Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 132 of 425
Found at i:39560550 original size:14 final size:14
Alignment explanation
Indices: 39560527--39560559 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39560517 TAATGTGGCT
39560527 AAAA-AAAAGAAAA
1 AAAAGAAAAGAAAA
*
39560540 AAAAGAAAAGAAGA
1 AAAAGAAAAGAAAA
39560554 AAAAGA
1 AAAAGA
39560560 TTGAATCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAA
Found at i:39563204 original size:37 final size:37
Alignment explanation
Indices: 39563154--39563225 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
39563144 TTTAGCTCGA
*
39563154 ATAATCCCCACACGTAGTCATCGGGTCTTACCCGGGC
1 ATAATCCCCACACGTAGCCATCGGGTCTTACCCGGGC
*
39563191 ATAATCTCCACACGTAGCCATCGGGTCTTACCCGG
1 ATAATCCCCACACGTAGCCATCGGGTCTTACCCGG
39563226 AATATATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.22
Consensus pattern (37 bp):
ATAATCCCCACACGTAGCCATCGGGTCTTACCCGGGC
Found at i:39563419 original size:48 final size:48
Alignment explanation
Indices: 39563359--39563464 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 48
39563349 CGGCCACAAT
* *
39563359 ATATACACATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
39563407 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
* *
39563455 ACATATATAT
1 ATATACATAT
39563465 ATTTATCTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (48 bp):
ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
Found at i:39565754 original size:28 final size:27
Alignment explanation
Indices: 39565688--39565757 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
39565678 ATAGTGAGTC
*
39565688 CGCACACTTAGTGCTATATAATCAGCT
1 CGCACACTTAGTGCTATATAATCAACT
* *
39565715 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATC-AACT
39565743 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39565758 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:39565830 original size:42 final size:42
Alignment explanation
Indices: 39565766--39565874 Score: 200
Period size: 42 Copynumber: 2.6 Consensus size: 42
39565756 CTGTACAAAT
*
39565766 TTTAAACCCGCACACTTAGTGCCGATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCGATCTTGTCACCGTGTCCA
*
39565808 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCGATCTTGTCACCGTGTCCA
39565850 TTTATACCCGCACACTTAGTGCCGA
1 TTTATACCCGCACACTTAGTGCCGA
39565875 GACCAATACT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (42 bp):
TTTATACCCGCACACTTAGTGCCGATCTTGTCACCGTGTCCA
Found at i:39570265 original size:29 final size:29
Alignment explanation
Indices: 39570223--39570304 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
39570213 ATTATTTTTT
39570223 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
39570252 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
*
39570281 TTTCCAGCACGCACACTTAGTGCC
1 TTTCCAGCATGCACACTTAGTGCC
39570305 TATCTCGTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:39578169 original size:29 final size:29
Alignment explanation
Indices: 39578127--39578208 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
39578117 TTATTTTTTT
39578127 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
39578156 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
*
39578185 TTTCCAGCACGCACACTTAGTGCC
1 TTTCCAGCATGCACACTTAGTGCC
39578209 TATCTCGTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:39589012 original size:29 final size:29
Alignment explanation
Indices: 39588970--39589051 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
39588960 GTATTTTTTT
39588970 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
39588999 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
*
39589028 TTTCCAGCACGCACACTTAGTGCC
1 TTTCCAGCATGCACACTTAGTGCC
39589052 TATCTCGTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:39596912 original size:29 final size:29
Alignment explanation
Indices: 39596870--39596951 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
39596860 TTATTTTTTT
39596870 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
39596899 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
*
39596928 TTTCCAGCACGCACACTTAGTGCC
1 TTTCCAGCATGCACACTTAGTGCC
39596952 TATCTCGTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:39600977 original size:78 final size:78
Alignment explanation
Indices: 39600817--39601051 Score: 299
Period size: 78 Copynumber: 3.0 Consensus size: 78
39600807 TCGTTCAAAC
* * ** * ** * * * *
39600817 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCAAGACTTAACCCGGGTATC
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTGCCTTC-GGGCTTAGCCCGGATATC
* *
39600882 ACAACTCGCACAATT
64 ACAATTCGCACATTT
39600897 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
39600962 AATTCGCACATTT
66 AATTCGCACATTT
* * * *
39600975 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATTTTCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
39601040 AATTCGCACATT
66 AATTCGCACATT
39601052 CATACACATC
Statistics
Matches: 138, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
78 100 0.72
79 29 0.21
80 9 0.07
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.25
Consensus pattern (78 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
AATTCGCACATTT
Found at i:39601050 original size:39 final size:39
Alignment explanation
Indices: 39600867--39601051 Score: 298
Period size: 39 Copynumber: 4.7 Consensus size: 39
39600857 GCCTTCAAGA
* * * *
39600867 CTTAACCCGGGTATCACAACTCGCACAATTGCCTTCGGG
1 CTTAGCCCGGATATCACAATTCGCACATTTGCCTTCGGG
* * *
39600906 CTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG
1 CTTAGCCCGGATATCACAATTCGCACATTTGCCTTCGGG
39600945 CTTAGCCCGGATATCACAATTCGCACATTTGCCTTCGGG
1 CTTAGCCCGGATATCACAATTCGCACATTTGCCTTCGGG
*
39600984 CTTAGCCCGGATATCACAATTCGCACATTTTCCTTCGGG
1 CTTAGCCCGGATATCACAATTCGCACATTTGCCTTCGGG
39601023 CTTAGCCCGGATATCACAATTCGCACATT
1 CTTAGCCCGGATATCACAATTCGCACATT
39601052 CATACACATC
Statistics
Matches: 139, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 139 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (39 bp):
CTTAGCCCGGATATCACAATTCGCACATTTGCCTTCGGG
Found at i:39608356 original size:39 final size:39
Alignment explanation
Indices: 39608163--39608357 Score: 311
Period size: 39 Copynumber: 5.0 Consensus size: 39
39608153 CCGCACAAAG
* * * *
39608163 GCCTTCGGGACTTAACCCGGGTATCACAACTCGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCACAATTCGCACATTT
* *
39608203 GCCTTCGGGCTTAGCCCGGATATCATAACTT-GCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAA-TTCGCACATTT
39608242 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATTT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATTT
39608281 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATTT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATTT
39608320 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATT
39608358 CATACACATC
Statistics
Matches: 147, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
38 2 0.01
39 135 0.92
40 10 0.07
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.27
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATTT
Found at i:39610445 original size:29 final size:29
Alignment explanation
Indices: 39610412--39610630 Score: 366
Period size: 29 Copynumber: 7.6 Consensus size: 29
39610402 CCTCCGAACT
** * * *
39610412 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
39610441 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
39610470 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
39610499 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
39610528 CGCATACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
39610557 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
39610586 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
39610615 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
39610631 ATCTCGTCAC
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 179 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:39610474 original size:87 final size:87
Alignment explanation
Indices: 39610354--39610631 Score: 308
Period size: 87 Copynumber: 3.2 Consensus size: 87
39610344 CACTCGATTT
** * * ** * *
39610354 CGCACACTTAGTGCCACGTAATTT-AAGCTCGCACACACAGTGCCATA-CCCTCCGAACTCGCAC
1 CGCACACTTAGTGCCAAAT-ATTTCCAGCACGCACACTTAGTGCCATATACCTCC-AACACGCAC
* * *
39610417 ACCCAGTGCCGTATTTTTCCAGCT
64 ACCCAGTGCCATATATTTCCAGCA
* ** *
39610441 TGCACACTTAGTGCCAAATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCACGCACAC
1 CGCACACTTAGTGCCAAATATTTCCAGCACGCACACTTAGTGCCATATACCTCCAACACGCACAC
**
39610506 TTAGTGCCATATATTTCCAGCA
66 CCAGTGCCATATATTTCCAGCA
* * ** *
39610528 CGCATACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCACGCACAC
1 CGCACACTTAGTGCCAAATATTTCCAGCACGCACACTTAGTGCCATATACCTCCAACACGCACAC
**
39610593 TTAGTGCCATATATTTCCAGCA
66 CCAGTGCCATATATTTCCAGCA
39610615 CGCACACTTAGTGCCAA
1 CGCACACTTAGTGCCAA
39610632 TCTCGTCACC
Statistics
Matches: 167, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
86 4 0.02
87 160 0.96
88 3 0.02
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (87 bp):
CGCACACTTAGTGCCAAATATTTCCAGCACGCACACTTAGTGCCATATACCTCCAACACGCACAC
CCAGTGCCATATATTTCCAGCA
Found at i:39613464 original size:30 final size:30
Alignment explanation
Indices: 39613430--39613486 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
39613420 TTTTCAAGCA
* *
39613430 TAGGGGTAAAATGGTCATTTTGCCAAAGTC
1 TAGGGGCAAAATGGTCATTTTACCAAAGTC
39613460 TAGGGGCAAAATGGTCATTTTACCAAA
1 TAGGGGCAAAATGGTCATTTTACCAAA
39613487 TATGTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTC
Found at i:39613953 original size:95 final size:95
Alignment explanation
Indices: 39613828--39614143 Score: 295
Period size: 95 Copynumber: 3.3 Consensus size: 95
39613818 GTACTTGTGT
* *
39613828 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-AATATGATAGCCAGTGTAAGACCATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAAGATGATAGCCAGTGTAAGACCATGT
* *
39613892 CTAGGACATGGCATCGACGTAGAGAATGAGC
66 CTAGGACATGGTATCGAC-TAGAGAATGAGA
* * * *
39613923 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGACGGTGATAGCCAGTGTAAGA-CGTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAAGATGATAGCCAGTGTAAGACCATGT
* * * * * *
39613987 ATAGGACA-CGTATCGGCTA-AGAGT-TGT
66 CTAGGACATGGTATCGACTAGAGAATGAGA
* * * * * *
39614014 GCTAGTGTAAGACATGTCTAGGACATGCATCAG-CACGTATAGACGAGAGCTAGTATAAGACCAT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACG-A-AGATGATAGCCAGTGTAAGACCAT
* * * *
39614078 GTCTGGGACATGGTATCAGCCTCGATG-ATGATA
64 GTCTAGGACATGGTATC-GACTAGA-GAATGAGA
*
39614111 GCCAGTGTAAGACCATGTCCGGGACATGGCATC
