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 62 of 100
Found at i:11357528 original size:30 final size:28
Alignment explanation
Indices: 11357418--11357540 Score: 78
Period size: 27 Copynumber: 4.4 Consensus size: 28
11357408 AAAAAAATCC
* *
11357418 ATAAAATTCAAAAAAAT-TAAATA-TTTA
1 ATAAAAAT-AAAAAAATCTAAAAATTTTA
* *
11357445 A-AAAATTAAAAAAAT-TATGAAAA-CTTA
1 ATAAAAATAAAAAAATCTA--AAAATTTTA
* * * *
11357472 A-AAAATTCAAAAAATCTCAAATTTTTA
1 ATAAAAATAAAAAAATCTAAAAATTTTA
*
11357499 ATAACAACTAAAAAAATTCTAAAAATTTTA
1 ATAA-AAATAAAAAAA-TCTAAAAATTTTA
11357529 ATAAAAATAAAA
1 ATAAAAATAAAA
11357541 TGTTAATAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
25 10 0.13
26 9 0.12
27 25 0.32
28 3 0.04
29 16 0.21
30 15 0.19
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.29
Consensus pattern (28 bp):
ATAAAAATAAAAAAATCTAAAAATTTTA
Found at i:11357898 original size:17 final size:17
Alignment explanation
Indices: 11357878--11357913 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11357868 TTTTTGAAAA
11357878 TTTTAAGTTTTCATAATT
1 TTTTAA-TTTTCATAATT
*
11357896 TTTTAATTTTTATAATT
1 TTTTAATTTTCATAATT
11357913 T
1 T
11357914 CTAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTAATTTTCATAATT
Found at i:11357931 original size:20 final size:21
Alignment explanation
Indices: 11357901--11357939 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11357891 TAATTTTTTA
11357901 ATTTTTATAATTTCTAAAAAT
1 ATTTTTATAATTTCTAAAAAT
*
11357922 ATTTTT-TAATTTTTAAAA
1 ATTTTTATAATTTCTAAAA
11357940 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTATAATTTCTAAAAAT
Found at i:11357935 original size:29 final size:29
Alignment explanation
Indices: 11357893--11357955 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
11357883 AGTTTTCATA
*
11357893 ATTTTTTAATTTTTATAATTTCTAAAAAT
1 ATTTTTTAATTTTTAAAATTTCTAAAAAT
*
11357922 ATTTTTTAATTTTTAAAATTTTTAAAAAT
1 ATTTTTTAATTTTTAAAATTTCTAAAAAT
11357951 ATTTT
1 ATTTT
11357956 AGATGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTTTTTAATTTTTAAAATTTCTAAAAAT
Found at i:11357973 original size:29 final size:27
Alignment explanation
Indices: 11357878--11357973 Score: 54
Period size: 29 Copynumber: 3.4 Consensus size: 27
11357868 TTTTTGAAAA
* * *
11357878 TTTTAAGTTTTCATAAT-TTTTTAA-T
1 TTTTAAATTTTAAAAATATTTTTAATT
**
11357903 TTTTATAATTTCTAAAAATATTTTTTAATT
1 TTTTA-AATTTTAAAAA-TA-TTTTTAATT
*
11357933 TTTAAAATTTTTAAAAATA-TTTTAGATGT
1 TTTTAAA-TTTTAAAAATATTTTTA-AT-T
11357962 TTTTAAACTTTT
1 TTTTAAA-TTTT
11357974 TTTAAAATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
25 5 0.09
26 7 0.13
27 6 0.11
28 2 0.04
29 22 0.41
30 12 0.22
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (27 bp):
TTTTAAATTTTAAAAATATTTTTAATT
Found at i:11357984 original size:9 final size:9
Alignment explanation
Indices: 11357752--11357948 Score: 73
Period size: 9 Copynumber: 21.2 Consensus size: 9
11357742 CCAATTTTTT
11357752 AATTTTTATA
1 AATTTTTA-A
*
11357762 ATATTTTTAG
1 A-ATTTTTAA
* *
11357772 AATATTTCA
1 AATTTTTAA
* *
11357781 GATTTTGAA
1 AATTTTTAA
11357790 AATTTTT--
1 AATTTTTAA
*
11357797 AATTTTTAG
1 AATTTTTAA
11357806 AATTTTTGAA
1 AATTTTT-AA
*
11357816 AATTTTAAAA
1 AATTTT-TAA
11357826 AACTTGTTTCATA
1 AA-TT-TTT-A-A
*
11357839 AATTTTTAG
1 AATTTTTAA
* *
11357848 TATTTTATTA
1 AATTTT-TAA
11357858 AA-TTTTAA
1 AATTTTTAA
*
11357866 GATTTTTGAA
1 AATTTTT-AA
11357876 AA-TTTT-A
1 AATTTTTAA
* * *
11357883 AGTTTTCAT
1 AATTTTTAA
*
11357892 AATTTTT-T
1 AATTTTTAA
*
11357900 AATTTTTAT
1 AATTTTTAA
*
11357909 AATTTCTAAA
1 AATTT-TTAA
**
11357919 AATATTTTTT
1 AAT-TTTTAA
11357929 AATTTTTAA
1 AATTTTTAA
11357938 AATTTTTAA
1 AATTTTTAA
11357947 AA
1 AA
11357949 ATATTTTAGA
Statistics
Matches: 137, Mismatches: 33, Indels: 35
0.67 0.16 0.17
Matches are distributed among these distances:
7 9 0.07
8 14 0.10
9 64 0.47
10 28 0.20
11 14 0.10
12 5 0.04
13 3 0.02
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (9 bp):
AATTTTTAA
Found at i:11367264 original size:45 final size:45
Alignment explanation
Indices: 11367194--11367295 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 45
11367184 AAATACTTTG
* *
11367194 CTTAAGTAAAAAA-AAAAGTTCAAGTTGAAAACCCGAAAGGGCAA
1 CTTAAGCAAAAAACTAAAGTTCAAGTTGAAAACCCGAAAGGGCAA
* * * *
11367238 CTTGAGCAAAAAACTAAAGTTTAAGTTGAAAATCTGAAAGGGCAA
1 CTTAAGCAAAAAACTAAAGTTCAAGTTGAAAACCCGAAAGGGCAA
11367283 CTTAAGCAAAAAA
1 CTTAAGCAAAAAA
11367296 GAAAAGAGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 11 0.22
45 39 0.78
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.19
Consensus pattern (45 bp):
CTTAAGCAAAAAACTAAAGTTCAAGTTGAAAACCCGAAAGGGCAA
Found at i:11368310 original size:55 final size:56
Alignment explanation
Indices: 11368201--11368487 Score: 185
Period size: 55 Copynumber: 5.2 Consensus size: 56
11368191 CCAAGTTAAC
* * * * * * * *
11368201 TTTTCAGACTTACGGTTCAATCTCAGTTATTCGATTTCG-GTTCTGTCCAAATCAT
1 TTTTCAGACTTACAGTTTAATCCCAGTCATTCGATCTCGACTTCAGTCCAGATCAT
* *
11368256 TTTTCAGACTTACAGTTTAATCCCAGTCATTTGATCTCGACTT-AGTTCAGATCAT
1 TTTTCAGACTTACAGTTTAATCCCAGTCATTCGATCTCGACTTCAGTCCAGATCAT
* ** *** * *
11368311 TTTTTAGACTT-GTGATTTAATCTTGGTCATTCGATCTCGGCTTCA-TCCAGATTAT
1 TTTTCAGACTTACAG-TTTAATCCCAGTCATTCGATCTCGACTTCAGTCCAGATCAT
* * * * * * * * *
11368366 TTTTCAAACATGCAATTCAATCCC-GATCGTTTGACCTTGAC-TCAGTCCA-AGTCAAT
1 TTTTCAGACTTACAGTTTAATCCCAG-TCATTCGATCTCGACTTCAGTCCAGA-TC-AT
* * * * * *
11368422 TTTTCAGACTTATAGTTTAATCACAGTCATTCAATCTCG-GTTCAGTCTAGATAAT
1 TTTTCAGACTTACAGTTTAATCCCAGTCATTCGATCTCGACTTCAGTCCAGATCAT
11368477 TTTTCAGACTT
1 TTTTCAGACTT
11368488 GTGATTCAAT
Statistics
Matches: 171, Mismatches: 50, Indels: 22
0.70 0.21 0.09
Matches are distributed among these distances:
54 6 0.04
55 125 0.73
56 38 0.22
57 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (56 bp):
TTTTCAGACTTACAGTTTAATCCCAGTCATTCGATCTCGACTTCAGTCCAGATCAT
Found at i:11368726 original size:3 final size:3
Alignment explanation
Indices: 11368712--11368877 Score: 90
Period size: 3 Copynumber: 58.3 Consensus size: 3
11368702 TTTTTGTTAC
* * *
11368712 TAT TAC TAT TAT TAT TCT T-G TAT TAT TAAT TAT TAT TA- TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
* * * *
11368755 TAT TAT TA- TAG TA- TAG TA- TAG CA- TAT TA- TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
11368797 TAT ATAG TAT GGTA- TAT TAT TAT TA- TAT TAT TA- TAT TA- TAT TAT
1 TAT -TAT TAT --TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
11368841 TAT T-T CTAT TTT TAT TCT CAT TAT TAT TAT TAT TAT T
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11368878 TTTTTACTTT
Statistics
Matches: 129, Mismatches: 15, Indels: 38
0.71 0.08 0.21
Matches are distributed among these distances:
2 25 0.19
3 96 0.74
4 6 0.05
5 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:11368745 original size:18 final size:17
Alignment explanation
Indices: 11368718--11368877 Score: 97
Period size: 16 Copynumber: 9.4 Consensus size: 17
11368708 TTACTATTAC
* *
11368718 TATTATTATTCTTGTAT
1 TATTATTATTATTATAT
11368735 TATTAATTATTATTATAT
1 TATT-ATTATTATTATAT
*
11368753 TA-TATTATTATAGTATAG
1 TATTATTATTAT--TATAT
**
11368771 TA-TAGCA-TATTATAT
1 TATTATTATTATTATAT
11368786 TATTATT-TTATTATAT
1 TATTATTATTATTATAT
11368802 AGTATGGTA-TATTATTAT-T
1 --TAT--TATTATTATTATAT
11368821 ATATTATTA-TATTATAT
1 -TATTATTATTATTATAT
11368838 TATTATT-TCTATT-T-T
1 TATTATTAT-TATTATAT
* *
11368853 TATTCTCATTATTATTAT
1 TATTATTATTATTA-TAT
11368871 TATTATT
1 TATTATT
11368878 TTTTTACTTT
Statistics
Matches: 112, Mismatches: 13, Indels: 35
0.70 0.08 0.22
Matches are distributed among these distances:
15 16 0.14
16 35 0.31
17 16 0.14
18 34 0.30
19 2 0.02
20 9 0.08
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (17 bp):
TATTATTATTATTATAT
Found at i:11368750 original size:13 final size:12
Alignment explanation
Indices: 11368732--11368877 Score: 61
Period size: 13 Copynumber: 11.6 Consensus size: 12
11368722 ATTATTCTTG
11368732 TATTATTAA-T-
1 TATTATTAATTA
11368742 TATTATTATATTA
1 TATTATTA-ATTA
*
11368755 TATTATTATAGTA
1 TATTATTA-ATTA
**
11368768 TAGTATAGCATATTA
1 TA-T-TATTA-ATTA
*
11368783 TATTATT-ATTT
1 TATTATTAATTA
11368794 TATTATATAGTATGGTA
1 TATTAT-TA--AT--TA
11368811 TATTATT-ATTA
1 TATTATTAATTA
11368822 TATTATTATATTA
1 TATTATTA-ATTA
* *
11368835 TATTATTATTTC
1 TATTATTAATTA
* *
11368847 TATT-TTTATTC
1 TATTATTAATTA
11368858 TCATTATT-ATTA
1 T-ATTATTAATTA
11368870 TTATTATT
1 -TATTATT
11368878 TTTTTACTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 30
0.71 0.09 0.20
Matches are distributed among these distances:
10 8 0.07
11 25 0.23
12 20 0.19
13 33 0.31
14 2 0.02
15 11 0.10
16 1 0.01
17 7 0.07
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.60
Consensus pattern (12 bp):
TATTATTAATTA
Found at i:11368755 original size:5 final size:5
Alignment explanation
Indices: 11368735--11368840 Score: 71
Period size: 5 Copynumber: 21.2 Consensus size: 5
11368725 ATTCTTGTAT
* * **
11368735 TATTA -ATTA TTATTA TATTA TA-T- TATTA TAGTA TAGTA TAGCA TATTA
1 TATTA TATTA -TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
*
11368783 TATTA TTATTT TATTA TA-TA GTATGGTA TATTA TTATTA TA-T- TATTA
1 TATTA -TATTA TATTA TATTA -TAT--TA TATTA -TATTA TATTA TATTA
11368830 TATTA TATTA T
1 TATTA TATTA T
11368841 TATTTCTATT
Statistics
Matches: 83, Mismatches: 6, Indels: 24
