Multiple sequence alignment - TraesCS6B01G443800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G443800 chr6B 100.000 1488 0 0 936 2423 706747262 706745775 0.000000e+00 2748.0
1 TraesCS6B01G443800 chr6B 100.000 690 0 0 1 690 706748197 706747508 0.000000e+00 1275.0
2 TraesCS6B01G443800 chr6A 92.880 632 23 5 945 1576 609983434 609982825 0.000000e+00 898.0
3 TraesCS6B01G443800 chr6A 85.812 437 29 18 265 690 609983885 609983471 1.330000e-117 433.0
4 TraesCS6B01G443800 chr6A 91.262 206 12 4 2222 2423 609981566 609981363 2.370000e-70 276.0
5 TraesCS6B01G443800 chr6A 82.951 305 31 6 1895 2180 609981865 609981563 3.090000e-64 255.0
6 TraesCS6B01G443800 chr6D 92.635 611 20 9 945 1555 463479010 463478425 0.000000e+00 856.0
7 TraesCS6B01G443800 chr6D 89.776 401 25 12 293 690 463479434 463479047 1.290000e-137 499.0
8 TraesCS6B01G443800 chr6D 90.323 279 26 1 2121 2398 463477869 463477591 4.920000e-97 364.0
9 TraesCS6B01G443800 chr6D 83.183 333 39 10 1603 1931 463477237 463476918 3.050000e-74 289.0
10 TraesCS6B01G443800 chr6D 86.364 88 12 0 3 90 451932929 451933016 1.980000e-16 97.1
11 TraesCS6B01G443800 chr6D 85.246 61 7 2 189 248 463224550 463224491 7.230000e-06 62.1
12 TraesCS6B01G443800 chr6D 81.333 75 10 3 189 261 395366123 395366195 9.360000e-05 58.4
13 TraesCS6B01G443800 chr4B 88.220 382 31 6 1194 1569 559277953 559278326 6.150000e-121 444.0
14 TraesCS6B01G443800 chr4B 90.476 84 8 0 7 90 657462347 657462264 7.080000e-21 111.0
15 TraesCS6B01G443800 chr4B 88.764 89 10 0 3 91 617431197 617431285 2.550000e-20 110.0
16 TraesCS6B01G443800 chr5A 82.972 323 51 4 1049 1369 459542752 459543072 3.050000e-74 289.0
17 TraesCS6B01G443800 chr5D 82.353 323 53 4 1049 1369 358798458 358798778 6.600000e-71 278.0
18 TraesCS6B01G443800 chr5D 85.075 67 6 2 189 251 546781648 546781714 5.590000e-07 65.8
19 TraesCS6B01G443800 chr5B 81.734 323 55 4 1049 1369 423796257 423796577 1.430000e-67 267.0
20 TraesCS6B01G443800 chr5B 88.506 87 10 0 4 90 600306059 600306145 3.290000e-19 106.0
21 TraesCS6B01G443800 chr5B 88.235 68 2 5 152 217 712082816 712082753 2.580000e-10 76.8
22 TraesCS6B01G443800 chr5B 85.714 63 6 1 189 248 336799832 336799770 2.010000e-06 63.9
23 TraesCS6B01G443800 chr4D 81.366 322 54 6 1049 1367 352525108 352525426 8.600000e-65 257.0
24 TraesCS6B01G443800 chr4D 85.000 60 9 0 189 248 19465549 19465608 7.230000e-06 62.1
25 TraesCS6B01G443800 chr4A 81.040 327 58 4 1049 1373 112853312 112852988 8.600000e-65 257.0
26 TraesCS6B01G443800 chr4A 80.734 327 59 4 1049 1373 112846963 112846639 4.000000e-63 252.0
27 TraesCS6B01G443800 chr2B 89.773 88 9 0 3 90 180549779 180549692 1.970000e-21 113.0
28 TraesCS6B01G443800 chr7A 90.123 81 8 0 3 83 436852871 436852791 3.290000e-19 106.0
29 TraesCS6B01G443800 chr7B 87.500 88 11 0 3 90 685323238 685323325 4.260000e-18 102.0
30 TraesCS6B01G443800 chr3B 87.500 88 11 0 3 90 436735690 436735603 4.260000e-18 102.0
31 TraesCS6B01G443800 chr1D 86.207 87 12 0 3 89 343366981 343366895 7.130000e-16 95.3
32 TraesCS6B01G443800 chr7D 88.889 63 4 1 189 248 530349295 530349357 9.290000e-10 75.0
33 TraesCS6B01G443800 chr3D 85.915 71 8 2 189 259 593276241 593276173 9.290000e-10 75.0
34 TraesCS6B01G443800 chr1B 84.058 69 7 1 189 257 656234115 656234051 2.010000e-06 63.9
35 TraesCS6B01G443800 chr2D 86.207 58 6 1 191 248 406943284 406943339 7.230000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G443800 chr6B 706745775 706748197 2422 True 2011.5 2748 100.00000 1 2423 2 chr6B.!!$R1 2422
1 TraesCS6B01G443800 chr6A 609981363 609983885 2522 True 465.5 898 88.22625 265 2423 4 chr6A.!!$R1 2158
2 TraesCS6B01G443800 chr6D 463476918 463479434 2516 True 502.0 856 88.97925 293 2398 4 chr6D.!!$R2 2105

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
980 1012 0.033109 ACCGTAGTACCACCCTACCC 60.033 60.0 0.0 0.0 32.85 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2394 3140 0.249398 GTAGTCCGACAGGTGCCAAT 59.751 55.0 0.4 0.0 39.05 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.703001 TTTTCCACTCTCTTAGCCCTG 57.297 47.619 0.00 0.00 0.00 4.45
21 22 2.623418 TTCCACTCTCTTAGCCCTGA 57.377 50.000 0.00 0.00 0.00 3.86
22 23 2.856760 TCCACTCTCTTAGCCCTGAT 57.143 50.000 0.00 0.00 0.00 2.90
23 24 3.121929 TCCACTCTCTTAGCCCTGATT 57.878 47.619 0.00 0.00 0.00 2.57
24 25 2.768527 TCCACTCTCTTAGCCCTGATTG 59.231 50.000 0.00 0.00 0.00 2.67
25 26 2.503356 CCACTCTCTTAGCCCTGATTGT 59.497 50.000 0.00 0.00 0.00 2.71
26 27 3.054802 CCACTCTCTTAGCCCTGATTGTT 60.055 47.826 0.00 0.00 0.00 2.83
27 28 3.937706 CACTCTCTTAGCCCTGATTGTTG 59.062 47.826 0.00 0.00 0.00 3.33
28 29 3.584848 ACTCTCTTAGCCCTGATTGTTGT 59.415 43.478 0.00 0.00 0.00 3.32
29 30 4.187694 CTCTCTTAGCCCTGATTGTTGTC 58.812 47.826 0.00 0.00 0.00 3.18
30 31 3.840666 TCTCTTAGCCCTGATTGTTGTCT 59.159 43.478 0.00 0.00 0.00 3.41
31 32 4.081420 TCTCTTAGCCCTGATTGTTGTCTC 60.081 45.833 0.00 0.00 0.00 3.36
32 33 3.055094 TCTTAGCCCTGATTGTTGTCTCC 60.055 47.826 0.00 0.00 0.00 3.71
33 34 1.067295 AGCCCTGATTGTTGTCTCCA 58.933 50.000 0.00 0.00 0.00 3.86
34 35 1.637553 AGCCCTGATTGTTGTCTCCAT 59.362 47.619 0.00 0.00 0.00 3.41
35 36 2.019984 GCCCTGATTGTTGTCTCCATC 58.980 52.381 0.00 0.00 0.00 3.51
