Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 97 of 141
Found at i:27582972 original size:18 final size:18
Alignment explanation
Indices: 27582945--27582985 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
27582935 AAAACTAATA
*
27582945 TATTAATATTATTATTAG
1 TATTAATATTAGTATTAG
*
27582963 TATTAGTATTAGTATTAG
1 TATTAATATTAGTATTAG
27582981 TATTA
1 TATTA
27582986 TTATCAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (18 bp):
TATTAATATTAGTATTAG
Found at i:27583442 original size:17 final size:17
Alignment explanation
Indices: 27583388--27583442 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
27583378 CATATGTTTT
*
27583388 TTTTTATATTTTCATAA
1 TTTTTATACTTTCATAA
*
27583405 -TTTTATAC-AT-ATATA
1 TTTTTATACTTTCATA-A
27583420 TATTTTATACTTTCATAA
1 T-TTTTATACTTTCATAA
27583438 TTTTT
1 TTTTT
27583443 GATCATTTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
14 3 0.10
15 2 0.07
16 7 0.23
17 12 0.40
18 3 0.10
19 3 0.10
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTATACTTTCATAA
Found at i:27595564 original size:44 final size:44
Alignment explanation
Indices: 27595386--27595569 Score: 151
Period size: 44 Copynumber: 4.2 Consensus size: 44
27595376 AAGATTACAG
*
27595386 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGA
* * ** ** *
27595430 GTTTTATCTTCCCT-AG-A-TAGTAGGAAGCAGATTTAAG-TCATCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCGAAGATGGTGA
* * * ** * * * *
27595473 GTCCTATCTCCCTGAGCAGTAGTGGAGTGGGTTGAAGATTGTAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGA
*
27595517 ATCTTATATCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGA
27595561 ATCTTATCT
1 ATCTTATCT
27595570 TCCCGAGGTA
Statistics
Matches: 105, Mismatches: 28, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
42 9 0.09
43 21 0.20
44 66 0.63
45 9 0.09
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGA
Found at i:27595585 original size:131 final size:131
Alignment explanation
Indices: 27595346--27595679 Score: 479
Period size: 131 Copynumber: 2.5 Consensus size: 131
27595336 TATCAAGCCT
* ** **
27595346 TATCTCCTTGAGCAGCAGCAGAGTAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * * * *
27595411 AGCAGATCGAAGACGGTGAGTTTTATCTTCCCTAGATAGTAGGAAGCAGATTTAAGTCATCAGTC
66 AGCAGATCGAAGACGGTGAATCTTATCTTCCCGAGATAATAGGAAGCAGATTTAAGCCACCAGTC
27595476 C
131 C
* * * *
27595477 TATCTCCCTGAGCAGTAGTGGAGTGGGTTGAAGATTGTAAATCTTATATCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* *
27595542 AGCAGATCGAAGATGGTGAATCTTATCTTCCCGAGGTAATAGGAAGCAGATTTAAGCCACCAGTC
66 AGCAGATCGAAGACGGTGAATCTTATCTTCCCGAGATAATAGGAAGCAGATTTAAGCCACCAGTC
*
27595607 T
131 C
* **
27595608 TACCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGCAG
1 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
27595673 AGCAGAT
66 AGCAGAT
27595680 TAAAACCATG
Statistics
Matches: 178, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
131 178 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (131 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACGGTGAATCTTATCTTCCCGAGATAATAGGAAGCAGATTTAAGCCACCAGTC
C
Found at i:27598873 original size:18 final size:20
Alignment explanation
Indices: 27598850--27598889 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
27598840 CCCTTTTTAC
27598850 ATATATTA-TTATA-TAAAT
1 ATATATTATTTATATTAAAT
27598868 ATATATTATTTATATTAAAT
1 ATATATTATTTATATTAAAT
27598888 AT
1 AT
27598890 TTCATTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTATTTATATTAAAT
Found at i:27599206 original size:14 final size:14
Alignment explanation
Indices: 27599187--27599214 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27599177 CTTTCGAACG
27599187 TTGATATTGATATT
1 TTGATATTGATATT
27599201 TTGATATTGATATT
1 TTGATATTGATATT
27599215 GACATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (14 bp):
TTGATATTGATATT
Found at i:27604500 original size:28 final size:28
Alignment explanation
Indices: 27604440--27604492 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
27604430 AAGTTTGTAA
* *
27604440 TAATTTTTTTATAATATTTTATGATTAC
1 TAATATTTTTATAATATTTTATCATTAC
*
27604468 TAATATTTTTATTATATTTTA-CATT
1 TAATATTTTTATAATATTTTATCATT
27604493 TTCTAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 3 0.14
28 19 0.86
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (28 bp):
TAATATTTTTATAATATTTTATCATTAC
Found at i:27604517 original size:101 final size:101
Alignment explanation
Indices: 27604404--27604605 Score: 377
Period size: 101 Copynumber: 2.0 Consensus size: 101
27604394 CTTTATTCCG
*
27604404 GGATACACTATTTTTTACTATTTTTAAAGTTTGTAATAATTTTTTTATAATATTTTATGATTACT
1 GGATACAATATTTTTTACTATTTTTAAAGTTTGTAATAATTTTTTTATAATATTTTATGATTACT
27604469 AATATTTTTATTATATTTTACATTTTCTAATAATGT
66 AATATTTTTATTATATTTTACATTTTCTAATAATGT
*
27604505 GGATACAATATTTTTTACTATTTTTAAAGTTTGTAATAATTTTTTTATAATCTTTTATGATTACT
1 GGATACAATATTTTTTACTATTTTTAAAGTTTGTAATAATTTTTTTATAATATTTTATGATTACT
*
27604570 AATATTTTTTTTATATTTTACATTTTCTAATAATGT
66 AATATTTTTATTATATTTTACATTTTCTAATAATGT
27604606 TTATAGTTTT
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (101 bp):
GGATACAATATTTTTTACTATTTTTAAAGTTTGTAATAATTTTTTTATAATATTTTATGATTACT
AATATTTTTATTATATTTTACATTTTCTAATAATGT
Found at i:27604707 original size:22 final size:22
Alignment explanation
Indices: 27604682--27604725 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
27604672 TTTTAGACAA
27604682 TTATATATATTTATA-ATTTTAG
1 TTATATAT-TTTATATATTTTAG
27604704 TTATATATTTTATATATTTTAG
1 TTATATATTTTATATATTTTAG
27604726 ATTTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (22 bp):
TTATATATTTTATATATTTTAG
Found at i:27604835 original size:20 final size:20
Alignment explanation
Indices: 27604812--27604872 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
27604802 TATATTTCTA
27604812 TTATATATTTTT-TACAATTT
1 TTATATATTTTTATA-AATTT
27604832 TTATATATTTTTAATAAATTT
1 TTATATATTTTT-ATAAATTT
27604853 TTA-ATA--TTTA-AAATTT
1 TTATATATTTTTATAAATTT
27604869 TTAT
1 TTAT
27604873 TAAAATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.24
17 1 0.03
18 3 0.08
20 15 0.39
21 8 0.21
22 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATATTTTTATAAATTT
Found at i:27604880 original size:19 final size:20
Alignment explanation
Indices: 27604841--27604892 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
27604831 TTTATATATT
*
27604841 TTTAATAA-ATTT-TTAATA
1 TTTAATAATATTTATTAAAA
*
27604859 TTTAA-AATTTTTATTAAAA
1 TTTAATAATATTTATTAAAA
27604878 TTTAATAATATTTAT
1 TTTAATAATATTTAT
27604893 AAATTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.07
18 8 0.29
19 10 0.36
20 8 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAATAATATTTATTAAAA
Found at i:27604895 original size:19 final size:19
Alignment explanation
Indices: 27604841--27604900 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
27604831 TTTATATATT
* *
27604841 TTTAATAA-ATTTTTAATA
1 TTTAATAATATTTATAAAA
*
27604859 TTTAA-AATTTTTATTAAAA
1 TTTAATAATATTTA-TAAAA
*
27604878 TTTAATAATATTTATAAAT
1 TTTAATAATATTTATAAAA
27604897 TTTA
1 TTTA
27604901 TTGATTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 2 0.06
18 8 0.24
19 17 0.50
20 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAATAATATTTATAAAA
Found at i:27619318 original size:13 final size:13
Alignment explanation
Indices: 27619300--27619326 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27619290 TTTCGGTTTA
27619300 ATTTAAACAATAT
1 ATTTAAACAATAT
27619313 ATTTAAACAATAT
1 ATTTAAACAATAT
27619326 A
1 A
27619327 GTTGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAACAATAT
Found at i:27620998 original size:23 final size:23
Alignment explanation
Indices: 27620963--27621007 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
27620953 CCTTATTTAA
**
27620963 TTCAAATTGATTAT-AATATTATT
1 TTCAAATAAATTATCAA-ATTATT
27620986 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
27621008 AAAATGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATT
Found at i:27624282 original size:91 final size:91
Alignment explanation
Indices: 27624156--27624363 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
27624146 TTGATTTTAG
* *
27624156 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
27624221 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
27624248 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
27624313 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
27624339 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
27624364 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:27624332 original size:26 final size:28
Alignment explanation
Indices: 27624278--27624338 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
27624268 TATTATCAAG
* *
27624278 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
27624306 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
27624332 AATTATA
1 AATTATA
27624339 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:27624338 original size:44 final size:43
Alignment explanation
Indices: 27624196--27624338 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
27624186 GAATTTTATG
* *
27624196 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
27624240 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
27624287 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
27624331 AAATTATA
1 AAATTATA
27624339 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:27624455 original size:59 final size:57
Alignment explanation
Indices: 27624390--27624578 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
27624380 ATTTTATTAA
27624390 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTATATTTTA-AGT
* * ** * *
27624449 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTAATTAGAATT-T-TATTAA--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATATTTTAAGT
* * * *
27624510 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTATATTTTA-AGT
27624569 ATCATATATT
1 ATCATATATT
27624579 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 13 0.13
55 8 0.08
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATATTTTAAGT
Found at i:27624507 original size:120 final size:120
Alignment explanation
Indices: 27624379--27624676 Score: 501
Period size: 120 Copynumber: 2.5 Consensus size: 120
27624369 AATTATTTTA
* *
27624379 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
*
27624443 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTAATT-AG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATT-ATTAAG
* *
27624499 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
