Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_pilon, 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: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 32
Found at i:2541755 original size:25 final size:25
Alignment explanation
Indices: 2541722--2541770 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2541712 TATTAATTTT
*
2541722 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
2541747 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
2541771 CGACTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:2541854 original size:7 final size:7
Alignment explanation
Indices: 2541842--2541868 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2541832 ATTTTTGGTT
2541842 CAATGAA
1 CAATGAA
2541849 CAATGAA
1 CAATGAA
2541856 CAATGAA
1 CAATGAA
2541863 CAATGA
1 CAATGA
2541869 TTTAGTAATA
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:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
CAATGAA
Found at i:2541903 original size:26 final size:26
Alignment explanation
Indices: 2541864--2542001 Score: 103
Period size: 26 Copynumber: 5.5 Consensus size: 26
2541854 AACAATGAAC
*
2541864 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAATAATAATCATTATAAA
*
2541890 AATGA-TT--TAATAATGATT-T--A
1 AATGATTTAATAATAATCATTATAAA
* * * **
2541910 AAT-ATTTAATGATTTGATGATT-TAGT
1 AATGATTTAAT-A-ATAATCATTATAAA
* **
2541936 AATGATTTGATAATAATCATTATAGT
1 AATGATTTAATAATAATCATTATAAA
*
2541962 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAATAATAATCATTATAAA
2541988 AATGATTTAATAAT
1 AATGATTTAATAAT
2542002 GATTTAAATA
Statistics
Matches: 90, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
19 1 0.01
20 6 0.07
22 2 0.02
23 11 0.12
24 8 0.09
25 8 0.09
26 48 0.53
27 6 0.07
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (26 bp):
AATGATTTAATAATAATCATTATAAA
Found at i:2542033 original size:98 final size:98
Alignment explanation
Indices: 2541864--2542082 Score: 404
Period size: 98 Copynumber: 2.2 Consensus size: 98
2541854 AACAATGAAC
2541864 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
1 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
*
2541929 ATTTAGTAATGATTTGATAATAATCATTATAGT
66 ATTTAGTAATGATTTGATAATAATCATTATAAT
2541962 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
1 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
2542027 ATTTAGTAATGATTTGATAATAATCATTATAAT
66 ATTTAGTAATGATTTGATAATAATCATTATAAT
*
2542060 AATGATTTTA-TAATAATTATTAT
1 AATGA-TTTAGTAATAATCATTAT
2542083 GTTATTATTT
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
98 114 0.97
99 4 0.03
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (98 bp):
AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
ATTTAGTAATGATTTGATAATAATCATTATAAT
Found at i:2542062 original size:26 final size:26
Alignment explanation
Indices: 2541935--2542082 Score: 121
Period size: 26 Copynumber: 5.9 Consensus size: 26
2541925 GATGATTTAG
*
2541935 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
2541961 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
2541987 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
2542010 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
2542033 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* *
2542059 TAATGATTTTATAATAATTATTAT
1 TAATGATTTGATAATAATCATTAT
2542083 GTTATTATTT
Statistics
Matches: 95, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.04
22 3 0.03
23 12 0.13
24 7 0.07
25 7 0.07
26 61 0.64
27 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:2542116 original size:24 final size:24
Alignment explanation
Indices: 2542044--2542135 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
2542034 AATGATTTGA
*
2542044 TAATAATCATTA-TAATAATGATT
1 TAATAATTATTACTAATAATGATT
* * * * * *
2542067 TTATAATAATTATTATGTTATTATT
1 TAATAATTATTACTA-ATAATGATT
*
2542092 TAGTAATTATTTA-TAATAATGATT
1 TAATAATTA-TTACTAATAATGATT
2542116 TAATAATTATTACTAATAAT
1 TAATAATTATTACTAATAAT
2542136 TATAGAATAC
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
23 13 0.25
24 23 0.43
25 14 0.26
26 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (24 bp):
TAATAATTATTACTAATAATGATT
Found at i:2542132 original size:13 final size:12
Alignment explanation
Indices: 2542043--2542138 Score: 81
Period size: 11 Copynumber: 7.9 Consensus size: 12
2542033 TAATGATTTG
*
2542043 ATAATAATCATT
1 ATAATAATTATT
*
2542055 ATAATAATGATTTT
1 ATAATAAT--TATT
2542069 ATAATAATTATT
1 ATAATAATTATT
* *
2542081 AT-GTTATTATT
1 ATAATAATTATT
*
2542092 -TAGTAATTATTT
1 ATAATAATTA-TT
*
2542104 ATAATAATGATT
1 ATAATAATTATT
2542116 -TAATAATTATT
1 ATAATAATTATT
2542127 ACTAATAATTAT
1 A-TAATAATTAT
2542139 AGAATACTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 1 0.01
11 23 0.34
12 17 0.25
13 17 0.25
14 10 0.15
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (12 bp):
ATAATAATTATT
Found at i:2542144 original size:24 final size:24
Alignment explanation
Indices: 2542095--2542144 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
2542085 TATTATTTAG
**
2542095 TAATTATTTATAATAATGATTTAA
1 TAATTATTTATAATAATGATAGAA
*
2542119 TAATTA-TTACTAATAATTATAGAA
1 TAATTATTTA-TAATAATGATAGAA
2542143 TA
1 TA
2542145 CTAACAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
TAATTATTTATAATAATGATAGAA
Found at i:2542243 original size:14 final size:13
Alignment explanation
Indices: 2542224--2542288 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
2542214 TTTAAATATT
2542224 TAATGATTTGATAC
1 TAATGATTT-ATAC
2542238 TAATGA-TT-TAC
1 TAATGATTTATAC
*
2542249 TAAT--TAT-TAC
1 TAATGATTTATAC
2542259 TAATGATTTAATAC
1 TAATGATTT-ATAC
*
2542273 TAATTATTTGATAC
1 TAATGATTT-ATAC
2542287 TA
1 TA
2542289 GTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.19
11 7 0.17
12 2 0.05
13 2 0.05
14 23 0.55
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATGATTTATAC
Found at i:2542260 original size:10 final size:11
Alignment explanation
Indices: 2542235--2542268 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2542225 AATGATTTGA
2542235 TACTAATGATT
1 TACTAATGATT
*
2542246 TACTAATTA-T
1 TACTAATGATT
2542256 TACTAATGATT
1 TACTAATGATT
2542267 TA
1 TA
2542269 ATACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TACTAATGATT
Found at i:2542278 original size:21 final size:21
Alignment explanation
Indices: 2542235--2542278 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2542225 AATGATTTGA
* *
2542235 TACTAATGATTTACTAATTAT
1 TACTAATGATTTAATAATAAT
*
2542256 TACTAATGATTTAATACTAAT
1 TACTAATGATTTAATAATAAT
2542277 TA
1 TA
2542279 TTTGATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TACTAATGATTTAATAATAAT
Found at i:2542295 original size:17 final size:17
Alignment explanation
Indices: 2542273--2542305 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2542263 GATTTAATAC
2542273 TAATTATTTGATACTAG
1 TAATTATTTGATACTAG
2542290 TAATTATTTGATACTA
1 TAATTATTTGATACTA
2542306 AACATCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
TAATTATTTGATACTAG
Found at i:2544477 original size:15 final size:14
Alignment explanation
Indices: 2544454--2544484 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2544444 TACAACACTA
2544454 AACTTTAATATAAT
1 AACTTTAATATAAT
2544468 AACTTATAATATAAT
1 AACTT-TAATATAAT
2544483 AA
1 AA
2544485 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:2544492 original size:16 final size:16
Alignment explanation
Indices: 2544459--2544505 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2544449 CACTAAACTT
*
2544459 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
2544474 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
2544490 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
2544506 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:2544616 original size:32 final size:34
Alignment explanation
Indices: 2544541--2544622 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
2544531 CCAAACCCTT
* *
2544541 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
2544574 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTTCA-TATAACTA
*
2544607 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
2544623 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 11 0.25
33 8 0.18
34 20 0.45
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:2544628 original size:12 final size:12
Alignment explanation
Indices: 2544603--2544655 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
2544593 TTTTTCATTA
*
2544603 TAATATACT-AC
1 TAATAAACTAAC
*
2544614 TAATAAACTTAC
1 TAATAAACTAAC
2544626 TAACTAAAACTAAC
1 TAA-T-AAACTAAC
2544640 TAATAAACTAAC
1 TAATAAACTAAC
2544652 TAAT
1 TAAT
2544656 TTTTATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
11 8 0.22
12 17 0.46
13 2 0.05
14 10 0.27
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (12 bp):
TAATAAACTAAC
Found at i:2544740 original size:43 final size:42
Alignment explanation
Indices: 2544692--2544786 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 42
2544682 AAATATAACT
2544692 TAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT-TATA
1 TAACTATTTAAC-AA-AACAAACTAATT-AATAATTTTTTATATA
* *
2544735 TAACTAACTTAACAAAACAAACTAATTAATTATTTTTTAACTATA
1 TAACT-ATTTAACAAAACAAACTAATTAATAATTTTTT-A-TATA
2544780 TAACTAT
1 TAACTAT
2544787 CAAACATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
42 12 0.27
43 16 0.36
44 7 0.16
45 9 0.20
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (42 bp):
TAACTATTTAACAAAACAAACTAATTAATAATTTTTTATATA
