Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 128 of 167
Found at i:42964975 original size:25 final size:25
Alignment explanation
Indices: 42964808--42965017 Score: 98
Period size: 25 Copynumber: 8.4 Consensus size: 25
42964798 CATAGATCTT
*
42964808 ATGAGCTTCCTGA-T-TATGGCTCTC
1 ATGAGCTTCCT-ATTATATGGCTCAC
**
42964832 ATGAGCTTCCTGATTA-ATGGCTTTTC
1 ATGAGCTTCCT-ATTATATGGC-TCAC
* *
42964858 A-GAGCTTCCCGA-TATTTGGCTCTA-
1 ATGAGCTT-CCTATTATATGGCTC-AC
* * **
42964882 TTGAGCTTCCCATT-TATGGCTCGT
1 ATGAGCTTCCTATTATATGGCTCAC
* *
42964906 ATGAGCTTCCCTATAAT-TGGCTCGC
1 ATGAGCTT-CCTATTATATGGCTCAC
* ** *
42964931 AAGAGCTTCCCGTTACATGGCTCAC
1 ATGAGCTTCCTATTATATGGCTCAC
*
42964956 ATGAGCTTCCTATTATATGGATCGA-
1 ATGAGCTTCCTATTATATGGCTC-AC
* * *
42964981 AAGAGCTACCCATTTATAT-GCTCAC
1 ATGAGCTTCCTA-TTATATGGCTCAC
42965006 ATGAGCATTCCT
1 ATGAGC-TTCCT
42965018 GAATATGAAT
Statistics
Matches: 139, Mismatches: 31, Indels: 30
0.69 0.16 0.15
Matches are distributed among these distances:
24 38 0.27
25 84 0.60
26 17 0.12
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCCTATTATATGGCTCAC
Found at i:42965058 original size:17 final size:19
Alignment explanation
Indices: 42965020--42965059 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42965010 GCATTCCTGA
*
42965020 ATATGAATTGATAGATATT
1 ATATGAATTGACAGATATT
42965039 ATATGAATTGACA-A-ATT
1 ATATGAATTGACAGATATT
42965056 ATAT
1 ATAT
42965060 TTTTGTACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (19 bp):
ATATGAATTGACAGATATT
Found at i:42969901 original size:11 final size:11
Alignment explanation
Indices: 42969881--42969913 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
42969871 CTGATTCACT
42969881 AAAA-ACATAG
1 AAAATACATAG
42969891 AAAATACATAG
1 AAAATACATAG
42969902 AAAATACATAG
1 AAAATACATAG
42969913 A
1 A
42969914 GTAAGCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.15
Consensus pattern (11 bp):
AAAATACATAG
Found at i:42988094 original size:180 final size:180
Alignment explanation
Indices: 42987792--42988151 Score: 711
Period size: 180 Copynumber: 2.0 Consensus size: 180
42987782 GGGAATGAAA
*
42987792 ACTAAGACGAGTCATGTTATTATTTTCTGAATCGTATGATAAATATTTAACTTGTTCTTAATTAT
1 ACTAAGACGAATCATGTTATTATTTTCTGAATCGTATGATAAATATTTAACTTGTTCTTAATTAT
42987857 GTGTTCTTAATTCTTGTTTTGATATCCCAGGATACTGATTCAAGATAAACTCTTATTTAGAGGTG
66 GTGTTCTTAATTCTTGTTTTGATATCCCAGGATACTGATTCAAGATAAACTCTTATTTAGAGGTG
42987922 GAATAGACCCTGGCTAAAAGTACATTTATCATAATTAAGCGGAGTTGATT
131 GAATAGACCCTGGCTAAAAGTACATTTATCATAATTAAGCGGAGTTGATT
42987972 ACTAAGACGAATCATGTTATTATTTTCTGAATCGTATGATAAATATTTAACTTGTTCTTAATTAT
1 ACTAAGACGAATCATGTTATTATTTTCTGAATCGTATGATAAATATTTAACTTGTTCTTAATTAT
42988037 GTGTTCTTAATTCTTGTTTTGATATCCCAGGATACTGATTCAAGATAAACTCTTATTTAGAGGTG
66 GTGTTCTTAATTCTTGTTTTGATATCCCAGGATACTGATTCAAGATAAACTCTTATTTAGAGGTG
42988102 GAATAGACCCTGGCTAAAAGTACATTTATCATAATTAAGCGGAGTTGATT
131 GAATAGACCCTGGCTAAAAGTACATTTATCATAATTAAGCGGAGTTGATT
42988152 GCGAGCCTAG
Statistics
Matches: 179, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 179 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.39
Consensus pattern (180 bp):
ACTAAGACGAATCATGTTATTATTTTCTGAATCGTATGATAAATATTTAACTTGTTCTTAATTAT
GTGTTCTTAATTCTTGTTTTGATATCCCAGGATACTGATTCAAGATAAACTCTTATTTAGAGGTG
GAATAGACCCTGGCTAAAAGTACATTTATCATAATTAAGCGGAGTTGATT
Found at i:42991267 original size:40 final size:40
Alignment explanation
Indices: 42991193--42991364 Score: 181
Period size: 40 Copynumber: 4.3 Consensus size: 40
42991183 GATAACCGGA
* * *
42991193 CTAAGATCCGAAGGCATTCATGCGAGTTGCTATAT-TCGGG
1 CTAAGACCCGAAGGCATTTATGCAAGTTGCTATATCT-GGG
* * * *
42991233 CTATGTCCCGAAGGCATTTATGCTAG-TGATTATATCTGGG
1 CTAAGACCCGAAGGCATTTATGCAAGTTG-CTATATCTGGG
*
42991273 CTAAGACCCGAAGGCATTTGTGCAAGTTGCTATATCTGGG
1 CTAAGACCCGAAGGCATTTATGCAAGTTGCTATATCTGGG
** * *
42991313 CTAAGACCCGAAGGCATTTGCGCGAGTTGTTATATCT-GG
1 CTAAGACCCGAAGGCATTTATGCAAGTTGCTATATCTGGG
42991352 CTAA-ATCCCGAAG
1 CTAAGA-CCCGAAG
42991365 ATACTTGGGT
Statistics
Matches: 114, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 95 0.83
41 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.28
Consensus pattern (40 bp):
CTAAGACCCGAAGGCATTTATGCAAGTTGCTATATCTGGG
Found at i:42991326 original size:80 final size:79
Alignment explanation
Indices: 42991193--42991364 Score: 206
Period size: 80 Copynumber: 2.2 Consensus size: 79
42991183 GATAACCGGA
* * * * * *
42991193 CTAAGATCCGAAGGCATTCATGCGAGTTGCTATATTCGGGCTATGTCCCGAAGGCATTTATGCTA
1 CTAAGACCCGAAGGCATTCATGCAAGTTGCTATATTCGGGCTAAGACCCGAAGGCATTTACGCGA
42991258 G-TGATTATATCTGGG
66 GTTG-TTATATCT-GG
** *
42991273 CTAAGACCCGAAGGCATTTGTGCAAGTTGCTATA-TCTGGGCTAAGACCCGAAGGCATTTGCGCG
1 CTAAGACCCGAAGGCATTCATGCAAGTTGCTATATTC-GGGCTAAGACCCGAAGGCATTTACGCG
42991337 AGTTGTTATATCTGG
65 AGTTGTTATATCTGG
42991352 CTAA-ATCCCGAAG
1 CTAAGA-CCCGAAG
42991365 ATACTTGGGT
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 15 0.19
80 62 0.77
81 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.28
Consensus pattern (79 bp):
CTAAGACCCGAAGGCATTCATGCAAGTTGCTATATTCGGGCTAAGACCCGAAGGCATTTACGCGA
GTTGTTATATCTGG
Found at i:42999258 original size:24 final size:24
Alignment explanation
Indices: 42999213--42999259 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
42999203 TATATATACC
42999213 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
42999237 AATTC-ATCATATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
42999260 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:43003178 original size:27 final size:27
Alignment explanation
Indices: 43003148--43003202 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
43003138 TTAAACCAAG
*
43003148 AATTGAAAACTAAATCCGAAAGCACAC
1 AATTGAAAACTAAAACCGAAAGCACAC
43003175 AATTGAAAACTAAAACCGAAAGCACAC
1 AATTGAAAACTAAAACCGAAAGCACAC
43003202 A
1 A
43003203 CACTTCCCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.55, C:0.22, G:0.11, T:0.13
Consensus pattern (27 bp):
AATTGAAAACTAAAACCGAAAGCACAC
Found at i:43007631 original size:40 final size:40
Alignment explanation
Indices: 43007572--43007851 Score: 408
Period size: 40 Copynumber: 7.1 Consensus size: 40
43007562 CGGATGATAA
*
43007572 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
43007612 CCGGGCTAAGTCCCAAAGGCA-TTGTGCGAGTTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
43007650 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
43007690 CCGGGCTAAGTCCCAAAGGCA-TTGTGCGAGTTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
43007728 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
43007768 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
43007808 CCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
43007848 CCGG
1 CCGG
43007852 TTAAATTCCG
Statistics
Matches: 214, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
38 40 0.19
39 61 0.29
40 113 0.53
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:43007700 original size:78 final size:78
Alignment explanation
Indices: 43007571--43007851 Score: 465
Period size: 78 Copynumber: 3.6 Consensus size: 78
43007561 TCGGATGATA
43007571 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCAAAGGCATTG
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCAAAGGCATTG
43007636 TGCGAGTTATTAT
66 TGCGAGTTATTAT
43007649 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCAAAGGCATTG
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCAAAGGCATTG
43007714 TGCGAGTTATTAT
66 TGCGAGTTATTAT
* * * *
43007727 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGCATTG
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCAAAGGCATT-
*
43007792 GTGCGAGTTACTAT
65 GTGCGAGTTATTAT
* *
43007806 AACCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCCGG
1 -ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTA-CTATATCCGG
43007852 TTAAATTCCG
Statistics
Matches: 191, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
78 138 0.72
79 15 0.08
80 38 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (78 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCAAAGGCATTG
TGCGAGTTATTAT
Found at i:43007780 original size:118 final size:118
Alignment explanation
Indices: 43007568--43007851 Score: 412
Period size: 118 Copynumber: 2.4 Consensus size: 118
43007558 TATTCGGATG
*
43007568 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCAAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCAAAGGCA
** * *
43007633 TTGTGCGAGTTATTATACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACT
66 TTGTGCGAGTTACCAAACCGGGCTAAGTCCCGAAGGCATTGGTGCGAGCTACT
* * * *
43007686 ATATCCGGGCTAAGTCCCAAAGGCA-TTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCAAAGGCA
*
43007749 TTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACT
66 -TTGTGCGAGTTACCAAA-CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGCTACT
* *
43007804 ATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCCGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG
43007852 TTAAATTCCG
Statistics
Matches: 146, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
116 20 0.14
117 29 0.20
118 81 0.55
119 12 0.08
120 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (118 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCAAAGGCA
TTGTGCGAGTTACCAAACCGGGCTAAGTCCCGAAGGCATTGGTGCGAGCTACT
Found at i:43016910 original size:40 final size:40
Alignment explanation
Indices: 43016855--43017142 Score: 488
Period size: 40 Copynumber: 7.2 Consensus size: 40
43016845 TATTCGGATG
43016855 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
43016895 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
43016935 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