27624564 ACAGTATCATATATTATGATTTGAGTAAATTCGTATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
27624619 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
27624677 ATGATTAAAT
Statistics
Matches: 167, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
119 3 0.02
120 157 0.94
121 7 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:27624539 original size:15 final size:15
Alignment explanation
Indices: 27624504--27624555 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
27624494 ATTAGAATTT
*
27624504 TATTAAATTAT-ATA
1 TATTTAATTATAATA
27624518 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
27624532 TATTTAATAATAAT-
1 TATTTAATTATAATA
27624546 TATGTTAATT
1 TAT-TTAATT
27624556 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:27624636 original size:59 final size:59
Alignment explanation
Indices: 27624453--27624636 Score: 157
Period size: 59 Copynumber: 3.1 Consensus size: 59
27624443 TATAGTATCA
27624453 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTAATTAGAATTTTATTAAAT
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTAATTAGAATTTTATTAAAT
* * * * * * * *
27624512 TATA-TAT--TTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-CAGTAT
1 TATATTATGATTTGAGTA-AAT-TCATATAAGAAT-ATTA-ATTAA-TTAGAATTTTATTA-AAT
*
27624571 CATATATTATGATTTGAGTAAATTCGTATAAGAATATTAATT-ATTAAGAATTTTATTAAAT
1 --TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTAATT-AGAATTTTATTAAAT
27624632 TATAT
1 TATAT
27624637 ATTTTAATTA
Statistics
Matches: 93, Mismatches: 17, Indels: 30
0.66 0.12 0.21
Matches are distributed among these distances:
56 6 0.06
57 11 0.12
58 9 0.10
59 23 0.25
60 5 0.05
61 14 0.15
62 9 0.10
63 10 0.11
64 6 0.06
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.48
Consensus pattern (59 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTAATTAGAATTTTATTAAAT
Found at i:27624648 original size:18 final size:17
Alignment explanation
Indices: 27624620--27624654 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27624610 ATTATTAAGA
*
27624620 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
27624637 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
27624655 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:27625321 original size:16 final size:18
Alignment explanation
Indices: 27625300--27625339 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
27625290 TGTATGCTTG
*
27625300 TGAAATTGTGAA-A-ATA
1 TGAAATTATGAACATATA
27625316 TGAAATTATGAACATATA
1 TGAAATTATGAACATATA
27625334 TGAAAT
1 TGAAAT
27625340 GCTATGGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 1 0.05
18 9 0.43
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.33
Consensus pattern (18 bp):
TGAAATTATGAACATATA
Found at i:27627399 original size:35 final size:35
Alignment explanation
Indices: 27627360--27627426 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
27627350 TGTTTCGGAG
27627360 GGACTAGCTGTTATGAGCATTGCTGTGTTTCGACT
1 GGACTAGCTGTTATGAGCATTGCTGTGTTTCGACT
* *
27627395 GGACTAGCTTTTATGAGCATTGGTGTGTTTCG
1 GGACTAGCTGTTATGAGCATTGCTGTGTTTCG
27627427 GAGGGGTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.16, C:0.15, G:0.30, T:0.39
Consensus pattern (35 bp):
GGACTAGCTGTTATGAGCATTGCTGTGTTTCGACT
Found at i:27636440 original size:50 final size:53
Alignment explanation
Indices: 27636342--27636517 Score: 141
Period size: 50 Copynumber: 3.4 Consensus size: 53
27636332 TGAGATCCAT
* * **
27636342 TGTAAGACCATGTCTGGGACATGGCATTGACATCATTGAGATTATGAGAGGTTTCA
1 TGTAAGACCATGTCTGGGACATAGCATTGACA-CATCGAG--TATGAGAGGTCCCA
* *
27636398 TGTAAGACCATGTCTGGGACATAGCGTTG-C-CATCGAG-ATGAGAGGTCCCC
1 TGTAAGACCATGTCTGGGACATAGCATTGACACATCGAGTATGAGAGGTCCCA
* * * * **
27636448 CGTAAGACCATGTCTAGGACAT-GACATGGGGCAC--CGA-TATGAGAACTCCCA
1 TGTAAGACCATGTCTGGGACATAG-CAT-TGACACATCGAGTATGAGAGGTCCCA
*
27636499 TGTAAGACCATATCTGGGA
1 TGTAAGACCATGTCTGGGA
27636518 TGTAGCGTTG
Statistics
Matches: 99, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
49 1 0.01
50 32 0.32
51 30 0.30
52 1 0.01
53 7 0.07
55 1 0.01
56 27 0.27
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (53 bp):
TGTAAGACCATGTCTGGGACATAGCATTGACACATCGAGTATGAGAGGTCCCA
Found at i:27638242 original size:26 final size:26
Alignment explanation
Indices: 27638194--27638243 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
27638184 ATAATTAATG
*
27638194 AATTTAAAATAAATAATATATATGAA
1 AATTTAAAATAAATAATAAATATGAA
*
27638220 AATTTGAAATAAATTAA-AAATATG
1 AATTTAAAATAAA-TAATAAATATG
27638244 GTTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (26 bp):
AATTTAAAATAAATAATAAATATGAA
Found at i:27638703 original size:27 final size:27
Alignment explanation
Indices: 27638656--27638716 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
27638646 TAGGTTAATT
* *
27638656 TTAAAAT-AAGTAATATGTAAAATAAC
1 TTAAAATAAAATAATATATAAAATAAC
*
27638682 TTAAAATAAAATAATATATAAAGTAAC
1 TTAAAATAAAATAATATATAAAATAAC
27638709 TTAAAATA
1 TTAAAATA
27638717 CTTAGGCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (27 bp):
TTAAAATAAAATAATATATAAAATAAC
Found at i:27638765 original size:21 final size:21
Alignment explanation
Indices: 27638736--27638775 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27638726 ATGAGTTAGG
27638736 TTAAAATAATAAATAAAAGGT
1 TTAAAATAATAAATAAAAGGT
* **
27638757 TTAATATAATCTATAAAAG
1 TTAAAATAATAAATAAAAG
27638776 AGAAAATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAAATAATAAATAAAAGGT
Found at i:27640428 original size:50 final size:48
Alignment explanation
Indices: 27640353--27641221 Score: 301
Period size: 50 Copynumber: 17.6 Consensus size: 48
27640343 TCGAGGAAGC
* * *
27640353 AAGATTCGCTGTTGTATCTTCAATCTGTTCCACTACACTGCCTGGAAAGT
1 AAGATTCGCTGTTGTAGCTTTAATCT-TTCCACTGCACTG-CTGGAAAGT
* * * * * * *
27640403 AAGATTCGCTATTGTAGCTTTAATCTTTCTAATTGCAATATCGGGAAAGC
1 AAGATTCGCTGTTGTAGCTTTAATCTTTC-CACTGCACT-GCTGGAAAGT
* * * * *
27640453 AAGATTCGCCGTTGTGGCATTAATCTATTCCACTGCACCGCTTGAGAAGT
1 AAGATTCGCTGTTGTAGCTTTAATCT-TTCCACTGCACTGCTGGA-AAGT
* ** * * * * * *
27640503 AAGATTCGCTGTTGTAGCTTTAATATTTTTAATTGTAATGTCGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTTAAT-CTTTCCACTGCACTG-CTGGAAAGT
* ** * * ** **
27640553 AAGGTTCGCCATTGTGGCTTTAATCTGTTCCACTGCGTCACCTGGGGAGT
1 AAGATTCGCTGTTGTAGCTTTAATCT-TTCCACTGC-ACTGCTGGAAAGT
* * * * * * *
27640603 AAGATTCGCTGTGGTAGC--T--T-TTT-AACTACAATGTTGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTTAATCTTTCCACTGCACTGCT-GGAAAGT
* * * * **
27640646 AAGATTCACCGATGTGGC-TTAATCTGTTCCACTGCA-TAGCTTGGGGAGT
1 AAGATTCGCTGTTGTAGCTTTAATCT-TTCCACTGCACT-GC-TGGAAAGT
** * *
27640695 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATG-TCGGAGAAGG
1 AAGATTCGCTGTTGTAGCTTTAATC-TTTCCACTGCACTGCT-GGA-AAGT
* * * * * *
27640745 AAGATTCACCGATGTGGCTTTAATATGTTCCACTGCA-TCGCCTGGAGAGT
1 AAGATTCGCTGTTGTAGCTTTAATCT-TTCCACTGCACT-G-CTGGAAAGT
* ** * * * *
27640795 AAGATTTGCTGTTGTAGCTTTAATCTTTGTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTTAATCTTT-CCACTGCACTG-CTGGAAAGT
* * * * * * **
27640845 AAGATTCACCGATGTGGCTTTAATCTATTCCGCTACATCT-CTTGGGGAGT
1 AAGATTCGCTGTTGTAGCTTTAATCT-TTCCACTGCA-CTGC-TGGAAAGT
** * * * *
27640895 AAGATTCGCTGTTGTAGCTTTAATCTTTTAACTGCAATGTCAGGGAAGC
1 AAGATTCGCTGTTGTAGCTTTAATCTTTCCACTGCACTG-CTGGAAAGT
* * * * **
27640944 AAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCA-TCGTCTGGGGAGT
1 AAGATTCGCTGTTGTAGCTTTAATCT-TTCCACTGCACT-G-CTGGAAAGT
** * * * *
27640994 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAAGC
1 AAGATTCGCTGTTGTAGCTTTAATC-TTTCCACTGCACTG-CTGGAAAGT
* * * * * **
27641044 AAGATTCACCGATGTGGCTTTAATCTGTTCCACTGTA-TCGTCTGGGGAGT
1 AAGATTCGCTGTTGTAGCTTTAATCT-TTCCACTGCACT-G-CTGGAAAGT
* ** * * * *
27641094 AAGATTCGCTGTTGTAGCTCTAATCTTTTTAACTGAAATGTCGGGGAAGT
1 AAGATTCGCTGTTGTAGCTTTAATC-TTTCCACTGCACTG-CTGGAAAGT
* * * * *
27641144 AAGATTCACTGATATGGCTTTAATCTGTTCCACTGCA-TCGCCTGTG-GAGT
1 AAGATTCGCTGTTGTAGCTTTAATCT-TTCCACTGCACT-G-CTG-GAAAGT
27641194 AAGATTCGCTGTTGTAGCTTTAATCTTT
1 AAGATTCGCTGTTGTAGCTTTAATCTTT
27641222 TTAATTGCAA
Statistics
Matches: 590, Mismatches: 185, Indels: 89
0.68 0.21 0.10
Matches are distributed among these distances:
42 1 0.00
43 22 0.04
44 3 0.01
45 1 0.00
46 2 0.00
47 1 0.00
48 6 0.01
49 79 0.13
50 454 0.77
51 20 0.03
52 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (48 bp):
AAGATTCGCTGTTGTAGCTTTAATCTTTCCACTGCACTGCTGGAAAGT
Found at i:27640503 original size:100 final size:100
Alignment explanation
Indices: 27640320--27641299 Score: 1268
Period size: 100 Copynumber: 9.9 Consensus size: 100
27640310 TAACTCGTAA
** * * * * ** *
27640320 CTTTAAT-TTGTTTAACTGTGATGTCGAGGAAGCAAGATTCGCTGTTGTATCTTCAATCTGTTCC
1 CTTTAATCTT-TTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCC
* * ** *
27640384 ACTACA-CTGCCTGGAAAGTAAGATTCGCTATTGTAG
65 ACTGCATC-GCTTGGGGAGTAAGATTCGCTGTTGTAG
* * * * * * * *
27640420 CTTTAATCTTTCTAATTGCAATATCGGGAAAGCAAGATTCGCCGTTGTGGCATTAATCTATTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* * *
27640485 CTGCACCGCTTGAGAAGTAAGATTCGCTGTTGTAG
66 CTGCATCGCTTGGGGAGTAAGATTCGCTGTTGTAG
* * * * *
27640520 CTTTAATATTTTTAATTGTAATGTCGGGGAAGCAAGGTTCGCC-ATTGTGGCTTTAATCTGTTCC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGTTCC
* * *
27640584 ACTGCGTCACCTGGGGAGTAAGATTCGCTG-TG--G
65 ACTGCATCGCTTGGGGAGTAAGATTCGCTGTTGTAG
* * *
27640617 ---T-AGCTTTTTAACTACAATGTTGGGGAAGCAAGATTCACCGATGTGGC-TTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
*
27640677 CTGCATAGCTTGGGGAGTAAGATTCGCTGTTGTAG
66 CTGCATCGCTTGGGGAGTAAGATTCGCTGTTGTAG
* * *
27640712 CTTTAATCTTTTTAACTGCAATGTCGGAGAAGGAAGATTCACCGATGTGGCTTTAATATGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* * *
27640777 CTGCATCGCCTGGAGAGTAAGATTTGCTGTTGTAG
66 CTGCATCGCTTGGGGAGTAAGATTCGCTGTTGTAG
* * *
27640812 CTTTAATCTTTGTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTATTCCG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* *
27640877 CTACATCTCTTGGGGAGTAAGATTCGCTGTTGTAG
66 CTGCATCGCTTGGGGAGTAAGATTCGCTGTTGTAG
*
27640912 CTTTAATC-TTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
27640976 CTGCATCG-TCTGGGGAGTAAGATTCGCTGTTGTAG
66 CTGCATCGCT-TGGGGAGTAAGATTCGCTGTTGTAG
*
27641011 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
*
27641076 CTGTATCG-TCTGGGGAGTAAGATTCGCTGTTGTAG
66 CTGCATCGCT-TGGGGAGTAAGATTCGCTGTTGTAG
* * * * *
27641111 CTCTAATCTTTTTAACTGAAATGTCGGGGAAGTAAGATTCACTGATATGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* *
27641176 CTGCATCGCCTGTGGAGTAAGATTCGCTGTTGTAG
66 CTGCATCGCTTGGGGAGTAAGATTCGCTGTTGTAG
* *
27641211 CTTTAATCTTTTTAATTGCAATATCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
*
