Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 128 of 310
Found at i:41105803 original size:11 final size:11
Alignment explanation
Indices: 41105767--41105808 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
41105757 ATGAATGTCT
41105767 CCTGGTAGC-G
1 CCTGGTAGCAG
*
41105777 CCTTGTAGCA-
1 CCTGGTAGCAG
41105787 -CTGGTAGCAG
1 CCTGGTAGCAG
41105797 CCTGGTAGCAG
1 CCTGGTAGCAG
41105808 C
1 C
41105809 AAGCTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 8 0.30
10 8 0.30
11 11 0.41
ACGTcount: A:0.17, C:0.29, G:0.33, T:0.21
Consensus pattern (11 bp):
CCTGGTAGCAG
Found at i:41111097 original size:24 final size:24
Alignment explanation
Indices: 41111032--41111102 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
41111022 GCCGGTTAGG
* *
41111032 TTCCCGGCGGTGCTCCGACGATCCA
1 TTCCCGGCGGTGCTCCGGCGA-GCA
* *
41111057 TT-CCGGCGGTGGTCCGGCGAGCT
1 TTCCCGGCGGTGCTCCGGCGAGCA
*
41111080 TTCCCGGCGGTGCTCCGGTGAGC
1 TTCCCGGCGGTGCTCCGGCGAGC
41111103 CATTTCGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 3 0.08
24 34 0.87
25 2 0.05
ACGTcount: A:0.07, C:0.35, G:0.37, T:0.21
Consensus pattern (24 bp):
TTCCCGGCGGTGCTCCGGCGAGCA
Found at i:41111685 original size:43 final size:43
Alignment explanation
Indices: 41111619--41112403 Score: 1032
Period size: 43 Copynumber: 18.5 Consensus size: 43
41111609 NNNNNNNNNN
* * **
41111619 CCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAAATAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* *
41111662 CCCTTGGTCGTGCGGGGGCCTCGGCCACCATCGGC-ACCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* * * *
41111704 CCCCTGGTCGTGCGGGAGCCTCGGGGACCATCGACACCCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* *
41111747 CCCTTGGTCGTGC--GAGACTCGGCCACCATCGGCAACCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* *
41111788 CCCTTGGTCGTGCGGGAGCCTCGGGCAACATCGGCAACCTAAG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* * *
41111831 CCTTTGGTCGTGCGAGAGCCTCGGGCACCATTGGCAACCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* **
41111874 CCCTTGGTCGTGCGAGAGCCTCGAACACCATCGGCAACCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* * * *
41111917 CCCCTGGTCGTGCGGGAGCCTCAGACACCATC-GTAACCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* * * *
41111959 CCCCTGGTCGTGCGGGAG-CTCGGACACCATCGGTAACTTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* *
41112001 CCCCTGGTCGTGCGAGAGCCTCGGG-ACCATCGGCAACCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* *
41112043 CCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* * * *
41112086 CCCCTAGTCGTGCGGGAGCCTCAGGCACCATCGGCACCCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* * * *
41112129 CCCCTGGTCGTGCGGGAGCCTCGGGGACCATCGACACCCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
*
41112172 CCCTTGGTCGTGCGAGAGCCTCGGG-ACCATCGGC-ACCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* *
41112213 CCCTTGGTCGTGGGGGAGCCTCGGGCACCATCGGC-ACCTTGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
** *
41112255 TGCTTGGAT-GTGCGGGAGCCTCGGACACCATCGGCAACCTAGG
1 CCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
* *
41112298 CCCTTGGTCGTGCCGGAGCCTCAGGCACCATCGGCAACCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
** *
41112341 CCCTTGGTCGTGCCAGAGCCTCGGGCACCATCGGAAACCTAGG
1 CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
41112384 CCCTTGGTCGTGCGGGAGCC
1 CCCTTGGTCGTGCGGGAGCC
41112404 GTGCGGGAGC
Statistics
Matches: 660, Mismatches: 72, Indels: 20
0.88 0.10 0.03
Matches are distributed among these distances:
41 77 0.12
42 180 0.27
43 403 0.61
ACGTcount: A:0.16, C:0.35, G:0.33, T:0.17
Consensus pattern (43 bp):
CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG
Found at i:41112034 original size:212 final size:211
Alignment explanation
Indices: 41111620--41112402 Score: 1046
Period size: 212 Copynumber: 3.7 Consensus size: 211
41111610 NNNNNNNNNC
* ** *
41111620 CCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAAATAGGCCCTTGGTCGTGCGGGGGCCTC-
1 CCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCA
*
41111684 GGCCACCATCGGC-ACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGGACCATCGACACCCTAGGC
66 GG-CACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGACACCCTAGGC
41111748 CCTTGGTCGTGCGAGA-CTCGGCCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGG
130 CCTTGGTCGTGCGAGAGCTCGG-CACCATCGG-AACCTAGGCCCTTGGTCGTGCGGGAGCCTCGG
* *
41111812 GCAACATCGGCAACCTAAG
193 GCACCATCGGCAACCTAGG
* *
41111831 CCTTTGGTCGTGCGAGAGCCTCGGGCACCATTGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTC
1 CC-TTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTC
* * *
41111896 -GAACACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCAGACACCATCGTA-A-CCTAG
65 AG-GCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCG-ACACCCTAG
* * * * *
41111958 GCCCCTGGTCGTGCGGGAGCTCGGACACCATCGGTAACTTAGGCCCCTGGTCGTGCGAGAGCCTC
128 GCCCTTGGTCGTGCGAGAGCTCGG-CACCATCGG-AACCTAGGCCCTTGGTCGTGCGGGAGCCTC
41112023 GGG-ACCATCGGCAACCTAGG
191 GGGCACCATCGGCAACCTAGG
* * * * *
41112043 CCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCCTAGGCCCCTAGTCGTGCGGGAGCCTC
1 -CCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTC
* *
41112108 AGGCACCATCGGCACCCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGGACCATCGACACCCTAGGC
65 AGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGACACCCTAGGC
* * *
41112173 CCTTGGTCGTGCGAGAGCCTCGGGACCATCGGCACCTAGGCCCTTGGTCGTGGGGGAGCCTCGGG
130 CCTTGGTCGTGCGAGAG-CTCGGCACCATCGGAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGG
*
41112238 CACCATCGGC-ACCTTGG
194 CACCATCGGCAACCTAGG
* * * *
41112255 TGCTTGGAT-GTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGCCGGAGCCT
1 -CCTTGG-TCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCT
* ** *
41112319 CAGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCCAGAGCCTCGGGCACCATCGGA-AACCTAG
64 CAGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATC-GACACCCTAG
*
41112383 GCCCTTGGTCGTGCGGGAGC
128 GCCCTTGGTCGTGCGAGAGC
41112403 CGTGCGGGAG
Statistics
Matches: 504, Mismatches: 55, Indels: 26
0.86 0.09 0.04
Matches are distributed among these distances:
211 4 0.01
212 367 0.73
213 127 0.25
214 6 0.01
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.17
Consensus pattern (211 bp):
CCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCA
GGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGACACCCTAGGCC
CTTGGTCGTGCGAGAGCTCGGCACCATCGGAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
CCATCGGCAACCTAGG
Found at i:41112077 original size:255 final size:256
Alignment explanation
Indices: 41111619--41112403 Score: 1069
Period size: 255 Copynumber: 3.1 Consensus size: 256
41111609 NNNNNNNNNN
* ** *
41111619 CCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAAATAGGCCCTTGGTCGTGCGGGGGCCTC
1 CCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTC
* * * *
41111684 GGCCACCATCGGCACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGGACCATCGACACCCTAGGCC
66 -GACACCATCGGCACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTTAGGCC
*
41111749 CTTGGTCGTGCGAGA--CTCGGCCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGG
130 CTTGGTCGTGCGAGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGG
* * * *
41111812 GCAACATCGGCAACCTAAGCCTTTGGTCGTGCGAGAGCCTCGGGCACCATTGGCAACCTAGG
195 GCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGG
** *
41111874 CCCTTGGTCGTGCGAGAGCCTCGAACACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTC
1 CCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTC
** * * *
41111939 AGACACCATCGTAACCTAGGCCCCTGGTCGTGCGGGAG-CTCGGACACCATCGGTAACTTAGGCC
66 -GACACCATCGGCACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTTAGGCC
* * *
41112003 CCTGGTCGTGCGAGAGCCTCGG-GACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGG
130 CTTGGTCGTGCGAGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGG
* * * * * *
41112067 GCACCATCGGCACCCTAGGCCCCTAGTCGTGCGGGAGCCTCAGGCACCATCGGCACCCTAGG
195 GCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGG
* * * * * *
41112129 CCCCTGGTCGTGCGGGAGCCTCGGGGACCATCGACACCCTAGGCCCTTGGTCGTGCGAGAGCCTC
1 CCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTC
** * * **
41112194 GGGACCATCGGCACCTAGGCCCTTGGTCGTGGGGGAGCCTCGGGCACCATCGGCACCTT-GGTGC
66 GACACCATCGGCACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTTAGGCCC
* * *
41112258 TTGGAT-GTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGCCGGAGCCTCAG
131 TTGG-TCGTGCGAGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGG
* *
41112322 GCACCATCGGCAACCTAGGCCCTTGGTCGTGCCAGAGCCTCGGGCACCATCGGAAACCTAGG
195 GCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGG
*
41112384 CCCTTGGTCGTGCGGGAGCC
1 CCCTTGGTCGTGCGAGAGCC
41112404 GTGCGGGAGC
Statistics
Matches: 460, Mismatches: 65, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
254 85 0.18
255 370 0.80
256 5 0.01
ACGTcount: A:0.16, C:0.35, G:0.33, T:0.17
Consensus pattern (256 bp):
CCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTC
GACACCATCGGCACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTTAGGCCC
TTGGTCGTGCGAGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGG
CACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCAACCTAGG
Found at i:41117676 original size:46 final size:46
Alignment explanation
Indices: 41117609--41117699 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
41117599 AGCCCGAATC
* *
41117609 AGGCAAAGAGTTTGTCATTTATAGTGATGCGTCCCTACTTGGGTTA
1 AGGCAAAGAGTTTGTCATTTATAGTGACGCATCCCTACTTGGGTTA
*
41117655 AGGCAAAGAGTTTGTCATTTATAGTGACGCATCCTTACTTGGGTT
1 AGGCAAAGAGTTTGTCATTTATAGTGACGCATCCCTACTTGGGTT
41117700 GGGTTACGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.35
Consensus pattern (46 bp):
AGGCAAAGAGTTTGTCATTTATAGTGACGCATCCCTACTTGGGTTA
Found at i:41119938 original size:74 final size:77
Alignment explanation
Indices: 41119850--41120017 Score: 243
Period size: 85 Copynumber: 2.1 Consensus size: 77
41119840 GGCCGGCCAT
41119850 GAGCATGGGTGGACAAGATGTTATGGCT-A-A-AAACATGTTGGGGTAGTGCATTATGTAAGGAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAATATAAACATGTTGGGGTAGTGCATTATGTAAGGAT
41119912 TAATAAAATAAA
66 TAATAAAATAAA
41119924 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCT----A-A--T-ATAAACATGTTGGGGTAGTGCATTAT
41119989 GTAAGGATTAATAAAATAAA
58 GTAAGGATTAATAAAATAAA
41120009 GAGCATGGG
1 GAGCATGGG
41120018 CAATAAAATA
Statistics
Matches: 83, Mismatches: 0, Indels: 11
0.88 0.00 0.12
Matches are distributed among these distances:
74 28 0.34
80 1 0.01
84 1 0.01
85 53 0.64
ACGTcount: A:0.38, C:0.08, G:0.29, T:0.26
Consensus pattern (77 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAATATAAACATGTTGGGGTAGTGCATTATGTAAGGAT
TAATAAAATAAA
Found at i:41121285 original size:39 final size:40
Alignment explanation
Indices: 41121184--41121368 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
41121174 TCGAATGATG
* * *
41121184 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
41121223 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
41121264 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGGTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
41121303 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * * *
41121342 AACCGGGCTATGTCCCAAAAGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41121369 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.29
40 77 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:41121320 original size:79 final size:80
Alignment explanation
Indices: 41121184--41121357 Score: 212
Period size: 79 Copynumber: 2.2 Consensus size: 80
41121174 TCGAATGATG
* * *
41121184 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTGGTGCGAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
41121249 GTGCGAGTTACTAAT
66 GTGCGAGTTACTAAT
* * **
