Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 120 of 203
Found at i:38019124 original size:17 final size:17
Alignment explanation
Indices: 38019099--38019132 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38019089 CCCTCTATCA
38019099 TTTTATTTATTCTCTTT
1 TTTTATTTATTCTCTTT
* *
38019116 TTTTTTTTATTTTCTTT
1 TTTTATTTATTCTCTTT
38019133 ACACCATATT
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:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTATTTATTCTCTTT
Found at i:38024024 original size:46 final size:46
Alignment explanation
Indices: 38023924--38024058 Score: 155
Period size: 46 Copynumber: 2.9 Consensus size: 46
38023914 AATATTCTTG
* * * ** *
38023924 TATTCTCGAGTCTACAACATATGCAGGAGCTTGGAACCTAAACCTA
1 TATTCTCGAGTCTGCAACATATGCAGGAGCTCGAAACCTATTCCCA
* * *
38023970 TATGCTCGAGTCTGCAACATATGTAGGAGCTCGAAACCTATTCCCC
1 TATTCTCGAGTCTGCAACATATGCAGGAGCTCGAAACCTATTCCCA
* *
38024016 TATTCTCGAGT-TCGGAACATATGCAGGAGCTCAAAACCTATTC
1 TATTCTCGAGTCT-GCAACATATGCAGGAGCTCGAAACCTATTC
38024059 ATGTATTCTT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
45 1 0.01
46 74 0.99
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (46 bp):
TATTCTCGAGTCTGCAACATATGCAGGAGCTCGAAACCTATTCCCA
Found at i:38024066 original size:46 final size:45
Alignment explanation
Indices: 38023916--38024072 Score: 138
Period size: 46 Copynumber: 3.4 Consensus size: 45
38023906 CAGGGCTTAA
* * *
38023916 TATTCTTGTATTCTCGAGTCTAC-AACATATGCAGGAGCTTGGAACC
1 TATTCCTGTATTCTCGAGT-T-CGAACATATGCAGGAGCTCGAAACC
** * * *
38023962 TAAACCTATATGCTCGAG-TCTGCAACATATGTAGGAGCTCGAAACC
1 TATTCCTGTATTCTCGAGTTC-G-AACATATGCAGGAGCTCGAAACC
** *
38024008 TATTCCCCTATTCTCGAGTTCGGAACATATGCAGGAGCTCAAAACC
1 TATTCCTGTATTCTCGAGTTC-GAACATATGCAGGAGCTCGAAACC
* *
38024054 TATTCATGTATTCTTGAGT
1 TATTCCTGTATTCTCGAGT
38024073 CCATAACATA
Statistics
Matches: 87, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
43 1 0.01
44 1 0.01
46 82 0.94
47 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (45 bp):
TATTCCTGTATTCTCGAGTTCGAACATATGCAGGAGCTCGAAACC
Found at i:38036019 original size:10 final size:10
Alignment explanation
Indices: 38036004--38036038 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
38035994 CATTAAATTT
38036004 AAATGAAAGC
1 AAATGAAAGC
*
38036014 AAATGAAAGT
1 AAATGAAAGC
38036024 AAATGAAAGC
1 AAATGAAAGC
38036034 AAATG
1 AAATG
38036039 TAGAACCTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.60, C:0.06, G:0.20, T:0.14
Consensus pattern (10 bp):
AAATGAAAGC
Found at i:38036667 original size:54 final size:54
Alignment explanation
Indices: 38036599--38036882 Score: 351
Period size: 54 Copynumber: 5.3 Consensus size: 54
38036589 CATCTCCTAA
* *
38036599 GGGTAATTCGGTCATTTTATCCTGTGGGGGTAATTCGGTCATTTTACCCTGTGG
1 GGGTAATTCGGTCATTTTACCCTGTGAGGGTAATTCGGTCATTTTACCCTGTGG
* ** * *
38036653 GGGTAATTCTGTCATTTTACCCTGTGAGGGTAATTTAGTCATTTTACCCTATAG
1 GGGTAATTCGGTCATTTTACCCTGTGAGGGTAATTCGGTCATTTTACCCTGTGG
** * *
38036707 GGGTAATTCGGTCATTTTACCCTGTGAGGGTAATTCTATCATTTTACCTTGTAG
1 GGGTAATTCGGTCATTTTACCCTGTGAGGGTAATTCGGTCATTTTACCCTGTGG
* * **
38036761 GGGTAATTCAGTCATTTTACCCTGTTAGGGTAATTTTGTCATTTTA-CCTAGTGG
1 GGGTAATTCGGTCATTTTACCCTGTGAGGGTAATTCGGTCATTTTACCCT-GTGG
* * * *
38036815 GGGTAATTCAGTCA--TTACACTGTG-GGGTAATTCGGTTATTTTACCTTGTGG
1 GGGTAATTCGGTCATTTTACCCTGTGAGGGTAATTCGGTCATTTTACCCTGTGG
*
38036866 AGGTAATTCGGTCATTT
1 GGGTAATTCGGTCATTT
38036883 ATTGACCTCT
Statistics
Matches: 199, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
51 32 0.16
52 10 0.05
53 3 0.02
54 154 0.77
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.40
Consensus pattern (54 bp):
GGGTAATTCGGTCATTTTACCCTGTGAGGGTAATTCGGTCATTTTACCCTGTGG
Found at i:38036717 original size:81 final size:81
Alignment explanation
Indices: 38036598--38036882 Score: 350
Period size: 81 Copynumber: 3.6 Consensus size: 81
38036588 TCATCTCCTA
* * *
38036598 AGGGTAATTCGGTCATTTTATCCTGTGGGGGTAATTCGGTCATTTTACCCTGTGGGGGTAATTCT
1 AGGGTAATTCAGTCATTTTACCCTGTAGGGGTAATTCGGTCATTTTACCCTGTGGGGGTAATTCT
38036663 GTCATTTTACCCTGTG
66 GTCATTTTACCCTGTG
* * *
38036679 AGGGTAATTTAGTCATTTTACCCTATAGGGGTAATTCGGTCATTTTACCCTGTGAGGGTAATTCT
1 AGGGTAATTCAGTCATTTTACCCTGTAGGGGTAATTCGGTCATTTTACCCTGTGGGGGTAATTCT
* *
38036744 ATCATTTTACCTTGT-
66 GTCATTTTACCCTGTG
**
38036759 AGGGGTAATTCAGTCATTTTACCCTGTTA-GGGTAATTTTGTCATTTTA-CCTAGTGGGGGTAAT
1 A-GGGTAATTCAGTCATTTTACCCTG-TAGGGGTAATTCGGTCATTTTACCCT-GTGGGGGTAAT
* *
38036822 TCAGTCA--TTACACTGTG
63 TCTGTCATTTTACCCTGTG
* * *
38036839 -GGGTAATTCGGTTATTTTACCTTGT-GGAGGTAATTCGGTCATTT
1 AGGGTAATTCAGTCATTTTACCCTGTAGG-GGTAATTCGGTCATTT
38036883 ATTGACCTCT
Statistics
Matches: 176, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
77 2 0.01
78 35 0.20
79 7 0.04
80 4 0.02
81 126 0.72
82 2 0.01
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.40
Consensus pattern (81 bp):
AGGGTAATTCAGTCATTTTACCCTGTAGGGGTAATTCGGTCATTTTACCCTGTGGGGGTAATTCT
GTCATTTTACCCTGTG
Found at i:38036805 original size:27 final size:27
Alignment explanation
Indices: 38036598--38036882 Score: 314
Period size: 27 Copynumber: 10.7 Consensus size: 27
38036588 TCATCTCCTA
*
38036598 AGGGTAATTCGGTCATTTTATCCTGTG
1 AGGGTAATTCGGTCATTTTACCCTGTG
*
38036625 GGGGTAATTCGGTCATTTTACCCTGTG
1 AGGGTAATTCGGTCATTTTACCCTGTG
* *
38036652 GGGGTAATTCTGTCATTTTACCCTGTG
1 AGGGTAATTCGGTCATTTTACCCTGTG
** *
38036679 AGGGTAATTTAGTCATTTTACCCTAT-
1 AGGGTAATTCGGTCATTTTACCCTGTG
38036705 AGGGGTAATTCGGTCATTTTACCCTGTG
1 A-GGGTAATTCGGTCATTTTACCCTGTG
** *
38036733 AGGGTAATTCTATCATTTTACCTTGT-
1 AGGGTAATTCGGTCATTTTACCCTGTG
* *
38036759 AGGGGTAATTCAGTCATTTTACCCTGTT
1 A-GGGTAATTCGGTCATTTTACCCTGTG
**
38036787 AGGGTAATTTTGTCATTTTA-CCTAGTG
1 AGGGTAATTCGGTCATTTTACCCT-GTG
* * *
38036814 GGGGTAATTCAGTCA--TTACACTGTG
1 AGGGTAATTCGGTCATTTTACCCTGTG
* *
38036839 -GGGTAATTCGGTTATTTTACCTTGTG
1 AGGGTAATTCGGTCATTTTACCCTGTG
38036865 -GAGGTAATTCGGTCATTT
1 AG-GGTAATTCGGTCATTT
38036883 ATTGACCTCT
Statistics
Matches: 221, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.05
25 6 0.03
26 16 0.07
27 185 0.84
28 2 0.01
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.40
Consensus pattern (27 bp):
AGGGTAATTCGGTCATTTTACCCTGTG
Found at i:38044655 original size:19 final size:19
Alignment explanation
Indices: 38044633--38044673 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
38044623 ATTGCATTTC
38044633 ATTCA-TTACATTTAGGTTA
1 ATTCATTTACATTTA-GTTA
*
38044652 ATTCATTTGCATTTAGTTA
1 ATTCATTTACATTTAGTTA
38044671 ATT
1 ATT
38044674 ATATTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (19 bp):
ATTCATTTACATTTAGTTA
Found at i:38049984 original size:112 final size:112
Alignment explanation
Indices: 38049787--38050010 Score: 448
Period size: 112 Copynumber: 2.0 Consensus size: 112
38049777 TTTTGGACAA
38049787 TAATTTTACCGAAACTACATGAATTTGAGTTAAAAAGAGCATGAAAAAGTGTGTATATTTTCGTG
1 TAATTTTACCGAAACTACATGAATTTGAGTTAAAAAGAGCATGAAAAAGTGTGTATATTTTCGTG
38049852 TTTCCAATAGGTTAGGTACTTTACAATTCTATCGTCGACTCAACATC
66 TTTCCAATAGGTTAGGTACTTTACAATTCTATCGTCGACTCAACATC
38049899 TAATTTTACCGAAACTACATGAATTTGAGTTAAAAAGAGCATGAAAAAGTGTGTATATTTTCGTG
1 TAATTTTACCGAAACTACATGAATTTGAGTTAAAAAGAGCATGAAAAAGTGTGTATATTTTCGTG
38049964 TTTCCAATAGGTTAGGTACTTTACAATTCTATCGTCGACTCAACATC
66 TTTCCAATAGGTTAGGTACTTTACAATTCTATCGTCGACTCAACATC
38050011 CAGAGACAAT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (112 bp):
TAATTTTACCGAAACTACATGAATTTGAGTTAAAAAGAGCATGAAAAAGTGTGTATATTTTCGTG
TTTCCAATAGGTTAGGTACTTTACAATTCTATCGTCGACTCAACATC
Found at i:38054197 original size:27 final size:27
Alignment explanation
Indices: 38054130--38054203 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
38054120 TGAAGTCAAT
* *
38054130 GACAGTAAACAT-GAGGTAGTCCGTCGG
1 GACAGTAAACATAG-GGTAGTCCATCAG
* *
38054157 GAAAGTAAAAATAGGGTAGTCCATCAG
1 GACAGTAAACATAGGGTAGTCCATCAG
*
38054184 GACAGTTAACATAGGGTAGT
1 GACAGTAAACATAGGGTAGT
38054204 TCGCTGGGAC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (27 bp):
GACAGTAAACATAGGGTAGTCCATCAG
Found at i:38063325 original size:151 final size:151
Alignment explanation
Indices: 38063051--38063352 Score: 595
Period size: 151 Copynumber: 2.0 Consensus size: 151
38063041 AGACCATCTG
38063051 AAAATACGGGCAATGCTAGTGGTGGTCAGAGAGGATCTAGAGATGCTACGAACAGATCTGAGGCT
1 AAAATACGGGCAATGCTAGTGGTGGTCAGAGAGGATCTAGAGATGCTACGAACAGATCTGAGGCT
38063116 CGTGCGCCTGCTAGAGCTTATGCTATACGTGCCCGTGAGGATGCTTCTTCGCCTGATGTTATTAC
66 CGTGCGCCTGCTAGAGCTTATGCTATACGTGCCCGTGAGGATGCTTCTTCGCCTGATGTTATTAC
38063181 CGGTACTTTTACTCTCTTGGA
131 CGGTACTTTTACTCTCTTGGA
*
38063202 AAAATACGGGCAATGCTGGTGGTGGTCAGAGAGGATCTAGAGATGCTACGAACAGATCTGAGGCT
1 AAAATACGGGCAATGCTAGTGGTGGTCAGAGAGGATCTAGAGATGCTACGAACAGATCTGAGGCT
38063267 CGTGCGCCTGCTAGAGCTTATGCTATACGTGCCCGTGAGGATGCTTCTTCGCCTGATGTTATTAC
66 CGTGCGCCTGCTAGAGCTTATGCTATACGTGCCCGTGAGGATGCTTCTTCGCCTGATGTTATTAC
38063332 CGGTACTTTTACTCTCTTGGA
131 CGGTACTTTTACTCTCTTGGA
38063353 TACTAATGTA
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 150 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (151 bp):
AAAATACGGGCAATGCTAGTGGTGGTCAGAGAGGATCTAGAGATGCTACGAACAGATCTGAGGCT
CGTGCGCCTGCTAGAGCTTATGCTATACGTGCCCGTGAGGATGCTTCTTCGCCTGATGTTATTAC
CGGTACTTTTACTCTCTTGGA
Found at i:38066727 original size:40 final size:40
Alignment explanation
Indices: 38066578--38066720 Score: 157
Period size: 40 Copynumber: 3.6 Consensus size: 40
38066568 AATGATGTCT
* * * *
38066578 GGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAATCC
* *
38066618 GGACTAAGAT-CTGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCC
* *
38066658 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCC
*
38066698 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
38066721 AACGAGTAGC
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 75 0.86
41 11 0.13
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:38068079 original size:96 final size:95
Alignment explanation
Indices: 38067907--38068105 Score: 276
Period size: 96 Copynumber: 2.1 Consensus size: 95
38067897 AAAAATATGT
*
38067907 AGATTGG-AATATGAGTCTAGTTTCAGGGAAAAATTACGAAACTGATTTTCAAGTTGTGAAACTC
1 AGATTGGCAATATGAGTCTAGTTTCAGGGAAAAATTACGAAACTGATTTCCAAGTTGTGAAACTC
38067971 AAGATATGATTTTTAAAGCGACTAGTACGC
66 AAGATATGATTTTTAAAGCGACTAGTACGC
* * * * **
38068001 AGATTGGCATATATGAGTCTAGTTTCAGGGAAAATTTACGGAACTGGA-TTCCGAGTTTTTTAAC
1 AGATTGGCA-ATATGAGTCTAGTTTCAGGGAAAAATTACGAAACT-GATTTCCAAGTTGTGAAAC
* * *
38068065 TCAAGATATTATTTTTTAAGCGACTAGTATGC
64 TCAAGATATGATTTTTAAAGCGACTAGTACGC
38068097 AGATTGGCA
1 AGATTGGCA
38068106 GTGTCTGGGA
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
94 7 0.08
95 1 0.01
96 82 0.89
97 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (95 bp):
AGATTGGCAATATGAGTCTAGTTTCAGGGAAAAATTACGAAACTGATTTCCAAGTTGTGAAACTC
AAGATATGATTTTTAAAGCGACTAGTACGC
Found at i:38072405 original size:18 final size:21
Alignment explanation
Indices: 38072362--38072406 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
38072352 ACTCGCAATA
38072362 TCTTTTTGCTCTTTTTCATTC
1 TCTTTTTGCTCTTTTTCATTC
