Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 123 of 373
Found at i:40253900 original size:79 final size:81
Alignment explanation
Indices: 40253764--40253948 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
40253754 TTGAATGATG
*
40253764 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGAAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGAAAT
40253828 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * ** *
40253843 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGAA
*
40253905 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
40253923 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40253949 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGAAAT
TGTGCGAGATACTATA
Found at i:40253955 original size:40 final size:40
Alignment explanation
Indices: 40253764--40253948 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
40253754 TTGAATGATG
* * * *
40253764 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * * *
40253804 TCCGGACTAAGAT-CCGAAGGAAATTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
40253844 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40253883 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40253924 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40253949 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 33 0.27
40 79 0.65
41 9 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40253970 original size:79 final size:79
Alignment explanation
Indices: 40253817--40253981 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
40253807 GGACTAAGAT
* **
40253817 CCGAAGGAAATTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGAAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
40253882 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
40253896 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGAAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
40253959 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
40253975 CCGAAGG
1 CCGAAGG
40253982 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (79 bp):
CCGAAGGAAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:40262132 original size:40 final size:40
Alignment explanation
Indices: 40261941--40262125 Score: 180
Period size: 40 Copynumber: 4.7 Consensus size: 40
40261931 TTGAATGATG
* * * *
40261941 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * * * * *
40261981 TCCAGACTAAGAT-CCAAAGGCAATTGTGTGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
40262021 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
40262060 TTCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40262101 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40262126 AACGAGTAGC
Statistics
Matches: 115, Mismatches: 25, Indels: 10
0.77 0.17 0.07
Matches are distributed among these distances:
39 31 0.27
40 76 0.66
41 8 0.07
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40262147 original size:79 final size:79
Alignment explanation
Indices: 40261997--40262158 Score: 186
Period size: 79 Copynumber: 2.1 Consensus size: 79
40261987 CTAAGATCCA
* * **
40261997 AAGGCAATTGTGTGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATT
1 AAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAATT
* *
40262062 CGGGTTAAGTCCCG
66 CCGGTTAAATCCCG
* * *
40262076 AAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTAT
1 AAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTAA
*
40262139 A-TCCGGTTAAATTCCG
63 ATTCCGGTTAAATCCCG
40262155 AAGG
1 AAGG
40262159 TACGTGATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.66
80 22 0.31
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (79 bp):
AAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAATT
CCGGTTAAATCCCG
Found at i:40265228 original size:29 final size:29
Alignment explanation
Indices: 40265165--40265232 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
40265155 TAATCAACCG
40265165 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
40265194 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
40265223 CGCACACTTA
1 CGCACACTTA
40265233 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:40265375 original size:29 final size:29
Alignment explanation
Indices: 40265341--40265406 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
40265331 ATCAACCGCG
40265341 CACACTTAGTGCCATGCACTTT-AAACTCA
1 CACACTTAGTGCCATGCA-TTTCAAACTCA
**
40265370 CACACTTAGTGCCATGCATTTCAAGTTCA
1 CACACTTAGTGCCATGCATTTCAAACTCA
40265399 CACACTTA
1 CACACTTA
40265407 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.29
Consensus pattern (29 bp):
CACACTTAGTGCCATGCATTTCAAACTCA
Found at i:40265547 original size:29 final size:30
Alignment explanation
Indices: 40265508--40265586 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
40265498 CTTAATAATC
40265508 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
40265538 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
40265567 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
40265587 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:40265580 original size:174 final size:174
Alignment explanation
Indices: 40265054--40265555 Score: 932
Period size: 174 Copynumber: 2.9 Consensus size: 174
40265044 AACTCAAGGT
* * *
40265054 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
40265119 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
40265184 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
40265228 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
40265293 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
40265358 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCACAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
40265402 ACTTACCTTTTCCGCTGTCCAAAATCGACTCAGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
* *
40265467 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
40265532 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
40265556 TGTACAATTT
Statistics
Matches: 320, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 320 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:40272510 original size:42 final size:43
Alignment explanation
Indices: 40272440--40272567 Score: 120
Period size: 42 Copynumber: 3.0 Consensus size: 43
40272430 TCTCAGATGT
* * * *
40272440 GGTCTTACATAGAATTC-AGTATCGATGCCTTTGTCCTAGGCA-A
1 GGTCTTACA-CGAATTCAAATA-CGATGCCTATGTCCTAGACATA
*
40272483 GGTCTTACACGAATTCAAATACGATGCCTATGTCCTTGACATA
1 GGTCTTACACGAATTCAAATACGATGCCTATGTCCTAGACATA
* *
40272526 -GTCTTACACGTAAATCTCAAAT-CGACGCCTGTGTCCTAGACA
1 GGTCTTACACG--AAT-TCAAATACGATGCCTATGTCCTAGACA
40272568 CGACCTTACA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
42 33 0.46
43 13 0.18
44 20 0.28
45 6 0.08
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (43 bp):
GGTCTTACACGAATTCAAATACGATGCCTATGTCCTAGACATA
Found at i:40277348 original size:19 final size:19
Alignment explanation
Indices: 40277316--40277353 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40277306 ACTTGGGTTG
*
40277316 AGAATTGGCCAAATGGGCC
1 AGAATAGGCCAAATGGGCC
*
40277335 AGAATAGGCTAAATGGGCC
1 AGAATAGGCCAAATGGGCC
40277354 TGATGGGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.16
Consensus pattern (19 bp):
AGAATAGGCCAAATGGGCC
Found at i:40277485 original size:29 final size:28
Alignment explanation
Indices: 40277431--40277547 Score: 107
Period size: 29 Copynumber: 4.2 Consensus size: 28
40277421 TTGAGCATGA
* *
40277431 ATAT-AATATGATTTGGGCCTAATGGGCC
1 ATATGAATATGA-ATGGGCCTAGTGGGCC
* *
40277459 ATATGAATTTGAATGGGGCCTAGTGGGCT
1 ATATGAATATGAAT-GGGCCTAGTGGGCC
*
40277488 ATAAGAATATGAATTGGG-C-AGATGGGCC
1 ATATGAATATGAA-TGGGCCTAG-TGGGCC
* *
40277516 ATTTGAATAAG-ATGGGCCTAGTGGGCC
1 ATATGAATATGAATGGGCCTAGTGGGCC
40277543 ATATG
1 ATATG
40277548 CATGTATGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
26 4 0.06
27 14 0.19
28 21 0.29
29 32 0.44
30 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (28 bp):
ATATGAATATGAATGGGCCTAGTGGGCC
Found at i:40277523 original size:57 final size:56
Alignment explanation
Indices: 40277435--40277541 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 56
40277425 GCATGAATAT
* **
40277435 AATATGATTTGGGCCTAATGGGCCATATGAATTTGAATGGGGCCTAGTGGGCTATAAG
1 AATATGAATTGGGCCTAATGGGCCATATGAATAAG-AT-GGGCCTAGTGGGCTATAAG
*
40277493 AATATGAATTGGG-C-AGATGGGCCATTTGAATAAGATGGGCCTAGTGGGC
1 AATATGAATTGGGCCTA-ATGGGCCATATGAATAAGATGGGCCTAGTGGGC
40277542 CATATGCATG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
55 13 0.30
56 3 0.07
57 16 0.36
58 12 0.27
ACGTcount: A:0.28, C:0.12, G:0.33, T:0.27
Consensus pattern (56 bp):
AATATGAATTGGGCCTAATGGGCCATATGAATAAGATGGGCCTAGTGGGCTATAAG
Found at i:40281683 original size:53 final size:54
Alignment explanation
Indices: 40281501--40281724 Score: 193
Period size: 54 Copynumber: 4.2 Consensus size: 54
40281491 ATTAGGGTTT
* * * * * *
40281501 AAGGATACCAAGTTAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCATAAGGA
* ** * * * ** *
40281555 AAGGAAATTATGTAAGACCATGTCAAGGCATGGCATTGATAAACTACGATAAGGCA
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTC-ATAAGG-A
* * *
40281611 AA-GATCCCATGTAAGACCATGCCAAGGCAAGGCAATGGTGAG-TTCATAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCATAAGGA
* * * * * *
40281663 AAGGATACCACGTAAGACCATGTCAAGACATGACAATGGTAAGTTTAAAAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCATAAGGA
40281717 AA-GATACC
1 AAGGATACC
40281725 CGTGTATCCT
Statistics
Matches: 133, Mismatches: 33, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
52 3 0.02
53 45 0.34
54 48 0.36
55 35 0.26
56 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCATAAGGA
Found at i:40284494 original size:35 final size:35
Alignment explanation
Indices: 40284448--40284730 Score: 118
Period size: 35 Copynumber: 7.7 Consensus size: 35
40284438 GCTTGTCGGT
* * *
40284448 TTATCCGACTAGGGCTAGGCGCAAATCTTTCTCCG
1 TTATCCGACTAGTGCTAGGCACAAATCTTTCTCAG
** * *
40284483 TTATCCGACTAGTGCTAGGCACACCTTTAATATCGTCGG
1 TTATCCGACTAGTGCTAGGCACAAATCT--T-TC-TCAG
* * *
40284522 TTTATCCGACTAGCGCTGGGCACAAATCTTTTTCAG
1 -TTATCCGACTAGTGCTAGGCACAAATCTTTCTCAG
* * ** * * *
40284558 TTATTCGACTAGTGCTAGGCGCACCTTTAATATAGTCATT
1 TTATCCGACTAGTGCTAGGCACAAATCT--T-T-CTCA-G
* ** * * * *
