Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 142 of 378
Found at i:40566305 original size:18 final size:18
Alignment explanation
Indices: 40566271--40566324 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
40566261 TATTTTTTCT
* *
40566271 TTTTTAAATA-TTGTAAA
1 TTTTAAAATATTTATAAA
40566288 TTTTAAAATATTTATAAA
1 TTTTAAAATATTTATAAA
** *
40566306 AATTAAAATTTTTATAAA
1 TTTTAAAATATTTATAAA
40566324 T
1 T
40566325 ATTTTGACTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 9 0.30
18 21 0.70
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTTTAAAATATTTATAAA
Found at i:40566877 original size:2 final size:2
Alignment explanation
Indices: 40566870--40566898 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40566860 CATGTTTACA
40566870 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40566899 AATCTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40575798 original size:43 final size:44
Alignment explanation
Indices: 40575733--40575886 Score: 162
Period size: 43 Copynumber: 3.6 Consensus size: 44
40575723 TCGTACAATA
* *
40575733 CCAATGTCCCAGA-CGTGGTCTTACATGTAATCAAATATCGATG
1 CCAACGTCCCAGATAGTGGTCTTACATGTAATCAAATATCGATG
* *
40575776 CC-ACTGTCCCAGATAG-GGTCTTACATGAAATCAAATA-CGATA
1 CCAAC-GTCCCAGATAGTGGTCTTACATGTAATCAAATATCGATG
* *
40575818 CCAACGTCCCA-A-ACGTGGTCTTACACGTAAATCATAA-GTCGATG
1 CCAACGTCCCAGATA-GTGGTCTTACATGT-AATCA-AATATCGATG
40575862 CCAACGTCCCAGAT-GTGGTCTTACA
1 CCAACGTCCCAGATAGTGGTCTTACA
40575887 CGAAAACACA
Statistics
Matches: 93, Mismatches: 8, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 23 0.25
43 37 0.40
44 29 0.31
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (44 bp):
CCAACGTCCCAGATAGTGGTCTTACATGTAATCAAATATCGATG
Found at i:40575870 original size:44 final size:42
Alignment explanation
Indices: 40575733--40575888 Score: 142
Period size: 44 Copynumber: 3.6 Consensus size: 42
40575723 TCGTACAATA
* * *
40575733 CCAATGTCCCAGACGTGGTCTTACATGT-AATCAAATATCGATG
1 CCAACGTCCCAAACGTGGTCTTACACGTAAATC-AA-ATCGATG
* *
40575776 CC-ACTGTCCCAGATA-G-GGTCTTACATG-AAATCAAATACGATA
1 CCAAC-GTCCCA-A-ACGTGGTCTTACACGTAAATCAAAT-CGATG
40575818 CCAACGTCCCAAACGTGGTCTTACACGTAAATCATAAGTCGATG
1 CCAACGTCCCAAACGTGGTCTTACACGTAAATCA-AA-TCGATG
* *
40575862 CCAACGTCCCAGATGTGGTCTTACACG
1 CCAACGTCCCAAACGTGGTCTTACACG
40575889 AAAACACATA
Statistics
Matches: 95, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
40 1 0.01
41 4 0.04
42 25 0.26
43 31 0.33
44 32 0.34
45 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (42 bp):
CCAACGTCCCAAACGTGGTCTTACACGTAAATCAAATCGATG
Found at i:40575882 original size:86 final size:85
Alignment explanation
Indices: 40575730--40575891 Score: 222
Period size: 86 Copynumber: 1.9 Consensus size: 85
40575720 AGCTCGTACA
* * *
40575730 ATACCAATGTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGATAGGGT
1 ATACCAACGTCCCAAACGTGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGATAGGGT
*
40575795 CTTACATGAAATCAAATACG
66 CTTACACGAAATCAAATACG
*
40575815 ATACCAACGTCCCAAACGTGGTCTTACACGTAAATCATAA-GTCGATGCCAAC-GTCCCAGAT-G
1 ATACCAACGTCCCAAACGTGGTCTTACACGT-AATCA-AATATCGATGCC-ACTGTCCCAGATAG
40575877 TGGTCTTACACGAAA
63 -GGTCTTACACGAAA
40575892 ACACATATCA
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
85 29 0.43
86 35 0.51
87 4 0.06
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (85 bp):
ATACCAACGTCCCAAACGTGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGATAGGGT
CTTACACGAAATCAAATACG
Found at i:40577557 original size:18 final size:18
Alignment explanation
Indices: 40577534--40577576 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
40577524 TGAACCGAAG
40577534 TACTTTCTTCCATGGGGA
1 TACTTTCTTCCATGGGGA
40577552 TACTTTCTTCCATGGGGA
1 TACTTTCTTCCATGGGGA
40577570 TACTTTC
1 TACTTTC
40577577 AAAAACACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (18 bp):
TACTTTCTTCCATGGGGA
Found at i:40581179 original size:4 final size:4
Alignment explanation
Indices: 40581170--40581212 Score: 52
Period size: 4 Copynumber: 10.2 Consensus size: 4
40581160 AGTCTTAAAT
40581170 TTTA TTTA TTTA TTATA TATTA TTTA TTTA TTTTA TTT- TTTA T
1 TTTA TTTA TTTA TT-TA T-TTA TTTA TTTA -TTTA TTTA TTTA T
40581213 ATTTTTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 3 0.09
4 21 0.60
5 10 0.29
6 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:40581216 original size:18 final size:18
Alignment explanation
Indices: 40581171--40581205 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40581161 GTCTTAAATT
*
40581171 TTATTTATTTATTATATA
1 TTATTTATTTATTTTATA
40581189 TTATTTATTTATTTTAT
1 TTATTTATTTATTTTAT
40581206 TTTTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTATTTATTTTATA
Found at i:40590762 original size:40 final size:40
Alignment explanation
Indices: 40590717--40590884 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
40590707 CGGAATATAA
40590717 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
40590757 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
40590797 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * * * * *
40590837 CCAGATATAATCTCCAGTATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
40590877 CCGGATAT
1 CCGGATAT
40590885 CATTCAATTT
Statistics
Matches: 101, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
39 1 0.01
40 99 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40597965 original size:40 final size:40
Alignment explanation
Indices: 40597920--40598087 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
40597910 CGGAATATAA
40597920 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
40597960 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
40598000 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40598040 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
40598080 CCGGATAT
1 CCGGATAT
40598088 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
39 1 0.01
40 101 0.98
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40598070 original size:80 final size:80
Alignment explanation
Indices: 40597936--40598085 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
40597926 ATAATCACGT
*
40597936 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
40598000 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
40598016 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
40598079 CCCGGAT
64 CCCGGAT
40598086 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:40602989 original size:40 final size:40
Alignment explanation
Indices: 40602944--40603111 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
40602934 CGGAATATAA
40602944 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
40602984 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
40603024 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * * * *
40603064 CCAGATATAATCTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
40603104 CCGGATAT
1 CCGGATAT
40603112 CATTCAATTT
Statistics
Matches: 102, Mismatches: 24, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
39 1 0.01
40 100 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40603094 original size:80 final size:80
Alignment explanation
Indices: 40602960--40603109 Score: 189
Period size: 80 Copynumber: 1.9 Consensus size: 80
40602950 ATAATCACGT
* * *
40602960 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCAGATAGAATCTCTCGCACGAATGCCTTCGGGAT-TTAGC
40603024 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * *
40603040 GCACAATTGCCTTCGGGTCTTAACCCAGATATAATCTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCAGATAGAATCTCTC-GCACGAA-TGCCTTCGGGATTTAG
40603103 CCCGGAT
64 CCCGGAT
40603110 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
79 3 0.05
80 56 0.93
81 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCAGATAGAATCTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:40605419 original size:5 final size:5
Alignment explanation
Indices: 40605409--40605491 Score: 75
Period size: 6 Copynumber: 16.0 Consensus size: 5
40605399 AAACTAAATT
40605409 AATAA AAT-A AATAA AAT-A AATAA AAT-A AATAAA AATAAA AATAAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AAT-AA AAT-AA AAT-AA
40605454 AATAAA AATAAA TAATAA AACT-A AATAA AATAA AATAA
1 AAT-AA AAT-AA -AATAA AA-TAA AATAA AATAA AATAA
40605492 TATCTTCTAT
Statistics
Matches: 71, Mismatches: 0, Indels: 14
0.84 0.00 0.16
Matches are distributed among these distances:
4 13 0.18
5 27 0.38
6 28 0.39
7 3 0.04
ACGTcount: A:0.78, C:0.01, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:40605421 original size:9 final size:9
Alignment explanation
Indices: 40605404--40605487 Score: 90
Period size: 9 Copynumber: 9.8 Consensus size: 9
40605394 GGCTAAAACT
*
40605404 AAATTAATA
1 AAATAAATA
40605413 AAATAAATA
1 AAATAAATA
40605422 AAATAAATA
1 AAATAAATA
40605431 AAATAAATA
1 AAATAAATA
*
40605440 AAA-ATA-A
1 AAATAAATA
40605447 AAATAAA-A
1 AAATAAATA
40605455 ATAA-AAAT-
1 A-AATAAATA
40605463 AAAT-AATA
1 AAATAAATA
40605471 AAACTAAATA
1 AAA-TAAATA
40605481 AAATAAA
1 AAATAAA
40605488 ATAATATCTT
Statistics
Matches: 65, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
7 9 0.14
8 13 0.20
9 36 0.55
10 7 0.11
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:40605493 original size:13 final size:13
Alignment explanation
Indices: 40605397--40605493 Score: 67
Period size: 14 Copynumber: 7.2 Consensus size: 13
40605387 AAAAATAGGC
*
40605397 TAAAACTAAATTAA
1 TAAAA-TAAAATAA
40605411 TAAAAT-AAATAA
1 TAAAATAAAATAA
*
40605423 AATAAATAAAATAAA
1 TA-AAATAAAAT-AA
40605438 TAAAA-ATAAA-AA
1 TAAAATA-AAATAA
40605450 TAAAAATAAAAATAA
1 T-AAAAT-AAAATAA
*
40605465 -ATAATAAAACTAAA
1 TAAAATAAAA-T-AA
40605479 TAAAATAAAATAA
1 TAAAATAAAATAA
40605492 TA
1 TA
