Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, whole genome shotgun sequence
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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 22 of 100
Found at i:4224661 original size:42 final size:42
Alignment explanation
Indices: 4224607--4224691 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
4224597 TGTTTATATG
* * * *
4224607 TCTATTATATATTATTATTTATCTGTTATTAT-TATTATTTA
1 TCTATTACATATTATCATTTATCTATTAATATATATTATTTA
*
4224648 TCTATTTACATATTATCATTTATCTATTAATATATATTTTTTA
1 TCTA-TTACATATTATCATTTATCTATTAATATATATTATTTA
4224691 T
1 T
4224692 TTTATTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 4 0.11
42 24 0.65
43 9 0.24
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (42 bp):
TCTATTACATATTATCATTTATCTATTAATATATATTATTTA
Found at i:4225074 original size:31 final size:31
Alignment explanation
Indices: 4225036--4225094 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
4225026 TTCGATTGAA
*
4225036 TTTTTCGGTAAAGTTTAAATTTTGTGGTGAC
1 TTTTTCGGCAAAGTTTAAATTTTGTGGTGAC
* * *
4225067 TTTTTCGGCCAAGTTTGAATTTTTTGGT
1 TTTTTCGGCAAAGTTTAAATTTTGTGGT
4225095 CAACTTTCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.19, C:0.08, G:0.22, T:0.51
Consensus pattern (31 bp):
TTTTTCGGCAAAGTTTAAATTTTGTGGTGAC
Found at i:4225568 original size:19 final size:19
Alignment explanation
Indices: 4225528--4225568 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4225518 CATTTTTTAT
*
4225528 TTATTATTTATTATTATTA
1 TTATTATTTATTATTATGA
4225547 TTATTATTTATTGATTA-GA
1 TTATTATTTATT-ATTATGA
4225566 TTA
1 TTA
4225569 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTATTATTTATTATTATGA
Found at i:4225687 original size:59 final size:59
Alignment explanation
Indices: 4225615--4225775 Score: 252
Period size: 59 Copynumber: 2.7 Consensus size: 59
4225605 TTAAATAAAA
* *
4225615 TTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATATGCT
1 TTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCT
* *
4225674 TTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTT
1 TTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCT
***
4225733 TTC-AAAAATGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1 TTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
4225776 TCCTGTACAA
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
58 36 0.38
59 58 0.62
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (59 bp):
TTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCT
Found at i:4228173 original size:2 final size:2
Alignment explanation
Indices: 4228161--4228230 Score: 61
Period size: 2 Copynumber: 35.0 Consensus size: 2
4228151 TCAATATAAA
* * *
4228161 AT AT GT AT AT AT AT AT AT AT AT -T AT AC AT GAT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
* * * *
4228203 AA AT AT AA AT AT TT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4228231 TTATTATTTT
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
1 1 0.02
2 49 0.94
3 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4228181 original size:12 final size:12
Alignment explanation
Indices: 4228154--4228230 Score: 75
Period size: 12 Copynumber: 6.3 Consensus size: 12
4228144 ACGGCTTTCA
4228154 ATATA-AAATAT
1 ATATATAAATAT
* *
4228165 GTATATATATAT
1 ATATATAAATAT
* *
4228177 ATATATTATACAT
1 ATATA-TAAATAT
4228190 GATATATAAATAT
1 -ATATATAAATAT
*
4228203 AAATATAAATAT
1 ATATATAAATAT
*
4228215 TTATATAAATAT
1 ATATATAAATAT
4228227 ATAT
1 ATAT
4228231 TTATTATTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
11 4 0.08
12 33 0.62
13 11 0.21
14 5 0.09
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:4228877 original size:2 final size:2
Alignment explanation
Indices: 4228870--4228914 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
4228860 AATTTTAGAG
4228870 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4228911 TA TA
1 TA TA
4228915 GCCAAAATAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4231388 original size:7 final size:7
Alignment explanation
Indices: 4231378--4231426 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
4231368 GATTTTTAGA
4231378 ATTTTGG
1 ATTTTGG
*
4231385 ATTTTAAG
1 ATTTT-GG
4231393 ATTTTGG
1 ATTTTGG
4231400 ATTTTAGG
1 ATTTT-GG
* *
4231408 GTTTGGG
1 ATTTTGG
4231415 ATTTTGG
1 ATTTTGG
4231422 ATTTT
1 ATTTT
4231427 AGGGTTTCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 23 0.68
8 11 0.32
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (7 bp):
ATTTTGG
Found at i:4231396 original size:15 final size:15
Alignment explanation
Indices: 4231363--4231419 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
4231353 GTGTACCAAA
*
4231363 TTTGAGATTTTTAGAAT
1 TTTG-GATTTTAAG-AT
4231380 TTTGGATTTTAAGAT
1 TTTGGATTTTAAGAT
* *
4231395 TTTGGATTTTAGGGT
1 TTTGGATTTTAAGAT
*
4231410 TTGGGATTTT
1 TTTGGATTTT
4231420 GGATTTTAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
15 24 0.67
16 8 0.22
17 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (15 bp):
TTTGGATTTTAAGAT
Found at i:4231417 original size:22 final size:21
Alignment explanation
Indices: 4231392--4231442 Score: 84
Period size: 22 Copynumber: 2.4 Consensus size: 21
4231382 TGGATTTTAA
*
4231392 GATTTTGGATTTTAGGGTTTGG
1 GATTTTGGATTTTAGGGTTT-C
4231414 GATTTTGGATTTTAGGGTTTC
1 GATTTTGGATTTTAGGGTTTC
4231435 GATTTTGG
1 GATTTTGG
4231443 GGTTTGAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.14, C:0.02, G:0.33, T:0.51
Consensus pattern (21 bp):
GATTTTGGATTTTAGGGTTTC
Found at i:4231588 original size:22 final size:22
Alignment explanation
Indices: 4231533--4231592 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
4231523 TTCAATTTTA
4231533 AGGTTTGGATGTTTAGAGTTTGG
1 AGGTTTGGAT-TTTAGAGTTTGG
*
4231556 AGGATTT-GATTTTAGGGTTTGG
1 AGG-TTTGGATTTTAGAGTTTGG
4231578 -GGTTTAGGATTTTAG
1 AGGTTT-GGATTTTAG
4231593 TTTTAAGGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 3 0.09
21 2 0.06
22 19 0.58
23 6 0.18
24 3 0.09
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (22 bp):
AGGTTTGGATTTTAGAGTTTGG
Found at i:4231613 original size:30 final size:30
Alignment explanation
Indices: 4231556--4231778 Score: 187
Period size: 30 Copynumber: 7.6 Consensus size: 30
4231546 TAGAGTTTGG
*
4231556 AGGATTTGA-TTTTAGGGTTT-G-GGGTTT
1 AGGATTTTAGTTTTAGGGTTTGGAGGGTTT
*
4231583 AGGATTTTAGTTTTAAGGTTTGGAGGGTTT
1 AGGATTTTAGTTTTAGGGTTTGGAGGGTTT
* ** *
4231613 AGGGTTTT-GATTTTAGGGTTTAAAGAGTTT
1 AGGATTTTAG-TTTTAGGGTTTGGAGGGTTT
* *
4231643 A-GAGTTTTAGTTTGAGGGTTTGGAGTGTTT
1 AGGA-TTTTAGTTTTAGGGTTTGGAGGGTTT
* * *
4231673 A-GAGTTTTGGTTTTAGGGTTTAGAGGGATTA
1 AGGA-TTTTAGTTTTAGGGTTTGGAGGG-TTT
4231704 AGG-TTTT-GATTTTAGGGTTTGGAGGGTTT
1 AGGATTTTAG-TTTTAGGGTTTGGAGGGTTT
* * * *
4231733 AGGGTTTTAGTTTTAGGATTTTGA--TTTT
1 AGGATTTTAGTTTTAGGGTTTGGAGGGTTT
*
4231761 AGGGTTTTAGTTTTAGGG
1 AGGATTTTAGTTTTAGGG
4231779 CTTCGATTTT
Statistics
Matches: 162, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
27 8 0.05
28 30 0.19
29 9 0.06
30 109 0.67
31 5 0.03
32 1 0.01
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (30 bp):
AGGATTTTAGTTTTAGGGTTTGGAGGGTTT
Found at i:4231663 original size:60 final size:59
Alignment explanation
Indices: 4231560--4231778 Score: 225
Period size: 60 Copynumber: 3.7 Consensus size: 59
4231550 GTTTGGAGGA
* *
4231560 TTTGATTTTAGGGTTT-GGGGTTTAG-GATTTTAGTTTTAAGGTTTGGAGGGTTTAGGGT
1 TTTGATTTTAGGGTTTAAGGGTTTAGAG-TTTTAGTTTTAGGGTTTGGAGGGTTTAGGGT
* * * *
4231618 TTTGATTTTAGGGTTTAAAGAGTTTAGAGTTTTAGTTTGAGGGTTTGGAGTGTTTAGAGT
1 TTTGATTTTAGGGTTT-AAGGGTTTAGAGTTTTAGTTTTAGGGTTTGGAGGGTTTAGGGT
* *
4231678 TTTGGTTTTAGGGTTTAGAGGGATTA-AGGTTTT-GATTTTAGGGTTTGGAGGGTTTAGGGT
1 TTTGATTTTAGGGTTTA-AGGGTTTAGA-GTTTTAG-TTTTAGGGTTTGGAGGGTTTAGGGT
* * ** *
4231738 TTT-AGTTTTAGGATTT-TGATTTTAGGGTTTTAGTTTTAGGG
1 TTTGA-TTTTAGGGTTTAAGGGTTTAGAGTTTTAGTTTTAGGG
4231779 CTTCGATTTT
Statistics
Matches: 133, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
58 33 0.25
59 4 0.03
60 95 0.71
61 1 0.01
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (59 bp):
TTTGATTTTAGGGTTTAAGGGTTTAGAGTTTTAGTTTTAGGGTTTGGAGGGTTTAGGGT
Found at i:4231699 original size:90 final size:89
Alignment explanation
Indices: 4231569--4231778 Score: 257
Period size: 90 Copynumber: 2.4 Consensus size: 89
4231559 ATTTGATTTT
* * * *
4231569 AGGGTTTGG-G-GTTTAGGATTTTAGTTTTAAGGTTTGGAGGGTTTAGGGTTTTGATTTTAGGGT
1 AGGGTTTGGAGTGTTTAGG-TTTTAGTTTTAGGGTTTAGAGGGATTAAGGTTTTGATTTTAGGGT
4231632 TTAAAGAGTTTAGAGTTTTAGTTTG
65 TTAAAGAGTTTAGAGTTTTAGTTTG
*
4231657 AGGGTTTGGAGTGTTTAGAGTTTTGGTTTTAGGGTTTAGAGGGATTAAGGTTTTGATTTTAGGGT
1 AGGGTTTGGAGTGTTTAG-GTTTTAGTTTTAGGGTTTAGAGGGATTAAGGTTTTGATTTTAGGGT
** * * *
4231722 TTGGAGGGTTTAGGGTTTTAGTTTT
65 TTAAAGAGTTTAGAGTTTTAGTTTG
* *
4231747 AGGATTTTGA-T-TTTAGGGTTTTAGTTTTAGGG
1 AGGGTTTGGAGTGTTTA-GGTTTTAGTTTTAGGG
4231779 CTTCGATTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
88 27 0.26
89 3 0.03
90 74 0.70
91 1 0.01
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (89 bp):
AGGGTTTGGAGTGTTTAGGTTTTAGTTTTAGGGTTTAGAGGGATTAAGGTTTTGATTTTAGGGTT
TAAAGAGTTTAGAGTTTTAGTTTG
Found at i:4231786 original size:28 final size:28
Alignment explanation
Indices: 4231730--4231788 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
4231720 GTTTGGAGGG
* *
4231730 TTTAGGGTTTTAGTTTTAGGATTTTGAT
1 TTTAGGGTTTTAGTTTTAGGACTTCGAT
*
4231758 TTTAGGGTTTTAGTTTTAGGGCTTCGAT
1 TTTAGGGTTTTAGTTTTAGGACTTCGAT
4231786 TTT
1 TTT
4231789 TAAAAACTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.15, C:0.03, G:0.25, T:0.56
Consensus pattern (28 bp):
TTTAGGGTTTTAGTTTTAGGACTTCGAT
Found at i:4231928 original size:6 final size:6
Alignment explanation
Indices: 4231920--4231981 Score: 79
Period size: 6 Copynumber: 10.0 Consensus size: 6
4231910 TGAAAATTTG
* * *
4231920 TTATTG TTACTA TTAATTTA TTATTA TTATTA TTATTA TTATTT TTATTA
1 TTATTA TTATTA TT-ATT-A TTATTA TTATTA TTATTA TTATTA TTATTA
4231970 TTATTA TTATTA
1 TTATTA TTATTA
4231982 ATGTCATAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
6 41 0.84
7 5 0.10
8 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (6 bp):
TTATTA
Found at i:4231945 original size:3 final size:3
Alignment explanation
Indices: 4231937--4231981 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
4231927 TACTATTAAT
*
4231937 TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4231982 ATGTCATAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4232542 original size:58 final size:58
Alignment explanation
Indices: 4232455--4232732 Score: 298
Period size: 58 Copynumber: 4.7 Consensus size: 58
4232445 TTGTACAGGA
* *
4232455 AAAATTGATACTTTCAACTTTT-CTCCAAAATATTTTTTTAG-AAACTTAAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAATATTTTTTTAGAAAACTT-ATTTTCAAGG
* ** * *
4232513 AAAATTGATACTTTGAACTTTTCCTCAAAA-ATCCACTTTT-GAAAACTTATTTTTAGGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAATAT--TTTTTTAGAAAACTTATTTTCAAGG
* *
4232571 AAAATTGATACTTTCAACTTTT-TTCCAAAA-ATATTTTTTAGAAAGCTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAATAT-TTTTTTAGAAAACTTATTTTCAAGG
* *
4232629 AAAATTAATACTTTCAACTTTTCTTCAAAAATATTTTTTTTTTTAGAAAAACTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTC-AAAATA----TTTTTTTAG-AAAACTTATTTTCAAGG
4232693 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTC-AAAATATTTTTTT
4232733 GAATTTTATT
Statistics
Matches: 187, Mismatches: 19, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
57 7 0.04
58 98 0.52
59 18 0.10
60 8 0.04
63 8 0.04
64 48 0.26
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTAGAAAACTTATTTTCAAGG
Found at i:4232630 original size:116 final size:121
Alignment explanation
Indices: 4232455--4232731 Score: 345
Period size: 116 Copynumber: 2.3 Consensus size: 121