Found at i:2544784 original size:41 final size:39
Alignment explanation
Indices: 2544691--2544815 Score: 112
Period size: 41 Copynumber: 3.1 Consensus size: 39
2544681 CAAATATAAC
* *
2544691 TTAACTATTTAACTAAC-AA-AAACTAATTAAATAATTTT
1 TTAACTATATAACTAACAAACAAACTAATT-AATTATTTT
*
2544729 TTTA-TATAACTAACTTAACAAAACAAACTAATTAATTATTTT
1 TTAACTAT-A-TAAC-TAAC-AAACAAACTAATTAATTATTTT
* * *
2544771 TTAACTATATAACTATCAAACATATACTAATTAAATAATTT
1 TTAACTATATAACTAACAAACA-A-ACTAATTAATTATTTT
2544812 TTAA
1 TTAA
2544816 TTTATGTATA
Statistics
Matches: 71, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
37 3 0.04
38 3 0.04
39 9 0.13
40 8 0.11
41 22 0.31
42 14 0.20
43 12 0.17
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (39 bp):
TTAACTATATAACTAACAAACAAACTAATTAATTATTTT
Found at i:2544841 original size:41 final size:40
Alignment explanation
Indices: 2544705--2544841 Score: 91
Period size: 41 Copynumber: 3.3 Consensus size: 40
2544695 CTATTTAACT
* *
2544705 AACAAAAACTAATTAAATAATTTTT--TTATATAACTAACTTAA
1 AACATAAACTAATTAAATAATTTTTAACTATATAACT-A--T-A
* * * *
2544747 CAAAACAAACTAATTAATTATTTTTTAACTATATAACTATCA
1 -AACATAAACTAATTAAATAATTTTTAACTATATAACTAT-A
* * *
2544789 AACATATACTAATTAAATAATTTTTAATTTATGTATACTAT-
1 AACATAAACTAATTAAATAATTTTTAA-CTATATA-ACTATA
*
2544830 AACTTAAACTAA
1 AACATAAACTAA
2544842 CAATCATATA
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
41 32 0.43
42 7 0.09
43 26 0.35
44 1 0.01
45 9 0.12
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (40 bp):
AACATAAACTAATTAAATAATTTTTAACTATATAACTATA
Found at i:2544906 original size:16 final size:18
Alignment explanation
Indices: 2544877--2544915 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
2544867 ACTAATTAAC
*
2544877 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
2544895 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
2544911 ATTTA
1 ATTTA
2544916 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:2545198 original size:50 final size:48
Alignment explanation
Indices: 2545127--2545233 Score: 173
Period size: 49 Copynumber: 2.2 Consensus size: 48
2545117 TAGGATCACA
*
2545127 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTAT-T
2545176 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
1 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
2545224 TGGC-TGCATG
1 TGGCATGCATG
2545234 TGCATGCATG
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
47 6 0.11
48 5 0.09
49 32 0.57
50 13 0.23
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (48 bp):
TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
Found at i:2545301 original size:29 final size:29
Alignment explanation
Indices: 2545268--2545362 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
2545258 TGGACGCCGG
2545268 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
2545297 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
2545326 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
2545355 GGCGACCT
1 GGCGACCT
2545363 CTCTATTGGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:2545391 original size:32 final size:32
Alignment explanation
Indices: 2545349--2545420 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
2545339 GTCGCCCAGA
*
2545349 CTGCATGGCGACCTCTCTATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
* *
2545381 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
2545413 CTGCATGG
1 CTGCATGG
2545421 TGAGTATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:2545485 original size:24 final size:19
Alignment explanation
Indices: 2545435--2545472 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2545425 TATATGGCTT
2545435 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
2545454 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
2545473 TGAGTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.37, T:0.32
Consensus pattern (19 bp):
GTATGGCTCGTCTGCATGG
Found at i:2546452 original size:58 final size:58
Alignment explanation
Indices: 2546386--2546679 Score: 341
Period size: 58 Copynumber: 5.1 Consensus size: 58
2546376 AATCGTGGGT
* * *
2546386 TGATTCTAACTTCGTAAGGAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTTATA
1 TGATTCTAACTTTGTAAGAAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTTAAA
* *
2546444 TGATTCTAACTTCGTAAGAAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTTATA
1 TGATTCTAACTTTGTAAGAAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTTAAA
* * * * *
2546502 TGATTCTAACTTTGTAAGAAAAATAAATAGTTAAATTTATTTCCTTAATAATTTTAAA
1 TGATTCTAACTTTGTAAGAAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTTAAA
* ** ** *
2546560 TGATTCTTACTTTGTAACCAAAATAAATAGTTGAATTTATTT-TTTTAGAATCTTGAAA
1 TGATTCTAACTTTGTAAGAAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTT-AAA
* * *
2546618 T-ATTCTAACTTTATAAGGAAAATAAATTGTT-AACTCTT-TTT---TGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGAAAAATAAATAGTTGAA-T-TTATTTCCCTGAGAATCTTAAA
2546672 TGATTCTA
1 TGATTCTA
2546680 TTTTGTTAAA
Statistics
Matches: 210, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
54 4 0.02
55 15 0.07
56 2 0.01
57 37 0.18
58 152 0.72
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAGAAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTTAAA
Found at i:2546707 original size:170 final size:172
Alignment explanation
Indices: 2546386--2546713 Score: 391
Period size: 174 Copynumber: 1.9 Consensus size: 172
2546376 AATCGTGGGT
** *
2546386 TGATTCTAACTTCGTAAGGAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTTATATGATTCT
1 TGATTCTAACTTCGTAACCAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTTAAATGATTCT
* *
2546451 AACTTCGTAAGAAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTTATATGATTCTAACTTTG
66 AACTTCATAAGAAAAATAAATAGTTGAATTTATTT--CTGAGAATCTTAAATGATTCTAACTTTG
*
2546516 TAAGAAAAATAAATAGTTAAATTTATTTCCTTAATAATTTTAAA
129 TAAGAAAAATAAATAGTTAAATTAATTTCCTTAATAATTTTAAA
* * ** *
2546560 TGATTCTTACTTTGTAACCAAAATAAATAGTTGAATTTATTT-TTTTAGAATCTTGAAAT-ATTC
1 TGATTCTAACTTCGTAACCAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTT-AAATGATTC
* * * *
2546623 TAACTTTATAAGGAAAATAAATTGTT-AACTCTT-TTT-TGAGAATCTTAAATGATTCT-ATTTT
65 TAACTTCATAAGAAAAATAAATAGTTGAA-T-TTATTTCTGAGAATCTTAAATGATTCTAACTTT
* *
2546684 GTTAA-AGGAAATAAATTGTTAAATTAATTT
128 G-TAAGA-AAAATAAATAGTTAAATTAATTT
2546714 TCTCAAGAAT
Statistics
Matches: 132, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
169 6 0.05
170 42 0.32
172 2 0.02
173 39 0.30
174 43 0.33
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (172 bp):
TGATTCTAACTTCGTAACCAAAATAAATAGTTGAATTTATTTCCCTGAGAATCTTAAATGATTCT
AACTTCATAAGAAAAATAAATAGTTGAATTTATTTCTGAGAATCTTAAATGATTCTAACTTTGTA
AGAAAAATAAATAGTTAAATTAATTTCCTTAATAATTTTAAA
Found at i:2546929 original size:39 final size:39
Alignment explanation
Indices: 2546872--2547021 Score: 120
Period size: 39 Copynumber: 3.9 Consensus size: 39
2546862 TATATGATTA
*
2546872 TATTTTGTAAAAGGAAATAAATCGTTGAATTTATTTTTC
1 TATTTTGTAAAAGAAAATAAATCGTTGAATTTATTTTTC
* *
2546911 TATTTTG-ATAAAGAAAATATATTGTTGAATTTA-TTTTC
1 TATTTTGTA-AAAGAAAATAAATCGTTGAATTTATTTTTC
* *
2546949 T-TGATTTATAAAAAAAAAT-AA---TTGAATTTATTTTAT-
1 TAT--TTTGTAAAAGAAAATAAATCGTTGAATTTATTTT-TC
* * *
2546985 TAATTTGTAAAATG-TAATAAATAGTTGAATTTATTTT
1 TATTTTGTAAAA-GAAAATAAATCGTTGAATTTATTTT
2547022 CATAAGAATC
Statistics
Matches: 89, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
35 20 0.22
36 6 0.07
37 2 0.02
38 8 0.09
39 52 0.58
40 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (39 bp):
TATTTTGTAAAAGAAAATAAATCGTTGAATTTATTTTTC
Found at i:2546981 original size:35 final size:37
Alignment explanation
Indices: 2546935--2547022 Score: 108
Period size: 35 Copynumber: 2.4 Consensus size: 37
2546925 AAATATATTG
*
2546935 TTGAATTTATTTTCTTGATTTATAAAA-AA-AAATAA
1 TTGAATTTATTTTCTTAATTTATAAAATAATAAATAA
* * *
2546970 TTGAATTTATTTTATTAATTTGTAAAATGTAATAAATAG
1 TTGAATTTATTTTCTTAATTTATAAAA--TAATAAATAA
2547009 TTGAATTTATTTTC
1 TTGAATTTATTTTC
2547023 ATAAGAATCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
35 24 0.55
38 2 0.05
39 18 0.41
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (37 bp):
TTGAATTTATTTTCTTAATTTATAAAATAATAAATAA
Found at i:2547200 original size:63 final size:62
Alignment explanation
Indices: 2547084--2547207 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 62
2547074 TATTTTCCTA
* *
2547084 TTTGTAAAAGAAAATAAATCGTTGGATTTATTTTCTTATTTTGCATAATGAAATAAATCATAT
1 TTTGTAAAAGAAAATAAATCGTTGGATTTATTTTCCTATTTT-CATAAGGAAATAAATCATAT
*
2547147 TTTGTAGAAGAAAATAAATCGTTGGATTTATTTTCCTATTTT-ATTAAAGGAAATAAATCAT
1 TTTGTAAAAGAAAATAAATCGTTGGATTTATTTTCCTATTTTCA-T-AAGGAAATAAATCAT
2547208 TAGATTTATT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
61 1 0.02
62 1 0.02
63 54 0.96
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (62 bp):
TTTGTAAAAGAAAATAAATCGTTGGATTTATTTTCCTATTTTCATAAGGAAATAAATCATAT
Found at i:2547201 original size:39 final size:39
Alignment explanation
Indices: 2547158--2547281 Score: 153
Period size: 39 Copynumber: 3.2 Consensus size: 39
2547148 TTGTAGAAGA
2547158 AAATAAATCGTTGGATTTATTTTCCTATTTTATTAAAGG
1 AAATAAATCGTTGGATTTATTTTCCTATTTTATTAAAGG
* * * *
2547197 AAATAAATCATTAGATTTATTTT-CTATTTTGTAAAAGG
1 AAATAAATCGTTGGATTTATTTTCCTATTTTATTAAAGG
* * * *
2547235 AAATAACTCGTTCGGTTTTATTTTCCTATTTTTTTAAA-A
1 AAATAAATCGTT-GGATTTATTTTCCTATTTTATTAAAGG
2547274 AAATAAAT
1 AAATAAAT
2547282 AAATCATTGA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
38 23 0.32
39 37 0.52
