Multiple sequence alignment - TraesCS4D01G324400

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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 TraesCS4D01G324400 chr4D 100.000 2302 0 0 916 3217 485043619 485041318 0.000000e+00 4252.0
1 TraesCS4D01G324400 chr4D 99.696 2301 6 1 916 3216 485065562 485063263 0.000000e+00 4209.0
2 TraesCS4D01G324400 chr4D 91.598 1464 101 12 919 2368 484952433 484950978 0.000000e+00 2002.0
3 TraesCS4D01G324400 chr4D 81.019 1570 209 39 916 2466 484927952 484926453 0.000000e+00 1166.0
4 TraesCS4D01G324400 chr4D 89.732 896 76 9 1486 2377 484929896 484929013 0.000000e+00 1131.0
5 TraesCS4D01G324400 chr4D 100.000 471 0 0 1 471 485044534 485044064 0.000000e+00 870.0
6 TraesCS4D01G324400 chr4D 90.261 421 27 8 916 1325 484934512 484934095 3.650000e-149 538.0
7 TraesCS4D01G324400 chr4D 77.477 222 42 6 74 291 99205926 99206143 3.370000e-25 126.0
8 TraesCS4D01G324400 chr5A 93.916 1578 68 12 950 2523 666117233 666115680 0.000000e+00 2357.0
9 TraesCS4D01G324400 chr5A 90.392 791 70 4 1468 2257 666073533 666072748 0.000000e+00 1035.0
10 TraesCS4D01G324400 chr5A 92.047 591 39 5 2630 3217 749100 749685 0.000000e+00 824.0
11 TraesCS4D01G324400 chr5A 85.984 371 43 5 957 1321 666074004 666073637 3.890000e-104 388.0
12 TraesCS4D01G324400 chr5A 89.130 138 7 4 2508 2638 666114685 666114549 7.140000e-37 165.0
13 TraesCS4D01G324400 chr5A 85.938 128 12 5 58 181 631671785 631671910 7.240000e-27 132.0
14 TraesCS4D01G324400 chr4B 95.983 1170 42 3 1465 2630 618251542 618250374 0.000000e+00 1895.0
15 TraesCS4D01G324400 chr4B 80.165 1573 214 37 916 2466 618227673 618226177 0.000000e+00 1086.0
16 TraesCS4D01G324400 chr4B 94.363 479 16 5 916 1393 618252284 618251816 0.000000e+00 725.0
17 TraesCS4D01G324400 chr4B 90.909 407 23 8 916 1310 618241641 618241237 4.720000e-148 534.0
18 TraesCS4D01G324400 chrUn 84.987 766 114 1 1493 2257 46203795 46204560 0.000000e+00 776.0
19 TraesCS4D01G324400 chrUn 89.216 102 8 2 2636 2735 352484393 352484493 1.210000e-24 124.0
20 TraesCS4D01G324400 chrUn 88.235 102 9 2 2636 2735 352502269 352502369 5.640000e-23 119.0
21 TraesCS4D01G324400 chr3B 82.781 784 132 2 1476 2258 813902530 813903311 0.000000e+00 697.0
22 TraesCS4D01G324400 chr3B 86.111 144 15 5 1 142 105181238 105181378 2.000000e-32 150.0
23 TraesCS4D01G324400 chr3B 90.278 72 7 0 2666 2737 804386899 804386828 9.500000e-16 95.3
24 TraesCS4D01G324400 chr3A 81.377 741 132 5 1483 2219 735976101 735975363 1.650000e-167 599.0
25 TraesCS4D01G324400 chr3A 89.216 102 9 2 2626 2727 265548077 265548176 3.370000e-25 126.0
26 TraesCS4D01G324400 chr3A 94.030 67 4 0 1202 1268 701219133 701219067 5.680000e-18 102.0
27 TraesCS4D01G324400 chr7D 84.574 188 25 4 1 185 45397699 45397513 1.970000e-42 183.0
28 TraesCS4D01G324400 chr2D 79.412 272 40 13 1 265 177453256 177452994 9.170000e-41 178.0
29 TraesCS4D01G324400 chr7B 78.656 253 33 16 23 264 203888246 203888488 7.190000e-32 148.0
30 TraesCS4D01G324400 chr7B 91.765 85 6 1 2635 2718 66466104 66466188 2.030000e-22 117.0
31 TraesCS4D01G324400 chr5D 86.667 135 10 6 1 133 431916702 431916574 3.350000e-30 143.0
32 TraesCS4D01G324400 chr5D 89.216 102 9 2 2624 2723 378899739 378899840 3.370000e-25 126.0
33 TraesCS4D01G324400 chr5B 86.567 134 12 4 1 133 524327353 524327481 3.350000e-30 143.0
34 TraesCS4D01G324400 chr5B 81.651 109 14 5 2 109 679200350 679200453 5.720000e-13 86.1
35 TraesCS4D01G324400 chr2B 78.261 184 26 10 86 263 169767360 169767535 4.390000e-19 106.0
36 TraesCS4D01G324400 chr3D 77.714 175 35 4 1096 1268 566080716 566080888 1.580000e-18 104.0
37 TraesCS4D01G324400 chr2A 83.036 112 16 2 2626 2734 677173609 677173720 7.340000e-17 99.0
38 TraesCS4D01G324400 chr6D 100.000 30 0 0 112 141 94749647 94749676 4.480000e-04 56.5


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 TraesCS4D01G324400 chr4D 485041318 485044534 3216 True 2561.0 4252 100.0000 1 3217 2 chr4D.!!$R5 3216
1 TraesCS4D01G324400 chr4D 485063263 485065562 2299 True 4209.0 4209 99.6960 916 3216 1 chr4D.!!$R3 2300
2 TraesCS4D01G324400 chr4D 484950978 484952433 1455 True 2002.0 2002 91.5980 919 2368 1 chr4D.!!$R2 1449
3 TraesCS4D01G324400 chr4D 484926453 484929896 3443 True 1148.5 1166 85.3755 916 2466 2 chr4D.!!$R4 1550
4 TraesCS4D01G324400 chr5A 666114549 666117233 2684 True 1261.0 2357 91.5230 950 2638 2 chr5A.!!$R2 1688
5 TraesCS4D01G324400 chr5A 749100 749685 585 False 824.0 824 92.0470 2630 3217 1 chr5A.!!$F1 587
6 TraesCS4D01G324400 chr5A 666072748 666074004 1256 True 711.5 1035 88.1880 957 2257 2 chr5A.!!$R1 1300
7 TraesCS4D01G324400 chr4B 618250374 618252284 1910 True 1310.0 1895 95.1730 916 2630 2 chr4B.!!$R3 1714
8 TraesCS4D01G324400 chr4B 618226177 618227673 1496 True 1086.0 1086 80.1650 916 2466 1 chr4B.!!$R1 1550
9 TraesCS4D01G324400 chrUn 46203795 46204560 765 False 776.0 776 84.9870 1493 2257 1 chrUn.!!$F1 764
10 TraesCS4D01G324400 chr3B 813902530 813903311 781 False 697.0 697 82.7810 1476 2258 1 chr3B.!!$F2 782
