Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 374 of 425
Found at i:115145206 original size:14 final size:14
Alignment explanation
Indices: 115145187--115145224 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
115145177 TGTTTAACTC
115145187 AAAATGACTTCTGA
1 AAAATGACTTCTGA
* *
115145201 AAAATGATTTCTGG
1 AAAATGACTTCTGA
115145215 AAAATGACTT
1 AAAATGACTT
115145225 ACGCTGCTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (14 bp):
AAAATGACTTCTGA
Found at i:115147629 original size:18 final size:18
Alignment explanation
Indices: 115147608--115147890 Score: 153
Period size: 18 Copynumber: 15.3 Consensus size: 18
115147598 GAACAATTAT
115147608 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* *
115147626 TTATTCAGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
115147644 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
115147662 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* * * *
115147688 TTATCCAATAACAATCAA
1 TTATTCAGTAACAGTCAG
*
115147706 TTATTCAGTAA-AATCA-
1 TTATTCAGTAACAGTCAG
* *
115147722 TATATTCAGTAACAATTAAG
1 T-TATTCAGTAAC-AGTCAG
115147742 TTATTCAGTAACAGTCA-
1 TTATTCAGTAACAGTCAG
** *
115147759 TTCATTCAGTGGCAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
115147778 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
115147796 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
115147814 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
115147832 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
115147850 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
115147868 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
115147886 TTATT
1 TTATT
115147891 TTATACCTTT
Statistics
Matches: 203, Mismatches: 44, Indels: 36
0.72 0.16 0.13
Matches are distributed among these distances:
16 1 0.00
17 18 0.09
18 151 0.74
19 17 0.08
20 1 0.00
21 2 0.01
22 1 0.00
23 2 0.01
26 10 0.05
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:115147648 original size:36 final size:35
Alignment explanation
Indices: 115147599--115147890 Score: 176
Period size: 36 Copynumber: 8.4 Consensus size: 35
115147589 TAACACTTAG
* *
115147599 AACAATTATTTATTCAGTAACAGTCAGTTATTCAGT
1 AACAATCAATTATTCAGTAACAGTCA-TTATTCAGT
* * **
115147635 AACAATCAATTATTCAATAATAACCAGTTATTCAGT
1 AACAATCAATTATTCAGTAACAGTCA-TTATTCAGT
* * * *
115147671 ATCGATCAATTGA-TC-G-----G---TTATCCAAT
1 AACAATCAATT-ATTCAGTAACAGTCATTATTCAGT
*
115147697 AACAATCAATTATTCAGTAA-AATCATATATTCAGT
1 AACAATCAATTATTCAGTAACAGTCAT-TATTCAGT
*
115147732 AACAATTAAGTTATTCAGTAACAGTCATTCATTCAGT
1 AACAATCAA-TTATTCAGTAACAGTCATT-ATTCAGT
** * *
115147769 GGCAATCAGTTATTCAGTAA-TGATCAATTATTCAGT
1 AACAATCAATTATTCAGTAACAG-TC-ATTATTCAGT
* * * * *
115147805 AATATTCAGTTATTCAGTAACAGTCTAATATCCAGT
1 AACAATCAATTATTCAGTAACAGTC-ATTATTCAGT
* * *
115147841 AACAGTCAATTATCCGGTAACAGTCAATTATTCAGT
1 AACAATCAATTATTCAGTAACAGTC-ATTATTCAGT
* *
115147877 AATAATCAGTTATT
1 AACAATCAATTATT
115147891 TTATACCTTT
Statistics
Matches: 195, Mismatches: 44, Indels: 34
0.71 0.16 0.12
Matches are distributed among these distances:
25 1 0.01
26 18 0.09
27 1 0.01
34 1 0.01
35 15 0.08
36 137 0.70
37 22 0.11
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (35 bp):
AACAATCAATTATTCAGTAACAGTCATTATTCAGT
Found at i:115147670 original size:54 final size:54
Alignment explanation
Indices: 115147599--115147890 Score: 198
Period size: 54 Copynumber: 5.3 Consensus size: 54
115147589 TAACACTTAG
* * *
115147599 AACAATTATTTATTCAGTAACAGTCAGTTATTCAGTAACAATCAATTATTCAAT
1 AACAATCAGTTATTCAGTAACAGTCAGTTATTCAGTAACAATCAATTATTCAGT
* * * * *
115147653 AATAACCAGTTATTCAGTATCGATCAATTGATCGGTTATCCAATAACAATCAATTATTCAGT
1 AACAATCAGTTATTCAGTA---A-C-A--G-TCAGTTATTCAGTAACAATCAATTATTCAGT
* * *
115147715 AA-AATCA-TATATTCAGTAACAATTAAGTTATTCAGTAACAGTC-ATTCATTCAGT
1 AACAATCAGT-TATTCAGTAAC-AGTCAGTTATTCAGTAACAATCAATT-ATTCAGT
** * * * * *
115147769 GGCAATCAGTTATTCAGTAA-TGATCAATTATTCAGTAATATTCAGTTATTCAGT
1 AACAATCAGTTATTCAGTAACAG-TCAGTTATTCAGTAACAATCAATTATTCAGT
* * * * * * *
115147823 AACAGTCTA-ATATCCAGTAACAGTCAATTATCCGGTAACAGTCAATTATTCAGT
1 AACAATC-AGTTATTCAGTAACAGTCAGTTATTCAGTAACAATCAATTATTCAGT
*
115147877 AATAATCAGTTATT
1 AACAATCAGTTATT
115147891 TTATACCTTT
Statistics
Matches: 182, Mismatches: 39, Indels: 34
0.71 0.15 0.13
Matches are distributed among these distances:
53 4 0.02
54 107 0.59
55 19 0.10
56 1 0.01
57 4 0.02
58 2 0.01
59 1 0.01
60 1 0.01
61 14 0.08
62 29 0.16
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (54 bp):
AACAATCAGTTATTCAGTAACAGTCAGTTATTCAGTAACAATCAATTATTCAGT
Found at i:115147816 original size:72 final size:71
Alignment explanation
Indices: 115147689--115147890 Score: 219
Period size: 72 Copynumber: 2.8 Consensus size: 71
115147679 ATTGATCGGT
* * *
115147689 TATCCAATAACAATCAATTATTCAGTAAAATC-ATATATTCAGTAACAATTAAGTTATTCAGTAA
1 TATCCAGTAACAATCAATTATTCAGTAAAATCAAT-TATTCAGTAA-TATTCAGTTATTCAGTAA
*
115147753 CAGTC-AT
64 CAGTCTAA
* ** * *
115147760 TCATTCAGTGGCAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTCAGTTATTCAGTAA
1 T-ATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATTCAGTAA
115147825 CAGTCTAA
64 CAGTCTAA
* * * * *
115147833 TATCCAGTAACAGTCAATTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATT
115147891 TTATACCTTT
Statistics
Matches: 107, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
71 1 0.01
72 89 0.83
73 15 0.14
74 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (71 bp):
TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAATATTCAGTTATTCAGTAACA
GTCTAA
Found at i:115148124 original size:6 final size:6
Alignment explanation
Indices: 115148109--115148142 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
115148099 TGCCAAATCG
*
115148109 GTAACA GTAACG GTAACA GTAACCA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAA-CA GTAACA GTA
115148143 TTCGGCACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:115148124 original size:12 final size:13
Alignment explanation
Indices: 115148107--115148142 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
115148097 AGTGCCAAAT
115148107 CGGTAACAGTAA-
1 CGGTAACAGTAAC
115148119 CGGTAACAGTAAC
1 CGGTAACAGTAAC
*
115148132 CAGTAACAGTA
1 CGGTAACAGTA
115148143 TTCGGCACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (13 bp):
CGGTAACAGTAAC
Found at i:115149823 original size:24 final size:24
Alignment explanation
Indices: 115149796--115149846 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
115149786 AACATAAAAA
115149796 TTAAGTAAAAAGGGCTAAATTGAC
1 TTAAGTAAAAAGGGCTAAATTGAC
115149820 TTAAGTAAAAAGGGCTAAATTGAC
1 TTAAGTAAAAAGGGCTAAATTGAC
115149844 TTA
1 TTA
115149847 CCTATTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (24 bp):
TTAAGTAAAAAGGGCTAAATTGAC
Found at i:115149982 original size:2 final size:2
Alignment explanation
Indices: 115149975--115150009 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
115149965 ATTAAACCTT
115149975 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
115150010 ATAACTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:115150013 original size:8 final size:9
Alignment explanation
Indices: 115149976--115150013 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
115149966 TTAAACCTTT
115149976 ATATATATA
1 ATATATATA
115149985 TATATATATA
1 -ATATATATA
115149995 TATATATATA
1 -ATATATATA
115150005 ATATA-ATA
1 ATATATATA
115150013 A
1 A
115150014 CTTAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 4 0.14
9 5 0.18
10 19 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATATATA
Found at i:115158454 original size:20 final size:20
Alignment explanation
Indices: 115158429--115158466 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
115158419 GAATCTGCCT
115158429 ATGTCCCAGGCCACACGGCC
1 ATGTCCCAGGCCACACGGCC
*
115158449 ATGTCCTAGGCCACACGG
1 ATGTCCCAGGCCACACGG
115158467 GCGTGTGCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.39, G:0.26, T:0.13
Consensus pattern (20 bp):
ATGTCCCAGGCCACACGGCC
Found at i:115159240 original size:30 final size:30
Alignment explanation
Indices: 115159204--115159260 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
115159194 TTAGTTAGGC
*
115159204 AATTTTTCAATTCAATCTTGATTCTAAGGT
1 AATTTTTCAATTCAATCTCGATTCTAAGGT
115159234 AATTTTTCAATTCAATCTCGATTCTAA
1 AATTTTTCAATTCAATCTCGATTCTAA
115159261 CCCTTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.46
Consensus pattern (30 bp):
AATTTTTCAATTCAATCTCGATTCTAAGGT
Found at i:115162366 original size:13 final size:13
Alignment explanation
Indices: 115162350--115162382 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
115162340 TTTGATTAAA
*
115162350 TTAGTTAATTAGT
1 TTAGATAATTAGT
115162363 TTAGATAATTAGT
1 TTAGATAATTAGT
115162376 TTA-ATAA
1 TTAGATAA
115162383 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:115162671 original size:5 final size:5
Alignment explanation
Indices: 115162661--115162686 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
115162651 ATTTTTCTTG
115162661 TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT T