40 11 0.15
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (39 bp):
AAATAAATCGTTGGATTTATTTTCCTATTTTATTAAAGG
Found at i:2547234 original size:38 final size:39
Alignment explanation
Indices: 2547144--2547266 Score: 140
Period size: 39 Copynumber: 3.2 Consensus size: 39
2547134 AAATAAATCA
* * * *
2547144 TATTTTGTAGAAGAAAATAAATCGTTGGATTTATTTTCC
1 TATTTTGTAAAAGGAAATAAATCATTAGATTTATTTTCC
* *
2547183 TATTTTATTAAAGGAAATAAATCATTAGATTTATTTT-C
1 TATTTTGTAAAAGGAAATAAATCATTAGATTTATTTTCC
* * * *
2547221 TATTTTGTAAAAGGAAATAACTCGTTCGGTTTTATTTTCC
1 TATTTTGTAAAAGGAAATAAATCATT-AGATTTATTTTCC
2547261 TATTTT
1 TATTTT
2547267 TTTAAAAAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
38 23 0.33
39 40 0.57
40 7 0.10
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (39 bp):
TATTTTGTAAAAGGAAATAAATCATTAGATTTATTTTCC
Found at i:2548608 original size:20 final size:21
Alignment explanation
Indices: 2548583--2548621 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2548573 GAAGATAAAG
*
2548583 AAAAT-ATGGAAAATGAAATA
1 AAAATAATCGAAAATGAAATA
2548603 AAAATAATCGAAAATGAAA
1 AAAATAATCGAAAATGAAA
2548622 CGAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.67, C:0.03, G:0.13, T:0.18
Consensus pattern (21 bp):
AAAATAATCGAAAATGAAATA
Found at i:2551358 original size:64 final size:64
Alignment explanation
Indices: 2551289--2551509 Score: 218
Period size: 64 Copynumber: 3.5 Consensus size: 64
2551279 TTGAAGGTGT
* *
2551289 ATCGATGCATTGGTAGTGCATCGATGCA-CTC-TT-TTAAAATAAAAACATCGAATGCAATTCAT
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTATT--AAT-AAAACATCGAATGCAATTCAT
2551351 GC
63 GC
* * **
2551353 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTATTAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTATTAATAAAACATCGAATGCAATTCATGC
** * * * ** *
2551417 ATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTATTAATAAAACATCGAATGCAATTCATGC
* *
2551481 ACCGATGCATCA-GTAGTACATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
2551510 ACATTCATTA
Statistics
Matches: 132, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
63 1 0.01
64 120 0.91
65 7 0.05
66 2 0.02
67 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTATTAATAAAACATCGAATGCAATTCATGC
Found at i:2552015 original size:15 final size:15
Alignment explanation
Indices: 2551997--2552029 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2551987 GAGGGTATAA
2551997 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2552012 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2552027 TAG
1 TAG
2552030 GGGTCCTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:2558296 original size:64 final size:64
Alignment explanation
Indices: 2558228--2558449 Score: 187
Period size: 64 Copynumber: 3.5 Consensus size: 64
2558218 TTGAAGGTGT
** ** *
2558228 ATCGATGCATTGGTAGTGCATCAATGCA-CTCTTTTAA-AATAAAAACATTGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCAATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
2558291 C
64 C
* * **
2558292 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCAATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* ** * ** * * ** *
2558356 ATCGATGCATAAGGAGTGCATTGATGTATCCCAGCAATAAATAATACATCGAATACCTTTTATGC
1 ATCGATGCATAAGTAGTGCATCAATGCATCCCATTAAT-AATAAAACATCGAATGCAATTCATGC
* * * *
2558421 ACCGATGCATCATTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCAATGCAT
2558450 ACCTTCATTA
Statistics
Matches: 128, Mismatches: 27, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
64 82 0.64
65 46 0.36
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCAATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:2558955 original size:15 final size:15
Alignment explanation
Indices: 2558937--2558969 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2558927 GAGGGTATAA
*
2558937 TAGTCCTTCGGGATG
1 TAGTCATTCGGGATG
2558952 TAGTCATTCGGGATG
1 TAGTCATTCGGGATG
2558967 TAG
1 TAG
2558970 GGGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.33
Consensus pattern (15 bp):
TAGTCATTCGGGATG
Found at i:2561182 original size:29 final size:30
Alignment explanation
Indices: 2561095--2561188 Score: 145
Period size: 30 Copynumber: 3.2 Consensus size: 30
2561085 GGTCCTTATA
2561095 GATAGTTACCGAGGATCTTTATGACCTCTG
1 GATAGTTACCGAGGATCTTTATGACCTCTG
* *
2561125 TACAGTTACCGAGGATCTTTATGACCTCTG
1 GATAGTTACCGAGGATCTTTATGACCTCTG
* *
2561155 GATAGTTACCG-GGGTCTTTGTGACCTCTG
1 GATAGTTACCGAGGATCTTTATGACCTCTG
2561184 GATAG
1 GATAG
2561189 GTCATTCGGG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 21 0.36
30 37 0.64
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (30 bp):
GATAGTTACCGAGGATCTTTATGACCTCTG
Found at i:2561911 original size:21 final size:21
Alignment explanation
Indices: 2561887--2561929 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2561877 AAAGAAGATA
2561887 TTGTATAAT-CTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
2561908 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
2561929 T
1 T
2561930 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.51
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:2565582 original size:30 final size:30
Alignment explanation
Indices: 2565546--2565638 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
2565536 GTGGTCCTTA
*
2565546 TGGACAGTTAGCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2565576 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
2565606 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2565635 TGGA
1 TGGA
2565639 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 18 0.31
30 41 0.69
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:2566353 original size:21 final size:21
Alignment explanation
Indices: 2566329--2566371 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2566319 AAAGAAGATA
2566329 TTGTATAAT-ATCTGAATAATT
1 TTGTA-AATGATCTGAATAATT
* *
2566350 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGATCTGAATAATT
2566371 T
1 T
2566372 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (21 bp):
TTGTAAATGATCTGAATAATT
Found at i:2572419 original size:64 final size:64
Alignment explanation
Indices: 2572350--2572559 Score: 235
Period size: 64 Copynumber: 3.3 Consensus size: 64
2572340 CAATGCATTG
* *
2572350 GTAGTGCATCAATGCA-CTCCTTTAA-AATAAAAACATCGAATGCAATTCATGCATCGATGCATA
1 GTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATGCATCGATGCATA
2572413 A
64 A
* **
2572414 GTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGCATCGATGCATAA
1 GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATGCATAA
* ** * * * ** * * *
2572478 GGAGTGCATCGATGCATCCCAGCAATAAATAATACATTGAATACCTTTTATGCACCGATGCATCA
1 GTAGTGCATCGATGCATCCCATTAAT-AATAAAACATCGAATGCAATTCATGCATCGATGCATAA
2572543 GTAGTGCATCGATGCAT
1 GTAGTGCATCGATGCAT
2572560 ACCTTCATTA
Statistics
Matches: 124, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
64 76 0.61
65 48 0.39
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATGCATAA
Found at i:2573065 original size:15 final size:15
Alignment explanation
Indices: 2573047--2573079 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2573037 GAGGGTATAA
2573047 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2573062 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2573077 TAG
1 TAG
2573080 GGGTCCTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:2579340 original size:64 final size:64
Alignment explanation
Indices: 2579271--2579491 Score: 227
Period size: 64 Copynumber: 3.5 Consensus size: 64
2579261 TTGAAGGTGT
* *
2579271 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAGGTAGTGCATCGATGCATCTC-ATTAATAAT-AAAACATCGAATGCAATTCATG
2579334 C
64 C
* * * **
2579335 ATCGATGCATAAGTAGTGCATTGATGCATCTCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCTCATTAATAATAAAACATCGAATGCAATTCATGC
** * * ** *
2579399 ATCGATGCATAAGG-AGTGCATCGATGCATC-CTAGCAATAATAATACATCGAATACCTTTTATG
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCTC-ATTAATAATAAAACATCGAATGCAATTCATG
2579462 C
64 C
*
2579463 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
2579492 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 122 0.92
65 8 0.06
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCTCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:2579997 original size:15 final size:15
Alignment explanation
Indices: 2579979--2580010 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2579969 GAGGGTATAA
2579979 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2579994 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
2580009 TA
1 TA
2580011 TGGGTCCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.31, T:0.34
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:2580895 original size:106 final size:106
Alignment explanation
Indices: 2580704--2580919 Score: 263
Period size: 106 Copynumber: 2.0 Consensus size: 106
2580694 GTATTGCTCC
* * *
2580704 GAGTCCAATATCCTCCGTCGTGAAGTTGAAACTGGCTCTGGAACTGGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTCCGTCGTGAAGTTGAAACTGACTCTGAAACTGGGAAATTGTTTGTTGACAA
* * *
2580769 TCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
66 CCAACCGCCCATTCGCTGTGAAGTTGAACTTGTGTTGTCTT
* * * * * * *
2580810 GAGTCTAATATCCTTCG-CTGTGAAGTTGAAATTGACTTTGAAATTGGGAAGTTGTTTGTTGGCA
1 GAGTCCAATATCCTCCGTC-GTGAAGTTGAAACTGACTCTGAAACTGGGAAATTGTTTGTTGACA
** * *
2580874 ACCAGTCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAACCGCCCATTCGCTGTGAAGTTGAACTTGTGTTGTCTT
2580916 GAGT
1 GAGT
2580920 GTTGAGCCTG