40605494 TCTTCTATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
12 13 0.19
13 19 0.28
14 21 0.31
15 14 0.21
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAATAAAATAA
Found at i:40611959 original size:79 final size:80
Alignment explanation
Indices: 40611858--40612041 Score: 196
Period size: 79 Copynumber: 2.3 Consensus size: 80
40611848 ACGACTCGCT
** * *
40611858 CAAATGCCTTCGGGACAAAGCCCGGTTATAGTAACTCGTACGAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTT-TAGTAACTCGCACGAACGCCTTC-GGATCTTAACCCG
* * **
40611922 GGTTTAGTAAC-TCCCA
64 GATATAGTAACTTAACA
* * **
40611938 CAAATGCCTTCGGG-CTTAGCCCGAATTTATTAACTCGCACGAACGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCG-GTTTAGTAACTCGCACGAACGCCTTCGGATCTTAACCCGG
*
40612002 ATATAGTCACTTAACA
65 ATATAGTAACTTAACA
40612018 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
40612042 ACATCATTCA
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
78 3 0.03
79 51 0.59
80 32 0.37
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTTAGTAACTCGCACGAACGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAACA
Found at i:40611986 original size:39 final size:40
Alignment explanation
Indices: 40611851--40611989 Score: 131
Period size: 40 Copynumber: 3.5 Consensus size: 40
40611841 GGATATAACG
* * * *
40611851 ACTCGCTCAAATGCCTTCGGGAC-AAAGCCCG-GTTATAGTA
1 ACTCGCACGAATGCCTTCGGGACTTAA-CCCGAATT-TAGTA
* **
40611891 ACTCGTACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCACGAATGCCTTCGGGACTTAACCCGAATTTAGTA
* * * *
40611931 ACTCCCACAAATGCCTTCGGG-CTTAGCCCGAATTTATTA
1 ACTCGCACGAATGCCTTCGGGACTTAACCCGAATTTAGTA
*
40611970 ACTCGCACGAACGCCTTCGG
1 ACTCGCACGAATGCCTTCGG
40611990 ATCTTAGTCC
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
39 31 0.37
40 47 0.57
41 5 0.06
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACGAATGCCTTCGGGACTTAACCCGAATTTAGTA
Found at i:40613776 original size:43 final size:46
Alignment explanation
Indices: 40613708--40613825 Score: 172
Period size: 45 Copynumber: 2.7 Consensus size: 46
40613698 GTCACATCGG
*
40613708 GCCTAGCAGGCTATAATGCCGGTGAAATGA-TA-TCG-GGCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGATTATTCGAGCCTTTGA
* * *
40613751 GCTTAGTAGGCTATGATGCCGGTGAAAT-ATTATTCGAGCCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGATTATTCGAGCCTTTGA
40613796 GCCTAGCAGGCTATAATGCCGGTGAAATGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGA
40613826 AATGTTATGT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.02
43 27 0.42
44 3 0.05
45 32 0.50
46 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (46 bp):
GCCTAGCAGGCTATAATGCCGGTGAAATGATTATTCGAGCCTTTGA
Found at i:40614280 original size:38 final size:38
Alignment explanation
Indices: 40614129--40614292 Score: 213
Period size: 38 Copynumber: 4.3 Consensus size: 38
40614119 ATATGCTAGA
*
40614129 ATTATATCCGGGTTAAATCCCGCAGGCTTCGTACAGGT
1 ATTATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGT
* * * *
40614167 AATATATCCGGGTTAAATCCAGCAGGCTTTGTGCTGGT
1 ATTATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGT
* *
40614205 AATT-TATCCGGGTTAATTCCCGCAGGCTTCGTGCTGGT
1 -ATTATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGT
* * *
40614243 ATTATATACGGGTTAAATCCCGCAGGCCTAGTACTGGT
1 ATTATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGT
*
40614281 ATTATATTCGGG
1 ATTATATCCGGG
40614293 CCTTTGAGCC
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
37 3 0.03
38 104 0.95
39 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (38 bp):
ATTATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGT
Found at i:40614428 original size:45 final size:45
Alignment explanation
Indices: 40614285--40614409 Score: 205
Period size: 45 Copynumber: 2.8 Consensus size: 45
40614275 ACTGGTATTA
* * * *
40614285 TATTCGGGCCTTTGAGCCTAGCAGGCTATTATGCCGGTGAGACAC
1 TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCCGATGAGATAC
*
40614330 TATTCGGGCTTTTGGGCCTAGCAGGCTATAATGCCGATGAGATAC
1 TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCCGATGAGATAC
40614375 TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCC
1 TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCC
40614410 AATAAAATGA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (45 bp):
TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCCGATGAGATAC
Found at i:40619941 original size:45 final size:43
Alignment explanation
Indices: 40619842--40619959 Score: 148
Period size: 45 Copynumber: 2.7 Consensus size: 43
40619832 CGGGCTTCGG
* *
40619842 GCCTAGCAGGTTATAATGCCGGTGAAATGATATCGGGCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGCCTTTGA
* * * *
40619885 GCTTAGTAGGCTATGATTCCGGTGAAAT-ATTATTCGAGCCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGA-TA-TCG-GCCTTTGA
40619930 GCCTAGCAGGCTATAATGCCGGTGAAATGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGA
40619960 AATGTTATGT
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
42 1 0.02
43 25 0.41
44 3 0.05
45 31 0.51
46 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (43 bp):
GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGCCTTTGA
Found at i:40620307 original size:38 final size:38
Alignment explanation
Indices: 40620265--40620426 Score: 218
Period size: 38 Copynumber: 4.3 Consensus size: 38
40620255 ATGCCGGAAT
40620265 TATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAA
* **
40620303 TATATCTGGGTTAAATCCCGCAGGCTTTGTGCTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAA
* * *
40620341 TATATCCGGGTTAATTCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAA
* * *
40620379 TATATCTGGGTTAAATCCCGCAGGCCT-AGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCA-TGCTGGTAA
*
40620417 TATATTCGGG
1 TATATCCGGG
40620427 CCTTTGAGCC
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 110 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAA
Found at i:40620363 original size:76 final size:76
Alignment explanation
Indices: 40620265--40620426 Score: 261
Period size: 76 Copynumber: 2.1 Consensus size: 76
40620255 ATGCCGGAAT
*
40620265 TATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAATATATCTGGGTTAAATCCCGCAGGCTT
1 TATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAATATATCTGGGTTAAATCCCGCAGGCCT
*
40620330 TGTGCTGGTAA
66 AGTGCTGGTAA
* * *
40620341 TATATCCGGGTTAATTCCCGCAGGCTTCGTGCTGGTATTATATCTGGGTTAAATCCCGCAGGCCT
1 TATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAATATATCTGGGTTAAATCCCGCAGGCCT
*
40620406 AGTGCTGGTAT
66 AGTGCTGGTAA
*
40620417 TATATTCGGG
1 TATATCCGGG
40620427 CCTTTGAGCC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (76 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAATATATCTGGGTTAAATCCCGCAGGCCT
AGTGCTGGTAA
Found at i:40620561 original size:45 final size:45
Alignment explanation
Indices: 40620419--40620591 Score: 201
Period size: 45 Copynumber: 3.9 Consensus size: 45
40620409 GCTGGTATTA
* *
40620419 TATTCGGGCCTTTGAGCCTAGCAGGCTATTATGCCGGTGAGACAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* *
40620464 TATTCGGGCCTTTGGGCCTAGTAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* * *
40620509 TATTCGGG-CTTTCGAGCCTAGCAGGCTATAATGCTGATGAAATGA-
1 TATTCGGGCCTTT-GAGCCTAGCAGGCTATAATGCCGGTGAGAT-AC
* * * *
40620554 TAATCGGGCC-TCGATCCTAGCAGGCGA-AATGCCGGTGA
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
40620592 TTTGAGAAAA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
43 9 0.08
44 17 0.15
45 82 0.75
46 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
Found at i:40640838 original size:27 final size:27
Alignment explanation
Indices: 40640800--40640861 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
40640790 CGTGCTAAAA
* *
40640800 AAATGAAAGCCTTTTTGAAAATATATG
1 AAATGGAAGCCTTTCTGAAAATATATG
* *
40640827 AAATGGAAGCCTTTCTGGAAATCTATG
1 AAATGGAAGCCTTTCTGAAAATATATG
*
40640854 GAATGGAA
1 AAATGGAA
40640862 AACTTTGTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (27 bp):
AAATGGAAGCCTTTCTGAAAATATATG
Found at i:40641085 original size:27 final size:27
Alignment explanation
Indices: 40641055--40641128 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
40641045 GACTTGAAGG
* *
40641055 TATGGTAAACACTGAAGGAATAGTACA
1 TATGGAAAACACTGAAAGAATAGTACA
** ** *
40641082 TATGGCGAACTTTGAAAGAATAGTGCA
1 TATGGAAAACACTGAAAGAATAGTACA
*
40641109 TATGGAAAACACTGAGAGAA
1 TATGGAAAACACTGAAAGAA
40641129 ACAGTTCCAT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (27 bp):
TATGGAAAACACTGAAAGAATAGTACA
Found at i:40642827 original size:45 final size:47
Alignment explanation
Indices: 40642615--40642884 Score: 193
Period size: 46 Copynumber: 5.7 Consensus size: 47
40642605 TCATTTGTGT
* * *
40642615 GAGCTAGTGTAAGA-CATGTCTCGGACATGCATCGGCCATATTATG-A
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGG-CACAGTATGTA
* * * * *
40642661 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGTATTGAG-ACG-A
1 GAGCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCA--CAGTATGTA
* * * * * * *
40642709 GTGCTAGTGTCAGA-CATGTCTGGGACATGCATCAGCCTCGGGACGTA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATC-GGCACAGTATGTA
* * *
40642756 -AGCTAGTATAAGA-CATGTCTGTGACATGTATCGGCTACGAG-ATGT-
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGC-AC-AGTATGTA
*
40642801 G-TC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGTTATGTGA
1 GAGCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCACAG-TATGT-A
40642849 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GAGCTAGTGTAAGACCATGTCTGGGACAT-GCATCG
40642885 ACACTTTACC
Statistics
Matches: 176, Mismatches: 30, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
44 10 0.06
45 19 0.11
46 62 0.35
47 31 0.18
48 21 0.12
49 2 0.01
50 31 0.18
