Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 66 of 189
Found at i:18412176 original size:11 final size:11
Alignment explanation
Indices: 18412146--18412170 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18412136 GAGAAATTTA
18412146 AGAGCAAATTG
1 AGAGCAAATTG
18412157 AGAGCAAATTG
1 AGAGCAAATTG
18412168 AGA
1 AGA
18412171 TTAAATATGG
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:0.28, T:0.16
Consensus pattern (11 bp):
AGAGCAAATTG
Found at i:18412231 original size:12 final size:12
Alignment explanation
Indices: 18412181--18412236 Score: 66
Period size: 11 Copynumber: 4.9 Consensus size: 12
18412171 TTAAATATGG
18412181 ATTTGAGA-GAA
1 ATTTGAGAGGAA
18412192 ATTTG-GAAGG-A
1 ATTTGAG-AGGAA
*
18412203 ATTTGAGAGCAA
1 ATTTGAGAGGAA
18412215 A-TTGAGAGGAA
1 ATTTGAGAGGAA
18412226 ATTTGAGAGGA
1 ATTTGAGAGGA
18412237 TTAGTTTGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 1 0.03
11 24 0.63
12 13 0.34
ACGTcount: A:0.41, C:0.02, G:0.32, T:0.25
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:18413096 original size:24 final size:23
Alignment explanation
Indices: 18413065--18413111 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
18413055 ACACTTTTTA
18413065 ATTATATTATTAAGTAATAATTT
1 ATTATATTATTAAGTAATAATTT
* * *
18413088 ATTAGTATTGTTATGTGATAATTT
1 ATTA-TATTATTAAGTAATAATTT
18413112 TGATGAAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (23 bp):
ATTATATTATTAAGTAATAATTT
Found at i:18414253 original size:59 final size:59
Alignment explanation
Indices: 18414187--18414308 Score: 244
Period size: 59 Copynumber: 2.1 Consensus size: 59
18414177 TAAAATCATG
18414187 AAAACATTCATTACGACACATAATTTTTATAAAAAATAAATATATATTTATATAAAAAT
1 AAAACATTCATTACGACACATAATTTTTATAAAAAATAAATATATATTTATATAAAAAT
18414246 AAAACATTCATTACGACACATAATTTTTATAAAAAATAAATATATATTTATATAAAAAT
1 AAAACATTCATTACGACACATAATTTTTATAAAAAATAAATATATATTTATATAAAAAT
18414305 AAAA
1 AAAA
18414309 ATAAAAATAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (59 bp):
AAAACATTCATTACGACACATAATTTTTATAAAAAATAAATATATATTTATATAAAAAT
Found at i:18418800 original size:18 final size:19
Alignment explanation
Indices: 18418779--18418816 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
18418769 TTAGTTTAGG
* *
18418779 TATTTTAAATTTTG-AATT
1 TATTTGAAAGTTTGTAATT
18418797 TATTTGAAAGTTTGTAATT
1 TATTTGAAAGTTTGTAATT
18418816 T
1 T
18418817 TTGGGACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (19 bp):
TATTTGAAAGTTTGTAATT
Found at i:18420952 original size:41 final size:41
Alignment explanation
Indices: 18420835--18420952 Score: 128
Period size: 41 Copynumber: 2.9 Consensus size: 41
18420825 ACATCCAGGA
* * * * *
18420835 GTACCGAAGTACAAACATGTGCACGTATGTGCAATCTAGGG
1 GTACCAAAGTACAAATAAGGGCACGTATGTGCAATTTAGGG
** * * *
18420876 GTTTCGAAGTACAAATAAGGACATGTATGTGCAATTTAGGG
1 GTACCAAAGTACAAATAAGGGCACGTATGTGCAATTTAGGG
* *
18420917 GTACCAAAGTTCAAATAGGGGCACGTATGTGCAATT
1 GTACCAAAGTACAAATAAGGGCACGTATGTGCAATT
18420953 CTTTATTATT
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (41 bp):
GTACCAAAGTACAAATAAGGGCACGTATGTGCAATTTAGGG
Found at i:18422658 original size:20 final size:20
Alignment explanation
Indices: 18422633--18422675 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
18422623 AAAACTTAGA
* *
18422633 CTTGTTGATAAAACTCGTTT
1 CTTGTTGATAAAAATCATTT
18422653 CTTGTTGATAAAAATCATTT
1 CTTGTTGATAAAAATCATTT
18422673 CTT
1 CTT
18422676 AAGTTTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.47
Consensus pattern (20 bp):
CTTGTTGATAAAAATCATTT
Found at i:18423797 original size:107 final size:105
Alignment explanation
Indices: 18423617--18423940 Score: 346
Period size: 107 Copynumber: 3.0 Consensus size: 105
18423607 TTTCGGTCAT
* * *
18423617 TTTACCC-TTCAGCGGTATTTTGATAATTTTACCCTTTGAAGGTATTTCAATAATTTTACCTTTC
1 TTTACCCTTTAAG-GGTATTTTGGTAATTTTACCC-TTGAGGGTATTTCAATAATTTTACCTTT-
* * *
18423681 AAGGCTATTTTGGTAATTTTACCCTTCGAGGGTGTTTCAGTAA
63 AAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCAGTAA
* * * *
18423724 TTTACTCTTTAAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGATAAATTTATCCTTTA
1 TTTACCCTTTAAGGGTATTTTGGTAATTTTACCCTT-GAGGGTATTTCAATAATTTTA-CCTTTA
* * * *
18423789 AGGGTATTTCGATAATTTTACCCTTC-AAGGTATTTCGGTTAT
64 AGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCAG-TAA
* * * * * * *
18423831 TTTACCCTTTAAGGGTATTTTGGTTATTTTACCCTTTAGGGGTATTTTAGTCATTTTACCCTTCA
1 TTTACCCTTTAAGGGTATTTTGGTAATTTTACCCTTGA-GGGTATTTCAATAATTTTACCTTTAA
* * *
18423896 GAGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCAGTCA
65 G-GGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCAGTAA
18423938 TTT
1 TTT
18423941 GCCTACGAAT
Statistics
Matches: 178, Mismatches: 32, Indels: 14
0.79 0.14 0.06
Matches are distributed among these distances:
106 18 0.10
107 141 0.79
108 19 0.11
ACGTcount: A:0.22, C:0.16, G:0.17, T:0.45
Consensus pattern (105 bp):
TTTACCCTTTAAGGGTATTTTGGTAATTTTACCCTTGAGGGTATTTCAATAATTTTACCTTTAAG
GGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCAGTAA
Found at i:18423940 original size:27 final size:26
Alignment explanation
Indices: 18423588--18423932 Score: 289
Period size: 27 Copynumber: 12.8 Consensus size: 26
18423578 TATAACGATT
*
18423588 ATTTTACCCTAT-AGGAGTATTTCGGTC
1 ATTTTACCCT-TCAGG-GTATTTCGGTA
* *
18423615 ATTTTACCCTTCAGCGGTATTTTGATA
1 ATTTTACCCTTCAG-GGTATTTCGGTA
* * **
18423642 ATTTTACCCTTTGAAGGTATTTCAATA
1 ATTTTACCC-TTCAGGGTATTTCGGTA
* * *
18423669 ATTTTACCTTTCAAGGCTATTTTGGTA
1 ATTTTACCCTTC-AGGGTATTTCGGTA
* *
18423696 ATTTTACCCTTCGAGGGTGTTTCAGTA
1 ATTTTACCCTTC-AGGGTATTTCGGTA
* *
18423723 A-TTTACTCTTTAAGGGTATTTCGGTA
1 ATTTTAC-CCTTCAGGGTATTTCGGTA
*
18423749 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTC-AGGGTATTTCGGTA
* * * *
18423776 AATTTATCCTTTAAGGGTATTTCGATA
1 ATTTTA-CCCTTCAGGGTATTTCGGTA
* *
18423803 ATTTTACCCTTCAAGGTATTTCGGTT
1 ATTTTACCCTTCAGGGTATTTCGGTA
* * *
18423829 ATTTTACCCTTTAAGGGTATTTTGGTT
1 ATTTTACCC-TTCAGGGTATTTCGGTA
* ** *
18423856 ATTTTACCCTTTAGGGGTATTTTAGTC
1 ATTTTACCCTTCA-GGGTATTTCGGTA
*
18423883 ATTTTACCCTTCAGAGGTATTTCGGTC
1 ATTTTACCCTTCAG-GGTATTTCGGTA
*
18423910 ATTTTACCCATCGAGGGTATTTC
1 ATTTTACCCTTC-AGGGTATTTC
18423933 AGTCATTTGC
Statistics
Matches: 260, Mismatches: 46, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
26 52 0.20
27 198 0.76
28 10 0.04
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (26 bp):
ATTTTACCCTTCAGGGTATTTCGGTA
Found at i:18428471 original size:25 final size:25
Alignment explanation
Indices: 18428412--18428669 Score: 99
Period size: 25 Copynumber: 10.4 Consensus size: 25
18428402 ACATGTATGT
*
18428412 TCATATGAG-CATATAAACGAGAAGC
1 TCATAAGAGCCATAT-AACGAGAAGC
* ** *
18428437 TCTTCCGAGCCATATAACGGGAAGC
1 TCATAAGAGCCATATAACGAGAAGC
** * *
18428462 TCATGTGAG-CAGTATAAAGGGAAGC
1 TCATAAGAGCCA-TATAACGAGAAGC
** * *
18428487 TCATTTGAG-C-TGAGAATCAAGAAGC
1 TCATAAGAGCCAT-ATAA-CGAGAAGC
**
18428512 TCATAAGAGCTGTA-AATC-AGGAAGC
1 TCATAAGAGCCATATAA-CGA-GAAGC
* **
18428537 TCATATGAGCCA-ATATTGAGAAGC
1 TCATAAGAGCCATATAACGAGAAGC
*
18428561 TC-TGGAGAGCCAT-TAATCGAGAAGC
1 TCAT-AAGAGCCATATAA-CGAGAAGC
*
18428586 TCATAAGAGCCA-ATTATCGAGAAGC
1 TCATAAGAGCCATA-TAACGAGAAGC
* *
18428611 TCATGAGAGCCAAATAACG-GCAAGC
1 TCATAAGAGCCATATAACGAG-AAGC
** * *
18428636 TCAGGAGAGCCATATATC-AGGATGC
1 TCATAAGAGCCATATAACGA-GAAGC
18428661 TCATAAGAG
1 TCATAAGAG
18428670 TTGTGGTGAG
Statistics
Matches: 179, Mismatches: 35, Indels: 38
0.71 0.14 0.15
Matches are distributed among these distances:
23 2 0.01
24 23 0.13
25 142 0.79
26 11 0.06
27 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (25 bp):
TCATAAGAGCCATATAACGAGAAGC
Found at i:18428636 original size:50 final size:49
Alignment explanation
Indices: 18428532--18428653 Score: 133
Period size: 50 Copynumber: 2.4 Consensus size: 49
18428522 TGTAAATCAG
* * *
18428532 GAAGCTCATATGAGCCAATATTGAGAAGCTCTGGAGAGCCATTAATCGA
1 GAAGCTCATAAGAGCCAATATCGAGAAGCTCTGGAGAGCCAATAATCGA
18428581 GAAGCTCATAAGAGCCAATTATCGAGAAGCTCAT-GAGAGCCAAATAA-CG-
1 GAAGCTCATAAGAGCCAA-TATCGAGAAGCTC-TGGAGAGCC-AATAATCGA
**
18428630 GCAAGCTCAGGAGAGCCATATATC
1 G-AAGCTCATAAGAGCCA-ATATC
18428654 AGGATGCTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
49 18 0.29
50 39 0.62
51 6 0.10
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (49 bp):
GAAGCTCATAAGAGCCAATATCGAGAAGCTCTGGAGAGCCAATAATCGA
Found at i:18439102 original size:14 final size:14
Alignment explanation
Indices: 18439083--18439114 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
18439073 AGTTTGAATG
*
18439083 TCAAATTATTTGAA
1 TCAAATTAATTGAA
18439097 TCAAATTAATTGAA
1 TCAAATTAATTGAA
18439111 TCAA
1 TCAA
18439115 CTTGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (14 bp):
TCAAATTAATTGAA
Found at i:18439556 original size:18 final size:19
Alignment explanation
Indices: 18439514--18439560 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
18439504 TATCAATTTC
*
18439514 ACATTTTATTTTAAAAATA
1 ACATTTTATTTAAAAAATA
*
18439533 AC-TTTTA-TTAAAAAATT
1 ACATTTTATTTAAAAAATA
18439550 ACATTTT-TTTA
1 ACATTTTATTTA
18439561 CATTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 10 0.42
18 12 0.50
19 2 0.08
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (19 bp):
ACATTTTATTTAAAAAATA
Found at i:18441053 original size:24 final size:24
Alignment explanation
Indices: 18441026--18441077 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
18441016 TTAGTAAGTC
*
18441026 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
18441050 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
18441074 AAAT
1 AAAT
18441078 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:18443396 original size:25 final size:23