27641276 CTGCACCGCTTGGGGAGTAAGATT
66 CTGCATCGCTTGGGGAGTAAGATT
27641300 TGCTATTCTC
Statistics
Matches: 773, Mismatches: 92, Indels: 30
0.86 0.10 0.03
Matches are distributed among these distances:
92 38 0.05
93 38 0.05
94 2 0.00
95 1 0.00
97 1 0.00
98 2 0.00
99 134 0.17
100 554 0.72
101 3 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
CTGCATCGCTTGGGGAGTAAGATTCGCTGTTGTAG
Found at i:27641248 original size:50 final size:50
Alignment explanation
Indices: 27640620--27641269 Score: 455
Period size: 50 Copynumber: 13.0 Consensus size: 50
27640610 GCTGTGGTAG
* * * * *
27640620 CTTTTTAACTACAATGTTGGGGAAGCAAGATTCACCGATGTGGC-TTAAT
1 CTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGATGTAGCTTTAAT
* ** * * *
27640669 CTGTTCCACTGC-ATAGCTTGGGG-AGTAAGATTCGCTGTTGTAGCTTTAAT
1 CTTTTTAACTGCAAT-G-TCGGGGAAGTAAGATTCACTGATGTAGCTTTAAT
* * * *
27640719 CTTTTTAACTGCAATGTCGGAGAAGGAAGATTCACCGATGTGGCTTTAAT
1 CTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGATGTAGCTTTAAT
* * ** ** ** *
27640769 ATGTTCCACTGC-ATCG-CCTGGAGAGTAAGATTTGCTGTTGTAGCTTTAAT
1 CTTTTTAACTGCAAT-GTCGGGGA-AGTAAGATTCACTGATGTAGCTTTAAT
* * * *
27640819 CTTTGTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAAT
1 CTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGATGTAGCTTTAAT
* *** * * * *
27640869 CTATTCCGCTAC-ATCTCTTGGGG-AGTAAGATTCGCTGTTGTAGCTTTAAT
1 CTTTTTAACTGCAATGTC--GGGGAAGTAAGATTCACTGATGTAGCTTTAAT
* * * *
27640919 C-TTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAAT
1 CTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGATGTAGCTTTAAT
* ** * *
27640968 CTGTTCCACTGC-ATCGTCTGGGG-AGTAAGATTCGCTGTTGTAGCTTTAAT
1 CTTTTTAACTGCAAT-GTC-GGGGAAGTAAGATTCACTGATGTAGCTTTAAT
* * * *
27641018 CTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAAT
1 CTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGATGTAGCTTTAAT
* ** * * * *
27641068 CTGTTCCACTG-TATCGTCTGGGG-AGTAAGATTCGCTGTTGTAGCTCTAAT
1 CTTTTTAACTGCAAT-GTC-GGGGAAGTAAGATTCACTGATGTAGCTTTAAT
* * *
27641118 CTTTTTAACTGAAATGTCGGGGAAGTAAGATTCACTGATATGGCTTTAAT
1 CTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGATGTAGCTTTAAT
* ** * * * *
27641168 CTGTTCCACTGC-ATCGCCTGTGG-AGTAAGATTCGCTGTTGTAGCTTTAAT
1 CTTTTTAACTGCAAT-GTC-GGGGAAGTAAGATTCACTGATGTAGCTTTAAT
* * * * *
27641218 CTTTTTAATTGCAATATCGGGGAAGCAAGATTCACCGATGTGGCTTTAAT
1 CTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGATGTAGCTTTAAT
27641268 CT
1 CT
27641270 GTTCCACTGC
Statistics
Matches: 446, Mismatches: 129, Indels: 51
0.71 0.21 0.08
Matches are distributed among these distances:
48 5 0.01
49 82 0.18
50 332 0.74
51 27 0.06
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (50 bp):
CTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGATGTAGCTTTAAT
Found at i:27641415 original size:44 final size:44
Alignment explanation
Indices: 27641366--27641516 Score: 132
Period size: 44 Copynumber: 3.4 Consensus size: 44
27641356 ACTCTACTGT
* *
27641366 AACTTCAGAGAGATAAGATCTATT-ACTTTAATCCGCTCCACTAC
1 AACTTCAGGGAGATAAGAT-TATTGACTTCAATCCGCTCCACTAC
* * *
27641410 AACTTCAGGGAGAT-AGAATTATTGGCTTCAATCTGCTCCACTGC
1 AACTTCAGGGAGATAAG-ATTATTGACTTCAATCCGCTCCACTAC
* * *
27641454 AACCTCAGGGAGATAAGA-T-TTGCCATCTTCGATCTG-TCCCACTAC
1 AACTTCAGGGAGATAAGATTATTG--A-CTTCAATCCGCT-CCACTAC
*
27641499 AACTTCAGGGGGATAAGA
1 AACTTCAGGGAGATAAGA
27641517 CCTACTTACT
Statistics
Matches: 89, Mismatches: 11, Indels: 13
0.79 0.10 0.12
Matches are distributed among these distances:
42 3 0.03
43 7 0.08
44 46 0.52
45 33 0.37
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (44 bp):
AACTTCAGGGAGATAAGATTATTGACTTCAATCCGCTCCACTAC
Found at i:27641507 original size:45 final size:45
Alignment explanation
Indices: 27641395--27641516 Score: 122
Period size: 45 Copynumber: 2.7 Consensus size: 45
27641385 CTATTACTTT
* ***
27641395 AATCCGCTCCACTACAACTTCAGGGAGAT-AGAATTATTGGCTTC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGAATTACCAGCTTC
* * * * *
27641439 AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGAATTACCAGCTTC
* *
27641484 GATCTG-TCCCACTACAACTTCAGGGGGATAAGA
1 AATCTGCT-CCACTACAACTTCAGGGAGATAAGA
27641517 CCTACTTACT
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
44 27 0.43
45 36 0.57
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (45 bp):
AATCTGCTCCACTACAACTTCAGGGAGATAAGAATTACCAGCTTC
Found at i:27641761 original size:44 final size:43
Alignment explanation
Indices: 27641658--27641903 Score: 295
Period size: 44 Copynumber: 5.7 Consensus size: 43
27641648 TAATTTCTCA
**
27641658 ACCTATTCCACTGCTGACCAGGGAGA-TAGGACTT--A-TCTTCC
1 ACCTATTCCACTGCTGGTCAGGGA-ACTAGG-CTTACAGTCTTCC
*
27641699 ACCTATTCCACTGCTGGTCAGGGAACTAGAGCTTACAGTTTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTAG-GCTTACAGTCTTCC
* * * *
27641743 ATCTATTCTATTGTTGGTCAGGGAACTAGGGCTTACAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTA-GGCTTACAGTCTTCC
* **
27641787 ACCTATTCCACTCCTGGTCAGGGAACTAGGACTTACAACCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTAGG-CTTACAGTCTTCC
*
27641831 ACCTATTCCACTGTTGGTCAGGG-ACTAGGACTTACAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTAGG-CTTACAGTCTTCC
*
27641874 ACCTATTCCGCTGCTGGTCAGGGAACTAGG
1 ACCTATTCCACTGCTGGTCAGGGAACTAGG
27641904 GCTTGTGATT
Statistics
Matches: 176, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
40 1 0.01
41 28 0.16
42 1 0.01
43 42 0.24
44 103 0.59
45 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (43 bp):
ACCTATTCCACTGCTGGTCAGGGAACTAGGCTTACAGTCTTCC
Found at i:27643207 original size:15 final size:17
Alignment explanation
Indices: 27643171--27643206 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
27643161 GCCTATCTAC
27643171 TTTTACTTTTTCATTTT
1 TTTTACTTTTTCATTTT
27643188 TTTTA-TTTTTCATTTT
1 TTTTACTTTTTCATTTT
27643204 TTT
1 TTT
27643207 ACTCAAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTACTTTTTCATTTT
Found at i:27644126 original size:20 final size:20
Alignment explanation
Indices: 27644087--27644127 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
27644077 TTGACCTATC
*
27644087 CTTTTCTCTTTTTTTCTTTT
1 CTTTTCTCTTTTTATCTTTT
27644107 CTTTT-TCTTTTTATCATTTT
1 CTTTTCTCTTTTTATC-TTTT
27644127 C
1 C
27644128 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (20 bp):
CTTTTCTCTTTTTATCTTTT
Found at i:27649410 original size:27 final size:27
Alignment explanation
Indices: 27649363--27649423 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
27649353 TAGGTTAATT
* *
27649363 TTAAAAT-AAGTAATATGTAAAATAAC
1 TTAAAATAAAATAATATATAAAATAAC
*
27649389 TTAAAATAAAATAATATATAAAGTAAC
1 TTAAAATAAAATAATATATAAAATAAC
27649416 TTAAAATA
1 TTAAAATA
27649424 CTTAGGCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (27 bp):
TTAAAATAAAATAATATATAAAATAAC
Found at i:27649472 original size:21 final size:21
Alignment explanation
Indices: 27649443--27649482 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27649433 ATGAGTTAGG
27649443 TTAAAATAATAAATAAAAGGT
1 TTAAAATAATAAATAAAAGGT
* **
27649464 TTAATATAATCTATAAAAG
1 TTAAAATAATAAATAAAAG
27649483 AGAAAATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAAATAATAAATAAAAGGT
Found at i:27654870 original size:15 final size:15
Alignment explanation
Indices: 27654850--27654885 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
27654840 TGTAAGGAGG
27654850 AAGAAATACAGTGTA
1 AAGAAATACAGTGTA
27654865 AAGAAATACAGTGTA
1 AAGAAATACAGTGTA
*
27654880 AGGAAA
1 AAGAAA
27654886 GGAATAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.17
Consensus pattern (15 bp):
AAGAAATACAGTGTA
Found at i:27655011 original size:14 final size:14
Alignment explanation
Indices: 27654994--27655031 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
27654984 GTGGAGGACC
27654994 GGAGGTGGATCGGT
1 GGAGGTGGATCGGT
27655008 GGAGGTGGATCGGT
1 GGAGGTGGATCGGT
27655022 GGAGGTGGAT
1 GGAGGTGGAT
27655032 TGGGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.16, C:0.05, G:0.58, T:0.21
Consensus pattern (14 bp):
GGAGGTGGATCGGT
Found at i:27656616 original size:3 final size:3
Alignment explanation
Indices: 27656608--27656636 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
27656598 TATATTAGTT
27656608 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
27656637 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:27658037 original size:14 final size:14
Alignment explanation
Indices: 27658018--27658045 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27658008 TAAAGTTATA
27658018 TTTAATATTTCATT
1 TTTAATATTTCATT
27658032 TTTAATATTTCATT
1 TTTAATATTTCATT
27658046 AATAAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTAATATTTCATT
Found at i:27667395 original size:19 final size:19
Alignment explanation
Indices: 27667368--27667437 Score: 51
Period size: 19 Copynumber: 3.8 Consensus size: 19
27667358 AAATAAGAGT
*
27667368 TCATTTCTCACTTTTTCAA
1 TCATCTCTCACTTTTTCAA
*
27667387 TCATCTCTCA----TCCAA
1 TCATCTCTCACTTTTTCAA
**
27667402 TCATCTCTCACTCATTC-A
1 TCATCTCTCACTTTTTCAA
27667420 TCATTCTCTCAACTTTTT
1 TCA-TCTCTC-ACTTTTT
27667438 TATCTATCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
15 14 0.35
18 4 0.10
19 17 0.43
20 5 0.12
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.46
Consensus pattern (19 bp):
TCATCTCTCACTTTTTCAA
Found at i:27669477 original size:26 final size:26
Alignment explanation
Indices: 27669448--27669516 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 26
27669438 TATTCAATAT
*
27669448 ATGTTATTAATTGTGTTACTACCTCC
1 ATGTTATTAATTGTGTTACTACCTCA
* * *
27669474 ATGTCATTTGAATCGTGTTACTACTTCA
1 ATGTTA-TT-AATTGTGTTACTACCTCA
*
27669502 ATGCTATTAATTGTG
1 ATGTTATTAATTGTG
27669517 CAGTTCATCT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
26 11 0.32
27 4 0.12
28 19 0.56
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (26 bp):
ATGTTATTAATTGTGTTACTACCTCA
Found at i:27673473 original size:25 final size:25
Alignment explanation
Indices: 27673409--27673477 Score: 93
Period size: 27 Copynumber: 2.7 Consensus size: 25
27673399 GGTGTTGCCT
*
27673409 CTCTCTTACCCTCCACCGGTGCCAC
1 CTCTCTCACCCTCCACCGGTGCCAC
* *
27673434 CTCTTTCTCACCCTCCACTGGTGTCAC
1 CTC--TCTCACCCTCCACCGGTGCCAC
27673461 CTCTCTCACCCTCCACC
1 CTCTCTCACCCTCCACC
27673478 AATTAAATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 16 0.42
27 22 0.58
ACGTcount: A:0.12, C:0.52, G:0.09, T:0.28
Consensus pattern (25 bp):
CTCTCTCACCCTCCACCGGTGCCAC
Found at i:27676030 original size:11 final size:11
Alignment explanation
Indices: 27676007--27676053 Score: 76
Period size: 11 Copynumber: 4.2 Consensus size: 11
27675997 AACAAATCCT
27676007 CTCTCATATTTC
