Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 63 of 208
Found at i:18112909 original size:20 final size:19
Alignment explanation
Indices: 18112886--18112952 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
18112876 AGGCAAAAAT
*
18112886 GTGCAATCAGAGGCACCGTA
1 GTGCAAT-AGAGGCACCGAA
*
18112906 GTGCAAATAGAGACACCGAA
1 GTGC-AATAGAGGCACCGAA
*
18112926 GTGTATATAGAGGCACCGAA
1 GTGCA-ATAGAGGCACCGAA
18112946 GTGCAAT
1 GTGCAAT
18112953 CCCGTACAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.08
20 34 0.85
21 3 0.08
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.16
Consensus pattern (19 bp):
GTGCAATAGAGGCACCGAA
Found at i:18115339 original size:5 final size:5
Alignment explanation
Indices: 18115329--18115354 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
18115319 GAAGAGAGAA
18115329 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
18115355 GGATTTAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:18116349 original size:75 final size:79
Alignment explanation
Indices: 18116261--18116446 Score: 247
Period size: 83 Copynumber: 2.4 Consensus size: 79
18116251 TAATTAATGG
*
18116261 TGGTGGAGCCATTCTAAATGGCGCCACCACTTTATGTTAG-GTTT-TTTT-TTT-AATTTAAAAA
1 TGGTGGAGCCATTCTAAATGGCGCCACCACTTTATGTTAGTGTTTGTTTTCTTTAAATTAAAAAA
*
18116322 AATGTTATTCTATT
66 AATATTATTCTATT
* *
18116336 TGGTGGAGTCATTCTAAATGGCGCCACCACTTTATGTTAGTTTTTTTAGGTTTTCTTTAAATTAA
1 TGGTGGAGCCATTCTAAATGGCGCCACCACTTTATGTTAG--TGTTT--GTTTTCTTTAAATTAA
*
18116401 AAAAAATATTATTTTATT
62 AAAAAATATTATTCTATT
*
18116419 TGGTGGAGCCATTCTAAATAGCG-CACCA
1 TGGTGGAGCCATTCTAAATGGCGCCACCA
18116447 GTGTAATCTA
Statistics
Matches: 96, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
75 39 0.41
78 3 0.03
81 4 0.04
82 8 0.08
83 42 0.44
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (79 bp):
TGGTGGAGCCATTCTAAATGGCGCCACCACTTTATGTTAGTGTTTGTTTTCTTTAAATTAAAAAA
AATATTATTCTATT
Found at i:18116473 original size:83 final size:82
Alignment explanation
Indices: 18116303--18116476 Score: 181
Period size: 83 Copynumber: 2.1 Consensus size: 82
18116293 TATGTTAGGT
* * * * * *
18116303 TTTTTTTTTAATTTAAAAAAATGTTATTCTATTTGGTGGAGTCATTCTAAATGGCGCCACCACTT
1 TTTTCTTTAAATTAAAAAAAATATTATTCTATTTGGTGGAGCCATTCTAAATAGCGCCACCACTT
* * * * *
18116368 TATGTTAGTTTTTTTAGG
66 AATCTTACTATTTTTA-C
* *
18116386 TTTTCTTTAAATTAAAAAAAATATTATTTTATTTGGTGGAGCCATTCTAAATAGCG-CACCAGTG
1 TTTTCTTTAAATTAAAAAAAATATTATTCTATTTGGTGGAGCCATTCTAAATAGCGCCACCACT-
18116450 TAATCTATCACTATTTTT-C
65 TAATCT-T-ACTATTTTTAC
18116469 TTTTCTTT
1 TTTTCTTT
18116477 TTTAATATAT
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
82 6 0.08
83 61 0.81
84 1 0.01
85 7 0.09
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (82 bp):
TTTTCTTTAAATTAAAAAAAATATTATTCTATTTGGTGGAGCCATTCTAAATAGCGCCACCACTT
AATCTTACTATTTTTAC
Found at i:18117037 original size:21 final size:20
Alignment explanation
Indices: 18117011--18117059 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
18117001 TTTTGGAATG
**
18117011 TTGTAAATGTAAAATTATATT
1 TTGTAAATAAAAAATT-TATT
18117032 TTGTAAA-AAAAAATTTATT
1 TTGTAAATAAAAAATTTATT
18117051 TATGTAAAT
1 T-TGTAAAT
18117060 TGATAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.21
20 12 0.50
21 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (20 bp):
TTGTAAATAAAAAATTTATT
Found at i:18117046 original size:20 final size:20
Alignment explanation
Indices: 18117021--18117058 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18117011 TTGTAAATGT
18117021 AAAATTATATTT-TGTAAAAA
1 AAAATT-TATTTATGTAAAAA
18117041 AAAATTTATTTATGTAAA
1 AAAATTTATTTATGTAAA
18117059 TTGATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
AAAATTTATTTATGTAAAAA
Found at i:18117307 original size:12 final size:12
Alignment explanation
Indices: 18117292--18117316 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18117282 TTTTAAATTT
18117292 AAAAAAAGAAAA
1 AAAAAAAGAAAA
18117304 AAAAAAAGAAAA
1 AAAAAAAGAAAA
18117316 A
1 A
18117317 TGGTGATAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:18117416 original size:9 final size:9
Alignment explanation
Indices: 18117385--18117419 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
18117375 TTTTTAAATT
18117385 TAAAAAAAC
1 TAAAAAAAC
*
18117394 TAAAAGAAAT
1 TAAAA-AAAC
18117404 TAAAAAAAC
1 TAAAAAAAC
18117413 TAAAAAA
1 TAAAAAA
18117420 TAATAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (9 bp):
TAAAAAAAC
Found at i:18121098 original size:22 final size:24
Alignment explanation
Indices: 18121076--18121135 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 24
18121066 CAAATCGTTC
18121076 TCTTTT-TT-ATTC-CT-CTTTTT
1 TCTTTTATTGATTCTCTCCTTTTT
18121096 TCTTTTATTGATTCTCTCC---TT
1 TCTTTTATTGATTCTCTCCTTTTT
18121117 T-TTTTATTGATTCTCTCCT
1 TCTTTTATTGATTCTCTCCT
18121136 CTCCTACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 23 0.66
21 5 0.14
22 4 0.11
23 2 0.06
24 1 0.03
ACGTcount: A:0.08, C:0.22, G:0.03, T:0.67
Consensus pattern (24 bp):
TCTTTTATTGATTCTCTCCTTTTT
Found at i:18121123 original size:20 final size:20
Alignment explanation
Indices: 18121098--18121135 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
18121088 CTCTTTTTTC
18121098 TTTTATTGATTCTCTCCTTT
1 TTTTATTGATTCTCTCCTTT
18121118 TTTTATTGATTCTCTCCT
1 TTTTATTGATTCTCTCCT
18121136 CTCCTACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.21, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTATTGATTCTCTCCTTT
Found at i:18121295 original size:21 final size:21
Alignment explanation
Indices: 18121269--18121365 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
18121259 AATCATATCT
*
18121269 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
*
18121290 TCTAAGATTACATATATCATA
1 TCTAAGATTGCATATATCATA
18121311 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
18121332 TCTAAGATTGCATATA--ATA
1 TCTAAGATTGCATATATCATA
*
18121351 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
18121366 CCTCGAAAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 17 0.24
21 55 0.76
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:18121326 original size:42 final size:42
Alignment explanation
Indices: 18121246--18121365 Score: 165
Period size: 42 Copynumber: 2.9 Consensus size: 42
18121236 AAATTAAATC
*
18121246 TCTAAGATTACA-AAATCATATCTTCTAAGATTGTATATATCATA
1 TCTAAGATTACATATATCATA---TCTAAGATTGTATATATCATA
*
18121290 TCTAAGATTACATATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTACATATATCATATCTAAGATTGTATATATCATA
*
18121332 TCTAAGATTGCATATA--ATATCTAAGATTGTATAT
1 TCTAAGATTACATATATCATATCTAAGATTGTATAT
18121366 CCTCGAAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
40 17 0.24
42 35 0.49
44 12 0.17
45 7 0.10
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.39
Consensus pattern (42 bp):
TCTAAGATTACATATATCATATCTAAGATTGTATATATCATA
Found at i:18121628 original size:44 final size:44
Alignment explanation
Indices: 18121569--18121653 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
18121559 AGGAATTCGT
*
18121569 GCTTCAATCTACTCCACTGTAACTTCAGG-GAGATAAGACTTATA
1 GCTTCAATCTACTCCACTGCAACTTCAGGAG-GATAAGACTTATA
* * *
18121613 GCTTTAATCTGCTCCACTGCCACTTCAGGAGGATAAGACTT
1 GCTTCAATCTACTCCACTGCAACTTCAGGAGGATAAGACTT
18121654 GCTGGCTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 35 0.97
45 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
GCTTCAATCTACTCCACTGCAACTTCAGGAGGATAAGACTTATA
Found at i:18121835 original size:132 final size:132
Alignment explanation
Indices: 18121651--18122576 Score: 1564
Period size: 132 Copynumber: 7.0 Consensus size: 132
18121641 GAGGATAAGA
* *
18121651 CTTGCTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
*
18121716 CACTACTGCTTAGGGAGATAAGATCTACAACCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
18121781 GG
131 GG
*
18121783 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTCCCGTCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
18121848 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
18121913 GG
131 GG
* * *
18121915 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATAAGATTTCCCATCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
*
18121980 CACTACTGCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
18122045 GG
131 GG
* * *
18122047 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCGTTGATCTACTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* * *
18122112 CACTACTACTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCATGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
18122177 GG
131 GG
* *
18122179 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTTCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
*
18122244 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGAGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
18122309 GG
131 GG
* *
18122311 CTTGTTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGACGTCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* * *
18122376 CTCTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCAACTCCGCTGCTGCTCAGGGAGATAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
*
18122441 TG
131 GG
* *
18122443 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCTTCTTTGATCTGCTT
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
** * * * * *
18122508 CACTACTGCTTAGGGAGATAAGATCTGTAATTTTAAACCTACTCCACTGCTGCTCAGGAAGATAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
18122573 GG
131 GG
18122575 CT
1 CT
18122577 GGAGTCTTTG
Statistics
Matches: 749, Mismatches: 45, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 749 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
GG
Found at i:18122570 original size:88 final size:88
Alignment explanation
Indices: 18122494--18122805 Score: 220
Period size: 88 Copynumber: 3.6 Consensus size: 88
18122484 AGATTTGCCT
* *
18122494 TCTTTGATCTGCTTCACTA-CTGCT-TAGGGAGATAAGATCTG-TAATTTTAAACCTACTCCACT
1 TCTTTGATCTGCTTCACTATC-GCTGTAGGAAGACAAGATCTGCT-ATTTTAAACCTACTCCACT
*
18122556 GCTGCTCAGGAAGATAAGGCTGGAG
64 GCTGCTCAGGAAGATAAGGCTGCAG
* * *
18122581 TCTTTGATCTGCTTCACTATCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTGC
1 TCTTTGATCTGCTTCACTATCGCTGTAGGAAGACAAGATCTGCTATTTTAAACCTACTCCACTGC
** * **
18122646 AACACAGGAAGGCAAGGCTG-ATG
66 TGCTCAGGAAGATAAGGCTGCA-G
* * * ** * * * * * ** *
18122669 TCTTCGATCTACTTCGCCGTCGGTGCAGGAAGGCAAGATCTGTTATTTTTAACCTGTTCCGCTGC
1 TCTTTGATCTGCTTCACTATCGCTGTAGGAAGACAAGATCTGCTATTTTAAACCTACTCCACTGC
** * * **
18122734 AACACAGGGAGGCAAGGCTG-ATG
66 TGCTCAGGAAGATAAGGCTGCA-G
* * * * * * *
18122757 TCTTCGGTCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTT
1 TCTTTGATCTGCTTCACTATCGCTGTAGGAAGACAAGATCTGCTATTTT
18122806 CACTAATCTG
Statistics
Matches: 196, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
87 22 0.11
88 173 0.88
89 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (88 bp):
TCTTTGATCTGCTTCACTATCGCTGTAGGAAGACAAGATCTGCTATTTTAAACCTACTCCACTGC
TGCTCAGGAAGATAAGGCTGCAG
Found at i:18122791 original size:44 final size:44
Alignment explanation
Indices: 18122650--18122793 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 44
18122640 CACTGCAACA
* *
18122650 CAGGAAGGCAAGGCTGATGTCTTCGATCTACTTCGCCGTCGGTG
1 CAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCGGTG
* * * * ** * ****
18122694 CAGGAAGGCAAGATCTGTTATTTTTAACCTG-TTCCGCTG-CAACA