0.73 0.05 0.21
Matches are distributed among these distances:
3 4 0.05
4 10 0.12
5 51 0.61
6 13 0.16
7 3 0.04
8 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:11368802 original size:28 final size:27
Alignment explanation
Indices: 11368749--11368850 Score: 97
Period size: 28 Copynumber: 3.8 Consensus size: 27
11368739 AATTATTATT
**
11368749 ATATTATATTATTATAGTA-TAGTATAG
1 ATATTATATTATTATTTTATTA-TATAG
11368776 CATATTATATTATTATTTTATTATATAG
1 -ATATTATATTATTATTTTATTATATAG
*
11368804 -TATGGTATATTATTATTATATTAT-T--
1 ATAT--TATATTATTATTTTATTATATAG
11368829 ATATTATATTATTATTTCTATT
1 ATATTATATTATTATTT-TATT
11368851 TTTATTCTCA
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
24 12 0.18
25 4 0.06
26 6 0.09
27 1 0.02
28 40 0.62
29 2 0.03
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (27 bp):
ATATTATATTATTATTTTATTATATAG
Found at i:11368836 original size:36 final size:36
Alignment explanation
Indices: 11368735--11368837 Score: 111
Period size: 36 Copynumber: 2.8 Consensus size: 36
11368725 ATTCTTGTAT
11368735 TATTAATTATTAT-TATATTATATTATTATAGTATAGTA
1 TATT-ATTATTATAT-TATTATATTA-TATAGTATAGTA
* * *
11368773 TAGCATATTA-TATTATTATTTTATTATATAGTATGGTA
1 TA--TTATTATTA-TATTATTATATTATATAGTATAGTA
11368811 TATTATTATTATATTATTATATTATAT
1 TATTATTATTATATTATTATATTATAT
11368838 TATTATTTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
36 20 0.36
37 2 0.04
38 17 0.31
39 14 0.25
40 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (36 bp):
TATTATTATTATATTATTATATTATATAGTATAGTA
Found at i:11369439 original size:13 final size:13
Alignment explanation
Indices: 11369421--11369445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11369411 GGATAAATTT
11369421 TTGAATTTTTTAG
1 TTGAATTTTTTAG
11369434 TTGAATTTTTTA
1 TTGAATTTTTTA
11369446 ACGATGTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
TTGAATTTTTTAG
Found at i:11369735 original size:13 final size:13
Alignment explanation
Indices: 11369719--11369778 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
11369709 CAAGTTTTCT
* *
11369719 TTTTTTTTTTTAA
1 TTTTATTTTTTGA
11369732 TTTTATTTTTTGA
1 TTTTATTTTTTGA
11369745 TTTTATTTTTTGA
1 TTTTATTTTTTGA
*
11369758 TTTCA-TTTTTGA
1 TTTTATTTTTTGA
11369770 TTTTATTTT
1 TTTTATTTT
11369779 ATATTTAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.26
13 31 0.74
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTTGA
Found at i:11369748 original size:25 final size:24
Alignment explanation
Indices: 11369720--11369778 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
11369710 AAGTTTTCTT
*
11369720 TTTTTTTTTTAATTTTATTTTTTGA
1 TTTTTTTTTTAATTTCA-TTTTTGA
*
11369745 TTTTATTTTTTGATTTCATTTTTGA
1 TTTT-TTTTTTAATTTCATTTTTGA
*
11369770 TTTTATTTT
1 TTTTTTTTT
11369779 ATATTTAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.13
25 15 0.50
26 11 0.37
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (24 bp):
TTTTTTTTTTAATTTCATTTTTGA
Found at i:11369784 original size:12 final size:13
Alignment explanation
Indices: 11369731--11369784 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
11369721 TTTTTTTTTA
*
11369731 ATTTTATTTTTTG
1 ATTTTATTTTATG
*
11369744 ATTTTATTTTTTG
1 ATTTTATTTTATG
*
11369757 ATTTCATTTT-TG
1 ATTTTATTTTATG
11369769 ATTTTATTTTAT-
1 ATTTTATTTTATG
11369781 ATTT
1 ATTT
11369785 AGTTTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
12 15 0.39
13 23 0.61
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.74
Consensus pattern (13 bp):
ATTTTATTTTATG
Found at i:11369791 original size:25 final size:25
Alignment explanation
Indices: 11369733--11369796 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
11369723 TTTTTTTAAT
*
11369733 TTTATTTTTTGATTTTATTTTTTGA
1 TTTATTTTTTGATTTTATTTTATGA
11369758 TTTCA-TTTTTGATTTTATTTTAT-A
1 TTT-ATTTTTTGATTTTATTTTATGA
11369782 TTTAGTTTTTT-ATTT
1 TTTA-TTTTTTGATTT
11369797 ATTCTATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
23 1 0.03
24 8 0.23
25 25 0.71
26 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (25 bp):
TTTATTTTTTGATTTTATTTTATGA
Found at i:11369861 original size:19 final size:18
Alignment explanation
Indices: 11369819--11369861 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
11369809 TATTTGTATC
*
11369819 ATTTATTTTTATTAAGTA
1 ATTTATTTTTATTAAATA
*
11369837 AATTATTATTTATTAAATA
1 ATTTATT-TTTATTAAATA
*
11369856 TTTTAT
1 ATTTAT
11369862 AAAAATTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
ATTTATTTTTATTAAATA
Found at i:11370023 original size:12 final size:13
Alignment explanation
Indices: 11369995--11370023 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11369985 AATCCATGAG
11369995 AAATTTCAAAAAT
1 AAATTTCAAAAAT
11370008 AAATTTCAAAAA-
1 AAATTTCAAAAAT
11370020 AAAT
1 AAAT
11370024 AAAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATTTCAAAAAT
Found at i:11371910 original size:26 final size:25
Alignment explanation
Indices: 11371863--11371916 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
11371853 AAATAGTAAT
* *
11371863 AAAATTTACTATAACTGCGATTGAAA
1 AAAAATTACTATAACTACGATT-AAA
* *
11371889 AAAAATTACTATAATTATGATTAAA
1 AAAAATTACTATAACTACGATTAAA
11371914 AAA
1 AAA
11371917 TTAATAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.31
Consensus pattern (25 bp):
AAAAATTACTATAACTACGATTAAA
Found at i:11371918 original size:23 final size:23
Alignment explanation
Indices: 11371888--11371932 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
11371878 TGCGATTGAA
*
11371888 AAAAAATTACT-ATAATTATGATT
1 AAAAAATTAATAATAATT-TGATT
11371911 AAAAAATTAATAATAATTTGAT
1 AAAAAATTAATAATAATTTGAT
11371933 CTCACTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAAAATTAATAATAATTTGATT
Found at i:11376208 original size:29 final size:30
Alignment explanation
Indices: 11376164--11376242 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 30
11376154 AGGCTTTTTA
11376164 CCTAACAAGTGGTATCAAAGCTGT-ATAAT
1 CCTAACAAGTGGTATCAAAGCTGTCATAAT
* * *
11376193 CTTAACAAGTGGTATCAAAACTGTCATGAT
1 CCTAACAAGTGGTATCAAAGCTGTCATAAT
* *
11376223 CCTAATAAGTGGTATTAAAG
1 CCTAACAAGTGGTATCAAAG
11376243 TTGAAAGTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 22 0.52
30 20 0.48
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (30 bp):
CCTAACAAGTGGTATCAAAGCTGTCATAAT
Found at i:11377895 original size:2 final size:2
Alignment explanation
Indices: 11377888--11377920 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
11377878 ATTAATCCTT
*
11377888 TA TA TA TA AA 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 T
11377921 TACGTTGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:11383270 original size:24 final size:24
Alignment explanation
Indices: 11383243--11383288 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
11383233 AGTTTCAATG
*
11383243 AAATCTCAATACTTAGTAAATATC
1 AAATATCAATACTTAGTAAATATC
* * *
11383267 AAATATTAATTCTTATTAAATA
1 AAATATCAATACTTAGTAAATA
11383289 CATATATACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (24 bp):
AAATATCAATACTTAGTAAATATC
Found at i:11384265 original size:18 final size:19
Alignment explanation
Indices: 11384217--11384266 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
11384207 TTTAATTATT
*
11384217 TATAA-AAATTAAAATTGA
1 TATAATAAATTAAAAATGA
* *
11384235 TAAAAATATATTAAAAATG-
1 T-ATAATAAATTAAAAATGA
11384254 TATAATAAATTAA
1 TATAATAAATTAA
11384267 TTATTTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 11 0.44
19 4 0.16
20 10 0.40
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (19 bp):
TATAATAAATTAAAAATGA
Found at i:11384706 original size:18 final size:18
Alignment explanation
Indices: 11384683--11384717 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
11384673 GAATTGTTAC
11384683 AAATATATATTTATTATA
1 AAATATATATTTATTATA
11384701 AAATATATATTTATTAT
1 AAATATATATTTATTAT
11384718 TTAGTTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATATATTTATTATA
Found at i:11389000 original size:48 final size:47
Alignment explanation
Indices: 11388943--11389044 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 47
11388933 ATTTGGACTT
* * *
11388943 AAAAGAAACAGGTTTAGACTTAGAAGAATTAATAGGCAAAAATGTTGA
1 AAAAGAAACAAGTTAAGACTCAGAAGAATTAATAGGCAAAAATGTT-A
* *
11388991 AAAAGAAACAAGTTAAGACTCAGAAGAATTAATGGGTAAAAATGTTA
1 AAAAGAAACAAGTTAAGACTCAGAAGAATTAATAGGCAAAAATGTTA
11389038 AAGAAGA
1 AA-AAGA
11389045 GGACAAGTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 3 0.06
48 45 0.94
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.21
Consensus pattern (47 bp):
AAAAGAAACAAGTTAAGACTCAGAAGAATTAATAGGCAAAAATGTTA
Found at i:11391907 original size:143 final size:142
Alignment explanation
Indices: 11391697--11392173 Score: 378
Period size: 143 Copynumber: 3.3 Consensus size: 142
11391687 TCAGGAAAGG
* * * * * *
11391697 TAAAGTTACCAAAATACCCTTTAGGGGTTTTTTGTAATTTGGTCTTCTCAAGATTAGATTTTCAT
1 TAAAATTACTAAAATA-CCTTTAAGGGTATTTTGTAATTTGATCTTCTCAAGATTAGAATTTCAT
* * * * * * *
11391762 GAAAA-CTTTCATATTATAATTAAACATTATTTTATGATTTTT-GATGTATTGAAAACGTTGATC
65 GAAAATC-TCCAAATCATAATTAAACATTATTTGATGATTTTTAGA-ATATTGAAAACCTTAATC
* * *
11391825 GTACCTTGAGATGTA
128 GTACCTCGAAAGGTA
* *
11391840 TAAAATTACTAAAATACCTTTAAGGGTATTTTCGTAAATTGATCTTCCCAAGA-TAGAAATTTCA
1 TAAAATTACTAAAATACCTTTAAGGGTATTTT-GTAATTTGATCTTCTCAAGATTAG-AATTTCA
* * * *
11391904 TGAAAATCTCCAAATCATGATTTAATATTATTTGATGATTTTTAGAATATTGAAAACCTTAATTG