115162687 TACTATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:115167779 original size:6 final size:6
Alignment explanation
Indices: 115167768--115167843 Score: 74
Period size: 6 Copynumber: 13.7 Consensus size: 6
115167758 AATCCTCCTA
*
115167768 TTTTAT TTTTAT TTTTA- -TTTAT TCTTAT TTTTA- TTTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * *
115167812 TTAT-T TTTTCT TATT-T TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
115167844 CAATTTTCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
4 4 0.07
5 18 0.31
6 37 0.63
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:115167790 original size:10 final size:10
Alignment explanation
Indices: 115167769--115167841 Score: 66
Period size: 10 Copynumber: 7.3 Consensus size: 10
115167759 ATCCTCCTAT
115167769 TTTATTTTTA
1 TTTATTTTTA
115167779 TTT-TTATTTA
1 TTTATT-TTTA
115167789 TTCTTATTTTTA
1 -T-TTATTTTTA
115167801 TTT-TATTTTA
1 TTTAT-TTTTA
115167811 TTTATTTTT-
1 TTTATTTTTA
115167820 TCTTA-TTTT-
1 T-TTATTTTTA
115167829 TTTATTTTTA
1 TTTATTTTTA
115167839 TTT
1 TTT
115167842 TTCAATTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
8 3 0.06
9 13 0.24
10 27 0.50
11 3 0.06
12 6 0.11
13 2 0.04
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:115167834 original size:38 final size:38
Alignment explanation
Indices: 115167766--115167842 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 38
115167756 TGAATCCTCC
115167766 TATTTTATTTTTATTTTTATTTATTCTTATTTTTATTT
1 TATTTTATTTTTATTTTTATTTATTCTTATTTTTATTT
*
115167804 TATTTTATTTATTTTTTCTTATTT-TT-TTATTTTTATTT
1 TATTTTATTT-TTATTT-TTATTTATTCTTATTTTTATTT
115167842 T
1 T
115167843 TCAATTTTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
38 23 0.64
39 7 0.19
40 6 0.17
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (38 bp):
TATTTTATTTTTATTTTTATTTATTCTTATTTTTATTT
Found at i:115167849 original size:22 final size:21
Alignment explanation
Indices: 115167768--115167858 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 21
115167758 AATCCTCCTA
115167768 TTTTATTTTTATTTTT-ATTT
1 TTTTATTTTTATTTTTAATTT
115167788 ATTCTTATTTTTA-TTTT-ATTT
1 -TT-TTATTTTTATTTTTAATTT
*
115167809 TATTTA-TTTT-TTCTT-ATTT
1 T-TTTATTTTTATTTTTAATTT
115167828 TTTTATTTTTATTTTTCAATTT
1 TTTTATTTTTATTTTT-AATTT
*
115167850 TCTTATTTT
1 TTTTATTTT
115167859 GAAAGACATA
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
18 4 0.07
19 16 0.27
20 8 0.13
21 11 0.18
22 21 0.35
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTATTTTTATTTTTAATTT
Found at i:115168800 original size:17 final size:18
Alignment explanation
Indices: 115168768--115168801 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
115168758 CGTTGAGCCT
*
115168768 ATTAACCCTTTTTCATTG
1 ATTAACCCTTTGTCATTG
115168786 ATTAA-CCTTTGTCATT
1 ATTAACCCTTTGTCATT
115168802 AACCCATTAA
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:0.24, C:0.21, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTAACCCTTTGTCATTG
Found at i:115170748 original size:13 final size:13
Alignment explanation
Indices: 115170732--115170764 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
115170722 TTTGATTAAA
*
115170732 TTAGTTAATTAGT
1 TTAGATAATTAGT
115170745 TTAGATAATTAGT
1 TTAGATAATTAGT
115170758 TTA-ATAA
1 TTAGATAA
115170765 ACAAACCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:115174697 original size:31 final size:31
Alignment explanation
Indices: 115174662--115174724 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
115174652 TCGAAGTGAT
115174662 TTTTTGCTATTGCCGTGTAGTTTTCTATGCA
1 TTTTTGCTATTGCCGTGTAGTTTTCTATGCA
* *
115174693 TTTTTGCTATTGTCGTGTGGTTTTCTATGCA
1 TTTTTGCTATTGCCGTGTAGTTTTCTATGCA
115174724 T
1 T
115174725 GACCACACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.11, C:0.14, G:0.21, T:0.54
Consensus pattern (31 bp):
TTTTTGCTATTGCCGTGTAGTTTTCTATGCA
Found at i:115182417 original size:35 final size:35
Alignment explanation
Indices: 115182371--115182464 Score: 143
Period size: 35 Copynumber: 2.7 Consensus size: 35
115182361 AAGAAAATAT
* *
115182371 ATTTTGTTTAACTTGATTTGTAAATAATCTCTTAG
1 ATTTTGTTTAACTTGACTTGTAAATAATCTCTTAA
* * *
115182406 ATTTTGTTTAACTTAACTTGTAAGTAATTTCTTAA
1 ATTTTGTTTAACTTGACTTGTAAATAATCTCTTAA
115182441 ATTTTGTTTAACTTGACTTGTAAA
1 ATTTTGTTTAACTTGACTTGTAAA
115182465 CAATATTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (35 bp):
ATTTTGTTTAACTTGACTTGTAAATAATCTCTTAA
Found at i:115182503 original size:17 final size:17
Alignment explanation
Indices: 115182477--115182510 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
115182467 ATATTTTAGA
115182477 ATTTAAATCACACAACT
1 ATTTAAATCACACAACT
* *
115182494 ATTTAGATCACATAACT
1 ATTTAAATCACACAACT
115182511 CTAATAGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (17 bp):
ATTTAAATCACACAACT
Found at i:115187089 original size:41 final size:38
Alignment explanation
Indices: 115187044--115187133 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 38
115187034 AAAAAAGTAT
* * *
115187044 TTATATTAAAAAGCACTACCATAAATATAATAAATGTTTTG
1 TTATATTAAAAA-CAC-A-AATAAATATAATAAATATTTTA
115187085 TTATATTACAAAACACAAATAAATATAATAAATATTTTA
1 TTATATTA-AAAACACAAATAAATATAATAAATATTTTA
115187124 TTATATTAAA
1 TTATATTAAA
115187134 CATAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.04
39 27 0.60
40 1 0.02
41 11 0.24
42 4 0.09
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (38 bp):
TTATATTAAAAACACAAATAAATATAATAAATATTTTA
Found at i:115187604 original size:16 final size:16
Alignment explanation
Indices: 115187583--115187613 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
115187573 TTTTCTAATA
*
115187583 TTTTTTTATAATTTAC
1 TTTTTTAATAATTTAC
115187599 TTTTTTAATAATTTA
1 TTTTTTAATAATTTA
115187614 ATAAATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTAATAATTTAC
Found at i:115189767 original size:24 final size:24
Alignment explanation
Indices: 115189738--115189786 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
115189728 AAAAGAGAAG
115189738 AGTAGAAAAATGAAAGGACGATCC
1 AGTAGAAAAATGAAAGGACGATCC
115189762 AGTAGAAAAATGAAAGGACGATCC
1 AGTAGAAAAATGAAAGGACGATCC
115189786 A
1 A
115189787 ACTTTCACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.24, T:0.12
Consensus pattern (24 bp):
AGTAGAAAAATGAAAGGACGATCC
Found at i:115197720 original size:39 final size:39
Alignment explanation
Indices: 115197666--115197745 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 39
115197656 TTATAATAGG
115197666 AGATTGTGTATTTTTTTTCCTTCATTAGTTTTTTTATCCC
1 AGATTGTGTATTTTTTTTCCTTCATTAG-TTTTTTATCCC
115197706 AGATTGTGTATTTTTTTTCCTTCATTAGTTTTTTATCCC
1 AGATTGTGTATTTTTTTTCCTTCATTAGTTTTTTATCCC
115197745 A
1 A
115197746 CAAGATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 12 0.30
40 28 0.70
ACGTcount: A:0.16, C:0.15, G:0.10, T:0.59
Consensus pattern (39 bp):
AGATTGTGTATTTTTTTTCCTTCATTAGTTTTTTATCCC
Found at i:115207624 original size:205 final size:205
Alignment explanation
Indices: 115207223--115208790 Score: 2417
Period size: 205 Copynumber: 7.6 Consensus size: 205
115207213 GCAGATCTGG
115207223 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGC-AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
* * *
115207288 GATTT-GCTTTTCGCGTGCTTAC-ACTGAAACAAATCTAAGATGATTTGGCATCTCTGTATTGTC
65 GATTTGGC-TTTCACGTGTTTACGA-TGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTC
* * * * *
115207351 AGAGAA-AAATCGAAGTTTGGCATCTCCATTTCGACGAAGAGCAGATACATAGTAGATCTAACCT
128 AGAGAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACACAGCAGATCTAACCT
115207415 TCAGATGTTTATA
193 TCAGATGTTTATA
*
115207428 CTGAAGCAGATCCAAGATGGTTTGGCATCATTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
* *
115207493 ATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATTTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * * *
115207558 GAACAAATTGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGTAGATCTAACCTTCA
131 GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACACAGCAGATCTAACCTTCA
115207623 GATGTTTATA
196 GATGTTTATA
115207633 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
* * *
115207698 ATTTGGATTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTTTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * * *
115207763 GAACAAATCAAAGTCTGGCATCTCCATTTCGACTGAGAGCAGATACATAGCAGATCTAACCTTCA
131 GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACACAGCAGATCTAACCTTCA
115207828 GATGTTTATA
196 GATGTTTATA
*
115207838 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTATGCTTACAAGGAACAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
*
115207903 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * * * *
115207968 AAACAAATTGAAGTCTGGCATCTCTATTTCAAAGGAGAGCAGATACACAGCAGATCTCACCTTCA
131 GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACACAGCAGATCTAACCTTCA
*
115208033 GATGTTTATG
196 GATGTTTATA
*
115208043 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
*
115208108 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * ** * *
115208173 GAGCAAATCGAAGTCTGGCATCTCCACTTCAATAGAGAGCAGATACACAGCAGATCTCACCTTAA
131 GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACACAGCAGATCTAACCTTCA
*
115208238 GATGTTTATG
196 GATGTTTATA
* * * *
115208248 CGGAAGCAGATCCAAGATGGTTTGGTATCCTTGTACTTACAAGGAACAAATTGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
* *
115208313 ATTTGGCTTTCACGTGTTTACGATGAAGTAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * *
115208378 GAACAAATCGAAGTCTGGCATCTCCACTTCAATGGAGAGCAGATACACAGCAGATCTCACCTTCA
131 GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACACAGCAGATCTAACCTTCA
*
115208443 GATGTTTATG
196 GATGTTTATA
* * * *
115208453 CTGAAGCAGATCTAAGATGGTTTGGTATCCTTGTGCTTACAAGTAACAAATCAAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
* * * *
115208518 ATTTGGCTTCCACGTGTTTACGATGAGGCAAATCTAAGATGATTTGGCATCTCTATATTGGCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * * * * * * *
115208583 GAGCAAATCGAAGTCTGGCATCTCCACTTCAATGGAGAGCAAACACAGAGTAGAT-TCAAACTTC
131 GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACACAGCAGATCT-AACCTTC
115208647 AGATGTTTATA
195 AGATGTTTATA
* * *
115208658 CTGAAGTAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCGAATCGAAGACATAG-TC
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT-
* * *
115208722 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATGTGTCATCTCTGTATTGTCAG
65 GATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
115208787 AGAA
130 AGAA
115208791 TGAATTGAAG
Statistics
Matches: 1272, Mismatches: 86, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
204 118 0.09
205 1154 0.91
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (205 bp):
CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
GAACAAATCGAAGTCTGGCATCTCCATTTCAACGGAGAGCAGATACACAGCAGATCTAACCTTCA
GATGTTTATA
Found at i:115210058 original size:7 final size:7
Alignment explanation
Indices: 115210040--115210069 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
115210030 AAATACTACT
115210040 TATATT-
1 TATATTA
115210046 TATATTA
1 TATATTA
115210053 TATATTA
1 TATATTA
115210060 TATATTA
1 TATATTA
115210067 TAT
1 TAT
115210070 TATCTATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TATATTA
Found at i:115210392 original size:2 final size:2
Alignment explanation
Indices: 115210374--115210407 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
115210364 TTATTCACTT
*
115210374 TA TA T- TA TA TT 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 TA TA TA TA TA T
115210408 TAATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:115212641 original size:21 final size:22
Alignment explanation
Indices: 115212605--115212645 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
115212595 ATATATAGGC
*
115212605 TTGTCATTTCAAAAAAAAAAGT
1 TTGTAATTTCAAAAAAAAAAGT
115212627 TTGTAATTT-AAAAAAAAAA
1 TTGTAATTTCAAAAAAAAAA
115212646 CAAAAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (22 bp):
TTGTAATTTCAAAAAAAAAAGT
Found at i:115213101 original size:31 final size:31
Alignment explanation
Indices: 115213057--115213117 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
115213047 CAGCCTAGTG
115213057 ACTTAAATAAAAACTTTTGAATAGTTCAGTA
1 ACTTAAATAAAAACTTTTGAATAGTTCAGTA
* *
115213088 ACTTCAATGAAAACTTTTGAATAGTTCAGT
1 ACTTAAATAAAAACTTTTGAATAGTTCAGT
115213118 GATCAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTTGAATAGTTCAGTA
Found at i:115218618 original size:50 final size:49
Alignment explanation
Indices: 115218545--115218682 Score: 152
Period size: 50 Copynumber: 2.8 Consensus size: 49
115218535 TGGACCATGG
* * * **
115218545 CAATACGTGTGATCCCATGTAAGACTATATTTGGGATTTGACATTGGCAT
1 CAATA-GTGTGATCTCATGTAAGACCATATTTGGGATATGACATCAGCAT
* * * *
115218595 CAATATGTGTGATCTCGTATAAGACCATATCTGGGATATGGCATCAGCAT
1 CAATA-GTGTGATCTCATGTAAGACCATATTTGGGATATGACATCAGCAT
* *
115218645 CGATA-TGTGATATCATGTAAGACCATATTTGGGATATG
1 CAATAGTGTGATCTCATGTAAGACCATATTTGGGATATG
115218683 GCGTTGATAT
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
48 29 0.40
50 44 0.60
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (49 bp):
CAATAGTGTGATCTCATGTAAGACCATATTTGGGATATGACATCAGCAT
Found at i:115218945 original size:36 final size:37
Alignment explanation
Indices: 115218848--115218946 Score: 114
Period size: 37 Copynumber: 2.7 Consensus size: 37
115218838 AGACATCGTA
115218848 TAAGACCATAGTTGGGCTATGGCATCGTGACAACATG
1 TAAGACCATAGTTGGGCTATGGCATCGTGACAACATG
* *
115218885 TAAGACCATA-TCTGGGCTATGGCATTGTGATATA-A-G
1 TAAGACCATAGT-TGGGCTATGGCATCGTGACA-ACATG
* * *
115218921 TAAGACTATAGTTGGACTACGGCATC
1 TAAGACCATAGTTGGGCTATGGCATC
115218947 AAGTAAACAA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
36 22 0.42
37 30 0.57
38 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (37 bp):
TAAGACCATAGTTGGGCTATGGCATCGTGACAACATG
Found at i:115221570 original size:13 final size:13
Alignment explanation
Indices: 115221552--115221579 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
115221542 CGGAAAAAAT
115221552 GGGTAGACCACAC
1 GGGTAGACCACAC
115221565 GGGTAGACCACAC
1 GGGTAGACCACAC
115221578 GG
1 GG
115221580 TCGTGTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.36, T:0.07
Consensus pattern (13 bp):
GGGTAGACCACAC
Found at i:115226910 original size:40 final size:39
Alignment explanation
Indices: 115226855--115227062 Score: 256
Period size: 40 Copynumber: 5.2 Consensus size: 39
115226845 TGAATGATAC
* * *
115226855 CCGGGCTAAGCCCCGAAGGCATCTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTG-TTATAT
115226895 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGTTATAT
* * *
115226935 CCAGGTTAAGACCCGAAGGCATTTGTGCGAGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGT-GTTATAT
* * *
115226975 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGTTATAT
* * *
115227015 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGT-GTTATAT
115227055 CC-GGCTAA
1 CCGGGCTAA
115227063 ATTTCGAAGA
Statistics
Matches: 147, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
39 7 0.05
40 137 0.93
41 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGTTATAT
Found at i:115226999 original size:80 final size:80
Alignment explanation
Indices: 115226851--115227062 Score: 300
Period size: 80 Copynumber: 2.7 Consensus size: 80
115226841 CATTTGAATG
* * * * * *
115226851 ATACCCGGGCTAAGCCCCGAAGGCATCTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCA
1 ATACCCAGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCA
* *
115226916 TTTGTGCTAGTTGTT
66 TTTGTGCGAGTTGCT
* *
115226931 ATATCCAGGTTAAGACCCGAAGGCATTTGTGCGAGTGGTTATATCCGGGCTAAGACCCGAAGGCA
1 ATACCCAGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCA
115226996 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGCT
* * *
115227011 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 ATACCCAGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAA
115227063 ATTTCGAAGA
Statistics
Matches: 117, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 6 0.05
80 111 0.95
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
ATACCCAGGTTAAGACCCGAAGGCATTTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGCT
Found at i:115234985 original size:40 final size:40
Alignment explanation
Indices: 115234906--115235151 Score: 338
Period size: 40 Copynumber: 6.2 Consensus size: 40
115234896 TGAATGATAC
* * *
115234906 CCGGGCTAAGCCCCGAAGGCA-TTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
115234945 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* *
115234985 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
115235025 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* *
115235064 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * ** *
115235104 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
115235144 CC-GGCTAA
1 CCGGGCTAA
115235152 ATTTCGAAGA
Statistics
Matches: 187, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 63 0.34
40 122 0.65
41 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:115235066 original size:79 final size:79
Alignment explanation
Indices: 115234906--115235151 Score: 352
Period size: 79 Copynumber: 3.1 Consensus size: 79
115234896 TGAATGATAC
* * * *
115234906 CCGGGCTAAGCCCCGAAGGCA-TTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTTG
115234970 TGCTAGTTGTTATAT
66 TGCTAG-TGTTATAT
*
115234985 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTTG
*
115235050 TGCGAGTGTTATAT
66 TGCTAGTGTTATAT
* * * * *
115235064 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTTG
*
115235129 TGCTTGTGGTTATAT
66 TGCTAGT-GTTATAT
115235144 CC-GGCTAA
1 CCGGGCTAA
115235152 ATTTCGAAGA
Statistics
Matches: 151, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
79 97 0.64
80 54 0.36
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTTG
TGCTAGTGTTATAT
Found at i:115235117 original size:119 final size:119
Alignment explanation
Indices: 115234906--115235151 Score: 388
Period size: 119 Copynumber: 2.1 Consensus size: 119
115234896 TGAATGATAC
* *
115234906 CCGGGCTAAGCCCCGAAGGCATTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTTGT
1 CCGGGCTAAGACCCGAAGGCATTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCATTTGT
* * * *
115234971 GCTAGTTGTTATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTGGTTATAT
66 GCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGGTTATAT
*
115235025 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG-TTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCA-TTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCATTTG
**
115235089 TGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
65 TGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGGTTATAT
115235144 CC-GGCTAA
1 CCGGGCTAA
115235152 ATTTCGAAGA
Statistics
Matches: 117, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
118 6 0.05
119 102 0.87
120 9 0.08
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.26
Consensus pattern (119 bp):
CCGGGCTAAGACCCGAAGGCATTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCATTTGT
GCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGGTTATAT
Found at i:115237076 original size:55 final size:55
Alignment explanation
Indices: 115236955--115237095 Score: 142
Period size: 55 Copynumber: 2.6 Consensus size: 55
115236945 ATGCGACATG
** * * **
115236955 CCGTGGGAAAACCTGCCAAAATAACACGGGCGATCGACACACCAGTGCCTTGAAC
1 CCGTGGGTGAACCTGTCAAATTAACACGGGCGATCGACACACCAGTGCCAAGAAC
* * *
115237010 CCCTGGCTGAACCTGTCAAATTAACACGGGCG-TACGACACACCCGTGCCAAGCAA-
1 CCGTGGGTGAACCTGTCAAATTAACACGGGCGAT-CGACACACCAGTGCCAAG-AAC
* * *
115237065 CCGTGGGTGAACTTGTTAAATTAACCCGGGC
1 CCGTGGGTGAACCTGTCAAATTAACACGGGC
115237096 ATGGGCCTAC
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
54 1 0.01
55 67 0.96
56 2 0.03
ACGTcount: A:0.29, C:0.30, G:0.24, T:0.16
Consensus pattern (55 bp):
CCGTGGGTGAACCTGTCAAATTAACACGGGCGATCGACACACCAGTGCCAAGAAC
Found at i:115241109 original size:13 final size:13
Alignment explanation
Indices: 115241091--115241117 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
115241081 GAAATAAACG
115241091 CACACGGGCGTGT
1 CACACGGGCGTGT
115241104 CACACGGGCGTGT
1 CACACGGGCGTGT
115241117 C
1 C
115241118 CCTGCTGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:115250887 original size:36 final size:36
Alignment explanation
Indices: 115250838--115250911 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
115250828 CTGCAAAGTA
*
115250838 GGTTGCAACATATTGTTAGGTTTAGTAGGATGGTGT
1 GGTTGCAACATATTGTTAGGTTTAGTAGAATGGTGT
*
115250874 GGTTGCAATATATTGTTAGGTTTAGTAGAATGGTGT
1 GGTTGCAACATATTGTTAGGTTTAGTAGAATGGTGT
115250910 GG
1 GG
115250912 ACCATTACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.23, C:0.04, G:0.34, T:0.39
Consensus pattern (36 bp):
GGTTGCAACATATTGTTAGGTTTAGTAGAATGGTGT
Found at i:115261383 original size:25 final size:25
Alignment explanation
Indices: 115261317--115261373 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
115261307 CTCATACTAG
*
115261317 CCAATATTAAGAAGGTTCAAGCGAA
1 CCAATATGAAGAAGGTTCAAGCGAA
*
115261342 CCAATATGAAAAAGGTTCAAGCGAA
1 CCAATATGAAGAAGGTTCAAGCGAA
*
115261367 CTAATAT
1 CCAATAT
115261374 CGGGAAGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.21
Consensus pattern (25 bp):
CCAATATGAAGAAGGTTCAAGCGAA
Found at i:115261513 original size:25 final size:25
Alignment explanation
Indices: 115261480--115261539 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
115261470 ACAACCAATA
*
115261480 GGGATGCTC-CAAAGAACCATATAAC
1 GGGAAGCTCGCAAA-AACCATATAAC
115261505 GGGAAGCTCGCAAAAACCATATAAC
1 GGGAAGCTCGCAAAAACCATATAAC
*
115261530 AGGAAGCTCG
1 GGGAAGCTCG
115261540 TGAGAGCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 28 0.88
26 4 0.12
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.13
Consensus pattern (25 bp):
GGGAAGCTCGCAAAAACCATATAAC
Found at i:115261587 original size:24 final size:24
Alignment explanation
Indices: 115261525--115261587 Score: 56
Period size: 25 Copynumber: 2.5 Consensus size: 24
115261515 CAAAAACCAT
*
115261525 ATAACAGGAAGCTCGTGAGAGCCAA
1 ATAAC-GGAAGCTCATGAGAGCCAA
* * *
115261550 ATATCGGGATGCTCATGAGAG-CTA
1 ATAAC-GGAAGCTCATGAGAGCCAA
115261574 ATAACGGAACGCTC
1 ATAACGGAA-GCTC
115261588 CTTTGAGCTA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 3 0.10
24 10 0.33
25 17 0.57
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (24 bp):
ATAACGGAAGCTCATGAGAGCCAA
Found at i:115268461 original size:20 final size:19
Alignment explanation
Indices: 115268436--115268495 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 19
115268426 TAATTTTGGG
115268436 ATTTATTTTCATTTATCTTT
1 ATTTATTTT-ATTTATCTTT
* *
115268456 ATTTATCTTAAATTATCTTT
1 ATTTAT-TTTATTTATCTTT
115268476 ATTTATTTGTATTTATCTTT
1 ATTTATTT-TATTTATCTTT
115268496 TAGAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATTTATCTTT
Found at i:115268492 original size:30 final size:30
Alignment explanation
Indices: 115268438--115268494 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
115268428 ATTTTGGGAT
115268438 TTATTTTCATTTATCTTTATTTATCTTAAA
1 TTATTTTCATTTATCTTTATTTATCTTAAA
115268468 TTATCTTT-ATTTAT-TTGTATTTATCTT
1 TTAT-TTTCATTTATCTT-TATTTATCTT
115268495 TTAGAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 2 0.08
30 20 0.80
31 3 0.12
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.67
Consensus pattern (30 bp):
TTATTTTCATTTATCTTTATTTATCTTAAA
Found at i:115269248 original size:17 final size:18
Alignment explanation
Indices: 115269215--115269248 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
115269205 TAGTCCTCAT
*
115269215 TTTAATTTTTGCCATTTA
1 TTTAATTTTTGCAATTTA
115269233 TTTAATTTTT-CAATTT
1 TTTAATTTTTGCAATTT
115269249 CAATTCACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTAATTTTTGCAATTTA
Found at i:115274856 original size:12 final size:13
Alignment explanation
Indices: 115274839--115274902 Score: 82
Period size: 12 Copynumber: 5.1 Consensus size: 13
115274829 AGACAACTCA
115274839 ATTT-TTATTTTT
1 ATTTATTATTTTT
115274851 ATTT-TTATTTTT
1 ATTTATTATTTTT
115274863 ATTTATT-TATTTT
1 ATTTATTAT-TTTT
115274876 ATCTTATTA-TTTT
1 AT-TTATTATTTTT
115274889 ATTTATTATTTTT
1 ATTTATTATTTTT
115274902 A
1 A
115274903 GATATTAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
12 23 0.49
13 19 0.40
14 5 0.11
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTATTATTTTT
Found at i:115274862 original size:18 final size:18
Alignment explanation
Indices: 115274839--115274902 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 18
115274829 AGACAACTCA
115274839 ATTTTTATTTTTATTTTT
1 ATTTTTATTTTTATTTTT
115274857 ATTTTTATTTATT-TATTTT
1 ATTTTTATTT-TTAT-TTTT
115274876 ATCTTATTA-TTTTATTTATT
1 AT-TT-TTATTTTTATTT-TT
115274896 ATTTTTA
1 ATTTTTA
115274903 GATATTAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
18 14 0.35
19 14 0.35
20 9 0.22
21 3 0.08
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTTATTTTTATTTTT
Found at i:115274873 original size:26 final size:27
Alignment explanation
Indices: 115274842--115274902 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
115274832 CAACTCAATT
115274842 TTTATTTTTAT-TT-TTATTTTTATTTA
1 TTTATTTTTATCTTATTA-TTTTATTTA
115274868 TTTA-TTTTATCTTATTATTTTATTTA
1 TTTATTTTTATCTTATTATTTTATTTA
115274894 -TTATTTTTA
1 TTTATTTTTA
115274903 GATATTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 9 0.28
26 20 0.62
27 3 0.09
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (27 bp):
TTTATTTTTATCTTATTATTTTATTTA
Found at i:115276646 original size:20 final size:19
Alignment explanation
Indices: 115276621--115276680 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 19
115276611 TAATTTTAGG
115276621 ATTTATTTTCATTTATCTTT
1 ATTTATTTT-ATTTATCTTT
* *
115276641 ATTTATCTTAAATTATCTTT
1 ATTTAT-TTTATTTATCTTT
115276661 ATTTATTTGTATTTATCTTT
1 ATTTATTT-TATTTATCTTT
115276681 TAGAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATTTATCTTT
Found at i:115276677 original size:30 final size:30
Alignment explanation
Indices: 115276623--115276679 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
115276613 ATTTTAGGAT
115276623 TTATTTTCATTTATCTTTATTTATCTTAAA
1 TTATTTTCATTTATCTTTATTTATCTTAAA
115276653 TTATCTTT-ATTTAT-TTGTATTTATCTT
1 TTAT-TTTCATTTATCTT-TATTTATCTT
115276680 TTAGAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 2 0.08
30 20 0.80
31 3 0.12
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.67
Consensus pattern (30 bp):
TTATTTTCATTTATCTTTATTTATCTTAAA
Found at i:115288323 original size:17 final size:17
Alignment explanation
Indices: 115288300--115288333 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
115288290 CAATATTGTT
*
115288300 TTTTTTCTTCTTTTTTTG
1 TTTTTCCTT-TTTTTTTG
115288318 TTTTTCCTTTTTTTTT
1 TTTTTCCTTTTTTTTT
115288334 CTAGAACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTCCTTTTTTTTTG
Found at i:115289472 original size:21 final size:21
Alignment explanation
Indices: 115289434--115289483 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
115289424 AAAGCTAAGC
*
115289434 ATAAGAAATATAAAAAATAAGA
1 ATAAAAAATATAAAAAATAA-A
115289456 A-AAAAAATA-AAACAAATAAA
1 ATAAAAAATATAAA-AAATAAA
115289476 ATAAAAAA
1 ATAAAAAA
115289484 CAAATAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 5 0.20
21 19 0.76
22 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (21 bp):
ATAAAAAATATAAAAAATAAA