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
105 1 0.01
106 91 0.99
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTCCGTCGTGAAGTTGAAACTGACTCTGAAACTGGGAAATTGTTTGTTGACAA
CCAACCGCCCATTCGCTGTGAAGTTGAACTTGTGTTGTCTT
Found at i:2581171 original size:279 final size:280
Alignment explanation
Indices: 2580670--2581199 Score: 873
Period size: 279 Copynumber: 1.9 Consensus size: 280
2580660 GGGTGTTACA
2580670 ATGAAGTTGAAATCCAAGTAAGTTGTATTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAA
1 ATGAAGTTGAAATCCAAGTAAGTTGTATTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAA
* * * *
2580735 CTGGCTCTGGAACTGGGAAATTGTTTGTTGACAGTCAACCGCCCCTTCGCTGTGAAGTTGAGCTT
66 CTGGCTCTGGAACTGGGAAATTATTTGTTAACAGCCAACCGCCCCTTCGCCGTGAAGTTGAGCTT
* * * * *
2580800 GTGTTGTCTTGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTTTGAAATTGGGAAGTTGT
131 GTGCTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTTTGAAACTAGGAAATTGT
*** * * *
2580865 TTGTTGGCAACCAGTCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTGTTGAGCCTG
196 TCACTGACAACCAGTCATCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGTTGAGCCTG
2580930 GTAATTGGATATCCTTCGTC
261 GTAATTGGATATCCTTCGTC
*
2580950 ATGAAGTTGAAATCCAAGTAAGTTGTATTGCTCTGAGTCCAATATCCTCCGTCGTGAAGTTGAAA
1 ATGAAGTTGAAATCCAAGTAAGTTGTATTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAA
* *
2581015 TTGGCTCT-GAACTGGTAAATTATTTGTTAACAGCCAACCGCCCCTTCGCCGTGAAGTTGAGCTT
66 CTGGCTCTGGAACTGGGAAATTATTTGTTAACAGCCAACCGCCCCTTCGCCGTGAAGTTGAGCTT
2581079 GTGCTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTTTGAAACTAGGAAATTGT
131 GTGCTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTTTGAAACTAGGAAATTGT
* *
2581144 TCACTGACAACCTGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTG
196 TCACTGACAACCAGTCATCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTG
2581200 GCACGATATC
Statistics
Matches: 230, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
279 159 0.69
280 71 0.31
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (280 bp):
ATGAAGTTGAAATCCAAGTAAGTTGTATTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAA
CTGGCTCTGGAACTGGGAAATTATTTGTTAACAGCCAACCGCCCCTTCGCCGTGAAGTTGAGCTT
GTGCTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTTTGAAACTAGGAAATTGT
TCACTGACAACCAGTCATCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGTTGAGCCTG
GTAATTGGATATCCTTCGTC
Found at i:2588152 original size:20 final size:21
Alignment explanation
Indices: 2588127--2588165 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2588117 GAAGATAAAG
*
2588127 AAAAT-ATGGAAAATGAAATA
1 AAAATAATCGAAAATGAAATA
2588147 AAAATAATCGAAAATGAAA
1 AAAATAATCGAAAATGAAA
2588166 CGAAGTAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.67, C:0.03, G:0.13, T:0.18
Consensus pattern (21 bp):
AAAATAATCGAAAATGAAATA
Found at i:2588350 original size:2 final size:2
Alignment explanation
Indices: 2588343--2588371 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2588333 AAAGAGGTAA
2588343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2588372 GTAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2588448 original size:15 final size:15
Alignment explanation
Indices: 2588408--2588452 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2588398 TATCTATACC
2588408 TATATATATATAATA
1 TATATATATATAATA
* *
2588423 AATA-ACGATATAATA
1 TATATA-TATATAATA
2588438 TATATATATATAATA
1 TATATATATATAATA
2588453 ATAAACGCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
TATATATATATAATA
Found at i:2595305 original size:19 final size:19
Alignment explanation
Indices: 2595278--2595322 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2595268 GGTATGTCCT
*
2595278 TGATTTTTATAGTAAAATG
1 TGATATTTATAGTAAAATG
*
2595297 TGATATTTATAGTAAACTG
1 TGATATTTATAGTAAAATG
2595316 TGATATT
1 TGATATT
2595323 GACTACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (19 bp):
TGATATTTATAGTAAAATG
Found at i:2605617 original size:13 final size:14
Alignment explanation
Indices: 2605592--2605626 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
2605582 CATCGGGATT
2605592 AAAAGTTTGAAAAA
1 AAAAGTTTGAAAAA
2605606 AAAAGTTT-AAAAA
1 AAAAGTTTGAAAAA
2605619 AAAAGTTT
1 AAAAGTTT
2605627 TCTATTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (14 bp):
AAAAGTTTGAAAAA
Found at i:2608656 original size:103 final size:103
Alignment explanation
Indices: 2608472--2608689 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
2608462 GTCGAGGGTC
* *
2608472 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTAAGACACATAC
* *
2608537 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
2608575 TATGTGGTCCTTCGGGATATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTAAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTAAGACACATAC
*
2608640 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2608678 TATGTGGTCCTT
1 TATGTGGTCCTT
2608690 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTAAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:2608772 original size:23 final size:23
Alignment explanation
Indices: 2608696--2608773 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
2608686 CCTTATGGAC
*
2608696 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * * *
2608720 ATTCTACGCGGCACTCCTGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
2608743 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
2608766 ATTATATG
1 ATTATATG
2608774 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 40 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:2613246 original size:64 final size:65
Alignment explanation
Indices: 2613173--2613334 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 65
2613163 ATTGTTTGAA
* *** *
2613173 GGTGTATCGATGCACAGGTAGTGCATCGATGCACT-CTTTTAATCTAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCACTCCCAGTAAT-AAACAAACATCGAATGCAAT
2613236 T
65 T
* * * *
2613237 GGTGCATCGATGCATAAGGCA-TGCATCGATGCA-TCCCAGTAATAAACAAACATCGAATGTATT
1 GGTGCATCGATGCA-CAGGTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAAT
2613300 T
65 T
** *
2613301 TATGCAACGATGCACAGGTAGTGCATCGATGCAC
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCAC
2613335 CGATAGGGAA
Statistics
Matches: 79, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
63 7 0.09
64 68 0.86
65 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (65 bp):
GGTGCATCGATGCACAGGTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAATT
Found at i:2614222 original size:103 final size:103
Alignment explanation
Indices: 2613989--2614206 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
2613979 GTCGAGGGTC
*
2613989 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
* *
2614054 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
2614092 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGATGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
*
2614157 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2614195 TATGTGGTCCTT
1 TATGTGGTCCTT
2614207 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:2617399 original size:20 final size:20
Alignment explanation
Indices: 2617305--2617673 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
2617295 GATTTTCCAT
* ** *
2617305 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2617325 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2617345 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2617365 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
2617385 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
2617405 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2617425 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2617445 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2617465 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
2617485 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2617505 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2617525 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2617545 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
2617565 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2617585 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2617605 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2617625 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2617645 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2617665 AATCACAAC
1 AATCGCAAC
2617674 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2618395 original size:24 final size:24
Alignment explanation
Indices: 2618356--2618402 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2618346 AAATTTGGTC
2618356 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2618380 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2618403 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2618594 original size:12 final size:12
Alignment explanation
Indices: 2618577--2618601 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2618567 ATATAATCCT
2618577 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2618589 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2618601 G
1 G
2618602 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2620902 original size:19 final size:19
Alignment explanation
Indices: 2620880--2621168 Score: 377
Period size: 19 Copynumber: 16.3 Consensus size: 19
2620870 CGGAAAATAC
*
2620880 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2620899 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