64 TGAAAATCTCCAAATCATAATTAAACATTATTTGATGATTTTTAGAATATTGAAAACCTTAATCG
11391969 TACCTCGAAAGGTA
129 TACCTCGAAAGGTA
* * * * * * *
11391983 TGAAATCACTAAAATACCCTT-AGGGATATTGTTGTAATTTGACCTTCTCAAGGTTAGTATTT-T
1 TAAAATTACTAAAATACCTTTAAGGG-TATT-TTGTAATTTGATCTTCTCAAGATTAGAATTTCA
* ** * * *
11392046 TCGAAACAT-TCCAGATCATGTTTTAAA-ATTATTTAATGATTTTTTA-TATATTAAAAACCTT-
64 T-GAAA-ATCTCCAAATCAT-AATTAAACATTATTTGATGA-TTTTTAGAATATTGAAAACCTTA
** * *
11392107 GGCAATACCTTGAAAGGTA
125 ATC-GTACCTCGAAAGGTA
* * * * *
11392126 TGAAATTACGAAAATACCCTTATGGGTAATTTTGTAATTTAATCTTCT
1 TAAAATTACTAAAATACCTTTAAGGGT-ATTTTGTAATTTGATCTTCT
11392174 TTAGGTAAGA
Statistics
Matches: 272, Mismatches: 48, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
142 22 0.08
143 224 0.82
144 26 0.10
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (142 bp):
TAAAATTACTAAAATACCTTTAAGGGTATTTTGTAATTTGATCTTCTCAAGATTAGAATTTCATG
AAAATCTCCAAATCATAATTAAACATTATTTGATGATTTTTAGAATATTGAAAACCTTAATCGTA
CCTCGAAAGGTA
Found at i:11396457 original size:17 final size:18
Alignment explanation
Indices: 11396424--11396458 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11396414 GACATTAAGG
11396424 AAAATTCAAAAGAGAAAA
1 AAAATTCAAAAGAGAAAA
11396442 AAAATTCAAAAG-GAAAA
1 AAAATTCAAAAGAGAAAA
11396459 TTGCAGATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.71, C:0.06, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAATTCAAAAGAGAAAA
Found at i:11396611 original size:58 final size:57
Alignment explanation
Indices: 11396473--11396618 Score: 204
Period size: 58 Copynumber: 2.5 Consensus size: 57
11396463 AGATGTTTCA
*
11396473 ACTTTCAACTTTTTCCTAAAAATATTCTTTTGAAACTTTAATTTCAAGAAAAATTGAT
1 ACTTTCAACTTTTCCCTAAAAATATT-TTTTGAAACTTTAATTTCAAGAAAAATTGAT
* * * * *
11396531 ACTTACAATTTTTCCTTAAAAATATTTTTTGGAAACTTTTAATTTCGAGGAAAATTGAT
1 ACTTTCAACTTTTCCCTAAAAATATTTTTT-GAAAC-TTTAATTTCAAGAAAAATTGAT
11396590 ACTTTCAACTTTTCCCT-AAAATATTTTTT
1 ACTTTCAACTTTTCCCTAAAAATATTTTTT
11396619 TTATTTTATT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
57 4 0.05
58 39 0.51
59 34 0.44
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (57 bp):
ACTTTCAACTTTTCCCTAAAAATATTTTTTGAAACTTTAATTTCAAGAAAAATTGAT
Found at i:11396637 original size:5 final size:5
Alignment explanation
Indices: 11396629--11396717 Score: 62
Period size: 5 Copynumber: 17.6 Consensus size: 5
11396619 TTATTTTATT
* *
11396629 AAATA AAATA AAAT- AAA-A AAATAA ATAATA AAA-A AATCCTA ATATA
1 AAATA AAATA AAATA AAATA AAAT-A A-AATA AAATA AA--ATA AAATA
*
11396675 ATAAT- AAATA AAATA AAATA AAATAA AAATA ATATA AAA-A AAA
1 A-AATA AAATA AAATA AAATA AAAT-A AAATA AAATA AAATA AAA
11396718 CATGAGAACG
Statistics
Matches: 68, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
4 16 0.24
5 36 0.53
6 11 0.16
7 5 0.07
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:11396820 original size:12 final size:12
Alignment explanation
Indices: 11396782--11396813 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
11396772 TCAGGGGTAT
11396782 CGGCTCGGCTAA
1 CGGCTCGGCTAA
11396794 CGGCTCGGCTAA
1 CGGCTCGGCTAA
11396806 CGGCTCGG
1 CGGCTCGG
11396814 GAAACGGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.34, G:0.38, T:0.16
Consensus pattern (12 bp):
CGGCTCGGCTAA
Found at i:11397007 original size:21 final size:23
Alignment explanation
Indices: 11396964--11397007 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
11396954 TTCAGCAGAA
**
11396964 CCTTTCTTCTCTTCTCTTTCTTC
1 CCTTTCTTCTCTTCTCTCCCTTC
11396987 CCTTT-TT-TCTTCTCTCCCTTC
1 CCTTTCTTCTCTTCTCTCCCTTC
11397008 TCTCTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (23 bp):
CCTTTCTTCTCTTCTCTCCCTTC
Found at i:11397562 original size:22 final size:22
Alignment explanation
Indices: 11397537--11397679 Score: 59
Period size: 22 Copynumber: 6.5 Consensus size: 22
11397527 AAGAAATCAG
11397537 ATAAATAAAAAAATATTAATAA
1 ATAAATAAAAAAATATTAATAA
* * *
11397559 ATAATTAGAAAAA-A--AA-AG
1 ATAAATAAAAAAATATTAATAA
11397577 ATAAAT-AAAAAATATTACA-AGA
1 ATAAATAAAAAAATATTA-ATA-A
*
11397599 AT-AAT-AAAAAATAATAATAACA
1 ATAAATAAAAAAATATTAAT-A-A
* * * * *
11397621 GATAAATTATAATATATAAATGA
1 -ATAAATAAAAAAATATTAATAA
*
11397644 ATAAATAATAATAAATATATAACTAG
1 ATAAATAA-AA-AAATAT-TAA-TAA
11397670 ATAAATAAAA
1 ATAAATAAAA
11397680 TACATATATA
Statistics
Matches: 88, Mismatches: 19, Indels: 25
0.67 0.14 0.19
Matches are distributed among these distances:
17 5 0.06
18 7 0.08
19 2 0.02
20 2 0.02
21 16 0.18
22 22 0.25
23 4 0.05
24 8 0.09
25 13 0.15
26 9 0.10
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (22 bp):
ATAAATAAAAAAATATTAATAA
Found at i:11397632 original size:7 final size:8
Alignment explanation
Indices: 11397622--11397694 Score: 53
Period size: 8 Copynumber: 9.0 Consensus size: 8
11397612 ATAATAACAG
11397622 ATAAAT-T
1 ATAAATAT
11397629 AT-AATAT
1 ATAAATAT
11397636 ATAAATGA-
1 ATAAAT-AT
11397644 ATAAATAAT
1 ATAAAT-AT
11397653 AATAAATAT
1 -ATAAATAT
* *
11397662 ATAACTAG
1 ATAAATAT
*
11397670 ATAAATAAA
1 ATAAAT-AT
*
11397679 ATACATAT
1 ATAAATAT
11397687 ATAAATAT
1 ATAAATAT
11397695 TAACAGAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
6 3 0.06
7 5 0.10
8 29 0.56
9 9 0.17
10 6 0.12
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (8 bp):
ATAAATAT
Found at i:11397660 original size:26 final size:25
Alignment explanation
Indices: 11397622--11397693 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 25
11397612 ATAATAACAG
*
11397622 ATAAATTATAATATATAAAT-GAATAA
1 ATAAAATA-AATATATAAATAG-ATAA
*
11397648 ATAATAATAAATATATAACTAGATAA
1 ATAA-AATAAATATATAAATAGATAA
*
11397674 ATAAAATACATATATAAATA
1 ATAAAATAAATATATAAATA
11397694 TTAACAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 14 0.35
26 22 0.55
27 4 0.10
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (25 bp):
ATAAAATAAATATATAAATAGATAA
Found at i:11397722 original size:16 final size:16
Alignment explanation
Indices: 11397701--11397731 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11397691 ATATTAACAG
*
11397701 AAAAGAAAGAAAAGAA
1 AAAAGAAAAAAAAGAA
11397717 AAAAGAAAAAAAAGA
1 AAAAGAAAAAAAAGA
11397732 TATATATATT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAAGAA
Found at i:11397804 original size:25 final size:25
Alignment explanation
Indices: 11397770--11397826 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
11397760 ATAAATAAAT
* * *
11397770 AATAAATACATAAGATACAAAGGAA
1 AATATATACATAAAATACAAAAGAA
*
11397795 AATATATACATAAAATATAAAAGAA
1 AATATATACATAAAATACAAAAGAA
11397820 AA-ATATA
1 AATATATA
11397827 AAATATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (25 bp):
AATATATACATAAAATACAAAAGAA
Found at i:11397816 original size:7 final size:7
Alignment explanation
Indices: 11397804--11397838 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
11397794 AAATATATAC
11397804 ATAAAAT
1 ATAAAAT
*
11397811 ATAAAAG
1 ATAAAAT
11397818 A-AAAAT
1 ATAAAAT
11397824 ATAAAAT
1 ATAAAAT
11397831 ATAAAAT
1 ATAAAAT
11397838 A
1 A
11397839 AAAGCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (7 bp):
ATAAAAT
Found at i:11397822 original size:13 final size:13
Alignment explanation
Indices: 11397806--11397848 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
11397796 ATATATACAT
11397806 AAAATATAAAAGA
1 AAAATATAAAAGA
*
11397819 AAAATATAAAATA
1 AAAATATAAAAGA
* *
11397832 TAAA-ATAAAAGC
1 AAAATATAAAAGA
11397844 AAAAT
1 AAAAT
11397849 TGGGCTTACC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (13 bp):
AAAATATAAAAGA
Found at i:11397827 original size:20 final size:20
Alignment explanation
Indices: 11397804--11397841 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11397794 AAATATATAC
11397804 ATAAAATATAAAAGAAAAAT
1 ATAAAATATAAAAGAAAAAT
*
11397824 ATAAAATATAAAATAAAA
1 ATAAAATATAAAAGAAAA
11397842 GCAAAATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (20 bp):
ATAAAATATAAAAGAAAAAT
Found at i:11397839 original size:25 final size:26
Alignment explanation
Indices: 11397743--11397848 Score: 76
Period size: 26 Copynumber: 3.9 Consensus size: 26
11397733 ATATATATTA
11397743 ATAAATAGTAACAATAAATA-AATAAATA-
1 ATAAATA-TAA-AATAAA-AGAA-AAATAT
* *
11397771 ATAAATACATAAGATACAAAGGAAAATAT
1 ATAAAT--ATAAAATA-AAAGAAAAATAT
*
11397800 ATACATA-AAATATAAAAGAAAAATAT
1 ATAAATATAAA-ATAAAAGAAAAATAT
*
11397826 A-AAATATAAAATAAAAGCAAAAT
1 ATAAATATAAAATAAAAGAAAAAT
11397849 TGGGCTTACC
Statistics
Matches: 64, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
25 16 0.25
26 17 0.27
27 4 0.06
28 15 0.23
29 11 0.17
30 1 0.02
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.22
Consensus pattern (26 bp):
ATAAATATAAAATAAAAGAAAAATAT
Found at i:11398004 original size:9 final size:9
Alignment explanation
Indices: 11397990--11398027 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
11397980 AACTCGACAT
11397990 TTTTTTTTG
1 TTTTTTTTG
**
11397999 TTTTTTTAA
1 TTTTTTTTG
11398008 TTTTTTTTG
1 TTTTTTTTG
11398017 TTTTTTTTG
1 TTTTTTTTG
11398026 TT
1 TT
11398028 CAAGATTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.87
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:11398111 original size:43 final size:43
Alignment explanation
Indices: 11398050--11398188 Score: 217
Period size: 43 Copynumber: 3.2 Consensus size: 43
11398040 AAAACTCCTT
11398050 TAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTTCTC
