Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 159 of 228
Found at i:47815766 original size:42 final size:42
Alignment explanation
Indices: 47815675--47815773 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
47815665 GACCTAATAG
* * * ** * *
47815675 AAACCCTTAAGGGTTGAATGGAAGCTCGTAAGAGCTGAGCGG
1 AAACCCATAAGGGTTAAATAGAAGCTCAAAAGAGCTGAACGA
47815717 AAACCCATAAGGGTTAAATAGAAGCTCAAAAGAGCTGAAC-A
1 AAACCCATAAGGGTTAAATAGAAGCTCAAAAGAGCTGAACGA
*
47815758 AAATCCCATGAGGGTT
1 AAA-CCCATAAGGGTT
47815774 GAACGGAAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 3 0.06
42 45 0.94
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.18
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAATAGAAGCTCAAAAGAGCTGAACGA
Found at i:47818245 original size:20 final size:20
Alignment explanation
Indices: 47818217--47818265 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
47818207 TAGAGCAGGA
*
47818217 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
*
47818237 ATATTGATACCTTAAGAAA-
1 ATATCGATACCTTAAGAAAT
47818256 AGTATCGATA
1 A-TATCGATA
47818266 TTGGATCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:47821569 original size:115 final size:114
Alignment explanation
Indices: 47821011--47821582 Score: 826
Period size: 114 Copynumber: 5.0 Consensus size: 114
47821001 AAAATAAGAA
** * * * *
47821011 TTAGCGGCGTTTTCCAGAAAGCGCCG--AAAAAACTTAAGCCCAACGACACCGTTTACCGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
47821074 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCTGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * * ** *
47821123 TTAGTGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCAAAGCCCAACGGTGCTGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
47821188 TCGGGGATTTAGTGGCGTTTTTAAGAAAGCGTCGCTAATGTTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * *
47821237 TTAGCGGCATTTTTGAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
47821302 TCGGAGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATG-TGCAGGGCG
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCT-CAGGGCT
* * *
47821351 TTAGCGGCGTTTTTGAGGAAGCGCCGCAAAAAAACCTAAGCCCAACGGCGTCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
47821416 TCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGAT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
47821465 TTAGCGGTGTTTTTGAGAAAGCGCCTCAAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* *
47821530 TTCGAGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGAT
65 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
47821580 TTA
1 TTA
47821583 AAATAATTTA
Statistics
Matches: 409, Mismatches: 46, Indels: 7
0.89 0.10 0.02
Matches are distributed among these distances:
112 22 0.05
113 1 0.00
114 299 0.73
115 87 0.21
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:47821863 original size:38 final size:37
Alignment explanation
Indices: 47821819--47821909 Score: 121
Period size: 38 Copynumber: 2.5 Consensus size: 37
47821809 GGATTTAAGG
* *
47821819 TTTAGGGGTTAGCTGTTATACTTTAGGGGTTATGGGGT
1 TTTAGGGGTTAGCGGTTATACTTTAGGGGTTA-GGGGA
* *
47821857 TTTAGGGGTTAGGGGTTATGCTTTAGGGGTTAGGGGA
1 TTTAGGGGTTAGCGGTTATACTTTAGGGGTTAGGGGA
*
47821894 TTTAGGAGTTAG-GGTT
1 TTTAGGGGTTAGCGGTT
47821910 TAGGGTTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 4 0.08
37 15 0.31
38 29 0.60
ACGTcount: A:0.16, C:0.03, G:0.41, T:0.40
Consensus pattern (37 bp):
TTTAGGGGTTAGCGGTTATACTTTAGGGGTTAGGGGA
Found at i:47821870 original size:7 final size:7
Alignment explanation
Indices: 47821841--47821914 Score: 58
Period size: 7 Copynumber: 9.9 Consensus size: 7
47821831 CTGTTATACT
47821841 TTAGGGG
1 TTAGGGG
47821848 TTATGGGG
1 TTA-GGGG
47821856 TTTTAGGGG
1 --TTAGGGG
47821865 TTAGGGG
1 TTAGGGG
* **
47821872 TTATGCT
1 TTAGGGG
47821879 TTAGGGG
1 TTAGGGG
47821886 TTAGGGG
1 TTAGGGG
*
47821893 ATTTAGGAG
1 --TTAGGGG
*
47821902 TTAGGGT
1 TTAGGGG
47821909 TTAGGG
1 TTAGGG
47821915 TTTCAACAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
7 36 0.68
8 4 0.08
9 10 0.19
10 3 0.06
ACGTcount: A:0.16, C:0.01, G:0.46, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:47821873 original size:16 final size:16
Alignment explanation
Indices: 47821840--47821907 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 16
47821830 GCTGTTATAC
47821840 TTTAGGGGTTATGGGGT
1 TTTAGGGGTTA-GGGGT
47821857 TTTAGGGGTTAGGGGTTAT
1 TTTAGGGGTTAGGGG---T
*
47821876 GCTTTAGGGGTTAGGGGA
1 --TTTAGGGGTTAGGGGT
*
47821894 TTTAGGAGTTAGGG
1 TTTAGGGGTTAGGG
47821908 TTTAGGGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
16 17 0.39
17 11 0.25
19 1 0.02
21 15 0.34
ACGTcount: A:0.16, C:0.01, G:0.46, T:0.37
Consensus pattern (16 bp):
TTTAGGGGTTAGGGGT
Found at i:47821899 original size:30 final size:28
Alignment explanation
Indices: 47821858--47821914 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
47821848 TTATGGGGTT
* *
47821858 TTAGGGGTTAGGGGTTATGCTTTAGGGG
1 TTAGGGGTTAGGAGTTAGGCTTTAGGGG
*
47821886 TTAGGGGATTTAGGAGTTAGGGTTTAGGG
1 TTAGGGG--TTAGGAGTTAGGCTTTAGGG
47821915 TTTCAACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.29
30 17 0.71
ACGTcount: A:0.18, C:0.02, G:0.46, T:0.35
Consensus pattern (28 bp):
TTAGGGGTTAGGAGTTAGGCTTTAGGGG
Found at i:47822939 original size:31 final size:32
Alignment explanation
Indices: 47822904--47822965 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
47822894 TTATTATTGG
*
47822904 ATAAAAAAAT-ACATTTTTTATACCAAATTTT
1 ATAAAAAAATAAAATTTTTTATACCAAATTTT
47822935 ATAAAAAAATAAAATTTTTTATACCAAATTT
1 ATAAAAAAATAAAATTTTTTATACCAAATTT
47822966 ATTATACCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 10 0.34
32 19 0.66
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (32 bp):
ATAAAAAAATAAAATTTTTTATACCAAATTTT
Found at i:47822965 original size:14 final size:14
Alignment explanation
Indices: 47822946--47822979 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
47822936 TAAAAAAATA
*
47822946 AAATTTTTTATACC
1 AAATTTATTATACC
47822960 AAATTTATTATACC
1 AAATTTATTATACC
47822974 AAATTT
1 AAATTT
47822980 CATCCGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTTATTATACC
Found at i:47823083 original size:15 final size:15
Alignment explanation
Indices: 47823065--47823095 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47823055 TACTTTATAC
47823065 AAAATATATTTAAAT
1 AAAATATATTTAAAT
47823080 AAAATATATTTAAAT
1 AAAATATATTTAAAT
47823095 A
1 A
47823096 TTAGTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATATTTAAAT
Found at i:47823105 original size:12 final size:11
Alignment explanation
Indices: 47823081--47823142 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
47823071 TATTTAAATA
47823081 AAATAT-ATTT
1 AAATATAATTT
*
47823091 AAATATTAGTTT
1 AAATA-TAATTT
*
47823103 AAATAGAATTAAT
1 AAATATAATT--T
47823116 AAATAT-ATTT
1 AAATATAATTT
47823126 AAATATTAATTT
1 AAATA-TAATTT
47823138 AAATA
1 AAATA
47823143 AAATAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 11 0.26
11 5 0.12
12 20 0.48
13 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
AAATATAATTT
Found at i:47826712 original size:24 final size:22
Alignment explanation
Indices: 47826685--47826728 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
47826675 AATTTCAAAA
47826685 ATAAAACATAATATAATATTTACC
1 ATAAAA-ATAA-ATAATATTTACC
*
47826709 ATAAAAATAAATATTATTTA
1 ATAAAAATAAATAATATTTA
47826729 ATTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAAAAATAAATAATATTTACC
Found at i:47826817 original size:43 final size:43
Alignment explanation
Indices: 47826741--47826893 Score: 195
Period size: 43 Copynumber: 3.6 Consensus size: 43
47826731 TAATTTTTTT
* * **
47826741 TAAAAGTCATG-T-TTTAGCGGCTTTTGTAATAGAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
*
47826782 TAAAGGTCATGATCTTTAGCGGCGCTTT-TGGTAGAAGCGCCGT
1 TAAAGGTCATGATCTTTAGCGGCG-TTTGTGGTAGAAGCGCCGC
* * *
47826825 TAAATGCCATGATCTTTAGTGGCGTTTGTGGTAGAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
*
47826868 TAAAGATCATGATCTTTAGCGGCGTT
1 TAAAGGTCATGATCTTTAGCGGCGTT
47826894 GCCAATAGCG
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
41 10 0.11
42 4 0.04
43 78 0.82
44 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
Found at i:47829803 original size:26 final size:26
Alignment explanation
Indices: 47829756--47829806 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
47829746 AAAATTTTTT
* *
47829756 GAATCGAGTCGAGTGAAATGAAATTC
1 GAATCGAGTCGAATCAAATGAAATTC
*
47829782 GAATCGAGTCGAATCAAGTGAAATT
1 GAATCGAGTCGAATCAAATGAAATT
47829807 TTTAGAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (26 bp):
GAATCGAGTCGAATCAAATGAAATTC
Found at i:47830000 original size:21 final size:21
Alignment explanation
Indices: 47829975--47830030 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
47829965 AAAATTATTG
*
47829975 TTTTAGAATTTTTTTAACTT-
1 TTTTAGAATTTTTTTAAATTC
*
47829995 TCTTTA-TATGTTTTTTAAATTC
1 T-TTTAGAAT-TTTTTTAAATTC
*
47830017 TTTTTGAATTTTTT
1 TTTTAGAATTTTTT
47830031 ATAATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
20 3 0.11
21 22 0.79
22 3 0.11
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTAGAATTTTTTTAAATTC
Found at i:47830020 original size:11 final size:10
Alignment explanation
Indices: 47829975--47830039 Score: 51
Period size: 11 Copynumber: 6.2 Consensus size: 10
47829965 AAAATTATTG
47829975 TTTTAGAATTT
1 TTTTA-AATTT
*
47829986 TTTTAACTTT
1 TTTTAAATTT
* *
47829996 CTTTATATGTT
1 TTTTAAAT-TT
47830007 TTTTAAATTCT
1 TTTTAAATT-T
*
47830018 TTTTGAA-TT
1 TTTTAAATTT
47830027 TTTTATAATTT
1 TTTTA-AATTT
47830038 TT
1 TT
47830040 AAAAAATATA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
9 5 0.12
10 13 0.31
11 24 0.57
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:47830078 original size:20 final size:19
Alignment explanation
Indices: 47830053--47830121 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
47830043 AAATATAAAA
*
47830053 TTTGAAAATTTTATAAATAT
1 TTTG-AAATTTTAAAAATAT
*
47830073 TTTG-AATTTAAAAAATAT
1 TTTGAAATTTTAAAAATAT
*
