Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 17 of 91
Found at i:5414839 original size:122 final size:122
Alignment explanation
Indices: 5414617--5414906 Score: 413
Period size: 122 Copynumber: 2.4 Consensus size: 122
5414607 GTGACAAATG
* * * *
5414617 CAACCATGCATGTGCGAAATGGGTAGTGCATATGCCAGTAATGATGCAGTCGTGATAATTATAAC
1 CAACCGTGCATGTGCGGAGTGGGTAGTGCACATGCCAGTAATGATGCAGTCGTGATAATTATAAC
5414682 CGTGCATGTGCAGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCATGATAATTA
66 CGTGCATGTGCAGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCATGATAATTA
* *
5414739 CAACCGTGCATGTGCGGAGTGGGCAGTGCACATGTC-GATAATGATG-ATGTCGTGATAATTATA
1 CAACCGTGCATGTGCGGAGTGGGTAGTGCACATGCCAG-TAATGATGCA-GTCGTGATAATTATA
* * * *
5414802 ATCGTGCATGTGCGGAGTGGGCAGTGCACATGTCGGTAATGATGCTTTCATGATAATTA
64 ACCGTGCATGTGCAGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCATGATAATTA
* * * * *
5414861 CAATCGTGCATATGCTGAGTGGGTAGTGCACATGCCGGTGATGATG
1 CAACCGTGCATGTGCGGAGTGGGTAGTGCACATGCCAGTAATGATG
5414907 TACATGAACT
Statistics
Matches: 149, Mismatches: 16, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
121 2 0.01
122 146 0.98
123 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (122 bp):
CAACCGTGCATGTGCGGAGTGGGTAGTGCACATGCCAGTAATGATGCAGTCGTGATAATTATAAC
CGTGCATGTGCAGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCATGATAATTA
Found at i:5416567 original size:54 final size:54
Alignment explanation
Indices: 5416487--5416603 Score: 121
Period size: 54 Copynumber: 2.2 Consensus size: 54
5416477 AATAGTTTGC
* ** * * *
5416487 ATTG-GAATGTTAAGCCATTGTGTGGC-AAGTTTCTTTTATGATAATATGTGAAT
1 ATTGTGAATGTTAAGCCATGGAATGGCAAAGTAT-TTTCATGAGAATATGTGAAT
* * *
5416540 ATTGTGAATGTTGAGCCATGGAATGGCAAAGTATTTTCATGGGATTATGTGAAT
1 ATTGTGAATGTTAAGCCATGGAATGGCAAAGTATTTTCATGAGAATATGTGAAT
*
5416594 ATTATGAATG
1 ATTGTGAATG
5416604 ATGGCATGTG
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
53 4 0.08
54 43 0.83
55 5 0.10
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (54 bp):
ATTGTGAATGTTAAGCCATGGAATGGCAAAGTATTTTCATGAGAATATGTGAAT
Found at i:5423310 original size:2 final size:2
Alignment explanation
Indices: 5423305--5423329 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5423295 ATATATACAT
5423305 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
5423330 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5423334 original size:2 final size:2
Alignment explanation
Indices: 5423329--5423377 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5423319 ACACACACAC
5423329 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
5423371 AT AT AT A
1 AT AT AT A
5423378 ACATTACAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5424780 original size:2 final size:2
Alignment explanation
Indices: 5424767--5424797 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5424757 TCAAAGCTTG
*
5424767 AT AT AT AA 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 AT AT AT A
5424798 ATTTTCTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5426589 original size:33 final size:34
Alignment explanation
Indices: 5426545--5426625 Score: 112
Period size: 33 Copynumber: 2.4 Consensus size: 34
5426535 TTTGGTATAT
** *
5426545 TAATATATCATAATTA-ACGAAAATATGACATGC
1 TAATATATCATAATTAGAAAAAAATATAACATGC
*
5426578 TGATATATCATAA-TAGAAAAAAATATAACATGC
1 TAATATATCATAATTAGAAAAAAATATAACATGC
5426611 TAATATATCATAATT
1 TAATATATCATAATT
5426626 GATGATGACG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 2 0.05
33 38 0.93
34 1 0.02
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.32
Consensus pattern (34 bp):
TAATATATCATAATTAGAAAAAAATATAACATGC
Found at i:5427019 original size:19 final size:19
Alignment explanation
Indices: 5426997--5427034 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5426987 AAAGGCATAG
5426997 TATTTAAAAAAATTTAAAT
1 TATTTAAAAAAATTTAAAT
*
5427016 TATTTAAAAATATTTAAAT
1 TATTTAAAAAAATTTAAAT
5427035 AAGTCTTTGT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTTAAAAAAATTTAAAT
Found at i:5434980 original size:2 final size:2
Alignment explanation
Indices: 5434973--5435036 Score: 92
Period size: 2 Copynumber: 31.0 Consensus size: 2
5434963 TTTGAAATAC
* *
5434973 AT AT AT AT AT AT AT AT AT AT AN AGT GGT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT
5435017 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
5435037 GTATGTATGT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 55 0.98
3 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5442757 original size:204 final size:204
Alignment explanation
Indices: 5442389--5442766 Score: 542
Period size: 204 Copynumber: 1.8 Consensus size: 204
5442379 ACTAGAATAG
* * * ** * *
5442389 AATTAAATAAATAAATTCTCTACTGATGAAATCTTTAGAAAACCAAAAGTGGCTTCTTGGGAATT
1 AATTAAATAAATAAATTCTCCAATGATAAAATCTCAAGAAAACCAAAAGTGACTTCTTGAGAATT
* * * *
5442454 TCTAGATGAGAGAATTTTTCAAAATTTACCATGACCGTTTGGGAGATTTTGAAAAATTTTCAATA
66 TCTAGA-GAGAGAATTTTCCAAAATTTACCATAAACGTTTAGGAGATTTTGAAAAATTTTCAATA
* ** *
5442519 TTAAGAATTTTTATTTATTTTGAACAACTAATAAAATAAAAATAGAAAAAAATAAATTAAAAGAT
130 TCAAGAATTTTTATTTATTTCAAAAAACTAATAAAATAAAAATAGAAAAAAATAAATTAAAAGAT
5442584 AAAATTATGA
195 AAAATTATGA
5442594 AATTAAATAAATAAATTCTCCAATGATAAAATCTCAAGAAAACCAAAAGTGACTTCTTGAGAATT
1 AATTAAATAAATAAATTCTCCAATGATAAAATCTCAAGAAAACCAAAAGTGACTTCTTGAGAATT
* * *
5442659 TCTAG-GTGAGAATTTTCCAAAATTTTACCATAAACGTTTAGGAGATTTTGAGAAATTTTCAATG
66 TCTAGAGAGAGAATTTTCCAAAA-TTTACCATAAACGTTTAGGAGATTTTGAAAAATTTTCAATA
* * *
5442723 TCAAGAATTTTTATTTATTTCAAAAAATTAATAAATTAGAAATA
130 TCAAGAATTTTTATTTATTTCAAAAAACTAATAAAATAAAAATA
5442767 TGTAAGGAAA
Statistics
Matches: 151, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
203 15 0.10
204 73 0.48
205 63 0.42
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (204 bp):
AATTAAATAAATAAATTCTCCAATGATAAAATCTCAAGAAAACCAAAAGTGACTTCTTGAGAATT
TCTAGAGAGAGAATTTTCCAAAATTTACCATAAACGTTTAGGAGATTTTGAAAAATTTTCAATAT
CAAGAATTTTTATTTATTTCAAAAAACTAATAAAATAAAAATAGAAAAAAATAAATTAAAAGATA
AAATTATGA
Found at i:5445072 original size:19 final size:19
Alignment explanation
Indices: 5445048--5445085 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5445038 CTGCCAAACC
*
5445048 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
5445067 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5445086 AGTTAATATG
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:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:5448171 original size:2 final size:2
Alignment explanation
Indices: 5448164--5448195 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5448154 ATTTTACAAC
5448164 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5448196 NATTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5449847 original size:85 final size:86
Alignment explanation
Indices: 5449668--5449864 Score: 240
Period size: 85 Copynumber: 2.3 Consensus size: 86
5449658 AAATCACTTT
* * * * * *
5449668 TTTTGATATATTAAATAG---ATGCTTGTCTTTGAAATTAAAAAGATAGTCTTCCATTTTTTTCT
1 TTTTGATATATTAAATAGAAAAT-CATATCTTTGAAAATAAAAAGATAGCCTTCAATTTTTTCCT
*
5449730 AAAAAAAAAGGTAAGTTATGTC
65 AAAAAAAAAGGTAAATTATGTC
* * *
5449752 ATTTGATATATTAAATAGAAAATCATATCTTTGAAAATAGAAAGATGGCCTTCAATTTTTTCCT-
1 TTTTGATATATTAAATAGAAAATCATATCTTTGAAAATAAAAAGATAGCCTTCAATTTTTTCCTA
*
5449816 AAAAAAAATGTAAATTATGTC
66 AAAAAAAAGGTAAATTATGTC
* *
5449837 TTTTGATATATTAAATACAAATTCATAT
1 TTTTGATATATTAAATAGAAAATCATAT
5449865 TACCTTTTAA
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
84 17 0.18
85 44 0.46
86 33 0.34
87 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.40
Consensus pattern (86 bp):
TTTTGATATATTAAATAGAAAATCATATCTTTGAAAATAAAAAGATAGCCTTCAATTTTTTCCTA
AAAAAAAAGGTAAATTATGTC
Found at i:5451410 original size:21 final size:21
Alignment explanation
Indices: 5451384--5451490 Score: 58
Period size: 21 Copynumber: 4.9 Consensus size: 21
5451374 TATGGACTGC
5451384 TGAGAGAGAGGGGAAGACGGG
1 TGAGAGAGAGGGGAAGACGGG
* * *
5451405 TGAGAGCGACTGAGAGAGA-GGG
1 TGAGAGAGA-GGGGA-AGACGGG
*
5451427 -GA-AGACGGACGGGTGAGAGAGCGGT
1 TGAGAGA--GA-GGG-GA-AGA-CGGG
* * *
5451452 TGAAAGAGAGGGGAAGACTGT
1 TGAGAGAGAGGGGAAGACGGG
5451473 TGAGAGAGAGGGGAAGAC
1 TGAGAGAGAGGGGAAGAC
5451491 AGACAGGTGA
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.03
21 30 0.44
22 13 0.19
23 11 0.16
24 3 0.04
25 4 0.06
26 2 0.03
27 3 0.04
ACGTcount: A:0.34, C:0.07, G:0.50, T:0.08
Consensus pattern (21 bp):
TGAGAGAGAGGGGAAGACGGG
Found at i:5451438 original size:35 final size:35
Alignment explanation
Indices: 5451383--5451469 Score: 101
Period size: 37 Copynumber: 2.5 Consensus size: 35
5451373 ATATGGACTG
5451383 CTGAGAGAGAGGGG-A-A-GACGGGT-GAGAGCGA
1 CTGAGAGAGAGGGGAAGACGACGGGTAGAGAGCGA
*
5451414 CTGAGAGAGAGGGGAAGACGGACGGGTGAGAGAGCGG
1 CTGAGAGAGAGGGGAAGAC-GACGGGT-AGAGAGCGA
* *
5451451 TTGAAAGAGAGGGGAAGAC
1 CTGAGAGAGAGGGGAAGAC
5451470 TGTTGAGAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
31 14 0.30
32 1 0.02
33 1 0.02
35 7 0.15
37 24 0.51
ACGTcount: A:0.33, C:0.09, G:0.51, T:0.07
Consensus pattern (35 bp):
CTGAGAGAGAGGGGAAGACGACGGGTAGAGAGCGA
Found at i:5452495 original size:19 final size:20
Alignment explanation
Indices: 5452457--5452506 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
5452447 TTATCTAAGT
*
5452457 ATAACAAATATTGAAAAATAA
1 ATAAAAAATA-TGAAAAATAA
5452478 ATAAAAAATATG-AAAATAA
1 ATAAAAAATATGAAAAATAA
*
5452497 A-AAAATATAT
1 ATAAAAAATAT
5452507 ATATAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 8 0.30
19 8 0.30
20 2 0.07
21 9 0.33
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
