Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 30 of 136
Found at i:9706589 original size:7 final size:7
Alignment explanation
Indices: 9706577--9706624 Score: 96
Period size: 7 Copynumber: 6.9 Consensus size: 7
9706567 TTTAACATTG
9706577 ATGATTA
1 ATGATTA
9706584 ATGATTA
1 ATGATTA
9706591 ATGATTA
1 ATGATTA
9706598 ATGATTA
1 ATGATTA
9706605 ATGATTA
1 ATGATTA
9706612 ATGATTA
1 ATGATTA
9706619 ATGATT
1 ATGATT
9706625 CAATTCTATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (7 bp):
ATGATTA
Found at i:9708311 original size:23 final size:24
Alignment explanation
Indices: 9708285--9708334 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
9708275 TATTATTTTT
9708285 ATTTG-TTATTTTTTATGTGTAGA
1 ATTTGTTTATTTTTTATGTGTAGA
*
9708308 ATTTGTTTTTTTTTTATGTGTAGA
1 ATTTGTTTATTTTTTATGTGTAGA
9708332 ATT
1 ATT
9708335 CATTTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (24 bp):
ATTTGTTTATTTTTTATGTGTAGA
Found at i:9713087 original size:301 final size:304
Alignment explanation
Indices: 9712510--9713097 Score: 792
Period size: 301 Copynumber: 1.9 Consensus size: 304
9712500 CCTAATCATC
**
9712510 ATAATGAGCCCCTTTGATTCATTGAAAATAAAGCAAATGCTATCTTGTCTAACAACATGCCTCCG
1 ATAATGAGCCCCTTTGATTCATCAAAAATAAAGCAAATGCTATCTTGTCTAACAACATGCCTCCG
* * *
9712575 CAAGTTTGTCAAAAAAAATTACCACAATTCCATGTTCCCTTTCTCCACAATTTGCAAAAGCTATC
66 CAAGTTTCTCAAAAAAAATTACCACAATTCCATGTTCCCTTTCTCCACAATTGGCAAAAGCAATC
* * * *
9712640 AGCAGTACATTTTAGTTATCATCTTGTACAACTGCGATAAGGAGGATTTGCCTATATTTCTCAAT
131 AGCAGTACATTCTAGTTACCATCTTGTACAACTGCAATAAGGAGGATTTGCATATATTTCTCAAT
* * * ** * * * *
9712705 ATAGCTAGGTTCCATCAACTTGTACAATCGGCTAATAGTGAGTAAAGACCCTACCGTATGGATTA
196 ACAACTAGGTTCCATAAACCAGCACAATCGGCTAATAGTGAGGAAAGACCCTAACGTATGGATCA
*
9712770 AATGTCTAGAACAAGCGATGGAAAATTTAGAACACCTAATTGTG
261 AATGTCAAGAACAAGCGATGGAAAATTTAGAACACCTAATTGTG
* * * * * *
9712814 ATAATGAGCCCTTTTGA-TCAATCAAAAATCAAGTAAATGTTGTCTTGTCTAACAACATGCCTCT
1 ATAATGAGCCCCTTTGATTC-ATCAAAAATAAAGCAAATGCTATCTTGTCTAACAACATGCCTCC
* * *
9712878 GCAAGTTTCTC-AAAAAAATTGCCACAATT-CATTGTTCTCTTTCTCCACAA-TGGCAAAGGCAA
65 GCAAGTTTCTCAAAAAAAATTACCACAATTCCA-TGTTCCCTTTCTCCACAATTGGCAAAAGCAA
* * * *
9712940 TCAGCAGTACGTTCTAGTTACCATCTTGTACAACTGTAATAAGGAGGATTTGTATATATTTC-CC
129 TCAGCAGTACATTCTAGTTACCATCTTGTACAACTGCAATAAGGAGGATTTGCATATATTTCTCA
* * *
9713004 ATACAATTAGGTTCCATAAACCAGCACAAAT-GGCTAATAGTGAGGAAAGGCCTTAACGTATGGA
194 ATACAACTAGGTTCCATAAACCAGCAC-AATCGGCTAATAGTGAGGAAAGACCCTAACGTATGGA
9713068 TCAAATGTCAAGAACAAGCGATGGAAAATT
258 TCAAATGTCAAGAACAAGCGATGGAAAATT
9713098 CTTTTCCCTG
Statistics
Matches: 246, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
301 78 0.32
302 69 0.28
303 36 0.15
304 63 0.26
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (304 bp):
ATAATGAGCCCCTTTGATTCATCAAAAATAAAGCAAATGCTATCTTGTCTAACAACATGCCTCCG
CAAGTTTCTCAAAAAAAATTACCACAATTCCATGTTCCCTTTCTCCACAATTGGCAAAAGCAATC
AGCAGTACATTCTAGTTACCATCTTGTACAACTGCAATAAGGAGGATTTGCATATATTTCTCAAT
ACAACTAGGTTCCATAAACCAGCACAATCGGCTAATAGTGAGGAAAGACCCTAACGTATGGATCA
AATGTCAAGAACAAGCGATGGAAAATTTAGAACACCTAATTGTG
Found at i:9715044 original size:12 final size:12
Alignment explanation
Indices: 9715015--9715053 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
9715005 GGTTTTCTCC
9715015 AAAATGGAAATG
1 AAAATGGAAATG
**
9715027 GGAATGGAAATG
1 AAAATGGAAATG
9715039 AAAATGAGAAATG
1 AAAATG-GAAATG
9715052 AA
1 AA
9715054 TTCATTTAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.15
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:9715080 original size:68 final size:69
Alignment explanation
Indices: 9714960--9715088 Score: 179
Period size: 68 Copynumber: 1.9 Consensus size: 69
9714950 TTTTCTCAAA
* *** * *
9714960 AATGAAAATGAAAATGGAGAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGGAAA
1 AATGAAAATGAAAATGGAGAAATGAAATCATTTAGAAATGAACAAGGATTTCTCAAAAATGGAAA
9715025 TGGG
66 TGGG
* *
9715029 AATGGAAATGAAAAT-GAGAAATGAATTCATTTAGAAATGAACAAGGATTTCTCAAAAATG
1 AATGAAAATGAAAATGGAGAAATGAAATCATTTAGAAATGAACAAGGATTTCTCAAAAATG
9715089 ATCGTAAGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
68 38 0.73
69 14 0.27
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.26
Consensus pattern (69 bp):
AATGAAAATGAAAATGGAGAAATGAAATCATTTAGAAATGAACAAGGATTTCTCAAAAATGGAAA
TGGG
Found at i:9715747 original size:9 final size:10
Alignment explanation
Indices: 9715728--9715765 Score: 62
Period size: 9 Copynumber: 4.0 Consensus size: 10
9715718 AGTTCATGTG
9715728 TTTGATTCGA
1 TTTGATTCGA
9715738 TTTG-TTCGA
1 TTTGATTCGA
9715747 TTTGATTCGA
1 TTTGATTCGA
9715757 TTTG-TTCGA
1 TTTGATTCGA
9715766 ACTTACACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 14 0.52
10 13 0.48
ACGTcount: A:0.16, C:0.11, G:0.21, T:0.53
Consensus pattern (10 bp):
TTTGATTCGA
Found at i:9715752 original size:19 final size:19
Alignment explanation
Indices: 9715728--9715765 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9715718 AGTTCATGTG
9715728 TTTGATTCGATTTGTTCGA
1 TTTGATTCGATTTGTTCGA
9715747 TTTGATTCGATTTGTTCGA
1 TTTGATTCGATTTGTTCGA
9715766 ACTTACACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.21, T:0.53
Consensus pattern (19 bp):
TTTGATTCGATTTGTTCGA
Found at i:9720765 original size:33 final size:33
Alignment explanation
Indices: 9720719--9720811 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
9720709 AGACTTCCCG
*
9720719 TGTTTACTGTCCCAACGAACTTACTCTATTCTA
1 TGTTTACTGTCCCAACGAACTTACTCTATTCCA
* * * *
9720752 TGTTTACTATCCCAATGAACTTACTTTATTCCC
1 TGTTTACTGTCCCAACGAACTTACTCTATTCCA
*
9720785 TGTTTACTGCCCCAACGAACTTACTCT
1 TGTTTACTGTCCCAACGAACTTACTCT
9720812 GTGGACGCCA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.39
Consensus pattern (33 bp):
TGTTTACTGTCCCAACGAACTTACTCTATTCCA
Found at i:9722547 original size:13 final size:15
Alignment explanation
Indices: 9722512--9722542 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9722502 AATAGTCTAA
9722512 ACATCCTCCTACCAC
1 ACATCCTCCTACCAC
9722527 ACATCCTCCTACCAC
1 ACATCCTCCTACCAC
9722542 A
1 A
9722543 ACCTCAATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.52, G:0.00, T:0.19
Consensus pattern (15 bp):
ACATCCTCCTACCAC
Found at i:9724261 original size:25 final size:25
Alignment explanation
Indices: 9724233--9724287 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
9724223 AAGAGAATGG
* *
9724233 AAAATAA-AGAAAAAGAAAGAAAGTT
1 AAAATAACA-AAAAAGAAAAAAAATT
* *
9724258 AAAAGAACATAAAAGAAAAAAAATT
1 AAAATAACAAAAAAGAAAAAAAATT
9724283 AAAAT
1 AAAAT
9724288 GCTCAAAACG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.13
Consensus pattern (25 bp):
AAAATAACAAAAAAGAAAAAAAATT
Found at i:9740049 original size:27 final size:27
Alignment explanation
Indices: 9740017--9740073 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
9740007 AAAAAAAAAA
9740017 TGATTGCAATCATTTCAAGAGAAATTC
1 TGATTGCAATCATTTCAAGAGAAATTC
*
9740044 TGATTGCAATCATTTCAAGAGACATTC
1 TGATTGCAATCATTTCAAGAGAAATTC
9740071 TGA
1 TGA
9740074 ATGTGCAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (27 bp):
TGATTGCAATCATTTCAAGAGAAATTC
Found at i:9741498 original size:22 final size:23
Alignment explanation
Indices: 9741466--9741529 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
9741456 ATAAATTAAA
9741466 ATATATTAAATT-ATTTTATAATT
1 ATATA-TAAATTAATTTTATAATT
* *
9741489 TTATATAAATTTAATTTTATTATT
1 ATATATAAA-TTAATTTTATAATT
*
9741513 ATATAATAAATAAATTT
1 ATAT-ATAAATTAATTT
9741530 AAATCATCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.12
23 6 0.18
24 19 0.56
25 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATATAAATTAATTTTATAATT
Found at i:9751216 original size:45 final size:45
Alignment explanation
Indices: 9751160--9751254 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
9751150 TACTATGTGA
* * *
9751160 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
9751205 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
9751250 ACCGA
1 ACCGA
9751255 GTATCTATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:9757211 original size:21 final size:21
Alignment explanation
Indices: 9757168--9757211 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
9757158 CCTCAATTAA
* * *
9757168 CAGGTGTAGGATTTGCAAGTG
1 CAGGAGTAGGATTAGCAACTG
*
9757189 CAGGAGTAGGATTAGCACCTG
1 CAGGAGTAGGATTAGCAACTG
9757210 CA
1 CA
9757212 ATCCTCTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.23
Consensus pattern (21 bp):
CAGGAGTAGGATTAGCAACTG
Found at i:9761377 original size:45 final size:45
Alignment explanation
Indices: 9761262--9761379 Score: 141
Period size: 45 Copynumber: 2.6 Consensus size: 45
9761252 GCTATACGCC
*
9761262 TAAAAA-GAGTAAGACCATAGCTAAAAGATGTTATGGCATCATGA
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGA
** * *
9761306 TAAAAATGAGTAAGATTATAGTTGAAATATGTTATGGCATCATGA
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGA
* * *
9761351 TAAATACT-ATTAATACCATAGCTGAAAGA
1 TAAA-AATGAGTAAGACCATAGCTGAAAGA
9761380 CGCTATTGCA
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
44 6 0.10
45 52 0.87
46 2 0.03
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (45 bp):
TAAAAATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGA
Found at i:9761470 original size:27 final size:26
Alignment explanation
Indices: 9761408--9761470 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
9761398 TAGTCCGTCG
* *
9761408 GGACAGTAAACATGGGTAGTCCACCA
1 GGACAGTAAACACGGGTACTCCACCA
* *
9761434 GGAAAATAAACACGGAGTACTCCACCA
1 GGACAGTAAACACGG-GTACTCCACCA
*
9761461 GGACCGTAAA
1 GGACAGTAAA
9761471 TACGAGAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.13