41121264 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGGT-ACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTGGTGCGAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
41121326 TTGTGCGAGTTACT-AT
64 TTGTGCGAGTTACTAAT
* *
41121342 AACCGGGCTATGTCCC
1 -TCCGGGCTAAGTCCC
41121358 AAAAGCATTT
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
78 3 0.04
79 55 0.68
80 23 0.28
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTGGTGCGAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTAAT
Found at i:41121390 original size:79 final size:79
Alignment explanation
Indices: 41121237--41121401 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
41121227 GGACTAAGAT
* * * **
41121237 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGGTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAAGCATTGGAACGAGGTACTAA
*
41121302 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
41121316 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCAAAAGCATTTGAACGA-GTAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCAAAAGCATTGGAACGAGGTA-C
* *
41121379 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
41121395 CCGAAGG
1 CCGAAGG
41121402 TACGCTATTC
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 50 0.68
80 21 0.29
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAAGCATTGGAACGAGGTACTAA
ATCCGGGTTAAATC
Found at i:41125910 original size:20 final size:21
Alignment explanation
Indices: 41125871--41125911 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41125861 ACTTGTATAA
*
41125871 CTATCATCAAACCTTCAAAAT
1 CTATCATCAAACCATCAAAAT
*
41125892 CTATCAT-AAATCATCAAAAT
1 CTATCATCAAACCATCAAAAT
41125912 ACATTCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.29
Consensus pattern (21 bp):
CTATCATCAAACCATCAAAAT
Found at i:41133687 original size:90 final size:90
Alignment explanation
Indices: 41133552--41133729 Score: 223
Period size: 90 Copynumber: 2.0 Consensus size: 90
41133542 AATAAGATGC
* * * * * *
41133552 CAACGCCATATCTCAGATATGGTCTTACATGGGATCACCACTCGATGCCAATGCCATGTCCCAGA
1 CAACGCCATATCCCAGATATGGTCTTACATGAGATAAACAATCGATGCCAATGCCATATCCCAGA
*
41133617 CATGGTCTTACATGGGATCTCATAT
66 CATGGTCTTACACGGGATCTCATAT
* ** *
41133642 CAACGCTATATCCCAGATATGGTCTTACATGAGA-AAACATATCGATGCCGGTGTCATATCCCAG
1 CAACGCCATATCCCAGATATGGTCTTACATGAGATAAACA-ATCGATGCCAATGCCATATCCCAG
* *
41133706 ATATGGTCTTATACGGGATCTCAT
65 ACATGGTCTTACACGGGATCTCAT
41133730 TAACCCAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 3 0.04
90 71 0.96
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (90 bp):
CAACGCCATATCCCAGATATGGTCTTACATGAGATAAACAATCGATGCCAATGCCATATCCCAGA
CATGGTCTTACACGGGATCTCATAT
Found at i:41134435 original size:10 final size:10
Alignment explanation
Indices: 41134420--41134444 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41134410 TCAAGGATAT
41134420 AAAAAACATC
1 AAAAAACATC
41134430 AAAAAACATC
1 AAAAAACATC
41134440 AAAAA
1 AAAAA
41134445 CTATCACCAA
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:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAACATC
Found at i:41140331 original size:42 final size:44
Alignment explanation
Indices: 41140226--41140345 Score: 136
Period size: 48 Copynumber: 2.7 Consensus size: 44
41140216 TAATAAGATG
* *
41140226 CCAAAGCCATATCCCAAATATGGTCTTACATGGGATCACCACTCGATA
1 CCAACGCCATATCCCAAATATGGTCTTACACGGGAT---C-CTCGATA
* * *
41140274 CCAATGCCATGTCCCAAACATGGTCTTACACGGGAT-CTC-ATA
1 CCAACGCCATATCCCAAATATGGTCTTACACGGGATCCTCGATA
*
41140316 TCAACGCCATATCCCAAATATGGTCTTACA
1 CCAACGCCATATCCCAAATATGGTCTTACA
41140346 TGATAACACA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 29 0.45
43 3 0.05
48 32 0.50
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (44 bp):
CCAACGCCATATCCCAAATATGGTCTTACACGGGATCCTCGATA
Found at i:41140397 original size:90 final size:90
Alignment explanation
Indices: 41140231--41140404 Score: 217
Period size: 90 Copynumber: 1.9 Consensus size: 90
41140221 AGATGCCAAA
* * *
41140231 GCCATATCCCAAATATGGTCTTACATGGGATCACCACTCGATACCAATGCCATGTCCCAAACATG
1 GCCATATCCCAAATATGGTCTTACATGAGAACACCACTCGATACCAATGCCATATCCCAAACATG
41140296 GTCTTACACGGGATCTCATATCAAC
66 GTCTTACACGGGATCTCATATCAAC
* * * ** * *
41140321 GCCATATCCCAAATATGGTCTTACATGATAACACATACT-GATGCTGATGCCATATCCCAGATAT
1 GCCATATCCCAAATATGGTCTTACATGAGAACAC-CACTCGATACCAATGCCATATCCCAAACAT
*
41140385 GG-CTTTATACGGGATCTCAT
65 GGTC-TTACACGGGATCTCAT
41140405 TAACCCAAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
89 1 0.01
90 67 0.94
91 3 0.04
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (90 bp):
GCCATATCCCAAATATGGTCTTACATGAGAACACCACTCGATACCAATGCCATATCCCAAACATG
GTCTTACACGGGATCTCATATCAAC
Found at i:41143845 original size:30 final size:30
Alignment explanation
Indices: 41143811--41143871 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
41143801 CATTTAATAC
41143811 AAACTTTGGAAAAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
* * *
41143841 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
41143871 A
1 A
41143872 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCCCT
Found at i:41145877 original size:30 final size:29
Alignment explanation
Indices: 41145782--41146156 Score: 199
Period size: 29 Copynumber: 12.9 Consensus size: 29
41145772 ATGAGCTAAA
* *
41145782 CGATGGTCGTAACCGTCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
*
41145811 CGATGGTCGAAACCATCCATTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * * *
41145840 TGATGGTTGAAACCATCCCTTTTAATTAAT
1 CGATGGTCGAAACCATCCCTTTTCA-TATT
* ** *
41145870 CGATGGTTGCCACCATCCCTTTTCATGGTT
1 CGATGGTCGAAACCATCCCTTTTCAT-ATT
* **
41145900 C-ATGGTTGTCACCATCCCTTTTCATAGTT
1 CGATGGTCGAAACCATCCCTTTTCATA-TT
***
41145929 -GATGGTCTTCACCATCCCTTTTCAT-TAT
1 CGATGGTCGAAACCATCCCTTTTCATAT-T
* * * *
41145957 CGATTG-CCAAAGCTATCCTTTTTCAT-TAT
1 CGATGGTCGAAA-CCATCCCTTTTCATAT-T
* * * **
41145986 CGATAGCCGAAGCTGTCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * * * *
41146015 CAATAG-CCAAAGCTATCCCATTTCATATT
1 CGATGGTCGAAA-CCATCCCTTTTCATATT
* *
41146044 TGATGGTC-ATCACCATCCCTTTTCATAGTT
1 CGATGGTCGA-AACCATCCCTTTTCATA-TT
* ** *
41146074 -GATGGTTGTCACCATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * * * *
41146102 CAATAGCCGAAGCTATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * * *
41146131 CGATAGCCGAAGCTATCCCTTTTCAT
1 CGATGGTCGAAACCATCCCTTTTCAT
41146157 TGGTCGATAA
Statistics
Matches: 278, Mismatches: 53, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
27 1 0.00
28 7 0.03
29 236 0.85
30 34 0.12
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:41146039 original size:116 final size:115
Alignment explanation
Indices: 41145913--41146156 Score: 314
Period size: 116 Copynumber: 2.1 Consensus size: 115
41145903 GGTTGTCACC
* *
41145913 ATCCCTTTTCATAGTTGATGGTCTTCACCATCCCTTTTC-A-TT-ATCGATTGCCAAAGCTATCC
1 ATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCAAGTTGAT-GATTGCC--A-CCATCC
* * * *
41145975 TTTTTCATTATCGATAGCCGAAGCTGTCCCTTTTCATATTCAATAGCCAAAGCT
62 CTTTTCATAATCAATAGCCGAAGCTATCCCTTTTCATATTCAATAGCCAAAGCT
* * * *
41146029 ATCCCATTTCATATTTGATGGTCATCACCATCCCTTTTCATAGTTGATGGTTGTCACCATCCCTT
1 ATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCA-AGTTGATGATTGCCACCATCCCTT
* *
41146094 TTCATAATCAATAGCCGAAGCTATCCCTTTTCATATTCGATAGCCGAAGCT
65 TTCATAATCAATAGCCGAAGCTATCCCTTTTCATATTCAATAGCCAAAGCT
41146145 ATCCCTTTTCAT
1 ATCCCTTTTCAT
41146157 TGGTCGATAA
Statistics
Matches: 111, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
116 100 0.90
117 1 0.01
118 1 0.01
119 7 0.06
120 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (115 bp):
ATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCAAGTTGATGATTGCCACCATCCCTTT
TCATAATCAATAGCCGAAGCTATCCCTTTTCATATTCAATAGCCAAAGCT
Found at i:41157189 original size:33 final size:33
Alignment explanation
Indices: 41157147--41157215 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
41157137 GTTGATAAAG
*
41157147 TTTGGAAGAATTGTCCATTGATGTTTCGAGACA
1 TTTGGAAGAATTGTCCATTGATGTCTCGAGACA
41157180 TTTGGAAGAATTGTCCATTGATGTCTCGAGACA
1 TTTGGAAGAATTGTCCATTGATGTCTCGAGACA
41157213 TTT
1 TTT
41157216 ATTTTCCAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (33 bp):
TTTGGAAGAATTGTCCATTGATGTCTCGAGACA
Found at i:41162920 original size:93 final size:93
Alignment explanation
Indices: 41162793--41163613 Score: 1579
Period size: 93 Copynumber: 8.8 Consensus size: 93
41162783 CCCATAAGCA
* * *** * *
41162793 AACTCGGACTCAACTCAACAAGCTCGGGTGTTCGCATCCATAAGTGAAGTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
41162858 GAGTTCGGATGCCTAGTTACATTTCACG
66 GAGTTCGGATGCCTAGTTACATTTCACG
41162886 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
41162951 GAGTTCGGATGCCTAGTTACATTTCACG
66 GAGTTCGGATGCCTAGTTACATTTCACG
41162979 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
41163044 GAGTTCGGATGCCTAGTTACATTTCACG
66 GAGTTCGGATGCCTAGTTACATTTCACG
41163072 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
41163137 GAGTTCGGATGCCTAGTTACATTTCACG
66 GAGTTCGGATGCCTAGTTACATTTCACG
41163165 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
41163230 GAGTTCGGATGCCTAGTTACATTTCACG
66 GAGTTCGGATGCCTAGTTACATTTCACG
41163258 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
41163323 GAGTTCGGATGCCTAGTTACATTTCACG
66 GAGTTCGGATGCCTAGTTACATTTCACG
41163351 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
41163416 GAGTTCGGATGCCTAGTTACATTTCACG
66 GAGTTCGGATGCCTAGTTACATTTCACG
41163444 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
41163509 GAGTTCGGATGCCTAGTTACATTTCACG
66 GAGTTCGGATGCCTAGTTACATTTCACG
41163537 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
41163602 GAGTTCGGATGC
66 GAGTTCGGATGC
41163614 TCAACCATCC
Statistics
Matches: 721, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 721 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTTCACG
Found at i:41171147 original size:93 final size:93
Alignment explanation
Indices: 41171020--41171842 Score: 1601
Period size: 93 Copynumber: 8.8 Consensus size: 93
41171010 CGGCCATAAG
* * * * *
41171020 CGAACTCAGACTCAACTCAATGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
41171085 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
41171113 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
41171178 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
41171206 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
41171271 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
41171299 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
41171364 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
41171392 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
41171457 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
41171485 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
41171550 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
41171578 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
41171643 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
41171671 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
41171736 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
41171764 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
41171829 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
41171843 TCAACCATCC
Statistics
Matches: 725, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 725 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTAGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:41174180 original size:51 final size:48
Alignment explanation
Indices: 41174014--41174201 Score: 198
Period size: 51 Copynumber: 3.8 Consensus size: 48
41174004 GCCGAAGCTA
* * *
41174014 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-ACAG
*
41174063 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGGTGACCTCACCA-
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACAC-GTGA-C-CA-CAG