1 CAGGAAGGCAAG-GCTGATGTCTTCGATCTGCTT-CGCTGTCGGTG
* *
18122738 CAGGGAGGCAAGGCTGATGTCTTCGGTCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCGGTG
18122782 CAGGAAGGCAAG
1 CAGGAAGGCAAG
18122794 ATCTGCTATT
Statistics
Matches: 69, Mismatches: 27, Indels: 8
0.66 0.26 0.08
Matches are distributed among these distances:
43 15 0.22
44 40 0.58
45 14 0.20
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCGGTG
Found at i:18130518 original size:22 final size:22
Alignment explanation
Indices: 18130493--18130546 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
18130483 TCTATTTTTT
*
18130493 ATTC-CTCCTTTTTCTTTTGTTG
1 ATTCTCTCCTTTTT-TTTTATTG
18130515 ATTCTCTCCTTTTTTTTTATTG
1 ATTCTCTCCTTTTTTTTTATTG
18130537 ATTCTCTCCT
1 ATTCTCTCCT
18130547 CTCCTACAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.07, C:0.24, G:0.06, T:0.63
Consensus pattern (22 bp):
ATTCTCTCCTTTTTTTTTATTG
Found at i:18130706 original size:21 final size:21
Alignment explanation
Indices: 18130680--18130776 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
18130670 AATCATATCT
*
18130680 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
*
18130701 TCTAAGATTACATATATCATA
1 TCTAAGATTGCATATATCATA
18130722 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
18130743 TCTAAGATTGCATATA--ATA
1 TCTAAGATTGCATATATCATA
*
18130762 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
18130777 CCTCGAAAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 17 0.24
21 55 0.76
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:18130737 original size:42 final size:42
Alignment explanation
Indices: 18130657--18130776 Score: 165
Period size: 42 Copynumber: 2.9 Consensus size: 42
18130647 AAATTAAATC
*
18130657 TCTAAGATTACA-AAATCATATCTTCTAAGATTGTATATATCATA
1 TCTAAGATTACATATATCATA---TCTAAGATTGTATATATCATA
*
18130701 TCTAAGATTACATATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTACATATATCATATCTAAGATTGTATATATCATA
*
18130743 TCTAAGATTGCATATA--ATATCTAAGATTGTATAT
1 TCTAAGATTACATATATCATATCTAAGATTGTATAT
18130777 CCTCGAAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
40 17 0.24
42 35 0.49
44 12 0.17
45 7 0.10
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.39
Consensus pattern (42 bp):
TCTAAGATTACATATATCATATCTAAGATTGTATATATCATA
Found at i:18131101 original size:13 final size:13
Alignment explanation
Indices: 18131083--18131134 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
18131073 GAGTTAGATA
*
18131083 AAATAATTAAAAT
1 AAATAAATAAAAT
* *
18131096 AAATAACTAAGAT
1 AAATAAATAAAAT
18131109 AAATAAAATAAAAT
1 AAAT-AAATAAAAT
18131123 -AATAAAATAAAA
1 AAAT-AAATAAAA
18131135 GATTGGACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 27 0.79
14 7 0.21
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:18131115 original size:22 final size:22
Alignment explanation
Indices: 18131080--18131133 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
18131070 TCCGAGTTAG
*
18131080 ATAAAATAATTAAAAT-AAATA
1 ATAAAATAAATAAAATAAAATA
*
18131101 ACTAAGATAAATAAAATAAAATA
1 A-TAAAATAAATAAAATAAAATA
18131124 ATAAAATAAA
1 ATAAAATAAA
18131134 AGATTGGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 21 0.75
23 6 0.21
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
ATAAAATAAATAAAATAAAATA
Found at i:18132944 original size:33 final size:33
Alignment explanation
Indices: 18132907--18132979 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
18132897 ACTTTCTGTT
* *
18132907 TGGTGTGTTGGTTGGACTAGCTCTTATGAGCAC
1 TGGTGTGATGGTTGGACTAGCTCTTATAAGCAC
* * * *
18132940 TGGTGTGATGGTTGGATTAGTTCTTCTAAGCAT
1 TGGTGTGATGGTTGGACTAGCTCTTATAAGCAC
18132973 TGGTGTG
1 TGGTGTG
18132980 GATGAAGGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.15, C:0.11, G:0.34, T:0.40
Consensus pattern (33 bp):
TGGTGTGATGGTTGGACTAGCTCTTATAAGCAC
Found at i:18142002 original size:50 final size:50
Alignment explanation
Indices: 18141899--18142140 Score: 238
Period size: 50 Copynumber: 4.7 Consensus size: 50
18141889 GGGAATGAGA
**
18141899 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ACCGAG---ATGAGAGG
* *
18141955 TCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * **
18142005 TCCTCA-GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCC-CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * **
18142055 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAGGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
* *
18142104 TCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
18142141 TGTTATTATC
Statistics
Matches: 161, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
48 1 0.01
49 40 0.25
50 80 0.50
51 2 0.01
53 4 0.02
56 34 0.21
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:18142368 original size:20 final size:20
Alignment explanation
Indices: 18142343--18142381 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
18142333 TGAGTTATTT
18142343 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
18142363 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
18142382 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:18157693 original size:27 final size:28
Alignment explanation
Indices: 18157661--18157784 Score: 97
Period size: 30 Copynumber: 4.2 Consensus size: 28
18157651 ATATCGCCGT
* *
18157661 AAAGGCTCACGTAT-AACAAAGAGCCAC
1 AAAGGCTCACGTATCAAAAAACAGCCAC
*
18157688 AAAGGCTTTCACTTATCAAAAAACAGCCAC
1 AAAGGC--TCACGTATCAAAAAACAGCCAC
* * * *
18157718 AAAGGCTTTCTCATATCTAATAACAGCCAC
1 AAAGGC--TCACGTATCAAAAAACAGCCAC
* * *
18157748 AAAGGCTTTCACATATCTAATAACAGCCAC
1 AAAGGC--TCACGTATCAAAAAACAGCCAC
18157778 AAAGGCT
1 AAAGGCT
18157785 TTCACATTTC
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
27 6 0.07
28 1 0.01
29 7 0.08
30 72 0.84
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (28 bp):
AAAGGCTCACGTATCAAAAAACAGCCAC
Found at i:18157718 original size:30 final size:30
Alignment explanation
Indices: 18157682--18157791 Score: 184
Period size: 30 Copynumber: 3.7 Consensus size: 30
18157672 TATAACAAAG
* * *
18157682 AGCCACAAAGGCTTTCACTTATCAAAAAAC
1 AGCCACAAAGGCTTTCACATATCTAATAAC
*
18157712 AGCCACAAAGGCTTTCTCATATCTAATAAC
1 AGCCACAAAGGCTTTCACATATCTAATAAC
18157742 AGCCACAAAGGCTTTCACATATCTAATAAC
1 AGCCACAAAGGCTTTCACATATCTAATAAC
18157772 AGCCACAAAGGCTTTCACAT
1 AGCCACAAAGGCTTTCACAT
18157792 TTCGATAATG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (30 bp):
AGCCACAAAGGCTTTCACATATCTAATAAC
Found at i:18158043 original size:55 final size:54
Alignment explanation
Indices: 18157900--18158050 Score: 171
Period size: 55 Copynumber: 2.7 Consensus size: 54
18157890 ATTTCCCTAC
* * * *
18157900 ATGACGCCATAGTCCCAAACTAGGTCTTATACTATGTGGTTCTCTTATCCCCAT
1 ATGATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTTCTCTTATCCCCAT
* **
18157954 ATGATGCCACAACCACCATGACTAGGTCTTACACTATATGGTT-T-TTCACTTCCCCAT
1 ATGATGCCATAGTC-CCA-GACTAGGTCTTACACTATATGGTTCTCTT-A--TCCCCAT
*
18158011 ATGATGCCATAGTCTCAGACTAGGTCTTACACTATATGGT
1 ATGATGCCATAGTCCCAGACTAGGTCTTACACTATATGGT
18158051 CTTCTTGCCA
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
54 12 0.15
55 28 0.35
56 23 0.28
57 18 0.22
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (54 bp):
ATGATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTTCTCTTATCCCCAT
Found at i:18158763 original size:34 final size:34
Alignment explanation
Indices: 18158720--18158789 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
18158710 ATATAGGCAG
18158720 AGAATACTTCCTAAGGAAGTAATGCGCAGTTCCC
1 AGAATACTTCCTAAGGAAGTAATGCGCAGTTCCC
* * *
18158754 AGAATACTTCCTGAGGAAGTAATGTGCAGTTGCC
1 AGAATACTTCCTAAGGAAGTAATGCGCAGTTCCC
18158788 AG
1 AG
18158790 CACTTATCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (34 bp):
AGAATACTTCCTAAGGAAGTAATGCGCAGTTCCC
Found at i:18161352 original size:27 final size:27
Alignment explanation
Indices: 18161322--18161375 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
18161312 ATTCACTGAA
*
18161322 TGACTT-ATGCTTGGACTGTCCACCATG
1 TGACTTCA-GCTTGAACTGTCCACCATG
18161349 TGACTTCGAGCTTGAACTGTCCACCAT
1 TGACTTC-AGCTTGAACTGTCCACCAT
18161376 ATGTACTCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 17 0.71
29 1 0.04
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.31
Consensus pattern (27 bp):
TGACTTCAGCTTGAACTGTCCACCATG
Found at i:18162677 original size:18 final size:18
Alignment explanation
Indices: 18162643--18162691 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
18162633 GGGTGTGCAT
18162643 AATTCGGTTAAAACCGAAAA
1 AATTCGGTT--AACCGAAAA
***
18162663 AATTCGGTTAACCGACCG
1 AATTCGGTTAACCGAAAA
18162681 AATTCGGTTAA
1 AATTCGGTTAA
18162692 GCGGTCGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 17 0.65
20 9 0.35
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (18 bp):
AATTCGGTTAACCGAAAA
Found at i:18163463 original size:27 final size:27
Alignment explanation
Indices: 18163425--18163504 Score: 151
Period size: 27 Copynumber: 3.0 Consensus size: 27
18163415 AACTATGTCG
18163425 TTGTATACTATTGTCTTAATTTTTTCA
1 TTGTATACTATTGTCTTAATTTTTTCA
18163452 TTGTATACTATTGTCTTAATTTTTTCA
1 TTGTATACTATTGTCTTAATTTTTTCA
*
18163479 TTGTATGCTATTGTCTTAATTTTTTC
1 TTGTATACTATTGTCTTAATTTTTTC
18163505 TTTCATCTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (27 bp):
TTGTATACTATTGTCTTAATTTTTTCA
Found at i:18163622 original size:8 final size:8
Alignment explanation
Indices: 18163609--18163633 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
18163599 CCTATATTGT
18163609 TAATTAAA
1 TAATTAAA
18163617 TAATTAAA
1 TAATTAAA
18163625 TAATTAAA
1 TAATTAAA
18163633 T
1 T
18163634 GCGAACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAATTAAA
Found at i:18163862 original size:17 final size:17
Alignment explanation
Indices: 18163840--18163875 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
18163830 AATTCAGTCG
18163840 TATAAGATTATTTTTCA
1 TATAAGATTATTTTTCA
18163857 TATAAGATTATTTTTCA
1 TATAAGATTATTTTTCA
18163874 TA
1 TA
18163876 CCTTAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
TATAAGATTATTTTTCA
Found at i:18166508 original size:24 final size:24
Alignment explanation
Indices: 18166453--18166511 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
18166443 GGTTTAATGC
* *
18166453 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
18166477 AAATGGATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
18166501 AAATGGATATA
1 AAATGGATATA
18166512 AAAGGAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:18166583 original size:17 final size:17
Alignment explanation
Indices: 18166561--18166658 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
18166551 AATTCAAGAC
18166561 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ***
18166578 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
18166597 CTTATGTAATATTTTTAA
1 -TTATGTAATATTTTTAA
* ** *
18166615 TTATGTAGTGATTCAAATAT
1 TTATGTAAT-ATT--TTTAA
*
18166635 TTATGTAATGTTTTTAA
1 TTATGTAATATTTTTAA
18166652 TTATGTA
1 TTATGTA
18166659 GTGATTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 25 0.43
18 8 0.14
19 7 0.12
20 18 0.31
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.51
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:18166606 original size:37 final size:37
Alignment explanation
Indices: 18166552--18166664 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
