440 TTTAAAAATTAAAAA-AA
1 TTTAAAAATTAAAAATAA
*
5141457 CTTTAAAAA-TAAAAATTA
1 -TTTAAAAATTAAAAATAA
5141475 TTTAAAAATT
1 TTTAAAAATT
5141485 CATTTTCGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAAAAATTAAAAATAA
Found at i:5141604 original size:20 final size:20
Alignment explanation
Indices: 5141579--5141629 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5141569 ATTTATTTAT
* *
5141579 TAAAATAATATTTTTATAGA
1 TAAAATAATATTCTTATAAA
*
5141599 TAAAATAATAATCTTATAAA
1 TAAAATAATATTCTTATAAA
*
5141619 TAAAAAAATAT
1 TAAAATAATAT
5141630 ACGGGGAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAATAATATTCTTATAAA
Found at i:5142948 original size:45 final size:45
Alignment explanation
Indices: 5142880--5143143 Score: 411
Period size: 45 Copynumber: 5.9 Consensus size: 45
5142870 AAGAGGTGGA
** * * *
5142880 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
5142925 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
5142970 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
5143015 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATCTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* *
5143060 CAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* * * *
5143105 CAACATCATGCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCA
5143144 CCATGGCCGA
Statistics
Matches: 203, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 203 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
Found at i:5147302 original size:45 final size:45
Alignment explanation
Indices: 5147234--5147497 Score: 420
Period size: 45 Copynumber: 5.9 Consensus size: 45
5147224 AAGAGGTAGA
** * * *
5147234 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
5147279 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
5147324 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
5147369 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* *
5147414 CAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* * * *
5147459 CAACATCATGCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCA
5147498 CCATGGCCGA
Statistics
Matches: 205, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 205 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
Found at i:5150319 original size:16 final size:15
Alignment explanation
Indices: 5150277--5150320 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
5150267 TTTATCAGTA
5150277 TTATTTTAGTTTAAAT
1 TTATTTTA-TTTAAAT
**
5150293 AAATTTTATTTAAAT
1 TTATTTTATTTAAAT
5150308 TTATTTTGATTTA
1 TTATTTT-ATTTA
5150321 GATCCAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (15 bp):
TTATTTTATTTAAAT
Found at i:5150727 original size:22 final size:22
Alignment explanation
Indices: 5150682--5150735 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
5150672 TGTCACACAA
* *
5150682 AAGATTTTAATAGAATAAATTT
1 AAGATTTTAACAGAATAAACTT
*
5150704 AACGATTTTAACA-AATAGACTT
1 AA-GATTTTAACAGAATAAACTT
*
5150726 AAAATTTTAA
1 AAGATTTTAA
5150736 ACCCAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.26
22 11 0.41
23 9 0.33
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (22 bp):
AAGATTTTAACAGAATAAACTT
Found at i:5152124 original size:14 final size:14
Alignment explanation
Indices: 5152105--5152148 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5152095 TTTGTCTTTT
5152105 TAATTTAATTCAAA
1 TAATTTAATTCAAA
* *
5152119 TAATTTTATTCAAT
1 TAATTTAATTCAAA
*
5152133 TCAATTTAATTTAAA
1 T-AATTTAATTCAAA
5152148 T
1 T
5152149 TTCATCTCAC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTTAATTCAAA
Found at i:5153697 original size:8 final size:8
Alignment explanation
Indices: 5153686--5153711 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5153676 AAAATATATA
5153686 AATAATTT
1 AATAATTT
5153694 AATAATTT
1 AATAATTT
5153702 AATAATTT
1 AATAATTT
5153710 AA
1 AA
5153712 ATAAAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AATAATTT
Found at i:5154580 original size:29 final size:30
Alignment explanation
Indices: 5154536--5154592 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
5154526 GAGATAATTT
* *
5154536 GACAAAAAATACAAATTAAAAATTAAAAGA
1 GACAAAAAATACAAATAAAAAACTAAAAGA
*
5154566 GACAAAAAA-ATAAATAAAAAACTAAAA
1 GACAAAAAATACAAATAAAAAACTAAAA
5154593 TATATAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.14
Consensus pattern (30 bp):
GACAAAAAATACAAATAAAAAACTAAAAGA
Found at i:5171178 original size:107 final size:107
Alignment explanation
Indices: 5171045--5171261 Score: 362
Period size: 107 Copynumber: 2.0 Consensus size: 107
5171035 ATCTTTATCT
* *
5171045 TAATAGGGCTCAAACTCTTATGTCTTAAATGTCTTTGGAAGTTAAAATGGTGTAGTTTTTATAAC
1 TAATAGGCCTCAAACTCTTATATCTTAAATGTCTTTGGAAGTTAAAATGGTGTAGTTTTTATAAC
* *
5171110 ACTTACTTGTTTATTGAAGAACATATATTTGAGAGTGTAAAG
66 ACTTACCTGTTCATTGAAGAACATATATTTGAGAGTGTAAAG
* *
5171152 TAATAGGCCTCAAACTCTTATATCTTAGATGTCTTTGGAAGTTAAAATGGTGTAGTTTTTATAGC
1 TAATAGGCCTCAAACTCTTATATCTTAAATGTCTTTGGAAGTTAAAATGGTGTAGTTTTTATAAC
* *
5171217 ACTTACCTGTTCATTGAATAACATGTATTTGAGAGTGTAAAG
66 ACTTACCTGTTCATTGAAGAACATATATTTGAGAGTGTAAAG
5171259 TAA
1 TAA
5171262 ATTGATATCA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 102 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (107 bp):
TAATAGGCCTCAAACTCTTATATCTTAAATGTCTTTGGAAGTTAAAATGGTGTAGTTTTTATAAC
ACTTACCTGTTCATTGAAGAACATATATTTGAGAGTGTAAAG
Found at i:5173432 original size:22 final size:21
Alignment explanation
Indices: 5173407--5173459 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5173397 CATTATTTAG
*
5173407 TTATATGAATACTAAATTTTTT
1 TTAT-TGAAAACTAAATTTTTT
*
5173429 TTATTTAAAACTAAATTTTTT
1 TTATTGAAAACTAAATTTTTT
*
5173450 TTATTTAAAA
1 TTATTGAAAA
5173460 ACGTAACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (21 bp):
TTATTGAAAACTAAATTTTTT
Found at i:5173461 original size:22 final size:21
Alignment explanation
Indices: 5173417--5173459 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5173407 TTATATGAAT
5173417 ACTAAATTTTTTTTATTTAAA
1 ACTAAATTTTTTTTATTTAAA
5173438 ACTAAATTTTTTTTATTTAAA
1 ACTAAATTTTTTTTATTTAAA
5173459 A
1 A
5173460 ACGTAACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
ACTAAATTTTTTTTATTTAAA
Found at i:5173733 original size:30 final size:30
Alignment explanation
Indices: 5173653--5173722 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
5173643 ATATATGAAG
5173653 AATATTAAATTATTATTAAAATAAAATTGA
1 AATATTAAATTATTATTAAAATAAAATTGA
*
5173683 ATTATTAAATTATTATTAAAATAAAATTGA
1 AATATTAAATTATTATTAAAATAAAATTGA
5173713 AATATTAAAT
1 AATATTAAAT
5173723 ATTTTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (30 bp):
AATATTAAATTATTATTAAAATAAAATTGA
Found at i:5184435 original size:83 final size:83
Alignment explanation
Indices: 5184332--5184534 Score: 282
Period size: 83 Copynumber: 2.4 Consensus size: 83
5184322 GACACATATG
* * * ** *
5184332 AAATATTTAGTGTCAAATTATAATATAATATTAAAGACATCGAAATTACTTATGTAGTTCG-GAA
1 AAATAATTAGTGTCAAATTATAATATAATATTAAAGACATCAAAATTAATTACATAGTTCGAAAA
*
5184396 AACATTTTACATTTGAAA