47830091 TTTGAATTTTTGAAAAATAT
1 TTTGAAATTTT-AAAAATAT
*
47830111 TTTGTAATTTT
1 TTTGAAATTTT
47830122 TTGAGAGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.39
19 4 0.10
20 21 0.51
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTGAAATTTTAAAAATAT
Found at i:47830080 original size:18 final size:18
Alignment explanation
Indices: 47830059--47830121 Score: 81
Period size: 18 Copynumber: 3.3 Consensus size: 18
47830049 AAAATTTGAA
*
47830059 AATTTTATAAATATTTTG
1 AATTTTAAAAATATTTTG
*
47830077 AATTTAAAAAATATTTTG
1 AATTTTAAAAATATTTTG
47830095 AATTTTTGAAAAATATTTTG
1 AA-TTTT-AAAAATATTTTG
47830115 TAATTTT
1 -AATTTT
47830122 TTGAGAGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 18 0.46
19 3 0.08
20 16 0.41
21 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
AATTTTAAAAATATTTTG
Found at i:47830213 original size:17 final size:18
Alignment explanation
Indices: 47830193--47830226 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
47830183 CAATTTGTTA
47830193 TTCGAATTATTC-AAATT
1 TTCGAATTATTCGAAATT
*
47830210 TTCGAGTTATTCGAAAT
1 TTCGAATTATTCGAAAT
47830227 GCAAAATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (18 bp):
TTCGAATTATTCGAAATT
Found at i:47833855 original size:57 final size:56
Alignment explanation
Indices: 47833791--47833918 Score: 134
Period size: 57 Copynumber: 2.2 Consensus size: 56
47833781 CCACTCCCCT
* * *
47833791 AGGCGGTCTAGATCAATTTCTCA-GGATCGT-GCCATGAGAGATGATTATCGCTCTCCC
1 AGGCGGTCTAGATCAATGTC-AAGGGATCGTGGCCA--AAAGATGATTATCGCTCTCCC
* * * *
47833848 AGTCGGTCCAGATCCATGTCAAGGGATCGTGGGGCAAAAGATGATTATCGCTCTCCC
1 AGGCGGTCTAGATCAATGTCAAGGGATCGT-GGCCAAAAGATGATTATCGCTCTCCC
*
47833905 AGGCGATCTAGATC
1 AGGCGGTCTAGATC
47833919 TGTTTCTCGG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
56 1 0.02
57 54 0.93
59 3 0.05
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (56 bp):
AGGCGGTCTAGATCAATGTCAAGGGATCGTGGCCAAAAGATGATTATCGCTCTCCC
Found at i:47837227 original size:3 final size:3
Alignment explanation
Indices: 47837219--47837254 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
47837209 TTCTTTTACC
47837219 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47837255 AGTTGTAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:47841804 original size:20 final size:21
Alignment explanation
Indices: 47841779--47841824 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
47841769 TTTTTTTTCT
47841779 TATAAAA-ATATTAAAAAAAC
1 TATAAAATATATTAAAAAAAC
*
47841799 TATAAAATTATATTAAAAAAAT
1 TATAAAA-TATATTAAAAAAAC
47841821 TATA
1 TATA
47841825 GACTAGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TATAAAATATATTAAAAAAAC
Found at i:47848557 original size:28 final size:25
Alignment explanation
Indices: 47848490--47848541 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
47848480 AAAATTGGTA
47848490 AGACATTTTCCATTCTTCTCTAAGC
1 AGACATTTTCCATTCTTCTCTAAGC
47848515 AGACATTTTCCATTC-TCTTCTAAGC
1 AGACATTTTCCATTCTTC-TCTAAGC
47848540 AG
1 AG
47848542 CAGGCATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (25 bp):
AGACATTTTCCATTCTTCTCTAAGC
Found at i:47850841 original size:14 final size:14
Alignment explanation
Indices: 47850822--47850849 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47850812 ACAATTTATT
47850822 AATATATATTAATA
1 AATATATATTAATA
47850836 AATATATATTAATA
1 AATATATATTAATA
47850850 TATGTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:47850923 original size:32 final size:31
Alignment explanation
Indices: 47850883--47850957 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
47850873 ACTTTTCCGA
* * *
47850883 AAAATATTTTCAGGAAATCTGCCAAACAGCAG
1 AAAATATTTTCA-CAAATCTACCAAACACCAG
* *
47850915 AAAATATTTTACACAGATTTACCAAACACCAG
1 AAAATATTTT-CACAAATCTACCAAACACCAG
47850947 AAAATATTTTC
1 AAAATATTTTC
47850958 CAGTTAATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 1 0.03
32 34 0.92
33 2 0.05
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (31 bp):
AAAATATTTTCACAAATCTACCAAACACCAG
Found at i:47853850 original size:41 final size:41
Alignment explanation
Indices: 47853763--47853946 Score: 184
Period size: 40 Copynumber: 4.6 Consensus size: 41
47853753 GCTACTCGTT
* * *
47853763 CAAATGCCTTCGGGACATAGCCCG-GTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGAATTTTAGTAACTCGCA
*
47853803 CAAATGCCTTCGGGACTTAACCCGAATTTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGAATTTTAGTAACTCGCA
* *
47853844 CCAATGCCTTCGGG-CTTAGCCCGGAA--TTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCC-GAATTTTAGTAACTCGCA
* * * * * *
47853883 CAAATGCCTTC-GGATCTTAGTCCGGA-TATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGAATTTTAGTAAC-TCGCA
47853924 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
47853947 GACATCATTC
Statistics
Matches: 121, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
38 2 0.02
39 24 0.20
40 55 0.45
41 40 0.33
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGAATTTTAGTAACTCGCA
Found at i:47853942 original size:80 final size:82
Alignment explanation
Indices: 47853763--47853948 Score: 204
Period size: 80 Copynumber: 2.3 Consensus size: 82
47853753 GCTACTCGTT
* * *
47853763 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCG
* *
47853827 AATTTTAGTAACTCGCAC
65 AATTATAGTAACTAGCAC
* **
47853845 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCACACAAATGCCTTC-GGATCTTAGTCCG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGGA-CTTAACCCG
* * *
47853907 GA-TATGGTCACTTAGCA-
65 AATTATAGTAAC-TAGCAC
47853924 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
47853949 CATCATTCGA
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
79 21 0.24
80 54 0.61
81 10 0.11
82 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (82 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGA
ATTATAGTAACTAGCAC
Found at i:47855241 original size:84 final size:85
Alignment explanation
Indices: 47855114--47855291 Score: 349
Period size: 84 Copynumber: 2.1 Consensus size: 85
47855104 TATTTTATTG
47855114 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATG-TTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
47855178 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
47855198 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
47855263 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
47855283 CCCATGCTC
1 CCCATGCTC
47855292 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 61 0.66
85 32 0.34
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:47865542 original size:314 final size:314
Alignment explanation
Indices: 47864973--47865583 Score: 1159
Period size: 314 Copynumber: 1.9 Consensus size: 314
47864963 TTCGATCAAC
*
47864973 ATGCTTACTAGTGGCCGCTGATCTATCAATAGATTGAATCGGAGCTTTCGAATCCTCCCCTTTAT
1 ATGCTTACTAGTGGCCGCTGATCTATCAATAGATTGAATCGGAGCTTCCGAATCCTCCCCTTTAT
* *
47865038 TGTAGTTGTCATGTATTGTTCGTTAACATTTCTTTCCTTTACAAATATCGATTGTTATATTCTTC
66 TGTAGTTGTCATGTATTGTTCGTTAACACTTCTTTCCTTTACAAATATCGATTGTTATATTCTCC
*
47865103 TGCATGGTTTCCCTTTGTTCTATAACTCGGTTTCCTTGGAATGTTACACTTTCGTCTAACCTTCC
131 TGCATGGTTTCCCTTTGTTCTATAACTCGGTTTCCTTGGAATGTTACACTTTCGTCTAACCCTCC
* *
47865168 TTTTTTCTATCTATAAATTTTTATGCTGACGGAGCTATTCTTTCTCTAGAACTCGCCTGGCCTTT
196 TTTTTTCTATCTATAAATTTTTATGCCGACGGAGCTATTCTTTCTCTAGAACCCGCCTGGCCTTT
47865233 TTTCTCTTAGCCATTTACTTTCAGCAAGTAATTCATTTCTATCTATAAATTTTT
261 TTTCTCTTAGCCATTTACTTTCAGCAAGTAATTCATTTCTATCTATAAATTTTT
47865287 ATGCTTACTAGTGGCCGCTGATCTATCAATAGATTGAATCGGAGCTTCCGAATCCTCCCCTTTAT
1 ATGCTTACTAGTGGCCGCTGATCTATCAATAGATTGAATCGGAGCTTCCGAATCCTCCCCTTTAT
47865352 TGTAGTTGTCATGTATTGTTCGTTAACACTTCTTTCCTTTACAAATATCGATTGTTATATTCTCC
66 TGTAGTTGTCATGTATTGTTCGTTAACACTTCTTTCCTTTACAAATATCGATTGTTATATTCTCC
47865417 TGCATGGTTTCCCTTTGTTCTATAACTCGGTTTCCTTGGAATGTTACACTTTCGTCTAACCCTCC
131 TGCATGGTTTCCCTTTGTTCTATAACTCGGTTTCCTTGGAATGTTACACTTTCGTCTAACCCTCC
*
47865482 TTTTTTCTATCTATAAATTTTTGTGCCGACGGAGCTATTCTTTCTCTAGAACCCGCCTGGCCTTT
196 TTTTTTCTATCTATAAATTTTTATGCCGACGGAGCTATTCTTTCTCTAGAACCCGCCTGGCCTTT
47865547 TTTCTCTTAGCCATTTACTTTCAGCAAGTAATTCATT
261 TTTCTCTTAGCCATTTACTTTCAGCAAGTAATTCATT
47865584 CCTCATGGGT
Statistics
Matches: 290, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
314 290 1.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (314 bp):
ATGCTTACTAGTGGCCGCTGATCTATCAATAGATTGAATCGGAGCTTCCGAATCCTCCCCTTTAT
TGTAGTTGTCATGTATTGTTCGTTAACACTTCTTTCCTTTACAAATATCGATTGTTATATTCTCC
TGCATGGTTTCCCTTTGTTCTATAACTCGGTTTCCTTGGAATGTTACACTTTCGTCTAACCCTCC
TTTTTTCTATCTATAAATTTTTATGCCGACGGAGCTATTCTTTCTCTAGAACCCGCCTGGCCTTT
TTTCTCTTAGCCATTTACTTTCAGCAAGTAATTCATTTCTATCTATAAATTTTT
Found at i:47876627 original size:15 final size:15
Alignment explanation
Indices: 47876604--47876633 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47876594 AAAAGCAAAG
47876604 CAAAATGGAAAAACA
1 CAAAATGGAAAAACA
*
47876619 CAAATTGGAAAAACA
1 CAAAATGGAAAAACA
47876634 TACTTCATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.13, G:0.13, T:0.10
Consensus pattern (15 bp):
CAAAATGGAAAAACA
Found at i:47888254 original size:16 final size:17
Alignment explanation
Indices: 47888233--47888268 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
47888223 CATTCCAAAT
47888233 AAACAAGAATCG-AATG
1 AAACAAGAATCGTAATG
*
47888249 AAACAATAATCGTAATG
1 AAACAAGAATCGTAATG
47888266 AAA
1 AAA
47888269 ATCATATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (17 bp):
AAACAAGAATCGTAATG
Found at i:47895849 original size:49 final size:48
Alignment explanation
Indices: 47895778--47895871 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 48
47895768 AGCTAGCGAG
47895778 TAGCTCCTGAATTGATGTATACCAATTGATAGATTCCTAATAAATCGC
1 TAGCTCCTGAATTGATGTATACCAATTGATAGATTCCTAATAAATCGC
47895826 TAGCTTCCTGAATTGATGTATACCAATTGATAGATTCCTAATAAAT
1 TAGC-TCCTGAATTGATGTATACCAATTGATAGATTCCTAATAAAT
47895872 AATTATCTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 4 0.09
49 41 0.91
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (48 bp):
TAGCTCCTGAATTGATGTATACCAATTGATAGATTCCTAATAAATCGC