18166542 TTATGTGTTA
18166552 ATTC-AAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
18166588 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* * *
18166625 ATTCAAATATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
18166662 ATT
1 ATT
18166665 TAATTCGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 4 0.05
37 69 0.95
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:18166679 original size:9 final size:9
Alignment explanation
Indices: 18166665--18166774 Score: 121
Period size: 9 Copynumber: 11.6 Consensus size: 9
18166655 TGTAGTGATT
18166665 TAATTCGGG
1 TAATTCGGG
18166674 TAATTCGGG
1 TAATTCGGG
*
18166683 TAATTTGGG
1 TAATTCGGG
18166692 TAATTTTCGGG
1 TAA--TTCGGG
*
18166703 TAATTTGGG
1 TAATTCGGG
*
18166712 TAATTTTTGGG
1 TAA--TTCGGG
18166723 TAATTCGGG
1 TAATTCGGG
18166732 TAATATTCGGG
1 T-A-ATTCGGG
18166743 TAATTCGGG
1 TAATTCGGG
*
18166752 TAAGTCGGG
1 TAATTCGGG
*
18166761 TAAGTCGGG
1 TAATTCGGG
18166770 TAATT
1 TAATT
18166775 TTTAACCAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
9 62 0.70
10 2 0.02
11 25 0.28
ACGTcount: A:0.23, C:0.07, G:0.32, T:0.38
Consensus pattern (9 bp):
TAATTCGGG
Found at i:18166702 original size:20 final size:20
Alignment explanation
Indices: 18166665--18166776 Score: 142
Period size: 20 Copynumber: 5.8 Consensus size: 20
18166655 TGTAGTGATT
18166665 TAATTCGGGTAA--TTCGGG
1 TAATTCGGGTAATTTTCGGG
*
18166683 TAATTTGGGTAATTTTCGGG
1 TAATTCGGGTAATTTTCGGG
* *
18166703 TAATTTGGGTAATTTTTGGG
1 TAATTCGGGTAATTTTCGGG
*
18166723 TAATTCGGGTAATATTCGGG
1 TAATTCGGGTAATTTTCGGG
*
18166743 TAATTCGGGTAA--GTCGGG
1 TAATTCGGGTAATTTTCGGG
*
18166761 TAAGTCGGGTAATTTT
1 TAATTCGGGTAATTTT
18166777 TAACCAAAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
18 27 0.33
20 55 0.67
ACGTcount: A:0.22, C:0.07, G:0.31, T:0.39
Consensus pattern (20 bp):
TAATTCGGGTAATTTTCGGG
Found at i:18166705 original size:29 final size:27
Alignment explanation
Indices: 18166665--18166775 Score: 132
Period size: 29 Copynumber: 3.9 Consensus size: 27
18166655 TGTAGTGATT
18166665 TAATTCGGGTAATTCGGGTAATTTGGG
1 TAATTCGGGTAATTCGGGTAATTTGGG
*
18166692 TAATTTTCGGGTAATTTGGGTAATTTTTGGG
1 TAA--TTCGGGTAATTCGGGTAA--TTTGGG
*
18166723 TAATTCGGGTAATATTCGGGTAATTCGGG
1 TAATTCGGGT-A-ATTCGGGTAATTTGGG
* *
18166752 TAAGTCGGGTAAGTCGGGTAATTT
1 TAATTCGGGTAATTCGGGTAATTT
18166776 TTAACCAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
27 14 0.19
28 1 0.01
29 38 0.53
30 1 0.01
31 18 0.25
ACGTcount: A:0.23, C:0.07, G:0.32, T:0.39
Consensus pattern (27 bp):
TAATTCGGGTAATTCGGGTAATTTGGG
Found at i:18169946 original size:9 final size:9
Alignment explanation
Indices: 18169932--18169956 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18169922 ATTATCTAAT
18169932 ATTAAATTA
1 ATTAAATTA
18169941 ATTAAATTA
1 ATTAAATTA
18169950 ATTAAAT
1 ATTAAAT
18169957 ACAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTAAATTA
Found at i:18178052 original size:10 final size:10
Alignment explanation
Indices: 18178033--18178130 Score: 55
Period size: 10 Copynumber: 9.8 Consensus size: 10
18178023 TTAAATTCTA
18178033 ATAAAAATAT
1 ATAAAAATAT
18178043 A-AAAATATAT
1 ATAAAA-ATAT
*
18178053 TTAAAAAT-T
1 ATAAAAATAT
18178062 ATAAAAA-ACT
1 ATAAAAATA-T
18178072 ATAAAAATCAT
1 ATAAAAAT-AT
*
18178083 A-AAAAAAACT
1 ATAAAAATA-T
18178093 ATAAAAAGT-T
1 ATAAAAA-TAT
* * *
18178103 GTAAAATTTT
1 ATAAAAATAT
18178113 ATAAAAATCAT
1 ATAAAAAT-AT
18178124 A-AAAAAT
1 ATAAAAAT
18178131 CATAAAATGA
Statistics
Matches: 68, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
9 13 0.19
10 41 0.60
11 13 0.19
12 1 0.01
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:18178347 original size:21 final size:20
Alignment explanation
Indices: 18178321--18178377 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
18178311 TTAGTATGAT
* *
18178321 AATTTTATAATTTTTTTTATG
1 AATTTTATAATTTTCTTTA-C
18178342 AATTTTAT-A-TTTCTTTAC
1 AATTTTATAATTTTCTTTAC
18178360 AATTTTTATAATTTTCTT
1 AA-TTTTATAATTTTCTT
18178378 ACGACTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 2 0.06
21 14 0.45
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTTTATAATTTTCTTTAC
Found at i:18178447 original size:29 final size:28
Alignment explanation
Indices: 18178408--18178521 Score: 117
Period size: 28 Copynumber: 3.9 Consensus size: 28
18178398 ATTTCTATAT
18178408 ATTTTATAATTTTTA-ACGATTTTTATAAA
1 ATTTTA-AATTTTTATA-GATTTTTATAAA
*
18178437 ATTTTACAATTTTTATAAATTTTTAT-AA
1 ATTTTA-AATTTTTATAGATTTTTATAAA
*
18178465 ATTTTAATATTTTTATAGTTTTTTATTAAA
1 ATTTTAA-ATTTTTATAGATTTTTA-TAAA
18178495 ATTTAATAAATTTTTTATA-ATTTTTAT
1 ATTT--TAAA-TTTTTATAGATTTTTAT
18178522 TGATTTTTAA
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
27 1 0.01
28 23 0.32
29 23 0.32
30 8 0.11
31 7 0.10
32 11 0.15
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
ATTTTAAATTTTTATAGATTTTTATAAA
Found at i:18178518 original size:41 final size:38
Alignment explanation
Indices: 18178445--18178530 Score: 100
Period size: 41 Copynumber: 2.2 Consensus size: 38
18178435 AAATTTTACA
* *
18178445 ATTTTTATAAATTTTTATAAATTTTAATATTTTTATAG
1 ATTTTTATAAAATTTAATAAATTTTAATATTTTTATAG
* * *
18178483 TTTTTTATTAAAATTTAATAAATTTTTTATAATTTTTATTG
1 ATTTTTA-TAAAATTTAATAAA-TTTTAAT-ATTTTTATAG
18178524 ATTTTTA
1 ATTTTTA
18178531 ATATTTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
38 6 0.15
39 12 0.31
40 6 0.15
41 15 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (38 bp):
ATTTTTATAAAATTTAATAAATTTTAATATTTTTATAG
Found at i:18178519 original size:10 final size:10
Alignment explanation
Indices: 18178383--18178521 Score: 89
Period size: 10 Copynumber: 14.5 Consensus size: 10
18178373 TTCTTACGAC
*
18178383 TTTATAAAAT
1 TTTATAAATT
18178393 TTTAT--ATT
1 TTTATAAATT
* *
18178401 TCTATATA-T
1 TTTATAAATT
18178410 TTTAT-AATT
1 TTTATAAATT
*
18178419 TTTA-ACGATT
1 TTTATA-AATT
*
18178429 TTTATAAAAT
1 TTTATAAATT
*
18178439 TTTA-CAATT
1 TTTATAAATT
18178448 TTTATAAATT
1 TTTATAAATT
18178458 TTTATAAA-T
1 TTTATAAATT
*
18178467 TTTA-ATATT
1 TTTATAAATT
**
18178476 TTTATAGTTT
1 TTTATAAATT
*
18178486 TTTATTAAAAT
1 TTTA-TAAATT
*
18178497 TTAATAAATT
1 TTTATAAATT
18178507 TTT-TATAATT
1 TTTATA-AATT
18178517 TTTAT
1 TTTAT
18178522 TGATTTTTAA
Statistics
Matches: 98, Mismatches: 19, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
8 9 0.09
9 29 0.30
10 52 0.53
11 8 0.08
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (10 bp):
TTTATAAATT
Found at i:18178527 original size:20 final size:20
Alignment explanation
Indices: 18178504--18178542 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
18178494 AATTTAATAA
*
18178504 ATTTTTTATAATTT-TTATTG
1 ATTTTTAAT-ATTTATTATTG
18178524 ATTTTTAATATTTATTATT
1 ATTTTTAATATTTATTATT
18178543 TTTTGGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
ATTTTTAATATTTATTATTG
Found at i:18178530 original size:19 final size:20
Alignment explanation
Indices: 18178383--18178521 Score: 89
Period size: 19 Copynumber: 7.2 Consensus size: 20
18178373 TTCTTACGAC
*
18178383 TTTATAAAATTTTAT--ATT
1 TTTATAAATTTTTATAAATT
* *
18178401 TCTATATA-TTTTAT-AATT
1 TTTATAAATTTTTATAAATT
* *
18178419 TTTA-ACGATTTTTATAAAAT
1 TTTATA-AATTTTTATAAATT
*
18178439 TTTA-CAATTTTTATAAATT
1 TTTATAAATTTTTATAAATT
*
18178458 TTTATAAA-TTTTA-ATATT
1 TTTATAAATTTTTATAAATT
** *
18178476 TTTATAGTTTTTTATTAAAAT
1 TTTATAAATTTTTA-TAAATT
*
18178497 TTAATAAATTTTT-TATAATT
1 TTTATAAATTTTTATA-AATT
18178517 TTTAT
1 TTTAT
18178522 TGATTTTTAA
Statistics
Matches: 93, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
17 7 0.08
18 23 0.25
19 34 0.37
20 16 0.17
21 13 0.14
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (20 bp):
TTTATAAATTTTTATAAATT
Found at i:18178537 original size:17 final size:16
Alignment explanation
Indices: 18178507--18178545 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
18178497 TTAATAAATT
*
18178507 TTTTATAATTTTTATTGA
1 TTTT-TAATATTTATT-A
18178525 TTTTTAATATTTATTA
1 TTTTTAATATTTATTA
18178541 TTTTT
1 TTTTT
18178546 TGGTGACACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 10 0.50
18 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTAATATTTATTA
Found at i:18179375 original size:17 final size:18
Alignment explanation
Indices: 18179343--18179376 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18179333 CCCTTTTTTT
*
18179343 CTTTTACCTTCCCCAAAA
1 CTTTTACCTACCCCAAAA
18179361 CTTTTA-CTACCCCAAA
1 CTTTTACCTACCCCAAA
18179377 CCTCCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.32
Consensus pattern (18 bp):
CTTTTACCTACCCCAAAA
Found at i:18179827 original size:19 final size:19
Alignment explanation
Indices: 18179803--18179840 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18179793 AAGTTAATAA
*
18179803 CAAATTTGATGACGGTGGG
1 CAAATTTCATGACGGTGGG
18179822 CAAATTTCATGACGGTGGG
1 CAAATTTCATGACGGTGGG
18179841 TGACAATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.34, T:0.26
Consensus pattern (19 bp):
CAAATTTCATGACGGTGGG
Found at i:18200386 original size:19 final size:20
Alignment explanation
Indices: 18200358--18200401 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
18200348 TTTATAGTTT
*
18200358 TAAATAATTTTTGGG-TAAAA
1 TAAATAA-TTTTGGGCCAAAA
18200378 TAAAT-ATTTTGGGCCAAAA
1 TAAATAATTTTGGGCCAAAA
18200397 TAAAT
1 TAAAT
18200402 TTAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (20 bp):
TAAATAATTTTGGGCCAAAA
Found at i:18203433 original size:9 final size:9
Alignment explanation
Indices: 18203419--18203456 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
18203409 TCTGTCTAAA
18203419 TTAATGAAT
1 TTAATGAAT
*
18203428 TTAATGAAA
1 TTAATGAAT
*
18203437 TT-ATTAAT
1 TTAATGAAT
18203445 TTAATGAAT
1 TTAATGAAT
18203454 TTA
1 TTA
18203457 TTAATTTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 6 0.25
9 18 0.75
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (9 bp):
TTAATGAAT
Found at i:18203447 original size:17 final size:17
Alignment explanation
Indices: 18203425--18203463 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
18203415 TAAATTAATG
18203425 AATTTAATGAAATTATT
1 AATTTAATGAAATTATT
*
18203442 AATTTAATGAATTTATT
1 AATTTAATGAAATTATT
18203459 AATTT
1 AATTT
18203464 GGATTAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
AATTTAATGAAATTATT
Found at i:18204591 original size:20 final size:20
Alignment explanation
Indices: 18204566--18204614 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
18204556 AAGTTTATCT
18204566 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
18204586 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGAAATGGAAAG
*
18204606 AAAGTAAAT
1 TAAGTAAAT
18204615 AGAGTGGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:18210264 original size:6 final size:6
Alignment explanation
Indices: 18210255--18210337 Score: 64
Period size: 6 Copynumber: 13.5 Consensus size: 6
18210245 TAAGTCTAAG
*
18210255 AAAATA AAAATA AAAATA ACACAACT- -AAA-A AAAATA AACATA AAAATA
1 AAAATA AAAATA AAAATA A-A-AA-TA AAAATA AAAATA AAAATA AAAATA
* * *
18210303 AACATAA AAAATA AAACTA AAAGAAA AAAATA AAA
1 AAAAT-A AAAATA AAAATA AAA-ATA AAAATA AAA
18210338 TCAAGGATCC
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
5 5 0.08
6 43 0.70
7 10 0.16
8 2 0.03
9 1 0.02