66 AACATTCTACATTTGAAA
5184414 AAATAAATTAGTGTCAAATTATAATATAATATTAAAGACATCAAAATTAATTACATAGTTCGAAA
1 AAAT-AATTAGTGTCAAATTATAATATAATATTAAAGACATCAAAATTAATTACATAGTTCGAAA
* *
5184479 AAACATTCTACGTTTGAAT
65 AAACATTCTACATTTGAAA
*
5184498 AAATAATATAGTGTCAATTTATAATATAATATGTAAA
1 AAATAAT-TAGTGTCAAATTATAATATAATAT-TAAA
5184535 ATTAATAGCT
Statistics
Matches: 107, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
82 4 0.04
83 55 0.51
84 44 0.41
85 4 0.04
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.35
Consensus pattern (83 bp):
AAATAATTAGTGTCAAATTATAATATAATATTAAAGACATCAAAATTAATTACATAGTTCGAAAA
AACATTCTACATTTGAAA
Found at i:5184738 original size:17 final size:16
Alignment explanation
Indices: 5184690--5184741 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
5184680 AAATATGATA
*
5184690 ATTTAAATATATATTT
1 ATTTAAATATAAATTT
*
5184706 -TTTAAA-AAATAATTT
1 ATTTAAATATA-AATTT
5184721 ATTTCAAATATAAATTT
1 ATTT-AAATATAAATTT
5184738 ATTT
1 ATTT
5184742 TTAAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.07
15 10 0.34
16 3 0.10
17 12 0.41
18 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTAAATATAAATTT
Found at i:5186071 original size:23 final size:23
Alignment explanation
Indices: 5186043--5186090 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5186033 TTTTTTAAAG
5186043 TTTGATTGTATTTATCTATGGGT
1 TTTGATTGTATTTATCTATGGGT
5186066 TTTGATTGTATTTATCTATGGGT
1 TTTGATTGTATTTATCTATGGGT
5186089 TT
1 TT
5186091 ATTATTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.04, G:0.21, T:0.58
Consensus pattern (23 bp):
TTTGATTGTATTTATCTATGGGT
Found at i:5192139 original size:80 final size:79
Alignment explanation
Indices: 5192006--5192155 Score: 246
Period size: 80 Copynumber: 1.9 Consensus size: 79
5191996 CCAAAAATTG
* *
5192006 ATTTGATCACAGCCTTCTACTACTTGCGTCCCAGTTAGCATTGATATTGGTACAACTTTTTGAGA
1 ATTTGATCACAGCCTTCAACTACTTGCGTCACAGTTAGCATTGATATTGGTACAAC-TTTTGAGA
5192071 TTAAAAGTTGTGTTA
65 TTAAAAGTTGTGTTA
* * *
5192086 ATTTGATTACAGCCTTCAACTACTTGCGTCACAGTTAGTATTGATTTTGGTACAACTTTTGAGAT
1 ATTTGATCACAGCCTTCAACTACTTGCGTCACAGTTAGCATTGATATTGGTACAACTTTTGAGAT
5192151 TAAAA
66 TAAAA
5192156 CAATGCTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 14 0.22
80 51 0.78
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (79 bp):
ATTTGATCACAGCCTTCAACTACTTGCGTCACAGTTAGCATTGATATTGGTACAACTTTTGAGAT
TAAAAGTTGTGTTA
Found at i:5193764 original size:13 final size:14
Alignment explanation
Indices: 5193746--5193774 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5193736 TAAATATGAC
5193746 TTTTTA-AAAATAA
1 TTTTTAGAAAATAA
5193759 TTTTTAGAAAATAA
1 TTTTTAGAAAATAA
5193773 TT
1 TT
5193775 AGCTTTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TTTTTAGAAAATAA
Found at i:5197756 original size:19 final size:19
Alignment explanation
Indices: 5197721--5197757 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5197711 TTGTTGTTTT
*
5197721 TTCACTATTTTACTACTAA
1 TTCACTATTATACTACTAA
*
5197740 TTCACTATTATATTACTA
1 TTCACTATTATACTACTA
5197758 CTATTTTATT
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:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (19 bp):
TTCACTATTATACTACTAA
Found at i:5197797 original size:25 final size:25
Alignment explanation
Indices: 5197769--5197821 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
5197759 TATTTTATTG
*
5197769 TTATT-ATTTAAATATTATATATTTA
1 TTATTAATTTAAAGA-TATATATTTA
* *
5197794 TTATTAATTTACAGATATTTATTTA
1 TTATTAATTTAAAGATATATATTTA
5197819 TTA
1 TTA
5197822 AATTGTACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
TTATTAATTTAAAGATATATATTTA
Found at i:5207414 original size:5 final size:5
Alignment explanation
Indices: 5207404--5207446 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
5207394 AACGTATTAT
** * *
5207404 ACCGC ACCGC ATTGT ACCGC ACCGT ACCGC ACCGC ACCGC ACC
1 ACCGC ACCGC ACCGC ACCGC ACCGC ACCGC ACCGC ACCGC ACC
5207447 ACCGCTCCAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.21, C:0.51, G:0.19, T:0.09
Consensus pattern (5 bp):
ACCGC
Found at i:5211738 original size:15 final size:15
Alignment explanation
Indices: 5211718--5211758 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
5211708 TTAAGATCCC
5211718 TTATAAATTATGAAA
1 TTATAAATTATGAAA
*
5211733 TTATAAATTAATGTAA
1 TTATAAATT-ATGAAA
*
5211749 TGATAAATTA
1 TTATAAATTA
5211759 CTTTATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
TTATAAATTATGAAA
Found at i:5212293 original size:21 final size:21
Alignment explanation
Indices: 5212255--5212303 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5212245 ATCATGATTC
*
5212255 TAAAACATTAAATAATTTAT-A
1 TAAAAAATTAAATAATTT-TCA
5212276 TAAAAAATATAAAT-ATTTTCA
1 TAAAAAAT-TAAATAATTTTCA
5212297 TAAAAAA
1 TAAAAAA
5212304 ACAATAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 5 0.20
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAAATTAAATAATTTTCA
Found at i:5212303 original size:23 final size:22
Alignment explanation
Indices: 5212256--5212312 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
5212246 TCATGATTCT
*
5212256 AAAACATTAAATAATTTATATAA
1 AAAACAATAAATAATTTATA-AA
* *
5212279 AAAA-TATAAATATTTTCATAAA
1 AAAACAATAAATAATTT-ATAAA
5212301 AAAACAATAAAT
1 AAAACAATAAAT
5212313 GTAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAACAATAAATAATTTATAAA
Found at i:5212817 original size:6 final size:6
Alignment explanation
Indices: 5212808--5212845 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
5212798 TTTATTTTAT
*
5212808 TTAATA TTAATA TTAATA TTAATA TTTAT- TTAATA TTA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTA
5212846 TTTTGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TTAATA
Found at i:5220867 original size:15 final size:15
Alignment explanation
Indices: 5220835--5220880 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
5220825 ATTCATCTAT
*
5220835 TTATATTTCAACTATTA
1 TTATATTTCTA-T-TTA
5220852 TTATATTTCTATTTA
1 TTATATTTCTATTTA
*
5220867 TTATATTTTTATTT
1 TTATATTTCTATTT
5220881 CTATTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 16 0.59
16 1 0.04
17 10 0.37
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:5220873 original size:23 final size:24
Alignment explanation
Indices: 5220845--5220913 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 24
5220835 TTATATTTCA
5220845 ACTATTATTATATTTCTATTTATT
1 ACTATTATTATATTTCTATTTATT
5220869 A-TATT-TT-TATTTCTATTTATAT
1 ACTATTATTATATTTCTATTTAT-T
*
5220891 ACTAATATTAT-TTTC-A-TTATT
1 ACTATTATTATATTTCTATTTATT
5220912 AC
1 AC
5220914 ATTTTTTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
21 16 0.40
22 8 0.20
23 8 0.20
24 7 0.17
25 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (24 bp):
ACTATTATTATATTTCTATTTATT
Found at i:5225564 original size:13 final size:13
Alignment explanation
Indices: 5225546--5225571 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5225536 TAATCACTTA
5225546 AAAAAATATATTT
1 AAAAAATATATTT
5225559 AAAAAATATATTT