** * * *
41174114 TCTAATACACGTAGTAGCCTGCACTTTGTACTACACACGTGATCACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCACAG
* *
41174162 TTTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
41174202 TGCGGCCTCA
Statistics
Matches: 117, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
47 2 0.02
48 2 0.02
49 35 0.30
50 7 0.06
51 68 0.58
52 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (48 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCACAG
Found at i:41176414 original size:42 final size:42
Alignment explanation
Indices: 41176359--41176481 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 42
41176349 AACTTATGAT
*
41176359 TTTCGTGTAAGACCATGTCTGGGATGTTGGCATTGTACTTGA
1 TTTCATGTAAGACCATGTCTGGGATGTTGGCATTGTACTTGA
* * * ** *
41176401 TTTCCTGTAAGACCCTGTCTGAGATAG-TGGCATCAATATTTGA
1 TTTCATGTAAGACCATGTCTGGGAT-GTTGGCAT-TGTACTTGA
* * *
41176444 TTACATATAAGACCATGTCTGGGACGTTGGCATTGTAC
1 TTTCATGTAAGACCATGTCTGGGATGTTGGCATTGTAC
41176482 AAGCTTTCCG
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
42 31 0.49
43 32 0.51
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (42 bp):
TTTCATGTAAGACCATGTCTGGGATGTTGGCATTGTACTTGA
Found at i:41181529 original size:16 final size:16
Alignment explanation
Indices: 41181504--41181534 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41181494 CCAAAATATT
41181504 ACCACATTGCAATGCA
1 ACCACATTGCAATGCA
*
41181520 ACCACCTTGCAATGC
1 ACCACATTGCAATGC
41181535 TTCTTACAAA
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:0.32, C:0.35, G:0.13, T:0.19
Consensus pattern (16 bp):
ACCACATTGCAATGCA
Found at i:41186607 original size:48 final size:48
Alignment explanation
Indices: 41186543--41186873 Score: 274
Period size: 48 Copynumber: 6.9 Consensus size: 48
41186533 GGTTATGTGG
* *
41186543 GAGCCAGTGTAAGACCATGTTTGGAACACGGCATCGGTATTGTTATGA
1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGA
* * * * ***
41186591 GAGCTAGTGTAAGACCATGTCTAGG-ACATGGCAACGGCCTCAATAT-A
1 GAGCCAGTGTAAGACCATGT-TTGGAACATGGCATCGGCATTGTTATGA
* * ** **
41186638 CGAGCCAGTGAAAGACCATGTTTGGAGCATGGCATCAACATTGCCATGA
1 -GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGA
* * * * * *** *
41186687 GAGCTAGTGTAAGACCATGTTTGGGACATGGCAACGACCTCAATATGG
1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGA
41186735 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTAT-A
1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGA
* * * * * *
41186782 TGTGTCAGTGTAGGACCATGTCTGGGACATGGCATCGGCACTGATGTATGA
1 -GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTG-T-TATGA
* * * *
41186833 AAGCCAATGTAAGACCATGTTCAGG-ACATGGCATCGACATT
1 GAGCCAGTGTAAGACCATGTT-TGGAACATGGCATCGGCATT
41186874 TTACCCTTTT
Statistics
Matches: 217, Mismatches: 57, Indels: 16
0.75 0.20 0.06
Matches are distributed among these distances:
47 4 0.02
48 173 0.80
49 5 0.02
50 32 0.15
51 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGA
Found at i:41186776 original size:96 final size:96
Alignment explanation
Indices: 41186540--41186873 Score: 395
Period size: 96 Copynumber: 3.5 Consensus size: 96
41186530 TAGGGTTATG
* **
41186540 TGGGAGCCAGTGTAAGACCATGTTTGGAACACGGCATCGGTATTGTTATGAGAGCTAGTGTAAGA
1 TGGGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGTTATGAGAGCTAGTGTAAGA
*
41186605 CCATGTCTAGGACATGGCAACGGCCTCAATA
66 CCATGTCTGGGACATGGCAACGGCCTCAATA
** * * * **
41186636 TACGAGCCAGTGAAAGACCATGTTTGGAGCATGGCATCAACATTGCCATGAGAGCTAGTGTAAGA
1 TGGGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGTTATGAGAGCTAGTGTAAGA
* *
41186701 CCATGTTTGGGACATGGCAACGACCTCAATA
66 CCATGTCTGGGACATGGCAACGGCCTCAATA
* * *
41186732 TGGGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTAT-ATGTG-TCAGTGTAG
1 TGGGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGTTATGA-GAGCT-AGTGTAA
* * *
41186795 GACCATGTCTGGGACATGGCATCGGCACTGATGTA
64 GACCATGTCTGGGACATGGCAACGGC-CTCA-ATA
** * *
41186830 TGAAAGCCAATGTAAGACCATGTTCAGG-ACATGGCATCGACATT
1 TGGGAGCCAGTGTAAGACCATGTT-TGGAACATGGCATCGACATT
41186874 TTACCCTTTT
Statistics
Matches: 200, Mismatches: 33, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
95 2 0.01
96 155 0.77
97 3 0.01
98 38 0.19
99 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (96 bp):
TGGGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGTTATGAGAGCTAGTGTAAGA
CCATGTCTGGGACATGGCAACGGCCTCAATA
Found at i:41189535 original size:40 final size:40
Alignment explanation
Indices: 41189452--41189644 Score: 212
Period size: 40 Copynumber: 4.8 Consensus size: 40
41189442 TTGAATGATG
* * * * *
41189452 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTAAA
*
41189492 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTACTAAA
* * *
41189532 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
* *
41189572 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTA-AA
* * *
41189613 -CCGGGCTATGTCCTGAAGGCATTTGAACGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
41189645 AGCTATATCC
Statistics
Matches: 133, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 123 0.92
41 9 0.07
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
Found at i:41189651 original size:40 final size:40
Alignment explanation
Indices: 41189452--41189670 Score: 205
Period size: 40 Copynumber: 5.5 Consensus size: 40
41189442 TTGAATGATG
* * * * * *
41189452 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTAC-GAGTTACTAAA
**
41189492 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTACGAGTTACTAAA
* *
41189532 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
*
41189572 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTA-AA
* * * * *
41189613 -CCGGGCTATGTCCTGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTA-CTAAA
* *
41189652 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
41189671 TACGTGATTT
Statistics
Matches: 151, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
39 15 0.10
40 127 0.84
41 9 0.06
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
Found at i:41197400 original size:40 final size:40
Alignment explanation
Indices: 41197342--41197519 Score: 245
Period size: 40 Copynumber: 4.5 Consensus size: 40
41197332 TGGATGATAA
** * *
41197342 CCGGGCTAAGTCCCGAAGGCATTTACGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
41197382 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
41197422 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
41197462 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
41197502 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41197520 TACTTGGCTT
Statistics
Matches: 127, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
39 17 0.13
40 110 0.87
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:41205475 original size:40 final size:40
Alignment explanation
Indices: 41205381--41205565 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
41205371 TATTCGAATG
* *
41205381 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCGA-GTGACT
* * *
41205422 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCGAG-TGACT
* * *
41205462 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTGACT
*
41205502 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTG-GTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGC-GAGTGACT
*
41205542 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
41205566 CTTGTGCAAG
Statistics
Matches: 122, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
39 1 0.01
40 91 0.75
41 29 0.24
42 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTGACT
Found at i:41205549 original size:80 final size:81
Alignment explanation
Indices: 41205381--41205565 Score: 252
Period size: 80 Copynumber: 2.3 Consensus size: 81
41205371 TATTCGAATG
* * *
41205381 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
*
41205446 ATTCGTGCGAGTTGCT
66 ATTCATGCGAGTTGCT
* *
41205462 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GCGACTATATCCGGGCTAAG-TCCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGAT-CCGAAGG
*
41205525 CATTTATGCTG-G-TGACT
65 CATTCATGC-GAGTTG-CT
41205542 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
41205566 CTTGTGCAAG
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
79 3 0.03
80 58 0.62
81 33 0.35
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (81 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
ATTCATGCGAGTTGCT
Found at i:41210280 original size:40 final size:40
Alignment explanation
Indices: 41210236--41210459 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
41210226 AAGTGAATAT
* * * * **
41210236 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTGTTAA
41210276 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
41210316 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
41210356 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * **
41210396 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * *
41210435 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
41210460 TGAACGAGGA
Statistics
Matches: 171, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.20
40 136 0.80
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
Found at i:41210334 original size:80 final size:80
Alignment explanation
Indices: 41210197--41210459 Score: 318
Period size: 80 Copynumber: 3.3 Consensus size: 80
41210187 TTGAATGCTG
* * * * *
41210197 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAATATATCCGGATTAAGAT-CCGAAGGCC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCC
*
41210259 TTTGTGCGAGATACTAAA
63 TTTGTGCGAGTTACTAAA
* * *
41210277 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
**
41210342 GTGCGAGTTGTTAAA
66 GTGCGAGTTACTAAA
* * *
41210357 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGG-CATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
*
41210421 GTGTGAGTTACTAAA
66 GTGCGAGTTACTAAA
* *
41210436 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
41210460 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
79 35 0.22
80 116 0.73
81 8 0.05
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
GTGCGAGTTACTAAA
Found at i:41210411 original size:120 final size:120
Alignment explanation
Indices: 41210197--41210459 Score: 318
Period size: 120 Copynumber: 2.2 Consensus size: 120
41210187 TTGAATGCTG
* * *
41210197 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
* **
41210261 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
66 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * * *
41210317 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAG-TGAATAAATCCGGATTAAGAT-CCGAAGGCA
* ** * *
41210379 TTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
64 TTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
41210436 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
41210460 TGAACGAGGA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 34 0.28
120 80 0.66
121 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:41218230 original size:40 final size:39
Alignment explanation
Indices: 41218199--41218408 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
41218189 GGACTAAGAT
* *
41218199 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
41218239 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
41218279 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
41218319 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
41218359 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
41218398 CCGAAGGCATT
1 CCGAAGGCATT
41218409 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:41218362 original size:120 final size:120
Alignment explanation
Indices: 41218146--41218408 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
41218136 TTGAATGCTG
* *
41218146 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
41218210 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
41218266 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