Alignment explanation
Indices: 18443368--18443412 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
18443358 ATGTTATAAT
*
18443368 TTTTTTATTTATCAAAATATATA
1 TTTTTTATTTACCAAAATATATA
18443391 TTTTTTATTTACCAAAATATAT
1 TTTTTTATTTACCAAAATATAT
18443413 CAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTTTATTTACCAAAATATATA
Found at i:18443487 original size:27 final size:27
Alignment explanation
Indices: 18443456--18443541 Score: 97
Period size: 27 Copynumber: 3.2 Consensus size: 27
18443446 GCCTGATCAG
*
18443456 GCCAATTAAATTGGCGGCACCATAGGT
1 GCCAAATAAATTGGCGGCACCATAGGT
*
18443483 GCCAAATAAATTGGTGGCACCA-ATGGT
1 GCCAAATAAATTGGCGGCACCATA-GGT
* *
18443510 GCCAAAGT-CATTGGCGGCACTAT-GGT
1 GCCAAA-TAAATTGGCGGCACCATAGGT
18443536 GCCAAA
1 GCCAAA
18443542 GGAAAAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.20
27 40 0.78
28 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (27 bp):
GCCAAATAAATTGGCGGCACCATAGGT
Found at i:18443640 original size:19 final size:19
Alignment explanation
Indices: 18443613--18443681 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
18443603 CTTCAAGTTT
*
18443613 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
18443632 TTTTAATTTAATAA--ATA
1 TTTTAATTTAATAACTCTA
* *
18443649 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
18443668 TTTTAATTTAATAA
1 TTTTAATTTAATAA
18443682 ACTATTAAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
17 14 0.34
19 27 0.66
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:18443661 original size:36 final size:37
Alignment explanation
Indices: 18443618--18443687 Score: 133
Period size: 36 Copynumber: 1.9 Consensus size: 37
18443608 AGTTTTTTTT
18443618 ATTTAATAACTCTATTTTAATTTAATAAA-TATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
18443654 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
18443688 AAGTAATACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 29 0.88
37 4 0.12
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:18443931 original size:19 final size:19
Alignment explanation
Indices: 18443904--18443973 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
18443894 TCAACTCAAT
*
18443904 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
18443923 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
18443941 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
18443960 TTTTAATTTAATAA
1 TTTTAATTTAATAA
18443974 AATATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:18443954 original size:37 final size:37
Alignment explanation
Indices: 18443909--18443979 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
18443899 TCAATTTTTT
*
18443909 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
18443946 ATTTAATAACTCTATTTTAATTTAATAAAATATT
1 ATTTAATAACTCTATTTTAATTTAATAAAATATT
18443980 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
Found at i:18444275 original size:19 final size:19
Alignment explanation
Indices: 18444251--18444324 Score: 87
Period size: 19 Copynumber: 3.9 Consensus size: 19
18444241 CTTAATTTTT
18444251 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
18444270 TTAAATGATAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
*
18444288 TTAAATTAAAATAGAATTA
1 TTAAATTAAAATAGAGTTA
* *
18444307 TTAAATAAAAAAAGAGTT
1 TTAAATTAAAATAGAGTT
18444325 GAAGGGAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 15 0.33
19 30 0.67
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.36
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:18444456 original size:27 final size:27
Alignment explanation
Indices: 18444386--18444471 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
18444376 TTTTTTTTCC
* *
18444386 TTTGGCACCA-TGGTGCCGCCAA-TGA
1 TTTGGCACCATTGGTGCCACCAATTTA
*
18444411 CTTTGGCACCATTGGTGCCACTAATTTA
1 -TTTGGCACCATTGGTGCCACCAATTTA
* *
18444439 TTTGGCA-CATTTGTTGCCGCCAATTTA
1 TTTGGCACCA-TTGGTGCCACCAATTTA
*
18444466 ATTGGC
1 TTTGGC
18444472 CTGATTAGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
26 12 0.24
27 36 0.72
28 2 0.04
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (27 bp):
TTTGGCACCATTGGTGCCACCAATTTA
Found at i:18444557 original size:26 final size:24
Alignment explanation
Indices: 18444503--18444558 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
18444493 TTTTTGATAT
* **
18444503 ATTTTGATAAATAAAAAATATATT
1 ATTTTAATAAATAAAAAATATAAC
*
18444527 TTTTTAATAAATAAAAAAATTATAAC
1 ATTTTAATAAAT-AAAAAA-TATAAC
18444553 ATTTTA
1 ATTTTA
18444559 GTTATTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 10 0.40
25 6 0.24
26 9 0.36
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTTTAATAAATAAAAAATATAAC
Found at i:18448187 original size:16 final size:18
Alignment explanation
Indices: 18448166--18448199 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18448156 AACTTTTTAC
18448166 ATTAA-TAA-TACGAAAA
1 ATTAATTAATTACGAAAA
18448182 ATTAATTAATTACGAAAA
1 ATTAATTAATTACGAAAA
18448200 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (18 bp):
ATTAATTAATTACGAAAA
Found at i:18449790 original size:11 final size:11
Alignment explanation
Indices: 18449763--18449819 Score: 78
Period size: 11 Copynumber: 5.1 Consensus size: 11
18449753 ATTAATGCTT
*
18449763 TCTCAATTATTC
1 TCTCAATT-TCC
18449775 TCTCAATTTCC
1 TCTCAATTTCC
18449786 TCTCAATTTCC
1 TCTCAATTTCC
* *
18449797 TTTCAATTTGC
1 TCTCAATTTCC
18449808 TCTCAATTTCC
1 TCTCAATTTCC
18449819 T
1 T
18449820 TCCAAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
11 32 0.80
12 8 0.20
ACGTcount: A:0.19, C:0.30, G:0.02, T:0.49
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:18449833 original size:22 final size:22
Alignment explanation
Indices: 18449786--18449835 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
18449776 CTCAATTTCC
* *
18449786 TCTCAATTTCCTTTCAATTTGC
1 TCTCAATTTCCTTCCAATTTGA
18449808 TCTCAATTTCCTTCCAAATTT-A
1 TCTCAATTTCCTTCC-AATTTGA
18449830 TCTCAA
1 TCTCAA
18449836 ATCCATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.24, C:0.28, G:0.02, T:0.46
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAATTTGA
Found at i:18449845 original size:17 final size:18
Alignment explanation
Indices: 18449820--18449853 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18449810 TCAATTTCCT
18449820 TCCAAATTT-ATCTCAAA
1 TCCAAATTTAATCTCAAA
*
18449837 TCCATATTTAATCTCAA
1 TCCAAATTTAATCTCAA
18449854 TTTCCTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (18 bp):
TCCAAATTTAATCTCAAA
Found at i:18449853 original size:40 final size:40
Alignment explanation
Indices: 18449808--18449885 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
18449798 TTCAATTTGC
18449808 TCTCAATTTCCT-TCCAAATTTATCTCAAATCCATATTTAA
1 TCTCAATTTCCTCT-CAAATTTATCTCAAATCCATATTTAA
* * *
18449848 TCTCAATTTCCTCTCAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTCCTCTCAAATTTATCTCAAATCCATATTT
18449886 TTAATTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.28, C:0.27, G:0.00, T:0.45
Consensus pattern (40 bp):
TCTCAATTTCCTCTCAAATTTATCTCAAATCCATATTTAA
Found at i:18451036 original size:7 final size:7
Alignment explanation
Indices: 18451024--18451052 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
18451014 AGCTAGTTGA
18451024 TTAGTAT
1 TTAGTAT
18451031 TTAGTAT
1 TTAGTAT
18451038 TTAGTAT
1 TTAGTAT
18451045 TTAGTAT
1 TTAGTAT
18451052 T
1 T
18451053 ATATATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (7 bp):
TTAGTAT
Found at i:18452021 original size:21 final size:21
Alignment explanation
Indices: 18451997--18452043 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
18451987 AGATACCCTA
* * *
18451997 CCGGAGGAACCAGAATCCCCG
1 CCGGAGCAACCACAACCCCCG
*
18452018 CCGGATCAACCACAACCCCCG
1 CCGGAGCAACCACAACCCCCG
18452039 CCGGA
1 CCGGA
18452044 AGCTAGACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.45, G:0.23, T:0.04
Consensus pattern (21 bp):
CCGGAGCAACCACAACCCCCG
Found at i:18452959 original size:18 final size:18
Alignment explanation
Indices: 18452936--18452970 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18452926 TTTCAGTACT
*
18452936 TCTGCTAACAAAGCATCC
1 TCTGCTAACAAAACATCC
18452954 TCTGCTAACAAAACATC
1 TCTGCTAACAAAACATC
18452971 TTGCTTAAAA
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:0.37, C:0.31, G:0.09, T:0.23
Consensus pattern (18 bp):
TCTGCTAACAAAACATCC
Found at i:18453207 original size:126 final size:126
Alignment explanation
Indices: 18453054--18453306 Score: 506
Period size: 126 Copynumber: 2.0 Consensus size: 126
18453044 TTTTGAAAAA
18453054 TTTAAAAATAATTTAATTGACAAACCCTAAACTAGAGGTGTTCATGGGCCAGGCAAAAAATATGG
1 TTTAAAAATAATTTAATTGACAAACCCTAAACTAGAGGTGTTCATGGGCCAGGCAAAAAATATGG
18453119 GAGGGTTCGGGTAAAAATATAGGCCCGAATTATGGGTTTGAGCAAAAAAGCGAGGCCCGTT
66 GAGGGTTCGGGTAAAAATATAGGCCCGAATTATGGGTTTGAGCAAAAAAGCGAGGCCCGTT
18453180 TTTAAAAATAATTTAATTGACAAACCCTAAACTAGAGGTGTTCATGGGCCAGGCAAAAAATATGG
1 TTTAAAAATAATTTAATTGACAAACCCTAAACTAGAGGTGTTCATGGGCCAGGCAAAAAATATGG
18453245 GAGGGTTCGGGTAAAAATATAGGCCCGAATTATGGGTTTGAGCAAAAAAGCGAGGCCCGTT
66 GAGGGTTCGGGTAAAAATATAGGCCCGAATTATGGGTTTGAGCAAAAAAGCGAGGCCCGTT
18453306 T
1 T
18453307 AAAAAACGGG
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 127 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.24
Consensus pattern (126 bp):
TTTAAAAATAATTTAATTGACAAACCCTAAACTAGAGGTGTTCATGGGCCAGGCAAAAAATATGG
GAGGGTTCGGGTAAAAATATAGGCCCGAATTATGGGTTTGAGCAAAAAAGCGAGGCCCGTT
Found at i:18453435 original size:29 final size:29
Alignment explanation
Indices: 18453402--18453459 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
18453392 TTATTCTTTA
*
18453402 ATTTTAAATT-TTTTTTAAAATACTTTTTT