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
39614144 GGCAACATAT
Statistics
Matches: 175, Mismatches: 35, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
90 3 0.02
91 33 0.19
92 18 0.10
93 12 0.07
94 11 0.06
95 49 0.28
96 20 0.11
97 12 0.07
98 12 0.07
99 5 0.03
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (95 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAAGATGATAGCCAGTGTAAGACCATGT
CTAGGACATGGTATCGACTAGAGAATGAGA
Found at i:39614087 original size:49 final size:49
Alignment explanation
Indices: 39613831--39614143 Score: 156
Period size: 49 Copynumber: 6.6 Consensus size: 49
39613821 CTTGTGTGCC
* * * * *
39613831 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACAAT-ATGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATGACGAGAGCT
* * * * *
39613877 AGTGTAAGACCATGTCTAGGACATGGCATC-G--ACGTAGAGAATGAGCGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACG-A-TG-ACGAGAGCT
* * ** * *
39613926 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGACGGTGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATGACGAGAGCT
* * * * * * * * *
39613973 AGTGTAAGA-CGTGTATAGGACA-CGTATCGGCTA--A-GA-GTTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATGACG-AGAGCT
*
39614017 AGTGTAAGA-CATGTCTAGGACAT-GCATCAG-CACGTATAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACG-AT-GACGAGAGCT
* * * * * *
39614065 AGTATAAGACCATGTCTGGGACATGGTATCAGCCTCGATGATGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATGACGAGAGCT
*
39614114 AGTGTAAGACCATGTCCGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
39614144 GGCAACATAT
Statistics
Matches: 206, Mismatches: 40, Indels: 39
0.72 0.14 0.14
Matches are distributed among these distances:
43 2 0.01
44 28 0.14
45 3 0.01
46 11 0.05
47 50 0.24
48 34 0.17
49 65 0.32
50 10 0.05
51 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATGACGAGAGCT
Found at i:39615006 original size:55 final size:55
Alignment explanation
Indices: 39614908--39615038 Score: 190
Period size: 55 Copynumber: 2.4 Consensus size: 55
39614898 ACACTTAAAA
*
39614908 TTTAAAGTCAGTGTTGTACACGGGCAAGCCACACCGGCGTGTGTCATGGTCATGT
1 TTTAAAGTCAGTGTTGTACACGGGCAAGCCACACCGGCGTGTGTCATGGCCATGT
* * * * * *
39614963 TTTAAAATCAGTGTTGTACACGGGCAGGCTACACGGGCTTGTGTCATGGCCGTGT
1 TTTAAAGTCAGTGTTGTACACGGGCAAGCCACACCGGCGTGTGTCATGGCCATGT
*
39615018 TTTAAAGTCAGTGTTGGACAC
1 TTTAAAGTCAGTGTTGTACAC
39615039 AGGCTAAGGG
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (55 bp):
TTTAAAGTCAGTGTTGTACACGGGCAAGCCACACCGGCGTGTGTCATGGCCATGT
Found at i:39615053 original size:55 final size:54
Alignment explanation
Indices: 39614908--39615059 Score: 180
Period size: 55 Copynumber: 2.8 Consensus size: 54
39614898 ACACTTAAAA
* * *
39614908 TTTAAAGTCAGTGTTGTACACGGGCAAGCCACACCGGCGTGTGTCATGGTCATGT
1 TTTAAAGTCAGTGTTGTACACGGGCAAG-GACACGGGCGTGTGTCATGGCCATGT
* * *
39614963 TTTAAAATCAGTGTTGTACACGGGC-AGGCTACACGGGCTTGTGTCATGGCCGTGT
1 TTTAAAGTCAGTGTTGTACACGGGCAAGG--ACACGGGCGTGTGTCATGGCCATGT
* * *
39615018 TTTAAAGTCAGTGTTGGACACAGGCTAAGGGCACGGGCGTGT
1 TTTAAAGTCAGTGTTGTACACGGGC-AAGGACACGGGCGTGT
39615060 CCTAAGCCAT
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
54 2 0.02
55 77 0.94
57 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.27
Consensus pattern (54 bp):
TTTAAAGTCAGTGTTGTACACGGGCAAGGACACGGGCGTGTGTCATGGCCATGT
Found at i:39618345 original size:26 final size:26
Alignment explanation
Indices: 39618316--39618423 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
39618306 TGGTACAAAT
39618316 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
39618342 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39618368 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39618394 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39618420 TGAT
1 TGAT
39618424 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39621770 original size:93 final size:93
Alignment explanation
Indices: 39621655--39621825 Score: 252
Period size: 93 Copynumber: 1.8 Consensus size: 93
39621645 GCCCCTAAGT
** * *
39621655 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCACATCCATAAATGAACTCAGACTCAACTCAA
*
39621720 TGAGTTCGGATGCCTAGTTACTTCTCAC
66 CGAGTTCGGATGCCTAGTTACTTCTCAC
* * ** *
39621748 GAACTCGGACTCAACTCAACGAGTTTGAACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCACATCCATAAATGAACTCAGACTCAACTCAA
39621813 CGAGTTCGGATGC
66 CGAGTTCGGATGC
39621826 TCAACCATCC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 68 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCACATCCATAAATGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACTTCTCAC
Found at i:39622278 original size:30 final size:30
Alignment explanation
Indices: 39622244--39622303 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
39622234 ATTTAATACG
39622244 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
39622274 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
39622304 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:39628823 original size:47 final size:49
Alignment explanation
Indices: 39628704--39628878 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 49
39628694 TAACCCCCCC
* *
39628704 TAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C-GTTCACATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTT-ACATCCA
**
39628750 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTACATCCA
* * *
39628798 TCA-CGAACTCGGACTCAACTCAACGAGTTC-GA---CATTTGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACATCCA
*
39628842 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
39628879 TCAACCATCC
Statistics
Matches: 109, Mismatches: 8, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
42 6 0.06
43 2 0.02
44 2 0.02
45 26 0.24
46 35 0.32
47 26 0.24
48 3 0.03
49 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (49 bp):
TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACATCCA
Found at i:39628867 original size:92 final size:93
Alignment explanation
Indices: 39628709--39628878 Score: 279
Period size: 92 Copynumber: 1.8 Consensus size: 93
39628699 CCCCCTAAGT
* *
39628709 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
39628774 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* ** *
39628802 GAACTCGGACTCAACTCAACGAGTTC-GACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
39628866 CGAGTTCGGATGC
66 CGAGTTCGGATGC
39628879 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 46 0.65
93 25 0.35
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:39629330 original size:30 final size:30
Alignment explanation
Indices: 39629296--39629355 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
39629286 ATTTAATACG
39629296 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
39629326 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
39629356 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:39635215 original size:26 final size:26
Alignment explanation
Indices: 39635186--39635292 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
39635176 TGGTACAAAT
39635186 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
39635212 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39635238 TGATAATGGGTTAGGTAAATGTT-CA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39635263 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39635289 TGAT
1 TGAT
39635293 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
25 24 0.32
26 51 0.68
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39635288 original size:51 final size:52
Alignment explanation
Indices: 39635186--39635292 Score: 189
Period size: 51 Copynumber: 2.1 Consensus size: 52
39635176 TGGTACAAAT
39635186 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
* *
39635238 TGATAATGGGTTAGGTAAATGTT-CATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
39635289 TGAT
1 TGAT
39635293 GGGCATTTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
51 30 0.57
52 23 0.43
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:39641343 original size:13 final size:13
Alignment explanation
Indices: 39641327--39641352 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39641317 ATATGTTTTA
39641327 TGATTGTTTTGGT
1 TGATTGTTTTGGT
39641340 TGATTGTTTTGGT
1 TGATTGTTTTGGT
39641353 ATGGGTTCAA
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:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TGATTGTTTTGGT
Found at i:39645919 original size:11 final size:11
Alignment explanation
Indices: 39645883--39645938 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
39645873 CATGGTATGT
39645883 ATGATATGCAC
1 ATGATATGCAC
* *
39645894 ATGACATG--T
1 ATGATATGCAC
39645903 ATGATATGCAC
1 ATGATATGCAC
*
39645914 ATGATATG--T
1 ATGATATGCAC
39645923 ATGATATGCAC
1 ATGATATGCAC
39645934 ATGAT
1 ATGAT
39645939 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:39645938 original size:20 final size:20
Alignment explanation
Indices: 39645872--39645938 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
39645862 ATTTTGATAA
*
39645872 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
39645892 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
39645912 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
39645932 ACATGAT
1 ACATGAT
39645939 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:39646018 original size:23 final size:23
Alignment explanation
Indices: 39645988--39646107 Score: 204
Period size: 23 Copynumber: 5.1 Consensus size: 23
39645978 AGGAAGTGAA
39645988 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
39646011 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
39646035 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
39646058 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
39646081 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
39646105 AAA
1 AAA
39646108 AGAGGCTAGG
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
23 48 0.52
24 44 0.48
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:39646043 original size:24 final size:23
Alignment explanation
Indices: 39645987--39646114 Score: 193
Period size: 24 Copynumber: 5.4 Consensus size: 23
39645977 GAGGAAGTGA
39645987 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
39646010 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
39646033 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
39646057 TAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
39646081 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
39646105 AAAAGAGGCT
1 AAAAG-GGCT
39646115 AGGCCTCCAG
Statistics
Matches: 97, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