11 TraesCS4D01G324400 chr3A 735975363 735976101 738 True 599.0 599 81.3770 1483 2219 1 chr3A.!!$R2 736

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
433 434 0.036952 CCTCTTCCCGCGCATCATAT 60.037 55.0 8.75 0.0 0.0 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3096 5434 3.074412 GAGAAGTCGCTTTCCATGGAAA 58.926 45.455 32.66 32.66 41.22 3.13 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
22 23 3.353836 GCATGTGTGCCGTCCGTT 61.354 61.111 0.00 0.00 45.76 4.44
23 24 2.555782 CATGTGTGCCGTCCGTTG 59.444 61.111 0.00 0.00 0.00 4.10
24 25 2.668212 ATGTGTGCCGTCCGTTGG 60.668 61.111 0.00 0.00 0.00 3.77
31 32 3.557824 CCGTCCGTTGGCAAGTAC 58.442 61.111 0.00 0.00 0.00 2.73
33 34 2.858158 GTCCGTTGGCAAGTACGC 59.142 61.111 0.00 0.00 36.49 4.42
41 42 3.889227 GCAAGTACGCCTGCATGA 58.111 55.556 11.33 0.00 0.00 3.07
42 43 2.170738 GCAAGTACGCCTGCATGAA 58.829 52.632 11.33 0.00 0.00 2.57
43 44 0.179189 GCAAGTACGCCTGCATGAAC 60.179 55.000 11.33 0.00 0.00 3.18
44 45 1.442769 CAAGTACGCCTGCATGAACT 58.557 50.000 0.00 0.00 0.00 3.01
45 46 1.129251 CAAGTACGCCTGCATGAACTG 59.871 52.381 0.00 0.00 0.00 3.16
46 47 0.321671 AGTACGCCTGCATGAACTGT 59.678 50.000 0.00 0.00 0.00 3.55
47 48 1.156736 GTACGCCTGCATGAACTGTT 58.843 50.000 0.00 0.00 0.00 3.16
49 50 0.534877 ACGCCTGCATGAACTGTTCA 60.535 50.000 23.94 23.94 45.01 3.18
50 51 0.167470 CGCCTGCATGAACTGTTCAG 59.833 55.000 25.40 18.30 43.98 3.02
52 53 1.068748 GCCTGCATGAACTGTTCAGTG 60.069 52.381 25.40 21.98 43.98 3.66
53 54 2.224606 CCTGCATGAACTGTTCAGTGT 58.775 47.619 25.40 9.07 43.98 3.55
54 55 2.620115 CCTGCATGAACTGTTCAGTGTT 59.380 45.455 25.40 8.72 43.98 3.32
55 56 3.067180 CCTGCATGAACTGTTCAGTGTTT 59.933 43.478 25.40 8.37 43.98 2.83
56 57 4.031418 TGCATGAACTGTTCAGTGTTTG 57.969 40.909 25.40 19.24 43.98 2.93
57 58 3.443329 TGCATGAACTGTTCAGTGTTTGT 59.557 39.130 25.40 7.01 43.98 2.83
58 59 4.082300 TGCATGAACTGTTCAGTGTTTGTT 60.082 37.500 25.40 6.32 43.98 2.83
59 60 4.864247 GCATGAACTGTTCAGTGTTTGTTT 59.136 37.500 25.40 5.64 43.98 2.83
60 61 5.348451 GCATGAACTGTTCAGTGTTTGTTTT 59.652 36.000 25.40 4.96 43.98 2.43
61 62 6.128580 GCATGAACTGTTCAGTGTTTGTTTTT 60.129 34.615 25.40 4.48 43.98 1.94
62 63 6.761731 TGAACTGTTCAGTGTTTGTTTTTG 57.238 33.333 18.69 0.00 34.08 2.44
65 66 5.848406 ACTGTTCAGTGTTTGTTTTTGGAA 58.152 33.333 4.58 0.00 0.00 3.53
67 68 4.688413 TGTTCAGTGTTTGTTTTTGGAAGC 59.312 37.500 0.00 0.00 0.00 3.86
68 69 4.799564 TCAGTGTTTGTTTTTGGAAGCT 57.200 36.364 0.00 0.00 0.00 3.74
69 70 4.493547 TCAGTGTTTGTTTTTGGAAGCTG 58.506 39.130 0.00 0.00 0.00 4.24
70 71 3.618150 CAGTGTTTGTTTTTGGAAGCTGG 59.382 43.478 0.00 0.00 0.00 4.85
73 74 3.205338 GTTTGTTTTTGGAAGCTGGCAT 58.795 40.909 0.00 0.00 0.00 4.40
74 75 2.529780 TGTTTTTGGAAGCTGGCATG 57.470 45.000 0.00 0.00 0.00 4.06
76 77 2.961741 TGTTTTTGGAAGCTGGCATGTA 59.038 40.909 0.00 0.00 0.00 2.29
77 78 3.577848 TGTTTTTGGAAGCTGGCATGTAT 59.422 39.130 0.00 0.00 0.00 2.29
78 79 3.872511 TTTTGGAAGCTGGCATGTATG 57.127 42.857 0.00 0.00 0.00 2.39
89 90 4.935495 ATGTATGCCGGCCGCTGG 62.935 66.667 26.77 14.51 38.78 4.85
106 107 3.589579 GCATGGTGCCGACATGAA 58.410 55.556 14.27 0.00 46.60 2.57
109 110 0.729116 CATGGTGCCGACATGAACTC 59.271 55.000 0.00 0.00 46.60 3.01
112 113 1.021390 GGTGCCGACATGAACTCTGG 61.021 60.000 0.00 0.00 0.00 3.86
113 114 1.021390 GTGCCGACATGAACTCTGGG 61.021 60.000 0.00 0.00 0.00 4.45
114 115 2.109126 GCCGACATGAACTCTGGGC 61.109 63.158 0.00 0.00 0.00 5.36
115 116 1.811266 CCGACATGAACTCTGGGCG 60.811 63.158 0.00 0.00 0.00 6.13
116 117 1.215382 CGACATGAACTCTGGGCGA 59.785 57.895 0.00 0.00 0.00 5.54
117 118 1.078759 CGACATGAACTCTGGGCGAC 61.079 60.000 0.00 0.00 0.00 5.19
118 119 1.078759 GACATGAACTCTGGGCGACG 61.079 60.000 0.00 0.00 0.00 5.12
119 120 1.811266 CATGAACTCTGGGCGACGG 60.811 63.158 0.00 0.00 0.00 4.79
120 121 3.665675 ATGAACTCTGGGCGACGGC 62.666 63.158 13.84 13.84 38.90 5.68
122 123 3.665675 GAACTCTGGGCGACGGCAT 62.666 63.158 23.66 1.39 42.47 4.40
124 125 4.147449 CTCTGGGCGACGGCATGA 62.147 66.667 23.66 17.64 42.47 3.07
125 126 4.451150 TCTGGGCGACGGCATGAC 62.451 66.667 23.66 6.09 42.47 3.06
135 136 3.896133 GGCATGACCGCTGGCATG 61.896 66.667 18.87 18.87 38.91 4.06
136 137 2.825387 GCATGACCGCTGGCATGA 60.825 61.111 26.33 0.00 38.51 3.07
137 138 2.191513 GCATGACCGCTGGCATGAT 61.192 57.895 26.33 0.00 38.51 2.45
138 139 1.947013 CATGACCGCTGGCATGATC 59.053 57.895 18.43 0.00 38.51 2.92
139 140 0.534427 CATGACCGCTGGCATGATCT 60.534 55.000 18.43 0.00 38.51 2.75
140 141 1.051008 ATGACCGCTGGCATGATCTA 58.949 50.000 0.00 0.00 0.00 1.98
141 142 1.051008 TGACCGCTGGCATGATCTAT 58.949 50.000 0.00 0.00 0.00 1.98
142 143 1.270465 TGACCGCTGGCATGATCTATG 60.270 52.381 0.00 0.00 39.88 2.23
143 144 1.001293 GACCGCTGGCATGATCTATGA 59.999 52.381 0.00 0.00 39.21 2.15
145 146 1.436600 CGCTGGCATGATCTATGACC 58.563 55.000 0.00 8.88 44.74 4.02
146 147 1.436600 GCTGGCATGATCTATGACCG 58.563 55.000 0.00 4.10 44.74 4.79