1 ATTTT-AATTATTTTTTAAAATAATTTTTT
*
18453431 ATTTTATTTATTTTTTAAAATAATTTTTT
1 ATTTTAATTATTTTTTAAAATAATTTTTT
18453460 TGGTGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (29 bp):
ATTTTAATTATTTTTTAAAATAATTTTTT
Found at i:18453468 original size:28 final size:29
Alignment explanation
Indices: 18453412--18453470 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
18453402 ATTTTAAATT
* **
18453412 TTTTTTAAAATACTTTTTTATTTTATTTA
1 TTTTTTAAAATAATTTTTTATGGTATTTA
*
18453441 TTTTTTAAAATAATTTTTT-TGGTGTTTA
1 TTTTTTAAAATAATTTTTTATGGTATTTA
18453469 TT
1 TT
18453471 AAAAATGGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (29 bp):
TTTTTTAAAATAATTTTTTATGGTATTTA
Found at i:18457146 original size:3 final size:3
Alignment explanation
Indices: 18457133--18457205 Score: 76
Period size: 3 Copynumber: 24.3 Consensus size: 3
18457123 TAATATTAAT
* * * **
18457133 TTA TCA TTA TTA TTTA TTA CTA TTA TTA CTA TCG TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
18457179 TTA TTA TTA TTA GTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
18457206 ATATATTAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:18464893 original size:13 final size:13
Alignment explanation
Indices: 18464875--18464899 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18464865 CTAAAAATCT
18464875 TTTTATAATTTTA
1 TTTTATAATTTTA
18464888 TTTTATAATTTT
1 TTTTATAATTTT
18464900 TTAAATTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTATAATTTTA
Found at i:18472908 original size:66 final size:66
Alignment explanation
Indices: 18472819--18472951 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
18472809 CTATATAGGA
18472819 AGAAAATCAAAATAAGTGATGTGTGTAAAAAGTATGTATTAAGAAAAATGAGATTAATAATAATA
1 AGAAAATCAAAATAAGTGATGTGTGTAAAAAGTATGTATTAAGAAAAATGAGATTAATAATAATA
18472884 C
66 C
18472885 AGAAAATCAAAATAAGTGATGTGTGTAAAAAGTATGTATTAAGAAAAATGAGATTAATAATAATA
1 AGAAAATCAAAATAAGTGATGTGTGTAAAAAGTATGTATTAAGAAAAATGAGATTAATAATAATA
18472950 C
66 C
18472951 A
1 A
18472952 TTAAGAATAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (66 bp):
AGAAAATCAAAATAAGTGATGTGTGTAAAAAGTATGTATTAAGAAAAATGAGATTAATAATAATA
C
Found at i:18473410 original size:3 final size:3
Alignment explanation
Indices: 18473402--18473460 Score: 59
Period size: 3 Copynumber: 20.3 Consensus size: 3
18473392 AGTTAGTAAG
*** *
18473402 TAA TAA TAA TAA TAA TAA TAA -AA GGC TAA TAA TAA -AA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
18473448 TAA TAA AAA TAA T
1 TAA TAA TAA TAA T
18473461 GGAGCTATTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:18486600 original size:3 final size:3
Alignment explanation
Indices: 18486537--18486580 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
18486527 TGCGTGCGCT
18486537 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18486581 TCAATTAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:18488488 original size:20 final size:20
Alignment explanation
Indices: 18488433--18488489 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
18488423 TGAAATTAGA
*
18488433 AAAAAATTAAATATAAAACT
1 AAAAAATTAAATTTAAAACT
* * *
18488453 ATAAAAA-TAATTTTTAATATT
1 A-AAAAATTAA-ATTTAAAACT
18488474 AAAAAATTAAATTTAA
1 AAAAAATTAAATTTAA
18488490 GTTTTAACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATTAAATTTAAAACT
Found at i:18488855 original size:9 final size:10
Alignment explanation
Indices: 18488843--18488885 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
18488833 TTTTTTTTAA
18488843 TTTTA-AATT
1 TTTTATAATT
18488852 TTTTATAACTT
1 TTTTATAA-TT
*
18488863 TTTTATATATA
1 TTTTATA-ATT
18488874 TTTTATAATT
1 TTTTATAATT
18488884 TT
1 TT
18488886 GTAAATATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 5 0.17
10 6 0.21
11 17 0.59
12 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:18495412 original size:20 final size:19
Alignment explanation
Indices: 18495386--18495431 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
18495376 AGCATATTAA
*
18495386 TTAAAATTTTTAAAAAAAT
1 TTAAAATTTATAAAAAAAT
18495405 TGTAAAATTTATAAAAAAAT
1 T-TAAAATTTATAAAAAAAT
18495425 TTAAAAT
1 TTAAAAT
18495432 AAAAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TTAAAATTTATAAAAAAAT
Found at i:18498875 original size:9 final size:9
Alignment explanation
Indices: 18498856--18498897 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
18498846 TTTTGGTTAA
*
18498856 AAATTACCC
1 AAATTAACC
*
18498865 GAATTAACC
1 AAATTAACC
*
18498874 GAATTAACC
1 AAATTAACC
18498883 AAATTAACC
1 AAATTAACC
18498892 AAATTA
1 AAATTA
18498898 TCGAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (9 bp):
AAATTAACC
Found at i:18499082 original size:13 final size:13
Alignment explanation
Indices: 18499064--18499093 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
18499054 TTTTAGTTTT
18499064 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
18499077 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
18499090 ATTG
1 ATTG
18499094 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:18505585 original size:20 final size:20
Alignment explanation
Indices: 18505549--18505588 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18505539 TCCTATTGTT
18505549 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
18505569 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
18505589 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:18506236 original size:44 final size:44
Alignment explanation
Indices: 18506122--18506238 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 44
18506112 TTTTAACCCA
* * ** * *
18506122 CTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
*
18506165 CTCCGCTGTAA-TCTC-GGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGG-GATAAGATCTCTGGCTTCAATCTG
*
18506209 CTCCACTGTAACTTCAGGGGGACAAGATCT
1 CTCCACTGTAACTTCAGGGGGATAAGATCT
18506239 GTAATTTCCA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
42 4 0.07
43 19 0.32
44 32 0.53
45 5 0.08
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGGGATAAGATCTCTGGCTTCAATCTG
Found at i:18506662 original size:88 final size:88
Alignment explanation
Indices: 18506399--18506941 Score: 726
Period size: 88 Copynumber: 6.2 Consensus size: 88
18506389 GCAACCAATG
* * * **
18506399 GAGGCAAGGCTTTGT-T-TTTGATCTGCTTTGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTT
1 GAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTT
* * * * **
18506461 TAACTAGCTCCA-CTGCAATCGATG
65 CAACCAGCTCCATC-ACAACCGAAA
* * * * **
18506485 GATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGACGGCAAGATCTGCT-TCTT
1 GAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTT
* *
18506547 TAACCAGCTCCA-CTACAACCGAGA
65 CAACCAGCTCCATC-ACAACCGAAA
* **
18506571 GAGGCAAGGTTTGTGTCTTCGACCTGCTTCAATGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
1 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
*
18506636 AACCAGCTCTATCACAACCGAAA
66 AACCAGCTCCATCACAACCGAAA
*
18506659 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTC
1 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
18506724 AACCAGCTCCATCACAACC-AAA
66 AACCAGCTCCATCACAACCGAAA
*
18506746 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTC
1 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
18506811 AACCAGCTCCATCACAACCGAAA
66 AACCAGCTCCATCACAACCGAAA
* *
18506834 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTT
1 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
*
18506899 AACCAGCTCCATCACAATCGAAA
66 AACCAGCTCCATCACAACCGAAA
*
18506922 GAGGCAAGGTTTGTGACTTC
1 GAGGCAAGGTTTGTGTCTTC
18506942 ATTGATCTGT
Statistics
Matches: 420, Mismatches: 32, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
85 5 0.01
86 85 0.20
87 121 0.29
88 208 0.50
89 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (88 bp):
GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTC
AACCAGCTCCATCACAACCGAAA
Found at i:18506711 original size:175 final size:176
Alignment explanation
Indices: 18506488--18506941 Score: 720
Period size: 175 Copynumber: 2.6 Consensus size: 176
18506478 ATCGATGGAT
* * **
18506488 GCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGACGGCAAGATCTGCT-TCTTTAA
1 GCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAA
*
18506550 CCAGCTCCA-CTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCAATGTCAATGCAG
65 CCAGCTCCATC-ACAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCAATGTCAATGCAG
* *
18506614 GAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAGAG
129 AAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAAGAG
* * *
18506662 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTCAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAAC
* **
18506727 CAGCTCCATCACAACC-AAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
66 CAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCAATGTCAATGCAGAA
18506791 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAAGAG
131 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAAGAG
18506837 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAAC
* *
18506902 CAGCTCCATCACAATCGAAAGAGGCAAGGTTTGTGACTTC
66 CAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
18506942 ATTGATCTGT
Statistics
Matches: 257, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
173 5 0.02
174 7 0.03
175 201 0.78
176 43 0.17
177 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (176 bp):
GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAAC
CAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCAATGTCAATGCAGAA
AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAAGAG
Found at i:18508665 original size:12 final size:12
Alignment explanation