ATAAAAAATATGAAAAATAA
Found at i:5452501 original size:16 final size:16
Alignment explanation
Indices: 5452474--5452517 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5452464 ATATTGAAAA
5452474 ATAAAT-AAAAAATAT
1 ATAAATAAAAAAATAT
5452489 GA-AAATAAAAAAATAT
1 -ATAAATAAAAAAATAT
*
5452505 ATATATAAAAAAA
1 ATAAATAAAAAAA
5452518 GAGAAGAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
ATAAATAAAAAAATAT
Found at i:5456869 original size:206 final size:205
Alignment explanation
Indices: 5456515--5456891 Score: 565
Period size: 206 Copynumber: 1.8 Consensus size: 205
5456505 TTGAACTAGA
* * * *
5456515 ATAGAATTAAATAAATAAACTCTCTAATGATAAAATCTTAAGAAAACCAAAAGTGACTTCTTGGG
1 ATAGAATTAAATAAATAAACTCTCCAATGATAAAATATCAAGAAAACCAAAAGTGACTTCTTGAG
* * * *
5456580 AATTTCTAGATGAGAGAATTTTTCAAAAATTTACGATAAGTGTATGGGAGATTTTAGAAAATTTT
66 AATTTCCAGATGAGAGAATTTTTCAAAAATTTACCATAAGTGTATGGGAGATTCTAAAAAATTTT
*
5456645 CAATATTAAGAATTTTTATTTATTTCAAAAAACTAATAAAATAAAAATAGACAAAAATAAATTAA
131 CAATATCAAGAATTTTTATTTATTTCAAAAAACTAA-AAAATAAAAATAGACAAAAATAAATTAA
5456710 AAGATAAAATT
195 AAGATAAAATT
* * * * *
5456721 ATAGAATTAAATAAATAAATTCTCCAATGATGAAATATCGAGAAAACCAAATGTGGCTTCTTGAG
1 ATAGAATTAAATAAATAAACTCTCCAATGATAAAATATCAAGAAAACCAAAAGTGACTTCTTGAG
* * * * *
5456786 AGTTTCCAGATGAGAGAATTTTTTAAAATTTTACCATGAGTGTTTGGGAGATTCTAAAAAATTTT
66 AATTTCCAGATGAGAGAATTTTTCAAAAATTTACCATAAGTGTATGGGAGATTCTAAAAAATTTT
*
5456851 CAATATCAAGAATTTTTATTTATTTCAAAAAATTAAAAAAT
131 CAATATCAAGAATTTTTATTTATTTCAAAAAACTAAAAAAT
5456892 TAGAAATATG
Statistics
Matches: 151, Mismatches: 20, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
205 5 0.03
206 146 0.97
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (205 bp):
ATAGAATTAAATAAATAAACTCTCCAATGATAAAATATCAAGAAAACCAAAAGTGACTTCTTGAG
AATTTCCAGATGAGAGAATTTTTCAAAAATTTACCATAAGTGTATGGGAGATTCTAAAAAATTTT
CAATATCAAGAATTTTTATTTATTTCAAAAAACTAAAAAATAAAAATAGACAAAAATAAATTAAA
AGATAAAATT
Found at i:5458806 original size:2 final size:2
Alignment explanation
Indices: 5458801--5458829 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5458791 TAAAAAATAA
5458801 AT AT 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 AT AT A
5458830 AAATATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5465145 original size:229 final size:229
Alignment explanation
Indices: 5464744--5465201 Score: 916
Period size: 229 Copynumber: 2.0 Consensus size: 229
5464734 ACAAGACAGA
5464744 TGATATTTTTACAAAATTAAAATCAGCAGATGCACCACACTTGAAGTTTGTAAGCAGATGTTGAG
1 TGATATTTTTACAAAATTAAAATCAGCAGATGCACCACACTTGAAGTTTGTAAGCAGATGTTGAG
5464809 CTGAAGAAAACAATAGGAGGATTTACAGAAAAGGCTTCTGAAAATGAATTTTTCCTACTACTAAG
66 CTGAAGAAAACAATAGGAGGATTTACAGAAAAGGCTTCTGAAAATGAATTTTTCCTACTACTAAG
5464874 GCTAATTTGTGTTTGAGACACTTGTTAAAGAAAATCATATCATGCAGGTATTGGTCATGGCACAA
131 GCTAATTTGTGTTTGAGACACTTGTTAAAGAAAATCATATCATGCAGGTATTGGTCATGGCACAA
5464939 TTTACAAGGGAAGAACCTTATAGCTCAAGCTTAG
196 TTTACAAGGGAAGAACCTTATAGCTCAAGCTTAG
5464973 TGATATTTTTACAAAATTAAAATCAGCAGATGCACCACACTTGAAGTTTGTAAGCAGATGTTGAG
1 TGATATTTTTACAAAATTAAAATCAGCAGATGCACCACACTTGAAGTTTGTAAGCAGATGTTGAG
5465038 CTGAAGAAAACAATAGGAGGATTTACAGAAAAGGCTTCTGAAAATGAATTTTTCCTACTACTAAG
66 CTGAAGAAAACAATAGGAGGATTTACAGAAAAGGCTTCTGAAAATGAATTTTTCCTACTACTAAG
5465103 GCTAATTTGTGTTTGAGACACTTGTTAAAGAAAATCATATCATGCAGGTATTGGTCATGGCACAA
131 GCTAATTTGTGTTTGAGACACTTGTTAAAGAAAATCATATCATGCAGGTATTGGTCATGGCACAA
5465168 TTTACAAGGGAAGAACCTTATAGCTCAAGCTTAG
196 TTTACAAGGGAAGAACCTTATAGCTCAAGCTTAG
5465202 AAGGAAAACT
Statistics
Matches: 229, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
229 229 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (229 bp):
TGATATTTTTACAAAATTAAAATCAGCAGATGCACCACACTTGAAGTTTGTAAGCAGATGTTGAG
CTGAAGAAAACAATAGGAGGATTTACAGAAAAGGCTTCTGAAAATGAATTTTTCCTACTACTAAG
GCTAATTTGTGTTTGAGACACTTGTTAAAGAAAATCATATCATGCAGGTATTGGTCATGGCACAA
TTTACAAGGGAAGAACCTTATAGCTCAAGCTTAG
Found at i:5467759 original size:36 final size:36
Alignment explanation
Indices: 5467719--5467793 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
5467709 AAAACTGTTG
5467719 ACAGACCAAGTTTTAATTTTAAGAAGATATTATGCC
1 ACAGACCAAGTTTTAATTTTAAGAAGATATTATGCC
5467755 ACAGACCAAGTTTTAATTTTAAGAAGATATTATGCC
1 ACAGACCAAGTTTTAATTTTAAGAAGATATTATGCC
5467791 ACA
1 ACA
5467794 AAGGTGGCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (36 bp):
ACAGACCAAGTTTTAATTTTAAGAAGATATTATGCC
Found at i:5468663 original size:24 final size:25
Alignment explanation
Indices: 5468626--5468709 Score: 95
Period size: 24 Copynumber: 3.5 Consensus size: 25
5468616 AGCCTTAATT
5468626 TATTTGAATTAAGATTACTATTCAA
1 TATTTGAATTAAGATTACTATTCAA
** *
5468651 TATTTG-ATTAAGATGCCT-TT-ATT
1 TATTTGAATTAAGATTACTATTCA-A
*
5468674 TATTTGAATTAGGATTACTATTCAA
1 TATTTGAATTAAGATTACTATTCAA
5468699 TATTTG-ATTAA
1 TATTTGAATTAA
5468710 AATTTATCCT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
22 1 0.02
23 8 0.17
24 23 0.49
25 14 0.30
26 1 0.02
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.48
Consensus pattern (25 bp):
TATTTGAATTAAGATTACTATTCAA
Found at i:5468675 original size:48 final size:48
Alignment explanation
Indices: 5468617--5468709 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
5468607 TATACATTAA
5468617 GCCTTAATTTATTTGAATTAAGATTACTATTCAATATTTGATTAAGAT
1 GCCTTAATTTATTTGAATTAAGATTACTATTCAATATTTGATTAAGAT
* *
5468665 GCCTTTATTTATTTGAATTAGGATTACTATTCAATATTTGATTAA
1 GCCTTAATTTATTTGAATTAAGATTACTATTCAATATTTGATTAA
5468710 AATTTATCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (48 bp):
GCCTTAATTTATTTGAATTAAGATTACTATTCAATATTTGATTAAGAT
Found at i:5474140 original size:10 final size:10
Alignment explanation
Indices: 5474117--5474151 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
5474107 ATCTTGCACA
5474117 AATTTCAGACC
1 AATTTCA-ACC
5474128 AATTTCAACC
1 AATTTCAACC
5474138 AATTTCAACC
1 AATTTCAACC
5474148 AATT
1 AATT
5474152 AAACCTGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.40, C:0.26, G:0.03, T:0.31
Consensus pattern (10 bp):
AATTTCAACC
Found at i:5475966 original size:2 final size:2
Alignment explanation
Indices: 5475961--5476002 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5475951 ATACACACAA
5475961 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
5476003 GGCAGACCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5495435 original size:8 final size:8
Alignment explanation
Indices: 5495422--5495448 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5495412 AAAAGAAATT
5495422 AAAAATGA
1 AAAAATGA
5495430 AAAAATGA
1 AAAAATGA
5495438 AAAAATGA
1 AAAAATGA
5495446 AAA
1 AAA
5495449 TAGAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAATGA
Found at i:5495457 original size:23 final size:22
Alignment explanation
Indices: 5495423--5495477 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 22
5495413 AAAGAAATTA
*
5495423 AAAATGAAAAAATGAAAAAATG
1 AAAATGAAAAAAAGAAAAAATG
* * *
5495445 AAAATAGAGAAAAAGAGAAAATT
1 AAAAT-GAAAAAAAGAAAAAATG
*
5495468 AAAATTAAAA
1 AAAATGAAAA
5495478 TATCATTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.15
Consensus pattern (22 bp):
AAAATGAAAAAAAGAAAAAATG
Found at i:5498444 original size:13 final size:13
Alignment explanation
Indices: 5498426--5498450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5498416 TTTCAGAAAA
5498426 TTTATAAAATCAT
1 TTTATAAAATCAT
5498439 TTTATAAAATCA
1 TTTATAAAATCA
5498451 CAATTTCCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:5499712 original size:20 final size:20
Alignment explanation
Indices: 5499695--5499732 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5499685 CCTCAAATCT
*
5499695 TACTCCAATGAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
5499715 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
5499733 GGGGCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:5500175 original size:19 final size:19
Alignment explanation
Indices: 5500136--5500184 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
5500126 TTAATATTTT
*
5500136 AATATTATTTTATTTGTAA
1 AATATTATTTTATTTGAAA
5500155 AATATTATTTTATTCT-AAA
1 AATATTATTTTATT-TGAAA
*
5500174 AATTTTATTTT
1 AATATTATTTT
5500185 GTCTCCTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
AATATTATTTTATTTGAAA
Found at i:5500512 original size:43 final size:43
Alignment explanation
Indices: 5500458--5500544 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
5500448 CTATTCTTGG
*
5500458 AGTGGTTTAATTTTTGTGAATTGTGAATTTGTGAAAAGTTAGA
1 AGTGGTCTAATTTTTGTGAATTGTGAATTTGTGAAAAGTTAGA
*
5500501 AGTGGTCTAATTTTTGTGAATTGTGAATTTGTGAAATGTTAGA
1 AGTGGTCTAATTTTTGTGAATTGTGAATTTGTGAAAAGTTAGA
5500544 A
1 A
5500545 AATGAATTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.30, C:0.01, G:0.25, T:0.44
Consensus pattern (43 bp):
AGTGGTCTAATTTTTGTGAATTGTGAATTTGTGAAAAGTTAGA
Found at i:5503053 original size:28 final size:28
Alignment explanation
Indices: 5503019--5503073 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5503009 GATTGAAATT
*
5503019 TTATTTATATTTGATGTAGTGTATTTGC
1 TTATTTATATTTGATGTAATGTATTTGC
* * *
5503047 TTATTTATGTTTGGTGTAATTTATTTG
1 TTATTTATATTTGATGTAATGTATTTG
5503074 TTTGTAACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.02, G:0.18, T:0.60
Consensus pattern (28 bp):
TTATTTATATTTGATGTAATGTATTTGC
Found at i:5505968 original size:31 final size:31
Alignment explanation
Indices: 5505933--5506015 Score: 116
Period size: 29 Copynumber: 2.7 Consensus size: 31
5505923 CATGGTTAGG
5505933 TTGTTACACGCCATGTTGAAAAAAAATACTA
1 TTGTTACACGCCATGTTGAAAAAAAATACTA
**
5505964 TTGTTACACGCCATGTTG--AAAAAATGTTA