1 CTCTCA-ATTTC
27676019 CTCTCAATTTC
1 CTCTCAATTTC
*
27676030 CTCTCAATTTT
1 CTCTCAATTTC
27676041 CTCTCAATTTC
1 CTCTCAATTTC
27676052 CT
1 CT
27676054 TCCAAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
11 27 0.82
12 6 0.18
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:27676089 original size:51 final size:51
Alignment explanation
Indices: 27676033--27676156 Score: 178
Period size: 51 Copynumber: 2.4 Consensus size: 51
27676023 CAATTTCCTC
* * *
27676033 TCAATTTTCTCTCAATTTCCTTCCAAAATTATCAT-AAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAAATATC-TCAAACCCATATTTAATT
* *
27676084 TCAATTTCCTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAAATATCTCAAACCCATATTTAATT
*
27676135 TCAATTTGCTCTCAATTTCCTT
1 TCAATTTCCTCTCAATTTCCTT
27676157 TTTTAAAATA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 1 0.02
51 64 0.98
ACGTcount: A:0.31, C:0.25, G:0.01, T:0.44
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCCAAAAATATCTCAAACCCATATTTAATT
Found at i:27677283 original size:7 final size:7
Alignment explanation
Indices: 27677267--27677298 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
27677257 TGCTAATAGA
*
27677267 TATTTTG
1 TATTTAG
27677274 TATTTAG
1 TATTTAG
27677281 TATTTAG
1 TATTTAG
27677288 TATTTAG
1 TATTTAG
27677295 TATT
1 TATT
27677299 ATGTATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
TATTTAG
Found at i:27677304 original size:14 final size:13
Alignment explanation
Indices: 27677270--27677304 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
27677260 TAATAGATAT
27677270 TTTGTATTTAGTA
1 TTTGTATTTAGTA
27677283 TTTAGTATTTAGTA
1 TTT-GTATTTAGTA
27677297 TTATGTAT
1 TT-TGTAT
27677305 ATAACTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 16 0.80
15 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (13 bp):
TTTGTATTTAGTA
Found at i:27678558 original size:29 final size:29
Alignment explanation
Indices: 27678500--27679155 Score: 773
Period size: 29 Copynumber: 22.7 Consensus size: 29
27678490 ATGTAATAAA
*
27678500 AACCCTAACCTAAACCCTAATTAAAAACCCT
1 AACCCTAACCT-AA-CTTAATTAAAAACCCT
*
27678531 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
*
27678560 AGCCCTAACCTAACTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* *
27678589 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* *
27678618 AACCCTAACTTAACTTAATTAAAAAACTCT
1 AACCCTAACCTAACTTAATT-AAAAACCCT
* *
27678648 AACCCTAACCTAATTTAATTACAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
*
27678677 AACCCTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* ** *
27678706 AACCCTAACATAACCCAATTAAAAACCTT
1 AACCCTAACCTAACTTAATTAAAAACCCT
*
27678735 AACCCTAAACCTAATTTAATTAGAAAACCCT
1 AACCCT-AACCTAACTTAATTA-AAAACCCT
* *
27678766 AACCCTAATCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
27678795 AA-CCTAAACC---C-TAATTAAAAACCCT
1 AACCCT-AACCTAACTTAATTAAAAACCCT
* *
27678820 AACCTTAACCTAAACCCTAATTAAAAACCCT
1 AACCCTAACCT-AA-CTTAATTAAAAACCCT
*
27678851 AA-CATAACC---C--AATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* *
27678874 AACTCC-AACCTAATTTAATTAAAAACACT
1 AAC-CCTAACCTAACTTAATTAAAAACCCT
27678903 AACCCTAACCTAACTTAATTAAAAAACCCT
1 AACCCTAACCTAACTTAATT-AAAAACCCT
* * *
27678933 AACTCC-AACCTAATTTAAATAAAAACACT
1 AAC-CCTAACCTAACTTAATTAAAAACCCT
27678962 AACCCTAACCTAACTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* * *
27678991 AACCCTAACCTAATTTAATTACAAACCTT
1 AACCCTAACCTAACTTAATTAAAAACCCT
*
27679020 AACCCTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* **
27679049 AACCCTAACATAACCCAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
* *
27679078 AACTCC-AACCTAATTTAATTAAAAACCGT
1 AAC-CCTAACCTAACTTAATTAAAAACCCT
* *
27679107 AACCATAACCCTAACCTAATTAAAAACCCT
1 AACCCTAA-CCTAACTTAATTAAAAACCCT
27679137 AACCCTAACCTAACTTAAT
1 AACCCTAACCTAACTTAAT
27679156 AATTTTTCAT
Statistics
Matches: 537, Mismatches: 63, Indels: 52
0.82 0.10 0.08
Matches are distributed among these distances:
23 15 0.03
24 4 0.01
25 22 0.04
26 2 0.00
28 8 0.01
29 334 0.62
30 110 0.20
31 42 0.08
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (29 bp):
AACCCTAACCTAACTTAATTAAAAACCCT
Found at i:27678668 original size:117 final size:116
Alignment explanation
Indices: 27678500--27679155 Score: 845
Period size: 117 Copynumber: 5.7 Consensus size: 116
27678490 ATGTAATAAA
* *
27678500 AACCCTAACCTAAACCCTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAGCCC
1 AACCCTAACCT-AA-CTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCC
27678565 TAACCTAACTTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCT
64 TAACCTAACTTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCT
* * *
27678618 AACCCTAACTTAACTTAATTAAAAAACTCTAACCCTAACCTAATTTAATTACAAACCCTAACCCT
1 AACCCTAACCTAACTTAATT-AAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
* * *
27678683 AACCTAAATTAATTAAAAACCCTAACCCTAACATAACCCAATTAAAAACCTT
65 AACCTAACTTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCT
* *
27678735 AACCCTAAACCTAATTTAATTAGAAAACCCTAACCCTAATCTAATTTAATTAAAAACCCTAA-CC
1 AACCCT-AACCTAACTTAATTA-AAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCC
* *
27678799 TAAACC---C-TAATTAAAAACCCTAACCTTAACCTAAACCCTAATTAAAAACCCT
64 T-AACCTAACTTAATTAAAAACCCTAACCCTAACAT-AA-CCTAATTAAAAACCCT
* *
27678851 AA-CATAACC---C--AATTAAAAACCCTAACTCC-AACCTAATTTAATTAAAAACACTAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCTAAC-CCTAACCTAATTTAATTAAAAACCCTAACCCT
* ** * *
27678909 AACCTAACTTAATTAAAAAACCCTAACTCC-AACCTAATTTAAATAAAAACACT
65 AACCTAACTTAATT-AAAAACCCTAAC-CCTAACATAACCTAATTAAAAACCCT
* *
27678962 AACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTACAAACCTTAACCCTA
1 AACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
* *
27679027 ACCTAAATTAATTAAAAACCCTAACCCTAACATAACCCAATTAAAAACCCT
66 ACCTAACTTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCT
* * * **
27679078 AACTCC-AACCTAATTTAATTAAAAACCGTAACCATAACCCTAACCTAATTAAAAACCCTAACCC
1 AAC-CCTAACCTAACTTAATTAAAAACCCTAACCCTAA-CCTAATTTAATTAAAAACCCTAACCC
27679142 TAACCTAACTTAAT
64 TAACCTAACTTAAT
27679156 AATTTTTCAT
Statistics
Matches: 468, Mismatches: 46, Indels: 49
0.83 0.08 0.09
Matches are distributed among these distances:
108 38 0.08
109 10 0.02
111 15 0.03
112 13 0.03
113 17 0.04
114 28 0.06
115 7 0.01
116 84 0.18
117 194 0.41
118 62 0.13
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (116 bp):
AACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
ACCTAACTTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCT
Found at i:27678681 original size:88 final size:87
Alignment explanation
Indices: 27678531--27679155 Score: 747
Period size: 88 Copynumber: 7.2 Consensus size: 87
27678521 TAAAAACCCT
* * *
27678531 AACCCTAACCTAATTTAATTAAAAACCCTAGCCCTAACCTAACTTAATTAAAAACCCTAACCCTA
1 AACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
* *
27678596 ACATAACCTAATTAAAAACCCT
66 ACCTAACTTAATTAAAAACCCT
* * *
27678618 AACCCTAACTTAACTTAATTAAAAAACTCTAACCCTAACCTAATTTAATTACAAACCCTAACCCT
1 AACCCTAACCTAACTTAATT-AAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
*
27678683 AACCTAAATTAATTAAAAACCCT
65 AACCTAACTTAATTAAAAACCCT
* ** *
27678706 AACCCTAACATAACCCAATTAAAAACCTTAACCCTAAACCTAATTTAATTAGAAAACCCTAACCC
1 AACCCTAACCTAACTTAATTAAAAACCCTAACCCT-AACCTAATTTAATTA-AAAACCCTAACCC
* *
27678771 TAATCTAATTTAATTAAAAACCCT
64 TAACCTAACTTAATTAAAAACCCT
* **
27678795 AA-CCTAAACC---C-TAATTAAAAACCCTAACCTTAACCTAAACCCTAATTAAAAACCCTAA-C
1 AACCCT-AACCTAACTTAATTAAAAACCCTAACCCTAACCT-AA-TTTAATTAAAAACCCTAACC
*
27678854 ATAACC---C--AATTAAAAACCCT
63 CTAACCTAACTTAATTAAAAACCCT
* * *
27678874 AACTCC-AACCTAATTTAATTAAAAACACTAACCCTAACCTAACTTAATTAAAAAACCCTAACTC
1 AAC-CCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATT-AAAAACCCTAAC-C
* * *
27678938 C-AACCTAATTTAAATAAAAACACT
63 CTAACCTAACTTAATTAAAAACCCT
* *
27678962 AACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTACAAACCTTAACCCTA
1 AACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
*
27679027 ACCTAAATTAATTAAAAACCCT
66 ACCTAACTTAATTAAAAACCCT
* ** * *
27679049 AACCCTAACATAACCCAATTAAAAACCCTAACTCC-AACCTAATTTAATTAAAAACCGTAACCAT
1 AACCCTAACCTAACTTAATTAAAAACCCTAAC-CCTAACCTAATTTAATTAAAAACCCTAACCCT
*
27679113 AACCCTAACCTAATTAAAAACCCT
65 AA-CCTAACTTAATTAAAAACCCT
27679137 AACCCTAACCTAACTTAAT
1 AACCCTAACCTAACTTAAT
27679156 AATTTTTCAT
Statistics
Matches: 461, Mismatches: 53, Indels: 47
0.82 0.09 0.08
Matches are distributed among these distances:
79 19 0.04
81 8 0.02
82 13 0.03
83 27 0.06
84 11 0.02
85 29 0.06
86 9 0.02
87 120 0.26
88 186 0.40
89 39 0.08
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (87 bp):
AACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
ACCTAACTTAATTAAAAACCCT
Found at i:27679210 original size:55 final size:55
Alignment explanation
Indices: 27679149--27679271 Score: 151
Period size: 57 Copynumber: 2.2 Consensus size: 55
27679139 CCCTAACCTA
* * * *
27679149 ACTTAATAATTTTTCATAATTTG-AT-AATTTTACTAACCATTAACACAATTTTTTG
1 ACTTAATAATTTTAC-T-ATGTGCATGAATTTTAATAACCATTAACACAAATTTTTG
*
27679204 ACTTAATAATTTTACTGTGTGCATGGCAATTTTAATAACCATTAACACAAATTTTTG
1 ACTTAATAATTTTACTATGTGCAT-G-AATTTTAATAACCATTAACACAAATTTTTG
27679261 ACTTAATAATT
1 ACTTAATAATT
27679272 ATAATTTTAC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
53 3 0.05
54 3 0.05
55 14 0.24
57 39 0.66
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.44
Consensus pattern (55 bp):
ACTTAATAATTTTACTATGTGCATGAATTTTAATAACCATTAACACAAATTTTTG
Found at i:27679711 original size:12 final size:12
Alignment explanation
Indices: 27679694--27679724 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27679684 TAAAAAAATA
27679694 AAAAGAATAAAG
1 AAAAGAATAAAG
*
27679706 AAAAGAATGAAG
1 AAAAGAATAAAG
27679718 AAAAGAA
1 AAAAGAA
27679725 GAAAAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (12 bp):
AAAAGAATAAAG
Found at i:27686557 original size:14 final size:13
Alignment explanation
Indices: 27686527--27686555 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27686517 TAAAATATAT
27686527 AAATATCTTTTTA
1 AAATATCTTTTTA
27686540 AAATATCTTTTTA
1 AAATATCTTTTTA
27686553 AAA
1 AAA
27686556 ATTAAATAAA
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:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATCTTTTTA
Found at i:27686927 original size:3 final size:3
Alignment explanation
Indices: 27686919--27686961 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
27686909 TTCATCAGCA
27686919 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
27686962 CGTAGCAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27687253 original size:6 final size:6