*
38072383 TCTTTTT-CT-TTTTTGATT-
1 TCTTTTTGCTCTTTTTCATTC
38072401 TCTTTT
1 TCTTTT
38072407 CTGTCTTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 8 0.35
20 2 0.09
21 7 0.30
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.73
Consensus pattern (21 bp):
TCTTTTTGCTCTTTTTCATTC
Found at i:38089669 original size:10 final size:10
Alignment explanation
Indices: 38089654--38089678 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38089644 TTAAATCAAG
38089654 AAAAAAACCA
1 AAAAAAACCA
38089664 AAAAAAACCA
1 AAAAAAACCA
38089674 AAAAA
1 AAAAA
38089679 TAAAGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACCA
Found at i:38090135 original size:42 final size:42
Alignment explanation
Indices: 38090086--38090472 Score: 444
Period size: 42 Copynumber: 9.2 Consensus size: 42
38090076 AGGAAAGCAA
** *
38090086 TCATTGCATTTAGAAGCTTAGGTGTGGAGGTCCATTAACTTT
1 TCATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTT
* * * *
38090128 TTATTGCATTTA-AAGGCCCATGTGTGGAGGTCTATTCACTTT
1 TCATTGCATTTAGAA-GCCCAGGTGTGGAGGTCCATTTACTTT
* *
38090170 TCATTGCATTTAG-AGTCCCAGGTGTGGAGGTCCATTCATTTT
1 TCATTGCATTTAGAAG-CCCAGGTGTGGAGGTCCATTTACTTT
* * * *
38090212 TCATTGCATTTAGGAA-CCTAAGTGTGGAGGTCCATTAAC-TG
1 TCATTGCATTTA-GAAGCCCAGGTGTGGAGGTCCATTTACTTT
* * * *
38090253 TCATTGCATTTAGAGGCCCAAGTGTAGAGGTCCATTCACTTT
1 TCATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTT
* *
38090295 TCATTGCAGTTAGAAGCCCAAGTGTGGAGGTCCATTTACTTT
1 TCATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTT
* *
38090337 TCATTGCATTTAG-AGACCCAGGTCTGAAGGTCCATTTACTTT
1 TCATTGCATTTAGAAG-CCCAGGTGTGGAGGTCCATTTACTTT
* * *
38090379 TCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTATTTT
1 TCATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTT
* * *
38090421 TCATTACATTTA-AAGGCACAGGTGTGGAGGTCCATTTACTCT
1 TCATTGCATTTAGAA-GCCCAGGTGTGGAGGTCCATTTACTTT
38090463 TCATTGCATT
1 TCATTGCATT
38090473 GTATATGAAG
Statistics
Matches: 295, Mismatches: 40, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
40 2 0.01
41 39 0.13
42 251 0.85
43 2 0.01
44 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.36
Consensus pattern (42 bp):
TCATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTT
Found at i:38090448 original size:209 final size:210
Alignment explanation
Indices: 38090086--38090472 Score: 546
Period size: 209 Copynumber: 1.8 Consensus size: 210
38090076 AGGAAAGCAA
* ** * * * *
38090086 TCATTGCATTTAGAAGCTTAGGTGTGGAGGTCCATTAACTTTTTATTGCATTTAAAGGCCCATGT
1 TCATTGCAGTTAGAAGCCCAAGTGTGGAGGTCCATTAACTTTTCATTGCATTTAAAGACCCAGGT
* * * *
38090151 GTGGAGGTCTATTCACTTTTCATTGCATTTAGAGTCCCAGGTGTGGAGGTCCATTCATTTTTCAT
66 CTGAAGGTCCATTCACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTCATTTTTCAT
*
38090216 TGCATTTAGGAACCTAAGTGTGGAGGTCCATTAACT-GTCATTGCATTTAGAGGCCCAAGTGTAG
131 TACATTTAGGAACCTAAGTGTGGAGGTCCATTAACTCGTCATTGCATTTAGAGGCCCAAGTGTAG
38090280 AGGTCCATTCACTTT
196 AGGTCCATTCACTTT
* *
38090295 TCATTGCAGTTAGAAGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGACCCAGGT
1 TCATTGCAGTTAGAAGCCCAAGTGTGGAGGTCCATTAACTTTTCATTGCATTTAAAGACCCAGGT
* * *
38090360 CTGAAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTATTTTTCAT
66 CTGAAGGTCCATTCACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTCATTTTTCAT
* * * *
38090425 TACATTTAAAGGCA-C-AGGTGTGGAGGTCCATTTACTCTTCATTGCATT
131 TACATTT--AGGAACCTAAGTGTGGAGGTCCATTAACTCGTCATTGCATT
38090473 GTATATGAAG
Statistics
Matches: 154, Mismatches: 21, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
209 139 0.90
210 11 0.07
211 4 0.03
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.36
Consensus pattern (210 bp):
TCATTGCAGTTAGAAGCCCAAGTGTGGAGGTCCATTAACTTTTCATTGCATTTAAAGACCCAGGT
CTGAAGGTCCATTCACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTCATTTTTCAT
TACATTTAGGAACCTAAGTGTGGAGGTCCATTAACTCGTCATTGCATTTAGAGGCCCAAGTGTAG
AGGTCCATTCACTTT
Found at i:38090951 original size:19 final size:18
Alignment explanation
Indices: 38090924--38090963 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
38090914 TATCATCACT
38090924 AATACTATTATTATTATGA
1 AATACTATTATTATTAT-A
*
38090943 AATATTATTATTATTATA
1 AATACTATTATTATTATA
38090961 AAT
1 AAT
38090964 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
AATACTATTATTATTATA
Found at i:38101692 original size:43 final size:43
Alignment explanation
Indices: 38101627--38101952 Score: 304
Period size: 43 Copynumber: 7.6 Consensus size: 43
38101617 TCAAACGTTT
* * *
38101627 GCGGCGTTTATTTCTAA-AAACGCCGCTATAGGTCATGACCTTTA
1 GCGGCGCTT-TTTC-AACAAACGCCGCTATAGATCAGGACCTTTA
* * *
38101671 GCGGCGCTTATACAACAAACGCCGCTATAGATCGGGACCTTTA
1 GCGGCGCTTTTTCAACAAACGCCGCTATAGATCAGGACCTTTA
* * *
38101714 GCGGCGCTTTTTCAACAAACGACACTGTAGATCAGGACCTTTA
1 GCGGCGCTTTTTCAACAAACGCCGCTATAGATCAGGACCTTTA
* * *
38101757 GCGGTGCTTTTTC-ACAAACACCACTATAGATC-GGAACCTTTA
1 GCGGCGCTTTTTCAACAAACGCCGCTATAGATCAGG-ACCTTTA
* * *
38101799 GCGGCGCTTTTTACAA-AAACGCCGCTATAGCTCAAGATCTTTA
1 GCGGCGCTTTTT-CAACAAACGCCGCTATAGATCAGGACCTTTA
* * * * * * * *
38101842 GCAGCG-ATTTCCCACAAATGCTGCTATAAATCAAGACCTTTA
1 GCGGCGCTTTTTCAACAAACGCCGCTATAGATCAGGACCTTTA
* * * * *
38101884 GCGGCGCATTTTCCACAAACGCCACTATAGATCA-AACCTTTG
1 GCGGCGCTTTTTCAACAAACGCCGCTATAGATCAGGACCTTTA
* *
38101926 GCGACGCTTTTTCCACAAACGCCGCTA
1 GCGGCGCTTTTTCAACAAACGCCGCTA
38101953 AAAACATATC
Statistics
Matches: 233, Mismatches: 42, Indels: 16
0.80 0.14 0.05
Matches are distributed among these distances:
41 4 0.02
42 96 0.41
43 123 0.53
44 10 0.04
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (43 bp):
GCGGCGCTTTTTCAACAAACGCCGCTATAGATCAGGACCTTTA
Found at i:38101790 original size:85 final size:84
Alignment explanation
Indices: 38101627--38101952 Score: 314
Period size: 85 Copynumber: 3.8 Consensus size: 84
38101617 TCAAACGTTT
* * * * *
38101627 GCGGCGTTTATTTCTAA-AAACGCCGCTATAGGTCATGACCTTTAGCGGCGCTTATACAACAAAC
1 GCGGCGCTT-TTTC-AACAAACGCCACTATAGATCA-GACCTTTAGCGGCGCTTTTTC-ACAAAC
38101691 GCCGCTATAGATCGGGACCTTTA
62 GCCGCTATAGATCGGGACCTTTA
* * * *
38101714 GCGGCGCTTTTTCAACAAACGACACTGTAGATCAGGACCTTTAGCGGTGCTTTTTCACAAACACC
1 GCGGCGCTTTTTCAACAAACGCCACTATAGATCA-GACCTTTAGCGGCGCTTTTTCACAAACGCC
* *
38101779 ACTATAGATCGGAACCTTTA
65 GCTATAGATCGGGACCTTTA
* * * * * ** *
38101799 GCGGCGCTTTTTACAA-AAACGCCGCTATAGCTCAAGATCTTTAGCAGCGATTTCCCACAAATGC
1 GCGGCGCTTTTT-CAACAAACGCCACTATAGATC-AGACCTTTAGCGGCGCTTTTTCACAAACGC
* * **
38101863 TGCTATAAATCAAGACCTTTA
64 CGCTATAGATCGGGACCTTTA
* * * * *
38101884 GCGGCGCATTTTCCACAAACGCCACTATAGATCAAACCTTTGGCGACGCTTTTTCCACAAACGCC
1 GCGGCGCTTTTTCAACAAACGCCACTATAGATCAGACCTTTAGCGGCGCTTTTT-CACAAACGCC
38101949 GCTA
65 GCTA
38101953 AAAACATATC
Statistics
Matches: 190, Mismatches: 44, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
84 15 0.08
85 127 0.67
86 40 0.21
87 8 0.04
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (84 bp):
GCGGCGCTTTTTCAACAAACGCCACTATAGATCAGACCTTTAGCGGCGCTTTTTCACAAACGCCG
CTATAGATCGGGACCTTTA
Found at i:38104228 original size:24 final size:24
Alignment explanation
Indices: 38104200--38104249 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
38104190 GCTTTACCTA
38104200 TACATATAAATTCAAGCATCAAAT
1 TACATATAAATTCAAGCATCAAAT
38104224 TACATATAAATTCAAGCATCAAAT
1 TACATATAAATTCAAGCATCAAAT
38104248 TA
1 TA
38104250 GACTCGTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (24 bp):
TACATATAAATTCAAGCATCAAAT
Found at i:38106024 original size:49 final size:49
Alignment explanation
Indices: 38105971--38106123 Score: 114
Period size: 49 Copynumber: 3.1 Consensus size: 49
38105961 TAAAAATTTT
38105971 TTATTTTGTTTTTTATAAATTGATTTAATTTTTGAAATGCCGCAAAAAA
1 TTATTTTGTTTTTTATAAATTGATTTAATTTTTGAAATGCCGCAAAAAA
** ** * * ***** *** * *
38106020 TTATTTCATTTTGAACAAAATGA-CGCCGTTTTCCTATG--GTAAAAATTTT
1 TTATTTTGTTTTTTATAAATTGATTTAATTTTTGAAATGCCGCAAAAA---A
38106069 TTATTTTGTTTTTTATAAATTGATTTAATTTTTGAAATGCCGCAAAAAA
1 TTATTTTGTTTTTTATAAATTGATTTAATTTTTGAAATGCCGCAAAAAA
38106118 TTATTT
1 TTATTT
38106124 CATTTTGAAC
Statistics
Matches: 66, Mismatches: 32, Indels: 12
0.60 0.29 0.11
Matches are distributed among these distances:
46 6 0.09
48 7 0.11
49 40 0.61
50 7 0.11
52 6 0.09
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.48
Consensus pattern (49 bp):
TTATTTTGTTTTTTATAAATTGATTTAATTTTTGAAATGCCGCAAAAAA
Found at i:38106025 original size:98 final size:98
Alignment explanation
Indices: 38105911--38106198 Score: 472
Period size: 98 Copynumber: 2.9 Consensus size: 98
38105901 TGAGAAAAAC
*
38105911 GCCGTAAAAAATTATTTCATTTTGAACAAAATGACGCCGTTTTCCTATGGTAAAAATTTTTTATT
1 GCCGCAAAAAATTATTTCATTTTGAACAAAATGACGCCGTTTTCCTATGGTAAAAATTTTTTATT
38105976 TTGTTTTTTATAAATTGATTTAATTTTTGAAAT
66 TTGTTTTTTATAAATTGATTTAATTTTTGAAAT
38106009 GCCGCAAAAAATTATTTCATTTTGAACAAAATGACGCCGTTTTCCTATGGTAAAAATTTTTTATT
1 GCCGCAAAAAATTATTTCATTTTGAACAAAATGACGCCGTTTTCCTATGGTAAAAATTTTTTATT
38106074 TTGTTTTTTATAAATTGATTTAATTTTTGAAAT
66 TTGTTTTTTATAAATTGATTTAATTTTTGAAAT
* * * ****
38106107 GCCGCAAAAAATTATTTCATTTTGAACAAAATGACACCGTTCTTCTTAT--CAAAAAAAAATTAT
1 GCCGCAAAAAATTATTTCATTTTGAACAAAATGACGCCGTT-TTCCTATGGTAAAAATTTTTTAT
*
38106170 TTTGTTTTTTATAAATTGATTTATTTTTT
65 TTTGTTTTTTATAAATTGATTTAATTTTT
38106199 ACGGTGTTTT
Statistics
Matches: 180, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
97 37 0.21
98 137 0.76
99 6 0.03
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (98 bp):
GCCGCAAAAAATTATTTCATTTTGAACAAAATGACGCCGTTTTCCTATGGTAAAAATTTTTTATT
TTGTTTTTTATAAATTGATTTAATTTTTGAAAT
Found at i:38106419 original size:98 final size:98
Alignment explanation
Indices: 38106250--38106426 Score: 282
Period size: 98 Copynumber: 1.8 Consensus size: 98
38106240 CGGCTTTTTT
*** ***
38106250 AAAATTATTTCATTTTGAACAAAATGACGCCGTTTTCCTATGGTAAAAATTTTTTATTTTGTTTT
1 AAAATTATTTCATTTTGAACAAAATGACGCCGTTTTCCTACACTAAAAAAAATTTATTTTGTTTT
38106315 TTATAAATTGATTTAATTTTTGAAATGCCGCAA
66 TTATAAATTGATTTAATTTTTGAAATGCCGCAA
* *
38106348 AAAATTATTTCATTTTGAACAAAATGACGTCGTTTTGCTACACTAAAAAAAATTTATTTTGTTTT
1 AAAATTATTTCATTTTGAACAAAATGACGCCGTTTTCCTACACTAAAAAAAATTTATTTTGTTTT
38106413 TTATAAATTGATTT
66 TTATAAATTGATTT
38106427 TTTATAAAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 71 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (98 bp):
AAAATTATTTCATTTTGAACAAAATGACGCCGTTTTCCTACACTAAAAAAAATTTATTTTGTTTT
TTATAAATTGATTTAATTTTTGAAATGCCGCAA
Found at i:38106905 original size:15 final size:15
Alignment explanation
Indices: 38106885--38107009 Score: 66
Period size: 14 Copynumber: 8.7 Consensus size: 15
38106875 TTAACCCGAC
38106885 CCTTAAATCCCTAAA
1 CCTTAAATCCCTAAA
38106900 CCTTAAATCCCT-AA
1 CCTTAAATCCCTAAA
* * *
38106914 CTTTTAACCCCT-AA
1 CCTTAAATCCCTAAA
* *
38106928 CGTCT-AACCCCTAAA
1 CCT-TAAATCCCTAAA
* *
38106943 CCCCT-AACCCCTAAA
1 -CCTTAAATCCCTAAA
* *
38106958 CCTTAAATCTC-AAC
1 CCTTAAATCCCTAAA
* *
38106972 CCTTAAA-CCATAAT
1 CCTTAAATCCCTAAA
* *
38106986 CCTT-AATCCATAAT
1 CCTTAAATCCCTAAA
38107000 CCTTAAATCC
1 CCTTAAATCC
38107010 ATACTCCCTA
Statistics
Matches: 90, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