4232445 TTGTACAGGA
* *
4232455 AAAATTGATACTTTCAACTTTTCTCC-AAAATATTTTTTTAGAAACTTAAATTTCGAGGAAAATT
1 AAAATTGATACTTTCAACTTTTTTCCAAAAATA-TTTTTTAGAAACTTAAATTTCAAGGAAAATT
* * * *
4232519 GATACTTTGAACTTTTCCTC-AAAA-A-TCCACTTTT-G-AAAACTTATTTTTAGGG
65 AATACTTTCAACTTTTCCTCAAAAATATTCCACTTTTAGAAAAACTTATTTTCAAGG
*
4232571 AAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTAGAAAGCTT-ATTTTCAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTAGAAA-CTTAAATTTCAAGGAAAATT
* ****
4232635 AATACTTTCAACTTTTCTTCAAAAATATTTTTTTTTTTAGAAAAACTTATTTTCAAGG
65 AATACTTTCAACTTTTCCTCAAAAATA-TTCCACTTTTAGAAAAACTTATTTTCAAGG
*
4232693 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTTTC-CAAAAATATTTTTT
4232732 TGAATTTTAT
Statistics
Matches: 139, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
116 67 0.48
117 13 0.09
118 1 0.01
120 5 0.04
121 6 0.04
122 47 0.34
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.43
Consensus pattern (121 bp):
AAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTAGAAACTTAAATTTCAAGGAAAATTA
ATACTTTCAACTTTTCCTCAAAAATATTCCACTTTTAGAAAAACTTATTTTCAAGG
Found at i:4232763 original size:6 final size:5
Alignment explanation
Indices: 4232748--4232821 Score: 94
Period size: 5 Copynumber: 13.6 Consensus size: 5
4232738 TTATTTAAAG
4232748 AAAAT AAAATT AAAAT AAAAAT AAAAT GAAAAT GAAAATT AAAAT AAAAT
1 AAAAT AAAA-T AAAAT -AAAAT AAAAT -AAAAT -AAAA-T AAAAT AAAAT
4232798 AAAAT AAAAT AAAAAT AAAAT AAA
1 AAAAT AAAAT -AAAAT AAAAT AAA
4232822 TGTATTAAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
5 34 0.53
6 29 0.45
7 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:4232764 original size:11 final size:10
Alignment explanation
Indices: 4232748--4232821 Score: 94
Period size: 11 Copynumber: 6.8 Consensus size: 10
4232738 TTATTTAAAG
4232748 AAAATAAAATT
1 AAAATAAAA-T
4232759 AAAATAAAAAT
1 AAAAT-AAAAT
4232770 AAAATGAAAAT
1 AAAAT-AAAAT
4232781 GAAAATTAAAAT
1 -AAAA-TAAAAT
4232793 AAAATAAAAT
1 AAAATAAAAT
4232803 AAAATAAAAAT
1 AAAAT-AAAAT
4232814 AAAATAAA
1 AAAATAAA
4232822 TGTATTAAAC
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
10 14 0.24
11 30 0.52
12 13 0.22
13 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:4232859 original size:3 final size:3
Alignment explanation
Indices: 4232851--4232890 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
4232841 CTAATCAATA
*
4232851 AAT AAT AAT AAT AAT AAT AAA AAT AAT GAAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AA
4232891 ATAAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:4232875 original size:15 final size:15
Alignment explanation
Indices: 4232851--4232908 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
4232841 CTAATCAATA
*
4232851 AATAATAATAATAAT
1 AATAAAAATAATAAT
4232866 AATAAAAATAATGAAT
1 AATAAAAATAAT-AAT
*
4232882 AAATAATAAATAAATAAA
1 -AATAA-AAAT-AATAAT
4232900 AATGAAAAA
1 AAT-AAAAA
4232909 AAAACTTGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 11 0.31
16 3 0.08
17 11 0.31
18 8 0.22
19 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAAAAATAATAAT
Found at i:4233786 original size:3 final size:3
Alignment explanation
Indices: 4233778--4233832 Score: 56
Period size: 3 Copynumber: 16.3 Consensus size: 3
4233768 TAAATAGATA
4233778 AAT AAT AAT AAT AGAT AAAT AAT AAT ATAT AAT AGAT ATAT AAT AAT
1 AAT AAT AAT AAT A-AT -AAT AAT AAT A-AT AAT A-AT A-AT AAT AAT
4233825 ATAT AAT A
1 A-AT AAT A
4233833 GATATATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
3 29 0.63
4 16 0.35
5 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:4233787 original size:14 final size:13
Alignment explanation
Indices: 4233779--4233841 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 13
4233769 AAATAGATAA
4233779 ATAATAATAATAG
1 ATAATAATAATAG
*
4233792 ATAAATAATAATAT
1 AT-AATAATAATAG
4233806 ATAATAGATATATA-
1 ATAATA-ATA-ATAG
4233820 ATAATATATAATAG
1 ATAATA-ATAATAG
4233834 ATATATAA
1 ATA-ATAA
4233842 ACAGATAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
13 9 0.21
14 28 0.65
15 6 0.14
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (13 bp):
ATAATAATAATAG
Found at i:4233795 original size:7 final size:6
Alignment explanation
Indices: 4233778--4233832 Score: 56
Period size: 7 Copynumber: 8.2 Consensus size: 6
4233768 TAAATAGATA
4233778 AATAAT AATAAT AGATAAAT AATAAT ATATAAT AGATATAT AATAAT ATATAAT
1 AATAAT AATAAT A-AT-AAT AATAAT A-ATAAT A-ATA-AT AATAAT A-ATAAT
4233832 A
1 A
4233833 GATATATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
6 14 0.33
7 22 0.51
8 7 0.16
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (6 bp):
AATAAT
Found at i:4233798 original size:11 final size:11
Alignment explanation
Indices: 4233784--4233898 Score: 69
Period size: 11 Copynumber: 10.5 Consensus size: 11
4233774 GATAAATAAT
4233784 AATAATAGATA
1 AATAATAGATA
4233795 AATAATA-ATA
1 AATAATAGATA
*
4233805 TATAATAGATA
1 AATAATAGATA
*
4233816 TATAATA-ATA
1 AATAATAGATA
*
4233826 TATAATAGATA
1 AATAATAGATA
* *
4233837 TATAAACAGATA
1 AAT-AATAGATA
* *
4233849 AAAAATATATA
1 AATAATAGATA
4233860 TTAATAAATAG-T-
1 --AAT-AATAGATA
*
4233872 TATAATAGATA
1 AATAATAGATA
*
4233883 AAAAAGTA-ATA
1 AATAA-TAGATA
4233894 AATAA
1 AATAA
4233899 ATAAATAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
9 5 0.06
10 22 0.27
11 39 0.47
12 10 0.12
13 3 0.04
14 4 0.05
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (11 bp):
AATAATAGATA
Found at i:4233799 original size:17 final size:17
Alignment explanation
Indices: 4233770--4233910 Score: 101
Period size: 17 Copynumber: 8.1 Consensus size: 17
4233760 ATATTATGTA
4233770 AATAGATAAATAATAAT
1 AATAGATAAATAATAAT
4233787 AATAGATAAATAATAAT
1 AATAGATAAATAATAAT
*
4233804 ATATA-ATAGATATATAAT
1 A-ATAGATAAATA-ATAAT
*
4233822 AATATAT-AATAGATATAT
1 AATAGATAAATA-ATA-AT
* *
4233840 AAACAGATAAAAAATATAT
1 -AATAGATAAATAATA-AT
* * *
4233859 ATTA-ATAAATAGTTAT
1 AATAGATAAATAATAAT
*
4233875 AATAGATAAAAAAGTAAT
1 AATAGATAAATAA-TAAT
*
4233893 AAATAAATAAATAA-AAT
1 -AATAGATAAATAATAAT
4233910 A
1 A
4233911 CAAAATACAA
Statistics
Matches: 98, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
16 6 0.06
17 49 0.50
18 18 0.18
19 22 0.22
20 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (17 bp):
AATAGATAAATAATAAT
Found at i:4233809 original size:21 final size:21
Alignment explanation
Indices: 4233733--4233841 Score: 113
Period size: 21 Copynumber: 5.4 Consensus size: 21
4233723 ATAAAATAAA
4233733 ATAAA-AA-AATATATTAATAG
1 ATAAATAATAATATA-TAATAG
* * *
4233753 ATAAATGATATTATGTAAATAG
1 ATAAATAATAATATAT-AATAG
4233775 AT--A-AATAATA-ATAATAG
1 ATAAATAATAATATATAATAG
4233792 ATAAATAATAATATATAATAG
1 ATAAATAATAATATATAATAG
*
4233813 ATATATAATAATATATAATAG
1 ATAAATAATAATATATAATAG
*
4233834 ATATATAA
1 ATAAATAA
4233842 ACAGATAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.09
18 1 0.01
19 6 0.08
20 13 0.17
21 37 0.49
22 11 0.15
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (21 bp):
ATAAATAATAATATATAATAG
Found at i:4233849 original size:19 final size:20
Alignment explanation
Indices: 4233785--4233860 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 20
4233775 ATAAATAATA
* * *
4233785 ATAATAGATAAATAATAATAT
1 ATAATAGATATAT-ATAACAG
* *
4233806 ATAATAGATATATAATAATAT
1 ATAATAGATATAT-ATAACAG
4233827 ATAATAGATATATA-AACAG
1 ATAATAGATATATATAACAG
* *
4233846 ATAAAAAATATATAT
1 ATAATAGATATATAT
4233861 TAATAAATAG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.31
20 1 0.02
21 33 0.67
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAATAGATATATATAACAG
Found at i:4233884 original size:42 final size:44
Alignment explanation
Indices: 4233775--4233898 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 44
4233765 ATGTAAATAG
*
4233775 ATAAATAATAATAATAGATAAATAATAATATATAATAGATATATA
1 ATAAAT-ATAATAATAGATAAACAATAATATATAATAGATATATA
* *
4233820 ATAATATATAATAGATATATAAACAGATAA-A-A-AATATATAT-TA
1 ATAA-ATATAATA-ATAGATAAACA-ATAATATATAATAGATATATA
* * *
4233863 ATAAATAGTTATAATAGATAAAAAAGTAATAAATAA
1 ATAAATA-TAATAATAGATAAACAA-TAATATATAA
4233899 ATAAATAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
41 1 0.02
42 15 0.23
43 11 0.17
44 9 0.14
45 13 0.20
46 12 0.18
47 4 0.06
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (44 bp):
ATAAATATAATAATAGATAAACAATAATATATAATAGATATATA
Found at i:4233886 original size:33 final size:31
Alignment explanation
Indices: 4233775--4233841 Score: 64
Period size: 32 Copynumber: 2.0 Consensus size: 31
4233765 ATGTAAATAG
4233775 ATAAATAATAATAATAGATAAATAATAATATATA
1 ATAAAT-AT-ATAATAGATAAA-AATAATATATA
* *
4233809 ATAGATATATAATA-ATATATAATAGATATATA
1 ATAAATATATAATAGATA-AAAATA-ATATATA
4233841 A
1 A
4233842 ACAGATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
31 7 0.24
32 15 0.52
33 2 0.07
34 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.34
Consensus pattern (31 bp):
ATAAATATATAATAGATAAAAATAATATATA
Found at i:4234239 original size:43 final size:43
Alignment explanation
Indices: 4234138--4234570 Score: 431
Period size: 43 Copynumber: 10.0 Consensus size: 43
4234128 AAATTTTGAT
* * *
4234138 CAAAACTCCTCTAAGCAAAGGCTCAACGAC-TTTGAAAAATATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTTG--AAA-ATAAA
* *
4234183 TAAAGCTCCTCTAATCAGAGGCTCAACGACTTTTGGAAATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAATAAA
* *
4234226 CAAAGCTCCTCTAATTAGAGGCTTAACGACTTTT-AAAA-AATA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAATAA-A
* *
4234268 -AAAGGCTCCTCTAATAAGAGGCTCAACAACTTTTGAAAGATAAA
1 CAAA-GCTCCTCTAATCAGAGGCTCAACGACTTTTGAAA-ATAAA
*
4234312 CAAAGCTCCTCTAATCAGAGGCTCTACGAC-TTTGAAAAT-AA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAATAAA
* * *
4234353 -ATAGCTCTTCTAATCAGAGGCTCAACAACTTTTGAAAGATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAA-ATAAA
* * * *
4234396 CAAAGCTCCTCTAATTAGAGGCTTAATGATCTTTTTTAAAA-AATA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGA-C-TTTTGAAAATAA-A
* *
4234441 -AAAGGCTCCTTTAATCAGAGGCTCAACAACTTTTGAAAGATAAA
1 CAAA-GCTCCTCTAATCAGAGGCTCAACGACTTTTGAAA-ATAAA
* **
4234485 CAAAGCTCCTCTAAACAGAGG--CATTGTAAC-TTTGAAAAATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACG--ACTTTTG-AAAATAAA
* *
4234528 CAAAGCTCCTCTAATCAGAGGCTCAACAACTTTTAAAAATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAATAAA
4234571 TTGCTCCTTG
Statistics
Matches: 322, Mismatches: 42, Indels: 50
0.78 0.10 0.12
Matches are distributed among these distances:
40 25 0.08
41 14 0.04
42 37 0.11
43 94 0.29
44 80 0.25
45 61 0.19
46 11 0.03
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (43 bp):
CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAATAAA
Found at i:4234388 original size:84 final size:85
Alignment explanation
Indices: 4234138--4234570 Score: 511
Period size: 84 Copynumber: 5.0 Consensus size: 85
4234128 AAATTTTGAT
* * * * *
4234138 CAAAACTCCTCTAAGCAAAGGCTCAACGACTTTGAAAAATATAAATAAAGCTCCTCTAATCAGAG
1 CAAAGCTCCTCTAATCAGAGGCTTAACGACTTTTAAAAA-AT--A-AAAGCTCCTCTAATCAGAG
* *
4234203 GCTCAACGACTTTTGGAA-ATAAA
62 GCTCAACAACTTTTGAAAGATAAA
* *
4234226 CAAAGCTCCTCTAATTAGAGGCTTAACGACTTTTAAAAAATAAAAGGCTCCTCTAATAAGAGGCT
1 CAAAGCTCCTCTAATCAGAGGCTTAACGACTTTTAAAAAATAAAA-GCTCCTCTAATCAGAGGCT
4234291 CAACAACTTTTGAAAGATAAA
65 CAACAACTTTTGAAAGATAAA
* *
4234312 CAAAGCTCCTCTAATCAGAGGCTCT-ACGAC-TTT-GAAAATAAATAGCTCTTCTAATCAGAGGC
1 CAAAGCTCCTCTAATCAGAGGCT-TAACGACTTTTAAAAAATAAA-AGCTCCTCTAATCAGAGGC
4234374 TCAACAACTTTTGAAAGATAAA
64 TCAACAACTTTTGAAAGATAAA
* * *
4234396 CAAAGCTCCTCTAATTAGAGGCTTAATGATCTTTTTTAAAAAATAAAAGGCTCCTTTAATCAGAG
1 CAAAGCTCCTCTAATCAGAGGCTTAACGA-C--TTTTAAAAAATAAAA-GCTCCTCTAATCAGAG
4234461 GCTCAACAACTTTTGAAAGATAAA
62 GCTCAACAACTTTTGAAAGATAAA
* * * *