148 149 2.410939 CTGGCATGATCTATGACCGTG 58.589 52.381 0.00 0.00 44.74 4.94
149 150 1.070601 TGGCATGATCTATGACCGTGG 59.929 52.381 0.00 0.00 44.74 4.94
152 153 3.557898 GGCATGATCTATGACCGTGGATT 60.558 47.826 0.00 0.00 39.01 3.01
153 154 4.067896 GCATGATCTATGACCGTGGATTT 58.932 43.478 0.00 0.00 39.21 2.17
154 155 4.516698 GCATGATCTATGACCGTGGATTTT 59.483 41.667 0.00 0.00 39.21 1.82
155 156 5.009010 GCATGATCTATGACCGTGGATTTTT 59.991 40.000 0.00 0.00 39.21 1.94
159 160 8.568676 TGATCTATGACCGTGGATTTTTAAAA 57.431 30.769 0.00 0.00 0.00 1.52
160 161 9.015367 TGATCTATGACCGTGGATTTTTAAAAA 57.985 29.630 15.38 15.38 0.00 1.94
169 170 9.026074 ACCGTGGATTTTTAAAAATTATATGCG 57.974 29.630 23.44 19.56 38.64 4.73
170 171 8.484008 CCGTGGATTTTTAAAAATTATATGCGG 58.516 33.333 23.44 22.85 38.64 5.69
171 172 9.239002 CGTGGATTTTTAAAAATTATATGCGGA 57.761 29.630 23.44 0.00 38.64 5.54
206 207 2.104729 GGGCGCGTTGGACGTATA 59.895 61.111 8.43 0.00 44.73 1.47
207 208 1.947642 GGGCGCGTTGGACGTATAG 60.948 63.158 8.43 0.00 44.73 1.31
208 209 1.064621 GGCGCGTTGGACGTATAGA 59.935 57.895 8.43 0.00 44.73 1.98
209 210 1.204856 GGCGCGTTGGACGTATAGAC 61.205 60.000 8.43 0.00 44.73 2.59
210 211 1.204856 GCGCGTTGGACGTATAGACC 61.205 60.000 8.43 0.00 44.73 3.85
211 212 0.593263 CGCGTTGGACGTATAGACCC 60.593 60.000 0.00 0.00 44.73 4.46
212 213 0.457035 GCGTTGGACGTATAGACCCA 59.543 55.000 2.27 0.00 44.73 4.51
214 215 2.674747 GCGTTGGACGTATAGACCCAAA 60.675 50.000 5.78 0.00 44.73 3.28
218 219 2.898612 TGGACGTATAGACCCAAACACA 59.101 45.455 0.00 0.00 33.63 3.72
219 220 3.324268 TGGACGTATAGACCCAAACACAA 59.676 43.478 0.00 0.00 33.63 3.33
220 221 4.202336 TGGACGTATAGACCCAAACACAAA 60.202 41.667 0.00 0.00 33.63 2.83
221 222 4.756135 GGACGTATAGACCCAAACACAAAA 59.244 41.667 0.00 0.00 0.00 2.44
222 223 5.334337 GGACGTATAGACCCAAACACAAAAC 60.334 44.000 0.00 0.00 0.00 2.43
223 224 4.211794 ACGTATAGACCCAAACACAAAACG 59.788 41.667 0.00 0.00 0.00 3.60
224 225 4.448395 CGTATAGACCCAAACACAAAACGA 59.552 41.667 0.00 0.00 0.00 3.85
225 226 5.389098 CGTATAGACCCAAACACAAAACGAG 60.389 44.000 0.00 0.00 0.00 4.18
226 227 2.993937 AGACCCAAACACAAAACGAGA 58.006 42.857 0.00 0.00 0.00 4.04
227 228 3.551846 AGACCCAAACACAAAACGAGAT 58.448 40.909 0.00 0.00 0.00 2.75
228 229 4.710324 AGACCCAAACACAAAACGAGATA 58.290 39.130 0.00 0.00 0.00 1.98
230 231 4.710324 ACCCAAACACAAAACGAGATAGA 58.290 39.130 0.00 0.00 0.00 1.98
231 232 4.514066 ACCCAAACACAAAACGAGATAGAC 59.486 41.667 0.00 0.00 0.00 2.59
232 233 4.377022 CCCAAACACAAAACGAGATAGACG 60.377 45.833 0.00 0.00 0.00 4.18
233 234 4.446385 CCAAACACAAAACGAGATAGACGA 59.554 41.667 0.00 0.00 34.70 4.20
235 236 3.231965 ACACAAAACGAGATAGACGACG 58.768 45.455 0.00 0.00 34.70 5.12
236 237 3.058708 ACACAAAACGAGATAGACGACGA 60.059 43.478 0.00 0.00 34.70 4.20
237 238 3.297461 CACAAAACGAGATAGACGACGAC 59.703 47.826 0.00 0.00 34.70 4.34
238 239 2.821307 AAACGAGATAGACGACGACC 57.179 50.000 0.00 0.00 34.70 4.79
239 240 0.649475 AACGAGATAGACGACGACCG 59.351 55.000 0.00 0.00 45.44 4.79
242 243 1.569708 GAGATAGACGACGACCGAGT 58.430 55.000 0.00 0.00 41.76 4.18
243 244 1.258458 GAGATAGACGACGACCGAGTG 59.742 57.143 0.00 0.00 41.76 3.51
244 245 0.304098 GATAGACGACGACCGAGTGG 59.696 60.000 0.00 0.00 41.76 4.00
245 246 1.712977 ATAGACGACGACCGAGTGGC 61.713 60.000 0.00 0.00 41.76 5.01
249 250 4.773117 GACGACCGAGTGGCCGAC 62.773 72.222 0.00 0.00 44.93 4.79
281 282 3.733443 AAAAAGGACAAAGCTCGCATT 57.267 38.095 0.00 0.00 0.00 3.56
283 284 1.896220 AAGGACAAAGCTCGCATTCA 58.104 45.000 0.00 0.00 0.00 2.57
286 287 2.821969 AGGACAAAGCTCGCATTCATTT 59.178 40.909 0.00 0.00 0.00 2.32
288 289 2.919229 GACAAAGCTCGCATTCATTTGG 59.081 45.455 0.00 0.00 35.64 3.28
289 290 2.264813 CAAAGCTCGCATTCATTTGGG 58.735 47.619 0.00 0.00 0.00 4.12
290 291 1.549203 AAGCTCGCATTCATTTGGGT 58.451 45.000 0.00 0.00 0.00 4.51
291 292 1.549203 AGCTCGCATTCATTTGGGTT 58.451 45.000 0.00 0.00 0.00 4.11
294 295 2.682856 GCTCGCATTCATTTGGGTTAGA 59.317 45.455 0.00 0.00 0.00 2.10
295 296 3.487544 GCTCGCATTCATTTGGGTTAGAC 60.488 47.826 0.00 0.00 0.00 2.59
296 297 3.941483 CTCGCATTCATTTGGGTTAGACT 59.059 43.478 0.00 0.00 0.00 3.24
299 300 4.176271 GCATTCATTTGGGTTAGACTTGC 58.824 43.478 0.00 0.00 0.00 4.01
302 303 4.640771 TCATTTGGGTTAGACTTGCTCT 57.359 40.909 0.00 0.00 0.00 4.09
304 305 5.734720 TCATTTGGGTTAGACTTGCTCTAG 58.265 41.667 0.00 0.00 32.75 2.43
305 306 4.553330 TTTGGGTTAGACTTGCTCTAGG 57.447 45.455 0.00 0.00 32.75 3.02
306 307 1.831736 TGGGTTAGACTTGCTCTAGGC 59.168 52.381 0.00 0.00 42.22 3.93
307 308 1.202428 GGGTTAGACTTGCTCTAGGCG 60.202 57.143 0.00 0.00 45.43 5.52
308 309 1.749634 GGTTAGACTTGCTCTAGGCGA 59.250 52.381 0.00 0.00 45.43 5.54
309 310 2.362717 GGTTAGACTTGCTCTAGGCGAT 59.637 50.000 0.00 0.00 45.43 4.58
310 311 3.376540 GTTAGACTTGCTCTAGGCGATG 58.623 50.000 0.00 0.00 45.43 3.84
311 312 0.103937 AGACTTGCTCTAGGCGATGC 59.896 55.000 0.00 0.00 45.43 3.91
312 313 1.211818 GACTTGCTCTAGGCGATGCG 61.212 60.000 0.00 0.00 45.43 4.73