13 3 0.03
14 51 0.57
15 35 0.39
16 1 0.01
ACGTcount: A:0.35, C:0.37, G:0.01, T:0.27
Consensus pattern (15 bp):
CCTTAAATCCCTAAA
Found at i:38106928 original size:7 final size:7
Alignment explanation
Indices: 38106918--38106956 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
38106908 CCCTAACTTT
38106918 TAACCCC
1 TAACCCC
**
38106925 TAACGTC
1 TAACCCC
38106932 TAACCCC
1 TAACCCC
38106939 TAAACCCC
1 T-AACCCC
38106947 TAACCCC
1 TAACCCC
38106954 TAA
1 TAA
38106957 ACCTTAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.33, C:0.46, G:0.03, T:0.18
Consensus pattern (7 bp):
TAACCCC
Found at i:38106964 original size:22 final size:22
Alignment explanation
Indices: 38106919--38106964 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
38106909 CCTAACTTTT
** *
38106919 AACCCCTAACGTCTAACCCCTA
1 AACCCCTAACCCCTAAACCCTA
*
38106941 AACCCCTAACCCCTAAACCTTA
1 AACCCCTAACCCCTAAACCCTA
38106963 AA
1 AA
38106965 TCTCAACCCT
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:0.37, C:0.43, G:0.02, T:0.17
Consensus pattern (22 bp):
AACCCCTAACCCCTAAACCCTA
Found at i:38106978 original size:21 final size:21
Alignment explanation
Indices: 38106948--38107028 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
38106938 CTAAACCCCT
38106948 AACCCCTAAACCTTAAATCTC
1 AACCCCTAAACCTTAAATCTC
* * *
38106969 AACCCTTAAACCAT-AATCCTT
1 AACCCCTAAACCTTAAAT-CTC
* * *
38106990 AATCCATAATCCTTAAATC-C
1 AACCCCTAAACCTTAAATCTC
38107010 ATACTCCCTAAACCTTAAA
1 A-AC-CCCTAAACCTTAAA
38107029 ATATGAACTC
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
20 4 0.09
21 26 0.58
22 15 0.33
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27
Consensus pattern (21 bp):
AACCCCTAAACCTTAAATCTC
Found at i:38106989 original size:14 final size:14
Alignment explanation
Indices: 38106972--38107023 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
38106962 AAATCTCAAC
38106972 CCTTAAACCATAAT
1 CCTTAAACCATAAT
*
38106986 CCTTAATCCATAAT
1 CCTTAAACCATAAT
*
38107000 CCTTAAATCCATACT
1 CCTTAAA-CCATAAT
*
38107015 CCCTAAACC
1 CCTTAAACC
38107024 TTAAAATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (14 bp):
CCTTAAACCATAAT
Found at i:38107021 original size:15 final size:15
Alignment explanation
Indices: 38106975--38107021 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
38106965 TCTCAACCCT
38106975 TAAA-CCATAAT-CC
1 TAAATCCATAATCCC
* *
38106988 TTAATCCATAATCCT
1 TAAATCCATAATCCC
*
38107003 TAAATCCATACTCCC
1 TAAATCCATAATCCC
38107018 TAAA
1 TAAA
38107022 CCTTAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 3 0.11
14 7 0.26
15 17 0.63
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:38107236 original size:8 final size:8
Alignment explanation
Indices: 38107223--38107257 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
38107213 TAACGCATCT
38107223 AACCCATA
1 AACCCATA
38107231 AACCCATA
1 AACCCATA
*
38107239 AACCCCTA
1 AACCCATA
38107247 AACCC-TA
1 AACCCATA
38107254 AACC
1 AACC
38107258 TTAAATCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.46, C:0.43, G:0.00, T:0.11
Consensus pattern (8 bp):
AACCCATA
Found at i:38107284 original size:20 final size:20
Alignment explanation
Indices: 38107223--38107286 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
38107213 TAACGCATCT
*
38107223 AACCCATAAACCCATAAACCCC
1 AACCC-TAAA-CCATAAATCCC
*
38107245 TAAACCCTAAACCTTAAATCCC
1 --AACCCTAAACCATAAATCCC
38107267 AACCCTTAAACCAT-AATCCC
1 AACCC-TAAACCATAAATCCC
38107287 TAATCCATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 11 0.31
21 7 0.19
22 9 0.25
23 4 0.11
24 5 0.14
ACGTcount: A:0.42, C:0.41, G:0.00, T:0.17
Consensus pattern (20 bp):
AACCCTAAACCATAAATCCC
Found at i:38107798 original size:23 final size:25
Alignment explanation
Indices: 38107771--38107825 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
38107761 TAAATAATAG
*
38107771 TATTTTAATT-TTTCCATGTGTT-T
1 TATTTTAATTATTTCCACGTGTTAT
* *
38107794 TATTTCAAATTATTTCTACGTGTTAT
1 TATTT-TAATTATTTCCACGTGTTAT
38107820 TATTTT
1 TATTTT
38107826 TTTCTGAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 5 0.20
24 4 0.16
25 10 0.40
26 6 0.24
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.62
Consensus pattern (25 bp):
TATTTTAATTATTTCCACGTGTTAT
Found at i:38108012 original size:40 final size:40
Alignment explanation
Indices: 38107910--38108027 Score: 182
Period size: 41 Copynumber: 2.9 Consensus size: 40
38107900 TAAAAAGTTT
*
38107910 TTAGTAGCGCTTTTCCAAAAACGCCGCTAAAGCCCCCATCA
1 TTAGT-GCGCTTTTCCAAAAACGCCGCTAAAGCCCCCAGCA
* * *
38107951 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAACCCCCAGCA
1 TTAG-TGCGCTTTTCCAAAAACGCCGCTAAAGCCCCCAGCA
38107992 TTAGTGCGCTTTTCCAAAAACGCCGCTAAAGCCCCC
1 TTAGTGCGCTTTTCCAAAAACGCCGCTAAAGCCCCC
38108028 GAAAGGTAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 29 0.42
41 40 0.58
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.20
Consensus pattern (40 bp):
TTAGTGCGCTTTTCCAAAAACGCCGCTAAAGCCCCCAGCA
Found at i:38108125 original size:39 final size:39
Alignment explanation
Indices: 38108081--38108214 Score: 117
Period size: 40 Copynumber: 3.4 Consensus size: 39
38108071 CGTTTTTCTG
38108081 TAAAACGCCGCTAATGCTC-ATTTTTAGCGGCATTTTTT
1 TAAAACGCCGCTAATGCTCGATTTTTAGCGGCATTTTTT
* * * * ***
38108119 TAAAAACACTGCTAATGCTCGATCTTTAGTGGCGATTTCCA
1 T-AAAACGCCGCTAATGCTCGATTTTTAGCGGC-ATTTTTT
* * * *
38108160 TAAAGCGCAGCTAATGCTCGATTTTTACCAGCATTTTTT
1 TAAAACGCCGCTAATGCTCGATTTTTAGCGGCATTTTTT
*
38108199 GTCCAAACGCCGCTAA
1 -T-AAAACGCCGCTAA
38108215 AAGTGTCGCT
Statistics
Matches: 71, Mismatches: 20, Indels: 7
0.72 0.20 0.07
Matches are distributed among these distances:
38 1 0.01
39 20 0.28
40 35 0.49
41 15 0.21
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (39 bp):
TAAAACGCCGCTAATGCTCGATTTTTAGCGGCATTTTTT
Found at i:38112660 original size:40 final size:40
Alignment explanation
Indices: 38112605--38113001 Score: 731
Period size: 40 Copynumber: 9.9 Consensus size: 40
38112595 GCATGAGCAT
38112605 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
38112645 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
38112685 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
38112725 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
38112765 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
38112805 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
38112845 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* * *
38112885 TTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
38112925 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* * * *
38112965 TTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
38113002 TTGCGGTTAT
Statistics
Matches: 347, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 347 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (40 bp):
TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
Found at i:38122908 original size:19 final size:19
Alignment explanation
Indices: 38122868--38122909 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
38122858 TTCAAAATCT
*
38122868 AAAATAATGAAATCAGCAG
1 AAAATAATGAAATCAACAG
38122887 AAAAT-ATGAAATCAACAGG
1 AAAATAATGAAATCAACA-G
38122906 AAAA
1 AAAA
38122910 ATAAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.62, C:0.10, G:0.14, T:0.14
Consensus pattern (19 bp):
AAAATAATGAAATCAACAG
Found at i:38126771 original size:15 final size:14
Alignment explanation
Indices: 38126733--38126763 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
38126723 CCAATTTATT
38126733 AATGAATTATTAAA
1 AATGAATTATTAAA
38126747 AATGAATTATTAAA
1 AATGAATTATTAAA
38126761 AAT
1 AAT
38126764 AACTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:38128707 original size:28 final size:28
Alignment explanation
Indices: 38128644--38128769 Score: 173
Period size: 28 Copynumber: 4.5 Consensus size: 28
38128634 ATATTAAGTC
*
38128644 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
38128671 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
38128699 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
38128727 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
38128756 CGCACACTTAGTGC
1 CGCACACTTAGTGC
38128770 CAATCTCATG
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 21 0.24
28 48 0.55
29 19 0.22
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:38132825 original size:25 final size:25
Alignment explanation
Indices: 38132783--38132836 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
38132773 TTTTCTCAAA
*
38132783 AATTTAATTAATATAAAATATTA-AT
1 AATTTAATAAATATAAAA-ATTAGAT
38132808 AATTTAATAAAT-TGAAAAATTAGAT
1 AATTTAATAAATAT-AAAAATTAGAT
38132833 AATT
1 AATT
38132837 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
AATTTAATAAATATAAAAATTAGAT
Found at i:38136120 original size:19 final size:18
Alignment explanation
Indices: 38136084--38136123 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38136074 TTTCCACTCG
*
38136084 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
38136102 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
38136121 TTT
1 TTT
38136124 GTTTCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:38137200 original size:15 final size:15
Alignment explanation
Indices: 38137180--38137220 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
38137170 TCAAAACTAG
*
38137180 CTTTTTTTTTCACGA
1 CTTTTTTTTTCACAA
38137195 C-TTTTTTTTCACAA
1 CTTTTTTTTTCACAA
*
38137209 ATTTTTTTTTCA
1 CTTTTTTTTTCA
38137221 GCTTGATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.63
Consensus pattern (15 bp):
CTTTTTTTTTCACAA
Found at i:38137277 original size:11 final size:11
Alignment explanation
Indices: 38137261--38137301 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
38137251 TAAACTAAAT
38137261 TTTTTTTTGAA
1 TTTTTTTTGAA
*
38137272 TTTTTTTTCAA
1 TTTTTTTTGAA
*
38137283 ATTTTTTTGAA
1 TTTTTTTTGAA
38137294 TTTTTTTT
1 TTTTTTTT
38137302 CGAAGATGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:38137782 original size:235 final size:236
Alignment explanation
Indices: 38137371--38137925 Score: 986
Period size: 235 Copynumber: 2.4 Consensus size: 236
38137361 CTGATACCAA
* * * ** * * *
38137371 TTTGATACAAACTCATTTCGTGATTGATTCGAGTCGTTAGTGATGCCCAATCATTAATTGAATAG
1 TTTGATACGAACTCGTTTCATGATTGATTCGAGTCGTTAGTGATGCCTGATCGTGAATTGAGTAG
* * *
38137436 AATAGAATCGTTTCGGTTTAAAAGTAACAAAATAGAGTTAATGGCTTCACACAGAGGTAATGAAT
66 AATAGAATCGTTTCGGTATAAAAGTAACAAAATAGAGTTAATGGCTTCAAACAAAGGTAATGAAT
38137501 AAAATAGATAGGAAACAATAACAAATTAATTGGCTAAGACC-AAAAAAATGAACCAACAATAACG
131 AAAATAGATAGGAAACAATAACAAATTAATTGGCTAAGACCAAAAAAAATGAACCAACAATAACG
38137565 AATTGTTGACCCAAATCTCAAAATGGTATTTAGGTTTTTTT
196 AATTGTTGACCCAAATCTCAAAATGGTATTTAGGTTTTTTT
38137606 TTTGATACGAACTCGTTTCATGATTGATTCGAGTCGTTAGTGATGCCTGATCGTGAATTGAGTAG
1 TTTGATACGAACTCGTTTCATGATTGATTCGAGTCGTTAGTGATGCCTGATCGTGAATTGAGTAG
* *
38137671 AATAGAATCGTTTCGGTATAAATGTAACAAAATAGAGTTAATGGCTTCAAATAAAGGTAATGAAT
66 AATAGAATCGTTTCGGTATAAAAGTAACAAAATAGAGTTAATGGCTTCAAACAAAGGTAATGAAT