Consensus pattern (26 bp):
GGACAGTAAACACGGGTACTCCACCA
Found at i:9763912 original size:21 final size:20
Alignment explanation
Indices: 9763883--9763922 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9763873 GAATTTGATT
*
9763883 TAAGAATTTTTTTGGAAAATC
1 TAAGAA-TTTTTGGGAAAATC
*
9763904 TAAGTATTTTTGGGAAAAT
1 TAAGAATTTTTGGGAAAAT
9763923 TAATTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (20 bp):
TAAGAATTTTTGGGAAAATC
Found at i:9772269 original size:90 final size:89
Alignment explanation
Indices: 9772069--9772419 Score: 374
Period size: 90 Copynumber: 3.9 Consensus size: 89
9772059 TTCAGGGTGT
* * * *
9772069 AAAAAGCCCCCAAACTTTCTT-AAAAAAAGCAATTAA-ACTCT--TTTTTTTTTCCACTCAATTA
1 AAAAAGCCCTCAAACTTT-TTCAAAAAAAGCAATTAAGCCTCTGCTTTTTTTTTACACTCAATTG
*
9772130 GGTACTTGAACTTTTAAAAATGCAT-
65 GGTACTTGAAC-TTTCAAAATGCATC
* * *
9772155 AAAAACGACCCTTAAACTTTTTCAAAAAAAGCCATTAAGCCTCTGCTTTTTTTTTTCACTCAATT
1 AAAAA-G-CCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCTCTGCTTTTTTTTTACACTCAATT
*
9772220 GGGAACTTGAACTTTCAAAATGCATC
64 GGGTACTTGAACTTTCAAAATGCATC
* * * * *
9772246 AAAAATGCCCTCAAACTTTTTCAATAAAAGCCATTAAACCCCTGC-TTTTTTTTACACTTAATTG
1 AAAAA-GCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCTCTGCTTTTTTTTTACACTCAATTG
* *
9772310 GGTACTTAAACTTTCAAAATGAATC
65 GGTACTTGAACTTTCAAAATGCATC
* * **
9772335 AAAAAGGCCCTCAAAATTTTTTCAAAAAAAGCAATTAAGCC-CTTACTTTTTTTTGGGCACTCAA
1 AAAAA-GCCCTC-AAACTTTTTCAAAAAAAGCAATTAAGCCTC-TGCTTTTTTTT-TACACTCAA
* *
9772399 TTGGGTACTTGATCTGTCAAA
62 TTGGGTACTTGAACTTTCAAA
9772420 TTGTTGATCT
Statistics
Matches: 224, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
86 5 0.02
87 3 0.01
88 24 0.11
89 55 0.25
90 72 0.32
91 41 0.18
92 24 0.11
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.34
Consensus pattern (89 bp):
AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCTCTGCTTTTTTTTTACACTCAATTGG
GTACTTGAACTTTCAAAATGCATC
Found at i:9772588 original size:9 final size:9
Alignment explanation
Indices: 9772552--9772648 Score: 65
Period size: 10 Copynumber: 10.6 Consensus size: 9
9772542 ACATGTGACA
9772552 AAAAATTAT
1 AAAAATTAT
9772561 AAAAA--AT
1 AAAAATTAT
*
9772568 AAAAATCAAT
1 AAAAAT-TAT
*
9772578 AAAAGTTAT
1 AAAAATTAT
9772587 AAAAATTATT
1 AAAAATTA-T
*
9772597 AAAATTTAAT
1 AAAAATT-AT
9772607 AAAAA-TAT
1 AAAAATTAT
*
9772615 AAAAATATTT
1 AAAAAT-TAT
* *
9772625 GAAATTTACT
1 AAAAATTA-T
*
9772635 AAAAATTAG
1 AAAAATTAT
9772644 AAAAA
1 AAAAA
9772649 AATATAAAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
7 7 0.10
8 7 0.10
9 21 0.31
10 32 0.47
11 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:9772590 original size:19 final size:20
Alignment explanation
Indices: 9772565--9772612 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
9772555 AATTATAAAA
9772565 AATAAAAATCAATAAAAGTT
1 AATAAAAATCAATAAAAGTT
* * *
9772585 -ATAAAAATTATTAAAATTT
1 AATAAAAATCAATAAAAGTT
9772604 AATAAAAAT
1 AATAAAAAT
9772613 ATAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAAAAATCAATAAAAGTT
Found at i:9772615 original size:28 final size:28
Alignment explanation
Indices: 9772575--9772658 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 28
9772565 AATAAAAATC
*
9772575 AATAAAAGTTATAAAAAT-TATTAAAATTT
1 AATAAAA-ATATAAAAATAT-TTAAAATTT
*
9772604 AATAAAAATATAAAAATATTTGAAATTT
1 AATAAAAATATAAAAATATTTAAAATTT
* * * *
9772632 ACTAAAAATTAGAAAAAAATATAAAAT
1 AATAAAAA-TATAAAAATATTTAAAAT
9772659 GCATCAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 24 0.52
29 22 0.48
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (28 bp):
AATAAAAATATAAAAATATTTAAAATTT
Found at i:9772871 original size:20 final size:19
Alignment explanation
Indices: 9772846--9772910 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
9772836 GTATAGTAAT
9772846 TTTTATATTTTTTTTACAAA
1 TTTTATA-TTTTTTTACAAA
* *
9772866 TTTTATATTTCTTTACATA
1 TTTTATATTTTTTTACAAA
*
9772885 TTTTATAATTTTCTTA-AAA
1 TTTTAT-ATTTTTTTACAAA
*
9772904 CTTTATA
1 TTTTATA
9772911 AAACTTTANN
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 1 0.03
19 23 0.61
20 14 0.37
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTATATTTTTTTACAAA
Found at i:9772882 original size:19 final size:20
Alignment explanation
Indices: 9772846--9772899 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
9772836 GTATAGTAAT
*
9772846 TTTTATATTTTTTTTACAAA
1 TTTTATATTTTCTTTACAAA
*
9772866 TTTTATA-TTTCTTTACATA
1 TTTTATATTTTCTTTACAAA
9772885 TTTTATAATTTTCTT
1 TTTTAT-ATTTTCTT
9772900 AAAACTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 16 0.53
20 8 0.27
21 6 0.20
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATATTTTCTTTACAAA
Found at i:9780705 original size:2 final size:2
Alignment explanation
Indices: 9780698--9780722 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9780688 TGTGAAAATA
9780698 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9780723 GTTATATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9783619 original size:17 final size:18
Alignment explanation
Indices: 9783593--9783628 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
9783583 GTTTAAAATT
*
9783593 AATTTTAGAAAA-TAAAA
1 AATTTAAGAAAATTAAAA
9783610 AATTTAAGAAAATTAAAA
1 AATTTAAGAAAATTAAAA
9783628 A
1 A
9783629 GATAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (18 bp):
AATTTAAGAAAATTAAAA
Found at i:9783665 original size:21 final size:20
Alignment explanation
Indices: 9783640--9783707 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
9783630 ATAAAATGAC
9783640 TTTTCCTGTAAAGACCCAAGT
1 TTTTCCTGTAAA-ACCCAAGT
* *
9783661 TTTTCCTATAAAATCC-AGT
1 TTTTCCTGTAAAACCCAAGT
*
9783680 TAATTTCCTGTAAAACCCTATGT
1 T--TTTCCTGTAAAACCC-AAGT
9783703 TTTTC
1 TTTTC
9783708 TCTTTTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 28 0.74
23 3 0.08
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (20 bp):
TTTTCCTGTAAAACCCAAGT
Found at i:9788044 original size:25 final size:25
Alignment explanation
Indices: 9788011--9788145 Score: 111
Period size: 25 Copynumber: 5.4 Consensus size: 25
9788001 GAGCCTATAA
*
9788011 CGGGTAGCTCCGAAGAGCCATTAAT
1 CGGGAAGCTCCGAAGAGCCATTAAT
* * *
9788036 CGGGGAGCTCCGGATAGCCA-TATAT
1 CGGGAAGCTCCGAAGAGCCATTA-AT
*
9788061 CGGGAAG-TTC-AAGCGAGCCA-T-AT
1 CGGGAAGCTCCGAA--GAGCCATTAAT
*
9788084 CGGGAAGCTCACAAAGAGCCAATTAA-
1 CGGGAAGCTC-CGAAGAGCC-ATTAAT
9788110 CGGGAAGCTCACGAAGAGCCATATAAT
1 CGGGAAGCTC-CGAAGAGCCAT-TAAT
9788137 CGGGAAGCT
1 CGGGAAGCT
9788146 TATAAGAGCT
Statistics
Matches: 90, Mismatches: 9, Indels: 20
0.76 0.08 0.17
Matches are distributed among these distances:
23 10 0.11
24 10 0.11
25 35 0.39
26 25 0.28
27 10 0.11
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16
Consensus pattern (25 bp):
CGGGAAGCTCCGAAGAGCCATTAAT
Found at i:9788154 original size:26 final size:27
Alignment explanation
Indices: 9788082--9788145 Score: 96
Period size: 26 Copynumber: 2.4 Consensus size: 27
9788072 AGCGAGCCAT
9788082 ATCGGGAAGCTCACAAAGAGCCAATTA
1 ATCGGGAAGCTCACAAAGAGCCAATTA
*
9788109 A-CGGGAAGCTCACGAAGAGCC-ATATA
1 ATCGGGAAGCTCACAAAGAGCCAAT-TA
9788135 ATCGGGAAGCT
1 ATCGGGAAGCT
9788146 TATAAGAGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 2 0.06
26 22 0.65
27 10 0.29
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.14
Consensus pattern (27 bp):
ATCGGGAAGCTCACAAAGAGCCAATTA
Found at i:9797311 original size:18 final size:18
Alignment explanation
Indices: 9797277--9797325 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
9797267 TATATCTCAC
9797277 ATCAAAAAATAATTTAAAA
1 ATCAAAAAAT-ATTTAAAA
* *
9797296 ATTATAAAATATTTAAAA
1 ATCAAAAAATATTTAAAA
9797314 ATCAAAAAATAT
1 ATCAAAAAATAT
9797326 AAAAAGTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
ATCAAAAAATATTTAAAA
Found at i:9797340 original size:18 final size:17
Alignment explanation
Indices: 9797291--9797347 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
9797281 AAAAATAATT
9797291 TAAAAATT-ATAAAATA
1 TAAAAATTCATAAAATA
*
9797307 TTTAAAAA-TCAAAAAATA
1 --TAAAAATTCATAAAATA
9797325 TAAAAAGTTCATAAAAT-
1 TAAAAA-TTCATAAAATA
9797342 TAAAAA
1 TAAAAA
9797348 AAATGAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 21 0.62
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (17 bp):
TAAAAATTCATAAAATA
Found at i:9813869 original size:17 final size:17
Alignment explanation
Indices: 9813831--9813879 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
9813821 AATTTTAAAA
*
9813831 TATTTTTAAAAT--ACT
1 TATTTTTAAAATAAATT
9813846 T-TTTTTAAAATAAATT
1 TATTTTTAAAATAAATT
9813862 TATTTTTAAAATAAATT
1 TATTTTTAAAATAAATT
9813879 T
1 T
9813880 TTAGTGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 3 0.10
17 16 0.53
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTTTAAAATAAATT
Found at i:9818996 original size:43 final size:43
Alignment explanation
Indices: 9818935--9819021 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
9818925 TCAAATTCCT
9818935 ACTTGCCTTTGAGTAGCCATTTAAGATTCTATAAAAGGCTAAA
1 ACTTGCCTTTGAGTAGCCATTTAAGATTCTATAAAAGGCTAAA
* *
9818978 ACTTGTCTTTGAGTAGCCATTTAAGATTCTATAATAGGCTAAA
1 ACTTGCCTTTGAGTAGCCATTTAAGATTCTATAAAAGGCTAAA
9819021 A
1 A
9819022 GTTTTCATGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (43 bp):
ACTTGCCTTTGAGTAGCCATTTAAGATTCTATAAAAGGCTAAA
Found at i:9822628 original size:20 final size:20
Alignment explanation
Indices: 9822605--9822659 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
9822595 ACATAGACAC
9822605 TAGTAAGTTCATTTAGAAAT
1 TAGTAAGTTCATTTAGAAAT
9822625 TAGTAAGTTCATTTAGAAAT