Found at i:115289476 original size:16 final size:16
Alignment explanation
Indices: 115289464--115289506 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
115289454 GAAAAAAAAT
115289464 AAAACAAATAAAATAA
1 AAAACAAATAAAATAA
*
115289480 AAAACAAATAATATAA
1 AAAACAAATAAAATAA
115289496 CAAAA-AAATAA
1 -AAAACAAATAA
115289507 GTAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAACAAATAAAATAA
Found at i:115289521 original size:21 final size:19
Alignment explanation
Indices: 115289443--115289522 Score: 54
Period size: 21 Copynumber: 3.9 Consensus size: 19
115289433 CATAAGAAAT
115289443 ATAA-AAAATAAGAAAAAAA
1 ATAATAAAATAAG-AAAAAA
* *
115289462 ATAAAACAAATAAAATAAAAA
1 ATAATA-AAATAAGA-AAAAA
* * *
115289483 ACAAATAATATAACAAAAAA
1 A-TAATAAAATAAGAAAAAA
115289503 ATAAGTAAAATAAAGAAAAA
1 ATAA-TAAAAT-AAGAAAAA
115289523 GGGTAAAAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
19 6 0.13
20 13 0.28
21 25 0.53
22 3 0.06
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.14
Consensus pattern (19 bp):
ATAATAAAATAAGAAAAAA
Found at i:115291787 original size:19 final size:19
Alignment explanation
Indices: 115291763--115291805 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
115291753 TACTATAAGG
115291763 GTTATTTTGAAGCCTAGAA
1 GTTATTTTGAAGCCTAGAA
115291782 GTTATTTTGAAGCCTAGAA
1 GTTATTTTGAAGCCTAGAA
115291801 -TTATT
1 GTTATT
115291806 ACCCATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (19 bp):
GTTATTTTGAAGCCTAGAA
Found at i:115294879 original size:13 final size:13
Alignment explanation
Indices: 115294861--115294891 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
115294851 GGGGTTGTTT
115294861 ACTAAACTAATTA
1 ACTAAACTAATTA
115294874 ACTAAACTAATTA
1 ACTAAACTAATTA
115294887 ACTAA
1 ACTAA
115294892 TTAAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (13 bp):
ACTAAACTAATTA
Found at i:115297825 original size:17 final size:17
Alignment explanation
Indices: 115297805--115297847 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
115297795 AATAAAATTG
115297805 AAATGAAAATAAACAT-A
1 AAAT-AAAATAAACATAA
*
115297822 AAATAAACATAAAAATAA
1 AAATAAA-ATAAACATAA
115297840 AAATAAAA
1 AAATAAAA
115297848 AGATAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 12 0.52
18 8 0.35
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (17 bp):
AAATAAAATAAACATAA
Found at i:115297826 original size:11 final size:11
Alignment explanation
Indices: 115297810--115297847 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
115297800 AATTGAAATG
115297810 AAAATAAACAT
1 AAAATAAACAT
115297821 AAAATAAACAT
1 AAAATAAACAT
*
115297832 AAAAATAAAAAT
1 -AAAATAAACAT
115297844 AAAA
1 AAAA
115297848 AGATAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAACAT
Found at i:115297838 original size:12 final size:12
Alignment explanation
Indices: 115297810--115297848 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
115297800 AATTGAAATG
115297810 AAAATAAACAT-
1 AAAATAAACATA
115297821 AAAATAAACATA
1 AAAATAAACATA
*
115297833 AAAATAAAAATA
1 AAAATAAACATA
115297845 AAAA
1 AAAA
115297849 GATAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAACATA
Found at i:115297848 original size:6 final size:6
Alignment explanation
Indices: 115297805--115297848 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
115297795 AATAAAATTG
* * *
115297805 AAATGA AAATAA ACAT-A AAATAA ACATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAA
115297849 GATAAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:115301594 original size:13 final size:13
Alignment explanation
Indices: 115301576--115301604 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
115301566 GGTTGTTTAT
115301576 TAAAGTAATTAAC
1 TAAAGTAATTAAC
115301589 TAAAGTAATTAAC
1 TAAAGTAATTAAC
115301602 TAA
1 TAA
115301605 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (13 bp):
TAAAGTAATTAAC
Found at i:115304084 original size:16 final size:16
Alignment explanation
Indices: 115304050--115304092 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
115304040 AATTGAAATG
*
115304050 AATAT-ATATATGTGTA
1 AATATGATA-ATGTGCA
*
115304066 AATGTGATAATGTGCA
1 AATATGATAATGTGCA
115304082 AATATGATAAT
1 AATATGATAAT
115304093 TAGATATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.37
Consensus pattern (16 bp):
AATATGATAATGTGCA
Found at i:115307962 original size:19 final size:19
Alignment explanation
Indices: 115307938--115307976 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
115307928 TTTGTTAGGT
115307938 AAGTTCATATAGTATAACC
1 AAGTTCATATAGTATAACC
115307957 AAGTTCATATAGTATAACC
1 AAGTTCATATAGTATAACC
115307976 A
1 A
115307977 GGTAAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (19 bp):
AAGTTCATATAGTATAACC
Found at i:115311068 original size:31 final size:31
Alignment explanation
Indices: 115310999--115311075 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
115310989 AAATATTATT
* * *
115310999 TTATTATTTTAATAATTTTTAAATGATAAAA
1 TTATAATTTTTATTATTTTTAAATGATAAAA
*
115311030 TTA-AATTTTTATTATTTTTAAGA-GATTAAA
1 TTATAATTTTTATTATTTTTAA-ATGATAAAA
115311060 TTATAA-TTTTATTATT
1 TTATAATTTTTATTATT
115311076 AATTTAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 34 0.85
31 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (31 bp):
TTATAATTTTTATTATTTTTAAATGATAAAA
Found at i:115311076 original size:19 final size:19
Alignment explanation
Indices: 115311054--115311090 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
115311044 TTTTTAAGAG
*
115311054 ATTAAATTATAATTTTATT
1 ATTAAATTAAAATTTTATT
*
115311073 ATTAATTTAAAATTTTAT
1 ATTAAATTAAAATTTTAT
115311091 AAAATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTAAATTAAAATTTTATT
Found at i:115313680 original size:3 final size:3
Alignment explanation
Indices: 115313674--115313701 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
115313664 GTAAAAAAAA
115313674 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
115313702 GGAATCTGAA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:115314603 original size:3 final size:3
Alignment explanation
Indices: 115314595--115314633 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
115314585 TATGAACAAA
115314595 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
115314634 GAACATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:115315928 original size:2 final size:2
Alignment explanation
Indices: 115315921--115315964 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
115315911 TGAACTAAAT
115315921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
115315963 TA
1 TA
115315965 AAACCGAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:115318489 original size:20 final size:20
Alignment explanation
Indices: 115318451--115318510 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 20
115318441 TTTTAAAAAC
*
115318451 ATATAAAAATTC-TAATAAA
1 ATATAAAAATTCAAAATAAA
*
115318470 ATATAAAATTTCAAAATAAA
1 ATATAAAAATTCAAAATAAA
* *
115318490 ATATATAACTT-AAAATAAA
1 ATATAAAAATTCAAAATAAA
115318509 AT
1 AT
115318511 CAACCTCAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 21 0.58
20 15 0.42
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATAAAAATTCAAAATAAA
Found at i:115326473 original size:16 final size:17
Alignment explanation
Indices: 115326448--115326497 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 17
115326438 TGGTAAATTA
115326448 TATAATATATAAAAATAG
1 TATAA-ATATAAAAATAG
*
115326466 TAT-AATAT-AAAATAT
1 TATAAATATAAAAATAG
*
115326481 TATAAATTTAAAAATAG
1 TATAAATATAAAAATAG
115326498 ATCGGATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 8 0.30
17 7 0.26
18 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (17 bp):
TATAAATATAAAAATAG
Found at i:115327099 original size:19 final size:18
Alignment explanation
Indices: 115327072--115327107 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
115327062 AGTTTATTCA
*
115327072 TTGATTTATTTTAATATAT
1 TTGAATTATTTT-ATATAT
115327091 TTGAATTATTTTATATA
1 TTGAATTATTTTATATA
115327108 AAAAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
TTGAATTATTTTATATAT
Found at i:115330662 original size:18 final size:19
Alignment explanation
Indices: 115330618--115330672 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
115330608 AAATCGTAAA
*
115330618 AAATGATAAAATA-TATAG
1 AAATCATAAAATATTATAG
*
115330636 AAATTATAAAATATTATA-
1 AAATCATAAAATATTATAG
* *
115330654 AAGTCATAAGAAAATTATA
1 AAATCATAA-AATATTATA
115330673 CAAAATGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 19 0.61
19 12 0.39
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (19 bp):
AAATCATAAAATATTATAG
Found at i:115330993 original size:9 final size:10
Alignment explanation
Indices: 115330969--115330994 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
115330959 ATTATTTATT
115330969 ATTTTTTGTA
1 ATTTTTTGTA
115330979 ATTTTTTGTA
1 ATTTTTTGTA
115330989 ATTTTT
1 ATTTTT
115330995 AATAAGAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (10 bp):
ATTTTTTGTA
Found at i:115335400 original size:55 final size:55
Alignment explanation
Indices: 115335334--115335443 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