38137736 AAAATAGATAGGAAACAATAACAAATTAATTGGCTAAGACCAAAAAAAATGAACCAACAATAACG
131 AAAATAGATAGGAAACAATAACAAATTAATTGGCTAAGACCAAAAAAAATGAACCAACAATAACG
38137801 AATTGTTGACCCAAATCTCAAAATGGTATTTAGGTTTTTTT
196 AATTGTTGACCCAAATCTCAAAATGGTATTTAGGTTTTTTT
38137842 TTTGATACGAACTCGTTTCATGATTGATTCGAGTCGTTAGTGATGCCTGATCGTGAATTGAGTAG
1 TTTGATACGAACTCGTTTCATGATTGATTCGAGTCGTTAGTGATGCCTGATCGTGAATTGAGTAG
38137907 AATAGAATCGTTTCGGTAT
66 AATAGAATCGTTTCGGTAT
38137926 GTTTTTCGGT
Statistics
Matches: 306, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
235 158 0.52
236 148 0.48
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (236 bp):
TTTGATACGAACTCGTTTCATGATTGATTCGAGTCGTTAGTGATGCCTGATCGTGAATTGAGTAG
AATAGAATCGTTTCGGTATAAAAGTAACAAAATAGAGTTAATGGCTTCAAACAAAGGTAATGAAT
AAAATAGATAGGAAACAATAACAAATTAATTGGCTAAGACCAAAAAAAATGAACCAACAATAACG
AATTGTTGACCCAAATCTCAAAATGGTATTTAGGTTTTTTT
Found at i:38139627 original size:30 final size:30
Alignment explanation
Indices: 38139593--38139652 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
38139583 GCTTTTTGAA
*
38139593 AATATTTACAAAAAGAGGC-ATCTAATTTTT
1 AATATTTACAAAAAGA-GCAATCAAATTTTT
38139623 AATATTTACAAAAAGAGCAATCAAATTTTT
1 AATATTTACAAAAAGAGCAATCAAATTTTT
38139653 TAAAAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (30 bp):
AATATTTACAAAAAGAGCAATCAAATTTTT
Found at i:38147507 original size:10 final size:10
Alignment explanation
Indices: 38147492--38147521 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
38147482 TAAAAAATAG
38147492 AAAATAAAGT
1 AAAATAAAGT
*
38147502 AAAATAAAAT
1 AAAATAAAGT
38147512 AAAATAAAGT
1 AAAATAAAGT
38147522 TCTAACGCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (10 bp):
AAAATAAAGT
Found at i:38149142 original size:19 final size:19
Alignment explanation
Indices: 38149118--38149160 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
38149108 CATGTTCAAA
* *
38149118 ATTTTAATACAATTTAATT
1 ATTTTAATAAAAATTAATT
38149137 ATTTT-ATAAAAATTAATT
1 ATTTTAATAAAAATTAATT
38149155 ATTTTA
1 ATTTTA
38149161 TGAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAATAAAAATTAATT
Found at i:38149154 original size:18 final size:19
Alignment explanation
Indices: 38149131--38149167 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
38149121 TTAATACAAT
38149131 TTAATTATTTTAT-AAAAA
1 TTAATTATTTTATGAAAAA
38149149 TTAATTATTTTATGAAAAA
1 TTAATTATTTTATGAAAAA
38149168 AATTCTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TTAATTATTTTATGAAAAA
Found at i:38149330 original size:24 final size:25
Alignment explanation
Indices: 38149289--38149335 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
38149279 AAATTTCAAA
*
38149289 AAGAATTTCTCAGAAAC-ACTTTTG
1 AAGAATTCCTCAGAAACAACTTTTG
38149313 AAGAATTCCTTCAG-AACAACTTT
1 AAGAATTCC-TCAGAAACAACTTT
38149336 CTTCTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (25 bp):
AAGAATTCCTCAGAAACAACTTTTG
Found at i:38156739 original size:56 final size:50
Alignment explanation
Indices: 38156479--38156775 Score: 265
Period size: 50 Copynumber: 5.8 Consensus size: 50
38156469 GAATATAAGA
* * * ** * * * *
38156479 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTC-TTTTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * * * ** *
38156528 TACCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATAT-AGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCA-G
* * * ** **
38156578 TTCCCATGCCATCTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* **
38156628 TGCGAGCGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
38156678 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC-A-G
*
38156733 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
38156776 TTACCCAAAT
Statistics
Matches: 200, Mismatches: 39, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
49 34 0.17
50 119 0.60
53 5 0.03
54 1 0.00
55 1 0.00
56 40 0.20
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:38165656 original size:32 final size:32
Alignment explanation
Indices: 38165605--38165797 Score: 219
Period size: 32 Copynumber: 6.1 Consensus size: 32
38165595 GAATGGCTAC
* * *
38165605 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * *
38165636 AAGCCATCAGTAGTAGTAATATGACCGGTACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
38165668 CAGCCATCAGTAATAGTAGTATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * *
38165700 AAGCCATTAGTAGTAGTAATATGATCGGCATA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * *
38165732 CAGCCATCAGTAATGGTAATATGATCGGTACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
38165764 CAA-CCATCAGTAATGGTAATATGATCGGTACA
1 -AAGCCATCAGTAATAGTAATATGATCGGCACA
38165796 AA
1 AA
38165798 TCCAACAATA
Statistics
Matches: 137, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
31 12 0.09
32 124 0.91
33 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:38165706 original size:64 final size:64
Alignment explanation
Indices: 38165602--38165795 Score: 250
Period size: 64 Copynumber: 3.1 Consensus size: 64
38165592 ATAGAATGGC
* * * *
38165602 TACA-AGCCATAAGT-ACAGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGACCGG
1 TACACAGCCATCAGTAATAGTAATATGATCGGCACAAAGCCATCAGTAGTAGTAATATGATCGG
* *
38165664 TACACAGCCATCAGTAATAGTAGTATGATCGGCACAAAGCCATTAGTAGTAGTAATATGATCGG
1 TACACAGCCATCAGTAATAGTAATATGATCGGCACAAAGCCATCAGTAGTAGTAATATGATCGG
* * * * * *
38165728 CATACAGCCATCAGTAATGGTAATATGATCGGTACACAA-CCATCAGTAATGGTAATATGATCGG
1 TACACAGCCATCAGTAATAGTAATATGATCGGCACA-AAGCCATCAGTAGTAGTAATATGATCGG
38165792 TACA
1 TACA
38165796 AATCCAACAA
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
62 4 0.04
63 9 0.08
64 98 0.87
65 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (64 bp):
TACACAGCCATCAGTAATAGTAATATGATCGGCACAAAGCCATCAGTAGTAGTAATATGATCGG
Found at i:38165787 original size:96 final size:95
Alignment explanation
Indices: 38165605--38165797 Score: 269
Period size: 96 Copynumber: 2.0 Consensus size: 95
38165595 GAATGGCTAC
* *
38165605 AAGCCATAAGTACAGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGACCGGTACACA
1 AAGCCATAAGTACAGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATATGACCGGTACACA
* *
38165670 GCCATCAGTAATAGTAGTATGATCGGCACA
66 ACCATCAGTAATAGTAATATGATCGGCACA
* * * * * *
38165700 AAGCCATTAGTAGTAGTAATATGATCGGCATACAGCCATCAGTAATGGTAATATGATCGGTACAC
1 AAGCCATAAGTA-CAGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATATGACCGGTACAC
* *
38165765 AACCATCAGTAATGGTAATATGATCGGTACA
65 AACCATCAGTAATAGTAATATGATCGGCACA
38165796 AA
1 AA
38165798 TCCAACAATA
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 11 0.13
96 74 0.87
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (95 bp):
AAGCCATAAGTACAGTAATATGATCGGCACAAAGCCATCAGTAATAGTAATATGACCGGTACACA
ACCATCAGTAATAGTAATATGATCGGCACA
Found at i:38165840 original size:26 final size:26
Alignment explanation
Indices: 38165810--38165863 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
38165800 CAACAATAGC
38165810 ATCGCAGCAAAGCTGCCAGCAACAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
* *
38165836 ATCGCAGCAAAGCTGCCAGTAATAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
38165862 AT
1 AT
38165864 ATGTGGCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAGCAACAGT
Found at i:38165881 original size:27 final size:27
Alignment explanation
Indices: 38165851--38165914 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
38165841 AGCAAAGCTG
*
38165851 CCAGTAATAGT-ATATGTGGCCA-AGCCA
1 CCAGTAACAGTGAT-TGTGG-CAGAGCCA
38165878 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAGAGCCA
38165905 CCAGT-ACAGT
1 CCAGTAACAGT
38165915 ACTTCCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.21
27 25 0.74
28 2 0.06
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAGAGCCA
Found at i:38166054 original size:23 final size:24
Alignment explanation
Indices: 38165980--38166063 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
38165970 CCATGCACGG
** * *
38165980 AATCAGTCATACAAATCATAGACA
1 AATCAGTCATTTAAATCACAAACA
38166004 AATCAGTCATTTAAATCACAAACA
1 AATCAGTCATTTAAATCACAAACA
*
38166028 AATCAGTCATTTCAATCAC-AACA
1 AATCAGTCATTTAAATCACAAACA
38166051 AATCAGTCATTTA
1 AATCAGTCATTTA
38166064 CATTTCGGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
23 16 0.30
24 38 0.70
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.26
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAAACA
Found at i:38166100 original size:24 final size:24
Alignment explanation
Indices: 38165980--38166111 Score: 108
Period size: 24 Copynumber: 5.5 Consensus size: 24
38165970 CCATGCACGG
** *
38165980 AATCAGTCATACAAATCATAGACA
1 AATCAGTCATTTACATCATAGACA
* * *
38166004 AATCAGTCATTTAAATCACAAACA
1 AATCAGTCATTTACATCATAGACA
*
38166028 AATCAGTCATTT-CAATCACA-ACA
1 AATCAGTCATTTAC-ATCATAGACA
* *
38166051 AATCAGTCATTTACAT-TTCGGACA
1 AATCAGTCATTTACATCAT-AGACA
* *
38166075 AATCAATCATTTACATCATAGGCA
1 AATCAGTCATTTACATCATAGACA
* *
38166099 AATTAATCATTTA
1 AATCAGTCATTTA
38166112 ACCCCGAGGG
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
23 17 0.19
24 72 0.80
25 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (24 bp):
AATCAGTCATTTACATCATAGACA
Found at i:38166161 original size:27 final size:27
Alignment explanation
Indices: 38166130--38166439 Score: 377
Period size: 27 Copynumber: 11.5 Consensus size: 27
38166120 GGGTAAAATA
*
38166130 GTCATTTTACCCTACAGGAGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
38166157 ATCATTTTACCCTATAGGGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
*
38166184 GTCATTTTATCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
38166211 GTCATTTTACCTTATAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
38166238 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
38166265 GTCATTTTACCTTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
38166292 ATCATTTTACCCTGCAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
38166319 GCCATTTTACCCTACAGAGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * * *
38166346 ATCACTTTACCCTACAAGGGCGTTGCG
1 GTCATTTTACCCTACAGGGGCATTACG
* **
38166373 GCCATTTTACCCTACAGGGGCATTATA
1 GTCATTTTACCCTACAGGGGCATTACG
* * * * *
38166400 GTCACTTTAGCCTATAGGGGCATTTCA
1 GTCATTTTACCCTACAGGGGCATTACG
*
38166427 GTAATTTTACCCT
1 GTCATTTTACCCT
38166440 TCGAGAGTAT
Statistics
Matches: 236, Mismatches: 47, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 236 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:38166458 original size:27 final size:26
Alignment explanation
Indices: 38166428--38166585 Score: 194
Period size: 27 Copynumber: 5.9 Consensus size: 26
38166418 GGCATTTCAG
*
38166428 TAATTTTACCCTTCGAGAGTATTCTGA
1 TAATTTTACCCTTCGAGGGTATT-TGA
* *
38166455 TAATTTTACCTTTCGAGGGT-TTTCCA
1 TAATTTTACCCTTCGAGGGTATTT-GA
* *
38166481 GTAATTTTATCCTTCGAGGGTATTTTA
1 -TAATTTTACCCTTCGAGGGTATTTGA
*
38166508 GTAATTTTACACTTCGAGGGTATTTCGA
1 -TAATTTTACCCTTCGAGGGTATTT-GA
38166536 TAATTTTACCCTTCGAGGGTATTTAGA
1 TAATTTTACCCTTCGAGGGTATTT-GA
38166563 TAATTTTACCCTTCGA-GGTATTT
1 TAATTTTACCCTTCGAGGGTATTT
38166586 CAGTAGTTTT
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
