Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 155 of 444
Found at i:42236174 original size:47 final size:47
Alignment explanation
Indices: 42236115--42236383 Score: 216
Period size: 46 Copynumber: 5.7 Consensus size: 47
42236105 TTAGAACCAA
42236115 TGTAAGACCATGTCTGGGACATGACATCGGCATTGAGACGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATG-CATCGGCATTGAGACGAGAGCTAG
* * * * *
42236163 TGTAAGA-CATGTCTGGGACATGCATCGGCCTCGAGATGTA-AGCCAC
1 TGTAAGACCATGTCTGGGACATGCATCGGCATTGAGACG-AGAGCTAG
* * * *
42236209 TATAAGA-CATGTCTGGGACATGCATCGGC--T-ACAAGATGTG-TCAG
1 TGTAAGACCATGTCTGGGACATGCATCGGCATTGAGACGA-GAGCT-AG
* ** *
42236253 TGTAAGACCATGTCTGGGACATGGCATTGGCACGGATATCTGAGAGCTAG
1 TGTAAGACCATGTCTGGGACAT-GCATCGGCATTGAGA-C-GAGAGCTAG
* * *
42236303 TGTAAGACCATGTTTGGGACATAGCATCGAC-TTGATG--GATGAGCCAG
1 TGTAAGACCATGTCTGGGACAT-GCATCGGCATTGA-GACGA-GAGCTAG
*
42236350 TGTAAGACCATGTCTGGGACATGGCATCGACATT
1 TGTAAGACCATGTCTGGGACAT-GCATCGGCATT
42236384 ATACCCTATG
Statistics
Matches: 178, Mismatches: 28, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
42 1 0.01
43 3 0.02
44 8 0.04
45 14 0.08
46 54 0.30
47 51 0.29
48 9 0.05
49 4 0.02
50 31 0.17
51 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
TGTAAGACCATGTCTGGGACATGCATCGGCATTGAGACGAGAGCTAG
Found at i:42239079 original size:40 final size:40
Alignment explanation
Indices: 42239013--42239163 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
42239003 AAATTGAATG
* * *
42239013 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
42239052 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
42239092 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
42239132 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
42239164 ACATGGTTAT
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
39 16 0.17
40 75 0.81
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:42239177 original size:40 final size:40
Alignment explanation
Indices: 42239050--42239179 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
42239040 ATGCTGGAAA
* * *
42239050 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * **
42239090 CTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* *
42239130 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
42239170 TTATATCCGG
1 TTATATCCGG
42239180 TTATATTCCG
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
39 1 0.01
40 74 0.99
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:42247061 original size:40 final size:40
Alignment explanation
Indices: 42246995--42247145 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
42246985 AAATTGAATG
* * *
42246995 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
42247034 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
42247074 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
42247114 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
42247146 ACATGGTTAT
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
39 16 0.17
40 75 0.81
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:42247159 original size:40 final size:40
Alignment explanation
Indices: 42247032--42247161 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
42247022 ATGCTGGAAA
* * *
42247032 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * **
42247072 CTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* *
42247112 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
42247152 TTATATCCGG
1 TTATATCCGG
42247162 TTATATTCCG
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
39 1 0.01
40 74 0.99
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:42251247 original size:93 final size:93
Alignment explanation
Indices: 42251135--42251306 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42251125 GCCCATAAGT
* *
42251135 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42251200 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
42251228 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42251293 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
42251307 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42251302 original size:46 final size:46
Alignment explanation
Indices: 42251127--42251302 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
42251117 TGTAACCCGC
* * *
42251127 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
42251173 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
42251223 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
42251266 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42251303 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:42256191 original size:15 final size:15
Alignment explanation
Indices: 42256171--42256239 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
42256161 GTATCTTGGG
42256171 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
42256186 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
42256201 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
42256216 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
42256231 TTTCTTTAT
1 TTTCTTTAT
42256240 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:42256240 original size:30 final size:30
Alignment explanation
Indices: 42256162--42256249 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
42256152 CATAGTATCG
* * * *
42256162 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
42256192 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
42256222 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
42256250 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:42258261 original size:93 final size:93
Alignment explanation
Indices: 42258149--42258320 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42258139 GCCCATAAGT
* *
42258149 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42258214 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
42258242 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42258307 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
42258321 CAAATATCCA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42258316 original size:46 final size:46
Alignment explanation
Indices: 42258141--42258316 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
42258131 TGTAACCCGC
* * *
42258141 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
42258187 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
42258237 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
42258280 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42258317 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:42260743 original size:30 final size:30
Alignment explanation
Indices: 42260699--42260787 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
42260689 CAAAGATAAC
42260699 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
42260728 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
42260758 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
42260788 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:42260747 original size:15 final size:15
Alignment explanation
Indices: 42260699--42260778 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
42260689 CAAAGATAAC
*
42260699 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
42260713 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
42260728 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
42260743 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
42260758 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
42260773 AAGAAA
1 AAGAAA
42260779 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:42260787 original size:15 final size:15
Alignment explanation
Indices: 42260710--42260787 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
42260700 AGAAAACCGA
42260710 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
42260725 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
42260739 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
42260754 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
42260770 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
42260785 ATA
1 ATA
42260788 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:42263852 original size:93 final size:93
Alignment explanation
Indices: 42263740--42263911 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42263730 GCCCATAAGT
* *
42263740 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42263805 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
42263833 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42263898 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
42263912 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42263907 original size:46 final size:46
Alignment explanation
Indices: 42263732--42263907 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
42263722 TGTAACCCGC
* * *
42263732 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
42263778 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
42263828 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
42263871 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42263908 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:42269295 original size:14 final size:16
Alignment explanation
Indices: 42269266--42269297 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42269256 GGATTATGTA
42269266 GAAAAAATAAAGAAAT
1 GAAAAAATAAAGAAAT
42269282 GAAAAAA-AAA-AAAT
1 GAAAAAATAAAGAAAT
42269296 GA
1 GA
42269298 GCATGGATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (16 bp):
GAAAAAATAAAGAAAT
Found at i:42270481 original size:29 final size:29
Alignment explanation
Indices: 42270448--42270579 Score: 108
Period size: 29 Copynumber: 4.6 Consensus size: 29
42270438 TGACGAGATC
*
42270448 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGAGCTGGAAATATAT
* * *
42270477 GGCACTAAGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGAGCTGGAAATATAT
** ***
42270506 GGCACTGGGTGTGCGAGCTCGG-AGGGTAT
1 GGCACTAAGTGTGCGAGCT-GGAAATATAT
* * *
42270535 GGCACTATGTGTGCGGGCT-TAAAT-TACGT
1 GGCACTAAGTGTGCGAGCTGGAAATATA--T
42270564 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
42270580 AATCGAGTAG
Statistics
Matches: 80, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
27 2 0.03
28 1 0.01
29 75 0.94