Indices: 18508621--18508665 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
18508611 TTGATTTCTC
18508621 TTTGTTTTT-AT
1 TTTGTTTTTGAT
*
18508632 TTTTTATTTTGAT
1 TTTGT-TTTTGAT
*
18508645 TTTGATTTTGAT
1 TTTGTTTTTGAT
18508657 TTTGTTTTT
1 TTTGTTTTT
18508666 TTTTTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 4 0.14
12 19 0.68
13 5 0.18
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (12 bp):
TTTGTTTTTGAT
Found at i:18508677 original size:18 final size:17
Alignment explanation
Indices: 18508621--18508676 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
18508611 TTGATTTCTC
*
18508621 TTTGTTTTTATTTTTTAT
1 TTTGTTTTT-TTTTTCAT
** *
18508639 TTTGATTTTGATTTTGAT
1 TTTG-TTTTTTTTTTCAT
18508657 TTTGTTTTTTTTTTCAT
1 TTTGTTTTTTTTTTCAT
18508674 TTT
1 TTT
18508677 TCCTTGTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 13 0.42
18 14 0.45
19 4 0.13
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.79
Consensus pattern (17 bp):
TTTGTTTTTTTTTTCAT
Found at i:18516491 original size:20 final size:20
Alignment explanation
Indices: 18516455--18516494 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18516445 TCCTATTGTT
18516455 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
18516475 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
18516495 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:18517832 original size:93 final size:92
Alignment explanation
Indices: 18517650--18517836 Score: 286
Period size: 93 Copynumber: 2.0 Consensus size: 92
18517640 GTACACCACT
*
18517650 TCTCCTGGAAGATACAATCTAGATCTGGGTGTTCCTTTTTCCCCTTTTTTCCAATATGCAACACA
1 TCTCCTGGAAGAGACAATCTAGATCTGGGTGTTCCTTTTTCCCCTTTTTTCCAATATGCAACACA
* *
18517715 GCTAGTGTATAAAGAATTATCTAATCC
66 GCCAGTATATAAAGAATTATCTAATCC
* * * *
18517742 TCTCCTGGAAGAGA-AATCTAGATTTGGGTGTTCTTTTTTCCCCTTTTTTTTCCATTGTGCAACA
1 TCTCCTGGAAGAGACAATCTAGATCTGGGTGTTCCTTTTTCCCC--TTTTTTCCAATATGCAACA
18517806 CAGCCAGTATATAAAGAATTATCTAATCC
64 CAGCCAGTATATAAAGAATTATCTAATCC
18517835 TC
1 TC
18517837 ATCTTTGTCA
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
91 27 0.31
92 13 0.15
93 46 0.53
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.37
Consensus pattern (92 bp):
TCTCCTGGAAGAGACAATCTAGATCTGGGTGTTCCTTTTTCCCCTTTTTTCCAATATGCAACACA
GCCAGTATATAAAGAATTATCTAATCC
Found at i:18518407 original size:20 final size:20
Alignment explanation
Indices: 18518382--18518421 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18518372 TCCTCTCTCC
18518382 CTCAAGGCAACACCTTTTAT
1 CTCAAGGCAACACCTTTTAT
18518402 CTCAAGGCAACACCTTTTAT
1 CTCAAGGCAACACCTTTTAT
18518422 GCTGAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (20 bp):
CTCAAGGCAACACCTTTTAT
Found at i:18520065 original size:21 final size:22
Alignment explanation
Indices: 18520041--18520081 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
18520031 TTAGTTTAAG
*
18520041 TAGTTAAAG-TATGTATTTAGT
1 TAGTTAAAGCTATCTATTTAGT
*
18520062 TAGTTCAAGCTATCTATTTA
1 TAGTTAAAGCTATCTATTTA
18520082 CTGATATTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (22 bp):
TAGTTAAAGCTATCTATTTAGT
Found at i:18522848 original size:9 final size:9
Alignment explanation
Indices: 18522834--18522912 Score: 52
Period size: 9 Copynumber: 9.8 Consensus size: 9
18522824 ATCAATTTTA
18522834 AAAAATTAT
1 AAAAATTAT
18522843 AAAAA-TAT
1 AAAAATTAT
18522851 AAAAATT-T
1 AAAAATTAT
18522859 AGAAAA-TAT
1 A-AAAATTAT
* *
18522868 --ACATAAT
1 AAAAATTAT
*
18522875 AAAAAGTAT
1 AAAAATTAT
18522884 -AAAA--AT
1 AAAAATTAT
18522890 AAAAATTAT
1 AAAAATTAT
18522899 AAAAA--AT
1 AAAAATTAT
18522906 AAAAATT
1 AAAAATT
18522913 CATTAATTCC
Statistics
Matches: 54, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
6 4 0.07
7 13 0.24
8 15 0.28
9 22 0.41
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.27
Consensus pattern (9 bp):
AAAAATTAT
Found at i:18522888 original size:24 final size:22
Alignment explanation
Indices: 18522841--18522911 Score: 63
Period size: 24 Copynumber: 3.1 Consensus size: 22
18522831 TTAAAAAATT
*
18522841 ATAAAAAT-ATAAAAATTTAGAAA
1 ATAAAAATAATAAAAA-ATA-AAA
* *
18522864 ATATACATAATAAAAAGTATAAAA
1 ATAAAAATAATAAAAA--ATAAAA
*
18522888 ATAAAAATTATAAAAAATAAAA
1 ATAAAAATAATAAAAAATAAAA
18522910 AT
1 AT
18522912 TCATTAATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 8 0.20
23 6 0.15
24 23 0.57
25 3 0.08
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (22 bp):
ATAAAAATAATAAAAAATAAAA
Found at i:18522912 original size:16 final size:15
Alignment explanation
Indices: 18522841--18522911 Score: 72
Period size: 16 Copynumber: 4.5 Consensus size: 15
18522831 TTAAAAAATT
18522841 ATAAAAATATAAAAA
1 ATAAAAATATAAAAA
* * *
18522856 TTTAGAAAATATACATA
1 -ATA-AAAATATAAAAA
18522873 ATAAAAAGTAT-AAAA
1 ATAAAAA-TATAAAAA
18522888 ATAAAAATTATAAAAA
1 ATAAAAA-TATAAAAA
18522904 ATAAAAAT
1 ATAAAAAT
18522912 TCATTAATTC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
15 17 0.38
16 18 0.40
17 10 0.22
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (15 bp):
ATAAAAATATAAAAA
Found at i:18529228 original size:32 final size:33
Alignment explanation
Indices: 18529164--18529232 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
18529154 AACAATTGAA
* * *
18529164 TTAAAAATATATATTTATTAATTAAATTAAATT
1 TTAAAAATATATATTTATCAAGTAAATAAAATT
18529197 TTAATAAATATATATTT-TCAAGTAAA-AAAATT
1 TTAA-AAATATATATTTATCAAGTAAATAAAATT
18529229 TTAA
1 TTAA
18529233 GTAATAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 9 0.28
33 11 0.34
34 12 0.38
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (33 bp):
TTAAAAATATATATTTATCAAGTAAATAAAATT
Found at i:18530066 original size:17 final size:18
Alignment explanation
Indices: 18530046--18530079 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18530036 AAAATGAACT
18530046 AAAAATAAAAA-ATAAAG
1 AAAAATAAAAAGATAAAG
*
18530063 AAAATTAAAAAGATAAA
1 AAAAATAAAAAGATAAA
18530080 ATAATTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (18 bp):
AAAAATAAAAAGATAAAG
Found at i:18538600 original size:62 final size:62
Alignment explanation
Indices: 18538503--18538626 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
18538493 ATGTTATTTG
* *
18538503 AATGAGTAATTAGGTTCAAGTGGTAAATACTTAAAGTCAAGTGGTTTTAGAAAATGAGGTAT
1 AATGAGTAATTAGGTTCAAGTGGTAAATACTTAAAGTCAAGCGGTTTTAAAAAATGAGGTAT
18538565 AATGAGTAATTAGGTTCAAGTGGTAAAT-CTTTAAAGTCAAGCGGTTTTAAAAAATGAGGTAT
1 AATGAGTAATTAGGTTCAAGTGGTAAATAC-TTAAAGTCAAGCGGTTTTAAAAAATGAGGTAT
18538627 TGGGACCTCG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 1 0.02
62 58 0.98
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (62 bp):
AATGAGTAATTAGGTTCAAGTGGTAAATACTTAAAGTCAAGCGGTTTTAAAAAATGAGGTAT
Found at i:18541291 original size:19 final size:18
Alignment explanation
Indices: 18541254--18541302 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
18541244 GTGACCCCTG
*
18541254 TTTCCCAATTTTTCACAT
1 TTTCCCAAATTTTCACAT
*
18541272 TTTCCCAAAATTTTCTCAT
1 TTTCCC-AAATTTTCACAT
*
18541291 TTGTTCCAAATT
1 TT-TCCCAAATT
18541303 AGTCCTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 6 0.23
19 17 0.65
20 3 0.12
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTCCCAAATTTTCACAT
Found at i:18543403 original size:3 final size:3
Alignment explanation
Indices: 18543397--18543462 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
18543387 ATTATTATTA
*
18543397 TTG TTG TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
18543445 TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG
18543463 ATATTGTAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.02, C:0.00, G:0.32, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:18547971 original size:15 final size:15
Alignment explanation
Indices: 18547950--18547989 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
18547940 AAAGTTCTAC
18547950 TATTATTATTGTT-A
1 TATTATTATTGTTAA
*
18547964 TGATTATTATCGTTAA
1 T-ATTATTATTGTTAA
18547980 TATTATTATT
1 TATTATTATT
18547990 TACTGATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 1 0.05
15 19 0.86
16 2 0.09
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (15 bp):
TATTATTATTGTTAA
Found at i:18550353 original size:9 final size:10
Alignment explanation
Indices: 18550335--18550380 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
18550325 AACGTCTCTT
18550335 TTTGCATTCA
1 TTTGCATTCA
18550345 TTT-CATTCA
1 TTTGCATTCA
18550354 TTTGCATTGCA
1 TTTGCATT-CA
18550365 -TTGCA-TCA
1 TTTGCATTCA
*
18550373 TATGCATT
1 TTTGCATT
18550381 AGATTTTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
8 2 0.06
9 14 0.45
10 13 0.42
11 2 0.06
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (10 bp):
TTTGCATTCA
Found at i:18550359 original size:19 final size:19
Alignment explanation
Indices: 18550335--18550380 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
18550325 AACGTCTCTT
*
18550335 TTTGCATT-CATTTCATTCA
1 TTTGCATTGCATTGCA-TCA
18550354 TTTGCATTGCATTGCATCA
1 TTTGCATTGCATTGCATCA
*
18550373 TATGCATT
1 TTTGCATT
18550381 AGATTTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (19 bp):
TTTGCATTGCATTGCATCA
Found at i:18553715 original size:7 final size:6
Alignment explanation
Indices: 18553695--18553777 Score: 73
Period size: 6 Copynumber: 13.7 Consensus size: 6
18553685 ACTTCACTTG
* * * *
18553695 AAAA-A AAAACA AAATGA AAAA-A AAATGAA AAAAGA AAAACA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAG-A AAAAGA AAAAGA AAAAGA
18553742 AAAATGA AAAA-A GAAAAGA AAAAGA AAGAAGA AAAA
1 AAAA-GA AAAAGA -AAAAGA AAAAGA AA-AAGA AAAA
18553778 ATAAAAAGGA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
5 9 0.14
6 37 0.58
7 18 0.28