23 43 0.44
24 50 0.52
25 4 0.04
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:39646056 original size:47 final size:47
Alignment explanation
Indices: 39645987--39646107 Score: 224
Period size: 47 Copynumber: 2.6 Consensus size: 47
39645977 GAGGAAGTGA
39645987 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
*
39646034 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
*
39646081 AAAAGGGCTTTTGCCCCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
39646108 AGAGGCTAGG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
Found at i:39646356 original size:31 final size:31
Alignment explanation
Indices: 39646321--39646381 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
39646311 CGTTTACAGT
39646321 AAAGGCTTCGGCCCAGTAATATGAAATATGG
1 AAAGGCTTCGGCCCAGTAATATGAAATATGG
**
39646352 AAAGGCTTCGGCCCAGTGTTATGAAATATG
1 AAAGGCTTCGGCCCAGTAATATGAAATATG
39646382 AAATATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGG
Found at i:39658335 original size:40 final size:39
Alignment explanation
Indices: 39658170--39658353 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
39658160 AAATTGAATG
* * *
39658170 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
39658210 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
39658250 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
39658290 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
39658329 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
39658354 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:39658378 original size:80 final size:81
Alignment explanation
Indices: 39658210--39658398 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
39658200 GCTGGAAATT
* * * *
39658210 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
39658275 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
39658291 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
39658354 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
39658370 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
39658399 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:39666401 original size:40 final size:39
Alignment explanation
Indices: 39666237--39666404 Score: 135
Period size: 40 Copynumber: 4.2 Consensus size: 39
39666227 AAATTGAATG
* *
39666237 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
39666276 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
39666316 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
39666356 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
39666395 GATATCCGGG
1 -ATATCCGGG
39666405 GTTAAGTCCC
Statistics
Matches: 101, Mismatches: 22, Indels: 11
0.75 0.16 0.08
Matches are distributed among these distances:
36 2 0.02
37 4 0.04
38 2 0.02
39 21 0.21
40 72 0.71
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:39673608 original size:40 final size:39
Alignment explanation
Indices: 39673443--39673626 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
39673433 AAATTGAATG
* * *
39673443 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
39673483 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
39673523 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
39673563 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
39673602 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
39673627 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:39673651 original size:80 final size:81
Alignment explanation
Indices: 39673483--39673671 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
39673473 GCTGGAAATT
* * * *
39673483 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
39673548 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
39673564 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
39673627 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
39673643 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
39673672 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:39676904 original size:26 final size:26
Alignment explanation
Indices: 39676867--39676950 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
39676857 TGATACAAAT
*
39676867 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39676893 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39676919 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39676945 TGATAA
1 TGATAA
39676951 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39678574 original size:27 final size:27
Alignment explanation
Indices: 39678533--39678645 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
39678523 GAGGAAGTGT
*
39678533 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
39678560 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
39678587 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
39678615 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
39678641 TCTGG
1 TCTGG
39678646 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:39678612 original size:54 final size:54
Alignment explanation
Indices: 39678530--39678645 Score: 171
Period size: 54 Copynumber: 2.1 Consensus size: 54
39678520 ATGGAGGAAG
*
39678530 TGTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGGCTCTGCCACATATATC
1 TGTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTGACTCTGCCACAT-TATC
* * * *
39678584 TGTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATC
1 TGTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTGACTCTGCCACATTATC
39678638 TGTTCTGG
1 TGTTCTGG
39678646 CAGCCATGCT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 38 0.68
55 18 0.32
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
TGTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTGACTCTGCCACATTATC
Found at i:39680100 original size:43 final size:42
Alignment explanation
Indices: 39679971--39680122 Score: 173
Period size: 42 Copynumber: 3.6 Consensus size: 42
39679961 AGATTTCGTA
* * * *
39679971 TAAGACCATATCTAGAATATGGCATCG-TCATGTGATTTCATA
1 TAAGACCATATCTGGGATATGGCATCGAT-ATGTGATCTCATG
* * *
39680013 TAAGACCATATCTGGGATATGGTATCGATATGAGA-CATCGTG
1 TAAGACCATATCTGGGATATGGCATCGATATGTGATC-TCATG
* * *
39680055 TAAGACCATAGCTGGGCTATTGGCATCGATATGTGATCCCATG
1 TAAGACCATATCTGGGATA-TGGCATCGATATGTGATCTCATG
39680098 TAAGACCATATCTGGGATATGGCAT
1 TAAGACCATATCTGGGATATGGCAT
39680123 TGGCATCTTA
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
42 55 0.60
43 35 0.38
44 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (42 bp):
TAAGACCATATCTGGGATATGGCATCGATATGTGATCTCATG
Found at i:39684214 original size:6 final size:6
Alignment explanation
Indices: 39684203--39684228 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39684193 GTGGAATGGA
39684203 GAGGAT GAGGAT GAGGAT GAGGAT GA
1 GAGGAT GAGGAT GAGGAT GAGGAT GA
39684229 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
GAGGAT
Found at i:39688328 original size:38 final size:38
Alignment explanation
Indices: 39688283--39688366 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
39688273 GCTTAAAGAA
* *
39688283 CCGCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAATC
1 CCGCAGGCTTCGTGCTGGTAAAATATCAGGGATAAATC
**
39688321 CCGCAGGCTTCGTGCTGGTATTATATCAGGGATAAATC
1 CCGCAGGCTTCGTGCTGGTAAAATATCAGGGATAAATC
39688359 CCGCAGGC
1 CCGCAGGC
39688367 CTAGTGTTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (38 bp):
CCGCAGGCTTCGTGCTGGTAAAATATCAGGGATAAATC
Found at i:39688378 original size:38 final size:38
Alignment explanation
Indices: 39688283--39688384 Score: 123
Period size: 38 Copynumber: 2.7 Consensus size: 38
39688273 GCTTAAAGAA
* * ** * *
39688283 CCGCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAATC
1 CCGCAGGCCTAGTGCTGGTATTATATCAGGGATAAATC
* *
39688321 CCGCAGGCTTCGTGCTGGTATTATATCAGGGATAAATC
1 CCGCAGGCCTAGTGCTGGTATTATATCAGGGATAAATC
*
39688359 CCGCAGGCCTAGTGTTGGTATTATAT
1 CCGCAGGCCTAGTGCTGGTATTATAT
39688385 TCGGGCCTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (38 bp):
CCGCAGGCCTAGTGCTGGTATTATATCAGGGATAAATC
Found at i:39688430 original size:43 final size:43
Alignment explanation
Indices: 39688382--39688501 Score: 195
Period size: 43 Copynumber: 2.8 Consensus size: 43
39688372 GTTGGTATTA
* *
39688382 TATTCGGGCCTTTGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATATG
*
39688425 TATTCGAGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATATG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATATG
* *
39688468 TATTAGGGCCTTCGTGCCTAGCAGCCTTCGTGCC
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCC
39688502 TAGCAGGCGT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.12, C:0.27, G:0.31, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATATG
Found at i:39688496 original size:16 final size:16
Alignment explanation
Indices: 39688475--39688507 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39688465 ATGTATTAGG
39688475 GCCTTCGTGCCTAGCA
1 GCCTTCGTGCCTAGCA
39688491 GCCTTCGTGCCTAGCA
1 GCCTTCGTGCCTAGCA
39688507 G
1 G
39688508 GCGTAATGCC
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:0.12, C:0.36, G:0.27, T:0.24
Consensus pattern (16 bp):
GCCTTCGTGCCTAGCA
Found at i:39693727 original size:2 final size:2
Alignment explanation
Indices: 39693716--39693744 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
39693706 ATTCAAGTCT
39693716 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39693745 GTAGCGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:39697055 original size:18 final size:18
Alignment explanation
Indices: 39697020--39697053 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39697010 AAATTAAAAT
*
39697020 ATATATAGTATATATTTA
1 ATATATAATATATATTTA
39697038 ATATATAATATA-ATTT
1 ATATATAATATATATTT
39697054 TACTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATATAATATATATTTA
Found at i:39701473 original size:50 final size:47
Alignment explanation
Indices: 39701307--39701591 Score: 175
Period size: 50 Copynumber: 5.9 Consensus size: 47
39701297 TAAGGTTATT
* * * * * *
39701307 CGAGAGCTAATGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATATA
1 CGAGAGCCAGTGTAAAACCATGTCTAGGACATGGCATCAGCCT-G--ATA
* * * * *
39701357 TGATAGTCAGTGTAAGACCATGTCT-GGAACATGGCATCTG-CT-ATGA
1 CGAGAGCCAGTGTAAAACCATGTCTAGG-ACATGGCATCAGCCTGAT-A
* ** * * *
39701403 -GATGTGTTAGTGTAAGACCATGTCTAGGACATGGCATCGGCACAGATGGA
1 CGA-GAGCCAGTGTAAAACCATGTCTAGGACATGGCATCAGC-CTGAT--A
* * *
39701453 CGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTAGCCTTGATA
1 CGAGAGCCAGTGTAAAACCATGTCTAGGACATGGCATCAGCC-TGATA
* * * *
39701501 CATGATAGTCAGTGTAAAACCATGTCTCGGACATGGCATCTA-CTTTGATA
1 C--GAGAGCCAGTGTAAAACCATGTCTAGGACATGGCATC-AGC-CTGATA
* *