1 TAGTAAGTTCATTTAGAAAT
9822645 TAGTAAGTTCATTTA
1 TAGTAAGTTCATTTA
9822660 AACATTGTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (20 bp):
TAGTAAGTTCATTTAGAAAT
Found at i:9823373 original size:21 final size:21
Alignment explanation
Indices: 9823349--9823397 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
9823339 CTAAACTTAG
*
9823349 CATCGCCTGAGGTTTGCCCAT
1 CATCGCCTAAGGTTTGCCCAT
9823370 CATCGCCTAAGGTTTGCCCAT
1 CATCGCCTAAGGTTTGCCCAT
*
9823391 CGTCGCC
1 CATCGCC
9823398 CCTGGGACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.14, C:0.37, G:0.22, T:0.27
Consensus pattern (21 bp):
CATCGCCTAAGGTTTGCCCAT
Found at i:9826261 original size:40 final size:39
Alignment explanation
Indices: 9826202--9826365 Score: 170
Period size: 40 Copynumber: 4.1 Consensus size: 39
9826192 CTTCTTTGAC
* * *
9826202 ACACAACTTGTCC-TTAGCTCACAAGGAAGTTGTGTTGAT
1 ACACAACTTATCCATAAGCTCACAAGGAAGTT-TGCTGAT
* *
9826241 ACACAACTTATCCATAAGCTCACAGAGGAACTTTACTGAT
1 ACACAACTTATCCATAAGCTCACA-AGGAAGTTTGCTGAT
**
9826281 ACACAGTTTATCCATAAGCTCAC-AGGAGAGCTTTGCTGAT
1 ACACAACTTATCCATAAGCTCACAAGGA-AG-TTTGCTGAT
* * * *
9826321 ACACAACTTATCCATAAACTCACATGGGAGCTTTTCTGAT
1 ACACAACTTATCCATAAGCTCACAAGGAAG-TTTGCTGAT
9826361 ACACA
1 ACACA
9826366 GCTTGGAAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
38 4 0.04
39 13 0.12
40 79 0.75
41 9 0.09
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (39 bp):
ACACAACTTATCCATAAGCTCACAAGGAAGTTTGCTGAT
Found at i:9831968 original size:44 final size:43
Alignment explanation
Indices: 9831920--9832034 Score: 133
Period size: 44 Copynumber: 2.7 Consensus size: 43
9831910 TGTGATTTCG
* *
9831920 TGTAAGACCACGCCTGGGACATTGGCATCGAT-TTGAGATTTACA
1 TGTAAGACCTCGTCTGGGACATTGGCATCGATATT-AGA-TTACA
* * * *
9831964 TGTAAGACCTTGTCTGGGATAGTGGCATCGATATTTGATTACA
1 TGTAAGACCTCGTCTGGGACATTGGCATCGATATTAGATTACA
* *
9832007 TGTAAAACCTCGTCTGGGACGTTGGCAT
1 TGTAAGACCTCGTCTGGGACATTGGCAT
9832035 TATACTAGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 28 0.47
44 29 0.49
45 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
TGTAAGACCTCGTCTGGGACATTGGCATCGATATTAGATTACA
Found at i:9832022 original size:43 final size:43
Alignment explanation
Indices: 9831906--9832034 Score: 127
Period size: 43 Copynumber: 3.0 Consensus size: 43
9831896 ATGGGATTCT
* * * * * *
9831906 GATATGTGATTTCGTGTAAGACCACGCCTGGGACATTGGCATC
1 GATATTTGATTACATGTAAGACCTCGTCTGGGACAGTGGCATC
* * *
9831949 GAT-TTGAGATTTACATGTAAGACCTTGTCTGGGATAGTGGCATC
1 GATATT-TGA-TTACATGTAAGACCTCGTCTGGGACAGTGGCATC
*
9831993 GATATTTGATTACATGTAAAACCTCGTCTGGGAC-GTTGGCAT
1 GATATTTGATTACATGTAAGACCTCGTCTGGGACAG-TGGCAT
9832035 TATACTAGCT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
42 2 0.03
43 33 0.48
44 32 0.46
45 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
GATATTTGATTACATGTAAGACCTCGTCTGGGACAGTGGCATC
Found at i:9834873 original size:21 final size:23
Alignment explanation
Indices: 9834828--9834877 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
9834818 CTACTTTTCA
*
9834828 AAATAAATATTATTTATTAATTT
1 AAATAAATATAATTTATTAATTT
*
9834851 AAATAAAT-TAATTTTTTAA-TT
1 AAATAAATATAATTTATTAATTT
9834872 AAATAA
1 AAATAA
9834878 TTTTCTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.32
22 9 0.36
23 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATAAATATAATTTATTAATTT
Found at i:9834880 original size:16 final size:17
Alignment explanation
Indices: 9834848--9834886 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
9834838 TATTTATTAA
9834848 TTTAAATAAATTAATTT
1 TTTAAATAAATTAATTT
*
9834865 TTTAATTAAA-TAATTT
1 TTTAAATAAATTAATTT
*
9834881 TCTAAA
1 TTTAAA
9834887 CCCGATTCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAATAAATTAATTT
Found at i:9838189 original size:50 final size:50
Alignment explanation
Indices: 9838017--9838501 Score: 571
Period size: 50 Copynumber: 9.6 Consensus size: 50
9838007 CGATCTCGTA
* * * * * *
9838017 TAAGACCATGTCTGGGACATGGCATCGACATCAATATGTGA-G--CCAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA-TG
* ** * *
9838065 TAAGACCATGTCTAGGACATGGCATTGGCATTATTGAAATTATGAGAGGTCTCATG
1 TAAGACCATGTCTGGGACATGGCATTGGC---ACCG--A-GATGAGAGGTCCCATG
* * * * * *
9838121 TAAAACCATATCTAGGACATGGCGTTGGCACCGAGATGAGATGTCCCATA
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
* *
9838171 TAAGACCATGTCTGGGACATGGCATTGGGGACCGAGATGAGAGGTCTCATG
1 TAAGACCATGTCTGGGACATGGCATT-GGCACCGAGATGAGAGGTCCCATG
9838222 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
*
9838272 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
***
9838322 TAAGACCATGTCTGGGACATGATGTTGGCACCGAGATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
* ***
9838372 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCA
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
* * * **
9838422 TAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
* *
9838472 TAAGACCATATCTGGGATATGGCATTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
9838502 GTATAGGAAA
Statistics
Matches: 380, Mismatches: 47, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
48 26 0.07
50 265 0.70
51 49 0.13
53 3 0.01
54 6 0.02
55 1 0.00
56 28 0.07
57 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
Found at i:9839487 original size:25 final size:25
Alignment explanation
Indices: 9839453--9839500 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
9839443 GGAGTTTAGC
9839453 GTGCTCTCTGATCATTAGCACATCG
1 GTGCTCTCTGATCATTAGCACATCG
* *
9839478 GTGCTTTCTGATTATTAGCACAT
1 GTGCTCTCTGATCATTAGCACAT
9839501 TTATGTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (25 bp):
GTGCTCTCTGATCATTAGCACATCG
Found at i:9846958 original size:10 final size:10
Alignment explanation
Indices: 9846930--9846963 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
9846920 TATTTTCGAG
9846930 TTAATGGAAA
1 TTAATGGAAA
9846940 TTAACTGGAAA
1 TTAA-TGGAAA
9846951 TTAATGGAAA
1 TTAATGGAAA
9846961 TTA
1 TTA
9846964 CTATCGTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (10 bp):
TTAATGGAAA
Found at i:9851602 original size:95 final size:94
Alignment explanation
Indices: 9851493--9851675 Score: 242
Period size: 94 Copynumber: 1.9 Consensus size: 94
9851483 ATATTGGGTA
* *
9851493 TTTTTACTATTTATGTTAAATAAAAAGGGTTAAGGAAGATGTGTGCTCAATTATCAAATAGATAA
1 TTTTTACTATTTATGTTAAATAAAAAGGG-AAAGGAAGAGGTGTGCTCAATTATCAAATAGATAA
*
9851558 ATTAAAAGAGTTTGATGAAAAATTTAGTTT
65 ATTAAAAGAGTATGATGAAAAATTTAGTTT
** * * * *
9851588 TTTTTA-TCATTTATGTTAAATAATGAGTGAAAGGGAGGGGTGTGCTCAATTATCAAATAGGTAA
1 TTTTTACT-ATTTATGTTAAATAAAAAGGGAAAGGAAGAGGTGTGCTCAATTATCAAATAGATAA
* *
9851652 ATTTAAAGTGTATGATGAAAAATT
65 ATTAAAAGAGTATGATGAAAAATT
9851676 CCATTTTTGT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
94 52 0.68
95 24 0.32
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.37
Consensus pattern (94 bp):
TTTTTACTATTTATGTTAAATAAAAAGGGAAAGGAAGAGGTGTGCTCAATTATCAAATAGATAAA
TTAAAAGAGTATGATGAAAAATTTAGTTT
Found at i:9851735 original size:83 final size:83
Alignment explanation
Indices: 9851595--9851760 Score: 226
Period size: 83 Copynumber: 2.0 Consensus size: 83
9851585 TTTTTTTTAT
* * * * * *
9851595 CATTTATGTTAAATAATGAGTGAAAGGGAGGGGTGTGCTCAATTATCAAATAGGTAAATTTAAAG
1 CATTTATGTTAAATAAAGAATGAAAGGAAGGGGTGTGCTAAATTACCAAATAAGTAAATTTAAAG
*
9851660 TGT-ATGATGAAAAATTC
66 AGTCATGATGAAAAATTC
* *
9851677 CATTTTTGTTAAATAAAGAATGTAAGGAAGGGGGTGTGCTAAATTACCAAATAAGTAAATTTAAA
1 CATTTATGTTAAATAAAGAATGAAAGGAA-GGGGTGTGCTAAATTACCAAATAAGTAAATTTAAA
*
9851742 GAGTCTTGATGAAAAATTC
65 GAGTCATGATGAAAAATTC
9851761 AGTTTTTTTG
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
82 24 0.33
83 35 0.49
84 13 0.18
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (83 bp):
CATTTATGTTAAATAAAGAATGAAAGGAAGGGGTGTGCTAAATTACCAAATAAGTAAATTTAAAG
AGTCATGATGAAAAATTC
Found at i:9851805 original size:178 final size:180
Alignment explanation
Indices: 9851533--9851951 Score: 459
Period size: 196 Copynumber: 2.3 Consensus size: 180
9851523 TAAGGAAGAT
* * * * *
9851533 GTGTGCTCAATTATCAAATAGATAAATTAAAAGAGTTTGATGAAAAATTTAGTTTTTTTTATCAT
1 GTGTGCTAAATTACCAAATAGATAAATTAAAAGAGTTTGATGAAAAATTCAGTTTTTTTGACCAT
* * *
9851598 TTATGTTAAATAATGAGTGAAAGGGA-GGG-GTG-TGCTCAATTATCAAATAGGTAAATTTAAAG
66 TTATGCTAAACAAAGAGTGAAAGGGAGGGGTGTGCTGCTCAATTATCAAATAGGTAAATTTAAAG
*
9851660 TGTATGATGAAAAATTCCATTTTTGTTAAATAAAGAATGTAAGGAAGGGG
131 AGTATGATGAAAAATTCCATTTTTGTTAAATAAAGAATGTAAGGAAGGGG
*
9851710 GTGTGCTAAATTACCAAATA-AGTAAATTTAAAGAGTCTTGATGAAAAATTCAGTTTTTTTGACC
1 GTGTGCTAAATTACCAAATAGA-TAAATTAAAAGAGT-TTGATGAAAAATTCAGTTTTTTTGACC
* * *
9851774 ATTTATGCTACACAAAGAGTGTAATGGAGGGGGTGTGCTCATTGCTCAATTATCAAATAGGTAAA
64 ATTTATGCTAAACAAAGAGTGAAAGGGA-GGGGTGTG--C--TGCTCAATTATCAAATAGGTAAA
* * * *
9851839 TTTAAAGAGTATGATGAAAAGTTCCATTTTTTGGCCATTTTGTTAAACAAAGAGTGTAAGGGAGG
124 TTTAAAGAGTATGATGAAAAATTCCA-----T-----TTTTGTTAAATAAAGAATGTAAGGAAGG
9851904 GG
179 GG
* * * * *
9851906 GTGTGCTAAATTATCAAATAGGTAAATTAAAATAGTGTGACGAAAA
1 GTGTGCTAAATTACCAAATAGATAAATTAAAAGAGTTTGATGAAAA
9851952 TTTTGGTTTT
Statistics
Matches: 198, Mismatches: 23, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
176 1 0.01
177 31 0.16
178 46 0.23
180 3 0.02
181 3 0.02
186 47 0.24
191 1 0.01
195 8 0.04
196 58 0.29
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (180 bp):
GTGTGCTAAATTACCAAATAGATAAATTAAAAGAGTTTGATGAAAAATTCAGTTTTTTTGACCAT
TTATGCTAAACAAAGAGTGAAAGGGAGGGGTGTGCTGCTCAATTATCAAATAGGTAAATTTAAAG
AGTATGATGAAAAATTCCATTTTTGTTAAATAAAGAATGTAAGGAAGGGG
Found at i:9851911 original size:100 final size:102