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:18553716 original size:8 final size:7
Alignment explanation
Indices: 18553714--18553784 Score: 62
Period size: 7 Copynumber: 10.7 Consensus size: 7
18553704 CAAAATGAAA
18553714 AAAAAATG
1 AAAAAA-G
18553722 AAAAAAG
1 AAAAAAG
18553729 -AAAAA-
1 AAAAAAG
*
18553734 CAAAAAG
1 AAAAAAG
*
18553741 AAAAATG
1 AAAAAAG
18553748 AAAAAAG
1 AAAAAAG
18553755 --AAAAG
1 AAAAAAG
18553760 -AAAAAG
1 AAAAAAG
*
18553766 AAAGAAG
1 AAAAAAG
*
18553773 AAAAAAT
1 AAAAAAG
18553780 AAAAA
1 AAAAA
18553785 GGAGAGGCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
5 5 0.09
6 15 0.28
7 27 0.51
8 6 0.11
ACGTcount: A:0.82, C:0.01, G:0.13, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:18553719 original size:19 final size:18
Alignment explanation
Indices: 18553695--18553784 Score: 76
Period size: 19 Copynumber: 4.8 Consensus size: 18
18553685 ACTTCACTTG
*
18553695 AAAAAAAAACAAAATGAA
1 AAAAAAAAAAAAAATGAA
*
18553713 AAAAAAATGAAAAAA-GAA
1 AAAAAAA-AAAAAAATGAA
*
18553731 AAACAAAAAGAAAAATGAA
1 AAA-AAAAAAAAAAATGAA
*
18553750 AAAAGAAAAGAAAAA-GAA
1 AAAA-AAAAAAAAAATGAA
18553768 AGAAGAAAAAATAAAAA
1 A-AA-AAAAAA-AAAAA
18553785 GGAGAGGCCA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
18 23 0.38
19 31 0.52
20 6 0.10
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.04
Consensus pattern (18 bp):
AAAAAAAAAAAAAATGAA
Found at i:18553744 original size:26 final size:26
Alignment explanation
Indices: 18553711--18553784 Score: 100
Period size: 25 Copynumber: 2.9 Consensus size: 26
18553701 AAACAAAATG
18553711 AAAA-AAAAATGAAAAAAGAAAAACA
1 AAAAGAAAAATGAAAAAAGAAAAACA
*
18553736 AAAAGAAAAATGAAAAAAG-AAAAGA
1 AAAAGAAAAATGAAAAAAGAAAAACA
*
18553761 AAAAGAAAGAA-GAAAAAATAAAAA
1 AAAAGAAA-AATGAAAAAAGAAAAA
18553785 GGAGAGGCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
25 24 0.55
26 20 0.45
ACGTcount: A:0.82, C:0.01, G:0.12, T:0.04
Consensus pattern (26 bp):
AAAAGAAAAATGAAAAAAGAAAAACA
Found at i:18553785 original size:26 final size:24
Alignment explanation
Indices: 18553697--18553785 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 24
18553687 TTCACTTGAA
*
18553697 AAAAAAACAAAATGAAAAA-AAAATG
1 AAAAAAA-AAAA-GAAAAAGAAAAAG
*
18553722 AAAAAAGAAAAACAAAAAGAAAAATG
1 AAAAAA-AAAAAGAAAAAGAAAAA-G
*
18553748 AAAAAAGAAAAGAAAAAGAAAGAAG
1 AAAAAAAAAAAGAAAAAGAAA-AAG
18553773 AAAAAATAAAAAG
1 AAAAAA-AAAAAG
18553786 GAGAGGCCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
24 5 0.09
25 34 0.63
26 15 0.28
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.04
Consensus pattern (24 bp):
AAAAAAAAAAAGAAAAAGAAAAAG
Found at i:18554894 original size:86 final size:87
Alignment explanation
Indices: 18554749--18554925 Score: 234
Period size: 86 Copynumber: 2.0 Consensus size: 87
18554739 GTAAAAATCA
** *
18554749 AAGACAAACCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGACAATAGATCTTGCCTTCCTG
1 AAGACAAACCTTGCCTCCATCGGTTGCAGCAGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTG
18554814 CA-TTGACAGCGAAGCAGATCG
66 CATTTGACAGCGAAGCAGATCG
* * *
18554835 AAGACAAACCTTGCCTCTC-TC-GTTCGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCC
1 AAGACAAACCTTGCCTC-CATCGGTT-GCAGCAGAGCTGGTTGAAGACAACAGATCTTGCCTTCC
* * *
18554898 TGTATTTGGCAGCGAAGTAGATCG
64 TGCATTTGACAGCGAAGCAGATCG
18554922 AAGA
1 AAGA
18554926 TGGCAGATTT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
85 3 0.04
86 54 0.68
87 22 0.28
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (87 bp):
AAGACAAACCTTGCCTCCATCGGTTGCAGCAGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTG
CATTTGACAGCGAAGCAGATCG
Found at i:18555135 original size:44 final size:44
Alignment explanation
Indices: 18555080--18555163 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
18555070 CCTCCCTGAT
* * * *
18555080 TACAGTGGAGTACATTGAAGCTGGTAGTTTTATCTCCCTGTGAC
1 TACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTGAC
18555124 TACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTG
1 TACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTG
18555164 GTTGGCAGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (44 bp):
TACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTGAC
Found at i:18555237 original size:176 final size:175
Alignment explanation
Indices: 18554944--18555298 Score: 500
Period size: 176 Copynumber: 2.0 Consensus size: 175
18554934 TTTACCTCCC
*
18554944 TGACTACAGTGGAGTACACTGAAGCCAATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
1 TGACTACAGTGGAGTACACTGAAGCCAATAACTCTATCTCCCTG-AGTTGGCAGTGGAATAGATT
* * *
18555009 GAAGATTACAGATCTTACCTTCCTAAGCAATAGTGGACCAGGTCGAAGATGGCGGATTTTACCTC
65 GAAGATTACAGATCTTACCTTCCT-AGCAATAGCGAACCAGATCGAAGATGGCGGATTTTACCTC
* *
18555074 CC-TGATTACAGTGGAGTACATTGAAGCTGGTAGTTTTATCTCCCTG
129 CCGTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTG
* * *
18555120 TGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTG-GTTGGCAGTGGAATAGATTG
1 TGACTACAGTGGAGTACACTGAAGCCAATAACTCTATCTCCCTGAGTTGGCAGTGGAATAGATTG
* * * *
18555184 AAGATTACAGATCTTGCCTTCCT-GTATTTGGCAGCGAAGCAGATCGAAGATGGCGGATTTTACC
66 AAGATTACAGATCTTACCTTCCTAGCA-AT---AGCGAACCAGATCGAAGATGGCGGATTTTACC
*
18555248 TCCCTGTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTTCCTG
127 TCCC-GTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTG
18555298 T
1 T
18555299 TCAACAGTGG
Statistics
Matches: 159, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
172 2 0.01
173 1 0.01
174 41 0.26
176 73 0.46
178 42 0.26
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (175 bp):
TGACTACAGTGGAGTACACTGAAGCCAATAACTCTATCTCCCTGAGTTGGCAGTGGAATAGATTG
AAGATTACAGATCTTACCTTCCTAGCAATAGCGAACCAGATCGAAGATGGCGGATTTTACCTCCC
GTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTG
Found at i:18555352 original size:44 final size:44
Alignment explanation
Indices: 18555300--18555475 Score: 126
Period size: 44 Copynumber: 4.0 Consensus size: 44
18555290 TCTTCCTGTT
*
18555300 CAACAGTGGAATAGAGTGAAGATTACAGATCTTATCTCCCTAAG
1 CAACAGTGGAATAGAGTGAAGATGACAGATCTTATCTCCCTAAG
* ** * * * * *
18555344 CAATAGTGGAGCAGA-TCGAAGATGGCGGATTTTACCTCCCTGA-
1 CAACAGTGGAATAGAGT-GAAGATGACAGATCTTATCTCCCTAAG
* * * * * * ** * **
18555387 CTACGGTGGAGTACATTGAAGCTGGTAGTTC-TATCTCCCTGGG
1 CAACAGTGGAATAGAGTGAAGATGACAGATCTTATCTCCCTAAG
18555430 CAACAGTGGAATAGAGTGAAGA-GCACAGATCTTATCTCCCTAAG
1 CAACAGTGGAATAGAGTGAAGATG-ACAGATCTTATCTCCCTAAG
18555474 CA
1 CA
18555476 GTAGTGGAGC
Statistics
Matches: 95, Mismatches: 32, Indels: 10
0.69 0.23 0.07
Matches are distributed among these distances:
42 10 0.11
43 40 0.42
44 45 0.47
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (44 bp):
CAACAGTGGAATAGAGTGAAGATGACAGATCTTATCTCCCTAAG
Found at i:18555421 original size:130 final size:131
Alignment explanation
Indices: 18555107--18555490 Score: 488
Period size: 130 Copynumber: 2.9 Consensus size: 131
18555097 AAGCTGGTAG
* * * * **
18555107 TTTTATCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGGTT-GGCA
1 TTTTACCTCCC-GTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCT-GTTCAACA
* ** * * * * *
18555171 GTGGAATAGATTGAAGATTACAGATCTTGCCTTCCT--GTATTTGGCAGCGAAGCAGATCGAAGA
64 GTGGAATAGAGTGAAGATTACAGATCTTATCTCCCTAAGCA-AT---AGTGGAGCAGATCGAAGA
18555234 TGGCGGA
125 TGGCGGA
*
18555241 TTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTTCCTGTTCAACAG
1 TTTTACCTCCC-GTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGTTCAACAG
18555306 TGGAATAGAGTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCG
65 TGGAATAGAGTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCG
18555371 GA
130 GA
* **
18555373 TTTTACCTCCC-TGACTACGGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGGGCAACAGT
1 TTTTACCTCCCGTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGTTCAACAGT
** *
18555437 GGAATAGAGTGAAGAGCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
66 GGAATAGAGTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATC
18555491 ACATCTAGTC
Statistics
Matches: 225, Mismatches: 22, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
130 100 0.44
132 34 0.15
133 3 0.01
134 85 0.38
135 1 0.00
136 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (131 bp):
TTTTACCTCCCGTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGTTCAACAGT
GGAATAGAGTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGG
A
Found at i:18555439 original size:43 final size:43
Alignment explanation
Indices: 18555259--18555439 Score: 112
Period size: 43 Copynumber: 4.2 Consensus size: 43
18555249 CCCTGTGACT
* * * **
18555259 ACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTTCCTGTTCA
1 ACAGTGGAGTACATTGAAGATGGCAGTTCTATCTCCCTGGGCA
* * * ** * **
18555302 ACAGTGGAATAGAGTGAAGATTACAGATCTTATCTCCCTAAGCA
1 ACAGTGGAGTACATTGAAGATGGCAGTTC-TATCTCCCTGGGCA
* * * * * * * * *
18555346 ATAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCT-GACT
1 ACAGTGGAGTACATTGAAGATGGCAG-TTCTATCTCCCTGGGCA
* * *
18555389 ACGGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGGGCA
1 ACAGTGGAGTACATTGAAGATGGCAGTTCTATCTCCCTGGGCA
18555432 ACAGTGGA
1 ACAGTGGA
18555440 ATAGAGTGAA
Statistics
Matches: 96, Mismatches: 39, Indels: 6
0.68 0.28 0.04
Matches are distributed among these distances:
42 10 0.10
43 49 0.51
44 36 0.38
45 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
ACAGTGGAGTACATTGAAGATGGCAGTTCTATCTCCCTGGGCA
Found at i:18555470 original size:308 final size:307
Alignment explanation
Indices: 18554873--18555450 Score: 865
Period size: 308 Copynumber: 1.9 Consensus size: 307
18554863 GCAGAGCTGG
*
18554873 TTGAAGATAGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGATGGCAGATTTTA
1 TTGAAGATAGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
***
18554938 CCTCCCTGACTACAGTGGAGTACACTGAAGCCAATAACTCTATCTCCCTGTATTTGGCAGTGGAA
66 CCTCCCTGACTACAGTGGAGTACACTGAAGCCAATAACTCTATCTCCCTG-ATTCAACAGTGGAA
* * *
18555003 TAGATTGAAGATTACAGATCTTACCTTCCTAAGCAATAGTGGACCAGGTCGAAGATGGCGGATTT
130 TAGAGTGAAGATTACAGATCTTACCTCCCTAAGCAATAGTGGACCAGATCGAAGATGGCGGATTT
* * *
18555068 TACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTTTATCTCCCTGTGACTACAGTGGA
195 TACCTCCCTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGTGACAACAGTGGA
* * *
18555133 GTACATTGAAGCCGATAATTCTATCTCCCTGGTTGGCAGTGGAATAGA
260 ATACAGTGAAGCCGACAATTCTATCTCCCTGGTTGGCAGTGGAATAGA
*
18555181 TTGAAGATTA-CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCGGATTTT
1 TTGAAGA-TAGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTT
* *** ** *
18555245 ACCTCCCTGTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTTCCTG-TTCAACAGTGG
65 ACCTCCC--TGACTACAGTGGAGTACACTGAAGCCAATAACTCTATCTCCCTGATTCAACAGTGG
* *
18555309 AATAGAGTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGGAT
128 AATAGAGTGAAGATTACAGATCTTACCTCCCTAAGCAATAGTGGACCAGATCGAAGATGGCGGAT
* *
18555374 TTTACCTCCCTGACTACGGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTG-GGCAACAGTG
193 TTTACCTCCCTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGTGACAACAGTG
*
18555438 GAATAGAGTGAAG
258 GAATACAGTGAAG
18555451 AGCACAGATC
Statistics
Matches: 242, Mismatches: 25, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
307 18 0.07
308 185 0.76
309 2 0.01
310 37 0.15
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (307 bp):
TTGAAGATAGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
CCTCCCTGACTACAGTGGAGTACACTGAAGCCAATAACTCTATCTCCCTGATTCAACAGTGGAAT
AGAGTGAAGATTACAGATCTTACCTCCCTAAGCAATAGTGGACCAGATCGAAGATGGCGGATTTT
ACCTCCCTGACTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGTGACAACAGTGGAA
TACAGTGAAGCCGACAATTCTATCTCCCTGGTTGGCAGTGGAATAGA
Found at i:18561029 original size:88 final size:88
Alignment explanation
Indices: 18560879--18561099 Score: 291
Period size: 88 Copynumber: 2.5 Consensus size: 88
18560869 AGCAGATCAG
* * *** **
18560879 TAAAAATAGCAGATCTTGCCTTCCTACACCGACAGTAAAGCAAATCAAAGACACCAGTCTTGCCT
1 TAAAAATAGCAGATCTTACCTTCCTGCACCGACAACGAAGCAAATCAAAGACACCAACCTTGCCT
* *
18560944 -CTCTGGGTTGCAGTGTAGCAGGT
66 CCT-TGGGTTGCAGCGGAGCAGGT
* * * *
18560967 TAAAAATAGTAGATCTTTCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAACCTTGCCT
1 TAAAAATAGCAGATCTTACCTTCCTGCACCGACAACGAAGCAAATCAAAGACACCAACCTTGCCT
18561032 CCTTGGGTTGCAGCGGAGCAGGT
66 CCTTGGGTTGCAGCGGAGCAGGT
* *
18561055 TAAAAATAGCAGATCTTACATTCCTGCACCTACAACGAAGCAAAT
1 TAAAAATAGCAGATCTTACCTTCCTGCACCGACAACGAAGCAAAT
18561100 TGATGACCCC
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
88 113 0.98
89 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTACCTTCCTGCACCGACAACGAAGCAAATCAAAGACACCAACCTTGCCT
CCTTGGGTTGCAGCGGAGCAGGT
Found at i:18561143 original size:88 final size:88
Alignment explanation
Indices: 18560879--18561146 Score: 241
Period size: 88 Copynumber: 3.0 Consensus size: 88
18560869 AGCAGATCAG
* * * *** * ** *
18560879 TAAAAATAGCAGATCTTGCCTTCCTACACCGACAGTAAAGCAAATCAAAGACACCAGTCTTGCCT
1 TAAAAATAGCAGATCTTACATTCCTGCACCGACAACGAAGCAAATCGAAGACACCAACCTTACCT
* * * * *
18560944 CTCTGGGTTGCAGTGTAGCAGGT
66 CCCTGGGTAGCAGCGGAACAGGT
* * * * *
18560967 TAAAAATAGTAGATCTTTCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAACCTTGCCT
1 TAAAAATAGCAGATCTTACATTCCTGCACCGACAACGAAGCAAATCGAAGACACCAACCTTACCT
* * *
18561032 CCTTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTAGCAGCGGAACAGGT
* * * * * *
18561055 TAAAAATAGCAGATCTTACATTCCTGCACCTACAACGAAGCAAATTGATGACCCCAGCCTTATCT
1 TAAAAATAGCAGATCTTACATTCCTGCACCGACAACGAAGCAAATCGAAGACACCAACCTTACCT
* *
18561120 CCCT-GGTCAGCAGTGGAATAGGT
66 CCCTGGGT-AGCAGCGGAACAGGT
18561143 TAAA
1 TAAA
18561147 GATTGTGAAT
Statistics
Matches: 149, Mismatches: 30, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
87 3 0.02
88 146 0.98
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTACATTCCTGCACCGACAACGAAGCAAATCGAAGACACCAACCTTACCT
CCCTGGGTAGCAGCGGAACAGGT
Found at i:18561179 original size:44 final size:44
Alignment explanation
Indices: 18561115--18561488 Score: 410
Period size: 44 Copynumber: 8.6 Consensus size: 44
18561105 ACCCCAGCCT
*
18561115 TATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCC
* *
18561159 TATCTCCCTGGACAGTAGTGGAATAGGTTAAATATTGTGAATCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCC
* * *
18561203 TATCTCCCT-GATCAGCAGTGGAATAGGTTGAAGATTGAGAATTC
1 TATCTCCCTGGA-CAGCAGTGGAATAGGTTAAAGATTGTGAATCC
* * *
18561247 TATCTCCTTGCG-CAAG-AGTGGAATAGATT-AA-A----GAACCC
1 TATCTCCCTG-GAC-AGCAGTGGAATAGGTTAAAGATTGTGAATCC
18561285 TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCC
* * * **
18561329 TATCTCCCTGGTCAGCAGTGGAATAGGTTAAAAATTGAGAATTT
1 TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCC
* * * * *
18561373 TATCTCCCTGGGCAGCAGTGGAATTGATTGAAGATTGT-AGGTCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGA-ATCC
* * * *
18561417 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAACCC
1 TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCC
*
18561461 TATCTCCCT-GAGCAGCAGTGGAGTAGGT
1 TATCTCCCTGGA-CAGCAGTGGAATAGGT
18561489 GGAAAATAGC
Statistics
Matches: 278, Mismatches: 37, Indels: 30
0.81 0.11 0.09
Matches are distributed among these distances:
37 3 0.01
38 26 0.09
39 2 0.01
40 1 0.00
42 1 0.00
43 6 0.02
44 235 0.85
45 3 0.01
46 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCC
Found at i:18561315 original size:126 final size:131
Alignment explanation
Indices: 18561115--18561488 Score: 467
Period size: 126 Copynumber: 2.9 Consensus size: 131
18561105 ACCCCAGCCT
* * * *
18561115 TATCTCCCTG-GTCAGCAGTGGAATAGGTTAAAGATTGT-GAATCCTATCTCCCTGGACAGTAGT
1 TATCTCCCTGCG-CAGCAGTGGAATAGATTGAAGA-TGTAG-ACCCTATCTCCCTGGACAGCAGT
* * *
18561178 GGAATAGGTTAAATATTGTGAATCCTATCTCCCTGATCAGCAGTGGAATAGGTTGAAGATTGAGA
63 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGATCAGCAGTGGAATAGGTTAAAAATTGAGA
18561243 ATTC
128 ATTC
*
18561247 TATCTCCTTGCGCAAG-AGTGGAATAGATT-AA-A-G-A-ACCCTATCTCCCTGGACAGCAGTGG
1 TATCTCCCTGCGC-AGCAGTGGAATAGATTGAAGATGTAGACCCTATCTCCCTGGACAGCAGTGG
*
18561306 AATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAAATTGAGAAT
65 AATAGGTTAAAGATTGTGAATCCTATCTCCCTGATCAGCAGTGGAATAGGTTAAAAATTGAGAAT
*
18561371 TT
130 TC
* * ** *
18561373 TATCTCCCTGGGCAGCAGTGGAATTGATTGAAGATTGTAGGTCCTATCTCCCTGGTCAGCAGTGG
1 TATCTCCCTGCGCAGCAGTGGAATAGATTGAAGA-TGTAGACCCTATCTCCCTGGACAGCAGTGG
* * * * *
18561438 AATAGGTTGAAGATCGTGAACCCTATCTCCCTGAGCAGCAGTGGAGTAGGT
65 AATAGGTTAAAGATTGTGAATCCTATCTCCCTGATCAGCAGTGGAATAGGT
18561489 GGAAAATAGC
Statistics
Matches: 211, Mismatches: 21, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
125 2 0.01
126 108 0.51
127 2 0.01
128 2 0.01
130 2 0.01
131 3 0.01
132 89 0.42
133 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (131 bp):
TATCTCCCTGCGCAGCAGTGGAATAGATTGAAGATGTAGACCCTATCTCCCTGGACAGCAGTGGA
ATAGGTTAAAGATTGTGAATCCTATCTCCCTGATCAGCAGTGGAATAGGTTAAAAATTGAGAATT
C
Found at i:18561422 original size:170 final size:173
Alignment explanation
Indices: 18561115--18561488 Score: 492
Period size: 170 Copynumber: 2.2 Consensus size: 173
18561105 ACCCCAGCCT
* *
18561115 TATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGTAGTGG
1 TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGCAGTGG
* * * *
18561180 AATAGGTTAAATATTGTGAATCCTATCTCCCTGATCAGCAGTGGAATAGGTTGAAGATTGAGAAT
66 AATAGGTTAAAAATTGAGAATCCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTGAGAAT
* *
18561245 TCTATCTCCTTGCG-CAAG-AGTGGAATAGATT-AA-A-GAACCC
131 CCTATCTCCCTG-GTC-AGCAGTGGAATAGATTGAAGATGAACCC
*
18561285 TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGG
1 TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGCAGTGG
** * * *
18561350 AATAGGTTAAAAATTGAGAATTTTATCTCCCTGGGCAGCAGTGGAATTGATTGAAGATTGTAG-G
66 AATAGGTTAAAAATTGAGAATCCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTG-AGAA
*
18561414 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAACCC
130 TCCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAGA---TGAACCC
*
18561461 TATCTCCCT-GAGCAGCAGTGGAGTAGGT
1 TATCTCCCTGGA-CAGCAGTGGAATAGGT
18561489 GGAAAATAGC
Statistics
Matches: 178, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
169 3 0.02
170 138 0.78
171 4 0.02
172 1 0.01
175 2 0.01
176 30 0.17
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (173 bp):
TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGCAGTGG
AATAGGTTAAAAATTGAGAATCCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATTGAGAAT
CCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAGATGAACCC
Found at i:18561549 original size:132 final size:132
Alignment explanation
Indices: 18561156--18561552 Score: 343
Period size: 126 Copynumber: 3.1 Consensus size: 132
18561146 AGATTGTGAA
* * * * *
18561156 TCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAATATTGTGAATCCTATCTCCCTGATCAGCAG
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATCGTGAACCCTATCTCCCTGGTCAGCAG
* * * * * * * *
18561221 TGGAATAGGTTG-AAGATTGAGAAT-TCTATCTCCTTGCGCAAG-AGTGGAATAGATTAAAGAA-
66 TGGAATAGG-TGAAAAATAGAGAATCT-TACCTCCCTGCAC-AGCAGTGAAACAGATTGAAGAAT
18561282 -C---
128 GCAGG
* *
18561283 -CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAG
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATCGTGAACCCTATCTCCCTGGTCAGCAG
* * * * ** * ** * *
18561347 TGGAATAGGTTAAAAATTGAGAATTTTATCTCCCTGGGCAGCAGTGGAATTGATTGAAGATTGTA
66 TGGAATAGGTGAAAAATAGAGAATCTTACCTCCCTGCACAGCAGTGAAACAGATTGAAGAATGCA
18561412 GG