ACGTcount: A:0.78, C:0.07, G:0.01, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:18210318 original size:19 final size:18
Alignment explanation
Indices: 18210255--18210337 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 18
18210245 TAAGTCTAAG
18210255 AAAATAAAAATAAAAATAA
1 AAAATAAAAAT-AAAATAA
*
18210274 CACAACT-AAAA-AAAAT-A
1 -A-AAATAAAAATAAAATAA
*
18210291 AACATAAAAATAAACATAA
1 AAAATAAAAATAAA-ATAA
* *
18210310 AAAATAAAACTAAAAGAAA
1 AAAATAAAAATAAAA-TAA
18210329 AAAATAAAA
1 AAAATAAAA
18210338 TCAAGGATCC
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
15 2 0.04
16 5 0.10
17 4 0.08
18 8 0.16
19 24 0.47
20 5 0.10
21 3 0.06
ACGTcount: A:0.78, C:0.07, G:0.01, T:0.13
Consensus pattern (18 bp):
AAAATAAAAATAAAATAA
Found at i:18210363 original size:3 final size:3
Alignment explanation
Indices: 18210348--18210530 Score: 64
Period size: 3 Copynumber: 62.0 Consensus size: 3
18210338 TCAAGGATCC
* * * * * *
18210348 TAA TAA GAA TAA TAA TAC TAA TAA TAC TAA -AA CTCA TAC TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
* * * * *
18210393 TAA TAA TAA CAG TAA -AA TAAA TAA TAA TTAA CTGA TGA TAA TGAA -AC
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA -TAA -TAA TAA TAA T-AA TAA
* * * * * *
18210440 GAA GAA TAA TAA GAA -AA TTA -AA TAA TAA TAA CAA TAAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
18210484 TAA CTAA -AA -AA TAA -AA TAA T-A TAA -AA -AA TAA TAA TAA TTAA
1 TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
18210525 TAA TAA
1 TAA TAA
18210531 ACAAATAAAT
Statistics
Matches: 136, Mismatches: 28, Indels: 32
0.69 0.14 0.16
Matches are distributed among these distances:
2 20 0.15
3 96 0.71
4 20 0.15
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:18210465 original size:16 final size:16
Alignment explanation
Indices: 18210444--18210558 Score: 53
Period size: 16 Copynumber: 7.3 Consensus size: 16
18210434 TGAAACGAAG
18210444 AATAATAAGAA-AATTA
1 AATAATAAGAACAA-TA
*
18210460 AATAATAATAACAATA
1 AATAATAAGAACAATA
* * *
18210476 AATAATTATAACTAAAA
1 AATAATAAGAAC-AATA
* *
18210493 AATAA-AATAA-TATA
1 AATAATAAGAACAATA
* * * *
18210507 AAAAATAATAATAATT
1 AATAATAAGAACAATA
18210523 AATAAT-A-AACAAATA
1 AATAATAAGAAC-AATA
*
18210538 AATAATTAGATA-AATA
1 AATAATAAGA-ACAATA
18210554 AATAA
1 AATAA
18210559 AAAATAAAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
14 8 0.10
15 15 0.19
16 44 0.56
17 11 0.14
18 1 0.01
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.27
Consensus pattern (16 bp):
AATAATAAGAACAATA
Found at i:18210540 original size:4 final size:4
Alignment explanation
Indices: 18210472--18210571 Score: 61
Period size: 4 Copynumber: 25.5 Consensus size: 4
18210462 TAATAATAAC
*
18210472 AATA AATA ATTATA ACTA AA-A AATAA AATA ATATA AA-A AAT- AAT-
1 AATA AATA A--ATA AATA AATA AAT-A AATA A-ATA AATA AATA AATA
* * * *
18210516 AAT- AATT AAT- AATA AACA AATA AATA ATTA GATA AATA AATA AA-A
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
18210561 AATAA AATA AA
1 AAT-A AATA AA
18210572 GAACAAGGGT
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
3 21 0.27
4 41 0.53
5 12 0.15
6 4 0.05
ACGTcount: A:0.71, C:0.02, G:0.01, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:18210557 original size:28 final size:25
Alignment explanation
Indices: 18210447--18210566 Score: 86
Period size: 27 Copynumber: 4.5 Consensus size: 25
18210437 AACGAAGAAT
18210447 AATAAGAAAATTAAATAATAATAACAATA
1 AATAA-AAAA-TAAATAATAAT-A-AATA
* *
18210476 AATAATTATAACTAAAAAAT-A-AAATA
1 AATAA--A-AAATAAATAATAATAAATA
*
18210502 ATATAAAAAAT-AATAATAATTAAT-
1 A-ATAAAAAATAAATAATAATAAATA
18210526 AATAAACAAATAAATAATTAGATAAATA
1 AATAAA-AAATAAATAA-TA-ATAAATA
18210554 AATAAAAAATAAA
1 AATAAAAAATAAA
18210567 ATAAAGAACA
Statistics
Matches: 74, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
23 10 0.14
24 9 0.12
25 9 0.12
26 7 0.09
27 17 0.23
28 6 0.08
29 6 0.08
30 8 0.11
31 2 0.03
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.26
Consensus pattern (25 bp):
AATAAAAAATAAATAATAATAAATA
Found at i:18210568 original size:16 final size:16
Alignment explanation
Indices: 18210483--18210571 Score: 74
Period size: 16 Copynumber: 5.3 Consensus size: 16
18210473 ATAAATAATT
*
18210483 ATAACTAAAAAATAAA
1 ATAAATAAAAAATAAA
18210499 ATAATATAAAAAATAATA
1 ATAA-ATAAAAAATAA-A
*
18210517 ATAATTAATAATAA-ACAA
1 ATAAATAA-AA-AATA-AA
* *
18210535 ATAAATAATTAGAT-AA
1 ATAAATAA-AAAATAAA
18210551 ATAAATAAAAAATAAA
1 ATAAATAAAAAATAAA
18210567 ATAAA
1 ATAAA
18210572 GAACAAGGGT
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
15 3 0.05
16 21 0.36
17 14 0.24
18 18 0.31
19 3 0.05
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.25
Consensus pattern (16 bp):
ATAAATAAAAAATAAA
Found at i:18210568 original size:28 final size:27
Alignment explanation
Indices: 18210497--18210570 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 27
18210487 CTAAAAAATA
18210497 AAATAATATAAAAAATAATAATAATTAAT
1 AAATAA-ATAAAAAATAA-AATAATTAAT
*
18210526 -AAT--A-AACAAAT-AAATAATTAGAT
1 AAATAAATAAAAAATAAAATAATTA-AT
18210549 AAATAAATAAAAAATAAAATAA
1 AAATAAATAAAAAATAAAATAA
18210571 AGAACAAGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
22 8 0.22
23 3 0.08
24 9 0.24
25 1 0.03
26 1 0.03
27 6 0.16
28 9 0.24
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (27 bp):
AAATAAATAAAAAATAAAATAATTAAT
Found at i:18231115 original size:43 final size:41
Alignment explanation
Indices: 18231054--18231326 Score: 262
Period size: 42 Copynumber: 6.4 Consensus size: 41
18231044 AAAAAACGCC
*
18231054 TTCTTTAGCAGCGCTTAGGAAAAAAACGCCGCTAATGATCATG
1 TTCTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAA-GATCATG
18231097 TTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAATGATCATG
1 TTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAA-GATCATG
* * *
18231139 TTCTTTAGCGGCGCTTTGGAAAAAACGCCACTAAAGAACATG
1 TTCTTTAGCGGCGCTTAGGAAAAAACGCCGCT-AAGATCATG
* * * *
18231181 ATCTTTAGCGGCGTTTAGGAAAAAAACGCCGCTAAAAGTAAATG
1 TTCTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAAGA-T-CATG
* * * *
18231225 TTCTATAGCGGCGCTT-GGTAAAAAACGCCACTAAAAGTAATG
1 TTCTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAAGA-TCATG
*** * * *
18231267 TTCTTTAGCGGCGCTTCATCTACAAACGCTGCTAA-ATGTAGTG
1 TTCTTTAGCGGCGCTT-AGGAAAAAACGCCGCTAAGAT-CA-TG
18231310 TTCTTTAGCGGCGCTTA
1 TTCTTTAGCGGCGCTTA
18231327 TTTCATAAAC
Statistics
Matches: 198, Mismatches: 24, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
41 1 0.01
42 100 0.51
43 81 0.41
44 16 0.08
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
TTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAGATCATG
Found at i:18231133 original size:42 final size:43
Alignment explanation
Indices: 18231054--18231282 Score: 270
Period size: 42 Copynumber: 5.4 Consensus size: 43
18231044 AAAAAACGCC
*
18231054 TTCTTTAGCAGCGCTTAGGAAAAAAACGCCGCTAATGATCATG
1 TTCTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAATGATCATG
18231097 TTCTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAATGATCATG
1 TTCTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAATGATCATG
* * * *
18231139 TTCTTTAGCGGCGCTTTGG-AAAAAACGCCACTAAAGAACATG
1 TTCTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAATGATCATG
* * * *
18231181 ATCTTTAGCGGCGTTTAGGAAAAAAACGCCGCTAA-AAGTAAATG
1 TTCTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAATGA-T-CATG
* * * * *
18231225 TTCTATAGCGGCGCTT-GGTAAAAAACGCCACTAA-AAGTAATG
1 TTCTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAATGA-TCATG
18231267 TTCTTTAGCGGCGCTT
1 TTCTTTAGCGGCGCTT
18231283 CATCTACAAA
Statistics
Matches: 165, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
42 97 0.59
43 52 0.32
44 16 0.10
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (43 bp):
TTCTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAATGATCATG
Found at i:18231248 original size:86 final size:83
Alignment explanation
Indices: 18231054--18231325 Score: 289
Period size: 86 Copynumber: 3.2 Consensus size: 83
18231044 AAAAAACGCC
* * * *
18231054 TTCTTTAGCAGCGCTTAGGAAAAAAACGCCGCTAATGATCATGTTCTTTAGCGGCGCTTAGGAAA
1 TTCTTTAGCGGCGCTT-GG-AAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGCTTAGGAAA
* *
18231119 AAACGCCGCTAATGATCATG
64 AAACGCCGCTAAAGATAATG
* *
18231139 TTCTTTAGCGGCGCTTTGGAAAAAACGCCACTAAAGAACATGATCTTTAGCGGCGTTTAGGAAAA
1 TTCTTTAGCGGCGC-TTGGAAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGCTTAGG-AAA
18231204 AAACGCCGCTAAA-AGTAAATG
64 AAACGCCGCTAAAGA-T-AATG
* * ***
18231225 TTCTATAGCGGCGCTTGGTAAAAAACGCCACTAAAAGTA-ATGTTCTTTAGCGGCGCTTCATCTA
1 TTCTTTAGCGGCGCTTGG-AAAAAACGCCACT-AAAGAACATGTTCTTTAGCGGCGCTT-AGGAA
* * *
18231289 CAAACGCTGCTAAATG-TAGTG
63 AAAACGCCGCTAAA-GATAATG
18231310 TTCTTTAGCGGCGCTT
1 TTCTTTAGCGGCGCTT
18231326 ATTTCATAAA
Statistics
Matches: 159, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
84 38 0.24
85 53 0.33
86 62 0.39
87 6 0.04
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (83 bp):
TTCTTTAGCGGCGCTTGGAAAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGCTTAGGAAAAA
ACGCCGCTAAAGATAATG
Found at i:18231338 original size:43 final size:43
Alignment explanation
Indices: 18231204--18231325 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 43
18231194 TTTAGGAAAA
* * ** * *
18231204 AAACGCCGCTAAAAGTAAATGTTCTATAGCGGCGCTTGGT-AAA
1 AAACGCTGCTAAAAGT-AATGTTCTTTAGCGGCGCTTCATCTAC
**
18231247 AAACGCCACTAAAAGTAATGTTCTTTAGCGGCGCTTCATCTAC
1 AAACGCTGCTAAAAGTAATGTTCTTTAGCGGCGCTTCATCTAC
* *
18231290 AAACGCTGCTAAATGTAGTGTTCTTTAGCGGCGCTT
1 AAACGCTGCTAAAAGTAATGTTCTTTAGCGGCGCTT
18231326 ATTTCATAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 20 0.29
43 48 0.71
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (43 bp):
AAACGCTGCTAAAAGTAATGTTCTTTAGCGGCGCTTCATCTAC
Found at i:18231798 original size:21 final size:21
Alignment explanation
Indices: 18231774--18231839 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
18231764 ACTTCTCTTG
18231774 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
18231795 CTGCTTCTCTCACTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
18231816 CTGCTTC-CTTCGCTGCCGCCT
1 CTGCTTCTC-TCGCTGCAGCCT
18231837 CTG
1 CTG
18231840 TTTTAAGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 1 0.03
21 39 0.98
ACGTcount: A:0.03, C:0.44, G:0.20, T:0.33
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:18237924 original size:21 final size:20
Alignment explanation
Indices: 18237892--18237932 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
18237882 TTAAGGACTA
*
18237892 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
18237912 GGGATTTAAGGTTTATGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
18237933 AGGGGTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:18243748 original size:66 final size:65
Alignment explanation
Indices: 18243641--18243811 Score: 227
Period size: 66 Copynumber: 2.6 Consensus size: 65
18243631 GAGCAAATTA
* * * **
18243641 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGTTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCGGATGCAGCAGCGAGAGAAGCAGAGGTTCAACAAAAG-TATGAAGAACTCCA
18243705 G
65 G
*
18243706 CTACAACTTAAAGCGGATGCAGCAGCGAGAGAAGCCGAGGTTCAACAAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCGGATGCAGCAGCGAGAGAAGCAGAGGTTCAACAAAAGTATGAAGAACTCCA
18243771 G
65 G
* * *