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (47 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCACAGTATGTA
Found at i:40649749 original size:35 final size:35
Alignment explanation
Indices: 40649703--40649774 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
40649693 TATGGAAGAA
40649703 AATGAGTCTTGGTTGCCTTATAAACAACTTTTGTG
1 AATGAGTCTTGGTTGCCTTATAAACAACTTTTGTG
*
40649738 AATGAGTCTTGGTTGTCTTATAAACAACTTTTGTG
1 AATGAGTCTTGGTTGCCTTATAAACAACTTTTGTG
40649773 AA
1 AA
40649775 AGGTGTTAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (35 bp):
AATGAGTCTTGGTTGCCTTATAAACAACTTTTGTG
Found at i:40650556 original size:45 final size:48
Alignment explanation
Indices: 40650336--40650647 Score: 165
Period size: 46 Copynumber: 6.6 Consensus size: 48
40650326 TGTATGAGCT
* * * * *
40650336 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCTACGATGATG-TAGTC
* * * * *
40650382 AGTGTAAGACCATATTTGGGACATGGCATC-GGTATTGA-GACG-AGTGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCTA-CGATGATGTAGT-C
* * ** *
40650429 GAGTGTAAGA-CATGTTTGGGACAT-GCATCAGCCT-CG-GGACATAAGCC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCAG-CTACGATGATGT-AGTC
*
40650476 AGTATAAGA-CATGTCTGGGACAT-GCATCAGCTACGA-GATGT-GTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCTACGATGATGTAGTC
* * * *
40650520 AGTGTAAGACCATGTCTGGGACATGGCAT-TGGTACGATTATGTGAGAGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCTACGATGATGT---AGTC
* * * *
40650570 AGTGTAAGACCGTGTCTGGGACATGGCATCGGCCT-CGAAGATGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CTACGATGATG-TAGTC
*
40650619 AGTGTAAGACCAT-T-TGTGGATATGGCATC
1 AGTGTAAGACCATGTCTG-GGACATGGCATC
40650648 GACACTTTAC
Statistics
Matches: 210, Mismatches: 32, Indels: 46
0.73 0.11 0.16
Matches are distributed among these distances:
44 10 0.05
45 22 0.10
46 61 0.29
47 32 0.15
48 31 0.15
49 15 0.07
50 30 0.14
51 7 0.03
52 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCTACGATGATGTAGTC
Found at i:40653694 original size:19 final size:19
Alignment explanation
Indices: 40653667--40653707 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
40653657 AAAAATCTAC
40653667 TTTTTTATTGTT-TTATT-T
1 TTTTTTATT-TTGTTATTAT
40653685 TTTTTCTATTTTGTTATTAT
1 TTTTT-TATTTTGTTATTAT
40653705 TTT
1 TTT
40653708 ATTGTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.35
19 9 0.45
20 4 0.20
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTTTTATTTTGTTATTAT
Found at i:40653701 original size:27 final size:28
Alignment explanation
Indices: 40653662--40653717 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
40653652 GCAACAAAAA
*
40653662 TCTACTTTTTTATTGTTTTATT-TTTTT
1 TCTACTTTTTTATTATTTTATTGTTTTT
40653689 TCTA-TTTTGTTATTATTTTATTGTTTTT
1 TCTACTTTT-TTATTATTTTATTGTTTTT
40653717 T
1 T
40653718 TCACTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 16 0.62
28 6 0.23
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.77
Consensus pattern (28 bp):
TCTACTTTTTTATTATTTTATTGTTTTT
Found at i:40676890 original size:67 final size:67
Alignment explanation
Indices: 40676780--40677205 Score: 403
Period size: 67 Copynumber: 6.4 Consensus size: 67
40676770 GCTGTAATGA
* * * *
40676780 GGTATGATGTGTAAGACCATATCTCAACTATGGA-AACATAGAGAGTTTGCCAGAACATTAAACA
1 GGTATGATGTGTAAGACCATAGCTCGACTAT-GACAACATAGAGAGTCTGCCAGGACATTAAACA
40676844 TAG
65 TAG
* * * **
40676847 GGTATGATGTGTAAAACCATAGCTCGTCTATGACAACAAAGAGAGTCTGTTAGGACATTAAACAT
1 GGTATGATGTGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCTGCCAGGACATTAAACAT
40676912 -G
66 AG
* * * ** *
40676913 AGGTATGATGTGTAAGACGATAGCTCGGCTATGGCAACATAGAGAGTCCACCAGGACATCAAACA
1 -GGTATGATGTGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCTGCCAGGACATTAAACA
*
40676978 TAA
65 TAG
* ** * * * *
40676981 GGTATGATGTGTAAAACCATATTTCGACGATGACAATATAGAGAGTCCGTCAGGACATTAAACAT
1 GGTATGATGTGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCTGCCAGGACATTAAACAT
40677046 -G
66 AG
* * * * * *
40677047 CGATATGATGTGTAAGACTATAGCTAGGCTATGACAACATAGAGTGTCTGCCAGGGCATTAAACA
1 -GGTATGATGTGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCTGCCAGGACATTAAACA
*
40677112 CAG
65 TAG
* ** * * * * *
40677115 GGTATGATGTGTAAGAACATTTCTTGACTATGTA-AACGTGGAGAGCCCT-CCATGACATTAAAC
1 GGTATGATGTGTAAGACCATAGCTCGACTATG-ACAACATAGAGAG-TCTGCCAGGACATTAAAC
*
40677178 ATGG
64 ATAG
* *
40677182 GGTATGATGTGTAAAACTATAGCT
1 GGTATGATGTGTAAGACCATAGCT
40677206 TGGCTATAGT
Statistics
Matches: 286, Mismatches: 66, Indels: 14
0.78 0.18 0.04
Matches are distributed among these distances:
66 3 0.01
67 279 0.98
68 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (67 bp):
GGTATGATGTGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCTGCCAGGACATTAAACAT
AG
Found at i:40677016 original size:134 final size:134
Alignment explanation
Indices: 40676776--40677212 Score: 466
Period size: 134 Copynumber: 3.3 Consensus size: 134
40676766 ATGGGCTGTA
* ** * * *
40676776 ATGAGGTATGATGTGTAAGACCATATCTCAACTATGGAAACATAGAGAGTTTGCCAGAACATTAA
1 ATGAGGTATGATGTGTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCTGCCAGGACATTAA
* * * *
40676841 ACATAGGGTATGATGTGTAAAACCATAGCTCGTCTATGACAACAAAGAGAGTCTGTTAGGACATT
66 ACATAGGGTATGATGTGTAAAACCATAGCTCGACGATGACAACAAAGAGAGTCCGTCAGGACATT
40676906 AAAC
131 AAAC
* ** *
40676910 ATGAGGTATGATGTGTAAGACGATAGCTCGGCTATGGCAACATAGAGAGTCCACCAGGACATCAA
1 ATGAGGTATGATGTGTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCTGCCAGGACATTAA
* ** * *
40676975 ACATAAGGTATGATGTGTAAAACCATATTTCGACGATGACAATATAGAGAGTCCGTCAGGACATT
66 ACATAGGGTATGATGTGTAAAACCATAGCTCGACGATGACAACAAAGAGAGTCCGTCAGGACATT
40677040 AAAC
131 AAAC
* * * * * * *
40677044 ATGCGATATGATGTGTAAGACTATAGCTAGGCTATGACAACATAGAGTGTCTGCCAGGGCATTAA
1 ATGAGGTATGATGTGTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCTGCCAGGACATTAA
* ** * * *** * *
40677109 ACACAGGGTATGATGTGTAAGAA-CATTTCTTGACTATGTA-AACGTGGAGAG-CCCTCCATGAC
66 ACATAGGGTATGATGTGTAA-AACCATAGCTCGACGATG-ACAACAAAGAGAGTCCGT-CAGGAC
40677171 ATTAAAC
128 ATTAAAC
* * * *
40677178 ATGGGGTATGATGTGTAAAACTATAGCTTGGCTAT
1 ATGAGGTATGATGTGTAAGACCATAGCTCGGCTAT
40677213 AGTAGCATAC
Statistics
Matches: 256, Mismatches: 44, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
133 3 0.01
134 250 0.98
135 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (134 bp):
ATGAGGTATGATGTGTAAGACCATAGCTCGGCTATGGCAACATAGAGAGTCTGCCAGGACATTAA
ACATAGGGTATGATGTGTAAAACCATAGCTCGACGATGACAACAAAGAGAGTCCGTCAGGACATT
AAAC
Found at i:40677188 original size:201 final size:201
Alignment explanation
Indices: 40676779--40677198 Score: 470
Period size: 201 Copynumber: 2.1 Consensus size: 201
40676769 GGCTGTAATG
* * **
40676779 AGGTATGATGTGTAAGACCATATCTCAACTATGGAAACATAGAGAGTTTGCCAGAACATTAAACA
1 AGGTATGATGTGTAAAACCATATCTCAACGATGGAAACATAGAGAGTCCGCCAGAACATTAAACA
* * * **
40676844 TAGGGTATGATGTGTAAAACCATAGCTCGTCTATGACAACAAAGAGAGTCTGTTAGGACATTAAA
66 TAGGATATGATGTGTAAAACCATAGCTAGGCTATGACAACAAAGAGAGTCTGCCAGGACATTAAA
* * * *
40676909 CATGAGGTATGATGTGTAAGACGATAGCTCGGCTATGGCAACATAGAGAGTCCACCAGGACATCA
131 CAAGAGGTATGATGTGTAAGACGATAGCTCGACTATGGAAACATAGAGAGCCCACCAGGACATCA
40676974 AACATA
196 AACATA
* * * * *
40676980 AGGTATGATGTGTAAAACCATATTTCGACGAT-GACAATATAGAGAGTCCGTCAGGACATTAAAC
1 AGGTATGATGTGTAAAACCATATCTCAACGATGGA-AACATAGAGAGTCCGCCAGAACATTAAAC
* * * * *
40677044 AT-GCGATATGATGTGTAAGACTATAGCTAGGCTATGACAACATAGAGTGTCTGCCAGGGCATTA
65 ATAG-GATATGATGTGTAAAACCATAGCTAGGCTATGACAACAAAGAGAGTCTGCCAGGACATTA
** * * * * * *
40677108 AACACAG-GGTATGATGTGTAAGAAC-ATTTCTTGACTATGTAAACGTGGAGAGCCCTCCATGAC
129 AACA-AGAGGTATGATGTGTAAG-ACGATAGCTCGACTATGGAAACATAGAGAGCCCACCAGGAC
* *
40677171 ATTAAACATG
192 ATCAAACATA
*
40677181 GGGTATGATGTGTAAAAC
1 AGGTATGATGTGTAAAAC
40677199 TATAGCTTGG
Statistics
Matches: 181, Mismatches: 34, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
200 3 0.02
201 175 0.97
202 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (201 bp):
AGGTATGATGTGTAAAACCATATCTCAACGATGGAAACATAGAGAGTCCGCCAGAACATTAAACA
TAGGATATGATGTGTAAAACCATAGCTAGGCTATGACAACAAAGAGAGTCTGCCAGGACATTAAA
CAAGAGGTATGATGTGTAAGACGATAGCTCGACTATGGAAACATAGAGAGCCCACCAGGACATCA
AACATA
Found at i:40678599 original size:15 final size:16
Alignment explanation
Indices: 40678571--40678600 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40678561 GTTGGACTAA
40678571 ATTGAATATGAGTTAT
1 ATTGAATATGAGTTAT
40678587 ATTGAAT-TGAGTTA
1 ATTGAATATGAGTTA
40678601 AATTCATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
ATTGAATATGAGTTAT
Found at i:40680191 original size:15 final size:15
Alignment explanation
Indices: 40680173--40680202 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40680163 TCAGCCTTGT
40680173 GTGAAACATGGCCAG
1 GTGAAACATGGCCAG
*
40680188 GTGACACATGGCCAG
1 GTGAAACATGGCCAG
40680203 ATGACACGGC
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:0.30, C:0.23, G:0.33, T:0.13
Consensus pattern (15 bp):
GTGAAACATGGCCAG
Found at i:40680207 original size:15 final size:15
Alignment explanation
Indices: 40680178--40680209 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40680168 CTTGTGTGAA
*
40680178 ACATGGCCAGGTGAC
1 ACATGGCCAGATGAC
40680193 ACATGGCCAGATGAC
1 ACATGGCCAGATGAC
40680208 AC
1 AC
40680210 GGCAAGTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.12
Consensus pattern (15 bp):
ACATGGCCAGATGAC
Found at i:40683636 original size:18 final size:17
Alignment explanation
Indices: 40683609--40683642 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40683599 AGAACACAAT
40683609 AATAAATTCTCTAAAAG
1 AATAAATTCTCTAAAAG
*
40683626 AATACAATTCTTTAAAA
1 AATA-AATTCTCTAAAA
40683643 TGTCTAAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (17 bp):
AATAAATTCTCTAAAAG
Found at i:40700239 original size:48 final size:47