30 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAGCTGGAAATATAT
Found at i:42277137 original size:21 final size:20
Alignment explanation
Indices: 42277113--42277184 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
42277103 TCTGATGAGC
42277113 TTCAGTTTAACCTTTCTGGGT
1 TTCAGTTTAACCTTT-TGGGT
* ** * *
42277134 TTCATTTTAGTTCTTTTGAGC
1 TTCAGTTTA-ACCTTTTGGGT
*
42277155 TTCAATTTAACCTTTTTGGGT
1 TTCAGTTTAACC-TTTTGGGT
*
42277176 TTCCGTTTA
1 TTCAGTTTA
42277185 GCTCCTATGA
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
20 1 0.03
21 32 0.86
22 4 0.11
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.53
Consensus pattern (20 bp):
TTCAGTTTAACCTTTTGGGT
Found at i:42277185 original size:42 final size:42
Alignment explanation
Indices: 42277091--42277240 Score: 149
Period size: 42 Copynumber: 3.6 Consensus size: 42
42277081 TCACTTTTAC
* *
42277091 TTTCCGTTTAGCTCTGATGAGCTTCAGTTTAACCTTTCTGGG
1 TTTCCGTTTAGCTCTTATGAGCTTCAATTTAACCTTTCTGGG
** * * *
42277133 TTTCATTTTAGTTCTTTTGAGCTTCAATTTAACCTTTTTGGG
1 TTTCCGTTTAGCTCTTATGAGCTTCAATTTAACCTTTCTGGG
* ** * *
42277175 TTTCCGTTTAGCTCCTATGAGCTTCCGTTCAACCCTTAC-GGG
1 TTTCCGTTTAGCTCTTATGAGCTTCAATTTAA-CCTTTCTGGG
* * *
42277217 TTTCTGTTTAGCACTTATGTGCTT
1 TTTCCGTTTAGCTCTTATGAGCTT
42277241 TTGTGCAGCC
Statistics
Matches: 86, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 82 0.95
43 4 0.05
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTCCGTTTAGCTCTTATGAGCTTCAATTTAACCTTTCTGGG
Found at i:42282400 original size:19 final size:20
Alignment explanation
Indices: 42282376--42282415 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
42282366 TAGCATGTGT
42282376 TTTGAA-GTTTCTTGATAGA
1 TTTGAATGTTTCTTGATAGA
*
42282395 TTTGAATGTTTGTTGATAGA
1 TTTGAATGTTTCTTGATAGA
42282415 T
1 T
42282416 ATACAAGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.25, C:0.03, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTGAATGTTTCTTGATAGA
Found at i:42284825 original size:27 final size:27
Alignment explanation
Indices: 42284535--42284824 Score: 463
Period size: 27 Copynumber: 10.7 Consensus size: 27
42284525 TACTGAAATG
** *
42284535 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
42284562 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
42284589 CCCTCGATTTACAGAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
42284616 CCCTCGTTTTACAGAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
42284643 CCCTCAATTTACAGAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
42284670 CCCTCGATTTACAGAATTACTGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
42284697 CCCTCGATTTACAGAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* * *
42284724 CCCTCAATTTATAGAATTATCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
42284751 CCCTCGATTTACAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
42284778 CCCTCGATTTACAGAATTACTGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
42284805 CCCTCGATTTACAAAATTAC
1 CCCTCGATTTACAGAATTAC
42284825 TAAAATACCC
Statistics
Matches: 244, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 244 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACCGTTTTA
Found at i:42284833 original size:27 final size:27
Alignment explanation
Indices: 42284749--42285022 Score: 162
Period size: 27 Copynumber: 10.2 Consensus size: 27
42284739 ATTATCGTTT
* * ***
42284749 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAAAATTACCAAAA
* * *****
42284776 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTATAAAATTACCAAAA
* *
42284803 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * *
42284830 TACCCTTGGTTTAAAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
*
42284857 TACCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAA
* * * * *
42284884 TACCCT-GGTCTGTAAAATTGCTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* *
42284910 TA-CCTCTGGTTTGTAAAATTACCAAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* * *
42284937 TACCC-CTAGTTTGTAAAGTTACCAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAA
* * * * *
42284964 TACCACTAG-TTTGTGAAATTATCGAAA
1 TACC-CTCGATTTATAAAATTACCAAAA
* *
42284991 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
42285018 TACCC
1 TACCC
42285023 CTAATTTACA
Statistics
Matches: 200, Mismatches: 38, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
25 3 0.01
26 19 0.09
27 175 0.88
28 3 0.01
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCAAAA
Found at i:42284931 original size:80 final size:79
Alignment explanation
Indices: 42284817--42285023 Score: 220
Period size: 80 Copynumber: 2.6 Consensus size: 79
42284807 CTCGATTTAC
**
42284817 AAAATTACTAAAATACCCTTGGTTTAAAAAATTACCAAAATACCCTCGA-TCAGTAAAATTACCA
1 AAAATT-CTAAAATACCC-TGGTTTGTAAAATTACCAAAATACCC-CGAGTCAGTAAAATTACCA
*
42284881 AAATACC-CTGGTCTGT
63 AAATACCACTAGTCTGT
* ** *
42284897 AAAATTGCTAAAATACCTCTGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAGTTACCAA
1 AAAATT-CTAAAATACC-CTGGTTTGTAAAATTACCAAAATACCCCGAGTCAGTAAAATTACCAA
*
42284962 AATACCACTAGTTTGT
64 AATACCACTAGTCTGT
* * * **
42284978 GAAATTATCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCC
1 AAAATTCT-AAAATACCCT-GGTTTGTAAAATTACCAAAATACCCC
42285024 TAATTTACAA
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
79 2 0.02
80 62 0.57
81 44 0.41
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (79 bp):
AAAATTCTAAAATACCCTGGTTTGTAAAATTACCAAAATACCCCGAGTCAGTAAAATTACCAAAA
TACCACTAGTCTGT
Found at i:42285028 original size:27 final size:27
Alignment explanation
Indices: 42284817--42285103 Score: 204
Period size: 27 Copynumber: 10.7 Consensus size: 27
42284807 CTCGATTTAC
* * * **
42284817 AAAATTACTAAAATACCCTTGGTTTAA
1 AAAATTACCAAAATACCCCTAGTTTGT
* **
42284844 AAAATTACCAAAATA-CCCTCGATCAGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
* *
42284871 AAAATTACCAAAATA-CCCTGGTCTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* * * *
42284897 AAAATTGCTAAAATACCTCTGGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
42284924 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* *
42284951 AAAGTTACCAAAATACCACTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* * * *
42284978 GAAATTATCGAAATA-CCCTCAATTTGT
1 AAAATTACCAAAATACCCCT-AGTTTGT
* **
42285005 AAAATTACCAAAATACCCCTAATTTAC
1 AAAATTACCAAAATACCCCTAGTTTGT
* ** **
42285032 AAAATTA-TAGAAATACCATTAGTTTAC
1 AAAATTACCA-AAATACCCCTAGTTTGT
** * *
42285059 AAAATTACTGAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* * *
42285086 AGATTTACCAAAACACCC
1 AAAATTACCAAAATACCC
42285104 TTGTAGGATG
Statistics
Matches: 210, Mismatches: 44, Indels: 12
0.79 0.17 0.05
Matches are distributed among these distances:
26 25 0.12
27 180 0.86
28 5 0.02
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTTTGT
Found at i:42285085 original size:81 final size:81
Alignment explanation
Indices: 42284812--42285103 Score: 263
Period size: 81 Copynumber: 3.6 Consensus size: 81
42284802 TTACCCTCGA
** * *
42284812 TTTACAAAATTACTAAAATACCCTTGGTTTAAAAAATTACCAAAATA-CCCTCGA-TCAGTAAAA
1 TTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCT-AATTTA-TAAAA
*
42284875 TTACCAAAATACC-CTGG
64 TTACCAAAATACCACTAG
* ** * * * *
42284892 TCTGTAAAATTGCTAAAATA-CCTCTGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAGT
1 TTTACAAAATTACTAAAATACCCT-TGGTTTGTAAAATTACCAAAATACCCCTAATTTATAAAAT
42284956 TACCAAAATACCACTAG
65 TACCAAAATACCACTAG
*** * *** *
42284973 TTTGTGAAATTA-TCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAAT
1 TTTACAAAATTACT-AAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAATTTATAAAAT
* *
42285037 TA-TAGAAATACCATTAG
65 TACCA-AAATACCACTAG
* * * *
42285054 TTTACAAAATTACTGAAATACCCTTGGTTTGTAGATTTACCAAAACACCC
1 TTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCC
42285104 TTGTAGGATG
Statistics
Matches: 170, Mismatches: 34, Indels: 15
0.78 0.16 0.07
Matches are distributed among these distances:
79 3 0.02
80 56 0.33
81 107 0.63
82 4 0.02
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (81 bp):
TTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAATTTATAAAATT
ACCAAAATACCACTAG
Found at i:42285201 original size:27 final size:27
Alignment explanation
Indices: 42285124--42285201 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
42285114 AAATGACTAC
* *
42285124 AATACCCTT-AATAGGTAAAAAGACCGT
1 AATACCCTTGTAT-GGTAAAATGACCGT
* * *
42285151 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCTTGTATGGTAAAATGACCGT
42285178 AATACCCTTGTATGGTAAAATGAC
1 AATACCCTTGTATGGTAAAATGAC
42285202 GAATATGCCC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 1 0.03
27 37 0.93
28 2 0.05
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (27 bp):
AATACCCTTGTATGGTAAAATGACCGT
Found at i:42285917 original size:20 final size:20
Alignment explanation
Indices: 42285883--42285958 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
42285873 GATACGTGGG
42285883 GTATGATAT--ACATGAT-T
1 GTATGATATGCACATGATAT
42285900 GATATGATATGCACATGATAT
1 G-TATGATATGCACATGATAT
*
42285921 GCATGATATGCACATGATAT
1 GTATGATATGCACATGATAT
* *
42285941 CTATGAAATGCACATGAT
1 GTATGATATGCACATGAT
42285959 GAATTCATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
17 1 0.02
18 8 0.16
20 40 0.78
21 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (20 bp):
GTATGATATGCACATGATAT
Found at i:42285919 original size:11 final size:11
Alignment explanation
Indices: 42285903--42285958 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
42285893 CATGATTGAT
42285903 ATGATATGCAC
1 ATGATATGCAC
42285914 ATGATATG--C
1 ATGATATGCAC
42285923 ATGATATGCAC
1 ATGATATGCAC
*
42285934 ATGATAT-C-T
1 ATGATATGCAC
*
42285943 ATGAAATGCAC
1 ATGATATGCAC
42285954 ATGAT
1 ATGAT
42285959 GAATTCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 15 0.41
10 2 0.05
11 20 0.54
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:42285946 original size:29 final size:29
Alignment explanation
Indices: 42285884--42285952 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
42285874 ATACGTGGGG
* *
42285884 TATGATATACATGATTGATATGATATGCA
1 TATGATATGCATGATTGACATGATATGCA
*
42285913 CATGATATGCATGATATGCACATGATAT-C-
1 TATGATATGCATGAT-TG-ACATGATATGCA
*
42285942 TATGAAATGCA
1 TATGATATGCA
42285953 CATGATGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 22 0.67