2620913 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
2620933 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2620947 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2620966 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2620985 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
2620999 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
2621018 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2621037 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2621056 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2621075 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2621094 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2621113 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
2621127 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
2621145 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2621164 AATCG
1 AATCG
2621169 GAACGAGATA
Statistics
Matches: 241, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 38 0.16
15 1 0.00
16 14 0.06
17 12 0.05
18 19 0.08
19 144 0.60
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2620995 original size:52 final size:55
Alignment explanation
Indices: 2620908--2621168 Score: 341
Period size: 52 Copynumber: 4.8 Consensus size: 55
2620898 AAATCCCAAC
*
2620908 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
2620961 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA-ATGAAAATCGCAATGCGAA
*
2621013 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
2621070 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
2621125 A-G--AATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAAATCG
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCG
2621169 GAACGAGATA
Statistics
Matches: 198, Mismatches: 2, Indels: 18
0.91 0.01 0.08
Matches are distributed among these distances:
51 25 0.13
52 80 0.40
53 16 0.08
54 6 0.03
55 7 0.04
57 64 0.32
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:2621309 original size:19 final size:19
Alignment explanation
Indices: 2621200--2621301 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2621190 AAATTATAAA
2621200 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2621219 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
2621239 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
2621255 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2621272 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2621291 CGCATTGCGAT
1 CGCATTGCGAT
2621302 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:2621427 original size:14 final size:14
Alignment explanation
Indices: 2621408--2621444 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2621398 CATCAATTAC
2621408 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2621422 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2621436 ACAAATCAA
1 ACAAATCAA
2621445 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2623419 original size:14 final size:14
Alignment explanation
Indices: 2623400--2623456 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2623390 GCGAAATGAA
*
2623400 AATCGCAACGACAG
1 AATCGCAACGAAAG
2623414 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2623431 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2623447 AATCGCAACG
1 AATCGCAACG
2623457 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2623427 original size:33 final size:33
Alignment explanation
Indices: 2623381--2623473 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2623371 GCGAAACCAA
*
2623381 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2623414 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2623447 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2623474 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2623438 original size:19 final size:19
Alignment explanation
Indices: 2623344--2623478 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2623334 TAGTTTACTT
* *
2623344 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2623364 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2623383 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2623402 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2623416 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2623435 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2623449 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2623468 TCGCAATGCGA
1 TCGCAACGCGA
2623479 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2623496 original size:19 final size:19
Alignment explanation
Indices: 2623474--2623602 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2623464 AAAATCGCAA
2623474 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2623493 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2623507 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2623526 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2623540 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2623559 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2623578 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2623598 TGCGA
1 TGCGA
2623603 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2623516 original size:33 final size:33
Alignment explanation
Indices: 2623474--2623565 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2623464 AAAATCGCAA
2623474 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2623507 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2623540 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2623566 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2623816 original size:92 final size:92
Alignment explanation
Indices: 2623646--2624301 Score: 1258
Period size: 92 Copynumber: 7.1 Consensus size: 92
2623636 TTGAATGGAT
2623646 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
2623711 AGTTTAGCAGAATTGGCAGCAACCGAAC
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
2623739 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
2623804 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
2623831 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
2623896 AGTTTAGCAGAATTGGCAGCAACCGAAC
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
2623924 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATATACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
2623989 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
2624016 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
2624081 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
*
2624108 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATATACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
2624173 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
2624200 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
*
2624265 AGTTTAGCAGAATTGGCAGCAACCGAAT
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
2624293 AAATTTACT
1 AAATTTACT
2624302 AAGCAATCTA
Statistics
Matches: 556, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 365 0.66
93 191 0.34
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (92 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2623958 original size:185 final size:185
Alignment explanation
Indices: 2623646--2624301 Score: 1287
Period size: 185 Copynumber: 3.6 Consensus size: 185
2623636 TTGAATGGAT
2623646 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2623711 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
2623776 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
2623831 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2623896 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2623961 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
2624016 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2624080 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2624145 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
2624200 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
2624265 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
2624302 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
184 184 0.39
185 284 0.61
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2626025 original size:14 final size:14
Alignment explanation
Indices: 2626006--2626095 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2625996 TTGAAATGAA
2626006 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2626020 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
2626037 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
2626053 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2626072 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2626086 AATCGCAACG
1 AATCGCAACG
2626096 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2626043 original size:33 final size:33
Alignment explanation
Indices: 2625998--2626112 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2625988 TCTTTTGGTT
2625998 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
2626031 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2626064 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2626097 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2626113 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2626044 original size:19 final size:18
Alignment explanation
Indices: 2626005--2626117 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
2625995 GTTGAAATGA
2626005 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
2626020 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