1 AAAAAATATATTT
5225572 TTAATTGTGA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAAAATATATTT
Found at i:5225575 original size:15 final size:14
Alignment explanation
Indices: 5225543--5225571 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5225533 AAATAATCAC
5225543 TTAAAAAAATATAT
1 TTAAAAAAATATAT
5225557 TT-AAAAAATATAT
1 TTAAAAAAATATAT
5225570 TT
1 TT
5225572 TTAATTGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.87
14 2 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAAAAAATATAT
Found at i:5226066 original size:2 final size:2
Alignment explanation
Indices: 5226061--5226088 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5226051 TTTCCTTCCC
5226061 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5226089 TGTTCCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5226542 original size:17 final size:18
Alignment explanation
Indices: 5226508--5226545 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5226498 CTGGTTAGAG
* *
5226508 TTTTAGCCATCTTTTCTT
1 TTTTAACCATCTTCTCTT
5226526 TTTTAACCATC-TCTCTT
1 TTTTAACCATCTTCTCTT
5226543 TTT
1 TTT
5226546 AATTCTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.13, C:0.24, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTAACCATCTTCTCTT
Found at i:5228766 original size:12 final size:12
Alignment explanation
Indices: 5228735--5228768 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
5228725 AAAAGAGAGA
5228735 AAATATTTGTCTG
1 AAAT-TTTGTCTG
5228748 AAGATTTTGTCTG
1 AA-ATTTTGTCTG
5228761 AAATTTTG
1 AAATTTTG
5228769 ATGTGGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 12 0.60
14 2 0.10
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (12 bp):
AAATTTTGTCTG
Found at i:5230937 original size:37 final size:37
Alignment explanation
Indices: 5230893--5231058 Score: 305
Period size: 37 Copynumber: 4.5 Consensus size: 37
5230883 CACTTGTCCC
5230893 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
5230930 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
*
5230967 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
* *
5231004 TGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
5231041 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
5231059 TAAAGCTATC
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 127 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
Found at i:5231075 original size:46 final size:46
Alignment explanation
Indices: 5231022--5231290 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
5231012 TAAGTGTAGC
* **
5231022 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
5231068 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
5231114 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
5231166 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
5231212 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
5231264 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
5231291 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:5231141 original size:52 final size:52
Alignment explanation
Indices: 5231065--5231284 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
5231055 TAGCTAAAGC
* *
5231065 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
5231118 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
5231170 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
5231216 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
5231268 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
5231285 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:5231187 original size:98 final size:98
Alignment explanation
Indices: 5231022--5231290 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
5231012 TAAGTGTAGC
* * *
5231022 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
5231087 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
5231121 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
5231186 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
5231219 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
5231284 GATCAGA
66 GATCAGA
5231291 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:5244050 original size:46 final size:46
Alignment explanation
Indices: 5243975--5244202 Score: 332
Period size: 46 Copynumber: 5.0 Consensus size: 46
5243965 TTATCTTCGG
* * * * * *
5243975 CATGATGCCATAGTGTCTTTCAACTATGGTCTTGCTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATAT
* *
5244021 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
* *
5244067 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACCCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
*
5244113 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
*
5244159 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
5244203 TTCAGAAAGC
Statistics
Matches: 169, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 4 0.02
46 165 0.98
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
Found at i:5246207 original size:50 final size:50
Alignment explanation
Indices: 5246148--5246248 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
5246138 GGGAAACAAG
5246148 TATGCTTATTAAAGAATAAGATTGTAAACATGAATGCTTGTGATGATATA
1 TATGCTTATTAAAGAATAAGATTGTAAACATGAATGCTTGTGATGATATA
*
5246198 TATGCTTATTAAAGAATAAGATTGTAAATATGAATGCTTGTGATGATATA
1 TATGCTTATTAAAGAATAAGATTGTAAACATGAATGCTTGTGATGATATA
5246248 T
1 T
5246249 CATGTTGAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.38
Consensus pattern (50 bp):
TATGCTTATTAAAGAATAAGATTGTAAACATGAATGCTTGTGATGATATA
Found at i:5247363 original size:46 final size:46
Alignment explanation
Indices: 5247302--5247621 Score: 507
Period size: 46 Copynumber: 7.0 Consensus size: 46
5247292 TTTGACATGA
* * * * * *
5247302 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * *
5247348 TGCCATGGTGCCTTTCAACCATGGTATTACACATTTCATATCAAGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5247394 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5247440 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5247486 TGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5247532 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5247578 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5247622 AGAGCACACT
Statistics
Matches: 258, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 4 0.02
46 254 0.98
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:5247675 original size:162 final size:163
Alignment explanation
Indices: 5247498--5247823 Score: 627
Period size: 162 Copynumber: 2.0 Consensus size: 163
5247488 CCATGGTGTC
*
5247498 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
1 TTTCAACCATGGTCTTACACATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACA
5247563 CATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAGAGCA
66 CATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAGAGCA
5247628 CACTCCCGCGAACCTCATCCTTACA-GTGGGAT
131 CACTCCCGCGAACCTCATCCTTACAGGTGGGAT
5247660 TTTCAACCATGGTCTTACACATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACA
1 TTTCAACCATGGTCTTACACATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACA
*
5247725 CATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGATAGCA
66 CATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAGAGCA
5247790 CACTCCCGCGAACCTCATCCTTACAGGTGGGAT
131 CACTCCCGCGAACCTCATCCTTACAGGTGGGAT
5247823 T
1 T
5247824 ACCAGTCCAG
Statistics
Matches: 161, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
162 153 0.95
163 8 0.05
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (163 bp):
TTTCAACCATGGTCTTACACATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACA
CATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAGAGAGCA
CACTCCCGCGAACCTCATCCTTACAGGTGGGAT
Found at i:5247727 original size:46 final size:46
Alignment explanation
Indices: 5247660--5247778 Score: 220
Period size: 46 Copynumber: 2.6 Consensus size: 46
5247650 ACAGTGGGAT
*
5247660 TTTCAACCATGGTCTTACACATTTCATATCAAGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCAAGCTGCCATGGTATC
*
5247706 TTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCAAGCTGCCATGGTATC
5247752 TTTCAACCATGGTCTTACACATTTCAT
1 TTTCAACCATGGTCTTACACATTTCAT
5247779 TTCAGATAGC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (46 bp):
TTTCAACCATGGTCTTACACATTTCATATCAAGCTGCCATGGTATC
Found at i:5250266 original size:30 final size:30
Alignment explanation
Indices: 5250199--5250266 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
5250189 CACCCTTAAA
* * *
5250199 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
5250229 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
5250258 AGTATTTAC
1 A-TATTTAC
5250267 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:5252764 original size:30 final size:31
Alignment explanation
Indices: 5252696--5252764 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
5252686 CACCCTTAAA
* *
5252696 ATATTTACACTATTAGTCCTTCAACTTTTTT
1 ATATTTACACTATTAGACCTTCAACTTTTTG
5252727 ATATTTACACT-TTA-ACCTCTCAA-TTTTTG
1 ATATTTACACTATTAGACCT-TCAACTTTTTG
5252756 AGTATTTAC
1 A-TATTTAC
5252765 TCTTGTGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 9 0.26
30 14 0.41
31 11 0.32
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.49
Consensus pattern (31 bp):
ATATTTACACTATTAGACCTTCAACTTTTTG
Found at i:5259316 original size:27 final size:27
Alignment explanation
Indices: 5259282--5259337 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
5259272 AACCTAAACA
*
5259282 TCGGGTTAAAGTATTGGGATGTTACAT
1 TCGGGTTAAAGTACTGGGATGTTACAT
5259309 TCGGGTTAAAGTACTGGGATGTTACAT
1 TCGGGTTAAAGTACTGGGATGTTACAT
5259336 TC
1 TC
5259338 TATACTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.36
Consensus pattern (27 bp):
TCGGGTTAAAGTACTGGGATGTTACAT
Found at i:5261281 original size:15 final size:15
Alignment explanation
Indices: 5261257--5261302 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
5261247 ATATAAATAG
*
5261257 AAATAAAAATATAAT
1 AAATAGAAATATAAT
5261272 AAATAGAAATATAAT
1 AAATAGAAATATAAT
5261287 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
5261303 ATAGATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:5261290 original size:23 final size:23
Alignment explanation
Indices: 5261225--5261335 Score: 71
Period size: 23 Copynumber: 5.0 Consensus size: 23
5261215 AGAAAAAAAG
*
5261225 TAAT-AAT-GAAA-ATAATATTA
1 TAATAAATAGAAATATAATAATA
5261245 GTATATAAATAGAAATA-AA-AATA
1 -TA-ATAAATAGAAATATAATAATA
5261268 TAATAAATAGAAATATAATAATA
1 TAATAAATAGAAATATAATAATA
* * *
5261291 GT-AGAAATATAAATA-GATAA-A
1 -TAATAAATAGAAATATAATAATA
5261312 TAA-AAATTAGATAA-ATAATAATA
1 TAATAAA-TAGA-AATATAATAATA
5261335 T
1 T
5261336 TAGAATAACA
Statistics
Matches: 72, Mismatches: 6, Indels: 22
0.72 0.06 0.22
Matches are distributed among these distances:
20 4 0.06
21 21 0.29
22 16 0.22
23 23 0.32
24 7 0.10
25 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (23 bp):
TAATAAATAGAAATATAATAATA
Found at i:5261299 original size:44 final size:44
Alignment explanation
Indices: 5261251--5261340 Score: 105
Period size: 44 Copynumber: 2.0 Consensus size: 44
5261241 ATTAGTATAT
5261251 AAATAGAAATA-A-AAATATAATAAATAGA-AATATAATAATAGTAG
1 AAATAGAAATAGATAAATA-AA-AAATAGATAA-ATAATAATAGTAG
* * *
5261295 AAATATAAATAGATAAATAAAAATTAGATAAATAATAATATTAG
1 AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATAGTAG
5261339 AA
1 AA
5261341 TAACAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
44 30 0.75
45 5 0.12
46 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.27
Consensus pattern (44 bp):
AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATAGTAG
Found at i:5261322 original size:15 final size:15
Alignment explanation
Indices: 5261295--5261339 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
5261285 ATAATAGTAG
*
5261295 AAATATAAA-TAGAT
1 AAATAAAAATTAGAT
5261309 AAATAAAAATTAGAT
1 AAATAAAAATTAGAT
5261324 AAATAATAATATTAGA
1 AAATAA-AA-ATTAGA
5261340 ATAACAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.30
15 11 0.41
16 2 0.07
17 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (15 bp):
AAATAAAAATTAGAT
Found at i:5261966 original size:20 final size:20
Alignment explanation
Indices: 5261943--5261987 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5261933 CACATCAGTT
*
5261943 TTTTATCTTGAATTTCAGGA
1 TTTTATCCTGAATTTCAGGA
* *
5261963 TTTTATCCTGAATTTTAGTA
1 TTTTATCCTGAATTTCAGGA
5261983 TTTTA
1 TTTTA
5261988 ATTTGTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.56
Consensus pattern (20 bp):
TTTTATCCTGAATTTCAGGA
Found at i:5268500 original size:5 final size:5
Alignment explanation
Indices: 5268490--5268543 Score: 60
Period size: 5 Copynumber: 11.4 Consensus size: 5
5268480 AATTAAAATA
* *
5268490 ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT A-TGT ATTAT -TTAT AATAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
*
5268537 TTTAT AT
1 ATTAT AT
5268544 ATGTAATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 11 0.27
5 30 0.73
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:5268542 original size:25 final size:27
Alignment explanation
Indices: 5268494--5268553 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
5268484 AAAATAATTA
5268494 TATTATATTATATTATATTATATATATG
1 TATTATATTATA-TATATTATATATATG
*
5268522 TATTAT-TTATA-ATATTTTATATATG
1 TATTATATTATATATATTATATATATG
*
5268547 TAATATA
1 TATTATA
5268554 AAGCTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 18 0.62
27 5 0.17
28 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (27 bp):
TATTATATTATATATATTATATATATG
Found at i:5269370 original size:21 final size:21
Alignment explanation
Indices: 5269344--5269387 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5269334 TTATCATGCC
*
5269344 TAAATGAACATATGTCACTCT
1 TAAATGAACATATATCACTCT
5269365 TAAATGAACATATATCACTCT
1 TAAATGAACATATATCACTCT
5269386 TA
1 TA
5269388 GAACGCTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (21 bp):
TAAATGAACATATATCACTCT