1 TTGTTACACGCCATGTTGAAAAAAAATACTA
* *
5505993 TTGTTACACGCCATATTCAAAAA
1 TTGTTACACGCCATGTTGAAAAA
5506016 CATTTTGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 25 0.54
31 21 0.46
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (31 bp):
TTGTTACACGCCATGTTGAAAAAAAATACTA
Found at i:5506023 original size:27 final size:28
Alignment explanation
Indices: 5505933--5506028 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 28
5505923 CATGGTTAGG
* * *
5505933 TTGTTACACGCCATGTTGAAAAAAAATACTA
1 TTGTTACACGCCATATT-CAAAAAAGT--TA
* *
5505964 TTGTTACACGCCATGTTGAAAAAATGTTA
1 TTGTTACACGCCATATTCAAAAAA-GTTA
5505993 TTGTTACACGCCATATTCAAAAACA-TT-
1 TTGTTACACGCCATATTCAAAAA-AGTTA
5506020 TTGTTACAC
1 TTGTTACAC
5506029 TTTAATGTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
27 9 0.15
28 2 0.03
29 23 0.39
30 7 0.12
31 18 0.31
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (28 bp):
TTGTTACACGCCATATTCAAAAAAGTTA
Found at i:5524145 original size:30 final size:30
Alignment explanation
Indices: 5524088--5524146 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
5524078 TAAAAATTTG
* **
5524088 TATTAATATTTTAATAATAAGTTATTAAAT
1 TATTAATATTTTAATAACAAGAAATTAAAT
5524118 TATTAATATTTTAATAACAAGAAATTAAA
1 TATTAATATTTTAATAACAAGAAATTAAA
5524147 AAGAGAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (30 bp):
TATTAATATTTTAATAACAAGAAATTAAAT
Found at i:5524847 original size:29 final size:27
Alignment explanation
Indices: 5524815--5524878 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
5524805 TATTATTTTT
*
5524815 TTAATATATTGA-AATTAATAACATTAATA
1 TTAATATATT-ATAATTAATAA-A-AAATA
* *
5524844 TTAATTTATTATATTTAATAAAAAATA
1 TTAATATATTATAATTAATAAAAAATA
5524871 TTAATATA
1 TTAATATA
5524879 AGTAATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 11 0.37
28 2 0.07
29 17 0.57
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TTAATATATTATAATTAATAAAAAATA
Found at i:5525100 original size:52 final size:52
Alignment explanation
Indices: 5525033--5525137 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 52
5525023 TATGAAAATA
* *
5525033 ACCTTAAAGGGTACTAATTCACTTTAAAATTATTATATTAATTAATTT-TTTC
1 ACCTAAAAGAGTACTAATTCACTTTAAAATTATTATATTAATT-ATTTCTTTC
5525085 ACCTAAAAGAGTACTAATTCACTTTAAAATTATTATATTAATTATTTCTTTC
1 ACCTAAAAGAGTACTAATTCACTTTAAAATTATTATATTAATTATTTCTTTC
5525137 A
1 A
5525138 ATTATTGCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
51 4 0.08
52 46 0.92
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (52 bp):
ACCTAAAAGAGTACTAATTCACTTTAAAATTATTATATTAATTATTTCTTTC
Found at i:5527439 original size:17 final size:17
Alignment explanation
Indices: 5527417--5527451 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5527407 CTACAAAAGT
*
5527417 ACAAATAAATTAATAAC
1 ACAAATAAATCAATAAC
5527434 ACAAATAAATCAATAAC
1 ACAAATAAATCAATAAC
5527451 A
1 A
5527452 AATTATCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (17 bp):
ACAAATAAATCAATAAC
Found at i:5541491 original size:2 final size:2
Alignment explanation
Indices: 5541484--5541531 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5541474 GTATGATGCA
5541484 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
5541526 AT AT AT
1 AT AT AT
5541532 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5542343 original size:20 final size:21
Alignment explanation
Indices: 5542292--5542346 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
5542282 TTATTTCACT
*
5542292 TATTATTTTTATTATTTTTATA
1 TATTATTTTTA-CATTTTTATA
*
5542314 TATAATTTTTTACATTTTTATA
1 TATTA-TTTTTACATTTTTATA
5542336 T-TTATTTTTAC
1 TATTATTTTTAC
5542347 CTAATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 7 0.24
21 2 0.07
22 14 0.48
23 6 0.21
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (21 bp):
TATTATTTTTACATTTTTATA
Found at i:5543446 original size:3 final size:3
Alignment explanation
Indices: 5543438--5543470 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
5543428 TCTTTTCTTT
5543438 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5543471 ATGAACTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:5543553 original size:37 final size:37
Alignment explanation
Indices: 5543471--5543922 Score: 420
Period size: 38 Copynumber: 11.8 Consensus size: 37
5543461 ATTATTTTAT
* * * * * *
5543471 ATGAACTTCTCAAAATTGAGGTAATGACACTTTTAAGA
1 ATGAACTCCTCAAAACTGAGGCAACGAAAC-TTTAAAA
* * *
5543509 ATAAACTCCTCAAAATTGAGGCAATGAAACTTTAAAA
1 ATGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAA
* *
5543546 ATGAACTCCTCAAAGCTGAGACAACGAAACTTTTAAAA
1 ATGAACTCCTCAAAACTGAGGCAACGAAAC-TTTAAAA
* * **
5543584 ATGAACTCCTCAAAGCTGAGGCAATGAAACCCTTTTTTTTTTAA
1 ATGAACTCCTCAAAACTGAGGCAACGAAA--C-----TTTAAAA
** *
5543628 ATGAACTCCTCAAAGTTGAGGCAACTG-GACTTTAAAA
1 ATGAACTCCTCAAAACTGAGGCAAC-GAAACTTTAAAA
* * *
5543665 ATGAACTCCTCAAAGCTGAGACAACGAGAATTTTAAAA
1 ATGAACTCCTCAAAACTGAGGCAACGA-AACTTTAAAA
* * *
5543703 ATAAACTCCTCAAAACTGAGGCAACTAGACTTTAAAA
1 ATGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAA
* *
5543740 ATGAACTCCTCAAAGCTGGGGCAACGAAACTTCTTTAAAA
1 ATGAACTCCTCAAAACTGAGGCAACGAAA---CTTTAAAA
* ** * *
5543780 ATGAACTCCTTAAAGTTAAGGCAACGAGACTTTAAAAA
1 ATGAACTCCTCAAAACTGAGGCAACGAAACTTT-AAAA
*
5543818 ATGAACTCCTCAAATCTGAGGCAACGAAACTTTAAAAA
1 ATGAACTCCTCAAAACTGAGGCAACGAAACTTT-AAAA
* * *
5543856 ATGAACTCCTCAAAACTAAGGCAACGAGACTTTTAAA
1 ATGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAA
* *
5543893 ATGAATTCCTCAAAATTGAGGCAACGAAAC
1 ATGAACTCCTCAAAACTGAGGCAACGAAAC
5543923 CTTTTTTCCT
Statistics
Matches: 348, Mismatches: 52, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
36 1 0.00
37 124 0.36
38 158 0.45
40 33 0.09
42 1 0.00
44 30 0.09
45 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (37 bp):
ATGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAA
Found at i:5543594 original size:75 final size:75
Alignment explanation
Indices: 5543471--5543922 Score: 453
Period size: 75 Copynumber: 5.9 Consensus size: 75
5543461 ATTATTTTAT
* ** * * * * * * *
5543471 ATGAACTTCTCAAAATTGAGGTAATGACACTTTTAAGAATAAACTCCTCAAAATTGAGGCAATGA
1 ATGAACTCCTCAAAGCTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGA
5543536 AACTTTAAAA
66 AACTTTAAAA
* * * *
5543546 ATGAACTCCTCAAAGCTGAGACAACGAAACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAATGA
1 ATGAACTCCTCAAAGCTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGA
**
5543611 AACCCTTTTTTTTTTAA
66 AA--C-----TTTAAAA
* * *
5543628 ATGAACTCCTCAAAGTTGAGGCAACTG-GAC-TTTAAAAATGAACTCCTCAAAGCTGAGACAACG
1 ATGAACTCCTCAAAGCTGAGGCAAC-GAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACG
*
5543691 AGAATTTTAAAA
65 A-AACTTTAAAA
* * * * *
5543703 ATAAACTCCTCAAAACTGAGGCAACTAGAC-TTTAAAAATGAACTCCTCAAAGCTGGGGCAACGA
1 ATGAACTCCTCAAAGCTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGA
5543767 AACTTCTTTAAAA
66 AA---CTTTAAAA
* * * * *
5543780 ATGAACTCCTTAAAGTTAAGGCAACGAGACTTTAAAAAATGAACTCCTCAAATCTGAGGCAACGA
1 ATGAACTCCTCAAAGCTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGA
5543845 AACTTTAAAAA
66 AACTTT-AAAA
* * * *
5543856 ATGAACTCCTCAAAACTAAGGCAACGAGACTTTT-AAAATGAATTCCTCAAAATTGAGGCAACGA
1 ATGAACTCCTCAAAGCTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGA
5543920 AAC
66 AAC
5543923 CTTTTTTCCT
Statistics
Matches: 318, Mismatches: 44, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
74 2 0.01
75 152 0.48
76 34 0.11
77 32 0.10
78 33 0.10
81 32 0.10
82 32 0.10
83 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (75 bp):
ATGAACTCCTCAAAGCTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGA
AACTTTAAAA
Found at i:5555968 original size:28 final size:25
Alignment explanation
Indices: 5555905--5555971 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 25
5555895 AATTAATTAN
5555905 ATTATTTTATTTATTATATTTTTATT
1 ATTATTTT-TTTATTATATTTTTATT
* * *
5555931 ATCATATTTTCTATTCTTATTTCTTATT
1 ATTAT-TTTTTTATT-ATATTT-TTATT
5555959 ATTATTTTTTTAT
1 ATTATTTTTTTAT
5555972 ACTTTACATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
26 9 0.27
27 15 0.45
28 9 0.27
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (25 bp):
ATTATTTTTTTATTATATTTTTATT
Found at i:5556286 original size:4 final size:4
Alignment explanation
Indices: 5556263--5556308 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
5556253 TTTAAATTAG
5556263 TTAT TT-T TTA- TTATT TTAT TTAT TTATT TTAT TT-T TTAT TTAT TTA
1 TTAT TTAT TTAT TTA-T TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTA
5556309 ATGTCATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
3 9 0.24
4 21 0.57
5 7 0.19
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTAT
Found at i:5557236 original size:51 final size:51
Alignment explanation
Indices: 5557181--5557277 Score: 185
Period size: 51 Copynumber: 1.9 Consensus size: 51
5557171 TCTCGATGCC
*
5557181 TTCCTCTCTCCTTTCTTGCTGCCCGAATGGCTTTCTCCCCTAGCCGGCGCT
1 TTCCTCTCTCCTTTCTCGCTGCCCGAATGGCTTTCTCCCCTAGCCGGCGCT
5557232 TTCCTCTCTCCTTTCTCGCTGCCCGAATGGCTTTCTCCCCTAGCCG
1 TTCCTCTCTCCTTTCTCGCTGCCCGAATGGCTTTCTCCCCTAGCCG
5557278 ACGTTACTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.06, C:0.42, G:0.16, T:0.35
Consensus pattern (51 bp):
TTCCTCTCTCCTTTCTCGCTGCCCGAATGGCTTTCTCCCCTAGCCGGCGCT
Found at i:5557391 original size:20 final size:20
Alignment explanation
Indices: 5557366--5557407 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5557356 TGTCGGGCTT
5557366 CCTCTCCCGCCGACACAAAC
1 CCTCTCCCGCCGACACAAAC
* * *
5557386 CCTCTCCTGCCGGCGCAAAC
1 CCTCTCCCGCCGACACAAAC
5557406 CC
1 CC
5557408 GAGCCCCCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.55, G:0.14, T:0.12