36 37 2.618816 GCCCTGATTGTTGTCTCCATCA 60.619 50.000 0.00 0.00 0.00 3.07
37 38 3.012518 CCCTGATTGTTGTCTCCATCAC 58.987 50.000 0.00 0.00 0.00 3.06
38 39 2.674852 CCTGATTGTTGTCTCCATCACG 59.325 50.000 0.00 0.00 0.00 4.35
39 40 3.588955 CTGATTGTTGTCTCCATCACGA 58.411 45.455 0.00 0.00 0.00 4.35
40 41 3.996363 CTGATTGTTGTCTCCATCACGAA 59.004 43.478 0.00 0.00 0.00 3.85
41 42 4.578871 TGATTGTTGTCTCCATCACGAAT 58.421 39.130 0.00 0.00 0.00 3.34
42 43 5.729510 TGATTGTTGTCTCCATCACGAATA 58.270 37.500 0.00 0.00 0.00 1.75
43 44 5.812127 TGATTGTTGTCTCCATCACGAATAG 59.188 40.000 0.00 0.00 0.00 1.73
44 45 3.521560 TGTTGTCTCCATCACGAATAGC 58.478 45.455 0.00 0.00 0.00 2.97
45 46 3.056179 TGTTGTCTCCATCACGAATAGCA 60.056 43.478 0.00 0.00 0.00 3.49
46 47 3.443099 TGTCTCCATCACGAATAGCAG 57.557 47.619 0.00 0.00 0.00 4.24
47 48 2.101415 TGTCTCCATCACGAATAGCAGG 59.899 50.000 0.00 0.00 0.00 4.85
48 49 1.688735 TCTCCATCACGAATAGCAGGG 59.311 52.381 0.00 0.00 0.00 4.45
49 50 0.106708 TCCATCACGAATAGCAGGGC 59.893 55.000 0.00 0.00 0.00 5.19
50 51 0.179048 CCATCACGAATAGCAGGGCA 60.179 55.000 0.00 0.00 0.00 5.36
51 52 1.224075 CATCACGAATAGCAGGGCAG 58.776 55.000 0.00 0.00 0.00 4.85
52 53 0.107456 ATCACGAATAGCAGGGCAGG 59.893 55.000 0.00 0.00 0.00 4.85
53 54 0.975556 TCACGAATAGCAGGGCAGGA 60.976 55.000 0.00 0.00 0.00 3.86
54 55 0.107703 CACGAATAGCAGGGCAGGAA 60.108 55.000 0.00 0.00 0.00 3.36
55 56 0.107654 ACGAATAGCAGGGCAGGAAC 60.108 55.000 0.00 0.00 0.00 3.62
56 57 0.179000 CGAATAGCAGGGCAGGAACT 59.821 55.000 0.00 0.00 43.88 3.01
57 58 1.407437 CGAATAGCAGGGCAGGAACTT 60.407 52.381 0.00 0.00 34.60 2.66
58 59 2.293170 GAATAGCAGGGCAGGAACTTC 58.707 52.381 0.00 0.00 34.60 3.01
59 60 1.589414 ATAGCAGGGCAGGAACTTCT 58.411 50.000 0.00 0.00 34.60 2.85
60 61 1.362224 TAGCAGGGCAGGAACTTCTT 58.638 50.000 0.00 0.00 34.60 2.52
61 62 0.251077 AGCAGGGCAGGAACTTCTTG 60.251 55.000 0.00 0.00 34.60 3.02
63 64 0.251077 CAGGGCAGGAACTTCTTGCT 60.251 55.000 21.39 4.24 46.99 3.91
64 65 0.480252 AGGGCAGGAACTTCTTGCTT 59.520 50.000 21.39 10.46 46.99 3.91
65 66 0.884514 GGGCAGGAACTTCTTGCTTC 59.115 55.000 21.39 12.60 46.99 3.86
66 67 1.609208 GGCAGGAACTTCTTGCTTCA 58.391 50.000 21.39 0.00 46.99 3.02
67 68 1.268079 GGCAGGAACTTCTTGCTTCAC 59.732 52.381 21.39 5.29 46.99 3.18
68 69 1.949525 GCAGGAACTTCTTGCTTCACA 59.050 47.619 16.56 0.00 44.80 3.58
69 70 2.358898 GCAGGAACTTCTTGCTTCACAA 59.641 45.455 16.56 0.00 44.80 3.33
70 71 3.005155 GCAGGAACTTCTTGCTTCACAAT 59.995 43.478 16.56 0.00 44.80 2.71
71 72 4.216257 GCAGGAACTTCTTGCTTCACAATA 59.784 41.667 16.56 0.00 44.80 1.90
72 73 5.693814 CAGGAACTTCTTGCTTCACAATAC 58.306 41.667 0.00 0.00 34.52 1.89
73 74 5.471456 CAGGAACTTCTTGCTTCACAATACT 59.529 40.000 0.00 0.00 34.52 2.12
74 75 5.471456 AGGAACTTCTTGCTTCACAATACTG 59.529 40.000 0.00 0.00 33.06 2.74
75 76 4.756084 ACTTCTTGCTTCACAATACTGC 57.244 40.909 0.00 0.00 37.72 4.40
76 77 3.187227 ACTTCTTGCTTCACAATACTGCG 59.813 43.478 0.00 0.00 37.72 5.18
77 78 3.038788 TCTTGCTTCACAATACTGCGA 57.961 42.857 0.00 0.00 37.72 5.10
78 79 3.398406 TCTTGCTTCACAATACTGCGAA 58.602 40.909 0.00 0.00 37.72 4.70
79 80 3.433274 TCTTGCTTCACAATACTGCGAAG 59.567 43.478 0.00 0.00 42.31 3.79
98 99 6.936222 CGAAGCTCGCAAACTATAGAATAT 57.064 37.500 6.78 0.00 31.14 1.28
99 100 6.746367 CGAAGCTCGCAAACTATAGAATATG 58.254 40.000 6.78 1.07 31.14 1.78
100 101 6.183360 CGAAGCTCGCAAACTATAGAATATGG 60.183 42.308 6.78 0.00 31.14 2.74
101 102 5.482908 AGCTCGCAAACTATAGAATATGGG 58.517 41.667 6.78 7.89 0.00 4.00
102 103 5.246203 AGCTCGCAAACTATAGAATATGGGA 59.754 40.000 6.78 11.27 0.00 4.37
103 104 6.070538 AGCTCGCAAACTATAGAATATGGGAT 60.071 38.462 6.78 0.00 0.00 3.85
104 105 6.036517 GCTCGCAAACTATAGAATATGGGATG 59.963 42.308 6.78 8.15 0.00 3.51
105 106 7.004555 TCGCAAACTATAGAATATGGGATGT 57.995 36.000 6.78 0.00 0.00 3.06
106 107 7.097192 TCGCAAACTATAGAATATGGGATGTC 58.903 38.462 6.78 0.00 0.00 3.06
107 108 6.873605 CGCAAACTATAGAATATGGGATGTCA 59.126 38.462 6.78 0.00 0.00 3.58
108 109 7.550551 CGCAAACTATAGAATATGGGATGTCAT 59.449 37.037 6.78 0.00 0.00 3.06
109 110 9.890629 GCAAACTATAGAATATGGGATGTCATA 57.109 33.333 6.78 0.00 34.55 2.15
118 119 9.872684 AGAATATGGGATGTCATAGAAACAAAT 57.127 29.630 0.00 0.00 33.69 2.32
119 120 9.903682 GAATATGGGATGTCATAGAAACAAATG 57.096 33.333 0.00 0.00 33.69 2.32
120 121 9.425248 AATATGGGATGTCATAGAAACAAATGT 57.575 29.630 0.00 0.00 33.69 2.71
123 124 8.224389 TGGGATGTCATAGAAACAAATGTATG 57.776 34.615 0.00 0.00 0.00 2.39
124 125 8.052141 TGGGATGTCATAGAAACAAATGTATGA 58.948 33.333 0.00 0.00 31.03 2.15
125 126 8.345565 GGGATGTCATAGAAACAAATGTATGAC 58.654 37.037 15.41 15.41 46.39 3.06
126 127 9.113838 GGATGTCATAGAAACAAATGTATGACT 57.886 33.333 19.82 10.89 46.37 3.41
134 135 7.910304 AGAAACAAATGTATGACTATCTTCGC 58.090 34.615 0.00 0.00 0.00 4.70
135 136 7.549134 AGAAACAAATGTATGACTATCTTCGCA 59.451 33.333 0.00 0.00 0.00 5.10
136 137 7.609760 AACAAATGTATGACTATCTTCGCAA 57.390 32.000 0.00 0.00 0.00 4.85
137 138 7.609760 ACAAATGTATGACTATCTTCGCAAA 57.390 32.000 0.00 0.00 0.00 3.68
138 139 8.039603 ACAAATGTATGACTATCTTCGCAAAA 57.960 30.769 0.00 0.00 0.00 2.44
139 140 8.511321 ACAAATGTATGACTATCTTCGCAAAAA 58.489 29.630 0.00 0.00 0.00 1.94