Alignment explanation
Indices: 9851713--9851912 Score: 280
Period size: 103 Copynumber: 2.0 Consensus size: 102
9851703 GAAGGGGGTG
*
9851713 TGCTAAATTACCAAATAAGTAAATTTAAAGAGTCTTGATGAAAAATTCAGTTTTTTTGACCATTT
1 TGCTAAATTACCAAATAAGTAAATTTAAAGAGTCATGATGAAAAATTCAG-TTTTTTGACCATTT
* *
9851778 ATGCTACACAAAGAGTGTAATGGAGGGGGTGTGCTCAT
65 ATGCTAAACAAAGAGTGTAAGGGAGGGGGTGTGCTCAT
* * * * *
9851816 TGCTCAATTATCAAATAGGTAAATTTAAAGAGT-ATGATGAAAAGTTCCA-TTTTTTGGCCATTT
1 TGCTAAATTACCAAATAAGTAAATTTAAAGAGTCATGATGAAAAATT-CAGTTTTTTGACCATTT
*
9851879 -TGTTAAACAAAGAGTGTAAGGGAGGGGGTGTGCT
65 ATGCTAAACAAAGAGTGTAAGGGAGGGGGTGTGCT
9851913 AAATTATCAA
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
100 31 0.36
101 13 0.15
102 11 0.13
103 32 0.37
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (102 bp):
TGCTAAATTACCAAATAAGTAAATTTAAAGAGTCATGATGAAAAATTCAGTTTTTTGACCATTTA
TGCTAAACAAAGAGTGTAAGGGAGGGGGTGTGCTCAT
Found at i:9867948 original size:29 final size:29
Alignment explanation
Indices: 9867914--9867972 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
9867904 ACAAATATTA
9867914 CAACTTTATGTATATAGTTGCAATAATTG
1 CAACTTTATGTATATAGTTGCAATAATTG
9867943 CAACTTTATGTATATAGTTGCAATAATTG
1 CAACTTTATGTATATAGTTGCAATAATTG
9867972 C
1 C
9867973 TTTACTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (29 bp):
CAACTTTATGTATATAGTTGCAATAATTG
Found at i:9874351 original size:20 final size:21
Alignment explanation
Indices: 9874326--9874365 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9874316 AGAAGAGGAT
*
9874326 GGAAAG-TAAAATAAAAAAAA
1 GGAAAGTTAAAAGAAAAAAAA
9874346 GGAAAGTTAAAAGAAAAAAA
1 GGAAAGTTAAAAGAAAAAAA
9874366 TTTAAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.10
Consensus pattern (21 bp):
GGAAAGTTAAAAGAAAAAAAA
Found at i:9875146 original size:3 final size:3
Alignment explanation
Indices: 9875140--9875165 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9875130 TCTAATGAAA
9875140 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
9875166 CATCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:9881017 original size:11 final size:11
Alignment explanation
Indices: 9881003--9881027 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9880993 GTTATTAAAG
9881003 TAATATAAGGC
1 TAATATAAGGC
9881014 TAATATAAGGC
1 TAATATAAGGC
9881025 TAA
1 TAA
9881028 AATAGGCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (11 bp):
TAATATAAGGC
Found at i:9881600 original size:109 final size:109
Alignment explanation
Indices: 9881404--9881742 Score: 549
Period size: 109 Copynumber: 3.1 Consensus size: 109
9881394 TGGATTAAAA
* *
9881404 TTTAGAAGGATATTTGGCTATTTGGTCGAACGAG--AAATCGAAACCCAGCACATTAGGGCATGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
9881467 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
9881511 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
*
9881576 TTTCTCGAATTTTCCAAACG-AAAACACTGCCTTATTTTGAAATT
66 TTTCTCGAA-TTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
* * * *
9881620 TTTGAAAGGATATTTGGTTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTTGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
* * *
9881685 TTTCTCGAATTTCCAAATGTAAAACATTGCCTTTTTTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
*
9881729 TTTTAAAGGATATT
1 TTTAAAAGGATATT
9881743 AGTATGCGTA
Statistics
Matches: 217, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
107 33 0.15
108 9 0.04
109 165 0.76
110 10 0.05
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (109 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
Found at i:9881974 original size:41 final size:41
Alignment explanation
Indices: 9881929--9882006 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
9881919 AAGAAAATGA
*
9881929 ATAGAACTATAAAAATAT-AAGAGATATATATATGTATCTAC
1 ATAGAACTATAAAAATATGAA-AAATATATATATGTATCTAC
* * *
9881970 ATAGAATTATAGAAATATGAAAAATATATGTATGTAT
1 ATAGAACTATAAAAATATGAAAAATATATATATGTAT
9882007 AAAATTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 30 0.94
42 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33
Consensus pattern (41 bp):
ATAGAACTATAAAAATATGAAAAATATATATATGTATCTAC
Found at i:9883825 original size:44 final size:43
Alignment explanation
Indices: 9883751--9884035 Score: 181
Period size: 44 Copynumber: 6.6 Consensus size: 43
9883741 GTGGTTTTAG
* *
9883751 TCTGCTCCACTACAACCTCAGGGA-AGTAAGACTTGTATCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGA-TAAGACTTGTAT-TTCAA
* *
9883795 TCTGCTCCACTGCAACTTCAGGGAGCTAAGA-TTG-ATTT-GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATTTCAA
* * * * *
9883835 TCTGCTCTACTGCAACTTCAGAGAGATGAGATCTGTGGTTTTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-T-G-TATTTCAA
* * * * * * **
9883882 TCCGCTCTACTGTAACTTCAAGGAGATAGGA-TTGGTTTCTTCTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTAT-TTCAA
* * * * *
9883926 TCTGCTCCACTGCAACTGCAGAGAGATAAGAC-TGGA-TGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATTTCAA
* * * *
9883967 TCTGCTCTACTGCAACTTCAGAGAGATAAGGTCTGTGT-TTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAA-GACT-TGTATTTCAA
*
9884011 TCCGCTCCACTGCAACTTCAGGGAG
1 TCTGCTCCACTGCAACTTCAGGGAG
9884036 GTAGGATTGG
Statistics
Matches: 186, Mismatches: 41, Indels: 28
0.73 0.16 0.11
Matches are distributed among these distances:
40 28 0.15
41 31 0.17
42 5 0.03
43 8 0.04
44 84 0.45
45 1 0.01
46 3 0.02
47 26 0.14
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATTTCAA
Found at i:9884002 original size:132 final size:128
Alignment explanation
Indices: 9883795--9884054 Score: 376
Period size: 129 Copynumber: 2.0 Consensus size: 128
9883785 GTATCTTCAA
* * * * **
9883795 TCTGCTCCACTGCAACTTCAGGGAGCTAAGATTGATTTGATCTGCTCTACTGCAACTTCAGAGAG
1 TCTGCTCCACTGCAACTGCAGAGAGATAAGATGGATGCGATCTGCTCTACTGCAACTTCAGAGAG
* * *
9883860 ATGAGATCTGTGGTTTTTTTAATCCGCTCTACTGTAACTTCAAGGAGATAGGATTGGTTTCTTCT
66 ATAAGATCTGT-G--TTTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATTGGTTTCTTCT
9883925 G
128 G
9883926 TCTGCTCCACTGCAACTGCAGAGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGA
1 TCTGCTCCACTGCAACTGCAGAGAGATAAGA-TGGATGCGATCTGCTCTACTGCAACTTCAGAGA
* * *
9883991 GATAAGGTCTGTGTTTTTAATCCGCTCCACTGCAACTTCAGGGAGGTAGGATTGGTTTCTTCTG
65 GATAAGATCTGTGTTTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATTGGTTTCTTCTG
9884055 CCTAATTAAC
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
129 47 0.41
131 29 0.25
132 40 0.34
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (128 bp):
TCTGCTCCACTGCAACTGCAGAGAGATAAGATGGATGCGATCTGCTCTACTGCAACTTCAGAGAG
ATAAGATCTGTGTTTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATTGGTTTCTTCTG
Found at i:9890059 original size:14 final size:15
Alignment explanation
Indices: 9890035--9890063 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9890025 TTTTTCTGTG
9890035 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
9890050 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
9890064 AGTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:9890301 original size:28 final size:28
Alignment explanation
Indices: 9890255--9890311 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
9890245 TATAGTTTTT
9890255 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
*
9890283 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
9890311 A
1 A
9890312 AACAAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:9891312 original size:60 final size:61
Alignment explanation
Indices: 9891233--9891346 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
9891223 AAGTAGTTCG
* * *
9891233 AATGTAAGATTTAATTTC-TTGAGTTGAA-ATTAA-AGTTATGAATTATATGTATAAAGTTTT
1 AATGTAAGATATAAGTTCTTTGAGTTGAACA-TAATA-TTATGAATTATATATATAAAGTTTT
*
9891293 AATGTATGATATAAGTTCTTTGAGTTGAACATAATATTATGAATTATATATATA
1 AATGTAAGATATAAGTTCTTTGAGTTGAACATAATATTATGAATTATATATATA
9891347 TGCCCATATG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
60 15 0.32
61 30 0.64
62 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.44
Consensus pattern (61 bp):
AATGTAAGATATAAGTTCTTTGAGTTGAACATAATATTATGAATTATATATATAAAGTTTT
Found at i:9891459 original size:64 final size:64
Alignment explanation
Indices: 9891375--9891551 Score: 240
Period size: 64 Copynumber: 2.8 Consensus size: 64
9891365 ATATATATTT
9891375 AAAGTTCTTGAGCT-ATATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTCTTGAGCTGA-ATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
* * *
9891439 AAAGTTTTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
*
9891503 AAA-TTCGTTGAGCTGAATTTTAATGT-TGTAA--AT-TATACATATGTGGTTC
1 AAAGTTC-TTGAGCTGAA-TTTAATGTATG-AATTTTATATACATATGTGGTTC
9891552 GAATGTTTGT
Statistics
Matches: 103, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
62 15 0.15
63 3 0.03
64 74 0.72
65 11 0.11
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.42
Consensus pattern (64 bp):
AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
Found at i:9892138 original size:2 final size:2
Alignment explanation
Indices: 9892131--9892155 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9892121 AGTATTAGTG
9892131 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
9892156 GAATTTTTGC
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:9893580 original size:18 final size:18
Alignment explanation
Indices: 9893554--9893589 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
9893544 GTGTGCTTTG
9893554 TTTAATAATGCCTCGTAA
1 TTTAATAATGCCTCGTAA
*
9893572 TTTAGTAATGCCTCGTAA
1 TTTAATAATGCCTCGTAA
9893590 CTCTAATCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (18 bp):