30 3 0.09
31 8 0.24
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (29 bp):
TATGATATGCATGATTGACATGATATGCA
Found at i:42286105 original size:25 final size:26
Alignment explanation
Indices: 42286008--42286130 Score: 187
Period size: 26 Copynumber: 4.8 Consensus size: 26
42285998 GAGGAAGTGC
* *
42286008 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
42286034 AAAAGGGCTTATGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
42286060 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
**
42286086 AAAAGGGCTT-TGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACTG
42286111 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
42286131 ATTAAAGAGG
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 32 0.35
26 59 0.65
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACTG
Found at i:42286383 original size:31 final size:31
Alignment explanation
Indices: 42286348--42286426 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
42286338 CGTTTACAAT
42286348 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
42286379 AAAGGCTTCGGCTCAGTGATTTGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
42286410 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
42286427 AACCGTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:42291847 original size:86 final size:86
Alignment explanation
Indices: 42291702--42291876 Score: 350
Period size: 86 Copynumber: 2.0 Consensus size: 86
42291692 ATGATAATTG
42291702 AAAATGATGACAAATTTGTTTTATTTATTTTTGTCATTAATAACCTAATTACATATTTAAGATTT
1 AAAATGATGACAAATTTGTTTTATTTATTTTTGTCATTAATAACCTAATTACATATTTAAGATTT
42291767 AAAATACTTATAAATTACACC
66 AAAATACTTATAAATTACACC
42291788 AAAATGATGACAAATTTGTTTTATTTATTTTTGTCATTAATAACCTAATTACATATTTAAGATTT
1 AAAATGATGACAAATTTGTTTTATTTATTTTTGTCATTAATAACCTAATTACATATTTAAGATTT
42291853 AAAATACTTATAAATTACACC
66 AAAATACTTATAAATTACACC
42291874 AAA
1 AAA
42291877 TACCAAGCCA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 89 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (86 bp):
AAAATGATGACAAATTTGTTTTATTTATTTTTGTCATTAATAACCTAATTACATATTTAAGATTT
AAAATACTTATAAATTACACC
Found at i:42294982 original size:21 final size:20
Alignment explanation
Indices: 42294943--42294986 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
42294933 TGTGATTTGG
*
42294943 ACTAAATTGAGTTTCAATTGT
1 ACTAAATTGAGTTTAAATT-T
42294964 ACTAAATTGA-TGTTAAATTT
1 ACTAAATTGAGT-TTAAATTT
42294984 ACT
1 ACT
42294987 CGTATAGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (20 bp):
ACTAAATTGAGTTTAAATTT
Found at i:42298744 original size:40 final size:39
Alignment explanation
Indices: 42298699--42298906 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 39
42298689 CGGAATACAA
*
42298699 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42298739 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42298779 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *** *
42298819 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
** * * *
42298859 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
42298899 CCGGATAT
1 CCGGATAT
42298907 CATTCAATTG
Statistics
Matches: 141, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.03
40 134 0.95
41 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42298839 original size:80 final size:80
Alignment explanation
Indices: 42298699--42298905 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 80
42298689 CGGAATACAA
* * *
42298699 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG
*
42298763 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAAC
* * **
42298779 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG
*
42298843 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
42298859 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
42298906 TCATTCAATT
Statistics
Matches: 107, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
79 3 0.03
80 102 0.95
81 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAAC
Found at i:42306770 original size:40 final size:39
Alignment explanation
Indices: 42306725--42306932 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 39
42306715 CGGAATACAA
*
42306725 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42306765 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42306805 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *** *
42306845 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
** * * *
42306885 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
42306925 CCGGATAT
1 CCGGATAT
42306933 CATTCAATTG
Statistics
Matches: 141, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.03
40 134 0.95
41 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42306865 original size:80 final size:80
Alignment explanation
Indices: 42306725--42306931 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 80
42306715 CGGAATACAA
* * *
42306725 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG
*
42306789 GCCTTCGGGTATTAGC
65 GCCTTCGGGTATTAAC
* * **
42306805 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG
*
42306869 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
42306885 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
42306932 TCATTCAATT
Statistics
Matches: 107, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
79 3 0.03
80 102 0.95
81 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAAC
Found at i:42311491 original size:40 final size:40
Alignment explanation
Indices: 42311432--42311618 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
42311422 CAATTGAATG
* * * *
42311432 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
42311472 ATATCCGGGTTAAGACCCGAAGGCCA-TTGTGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGG-CATTTGTGCAAGTAATT
* * * **
42311512 ACATCCAGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
42311552 AAATCCGGGCTAATACCCGAAGGCATTTGTACAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
*
42311592 CTATCCGGGCTAAGACCCGAAGGCATT
1 ATATCCGGGCTAAGACCCGAAGGCATT
42311619 CGTACATGTG
Statistics
Matches: 120, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
39 2 0.02
40 116 0.97
41 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:42311624 original size:40 final size:40
Alignment explanation
Indices: 42311432--42311639 Score: 177
Period size: 40 Copynumber: 5.2 Consensus size: 40
42311422 CAATTGAATG
* * ** * * **
42311432 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTACAAGTCGTT
* * * **
42311472 ATATCCGGGTTAAGACCCGAAGGCCATT-GTGCTAGT-GACC
1 ATATCCGGGCTAAGACCCGAAGG-CATTCGTACAAGTCG-TT
* * * *
42311512 ACATCCAGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTACAAGTCGTT
* * *
42311552 AAATCCGGGCTAATACCCGAAGGCATTTGTACAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTACAAGTCGTT
* * *
42311592 CTATCCGGGCTAAGACCCGAAGGCATTCGTACATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTACAAGTCGTT
42311632 ATATCCGG
1 ATATCCGG
42311640 TTGTATTCCG
Statistics
Matches: 138, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
39 4 0.03
40 129 0.93
41 5 0.04
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTACAAGTCGTT
Found at i:42331639 original size:17 final size:18
Alignment explanation
Indices: 42331597--42331640 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
42331587 AAAATCGATT
42331597 AATGATAATGCCTGAAATA
1 AATGATAATGCCTG-AATA
*
42331616 AATGATAATGTCTG-ATA
1 AATGATAATGCCTGAATA
*
42331633 CATGATAA
1 AATGATAA
42331641 AAGATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
19 13 0.57
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (18 bp):
AATGATAATGCCTGAATA
Found at i:42336990 original size:19 final size:19
Alignment explanation
Indices: 42336966--42337015 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
42336956 TTTTCACATG
42336966 GCCTGGCACATGCCCGTGT
1 GCCTGGCACATGCCCGTGT
* * *
42336985 GCCTGGCATACGCTCGTGT
1 GCCTGGCACATGCCCGTGT
42337004 GCCTGGCACATG
1 GCCTGGCACATG
42337016 TCCTTCACAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.12, C:0.34, G:0.32, T:0.22
Consensus pattern (19 bp):
GCCTGGCACATGCCCGTGT
Found at i:42338055 original size:47 final size:46
Alignment explanation
Indices: 42337980--42338198 Score: 162
Period size: 47 Copynumber: 4.7 Consensus size: 46
42337970 AGGGTAAGGT
* * *
42337980 GTCGATGCCATGTCCTAGACACGATCTTATACTGGCTCATATCTCAA
1 GTCGATGCCATGTCCCAGACATG-TCTTACACTGGCTCATATCTCAA
*
42338027 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTCATA
1 GTCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCAT-ATCTCA-A
* * * * ** *
42338075 G-CAGATGCACA--TCCCAGACATGTATTTTCACTGCCTTACGT-TCGA
1 GTC-GATGC-CATGTCCCAGACATGT-CTTACACTGGCTCATATCTCAA
* * * * *
42338120 GGCAGTTG-CATGTCCCAGACATGTCTTACACTAGCCCTTATCTCAA
1 GTC-GATGCCATGTCCCAGACATGTCTTACACTGGCTCATATCTCAA
*
42338166 TGTCGATGCCATGTCCGAGACATGTCTTACACT
1 -GTCGATGCCATGTCCCAGACATGTCTTACACT
42338199 AACTCACACA
Statistics
Matches: 135, Mismatches: 24, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
44 2 0.01
45 10 0.07
46 29 0.21
47 83 0.61
48 9 0.07
49 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (46 bp):
GTCGATGCCATGTCCCAGACATGTCTTACACTGGCTCATATCTCAA
Found at i:42354841 original size:21 final size:21
Alignment explanation
Indices: 42354815--42354869 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
42354805 CACTAGACAT
*
42354815 AGGGGCACATGCCCATATGAA
1 AGGGGCACACGCCCATATGAA
* *
42354836 AGGGGCATACGCCCATGTGAA
1 AGGGGCACACGCCCATATGAA
42354857 AGGGGCACACGCC
1 AGGGGCACACGCC
42354870 TGTGTAGCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.27, G:0.33, T:0.11
Consensus pattern (21 bp):
AGGGGCACACGCCCATATGAA
Found at i:42365402 original size:40 final size:40
Alignment explanation
Indices: 42365357--42365524 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
42365347 CGGAATATAA
42365357 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
42365397 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
42365437 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
42365477 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
42365517 CCGGATAT
1 CCGGATAT
42365525 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42373810 original size:46 final size:46
Alignment explanation