2626037 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
2626053 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
2626070 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
2626086 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
2626103 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
2626118 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:2626148 original size:14 final size:14
Alignment explanation
Indices: 2626129--2626183 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2626119 TTTGGTTTCG
2626129 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2626143 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2626162 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2626176 CGTTGCGA
1 CGTTGCGA
2626184 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2626161 original size:33 final size:33
Alignment explanation
Indices: 2626113--2626183 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2626103 AAAATCGCAA
**
2626113 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2626146 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2626179 TGCGA
1 TGCGA
2626184 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2626191 original size:33 final size:33
Alignment explanation
Indices: 2626124--2626205 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
2626114 GCGATTTTGG
***
2626124 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
2626157 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
2626190 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
2626206 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:2626210 original size:20 final size:20
Alignment explanation
Indices: 2626136--2626224 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
2626126 TCGCGTTGCG
2626136 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2626156 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
2626169 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
2626189 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2626209 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
2626225 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2626346 original size:33 final size:33
Alignment explanation
Indices: 2626304--2626374 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2626294 AATACTAACT
*
2626304 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2626337 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2626370 TGAAA
1 TGAAA
2626375 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2626608 original size:22 final size:22
Alignment explanation
Indices: 2626556--2626610 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2626546 TGGTTGTGAG
**
2626556 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2626578 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2626600 GGATTTCTTCG
1 GGATTTCTTCG
2626611 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2626781 original size:20 final size:20
Alignment explanation
Indices: 2626756--2626948 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
2626746 CTTTAAATAT
2626756 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2626776 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2626798 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2626817 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2626837 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2626857 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2626877 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2626897 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2626917 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2626937 CGCGTTGCGATT
1 CGCGTTGCGATT
2626949 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2626943 original size:60 final size:60
Alignment explanation
Indices: 2626756--2626948 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2626746 CTTTAAATAT
**
2626756 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
2626817 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
2626877 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
2626937 CGCGTTGCGATT
1 CGCGTTGCGATT
2626949 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:2627036 original size:20 final size:20
Alignment explanation
Indices: 2627007--2627055 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2626997 AATCGCGTTA
*
2627007 CGATTTTGGAAACTGATTTG
1 CGATTCTGGAAACTGATTTG
2627027 CGATTCTGGAAACTGATTTG
1 CGATTCTGGAAACTGATTTG
2627047 CGATTCTGG
1 CGATTCTGG
2627056 GGATCGCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (20 bp):
CGATTCTGGAAACTGATTTG
Found at i:2627352 original size:21 final size:21
Alignment explanation
Indices: 2627328--2627388 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2627318 AACTTTGAAA
2627328 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
2627349 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
2627363 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
2627384 AAATG
1 AAATG
2627389 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:2627419 original size:37 final size:37
Alignment explanation
Indices: 2627320--2627438 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
2627310 TGGTAACCAA
2627320 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
2627357 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
2627392 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
2627429 -GTTGAAAAAT
1 CTTTGAAAAAT
2627439 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2640301 original size:51 final size:51
Alignment explanation
Indices: 2640242--2640344 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
2640232 TCCTAATAAT
2640242 AAAATATCGATGATCTCGTATGGTTAGAACATGAAACATATATTCAATAGG
1 AAAATATCGATGATCTCGTATGGTTAGAACATGAAACATATATTCAATAGG
2640293 AAAATATCGATGATCTCGTATGGTTAGAACATGAAACATATATTCAATAGG
1 AAAATATCGATGATCTCGTATGGTTAGAACATGAAACATATATTCAATAGG
2640344 A
1 A
2640345 GATTTGGACG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (51 bp):
AAAATATCGATGATCTCGTATGGTTAGAACATGAAACATATATTCAATAGG
Found at i:2643242 original size:2 final size:2
Alignment explanation
Indices: 2643235--2643282 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2643225 GAAGAATCAA
2643235 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
2643277 AT AT AT
1 AT AT AT
2643283 TCTCCATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2644614 original size:18 final size:18
Alignment explanation
Indices: 2644588--2644625 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2644578 GAAAGCTTCT
2644588 TTCAACGAAAAAAAATTG
1 TTCAACGAAAAAAAATTG
*
2644606 TTCAGCGAAAAAAAATTG
1 TTCAACGAAAAAAAATTG
2644624 TT
1 TT
2644626 AAAGAAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (18 bp):
TTCAACGAAAAAAAATTG
Found at i:2648481 original size:25 final size:25
Alignment explanation
Indices: 2648435--2648484 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
2648425 ATATGATAAT
2648435 TTAAAAAATTGTTTTTTAAAAAAAC
1 TTAAAAAATTGTTTTTTAAAAAAAC
2648460 TTAAAAATATT-TTGTTTTAAAAAAA
1 TTAAAAA-ATTGTT-TTTTAAAAAAA
2648485 ACCCAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
TTAAAAAATTGTTTTTTAAAAAAAC
Found at i:2648991 original size:31 final size:31
Alignment explanation
Indices: 2648922--2648991 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
2648912 ATAACCGAGG
* * *
2648922 TACCTAAAGTGGTAACGTTTTTAACTTCAGA
1 TACCTAAAGTGGTAACGTTTTAAAATTCAAA
* *
2648953 TATCTAAAGTGGTAATGTTTATAAAATT-AAA
1 TACCTAAAGTGGTAACGTTT-TAAAATTCAAA
2648984 TACCTAAA
1 TACCTAAA
2648992 TGAGTCAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (31 bp):
TACCTAAAGTGGTAACGTTTTAAAATTCAAA
Found at i:2652300 original size:21 final size:21
Alignment explanation
Indices: 2652274--2652354 Score: 144
Period size: 21 Copynumber: 3.9 Consensus size: 21
2652264 CAATTAAGAA
* *
2652274 TCAAGGAGCTTTACTTCATAG
1 TCAAGGCGCCTTACTTCATAG
2652295 TCAAGGCGCCTTACTTCATAG
1 TCAAGGCGCCTTACTTCATAG
2652316 TCAAGGCGCCTTACTTCATAG
1 TCAAGGCGCCTTACTTCATAG
2652337 TCAAGGCGCCTTACTTCA
1 TCAAGGCGCCTTACTTCA
2652355 AAGCCATAGC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (21 bp):
TCAAGGCGCCTTACTTCATAG
Found at i:2656922 original size:19 final size:21
Alignment explanation
Indices: 2656885--2656927 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
2656875 TAACTTTTTC
*
2656885 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTCCATTATTAACT
*
2656905 TTTTCTCTTCCATT-TTAACT
1 TTTTATCTTCCATTATTAACT
2656925 TTT
1 TTT
2656928 ACCTTTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATCTTCCATTATTAACT
Found at i:2660786 original size:17 final size:16
Alignment explanation
Indices: 2660755--2660788 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2660745 CACGTGAGGA
2660755 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
2660771 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
2660788 T
1 T
2660789 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:2664680 original size:21 final size:21
Alignment explanation
Indices: 2664651--2664693 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2664641 TGAAAATATT
*
2664651 AAAATATTAAAATTTTAAATA
1 AAAAAATTAAAATTTTAAATA
*
2664672 AAAAAATTAACATTTTAAATA
1 AAAAAATTAAAATTTTAAATA
2664693 A
1 A
2664694 TACTCCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAATTAAAATTTTAAATA
Found at i:2664776 original size:17 final size:18
Alignment explanation