Found at i:5270179 original size:12 final size:12
Alignment explanation
Indices: 5270162--5270194 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5270152 GTTCGCCAAT
5270162 AAAAACATAAAG
1 AAAAACATAAAG
5270174 AAAAACAT-AAG
1 AAAAACATAAAG
5270185 -AAAACATAAA
1 AAAAACATAAA
5270195 AATAACTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.35
11 5 0.25
12 8 0.40
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAACATAAAG
Found at i:5272809 original size:48 final size:48
Alignment explanation
Indices: 5272747--5273221 Score: 851
Period size: 48 Copynumber: 9.9 Consensus size: 48
5272737 TATATATGTG
* *
5272747 TGTGGCAAAGCCGAATGACTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
5272795 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATACGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
5272843 TGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 --TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
5272893 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
5272941 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
5272989 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
5273037 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
* *
5273085 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
5273133 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
*
5273181 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAAGAGAT
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
5273222 GTGTGTACAT
Statistics
Matches: 410, Mismatches: 15, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
48 363 0.89
50 47 0.11
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.31
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
Found at i:5273417 original size:37 final size:37
Alignment explanation
Indices: 5273362--5273464 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
5273352 GGAAATATAT
*
5273362 TCCGGGTAAGACCTGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
5273399 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
5273436 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
5273465 GGACTATTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:5275728 original size:39 final size:40
Alignment explanation
Indices: 5275623--5275830 Score: 237
Period size: 40 Copynumber: 5.2 Consensus size: 40
5275613 TATTCGAATG
* * * *
5275623 ATATCCGGGCTAAGTCTCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACT
* *
5275664 ATATCCGGACTCAGAT-CCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
*
5275704 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACT
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
5275743 AAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
5275783 ATAACCGGGC-AATGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATATCCGGGCTAA-GTCCCGAAGGCATTTGTGCGAGTTA-CT
5275823 ATATCCGG
1 ATATCCGG
5275831 TTAAATTCTG
Statistics
Matches: 144, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
39 39 0.27
40 78 0.54
41 26 0.18
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:5275763 original size:79 final size:79
Alignment explanation
Indices: 5275680--5275834 Score: 210
Period size: 79 Copynumber: 2.0 Consensus size: 79
5275670 GGACTCAGAT
* *
5275680 CCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGGCTAA-G-CCCGAAGGCATTGGTGCGAGTTA-
1 CCGAAGGCATTTGTGCGAGTTACTATA-ACCGGGC-AATGTCCCGAAGGCATTGGAGCGAG-TAG
5275741 CTAAATCCGGGTTAAGTC
63 CTAAATCC-GGTTAAGTC
*
5275759 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCAATGTCCCGAAGGCATTTGAGCGAGTAGCTA
1 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCAATGTCCCGAAGGCATTGGAGCGAGTAGCTA
*
5275824 TATCCGGTTAA
66 AATCCGGTTAA
5275835 ATTCTGAAGG
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
78 2 0.03
79 40 0.59
80 26 0.38
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCAATGTCCCGAAGGCATTGGAGCGAGTAGCTA
AATCCGGTTAAGTC
Found at i:5285703 original size:106 final size:106
Alignment explanation
Indices: 5285497--5285704 Score: 249
Period size: 106 Copynumber: 2.0 Consensus size: 106
5285487 ACTATCACAG
* * *
5285497 CTTGCCAGGCCCACTGACGATCCCTGCTTCATCAAGTCCACTGGCAATTATAGTTTGCTAAATCT
1 CTTGCCAGGCCCACTGACGATCCCTACTTCATCAAGTCCACTAGCAATCATAGTTTGCTAAATCT
* * * * **
5285562 ACTGGCAACCCTAGTTCGCTAGGCCTTTTGACGAACCCCAA
66 ACTGGCAACCCCAGCTCGCCAGACCTGCTGACGAACCCCAA
* * * **
5285603 CTTGCCAGGCTCACTGGCGATCCCTACTTCGTCAAG-CCTACTAGTGATCATAGTTCT-CTAAAT
1 CTTGCCAGGCCCACTGACGATCCCTACTTCATCAAGTCC-ACTAGCAATCATAGTT-TGCTAAAT
*
5285666 CTACTGGCAACCCCAGCTCGCCAGACCTGCTGGCGAACC
64 CTACTGGCAACCCCAGCTCGCCAGACCTGCTGACGAACC
5285705 TCTTCTTGTA
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
105 2 0.02
106 82 0.96
107 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.25
Consensus pattern (106 bp):
CTTGCCAGGCCCACTGACGATCCCTACTTCATCAAGTCCACTAGCAATCATAGTTTGCTAAATCT
ACTGGCAACCCCAGCTCGCCAGACCTGCTGACGAACCCCAA
Found at i:5286692 original size:21 final size:21
Alignment explanation
Indices: 5286666--5286705 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5286656 TATAGGTGGA
5286666 TCAACTCTCACGAGCTTCTAT
1 TCAACTCTCACGAGCTTCTAT
5286687 TCAACTCTCACGAGCTTCT
1 TCAACTCTCACGAGCTTCT
5286706 GTTTAGCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.35, G:0.10, T:0.33
Consensus pattern (21 bp):
TCAACTCTCACGAGCTTCTAT
Found at i:5293104 original size:17 final size:18
Alignment explanation
Indices: 5293071--5293106 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5293061 TGCTTCGAAG
5293071 AAGCACTTTTGGGACAAA
1 AAGCACTTTTGGGACAAA
5293089 AAGCACTTTT-GGACAAA
1 AAGCACTTTTGGGACAAA
5293106 A
1 A
5293107 TCATTCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (18 bp):
AAGCACTTTTGGGACAAA
Found at i:5297532 original size:15 final size:17
Alignment explanation
Indices: 5297503--5297539 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
5297493 CGTACTTTCA
5297503 TAACTTTTTATACAAT-
1 TAACTTTTTATACAATC
5297519 TAACTTTTTA-ACAATC
1 TAACTTTTTATACAATC
5297535 TAACT
1 TAACT
5297540 GTTGAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (17 bp):
TAACTTTTTATACAATC
Found at i:5297941 original size:21 final size:20
Alignment explanation
Indices: 5297903--5297941 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5297893 TTCTACTGTT
* *
5297903 GTTGGTTCTTGCCTTCTTGG
1 GTTGGTACTTGCCATCTTGG
5297923 GTTGGTACTCTGCCATCTT
1 GTTGGTACT-TGCCATCTT
5297942 TGTTACCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.05, C:0.23, G:0.26, T:0.46
Consensus pattern (20 bp):
GTTGGTACTTGCCATCTTGG
Found at i:5314128 original size:16 final size:16
Alignment explanation
Indices: 5314107--5314138 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5314097 CTTATGTAAA
5314107 GGCTAAGCTATTTGGT
1 GGCTAAGCTATTTGGT
5314123 GGCTAAGCTATTTGGT
1 GGCTAAGCTATTTGGT
5314139 TTTAAGGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.38
Consensus pattern (16 bp):
GGCTAAGCTATTTGGT
Found at i:5322204 original size:16 final size:16
Alignment explanation