Indices: 42373760--42373935 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
42373750 TGGTTGAGCA
42373760 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42373806 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
42373851 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42373899 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42373936 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:42373916 original size:93 final size:93
Alignment explanation
Indices: 42373757--42373928 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42373747 GGATGGTTGA
* *
42373757 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42373822 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
42373850 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42373915 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
42373929 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42381378 original size:46 final size:46
Alignment explanation
Indices: 42381328--42381503 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
42381318 TGGTTGAGCA
42381328 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42381374 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
42381419 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42381467 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42381504 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:42381484 original size:93 final size:93
Alignment explanation
Indices: 42381325--42381496 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42381315 GGATGGTTGA
* *
42381325 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42381390 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
42381418 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42381483 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
42381497 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42394824 original size:43 final size:43
Alignment explanation
Indices: 42394700--42394859 Score: 184
Period size: 43 Copynumber: 3.7 Consensus size: 43
42394690 ATATGTGTTA
* *
42394700 TCGTGTAAGACCACGTTTGGGACGTTGGCATCGACT-TATGATT
1 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGATT
* * *
42394743 TATGTGTAAGACCACGTTTGGGATGTTGGCATCG-TATTTGATT
1 T-CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATT
42394786 TCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTTGATT
1 TCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATT
* * *
42394829 ACATGGAAGACCACGTCTGGGACGTTGGCAT
1 TCGTGTAAGACCACGTCTGGGACGTTGGCAT
42394860 TGTATGAGCT
Statistics
Matches: 101, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
41 1 0.01
42 27 0.27
43 42 0.42
44 31 0.31
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (43 bp):
TCGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATT
Found at i:42397449 original size:33 final size:34
Alignment explanation
Indices: 42397378--42397442 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
42397368 TGCATTTTGT
*
42397378 ACTGATACTGTTACTGAATTAGTCTAAAGCCCAC
1 ACTGATACTGTTACTGAATTAGGCTAAAGCCCAC
*
42397412 ACTGATACTGTTACTGAA-TGGGCTAAAGCCC
1 ACTGATACTGTTACTGAATTAGGCTAAAGCCC
42397443 TAACTGAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (34 bp):
ACTGATACTGTTACTGAATTAGGCTAAAGCCCAC
Found at i:42398309 original size:10 final size:10
Alignment explanation
Indices: 42398269--42398311 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
42398259 TATTGAATCA
*
42398269 TATGCTTTGG
1 TATGATTTGG
42398279 TATGACTTTGG
1 TATGA-TTTGG
*
42398290 TTTAGATTTGG
1 TAT-GATTTGG
42398301 TATGATTTGG
1 TATGATTTGG
42398311 T
1 T
42398312 TAGTGAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 12 0.43
11 14 0.50
12 2 0.07
ACGTcount: A:0.16, C:0.05, G:0.28, T:0.51
Consensus pattern (10 bp):
TATGATTTGG
Found at i:42400581 original size:39 final size:40
Alignment explanation
Indices: 42400536--42400631 Score: 104
Period size: 39 Copynumber: 2.4 Consensus size: 40
42400526 GATTTAGAGT
* * * *
42400536 TACCAAAATATAAATAGGGGCACGAATGTGC-ATTAAGGG
1 TACCAAAATACAAACAAGGCCACGAATGTGCAATTAAGGG
* * *
42400575 TACCAAAGTACAAACAAGGCCACGTATGTGCAATTAGGGG
1 TACCAAAATACAAACAAGGCCACGAATGTGCAATTAAGGG
* *
42400615 TACCAAAGTACAGACAA
1 TACCAAAATACAAACAA
42400632 TGGCATATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 25 0.52
40 23 0.48
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.18
Consensus pattern (40 bp):
TACCAAAATACAAACAAGGCCACGAATGTGCAATTAAGGG
Found at i:42400620 original size:40 final size:39
Alignment explanation
Indices: 42400554--42400667 Score: 124
Period size: 40 Copynumber: 2.9 Consensus size: 39
42400544 TATAAATAGG
*
42400554 GGCACGAATGTGC-ATTAAGGGTACCAAAGTACAAACAA-
1 GGCACGTATGTGCAATT-AGGGTACCAAAGTACAAACAAT
*
42400592 GGCCACGTATGTGCAATTAGGGGTACCAAAGTACAGACAAT
1 GG-CACGTATGTGCAATTA-GGGTACCAAAGTACAAACAAT
** * * *
42400633 GGCATATATGTGCAATCAGGGTGCCGAAGTACAAA
1 GGCACGTATGTGCAATTAGGGTACCAAAGTACAAA
42400668 TAGAGGCACA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
38 2 0.03
39 25 0.39
40 35 0.55
41 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (39 bp):
GGCACGTATGTGCAATTAGGGTACCAAAGTACAAACAAT
Found at i:42405407 original size:48 final size:48
Alignment explanation
Indices: 42405284--42405663 Score: 309
Period size: 48 Copynumber: 7.9 Consensus size: 48
42405274 GGTAAAATAT
* * * * *
42405284 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATACATCAGTGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATA-A-CAATGC
* * * * * **
42405334 CGATGCCATGTCCCAGACATAGTCTTACACTAACACGTATAACAATGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAACAATGC
* *
42405382 TGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAACAATGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAACAATGC
* * *** *
42405430 CGATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATTGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAACAATGC
*
42405478 CGATGCCATG-TCCTAGACATGGTCTTACACTAGCTCACATAACAATGC
1 CGATGCCATGTTCC-AAACATGGTCTTACACTAGCTCACATAACAATGC
* * * * * *
42405526 CGATGTCATGTTCCAAACATGGTCGTACACTGGCTCTCATAAACTAGTGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACAT-AAC-AATGC
* * * * * * * * *
42405576 CGGTGCTATGTCCCAGATATGGTCTTACACT-G-ACACATATCGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAACAATGC
** * ** *
42405622 CGAT-AAATGTCCCTGACATGGTCTTACACTAGCTCTCATAAC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAAC
42405664 CCTAGTATCA
Statistics
Matches: 264, Mismatches: 60, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
45 22 0.08
46 5 0.02
47 11 0.04
48 156 0.59
49 8 0.03
50 62 0.23
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAACAATGC
Found at i:42405545 original size:144 final size:146
Alignment explanation
Indices: 42405283--42405663 Score: 459
Period size: 144 Copynumber: 2.6 Consensus size: 146
42405273 GGGTAAAATA
* * * *
42405283 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATACATCAGTGCCGATGCCATGTCCC
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATA-TTGAG-GCCGATGCCATGTCCT
* * * ** * *
42405348 AGACATAGTCTTACACTAACACGTATAACAATGCTGATGCCATGTTCCAAACATGGTCTTACACT
64 AGACATGGTCTTACACTAGCTCACATAACAATGCCGATGCCATGTTCCAAACATGGTCGTACACT
42405413 AGCTCACAT-AAC-AATG
129 AGCTCACATAAACTAATG
* * *
42405429 TCGATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATTGAGGCCGATGCCATGTCCTAG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATTGAGGCCGATGCCATGTCCTAG
* *
42405494 ACATGGTCTTACACTAGCTCACATAACAATGCCGATGTCATGTTCCAAACATGGTCGTACACTGG
66 ACATGGTCTTACACTAGCTCACATAACAATGCCGATGCCATGTTCCAAACATGGTCGTACACTAG
* *
42405559 CTCTCATAAACTAGTG
131 CTCACATAAACTAATG
* * * * * **
42405575 TCGGTGCTATGTCCCAGATATGGTCTTACACT-G-ACACATATCGAGGCCGAT-AAATGTCCCT-
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATTGAGGCCGATGCCATGT-CCTA
*
42405636 GACATGGTCTTACACTAGCTCTCATAAC
65 GACATGGTCTTACACTAGCTCACATAAC
42405664 CCTAGTATCA
Statistics
Matches: 203, Mismatches: 29, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
143 31 0.15
144 98 0.48
145 7 0.03
146 67 0.33
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (146 bp):
TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATTGAGGCCGATGCCATGTCCTAG
ACATGGTCTTACACTAGCTCACATAACAATGCCGATGCCATGTTCCAAACATGGTCGTACACTAG
CTCACATAAACTAATG
Found at i:42415776 original size:96 final size:96
Alignment explanation
Indices: 42415671--42415844 Score: 260
Period size: 96 Copynumber: 1.8 Consensus size: 96
42415661 TATAACAATA
* * * *
42415671 CCGATGCCATGTTCC-AAACATGGTCTTACACTAACTCACATAACAATGTCGATGTCATGCTCCA
1 CCGACGCCATG-TCCTAAACATGGTCTTACACTAACTCACATAACAATGCCAATGCCATGCTCCA
42415735 AAAATGGTCTTACATTAGCTAGCATATTGAGG
65 AAAATGGTCTTACATTAGCTAGCATATTGAGG
* * *
42415767 CCGACGCCATGTCCTAGACATGGTCTTACACTAGCTCACATAACAATGCCAATGCCATGTTCCAA
1 CCGACGCCATGTCCTAAACATGGTCTTACACTAACTCACATAACAATGCCAATGCCATGCTCCAA
*
42415832 ACATGGTCTTACA
66 AAATGGTCTTACA
42415845 CTGGCTCTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
95 3 0.04
96 66 0.96
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (96 bp):
CCGACGCCATGTCCTAAACATGGTCTTACACTAACTCACATAACAATGCCAATGCCATGCTCCAA
AAATGGTCTTACATTAGCTAGCATATTGAGG
Found at i:42415887 original size:50 final size:48
Alignment explanation
Indices: 42415579--42415908 Score: 193
Period size: 48 Copynumber: 6.8 Consensus size: 48
42415569 AATACCGATT
* * * * *
42415579 CCATGTCCCGGACATGGTCTTACACT-GACTCTCATACATCAGTGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTAG-CTCACATA-A-CAATGCCAATG
* ** * * * *
42415629 CAACATCCTAGACATGGTCTTACACT-G-ACACGTATAACAATACCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCAC--ATAACAATGCCAATG
* * * * *
42415677 CCATGTTCCAAACATGGTCTTACACTAACTCACATAACAATGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCACATAACAATGCCAATG
* * * * *** * * *
42415725 TCATG-CTCCAAAAATGGTCTTACATTAGCT-AGCATATTGAGGCCGACG
1 CCATGTC-CCAGACATGGTCTTACACTAGCTCA-CATAACAATGCCAATG
*
42415773 CCATGTCCTAGACATGGTCTTACACTAGCTCACATAACAATGCCAATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCACATAACAATGCCAATG
* * * ** ** * *
42415821 CCATGTTCCAAACATGGTCTTACACTGGCTCTTATAAACCGGTGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCACAT-AA-CAATGCCAATG
* *
