Multiple sequence alignment - TraesCS1B01G343700

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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 TraesCS1B01G343700 chr1B 100.000 4251 0 0 1 4251 572291451 572287201 0.000000e+00 7851.0
1 TraesCS1B01G343700 chr1B 80.104 960 105 42 1559 2497 572288161 572287267 1.670000e-178 636.0
2 TraesCS1B01G343700 chr1B 80.104 960 105 42 3291 4185 572289893 572288955 1.670000e-178 636.0
3 TraesCS1B01G343700 chr1B 95.122 82 2 2 4170 4251 679712993 679713072 1.240000e-25 128.0
4 TraesCS1B01G343700 chr1A 90.719 2780 140 40 1470 4185 518955469 518952744 0.000000e+00 3596.0
5 TraesCS1B01G343700 chr1A 80.271 958 123 29 1559 2500 518953648 518952741 0.000000e+00 662.0
6 TraesCS1B01G343700 chr1A 84.718 674 61 12 2628 3287 518952582 518951937 1.670000e-178 636.0
7 TraesCS1B01G343700 chr1A 93.674 411 21 3 909 1315 518955983 518955574 1.010000e-170 610.0
8 TraesCS1B01G343700 chr1A 89.641 473 40 5 2615 3082 111988643 111988175 1.020000e-165 593.0
9 TraesCS1B01G343700 chr1A 79.828 233 30 10 3081 3296 518866954 518866722 2.050000e-33 154.0
10 TraesCS1B01G343700 chr1A 98.684 76 1 0 4176 4251 84176181 84176106 7.410000e-28 135.0
11 TraesCS1B01G343700 chr1A 93.878 49 3 0 670 718 518966149 518966101 1.640000e-09 75.0
12 TraesCS1B01G343700 chr1D 89.614 2773 158 60 1499 4185 423037162 423034434 0.000000e+00 3406.0
13 TraesCS1B01G343700 chr1D 95.753 518 17 3 823 1337 423037801 423037286 0.000000e+00 830.0
14 TraesCS1B01G343700 chr1D 80.816 980 104 36 1559 2503 423035358 423034428 0.000000e+00 691.0
15 TraesCS1B01G343700 chr1D 82.494 794 77 30 3430 4185 423036927 423036158 1.290000e-179 640.0
16 TraesCS1B01G343700 chr1D 86.306 314 33 8 263 573 423038987 423038681 2.450000e-87 333.0
17 TraesCS1B01G343700 chr1D 88.832 197 12 4 41 228 423039163 423038968 2.560000e-57 233.0
18 TraesCS1B01G343700 chr1D 89.928 139 14 0 1071 1209 224139520 224139658 3.380000e-41 180.0
19 TraesCS1B01G343700 chr1D 93.750 48 3 0 1420 1467 423037216 423037169 5.900000e-09 73.1
20 TraesCS1B01G343700 chr2B 93.782 579 27 3 1300 1876 289226147 289226718 0.000000e+00 861.0
21 TraesCS1B01G343700 chr2B 88.821 653 49 12 2615 3248 776687467 776688114 0.000000e+00 780.0
22 TraesCS1B01G343700 chr2B 89.429 473 41 5 2615 3082 138122061 138121593 4.730000e-164 588.0
23 TraesCS1B01G343700 chr2B 84.138 145 19 3 1047 1190 776687266 776687407 2.060000e-28 137.0
24 TraesCS1B01G343700 chr2A 88.588 701 54 10 2615 3295 780743831 780743137 0.000000e+00 828.0
25 TraesCS1B01G343700 chr2A 84.358 179 23 4 1047 1224 780744062 780743888 2.030000e-38 171.0
26 TraesCS1B01G343700 chr2D 87.896 694 51 12 2615 3280 633593294 633593982 0.000000e+00 785.0
27 TraesCS1B01G343700 chr2D 88.550 131 15 0 1084 1214 633592211 633592341 4.400000e-35 159.0
28 TraesCS1B01G343700 chr2D 100.000 43 0 0 1 43 272263129 272263171 3.520000e-11 80.5