Indices: 5322178--5322213 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
5322168 AATCACGATG
5322178 ATAACATGCGTAATAAA
1 ATAACATGCGTAA-AAA
5322195 ATAA-ATGCGTAAAAA
1 ATAACATGCGTAAAAA
5322210 ATAA
1 ATAA
5322214 TAAAAAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 8 0.42
17 4 0.21
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.22
Consensus pattern (16 bp):
ATAACATGCGTAAAAA
Found at i:5322535 original size:3 final size:3
Alignment explanation
Indices: 5322527--5322573 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
5322517 ACAATATTAG
* * * *
5322527 TAA TAA TAA TAA TAG TAA AAA TAA TAG TAA TGA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5322574 TAAATAAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5322738 original size:3 final size:3
Alignment explanation
Indices: 5322730--5322820 Score: 57
Period size: 3 Copynumber: 30.3 Consensus size: 3
5322720 AGAAAGAACT
* * *
5322730 ATA ATA ATA ATA GTA ATA ATA ATA CTA AGTTA ATTA AT- TTA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A--TA A-TA ATA ATA ATA ATA
* *
5322776 ATA ATA ATA ATA AGTA GTA A-A CATA AAA ATA A-A AT- ATA ATA ATA
1 ATA ATA ATA ATA A-TA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
5322820 A
1 A
5322821 CATTAAATTA
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
2 8 0.12
3 51 0.74
4 7 0.10
5 3 0.04
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5324303 original size:31 final size:32
Alignment explanation
Indices: 5324262--5324324 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
5324252 TTATTTATAA
*
5324262 AAGATATTTAT-TAATTAAATA-ATTATATTAT
1 AAGATATTTATGTAA-TAAATATATTAAATTAT
*
5324293 AAGATTTTTATGTAATAAATATATTAAATTAT
1 AAGATATTTATGTAATAAATATATTAAATTAT
5324325 GACAAGTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (32 bp):
AAGATATTTATGTAATAAATATATTAAATTAT
Found at i:5329461 original size:89 final size:88
Alignment explanation
Indices: 5329331--5329651 Score: 322
Period size: 86 Copynumber: 3.7 Consensus size: 88
5329321 GCCTACTCCA
* * *
5329331 CTACTGCTTAGGGAGATAGGGTC--TACAATTTCTAGCCTATTACCTTACTGCTTAAGGGG-TTA
1 CTACTGCTTAGGGAGATAAGATCTGTA-AATTT-TAGCCTATTACCCTACTGCTTAAGGGGTTTA
* *
5329393 AGGCTCGTCGTCTTTGATCTGTTTCC
64 AGGC-CTTCGTCTTCGATCTGTTTCC
* **
5329419 CTACTGCTTAGGGTGATAAGATCTGTAAATTTTTAGCCTATTACCCTACTG-TTTGGGGGTTTAA
1 CTACTGCTTAGGGAGATAAGATCTGTAAA-TTTTAGCCTATTACCCTACTGCTTAAGGGGTTTAA
*
5329483 GGCCCTTCGTCTTCGATCTG-CTCC
65 GG-CCTTCGTCTTCGATCTGTTTCC
* * * *
5329507 ACTACTGCTTAGGGAGATAAAATCTGT-AA-TTTGGTCC-GTTACCCTACTTCTT-AGGGGTTTA
1 -CTACTGCTTAGGGAGATAAGATCTGTAAATTTTAG-CCTATTACCCTACTGCTTAAGGGGTTTA
*
5329568 AGACCTTTCGTCTTCGATCTGTTTCC
64 AGGCC-TTCGTCTTCGATCTGTTTCC
* * * *
5329594 CTACTGCTTAGGG-GATTAAGATCTG-AAAATTCAGCCTGTTACCCTACTGCTTAGGGGG
1 CTACTGCTTAGGGAGA-TAAGATCTGTAAATTTTAGCCTATTACCCTACTGCTTAAGGGG
5329652 ACAGGATGGT
Statistics
Matches: 196, Mismatches: 22, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
85 4 0.02
86 64 0.33
87 24 0.12
88 35 0.18
89 63 0.32
90 6 0.03
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (88 bp):
CTACTGCTTAGGGAGATAAGATCTGTAAATTTTAGCCTATTACCCTACTGCTTAAGGGGTTTAAG
GCCTTCGTCTTCGATCTGTTTCC
Found at i:5338801 original size:6 final size:6
Alignment explanation
Indices: 5338790--5338829 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
5338780 TGTCGGATAT
5338790 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTT
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTT
5338830 TCGGATTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53
Consensus pattern (6 bp):
TGTTAC
Found at i:5339016 original size:18 final size:18
Alignment explanation
Indices: 5338993--5339288 Score: 161
Period size: 18 Copynumber: 16.1 Consensus size: 18
5338983 AAAGGTATAA
*
5338993 AATAATTGATTATTACTG
1 AATAATTGATTGTTACTG
** *
5339011 AATAATTGACAGTTACCG
1 AATAATTGATTGTTACTG
* *
5339029 GATAATTGACTGTTACTG
1 AATAATTGATTGTTACTG
* *
5339047 GAT-ATTAGACTGTTACTG
1 AATAATT-GATTGTTACTG
* *
5339065 AATAATTGAATATTACTG
1 AATAATTGATTGTTACTG
**
5339083 AATAATTGATCATTACTG
1 AATAATTGATTGTTACTG
* *
5339101 AATAACTGATTGTCACTG
1 AATAATTGATTGTTACTG
* * *
5339119 AATGAA-TAACTGTTACCG
1 AAT-AATTGATTGTTACTG
*
5339137 AATAACTTAATTGTTACTG
1 AATAA-TTGATTGTTACTG
*
5339156 AAT-ATCTTATT-TTACTG
1 AATAAT-TGATTGTTACTG
*
5339173 AATAATTGACTGTTACTGG
1 AATAATTGATTGTTACT-G
* *
5339192 ATAACCGATCAATTGATCGATACTG
1 ---A---AT-AATTGATTGTTACTG
* * * * *
5339217 AATAACTGGTTATCATTG
1 AATAATTGATTGTTACTG
*
5339235 AATAATTGATTGTTACCG
1 AATAATTGATTGTTACTG
* *
5339253 AATAACTGACTGTTACTG
1 AATAATTGATTGTTACTG
* *
5339271 AATAAATAATTGTT-CTG
1 AATAATTGATTGTTACTG
5339288 A
1 A
5339289 TTGTTAATAA
Statistics
Matches: 215, Mismatches: 47, Indels: 33
0.73 0.16 0.11
Matches are distributed among these distances:
17 22 0.10
18 156 0.73
19 21 0.10
22 2 0.01
25 3 0.01
26 11 0.05
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
AATAATTGATTGTTACTG
Found at i:5339131 original size:72 final size:72
Alignment explanation
Indices: 5338993--5339159 Score: 187
Period size: 72 Copynumber: 2.3 Consensus size: 72
5338983 AAAGGTATAA
* * * * * *
5338993 AATAATTGATTATTACTGAATAATTGACAGTTACCGGATAATTGACTGTTACTGGATATTAGACT
1 AATAATTGAATATTACTGAATAATTGACAGTTACCGAATAACTGACTGTCACTGAATAATAGACT
*
5339058 GTTACTG
66 GTTACCG
* *
5339065 AATAATTGAATATTACTGAATAATTGATCA-TTACTGAATAACTGATTGTCACTGAATGAATA-A
1 AATAATTGAATATTACTGAATAATTGA-CAGTTACCGAATAACTGACTGTCACTGAAT-AATAGA
5339128 CTGTTACCG
64 CTGTTACCG
*
5339137 AATAACTT-AATTGTTACTGAATA
1 AATAA-TTGAA-TATTACTGAATA
5339160 TCTTATTTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
72 63 0.78
73 18 0.22
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (72 bp):
AATAATTGAATATTACTGAATAATTGACAGTTACCGAATAACTGACTGTCACTGAATAATAGACT
GTTACCG
Found at i:5341051 original size:75 final size:75
Alignment explanation
Indices: 5340936--5341141 Score: 283
Period size: 75 Copynumber: 2.7 Consensus size: 75
5340926 CGCCCAGCGT
* *
5340936 TAGTCAGAT-TAACCGAC-AGTATTAAATGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATT
1 TAGTCAGATAT-ACCGACGA-TAGTAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATT
* *
5340999 TGCACCCAGTGT
64 TGCACCCAATGC
* * *
5341011 TAGTC-GAATATACCGATGATAGTAATTGTGAGCCTAGCTCTAGGTGGATAAACCAACGATATTT
1 TAGTCAG-ATATACCGACGATAGTAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATTT
5341075 GCACCCAATGC
65 GCACCCAATGC
* *
5341086 TAGTCAGGTATACCGACGATAGTAATTGTGAGCCCAGCTCTAGTTAGATAAACCAA
1 TAGTCAGATATACCGACGATAGTAATTGTGAGCCCAGCTCTAGTTGGATAAACCAA
5341142 TGGTAATTGC
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
74 1 0.01
75 111 0.97
76 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (75 bp):
TAGTCAGATATACCGACGATAGTAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTG
CACCCAATGC
Found at i:5341163 original size:75 final size:75
Alignment explanation
Indices: 5340922--5341179 Score: 279
Period size: 75 Copynumber: 3.4 Consensus size: 75