131 GG
* *
18561414 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAACCCTATCTCCCTGAG-CAGCA
1 TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATCGTGAACCCTATCTCCCTG-GTCAGCA
* * * * *
18561478 GTGGAGTAGGTGGAAAATAGCAG-ATCTTGCCTTCCTGCACCGACAGTGAAACAGATTGAAGACA
65 GTGGAATAGGTGAAAAATAG-AGAATCTTACCTCCCTGCACAG-CAGTGAAACAGATTGAAGA-A
18561542 T-CA-G
127 TGCAGG
18561546 TCCTATC
1 TCCTATC
18561553 GCCTTGATGT
Statistics
Matches: 226, Mismatches: 31, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
125 3 0.01
126 108 0.48
127 1 0.00
132 93 0.41
133 20 0.09
134 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (132 bp):
TCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATCGTGAACCCTATCTCCCTGGTCAGCAG
TGGAATAGGTGAAAAATAGAGAATCTTACCTCCCTGCACAGCAGTGAAACAGATTGAAGAATGCA
GG
Found at i:18561888 original size:44 final size:43
Alignment explanation
Indices: 18561795--18561910 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 43
18561785 ATGGCAAATT
* * *
18561795 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATC
1 TTATCTTCTTGAAGTTGCAGT-GAGCAGATTAAAACCGATAATC
* *
18561839 CTATCTTCTTGAAGTTGCAGTGAAGCAGATTAAAACC-TTAGATC
1 TTATCTTCTTGAAGTTGCAGTG-AGCAGATTAAAACCGATA-ATC
* *
18561883 TTATC-TCTCAGAAGTTGCAGAGAGCAGA
1 TTATCTTCT-TGAAGTTGCAGTGAGCAGA
18561911 ACGCATCTAG
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
43 12 0.20
44 49 0.80
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
TTATCTTCTTGAAGTTGCAGTGAGCAGATTAAAACCGATAATC
Found at i:18563359 original size:3 final size:3
Alignment explanation
Indices: 18563353--18563424 Score: 126
Period size: 3 Copynumber: 24.0 Consensus size: 3
18563343 ATTATTATTA
* *
18563353 TTG TTG TTG TTG TTG TTG TTA TTG TTG TTA TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
18563401 TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG
18563425 ATATTGTAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.03, C:0.00, G:0.31, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:18565238 original size:17 final size:18
Alignment explanation
Indices: 18565199--18565238 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
18565189 GTTTGTTTGG
*
18565199 ATTAAACTTTAGTTATGA
1 ATTAAACTTTAGTTATAA
18565217 A-TAAACTTTAGTTA-AA
1 ATTAAACTTTAGTTATAA
18565233 ATTAAA
1 ATTAAA
18565239 ATTTTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 17 0.85
18 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (18 bp):
ATTAAACTTTAGTTATAA
Found at i:18575409 original size:27 final size:26
Alignment explanation
Indices: 18575344--18575433 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 26
18575334 TTAAAAAAAT
18575344 TAAAAA-T-TAAAAATATAAAATATA
1 TAAAAATTATAAAAATATAAAATATA
* * *
18575368 AAAAAATTCA-AAAAAGTATATAATGTA
1 TAAAAATT-ATAAAAA-TATAAAATATA
*
18575395 TAAAAATTATAAAAATGA-AAAGAAATGA
1 TAAAAATTATAAAAAT-ATAAA-ATAT-A
18575423 TAAAAATTATA
1 TAAAAATTATA
18575434 TATAAAGTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
24 5 0.10
25 1 0.02
26 9 0.18
27 24 0.47
28 12 0.24
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.27
Consensus pattern (26 bp):
TAAAAATTATAAAAATATAAAATATA
Found at i:18575411 original size:19 final size:20
Alignment explanation
Indices: 18575389--18575433 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
18575379 AAAAGTATAT
*
18575389 AATGTATAA-AAATTATAAA
1 AATGTATAAGAAATGATAAA
*
18575408 AATG-AAAAGAAATGATAAA
1 AATGTATAAGAAATGATAAA
18575427 AAT-TATA
1 AATGTATA
18575434 TATAAAGTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (20 bp):
AATGTATAAGAAATGATAAA
Found at i:18575878 original size:20 final size:19
Alignment explanation
Indices: 18575837--18575897 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
18575827 ACATAATTTT
*
18575837 TATT-TTTTTATATATTTA
1 TATTATTTTTATATATATA
18575855 -ATTATTTTGTATATATATA
1 TATTATTTT-TATATATATA
**
18575874 TATTAGAGTTTATATATATA
1 TATTA-TTTTTATATATATA
18575894 TATT
1 TATT
18575898 TTAGAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.08
18 4 0.11
19 9 0.25
20 18 0.50
21 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TATTATTTTTATATATATA
Found at i:18577208 original size:40 final size:40
Alignment explanation
Indices: 18577164--18577251 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 40
18577154 CACGTAAGCC
* *
18577164 CGATTTGCTT-CCACGTCAGCAAATCGTGCTTACATGGACG
1 CGATTTGCTTGCCACGTAAG-AAATCGCGCTTACATGGACG
* *
18577204 CGATTTG-TTGCCACGTAAGTAATCGCGCTTACGTGGACG
1 CGATTTGCTTGCCACGTAAGAAATCGCGCTTACATGGACG
*
18577243 CAATTTGCT
1 CGATTTGCT
18577252 GACACGTCCC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 25 0.61
40 16 0.39
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.30
Consensus pattern (40 bp):
CGATTTGCTTGCCACGTAAGAAATCGCGCTTACATGGACG
Found at i:18577630 original size:28 final size:28
Alignment explanation
Indices: 18577598--18577654 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
18577588 CTATTGAAGT
*
18577598 ATATTTAGTT-TCACATTTTGGTACTTAA
1 ATATTT-GTTGTCACAATTTGGTACTTAA
* *
18577626 ATATTTTTTGTCTCAATTTGGTACTTAA
1 ATATTTGTTGTCACAATTTGGTACTTAA
18577654 A
1 A
18577655 GAATCAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51
Consensus pattern (28 bp):
ATATTTGTTGTCACAATTTGGTACTTAA
Found at i:18577863 original size:21 final size:19
Alignment explanation
Indices: 18577839--18577904 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 19
18577829 ATGAAAAACA
18577839 AAAATAAATATATAAAATTT
1 AAAA-AAATATATAAAATTT
* *
18577859 CAAAAAAGATACATAAAATCT
1 -AAAAAA-ATATATAAAATTT
*
18577880 AGAAAAAATATATAAATTTT
1 A-AAAAAATATATAAAATTT
18577900 AAAAA
1 AAAAA
18577905 TAATTTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 4 0.11
20 14 0.37
21 20 0.53
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAAAAATATATAAAATTT
Found at i:18580624 original size:20 final size:20
Alignment explanation
Indices: 18580599--18580637 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
18580589 TAAATGTATA
18580599 TTAAAAAAT-TACTAAAAATC
1 TTAAAAAATATA-TAAAAATC
*
18580619 TTAAAAGATATATAAAAAT
1 TTAAAAAATATATAAAAAT
18580638 ACTAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (20 bp):
TTAAAAAATATATAAAAATC
Found at i:18585524 original size:19 final size:20
Alignment explanation
Indices: 18585500--18585537 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18585490 TGTTATGGTT
18585500 TAGGG-TTAAGGTTTTAAAG
1 TAGGGTTTAAGGTTTTAAAG
*
18585519 TAGGGTTTAGGGTTTTAAA
1 TAGGGTTTAAGGTTTTAAA
18585538 TTTTAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (20 bp):
TAGGGTTTAAGGTTTTAAAG
Found at i:18586096 original size:32 final size:32
Alignment explanation
Indices: 18586053--18586157 Score: 131
Period size: 32 Copynumber: 3.3 Consensus size: 32
18586043 TGGTTCTATA
*
18586053 AAATGATAACAATTATCAACTTTCATTTTGTG
1 AAATGATAACAATTATCAACTTTAATTTTGTG
* * *
18586085 ACATGATAACAAATTA-CAAGTTTAATTTTTTG
1 AAATGATAAC-AATTATCAACTTTAATTTTGTG
* * *
18586117 AAATGATAATAAATATCAACTTTAATTTTGTT
1 AAATGATAACAATTATCAACTTTAATTTTGTG
18586149 AAATGATAA
1 AAATGATAA
18586158 TAATATTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
31 4 0.07
32 52 0.85
33 5 0.08
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (32 bp):
AAATGATAACAATTATCAACTTTAATTTTGTG
Found at i:18598443 original size:31 final size:31
Alignment explanation
Indices: 18598408--18598473 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
18598398 ACGATGAAAA
18598408 TTATCTTATTAAAGCTTATACACCACATGAC
1 TTATCTTATTAAAGCTTATACACCACATGAC
* *
18598439 TTATCTTATTAAAGCTTATGCGCCACATGAC
1 TTATCTTATTAAAGCTTATACACCACATGAC
18598470 TTAT
1 TTAT
18598474 ACTTTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (31 bp):
TTATCTTATTAAAGCTTATACACCACATGAC
Found at i:18605763 original size:36 final size:36
Alignment explanation
Indices: 18605689--18605763 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
18605679 ATGACTAAAC
* *
18605689 AATTCAATAATATAAATAATATAAAATGTGAAATTT
1 AATTCAATAATATAAATAATATAAAATATGAAAATT
*
18605725 AATTTAATAATATAAATAATATATATAA-AT-AAAATT
1 AATTCAATAATATAAATAATATA-A-AATATGAAAATT
18605761 AAT
1 AAT
18605764 ACTATTTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 30 0.88
37 2 0.06
38 2 0.06
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (36 bp):
AATTCAATAATATAAATAATATAAAATATGAAAATT
Found at i:18608422 original size:23 final size:23
Alignment explanation
Indices: 18608396--18608540 Score: 236
Period size: 23 Copynumber: 6.3 Consensus size: 23
18608386 ATAAGTGCCA
18608396 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
18608419 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
18608442 CACTGAAATGTAGGCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
18608465 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
18608488 CACTGATACGTAGCAGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
18608511 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
18608534 CACTGAT
1 CACTGAT
18608541 CAATAACACT
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 110 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:18614603 original size:13 final size:13
Alignment explanation
Indices: 18614585--18614611 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18614575 AAGTTGATTG
18614585 AATTGAAGATATT
1 AATTGAAGATATT
18614598 AATTGAAGATATT
1 AATTGAAGATATT
18614611 A
1 A
18614612 TTAATTAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (13 bp):
AATTGAAGATATT
Found at i:18614848 original size:24 final size:24
Alignment explanation
Indices: 18614821--18614870 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
18614811 GTATAGTACA
* * *