1 TAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTTCTC
*
11398093 TAATCAGAGGCTCAACGACTTTGAAAATTAAATAAAGC-TCATC
1 TAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTTC-TC
* * *
11398136 TAATCAGAGGCTCAATGACTTTGAAAAATAAACAAAGCTCCTC
1 TAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTTCTC
*
11398179 TAAACAGAGG
1 TAATCAGAGG
11398189 TAATTTTTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
42 2 0.02
43 85 0.97
44 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (43 bp):
TAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTTCTC
Found at i:11398205 original size:1 final size:1
Alignment explanation
Indices: 11398201--11398259 Score: 64
Period size: 1 Copynumber: 59.0 Consensus size: 1
11398191 ATTTTTTTAC
* * * * * *
11398201 TTTTTTTTGTTTTTTGTTTTTTTTTTGTTTTTGTTTTTTTTTTTTCTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11398260 AATTTGATCA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:11398232 original size:34 final size:34
Alignment explanation
Indices: 11398194--11398259 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
11398184 AGAGGTAATT
11398194 TTTTTACTTTTTTTTGTTT-TTTGTTTTTTTTTTG
1 TTTTT-CTTTTTTTTGTTTCTTTGTTTTTTTTTTG
* *
11398228 TTTTTGTTTTTTTTTTTTCTTTGTTTTTTTTT
1 TTTTTCTTTTTTTTGTTTCTTTGTTTTTTTTT
11398260 AATTTGATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.88
Consensus pattern (34 bp):
TTTTTCTTTTTTTTGTTTCTTTGTTTTTTTTTTG
Found at i:11398233 original size:17 final size:17
Alignment explanation
Indices: 11398201--11398259 Score: 93
Period size: 17 Copynumber: 3.4 Consensus size: 17
11398191 ATTTTTTTAC
11398201 TTTTTTTTGTTTTTTGTT
1 TTTTTTTTG-TTTTTGTT
11398219 TTTTTTTTGTTTTTGTT
1 TTTTTTTTGTTTTTGTT
11398236 TTTTTTTT-TTCTTTGTT
1 TTTTTTTTGTT-TTTGTT
11398253 TTTTTTT
1 TTTTTTT
11398260 AATTTGATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
16 2 0.05
17 29 0.73
18 9 0.22
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (17 bp):
TTTTTTTTGTTTTTGTT
Found at i:11398446 original size:41 final size:41
Alignment explanation
Indices: 11398272--11398611 Score: 360
Period size: 41 Copynumber: 8.1 Consensus size: 41
11398262 TTTGATCAAA
* *
11398272 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAAATA
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGA-AAA-ATAAATT
* * *
11398315 GCTCCTCTAATCAGAGGTTCAACGACTTTTAGAAAAATGAATG
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTT-GAAAAATAAATT
* * *
11398358 GCTCCTCTAATTAGAGGCTCAACGACTTTTAGAAAAATGAATG
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTT-GAAAAATAAATT
* * *
11398401 GCTCCTCTAATTAGAGGCTCAACAACTTTGAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATT
* * *
11398442 GCTCCTCTAATCAGAGGCTCAGCAACTTTGAAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATT
* * * *
11398483 GCTCCTCTAAAT-AGAGGCACCATGACTTTGAAAAGTAAATT
1 GCTCCTCT-AATCAGAGGCTCAACGACTTTGAAAAATAAATT
* * * *
11398524 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATT
* * * *
11398565 GCTCCTTTAAACAGAGGCACTACGACTTT-AAAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAA-TAAATT
11398606 GCTCCT
1 GCTCCT
11398612 TGACAATCAT
Statistics
Matches: 270, Mismatches: 22, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
40 6 0.02
41 155 0.57
42 6 0.02
43 95 0.35
44 6 0.02
45 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATT
Found at i:11399614 original size:8 final size:8
Alignment explanation
Indices: 11399593--11399678 Score: 79
Period size: 8 Copynumber: 10.8 Consensus size: 8
11399583 TTTTCATTCA
11399593 CTTTTTTT
1 CTTTTTTT
*
11399601 -TCTTTTT
1 CTTTTTTT
11399608 CTTTTTTT
1 CTTTTTTT
11399616 CATTTTTTT
1 C-TTTTTTT
*
11399625 CATTTTTT
1 CTTTTTTT
*
11399633 C-GTTTTT
1 CTTTTTTT
11399640 CATTTTTTT
1 C-TTTTTTT
*
11399649 CATTTTTT
1 CTTTTTTT
*
11399657 CATTTTTT
1 CTTTTTTT
11399665 CATTTTTTT
1 C-TTTTTTT
11399674 -TTTTT
1 CTTTTT
11399679 ATTTTTTCTT
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
7 17 0.26
8 29 0.44
9 20 0.30
ACGTcount: A:0.07, C:0.12, G:0.01, T:0.80
Consensus pattern (8 bp):
CTTTTTTT
Found at i:11399630 original size:24 final size:23
Alignment explanation
Indices: 11399595--11399685 Score: 105
Period size: 24 Copynumber: 3.9 Consensus size: 23
11399585 TTCATTCACT
11399595 TTTTTTTCTTTTTCTTTTTTTCA
1 TTTTTTTCTTTTTCTTTTTTTCA
*
11399618 TTTTTTTCATTTTT-TCGTTTTTCA
1 TTTTTTTC-TTTTTCT-TTTTTTCA
*
11399642 TTTTTTTCATTTTTTCATTTTTTCA
1 TTTTTTTC--TTTTTCTTTTTTTCA
*
11399667 TTTTTTT-TTTTTATTTTTT
1 TTTTTTTCTTTTTCTTTTTT
11399686 CTTTAAGCAT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
22 10 0.17
23 9 0.16
24 20 0.34
25 19 0.33
ACGTcount: A:0.08, C:0.10, G:0.01, T:0.81
Consensus pattern (23 bp):
TTTTTTTCTTTTTCTTTTTTTCA
Found at i:11410142 original size:61 final size:60
Alignment explanation
Indices: 11410075--11410233 Score: 209
Period size: 60 Copynumber: 2.6 Consensus size: 60
11410065 TATGCAGGAA
* * * *
11410075 AAAATTGATACTTTCAAC-TTTCCCTCAAAACCTCTTTTTTTTG-GAAA-TTTTACTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAA---ATATTTTTTGAAAAACTTTTAATTTTAAGG
*
11410136 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAAACTTTTAATTTTGAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAAACTTTTAATTTTAAGG
11410196 AAAATTGATACTTTCAACTTTTCCCT-AAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
11410234 TTATTTTATT
Statistics
Matches: 90, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
58 8 0.09
59 15 0.17
60 38 0.42
61 22 0.24
62 7 0.08
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (60 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAAACTTTTAATTTTAAGG
Found at i:11410268 original size:21 final size:21
Alignment explanation
Indices: 11410244--11410285 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11410234 TTATTTTATT
11410244 TAAAGAAAAGAAAATAAATAA
1 TAAAGAAAAGAAAATAAATAA
* *
11410265 TAAATAAATGAAAATAAATAA
1 TAAAGAAAAGAAAATAAATAA
11410286 AAAAATCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (21 bp):
TAAAGAAAAGAAAATAAATAA
Found at i:11410271 original size:11 final size:11
Alignment explanation
Indices: 11410255--11410321 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
11410245 AAAGAAAAGA
11410255 AAATAAATAAT
1 AAATAAATAAT
*
11410266 AAATAAATGA-
1 AAATAAATAAT
11410276 AAATAAATAA-
1 AAATAAATAAT
*
11410286 AAA-AATCCTAAT
1 AAATAA--ATAAT
11410298 ATAATAATAATAAT
1 A-AAT-A-AATAAT
11410312 AAATAAATAA
1 AAATAAATAA
11410322 AATAATATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
9 2 0.04
10 12 0.27
11 17 0.38
12 2 0.04
13 5 0.11
14 5 0.11
15 1 0.02
16 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.25
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:11410337 original size:14 final size:13
Alignment explanation
Indices: 11410263--11410337 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 13
11410253 GAAAATAAAT
*
11410263 AATAAATAAATGAA
1 AATAAATAAA-AAA
11410277 AATAAATAAAAAA
1 AATAAATAAAAAA
*
11410290 ATCCTAATATAATAATAA
1 A--ATAA-ATAA-AA-AA
*
11410308 TAATAAATAAATAA
1 -AATAAATAAAAAA
11410322 AATAATATAAAAAA
1 AATAA-ATAAAAAA
11410336 AA
1 AA
11410338 ACCTGAGAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
13 8 0.16
14 21 0.43
15 4 0.08
16 8 0.16
17 5 0.10
18 2 0.04
19 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (13 bp):
AATAAATAAAAAA
Found at i:11410656 original size:20 final size:20
Alignment explanation
Indices: 11410631--11410680 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
11410621 CGGTTGAATA
*
11410631 TTCATCGGATTCTGAAAATT
1 TTCATCGGAATCTGAAAATT
* *
11410651 TTCATCGGAATCTGGAATTT
1 TTCATCGGAATCTGAAAATT
*
11410671 TTCGTCGGAA
1 TTCATCGGAA
11410681 GTTCGTCGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (20 bp):
TTCATCGGAATCTGAAAATT
Found at i:11410671 original size:19 final size:20
Alignment explanation
Indices: 11410626--11410671 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
11410616 AACTCCGGTT
* *
11410626 GAATATTCATCGGATTCTGA
1 GAATTTTCATCGGAATCTGA
*
11410646 AAATTTTCATCGGAATCTG-
1 GAATTTTCATCGGAATCTGA
11410665 GAATTTT
1 GAATTTT
11410672 TCGTCGGAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (20 bp):
GAATTTTCATCGGAATCTGA
Found at i:11411201 original size:4 final size:4
Alignment explanation
Indices: 11411194--11411310 Score: 50
Period size: 4 Copynumber: 29.8 Consensus size: 4
11411184 AAAAAAAAAG
* * *
11411194 ATAA ATAA ATAA TATTAA A-AG ATAA ATAA AT-A AT-A AT-A AT-A ACAG
1 ATAA ATAA ATAA -A-TAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * * *
11411239 ATAA ATTATA ATAT ATAA ATGA ATAA AT-A AT-A ATAA ATAT ATAA CTAG
1 ATAA A-TA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* *
11411287 ATAA ATAAA ATAC ATAT ATAA ATA
1 ATAA AT-AA ATAA ATAA ATAA ATA
11411311 TTAACAGAAA
Statistics
Matches: 86, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
3 19 0.22
4 52 0.60
5 10 0.12
6 5 0.06
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (4 bp):
ATAA
Found at i:11411213 original size:25 final size:24
Alignment explanation
Indices: 11411158--11411231 Score: 60
Period size: 26 Copynumber: 3.0 Consensus size: 24
11411148 ATCAGATAAA
* *
11411158 TAAAAAAAATATTAATAGATAACTAG
1 TAAAAAAAA-ATAAATAAATAA-TAG
* *
11411184 AAAAAAAAAGATAAATAAATAATAT
1 TAAAAAAAA-ATAAATAAATAATAG
*
11411209 TAAAAGATAAATAAAT-AATAATA