42415871 CCATGTCCCAGACATGGTCTTACACTAGCACTCATAAC
1 CCATGTCCCAGACATGGTCTTACACTAGCTCACATAAC
42415909 CCTAGTATCA
Statistics
Matches: 213, Mismatches: 57, Indels: 22
0.73 0.20 0.08
Matches are distributed among these distances:
47 1 0.00
48 140 0.66
49 7 0.03
50 65 0.31
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (48 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTCACATAACAATGCCAATG
Found at i:42416040 original size:21 final size:21
Alignment explanation
Indices: 42416015--42416066 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
42416005 AATTTCATAC
42416015 AATAGCAATAATTTAATGCAT
1 AATAGCAATAATTTAATGCAT
42416036 AATAGCAATAATTTAATGCAT
1 AATAGCAATAATTTAATGCAT
*
42416057 AATAACAATA
1 AATAGCAATA
42416067 GAGTTGGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.31
Consensus pattern (21 bp):
AATAGCAATAATTTAATGCAT
Found at i:42424202 original size:28 final size:28
Alignment explanation
Indices: 42424170--42424296 Score: 188
Period size: 28 Copynumber: 4.5 Consensus size: 28
42424160 AATGAGATTG
42424170 GCACTAAGTGTGCGAGTTT-AAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
42424198 GCACTAAGTGTGCGAGTTTGAAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
42424227 GCACTAAGTGTGCGAGTTTGAATATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
42424255 GCACTAAGTGTGCGAGTTTGAATATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
*
42424283 GCTCTAAGTGTGCG
1 GCACTAAGTGTGCG
42424297 GACTTACTGT
Statistics
Matches: 96, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
28 61 0.64
29 34 0.35
30 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:42424258 original size:57 final size:56
Alignment explanation
Indices: 42424170--42424296 Score: 188
Period size: 57 Copynumber: 2.2 Consensus size: 56
42424160 AATGAGATTG
42424170 GCACTAAGTGTGCGAGTTTAATTGTATAGCACTAAGTGTGCGAGTTTGAAT-TGTATA
1 GCACTAAGTGTGCGAGTTTAATTGTATAGCACTAAGTGTGCGAGTTTGAATAT-TA-A
42424227 GCACTAAGTGTGCGAGTTTGAATAT-TA-AGCACTAAGTGTGCGAGTTTGAATATTAA
1 GCACTAAGTGTGCGAGTTT-AAT-TGTATAGCACTAAGTGTGCGAGTTTGAATATTAA
*
42424283 GCTCTAAGTGTGCG
1 GCACTAAGTGTGCG
42424297 GACTTACTGT
Statistics
Matches: 66, Mismatches: 1, Indels: 7
0.89 0.01 0.09
Matches are distributed among these distances:
56 14 0.21
57 45 0.68
58 6 0.09
59 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (56 bp):
GCACTAAGTGTGCGAGTTTAATTGTATAGCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:42427434 original size:39 final size:40
Alignment explanation
Indices: 42427215--42427401 Score: 317
Period size: 40 Copynumber: 4.7 Consensus size: 40
42427205 TATTCGGATG
* *
42427215 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
42427255 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
42427294 AT-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
42427333 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
42427373 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
42427402 AGCAAGTAGC
Statistics
Matches: 139, Mismatches: 4, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
38 10 0.07
39 52 0.37
40 77 0.55
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:42435369 original size:37 final size:38
Alignment explanation
Indices: 42435255--42435429 Score: 232
Period size: 37 Copynumber: 4.6 Consensus size: 38
42435245 CGGATGATAA
* *
42435255 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGT-CCGAAGGCA-TTGTGCGAGTTACTATA-T
*
42435295 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCGAAGGCA-TTGTGCGAGTTACTATAT
*
42435334 CCGGGCTAAGTCCGAAGGCATT-TGCGAGTTACTATAA
1 CCGGGCTAAGTCCGAAGGCATTGTGCGAGTTACTATAT
42435371 CCGGGCTAAGTCCGAAGGCATTGTGCGAGTTACTATA-
1 CCGGGCTAAGTCCGAAGGCATTGTGCGAGTTACTATAT
*
42435408 -AGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGT-CCGAAGGCATT
42435430 TGAGCAAGTA
Statistics
Matches: 126, Mismatches: 6, Indels: 9
0.89 0.04 0.06
Matches are distributed among these distances:
36 9 0.07
37 47 0.37
38 16 0.13
39 43 0.34
40 11 0.09
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (38 bp):
CCGGGCTAAGTCCGAAGGCATTGTGCGAGTTACTATAT
Found at i:42441477 original size:29 final size:29
Alignment explanation
Indices: 42441436--42441538 Score: 188
Period size: 29 Copynumber: 3.6 Consensus size: 29
42441426 TTTTCCAGTT
42441436 GCACACTTAGTGCCAAATATTTCCAGCAC
1 GCACACTTAGTGCCAAATATTTCCAGCAC
*
42441465 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCAAATATTTCCAGCAC
*
42441494 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCAAATATTTCCAGCAC
42441523 GCACACTTAGTGCCAA
1 GCACACTTAGTGCCAA
42441539 TCTCGTCACC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (29 bp):
GCACACTTAGTGCCAAATATTTCCAGCAC
Found at i:42448634 original size:29 final size:29
Alignment explanation
Indices: 42448623--42448724 Score: 177
Period size: 29 Copynumber: 3.5 Consensus size: 29
42448613 TTTCCAGTTT
* *
42448623 GCACACTTAGTGCCAAATATTTCCAGTAC
1 GCACACTTAGTGCCATATATTTCCAGCAC
42448652 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCATATATTTCCAGCAC
*
42448681 ACACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCATATATTTCCAGCAC
42448710 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
42448725 ATCTCGTCAC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAC
Found at i:42448655 original size:58 final size:58
Alignment explanation
Indices: 42448593--42448724 Score: 156
Period size: 58 Copynumber: 2.3 Consensus size: 58
42448583 CCTCCGAACT
* * **** *
42448593 CGCACACCCAGTGCCGTATTTTTCCAGTTTGCACACTTAGTGCCAAATATTTCCAGTA
1 CGCACACCCAGTGCCATATATTTCCAGCACACACACTTAGTGCCAAATATTTCCAGCA
** *
42448651 CGCACACTTAGTGCCATATATTTCCAGCACACACACTTAGTGCCATATATTTCCAGCA
1 CGCACACCCAGTGCCATATATTTCCAGCACACACACTTAGTGCCAAATATTTCCAGCA
**
42448709 CGCACACTTAGTGCCA
1 CGCACACCCAGTGCCA
42448725 ATCTCGTCAC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 64 1.00
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.28
Consensus pattern (58 bp):
CGCACACCCAGTGCCATATATTTCCAGCACACACACTTAGTGCCAAATATTTCCAGCA
Found at i:42452605 original size:21 final size:22
Alignment explanation
Indices: 42452564--42452621 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
42452554 ATATTGTTAT
*
42452564 ACATGATATGACATG-GTATGC
1 ACATGATATGATATGAGTATGC
*
42452585 ACATGATATGTTATGAG-ATGC
1 ACATGATATGATATGAGTATGC
* *
42452606 ATATGATATGCTATGA
1 ACATGATATGATATGA
42452622 TATACTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.33
Consensus pattern (22 bp):
ACATGATATGATATGAGTATGC
Found at i:42452729 original size:24 final size:24
Alignment explanation
Indices: 42452697--42452743 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
42452687 CAATTTACCA
**
42452697 AAAAGGGCTTTGCC-CCAGTTATT
1 AAAAGGGCTAGGCCTCCAGTTATT
42452720 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAG-GGCTAGGCCTCCAGTTAT
42452744 ATGATAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTAGGCCTCCAGTTATT
Found at i:42464866 original size:40 final size:39
Alignment explanation
Indices: 42464821--42465028 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 39
42464811 CGGAATACAA
*
42464821 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42464861 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTTTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
42464901 CCGGATTTAACAACTTGCACGAATGCCTTCGAGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
42464941 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * *
42464981 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
*
42465021 CCAGATAT
1 CCGGATAT
42465029 CATTCAATTG
Statistics
Matches: 140, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
39 1 0.01
40 139 0.99
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42464961 original size:80 final size:80
Alignment explanation
Indices: 42464821--42465027 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 80
42464811 CGGAATACAA
* * *
42464821 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATG
* *
42464886 CCTTCGGGTTTTAGC
66 CCTTCGGGTCTTAAC
* * * *
42464901 CCGGATTTAACAACTTGCACGAATGCCTTCGAGTCTTAGCCCGGAT-GTA-GTCACTAGCACAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACG--ACTAGCACAAA
42464964 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTCTTAAC
** * * * * *
42464981 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGCCCAGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
42465028 TCATTCAATT
Statistics
Matches: 106, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.02
80 103 0.97
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATG
CCTTCGGGTCTTAAC
Found at i:42472244 original size:80 final size:81
Alignment explanation
Indices: 42472104--42472309 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
42472094 CGGAATACAA
* * *
42472104 CCAGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCAGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
42472168 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
42472184 CCAGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCACAAT
1 CCAGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAA
*
42472247 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
* ** * * * *
42472264 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGCCCGGAT
1 CCAGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
42472310 ATCATTCAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
80 104 0.96
81 1 0.01
82 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
CCAGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:42472311 original size:40 final size:40
Alignment explanation
Indices: 42472107--42472311 Score: 216
Period size: 40 Copynumber: 5.1 Consensus size: 40
42472097 AATACAACCA
* *
42472107 GATATAACCAC-ATGCACGAATGCCTTCGGGTCTTAGCCCG
1 GATATAACAACTA-GCACAAATGCCTTCGGGTCTTAGCCCG
* * * * *
42472147 GATAGAACGACTTGCACAAATGCCTTCGGGTATTAGCCCA
1 GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
* * *
42472187 GATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCG
1 GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
* * * *
42472227 GATGTAGTC-ACTAGCACAATTGCCTTCGGGTCTTAACCCG
1 GATATA-ACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
** * *
42472267 GATATAATTACTAGCACAAATGTCTTCGGGACTTAGCCCG