41218329 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
41218385 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
41218409 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:41218428 original size:79 final size:80
Alignment explanation
Indices: 41218147--41218443 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
41218137 TGAATGCTGT
* ** * * * **
41218147 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
41218210 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
41218227 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
41218291 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
41218307 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
41218371 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
41218386 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
41218444 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:41224920 original size:19 final size:19
Alignment explanation
Indices: 41224896--41224934 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
41224886 GCTATAAAAC
*
41224896 TTAGTAAGCTCGTATGAAA
1 TTAGTAAGCTCATATGAAA
41224915 TTAGTAAGCTCATATGAAA
1 TTAGTAAGCTCATATGAAA
41224934 T
1 T
41224935 AATAATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (19 bp):
TTAGTAAGCTCATATGAAA
Found at i:41229864 original size:43 final size:43
Alignment explanation
Indices: 41229803--41229909 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 43
41229793 TCGATGTTAC
* * *
41229803 TGTCCCAGACAG-GGTCTTACACGAAATC-GATTAACGATACCAA
1 TGTCCCAGAC-GTGGTCTTACACGAAATCTCAAT-ACAATACCAA
* * *
41229846 TGTCCCAGACGTGGTCTTACATGTAATCTCAATACAATGCCAA
1 TGTCCCAGACGTGGTCTTACACGAAATCTCAATACAATACCAA
*
41229889 TGTCCCAGACATGGTCTTACA
1 TGTCCCAGACGTGGTCTTACA
41229910 TGTAATCACA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.02
43 52 0.95
44 2 0.04
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
TGTCCCAGACGTGGTCTTACACGAAATCTCAATACAATACCAA
Found at i:41232768 original size:31 final size:31
Alignment explanation
Indices: 41232725--41232785 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
41232715 AATAATAAAA
*
41232725 TAAAAGGTTGGTAATAAAGTAATGAAAAGGT
1 TAAAAGGCTGGTAATAAAGTAATGAAAAGGT
41232756 TAAAAGGCTGGTAATAAAGTAATGAAAAGG
1 TAAAAGGCTGGTAATAAAGTAATGAAAAGG
41232786 GAGGGGTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.49, C:0.02, G:0.26, T:0.23
Consensus pattern (31 bp):
TAAAAGGCTGGTAATAAAGTAATGAAAAGGT
Found at i:41233360 original size:40 final size:40
Alignment explanation
Indices: 41233278--41233363 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
41233268 TATTCAGATG
* *
41233278 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTCATGCGAGTGACT
**
41233318 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTCATGCGAG-TGACT
41233358 ATATCC
1 ATATCC
41233364 TTCTAAATCC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 39 0.95
41 2 0.05
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCATGCGAGTGACT
Found at i:41239717 original size:305 final size:305
Alignment explanation
Indices: 41239160--41239770 Score: 841
Period size: 305 Copynumber: 2.0 Consensus size: 305
41239150 GAGTCCGAGG
*
41239160 TTCATAGGGCCGTATGAAATATCCGAACGAGTTGGCCTAGTGGCATATAGATTGATTTTACCCCC
1 TTCATAGGGCCGTACGAAATATCCGAACGAGTTGGCCTAGTGGCATATAGATTGATTTTACCCCC
* * * * *
41239225 TGACCTCGAGAAGATTCACAACGTTTTTCATGTCTCAATGCTTCAACGTTACAGATCTGATCCTT
66 GGACCTCGAAAAGATTCACAACGTCTTTCATGTCTCAATGCTTCAACGCTACAGATCTGATCCAT
* * * * * *
41239290 CGCACATAATAAATCCCTCCGAGGTTGAAATTCAAGCCGATATGAGTTATGAAGAAAAACTGATT
131 CGCACATAATAAAGCCCTCAGAGGTTGAAATTCAAGCCGACATGAGCTATGAAGAAAAACCGATG
* * * *
41239355 TGCATCCTAGCTCGTGAACTGAAAGAGTTGCGAAACAAGAGGGTTCCGTTAGTAAAGGTGTTATG
196 CGCATCCTAGCTCGTGAACTGAAAGAGTTGCGAAACAAAAGAGTTCCGCTAGTAAAGGTGTTATG
41239420 GCTCAAACACGGGATCGAAGAAGCTACTTGGGAAACCGAGAACTC
261 GCTCAAACACGGGATCGAAGAAGCTACTTGGGAAACCGAGAACTC
* * * * * *
41239465 TTCATTGGGCCGTACGAAATCTCCGAACGAGTTGGTCC-GGTTGCGTATAGATTGATTTTGCCCC
1 TTCATAGGGCCGTACGAAATATCCGAACGAGTTGG-CCTAGTGGCATATAGATTGATTTTACCCC
* * ** * * *
41239529 CGGAGCTTGAAAAGATTCATGACGTCTTTCATGTTTCGATGCTTCGACGCTATC-GATCTGATCC
65 CGGACCTCGAAAAGATTCACAACGTCTTTCATGTCTCAATGCTTCAACGCTA-CAGATCTGATCC
* * *
41239593 ATCGCACATAAT-TAGCCCATCAGAGGTTGAAATTCAAGTCGACATGAGCTATGAAGAAGAACCG
129 ATCGCACATAATAAAGCCC-TCAGAGGTTGAAATTCAAGCCGACATGAGCTATGAAGAAAAACCG
* * *
41239657 ATGCGTATCCTAGCTCGTGAAGTGAAGGAGTTGCGAAACAAAAGAGTTCCGCTAGTAAAGGTGTT
193 ATGCGCATCCTAGCTCGTGAACTGAAAGAGTTGCGAAACAAAAGAGTTCCGCTAGTAAAGGTGTT
* *
41239722 ATGGCTCAAACACGGGATCGAGGAAGCTACTTGGGAGACCGAGAACTC
258 ATGGCTCAAACACGGGATCGAAGAAGCTACTTGGGAAACCGAGAACTC
41239770 T
1 T
41239771 ATGAAAGAAC
Statistics
Matches: 266, Mismatches: 37, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
304 4 0.02
305 259 0.97
306 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (305 bp):
TTCATAGGGCCGTACGAAATATCCGAACGAGTTGGCCTAGTGGCATATAGATTGATTTTACCCCC
GGACCTCGAAAAGATTCACAACGTCTTTCATGTCTCAATGCTTCAACGCTACAGATCTGATCCAT
CGCACATAATAAAGCCCTCAGAGGTTGAAATTCAAGCCGACATGAGCTATGAAGAAAAACCGATG
CGCATCCTAGCTCGTGAACTGAAAGAGTTGCGAAACAAAAGAGTTCCGCTAGTAAAGGTGTTATG
GCTCAAACACGGGATCGAAGAAGCTACTTGGGAAACCGAGAACTC
Found at i:41240773 original size:40 final size:40
Alignment explanation
Indices: 41240714--41240805 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
41240704 TATTCAGATG
* *
41240714 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAG-TGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTCATGCGAGTTG-CT
**
41240754 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTCATGCGAGTTGCT
41240794 ATATCC-GGCTAA
1 ATATCCGGGCTAA
41240806 ATCCCAAAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
39 6 0.13
40 39 0.83
41 2 0.04
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCATGCGAGTTGCT
Found at i:41251737 original size:66 final size:66
Alignment explanation
Indices: 41251659--41251791 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
41251649 AATGGGAAAA
*
41251659 AATCCCGATTGAATGAAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAAGGATC
1 AATCCCGATTGAATGAAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGGAAAAAGGATC
41251724 T
66 T
* * * *
41251725 AATCCCGGTTGAATGAAATGAAAATTTGTTGGATCTCTGAAAAGGAATTGACGGGAAAAAGGATC
1 AATCCCGATTGAATGAAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGGAAAAAGGATC
41251790 T
66 T
41251791 A
1 A
41251792 GCCCGGACGG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (66 bp):
AATCCCGATTGAATGAAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGGAAAAAGGATC
T
Found at i:41257196 original size:73 final size:73
Alignment explanation
Indices: 41257109--41257255 Score: 231
Period size: 73 Copynumber: 2.0 Consensus size: 73
41257099 TAAGAGTCTA
*
41257109 ATGAGAAAAAATTTAAAAGGAAATTAGACCCAAAATTTACTTGGGCTGGACCGCAAGGGCATGAA
1 ATGAGAAAAAATTTAAAAGGAAATTAGACCCAAAAGTTACTTGGGCTGGACCGCAAGGGCATGAA
41257174 ATCAGCAG
66 ATCAGCAG
** * * * *
41257182 ATGAGAAAGGATTTAAAAGGCAATTAGACCCAAAAGTTATTTGGGCTGGACGGCAAGGGTATGAA
1 ATGAGAAAAAATTTAAAAGGAAATTAGACCCAAAAGTTACTTGGGCTGGACCGCAAGGGCATGAA
41257247 ATCAGCAG
66 ATCAGCAG
41257255 A
1 A
41257256 AAAATTGATA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.20
Consensus pattern (73 bp):
ATGAGAAAAAATTTAAAAGGAAATTAGACCCAAAAGTTACTTGGGCTGGACCGCAAGGGCATGAA
ATCAGCAG
Found at i:41257273 original size:20 final size:20
Alignment explanation
Indices: 41257245--41257289 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
41257235 CAAGGGTATG
*
41257245 AAATCAGCAGAAAAATTGAT
1 AAATTAGCAGAAAAATTGAT
*
41257265 AAATTAGCAGGAAAATTGAT
1 AAATTAGCAGAAAAATTGAT
41257285 AAATT
1 AAATT
41257290 GCAAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.24
Consensus pattern (20 bp):
AAATTAGCAGAAAAATTGAT
Found at i:41261273 original size:47 final size:48
Alignment explanation
Indices: 41261199--41261370 Score: 164
Period size: 46 Copynumber: 3.7 Consensus size: 48
41261189 TCACTTGTGT
* *
41261199 GAGCTAGTGTAAGACATGTCTGAGACATGCATCAGCCACATT-A-TGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGAGCGA
* *
41261245 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-G--GCATTGAGCGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCACATTGAGCGA
* * *
41261292 GTGCTAGTGTAAGACATGTCTGGGACAGGCATCAG-C-C-TCGAGACGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGAG-CG-A
* *
41261339 -AGCTAGTGTAATATATGTCTGGGACATGCATC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATC
41261371 GGCTACGTAA
Statistics
Matches: 106, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
45 13 0.12
46 59 0.56
47 29 0.27
48 5 0.05
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (48 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGAGCGA
Found at i:41262128 original size:22 final size:22
Alignment explanation
Indices: 41262098--41262146 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
41262088 GGTTGTGTAA
* *
41262098 GTAATGGTGGCAAAGAGGCTTT
1 GTAAAGGTGGCAAAGAGGCTTG
*
41262120 GTAAAGGTGGCAAAGAGTCTTG
1 GTAAAGGTGGCAAAGAGGCTTG
41262142 GTAAA
1 GTAAA
41262147 TAGCCTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.35, T:0.24
Consensus pattern (22 bp):
GTAAAGGTGGCAAAGAGGCTTG
Found at i:41262638 original size:20 final size:21
Alignment explanation
Indices: 41262600--41262638 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41262590 CTGAAATGGC
*
41262600 CACACGGGCGTGTTGCCCTTG
1 CACACGGACGTGTTGCCCTTG
41262621 CACACGGACGTG-TGCCCT
1 CACACGGACGTGTTGCCCT
41262639 GTCTCAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.13, C:0.36, G:0.31, T:0.21
Consensus pattern (21 bp):
CACACGGACGTGTTGCCCTTG
Found at i:41269939 original size:35 final size:35
Alignment explanation
Indices: 41269888--41269959 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
41269878 AACATCAGAT
* *
41269888 CAGCAGGAAAATAGATATCTCGAATCAATAACGGG
1 CAGCAGGAAAACAGATATCTCAAATCAATAACGGG
*
41269923 CAGCAGGAAAGCAGATATCTCAAATCAATAACGGG
1 CAGCAGGAAAACAGATATCTCAAATCAATAACGGG
41269958 CA
1 CA
41269960 ATTTTTGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.15
Consensus pattern (35 bp):
CAGCAGGAAAACAGATATCTCAAATCAATAACGGG
Found at i:41290975 original size:27 final size:27
Alignment explanation
Indices: 41290945--41291007 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
41290935 TTTATTCAGT
41290945 AAACCAACTGGCAAACAGCAACTTGCC
1 AAACCAACTGGCAAACAGCAACTTGCC
* * * * *
41290972 AAACCAATTGGCGAACTGCAGCTTTCC
1 AAACCAACTGGCAAACAGCAACTTGCC
41290999 AAACCAACT
1 AAACCAACT
41291008 AGTGAACCAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.16
Consensus pattern (27 bp):
AAACCAACTGGCAAACAGCAACTTGCC
Found at i:41293919 original size:17 final size:17
Alignment explanation
Indices: 41293899--41293937 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
41293889 TCACCAGACA
*
41293899 ATACTGTCCACCATGTG
1 ATACTGTCCACCAGGTG
* *
41293916 ATACAGTTCACCAGGTG
1 ATACTGTCCACCAGGTG
41293933 ATACT
1 ATACT
41293938 ATCCGCTAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (17 bp):
ATACTGTCCACCAGGTG
Found at i:41297883 original size:26 final size:26
Alignment explanation
Indices: 41297854--41297906 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
41297844 TCCAACATGC
41297854 ATTTAGGTCAATTTA-CTCCTAGAGGT
1 ATTTAGGT-AATTTATCTCCTAGAGGT
* * *
41297880 ATTTCGGTACTTTATCTCCTAGGGGT
1 ATTTAGGTAATTTATCTCCTAGAGGT
41297906 A
1 A
41297907 AAACTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (26 bp):
ATTTAGGTAATTTATCTCCTAGAGGT
Found at i:41298816 original size:24 final size:24
Alignment explanation
Indices: 41298782--41298881 Score: 132
Period size: 24 Copynumber: 4.2 Consensus size: 24
41298772 CCAACTCCTG
* *
41298782 CTCCTTGATCAGCTCCGAAATCTT
1 CTCCTTTATCAGCTCCTAAATCTT
*
41298806 CTCCTTTATCAGCTCCTAAATCCT
1 CTCCTTTATCAGCTCCTAAATCTT
*
41298830 CTCCCTTATCAGCTCCTAAA-CTCT