4234485 CAAAGCTCCTCTAAACAGAGGCATTGTA--ACTTTGAAAAATAAACAAAGCTCCTCTAATCAGAG
1 CAAAGCTCCTCTAATCAGAGGC-TT-AACGACTTTTAAAAA-ATA-AAAGCTCCTCTAATCAGAG
*
4234548 GCTCAACAACTTTT-AAAAATAAA
62 GCTCAACAACTTTTGAAAGATAAA
4234571 TTGCTCCTTG
Statistics
Matches: 305, Mismatches: 25, Indels: 32
0.84 0.07 0.09
Matches are distributed among these distances:
83 1 0.00
84 74 0.24
85 37 0.12
86 48 0.16
87 34 0.11
88 41 0.13
89 67 0.22
90 2 0.01
91 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (85 bp):
CAAAGCTCCTCTAATCAGAGGCTTAACGACTTTTAAAAAATAAAAGCTCCTCTAATCAGAGGCTC
AACAACTTTTGAAAGATAAA
Found at i:4234465 original size:173 final size:170
Alignment explanation
Indices: 4234138--4234570 Score: 611
Period size: 173 Copynumber: 2.5 Consensus size: 170
4234128 AAATTTTGAT
* * * *
4234138 CAAAACTCCTCTAAGCAAAGGCTCAACGACTTTGAAAAATATAAATAAAGCTCCTCTAATCAGAG
1 CAAAGCTCCTCTAAACAGAGGCTCTACGACTTTG-AAAA-ATAAAT--AGCTCCTCTAATCAGAG
* *
4234203 GCTCAACGACTTTTGGAAATAAACAAAGCTCCTCTAATTAGAGGCTTAACGACTTTTAAAAAATA
62 GCTCAACAACTTTTGAAAATAAACAAAGCTCCTCTAATTAGAGGCTTAACGACTTTTAAAAAATA
4234268 AAAGGCTCCTCTAATAAGAGGCTCAACAACTTTTGAAAGATAAA
127 AAAGGCTCCTCTAATAAGAGGCTCAACAACTTTTGAAAGATAAA
* *
4234312 CAAAGCTCCTCTAATCAGAGGCTCTACGACTTTG-AAAATAAATAGCTCTTCTAATCAGAGGCTC
1 CAAAGCTCCTCTAAACAGAGGCTCTACGACTTTGAAAAATAAATAGCTCCTCTAATCAGAGGCTC
*
4234376 AACAACTTTTGAAAGATAAACAAAGCTCCTCTAATTAGAGGCTTAATGATCTTTTTTAAAAAATA
66 AACAACTTTTGAAA-ATAAACAAAGCTCCTCTAATTAGAGGCTTAACGA-C--TTTTAAAAAATA
* *
4234441 AAAGGCTCCTTTAATCAGAGGCTCAACAACTTTTGAAAGATAAA
127 AAAGGCTCCTCTAATAAGAGGCTCAACAACTTTTGAAAGATAAA
* *
4234485 CAAAGCTCCTCTAAACAGAGGCATTGTA--ACTTTGAAAAATAAACAAAGCTCCTCTAATCAGAG
1 CAAAGCTCCTCTAAACAGAGGC--TCTACGACTTTGAAAAAT-AA-ATAGCTCCTCTAATCAGAG
*
4234548 GCTCAACAACTTTTAAAAATAAA
62 GCTCAACAACTTTTGAAAATAAA
4234571 TTGCTCCTTG
Statistics
Matches: 235, Mismatches: 15, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
169 32 0.14
170 33 0.14
171 7 0.03
172 3 0.01
173 81 0.34
174 35 0.15
175 10 0.04
176 34 0.14
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (170 bp):
CAAAGCTCCTCTAAACAGAGGCTCTACGACTTTGAAAAATAAATAGCTCCTCTAATCAGAGGCTC
AACAACTTTTGAAAATAAACAAAGCTCCTCTAATTAGAGGCTTAACGACTTTTAAAAAATAAAAG
GCTCCTCTAATAAGAGGCTCAACAACTTTTGAAAGATAAA
Found at i:4235585 original size:10 final size:9
Alignment explanation
Indices: 4235566--4235607 Score: 66
Period size: 9 Copynumber: 4.6 Consensus size: 9
4235556 ACCTTTTTTA
4235566 TTTTTCTTT
1 TTTTTCTTT
4235575 TTTTTCATTT
1 TTTTTC-TTT
*
4235585 TTTTTCATT
1 TTTTTCTTT
4235594 TTTTTCTTT
1 TTTTTCTTT
4235603 TTTTT
1 TTTTT
4235608 AAGCATAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 21 0.70
10 9 0.30
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:4235588 original size:19 final size:18
Alignment explanation
Indices: 4235566--4235607 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
4235556 ACCTTTTTTA
*
4235566 TTTTTCTTTTTTTTCATTT
1 TTTTTCATTTTTTTC-TTT
4235585 TTTTTCATTTTTTTCTTT
1 TTTTTCATTTTTTTCTTT
4235603 TTTTT
1 TTTTT
4235608 AAGCATAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTCATTTTTTTCTTT
Found at i:4246104 original size:133 final size:133
Alignment explanation
Indices: 4245884--4246149 Score: 505
Period size: 133 Copynumber: 2.0 Consensus size: 133
4245874 GTTTCACTTG
*
4245884 CAGATGCTCCATCGTCAGATTATTTACATCCAAGAAAATAAAAAGGGAAAAAAATGATTGCTTTT
1 CAGATGCTCCATCGTCAGATTATTTACATCCAAAAAAATAAAAAGGGAAAAAAATGATTGCTTTT
*
4245949 GTACAGGAAAAATTGATACTTTCAATTTTTCCTCAAAAATCTATTTTTGGAAACTTATTTTTAAA
66 GTACAGGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTATTTTTGGAAACTTATTTTTAAA
4246014 GAA
131 GAA
4246017 CAGATGCTCCATCGTCAGATTATTTACATCCAAAAAAATAAAAAGGGAAAAAAATGATTGCTTTT
1 CAGATGCTCCATCGTCAGATTATTTACATCCAAAAAAATAAAAAGGGAAAAAAATGATTGCTTTT
*
4246082 GTACAGGGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTATTTTTGGAAACTTATTTTTAAA
66 GTACAGGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTATTTTTGGAAACTTATTTTTAAA
4246147 GAA
131 GAA
4246150 AATTGATACT
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 130 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (133 bp):
CAGATGCTCCATCGTCAGATTATTTACATCCAAAAAAATAAAAAGGGAAAAAAATGATTGCTTTT
GTACAGGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTATTTTTGGAAACTTATTTTTAAA
GAA
Found at i:4246159 original size:58 final size:57
Alignment explanation
Indices: 4246089--4246385 Score: 352
Period size: 58 Copynumber: 5.1 Consensus size: 57
4246079 TTTGTACAGG
* *
4246089 GAAAATTGATACTTTCAACTTTTCCTCAAAAATCTATTTTTGGAAACTTATTTTTAAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTAGAAACTTATTTTTAAA
* *
4246147 GAAAATTGATACTTTCAACTTTTTCCT-AAAAATATTTTTTAGAAAGCTTATTTTCAAG
1 GAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTAGAAA-CTTATTTTTAAA
*
4246205 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAGCTTA-TTTTCAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAA-CTTATTTTTAAA
* * * *
4246262 GAAAAATTGATACTTCCAACTTTTCCTCAAAAATATTTTTTTTGAAAAATACTTATTTTCAAG
1 G-AAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTT--AGAA-ACTTATTTTTAAA
* * *
4246325 GAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTTG-AA-TT-TTATTTAAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAACTTATT-TTTAAA
4246380 GAAAAT
1 GAAAAT
4246386 AAAATAAAAT
Statistics
Matches: 209, Mismatches: 19, Indels: 25
0.83 0.08 0.10
Matches are distributed among these distances:
54 2 0.01
55 12 0.06
56 1 0.00
57 22 0.11
58 110 0.53
59 7 0.03
60 12 0.06
62 37 0.18
63 6 0.03
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.43
Consensus pattern (57 bp):
GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAACTTATTTTTAAA
Found at i:4246294 original size:116 final size:118
Alignment explanation
Indices: 4246088--4246385 Score: 403
Period size: 116 Copynumber: 2.5 Consensus size: 118
4246078 TTTTGTACAG
* * *
4246088 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTATTTTTGGAAACTTATTTTTAAAGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTAGAAACTTATTTTCAAAGAAAAT
* * *
4246153 TGATACTTTCAACTTTTTCCTAAAAATA-TTTTTT-AGAAA-GCTTATTTTCAA
65 TGATACTTCCAACTTTTTCCTAAAAATATTTTTTTGAAAAATACTTATTTTCAA
4246204 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAGCTTATTTTC-AAGAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAA-CTTATTTTCAAAG-AAAA
4246268 TTGATACTTCCAAC-TTTTCCTCAAAAATATTTTTTTTGAAAAATACTTATTTTCAA
64 TTGATACTTCCAACTTTTTCCT-AAAAATA-TTTTTTTGAAAAATACTTATTTTCAA
* * * **
4246324 GGAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTTGAATTTTA-TTT-AAAGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAACTTATTTTCAAAGAAAAT
4246386 AAAATAAAAT
Statistics
Matches: 163, Mismatches: 11, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
115 19 0.12
116 67 0.41
117 5 0.03
118 12 0.07
119 7 0.04
120 53 0.33
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.43
Consensus pattern (118 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAACTTATTTTCAAAGAAAATT
GATACTTCCAACTTTTTCCTAAAAATATTTTTTTGAAAAATACTTATTTTCAA
Found at i:4246389 original size:5 final size:5
Alignment explanation
Indices: 4246381--4246427 Score: 60
Period size: 5 Copynumber: 9.0 Consensus size: 5
4246371 TTATTTAAAG
4246381 AAAAT AAAAT AAAAT GAAAAT AAAAAT AAAGA- AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT -AAAAT -AAAAT AAA-AT AAAAT AAAAT AAAAT
4246428 GTATTAAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
4 1 0.03
5 26 0.68
6 11 0.29
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:4246401 original size:16 final size:16
Alignment explanation
Indices: 4246380--4246428 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
4246370 TTTATTTAAA
4246380 GAAAATAAAATAAAAT
1 GAAAATAAAATAAAAT
4246396 GAAAATAAAA-ATAAA-
1 GAAAATAAAATA-AAAT
4246411 GAAAAATAAAATAAAAT
1 G-AAAATAAAATAAAAT
4246428 G
1 G
4246429 TATTAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.07
16 25 0.86
17 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (16 bp):
GAAAATAAAATAAAAT
Found at i:4246464 original size:3 final size:3
Alignment explanation
Indices: 4246456--4246489 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4246446 CTAATCAATA
4246456 AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4246490 ATAAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:4246495 original size:17 final size:17
Alignment explanation
Indices: 4246447--4246502 Score: 71
Period size: 17 Copynumber: 3.2 Consensus size: 17
4246437 AATTCTAATC
4246447 TAATCAATAAAT-AATAA
1 TAAT-AATAAATAAATAA
4246464 TAATAAT-AATAAAATAA
1 TAATAATAAAT-AAATAA
4246481 TAATAATAAATAAATAAA
1 TAATAATAAATAAAT-AA
4246499 TAAT
1 TAAT
4246503 GAAAAAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.09
16 3 0.09
17 20 0.57
18 9 0.26
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
TAATAATAAATAAATAA
Found at i:4246496 original size:14 final size:13
Alignment explanation
Indices: 4246447--4246502 Score: 64
Period size: 11 Copynumber: 4.3 Consensus size: 13
4246437 AATTCTAATC
4246447 TAATCAATAAATAA
1 TAAT-AATAAATAA
4246461 TAATAAT-AATAA
1 TAATAATAAATAA
4246473 TAA-AAT-AATAA
1 TAATAATAAATAA
4246484 TAATAAATAAATAAA
1 TAAT-AATAAAT-AA
4246499 TAAT
1 TAAT
4246503 GAAAAAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 11 0.29
12 8 0.21
13 6 0.16
14 7 0.18
15 6 0.16
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:4246801 original size:15 final size:15
Alignment explanation
Indices: 4246777--4246817 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
4246767 ACCTCTCCTC
4246777 CCCTCTCTTTCTCT-T
1 CCCT-TCTTTCTCTCT
4246792 CCCTTCCTTT-TCTCT
1 CCCTT-CTTTCTCTCT
4246807 CCCTTCTTTCT
1 CCCTTCTTTCT
4246818 AAACCAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (15 bp):
CCCTTCTTTCTCTCT
Found at i:4246903 original size:19 final size:18
Alignment explanation
Indices: 4246862--4246906 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
4246852 ATTTTGGAAA
*
4246862 TTTCATTGTAATCTGGGT
1 TTTCATCGTAATCTGGGT
4246880 TTTCATCGTAATCTGGGTT
1 TTTCATCGTAATCTGGG-T
4246899 TTTCATCG
1 TTTCATCG
4246907 AAAGTTTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.49
Consensus pattern (18 bp):
TTTCATCGTAATCTGGGT
Found at i:4247422 original size:46 final size:45
Alignment explanation
Indices: 4247372--4247514 Score: 116
Period size: 46 Copynumber: 3.1 Consensus size: 45
4247362 TAGATAAATG
4247372 ATAATATGTAAATAGATAAATAATAACAAACAAATAATAATATATA
1 ATAATATGTAAATAGATAAATAATAACAAA-AAATAATAATATATA
* * *
4247418 ATAATATAT-AATAGATATAT-A-AACAGATAAAAAAAT-ATATATTA
1 ATAATATGTAAATAGATAAATAATAACA-A-AAAATAATAATATA-TA
* *
4247462 ATAATA-GTAATAATAGATAAATAAGTAATAAATAAAATACATAATACATA
1 ATAATATGT-A-AATAGATAAATAA-TAA-CAA-AAAATA-ATAATATATA
4247512 ATA
1 ATA
4247515 CATAATACAA
Statistics
Matches: 77, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
43 10 0.13
44 16 0.21
45 11 0.14
46 18 0.23
47 1 0.01
49 9 0.12
50 8 0.10
51 4 0.05
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.29
Consensus pattern (45 bp):
ATAATATGTAAATAGATAAATAATAACAAAAAATAATAATATATA
Found at i:4247507 original size:7 final size:7
Alignment explanation
Indices: 4247497--4247523 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4247487 TAATAAATAA
4247497 AATACAT
1 AATACAT
4247504 AATACAT
1 AATACAT
4247511 AATACAT
1 AATACAT
4247518 AATACA
1 AATACA
4247524 AGATACAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (7 bp):
AATACAT
Found at i:4247523 original size:21 final size:21
Alignment explanation
Indices: 4247488--4247540 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
4247478 ATAAATAAGT
*
4247488 AATAAATAAAATACATA-ATACAT
1 AATAAAT--AATACA-AGATACAG
*
4247511 AATACATAATACAAGATACAG
1 AATAAATAATACAAGATACAG