1 GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
42472307 GATAT
1 GATAT
42472312 CATTCAATTG
Statistics
Matches: 137, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
40 136 0.99
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
Found at i:42476604 original size:37 final size:36
Alignment explanation
Indices: 42476554--42476640 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
42476544 TACGAAGTCT
42476554 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
42476590 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
42476627 TCACCCGGCACATA
1 T-ACCCGG-ACATA
42476641 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:42476779 original size:49 final size:49
Alignment explanation
Indices: 42476710--42477028 Score: 343
Period size: 49 Copynumber: 6.2 Consensus size: 49
42476700 TACCACATAT
*
42476710 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * * *
42476759 ATATACATACACTTTCACATTCACCACATCACATTC-ACCACATCGGCCATTAGGCCTTATC
1 ATATACATACACTTTCACATT-----CATCACA-TCGGCCA-TTAGGCC-TTA----TCA-C
* *
42476820 ACATATACATATACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATA--CATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
42476871 ATATACATATACTTTCACATTCACCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * * *
42476920 ATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCCTCATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * *
42476969 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
42477018 ATATATATACA
1 ATATACATACA
42477029 TTTTACGAAT
Statistics
Matches: 232, Mismatches: 22, Indels: 32
0.81 0.08 0.11
Matches are distributed among these distances:
49 163 0.70
51 5 0.02
52 2 0.01
54 10 0.04
55 7 0.03
56 6 0.03
57 7 0.03
58 10 0.04
60 2 0.01
61 5 0.02
63 15 0.06
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.31
Consensus pattern (49 bp):
ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:42476792 original size:14 final size:14
Alignment explanation
Indices: 42476773--42476802 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
42476763 ACATACACTT
42476773 TCACATTCACCACA
1 TCACATTCACCACA
42476787 TCACATTCACCACA
1 TCACATTCACCACA
42476801 TC
1 TC
42476803 GGCCATTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.43, G:0.00, T:0.23
Consensus pattern (14 bp):
TCACATTCACCACA
Found at i:42476792 original size:63 final size:63
Alignment explanation
Indices: 42476724--42476851 Score: 229
Period size: 63 Copynumber: 2.0 Consensus size: 63
42476714 ATATACACTT
*
42476724 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACA
1 TCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACA
* *
42476787 TCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCACATTCATCACA
1 TCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACA
42476850 TC
1 TC
42476852 GGCCATTAGG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.30
Consensus pattern (63 bp):
TCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACA
Found at i:42477029 original size:49 final size:49
Alignment explanation
Indices: 42476787--42477032 Score: 384
Period size: 49 Copynumber: 5.0 Consensus size: 49
42476777 ATTCACCACA
* * *
42476787 TCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACATTT
* *
42476836 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATATACTT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACATTT
*
42476885 TCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACATTT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACATTT
* * * *
42476934 TCGCATTCATCGCATCGGCCATTAGGCCTCATCACATATATATACATTT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACATTT
* *
42476983 TCACATTCATCACATCGGCCATTAGGCCTCATCACATATATATACATTT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACATTT
42477032 T
1 T
42477033 ACGAATCTTG
Statistics
Matches: 186, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 186 1.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (49 bp):
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACATTT
Found at i:42479655 original size:43 final size:43
Alignment explanation
Indices: 42479487--42479655 Score: 132
Period size: 43 Copynumber: 4.0 Consensus size: 43
42479477 ATATCATACA
** *
42479487 ATGCCAACATCCCAGACGTGGTCTTACATGCTATCTCATATCG
1 ATGCCAACATCCCAGACGTGGTCTTACATGAAATCACATATCG
* *
42479530 ATGCC-ACTATCCCAGACAG-GGTCTTACA-CAAATCAAATA-CG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACATGAAATCACATATCG
* * ** * * * * *
42479571 GTGCCGATGTCCTAGACATGGTCTTAC-TCGTAACCATATATCG
1 ATGCCAACATCCCAGACGTGGTCTTACAT-GAAATCACATATCG
* *
42479614 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACATATC
1 ATGCCAACATCCCAGACGTGGTCTTACATGAAATCACATATC
42479656 AGAATCCTAT
Statistics
Matches: 96, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
41 21 0.22
42 16 0.17
43 57 0.59
44 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAACATCCCAGACGTGGTCTTACATGAAATCACATATCG
Found at i:42488597 original size:20 final size:19
Alignment explanation
Indices: 42488561--42488611 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
42488551 AAGGACTATT
*
42488561 TTGTAAA-GTGGTAAAATAA
1 TTGTAAATGT-GTGAAATAA
42488580 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
42488600 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
42488612 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 15 0.52
21 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:42489351 original size:46 final size:44
Alignment explanation
Indices: 42489262--42489382 Score: 136
Period size: 46 Copynumber: 2.7 Consensus size: 44
42489252 TATGTGTGCT
* *
42489262 AGTGTAAGACATGTTTGGGACATGCATCAGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-G-CACATTACGAGAGCC
* *
42489308 AGTGTAAGACATGTCTGGGAAATGCATCG-ACATTGAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGCACATT---ACGAGAGCC
* *
42489354 ACTGTAAGACATGTCCGGGACATGCATCG
1 AGTGTAAGACATGTCTGGGACATGCATCG
42489383 GCCTCGAGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
43 5 0.08
45 1 0.02
46 59 0.91
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGCACATTACGAGAGCC
Found at i:42489504 original size:49 final size:49
Alignment explanation
Indices: 42489262--42489575 Score: 156
Period size: 49 Copynumber: 6.7 Consensus size: 49
42489252 TATGTGTGCT
* * * * *
42489262 AGTGTAAGACATGTTTGGGACAT-GCATC-AGC-CACAT-TATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCA-ATAGATGAAAGCC
* * * * * *
42489308 AGTGTAAGACATGTCTGGGAAAT-GCATCGA---CATTGAGACGAGAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAAT-AGATGAAAGCC
* * * * * * * *
42489354 ACTGTAAGACATGTCCGGGACAT-GCATCGGCCTCGAGATAT-ACAAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGA-AAGCC
* * * *** *
42489402 AGTGTAAGACCTGTCTGGGACATGGCGTC-AGCT---T-GTTGTGTGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGAAAGCC
* *
42489446 AGTGTAAGACCTGTTTGGGACATGGCATCGACAC-CAATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCAATAGATGAAAGCC
* * * * *
42489495 AGTGTAAGACCTGTCTGGGACACGGCATCGGCCTCGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGAAAGCC
* * *
42489544 AGTGTAAGACCTATCTAGGACATGCCATCGAC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGAC
42489576 TTTGATGTCC
Statistics
Matches: 203, Mismatches: 49, Indels: 29
0.72 0.17 0.10
Matches are distributed among these distances:
44 30 0.15
45 3 0.01
46 60 0.30
47 2 0.01
48 30 0.15
49 78 0.38
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGAAAGCC
Found at i:42493660 original size:40 final size:40
Alignment explanation
Indices: 42493469--42493653 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
42493459 TCGAATGATG
* * *
42493469 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
42493509 TCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42493549 TCC-GACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42493588 TCCGGGTTAAGTCCCGAAGGCATCTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42493629 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42493654 AACGAGTAGC
Statistics
Matches: 128, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
39 39 0.30
40 80 0.62
41 9 0.07
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42493675 original size:79 final size:79
Alignment explanation
Indices: 42493469--42493686 Score: 220
Period size: 79 Copynumber: 2.7 Consensus size: 79
42493459 TCGAATGATG
* *
42493469 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAGATCCGAAGGCAT
42493532 TCGTGCGAGTTACTAAA
63 TCGTGCGAGTTACTAAA
* *
42493549 TCC-GACTAAGAT-CCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TAGCTATATCC-GGTTAAGAT-CCGAAGGCA
42493610 -TCTGTGCGAGTTACTATAA
62 TTC-GTGCGAGTTACTA-AA
* **
42493629 -CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAA-ACTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGA-TCCGAAGG
42493687 TACGTGATTC
Statistics
Matches: 116, Mismatches: 9, Indels: 27
0.76 0.06 0.18
Matches are distributed among these distances:
78 3 0.03
79 67 0.58
80 46 0.40
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGATCCGAAGGCATTCG
TGCGAGTTACTAAA
Found at i:42500214 original size:40 final size:40
Alignment explanation
Indices: 42500022--42500207 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
42500012 TCGAATGATG
* * *
42500022 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
42500062 TCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42500102 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42500142 TCCGGGTTAAGTCCCGAAGGCATCTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42500183 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42500208 AACGAGTAGC
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 120 0.92
41 9 0.07
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42500214 original size:80 final size:80
Alignment explanation
Indices: 42500022--42500240 Score: 238
Period size: 80 Copynumber: 2.8 Consensus size: 80
42500012 TCGAATGATG
* * **
42500022 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGTTAAGATCCGAAGGCATT
42500086 CGTGCGAGTTACTAAA
65 CGTGCGAGTTACTAAA
* *
42500102 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGAT-CCGAAGGCAT
42500164 TCTGTGCGAGTTACTATAA
64 TC-GTGCGAGTTACTA-AA
* **