40284598 TTATCCAACTAGCACTATGCGCAAATATTTTTCAG
1 TTATCCGACTAGTGCTAGGCACAAATCTTTCTCAG
* * *
40284633 TTATCCGACTAGTGCTGGGCACACCTTTAATATTT-TCGG
1 TTATCCGACTAGTGCTAGGCACA-----AATCTTTCTCAG
* * * *
40284672 TTTATCCGACTAGCGCTGGGCGCAAATCTTTGTCAG
1 -TTATCCGACTAGTGCTAGGCACAAATCTTTCTCAG
* *
40284708 TTATCCAACTAGTGCTGGGCACA
1 TTATCCGACTAGTGCTAGGCACA
40284731 CCTTTAATAT
Statistics
Matches: 185, Mismatches: 46, Indels: 34
0.70 0.17 0.13
Matches are distributed among these distances:
35 87 0.47
36 9 0.05
37 4 0.02
38 5 0.03
39 9 0.05
40 71 0.38
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (35 bp):
TTATCCGACTAGTGCTAGGCACAAATCTTTCTCAG
Found at i:40284527 original size:40 final size:39
Alignment explanation
Indices: 40284483--40284759 Score: 159
Period size: 40 Copynumber: 7.3 Consensus size: 39
40284473 TCTTTCTCCG
* *
40284483 TTATCCGACTAGTGCTAGGCACACCTTTAATATCGTCGGT
1 TTATCCGACTAGTGCTGGGCACACCTTTAATAT-GTCAGT
* **
40284523 TTATCCGACTAGCGCTGGGCACAAATCTT--T-T-TCAG-
1 TTATCCGACTAGTGCTGGGCACACCT-TTAATATGTCAGT
* * * *
40284558 TTATTCGACTAGTGCTAGGCGCACCTTTAATATAGTCATT
1 TTATCCGACTAGTGCTGGGCACACCTTTAATAT-GTCAGT
* ** ** * **
40284598 TTATCCAACTAGCACTATGCGCAAATATT--T-T-TCAG-
1 TTATCCGACTAGTGCTGGGCACACCT-TTAATATGTCAGT
* *
40284633 TTATCCGACTAGTGCTGGGCACACCTTTAATATTTTCGGT
1 TTATCCGACTAGTGCTGGGCACACCTTTAATA-TGTCAGT
* * ** *
40284673 TTATCCGACTAGCGCTGGGCGCAAATCT--T-TGTCAG-
1 TTATCCGACTAGTGCTGGGCACACCTTTAATATGTCAGT
* *
40284708 TTATCCAACTAGTGCTGGGCACACCTTTAATATCGTCGGT
1 TTATCCGACTAGTGCTGGGCACACCTTTAATAT-GTCAGT
*
40284748 TTATCTGACTAG
1 TTATCCGACTAG
40284760 CGCTTGGTGC
Statistics
Matches: 173, Mismatches: 45, Indels: 38
0.68 0.18 0.15
Matches are distributed among these distances:
34 4 0.02
35 60 0.35
36 12 0.07
37 2 0.01
38 5 0.03
39 12 0.07
40 74 0.43
41 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (39 bp):
TTATCCGACTAGTGCTGGGCACACCTTTAATATGTCAGT
Found at i:40284567 original size:75 final size:75
Alignment explanation
Indices: 40284442--40284776 Score: 447
Period size: 75 Copynumber: 4.5 Consensus size: 75
40284432 GTATGTGCTT
* * *
40284442 GTCGGTTTATCCGACTAGGGCTAGGCGCAAATCTTTCTCCGTTATCCGACTAGTGCTAGGCACAC
1 GTCGGTTTATCCGACTAGCGCTAGGCGCAAATCTTTTTCAGTTATCCGACTAGTGCTAGGCACAC
40284507 CTTTAATATC
66 CTTTAATATC
* * * *
40284517 GTCGGTTTATCCGACTAGCGCTGGGCACAAATCTTTTTCAGTTATTCGACTAGTGCTAGGCGCAC
1 GTCGGTTTATCCGACTAGCGCTAGGCGCAAATCTTTTTCAGTTATCCGACTAGTGCTAGGCACAC
*
40284582 CTTTAATATA
66 CTTTAATATC
** * * * * *
40284592 GTCATTTTATCCAACTAGCACTATGCGCAAATATTTTTCAGTTATCCGACTAGTGCTGGGCACAC
1 GTCGGTTTATCCGACTAGCGCTAGGCGCAAATCTTTTTCAGTTATCCGACTAGTGCTAGGCACAC
*
40284657 CTTTAATATT
66 CTTTAATATC
* * * * *
40284667 TTCGGTTTATCCGACTAGCGCTGGGCGCAAATCTTTGTCAGTTATCCAACTAGTGCTGGGCACAC
1 GTCGGTTTATCCGACTAGCGCTAGGCGCAAATCTTTTTCAGTTATCCGACTAGTGCTAGGCACAC
40284732 CTTTAATATC
66 CTTTAATATC
* * *
40284742 GTCGGTTTATCTGACTAGCGCTTGGTGCAAA-CTTT
1 GTCGGTTTATCCGACTAGCGCTAGGCGCAAATCTTT
40284777 GTTATGGTTT
Statistics
Matches: 225, Mismatches: 35, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
74 4 0.02
75 221 0.98
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (75 bp):
GTCGGTTTATCCGACTAGCGCTAGGCGCAAATCTTTTTCAGTTATCCGACTAGTGCTAGGCACAC
CTTTAATATC
Found at i:40286662 original size:15 final size:15
Alignment explanation
Indices: 40286644--40286672 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40286634 ATATTTATAA
40286644 AATTATTATTATTAT
1 AATTATTATTATTAT
40286659 AATTATTATTATTA
1 AATTATTATTATTA
40286673 GATAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTATTATTATTAT
Found at i:40290385 original size:39 final size:40
Alignment explanation
Indices: 40290253--40290385 Score: 173
Period size: 40 Copynumber: 3.4 Consensus size: 40
40290243 TGATAACCGA
40290253 GCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* * *
40290292 GCTAAGTCTCGAAGGCAATTGTGCGAGTTACTATAACCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* *
40290332 GCTAAGTCCCGAAGGCATTTGAGCGAG-AAGCTATATCC-G
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG
**
40290371 GCTAAACCCCGAAGG
1 GCTAAGTCCCGAAGG
40290386 TACTTGGTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
39 21 0.26
40 61 0.74
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
Found at i:40294691 original size:29 final size:29
Alignment explanation
Indices: 40294655--40294711 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
40294645 TTTGAGTGGT
*
40294655 GCGATCCTATTCGCCTAATTGATGCCTGC
1 GCGATCCTATTCACCTAATTGATGCCTGC
40294684 GCGATCCTATTCACCTAATTGATGCCTG
1 GCGATCCTATTCACCTAATTGATGCCTG
40294712 AGCATATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (29 bp):
GCGATCCTATTCACCTAATTGATGCCTGC
Found at i:40296086 original size:27 final size:26
Alignment explanation
Indices: 40296018--40296118 Score: 123
Period size: 27 Copynumber: 3.8 Consensus size: 26
40296008 ACACACTGAA
*
40296018 GAAATGGAAGCCTTTGTGGCAAATATAT
1 GAAATGGAAGCCTTTGTGGC-AAT-TTT
*
40296046 GAAATGGAAG-CTTTATGGCAACTTTT
1 GAAATGGAAGCCTTTGTGGCAA-TTTT
*
40296072 GAAATAGAAGCCTTTGTGGCAATTTAT
1 GAAATGGAAGCCTTTGTGGCAATTT-T
*
40296099 GAAATGGAAGCCTTGGTGGC
1 GAAATGGAAGCCTTTGTGGC
40296119 GATCTACGGA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
26 16 0.25
27 38 0.59
28 10 0.16
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (26 bp):
GAAATGGAAGCCTTTGTGGCAATTTT
Found at i:40307439 original size:27 final size:27
Alignment explanation
Indices: 40307409--40307586 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40307399 ATATTGAGTC
* * * *
40307409 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40307436 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40307463 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40307491 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40307518 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40307545 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40307572 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40307587 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40307548 original size:82 final size:81
Alignment explanation
Indices: 40307430--40307585 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40307420 TGCTATATAA
* *
40307430 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40307495 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40307512 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40307576 CACTTAGTGC
65 CACTTAGTGC
40307586 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40312935 original size:40 final size:40
Alignment explanation
Indices: 40312890--40313081 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
40312880 ATAACCACAA
* * *
40312890 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
40312930 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
40312970 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
40313010 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
40313050 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
40313082 CATTCAAATG
Statistics
Matches: 142, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 137 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:40320482 original size:40 final size:40
Alignment explanation
Indices: 40320438--40320629 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
40320428 ATAACCACAA
* * *
40320438 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
40320478 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
40320518 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
40320558 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
40320598 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
40320630 CATTCAAATG
Statistics
Matches: 142, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 137 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:40324122 original size:48 final size:48
Alignment explanation
Indices: 40324022--40324132 Score: 150
Period size: 48 Copynumber: 2.3 Consensus size: 48
40324012 AACAATATGT
* * * **
40324022 GATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATTGATCTAC
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCGATAGAC
* **
40324070 GATCCCACGTAAGACCATGTCTGGGACATGGCATTAGCATCGATAGGG
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCGATAGAC
40324118 GATCCCATGTAAGAC
1 GATCCCATGTAAGAC
40324133 AATATCCGCG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCGATAGAC
Found at i:40326543 original size:60 final size:60
Alignment explanation
Indices: 40326479--40326601 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 60
40326469 ATTTATTGTT
40326479 ATTATTGGTATTGATTTGAAATAAGTGTGTTTATTGATTAAAGTTGTGATTGACAGAGAG
1 ATTATTGGTATTGATTTGAAATAAGTGTGTTTATTGATTAAAGTTGTGATTGACAGAGAG
*
40326539 ATTATTGGTATTGATTTGAAATAAGTGTGTTTATTGATTAAAGTTGTGATTGACAGGGAG
1 ATTATTGGTATTGATTTGAAATAAGTGTGTTTATTGATTAAAGTTGTGATTGACAGAGAG
40326599 ATT
1 ATT
40326602 GCATGAATAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.31, C:0.02, G:0.25, T:0.42
Consensus pattern (60 bp):
ATTATTGGTATTGATTTGAAATAAGTGTGTTTATTGATTAAAGTTGTGATTGACAGAGAG
Found at i:40335907 original size:15 final size:15
Alignment explanation
Indices: 40335889--40335921 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40335879 GAAGCCTAGA
40335889 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
40335904 ATAAAGAAATCCATG
1 ATAAAGAAATCCAAG
40335919 ATA
1 ATA
40335922 CGAGAATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:40352969 original size:13 final size:13
Alignment explanation
Indices: 40352951--40352977 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40352941 GCTCGGCAGG
40352951 GACACGCCTGTGT
1 GACACGCCTGTGT
40352964 GACACGCCTGTGT
1 GACACGCCTGTGT
40352977 G
1 G
40352978 CGATTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.22
Consensus pattern (13 bp):
GACACGCCTGTGT
Found at i:40362265 original size:15 final size:15
Alignment explanation
Indices: 40362245--40362274 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40362235 GCACCATCGC
40362245 GCCATCGCTCCTCCA
1 GCCATCGCTCCTCCA
*
40362260 GCCATCGGTCCTCCA
1 GCCATCGCTCCTCCA
40362275 CTAACGGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.50, G:0.17, T:0.20