18614821 AAATTTATACAAGTGTAATTATAT
1 AAATATATACAAATGTAATTAAAT
*
18614845 AAATATGTACAAATGTAATTAAAT
1 AAATATATACAAATGTAATTAAAT
18614869 AA
1 AA
18614871 TTGGTTTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (24 bp):
AAATATATACAAATGTAATTAAAT
Found at i:18614921 original size:14 final size:14
Alignment explanation
Indices: 18614902--18614931 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
18614892 CATAAGATAC
18614902 AATAAAGTAAATAA
1 AATAAAGTAAATAA
18614916 AATAAAGTAAATAA
1 AATAAAGTAAATAA
18614930 AA
1 AA
18614932 GAAACTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AATAAAGTAAATAA
Found at i:18615487 original size:3 final size:3
Alignment explanation
Indices: 18615479--18615509 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
18615469 TAATTAATAG
18615479 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18615510 TTCGTAGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:18615935 original size:21 final size:21
Alignment explanation
Indices: 18615906--18615987 Score: 87
Period size: 23 Copynumber: 3.8 Consensus size: 21
18615896 GCCTTGCCGA
*
18615906 TCAGACACTT-TGTGTCGTTT
1 TCAGGCACTTATGTGTCGTTT
*
18615926 ATCAGGCACTTTATATGTCGTATT
1 -TCAGGCAC-TTATGTGTCGT-TT
*
18615950 TCAGGCACCTCATGTGTCG-TT
1 TCAGGCA-CTTATGTGTCGTTT
18615971 TCAGGCACTTATGTGTC
1 TCAGGCACTTATGTGTC
18615988 ATATACTGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
20 9 0.17
21 16 0.31
22 2 0.04
23 22 0.42
24 3 0.06
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (21 bp):
TCAGGCACTTATGTGTCGTTT
Found at i:18622367 original size:34 final size:34
Alignment explanation
Indices: 18622318--18622383 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
18622308 CATCATTTAC
* *
18622318 TGCCAAGCAATAACTCCA-TTGACAATAATAGAAA
1 TGCCAAGAAAGAACTCCACTT-ACAATAATAGAAA
18622352 TGCCAAGAAAGAACTCCACTTACAATAATAGA
1 TGCCAAGAAAGAACTCCACTTACAATAATAGA
18622384 CACCCTACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.20
Consensus pattern (34 bp):
TGCCAAGAAAGAACTCCACTTACAATAATAGAAA
Found at i:18627976 original size:14 final size:14
Alignment explanation
Indices: 18627957--18627983 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18627947 ATAATCTGTC
18627957 GTTGTTGCCTTACT
1 GTTGTTGCCTTACT
18627971 GTTGTTGCCTTAC
1 GTTGTTGCCTTAC
18627984 AATTCCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (14 bp):
GTTGTTGCCTTACT
Found at i:18628033 original size:59 final size:59
Alignment explanation
Indices: 18627941--18628059 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
18627931 GCTCAAAACC
18627941 TTGTTTATAATCTGTCGTTGTTGCCTTACTGTTGTTGCCTTACAATTCCATTTGTTTAG
1 TTGTTTATAATCTGTCGTTGTTGCCTTACTGTTGTTGCCTTACAATTCCATTTGTTTAG
*
18628000 TTGTTTATAATCTGTCGTTGTTGCCTTACTGTTGTTGCCTTACAGTTCCATTTGTTTAG
1 TTGTTTATAATCTGTCGTTGTTGCCTTACTGTTGTTGCCTTACAATTCCATTTGTTTAG
18628059 T
1 T
18628060 CGTTCAAAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (59 bp):
TTGTTTATAATCTGTCGTTGTTGCCTTACTGTTGTTGCCTTACAATTCCATTTGTTTAG
Found at i:18628035 original size:14 final size:14
Alignment explanation
Indices: 18628016--18628042 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18628006 ATAATCTGTC
18628016 GTTGTTGCCTTACT
1 GTTGTTGCCTTACT
18628030 GTTGTTGCCTTAC
1 GTTGTTGCCTTAC
18628043 AGTTCCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (14 bp):
GTTGTTGCCTTACT
Found at i:18628238 original size:47 final size:47
Alignment explanation
Indices: 18628169--18628290 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
18628159 TACTTTCTCT
* *
18628169 TATTTTAAATTTTATAATCTGGTTTATACCTTGTTGCTTCTTTTTTA
1 TATTTGAAATTTTATATTCTGGTTTATACCTTGTTGCTTCTTTTTTA
18628216 TATTTGAAATTTTATATTCTGGTTTATACCTTGTTGCTTCTTTTTTA
1 TATTTGAAATTTTATATTCTGGTTTATACCTTGTTGCTTCTTTTTTA
*
18628263 TATCTGAAATTTTATATTCTGGTTTATA
1 TATTTGAAATTTTATATTCTGGTTTATA
18628291 ATCTGGTTTA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.58
Consensus pattern (47 bp):
TATTTGAAATTTTATATTCTGGTTTATACCTTGTTGCTTCTTTTTTA
Found at i:18628290 original size:12 final size:12
Alignment explanation
Indices: 18628273--18628302 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18628263 TATCTGAAAT
*
18628273 TTTATATTCTGG
1 TTTATAATCTGG
18628285 TTTATAATCTGG
1 TTTATAATCTGG
18628297 TTTATA
1 TTTATA
18628303 CCTTGTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (12 bp):
TTTATAATCTGG
Found at i:18639592 original size:16 final size:16
Alignment explanation
Indices: 18639571--18639602 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18639561 TAAAATTGTG
18639571 TTGCTAATTTTTATTT
1 TTGCTAATTTTTATTT
18639587 TTGCTAATTTTTATTT
1 TTGCTAATTTTTATTT
18639603 ACTACAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (16 bp):
TTGCTAATTTTTATTT
Found at i:18642181 original size:27 final size:28
Alignment explanation
Indices: 18642151--18642205 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
18642141 ATAACTTTTT
18642151 TTTATTTACCAAAATATAT-AAAAAAAA
1 TTTATTTACCAAAATATATCAAAAAAAA
18642178 TTTATTTACCAAAATATATCAAAAAAAA
1 TTTATTTACCAAAATATATCAAAAAAAA
18642206 CAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (28 bp):
TTTATTTACCAAAATATATCAAAAAAAA
Found at i:18642338 original size:27 final size:27
Alignment explanation
Indices: 18642254--18642347 Score: 127
Period size: 27 Copynumber: 3.5 Consensus size: 27
18642244 CGCCAATGGT
* *
18642254 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
18642281 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAATGGTGCCAATACC
* *
18642308 ATTGGCGGCACCAATGGTGCC-GTACTA
1 ATTGGCGGCACCAATGGTGCCAATAC-C
18642335 ATTGGCGGCACCA
1 ATTGGCGGCACCA
18642348 CTCGTATTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
26 2 0.03
27 58 0.97
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.17
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:18642517 original size:19 final size:21
Alignment explanation
Indices: 18642479--18642517 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
18642469 AATAATTGAT
*
18642479 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
18642500 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
18642518 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:18642579 original size:3 final size:3
Alignment explanation
Indices: 18642563--18642621 Score: 100
Period size: 3 Copynumber: 19.3 Consensus size: 3
18642553 AAAATAATAG
*
18642563 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18642609 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
18642622 GTTGTTGTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:18642626 original size:3 final size:3
Alignment explanation
Indices: 18642620--18642657 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
18642610 ATTATTATTA
18642620 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
18642658 AGTATTAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:18642899 original size:26 final size:26
Alignment explanation
Indices: 18642847--18642899 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
18642837 TTTTAGTGTG
* *
18642847 TATTATTTTGAGTATAAATTTATTAA
1 TATTATTTTGAGTATAAACTTAATAA
*
18642873 TATTATTTTGAGTATACACTTAATAA
1 TATTATTTTGAGTATAAACTTAATAA
18642899 T
1 T
18642900 TTTAGTGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (26 bp):
TATTATTTTGAGTATAAACTTAATAA
Found at i:18642922 original size:12 final size:12
Alignment explanation
Indices: 18642905--18642935 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
18642895 ATAATTTTAG
18642905 TGTGTATTATTT
1 TGTGTATTATTT
18642917 TGTGTATTATTT
1 TGTGTATTATTT
*
18642929 TGAGTAT
1 TGTGTAT
18642936 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:18643528 original size:18 final size:18
Alignment explanation
Indices: 18643485--18643529 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
18643475 TTGACATGGT
*
18643485 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
**
18643503 TGCCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
18643521 TGGTGGCGA
1 TGGTGGCGA
18643530 TAATTGGGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.49, T:0.13
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:18649196 original size:14 final size:13
Alignment explanation
Indices: 18649170--18649207 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
18649160 TATATATGCT
*
18649170 AAATAAAATAATA
1 AAATAACATAATA
18649183 AAATAACTATAATA
1 AAATAAC-ATAATA
18649197 AAATAACATAA
1 AAATAACATAA
18649208 ATTTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAACATAATA
Found at i:18649315 original size:34 final size:37
Alignment explanation
Indices: 18649263--18649467 Score: 133
Period size: 38 Copynumber: 5.4 Consensus size: 37
18649253 ATTACATTTT
18649263 TTTC-TTTTTTTTC-C--CTCC-TTCCCTCTTC-TTC
1 TTTCTTTTTTTTTCTCTTCTCCTTTCCCTCTTCTTTC
*
18649294 -TTCTTTTTTTTTCTCTTCTCCTTT-CCTTTTCTTTC
1 TTTCTTTTTTTTTCTCTTCTCCTTTCCCTCTTCTTTC
* * *
18649329 CTTCTTTCTTTCTTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTC
1 TTTC-TT-TTT-TTTTCTCTTCTCCTTTCC--CTCTTC-T-TTC
18649373 TTTCTTTCTTTTTTTCTCTTCTCCTTTCCCT-TTCTTTC
1 TTTC-TT-TTTTTTTCTCTTCTCCTTTCCCTCTTCTTTC
* * *
18649411 CTTCTTTTTCTTTCTTCCCTCTCCTTTCTTCCT-TTCTTTC
1 TTTCTTTTTTTTTC-T-CTTCTCCTTTC--CCTCTTCTTTC
*
18649451 TCTCTTTCTTTCTTTCT
1 TTTCTTT-TTT-TTTCT
18649468 TTCCCTCTCC
Statistics
Matches: 140, Mismatches: 13, Indels: 32
0.76 0.07 0.17
Matches are distributed among these distances:
30 3 0.02
31 9 0.06
32 1 0.01
34 10 0.07
35 5 0.04
36 10 0.07
37 5 0.04
38 19 0.14
39 15 0.11
40 19 0.14
41 5 0.04
42 9 0.06
43 17 0.12
44 13 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (37 bp):
TTTCTTTTTTTTTCTCTTCTCCTTTCCCTCTTCTTTC
Done.