18243772 CAGCAGCTTAAAGCAGATGCGGCAGCGAGAGAAGCAGAGG
1 CA-CAACTTAAAGCGGATGCAGCAGCGAGAGAAGCAGAGG
18243812 CTGCAACGAG
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
65 2 0.02
66 87 0.93
67 5 0.05
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCGGATGCAGCAGCGAGAGAAGCAGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:18243807 original size:21 final size:21
Alignment explanation
Indices: 18243782--18243831 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
18243772 CAGCAGCTTA
* *
18243782 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAACGAGAG
* *
18243803 AAGCAGAGGCTGCAACGAGGG
1 AAGCAGAGGCGGCAACGAGAG
18243824 AAGCAGAG
1 AAGCAGAG
18243832 ACTAAAGCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.42, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAACGAGAG
Found at i:18243842 original size:21 final size:21
Alignment explanation
Indices: 18243795--18243873 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
18243785 CAGATGCGGC
* *
18243795 AGCGAGAGAAGCAGAGGCTGCA
1 AGCGAGGGAAGCAGAGGCT-AA
*
18243817 A-CGAGGGAAGCAGAGACTAA
1 AGCGAGGGAAGCAGAGGCTAA
* **
18243837 AGCGAGGGAAGTAGAGGCTGC
1 AGCGAGGGAAGCAGAGGCTAA
18243858 AGCGAGGGAAGCAGAG
1 AGCGAGGGAAGCAGAG
18243874 CAGCGTAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 2 0.04
21 45 0.94
22 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.43, T:0.05
Consensus pattern (21 bp):
AGCGAGGGAAGCAGAGGCTAA
Found at i:18244299 original size:43 final size:43
Alignment explanation
Indices: 18244252--18244600 Score: 407
Period size: 43 Copynumber: 8.1 Consensus size: 43
18244242 AAAAATACCA
* *
18244252 CTAAAGAGAAGGGTCTTTAGCGGCGTTTGTGTAGAAAGCGCCG
1 CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAGAAAGCGCCG
*
18244295 CTAAAGATAAGGGTCTTTTGCGGCGTTTGTGGAGAAAGCGCCG
1 CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAGAAAGCGCCG
* * * *
18244338 CTAAAGATAGGGGTCTTTTGCGACGTTTGTAGAGAAAGCGCCG
1 CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAGAAAGCGCCG
** **
18244381 CTAAAGACCAGATTCTTTAGCGGCGTTTGTGGA-AAAGCGCCG
1 CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAGAAAGCGCCG
* * *
18244423 CTAAGGATTAGGTTCTTTAGCGGCGTTTGTGGAGAAAGCGCCG
1 CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAGAAAGCGCCG
* * *
18244466 CTAAGGATTAGGTTCTTTAGCGGCGTTTGTGGAGAAAGCGCCG
1 CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAGAAAGCGCCG
* *** * *
18244509 CTAAAGGTCCTGCTCTTTAGCGGCGTTTGT-GAGAAAAGTGCCG
1 CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAG-AAAGCGCCG
* *** *
18244552 CTAAAGGTCCTGCTCTTTAGCGGCGTTTGT-GAGAAAAGCGCCG
1 CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAG-AAAGCGCCG
18244595 CTAAAG
1 CTAAAG
18244601 GTCCTCGTCT
Statistics
Matches: 278, Mismatches: 26, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
42 41 0.15
43 237 0.85
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.26
Consensus pattern (43 bp):
CTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAGAAAGCGCCG
Found at i:18244554 original size:171 final size:172
Alignment explanation
Indices: 18244265--18244598 Score: 485
Period size: 171 Copynumber: 1.9 Consensus size: 172
18244255 AAGAGAAGGG
* *
18244265 TCTTTAGCGGCGTTTGTGTAGAAAGCGCCGCTAAAGATAAGGGTCTTTTGCGGCGTTTGTGGAGA
1 TCTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAGA
* * * *
18244330 AAGCGCCGCTAAAGATAGGGGTCTTTTGCGACGTTTGTAGAGAAAGCGCCGCTAAA-GACCAGAT
66 AAGCGCCGCTAAAGATACGGCTCTTTAGCGACGTTTGTAGAGAAAGCGCCGCTAAAGGACCAG-C
18244394 TCTTTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAGGATTAGGT
130 TCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAGGATTAGGT
* * *
18244436 TCTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAGGATTAGGTTCTTTAGCGGCGTTTGTGGAGA
1 TCTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAGA
* * * * * * *
18244501 AAGCGCCGCTAAAGGTCCTGCTCTTTAGCGGCGTTTGT-GAGAAAAGTGCCGCTAAAGGTCCTGC
66 AAGCGCCGCTAAAGATACGGCTCTTTAGCGACGTTTGTAGAG-AAAGCGCCGCTAAAGGACCAGC
18244565 TCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAA
130 TCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAA
18244599 AGGTCCTCGT
Statistics
Matches: 144, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
170 3 0.02
171 122 0.85
172 19 0.13
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (172 bp):
TCTTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAGA
AAGCGCCGCTAAAGATACGGCTCTTTAGCGACGTTTGTAGAGAAAGCGCCGCTAAAGGACCAGCT
CTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAGGATTAGGT
Found at i:18244628 original size:23 final size:23
Alignment explanation
Indices: 18244602--18244647 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
18244592 CCGCTAAAGG
*
18244602 TCCTCGTCTTTAGCGGCGTTTTT
1 TCCTCGTCTTTAGCAGCGTTTTT
18244625 TCCTCGTCTTTAGCAGCGTTTTT
1 TCCTCGTCTTTAGCAGCGTTTTT
18244648 AATAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.07, C:0.26, G:0.20, T:0.48
Consensus pattern (23 bp):
TCCTCGTCTTTAGCAGCGTTTTT
Found at i:18245211 original size:41 final size:40
Alignment explanation
Indices: 18245157--18245378 Score: 246
Period size: 41 Copynumber: 5.4 Consensus size: 40
18245147 GCGCTTCGGC
* *
18245157 AAAAACGTCGCTAAAGGCAAATGCATTAGCGGCGCTTAGAT
1 AAAAACGCCGCTAAAGGCAGA-GCATTAGCGGCGCTTAGAT
* * * * * *
18245198 ACAAACACAGCTAAAGGCCAGAGAATTAGTGGCGCTCAGAT
1 AAAAACGCCGCTAAAGG-CAGAGCATTAGCGGCGCTTAGAT
* *
18245239 AAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTAGAT
1 AAAAACGCCGCTAAAG-GCAGAGCATTAGCGGCGCTTAGAT
* * * *
18245280 AAAATCGCCACTAAAGGCCAGAGAATTAGCGGCGCTCAGAT
1 AAAAACGCCGCTAAAGG-CAGAGCATTAGCGGCGCTTAGAT
** *
18245321 AAAAACGCCGCTAAATATCCGAGCATTAGCGGCGCTTAGAT
1 AAAAACGCCGCTAAA-GGCAGAGCATTAGCGGCGCTTAGAT
18245362 AAAAACGCCGCTAAAGG
1 AAAAACGCCGCTAAAGG
18245379 TTTAAAAAAT
Statistics
Matches: 146, Mismatches: 31, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
41 143 0.98
42 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.17
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGGCAGAGCATTAGCGGCGCTTAGAT
Found at i:18245376 original size:82 final size:82
Alignment explanation
Indices: 18245179--18245378 Score: 328
Period size: 82 Copynumber: 2.4 Consensus size: 82
18245169 AAAGGCAAAT
* * * *
18245179 GCATTAGCGGCGCTTAGATACAAACACAGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAAAA
1 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGCGGCGCTCAGATAAAAA
*
18245244 CGCCGCTAAAGATCTGA
66 CGCCGCTAAAGATCCGA
* *
18245261 GCATTAGCGGCGCTTAGATAAAATCGCCACTAAAGGCCAGAGAATTAGCGGCGCTCAGATAAAAA
1 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGCGGCGCTCAGATAAAAA
*
18245326 CGCCGCTAAATATCCGA
66 CGCCGCTAAAGATCCGA
18245343 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
1 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
18245379 TTTAAAAAAT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 108 1.00
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.17
Consensus pattern (82 bp):
GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGCGGCGCTCAGATAAAAA
CGCCGCTAAAGATCCGA
Found at i:18249119 original size:277 final size:274
Alignment explanation
Indices: 18248627--18249695 Score: 1567
Period size: 269 Copynumber: 3.9 Consensus size: 274
18248617 GTTATAGTCA
* *
18248627 GATTATGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGAAGAACCAATTCCAGCAA
1 GATTACGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGAAGAACCAATTCCAGCAG
* ** *
18248692 GTTAAAACTTTATTGTC-TCATTTAAAAGAAAAGAACATTTCAAACATGTCAAAATATTAAGTTA
66 GTTAAAACTTCATTGTCTTTTTTTAAAA-AAAA-AACATTTCAAACATGTCAAAATATCAAGTTA
* *
18248756 AATTCTCTTATAAATGTACCCACTGAAATTATTTTTAATGAAAACCTCAAACTTAATTTGTAGCG
129 AATTCTCTTATAAACGTACCCACTGAAATTATTTTTAATGAAAACCTCAAACTTAATTTGCAGCG
* * * *
18248821 ACAATTACTTGAAAACTTAAAGTTTCGTTTTAGTCTCTTTAGGAAAAAATATTTATAAACCCGGC
194 ACAATTACTTGAAAACTTAAAGTTTCATTTTGGTCTCTTTAGGAAAAATTATTTATAAACCTGGC
18248886 CTAGACGTTACGGTCG
259 CTAGACGTTACGGTCG
* * *
18248902 GATTATGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGAATAATCAATTCCAGCAG
1 GATTACGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGAAGAACCAATTCCAGCAG
*** *
18248967 GTTAAAACTTCATTGTCTTGTTTTTTTTCTAAAAAAACATTTCAAACATGTCAAAATATCAAGCT
66 GTTAAAACTTCATTGTC---TTTTTTTAAAAAAAAAACATTTCAAACATGTCAAAATATCAAGTT
* * * *
18249032 AAATTCTCTTATAAACGTGCCCGCTGAAATTTTTTTTAATGAAAACTTCAAACTTAATTTGCAGC
128 AAATTCTCTTATAAACGTACCCACTGAAATTATTTTTAATGAAAACCTCAAACTTAATTTGCAGC
* * * **
18249097 AACAATTACTTGAAAACTTAAAGTTTTATTTTGGTTTCTTTAGGAAGGATTATTTATAAACCTGG
193 GACAATTACTTGAAAACTTAAAGTTTCATTTTGGTCTCTTTAGGAAAAATTATTTATAAACCTGG
*
18249162 CCTAGACGTTACGGTTG
258 CCTAGACGTTACGGTCG
* *
18249179 GATTACGGAGGTTACATCACTAGATAAAAGAAAGTACTAGTGTTTTGAAGAACCAATTCCAGTAG
1 GATTACGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGAAGAACCAATTCCAGCAG
** * *
18249244 GTTAAAACTTCATTGTC-TCGTTTAAAAAAAAAAC--GT--AACATGTCAAAATATCAAGTTATA
66 GTTAAAACTTCATTGTCTTTTTTTAAAAAAAAAACATTTCAAACATGTCAAAATATCAAGTTAAA
*
18249304 TTCTCTTATAAACGTACCCACTAAAATTATTTTTAATGAAAACCTCAAACTTAATTTGCAGCGAC
131 TTCTCTTATAAACGTACCCACTGAAATTATTTTTAATGAAAACCTCAAACTTAATTTGCAGCGAC
* * * **
18249369 AATTACTTGAAAGCTTAAAGTTTCGTTTTTGTCTCTTTAGGAAGGATTATTTATAAACCTGGCCT
196 AATTACTTGAAAACTTAAAGTTTCATTTTGGTCTCTTTAGGAAAAATTATTTATAAACCTGGCCT
18249434 AGACGTTACGGTCG
261 AGACGTTACGGTCG
* *
18249448 GATTACAGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGAAAAACCAATTCCAGCAG
1 GATTACGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGAAGAACCAATTCCAGCAG
* **
18249513 GTTAAAACTTCTTTGTC-TCATTTAAAAAAAAAACATTTCAAACATGTCAAAATATCAAGTTAAA
66 GTTAAAACTTCATTGTCTTTTTTTAAAAAAAAAACATTTCAAACATGTCAAAATATCAAGTTAAA
* * ** *
18249577 TTCTTTTATAAATGTGTCCGCTGAAATTATTTTTAATGAAAACCTCAAACTTAATTTGCAGCGAC
131 TTCTCTTATAAACGTACCCACTGAAATTATTTTTAATGAAAACCTCAAACTTAATTTGCAGCGAC
* *
18249642 AGTTACTTGAAAACTTAAAGTTTCATTTTGGTCTCTATAGGAAAAATTATTTAT
196 AATTACTTGAAAACTTAAAGTTTCATTTTGGTCTCTTTAGGAAAAATTATTTAT
18249696 CATTTGAGCT
Statistics
Matches: 713, Mismatches: 73, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
269 247 0.35
271 2 0.00
273 141 0.20
275 78 0.11
277 236 0.33
278 4 0.01
279 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (274 bp):
GATTACGGAGGTCACATCACTAGATAAAAGAAAGTACTAGTGTTTTGAAGAACCAATTCCAGCAG
GTTAAAACTTCATTGTCTTTTTTTAAAAAAAAAACATTTCAAACATGTCAAAATATCAAGTTAAA
TTCTCTTATAAACGTACCCACTGAAATTATTTTTAATGAAAACCTCAAACTTAATTTGCAGCGAC
AATTACTTGAAAACTTAAAGTTTCATTTTGGTCTCTTTAGGAAAAATTATTTATAAACCTGGCCT
AGACGTTACGGTCG
Found at i:18252084 original size:9 final size:9
Alignment explanation
Indices: 18252070--18252099 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
18252060 GTTTGAATAA
18252070 TTATAAAAT
1 TTATAAAAT
18252079 TTATAAAAT
1 TTATAAAAT
18252088 TTATAAAAT
1 TTATAAAAT
18252097 TTA
1 TTA
18252100 CAATTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTATAAAAT
Found at i:18253253 original size:21 final size:21
Alignment explanation
Indices: 18253213--18253253 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18253203 ATAAAGTAGA
*
18253213 TTATATATTATTTTTATAGTG
1 TTATATATTATATTTATAGTG
18253234 TTATATATTATGATTT-TAGT
1 TTATATATTAT-ATTTATAGT
18253254 AAATTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (21 bp):
TTATATATTATATTTATAGTG
Found at i:18253490 original size:39 final size:40
Alignment explanation