Alignment explanation
Indices: 40700165--40700396 Score: 143
Period size: 48 Copynumber: 4.9 Consensus size: 47
40700155 CAAGGTAGGG
* **
40700165 TGCCAATGCCATATCTTAGATATGGTCTTACATGGGACCACATAACGA
1 TGCCAATGCCATGTCCCA-ATATGGTCTTACATGGGACCACATAACGA
* * *
40700213 TGCCAATTCCATGTCCCAATTATGGTCTTATATGGGATCACACATATCGA
1 TGCCAATGCCATGTCCCAA-TATGGTCTTACATGGGA-C-CACATAACGA
* * * * * * * *
40700263 AGACGAT---A-G-CCCAACTATGGTCTTACACGATGTCC-CATTATGA
1 TGCCAATGCCATGTCCCAA-TATGGTCTTACATG-GGACCACATAACGA
** * * *
40700306 TGCCAATGCCATGTCCTTGACACGGTCTTACATGGGATCACATAACGA
1 TGCCAATGCCATGTCC-CAATATGGTCTTACATGGGACCACATAACGA
* * * *
40700354 TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATCACAT
1 TGCCAATGCCATGTCCCA-ATATGGTCTTACATGGGACCACAT
40700397 GTAACTGCCG
Statistics
Matches: 137, Mismatches: 35, Indels: 24
0.70 0.18 0.12
Matches are distributed among these distances:
43 9 0.07
44 1 0.01
45 18 0.13
46 3 0.02
47 5 0.04
48 86 0.63
49 2 0.01
50 13 0.09
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (47 bp):
TGCCAATGCCATGTCCCAATATGGTCTTACATGGGACCACATAACGA
Found at i:40700411 original size:48 final size:46
Alignment explanation
Indices: 40700330--40700430 Score: 132
Period size: 48 Copynumber: 2.1 Consensus size: 46
40700320 CCTTGACACG
*
40700330 GTCTTACATGGGATCACATAACGATGCCAAAGCCATGTCCCAGACAT
1 GTCTTACATGGGATCACATAAC-ATGCCAAAGCCATATCCCAGACAT
* *
40700377 AGTCTTACATGGGATCACATGTAAC-TGCCGAAGCCATATCCCAGATAT
1 -GTCTTACATGGGATCACA--TAACATGCCAAAGCCATATCCCAGACAT
40700425 GTCTTA
1 GTCTTA
40700431 TACAGGAGCT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
47 6 0.12
48 38 0.79
50 4 0.08
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.25
Consensus pattern (46 bp):
GTCTTACATGGGATCACATAACATGCCAAAGCCATATCCCAGACAT
Found at i:40708455 original size:39 final size:39
Alignment explanation
Indices: 40708401--40708489 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
40708391 GAATGTTCGA
*
40708401 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAACT
*
40708440 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAACT
*
40708479 ATGATATCCGG
1 GTGATATCCGG
40708490 TTGTGGAGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.22
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAACT
Found at i:40713038 original size:39 final size:39
Alignment explanation
Indices: 40712984--40713136 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
40712974 GAATGTTCGA
*
40712984 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
40713023 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
40713062 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
* *
40713101 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
40713137 GGTTACCATA
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
Found at i:40713152 original size:40 final size:39
Alignment explanation
Indices: 40712985--40713166 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
40712975 AATGTTCGAG
* *
40712985 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
40713024 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
40713063 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
40713102 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
40713142 CCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGG
40713167 TGTTTTGAAC
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:40715856 original size:13 final size:13
Alignment explanation
Indices: 40715838--40715865 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40715828 GCTACCACAC
40715838 TCGAGGTAGGCCG
1 TCGAGGTAGGCCG
40715851 TCGAGGTAGGCCG
1 TCGAGGTAGGCCG
40715864 TC
1 TC
40715866 TAGAAACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (13 bp):
TCGAGGTAGGCCG
Found at i:40717622 original size:29 final size:29
Alignment explanation
Indices: 40717560--40717662 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 29
40717550 CGGTGACGAT
* * *
40717560 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
40717589 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * **
40717618 TGGCACTATGTGTGCGGGCTT-GAATCACG
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
40717647 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40717663 TGATTGAGTA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
28 3 0.05
29 56 0.95
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:40730103 original size:28 final size:30
Alignment explanation
Indices: 40730060--40730119 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
40730050 AAAGCTTATC
* *
40730060 TTTTATTTAAACATTTGA-TTTT-ACTCAA
1 TTTTAATTAAAAATTTGAGTTTTGACTCAA
*
40730088 TTTTAATTAAAAATTTTAGTTTTGACTCAA
1 TTTTAATTAAAAATTTGAGTTTTGACTCAA
40730118 TT
1 TT
40730120 AAGGGTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 15 0.56
29 4 0.15
30 8 0.30
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTTAATTAAAAATTTGAGTTTTGACTCAA
Found at i:40730256 original size:29 final size:28
Alignment explanation
Indices: 40730215--40730278 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
40730205 TATAATTTTA
*
40730215 TATTCTTTAGAAAGATT-AAATCAAAATTT
1 TATTATTTAGAAAG-TTAAAAT-AAAATTT
* *
40730244 TATTATTTTGAAAGTTCAAAATGAAATTT
1 TATTATTTAGAAAGTT-AAAATAAAATTT
40730273 TATTAT
1 TATTAT
40730279 GTATTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 2 0.07
29 24 0.80
30 4 0.13
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (28 bp):
TATTATTTAGAAAGTTAAAATAAAATTT
Found at i:40730955 original size:29 final size:29
Alignment explanation
Indices: 40730913--40730970 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
40730903 TATTGTCATT
40730913 TAGATTTGAAGTTTGTTGTTGGATTTGAA
1 TAGATTTGAAGTTTGTTGTTGGATTTGAA
40730942 TAGATTTGAAGTTTGTTGTTGGATTTGAA
1 TAGATTTGAAGTTTGTTGTTGGATTTGAA
40730971 GTTACAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (29 bp):
TAGATTTGAAGTTTGTTGTTGGATTTGAA
Found at i:40734475 original size:197 final size:196
Alignment explanation
Indices: 40734141--40734527 Score: 711
Period size: 197 Copynumber: 2.0 Consensus size: 196
40734131 ATAGCAACAA
*
40734141 GCTATCTCATCAAACTCTTCCTAGCGTTTTCTAGCCTTAACTTGAGTGGTCGAGGGCACTTAGTA
1 GCTATCTCATCAAACTCTTCCTAGCATTTTCTAGCCTTAACTTGAGTGGTCGAGGGCACTTAGTA
*
40734206 TCAAGAACAATTTTAAGTTTCTCACAACTTAAGACAATTATCAATTTCCTTTTCCATTCATTACA
66 TCAAGAACAATTTTAAGTTTCTCACAACTTAAGACAATTATCAAGTTCCTTTTCCATTCATTACA
40734271 GTTGTTTCCGTTGAGTTTGTTTTCAGTGACTATGTTCAATAAGGGAGTTGGTGCCATTTTTTTGT
131 GTTGTTTCCGTTGAGTTTGTTTTCAGTGACTATGTTCAATAAGGGAGTTGGTGCCATTTTTTTGT
40734336 T
196 T
*
40734337 GCTATCTCATCAAACTCTTCCTAGCATTTTCTGGCCTTAACTTGAGTGGTCGGAGGGCACTTAGT
1 GCTATCTCATCAAACTCTTCCTAGCATTTTCTAGCCTTAACTTGAGTGGTC-GAGGGCACTTAGT
* * *
40734402 ATCAAGAACATTTTTAAGTTTCTCACAACTTAAGACAATTATCAAGTTCCTTTTCCATTCCTTAT
65 ATCAAGAACAATTTTAAGTTTCTCACAACTTAAGACAATTATCAAGTTCCTTTTCCATTCATTAC
40734467 AGTTGTTTCCGTTGAGTTTGTTTTCAGTGACTATGTTCAATAAGGGAGTTGGTGCCATTTT
130 AGTTGTTTCCGTTGAGTTTGTTTTCAGTGACTATGTTCAATAAGGGAGTTGGTGCCATTTT
40734528 CATATTGAAA
Statistics
Matches: 184, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
196 49 0.27
197 135 0.73
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (196 bp):
GCTATCTCATCAAACTCTTCCTAGCATTTTCTAGCCTTAACTTGAGTGGTCGAGGGCACTTAGTA
TCAAGAACAATTTTAAGTTTCTCACAACTTAAGACAATTATCAAGTTCCTTTTCCATTCATTACA
GTTGTTTCCGTTGAGTTTGTTTTCAGTGACTATGTTCAATAAGGGAGTTGGTGCCATTTTTTTGT
T
Found at i:40739900 original size:54 final size:54
Alignment explanation
Indices: 40739828--40739950 Score: 138
Period size: 54 Copynumber: 2.3 Consensus size: 54
40739818 GTTTTATCAA
* * * * * *
40739828 AAAACCCTAAAACTCTAAACCCCAAAAAATCATAAACATTAATCTATAACCCTT
1 AAAACCCTAAACCCCTAAACCCCAAAAAACCATAAACACTAAACTATAACCCCT
* ** * * *
40739882 AAAACACTAAACCCCTAAACCTTAAGAAACCTTAAACACTAAAGTATAACCCCT
1 AAAACCCTAAACCCCTAAACCCCAAAAAACCATAAACACTAAACTATAACCCCT
40739936 AAAACCCTAAACCCC
1 AAAACCCTAAACCCC
40739951 AAAAAACATC
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.19
Consensus pattern (54 bp):
AAAACCCTAAACCCCTAAACCCCAAAAAACCATAAACACTAAACTATAACCCCT
Found at i:40740068 original size:7 final size:7
Alignment explanation
Indices: 40740057--40740120 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
40740047 TTTATTTTTG
*
40740057 GGTTTAG
1 GGTTTAA
40740064 GGTTTAA
1 GGTTTAA
**
40740071 TATTTAA
1 GGTTTAA
40740078 GGTTTAA
1 GGTTTAA
* *
40740085 GGTCTAT
1 GGTTTAA
*
40740092 GGTTTAG
1 GGTTTAA
*
40740099 GGTTTTAT
1 GG-TTTAA
40740107 GGTTTAA
1 GGTTTAA
40740114 GGTTTAA
1 GGTTTAA
40740121 TGGCCATGGG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (7 bp):
GGTTTAA
Found at i:40740109 original size:15 final size:15
Alignment explanation
Indices: 40740073--40740123 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
40740063 GGGTTTAATA
*
40740073 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* *
40740087 TCTATGGTTTAGGGT
1 TTTATGGTTTAAGGT
40740102 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
40740117 TTAATGG
1 TTTATGG
40740124 CCATGGGTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:40740435 original size:7 final size:7
Alignment explanation
Indices: 40740359--40740437 Score: 59
Period size: 7 Copynumber: 10.9 Consensus size: 7
40740349 AGGGGTAGAA
40740359 GTTTAGG
1 GTTTAGG
*
40740366 GTTTATG
1 GTTTAGG
* *
40740373 TTTTATG
1 GTTTAGG
*
40740380 GCTTAGG
1 GTTTAGG
40740387 GTTTAAGG
1 GTTT-AGG
* *
40740395 GTTAAGA
1 GTTTAGG
*
40740402 GTTAAGG
1 GTTTAGG
40740409 GTTTACGG
1 GTTTA-GG
*
40740417 GTTATGGG
1 GTT-TAGG
40740425 GTTTAGG
1 GTTTAGG
40740432 GTTTAG
1 GTTTAG
40740438 AATTTAAGTG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
7 40 0.70
8 16 0.28
9 1 0.02