1 TAAAA-AAAAATAAATAAATAATA
11411232 ATAACAGATA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 7 0.17
25 12 0.30
26 21 0.52
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.24
Consensus pattern (24 bp):
TAAAAAAAAATAAATAAATAATAG
Found at i:11411215 original size:21 final size:21
Alignment explanation
Indices: 11411189--11411273 Score: 91
Period size: 21 Copynumber: 3.9 Consensus size: 21
11411179 ACTAGAAAAA
11411189 AAAAGATAAATAAATAATAT-T
1 AAAAGATAAAT-AATAATATAT
11411210 AAAAGATAAATAAATAATAATAAT
1 AAAAGATAAAT-AATAAT-AT-AT
* *
11411234 AACAGATAAATTATAATATAT
1 AAAAGATAAATAATAATATAT
*
11411255 AAATGAATAAATAATAATA
1 AAAAG-ATAAATAATAATA
11411274 AATATATAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
21 23 0.42
22 16 0.29
23 5 0.09
24 11 0.20
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAAGATAAATAATAATATAT
Found at i:11411241 original size:45 final size:49
Alignment explanation
Indices: 11411192--11411308 Score: 147
Period size: 45 Copynumber: 2.4 Consensus size: 49
11411182 AGAAAAAAAA
11411192 AGATAAATAAATAATAT-TAAAAG-ATAAATAAATAAT-AATA-ATAAC-
1 AGATAAATAAATAATATATAAAAGAATAAAT-AATAATAAATATATAACT
* *
11411237 AGATAAAT-TATAATATATAAATGAATAAATAATAATAAATATATAACT
1 AGATAAATAAATAATATATAAAAGAATAAATAATAATAAATATATAACT
11411285 AGATAAATAAAATACATATATAAA
1 AGATAAAT-AAATA-ATATATAAA
11411309 TATTAACAGA
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
44 7 0.11
45 19 0.31
46 10 0.16
47 5 0.08
48 8 0.13
50 3 0.05
51 9 0.15
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (49 bp):
AGATAAATAAATAATATATAAAAGAATAAATAATAATAAATATATAACT
Found at i:11411268 original size:26 final size:25
Alignment explanation
Indices: 11411192--11411310 Score: 91
Period size: 24 Copynumber: 5.0 Consensus size: 25
11411182 AGAAAAAAAA
11411192 AGATAAAT-AA-ATAATAT-TAAA-
1 AGATAAATAAATATAATATATAAAT
*
11411213 AGATAAATAAATAATAATA-AT-AAC
1 AGATAAATAAAT-ATAATATATAAAT
11411237 AGATAAAT---TATAATATATAAAT
1 AGATAAATAAATATAATATATAAAT
*
11411259 -GAATAAAT-AATAATAAATATATAACT
1 AG-ATAAATAAAT-AT-AATATATAAAT
11411285 AGATAAATAAA-ATACATATATAAAT
1 AGATAAATAAATATA-ATATATAAAT
11411310 A
1 A
11411311 TTAACAGAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 26
0.73 0.03 0.24
Matches are distributed among these distances:
20 6 0.08
21 12 0.15
22 10 0.12
23 2 0.03
24 17 0.21
25 14 0.17
26 16 0.20
27 3 0.04
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (25 bp):
AGATAAATAAATATAATATATAAAT
Found at i:11411430 original size:25 final size:26
Alignment explanation
Indices: 11411385--11411461 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 26
11411375 TAAATAAATA
* * * *
11411385 AATAATAAATACGTAAGATATAAAGG
1 AATAATATATACATAAAATATAAAAG
*
11411411 AA-AATATATACATAAAATATAAAAT
1 AATAATATATACATAAAATATAAAAG
11411436 AATAATAATAATA-ATAAAATATAAAA
1 AATAAT-AT-ATACATAAAATATAAAA
11411462 TACAAAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
25 20 0.47
26 5 0.12
27 15 0.35
28 3 0.07
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (26 bp):
AATAATATATACATAAAATATAAAAG
Found at i:11411436 original size:20 final size:21
Alignment explanation
Indices: 11411411--11411463 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
11411401 GATATAAAGG
11411411 AAAATATATACATAA-AAT-AT
1 AAAATATATA-ATAATAATAAT
11411431 AAAATA-ATAATAATAATAAT
1 AAAATATATAATAATAATAAT
*
11411451 AAAATATAAAATA
1 AAAATATATAATA
11411464 CAAAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 14 0.48
21 5 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATATATAATAATAATAAT
Found at i:11411437 original size:12 final size:12
Alignment explanation
Indices: 11411411--11411480 Score: 70
Period size: 13 Copynumber: 5.4 Consensus size: 12
11411401 GATATAAAGG
*
11411411 AAAATATATACAT
1 AAAATATA-AAAT
11411424 AAAATATAAAAT
1 AAAATATAAAAT
11411436 AATAATAATAATAAT
1 AA-AAT-ATAA-AAT
11411451 AAAATATAAAAT
1 AAAATATAAAAT
11411463 ACAAA-ATAAAAGT
1 A-AAATATAAAA-T
11411476 AAAAT
1 AAAAT
11411481 TGGGCTTACC
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
12 18 0.36
13 20 0.40
14 7 0.14
15 5 0.10
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (12 bp):
AAAATATAAAAT
Found at i:11416388 original size:71 final size:71
Alignment explanation
Indices: 11416300--11416435 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 71
11416290 ACATGCATTG
* * *
11416300 CATTTGCATTATTGTTTGAACCATACATGTGCATAATTTGGTGAGTATATAGATCATTGTTTTGA
1 CATTTGCATCATCGTTTGAACCATACATGTGCATAACTTGGTGAGTATATAGATCATTGTTTTGA
11416365 AAGTTA
66 AAGTTA
* * * * *
11416371 CATTTGCATCATCGTTTGAACCCTGCATTTGTATTACTTGGTGAGTATATAGATCATTGTTTTGA
1 CATTTGCATCATCGTTTGAACCATACATGTGCATAACTTGGTGAGTATATAGATCATTGTTTTGA
11416436 GTATTGAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.43
Consensus pattern (71 bp):
CATTTGCATCATCGTTTGAACCATACATGTGCATAACTTGGTGAGTATATAGATCATTGTTTTGA
AAGTTA
Found at i:11416447 original size:71 final size:70
Alignment explanation
Indices: 11416296--11416452 Score: 190
Period size: 71 Copynumber: 2.2 Consensus size: 70
11416286 CATTACATGC
* * * *
11416296 ATTGCATTTGCATTATTGTTTGAACCATACATGTGCATAATTTGGTGAGTATATAGATCATTGTT
1 ATTGAATTTGCATCATCGTTTGAACCATACATGTGCATAACTTGGTGAGTATATAGATCATTGTT
11416361 TTGAA
66 TTGAA
* * * * *
11416366 AGTT-ACATTTGCATCATCGTTTGAACCCTGCATTTGTATTACTTGGTGAGTATATAGATCATTG
1 A-TTGA-ATTTGCATCATCGTTTGAACCATACATGTGCATAACTTGGTGAGTATATAGATCATTG
*
11416430 TTTTGAGT
64 TTTTGA-A
11416438 ATTGAATTTGCATCA
1 ATTGAATTTGCATCA
11416453 ATGATTGGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
70 1 0.01
71 70 0.96
72 2 0.03
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (70 bp):
ATTGAATTTGCATCATCGTTTGAACCATACATGTGCATAACTTGGTGAGTATATAGATCATTGTT
TTGAA
Found at i:11416505 original size:71 final size:70
Alignment explanation
Indices: 11416430--11416566 Score: 161
Period size: 70 Copynumber: 1.9 Consensus size: 70
11416420 TAGATCATTG
* * * * *
11416430 TTTTGAGT-ATTGAATTTGCATCAAT-GATTGGATCATACATTTGCGTTATTTAGTGAAGATTTG
1 TTTTGA-TAATTGAATTTGCATC-ATGGATTGGA-CATACATGTGCATCATGTAGTGAACATTTG
11416493 AATCTTTA
63 AATCTTTA
* * *
11416501 TTTTGATAATTGCATTTGCATCATGGTTTGGACATGCATGTGCATCATGTAGTGAACATTTGAAT
1 TTTTGATAATTGAATTTGCATCATGGATTGGACATACATGTGCATCATGTAGTGAACATTTGAAT
11416566 C
66 C
11416567 ATAGTTTAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
70 31 0.55
71 25 0.45
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (70 bp):
TTTTGATAATTGAATTTGCATCATGGATTGGACATACATGTGCATCATGTAGTGAACATTTGAAT
CTTTA
Found at i:11416539 original size:24 final size:23
Alignment explanation
Indices: 11416511--11416619 Score: 73
Period size: 26 Copynumber: 4.6 Consensus size: 23
11416501 TTTTGATAAT
11416511 TGCATTTGCATCATGGTTTGGACA
1 TGCATTTGCATCAT-GTTTGGACA
* *
11416535 TGCATGTGCATCATG-TAGTGA-A
1 TGCATTTGCATCATGTTTG-GACA
* *
11416557 --CATTTGAATCATAGTTTAGAGCA
1 TGCATTTGCATCAT-GTTTGGA-CA
*
11416580 TGCCATTTGCATTATTGTTTAGGACA
1 TG-CATTTGCATCA-TGTTT-GGACA
*
11416606 TGCATTTGTATCAT
1 TGCATTTGCATCAT
11416620 TTAGTGACAA
Statistics
Matches: 64, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
20 10 0.16
21 3 0.05
22 4 0.06
23 4 0.06
24 14 0.22
25 9 0.14
26 17 0.27
27 3 0.05
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (23 bp):
TGCATTTGCATCATGTTTGGACA
Found at i:11416817 original size:39 final size:40
Alignment explanation
Indices: 11416769--11416905 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 40
11416759 TTTGAATAAC
* *
11416769 AAAAGCTTTTCAAGAT-ACGATTTTGAATCCTCAAATAAGT
1 AAAACCTTTTCAAGATGA-GATTTTGAATCCTCAAATAAGA
* * * * * * * *
11416809 AAAACTTTTTCTATATGAGATTTTGATTCTTTAAATGAGG
1 AAAACCTTTTCAAGATGAGATTTTGAATCCTCAAATAAGA
* *
11416849 AAAACCTTTTTAAGATGAGATTTTGAATTCTCAAATAAGA
1 AAAACCTTTTCAAGATGAGATTTTGAATCCTCAAATAAGA
* *
11416889 AAAATC-TTTCATGATGA
1 AAAACCTTTTCAAGATGA
11416906 AATCTTTTAG
Statistics
Matches: 74, Mismatches: 22, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
39 9 0.12
40 64 0.86
41 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (40 bp):
AAAACCTTTTCAAGATGAGATTTTGAATCCTCAAATAAGA
Found at i:11417306 original size:24 final size:23
Alignment explanation
Indices: 11417233--11417376 Score: 73
Period size: 21 Copynumber: 6.3 Consensus size: 23
11417223 ACGAATCCTA
11417233 AAAATTTTCTTGAATGTGAATCTTT
1 AAAA-TTTC-TGAATGTGAATCTTT
* * * *
11417258 GAAATGT-TGGATGTGAATCTCT
1 AAAATTTCTGAATGTGAATCTTT
11417280 AAAATTTCTCGAATGTGAAT-TTT
1 AAAATTTCT-GAATGTGAATCTTT
* * * * *
11417303 TAAATTT-TGGATATAAATCTCT
1 AAAATTTCTGAATGTGAATCTTT
* * *
11417325 AAGATTTTTTAAATGTGAATCTTT
1 AA-AATTTCTGAATGTGAATCTTT
* * *
11417349 GAAATTT-AG-ATGTGAATCTCT
1 AAAATTTCTGAATGTGAATCTTT
*
11417370 AACATTT
1 AAAATTT
11417377 TTCAAATATA
Statistics
Matches: 87, Mismatches: 27, Indels: 14
0.68 0.21 0.11
Matches are distributed among these distances:
21 23 0.26
22 22 0.25
23 17 0.20
24 22 0.25
25 3 0.03
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (23 bp):
AAAATTTCTGAATGTGAATCTTT
Found at i:11417367 original size:45 final size:45
Alignment explanation
Indices: 11417245--11417396 Score: 173
Period size: 45 Copynumber: 3.4 Consensus size: 45
11417235 AATTTTCTTG
* *
11417245 AATGTGAATCTTTGAAATGTTGGATGTGAATCTCTAAAATTTCTCG
1 AATGTGAATCTTTGAAAT-TTGGATGTGAATCTCTAAAATTTTTCA
* * * * *
11417291 AATGTGAAT-TTTTAAATTTTGGATATAAATCTCTAAGATTTTTTA