Alignment explanation
Indices: 27687242--27687272 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
27687232 GGATATGGCA
*
27687242 GAGGCG GAGGCG GAGGCG GAGGCG GGGGCG G
1 GAGGCG GAGGCG GAGGCG GAGGCG GAGGCG G
27687273 CGGAGGTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.71, T:0.00
Consensus pattern (6 bp):
GAGGCG
Found at i:27688565 original size:3 final size:3
Alignment explanation
Indices: 27688559--27688624 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
27688549 CCCTTATTAT
27688559 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27688607 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
27688625 ACTCAATCAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:27688773 original size:11 final size:11
Alignment explanation
Indices: 27688747--27688793 Score: 60
Period size: 12 Copynumber: 4.1 Consensus size: 11
27688737 TATCAGCAAA
27688747 AATTTAAAAAT
1 AATTTAAAAAT
27688758 AAATTTAAAAAT
1 -AATTTAAAAAT
27688770 AATTT-AAAAT
1 AATTTAAAAAT
27688780 AATTAATAAAAAT
1 AATT--TAAAAAT
27688793 A
1 A
27688794 TATTAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.28
11 5 0.16
12 12 0.38
13 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATTTAAAAAT
Found at i:27688901 original size:8 final size:8
Alignment explanation
Indices: 27688881--27688927 Score: 69
Period size: 8 Copynumber: 5.8 Consensus size: 8
27688871 AGACGAGTGC
27688881 AAAAATAT
1 AAAAATAT
27688889 AAAAAATAT
1 -AAAAATAT
27688898 AAAAATAT
1 AAAAATAT
27688906 AAAAATAT
1 AAAAATAT
27688914 -AAAATAT
1 AAAAATAT
27688921 GAAAAAT
1 -AAAAAT
27688928 TCAAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.19
8 16 0.44
9 13 0.36
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (8 bp):
AAAAATAT
Found at i:27689279 original size:17 final size:17
Alignment explanation
Indices: 27689259--27689292 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27689249 TTCATACTTA
* *
27689259 ATTTTTAGAATATTTAT
1 ATTTTTAAAATAATTAT
27689276 ATTTTTAAAATAATTAT
1 ATTTTTAAAATAATTAT
27689293 TAATATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTTTAAAATAATTAT
Found at i:27693973 original size:15 final size:16
Alignment explanation
Indices: 27693941--27693978 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
27693931 CCTACACGGG
*
27693941 ACACACGGTCGTGTGTC
1 ACACACGGTC-TGAGTC
27693958 ACACACGGT-TGAGTC
1 ACACACGGTCTGAGTC
27693973 ACACAC
1 ACACAC
27693979 CGGTGTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
17 9 0.45
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (16 bp):
ACACACGGTCTGAGTC
Found at i:27694902 original size:35 final size:35
Alignment explanation
Indices: 27694821--27694908 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
27694811 ACGAGCCAAT
* *
27694821 CCCTCCGAAAA-ACACCAATGCTTATAAGAGCTAGT
1 CCCTCC-AAAACACACCAATACTTATAAGAGCTAGC
** * *
27694856 CCAACCGAAACACATCAATACTTATAAGAGCTAGC
1 CCCTCCAAAACACACCAATACTTATAAGAGCTAGC
27694891 CCCTCCAAAACACACCAA
1 CCCTCCAAAACACACCAA
27694909 ATAAAGAGTA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
34 3 0.07
35 39 0.93
ACGTcount: A:0.41, C:0.33, G:0.10, T:0.16
Consensus pattern (35 bp):
CCCTCCAAAACACACCAATACTTATAAGAGCTAGC
Found at i:27698789 original size:32 final size:33
Alignment explanation
Indices: 27698744--27698806 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
27698734 TCACATCAAT
* *
27698744 TGGTGTCGTCTACT-TCAGTCCTCCACCAGCAC
1 TGGTGTCGCCTACTGTCAGCCCTCCACCAGCAC
*
27698776 TGGTGTTGCCTACTGTCAGCCCTCCACCAGC
1 TGGTGTCGCCTACTGTCAGCCCTCCACCAGC
27698807 CCACTGAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.14, C:0.38, G:0.21, T:0.27
Consensus pattern (33 bp):
TGGTGTCGCCTACTGTCAGCCCTCCACCAGCAC
Found at i:27707171 original size:39 final size:40
Alignment explanation
Indices: 27707072--27707215 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 40
27707062 CGAATGATGT
* * *
27707072 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATAA
* * *
27707112 CCAGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-A
*
27707152 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
*
27707191 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
27707216 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
39 34 0.39
40 43 0.49
41 10 0.11
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
Found at i:27707229 original size:40 final size:39
Alignment explanation
Indices: 27707124--27707222 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
27707114 AGACTAAGAT
** * *
27707124 CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAGC
1 CCGAAGGCATTTGAACGAGTTACTATA-ACCGGGCTAAGC
** *
27707163 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAG-C
27707203 CCGAAGGCATTTGAACGAGT
1 CCGAAGGCATTTGAACGAGT
27707223 AGCTATATCC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 33 0.62
40 20 0.38
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAGC
Found at i:27707234 original size:79 final size:80
Alignment explanation
Indices: 27707071--27707221 Score: 182
Period size: 79 Copynumber: 1.9 Consensus size: 80
27707061 TCGAATGATG
*
27707071 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
**
27707136 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * * *
27707151 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCAGACTAAGAT-CCGAAGGCAT
27707213 TTGAACGAG
64 TTGAACGAG
27707222 TAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.02
79 41 0.68
80 18 0.30
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:27717643 original size:11 final size:10
Alignment explanation
Indices: 27717619--27717643 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
27717609 AATAAAATCT
27717619 AAAAACTACG
1 AAAAACTACG
27717629 AAAAACTACG
1 AAAAACTACG
27717639 AAAAA
1 AAAAA
27717644 GACGTTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAACTACG
Found at i:27726499 original size:22 final size:22
Alignment explanation
Indices: 27726470--27726512 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
27726460 AGTTTGATAA
27726470 ATTTTAATATATAA-TTATATT
1 ATTTTAATATATAATTTATATT
*
27726491 ATTTATAATTTATAATTTATAT
1 ATTT-TAATATATAATTTATAT
27726513 ATTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTAATATATAATTTATATT
Found at i:27726501 original size:7 final size:7
Alignment explanation
Indices: 27726469--27726511 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
27726459 TAGTTTGATA
27726469 AATTT-T
1 AATTTAT
*
27726475 AATATAT
1 AATTTAT
27726482 AATTATAT
1 AATT-TAT
*
27726490 TATTTAT
1 AATTTAT
27726497 AATTTAT
1 AATTTAT
27726504 AATTTAT
1 AATTTAT
27726511 A
1 A
27726512 TATTAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 21 0.68
8 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTAT
Found at i:27726595 original size:32 final size:32
Alignment explanation
Indices: 27726554--27726619 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
27726544 GATTAATTAG
27726554 GAATTTCTATATTTCTACACAATAAAAAAAGA
1 GAATTTCTATATTTCTACACAATAAAAAAAGA
*
27726586 GAATTTCTATATTTCTACACAATAAAATAAGA
1 GAATTTCTATATTTCTACACAATAAAAAAAGA
27726618 GA
1 GA
27726620 TGGGAATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (32 bp):
GAATTTCTATATTTCTACACAATAAAAAAAGA
Found at i:27730385 original size:21 final size:23
Alignment explanation
Indices: 27730343--27730385 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
27730333 TAATTAATTA
*
27730343 TAAAGAGAAGCAAATCTCTTTTC
1 TAAAGAGAAGCAAATATCTTTTC
*
27730366 TAAA-AGAAG-AAATATGTTTT
1 TAAAGAGAAGCAAATATCTTTT
27730386 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (23 bp):
TAAAGAGAAGCAAATATCTTTTC
Found at i:27733346 original size:39 final size:34
Alignment explanation
Indices: 27733269--27733341 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
27733259 AAATAATATC
*
27733269 AGAAATGATGTATGAACAGGAGATATTCCCTGCA
1 AGAAATGATGTATGAACAGGAGAGATTCCCTGCA
*
27733303 AGAAATGATGTGTGAACAGGAGAGATTCCCTGCA
1 AGAAATGATGTATGAACAGGAGAGATTCCCTGCA
27733337 AGAAA
1 AGAAA
27733342 AGAAAGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (34 bp):
AGAAATGATGTATGAACAGGAGAGATTCCCTGCA
Found at i:27733605 original size:14 final size:13
Alignment explanation
Indices: 27733578--27733614 Score: 65
Period size: 14 Copynumber: 2.8 Consensus size: 13
27733568 AGTTTCCAAA
27733578 TTTTCAAATTAAG
1 TTTTCAAATTAAG
27733591 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
27733605 TTTTCAAATT
1 TTTTCAAATT
27733615 TCAAATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:27737118 original size:17 final size:17
Alignment explanation
Indices: 27737092--27737124 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27737082 ATATTTAATA
*
27737092 TATATTTGATTAAAAAG
1 TATATGTGATTAAAAAG
27737109 TATATGTGATTAAAAA
1 TATATGTGATTAAAAA
27737125 TAAAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (17 bp):
TATATGTGATTAAAAAG
Found at i:27739388 original size:26 final size:26
Alignment explanation
Indices: 27739359--27739411 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
27739349 TCATGCCACC
27739359 GGGTTATAGGTGTTAAAGAATGGATT
1 GGGTTATAGGTGTTAAAGAATGGATT
27739385 GGGTTATAGGTGTTAAAGAATGGATT
1 GGGTTATAGGTGTTAAAGAATGGATT
27739411 G
1 G
27739412 TATCCTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.34
Consensus pattern (26 bp):
GGGTTATAGGTGTTAAAGAATGGATT
Found at i:27740963 original size:25 final size:26
Alignment explanation
Indices: 27740935--27740991 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
27740925 ACCTCTAGCA
* *
27740935 AAAATTTT-ATGACTTTATCCCTGGT
1 AAAATTTTGACGACTTTACCCCTGGT
* *
27740960 AAAATTTTGACGATTTTGCCCCTGGT
1 AAAATTTTGACGACTTTACCCCTGGT
27740986 AAAATT
1 AAAATT
27740992 CCAAGAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (26 bp):
AAAATTTTGACGACTTTACCCCTGGT
Found at i:27743024 original size:21 final size:20
Alignment explanation
Indices: 27742980--27743035 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
27742970 AAAAACATTT
** *
27742980 TATCGATACCTGGTAAAAGG
1 TATCGATACCTTTTAAAAGA
27743000 TATCGATACCTTTTGAAAAGA
1 TATCGATACCTTTT-AAAAGA
*
27743021 TATCGATACTTTTTA
1 TATCGATACCTTTTA
27743036 TGATTGTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (20 bp):
TATCGATACCTTTTAAAAGA
Found at i:27743093 original size:18 final size:18
Alignment explanation
Indices: 27743067--27743101 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27743057 AGTAAGAATG
*
27743067 CAAAAATGGTATTGATAT
1 CAAAAATGGTATCGATAT
*
27743085 CAAAGATGGTATCGATA
1 CAAAAATGGTATCGATA
27743102 AAAATACAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.29