115335324 AAAAATAAGG
115335334 CACTAATCTTCAATTATACCTCTTGTCAAACTAAATGCACTTGTCAGTATCAATC
1 CACTAATCTTCAATTATACCTCTTGTCAAACTAAATGCACTTGTCAGTATCAATC
*
115335389 CACTAATCTTCAATTATACCTCTTGTGAAACTAAATGCACTTGTCAGTATCAATC
1 CACTAATCTTCAATTATACCTCTTGTCAAACTAAATGCACTTGTCAGTATCAATC
115335444 TACTTCTTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.35
Consensus pattern (55 bp):
CACTAATCTTCAATTATACCTCTTGTCAAACTAAATGCACTTGTCAGTATCAATC
Found at i:115336436 original size:18 final size:19
Alignment explanation
Indices: 115336410--115336445 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
115336400 TTTTTAGTAT
115336410 TTTTGATGTATTTTTAATG
1 TTTTGATGTATTTTTAATG
*
115336429 TTTT-ATGTTTTTTTAAT
1 TTTTGATGTATTTTTAAT
115336446 TAAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.69
Consensus pattern (19 bp):
TTTTGATGTATTTTTAATG
Found at i:115338446 original size:3 final size:3
Alignment explanation
Indices: 115338438--115338514 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
115338428 TAATAAAGTA
115338438 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
115338486 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
115338515 AATGAAATAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:115340292 original size:44 final size:44
Alignment explanation
Indices: 115340217--115340475 Score: 159
Period size: 44 Copynumber: 5.9 Consensus size: 44
115340207 TCGTAGCTTT
* * * *
115340217 AATCTGTTCCACTACAACTCCAGGGAA-ATAAGAATCGCATCTTC
1 AATCTGCTCCACTGCAACTTCA-GGAAGATAAGATTCGCATCTTC
* * * *
115340261 AATCTGCTCCACTGCAACTTCAAGAAGATAAGATTTGTAAC-TC
1 AATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCATCTTC
* * * *** * *
115340304 TAACCTGCTCCACTGCAACTTTAGGGAA-ATAAGGTTTATAGCTTT
1 -AATCTGCTCCACTGCAACTTCA-GGAAGATAAGATTCGCATCTTC
* * *
115340349 AATCTGCTCTACTGCAACTTTA-GAGAGATAAGATTCGCTATCTTT
1 AATCTGCTCCACTGCAACTTCAGGA-AGATAAGATTCGC-ATCTTC
* * *** *
115340394 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGAAGATAAGA-TTCGCATCTTC
** * * *
115340438 AATCTATTCCATTGTAACTTCAGGGAGATAAGATTCGC
1 AATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGC
115340476 CATAATAACT
Statistics
Matches: 170, Mismatches: 35, Indels: 20
0.76 0.16 0.09
Matches are distributed among these distances:
42 2 0.01
43 8 0.05
44 120 0.71
45 37 0.22
46 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCATCTTC
Found at i:115340437 original size:89 final size:89
Alignment explanation
Indices: 115340224--115340475 Score: 247
Period size: 89 Copynumber: 2.8 Consensus size: 89
115340214 TTTAATCTGT
* * * *** * *
115340224 TCCACTACAACTCCAGGGAAATAAGAATCGCATCTTCAATCTGCTCCACTGCAACTTCA-AGAAG
1 TCCACTGCAACTTCAGGGAAATAAGACTTATAGCTTTAATCTGCTCCACTGCAACTTCAGAG-AG
*
115340288 ATAAGATTTG-TAACTCTAACCTGC
65 ATAAGATTCGCTAACTCTAACCTGC
* ** * *
115340312 TCCACTGCAACTTTAGGGAAATAAGGTTTATAGCTTTAATCTGCTCTACTGCAACTTTAGAGAGA
1 TCCACTGCAACTTCAGGGAAATAAGACTTATAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGA
* * **
115340377 TAAGATTCGCTATCTTTAGTCTGC
66 TAAGATTCGCTAACTCTAACCTGC
* * * ** * * *
115340401 TCCACTGCAACTTCAGGGAGATAAGACTTGTGGCTTTAATCTATTCCATTGTAACTTCAGGGAGA
1 TCCACTGCAACTTCAGGGAAATAAGACTTATAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGA
115340466 TAAGATTCGC
66 TAAGATTCGC
115340476 CATAATAACT
Statistics
Matches: 132, Mismatches: 30, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
88 58 0.44
89 74 0.56
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (89 bp):
TCCACTGCAACTTCAGGGAAATAAGACTTATAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGA
TAAGATTCGCTAACTCTAACCTGC
Found at i:115340457 original size:133 final size:132
Alignment explanation
Indices: 115340210--115340469 Score: 304
Period size: 133 Copynumber: 2.0 Consensus size: 132
115340200 TTTTAACTCG
* *
115340210 TAGCTTTAATCTGTTCCACTACAACTCCAGGGAAATAAGAATCGCATCTTCAATCTGCTCCACTG
1 TAGCTTTAATCTGCTCCACTACAACTCCAGAGAAATAAGAATCGCATCTTCAATCTGCTCCACTG
* * *
115340275 CAACTTCAAGAAGATAAGATTTGTAACTCTAACCTGCTCCACTGCAACTTTAGGGAAATAAGGTT
66 CAACTTCAAGAAGATAAGACTTGTAACTCTAACCTACTCCACTGCAACTTCAGGGAAATAAGGTT
115340340 TA
131 TA
* * ** * * * *
115340342 TAGCTTTAATCTGCTCTACTGCAACTTTAGAGAGATAAGATTCGCTATCTTTAGTCTGCTCCACT
1 TAGCTTTAATCTGCTCCACTACAACTCCAGAGAAATAAGAATCGC-ATCTTCAATCTGCTCCACT
* * ** * * * * * *
115340407 GCAACTTCAGGGAGATAAGACTTGTGGCTTTAATCTATTCCATTGTAACTTCAGGGAGATAAG
65 GCAACTTCAAGAAGATAAGACTTGTAACTCTAACCTACTCCACTGCAACTTCAGGGAAATAAG
115340470 ATTCGCCATA
Statistics
Matches: 104, Mismatches: 23, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
132 37 0.36
133 67 0.64
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (132 bp):
TAGCTTTAATCTGCTCCACTACAACTCCAGAGAAATAAGAATCGCATCTTCAATCTGCTCCACTG
CAACTTCAAGAAGATAAGACTTGTAACTCTAACCTACTCCACTGCAACTTCAGGGAAATAAGGTT
TA
Found at i:115341196 original size:44 final size:44
Alignment explanation
Indices: 115341096--115341209 Score: 133
Period size: 44 Copynumber: 2.6 Consensus size: 44
115341086 TTTAATTTGT
* *
115341096 TCCACTACAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGC
1 TCCACTACAACTTCAGGGAAATAAGATT-ACTAACTTCAGTCTAC
* * *
115341141 TCCACTGCAACTTTAGGGAAATAAGACTT-GTAACTTCA-TCCTAC
1 TCCACTACAACTTCAGGGAAATAAGA-TTACTAACTTCAGT-CTAC
*
115341185 TCCACTACAACTTCAGGGAGATAAG
1 TCCACTACAACTTCAGGGAAATAAG
115341210 GTTTGTGGCT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
43 1 0.02
44 32 0.54
45 24 0.41
46 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (44 bp):
TCCACTACAACTTCAGGGAAATAAGATTACTAACTTCAGTCTAC
Found at i:115341349 original size:94 final size:94
Alignment explanation
Indices: 115341226--115341400 Score: 235
Period size: 94 Copynumber: 1.9 Consensus size: 94
115341216 GGCTTTAATT
* * *
115341226 TGCTCCACTGCAACTTTAGGAAGATAAGATTCACCATGATAACTTTAATCCGTCCCACTGCCAT-
1 TGCTCCACTGCAACTTCAGGAAGATAAGATTCACCATAATAACTTTAATCCATCCCACTG-CATC
* *
115341290 TTTAGGGGTGTAGGATTAATGGTTTCAATA
65 TTTAGAGGTATAGGATTAATGGTTTCAATA
* ** * * *
115341320 TGCTCCACTGCATCTTCAGGGGGATAAGATTCGCCATAATGATTTTAATCCATCCCACTGCATCT
1 TGCTCCACTGCAACTTCAGGAAGATAAGATTCACCATAATAACTTTAATCCATCCCACTGCATCT
115341385 TTAGAGGTATAGGATT
66 TTAGAGGTATAGGATT
115341401 TTTCGTTTCT
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
93 3 0.04
94 66 0.96
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (94 bp):
TGCTCCACTGCAACTTCAGGAAGATAAGATTCACCATAATAACTTTAATCCATCCCACTGCATCT
TTAGAGGTATAGGATTAATGGTTTCAATA
Found at i:115342283 original size:14 final size:13
Alignment explanation
Indices: 115342245--115342283 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
115342235 CTTTTTCTTC
115342245 TTTTTTGTTTTT-G
1 TTTTTT-TTTTTGG
115342258 TTTTTTTTTTTGG
1 TTTTTTTTTTTGG
115342271 TTTTTTTATTTTG
1 TTTTTTT-TTTTG
115342284 TAGTGAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
14 5 0.21
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTTGG
Found at i:115345972 original size:47 final size:47
Alignment explanation
Indices: 115345910--115346035 Score: 146
Period size: 47 Copynumber: 2.7 Consensus size: 47
115345900 CTTTACATAA
* * * *
115345910 TGATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCTCAC
1 TGATGCCATATCCCAGATATGGTCTTACACAGT-AGCACATATCACAC
* * **
115345957 TGATGTCATATCCCAGATATGGTCTTATACAGTAGCTTATATCACAC
1 TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC
* *
115346004 CGATGCCATATCCCAGATATGGTCTTATACAG
1 TGATGCCATATCCCAGATATGGTCTTACACAG
115346036 AAATCACTTG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 66 0.97
48 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (47 bp):
TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC
Found at i:115346051 original size:7 final size:7
Alignment explanation
Indices: 115346039--115346067 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
115346029 TATACAGAAA
115346039 TCACTTG
1 TCACTTG
115346046 TCACTTG
1 TCACTTG
115346053 TCACTTG
1 TCACTTG
115346060 TCACTTG
1 TCACTTG
115346067 T
1 T
115346068 AGCCAAAGCT
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:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Found at i:115346101 original size:31 final size:31
Alignment explanation
Indices: 115346066--115346274 Score: 301
Period size: 31 Copynumber: 6.7 Consensus size: 31
115346056 CTTGTCACTT
* *
115346066 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** *
115346097 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
115346128 GTAGCCGGAGCTACCACTTTTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
115346159 GTAGCCGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
115346190 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
115346221 GTAGCTGAAACTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
115346252 GTAGCTGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
115346275 GTTGTCATTT
Statistics
Matches: 160, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 160 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:115346358 original size:50 final size:50
Alignment explanation
Indices: 115346252--115346428 Score: 257