5340912 CGTAGAAAAG
* * * * *
5340922 ATTGCGCCCAGCGTTAGTCAGAT-TAACCGAC-AGTATTAAATGTGAGCCCAGCTCTAGTTGGAT
1 ATTGCACCCAGTGCTAGTCAGATAT-ACCGACGA-TAGTAATTGTGAGCCCAGCTCTAGTTGGAT
5340985 AAACCAACGATA
64 AAACCAACGATA
* * * * *
5340997 TTTGCACCCAGTGTTAGTC-GAATATACCGATGATAGTAATTGTGAGCCTAGCTCTAGGTGGATA
1 ATTGCACCCAGTGCTAGTCAG-ATATACCGACGATAGTAATTGTGAGCCCAGCTCTAGTTGGATA
5341061 AACCAACGATA
65 AACCAACGATA
* * * *
5341072 TTTGCACCCAATGCTAGTCAGGTATACCGACGATAGTAATTGTGAGCCCAGCTCTAGTTAGATAA
1 ATTGCACCCAGTGCTAGTCAGATATACCGACGATAGTAATTGTGAGCCCAGCTCTAGTTGGATAA
* *
5341137 ACCAATGGTA
66 ACCAACGATA
* * * *
5341147 ATTGCGCCCAGGGCTAGTCGGGATAAACCGACG
1 ATTGCACCCAGTGCTAGTC-AGATATACCGACG
5341180 GTTATACAAT
Statistics
Matches: 154, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
74 1 0.01
75 140 0.91
76 13 0.08
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (75 bp):
ATTGCACCCAGTGCTAGTCAGATATACCGACGATAGTAATTGTGAGCCCAGCTCTAGTTGGATAA
ACCAACGATA
Found at i:5343485 original size:45 final size:45
Alignment explanation
Indices: 5343434--5343565 Score: 219
Period size: 45 Copynumber: 2.9 Consensus size: 45
5343424 TATGCCTAAA
*
5343434 ATGAGTAAGGCCATAACTGAAACATGCTATGGCATCATGATAAGG
1 ATGAGTAAGGCCATAACTGAAAGATGCTATGGCATCATGATAAGG
5343479 ATGAGTAAGGCCATAACTGAAAGATGCTATGGCATCATGATAAGG
1 ATGAGTAAGGCCATAACTGAAAGATGCTATGGCATCATGATAAGG
* * * *
5343524 ATGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGATA
1 ATGAGTAAGGCCATAACTGAAAGATGCTATGGCATCATGATA
5343566 TAAATGAGTA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (45 bp):
ATGAGTAAGGCCATAACTGAAAGATGCTATGGCATCATGATAAGG
Found at i:5343526 original size:22 final size:22
Alignment explanation
Indices: 5343457--5343526 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
5343447 TAACTGAAAC
5343457 ATGCTATGGCATCATGATAAGG
1 ATGCTATGGCATCATGATAAGG
* * *
5343479 ATGAGTAAGGCCATAACTGA-AA-G
1 ATG-CTATGG-CATCA-TGATAAGG
5343502 ATGCTATGGCATCATGATAAGG
1 ATGCTATGGCATCATGATAAGG
5343524 ATG
1 ATG
5343527 AGTAAGACCA
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
20 3 0.08
21 6 0.16
22 11 0.30
23 8 0.22
24 6 0.16
25 3 0.08
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (22 bp):
ATGCTATGGCATCATGATAAGG
Found at i:5343573 original size:45 final size:45
Alignment explanation
Indices: 5343433--5343581 Score: 192
Period size: 45 Copynumber: 3.3 Consensus size: 45
5343423 ATATGCCTAA
* * *
5343433 AATGAGTAAGGCCATAACTGAAACATGCTATGGCATCATGATAAG
1 AATGAGTAAGACCATAACTAAAAGATGCTATGGCATCATGATAAG
* * *
5343478 GATGAGTAAGGCCATAACTGAAAGATGCTATGGCATCATGATAAG
1 AATGAGTAAGACCATAACTAAAAGATGCTATGGCATCATGATAAG
* * *
5343523 GATGAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGATATA-
1 AATGAGTAAGACCATAACTAAAAGATGCTATGGCATCATGATA-AG
*
5343568 AATGAGTAGGACCA
1 AATGAGTAAGACCA
5343582 CGGCTAAAGG
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 94 0.99
46 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (45 bp):
AATGAGTAAGACCATAACTAAAAGATGCTATGGCATCATGATAAG
Found at i:5343656 original size:27 final size:27
Alignment explanation
Indices: 5343626--5343720 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 27
5343616 CGACGGGACG
* *
5343626 TTAAATACAGGATAATCTAACGAGACA
1 TTAAACACAGGATAATCTAACAAGACA
** * * *
5343653 TTAAACATGGGATAGTCTGATAAGACA
1 TTAAACACAGGATAATCTAACAAGACA
* *
5343680 TTAAACACAGGATAGT-TCAACAGGACA
1 TTAAACACAGGATAATCT-AACAAGACA
*
5343707 TTAAACACAAGATA
1 TTAAACACAGGATA
5343721 GTTCGATGGG
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
26 1 0.02
27 53 0.98
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (27 bp):
TTAAACACAGGATAATCTAACAAGACA
Found at i:5343765 original size:27 final size:27
Alignment explanation
Indices: 5343677--5343769 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 27
5343667 GTCTGATAAG
*
5343677 ACATTAAACAC-AGGATAGTTCAACAGG-
1 ACATTAAACACGA-GATAGTTCGAC-GGA
* * *
5343704 ACATTAAACACAAGATAGTTCGATGGG
1 ACATTAAACACGAGATAGTTCGACGGA
* * *
5343731 ACAATAAACACGAGATATTTTGACGGA
1 ACATTAAACACGAGATAGTTCGACGGA
5343758 ACATTAAACACG
1 ACATTAAACACG
5343770 GGTTAGTCCG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.04
27 52 0.95
28 1 0.02
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.20
Consensus pattern (27 bp):
ACATTAAACACGAGATAGTTCGACGGA
Found at i:5356677 original size:23 final size:21
Alignment explanation
Indices: 5356630--5356670 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
5356620 TTTGGTTAAA
5356630 AATTGAATAGAAATGAAGTATG
1 AATTGAATAGAAA-GAAGTATG
5356652 AATTGAGATAGAAA-AAGTA
1 AATTGA-ATAGAAAGAAGTA
5356671 AGTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTGAATAGAAAGAAGTATG
Found at i:5359713 original size:13 final size:13
Alignment explanation
Indices: 5359661--5359730 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
5359651 TTGTACATAT
5359661 ATTTCCATATAACC
1 ATTT-CATATAACC
* * * *
5359675 AATTCCTGTAAAC
1 ATTTCATATAACC
* *
5359688 ATTTCACACAACC
1 ATTTCATATAACC
**
5359701 ATTTTGTATAACC
1 ATTTCATATAACC
*
5359714 AATTCATATAACC
1 ATTTCATATAACC
5359727 ATTT
1 ATTT
5359731 GTCATCTGGT
Statistics
Matches: 38, Mismatches: 18, Indels: 1
0.67 0.32 0.02
Matches are distributed among these distances:
13 35 0.92
14 3 0.08
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (13 bp):
ATTTCATATAACC
Found at i:5359875 original size:46 final size:47
Alignment explanation
Indices: 5359818--5359984 Score: 223
Period size: 46 Copynumber: 3.6 Consensus size: 47
5359808 TTCGACTTGA
* ** ** *
5359818 TGCCATAGTATCTTTCAATTATGGTCTTACTTGTTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTTCATTTCATGTCACGT
5359864 TGCCATGGTATCTTTCAACCATGGTCTTA-TTCATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTTCATTTCATGTCACGT
* * *
5359910 TGCCATGGTATCTTTCAACCATGGTCTTAC-ACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTTCATTTCATGTCACGT
*
5359956 TGCCATGGTCTCTTTCAACCATGGTCTTA
1 TGCCATGGTATCTTTCAACCATGGTCTTA
5359985 GACATTTCAT
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
45 6 0.06
46 103 0.94
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.42
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTTCATTTCATGTCACGT
Found at i:5360404 original size:24 final size:23
Alignment explanation
Indices: 5360372--5360420 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5360362 ATCAGGTAGT
*
5360372 TCACAAAGAACCATATCGTGAAGC
1 TCACAAAGAACC-TATCGAGAAGC
* *
5360396 TCACGAAGAGCCTATCGAGAAGC
1 TCACAAAGAACCTATCGAGAAGC
5360419 TC
1 TC
5360421 CGGATAGCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (23 bp):
TCACAAAGAACCTATCGAGAAGC
Found at i:5360417 original size:23 final size:23
Alignment explanation
Indices: 5360385--5360500 Score: 94
Period size: 23 Copynumber: 5.0 Consensus size: 23
5360375 CAAAGAACCA
*
5360385 TATCGTGAAGCTCACGAAGAGCC
1 TATCGAGAAGCTCACGAAGAGCC
* *
5360408 TATCGAGAAGCTC-CGGATAGCC
1 TATCGAGAAGCTCACGAAGAGCC
* * *
5360430 ATATATCGGGAAGTTCAAG-AGAGCAC
1 ---TATCGAGAAGCTCACGAAGAGC-C