313 314 1.066422 CTTGCTCTAGGCGATGCGA 59.934 57.895 0.00 0.00 45.43 5.10
315 316 1.667154 TTGCTCTAGGCGATGCGAGT 61.667 55.000 0.00 0.00 45.43 4.18
317 318 1.082431 CTCTAGGCGATGCGAGTCG 60.082 63.158 8.54 8.54 44.14 4.18
318 319 2.050895 CTAGGCGATGCGAGTCGG 60.051 66.667 15.52 0.00 41.72 4.79
326 327 3.062466 TGCGAGTCGGCAGTAGCT 61.062 61.111 15.52 0.00 41.70 3.32
327 328 2.182030 GCGAGTCGGCAGTAGCTT 59.818 61.111 15.52 0.00 41.70 3.74
328 329 1.446272 GCGAGTCGGCAGTAGCTTT 60.446 57.895 15.52 0.00 41.70 3.51
329 330 0.179145 GCGAGTCGGCAGTAGCTTTA 60.179 55.000 15.52 0.00 41.70 1.85
330 331 1.546834 CGAGTCGGCAGTAGCTTTAC 58.453 55.000 4.10 0.00 41.70 2.01
332 333 0.886563 AGTCGGCAGTAGCTTTACGT 59.113 50.000 0.00 0.00 41.70 3.57
333 334 1.135460 AGTCGGCAGTAGCTTTACGTC 60.135 52.381 0.00 0.00 41.70 4.34
334 335 0.171903 TCGGCAGTAGCTTTACGTCC 59.828 55.000 0.00 0.00 41.70 4.79
335 336 0.108992 CGGCAGTAGCTTTACGTCCA 60.109 55.000 0.00 0.00 41.70 4.02
336 337 1.641577 GGCAGTAGCTTTACGTCCAG 58.358 55.000 0.00 0.00 41.70 3.86
337 338 1.641577 GCAGTAGCTTTACGTCCAGG 58.358 55.000 0.00 0.00 37.91 4.45
338 339 1.739371 GCAGTAGCTTTACGTCCAGGG 60.739 57.143 0.00 0.00 37.91 4.45
339 340 1.549170 CAGTAGCTTTACGTCCAGGGT 59.451 52.381 0.00 0.00 0.00 4.34
342 343 1.447314 GCTTTACGTCCAGGGTCGG 60.447 63.158 9.59 0.00 0.00 4.79
343 344 1.969862 CTTTACGTCCAGGGTCGGT 59.030 57.895 9.59 0.00 0.00 4.69
344 345 0.108945 CTTTACGTCCAGGGTCGGTC 60.109 60.000 9.59 0.00 0.00 4.79
346 347 0.962356 TTACGTCCAGGGTCGGTCTC 60.962 60.000 9.59 0.00 0.00 3.36
349 350 3.596799 TCCAGGGTCGGTCTCCCA 61.597 66.667 3.79 0.00 46.82 4.37
351 352 2.037367 CAGGGTCGGTCTCCCAGA 59.963 66.667 3.79 0.00 46.82 3.86
353 354 3.450115 GGGTCGGTCTCCCAGACG 61.450 72.222 0.00 0.00 45.96 4.18
355 356 1.377725 GGTCGGTCTCCCAGACGTA 60.378 63.158 0.00 0.00 45.96 3.57
356 357 1.375098 GGTCGGTCTCCCAGACGTAG 61.375 65.000 0.00 0.00 45.96 3.51
357 358 0.392193 GTCGGTCTCCCAGACGTAGA 60.392 60.000 0.00 0.00 45.96 2.59
358 359 0.107800 TCGGTCTCCCAGACGTAGAG 60.108 60.000 0.00 0.00 45.96 2.43
361 362 1.950909 GGTCTCCCAGACGTAGAGATG 59.049 57.143 9.46 0.00 45.96 2.90
362 363 1.335496 GTCTCCCAGACGTAGAGATGC 59.665 57.143 9.46 0.00 38.81 3.91
363 364 1.064685 TCTCCCAGACGTAGAGATGCA 60.065 52.381 0.00 0.00 31.80 3.96
364 365 1.959985 CTCCCAGACGTAGAGATGCAT 59.040 52.381 0.00 0.00 0.00 3.96
365 366 1.957177 TCCCAGACGTAGAGATGCATC 59.043 52.381 19.37 19.37 0.00 3.91
366 367 1.683385 CCCAGACGTAGAGATGCATCA 59.317 52.381 27.81 5.22 0.00 3.07
367 368 2.544694 CCCAGACGTAGAGATGCATCAC 60.545 54.545 27.81 21.68 0.00 3.06
368 369 2.379732 CAGACGTAGAGATGCATCACG 58.620 52.381 27.06 27.06 38.52 4.35
370 371 2.112522 GACGTAGAGATGCATCACGTG 58.887 52.381 34.52 22.52 45.03 4.49
371 372 1.202302 ACGTAGAGATGCATCACGTGG 60.202 52.381 31.05 20.02 43.54 4.94
372 373 1.858091 GTAGAGATGCATCACGTGGG 58.142 55.000 27.81 9.74 0.00 4.61
373 374 1.409064 GTAGAGATGCATCACGTGGGA 59.591 52.381 27.81 1.49 0.00 4.37
374 375 1.126488 AGAGATGCATCACGTGGGAT 58.874 50.000 27.81 7.14 0.00 3.85
375 376 1.202615 AGAGATGCATCACGTGGGATG 60.203 52.381 27.81 13.97 45.89 3.51
379 380 3.928769 CATCACGTGGGATGCGCG 61.929 66.667 17.00 0.00 38.35 6.86
390 391 4.383602 ATGCGCGCAACGGTCAAC 62.384 61.111 39.68 1.18 43.93 3.18
392 393 4.599434 GCGCGCAACGGTCAACAA 62.599 61.111 29.10 0.00 43.93 2.83
393 394 2.720750 CGCGCAACGGTCAACAAC 60.721 61.111 8.75 0.00 38.44 3.32
394 395 2.713154 GCGCAACGGTCAACAACT 59.287 55.556 0.30 0.00 0.00 3.16
395 396 1.063488 GCGCAACGGTCAACAACTT 59.937 52.632 0.30 0.00 0.00 2.66
396 397 0.524604 GCGCAACGGTCAACAACTTT 60.525 50.000 0.30 0.00 0.00 2.66
397 398 1.462791 CGCAACGGTCAACAACTTTC 58.537 50.000 0.00 0.00 0.00 2.62
399 400 1.535226 GCAACGGTCAACAACTTTCCC 60.535 52.381 0.00 0.00 0.00 3.97
402 403 2.842457 ACGGTCAACAACTTTCCCTAC 58.158 47.619 0.00 0.00 0.00 3.18
403 404 2.436911 ACGGTCAACAACTTTCCCTACT 59.563 45.455 0.00 0.00 0.00 2.57
404 405 3.118149 ACGGTCAACAACTTTCCCTACTT 60.118 43.478 0.00 0.00 0.00 2.24
405 406 3.497262 CGGTCAACAACTTTCCCTACTTC 59.503 47.826 0.00 0.00 0.00 3.01
406 407 3.497262 GGTCAACAACTTTCCCTACTTCG 59.503 47.826 0.00 0.00 0.00 3.79
407 408 4.374399 GTCAACAACTTTCCCTACTTCGA 58.626 43.478 0.00 0.00 0.00 3.71
409 410 5.120363 GTCAACAACTTTCCCTACTTCGATC 59.880 44.000 0.00 0.00 0.00 3.69
410 411 3.846360 ACAACTTTCCCTACTTCGATCG 58.154 45.455 9.36 9.36 0.00 3.69
413 414 3.087031 ACTTTCCCTACTTCGATCGTCA 58.913 45.455 15.94 2.16 0.00 4.35
414 415 3.119566 ACTTTCCCTACTTCGATCGTCAC 60.120 47.826 15.94 0.00 0.00 3.67
416 417 1.064906 TCCCTACTTCGATCGTCACCT 60.065 52.381 15.94 0.00 0.00 4.00
417 418 1.334243 CCCTACTTCGATCGTCACCTC 59.666 57.143 15.94 0.00 0.00 3.85
418 419 2.290464 CCTACTTCGATCGTCACCTCT 58.710 52.381 15.94 0.00 0.00 3.69
419 420 2.683867 CCTACTTCGATCGTCACCTCTT 59.316 50.000 15.94 0.00 0.00 2.85
420 421 2.923605 ACTTCGATCGTCACCTCTTC 57.076 50.000 15.94 0.00 0.00 2.87
421 422 1.473278 ACTTCGATCGTCACCTCTTCC 59.527 52.381 15.94 0.00 0.00 3.46