Found at i:47906722 original size:32 final size:32
Alignment explanation
Indices: 47906686--47906746 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
47906676 TTGTTTTATT
47906686 TTATTTCAAGTGATTTATGAGTTGATGCTATG
1 TTATTTCAAGTGATTTATGAGTTGATGCTATG
47906718 TTATTTCAAGTGATTTATGAGTTGATGCT
1 TTATTTCAAGTGATTTATGAGTTGATGCT
47906747 CTAACATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.48
Consensus pattern (32 bp):
TTATTTCAAGTGATTTATGAGTTGATGCTATG
Found at i:47907220 original size:20 final size:20
Alignment explanation
Indices: 47907195--47907261 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
47907185 GCTAAAGAAA
*
47907195 GTAAATGCAATGGGAAGTAT
1 GTAAATGCAATGGAAAGTAT
*
47907215 GTAAATACAATGGAAAGTAT
1 GTAAATGCAATGGAAAGTAT
*
47907235 GTAAATGCAATGGAAAGTAA
1 GTAAATGCAATGGAAAGTAT
47907255 GTAAATG
1 GTAAATG
47907262 AAAGGGGTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.46, C:0.04, G:0.25, T:0.24
Consensus pattern (20 bp):
GTAAATGCAATGGAAAGTAT
Found at i:47912943 original size:20 final size:20
Alignment explanation
Indices: 47912911--47912984 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
47912901 TATTTGAGCT
*
47912911 AAAGAAAGTAAATGCAATGG
1 AAAGTAAGTAAATGCAATGG
* *
47912931 GAAGTATGTAAATGCAATGG
1 AAAGTAAGTAAATGCAATGG
*
47912951 AAAGTAAGTAAATGCAATGA
1 AAAGTAAGTAAATGCAATGG
47912971 AAAGTAAGTAAATG
1 AAAGTAAGTAAATG
47912985 AAAGGGGTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.51, C:0.04, G:0.24, T:0.20
Consensus pattern (20 bp):
AAAGTAAGTAAATGCAATGG
Found at i:47916646 original size:13 final size:14
Alignment explanation
Indices: 47916625--47916671 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
47916615 CATGTACAGT
*
47916625 CAGATTCAGATA-A
1 CAGAATCAGATATA
*
47916638 CAGAATCAGAAATA
1 CAGAATCAGATATA
*
47916652 TAGAAT-AGATATA
1 CAGAATCAGATATA
47916665 CAGAATC
1 CAGAATC
47916672 CTACCCCTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
13 21 0.78
14 6 0.22
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (14 bp):
CAGAATCAGATATA
Found at i:47929072 original size:42 final size:42
Alignment explanation
Indices: 47929012--47929163 Score: 187
Period size: 42 Copynumber: 3.6 Consensus size: 42
47929002 TAATCTGAAA
* *
47929012 TGTTTCACCGGCATTAAGCCTATTAGACGTAAAGTCTGATAT
1 TGTTTCACCGGCAATAAGCCTACTAGACGTAAAGTCTGATAT
* *
47929054 TGTTTCACTGGCAATAAGCCTACTAGACGTAAAGTCTGAAAT
1 TGTTTCACCGGCAATAAGCCTACTAGACGTAAAGTCTGATAT
* * ** * * *
47929096 TATTTCACCGACCTTAAGCCTGCTATATGTAAAGTCTGATAT
1 TGTTTCACCGGCAATAAGCCTACTAGACGTAAAGTCTGATAT
* *
47929138 TGTTTCACTGGCAATAAGCCTGCTAG
1 TGTTTCACCGGCAATAAGCCTACTAG
47929164 GCGTTAAGCC
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (42 bp):
TGTTTCACCGGCAATAAGCCTACTAGACGTAAAGTCTGATAT
Found at i:47929114 original size:84 final size:84
Alignment explanation
Indices: 47929005--47929179 Score: 244
Period size: 84 Copynumber: 2.1 Consensus size: 84
47928995 AGACATATAA
* * *
47929005 TCTGAAA-TGTTTCACCGGCATTAAGCCTATTAGACGTAAAGTCTGATATTGTTTCACTGGCAAT
1 TCTGAAATTATTTCACCGACATTAAGCCTACTAGACGTAAAGTCTGATATTGTTTCACTGGCAAT
47929069 AAGCCTACTAGACGTAAAG
66 AAGCCTACTAGACGTAAAG
* * * *
47929088 TCTGAAATTATTTCACCGACCTTAAGCCTGCTATATGTAAAGTCTGATATTGTTTCACTGGCAAT
1 TCTGAAATTATTTCACCGACATTAAGCCTACTAGACGTAAAGTCTGATATTGTTTCACTGGCAAT
* * *
47929153 AAGCCTGCTAGGCGTTAAG
66 AAGCCTACTAGACGTAAAG
*
47929172 CCTGAAAT
1 TCTGAAAT
47929180 CTCAATTTCA
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
83 7 0.09
84 73 0.91
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (84 bp):
TCTGAAATTATTTCACCGACATTAAGCCTACTAGACGTAAAGTCTGATATTGTTTCACTGGCAAT
AAGCCTACTAGACGTAAAG
Found at i:47929368 original size:30 final size:30
Alignment explanation
Indices: 47929332--47929393 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
47929322 ATATATAATC
47929332 TAACCTCACATATAAAAATATAAGATTTTA
1 TAACCTCACATATAAAAATATAAGATTTTA
47929362 TAACCTCACATATAAAAATATAAGATTTTA
1 TAACCTCACATATAAAAATATAAGATTTTA
47929392 TA
1 TA
47929394 TCTTTAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (30 bp):
TAACCTCACATATAAAAATATAAGATTTTA
Found at i:47937840 original size:3 final size:3
Alignment explanation
Indices: 47937832--47937869 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
47937822 AAAAAACTAG
47937832 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
47937870 TGAAAAGGCT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47940542 original size:14 final size:14
Alignment explanation
Indices: 47940520--47940554 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
47940510 ATGGTATGGG
47940520 TTTATGGGTTTTGGT
1 TTTA-GGGTTTTGGT
47940535 TTTAGGGTTTTGGT
1 TTTAGGGTTTTGGT
*
47940549 TATAGG
1 TTTAGG
47940555 CAAATGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.54
Consensus pattern (14 bp):
TTTAGGGTTTTGGT
Found at i:47940708 original size:22 final size:22
Alignment explanation
Indices: 47940683--47940728 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
47940673 GAGGAAAGTT
47940683 TAAAGAACATAAAATAAAAAAA
1 TAAAGAACATAAAATAAAAAAA
** * *
47940705 TAAATTACTTAAAATGAAAAAA
1 TAAAGAACATAAAATAAAAAAA
47940727 TA
1 TA
47940729 TGGGGATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (22 bp):
TAAAGAACATAAAATAAAAAAA
Found at i:47960938 original size:36 final size:35
Alignment explanation
Indices: 47960898--47960973 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 35
47960888 TGATGGTTGT
47960898 TGTGAAAG-AGAATATGTGGGTATGATATTCATGCCA
1 TGTGAAAGTA-AATATGTGGGTAT-ATATTCATGCCA
* * *
47960934 TGTGACAGTAAATATGTGGGTATATTTTCATTCCA
1 TGTGAAAGTAAATATGTGGGTATATATTCATGCCA
47960969 TGTGA
1 TGTGA
47960974 CAGTGATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 15 0.42
36 20 0.56
37 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (35 bp):
TGTGAAAGTAAATATGTGGGTATATATTCATGCCA
Found at i:47960971 original size:35 final size:36
Alignment explanation
Indices: 47960908--47960977 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
47960898 TGTGAAAGAG
47960908 AATATGTGGGTATGATATTCATGCCATGTGACAGTA
1 AATATGTGGGTATGATATTCATGCCATGTGACAGTA
* *
47960944 AATATGTGGGTAT-ATTTTCATTCCATGTGACAGT
1 AATATGTGGGTATGATATTCATGCCATGTGACAGT
47960978 GATTATAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.59
36 13 0.41
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (36 bp):
AATATGTGGGTATGATATTCATGCCATGTGACAGTA
Found at i:47976569 original size:394 final size:393
Alignment explanation
Indices: 47975837--47976617 Score: 1230
Period size: 394 Copynumber: 2.0 Consensus size: 393
47975827 GAAAATTGTT
** *
47975837 TCTCCCAGTTGTAAGAGATCTTAATAATTCCCTTAGGATTCATAGATTTCCCTTAGAAGATATTC
1 TCTCCCAACTGTAAGAGACCTTAATAATTCCCTTAGGATTCATAGATTTCCCTTAGAAGATATTC
* * * *
47975902 AAGTTTCGATTCTTCCAAATTCGTCAAAGAATTAAACTGAAGAAACAGGCCCATACTGAACCTCT
66 AAGTTCCAATTCTTCCAAATTCG-CAAAGAATTAAACCGAAGAAACAGGCCCATACTAAACCTCT
* * * * *
47975967 CGTGCTATTATCTGACTGGTCACGTAGATTACAGAGTAACCATTCCGATAGATTACCGTTGAAGA
130 AGTGCTATTATCCGACTGGTCACATAGATTACAGAGTAACCATTCCGATAGATTACCATTAAAGA
47976032 ACCATCTATGTTGATTAGAAGGGATGACTTGATTCCAAATATCCTTCGCGAACAGGCAATCTCTA
195 ACCATCTATGTTGATTAGAAGGGATGACTTGATTCCAAATATCCTTCGCGAACAGGCAATCTCTA
* * *
47976097 AGGACATGTAAAGCATCCTCAGTATTATAACCACATAAGTGGCATGACTCTTCTTGTCCAATCCC
260 AGGACATGTAAAGCATACTCAATATTATAACCACATAAGTGACATGACTCTTCTTGTCCAATCCC
*
47976162 TCTCCGAACTCTTTCAGAGTTAGTTAATAGTCTTTGTTTAAAGACCAACCAGATGAATTGTCCAA
325 TCTCCGAACTCTTTCAGAGTTAGTTAATAGTCTTTGTTTAAAGACCAACCAGATGAACTGTCCAA
47976227 TCCC
390 TCCC
*
47976231 TCTCCCAACTGTAAGAGACCTTAATAATTTCCC-TCGGATTCATAGATGTT-CCTTAGAAGATAT
1 TCTCCCAACTGTAAGAGACCTTAATAA-TTCCCTTAGGATTCATAGAT-TTCCCTTAGAAGATAT
*
47976294 TCAAGTTCCAATTCTTCCTAAATTTC-CAAAGAATTAAACCGAAGAAATAGGCCCATACTAAACC
64 TCAAGTTCCAATTCTTCC-AAA-TTCGCAAAGAATTAAACCGAAGAAACAGGCCCATACTAAACC
* *
47976358 TCTAGTGCTATTATCCGTCTGGTCACATAGATTAGAGAGTAACCATTCCGATAGATTACCATTAA
127 TCTAGTGCTATTATCCGACTGGTCACATAGATTACAGAGTAACCATTCCGATAGATTACCATTAA
* * *
47976423 AGAACCATCTATGTTTATTAGAAGGGATGACTTGATTCCAAATATCCTTTGTGAA-AGGGCAATC
192 AGAACCATCTATGTTGATTAGAAGGGATGACTTGATTCCAAATATCCTTCGCGAACA-GGCAATC
*
47976487 TCTAAGGACATGTAAAGCATATTCAATATTATAACCACATAAGTGACATGACTCTTCTTGTCCAA
256 TCTAAGGACATGTAAAGCATACTCAATATTATAACCACATAAGTGACATGACTCTTCTTGTCCAA
* *
47976552 TCCCTCTCC-AGACTCTTTTAGAGTTAGTTAATAGTCTTTGTTTAAAGACCAACTAGATGAACTG
321 TCCCTCTCCGA-ACTCTTTCAGAGTTAGTTAATAGTCTTTGTTTAAAGACCAACCAGATGAACTG
47976616 TC
385 TC
47976618 TGACTCTTTG
Statistics
Matches: 355, Mismatches: 26, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
393 2 0.01
394 340 0.96
395 10 0.03
396 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (393 bp):
TCTCCCAACTGTAAGAGACCTTAATAATTCCCTTAGGATTCATAGATTTCCCTTAGAAGATATTC
AAGTTCCAATTCTTCCAAATTCGCAAAGAATTAAACCGAAGAAACAGGCCCATACTAAACCTCTA
GTGCTATTATCCGACTGGTCACATAGATTACAGAGTAACCATTCCGATAGATTACCATTAAAGAA
CCATCTATGTTGATTAGAAGGGATGACTTGATTCCAAATATCCTTCGCGAACAGGCAATCTCTAA
GGACATGTAAAGCATACTCAATATTATAACCACATAAGTGACATGACTCTTCTTGTCCAATCCCT
CTCCGAACTCTTTCAGAGTTAGTTAATAGTCTTTGTTTAAAGACCAACCAGATGAACTGTCCAAT
CCC
Found at i:47978428 original size:19 final size:19
Alignment explanation
Indices: 47978378--47978417 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
47978368 ATGGGTTCAA
47978378 ACCAATTTTTGAATTAATT
1 ACCAATTTTTGAATTAATT
47978397 ACCAATTTTTGAATTAATT
1 ACCAATTTTTGAATTAATT
47978416 AC
1 AC
47978418 TATTTTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (19 bp):
ACCAATTTTTGAATTAATT
Found at i:47978610 original size:42 final size:43
Alignment explanation
Indices: 47978563--47978646 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
47978553 ATCCTAGAAC
* *
47978563 AAAAAGAATTTAAAAA-AGGAGAAGATAATCTTGGGTTGTTGA
1 AAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTTGA
47978605 AAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTTG
1 AAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTTG
47978647 GATTTACCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 16 0.41