TTTAATAATGCCTCGTAA
Found at i:9899322 original size:109 final size:109
Alignment explanation
Indices: 9899124--9899575 Score: 757
Period size: 109 Copynumber: 4.2 Consensus size: 109
9899114 GACATGGATT
* * *
9899124 AAAA-TTTAGAAGGATATTTGGCTATTTGGTCGAACGAG--AAACCGAAACCCAACACATTAGGG
1 AAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGG
9899186 CACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG
66 CACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG
9899230 AAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGG
1 AAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGG
*
9899295 CACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTAATTTTG
66 CACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG
* * * * *
9899339 AAATTTTTGAAAGGATATTTGGCTATTTGGTTGAATGAGAAAAATCGAAACCTAGCACATTAGGG
1 AAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGG
*
9899404 CACATTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG
66 CACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG
*
9899448 AAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTTGGG
1 AAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGG
*
9899513 CACGTTTTCTTGAATTTCCAAACGCAAAACATTGCCTTATTTTG
66 CACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG
* *
9899557 AAATTTTTTAAAGGATATT
1 AAAATTTTAAAAGGATATT
9899576 AGTATGCATA
Statistics
Matches: 322, Mismatches: 21, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
106 4 0.01
107 33 0.10
109 285 0.89
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (109 bp):
AAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGG
CACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG
Found at i:9905092 original size:25 final size:25
Alignment explanation
Indices: 9905064--9905131 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
9905054 CTTGTACAAG
* * *
9905064 TATGCTCACACGAGCTGTAAATTGA
1 TATGCTCTCACAAGCTGTAAATCGA
*
9905089 TATGCTCTCACAAGCTGTAAATCGG
1 TATGCTCTCACAAGCTGTAAATCGA
*
9905114 TATGCTCTCACCAGCTGT
1 TATGCTCTCACAAGCTGT
9905132 GGGTCGAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (25 bp):
TATGCTCTCACAAGCTGTAAATCGA
Found at i:9912245 original size:18 final size:18
Alignment explanation
Indices: 9912188--9912248 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
9912178 TCCTCACATA
* *
9912188 CATCTTCTTCCTCGGTCG
1 CATCTTCTTCCTCGATTG
* * *
9912206 TATCTTCTTCCT-TATCTA
1 CATCTTCTTCCTCGAT-TG
9912224 CATCTTCTTCCTCGATTG
1 CATCTTCTTCCTCGATTG
9912242 CATCTTC
1 CATCTTC
9912249 ATCATCATCT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 1 0.03
18 30 0.91
19 2 0.06
ACGTcount: A:0.11, C:0.34, G:0.08, T:0.46
Consensus pattern (18 bp):
CATCTTCTTCCTCGATTG
Found at i:9912259 original size:36 final size:36
Alignment explanation
Indices: 9912186--9912259 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
9912176 GTTCCTCACA
* * * * *
9912186 TACATCTTCTTCCTCGGTCGTATCTTCTTCCTTATC
1 TACATCTTCTTCCTCGATCGCATCTTCATCATCATC
*
9912222 TACATCTTCTTCCTCGATTGCATCTTCATCATCATC
1 TACATCTTCTTCCTCGATCGCATCTTCATCATCATC
9912258 TA
1 TA
9912260 TGCCTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.16, C:0.32, G:0.07, T:0.45
Consensus pattern (36 bp):
TACATCTTCTTCCTCGATCGCATCTTCATCATCATC
Found at i:9913503 original size:22 final size:22
Alignment explanation
Indices: 9913475--9913521 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
9913465 GATATGTGAC
9913475 CATTAGGAAATTTATCTATAAA
1 CATTAGGAAATTTATCTATAAA
9913497 CATTAGGAAATTTATCTATAAA
1 CATTAGGAAATTTATCTATAAA
9913519 CAT
1 CAT
9913522 GTTTTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (22 bp):
CATTAGGAAATTTATCTATAAA
Found at i:9916188 original size:33 final size:35
Alignment explanation
Indices: 9916151--9916215 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
9916141 TCTCCTACTA
*
9916151 GTTAGGGTTTT-GGGTTTTT-GGTTTAGGGTTAGG
1 GTTAGGGTTTTGGGGTTTTTAGGTTTAAGGTTAGG
9916184 GTTAGGGTTTTGGGGTTTTTAGGTTTAAGGTT
1 GTTAGGGTTTTGGGGTTTTTAGGTTTAAGGTT
9916216 TTAAAGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 11 0.38
34 8 0.28
35 10 0.34
ACGTcount: A:0.11, C:0.00, G:0.40, T:0.49
Consensus pattern (35 bp):
GTTAGGGTTTTGGGGTTTTTAGGTTTAAGGTTAGG
Found at i:9916501 original size:96 final size:95
Alignment explanation
Indices: 9916201--9916539 Score: 380
Period size: 97 Copynumber: 3.5 Consensus size: 95
9916191 TTTTGGGGTT
* * * * * * * * *
9916201 TTTA-GGTTTAAGGTTTTAAAGAAAAAAAT-AAATAAATAAGAGTTTAGGGTTTCTTAATTAGAT
1 TTTAGGGTTTAGGGTTTTTAAG-GAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAAT
* *
9916264 TAATTATAAATTTTT-CAAAATTGGATTAGG
65 TAATTATAAATTTTTAAAAAATTAGATTAGG
* * * * *
9916294 TTTTGTGTTTATGGG-TTTTAAAGAAAAATTAATTAAATTAGGGTTTAGGGTTACTTGAGTAAAT
1 TTTAGGGTTTA-GGGTTTTTAAGGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAAT
* *
9916358 TAATTAAAAAATTTTAAAAAATTTAGATTAGGG
65 TAATTATAAATTTTTAAAAAA-TTAGATTA-GG
** * *
9916391 TTTAATGTTAAGGGTTTTTAAGGAAAAATCAAATAAATTCGGGTTTAGGGTTACTTGAGTAAATT
1 TTTAGGGTTTAGGGTTTTTAAGGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATT
*
9916456 AATTATAAATTTTTAAAAAAATAGATTAGAG
66 AATTATAAATTTTTAAAAAATTAGATTAG-G
*
9916487 TTTAGGGTTTAGGGTTTTTAAGGAAAAACTCAAATAAATTAGGGTTTGGGGTT
1 TTTAGGGTTTAGGGTTTTTAAGGAAAAA-TCAAATAAATTAGGGTTTAGGGTT
9916540 TAGGGTTACT
Statistics
Matches: 205, Mismatches: 32, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
93 9 0.04
94 50 0.24
95 7 0.03
96 43 0.21
97 96 0.47
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.39
Consensus pattern (95 bp):
TTTAGGGTTTAGGGTTTTTAAGGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATT
AATTATAAATTTTTAAAAAATTAGATTAGG
Found at i:9916799 original size:125 final size:126
Alignment explanation
Indices: 9916576--9916865 Score: 449
Period size: 125 Copynumber: 2.3 Consensus size: 126
9916566 TAATTTAAAA
* * *
9916576 AAGCTCCCACGTGGATGCTCTTTTACTACAGTAG-TCCTGAAAAAATAATTTCGAGAAGACGTTT
1 AAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTT
* * *
9916640 CTGAGAAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
66 CTGAGAAAATAGTATCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAATACTGAAAG
* *
9916701 AAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTT
* * *
9916766 CTGAGCAAATAGTAT-AAAAACGTTTTAAACAGGATGCTTTGTCAGCAAAAATACTGAAAG
66 CTGAGAAAATAGTATCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAATACTGAAAG
* *
9916826 AAGCTCCCATGTGGACGCGCTTTTGCTACAGTAGCTCCTG
1 AAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTG
9916866 TTTGGCCTGA
Statistics
Matches: 151, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
125 110 0.73
126 41 0.27
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTT
CTGAGAAAATAGTATCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAATACTGAAAG
Found at i:9919915 original size:58 final size:59
Alignment explanation
Indices: 9919853--9920008 Score: 135
Period size: 58 Copynumber: 2.6 Consensus size: 59
9919843 TTTTTAAATC
9919853 AAATAATATAGAAATATTCAGAATATTGACTTATTTAAAACAAAATCT-ATTTTATT-AA-
1 AAATAATATAGAAATATTCA-AATATT-ACTTATTTAAAACAAAATCTCATTTTATTAAAG
* * * * * ** *
9919911 AAATATTAAAGTAA-ATT-ACA-ATTACTTTATTCAAAACAACTTTTCATTTTATTAAATG
1 AAATAATATAGAAATATTCAAATATTAC-TTATTTAAAACAAAATCTCATTTTATTAAA-G
*
9919969 AAATAATATAGCAATATTCAAAATATTACCTTATTTAAAA
1 AAATAATATAGAAATATTC-AAATATTA-CTTATTTAAAA
9920009 GAATATTACC
Statistics
Matches: 75, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
53 2 0.03
54 17 0.23
55 9 0.12
56 3 0.04
57 3 0.04
58 22 0.29
59 3 0.04
61 2 0.03
62 13 0.17
63 1 0.01
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (59 bp):
AAATAATATAGAAATATTCAAATATTACTTATTTAAAACAAAATCTCATTTTATTAAAG
Found at i:9920026 original size:19 final size:20
Alignment explanation
Indices: 9919990--9920031 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
9919980 CAATATTCAA
9919990 AATATTACCTTATTTAAAAG
1 AATATTACCTTATTTAAAAG
9920010 AATATTACCTT-TTTAAAAG
1 AATATTACCTTATTTAAAAG
9920029 AAT
1 AAT
9920032 TTCTATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
AATATTACCTTATTTAAAAG
Found at i:9920696 original size:29 final size:30
Alignment explanation
Indices: 9920646--9920718 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
9920636 GATTGTGTCA
*
9920646 GTGCTGTTGCTGGGCCTGGTGATTGTAT-G
1 GTGCTGTTGATGGGCCTGGTGATTGTATGG
*
9920675 G-GCATGTTGATGGG-CTGAGTGATTGTGTGG
1 GTGC-TGTTGATGGGCCTG-GTGATTGTATGG
9920705 GTGCTGTTGATGGG
1 GTGCTGTTGATGGG
9920719 TCTGCGTCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 5 0.13
29 19 0.50
30 12 0.32
31 2 0.05
ACGTcount: A:0.10, C:0.10, G:0.45, T:0.36
Consensus pattern (30 bp):
GTGCTGTTGATGGGCCTGGTGATTGTATGG
Found at i:9922394 original size:22 final size:21
Alignment explanation
Indices: 9922346--9922386 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
9922336 CAAAAAAAAT
9922346 AAAATTAAAGCTTTTTTTAAA
1 AAAATTAAAGCTTTTTTTAAA
9922367 AAAATTAAAGCTTTTTTTAA
1 AAAATTAAAGCTTTTTTTAA
9922387 GAGGAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
AAAATTAAAGCTTTTTTTAAA
Found at i:9922406 original size:11 final size:10
Alignment explanation
Indices: 9922390--9922435 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 10
9922380 TTTTTAAGAG
9922390 GAATTTGAGA
1 GAATTTGAGA
9922400 CGAATTTGAGA
1 -GAATTTGAGA
9922411 GAATATTGGAGA
1 GAAT-TT-GAGA
*
9922423 GAAATTGAGA
1 GAATTTGAGA
9922433 GAA
1 GAA
9922436 AGGATTTAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 11 0.34
11 14 0.44
12 7 0.22
ACGTcount: A:0.43, C:0.02, G:0.30, T:0.24
Consensus pattern (10 bp):