422 423 0.815734 TTCGATCGTCACCTCTTCCC 59.184 55.000 15.94 0.00 0.00 3.97
423 424 1.064296 CGATCGTCACCTCTTCCCG 59.936 63.158 7.03 0.00 0.00 5.14
424 425 1.227002 GATCGTCACCTCTTCCCGC 60.227 63.158 0.00 0.00 0.00 6.13
425 426 2.938539 GATCGTCACCTCTTCCCGCG 62.939 65.000 0.00 0.00 0.00 6.46
428 429 3.390521 TCACCTCTTCCCGCGCAT 61.391 61.111 8.75 0.00 0.00 4.73
429 430 2.892425 CACCTCTTCCCGCGCATC 60.892 66.667 8.75 0.00 0.00 3.91
431 432 2.109799 CCTCTTCCCGCGCATCAT 59.890 61.111 8.75 0.00 0.00 2.45
432 433 1.367471 CCTCTTCCCGCGCATCATA 59.633 57.895 8.75 0.00 0.00 2.15
433 434 0.036952 CCTCTTCCCGCGCATCATAT 60.037 55.000 8.75 0.00 0.00 1.78
434 435 1.204704 CCTCTTCCCGCGCATCATATA 59.795 52.381 8.75 0.00 0.00 0.86
435 436 2.353704 CCTCTTCCCGCGCATCATATAA 60.354 50.000 8.75 0.00 0.00 0.98
436 437 3.325870 CTCTTCCCGCGCATCATATAAA 58.674 45.455 8.75 0.00 0.00 1.40
440 441 3.006940 TCCCGCGCATCATATAAAATCC 58.993 45.455 8.75 0.00 0.00 3.01
442 443 2.746904 CCGCGCATCATATAAAATCCCA 59.253 45.455 8.75 0.00 0.00 4.37
443 444 3.378112 CCGCGCATCATATAAAATCCCAT 59.622 43.478 8.75 0.00 0.00 4.00
444 445 4.345288 CGCGCATCATATAAAATCCCATG 58.655 43.478 8.75 0.00 0.00 3.66
445 446 4.107622 GCGCATCATATAAAATCCCATGC 58.892 43.478 0.30 0.00 33.35 4.06
446 447 4.380761 GCGCATCATATAAAATCCCATGCA 60.381 41.667 0.30 0.00 35.87 3.96
448 449 5.574055 CGCATCATATAAAATCCCATGCAAC 59.426 40.000 0.00 0.00 35.87 4.17
449 450 6.457355 GCATCATATAAAATCCCATGCAACA 58.543 36.000 0.00 0.00 36.11 3.33
450 451 6.366877 GCATCATATAAAATCCCATGCAACAC 59.633 38.462 0.00 0.00 36.11 3.32
451 452 7.435305 CATCATATAAAATCCCATGCAACACA 58.565 34.615 0.00 0.00 0.00 3.72
452 453 6.804677 TCATATAAAATCCCATGCAACACAC 58.195 36.000 0.00 0.00 0.00 3.82
453 454 6.379417 TCATATAAAATCCCATGCAACACACA 59.621 34.615 0.00 0.00 0.00 3.72
454 455 5.680594 ATAAAATCCCATGCAACACACAT 57.319 34.783 0.00 0.00 0.00 3.21
456 457 1.477553 ATCCCATGCAACACACATCC 58.522 50.000 0.00 0.00 0.00 3.51
457 458 0.112025 TCCCATGCAACACACATCCA 59.888 50.000 0.00 0.00 0.00 3.41
458 459 1.187974 CCCATGCAACACACATCCAT 58.812 50.000 0.00 0.00 0.00 3.41
459 460 1.135527 CCCATGCAACACACATCCATC 59.864 52.381 0.00 0.00 0.00 3.51
461 462 1.819903 CATGCAACACACATCCATCCA 59.180 47.619 0.00 0.00 0.00 3.41
462 463 2.219080 TGCAACACACATCCATCCAT 57.781 45.000 0.00 0.00 0.00 3.41
464 465 2.291089 TGCAACACACATCCATCCATCT 60.291 45.455 0.00 0.00 0.00 2.90
465 466 2.756760 GCAACACACATCCATCCATCTT 59.243 45.455 0.00 0.00 0.00 2.40
466 467 3.947196 GCAACACACATCCATCCATCTTA 59.053 43.478 0.00 0.00 0.00 2.10
468 469 5.278169 GCAACACACATCCATCCATCTTATC 60.278 44.000 0.00 0.00 0.00 1.75
469 470 5.635278 ACACACATCCATCCATCTTATCA 57.365 39.130 0.00 0.00 0.00 2.15
470 471 6.005066 ACACACATCCATCCATCTTATCAA 57.995 37.500 0.00 0.00 0.00 2.57
3096 5434 4.993584 TGATTTTTACGCCATGCATTTTGT 59.006 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.555782 CAACGGACGGCACACATG 59.444 61.111 0.00 0.00 0.00 3.21
14 15 2.377310 CGTACTTGCCAACGGACGG 61.377 63.158 4.39 0.00 35.51 4.79
15 16 3.007070 GCGTACTTGCCAACGGACG 62.007 63.158 7.13 7.13 39.46 4.79
16 17 2.858158 GCGTACTTGCCAACGGAC 59.142 61.111 0.00 0.00 39.46 4.79
24 25 0.179189 GTTCATGCAGGCGTACTTGC 60.179 55.000 0.00 6.86 0.00 4.01
26 27 1.270839 ACAGTTCATGCAGGCGTACTT 60.271 47.619 0.00 0.00 0.00 2.24
27 28 0.321671 ACAGTTCATGCAGGCGTACT 59.678 50.000 0.00 0.00 0.00 2.73
29 30 1.270571 TGAACAGTTCATGCAGGCGTA 60.271 47.619 12.24 0.00 34.08 4.42
31 32 0.167470 CTGAACAGTTCATGCAGGCG 59.833 55.000 16.53 0.00 39.30 5.52
33 34 2.224606 ACACTGAACAGTTCATGCAGG 58.775 47.619 16.53 7.14 40.20 4.85
35 36 3.443329 ACAAACACTGAACAGTTCATGCA 59.557 39.130 16.53 0.00 40.20 3.96
36 37 4.032703 ACAAACACTGAACAGTTCATGC 57.967 40.909 16.53 0.00 40.20 4.06
37 38 6.949578 AAAACAAACACTGAACAGTTCATG 57.050 33.333 16.53 17.07 40.20 3.07
38 39 6.368516 CCAAAAACAAACACTGAACAGTTCAT 59.631 34.615 16.53 4.64 40.20 2.57
39 40 5.694006 CCAAAAACAAACACTGAACAGTTCA 59.306 36.000 15.39 15.39 40.20 3.18
41 42 5.848406 TCCAAAAACAAACACTGAACAGTT 58.152 33.333 4.63 0.00 40.20 3.16
42 43 5.461032 TCCAAAAACAAACACTGAACAGT 57.539 34.783 1.32 1.32 43.61 3.55
43 44 5.163963 GCTTCCAAAAACAAACACTGAACAG 60.164 40.000 0.00 0.00 0.00 3.16
44 45 4.688413 GCTTCCAAAAACAAACACTGAACA 59.312 37.500 0.00 0.00 0.00 3.18
45 46 4.929211 AGCTTCCAAAAACAAACACTGAAC 59.071 37.500 0.00 0.00 0.00 3.18
46 47 4.928615 CAGCTTCCAAAAACAAACACTGAA 59.071 37.500 0.00 0.00 0.00 3.02
47 48 4.493547 CAGCTTCCAAAAACAAACACTGA 58.506 39.130 0.00 0.00 0.00 3.41
49 50 3.860641 CCAGCTTCCAAAAACAAACACT 58.139 40.909 0.00 0.00 0.00 3.55
50 51 2.351418 GCCAGCTTCCAAAAACAAACAC 59.649 45.455 0.00 0.00 0.00 3.32
52 53 2.626840 TGCCAGCTTCCAAAAACAAAC 58.373 42.857 0.00 0.00 0.00 2.93
53 54 3.204526 CATGCCAGCTTCCAAAAACAAA 58.795 40.909 0.00 0.00 0.00 2.83
54 55 2.170187 ACATGCCAGCTTCCAAAAACAA 59.830 40.909 0.00 0.00 0.00 2.83
55 56 1.761784 ACATGCCAGCTTCCAAAAACA 59.238 42.857 0.00 0.00 0.00 2.83