4247532 AATAAATAA
1 AATAAATAA
4247541 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 19 0.73
23 6 0.23
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.23
Consensus pattern (21 bp):
AATAAATAATACAAGATACAG
Found at i:4248313 original size:19 final size:20
Alignment explanation
Indices: 4248279--4248316 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4248269 CCTTTGTCTC
*
4248279 TCTTTTTTTCTCCTTTTTTT
1 TCTTCTTTTCTCCTTTTTTT
4248299 TCTTCTTTT-TCCTTTTTT
1 TCTTCTTTTCTCCTTTTTT
4248317 ATTATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTCTTTTCTCCTTTTTTT
Found at i:4248338 original size:16 final size:18
Alignment explanation
Indices: 4248312--4248358 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
4248302 TCTTTTTCCT
*
4248312 TTTTTATTATTAATAT-A
1 TTTTAATTATTAATATAA
4248329 -TTTAATTATTAAT-TAA
1 TTTTAATTATTAATATAA
4248345 TTTTAA-TATTAATA
1 TTTTAATTATTAATA
4248359 AACAGAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.04
16 20 0.77
17 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAATTATTAATATAA
Found at i:4249658 original size:20 final size:20
Alignment explanation
Indices: 4249619--4249658 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4249609 TGATATTGTT
*
4249619 TTTAAAATGTATTAAGAAAA
1 TTTAAAATGTATTAAAAAAA
*
4249639 TTTAAAATGTCTTAAAAAAA
1 TTTAAAATGTATTAAAAAAA
4249659 GATATTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (20 bp):
TTTAAAATGTATTAAAAAAA
Found at i:4250363 original size:158 final size:158
Alignment explanation
Indices: 4250123--4250441 Score: 521
Period size: 158 Copynumber: 2.0 Consensus size: 158
4250113 TTAATTATTC
* *
4250123 CATATAATTACATTCAAAAAGTAACATCTAGTAAATTTGATGTTCGAAACTCAAACCCTGTGACT
1 CATATAATTACATTCAAAAAGTAACATCTAGTAAATTTGATGTTCGAAACTCAAACCCTATAACT
* * *
4250188 CTTTTTCTTACTTCTAGACTACGGCTTTCAATATAAAATATGTATATATTGAAACAATGGCAAAA
66 CTTTTTCTTACTCCTAGACTACGGCTTTCAATATAAAATATGTATACATTGAAAAAATGGCAAAA
4250253 GTCAATCTGATATTGGAAAACTTTTTTT
131 GTCAATCTGATATTGGAAAACTTTTTTT
* * **
4250281 CATATAATTACATTCAAAAAGTAACATCTAGTAAATTTGATGTTTGAAACTTAATTCCTATAACT
1 CATATAATTACATTCAAAAAGTAACATCTAGTAAATTTGATGTTCGAAACTCAAACCCTATAACT
4250346 CTTTTTCTTACTCCTAGACTACGGCTTTCAATATAAAATATGTATACATTGAAAAAATGGCAAAA
66 CTTTTTCTTACTCCTAGACTACGGCTTTCAATATAAAATATGTATACATTGAAAAAATGGCAAAA
*** *
4250411 GTTGGTCTGATATTGGAGAACTTTTTTT
131 GTCAATCTGATATTGGAAAACTTTTTTT
4250439 CAT
1 CAT
4250442 GCCTTTTTCT
Statistics
Matches: 148, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
158 148 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (158 bp):
CATATAATTACATTCAAAAAGTAACATCTAGTAAATTTGATGTTCGAAACTCAAACCCTATAACT
CTTTTTCTTACTCCTAGACTACGGCTTTCAATATAAAATATGTATACATTGAAAAAATGGCAAAA
GTCAATCTGATATTGGAAAACTTTTTTT
Found at i:4250782 original size:431 final size:431
Alignment explanation
Indices: 4249965--4251098 Score: 1835
Period size: 431 Copynumber: 2.6 Consensus size: 431
4249955 TTGGAATATC
* *
4249965 GAAAAAATGGCAAAAGTCGGTCTGAGATTGGAAAACTTTTTTTCATGCCTTTTTCTTTGATGTTC
1 GAAAAAATGGCAAAAGTTGGTCTGATATTGGAAAACTTTTTTTCATGCCTTTTTCTTTGATGTTC
4250030 GAAATAAATTAATTAAAGAGTTAAAAGCAAAATCATACTAATTATATACTCAAATTATTTTATAT
66 GAAATAAATTAATTAAAGAGTTAAAAGCAAAATCATACTAATTATATACTCAAATTATTTTATAT
*
4250095 TGAAATTCAAATTTTGACTTAATTATTCCATATAATTACATTCAAAAAGTAACATCTAGTAAATT
131 TGAAATTCAAATTTTAACTTAATTATTCCATATAATTACATTCAAAAAGTAACATCTAGTAAATT
* * *
4250160 TGATGTTCGAAACTCAAACCCTGTGACTCTTTTTCTTACTTCTAGACTACGGCTTTCAATATAAA
196 TGATGTTTGAAACTCAAACCCTGTGACTCTTTTTCTTACTTCCAAACTACGGCTTTCAATATAAA
*
4250225 ATATGTATATATTGAAACAATGGCAAAAGTCAATCTGATATTGGAAAACTTTTTTTCATATAATT
261 ATATGTATATATTGAAACAATGGCAAAAGTCAATATGATATTGGAAAACTTTTTTTCATATAATT
* *
4250290 ACATTCAAAAAGTAACATCTAGTAAATTTGATGTTTGAAACTTAATTCCTATAACTCTTTTTCTT
326 ACATTCAAAAAGTAACATCTAGTAAATTTGATGTTTGAAAATTAATTACTATAACTCTTTTTCTT
4250355 ACTC-CTAGACTACGGCTTTCAATATAAAATATGTATACATT
391 ACTCTC-AGACTACGGCTTTCAATATAAAATATGTATACATT
*
4250396 GAAAAAATGGCAAAAGTTGGTCTGATATTGGAGAACTTTTTTTCATGCCTTTTTCTTTGATGTTC
1 GAAAAAATGGCAAAAGTTGGTCTGATATTGGAAAACTTTTTTTCATGCCTTTTTCTTTGATGTTC
4250461 GAAATAAATTAATTAAAGAGTTAAAAGCAAAATCATACTAATTATATACTCAAATTATTTTATAT
66 GAAATAAATTAATTAAAGAGTTAAAAGCAAAATCATACTAATTATATACTCAAATTATTTTATAT
* * *
4250526 TGAAATTCTAATTTTTACTTAATTATTCCATATAATTACATTCAAAAAGTAATATCTAGTAAATT
131 TGAAATTCAAATTTTAACTTAATTATTCCATATAATTACATTCAAAAAGTAACATCTAGTAAATT
* *
4250591 TGATGTTTGAAACTCAAACCCTGTGACTCTTTTTCTTACTTCCAAACTATGACTTTCAATATAAA
196 TGATGTTTGAAACTCAAACCCTGTGACTCTTTTTCTTACTTCCAAACTACGGCTTTCAATATAAA
* *
4250656 ATGTGTATATATTGAAACAATGGCAAAAGTTAATATGATATTGGAAAACTTTTTTTCATATAATT
261 ATATGTATATATTGAAACAATGGCAAAAGTCAATATGATATTGGAAAACTTTTTTTCATATAATT
*
4250721 ACATTCAAAAAGTAACATCTAGTAAATTTGATGTTT-AAAATTCAA-TACT-TGAATTTCTTTTT
326 ACATTCAAAAAGTAACATCTAGTAAATTTGATGTTTGAAAATT-AATTACTAT-AA-CTCTTTTT
* *
4250783 CTTACTCTCAGACTACGGCTTTCAATATAAAATATGTGTATATT
388 CTTACTCTCAGACTACGGCTTTCAATATAAAATATGTATACATT
* *
4250827 GAAAAATTGGCAAAAGTTGGTCTGATATTGGAAAACTTTTTTTCATGCCTTTTTCTTTGATGTTA
1 GAAAAAATGGCAAAAGTTGGTCTGATATTGGAAAACTTTTTTTCATGCCTTTTTCTTTGATGTTC
*
4250892 GAAATAAATTAATTAAAGAGTTAAAAGCAAAAGCATACTAATTATATACTCAAATTATTTTATAT
66 GAAATAAATTAATTAAAGAGTTAAAAGCAAAATCATACTAATTATATACTCAAATTATTTTATAT
* * * * * * * * * *
4250957 TGAAATTAAAAATTTAACTTAATTGTTTCTTATAATTATATTAAAAAAATAACATATAATAAATT
131 TGAAATTCAAATTTTAACTTAATTATTCCATATAATTACATTCAAAAAGTAACATCTAGTAAATT
* *** * * * *
4251022 TGATGTTTGAAACTCAATCCGAATAATTCTTTTTCTTATTTCCTAACTACGGCTTTCAATATAAA
196 TGATGTTTGAAACTCAAACCCTGTGACTCTTTTTCTTACTTCCAAACTACGGCTTTCAATATAAA
4251087 ATATGTATATAT
261 ATATGTATATAT
4251099 ATATATATAT
Statistics
Matches: 652, Mismatches: 47, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
429 1 0.00
430 10 0.02
431 640 0.98
432 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.39
Consensus pattern (431 bp):
GAAAAAATGGCAAAAGTTGGTCTGATATTGGAAAACTTTTTTTCATGCCTTTTTCTTTGATGTTC
GAAATAAATTAATTAAAGAGTTAAAAGCAAAATCATACTAATTATATACTCAAATTATTTTATAT
TGAAATTCAAATTTTAACTTAATTATTCCATATAATTACATTCAAAAAGTAACATCTAGTAAATT
TGATGTTTGAAACTCAAACCCTGTGACTCTTTTTCTTACTTCCAAACTACGGCTTTCAATATAAA
ATATGTATATATTGAAACAATGGCAAAAGTCAATATGATATTGGAAAACTTTTTTTCATATAATT
ACATTCAAAAAGTAACATCTAGTAAATTTGATGTTTGAAAATTAATTACTATAACTCTTTTTCTT
ACTCTCAGACTACGGCTTTCAATATAAAATATGTATACATT
Found at i:4250805 original size:158 final size:157
Alignment explanation
Indices: 4250554--4250872 Score: 448
Period size: 158 Copynumber: 2.0 Consensus size: 157
4250544 TTAATTATTC
* *
4250554 CATATAATTACATTCAAAAAGTAATATCTAGTAAATTTGATGTTTGAAACTCAAACCCTGTGACT
1 CATATAATTACATTCAAAAAGTAACATCTAGTAAATTTGATGTTTAAAACTCAAA-CCTGTGACT
* *
4250619 CTTTTTCTTACTTCCAAACTATGACTTTCAATATAAAATGTGTATATATTGAAACAA-TGGCAAA
65 CTTTTTCTTACTTCCAAACTACGACTTTCAATATAAAATATGTATATATTGAAA-AATTGGCAAA
4250683 AGTTAATATGATATTGGAAAACTTTTTTT
129 AGTTAATATGATATTGGAAAACTTTTTTT
*
4250712 CATATAATTACATTCAAAAAGTAACATCTAGTAAATTTGATGTTTAAAATTCAATA-CT-TGAAT
1 CATATAATTACATTCAAAAAGTAACATCTAGTAAATTTGATGTTTAAAACTCAA-ACCTGTG-A-
* * * *
4250775 TTCTTTTTCTTAC-TCTCAGACTACGGCTTTCAATATAAAATATGTGTATATTGAAAAATTGGCA
63 CTCTTTTTCTTACTTC-CAAACTACGACTTTCAATATAAAATATGTATATATTGAAAAATTGGCA
** *
4250839 AAAGTTGGTCTGATATTGGAAAACTTTTTTT
127 AAAGTTAATATGATATTGGAAAACTTTTTTT
4250870 CAT
1 CAT
4250873 GCCTTTTTCT
Statistics
Matches: 144, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
156 2 0.01
157 7 0.05
158 134 0.93
159 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (157 bp):
CATATAATTACATTCAAAAAGTAACATCTAGTAAATTTGATGTTTAAAACTCAAACCTGTGACTC
TTTTTCTTACTTCCAAACTACGACTTTCAATATAAAATATGTATATATTGAAAAATTGGCAAAAG
TTAATATGATATTGGAAAACTTTTTTT
Found at i:4251099 original size:2 final size:2
Alignment explanation
Indices: 4251087--4251142 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
4251077 TCAATATAAA
* * *
4251087 AT AT GT AT AT AT AT AT AT AT AT -T AT AC AT GAT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
*
4251129 AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
4251143 TTTTATGCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4251784 original size:2 final size:2
Alignment explanation
Indices: 4251779--4251803 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4251769 AATTTTAAAG
4251779 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4251804 TAGTCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4262218 original size:3 final size:3
Alignment explanation
Indices: 4262210--4262248 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4262200 AGAATTCATG
4262210 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4262249 AATCATATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4262684 original size:128 final size:128
Alignment explanation
Indices: 4262453--4262710 Score: 473
Period size: 128 Copynumber: 2.0 Consensus size: 128
4262443 TCCAAATTTT
4262453 CACTTAAAAAATTGATTTTTTTCAATAAAATTATGTTGTTATAGTAATTGGTACATGAATATTGC
1 CACTTAAAAAATTGATTTTTTTCAATAAAATTA--TTGTTATAGTAATTGGTACATGAATATTGC
4262518 TTTAATCATTTATATATGTGTGCAATATCCACAAATATTTGTAATTCAATACCTTAGTATTAAAT
64 TTTAATCATTTATATATGTGTGCAATATCCACAAATATTTGTAATTCAATA-CTTAGTATTAAAT
4262583 G
128 G
*
4262584 CACTTAAAAAATTGATTTTTTTCAATACAATTA-TGTTATAGTAATTGGTACATGAATATTGCTT
1 CACTTAAAAAATTGATTTTTTTCAATAAAATTATTGTTATAGTAATTGGTACATGAATATTGCTT
4262648 TAATCATTTATATATGTGTGCAATATCCACAAATATTTGTAATTCAATACTTAGTATTAAATG
66 TAATCATTTATATATGTGTGCAATATCCACAAATATTTGTAATTCAATACTTAGTATTAAATG
4262711 GCAATAAATA
Statistics
Matches: 126, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
127 14 0.11
128 80 0.63
131 32 0.25
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (128 bp):
CACTTAAAAAATTGATTTTTTTCAATAAAATTATTGTTATAGTAATTGGTACATGAATATTGCTT
TAATCATTTATATATGTGTGCAATATCCACAAATATTTGTAATTCAATACTTAGTATTAAATG
Found at i:4262962 original size:21 final size:22
Alignment explanation
Indices: 4262887--4262961 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
4262877 AAAATTTGAA
*
4262887 TAATTTATTATTAAGTTATCCA-
1 TAATTTATTACTAAGTTAT-CAT
* * * **
4262909 TACTTTACTACTAAGCTAAAAT
1 TAATTTATTACTAAGTTATCAT
4262931 TAATTTATTA-TAAGTTATCAT
1 TAATTTATTACTAAGTTATCAT
4262952 TAATTTATTA
1 TAATTTATTA
4262962 TTATCACTGA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
21 19 0.46
22 22 0.54
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (22 bp):
TAATTTATTACTAAGTTATCAT
Found at i:4263244 original size:44 final size:44
Alignment explanation
Indices: 4263196--4263304 Score: 105
Period size: 44 Copynumber: 2.5 Consensus size: 44
4263186 TATTAGTAAA
* *
4263196 TTATTAATGATTTACTATTAAGCTATGAA-TGATTTACTACT-ACG
1 TTATTAATGATTTACTATTAAGCTAT-AATTAATTTACTA-TGAAG
* * * * * *
4263240 TTATTGATAATTTATTATAAAGTTATAATTAATTTTCTATGAAG
1 TTATTAATGATTTACTATTAAGCTATAATTAATTTACTATGAAG
*
4263284 TTATCAATGATTTACTATTAA
1 TTATTAATGATTTACTATTAA
4263305 ATTATCATTG
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
43 3 0.06
44 47 0.94
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (44 bp):
TTATTAATGATTTACTATTAAGCTATAATTAATTTACTATGAAG
Found at i:4263310 original size:22 final size:22
Alignment explanation
Indices: 4263173--4263527 Score: 95
Period size: 22 Copynumber: 16.4 Consensus size: 22
4263163 TTATTGCTAT
* * *
4263173 ATTATCAGTGATTTATTAGTAA
1 ATTATCAATGATTTACTATTAA
*
4263195 ATTATTAATGATTTACTATTAA
1 ATTATCAATGATTTACTATTAA
** * * *
4263217 GCTATGAATGATTTACTACTAC
1 ATTATCAATGATTTACTATTAA
* ** * *
4263239 GTTATTGATAATTTATTA-TAA
1 ATTATCAATGATTTACTATTAA
* * *
4263260 AGTTAT-AATTAATTTTCTATGAA
1 A-TTATCAA-TGATTTACTATTAA
*
4263283 GTTATCAATGATTTACTATTAA
1 ATTATCAATGATTTACTATTAA
* * **
4263305 ATTATCATTGATATAC-AACAA
1 ATTATCAATGATTTACTATTAA