Consensus pattern (18 bp):
CAAAAATGGTATCGATAT
Found at i:27743307 original size:20 final size:20
Alignment explanation
Indices: 27743265--27743307 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
27743255 GAGAGCGATT
* *
27743265 TTTCAATTGATTTAAACATG
1 TTTCAATTGAGTTAAACAAG
27743285 TTTCAATTGAGTTAGAA-AAG
1 TTTCAATTGAGTTA-AACAAG
27743305 TTT
1 TTT
27743308 AAACCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (20 bp):
TTTCAATTGAGTTAAACAAG
Found at i:27772797 original size:16 final size:16
Alignment explanation
Indices: 27772776--27772810 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27772766 CAATGTCCCA
27772776 TTTAGTCCCTAATTCT
1 TTTAGTCCCTAATTCT
* *
27772792 TTTAGTCTCTAGTTCT
1 TTTAGTCCCTAATTCT
27772808 TTT
1 TTT
27772811 CGCGCATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.20, G:0.09, T:0.57
Consensus pattern (16 bp):
TTTAGTCCCTAATTCT
Found at i:27773394 original size:12 final size:12
Alignment explanation
Indices: 27773377--27773402 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27773367 ATCATTACTA
27773377 TAATATGATTAT
1 TAATATGATTAT
27773389 TAATATGATTAT
1 TAATATGATTAT
27773401 TA
1 TA
27773403 TAATTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TAATATGATTAT
Found at i:27776171 original size:44 final size:44
Alignment explanation
Indices: 27776102--27776560 Score: 333
Period size: 44 Copynumber: 10.5 Consensus size: 44
27776092 AGTTATTGTG
* *
27776102 ACAAATCTTATCT-CTCTGAAGTTGCAGTGGAGCAGATTAAAGCT
1 ACAAATCTTATCTCCT-TGAAGTTGCAGTAGAGCAGATTGAAGCT
* * * * * *
27776146 ACAAATCTTATCTCCTTAAAATTGCAATGGAACAGATTGAAGAT
1 ACAAATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTGAAGCT
* * *
27776190 AGCAAATCTTATCT-CTCTAAAGTTGCAGTAAAGC-GATTGAAGTT
1 A-CAAATCTTATCTCCT-TGAAGTTGCAGTAGAGCAGATTGAAGCT
* * *
27776234 ACAAACCTTATCT-CTCTGAAGTTGCAGTTGAGCATATT---G-T
1 ACAAATCTTATCTCCT-TGAAGTTGCAGTAGAGCAGATTGAAGCT
* *
27776274 --GATTCTTATCT-CTCTGAAGTTGCAGTAGAGCAGATTGAAGCT
1 ACAAATCTTATCTCCT-TGAAGTTGCAGTAGAGCAGATTGAAGCT
* * * * *
27776316 ACAAATCTTATCTCCCTAAAGTTGCA-TGGACCAGATTAAAGCTACAAGTT
1 ACAAATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATT---G----AAGCT
*
27776366 ACAAATCTTATCTCCTTGAAGTTGTAGTAGAGCAGATT---G-T
1 ACAAATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTGAAGCT
* *
27776406 --GAATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATTGAAGCT
1 ACAAATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTGAAGCT
* * * * * *
27776448 GCAAATCTTATCTCCCTAAATTTGCAGTGGAGCAGATTGAAGAT
1 ACAAATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTGAAGCT
* * * * * * *
27776492 AGTAAATCTTATCTCCCTGAAGCTGCAGCAGAGTAGATTAAAGGT
1 A-CAAATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTGAAGCT
*
27776537 ACAAATCTTATCTCCCTGAAGTTG
1 ACAAATCTTATCTCCTTGAAGTTG
27776561 TAGTGAAAGT
Statistics
Matches: 333, Mismatches: 56, Indels: 52
0.76 0.13 0.12
Matches are distributed among these distances:
38 64 0.19
40 2 0.01
41 4 0.01
42 2 0.01
43 37 0.11
44 125 0.38
45 62 0.19
46 1 0.00
50 27 0.08
51 9 0.03
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (44 bp):
ACAAATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTGAAGCT
Found at i:27776258 original size:132 final size:127
Alignment explanation
Indices: 27776102--27776530 Score: 438
Period size: 132 Copynumber: 3.3 Consensus size: 127
27776092 AGTTATTGTG
* * *
27776102 ACAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCTTAAAA
1 ACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT---G-T--AAATCTTATCTCCTTGAAG
* * * * * **
27776167 TTGCAATGGAACAGATTGAAGATAGCAAATCTTATCTCTCTAAAGTTGCAGTAAAGC-GATTGAA
60 TTGCAGTAGAGCAGATTGAAGCTAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAA
27776231 GTT
125 GTT
* * * * *
27776234 ACAAACCTTATCTCTCTGAAGTTGCAGTTGAGCATATTGTGATTCTTATCT-CTCTGAAGTTGCA
1 ACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGTAAATCTTATCTCCT-TGAAGTTGCA
*
27776298 GTAGAGCAGATTGAAGCTA-CAAATCTTATCTCCCTAAAGTTGCA-TGGACCAGATTAAAGCTAC
65 GTAGAGCAGATTGAAGCTAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATT---G----
27776361 AAGTT
123 AAGTT
* * *
27776366 ACAAATCTTATCTC-CTTGAAGTTGTAGTAGAGCAGATTGTGAATCTTATCTCTTTGAAGTTGCA
1 ACAAATCTTATCTCTC-TGAAGTTGCAGTAGAGCAGATTGTAAATCTTATCTCCTTGAAGTTGCA
* *
27776430 GTAGAGCAGATTGAAGCT-GCAAATCTTATCTCCCTAAATTTGCAGTGGAGCAGATTGAAGAT
65 GTAGAGCAGATTGAAGCTAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTT
* * * * *
27776492 AGTAAATCTTATCTCCCTGAAGCTGCAGCAGAGTAGATT
1 A-CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT
27776531 AAAGGTACAA
Statistics
Matches: 253, Mismatches: 29, Indels: 35
0.80 0.09 0.11
Matches are distributed among these distances:
124 3 0.01
125 30 0.12
126 37 0.15
127 30 0.12
128 3 0.01
129 1 0.00
130 1 0.00
131 1 0.00
132 136 0.54
133 11 0.04
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (127 bp):
ACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGTAAATCTTATCTCCTTGAAGTTGCAG
TAGAGCAGATTGAAGCTAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTT
Found at i:27776423 original size:38 final size:38
Alignment explanation
Indices: 27776369--27776442 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
27776359 ACAAGTTACA
*
27776369 AATCTTATCTCCTTGAAGTTGTAGTAGAGCAGATTGTG
1 AATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTGTG
*
27776407 AATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATTG
1 AATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTG
27776443 AAGCTGCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (38 bp):
AATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTGTG
Found at i:27778158 original size:3 final size:3
Alignment explanation
Indices: 27778150--27778180 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
27778140 TTTTATGTCT
27778150 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
27778181 CTTTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:27778437 original size:14 final size:14
Alignment explanation
Indices: 27778418--27778450 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
27778408 ATAATACGAT
27778418 TATTAATATTATAA
1 TATTAATATTATAA
*
27778432 TATTAATATTATAT
1 TATTAATATTATAA
27778446 TATTA
1 TATTA
27778451 TTACAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTAATATTATAA
Found at i:27779145 original size:80 final size:80
Alignment explanation
Indices: 27779007--27779166 Score: 293
Period size: 80 Copynumber: 2.0 Consensus size: 80
27778997 TCCTTCCTCG
* *
27779007 TGCGTAACCGACTCCCGAACCAATTTCTTGGATTTTGTAGATCGAAAAGTATTTTTTTAATAAGT
1 TGCGTAACCAACTCCCGAACCAATTTCTTGGATTTTGTAGATCGAAAAGTATTGTTTTAATAAGT
27779072 CTAACATTTTATTAA
66 CTAACATTTTATTAA
*
27779087 TGCGTAACCAACTCCCGAACCCATTTCTTGGATTTTGTAGATCGAAAAGTATTGTTTTAATAAGT
1 TGCGTAACCAACTCCCGAACCAATTTCTTGGATTTTGTAGATCGAAAAGTATTGTTTTAATAAGT
27779152 CTAACATTTTATTAA
66 CTAACATTTTATTAA
27779167 AATGAGTTTT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (80 bp):
TGCGTAACCAACTCCCGAACCAATTTCTTGGATTTTGTAGATCGAAAAGTATTGTTTTAATAAGT
CTAACATTTTATTAA
Found at i:27780477 original size:17 final size:17
Alignment explanation
Indices: 27780455--27780509 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
27780445 GATAGTCCCT
*
27780455 CATAATTGTTGGTACTC
1 CATAATTTTTGGTACTC
*
27780472 CATAATTTTTTGTAATCTC
1 CATAATTTTTGGT-A-CTC
27780491 TCATAATTTTTGGTACTC
1 -CATAATTTTTGGTACTC
27780509 C
1 C
27780510 CTCATGTCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 12 0.38
18 4 0.12
19 4 0.12
20 12 0.38
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (17 bp):
CATAATTTTTGGTACTC
Found at i:27780513 original size:20 final size:20
Alignment explanation
Indices: 27780450--27780514 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
27780440 TATTTGATAG
*
27780450 TCCCTCATAATTGTTGGTAC
1 TCCCTCATAATTTTTGGTAC
* *
27780470 T--C-CATAATTTTTTGTAA
1 TCCCTCATAATTTTTGGTAC
*
27780487 TCTCTCATAATTTTTGGTAC
1 TCCCTCATAATTTTTGGTAC
27780507 TCCCTCAT
1 TCCCTCAT
27780515 GTCTGTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 13 0.36
18 1 0.03
19 1 0.03
20 21 0.58
ACGTcount: A:0.22, C:0.23, G:0.09, T:0.46
Consensus pattern (20 bp):
TCCCTCATAATTTTTGGTAC
Found at i:27780603 original size:21 final size:21
Alignment explanation
Indices: 27780579--27780632 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
27780569 TGAAACTCTT
* *
27780579 TCATATCTTTTTGGTATTTTA
1 TCATATTTTTTTGGTATTCTA
* *
27780600 TCATGTTTTTTTGGTATTCTC
1 TCATATTTTTTTGGTATTCTA
27780621 TCATATTTTTTT
1 TCATATTTTTTT
27780633 TACTTAGCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.15, C:0.11, G:0.09, T:0.65
Consensus pattern (21 bp):
TCATATTTTTTTGGTATTCTA
Found at i:27780629 original size:20 final size:20
Alignment explanation
Indices: 27780546--27780631 Score: 64
Period size: 21 Copynumber: 4.2 Consensus size: 20
27780536 TTCTTGTGAC
* * *
27780546 TTTTGGTAGTCCCTCATAAT
1 TTTTGGTATTCTCTCATATT
** * *
27780566 TTTTGAAACTCTTTCATATCT
1 TTTTGGTATTCTCTCATAT-T
* * *
27780587 TTTTGGTATTTTATCATGTTT
1 TTTTGGTATTCTCTCAT-ATT
27780608 TTTTGGTATTCTCTCATATT
1 TTTTGGTATTCTCTCATATT
27780628 TTTT
1 TTTT
27780632 TTACTTAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 19 0.39
21 29 0.59
22 1 0.02
ACGTcount: A:0.17, C:0.14, G:0.10, T:0.58
Consensus pattern (20 bp):
TTTTGGTATTCTCTCATATT
Found at i:27781157 original size:20 final size:19
Alignment explanation
Indices: 27781134--27781216 Score: 55
Period size: 20 Copynumber: 4.3 Consensus size: 19
27781124 AGGGTGTACA
27781134 AAAAAATATAAGAGAATACT
1 AAAAAATATAA-AGAATACT
*
27781154 AAAAAA-ATAAATAAGTAC-
1 AAAAAATATAAAGAA-TACT
* *
27781172 CAAAAATATGAAAGGATA-T
1 AAAAAATAT-AAAGAATACT
**
27781191 AGAAAAATATGAGGGAATACT
1 A-AAAAATAT-AAAGAATACT
27781212 AAAAA
1 AAAAA
27781217 TTATGAGGGG
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
18 8 0.16
19 11 0.22
20 28 0.57
21 2 0.04
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (19 bp):
AAAAAATATAAAGAATACT
Found at i:27781221 original size:20 final size:18
Alignment explanation
Indices: 27781172--27781235 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 18
27781162 AAATAAGTAC
*
27781172 CAAAAATATGAAAGGATATA
1 CAAAAATATG-AGGGA-ATA
*
27781192 GAAAAATATGAGGGAATA
1 CAAAAATATGAGGGAATA
*
27781210 CTAAAAATTATGAGGGGATA
1 C-AAAAA-TATGAGGGAATA
27781230 CAAAAA
1 CAAAAA
27781236 CATATGAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 3 0.08
19 14 0.37
20 21 0.55
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.19
Consensus pattern (18 bp):
CAAAAATATGAGGGAATA
Found at i:27781241 original size:20 final size:20