56 57 2.531522 ACATGCCAGCTTCCAAAAAC 57.468 45.000 0.00 0.00 0.00 2.43
57 58 4.191033 CATACATGCCAGCTTCCAAAAA 57.809 40.909 0.00 0.00 0.00 1.94
58 59 3.872511 CATACATGCCAGCTTCCAAAA 57.127 42.857 0.00 0.00 0.00 2.44
89 90 1.137404 GTTCATGTCGGCACCATGC 59.863 57.895 0.00 0.00 44.08 4.06
90 91 0.729116 GAGTTCATGTCGGCACCATG 59.271 55.000 0.00 6.97 40.82 3.66
92 93 0.320683 CAGAGTTCATGTCGGCACCA 60.321 55.000 0.00 0.00 0.00 4.17
93 94 1.021390 CCAGAGTTCATGTCGGCACC 61.021 60.000 0.00 0.00 0.00 5.01
94 95 1.021390 CCCAGAGTTCATGTCGGCAC 61.021 60.000 0.00 0.00 0.00 5.01
95 96 1.296392 CCCAGAGTTCATGTCGGCA 59.704 57.895 0.00 0.00 0.00 5.69
97 98 1.811266 CGCCCAGAGTTCATGTCGG 60.811 63.158 0.00 0.00 0.00 4.79
99 100 1.078759 CGTCGCCCAGAGTTCATGTC 61.079 60.000 0.00 0.00 0.00 3.06
101 102 1.811266 CCGTCGCCCAGAGTTCATG 60.811 63.158 0.00 0.00 0.00 3.07
102 103 2.579201 CCGTCGCCCAGAGTTCAT 59.421 61.111 0.00 0.00 0.00 2.57
103 104 4.373116 GCCGTCGCCCAGAGTTCA 62.373 66.667 0.00 0.00 0.00 3.18
104 105 3.665675 ATGCCGTCGCCCAGAGTTC 62.666 63.158 0.00 0.00 0.00 3.01
105 106 3.706373 ATGCCGTCGCCCAGAGTT 61.706 61.111 0.00 0.00 0.00 3.01
106 107 4.457496 CATGCCGTCGCCCAGAGT 62.457 66.667 0.00 0.00 0.00 3.24
118 119 3.896133 CATGCCAGCGGTCATGCC 61.896 66.667 3.70 0.00 33.32 4.40
119 120 2.126417 GATCATGCCAGCGGTCATGC 62.126 60.000 10.51 2.89 37.24 4.06
120 121 0.534427 AGATCATGCCAGCGGTCATG 60.534 55.000 9.38 9.38 38.01 3.07
122 123 1.051008 ATAGATCATGCCAGCGGTCA 58.949 50.000 0.00 0.00 0.00 4.02
124 125 1.051008 TCATAGATCATGCCAGCGGT 58.949 50.000 0.00 0.00 34.35 5.68
125 126 1.436600 GTCATAGATCATGCCAGCGG 58.563 55.000 0.00 0.00 34.35 5.52
126 127 1.436600 GGTCATAGATCATGCCAGCG 58.563 55.000 0.00 0.00 34.35 5.18
127 128 1.270518 ACGGTCATAGATCATGCCAGC 60.271 52.381 0.00 0.00 34.35 4.85
129 130 1.070601 CCACGGTCATAGATCATGCCA 59.929 52.381 0.00 0.00 34.35 4.92
130 131 1.344438 TCCACGGTCATAGATCATGCC 59.656 52.381 0.00 2.82 34.35 4.40
131 132 2.820059 TCCACGGTCATAGATCATGC 57.180 50.000 0.00 0.00 34.35 4.06
143 144 9.026074 CGCATATAATTTTTAAAAATCCACGGT 57.974 29.630 22.96 11.30 37.62 4.83
145 146 9.239002 TCCGCATATAATTTTTAAAAATCCACG 57.761 29.630 22.96 18.94 37.62 4.94
159 160 7.360353 CGACTCATTTCATGTCCGCATATAATT 60.360 37.037 0.00 0.00 33.30 1.40
160 161 6.091305 CGACTCATTTCATGTCCGCATATAAT 59.909 38.462 0.00 0.00 33.30 1.28
161 162 5.405269 CGACTCATTTCATGTCCGCATATAA 59.595 40.000 0.00 0.00 33.30 0.98
162 163 4.923281 CGACTCATTTCATGTCCGCATATA 59.077 41.667 0.00 0.00 33.30 0.86
164 165 3.123050 CGACTCATTTCATGTCCGCATA 58.877 45.455 0.00 0.00 33.30 3.14
165 166 1.935873 CGACTCATTTCATGTCCGCAT 59.064 47.619 0.00 0.00 35.32 4.73
166 167 1.358877 CGACTCATTTCATGTCCGCA 58.641 50.000 0.00 0.00 0.00 5.69
167 168 0.652592 CCGACTCATTTCATGTCCGC 59.347 55.000 0.00 0.00 0.00 5.54
168 169 0.652592 GCCGACTCATTTCATGTCCG 59.347 55.000 0.00 0.00 0.00 4.79
169 170 1.017387 GGCCGACTCATTTCATGTCC 58.983 55.000 0.00 0.00 0.00 4.02
170 171 0.652592 CGGCCGACTCATTTCATGTC 59.347 55.000 24.07 0.00 0.00 3.06
171 172 0.744414 CCGGCCGACTCATTTCATGT 60.744 55.000 30.73 0.00 0.00 3.21
172 173 1.439353 CCCGGCCGACTCATTTCATG 61.439 60.000 30.73 4.42 0.00 3.07
173 174 1.153168 CCCGGCCGACTCATTTCAT 60.153 57.895 30.73 0.00 0.00 2.57
174 175 2.267642 CCCGGCCGACTCATTTCA 59.732 61.111 30.73 0.00 0.00 2.69
175 176 3.202706 GCCCGGCCGACTCATTTC 61.203 66.667 30.73 1.81 0.00 2.17
195 196 3.681417 GTGTTTGGGTCTATACGTCCAAC 59.319 47.826 3.80 1.76 38.78 3.77
196 197 3.324268 TGTGTTTGGGTCTATACGTCCAA 59.676 43.478 0.00 0.00 37.48 3.53
197 198 2.898612 TGTGTTTGGGTCTATACGTCCA 59.101 45.455 0.00 0.00 0.00 4.02
199 200 5.613142 CGTTTTGTGTTTGGGTCTATACGTC 60.613 44.000 0.00 0.00 0.00 4.34
201 202 4.448395 TCGTTTTGTGTTTGGGTCTATACG 59.552 41.667 0.00 0.00 0.00 3.06
202 203 5.697633 TCTCGTTTTGTGTTTGGGTCTATAC 59.302 40.000 0.00 0.00 0.00 1.47
203 204 5.856156 TCTCGTTTTGTGTTTGGGTCTATA 58.144 37.500 0.00 0.00 0.00 1.31
204 205 4.710324 TCTCGTTTTGTGTTTGGGTCTAT 58.290 39.130 0.00 0.00 0.00 1.98
205 206 4.139859 TCTCGTTTTGTGTTTGGGTCTA 57.860 40.909 0.00 0.00 0.00 2.59
206 207 2.993937 TCTCGTTTTGTGTTTGGGTCT 58.006 42.857 0.00 0.00 0.00 3.85
207 208 3.982576 ATCTCGTTTTGTGTTTGGGTC 57.017 42.857 0.00 0.00 0.00 4.46
208 209 4.514066 GTCTATCTCGTTTTGTGTTTGGGT 59.486 41.667 0.00 0.00 0.00 4.51
209 210 4.377022 CGTCTATCTCGTTTTGTGTTTGGG 60.377 45.833 0.00 0.00 0.00 4.12
210 211 4.446385 TCGTCTATCTCGTTTTGTGTTTGG 59.554 41.667 0.00 0.00 0.00 3.28
211 212 5.363517 GTCGTCTATCTCGTTTTGTGTTTG 58.636 41.667 0.00 0.00 0.00 2.93
212 213 4.147653 CGTCGTCTATCTCGTTTTGTGTTT 59.852 41.667 0.00 0.00 0.00 2.83
214 215 3.058708 TCGTCGTCTATCTCGTTTTGTGT 60.059 43.478 0.00 0.00 0.00 3.72
218 219 2.475187 CGGTCGTCGTCTATCTCGTTTT 60.475 50.000 0.00 0.00 0.00 2.43
219 220 1.061711 CGGTCGTCGTCTATCTCGTTT 59.938 52.381 0.00 0.00 0.00 3.60
220 221 0.649475 CGGTCGTCGTCTATCTCGTT 59.351 55.000 0.00 0.00 0.00 3.85