192 193 8.057536 ACATCTTATATTATGAGACGGACTCC 57.942 38.462 5.08 0.00 44.34 3.85
193 194 7.122948 ACATCTTATATTATGAGACGGACTCCC 59.877 40.741 5.08 0.00 44.34 4.30
194 195 6.791371 TCTTATATTATGAGACGGACTCCCT 58.209 40.000 5.08 0.00 44.34 4.20
195 196 6.885376 TCTTATATTATGAGACGGACTCCCTC 59.115 42.308 5.08 0.00 44.34 4.30
196 197 2.068834 TTATGAGACGGACTCCCTCC 57.931 55.000 5.08 0.00 44.34 4.30
203 204 2.041819 GGACTCCCTCCGTCCCAT 60.042 66.667 0.00 0.00 44.08 4.00
204 205 1.232216 GGACTCCCTCCGTCCCATA 59.768 63.158 0.00 0.00 44.08 2.74
205 206 0.398098 GGACTCCCTCCGTCCCATAA 60.398 60.000 0.00 0.00 44.08 1.90
206 207 1.718280 GACTCCCTCCGTCCCATAAT 58.282 55.000 0.00 0.00 0.00 1.28
207 208 1.344763 GACTCCCTCCGTCCCATAATG 59.655 57.143 0.00 0.00 0.00 1.90
208 209 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
209 210 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
210 211 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
211 212 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
212 213 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
213 214 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
215 216 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
216 217 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
217 218 4.644234 TCCGTCCCATAATGTAAGACGTTA 59.356 41.667 9.63 0.00 46.62 3.18
218 219 5.126869 TCCGTCCCATAATGTAAGACGTTAA 59.873 40.000 9.63 0.00 46.62 2.01
219 220 5.811613 CCGTCCCATAATGTAAGACGTTAAA 59.188 40.000 9.63 0.00 46.62 1.52
220 221 6.237915 CCGTCCCATAATGTAAGACGTTAAAC 60.238 42.308 9.63 0.00 46.62 2.01
221 222 9.288309 CCGTCCCATAATGTAAGACGTTAAACG 62.288 44.444 9.63 0.00 46.62 3.60
237 238 7.728580 CGTTAAACGTTTTACATTATGGCAT 57.271 32.000 24.72 4.88 36.74 4.40
238 239 7.596576 CGTTAAACGTTTTACATTATGGCATG 58.403 34.615 24.72 0.00 36.74 4.06
239 240 7.253486 CGTTAAACGTTTTACATTATGGCATGG 60.253 37.037 24.72 2.07 36.74 3.66
240 241 5.906113 AACGTTTTACATTATGGCATGGA 57.094 34.783 10.98 0.00 0.00 3.41
241 242 5.499139 ACGTTTTACATTATGGCATGGAG 57.501 39.130 10.98 1.72 0.00 3.86
242 243 4.338118 ACGTTTTACATTATGGCATGGAGG 59.662 41.667 10.98 2.99 0.00 4.30
243 244 4.261572 CGTTTTACATTATGGCATGGAGGG 60.262 45.833 10.98 0.00 0.00 4.30
244 245 4.805140 TTTACATTATGGCATGGAGGGA 57.195 40.909 10.98 0.00 0.00 4.20
245 246 2.965671 ACATTATGGCATGGAGGGAG 57.034 50.000 10.98 0.00 0.00 4.30
246 247 2.138542 ACATTATGGCATGGAGGGAGT 58.861 47.619 10.98 0.00 0.00 3.85
247 248 3.326521 ACATTATGGCATGGAGGGAGTA 58.673 45.455 10.98 0.00 0.00 2.59
248 249 3.328931 ACATTATGGCATGGAGGGAGTAG 59.671 47.826 10.98 0.00 0.00 2.57
249 250 3.344535 TTATGGCATGGAGGGAGTAGA 57.655 47.619 10.98 0.00 0.00 2.59
250 251 2.196742 ATGGCATGGAGGGAGTAGAA 57.803 50.000 0.00 0.00 0.00 2.10
251 252 1.965414 TGGCATGGAGGGAGTAGAAA 58.035 50.000 0.00 0.00 0.00 2.52
252 253 2.274542 TGGCATGGAGGGAGTAGAAAA 58.725 47.619 0.00 0.00 0.00 2.29
253 254 2.852449 TGGCATGGAGGGAGTAGAAAAT 59.148 45.455 0.00 0.00 0.00 1.82
254 255 3.269381 TGGCATGGAGGGAGTAGAAAATT 59.731 43.478 0.00 0.00 0.00 1.82
255 256 4.476846 TGGCATGGAGGGAGTAGAAAATTA 59.523 41.667 0.00 0.00 0.00 1.40
256 257 4.822350 GGCATGGAGGGAGTAGAAAATTAC 59.178 45.833 0.00 0.00 0.00 1.89
257 258 5.398012 GGCATGGAGGGAGTAGAAAATTACT 60.398 44.000 0.00 0.00 36.61 2.24
258 259 6.183361 GGCATGGAGGGAGTAGAAAATTACTA 60.183 42.308 0.00 0.00 34.13 1.82
259 260 6.706716 GCATGGAGGGAGTAGAAAATTACTAC 59.293 42.308 12.12 12.12 40.04 2.73
313 314 9.986833 AAAAACAATTCTTTTGTGCAAATCTAC 57.013 25.926 0.00 0.00 32.22 2.59
349 378 8.003784 GCACATTGTAGCTTTTGTGTTTTATTC 58.996 33.333 15.11 0.09 41.14 1.75
360 389 5.090652 TGTGTTTTATTCACACGAGAAGC 57.909 39.130 0.00 0.00 46.47 3.86
418 448 3.763897 GGGAATATGCTGTTTCAAGTGGT 59.236 43.478 0.00 0.00 0.00 4.16
419 449 4.220602 GGGAATATGCTGTTTCAAGTGGTT 59.779 41.667 0.00 0.00 0.00 3.67
485 516 0.911769 AACGCAGATGATTCCCTCCA 59.088 50.000 0.00 0.00 0.00 3.86
486 517 0.911769 ACGCAGATGATTCCCTCCAA 59.088 50.000 0.00 0.00 0.00 3.53
488 519 2.092212 ACGCAGATGATTCCCTCCAAAT 60.092 45.455 0.00 0.00 0.00 2.32
489 520 2.292569 CGCAGATGATTCCCTCCAAATG 59.707 50.000 0.00 0.00 0.00 2.32
490 521 3.559069 GCAGATGATTCCCTCCAAATGA 58.441 45.455 0.00 0.00 0.00 2.57
491 522 3.956199 GCAGATGATTCCCTCCAAATGAA 59.044 43.478 0.00 0.00 0.00 2.57
492 523 4.403432 GCAGATGATTCCCTCCAAATGAAA 59.597 41.667 0.00 0.00 0.00 2.69
493 524 5.680665 GCAGATGATTCCCTCCAAATGAAAC 60.681 44.000 0.00 0.00 0.00 2.78
563 595 2.621668 CCAAACCCAAATCTCCTCCCTC 60.622 54.545 0.00 0.00 0.00 4.30
977 1009 0.704076 ACCACCGTAGTACCACCCTA 59.296 55.000 0.00 0.00 0.00 3.53
978 1010 1.106285 CCACCGTAGTACCACCCTAC 58.894 60.000 0.00 0.00 33.08 3.18
980 1012 0.033109 ACCGTAGTACCACCCTACCC 60.033 60.000 0.00 0.00 32.85 3.69
981 1013 0.756815 CCGTAGTACCACCCTACCCC 60.757 65.000 0.00 0.00 32.85 4.95
982 1014 1.103398 CGTAGTACCACCCTACCCCG 61.103 65.000 0.00 0.00 32.85 5.73
1425 1457 1.754226 CAGTCCCAGGAGTTCTAGAGC 59.246 57.143 0.00 0.00 0.00 4.09
1426 1458 0.741915 GTCCCAGGAGTTCTAGAGCG 59.258 60.000 0.47 0.00 0.00 5.03
1436 1468 1.000717 GTTCTAGAGCGCCAGAGATCC 60.001 57.143 2.29 0.00 0.00 3.36
1439 1471 0.250945 TAGAGCGCCAGAGATCCGAT 60.251 55.000 2.29 0.00 0.00 4.18