* * *
4263326 ATTAT-AAGTGATTTATTAGTAT
1 ATTATCAA-TGATTTACTATTAA
* * ** *
4263348 GTTATTAGCGATTTACTACTAA
1 ATTATCAATGATTTACTATTAA
* *
4263370 A-T-TCAATGATTTACTACTAT
1 ATTATCAATGATTTACTATTAA
* *
4263390 AGTAT-TATGCATTTAC---T-A
1 ATTATCAATG-ATTTACTATTAA
* * **
4263408 ATTACCATTGATTTGTTATTAA
1 ATTATCAATGATTTACTATTAA
* * * *
4263430 CTTTTTAAT-AATTAGCTATTAA
1 ATTATCAATGATTTA-CTATTAA
* * *
4263452 GTTATCAATTATTTACTACTAA
1 ATTATCAATGATTTACTATTAA
* * * *
4263474 ATTATCCATTCAATTACTGTTAA
1 ATTAT-CAATGATTTACTATTAA
* **
4263497 GTTATTTATGATTTACTATTAA
1 ATTATCAATGATTTACTATTAA
*
4263519 TTTATCAAT
1 ATTATCAAT
4263528 AAATTACAAT
Statistics
Matches: 232, Mismatches: 83, Indels: 36
0.66 0.24 0.10
Matches are distributed among these distances:
18 7 0.03
19 3 0.01
20 16 0.07
21 26 0.11
22 155 0.67
23 25 0.11
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.46
Consensus pattern (22 bp):
ATTATCAATGATTTACTATTAA
Found at i:4263805 original size:11 final size:11
Alignment explanation
Indices: 4263769--4263816 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
4263759 TATTACTATC
4263769 TTATCACTAAT
1 TTATCACTAAT
*
4263780 TT-TCTACTAAA
1 TTATC-ACTAAT
*
4263791 TTATCATTAAT
1 TTATCACTAAT
*
4263802 TTATCACTAAG
1 TTATCACTAAT
4263813 TTAT
1 TTAT
4263817 AGATGATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
10 2 0.07
11 26 0.87
12 2 0.07
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (11 bp):
TTATCACTAAT
Found at i:4263832 original size:66 final size:66
Alignment explanation
Indices: 4263762--4263892 Score: 147
Period size: 66 Copynumber: 2.0 Consensus size: 66
4263752 AATTACTTAT
* * * * * * *
4263762 TACTATCTTATCACTAATTTTCTACTAAATTATCATTAATTTA-TCACTAAGTTATAGATGATTT
1 TACTAACTTATAAATAATTTACTACTAAATTATCAATAATTTACT-ACTAAATTATAGATAATTT
4263826 AC
65 AC
* * * *
4263828 TACTAAGTTATAAATGATTTACTACTAAATTATTAATAATTTACTATTAAATTATAGATAATTTA
1 TACTAACTTATAAATAATTTACTACTAAATTATCAATAATTTACTACTAAATTATAGATAATTTA
4263893 TTATAAAGTT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
66 52 0.98
67 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.45
Consensus pattern (66 bp):
TACTAACTTATAAATAATTTACTACTAAATTATCAATAATTTACTACTAAATTATAGATAATTTA
C
Found at i:4263888 original size:22 final size:22
Alignment explanation
Indices: 4263776--4263917 Score: 121
Period size: 22 Copynumber: 6.5 Consensus size: 22
4263766 ATCTTATCAC
* *
4263776 TAATTTTCTACTAAATTATCA-T
1 TAATTTACTACTAAATTAT-AGA
*
4263798 TAATTTA-TCACTAAGTTATAGA
1 TAATTTACT-ACTAAATTATAGA
* * *
4263820 TGATTTACTACTAAGTTATAAA
1 TAATTTACTACTAAATTATAGA
*
4263842 TGATTTACTACTAAATTATTA-A
1 TAATTTACTACTAAATTA-TAGA
*
4263864 TAATTTACTATTAAATTATAGA
1 TAATTTACTACTAAATTATAGA
* * *
4263886 TAATTTATTA-TAAAGTTGTTGA
1 TAATTTACTACTAAA-TTATAGA
4263908 TAATTTACTA
1 TAATTTACTA
4263918 TGAAGTTGTT
Statistics
Matches: 102, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
21 8 0.08
22 91 0.89
23 3 0.03
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (22 bp):
TAATTTACTACTAAATTATAGA
Found at i:4263923 original size:22 final size:22
Alignment explanation
Indices: 4263844--4263939 Score: 88
Period size: 22 Copynumber: 4.4 Consensus size: 22
4263834 GTTATAAATG
* *
4263844 ATTTACTACTAAA-TTATTAATA
1 ATTTACTA-TAAAGTTGTTGATA
* *
4263866 ATTTACTATTAAA-TTATAGATA
1 ATTTACTA-TAAAGTTGTTGATA
*
4263888 ATTTATTATAAAGTTGTTGATA
1 ATTTACTATAAAGTTGTTGATA
* *
4263910 ATTTACTATGAAGTTGTTAATA
1 ATTTACTATAAAGTTGTTGATA
*
4263932 ATTAACTA
1 ATTTACTA
4263940 ATTTATGATT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 4 0.06
22 59 0.94
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (22 bp):
ATTTACTATAAAGTTGTTGATA
Found at i:4263977 original size:22 final size:22
Alignment explanation
Indices: 4263952--4263994 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4263942 TTATGATTAA
* *
4263952 ATTATCATTAATTTATAGCTAT
1 ATTATCACTAATTTACAGCTAT
*
4263974 ATTATCACTGATTTACAGCTA
1 ATTATCACTAATTTACAGCTA
4263995 AGTTGTCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTATCACTAATTTACAGCTAT
Found at i:4264022 original size:44 final size:43
Alignment explanation
Indices: 4263974--4264078 Score: 104
Period size: 44 Copynumber: 2.4 Consensus size: 43
4263964 TTATAGCTAT
* * * * *
4263974 ATTATCACTGATTTAC-AGCTAAGTTGTCAATGATTTACCATTA
1 ATTATCAATGATTTACTA-CTAAATTATCAATAATTGACCATTA
* * * *
4264017 CATTATTAGTGATTTACTACTAAATTATTAATAATTGACTATTA
1 -ATTATCAATGATTTACTACTAAATTATCAATAATTGACCATTA
4264061 ATTATCAATGATTTACTA
1 ATTATCAATGATTTACTA
4264079 TATACTGTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
43 16 0.32
44 33 0.66
45 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (43 bp):
ATTATCAATGATTTACTACTAAATTATCAATAATTGACCATTA
Found at i:4264043 original size:22 final size:21
Alignment explanation
Indices: 4264003--4264284 Score: 70
Period size: 22 Copynumber: 13.0 Consensus size: 21
4263993 TAAGTTGTCA
* * *
4264003 ATGATTTACCATTACATTATT
1 ATGATTTACTACTAAATTATT
4264024 AGTGATTTACTACTAAATTATT
1 A-TGATTTACTACTAAATTATT
* * * *
4264046 AATAATTGACTA-TTAATTATCA
1 -ATGATTTACTACTAAATTAT-T
* * *
4264068 ATGATTTACTA-TATACTGTT
1 ATGATTTACTACTAAATTATT
* ** *
4264088 ATGCATTTGCTACTATGTTATC
1 ATG-ATTTACTACTAAATTATT
* * *
4264110 ATTGATTTA-TCATTGAGTT-TT
1 A-TGATTTACT-ACTAAATTATT
* *
4264131 AGTGATTAACTACTAAATTATC
1 A-TGATTTACTACTAAATTATT
* * *
4264153 ATTGTTTTATTGCTAAATTATTT
1 A-TGATTTACTACTAAATTA-TT
* *
4264176 ATGATTTACTACTAAGTTTATA
1 ATGATTTACTACTAA-ATTATT
* * * * **
4264198 ATTTACTTACTATTAAACTAAA
1 A-TGATTTACTACTAAATTATT
* *
4264220 ATAGATTTACTATTAAGTTATCT
1 AT-GATTTACTACTAAATTAT-T
* * *
4264243 GTAATTTATTACTAAATT-TT
1 ATGATTTACTACTAAATTATT
*
4264263 CATTGATTTACTATTAAATTAT
1 -A-TGATTTACTACTAAATTAT
4264285 CAATTATTAA
Statistics
Matches: 182, Mismatches: 62, Indels: 32
0.66 0.22 0.12
Matches are distributed among these distances:
20 4 0.02
21 44 0.24
22 113 0.62
23 21 0.12
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (21 bp):
ATGATTTACTACTAAATTATT
Found at i:4264065 original size:21 final size:21
Alignment explanation
Indices: 4264039--4264079 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4264029 TTTACTACTA
*
4264039 AATTATTAATAATTGACTATT
1 AATTATCAATAATTGACTATT
* *
4264060 AATTATCAATGATTTACTAT
1 AATTATCAATAATTGACTAT
4264080 ATACTGTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (21 bp):
AATTATCAATAATTGACTATT
Found at i:4264495 original size:22 final size:22
Alignment explanation
Indices: 4264224--4264639 Score: 195
Period size: 22 Copynumber: 18.8 Consensus size: 22
4264214 ACTAAAATAG
4264224 ATTTACTATTAAGTTATC-TGTA
1 ATTTACTATTAAGTTATCAT-TA
* * * * *
4264246 ATTTATTACTAAATTTTCATTG
1 ATTTACTATTAAGTTATCATTA
*
4264268 ATTTACTATTAAATTATCAATT-
1 ATTTACTATTAAGTTATC-ATTA
*
4264290 ATTAACTATTAAGTTATCATTTA
1 ATTTACTATTAAGTTATCA-TTA
* ** *
4264313 TTTTTTTATTAAATTATCATTA
1 ATTTACTATTAAGTTATCATTA
* * * * *
4264335 ATTTACTACTATGCTAT-TTTGC
1 ATTTACTATTAAGTTATCATT-A
* * * *
4264357 ATTTACAATTATGTTATAATTG
1 ATTTACTATTAAGTTATCATTA
* * **
4264379 ATTTACTGTTAAGTTATTATGC
1 ATTTACTATTAAGTTATCATTA
* *
4264401 ATTTACTATTATA-TTATTATTG
1 ATTTACTATTA-AGTTATCATTA
*
4264423 ATTTACAATTAAGTTATCAATT-
1 ATTTACTATTAAGTTATC-ATTA
* *
4264445 ATTTACTATTAAATTATTATT-
1 ATTTACTATTAAGTTATCATTA
*
4264466 ATTATACTATTAAGTTATCACTA
1 ATT-TACTATTAAGTTATCATTA
* * *
4264489 ATTTACTATACCAAATTATCACTA
1 ATTTACTAT--TAAGTTATCATTA
* * * *
4264513 ATTAACTATTAATTTATCAATG
1 ATTTACTATTAAGTTATCATTA
* *
4264535 A-TTACTATTAAATTAT-ATTG
1 ATTTACTATTAAGTTATCATTA
* *
4264555 ATTTACTTTTAA-TTTTCAATTA
1 ATTTACTATTAAGTTATC-ATTA
* * * * *
4264577 TTAATTACTACTATGTTCTAAATT-
1 --ATTTACTATTAAGTTAT-CATTA
* *
4264601 ATTTACTACTAAATTATCATTA
1 ATTTACTATTAAGTTATCATTA
* *
4264623 ATTTATTATTAAATTAT
1 ATTTACTATTAAGTTAT
4264640 TTATGATTTA
Statistics
Matches: 301, Mismatches: 72, Indels: 42
0.73 0.17 0.10
Matches are distributed among these distances:
20 7 0.02
21 35 0.12
22 199 0.66
23 27 0.09
24 27 0.09
25 6 0.02
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTACTATTAAGTTATCATTA
Found at i:4264976 original size:22 final size:22
Alignment explanation
Indices: 4264951--4265093 Score: 66
Period size: 22 Copynumber: 6.7 Consensus size: 22
4264941 GAATCTTATC
4264951 TACTATTAAATTATTATTAATT
1 TACTATTAAATTATTATTAATT
* * * * * *
4264973 TACTACTAATTTGTCAATGATT
1 TACTATTAAATTATTATTAATT
*
4264995 TACTATTAAGTTATTAGTT--TT
1 TACTATTAAATTATTA-TTAATT
**
4265016 T--TATTAAATTATCCTTAATT
1 TACTATTAAATTATTATTAATT
* * * *
4265036 TACTGTTATATTGTTATGT-GTT
1 TACTATTAAATTATTAT-TAATT
* * *
4265058 TACAATT--ATGTATAAATAATT
1 TACTATTAAAT-TATTATTAATT
4265079 TACTATTAAATTATT
1 TACTATTAAATTATT
4265094 TGTTATTTAT
Statistics
Matches: 83, Mismatches: 28, Indels: 20
0.63 0.21 0.15
Matches are distributed among these distances:
18 2 0.02
19 10 0.12
20 6 0.07
21 14 0.17
22 47 0.57
23 4 0.05
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.52
Consensus pattern (22 bp):
TACTATTAAATTATTATTAATT
Found at i:4265102 original size:22 final size:22
Alignment explanation
Indices: 4265076--4265130 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4265066 TGTATAAATA
*
4265076 ATTTACTATTAAATTATT-TGTT
1 ATTTATTATTAAATTATTATG-T
* *
4265098 ATTTATTACTATATTATTATGT
1 ATTTATTATTAAATTATTATGT
4265120 ATTTATTATTA
1 ATTTATTATTA
4265131 TGTTATCACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (22 bp):
ATTTATTATTAAATTATTATGT
Found at i:4265136 original size:22 final size:22
Alignment explanation
Indices: 4265088--4265136 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
4265078 TTACTATTAA
4265088 ATTATTTGTTATTTATTACTAT
1 ATTATTTGTTATTTATTACTAT
*
4265110 ATTATTATG-TATTTATTATTAT
1 ATTATT-TGTTATTTATTACTAT
*
4265132 GTTAT
1 ATTAT
4265137 CACTGGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (22 bp):
ATTATTTGTTATTTATTACTAT
Found at i:4265174 original size:22 final size:22
Alignment explanation
Indices: 4265155--4265227 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
4265145 TATAACTATC
4265155 TTATCAATTATTTACTACTAAA
1 TTATCAATTATTTACTACTAAA
* * * *
4265177 TTATTATTTATTTACTAATAAG
1 TTATCAATTATTTACTACTAAA
* * *
4265199 TTATCCATAATTTAATA-TACAA
1 TTATCAATTATTTACTACTA-AA
4265221 TTATCAA
1 TTATCAA
4265228 CGATTTAATA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
21 2 0.05
22 37 0.95
ACGTcount: A:0.41, C:0.11, G:0.01, T:0.47
Consensus pattern (22 bp):
TTATCAATTATTTACTACTAAA
Found at i:4268766 original size:54 final size:53
Alignment explanation
Indices: 4268691--4268901 Score: 188
Period size: 54 Copynumber: 3.7 Consensus size: 53
4268681 CGAAAACAAA
* *
4268691 AAAAAAAGAAAAAGGATTTCTAAATAGGCCCAAATGATGAAAAATTTAGAAATTT
1 AAAAAAAG-AAAA-TATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAATTT
* *
4268746 CAAAAAAAGAAAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAATCCAATAAAAAT
1 -AAAAAAAGAAAATATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAAT----T-----T
* * *
4268809 AAATAAATAAAGATAATTTCTAAATAGGCCCAAATGGTGAAAAATTTATAAATTT
1 AAAAAAAGAAA-AT-ATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAATTT
* * * *
4268864 AAAAAAGAGAAAATATTTTTAATTTGGCCTAAATGGTG
1 AAAAAA-AGAAAATATTTCTAAATAGGCCCAAATGGTG
4268902 GAATAATTAG
Statistics
Matches: 128, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
54 55 0.43
55 12 0.09
56 12 0.09
58 1 0.01
60 1 0.01
62 9 0.07
63 3 0.02
64 35 0.27
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.27
Consensus pattern (53 bp):
AAAAAAAGAAAATATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAATTT
Found at i:4272468 original size:15 final size:16
Alignment explanation
Indices: 4272448--4272477 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4272438 TTAAAGATAG