221 222 0.179127 TCGGTCGTCGTCTATCTCGT 60.179 55.000 0.00 0.00 40.32 4.18
222 223 0.503539 CTCGGTCGTCGTCTATCTCG 59.496 60.000 0.00 0.00 40.32 4.04
223 224 1.258458 CACTCGGTCGTCGTCTATCTC 59.742 57.143 0.00 0.00 40.32 2.75
224 225 1.288350 CACTCGGTCGTCGTCTATCT 58.712 55.000 0.00 0.00 40.32 1.98
225 226 0.304098 CCACTCGGTCGTCGTCTATC 59.696 60.000 0.00 0.00 40.32 2.08
226 227 1.712977 GCCACTCGGTCGTCGTCTAT 61.713 60.000 0.00 0.00 40.32 1.98
227 228 2.393768 GCCACTCGGTCGTCGTCTA 61.394 63.158 0.00 0.00 40.32 2.59
228 229 3.735029 GCCACTCGGTCGTCGTCT 61.735 66.667 0.00 0.00 40.32 4.18
235 236 2.981977 TTTGTGTCGGCCACTCGGTC 62.982 60.000 2.24 0.00 44.81 4.79
236 237 3.096633 TTTGTGTCGGCCACTCGGT 62.097 57.895 2.24 0.00 44.81 4.69
237 238 2.280524 TTTGTGTCGGCCACTCGG 60.281 61.111 2.24 0.00 44.81 4.63
238 239 2.935955 GTTTGTGTCGGCCACTCG 59.064 61.111 2.24 0.00 44.81 4.18
239 240 2.604174 CCGTTTGTGTCGGCCACTC 61.604 63.158 2.24 1.97 44.81 3.51
242 243 2.280524 CTCCGTTTGTGTCGGCCA 60.281 61.111 2.24 0.00 46.49 5.36
243 244 1.161563 TTTCTCCGTTTGTGTCGGCC 61.162 55.000 0.00 0.00 46.49 6.13
244 245 0.658897 TTTTCTCCGTTTGTGTCGGC 59.341 50.000 0.00 0.00 46.49 5.54
262 263 2.622942 TGAATGCGAGCTTTGTCCTTTT 59.377 40.909 0.84 0.00 0.00 2.27
264 265 1.896220 TGAATGCGAGCTTTGTCCTT 58.104 45.000 0.84 0.00 0.00 3.36
265 266 2.119801 ATGAATGCGAGCTTTGTCCT 57.880 45.000 0.84 0.00 0.00 3.85
267 268 2.919229 CCAAATGAATGCGAGCTTTGTC 59.081 45.455 0.84 0.00 0.00 3.18
268 269 2.353011 CCCAAATGAATGCGAGCTTTGT 60.353 45.455 0.84 0.00 0.00 2.83
270 271 1.895131 ACCCAAATGAATGCGAGCTTT 59.105 42.857 0.00 0.00 0.00 3.51
271 272 1.549203 ACCCAAATGAATGCGAGCTT 58.451 45.000 0.00 0.00 0.00 3.74
272 273 1.549203 AACCCAAATGAATGCGAGCT 58.451 45.000 0.00 0.00 0.00 4.09
273 274 2.682856 TCTAACCCAAATGAATGCGAGC 59.317 45.455 0.00 0.00 0.00 5.03
275 276 3.950397 AGTCTAACCCAAATGAATGCGA 58.050 40.909 0.00 0.00 0.00 5.10
276 277 4.414852 CAAGTCTAACCCAAATGAATGCG 58.585 43.478 0.00 0.00 0.00 4.73
278 279 5.416952 AGAGCAAGTCTAACCCAAATGAATG 59.583 40.000 0.00 0.00 31.71 2.67
279 280 5.574188 AGAGCAAGTCTAACCCAAATGAAT 58.426 37.500 0.00 0.00 31.71 2.57
280 281 4.985538 AGAGCAAGTCTAACCCAAATGAA 58.014 39.130 0.00 0.00 31.71 2.57
281 282 4.640771 AGAGCAAGTCTAACCCAAATGA 57.359 40.909 0.00 0.00 31.71 2.57
283 284 4.626529 GCCTAGAGCAAGTCTAACCCAAAT 60.627 45.833 0.00 0.00 42.97 2.32
286 287 1.831736 GCCTAGAGCAAGTCTAACCCA 59.168 52.381 0.00 0.00 42.97 4.51
288 289 1.749634 TCGCCTAGAGCAAGTCTAACC 59.250 52.381 0.00 0.00 44.04 2.85
289 290 3.376540 CATCGCCTAGAGCAAGTCTAAC 58.623 50.000 0.00 0.00 44.04 2.34
290 291 2.223829 GCATCGCCTAGAGCAAGTCTAA 60.224 50.000 0.00 0.00 44.04 2.10
291 292 1.338337 GCATCGCCTAGAGCAAGTCTA 59.662 52.381 0.00 0.00 44.04 2.59
294 295 1.227089 CGCATCGCCTAGAGCAAGT 60.227 57.895 0.00 0.00 44.04 3.16
295 296 0.938637 CTCGCATCGCCTAGAGCAAG 60.939 60.000 0.00 0.00 44.04 4.01
296 297 1.066422 CTCGCATCGCCTAGAGCAA 59.934 57.895 0.00 0.00 44.04 3.91
299 300 1.082431 CGACTCGCATCGCCTAGAG 60.082 63.158 0.00 0.00 34.90 2.43
302 303 4.266070 GCCGACTCGCATCGCCTA 62.266 66.667 2.93 0.00 40.87 3.93
305 306 3.751401 TACTGCCGACTCGCATCGC 62.751 63.158 2.93 0.00 40.87 4.58
306 307 1.655654 CTACTGCCGACTCGCATCG 60.656 63.158 1.58 1.58 38.30 3.84
307 308 1.946650 GCTACTGCCGACTCGCATC 60.947 63.158 0.00 0.00 38.30 3.91
308 309 1.949847 AAGCTACTGCCGACTCGCAT 61.950 55.000 0.00 0.00 38.30 4.73
309 310 2.154798 AAAGCTACTGCCGACTCGCA 62.155 55.000 0.00 0.00 40.80 5.10
310 311 0.179145 TAAAGCTACTGCCGACTCGC 60.179 55.000 0.00 0.00 40.80 5.03
311 312 1.546834 GTAAAGCTACTGCCGACTCG 58.453 55.000 0.00 0.00 40.80 4.18
312 313 1.135460 ACGTAAAGCTACTGCCGACTC 60.135 52.381 0.00 0.00 40.80 3.36
313 314 0.886563 ACGTAAAGCTACTGCCGACT 59.113 50.000 0.00 0.00 40.80 4.18
315 316 0.171903 GGACGTAAAGCTACTGCCGA 59.828 55.000 0.00 0.00 40.80 5.54
317 318 1.641577 CTGGACGTAAAGCTACTGCC 58.358 55.000 0.00 0.00 40.80 4.85
318 319 1.641577 CCTGGACGTAAAGCTACTGC 58.358 55.000 0.00 0.00 40.05 4.40
319 320 1.549170 ACCCTGGACGTAAAGCTACTG 59.451 52.381 0.00 0.00 0.00 2.74
320 321 1.823610 GACCCTGGACGTAAAGCTACT 59.176 52.381 0.00 0.00 0.00 2.57
322 323 0.813184 CGACCCTGGACGTAAAGCTA 59.187 55.000 0.00 0.00 0.00 3.32
323 324 1.590147 CGACCCTGGACGTAAAGCT 59.410 57.895 0.00 0.00 0.00 3.74
324 325 1.447314 CCGACCCTGGACGTAAAGC 60.447 63.158 7.24 0.00 0.00 3.51
325 326 0.108945 GACCGACCCTGGACGTAAAG 60.109 60.000 7.24 0.00 0.00 1.85
326 327 0.540365 AGACCGACCCTGGACGTAAA 60.540 55.000 7.24 0.00 0.00 2.01
327 328 0.962356 GAGACCGACCCTGGACGTAA 60.962 60.000 7.24 0.00 0.00 3.18
328 329 1.377725 GAGACCGACCCTGGACGTA 60.378 63.158 7.24 0.00 0.00 3.57
329 330 2.675772 GAGACCGACCCTGGACGT 60.676 66.667 7.24 0.00 0.00 4.34
330 331 3.450115 GGAGACCGACCCTGGACG 61.450 72.222 0.00 1.00 0.00 4.79
342 343 1.335496 GCATCTCTACGTCTGGGAGAC 59.665 57.143 10.93 0.00 41.71 3.36
343 344 1.064685 TGCATCTCTACGTCTGGGAGA 60.065 52.381 0.00 1.88 39.87 3.71