ACGTcount: A:0.19, C:0.03, G:0.37, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:40740482 original size:21 final size:20
Alignment explanation
Indices: 40740457--40740511 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
40740447 GTTAGTAGTT
*
40740457 TTAGGGTTAAGAGGACATGGG
1 TTAGGGTTAAG-GGACAGGGG
**
40740478 TTAGGGGTTAAGGGTTAGGGG
1 TTA-GGGTTAAGGGACAGGGG
*
40740499 TTAGGGTTTAGGG
1 TTAGGGTTAAGGG
40740512 TAATTAGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 9 0.31
21 12 0.41
22 8 0.28
ACGTcount: A:0.22, C:0.02, G:0.47, T:0.29
Consensus pattern (20 bp):
TTAGGGTTAAGGGACAGGGG
Found at i:40740487 original size:7 final size:7
Alignment explanation
Indices: 40740475--40740511 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
40740465 AAGAGGACAT
40740475 GGGTTAG
1 GGGTTAG
*
40740482 GGGTTAA
1 GGGTTAG
40740489 GGGTTAG
1 GGGTTAG
40740496 GGGTTAG
1 GGGTTAG
*
40740503 GGTTTAG
1 GGGTTAG
40740510 GG
1 GG
40740512 TAATTAGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.16, C:0.00, G:0.54, T:0.30
Consensus pattern (7 bp):
GGGTTAG
Found at i:40740640 original size:17 final size:17
Alignment explanation
Indices: 40740614--40740657 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
40740604 AATCTATATA
* *
40740614 TTAAATAATTTCAAATT
1 TTAAAAAATTTAAAATT
*
40740631 TTAAAGAA-TTAAAATT
1 TTAAAAAATTTAAAATT
40740647 TTAAAAAATTT
1 TTAAAAAATTT
40740658 TCAAGATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAAAAAATTTAAAATT
Found at i:40740655 original size:26 final size:26
Alignment explanation
Indices: 40740626--40740675 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
40740616 AAATAATTTC
40740626 AAATTTTAAAGAATTAAAATTTTAAA
1 AAATTTTAAAGAATTAAAATTTTAAA
* * *
40740652 AAATTTTCAAGATTTCAAATTTTA
1 AAATTTTAAAGAATTAAAATTTTA
40740676 TCTAATTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (26 bp):
AAATTTTAAAGAATTAAAATTTTAAA
Found at i:40740808 original size:15 final size:16
Alignment explanation
Indices: 40740788--40740818 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40740778 TAAGTGATTG
40740788 TTTTTAA-TTTATATT
1 TTTTTAATTTTATATT
40740803 TTTTTAATTTTATATT
1 TTTTTAATTTTATATT
40740819 AAATAGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTAATTTTATATT
Found at i:40741354 original size:115 final size:114
Alignment explanation
Indices: 40740924--40741375 Score: 573
Period size: 116 Copynumber: 3.9 Consensus size: 114
40740914 ATATAATTAT
* * * * * * *
40740924 GTTTTAAACAAAACGACG-CTGTTTTATTGGATTTGTTAGTGGCGTTTTGTGTAAAATGTCGCAA
1 GTTTAAAACAAAACGGCGAC-GTTTTGTTGGA-TTATTAGTGGCGTTTTGAGTAAAACGCCGCAA
* *
40740988 TAGGTGTGTTTTTAGCGGCACTAGGGTATAAACGCCACTAAAGGTGATTTC
64 TAGGTGCGTTTTTAGCGGCGCTAGGGTATAAACGCCACTAAAGGTGATTTC
* **
40741039 GTTTAAAACAAAACGGCGAAGTTTTGTTGGATTATTAGTGGCGTTTTAGGAAAAAAACGCCGCAA
1 GTTTAAAACAAAACGGCGACGTTTTGTTGGATTATTAGTGGCGTTTT--GAGTAAAACGCCGCAA
* *
40741104 TTGGTGCGTTTTTAGCGGCGCTAGGGTATAAACGCCACTAAAGGTGATTCC
64 TAGGTGCGTTTTTAGCGGCGCTAGGGTATAAACGCCACTAAAGGTGATTTC
* * * * * *
40741155 GGTTAAAACAAAAAGGGCGACGTTTTGTTGGATTATTAGTGGCATTTTAAGGTTAAATGCCGCAA
1 GTTTAAAAC-AAAACGGCGACGTTTTGTTGGATTATTAGTGGCGTTTTGA-GTAAAACGCCGCAA
* * * * * *
40741220 TATGTGCGTTTTTAACGGCGCTAGGTTAAAAACGCCGCTAAAGATGATTTC
64 TAGGTGCGTTTTTAGCGGCGCTAGGGTATAAACGCCACTAAAGGTGATTTC
* *
40741271 GTTTAAAACAAAACGGTGACGTTTTGTTGAATTATTAGTGGCGTTTTGGAGTAAAACGCCGCAAT
1 GTTTAAAACAAAACGGCGACGTTTTGTTGGATTATTAGTGGCGTTTT-GAGTAAAACGCCGCAAT
*
40741336 AGGTGCGTTTTTAGCGGCGCTAGGGTATAAACGCCGCTAA
65 AGGTGCGTTTTTAGCGGCGCTAGGGTATAAACGCCACTAA
40741376 TGTTAAATTA
Statistics
Matches: 288, Mismatches: 43, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
114 15 0.05
115 110 0.38
116 128 0.44
117 35 0.12
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.31
Consensus pattern (114 bp):
GTTTAAAACAAAACGGCGACGTTTTGTTGGATTATTAGTGGCGTTTTGAGTAAAACGCCGCAATA
GGTGCGTTTTTAGCGGCGCTAGGGTATAAACGCCACTAAAGGTGATTTC
Found at i:40744225 original size:52 final size:52
Alignment explanation
Indices: 40744157--40744382 Score: 303
Period size: 52 Copynumber: 4.3 Consensus size: 52
40744147 ATATCATATA
* * *
40744157 ATAATTTAGAAAACTTACATAATACATAAATATATATCATATCATAACTTAC
1 ATAACTTACAAAACTTACATAATACATAAATATATATCATATAATAACTTAC
*
40744209 GTAACTTACAAAACTTACATAATACATAAATATATATCATATAATAACTTAC
1 ATAACTTACAAAACTTACATAATACATAAATATATATCATATAATAACTTAC
40744261 ATAACTTACAAAACTTACATAATACATAAATATATATCATATAATAACTTAC
1 ATAACTTACAAAACTTACATAATACATAAATATATATCATATAATAACTTAC
* * * * * * * *
40744313 AAAACTTACATAA--TACATACCTTATATAATTTTATATCATATCATAACTTGC
1 ATAACTTACAAAACTTACATA--ATACATAAATATATATCATATAATAACTTAC
*
40744365 ATAACATACAAAACTTAC
1 ATAACTTACAAAACTTAC
40744383 TTACCTTACG
Statistics
Matches: 154, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
50 6 0.04
52 145 0.94
54 3 0.02
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.34
Consensus pattern (52 bp):
ATAACTTACAAAACTTACATAATACATAAATATATATCATATAATAACTTAC
Found at i:40744264 original size:9 final size:9
Alignment explanation
Indices: 40744252--40744382 Score: 60
Period size: 9 Copynumber: 15.0 Consensus size: 9
40744242 ATATCATATA
40744252 ATAACTTAC
1 ATAACTTAC
40744261 ATAACTTAC
1 ATAACTTAC
*
40744270 AAAACTTAC
1 ATAACTTAC
40744279 ATAA--TAC
1 ATAACTTAC
* *
40744286 ATAA-ATAT
1 ATAACTTAC
*
40744294 ATATCATATA-
1 ATAAC-T-TAC
40744304 ATAACTTAC
1 ATAACTTAC
*
40744313 AAAACTTAC
1 ATAACTTAC
40744322 ATAA--TAC
1 ATAACTTAC
* *
40744329 ATACCTTAT
1 ATAACTTAC
**
40744338 ATAA-TTTT
1 ATAACTTAC
* *
40744346 ATATCATATC
1 ATAACTTA-C
*
40744356 ATAACTTGC
1 ATAACTTAC
*
40744365 ATAACATAC
1 ATAACTTAC
*
40744374 AAAACTTAC
1 ATAACTTAC
40744383 TTACCTTACG
Statistics
Matches: 90, Mismatches: 23, Indels: 18
0.69 0.18 0.14
Matches are distributed among these distances:
7 13 0.14
8 13 0.14
9 53 0.59
10 9 0.10
11 2 0.02
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:40744277 original size:18 final size:18
Alignment explanation
Indices: 40744202--40744282 Score: 71
Period size: 18 Copynumber: 4.6 Consensus size: 18
40744192 ATCATATCAT
*
40744202 AACTTACGTAACTTACAA
1 AACTTACATAACTTACAA
40744220 AACTTACATAA--TACATA
1 AACTTACATAACTTACA-A
* * * *
40744237 AA--TATATATCATATAA
1 AACTTACATAACTTACAA
40744253 TAACTTACATAACTTACAA
1 -AACTTACATAACTTACAA
40744272 AACTTACATAA
1 AACTTACATAA
40744283 TACATAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
15 5 0.10
16 5 0.10
17 8 0.16
18 21 0.43
19 10 0.20
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (18 bp):
AACTTACATAACTTACAA
Found at i:40748674 original size:27 final size:28
Alignment explanation
Indices: 40748617--40748686 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
40748607 AAAATTGTAC
**
40748617 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
40748645 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
40748672 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
40748687 GACTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:40748695 original size:27 final size:28
Alignment explanation
Indices: 40748588--40748698 Score: 102
Period size: 27 Copynumber: 4.0 Consensus size: 28
40748578 GACAAGATTG
* * *
40748588 GCACTAAGTGTGCGGATTTAAAATTGTACA
1 GCACTAAGTGTGCGGACTT--AATTATATA
* * *
40748618 GCACTAAGTGTGCGAATTTGATTATATA
1 GCACTAAGTGTGCGGACTTAATTATATA
* *
40748646 GCACTATGTGTGC-GAGC-TGATTATATA
1 GCACTAAGTGTGCGGA-CTTAATTATATA
40748673 GCACTAAGTGTGCGGACTT-ATTATAT
1 GCACTAAGTGTGCGGACTTAATTATAT
40748699 GCTTTTGTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
27 31 0.44
28 21 0.30
30 18 0.26
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGGACTTAATTATATA
Found at i:40756595 original size:27 final size:28
Alignment explanation
Indices: 40756538--40756607 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
40756528 AAAATTGTAC
**
40756538 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
40756566 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
40756593 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
40756608 GACTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:40756616 original size:27 final size:28
Alignment explanation
Indices: 40756509--40756619 Score: 102
Period size: 27 Copynumber: 4.0 Consensus size: 28
40756499 GACAAGATTG
* * *
40756509 GCACTAAGTGTGCGGATTTAAAATTGTACA
1 GCACTAAGTGTGCGGACTT--AATTATATA
* * *
40756539 GCACTAAGTGTGCGAATTTGATTATATA
1 GCACTAAGTGTGCGGACTTAATTATATA
* *
40756567 GCACTATGTGTGC-GAGC-TGATTATATA
1 GCACTAAGTGTGCGGA-CTTAATTATATA
40756594 GCACTAAGTGTGCGGACTT-ATTATAT
1 GCACTAAGTGTGCGGACTTAATTATAT
40756620 GCTTTTGCAT
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
27 31 0.44
28 21 0.30
30 18 0.26
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGGACTTAATTATATA
Found at i:40760584 original size:13 final size:13
Alignment explanation
Indices: 40760568--40760600 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
40760558 TTATAAATAT
*
40760568 TTATAATGTTTCA
1 TTATAATGTTTAA
40760581 TTATAATGTTTAA
1 TTATAATGTTTAA
40760594 TTATAAT
1 TTATAAT
40760601 TCATCGTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (13 bp):
TTATAATGTTTAA
Found at i:40761013 original size:21 final size:21
Alignment explanation
Indices: 40760980--40761019 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40760970 TAGAGTGGAT
*
40760980 GCAGAAGCGAGGGAGGCAGTG
1 GCAGAAGCAAGGGAGGCAGTG
*
40761001 GCAGCAGCAAGGGAGGCAG
1 GCAGAAGCAAGGGAGGCAG
40761020 AGCAGAGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.50, T:0.03
Consensus pattern (21 bp):
GCAGAAGCAAGGGAGGCAGTG
Found at i:40761305 original size:31 final size:32
Alignment explanation
Indices: 40761243--40761323 Score: 110
Period size: 31 Copynumber: 2.5 Consensus size: 32
40761233 TTAGATTTAA