1 CTCCTTTATCAGCTCCTAAATCT-T
*
41298854 CTCCCTTATCAGCT-CTAAATCTT
1 CTCCTTTATCAGCTCCTAAATCTT
41298877 CTCCT
1 CTCCT
41298882 GACAACCTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
23 11 0.16
24 57 0.84
ACGTcount: A:0.20, C:0.38, G:0.06, T:0.36
Consensus pattern (24 bp):
CTCCTTTATCAGCTCCTAAATCTT
Found at i:41305438 original size:26 final size:26
Alignment explanation
Indices: 41305409--41305461 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
41305399 TCTAACATGC
41305409 ATTTAGGTCAATTTA-CTCCTAGGGGT
1 ATTTAGGT-AATTTATCTCCTAGGGGT
* *
41305435 ATTTCGGTACTTTATCTCCTAGGGGT
1 ATTTAGGTAATTTATCTCCTAGGGGT
41305461 A
1 A
41305462 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTTAGGTAATTTATCTCCTAGGGGT
Found at i:41306744 original size:24 final size:24
Alignment explanation
Indices: 41306710--41306810 Score: 125
Period size: 24 Copynumber: 4.2 Consensus size: 24
41306700 CCAACTCCTG
*
41306710 CTCCTTGATCAGCT-CTGAAATCTT
1 CTCCTTTATCAGCTCCT-AAATCTT
*
41306734 CTCCTTTATCAGCTCCTAAATCCT
1 CTCCTTTATCAGCTCCTAAATCTT
*
41306758 CTCCCTTATCAGCTCCTAAA-CTCT
1 CTCCTTTATCAGCTCCTAAATCT-T
* *
41306782 CTCCCTTATCAACTCCTAAATCTT
1 CTCCTTTATCAGCTCCTAAATCTT
41306806 CTCCT
1 CTCCT
41306811 GACAGCCTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.01
24 63 0.93
25 4 0.06
ACGTcount: A:0.21, C:0.38, G:0.05, T:0.37
Consensus pattern (24 bp):
CTCCTTTATCAGCTCCTAAATCTT
Found at i:41312970 original size:27 final size:28
Alignment explanation
Indices: 41312886--41312983 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
41312876 CATGAGATTG
* * * *
41312886 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
41312915 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
41312943 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
41312970 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
41312984 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:41312994 original size:27 final size:27
Alignment explanation
Indices: 41312914--41312996 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
41312904 TAAATTGTAC
* *
41312914 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
41312942 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
41312969 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
41312996 A
1 A
41312997 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:41312997 original size:29 final size:27
Alignment explanation
Indices: 41312886--41312997 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
41312876 CATGAGATTG
** * *
41312886 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
41312915 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
41312943 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
41312970 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
41312998 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:41317778 original size:28 final size:28
Alignment explanation
Indices: 41317745--41317801 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41317735 TTCCCTTATG
41317745 CTTCTTCTGTTAGCCGAAACCTTCTGAT
1 CTTCTTCTGTTAGCCGAAACCTTCTGAT
41317773 CTTCTTCTGTTAGCCGAAACCTTCTGAT
1 CTTCTTCTGTTAGCCGAAACCTTCTGAT
41317801 C
1 C
41317802 ACCCTACTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.39
Consensus pattern (28 bp):
CTTCTTCTGTTAGCCGAAACCTTCTGAT
Found at i:41323497 original size:47 final size:47
Alignment explanation
Indices: 41323427--41323585 Score: 228
Period size: 47 Copynumber: 3.4 Consensus size: 47
41323417 GGTGTACAAG
* *
41323427 GTGTGTATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGGATGTGAAA
* * * **
41323474 GTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGATG
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGGATGTGAAA
* *
41323521 GTGTCTATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGGATGTGAAA
*
41323568 GTGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
41323586 TCCCGAAGGG
Statistics
Matches: 96, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 96 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGGATGTGAAA
Found at i:41330424 original size:41 final size:39
Alignment explanation
Indices: 41330390--41330543 Score: 116
Period size: 38 Copynumber: 3.9 Consensus size: 39
41330380 GAATCCAGTC
*
41330390 ACCAGCACAAAACCTGCGGGACTTTAAGCTCGAATATAAT
1 ACCAGCACAAAACCTGCGGGA-TTTAAGCTCGAATACAAT
* * * *
41330430 ACCAGCACTAAGCCTGCGGGATTTAA-C-CCAGATATAAT
1 ACCAGCACAAAACCTGCGGGATTTAAGCTCGA-ATACAAT
* * * * * *
41330468 ACCGGCACGAAGCCTGCGGGATTTAA-CCCGGATATAAT
1 ACCAGCACAAAACCTGCGGGATTTAAGCTCGAATACAAT
* * * * *
41330506 ACCAGCACATAGCCTGCGGGTCTTTAAGCCCGGATACA
1 ACCAGCACAAAACCTGCGGG-ATTTAAGCTCGAATACA
41330544 CATCAAATAT
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
37 2 0.02
38 57 0.58
39 11 0.11
40 28 0.29
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.19
Consensus pattern (39 bp):
ACCAGCACAAAACCTGCGGGATTTAAGCTCGAATACAAT
Found at i:41330481 original size:38 final size:37
Alignment explanation
Indices: 41330390--41330525 Score: 166
Period size: 38 Copynumber: 3.5 Consensus size: 37
41330380 GAATCCAGTC
* *
41330390 ACCAGCACAAAACCTGCGGGACTTTAAGCTC-GAATATAAT
1 ACCAGCAC-AAGCCTGCGGGA-TTTAA-CCCAG-ATATAAT
41330430 ACCAGCACTAAGCCTGCGGGATTTAACCCAGATATAAT
1 ACCAGCAC-AAGCCTGCGGGATTTAACCCAGATATAAT
* *
41330468 ACCGGCACGAAGCCTGCGGGATTTAACCCGGATATAAT
1 ACCAGCAC-AAGCCTGCGGGATTTAACCCAGATATAAT
41330506 ACCAGCACATAGCCTGCGGG
1 ACCAGCACA-AGCCTGCGGG
41330526 TCTTTAAGCC
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
37 1 0.01
38 61 0.70
39 6 0.07
40 19 0.22
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.18
Consensus pattern (37 bp):
ACCAGCACAAGCCTGCGGGATTTAACCCAGATATAAT
Found at i:41340583 original size:40 final size:40
Alignment explanation
Indices: 41340485--41341587 Score: 2005
Period size: 40 Copynumber: 27.6 Consensus size: 40
41340475 TCCTCGTTCA
* * * * *
41340485 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41340524 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41340564 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41340604 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41340644 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41340684 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41340724 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41340764 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41340804 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41340844 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41340884 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41340924 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41340964 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341004 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341044 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341084 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341124 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341164 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341204 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341244 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341284 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341324 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341364 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341404 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41341444 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41341484 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
41341524 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
41341564 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41341588 CAGCATTCAA
Statistics
Matches: 1040, Mismatches: 20, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
39 37 0.04
40 995 0.96
41 8 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41347908 original size:14 final size:13
Alignment explanation
Indices: 41347863--41347913 Score: 75
Period size: 13 Copynumber: 3.7 Consensus size: 13
41347853 ATGCAATTTT
41347863 TTTTTTCTTTTCAA
1 TTTTTT-TTTTCAA
41347877 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
41347890 TTTTTTTTTTCAAA
1 TTTTTTTTTTC-AA
41347904 CTTTTTTTTT
1 -TTTTTTTTT
41347914 ACGTACCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
13 18 0.51
14 8 0.23
15 9 0.26
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:41348242 original size:22 final size:22
Alignment explanation
Indices: 41348212--41348255 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41348202 TTTGGTATTT
41348212 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
41348234 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
41348256 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:41349090 original size:31 final size:30
Alignment explanation
Indices: 41349053--41349111 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
41349043 CATGCACCAA
* *
41349053 GCTAAATGAATCTCCACATTCGGCTCACCTT
1 GCTAAATGAACCCCCACATTCGGC-CACCTT
41349084 GCTAAATGAACCCCCACATTCGGCCACC
1 GCTAAATGAACCCCCACATTCGGCCACC
41349112 CTACAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.27, C:0.37, G:0.14, T:0.22
Consensus pattern (30 bp):
GCTAAATGAACCCCCACATTCGGCCACCTT
Found at i:41354575 original size:55 final size:55
Alignment explanation
Indices: 41354509--41354619 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
41354499 AAGGTCTTGA
*
41354509 GTGATAGTGTGATCAAAGCTTTTGATGTCACTAGATTCC-CAATGCTAGCTTGGCG
1 GTGATAGTGTGATCAAAGCTTTTGATGTCACCAGA-TCCTCAATGCTAGCTTGGCG
* *
41354564 GTGATAGTGTGATCGAAGCTTTTGATGTCACCAGATCCTCGATGCTAGCTTGGCG
1 GTGATAGTGTGATCAAAGCTTTTGATGTCACCAGATCCTCAATGCTAGCTTGGCG
41354619 G
1 G
41354620 CACTATAAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 3 0.06
55 49 0.94
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.32
Consensus pattern (55 bp):
GTGATAGTGTGATCAAAGCTTTTGATGTCACCAGATCCTCAATGCTAGCTTGGCG
Found at i:41358840 original size:21 final size:21
Alignment explanation
Indices: 41358816--41358877 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
41358806 ATACCGGACT
41358816 TAATCTCAATCTCTGACAGGC
1 TAATCTCAATCTCTGACAGGC
* *
41358837 TAATCAC-A--TGTGA-A-G-
1 TAATCTCAATCTCTGACAGGC
*
41358852 AAATCTCAATCTCTGACAGGC
1 TAATCTCAATCTCTGACAGGC
41358873 TAATC
1 TAATC
41358878 ACATGTGAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 12
0.62 0.13 0.26
Matches are distributed among these distances:
15 5 0.17
16 2 0.07
17 1 0.03
18 8 0.28
19 1 0.03
20 2 0.07
21 10 0.34
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (21 bp):
TAATCTCAATCTCTGACAGGC
Found at i:41358864 original size:36 final size:36
Alignment explanation
Indices: 41358817--41358887 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
41358807 TACCGGACTT
41358817 AATCTCAATCTCTGACAGGCTAATCACATGTGAAGA
1 AATCTCAATCTCTGACAGGCTAATCACATGTGAAGA
41358853 AATCTCAATCTCTGACAGGCTAATCACATGTGAAG
1 AATCTCAATCTCTGACAGGCTAATCACATGTGAAG
41358888 GATCAGATCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (36 bp):
AATCTCAATCTCTGACAGGCTAATCACATGTGAAGA
Found at i:41373735 original size:40 final size:43
Alignment explanation
Indices: 41373691--41373794 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 43
41373681 GTTATAAATA
* *
41373691 GCACTAAGTGTGTGAAATGGA-ATAGCTTCAGCTATAT-GA-G
1 GCACTAAGTGTGTGAAATCGAGATAACTTCAGCTATATAGATG
* * * *
41373731 GCACTAAGTGTGCGATATCGAGATAACTTCAGTTATTTGAGATG
1 GCACTAAGTGTGTGAAATCGAGATAACTTCAGCTATAT-AGATG
*
41373775 GCACTAAGTGTGTGGAATCG
1 GCACTAAGTGTGTGAAATCG
41373795 TTCTAGCTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
40 18 0.35
41 13 0.25
43 2 0.04
44 18 0.35
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (43 bp):
GCACTAAGTGTGTGAAATCGAGATAACTTCAGCTATATAGATG
Found at i:41398724 original size:46 final size:46
Alignment explanation