Indices: 18253447--18253551 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
18253437 TTTCATTATG
18253447 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
18253486 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
18253531 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
18253552 ACGTCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:18253545 original size:45 final size:44
Alignment explanation
Indices: 18253445--18253553 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 44
18253435 TTTTTCATTA
18253445 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
18253484 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
18253529 TGCTATTACACCTCTATTCCATTAC
1 TGCTATTACACCTCTATTCCATTAC
18253554 GTCTCTAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 24 0.42
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:18254027 original size:29 final size:30
Alignment explanation
Indices: 18253995--18254053 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
18253985 TATGGTTTAA
18253995 TGTGCAAT-TGTATAAATG-AATTTTGATTT
1 TGTGCAATGT-TATAAATGAAATTTTGATTT
*
18254024 TGTGCAATGTTATACATGAAATTTTGATTT
1 TGTGCAATGTTATAAATGAAATTTTGATTT
18254054 GATCCAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (30 bp):
TGTGCAATGTTATAAATGAAATTTTGATTT
Found at i:18255810 original size:19 final size:20
Alignment explanation
Indices: 18255772--18255811 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
18255762 GGGTTTTTTT
18255772 TAATTTTTTTAATATTAATA
1 TAATTTTTTTAATATTAATA
18255792 TAATTATTTTT-AT-TTAATA
1 TAATT-TTTTTAATATTAATA
18255811 T
1 T
18255812 TAATGTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATTTTTTTAATATTAATA
Found at i:18255815 original size:20 final size:21
Alignment explanation
Indices: 18255771--18255815 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
18255761 AGGGTTTTTT
18255771 TTAATTTTTTTAATATTAATA
1 TTAATTTTTTTAATATTAATA
18255792 -TAATTATTTTT-AT-TTAATA
1 TTAATT-TTTTTAATATTAATA
18255811 TTAAT
1 TTAAT
18255816 GTCAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.27
20 11 0.50
21 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTAATTTTTTTAATATTAATA
Found at i:18255857 original size:22 final size:20
Alignment explanation
Indices: 18255821--18255865 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
18255811 TTAATGTCAA
*
18255821 TTTTAAATTTATTATTATATT
1 TTTTAAAATTATTA-TATATT
*
18255842 TTTTAAAATTATTTATGTATT
1 TTTTAAAATTA-TTATATATT
18255863 TTT
1 TTT
18255866 ATATATTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTAAAATTATTATATATT
Found at i:18257673 original size:20 final size:19
Alignment explanation
Indices: 18257623--18257673 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
18257613 AATAGTTCTG
*
18257623 TCTCTTGATGAACAGTTGTA
1 TCTCTTG-TGAACAATTGTA
18257643 TCT-TT-TGAACAATTGTA
1 TCTCTTGTGAACAATTGTA
18257660 TCTCTTGGTGAACA
1 TCTCTT-GTGAACA
18257674 GATTCATTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 2 0.07
20 9 0.33
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (19 bp):
TCTCTTGTGAACAATTGTA
Found at i:18259111 original size:30 final size:30
Alignment explanation
Indices: 18259051--18259111 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
18259041 AAGTTCTTCC
* *
18259051 TTTTTTATAAATTATAATATTATAATATTA
1 TTTTTTATAAATCATAATATTATAACATTA
* *
18259081 TTTTTTAATAACTCATAAT-TTATGACATTA
1 TTTTTT-ATAAATCATAATATTATAACATTA
18259111 T
1 T
18259112 AGATTAACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTTTTATAAATCATAATATTATAACATTA
Found at i:18259812 original size:30 final size:29
Alignment explanation
Indices: 18259768--18259829 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
18259758 ATTATAAATT
*
18259768 ATTTTTAATATTTTAA-TATATGAAATATTA
1 ATTTTAAATATTTTAAGTA-AT-AAATATTA
* *
18259798 ATTTTAAATGTTTTAAGTAATTAATATTA
1 ATTTTAAATATTTTAAGTAATAAATATTA
18259827 ATT
1 ATT
18259830 ATTTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.36
30 16 0.57
31 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (29 bp):
ATTTTAAATATTTTAAGTAATAAATATTA
Found at i:18262981 original size:32 final size:32
Alignment explanation
Indices: 18262613--18262959 Score: 469
Period size: 32 Copynumber: 10.8 Consensus size: 32
18262603 ATATTTTATG
* * * ***
18262613 TATTGTCGAATTGAATTGTAAAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
18262645 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
18262677 TATTGCCGAATTGAATTGTATGTGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* ***
18262709 TATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
18262741 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* * *
18262773 TGTTGCTGAATTGAATTGTATATGTATAATTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
*
18262805 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* ***
18262837 TATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGCCGAATTGAATTGTATATGTATACTTA
**
18262869 TATTGTTGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
18262901 TATTGCCGAATTGAATTGTATATGTATACTTA
1 TATTGCCGAATTGAATTGTATATGTATACTTA
* *
18262933 TGTTGCCGAATTGATTTGTATATGTAT
1 TATTGCCGAATTGAATTGTATATGTAT
18262960 TTATATATTG
Statistics
Matches: 275, Mismatches: 40, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 275 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.43
Consensus pattern (32 bp):
TATTGCCGAATTGAATTGTATATGTATACTTA
Found at i:18272954 original size:32 final size:32
Alignment explanation
Indices: 18272911--18273321 Score: 450
Period size: 32 Copynumber: 12.8 Consensus size: 32
18272901 ATATTTTATG
* * ***
18272911 TATTTTCGAATTGAATTGTATAGGTATACACC
1 TATTGTCGAATTGAATTGTATATGTATACTTA
18272943 TATTGTCGAATTGAATTGTATATGTATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
18272975 TATTG-CTGAATTGAATTGTATATGTATACTTA
1 TATTGTC-GAATTGAATTGTATATGTATACTTA
* * ***
18273007 TATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGTCGAATTGAATTGTATATGTATACTTA
*
18273039 TATTGTTGAATTGAATTGTATATGTATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
* *
18273071 TACTGCCGAATTGAATTGTATATGTATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
* * * * * ***
18273103 TATT-TCTGAATTAAAATATAGAGGTATACACC
1 TATTGTC-GAATTGAATTGTATATGTATACTTA
* *
18273135 TATTTTTGAATTGAATTGTATATGTATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
18273167 TATTGTCGAATTGAATTGTA-ATAGTATACTTA
1 TATTGTCGAATTGAATTGTATAT-GTATACTTA
* * ***
18273199 TATTGCCGAATTGAATTGTATAGGTATACACC
1 TATTGTCGAATTGAATTGTATATGTATACTTA
* * *
18273231 TATTATCAAATTGAATTGTATATATATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
*
18273263 TATTGCCGAATTGAATTGTATATGTATACTTA
1 TATTGTCGAATTGAATTGTATATGTATACTTA
* * * *
18273295 TGTTGCCAAATTGATTTGTATATGTAT
1 TATTGTCGAATTGAATTGTATATGTAT
18273322 TTATATATTG
Statistics
Matches: 314, Mismatches: 59, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
31 4 0.01
32 307 0.98
33 3 0.01
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (32 bp):
TATTGTCGAATTGAATTGTATATGTATACTTA
Found at i:18273024 original size:96 final size:96
Alignment explanation
Indices: 18272917--18273321 Score: 623
Period size: 96 Copynumber: 4.2 Consensus size: 96
18272907 TATGTATTTT
*
18272917 CGAATTGAATTGTATAGGTATACACCTATTGTCGAATTGAATTGTATATGTATACTTATATTGCT
1 CGAATTGAATTGTATAGGTATACACCTATTGTCGAATTGAATTGTATATGTATACTTATATTGCC
18272982 GAATTGAATTGTATATGTATACTTATATTGC
66 GAATTGAATTGTATATGTATACTTATATTGC
* *
18273013 CGAATTGAATTGTATAGGTATACACCTATTGTTGAATTGAATTGTATATGTATACTTATACTGCC
1 CGAATTGAATTGTATAGGTATACACCTATTGTCGAATTGAATTGTATATGTATACTTATATTGCC
*
18273078 GAATTGAATTGTATATGTATACTTATATTTC
66 GAATTGAATTGTATATGTATACTTATATTGC
* * * * * * * *
18273109 TGAATTAAAATATAGAGGTATACACCTATTTTTGAATTGAATTGTATATGTATACTTATATTGTC
1 CGAATTGAATTGTATAGGTATACACCTATTGTCGAATTGAATTGTATATGTATACTTATATTGCC
18273174 GAATTGAATTGTA-ATAGTATACTTATATTGC
66 GAATTGAATTGTATAT-GTATACTTATATTGC
* * *
18273205 CGAATTGAATTGTATAGGTATACACCTATTATCAAATTGAATTGTATATATATACTTATATTGCC
1 CGAATTGAATTGTATAGGTATACACCTATTGTCGAATTGAATTGTATATGTATACTTATATTGCC
*
18273270 GAATTGAATTGTATATGTATACTTATGTTGC
66 GAATTGAATTGTATATGTATACTTATATTGC
* * *
18273301 CAAATTGATTTGTATATGTAT
1 CGAATTGAATTGTATAGGTAT
18273322 TTATATATTG
Statistics
Matches: 280, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
95 2 0.01
96 276 0.99
97 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (96 bp):
CGAATTGAATTGTATAGGTATACACCTATTGTCGAATTGAATTGTATATGTATACTTATATTGCC
GAATTGAATTGTATATGTATACTTATATTGC
Found at i:18276884 original size:41 final size:40
Alignment explanation
Indices: 18276810--18276951 Score: 176
Period size: 41 Copynumber: 3.5 Consensus size: 40
18276800 AAAAAGGGGT
* *
18276810 ACATATGTGCAATTCAGGGGGTACCGAAGTACAAACAGCGGC
1 ACATAAGTGCAATTCA-GGGGTAACGAAGTACAAACAG-GGC
* * *
18276852 ACATTAGTGCAATTCAGGGGTAACAAAGTACAAATAGGGGC
1 ACATAAGTGCAATTCAGGGGTAACGAAGTACAAACA-GGGC
**
18276893 ACATAAGTGCAATTCAGGGGTATTGAAGTACAAACAGGTGC
1 ACATAAGTGCAATTCAGGGGTAACGAAGTACAAACAGG-GC
*
18276934 ACGTAAGTGCAATTCAGG
1 ACATAAGTGCAATTCAGG
18276952 TATAATTAAC
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.02
41 70 0.80
42 15 0.17
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (40 bp):
ACATAAGTGCAATTCAGGGGTAACGAAGTACAAACAGGGC
Found at i:18276911 original size:21 final size:21
Alignment explanation
Indices: 18276804--18276951 Score: 72
Period size: 20 Copynumber: 7.1 Consensus size: 21
18276794 AGTGTAAAAA
* *
18276804 AGGGGTACATATGTGCAATTC
1 AGGGGCACATAAGTGCAATTC
* ** * *
18276825 AGGGGGTACCGAAGTACAA-AC
1 A-GGGGCACATAAGTGCAATTC
* *
18276846 AGCGGCACATTAGTGCAATTC
1 AGGGGCACATAAGTGCAATTC
* * *
18276867 AGGGGTAACA-AAGTACAAAT-
1 AGGGG-CACATAAGTGCAATTC
18276887 AGGGGCACATAAGTGCAATTC
1 AGGGGCACATAAGTGCAATTC
* * * *
18276908 AGGGGTA-TTGAAGTACAA-AC
1 AGGGGCACAT-AAGTGCAATTC
* *
18276928 AGGTGCACGTAAGTGCAATTC
1 AGGGGCACATAAGTGCAATTC
18276949 AGG
1 AGG
18276952 TATAATTAAC
Statistics
Matches: 90, Mismatches: 29, Indels: 16
0.67 0.21 0.12
Matches are distributed among these distances:
19 3 0.03
20 38 0.42
21 33 0.37
22 16 0.18
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (21 bp):
AGGGGCACATAAGTGCAATTC
Found at i:18283464 original size:41 final size:41
Alignment explanation
Indices: 18283407--18283627 Score: 194
Period size: 41 Copynumber: 5.4 Consensus size: 41
18283397 ACCAGAGTGT
* * *
18283407 AAACAGAGGCACGTAAGTGCAATTGT-GGTGTACCAAAGTAC
1 AAACAGGGGCATGTAAGTGCAATT-TAGGTGTACCGAAGTAC
* * * *
18283448 AAACTGGAGCATGTAAGTGCAATTTAGGGGTACCGAGGTAC
1 AAACAGGGGCATGTAAGTGCAATTTAGGTGTACCGAAGTAC
** * * *
18283489 AAACAGGGGCACATAAGTGCAATTCAGGAGTACCGAAGTAG
1 AAACAGGGGCATGTAAGTGCAATTTAGGTGTACCGAAGTAC
* * *
18283530 AAACAGGGGCATGTAAATGCAATTTAAGTGTATCGAAGTAC
1 AAACAGGGGCATGTAAGTGCAATTTAGGTGTACCGAAGTAC
* * ** * *
18283571 AAACTGGGGTACATAAGTGTAATTCAAGG-GTACCGAAGTAC
1 AAACAGGGGCATGTAAGTGCAATT-TAGGTGTACCGAAGTAC
* * *
18283612 AGACAAGGGCACGTAA
1 AAACAGGGGCATGTAA
18283628 CAATAATTCA
Statistics
Matches: 141, Mismatches: 37, Indels: 4
0.77 0.20 0.02
Matches are distributed among these distances:
40 1 0.01
41 138 0.98
42 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.19
Consensus pattern (41 bp):
AAACAGGGGCATGTAAGTGCAATTTAGGTGTACCGAAGTAC
Found at i:18283622 original size:82 final size:82