39701551 CGTGAGCTAGTGTAAAACCATGTCTAGGACATGGCATCAGC
1 CGAGAGCCAGTGTAAAACCATGTCTAGGACATGGCATCAGC
39701592 TTCCTGCCCT
Statistics
Matches: 190, Mismatches: 30, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
45 4 0.02
46 31 0.16
47 3 0.02
48 36 0.19
49 7 0.04
50 106 0.56
51 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (47 bp):
CGAGAGCCAGTGTAAAACCATGTCTAGGACATGGCATCAGCCTGATA
Found at i:39707451 original size:36 final size:35
Alignment explanation
Indices: 39707404--39707478 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 35
39707394 AAATTCAAAG
39707404 TAAAACACAATTATACACTTGTAAATAATCTTGAT
1 TAAAACACAATTATACACTTGTAAATAATCTTGAT
39707439 ATAAAACACAATTATACACTTGTAAATAATCTTGAT
1 -TAAAACACAATTATACACTTGTAAATAATCTTGAT
39707475 TAAA
1 TAAA
39707479 CTAGACGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
35 4 0.10
36 35 0.90
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.33
Consensus pattern (35 bp):
TAAAACACAATTATACACTTGTAAATAATCTTGAT
Found at i:39713467 original size:48 final size:48
Alignment explanation
Indices: 39713415--39713743 Score: 426
Period size: 48 Copynumber: 6.8 Consensus size: 48
39713405 TACGAAGTCT
* * * * *
39713415 CATATCAGTGTCGATGCCATGTCTCAAACATGGTCTTACACTAGCACA
1 CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
*
39713463 CATATC-ATCGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
1 CATATCAAT-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* *
39713511 CATATCAATGCCAATGCCATGTCCCAAACATGGTCTTACACTGGCACA
1 CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
** ** *
39713559 CATATCAACACCGATGCCATGTCCCAGACATGGTCTTACTTTGGCATA
1 CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* **
39713607 CATATCAATACCGATGCCATGTCCCAGACATTTTCTTACACTGGCACA
1 CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* * *
39713655 CATATCAATGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT
1 CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* * * *
39713703 CATTTCGGATGCCAATGCCATGTCCCAGACATGGTTTTACA
1 CATATC-AATGCCGATGCCATGTCCCAGACATGGTCTTACA
39713744 TAGGATCTCA
Statistics
Matches: 245, Mismatches: 33, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
47 1 0.00
48 212 0.87
49 32 0.13
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (48 bp):
CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
Found at i:39718102 original size:378 final size:377
Alignment explanation
Indices: 39717408--39718162 Score: 1357
Period size: 378 Copynumber: 2.0 Consensus size: 377
39717398 TCAATACACA
39717408 ACATATAACTTTATTTTCTCATACAAGATTCAATTTCACATAGATATCAATCAAACACAATCATA
1 ACATATAACTTTATTTTCTCATACAAGATTCAATTTCACATAGATATCAATCAAACACAATCATA
*
39717473 TTGTCCCTTATAAAGTTCTATGAGACCTTAAAACATCTCAGAAGAGATTCGGGACTAAATCGATA
66 TTGTCCCTTATAAAGTTCCATGAGACCTTAAAACATCTCAGAAGAGATTCGGGACTAAATCGATA
*
39717538 ACATTTGCAAACTTTAGGAAACACATAAAATTTTCAAGCATTCAAGGGTCACACGCCCGTGTGAA
131 ACATTTGCAAACTTTAGGAAACACATAAAATTTTCAAGCATTCAAGGGTCACACGCCCATGTGAA
* * * *
39717603 TAGACCGTCTGCCTCACACGGCCACCAGACATGCCTGTGTCTAGGCGATGTGGAAATGGGGCATA
196 CAGACCGTCTGCCTCACACGGCCACCAGACATGCCTATGTCTAGGCGATGTAGAAATAGGGCATA
*
39717668 CATACTGACTTACATCACACGGTCGGGGACACACCCATGTGCCATGGCCATGTGAGAACTGGAGG
261 CATACTAACTTACATCACACGGTCGGGGACACACCCATGTGCCATGGCCATGTGAGAACTGGAGG
*
39717733 GTATATTGACTTGGGTCACATGGCCAACCACATGTCCGTGGGCCACACACGG
326 GTATATTGACTTGGGTCACATGGCCAACCACATGTCCATGGGCCACACACGG
39717785 ACATATAACTTTATTTTCTCATACAAGATTCAATTTCACATAGATATCAATCAAACACAATCATA
1 ACATATAACTTTATTTTCTCATACAAGATTCAATTTCACATAGATATCAATCAAACACAATCATA
39717850 TTGTCCCTTATAAAGTTCCATGAGACCTTAAAACATGCTCAGAAGAGATTCGGGACTAAATCGAT
66 TTGTCCCTTATAAAGTTCCATGAGACCTTAAAACAT-CTCAGAAGAGATTCGGGACTAAATCGAT
* * * *
39717915 AACATTTGCAAACTTTAGGAAACACATAAAATTTTTAGGCATTCAAGGGTCGCGCGCCCATGTGA
130 AACATTTGCAAACTTTAGGAAACACATAAAATTTTCAAGCATTCAAGGGTCACACGCCCATGTGA
*
39717980 ACAGACCGTGTGCCTCACACGGCCACCAGACATGCCTATGTCTAGGCGATGTAGAAATAGGGCAT
195 ACAGACCGTCTGCCTCACACGGCCACCAGACATGCCTATGTCTAGGCGATGTAGAAATAGGGCAT
*
39718045 ACATACTAACTTACATCACACGGTCGGGGACACACCCGTGTGCCATGGCCATGTGAGAACTGGAG
260 ACATACTAACTTACATCACACGGTCGGGGACACACCCATGTGCCATGGCCATGTGAGAACTGGAG
* *
39718110 GGTATATTGACTTGGGTCACATGGCCAACCACATGTCTATGTGCCACACACGG
325 GGTATATTGACTTGGGTCACATGGCCAACCACATGTCCATGGGCCACACACGG
39718163 CCAGTAAACA
Statistics
Matches: 361, Mismatches: 16, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
377 100 0.28
378 261 0.72
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (377 bp):
ACATATAACTTTATTTTCTCATACAAGATTCAATTTCACATAGATATCAATCAAACACAATCATA
TTGTCCCTTATAAAGTTCCATGAGACCTTAAAACATCTCAGAAGAGATTCGGGACTAAATCGATA
ACATTTGCAAACTTTAGGAAACACATAAAATTTTCAAGCATTCAAGGGTCACACGCCCATGTGAA
CAGACCGTCTGCCTCACACGGCCACCAGACATGCCTATGTCTAGGCGATGTAGAAATAGGGCATA
CATACTAACTTACATCACACGGTCGGGGACACACCCATGTGCCATGGCCATGTGAGAACTGGAGG
GTATATTGACTTGGGTCACATGGCCAACCACATGTCCATGGGCCACACACGG
Found at i:39718362 original size:57 final size:57
Alignment explanation
Indices: 39718269--39718382 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
39718259 CAACCGTGTG
*
39718269 GTACAAAAATAGGCTTAATTTAAGCCAATTTTCCACCTATCTTTTATGTACCTAAAA
1 GTACAAAAATAGGCTTAATTTAAGCCAATTTTCCACCTATCTTTCATGTACCTAAAA
* *
39718326 GTACGAAAATAGGCTTAATTTAAGCCAGTTTTCCACCTATCTTTCATGTACCTAAAA
1 GTACAAAAATAGGCTTAATTTAAGCCAATTTTCCACCTATCTTTCATGTACCTAAAA
39718383 ACATTCTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (57 bp):
GTACAAAAATAGGCTTAATTTAAGCCAATTTTCCACCTATCTTTCATGTACCTAAAA
Found at i:39719383 original size:43 final size:43
Alignment explanation
Indices: 39719279--39719386 Score: 112
Period size: 43 Copynumber: 2.5 Consensus size: 43
39719269 TATCCCGAAT
* * *
39719279 ATGGTCTTACATGTTATCACATATCGATGCCACTGTCCTAGAC
1 ATGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAAAC
* * * * *
39719322 AGGGTCTTATACGAAATCATATAAT-GATGCCGA-TGTCCCAAAC
1 ATGGTCTTACATGTAATCACAT-ATCGATGCC-ACTGTCCCAAAC
39719365 ATGGTCTTACATGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
39719387 CTCGGTAAAC
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
43 47 0.94
44 3 0.06
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAAAC
Found at i:39729881 original size:14 final size:14
Alignment explanation
Indices: 39729862--39729889 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39729852 GTTTAAGTTG
39729862 ATTATATATGTATT
1 ATTATATATGTATT
39729876 ATTATATATGTATT
1 ATTATATATGTATT
39729890 CGAGTCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
ATTATATATGTATT
Found at i:39731303 original size:30 final size:30
Alignment explanation
Indices: 39731258--39731318 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
39731248 TAATTCAATT
*
39731258 TTTTAAAAAATAAAA-TTATATATAAAAAA
1 TTTTAAAAAATAAAATTTAGATATAAAAAA
*
39731287 TTTTAAAATCATAAAATTTAGATATAAAAAA
1 TTTTAAAA-AATAAAATTTAGATATAAAAAA
39731318 T
1 T
39731319 ATAGTAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 8 0.29
30 6 0.21
31 14 0.50
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (30 bp):
TTTTAAAAAATAAAATTTAGATATAAAAAA
Found at i:39731315 original size:29 final size:29
Alignment explanation
Indices: 39731258--39731316 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
39731248 TAATTCAATT
*
39731258 TTTTAAAAAATAAAATTATATATAAAAAA
1 TTTTAAAAAATAAAATTATAGATAAAAAA
*
39731287 TTTTAAAATCATAAAATT-TAGATATAAAAA
1 TTTTAAAA-AATAAAATTATAGATA-AAAAA
39731317 ATATAGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (29 bp):
TTTTAAAAAATAAAATTATAGATAAAAAA
Found at i:39732593 original size:2 final size:2
Alignment explanation
Indices: 39732586--39732624 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
39732576 ACTAAGACTA
39732586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39732625 AATACCAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39738568 original size:47 final size:45
Alignment explanation
Indices: 39738451--39738671 Score: 173
Period size: 46 Copynumber: 4.8 Consensus size: 45
39738441 TCATACATGT
* * * *
39738451 GAGCTAGTGTAAGACATGTCTGGGACATGCATTAGCCACAATATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCA-TCGGCACAAGACGA
* *
39738497 GAGCCAGTGTAAGACCATGTCTGGGACATGACATCGGCACTGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCAC-AAGACGA
* * *
39738545 GAGCTAGTGTAAGATATGCCTGGGACATGCATCGGC-CTCAGAACGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCAC-AAG-ACG-A
* * * *
39738592 -AACCAGTGTAAGACATGTCTGAGACATACATCGGCTAC--GA-GA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGC-ACAAGACGA
* *
39738634 TGTGTTAGTGTAAGACCATGTCTGGGACATGGCATCGG
1 -GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGG
39738672 TATGGATATG
Statistics
Matches: 142, Mismatches: 22, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 10 0.07
45 18 0.13
46 58 0.41
47 34 0.24
48 20 0.14
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (45 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCACAAGACGA
Found at i:39738928 original size:17 final size:17
Alignment explanation
Indices: 39738906--39738941 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
39738896 TGCATGGTGA
39738906 TAAGTTACACCTATACT
1 TAAGTTACACCTATACT
39738923 TAAGTTACACCTATACT
1 TAAGTTACACCTATACT
39738940 TA
1 TA
39738942 CTTTGGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (17 bp):
TAAGTTACACCTATACT
Found at i:39750647 original size:30 final size:30
Alignment explanation
Indices: 39750613--39750670 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39750603 TTTTCGAATA
* * *
39750613 TAGGGGTAAAATGGTCATTTTGCCAAAGTC
1 TAGGGGCAAAATGGTAATTTTACCAAAGTC
39750643 TAGGGGCAAAATGGTAATTTTACCAAAG
1 TAGGGGCAAAATGGTAATTTTACCAAAG
39750671 ATGTGAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTTTACCAAAGTC
Found at i:39753781 original size:40 final size:39
Alignment explanation
Indices: 39753684--39753796 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 39
39753674 TTCGAATGGT
* * *
39753684 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACCAA
1 ATCCGGGTTAAGTCCCGAAGGC-ATTGTGC-GAGTGACCAA
* * *
39753725 AACCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTGACCAA
*
39753765 ATCCGGGTTAATTCCCGAAGGCAATTGTGCGA
1 ATCCGGGTTAAGTCCCGAAGGC-ATTGTGCGA
39753797 ATCACTATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
40 35 0.56
41 27 0.44
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (39 bp):
ATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTGACCAA
Found at i:39753811 original size:40 final size:39
Alignment explanation
Indices: 39753724--39753824 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 39
39753714 TAAGTGACCA