1 AATGTGAATCTTTGAAA-TTTGGATGTGAATCTCTAAAATTTTTCA
* *
11417336 AATGTGAATCTTTGAAATTTAGATGTGAATCTCTAACATTTTTCA
1 AATGTGAATCTTTGAAATTTGGATGTGAATCTCTAAAATTTTTCA
*
11417381 AATAT-AGATCTTTGAA
1 AATGTGA-ATCTTTGAA
11417397 TTTTTTATGT
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
44 1 0.01
45 72 0.81
46 16 0.18
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (45 bp):
AATGTGAATCTTTGAAATTTGGATGTGAATCTCTAAAATTTTTCA
Found at i:11417430 original size:90 final size:91
Alignment explanation
Indices: 11417238--11417436 Score: 215
Period size: 90 Copynumber: 2.2 Consensus size: 91
11417228 TCCTAAAAAT
* * * *
11417238 TTTCTTGAATGTGAATCTTTGAAATGTTGGATGTGAATCTCTAAAATTTCTCGAATGTGAATTTT
1 TTTCTTGAATGTGAATCTTTGAAATGTTAGATGTGAATCTCTAAAATTTCTCAAATATGAATCTT
*
11417303 TAAATTTTGGATATAAATCTCTAAGA
66 TAAATTTTGGATATAAATATCTAAGA
* * * *
11417329 TTTTTTAAATGTGAATCTTTGAAAT-TTAGATGTGAATCTCTAACATTTTTCAAATAT-AGATCT
1 TTTCTTGAATGTGAATCTTTGAAATGTTAGATGTGAATCTCTAAAATTTCTCAAATATGA-ATCT
* ** * *
11417392 TTGAATTTTTTATGTAAATATGTAA-A
65 TTAAATTTTGGATATAAATATCTAAGA
* *
11417418 GTTTCTGGAATGTAAATCT
1 -TTTCTTGAATGTGAATCT
11417437 CCAAAATTTT
Statistics
Matches: 88, Mismatches: 18, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
89 2 0.02
90 63 0.72
91 23 0.26
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.45
Consensus pattern (91 bp):
TTTCTTGAATGTGAATCTTTGAAATGTTAGATGTGAATCTCTAAAATTTCTCAAATATGAATCTT
TAAATTTTGGATATAAATATCTAAGA
Found at i:11417835 original size:54 final size:54
Alignment explanation
Indices: 11417720--11417962 Score: 195
Period size: 54 Copynumber: 4.5 Consensus size: 54
11417710 ATTTCTTTGT
* * * * * *
11417720 GAATCTTTGAAATCTTGCAAACCTTTGAATTTTTA-GAAATCCTTGAGTTCTCAC
1 GAATCTTTGAAATCTTGCAAATCTTTGAAATCTTACG-AATCTTTGAATTCTTAC
* * * * *
11417774 -AAGTCTTTAAAATCTTGCAAACCTTTGAAATCTTACGAATTTTTAAATTCTTGC
1 GAA-TCTTTGAAATCTTGCAAATCTTTGAAATCTTACGAATCTTTGAATTCTTAC
** ** ** * *
11417828 GAATCTTTGAGTTCTTGTGAATCTTTGAAATCTTGTGAACCTTTGAATTCTTGC
1 GAATCTTTGAAATCTTGCAAATCTTTGAAATCTTACGAATCTTTGAATTCTTAC
* ** * * *
11417882 GAATATTTGAGTTCTTGTGATATCTTTGAAATCTTACGAATCTTTGAATTCTTAT
1 GAATCTTTGAAATCTTG-CAAATCTTTGAAATCTTACGAATCTTTGAATTCTTAC
*
11417937 GAA-CTTTGAAAATTTTGCAAATCTTT
1 GAATCTTTG-AAATCTTGCAAATCTTT
11417963 AAGCTCTTTT
Statistics
Matches: 149, Mismatches: 35, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
53 2 0.01
54 107 0.72
55 40 0.27
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.43
Consensus pattern (54 bp):
GAATCTTTGAAATCTTGCAAATCTTTGAAATCTTACGAATCTTTGAATTCTTAC
Found at i:11417852 original size:9 final size:8
Alignment explanation
Indices: 11417828--11417946 Score: 60
Period size: 9 Copynumber: 13.4 Consensus size: 8
11417818 AAATTCTTGC
11417828 GAATCTTT
1 GAATCTTT
*
11417836 GAGTTCTTGT
1 GA-ATCTT-T
11417846 GAATCTTT
1 GAATCTTT
11417854 GAAATCTTGT
1 G-AATCTT-T
*
11417864 GAACCTTT
1 GAATCTTT
*
11417872 GAATTCTTGC
1 GAA-TCTT-T
*
11417882 GAATATTT
1 GAATCTTT
*
11417890 GAGTTCTTGT
1 GA-ATCTT-T
11417900 GATATCTTT
1 GA-ATCTTT
*
11417909 GAAATCTTAC
1 G-AATCTT-T
11417919 GAATCTTT
1 GAATCTTT
11417927 GAATTCTTAT
1 GAA-TCTT-T
11417937 GAA-CTTT
1 GAATCTTT
11417944 GAA
1 GAA
11417947 AATTTTGCAA
Statistics
Matches: 86, Mismatches: 13, Indels: 25
0.69 0.10 0.20
Matches are distributed among these distances:
7 4 0.05
8 16 0.19
9 45 0.52
10 21 0.24
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (8 bp):
GAATCTTT
Found at i:11417935 original size:18 final size:18
Alignment explanation
Indices: 11417720--11417934 Score: 146
Period size: 18 Copynumber: 11.9 Consensus size: 18
11417710 ATTTCTTTGT
*
11417720 GAATCTTTGAAATCTTGC
1 GAATCTTTGAATTCTTGC
* * *
11417738 AAACCTTTGAATTTTTAG-
1 GAATCTTTGAATTCTT-GC
* * * **
11417756 AAATCCTTGAGTTCTCAC
1 GAATCTTTGAATTCTTGC
* *
11417774 -AAGTCTTTAAAATCTTGC
1 GAA-TCTTTGAATTCTTGC
* * * *
11417792 AAACCTTTGAAATCTTAC
1 GAATCTTTGAATTCTTGC
* *
11417810 GAATTTTTAAATTCTTGC
1 GAATCTTTGAATTCTTGC
* *
11417828 GAATCTTTGAGTTCTTGT
1 GAATCTTTGAATTCTTGC
* *
11417846 GAATCTTTGAAATCTTGT
1 GAATCTTTGAATTCTTGC
*
11417864 GAACCTTTGAATTCTTGC
1 GAATCTTTGAATTCTTGC
* * *
11417882 GAATATTTGAGTTCTTGT
1 GAATCTTTGAATTCTTGC
* *
11417900 GATATCTTTGAAATCTTAC
1 GA-ATCTTTGAATTCTTGC
11417919 GAATCTTTGAATTCTT
1 GAATCTTTGAATTCTT
11417935 ATGAACTTTG
Statistics
Matches: 148, Mismatches: 44, Indels: 10
0.73 0.22 0.05
Matches are distributed among these distances:
17 2 0.01
18 130 0.88
19 16 0.11
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (18 bp):
GAATCTTTGAATTCTTGC
Found at i:11418396 original size:19 final size:19
Alignment explanation
Indices: 11418361--11418400 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
11418351 TTACTTATAT
*
11418361 TTTTATTTTTTTCTTTTAC
1 TTTTATTTTATTCTTTTAC
11418380 TTTTATTTTCATT-TTTTAC
1 TTTTATTTT-ATTCTTTTAC
11418399 TT
1 TT
11418401 CTCATCTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATTTTATTCTTTTAC
Found at i:11423955 original size:40 final size:40
Alignment explanation
Indices: 11423900--11423979 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
11423890 TAGCACGCTG
11423900 ACCAATAATAAGCTTGGTTTTTGCTGTTAACATCAAAGTC
1 ACCAATAATAAGCTTGGTTTTTGCTGTTAACATCAAAGTC
11423940 ACCAATAATAAGCTTGGTTTTTGCTGTTAACATCAAAGTC
1 ACCAATAATAAGCTTGGTTTTTGCTGTTAACATCAAAGTC
11423980 GCAGTAAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (40 bp):
ACCAATAATAAGCTTGGTTTTTGCTGTTAACATCAAAGTC
Found at i:11424132 original size:2 final size:2
Alignment explanation
Indices: 11424125--11424151 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11424115 TGAGCTAAAC
11424125 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 T
11424152 TTGACTTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11431902 original size:15 final size:15
Alignment explanation
Indices: 11431882--11431918 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
11431872 TATTATTATT
11431882 ATTATCATCATCATC
1 ATTATCATCATCATC
*
11431897 ATTATCATCATCATT
1 ATTATCATCATCATC
11431912 ATTATCA
1 ATTATCA
11431919 GTATTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTATCATCATCATC
Found at i:11432261 original size:23 final size:22
Alignment explanation
Indices: 11432209--11432273 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
11432199 AACAATTCAC
11432209 GAGTTAATTTTT-AGAAAAGAA
1 GAGTTAATTTTTGAGAAAAGAA
* *
11432230 GGGTGAATTTTTAGAGAAAAGATA
1 GAGTTAATTTTT-GAGAAAAGA-A
11432254 -AGTTAATTATTTGGAGAAAA
1 GAGTTAATT-TTT-GAGAAAA
11432274 TATTTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 10 0.29
23 14 0.40
24 11 0.31
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
GAGTTAATTTTTGAGAAAAGAA
Found at i:11432366 original size:27 final size:26
Alignment explanation
Indices: 11432327--11432390 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
11432317 ATTTTTCAGG
** *
11432327 GTTTGAATTTCTAGATTTTGATTTGAA
1 GTTTGAAAATCTAGATTTAGATTT-AA
*
11432354 GTTTGAAAATCTAGGTTTAGATTTAA
1 GTTTGAAAATCTAGATTTAGATTTAA
11432380 GCTTTTGAAAA
1 G--TTTGAAAA
11432391 ATTTTTGGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 3 0.10
27 20 0.65
28 8 0.26
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (26 bp):
GTTTGAAAATCTAGATTTAGATTTAA
Found at i:11432404 original size:41 final size:41
Alignment explanation
Indices: 11432359--11432458 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 41
11432349 TTGAAGTTTG
* * * *
11432359 AAAATCTAGGTTTAGATTTAAGCTTT-TGAAAAATTTTTGGA
1 AAAATCTAGGTTTAGATTTAA-ATTTCTAAAAAATTTCTAGA
* * *
11432400 AAAATCTGGGTCTAGGTTTAAATTTCTAAAAAATTTCTAGA
1 AAAATCTAGGTTTAGATTTAAATTTCTAAAAAATTTCTAGA
* *
11432441 AAAATCTAAGTTTGGATT
1 AAAATCTAGGTTTAGATT
11432459 GAATGTTTGA
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
40 3 0.07
41 43 0.93
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (41 bp):
AAAATCTAGGTTTAGATTTAAATTTCTAAAAAATTTCTAGA
Found at i:11432755 original size:11 final size:10
Alignment explanation
Indices: 11432739--11432805 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
11432729 TGATTGAAGG
*
11432739 TTTTTTTTCT
1 TTTTTTTTAT
*
11432749 ATTTTTTTAT
1 TTTTTTTTAT
11432759 TTTTATTTTA-
1 TTTT-TTTTAT
* *
11432769 TTTTTTATCT
1 TTTTTTTTAT
*
11432779 TTTTTCTTAT
1 TTTTTTTTAT
*
11432789 TTTATTTTAT
1 TTTTTTTTAT
11432799 TGTTTTT
1 T-TTTTT
11432806 AAATTAAGTA
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
9 3 0.07
10 31 0.72
11 9 0.21
ACGTcount: A:0.12, C:0.04, G:0.01, T:0.82
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:11432770 original size:19 final size:18
Alignment explanation
Indices: 11432739--11432805 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 18
11432729 TGATTGAAGG
11432739 TTTTTTTTCTATTTTTTTA
1 TTTTTTTT-TATTTTTTTA
11432758 TTTTTATTTTA-TTTTTTA
1 TTTTT-TTTTATTTTTTTA
11432776 TCTTTTTTCTTATTTTATTTTA
1 T-TTTTTT-TTA-TTT-TTTTA
11432798 TTGTTTTT
1 TT-TTTTT
11432806 AAATTAAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
18 10 0.24
19 14 0.34
20 3 0.07
21 3 0.07
22 11 0.27
ACGTcount: A:0.12, C:0.04, G:0.01, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTATTTTTTTA
Found at i:11432782 original size:29 final size:30
Alignment explanation
Indices: 11432739--11432804 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
11432729 TGATTGAAGG
*
11432739 TTTTTTTTCTATTTTT-TTATTTTTATTTTA