Alignment explanation
Indices: 18283407--18283627 Score: 239
Period size: 82 Copynumber: 2.7 Consensus size: 82
18283397 ACCAGAGTGT
* * ** * * * *
18283407 AAACAGAGGCACGTAAGTGCAATTGTGGTGTACCAAAGTACAAAC-TGGAGCATGTAAGTGCAAT
1 AAACAGGGGCACATAAGTGCAATTCAGGAGTACCGAAGTACAAACAAGG-GCATGTAAATGCAAT
* *
18283471 TTAGGGGTACCGAGGTAC
65 TTAAGGGTACCGAAGTAC
* *
18283489 AAACAGGGGCACATAAGTGCAATTCAGGAGTACCGAAGTAGAAACAGGGGCATGTAAATGCAATT
1 AAACAGGGGCACATAAGTGCAATTCAGGAGTACCGAAGTACAAACAAGGGCATGTAAATGCAATT
* *
18283554 TAAGTGTATCGAAGTAC
66 TAAGGGTACCGAAGTAC
* * * * *
18283571 AAACTGGGGTACATAAGTGTAATTCAAGG-GTACCGAAGTACAGACAAGGGCACGTAA
1 AAACAGGGGCACATAAGTGCAATTC-AGGAGTACCGAAGTACAAACAAGGGCATGTAA
18283628 CAATAATTCA
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
82 112 0.96
83 5 0.04
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.19
Consensus pattern (82 bp):
AAACAGGGGCACATAAGTGCAATTCAGGAGTACCGAAGTACAAACAAGGGCATGTAAATGCAATT
TAAGGGTACCGAAGTAC
Found at i:18288580 original size:253 final size:253
Alignment explanation
Indices: 18288116--18288583 Score: 731
Period size: 253 Copynumber: 1.8 Consensus size: 253
18288106 AAATACATTT
18288116 TTTTATCTTTAATTTCTCACTTTTCCTTTACATAAATTTTCATATTCTTTTGCTCAAAATTTATT
1 TTTTATCTTTAATTTCTCACTTTTCCTTTACATAAATTTTCATATTCTTTTGCTCAAAATTTATT
* * * * *
18288181 TGTTGAATCCCGAACCCGAATTCCACCCTGTTCAATTCGTTCTTCGTATTGTTTTAGCGTAACAC
66 TGTTGAATCCCAAACCCGAATTCCACCCCGTTCAATTCATTCTTCATATTGTTTTAACGTAACAC
* *
18288246 CGTCAAAATCCGTTTCTAACATGCCAATATCAGTAAGAATTATTACTTTTATTTTCGTAGAACAC
131 AGTCAAAATCCGTTTCTAACATGCCAATATCAGTAAGAATTATTACTTTTATTCTCGTAGAACAC
18288311 TAACATTCTAAAATAAATAACGTTATTTCCAATCTTTTAATCAATTTCGTAAAACATA
196 TAACATTCTAAAATAAATAACGTTATTTCCAATCTTTTAATCAATTTCGTAAAACATA
* *
18288369 TTTTATCCTTT-ATTTCTCACTTTTCCTTTTCATAAATTTTCATATTGTTTTGCTCAAAATTTAT
1 TTTTAT-CTTTAATTTCTCACTTTTCCTTTACATAAATTTTCATATTCTTTTGCTCAAAATTTAT
* * *
18288433 TTGTTGAATCCTAAACCCGAATTCCACCCCGTTCAATTTATTCTTCATATTTTTTTAACGTAACA
65 TTGTTGAATCCCAAACCCGAATTCCACCCCGTTCAATTCATTCTTCATATTGTTTTAACGTAACA
*** * * * *
18288498 CAGTCAAAATTTTTTTCTAACGTGCCAATATCGGTAAGAATTCTTACTTTTATTCTCGTAGAACC
130 CAGTCAAAATCCGTTTCTAACATGCCAATATCAGTAAGAATTATTACTTTTATTCTCGTAGAACA
* *
18288563 CTAGCATTCTGAAATAAATAA
195 CTAACATTCTAAAATAAATAA
18288584 TGTTCTTGTT
Statistics
Matches: 193, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
253 189 0.98
254 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (253 bp):
TTTTATCTTTAATTTCTCACTTTTCCTTTACATAAATTTTCATATTCTTTTGCTCAAAATTTATT
TGTTGAATCCCAAACCCGAATTCCACCCCGTTCAATTCATTCTTCATATTGTTTTAACGTAACAC
AGTCAAAATCCGTTTCTAACATGCCAATATCAGTAAGAATTATTACTTTTATTCTCGTAGAACAC
TAACATTCTAAAATAAATAACGTTATTTCCAATCTTTTAATCAATTTCGTAAAACATA
Found at i:18297336 original size:3 final size:3
Alignment explanation
Indices: 18297330--18297364 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
18297320 CTCTTATTAT
18297330 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
18297365 TTATTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:18309978 original size:51 final size:51
Alignment explanation
Indices: 18309860--18309980 Score: 129
Period size: 51 Copynumber: 2.4 Consensus size: 51
18309850 GAAGGCAACA
* *
18309860 AATCCTATCTCAT-TGGCGTTACAGTGGAATAGATTAAAGTAAAAGGTAGCG
1 AATCTTATCTC-TCTGGCGTTACAGTGGAACAGATTAAAGTAAAAGGTAGCG
* * * * * * *
18309911 AATCTTGTTTCCCTGGCGTTGCAGTGGAGCAGATTAAAGCT-GAAGGTAGTG
1 AATCTTATCTCTCTGGCGTTACAGTGGAACAGATTAAAG-TAAAAGGTAGCG
18309962 AATCTTATCTCTCTGGCGT
1 AATCTTATCTCTCTGGCGT
18309981 AGATTAAAGA
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (51 bp):
AATCTTATCTCTCTGGCGTTACAGTGGAACAGATTAAAGTAAAAGGTAGCG
Found at i:18310177 original size:128 final size:128
Alignment explanation
Indices: 18309998--18310232 Score: 298
Period size: 128 Copynumber: 1.8 Consensus size: 128
18309988 AGATGGCGAA
* * * * *
18309998 TCTTATCTCCCTGAAGTTGCAGTGGAGCTGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGCAAATAATCCTATCTCCCTGAAATTACA
* *
18310063 GTGGAGC-GAGTT-AAAATCAC-AAGTCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCCA
66 GTGGAGCAGA-TTGAAAA-AACTAA-TCCTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCCA
18310125 G
128 G
* * * * *
18310126 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-TAAATCGATCTTATCTCCCTGAAATTAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGCAAAT-AATCCTATCTCCCTGAAATTAC
18310190 AGTGGAGCAGATTGAAAAAACTAATCCTATCTCTCTGAAGTTG
65 AGTGGAGCAGATTGAAAAAACTAATCCTATCTCTCTGAAGTTG
18310233 TAGTGGAGCG
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
127 3 0.03
128 80 0.88
129 8 0.09
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (128 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGCAAATAATCCTATCTCCCTGAAATTACA
GTGGAGCAGATTGAAAAAACTAATCCTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCCAG
Found at i:18310181 original size:44 final size:42
Alignment explanation
Indices: 18309996--18310443 Score: 268
Period size: 44 Copynumber: 10.6 Consensus size: 42
18309986 AAAGATGGCG
* *
18309996 AATCTTATCTCCCTGAAGTTGCAGTGGAGCTGATTAAAGCCAAT-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAA---AATC
* *
18310040 AATCCTATCTCCCTGAAGTTGCAGTGGAGC-GA-GTTAAAATCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATG-AAAAAT--C
* * *
18310083 AAGTCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCG---CATCC
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-GAAAAAT-C
*
18310124 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAAATC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAA-AAATC
* * ** *
18310168 GATCTTATCTCCCTGAAATTATAGTGGAGCAGATTGAAAAAAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAAAATC
* * * *
18310211 TAATCCTATCTCTCTGAAGTTGTAGTGGAGCGGATG-AAAATC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAAATC
** * *
18310253 -A-CAGATCT---T-AAGTTGCAG-AGAGCAGATCG---CATC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-GAAAAATC
* * * *
18310286 AAGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAATGAACC
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAA-AAATC
* *
18310331 AATCTTATCTCCCTGAAGTTGCAGTCGAACAGATTGAAGAAA-C
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAA-AAATC
* * * *
18310374 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATGATG
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAA--ATC
* *
18310419 GATCTTATCTCTCTGAAGTTGCAGT
1 AATCTTATCTCCCTGAAGTTGCAGT
18310444 AGAATAGATC
Statistics
Matches: 320, Mismatches: 51, Indels: 66
0.73 0.12 0.15
Matches are distributed among these distances:
33 3 0.01
34 8 0.03
35 9 0.03
36 6 0.02
39 6 0.02
40 34 0.11
41 19 0.06
42 11 0.03
43 20 0.06
44 197 0.62
45 6 0.02
46 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (42 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAAATC
Found at i:18310338 original size:163 final size:168
Alignment explanation
Indices: 18309996--18310414 Score: 566
Period size: 163 Copynumber: 2.5 Consensus size: 168
18309986 AAAGATGGCG
* *
18309996 AATCTTATCTCCCTGAAGTTGCAGTGGAGCTGATT-AAAGCCAA-TAATCCTATCTCCCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA--AAACTAATCCTATCTCCCTGAAGT
18310059 TGCAGTGGAGC-GAGTTAAAATCACAAGTCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
64 TGCAGTGGAGCGGA-TTAAAATCACAAG---TA-CTCTCTGAAGTTGCAGAGAGCAGATCGCATC
* * * *
18310123 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAAATC
124 AAGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGAATAAACC
* * ** *
18310168 GATCTTATCTCCCTGAAATTATAGTGGAGCAGATTGAAAAAACTAATCCTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAACTAATCCTATCTCCCTGAAGTTG
* *
18310233 TAGTGGAGCGGATGAAAATCAC-AG-A-TCT-T-AAGTTGCAGAGAGCAGATCGCATCAAGTCTT
66 CAGTGGAGCGGATTAAAATCACAAGTACTCTCTGAAGTTGCAGAGAGCAGATCGCATCAAGTCTT
*
18310293 ATCTCCCTAAAGTTGCAGTAGAGCAGACTGAATGAACC
131 ATCTCCCTAAAGTTGCAGTAGAGCAGACTGAATAAACC
* * *
18310331 AATCTTATCTCCCTGAAGTTGCAGTCGAACAGATTGAAGAAACTAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAACTAATCCTATCTCCCTGAAGTTG
18310396 CAGTGGAGCGGATTAAAAT
66 CAGTGGAGCGGATTAAAAT
18310415 GATGGATCTT
Statistics
Matches: 220, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
163 138 0.63
164 1 0.00
165 3 0.01
167 1 0.00
171 4 0.02
172 68 0.31
173 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (168 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAACTAATCCTATCTCCCTGAAGTTG
CAGTGGAGCGGATTAAAATCACAAGTACTCTCTGAAGTTGCAGAGAGCAGATCGCATCAAGTCTT
ATCTCCCTAAAGTTGCAGTAGAGCAGACTGAATAAACC
Found at i:18311396 original size:29 final size:29
Alignment explanation
Indices: 18311354--18311411 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
18311344 AAAAGAAAAA
18311354 AGAAGACTTACCTGTGGTTTTGTGACACC
1 AGAAGACTTACCTGTGGTTTTGTGACACC
18311383 AGAAGACTTACCTGTGGTTTTGTGACACC
1 AGAAGACTTACCTGTGGTTTTGTGACACC
18311412 CCGCCTTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (29 bp):
AGAAGACTTACCTGTGGTTTTGTGACACC
Found at i:18312029 original size:3 final size:3
Alignment explanation
Indices: 18312021--18312111 Score: 92
Period size: 3 Copynumber: 30.3 Consensus size: 3
18312011 TTTAATACTC
* * * *
18312021 TTA TTA TTA TTA CTA TTA TAA TTA TTA TTA TTA TTA TTA TTA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
18312069 CTA CTA CTA CTA TTA TTA TTA GTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
18312112 ATCAATTGAA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:18316531 original size:34 final size:36
Alignment explanation
Indices: 18316476--18316568 Score: 122
Period size: 34 Copynumber: 2.7 Consensus size: 36
18316466 TATAATTTGA
* * *
18316476 AATAAAATACTTTAATTTAATTTAATATAAAA-A-T
1 AATAAAATATTTTAATATAATTTAAAATAAAATATT
18316510 AA-AATAATATTTTAATATAATTTAAAATAAAATATT
1 AATAA-AATATTTTAATATAATTTAAAATAAAATATT
18316546 AATAAAATATTTT-ATATAATTTA
1 AATAAAATATTTTAATATAATTTA
18316569 GACTAAATGA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
33 2 0.04
34 26 0.50
35 11 0.21
36 11 0.21
37 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (36 bp):
AATAAAATATTTTAATATAATTTAAAATAAAATATT
Found at i:18332948 original size:17 final size:18
Alignment explanation
Indices: 18332917--18332951 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
18332907 AATAAAAATA
*
18332917 ATAAAAATAATAATTTAG
1 ATAAAAATAAGAATTTAG
18332935 ATAAAAAT-AGAATTTAG
1 ATAAAAATAAGAATTTAG
18332952 GAAAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (18 bp):
ATAAAAATAAGAATTTAG
Found at i:18370168 original size:50 final size:49
Alignment explanation
Indices: 18370109--18370445 Score: 192
Period size: 50 Copynumber: 6.8 Consensus size: 49
18370099 TCGAGGAAGC
* *
18370109 AAGATTCGTTGTTGTAGCTTCAATCTGTTCCACTACACCGCCTGGGGAGT
1 AAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTGCACCGCC-GGGGAGT
* ** * * *
18370159 AAGATTCGTTGTTGTAGCTTTAATCTTTTTAACTGC-CATGTCGGGGAAGC
1 AAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTGCAC-CGCCGGGG-AGT
*** * * *
18370209 AAGATTCACCGTTGTGGCGTTAATCTGTTCCACTGCACCGCCAGGGAAGT
1 AAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTGCACCGCC-GGGGAGT
* * ** * ** * * *
18370259 AAGATTCGTTGTTGTCGCTTTAATCTTTTTAAATGCAATGTCAGGGAAGC
1 AAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTGCACCG-CCGGGGAGT
* * ** * * * * *
18370309 AAGGTTTG-CCTTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGT
1 AAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTGCACCGC-CGGGGAGT
* * ** ** * *
18370358 AAGATTCGTTGTGGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGA
1 AAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTGCACCGCCGGGG-AGT
* * * *
18370408 AAGGTTCGTCGTTGTGGCGTTAATCTGTTCCACTGCAC
1 AAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTGCAC
18370446 TGCTTGAGAA
Statistics
Matches: 205, Mismatches: 74, Indels: 16
0.69 0.25 0.05
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 160 0.78
51 5 0.02
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (49 bp):
AAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTGCACCGCCGGGGAGT
Found at i:18370210 original size:100 final size:100
Alignment explanation
Indices: 18370076--18370745 Score: 862
Period size: 100 Copynumber: 6.7 Consensus size: 100
18370066 TTACTCGTTA
* * ** * * ** *
18370076 CTTTAATATGTTTAACTGTGATGTCGAGGAAGCAAGATTCGTTGTTGTAGC-TTCAATCTGTTCC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCCGTTGTGGCGTT-AATCTGTTCC
* * * * *
18370140 ACTACACCGCCTGGGGAGTAAGATTCGTTGTTGTAG
65 ACTGCACCGCTTGAGAAGTAAGATTCGTTGTGGTAG
* * *
18370176 CTTTAATCTTTTTAACTGCCATGTCGGGGAAGCAAGATTCACCGTTGTGGCGTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCCGTTGTGGCGTTAATCTGTTCCA
** * * *
18370241 CTGCACCGCCAGGGAAGTAAGATTCGTTGTTGTCG
66 CTGCACCGCTTGAGAAGTAAGATTCGTTGTGGTAG
* * *
18370276 CTTTAATCTTTTTAAATGCAATGTCAGGGAAGCAAGGTTTGCC-TTGTGGCGTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCCGTTGTGGCGTTAATCTGTTCCA
18370340 CTGCACCGCTTGAGAAGTAAGATTCGTTGTGGTAG
66 CTGCACCGCTTGAGAAGTAAGATTCGTTGTGGTAG
* *
18370375 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGAAAGGTTCGTCGTTGTGGCGTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCCGTTGTGGCGTTAATCTGTTCCA
* *
18370440 CTGCACTGCTTGAGAAGTAAGATT-TTCTGTGGTAG
66 CTGCACCGCTTGAGAAGTAAGATTCGT-TGTGGTAG
*
18370475 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCCGTTGTGGCGTTAATCTTTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCCGTTGTGGCGTTAATCTGTTCCA
* ** *
18370540 CTACACCGCTTGAGAAGTAAGATTCACTGCGGTAG
66 CTGCACCGCTTGAGAAGTAAGATTCGTTGTGGTAG
*
18370575 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCCGTTGTGGCGTTAATCTATTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCCGTTGTGGCGTTAATCTGTTCCA
* * * *
18370640 CTGCACCGCTTGACAAGTAAGATTCGCTGTTGTGG
66 CTGCACCGCTTGAGAAGTAAGATTCGTTGTGGTAG
* * * * * *
18370675 CTTTAATCATTTTAACGGCAATGTCGAGGAAGC-AGGATTCACCGTTGTGGCTTTCATCTTGTTC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGG-TTCGCCGTTGTGGCGTTAATC-TGTTC
*
18370739 CATTGCA
64 CACTGCA
18370746 TTGTCAGGGA
Statistics
Matches: 510, Mismatches: 54, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
99 93 0.18
100 405 0.79
101 12 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCCGTTGTGGCGTTAATCTGTTCCA
CTGCACCGCTTGAGAAGTAAGATTCGTTGTGGTAG
Found at i:18370481 original size:50 final size:50
Alignment explanation
Indices: 18370327--18370687 Score: 201
Period size: 50 Copynumber: 7.2 Consensus size: 50
18370317 CCTTGTGGCG
* *
18370327 TTAATCTGTTCCACTGCACCGCTTGAGAAGTAAGATTCGT-TGTGGTAGCT
1 TTAATCTTTTCCACTGCACTGCTTGAGAAGTAAGATTC-TCTGTGGTAGCT
** * * * * * * * *
18370377 TTAATCTTTTTAACTGCAATG-TCGGGGAAGAAAGGTTCGTC-GTTGTGGCG
1 TTAATCTTTTCCACTGCACTGCT-TGAGAAGTAAGATTC-TCTGTGGTAGCT
* *
18370427 TTAATCTGTTCCACTGCACTGCTTGAGAAGTAAGATTTTCTGTGGTAGCT
1 TTAATCTTTTCCACTGCACTGCTTGAGAAGTAAGATTCTCTGTGGTAGCT
** * * * * * * * * * *
18370477 TTAATCTTTTTAACTGCAATG-TCGGGGAAGCAAGGTTCGCCGTTGTGGCG
1 TTAATCTTTTCCACTGCACTGCT-TGAGAAGTAAGATTCTCTGTGGTAGCT
* * * *
18370527 TTAATCTTTTCCACTACACCGCTTGAGAAGTAAGATTCACTGCGGTAGCT
1 TTAATCTTTTCCACTGCACTGCTTGAGAAGTAAGATTCTCTGTGGTAGCT
** * * * * * * * * * *
18370577 TTAATCTTTTTAACTGCAATG-TCGGGGAAGCAAGGTTCGCCGTTGTGGCG
1 TTAATCTTTTCCACTGCACTGCT-TGAGAAGTAAGATTCTCTGTGGTAGCT
* * * * * *
18370627 TTAATCTATTCCACTGCACCGCTTGACAAGTAAGATTCGCTGTTGTGGCT
1 TTAATCTTTTCCACTGCACTGCTTGAGAAGTAAGATTCTCTGTGGTAGCT
18370677 TTAATCATTTT
1 TTAATC-TTTT
18370688 AACGGCAATG
Statistics
Matches: 221, Mismatches: 81, Indels: 17
0.69 0.25 0.05
Matches are distributed among these distances:
49 5 0.02
50 210 0.95
51 6 0.03
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (50 bp):
TTAATCTTTTCCACTGCACTGCTTGAGAAGTAAGATTCTCTGTGGTAGCT
Found at i:18372426 original size:15 final size:15
Alignment explanation
Indices: 18372408--18372442 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18372398 CATTTTTTTA
18372408 TTTTTAATTTTCACT
1 TTTTTAATTTTCACT
* *
18372423 TTTTCATTTTTCACT
1 TTTTTAATTTTCACT
18372438 TTTTT
1 TTTTT
18372443 TTGACTCGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTAATTTTCACT
Found at i:18373301 original size:8 final size:8
Alignment explanation
Indices: 18373288--18373327 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
18373278 TGACCTCTCC
18373288 TTTTTCTT
1 TTTTTCTT
18373296 TTTTTCTT
1 TTTTTCTT
18373304 TTTTTC--
1 TTTTTCTT
18373310 TTTTTCTT
1 TTTTTCTT
18373318 TTTTTCTT
1 TTTTTCTT
18373326 TT
1 TT
18373328 ATTTTTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.20
8 24 0.80
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTCTT
Found at i:18373333 original size:14 final size:14
Alignment explanation
Indices: 18373287--18373327 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
18373277 TTGACCTCTC
18373287 CTTTTTCTT-TTTTT
1 CTTTTT-TTCTTTTT
18373301 CTTTTTTTCTTTTT
1 CTTTTTTTCTTTTT
18373315 CTTTTTTTCTTTT
1 CTTTTTTTCTTTT
18373328 ATTTTTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 2 0.08
14 24 0.92
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
CTTTTTTTCTTTTT
Found at i:18373352 original size:30 final size:31
Alignment explanation
Indices: 18373318--18373376 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
18373308 TCTTTTTCTT
18373318 TTTTTCTTTTATTTT-TGATTTTG-ATTTTGA
1 TTTTTCTTTT-TTTTGTGATTTTGAATTTTGA
*
18373348 TTTTTCTTTTTTTTGTTATTTTGAATTTT
1 TTTTTCTTTTTTTTGTGATTTTGAATTTT
18373377 TTGAATTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 4 0.15
30 17 0.65
31 5 0.19
ACGTcount: A:0.12, C:0.03, G:0.08, T:0.76
Consensus pattern (31 bp):
TTTTTCTTTTTTTTGTGATTTTGAATTTTGA
Found at i:18374092 original size:35 final size:35
Alignment explanation
Indices: 18374052--18374130 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
18374042 GAATAAATTC
18374052 ATGAATAATTATTTGTACCATATGATTATGAATGA
1 ATGAATAATTATTTGTACCATATGATTATGAATGA
*
18374087 ATGAATAATAATTTGTACCATATGATTATGAATGA
1 ATGAATAATTATTTGTACCATATGATTATGAATGA
18374122 AT-AATAATT
1 ATGAATAATT
18374131 TGGAAGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 6 0.14
35 36 0.86
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.39
Consensus pattern (35 bp):
ATGAATAATTATTTGTACCATATGATTATGAATGA
Found at i:18388818 original size:84 final size:84
Alignment explanation
Indices: 18388667--18388828 Score: 216
Period size: 84 Copynumber: 1.9 Consensus size: 84
18388657 ACTTTCATCA
* * * *
18388667 TAGGTAAGACAATGTTAGAGATAAGGTCAGAATCCAATTTTGGATGACCCTATGACACACTTACA
1 TAGGTAAGACAATGTCAGAGATAAGGTCAGAATCCAATTTCGGACGACCCTATAACACACTTACA
*
18388732 ACAGCACAAGTATTTCACC
66 ACAACACAAGTATTTCACC
* * * * * * *
18388751 TAGGTAAGATAATGTCAGAGGTAAGGTTAGAATCCAATTTCGGACGATCCTGTAACATACTTGCA
1 TAGGTAAGACAATGTCAGAGATAAGGTCAGAATCCAATTTCGGACGACCCTATAACACACTTACA
18388816 ACAACACAAGTAT
66 ACAACACAAGTAT
18388829 GTGGAGCGTC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (84 bp):
TAGGTAAGACAATGTCAGAGATAAGGTCAGAATCCAATTTCGGACGACCCTATAACACACTTACA
ACAACACAAGTATTTCACC
Found at i:18389743 original size:41 final size:41
Alignment explanation
Indices: 18389686--18389768 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
18389676 ACCTTCCTCT
18389686 ACATAGACAATCTGGGTATATAACTCTAATATAGCATTTCC
1 ACATAGACAATCTGGGTATATAACTCTAATATAGCATTTCC
18389727 ACATAGACAATCTGGGTATATAACTCTAATATAGCATTTCC
1 ACATAGACAATCTGGGTATATAACTCTAATATAGCATTTCC
18389768 A
1 A
18389769 GTTGAGCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.31
Consensus pattern (41 bp):
ACATAGACAATCTGGGTATATAACTCTAATATAGCATTTCC
Found at i:18397869 original size:26 final size:27
Alignment explanation
Indices: 18397813--18397898 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 27
18397803 ATAAAAGTCG
* * * *
18397813 TTGTGGCGAACCATGAAAATAAAGGCG
1 TTGTGGTGAACCATGAAAAGAAAGCCC
18397840 TTGTGGTGAACCATG-AAAGAAAGCCC
1 TTGTGGTGAACCATGAAAAGAAAGCCC
*
18397866 TTGTGGTGAACCATGAAAAGAAAGCCT
1 TTGTGGTGAACCATGAAAAGAAAGCCC
18397893 TTGTGG
1 TTGTGG
18397899 CAAATCTTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
26 23 0.43
27 30 0.57
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (27 bp):
TTGTGGTGAACCATGAAAAGAAAGCCC
Found at i:18398074 original size:27 final size:27
Alignment explanation
Indices: 18397988--18398074 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 27
18397978 CCTCTGTGGA
* * * * *
18397988 GAACTCTAAAAGAATAGTACTCATAGT
1 GAACTATAAAGGAATGGTACTCATGGC
**
18398015 GAACCCTAAAGGAATGGTACTCATGGC
1 GAACTATAAAGGAATGGTACTCATGGC
*
18398042 GAACTATAAAGGAATGGTATTCATGGC
1 GAACTATAAAGGAATGGTACTCATGGC
18398069 GAACTA
1 GAACTA
18398075 CGAAAGAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (27 bp):
GAACTATAAAGGAATGGTACTCATGGC
Found at i:18404823 original size:12 final size:13
Alignment explanation
Indices: 18404799--18404827 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
18404789 ATTGAAGCCT
18404799 TTTTCTCTTTTTC
1 TTTTCTCTTTTTC
18404812 TTTTCT-TTTTTC
1 TTTTCTCTTTTTC
18404824 TTTT
1 TTTT
18404828 ATTAATTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTCTTTTTC
Found at i:18407178 original size:103 final size:103
Alignment explanation
Indices: 18406999--18407229 Score: 392
Period size: 103 Copynumber: 2.2 Consensus size: 103
18406989 TAGCCGTTAT
*
18406999 TGGTGGATCCCGCACTTAGCACCACCACTGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGAT-ACGCACTTAGCACCACCACTGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGGG
**
18407064 AATCAGCACATAGCAACCCCCTTT-TTATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
18407102 TGGTGGATATCGCACTTAGCACCACCACTGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATA-CGCACTTAGCACCACCACTGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGGG
18407167 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
18407206 TGGTGGATCACGCACATAGCACCA
1 TGGTGGAT-ACGCACTTAGCACCA
18407230 NNNNNNNNNN
Statistics
Matches: 121, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
103 87 0.72
104 33 0.27
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (103 bp):
TGGTGGATACGCACTTAGCACCACCACTGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:18412328 original size:44 final size:44
Alignment explanation
Indices: 18412278--18412368 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
18412268 GTGTTTCTTT
18412278 TTTCCTAAAATTTCCTCTTTC-TGACATTTTTCTCTCCTCCCTTG
1 TTTCCTAAAATTTCCTCTTTCTTG-CATTTTTCTCTCCTCCCTTG
18412322 TTTCCTAAAATTTCCTCTTTCTTGCATTTTTCTCTCCTCCCTTG
1 TTTCCTAAAATTTCCTCTTTCTTGCATTTTTCTCTCCTCCCTTG
18412366 TTT
1 TTT
18412369 TCTCACTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 44 0.96
45 2 0.04
ACGTcount: A:0.12, C:0.31, G:0.04, T:0.53
Consensus pattern (44 bp):
TTTCCTAAAATTTCCTCTTTCTTGCATTTTTCTCTCCTCCCTTG
Done.