43016975 AAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
43017015 AAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
43017055 AAATCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
43017095 ATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
43017135 ATATCCGG
1 ATATCCGG
43017143 TTAAATTCCG
Statistics
Matches: 237, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
39 2 0.01
40 235 0.99
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:43022329 original size:48 final size:48
Alignment explanation
Indices: 43022243--43022386 Score: 184
Period size: 48 Copynumber: 3.0 Consensus size: 48
43022233 CGCATAGTAA
* * *
43022243 GATGCCAATGCCATA-TCCTAGATAT-GTCTTACATGGGATCAAATATC
1 GATGCCAATGCCA-AGTCCCAGACATGGTCTTACATGGGATCACATATC
* * * *
43022290 GATGCCAATGCCAAGTCTCAGGCATGGTCTTATATGGGATCACATATT
1 GATGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGATCACATATC
* *
43022338 GATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGATCACATATC
43022386 G
1 G
43022387 CCCTAATGTA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
46 1 0.01
47 19 0.23
48 62 0.76
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (48 bp):
GATGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:43046138 original size:38 final size:38
Alignment explanation
Indices: 43046095--43046170 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
43046085 TTCATCCTTT
*
43046095 TTCATTTCTTCTGGCCGAAAATTCTAAGGAATGAGGAA
1 TTCATTTCTTCTGGCCGAAAATTCTAAGGAAGGAGGAA
*
43046133 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTCTGGCCGAAAATTCTAAGGAAGGAGGAA
43046171 GGAGTTCTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTCTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:43047453 original size:40 final size:40
Alignment explanation
Indices: 43047359--43047503 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
43047349 TACTCGAATG
*
43047359 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
43047400 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
43047440 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
43047480 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
43047504 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:43062865 original size:50 final size:50
Alignment explanation
Indices: 43062811--43062930 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
43062801 GAGGAAGTGC
* * *
43062811 AAAAGGGCTATGCCCTAGTTTACCGAAAAGGGTTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTATCA
* * * *
43062861 AAAAGGGTTTTGCCCCAGTTTATCAAAAAGGGCTTTGCCCCAG-TTAT-T
1 AAAAGGGCTATGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTATCA
*
43062909 AAAAGAGGCTAGGCCTCCAGTT
1 AAAAG-GGCTATGCC-CCAGTT
43062931 ATATGATAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
48 5 0.09
49 10 0.17
50 43 0.74
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (50 bp):
AAAAGGGCTATGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTATCA
Found at i:43062918 original size:24 final size:25
Alignment explanation
Indices: 43062811--43062905 Score: 136
Period size: 25 Copynumber: 3.8 Consensus size: 25
43062801 GAGGAAGTGC
* * * *
43062811 AAAAGGGCTATGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
43062836 AAAAGGGTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
43062861 AAAAGGGTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
43062886 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
43062906 ATTAAAAGAG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:43063859 original size:12 final size:13
Alignment explanation
Indices: 43063842--43063870 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
43063832 CATTAGAACT
43063842 TTTATTTTA-TTA
1 TTTATTTTACTTA
43063854 TTTATTTTACTTA
1 TTTATTTTACTTA
43063867 TTTA
1 TTTA
43063871 AAATTCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTTACTTA
Found at i:43071698 original size:76 final size:73
Alignment explanation
Indices: 43071574--43071718 Score: 236
Period size: 76 Copynumber: 1.9 Consensus size: 73
43071564 TGACTTATGC
*
43071574 CAGACGGCCAAGCACGCCCATGTGCTGAGCCATGTGGAGCATATTGACTTGGTTTCTAATAAACA
1 CAGACGGCCAAGCACGCCCATGTGCTGAGCCATGTGGAGCATACTGACTTGGTTTCTAATAAACA
43071639 TCAGCAGA
66 TCAGCAGA
* *
43071647 CAGACGGCCAAGTTACACGCCCATGTGCTGGGCCGTGTGGAGCATACTGACTTGGTTTCTAATAA
1 CAGACGGCCAAG---CACGCCCATGTGCTGAGCCATGTGGAGCATACTGACTTGGTTTCTAATAA
43071712 ACATCAG
63 ACATCAG
43071719 GGGATACACG
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
73 12 0.18
76 54 0.82
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.23
Consensus pattern (73 bp):
CAGACGGCCAAGCACGCCCATGTGCTGAGCCATGTGGAGCATACTGACTTGGTTTCTAATAAACA
TCAGCAGA
Found at i:43077254 original size:15 final size:15
Alignment explanation
Indices: 43077234--43077270 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
43077224 AGCTTCAACT
43077234 CGGACACACAGTGTA
1 CGGACACACAGTGTA
43077249 CGGACACACAGTGTA
1 CGGACACACAGTGTA
43077264 CGGACAC
1 CGGACAC
43077271 TTAGAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.30, G:0.27, T:0.11
Consensus pattern (15 bp):
CGGACACACAGTGTA
Found at i:43079598 original size:6 final size:6
Alignment explanation
Indices: 43079587--43079617 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
43079577 TTTTTTGCTT
*
43079587 GGTTAG GGTTAG GGTTAG GGTTAG AGTTAG G
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG G
43079618 ATTTTAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.32
Consensus pattern (6 bp):
GGTTAG
Found at i:43080114 original size:128 final size:126
Alignment explanation
Indices: 43079730--43080124 Score: 583
Period size: 126 Copynumber: 3.1 Consensus size: 126
43079720 TAAAAACTTT
*
43079730 TTTTTCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTTCAAA
1 TTTTTCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCCAAA
** * * *
43079795 ACACTTCAAGCAGGATGGACTGTCAGCAAAATTACAGGAAAAAGCTCCCACGTGGATGCTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGATGCTC
43079856 TTTTTCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCCAAA
1 TTTTTCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCCAAA
* * * * * * *
43079921 ATGGTTCAAGCAGGATACACTGTCACCAAAATTACTGAAAAAAACTCCCACGTGAATGTTTTT
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGATG--CTC
* * * *
43079984 TTTTTCTACAGTAGCATCTGAAAAAATAATTTTGAAAAGACATTTCTGAACAAATAGTATCCAAA
1 TTTTTCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCCAAA
* * **
43080049 ATGCTTCAAGCAGGATGCACTGTCAGGAAAATTACTGAAAAAAGCTCCAACGTGGACACTC
66 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGATGCTC
43080110 TTTTTCTACAGTAGT
1 TTTTTCTACAGTAGT
43080125 TCCTATTTGG
Statistics
Matches: 238, Mismatches: 29, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
126 127 0.53
128 111 0.47
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCCAAA
ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGATGCTC
Found at i:43082060 original size:42 final size:41
Alignment explanation
Indices: 43082000--43082104 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 41
43081990 ATTAGCCGCT
*
43082000 GCAAAAGGTAAAGCAATAGTGGCATTTTT-TACATAAATGTC
1 GCAAAAGGTAAAGCAATAGTGGCATTTTTCT-CATAAACGTC
* *
43082041 GCCAAAAGGTAAAGCAATAGCGGCATTTTTCTCATAAACGTT
1 G-CAAAAGGTAAAGCAATAGTGGCATTTTTCTCATAAACGTC
* *
43082083 GCAAAACGTAAAGGAATAGTGG
1 GCAAAAGGTAAAGCAATAGTGG
43082105 TGATTATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
41 19 0.34
42 36 0.64
43 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (41 bp):
GCAAAAGGTAAAGCAATAGTGGCATTTTTCTCATAAACGTC
Found at i:43084360 original size:30 final size:30
Alignment explanation
Indices: 43084324--43084409 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 30
43084314 TAGTGATTTG
*
43084324 TGAAAATTGAATTAAATTTAAATTTTATGTA
1 TGAAAATT-AATTAAATTTAAATTTCATGTA
* *
43084355 T-AAAATT-ATAAAAAATTAAATTTCATGTA
1 TGAAAATTAAT-TAAATTTAAATTTCATGTA
* *
43084384 TGAAAATACACATTAAATTAAAATTT
1 TGAAAAT-TA-ATTAAATTTAAATTT
43084410 ATATTTAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.05
29 17 0.40
30 11 0.26
31 1 0.02
32 10 0.23
33 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (30 bp):
TGAAAATTAATTAAATTTAAATTTCATGTA
Found at i:43086522 original size:43 final size:43
Alignment explanation
Indices: 43086438--43086563 Score: 182
Period size: 43 Copynumber: 3.0 Consensus size: 43
43086428 GCGTTTATAA
* * * *
43086438 GGAAAGCGTCACTAAAGATCATG-TCTTTAGCGGAATTTTTGG
1 GGAAAGCGCCACTAAAGGTCATGTTCTTTAGTGGCATTTTTGG
*
43086480 GGAAAGCGCCGCTAAAGGTCATGTTCTTTAGTGGCATTTTTGG
1 GGAAAGCGCCACTAAAGGTCATGTTCTTTAGTGGCATTTTTGG
* *
43086523 GGAAAGTGCCACTAAAGGTCATGTTCTTTTGTGGCATTTTT
1 GGAAAGCGCCACTAAAGGTCATGTTCTTTAGTGGCATTTTT
43086564 TTGTAAAAAC
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 20 0.27
43 55 0.73
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (43 bp):
GGAAAGCGCCACTAAAGGTCATGTTCTTTAGTGGCATTTTTGG
Found at i:43090689 original size:9 final size:9
Alignment explanation
Indices: 43090677--43090751 Score: 55
Period size: 9 Copynumber: 8.4 Consensus size: 9
43090667 AGAATTTTTT
43090677 AAAATTATA
1 AAAATTATA
*
43090686 AAAATTAAA
1 AAAATTATA
*
43090695 AAAAGTATA
1 AAAATTATA
*
43090704 TAAA-TAT-
1 AAAATTATA
*
43090711 AAAATTATT
1 AAAATTATA
*
43090720 AAAATTACA
1 AAAATTATA
** *
43090729 TTAATATATT
1 AAAAT-TATA
43090739 AAAATTATA
1 AAAATTATA
43090748 AAAA
1 AAAA
43090752 AATTTAAATT
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
7 3 0.06
8 6 0.12
9 35 0.71
10 5 0.10
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:43090723 original size:25 final size:28
Alignment explanation
Indices: 43090686--43090751 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 28