42500183 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAA-ACTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTTAAGA-TCCGAAGG
42500241 TACGTGATTC
Statistics
Matches: 119, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
79 19 0.16
80 90 0.76
81 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGATCCGAAGGCATTC
GTGCGAGTTACTAAA
Found at i:42505150 original size:40 final size:40
Alignment explanation
Indices: 42505105--42505271 Score: 194
Period size: 40 Copynumber: 4.2 Consensus size: 40
42505095 CGGAATATAA
42505105 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
42505145 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** *
42505185 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
42505225 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
42505264 CCGGATAT
1 CCGGATAT
42505272 CATTCAATTT
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
39 15 0.14
40 94 0.86
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42509598 original size:2 final size:2
Alignment explanation
Indices: 42509591--42509615 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42509581 GTTAATTCTA
42509591 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
42509616 AGCATCAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42513588 original size:13 final size:13
Alignment explanation
Indices: 42513570--42513594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42513560 ATTTTTGTCA
42513570 ATTCATCCACAAC
1 ATTCATCCACAAC
42513583 ATTCATCCACAA
1 ATTCATCCACAA
42513595 TATTATTCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (13 bp):
ATTCATCCACAAC
Found at i:42517012 original size:29 final size:29
Alignment explanation
Indices: 42516970--42517051 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
42516960 AGTGCGTATT
**
42516970 TTTCCAGCTTGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCATATA
42516999 TTTCCAGCACGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCATATA
42517028 TTTCCAGCACGCACACTTAGTGCC
1 TTTCCAGCACGCACACTTAGTGCC
42517052 GATCTCGTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (29 bp):
TTTCCAGCACGCACACTTAGTGCCATATA
Found at i:42524836 original size:29 final size:29
Alignment explanation
Indices: 42524808--42524909 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
42524798 CCTCCGAGCT
** * * *
42524808 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
42524837 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
42524866 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
42524895 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
42524910 GATCTCGTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:42529712 original size:40 final size:40
Alignment explanation
Indices: 42529663--42529870 Score: 253
Period size: 40 Copynumber: 5.2 Consensus size: 40
42529653 CAGAATTTAA
* *
42529663 CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
42529703 CCGGTTATAGTATCTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42529743 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
42529782 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42529822 CCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42529863 CCGGATAT
1 CCGGATAT
42529871 CATTCGAATA
Statistics
Matches: 144, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 78 0.54
41 28 0.19
42 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42529793 original size:79 final size:79
Alignment explanation
Indices: 42529659--42529867 Score: 246
Period size: 79 Copynumber: 2.6 Consensus size: 79
42529649 CCTTCAGAAT
* * * *
42529659 TTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTATAGTATCTCGCAC
1 TTAACCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCAC
42529723 AAATGCCTTCGGGA-C
65 AAATGCCTTC-GGATC
* *
42529738 TTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
1 TTAA-CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCA
42529801 CAAATGCCTTCGGATC
64 CAAATGCCTTCGGATC
* * *
42529817 TTAGTCCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 TTA-ACCGGATATAGT-AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
42529868 TATCATTCGA
Statistics
Matches: 111, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.03
79 52 0.47
80 45 0.41
81 11 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
TTAACCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACA
AATGCCTTCGGATC
Found at i:42530585 original size:2 final size:2
Alignment explanation
Indices: 42530578--42530609 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42530568 ATGTGCAAAC
42530578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42530610 GTGCAAGAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42532138 original size:43 final size:43
Alignment explanation
Indices: 42532089--42532187 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
42532079 AAAAACACTG
* * *
42532089 CTAAAGGTCATGATCTTTAGCGGCGCTTTTACCACAAACGCCG
1 CTAAAGGTCATGACCTTTAGCGGCGCTTTTACCAAAAACGCCA
* * * * *
42532132 TTAAAGGTCAAGACCTTTAGTGGTGCTTTTCCCAAAAACGCCA
1 CTAAAGGTCATGACCTTTAGCGGCGCTTTTACCAAAAACGCCA
42532175 CTAAAGGTCATGA
1 CTAAAGGTCATGA
42532188 AATTTAAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.26
Consensus pattern (43 bp):
CTAAAGGTCATGACCTTTAGCGGCGCTTTTACCAAAAACGCCA
Found at i:42532492 original size:19 final size:19
Alignment explanation
Indices: 42532447--42532493 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
42532437 TAAATATTAA
*
42532447 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
42532466 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
42532485 AATAAAAAT
1 AATAAAAAT
42532494 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:42532986 original size:23 final size:24
Alignment explanation
Indices: 42532896--42532992 Score: 108
Period size: 23 Copynumber: 4.1 Consensus size: 24
42532886 TTCCAGCAAC
* **
42532896 TAAACACTTCAATTTGCATTACTT
1 TAAACACTTCAATTTACAGCACTT
* *
42532920 AAAACACTTCAATTTACAACA-TT
1 TAAACACTTCAATTTACAGCACTT
* *
42532943 TAAGCACTTCAATTTATAGCA-TT
1 TAAACACTTCAATTTACAGCACTT
*
42532966 TAAACACTTCAATTTGCAGCACTT
1 TAAACACTTCAATTTACAGCACTT
42532990 TAA
1 TAA
42532993 TTTAGTAGGG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 39 0.64
24 22 0.36
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (24 bp):
TAAACACTTCAATTTACAGCACTT
Found at i:42536930 original size:7 final size:7
Alignment explanation
Indices: 42536902--42536951 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
42536892 TTAAATATTA
42536902 AATTTTT
1 AATTTTT
42536909 AAGTTTTT
1 AA-TTTTT
*
42536917 -TTTTTT
1 AATTTTT
*
42536923 ATTTTTT
1 AATTTTT
42536930 AATTTTT
1 AATTTTT
42536937 AATTTTT
1 AATTTTT
42536944 AAATTTTT
1 -AATTTTT
42536952 TTTGAAGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
6 5 0.13
7 21 0.55
8 12 0.32
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (7 bp):
AATTTTT
Found at i:42536935 original size:15 final size:15
Alignment explanation
Indices: 42536917--42536952 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
42536907 TTAAGTTTTT
*
42536917 TTTTTTATTTTTTAA
1 TTTTTTATTTTTAAA
*
42536932 TTTTTAATTTTTAAA
1 TTTTTTATTTTTAAA
42536947 TTTTTT
1 TTTTTT
42536953 TTGAAGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTATTTTTAAA
Found at i:42537570 original size:15 final size:15
Alignment explanation
Indices: 42537538--42537580 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
42537528 TTATCTCTTA
42537538 CATAA-CCATAAA-C
1 CATAATCCATAAACC
*
42537551 CATAATCCCTAAACC
1 CATAATCCATAAACC
42537566 CATAATCCATAAACC
1 CATAATCCATAAACC
42537581 TTAAAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 5 0.19
14 6 0.23
15 15 0.58
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.19
Consensus pattern (15 bp):
CATAATCCATAAACC
Found at i:42537585 original size:22 final size:22
Alignment explanation
Indices: 42537543--42537585 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42537533 TCTTACATAA
*
42537543 CCATAAACCATAATCCCTAAAC
1 CCATAAACCATAAACCCTAAAC
* *
42537565 CCATAATCCATAAACCTTAAA
1 CCATAAACCATAAACCCTAAA
42537586 ATAGTAACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.21
Consensus pattern (22 bp):
CCATAAACCATAAACCCTAAAC
Found at i:42538509 original size:19 final size:19
Alignment explanation
Indices: 42538473--42538511 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
42538463 TTTTCATCAT
* *
42538473 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
42538492 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
42538511 A
1 A
42538512 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:42539024 original size:28 final size:29
Alignment explanation
Indices: 42538950--42539038 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 29
42538940 CAGCATGGCT
* * *
42538950 ACCAGATACAGA-AA-ATGTGACAGAGTC
1 ACCAGATACAGATAATTTGTGGCAGAGCC
* *
42538977 ACCAGATATAGATAATTTGTGGCAGGGCC
1 ACCAGATACAGATAATTTGTGGCAGAGCC
*
42539006 ACCAGA-ACAGATAATTTGTGGCATAGCC
1 ACCAGATACAGATAATTTGTGGCAGAGCC
42539034 ACCAG
1 ACCAG
42539039 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
27 11 0.21
28 26 0.50
29 15 0.29
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (29 bp):
ACCAGATACAGATAATTTGTGGCAGAGCC
Found at i:42539191 original size:28 final size:28
Alignment explanation
Indices: 42539144--42539235 Score: 141
Period size: 28 Copynumber: 3.3 Consensus size: 28
42539134 AAATTAACCC
*
42539144 TAGGGGTATAGA-GGTCATTTTGCATACA
1 TAGGGGTATA-ATGGTAATTTTGCATACA
*
42539172 TAGGGGTATAATGGTAATTTTGTATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
42539200 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
*
42539228 TAAGGGTA
1 TAGGGGTA
42539236 CTCTAGTACA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 1 0.02
28 58 0.98
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:42543709 original size:39 final size:39
Alignment explanation
Indices: 42543591--42543773 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
42543581 TCGTTCAAAC
* * ** * **
42543591 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
42543631 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
*
42543671 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
42543710 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