1 TTTTTTATCTATTTTTCTTA-TTTTATTTTA
11432769 TTTTTTATCT-TTTTTCTTATTTTATTTTA
1 TTTTTTATCTATTTTTCTTATTTTATTTTA
11432798 TTGTTTT
1 TT-TTTT
11432805 TAAATTAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.82
Consensus pattern (30 bp):
TTTTTTATCTATTTTTCTTATTTTATTTTA
Found at i:11454083 original size:7 final size:7
Alignment explanation
Indices: 11454071--11454096 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11454061 TAAATTTAAA
11454071 AATTTTT
1 AATTTTT
11454078 AATTTTT
1 AATTTTT
11454085 AATTTTT
1 AATTTTT
11454092 AATTT
1 AATTT
11454097 AAAAATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:11458100 original size:21 final size:21
Alignment explanation
Indices: 11458074--11458127 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
11458064 AAACCCAGAA
**
11458074 AAGGGATCGATCCTTTCATAT
1 AAGGGATCGATCCCCTCATAT
11458095 AAGGGATCGATCCCCTCATAT
1 AAGGGATCGATCCCCTCATAT
11458116 -AGGAGATCGATC
1 AAGG-GATCGATC
11458128 ACCTAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.10
21 27 0.90
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (21 bp):
AAGGGATCGATCCCCTCATAT
Found at i:11465665 original size:20 final size:20
Alignment explanation
Indices: 11465640--11465678 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11465630 TGAAAATCTG
*
11465640 ATGATGTTTTGATATTGATA
1 ATGATGCTTTGATATTGATA
11465660 ATGATGCTTTGATATTGAT
1 ATGATGCTTTGATATTGAT
11465679 GGATATATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (20 bp):
ATGATGCTTTGATATTGATA
Found at i:11466056 original size:21 final size:21
Alignment explanation
Indices: 11466030--11466069 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11466020 AAGTTTTGAT
11466030 AGAAGGGATCGATCCCCTCAA
1 AGAAGGGATCGATCCCCTCAA
*
11466051 AGAAGGGATCGATCTCCTC
1 AGAAGGGATCGATCCCCTC
11466070 TATTACCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (21 bp):
AGAAGGGATCGATCCCCTCAA
Found at i:11470951 original size:18 final size:18
Alignment explanation
Indices: 11470928--11470963 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11470918 AAACATTGGC
*
11470928 ATGAAAATTTGATGATGT
1 ATGAAAATCTGATGATGT
11470946 ATGAAAATCTGATGATGT
1 ATGAAAATCTGATGATGT
11470964 TTTTATATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
ATGAAAATCTGATGATGT
Found at i:11470982 original size:20 final size:20
Alignment explanation
Indices: 11470957--11470995 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11470947 TGAAAATCTG
* *
11470957 ATGATGTTTTTATATTGATA
1 ATGATGCTTTGATATTGATA
11470977 ATGATGCTTTGATATTGAT
1 ATGATGCTTTGATATTGAT
11470996 GGATATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.51
Consensus pattern (20 bp):
ATGATGCTTTGATATTGATA
Found at i:11471398 original size:20 final size:21
Alignment explanation
Indices: 11471349--11471401 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
11471339 GTTTTGATAG
**
11471349 AAAGGATCGATCCCCTCAGGG
1 AAAGGATCGATCCCCTCAGCA
*
11471370 AAGGGATCGATCCCCT-AGCA
1 AAAGGATCGATCCCCTCAGCA
11471390 AAAGGATCGATC
1 AAAGGATCGATC
11471402 ATGTTTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.15
Consensus pattern (21 bp):
AAAGGATCGATCCCCTCAGCA
Found at i:11474636 original size:13 final size:13
Alignment explanation
Indices: 11474618--11474646 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
11474608 AAAAATTATT
11474618 TTTTAATTATTTA
1 TTTTAATTATTTA
11474631 TTTTAATTATTTA
1 TTTTAATTATTTA
11474644 TTT
1 TTT
11474647 ATATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTAATTATTTA
Found at i:11474659 original size:8 final size:8
Alignment explanation
Indices: 11474648--11474688 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
11474638 TATTTATTTA
11474648 TATATATT
1 TATATATT
*
11474656 TATATAGT
1 TATATATT
11474664 TATATATT
1 TATATATT
*
11474672 TAAATATT
1 TATATATT
11474680 TATAT-TT
1 TATATATT
11474687 TA
1 TA
11474689 AAAATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
TATATATT
Found at i:11474708 original size:21 final size:21
Alignment explanation
Indices: 11474674--11474724 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
11474664 TATATATTTA
11474674 AATA-TTTATATTTTAAAAAT
1 AATATTTTATATTTTAAAAAT
*
11474694 AATATTTTATGTTTTAAAAAT
1 AATATTTTATATTTTAAAAAT
11474715 AATATTTTAT
1 AATATTTTAT
11474725 TAATTTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
AATATTTTATATTTTAAAAAT
Found at i:11477486 original size:12 final size:12
Alignment explanation
Indices: 11477469--11477505 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
11477459 AGTATAGTAT
*
11477469 TAATAATTTTAA
1 TAATAATATTAA
11477481 TAATAATATTAA
1 TAATAATATTAA
*
11477493 TAATAATAATAA
1 TAATAATATTAA
11477505 T
1 T
11477506 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:11477505 original size:30 final size:33
Alignment explanation
Indices: 11477469--11477531 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
11477459 AGTATAGTAT
*
11477469 TAATAA-TTTT-AATAATAA-TATTAATAATAA
1 TAATAATTTTTAAAAAATAATTATTAATAATAA
*
11477499 TAATAATTTTTAAAAAATAATTATTAATTATAA
1 TAATAATTTTTAAAAAATAATTATTAATAATAA
11477532 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 6 0.21
31 4 0.14
32 7 0.25
33 11 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
TAATAATTTTTAAAAAATAATTATTAATAATAA
Found at i:11477519 original size:20 final size:20
Alignment explanation
Indices: 11477494--11477544 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
11477484 TAATATTAAT
* *
11477494 AATAATAATAATTTTTAAAA
1 AATAATAATAATTATAAAAA
*
11477514 AATAATTATTAATTATAAAAA
1 AATAA-TAATAATTATAAAAA
11477535 AATAA-AATAA
1 AATAATAATAA
11477545 AAAATAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 5 0.19
21 17 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AATAATAATAATTATAAAAA
Found at i:11477553 original size:11 final size:12
Alignment explanation
Indices: 11477531--11477564 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
11477521 ATTAATTATA
11477531 AAAAAATAAAAT
1 AAAAAATAAAAT
11477543 AAAAAAT-AAAT
1 AAAAAATAAAAT
*
11477554 AAAAAACAAAA
1 AAAAAATAAAA
11477565 AAAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:11477564 original size:16 final size:15
Alignment explanation
Indices: 11477530--11477567 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
11477520 TATTAATTAT
11477530 AAAAAAATAAAATAA
1 AAAAAAATAAAATAA
11477545 AAAATAAATAAAA-AA
1 AAAA-AAATAAAATAA
11477560 CAAAAAAA
1 -AAAAAAA
11477568 GAGAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAAATAAAATAA
Found at i:11478578 original size:17 final size:19
Alignment explanation
Indices: 11478552--11478591 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
11478542 TTTTTTTGAA
11478552 TTTTGTTTATATT-AGTAT
1 TTTTGTTTATATTAAGTAT
*
11478570 TTTTG-TTATTTTAAGTAT
1 TTTTGTTTATATTAAGTAT
11478588 TTTT
1 TTTT
11478592 TTAGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (19 bp):
TTTTGTTTATATTAAGTAT
Found at i:11478992 original size:17 final size:16
Alignment explanation
Indices: 11478970--11479122 Score: 84
Period size: 16 Copynumber: 9.6 Consensus size: 16
11478960 TAAAACCCCA
11478970 AAAATCCAAAATCTCCT
1 AAAATCCAAAA-CTCCT
**
11478987 AAAATCTTAAA-TCCT
1 AAAATCCAAAACTCCT
*
11479002 AAAATCCATAA-TCCTT
1 AAAATCCAAAACTCC-T
* * *
11479018 TAAAT-CGAAACCCCTT
1 AAAATCCAAAACTCC-T
* *
11479034 AAAATCCGAAACCCCTT
1 AAAATCCAAAACTCC-T
* *
11479051 AAAATTCAAACCTCCT
1 AAAATCCAAAACTCCT
* * *
11479067 AAAGTCCGAAACCCCT
1 AAAATCCAAAACTCCT
*
11479083 AAAATCCAAACCT-C-
1 AAAATCCAAAACTCCT
*
11479097 AAATTCCAAAA-TCCTT
1 AAAATCCAAAACTCC-T
11479113 AAAATCCAAA
1 AAAATCCAAA
11479123 CCCTTAAATC
Statistics
Matches: 104, Mismatches: 26, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
13 1 0.01
14 10 0.10
15 19 0.18
16 43 0.41
17 31 0.30
ACGTcount: A:0.45, C:0.29, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAATCCAAAACTCCT
Found at i:11479075 original size:33 final size:33
Alignment explanation
Indices: 11479019--11479096 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
11479009 ATAATCCTTT
*
11479019 AAATCGAAACC-CCTTAAAATCCGAAACCCCTTA
1 AAATCCAAACCTCCTTAAAATCCGAAACCCC-TA
* *
11479052 AAATTCAAACCTCC-TAAAGTCCGAAACCCCTA
1 AAATCCAAACCTCCTTAAAATCCGAAACCCCTA
11479084 AAATCCAAACCTC
1 AAATCCAAACCTC
11479097 AAATTCCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 14 0.35
33 24 0.60
34 2 0.05
ACGTcount: A:0.42, C:0.35, G:0.05, T:0.18
Consensus pattern (33 bp):
AAATCCAAACCTCCTTAAAATCCGAAACCCCTA
Found at i:11479129 original size:15 final size:15
Alignment explanation
Indices: 11479001--11479139 Score: 102
Period size: 16 Copynumber: 8.9 Consensus size: 15
11478991 TCTTAAATCC
*
11479001 TAAAATCCATAATCCT
1 TAAAATCCA-AACCCT
* *
11479017 TTAAATCGAAACCCCT
1 TAAAATCCAAA-CCCT
11479033 TAAAATCCGAAACCCCT
1 TAAAATCC-AAA-CCCT
* *
11479050 TAAAATTCAAACCTCC
1 TAAAATCCAAACC-CT
* *
11479066 TAAAGTCCGAAACCCC
1 TAAAATCC-AAACCCT
11479082 TAAAATCCAAA-CCT
1 TAAAATCCAAACCCT
* * *
11479096 CAAATTCCAAAATCCT
1 TAAAATCC-AAACCCT
11479112 TAAAATCCAAACCCT
1 TAAAATCCAAACCCT
*
11479127 T-AAATCAAAACCC
1 TAAAATCCAAACCC
11479140 CAAACCTCAA
Statistics
Matches: 100, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
14 19 0.19
15 17 0.17
16 44 0.44
17 20 0.20
ACGTcount: A:0.44, C:0.32, G:0.03, T:0.22
Consensus pattern (15 bp):
TAAAATCCAAACCCT
Found at i:11479148 original size:51 final size:50