25 1 0.01
26 10 0.09
27 101 0.87
28 4 0.03
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (26 bp):
TAATTTTACCCTTCGAGGGTATTTGA
Found at i:38166484 original size:54 final size:53
Alignment explanation
Indices: 38166421--38166597 Score: 220
Period size: 54 Copynumber: 3.3 Consensus size: 53
38166411 CTATAGGGGC
*
38166421 ATTT-CAGTAATTTTACCCTTCGAGAGTATTCTGATAATTTTACCTTTCGAGGGT
1 ATTTCCAGTAATTTTACCCTTCGAGGGTATT-TGATAATTTTACC-TTCGAGGGT
* *
38166475 -TTTCCAGTAATTTTATCCTTCGAGGGTATTTTAGTAATTTTACACTTCGAGGGT
1 ATTTCCAGTAATTTTACCCTTCGAGGGTATTTGA-TAATTTTAC-CTTCGAGGGT
*
38166529 ATTTCGA-TAATTTTACCCTTCGAGGGTATTTAGATAATTTTACCCTTCGA-GGT
1 ATTTCCAGTAATTTTACCCTTCGAGGGTATTT-GATAATTTTA-CCTTCGAGGGT
*
38166582 ATTT-CAGTAGTTTTAC
1 ATTTCCAGTAATTTTAC
38166598 AACCTTTCCG
Statistics
Matches: 108, Mismatches: 8, Indels: 15
0.82 0.06 0.11
Matches are distributed among these distances:
52 1 0.01
53 20 0.19
54 79 0.73
55 8 0.07
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.44
Consensus pattern (53 bp):
ATTTCCAGTAATTTTACCCTTCGAGGGTATTTGATAATTTTACCTTCGAGGGT
Found at i:38166531 original size:81 final size:80
Alignment explanation
Indices: 38166421--38166598 Score: 245
Period size: 81 Copynumber: 2.2 Consensus size: 80
38166411 CTATAGGGGC
* *
38166421 ATTTCAGTAATTTTACCCTTCGAGAGTA-TTCTGATAATTTTACCTTTCGAGGGT-TTTCCAG-T
1 ATTTCAGTAATTTTACACTTCGAGAGTATTTC-GATAATTTTACCCTTCGAGGGTATTT--AGAT
*
38166483 AATTTTATCCTTCGAGGGT
63 AATTTTACCCTTCGA-GGT
* *
38166502 ATTTTAGTAATTTTACACTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTAGATAAT
1 ATTTCAGTAATTTTACACTTCGAGAGTATTTCGATAATTTTACCCTTCGAGGGTATTTAGATAAT
38166567 TTTACCCTTCGAGGT
66 TTTACCCTTCGAGGT
*
38166582 ATTTCAGTAGTTTTACA
1 ATTTCAGTAATTTTACA
38166599 ACCTTTCCGA
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
80 20 0.23
81 61 0.70
82 6 0.07
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (80 bp):
ATTTCAGTAATTTTACACTTCGAGAGTATTTCGATAATTTTACCCTTCGAGGGTATTTAGATAAT
TTTACCCTTCGAGGT
Found at i:38172052 original size:50 final size:50
Alignment explanation
Indices: 38171977--38172267 Score: 393
Period size: 50 Copynumber: 5.8 Consensus size: 50
38171967 ATTTGGGTAA
* *
38171977 AGAGGTCCCATGTAAGACCATGTCTGGGACATGCCGTTGGCACCCAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * * *
38172027 AGAGGTTGCATGTACGAACATGTCTGGGACATGACATTAGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
38172077 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
38172127 AGAGGTCCCATGTAAGACCATGTCTGGGACAAGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * *** *
38172177 AGAGGTCCCCCGTAAGACCATGTCTGGGACATTGCAAGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
38172227 AGAAAATCCCATGTAAGACCATGTCTGGGACATGGCTTTGG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGG
38172268 AATGTTATTA
Statistics
Matches: 208, Mismatches: 32, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
50 178 0.86
51 30 0.14
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:38173477 original size:108 final size:108
Alignment explanation
Indices: 38173288--38173503 Score: 423
Period size: 108 Copynumber: 2.0 Consensus size: 108
38173278 TTATTTCTTG
38173288 CTGTTTCGTTTTATTTCTTTATTCCTACTTGTGCCGATTCTTTATCTCATTTGTTTACTGTTCTT
1 CTGTTTCGTTTTATTTCTTTATTCCTACTTGTGCCGATTCTTTATCTCATTTGTTTACTGTTCTT
38173353 CTTGTGTTTTTCCAGCCATATTCAACTCAAAGAATCGAATTAA
66 CTTGTGTTTTTCCAGCCATATTCAACTCAAAGAATCGAATTAA
*
38173396 CTGTTTCGTTTTATTTCTTTATTCCTACTTGTGCCGATTCTTTATCTCATTTGTTTGCTGTTCTT
1 CTGTTTCGTTTTATTTCTTTATTCCTACTTGTGCCGATTCTTTATCTCATTTGTTTACTGTTCTT
38173461 CTTGTGTTTTTCCAGCCATATTCAACTCAAAGAATCGAATTAA
66 CTTGTGTTTTTCCAGCCATATTCAACTCAAAGAATCGAATTAA
38173504 ATCATCATTC
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.19, C:0.20, G:0.12, T:0.49
Consensus pattern (108 bp):
CTGTTTCGTTTTATTTCTTTATTCCTACTTGTGCCGATTCTTTATCTCATTTGTTTACTGTTCTT
CTTGTGTTTTTCCAGCCATATTCAACTCAAAGAATCGAATTAA
Found at i:38178239 original size:50 final size:50
Alignment explanation
Indices: 38178159--38178332 Score: 204
Period size: 50 Copynumber: 3.5 Consensus size: 50
38178149 GGCTAAATTG
* *
38178159 ATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCATGTAAGACC
1 ATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACC
* * ** *
38178209 ATGCCTGGGACATGGCATTGGTACCGAGATGAGAGGTCCCCCGTAACACC
1 ATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACC
* * * * **
38178259 ATGTCTAGGACATGGAATGGGCACCGATATGAGAACATCCCATGTAAGACC
1 ATGTCTGGGACATGGCATTGGCACCGAGATGAG-AGGTCCCATGTAAGACC
* *
38178310 ATGTCTGAGACATGGCTTTGGCA
1 ATGTCTGGGACATGGCATTGGCA
38178333 TGTTATTATC
Statistics
Matches: 100, Mismatches: 23, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
50 70 0.70
51 30 0.30
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
ATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACC
Found at i:38183518 original size:45 final size:45
Alignment explanation
Indices: 38183467--38183555 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
38183457 TGTGAACCAA
* * *
38183467 ACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
*
38183512 ACATCATTGATTAATAAGGTGGTTTCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
38183556 AGTATCTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:38189535 original size:17 final size:17
Alignment explanation
Indices: 38189513--38189548 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
38189503 ACATGACAAC
*
38189513 TTAGTTTAGGATTATGT
1 TTAGTTGAGGATTATGT
38189530 TTAGTTGAGGATTATGT
1 TTAGTTGAGGATTATGT
38189547 TT
1 TT
38189549 TGTATGCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (17 bp):
TTAGTTGAGGATTATGT
Found at i:38192493 original size:20 final size:20
Alignment explanation
Indices: 38192453--38192498 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
38192443 TTAAAGAAAA
*
38192453 TATTGATACCCTAGTGTCAG
1 TATTGATACCCTAGTGACAG
38192473 TATTGATA-CCTATGTGACAG
1 TATTGATACCCTA-GTGACAG
*
38192493 TTTTGA
1 TATTGA
38192499 GATTTTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (20 bp):
TATTGATACCCTAGTGACAG
Found at i:38206774 original size:50 final size:50
Alignment explanation
Indices: 38206659--38206851 Score: 251
Period size: 50 Copynumber: 3.8 Consensus size: 50
38206649 GATAATAACA
* * ** * *
38206659 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
38206710 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** * *
38206760 TGCCAATGCCATGTCTTAGAAATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
38206810 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
38206852 TTACCCAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 90 0.74
51 32 0.26
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:38211232 original size:27 final size:27
Alignment explanation
Indices: 38211196--38211417 Score: 304
Period size: 27 Copynumber: 8.2 Consensus size: 27
38211186 CCCCAAAATA
*
38211196 GGTAAAATGATCGAAATACCTCCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
38211223 GGTAAAATGA-CTGAAATACCCCCATAG
1 GGTAAAATGATC-GAAATACCCCCATAG
* * *
38211250 GGTAGAATGATTGAAATACCTCCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
* *
38211277 GGTAAAATGA-CTGAAATACTCCTATAG
1 GGTAAAATGATC-GAAATACCCCCATAG
* * *
38211304 GGTAAAATGACCAAAATACCCCCATAA
1 GGTAAAATGATCGAAATACCCCCATAG
* *
38211331 GGTAGAATGACCGAAATACCCCCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
38211358 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
*
38211385 GGTAAAATGATCAAAATACCCCCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
38211412 GGTAAA
1 GGTAAA
38211418 GTAACTGTTA
Statistics
Matches: 172, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.01
27 170 0.99
28 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (27 bp):
GGTAAAATGATCGAAATACCCCCATAG
Found at i:38213622 original size:17 final size:18
Alignment explanation
Indices: 38213594--38213628 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
38213584 GGGCTGAAAG
*
38213594 GGGCCATGTGGGGCCAAT
1 GGGCCATGTGGGCCCAAT
38213612 GGGCC-TGTGGGCCCAAT
1 GGGCCATGTGGGCCCAAT
38213629 CGGATAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.14, C:0.26, G:0.43, T:0.17
Consensus pattern (18 bp):
GGGCCATGTGGGCCCAAT
Found at i:38213807 original size:27 final size:26
Alignment explanation
Indices: 38213776--38213874 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 26
38213766 TTTGGTTTAC
*
38213776 AAAATTACTAAAATACCCTCAACTTGT
1 AAAATTACTAAAATACCCTCGA-TTGT
** *
38213803 AAAATTACCGAAGTACCCTCGATTCGT
1 AAAATTACTAAAATACCCTCGATT-GT
* *
38213830 GAAATTAC-AAAAGTACCCTTGATTTGT
1 AAAATTACTAAAA-TACCCTCGA-TTGT
38213857 AAAATTACTAAAATACCC
1 AAAATTACTAAAATACCC
38213875 CTGAACGGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
26 4 0.07
27 49 0.83
28 6 0.10
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.28
Consensus pattern (26 bp):
AAAATTACTAAAATACCCTCGATTGT
Found at i:38214966 original size:16 final size:17
Alignment explanation
Indices: 38214934--38214966 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
38214924 AATTAAGAAG
38214934 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
38214952 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
38214967 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:38216233 original size:20 final size:20
Alignment explanation
Indices: 38216154--38216237 Score: 105
Period size: 20 Copynumber: 4.1 Consensus size: 20
38216144 AAAGTCTGTG
* *
38216154 GCAGCCTATGTTGAGCCGTG
1 GCAGCCTATGTTGAGCCATA
*
38216174 GCGGCCTATGTTGAGCCATA
1 GCAGCCTATGTTGAGCCATA
*
38216194 GCAGCCCCTGTGTTGAGCCATA
1 GCAG--CCTATGTTGAGCCATA
*
38216216 GTAGCCTATGTTGAGCCATA
1 GCAGCCTATGTTGAGCCATA
38216236 GC
1 GC
38216238 CTGAACATGG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
20 36 0.67
22 18 0.33
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.25
Consensus pattern (20 bp):
GCAGCCTATGTTGAGCCATA
Found at i:38218811 original size:13 final size:14
Alignment explanation
Indices: 38218786--38218828 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
38218776 TACTCTTGAA
*
38218786 TTTTCGAATTTTTT
1 TTTTCAAATTTTTT
38218800 TTTTCAAATTTTTT
1 TTTTCAAATTTTTT
38218814 TTTTCAAATTTTTT
1 TTTTCAAATTTTTT
38218828 T
1 T
38218829 ACAAACTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTTCAAATTTTTT
Found at i:38220037 original size:29 final size:29
Alignment explanation
Indices: 38220004--38220076 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
38219994 ATGTATTAGT
* *
38220004 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
38220033 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
38220062 TTAGGACATATTTAA
1 TTAGGACATATTTAA
38220077 TAATATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:38221916 original size:60 final size:58
Alignment explanation
Indices: 38221758--38221981 Score: 236
Period size: 60 Copynumber: 3.7 Consensus size: 58
38221748 AAACATGATA
* * *
38221758 GAAATAGGATGCCTTTGTGGAAAATCTCTAAAAAGGAAAACCTTTTGGCGAGTACTGAAT
1 GAAA-AGGATGCATTTGTGGAAAATCTCT-AAAAGGAAAGCCTTTAGGCGAGTACTGAAT