43 23 0.59
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.24
Consensus pattern (43 bp):
AAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTTGA
Found at i:47982661 original size:21 final size:20
Alignment explanation
Indices: 47982624--47982667 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
47982614 ACCAATGCCA
* *
47982624 AAAAAAAAGGATTCAAAGAG
1 AAAAAAAAGAATTCAAAAAG
*
47982644 AAAAAAAATAATTACAAAAAG
1 AAAAAAAAGAATT-CAAAAAG
47982665 AAA
1 AAA
47982668 TCCCCTAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.73, C:0.05, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAAAAAAGAATTCAAAAAG
Found at i:47985245 original size:12 final size:11
Alignment explanation
Indices: 47985228--47985262 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
47985218 AACAAATCCT
47985228 CTCTCATATTTC
1 CTCTCA-ATTTC
47985240 CTCTCAA-TTC
1 CTCTCAATTTC
47985250 CTCTCAATTTC
1 CTCTCAATTTC
47985261 CT
1 CT
47985263 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:47985275 original size:22 final size:22
Alignment explanation
Indices: 47985245--47985300 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
47985235 ATTTCCTCTC
47985245 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
*
47985268 AATTCTCTCAGTTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
47985290 AATTCTCTCAA
1 AATTCTCTCAA
47985301 ATCCATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:47986477 original size:7 final size:7
Alignment explanation
Indices: 47986467--47986491 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47986457 ATTCGATTGA
47986467 TATTTAG
1 TATTTAG
47986474 TATTTAG
1 TATTTAG
47986481 TATTTAG
1 TATTTAG
47986488 TATT
1 TATT
47986492 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:47987695 original size:23 final size:22
Alignment explanation
Indices: 47987663--47988223 Score: 208
Period size: 23 Copynumber: 23.8 Consensus size: 22
47987653 TTATTTGATG
* *
47987663 TAATAAAAACCCTAACCTAATT
1 TAATTAAAACCCTAACCTAAAT
47987685 TAACCTT-AAACCCTAACCTAAAT
1 TAA--TTAAAACCCTAACCTAAAT
47987708 TAATTAAAAACCCTAACCTTAACCTAATT
1 TAATT-AAAACCCTAACC-T-A---AA-T
* *
47987737 TAATTAAAAATCCTAACCTAATT
1 TAATT-AAAACCCTAACCTAAAT
*
47987760 TAATTAAAAACCCTAACCTAATT
1 TAATT-AAAACCCTAACCTAAAT
* *
47987783 TAATTAAAAACTCTAAACC---CT
1 TAATT-AAAACCCT-AACCTAAAT
*
47987804 TAATTAAAACCCTAACCTAATT
1 TAATTAAAACCCTAACCTAAAT
47987826 TAATTAAATACCCTAACCT-AA-
1 TAATTAAA-ACCCTAACCTAAAT
*
47987847 T--TT-AAACCCTAAACCCTAATT
1 TAATTAAAACCCT-AA-CCTAAAT
* *
47987868 TAATTAAAAATCCTAACATTCACCTAATT
1 TAATT-AAAA-CC---C--TAACCTAAAT
*
47987897 TAATTAAAAACCCTAACCTAATT
1 TAATT-AAAACCCTAACCTAAAT
*
47987920 TAATTAAAAACCCTAAACCCTTAAT
1 TAATT-AAAACCCT-AA-CCTAAAT
* * *
47987945 TAA-AAACTCTAACCTTAACCTAATT
1 TAATTAA----AACCCTAACCTAAAT
*
47987970 TAATTAAAACCCCTAACCTAATT
1 TAATTAAAA-CCCTAACCTAAAT
*
47987993 TAATTAAAAACCCTAAACCCTTAAT
1 TAATT-AAAACCCT-AA-CCTAAAT
* * *
47988018 TAA-AAACCCTAACCTTAACCTAATT
1 TAATTAA----AACCCTAACCTAAAT
47988043 TAATTAAAAACCCTAACCT-AA-
1 TAATT-AAAACCCTAACCTAAAT
*
47988064 T--TT-AAACCCTAACCCTAATT
1 TAATTAAAACCCTAA-CCTAAAT
*
47988084 TAATAAAAAACCCTAACCTTAACTTAATT
1 TAAT-TAAAACCCTAACC-T-A---AA-T
*
47988113 TAATTAAAACCCTAACCTAATT
1 TAATTAAAACCCTAACCTAAAT
*
47988135 TAATTAAAAACCCTAAACC---CT
1 TAATT-AAAACCCT-AACCTAAAT
* * *
47988156 TAATTAAAAATCCTAATCTAATT
1 TAATT-AAAACCCTAACCTAAAT
*
47988179 TAAACCTT-AAACCCTAAACCCTAATT
1 T-AA--TTAAAACCCT-AA-CCTAAAT
47988205 TAATTAAAAACCCTAACCT
1 TAATT-AAAACCCTAACCT
47988224 TAACGTAATG
Statistics
Matches: 427, Mismatches: 41, Indels: 141
0.70 0.07 0.23
Matches are distributed among these distances:
17 14 0.03
18 7 0.02
19 12 0.03
20 12 0.03
21 25 0.06
22 23 0.05
23 153 0.36
24 39 0.09
25 49 0.11
26 18 0.04
27 14 0.03
28 18 0.04
29 41 0.10
30 1 0.00
31 1 0.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATTAAAACCCTAACCTAAAT
Found at i:47987730 original size:29 final size:29
Alignment explanation
Indices: 47987693--47987778 Score: 112
Period size: 29 Copynumber: 3.2 Consensus size: 29
47987683 TTTAACCTTA
* *
47987693 AACCCTAACCTAAATTAATTAAAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACCCT
47987722 AACCTTAACCTAATTTAATTAAAAA---T
1 AACCTTAACCTAATTTAATTAAAAACCCT
47987748 --CC-TAACCTAATTTAATTAAAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACCCT
47987774 AACCT
1 AACCT
47987779 AATTTAATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
23 20 0.41
24 2 0.04
26 2 0.04
28 2 0.04
29 23 0.47
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (29 bp):
AACCTTAACCTAATTTAATTAAAAACCCT
Found at i:47987753 original size:52 final size:50
Alignment explanation
Indices: 47987673--47988146 Score: 293
Period size: 52 Copynumber: 9.9 Consensus size: 50
47987663 TAATAAAAAC
*
47987673 CCTAACCTAATTTAACCTT--AAACCCTAACCTAAATTAATTAAAAACCCTAA
1 CCTAACCTAATTTAA--TTAAAAACCCTAACCTAATTTAATTAAAAA-CCTAA
*
47987724 CCTTAACCTAATTTAATTAAAAATCCTAACCTAATTTAATTAAAAA-C---
1 CC-TAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCTAA
* *
47987771 CCTAACCTAATTTAATTAAAAACTCTAAACC---CTTAATT-AAAA-C---
1 CCTAACCTAATTTAATTAAAAACCCT-AACCTAATTTAATTAAAAACCTAA
* *
47987814 CCTAACCTAATTTAATTAAATACCCTAACCTAA--T--TT-AAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCTAA
* *
47987859 ---ACCCTAATTTAATTAAAAATCCTAACATTCACCTAATTTAATTAAAAA-C---
1 CCTAACCTAATTTAATTAAAAA-CC---C--TAACCTAATTTAATTAAAAACCTAA
*
47987908 CCTAACCTAATTTAATTAAAAACCCTAAACC---CTTAATTAAAAACTCTAA
1 CCTAACCTAATTTAATTAAAAACCCT-AACCTAATTTAATTAAAAAC-CTAA
*
47987957 CCTTAACCTAATTTAATTAAAACCCCTAACCTAATTTAATTAAAAACCCTAAA
1 CC-TAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAA-CCT-AA
* *
47988010 CC---CTTAA-TTAA--AAACCCTAACCTTAACCTAATTTAATTAAAAA-C---
1 CCTAACCTAATTTAATTAAA----AACCCTAACCTAATTTAATTAAAAACCTAA
*
47988054 CCTAACCTAA--T--TT--AAACCCTAACCCTAATTTAATAAAAAACCCTAA
1 CCTAACCTAATTTAATTAAAAACCCTAA-CCTAATTTAATTAAAAA-CCTAA
*
47988100 CCTTAACTTAATTTAATT-AAAACCCTAACCTAATTTAATTAAAAACC
1 CC-TAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACC
47988147 CTAAACCCTT
Statistics
Matches: 340, Mismatches: 25, Indels: 117
0.71 0.05 0.24
Matches are distributed among these distances:
40 7 0.02
41 21 0.06
42 22 0.06
43 33 0.10
44 20 0.06
46 31 0.09
47 20 0.06
48 13 0.04
49 11 0.03
50 52 0.15
51 22 0.06
52 80 0.24
53 8 0.02
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (50 bp):
CCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCTAA
Found at i:47987945 original size:21 final size:22
Alignment explanation
Indices: 47987896--47987956 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
47987886 TTCACCTAAT
*
47987896 TTAATTAAAAACCCT-AACCTAAT
1 TTAATTAAAAACCCTAAACC--AC
47987919 TTAATTAAAAACCCTAAACC-C
1 TTAATTAAAAACCCTAAACCAC
*
47987940 TTAATTAAAAACTCTAA
1 TTAATTAAAAACCCTAA
47987957 CCTTAACCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.46
23 15 0.43
24 4 0.11
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (22 bp):
TTAATTAAAAACCCTAAACCAC
Found at i:47987973 original size:29 final size:27
Alignment explanation
Indices: 47987940--47988063 Score: 108
Period size: 29 Copynumber: 4.8 Consensus size: 27
47987930 CCCTAAACCC
47987940 TTAATTAAAAACTCTAACCTTAACCTAAT
1 TTAATTAAAAAC-CTAACC-TAACCTAAT
47987969 TTAATT-AAAACC---CCTAACCTAAT
1 TTAATTAAAAACCTAACCTAACCTAAT
*
47987992 TTAATTAAAAA-C---CCTAAACC---C
1 TTAATTAAAAACCTAACCT-AACCTAAT
47988013 TTAATTAAAAACCCTAACCTTAACCTAAT
1 TTAATTAAAAA-CCTAACC-TAACCTAAT
47988042 TTAATTAAAAACCCTAACCTAA
1 TTAATTAAAAA-CCTAACCTAA
47988064 TTTAAACCCT
Statistics
Matches: 82, Mismatches: 2, Indels: 23
0.77 0.02 0.21
Matches are distributed among these distances:
21 11 0.13
23 20 0.24
24 10 0.12
26 6 0.07
27 2 0.02
28 8 0.10
29 25 0.30
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (27 bp):
TTAATTAAAAACCTAACCTAACCTAAT
Found at i:47987975 original size:73 final size:73
Alignment explanation
Indices: 47987811--47988171 Score: 475
Period size: 73 Copynumber: 5.0 Consensus size: 73
47987801 CCTTAATTAA
* * **** *
47987811 AACCCTAACCTAATTTAATTAAATACCCTAACCTAATTTAAACCCTAAACCCT-AA--TTTAATT
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTT-AATTAAAAACCCTAAACCCTTAATT
*
47987873 AAAAATCCT
65 AAAAACCCT
* *
47987882 AACATTCACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTA
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTA
*
47987947 AAAACTCT
66 AAAACCCT
*
47987955 AACCTTAACCTAATTTAATTAAAACCCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTA
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTA
47988020 AAAACCCT
66 AAAACCCT
***** * *
47988028 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAACCCTAACCCT-AA--TTTAATAA
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTA
47988090 AAAACCCT
66 AAAACCCT
*
47988098 AACCTTAACTTAATTTAATT-AAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTA
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTA
*
47988162 AAAATCCT
66 AAAACCCT
47988170 AA
1 AA
47988172 TCTAATTTAA
Statistics
Matches: 252, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
69 26 0.10
70 44 0.17
71 37 0.15
72 17 0.07
73 128 0.51
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (73 bp):
AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTA
AAAACCCT
Found at i:47988007 original size:18 final size:18
Alignment explanation
Indices: 47987986--47988099 Score: 53
Period size: 18 Copynumber: 6.3 Consensus size: 18
47987976 AAACCCCTAA
47987986 CCTAATTTAATTAAAAAC
1 CCTAATTTAATTAAAAAC
*
47988004 CCTAAACCCTTAATTAAAAAC
1 CCT-AA--TTTAATTAAAAAC
**
47988025 CCTAA---CCTT--A-AC
1 CCTAATTTAATTAAAAAC
47988037 C-TAATTTAATTAAAAAC
1 CCTAATTTAATTAAAAAC
**
47988054 CCTAACCTAATTTAAACCCTAAC
1 CCTAATTTAA-TTAAA----AAC
*
47988077 CCTAATTTAATAAAAAAC
1 CCTAATTTAATTAAAAAC
47988095 CCTAA
1 CCTAA
47988100 CCTTAACTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 30
0.64 0.09 0.27
Matches are distributed among these distances:
11 3 0.04
12 3 0.04
13 1 0.01
14 2 0.03
15 2 0.03
16 1 0.01