* * *
39753724 AAACCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACT
1 AAACCGGGTTAATTCCCGAAGGCATTCGTGCGAATCACT
39753763 AAATCCGGGTTAATTCCCGAAGGCAATT-GTGCGAATCACT
1 AAA-CCGGGTTAATTCCCGAAGGC-ATTCGTGCGAATCACT
*
39753803 ATAACCGGG-CAATGTCCCGAAG
1 A-AACCGGGTTAAT-TCCCGAAG
39753825 ATAATCGAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
39 6 0.11
40 43 0.80
41 5 0.09
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.22
Consensus pattern (39 bp):
AAACCGGGTTAATTCCCGAAGGCATTCGTGCGAATCACT
Found at i:39755831 original size:40 final size:40
Alignment explanation
Indices: 39755740--39756076 Score: 463
Period size: 40 Copynumber: 8.5 Consensus size: 40
39755730 TGGATGATAA
*
39755740 CCGGGCTAAGTCCCGAAGGCATTT-TGCGTTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* * *
39755781 CCGAGG-TAAGTCCCGAAGGCATTTGCGCGAGTTATTACAT
1 CCG-GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
39755821 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
39755861 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
39755901 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
39755941 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
39755981 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39756021 CCGGGCTATGT-CCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
39756059 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39756077 TACTTGGCTT
Statistics
Matches: 269, Mismatches: 21, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
37 7 0.03
38 23 0.09
39 11 0.04
40 202 0.75
41 21 0.08
42 5 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39764020 original size:40 final size:40
Alignment explanation
Indices: 39763897--39764153 Score: 328
Period size: 40 Copynumber: 6.5 Consensus size: 40
39763887 TGGATGATAA
*
39763897 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* * *
39763938 CCGGGCTAAGTCCCGAAGGCATTTGCG-GAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
39763977 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
39764017 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
39764057 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39764097 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
39764136 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39764154 TACTTGGCTT
Statistics
Matches: 193, Mismatches: 19, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
38 15 0.08
39 49 0.25
40 103 0.53
41 25 0.13
42 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39765898 original size:46 final size:48
Alignment explanation
Indices: 39765743--39766016 Score: 187
Period size: 46 Copynumber: 5.8 Consensus size: 48
39765733 TGGGTCATGT
* * * * *
39765743 ATGTGAGCTAGTGTAAGA-CATGTTTGAGACATGCATCGGCCAC--A-
1 ATGTAAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTACGGAG
* * * * ** *
39765787 ATATAAGATCCAGTGTAAGACCATGTTTGGCACATGGCATCGAC-ATTGAC
1 ATGTAAG--CCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCTACGGAG
* * *
39765837 A-CTAGAGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCTTCGGA-
1 ATGTA-AGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTACGGAG
* * *
39765883 ACGTAAGCCAATGTAAGA-CATGTCTGGGACATGTATCGGCTAC-GAG
1 ATGTAAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTACGGAG
** * *
39765929 ATGT--GTTAGTGTAAGACCATGTCTGGGACATGGCATCAGC-ACGGAT
1 ATGTAAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCTACGGAG
39765975 ATGTGAAAGCCAGTGTAAGACCATGTCTGGGACATGACATCG
1 ATGT--AAGCCAGTGTAAGACCATGTCTGGGACATG-CATCG
39766017 ACACCTTACC
Statistics
Matches: 181, Mismatches: 30, Indels: 32
0.74 0.12 0.13
Matches are distributed among these distances:
44 14 0.08
45 18 0.10
46 67 0.37
47 29 0.16
48 17 0.09
49 4 0.02
50 32 0.18
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (48 bp):
ATGTAAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTACGGAG
Found at i:39769738 original size:18 final size:18
Alignment explanation
Indices: 39769717--39769761 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
39769707 TAAAAGTTCA
39769717 AATTGAGTAGAACGCAGG
1 AATTGAGTAGAACGCAGG
39769735 AATTGAGTAGAACGCAGG
1 AATTGAGTAGAACGCAGG
39769753 AATTGAGTA
1 AATTGAGTA
39769762 CGATCGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.31, T:0.20
Consensus pattern (18 bp):
AATTGAGTAGAACGCAGG
Found at i:39769875 original size:29 final size:29
Alignment explanation
Indices: 39769833--39769888 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
39769823 TTAAATGTAA
39769833 GATCATAGCTGGGGCTATGGCATTTCAAG
1 GATCATAGCTGGGGCTATGGCATTTCAAG
*
39769862 GATCATATCTGGGGCTATGGCATTTCA
1 GATCATAGCTGGGGCTATGGCATTTCA
39769889 GTGAAAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (29 bp):
GATCATAGCTGGGGCTATGGCATTTCAAG
Found at i:39770340 original size:20 final size:20
Alignment explanation
Indices: 39770315--39770355 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
39770305 AACTTACTAA
39770315 GCTTCTATAAGCTTCCTCTT
1 GCTTCTATAAGCTTCCTCTT
39770335 GCTTCTATAAGCTTCCTCTT
1 GCTTCTATAAGCTTCCTCTT
39770355 G
1 G
39770356 TGTGTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.29, G:0.12, T:0.44
Consensus pattern (20 bp):
GCTTCTATAAGCTTCCTCTT
Found at i:39781867 original size:18 final size:18
Alignment explanation
Indices: 39781841--39781875 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39781831 AATTAAATAT
39781841 ATGCATATTAAATTATTA
1 ATGCATATTAAATTATTA
* *
39781859 ATGCTTATTAATTTATT
1 ATGCATATTAAATTATT
39781876 TAAACAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
ATGCATATTAAATTATTA
Found at i:39801982 original size:25 final size:26
Alignment explanation
Indices: 39801954--39802007 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
39801944 TAGTTAGTAT
*
39801954 AAAATATT-AATAATTCAAT-AAATTG
1 AAAA-ATTAAATAATTAAATAAAATTG
39801979 AAAAATTAAATAATTAAATAAAATTG
1 AAAAATTAAATAATTAAATAAAATTG
39802005 AAA
1 AAA
39802008 TTTAGGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.12
25 14 0.54
26 9 0.35
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (26 bp):
AAAAATTAAATAATTAAATAAAATTG
Found at i:39818491 original size:40 final size:39
Alignment explanation
Indices: 39818323--39818493 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
39818313 AGAAATTGAA
* *
39818323 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
39818363 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
39818403 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
39818443 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
39818483 TGATATCCGGG
1 TGATATCCGGG
39818494 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:39826473 original size:40 final size:39
Alignment explanation
Indices: 39826305--39826475 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
39826295 AGAAATTGAA
* *
39826305 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
39826345 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
39826385 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
39826425 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
39826465 TGATATCCGGG
1 TGATATCCGGG
39826476 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:39828977 original size:47 final size:48
Alignment explanation
Indices: 39828813--39829085 Score: 235
Period size: 46 Copynumber: 5.8 Consensus size: 48
39828803 TGAGGTAAGG
* * ** * * *
39828813 TGCCAATGCCATGTCCCATACATGGTCTTACAGAAGCTCTAGCATGTCT-G
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTA--ATCT-TAA
*
39828863 TGCCGATGCCATGTGCCAGACATGGTCTTACACT-G-AC-ACATCTCATAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTA-ATCT--TAA
39828911 --CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTAATCTTAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTAATCTTAA
* * * * ** *
39828955 TGCCGATGCCATGTCCCTGACATGGTCTTACACTGGCTCTCATAAT-G
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTAATCTTAA
* *
39829002 TGGTCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCATCTTAA
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTAATCTTAA
* *
39829049 TACCGATGCCATGTCCCTGACATGGTCTTACACTAGC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
39829086 TCACAATAAC
Statistics
Matches: 183, Mismatches: 27, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
44 13 0.07
45 14 0.08
46 45 0.25
47 44 0.24
48 37 0.20
49 1 0.01
50 29 0.16
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (48 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTAATCTTAA
Found at i:39829028 original size:94 final size:89
Alignment explanation
Indices: 39828863--39829096 Score: 315
Period size: 94 Copynumber: 2.5 Consensus size: 89
39828853 AGCATGTCTG
* * *
39828863 TGCCGATGCCATGTGCCAGACATGGTCTTACACTGACACATCTCATAACCGATGCATGTCCCAGA
1 TGCCGATGCCATGTCCCTGACATGGTCTTACACTG--GC-TCTCATAACCGATGCATGTCCCAGA
39828928 CATGTCTTACACTAGCACTAATCTTAA
63 CATGTCTTACACTAGCACTAATCTTAA
*
39828955 TGCCGATGCCATGTCCCTGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATGCATGTCCCA
1 TGCCGATGCCATGTCCCTGACATGGTCTTACACTGGCTCTCATAA-----CCGATGCATGTCCCA
*
39829020 GACATGTCTTACACTAGCACTCATCTTAA
61 GACATGTCTTACACTAGCACTAATCTTAA
* * *
39829049 TACCGATGCCATGTCCCTGACATGGTCTTACACTAGCTCACAATAACC
1 TGCCGATGCCATGTCCCTGACATGGTCTTACACTGGCTCTC-ATAACC
39829097 CATATGTTAT
Statistics
Matches: 127, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
89 8 0.06
90 2 0.02
92 33 0.26
94 80 0.63
95 4 0.03
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (89 bp):
TGCCGATGCCATGTCCCTGACATGGTCTTACACTGGCTCTCATAACCGATGCATGTCCCAGACAT
GTCTTACACTAGCACTAATCTTAA
Found at i:39834035 original size:29 final size:29
Alignment explanation
Indices: 39833900--39834034 Score: 207
Period size: 29 Copynumber: 4.7 Consensus size: 29
39833890 GCTTGGAAGG
39833900 TATGGCACTAAGTGTGCGAACTTAAATTA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
39833929 TATGGCACTAAGTGTGCGAACTTAAATTA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
*
39833958 TATGGCACTAAGTGTGCAAACTTAAATTA
1 TATGGCACTAAGTGTGCGAACTTAAATTA
* * **
39833987 TATGGCACTATGTGTGCGAGCTTAAATCG
1 TATGGCACTAAGTGTGCGAACTTAAATTA
* *
39834016 CATGGCACCAAGTGTGCGA
1 TATGGCACTAAGTGTGCGA
39834035 GATCGTTTAT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 97 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (29 bp):
TATGGCACTAAGTGTGCGAACTTAAATTA
Found at i:39835766 original size:2 final size:2
Alignment explanation
Indices: 39835761--39835786 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39835751 AAATGTCTTC
39835761 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