1440 1472 1.372748 GAGCGCCAGAGATCCGATG 60.373 63.158 2.29 0.00 0.00 3.84
1442 1474 1.372748 GCGCCAGAGATCCGATGAG 60.373 63.158 0.00 0.00 0.00 2.90
1443 1475 2.037053 CGCCAGAGATCCGATGAGT 58.963 57.895 0.00 0.00 0.00 3.41
1445 1477 0.033228 GCCAGAGATCCGATGAGTGG 59.967 60.000 0.00 0.00 0.00 4.00
1446 1478 0.033228 CCAGAGATCCGATGAGTGGC 59.967 60.000 0.00 0.00 0.00 5.01
1447 1479 0.318529 CAGAGATCCGATGAGTGGCG 60.319 60.000 0.00 0.00 0.00 5.69
1448 1480 0.753479 AGAGATCCGATGAGTGGCGT 60.753 55.000 0.00 0.00 0.00 5.68
1449 1481 0.596083 GAGATCCGATGAGTGGCGTG 60.596 60.000 0.00 0.00 0.00 5.34
1450 1482 1.592669 GATCCGATGAGTGGCGTGG 60.593 63.158 0.00 0.00 0.00 4.94
1451 1483 3.740128 ATCCGATGAGTGGCGTGGC 62.740 63.158 0.00 0.00 0.00 5.01
1454 1486 3.490759 GATGAGTGGCGTGGCGTG 61.491 66.667 0.00 0.00 0.00 5.34
1504 1536 5.119694 GGTAGATTAGTTCTTCTTGGCCAG 58.880 45.833 5.11 0.00 35.79 4.85
1505 1537 3.615155 AGATTAGTTCTTCTTGGCCAGC 58.385 45.455 5.11 0.00 0.00 4.85
1565 1597 3.118884 GGAATGGAATGCTTGCAATCTGT 60.119 43.478 0.00 0.00 32.29 3.41
1576 1608 4.498682 GCTTGCAATCTGTTTCTTGTCTGT 60.499 41.667 0.00 0.00 0.00 3.41
1578 1610 5.581126 TGCAATCTGTTTCTTGTCTGTTT 57.419 34.783 0.00 0.00 0.00 2.83
1579 1611 5.342433 TGCAATCTGTTTCTTGTCTGTTTG 58.658 37.500 0.00 0.00 0.00 2.93
1580 1612 4.741676 GCAATCTGTTTCTTGTCTGTTTGG 59.258 41.667 0.00 0.00 0.00 3.28
1581 1613 5.450412 GCAATCTGTTTCTTGTCTGTTTGGA 60.450 40.000 0.00 0.00 0.00 3.53
1582 1614 6.736794 GCAATCTGTTTCTTGTCTGTTTGGAT 60.737 38.462 0.00 0.00 0.00 3.41
1583 1615 5.756195 TCTGTTTCTTGTCTGTTTGGATG 57.244 39.130 0.00 0.00 0.00 3.51
1586 1618 4.952957 TGTTTCTTGTCTGTTTGGATGGAA 59.047 37.500 0.00 0.00 0.00 3.53
1588 1620 5.710513 TTCTTGTCTGTTTGGATGGAATG 57.289 39.130 0.00 0.00 0.00 2.67
1589 1621 3.507233 TCTTGTCTGTTTGGATGGAATGC 59.493 43.478 0.00 0.00 33.97 3.56
1590 1622 1.811965 TGTCTGTTTGGATGGAATGCG 59.188 47.619 0.00 0.00 37.56 4.73
1596 1734 2.880890 GTTTGGATGGAATGCGCTCTAT 59.119 45.455 9.73 1.29 37.56 1.98
1600 1738 3.181451 TGGATGGAATGCGCTCTATTTCT 60.181 43.478 9.73 0.00 37.56 2.52
1627 1765 2.698855 ACTTGTCGCTGCCTATGATT 57.301 45.000 0.00 0.00 0.00 2.57
1629 1767 2.679837 ACTTGTCGCTGCCTATGATTTG 59.320 45.455 0.00 0.00 0.00 2.32
1630 1768 1.016627 TGTCGCTGCCTATGATTTGC 58.983 50.000 0.00 0.00 0.00 3.68
1652 1790 7.144722 TGCGAATGTTAATCTGAATGAAACT 57.855 32.000 0.00 0.00 0.00 2.66
1662 1800 4.801891 TCTGAATGAAACTGAAATGCTGC 58.198 39.130 0.00 0.00 0.00 5.25
1665 1803 5.946298 TGAATGAAACTGAAATGCTGCTAG 58.054 37.500 0.00 0.00 0.00 3.42
1669 1807 4.580167 TGAAACTGAAATGCTGCTAGTGTT 59.420 37.500 0.00 0.00 0.00 3.32
1670 1808 4.494350 AACTGAAATGCTGCTAGTGTTG 57.506 40.909 0.00 0.00 0.00 3.33
1671 1809 3.480470 ACTGAAATGCTGCTAGTGTTGT 58.520 40.909 0.00 0.00 0.00 3.32
1673 1811 4.023707 ACTGAAATGCTGCTAGTGTTGTTC 60.024 41.667 0.00 0.00 0.00 3.18
1676 1814 5.762711 TGAAATGCTGCTAGTGTTGTTCTAA 59.237 36.000 0.00 0.00 0.00 2.10
1682 1820 5.290643 GCTGCTAGTGTTGTTCTAATCTGAG 59.709 44.000 0.00 0.00 0.00 3.35
1694 1832 7.405292 TGTTCTAATCTGAGGAATGAATGGTT 58.595 34.615 0.00 0.00 0.00 3.67
1700 1838 3.349927 TGAGGAATGAATGGTTCAGCAG 58.650 45.455 0.00 0.00 43.98 4.24
1715 1853 4.806936 CAGTTCCTGCTGCAAGGA 57.193 55.556 14.24 14.24 44.88 3.36
1716 1854 2.251600 CAGTTCCTGCTGCAAGGAC 58.748 57.895 16.84 10.41 46.24 3.85
1718 1856 1.301716 GTTCCTGCTGCAAGGACGA 60.302 57.895 16.84 4.91 46.24 4.20
1720 1858 0.036732 TTCCTGCTGCAAGGACGATT 59.963 50.000 16.84 0.00 46.24 3.34
1760 1903 2.426522 TCGATTCTTTTGCCCTGACAG 58.573 47.619 0.00 0.00 0.00 3.51
1761 1904 1.135575 CGATTCTTTTGCCCTGACAGC 60.136 52.381 0.00 0.00 0.00 4.40
1763 1906 0.465460 TTCTTTTGCCCTGACAGCGT 60.465 50.000 0.00 0.00 0.00 5.07
1764 1907 1.165907 TCTTTTGCCCTGACAGCGTG 61.166 55.000 0.00 0.00 0.00 5.34
1805 1948 1.217916 TCAGTCCAAGGTCCACCAAA 58.782 50.000 0.00 0.00 38.89 3.28
1807 1950 2.176798 TCAGTCCAAGGTCCACCAAAAT 59.823 45.455 0.00 0.00 38.89 1.82
1813 1956 2.009681 AGGTCCACCAAAATCCAACC 57.990 50.000 0.00 0.00 38.89 3.77
1818 1961 2.038659 CCACCAAAATCCAACCACTGT 58.961 47.619 0.00 0.00 0.00 3.55
1831 1974 4.478699 CAACCACTGTGCAGATTGTTATG 58.521 43.478 6.17 0.00 0.00 1.90
1843 1990 7.213252 GCAGATTGTTATGCAACATGTTTAG 57.787 36.000 8.77 0.00 44.01 1.85
1845 1992 7.967854 GCAGATTGTTATGCAACATGTTTAGTA 59.032 33.333 8.77 0.00 44.01 1.82
1851 1998 9.838975 TGTTATGCAACATGTTTAGTATTCTTG 57.161 29.630 8.77 0.00 39.75 3.02
1852 1999 9.840427 GTTATGCAACATGTTTAGTATTCTTGT 57.160 29.630 8.77 0.00 34.60 3.16
1855 2002 9.762933 ATGCAACATGTTTAGTATTCTTGTTTT 57.237 25.926 8.77 0.00 30.79 2.43
1856 2003 9.593134 TGCAACATGTTTAGTATTCTTGTTTTT 57.407 25.926 8.77 0.00 30.79 1.94
1873 2020 4.081420 TGTTTTTAAAAGTTGCAGCCAGGA 60.081 37.500 0.14 0.00 0.00 3.86
1879 2026 2.719376 GTTGCAGCCAGGAACTTCA 58.281 52.632 0.00 0.00 44.29 3.02
1880 2027 1.032014 GTTGCAGCCAGGAACTTCAA 58.968 50.000 0.00 0.00 44.29 2.69
1909 2575 9.871238 TCTATACAGATTGTTTACTGAAGAACC 57.129 33.333 0.00 0.00 37.54 3.62
1910 2576 5.924475 ACAGATTGTTTACTGAAGAACCG 57.076 39.130 0.00 0.00 37.54 4.44
1919 2585 2.417719 ACTGAAGAACCGACAATCTGC 58.582 47.619 0.00 0.00 0.00 4.26