Alignment explanation
Indices: 27781193--27781242 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
27781183 AAGGATATAG
27781193 AAAAATATGAGGGAATACTA
1 AAAAATATGAGGGAATACTA
* *
27781213 AAAATTATGAGGGGATAC-A
1 AAAAATATGAGGGAATACTA
27781232 AAAACATATGA
1 AAAA-ATATGA
27781243 AGTACAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (20 bp):
AAAAATATGAGGGAATACTA
Found at i:27782382 original size:3 final size:3
Alignment explanation
Indices: 27782362--27782427 Score: 55
Period size: 3 Copynumber: 21.3 Consensus size: 3
27782352 GGGTCCCTTG
** *
27782362 TTA TTAA TTA TT- TTA TTA TTA AAA TTA TTTA TTT TTA TTA -TA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
27782407 TTTA TTA TTA TTAA TTA TTA T
1 -TTA TTA TTA TT-A TTA TTA T
27782428 CATATTTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
2 4 0.08
3 35 0.69
4 12 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:27782408 original size:18 final size:17
Alignment explanation
Indices: 27782362--27782425 Score: 85
Period size: 18 Copynumber: 3.7 Consensus size: 17
27782352 GGGTCCCTTG
27782362 TTATTAATTATTTTATTA
1 TTATTAATTA-TTTATTA
* *
27782380 TTA-AAATTATTTATTT
1 TTATTAATTATTTATTA
27782396 TTATTATATTATTTATTA
1 TTATTA-ATTATTTATTA
27782414 TTATTAATTATT
1 TTATTAATTATT
27782426 ATCATATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 9 0.22
17 12 0.30
18 19 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTAATTATTTATTA
Found at i:27782415 original size:10 final size:10
Alignment explanation
Indices: 27782385--27782427 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
27782375 TATTATTAAA
27782385 ATTATTTATT
1 ATTATTTATT
*
27782395 TTTA-TTA-T
1 ATTATTTATT
27782403 ATTATTTATT
1 ATTATTTATT
*
27782413 ATTATTAATT
1 ATTATTTATT
27782423 ATTAT
1 ATTAT
27782428 CATATTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 4 0.14
9 6 0.21
10 18 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
ATTATTTATT
Found at i:27782425 original size:31 final size:32
Alignment explanation
Indices: 27782362--27782425 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 32
27782352 GGGTCCCTTG
*
27782362 TTATTAATTATTTTATTATTAAAATTATTTATTT
1 TTATTAATTATTTTATTATT--AATTAATTATTT
27782396 TTATTATATTA-TTTATTATT-ATTAATTATT
1 TTATTA-ATTATTTTATTATTAATTAATTATT
27782426 ATCATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 9 0.32
34 15 0.54
35 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (32 bp):
TTATTAATTATTTTATTATTAATTAATTATTT
Found at i:27782594 original size:20 final size:20
Alignment explanation
Indices: 27782571--27782630 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
27782561 TTTTTTGTTT
*
27782571 TTTTTACTTTTTTATATATA-
1 TTTTTA-TTTTATATATATAC
27782591 TTTTATATTTTATATATATAC
1 TTTT-TATTTTATATATATAC
* *
27782612 TTTTT-TTGTAAATATATAC
1 TTTTTATTTTATATATATAC
27782631 ACATGTACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 12 0.34
20 17 0.49
21 6 0.17
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTATTTTATATATATAC
Found at i:27785165 original size:36 final size:37
Alignment explanation
Indices: 27785099--27785177 Score: 133
Period size: 36 Copynumber: 2.1 Consensus size: 37
27785089 TCAGGTTCCA
27785099 ATCTTAGGGGCAATCTAACTAATCCTGTTGTCCTCGATG
1 ATCTTAGGGGCAATCT-A-TAATCCTGTTGTCCTCGATG
27785138 ATCTTAGGGGCAATCT-TAATCCTGTTGTCCTCGATG
1 ATCTTAGGGGCAATCTATAATCCTGTTGTCCTCGATG
27785174 ATCT
1 ATCT
27785178 AGCAGAAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
36 24 0.60
39 16 0.40
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (37 bp):
ATCTTAGGGGCAATCTATAATCCTGTTGTCCTCGATG
Found at i:27788471 original size:133 final size:133
Alignment explanation
Indices: 27788287--27789740 Score: 1190
Period size: 133 Copynumber: 10.8 Consensus size: 133
27788277 TGAAGATAGC
* *
27788287 AGATCTTGCCTTCCTGCATAGACAGC-AGAGCAGATCAAAGATGGC-GAATTTTACCTCCATGTG
1 AGATCTTGCCTTCCTGCATAGACAGCGA-AGCAGATCAAAGACGGCAG-ATTTTACCTCCCTGTG
27788350 GTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAATAGACTGAAG
64 GTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAATAGACTGAAG
27788415 ATTTT
129 ATTTT
* * *
27788420 AGATCTTGCCTTCCTGCATAGACACCGAAGCAGGTCGAAGACGGCAGATTTTACCTCCCTGTGGT
1 AGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGT
* *
27788485 TACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTAGGTAGCAGTGGAATAGACTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAATAGACTGAAGAT
27788550 TTT
131 TTT
* * ** *
27788553 AGATCTTGCCTTCCTGCATAGACAGCAAAACAGATTGAAGACGGCAGATTTTACCTCTCTGTGGT
1 AGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGT
*
27788618 TACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGACTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAATAGACTGAAGAT
27788683 TTT
131 TTT
* * * * *
27788686 AGATCTTACCTTCCTGCATAGATAGTGAAGCAGATCAAAAACGGTAGATTTTACCTCCCTGTGGT
1 AGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGT
*
27788751 TACAGTGGAGTACATTGAAGCCAATAATTCTA-CTTCCCTGGGCAGCAGTGGAATAGATTGAAGA
66 TACAGTGGAGTACATTGAAGCCAATAATTCTATC-TCCCTGGGCAGCAGTGGAATAGACTGAAGA
*
27788815 TTTC
130 TTTT
* * * * ** * * * * * *
27788819 ATATATTGTCTCCCTAAACAG-TAGTGGAGCAGATCAAAGATGG-TGAATTTTACCTCCCTGTGG
1 AGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGACGGCAG-ATTTTACCTCCCTGTGG
* *
27788882 TTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCAGCAGTGGAATAGACTGAAGA
65 TTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAATAGACTGAAGA
27788947 TTTT
130 TTTT
* * * ** *
27788951 AGATCTTGCCTTCCTGCATAGACAGCGACGCATATCAAAGATGGTGGATTTTACCTCCCTGAGGT
1 AGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGT
* * * *
27789016 TGCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAATAGACTGAAGAT
*
27789081 TTC
131 TTT
* * * * * **
27789084 AGATCTTGCCTCCCTAAGCAATAG--TG-G-AGCAGATCGAAGATGGCAGATTTTATCTCCCTAA
1 AGATCTTGCCTTCCT--GC-ATAGACAGCGAAGCAGATCAAAGACGGCAGATTTTACCTCCCTGT
* * * * * * * *** *
27789145 AGTTGCAGTAGAGTATATTGAAGCCAGTAATTCTACCTCCCCGGTTGGC-GT-GAAGTAGA-TCA
63 GGTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAA-TAGACT-G
***
27789207 AAGATAGC
126 AAGATTTT
* * * * **
27789215 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG-AAAGCAGATCAAATATGGTGGATT
1 AGATCTTGCCTT--C---C---T-GC--A-TAGA-C--AGCGAAGCAGATCAAAGACGGCAGATT
* * * * *
27789279 TTACCCCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTG
51 TTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTG
* **
27789344 GAATAGATTGAAGATTAC
116 GAATAGACTGAAGATTTT
** * ** * * * * * ** **
27789362 AGATCTTATCTCCCTAAACAG-TAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAAGT
1 AGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGT
* * * * * * *
27789426 TGCAGTGGAGTATATTGAAGCCAGTAATTCTACCTCCC-CGGCTGGCA-T-GAAGTAGA-TCAAA
66 TACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGC-AGCAGTGGAA-TAGACT-GAA
***
27789487 GATAGC
128 GATTTT
* * * ** **
27789493 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG-AAAGTAGATCAAAGATAGTGGATT
1 AGATCTTGCCTT--C---C---T-GC--A-TAGA-C--AGCGAAGCAGATCAAAGACGGCAGATT
** * *
27789557 TTACCTCCCTAAGGTTGCAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAACAGTG
51 TTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTG
* **
27789622 GAATAGATTGAAGATTAC
116 GAATAGACTGAAGATTTT
** * * * * ** *
27789640 AGATCTTATCTCCCT--A-AG-CAGTGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAG
1 AGATCTTGCCTTCCTGCATAGACA--GCGAAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTG
**
27789701 GTTACAGTGGAGTACATTGAAGCCGGTAATTCTATCTCCC
64 GTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCC
27789741 GAAACAACAG
Statistics
Matches: 1104, Mismatches: 159, Indels: 118
0.80 0.12 0.09
Matches are distributed among these distances:
128 1 0.00
130 10 0.01
131 118 0.11
132 255 0.23
133 492 0.45
134 5 0.00
135 4 0.00
136 7 0.01
138 2 0.00
139 6 0.01
140 3 0.00
142 3 0.00
143 2 0.00
145 3 0.00
146 137 0.12
147 48 0.04
148 8 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (133 bp):
AGATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGACGGCAGATTTTACCTCCCTGTGGT
TACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAATAGACTGAAGAT
TTT
Found at i:27788965 original size:265 final size:265
Alignment explanation
Indices: 27788314--27789760 Score: 1532
Period size: 278 Copynumber: 5.4 Consensus size: 265
27788304 ATAGACAGCA
* * * *
27788314 GAGCAGATCAAAGATGGCGAATTTTACCTCCATGTGGTTACAGTGGAGTACATTGAAGCCAATAA
1 GAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
* *
27788379 TTCTATCTCCCTGGGCAGCAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCTGCATAGACA
66 TTCTATCTCCCTAGGCAGCAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCTGCATAGATA
** * * * ** * *
27788444 CCGAAGCAGGTCGAAGACGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAA
131 GAGAAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAA
* * * * * * * ** *
27788509 TAATTCTATCTCCCTAGGTAGCAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCTGCATAG
196 TAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAACAG
* **
27788574 ACAGCA
261 -TAGTG
* * ** * * * *
27788580 AAACAGATTGAAGACGG-CAGATTTTACCTCTCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
1 GAGCAGATCAAAGATGGTGA-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
* *
27788644 ATTCTATCTCCCTGGGCAGCAGTGGAATAGACTGAAGATTTTAGATCTTACCTTCCTGCATAGAT
65 ATTCTATCTCCCTAGGCAGCAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCTGCATAGAT
* * * * * *
27788709 AGTGAAGCAGATCAAAAACGGTAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
130 AGAGAAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCA
* * *
27788774 ATAATTCTA-CTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCATATATTGTCTCCCTAAAC
195 ATAATTCTATC-TCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAAC
27788838 AGTAGTG
259 AGTAGTG
*
27788845 GAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 GAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
*
27788910 TTCTATCTCCCTAGGCAGCAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCTGCATAGACA
66 TTCTATCTCCCTAGGCAGCAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCTGCATAGATA
* * * *
27788975 GCGACGCATATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAG
131 GAGAAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAA
* * *
27789040 TAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAA
196 TAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAACAG
27789105 TAGTG
261 TAGTG
* * * * * * * *
27789110 GAGCAGATCGAAGATGG-CAGATTTTATCTCCCTAAAGTTGCAGTAGAGTATATTGAAGCCAGTA
1 GAGCAGATCAAAGATGGTGA-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