17 3 0.04
18 17 0.24
19 7 0.10
20 2 0.03
21 15 0.21
22 4 0.06
23 11 0.15
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.28
Consensus pattern (18 bp):
CCTAATTTAATTAAAAAC
Found at i:47988070 original size:17 final size:18
Alignment explanation
Indices: 47988050--47988086 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
47988040 ATTTAATTAA
47988050 AAACCCTAA-CCTAATTT
1 AAACCCTAACCCTAATTT
47988067 AAACCCTAACCCTAATTT
1 AAACCCTAACCCTAATTT
47988085 AA
1 AA
47988087 TAAAAAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (18 bp):
AAACCCTAACCCTAATTT
Found at i:47988130 original size:28 final size:28
Alignment explanation
Indices: 47988079--47988139 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
47988069 ACCCTAACCC
47988079 TAATTTAATAAAAAACCCTAACCTTAACT
1 TAATTTAATAAAAAACCCTAACC-TAACT
* *
47988108 TAATTTAAT-TAAAACCCTAACCTAATT
1 TAATTTAATAAAAAACCCTAACCTAACT
47988135 TAATT
1 TAATT
47988140 AAAAACCCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 9 0.30
28 12 0.40
29 9 0.30
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (28 bp):
TAATTTAATAAAAAACCCTAACCTAACT
Found at i:47988378 original size:116 final size:116
Alignment explanation
Indices: 47988229--47988439 Score: 368
Period size: 116 Copynumber: 1.8 Consensus size: 116
47988219 AACCTTAACG
*
47988229 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
1 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTCTACATAATTTGATA
*
47988294 ATTTTATTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
* * * *
47988345 TAATGTTAGATTTGGAAAAATGTTTTGATTGGTACTAACAATTAATAATTCTATATAATTTGATA
1 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTCTACATAATTTGATA
47988410 ATTTTACTAACCATTAATACAATTTTTTGA
66 ATTTTACTAACCATTAATACAATTTTTTGA
47988440 TGTTATACAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 89 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (116 bp):
TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTCTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
Found at i:47991702 original size:126 final size:126
Alignment explanation
Indices: 47991477--47991704 Score: 420
Period size: 126 Copynumber: 1.8 Consensus size: 126
47991467 CCCAAACATG
* *
47991477 CTACTGTAGCAAAAGCGCGTCCACGATGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGC
* *
47991542 TAGAAGCGATTTTATATTATTTTCTCAGAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
66 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
47991603 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGC
47991668 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAA
47991705 CTCGAAATTA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 98 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGC
TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
Found at i:47996513 original size:42 final size:42
Alignment explanation
Indices: 47996410--47996515 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
47996400 ATGCCACAGG
* * * *
47996410 GCCTGAACACACGCCTATGTCCTTGCTCGTGTGGCTCACACA
1 GCCTGGACACACGCCCATGTCCTTGCTCGTATGACTCACACA
* * *
47996452 GCCTGGAAACACACTCATGTCCTTGCTCGTATGACTCACACA
1 GCCTGGACACACGCCCATGTCCTTGCTCGTATGACTCACACA
* * *
47996494 TCTTGGGCACACGCCCATGTCC
1 GCCTGGACACACGCCCATGTCC
47996516 CTGGCCGTGT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.24
Consensus pattern (42 bp):
GCCTGGACACACGCCCATGTCCTTGCTCGTATGACTCACACA
Found at i:48000767 original size:28 final size:27
Alignment explanation
Indices: 48000736--48000801 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
48000726 GAGCCCTATT
*
48000736 CAATAACAGTACAGTATGGGCCTTAGCC
1 CAAT-ACAGTACAATATGGGCCTTAGCC
* * *
48000764 CAATACAATAATAATGTGGGCCTTAGCC
1 CAATACAGT-ACAATATGGGCCTTAGCC
48000792 CAATACAGTA
1 CAATACAGTA
48000802 TTGGTACAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 5 0.16
28 27 0.84
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (27 bp):
CAATACAGTACAATATGGGCCTTAGCC
Found at i:48003434 original size:51 final size:48
Alignment explanation
Indices: 48003342--48003436 Score: 120
Period size: 51 Copynumber: 1.9 Consensus size: 48
48003332 CTTCACCATC
* *
48003342 GTCTTCAACATTTTTCCTGACTACTTTCTCTTTCGTTTTCTTTGAATT
1 GTCTTCAACATTTTTCCTGACTACTTTCTATATCGTTTTCTTTGAATT
*
48003390 GTCTTCAACATTTTTCATTCATGTCT-CTTTCTATATCGTTTTCTTTG
1 GTCTTCAACATTTTTC---C-TGACTACTTTCTATATCGTTTTCTTTG
48003437 CCATCTCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
48 16 0.40
51 20 0.50
52 4 0.10
ACGTcount: A:0.15, C:0.22, G:0.08, T:0.55
Consensus pattern (48 bp):
GTCTTCAACATTTTTCCTGACTACTTTCTATATCGTTTTCTTTGAATT
Found at i:48004343 original size:26 final size:26
Alignment explanation
Indices: 48004314--48004379 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
48004304 GGATCAACAT
*
48004314 AAAATGTCCATCAAAATACAACCATC
1 AAAATGTCCATCAAAATAAAACCATC
* * *
48004340 AAAATGATCTAACAAAATAAAACCATT
1 AAAATG-TCCATCAAAATAAAACCATC
* *
48004367 AAATTATCCATCA
1 AAAATGTCCATCA
48004380 TATGTTAACT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.23
Consensus pattern (26 bp):
AAAATGTCCATCAAAATAAAACCATC
Found at i:48004399 original size:35 final size:35
Alignment explanation
Indices: 48004355--48004471 Score: 164
Period size: 35 Copynumber: 3.3 Consensus size: 35
48004345 GATCTAACAA
*
48004355 AATAAAACCATTAAATTATCCATCATATGTTAACT
1 AATAAAACCATCAAATTATCCATCATATGTTAACT
* *
48004390 AACT-AAACCATCAAATTATCCATCGTATGTTAACAA
1 AA-TAAAACCATCAAATTATCCATCATATGTTAAC-T
*
48004426 AATAAAACCATCAAATTATCCATGATATGTTAACT
1 AATAAAACCATCAAATTATCCATCATATGTTAACT
*
48004461 AATGAAACCAT
1 AATAAAACCAT
48004472 ATTGACATTA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 41 0.57
36 31 0.43
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (35 bp):
AATAAAACCATCAAATTATCCATCATATGTTAACT
Found at i:48004441 original size:36 final size:36
Alignment explanation
Indices: 48004349--48004459 Score: 163
Period size: 36 Copynumber: 3.1 Consensus size: 36
48004339 CAAAATGATC
* *
48004349 TAACAAAATAAAACCATTAAATTATCCATCATATGT
1 TAACAAAATAAAACCATCAAATTATCCATCGTATGT
* *
48004385 TAACTAACT-AAACCATCAAATTATCCATCGTATGT
1 TAACAAAATAAAACCATCAAATTATCCATCGTATGT
48004420 TAACAAAATAAAACCATCAAATTATCCAT-GATATGT
1 TAACAAAATAAAACCATCAAATTATCCATCG-TATGT
48004456 TAAC
1 TAAC
48004460 TAATGAAACC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 32 0.48
36 35 0.52
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.30
Consensus pattern (36 bp):
TAACAAAATAAAACCATCAAATTATCCATCGTATGT
Found at i:48007743 original size:4 final size:4
Alignment explanation
Indices: 48007729--48007821 Score: 91
Period size: 4 Copynumber: 22.5 Consensus size: 4
48007719 AATAAACCTA
*
48007729 ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-A-
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
48007775 ACAATT ATAT ACAT AACAT ACAT AGTAT ACAT ACAT AACAA ACAT AC
1 AC-A-T ACAT ACAT -ACAT ACAT A-CAT ACAT ACAT -ACAT ACAT AC
48007822 TAATAGACAT
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
2 1 0.01
3 1 0.01
4 60 0.81
5 11 0.15
6 1 0.01
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:48007840 original size:63 final size:62
Alignment explanation
Indices: 48007710--48007918 Score: 212
Period size: 63 Copynumber: 3.4 Consensus size: 62
48007700 CATACATATA
* * * * *
48007710 ATAAACAATAATAAACCTAACATGCATACATACATACAT-ACATACATACATACAT--ACATAC
1 ATAAACAATAATATACATAACATACATATATACATACATAACAAACATAC-TA-ATAGACATAC
* *
48007771 ATAAACAATTATATACATAACATACATAGTATACATACATAACAAACATACTAATAGACATCC
1 ATAAACAATAATATACATAACATACATA-TATACATACATAACAAACATACTAATAGACATAC
* *** * *
48007834 ATAAACAACAATATTTGTAACATACATAATATACATACATAACAGACATACTAACATG-CATAC
1 ATAAACAATAATATACATAACATACAT-ATATACATACATAACAAACATACTAATA-GACATAC
48007897 ATAAA-AAGTAATATACATAACA
1 ATAAACAA-TAATATACATAACA
48007919 GATTGACCTT
Statistics
Matches: 122, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
61 26 0.21
62 14 0.11
63 80 0.66
64 2 0.02
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.24
Consensus pattern (62 bp):
ATAAACAATAATATACATAACATACATATATACATACATAACAAACATACTAATAGACATAC
Found at i:48007843 original size:25 final size:26
Alignment explanation
Indices: 48007741--48007900 Score: 72
Period size: 25 Copynumber: 6.4 Consensus size: 26
48007731 ATGCATACAT
*
48007741 ACATACATACAT--ACATACAT-ACAT
1 ACATACATA-ATAGACATACATAACAA
* *
48007765 ACATACATAA-ACA-AT-TATATACATA
1 ACATACATAATAGACATACATA-ACA-A
* *
48007790 ACATACATAGTATACATACATAACAA
1 ACATACATAATAGACATACATAACAA
*
48007816 ACATAC-TAATAGACATCCATAA-ACA
1 ACATACATAATAGACATACATAACA-A
* ** * *
48007841 ACAATA-TTTGTA-ACATACATAATAT
1 AC-ATACATAATAGACATACATAACAA
* *
48007866 ACATACATAACAGACATAC-TAACAT
1 ACATACATAATAGACATACATAACAA
*
48007891 GCATACATAA
1 ACATACATAA
48007901 AAAGTAATAT
Statistics
Matches: 104, Mismatches: 18, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
22 2 0.02
23 3 0.03
24 17 0.16
25 52 0.50
26 22 0.21
27 5 0.05
28 3 0.03
ACGTcount: A:0.52, C:0.20, G:0.03, T:0.25
Consensus pattern (26 bp):
ACATACATAATAGACATACATAACAA
Found at i:48007895 original size:12 final size:13
Alignment explanation
Indices: 48007853--48007900 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
48007843 AATATTTGTA
* *
48007853 ACATACATAATAT
1 ACATACATAACAG
48007866 ACATACATAACAG
1 ACATACATAACAG
48007879 ACATAC-TAACATG
1 ACATACATAACA-G
48007892 -CATACATAA
1 ACATACATAA
48007901 AAAGTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.52, C:0.21, G:0.04, T:0.23
Consensus pattern (13 bp):
ACATACATAACAG
Found at i:48009290 original size:26 final size:26
Alignment explanation
Indices: 48009227--48009293 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
48009217 CTTAAAAAAA
*
48009227 TATATATTAAAAATATGCATATATAT
1 TATATATAAAAAATATGCATATATAT
* *
48009253 TATATATAAAAAATATGCGTATGTA-
1 TATATATAAAAAATATGCATATATAT
* *
48009278 TATGTATAGAAAATAT
1 TATATATAAAAAATAT
48009294 AATAGTAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 14 0.39
26 22 0.61