Consensus pattern (20 bp):
CCTCTCCCGCCGACACAAAC
Found at i:5558772 original size:12 final size:12
Alignment explanation
Indices: 5558750--5558788 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5558740 TGTAAATTTT
*
5558750 AATAAACAATTG
1 AATAAAAAATTG
*
5558762 TATAAAAAATTG
1 AATAAAAAATTG
5558774 AATGAAAAAATTG
1 AAT-AAAAAATTG
5558787 AA
1 AA
5558789 GTTAGTGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (12 bp):
AATAAAAAATTG
Found at i:5561249 original size:2 final size:2
Alignment explanation
Indices: 5561242--5561284 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5561232 CTCTAGTATG
5561242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5561284 T
1 T
5561285 GACTTAATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5568873 original size:6 final size:6
Alignment explanation
Indices: 5568864--5568930 Score: 57
Period size: 6 Copynumber: 11.2 Consensus size: 6
5568854 CGTCTTCAAG
* * *
5568864 TTCATC TTCATC TTCATC TTCATC TTTATT TTCATC -TCCT- TTCATGTC
1 TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCA--TC
* *
5568912 ATCTTC TTCATC TTCATC T
1 TTCATC TTCATC TTCATC T
5568931 CTTTGCATGT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
5 5 0.11
6 39 0.83
7 1 0.02
8 2 0.04
ACGTcount: A:0.15, C:0.30, G:0.01, T:0.54
Consensus pattern (6 bp):
TTCATC
Found at i:5568913 original size:15 final size:14
Alignment explanation
Indices: 5568895--5568945 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
5568885 ATCTTTATTT
5568895 TCATCTCCTTTCATG
1 TCATCT-CTTTCATG
*
5568910 TCATCT-TCTTCATCT
1 TCATCTCT-TTCAT-G
5568925 TCATCTCTTTGCATG
1 TCATCTCTTT-CATG
5568940 TCATCT
1 TCATCT
5568946 TCTTCATCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 20 0.67
16 4 0.13
ACGTcount: A:0.14, C:0.31, G:0.06, T:0.49
Consensus pattern (14 bp):
TCATCTCTTTCATG
Found at i:5568916 original size:27 final size:28
Alignment explanation
Indices: 5568883--5568946 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
5568873 ATCTTCATCT
*
5568883 TCATCTTT-ATTTTCATCTCCTTT-CATG
1 TCATCTTTCATCTTCATCT-CTTTGCATG
5568910 TCATCTTCTTCATCTTCATCTCTTTGCATG
1 TCATC-T-TTCATCTTCATCTCTTTGCATG
5568940 TCATCTT
1 TCATCTT
5568947 CTTCATCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
27 5 0.16
28 2 0.06
29 7 0.22
30 18 0.56
ACGTcount: A:0.14, C:0.28, G:0.05, T:0.53
Consensus pattern (28 bp):
TCATCTTTCATCTTCATCTCTTTGCATG
Found at i:5568928 original size:30 final size:30
Alignment explanation
Indices: 5568894--5568953 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
5568884 CATCTTTATT
5568894 TTCATCTCCTTT-CATGTCATCTTCTTCATC
1 TTCATCT-CTTTGCATGTCATCTTCTTCATC
5568924 TTCATCTCTTTGCATGTCATCTTCTTCATC
1 TTCATCTCTTTGCATGTCATCTTCTTCATC
5568954 CTCAATCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.13, C:0.32, G:0.05, T:0.50
Consensus pattern (30 bp):
TTCATCTCTTTGCATGTCATCTTCTTCATC
Found at i:5574928 original size:45 final size:45
Alignment explanation
Indices: 5574878--5575044 Score: 184
Period size: 45 Copynumber: 3.8 Consensus size: 45
5574868 CAAGCCATGA
* * *
5574878 TGTTACATGTCATGTACAAAAATATGTTACACGTCATGGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTTACACGTCATGGTTAGGT
* * *
5574923 TGTTACACGTCATGTACAAAAACATATAACACGTCATGGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTTACACGTCATGGTTAGGT
* * * *
5574968 TG------GCCATGTCCAAAAACATGTTATATGGCATGGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTTACACGTCATGGTTAGGT
* *
5575007 TGTTACACGCCATGAACAAAAACATGTTACATGTCATG
1 TGTTACACGCCATGTACAAAAACATGTTACACGTCATG
5575045 TACAAAAACA
Statistics
Matches: 101, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
39 32 0.32
45 69 0.68
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (45 bp):
TGTTACACGCCATGTACAAAAACATGTTACACGTCATGGTTAGGT
Found at i:5575034 original size:24 final size:24
Alignment explanation
Indices: 5575007--5575068 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
5574997 ATGGTTAGGT
*
5575007 TGTTACACGCCATGAACAAAAACA
1 TGTTACACGTCATGAACAAAAACA
* *
5575031 TGTTACATGTCATGTACAAAAACA
1 TGTTACACGTCATGAACAAAAACA
*
5575055 TGTGACACGTCATG
1 TGTTACACGTCATG
5575069 GTTAGGTTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
TGTTACACGTCATGAACAAAAACA
Found at i:5575066 original size:108 final size:106
Alignment explanation
Indices: 5574923--5575191 Score: 296
Period size: 108 Copynumber: 2.5 Consensus size: 106
5574913 ATGGTTAGGT
* * *
5574923 TGTTACACGTCATGTACAAAAACATATAACACGTCATGGTTAGGTTGGCCATGTC-CAAAAACAT
1 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGTTGG---TGACACAAAAACAT
* ** * ***
5574987 GTTATATGGCATGGT-TAGGTTGTTACACGCCATGA-ACAAAAACA
63 GTTACATACCAT-GTAAAACATGTTACACGCCAT-ATACAAAAACA
* ** **
5575031 TGTTACATGTCATGTACAAAAACATGTGACACGTCATGGTTAGGTT-GTGACACACCATGATGTT
1 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGTTGGTGACACAAAAACATGTT
5575095 ACATACCATGTACAAAAACATGTTACACGCCATATACAAAAACA
66 ACATACCATGT---AAAACATGTTACACGCCATATACAAAAACA
5575139 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGTT-GTGACAC
1 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGTTGGTGACAC
5575192 GCCATGGTTA
Statistics
Matches: 139, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
104 5 0.04
105 14 0.10
107 2 0.01
108 118 0.85
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (106 bp):
TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGTTGGTGACACAAAAACATGTT
ACATACCATGTAAAACATGTTACACGCCATATACAAAAACA
Found at i:5575117 original size:24 final size:24
Alignment explanation
Indices: 5575090--5575176 Score: 120
Period size: 24 Copynumber: 3.6 Consensus size: 24
5575080 ACACACCATG
**
5575090 ATGTTACATACCATGTACAAAAAC
1 ATGTTACACGCCATGTACAAAAAC
*
5575114 ATGTTACACGCCATATACAAAAAC
1 ATGTTACACGCCATGTACAAAAAC
*
5575138 ATGTTACACGTCATGTACAAAAAC
1 ATGTTACACGCCATGTACAAAAAC
* *
5575162 ATGTGACACGTCATG
1 ATGTTACACGCCATG
5575177 GTTAGGTTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (24 bp):
ATGTTACACGCCATGTACAAAAAC
Found at i:5575189 original size:21 final size:21
Alignment explanation
Indices: 5575163--5575219 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
5575153 TACAAAAACA
5575163 TGTGACACGTCATGGTTAGGT
1 TGTGACACGTCATGGTTAGGT
*
5575184 TGTGACACGCCATGGTTAGGT
1 TGTGACACGTCATGGTTAGGT
*
5575205 TGTTACACGTCATGG
1 TGTGACACGTCATGG
5575220 ACAAAAACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.32
Consensus pattern (21 bp):
TGTGACACGTCATGGTTAGGT
Found at i:5575228 original size:66 final size:66
Alignment explanation
Indices: 5575139--5575283 Score: 227
Period size: 66 Copynumber: 2.2 Consensus size: 66
5575129 TACAAAAACA
* * * * *
5575139 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGTTGTGACACGCCATGGTTAGG
1 TGTTACACGTCATGGACAAAAACATGTGACACGCCATAGTTAGGTTCTGACACGCCATAGTTAGG
5575204 T
66 T
*
5575205 TGTTACACGTCATGGACAAAAACATGTGACACGCCATAGTTAGGTTCTTACACGCCATAGTTAGG
1 TGTTACACGTCATGGACAAAAACATGTGACACGCCATAGTTAGGTTCTGACACGCCATAGTTAGG
5575270 T
66 T
*
5575271 TCTTACACGTCAT
1 TGTTACACGTCAT
5575284 ATTGAAAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (66 bp):
TGTTACACGTCATGGACAAAAACATGTGACACGCCATAGTTAGGTTCTGACACGCCATAGTTAGG
T
Found at i:5575258 original size:21 final size:21
Alignment explanation
Indices: 5575233--5575284 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
5575223 AAAACATGTG
5575233 ACACGCCATAGTTAGGTTCTT
1 ACACGCCATAGTTAGGTTCTT
5575254 ACACGCCATAGTTAGGTTCTT
1 ACACGCCATAGTTAGGTTCTT
*
5575275 ACACGTCATA
1 ACACGCCATA
5575285 TTGAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (21 bp):
ACACGCCATAGTTAGGTTCTT
Found at i:5575321 original size:32 final size:29
Alignment explanation
Indices: 5575273--5575339 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
5575263 AGTTAGGTTC
*
5575273 TTACACGTCATATTGAAAAAAAAATATTGTTG
1 TTACACGCCATATTG---AAAAAATATTGTTG
*
5575305 TTACACGCCATGTTGAAAAAATATTGTTG
1 TTACACGCCATATTGAAAAAATATTGTTG
5575334 TTACAC
1 TTACAC
5575340 ATCATATTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 20 0.61
32 13 0.39
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (29 bp):
TTACACGCCATATTGAAAAAATATTGTTG
Found at i:5576403 original size:2 final size:2
Alignment explanation
Indices: 5576396--5576440 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5576386 NNNNNNNNNN
5576396 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5576438 TA T
1 TA T
5576441 TCTATAGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5589151 original size:28 final size:30
Alignment explanation
Indices: 5589093--5589152 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
5589083 TTTTTGAAAT
*
5589093 TTACACTTTTGCCCCTATAAAAGTCAAAAA
1 TTACACTTTTGCCCCTATAAAACTCAAAAA
* *
5589123 TTACATTTTTGCCCC-A-AAAACTGAAAAA
1 TTACACTTTTGCCCCTATAAAACTCAAAAA
5589151 TT
1 TT
5589153 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 1 0.04
30 14 0.52
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.32
Consensus pattern (30 bp):
TTACACTTTTGCCCCTATAAAACTCAAAAA
Found at i:5589682 original size:10 final size:10
Alignment explanation
Indices: 5589667--5589706 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
5589657 GCTTGACAGA
5589667 AAAGAAAAAG
1 AAAGAAAAAG
5589677 AAAGAAAAAAG
1 AAAG-AAAAAG
5589688 AAA-AAAAAG
1 AAAGAAAAAG
*
5589697 AGAGAAAAAG
1 AAAGAAAAAG
5589707 GGGGGGTCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 8 0.30
10 10 0.37
11 9 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:5589688 original size:17 final size:16
Alignment explanation