* ** *
40761243 TGTTTTTGGTTGTATTTTTTATGCTATATTTGT
1 TGTTTTTGGTTGGATTTACTAT-CTATATTTGC
40761276 TGTTTTTGGTTGGATTTACTAT-TATATTTGC
1 TGTTTTTGGTTGGATTTACTATCTATATTTGC
40761307 TGTTTTTGGTTGGATTT
1 TGTTTTTGGTTGGATTT
40761324 TAATGCAGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 25 0.57
33 19 0.43
ACGTcount: A:0.12, C:0.04, G:0.21, T:0.63
Consensus pattern (32 bp):
TGTTTTTGGTTGGATTTACTATCTATATTTGC
Found at i:40761428 original size:43 final size:43
Alignment explanation
Indices: 40761379--40761515 Score: 150
Period size: 43 Copynumber: 3.2 Consensus size: 43
40761369 TCTGTCAAAA
* * *
40761379 TTAGCGGC-GTTTGTAACAAAAATGCCGCAAAAAGTCATGACTT
1 TTAGCGGCACTTT-TAACACAAATGCCGCTAAAAGTCATGACTT
* * * **
40761422 TTAGCGGCACTTTTATCACAAACGCCTCTAAAAGAAATGACTT
1 TTAGCGGCACTTTTAACACAAATGCCGCTAAAAGTCATGACTT
* ** *
40761465 TTAGAGGCACTTTTCCCACAAATGCCGCTAAAAGTCATGGCTT
1 TTAGCGGCACTTTTAACACAAATGCCGCTAAAAGTCATGACTT
40761508 TTAGCGGC
1 TTAGCGGC
40761516 GTTTTTTCAG
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
43 73 0.96
44 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (43 bp):
TTAGCGGCACTTTTAACACAAATGCCGCTAAAAGTCATGACTT
Found at i:40765380 original size:2 final size:2
Alignment explanation
Indices: 40765373--40765404 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40765363 GTTCATGCTC
40765373 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40765405 GTATCCTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40766111 original size:132 final size:131
Alignment explanation
Indices: 40765619--40766121 Score: 559
Period size: 132 Copynumber: 3.8 Consensus size: 131
40765609 TTATTTGGGC
* * * *** *
40765619 TCGTTGACCTAAGATCACAACCAATACAGCTCGCTGACCTAA-ATCGCAGCCAAAATTATTTGGT
1 TCGTTGACATAAGATCACGACCTATGTGGCTCGCTGACCTAAGATCGCAGCCAAAATTATTTGGG
* ** * * **
40765683 TTCACTGACCTAAGATCACATGCCATACAACT-AGCCGACCTAAGATTGTGACTGAAATTATTTG
66 TTCGCTGACCTAAGATCACAACCCATACAGCTCA-CCGACCTAAGA-TCTGACTGAAATTATTCA
40765747 GGT
129 GGT
* * * * * *
40765750 TCGCTGACGTAAGATCACGACCTATGTGGCTTGTTGACCTAAGATCGCATCCAAAATAATTTGGG
1 TCGTTGACATAAGATCACGACCTATGTGGCTCGCTGACCTAAGATCGCAGCCAAAATTATTTGGG
** **
40765815 TTCGCTGACCTAAGATCACAACCCATACAGCTTGCCGACCTAAGATC-GCAGCCAAAATTATTCA
66 TTCGCTGACCTAAGATCACAACCCATACAGCTCACCGACCTAAGATCTG-A-CTGAAATTATTCA
40765879 GGT
129 GGT
* ** * *
40765882 TCGTTGACATAAGATCACGACCTATGTGGCTCACCAACCTAAAATTGCAGCCAAAATT-TTTCGG
1 TCGTTGACATAAGATCACGACCTATGTGGCTCGCTGACCTAAGATCGCAGCCAAAATTATTT-GG
40765946 GTTCG-TAGACCTAAGATCACAACCCATACAGCTCACCGACCTAAGATCATGACTGAAATTATTC
65 GTTCGCT-GACCTAAGATCACAACCCATACAGCTCACCGACCTAAGATC-TGACTGAAATTATTC
40766010 AGGT
128 AGGT
* * * *
40766014 CCATTGACATAAGATCACGACCTATGTGGCTCGCCT-ACCTAAGATTGCAACCAAAATTATTTGG
1 TCGTTGACATAAGATCACGACCTATGTGGCTCG-CTGACCTAAGATCGCAGCCAAAATTATTTGG
* * * *
40766078 GTTTGTTGACCTAAGATCACAACCCATATAGCTCACTGACCTAA
65 GTTCGCTGACCTAAGATCACAACCCATACAGCTCACCGACCTAA
40766122 AATTGCGGCT
Statistics
Matches: 315, Mismatches: 46, Indels: 21
0.82 0.12 0.05
Matches are distributed among these distances:
130 1 0.00
131 39 0.12
132 268 0.85
133 6 0.02
134 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (131 bp):
TCGTTGACATAAGATCACGACCTATGTGGCTCGCTGACCTAAGATCGCAGCCAAAATTATTTGGG
TTCGCTGACCTAAGATCACAACCCATACAGCTCACCGACCTAAGATCTGACTGAAATTATTCAGG
T
Found at i:40766120 original size:66 final size:66
Alignment explanation
Indices: 40765587--40766127 Score: 392
Period size: 66 Copynumber: 8.2 Consensus size: 66
40765577 TAACCTTCAT
** * * *
40765587 TGACCTAAGATTGCAAGTAAAATTATTTGGGCTCGTTGACCTAAGATCACAACCAATACAGCTCG
1 TGACCTAAGATTGCAACCAAAATTATTTGGGTTCGTTGACCTAAGATCACAACCCATACAGCTCA
40765652 C
66 C
* * * ** ** *
40765653 TGACCTAA-ATCGCAGCCAAAATTATTTGGTTTCACTGACCTAAGATCACATGCCATACAACT-A
1 TGACCTAAGATTGCAACCAAAATTATTTGGGTTCGTTGACCTAAGATCACAACCCATACAGCTCA
40765716 GC
66 -C
* ** ** * * * * *** **
40765718 CGACCTAAGATTGTGACTGAAATTATTTGGGTTCGCTGACGTAAGATCACGACCTATGTGGCTTG
1 TGACCTAAGATTGCAACCAAAATTATTTGGGTTCGTTGACCTAAGATCACAACCCATACAGCTCA
*
40765783 T
66 C
* * * * **
40765784 TGACCTAAGATCGCATCCAAAATAATTTGGGTTCGCTGACCTAAGATCACAACCCATACAGCTTG
1 TGACCTAAGATTGCAACCAAAATTATTTGGGTTCGTTGACCTAAGATCACAACCCATACAGCTCA
40765849 C
66 C
* * * ** * * * ***
40765850 CGACCTAAGATCGCAGCCAAAATTATTCAGGTTCGTTGACATAAGATCACGACCTATGTGGCTCA
1 TGACCTAAGATTGCAACCAAAATTATTTGGGTTCGTTGACCTAAGATCACAACCCATACAGCTCA
40765915 C
66 C
** * * *
40765916 CAACCTAAAATTGCAGCCAAAATT-TTTCGGGTTCGTAGACCTAAGATCACAACCCATACAGCTC
1 TGACCTAAGATTGCAACCAAAATTATTT-GGGTTCGTTGACCTAAGATCACAACCCATACAGCTC
40765980 AC
65 AC
* ** ** * * * * * ***
40765982 CGACCTAAGA-T-CATGACTGAAATTATTCAGGTCCATTGACATAAGATCACGACCTATGTGGCT
1 TGACCTAAGATTGCA--ACCAAAATTATTTGGGTTCGTTGACCTAAGATCACAACCCATACAGCT
*
40766045 CGCC
64 C-AC
* *
40766049 T-ACCTAAGATTGCAACCAAAATTATTTGGGTTTGTTGACCTAAGATCACAACCCATATAGCTCA
1 TGACCTAAGATTGCAACCAAAATTATTTGGGTTCGTTGACCTAAGATCACAACCCATACAGCTCA
40766113 C
66 C
*
40766114 TGACCTAAAATTGC
1 TGACCTAAGATTGC
40766128 GGCTAATGTA
Statistics
Matches: 358, Mismatches: 106, Indels: 22
0.74 0.22 0.05
Matches are distributed among these distances:
64 2 0.01
65 55 0.15
66 295 0.82
67 4 0.01
68 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (66 bp):
TGACCTAAGATTGCAACCAAAATTATTTGGGTTCGTTGACCTAAGATCACAACCCATACAGCTCA
C
Found at i:40766682 original size:17 final size:17
Alignment explanation
Indices: 40766650--40766682 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40766640 CAACTTCTAC
40766650 TTAGTTTTAAACATTAT
1 TTAGTTTTAAACATTAT
40766667 TTAGTCTTTAAA-ATTA
1 TTAGT-TTTAAACATTA
40766683 AGTTTTTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
TTAGTTTTAAACATTAT
Found at i:40776081 original size:3 final size:3
Alignment explanation
Indices: 40776067--40776115 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
40776057 ACCAAATGCA
* * *
40776067 AAG AAG ACG AAG AAG AAG AAA AAG AAG AAA AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
40776115 A
1 A
40776116 GAAAAGTAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40777773 original size:16 final size:16
Alignment explanation
Indices: 40777752--40777803 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
40777742 TTCTATTTAA
40777752 TAATATAATAAATTAT
1 TAATATAATAAATTAT
40777768 TAATATAAT---TTAT
1 TAATATAATAAATTAT
* *
40777781 TATTTTAATAAATTATT
1 TAATATAATAAATTA-T
40777798 TAATAT
1 TAATAT
40777804 TACAAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
13 11 0.39
16 12 0.43
17 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATATAATAAATTAT
Found at i:40777778 original size:29 final size:30
Alignment explanation
Indices: 40777746--40777803 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
40777736 AAGTATTTCT
40777746 ATTTAATAATATAATAAATTA-TTAATATA
1 ATTTAATAATATAATAAATTATTTAATATA
* * *
40777775 ATTTATTATTTTAATAAATTATTTAATAT
1 ATTTAATAATATAATAAATTATTTAATAT
40777804 TACAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTAATAATATAATAAATTATTTAATATA
Found at i:40777837 original size:16 final size:15
Alignment explanation
Indices: 40777818--40777847 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40777808 AATTTATTTT
40777818 AATAATAATTATTAAC
1 AATAATAATT-TTAAC
40777834 AATAATAATTTTAA
1 AATAATAATTTTAA
40777848 ATTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAATAATTTTAAC
Found at i:40778441 original size:23 final size:23
Alignment explanation
Indices: 40778390--40778451 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
40778380 TTGCATTAAA
40778390 AAAATAATAAATATTTTATAGTAT
1 AAAAT-ATAAATATTTTATAGTAT
*
40778414 AAAATATGAAA-ATTTTA-ATTAT
1 AAAATAT-AAATATTTTATAGTAT
40778436 ATAAATATAAATATTT
1 A-AAATATAAATATTT
40778452 GTTTAAATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
22 8 0.24
23 18 0.53
24 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
AAAATATAAATATTTTATAGTAT
Found at i:40779123 original size:31 final size:29
Alignment explanation
Indices: 40779055--40779126 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 29
40779045 TAATACATGG
40779055 ACTTTAATTTGGTTCAATTATAAATATGAA
1 ACTTTAATTTGGTTCAATTATAAATA-GAA
*
40779085 ACTTTTAATTGTGGTTCAAAGTTATACATA-AA
1 AC-TTTAATT-TGGTTC-AA-TTATAAATAGAA
40779117 ACTTTAATTT
1 ACTTTAATTT
40779127 TGATTTAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
30 3 0.08
31 14 0.38
32 10 0.27
33 2 0.05
34 8 0.22
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (29 bp):
ACTTTAATTTGGTTCAATTATAAATAGAA
Found at i:40786242 original size:3 final size:3
Alignment explanation
Indices: 40786236--40786262 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40786226 CTTGAGGTGA
40786236 AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG
40786263 GAATTTAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:40796036 original size:47 final size:47
Alignment explanation
Indices: 40795933--40796058 Score: 170
Period size: 47 Copynumber: 2.7 Consensus size: 47
40795923 GTATAATACT
40795933 GATGCCATGTCCCAGACATGGTCTTACACT-GACTTACATCAAGAGGCC
1 GATGCCATGTCCCAGACAT-GTCTTACACTAG-CTTACATCAAGAGGCC
* *
40795981 GATG-CATGTCCCAGACATGTCTTACACTAGCTCT-CATCTCA-ATGCC
1 GATGCCATGTCCCAGACATGTCTTACACTAGCT-TACATC-AAGAGGCC
40796027 GATGCCATGTCCCAGACATGTCTTACACTAGC
1 GATGCCATGTCCCAGACATGTCTTACACTAGC
40796059 ACACAAATAT
Statistics
Matches: 72, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
46 24 0.33
47 44 0.61
48 4 0.06
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGTCTTACACTAGCTTACATCAAGAGGCC
Found at i:40796778 original size:22 final size:22
Alignment explanation
Indices: 40796759--40796802 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
40796749 CCTCAAAAGT
40796759 ACAAAAATATTCAAGAAAAACC