Consensus pattern (15 bp):
GCCATCGCTCCTCCA
Found at i:40364651 original size:96 final size:96
Alignment explanation
Indices: 40364467--40364654 Score: 259
Period size: 96 Copynumber: 2.0 Consensus size: 96
40364457 CTTTTTGCTT
* * * *
40364467 CTCTTAGCCCTTTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTGTCTGC
1 CTCTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCGTATCTAC
** * * *
40364532 TCCATCGTTCCCTTCGATGACAGACTTACTC
66 TCCATCACTCCCATCAATAACAGACTTACTC
* * *
40364563 CTCTTTGCCCTCTTGGCTTCGGCTTTTCCCTTGCTCGAACCAAGCTTCTTGGGCTCCGTATCTAT
1 CTCTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCGTATCTAC
*
40364628 TCGATCACTCCCATCAATAACAGACTT
66 TCCATCACTCCCATCAATAACAGACTT
40364655 CCTCAGACAC
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.14, C:0.34, G:0.16, T:0.35
Consensus pattern (96 bp):
CTCTTAGCCCTCTTGGCTTCGGCTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCGTATCTAC
TCCATCACTCCCATCAATAACAGACTTACTC
Found at i:40367319 original size:25 final size:23
Alignment explanation
Indices: 40367263--40367323 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 23
40367253 TGAAGACTCT
*
40367263 TTATTTTTATTTTTTTTTTAATT
1 TTATTTTTATTTTTTTTTTAATC
*
40367286 TTATATTTATTTATCTTTTTTAA-C
1 TTATTTTTATTT-T-TTTTTTAATC
40367310 TTACTTTTTATTTT
1 TTA-TTTTTATTTT
40367324 AGTTCTCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 11 0.34
24 5 0.16
25 16 0.50
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (23 bp):
TTATTTTTATTTTTTTTTTAATC
Found at i:40378355 original size:79 final size:81
Alignment explanation
Indices: 40378219--40378403 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
40378209 TTGAATGATG
*
40378219 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
40378283 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
40378298 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
40378360 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
40378378 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40378404 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:40378410 original size:40 final size:40
Alignment explanation
Indices: 40378219--40378403 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
40378209 TTGAATGATG
* * * *
40378219 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
40378259 TCCGGACTAAGAT-CCGAAGGCAATTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
40378299 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40378338 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40378379 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40378404 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 34 0.28
40 80 0.65
41 9 0.07
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40378425 original size:79 final size:79
Alignment explanation
Indices: 40378272--40378436 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
40378262 GGACTAAGAT
* **
40378272 CCGAAGGCAATTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
40378337 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
40378351 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
40378414 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
40378430 CCGAAGG
1 CCGAAGG
40378437 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:40380423 original size:29 final size:29
Alignment explanation
Indices: 40380360--40380427 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
40380350 TAATCAACCG
*
40380360 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
40380389 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
40380418 CGCACACTTA
1 CGCACACTTA
40380428 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:40380539 original size:174 final size:174
Alignment explanation
Indices: 40380249--40380576 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
40380239 AACTCAAGGT
* *
40380249 ACTTACCCTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCCTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
40380314 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
40380379 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
40380423 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCCTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
40380488 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
**
40380553 ACTTTAAACTCGTACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
40380577 TGTACAATTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCCTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:40380571 original size:29 final size:30
Alignment explanation
Indices: 40380529--40380607 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
40380519 CTTAATAATC
40380529 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
* *
40380559 AACTCGTACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
40380588 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
40380608 ATCTCATGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 31 0.76
30 4 0.10
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:40388586 original size:29 final size:29
Alignment explanation
Indices: 40388523--40388590 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
40388513 TAATCAACCG
*
40388523 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
40388552 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
40388581 CGCACACTTA
1 CGCACACTTA
40388591 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:40388702 original size:174 final size:174
Alignment explanation
Indices: 40388412--40388739 Score: 629
Period size: 174 Copynumber: 1.9 Consensus size: 174
40388402 AACTCAAGGT
* *
40388412 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
40388477 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
40388542 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
40388586 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
40388651 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
*
40388716 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
40388740 TGTACAATTT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 151 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:40388731 original size:29 final size:30
Alignment explanation
Indices: 40388692--40388770 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
40388682 CTTAATAATC
40388692 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
40388722 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
40388751 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
40388771 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:40391864 original size:5 final size:5
Alignment explanation
Indices: 40391854--40391883 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
40391844 GATGCCAACC
40391854 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
40391884 TTTTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:40394898 original size:50 final size:50
Alignment explanation
Indices: 40394821--40395064 Score: 256
Period size: 50 Copynumber: 4.9 Consensus size: 50
40394811 TCCTTTGTGA
* * *
40394821 GTCACGTGTGTAGTACTAAGTGTAGGCTAATACGTGTACCAGATTGATAG
1 GTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAG
* ** * * *
40394871 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCG-TTAACTTTG
1 GTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGA--TAG
* * * ** * * *
40394922 ATCACGTGTGAAGTACTAAGTGCAGGATACTATGTGTATTAGATGGTTAA
1 GTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAG
* * *
40394972 GTCACGTGTGTAGTACTAAGTGCATGCTACTACGTGTACCAGATTCATAG
1 GTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAG
* * *
40395022 GTCACATGTGTAGTACTGAGTGCAGGCTACTATGCGTACCAGA
1 GTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
40395065 GAGCTTCAGT
Statistics
Matches: 152, Mismatches: 39, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
49 3 0.02
50 113 0.74
51 35 0.23
52 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (50 bp):
GTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAG
Found at i:40395001 original size:101 final size:101
Alignment explanation
Indices: 40394822--40395003 Score: 256
Period size: 101 Copynumber: 1.8 Consensus size: 101
40394812 CCTTTGTGAG
* * * * *
40394822 TCACGTGTGTAGTACTAAGTGTAGGCTAATACGTGTACCAGATTGATAGGTCACATGTGTAGTAC
1 TCACGTGTGAAGTACTAAGTGCAGGATAATACGTGTACCAGATGGATAAGTCACATGTGTAGTAC
40394887 TAAGTGCAGGCTACTATGCATACCCGTTAACTTTGA
66 TAAGTGCAGGCTACTATGCATACCCGTTAACTTTGA
* * ** * *
40394923 TCACGTGTGAAGTACTAAGTGCAGGATACTATGTGTATTAGATGGTTAAGTCACGTGTGTAGTAC
1 TCACGTGTGAAGTACTAAGTGCAGGATAATACGTGTACCAGATGGATAAGTCACATGTGTAGTAC
*
40394988 TAAGTGCATGCTACTA
66 TAAGTGCAGGCTACTA
40395004 CGTGTACCAG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 69 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (101 bp):
TCACGTGTGAAGTACTAAGTGCAGGATAATACGTGTACCAGATGGATAAGTCACATGTGTAGTAC
TAAGTGCAGGCTACTATGCATACCCGTTAACTTTGA
Found at i:40410597 original size:50 final size:50
Alignment explanation
Indices: 40410540--40410639 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
40410530 TTGCTCATTA
40410540 TGTATTATGATTCATGTTTGGTTCCACTGCATTGTGATAACCTAACTTAC
1 TGTATTATGATTCATGTTTGGTTCCACTGCATTGTGATAACCTAACTTAC
40410590 TGTATTATGATTCATGTTTGGTTCCACTGCATTGTGATAACCTAACTTAC
1 TGTATTATGATTCATGTTTGGTTCCACTGCATTGTGATAACCTAACTTAC
40410640 CTTTATGATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (50 bp):
TGTATTATGATTCATGTTTGGTTCCACTGCATTGTGATAACCTAACTTAC
Found at i:40410627 original size:27 final size:27
Alignment explanation
Indices: 40410547--40410627 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 27
40410537 TTATGTATTA
40410547 TGATTCATGTTTGGTTCCACTGCATTG
1 TGATTCATGTTTGGTTCCACTGCATTG
*** *** * *
40410574 TGA-T-AACCTAACTT--ACTGTATTA
1 TGATTCATGTTTGGTTCCACTGCATTG
40410597 TGATTCATGTTTGGTTCCACTGCATTG
1 TGATTCATGTTTGGTTCCACTGCATTG
40410624 TGAT
1 TGAT
40410628 AACCTAACTT
Statistics
Matches: 34, Mismatches: 16, Indels: 8
0.59 0.28 0.14
Matches are distributed among these distances:
23 10 0.29
24 1 0.03
25 8 0.24
26 1 0.03
27 14 0.41
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (27 bp):
TGATTCATGTTTGGTTCCACTGCATTG
Found at i:40413961 original size:27 final size:27
Alignment explanation