Indices: 5589666--5589697 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5589656 GGCTTGACAG
5589666 AAAAGAAAAAGAAAGAA
1 AAAAGAAAAA-AAAGAA
5589683 AAAAGAAAAAAAAGA
1 AAAAGAAAAAAAAGA
5589698 GAGAAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAAGAA
Found at i:5589769 original size:19 final size:20
Alignment explanation
Indices: 5589732--5589780 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
5589722 AAGAAAGAAG
*
5589732 AAAG-AGAAAGACAAGAAAA
1 AAAGAAGAAAGACAAAAAAA
5589751 AAAGAAGAAAGA-AAAAAAA
1 AAAGAAGAAAGACAAAAAAA
*
5589770 AAGGAAGAAAG
1 AAAGAAGAAAG
5589781 GTTCAAACGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAAGACAAAAAAA
Found at i:5589780 original size:26 final size:26
Alignment explanation
Indices: 5589722--5589780 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
5589712 GTCGGCTGCT
* * *
5589722 AAGAAAGAAGAAAGAGAAAGACAAGA
1 AAGAAAGAAGAAAGAAAAAAAAAAGA
* *
5589748 AAAAAAGAAGAAAGAAAAAAAAAAGG
1 AAGAAAGAAGAAAGAAAAAAAAAAGA
5589774 AAGAAAG
1 AAGAAAG
5589781 GTTCAAACGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.75, C:0.02, G:0.24, T:0.00
Consensus pattern (26 bp):
AAGAAAGAAGAAAGAAAAAAAAAAGA
Found at i:5590402 original size:118 final size:116
Alignment explanation
Indices: 5590193--5590410 Score: 310
Period size: 118 Copynumber: 1.9 Consensus size: 116
5590183 ATAAATTTAC
* ** * * *
5590193 ATAATGTTCGAGACGGATTCTCATCGAAGTGTCGGGATGAATCCGAATTCTATATTCTAGTACCT
1 ATAAAGTTCGAGACGGATTCTCATCGAAGCATCGGGATGAATCCGAATTCTATACTCTAATACCC
**
5590258 ATTAACTCAAATAATCATTTTTAAAAAATAATATATATATATTTTAAAAATAA
66 ATTAACTCAAATAATCA-TTACAAAAAAT-ATATATATATATTTTAAAAATAA
* * *
5590311 ATAAAGTTCGAGACGGATTCTCATCGGAGCATCGGGATGAATCTGAATTTTATACTCTAATACCC
1 ATAAAGTTCGAGACGGATTCTCATCGAAGCATCGGGATGAATCCGAATTCTATACTCTAATACCC
*
5590376 ATTAACTCAAATAATCGTTACAAAAAATATATATA
66 ATTAACTCAAATAATCATTACAAAAAATATATATA
5590411 CATAATACTA
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
116 7 0.08
117 9 0.10
118 72 0.82
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (116 bp):
ATAAAGTTCGAGACGGATTCTCATCGAAGCATCGGGATGAATCCGAATTCTATACTCTAATACCC
ATTAACTCAAATAATCATTACAAAAAATATATATATATATTTTAAAAATAA
Found at i:5592019 original size:2 final size:2
Alignment explanation
Indices: 5592012--5592041 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5592002 ATCTTTGGGA
5592012 AT AT 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 AT AT
5592042 GTTGCATATT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5597356 original size:34 final size:35
Alignment explanation
Indices: 5597292--5597358 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
5597282 TGCTGTTGAT
*
5597292 TTGTGCAGGAAAAGTGGAGGCTGTTTGCTGCCGGA
1 TTGTGAAGGAAAAGTGGAGGCTGTTTGCTGCCGGA
5597327 TTGTGAAGGATAAAG-GGA-GCT-TTATGCTGCCG
1 TTGTGAAGGA-AAAGTGGAGGCTGTT-TGCTGCCG
5597359 ATTTTTGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 2 0.07
34 11 0.38
35 12 0.41
36 4 0.14
ACGTcount: A:0.22, C:0.13, G:0.37, T:0.27
Consensus pattern (35 bp):
TTGTGAAGGAAAAGTGGAGGCTGTTTGCTGCCGGA
Found at i:5598860 original size:29 final size:28
Alignment explanation
Indices: 5598806--5598865 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
5598796 ATGTCTATGG
*
5598806 GTAATTTTTCAGTTTTTTGGGTAAAAAT
1 GTAATTTTTCACTTTTTTGGGTAAAAAT
5598834 GTAATTTTTCACTTTTTTGGGTAAAAAT
1 GTAATTTTTCACTTTTTTGGGTAAAAAT
5598862 GTAA
1 GTAA
5598866 AAATGGTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.48
Consensus pattern (28 bp):
GTAATTTTTCACTTTTTTGGGTAAAAAT
Found at i:5602045 original size:32 final size:33
Alignment explanation
Indices: 5602004--5602074 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 33
5601994 TTGTGAATAA
5602004 ATGGTTTAAAGATTGAATTGATTATTATG-TTT
1 ATGGTTTAAAGATTGAATTGATTATTATGTTTT
*
5602036 ATGGTTTAAAGATTGAATTGCTTATTATGTTTT
1 ATGGTTTAAAGATTGAATTGATTATTATGTTTT
5602069 ATGGTT
1 ATGGTT
5602075 CAAATCATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 28 0.76
33 9 0.24
ACGTcount: A:0.28, C:0.01, G:0.20, T:0.51
Consensus pattern (33 bp):
ATGGTTTAAAGATTGAATTGATTATTATGTTTT
Found at i:5604997 original size:109 final size:108
Alignment explanation
Indices: 5604831--5605047 Score: 425
Period size: 109 Copynumber: 2.0 Consensus size: 108
5604821 TATAGAAAAG
5604831 AATCAAGTCTTTTTATATAATTAAGTATGTCGATTAGACTATTATTTTTCATTTGTATAATTTCG
1 AATCAAGTCTTTTTATATAATTAAGTATGTCGATTAGACTATTATTTTTCATTTGTATAATTTCG
5604896 TTTAAAATTTTTAACTCAATAATAAATCTAAACCATCATTGTT
66 TTTAAAATTTTTAACTCAATAATAAATCTAAACCATCATTGTT
5604939 NAATCAAGTCTTTTTATATAATTAAGTATGTCGATTAGACTATTATTTTTCATTTGTATAATTTC
1 -AATCAAGTCTTTTTATATAATTAAGTATGTCGATTAGACTATTATTTTTCATTTGTATAATTTC
5605004 GTTTAAAATTTTTAACTCAATAATAAATCTAAACCATCATTGTT
65 GTTTAAAATTTTTAACTCAATAATAAATCTAAACCATCATTGTT
5605048 GTATTTTAAA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (108 bp):
AATCAAGTCTTTTTATATAATTAAGTATGTCGATTAGACTATTATTTTTCATTTGTATAATTTCG
TTTAAAATTTTTAACTCAATAATAAATCTAAACCATCATTGTT
Found at i:5616304 original size:20 final size:20
Alignment explanation
Indices: 5616279--5616324 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
5616269 TTTTGACCCC
5616279 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
5616299 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
5616319 ATTTGA
1 ATTTGA
5616325 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:5616400 original size:28 final size:27
Alignment explanation
Indices: 5616369--5616421 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
5616359 TTTGGAGTAT
*
5616369 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
5616397 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
5616422 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:5616427 original size:28 final size:28
Alignment explanation
Indices: 5616369--5616427 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
5616359 TTTGGAGTAT
* *
5616369 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
5616397 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
5616425 AGG
1 AGG
5616428 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:5625710 original size:176 final size:174
Alignment explanation
Indices: 5625281--5625732 Score: 482
Period size: 175 Copynumber: 2.6 Consensus size: 174
5625271 GACACTTTAT
* * ** * *
5625281 CCCACCCAATTGTGCAACGCCCCTGTTGCACTAGCTCTTTACCCATAGAGGAGAGGGACT-TTAC
1 CCCACTCAATTATGCAACGCCCCCATTGCACTAGCTCTTTACCCATAAAGGAGAGAGACTCTTAC
* * * * * ** ** * *
5625345 ACTAGTCCAAGTCTATCCTAAACCTTGTAACTATCATGGGAGCTTCACATCAGTGAAGATCCATG
66 ATTAGTTCAAGTCTA-CCTGACCCTTGTATCTATCATAAGAGCCCCACATCAATGAAGATCCAGG
* * *
5625410 TCCGCTCTGAAACTAAATGTTGCAGCTTTAAACTCTAAATTTTAC
130 TCCACTCTGAAACTAAATGTTGCAACTTTAAACTCTAAATTCTAC
** * *
5625455 CTTACTCAATTATGCAACGTCCCCATTGCACTAGCTCTTTACCCGTAGAA-GAGAGAGACTCTTA
1 CCCACTCAATTATGCAACGCCCCCATTGCACTAGCTCTTTACCCATA-AAGGAGAGAGACTCTTA
* * *
5625519 CATTAG-TCTAAGTCTACCTCGACCCTTGTATCTATCATAAGAGCCCCACATTAATGAAGATTCG
65 CATTAGTTC-AAGTCTACCT-GACCCTTGTATCTATCATAAGAGCCCCACATCAATGAAGATCCA
*
5625583 GGTCCACTCT-AATACTAAATGTTGCAACTTTAAACTTTAACATTCTAC
128 GGTCCACTCTGAA-ACTAAATGTTGCAACTTTAAACTCTAA-ATTCTAC
* *
5625631 CCCA-TCAAATTATGCAATGCCCCCATTGCACTAGCTCTTTACCCATAAAGGAGAGATACTCTTA
1 CCCACTC-AATTATGCAACGCCCCCATTGCACTAGCTCTTTACCCATAAAGGAGAGAGACTCTTA
** ** *
5625695 GTTTAGTTCAAGTCTATTTTGACCCTTATATCTATCAT
65 CATTAGTTCAAGTCTA-CCTGACCCTTGTATCTATCAT
5625733 GGGATCCTCA
Statistics
Matches: 229, Mismatches: 39, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
174 54 0.24
175 86 0.38
176 86 0.38
177 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (174 bp):
CCCACTCAATTATGCAACGCCCCCATTGCACTAGCTCTTTACCCATAAAGGAGAGAGACTCTTAC
ATTAGTTCAAGTCTACCTGACCCTTGTATCTATCATAAGAGCCCCACATCAATGAAGATCCAGGT
CCACTCTGAAACTAAATGTTGCAACTTTAAACTCTAAATTCTAC
Found at i:5625771 original size:176 final size:175
Alignment explanation
Indices: 5625281--5625772 Score: 544
Period size: 176 Copynumber: 2.8 Consensus size: 175
5625271 GACACTTTAT
* * ** * *
5625281 CCCACCCAATTGTGCAACGCCCCTGTTGCACTAGCTCTTTACCCATAGAGGAGAGGGACT-TTAC
1 CCCACTCAATTATGCAACGCCCCCATTGCACTAGCTCTTTACCCATAAAGGAGAGAGACTCTTAC
* * * * * * * * *
5625345 ACTAGTCCAAGTCTATCCTAAACCTTGTAACTATCATGGGAGCTTCACATCAGTGAAGATCCATG
66 ATTAGTTCAAGTCTATCTTGACCCTTGTATCTATCATGGGAGCCTCACATTAGTGAAGATCCAGG
* *
5625410 TCCGCTCTGAA-ACTAAATGTTGCAGCTTTAAACTCTAAATTTTAC
131 TCCGCTCT-AATACTAAATGTTGCAACTTTAAACTCTAAATTCTAC
** * *
5625455 CTTACTCAATTATGCAACGTCCCCATTGCACTAGCTCTTTACCCGTAGAA-GAGAGAGACTCTTA
1 CCCACTCAATTATGCAACGCCCCCATTGCACTAGCTCTTTACCCATA-AAGGAGAGAGACTCTTA
* * ** * * * *
5625519 CATTAG-TCTAAGTCTACCTCGACCCTTGTATCTATCATAAGAGCCCCACATTAATGAAGATTCG
65 CATTAGTTC-AAGTCTATCTTGACCCTTGTATCTATCATGGGAGCCTCACATTAGTGAAGATCCA
* *
5625583 GGTCCACTCTAATACTAAATGTTGCAACTTTAAACTTTAACATTCTAC
129 GGTCCGCTCTAATACTAAATGTTGCAACTTTAAACTCTAA-ATTCTAC
* *
5625631 CCCA-TCAAATTATGCAATGCCCCCATTGCACTAGCTCTTTACCCATAAAGGAGAGATACTCTTA
1 CCCACTC-AATTATGCAACGCCCCCATTGCACTAGCTCTTTACCCATAAAGGAGAGAGACTCTTA
** * * * *
5625695 GTTTAGTTCAAGTCTATTTTGACCCTTATATCTATCATGGGATCCTCACATTAGTGAGGATCCAG
65 CATTAGTTCAAGTCTATCTTGACCCTTGTATCTATCATGGGAGCCTCACATTAGTGAAGATCCAG
*
5625760 GTCTGCTCTAATA
130 GTCCGCTCTAATA
5625773 TCAAATATTA
Statistics
Matches: 257, Mismatches: 53, Indels: 14
0.79 0.16 0.04
Matches are distributed among these distances:
174 51 0.20
175 87 0.34
176 117 0.46
177 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (175 bp):
CCCACTCAATTATGCAACGCCCCCATTGCACTAGCTCTTTACCCATAAAGGAGAGAGACTCTTAC
ATTAGTTCAAGTCTATCTTGACCCTTGTATCTATCATGGGAGCCTCACATTAGTGAAGATCCAGG