43090676 TAAAATTATA
* *
43090686 AAAATTAAAAAAAGTATA-TAA-ATA-T
1 AAAATTATAAAAAGTACATTAATATATT
* *
43090711 AAAATTATTAAAATTACATTAATATATT
1 AAAATTATAAAAAGTACATTAATATATT
43090739 AAAATTATAAAAA
1 AAAATTATAAAAA
43090752 AATTTAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 14 0.42
26 3 0.09
27 3 0.09
28 13 0.39
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAATTATAAAAAGTACATTAATATATT
Found at i:43091306 original size:21 final size:21
Alignment explanation
Indices: 43091280--43091353 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
43091270 TTTTCAATAT
43091280 TTTATAGTTTTTAAATATTTC
1 TTTATAGTTTTTAAATATTTC
*
43091301 TTTATA-ATTTTATAAT-TTTC
1 TTTATAGTTTTTA-AATATTTC
* *
43091321 TAT-TAGTTTTT-AATAATT-
1 TTTATAGTTTTTAAATATTTC
*
43091339 TTTATGGTTTTTAAA
1 TTTATAGTTTTTAAA
43091354 CTTTTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
18 5 0.12
19 11 0.26
20 17 0.40
21 9 0.21
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTATAGTTTTTAAATATTTC
Found at i:43091311 original size:29 final size:29
Alignment explanation
Indices: 43091270--43091353 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
43091260 TCTTAAAACA
*
43091270 TTTTCAAT-ATTTTATAGTTTTTAAATA-
1 TTTTTAATAATTTTATAGTTTTTAAATAG
* * *
43091297 TTTCTTTATAATTTTATAATTTTCT-ATTAG
1 TTT-TTAATAATTTTATAGTTTT-TAAATAG
*
43091327 TTTTTAATAATTTTTATGGTTTTTAAA
1 TTTTTAATAA-TTTTATAGTTTTTAAA
43091354 CTTTTTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
27 3 0.07
28 3 0.07
29 22 0.51
30 15 0.35
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.62
Consensus pattern (29 bp):
TTTTTAATAATTTTATAGTTTTTAAATAG
Found at i:43102773 original size:23 final size:23
Alignment explanation
Indices: 43102747--43102834 Score: 99
Period size: 23 Copynumber: 3.9 Consensus size: 23
43102737 CTGACCACAA
*
43102747 CTCATAAGAGCCTACTGTTTCAG
1 CTCATAAGAGCTTACTGTTTCAG
** * *
43102770 CTCATTGGAGCTTACCGATTCAG
1 CTCATAAGAGCTTACTGTTTCAG
*
43102793 CTCAAAAGAGCTTACTGTTT-AG
1 CTCATAAGAGCTTACTGTTTCAG
43102815 CTCA-ATAGAGCTTACTGTTT
1 CTCATA-AGAGCTTACTGTTT
43102835 ATTAGCTTAG
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
21 1 0.02
22 20 0.37
23 33 0.61
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (23 bp):
CTCATAAGAGCTTACTGTTTCAG
Found at i:43109573 original size:30 final size:30
Alignment explanation
Indices: 43109539--43109600 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
43109529 GAGGGGACGA
43109539 ATCTTGTCCTTAATCGGAAGAAACCATTTT
1 ATCTTGTCCTTAATCGGAAGAAACCATTTT
* *
43109569 ATCTTGTCCTTAATTGGGAGAAACCATTTT
1 ATCTTGTCCTTAATCGGAAGAAACCATTTT
43109599 AT
1 AT
43109601 GTTAAGGAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (30 bp):
ATCTTGTCCTTAATCGGAAGAAACCATTTT
Found at i:43111970 original size:14 final size:14
Alignment explanation
Indices: 43111951--43111977 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43111941 TTTTTAGTGT
43111951 TTATATGTGTGAAC
1 TTATATGTGTGAAC
43111965 TTATATGTGTGAA
1 TTATATGTGTGAA
43111978 ATTTTTGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (14 bp):
TTATATGTGTGAAC
Found at i:43118625 original size:40 final size:40
Alignment explanation
Indices: 43118570--43119243 Score: 1348
Period size: 40 Copynumber: 16.9 Consensus size: 40
43118560 CGGATGATAA
43118570 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43118610 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43118650 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43118690 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43118730 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43118770 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43118810 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43118850 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43118890 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43118930 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43118970 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43119010 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43119050 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43119090 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43119130 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43119170 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
43119210 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA
43119244 AATATCATGC
Statistics
Matches: 634, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 634 1.00
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
Found at i:43119706 original size:22 final size:21
Alignment explanation
Indices: 43119665--43119708 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
43119655 GAATGTGCAT
43119665 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
43119687 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
43119709 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:43122180 original size:20 final size:20
Alignment explanation
Indices: 43122146--43122195 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
43122136 TTTATAGCAC
*
43122146 ATTTATTCATAAAATTTTAGA
1 ATTT-TTCATAAAATTTTACA
*
43122167 ATTTTTCATCAAATTTTACA
1 ATTTTTCATAAAATTTTACA
*
43122187 ACTTTTCAT
1 ATTTTTCAT
43122196 TTCAGTCCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTTTTCATAAAATTTTACA
Found at i:43124001 original size:39 final size:39
Alignment explanation
Indices: 43123947--43124268 Score: 502
Period size: 39 Copynumber: 8.2 Consensus size: 39
43123937 GGTTTTACGA
43123947 AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
1 AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
43123986 AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
1 AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
43124025 AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
1 AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
43124064 AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
1 AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
* *
43124103 AGCCCGGTATAGTAACTTGCACAAATGCCTTCGGGACTT
1 AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
43124142 AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
1 AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
** * *
43124181 AGCCCGAAATTAGTAGCTCGCACAAATGCCTTCGGGACTT
1 AGCCCGGTA-TAATAACTCGCACAAATGCCTTCGGGACTT
* *** * *
43124221 AGCCCGGAATTAGCCACTAGCTCAAATG-CTCTCGGGACTT
1 AGCCCGGTA-TAATAACTCGCACAAATGCCT-TCGGGACTT
43124261 AGCCCGGT
1 AGCCCGGT
43124269 TATCATCCGA
Statistics
Matches: 266, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
39 200 0.75
40 66 0.25
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (39 bp):
AGCCCGGTATAATAACTCGCACAAATGCCTTCGGGACTT
Found at i:43124430 original size:14 final size:14
Alignment explanation
Indices: 43124411--43124440 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
43124401 GTTTAGTTTG
43124411 CTTTATAACACGAT
1 CTTTATAACACGAT
43124425 CTTTATAACACGAT
1 CTTTATAACACGAT
43124439 CT
1 CT
43124441 CTATGCACAT
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:0.23, G:0.07, T:0.37
Consensus pattern (14 bp):
CTTTATAACACGAT
Found at i:43125605 original size:200 final size:200
Alignment explanation
Indices: 43125262--43125662 Score: 748
Period size: 200 Copynumber: 2.0 Consensus size: 200
43125252 TTCAAGAGTC
43125262 ATCAATCCACCACCACATGCATCATTACAAAGCTTCACTTTTAGCATGGAAATGACATCAACACC
1 ATCAATCCACCACCACATGCATCATTACAAAGCTTCACTTTTAGCATGGAAATGACATCAACACC
* *
43125327 AATCCACCTTAGTCGAATATCATCTCCATGACATAGCAAAGATTTGAACCATGGGCTAGTTAGAA
66 AATCCACCTTAGCCGAATATCATCACCATGACATAGCAAAGATTTGAACCATGGGCTAGTTAGAA
* * *
43125392 CTCAAGCTAACAACTAAAAACATGCATGAGTCTTATGGCACAACATCAAACATACCTTATTCTAG
131 CTCAAGCTAACAACTAAAAACAAGCATGAGTCTCATGGCACAACATCAAACATACCTTATCCTAG
43125457 ACACA
196 ACACA
*
43125462 ATCAATCCACCATCACATGCATCATTACAAAGCTTCACTTTTAGCATGGAAATGACATCAACACC
1 ATCAATCCACCACCACATGCATCATTACAAAGCTTCACTTTTAGCATGGAAATGACATCAACACC
43125527 AATCCACCTTAGCCGAATATCATCACCATGACATAGCAAAGATTTGAACCATGGGCTAGTTAGAA
66 AATCCACCTTAGCCGAATATCATCACCATGACATAGCAAAGATTTGAACCATGGGCTAGTTAGAA
43125592 CTCAAGCTAACAACTAAAAACAAGCATGAGTCTCATGGCACAACATCAAACATACCTTATCCTAG
131 CTCAAGCTAACAACTAAAAACAAGCATGAGTCTCATGGCACAACATCAAACATACCTTATCCTAG
43125657 ACACA
196 ACACA
43125662 A
1 A
43125663 GTATGGCCGA
Statistics
Matches: 195, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
200 195 1.00
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.23
Consensus pattern (200 bp):
ATCAATCCACCACCACATGCATCATTACAAAGCTTCACTTTTAGCATGGAAATGACATCAACACC
AATCCACCTTAGCCGAATATCATCACCATGACATAGCAAAGATTTGAACCATGGGCTAGTTAGAA
CTCAAGCTAACAACTAAAAACAAGCATGAGTCTCATGGCACAACATCAAACATACCTTATCCTAG
ACACA
Found at i:43132422 original size:39 final size:38
Alignment explanation
Indices: 43132378--43132461 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 38
43132368 CCTTCAGAGT
* * *
43132378 TTAGCCGGATATAGCCACTAGCTCAAATGCCTTCGAGAC
1 TTAGCCGG-TATAACAACTAGCACAAATGCCTTCGAGAC
* * *
43132417 TTAGCCCGGTATAATAACTCGCACAAATGCCTTCGGGAC
1 TTAG-CCGGTATAACAACTAGCACAAATGCCTTCGAGAC
43132456 TTAGCC
1 TTAGCC
43132462 CAGNNNNNNN
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.05
39 32 0.84
40 4 0.11
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (38 bp):
TTAGCCGGTATAACAACTAGCACAAATGCCTTCGAGAC
Found at i:43140975 original size:20 final size:21
Alignment explanation
Indices: 43140943--43140981 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
43140933 AATGAAATAG
43140943 ATTTAGCAAAATTA-AACACA
1 ATTTAGCAAAATTATAACACA
43140963 ATTT-GCAACAATTATAACA
1 ATTTAGCAA-AATTATAACA
43140982 TAAATAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.28