* * * * * * * *
38221818 GAAAAGGATACCTTTGTGGCAAACCTATGGAAAA-GAAAGCCTTTGAGGCGATTAATGTAT
1 GAAAAGGATGCATTTGTGGAAAATCTCT--AAAAGGAAAGCCTTT-AGGCGAGTACTGAAT
* *
38221878 GAAAAGAATGCATTTATGGAAAATCTCTCAAAAGGAAAGCCTTTATGGCGAGTACTGAAT
1 GAAAAGGATGCATTTGTGGAAAATCTCT-AAAAGGAAAGCCTTTA-GGCGAGTACTGAAT
38221938 GAAAAGGATGCCA-TTGTGGAAAATCTCTAGAAAGGAAAGCCTTT
1 GAAAAGGATG-CATTTGTGGAAAATCTCTA-AAAGGAAAGCCTTT
38221982 CTGGCAAATC
Statistics
Matches: 135, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
59 35 0.26
60 98 0.73
61 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (58 bp):
GAAAAGGATGCATTTGTGGAAAATCTCTAAAAGGAAAGCCTTTAGGCGAGTACTGAAT
Found at i:38228219 original size:26 final size:26
Alignment explanation
Indices: 38228190--38228240 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
38228180 ACACACCAAT
*
38228190 ATCGCAGC-AGAGCTGCCAGTAATAGA
1 ATCGCAGCGA-AGCTACCAGTAATAGA
38228216 ATCGCAGCGAAGCTACCAGTAATAG
1 ATCGCAGCGAAGCTACCAGTAATAG
38228241 TATATGTGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (26 bp):
ATCGCAGCGAAGCTACCAGTAATAGA
Found at i:38228436 original size:27 final size:27
Alignment explanation
Indices: 38228418--38228658 Score: 241
Period size: 27 Copynumber: 9.2 Consensus size: 27
38228408 GGTATAACAG
38228418 TCATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
** *
38228445 TCATTTTATGCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
38228472 TCATTTTACCCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * * * *
38228499 TCAATTTACCATTTGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
38228526 TC-----A---TTCGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
38228545 TC-TTTTCACCCTTCGAGGGTATTTTGG
1 TCATTTT-ACCCTTCGAGGGTATTTCGA
* * *
38228572 TCAATTTACCCTTCGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
38228599 TCATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
38228626 TCATTTTACCCTCCGAGGGTATTTC-A
1 TCATTTTACCCTTCGAGGGTATTTCGA
38228652 GTCATTT
1 -TCATTT
38228659 GCCCATGAAT
Statistics
Matches: 187, Mismatches: 17, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
19 15 0.08
22 1 0.01
24 1 0.01
26 1 0.01
27 166 0.89
28 3 0.02
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCGA
Found at i:38228580 original size:73 final size:73
Alignment explanation
Indices: 38228456--38228650 Score: 203
Period size: 73 Copynumber: 2.6 Consensus size: 73
38228446 CATTTTATGC
* * * *
38228456 TTCGGGGGTATTTCGATCATTTTACCCTTCGGGGGTATTTCGATCAATTTACCATTTGGGGGTAT
1 TTCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGATCAATTTACCATTCGAGGGTAT
38228521 TTCGGTCA
66 TTCGGTCA
* * * * *
38228529 TTCGAGGGTATTTTGGTC-TTTTCACCCTTCGAGGGTATTTTGGTCAATTTACCCTTCGAGGGTA
1 TTCGAGGGTATTTCGATCATTTT-ACCCTTCGAGGGTATTTCGATCAATTTACCATTCGAGGGTA
*
38228593 TTTTGGTCATTTTA
65 TTTCGGTC-----A
*
38228607 CCCTTCGAGGGTATTTCGATCATTTTACCCTCCGAGGGTATTTC
1 ---TTCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTC
38228651 AGTCATTTGC
Statistics
Matches: 98, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
72 4 0.04
73 57 0.58
78 1 0.01
81 32 0.33
82 4 0.04
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (73 bp):
TTCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGATCAATTTACCATTCGAGGGTAT
TTCGGTCA
Found at i:38228607 original size:100 final size:100
Alignment explanation
Indices: 38228429--38228630 Score: 244
Period size: 100 Copynumber: 2.0 Consensus size: 100
38228419 CATTTTACCC
** * * *
38228429 TTCGAGGGTATTTCGATCATTTTATGCTTCGGGGGTATTTCGATCATTTTACCCTTCGGGGGTAT
1 TTCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGATCAATTTACCCTTCGAGGGTAT
* * *
38228494 TTCGATCAATTTACCATTTGGGGGTATTTCGGTCA
66 TTCGATCAATTTACCATTCGAGGGTATTTCGATCA
* * * *
38228529 TTCGAGGGTATTTTGGTC-TTTTCACCCTTCGAGGGTATTTTGGTCAATTTACCCTTCGAGGGTA
1 TTCGAGGGTATTTCGATCATTTT-ACCCTTCGAGGGTATTTCGATCAATTTACCCTTCGAGGGTA
* * * *
38228593 TTTTGGTCATTTTACCCTTCGAGGGTATTTCGATCA
65 TTTCGATCAATTTACCATTCGAGGGTATTTCGATCA
38228629 TT
1 TT
38228631 TTACCCTCCG
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
99 4 0.05
100 81 0.95
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (100 bp):
TTCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTCGATCAATTTACCCTTCGAGGGTAT
TTCGATCAATTTACCATTCGAGGGTATTTCGATCA
Found at i:38228646 original size:127 final size:126
Alignment explanation
Indices: 38228421--38228657 Score: 330
Period size: 127 Copynumber: 1.9 Consensus size: 126
38228411 ATAACAGTCA
* ** *
38228421 TTTTACCCTTCGAGGGTATTTCGATCATTTTATGCTTCGGGGGTATTTCGATCATTTTACCCTTC
1 TTTTACCCTTCGAGGGTATTTCGATCAATTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTC
* ** * *
38228486 GGGGGTATTTCGATCAATTTACCATTTGGGGGTATTTCGGTCATTCGAGGGTATTTTGGTC
66 GAGGGTATTTCGATCAATTTACCATCCGAGGGTATTTCAGTCATTCGAGGGTATTTTGGTC
* * * *
38228547 TTTTCACCCTTCGAGGGTATTTTGGTCAATTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTT
1 TTTT-ACCCTTCGAGGGTATTTCGATCAATTTACCCTTCGAGGGTATTTCGATCATTTTACCCTT
* *
38228612 CGAGGGTATTTCGATCATTTTACCCTCCGAGGGTATTTCAGTCATT
65 CGAGGGTATTTCGATCAATTTACCATCCGAGGGTATTTCAGTCATT
38228658 TGCCCATGAA
Statistics
Matches: 95, Mismatches: 15, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
126 4 0.04
127 91 0.96
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.42
Consensus pattern (126 bp):
TTTTACCCTTCGAGGGTATTTCGATCAATTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTC
GAGGGTATTTCGATCAATTTACCATCCGAGGGTATTTCAGTCATTCGAGGGTATTTTGGTC
Found at i:38231187 original size:43 final size:43
Alignment explanation
Indices: 38231139--38231224 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
38231129 AGGGTAAATC
* *
38231139 CAACAACCC-ATGTTTATTTTCTCCTCTTTTTAAATTATGTTTT
1 CAACAACCCAAT-ATTATCTTCTCCTCTTTTTAAATTATGTTTT
*
38231182 CAACAACCCAATATTATCTTCTCCTCTTTTTAAATTATTTTTT
1 CAACAACCCAATATTATCTTCTCCTCTTTTTAAATTATGTTTT
38231225 ATAGGATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
43 37 0.95
44 2 0.05
ACGTcount: A:0.26, C:0.22, G:0.02, T:0.50
Consensus pattern (43 bp):
CAACAACCCAATATTATCTTCTCCTCTTTTTAAATTATGTTTT
Found at i:38234573 original size:25 final size:24
Alignment explanation
Indices: 38234526--38234573 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
38234516 AACAAAGAAC
* *
38234526 AAATAAAAATAATGATATATAAAT
1 AAATAAAAATAACGAAATATAAAT
*
38234550 AAATAAAAATAGACGAAATTTAAA
1 AAATAAAAATA-ACGAAATATAAA
38234574 AGTGGAAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (24 bp):
AAATAAAAATAACGAAATATAAAT
Found at i:38234815 original size:17 final size:18
Alignment explanation
Indices: 38234779--38234817 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38234769 TTCTAAAAAT
*
38234779 CAAAAGAAAGAAATCTTC
1 CAAAAGAAACAAATCTTC
*
38234797 CAAATGAAACAAA-CTTC
1 CAAAAGAAACAAATCTTC
38234814 CAAA
1 CAAA
38234818 GCTGAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.56, C:0.21, G:0.08, T:0.15
Consensus pattern (18 bp):
CAAAAGAAACAAATCTTC
Found at i:38236369 original size:23 final size:23
Alignment explanation
Indices: 38236338--38236385 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
38236328 CTTTTCTGAC
38236338 TATAAATTTCGTATACCAGACCT
1 TATAAATTTCGTATACCAGACCT
* *
38236361 TATACATTTCGTATACTAGACCT
1 TATAAATTTCGTATACCAGACCT
38236384 TA
1 TA
38236386 CATGCCTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (23 bp):
TATAAATTTCGTATACCAGACCT
Found at i:38241118 original size:15 final size:15
Alignment explanation
Indices: 38241083--38241111 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38241073 GAATGTTATC
38241083 ATTATTATTATTTTT
1 ATTATTATTATTTTT
38241098 ATTATTATTATTTT
1 ATTATTATTATTTT
38241112 GTATATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTATTATTATTTTT
Found at i:38262034 original size:13 final size:13
Alignment explanation
Indices: 38262016--38262040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38262006 AATCTGTGTG
38262016 TTCTTATTTTTTT
1 TTCTTATTTTTTT
38262029 TTCTTATTTTTT
1 TTCTTATTTTTT
38262041 GCTTTACAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (13 bp):
TTCTTATTTTTTT
Found at i:38263057 original size:24 final size:24
Alignment explanation
Indices: 38263025--38263081 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
38263015 TTTACTAAAA
* **
38263025 TATTAAGTGGCTTTG-CCACAACGT
1 TATTGAGTGGC-TTGACCACAACAC
38263049 TATTGAGTGGCTTGACCACAACAC
1 TATTGAGTGGCTTGACCACAACAC
38263073 TATTGAGTG
1 TATTGAGTG
38263082 ACATGCCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (24 bp):
TATTGAGTGGCTTGACCACAACAC
Found at i:38263091 original size:24 final size:24
Alignment explanation
Indices: 38263040--38263094 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
38263030 AGTGGCTTTG
** * *
38263040 CCACAACGTTATTGAGTGGCTTGA
1 CCACAACACTATTGAGTGACATGA
*
38263064 CCACAACACTATTGAGTGACATGC
1 CCACAACACTATTGAGTGACATGA
38263088 CCACAAC
1 CCACAAC
38263095 GTGCAGCTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (24 bp):
CCACAACACTATTGAGTGACATGA
Found at i:38266989 original size:27 final size:27
Alignment explanation
Indices: 38266951--38267116 Score: 126
Period size: 27 Copynumber: 6.2 Consensus size: 27
38266941 ATTCGTAGGC
*
38266951 AAATTATCGAAATACCCCCTAAGGGTA
1 AAATTATCGAAATACCCCCGAAGGGTA
** *
38266978 AAATTATCGAAATACCCTTGAAGGATA
1 AAATTATCGAAATACCCCCGAAGGGTA
* *
38267005 AAATTA-CCAAA-ACACCTCGACA-GGTA
1 AAATTATCGAAATAC-CCCCGA-AGGGTA
* * * *
38267031 AATTTACCGTAATACCCTCGAAGGGTA
1 AAATTATCGAAATACCCCCGAAGGGTA
*
38267058 AAATGAAT-GAAATACCCCCGAAGGGTA
1 AAAT-TATCGAAATACCCCCGAAGGGTA
* * * * *
38267085 AAATGACCAAAATACCCCTG-GGGGTA
1 AAATTATCGAAATACCCCCGAAGGGTA
38267111 AAATTA
1 AAATTA
38267117 CCATTTTACC
Statistics
Matches: 111, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
25 2 0.02
26 29 0.26
27 77 0.69
28 3 0.03
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATTATCGAAATACCCCCGAAGGGTA
Found at i:38267118 original size:80 final size:80
Alignment explanation
Indices: 38266951--38267102 Score: 180
Period size: 80 Copynumber: 1.9 Consensus size: 80
38266941 ATTCGTAGGC
* * * ** *
38266951 AAATTATCGAAATACCCCCTAAGGGTAAAATTATCGAAATACCCTTGAAGGATAAAATTACCAAA
1 AAATTACCGAAATACCCCCGAAGGGTAAAATAATCGAAATACCCCCGAAGGATAAAATGACCAAA
*
38267016 ACACCTCGACAGGTA
66 ACACCCCGACAGGTA
* * * *
38267031 AATTTACCGTAATACCCTCGAAGGGTAAAATGAAT-GAAATACCCCCGAAGGGTAAAATGACCAA
1 AAATTACCGAAATACCCCCGAAGGGTAAAAT-AATCGAAATACCCCCGAAGGATAAAATGACCAA
*
38267095 AATACCCC
65 AACACCCC
38267103 TGGGGGTAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
80 57 0.97
81 2 0.03
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (80 bp):
AAATTACCGAAATACCCCCGAAGGGTAAAATAATCGAAATACCCCCGAAGGATAAAATGACCAAA
ACACCCCGACAGGTA
Found at i:38277694 original size:55 final size:55
Alignment explanation
Indices: 38277633--38277738 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
38277623 ATTTACTAAT
* *
38277633 TCAACTCAATAAATCTAATCGAAAACCGAATTTTTCAACAGCATTAAGAATTAAC
1 TCAACTCAATAAATCTAATCGAAAACCGAACTTTTCAACACCATTAAGAATTAAC
* * *
38277688 TCAACTCAATAAATCTGATCTAAAACTGAACTTTTCAACACCATTAAGAAT