TCCGCTCTAATACTAAATGTTGCAACTTTAAACTCTAAATTCTAC
Found at i:5626840 original size:41 final size:41
Alignment explanation
Indices: 5626782--5626865 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 41
5626772 TCTTGGACTT
*
5626782 CTATGATATACCTTACAAAGTCGTGCAAGTCC-ATTCCTTTA
1 CTATGATATACCATACAAAGTCGTGCAAGTCCAATT-CTTTA
* *
5626823 CTATGATATACCATACAAAGTTGTGGAAGTCCAATTCTTTA
1 CTATGATATACCATACAAAGTCGTGCAAGTCCAATTCTTTA
5626864 CT
1 CT
5626866 CGTGGTCGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
41 36 0.92
42 3 0.08
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (41 bp):
CTATGATATACCATACAAAGTCGTGCAAGTCCAATTCTTTA
Found at i:5632549 original size:97 final size:98
Alignment explanation
Indices: 5632317--5632705 Score: 414
Period size: 99 Copynumber: 4.0 Consensus size: 98
5632307 TGTAAGTTAG
* * *
5632317 TATTTATCTTTGCATTTCACT-AGCATATAAACTCTTA-GAGTTAAACACCTTAAATATGGCACG
1 TATTTATCTTTGTATTTCACTAAG-ACATAAACTCTTAGGAGTTAAACACCTTAAATATGGCATG
** * **
5632380 TAACAACTTTTTTTTTTTACATGGTGTGTAACTTGA
65 TAACAAC--TTTTTTTCAACATAGTGTGTAACAAGA
* * * * * *
5632416 TCTTTATATTTGTATTTCACTAAGACATAAATTCTTA-GAGTTAAATACCTTAATTATGGCGTGT
1 TATTTATCTTTGTATTTCACTAAGACATAAACTCTTAGGAGTTAAACACCTTAAATATGGCATGT
*
5632480 AACAACTTTTTTTCAACATAGTGTGTAACAAGG
66 AACAACTTTTTTTCAACATAGTGTGTAACAAGA
* *
5632513 TTTTTATTTTTGTATTTCACTAAGACATAAACTCTTAGGAGTTAAACA-CTTAAATATGGCATGT
1 TATTTATCTTTGTATTTCACTAAGACATAAACTCTTAGGAGTTAAACACCTTAAATATGGCATGT
* * ***
5632577 AACAA-TTGTTTTCAACAT-GACGTGTAATTTGA
66 AACAACTTTTTTTCAACATAG-TGTGTAACAAGA
* * * * *
5632609 TATTTATCTTTGTATTTTATTAGGACATAAACTC-TAGGAGTCAAACATCTTAAATATGGCATGT
1 TATTTATCTTTGTATTTCACTAAGACATAAACTCTTAGGAGTTAAACACCTTAAATATGGCATGT
* *
5632673 AACAACTCTTTTTTTCAATATAATGTGTAACAA
66 AACAA--CTTTTTTTCAACATAGTGTGTAACAA
5632706 CTTTTTTTCA
Statistics
Matches: 242, Mismatches: 40, Indels: 16
0.81 0.13 0.05
Matches are distributed among these distances:
95 13 0.05
96 69 0.29
97 74 0.31
98 9 0.04
99 75 0.31
100 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (98 bp):
TATTTATCTTTGTATTTCACTAAGACATAAACTCTTAGGAGTTAAACACCTTAAATATGGCATGT
AACAACTTTTTTTCAACATAGTGTGTAACAAGA
Found at i:5638279 original size:2 final size:2
Alignment explanation
Indices: 5638272--5638304 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5638262 TATATTTTTA
5638272 AT AT AT AT 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 AT AT AT AT A
5638305 AGTAAAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5641409 original size:28 final size:29
Alignment explanation
Indices: 5641351--5641414 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
5641341 GCAAATTTTT
** *
5641351 AAAAATTACACTTTTACCCCCGTAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
* *
5641380 AAAAATTATATTTTTA-CCCCAAAAACTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
5641408 AAAAATT
1 AAAAATT
5641415 GCCCATAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAACTG
Found at i:5643302 original size:61 final size:61
Alignment explanation
Indices: 5643207--5643343 Score: 195
Period size: 61 Copynumber: 2.2 Consensus size: 61
5643197 GAATCTGACT
* * * *
5643207 CCGGATCTAGTGTTGGGAGTTACCGCTGTTTAGCTTGGGAAGAGAAAGAGTGAAATCGGCG
1 CCGGATCTAGTGTTGGGAGTTACAGCCGTTTAGCTTGGGAAGAGAAAGAGCGAAACCGGCG
* * *
5643268 CCGGATCTGGTGCTT-GGAGTTACAGCCGTTTAGCTTGGGAAGAGAGAGAGCGAAGCCGGCG
1 CCGGATCTAGTG-TTGGGAGTTACAGCCGTTTAGCTTGGGAAGAGAAAGAGCGAAACCGGCG
5643329 CCGGATCTAGTGTTG
1 CCGGATCTAGTGTTG
5643344 TCGCTGTTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 2 0.03
61 62 0.94
62 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (61 bp):
CCGGATCTAGTGTTGGGAGTTACAGCCGTTTAGCTTGGGAAGAGAAAGAGCGAAACCGGCG
Found at i:5661900 original size:52 final size:52
Alignment explanation
Indices: 5661835--5662226 Score: 317
Period size: 52 Copynumber: 7.4 Consensus size: 52
5661825 TTTGGAGAAG
* * * *
5661835 TTTGATTCATCATATCTTCCTTATTGGATTTGTTTGTGGAACTATGGAGAGGC
1 TTTGA-TCTTCATATCTTCCTTCTTGGATTTGTTTGTGGAACTTTAGAGAGGC
** * ** * * * * *
5661888 TTTGATCTTCATATCTTTATTCTTGGATTTATTTGCAGAGCTTCAAAAAGGA
1 TTTGATCTTCATATCTTCCTTCTTGGATTTGTTTGTGGAACTTTAGAGAGGC
** * * * *
5661940 TTTGATTCTTCATATCTTTTTTTTTAGATTTGTTTGTGGAAATCTCA-AGAGGC
1 TTTGA-TCTTCATATCTTCCTTCTTGGATTTGTTTGTGGAACT-TTAGAGAGGC
* ** *
5661993 TTTGATCTTCAGATCTTTTTTCTTGGATTTATTTGTGGAGTTAACTTTAGAGAGGC
1 TTTGATCTTCATATCTTCCTTCTTGGATTTGTTTGT-G-G--AACTTTAGAGAGGC
* * *
5662049 TTTGATCTTCACATCTTCCTTCTTGGATTTGTTTGTGGAACTTTAAAGAGGT
1 TTTGATCTTCATATCTTCCTTCTTGGATTTGTTTGTGGAACTTTAGAGAGGC
* ** * * *
5662101 TTTGATCTTCAAATCTTTTTTCTTGGATTTATTTGTGGAAATCTAGAGAGGC
1 TTTGATCTTCATATCTTCCTTCTTGGATTTGTTTGTGGAACTTTAGAGAGGC
* * * *
5662153 TTTGATTATTTAGATCTTCATTCTTGGATTTG-TT-T--AACTTTAGAGAGGC
1 TTTGA-TCTTCATATCTTCCTTCTTGGATTTGTTTGTGGAACTTTAGAGAGGC
*
5662202 TTTGGATCTTCAGAATCTTCCTTCT
1 TTT-GATCTTCA-TATCTTCCTTCT
5662227 GAAGGCCTTG
Statistics
Matches: 273, Mismatches: 56, Indels: 23
0.78 0.16 0.07
Matches are distributed among these distances:
49 19 0.07
50 12 0.04
51 1 0.00
52 128 0.47
53 64 0.23
54 5 0.02
55 3 0.01
56 41 0.15
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (52 bp):
TTTGATCTTCATATCTTCCTTCTTGGATTTGTTTGTGGAACTTTAGAGAGGC
Found at i:5662017 original size:105 final size:106
Alignment explanation
Indices: 5661835--5662135 Score: 354
Period size: 105 Copynumber: 2.8 Consensus size: 106
5661825 TTTGGAGAAG
* ** *
5661835 TTTGATTCATCATATCTTCCTTATTGGATTTGTTTGTGGAACTATGGAGAGGCTTTGATCTTCAT
1 TTTGATTCTTCATATCTTCCTTATTGGATTTGTTTGTGGAACTATAAAGAGGCTTTGATCTTCAA
* *
5661900 ATCTTTATTCTTGGATTTATTTGCAG-AGCTTCAAAAAGGA
66 ATCTTTTTTCTTGGATTTATTTGCAGTAACTTCAAAAAGGA
** * * * * * *
5661940 TTTGATTCTTCATATCTTTTTTTTTAGATTTGTTTGTGGAAATCTCAAGAGGCTTTGATCTTCAG
1 TTTGATTCTTCATATCTTCCTTATTGGATTTGTTTGTGGAACTATAAAGAGGCTTTGATCTTCAA
* * * * *
5662005 ATCTTTTTTCTTGGATTTATTTGTGGAGTTAACTTTAGAGAGGC
66 ATCTTTTTTCTTGGATTTA-TT-TGCAG-TAACTTCAAAAAGGA
* * * *
5662049 TTTGA-TCTTCACATCTTCCTTCTTGGATTTGTTTGTGGAACTTTAAAGAGGTTTTGATCTTCAA
1 TTTGATTCTTCATATCTTCCTTATTGGATTTGTTTGTGGAACTATAAAGAGGCTTTGATCTTCAA
5662113 ATCTTTTTTCTTGGATTTATTTG
66 ATCTTTTTTCTTGGATTTATTTG
5662136 TGGAAATCTA
Statistics
Matches: 165, Mismatches: 27, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
105 73 0.44
106 4 0.02
107 6 0.04
108 68 0.41
109 14 0.08
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (106 bp):
TTTGATTCTTCATATCTTCCTTATTGGATTTGTTTGTGGAACTATAAAGAGGCTTTGATCTTCAA
ATCTTTTTTCTTGGATTTATTTGCAGTAACTTCAAAAAGGA
Found at i:5662075 original size:161 final size:153
Alignment explanation
Indices: 5661881--5662226 Score: 399
Period size: 161 Copynumber: 2.2 Consensus size: 153
5661871 TGGAACTATG
* ** *
5661881 GAGAGGCTTTGATCTTCATATCTTTATTCTTGGATTTATTTGCAGAGCTTCAAAAAGGATTTGAT
1 GAGAGGCTTTGATCTTCAAATCTTCCTTCTTGGATTTATTTGCAGAACTTCAAAAAGGATTTGA-
* * * *
5661946 TCTTCATATCTTTTTTTTTAGATTTGTTTGTGGAAATCTCA-AGAGGCTTTGA-TCTTCAGATCT
65 TCTTCAAATCTTTTTTCTTAGATTTATTTGTGGAAATCT-AGAGAGGCTTTGATTATTCAGATCT
**
5662009 TTTTTCTTGGATTTATTTGTGGAGTTAACTTTA
129 TCATTCTTGG----ATTTGT----TTAACTTTA
* * ** * * *
5662042 GAGAGGCTTTGATCTTCACATCTTCCTTCTTGGATTTGTTTGTGGAACTTTAAAGAGGTTTTGAT
1 GAGAGGCTTTGATCTTCAAATCTTCCTTCTTGGATTTATTTGCAGAACTTCAAAAAGGATTTGAT
* *
5662107 CTTCAAATCTTTTTTCTTGGATTTATTTGTGGAAATCTAGAGAGGCTTTGATTATTTAGATCTTC
66 CTTCAAATCTTTTTTCTTAGATTTATTTGTGGAAATCTAGAGAGGCTTTGATTATTCAGATCTTC
5662172 ATTCTTGGATTTGTTTAACTTTA
131 ATTCTTGGATTTGTTTAACTTTA
5662195 GAGAGGCTTTGGATCTTCAGAATCTTCCTTCT
1 GAGAGGCTTT-GATCTTCA-AATCTTCCTTCT
5662227 GAAGGCCTTG
Statistics
Matches: 162, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
153 19 0.12
154 8 0.05
155 11 0.07
157 6 0.04
159 1 0.01
160 46 0.28
161 71 0.44
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (153 bp):
GAGAGGCTTTGATCTTCAAATCTTCCTTCTTGGATTTATTTGCAGAACTTCAAAAAGGATTTGAT
CTTCAAATCTTTTTTCTTAGATTTATTTGTGGAAATCTAGAGAGGCTTTGATTATTCAGATCTTC
ATTCTTGGATTTGTTTAACTTTA
Found at i:5667162 original size:6 final size:6
Alignment explanation
Indices: 5667151--5667177 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5667141 TTCATATATA
5667151 TGAAAG TGAAAG TGAAAG TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGA
5667178 TAGAAACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (6 bp):
TGAAAG
Found at i:5670263 original size:43 final size:43
Alignment explanation
Indices: 5670202--5670285 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
5670192 TGTGATAATA
** *
5670202 ATGACCCAGCTATGTGCGATG-TGGGAGTGTACATGAGCTGATG
1 ATGACCCAGCTATGTGCGA-GAAAGGAGTGCACATGAGCTGATG
*
5670245 ATGACCCGGCTATGTGCGAGAAAGGAGTGCACATGAGCTGA
1 ATGACCCAGCTATGTGCGAGAAAGGAGTGCACATGAGCTGA
5670286 GTGTGGCAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (43 bp):
ATGACCCAGCTATGTGCGAGAAAGGAGTGCACATGAGCTGATG
Found at i:5673895 original size:21 final size:19
Alignment explanation
Indices: 5673869--5673909 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
5673859 AATTTAAAAC
5673869 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
5673890 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
5673909 A
1 A
5673910 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:5679949 original size:21 final size:19
Alignment explanation
Indices: 5679923--5679963 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
5679913 AATTTAAAAC
5679923 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
5679944 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
5679963 A
1 A
5679964 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:5680748 original size:116 final size:117