Indices: 2664754--2664788 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2664744 CTTTAATCTT
2664754 ATATT-AACTGCTTTCCC
1 ATATTAAACTGCTTTCCC
2664771 ATATTAAACTGCTTTCCC
1 ATATTAAACTGCTTTCCC
2664789 TCCGTGTAGT
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:0.26, C:0.29, G:0.06, T:0.40
Consensus pattern (18 bp):
ATATTAAACTGCTTTCCC
Found at i:2677124 original size:15 final size:16
Alignment explanation
Indices: 2677099--2677144 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
2677089 GAGATTGAGT
*
2677099 ATTTGAGATTTTAGGG
1 ATTTGAAATTTTAGGG
*
2677115 A-TTGAAA-TTTAGAG
1 ATTTGAAATTTTAGGG
2677129 ATTTGAGAATTTTAGG
1 ATTTGA-AATTTTAGG
2677145 TTTTGAGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
14 7 0.29
15 9 0.38
16 3 0.12
17 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (16 bp):
ATTTGAAATTTTAGGG
Found at i:2677149 original size:16 final size:16
Alignment explanation
Indices: 2677099--2677152 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
2677089 GAGATTGAGT
2677099 ATTTGAG-ATTTTAGGG
1 ATTTGAGAATTTTA-GG
2677115 A-TTGA-AA-TTTAGAG
1 ATTTGAGAATTTTAG-G
2677129 ATTTGAGAATTTTAGG
1 ATTTGAGAATTTTAGG
*
2677145 TTTTGAGA
1 ATTTGAGA
2677153 TGAAATTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
13 1 0.03
14 6 0.19
15 9 0.28
16 11 0.34
17 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (16 bp):
ATTTGAGAATTTTAGG
Found at i:2682201 original size:13 final size:12
Alignment explanation
Indices: 2682171--2682195 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2682161 TATGTAAATC
2682171 AAATATGAAAAA
1 AAATATGAAAAA
2682183 AAATATGAAAAA
1 AAATATGAAAAA
2682195 A
1 A
2682196 CTATATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAATATGAAAAA
Found at i:2685364 original size:108 final size:105
Alignment explanation
Indices: 2685173--2685567 Score: 300
Period size: 108 Copynumber: 3.7 Consensus size: 105
2685163 AACAGTATTG
* * * *
2685173 TTGTTCTCATTCTGTCTTGCATTCTCACTG---TTGTTGCAGCTCTGGGAAGCATTGTTCCCA-T
1 TTGTTCTCATTCTGACTTGCATTCTCACTGTTATTGTTGTAGCTCTGGGAAGCATTATTCTCATT
* * * * *
2685234 CCATACCTGCATGCTCGTTGTTGGTGGCTAT-TTGAACAGCG
66 CC-GACCTGCATTCTCATTGTTGTTGG-TATATTGAACAGCA
*
2685275 TTGTTCTCATTCTGACTTGCATTCTCACTGTTATTGCTGTTGTAGTTCTGGGAAGCATTATTCTC
1 TTGTTCTCATTCTGACTTGCATTCTCACTGTTA-T--TGTTGTAGCTCTGGGAAGCATTATTCTC
* * * * * * *
2685340 ATTCCGACCTGCATTTTCTTTGTTGTT-ATTTCTCTTAGCAGCA
63 ATTCCGACCTGCATTCTCATTGTTGTTGGTATAT-TGAACAGCA
* ** * * * * * *
2685383 TTGTTCTCATTCTCACTTGCATTCTCGTTGTTGTTGGTGTTGATCT-GAACAGCATCATTGTTCT
1 TTGTTCTCATTCTGACTTGCATTCTCACTGTTATTGTTGTAGCTCTGGGA-AG---CATTATTCT
* * *
2685447 CAATCCGACTTGTATTCTCATTGTTGTTGGTATTGATCTGAACATGATCA
62 CATTCCGACCTGCATTCTCATTGTTGTTGGTA-T-AT-TGAACA-G--CA
* * *
2685497 TTGTTCTCAATCTGACTTGCATTCTCATTGTTATTGTTGTTGCTCTGGGAAGCATTATTCTCATT
1 TTGTTCTCATTCTGACTTGCATTCTCACTGTTATTGTTGTAGCTCTGGGAAGCATTATTCTCATT
*
2685562 CTGACC
66 CCGACC
2685568 AACATTCTGG
Statistics
Matches: 228, Mismatches: 45, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
102 29 0.13
104 2 0.01
105 11 0.05
106 3 0.01
107 2 0.01
108 108 0.47
109 4 0.02
110 1 0.00
111 21 0.09
112 1 0.00
114 44 0.19
115 2 0.01
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (105 bp):
TTGTTCTCATTCTGACTTGCATTCTCACTGTTATTGTTGTAGCTCTGGGAAGCATTATTCTCATT
CCGACCTGCATTCTCATTGTTGTTGGTATATTGAACAGCA
Found at i:2685442 original size:57 final size:57
Alignment explanation
Indices: 2685376--2685543 Score: 223
Period size: 57 Copynumber: 2.9 Consensus size: 57
2685366 TATTTCTCTT
* * *
2685376 AGCAGCATTGTTCTCATTCTCACTTGCATTCTCGTTGTTGTTGGTGTTGATCTGAAC
1 AGCATCATTGTTCTCAATCTCACTTGCATTCTCATTGTTGTTGGTGTTGATCTGAAC
* *
2685433 AGCATCATTGTTCTCAATC-CGACTTGTATTCTCATTGTTGTTGGTATTGATCTGAAC
1 AGCATCATTGTTCTCAATCTC-ACTTGCATTCTCATTGTTGTTGGTGTTGATCTGAAC
* * * *
2685490 ATG-ATCATTGTTCTCAATCTGACTTGCATTCTCATTGTTATTGTTGTTGCTCTG
1 A-GCATCATTGTTCTCAATCTCACTTGCATTCTCATTGTTGTTGGTGTTGATCTG
2685544 GGAAGCATTA
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
56 1 0.01
57 95 0.98
58 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (57 bp):
AGCATCATTGTTCTCAATCTCACTTGCATTCTCATTGTTGTTGGTGTTGATCTGAAC
Found at i:2685601 original size:219 final size:221
Alignment explanation
Indices: 2685275--2685691 Score: 509
Period size: 219 Copynumber: 1.9 Consensus size: 221
2685265 TTGAACAGCG
* *
2685275 TTGTTCTCATTCTGACTTGCATTCTCACTGTTATTGCTGTTGTAGTTCTGGGAAGCATTATTCTC
1 TTGTTCTCAATCTGACTTGCATTCTCACTGTTATT-CTGTTGTAGCTCTGGGAAGCATTATTCTC
** * * * ** *** * **
2685340 ATTCCGACCTGCATTTTCTTTGTTGTTATTTCTCTTAGCAGCATTGTTCTCATTCT-CACTTGCA
65 ATTCCGACCAACATTCTCGTTGTCGGCAACGCTCTGAGCAGCATTGTTCTCATTCTGC-CCAGCA
* * * *
2685404 TTCTCGTTGTTGTTGGTGTTGATCTGAACAGCATCATTGTTCTCAATCCGACTTG-TATTCTCAT
129 TTCTCGTTGTTGTTGGTATTGAGCAGAACAGCATCATTGCTCTCAATCCGACTTGCT-TTCTCAT
2685468 TGTTGTTGGTATTGATCTGAACATGATCA
193 TGTTGTTGGTATTGATCTGAACATGATCA
* *
2685497 TTGTTCTCAATCTGACTTGCATTCTCATTGTTA-T-TGTTGTTGCTCTGGGAAGCATTATTCTCA
1 TTGTTCTCAATCTGACTTGCATTCTCACTGTTATTCTGTTGTAGCTCTGGGAAGCATTATTCTCA
* * *
2685560 TTCTGACCAACATTCTGGTTGTCGGCAACGCTCTGAGCAGCATTGTTCTCATTTTGCCCAGCATT
66 TTCCGACCAACATTCTCGTTGTCGGCAACGCTCTGAGCAGCATTGTTCTCATTCTGCCCAGCATT
* * * * * *
2685625 CTCGTTGTTGTTGTTATTGCGCAGAACAGTATCGTTGCTCTCATTCTGACTTGCTTTCTCATTGT
131 CTCGTTGTTGTTGGTATTGAGCAGAACAGCATCATTGCTCTCAATCCGACTTGCTTTCTCATTGT
2685690 TG
196 TG
2685692 CTCTGGGAAG
Statistics
Matches: 163, Mismatches: 30, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
219 129 0.79
220 2 0.01
221 1 0.01
222 31 0.19
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.43
Consensus pattern (221 bp):
TTGTTCTCAATCTGACTTGCATTCTCACTGTTATTCTGTTGTAGCTCTGGGAAGCATTATTCTCA
TTCCGACCAACATTCTCGTTGTCGGCAACGCTCTGAGCAGCATTGTTCTCATTCTGCCCAGCATT
CTCGTTGTTGTTGGTATTGAGCAGAACAGCATCATTGCTCTCAATCCGACTTGCTTTCTCATTGT
TGTTGGTATTGATCTGAACATGATCA
Found at i:2689772 original size:13 final size:13
Alignment explanation
Indices: 2689754--2689781 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2689744 ATATAATGTA
2689754 TTGTTGACATTTG
1 TTGTTGACATTTG
2689767 TTGTTGACATTTG
1 TTGTTGACATTTG
2689780 TT
1 TT
2689782 ATGAATCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.57
Consensus pattern (13 bp):
TTGTTGACATTTG
Found at i:2691267 original size:124 final size:126
Alignment explanation
Indices: 2691102--2691333 Score: 321
Period size: 124 Copynumber: 1.9 Consensus size: 126
2691092 AATGTCAAAA
* *
2691102 TTAGCGGCGTTTATCATTAAAACGTCGCTATAGATATGTACCTTAGTGGCATTTGTTAT-ATAAA
1 TTAGCGGCGTTTATCATTAAAACGTCGCTATAGAGACGTACCTTAGTGGCATTTGTTATCA-AAA
* * *
2691166 CG-C-C-TTAATAGAGACACCTTAGTGGCGTTTGTTACTAAAACGCTGCTATTGAGGCGAACT
65 CGCCGCAATAAAAGAGA-ACCTTAGTAGCGTTTGTTACTAAAACGCTGCTATTGAGGCGAACT
* *
2691226 TTAGTGGCGTTTATCATTAAAACG-CTGCTATAGAGCCGTACCTTAGTGGCATTTGTTATCAAAA
1 TTAGCGGCGTTTATCATTAAAACGTC-GCTATAGAGACGTACCTTAGTGGCATTTGTTATCAAAA
* *
2691290 CGCCGCAATAAAAGAGAACTTTAGTAGCGTTTGTTATTAAAACG
65 CGCCGCAATAAAAGAGAACCTTAGTAGCGTTTGTTACTAAAACG
2691334 TCGCAATAGA
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
123 1 0.01
124 58 0.62
125 2 0.02
126 25 0.27
127 8 0.09
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (126 bp):
TTAGCGGCGTTTATCATTAAAACGTCGCTATAGAGACGTACCTTAGTGGCATTTGTTATCAAAAC
GCCGCAATAAAAGAGAACCTTAGTAGCGTTTGTTACTAAAACGCTGCTATTGAGGCGAACT
Found at i:2691290 original size:42 final size:42
Alignment explanation
Indices: 2691120--2691292 Score: 144
Period size: 42 Copynumber: 4.2 Consensus size: 42
2691110 GTTTATCATT
* *
2691120 AAAACG-TCGCTATAGATATGTACCTTAGTGGCATTTGTTAT-
1 AAAACGCT-GCTATAGAGACGTACCTTAGTGGCATTTGTTATC
*
2691161 ATAAACGC--CTTAATAGAGAC--ACCTTAGTGGCGTTTGTTA-C
1 A-AAACGCTGC-T-ATAGAGACGTACCTTAGTGGCATTTGTTATC
* * * * * * * *
2691201 TAAAACGCTGCTATTGAGGCGAACTTTAGTGGCGTTTATCATT
1 -AAAACGCTGCTATAGAGACGTACCTTAGTGGCATTTGTTATC
*
2691244 AAAACGCTGCTATAGAGCCGTACCTTAGTGGCATTTGTTATC
1 AAAACGCTGCTATAGAGACGTACCTTAGTGGCATTTGTTATC
2691286 AAAACGC
1 AAAACGC
2691293 CGCAATAAAA
Statistics
Matches: 104, Mismatches: 17, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
40 31 0.30
41 4 0.04
42 69 0.66
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (42 bp):
AAAACGCTGCTATAGAGACGTACCTTAGTGGCATTTGTTATC
Found at i:2691292 original size:84 final size:85
Alignment explanation
Indices: 2691181--2691381 Score: 210
Period size: 84 Copynumber: 2.4 Consensus size: 85
2691171 TAATAGAGAC
* * * ** * * *
2691181 ACCTTAGTGGCGTTTGTTA-CTAAAACGCTGCTATTGAGGCGAACTTTAGTGGCGTTTATCATTA
1 ACCTTAGTGGCATTTGTTATC-AAAACGCCGCAATAAAAGAGAACTTTAGTAGCGTTTATCATTA
* *
2691245 AAACG-CTGCTATAG-AGCCGT
65 AAACGTC-GCAATAGAAGCCAT
* *
2691265 ACCTTAGTGGCATTTGTTATCAAAACGCCGCAATAAAAGAGAACTTTAGTAGCGTTTGTTATTAA
1 ACCTTAGTGGCATTTGTTATCAAAACGCCGCAATAAAAGAGAACTTTAGTAGCGTTTATCATTAA
* *
2691330 AACGTCGCAATAGAATCTAT
66 AACGTCGCAATAGAAGCCAT
* * *
2691350 ACTTTAGTGGCATTTGTTATTAAAATGCCGCA
1 ACCTTAGTGGCATTTGTTATCAAAACGCCGCA
2691382 GTAGAGGCTC
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
84 63 0.65
85 34 0.35
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (85 bp):
ACCTTAGTGGCATTTGTTATCAAAACGCCGCAATAAAAGAGAACTTTAGTAGCGTTTATCATTAA
AACGTCGCAATAGAAGCCAT
Found at i:2691368 original size:43 final size:42
Alignment explanation
Indices: 2691144--2691381 Score: 144
Period size: 42 Copynumber: 5.7 Consensus size: 42
2691134 GATATGTACC
* * *
2691144 TTAGTGGCATTTGTTA-TATAAACG-C-C-TTAATAGAGACACC
1 TTAGTGGCATTTGTTATTA-AAACGCCGCAATAAAAGAGA-ACT
* * * * ** * *