Indices: 40413931--40413984 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
40413921 TCATACAACC
* *
40413931 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
40413958 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
40413985 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:40423782 original size:18 final size:19
Alignment explanation
Indices: 40423759--40423796 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40423749 GGTACCACCA
40423759 AAACAT-ATATCA-CATCTT
1 AAACATCAT-TCATCATCTT
40423777 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
40423796 A
1 A
40423797 CCACCTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (19 bp):
AAACATCATTCATCATCTT
Found at i:40424086 original size:46 final size:46
Alignment explanation
Indices: 40424019--40424185 Score: 173
Period size: 46 Copynumber: 3.6 Consensus size: 46
40424009 CGCCCCTAAG
* *
40424019 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGGCGTTAGCATCCATAAA
*
40424065 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTAG-AT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTAGCATCCATAAA
* *** * *
40424112 CGAACTCGGACTCAACTCAACGAGTTC-GATATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGGCGTTAGCATCCATAAA
40424157 TGAACTCGGACTCAACTCAACGAGTTCGG
1 TGAACTCGGACTCAACTCAACGAGTTCGG
40424186 ATGCTCAACC
Statistics
Matches: 100, Mismatches: 11, Indels: 20
0.76 0.08 0.15
Matches are distributed among these distances:
41 3 0.03
42 2 0.02
43 1 0.01
44 1 0.01
45 26 0.26
46 30 0.30
47 27 0.27
48 2 0.02
49 2 0.02
50 2 0.02
51 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGGCGTTAGCATCCATAAA
Found at i:40424178 original size:92 final size:93
Alignment explanation
Indices: 40424020--40424189 Score: 279
Period size: 92 Copynumber: 1.8 Consensus size: 93
40424010 GCCCCTAAGT
* *
40424020 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
40424085 CGAGTTCGGATGCCTAGTTAGATCTCAC
66 CGAGTTCGGATGCCTAGTTAGATCTCAC
* * * *
40424113 GAACTCGGACTCAACTCAACGAGTTC-GATATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
40424177 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40424190 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:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTAGATCTCAC
Found at i:40444456 original size:50 final size:50
Alignment explanation
Indices: 40444399--40444498 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
40444389 TTGCTCATTA
40444399 TGTATTATGATTCATGTTTGGTTCCACTGCATTGTGATAACCTAACTTAC
1 TGTATTATGATTCATGTTTGGTTCCACTGCATTGTGATAACCTAACTTAC
40444449 TGTATTATGATTCATGTTTGGTTCCACTGCATTGTGATAACCTAACTTAC
1 TGTATTATGATTCATGTTTGGTTCCACTGCATTGTGATAACCTAACTTAC
40444499 CTTTATGATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (50 bp):
TGTATTATGATTCATGTTTGGTTCCACTGCATTGTGATAACCTAACTTAC
Found at i:40444486 original size:27 final size:27
Alignment explanation
Indices: 40444406--40444486 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 27
40444396 TTATGTATTA
40444406 TGATTCATGTTTGGTTCCACTGCATTG
1 TGATTCATGTTTGGTTCCACTGCATTG
*** *** * *
40444433 TGA-T-AACCTAACTT--ACTGTATTA
1 TGATTCATGTTTGGTTCCACTGCATTG
40444456 TGATTCATGTTTGGTTCCACTGCATTG
1 TGATTCATGTTTGGTTCCACTGCATTG
40444483 TGAT
1 TGAT
40444487 AACCTAACTT
Statistics
Matches: 34, Mismatches: 16, Indels: 8
0.59 0.28 0.14
Matches are distributed among these distances:
23 10 0.29
24 1 0.03
25 8 0.24
26 1 0.03
27 14 0.41
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (27 bp):
TGATTCATGTTTGGTTCCACTGCATTG
Found at i:40447821 original size:27 final size:27
Alignment explanation
Indices: 40447791--40447844 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
40447781 TCATACAACC
* *
40447791 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
40447818 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
40447845 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:40457765 original size:19 final size:20
Alignment explanation
Indices: 40457741--40457778 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
40457731 TGGTACACCA
40457741 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
40457760 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
40457779 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:40458114 original size:93 final size:93
Alignment explanation
Indices: 40458007--40458177 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
40457997 GCCCATAAGT
***
40458007 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40458072 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
40458100 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40458165 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40458178 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40458174 original size:46 final size:46
Alignment explanation
Indices: 40457999--40458174 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
40457989 TGTAACCCGC
* *** *
40457999 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* *
40458045 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
40458095 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
40458138 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40458175 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 2 0.02
46 64 0.58
47 29 0.26
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:40458633 original size:30 final size:30
Alignment explanation
Indices: 40458599--40458658 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
40458589 ATTTAATACG
40458599 AACTTTGGAAAAATTACACTTTTACCCCTA
1 AACTTTGGAAAAATTACACTTTTACCCCTA
* * * *
40458629 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTACCCCTA
40458659 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTACCCCTA
Found at i:40461143 original size:23 final size:24
Alignment explanation
Indices: 40461117--40461162 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
40461107 CTTCGCTGTC
*
40461117 TCAA-ATTCAAGTCTTTTGTGACA
1 TCAAGATTCAAGACTTTTGTGACA
*
40461140 TCAAGTATTTAAGACTTTTGTGA
1 TCAAG-ATTCAAGACTTTTGTGA
40461163 TCGGTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
25 15 0.79
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
TCAAGATTCAAGACTTTTGTGACA
Found at i:40466187 original size:30 final size:30
Alignment explanation
Indices: 40466153--40466209 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
40466143 ATTTAATATG
40466153 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40466183 AACTTTTGCATAATTACACTTTTGCCC
1 AACTTTGGAAAAATTACACTTTTGCCC
40466210 TAGGCTCGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:40469145 original size:40 final size:40
Alignment explanation
Indices: 40469075--40469327 Score: 335
Period size: 40 Copynumber: 6.3 Consensus size: 40
40469065 AGGCATGAAG
* * * *
40469075 GCCCGAATATACATCACCAGCATGATTGCTCTTCGGGACCTA
1 GCCCGGATATA-A-CACCAGCACGAATGCTCTTCGGGACTTA
40469117 GCCCGGATATAACACCAGCACGAATGCTCTTCGGGACTTA
1 GCCCGGATATAACACCAGCACGAATGCTCTTCGGGACTTA
* * * * * * *
40469157 ACCCTGATATAACTCTAACACGAATGCTCTCCGAGACTTA
1 GCCCGGATATAACACCAGCACGAATGCTCTTCGGGACTTA
*
40469197 GCCCGGACATAACACCAGCACGAATGCTCTTCGGGACTTA
1 GCCCGGATATAACACCAGCACGAATGCTCTTCGGGACTTA
*
40469237 GCCCGGACATAACACCAGCACGAATGCTCTTCGGGACTTA
1 GCCCGGATATAACACCAGCACGAATGCTCTTCGGGACTTA
* *
40469277 GCCCGGACATAACACCAGCACGAATGCTCTTCAGGACTTA
1 GCCCGGATATAACACCAGCACGAATGCTCTTCGGGACTTA
* *
40469317 GCTCGGCTATA
1 GCCCGGATATA
40469328 TAACTCTCAA
Statistics
Matches: 188, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 177 0.94
41 1 0.01
42 10 0.05
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (40 bp):
GCCCGGATATAACACCAGCACGAATGCTCTTCGGGACTTA
Found at i:40470673 original size:37 final size:37
Alignment explanation
Indices: 40470592--40470693 Score: 170
Period size: 37 Copynumber: 2.8 Consensus size: 37
40470582 CGAATAGTCC
*
40470592 CCACACGTAGTTATCGGGTCTTACCC-GACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
40470628 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
40470665 CCATACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
40470694 ATATATTTCC
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
36 25 0.40
37 37 0.60
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:40470891 original size:48 final size:48
Alignment explanation
Indices: 40470833--40471137 Score: 470
Period size: 48 Copynumber: 6.6 Consensus size: 48
40470823 ATATACACAC
* * * *
40470833 ATCTCCTACATATTTCACACTAGCCATTTGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
40470881 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
40470929 ATCTCATA-ATATTTCACATTAGCCATT-GGCTTTACCA-ATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
40470974 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
40471022 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAC
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
40471070 ATCTCATATATATTTCACATTAGCCATTCGGC-TTACCA-ATATAC--
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
40471114 A--TC-TATATATTTCACA-TAGCCATT
1 ATCTCATATATATTTCACATTAGCCATT
40471138 ATCTCATATA
Statistics
Matches: 250, Mismatches: 4, Indels: 14
0.93 0.01 0.05
Matches are distributed among these distances:
40 8 0.03
41 13 0.05
42 2 0.01
44 1 0.00
45 16 0.06
46 35 0.14
47 34 0.14
48 141 0.56
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.36
Consensus pattern (48 bp):
ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:40470990 original size:141 final size:138
Alignment explanation
Indices: 40470831--40471137 Score: 478
Period size: 141 Copynumber: 2.2 Consensus size: 138
40470821 CAATATACAC
* *
40470831 ACATCTCCTACATATTTCACACTAGCCATTTGGCTTTACCACATATACATATCTCATACATATTT
1 ACATCT-CTATATATTTCACA-TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTT
*
40470896 CACACTAGCCATTCGGCTTTACCACATATACATATCTCATA-ATATTTCACATTAGCCATT-GGC
64 CACACTAGCCATTCGGCTTTACCACATATACACATCTCATATATATTTCACATTAGCCATTCGGC
40470959 TTTACCAATAT
129 -TTACCAATAT
*
40470970 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
1 AC--ATCTC-TATATATTTCACA-TAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
*
40471035 TTCACATTAGCCATTCGGCTTTACCACATATACACATCTCATATATATTTCACATTAGCCATTCG