344 345 1.393603 TGCATCTCTACGTCTGGGAG 58.606 55.000 0.00 0.00 0.00 4.30
346 347 1.683385 TGATGCATCTCTACGTCTGGG 59.317 52.381 26.32 0.00 0.00 4.45
349 350 2.017782 ACGTGATGCATCTCTACGTCT 58.982 47.619 28.11 13.91 43.57 4.18
353 354 1.409064 TCCCACGTGATGCATCTCTAC 59.591 52.381 26.32 15.65 0.00 2.59
355 356 1.126488 ATCCCACGTGATGCATCTCT 58.874 50.000 26.32 10.75 0.00 3.10
356 357 1.224075 CATCCCACGTGATGCATCTC 58.776 55.000 26.32 21.51 36.07 2.75
357 358 3.391736 CATCCCACGTGATGCATCT 57.608 52.632 26.32 4.61 36.07 2.90
362 363 3.928769 CGCGCATCCCACGTGATG 61.929 66.667 19.30 14.84 43.44 3.07
372 373 4.083600 TTGACCGTTGCGCGCATC 62.084 61.111 36.83 31.77 39.71 3.91
373 374 4.383602 GTTGACCGTTGCGCGCAT 62.384 61.111 36.83 21.17 39.71 4.73
375 376 4.599434 TTGTTGACCGTTGCGCGC 62.599 61.111 27.26 27.26 39.71 6.86
376 377 2.640736 AAGTTGTTGACCGTTGCGCG 62.641 55.000 0.00 0.00 40.95 6.86
379 380 1.535226 GGGAAAGTTGTTGACCGTTGC 60.535 52.381 0.00 0.00 0.00 4.17
380 381 2.021457 AGGGAAAGTTGTTGACCGTTG 58.979 47.619 0.00 0.00 0.00 4.10
382 383 2.436911 AGTAGGGAAAGTTGTTGACCGT 59.563 45.455 0.00 0.00 0.00 4.83
383 384 3.121738 AGTAGGGAAAGTTGTTGACCG 57.878 47.619 0.00 0.00 0.00 4.79
385 386 4.374399 TCGAAGTAGGGAAAGTTGTTGAC 58.626 43.478 0.00 0.00 0.00 3.18
386 387 4.675976 TCGAAGTAGGGAAAGTTGTTGA 57.324 40.909 0.00 0.00 0.00 3.18
387 388 4.091509 CGATCGAAGTAGGGAAAGTTGTTG 59.908 45.833 10.26 0.00 0.00 3.33
388 389 4.243270 CGATCGAAGTAGGGAAAGTTGTT 58.757 43.478 10.26 0.00 0.00 2.83
390 391 3.846360 ACGATCGAAGTAGGGAAAGTTG 58.154 45.455 24.34 0.00 0.00 3.16
391 392 3.508793 TGACGATCGAAGTAGGGAAAGTT 59.491 43.478 24.34 0.00 0.00 2.66
392 393 3.087031 TGACGATCGAAGTAGGGAAAGT 58.913 45.455 24.34 0.00 0.00 2.66
393 394 3.436496 GTGACGATCGAAGTAGGGAAAG 58.564 50.000 24.34 0.00 0.00 2.62
394 395 2.165030 GGTGACGATCGAAGTAGGGAAA 59.835 50.000 24.34 0.00 0.00 3.13
395 396 1.747355 GGTGACGATCGAAGTAGGGAA 59.253 52.381 24.34 0.00 0.00 3.97
396 397 1.064906 AGGTGACGATCGAAGTAGGGA 60.065 52.381 24.34 0.00 0.00 4.20
397 398 1.334243 GAGGTGACGATCGAAGTAGGG 59.666 57.143 24.34 0.00 0.00 3.53
399 400 3.242804 GGAAGAGGTGACGATCGAAGTAG 60.243 52.174 24.34 0.00 0.00 2.57
402 403 1.202313 GGGAAGAGGTGACGATCGAAG 60.202 57.143 24.34 0.00 0.00 3.79
403 404 0.815734 GGGAAGAGGTGACGATCGAA 59.184 55.000 24.34 6.64 0.00 3.71
404 405 1.374343 CGGGAAGAGGTGACGATCGA 61.374 60.000 24.34 0.00 0.00 3.59
405 406 1.064296 CGGGAAGAGGTGACGATCG 59.936 63.158 14.88 14.88 0.00 3.69
406 407 1.227002 GCGGGAAGAGGTGACGATC 60.227 63.158 0.00 0.00 0.00 3.69
407 408 2.893398 GCGGGAAGAGGTGACGAT 59.107 61.111 0.00 0.00 0.00 3.73
410 411 3.665675 ATGCGCGGGAAGAGGTGAC 62.666 63.158 8.83 0.00 0.00 3.67
413 414 1.399744 TATGATGCGCGGGAAGAGGT 61.400 55.000 8.83 0.00 0.00 3.85
414 415 0.036952 ATATGATGCGCGGGAAGAGG 60.037 55.000 8.83 0.00 0.00 3.69
416 417 3.394674 TTTATATGATGCGCGGGAAGA 57.605 42.857 8.83 0.00 0.00 2.87
417 418 4.437390 GGATTTTATATGATGCGCGGGAAG 60.437 45.833 8.83 0.00 0.00 3.46
418 419 3.438781 GGATTTTATATGATGCGCGGGAA 59.561 43.478 8.83 0.00 0.00 3.97
419 420 3.006940 GGATTTTATATGATGCGCGGGA 58.993 45.455 8.83 0.00 0.00 5.14
420 421 2.097466 GGGATTTTATATGATGCGCGGG 59.903 50.000 8.83 0.00 0.00 6.13
421 422 2.746904 TGGGATTTTATATGATGCGCGG 59.253 45.455 8.83 0.00 0.00 6.46
422 423 4.345288 CATGGGATTTTATATGATGCGCG 58.655 43.478 0.00 0.00 0.00 6.86
423 424 4.107622 GCATGGGATTTTATATGATGCGC 58.892 43.478 0.00 0.00 0.00 6.09
424 425 5.313520 TGCATGGGATTTTATATGATGCG 57.686 39.130 0.00 0.00 38.02 4.73
425 426 6.366877 GTGTTGCATGGGATTTTATATGATGC 59.633 38.462 0.00 0.00 36.19 3.91
426 427 7.383029 GTGTGTTGCATGGGATTTTATATGATG 59.617 37.037 0.00 0.00 0.00 3.07
428 429 6.379417 TGTGTGTTGCATGGGATTTTATATGA 59.621 34.615 0.00 0.00 0.00 2.15
429 430 6.571605 TGTGTGTTGCATGGGATTTTATATG 58.428 36.000 0.00 0.00 0.00 1.78
431 432 6.183360 GGATGTGTGTTGCATGGGATTTTATA 60.183 38.462 0.00 0.00 0.00 0.98
432 433 5.395546 GGATGTGTGTTGCATGGGATTTTAT 60.396 40.000 0.00 0.00 0.00 1.40
433 434 4.081752 GGATGTGTGTTGCATGGGATTTTA 60.082 41.667 0.00 0.00 0.00 1.52
434 435 3.306919 GGATGTGTGTTGCATGGGATTTT 60.307 43.478 0.00 0.00 0.00 1.82
435 436 2.234414 GGATGTGTGTTGCATGGGATTT 59.766 45.455 0.00 0.00 0.00 2.17
436 437 1.826720 GGATGTGTGTTGCATGGGATT 59.173 47.619 0.00 0.00 0.00 3.01
440 441 1.135527 GGATGGATGTGTGTTGCATGG 59.864 52.381 0.00 0.00 0.00 3.66
442 443 2.219080 TGGATGGATGTGTGTTGCAT 57.781 45.000 0.00 0.00 0.00 3.96
443 444 2.093890 GATGGATGGATGTGTGTTGCA 58.906 47.619 0.00 0.00 0.00 4.08
444 445 2.372264 AGATGGATGGATGTGTGTTGC 58.628 47.619 0.00 0.00 0.00 4.17
445 446 5.824097 TGATAAGATGGATGGATGTGTGTTG 59.176 40.000 0.00 0.00 0.00 3.33
446 447 6.005066 TGATAAGATGGATGGATGTGTGTT 57.995 37.500 0.00 0.00 0.00 3.32
3096 5434 3.074412 GAGAAGTCGCTTTCCATGGAAA 58.926 45.455 32.66 32.66 41.22 3.13


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

AutoCloner maintained by Alex Coulton.