1932 2598 4.092091 CGACAATCTGCTTACTGAAGAACC 59.908 45.833 0.00 0.00 33.23 3.62
1933 2599 3.997021 ACAATCTGCTTACTGAAGAACCG 59.003 43.478 0.00 0.00 33.23 4.44
1975 2662 3.318275 ACGAGCACTCTGTTTACTGAAGA 59.682 43.478 0.00 0.00 0.00 2.87
1980 2667 4.149046 GCACTCTGTTTACTGAAGAACGAG 59.851 45.833 0.00 0.00 35.06 4.18
1985 2672 3.802139 TGTTTACTGAAGAACGAGCACTG 59.198 43.478 0.00 0.00 0.00 3.66
1987 2674 2.604046 ACTGAAGAACGAGCACTGTT 57.396 45.000 0.00 0.00 0.00 3.16
1989 2676 2.609459 ACTGAAGAACGAGCACTGTTTG 59.391 45.455 0.00 0.00 0.00 2.93
1994 2683 2.609459 AGAACGAGCACTGTTTGTTGAG 59.391 45.455 3.37 0.00 0.00 3.02
2013 2702 3.449018 TGAGAAACTCTGTATGGAGGCTC 59.551 47.826 5.78 5.78 37.63 4.70
2048 2737 6.073003 CGCTTTCTCCAAATCTACTTTCAACT 60.073 38.462 0.00 0.00 0.00 3.16
2078 2767 3.252554 AGGCATGGGGAAAAGTTTACA 57.747 42.857 0.00 0.00 0.00 2.41
2079 2768 3.582164 AGGCATGGGGAAAAGTTTACAA 58.418 40.909 0.00 0.00 0.00 2.41
2088 2777 8.485578 TGGGGAAAAGTTTACAAGAACATAAT 57.514 30.769 0.00 0.00 31.94 1.28
2089 2778 8.929487 TGGGGAAAAGTTTACAAGAACATAATT 58.071 29.630 0.00 0.00 31.94 1.40
2108 2797 2.682155 TTTTTGAGCACCCAACAACC 57.318 45.000 0.00 0.00 0.00 3.77
2118 2824 2.433970 CACCCAACAACCAACCTTCATT 59.566 45.455 0.00 0.00 0.00 2.57
2123 2829 4.141959 CCAACAACCAACCTTCATTCAAGT 60.142 41.667 0.00 0.00 0.00 3.16
2125 2831 5.675684 ACAACCAACCTTCATTCAAGTTT 57.324 34.783 0.00 0.00 0.00 2.66
2183 2889 5.064071 GCAGATTGTAGAAACCTGAGTAAGC 59.936 44.000 8.82 0.00 0.00 3.09
2191 2897 3.305398 AACCTGAGTAAGCGAGTCAAG 57.695 47.619 0.00 0.00 37.05 3.02
2220 2926 7.661040 AGTGATGATGAAAATTCGTTTTCCTT 58.339 30.769 10.18 0.30 39.51 3.36
2245 2951 6.650807 TGAGTGACATATTTGACCTCTTTGTC 59.349 38.462 0.00 0.00 35.77 3.18
2255 2961 1.018226 CCTCTTTGTCTGCTCGCTGG 61.018 60.000 0.00 0.00 0.00 4.85
2292 2998 1.320344 TTCCATGGTCCTCGAGGTCG 61.320 60.000 30.17 12.50 41.45 4.79
2297 3003 0.824595 TGGTCCTCGAGGTCGTTGAA 60.825 55.000 30.17 7.04 40.80 2.69
2322 3028 3.187227 GCTCATCAACAACAATGACGAGT 59.813 43.478 0.00 0.00 38.87 4.18
2394 3140 0.892755 ACGGCATTGTAGGTCGAAGA 59.107 50.000 0.00 0.00 36.74 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.248024 TCAGGGCTAAGAGAGTGGAAAA 58.752 45.455 0.00 0.00 0.00 2.29
1 2 2.902608 TCAGGGCTAAGAGAGTGGAAA 58.097 47.619 0.00 0.00 0.00 3.13
2 3 2.623418 TCAGGGCTAAGAGAGTGGAA 57.377 50.000 0.00 0.00 0.00 3.53
3 4 2.768527 CAATCAGGGCTAAGAGAGTGGA 59.231 50.000 0.00 0.00 0.00 4.02
4 5 2.503356 ACAATCAGGGCTAAGAGAGTGG 59.497 50.000 0.00 0.00 31.06 4.00
5 6 3.902881 ACAATCAGGGCTAAGAGAGTG 57.097 47.619 0.00 0.00 32.86 3.51
6 7 3.584848 ACAACAATCAGGGCTAAGAGAGT 59.415 43.478 0.00 0.00 0.00 3.24
7 8 4.081198 AGACAACAATCAGGGCTAAGAGAG 60.081 45.833 0.00 0.00 0.00 3.20
8 9 3.840666 AGACAACAATCAGGGCTAAGAGA 59.159 43.478 0.00 0.00 0.00 3.10
9 10 4.187694 GAGACAACAATCAGGGCTAAGAG 58.812 47.826 0.00 0.00 0.00 2.85
10 11 3.055094 GGAGACAACAATCAGGGCTAAGA 60.055 47.826 0.00 0.00 0.00 2.10
11 12 3.274288 GGAGACAACAATCAGGGCTAAG 58.726 50.000 0.00 0.00 0.00 2.18
12 13 2.642311 TGGAGACAACAATCAGGGCTAA 59.358 45.455 0.00 0.00 37.44 3.09
13 14 2.265367 TGGAGACAACAATCAGGGCTA 58.735 47.619 0.00 0.00 37.44 3.93
14 15 1.067295 TGGAGACAACAATCAGGGCT 58.933 50.000 0.00 0.00 37.44 5.19
15 16 3.650647 TGGAGACAACAATCAGGGC 57.349 52.632 0.00 0.00 37.44 5.19
16 17 3.012518 GTGATGGAGACAACAATCAGGG 58.987 50.000 0.00 0.00 45.31 4.45
17 18 2.674852 CGTGATGGAGACAACAATCAGG 59.325 50.000 0.00 0.00 45.31 3.86
18 19 3.588955 TCGTGATGGAGACAACAATCAG 58.411 45.455 0.00 0.00 45.31 2.90
19 20 3.676291 TCGTGATGGAGACAACAATCA 57.324 42.857 0.00 0.00 45.31 2.57
20 21 5.277058 GCTATTCGTGATGGAGACAACAATC 60.277 44.000 0.00 0.00 45.31 2.67
21 22 4.572389 GCTATTCGTGATGGAGACAACAAT 59.428 41.667 0.00 0.00 45.31 2.71
22 23 3.932710 GCTATTCGTGATGGAGACAACAA 59.067 43.478 0.00 0.00 45.31 2.83
27 28 2.546795 CCCTGCTATTCGTGATGGAGAC 60.547 54.545 0.00 0.00 0.00 3.36
28 29 1.688735 CCCTGCTATTCGTGATGGAGA 59.311 52.381 0.00 0.00 0.00 3.71
29 30 1.875576 GCCCTGCTATTCGTGATGGAG 60.876 57.143 0.00 0.00 0.00 3.86
30 31 0.106708 GCCCTGCTATTCGTGATGGA 59.893 55.000 0.00 0.00 0.00 3.41
31 32 0.179048 TGCCCTGCTATTCGTGATGG 60.179 55.000 0.00 0.00 0.00 3.51
32 33 1.224075 CTGCCCTGCTATTCGTGATG 58.776 55.000 0.00 0.00 0.00 3.07
33 34 0.107456 CCTGCCCTGCTATTCGTGAT 59.893 55.000 0.00 0.00 0.00 3.06
34 35 0.975556 TCCTGCCCTGCTATTCGTGA 60.976 55.000 0.00 0.00 0.00 4.35
35 36 0.107703 TTCCTGCCCTGCTATTCGTG 60.108 55.000 0.00 0.00 0.00 4.35
36 37 0.107654 GTTCCTGCCCTGCTATTCGT 60.108 55.000 0.00 0.00 0.00 3.85
37 38 0.179000 AGTTCCTGCCCTGCTATTCG 59.821 55.000 0.00 0.00 0.00 3.34
38 39 2.092699 AGAAGTTCCTGCCCTGCTATTC 60.093 50.000 0.00 0.00 0.00 1.75
39 40 1.918957 AGAAGTTCCTGCCCTGCTATT 59.081 47.619 0.00 0.00 0.00 1.73
40 41 1.589414 AGAAGTTCCTGCCCTGCTAT 58.411 50.000 0.00 0.00 0.00 2.97
41 42 1.003580 CAAGAAGTTCCTGCCCTGCTA 59.996 52.381 0.00 0.00 0.00 3.49
42 43 0.251077 CAAGAAGTTCCTGCCCTGCT 60.251 55.000 0.00 0.00 0.00 4.24
43 44 1.871126 GCAAGAAGTTCCTGCCCTGC 61.871 60.000 14.46 4.07 0.00 4.85
44 45 0.251077 AGCAAGAAGTTCCTGCCCTG 60.251 55.000 20.39 1.58 0.00 4.45