62 TTCACACTAGCCATTCGGCTTTACCACATATACACATCTCATATATATTTCACATTAGCCATTCG
40471100 GCTTACCAATAT
127 GCTTACCAATAT
40471112 ACA--TCTATATATTTCACATAGCCATT
1 ACATCTCTATATATTTCACATAGCCATT
40471138 ATCTCATATA
Statistics
Matches: 157, Mismatches: 6, Indels: 13
0.89 0.03 0.07
Matches are distributed among these distances:
136 8 0.05
137 13 0.08
138 2 0.01
139 2 0.01
140 2 0.01
141 96 0.61
142 31 0.20
143 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (138 bp):
ACATCTCTATATATTTCACATAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
CACTAGCCATTCGGCTTTACCACATATACACATCTCATATATATTTCACATTAGCCATTCGGCTT
ACCAATAT
Found at i:40474289 original size:46 final size:45
Alignment explanation
Indices: 40474222--40474392 Score: 195
Period size: 46 Copynumber: 3.7 Consensus size: 45
40474212 AACCCGCCCC
*
40474222 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCCTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCCTTC-CATCCA
*
40474268 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCC---TTCCATCCA
* * * * *
40474316 TCA-CGAACTCGGACTCAACTCAATGAGTTCGGACATTCCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCCTTCCATCCA
*
40474360 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
40474393 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 12, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
42 5 0.05
43 1 0.01
44 1 0.01
45 28 0.27
46 32 0.30
47 27 0.26
48 5 0.05
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCCTTCCATCCA
Found at i:40474385 original size:92 final size:93
Alignment explanation
Indices: 40474227--40474396 Score: 288
Period size: 92 Copynumber: 1.8 Consensus size: 93
40474217 GCCCCTAAGT
* *
40474227 GAACTCGGACTCAACTCAACGAGCTCGGGCCTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40474292 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
40474320 GAACTCGGACTCAACTCAATGAGTTCGGACATTC-CATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40474384 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40474397 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 42 0.58
93 30 0.42
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40474849 original size:30 final size:29
Alignment explanation
Indices: 40474815--40474873 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
40474805 ATTTAATACG
40474815 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTT-GAAAAATTACACTTTTGCCCCTA
* *
40474845 AACTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGAAAAATTACACTTTTGCCCCTA
40474874 GGCTCGGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (29 bp):
AACTTTGAAAAATTACACTTTTGCCCCTA
Found at i:40477756 original size:39 final size:40
Alignment explanation
Indices: 40477712--40477933 Score: 289
Period size: 39 Copynumber: 5.8 Consensus size: 40
40477702 GAATATACAT
* * * *
40477712 CACCAGCATGATTGCTCTTCGGGACCTAGCCC-GATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
* * *
40477751 CACCAGCACGAATGCTCTTCGGGACTTAACCCTGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
* * * *
40477791 CTCTAACACGAATGCTC-TCGAGACTTAGCCC-GACATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
40477829 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACAT-A
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
40477868 CACCAGCACGAAT--TCTTCGGGACTTAGCCCGGACATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
40477906 C-CCAGCACGAATGCTCTTC-GGACTTAGC
1 CACCAGCACGAATGCTCTTCGGGACTTAGC
40477934 TCGGCTATAT
Statistics
Matches: 163, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
37 34 0.21
38 31 0.19
39 72 0.44
40 26 0.16
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.21
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
Found at i:40479248 original size:36 final size:37
Alignment explanation
Indices: 40479196--40479297 Score: 170
Period size: 36 Copynumber: 2.8 Consensus size: 37
40479186 CGAATAGTCC
*
40479196 CCACACGTAGTTATCGGGTCTTACCCGGACAAAAT-T
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
40479232 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
40479269 CCATACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
40479298 ATATATTTCC
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
36 33 0.53
37 29 0.47
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:40479488 original size:47 final size:48
Alignment explanation
Indices: 40479437--40479699 Score: 373
Period size: 47 Copynumber: 5.6 Consensus size: 48
40479427 ATATACACAC
* * *
40479437 ATCTCCTACATATTTCACACTAGCCATT-GGCTTTACCACATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
40479484 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCA-ATATACAT
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
40479531 ATCTCATATATATTTCACATTAATTAG-CATTCGGCTTTACCA-ATATACAT
1 ATCTCATATATATTTCAC----ATTAGCCATTCGGCTTTACCACATATACAT
40479581 ATCTC--ATATATTTCACATTAGCCATTCGGC-TTACCACATATAC--
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
40479624 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAC
1 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
40479672 ATCTCATATATATTTCACATTAGCCATT
1 ATCTCATATATATTTCACATTAGCCATT
40479700 ATCTCATATA
Statistics
Matches: 201, Mismatches: 3, Indels: 23
0.89 0.01 0.10
Matches are distributed among these distances:
43 5 0.02
44 11 0.05
45 39 0.19
46 13 0.06
47 52 0.26
48 49 0.24
50 28 0.14
51 4 0.02
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.37
Consensus pattern (48 bp):
ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:40479691 original size:93 final size:93
Alignment explanation
Indices: 40479435--40479699 Score: 371
Period size: 93 Copynumber: 2.8 Consensus size: 93
40479425 CAATATACAC
* * * *
40479435 ACATCTCCTACATATTTCACACTAGCCATT-GGCTTTACCACATATACATATCTCATACATATTT
1 ACATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATTT
*
40479499 CACACTAGCCATTCGGCTTTACCAATAT
66 CACATTAGCCATTCGGCTTTACCAATAT
40479527 ACATATCTCATATATATTTCACATTAATTAG-CATTCGGCTTTACCA-ATATACATATCTC--AT
1 AC--ATCTCATATATATTTCAC----ATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
40479588 ATATTTCACATTAGCCATTCGGC-TTACCACATAT
60 ATATTTCACATTAGCCATTCGGCTTTACCA-ATAT
*
40479622 ACATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACACATCTCATATATATTT
1 ACATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATTT
40479687 CACATTAGCCATT
66 CACATTAGCCATT
40479700 ATCTCATATA
Statistics
Matches: 155, Mismatches: 6, Indels: 23
0.84 0.03 0.12
Matches are distributed among these distances:
89 5 0.03
90 15 0.10
91 12 0.08
92 2 0.01
93 39 0.25
94 22 0.14
95 29 0.19
97 17 0.11
98 14 0.09
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (93 bp):
ACATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATTT
CACATTAGCCATTCGGCTTTACCAATAT
Found at i:40479704 original size:28 final size:28
Alignment explanation
Indices: 40479672--40479727 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
40479662 ACATATACAC
*
40479672 ATCTCATATATATTTCACATTAGCCATT
1 ATCTCATATATATTTCAAATTAGCCATT
40479700 ATCTCATATATATTTCAAATTAGCCATT
1 ATCTCATATATATTTCAAATTAGCCATT
40479728 CGACTTTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.43
Consensus pattern (28 bp):
ATCTCATATATATTTCAAATTAGCCATT
Found at i:40482864 original size:46 final size:46
Alignment explanation
Indices: 40482797--40482969 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
40482787 AACCCGCCCC
* *
40482797 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
40482843 TAAGTGAACTCGGACTCAACTCAGCGAGTTCAGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-G--GAC-A-TTCGCATCCA
* *
40482891 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
40482936 TAGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40482970 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 1 0.01
46 59 0.56
47 26 0.25
48 2 0.02
49 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:40482909 original size:93 final size:93
Alignment explanation
Indices: 40482802--40482972 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
40482792 GCCCCTAAGT
* *
40482802 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAG
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40482867 CGAGTTCAGATGCCTAGTTACATCTCAC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
* *
40482895 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
40482960 CGAGTTCGGATGC
66 CGAGTTCAGATGC
40482973 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:40483426 original size:30 final size:30
Alignment explanation
Indices: 40483392--40483451 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
40483382 ATTTAATACG
*
40483392 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTAGAAAAATTACACTTTTGCCCCTA
* * *
40483422 AACTTTAGCATAATTACACTTTTTCCCCTA
1 AACTTTAGAAAAATTACACTTTTGCCCCTA
40483452 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTAGAAAAATTACACTTTTGCCCCTA
Found at i:40486401 original size:40 final size:40
Alignment explanation
Indices: 40486345--40486574 Score: 318
Period size: 40 Copynumber: 5.8 Consensus size: 40
40486335 GAATACACAT
* * * * *
40486345 CACCAGCATGATTGCTCTTCGGGACCTAGCCCAGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
* * *
40486385 CACCAGCACGAATGCTCTTCGGGACTTAACCCTGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
* * * *
40486425 CTCTAACACGAATGCTC-TCTGAGACTTAGCCCGGACATAA
1 CACCAGCACGAATGCTCTTC-GGGACTTAGCCCGGACATAA
40486465 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
*
40486505 CACCAGCACGAATACTCTTCGGGACTTAGCCCGGACATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
*
40486545 CACCGGCACGAATGCTCTTCGGGACTTAGC
1 CACCAGCACGAATGCTCTTCGGGACTTAGC
40486575 TCGGCTATAT
Statistics
Matches: 169, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 165 0.98
41 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
Found at i:40487924 original size:37 final size:37
Alignment explanation
Indices: 40487883--40487968 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 37
40487873 TAGTAATTGA
* *
40487883 GTCTTACCTGGACAAAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCTCCACACATAGTCATCGG
*
40487920 GTCTTACCCGGACATAATCTCCACACATAGTCATCGG
1 GTCTTACCCGGACAAAATCTCCACACATAGTCATCGG
40487957 GTCTTACCCGGA
1 GTCTTACCCGGA