4272448 AAAGCAAAA-AAAAAA
1 AAAGCAAAACAAAAAA
4272463 AAAGCAAAACAAAAA
1 AAAGCAAAACAAAAA
4272478 CATAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAGCAAAACAAAAAA
Found at i:4272865 original size:13 final size:12
Alignment explanation
Indices: 4272848--4272902 Score: 74
Period size: 13 Copynumber: 4.3 Consensus size: 12
4272838 CTAATGGATG
4272848 AAAAAAGAGAAA
1 AAAAAAGAGAAA
*
4272860 GAAAAAAAAGAAA
1 -AAAAAAGAGAAA
4272873 AAAAAAGAGAAA
1 AAAAAAGAGAAA
4272885 AAAGAAAGAGGAAA
1 AAA-AAAGA-GAAA
4272899 AAAA
1 AAAA
4272903 GAAAAAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
12 14 0.37
13 17 0.45
14 7 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAGAGAAA
Found at i:4272879 original size:25 final size:25
Alignment explanation
Indices: 4272848--4272909 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
4272838 CTAATGGATG
4272848 AAAAAAGAGAAAGAAA-AAAAAGAAA
1 AAAAAAGAGAAA-AAAGAAAAAGAAA
* *
4272873 AAAAAAGAGAAAAAAGAAAGAG-GA
1 AAAAAAGAGAAAAAAGAAAAAGAAA
4272897 AAAAAAGA-AAAAA
1 AAAAAAGAGAAAAA
4272910 TTAAAGGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 5 0.15
24 12 0.35
25 17 0.50
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (25 bp):
AAAAAAGAGAAAAAAGAAAAAGAAA
Found at i:4272887 original size:23 final size:23
Alignment explanation
Indices: 4272848--4272909 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
4272838 CTAATGGATG
4272848 AAAAAAGAGAAAGAAAAAAAAGAAA
1 AAAAAAGAG-AA-AAAAAAAAGAAA
* **
4272873 AAAAAAGAGAAAAAAGAAAGAGG
1 AAAAAAGAGAAAAAAAAAAGAAA
4272896 AAAAAA-AGAAAAAA
1 AAAAAAGAGAAAAAA
4272910 TTAAAGGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.24
23 15 0.44
24 2 0.06
25 9 0.26
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAAAAGAGAAAAAAAAAAGAAA
Found at i:4272905 original size:15 final size:13
Alignment explanation
Indices: 4272851--4272906 Score: 62
Period size: 12 Copynumber: 4.2 Consensus size: 13
4272841 ATGGATGAAA
4272851 AAAGAGAAAGAAA-
1 AAAGAGAAA-AAAG
*
4272864 AAAAAGAAAAAA-
1 AAAGAGAAAAAAG
4272876 AAAGAGAAAAAAG
1 AAAGAGAAAAAAG
4272889 AAAGAGGAAAAAAAG
1 AAAGA-G-AAAAAAG
4272904 AAA
1 AAA
4272907 AAATTAAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
12 14 0.37
13 13 0.34
14 1 0.03
15 10 0.26
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAGAAAAAAG
Found at i:4272908 original size:9 final size:9
Alignment explanation
Indices: 4272857--4272891 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4272847 GAAAAAAGAG
4272857 AAAGAAAAA
1 AAAGAAAAA
4272866 AAAGAAAAAA
1 AAAG-AAAAA
*
4272876 AAAGAGAAA
1 AAAGAAAAA
4272885 AAAGAAA
1 AAAGAAA
4272892 GAGGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:4272922 original size:24 final size:23
Alignment explanation
Indices: 4272847--4272932 Score: 75
Period size: 24 Copynumber: 3.6 Consensus size: 23
4272837 ACTAATGGAT
*
4272847 GAAAAAAGAGAAAGAAAAAAAAGA-
1 GAAAAAA-AGAAA-AAAAGAAAGAG
*
4272871 AAAAAAAAGAGAAAAAAGAAAGAG
1 GAAAAAAAGA-AAAAAAGAAAGAG
** *
4272895 GAAAAAAAGAAAAAATTAAAGGAT
1 GAAAAAAAGAAAAAAAGAAA-GAG
*
4272919 GAAAAAATGAAAAA
1 GAAAAAAAGAAAAA
4272933 GGAGAGAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 20 0.38
24 32 0.62
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (23 bp):
GAAAAAAAGAAAAAAAGAAAGAG
Found at i:4274467 original size:16 final size:16
Alignment explanation
Indices: 4274446--4274476 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4274436 AATCTTGAAA
4274446 TCTTGCAAATCTAAAT
1 TCTTGCAAATCTAAAT
*
4274462 TCTTGCATATCTAAA
1 TCTTGCAAATCTAAA
4274477 ATTTTGTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (16 bp):
TCTTGCAAATCTAAAT
Found at i:4274496 original size:31 final size:31
Alignment explanation
Indices: 4274453--4274524 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
4274443 AAATCTTGCA
* *
4274453 AATCTAAATTCTTG-CATATCTAAAATTTTGTG
1 AATC-AAATTCTTGTCA-AACTAAAATTTTGAG
* *
4274485 ATTCAAATTCTTGTGAAACTAAAATTTTGAG
1 AATCAAATTCTTGTCAAACTAAAATTTTGAG
4274516 AATCAAATT
1 AATCAAATT
4274525 TCAACGAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (31 bp):
AATCAAATTCTTGTCAAACTAAAATTTTGAG
Found at i:4274768 original size:40 final size:40
Alignment explanation
Indices: 4274667--4275285 Score: 539
Period size: 40 Copynumber: 14.9 Consensus size: 40
4274657 TCGAAGAGTA
* * * *
4274667 TTATTTTTCAAAGTTGTTGTGCCTCTATTTATAGGAGCTT
1 TTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCCT
* *
4274707 TTATTTTTTCAAAGTTGTTGAGCCTTTGA-TTAGAGGAGCCT
1 TTA-TTTTTCAAAGTCGTTGAGCCTCT-ATTTAGAGGAGCCT
* *
4274748 TTATTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCAT
1 TTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCCT
* * * * ** *
4274788 TTATTTTTCAAAGTTGTTGTGCCTCTGTATAGAAAAGCTTT
1 TTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGC-CT
*
4274829 TTATTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCCT
1 TTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCCT
* * * **
4274869 TTATTTCTCAAAGTCATTGAGCTTCTGCTTAGAGGAGCCTT
1 TTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCC-T
* * * *
4274910 TTATTTTTTAAAGTTGTTGAGCCTATATTTAGAGAAGCCT
1 TTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCCT
* * *
4274950 TTATTTTTCAAAAGGCATTGAGCCTCTACTTAGAGGAGCCTTAT
1 TTATTTTTC-AAAGTCGTTGAGCCTCTATTTAGAGGAGCC---T
* * * * *
4274994 TTATTTTTCAAAATTG-TAAGCCTCTATTTAGAAGAGCTT
1 TTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCCT
* **
4275033 TTATTTTTCAAAG-CATTGAGCCTCCGTTTAGAGGAGCCT
1 TTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCCT
*
4275072 TTATTTTTCAAAGTTGTTGAGCCTCTCCTTACTCAACTTAGAGGAGCCTTAT
1 TTATTTTTCAAAGTCGTTGAG-C-CT-C-TA-T----TTAGAGGAGCC---T
*
4275124 TTATTTTTCAAAGTTGTTGAGCCTCTGA-TTAGAGGAGCCT
1 TTATTTTTCAAAGTCGTTGAGCCTCT-ATTTAGAGGAGCCT
* * * * *
4275164 TTATTTTTCAAAGTTGTTAAGCCTTTGA-TTAAATGAG-CT
1 TTATTTTTCAAAGTCGTTGAGCCTCT-ATTTAGAGGAGCCT
* *
4275203 TTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTGAT
1 TTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGC---CT
*
4275246 TTATTTTTTCTAAAGTCATTGAGCCTCTATTTAGAGGAGC
1 TTA-TTTTTC-AAAGTCGTTGAGCCTCTATTTAGAGGAGC
4275286 TTTGTTTACA
Statistics
Matches: 471, Mismatches: 77, Indels: 57
0.78 0.13 0.09
Matches are distributed among these distances:
39 77 0.16
40 149 0.32
41 122 0.26
42 21 0.04
43 19 0.04
44 16 0.03
45 28 0.06
48 1 0.00
49 13 0.03
50 2 0.00
51 1 0.00
52 22 0.05
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (40 bp):
TTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCCT
Found at i:4274832 original size:81 final size:80
Alignment explanation
Indices: 4274667--4275285 Score: 525
Period size: 81 Copynumber: 7.5 Consensus size: 80
4274657 TCGAAGAGTA
* * * * *
4274667 TTATTTTTCAAAGTTGTTGTGCCTCTATTTATAGGAGCTTTTATTTTTTCAAAGTTGTTGAGCCT
1 TTATTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGCATTTA-TTTTTCAAAGTCGTTGAGCCT
* *
4274732 TTG-ATTAGAGGAGCCT
65 CTGTA-TAGAGGAGCTT
* * *
4274748 TTATTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCATTTATTTTTCAAAGTTGTTGTGCCTC
1 TTATTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGCATTTATTTTTCAAAGTCGTTGAGCCTC
**
4274813 TGTATAGAAAAGCTTT
66 TGTATAGAGGAGC-TT
* * * * *
4274829 TTATTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCCTTTATTTCTCAAAGTCATTGAGCTTC
1 TTATTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGCATTTATTTTTCAAAGTCGTTGAGCCTC
4274894 TGCT-TAGAGGAGCCTT
66 TG-TATAGAGGAG-CTT
* * * * * * *
4274910 TTATTTTTTAAAGTTGTTGAGCCTATATTTAGAGAAGCCTTTATTTTTCAAAAGGCATTGAGCCT
1 TTATTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGCATTTATTTTTC-AAAGTCGTTGAGCCT
*
4274975 CTACT-TAGAGGAGCCTTAT
65 CT-GTATAGAGGAG-C-T-T
* * * * * *
4274994 TTATTTTTCAAAATT-GTAAGCCTCTATTTAGAAGAGCTTTTATTTTTCAAAG-CATTGAGCCTC
1 TTATTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGCATTTATTTTTCAAAGTCGTTGAGCCTC
* * *
4275057 CGTTTAGAGGAGCCT
66 TGTATAGAGGAGCTT
*
4275072 TTATTTTTCAAAGTTGTTGAGCCTCTCCTTACTCAACTTAGAGGAGCCTTATTTATTTTTCAAAG
1 TTATTTTTCAAAGTTATTGAG-C-CT-C-TA-T----TTAGAGGAG-C--ATTTATTTTTCAAAG
* *
4275137 TTGTTGAGCCTCTG-ATTAGAGGAGCCT
54 TCGTTGAGCCTCTGTA-TAGAGGAGCTT
* * * * *
4275164 TTATTTTTCAAAGTTGTTAAGCCTTTGA-TTAAATGAGC-TTTATTTTTCAAAGTCGTTGAGCCT
1 TTATTTTTCAAAGTTATTGAGCCTCT-ATTTAGAGGAGCATTTATTTTTCAAAGTCGTTGAGCCT
*
4275227 CTGTTTAGAGGAGCTTGAT
65 CTGTATAGAGGAGC-T--T
*
4275246 TTATTTTTTCTAAAGTCATTGAGCCTCTATTTAGAGGAGC
1 TTA-TTTTTC-AAAGTTATTGAGCCTCTATTTAGAGGAGC
4275286 TTTGTTTACA
Statistics
Matches: 446, Mismatches: 60, Indels: 61
0.79 0.11 0.11
Matches are distributed among these distances:
78 15 0.03
79 39 0.09
80 32 0.07
81 173 0.39
82 38 0.09
83 44 0.10
84 36 0.08
88 9 0.02
89 2 0.00
90 2 0.00
91 15 0.03
92 41 0.09
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (80 bp):
TTATTTTTCAAAGTTATTGAGCCTCTATTTAGAGGAGCATTTATTTTTCAAAGTCGTTGAGCCTC
TGTATAGAGGAGCTT
Found at i:4274881 original size:121 final size:120
Alignment explanation
Indices: 4274667--4275288 Score: 592
Period size: 121 Copynumber: 5.0 Consensus size: 120
4274657 TCGAAGAGTA
* * * * *
4274667 TTATTTTTCAAAGTTGTTGTGCCTCTATTTATAGGAGCTTTTATTTTTTCAAAGTTGTTGAGCCT
1 TTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCCTTTA-TTTTTCAAAGTCGTTGAGCCT
* *
4274732 TTGA-TTAGAGGAGCCTTTATTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCAT
65 CT-ATTTAGAGGAGCCTTTATTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCTT
* * ** * *
4274788 TTATTTTTCAAAGTTGTTGTGCCTCTGTATAGAAAAGCTTTTTATTTTTCAAAGTCATTGAGCCT
1 TTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGC-CTTTATTTTTCAAAGTCGTTGAGCCT
* * **
4274853 CTATTTAGAGGAGCCTTTATTTCTCAAAGTCATTGAGCTTCTGCTTAGAGGAGCCTT
65 CTATTTAGAGGAGCCTTTATTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAG-CTT
* * * * * *
4274910 TTATTTTTTAAAGTTGTTGAGCCTATATTTAGAGAAGCCTTTATTTTTCAAAAGGCATTGAGCCT
1 TTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCCTTTATTTTTC-AAAGTCGTTGAGCCT
* *
4274975 CTACTTAGAGGAGCCTTATTTATTTTTCAAA---ATTGTAAGCCTCTATTTAGAAGAGCTT
65 CTATTTAGAGGAGCC---TTTATTTTTCAAAGTCATTG--AGCCTCTATTTAGAGGAGCTT
** * *
4275033 TTATTTTTCAAAG-CATTGAGCCTCCGTTTAGAGGAGCCTTTATTTTTCAAAGTTGTTGAGCCTC
1 TTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCCTTTATTTTTCAAAGTCGTTGAG-C-C
**
4275097 TCCTTACTCAACTTAGAGGAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGA-TTAGAGGAG
64 T-C-TA-T----TTAGAGGAGCC---TTTATTTTTCAAAGTCATTGAGCCTCT-ATTTAGAGGAG
*
4275161 CCT
118 CTT
* * * * *
4275164 TTATTTTTCAAAGTTGTTAAGCCTTTGATTAAATGAG-CTTTATTTTTCAAAGTCGTTGAGCCTC
1 TTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCCTTTATTTTTCAAAGTCGTTGAGCCTC
* *
4275228 TGTTTAGAGGAGCTTGATTTATTTTTTCTAAAGTCATTGAGCCTCTATTTAGAGGAGCTT
66 TATTTAGAGGAGC---CTTTA-TTTTTC-AAAGTCATTGAGCCTCTATTTAGAGGAGCTT
4275288 T
1 T
4275289 GTTTACATTT
Statistics
Matches: 417, Mismatches: 55, Indels: 55
0.79 0.10 0.10
Matches are distributed among these distances:
120 1 0.00
121 117 0.28
122 115 0.28
123 24 0.06
124 42 0.10
125 14 0.03
126 1 0.00
127 1 0.00
128 1 0.00
129 2 0.00
130 28 0.07
131 52 0.12
132 16 0.04
133 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (120 bp):
TTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCCTTTATTTTTCAAAGTCGTTGAGCCTC
TATTTAGAGGAGCCTTTATTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCTT
Found at i:4275205 original size:131 final size:130
Alignment explanation
Indices: 4274977--4275228 Score: 346
Period size: 131 Copynumber: 1.9 Consensus size: 130
4274967 TTGAGCCTCT
*
4274977 ACTTAGAGGAGCCTTATTTATTTTTCAAAATTGTAAGCCTCTATTTAGAAGAGCTTTTATTTTTC
1 ACTTAGAGGAGCCTTATTTATTTTTCAAAATTGTAAGCCTCTATTTAGAAGAGCCTTTATTTTTC
* * * *
4275042 AAAGCATTGAGCCTCCGTTTAGAGGAGCCTTTATTTTTCAAAGTTGTTGAGCCTCTCCTTACTCA