39835787 AGATACAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39837039 original size:24 final size:26
Alignment explanation
Indices: 39837012--39837070 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
39837002 AATAATATAG
*
39837012 AATAATATATAATATGTATA-TAA-A
1 AATAATATATAATATATATATTAATA
* *
39837036 AATAATGTATAGTATATATATTAATA
1 AATAATATATAATATATATATTAATA
*
39837062 TATAATATA
1 AATAATATA
39837071 AGCACAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 17 0.61
25 3 0.11
26 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (26 bp):
AATAATATATAATATATATATTAATA
Found at i:39837114 original size:30 final size:30
Alignment explanation
Indices: 39837080--39837141 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
39837070 AAGCACAAAT
*
39837080 ATAATAACCATATATAAATAATA-ATGTAAA
1 ATAATAACAATATA-AAATAATATATGTAAA
* *
39837110 ATAATAATAATATAAAATAATATATTTAAA
1 ATAATAACAATATAAAATAATATATGTAAA
39837140 AT
1 AT
39837142 GTAAGATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (30 bp):
ATAATAACAATATAAAATAATATATGTAAA
Found at i:39837117 original size:16 final size:16
Alignment explanation
Indices: 39837096--39837131 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
39837086 ACCATATATA
*
39837096 AATAATAATGTAAAAT
1 AATAATAATATAAAAT
39837112 AATAATAATATAAAAT
1 AATAATAATATAAAAT
39837128 AATA
1 AATA
39837132 TATTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAATAATATAAAAT
Found at i:39839273 original size:250 final size:249
Alignment explanation
Indices: 39838946--39839405 Score: 668
Period size: 249 Copynumber: 1.8 Consensus size: 249
39838936 AGAGATGAAA
* * * * *
39838946 AAATCATCTTAGATTTGCTTCATCGTAAGCACGTGAAAGCTAAATCAACTATGTCTTCGATTTGC
1 AAATCATCTTAGACTTACTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATTTGC
* * * *
39839011 TCCTTATAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCGTCTGAAGGTGA
66 TCCTTATAAGCACAAGGATGCCAAATCATCTTGGATC-TGATTCAGTATAACCATCTGAAGGTGA
* * * ** *
39839076 GATCTGCTTTGTATCTGCTCTCCATCGAAGTGGAGATGCCAGACTTCGATTTGCTCTTTGCCAAT
130 GATCTACTATGTATCTGCTCCCCATCGAAGTGGAGATGCCAGACTTCGATTTGCTCCCTGACAAT
39839141 ACAGAGATGCCAAATCTGGTATCTTCGATCTGCTCTCCACCAATACAGAGATGCC
195 ACAGAGATGCCAAATCTGGTATCTTCGATCTGCTCTCCACCAATACAGAGATGCC
* * *
39839196 AAATCATCTTAGACTTACTTTAACGTAAACACGTGAAAGCCAAATCAGCTGTGTCTTCGATTTGC
1 AAATCATCTTAGACTTACTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATTTGC
* * * *
39839261 TCCTTGTAAGCACAAGGATGCTAAATCGTGTTGGATCTGATTCAGTATAACCATCTGAAGGTGAG
66 TCCTTATAAGCACAAGGATGCCAAATCATCTTGGATCTGATTCAGTATAACCATCTGAAGGTGAG
* * * *
39839326 ATCTACTATGTATCTGCTCCCCATTGAAGTGGATATGTCAGACTTTGATTTGCTCCCTGACAATA
131 ATCTACTATGTATCTGCTCCCCATCGAAGTGGAGATGCCAGACTTCGATTTGCTCCCTGACAATA
*
39839391 CGGAGATGCCAAATC
196 CAGAGATGCCAAATC
39839406 ATCTTAGATT
Statistics
Matches: 183, Mismatches: 27, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
249 93 0.51
250 90 0.49
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (249 bp):
AAATCATCTTAGACTTACTTCAACGTAAACACGTGAAAGCCAAATCAACTATGTCTTCGATTTGC
TCCTTATAAGCACAAGGATGCCAAATCATCTTGGATCTGATTCAGTATAACCATCTGAAGGTGAG
ATCTACTATGTATCTGCTCCCCATCGAAGTGGAGATGCCAGACTTCGATTTGCTCCCTGACAATA
CAGAGATGCCAAATCTGGTATCTTCGATCTGCTCTCCACCAATACAGAGATGCC
Found at i:39839575 original size:205 final size:205
Alignment explanation
Indices: 39839181--39839672 Score: 686
Period size: 205 Copynumber: 2.4 Consensus size: 205
39839171 TGCTCTCCAC
* * *
39839181 CAATACAGAGATGCCAAATCATCTTAGACTTACTTTAACGTAAACACGTGAAAGCCAAATCAGCT
1 CAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCT
* * * * *
39839246 GTGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCTAAATCGTGTTGGATCTGATTCAGTATAA
66 ATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTGATTCAGTATAA
* * * * * *
39839311 CCATCTGAAGGTGAGATCTACTATGTATCTGCTCCCCATTGAAGTGGATATGTCAGACTTTGATT
131 CCATCTAAAGGTGAGATCTACTATGTATCTGCTCCCCATCGAAGTAGAGATGCCAGACTTCGATT
39839376 TGCTCCCTGA
196 TGCTCCCTGA
* * *
39839386 CAATACGGAGATGCCAAATCATCTTAGATTTGCTTCGACGTAAGCACGTGAAAGCCAAATCAGCT
1 CAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCT
* *
39839451 ATGTCTTCGATTTTCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCT-ACTTTAGTATA
66 ATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTGA-TTCAGTATA
* * * *
39839515 GA-CATCTAAAGTTTG-GATCTGCTATGTGTCTGC-CCTCCGTCGAAGTAGAGATGCCAGACTTC
130 -ACCATCTAAAG-GTGAGATCTACTATGTATCTGCTCC-CCATCGAAGTAGAGATGCCAGACTTC
* *
39839577 GATTTGTTCTCTGA
192 GATTTGCTCCCTGA
39839591 CAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCT
1 CAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCT
*
39839656 ATGTCTTCGATCTGCTC
66 ATGTCTTCGATTTGCTC
39839673 TCCGCCAATA
Statistics
Matches: 253, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
204 3 0.01
205 247 0.98
206 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (205 bp):
CAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCT
ATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTGATTCAGTATAA
CCATCTAAAGGTGAGATCTACTATGTATCTGCTCCCCATCGAAGTAGAGATGCCAGACTTCGATT
TGCTCCCTGA
Found at i:39839713 original size:42 final size:43
Alignment explanation
Indices: 39839664--39839747 Score: 125
Period size: 44 Copynumber: 2.0 Consensus size: 43
39839654 CTATGTCTTC
* *
39839664 GATCTGCTCTCCGCCAAT-AGAGATGCCAAATCTAGTATCTAT
1 GATCTGCTCTCCGACAATAAGAGATGCCAAATCTACTATCTAT
*
39839706 GATCTGCTCTCTGACAATACAGAGATGCCAAATCTACTATCT
1 GATCTGCTCTCCGACAATA-AGAGATGCCAAATCTACTATCT
39839748 TCAACTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 16 0.43
44 21 0.57
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (43 bp):
GATCTGCTCTCCGACAATAAGAGATGCCAAATCTACTATCTAT
Found at i:39847894 original size:14 final size:16
Alignment explanation
Indices: 39847859--39847895 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
39847849 CAAAAGATAT
39847859 GATG-AAATGCTATGA
1 GATGCAAATGCTATGA
39847874 GATGCAAATGC-ATGA
1 GATGCAAATGCTATGA
39847889 -ATGCAAA
1 GATGCAAA
39847896 AAGGATATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
GATGCAAATGCTATGA
Found at i:39854849 original size:21 final size:21
Alignment explanation
Indices: 39854788--39854859 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
39854778 TAAAAATGGC
*
39854788 ATAATA-ATATAGAATAATAT
1 ATAATATATATAAAATAATAT
*
39854808 ATAATATGTATATAAAATAATGT
1 ATAATA--TATATAAAATAATAT
* * *
39854831 ATAGTATATATATATTAATAT
1 ATAATATATATAAAATAATAT
39854852 ATAATATA
1 ATAATATA
39854860 AGCAAAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
20 6 0.14
21 19 0.45
23 17 0.40
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (21 bp):
ATAATATATATAAAATAATAT
Found at i:39854903 original size:30 final size:30
Alignment explanation
Indices: 39854869--39854930 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
39854859 AAGCAAAAAT
*
39854869 ATAATAACCATATATAAATAATA-ATGTAAA
1 ATAATAACAATATA-AAATAATATATGTAAA
* *
39854899 ATAATAATAATATAAAATAATATATTTAAA
1 ATAATAACAATATAAAATAATATATGTAAA
39854929 AT
1 AT
39854931 GTAAGATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (30 bp):
ATAATAACAATATAAAATAATATATGTAAA
Found at i:39854906 original size:16 final size:16
Alignment explanation
Indices: 39854885--39854920 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
39854875 ACCATATATA
*
39854885 AATAATAATGTAAAAT
1 AATAATAATATAAAAT
39854901 AATAATAATATAAAAT
1 AATAATAATATAAAAT
39854917 AATA
1 AATA
39854921 TATTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAATAATATAAAAT
Found at i:39857413 original size:18 final size:20
Alignment explanation
Indices: 39857373--39857413 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
39857363 CCAAAATTTA
*
39857373 CAAGTATATAACAGCCAATT
1 CAAGTATATAACAGCCAAGT
*
39857393 CAAGTAT-TAA-ATCCAAGT
1 CAAGTATATAACAGCCAAGT
39857411 CAA
1 CAA
39857414 TTCTAACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 9 0.47
19 3 0.16
20 7 0.37
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (20 bp):
CAAGTATATAACAGCCAAGT
Found at i:39858873 original size:19 final size:19
Alignment explanation
Indices: 39858849--39858886 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39858839 TCTATTGAAC
39858849 TCAATTTACATCCTAGGCA
1 TCAATTTACATCCTAGGCA
39858868 TCAATTTACATCCTAGGCA
1 TCAATTTACATCCTAGGCA
39858887 AAATTATCAT
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:0.26, G:0.11, T:0.32
Consensus pattern (19 bp):
TCAATTTACATCCTAGGCA
Found at i:39860506 original size:45 final size:45
Alignment explanation
Indices: 39860445--39860553 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
39860435 TAGACGAACT
* * *
39860445 ACTCATTATTGCAGATAAAAATTGCTAATACGGTGTGGATAAACC
1 ACTCAATAGTGCAGATAAAAATTGCTAATACGATGTGGATAAACC
* * * *
39860490 ACTCAATAGTGTAGATAGAAGTTGCTAATACGATGTGGATAAATC
1 ACTCAATAGTGCAGATAAAAATTGCTAATACGATGTGGATAAACC
* *
39860535 ACTCCATGGTGCAGATAAA
1 ACTCAATAGTGCAGATAAA
39860554 CCACTCAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (45 bp):
ACTCAATAGTGCAGATAAAAATTGCTAATACGATGTGGATAAACC
Found at i:39866382 original size:14 final size:14
Alignment explanation
Indices: 39866360--39866418 Score: 64
Period size: 15 Copynumber: 4.1 Consensus size: 14
39866350 GTATCGTATC
*
39866360 TTGGGTTTCTTTAT
1 TTGGATTTCTTTAT
39866374 TTGGATTTCTTTAT
1 TTGGATTTCTTTAT
* **
39866388 TCTGGGTTTCTCAAT
1 T-TGGATTTCTTTAT
39866403 CTTGGATTTCTTTAT
1 -TTGGATTTCTTTAT
39866418 T
1 T
39866419 CAGTTTTCTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
14 15 0.42
15 20 0.56
16 1 0.03
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (14 bp):
TTGGATTTCTTTAT
Found at i:39866410 original size:30 final size:29
Alignment explanation
Indices: 39866361--39866419 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
39866351 TATCGTATCT
**
39866361 TGGGTTTCTTTATTTGGATTTCTTTATTC
1 TGGGTTTCTCAATTTGGATTTCTTTATTC
39866390 TGGGTTTCTCAATCTTGGATTTCTTTATTC
1 TGGGTTTCTCAAT-TTGGATTTCTTTATTC
39866420 AGTTTTCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.58
Consensus pattern (29 bp):
TGGGTTTCTCAATTTGGATTTCTTTATTC
Found at i:39869177 original size:46 final size:45
Alignment explanation
Indices: 39869126--39869248 Score: 176
Period size: 46 Copynumber: 2.7 Consensus size: 45
39869116 GGCATCCGAA
*
39869126 CTCGTTGAGTTGAGTTAGAGTTCACTTATGGATGCGAATGT-TCGAG
1 CTCGTTGAGTTGAGTT-GAGTTCACTTATGGATGCGAACGTCT-GAG
*
39869172 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCTGAG
1 CTCGTTGAGTTGAGT-TGAGTTCACTTATGGATGCGAACGTCTGAG
*
39869218 CTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 CTCGTTGAGTTGAGT-TGAGTTCACTTATGG
39869249 GCGGGTTACA