GAATTTGAGA
Found at i:9922432 original size:10 final size:10
Alignment explanation
Indices: 9922394--9922436 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
9922384 TAAGAGGAAT
*
9922394 TTGAGACGAAT
1 TTGAGA-GAAA
9922405 TTGAGAGAATA
1 TTGAGAGAA-A
9922416 TTGGAGAGAAA
1 TT-GAGAGAAA
9922427 TTGAGAGAAA
1 TTGAGAGAAA
9922437 GGATTTAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 11 0.38
11 11 0.38
12 7 0.24
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.23
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:9923494 original size:19 final size:19
Alignment explanation
Indices: 9923470--9923508 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9923460 GTTAATAATA
9923470 AAAATA-ATTGAATATTATT
1 AAAATATATT-AATATTATT
*
9923489 AAAATATATTATTATTATT
1 AAAATATATTAATATTATT
9923508 A
1 A
9923509 TTATTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AAAATATATTAATATTATT
Found at i:9923501 original size:3 final size:3
Alignment explanation
Indices: 9923495--9923522 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9923485 TATTAAAATA
9923495 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9923523 GATTTTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9927462 original size:3 final size:3
Alignment explanation
Indices: 9927454--9927488 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
9927444 ACCAACAAAC
9927454 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
9927489 CTGACATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:9927823 original size:21 final size:21
Alignment explanation
Indices: 9927784--9927824 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9927774 TTAAAATATT
*
9927784 AATAAATTTTCATATATTTTC
1 AATAAATTTTCATAGATTTTC
9927805 AATAAATTGTTC-TAGATTTT
1 AATAAATT-TTCATAGATTTT
9927825 TCATTGCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (21 bp):
AATAAATTTTCATAGATTTTC
Found at i:9930050 original size:166 final size:166
Alignment explanation
Indices: 9929726--9930086 Score: 498
Period size: 168 Copynumber: 2.2 Consensus size: 166
9929716 TGAATACCTC
* * *
9929726 TAGTTTCAAGCCTTATGTTTCATTTTTATTGTGTTTAAAAATAATTGTAGTGGATTTAGTATTGT
1 TAGTTTCAAGCCTTATATTTCATTTTTATTGTGTTTAAAAATAATTGTAGTGCATTTAGTATTCT
*
9929791 TTATCAATGTATTTGTGTGTTTAAATTTCGTTTTACTTCTAATTTAATCTATTTTTTAAAATTTT
66 TTATCAATGTATTTATGTGTTTAAATTTCGTTTTACTTCTAATTTAATCTATTTTTTAAAATTTT
9929856 AATATCATACATATTTATTGTGTTATTATAATTACT
131 AATATCATACATATTTATTGTGTTATTATAATTACT
9929892 TAGTTTCAAGCCTTATATTTCATTTTTATTGTGTGTTTAAAAATAATTGTAGTGCATTTAGTATT
1 TAGTTTCAAGCCTTATATTTCATTTTTA-T-TGTGTTTAAAAATAATTGTAGTGCATTTAGTATT
** *
9929957 CTTTATCTAATGTATTTATGTGTTTGTATTTCG-TTTAC-TCATAATTTAATCTAATTTTTT-TA
64 CTTTATC-AATGTATTTATGTGTTTAAATTTCGTTTTACTTC-TAATTTAATCT-ATTTTTTAAA
* ** * **
9930019 TTTTTAATATTGTGCATA-TT-TTGTGTTATTATCGTTACT
126 ATTTTAATATCATACATATTTATTGTGTTATTATAATTACT
* *
9930058 TAGTTTCAAGGCTTACATTTCATTATTTA
1 TAGTTTCAAGCCTTATATTTCATT-TTTA
9930087 ATTTATGCTA
Statistics
Matches: 174, Mismatches: 15, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
166 66 0.38
167 9 0.05
168 70 0.40
169 29 0.17
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (166 bp):
TAGTTTCAAGCCTTATATTTCATTTTTATTGTGTTTAAAAATAATTGTAGTGCATTTAGTATTCT
TTATCAATGTATTTATGTGTTTAAATTTCGTTTTACTTCTAATTTAATCTATTTTTTAAAATTTT
AATATCATACATATTTATTGTGTTATTATAATTACT
Found at i:9941315 original size:58 final size:59
Alignment explanation
Indices: 9941223--9941368 Score: 151
Period size: 58 Copynumber: 2.5 Consensus size: 59
9941213 TCAGATAAAG
* ** * *
9941223 GGGTGCCGGCCATC-AGTGTGCCAGCACCCCAAAAT-TTTTTTTGAA-AAAAAAAATACAT
1 GGGTGCCGGCCATCTAGTGTCCCAAAACCCAAAAATCATTTTTT-AATAAAAAAAATA-AT
* *
9941281 GGGTGCCGGCCATCTAGTGT-CCAAAACCCAAAAATCATTTTTTAATAGAAAAAATAGT
1 GGGTGCCGGCCATCTAGTGTCCCAAAACCCAAAAATCATTTTTTAATAAAAAAAATAAT
* *
9941339 -GTTGCCGGCCATCTAGT-TCCCATAACCCAA
1 GGGTGCCGGCCATCTAGTGTCCCAAAACCCAA
9941369 TTTTCCTGTT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
56 1 0.01
57 26 0.34
58 29 0.38
59 20 0.26
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (59 bp):
GGGTGCCGGCCATCTAGTGTCCCAAAACCCAAAAATCATTTTTTAATAAAAAAAATAAT
Found at i:9943830 original size:23 final size:24
Alignment explanation
Indices: 9943783--9943832 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
9943773 CAAAGTGTTG
9943783 TATAATTGAGATATGCAAATTATA
1 TATAATTGAGATATGCAAATTATA
*
9943807 TATACTTGAG-TATG-AAATTGATA
1 TATAATTGAGATATGCAAATT-ATA
9943830 TAT
1 TAT
9943833 GAATGAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 5 0.21
23 10 0.42
24 9 0.38
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (24 bp):
TATAATTGAGATATGCAAATTATA
Found at i:9946610 original size:5 final size:5
Alignment explanation
Indices: 9946600--9946657 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
9946590 GATATATATA
* * *
9946600 ATAAT ATAAT ATAAT ATAAC ATAAC ATAAC ATAAT ATATTAT ATAAT A-AA-
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT
9946650 ATAAT ATA
1 ATAAT ATA
9946658 CATAACATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
3 1 0.02
4 4 0.09
5 37 0.79
7 5 0.11
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:9946613 original size:10 final size:10
Alignment explanation
Indices: 9946600--9946667 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
9946590 GATATATATA
*
9946600 ATAATATAAT
1 ATAATATAAC
9946610 ATAATATAAC
1 ATAATATAAC
*
9946620 ATAACATAAC
1 ATAATATAAC
*
9946630 ATAATATATTAT
1 ATAATATA--AC
9946642 ATAATA-AA-
1 ATAATATAAC
9946650 ATAATAT-AC
1 ATAATATAAC
*
9946659 ATAACATAA
1 ATAATATAA
9946668 AAATCTCATA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
8 7 0.15
9 7 0.15
10 26 0.54
11 1 0.02
12 7 0.15
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAATATAAC
Found at i:9946671 original size:20 final size:19
Alignment explanation
Indices: 9946595--9946669 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
9946585 TTATTGATAT
* *
9946595 ATATA-ATAATATAATATA
1 ATATACATAACATAAAATA
*
9946613 ATATAACATAACATAACATA
1 ATAT-ACATAACATAAAATA
*
9946633 ATATATTATATA-ATAAAATA
1 ATATA-CATA-ACATAAAATA
9946653 ATATACATAACATAAAA
1 ATATACATAACATAAAA
9946670 ATCTCATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 5 0.11
19 11 0.23
20 30 0.64
21 1 0.02
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATACATAACATAAAATA
Found at i:9947290 original size:14 final size:14
Alignment explanation
Indices: 9947268--9947298 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9947258 TTAATGTCTG
9947268 TTTGGTTGATTGAA
1 TTTGGTTGATTGAA
*
9947282 TTTGTTTGATTGAA
1 TTTGGTTGATTGAA
9947296 TTT
1 TTT
9947299 ATTAAATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (14 bp):
TTTGGTTGATTGAA
Found at i:9949164 original size:26 final size:26
Alignment explanation
Indices: 9949135--9949194 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
9949125 CCATATTTTC
* *
9949135 TCAAAATTTTACTAGGGGCAAAATCG
1 TCAAAATTTTACCAAGGGCAAAATCG
*
9949161 TCAAAATTTTACCAAGGGTAAAATCG
1 TCAAAATTTTACCAAGGGCAAAATCG
9949187 TCAAAATT
1 TCAAAATT
9949195 AAGCTGGGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (26 bp):
TCAAAATTTTACCAAGGGCAAAATCG
Found at i:9957446 original size:19 final size:19
Alignment explanation
Indices: 9957392--9957446 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
9957382 TAATAGTAAT
* * *
9957392 AAAATTTATATTAAATAAT
1 AAAATTTATGTTAAATTAC
*
9957411 AAAATATA-GTTAAAATTAC
1 AAAATTTATGTT-AAATTAC
9957430 AAAATTTATGTTAAATT
1 AAAATTTATGTTAAATT
9957447 TTCAAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 2 0.07
19 24 0.83
20 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATTTATGTTAAATTAC
Found at i:9958090 original size:21 final size:22
Alignment explanation
Indices: 9958057--9958097 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
9958047 ATTTTCACAT
* *
9958057 ATTTTT-ATTTTTTTAAAAATA
1 ATTTTTAAATTTTTCAAAAATA
9958078 ATTTTTAAATTTTTCAAAAA
1 ATTTTTAAATTTTTCAAAAA
9958098 AAAAAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTAAATTTTTCAAAAATA
Found at i:9959040 original size:11 final size:11
Alignment explanation
Indices: 9959024--9959075 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
9959014 CTTGAATAAG
*
9959024 CTATTTTGCCA
1 CTATTTTGCTA
9959035 CTATTTTGCTA
1 CTATTTTGCTA
* *
9959046 CCATTTCGCTA
1 CTATTTTGCTA
* *
9959057 TTATATTGCTA
1 CTATTTTGCTA
9959068 CTATTTTG
1 CTATTTTG
9959076 TTATTAGTGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:9967974 original size:25 final size:25
Alignment explanation
Indices: 9967944--9968021 Score: 111
Period size: 25 Copynumber: 3.1 Consensus size: 25
9967934 AATTCACCAT
* * *
9967944 AAAGGCTTTTTAGAGAGTTTGTCAC
1 AAAGGCTTTTCAGAGAATTTGCCAC
*
9967969 AAAGGCTTTTCAGAGAATTCGCCAC
1 AAAGGCTTTTCAGAGAATTTGCCAC
*
9967994 AAAAGCTTTTCAGAGAATTTGCCAC
1 AAAGGCTTTTCAGAGAATTTGCCAC
9968019 AAA
1 AAA
9968022 AGCACCACAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (25 bp):
AAAGGCTTTTCAGAGAATTTGCCAC
Found at i:9970367 original size:155 final size:154
Alignment explanation
Indices: 9970079--9970368 Score: 436
Period size: 155 Copynumber: 1.9 Consensus size: 154
9970069 ACAAACGTCG
9970079 CTATAGATCGAGCATTAGCGGCACTTTTCAGAAAATGACACAAAAAAATTGAGCAAAACACGTAG
1 CTATAGATCGAGCATTAGCGGCACTTTTCAGAAAATGACACAAAAAAATTGAGCAAAACACGTAG
* * *
9970144 TTTGATGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTTAAAAAGCGCCACAATAGATCGAGCATT
66 TTTGATGTTGAGCTTTAGTGACATTAGCGGCGCTTTTTAAAAAGCGCCACAATAGATCGAGAAAT
9970209 AGCGGAAATATTTGAGAAACGCCA
131 AGCGGAAATATTTGAGAAACGCCA