Consensus pattern (21 bp):
ATTTAGCAAAATTATAACACA
Found at i:43145377 original size:18 final size:18
Alignment explanation
Indices: 43145354--43145389 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
43145344 AGTAGCAATG
43145354 ACGGCGCTTCGACAATCT
1 ACGGCGCTTCGACAATCT
43145372 ACGGCGCTTCGACAATCT
1 ACGGCGCTTCGACAATCT
43145390 TCTTACAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (18 bp):
ACGGCGCTTCGACAATCT
Found at i:43152738 original size:54 final size:54
Alignment explanation
Indices: 43152557--43152753 Score: 254
Period size: 55 Copynumber: 3.6 Consensus size: 54
43152547 AACTTGCCAT
* * * *
43152557 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* * **
43152610 TGCCATGCCTTGGCATGGTTTTACATGGGA-CCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATAG-AACTCATCAA
* * *
43152665 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
*
43152719 TGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTT
43152754 ATCTTACCAA
Statistics
Matches: 124, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
52 2 0.02
53 34 0.27
54 42 0.34
55 44 0.35
56 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
TGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
Found at i:43153012 original size:44 final size:44
Alignment explanation
Indices: 43152943--43153073 Score: 183
Period size: 44 Copynumber: 3.0 Consensus size: 44
43152933 GTATCCTTAA
* * * * *
43152943 CCGTCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGACTTTT
1 CCGTCAATTCTTCCTTAATTTCCATGGTA-CAACCATGGACTTTT
*
43152987 CCGTCAATTCTTCCTTAGTTTCCATGGTACAACCATGGACTTTT
1 CCGTCAATTCTTCCTTAATTTCCATGGTACAACCATGGACTTTT
*
43153031 CCGTCAATTCTTCCTTAATTTCCTTGGTACAACCATGGACTTT
1 CCGTCAATTCTTCCTTAATTTCCATGGTACAACCATGGACTTT
43153074 GAGATATCAA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 2 0.03
44 76 0.97
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (44 bp):
CCGTCAATTCTTCCTTAATTTCCATGGTACAACCATGGACTTTT
Found at i:43163999 original size:16 final size:16
Alignment explanation
Indices: 43163978--43164014 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
43163968 CAAATTTTAG
43163978 AAACCTAGAAAAACTT
1 AAACCTAGAAAAACTT
43163994 AAACCTAGAAAAACTT
1 AAACCTAGAAAAACTT
43164010 AAACC
1 AAACC
43164015 ATTTTAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.22, G:0.05, T:0.16
Consensus pattern (16 bp):
AAACCTAGAAAAACTT
Found at i:43165730 original size:8 final size:8
Alignment explanation
Indices: 43165717--43165746 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
43165707 ACAAATGCCG
43165717 GCTTTTCA
1 GCTTTTCA
43165725 GCTTTTCA
1 GCTTTTCA
*
43165733 GCTTTTCG
1 GCTTTTCA
43165741 GCTTTT
1 GCTTTT
43165747 GCCGATCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.07, C:0.23, G:0.17, T:0.53
Consensus pattern (8 bp):
GCTTTTCA
Found at i:43166560 original size:18 final size:17
Alignment explanation
Indices: 43166509--43166563 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
43166499 ATTCAGCTAT
43166509 AGAG-GAAAAGAAGAAG
1 AGAGAGAAAAGAAGAAG
*
43166525 A-AGAGTAAATAGATGAAG
1 AGAGAG-AAA-AGAAGAAG
43166543 AGAGGAGAAAAGAAGAAG
1 AGA-GAGAAAAGAAGAAG
43166561 AGA
1 AGA
43166564 AAAGAATTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 2 0.06
16 2 0.06
17 3 0.09
18 18 0.56
19 4 0.12
20 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.35, T:0.05
Consensus pattern (17 bp):
AGAGAGAAAAGAAGAAG
Found at i:43166569 original size:18 final size:18
Alignment explanation
Indices: 43166513--43166569 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
43166503 AGCTATAGAG
43166513 GAAAAGAAG-A-AGAAGA
1 GAAAAGAAGAAGAGAAGA
* *
43166529 GTAAATAGATGAAGAGAGGA
1 G-AAA-AGAAGAAGAGAAGA
*
43166549 GAAAAGAAGAAGAGAAAA
1 GAAAAGAAGAAGAGAAGA
43166567 GAA
1 GAA
43166570 TTGCCAGAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 1 0.03
17 3 0.09
18 18 0.56
19 4 0.12
20 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.32, T:0.05
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAAGA
Found at i:43168540 original size:19 final size:20
Alignment explanation
Indices: 43168507--43168548 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 20
43168497 TGTTATAATT
43168507 AAAATATAAAGTAAATAAAAG
1 AAAATATAAAGTAAAT-AAAG
43168528 AAAATA-AAA-TAAATAAAG
1 AAAATATAAAGTAAATAAAG
43168546 AAA
1 AAA
43168549 CAAAGCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 5 0.24
20 3 0.14
21 6 0.29
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (20 bp):
AAAATATAAAGTAAATAAAG
Found at i:43173118 original size:99 final size:100
Alignment explanation
Indices: 43172920--43173127 Score: 314
Period size: 99 Copynumber: 2.1 Consensus size: 100
43172910 CGGGGATTAA
43172920 TTTGTAAAACCATTAAAGTATTAGGATTTTTCCATGGATGATATGCTTGAATTATGAAGTTTTAT
1 TTTGTAAAACCATTAAAGTATTAGGATTTTTCCATGGATGATATGCTTGAATTATGAAG-TTTAT
43172985 GATAGAAAATGAAAGGTTGTTATTAGATAAACAACC
65 GATAGAAAATGAAAGGTTGTTATTAGATAAACAACC
* *
43173021 TTTGTAAAACCGTTAATGTATTAGGGA-TTTTCCATGGATGAGTATGCTTGAATTATG-A-TTTA
1 TTTGTAAAACCATTAAAGTATTA-GGATTTTTCCATGGATGA-TATGCTTGAATTATGAAGTTTA
* * * *
43173083 TGATAGAAAATGAAAGTTTTTTGTTAGATAAACAACT
64 TGATAGAAAATGAAAGGTTGTTATTAGATAAACAACC
43173120 TTTGTAAA
1 TTTGTAAA
43173128 GAGAATTTTG
Statistics
Matches: 99, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
99 45 0.45
101 36 0.36
102 18 0.18
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.38
Consensus pattern (100 bp):
TTTGTAAAACCATTAAAGTATTAGGATTTTTCCATGGATGATATGCTTGAATTATGAAGTTTATG
ATAGAAAATGAAAGGTTGTTATTAGATAAACAACC
Found at i:43173767 original size:25 final size:25
Alignment explanation
Indices: 43173738--43173806 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
43173728 TGACTCTCAC
* *
43173738 GAGCTTCTCGATTAATGGCGCTCTT
1 GAGCTTCTCGATTAATGGCGCACAT
* *
43173763 GAGCTTCCCGA-TAATTGGCTCACAT
1 GAGCTTCTCGATTAA-TGGCGCACAT
43173788 GAGCTTCTCG-TTATATGGC
1 GAGCTTCTCGATTA-ATGGC
43173807 TTGGAAGAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
24 3 0.08
25 32 0.89
26 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (25 bp):
GAGCTTCTCGATTAATGGCGCACAT
Found at i:43189299 original size:19 final size:17
Alignment explanation
Indices: 43189264--43189306 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
43189254 GGTAAGATCG
43189264 AATTTTTTCTTAAATTTT
1 AATTTTTTCTTAAA-TTT
43189282 AATTTTATTC-TAATATTT
1 AATTTT-TTCTTAA-ATTT
43189300 AATTTTT
1 AATTTTT
43189307 CAATTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 18 0.78
19 4 0.17
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTTTTTCTTAAATTT
Found at i:43195976 original size:47 final size:47
Alignment explanation
Indices: 43195913--43196066 Score: 245
Period size: 47 Copynumber: 3.3 Consensus size: 47
43195903 CCCTTCGGGA
*
43195913 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
* * * *
43195960 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
* *
43196007 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
43196054 CTTATCACATATA
1 CTTATCACATATA
43196067 CATATCTTGT
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 95 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:43213060 original size:10 final size:10
Alignment explanation
Indices: 43213045--43213178 Score: 53
Period size: 10 Copynumber: 13.4 Consensus size: 10
43213035 ACATGTAGCA
43213045 AAAAAATTAT
1 AAAAAATTAT
**
43213055 AAAAAAAAAT
1 AAAAAATTAT
*
43213065 ATATAAATTAT
1 A-AAAAATTAT
* **
43213076 TAAATTTTAAT
1 AAAAAATT-AT
*
43213087 AAAAATATT-G
1 AAAAA-ATTAT
43213097 A-AAA-TTAT
1 AAAAAATTAT
*
43213105 GAAAAATT-T
1 AAAAAATTAT
* *
43213114 ATAAAGATTGT
1 A-AAAAATTAT
43213125 AAAAAAATTAT
1 A-AAAAATTAT
*
43213136 AAAAAATTGT
1 AAAAAATTAT
**
43213146 AAAATTTTAT
1 AAAAAATTAT
*
43213156 -AAAAATCAT
1 AAAAAATTAT
*
43213165 AAATAATTAT
1 AAAAAATTAT
43213175 AAAA
1 AAAA
43213179 TGCACCATTA
Statistics
Matches: 85, Mismatches: 30, Indels: 18
0.64 0.23 0.14
Matches are distributed among these distances:
7 2 0.02
9 13 0.15
10 47 0.55
11 21 0.25
12 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.34
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:43213129 original size:20 final size:19
Alignment explanation
Indices: 43213106--43213161 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
43213096 GAAAATTATG
*
43213106 AAAAATTTATAAAGATTGT
1 AAAAATTTATAAAAATTGT
*
43213125 AAAAAAATTATAAAAAATTGT
1 -AAAAATTTAT-AAAAATTGT
*
43213146 AAAATTTTATAAAAAT
1 AAAAATTTATAAAAAT
43213162 CATAAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 6 0.19
20 17 0.55
21 8 0.26
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AAAAATTTATAAAAATTGT
Found at i:43213131 original size:21 final size:21
Alignment explanation
Indices: 43213106--43213149 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43213096 GAAAATTATG
*
43213106 AAAAATT-TATAAAGATTGTAA
1 AAAAATTATA-AAAAATTGTAA
43213127 AAAAATTATAAAAAATTGTAA
1 AAAAATTATAAAAAATTGTAA
43213148 AA
1 AA
43213150 TTTTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAATTATAAAAAATTGTAA
Found at i:43213160 original size:29 final size:29
Alignment explanation
Indices: 43213097--43213179 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
43213087 AAAAATATTG
*
43213097 AAAATTATGAAAAATTTATAAAGATTGTAAA
1 AAAATTAT-AAAAAATTATAAA-ATTGTAAA
* * *
43213128 AAAATTATAAAAAATTGTAAAATTTTATA
1 AAAATTATAAAAAATTATAAAATTGTAAA
* *
43213157 AAAATCATAAATAATTATAAAAT
1 AAAATTATAAAAAATTATAAAAT
43213180 GCACCATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 26 0.58
30 11 0.24
31 8 0.18
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAATTATAAAAAATTATAAAATTGTAAA
Found at i:43213345 original size:9 final size:9