1 ACAAAAATATTCAAGAAAAACC
40796781 ACAAAAATATTCAAGAAAAACC
1 ACAAAAATATTCAAGAAAAACC
40796803 CTCAAACCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.64, C:0.18, G:0.05, T:0.14
Consensus pattern (22 bp):
ACAAAAATATTCAAGAAAAACC
Found at i:40803861 original size:29 final size:29
Alignment explanation
Indices: 40803828--40803901 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
40803818 GTGACGAGAT
40803828 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
40803857 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
40803886 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40803902 AGCTCGAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:40803917 original size:29 final size:29
Alignment explanation
Indices: 40803885--40803960 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
40803875 CTGGAAATAT
* *
40803885 ATGGCACTAAGTGTGCGAGCTCGAAGGGC
1 ATGGCACTAAGTGTGCGAGCTCAAAGCGC
** * * *
40803914 ATGGCACTGTGTGTGCGGGCTTAAATCGC
1 ATGGCACTAAGTGTGCGAGCTCAAAGCGC
40803943 ATGGCACTAAGTGTGCGA
1 ATGGCACTAAGTGTGCGA
40803961 AATCGAGTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGCTCAAAGCGC
Found at i:40803928 original size:58 final size:58
Alignment explanation
Indices: 40803828--40803960 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
40803818 GTGACGAGAT
* * * * * *
40803828 TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAAT-ATA
1 TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCT-GAAATCACA
* * ** * * *
40803886 TGGCACTAAGTGTGCGAGCTCGAAGGGCATGGCACTGTGTGTGCGGGCTTAAATCGCA
1 TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCTGAAATCACA
40803944 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
40803961 AATCGAGTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (58 bp):
TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCTGAAATCACA
Found at i:40811744 original size:29 final size:29
Alignment explanation
Indices: 40811711--40811784 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
40811701 GTGACGAGAT
40811711 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
40811740 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
40811769 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40811785 AGCTCGAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:40811800 original size:29 final size:29
Alignment explanation
Indices: 40811768--40811843 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
40811758 CTGGAAATAT
* *
40811768 ATGGCACTAAGTGTGCGAGCTCGAAGGGC
1 ATGGCACTAAGTGTGCGAGCTCAAAGCGC
** * * *
40811797 ATGGCACTGTGTGTGCGGGCTTAAATCGC
1 ATGGCACTAAGTGTGCGAGCTCAAAGCGC
40811826 ATGGCACTAAGTGTGCGA
1 ATGGCACTAAGTGTGCGA
40811844 AATCGAGTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGCTCAAAGCGC
Found at i:40811811 original size:58 final size:58
Alignment explanation
Indices: 40811711--40811843 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
40811701 GTGACGAGAT
* * * * * *
40811711 TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAAT-ATA
1 TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCT-GAAATCACA
* * ** * * *
40811769 TGGCACTAAGTGTGCGAGCTCGAAGGGCATGGCACTGTGTGTGCGGGCTTAAATCGCA
1 TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCTGAAATCACA
40811827 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
40811844 AATCGAGTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (58 bp):
TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCTGAAATCACA
Found at i:40817216 original size:14 final size:13
Alignment explanation
Indices: 40817187--40817231 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
40817177 AGTGGGTGGA
40817187 AATAATATT-A-T
1 AATAATATTAAGT
40817198 AATAATATTAAAGT
1 AATAATATT-AAGT
*
40817212 TATAATA-TAAGT
1 AATAATATTAAGT
40817224 AATAATAT
1 AATAATAT
40817232 GTATATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 9 0.32
12 10 0.36
13 2 0.07
14 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AATAATATTAAGT
Found at i:40817623 original size:9 final size:9
Alignment explanation
Indices: 40817609--40817637 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
40817599 GACTAAAATG
40817609 TGAAATAAA
1 TGAAATAAA
40817618 TGAAATAAA
1 TGAAATAAA
40817627 TGAAATAAA
1 TGAAATAAA
40817636 TG
1 TG
40817638 GACTAGTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (9 bp):
TGAAATAAA
Found at i:40818578 original size:50 final size:51
Alignment explanation
Indices: 40818385--40818577 Score: 162
Period size: 50 Copynumber: 3.8 Consensus size: 51
40818375 ATCTTGTATT
* * *
40818385 TATTCGGCCACATAGGTATGTACATATGTGATGTTATA-TTGAATCTTGAA
1 TATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGAATCTTGAA
* * * * *
40818435 TATTTGACCATGA-AGGTATGCACAAAAGTGATATTATATTTGAAT-TTGTA
1 TATTCGGCCAT-ATAGGTATGCACATATGTGATATTATATTTGAATCTTGAA
* * * * * * * *
40818485 TATTCAGCCATAT-GAGTAAGTACTTAGGTGATGTTAAATTTG-ATCTTGCA
1 TATTCGGCCATATAG-GTATGCACATATGTGATATTATATTTGAATCTTGAA
* * *
40818535 TATTTGGCCATATAGGTATGCACATTTGTGATATTATCTTTGA
1 TATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGA
40818578 TTCTCTATAA
Statistics
Matches: 107, Mismatches: 29, Indels: 13
0.72 0.19 0.09
Matches are distributed among these distances:
49 4 0.04
50 95 0.89
51 8 0.07
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (51 bp):
TATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGAATCTTGAA
Found at i:40818644 original size:2 final size:2
Alignment explanation
Indices: 40818637--40818661 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40818627 GATTCACGAG
40818637 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40818662 TTGAATGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40822125 original size:10 final size:10
Alignment explanation
Indices: 40822110--40822138 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
40822100 TACATTCAGT
40822110 AAAACATTTC
1 AAAACATTTC
40822120 AAAACATTTC
1 AAAACATTTC
40822130 AAAACATTT
1 AAAACATTT
40822139 GAAAGCAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAACATTTC
Found at i:40834714 original size:28 final size:29
Alignment explanation
Indices: 40834631--40834726 Score: 158
Period size: 29 Copynumber: 3.3 Consensus size: 29
40834621 GAAAGCATGA
40834631 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
40834660 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
40834689 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
40834717 ATATGCATGT
1 ATATGAATGT
40834727 ATGTAGACTT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
28 23 0.37
29 40 0.63
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:40838204 original size:39 final size:39
Alignment explanation
Indices: 40838160--40838234 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
40838150 TTCCTAAACT
40838160 TAGGGAAACAACCTAAAAGTTTTTAATTCTTCAAAAATC
1 TAGGGAAACAACCTAAAAGTTTTTAATTCTTCAAAAATC
40838199 TAGGGAAACAACCTAAAAGTTTTTAATTCTTCAAAA
1 TAGGGAAACAACCTAAAAGTTTTTAATTCTTCAAAA
40838235 GTCAACTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (39 bp):
TAGGGAAACAACCTAAAAGTTTTTAATTCTTCAAAAATC
Found at i:40849366 original size:16 final size:16
Alignment explanation
Indices: 40849345--40849391 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
40849335 GGCAAATCCC
*
40849345 GAAATGCCGAAAAGCA
1 GAAATGCTGAAAAGCA
*
40849361 GAAATGCTAAAAAGCA
1 GAAATGCTGAAAAGCA
40849377 GAAATGCTGAAAAGC
1 GAAATGCTGAAAAGC
40849392 TGAAGGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.23, T:0.11
Consensus pattern (16 bp):
GAAATGCTGAAAAGCA
Found at i:40849718 original size:28 final size:29
Alignment explanation
Indices: 40849607--40849781 Score: 284
Period size: 28 Copynumber: 6.1 Consensus size: 29
40849597 GAAAGCATGA
*
40849607 ATATGAATGTTATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
40849636 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
40849665 ATATGAATGTGATTTGGGCCAAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
40849694 ATATGAATGTGA-TTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
40849722 ATATGAATGTGA-TTGGGTCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
40849750 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
40849778 ATAT
1 ATAT
40849782 ACATGTATGT
Statistics
Matches: 139, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
28 71 0.51
29 68 0.49
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:40853722 original size:25 final size:25
Alignment explanation
Indices: 40853683--40853740 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
40853673 TCATGTACAA
* *
40853683 GTATGCTTATATGAGCTGTGAATCG
1 GTATGCTCATATGAGCTGTAAATCG
* *
40853708 GTATGCTCATTTGAGCTGTAAATTG
1 GTATGCTCATATGAGCTGTAAATCG
40853733 GTATGCTC
1 GTATGCTC
40853741 TCACAAGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (25 bp):
GTATGCTCATATGAGCTGTAAATCG
Found at i:40857944 original size:4 final size:4
Alignment explanation
Indices: 40857935--40857969 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
40857925 ACAATAAACT
40857935 TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAA
1 TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAA
40857970 TATAGCATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAC
Found at i:40862421 original size:21 final size:20
Alignment explanation
Indices: 40862381--40862421 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
40862371 GGCCACCGAA
*
40862381 GGGTGGTCGCAGCTGCCAAG
1 GGGTGGTCGCAGCCGCCAAG
*
40862401 GGGTGGTCAGTAGCCGCCAAG
1 GGGTGGTC-GCAGCCGCCAAG
40862422 AGGCCGTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.24, G:0.44, T:0.15
Consensus pattern (20 bp):
GGGTGGTCGCAGCCGCCAAG
Found at i:40870710 original size:27 final size:28
Alignment explanation