Indices: 41398623--41398710 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
41398613 TGTAACCCGC
* * * *
41398623 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
* *
41398669 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTC
41398711 AACCATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:41410155 original size:93 final size:93
Alignment explanation
Indices: 41410041--41410212 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
41410031 CGCCCATAAG
* *
41410041 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
41410106 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
41410134 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
41410199 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
41410213 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:41410209 original size:46 final size:46
Alignment explanation
Indices: 41410034--41410209 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
41410024 TGTAACCCGC
* * * *
41410034 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
41410080 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
41410130 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
41410173 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
41410210 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:41410228 original size:46 final size:46
Alignment explanation
Indices: 41410083--41410221 Score: 144
Period size: 47 Copynumber: 3.0 Consensus size: 46
41410073 TTCGCATCCA
41410083 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * *
41410131 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
41410176 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
41410222 CTAGTGACAT
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 28 0.37
47 30 0.40
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:41416349 original size:659 final size:659
Alignment explanation
Indices: 41415091--41416406 Score: 2632
Period size: 659 Copynumber: 2.0 Consensus size: 659
41415081 TATGTCTCTT
41415091 TAAATGAGAGGTCCTTATGATGCAAATGGACCATTGGTTTAATGAATGGACAAGTATTGTGTAAC
1 TAAATGAGAGGTCCTTATGATGCAAATGGACCATTGGTTTAATGAATGGACAAGTATTGTGTAAC
41415156 GCCCCGTACCCAAGACCGTCGCCGGAGTCGAACACGAGGTGTTAACGGACTTAATTCATTAATTA
66 GCCCCGTACCCAAGACCGTCGCCGGAGTCGAACACGAGGTGTTAACGGACTTAATTCATTAATTA
41415221 AACAACTTAAACAACTTATTACCAACCATGCATATGCACATCACCAATATCAAACATAACATAAA
131 AACAACTTAAACAACTTATTACCAACCATGCATATGCACATCACCAATATCAAACATAACATAAA
41415286 TAGCCAGATTTATAAGTCAAAATCATTAGCTCACTAAAGACCAATATATTTGGCCAAATTATAAT
196 TAGCCAGATTTATAAGTCAAAATCATTAGCTCACTAAAGACCAATATATTTGGCCAAATTATAAT
41415351 AATACATGTTATAAAACTAGGTCCTTATACGTGCCACTCACTTGATAATTCTAGCATATGTGTTT
261 AATACATGTTATAAAACTAGGTCCTTATACGTGCCACTCACTTGATAATTCTAGCATATGTGTTT
41415416 ATACTGTCAAGGTGTTGGCTTGATAGTGTGATGCTGCCTCCGACGATCTCCAACCCTGAGCTAAC
326 ATACTGTCAAGGTGTTGGCTTGATAGTGTGATGCTGCCTCCGACGATCTCCAACCCTGAGCTAAC
41415481 CTAACAACACTAAAAGAAATGGAAAGGAGGGGGTAAGCTTTATGCTTAGGAAGCTCACATGAAAT
391 CTAACAACACTAAAAGAAATGGAAAGGAGGGGGTAAGCTTTATGCTTAGGAAGCTCACATGAAAT
41415546 AATAATAAGCAATTTACTAACATGCTTTCCACAGTAAAACTAACCCAATTGTACATTTACACATG
456 AATAATAAGCAATTTACTAACATGCTTTCCACAGTAAAACTAACCCAATTGTACATTTACACATG
41415611 TTCTGGTTAAGCTGCTTTCTTGAGTAACAATCACTAAATCATTTATATCTAGAGTTAAGGAACTC
521 TTCTGGTTAAGCTGCTTTCTTGAGTAACAATCACTAAATCATTTATATCTAGAGTTAAGGAACTC
41415676 GAAATTAAGATCTGTAAATTTTCCCAGAAACTAGACTCATATATATTTCCACCATAAAATTTTCA
586 GAAATTAAGATCTGTAAATTTTCCCAGAAACTAGACTCATATATATTTCCACCATAAAATTTTCA
41415741 TAATTTTAA
651 TAATTTTAA
41415750 TAAATGAGAGGTCCTTATGATGCAAATGGACCATTGGTTTAATGAATGGACAAGTATTGTGTAAC
1 TAAATGAGAGGTCCTTATGATGCAAATGGACCATTGGTTTAATGAATGGACAAGTATTGTGTAAC
41415815 GCCCCGTACCCAAGACCGTCGCCGGAGTCGAACACGAGGTGTTAACGGACTTAATTCATTAATTA
66 GCCCCGTACCCAAGACCGTCGCCGGAGTCGAACACGAGGTGTTAACGGACTTAATTCATTAATTA
41415880 AACAACTTAAACAACTTATTACCAACCATGCATATGCACATCACCAATATCAAACATAACATAAA
131 AACAACTTAAACAACTTATTACCAACCATGCATATGCACATCACCAATATCAAACATAACATAAA
41415945 TAGCCAGATTTATAAGTCAAAATCATTAGCTCACTAAAGACCAATATATTTGGCCAAATTATAAT
196 TAGCCAGATTTATAAGTCAAAATCATTAGCTCACTAAAGACCAATATATTTGGCCAAATTATAAT
41416010 AATACATGTTATAAAACTAGGTCCTTATACGTGCCACTCACTTGATAATTCTAGCATATGTGTTT
261 AATACATGTTATAAAACTAGGTCCTTATACGTGCCACTCACTTGATAATTCTAGCATATGTGTTT
41416075 ATACTGTCAAGGTGTTGGCTTGATAGTGTGATGCTGCCTCCGACGATCTCCAACCCTGAGCTAAC
326 ATACTGTCAAGGTGTTGGCTTGATAGTGTGATGCTGCCTCCGACGATCTCCAACCCTGAGCTAAC
41416140 CTAACAACACTAAAAGAAATGGAAAGGAGGGGGTAAGCTTTATGCTTAGGAAGCTCACATGAAAT
391 CTAACAACACTAAAAGAAATGGAAAGGAGGGGGTAAGCTTTATGCTTAGGAAGCTCACATGAAAT
41416205 AATAATAAGCAATTTACTAACATGCTTTCCACAGTAAAACTAACCCAATTGTACATTTACACATG
456 AATAATAAGCAATTTACTAACATGCTTTCCACAGTAAAACTAACCCAATTGTACATTTACACATG
41416270 TTCTGGTTAAGCTGCTTTCTTGAGTAACAATCACTAAATCATTTATATCTAGAGTTAAGGAACTC
521 TTCTGGTTAAGCTGCTTTCTTGAGTAACAATCACTAAATCATTTATATCTAGAGTTAAGGAACTC
41416335 GAAATTAAGATCTGTAAATTTTCCCAGAAACTAGACTCATATATATTTCCACCATAAAATTTTCA
586 GAAATTAAGATCTGTAAATTTTCCCAGAAACTAGACTCATATATATTTCCACCATAAAATTTTCA
41416400 TAATTTT
651 TAATTTT
41416407 TGGTCCAGCA
Statistics
Matches: 657, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
659 657 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (659 bp):
TAAATGAGAGGTCCTTATGATGCAAATGGACCATTGGTTTAATGAATGGACAAGTATTGTGTAAC
GCCCCGTACCCAAGACCGTCGCCGGAGTCGAACACGAGGTGTTAACGGACTTAATTCATTAATTA
AACAACTTAAACAACTTATTACCAACCATGCATATGCACATCACCAATATCAAACATAACATAAA
TAGCCAGATTTATAAGTCAAAATCATTAGCTCACTAAAGACCAATATATTTGGCCAAATTATAAT
AATACATGTTATAAAACTAGGTCCTTATACGTGCCACTCACTTGATAATTCTAGCATATGTGTTT
ATACTGTCAAGGTGTTGGCTTGATAGTGTGATGCTGCCTCCGACGATCTCCAACCCTGAGCTAAC
CTAACAACACTAAAAGAAATGGAAAGGAGGGGGTAAGCTTTATGCTTAGGAAGCTCACATGAAAT
AATAATAAGCAATTTACTAACATGCTTTCCACAGTAAAACTAACCCAATTGTACATTTACACATG
TTCTGGTTAAGCTGCTTTCTTGAGTAACAATCACTAAATCATTTATATCTAGAGTTAAGGAACTC
GAAATTAAGATCTGTAAATTTTCCCAGAAACTAGACTCATATATATTTCCACCATAAAATTTTCA
TAATTTTAA
Found at i:41417119 original size:49 final size:49
Alignment explanation
Indices: 41417063--41417251 Score: 234
Period size: 50 Copynumber: 3.8 Consensus size: 49
41417053 TAGCTAAAGC
* **
41417063 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATTTGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
41417112 TATCTGGTACACATAGTAACCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-AAT
* * ** *
41417162 GATCTGATACATGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-T
* * *
41417213 TATCAGGTACGCATAGTAGCCTACACTTAGTACTACACA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
41417252 TGCGACCTCA
Statistics
Matches: 118, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 42 0.36
50 43 0.36
51 33 0.28
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:41417259 original size:101 final size:99
Alignment explanation
Indices: 41417076--41417259 Score: 269
Period size: 101 Copynumber: 1.8 Consensus size: 99
41417066 CTGGTACGCA
** * *
41417076 TAGTAGCCTGCACTTAGTACTACACATTTGACCAATTATCTGGTACACATAGTAACCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAACCTACACTTA
*
41417141 GTACTACACACGTGACCTAACGATCTGATACATG
66 GTACTACACACGCGACCTAACGATCTGATACATG
* * *
41417175 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTACACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCAGGTACACATAGTAACCTACACT
*
41417240 TAGTACTACACATGCGACCT
64 TAGTACTACACACGCGACCT
41417260 CACAATAGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 29 0.39
100 3 0.04
101 42 0.57
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAACCTACACTTA
GTACTACACACGCGACCTAACGATCTGATACATG
Found at i:41426095 original size:16 final size:16
Alignment explanation
Indices: 41426074--41426104 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41426064 TAAAAAAAAA
*
41426074 ACATGAATATAAATAG
1 ACATGAAAATAAATAG
41426090 ACATGAAAATAAATA
1 ACATGAAAATAAATA
41426105 AAGATAAAAT
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:0.61, C:0.06, G:0.10, T:0.23
Consensus pattern (16 bp):
ACATGAAAATAAATAG
Found at i:41433241 original size:40 final size:40
Alignment explanation
Indices: 41433193--41433500 Score: 562
Period size: 40 Copynumber: 7.7 Consensus size: 40
41433183 GCAAACACCT
* * *
41433193 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
41433233 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
41433273 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
41433313 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
41433353 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
41433393 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
41433433 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
41433473 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
41433501 NNNNNNNNNN
Statistics
Matches: 262, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 262 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:41440582 original size:27 final size:27
Alignment explanation
Indices: 41440543--41440711 Score: 196
Period size: 27 Copynumber: 6.2 Consensus size: 27
41440533 NNNNNNNNNC
* * *
41440543 AGTGCTATATAATCAACTCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
* *
41440570 AGTGCTACGTAATCAAATCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
41440597 AGTGCTACATAGTCAAACTCGCACACTT
1 AGTGCTACATAGTCAAA-TCGCACACTT
** * *
41440625 AGTGCCGCATGGTCAATTCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
* **
41440652 AGTGC-ATCATATTCATTTCGCACACTT
1 AGTGCTA-CATAGTCAAATCGCACACTT
*
41440679 AGTGCAACATAGTCAAATCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
41440706 AGTGCT
1 AGTGCT
41440712 GTACAATTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 98 0.80
28 24 0.20
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
AGTGCTACATAGTCAAATCGCACACTT
Found at i:41440680 original size:82 final size:81
Alignment explanation
Indices: 41440555--41440710 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41440545 TGCTATATAA
* *
41440555 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41440620 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41440637 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41440701 CACTTAGTGC
65 CACTTAGTGC
41440711 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41444140 original size:2 final size:2
Alignment explanation
Indices: 41444135--41444170 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41444125 TTTAAACATT
41444135 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
41444171 ATCTTCGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:41445725 original size:49 final size:50
Alignment explanation
Indices: 41445672--41445960 Score: 242
Period size: 50 Copynumber: 5.7 Consensus size: 50
41445662 AACCGAAGCT
* *
41445672 ATTTGGTACACATATTAGCCTGCACTTAGTACTACACATGTGACC-AACA
1 ATTTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACA
** *
41445721 ATTTGGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
1 ATTTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACA
* * * * *
41445771 ATTTGATACACGTAGTAGCCTGCACTCAGTACTACACACGTGA-TTGAA-G
1 ATTTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCT-AACA
* * * * * * * *
41445820 TTGTCTGGTACGCATAGTAGCCTGCACTCAATGCTACACATGCGACCTAACT
1 AT-T-TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACA
* * * * * *
41445872 ATCTAGTACACATAGTATCCTGCACTTTGTACTACACACATGACCTAAAACC
1 ATTTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCT--AACA
*** ** *
41445924 ATTTTAAACACATAGTATTCTGCACATAGTACTACAC
1 ATTTGGTACACATAGTAGCCTGCACTTAGTACTACAC
41445961 TTGTGTTCTT
Statistics
Matches: 192, Mismatches: 40, Indels: 13
0.78 0.16 0.05
Matches are distributed among these distances:
49 43 0.22
50 79 0.41
51 35 0.18
52 35 0.18
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (50 bp):
ATTTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACA
Found at i:41445916 original size:151 final size:151
Alignment explanation