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (26 bp):
TATATATAAAAAATATGCATATATAT
Found at i:48010915 original size:44 final size:44
Alignment explanation
Indices: 48010832--48011362 Score: 624
Period size: 44 Copynumber: 12.0 Consensus size: 44
48010822 ATAAGACTTG
* * *
48010832 TATCTTCGATCTGCTTCAGTGTCGATACAGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCA-TGTCAATACATGAAGACAAGATCTGC
***
48010877 TATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCAT
1 TATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCTGC
48010921 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
*
48010965 TATC-CCTGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
1 TATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCTGC
* **
48011009 TATC-TCTGATCTACTTCATGTCAATACATGAAGTCAAGATCTAT
1 TATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCTGC
* *
48011053 TATCTTCGATCTACTTCATGTCAATACATGAAGATAATATCTGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
* * ***
48011097 TATC-CCTAATCTACTTCATGTCAATACATGACA-ACAAGATCCAT
1 TATCTTC-GATCTACTTCATGTCAATACATGA-AGACAAGATCTGC
*** * ***
48011141 TATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCA-TGTCAATACATGAAGACAAGATCTGC
* ***
48011186 TATC-TCTGATCTACTTCATGTCACTACATGAAGACAAGATCCAT
1 TATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCTGC
48011230 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
* *** *
48011274 TTTCTTCGATCTACTTCACACCAATACACGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
* * *
48011318 TTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
48011362 T
1 T
48011363 GCTTTTCAAC
Statistics
Matches: 416, Mismatches: 59, Indels: 23
0.84 0.12 0.05
Matches are distributed among these distances:
43 2 0.00
44 363 0.87
45 51 0.12
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (44 bp):
TATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCTGC
Found at i:48012672 original size:14 final size:13
Alignment explanation
Indices: 48012657--48012702 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
48012647 AGCCTCTCCA
48012657 TTTTACTTTTTCC
1 TTTTACTTTTTCC
*
48012670 ATTTTTCATTTTTCC
1 -TTTTAC-TTTTTCC
48012685 TTTTCACTTTTTCC
1 TTTT-ACTTTTTCC
48012699 TTTT
1 TTTT
48012703 TTCATTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 20 0.71
15 8 0.29
ACGTcount: A:0.09, C:0.22, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTACTTTTTCC
Found at i:48012710 original size:21 final size:21
Alignment explanation
Indices: 48012671--48012711 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
48012661 ACTTTTTCCA
*
48012671 TTTTTCATTTTTCCTTTTCAC
1 TTTTTCATTTTTCCATTTCAC
* *
48012692 TTTTTCCTTTTTTCATTTCA
1 TTTTTCATTTTTCCATTTCA
48012712 TCATTTTTTA
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:0.10, C:0.22, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTCATTTTTCCATTTCAC
Found at i:48013638 original size:18 final size:18
Alignment explanation
Indices: 48013612--48013655 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
48013602 TGGTTTGGCA
*
48013612 GAAAAAATCCAAAAAAAT
1 GAAAGAATCCAAAAAAAT
**
48013630 GAAAGAATCGTAAAAAAT
1 GAAAGAATCCAAAAAAAT
48013648 GAAAGAAT
1 GAAAGAAT
48013656 ATTTGCTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (18 bp):
GAAAGAATCCAAAAAAAT
Found at i:48017436 original size:26 final size:25
Alignment explanation
Indices: 48017396--48017463 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 25
48017386 GCTTAAAAAA
* *
48017396 ATATATATTAAAAATATGCATATAT
1 ATATGTATAAAAAATATGCATATAT
* * *
48017421 ATTATTTATAAAAAATATGCGTATGT
1 A-TATGTATAAAAAATATGCATATAT
*
48017447 ATATGTATAGAAAATAT
1 ATATGTATAAAAAATAT
48017464 AATAGTAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.40
Consensus pattern (25 bp):
ATATGTATAAAAAATATGCATATAT
Found at i:48022726 original size:34 final size:34
Alignment explanation
Indices: 48022677--48022755 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
48022667 GGATTTGTTT
* * ** *
48022677 TGATCTGATACATGTTTCTGAAAATATTAGATTC
1 TGATATGATATATGTTTCTGAAAATAGGACATTC
**
48022711 TGATATGATATATGTTTCTGGTAATAGGACATTC
1 TGATATGATATATGTTTCTGAAAATAGGACATTC
48022745 TGATATGATAT
1 TGATATGATAT
48022756 TTGTATATGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.42
Consensus pattern (34 bp):
TGATATGATATATGTTTCTGAAAATAGGACATTC
Found at i:48023841 original size:29 final size:29
Alignment explanation
Indices: 48023809--48023873 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
48023799 AGCAACACCA
*
48023809 AAGTGAAATATCATAATAGAATGACACTG
1 AAGTGAAATAGCATAATAGAATGACACTG
*** * *
48023838 AAGTGCTTTAGCATAATAGAGTGGCACTG
1 AAGTGAAATAGCATAATAGAATGACACTG
48023867 AAGTGAA
1 AAGTGAA
48023874 TTAACAGAAC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.25
Consensus pattern (29 bp):
AAGTGAAATAGCATAATAGAATGACACTG
Found at i:48024890 original size:15 final size:16
Alignment explanation
Indices: 48024870--48024902 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
48024860 AACCATTAAG
48024870 TAAAATAATT-TAAAA
1 TAAAATAATTCTAAAA
48024885 TAAAATAATTCTAAAA
1 TAAAATAATTCTAAAA
48024901 TA
1 TA
48024903 TTCTAACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATAATTCTAAAA
Found at i:48028830 original size:35 final size:35
Alignment explanation
Indices: 48028790--48028893 Score: 102
Period size: 35 Copynumber: 2.9 Consensus size: 35
48028780 AATAATGTTT
* *
48028790 TGTGCCTAGCACTAGTCGGATACACTGACAATAGG
1 TGTGCCTAGCACTAGTCGGATAAACCGACAATAGG
* * *
48028825 TGTGCCTAGCACTGGTCGGGTAAACCGACAATA-T
1 TGTGCCTAGCACTAGTCGGATAAACCGACAATAGG
* * * *
48028859 TTTGCACCCAACACTAGTCGGATAAACCGATAATA
1 TGTG--CCTAGCACTAGTCGGATAAACCGACAATA
48028894 TCAAATGTGG
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
34 3 0.05
35 29 0.52
36 24 0.43
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (35 bp):
TGTGCCTAGCACTAGTCGGATAAACCGACAATAGG
Found at i:48030946 original size:6 final size:6
Alignment explanation
Indices: 48030937--48030963 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
48030927 TAATGATGCA
48030937 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
48030964 AAAAAGGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:48037027 original size:17 final size:15
Alignment explanation
Indices: 48037005--48037038 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
48036995 AACAAATATT
48037005 TTAAAATTATTAAAAAA
1 TTAAAATTA--AAAAAA
48037022 TTAAAATTAAAAAAA
1 TTAAAATTAAAAAAA
48037037 TT
1 TT
48037039 GATACAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAAATTAAAAAAA
Found at i:48037063 original size:18 final size:19
Alignment explanation
Indices: 48037025--48037064 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
48037015 TAAAAAATTA
* *
48037025 AAATTAAAAAAATTGATAC
1 AAATTAAAAAAATAGACAC
48037044 AAATTAAAAAAATAG-CAC
1 AAATTAAAAAAATAGACAC
48037062 AAA
1 AAA
48037065 GTATATGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (19 bp):
AAATTAAAAAAATAGACAC
Found at i:48046669 original size:35 final size:34
Alignment explanation
Indices: 48046579--48046677 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 34
48046569 AATCCGCGAA
* *
48046579 AGAGTTTGCGCCCAACACTAGTCGGATAAATCGAC
1 AGAGGTTGC-CCCAACACTAGTCAGATAAATCGAC
* * * *
48046614 AAATGTGTG-CCCAGCACTAGTCAGATAAATTGAC
1 AGAGGT-TGCCCCAACACTAGTCAGATAAATCGAC
48046648 AGAGGTTGCACCCAACACTAGTCAGATAAA
1 AGAGGTTGC-CCCAACACTAGTCAGATAAA
48046678 CTAACGAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
33 2 0.04
34 26 0.50
35 22 0.42
36 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.20
Consensus pattern (34 bp):
AGAGGTTGCCCCAACACTAGTCAGATAAATCGAC
Found at i:48046900 original size:143 final size:143
Alignment explanation
Indices: 48046583--48046901 Score: 399
Period size: 143 Copynumber: 2.2 Consensus size: 143
48046573 CGCGAAAGAG
* * * * *
48046583 TTTGCGCCCAACACTAGTCGGATAAATCGACAAATGTGTGCCCAGCACTAGTCAGATAAATTGAC
1 TTTGCGCCCAGCGCTAGTCGAATAAATCGACGAATGTGTGCCCAGCACTAGTCAGATAAACTGAC
* *
48046648 AGAGGTTGCACCCAACACTAGTCAGATAAACTAACGAATAATTAGTGAGCCCAACTCTAGTTGGA
66 AGAAGTTGCACCCAACACTAATCAGATAAACTAACGAATAATTAGTGAGCCCAACTCTAGTTGGA
*
48046713 TAAATCAACGATA
131 TAAACCAACGATA
** * * * *
48046726 TTTTTGCACAGCGCTAG-CCAGATAAACCGACGAATGTGTGCCCAGCGCTAGTCAGATAAACTGA
1 TTTGCGCCCAGCGCTAGTCGA-ATAAATCGACGAATGTGTGCCCAGCACTAGTCAGATAAACTGA
* * * * * * *
48046790 -TGAAAGTTGCGCCCAGCACTAATCGGATAAACTAACTAATAATTAGTGAGCCTAGCTCTAGTTG
65 CAG-AAGTTGCACCCAACACTAATCAGATAAACTAACGAATAATTAGTGAGCCCAACTCTAGTTG
48046854 GATAAACCAACGATA
129 GATAAACCAACGATA
* *
48046869 TTTGCGCCCAGCGCTAGTTGAACAAATCGACGA
1 TTTGCGCCCAGCGCTAGTCGAATAAATCGACGA
48046902 TGTCAATTAC
Statistics
Matches: 145, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
142 2 0.01
143 142 0.98
144 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (143 bp):
TTTGCGCCCAGCGCTAGTCGAATAAATCGACGAATGTGTGCCCAGCACTAGTCAGATAAACTGAC
AGAAGTTGCACCCAACACTAATCAGATAAACTAACGAATAATTAGTGAGCCCAACTCTAGTTGGA
TAAACCAACGATA
Found at i:48053598 original size:47 final size:47
Alignment explanation
Indices: 48053542--48053636 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
48053532 TTTATTTTGA
48053542 GTATGATCCTACTAATTTGAGCTATTTATGATTTTTTATGTTGTAGG
1 GTATGATCCTACTAATTTGAGCTATTTATGATTTTTTATGTTGTAGG
48053589 GTATGATCCTACTAATTTGAGCTATTTATGATTTTTTATGTTGTAGG
1 GTATGATCCTACTAATTTGAGCTATTTATGATTTTTTATGTTGTAGG
48053636 G
1 G
48053637 ACTAAATTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.23, C:0.08, G:0.20, T:0.48
Consensus pattern (47 bp):
GTATGATCCTACTAATTTGAGCTATTTATGATTTTTTATGTTGTAGG
Found at i:48055013 original size:33 final size:33
Alignment explanation
Indices: 48054970--48055047 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
48054960 AGCTAATGTG
*
48054970 CTTGATTTCCAACAGCAGATACAACGACAAACT
1 CTTGATTTCCAACAGCAAATACAACGACAAACT
* * * *
48055003 GTTGATTTCCAGCAGTAAATACAACGGCAAACT
1 CTTGATTTCCAACAGCAAATACAACGACAAACT
48055036 CTTGATTTCCAA
1 CTTGATTTCCAA
48055048 AAGGAAACAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (33 bp):