40487969 ATATATTTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACATAGTCATCGG
Found at i:40488167 original size:48 final size:48
Alignment explanation
Indices: 40488109--40488533 Score: 796
Period size: 48 Copynumber: 8.9 Consensus size: 48
40488099 ATATACACAC
* *
40488109 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
40488157 ATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
40488205 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
40488253 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
40488301 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
40488349 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
40488397 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
40488445 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
40488493 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
40488534 CACATATACA
Statistics
Matches: 371, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 371 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:40493899 original size:46 final size:45
Alignment explanation
Indices: 40493849--40494020 Score: 197
Period size: 46 Copynumber: 3.7 Consensus size: 45
40493839 TGAGCATCCA
40493849 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCCG
*** * *
40493895 AACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-TCCG
1 AACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTCCG
*
40493942 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCC-G
*
40493988 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40494021 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 3 0.03
46 63 0.59
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTCCG
Found at i:40494001 original size:93 final size:93
Alignment explanation
Indices: 40493842--40494012 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
40493832 GGATGGTTGA
*
40493842 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
40493907 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
40493935 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
40493999 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
40494013 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:40497193 original size:44 final size:44
Alignment explanation
Indices: 40497128--40497212 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
40497118 ACATGTATCA
* *
40497128 CATCCATTATGAACTCGGACCAATTCAACGAGTTCAGATGCTCC
1 CATCCATAATGAACTCAGACCAATTCAACGAGTTCAGATGCTCC
40497172 CATCCATAATGAACTCAGACCAATTCAACGAGTTCAGATGC
1 CATCCATAATGAACTCAGACCAATTCAACGAGTTCAGATGC
40497213 CTCATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (44 bp):
CATCCATAATGAACTCAGACCAATTCAACGAGTTCAGATGCTCC
Found at i:40497416 original size:60 final size:60
Alignment explanation
Indices: 40497323--40497442 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 60
40497313 GATTTTTCGA
*
40497323 TACTCTATCTCTGTCGAACTTACTCAAAGTGTCGATCTCACTATCCATAGTATCAATTGC
1 TACTCTATCTCTGTCGAACTTACTCAAAGTGTCGATCTCACAATCCATAGTATCAATTGC
* * *
40497383 TACTCTATCTCTTTCGAACTTACTCGAAGTGTCGATCTCACAATCCTTAGTATCAATTGC
1 TACTCTATCTCTGTCGAACTTACTCAAAGTGTCGATCTCACAATCCATAGTATCAATTGC
40497443 ACTTTCATAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.36
Consensus pattern (60 bp):
TACTCTATCTCTGTCGAACTTACTCAAAGTGTCGATCTCACAATCCATAGTATCAATTGC
Found at i:40499725 original size:27 final size:27
Alignment explanation
Indices: 40499686--40499766 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
40499676 AGCATGGCTG
* *
40499686 CCAGAACT-GATATTGTGACAGAGTCA
1 CCAGAATTAGATATTGTGACAGAGCCA
*
40499712 CCAG-ATATAGATATTGTGGCAGAGCCA
1 CCAGAAT-TAGATATTGTGACAGAGCCA
* * *
40499739 CCAGAATTAGATAATGTGGCAAAGCCA
1 CCAGAATTAGATATTGTGACAGAGCCA
40499766 C
1 C
40499767 TTAACAGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.02
26 5 0.11
27 39 0.83
28 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (27 bp):
CCAGAATTAGATATTGTGACAGAGCCA
Found at i:40499863 original size:20 final size:20
Alignment explanation
Indices: 40499816--40499853 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40499806 TATAATCGGA
*
40499816 ACGAAGCCCACAATACCGAT
1 ACGAAGCCCACAATAACGAT
40499836 ACGAAGCCCACAATAACG
1 ACGAAGCCCACAATAACG
40499854 GTACACAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.34, G:0.16, T:0.08
Consensus pattern (20 bp):
ACGAAGCCCACAATAACGAT
Found at i:40499950 original size:98 final size:98
Alignment explanation
Indices: 40499788--40499993 Score: 358
Period size: 98 Copynumber: 2.1 Consensus size: 98
40499778 CGTGGCACAA
40499788 AGCCATCGATAACGGGTCTATAATCGGAACGAAGCCCACAATACCGATACGAAGCCCACAATAAC
1 AGCCATCGATAACGGGTCTATAATCGGAACGAAGCCCACAATACCGATACGAAGCCCACAATAAC
*
40499853 GGTACACAGCCTTCGGTAACATGATCGGCACTC
66 GGCACACAGCCTTCGGTAACATGATCGGCACTC
* * * * *
40499886 AGCCATTGATAACGGGTGTATAATCGGCACGAAGCCTACAATATCGATACGAAGCCCACAATAAC
1 AGCCATCGATAACGGGTCTATAATCGGAACGAAGCCCACAATACCGATACGAAGCCCACAATAAC
40499951 GGCACACAGCCTTCGGTAACATGATCGGCACTC
66 GGCACACAGCCTTCGGTAACATGATCGGCACTC
40499984 AGCCATCGAT
1 AGCCATCGAT
40499994 CGGTCAACAG
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 101 1.00
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.17
Consensus pattern (98 bp):
AGCCATCGATAACGGGTCTATAATCGGAACGAAGCCCACAATACCGATACGAAGCCCACAATAAC
GGCACACAGCCTTCGGTAACATGATCGGCACTC
Found at i:40500050 original size:27 final size:26
Alignment explanation
Indices: 40500000--40500079 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 26
40499990 CGATCGGTCA
*
40500000 ACAGATATTGTGACAAAGTCACCAGAT
1 ACAGATATTGTGGCAAAG-CACCAGAT
*
40500027 ACAGATATTGTGGCAGAGCAACCAGAAT
1 ACAGATATTGTGGCAAAGC-ACCAG-AT
*
40500055 A-A-ATATTTGTGGCATAGCCACCAGA
1 ACAGATA-TTGTGGCAAAG-CACCAGA
40500080 ACGCTTCCTC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
26 5 0.11
27 37 0.80
28 4 0.09
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (26 bp):
ACAGATATTGTGGCAAAGCACCAGAT
Found at i:40500363 original size:27 final size:27
Alignment explanation
Indices: 40500313--40500661 Score: 445
Period size: 27 Copynumber: 13.0 Consensus size: 27
40500303 ATTACCATTT
* *
40500313 TACCC-ACAAGGGTATCTCGGTAATTC
1 TACCCTACAAGGGTATTTCAGTAATTC
* *
40500339 TACCCTACAGGGGTATTTCAATAATTC
1 TACCCTACAAGGGTATTTCAGTAATTC
*
40500366 TACCCTACAAGGGTATTTCGGTAATTC
1 TACCCTACAAGGGTATTTCAGTAATTC
*
40500393 TACCTTACAAGGGTATTTCAGTAATTC
1 TACCCTACAAGGGTATTTCAGTAATTC
*
40500420 TACCCTACAGGGGTATTTCAGTAATTC
1 TACCCTACAAGGGTATTTCAGTAATTC
40500447 TACCCTACAAGGGTATTTCAGTAATTC
1 TACCCTACAAGGGTATTTCAGTAATTC
* *
40500474 TACCCTATAGGGGTATTTCAGTAATTC
1 TACCCTACAAGGGTATTTCAGTAATTC
* *
40500501 TACCTTAC-AGGAGTATTTCAGTATTTC
1 TACCCTACAAGG-GTATTTCAGTAATTC
*
40500528 TACCCTACAAGGGTATTTCGGTAATTC
1 TACCCTACAAGGGTATTTCAGTAATTC
**
40500555 TACCCTACAAGGGTATTTTGGTAATTC
1 TACCCTACAAGGGTATTTCAGTAATTC
* *
40500582 TACCCTA-TAGTGGTATTTTAGTAATTC
1 TACCCTACAAG-GGTATTTCAGTAATTC
* * *
40500609 TACCCTATAAGGGTATTTTAGTAATTT
1 TACCCTACAAGGGTATTTCAGTAATTC
** *
40500636 TA-CAAATCGAGGGTATTTCAGTAATT
1 TACCCTA-CAAGGGTATTTCAGTAATT
40500662 TTGCAAACTG
Statistics
Matches: 286, Mismatches: 31, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
26 11 0.04
27 270 0.94
28 5 0.02
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (27 bp):
TACCCTACAAGGGTATTTCAGTAATTC
Found at i:40500662 original size:27 final size:27
Alignment explanation
Indices: 40500618--40500877 Score: 253
Period size: 27 Copynumber: 9.7 Consensus size: 27
40500608 CTACCCTATA
*
40500618 AGGGTATTTTAGTAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
*
40500645 AGGGTATTTCAGTAATTTTGCAAA-CTG
1 AGGGTATTTCAGTAATTTTACAAATC-G
** *
40500672 AGGGTATTTTGGTAATTTTACAAGTCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* *
40500699 AGGGTATTTTAGTAATTTTAC-AATGG
1 AGGGTATTTCAGTAATTTTACAAATCG
* * * *
40500725 ACGGTATTTCGGTAATTTTATAAACCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* * *
40500752 GGGGTACTTT-GGTAATTTTACAAGTCG
1 AGGGTA-TTTCAGTAATTTTACAAATCG
40500779 AGGGTATTTCAGTAATTTTAC-AATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* * * *
40500805 ACGGCATTTCGGTAATTTTATAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* * *
40500832 GGGGTACTTT-GGTAATTTTACAACT-G
1 AGGGTA-TTTCAGTAATTTTACAAATCG
*
40500858 GGGGTATTTCAGTAATTTTA
1 AGGGTATTTCAGTAATTTTA
40500878 GTAAACTAAA
Statistics
Matches: 192, Mismatches: 33, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
25 3 0.02
26 61 0.32
27 121 0.63
28 7 0.04
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAAATCG
Found at i:40500678 original size:81 final size:80
Alignment explanation
Indices: 40500349--40500823 Score: 293
Period size: 81 Copynumber: 5.9 Consensus size: 80
40500339 TACCCTACAG
* * ** *
40500349 GGGTATTTCAATAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCAG
1 GGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACAAT-CGAGGGTATTTCAG
* ** *
40500414 TAATTCTACCCTACAG-
65 TAATT-TTCCAAACTGA
* *
40500430 GGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAG-GGGTATTTCA
1 GGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTA--CAATCGAGGGTATTTCA
* **
40500494 GTAATTCTACCTTAC--A
64 GTAATT-TTCCAAACTGA
* * ** * **
40500510 GGAGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTG
1 GG-GTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACAAT-CGAGGGTATTTCA
* **
40500575 GTAATTCTACCCTA-T-A
64 GTAATT-TTCCAAACTGA
* * * *
40500591 GTGGTATTTTAGTAATTCTACCCTATAAGGGTATTTTAGTAATTTTACAAATCGAGGGTATTTCA
1 G-GGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTAC-AATCGAGGGTATTTCA
*
40500656 GTAATTTTGCAAACTGA
64 GTAATTTTCCAAACTGA
** * ** * * * * * *
40500673 GGGTATTTTGGTAATTTTACAAGT-CGAGGGTATTTTAGTAATTTTACAATGGACGGTATTTCGG
1 GGGTATTTCAGTAATTCTAC-CCTACAAGGGTATTTCAGTAATTCTACAATCGAGGGTATTTCAG
** * *
40500737 TAATTTTATAAACCGG
65 TAATTTTCCAAACTGA
* * ** * * * * *
40500753 GGGTACTTT-GGTAATTTTACAAGT-CGAGGGTATTTCAGTAATTTTACAATCGACGGCATTTCG
1 GGGTA-TTTCAGTAATTCTAC-CCTACAAGGGTATTTCAGTAATTCTACAATCGAGGGTATTTCA
40500816 GTAATTTT
64 GTAATTTT
40500824 ATAAATCGGG
Statistics
Matches: 334, Mismatches: 47, Indels: 27
0.82 0.12 0.07
Matches are distributed among these distances:
79 2 0.01
80 95 0.28
81 230 0.69
82 5 0.01
83 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (80 bp):
GGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACAATCGAGGGTATTTCAGT
AATTTTCCAAACTGA
Found at i:40500766 original size:80 final size:80
Alignment explanation
Indices: 40500618--40500877 Score: 378
Period size: 80 Copynumber: 3.2 Consensus size: 80
40500608 CTACCCTATA
* * * ** * * *
40500618 AGGGTATTTTAGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTGCAAACTGAGGGTATTTTG
1 AGGGTATTTCAGTAATTTTAC-AATCGACGGTATTTCGGTAATTTTATAAACCGGGGGTACTTTG
40500683 GTAATTTTACAAGTCG
65 GTAATTTTACAAGTCG
* *
40500699 AGGGTATTTTAGTAATTTTACAATGGACGGTATTTCGGTAATTTTATAAACCGGGGGTACTTTGG
1 AGGGTATTTCAGTAATTTTACAATCGACGGTATTTCGGTAATTTTATAAACCGGGGGTACTTTGG
40500764 TAATTTTACAAGTCG
66 TAATTTTACAAGTCG
* *
40500779 AGGGTATTTCAGTAATTTTACAATCGACGGCATTTCGGTAATTTTATAAATCGGGGGTACTTTGG
1 AGGGTATTTCAGTAATTTTACAATCGACGGTATTTCGGTAATTTTATAAACCGGGGGTACTTTGG
*
40500844 TAATTTTACAACT-G
66 TAATTTTACAAGTCG
*
40500858 GGGGTATTTCAGTAATTTTA
1 AGGGTATTTCAGTAATTTTA
40500878 GTAAACTAAA
Statistics
Matches: 165, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
79 20 0.12
80 124 0.75
81 21 0.13
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (80 bp):
AGGGTATTTCAGTAATTTTACAATCGACGGTATTTCGGTAATTTTATAAACCGGGGGTACTTTGG
TAATTTTACAAGTCG
Found at i:40500819 original size:53 final size:52
Alignment explanation
Indices: 40500618--40500877 Score: 247
Period size: 53 Copynumber: 4.9 Consensus size: 52
40500608 CTACCCTATA
** * *
40500618 AGGGTATTTTAGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTGCAAACTG
1 AGGGTATTTCGGTAATTTTAC-AATCGAGGGTATTTCAGTAATTTTACAATC-G
* * *
40500672 AGGGTATTTTGGTAATTTTACAAGTCGAGGGTATTTTAGTAATTTTACAATGG
1 AGGGTATTTCGGTAATTTTACAA-TCGAGGGTATTTCAGTAATTTTACAATCG
* * * * *
40500725 ACGGTATTTCGGTAATTTTATAAACCGGGGGTACTTT-GGTAATTTTACAAGTCG
1 AGGGTATTTCGGTAATTTTA-CAATCGAGGGTA-TTTCAGTAATTTTACAA-TCG
* * * * *
40500779 AGGGTATTTCAGTAATTTTACAATCGACGGCATTTCGGTAATTTTATAAATCG
1 AGGGTATTTCGGTAATTTTACAATCGAGGGTATTTCAGTAATTTTA-CAATCG
* *
40500832 GGGGTACTTT-GGTAATTTTACAA-CTGGGGGTATTTCAGTAATTTTA
1 AGGGTA-TTTCGGTAATTTTACAATC-GAGGGTATTTCAGTAATTTTA
40500878 GTAAACTAAA
Statistics
Matches: 172, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
52 4 0.02
53 94 0.55
54 74 0.43
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (52 bp):
AGGGTATTTCGGTAATTTTACAATCGAGGGTATTTCAGTAATTTTACAATCG
Found at i:40501963 original size:23 final size:22
Alignment explanation
Indices: 40501933--40501996 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
40501923 CCACAACTCG
40501933 TATGAGCTTATTGTTTCAGCTCT
1 TATGAGCTTATT-TTTCAGCTCT
**
40501956 TATGAGCTTACCATTT-AGCTCT
1 TATGAGCTTA-TTTTTCAGCTCT
*
40501978 TCTGAGCTTATCTTTTCAG
1 TATGAGCTTAT-TTTTCAG
40501997 TCCTTACGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
22 18 0.55
23 15 0.45
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (22 bp):
TATGAGCTTATTTTTCAGCTCT
Found at i:40501978 original size:22 final size:22
Alignment explanation
Indices: 40501950--40502062 Score: 79
Period size: 22 Copynumber: 5.0 Consensus size: 22
40501940 TTATTGTTTC
40501950 AGCTCTTATGAGCTTACCATTT
1 AGCTCTTATGAGCTTACCATTT
* * *
40501972 AGCTCTTCTGAGCTTATCTTTT
1 AGCTCTTATGAGCTTACCATTT
* * *
40501994 CAG-TCCTTACGGGGTTACCATTTT
1 -AGCT-CTTATGAGCTTACCA-TTT
* *
40502018 AGCT-TTATGGAGCTTACCGTTC
1 AGCTCTTAT-GAGCTTACCATTT
*
40502040 AGCTC-AATTGAGCTTACCATTT
1 AGCTCTTA-TGAGCTTACCATTT
40502062 A
1 A
40502063 TCGGCTCTGG
Statistics
Matches: 67, Mismatches: 17, Indels: 14
0.68 0.17 0.14
Matches are distributed among these distances:
22 42 0.63
23 21 0.31
24 4 0.06
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (22 bp):
AGCTCTTATGAGCTTACCATTT
Found at i:40502270 original size:16 final size:16
Alignment explanation
Indices: 40502219--40502272 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
40502209 GATAAAGTAC
40502219 ATGTTACATGAATAAT
1 ATGTTACATGAATAAT
* * *
40502235 ATATTACATGAATCAC
1 ATGTTACATGAATAAT
* *
40502251 ATGTTACATGGATTAT
1 ATGTTACATGAATAAT
40502267 ATGTTA
1 ATGTTA
40502273 TAAGAGCGCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (16 bp):
ATGTTACATGAATAAT
Found at i:40504124 original size:16 final size:16
Alignment explanation
Indices: 40504099--40504131 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40504089 AAAGTCACTT
40504099 ACTTGCAAGAGAACTA
1 ACTTGCAAGAGAACTA
*
40504115 ACTTGTAAGAGAACTA
1 ACTTGCAAGAGAACTA
40504131 A
1 A
40504132 GTGGCTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.21
Consensus pattern (16 bp):
ACTTGCAAGAGAACTA
Found at i:40504814 original size:35 final size:35
Alignment explanation
Indices: 40504775--40504845 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
40504765 GAAATACGTT
40504775 GTGAATATTTTCTAATTCTGAAGGTAAAGCTAGTC
1 GTGAATATTTTCTAATTCTGAAGGTAAAGCTAGTC
*
40504810 GTGAATATTTTCTAATTTTGAAGGTAAAGCTAGTC
1 GTGAATATTTTCTAATTCTGAAGGTAAAGCTAGTC
40504845 G
1 G
40504846 ATATGCCACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (35 bp):
GTGAATATTTTCTAATTCTGAAGGTAAAGCTAGTC
Found at i:40514893 original size:28 final size:28
Alignment explanation
Indices: 40514853--40514982 Score: 170
Period size: 28 Copynumber: 4.6 Consensus size: 28
40514843 ATTGCATGAC
* * *
40514853 TATGAGTGTGATTGGGCCTGACGGGCCA
1 TATGAATGTGATTGGGCCCGATGGGCCA
*
40514881 TATGAAAGTGATTGGGCCCGATGGGCCA
1 TATGAATGTGATTGGGCCCGATGGGCCA
* *
40514909 TATGAATGTGATTAGGCCCGATGGGCAA
1 TATGAATGTGATTGGGCCCGATGGGCCA
* **
40514937 TATGAATGTGATTGGGCTCGATGGGTGA
1 TATGAATGTGATTGGGCCCGATGGGCCA
*
40514965 TATGAATGAGATTGGGCC
1 TATGAATGTGATTGGGCC
40514983 TAAAAGGGCC
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 89 1.00
ACGTcount: A:0.24, C:0.14, G:0.36, T:0.26
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCCGATGGGCCA
Found at i:40537815 original size:40 final size:40
Alignment explanation
Indices: 40537770--40537921 Score: 198
Period size: 40 Copynumber: 3.8 Consensus size: 40
40537760 ATAACCACAA
* * *
40537770 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* *
40537810 GCACAAATGCCTTCGGGTCTTAGCCCAGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
40537850 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
40537890 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
40537922 CATTCAAATG
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
39 1 0.01
40 95 0.95
41 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:40549158 original size:18 final size:18
Alignment explanation
Indices: 40549135--40549177 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
40549125 TGCCATATGC
*
40549135 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
40549153 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
40549171 GTTTCCT
1 GTATCCT
40549178 TTTCCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:40549702 original size:8 final size:9
Alignment explanation
Indices: 40549686--40549715 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40549676 TGAATAAGAC
40549686 AATATTTTT
1 AATATTTTT
40549695 AATATTTTT
1 AATATTTTT
40549704 -ATATTTTT
1 AATATTTTT
40549712 AATA
1 AATA
40549716 AAATATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:40560152 original size:47 final size:47
Alignment explanation
Indices: 40560051--40560407 Score: 462
Period size: 46 Copynumber: 7.8 Consensus size: 47
40560041 TGATGTCATA
* * * * *
40560051 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTTCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATG
* ***
40560097 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATG
* ***
40560144 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATG
40560191 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCA-GTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATG
* *
40560236 GTATCTTTCAA-CAT-GTCTTATTCA-TTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATG
* *
40560280 GTATCTTTCAACCATGGTCTTACACATTTT-ATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATG
* *
40560326 GTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATG
* *
40560372 GTATCTTTCAACCATGGTCTTACACA-TTCCATATCA
1 GTATCTTTCAACCATGGTCTTACTCATTTTCATATCA
40560408 GAGAGCACAC
Statistics
Matches: 290, Mismatches: 15, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
43 19 0.07
44 23 0.08
45 26 0.09
46 134 0.46
47 88 0.30
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (47 bp):
GTATCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATG
Found at i:40567670 original size:53 final size:54
Alignment explanation
Indices: 40567602--40567806 Score: 225
Period size: 53 Copynumber: 3.8 Consensus size: 54
40567592 TTTCCTTTTT
* * * *
40567602 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * *
40567655 GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CATTTGCCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATC-CTTGCCTTATA
* * * * * *
40567709 GTAACTCATCAATTCCATGTCTTGACATGGTGTTACATGATTTCCTTGCCTTATA
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * * *
40567764 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATC
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATC
40567807 TTTATCTTAC
Statistics
Matches: 126, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
52 1 0.01
53 44 0.35
54 37 0.29
55 43 0.34
56 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (54 bp):
GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
Found at i:40567745 original size:55 final size:53
Alignment explanation
Indices: 40567613--40567801 Score: 200
Period size: 55 Copynumber: 3.5 Consensus size: 53
40567603 AACTTACCAT
* * * * *
40567613 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGGA-CTTTGCCTTATAGAACTCATCAA
*
40567666 TGCCATGCCTTGGCATGGTCTTACATGGGACATTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGGGAC-TTTGCCTTATAG-AACTCATCAA
* * * *** * *
40567721 TTCCATGTCTTGACATGGTGTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATG-GGACTTTGCCTTATAGAACTCATCAA
*
40567775 TGCCATGCCTTGGCATGGTCTTACATG
1 TGCCATGCCTTGACATGGTCTTACATG
40567802 ATATCTTTAT
Statistics
Matches: 113, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
52 1 0.01
53 35 0.31
54 33 0.29
55 43 0.38
56 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (53 bp):