Alignment explanation
Indices: 5680534--5680838 Score: 443
Period size: 116 Copynumber: 2.6 Consensus size: 117
5680524 ATCCCATGTG
* * *
5680534 GCAATTTCAAATTTGAATGAAGATTCTACTAAGGAGAATTCTGAGGCTGTGGAACTCTTTCAAAA
1 GCAAATTCAAATTTGAATGAAGATTCTGCTAAGGAGAATTCTAAGGCTGTGGAACTCTTTCAAAA
* * *
5680599 -TCTAAATTTCGATTGTAGCCAACCATATATGGATAAATTGCATTATCCTATA
66 TTC-AAATTTCAATTGCAGCCAACCATATATGGATAAATTGCACTATCCTATA
* * * *
5680651 GCAAATTCAAATTTGAATGCAGATTTTGCTAA-GAGAATTCTAAGGTTGTGGAACTCTTTGAAAA
1 GCAAATTCAAATTTGAATGAAGATTCTGCTAAGGAGAATTCTAAGGCTGTGGAACTCTTTCAAAA
* *
5680715 TTCAAATTTCAATTGCAGTCAACCATATCTGGATAAATTGCACTATCCTATA
66 TTCAAATTTCAATTGCAGCCAACCATATATGGATAAATTGCACTATCCTATA
* * * *
5680767 GCAAATTCAAAATTAAATAAAGATTCTGCTAAGGAGAATTCTAAGGCTATGGAACTCTTTCAAAA
1 GCAAATTCAAATTTGAATGAAGATTCTGCTAAGGAGAATTCTAAGGCTGTGGAACTCTTTCAAAA
5680832 TTCAAAT
66 TTCAAAT
5680839 ATGGAAGAGG
Statistics
Matches: 166, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
116 100 0.60
117 66 0.40
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (117 bp):
GCAAATTCAAATTTGAATGAAGATTCTGCTAAGGAGAATTCTAAGGCTGTGGAACTCTTTCAAAA
TTCAAATTTCAATTGCAGCCAACCATATATGGATAAATTGCACTATCCTATA
Found at i:5703541 original size:27 final size:27
Alignment explanation
Indices: 5703511--5703563 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
5703501 ATCCTATCCT
*
5703511 TACATTGCTTGAATTGTAGACCAAGGA
1 TACATTGCTTGAATTGTAGACAAAGGA
*
5703538 TACATTGCTTGATTTGTAGACAAAGG
1 TACATTGCTTGAATTGTAGACAAAGG
5703564 GAGAAAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (27 bp):
TACATTGCTTGAATTGTAGACAAAGGA
Found at i:5706254 original size:14 final size:14
Alignment explanation
Indices: 5706223--5706261 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5706213 GAATCGATTC
5706223 TTTCT-TCTTTGCA
1 TTTCTATCTTTGCA
5706236 TTTCTATCTTCTGCA
1 TTTCTATCTT-TGCA
5706251 -TTCTATCTTTG
1 TTTCTATCTTTG
5706262 TAGTATCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.29
14 13 0.54
15 4 0.17
ACGTcount: A:0.10, C:0.23, G:0.08, T:0.59
Consensus pattern (14 bp):
TTTCTATCTTTGCA
Found at i:5710098 original size:24 final size:24
Alignment explanation
Indices: 5710042--5710131 Score: 90
Period size: 24 Copynumber: 3.7 Consensus size: 24
5710032 AATGTGACAA
* ** *
5710042 AATACATGACAGAACATGTGGCAG
1 AATACGTGACAGAACACATGGTAG
* *
5710066 AGTATGTGACAGAACACATGGTAG
1 AATACGTGACAGAACACATGGTAG
*
5710090 AATACGTGATAGAACACATGGTAG
1 AATACGTGACAGAACACATGGTAG
* *
5710114 GATGGCGTGACAGAACAC
1 AAT-ACGTGACAGAACAC
5710132 GTCTCAAGCA
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 41 0.77
25 12 0.23
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.18
Consensus pattern (24 bp):
AATACGTGACAGAACACATGGTAG
Found at i:5716911 original size:18 final size:18
Alignment explanation
Indices: 5716888--5716928 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5716878 GTAGTCAAAG
5716888 TAAAAAT-GAAAATGAAAA
1 TAAAAATAGAAAAT-AAAA
*
5716906 TAAAAATATAAAATAAAA
1 TAAAAATAGAAAATAAAA
5716924 TAAAA
1 TAAAA
5716929 GATAATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
TAAAAATAGAAAATAAAA
Found at i:5717178 original size:13 final size:12
Alignment explanation
Indices: 5717152--5717190 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
5717142 AGCAAGCAAC
5717152 AAAAA-AATATAT
1 AAAAATAATA-AT
5717164 AAAAATAATGAAT
1 AAAAATAAT-AAT
5717177 AAAAATAATAAT
1 AAAAATAATAAT
5717189 AA
1 AA
5717191 TGATAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.40
13 14 0.56
14 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:5722708 original size:16 final size:16
Alignment explanation
Indices: 5722689--5722719 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5722679 GAATTGAATA
5722689 TATGAAATTTGTTTTG
1 TATGAAATTTGTTTTG
*
5722705 TATGATATTTGTTTT
1 TATGAAATTTGTTTT
5722720 ATAACAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.16, T:0.61
Consensus pattern (16 bp):
TATGAAATTTGTTTTG
Found at i:5729078 original size:15 final size:16
Alignment explanation
Indices: 5729058--5729087 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5729048 CTAGGAGAGA
5729058 GAAAGG-AAGAAAGAC
1 GAAAGGAAAGAAAGAC
5729073 GAAAGGAAAGAAAGA
1 GAAAGGAAAGAAAGA
5729088 AAGGAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (16 bp):
GAAAGGAAAGAAAGAC
Found at i:5730400 original size:36 final size:39
Alignment explanation
Indices: 5730243--5730384 Score: 205
Period size: 39 Copynumber: 3.6 Consensus size: 39
5730233 GGTGCCAGTA
* **
5730243 ATGTGC-GTTGTGGGAGAGCACACGCCGATGATATATGCC
1 ATGTGCAG-TGTGGGAGAGCACATGATGATGATATATGCC
5730282 ATGTGCAGTGTGGGAGAGCACATGATGATGATATATGCC
1 ATGTGCAGTGTGGGAGAGCACATGATGATGATATATGCC
*
5730321 ATGTGCAGTGTGTGAGAGCACATGATGATGATATATGCC
1 ATGTGCAGTGTGGGAGAGCACATGATGATGATATATGCC
* * *
5730360 ATGTGCGGTGTGGGAGTGCATATGA
1 ATGTGCAGTGTGGGAGAGCACATGA
5730385 GGATATTAGC
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 93 0.99
40 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.26
Consensus pattern (39 bp):
ATGTGCAGTGTGGGAGAGCACATGATGATGATATATGCC
Found at i:5742828 original size:14 final size:13
Alignment explanation
Indices: 5742784--5742829 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 13
5742774 AATATGCAAA
5742784 ATAATAAAATAAAG
1 ATAAT-AAATAAAG
*
5742798 ATAAAAAATAAA-
1 ATAATAAATAAAG
5742810 A-AATAAATAAAG
1 ATAATAAATAAAG
5742822 ACTAATAA
1 A-TAATAA
5742830 CTTAAAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 9 0.33
12 2 0.07
13 7 0.26
14 9 0.33
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (13 bp):
ATAATAAATAAAG
Found at i:5742836 original size:25 final size:24
Alignment explanation
Indices: 5742781--5742846 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
5742771 CTAAATATGC
5742781 AAAATAATAAAATAAAGATAAAAAAT
1 AAAA-AAT-AAATAAAGATAAAAAAT
* *
5742807 AAAAAATAAATAAAGACTAATAACT
1 AAAAAATAAATAAAGA-TAAAAAAT
* *
5742832 TAAAAGTAAATAAAG
1 AAAAAATAAATAAAG
5742847 GCACAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.26
25 22 0.63
26 4 0.11
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (24 bp):
AAAAAATAAATAAAGATAAAAAAT
Found at i:5745525 original size:198 final size:198
Alignment explanation
Indices: 5745175--5745567 Score: 590
Period size: 198 Copynumber: 2.0 Consensus size: 198
5745165 GAATACCTCC
* * * *
5745175 GCTTGGCCACTTGTTTGAGGATGGTAAGCAGTTGTAACTTTGTGTTTAACTCCATATTTTGTAAG
1 GCTTGACCACTTGTTTGAGGATGGTAAGCAGTTGAAACTTTGGGTTTAACTCCATATTTTGCAAG
* * * * * * * *
5745240 TAGTGCATCAAAATACTTGTTGCAAAAGTGTCTACCCTCATCACTAATGATTGCCCTTGGAGTGC
66 AAATGCATCAAAATACTTATTACAAAACTGTCGACCCTCATCACTAATGAATGCCCTTAGAGTGC
* * *
5745305 CAAATCGGAAAAAGATATTTTTCTTCATGAAATTTACCTCTAACTTGGAGTCATTAG-TAGGAAG
131 CAAATCGGAAAAAGAAATTTTTCTTCATGAAATTCACCACTAACTTGGAGTC-TTAGATAGGAAG
5745369 ACTT
195 ACTT
5745373 GCTTGACCACTTGTTTGAGGATGGTAAGCAGTTGAAACTTTGGGTTTAACTCCATATTTTGCAAG
1 GCTTGACCACTTGTTTGAGGATGGTAAGCAGTTGAAACTTTGGGTTTAACTCCATATTTTGCAAG
*
5745438 AAATGCATCAAAATTCTTATTACAAAACTGTCGACCCTCATCACTAATGAATGCCCTTAGAGTGC
66 AAATGCATCAAAATACTTATTACAAAACTGTCGACCCTCATCACTAATGAATGCCCTTAGAGTGC
* * * *
5745503 CAAATCGGGAAAAGAAATTTTTCTTCATGAAATTCATCACTACCTTGGAGTCTTTGATAGGAAGA
131 CAAATCGGAAAAAGAAATTTTTCTTCATGAAATTCACCACTAACTTGGAGTCTTAGATAGGAAGA
5745568 GCTGCTGCTT
Statistics
Matches: 174, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
197 3 0.02
198 171 0.98
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (198 bp):
GCTTGACCACTTGTTTGAGGATGGTAAGCAGTTGAAACTTTGGGTTTAACTCCATATTTTGCAAG
AAATGCATCAAAATACTTATTACAAAACTGTCGACCCTCATCACTAATGAATGCCCTTAGAGTGC
CAAATCGGAAAAAGAAATTTTTCTTCATGAAATTCACCACTAACTTGGAGTCTTAGATAGGAAGA
CTT
Found at i:5756532 original size:2 final size:2
Alignment explanation
Indices: 5756525--5756559 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
5756515 TATACGTGTT
*
5756525 TA TA TA TA TA TA TA TA TA TA TA TA TT TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
5756560 GAGAGGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5762535 original size:5 final size:5
Alignment explanation
Indices: 5762513--5762562 Score: 57
Period size: 5 Copynumber: 10.2 Consensus size: 5
5762503 AGATTTTCAA
* * * *
5762513 TTTTC TTTTC -CTTG TTTTC TTTTC TTTCC TTTTC TTTCC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
5762562 T
1 T
5762563 AACTCCTTCC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
4 2 0.06
5 34 0.94
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTC
Found at i:5771725 original size:21 final size:21
Alignment explanation
Indices: 5771701--5771755 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
5771691 GTTCATGCAA
*
5771701 TTCATGACAAAGACTGATGCC
1 TTCATGACAAAGACTAATGCC
5771722 TTCATGACAAAGACTAATGCC
1 TTCATGACAAAGACTAATGCC
*
5771743 TACATGACAAAGA
1 TTCATGACAAAGA
5771756 ATTACACCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (21 bp):
TTCATGACAAAGACTAATGCC
Found at i:5777135 original size:28 final size:28
Alignment explanation
Indices: 5777103--5777160 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
5777093 AAAAACAAAC
5777103 TTATGGGATTCTAGTGTTAAACTATGTT
1 TTATGGGATTCTAGTGTTAAACTATGTT
* *
5777131 TTATGGGATTCTAGTGTTAAATTGTGTT
1 TTATGGGATTCTAGTGTTAAACTATGTT
5777159 TT
1 TT
5777161 GAATTAGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.50
Consensus pattern (28 bp):
TTATGGGATTCTAGTGTTAAACTATGTT
Found at i:5783585 original size:43 final size:43
Alignment explanation
Indices: 5783524--5783781 Score: 276
Period size: 43 Copynumber: 6.1 Consensus size: 43