CTTGATTTCCAACAGCAAATACAACGACAAACT
Found at i:48056441 original size:6 final size:6
Alignment explanation
Indices: 48056430--48056479 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
48056420 GGTAACCCAA
* *
48056430 TTTTAT TTTTAT TTTTA- TTTTAT TTATAT ATTTA- TTTTATT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT
48056477 TTT
1 TTT
48056480 CTTGCATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 9 0.24
6 23 0.62
7 5 0.14
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:48056451 original size:17 final size:17
Alignment explanation
Indices: 48056429--48056479 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
48056419 AGGTAACCCA
48056429 ATTTTATTTTTATTTTT
1 ATTTTATTTTTATTTTT
* *
48056446 ATTTTATTTATATATTT
1 ATTTTATTTTTATTTTT
48056463 ATTTTATTTTTTATTTT
1 ATTTTA-TTTTTATTTT
48056480 CTTGCATGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 21 0.72
18 8 0.28
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
ATTTTATTTTTATTTTT
Found at i:48056479 original size:5 final size:5
Alignment explanation
Indices: 48056429--48056472 Score: 52
Period size: 5 Copynumber: 8.0 Consensus size: 5
48056419 AGGTAACCCA
48056429 ATTTT ATTTTT ATTTTT ATTTT ATTTAT ATATTT ATTTT ATTTT
1 ATTTT A-TTTT A-TTTT ATTTT ATTT-T AT-TTT ATTTT ATTTT
48056473 TTATTTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 17 0.47
6 17 0.47
7 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:48057441 original size:18 final size:19
Alignment explanation
Indices: 48057406--48057447 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
48057396 ATATATTATT
48057406 AAGAAAAAAAGAAGGAAAA
1 AAGAAAAAAAGAAGGAAAA
48057425 AAGAAAAGAAA-AA-GAAAA
1 AAGAAAA-AAAGAAGGAAAA
48057443 AAGAA
1 AAGAA
48057448 GTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.45
19 9 0.41
20 3 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAGAAGGAAAA
Found at i:48059655 original size:39 final size:39
Alignment explanation
Indices: 48059504--48059673 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 39
48059494 GGACTAAGAT
*
48059504 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCA-TTGTGCGAGATACTAAA-TCCGGGTTAAGTC
*
48059544 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGG-CATTGTGCGAGATACTAAATCCGGGTTAAGTC
* * *
48059584 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATT-GTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
48059624 CCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTGTGCGAGATACTAAATCCGGGTTAAGTC
48059663 CCGAAGGCATT
1 CCGAAGGCATT
48059674 TGAACGAGGA
Statistics
Matches: 117, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
39 38 0.32
40 75 0.64
41 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:48059693 original size:79 final size:80
Alignment explanation
Indices: 48059531--48059708 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
48059521 AGATACAAAT
* * * *
48059531 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
48059596 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
48059611 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
48059675 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
48059690 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
48059709 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:48062184 original size:14 final size:13
Alignment explanation
Indices: 48062167--48062206 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
48062157 AATACAAAAC
48062167 TTTTTTCTTTTTCT
1 TTTTTTCTTTTT-T
48062181 TTTTTTCTTTCTTT
1 TTTTTTCTTT-TTT
48062195 TTTTTT-TTTTTT
1 TTTTTTCTTTTTT
48062207 GAGTCATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 3 0.12
14 17 0.68
15 2 0.08
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:48062204 original size:18 final size:18
Alignment explanation
Indices: 48062170--48062203 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48062160 ACAAAACTTT
48062170 TTTCTTTTTCTTTTTTTC
1 TTTCTTTTTCTTTTTTTC
48062188 TTTCTTTTT-TTTTTTT
1 TTTCTTTTTCTTTTTTT
48062204 TTTGAGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTCTTTTTCTTTTTTTC
Found at i:48062287 original size:22 final size:22
Alignment explanation
Indices: 48062259--48062328 Score: 131
Period size: 22 Copynumber: 3.2 Consensus size: 22
48062249 TAGTTCGGTA
48062259 CTAAAGTAGAAAATAACGTATC
1 CTAAAGTAGAAAATAACGTATC
48062281 CTAAAGTAGAAAATAACGTATC
1 CTAAAGTAGAAAATAACGTATC
*
48062303 CTAAAGTAGAAAATAACTTATC
1 CTAAAGTAGAAAATAACGTATC
48062325 CTAA
1 CTAA
48062329 TATTCTTCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.24
Consensus pattern (22 bp):
CTAAAGTAGAAAATAACGTATC
Found at i:48074371 original size:30 final size:29
Alignment explanation
Indices: 48074331--48074407 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 29
48074321 TTGGTTGGAA
* *
48074331 AAAAATAAAAAAAATATATATT-AACTTATG
1 AAAAAGAAAAAAAATAT-TATTAAAATT-TG
48074361 AAAAAGAAAAAAAA-ATTATTAAAATTTG
1 AAAAAGAAAAAAAATATTATTAAAATTTG
*
48074389 TAAAAGAAGAAAAAATATT
1 AAAAAGAA-AAAAAATATT
48074408 TGTTTATGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.32
29 12 0.29
30 16 0.39
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.26
Consensus pattern (29 bp):
AAAAAGAAAAAAAATATTATTAAAATTTG
Found at i:48074380 original size:28 final size:29
Alignment explanation
Indices: 48074331--48074406 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 29
48074321 TTGGTTGGAA
* *
48074331 AAAAATAAAAAAAATATATATT-AACTTATG
1 AAAAAGAAAAAAAA-ATATATTAAAATT-TG
48074361 AAAAAGAAAAAAAAAT-TATTAAAATTTG
1 AAAAAGAAAAAAAAATATATTAAAATTTG
* *
48074389 TAAAAGAAGAAAAAATAT
1 AAAAAGAAAAAAAAATAT
48074407 TTGTTTATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 20 0.50
29 7 0.17
30 13 0.32
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (29 bp):
AAAAAGAAAAAAAAATATATTAAAATTTG
Found at i:48074899 original size:19 final size:21
Alignment explanation
Indices: 48074877--48074921 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
48074867 TTAGTAATAG
*
48074877 TAATATTTAAT-T-TTTTTTA
1 TAATACTTAATATATTTTTTA
48074896 TAATACTTAATATATTTTTTA
1 TAATACTTAATATATTTTTTA
*
48074917 AAATA
1 TAATA
48074922 AGTGATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 1 0.05
21 11 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TAATACTTAATATATTTTTTA
Found at i:48075257 original size:42 final size:42
Alignment explanation
Indices: 48075115--48075447 Score: 352
Period size: 43 Copynumber: 7.9 Consensus size: 42
48075105 TTTTAGAAAT
* * *
48075115 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTT-TCCAC
* *
48075158 AAATGCCGCTATAGATCAGGACCTTTAGCGGCGCATTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTTCCAC
** ** * *
48075201 AAACATCGCTATAGATCGGGACCATTAGCGGCGCTTTTTCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCAC
**
48075243 AAACGCCATTATAGATCAAGACCTTTAGCGGCGC-TTTCCGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCC-AC
* *
48075285 AAACGCCACTATA-ACTCAAGACCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTATAGA-TCAAGACCTTTAGCGGCGCTTTT-CCAC
* *
48075328 AAACGCCGCTATAGATCAAGACCTTTATCGGTGCTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTTCCAC
* * **
48075371 AAACGTCGCTAT-GTCTCAAGACCTTTAATGGCGCTTTTCCCAC
1 AAACGCCGCTATAG-ATCAAGACCTTTAGCGGCGCTTTT-CCAC
* *
48075414 AAACGCCGCTATAGAACAA-A-CTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
48075448 CTCGTTAAAC
Statistics
Matches: 245, Mismatches: 35, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
41 16 0.07
42 73 0.30
43 145 0.59
44 11 0.04
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCAC
Found at i:48075406 original size:170 final size:169
Alignment explanation
Indices: 48075115--48075447 Score: 420
Period size: 170 Copynumber: 2.0 Consensus size: 169
48075105 TTTTAGAAAT
* * * * *
48075115 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTACCCACAAATGCCGCTATAGATCAGGAC
1 AAACGCCACTATAGACCAAGACCTTTAGCGGCGCTTTACCCAAAAACGCCGCTATAGATCAAGAC
** * *
48075180 CTTTAGCGGCGCATTTTCCACAAACATCGCTATAGATCGGGACCATTAGCGGCGCTTTT-TCACA
66 CTTTAGCGGCGCATTTTCCACAAACATCGCTATAGATCAAGACCATTAACGGCGCTTTTCCCACA
* * *
48075244 AACGCCATTATAGATCAAGACCTTTAGCGGCGCTTTCCGAC
131 AACGCCACTATAGAACAA-A-CTTTAGCGACGCTTTCCGAC
*
48075285 AAACGCCACTATA-ACTCAAGACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAGATCAAGA
1 AAACGCCACTATAGAC-CAAGACCTTTAGCGGCGCTTTACCCAAAAACGCCGCTATAGATCAAGA
* * * * * * *
48075349 CCTTTATCGGTGCTTTTTCCACAAACGTCGCTAT-GTCTCAAGACCTTTAATGGCGCTTTTCCCA
65 CCTTTAGCGGCGCATTTTCCACAAACATCGCTATAG-ATCAAGACCATTAACGGCGCTTTTCCCA
*
48075413 CAAACGCCGCTATAGAACAAACTTTAGCGACGCTT
129 CAAACGCCACTATAGAACAAACTTTAGCGACGCTT
48075448 CTCGTTAAAC
Statistics
Matches: 139, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
169 16 0.12
170 104 0.75
171 19 0.14
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (169 bp):
AAACGCCACTATAGACCAAGACCTTTAGCGGCGCTTTACCCAAAAACGCCGCTATAGATCAAGAC
CTTTAGCGGCGCATTTTCCACAAACATCGCTATAGATCAAGACCATTAACGGCGCTTTTCCCACA
AACGCCACTATAGAACAAACTTTAGCGACGCTTTCCGAC
Found at i:48079200 original size:27 final size:27
Alignment explanation
Indices: 48079170--48079256 Score: 99
Period size: 27 Copynumber: 3.2 Consensus size: 27
48079160 CTTAAATAAT
48079170 TTAAACTATAATCATAATTTTAATATA
1 TTAAACTATAATCATAATTTTAATATA
* *
48079197 TTAAAAT-TAAT-ATTATCTCTTAA-ATAA
1 TTAAACTATAATCATAAT-T-TTAATAT-A
48079224 TTTAAACTATAATCATAATTTTAATATA
1 -TTAAACTATAATCATAATTTTAATATA
48079252 TTAAA
1 TTAAA
48079257 ATTAATATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
25 4 0.08
26 7 0.14
27 16 0.33
28 11 0.22
29 7 0.14
30 4 0.08
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (27 bp):
TTAAACTATAATCATAATTTTAATATA
Found at i:48079211 original size:55 final size:55
Alignment explanation
Indices: 48079152--48079272 Score: 242
Period size: 55 Copynumber: 2.2 Consensus size: 55
48079142 AAAATGGATT
48079152 TATTATCTCTTAAATAATTTAAACTATAATCATAATTTTAATATATTAAAATTAA
1 TATTATCTCTTAAATAATTTAAACTATAATCATAATTTTAATATATTAAAATTAA