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
46 70 0.99
47 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (45 bp):
CTCGTTGAGTTGAGTTGAGTTCACTTATGGATGCGAACGTCTGAG
Found at i:39877986 original size:39 final size:39
Alignment explanation
Indices: 39877905--39878095 Score: 287
Period size: 39 Copynumber: 4.9 Consensus size: 39
39877895 TATGGTAACC
* * * * *
39877905 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGGTATCATAGCT
39877945 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
*
39877984 CGCACAATTGCCTTCGAGCTTAG-CCGGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGG-TATCATAGCT
39878023 CGCACAATTGCCTTCGGGCTTAGCCC-GGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
*
39878061 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCAT
39878096 TCGAACATTC
Statistics
Matches: 140, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
38 41 0.29
39 80 0.57
40 19 0.14
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.25
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
Found at i:39878091 original size:77 final size:78
Alignment explanation
Indices: 39877905--39878095 Score: 312
Period size: 77 Copynumber: 2.4 Consensus size: 78
39877895 TATGGTAACC
* * *
39877905 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCC
39877970 CGGGTATCATAGCT
65 CGGGTATCATAGCT
* * *
39877984 CGCACAATTGCCTTCGAGCTTAGCCGGGATATCATAGCTCGCACAATTGCCTTCGGGCTTAGCCC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCC
39878049 -GGTATCATAGCT
66 GGGTATCATAGCT
39878061 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAT
39878096 TCGAACATTC
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
77 45 0.43
78 43 0.41
79 16 0.15
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.25
Consensus pattern (78 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCC
GGGTATCATAGCT
Found at i:39886183 original size:21 final size:21
Alignment explanation
Indices: 39886154--39886193 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39886144 TTGAAATGGC
39886154 CACACGGGCGTGCGCCCCTTT
1 CACACGGGCGTGCGCCCCTTT
* *
39886175 CACATGGGCGTGTGCCCCT
1 CACACGGGCGTGCGCCCCT
39886194 ATGTCAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.40, G:0.30, T:0.20
Consensus pattern (21 bp):
CACACGGGCGTGCGCCCCTTT
Found at i:39888260 original size:980 final size:981
Alignment explanation
Indices: 39886447--39888318 Score: 2531
Period size: 980 Copynumber: 1.9 Consensus size: 981
39886437 CATTTTAACG
* *
39886447 TTTCCAGACAAGCTGGCTAACTGCATCACTGTCACCTTAAAAATCATATCTCGAGTTCCAGAGAC
1 TTTCCAGACAAACTGGCTAACTGCATCACTGTCACCTTAAAAATCATATCTCGAGTTCCAGAAAC
* * ** *
39886512 CGAAAATCAGTTATGTAAATTTTTCCTGGAACTAAACTCATAATTCCATCTACATATTTTTTTCT
66 CGAAAATCAGCTACGTAAATTTTTCCCCGAACTAAACTCATAATTCCATC-ACATATTTATTTCT
*
39886577 AGAATTTTTGGTCTAGCCAATTAGTACAGTTTATTAGTTAAAGTCTCCCCTGTTTCAGGGTTCAA
130 AGAATTTTTGGTCTAGCCAATTAGTACAGTTTATTAGTTAAAGTCACCCCTGTTTCAGGGTTCAA
* * * * * *
39886642 CTACACTAACCTTTGCGCGTTACAACTTAGATATCTTTCAGTACAGGGCTCCAACACTTATGTCG
195 CTACACTAACCTTTGCGCATTACAACCTAGATATCTTTCAGTACAGAGCTCAAACACTCATGCCG
* * *
39886707 TTTGTTTCTAAAGAAACTAGACTCACAAAGAAATCTGTAAATATACAGAATGACTTCTAATTCTC
260 TTTGTTTCTAAAGAAACTAGACTCACAAAGAAATATATAAATATACAGAATGACTTCTAATTATC
* * * * *
39886772 TCTGGTTAATTTATAGTGAATTTTCAAAGTCAGAACAGGGGATCCAGAAACTGTTCTGGCCCTGT
325 TCTGGATAATTTATAGTAAATTTTCAAAGACAGAACAGAGGATCCAGAAACCGTTCTGGCCCTGT
* * * * * *
39886837 TTCGCGAAAACTTGAATATCTCTTAAATTTCGACTCATATGACCGTTTCTTTTCTTCCATATGAA
390 CTCACGAAAACTTGAATATCTCTTAAAATCCGACTCATATGACCATTTCGTTTCTTCCATATGAA
*
39886902 AATAGATTCATCAAGGTTCAATTACATAATTTATTCACTATTTAATTCTACTTCTACTATTTTTA
455 AATAGATTCATCAAGGTTCAATTACATAATTTATTCACTATTTAATTCCACTTCTACTATTTTTA
* * *
39886967 GTGATTTTTCAATCTCCCAGCACTGCTGCTGTCAGCATCTATTACTAAGTAAACAATGCCTATTT
520 GTGATTTTTCAATCTCACAGCACTGCTGCTGTCAGCATCTATTACTAAGCAAACAATGACTATTT
* * *
39887032 CATAATTCTTCCATGACATAACTAATCATCCATCATGCATATCACAATTTATGACCACCTTATCA
585 CATAATTCTTCCATGACATAACTAATAATCCATCATACATATCACAAATTATGACCACCTTATCA
* * * *
39887097 AAATTAAGATTTCTAAGACTCATGAATAAGAGTTTTGGAGCCAAATTCAACCGACCATATAAGCC
650 AAATTAAGATTTCTAAGACTCATGAATAAGAGTTTTAGAACCAAACTCAACCGACCACATAAGCC
* *
39887162 ATTTTCGCATGGCTAAAAGTTTACAACCCAAAGTTCACAAAACAAAAGAGCCTATACATGCCAAA
715 ATTTTCACATGGCTAAAAGTTTACAACCCAAAATTCACAAAACAAAAGAGCCTATACATGCCAAA
* * * *
39887227 TGTTCTCCTAGATCAACTATGAAGGCAATACCAAAAGTTTTCCAGCAGGTGTGATGACTTCGATG
780 TGTTCTCCTAGATCAACTAAGAAGACAATACCAAAAATTCTCCAGCAGGTGTGATGACTTCGATG
* **
39887292 ACGGTCCCAAGCACGCAAACA-AGTTGAGTCCAAGAAACCTAAAAGGTGTAACACCCCGTACCCG
845 ACGGTCCCAAGCACGCAAAAAGAGACGAGTCCAAGAAACCTAAAAGGTGTAACACCCCGTACCCG
39887356 AGTCCGTTACCGGAGTTGAACACGAGGTGCACACAGACTTAACTTAATGATTTTCACAGTCCATT
910 AGTCCGTTACCGGAGTTGAACACGAGGTGCACACAGACTTAACTTAATGATTTTCACAGTCCATT
39887421 TAAAAAA
975 TAAAAAA
* * * *
39887428 TTTCCAGACAAACTGG-TTACTGCATCACTGTCGCCTTAAAAATCATATCTTGAGTTTCA-AAAC
1 TTTCCAGACAAACTGGCTAACTGCATCACTGTCACCTTAAAAATCATATCTCGAGTTCCAGAAAC
* * * * *
39887491 TCGAAAA-CTGACTCCGTAAA-TTTTCCCCGAATTTAGACTCAT-ATATCTATC-CATGGATTTA
66 -CGAAAATCAG-CTACGTAAATTTTTCCCCGAA-CTAAACTCATAAT-TCCATCACAT--ATTTA
* * *
39887552 TTTCTAGAATTTTTGGT-TGGGCCAATTGGTACAGTTTATTAGTTAAAGTCAGCCCTGTTTCAGG
125 TTTCTAGAATTTTTGGTCT-AGCCAATTAGTACAGTTTATTAGTTAAAGTCACCCCTGTTTCAGG
* * * * * * **
39887616 GTTCGACTACACTGACCTTTGTGCATTACGACCTGGATATCTTCTC-GTACAGAGCTTAAATGCT
189 GTTCAACTACACTAACCTTTGCGCATTACAACCTAGATATCTT-TCAGTACAGAGCTCAAACACT
* * * * *
39887680 CATGCCGTTTGTTTCTAATGAAACTAGACTCA-AAGGGGAATATATACATATA-AGGTATGACTT
253 CATGCCGTTTGTTTCTAAAGAAACTAGACTCACAA-AGAAATATATAAATATACA-GAATGACTT
* *
39887743 CTAATTATTTCTGGATAATTTATGGTAAATTTTCAAAGAC-GAAACAGAGGATCCAGAAACCGTT
316 CTAATTATCTCTGGATAATTTATAGTAAATTTTCAAAGACAG-AACAGAGGATCCAGAAACCGTT
*
39887807 CTGGCCCTGTCTCACGAAATCTTGAATATCTCTTAAAATCCGACTCATATGACCATTTCGTTTCT
380 CTGGCCCTGTCTCACGAAAACTTGAATATCTCTTAAAATCCGACTCATATGACCATTTCGTTTCT
* * * *
39887872 TTCATATGAAAGTAGGTTCATCAAGGTTCAATTTCATAATTTATTCACTATTTAATTCCA-TTCC
445 TCCATATGAAAATAGATTCATCAAGGTTCAATTACATAATTTATTCACTATTTAATTCCACTT-C
* *
39887936 TACTATTTTTAGTGATTTTTCAATCTCACATCACTGCTGCTGTCAGCATCTGTTACTAAAGCAAA
509 TACTATTTTTAGTGATTTTTCAATCTCACAGCACTGCTGCTGTCAGCATCTATTACT-AAGCAAA
* * *
39888001 CATTGACTATTTCATAATTCTTCCATGGCCA-AACT-ATAATTCATCATACATGA-CACAAATTA
573 CAATGACTATTTCATAATTCTTCCAT-GACATAACTAATAATCCATCATACAT-ATCACAAATTA
* * * * **
39888063 TGGCCACCTTATCAAAATTAAGGTTTCTAAGACTCGTGACTATAG-GTTTTAGAACCCCACTCAA
636 TGACCACCTTATCAAAATTAAGATTTCTAAGACTCATGAATA-AGAGTTTTAGAACCAAACTCAA
* * * *
39888127 CCGACCACATAGGCCATTTTCACATGGCTTAAAGTTTACAGCCCAAAATTCAACAAAACAAAATA
700 CCGACCACATAAGCCATTTTCACATGGCTAAAAGTTTACAACCCAAAATTC-ACAAAACAAAAGA
* *
39888192 GCCTATACATGCCAAATGTTCTCCTAGATCGACTAAGAAGACAATACCAAAAATTGCT-C-GCCG
764 GCCTATACATGCCAAATGTTCTCCTAGATCAACTAAGAAGACAATACCAAAAATT-CTCCAGCAG
* * * *
39888255 GTGTGATGACTTCGATGACGGTTCCGAGCACTCAAAAAGAGACGAGTCCAAGAGACCTAAAAGG
828 GTGTGATGACTTCGATGACGGTCCCAAGCACGCAAAAAGAGACGAGTCCAAGAAACCTAAAAGG
39888319 GGTGACAAGA
Statistics
Matches: 771, Mismatches: 101, Indels: 38
0.85 0.11 0.04
Matches are distributed among these distances:
978 3 0.00
979 23 0.03
980 601 0.78
981 140 0.18
982 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (981 bp):
TTTCCAGACAAACTGGCTAACTGCATCACTGTCACCTTAAAAATCATATCTCGAGTTCCAGAAAC
CGAAAATCAGCTACGTAAATTTTTCCCCGAACTAAACTCATAATTCCATCACATATTTATTTCTA
GAATTTTTGGTCTAGCCAATTAGTACAGTTTATTAGTTAAAGTCACCCCTGTTTCAGGGTTCAAC
TACACTAACCTTTGCGCATTACAACCTAGATATCTTTCAGTACAGAGCTCAAACACTCATGCCGT
TTGTTTCTAAAGAAACTAGACTCACAAAGAAATATATAAATATACAGAATGACTTCTAATTATCT
CTGGATAATTTATAGTAAATTTTCAAAGACAGAACAGAGGATCCAGAAACCGTTCTGGCCCTGTC
TCACGAAAACTTGAATATCTCTTAAAATCCGACTCATATGACCATTTCGTTTCTTCCATATGAAA
ATAGATTCATCAAGGTTCAATTACATAATTTATTCACTATTTAATTCCACTTCTACTATTTTTAG
TGATTTTTCAATCTCACAGCACTGCTGCTGTCAGCATCTATTACTAAGCAAACAATGACTATTTC
ATAATTCTTCCATGACATAACTAATAATCCATCATACATATCACAAATTATGACCACCTTATCAA
AATTAAGATTTCTAAGACTCATGAATAAGAGTTTTAGAACCAAACTCAACCGACCACATAAGCCA
TTTTCACATGGCTAAAAGTTTACAACCCAAAATTCACAAAACAAAAGAGCCTATACATGCCAAAT
GTTCTCCTAGATCAACTAAGAAGACAATACCAAAAATTCTCCAGCAGGTGTGATGACTTCGATGA
CGGTCCCAAGCACGCAAAAAGAGACGAGTCCAAGAAACCTAAAAGGTGTAACACCCCGTACCCGA
GTCCGTTACCGGAGTTGAACACGAGGTGCACACAGACTTAACTTAATGATTTTCACAGTCCATTT
AAAAAA
Found at i:39888836 original size:29 final size:29
Alignment explanation
Indices: 39888802--39888933 Score: 176
Period size: 29 Copynumber: 4.6 Consensus size: 29
39888792 TAATCGATCA
* *
39888802 CGCACACTTAGTGCCATGTGATTTAAGCT
1 CGCACACTTAGTGCCATATAATTTAAGCT
* *
39888831 CGCACACATAGTGCCATATAATTTAAGTT
1 CGCACACTTAGTGCCATATAATTTAAGCT
* **
39888860 CGCACACTTAGTGCCATGTAATTTAAATT
1 CGCACACTTAGTGCCATATAATTTAAGCT
39888889 CGCACACTTAGTGCCATAT-ATTTCAAGCT
1 CGCACACTTAGTGCCATATAATTT-AAGCT
*
39888918 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
39888934 ATCTTGTCAC
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
28 4 0.04
29 87 0.96
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATAATTTAAGCT
Found at i:39888878 original size:58 final size:59
Alignment explanation
Indices: 39888802--39888933 Score: 198
Period size: 58 Copynumber: 2.3 Consensus size: 59
39888792 TAATCGATCA
* *
39888802 CGCACACTTAGTGCCATGTGATTTAAGCTCGCACACATAGTGCCATATAATTT-AAG-TT
1 CGCACACTTAGTGCCATGTAATTTAAACTCGCACACATAGTGCCATAT-ATTTCAAGCTT
* *
39888860 CGCACACTTAGTGCCATGTAATTTAAATTCGCACACTTAGTGCCATATATTTCAAGCTT
1 CGCACACTTAGTGCCATGTAATTTAAACTCGCACACATAGTGCCATATATTTCAAGCTT
39888919 -GCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
39888934 ATCTTGTCAC
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
57 4 0.06
58 62 0.91
59 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (59 bp):
CGCACACTTAGTGCCATGTAATTTAAACTCGCACACATAGTGCCATATATTTCAAGCTT
Found at i:39895960 original size:29 final size:28
Alignment explanation
Indices: 39895928--39896006 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
39895918 GTGACGAGAT
*
39895928 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACT-AGTGTGCGAGCTTGAAATATA
* * *
39895957 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACT-AGTGTGCGAGCTTGAAATATA
*
39895986 TGGCACTATGTGTGCGGGCTT
1 TGGCACTA-GTGTGCGAGCTT
39896007 AAACCACATG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 1 0.02
29 41 0.98
ACGTcount: A:0.20, C:0.15, G:0.34, T:0.30
Consensus pattern (28 bp):
TGGCACTAGTGTGCGAGCTTGAAATATA
Found at i:39903123 original size:29 final size:28
Alignment explanation
Indices: 39903091--39903191 Score: 87
Period size: 29 Copynumber: 3.5 Consensus size: 28