* * ** * *** *
27789174 ATTCTACCTCCC-CGGTTGGC-GT-GAAGTAGA-TCAAAGATAGCAGATCTTGTCTTCCCATACT
65 ATTCTATCTCCCTAGG-CAGCAGTGGAA-TAGACT-GAAGATTTTAGATCTTGCCTT--C---C-
* * *
27789235 GGTGGCGAAGTAGATCGAAGAAAGCAGATCAAATATGGTGGATTTTACCCCCCTGAGGTTGCAGT
121 --T-GC--A-TAGATAG-AG-AAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGT
* *
27789300 GGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGA
178 GGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGA
*
27789365 TCTTATCTCCCTAAACAGTAGTG
243 TCTTGTCTCCCTAAACAGTAGTG
* * * *
27789388 GAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAA
1 GAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * * * *** *
27789453 TTCTACCTCCC-CGGCTGGCA-T-GAAGTAGA-TCAAAGATAGCAGATCTTGTCTTCCCATACTG
66 TTCTATCTCCCTAGGC-AGCAGTGGAA-TAGACT-GAAGATTTTAGATCTTGCCTT--C---C--
* * * *
27789514 GTGGCGAAGTAGATCGAAGAAAGTAGATCAAAGATAGTGGATTTTACCTCCCTAAGGTTGCAGTG
121 -T-GC--A-TAGATAG-AG-AAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTG
*
27789579 GAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGAT
179 GAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGAT
* *
27789644 CTTATCTCCCTAAGCAGT-GTG
244 CTTGTCTCCCTAAACAGTAGTG
* *
27789665 GAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCGGTAA
1 GAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
* ** *
27789730 TTCTATCTCCCGAAACAACAGTGGAATAGAC
66 TTCTATCTCCCTAGGCAGCAGTGGAATAGAC
27789761 AGAATAAATC
Statistics
Matches: 1042, Mismatches: 110, Indels: 45
0.87 0.09 0.04
Matches are distributed among these distances:
263 4 0.00
264 25 0.02
265 306 0.29
266 231 0.22
269 1 0.00
272 1 0.00
273 2 0.00
275 1 0.00
276 5 0.00
277 77 0.07
278 386 0.37
279 3 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (265 bp):
GAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
TTCTATCTCCCTAGGCAGCAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCTGCATAGATA
GAGAAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAA
TAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAACAG
TAGTG
Found at i:27791263 original size:3 final size:3
Alignment explanation
Indices: 27791243--27791308 Score: 55
Period size: 3 Copynumber: 21.3 Consensus size: 3
27791233 GGGTCCCTTG
** *
27791243 TTA TTAA TTA TT- TTA TTA TTA AAA TTAA TTA TTT TTA TTA -TA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
27791288 TTTA TTA TTA TTAA TTA TTA T
1 -TTA TTA TTA TT-A TTA TTA T
27791309 CATATTTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
2 4 0.08
3 35 0.69
4 12 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:27791292 original size:18 final size:17
Alignment explanation
Indices: 27791243--27791306 Score: 76
Period size: 18 Copynumber: 3.7 Consensus size: 17
27791233 GGGTCCCTTG
27791243 TTATTAATTATTTTATTA
1 TTATTAATTA-TTTATTA
* * *
27791261 TTA-AAATTAATTATTT
1 TTATTAATTATTTATTA
27791277 TTATTATATTATTTATTA
1 TTATTA-ATTATTTATTA
27791295 TTATTAATTATT
1 TTATTAATTATT
27791307 ATCATATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 8 0.21
17 12 0.32
18 18 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTAATTATTTATTA
Found at i:27791294 original size:21 final size:21
Alignment explanation
Indices: 27791243--27791305 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
27791233 GGGTCCCTTG
27791243 TTATTAATTA-TTTTATTATTA
1 TTATTAATTATTTTTATTA-TA
**
27791264 AAATTAATTATTTTTATTATA
1 TTATTAATTATTTTTATTATA
* *
27791285 TTATTTATTATTATTAATTAT
1 TTATTAATTATT-TTTATTAT
27791306 TATCATATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTAATTATTTTTATTATA
Found at i:27791301 original size:31 final size:32
Alignment explanation
Indices: 27791243--27791306 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
27791233 GGGTCCCTTG
27791243 TTATTAATTATTTTATTATTAAAATTAATTATTT
1 TTATTAATTATTTTATTATT--AATTAATTATTT
27791277 TTATTATATTA-TTTATTATT-ATTAATTATT
1 TTATTA-ATTATTTTATTATTAATTAATTATT
27791307 ATCATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 10 0.34
34 15 0.52
35 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TTATTAATTATTTTATTATTAATTAATTATTT
Found at i:27791363 original size:34 final size:32
Alignment explanation
Indices: 27791325--27791400 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
27791315 TTCTATACAT
27791325 ATATATATATACGCATAGTTTTTTATTATATATA-
1 ATATATATATACGCAT--TTTTTTA-TATATATAG
* **
27791359 ATATACATATGGGCATTTTTTTATATATATAG
1 ATATATATATACGCATTTTTTTATATATATAG
*
27791391 GTATATATAT
1 ATATATATAT
27791401 TTTTAAGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 8 0.22
32 15 0.42
34 13 0.36
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (32 bp):
ATATATATATACGCATTTTTTTATATATATAG
Found at i:27791488 original size:18 final size:17
Alignment explanation
Indices: 27791465--27791509 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
27791455 TTTTTTTTAC
27791465 TTTTTTATA-TATACTT
1 TTTTTTATAGTATACTT
27791481 TATATTTTATATGTATACTT
1 T-T-TTTTATA-GTATACTT
27791501 TTTTTTATA
1 TTTTTTATA
27791510 AATATATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.04
17 1 0.04
18 14 0.56
19 1 0.04
20 8 0.32
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTTTATAGTATACTT
Found at i:27791515 original size:18 final size:17
Alignment explanation
Indices: 27791465--27791515 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
27791455 TTTTTTTTAC
27791465 TTTTTTAT-ATATACTT
1 TTTTTTATAATATACTT
*
27791481 TATATTTTATATGTATACTT
1 T-T-TTTTATA-ATATACTT
27791501 TTTTTTATAAATATA
1 TTTTTTAT-AATATA
27791516 TACACATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 1 0.04
17 1 0.04
18 16 0.57
19 2 0.07
20 8 0.29
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTTTATAATATACTT
Found at i:27791518 original size:20 final size:20
Alignment explanation
Indices: 27791465--27791515 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
27791455 TTTTTTTTAC
*
27791465 TTTTTTATATATACTTTATA
1 TTTTATATATATACTTTATA
*
27791485 TTTTATATGTATACTTT-T-
1 TTTTATATATATACTTTATA
*
27791503 TTTTATAAATATA
1 TTTTATATATATA
27791516 TACACATGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 11 0.41
19 1 0.04
20 15 0.56
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATATATATACTTTATA
Found at i:27792833 original size:20 final size:19
Alignment explanation
Indices: 27792786--27792837 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
27792776 AAACTAAGGA
27792786 AATACAAAGAAAGTATGATGG
1 AATACAAA-AAAGTATGA-GG
* *
27792807 AAAACAAAAAATTATGAGG
1 AATACAAAAAAGTATGAGG
27792826 AGATACAAAAAA
1 A-ATACAAAAAA
27792838 AAAATGGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 17 0.63
21 7 0.26
ACGTcount: A:0.62, C:0.06, G:0.17, T:0.15
Consensus pattern (19 bp):
AATACAAAAAAGTATGAGG
Found at i:27792856 original size:20 final size:20
Alignment explanation
Indices: 27792810--27792881 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
27792800 ATGATGGAAA
**
27792810 ACAAAAAATTATGAG-GAGAT
1 ACAAAAAAAAATGAGAGA-AT
27792830 ACAAAAAAAAAATG-GAGAAGT
1 AC-AAAAAAAAATGAGAGAA-T
* *
27792851 ACAAAAAGAAATGAGGGAAT
1 ACAAAAAAAAATGAGAGAAT
27792871 ACAAAAAAAAA
1 ACAAAAAAAAA
27792882 ACCAAAAGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 25 0.58
21 18 0.42
ACGTcount: A:0.65, C:0.06, G:0.18, T:0.11
Consensus pattern (20 bp):
ACAAAAAAAAATGAGAGAAT
Found at i:27792970 original size:18 final size:19
Alignment explanation
Indices: 27792947--27792992 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
27792937 TAAAAAAATT
27792947 CATTTATTTAAT-TTTTCA
1 CATTTATTTAATATTTTCA
*
27792965 CATTTA-TTCATATTTTCA
1 CATTTATTTAATATTTTCA
27792983 CATTT-TTTAA
1 CATTTATTTAA
27792993 AACATGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (19 bp):
CATTTATTTAATATTTTCA
Found at i:27793016 original size:36 final size:38
Alignment explanation
Indices: 27792976--27793050 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
27792966 ATTTATTCAT
* *
27792976 ATTTTCACA-TTTTTT-AAAACATGAAAGAATGCCAAA
1 ATTTTAACATTTTTTTAAAAACATGAAAGAATACCAAA
27793012 ATTTTAACATTTTTTTAAAAACATGAAAGAATACCAAA
1 ATTTTAACATTTTTTTAAAAACATGAAAGAATACCAAA
27793050 A
1 A
27793051 AATCTAAGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 8 0.23
37 6 0.17
38 21 0.60
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (38 bp):
ATTTTAACATTTTTTTAAAAACATGAAAGAATACCAAA
Found at i:27795896 original size:22 final size:20
Alignment explanation
Indices: 27795871--27795910 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
27795861 TTATTATCCC
27795871 TATCATTATTGATCAATGGTGT
1 TATCATTATT-AT-AATGGTGT
27795893 TATCATTATTATAATGGT
1 TATCATTATTATAATGGT
27795911 TATATTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (20 bp):
TATCATTATTATAATGGTGT
Found at i:27801588 original size:22 final size:22
Alignment explanation
Indices: 27801563--27801623 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
27801553 TTAAATATGG
*
27801563 ATTTCAGA-GAAATTTGGAAGGA
1 ATTTGAGAGGAAATTTGG-AGGA
*
27801585 ATTTGAGAGGAAATTTAGAGGA
1 ATTTGAGAGGAAATTTGGAGGA
*
27801607 AATTGAGAGGAAATTTG
1 ATTTGAGAGGAAATTTG
27801624 AGAGAGGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.28
Consensus pattern (22 bp):
ATTTGAGAGGAAATTTGGAGGA
Found at i:27801595 original size:11 final size:11
Alignment explanation
Indices: 27801563--27801627 Score: 62
Period size: 11 Copynumber: 5.8 Consensus size: 11
27801553 TTAAATATGG
* *
27801563 ATTTCAGAGAA
1 ATTTGAGAGGA
27801574 ATTTG-GAAGGA
1 ATTTGAG-AGGA
27801585 ATTTGAGAGGAA
1 ATTTGAGAGG-A
27801597 ATTT-AGAGGA
1 ATTTGAGAGGA
*
27801607 AATTGAGAGGAA
1 ATTTGAGAGG-A
27801619 ATTTGAGAG
1 ATTTGAGAG
27801628 AGGATTAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
10 5 0.11
11 25 0.56
12 15 0.33
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGGA
Found at i:27803362 original size:6 final size:6
Alignment explanation
Indices: 27803351--27803387 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
27803341 TTTTACAACC
* *
27803351 ATAGAT ATAGAT ATAGAT ATAAAT ATAGAT ACAGAT A
1 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT A
27803388 AGGAAACCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.30
Consensus pattern (6 bp):
ATAGAT
Found at i:27803684 original size:34 final size:35
Alignment explanation
Indices: 27803640--27803706 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
27803630 CAGTAAAATA
*
27803640 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
27803674 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
27803707 CTAGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Done.