TGCCATGCCTTGACATGGTCTTACATGGGACTTTGCCTTATAGAACTCATCAA
Found at i:40567843 original size:47 final size:47
Alignment explanation
Indices: 40567788--40567909 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
40567778 CATGCCTTGG
* *
40567788 CATGGTCTTACATGATATCTTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
*
40567835 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTGCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
40567882 CATGGTCTTACATGGTATCCTTATCTTA
1 CATGGTCTTACATGGTATCCTTATCTTA
40567910 GTGCCAATGC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
Found at i:40571188 original size:32 final size:32
Alignment explanation
Indices: 40571147--40571210 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
40571137 ATCACAAGAC
*
40571147 TTCGAGACCAATCTTTTCTTCTGGGGCGTACT
1 TTCGAGACCAATCTTTTCTGCTGGGGCGTACT
40571179 TTCGAGACCAATCTTTTCTGCTGGGGCGTACT
1 TTCGAGACCAATCTTTTCTGCTGGGGCGTACT
40571211 ATCTTTTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (32 bp):
TTCGAGACCAATCTTTTCTGCTGGGGCGTACT
Found at i:40580304 original size:50 final size:50
Alignment explanation
Indices: 40580245--40580345 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
40580235 AATAGCATAT
* *
40580245 ACTAGTTTTAGGATTCTTGCTTAGCTGTTGATGCATCTTTGATTCCAGTA
1 ACTAGTTTTAGGATTCTTGCTTAGCTGCTGATGCATATTTGATTCCAGTA
40580295 ACTAGTTTTAGGATTCTTGCTTAGCTGCTGATGCATATTTGATTCCAGTA
1 ACTAGTTTTAGGATTCTTGCTTAGCTGCTGATGCATATTTGATTCCAGTA
40580345 A
1 A
40580346 ATGTTTCTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (50 bp):
ACTAGTTTTAGGATTCTTGCTTAGCTGCTGATGCATATTTGATTCCAGTA
Found at i:40581726 original size:6 final size:6
Alignment explanation
Indices: 40581715--40581747 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
40581705 TCCTCCTATC
*
40581715 TTTTTA TTTTTA TTTTTA TTTTTA TTTTCA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
40581748 CAATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:40581753 original size:18 final size:18
Alignment explanation
Indices: 40581715--40581754 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40581705 TCCTCCTATC
* **
40581715 TTTTTATTTTTATTTTTA
1 TTTTTATTTTCATTTCAA
40581733 TTTTTATTTTCATTTCAA
1 TTTTTATTTTCATTTCAA
40581751 TTTT
1 TTTT
40581755 ATTATTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTATTTTCATTTCAA
Found at i:40586271 original size:41 final size:40
Alignment explanation
Indices: 40586221--40586321 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
40586211 GAAGACTGCC
* * *
40586221 AGGCTCAAAGCCTGATATAACATACTGGCATAAAGCCTACT
1 AGGCACAAAGCCTGATATAACATACCGACA-AAAGCCTACT
* *
40586262 AGGCACAAAGCCTGATATAATATACCGACACAAGCCTACT
1 AGGCACAAAGCCTGATATAACATACCGACAAAAGCCTACT
* *
40586302 GGGTACAAAGCCTGATATAA
1 AGGCACAAAGCCTGATATAA
40586322 TACACCAACA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 27 0.51
41 26 0.49
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (40 bp):
AGGCACAAAGCCTGATATAACATACCGACAAAAGCCTACT
Found at i:40586310 original size:40 final size:40
Alignment explanation
Indices: 40586221--40586351 Score: 136
Period size: 41 Copynumber: 3.2 Consensus size: 40
40586211 GAAGACTGCC
* * * * *
40586221 AGGCTCAAAGCCTGATATAACATACTGGCATAAAGCCTACT
1 AGGCACAAAGCCTGATATAATATACCGACA-CAAGCCTACT
40586262 AGGCACAAAGCCTGATATAATATACCGACACAAGCCTACT
1 AGGCACAAAGCCTGATATAATATACCGACACAAGCCTACT
* * * * * **
40586302 GGGTACAAAGCCTGATATAATACACCAACACGAAGCTTGTT
1 AGGCACAAAGCCTGATATAATATACCGACAC-AAGCCTACT
40586343 AGGCACAAA
1 AGGCACAAA
40586352 TCCTAAAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
40 36 0.48
41 39 0.52
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
AGGCACAAAGCCTGATATAATATACCGACACAAGCCTACT
Found at i:40586417 original size:38 final size:38
Alignment explanation
Indices: 40586361--40586477 Score: 148
Period size: 38 Copynumber: 3.1 Consensus size: 38
40586351 ATCCTAAAAA
* *
40586361 AATA-CACTGGCACGAAGCCTGCTAGGCACAGAGCCCG
1 AATATCACTGGTACAAAGCCTGCTAGGCACAGAGCCCG
* * *
40586398 AATATCACTGGTACAAAGCCTGCTAGGCATAAAGCTCG
1 AATATCACTGGTACAAAGCCTGCTAGGCACAGAGCCCG
* *
40586436 AATATCACT-GTCACAAAGTCTGCTAGGCACAGAGCCTG
1 AATATCACTGGT-ACAAAGCCTGCTAGGCACAGAGCCCG
40586474 AATA
1 AATA
40586478 ACGTTACGTT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
37 6 0.09
38 62 0.91
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.18
Consensus pattern (38 bp):
AATATCACTGGTACAAAGCCTGCTAGGCACAGAGCCCG
Found at i:40588087 original size:21 final size:21
Alignment explanation
Indices: 40588053--40588098 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40588043 CTAAGGTGTG
*
40588053 AATTGGATTGAATTGAATG-TA
1 AATTGGATTAAATTG-ATGTTA
*
40588074 AATTGTATTAAATTGATGTTA
1 AATTGGATTAAATTGATGTTA
40588095 AATT
1 AATT
40588099 CATTCATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.43
Consensus pattern (21 bp):
AATTGGATTAAATTGATGTTA
Found at i:40588572 original size:26 final size:25
Alignment explanation
Indices: 40588534--40588608 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 25
40588524 GTAGCTCTTA
* *
40588534 TGAGCATCCCAATACATGGCTCTTCG
1 TGAGCTTCTCAATA-ATGGCTCTTCG
* *
40588560 TGAGCTTCTCAATTAAAGGCTCTTTG
1 TGAGCTTCTCAA-TAATGGCTCTTCG
* *
40588586 CGAGCTTCTCGATTAATGGCTCT
1 TGAGCTTCTC-AATAATGGCTCT
40588609 CCGAAGCTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 37 0.93
27 3 0.08
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.33
Consensus pattern (25 bp):
TGAGCTTCTCAATAATGGCTCTTCG
Found at i:40588713 original size:25 final size:25
Alignment explanation
Indices: 40588685--40588743 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
40588675 TGGCTCCCTT
40588685 GAGCTTCCCGTTATATG-GCTCAAAA
1 GAGCTTCCCGTT-TATGTGCTCAAAA
** *
40588710 GAGCTTCTTGTTTATGTGCTCGAAA
1 GAGCTTCCCGTTTATGTGCTCAAAA
40588735 GAGCATTCC
1 GAGC-TTCC
40588744 TGAATATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 4 0.14
25 21 0.75
26 3 0.11
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGTTTATGTGCTCAAAA
Found at i:40589444 original size:22 final size:22
Alignment explanation
Indices: 40589418--40589462 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
40589408 ATTATGTGTA
40589418 TTAATTCATGATATAA-TTAATT
1 TTAATTCAT-ATATAATTTAATT
* *
40589440 TTAATTTATATCTAATTTAATT
1 TTAATTCATATATAATTTAATT
40589462 T
1 T
40589463 GGATAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAATTCATATATAATTTAATT
Found at i:40591643 original size:39 final size:39
Alignment explanation
Indices: 40591598--40591874 Score: 455
Period size: 39 Copynumber: 7.1 Consensus size: 39
40591588 ATGCAAGACA
*
40591598 CTGGAAATGTATCCGGGCTAAAGTCCCCCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
40591637 CTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
40591676 CTGGAAATGTATTCGGGTTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
40591715 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
40591754 CTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
40591793 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* * *
40591832 CTGGAAATGTATCCGGGTTAAAGTCCCGTAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
40591871 CTGG
1 CTGG
40591875 TAATATAATT
Statistics
Matches: 222, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 222 1.00
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:40597752 original size:32 final size:32
Alignment explanation
Indices: 40597711--40597777 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
40597701 ATGTTGTATA
40597711 TTAGAATTAAAAATACTTGAGACTAGGTTACC
1 TTAGAATTAAAAATACTTGAGACTAGGTTACC
40597743 TTAGAATTAAAAATACTTGAGACTAGGTTACC
1 TTAGAATTAAAAATACTTGAGACTAGGTTACC
40597775 TTA
1 TTA
40597778 ATAGTGATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (32 bp):
TTAGAATTAAAAATACTTGAGACTAGGTTACC
Found at i:40600651 original size:39 final size:39
Alignment explanation
Indices: 40600606--40600919 Score: 529
Period size: 39 Copynumber: 8.1 Consensus size: 39
40600596 ATGCAAGACA
* *
40600606 CTGGAAATGTATCCGGGCTAAAGTCCCCCAAGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
40600645 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
40600684 CTGGAAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
40600723 CTGGAAATGTATTCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* * *
40600762 CTGGAAATATATCCGGGCCAAAGTCCCGTAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
40600801 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
40600840 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
40600879 CTGGAAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
40600918 CT
1 CT
40600920 AGTAATATAA
Statistics
Matches: 257, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 257 1.00
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:40604928 original size:19 final size:19
Alignment explanation
Indices: 40604904--40604942 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
40604894 CGTGTCATCA
40604904 TAAATTCATAGGCATAACT
1 TAAATTCATAGGCATAACT
*
40604923 TAAATTTATAGGCATAACT
1 TAAATTCATAGGCATAACT
40604942 T
1 T
40604943 CCACATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (19 bp):
TAAATTCATAGGCATAACT
Found at i:40611412 original size:53 final size:53
Alignment explanation
Indices: 40611308--40611412 Score: 120
Period size: 53 Copynumber: 2.0 Consensus size: 53
40611298 TTCCTTTTAA
* * * *
40611308 AACTTACCATTTCCATGTCTTGACATGGTATTACGTGGTATCCTTGCCTTATG
1 AACTCACCATTTCCATGCCTTGACATGGTATTACATGGGATCCTTGCCTTATG
* * * * * *
40611361 AACTCACCATTTTCATGCCTTGGCATGGTCTTCCATGGGATCTTTGTCTTAT
1 AACTCACCATTTCCATGCCTTGACATGGTATTACATGGGATCCTTGCCTTAT
40611413 TGTAGTTTAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (53 bp):
AACTCACCATTTCCATGCCTTGACATGGTATTACATGGGATCCTTGCCTTATG
Found at i:40615684 original size:18 final size:18
Alignment explanation
Indices: 40615661--40615707 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
40615651 GCGTAGTTTT
40615661 GGTTTATCGTGTGTTCTC
1 GGTTTATCGTGTGTTCTC
40615679 GGTTTATCGTGTGTTCTC
1 GGTTTATCGTGTGTTCTC
*
40615697 AGTTTAT-GTGT
1 GGTTTATCGTGT
40615708 CCACCATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.09, C:0.13, G:0.28, T:0.51
Consensus pattern (18 bp):
GGTTTATCGTGTGTTCTC
Done.