39903081 GTGACGAGAT
*
39903091 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACT-AGTGTGCGAGCTTGAAATATA
* * *
39903120 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACT-AGTGTGCGAGCTTGAAATATA
* * *
39903149 TGGCACTATGTGTGCGGGCTT-AAACCACA
1 TGGCACTA-GTGTGCGAGCTTGAAA-TATA
39903178 TGGCACTAAGTGTG
1 TGGCACT-AGTGTG
39903192 TGTGATCGAG
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
28 2 0.03
29 55 0.95
30 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.28
Consensus pattern (28 bp):
TGGCACTAGTGTGCGAGCTTGAAATATA
Found at i:39904230 original size:28 final size:29
Alignment explanation
Indices: 39904191--39904260 Score: 108
Period size: 28 Copynumber: 2.4 Consensus size: 29
39904181 AAAATTGTAC
*
39904191 AGCACTAAGTGTGTGAGTTTG-AT-TATAT
1 AGCACTAAGTGTGTGAG-TTGAATACATAT
39904219 AGCACTAAGTGTGTGAGTTGAATACATAT
1 AGCACTAAGTGTGTGAGTTGAATACATAT
39904248 AGCACTAAGTGTG
1 AGCACTAAGTGTG
39904261 CGGATTCACT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 3 0.08
28 19 0.49
29 17 0.44
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (29 bp):
AGCACTAAGTGTGTGAGTTGAATACATAT
Found at i:39911376 original size:27 final size:28
Alignment explanation
Indices: 39911302--39911400 Score: 121
Period size: 27 Copynumber: 3.5 Consensus size: 28
39911292 GACAAGATTG
* *
39911302 GCACTAAGTGTGCGAGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--AATTATATA
*
39911332 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAATTATATA
*
39911360 GCACT-AGTGTGCGAG-TTAATACATATA
1 GCACTAAGTGTGCGAGTTTAAT-TATATA
39911387 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39911401 GATTCACTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
26 4 0.06
27 20 0.32
28 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATATA
Found at i:39913353 original size:27 final size:28
Alignment explanation
Indices: 39913307--39913374 Score: 113
Period size: 27 Copynumber: 2.5 Consensus size: 28
39913297 GCGTAGATCA
39913307 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
39913335 CGAAATTA-CCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
39913362 CGATA-TACCCCTA
1 CGAAATTACCCCTA
39913375 GGGTTTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
26 2 0.05
27 28 0.74
28 8 0.21
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:39914723 original size:11 final size:11
Alignment explanation
Indices: 39914707--39914737 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
39914697 TTATTTTTAG
39914707 TAAAAAAAAAA
1 TAAAAAAAAAA
39914718 TAAAAAAAAAA
1 TAAAAAAAAAA
*
39914729 CAAAAAAAA
1 TAAAAAAAA
39914738 TAGGGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.06
Consensus pattern (11 bp):
TAAAAAAAAAA
Found at i:39921489 original size:28 final size:28
Alignment explanation
Indices: 39921457--39921525 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
39921447 GCGTAGATCA
39921457 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
39921485 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
39921513 CGATA-TACCCCTA
1 CGAAATTACCCCTA
39921526 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:39928626 original size:39 final size:39
Alignment explanation
Indices: 39928545--39928707 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
39928535 TATGGTAACC
* *
39928545 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
39928585 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
39928624 CGCACCATTGCCTTCGGGCTTAGCCCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
39928663 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
39928702 CGCACA
1 CGCACA
39928708 TTCATACACA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 97 0.85
40 17 0.15
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:39936534 original size:39 final size:39
Alignment explanation
Indices: 39936453--39936615 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
39936443 TATGGTAACC
* *
39936453 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
39936493 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
39936532 CGCACCATTGCCTTCGGGCTTAGCCCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
39936571 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
39936610 CGCACA
1 CGCACA
39936616 TTCATACACA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 97 0.85
40 17 0.15
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:39938230 original size:30 final size:30
Alignment explanation
Indices: 39938194--39938353 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
39938184 GACAAGATTG
* * * * * *
39938194 GCACTAAGTGTACGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
39938224 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
39938252 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
39938281 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
39938311 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
39938340 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39938354 GATTCACTAT
Statistics
Matches: 119, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 49 0.41
30 44 0.37
31 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:39938319 original size:59 final size:57
Alignment explanation
Indices: 39938223--39938353 Score: 219
Period size: 59 Copynumber: 2.3 Consensus size: 57
39938213 AAAATTGTAC
*
39938223 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGTCTGATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
39938280 AGCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGTCTG---ATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
39938339 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
39938354 GATTCACTAT
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
56 2 0.03
57 17 0.24
59 51 0.73
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (57 bp):
AGCACTAAGTGTGCGAGTCTGATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:39946140 original size:30 final size:30
Alignment explanation
Indices: 39946104--39946204 Score: 127
Period size: 28 Copynumber: 3.5 Consensus size: 30
39946094 GACAAGATTG
* * *
39946104 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
*
39946134 GCACTAAGTGTGCGAGTTT--GATTATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
39946162 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
39946191 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39946205 GATTCACTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 23 0.37
29 20 0.32
30 19 0.31
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:39946198 original size:29 final size:29
Alignment explanation
Indices: 39946104--39946204 Score: 116
Period size: 29 Copynumber: 3.5 Consensus size: 29
39946094 GACAAGATTG
* * * *
39946104 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTGAAAA-TATATA
*
39946134 GCACTAAGTGTGCGAGTTTG--ATTATATA
1 GCACTAAGTGTGCGAG-TTGAAAATATATA
*
39946162 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGTTGAAAATATATA
39946191 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39946205 GATTCACTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 20 0.33
29 22 0.36
30 15 0.25
31 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGTTGAAAATATATA
Found at i:39953090 original size:15 final size:15
Alignment explanation
Indices: 39953070--39953103 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39953060 GTGTTGTAAA
39953070 TTGGATTTCCTTATC
1 TTGGATTTCCTTATC
* *
39953085 TTGGATTTCTTTATT
1 TTGGATTTCCTTATC
39953100 TTGG
1 TTGG
39953104 GCTTCTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (15 bp):
TTGGATTTCCTTATC
Found at i:39953785 original size:14 final size:15
Alignment explanation
Indices: 39953766--39953794 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39953756 AAAGTTAATA
39953766 TGGATT-TTCTTGTC
1 TGGATTATTCTTGTC
39953780 TGGATTATTCTTGTC
1 TGGATTATTCTTGTC
39953795 CTTGAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.10, C:0.14, G:0.21, T:0.55
Consensus pattern (15 bp):
TGGATTATTCTTGTC
Found at i:39959886 original size:31 final size:31
Alignment explanation
Indices: 39959851--39959919 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
39959841 TTAAATGGTG
* * *
39959851 CATAATTCCCTCCTTAAATGTTGTCGATATA
1 CATAACTCCCTCCTTAAATATTGTCCATATA
*
39959882 CATAACTCCCTCCTTAAATATTGTCCATGTA
1 CATAACTCCCTCCTTAAATATTGTCCATATA
39959913 CATAACT
1 CATAACT
39959920 GACATAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.36
Consensus pattern (31 bp):
CATAACTCCCTCCTTAAATATTGTCCATATA
Found at i:39963095 original size:20 final size:21
Alignment explanation
Indices: 39963061--39963100 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
39963051 CTCCACTCTC
39963061 TCATGTTTTCCTTTCTTTCTA
1 TCATGTTTTCCTTTCTTTCTA
*
39963082 TCAT-TTTTCTTTTCTTTCT
1 TCATGTTTTCCTTTCTTTCT
39963101 CTTTTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.07, C:0.23, G:0.03, T:0.68
Consensus pattern (21 bp):
TCATGTTTTCCTTTCTTTCTA
Found at i:39968458 original size:27 final size:25
Alignment explanation
Indices: 39968414--39968564 Score: 95
Period size: 27 Copynumber: 5.6 Consensus size: 25
39968404 TTAGTTTACC
*
39968414 AAATTACTGAAATACCCCCAGTTGTA
1 AAATTAC-CAAATACCCCCAGTTGTA
* *
39968440 AAATTACCAAAGTACCCCCGGTTTATA
1 AAATTACCAAA-TACCCCCAG-TTGTA
* * *
39968467 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTA-CCAAATA-CCCCCAGTTGTA
** *
39968494 AAATTACCGAAATACCCTTAGTTTGCA
1 AAATTACC-AAATACCCCCAG-TTGTA
* * *
39968521 AAATTACTAAAATACCCTCGACTTGTA
1 AAATTAC-CAAATACCC-CCAGTTGTA
*
39968548 AAATTATCAAAGTACCC
1 AAATTACCAAA-TACCC
39968565 TCGAATTACA
Statistics
Matches: 96, Mismatches: 20, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
25 3 0.03
26 23 0.24
27 61 0.64
28 9 0.09
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.28
Consensus pattern (25 bp):
AAATTACCAAATACCCCCAGTTGTA
Found at i:39968565 original size:27 final size:26
Alignment explanation
Indices: 39968435--39968568 Score: 126
Period size: 27 Copynumber: 5.0 Consensus size: 26
39968425 ATACCCCCAG
* *
39968435 TTGTAAAATTACCAAAGTACCCCCGGT
1 TTGTAAAATTACCAAA-TACCCTCGAT
* *
39968462 TTATAAAATTACCCAAATATCCTCGAT
1 TTGTAAAATTA-CCAAATACCCTCGAT
*
39968489 TTGTAAAATTACCGAAATACCCT-TAGT
1 TTGTAAAATTACC-AAATACCCTCGA-T
* * *
39968516 TTGCAAAATTACTAAAATACCCTCGAC
1 TTGTAAAATTAC-CAAATACCCTCGAT
*
39968543 TTGTAAAATTATCAAAGTACCCTCGA
1 TTGTAAAATTACCAAA-TACCCTCGA
39968569 ATTACAAAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
26 6 0.07
27 75 0.86
28 6 0.07
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (26 bp):
TTGTAAAATTACCAAATACCCTCGAT
Done.