Indices: 40870654--40870723 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
40870644 AAATTTGTAC
40870654 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
40870682 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
40870709 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40870724 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:40870734 original size:27 final size:27
Alignment explanation
Indices: 40870654--40870735 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
40870644 AAATTTGTAC
* *
40870654 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
40870682 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
*
40870709 AGCACTGAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
40870736 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:40875736 original size:41 final size:41
Alignment explanation
Indices: 40875691--40875808 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
40875681 TGAAAGATAA
40875691 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
40875732 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
40875762 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
40875803 ATGTAG
1 ATGTAG
40875809 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:40875745 original size:71 final size:71
Alignment explanation
Indices: 40875659--40875822 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
40875649 GAGATGTATC
40875659 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
40875724 AGGACA
66 AGGACA
40875730 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
40875795 AGGACA
66 AGGACA
40875801 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
40875823 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:40877670 original size:22 final size:22
Alignment explanation
Indices: 40877606--40877670 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 22
40877596 GGAAATACGT
* * * *
40877606 TTGGCACAAAGCCATAGTCAAG
1 TTGGCACAGAGCCATAATTAGG
* * **
40877628 ATGGCATAGAGCCATTTTTAGG
1 TTGGCACAGAGCCATAATTAGG
40877650 TTGGCACAGAGCCATAATTAG
1 TTGGCACAGAGCCATAATTAG
40877671 ATTAAACGGC
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (22 bp):
TTGGCACAGAGCCATAATTAGG
Found at i:40878052 original size:27 final size:27
Alignment explanation
Indices: 40878019--40878106 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
40878009 CAAAATAGTC
* *
40878019 ATTTTACCCTACAAGCGTATTTCAGTA
1 ATTTTACACTACAAGCGTATTTCAATA
* *
40878046 ATTTTACACTACAAGGGTATTTTAATA
1 ATTTTACACTACAAGCGTATTTCAATA
* * * *
40878073 A-TTTACA-AACTAGGGGTATTTCAGTA
1 ATTTTACACTAC-AAGCGTATTTCAATA
40878099 ATTTTACA
1 ATTTTACA
40878107 AGTCGGGGGT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 2 0.04
26 19 0.37
27 30 0.59
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (27 bp):
ATTTTACACTACAAGCGTATTTCAATA
Found at i:40878114 original size:26 final size:26
Alignment explanation
Indices: 40878035--40878114 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 26
40878025 CCCTACAAGC
*
40878035 GTATTTCAGTAATTTTAC-ACTACAAGG
1 GTATTTCAGTAATTTTACAACT-C-GGG
* * *
40878062 GTATTTTAATAA-TTTACAAACTAGGG
1 GTATTTCAGTAATTTTAC-AACTCGGG
*
40878088 GTATTTCAGTAATTTTACAAGTCGGG
1 GTATTTCAGTAATTTTACAACTCGGG
40878114 G
1 G
40878115 GTCTTAACGA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
26 24 0.57
27 15 0.36
28 3 0.07
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.38
Consensus pattern (26 bp):
GTATTTCAGTAATTTTACAACTCGGG
Found at i:40879322 original size:34 final size:34
Alignment explanation
Indices: 40879279--40879349 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
40879269 ACGTAAGAAC
*
40879279 AACTCCTATATTCAACTTTTCAATTCTATACTAA
1 AACTCCTATATTCAACCTTTCAATTCTATACTAA
**
40879313 AACTCCTATATTCGGCCTTTCAATTCTATACTAA
1 AACTCCTATATTCAACCTTTCAATTCTATACTAA
40879347 AAC
1 AAC
40879350 AACAAAGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (34 bp):
AACTCCTATATTCAACCTTTCAATTCTATACTAA
Found at i:40885287 original size:23 final size:24
Alignment explanation
Indices: 40885243--40885287 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
40885233 ATGCTCAGAT
*
40885243 TCATCACATGAATAAATTAATATG
1 TCATCACATGAATAAATCAATATG
40885267 TCATCA-ATGAATACAA-CAATA
1 TCATCACATGAATA-AATCAATA
40885288 AATTGATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.29
Consensus pattern (24 bp):
TCATCACATGAATAAATCAATATG
Found at i:40892217 original size:42 final size:43
Alignment explanation
Indices: 40892120--40892273 Score: 154
Period size: 42 Copynumber: 3.6 Consensus size: 43
40892110 GGTACAATGT
** * *
40892120 CGATGTCCCAGACATGGTCTTACATGTAATTCAG-TATTGATGC
1 CGATGTCCCAGACATGGTCTTACA-CAAAATCAGATATCGATGC
** *
40892163 CTCTGTCCCAGACAAGGTCTTACACAAAATCAGATA-CGATGC
1 CGATGTCCCAGACATGGTCTTACACAAAATCAGATATCGATGC
* *
40892205 CGATGTCCCAGACATGGTCTTACACATAAATCTCGA-ATCGAGGC
1 CGATGTCCCAGACATGGTCTTACACA-AAATC-AGATATCGATGC
*
40892249 C-AGTGTCCCAGACACGGTCTTACAC
1 CGA-TGTCCCAGACATGGTCTTACAC
40892274 GACATCTCAG
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
42 34 0.37
43 30 0.32
44 29 0.31
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
CGATGTCCCAGACATGGTCTTACACAAAATCAGATATCGATGC
Found at i:40894418 original size:20 final size:20
Alignment explanation
Indices: 40894381--40894417 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
40894371 GACTAAACCG
40894381 AGAACTATAGAAATTTTTAC
1 AGAACTATAGAAATTTTTAC
40894401 AGAACT-TAGAAATTTTT
1 AGAACTATAGAAATTTTT
40894418 TCTACTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (20 bp):
AGAACTATAGAAATTTTTAC
Found at i:40899606 original size:43 final size:43
Alignment explanation
Indices: 40899470--40899621 Score: 150
Period size: 43 Copynumber: 3.5 Consensus size: 43
40899460 ATACGATTAC
* *
40899470 CGATATTTGATTTCGTGTAAGACCATGTTTGGGA-TGTCGGCAT
1 CGATATTTGATTTCATGTAAGACCATGTTTGGGACAGT-GGCAT
* ** ** *
40899513 AGAT-TTGTGATTTACATGTAAGACCATGTCCGAGG-CAACGACAT
1 CGATATT-TGATTT-CATGTAAGACCATGTTTG-GGACAGTGGCAT
*
40899557 CG-TATTTGATTTCATGTAAGACCCTGTTTGGGACAGTGGCAT
1 CGATATTTGATTTCATGTAAGACCATGTTTGGGACAGTGGCAT
*
40899599 CGATATTTGATTACATGTAAGAC
1 CGATATTTGATTTCATGTAAGAC
40899622 GACATATGGA
Statistics
Matches: 86, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
41 2 0.02
42 25 0.29
43 35 0.41
44 22 0.26
45 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (43 bp):
CGATATTTGATTTCATGTAAGACCATGTTTGGGACAGTGGCAT
Found at i:40901520 original size:23 final size:22
Alignment explanation
Indices: 40901493--40901542 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
40901483 TGCCTAAAAT
40901493 GACACACGAGGTGCCTG-ATAC
1 GACACACGAGGTGCCTGAATAC
40901514 GACACACGAGGTGCCTGAAATAC
1 GACACACGAGGTGCCTG-AATAC
40901537 GACACA
1 GACACA
40901543 TAAAGTGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.63
23 10 0.37
ACGTcount: A:0.34, C:0.28, G:0.26, T:0.12
Consensus pattern (22 bp):
GACACACGAGGTGCCTGAATAC
Found at i:40901550 original size:23 final size:23
Alignment explanation
Indices: 40901468--40901554 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
40901458 CCTGATCAGT
*
40901468 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* * *
40901490 A-ATGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
40901510 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
40901533 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
40901555 TCAGTACAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 32 0.60
22 1 0.02
23 19 0.36
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:40901953 original size:15 final size:14
Alignment explanation
Indices: 40901929--40901968 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
40901919 TATATATTAT
40901929 ATAATTCAATCAAA
1 ATAATTCAATCAAA
*
40901943 ATAATTTCAATCAAT
1 ATAA-TTCAATCAAA
40901958 ATAAATTCAAT
1 AT-AATTCAAT
40901969 AAATTCATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 17 0.74
16 2 0.09
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATTCAATCAAA
Found at i:40905572 original size:31 final size:31
Alignment explanation
Indices: 40905537--40905600 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40905527 CCTTTTCATG
40905537 TTTCATATTCCATAACACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
* **
40905568 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
40905599 TT
1 TT
40905601 ACTGTAACGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATATTCCATAACACTGGGCCGAAGCCT
Found at i:40905866 original size:47 final size:48
Alignment explanation
Indices: 40905791--40905932 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
40905781 GCTTTATCAT
* *
40905791 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
40905840 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
40905887 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
40905933 TGCACTTCCT
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
47 44 0.51
48 30 0.35
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:40905891 original size:71 final size:72
Alignment explanation
Indices: 40905791--40905932 Score: 216
Period size: 71 Copynumber: 2.0 Consensus size: 72
40905781 GCTTTATCAT
*
40905791 ATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAG
1 ATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAG
40905856 CCCTTTA
66 CCCTTTA
* * **
40905863 ATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAA
1 ATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
40905926 GCCCTTT
65 GCCCTTT
40905933 TGCACTTCCT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 52 0.81
72 12 0.19
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (72 bp):
ATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAG
CCCTTTA
Done.