5783514 TTTTGTGTGA
* * *
5783524 TGATAATGACCCAGCCATGTGCGATGCA-AGAGTGCACATGAGC
1 TGATGATGACCCAGCCATGTGCGA-GTAGGGAGTGCACATGAGC
* * * *
5783567 TGATGATAACCCAGCCATGTGTGGGTAGGGAGTGCACATAAGC
1 TGATGATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGC
* *
5783610 TGATGATGACCCAACTATGTGCGAGTAGGGAGTGCACATGAGC
1 TGATGATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGC
* * *
5783653 TGATGATGACCCAACAATGTGTG-G-A-GGAGCT-CACATGAGC
1 TGATGATGACCCAGCCATGTGCGAGTAGGGAG-TGCACATGAGC
* *
5783693 TGATGATGACCTAGCTATGTGCGAGTAGGGAGTGCACATGAGC
1 TGATGATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGC
*** * *
5783736 TGATGATGACCCAATTATGTGCG-GTGTGGGAGTGCACATAAGC
1 TGATGATGACCCAGCCATGTGCGAGT-AGGGAGTGCACATGAGC
5783779 TGA
1 TGA
5783782 GAGAGAGTTA
Statistics
Matches: 184, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
40 32 0.17
41 3 0.02
42 7 0.04
43 142 0.77
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.22
Consensus pattern (43 bp):
TGATGATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGC
Found at i:5783727 original size:83 final size:86
Alignment explanation
Indices: 5783553--5783781 Score: 324
Period size: 83 Copynumber: 2.7 Consensus size: 86
5783543 TGCGATGCAA
* * *
5783553 GAGTGCACATGAGCTGATGATAACCCAGCCATGTGTGGGTAGGGAGTGCACATAAGCTGATGATG
1 GAGTGCACATGAGCTGATGATGACCCAACAATGTGTGGGTAGGGAGTGCACATAAGCTGATGATG
5783618 ACCCAACTATGTGCGAGTAGG
66 ACCCAACTATGTGCGAGTAGG
*
5783639 GAGTGCACATGAGCTGATGATGACCCAACAATGTGT-GG-A-GGAGCT-CACATGAGCTGATGAT
1 GAGTGCACATGAGCTGATGATGACCCAACAATGTGTGGGTAGGGAG-TGCACATAAGCTGATGAT
* *
5783700 GACCTAGCTATGTGCGAGTAGG
65 GACCCAACTATGTGCGAGTAGG
** *
5783722 GAGTGCACATGAGCTGATGATGACCCAATTATGTGCGGTGT-GGGAGTGCACATAAGCTGA
1 GAGTGCACATGAGCTGATGATGACCCAACAATGTGTGG-GTAGGGAGTGCACATAAGCTGA
5783782 GAGAGAGTTA
Statistics
Matches: 127, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
83 72 0.57
84 3 0.02
85 4 0.03
86 48 0.38
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.22
Consensus pattern (86 bp):
GAGTGCACATGAGCTGATGATGACCCAACAATGTGTGGGTAGGGAGTGCACATAAGCTGATGATG
ACCCAACTATGTGCGAGTAGG
Found at i:5786419 original size:25 final size:25
Alignment explanation
Indices: 5786354--5786421 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
5786344 TTCCTTTATT
* * *
5786354 AATTAACATAATTATTA-GAATTAGG
1 AATTACCATAATTA-TAGGAAGTAAG
*
5786379 AATCACCATAATTATAGGAAGTAAG
1 AATTACCATAATTATAGGAAGTAAG
5786404 AATTACCATAATTATAGG
1 AATTACCATAATTATAGG
5786422 GATTTTAGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 2 0.05
25 35 0.95
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (25 bp):
AATTACCATAATTATAGGAAGTAAG
Found at i:5787633 original size:20 final size:20
Alignment explanation
Indices: 5787591--5787634 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5787581 GACCACTTAG
*
5787591 TTGAAAATGTATCGATGCAT
1 TTGAAAATGTATCGATACAT
* * *
5787611 TTGATAATGTATTGATACTT
1 TTGAAAATGTATCGATACAT
5787631 TTGA
1 TTGA
5787635 GGCCAAGAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (20 bp):
TTGAAAATGTATCGATACAT
Found at i:5787863 original size:15 final size:15
Alignment explanation
Indices: 5787843--5787872 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5787833 ATGAAGAACA
*
5787843 TATATCAATAGATTT
1 TATATCAATAAATTT
5787858 TATATCAATAAATTT
1 TATATCAATAAATTT
5787873 GGACCATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (15 bp):
TATATCAATAAATTT
Found at i:5804302 original size:2 final size:2
Alignment explanation
Indices: 5804295--5804319 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5804285 GTAGTCATAA
5804295 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
5804320 CACACAATTG
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:5806027 original size:4 final size:4
Alignment explanation
Indices: 5806013--5806109 Score: 50
Period size: 4 Copynumber: 21.5 Consensus size: 4
5806003 TACCATTTTT
* * *
5806013 TTTC TTCC TTTC TTTC TTTGT TTTC TTTCC TCTC TTTC TCTCTC TTTC
1 TTTC TTTC TTTC TTTC TTT-C TTTC TTT-C TTTC TTTC T-T-TC TTTC
* *
5806061 TTTTCC GTTCC TCTC TTTC TCTCTC TTTC TTTTCC TTTC TTTC TTTC TT
1 -TTT-C -TTTC TTTC TTTC T-T-TC TTTC -TTT-C TTTC TTTC TTTC TT
5806110 CAACTGCCGC
Statistics
Matches: 72, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
4 42 0.58
5 20 0.28
6 10 0.14
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:5806057 original size:10 final size:10
Alignment explanation
Indices: 5806036--5806090 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
5806026 TTCTTTGTTT
5806036 TCTTTC-CTC
1 TCTTTCTCTC
5806045 TCTTTCTCTC
1 TCTTTCTCTC
*
5806055 TCTTTCT-TT
1 TCTTTCTCTC
*
5806064 TCCGTTC-CTC
1 T-CTTTCTCTC
5806074 TCTTTCTCTC
1 TCTTTCTCTC
5806084 TCTTTCT
1 TCTTTCT
5806091 TTTCCTTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 12 0.32
10 26 0.68
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.60
Consensus pattern (10 bp):
TCTTTCTCTC
Found at i:5806060 original size:19 final size:20
Alignment explanation
Indices: 5806036--5806090 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
5806026 TTCTTTGTTT
5806036 TCTTTC-CTCTCTTTCTCTC
1 TCTTTCTCTCTCTTTCTCTC
* *
5806055 TCTTTCT-TTTCCGTTC-CTC
1 TCTTTCTCTCT-CTTTCTCTC
5806074 TCTTTCTCTCTCTTTCT
1 TCTTTCTCTCTCTTTCT
5806091 TTTCCTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.60
Consensus pattern (20 bp):
TCTTTCTCTCTCTTTCTCTC
Found at i:5806077 original size:29 final size:28
Alignment explanation
Indices: 5806020--5806108 Score: 119
Period size: 29 Copynumber: 3.2 Consensus size: 28
5806010 TTTTTTCTTC
* *
5806020 CTTTCT-T-TCTTTGTTTTCTTTCCTCT
1 CTTTCTCTCTCTTTCTTTTCCTTCCTCT
5806046 CTTTCTCTCTCTTTCTTTTCCGTTCCTCT
1 CTTTCTCTCTCTTTCTTTTCC-TTCCTCT
* *
5806075 CTTTCTCTCTCTTTCTTTTCCTTTCTTT
1 CTTTCTCTCTCTTTCTTTTCCTTCCTCT
5806103 CTTTCT
1 CTTTCT
5806109 TCAACTGCCG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
26 6 0.11
27 1 0.02
28 21 0.38
29 28 0.50
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (28 bp):
CTTTCTCTCTCTTTCTTTTCCTTCCTCT
Found at i:5808040 original size:18 final size:19
Alignment explanation
Indices: 5808002--5808052 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
5807992 TATATGACAC
5808002 AACATGATTAATAACACGTTT
1 AACATGATT-A-AACACGTTT
5808023 AACATGATTAAA-ACGTTT
1 AACATGATTAAACACGTTT
*
5808041 AACACGATTAAA
1 AACATGATTAAA
5808053 TAAAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 17 0.59
19 2 0.07
20 1 0.03
21 9 0.31
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (19 bp):
AACATGATTAAACACGTTT
Found at i:5808072 original size:20 final size:20
Alignment explanation
Indices: 5808047--5808136 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 20
5808037 GTTTAACACG
5808047 ATTAAATAAAAATATTTATA
1 ATTAAATAAAAATATTTATA
*
5808067 ATTAAAT-ATAAT-TTTATTA
1 ATTAAATAAAAATATTTA-TA
* ** *
5808086 TTTAAATTTAAA-ATCTATA
1 ATTAAATAAAAATATTTATA
*
5808105 ATT--ATAAAAATAATTATA
1 ATTAAATAAAAATATTTATA
* *
5808123 ATAAAACAAAAATA
1 ATTAAATAAAAATA
5808137 ATAATAACAT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
17 5 0.10
18 11 0.21
19 16 0.31
20 20 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAAATAAAAATATTTATA
Found at i:5808340 original size:18 final size:18
Alignment explanation
Indices: 5808313--5808376 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
5808303 TGTCACGTAT
* *
5808313 ACACGTTTAAATATGATA
1 ACACGATTAAACATGATA
5808331 ACACGATTAAACATGATA
1 ACACGATTAAACATGATA
* * *
5808349 ACACAATTAAGCACGATA
1 ACACGATTAAACATGATA
5808367 ACACGATTAA
1 ACACGATTAA
5808377 GTAAACGTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.23
Consensus pattern (18 bp):
ACACGATTAAACATGATA
Found at i:5825625 original size:71 final size:71
Alignment explanation
Indices: 5825540--5825690 Score: 284
Period size: 71 Copynumber: 2.1 Consensus size: 71
5825530 GCATGTGTAC
5825540 TCTGCTTCTAAAAGATTATGACATGGTGTGGTTTTAAATTTATGAAGCTGAATTTAGGCTGCATG
1 TCTGCTTCTAAAAGATTATGACATGGTGTGGTTTTAAATTTATGAAGCTGAATTTAGGCTGCATG
5825605 TCCTTT
66 TCCTTT
*
5825611 TCTGCTTCTGAAAGATTATGACATGGTGTGGTTTTAAATTTATGAAGCTGAATTTAGGCTGCATG
1 TCTGCTTCTAAAAGATTATGACATGGTGTGGTTTTAAATTTATGAAGCTGAATTTAGGCTGCATG
5825676 TCCTTT
66 TCCTTT
*
5825682 TCTCCTTCT
1 TCTGCTTCT
5825691 CATACATTAC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.42
Consensus pattern (71 bp):
TCTGCTTCTAAAAGATTATGACATGGTGTGGTTTTAAATTTATGAAGCTGAATTTAGGCTGCATG
TCCTTT
Found at i:5825884 original size:131 final size:131
Alignment explanation
Indices: 5825650--5825924 Score: 435
Period size: 131 Copynumber: 2.1 Consensus size: 131
5825640 GGTTTTAAAT
* *
5825650 TTATGAAGCTGAATTTAGGCTGCATGTCCTTTTCTCCTTCTCATACATTACCTGTGGAAAGCATT
1 TTATGAAGCTGAATTTAAGCTGCATGTCCTTTTCTCCTTCTCATACATTACCTGAGGAAAGCATT
* *
5825715 TACTTTGCATGTGTACTCTGCTTCTAGAAGAATATGACATGGTGTGGTTCTAAAATTAATTGTAC
66 TACTTTGCATGTGTACTCTGCTTCTAGAAGAATATGACATGGTGTGGTTCTAAAATAAATTATAC
5825780 A
131 A
* **
5825781 TTATGAAGCTGAATTTAAGCTGCATGTCCTTTTTTCCTTCTCATATTTTACCTGAGGAAAGCATT
1 TTATGAAGCTGAATTTAAGCTGCATGTCCTTTTCTCCTTCTCATACATTACCTGAGGAAAGCATT
* * *
5825846 TACTTTGCATGTGTACTCTGCTTCT-GAAAGATTCTGACATGGTTTGGTTCTAAAATAAATTATA
66 TACTTTGCATGTGTACTCTGCTTCTAG-AAGAATATGACATGGTGTGGTTCTAAAATAAATTATA
5825910 CA
130 CA
*
5825912 TTAAGAAGCTGAA
1 TTATGAAGCTGAA
5825925 GTTAGGTTCT
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
130 1 0.01
131 131 0.99
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (131 bp):
TTATGAAGCTGAATTTAAGCTGCATGTCCTTTTCTCCTTCTCATACATTACCTGAGGAAAGCATT
TACTTTGCATGTGTACTCTGCTTCTAGAAGAATATGACATGGTGTGGTTCTAAAATAAATTATAC
A
Done.