Alignment explanation
Indices: 43213331--43213526 Score: 73
Period size: 9 Copynumber: 20.9 Consensus size: 9
43213321 TTTTTGTACG
43213331 ATAATTTTT
1 ATAATTTTT
43213340 ATAATTTTTTTT
1 ATAA---TTTTT
43213352 ATGAA-TTTT
1 AT-AATTTTT
*
43213361 ATATTTCTTT
1 ATAATT-TTT
* *
43213371 ACATTTTTT
1 ATAATTTTT
43213380 ATAATTTTCTTT
1 ATAA--TT-TTT
*
43213392 ATAAAATTTT
1 AT-AATTTTT
43213402 AT-ATTTTT
1 ATAATTTTT
*
43213410 CTATATTTTT
1 ATA-ATTTTT
*
43213420 CT-ATATTTT
1 ATAAT-TTTT
43213429 ATAATTTTT
1 ATAATTTTT
*
43213438 ATAAAATTTT
1 AT-AATTTTT
*
43213448 AAAATTTTT
1 ATAATTTTT
43213457 -T-ATTTTT
1 ATAATTTTT
*
43213464 TTAATTTTT
1 ATAATTTTT
* **
43213473 AATAAAATTGA
1 -AT-AATTTTT
43213484 ATAATTTTT
1 ATAATTTTT
* *
43213493 ATAACTTTC
1 ATAATTTTT
43213502 ATTAATTTTT
1 A-TAATTTTT
43213512 AT--TTTTT
1 ATAATTTTT
*
43213519 ATCATTTT
1 ATAATTTT
43213527 ATTTGTTACA
Statistics
Matches: 142, Mismatches: 23, Indels: 44
0.68 0.11 0.21
Matches are distributed among these distances:
7 13 0.09
8 10 0.07
9 56 0.39
10 40 0.28
11 7 0.05
12 12 0.08
13 4 0.03
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:43213362 original size:21 final size:20
Alignment explanation
Indices: 43213331--43213408 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 20
43213321 TTTTTGTACG
* *
43213331 ATAATTTTTATAATTTTTTTT
1 ATAAATTTTAT-ATTTTCTTT
*
43213352 ATGAATTTTATA-TTTCTTT
1 ATAAATTTTATATTTTCTTT
* **
43213371 ACATTTTTTATAATTTTCTTT
1 ATAAATTTTAT-ATTTTCTTT
43213392 ATAAAATTTTATATTTT
1 AT-AAATTTTATATTTT
43213409 TCTATATTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
19 13 0.30
20 2 0.05
21 22 0.50
22 7 0.16
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (20 bp):
ATAAATTTTATATTTTCTTT
Found at i:43213380 original size:40 final size:41
Alignment explanation
Indices: 43213335--43213428 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
43213325 TGTACGATAA
* *
43213335 TTTTTATAATTTTTTTTAT-GAATTTTATATTTCTT-TACAT
1 TTTTTATAATTTTCTTTATAAAATTTTATATTT-TTCTACAT
*
43213375 TTTTTATAATTTTCTTTATAAAATTTTATATTTTTCTATAT
1 TTTTTATAATTTTCTTTATAAAATTTTATATTTTTCTACAT
43213416 TTTTCTAT-ATTTT
1 TTTT-TATAATTTT
43213429 ATAATTTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
40 20 0.42
41 25 0.52
42 3 0.06
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.68
Consensus pattern (41 bp):
TTTTTATAATTTTCTTTATAAAATTTTATATTTTTCTACAT
Found at i:43213414 original size:10 final size:10
Alignment explanation
Indices: 43213401--43213428 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
43213391 TATAAAATTT
43213401 TATATTTTTC
1 TATATTTTTC
43213411 TATATTTTTC
1 TATATTTTTC
43213421 TATATTTT
1 TATATTTT
43213429 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (10 bp):
TATATTTTTC
Found at i:43213490 original size:36 final size:37
Alignment explanation
Indices: 43213414--43213492 Score: 101
Period size: 35 Copynumber: 2.2 Consensus size: 37
43213404 ATTTTTCTAT
*
43213414 ATTTTTCTATATTTTATAATTTTTATAAAATTTTAAA
1 ATTTTTCTATATTTTATAATTTTTATAAAATTTGAAA
*
43213451 ATTTTT-TAT-TTTTTTAATTTTTAATAAAA-TTGAATA
1 ATTTTTCTATATTTTATAATTTTT-ATAAAATTTGAA-A
43213487 ATTTTT
1 ATTTTT
43213493 ATAACTTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
35 16 0.42
36 16 0.42
37 6 0.16
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (37 bp):
ATTTTTCTATATTTTATAATTTTTATAAAATTTGAAA
Found at i:43217908 original size:3 final size:3
Alignment explanation
Indices: 43217900--43217925 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43217890 AAATGATCTA
43217900 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
43217926 ACATTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:43219181 original size:19 final size:17
Alignment explanation
Indices: 43219130--43219182 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
43219120 ATACAATAAT
*
43219130 AATAGTATTTTAATTTTA
1 AATA-TATTTTATTTTTA
*
43219148 AGATATATATTATTTTTGA
1 A-ATATATTTTATTTTT-A
43219167 AATATTATTTTATTTT
1 AATA-TATTTTATTTT
43219183 ATTTTACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
AATATATTTTATTTTTA
Found at i:43222660 original size:23 final size:24
Alignment explanation
Indices: 43222626--43222678 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
43222616 ATCCCCGGTG
*
43222626 GAAATA-TAGAAAGCTCTTAAAGA
1 GAAATACTAGAAAGCTCCTAAAGA
*
43222649 GAAATACT-GAAAGTTCCTAAAGA
1 GAAATACTAGAAAGCTCCTAAAGA
43222672 GAAATAC
1 GAAATAC
43222679 AACACCGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (24 bp):
GAAATACTAGAAAGCTCCTAAAGA
Found at i:43222783 original size:15 final size:15
Alignment explanation
Indices: 43222763--43222799 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
43222753 GATCATAGAT
*
43222763 CAAGTCTATGAATTA
1 CAAGTCCATGAATTA
43222778 CAAGTCCATGAATTA
1 CAAGTCCATGAATTA
43222793 CAAGTCC
1 CAAGTCC
43222800 TCGTAAGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (15 bp):
CAAGTCCATGAATTA
Found at i:43226712 original size:29 final size:30
Alignment explanation
Indices: 43226674--43226760 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 30
43226664 TTTATGAGCA
43226674 CTATTCAAATTAAAAGTGATGATTTATCAT
1 CTATTCAAATTAAAAGTGATGATTTATCAT
* * * * *
43226704 CT-TTCAAATT-TAA-TTATTCA-TAAGCA-
1 CTATTCAAATTAAAAGTGA-TGATTTATCAT
43226730 CTATTCAAATTAAAAGTGATGATTTATCAT
1 CTATTCAAATTAAAAGTGATGATTTATCAT
43226760 C
1 C
43226761 CAATGGATAC
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
26 2 0.05
27 14 0.34
28 8 0.20
29 14 0.34
30 3 0.07
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (30 bp):
CTATTCAAATTAAAAGTGATGATTTATCAT
Found at i:43226718 original size:56 final size:55
Alignment explanation
Indices: 43226653--43226760 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 55
43226643 TTATAGATTG
* * *
43226653 CAAATTAATTTTTTATGAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTT
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTT
43226708 CAAATTTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATTTATCATC
1 CAAA-TTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATTTATCATC
43226761 CAATGGATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 4 0.08
56 45 0.92
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (55 bp):
CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTT
Found at i:43227153 original size:80 final size:80
Alignment explanation
Indices: 43227020--43227259 Score: 480
Period size: 80 Copynumber: 3.0 Consensus size: 80
43227010 GCAACTTTGT
43227020 GCGGGGGCAAATAGTACTCTTTAGAAAGAGTCATCCGCGTCTCGAAGTCTACTGTTTATTTTTAT
1 GCGGGGGCAAATAGTACTCTTTAGAAAGAGTCATCCGCGTCTCGAAGTCTACTGTTTATTTTTAT
43227085 ATAAGCCTCTGATTC
66 ATAAGCCTCTGATTC
43227100 GCGGGGGCAAATAGTACTCTTTAGAAAGAGTCATCCGCGTCTCGAAGTCTACTGTTTATTTTTAT
1 GCGGGGGCAAATAGTACTCTTTAGAAAGAGTCATCCGCGTCTCGAAGTCTACTGTTTATTTTTAT
43227165 ATAAGCCTCTGATTC
66 ATAAGCCTCTGATTC
43227180 GCGGGGGCAAATAGTACTCTTTAGAAAGAGTCATCCGCGTCTCGAAGTCTACTGTTTATTTTTAT
1 GCGGGGGCAAATAGTACTCTTTAGAAAGAGTCATCCGCGTCTCGAAGTCTACTGTTTATTTTTAT
43227245 ATAAGCCTCTGATTC
66 ATAAGCCTCTGATTC
43227260 TATCGTCTCC
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 160 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (80 bp):
GCGGGGGCAAATAGTACTCTTTAGAAAGAGTCATCCGCGTCTCGAAGTCTACTGTTTATTTTTAT
ATAAGCCTCTGATTC
Found at i:43227353 original size:3 final size:3
Alignment explanation
Indices: 43227345--43227378 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
43227335 TTTTCACATG
43227345 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
43227379 TTAAATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:43233050 original size:39 final size:39
Alignment explanation
Indices: 43233007--43233082 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
43232997 GTTTTCCTTT
* *
43233007 TTTTTTTCAAAACCTTAAAAAAAAGTGGGGGGGGGGGAA
1 TTTTTTTCAAAACCTAAAAAAAAAGGGGGGGGGGGGGAA
43233046 TTTTTTTCAAAACCTAAAAAAAAAGGGGGGGGGGGGG
1 TTTTTTTCAAAACCTAAAAAAAAAGGGGGGGGGGGGG
43233083 GGAGAGTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.08, G:0.33, T:0.24
Consensus pattern (39 bp):
TTTTTTTCAAAACCTAAAAAAAAAGGGGGGGGGGGGGAA
Found at i:43233479 original size:16 final size:16
Alignment explanation
Indices: 43233460--43233492 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
43233450 GATAATAATA
43233460 TTATTTTAATACATCT
1 TTATTTTAATACATCT
43233476 TTATTTTAATACATCT
1 TTATTTTAATACATCT
43233492 T
1 T
43233493 GATACAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTTTAATACATCT
Found at i:43235289 original size:35 final size:35
Alignment explanation
Indices: 43235250--43235320 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
43235240 AAAATTATTA
43235250 ATTAATTTCAATAAATTAATTAAATGGTTATATAT
1 ATTAATTTCAATAAATTAATTAAATGGTTATATAT
43235285 ATTAATTTCAATAAATTAATTAAATGGTTATATAT
1 ATTAATTTCAATAAATTAATTAAATGGTTATATAT
43235320 A
1 A
43235321 AATTTTTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (35 bp):
ATTAATTTCAATAAATTAATTAAATGGTTATATAT
Found at i:43243987 original size:14 final size:13
Alignment explanation
Indices: 43243962--43243986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43243952 TTTTTAGAAT
43243962 TACTTTTGAAAAG
1 TACTTTTGAAAAG
43243975 TACTTTTGAAAA
1 TACTTTTGAAAA
43243987 ATTTAGTTTA
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:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:43244277 original size:33 final size:30
Alignment explanation
Indices: 43244201--43244281 Score: 78
Period size: 33 Copynumber: 2.7 Consensus size: 30
43244191 ATTTTTAAGC
43244201 AATA-AATATT-AATTATTTATAAAATTTA
1 AATATAATATTAAATTATTTATAAAATTTA
* * *
43244229 ATTAGAATATATAAATTATATTTTAAATATTTA