45 46 0.480252 AAGCAAGAAGTTCCTGCCCT 59.520 50.000 20.39 7.66 0.00 5.19
46 47 0.884514 GAAGCAAGAAGTTCCTGCCC 59.115 55.000 20.39 10.78 0.00 5.36
47 48 1.268079 GTGAAGCAAGAAGTTCCTGCC 59.732 52.381 20.39 8.85 0.00 4.85
48 49 1.949525 TGTGAAGCAAGAAGTTCCTGC 59.050 47.619 17.14 17.14 0.00 4.85
49 50 4.843220 ATTGTGAAGCAAGAAGTTCCTG 57.157 40.909 0.00 0.00 40.86 3.86
50 51 5.471456 CAGTATTGTGAAGCAAGAAGTTCCT 59.529 40.000 0.00 0.00 40.86 3.36
51 52 5.693814 CAGTATTGTGAAGCAAGAAGTTCC 58.306 41.667 0.00 0.00 40.86 3.62
52 53 5.149977 GCAGTATTGTGAAGCAAGAAGTTC 58.850 41.667 0.00 0.00 40.86 3.01
53 54 4.319766 CGCAGTATTGTGAAGCAAGAAGTT 60.320 41.667 0.00 0.00 40.86 2.66
54 55 3.187227 CGCAGTATTGTGAAGCAAGAAGT 59.813 43.478 0.00 0.00 40.86 3.01
55 56 3.433274 TCGCAGTATTGTGAAGCAAGAAG 59.567 43.478 0.00 0.00 40.68 2.85
56 57 3.398406 TCGCAGTATTGTGAAGCAAGAA 58.602 40.909 0.00 0.00 40.68 2.52
57 58 3.038788 TCGCAGTATTGTGAAGCAAGA 57.961 42.857 0.00 0.00 40.68 3.02
58 59 3.811722 TTCGCAGTATTGTGAAGCAAG 57.188 42.857 9.88 0.00 46.01 4.01
64 65 1.629013 CGAGCTTCGCAGTATTGTGA 58.371 50.000 0.00 0.00 41.84 3.58
75 76 6.183360 CCATATTCTATAGTTTGCGAGCTTCG 60.183 42.308 0.00 0.00 43.89 3.79
76 77 6.091441 CCCATATTCTATAGTTTGCGAGCTTC 59.909 42.308 0.00 0.00 0.00 3.86
77 78 5.934625 CCCATATTCTATAGTTTGCGAGCTT 59.065 40.000 0.00 0.00 0.00 3.74
78 79 5.246203 TCCCATATTCTATAGTTTGCGAGCT 59.754 40.000 0.00 0.00 0.00 4.09
79 80 5.479306 TCCCATATTCTATAGTTTGCGAGC 58.521 41.667 0.00 0.00 0.00 5.03
80 81 7.099764 ACATCCCATATTCTATAGTTTGCGAG 58.900 38.462 0.00 0.00 0.00 5.03
81 82 7.004555 ACATCCCATATTCTATAGTTTGCGA 57.995 36.000 0.00 0.00 0.00 5.10
82 83 6.873605 TGACATCCCATATTCTATAGTTTGCG 59.126 38.462 0.00 0.00 0.00 4.85
83 84 8.798859 ATGACATCCCATATTCTATAGTTTGC 57.201 34.615 0.00 0.00 0.00 3.68
92 93 9.872684 ATTTGTTTCTATGACATCCCATATTCT 57.127 29.630 0.00 0.00 0.00 2.40
93 94 9.903682 CATTTGTTTCTATGACATCCCATATTC 57.096 33.333 0.00 0.00 0.00 1.75
94 95 9.425248 ACATTTGTTTCTATGACATCCCATATT 57.575 29.630 0.00 0.00 0.00 1.28
97 98 8.853126 CATACATTTGTTTCTATGACATCCCAT 58.147 33.333 0.00 0.00 0.00 4.00
98 99 8.052141 TCATACATTTGTTTCTATGACATCCCA 58.948 33.333 0.00 0.00 0.00 4.37
99 100 8.345565 GTCATACATTTGTTTCTATGACATCCC 58.654 37.037 14.84 0.00 38.86 3.85
100 101 9.113838 AGTCATACATTTGTTTCTATGACATCC 57.886 33.333 19.07 1.68 40.27 3.51
108 109 9.031360 GCGAAGATAGTCATACATTTGTTTCTA 57.969 33.333 0.00 0.00 0.00 2.10
109 110 7.549134 TGCGAAGATAGTCATACATTTGTTTCT 59.451 33.333 0.00 0.00 0.00 2.52
110 111 7.684670 TGCGAAGATAGTCATACATTTGTTTC 58.315 34.615 0.00 0.00 0.00 2.78
111 112 7.609760 TGCGAAGATAGTCATACATTTGTTT 57.390 32.000 0.00 0.00 0.00 2.83
112 113 7.609760 TTGCGAAGATAGTCATACATTTGTT 57.390 32.000 0.00 0.00 0.00 2.83
113 114 7.609760 TTTGCGAAGATAGTCATACATTTGT 57.390 32.000 0.00 0.00 0.00 2.83
114 115 8.894409 TTTTTGCGAAGATAGTCATACATTTG 57.106 30.769 0.00 0.00 0.00 2.32
166 167 8.524487 GGAGTCCGTCTCATAATATAAGATGTT 58.476 37.037 0.00 0.00 44.40 2.71
167 168 7.122948 GGGAGTCCGTCTCATAATATAAGATGT 59.877 40.741 2.26 0.00 44.40 3.06
168 169 7.340743 AGGGAGTCCGTCTCATAATATAAGATG 59.659 40.741 2.26 0.00 44.40 2.90
169 170 7.415086 AGGGAGTCCGTCTCATAATATAAGAT 58.585 38.462 2.26 0.00 44.40 2.40
170 171 6.791371 AGGGAGTCCGTCTCATAATATAAGA 58.209 40.000 2.26 0.00 44.40 2.10
171 172 6.095720 GGAGGGAGTCCGTCTCATAATATAAG 59.904 46.154 26.66 0.00 44.40 1.73
172 173 5.950549 GGAGGGAGTCCGTCTCATAATATAA 59.049 44.000 26.66 0.00 44.40 0.98
173 174 5.507637 GGAGGGAGTCCGTCTCATAATATA 58.492 45.833 26.66 0.00 44.40 0.86
174 175 4.345854 GGAGGGAGTCCGTCTCATAATAT 58.654 47.826 26.66 0.00 44.40 1.28
175 176 3.764218 GGAGGGAGTCCGTCTCATAATA 58.236 50.000 26.66 0.00 44.40 0.98
176 177 2.599677 GGAGGGAGTCCGTCTCATAAT 58.400 52.381 26.66 0.00 44.40 1.28
177 178 2.068834 GGAGGGAGTCCGTCTCATAA 57.931 55.000 26.66 0.00 44.40 1.90
178 179 3.823369 GGAGGGAGTCCGTCTCATA 57.177 57.895 26.66 0.00 44.40 2.15
179 180 4.688770 GGAGGGAGTCCGTCTCAT 57.311 61.111 26.66 0.00 44.40 2.90
187 188 1.344763 CATTATGGGACGGAGGGAGTC 59.655 57.143 0.00 0.00 37.86 3.36
188 189 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
189 190 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
190 191 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
191 192 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
192 193 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
193 194 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
194 195 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
197 198 6.699063 CGTTTAACGTCTTACATTATGGGAC 58.301 40.000 9.54 1.75 36.74 4.46
198 199 6.890663 CGTTTAACGTCTTACATTATGGGA 57.109 37.500 9.54 0.00 36.74 4.37
214 215 7.755822 TCCATGCCATAATGTAAAACGTTTAAC 59.244 33.333 15.03 0.08 0.00 2.01
215 216 7.827701 TCCATGCCATAATGTAAAACGTTTAA 58.172 30.769 15.03 3.67 0.00 1.52
216 217 7.392494 TCCATGCCATAATGTAAAACGTTTA 57.608 32.000 15.03 0.00 0.00 2.01
217 218 6.274157 TCCATGCCATAATGTAAAACGTTT 57.726 33.333 7.96 7.96 0.00 3.60
218 219 5.163561 CCTCCATGCCATAATGTAAAACGTT 60.164 40.000 0.00 0.00 0.00 3.99
219 220 4.338118 CCTCCATGCCATAATGTAAAACGT 59.662 41.667 0.00 0.00 0.00 3.99