1 TCAACTCAATAAATCTAATCGAAAACCGAACTTTTCAACACCATTAAGAAT
38277739 CTGTTTGTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (55 bp):
TCAACTCAATAAATCTAATCGAAAACCGAACTTTTCAACACCATTAAGAATTAAC
Found at i:38286215 original size:27 final size:28
Alignment explanation
Indices: 38286172--38286238 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
38286162 AAACATCATT
*
38286172 AAAA-ATAATAGAAAATACAAATT-T-TA
1 AAAATATAATATAAAATA-AAATTATATA
*
38286198 AAAATATAATATATAATAAAATTATATA
1 AAAATATAATATAAAATAAAATTATATA
*
38286226 AATAATTTAATAT
1 AA-AATATAATAT
38286239 TTTAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 9 0.26
27 12 0.35
28 4 0.12
29 9 0.26
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAATATAATATAAAATAAAATTATATA
Found at i:38293770 original size:25 final size:27
Alignment explanation
Indices: 38293742--38293794 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
38293732 AAAAATCATC
38293742 CCAAATAATA-ATATAG-TG-CAAAAAT
1 CCAAA-AATATATATAGATGTCAAAAAT
*
38293767 CCAAACATATATATAGATGTCAAAAAT
1 CCAAAAATATATATAGATGTCAAAAAT
38293794 C
1 C
38293795 TATTTCGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 3 0.12
25 11 0.46
26 2 0.08
27 8 0.33
ACGTcount: A:0.53, C:0.15, G:0.08, T:0.25
Consensus pattern (27 bp):
CCAAAAATATATATAGATGTCAAAAAT
Found at i:38303300 original size:10 final size:10
Alignment explanation
Indices: 38303285--38303320 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
38303275 AATGGACATG
38303285 AAAATAAATA
1 AAAATAAATA
38303295 AAAATAAAATA
1 AAAAT-AAATA
*
38303306 AGAATAAATA
1 AAAATAAATA
38303316 AAAAT
1 AAAAT
38303321 TATATAAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (10 bp):
AAAATAAATA
Found at i:38303745 original size:22 final size:22
Alignment explanation
Indices: 38303720--38303776 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
38303710 GAAATAGTTG
**
38303720 AAAAAGATTAAAATTTTGTTTT
1 AAAAAGATTAAAATTTTACTTT
38303742 AAAAA-ATTTAAAATTTTACTTT
1 AAAAAGA-TTAAAATTTTACTTT
* *
38303764 AAAATGACTAAAA
1 AAAAAGATTAAAA
38303777 AACATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.39
Consensus pattern (22 bp):
AAAAAGATTAAAATTTTACTTT
Found at i:38303814 original size:22 final size:21
Alignment explanation
Indices: 38303783--38303851 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 21
38303773 AAAAAACATA
*
38303783 TTTTTATTTTAAAAATCTAAAC
1 TTTTTTTTTTAAAAATC-AAAC
38303805 TTTTTTTTTT--AAATC--AC
1 TTTTTTTTTTAAAAATCAAAC
*
38303822 TTTTTTTCTTAAAAATCAAAAC
1 TTTTTTTTTTAAAAATC-AAAC
*
38303844 TTTATTTT
1 TTTTTTTT
38303852 CGAAATAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
17 11 0.29
19 5 0.13
20 5 0.13
22 17 0.45
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTTTTTTAAAAATCAAAC
Found at i:38304788 original size:42 final size:42
Alignment explanation
Indices: 38304741--38305255 Score: 654
Period size: 42 Copynumber: 12.3 Consensus size: 42
38304731 CTTAATACAC
* *
38304741 AATGCAATGAAAAGTAAATGGACCTTCACACCTGGGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
38304783 AATGCAATGAAAAGTGAATGAACCTCCACACCTAGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* ** * *
38304825 GATGCAATGAAAAGTAAATGGACCTTTACACTTGAGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * * *
38304867 AATACAATAAAAAGTAAATGAACCTTCACACCTAGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
38304909 AATGCAATGAAAAGTGAATGGGCCTCCACACTTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
38304951 AATGCAAGGAAAAGTAAATGGGCCTCCACACCTGGGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
38304993 AATGCAAT-AAATAGTAAATGGACCTCCACACCTGGGCCTCTA
1 AATGCAATGAAA-AGTAAATGGACCTCCACACCTGGGCCTCTA
* * * *
38305035 AATTCAACGAAAAGAAAATAGACCTCCACACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* *
38305077 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGTCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * * *
38305119 AATGTAATAAAAAGTGAATGGACCTCCACACTTAGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * *
38305161 AATGCAATGAAAAGTAAATGGACCTCCACACTTGGACCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
* * * *
38305203 AATGCAATCAAAAGTGAATGGACATCCACACTTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
*
38305245 AATGGAATGAA
1 AATGCAATGAA
38305256 TAATTTCATT
Statistics
Matches: 405, Mismatches: 66, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
41 3 0.01
42 399 0.99
43 3 0.01
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
AATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTA
Found at i:38307049 original size:34 final size:34
Alignment explanation
Indices: 38307010--38307077 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
38307000 TTTGAACATG
38307010 GTGGCTAGAGTAGCTAATGCACCTGCTAACTGGT
1 GTGGCTAGAGTAGCTAATGCACCTGCTAACTGGT
* *
38307044 GTGGCTAGAGTAGCTAATGCATCTGCTTACTGGT
1 GTGGCTAGAGTAGCTAATGCACCTGCTAACTGGT
38307078 TTTCTTCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (34 bp):
GTGGCTAGAGTAGCTAATGCACCTGCTAACTGGT
Found at i:38310350 original size:37 final size:37
Alignment explanation
Indices: 38310300--38310378 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
38310290 TTATTACGAA
* * *
38310300 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
38310337 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
38310374 GTCTT
1 GTCTT
38310379 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:38310575 original size:47 final size:47
Alignment explanation
Indices: 38310497--38310817 Score: 525
Period size: 47 Copynumber: 6.8 Consensus size: 47
38310487 CCCTTCGGGA
* * * * * *
38310497 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
38310544 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38310591 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38310640 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38310687 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38310734 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38310781 CTTATCACACATATACACTTTCACATTCATCACATCG
1 CTTATCACATATATACACTTTCACATTCATCACATCG
38310818 AATCCTAAAT
Statistics
Matches: 261, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 214 0.82
49 47 0.18
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:38315747 original size:28 final size:28
Alignment explanation
Indices: 38315706--38315763 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
38315696 TTCTCGATGG
*
38315706 TATGATCTTTTACCTTGTATTTTAACGC
1 TATGATCTTGTACCTTGTATTTTAACGC
38315734 TATGATCTTGTACCTTGTATTTTAACGC
1 TATGATCTTGTACCTTGTATTTTAACGC
38315762 TA
1 TA
38315764 AGCAGTTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.48
Consensus pattern (28 bp):
TATGATCTTGTACCTTGTATTTTAACGC
Found at i:38317251 original size:12 final size:13
Alignment explanation
Indices: 38317235--38317274 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
38317225 GAATAAACAA
38317235 ATGAACGAATGAG
1 ATGAACGAATGAG
38317248 -TGAACGAATG-G
1 ATGAACGAATGAG
*
38317259 ATGAATGAATGA-
1 ATGAACGAATGAG
38317271 ATGA
1 ATGA
38317275 TTGATTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 1 0.04
12 23 0.96
ACGTcount: A:0.45, C:0.05, G:0.30, T:0.20
Consensus pattern (13 bp):
ATGAACGAATGAG
Found at i:38318531 original size:24 final size:25
Alignment explanation
Indices: 38318504--38318550 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
38318494 ACTGGTCATA
*
38318504 GAGAGAATTGATGAG-GAATATTTG
1 GAGAGAATTGAGGAGAGAATATTTG
*
38318528 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAGAGAATATT
38318551 GAGAATTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (25 bp):
GAGAGAATTGAGGAGAGAATATTTG
Found at i:38319525 original size:134 final size:133
Alignment explanation
Indices: 38319236--38319651 Score: 482
Period size: 134 Copynumber: 3.1 Consensus size: 133
38319226 AGACCCAAAA
* * * * *
38319236 ATAGGTAAAATGATCGAAAA-ACCCCCATAGGATAAAATGA-CAGAAATACCTCCATAAGGTAAA
1 ATAGGTAAAATGA-CCAAAATACCCTCATAGGGTAAAATGATC-GAAATACCCCCATAGGGTAAA
* * ** * *
38319299 ATGACTGAAATACCCCCATACAGTAAAATGACCAAAATACCCCCATAGGGTAAAATTACCAAAAT
64 ATGACCGAAATAACCCCATAGGGTAAAATGACCAAAATA-CCCTATAGGGTAAAATAACCAAAAT
38319364 ACCCTC
128 ACCCTC
* ** *
38319370 ATAGGGTAAAATGTCTGAAATACCCTCATAGGGTAAAATGATCGAAATACCCCCATAGGGTATAA
1 ATA-GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAA
* *
38319435 TGACCAAAATAACCCCATAGGGT-AAATTACCAAAATACCACTATAGGGTAAAATAACCAAAATA
65 TGACCGAAATAACCCCATAGGGTAAAATGACCAAAATACC-CTATAGGGTAAAATAACCAAAATA
38319499 CCCTC
129 CCCTC
* *
38319504 ATAGGTTAAAATGACCAAAATACCCTTATAGGGTAAAATAATCGAAATACCCCCATAGGGTAAAA
1 ATAGG-TAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAA
* * * * *
38319569 TGATCGAAAT-ACCCCATAGGGTAAAATGA-CAGAAATACCCTCATAAGGTAAAATGATCGAAAT
65 TGACCGAAATAACCCCATAGGGTAAAATGACCA-AAATACCCT-ATAGGGTAAAATAACCAAAAT
*
38319632 ACCCCC
128 ACCCTC
*
38319638 ATAAGATAAAATGA
1 AT-AGGTAAAATGA
38319652 TTGTTATACC
Statistics
Matches: 242, Mismatches: 31, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
133 20 0.08
134 155 0.64
135 66 0.27
136 1 0.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.20
Consensus pattern (133 bp):
ATAGGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAAT
GACCGAAATAACCCCATAGGGTAAAATGACCAAAATACCCTATAGGGTAAAATAACCAAAATACC
CTC
Found at i:38319652 original size:27 final size:27
Alignment explanation
Indices: 38319239--38319652 Score: 426
Period size: 27 Copynumber: 15.4 Consensus size: 27
38319229 CCCAAAAATA
*
38319239 GGTAAAATGATCGAAAAACCCCCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
* * *
38319266 GATAAAATGA-CAGAAATACCTCCATAA
1 GGTAAAATGATC-GAAATACCCCCATAG
*
38319293 GGTAAAATGA-CTGAAATACCCCCATAC
1 GGTAAAATGATC-GAAATACCCCCATAG
* * *
38319320 AGTAAAATGACCAAAATACCCCCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
* * * *
38319347 GGTAAAATTACCAAAATACCCTCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
*
38319374 GGTAAAATG-TCTGAAATACCCTCATAG
1 GGTAAAATGATC-GAAATACCCCCATAG
38319401 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
* * * *
38319428 GGTATAATGACCAAAATAACCCCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
* * * * *
38319455 GGT-AAATTACCAAAATACCACTATAG
1 GGTAAAATGATCGAAATACCCCCATAG
* * * *
38319481 GGTAAAATAACCAAAATACCCTCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
* * * **
38319508 GTTAAAATGACCAAAATACCCTTATAG
1 GGTAAAATGATCGAAATACCCCCATAG
*
38319535 GGTAAAATAATCGAAATACCCCCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
38319562 GGTAAAATGATCGAAATA-CCCCATAG
1 GGTAAAATGATCGAAATACCCCCATAG
* *
38319588 GGTAAAATGA-CAGAAATACCCTCATAA
1 GGTAAAATGATC-GAAATACCCCCATAG
*
38319615 GGTAAAATGATCGAAATACCCCCATAA
1 GGTAAAATGATCGAAATACCCCCATAG
*
38319642 GATAAAATGAT
1 GGTAAAATGAT
38319653 TGTTATACCC
Statistics
Matches: 334, Mismatches: 45, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
25 1 0.00
26 47 0.14
27 282 0.84
28 4 0.01
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.20
Consensus pattern (27 bp):
GGTAAAATGATCGAAATACCCCCATAG
Found at i:38320161 original size:33 final size:35