1 AATATAATAT-TAAATTAT-TTATAAA-ATTTA
43244262 AATATAACTATTAAA-TATTT
1 AATATAA-TATTAAATTATTT
43244282 GTAATTAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 3 0.07
29 5 0.12
30 1 0.02
31 8 0.19
32 9 0.21
33 14 0.33
34 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
AATATAATATTAAATTATTTATAAAATTTA
Found at i:43246588 original size:13 final size:13
Alignment explanation
Indices: 43246570--43246595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43246560 TATTAAAATT
43246570 TAAAATAGATCAA
1 TAAAATAGATCAA
43246583 TAAAATAGATCAA
1 TAAAATAGATCAA
43246596 AACTTACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
TAAAATAGATCAA
Found at i:43249143 original size:26 final size:26
Alignment explanation
Indices: 43249107--43249268 Score: 261
Period size: 26 Copynumber: 6.2 Consensus size: 26
43249097 TGATACAAAT
* *
43249107 TGATAATAGGTTAGGTAAATATTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
43249133 TGATAATAGGTTAGGTAAATGTTCCG
1 TGATAATAGGTTAGGTAAATGTTCCA
43249159 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
43249185 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
43249211 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
43249237 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
43249263 TGATAA
1 TGATAA
43249269 GAATTTCATG
Statistics
Matches: 130, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 130 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:43250754 original size:28 final size:26
Alignment explanation
Indices: 43250708--43250782 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
43250698 AAAAGTAGCT
* * *
43250708 AAATTACTATAATATCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGGA
* *
43250736 AAATTACTGTTATACCCCTAGGTGTA
1 AAATTACTGTTATACCCCTAGATGGA
*
43250762 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
43250783 GGTTAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 23 0.56
27 1 0.02
28 17 0.41
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGGA
Found at i:43250991 original size:27 final size:26
Alignment explanation
Indices: 43250884--43250998 Score: 133
Period size: 27 Copynumber: 4.3 Consensus size: 26
43250874 TGGAGGAAGC
*
43250884 GTTCTGGTGGCTCTGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
43250911 GATT-TGGTGGCTCTGCCACATATATCT
1 G-TTCTGGTGGCTCTGCCACAT-TATCT
*
43250938 GTTCTGGTGGCCCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* * *
43250965 GTATCTGGTGACTCTGTCACATCATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
43250992 GTTCTGG
1 GTTCTGG
43250999 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.10
27 51 0.66
28 18 0.23
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:43250992 original size:54 final size:54
Alignment explanation
Indices: 43250884--43250998 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
43250874 TGGAGGAAGC
* * * *
43250884 GTTCTGGTGGCTCTGCCACAAATATCTGATTTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCCCTGCCACAAATATCTGATCTGGTGACTCTGCCACATACATCT
* * *
43250938 GTTCTGGTGGCCCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-CATCT
1 GTTCTGGTGGCCCTGCCACAAATATCTG-ATCTGGTGACTCTGCCACATACATCT
43250992 GTTCTGG
1 GTTCTGG
43250999 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 36 0.68
55 17 0.32
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (54 bp):
GTTCTGGTGGCCCTGCCACAAATATCTGATCTGGTGACTCTGCCACATACATCT
Found at i:43252885 original size:3 final size:3
Alignment explanation
Indices: 43252877--43252943 Score: 52
Period size: 3 Copynumber: 23.0 Consensus size: 3
43252867 TATATATTAA
*
43252877 ATT ATT ATT ATT ATTT ATT A-T AGTT -TT A-T ATT -TA ATT ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
* * *
43252920 GTT ATT GTT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
43252944 TAAATTGATA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
2 7 0.14
3 39 0.78
4 4 0.08
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:43252932 original size:12 final size:12
Alignment explanation
Indices: 43252877--43252943 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
43252867 TATATATTAA
*
43252877 ATTATTATTATT
1 ATTATTATTGTT
*
43252889 ATTTATTATAGTT
1 A-TTATTATTGTT
*
43252902 -TTA-TATT-TA
1 ATTATTATTGTT
43252911 ATTATTATTGTT
1 ATTATTATTGTT
*
43252923 ATTGTTATTGTT
1 ATTATTATTGTT
43252935 ATTATTATT
1 ATTATTATT
43252944 TAAATTGATA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
9 1 0.02
10 6 0.14
11 7 0.16
12 21 0.48
13 9 0.20
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (12 bp):
ATTATTATTGTT
Found at i:43252950 original size:18 final size:18
Alignment explanation
Indices: 43252873--43252957 Score: 61
Period size: 18 Copynumber: 4.8 Consensus size: 18
43252863 AAAATATATA
*
43252873 TTAAATTATTATTATTAT
1 TTAAATTGTTATTATTAT
* *
43252891 TTATTATAGTT-TTA-TAT
1 TTA-AATTGTTATTATTAT
* *
43252908 TT-AATTATTATTGTTAT
1 TTAAATTGTTATTATTAT
*
43252925 TGT-TATTGTTATTATTAT
1 T-TAAATTGTTATTATTAT
*
43252943 TTAAATTGATATTAT
1 TTAAATTGTTATTAT
43252958 ATTATAAAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
15 4 0.08
16 2 0.04
17 10 0.20
18 30 0.60
19 4 0.08
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (18 bp):
TTAAATTGTTATTATTAT
Found at i:43253555 original size:23 final size:21
Alignment explanation
Indices: 43253508--43253548 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
43253498 TTTGGTTAAA
43253508 AATTGAATAGAAATGAAGTATG
1 AATTGAATAGAAA-GAAGTATG
43253530 AATTGAGATAGAAA-AAGTA
1 AATTGA-ATAGAAAGAAGTA
43253549 AGTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTGAATAGAAAGAAGTATG
Found at i:43254860 original size:6 final size:7
Alignment explanation
Indices: 43254845--43254870 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43254835 CGCTTTGAAA
43254845 TTTTATT
1 TTTTATT
43254852 TTTTATT
1 TTTTATT
43254859 TTTTATT
1 TTTTATT
43254866 TTTTA
1 TTTTA
43254871 AAAGGGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:43254970 original size:19 final size:19
Alignment explanation
Indices: 43254946--43254983 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
43254936 TAAATGAATA
43254946 ATTTCAGGCAAATAGGTTG
1 ATTTCAGGCAAATAGGTTG
43254965 ATTTCAGGCAAATAGGTTG
1 ATTTCAGGCAAATAGGTTG
43254984 GCAATCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
ATTTCAGGCAAATAGGTTG
Found at i:43255888 original size:19 final size:20
Alignment explanation
Indices: 43255855--43255894 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
43255845 AATTATGTAT
43255855 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
43255874 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
43255894 A
1 A
43255895 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:43256543 original size:44 final size:44
Alignment explanation
Indices: 43256480--43257588 Score: 1991
Period size: 44 Copynumber: 25.4 Consensus size: 44
43256470 CCCTGTCTAA
*
43256480 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43256524 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43256568 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43256612 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43256656 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43256700 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43256744 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43256788 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43256832 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43256876 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43256920 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43256964 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43257008 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43257052 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43257096 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43257140 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43257184 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43257228 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43257272 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
43257316 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * **
43257360 TACAGAGACGCCAAATCTGCTATATTCGATCTGCTCTTTGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
43257404 TACAAAGACGCCAAATCTGTTATC-T---TCT-CTCT--GCCAC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * ** *
43257441 TACAGAG-AGCAAAATCTACTATCTTCAATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
43257484 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
43257528 TACAGAGACTCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
**
43257572 TACAGAGATGCCAAATC
1 TACAGAGCCGCCAAATC
43257589 ATATTAGATT
Statistics
Matches: 1033, Mismatches: 24, Indels: 16
0.96 0.02 0.01
Matches are distributed among these distances:
36 12 0.01
37 11 0.01
39 4 0.00
40 6 0.01
41 4 0.00
43 12 0.01
44 984 0.95
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (44 bp):
TACAGAGCCGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
Found at i:43257456 original size:36 final size:37
Alignment explanation
Indices: 43257388--43257466 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 37
43257378 GCTATATTCG
* * * * **
43257388 ATCTGCTCTTTGCCGCTACAAAGACGCCAAATCTGTT
1 ATCTTCTCTCTGCCACTACAAAGACGCAAAATCTACT
*
43257425 ATCTTCTCTCTGCCACTACAGAGA-GCAAAATCTACT
1 ATCTTCTCTCTGCCACTACAAAGACGCAAAATCTACT
43257461 ATCTTC
1 ATCTTC
43257467 AATCTGCTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
36 15 0.43
37 20 0.57
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (37 bp):
ATCTTCTCTCTGCCACTACAAAGACGCAAAATCTACT
Found at i:43257475 original size:80 final size:81