220 221 4.261572 CCCTCCATGCCATAATGTAAAACG 60.262 45.833 0.00 0.00 0.00 3.60
221 222 4.892934 TCCCTCCATGCCATAATGTAAAAC 59.107 41.667 0.00 0.00 0.00 2.43
222 223 5.136068 TCCCTCCATGCCATAATGTAAAA 57.864 39.130 0.00 0.00 0.00 1.52
223 224 4.167892 ACTCCCTCCATGCCATAATGTAAA 59.832 41.667 0.00 0.00 0.00 2.01
224 225 3.721575 ACTCCCTCCATGCCATAATGTAA 59.278 43.478 0.00 0.00 0.00 2.41
225 226 3.326521 ACTCCCTCCATGCCATAATGTA 58.673 45.455 0.00 0.00 0.00 2.29
226 227 2.138542 ACTCCCTCCATGCCATAATGT 58.861 47.619 0.00 0.00 0.00 2.71
227 228 2.965671 ACTCCCTCCATGCCATAATG 57.034 50.000 0.00 0.00 0.00 1.90
228 229 3.874316 TCTACTCCCTCCATGCCATAAT 58.126 45.455 0.00 0.00 0.00 1.28
229 230 3.344535 TCTACTCCCTCCATGCCATAA 57.655 47.619 0.00 0.00 0.00 1.90
230 231 3.344535 TTCTACTCCCTCCATGCCATA 57.655 47.619 0.00 0.00 0.00 2.74
231 232 2.196742 TTCTACTCCCTCCATGCCAT 57.803 50.000 0.00 0.00 0.00 4.40
232 233 1.965414 TTTCTACTCCCTCCATGCCA 58.035 50.000 0.00 0.00 0.00 4.92
233 234 3.584733 ATTTTCTACTCCCTCCATGCC 57.415 47.619 0.00 0.00 0.00 4.40
234 235 5.685728 AGTAATTTTCTACTCCCTCCATGC 58.314 41.667 0.00 0.00 0.00 4.06
235 236 8.024145 AGTAGTAATTTTCTACTCCCTCCATG 57.976 38.462 9.24 0.00 42.74 3.66
288 289 9.382275 AGTAGATTTGCACAAAAGAATTGTTTT 57.618 25.926 7.46 7.46 33.56 2.43
291 292 8.947055 AAAGTAGATTTGCACAAAAGAATTGT 57.053 26.923 0.00 0.00 33.56 2.71
336 337 5.968848 GCTTCTCGTGTGAATAAAACACAAA 59.031 36.000 0.00 0.00 46.68 2.83
338 339 4.814234 AGCTTCTCGTGTGAATAAAACACA 59.186 37.500 7.40 0.00 46.68 3.72
339 340 5.344207 AGCTTCTCGTGTGAATAAAACAC 57.656 39.130 0.00 0.00 43.62 3.32
349 378 0.861837 GGTGTCAAGCTTCTCGTGTG 59.138 55.000 0.00 0.00 0.00 3.82
485 516 4.388378 TTCGAAAAACGGGGTTTCATTT 57.612 36.364 0.00 0.00 42.82 2.32
486 517 4.142116 ACTTTCGAAAAACGGGGTTTCATT 60.142 37.500 12.41 0.00 42.82 2.57
488 519 2.754002 ACTTTCGAAAAACGGGGTTTCA 59.246 40.909 12.41 0.00 42.82 2.69
489 520 3.425577 ACTTTCGAAAAACGGGGTTTC 57.574 42.857 12.41 0.00 42.82 2.78
490 521 3.872511 AACTTTCGAAAAACGGGGTTT 57.127 38.095 12.41 0.00 42.82 3.27
491 522 3.772932 GAAACTTTCGAAAAACGGGGTT 58.227 40.909 12.41 8.42 42.82 4.11
492 523 3.425577 GAAACTTTCGAAAAACGGGGT 57.574 42.857 12.41 2.20 42.82 4.95
935 967 1.152652 GGAGAGATGGAGGGAGCGA 60.153 63.158 0.00 0.00 0.00 4.93
936 968 2.560119 CGGAGAGATGGAGGGAGCG 61.560 68.421 0.00 0.00 0.00 5.03
937 969 2.206536 CCGGAGAGATGGAGGGAGC 61.207 68.421 0.00 0.00 0.00 4.70
942 974 2.725008 GTCGCCGGAGAGATGGAG 59.275 66.667 8.65 0.00 0.00 3.86
943 975 2.833582 GGTCGCCGGAGAGATGGA 60.834 66.667 8.65 0.00 0.00 3.41
965 997 0.258774 GACGGGGTAGGGTGGTACTA 59.741 60.000 0.00 0.00 0.00 1.82
977 1009 4.716977 GAGTGGGGAGGACGGGGT 62.717 72.222 0.00 0.00 0.00 4.95
980 1012 3.077556 CTGGAGTGGGGAGGACGG 61.078 72.222 0.00 0.00 0.00 4.79
981 1013 3.775654 GCTGGAGTGGGGAGGACG 61.776 72.222 0.00 0.00 0.00 4.79
982 1014 3.775654 CGCTGGAGTGGGGAGGAC 61.776 72.222 0.00 0.00 0.00 3.85
1044 1076 3.470567 CGCGACACCGACTTGCTC 61.471 66.667 0.00 0.00 38.22 4.26
1152 1184 4.874977 GCGCAGAGGTAGACGGGC 62.875 72.222 0.30 0.00 0.00 6.13
1425 1457 0.318529 CACTCATCGGATCTCTGGCG 60.319 60.000 0.00 0.00 0.00 5.69
1426 1458 0.033228 CCACTCATCGGATCTCTGGC 59.967 60.000 0.00 0.00 0.00 4.85
1451 1483 4.901123 TCACACCACCACGCCACG 62.901 66.667 0.00 0.00 0.00 4.94
1452 1484 2.281484 ATCACACCACCACGCCAC 60.281 61.111 0.00 0.00 0.00 5.01
1453 1485 2.281414 CATCACACCACCACGCCA 60.281 61.111 0.00 0.00 0.00 5.69
1454 1486 3.737172 GCATCACACCACCACGCC 61.737 66.667 0.00 0.00 0.00 5.68
1455 1487 1.795170 AAAGCATCACACCACCACGC 61.795 55.000 0.00 0.00 0.00 5.34
1456 1488 0.667993 AAAAGCATCACACCACCACG 59.332 50.000 0.00 0.00 0.00 4.94
1457 1489 2.228822 CCTAAAAGCATCACACCACCAC 59.771 50.000 0.00 0.00 0.00 4.16
1458 1490 2.158534 ACCTAAAAGCATCACACCACCA 60.159 45.455 0.00 0.00 0.00 4.17
1459 1491 2.514803 ACCTAAAAGCATCACACCACC 58.485 47.619 0.00 0.00 0.00 4.61
1460 1492 3.305335 CCAACCTAAAAGCATCACACCAC 60.305 47.826 0.00 0.00 0.00 4.16
1461 1493 2.890311 CCAACCTAAAAGCATCACACCA 59.110 45.455 0.00 0.00 0.00 4.17
1462 1494 2.890945 ACCAACCTAAAAGCATCACACC 59.109 45.455 0.00 0.00 0.00 4.16
1463 1495 5.001232 TCTACCAACCTAAAAGCATCACAC 58.999 41.667 0.00 0.00 0.00 3.82
1464 1496 5.235850 TCTACCAACCTAAAAGCATCACA 57.764 39.130 0.00 0.00 0.00 3.58
1505 1537 1.823260 TACACGCGCCAACAAGAACG 61.823 55.000 5.73 0.00 0.00 3.95
1517 1549 2.071844 ATCCACCCTCGATACACGCG 62.072 60.000 3.53 3.53 42.26 6.01
1565 1597 5.509501 GCATTCCATCCAAACAGACAAGAAA 60.510 40.000 0.00 0.00 0.00 2.52
1576 1608 2.708216 TAGAGCGCATTCCATCCAAA 57.292 45.000 11.47 0.00 0.00 3.28
1578 1610 2.936919 AATAGAGCGCATTCCATCCA 57.063 45.000 11.47 0.00 0.00 3.41
1579 1611 3.406764 AGAAATAGAGCGCATTCCATCC 58.593 45.455 11.47 0.00 0.00 3.51
1580 1612 5.429957 AAAGAAATAGAGCGCATTCCATC 57.570 39.130 11.47 0.61 0.00 3.51
1581 1613 5.841957 AAAAGAAATAGAGCGCATTCCAT 57.158 34.783 11.47 0.00 0.00 3.41
1582 1614 5.401550 CAAAAAGAAATAGAGCGCATTCCA 58.598 37.500 11.47 0.00 0.00 3.53
1583 1615 4.266265 GCAAAAAGAAATAGAGCGCATTCC 59.734 41.667 11.47 0.00 0.00 3.01
1586 1618 4.708726 AGCAAAAAGAAATAGAGCGCAT 57.291 36.364 11.47 0.00 0.00 4.73