42543749 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
42543774 CTCGAACATT
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:42551143 original size:39 final size:39
Alignment explanation
Indices: 42551025--42551207 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
42551015 TCGTTCAAAC
* * ** * **
42551025 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
42551065 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
*
42551105 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
42551144 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
42551183 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
42551208 CTCGAACATT
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:42554997 original size:19 final size:19
Alignment explanation
Indices: 42554961--42554999 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
42554951 TTTTCATCAT
* *
42554961 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
42554980 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
42554999 A
1 A
42555000 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:42555514 original size:28 final size:28
Alignment explanation
Indices: 42555464--42555554 Score: 130
Period size: 28 Copynumber: 3.2 Consensus size: 28
42555454 GTGACAGAGT
* *
42555464 CACCAGATATAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGTGC
*
42555493 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGTGC
42555521 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGATAATTTGTGGCAGT-GC
42555549 CACCAG
1 CACCAG
42555555 GATGCTTCCT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
28 50 0.88
29 7 0.12
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGTGC
Found at i:42555707 original size:28 final size:28
Alignment explanation
Indices: 42555676--42555752 Score: 154
Period size: 28 Copynumber: 2.8 Consensus size: 28
42555666 TGTAGAGGTC
42555676 ATTTTGCATACATAGGGGTATAATGGTA
1 ATTTTGCATACATAGGGGTATAATGGTA
42555704 ATTTTGCATACATAGGGGTATAATGGTA
1 ATTTTGCATACATAGGGGTATAATGGTA
42555732 ATTTTGCATACATAGGGGTAT
1 ATTTTGCATACATAGGGGTAT
42555753 TCTAGTACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (28 bp):
ATTTTGCATACATAGGGGTATAATGGTA
Found at i:42556017 original size:8 final size:8
Alignment explanation
Indices: 42556001--42556032 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
42555991 CCCAAAAAAC
42556001 CGGCTTTT
1 CGGCTTTT
*
42556009 CGGCATTT
1 CGGCTTTT
42556017 CGGCTTTT
1 CGGCTTTT
42556025 CGGCTTTT
1 CGGCTTTT
42556033 ACCGATCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.25, G:0.25, T:0.47
Consensus pattern (8 bp):
CGGCTTTT
Found at i:42557957 original size:17 final size:18
Alignment explanation
Indices: 42557931--42557965 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42557921 AGGGTTATAG
*
42557931 TTTAGTGTTTAG-GGTTT
1 TTTAGGGTTTAGAGGTTT
42557948 TTTAGGGTTTAGAGGTTT
1 TTTAGGGTTTAGAGGTTT
42557966 AGTGTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.54
Consensus pattern (18 bp):
TTTAGGGTTTAGAGGTTT
Found at i:42557974 original size:54 final size:54
Alignment explanation
Indices: 42557907--42558019 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 54
42557897 TTTTTTTGGG
* * *
42557907 GGTTTAGGGTTTTAAGGGTTATAGTTTAGTGTTTAGGGTTTTTTAG-GGTTTAGA
1 GGTTTAGGGTTTTAAGGGTTATAGATTAATGTTTAGGATTTTTTAGAGGTTTA-A
* * *
42557961 GGTTTAGTGTTTTAAGGGTTATAGATTAATGTTTATGATTTTTTGGAGGTTTAA
1 GGTTTAGGGTTTTAAGGGTTATAGATTAATGTTTAGGATTTTTTAGAGGTTTAA
42558015 GGTTT
1 GGTTT
42558020 TAAGGGTTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 46 0.88
55 6 0.12
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (54 bp):
GGTTTAGGGTTTTAAGGGTTATAGATTAATGTTTAGGATTTTTTAGAGGTTTAA
Found at i:42558104 original size:41 final size:40
Alignment explanation
Indices: 42558059--42558138 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
42558049 TACTGAAAGT
* * *
42558059 GCCACTAATACTCTGGTTTTTAGCGGCTTTTTACCAAAAAC
1 GCCACTAATACT-TGGTTTTTAGCAGCGTTTTAACAAAAAC
* * *
42558100 GCCACTATTGCTTTGTTTTTAGCAGCGTTTTAACAAAAA
1 GCCACTAATACTTGGTTTTTAGCAGCGTTTTAACAAAAA
42558139 ATGCCGCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 23 0.70
41 10 0.30
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (40 bp):
GCCACTAATACTTGGTTTTTAGCAGCGTTTTAACAAAAAC
Found at i:42558131 original size:40 final size:41
Alignment explanation
Indices: 42558074--42558164 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
42558064 TAATACTCTG
* * *
42558074 GTTTTTAGCGGC-TTTTTACCAAAAACGCCACTATTGCTTT
1 GTTTTTAGCAGCGTTTTAACAAAAAACGCCACTATTGCTTT
* *
42558114 GTTTTTAGCAGCGTTTTAACAAAAAATGCCGCTATTGCTTT
1 GTTTTTAGCAGCGTTTTAACAAAAAACGCCACTATTGCTTT
42558155 GTTTTTAGCA
1 GTTTTTAGCA
42558165 TTTTACAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 11 0.24
41 34 0.76
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (41 bp):
GTTTTTAGCAGCGTTTTAACAAAAAACGCCACTATTGCTTT
Found at i:42559527 original size:20 final size:21
Alignment explanation
Indices: 42559502--42559548 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
42559492 TTAATTAAGG
42559502 TTAAAATTATAAT-TTAATAA
1 TTAAAATTATAATCTTAATAA
42559522 TTAAAA-TATAATCTTAATAA
1 TTAAAATTATAATCTTAATAA
*
42559542 TAAAAAT
1 TTAAAAT
42559549 AACATGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAAATTATAATCTTAATAA
Found at i:42560044 original size:13 final size:13
Alignment explanation
Indices: 42560026--42560050 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42560016 CTTATGATAT
42560026 GTGTGAAAATTTC
1 GTGTGAAAATTTC
42560039 GTGTGAAAATTT
1 GTGTGAAAATTT
42560051 GATCATTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:42561206 original size:44 final size:42
Alignment explanation
Indices: 42561140--42561291 Score: 108
Period size: 43 Copynumber: 3.5 Consensus size: 42
42561130 ATATATGTTA
* ** *
42561140 TCGTGTAAGACCACATCCGGGACATTAACATCG-ACTTATGATT
1 TCGTATAAGACCATGTCTGGGACATTAACATCGTA-TT-TGATT
* * * *
42561183 TACGTGTAAGGCCATGTCTGGGACGTTGACATCGTATTTGATT
1 T-CGTATAAGACCATGTCTGGGACATTAACATCGTATTTGATT
* * * **
42561226 TTGTATAAGACCCTGTCTGGGACAGTGGCATCGATATTTGATT
1 TCGTATAAGACCATGTCTGGGACATTAACATCG-TATTTGATT
* * * *
42561269 ACATGTAAGACCACGTCTGGGAC
1 TCGTATAAGACCATGTCTGGGAC
42561292 GTTGGCATTG
Statistics
Matches: 87, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
42 25 0.29
43 33 0.38
44 28 0.32
45 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (42 bp):
TCGTATAAGACCATGTCTGGGACATTAACATCGTATTTGATT
Found at i:42561278 original size:43 final size:42
Alignment explanation
Indices: 42561182--42561299 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 42
42561172 GACTTATGAT
* * *
42561182 TTACGTGTAAGGCCATGTCTGGGACGTTGACATCGTATTTGA
1 TTACGTGTAAGACCCTGTCTGGGACGTTGGCATCGTATTTGA
** *
42561224 TTTTGTATAAGACCCTGTCTGGGACAG-TGGCATCGATATTTGA
1 TTACGTGTAAGACCCTGTCTGGGAC-GTTGGCATCG-TATTTGA
*
42561267 TTACATGTAAGACCAC-GTCTGGGACGTTGGCAT
1 TTACGTGTAAGACC-CTGTCTGGGACGTTGGCAT
42561300 TGTACGAGCT
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
42 28 0.45
43 33 0.53
44 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
TTACGTGTAAGACCCTGTCTGGGACGTTGGCATCGTATTTGA
Found at i:42564701 original size:46 final size:46
Alignment explanation
Indices: 42564613--42564785 Score: 138
Period size: 46 Copynumber: 3.7 Consensus size: 46
42564603 ACATCTGGTA
* * *
42564613 GCCGATGCATGTCCTAAACATGTCTTACCCTGATTTA-T-GTCTCGAG
1 GCCGATGCATGTCCCAAACATGTCTTACACT-A-GTACTCGTCTCGAG
* * *
42564659 GCCAATGCATGTCCCAAACATGTCTTACACTAGTACTCGTCTCAAT
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGTACTCGTCTCGAG
* * * * * *
42564705 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCT-CTCATAAT-GTG
1 GCCGATG-CATGTCCCAAACAT-GTCTTACACTAG-TACTCGT-CTCGAG
* *
42564753 GTCGATGCATGTCCCAGACATGTCTTACACTAG
1 GCCGATGCATGTCCCAAACATGTCTTACACTAG
42564786 CTCACAGTAA
Statistics
Matches: 103, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
44 2 0.02
45 2 0.02
46 50 0.49
47 27 0.26
48 20 0.19
49 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (46 bp):
GCCGATGCATGTCCCAAACATGTCTTACACTAGTACTCGTCTCGAG
Found at i:42576246 original size:27 final size:27
Alignment explanation
Indices: 42576216--42576647 Score: 321
Period size: 27 Copynumber: 16.0 Consensus size: 27
42576206 TGTAAGGTAG
* **
42576216 AATTACTGAAATACCCTTGGTTTACAA
1 AATTACTGAAATACCCTTGATTTGTAA
* * * * * **
42576243 AATTATTG-AGTATCTTTGGTTTAAAA
1 AATTACTGAAATACCCTTGATTTGTAA
* * * * *
42576269 AATTACTAAAACACCCTCGATTAGCAA
1 AATTACTGAAATACCCTTGATTTGTAA
* * *
42576296 AATTAC-CAAATTACCATTGATTTATAA
1 AATTACTGAAA-TACCCTTGATTTGTAA
** * *
42576323 AATTACCAAAATACCCTTAATTTGTGA
1 AATTACTGAAATACCCTTGATTTGTAA
* ** * *
42576350 AATTATTGAAATACCCTCAACTTGTGA
1 AATTACTGAAATACCCTTGATTTGTAA
* *
42576377 AATTACTGAAATACCCTCGACTTGTAA
1 AATTACTGAAATACCCTTGATTTGTAA
* *
42576404 AATTACTGAAATACCCTCGACTTGTAA
1 AATTACTGAAATACCCTTGATTTGTAA
*
42576431 AATTACTGAAATACCCTTGACTTGTAA
1 AATTACTGAAATACCCTTGATTTGTAA
* ** *
42576458 AATTACCGAAATACCCTCAACTTGTAA
1 AATTACTGAAATACCCTTGATTTGTAA
* *
42576485 AATTACTGAAATACCCCTGATTTGGAA
1 AATTACTGAAATACCCTTGATTTGTAA
* *
42576512 AATTACCGAAATACCCTTGATTTGGAA
1 AATTACTGAAATACCCTTGATTTGTAA
** * * **
42576539 AATTACAAAAATACCCCTAATTTACAA
1 AATTACTGAAATACCCTTGATTTGTAA
**
42576566 AATTA-TAGAAATACCCTTGACTTTAAAAA
1 AATTACT-GAAATACCCTTGA-TTT-GTAA
* * * *
42576595 AATTACAGAAATACCATTGGTTTGCAA
1 AATTACTGAAATACCCTTGATTTGTAA
* *
42576622 AATTACTAAAATACCCTTGGTTTGTA
1 AATTACTGAAATACCCTTGATTTGTA
42576648 GATTTACCAA
Statistics
Matches: 330, Mismatches: 68, Indels: 14
0.80 0.17 0.03
Matches are distributed among these distances:
26 23 0.07
27 279 0.85
28 9 0.03
29 19 0.06
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (27 bp):
AATTACTGAAATACCCTTGATTTGTAA
Found at i:42576654 original size:27 final size:27
Alignment explanation
Indices: 42576593--42576667 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
42576583 TGACTTTAAA
42576593 AAAATTA-CAGAAATACCATTGGTTTGC
1 AAAATTACCA-AAATACCATTGGTTTGC
* * *
42576620 AAAATTACTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCATTGGTTTGC
* * *
42576647 AGATTTACCAAAACACCATTG
1 AAAATTACCAAAATACCATTG
42576668 TAGGGTGAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCATTGGTTTGC
Done.