Alignment explanation
Indices: 43257344--43257588 Score: 249
Period size: 80 Copynumber: 3.0 Consensus size: 81
43257334 GTTATCTTCG
* * * * * **
43257344 ATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGCTATATTCGATCTGCTCTTTGCCGCTACAA
1 ATCTTCTCTCCGCCACTACAGAGACGCAAAATCTACTATATTCAATCTGCTCTCCGCCGCTACAA
43257409 AGACGCCAAATCTGTT
66 AGACGCCAAATCTGTT
* * *
43257425 ATCTTCTCTCTGCCACTACAGAGA-GCAAAATCTACTATCTTCAATCTGCTCTCCGCCGCTACAG
1 ATCTTCTCTCCGCCACTACAGAGACGCAAAATCTACTATATTCAATCTGCTCTCCGCCGCTACAA
43257489 AGACGCCAAATCTGTT
66 AGACGCCAAATCTGTT
* * * ** * *
43257505 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACTCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
1 A---TC--T-T-CTCTCCGCCACTACAGAGACGCAAAATCTACTATATTCAATCTGCTCTCCGCC
* *
43257570 GCTACAGAGATGCCAAATC
59 GCTACAAAGACGCCAAATC
43257589 ATATTAGATT
Statistics
Matches: 138, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
80 50 0.36
81 21 0.15
83 2 0.01
85 1 0.01
86 1 0.01
87 17 0.12
88 46 0.33
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (81 bp):
ATCTTCTCTCCGCCACTACAGAGACGCAAAATCTACTATATTCAATCTGCTCTCCGCCGCTACAA
AGACGCCAAATCTGTT
Found at i:43257767 original size:88 final size:88
Alignment explanation
Indices: 43257550--43257773 Score: 324
Period size: 88 Copynumber: 2.6 Consensus size: 88
43257540 AAATCTGTTA
* * * * * *
43257550 TCTTCGATCTGCTCTCCGCC-GCTACAGAGATGCCAAATCATATTAGATTTGCTTCAACGTAAAC
1 TCTTCGATCTACTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACGTAAAC
43257614 ACGTGAAAGCCAAATCAGCTATG
66 ACGTGAAAGCCAAATCAGCTATG
* * * *
43257637 TCTTCGATCTGCTCCCTGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTTAATGTAAAC
1 TCTTCGATCTACTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACGTAAAC
*
43257702 ACGTGAAAGCCAAATTAGCTATG
66 ACGTGAAAGCCAAATCAGCTATG
* *
43257725 TCTTCGATCTACTCCCCGCTTGATGCAGAGATGCCAAATCATCTTGGAT
1 TCTTCGATCTACTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGAT
43257774 ATCTTCAGCT
Statistics
Matches: 123, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 18 0.15
88 105 0.85
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (88 bp):
TCTTCGATCTACTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACGTAAAC
ACGTGAAAGCCAAATCAGCTATG
Found at i:43259639 original size:6 final size:6
Alignment explanation
Indices: 43259620--43259649 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
43259610 TCTTGTTTTT
*
43259620 TTTGCC TTTACC TTTGCC TTTGCC TTTGCC
1 TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC
43259650 ATATAGCGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.03, C:0.33, G:0.13, T:0.50
Consensus pattern (6 bp):
TTTGCC
Found at i:43261771 original size:19 final size:19
Alignment explanation
Indices: 43261747--43261795 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
43261737 TGGGAAAATC
43261747 TAATGCAAATGATACAATG
1 TAATGCAAATGATACAATG
*
43261766 TAATGCAAATGATGCAATG
1 TAATGCAAATGATACAATG
*
43261785 CAATGCAAATG
1 TAATGCAAATG
43261796 CATGTGATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (19 bp):
TAATGCAAATGATACAATG
Found at i:43263767 original size:6 final size:7
Alignment explanation
Indices: 43263752--43263777 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43263742 CGCTTTGAAA
43263752 TTTTATT
1 TTTTATT
43263759 TTTTATT
1 TTTTATT
43263766 TTTTATT
1 TTTTATT
43263773 TTTTA
1 TTTTA
43263778 AAAGGGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:43263877 original size:19 final size:19
Alignment explanation
Indices: 43263853--43263890 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
43263843 GAAATGAATA
43263853 ATTTCAGGCAAATAGGTTG
1 ATTTCAGGCAAATAGGTTG
43263872 ATTTCAGGCAAATAGGTTG
1 ATTTCAGGCAAATAGGTTG
43263891 GCAATCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
ATTTCAGGCAAATAGGTTG
Found at i:43264215 original size:78 final size:77
Alignment explanation
Indices: 43264120--43264282 Score: 299
Period size: 78 Copynumber: 2.1 Consensus size: 77
43264110 AATGTTAAAA
43264120 CAAATAAACTTGAAATGAACAATTTAAAAGTAGGTAAATTATATATAAATATATATATACATAAA
1 CAAA-AAACTTGAAATGAACAATTTAAAAGTAGGTAAATTATATATAAATATATATATACATAAA
*
43264185 TAGATAATACATG
65 CAGATAATACATG
43264198 CAAAAAAGCTTGAAATGAACAATTTAAAAGTAGGTAAATTATATATAAATATATATATACATAAA
1 CAAAAAA-CTTGAAATGAACAATTTAAAAGTAGGTAAATTATATATAAATATATATATACATAAA
43264263 CAGATAATACATG
65 CAGATAATACATG
43264276 CAAAAAA
1 CAAAAAA
43264283 ATTACAATAT
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
77 3 0.04
78 80 0.96
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.28
Consensus pattern (77 bp):
CAAAAAACTTGAAATGAACAATTTAAAAGTAGGTAAATTATATATAAATATATATATACATAAAC
AGATAATACATG
Found at i:43264876 original size:19 final size:20
Alignment explanation
Indices: 43264843--43264882 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
43264833 AATTATGTAT
43264843 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
43264862 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
43264882 A
1 A
43264883 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:43265532 original size:44 final size:44
Alignment explanation
Indices: 43265465--43266269 Score: 1204
Period size: 44 Copynumber: 18.4 Consensus size: 44
43265455 CCACGTCTAA
* *
43265465 TACAGAGACGCCAAATCCGTTATCTTCGATCTGCTCTCCGTCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * *
43265509 TACAGAGACGCCCAATCTATTATCTTTGATCTGGTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
43265553 TACAGAGACGCCAAATCTGTTATCTTTGATCTGCTCTCCGCTGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * * *
43265597 TACAGAGATGCCAAATC----ATCTTCGATCAGCTTTCCACCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
43265637 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGTCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
43265681 TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
43265725 TACAGAGACGCCAAATCTGCTATCTTCGATCTACCCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
** *
43265769 TACAGAGAATCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
43265813 TACAGAGATGCCAAATCTGTTATCTTCGATTTGCTCTCCGCCAC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
43265857 TACAGAGACGCCAAATTTGCTATCTTCGATCTGCTCTTCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
43265901 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
43265945 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
43265989 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
43266033 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCTGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
43266077 TACAGAGACGCCAAATCTGCTACCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
43266121 TAGAGAGACGCCAAATTTGTTATCTTCGATCTGCTCTCCACCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
43266165 TACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCCCCGCCCC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
43266209 TACAGAGACGCCAAATCTGTTATCTTTGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
43266253 TATAGAGATGCCAAATC
1 TACAGAGACGCCAAATC
43266270 ATCTTAGATT
Statistics
Matches: 687, Mismatches: 70, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
40 34 0.05
44 653 0.95
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (44 bp):
TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
Found at i:43266405 original size:88 final size:87
Alignment explanation
Indices: 43266231--43266454 Score: 342
Period size: 88 Copynumber: 2.6 Consensus size: 87
43266221 AAATCTGTTA
* * * * *
43266231 TCTTTGATCTGCTCTCCGCC-GCTATAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAAC
1 TCTTCGATCTGCTC-CCGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACGTAAAC
*
43266295 ACGTGAAAGCGAAATTAGCTATG
65 ACGTGAAAGCCAAATTAGCTATG
*
43266318 TCTTCGATCTGCTCCCTGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTTAACGTAAAC
1 TCTTCGATCTGCTCCC-GCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACGTAAAC
43266383 ACGTGAAAGCCAAATTAGCTATG
65 ACGTGAAAGCCAAATTAGCTATG
*
43266406 TCTTCGATCTACTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGAT
1 TCTTCGATCTGCT-CCCGCCTGATACAGAGATGCCAAATCATCTTGGAT
43266455 ATCTTCAGCT
Statistics
Matches: 126, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
86 2 0.02
87 16 0.13
88 105 0.83
89 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (87 bp):
TCTTCGATCTGCTCCCGCCTGATACAGAGATGCCAAATCATCTTGGATCTGCTTCAACGTAAACA
CGTGAAAGCCAAATTAGCTATG
Found at i:43268323 original size:6 final size:6
Alignment explanation
Indices: 43268304--43268333 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
43268294 CTTGTTTTTT
*
43268304 TTTGCC TTTACC TTTGCC TTTGCC TTTGCC
1 TTTGCC TTTGCC TTTGCC TTTGCC TTTGCC
43268334 ATATAGCGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.03, C:0.33, G:0.13, T:0.50
Consensus pattern (6 bp):
TTTGCC
Found at i:43270447 original size:19 final size:19
Alignment explanation
Indices: 43270423--43270470 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
43270413 GGGAAAATCT
43270423 AATGCAAATGATGCAATGC
1 AATGCAAATGATGCAATGC
*
43270442 AATGCACATGATGCAATGC
1 AATGCAAATGATGCAATGC
43270461 AATGCAAATG
1 AATGCAAATG
43270471 CCTGGGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGCAAATGATGCAATGC
Found at i:43272677 original size:286 final size:286
Alignment explanation
Indices: 43272165--43272736 Score: 1090
Period size: 286 Copynumber: 2.0 Consensus size: 286
43272155 TGAACAAATG
43272165 AAAAAGCGCAACCCGGCACGATAGGACACAACATTTCAAATCCTCGATACAAGATCATTTTATAA
1 AAAAAGCGCAACCCGGCACGATAGGACACAACATTTCAAATCCTCGATACAAGATCATTTTATAA
43272230 TTTCCAAAACTCATGCATTTGAAATTTCAAAAGGATATTTAGTTATTTAGGTTAAACAAGAAAAA