48079207 TATTATCTCTTAAATAATTTAAACTATAATCATAATTTTAATATATTAAAATTAA
1 TATTATCTCTTAAATAATTTAAACTATAATCATAATTTTAATATATTAAAATTAA
48079262 TATTATCTCTT
1 TATTATCTCTT
48079273 TTACAATTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (55 bp):
TATTATCTCTTAAATAATTTAAACTATAATCATAATTTTAATATATTAAAATTAA
Found at i:48079228 original size:28 final size:28
Alignment explanation
Indices: 48079152--48079272 Score: 96
Period size: 27 Copynumber: 4.4 Consensus size: 28
48079142 AAAATGGATT
*
48079152 TATTATCTCTTAA-ATAATTTAAACTATAA
1 TATTATCTCTTAATAT-A-TTAAAATATAA
*
48079181 TCATAAT-T-TTAATATATTAAAAT-TAA
1 T-ATTATCTCTTAATATATTAAAATATAA
*
48079207 TATTATCTCTTAA-ATAATTTAAACTATAA
1 TATTATCTCTTAATAT-A-TTAAAATATAA
*
48079236 TCATAAT-T-TTAATATATTAAAAT-TAA
1 T-ATTATCTCTTAATATATTAAAATATAA
48079262 TATTATCTCTT
1 TATTATCTCTT
48079273 TTACAATTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
25 8 0.11
26 12 0.16
27 19 0.26
28 16 0.22
29 11 0.15
30 8 0.11
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (28 bp):
TATTATCTCTTAATATATTAAAATATAA
Found at i:48079514 original size:121 final size:126
Alignment explanation
Indices: 48079268--48079520 Score: 308
Period size: 130 Copynumber: 2.0 Consensus size: 126
48079258 TTAATATTAT
* *
48079268 CTCTTTTACAATTATATAAGAAATTATTTAATATATAAATTAAGAAACACCAATTAATCTAAACT
1 CTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAAAAAACACCAATTAATCTAAACT
* *
48079333 CTAAACCCCTACCCCCTACATCTTAAACCTTAAATCATAAAACATAAACCTTAAACCCCTAACCC
66 CTAAACCCCGACCCCCGACATCTTAAACCTTAAATCAT-AAACAT--A-CTTAAACCCCTAACCC
* * *
48079398 CTCTTTTACAATTATATAAGAACTTAATTAATATATAAATTAAAAAATACTAATTAATCTAAAC-
1 CTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAAAAAACACCAATTAATCTAAACT
48079462 CTTAAA-CCCGA-CCCCGA-ATCTCTAAATCC-TAAATCACT-AAC-T-CTT-AACCCCTAACCC
66 C-TAAACCCCGACCCCCGACATCT-TAAA-CCTTAAATCA-TAAACATACTTAAACCCCTAACCC
48079519 CT
1 CT
48079521 AACCACTAAC
Statistics
Matches: 112, Mismatches: 7, Indels: 17
0.82 0.05 0.12
Matches are distributed among these distances:
121 14 0.12
122 3 0.03
126 1 0.01
127 7 0.06
128 16 0.14
129 8 0.07
130 63 0.56
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (126 bp):
CTCTTTTACAATTATATAAGAAATTAATTAATATATAAATTAAAAAACACCAATTAATCTAAACT
CTAAACCCCGACCCCCGACATCTTAAACCTTAAATCATAAACATACTTAAACCCCTAACCC
Found at i:48079516 original size:7 final size:7
Alignment explanation
Indices: 48079506--48079536 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
48079496 CACTAACTCT
48079506 TAACCCC
1 TAACCCC
48079513 TAACCCC
1 TAACCCC
*
48079520 TAACCAC
1 TAACCCC
48079527 TAACCCC
1 TAACCCC
48079534 TAA
1 TAA
48079537 ACTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.35, C:0.48, G:0.00, T:0.16
Consensus pattern (7 bp):
TAACCCC
Found at i:48079523 original size:14 final size:14
Alignment explanation
Indices: 48079496--48079536 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
48079486 AATCCTAAAT
* *
48079496 CACTAACTCTTAAC
1 CACTAACCCCTAAC
*
48079510 CCCTAACCCCTAAC
1 CACTAACCCCTAAC
48079524 CACTAACCCCTAA
1 CACTAACCCCTAA
48079537 ACTTTATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (14 bp):
CACTAACCCCTAAC
Found at i:48079657 original size:126 final size:119
Alignment explanation
Indices: 48079425--48079663 Score: 293
Period size: 126 Copynumber: 1.9 Consensus size: 119
48079415 AAGAACTTAA
* * * *
48079425 TTAATATATAAATTAAAAAATACTAATTAATCTAAACCTTAAACCCGACCCCGAATCTCTAAATC
1 TTAATATATAAATAAAAAAATACTAATTAATCTAAACCCTAAACCCGACACCGAATCTATAAATC
* *
48079490 CTAAATCACTAACTCTTAACCCCTAACCCCTAACCACTAACCCCTAAACTTTAT
66 CTAAATCACTAACTCATAACCCCTAACCACTAACCACTAACCCCTAAACTTTAT
*
48079544 TTAATATATAAATCAAAAAAATACTAATTAATCTAAACCCTAAACCCTAACTTGACATCGAATCT
1 TTAATATATAAAT-AAAAAAATACTAATTAATCTAAACCCTAAA-CC---C--GACACCGAATCT
* * *
48079609 ATAAA-CCTTAAATTC-CTAACTCATAATCTCTAACCACTAACCCCTAACCCCTAAA
59 ATAAATCC-TAAA-TCACTAACTCATAACCCCTAACCACTAACCACTAACCCCTAAA
48079664 TCACAACCCT
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
119 13 0.13
120 28 0.28
121 2 0.02
124 1 0.01
125 2 0.02
126 53 0.52
127 2 0.02
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.28
Consensus pattern (119 bp):
TTAATATATAAATAAAAAAATACTAATTAATCTAAACCCTAAACCCGACACCGAATCTATAAATC
CTAAATCACTAACTCATAACCCCTAACCACTAACCACTAACCCCTAAACTTTAT
Found at i:48080238 original size:41 final size:41
Alignment explanation
Indices: 48080181--48080390 Score: 321
Period size: 41 Copynumber: 5.1 Consensus size: 41
48080171 CGCTAATGCT
* * * **
48080181 CTAAAAGCCTGAGCATTAGCGCCGCTTTTTCAAAATTGCCG
1 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
*
48080222 CTAAAAGCCTAAGCATTCGCGGCGCTTTTTTAAAAACGCCG
1 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
*
48080263 CTAAAAGCCTGAGCATTAGCGGCGCTTTTTTAAAAACGCCG
1 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
* *
48080304 CTAAAAGCCTAAGCATTAGCGGTGCTTTTTTAAAAACGCCA
1 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
* *
48080345 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTCAAAAACACCG
1 CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
48080386 CTAAA
1 CTAAA
48080391 GCCCCAAAAT
Statistics
Matches: 154, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 154 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (41 bp):
CTAAAAGCCTAAGCATTAGCGGCGCTTTTTTAAAAACGCCG
Found at i:48082948 original size:6 final size:6
Alignment explanation
Indices: 48082927--48082960 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
48082917 AAATAAAGAC
48082927 AATTAA AATTGCAA AATTAA AATTAA AATTAA AA
1 AATTAA AATT--AA AATTAA AATTAA AATTAA AA
48082961 ACTTTTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.77
8 6 0.23
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (6 bp):
AATTAA
Found at i:48089791 original size:15 final size:16
Alignment explanation
Indices: 48089771--48089800 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
48089761 GATTTGAAGA
48089771 ATGAGGGAT-ATTGAG
1 ATGAGGGATGATTGAG
48089786 ATGAGGGATGATTGA
1 ATGAGGGATGATTGA
48089801 AATGGAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.40, T:0.27
Consensus pattern (16 bp):
ATGAGGGATGATTGAG
Found at i:48091773 original size:63 final size:63
Alignment explanation
Indices: 48091695--48091835 Score: 178
Period size: 63 Copynumber: 2.3 Consensus size: 63
48091685 AATATCTCTC
** * * * *
48091695 ACACGGCCTGGACACACGTTCATGTCTCTGGCCTGTGTGACTCTAATTC-CAAAACAATGAGTT
1 ACACGGCCTGGACACACGACCATGTCCCTGGCCCGTGGGACACTAATTCAC-AAACAATGAGTT
* * *
48091758 ACATGGCCTGGACACACGACCGTGTCCCTGGCCCGTGGGACACTAATTCACAAACAGTGAGTT
1 ACACGGCCTGGACACACGACCATGTCCCTGGCCCGTGGGACACTAATTCACAAACAATGAGTT
48091821 ACACGGCCTGG-CACA
1 ACACGGCCTGGACACA
48091836 TGGTTATGTG
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
62 4 0.06
63 62 0.93
64 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (63 bp):
ACACGGCCTGGACACACGACCATGTCCCTGGCCCGTGGGACACTAATTCACAAACAATGAGTT
Found at i:48092351 original size:14 final size:14
Alignment explanation
Indices: 48092332--48092378 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
48092322 TGTGAAAACC
48092332 AAAAAGAATAAGAG
1 AAAAAGAATAAGAG
48092346 AAAAAGAAT-A-A-
1 AAAAAGAATAAGAG
*
48092357 TAAAAGAATAAGAG
1 AAAAAGAATAAGAG
48092371 AAAAAGAA
1 AAAAAGAA
48092379 CGAACGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 8 0.29
12 2 0.07
13 2 0.07
14 16 0.57
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAAAGAATAAGAG
Found at i:48092763 original size:4 final size:4
Alignment explanation
Indices: 48092754--48092874 Score: 228
Period size: 4 Copynumber: 30.8 Consensus size: 4
48092744 TGGGCGTTAC
48092754 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
48092802 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
48092850 AGAT AGAT AGAT AGAT --AT AGAT AGA
1 AGAT AGAT AGAT AGAT AGAT AGAT AGA
48092875 ATGCCTAAAC
Statistics
Matches: 115, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.02
4 113 0.98
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:48093492 original size:28 final size:28
Alignment explanation
Indices: 48093452--48093509 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
48093442 CAAATCAAAA
48093452 GTAGTTTAAATACTTGAGATTTGTATAG
1 GTAGTTTAAATACTTGAGATTTGTATAG
48093480 GTAGTTTAAATACTTGAGATTTGTATAG
1 GTAGTTTAAATACTTGAGATTTGTATAG
48093508 GT
1 GT
48093510 TTTATACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.43
Consensus pattern (28 bp):
GTAGTTTAAATACTTGAGATTTGTATAG
Found at i:48093516 original size:24 final size:26
Alignment explanation
Indices: 48093460--48093517 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
48093450 AAGTAGTTTA
48093460 AATACTTGAGATTTGTATAGGTAGTTT
1 AATACTTGAGATTTGTATAGGTA-TTT
48093487 AAATACTTGAGATTTGTATAGGT-TTT
1 -AATACTTGAGATTTGTATAGGTATTT
48093513 -ATACT
1 AATACT
48093518 AAGAGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.17
26 3 0.10
28 22 0.73
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (26 bp):
AATACTTGAGATTTGTATAGGTATTT
Found at i:48099368 original size:17 final size:17
Alignment explanation
Indices: 48099345--48099386 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
48099335 TAAGTAAAAT
*
48099345 AAAATAAAGCAAAGTAA
1 AAAATAAAGCAAAGAAA
* *
48099362 TAAATAAAGTAAAGAAA
1 AAAATAAAGCAAAGAAA
48099379 AAAATAAA
1 AAAATAAA
48099387 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14
Consensus pattern (17 bp):
AAAATAAAGCAAAGAAA
Found at i:48105783 original size:44 final size:44
Alignment explanation
Indices: 48105720--48105805 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
48105710 CCTATCCGTG
*
48105720 AACACCTTATCCTGAACCGGTCTGGATTGTGAGGTCGAGAGATA
1 AACACCTTATCCTGAACCGGTCTGGACTGTGAGGTCGAGAGATA
48105764 AACACCTTA-CCTTGAACCGGTCTGGACTGTGAGGTCGAGAGA
1 AACACCTTATCC-TGAACCGGTCTGGACTGTGAGGTCGAGAGA
48105806 AAAATAGTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 2 0.05
44 38 0.95
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (44 bp):
AACACCTTATCCTGAACCGGTCTGGACTGTGAGGTCGAGAGATA
Done.