* *
5360456 TATCGAGAGGCTCACAAAGAGCC
1 TATCGAGAAGCTCACGAAGAGCC
5360479 TATC-AGGAAGCTCACGAAGAGC
1 TATCGA-GAAGCTCACGAAGAGC
5360501 TGTATTTCGG
Statistics
Matches: 72, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
22 8 0.11
23 42 0.58
24 5 0.07
25 15 0.21
26 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (23 bp):
TATCGAGAAGCTCACGAAGAGCC
Found at i:5362295 original size:15 final size:15
Alignment explanation
Indices: 5362275--5362304 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5362265 TTAAGTAAAA
5362275 AGGGCTAAATTGACT
1 AGGGCTAAATTGACT
5362290 AGGGCTAAATTGACT
1 AGGGCTAAATTGACT
5362305 CACCTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (15 bp):
AGGGCTAAATTGACT
Found at i:5377630 original size:6 final size:6
Alignment explanation
Indices: 5377619--5377644 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5377609 CATTCCTCTT
5377619 CTGCTA CTGCTA CTGCTA CTGCTA CT
1 CTGCTA CTGCTA CTGCTA CTGCTA CT
5377645 AGGTCTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.15, T:0.35
Consensus pattern (6 bp):
CTGCTA
Found at i:5383840 original size:31 final size:31
Alignment explanation
Indices: 5383800--5383858 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
5383790 AAGACATTTA
5383800 TTTACATGTGTAG-AATTGAATCAAAATCACAG
1 TTTACATGTGT-GTAATTGAAT-AAAATCACAG
*
5383832 TTTA-ATGTGTGTAATTGCATAAAATCA
1 TTTACATGTGTGTAATTGAATAAAATCA
5383859 AAATTCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 8 0.32
31 13 0.52
32 4 0.16
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (31 bp):
TTTACATGTGTGTAATTGAATAAAATCACAG
Found at i:5384379 original size:28 final size:28
Alignment explanation
Indices: 5384338--5384395 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5384328 CAAGTTCACT
5384338 TTCAACCTACTAAAAACATAAAAACACA
1 TTCAACCTACTAAAAACATAAAAACACA
*
5384366 TTCAACCTAGTAAAAACATAAAAACACA
1 TTCAACCTACTAAAAACATAAAAACACA
5384394 TT
1 TT
5384396 TTCAATACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.55, C:0.22, G:0.02, T:0.21
Consensus pattern (28 bp):
TTCAACCTACTAAAAACATAAAAACACA
Found at i:5385613 original size:39 final size:39
Alignment explanation
Indices: 5385570--5385661 Score: 121
Period size: 39 Copynumber: 2.4 Consensus size: 39
5385560 CCACGACAAG
* *
5385570 GCTAGATCTCGTTACATTACTCGAGAATCTGCAACAAAT
1 GCTAGATCTCGTTACATTACCCAAGAATCTGCAACAAAT
* * * *
5385609 GCTAGATCTCGTTATATTACCCAATAGTTTGCAACAAAT
1 GCTAGATCTCGTTACATTACCCAAGAATCTGCAACAAAT
*
5385648 GCTAGATCTTGTTA
1 GCTAGATCTCGTTA
5385662 TAACTTGTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.33
Consensus pattern (39 bp):
GCTAGATCTCGTTACATTACCCAAGAATCTGCAACAAAT
Found at i:5404774 original size:18 final size:17
Alignment explanation
Indices: 5404751--5404786 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
5404741 AGAGTGGATG
5404751 AGTTTGGACAAAAATATA
1 AGTTTGGACAAAAA-ATA
5404769 AGTTTGGACAAAAAATA
1 AGTTTGGACAAAAAATA
5404786 A
1 A
5404787 TGCACATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.25
Consensus pattern (17 bp):
AGTTTGGACAAAAAATA
Found at i:5405942 original size:20 final size:21
Alignment explanation
Indices: 5405914--5405966 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
5405904 AATACGACAG
*
5405914 ATAATAAAAATGATAGTAATA
1 ATAATAAAAATAATAGTAATA
*
5405935 ATAA-AAAAATAATGGTAATA
1 ATAATAAAAATAATAGTAATA
* *
5405955 CTATTAAAAATA
1 ATAATAAAAATA
5405967 GCAAGTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (21 bp):
ATAATAAAAATAATAGTAATA
Found at i:5415394 original size:16 final size:16
Alignment explanation
Indices: 5415373--5415404 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5415363 AAGGTTATAT
5415373 CATACCGGGATAACAC
1 CATACCGGGATAACAC
5415389 CATACCGGGATAACAC
1 CATACCGGGATAACAC
5415405 GTGACCCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.19, T:0.12
Consensus pattern (16 bp):
CATACCGGGATAACAC
Found at i:5416753 original size:22 final size:21
Alignment explanation
Indices: 5416715--5416758 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
5416705 TAAAGAATGT
*
5416715 ATAAAATTATTAAATATTAAA
1 ATAAAATAATTAAATATTAAA
5416736 ATAAAATAATATAAATATTAAA
1 ATAAAATAAT-TAAATATTAAA
5416758 A
1 A
5416759 AAATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAAATAATTAAATATTAAA
Found at i:5416771 original size:22 final size:22
Alignment explanation
Indices: 5416725--5416767 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5416715 ATAAAATTAT
*
5416725 TAAATATTAAAATAAAATAATA
1 TAAATATTAAAATAAAATAAAA
*
5416747 TAAATATTAAAA-AAATTAAAA
1 TAAATATTAAAATAAAATAAAA
5416768 ATAATATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAATATTAAAATAAAATAAAA
Found at i:5428122 original size:22 final size:22
Alignment explanation
Indices: 5428098--5428140 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
5428088 TTAAATTTTT
5428098 AAAT-TTAAGAAATAGAAATACTA
1 AAATCTTAA-AAATA-AAATACTA
5428121 AAATCTTAAAAATAAAATAC
1 AAATCTTAAAAATAAAATAC
5428141 GGAGATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.26
Consensus pattern (22 bp):
AAATCTTAAAAATAAAATACTA
Found at i:5429119 original size:21 final size:21
Alignment explanation
Indices: 5429066--5429125 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
5429056 ATTGATGTAA
* *
5429066 AATTTTATAATATTATGTTTAT
1 AATTTTA-AATAATATTTTTAT
* * *
5429088 ACTATTGAATAATATTTTTAT
1 AATTTTAAATAATATTTTTAT
5429109 AATTTTAAATAAT-TTTT
1 AATTTTAAATAATATTTT
5429126 ACAATTTGGT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 4 0.13
21 22 0.73
22 4 0.13
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (21 bp):
AATTTTAAATAATATTTTTAT
Found at i:5429339 original size:9 final size:9
Alignment explanation
Indices: 5429317--5429369 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
5429307 AATGAAATTT
*
5429317 ATTTTTTAA
1 ATTTTTAAA
*
5429326 TTTTTTAAA
1 ATTTTTAAA
5429335 ATTTTTACAA
1 ATTTTTA-AA
*
5429345 ATTATTAAA
1 ATTTTTAAA
5429354 TATTTTTAATA
1 -ATTTTTAA-A
5429365 ATTTT
1 ATTTT
5429370 ATATTCTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 15 0.42
10 20 0.56
11 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:5436275 original size:15 final size:15
Alignment explanation
Indices: 5436255--5436288 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
5436245 TTATTTTTAA
5436255 TTTAATATTTAATGT
1 TTTAATATTTAATGT
5436270 TTTAATATTTAATGT
1 TTTAATATTTAATGT
5436285 TTTA
1 TTTA
5436289 GATGAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTAATATTTAATGT
Found at i:5443597 original size:18 final size:18
Alignment explanation
Indices: 5443576--5443642 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
5443566 AATCGGTTAA
5443576 TCAGTAACAATCATTTAT
1 TCAGTAACAATCATTTAT
* * *
5443594 TCAGTATCAGTCGTTTAT
1 TCAGTAACAATCATTTAT
* ** *
5443612 TCAATAACGGTCAATTAT
1 TCAGTAACAATCATTTAT
*
5443630 TCAGTAGCAATCA
1 TCAGTAACAATCA
5443643 GTCTTTAATA
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (18 bp):
TCAGTAACAATCATTTAT
Done.