66 TTTCCAAAACTCATGCATTTGAAATTTCAAAAGGATATTTAGTTATTTAGGTTAAACAAGAAAAA
*
43272295 TTGAAACCTAGTAAGTTAGAGTACTATTTTCTTGAATTTCCTAAATTCGAAATATTGTCTTATTT
131 TTGAAACCTAGTAAGTTAGAGTACTATTTTCTTGAATTTCCTAAATTCGAAATATTGCCTTATTT
43272360 TTAATTTAAAAAAACATGGACAAAATCTCGAGAGAATATTTATTTGGTCAAACAGAAAATCGAAA
196 TTAATTTAAAAAAACATGGACAAAATCTCGAGAGAATATTTATTTGGTCAAACAGAAAATCGAAA
*
43272425 CCCAACACGTTAGGGCACAATTTCTT
261 CCCAACACGCTAGGGCACAATTTCTT
*
43272451 AAAAAGCGCAACCCGGCACGATAGGACACAATATTTCAAATCCTCGATACAAGATCATTTTATAA
1 AAAAAGCGCAACCCGGCACGATAGGACACAACATTTCAAATCCTCGATACAAGATCATTTTATAA
43272516 TTTCCAAAACTCATGCATTTGAAATTTCAAAAGGATATTTAGTTATTTAGGTTAAACAAGAAAAA
66 TTTCCAAAACTCATGCATTTGAAATTTCAAAAGGATATTTAGTTATTTAGGTTAAACAAGAAAAA
*
43272581 TTGAAACCTAGTAAGTTAGGGTACTATTTTCTTGAATTTCCTAAATTCGAAATATTGCCTTATTT
131 TTGAAACCTAGTAAGTTAGAGTACTATTTTCTTGAATTTCCTAAATTCGAAATATTGCCTTATTT
*
43272646 TTAATTTAAAAAAACATGGACGAAATCTCGAGAGAATATTTATTTGGTCAAACAGAAAATCGAAA
196 TTAATTTAAAAAAACATGGACAAAATCTCGAGAGAATATTTATTTGGTCAAACAGAAAATCGAAA
*
43272711 CCCAACACGCTAGGGCGCAATTTCTT
261 CCCAACACGCTAGGGCACAATTTCTT
43272737 GAATTACCAA
Statistics
Matches: 280, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
286 280 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (286 bp):
AAAAAGCGCAACCCGGCACGATAGGACACAACATTTCAAATCCTCGATACAAGATCATTTTATAA
TTTCCAAAACTCATGCATTTGAAATTTCAAAAGGATATTTAGTTATTTAGGTTAAACAAGAAAAA
TTGAAACCTAGTAAGTTAGAGTACTATTTTCTTGAATTTCCTAAATTCGAAATATTGCCTTATTT
TTAATTTAAAAAAACATGGACAAAATCTCGAGAGAATATTTATTTGGTCAAACAGAAAATCGAAA
CCCAACACGCTAGGGCACAATTTCTT
Found at i:43272788 original size:6 final size:7
Alignment explanation
Indices: 43272773--43272798 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43272763 CGCTTTGAAA
43272773 TTTTATT
1 TTTTATT
43272780 TTTTATT
1 TTTTATT
43272787 TTTTATT
1 TTTTATT
43272794 TTTTA
1 TTTTA
43272799 AAAGGGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:43273812 original size:19 final size:19
Alignment explanation
Indices: 43273774--43273812 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
43273764 AATTATGTAT
*
43273774 ATAAAATAAAGAAAATAAA
1 ATAAAATAAACAAAATAAA
43273793 ATAAAAT-AACAAAATGAAA
1 ATAAAATAAACAAAAT-AAA
43273812 A
1 A
43273813 ATGAACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (19 bp):
ATAAAATAAACAAAATAAA
Found at i:43274280 original size:15 final size:15
Alignment explanation
Indices: 43274232--43274281 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
43274222 TTTATCAAAT
43274232 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
43274247 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
43274262 TTATATTGATTGAAA
1 TTATATTGATTGAAA
43274277 TTATA
1 TTATA
43274282 ATATATATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:43274946 original size:18 final size:19
Alignment explanation
Indices: 43274925--43274965 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
43274915 AATGAAATGA
43274925 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
43274943 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
43274962 GAAA
1 GAAA
43274966 ATATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:43279863 original size:21 final size:22
Alignment explanation
Indices: 43279836--43279892 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
43279826 ATATATTAAA
43279836 TTATTATTATTATTTATTATAG
1 TTATTATTATTATTTATTATAG
* *
43279858 TT-TTA-TATTTAATTATTATTG
1 TTATTATTA-TTATTTATTATAG
*
43279879 TTATTGTTATTATT
1 TTATTATTATTATT
43279893 ATTTAAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 2 0.07
21 16 0.57
22 8 0.29
23 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTATTATTATTATTTATTATAG
Found at i:43280514 original size:23 final size:21
Alignment explanation
Indices: 43280467--43280507 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
43280457 TTTGGTTAAA
43280467 AATTGAATAGAAATGAAGTATG
1 AATTGAATAGAAA-GAAGTATG
43280489 AATTGAGATAGAAA-AAGTA
1 AATTGA-ATAGAAAGAAGTA
43280508 AGTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTGAATAGAAAGAAGTATG
Found at i:43280980 original size:15 final size:15
Alignment explanation
Indices: 43280937--43280985 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
43280927 TTATCAAATA
*
43280937 TATATTGATTGAAAT
1 TATATTGATTGAATT
* *
43280952 CATTTTGATTGAATT
1 TATATTGATTGAATT
43280967 TATATTGATTGAATT
1 TATATTGATTGAATT
43280982 TATA
1 TATA
43280986 ATATATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (15 bp):
TATATTGATTGAATT
Found at i:43281650 original size:18 final size:19
Alignment explanation
Indices: 43281629--43281669 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
43281619 AATGAAATGA
43281629 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
43281647 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
43281666 GAAA
1 GAAA
43281670 ATATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:43296069 original size:27 final size:27
Alignment explanation
Indices: 43296039--43296091 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
43296029 TTAAAATAAG
*
43296039 ATTGTTTTTATTTTGTTATTTTTTTTT
1 ATTGTTTTCATTTTGTTATTTTTTTTT
43296066 ATTGTTTTCATTTTGTTATTTTTTTT
1 ATTGTTTTCATTTTGTTATTTTTTTT
43296092 GTCAAATTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.11, C:0.02, G:0.08, T:0.79
Consensus pattern (27 bp):
ATTGTTTTCATTTTGTTATTTTTTTTT
Found at i:43296087 original size:14 final size:13
Alignment explanation
Indices: 43296044--43296093 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
43296034 ATAAGATTGT
43296044 TTTTATTTTGTTA
1 TTTTATTTTGTTA
* * *
43296057 TTTTTTTTTATTG
1 TTTTATTTTGTTA
43296070 TTTTCATTTTGTTA
1 TTTT-ATTTTGTTA
43296084 TTTT-TTTTGT
1 TTTTATTTTGT
43296094 CAAATTAGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 6 0.20
13 14 0.47
14 10 0.33
ACGTcount: A:0.10, C:0.02, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTATTTTGTTA
Found at i:43298615 original size:22 final size:21
Alignment explanation
Indices: 43298569--43298633 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
43298559 GCAAGCCCAG
43298569 AAAAAGAA-AAAGAAAAATAA
1 AAAAAGAAGAAAGAAAAATAA
* *
43298589 GAAAAGAAGAATGAAAAATGAA
1 AAAAAGAAGAAAGAAAAAT-AA
* * *
43298611 AAAAACAAG-AGGGAAAATAA
1 AAAAAGAAGAAAGAAAAATAA
43298631 AAA
1 AAA
43298634 TAACAAAACA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 12 0.32
21 16 0.43
22 9 0.24
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (21 bp):
AAAAAGAAGAAAGAAAAATAA
Found at i:43307148 original size:5 final size:5
Alignment explanation
Indices: 43307138--43307162 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
43307128 AAATAAGCAC
43307138 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
43307163 TTTTTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:43308319 original size:19 final size:19
Alignment explanation
Indices: 43308295--43308334 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
43308285 TCTGGTTTCG
43308295 TTCTCCCGTTCGTTCTCCC
1 TTCTCCCGTTCGTTCTCCC
*
43308314 TTCTCCCTTTCGTTCTCCC
1 TTCTCCCGTTCGTTCTCCC
43308333 TT
1 TT
43308335 GATTTGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.45, G:0.07, T:0.47
Consensus pattern (19 bp):
TTCTCCCGTTCGTTCTCCC
Found at i:43310022 original size:18 final size:18
Alignment explanation
Indices: 43309999--43310037 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
43309989 TTTACCAACT
43309999 TTATGGATAATAATTTAA
1 TTATGGATAATAATTTAA
43310017 TTATGGATAATAATTTAA
1 TTATGGATAATAATTTAA
43310035 TTA
1 TTA
43310038 AAGATACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (18 bp):
TTATGGATAATAATTTAA
Found at i:43310043 original size:18 final size:18
Alignment explanation
Indices: 43310004--43310043 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
43309994 CAACTTTATG
**
43310004 GATAATAATTTAATTATG
1 GATAATAATTTAATTAAA
43310022 GATAATAATTTAATTAAA
1 GATAATAATTTAATTAAA
43310040 GATA
1 GATA
43310044 CAACATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (18 bp):
GATAATAATTTAATTAAA
Found at i:43310570 original size:20 final size:19
Alignment explanation
Indices: 43310520--43310572 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
43310510 TAAATCATTG
*
43310520 TAATATATGTAAAAGCAATT
1 TAATATATGTAAAA-AAATT
*
43310540 TAA-A-ATATAAAAAAATAT
1 TAATATATGTAAAAAAAT-T
43310558 TAATATATGTAAAAA
1 TAATATATGTAAAAA
43310573 TAACTTTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 3 0.11
18 11 0.41
19 2 0.07
20 11 0.41
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (19 bp):
TAATATATGTAAAAAAATT
Found at i:43310687 original size:20 final size:20
Alignment explanation
Indices: 43310662--43310701 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43310652 AATATTTTCC
*
43310662 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
43310682 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
43310702 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:43310707 original size:34 final size:35
Alignment explanation
Indices: 43310650--43310716 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
43310640 CAAACACTAG
*
43310650 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
43310685 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
43310717 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:43317450 original size:19 final size:20
Alignment explanation
Indices: 43317414--43317451 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
43317404 AATTTTTTAA
43317414 TATTTTATTTAAAATAATAT
1 TATTTTATTTAAAATAATAT
*
43317434 TATTTTA-TTAAAGTAATA
1 TATTTTATTTAAAATAATA
43317452 AAATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTTATTTAAAATAATAT
Done.