66 AAAGCATTAAGCCTCCGATTAAAGGAGCCTTTATTTTTCAAAGTCGTTGAGCCTCTCCTTACTCA
* * *
4275107 ACTTAGAGGAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGA-TTAGAGGAGCCTTTATTTT
1 ACTTAGAGGAGCCTTATTTATTTTTCAAAATTG-TAAGCCTCT-ATTTAGAAGAGCCTTTATTTT
** ** *
4275171 TCAAAGTTGTTAAGCCTTTGATTAAATGAG-CTTTATTTTTCAAAGTCGTTGAGCCTCT
64 TCAAAG-CATTAAGCCTCCGATTAAAGGAGCCTTTATTTTTCAAAGTCGTTGAGCCTCT
4275229 GTTTAGAGGA
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
130 32 0.30
131 58 0.55
132 16 0.15
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (130 bp):
ACTTAGAGGAGCCTTATTTATTTTTCAAAATTGTAAGCCTCTATTTAGAAGAGCCTTTATTTTTC
AAAGCATTAAGCCTCCGATTAAAGGAGCCTTTATTTTTCAAAGTCGTTGAGCCTCTCCTTACTCA
Found at i:4283670 original size:17 final size:17
Alignment explanation
Indices: 4283650--4283688 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
4283640 TAATTTAATA
*
4283650 ATGAACACATTTATCAT
1 ATGAACACAGTTATCAT
**
4283667 ATGAATGCAGTTATCAT
1 ATGAACACAGTTATCAT
4283684 ATGAA
1 ATGAA
4283689 TGTAATTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (17 bp):
ATGAACACAGTTATCAT
Found at i:4283697 original size:17 final size:17
Alignment explanation
Indices: 4283660--4283697 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4283650 ATGAACACAT
*
4283660 TTATCATATGAATGCAG
1 TTATCATATGAATGCAA
*
4283677 TTATCATATGAATGTAA
1 TTATCATATGAATGCAA
4283694 TTAT
1 TTAT
4283698 GAATGTAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (17 bp):
TTATCATATGAATGCAA
Found at i:4292039 original size:23 final size:23
Alignment explanation
Indices: 4292007--4292056 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
4291997 TGTAAACACC
*
4292007 ATTTATTATTATTATT-ATTATTT
1 ATTTAATATT-TTATTCATTATTT
* *
4292030 ATTTAATATTTTTTTCATTTTTT
1 ATTTAATATTTTATTCATTATTT
4292053 ATTT
1 ATTT
4292057 TTTTTCCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (23 bp):
ATTTAATATTTTATTCATTATTT
Found at i:4292058 original size:17 final size:16
Alignment explanation
Indices: 4292038--4292078 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
4292028 TTATTTAATA
4292038 TTTTTTTCATTTTTTAT
1 TTTTTTTCATTTTTT-T
*
4292055 TTTTTTTCCTTTTTTT
1 TTTTTTTCATTTTTTT
4292071 TTTCTTTT
1 TTT-TTTT
4292079 TTTTTTTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTCATTTTTTT
Found at i:4292071 original size:12 final size:12
Alignment explanation
Indices: 4292054--4292089 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
4292044 TCATTTTTTA
4292054 TTTTTTTTCCTT
1 TTTTTTTTCCTT
*
4292066 TTTTTTTTCTTT
1 TTTTTTTTCCTT
4292078 TTTTTTTTCCTT
1 TTTTTTTTCCTT
4292090 CTTCTTCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTCCTT
Found at i:4292084 original size:11 final size:11
Alignment explanation
Indices: 4292054--4292084 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4292044 TCATTTTTTA
*
4292054 TTTTTTTTCCT
1 TTTTTTTTTCT
4292065 TTTTTTTTTCT
1 TTTTTTTTTCT
4292076 TTTTTTTTT
1 TTTTTTTTT
4292085 TCCTTCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:4292084 original size:17 final size:17
Alignment explanation
Indices: 4292038--4292085 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
4292028 TTATTTAATA
4292038 TTTTTTTCATTTTTTATT
1 TTTTTTTC-TTTTTTATT
*
4292056 TTTTTTCCTTTTTT-TT
1 TTTTTTTCTTTTTTATT
4292072 TTCTTTTT-TTTTTT
1 TT-TTTTTCTTTTTT
4292086 CCTTCTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 10 0.37
17 10 0.37
18 7 0.26
ACGTcount: A:0.04, C:0.08, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTCTTTTTTATT
Found at i:4292092 original size:16 final size:14
Alignment explanation
Indices: 4292038--4292085 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
4292028 TTATTTAATA
4292038 TTTTTTTCATTTTTT
1 TTTTTTTC-TTTTTT
**
4292053 ATTTTTTT-TCCTTT
1 -TTTTTTTCTTTTTT
4292067 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
4292081 TTTTT
1 TTTTT
4292086 CCTTCTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 7 0.26
14 13 0.48
16 7 0.26
ACGTcount: A:0.04, C:0.08, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTCTTTTTT
Found at i:4292262 original size:23 final size:23
Alignment explanation
Indices: 4292236--4292290 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
4292226 AATGGGACTC
*
4292236 GAATCCCTGATGATCTGGGATTT
1 GAATCCCAGATGATCTGGGATTT
4292259 GAATCCCAGATGATCTGGGATTT
1 GAATCCCAGATGATCTGGGATTT
4292282 GAATCCCAG
1 GAATCCCAG
4292291 CAAGCTCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (23 bp):
GAATCCCAGATGATCTGGGATTT
Found at i:4293101 original size:15 final size:15
Alignment explanation
Indices: 4293081--4293113 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4293071 ATTTTTAAAG
4293081 ATTTTT-TTATATATT
1 ATTTTTATTAT-TATT
4293096 ATTTTTATTATTATT
1 ATTTTTATTATTATT
4293111 ATT
1 ATT
4293114 AATATTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTTTATTATTATT
Found at i:4293583 original size:202 final size:201
Alignment explanation
Indices: 4293196--4293583 Score: 479
Period size: 202 Copynumber: 1.9 Consensus size: 201
4293186 ATAATAAAAA
* * * * *
4293196 AAATAAAAAAAAGAAAATTTTGTCTGACGATGAGATTCAGAGGTACTTCGAGTAGTGATACCTAT
1 AAATAAAAAAAAGAAAATTTTATCTAACGATGAGATTCAAAAGTACTTCGAGTAGTGATACCTAC
* * *
4293261 GAAATCTCTAGGTGAGAAGATTTTTTTTAATATTACTAGTGTATTGAAGTATTTATAAAAAAATT
66 GAAATCTCTAGGTGAGAAGATTTTTTTTAATATTACCAGTATATTGAAGTATTTATAAAAAAATC
*
4293326 TTCAATAAAATAAAAATTTTCTTCTTTTATAGAATAATAAATAAAAATTAATTAATTTATTAAAA
131 TTCAATAAAATAAAAATTTTCTTCTTTTATAAAATAATAAATAAAAA-TAATTAATTTATTAAAA
4293391 ATAGTAT
195 ATAGTAT
* * *
4293398 AAAT-AAAAAAAG-AAATTTTATCTAATGATGGGATTCTAAAAGTA-TTCCGAGTAGTGATACTT
1 AAATAAAAAAAAGAAAATTTTATCTAACGATGAGATTC-AAAAGTACTT-CGAGTAGTGATAC-C
*
4293460 TACGAAATCTCTAGGTGAGAAGATTTTTTTTAAAATATTACCAGTATATTGGAA-TATTTATAGA
63 TACGAAATCTCTAGGTGAGAAGATTTTTTTT--AATATTACCAGTATATT-GAAGTATTTATAAA
* *
4293524 AAAA-CTTCAATACAATAAAAATTCTT-TT-TTTTCTTCAAAATTAA-AAATAAAAA-AATTAAT
125 AAAATCTTCAATAAAATAAAAATT-TTCTTCTTTT-AT-AAAA-TAATAAATAAAAATAATTAAT
4293584 AAAACAATTA
Statistics
Matches: 161, Mismatches: 15, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
200 22 0.14
201 26 0.16
202 45 0.28
203 20 0.12
204 42 0.26
205 6 0.04
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (201 bp):
AAATAAAAAAAAGAAAATTTTATCTAACGATGAGATTCAAAAGTACTTCGAGTAGTGATACCTAC
GAAATCTCTAGGTGAGAAGATTTTTTTTAATATTACCAGTATATTGAAGTATTTATAAAAAAATC
TTCAATAAAATAAAAATTTTCTTCTTTTATAAAATAATAAATAAAAATAATTAATTTATTAAAAA
TAGTAT
Found at i:4293584 original size:12 final size:12
Alignment explanation
Indices: 4293569--4293599 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4293559 CAAAATTAAA
4293569 AATAAAAAAATT
1 AATAAAAAAATT
*
4293581 AATAAAACAATT
1 AATAAAAAAATT
4293593 AATAAAA
1 AATAAAA
4293600 GTAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAAAAAAATT
Found at i:4293853 original size:19 final size:19
Alignment explanation
Indices: 4293817--4293853 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4293807 ATATTTGAAT
*
4293817 ATAAAAAAATAAATAAAAA
1 ATAAAAAAATAAAGAAAAA
*
4293836 ATAAAAAAATCAAGAAAA
1 ATAAAAAAATAAAGAAAA
4293854 TTAATTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.14
Consensus pattern (19 bp):
ATAAAAAAATAAAGAAAAA
Found at i:4296312 original size:100 final size:100
Alignment explanation
Indices: 4296139--4296339 Score: 366
Period size: 100 Copynumber: 2.0 Consensus size: 100
4296129 GTATAGCACA
*
4296139 AAGCTCAACCCGAGCAAATGCACTTTTGAGGTTATGTTAGGAAAATTCCTAGGATACATGATCAA
1 AAGCTCAACCCGAGCAAATGCACTTTTGAGGTTATGTTAGGAAAATTACTAGGATACATGATCAA
4296204 CTAGAAAGGAATAGAAGCTAACCTTGAAAAAGTTT
66 CTAGAAAGGAATAGAAGCTAACCTTGAAAAAGTTT
*
4296239 AAGCTCAACCCGAGCAAATGCACTTTTGAGGTTATGTTAGGCAAATTACTAGGATACATGATCAA
1 AAGCTCAACCCGAGCAAATGCACTTTTGAGGTTATGTTAGGAAAATTACTAGGATACATGATCAA
* *
4296304 CTAGAAAGGAATAGATGCTAACCTTGAAAATGTTT
66 CTAGAAAGGAATAGAAGCTAACCTTGAAAAAGTTT
4296339 A
1 A
4296340 GGCTATTTTC
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (100 bp):
AAGCTCAACCCGAGCAAATGCACTTTTGAGGTTATGTTAGGAAAATTACTAGGATACATGATCAA
CTAGAAAGGAATAGAAGCTAACCTTGAAAAAGTTT
Found at i:4299523 original size:36 final size:36
Alignment explanation
Indices: 4299476--4299547 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
4299466 CTTAAGCCTC
4299476 GTCATATATATTGTATTAATTATAAAGCTGTACATT
1 GTCATATATATTGTATTAATTATAAAGCTGTACATT
4299512 GTCATATATATTGTATTAATTATAAAGCTGTACATT
1 GTCATATATATTGTATTAATTATAAAGCTGTACATT
4299548 TGTCGTTGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (36 bp):
GTCATATATATTGTATTAATTATAAAGCTGTACATT
Found at i:4300649 original size:2 final size:2
Alignment explanation
Indices: 4300637--4300676 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
4300627 TCAATATAAA
* * *
4300637 AT AT GT AT AT AT AT AT AT AT AT AT AA AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4300677 TTATTATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4302496 original size:39 final size:40
Alignment explanation
Indices: 4302409--4302510 Score: 145
Period size: 39 Copynumber: 2.6 Consensus size: 40
4302399 GGTCAACGCT
* *
4302409 GGTCCGGGCGGTCTGACCGGTTCGGCGGGTTGGGATCGGC
1 GGTCCGGGCGATCTGACCGGTTCGGCGGGTTCGGATCGGC
* *
4302449 GGTTCGGGCTATCTGACCGGTTCGG-GCGG-TCGGATCGGC
1 GGTCCGGGCGATCTGACCGGTTCGGCG-GGTTCGGATCGGC
4302488 GGTCCGGGCGATCTGACCGGTTC
1 GGTCCGGGCGATCTGACCGGTTC
4302511 AGTCCGGTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 31 0.56
40 24 0.44
ACGTcount: A:0.07, C:0.26, G:0.45, T:0.22
Consensus pattern (40 bp):
GGTCCGGGCGATCTGACCGGTTCGGCGGGTTCGGATCGGC
Found at i:4303322 original size:17 final size:18
Alignment explanation
Indices: 4303302--4303340 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
4303292 ATTTTCATTT
4303302 TTTTTGTTTGTTTG-TTG
1 TTTTTGTTTGTTTGTTTG
*
4303319 TTTTTGTTTTTTTGTTTG
1 TTTTTGTTTGTTTGTTTG
4303337 TTTT
1 TTTT
4303341 GTTAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (18 bp):
TTTTTGTTTGTTTGTTTG
Found at i:4303332 original size:21 final size:20
Alignment explanation
Indices: 4303299--4303338 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
4303289 CTTATTTTCA
4303299 TTTTTTTTGTTTGTTTGTTG
1 TTTTTTTTGTTTGTTTGTTG
*
4303319 TTTTTGTTTTTTTGTTTGTT
1 TTTTT-TTTGTTTGTTTGTT
4303339 TTGTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.82
Consensus pattern (20 bp):
TTTTTTTTGTTTGTTTGTTG
Found at i:4304045 original size:45 final size:45
Alignment explanation
Indices: 4303470--4304588 Score: 1673
Period size: 46 Copynumber: 24.2 Consensus size: 45
4303460 TCCGAAAGTG
* * *
4303470 AATTCTCTTGGAAAAGCTCCTCTCAGCAGAGGCCTCAACGACTTTAA
1 AATTCTCTTGAAAAAGCTCCTCTCAACAGAGG-CTC-ACAACTTTAA
* *
4303517 AATTCATCTT--AAAAGCTCATCTCAGCAGAGGCTCCACAACTTTAA
1 AATTC-TCTTGAAAAAGCTCCTCTCAACAGAGGCT-CACAACTTTAA
* * *
4303562 AATTCTCATGAAAAAGTTCCTCTCAGCAGAGGCTCAACAACTTTAA
1 AATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTC-ACAACTTTAA
4303608 AATTCTCTCTG-AAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAA
1 AATTCTCT-TGAAAAAGCTCCTCTCAACAGAGGCT-CACAACTTTAA
*
4303654 AATTCTCATCTGAAAAAGTCCTCTGCTCTCAGCAGAGGCTCAACAACTTTAA
1 AATTCTC-T-TGAAAAAG--CTC--CTCTCAACAGAGGCTC-ACAACTTTAA
4303706 AATTCTTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAA
1 AATTC--TCTTGAAAAAGCTCCTCTCAACAGAGGCT-CACAACTTTAA
4303754 AATT-TCATTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAA
1 AATTCTC--TTGAAAAAGCTCCTCTCAACAGAGGCTC-ACAACTTTAA
4303801 AATTCTTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAA
1 AATTC--TCTTGAAAAAGCTCCTCTCAACAGAGGCTC-ACAACTTTAA
4303849 AATTCTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAA
1 AATTC-TCTTGAAAAAGCTCCTCTCAACAGAGGCT-CACAACTTTAA
4303896 AATTTCTTCTTGAAAAAGCTCCTCTCAACAGAGGC-CACAACTTTAA