Period size: 50 Copynumber: 3.5 Consensus size: 50
115346242 CACTGATCAG
* * * *
115346252 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTG-CCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCC-TTGATCAGATAAGT
* *
115346303 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
115346353 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
115346403 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
115346429 GTTTCCATGG
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
50 89 0.79
51 24 0.21
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:115350768 original size:47 final size:47
Alignment explanation
Indices: 115350704--115350825 Score: 147
Period size: 47 Copynumber: 2.6 Consensus size: 47
115350694 ACATAATGAG
* * * * *
115350704 GCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCTCACTGAT
1 GCCATATCCCAGATATGGTCTTACACAGT-AGCACATATCACACCGAT
* * *
115350751 GTCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACCGAT
1 GCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACACCGAT
*
115350798 GCCATATCCCAGATATGGTCTTATACAG
1 GCCATATCCCAGATATGGTCTTACACAG
115350826 AAATCACTTG
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
47 63 0.97
48 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (47 bp):
GCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACACCGAT
Found at i:115350841 original size:7 final size:7
Alignment explanation
Indices: 115350829--115350857 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
115350819 TATACAGAAA
115350829 TCACTTG
1 TCACTTG
115350836 TCACTTG
1 TCACTTG
115350843 TCACTTG
1 TCACTTG
115350850 TCACTTG
1 TCACTTG
115350857 T
1 T
115350858 AGCCAAAGCT
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:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Found at i:115350891 original size:31 final size:31
Alignment explanation
Indices: 115350856--115351064 Score: 310
Period size: 31 Copynumber: 6.7 Consensus size: 31
115350846 CTTGTCACTT
* *
115350856 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** *
115350887 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
115350918 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
115350949 GTAGCCGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
115350980 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
115351011 GTAGCTGAAACTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
115351042 GTAGCTGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
115351065 GTTGTCATTT
Statistics
Matches: 162, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 162 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:115351191 original size:50 final size:50
Alignment explanation
Indices: 115351042--115351217 Score: 248
Period size: 50 Copynumber: 3.5 Consensus size: 50
115351032 CACTGATCAG
* * * *
115351042 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTG-CCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCC-TTGATCAGATAAGT
* *
115351093 GTAGCCGAAGCTATCACTTATCA-TTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
115351142 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
115351192 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
115351218 GTTTCCATGG
Statistics
Matches: 112, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
49 40 0.36
50 52 0.46
51 20 0.18
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:115354120 original size:26 final size:26
Alignment explanation
Indices: 115354084--115354192 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
115354074 TGATACAAAT
115354084 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
115354110 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
115354136 TGA-AATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
115354161 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
115354187 TGATAA
1 TGATAA
115354193 GAATTTCATG
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
25 23 0.29
26 53 0.68
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:115354152 original size:51 final size:51
Alignment explanation
Indices: 115354092--115354189 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
115354082 ATTGATAATA
115354092 GGTTAGGTAAATG-TTCAATGATAATAGGTTAGGTAAATGTTCCATGAAATG
1 GGTTAGGTAAATGTTTC-ATGATAATAGGTTAGGTAAATGTTCCATGAAATG
* *
115354143 GGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATGTTTCATGA
1 GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGA
115354190 TAAGAATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 41 0.93
52 3 0.07
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.36
Consensus pattern (51 bp):
GGTTAGGTAAATGTTTCATGATAATAGGTTAGGTAAATGTTCCATGAAATG
Found at i:115355866 original size:27 final size:26
Alignment explanation
Indices: 115355788--115355901 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
115355778 TGGAGGAAGC
* *
115355788 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
115355815 GATCTGGT-GCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
115355841 GTTCTGGTGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* *
115355868 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
115355895 GTTCTGG
1 GTTCTGG
115355902 CAGCCATACT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
25 1 0.01
26 26 0.34
27 33 0.43
28 17 0.22
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:115355868 original size:53 final size:54
Alignment explanation
Indices: 115355788--115355901 Score: 169
Period size: 53 Copynumber: 2.1 Consensus size: 54
115355778 TGGAGGAAGC
115355788 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTG-CTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTGACTCTGCCACAT-TATCT
* * * *
115355841 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTGACTCTGCCACATTATCT
115355895 GTTCTGG
1 GTTCTGG
115355902 CAGCCATACT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
53 25 0.45
54 20 0.36
55 10 0.18
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTGACTCTGCCACATTATCT
Found at i:115357372 original size:12 final size:12
Alignment explanation
Indices: 115357355--115357397 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
115357345 ACTCGGGGAA
*
115357355 GAGGCCATGGTC
1 GAGGCCGTGGTC
115357367 GAGGCCGTGGTC
1 GAGGCCGTGGTC
115357379 GAGGCCGTGGTC
1 GAGGCCGTGGTC
115357391 GAGGCCG
1 GAGGCCG
115357398 AGGTAGTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.12, C:0.26, G:0.49, T:0.14
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:115362298 original size:26 final size:26
Alignment explanation
Indices: 115362262--115362371 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
115362252 TGATACAAAT
115362262 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
115362288 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
115362314 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
115362340 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
115362366 TGATAA
1 TGATAA
115362372 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:115364008 original size:27 final size:27
Alignment explanation
Indices: 115363967--115364079 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
115363957 GAGGAAGCGT
*
115363967 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
115363994 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
115364021 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
115364049 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
115364075 TCTGG
1 TCTGG
115364080 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:115364072 original size:54 final size:54
Alignment explanation
Indices: 115363965--115364079 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
115363955 TGGAGGAAGC
*
115363965 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
115364019 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
115364073 GTTCTGG
1 GTTCTGG
115364080 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:115365523 original size:5 final size:5
Alignment explanation
Indices: 115365513--115365541 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
115365503 GCAATTACAG
115365513 ACAAA ACAAA ACAAA ACAAA ACAAA ACAA
1 ACAAA ACAAA ACAAA ACAAA ACAAA ACAA
115365542 GTCAGTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (5 bp):
ACAAA
Found at i:115367076 original size:3 final size:3
Alignment explanation
Indices: 115367068--115367140 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
115367058 AATAAAGTAC
115367068 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
115367116 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
115367141 AACGAAATAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:115367451 original size:17 final size:19
Alignment explanation
Indices: 115367429--115367467 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
115367419 TTGAAGAACC
*
115367429 AAATTAAA-AGTGAAA-TA
1 AAATTAAAGAGTCAAATTA
115367446 AAATTAAAGAGTCAAATTA
1 AAATTAAAGAGTCAAATTA
115367465 AAA
1 AAA
115367468 AAAAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (19 bp):
AAATTAAAGAGTCAAATTA
Found at i:115368758 original size:18 final size:18