1588 1620 5.223225 AGTAGCAAAAAGAAATAGAGCGC 57.777 39.130 0.00 0.00 0.00 5.92
1589 1621 6.603095 ACAAGTAGCAAAAAGAAATAGAGCG 58.397 36.000 0.00 0.00 0.00 5.03
1590 1622 6.738649 CGACAAGTAGCAAAAAGAAATAGAGC 59.261 38.462 0.00 0.00 0.00 4.09
1596 1734 4.597079 CAGCGACAAGTAGCAAAAAGAAA 58.403 39.130 7.99 0.00 33.49 2.52
1600 1738 1.001815 GGCAGCGACAAGTAGCAAAAA 60.002 47.619 7.99 0.00 33.49 1.94
1627 1765 7.538334 CAGTTTCATTCAGATTAACATTCGCAA 59.462 33.333 0.00 0.00 0.00 4.85
1629 1767 7.243487 TCAGTTTCATTCAGATTAACATTCGC 58.757 34.615 0.00 0.00 0.00 4.70
1630 1768 9.611284 TTTCAGTTTCATTCAGATTAACATTCG 57.389 29.630 0.00 0.00 0.00 3.34
1652 1790 4.136796 AGAACAACACTAGCAGCATTTCA 58.863 39.130 0.00 0.00 0.00 2.69
1662 1800 8.253810 TCATTCCTCAGATTAGAACAACACTAG 58.746 37.037 0.00 0.00 0.00 2.57
1665 1803 7.672983 TTCATTCCTCAGATTAGAACAACAC 57.327 36.000 0.00 0.00 0.00 3.32
1669 1807 6.962182 ACCATTCATTCCTCAGATTAGAACA 58.038 36.000 0.00 0.00 0.00 3.18
1670 1808 7.554118 TGAACCATTCATTCCTCAGATTAGAAC 59.446 37.037 0.00 0.00 34.08 3.01
1671 1809 7.632861 TGAACCATTCATTCCTCAGATTAGAA 58.367 34.615 0.00 0.00 34.08 2.10
1673 1811 6.017275 GCTGAACCATTCATTCCTCAGATTAG 60.017 42.308 1.21 0.00 39.30 1.73
1676 1814 4.205587 GCTGAACCATTCATTCCTCAGAT 58.794 43.478 1.21 0.00 39.30 2.90
1682 1820 3.119352 GGAACTGCTGAACCATTCATTCC 60.119 47.826 0.00 6.11 37.71 3.01
1700 1838 0.674895 ATCGTCCTTGCAGCAGGAAC 60.675 55.000 8.75 0.00 45.03 3.62
1720 1858 4.514816 TCGATCTGCTGAACATGTGAAAAA 59.485 37.500 0.00 0.00 0.00 1.94
1739 1882 3.012518 CTGTCAGGGCAAAAGAATCGAT 58.987 45.455 0.00 0.00 0.00 3.59
1741 1884 1.135575 GCTGTCAGGGCAAAAGAATCG 60.136 52.381 1.14 0.00 0.00 3.34
1760 1903 0.804989 CCACAAGAGGGATTTCACGC 59.195 55.000 0.00 0.00 0.00 5.34
1761 1904 2.472695 TCCACAAGAGGGATTTCACG 57.527 50.000 0.00 0.00 0.00 4.35
1805 1948 2.559668 CAATCTGCACAGTGGTTGGATT 59.440 45.455 1.84 0.00 0.00 3.01
1807 1950 1.133823 ACAATCTGCACAGTGGTTGGA 60.134 47.619 1.84 0.00 0.00 3.53
1813 1956 3.835378 TGCATAACAATCTGCACAGTG 57.165 42.857 0.00 0.00 43.11 3.66
1842 1989 8.817100 GCTGCAACTTTTAAAAACAAGAATACT 58.183 29.630 1.66 0.00 0.00 2.12
1843 1990 8.061857 GGCTGCAACTTTTAAAAACAAGAATAC 58.938 33.333 0.50 0.00 0.00 1.89
1845 1992 6.597280 TGGCTGCAACTTTTAAAAACAAGAAT 59.403 30.769 0.50 0.00 0.00 2.40
1848 1995 5.220643 CCTGGCTGCAACTTTTAAAAACAAG 60.221 40.000 0.50 0.00 0.00 3.16
1849 1996 4.633565 CCTGGCTGCAACTTTTAAAAACAA 59.366 37.500 0.50 0.00 0.00 2.83
1850 1997 4.081420 TCCTGGCTGCAACTTTTAAAAACA 60.081 37.500 0.50 0.00 0.00 2.83
1851 1998 4.438148 TCCTGGCTGCAACTTTTAAAAAC 58.562 39.130 0.50 0.00 0.00 2.43
1852 1999 4.744795 TCCTGGCTGCAACTTTTAAAAA 57.255 36.364 0.50 0.00 0.00 1.94
1853 2000 4.161377 AGTTCCTGGCTGCAACTTTTAAAA 59.839 37.500 0.50 0.00 0.00 1.52
1854 2001 3.704061 AGTTCCTGGCTGCAACTTTTAAA 59.296 39.130 0.50 0.00 0.00 1.52
1855 2002 3.295973 AGTTCCTGGCTGCAACTTTTAA 58.704 40.909 0.50 0.00 0.00 1.52
1856 2003 2.944129 AGTTCCTGGCTGCAACTTTTA 58.056 42.857 0.50 0.00 0.00 1.52
1857 2004 1.780503 AGTTCCTGGCTGCAACTTTT 58.219 45.000 0.50 0.00 0.00 2.27
1858 2005 1.683385 GAAGTTCCTGGCTGCAACTTT 59.317 47.619 13.69 0.00 39.84 2.66
1867 2014 5.428253 TGTATAGATGTTGAAGTTCCTGGC 58.572 41.667 0.00 0.00 0.00 4.85
1899 2565 2.037772 AGCAGATTGTCGGTTCTTCAGT 59.962 45.455 0.00 0.00 0.00 3.41
1909 2575 4.092091 GGTTCTTCAGTAAGCAGATTGTCG 59.908 45.833 0.00 0.00 32.36 4.35
1910 2576 4.092091 CGGTTCTTCAGTAAGCAGATTGTC 59.908 45.833 0.00 0.00 32.36 3.18
1919 2585 4.230657 CAGAGTGTCGGTTCTTCAGTAAG 58.769 47.826 0.00 0.00 0.00 2.34
1932 2598 4.146616 CGTTCTTCAGTAAACAGAGTGTCG 59.853 45.833 0.00 0.00 0.00 4.35
1933 2599 5.279384 TCGTTCTTCAGTAAACAGAGTGTC 58.721 41.667 0.00 0.00 0.00 3.67
1975 2662 2.627945 TCTCAACAAACAGTGCTCGTT 58.372 42.857 0.00 0.00 0.00 3.85
1980 2667 4.142600 ACAGAGTTTCTCAACAAACAGTGC 60.143 41.667 0.00 0.00 38.53 4.40
1985 2672 6.073003 CCTCCATACAGAGTTTCTCAACAAAC 60.073 42.308 0.00 0.00 36.64 2.93
1987 2674 5.551233 CCTCCATACAGAGTTTCTCAACAA 58.449 41.667 0.00 0.00 35.05 2.83
1989 2676 3.935828 GCCTCCATACAGAGTTTCTCAAC 59.064 47.826 0.00 0.00 32.06 3.18
1994 2683 4.053469 GAGAGCCTCCATACAGAGTTTC 57.947 50.000 0.00 0.00 31.53 2.78
2013 2702 3.045601 TGGAGAAAGCGAAGAAAGGAG 57.954 47.619 0.00 0.00 0.00 3.69
2089 2778 1.902508 TGGTTGTTGGGTGCTCAAAAA 59.097 42.857 0.00 0.00 0.00 1.94
2118 2824 4.136796 CAGTTCCCAGATGACAAACTTGA 58.863 43.478 0.00 0.00 0.00 3.02
2123 2829 2.061848 TCCCAGTTCCCAGATGACAAA 58.938 47.619 0.00 0.00 0.00 2.83
2125 2831 0.984230 GTCCCAGTTCCCAGATGACA 59.016 55.000 0.00 0.00 0.00 3.58
2183 2889 7.761651 TTTCATCATCACTATTCTTGACTCG 57.238 36.000 0.00 0.00 0.00 4.18
2220 2926 6.533730 ACAAAGAGGTCAAATATGTCACTCA 58.466 36.000 0.00 0.00 0.00 3.41
2245 2951 1.729470 ATCCGTCTACCAGCGAGCAG 61.729 60.000 0.00 0.00 0.00 4.24
2255 2961 3.698040 TGGAAGAGGTGTTATCCGTCTAC 59.302 47.826 0.00 0.00 34.60 2.59
2297 3003 4.216042 TCGTCATTGTTGTTGATGAGCATT 59.784 37.500 0.00 0.00 34.91 3.56
2314 3020 8.470805 AGATGAAACACTTATTCTACTCGTCAT 58.529 33.333 0.00 0.00 0.00 3.06
2394 3140 0.249398 GTAGTCCGACAGGTGCCAAT 59.751 55.000 0.40 0.00 39.05 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.