Alignment explanation
Indices: 11479088--11479197 Score: 132
Period size: 51 Copynumber: 2.2 Consensus size: 50
11479078 CCCCTAAAAT
* *
11479088 CCAAACCTCAAATTCCAAAATCCTTAAAATC-CAAACCCTTAAATCAAAACC
1 CCAAACCTCAAA-ACCAAAATCC-TAAAATCTCAAACCCTAAAATCAAAACC
* * *
11479139 CCAAACCTCAAAACCCAAATCCTAAAATCTTCAAACTCTAAAATTAAAACC
1 CCAAACCTCAAAACCAAAATCCTAAAATC-TCAAACCCTAAAATCAAAACC
*
11479190 CTAAACCT
1 CCAAACCT
11479198 TTCATATCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
49 7 0.14
50 8 0.16
51 36 0.71
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (50 bp):
CCAAACCTCAAAACCAAAATCCTAAAATCTCAAACCCTAAAATCAAAACC
Found at i:11480375 original size:21 final size:22
Alignment explanation
Indices: 11480349--11480395 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11480339 CAATAGTTAG
*
11480349 ATTTAA-TTGATTTTATTTTAT
1 ATTTAATTTAATTTTATTTTAT
*
11480370 ATTTAATTTAATTTTTTTTTAT
1 ATTTAATTTAATTTTATTTTAT
11480392 -TTTA
1 ATTTA
11480396 TTTTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTAATTTAATTTTATTTTAT
Found at i:11487232 original size:33 final size:33
Alignment explanation
Indices: 11487190--11487698 Score: 613
Period size: 33 Copynumber: 15.5 Consensus size: 33
11487180 AAAAAAAAAA
* *
11487190 CTTTAAGCCCAGTTTATTTGGCCATCAATAAAG
1 CTTTAAGCCCAGTTTATCTGGCCATCAATGAAG
11487223 CTTTAAGCCCAGTTTATCTGGCC-TCAAATGAAG
1 CTTTAAGCCCAGTTTATCTGGCCATC-AATGAAG
* * *
11487256 TTTTAAGCCTAATTTATCTGGCCATCAATGAAG
1 CTTTAAGCCCAGTTTATCTGGCCATCAATGAAG
* *
11487289 CTTTAAGCCTAGTTTATCTGGCC-TCAAATAAAG
1 CTTTAAGCCCAGTTTATCTGGCCATC-AATGAAG
* * * * *
11487322 ATTTAAGCCTAGTTTATTTGGCCGTCAATGAAA
1 CTTTAAGCCCAGTTTATCTGGCCATCAATGAAG
* *
11487355 CTTTAAGCCCAGTTGATCTGGTCATCAATG-A-
1 CTTTAAGCCCAGTTTATCTGGCCATCAATGAAG
*
11487386 CATTTAAGCCCAATTTATCTGGCCATCAATGAAG
1 C-TTTAAGCCCAGTTTATCTGGCCATCAATGAAG
*
11487420 CTTTAAGCCCAGTTTATCTGGTCATCAATG-A-
1 CTTTAAGCCCAGTTTATCTGGCCATCAATGAAG
*
11487451 CATTTAAGCCCAGTTTATCTGGCCATTAATGAAG
1 C-TTTAAGCCCAGTTTATCTGGCCATCAATGAAG
* *
11487485 TTTTAAGCCCAGTTTATATGGCC-TCAAATGAAG
1 CTTTAAGCCCAGTTTATCTGGCCATC-AATGAAG
*
11487518 TTTTAAGCCCAGTTTATCTGGCCATCAATGAAG
1 CTTTAAGCCCAGTTTATCTGGCCATCAATGAAG
* * *
11487551 CTTTAAACCCAGTTTATTTGGCC-TCAAATAAAG
1 CTTTAAGCCCAGTTTATCTGGCCATC-AATGAAG
* *
11487584 ATTTAAGCCCATTTTATCTGGCCATCAATGAAG
1 CTTTAAGCCCAGTTTATCTGGCCATCAATGAAG
* *
11487617 CTTTAAGTCCAGTTTATCTGACCATCAATGAAG
1 CTTTAAGCCCAGTTTATCTGGCCATCAATGAAG
* * *
11487650 TTTTAAGCCCAATTTATCTGACC-TCAAATGAAG
1 CTTTAAGCCCAGTTTATCTGGCCATC-AATGAAG
*
11487683 TTTTAAGCCCAGTTTA
1 CTTTAAGCCCAGTTTA
11487699 GTTGGCTTTC
Statistics
Matches: 415, Mismatches: 46, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
31 2 0.00
32 64 0.15
33 340 0.82
34 9 0.02
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (33 bp):
CTTTAAGCCCAGTTTATCTGGCCATCAATGAAG
Found at i:11488777 original size:22 final size:22
Alignment explanation
Indices: 11488752--11488795 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
11488742 ATCAATTCTG
* *
11488752 TAAGACCTTCGGGCATGATTTC
1 TAAGACCTCCGGGCATAATTTC
11488774 TAAGACCTCCGGGCATAATTTC
1 TAAGACCTCCGGGCATAATTTC
11488796 AATTCCCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (22 bp):
TAAGACCTCCGGGCATAATTTC
Found at i:11488778 original size:111 final size:111
Alignment explanation
Indices: 11488634--11488860 Score: 269
Period size: 111 Copynumber: 2.0 Consensus size: 111
11488624 ATCTCAATTG
* * * *
11488634 ATTCTGTAAGACCTCCGGACATGATTCTGTAAGACTTTCGGGCATAAATT-AGATTCGCGATATT
1 ATTCTGTAAGACCTCCGGACATGATTCTCTAAGACCTCCGGGCATAAATTCA-ATTCCCGATATT
* *
11488698 ATATCGATCGATTCCTTATTTTTTTGACTTGCGGTATTATCCCGATCA
65 ATATCGATCGATTCCTTA-TCTTTCGACTTGCGGTATTATCCCGATCA
* * * *
11488746 ATTCTGTAAGACCTTCGGGCATGATT-TCTAAGACCTCCGGGCATAATTTCAATTCCCGATGTTA
1 ATTCTGTAAGACCTCCGGACATGATTCTCTAAGACCTCCGGGCATAAATTCAATTCCCGATATTA
* * ** * * *
11488810 TCTTGATCGATTTTTTATCTTTCGACTTGTGGTGTTATCCCGATCG
66 TATCGATCGATTCCTTATCTTTCGACTTGCGGTATTATCCCGATCA
11488856 ATTCT
1 ATTCT
11488861 TTATCTTTCG
Statistics
Matches: 97, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
110 29 0.30
111 43 0.44
112 25 0.26
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (111 bp):
ATTCTGTAAGACCTCCGGACATGATTCTCTAAGACCTCCGGGCATAAATTCAATTCCCGATATTA
TATCGATCGATTCCTTATCTTTCGACTTGCGGTATTATCCCGATCA
Found at i:11488855 original size:37 final size:37
Alignment explanation
Indices: 11488805--11488897 Score: 143
Period size: 37 Copynumber: 2.5 Consensus size: 37
11488795 CAATTCCCGA
** *
11488805 TGTTATCTTGATCGATTTTTTATCTTTCGACTTGTGG
1 TGTTATCCCGATCGATTCTTTATCTTTCGACTTGTGG
11488842 TGTTATCCCGATCGATTCTTTATCTTTCGACTTGTGG
1 TGTTATCCCGATCGATTCTTTATCTTTCGACTTGTGG
11488879 TGTTATCCC-AGTCGATTCT
1 TGTTATCCCGA-TCGATTCT
11488898 GTAAGACCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
36 1 0.02
37 51 0.98
ACGTcount: A:0.14, C:0.19, G:0.18, T:0.48
Consensus pattern (37 bp):
TGTTATCCCGATCGATTCTTTATCTTTCGACTTGTGG
Found at i:11489179 original size:21 final size:20
Alignment explanation
Indices: 11489137--11489180 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
11489127 GTATTAATAA
*
11489137 TTTTAATAATAATAATAATAAT
1 TTTTAA-AA-AATAATATTAAT
11489159 TTTTAAAAAATAATTATTAAT
1 TTTTAAAAAATAA-TATTAAT
11489180 T
1 T
11489181 ATAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTAAAAAATAATATTAAT
Found at i:11489206 original size:16 final size:15
Alignment explanation
Indices: 11489183--11489229 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
11489173 TATTAATTAT
11489183 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
*
11489198 AATAAAAAAACAAAA
1 AAAAAAAAAACAAAA
11489213 AAAAAGAAAAACAAAA
1 AAAAA-AAAAACAAAA
11489229 A
1 A
11489230 GTATGGTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.89, C:0.06, G:0.02, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAACAAAA
Found at i:11490614 original size:16 final size:16
Alignment explanation
Indices: 11490595--11490774 Score: 140
Period size: 16 Copynumber: 11.5 Consensus size: 16
11490585 CTAGGTTTCT
11490595 AAAACCCCTAAAATCC
1 AAAACCCCTAAAATCC
*
11490611 AAAATCTCCTAAAATCC
1 AAAA-CCCCTAAAATCC
* *
11490628 AAAA-TCCTAAAATTC
1 AAAACCCCTAAAATCC
* *
11490643 GAAACCCCTAAAAATCT
1 AAAACCCCT-AAAATCC
* *
11490660 AAAATCCCTTAAATCC
1 AAAACCCCTAAAATCC
*
11490676 -AAACCCCATAAAATGC
1 AAAACCCC-TAAAATCC
* *
11490692 AAACCCCCTAAAATTC
1 AAAACCCCTAAAATCC
* *
11490708 GAAGCCCCTAAAATCC
1 AAAACCCCTAAAATCC
* *
11490724 -AAACCTC-AAAATCA
1 AAAACCCCTAAAATCC
*
11490738 AAAATCCCTAAAATCC
1 AAAACCCCTAAAATCC
*
11490754 -AAA-CCCTTAAAT-C
1 AAAACCCCTAAAATCC
11490767 AAAACCCC
1 AAAACCCC
11490775 AAACCCTAAA
Statistics
Matches: 130, Mismatches: 25, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
13 1 0.01
14 17 0.13
15 35 0.27
16 44 0.34
17 33 0.25
ACGTcount: A:0.48, C:0.32, G:0.02, T:0.18
Consensus pattern (16 bp):
AAAACCCCTAAAATCC
Found at i:11490808 original size:37 final size:35
Alignment explanation
Indices: 11490713--11490816 Score: 94
Period size: 37 Copynumber: 3.1 Consensus size: 35
11490703 AATTCGAAGC
*
11490713 CCCTAAAATCCAAA-CCTCAAAATC-AAA----AAT
1 CCCTAAAATCCAAACCCT-AAAATCAAAACCCCAAA
*
11490743 CCCTAAAATCCAAACCCTTAAATCAAAACCCCAAA
1 CCCTAAAATCCAAACCCTAAAATCAAAACCCCAAA
* * *
11490778 CCCTAAAATCTTCAAACTCTAAAATTAAAACCCTAAA
1 CCCTAAAATC--CAAACCCTAAAATCAAAACCCCAAA
11490815 CC
1 CC
11490817 TTCCATATCC
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
30 19 0.32
31 6 0.10
35 12 0.20
37 23 0.38
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (35 bp):
CCCTAAAATCCAAACCCTAAAATCAAAACCCCAAA
Found at i:11493100 original size:26 final size:26
Alignment explanation
Indices: 11493044--11493093 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
11493034 GGTTTTCTTT
*
11493044 ATAAAAGATCCACTTTTAGGATTTTC
1 ATAAAAGATCCACTTTTAAGATTTTC
* *
11493070 ATAAATGATCCATTTTTAAGATTT
1 ATAAAAGATCCACTTTTAAGATTT
11493094 CTTTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (26 bp):
ATAAAAGATCCACTTTTAAGATTTTC
Found at i:11496389 original size:63 final size:63
Alignment explanation
Indices: 11496321--11496449 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 63
11496311 AATATGTTGG
11496321 TTAACAGTTTACAAGTATCTAATCCGACAAAATCAAACACAATAATACCAAATAGCTATTTAT
1 TTAACAGTTTACAAGTATCTAATCCGACAAAATCAAACACAATAATACCAAATAGCTATTTAT
*
11496384 TTAACAGTTTACAAGTATCTAATCCGACAAAATCAAACACAATAATACCAAATATCTATTTAT
1 TTAACAGTTTACAAGTATCTAATCCGACAAAATCAAACACAATAATACCAAATAGCTATTTAT
11496447 TTA
1 TTA
11496450 TCATCCATCG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (63 bp):
TTAACAGTTTACAAGTATCTAATCCGACAAAATCAAACACAATAATACCAAATAGCTATTTAT
Found at i:11498841 original size:13 final size:13
Alignment explanation
Indices: 11498823--11498847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11498813 GAATCAGAAA
11498823 AAGTCTACATTGG
1 AAGTCTACATTGG
11498836 AAGTCTACATTG
1 AAGTCTACATTG
11498848 AAACAGATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
AAGTCTACATTGG
Found at i:11502172 original size:2 final size:2
Alignment explanation
Indices: 11502165--11502192 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11502155 TCTTTGTAAC
11502165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11502193 GTACACTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.