2691184 TTAGTGGCGTTTGTTACTAAAACGCTGCTATTGAGGCGAACT
1 TTAGTGGCATTTGTTATTAAAACGCCGCAATAAAAGAGAACT
* * * * * * * * *
2691226 TTAGTGGCGTTTATCATTAAAACGCTGCTAT-AGAGCCGTACC
1 TTAGTGGCATTTGTTATTAAAACGCCGCAATAAAAG-AGAACT
*
2691268 TTAGTGGCATTTGTTATCAAAACGCCGCAATAAAAGAGAACT
1 TTAGTGGCATTTGTTATTAAAACGCCGCAATAAAAGAGAACT
* * * * ***
2691310 TTAGTAGCGTTTGTTATTAAAACGTCGCAATAGAATCTATACT
1 TTAGTGGCATTTGTTATTAAAACGCCGCAATAAAAGAGA-ACT
*
2691353 TTAGTGGCATTTGTTATTAAAATGCCGCA
1 TTAGTGGCATTTGTTATTAAAACGCCGCA
2691382 GTAGAGGCTC
Statistics
Matches: 152, Mismatches: 39, Indels: 11
0.75 0.19 0.05
Matches are distributed among these distances:
40 20 0.13
41 3 0.02
42 94 0.62
43 35 0.23
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (42 bp):
TTAGTGGCATTTGTTATTAAAACGCCGCAATAAAAGAGAACT
Found at i:2691409 original size:42 final size:42
Alignment explanation
Indices: 2691353--2691460 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
2691343 AATCTATACT
*
2691353 TTAGTGGCA-TTTGTTATTAAAATGCCGCAGTAGAGGCT-CACA
1 TTAGTGG-AGTTTGTTATTAAAATGCCACAGTAGAGG-TGCACA
* * * * *
2691395 TTAGTGGTGTTTGTTGTTGAAACGCCACAGTAGAGGTGCACG
1 TTAGTGGAGTTTGTTATTAAAATGCCACAGTAGAGGTGCACA
*
2691437 TTATTGGAGTTTGTTATTAAAATG
1 TTAGTGGAGTTTGTTATTAAAATG
2691461 TTGCTATAGA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (42 bp):
TTAGTGGAGTTTGTTATTAAAATGCCACAGTAGAGGTGCACA
Found at i:2696115 original size:72 final size:72
Alignment explanation
Indices: 2695998--2696135 Score: 231
Period size: 72 Copynumber: 1.9 Consensus size: 72
2695988 TCTCCTCTTA
* * *
2695998 GCGTGGTTCCCACCCATGTTGATACTTCAATAAACGCATGGGTCCAAGAATTAAATAATGGTAAT
1 GCGTGGTGCCCACCCACGTTGATACTTCAACAAACGCATGGGTCCAAGAATTAAATAATGGTAAT
2696063 GTGCATG
66 GTGCATG
* *
2696070 GCGTGGTGCCTACCCACGTTGATACTTCAACAAACGTATGGGTCCAAGAATTAAATAATGGTAAT
1 GCGTGGTGCCCACCCACGTTGATACTTCAACAAACGCATGGGTCCAAGAATTAAATAATGGTAAT
2696135 G
66 G
2696136 CATATGACGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (72 bp):
GCGTGGTGCCCACCCACGTTGATACTTCAACAAACGCATGGGTCCAAGAATTAAATAATGGTAAT
GTGCATG
Found at i:2699553 original size:26 final size:26
Alignment explanation
Indices: 2699524--2699587 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
2699514 CTGATGTGGT
* *
2699524 AGTTTCTAGAAGGTCCAATCAATGGC
1 AGTTTCTAGAAGGTCCAATCAACGAC
*
2699550 AGTTTCTAGAAGGTCCAGTCAACGAC
1 AGTTTCTAGAAGGTCCAATCAACGAC
2699576 AGTTTCTAGAAG
1 AGTTTCTAGAAG
2699588 ATCTAGTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (26 bp):
AGTTTCTAGAAGGTCCAATCAACGAC
Found at i:2705260 original size:63 final size:63
Alignment explanation
Indices: 2705183--2705305 Score: 228
Period size: 63 Copynumber: 2.0 Consensus size: 63
2705173 GAGGCCGCCG
2705183 ATACTGCAAATGACCCATAGTCTTAGGGCTCTCAAATATCCTAAGTTTGGCTGGTAAGAACCA
1 ATACTGCAAATGACCCATAGTCTTAGGGCTCTCAAATATCCTAAGTTTGGCTGGTAAGAACCA
* *
2705246 ATACTGCAAATGACCCATAGTCTTAGGGCTCTCAAATCTCTTAAGTTTGGCTGGTAAGAA
1 ATACTGCAAATGACCCATAGTCTTAGGGCTCTCAAATATCCTAAGTTTGGCTGGTAAGAA
2705306 TTGAGATGCG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (63 bp):
ATACTGCAAATGACCCATAGTCTTAGGGCTCTCAAATATCCTAAGTTTGGCTGGTAAGAACCA
Found at i:2707847 original size:21 final size:21
Alignment explanation
Indices: 2707781--2707849 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
2707771 AGCATTATCA
* *
2707781 AATAAACTTGACATTCATAAC
1 AATAAACTTGAAATCCATAAC
*
2707802 AACAAACTTGAAATCCATAAC
1 AATAAACTTGAAATCCATAAC
* *
2707823 AATAAACTTTAAATCCATAAT
1 AATAAACTTGAAATCCATAAC
2707844 AATAAA
1 AATAAA
2707850 ACAAAGTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.26
Consensus pattern (21 bp):
AATAAACTTGAAATCCATAAC
Found at i:2708446 original size:43 final size:43
Alignment explanation
Indices: 2708398--2708482 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
2708388 AATTAATCAG
* *
2708398 ATAAGTATATGAATTATAAATATTAAAATTTAAATCTAGTATT
1 ATAAGTATAGGAATTATAAATATTAAAATTTAAATCAAGTATT
2708441 ATAAGTATAGGAATTATAAATATTAAAATTTAAATCAAGTAT
1 ATAAGTATAGGAATTATAAATATTAAAATTTAAATCAAGTAT
2708483 AAGTTAGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (43 bp):
ATAAGTATAGGAATTATAAATATTAAAATTTAAATCAAGTATT
Found at i:2709404 original size:40 final size:39
Alignment explanation
Indices: 2709344--2709431 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 39
2709334 TTCCGCGAAT
*
2709344 CAGCAGATTTCGCAAGGAGAAAGTGAGATCGGCGAAGAAG
1 CAGCAGA-TTCGCAAAGAGAAAGTGAGATCGGCGAAGAAG
*
2709384 CAGCAGATTCAGCAAAGAGAAAGTGAGATCGGGGAAGAAG
1 CAGCAGATTC-GCAAAGAGAAAGTGAGATCGGCGAAGAAG
2709424 CAGCAGAT
1 CAGCAGAT
2709432 GGGTTTGGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 3 0.07
40 42 0.93
ACGTcount: A:0.40, C:0.15, G:0.34, T:0.11
Consensus pattern (39 bp):
CAGCAGATTCGCAAAGAGAAAGTGAGATCGGCGAAGAAG
Found at i:2709644 original size:42 final size:41
Alignment explanation
Indices: 2709598--2709726 Score: 168
Period size: 41 Copynumber: 3.1 Consensus size: 41
2709588 GCCATTACAA
* * * * *
2709598 TACGAGTCTTTAGCGGCATTTGTGCTTAAAACACCATTACAG
1 TACGAGTCTTTAGCGGCGTTTGT-ATAAAAACACCACTAAAG
* * * *
2709640 TACGACTCTTTAGCGGTGTCTGTATAAAAACGCCACTAAAG
1 TACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACTAAAG
2709681 TACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACTAAAG
1 TACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACTAAAG
2709722 TACGA
1 TACGA
2709727 ATATATATAT
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 55 0.74
42 19 0.26
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (41 bp):
TACGAGTCTTTAGCGGCGTTTGTATAAAAACACCACTAAAG
Found at i:2714425 original size:82 final size:82
Alignment explanation
Indices: 2714288--2714482 Score: 268
Period size: 82 Copynumber: 2.4 Consensus size: 82
2714278 CCAAATAATG
* * * *
2714288 GTGGTGCATTACCATCTTCTGCAACTTTTCATAGGTCATTTAATGTATAAGTTAAACAACTTTTC
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTTAATGCATAAGTTAAACAACATTTC
*
2714353 AGAAAAATAGTGAAATA
66 AGAAAAAGAGTGAAATA
* *
2714370 GTGGTGCATTATCATCTTCTGCAACTTTTTAGAGGTCATTTAATGCATAATTTAAACAACATTTC
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTTAATGCATAAGTTAAACAACATTTC
* *
2714435 AGACAACGAGTGAAATA
66 AGAAAAAGAGTGAAATA
*
2714452 GTTGTGTC-TTATCATCTTCAT-CAACTTTTCA
1 GTGGTG-CATTATCATCTTC-TGCAACTTTTCA
2714483 ATGATGTATC
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
82 98 0.98
83 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (82 bp):
GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTTAATGCATAAGTTAAACAACATTTC
AGAAAAAGAGTGAAATA
Found at i:2717845 original size:3 final size:3
Alignment explanation
Indices: 2717837--2717888 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
2717827 TACATTAGTC
*
2717837 ATT ATT ATT ATT AGTC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2717883 ATT ATT
1 ATT ATT
2717889 GTGGTGGTCG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 44 0.96
4 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2720483 original size:41 final size:41
Alignment explanation
Indices: 2720416--2720512 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
2720406 ACTCAACAAA
* *
2720416 AACA-ATTCTTCACTTCTACAACCAAGTTCTCCACCTTGAG
1 AACATATTCTTCACTTCAACAACCAAGTTATCCACCTTGAG
* * *
2720456 AACATATTCTTCACTTCAACGATCAAGTTATCCACCTTTAG
1 AACATATTCTTCACTTCAACAACCAAGTTATCCACCTTGAG
* *
2720497 AATATATTCTACACTT
1 AACATATTCTTCACTT
2720513 TTTTCATGGA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 4 0.08
41 45 0.92
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (41 bp):
AACATATTCTTCACTTCAACAACCAAGTTATCCACCTTGAG
Found at i:2722048 original size:6 final size:6
Alignment explanation
Indices: 2722037--2722066 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2722027 CACTCAATTA
2722037 TATATT TATATT TATATT TATATT T-TATT T
1 TATATT TATATT TATATT TATATT TATATT T
2722067 TAATAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TATATT
Found at i:2722755 original size:22 final size:23
Alignment explanation
Indices: 2722723--2722765 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2722713 ATCGGTTAAA
**
2722723 ATTTATACCGGTTATATTATATT
1 ATTTATACCGGAAATATTATATT
2722746 ATTTA-ACCGGAAATATTATA
1 ATTTATACCGGAAATATTATA
2722766 AAGTACAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (23 bp):
ATTTATACCGGAAATATTATATT
Found at i:2722799 original size:23 final size:23
Alignment explanation
Indices: 2722773--2722820 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2722763 ATAAAGTACA
*
2722773 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
2722796 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
2722819 AT
1 AT
2722821 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2723065 original size:30 final size:29
Alignment explanation
Indices: 2723025--2723091 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
2723015 TCATTTGCAC
* * *
2723025 AAAAAATTATTT-GATTTTTTGATATTTTAT
1 AAAATATTATTTAGAATTTTT-A-ATTTAAT
2723055 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
2723084 AATAATAT
1 AA-AATAT
2723092 ATATCGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:2723276 original size:23 final size:23
Alignment explanation
Indices: 2723247--2723309 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2723237 ATATAACCAC
2723247 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
2723270 TATCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2723293 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2723310 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Done.