Alignment explanation
Indices: 115368735--115368777 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
115368725 GAATAGGTTT
115368735 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
115368753 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
115368771 TTAATTA
1 TTAATTA
115368778 CACCTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:115369063 original size:22 final size:22
Alignment explanation
Indices: 115369038--115369079 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
115369028 TTGGTAAACA
115369038 AAAATGACTATTTTTATAATCT
1 AAAATGACTATTTTTATAATCT
115369060 AAAATGACTATTTTTATAAT
1 AAAATGACTATTTTTATAAT
115369080 TTATATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (22 bp):
AAAATGACTATTTTTATAATCT
Found at i:115377593 original size:22 final size:23
Alignment explanation
Indices: 115377568--115377613 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
115377558 CAACCAATCC
* *
115377568 AATTCA-ACATATTTTTAAGATA
1 AATTCATACATATTTATAAAATA
*
115377590 AATTCATGCATATTTATAAAATA
1 AATTCATACATATTTATAAAATA
115377613 A
1 A
115377614 CGTCATCACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (23 bp):
AATTCATACATATTTATAAAATA
Found at i:115377619 original size:23 final size:23
Alignment explanation
Indices: 115377575--115377619 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
115377565 TCCAATTCAA
* * *
115377575 CATATTTTTAAGATAAATTCATG
1 CATATTTATAAAATAAAGTCATG
*
115377598 CATATTTATAAAATAACGTCAT
1 CATATTTATAAAATAAAGTCAT
115377620 CACATAGCTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (23 bp):
CATATTTATAAAATAAAGTCATG
Found at i:115380084 original size:2 final size:2
Alignment explanation
Indices: 115380077--115380103 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
115380067 GCATATAAAC
115380077 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
115380104 ACTCCTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:115380595 original size:21 final size:20
Alignment explanation
Indices: 115380551--115380620 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
115380541 ACTGAAGCAT
* * *
115380551 ATAAGTGTTAAATGGAAACCC
1 ATAAGGGTTAAACGG-AAGCC
115380572 ATAAGGGTTAAACGGAAGCTC
1 ATAAGGGTTAAACGGAAGC-C
*
115380593 AT-AGGAGTTGAACGGAAAGCC
1 ATAAGG-GTTAAACGG-AAGCC
115380614 ATAAGGG
1 ATAAGGG
115380621 CTAATCTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 6 0.15
21 28 0.68
22 7 0.17
ACGTcount: A:0.40, C:0.13, G:0.29, T:0.19
Consensus pattern (20 bp):
ATAAGGGTTAAACGGAAGCC
Found at i:115380658 original size:21 final size:21
Alignment explanation
Indices: 115380634--115380674 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
115380624 ATCTTAAGCT
115380634 CAAAAGAGCTAAACTGAAACC
1 CAAAAGAGCTAAACTGAAACC
* * *
115380655 CAAAAGGGTTGAACTGAAAC
1 CAAAAGAGCTAAACTGAAAC
115380675 TTATATGAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.12
Consensus pattern (21 bp):
CAAAAGAGCTAAACTGAAACC
Found at i:115383365 original size:47 final size:47
Alignment explanation
Indices: 115383234--115383366 Score: 158
Period size: 47 Copynumber: 2.8 Consensus size: 47
115383224 CGTTGGCAGT
* * * * *
115383234 TCATCTATTCGACCAATGGTTTATCCACAATGTATTTCAGTCGGCAA
1 TCATCTGTTCGACCAATGGTTTATCCACAACGTATTTTAATCGCCAA
* * * * *
115383281 TCATCTGCTCGACCAATTGTTCATCCACAACGTATTTTAATTGCCAG
1 TCATCTGTTCGACCAATGGTTTATCCACAACGTATTTTAATCGCCAA
* *
115383328 TCATCTGTTCGGCCAGTGGTTTATCCACAACGTATTTTA
1 TCATCTGTTCGACCAATGGTTTATCCACAACGTATTTTA
115383367 GTTGATCTGC
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (47 bp):
TCATCTGTTCGACCAATGGTTTATCCACAACGTATTTTAATCGCCAA
Found at i:115387104 original size:2 final size:2
Alignment explanation
Indices: 115387097--115387145 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
115387087 AGTGTTCATC
115387097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
115387139 TA TA TA T
1 TA TA TA T
115387146 TTAGTTATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:115389210 original size:14 final size:14
Alignment explanation
Indices: 115389172--115389212 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
115389162 CTTACCTAAT
*
115389172 TGTGCAAGTTATGA
1 TGTGCAAGTTGTGA
*
115389186 TTTGCAAGTTGTGA
1 TGTGCAAGTTGTGA
115389200 TGTGCAAGTTGTG
1 TGTGCAAGTTGTG
115389213 CAAGTTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.22, C:0.07, G:0.32, T:0.39
Consensus pattern (14 bp):
TGTGCAAGTTGTGA
Found at i:115400541 original size:23 final size:23
Alignment explanation
Indices: 115400511--115400557 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
115400501 AGTAGTAGCA
*
115400511 TCAACAATTACTGAATCTCAAAG
1 TCAACAATTACTAAATCTCAAAG
115400534 TCAACAATTACTAAATCTCAAAG
1 TCAACAATTACTAAATCTCAAAG
115400557 T
1 T
115400558 TGAACAGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (23 bp):
TCAACAATTACTAAATCTCAAAG
Found at i:115401631 original size:10 final size:10
Alignment explanation
Indices: 115401616--115401664 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
115401606 TATTTTAGCT
115401616 TTTATCTTTA
1 TTTATCTTTA
*
115401626 TTTATCCTTA
1 TTTATCTTTA
*
115401636 ATTATCTTTA
1 TTTATCTTTA
* * *
115401646 ATTATATGTA
1 TTTATCTTTA
115401656 TTTATCTTT
1 TTTATCTTT
115401665 TAGAATTTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:115402723 original size:401 final size:401
Alignment explanation
Indices: 115401980--115402783 Score: 1608
Period size: 401 Copynumber: 2.0 Consensus size: 401
115401970 TCACGCTACA
115401980 GTATCGCTACAGTATCTAATCTCACCGCCATCGCTGTTTTTACTCTAACCGCAGCTAAACGCACC
1 GTATCGCTACAGTATCTAATCTCACCGCCATCGCTGTTTTTACTCTAACCGCAGCTAAACGCACC
115402045 GCCCATCCAAACTCACCCTTAGAATCCATATTTAGCCTTCTCGACGAATATACATCATTTCTCCG
66 GCCCATCCAAACTCACCCTTAGAATCCATATTTAGCCTTCTCGACGAATATACATCATTTCTCCG
115402110 CATTACGGGGCTGACGCTTCCGTCCATGTCCCTTATAAGGTAATCTTTTCAATGTGTGCAAAGGT
131 CATTACGGGGCTGACGCTTCCGTCCATGTCCCTTATAAGGTAATCTTTTCAATGTGTGCAAAGGT
115402175 GGCCGCTTTGTATGTTTTGGGAAGGTTGCACAGTCAATTCGTTAGCTTACTGCATCAGAGCTTGG
196 GGCCGCTTTGTATGTTTTGGGAAGGTTGCACAGTCAATTCGTTAGCTTACTGCATCAGAGCTTGG
115402240 CGAGCCCAATAGACAAAATGGCATGGGATTCGCCATTGAGAAGTGATGATCTAGCATAAGATGAT
261 CGAGCCCAATAGACAAAATGGCATGGGATTCGCCATTGAGAAGTGATGATCTAGCATAAGATGAT
115402305 CCCACAGAAGAGATTATTGGCTAGAGTCAGGTTCCACTAAATTGTAAGTTTAAATTCTTGGAACT
326 CCCACAGAAGAGATTATTGGCTAGAGTCAGGTTCCACTAAATTGTAAGTTTAAATTCTTGGAACT
115402370 GGTGGTCATAT
391 GGTGGTCATAT
115402381 GTATCGCTACAGTATCTAATCTCACCGCCATCGCTGTTTTTACTCTAACCGCAGCTAAACGCACC
1 GTATCGCTACAGTATCTAATCTCACCGCCATCGCTGTTTTTACTCTAACCGCAGCTAAACGCACC
115402446 GCCCATCCAAACTCACCCTTAGAATCCATATTTAGCCTTCTCGACGAATATACATCATTTCTCCG
66 GCCCATCCAAACTCACCCTTAGAATCCATATTTAGCCTTCTCGACGAATATACATCATTTCTCCG
115402511 CATTACGGGGCTGACGCTTCCGTCCATGTCCCTTATAAGGTAATCTTTTCAATGTGTGCAAAGGT
131 CATTACGGGGCTGACGCTTCCGTCCATGTCCCTTATAAGGTAATCTTTTCAATGTGTGCAAAGGT
115402576 GGCCGCTTTGTATGTTTTGGGAAGGTTGCACAGTCAATTCGTTAGCTTACTGCATCAGAGCTTGG
196 GGCCGCTTTGTATGTTTTGGGAAGGTTGCACAGTCAATTCGTTAGCTTACTGCATCAGAGCTTGG
115402641 CGAGCCCAATAGACAAAATGGCATGGGATTCGCCATTGAGAAGTGATGATCTAGCATAAGATGAT
261 CGAGCCCAATAGACAAAATGGCATGGGATTCGCCATTGAGAAGTGATGATCTAGCATAAGATGAT
115402706 CCCACAGAAGAGATTATTGGCTAGAGTCAGGTTCCACTAAATTGTAAGTTTAAATTCTTGGAACT
326 CCCACAGAAGAGATTATTGGCTAGAGTCAGGTTCCACTAAATTGTAAGTTTAAATTCTTGGAACT
115402771 GGTGGTCATAT
391 GGTGGTCATAT
115402782 GT
1 GT
115402784 GTCCTTTTCC
Statistics
Matches: 403, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
401 403 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (401 bp):
GTATCGCTACAGTATCTAATCTCACCGCCATCGCTGTTTTTACTCTAACCGCAGCTAAACGCACC
GCCCATCCAAACTCACCCTTAGAATCCATATTTAGCCTTCTCGACGAATATACATCATTTCTCCG
CATTACGGGGCTGACGCTTCCGTCCATGTCCCTTATAAGGTAATCTTTTCAATGTGTGCAAAGGT
GGCCGCTTTGTATGTTTTGGGAAGGTTGCACAGTCAATTCGTTAGCTTACTGCATCAGAGCTTGG
CGAGCCCAATAGACAAAATGGCATGGGATTCGCCATTGAGAAGTGATGATCTAGCATAAGATGAT
CCCACAGAAGAGATTATTGGCTAGAGTCAGGTTCCACTAAATTGTAAGTTTAAATTCTTGGAACT
GGTGGTCATAT
Found at i:115403028 original size:37 final size:39
Alignment explanation
Indices: 115402953--115403028 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 39
115402943 CAAAATTTCA
115402953 ATCAAAACTTTTAATTCTGTTTTTATTTTATTTTTTTCTAG
1 ATCAAAACTTTTAATTC--TTTTTATTTTATTTTTTTCTAG
115402994 ATCAAAACTTTTAATTC-TTTT-TTTTATTTTTTTCT
1 ATCAAAACTTTTAATTCTTTTTATTTTATTTTTTTCT
115403029 CAGGTACGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
37 14 0.40
38 4 0.11
41 17 0.49
ACGTcount: A:0.24, C:0.11, G:0.03, T:0.63
Consensus pattern (39 bp):
ATCAAAACTTTTAATTCTTTTTATTTTATTTTTTTCTAG
Found at i:115404602 original size:33 final size:33
Alignment explanation
Indices: 115404560--115404636 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
115404550 GTTAATGTGC
* *
115404560 TTGATTTCCAACAGCAGATACAACAGCAAACTA
1 TTGATTTCCAACAGAAAATACAACAGCAAACTA
* * * *
115404593 TTGATTTCCAACGGAAAATACTACGGCAAACTC
1 TTGATTTCCAACAGAAAATACAACAGCAAACTA
115404626 TTGATTTCCAA
1 TTGATTTCCAA
115404637 AAGGAAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (33 bp):
TTGATTTCCAACAGAAAATACAACAGCAAACTA
Done.