** * ** * * *
9970233 CTATAGATCGAGCATTAGTTGCGCTTTTTGGAAAATGCCACAAAAAAGTTGAGCAAAACGACGTC
1 CTATAGATCGAGCATTAGCGGCACTTTTCAGAAAATGACACAAAAAAATTGAGCAAAAC-ACGTA
* * * *
9970298 GTTTGTTGTTGAGCTTTAGTGACATTAGCGGCGCTTTTTAAAAAGCGTCGCAATAGATTGAGAAA
65 GTTTGATGTTGAGCTTTAGTGACATTAGCGGCGCTTTTTAAAAAGCGCCACAATAGATCGAGAAA
9970363 TAGCGG
130 TAGCGG
9970369 CGCTTTGTCA
Statistics
Matches: 120, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
154 52 0.43
155 68 0.57
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (154 bp):
CTATAGATCGAGCATTAGCGGCACTTTTCAGAAAATGACACAAAAAAATTGAGCAAAACACGTAG
TTTGATGTTGAGCTTTAGTGACATTAGCGGCGCTTTTTAAAAAGCGCCACAATAGATCGAGAAAT
AGCGGAAATATTTGAGAAACGCCA
Found at i:9970525 original size:41 final size:41
Alignment explanation
Indices: 9970366--9970505 Score: 273
Period size: 41 Copynumber: 3.4 Consensus size: 41
9970356 TGAGAAATAG
9970366 CGGCGCTTTGTCAAAAAACACCGCTATAGATCGAGCATTAA
1 CGGCGCTTTGTCAAAAAACACCGCTATAGATCGAGCATTAA
9970407 CGGCGCTTTGTCAAAAAACACCGCTATAGATCGAGCATTAA
1 CGGCGCTTTGTCAAAAAACACCGCTATAGATCGAGCATTAA
9970448 CGGCGCTTTGTCAAAAAACACCGCTATAGATCGAGCATTAA
1 CGGCGCTTTGTCAAAAAACACCGCTATAGATCGAGCATTAA
9970489 CGGCGCTTT-TCAAAAAA
1 CGGCGCTTTGTCAAAAAA
9970506 ACACGACAAA
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
40 8 0.08
41 91 0.92
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (41 bp):
CGGCGCTTTGTCAAAAAACACCGCTATAGATCGAGCATTAA
Found at i:9970633 original size:40 final size:40
Alignment explanation
Indices: 9970577--9970652 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
9970567 CACTTTTTAA
** *
9970577 AAAAAAGCCGCAATAGATTGAGAATTAGCGGCGCTTGTTG
1 AAAAAAGCCGCAATAGATCAAGAATTAGCAGCGCTTGTTG
* * *
9970617 AAAAACGCCGCTATAGATCAAGCATTAGCAGCGCTT
1 AAAAAAGCCGCAATAGATCAAGAATTAGCAGCGCTT
9970653 TTCGCAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.21
Consensus pattern (40 bp):
AAAAAAGCCGCAATAGATCAAGAATTAGCAGCGCTTGTTG
Found at i:9970735 original size:156 final size:156
Alignment explanation
Indices: 9970419--9970719 Score: 410
Period size: 156 Copynumber: 1.9 Consensus size: 156
9970409 GCGCTTTGTC
* * * *
9970419 AAAAAACACCGCTATAGATCGAGCATTAACGGCGCTTTGTCAAAAAACACCGCTATAGATCGAGC
1 AAAAAAAACCGCAATAGATCGAGAATTAACGGCGCTTTGTCAAAAAACACCGCTATAGATCAAGC
* *
9970484 ATTAACGGCGCTTTTCAAAAAAACACGACAAAAAGTTGAGCAAAACGACGTCATTTGTTGTTGAG
66 ATTAACAGCGCTTTTCAAAAAAACACGACAAAAAGTTGAGCAAAACGACGTCATTTATTGTTGAG
9970549 CTTTAGTGGCATTAGCGACACTTTTT
131 CTTTAGTGGCATTAGCGACACTTTTT
* * ** *
9970575 AAAAAAAAGCCGCAATAGATTGAGAATTAGCGGCGC-TTGTTGAAAAACGCCGCTATAGATCAAG
1 AAAAAAAA-CCGCAATAGATCGAGAATTAACGGCGCTTTGTCAAAAAACACCGCTATAGATCAAG
* ** *** *
9970639 CATTAGCAGCGCTTTTCGCAAAATGTCG-CAAAAAGTTGAG-AAAACGACGTCGTTTATTGTTGA
65 CATTAACAGCGCTTTTCAAAAAAACACGACAAAAAGTTGAGCAAAACGACGTCATTTATTGTTGA
9970702 GCTTTAGTGGCATTAGCG
130 GCTTTAGTGGCATTAGCG
9970720 GAGTTTTTGA
Statistics
Matches: 126, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
154 39 0.31
155 12 0.10
156 52 0.41
157 23 0.18
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (156 bp):
AAAAAAAACCGCAATAGATCGAGAATTAACGGCGCTTTGTCAAAAAACACCGCTATAGATCAAGC
ATTAACAGCGCTTTTCAAAAAAACACGACAAAAAGTTGAGCAAAACGACGTCATTTATTGTTGAG
CTTTAGTGGCATTAGCGACACTTTTT
Found at i:9970787 original size:14 final size:14
Alignment explanation
Indices: 9970768--9970802 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
9970758 TTAGGGTTAG
9970768 GGTTTAATATTTAA
1 GGTTTAATATTTAA
* *
9970782 GGTTTAATGTTTAT
1 GGTTTAATATTTAA
9970796 GGTTTAA
1 GGTTTAA
9970803 GGGTTTAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (14 bp):
GGTTTAATATTTAA
Found at i:9971086 original size:27 final size:28
Alignment explanation
Indices: 9971056--9971121 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
9971046 GTAATATATA
9971056 TTTAGGGTTTAAGATGTAG-GTTTAAG-G
1 TTTAGGGTTTAAGATGTAGTG-TTAAGAG
* *
9971083 TTTAGGGTTTATGATTTAGTGTTAAGAG
1 TTTAGGGTTTAAGATGTAGTGTTAAGAG
*
9971111 TTTAGTGTTTA
1 TTTAGGGTTTA
9971122 TAGTTTAGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 22 0.65
28 12 0.35
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (28 bp):
TTTAGGGTTTAAGATGTAGTGTTAAGAG
Found at i:9971091 original size:14 final size:14
Alignment explanation
Indices: 9971056--9971272 Score: 117
Period size: 14 Copynumber: 15.6 Consensus size: 14
9971046 GTAATATATA
*
9971056 TTTAGGGTTTAAGA
1 TTTAGGGTTTAAGG
*
9971070 TGTA-GGTTTAAGG
1 TTTAGGGTTTAAGG
* *
9971083 TTTAGGGTTTATGA
1 TTTAGGGTTTAAGG
*
9971097 TTTAGTG-TTAAGAG
1 TTTAGGGTTTAAG-G
*
9971111 TTTAGTGTTTATA-G
1 TTTAGGGTTTA-AGG
*
9971125 TTTAGGGTGT-AGG
1 TTTAGGGTTTAAGG
*
9971138 TTTATGGTTT-AGTG
1 TTTAGGGTTTAAG-G
*
9971152 TTTAGTGTTT-AGTG
1 TTTAGGGTTTAAG-G
*
9971166 TTTAAGG-TTAATGG
1 TTTAGGGTTTAA-GG
* *
9971180 TTTATGGTTTAGGG
1 TTTAGGGTTTAAGG
* * *
9971194 CTTAGGGGCTTAGGG
1 TTTA-GGGTTTAAGG
* *
9971209 TTTAGTGTTTAAAG
1 TTTAGGGTTTAAGG
* *
9971223 TTTATGGTTTATGG
1 TTTAGGGTTTAAGG
*
9971237 TTTAGGGGCTT-AGG
1 TTTA-GGGTTTAAGG
* *
9971251 TTTATGGTTTAATG
1 TTTAGGGTTTAAGG
9971265 TTTAGGGT
1 TTTAGGGT
9971273 CTGATTTTAA
Statistics
Matches: 154, Mismatches: 37, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
12 1 0.01
13 32 0.21
14 98 0.64
15 22 0.14
16 1 0.01
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:9971142 original size:20 final size:19
Alignment explanation
Indices: 9971072--9971199 Score: 71
Period size: 21 Copynumber: 6.2 Consensus size: 19
9971062 GTTTAAGATG
*
9971072 TAGGTTTAAGGTTTAGGGTT
1 TAGGTTTATGGTTTAGGG-T
* * *
9971092 TATGATTTA-GTGTTAAGAGTT
1 TA-GGTTTATG-GTTTAG-GGT
*
9971113 TAGTGTTTATAGTTTAGGGT
1 TAG-GTTTATGGTTTAGGGT
*
9971133 GTAGGTTTATGGTTTAGTGTT
1 -TAGGTTTATGGTTTAG-GGT
*
9971154 TAGTGTTTA-GTGTTTAAGGT
1 TAG-GTTTATG-GTTTAGGGT
9971174 TAATGGTTTATGGTTTAGGGCT
1 T-A-GGTTTATGGTTTAGGG-T
9971196 TAGG
1 TAGG
9971200 GGCTTAGGGT
Statistics
Matches: 83, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
20 27 0.33
21 51 0.61
22 5 0.06
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (19 bp):
TAGGTTTATGGTTTAGGGT
Found at i:9971153 original size:34 final size:35
Alignment explanation
Indices: 9971110--9971200 Score: 98
Period size: 35 Copynumber: 2.6 Consensus size: 35
9971100 AGTGTTAAGA
*
9971110 GTTTAGTGTTTA-TAGTTTAGGGTGT-AGGTTTATG
1 GTTTAGTGTTTAGT-GTTTAGGGTGTAAGGTTAATG
* *
9971144 GTTTAGTGTTTAGTGTTTAGTGTTTAAGGTTAATG
1 GTTTAGTGTTTAGTGTTTAGGGTGTAAGGTTAATG
* *
9971179 GTTTA-TGGTTTAGGGCTTAGGG
1 GTTTAGT-GTTTAGTGTTTAGGG
9971201 GCTTAGGGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
34 22 0.46
35 26 0.54
ACGTcount: A:0.18, C:0.01, G:0.33, T:0.48
Consensus pattern (35 bp):
GTTTAGTGTTTAGTGTTTAGGGTGTAAGGTTAATG
Found at i:9971163 original size:62 final size:63
Alignment explanation
Indices: 9971070--9971219 Score: 166
Period size: 62 Copynumber: 2.4 Consensus size: 63
9971060 GGGTTTAAGA
* *
9971070 TGTAGGTTTAAGGTTTAGGGTTTATGATTTAGTG-TTAAGAGTTTA-GTGTTTATAGTTTAGGG-
1 TGTAGGTTTAAGGTTTAGTGTTTATGATTTAGTGTTTAAG-GTTAATG-GTTTATAGTTTAGGGC
* *
9971132 TGTAGGTTTATGGTTTAGTGTTTAGTG-TTTAGTGTTTAAGGTTAATGGTTTATGGTTTAGGGC
1 TGTAGGTTTAAGGTTTAGTGTTTA-TGATTTAGTGTTTAAGGTTAATGGTTTATAGTTTAGGGC
* *
9971195 T-TAGGGGCTTAGGGTTTAGTGTTTA
1 TGTA--GGTTTAAGGTTTAGTGTTTA
9971220 AAGTTTATGG
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
62 49 0.64
63 9 0.12
64 18 0.24
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.47
Consensus pattern (63 bp):
TGTAGGTTTAAGGTTTAGTGTTTATGATTTAGTGTTTAAGGTTAATGGTTTATAGTTTAGGGC
Found at i:9971189 original size:21 final size:21
Alignment explanation
Indices: 9971135--9971233 Score: 55
Period size: 21 Copynumber: 4.7 Consensus size: 21
9971125 TTTAGGGTGT
*
9971135 AGGTTTATGGTTT-AGTGTTT
1 AGGTTTATGGTTTAAGTGTTA
9971155 AGTGTTTA-GTGTTTAAG-GTTA
1 AG-GTTTATG-GTTTAAGTGTTA
*
9971176 ATGGTTTATGGTTT-AGGGCTTA
1 A-GGTTTATGGTTTAAGTG-TTA
* * *
9971198 GGGGCTTAGGGTTT-AGTGTTTA
1 -AGGTTTATGGTTTAAGTG-TTA
*
9971220 AAGTTTATGGTTTA
1 AGGTTTATGGTTTA
9971234 TGGTTTAGGG
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
20 5 0.08
21 32 0.53
22 23 0.38
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.47
Consensus pattern (21 bp):
AGGTTTATGGTTTAAGTGTTA
Found at i:9971217 original size:50 final size:51
Alignment explanation
Indices: 9971153--9971250 Score: 162
Period size: 50 Copynumber: 1.9 Consensus size: 51
9971143 GGTTTAGTGT
* *
9971153 TTAGTGTTTAGTGTTTAAGGTTAATGGTTTATGGTTTA-GGGCTTAGGGGC
1 TTAGGGTTTAGTGTTTAAAGTTAATGGTTTATGGTTTAGGGGCTTAGGGGC
*
9971203 TTAGGGTTTAGTGTTTAAAGTTTATGGTTTATGGTTTAGGGGCTTAGG
1 TTAGGGTTTAGTGTTTAAAGTTAATGGTTTATGGTTTAGGGGCTTAGG
9971251 TTTATGGTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 35 0.80
51 9 0.20
ACGTcount: A:0.18, C:0.03, G:0.34, T:0.45
Consensus pattern (51 bp):
TTAGGGTTTAGTGTTTAAAGTTAATGGTTTATGGTTTAGGGGCTTAGGGGC
Found at i:9971227 original size:43 final size:42
Alignment explanation
Indices: 9971179--9971268 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 42
9971169 AAGGTTAATG
9971179 GTTTATGGTTTAGGGCTTAGGGGCTTAGGGTTTA-GTGTTTAAA
1 GTTTATGGTTTAGGGCTTAGGGGCTTA-GGTTTATG-GTTTAAA
* * *
9971222 GTTTATGGTTTATGGTTTAGGGGCTTAGGTTTATGGTTTAAT
1 GTTTATGGTTTAGGGCTTAGGGGCTTAGGTTTATGGTTTAAA
9971264 GTTTA
1 GTTTA
9971269 GGGTCTGATT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 17 0.40
43 26 0.60
ACGTcount: A:0.18, C:0.03, G:0.32, T:0.47
Consensus pattern (42 bp):
GTTTATGGTTTAGGGCTTAGGGGCTTAGGTTTATGGTTTAAA
Found at i:9975779 original size:43 final size:43
Alignment explanation
Indices: 9975682--9975891 Score: 203