Alignment explanation
Indices: 38320115--38320186 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 35
38320105 ACTGCATGAC
* ** *
38320115 TGATATCTGTTACTGTTA-TGGGCTAAGGCCCCAT
1 TGATATCTATTACTGAAATTGGGCAAAGGCCCCAT
*
38320149 TGATA-CTATTACTGAAATTGGGCAAAGGCCCTAT
1 TGATATCTATTACTGAAATTGGGCAAAGGCCCCAT
38320183 TGAT
1 TGAT
38320187 TACTGGCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 9 0.28
34 23 0.72
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (35 bp):
TGATATCTATTACTGAAATTGGGCAAAGGCCCCAT
Found at i:38322287 original size:17 final size:19
Alignment explanation
Indices: 38322265--38322307 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 19
38322255 ACAGACACAA
38322265 AAAAAAATAAAGTC-AAT-
1 AAAAAAATAAAGTCAAATG
38322282 -AAAAAATAAAGTCAAATG
1 AAAAAAATAAAGTCAAATG
38322300 AAAAAAAT
1 AAAAAAAT
38322308 GTGAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.57
17 3 0.13
19 7 0.30
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.16
Consensus pattern (19 bp):
AAAAAAATAAAGTCAAATG
Found at i:38324829 original size:140 final size:142
Alignment explanation
Indices: 38324586--38324869 Score: 430
Period size: 140 Copynumber: 2.0 Consensus size: 142
38324576 CTTTAAAAAG
* * * *
38324586 AATCACTATTTGTCTTAAAAATCAAAAATTTATTTCGAAATAGTTGAAAGAGATCAAAATTTTGT
1 AATCACTATTTGTCTTAAAAATCAAAAATTTATTTCAAAATAGTTGAAAAAGATCAAAACTTTAT
* * *
38324651 TTTAAAAAATTTAAAATTTTCCTTTAAAATGATTAAAAAACATATTTTTATTTTAAAAATCTAAA
66 TTTAAAAAATTTAAAATTTTCCTTTAAAATGATAAAAAAACAAATTTTTAGTTTAAAAATCTAAA
38324716 CT-T-TTTTTTA
131 CTCTCTTTTTTA
* *
38324726 AATCACTATTTTTCTTAAAAATCAAAACTTTATTTCAAAATAGTTGAAAAAGATCAAAACTTTAT
1 AATCACTATTTGTCTTAAAAATCAAAAATTTATTTCAAAATAGTTGAAAAAGATCAAAACTTTAT
* * *
38324791 TTT-AAAAATTTAAACTTTTCCTTTAAGATGACTAAAAAAACAAATTTTTAGTTTAGAAATCTAA
66 TTTAAAAAATTTAAAATTTTCCTTTAAAATGA-TAAAAAAACAAATTTTTAGTTTAAAAATCTAA
38324855 ACTCTCTTTTTTA
130 ACTCTCTTTTTTA
38324868 AA
1 AA
38324870 AAAAAAATCA
Statistics
Matches: 129, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
139 26 0.20
140 93 0.72
141 1 0.01
142 9 0.07
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (142 bp):
AATCACTATTTGTCTTAAAAATCAAAAATTTATTTCAAAATAGTTGAAAAAGATCAAAACTTTAT
TTTAAAAAATTTAAAATTTTCCTTTAAAATGATAAAAAAACAAATTTTTAGTTTAAAAATCTAAA
CTCTCTTTTTTA
Found at i:38325255 original size:125 final size:125
Alignment explanation
Indices: 38325106--38325358 Score: 479
Period size: 125 Copynumber: 2.0 Consensus size: 125
38325096 TTAAGAACAA
*
38325106 AATATGAAAAACCTCCCTTTTTTTCTTTCATTTCAATTCATGTATATATATTGTTTTTTTATCTT
1 AATATGAAAAACCTCCCTTTTTTTCTTTCATTTCAATTCATGTATATATATTGTTTTTTAATCTT
38325171 GTTTATTTGTAAAAAATGATAATAATATTTAATAATAGTAGTAGTAGTGATGATAATAAT
66 GTTTATTTGTAAAAAATGATAATAATATTTAATAATAGTAGTAGTAGTGATGATAATAAT
* *
38325231 AATATGAAAAACCTCCCTTTTTTTCTTTCATTTCATTTCATGTATATATGTTGTTTTTTAATCTT
1 AATATGAAAAACCTCCCTTTTTTTCTTTCATTTCAATTCATGTATATATATTGTTTTTTAATCTT
38325296 GTTTATTTGTAAAAAATGATAATAATATTTAATAATAGTAGTAGTAGTGATGATAATAAT
66 GTTTATTTGTAAAAAATGATAATAATATTTAATAATAGTAGTAGTAGTGATGATAATAAT
38325356 AAT
1 AAT
38325359 TTAGGCCCTT
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (125 bp):
AATATGAAAAACCTCCCTTTTTTTCTTTCATTTCAATTCATGTATATATATTGTTTTTTAATCTT
GTTTATTTGTAAAAAATGATAATAATATTTAATAATAGTAGTAGTAGTGATGATAATAAT
Found at i:38326132 original size:28 final size:28
Alignment explanation
Indices: 38326087--38326153 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
38326077 AATGGGCCTA
* *
38326087 CTACACGAGTTGTAGGTTGGAATGTAAG
1 CTACACGAGCTATAGGTTGGAATGTAAG
*
38326115 CTACACGAGCTATGGGTTGGAATGTAAG
1 CTACACGAGCTATAGGTTGGAATGTAAG
*
38326143 CTACATGAGCT
1 CTACACGAGCT
38326154 CTGGAAAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (28 bp):
CTACACGAGCTATAGGTTGGAATGTAAG
Found at i:38340354 original size:40 final size:40
Alignment explanation
Indices: 38340264--38340342 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
38340254 GCAATCAAGT
* * *
38340264 TGCCAGTATTATGGGCAAGCTACCAATAATGCAAATAAAC
1 TGCCAGTATTGTGGACAAGCCACCAATAATGCAAATAAAC
*
38340304 TGCCAGTATTGTGGACAAGCCACCAGTAATGCAAATAAA
1 TGCCAGTATTGTGGACAAGCCACCAATAATGCAAATAAA
38340343 TTGTTAGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (40 bp):
TGCCAGTATTGTGGACAAGCCACCAATAATGCAAATAAAC
Found at i:38340370 original size:40 final size:40
Alignment explanation
Indices: 38340279--38340371 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
38340269 GTATTATGGG
* **
38340279 CAAGCTACCAATAATGCAAATAAACTGCCAGTATTGTGGA
1 CAAGCTACCAGTAATGCAAATAAACTGCCAGTATTGCAGA
* * **
38340319 CAAGCCACCAGTAATGCAAATAAATTGTTAGTATTGCAGA
1 CAAGCTACCAGTAATGCAAATAAACTGCCAGTATTGCAGA
*
38340359 CAAGCTGCCAGTA
1 CAAGCTACCAGTA
38340372 TAATGGACAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (40 bp):
CAAGCTACCAGTAATGCAAATAAACTGCCAGTATTGCAGA
Found at i:38340510 original size:38 final size:38
Alignment explanation
Indices: 38340428--38340511 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
38340418 TCATAACAAT
* ** *
38340428 ACAGTAGGCATGATTAAATTATGCAATCAGTAGTAGAA
1 ACAGTAGGCATGATTAAATCATGCAATCAGTAACAAAA
*
38340466 ACAGTAGGCATGATTTAAA-CATGCGATCAGTAACAAAA
1 ACAGTAGGCATGA-TTAAATCATGCAATCAGTAACAAAA
*
38340504 ATAGTAGG
1 ACAGTAGG
38340512 TGCATTTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 34 0.87
39 5 0.13
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (38 bp):
ACAGTAGGCATGATTAAATCATGCAATCAGTAACAAAA
Found at i:38349369 original size:12 final size:13
Alignment explanation
Indices: 38349337--38349378 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
38349327 ATATTTTAAG
38349337 TTAAATAAATTATT
1 TTAAAT-AATTATT
*
38349351 ATAAATAATT-TT
1 TTAAATAATTATT
*
38349363 TTAAATATTTATT
1 TTAAATAATTATT
38349376 TTA
1 TTA
38349379 TTATTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.42
13 9 0.38
14 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAAATAATTATT
Found at i:38350040 original size:24 final size:24
Alignment explanation
Indices: 38349988--38350040 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
38349978 AGACGTTATG
*
38349988 GCCAAATCATGAAAGATTACATTA
1 GCCACATCATGAAAGATTACATTA
38350012 GCCACATCATGAAAGATTACATTA
1 GCCACATCATGAAAGATTACATTA
38350036 GCCAC
1 GCCAC
38350041 CAAAATGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (24 bp):
GCCACATCATGAAAGATTACATTA
Found at i:38355636 original size:51 final size:51
Alignment explanation
Indices: 38355519--38356010 Score: 483
Period size: 51 Copynumber: 9.7 Consensus size: 51
38355509 TCATTCGATA
* * *
38355519 CACGTAATGGCCTTCACATAGTACTACACACGTGATC-AAGTTT-TACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTAT-CGGTT
* * *
38355569 CACGTAGTAGCTTTCACATAGTACTACACACGTGACCAAAGTTTTTCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTATCGGTT
* * * * *
38355620 CACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCA-TTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTTATCGGTT
* * * * *
38355671 CACGTAGTAGCCTTCACACAGTACTACAGACGTGACCAAAGCTTCTCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTATCGGTT
* * * * * *
38355722 CACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCA-TTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTTATCGGTT
* * * * *
38355773 CACGTAGTAGCCTTCACACAGTACTACAGACGTGACCAAAGCTTCTCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTATCGGTT
* * * * * **
38355824 CACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCA-TTTATCAATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTTATCGGTT
* * * * *
38355875 CACGTAGTAGCCTTCACACAGTACTACAGACGTGACCAAAGCTTCTCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTATCGGTT
* * * * * **
38355926 CACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCA-TTTATCAATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTTATCGGTT
38355977 CACGTAGTAGCCTTCACATAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
38356011 TTCATCGATA
Statistics
Matches: 348, Mismatches: 85, Indels: 17
0.77 0.19 0.04
Matches are distributed among these distances:
50 36 0.10
51 307 0.88
52 5 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (51 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTATCGGTT
Found at i:38355696 original size:102 final size:102
Alignment explanation
Indices: 38355528--38356010 Score: 806
Period size: 102 Copynumber: 4.7 Consensus size: 102
38355518 ACACGTAATG
* * * *** * * *
38355528 GCCTTCACATAGTACTACACACGTGATCAAGTTTTA-CGGTTCACGTAGTAGCTTTCACATAGTA
1 GCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACACAGTA
* * * *
38355592 CTACACACGTGACCAAAGTTTTTCGGTACACATAGTA
66 CTACAGACGTGACCAAAGCTTCTCGGTACACATTGTA
38355629 GCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACACAGTA
1 GCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACACAGTA
38355694 CTACAGACGTGACCAAAGCTTCTCGGTACACATTGTA
66 CTACAGACGTGACCAAAGCTTCTCGGTACACATTGTA
38355731 GCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACACAGTA
1 GCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACACAGTA
38355796 CTACAGACGTGACCAAAGCTTCTCGGTACACATTGTA
66 CTACAGACGTGACCAAAGCTTCTCGGTACACATTGTA
*
38355833 GCCTTCACTTAGTACTACACATGTGACCATCATTTATCAATTCACGTAGTAGCCTTCACACAGTA
1 GCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACACAGTA
38355898 CTACAGACGTGACCAAAGCTTCTCGGTACACATTGTA
66 CTACAGACGTGACCAAAGCTTCTCGGTACACATTGTA
* *
38355935 GCCTTCACTTAGTACTACACATGTGACCATCATTTATCAATTCACGTAGTAGCCTTCACATAGTA
1 GCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACACAGTA
*
38356000 CTACACACGTG
66 CTACAGACGTG
38356011 TTCATCGATA
Statistics
Matches: 365, Mismatches: 16, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
101 30 0.08
102 335 0.92
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (102 bp):
GCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACACAGTA
CTACAGACGTGACCAAAGCTTCTCGGTACACATTGTA
Found at i:38356533 original size:30 final size:31
Alignment explanation
Indices: 38356479--38356537 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
38356469 GCTTCGACTC
38356479 AACTTTTGTCAAAATTACGATTTTGTCCCTA
1 AACTTTTGTCAAAATTACGATTTTGTCCCTA
*
38356510 AACTTTTG-CATAATTAC-ATTTTTGTCCC
1 AACTTTTGTCAAAATTACGA-TTTTGTCCC
38356538 CAAGCTCGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 1 0.04
30 17 0.65
31 8 0.31
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.44
Consensus pattern (31 bp):
AACTTTTGTCAAAATTACGATTTTGTCCCTA
Found at i:38362955 original size:48 final size:47
Alignment explanation
Indices: 38362892--38362982 Score: 128
Period size: 48 Copynumber: 1.9 Consensus size: 47
38362882 AACACACCAT
* * * *
38362892 TTGTGGACAAGCCACCACATTATTGTCGATAAACGACCACATAACACA
1 TTGTGGACAAACCACCACATAATTGCCAAT-AACGACCACATAACACA
*
38362940 TTGTGGACAAACCACCACATAATTGCCAATAACGACCATATAA
1 TTGTGGACAAACCACCACATAATTGCCAATAACGACCACATAA
38362983 TCATAGATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 12 0.32
48 26 0.68
ACGTcount: A:0.40, C:0.26, G:0.13, T:0.21
Consensus pattern (47 bp):
TTGTGGACAAACCACCACATAATTGCCAATAACGACCACATAACACA
Done.