1 AA-TTC-TCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
4303942 AATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAA
1 AATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCT-CACAACTTTAA
*
4303988 AATCTTTCTTG-AAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
1 AAT-TCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
4304033 AATTCTCATTG-AAAAGCTCCTCTCAACAGAGGC-CACAACTTTAA
1 AATTCTC-TTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
4304077 AATTCTTCTTGAAAAAGCTCCTCTC-ACAGAGGCTCACAACTTTAA
1 AATTC-TCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
4304122 AATTCTCATTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
1 AATTCTC--TTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
4304169 AATTCTTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
1 AATTC--TCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
4304216 AATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
1 AATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
4304261 AATTCTCATTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
1 AATTCTC-TTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
*
4304307 AATTCTTTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
1 AATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
*
4304352 AATTCTTTTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
1 AATTC-TCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
4304398 AATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAA
1 AATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCT-CACAACTTTAA
4304444 AATTCTTTCTTG-AAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
1 AATTC--TCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
4304490 AATTCTCTTTCGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
1 AATTCTC-TT-GAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
4304537 AATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
1 AATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
*
4304582 AAATCTC
1 AATTCTC
4304589 ATTTGTTTTC
Statistics
Matches: 1012, Mismatches: 15, Indels: 92
0.90 0.01 0.08
Matches are distributed among these distances:
44 65 0.06
45 254 0.25
46 289 0.29
47 233 0.23
48 119 0.12
49 3 0.00
50 8 0.01
51 1 0.00
52 37 0.04
53 1 0.00
54 2 0.00
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (45 bp):
AATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
Found at i:4304633 original size:321 final size:315
Alignment explanation
Indices: 4303475--4304635 Score: 1234
Period size: 321 Copynumber: 3.6 Consensus size: 315
4303465 AAGTGAATTC
* * * * *
4303475 TCTTGGAAAAGCTCCTCTCAGCAGAGGCCTCAACGACTTTAAAATTCATCTT--AAAAGCTCATC
1 TCTTGAAAAAGCTCCTCTCAACAGAGG-CTC-ACAACTTTAAAATTC-TTTTGAAAAAGCTCCTC
* * * *
4303538 TCAGCAGAGGCTCCACAACTTTAAAATTCTCATGAAAAAGTTCCTCTCAGCAGAGGCTCAACAAC
63 TCAACAGAGGCT-CACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTC-ACAAC
* * *
4303603 TTTAAAATTCTC-TCTGAAAAGCTCCTCTCAACA-GAGGCTCCACAACTTT-----A-AAATTCT
126 TTTAAAATTCTCAT-T----TG-T--T-TCAA-ATGA-G-TTCTCAACTTTGAACAATAAATTCT
*
4303660 CATCTGAAAAAGTCCTCTGCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTTCTTGAAAAAGC
179 C-T-TG-AAAAG--CTC--CTCTCAACAGAGGCTC-ACAACTTTAAAATTCTTT-TTGAAAAAGC
4303725 TCCTCTCAACAGAGGCTCCACAACTTTAAAATT-TCATTTGAAAAAGCTCCTCTCAACAGAGGCT
235 TCCTCTCAACAGAGGCT-CACAACTTTAAAATTCTC--TTGAAAAAGCTCCTCTCAACAGAGGCT
*
4303789 CAACAACTTTAAAATTCTT
297 CCACAACTTTAAAATTCTT
4303808 TCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCTTCTTGAAAAAGCTCCTCT
1 TCTTGAAAAAGCTCCTCTCAACAGAGGCTC-ACAACTTTAAAATTCTT-TTGAAAAAGCTCCTCT
4303873 CAACAGAGGCTCCACAACTTTAAAATTTCTTCTTGAAAAAGCTCCTCTCAACAGAGGC-CACAAC
64 CAACAGAGGCT-CACAACTTTAAAA-TTC-TCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAAC
* * * *
4303937 TTTAAAATTCTC-TTGAAAAAGCTCCTCTCAACA-GAGGCTCCACAACTTT-AA-AAT--CTT-T
126 TTTAAAATTCTCATT-----TG-T--T-TCAA-ATGA-G-TTCTCAACTTTGAACAATAAATTCT
**
4303995 CTTGAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAAAATTCTCATTG-AAAAGCTCCTCTCAA
179 CTTGAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAAAATTCTTTTTGAAAAAGCTCCTCTCAA
4304059 CAGAGGC-CACAACTTTAAAATTCTTCTTGAAAAAGCTCCTCTC-ACAGAGGCT-CACAACTTTA
244 CAGAGGCTCACAACTTTAAAATTC-TCTTGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTA
*
4304121 AAATTCTCA
308 AAATTCT-T
4304130 T-TTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAAAATTCTTTCTTGAAAAAGCTCCTCT
1 TCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAAAATTC-TT-TTGAAAAAGCTCCTCT
4304194 CAACAGAGGCTCACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTT
64 CAACAGAGGCTCACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTT
* * * *
4304259 AAAATTCTCATTGAAAAAGCTCCTCTCAACA-GAGGCTCACAACTTT-----A-AAATTCTTTTG
129 AAAATTCTCATT-----TG-T--T-TCAA-ATGA-GTTCTCAACTTTGAACAATAAATTCTCTTG
4304317 AAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAAAATTCTTTTTGAAAAAGCTCCTCTCAACAG
183 -AAAAGCTCCTCTCAACAGAGGCTCACAACTTTAAAATTCTTTTTGAAAAAGCTCCTCTCAACAG
4304382 AGGCTCACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAAT
247 AGGCTCACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAAT
4304447 TCTT
312 TCTT
4304451 TCTTG-AAAAGCTCCTCTCAACAGAGGCTCACAACTTTAAAATTCTCTTTCGAAAAAGCTCCTCT
1 TCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAAAATTCT-TTT-GAAAAAGCTCCTCT
4304515 CAACAGAGGCTCACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTT
64 CAACAGAGGCTCACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTT
* * *
4304580 AAAAATCTCATTTGTTTTCAAATTTGAGTTTTCATCTTTGAACAAGTAAATTCTCT
129 AAAATTCTCATTTG-TTTCAAA--TGAGTTCTCAACTTTGAACAA-TAAATTCTCT
4304636 CTTTTGAATT
Statistics
Matches: 760, Mismatches: 31, Indels: 86
0.87 0.04 0.10
Matches are distributed among these distances:
312 1 0.00
313 4 0.01
314 9 0.01
315 2 0.00
316 3 0.00
317 2 0.00
318 32 0.04
319 74 0.10
320 97 0.13
321 238 0.31
322 30 0.04
323 32 0.04
325 24 0.03
326 3 0.00
327 16 0.02
328 15 0.02
330 3 0.00
331 1 0.00
332 25 0.03
333 28 0.04
334 87 0.11
335 6 0.01
336 27 0.04
337 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (315 bp):
TCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAAAATTCTTTTGAAAAAGCTCCTCTCA
ACAGAGGCTCACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTTAA
AATTCTCATTTGTTTCAAATGAGTTCTCAACTTTGAACAATAAATTCTCTTGAAAAGCTCCTCTC
AACAGAGGCTCACAACTTTAAAATTCTTTTTGAAAAAGCTCCTCTCAACAGAGGCTCACAACTTT
AAAATTCTCTTGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTCTT
Found at i:4317299 original size:38 final size:38
Alignment explanation
Indices: 4317246--4317344 Score: 153
Period size: 38 Copynumber: 2.6 Consensus size: 38
4317236 GATCAACGCT
* *
4317246 GGTCCGGGCGGTCTGACCGGTTCGACGGTTGGATCGGC
1 GGTCCGGGCGATCTGACCGGTTCGACGGTCGGATCGGC
* * *
4317284 GGTTCGGGCTATCTGACCGGTTCGGCGGTCGGATCGGC
1 GGTCCGGGCGATCTGACCGGTTCGACGGTCGGATCGGC
4317322 GGTCCGGGCGATCTGACCGGTTC
1 GGTCCGGGCGATCTGACCGGTTC
4317345 AGTCCGGTCC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.08, C:0.27, G:0.42, T:0.22
Consensus pattern (38 bp):
GGTCCGGGCGATCTGACCGGTTCGACGGTCGGATCGGC
Found at i:4318161 original size:9 final size:9
Alignment explanation
Indices: 4318149--4318190 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
4318139 TTTTATTTTT
4318149 TTTTGTTTG
1 TTTTGTTTG
*
4318158 TTTTGTTTT
1 TTTTGTTTG
4318167 TTTTGTTT-
1 TTTTGTTTG
4318175 TTTTGTTTG
1 TTTTGTTTG
4318184 -TTTGTTT
1 TTTTGTTT
4318191 AAATATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
8 15 0.48
9 16 0.52
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (9 bp):
TTTTGTTTG
Found at i:4318166 original size:18 final size:17
Alignment explanation
Indices: 4318145--4318182 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
4318135 TTATTTTTAT
4318145 TTTTTTTTGTTTGTTTTG
1 TTTTTTTTGTTT-TTTTG
4318163 TTTTTTTTGTTTTTTTG
1 TTTTTTTTGTTTTTTTG
4318180 TTT
1 TTT
4318183 GTTTGTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (17 bp):
TTTTTTTTGTTTTTTTG
Found at i:4318169 original size:8 final size:8
Alignment explanation
Indices: 4318146--4318190 Score: 63
Period size: 8 Copynumber: 5.4 Consensus size: 8
4318136 TATTTTTATT
4318146 TTTTTTTG
1 TTTTTTTG
4318154 TTTGTTTTG
1 TTT-TTTTG
4318163 TTTTTTTTG
1 -TTTTTTTG
4318172 TTTTTTTG
1 TTTTTTTG
*
4318180 TTTGTTTG
1 TTTTTTTG
4318188 TTT
1 TTT
4318191 AAATATTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
8 21 0.62
9 10 0.29
10 3 0.09
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:4318175 original size:26 final size:24
Alignment explanation
Indices: 4318138--4318190 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 24
4318128 TTTTATCTTA
4318138 TTTTTATTTTTTTTTGTTTGTTTTG
1 TTTTTATTTTTTTTTGTTTG-TTTG
*
4318163 TTTTTTTTGTTTTTTTGTTTGTTTG
1 TTTTTATT-TTTTTTTGTTTGTTTG
4318188 TTT
1 TTT
4318191 AAATATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (24 bp):
TTTTTATTTTTTTTTGTTTGTTTG
Found at i:4319112 original size:84 final size:84
Alignment explanation
Indices: 4318969--4319140 Score: 202
Period size: 84 Copynumber: 2.0 Consensus size: 84
4318959 AAATTCAGAT
* * *
4318969 ATTTAAACATTCTGTTTAGCAATTTCTGACCCAACATCTTTCTTATATCTTATTCGCTACAAATG
1 ATTTAAACATTCTGTTTAGCAACTTCTGACCCAACATCTTTCTTATACCTCATTCGCTACAAATG
*
4319034 AGTTTCTAAAATCAGAATC
66 AGTTTCTAAAATCAAAATC
* * * * * * * *
4319053 ATTTAAATATTCTGTTTAGTAACTTCTGACCTACCATCTTTGTTCA-ACCTCGTTTGCTACTAAT
1 ATTTAAACATTCTGTTTAGCAACTTCTGACCCAACATCTTTCTT-ATACCTCATTCGCTACAAAT
* *
4319117 TAGTTTCTAAAATTAAAATC
65 GAGTTTCTAAAATCAAAATC
4319137 ATTT
1 ATTT
4319141 GTTTATCTTA
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
84 72 0.99
85 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (84 bp):
ATTTAAACATTCTGTTTAGCAACTTCTGACCCAACATCTTTCTTATACCTCATTCGCTACAAATG
AGTTTCTAAAATCAAAATC
Found at i:4322692 original size:19 final size:19
Alignment explanation
Indices: 4322670--4322708 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
4322660 AGTTTAAATG
4322670 ATTTTTTTATTATTAAACT
1 ATTTTTTTATTATTAAACT
4322689 ATTTTTTTATTATTAAACT
1 ATTTTTTTATTATTAAACT
4322708 A
1 A
4322709 AAAAAATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTTTATTATTAAACT
Found at i:4323473 original size:148 final size:146
Alignment explanation
Indices: 4323187--4323478 Score: 318
Period size: 148 Copynumber: 2.0 Consensus size: 146
4323177 AACCTTTTAC
* * * *
4323187 AATATTCTTTACTCTTTTCAAATGAAGAAATTGATTGGCATTAAAATATCAAAAAAGCCATTTTG
1 AATATTCTTTACTCTTTTCAAATGAAGAAATTGATTGACATGAAAATATAAAAAAAACCATTTTG
* * *
4323252 AATGATGGTAATAAAAATGAAGCAACAATTAAACATATACCATCTTTTCATTTACTAAAATAAAT
66 AATGACGGTAATAAAAATGAAGCAACAATTAAAAATATACAATCTTTTCATTTACTAAAAT-AAT
4323317 TTTTATGGAGAATGCAA
130 TTTTATGGAGAATGCAA
* * * * * **
4323334 AATATTCTTTACTTTTTTCCGAATGGAGAAGTTGATTGATATGAAAATATAAAAAAAATTATTTT
1 AATATTCTTTACTCTTTT-CAAATGAAGAAATTGATTGACATGAAAATATAAAAAAAACCATTTT
* * * ** * * *
4323399 GAATTACGGTAATAAGAATGAAAG-AATAATTAAAAATATTTAATGTTTTCGTTTAGTAGAAAT-
65 GAATGACGGTAATAAAAATG-AAGCAACAATTAAAAATATACAATCTTTTCATTTACTA-AAATA
*
4323462 TTTTTTCATGGAGAATG
128 ATTTTT-ATGGAGAATG
4323479 TGAAAGTAAT
Statistics
Matches: 118, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
147 22 0.19
148 89 0.75
149 7 0.06
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (146 bp):
AATATTCTTTACTCTTTTCAAATGAAGAAATTGATTGACATGAAAATATAAAAAAAACCATTTTG
AATGACGGTAATAAAAATGAAGCAACAATTAAAAATATACAATCTTTTCATTTACTAAAATAATT
TTTATGGAGAATGCAA
Found at i:4324044 original size:2 final size:2
Alignment explanation
Indices: 4324037--4324066 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4324027 TGATTACTTT
4324037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4324067 CACAAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.