Period size: 43 Copynumber: 4.9 Consensus size: 43
9975672 GAACGGTACT
* *
9975682 TTTAGCGGCGTTTGTGAAAAAAAAGCCGCTAAA-GTCATTCTC
1 TTTAGCGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATTCTC
* * * *
9975724 TATAGCGGCGTTTGTGATAAAAGCGCCACTAAAGGTTATTCTC
1 TTTAGCGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATTCTC
* * *
9975767 TTTAACGGCGTTTGTGATAAAAACACCGTTAAAGGTCATGT-TC
1 TTTAGCGGCGTTTGTGATAAAAACGCCGCTAAAGGTCAT-TCTC
*** * * *
9975810 TTTAGCAATGTTTGTGATAAAAGCGCCGCTAAAGATCACGT-TC
1 TTTAGCGGCGTTTGTGATAAAAACGCCGCTAAAGGTCA-TTCTC
* * *
9975853 TTTAGCGGCGTTTGTGGGT-AAAGCGTCGCTAAAGGTCAT
1 TTTAGCGGCGTTTGT-GATAAAAACGCCGCTAAAGGTCAT
9975892 GTTTTTTAAC
Statistics
Matches: 135, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
42 28 0.21
43 104 0.77
44 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATTCTC
Found at i:9991011 original size:13 final size:14
Alignment explanation
Indices: 9990990--9991023 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
9990980 TAAAAGTGTC
*
9990990 CTTTTTTTTCTTT-
1 CTTTCTTTTCTTTG
9991003 CTTTCTTTTCTTTG
1 CTTTCTTTTCTTTG
9991017 CTTTCTT
1 CTTTCTT
9991024 ATGTAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (14 bp):
CTTTCTTTTCTTTG
Found at i:9995380 original size:6 final size:6
Alignment explanation
Indices: 9995366--9995396 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
9995356 GAGAAGTGAA
*
9995366 GTGACG GTGAGG GTGAGG GTGAGG GTGAGG G
1 GTGAGG GTGAGG GTGAGG GTGAGG GTGAGG G
9995397 GTTGCTTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.03, G:0.65, T:0.16
Consensus pattern (6 bp):
GTGAGG
Found at i:9999532 original size:16 final size:15
Alignment explanation
Indices: 9999505--9999559 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
9999495 TTTTTCATAA
9999505 ATATATATTATT-TT
1 ATATATATTATTATT
9999519 ATATATATCCTATTATT
1 ATATATAT--TATTATT
*
9999536 -TATATACTTATTATAC
1 ATATATA-TTATTAT-T
9999552 ATATATAT
1 ATATATAT
9999560 ATAAGTGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 8 0.24
15 6 0.18
16 11 0.32
17 9 0.26
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATATATTATTATT
Found at i:10000431 original size:40 final size:40
Alignment explanation
Indices: 10000382--10000521 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 40
10000372 AACACACCAG
* * *
10000382 TTTGGCACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
* *
10000422 TTTGACACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
* * * * *
10000460 -TTGGCACCTAGTGTCTCATCGAATTAATCCAAAGTAGTAA
1 TTTGACACCCAGTGTCTCATCGGA-TAATCCGAAGTAATAA
* *
10000500 ATTGACACCTAGTGTCTCATCG
1 TTTGACACCCAGTGTCTCATCG
10000522 ACTCGAAGTC
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
37 19 0.23
38 11 0.13
39 1 0.01
40 32 0.39
41 20 0.24
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (40 bp):
TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
Found at i:10001382 original size:11 final size:10
Alignment explanation
Indices: 10001359--10001408 Score: 55
Period size: 11 Copynumber: 4.6 Consensus size: 10
10001349 CTTTCTCCAT
10001359 TTTCTTTTTC
1 TTTCTTTTTC
10001369 TTTCTTTCTTC
1 TTTCTTT-TTC
*
10001380 TTTCTATTTC
1 TTTCTTTTTC
10001390 GTTTCTATCTTTC
1 -TTTCT-T-TTTC
10001403 TTTCTT
1 TTTCTT
10001409 CATTTCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 10 0.29
11 15 0.44
12 5 0.15
13 4 0.12
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:10003706 original size:43 final size:42
Alignment explanation
Indices: 10003638--10003788 Score: 178
Period size: 42 Copynumber: 3.5 Consensus size: 42
10003628 CAATGTCAAA
* * *
10003638 GTCCCAGACGTGGTCTTACATGTAATCAAATAACGATGCCATT
1 GTCCCAGACATGGTCTTACACGTAATCAAAT-ACGATGCCAAT
* * *
10003681 GTCTCAGACATGGTCTTACACGTAATCATATATGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAATCAAATACGATGCCAAT
* *
10003723 GTCCCAGACATGGTCTTACACGTAAATCTCAAAT-CGATGCAAAC
1 GTCCCAGACATGGTCTTACACGT-AA--TCAAATACGATGCCAAT
*
10003767 GTCCCAGACGTGGTCTTACACG
1 GTCCCAGACATGGTCTTACACG
10003789 ATATCACATT
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
42 31 0.33
43 29 0.31
44 28 0.30
45 5 0.05
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGTAATCAAATACGATGCCAAT
Found at i:10003731 original size:42 final size:42
Alignment explanation
Indices: 10003638--10003788 Score: 169
Period size: 43 Copynumber: 3.5 Consensus size: 42
10003628 CAATGTCAAA
* * * * *
10003638 GTCCCAGACGTGGTCTTACATGTAATCAAATAACGATGCCATT
1 GTCCCAGACATGGTCTTACACGTAATCATAT-ATGATGCCAAT
*
10003681 GTCTCAGACATGGTCTTACACGTAATCATATATGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAATCATATATGATGCCAAT
* * *
10003723 GTCCCAGACATGGTCTTACACGTAAATC-TCAAATCGATGCAAAC
1 GTCCCAGACATGGTCTTACACGT-AATCAT-ATAT-GATGCCAAT
*
10003767 GTCCCAGACGTGGTCTTACACG
1 GTCCCAGACATGGTCTTACACG
10003789 ATATCACATT
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.34
43 34 0.36
44 28 0.30
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGTAATCATATATGATGCCAAT
Found at i:10006088 original size:12 final size:12
Alignment explanation
Indices: 10006071--10006125 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
10006061 AAGAGAATTT
10006071 TTTAAAATTTAA
1 TTTAAAATTTAA
10006083 TTTAAAATTTAA
1 TTTAAAATTTAA
10006095 -TT--AATGTTAA
1 TTTAAAAT-TTAA
*
10006105 TTTAAATATTTTA
1 TTTAAA-ATTTAA
10006118 -TTAAAATT
1 TTTAAAATT
10006126 AAAATACCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
9 3 0.08
10 4 0.11
11 7 0.19
12 17 0.46
13 4 0.11
14 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (12 bp):
TTTAAAATTTAA
Found at i:10006104 original size:22 final size:23
Alignment explanation
Indices: 10006079--10006121 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
10006069 TTTTTAAAAT
10006079 TTAATTTAAA-ATTTAATTAATG
1 TTAATTTAAATATTTAATTAATG
*
10006101 TTAATTTAAATATTTTATTAA
1 TTAATTTAAATATTTAATTAA
10006122 AATTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAATTTAAATATTTAATTAATG
Found at i:10006127 original size:23 final size:22
Alignment explanation
Indices: 10006066--10006127 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
10006056 GGAAAAAGAG
10006066 AATTTT-TTAAAATTTAATTTAA
1 AATTTTATTAAAA-TTAATTTAA
* **
10006088 AATTTAATTAATGTTAATTTAA
1 AATTTTATTAAAATTAATTTAA
10006110 ATATTTTATTAAAATTAA
1 A-ATTTTATTAAAATTAA
10006128 AATACCATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTTTATTAAAATTAATTTAA
Found at i:10006544 original size:13 final size:12
Alignment explanation
Indices: 10006519--10006543 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10006509 GATATTTAAT
10006519 ATCATTAAAAAA
1 ATCATTAAAAAA
10006531 ATCATTAAAAAA
1 ATCATTAAAAAA
10006543 A
1 A
10006544 AGAATCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
ATCATTAAAAAA
Found at i:10006620 original size:29 final size:30
Alignment explanation
Indices: 10006587--10006662 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 30
10006577 AAACTATAAA
*
10006587 ATATATAAAATAC-AAACATTATA-AAATT
1 ATATATAAAATACAAAAAATTATATAAATT
*
10006615 AT-TATAAATTACAAAAAATTATATAAATT
1 ATATATAAAATACAAAAAATTATATAAATT
*
10006644 AT-TAAAAAATGA-AAAAAAT
1 ATATATAAAAT-ACAAAAAAT
10006663 AAAAAAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 9 0.22
28 11 0.27
29 20 0.49
30 1 0.02
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (30 bp):
ATATATAAAATACAAAAAATTATATAAATT
Found at i:10006639 original size:19 final size:19
Alignment explanation
Indices: 10006609--10006697 Score: 65
Period size: 19 Copynumber: 4.6 Consensus size: 19
10006599 CAAACATTAT
10006609 AAAATTATTATAAATTACAA
1 AAAATTA-TATAAATTACAA
*
10006629 AAAATTATATAAATTATTAA
1 AAAATTATATAAATTA-CAA
* * * *
10006649 AAAATGA-AAAAAATAAAA
1 AAAATTATATAAATTACAA
* * *
10006667 AAAACTA-ATAAAATAACAT
1 AAAATTATAT-AAATTACAA
10006686 AAAATTATATAA
1 AAAATTATATAA
10006698 GTTATGAAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
18 8 0.15
19 28 0.53
20 17 0.32
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.28
Consensus pattern (19 bp):
AAAATTATATAAATTACAA
Found at i:10006650 original size:20 final size:21
Alignment explanation
Indices: 10006604--10006653 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
10006594 AAATACAAAC
*
10006604 ATTATAAAATTATTATAAATT
1 ATTAAAAAATTATTATAAATT
*
10006625 A-CAAAAAATTA-TATAAATT
1 ATTAAAAAATTATTATAAATT
10006644 ATTAAAAAAT
1 ATTAAAAAAT
10006654 GAAAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.36
20 15 0.60
21 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAAAAAATTATTATAAATT
Found at i:10007190 original size:16 final size:17
Alignment explanation
Indices: 10007169--10007203 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
10007159 ATATTTTTAA
*
10007169 TAATTTTCTAT-ATTTT
1 TAATTTTCCATGATTTT
10007185 TAATTTTCCATGATTTT
1 TAATTTTCCATGATTTT
10007202 TA
1 TA
10007204 CAAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.63
Consensus pattern (17 bp):
TAATTTTCCATGATTTT
Found at i:10012691 original size:44 final size:43
Alignment explanation
Indices: 10012606--10012697 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 43
10012596 TAATAAGAGT
* *
10012606 ATATCTAAATATTAATTTAGTAAAAATAAATTTTAATAATTAAA
1 ATATCTAAATATTAATTTAGTAAAAATAAA-TGTAAAAATTAAA
*
10012650 ATATCTAAATATTAA-TTACGTAAAAAATTAAA-GTAAAAATTATA
1 ATATCTAAATATTAATTTA-GT-AAAAA-TAAATGTAAAAATTAAA
10012694 ATAT
1 ATAT
10012698 TCAATAAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
43 3 0.07
44 30 0.71
45 5 0.12
46 4 0.10
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (43 bp):
ATATCTAAATATTAATTTAGTAAAAATAAATGTAAAAATTAAA
Done.