Indices: 41445675--41445960 Score: 360
Period size: 151 Copynumber: 1.9 Consensus size: 151
41445665 CGAAGCTATT
* * * * * * **
41445675 TGGTACACATATTAGCCTGCACTTAGTACTACACATGTGACCAACAATTTGGTACATGTAGTAGC
1 TGGTACACATAGTAGCCTGCACTCAATACTACACATGCGACCAACAATCTAGTACACATAGTAGC
* * *
41445740 CTGCACTTAGTACTACACACGTGACCT-AACCATTTGATACACGTAGTAGCCTGCAC-TCAGTAC
66 CTGCACTTAGTACTACACACATGACCTAAACCATTTGAAACACATAGTAGCCTGCACAT-AGTAC
41445803 TACACACGTGATTGAAGTTGTC
130 TACACACGTGATTGAAGTTGTC
* * * *
41445825 TGGTACGCATAGTAGCCTGCACTCAATGCTACACATGCGACCTAACTATCTAGTACACATAGTAT
1 TGGTACACATAGTAGCCTGCACTCAATACTACACATGCGACC-AACAATCTAGTACACATAGTAG
* * **
41445890 CCTGCACTTTGTACTACACACATGACCTAAAACCATTTTAAACACATAGTATTCTGCACATAGTA
65 CCTGCACTTAGTACTACACACATGACCT-AAACCATTTGAAACACATAGTAGCCTGCACATAGTA
41445955 CTACAC
129 CTACAC
41445961 TTGTGTTCTT
Statistics
Matches: 113, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
150 36 0.32
151 42 0.37
153 34 0.30
154 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (151 bp):
TGGTACACATAGTAGCCTGCACTCAATACTACACATGCGACCAACAATCTAGTACACATAGTAGC
CTGCACTTAGTACTACACACATGACCTAAACCATTTGAAACACATAGTAGCCTGCACATAGTACT
ACACACGTGATTGAAGTTGTC
Found at i:41455776 original size:57 final size:57
Alignment explanation
Indices: 41455668--41455778 Score: 134
Period size: 57 Copynumber: 1.9 Consensus size: 57
41455658 TTTACTCAAT
* * * *
41455668 AGAGCTTAGTCAGGATTACCAGTCCAGACTAAATTCTTTATGTAACGTATGCTCAGA
1 AGAGCTTAATCAGGATTACCAGTCCAGACTAAATCCTATATGTAACATATGCTCAGA
* * * *
41455725 AGAGCTTAATTAGGATTACCAGTCTAGGCTAAATCCTA-ATTGTATCATATGCTC
1 AGAGCTTAATCAGGATTACCAGTCCAGACTAAATCCTATA-TGTAACATATGCTC
41455779 GAGAGGAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
56 1 0.02
57 44 0.98
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (57 bp):
AGAGCTTAATCAGGATTACCAGTCCAGACTAAATCCTATATGTAACATATGCTCAGA
Found at i:41456214 original size:20 final size:20
Alignment explanation
Indices: 41456189--41456235 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
41456179 TCTATCCCCT
*
41456189 AATTTGGTCTATCTAG-ATCC
1 AATTTGGTCGAT-TAGAATCC
*
41456209 AATTTGGTCGATTCGAATCC
1 AATTTGGTCGATTAGAATCC
41456229 AATTTGG
1 AATTTGG
41456236 CCAAGAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (20 bp):
AATTTGGTCGATTAGAATCC
Found at i:41458065 original size:21 final size:21
Alignment explanation
Indices: 41458039--41458079 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
41458029 CAACTTAACC
41458039 ATATTTTTACCTATTTTGATA
1 ATATTTTTACCTATTTTGATA
41458060 ATATTTTTACCTATTTTGAT
1 ATATTTTTACCTATTTTGAT
41458080 CCCTATAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.10, G:0.05, T:0.59
Consensus pattern (21 bp):
ATATTTTTACCTATTTTGATA
Found at i:41464430 original size:48 final size:48
Alignment explanation
Indices: 41464359--41464502 Score: 180
Period size: 48 Copynumber: 3.0 Consensus size: 48
41464349 TGGTATGATA
* * * *
41464359 CCAATGCCATATCTCGGATATGGTCTTACATGGGATCACATATCGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATG
* ** ** *
41464407 CCAATGCCATGTCCTAGACATGGTCTTACATGGGATCGTAGGTTGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATG
* *
41464455 CCAATGCCATGTCCCAGATATGGTCTTACATAGGATCACATATCGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATG
41464503 TCGATAGCCA
Statistics
Matches: 78, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (48 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATG
Found at i:41466713 original size:32 final size:33
Alignment explanation
Indices: 41466648--41466716 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
41466638 TTTTTCCTAG
*
41466648 TTTTATTTAATTAATTTTCTTTTGATTTCTTTC
1 TTTTATTGAATTAATTTTCTTTTGATTTCTTTC
*
41466681 TTTTATTGATTTAATTTAT-TTTT-ATTTCTTTC
1 TTTTATTGAATTAATTT-TCTTTTGATTTCTTTC
41466713 TTTT
1 TTTT
41466717 GTTGCAGGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 13 0.39
33 19 0.58
34 1 0.03
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (33 bp):
TTTTATTGAATTAATTTTCTTTTGATTTCTTTC
Found at i:41468680 original size:12 final size:12
Alignment explanation
Indices: 41468663--41468693 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
41468653 GAACATTAGA
*
41468663 TCATTTTGTCAT
1 TCATTTTGTCAC
41468675 TCATTTTGTCAC
1 TCATTTTGTCAC
41468687 TCATTTT
1 TCATTTT
41468694 TCCATGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.06, T:0.58
Consensus pattern (12 bp):
TCATTTTGTCAC
Found at i:41476076 original size:31 final size:31
Alignment explanation
Indices: 41476041--41476106 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
41476031 CGTTTACAGT
*
41476041 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCAGCCCAGTGATATGATTTATGA
41476072 AAAGGCTTCAGCCCAGTGATATGATTTATGA
1 AAAGGCTTCAGCCCAGTGATATGATTTATGA
41476103 AAAG
1 AAAG
41476107 NGATGTGGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTGATATGATTTATGA
Found at i:41483485 original size:25 final size:25
Alignment explanation
Indices: 41483456--41483503 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41483446 TTATAATATG
* * *
41483456 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
41483481 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
41483504 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:41483570 original size:20 final size:20
Alignment explanation
Indices: 41483547--41483585 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
41483537 TAAACATGGT
41483547 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
41483567 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
41483586 TGTATTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:41483667 original size:23 final size:23
Alignment explanation
Indices: 41483637--41483709 Score: 128
Period size: 23 Copynumber: 3.1 Consensus size: 23
41483627 AGGAAGTGCA
41483637 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
41483660 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
41483683 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
41483707 AAA
1 AAA
41483710 AGAGGCTAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
23 26 0.54
24 22 0.46
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:41483726 original size:25 final size:24
Alignment explanation
Indices: 41483636--41483730 Score: 140
Period size: 24 Copynumber: 4.0 Consensus size: 24
41483626 GAGGAAGTGC
41483636 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
41483660 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
41483683 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
41483707 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
41483731 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.35
24 31 0.48
25 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:41483959 original size:31 final size:31
Alignment explanation
Indices: 41483924--41483987 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
41483914 CGTTTACAGT
41483924 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
41483955 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
41483986 AA
1 AA
41483988 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:41489715 original size:27 final size:27
Alignment explanation
Indices: 41489685--41489862 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41489675 ATATTGAGTC
* * * *
41489685 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41489712 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41489739 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41489767 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41489794 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41489821 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41489848 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41489863 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41489824 original size:82 final size:81
Alignment explanation
Indices: 41489706--41489861 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41489696 TGCTATATAA
* *
41489706 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41489771 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41489788 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41489852 CACTTAGTGC
65 CACTTAGTGC
41489862 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41503934 original size:21 final size:21
Alignment explanation
Indices: 41503910--41503985 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
41503900 CATCATGAAC
41503910 TCAGACCACAACTCAATGAGT
1 TCAGACCACAACTCAATGAGT
* * **
41503931 TCAGATGTCACATATATC-ATGAAC
1 TCAGA--CCACA-A-CTCAATGAGT
*
41503955 TCAGACCACAACTCAATGCGT
1 TCAGACCACAACTCAATGAGT
*
41503976 TCAGATCACA
1 TCAGACCACA
41503986 TAGTTCCTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
20 2 0.05
21 18 0.45
22 4 0.10
23 4 0.10
24 10 0.25
25 2 0.05
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.22
Consensus pattern (21 bp):
TCAGACCACAACTCAATGAGT
Found at i:41521492 original size:14 final size:14
Alignment explanation
Indices: 41521473--41521528 Score: 78
Period size: 14 Copynumber: 3.9 Consensus size: 14
41521463 AGTTCAACGA
41521473 ATGTAAAATCATAT
1 ATGTAAAATCATAT
41521487 ATGTAAAATCATACT
1 ATGTAAAATCATA-T
*
41521502 CA-GTACAATCATAT
1 -ATGTAAAATCATAT
41521516 ATGTAAAATCATA
1 ATGTAAAATCATA
41521529 AGCACATCAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
13 1 0.03
14 24 0.65
15 11 0.30
16 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.32
Consensus pattern (14 bp):
ATGTAAAATCATAT
Found at i:41521594 original size:27 final size:27
Alignment explanation
Indices: 41521564--41521623 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
41521554 GGGCATACTC
*
41521564 GTCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
41521591 GTCATTTTACCTTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
41521618 GTCATT
1 GTCATT
41521624 GGGGGAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:41532954 original size:42 final size:42
Alignment explanation
Indices: 41532908--41533065 Score: 183
Period size: 42 Copynumber: 3.7 Consensus size: 42
41532898 GACTATGTGC
* * * *
41532908 AAGACCATATCTGGGATATGGCATCT-ATATAAGACTGCGTGT
1 AAGACCATATCTGAGATATGGCAT-TGATATGAGATTACGTGT
* * *
41532950 AAGACCATATCTGGGATATGGCTTTGATATGAGATTTCGTGT
1 AAGACCATATCTGAGATATGGCATTGATATGAGATTACGTGT
* * * *
41532992 AAGACCATAGCTGAGTTATTGGCATTGATACGAGATTACATGT
1 AAGACCATATCTGAGATA-TGGCATTGATATGAGATTACGTGT
*
41533035 AAGACCATATCTGAGATATGGCATTGGTATG
1 AAGACCATATCTGAGATATGGCATTGATATG
41533066 GTACCAAGTG
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
41 1 0.01
42 62 0.63
43 36 0.36
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (42 bp):
AAGACCATATCTGAGATATGGCATTGATATGAGATTACGTGT
Found at i:41536322 original size:46 final size:46
Alignment explanation
Indices: 41536050--41536322 Score: 352
Period size: 46 Copynumber: 5.9 Consensus size: 46
41536040 TTGTCTTCGA
* * * * * *
41536050 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-AAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCGTAT
* * * ** ***
41536096 CATGTTGTCATGGTATCTTTTAACCATAGTCTTATTCATTTCCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT-CGTAT
41536143 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCGTAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCGTAT
* *
41536189 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACATATTTCGTAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCGTAT
*
41536235 CATGTTGCCATGATATCTTTCAACCATGGT-TCTACACATTTCGTAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCT-TACACATTTCGTAT
41536281 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
41536323 ATTTCAGAAA
Statistics
Matches: 199, Mismatches: 24, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
45 4 0.02
46 157 0.79
47 38 0.19
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCGTAT
Found at i:41538445 original size:8 final size:8
Alignment explanation
Indices: 41538432--41538466 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
41538422 TATACTAAAT
41538432 AAATAATA
1 AAATAATA
41538440 AAATAAT-
1 AAATAATA
41538447 -AATAATA
1 AAATAATA
41538454 AAATAATA
1 AAATAATA
41538462 AAATA
1 AAATA
41538467 TCTCATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
8 19 0.76
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAATAATA
Found at i:41538452 original size:14 final size:14
Alignment explanation
Indices: 41538433--41538466 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
41538423 ATACTAAATA
41538433 AATAATAAAATAAT
1 AATAATAAAATAAT
41538447 AATAATAAAATAAT
1 AATAATAAAATAAT
41538461 AA-AATA
1 AATAATA
41538467 TCTCATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:41541402 original size:46 final size:47
Alignment explanation
Indices: 41541333--41541752 Score: 510
Period size: 46 Copynumber: 8.9 Consensus size: 47
41541323 TTATATTCAA
* * * * * *
41541333 CATGATGCCATAGTAACTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
* * ** * **
41541379 CATGTTTCTATGGTATCTTTCAACCATGGTCTTATTCATTTCCCCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
*
41541426 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCGTAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TT--T-TCATAT
** *
41541477 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
*
41541523 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATTGTAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC--A---TAT
*
41541574 CATGTTGCCATGGTATCTTTCAACCATGTTCTTACACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
*
41541620 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCGTAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
* *
41541666 CATGTTTCCATGGTATCTTTCAACCATGGTCTTACACATTTT-GTAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
*
41541712 CATGTTGCCATGGTATCTTTCAACCATGATCTTACACATTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
41541753 CATTTCAGAA
Statistics
Matches: 331, Mismatches: 32, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
46 205 0.62
47 39 0.12
48 3 0.01
49 2 0.01
50 1 0.00
51 81 0.24
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (47 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATAT
Found at i:41541565 original size:97 final size:96
Alignment explanation
Indices: 41541333--41541756 Score: 567
Period size: 97 Copynumber: 4.5 Consensus size: 96
41541323 TTATATTCAA
* * * * * * * *
41541333 CATGATGCCATAGTAACTTTCAACTATGGTCTTACTCA-TT--TTC-TGTCATGTTTCTATGGTA
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTCGTATCATGTTGCCATGGTA
** **
41541394 TCTTTCAACCATGGTCTTATTCATTTCCCCAT
66 TCTTTCAACCATGGTCTTACACATTT-CATAT
41541426 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCGTATCATGTTGCCATGGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT-TCGTATCATGTTGCCATGGT
** *
41541491 ATCTTTCAACCATGGTCTTATTCATTTCATGT
65 ATCTTTCAACCATGGTCTTACACATTTCATAT
* *
41541523 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTGTATCATGTTGCCATGGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT-TCGTATCATGTTGCCATGGT
*
41541588 ATCTTTCAACCATGTTCTTACACATTTCATAT
65 ATCTTTCAACCATGGTCTTACACATTTCATAT
*
41541620 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA--T--TTCGTATCATGTTTCCATGGTA
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTCGTATCATGTTGCCATGGTA
**
41541681 TCTTTCAACCATGGTCTTACACATTTTGTAT
66 TCTTTCAACCATGGTCTTACACATTTCATAT
*
41541712 CATGTTGCCATGGTATCTTTCAACCATGATCTTACACATTTCATT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATT
41541757 TCAGAAAGCA
Statistics
Matches: 298, Mismatches: 24, Indels: 15
0.88 0.07 0.04
Matches are distributed among these distances:
92 84 0.28
93 34 0.11
94 3 0.01
95 1 0.00
96 3 0.01
97 132 0.44
98 41 0.14
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (96 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATTCGTATCATGTTGCCATGGTA
TCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:41541601 original size:24 final size:24
Alignment explanation
Indices: 41541574--41541647 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
41541564 CATATTGTAT
41541574 CATGTTGCCATGGTATCTTTCAAC
1 CATGTTGCCATGGTATCTTTCAAC
* *
41541598 CATGTT--C-T--TACACATTTCATAT
1 CATGTTGCCATGGTA-TC-TTTCA-AC
41541620 CATGTTGCCATGGTATCTTTCAAC
1 CATGTTGCCATGGTATCTTTCAAC
41541644 CATG
1 CATG
41541648 GTCTTACACA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 6 0.16
22 8 0.21
24 12 0.32
25 6 0.16
26 1 0.03
27 2 0.05
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (24 bp):
CATGTTGCCATGGTATCTTTCAAC
Found at i:41543446 original size:24 final size:21
Alignment explanation
Indices: 41543419--41543465 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
41543409 CTCTTATTTT
41543419 CTTTCTCTATACTATTTCTCATCA
1 CTTTCTCT-TA-T-TTTCTCATCA
*
41543443 CTTTCTCTTATTTTCTCTTCA
1 CTTTCTCTTATTTTCTCATCA
41543464 CT
1 CT
41543466 AACATGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 1 0.05
23 2 0.09
24 8 0.36
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.55
Consensus pattern (21 bp):
CTTTCTCTTATTTTCTCATCA
Found at i:41547789 original size:79 final size:81
Alignment explanation
Indices: 41547680--41547862 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
41547670 TACTCGTTCA
* *
41547680 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
41547743 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
41547760 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
41547823 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
41547839 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
41547863 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:41547862 original size:40 final size:40
Alignment explanation
Indices: 41547659--41547862 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
41547649 CGGAATTTAA
** *
41547659 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41547699 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41547739 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
41547778 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
41547818 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41547858 CCGGA
1 CCGGA
41547863 CATCATTCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 95 0.67
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41551936 original size:10 final size:10
Alignment explanation
Indices: 41551921--41551948 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
41551911 ATAGTTCATG
41551921 TTTACTTTGT
1 TTTACTTTGT
41551931 TTTACTTTGT
1 TTTACTTTGT
41551941 TTTACTTT
1 TTTACTTT
41551949 TTCCCCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTACTTTGT
Found at i:41566163 original size:14 final size:14
Alignment explanation
Indices: 41566144--41566180 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
41566134 AAATAGGTAA
41566144 ATGAGATATATTTT
1 ATGAGATATATTTT
41566158 ATGAGATATATTTT
1 ATGAGATATATTTT
*
41566172 CTGAGATAT
1 ATGAGATAT
41566181 TTAAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (14 bp):
ATGAGATATATTTT
Found at i:41569005 original size:420 final size:420
Alignment explanation
Indices: 41568226--41569060 Score: 1517
Period size: 420 Copynumber: 2.0 Consensus size: 420
41568216 AGAATCTACA
*
41568226 GAATTTGTGATTAAAGTATCGAATCCATTAGGCAAGCATGTATTAGTAGATAAAGTATGTAGAAA
1 GAATTTGTGATTAAAGTATCGAATCCATTAGGCAAGCATGTATTAGTAGATAAAGCATGTAGAAA
** * * *
41568291 TTGTCCTTTGATGATTAGAGGCTATTGTTTTTCGGCCGATCTCATGCTATTGCCATTTGATGAGT
66 TTACCCTTTAATGATTAGAGGCTACTGTTTTCCGGCCGATCTCATGCTATTGCCATTTGATGAGT
41568356 TTGATGTGATTCTTGGTATGGATTGGTTGACTACACATGATGTGATAGTGAATTGTGGAAAGAAA
131 TTGATGTGATTCTTGGTATGGATTGGTTGACTACACATGATGTGATAGTGAATTGTGGAAAGAAA
41568421 TTCATTGAGTTGAAGTGTGAAAATGGTGAAATTCTTCGGGTTAATTCAGAAGAGTCAGATAGTTC
196 TTCATTGAGTTGAAGTGTGAAAATGGTGAAATTCTTCGGGTTAATTCAGAAGAGTCAGATAGTTC
**
41568486 ATTTCCCATAATTTCTGTTATGTCTGCTCAAAAATGTTTGAGAAAAGGGTATGAAGCTTATCTTG
261 ATTTCCCATAATTTCTGTTATGTCTGCTCAAAAATACTTGAGAAAAGGGTATGAAGCTTATCTTG
*
41568551 CTTTTGTGTTAAACACTAAAGATCCAGAATTGAAAATTGAATCAGTGTCTGTGGTATGTGAGTTT
326 CTTTTGTGTTAAACACTAAAGATCCAGAATTGAAAATTGAATCAGTGCCTGTGGTATGTGAGTTT
*
41568616 CCCGATGTGTTTCTGAAAGAACTACTAGGC
391 CCCGATGTGTTTCCGAAAGAACTACTAGGC
*
41568646 GAATTTGTGATTAAAGTATCGAATTCATTAGGCAAGCATGTATTAGTAGATAAAGCATGTAGAAA
1 GAATTTGTGATTAAAGTATCGAATCCATTAGGCAAGCATGTATTAGTAGATAAAGCATGTAGAAA
** *
41568711 TTACCCTTTAATGATTAGAGGCTACTGTTTTCCGGTTGATCTCATGCTATTTCCATTTGATGAGT
66 TTACCCTTTAATGATTAGAGGCTACTGTTTTCCGGCCGATCTCATGCTATTGCCATTTGATGAGT
41568776 TTGATGTGATTCTTGGTATGGATTGGTTGACTACACATGATGTGATAGTGAATTGTGGAAAGAAA
131 TTGATGTGATTCTTGGTATGGATTGGTTGACTACACATGATGTGATAGTGAATTGTGGAAAGAAA
41568841 TTCATTGAGTTGAAGTGTGAAAATGGTGAAATTCTTCGGGTTAATTCAGAAGAGTCAGATAGTTC
196 TTCATTGAGTTGAAGTGTGAAAATGGTGAAATTCTTCGGGTTAATTCAGAAGAGTCAGATAGTTC
*
41568906 ATTTCCCATAATTTCTGTTATGTCTGCTCAGAAATACTTGAGAAAAGGGTATGAAGCTTATCTTG
261 ATTTCCCATAATTTCTGTTATGTCTGCTCAAAAATACTTGAGAAAAGGGTATGAAGCTTATCTTG
*
41568971 CTTTTGTGTTGAACACTAAAGATCCAGAATTGAAAATTGAATCAGTGCCTGTGGTATGTGAGTTT
326 CTTTTGTGTTAAACACTAAAGATCCAGAATTGAAAATTGAATCAGTGCCTGTGGTATGTGAGTTT
*
41569036 CCCGATGTGTTTCCGGAAGAACTAC
391 CCCGATGTGTTTCCGAAAGAACTAC
41569061 CAGGTTTGCC
Statistics
Matches: 398, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
420 398 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.35
Consensus pattern (420 bp):
GAATTTGTGATTAAAGTATCGAATCCATTAGGCAAGCATGTATTAGTAGATAAAGCATGTAGAAA
TTACCCTTTAATGATTAGAGGCTACTGTTTTCCGGCCGATCTCATGCTATTGCCATTTGATGAGT
TTGATGTGATTCTTGGTATGGATTGGTTGACTACACATGATGTGATAGTGAATTGTGGAAAGAAA
TTCATTGAGTTGAAGTGTGAAAATGGTGAAATTCTTCGGGTTAATTCAGAAGAGTCAGATAGTTC
ATTTCCCATAATTTCTGTTATGTCTGCTCAAAAATACTTGAGAAAAGGGTATGAAGCTTATCTTG
CTTTTGTGTTAAACACTAAAGATCCAGAATTGAAAATTGAATCAGTGCCTGTGGTATGTGAGTTT
CCCGATGTGTTTCCGAAAGAACTACTAGGC
Found at i:41597582 original size:15 final size:15
Alignment explanation
Indices: 41597558--41597594 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
41597548 TTTTTATAAT
41597558 AATAAAATAAAAGAA
1 AATAAAATAAAAGAA
*
41597573 AATAACATAAAAG-A
1 AATAAAATAAAAGAA
41597587 AATAAAAT
1 AATAAAAT
41597595 TTCAAGAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (15 bp):
AATAAAATAAAAGAA
Found at i:41602454 original size:24 final size:23
Alignment explanation
Indices: 41602406--41602455 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
41602396 TATGAAAATA
*
41602406 ATATAATAAATATGAGATTTTTT
1 ATATAATAAATATGAGATTTGTT
*
41602429 ATATGAATATATATGA-ATTGTGTT
1 ATAT-AATAAATATGAGATT-TGTT
41602453 ATA
1 ATA
41602456 ATTGGGTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (23 bp):
ATATAATAAATATGAGATTTGTT
Found at i:41602514 original size:13 final size:13
Alignment explanation
Indices: 41602496--41602522 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41602486 ATAATGAATT
41602496 TAACTTGTTAATA
1 TAACTTGTTAATA
41602509 TAACTTGTTAATA
1 TAACTTGTTAATA
41602522 T
1 T
41602523 GAATAGCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TAACTTGTTAATA
Found at i:41614290 original size:7 final size:7
Alignment explanation
Indices: 41614278--41614302 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41614268 CTATAAAATG
41614278 AAAATTA
1 AAAATTA
41614285 AAAATTA
1 AAAATTA
41614292 AAAATTA
1 AAAATTA
41614299 AAAA
1 AAAA
41614303 GATCAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:41616839 original size:3 final size:3
Alignment explanation
Indices: 41616833--41616866 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
41616823 TACTACTACT
41616833 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC -TC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
41616867 TTCATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Done.