29 TraesCS1B01G343700 chr2D 91.071 56 3 2 1 55 142839907 142839853 1.640000e-09 75.0
30 TraesCS1B01G343700 chr5A 84.257 686 82 11 2615 3280 565940987 565940308 0.000000e+00 645.0
31 TraesCS1B01G343700 chr5A 87.742 155 13 5 3115 3263 622380552 622380706 4.370000e-40 176.0
32 TraesCS1B01G343700 chr5A 98.718 78 1 0 4174 4251 293066494 293066417 5.730000e-29 139.0
33 TraesCS1B01G343700 chr3B 89.641 473 40 5 2615 3082 646715372 646714904 1.020000e-165 593.0
34 TraesCS1B01G343700 chr3A 89.006 473 43 6 2615 3082 565331386 565331854 1.020000e-160 577.0
35 TraesCS1B01G343700 chr3A 97.436 78 1 1 4175 4251 146405187 146405110 9.590000e-27 132.0
36 TraesCS1B01G343700 chr3A 100.000 29 0 0 1003 1031 736803654 736803682 2.000000e-03 54.7
37 TraesCS1B01G343700 chr4D 81.754 285 16 15 3011 3263 49872913 49872633 5.570000e-49 206.0
38 TraesCS1B01G343700 chr4D 80.714 280 23 16 3011 3263 461529342 461529067 5.610000e-44 189.0
39 TraesCS1B01G343700 chr4D 94.118 85 3 2 4167 4251 335294445 335294527 1.240000e-25 128.0
40 TraesCS1B01G343700 chr6A 95.238 84 2 2 4170 4251 372215760 372215677 9.590000e-27 132.0
41 TraesCS1B01G343700 chr6A 95.238 84 2 2 4170 4251 372279951 372279868 9.590000e-27 132.0
42 TraesCS1B01G343700 chr4A 93.258 89 3 3 4164 4251 570369776 570369690 1.240000e-25 128.0
43 TraesCS1B01G343700 chr4B 93.103 87 3 3 4165 4251 172583600 172583517 1.600000e-24 124.0
44 TraesCS1B01G343700 chr6B 97.826 46 1 0 1 46 280092519 280092474 3.520000e-11 80.5
45 TraesCS1B01G343700 chr6B 97.826 46 0 1 1 46 333551483 333551439 1.270000e-10 78.7
46 TraesCS1B01G343700 chr6B 95.918 49 1 1 1 49 455146472 455146519 1.270000e-10 78.7
47 TraesCS1B01G343700 chr6B 94.000 50 2 1 1 50 30889141 30889189 1.640000e-09 75.0
48 TraesCS1B01G343700 chr3D 100.000 43 0 0 1 43 435646784 435646742 3.520000e-11 80.5
49 TraesCS1B01G343700 chr3D 88.889 63 7 0 125 187 515964149 515964211 1.270000e-10 78.7
50 TraesCS1B01G343700 chrUn 97.778 45 1 0 1 45 218382200 218382244 1.270000e-10 78.7
51 TraesCS1B01G343700 chrUn 97.778 45 1 0 1 45 218399748 218399792 1.270000e-10 78.7


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 TraesCS1B01G343700 chr1B 572287201 572291451 4250 True 7851.000000 7851 100.000000 1 4251 1 chr1B.!!$R1 4250
1 TraesCS1B01G343700 chr1B 572287267 572289893 2626 True 636.000000 636 80.104000 1559 4185 2 chr1B.!!$R2 2626
2 TraesCS1B01G343700 chr1A 518951937 518955983 4046 True 1376.000000 3596 87.345500 909 4185 4 chr1A.!!$R5 3276
3 TraesCS1B01G343700 chr1D 423034428 423039163 4735 True 886.585714 3406 88.223571 41 4185 7 chr1D.!!$R1 4144
4 TraesCS1B01G343700 chr2B 289226147 289226718 571 False 861.000000 861 93.782000 1300 1876 1 chr2B.!!$F1 576
5 TraesCS1B01G343700 chr2B 776687266 776688114 848 False 458.500000 780 86.479500 1047 3248 2 chr2B.!!$F2 2201
6 TraesCS1B01G343700 chr2A 780743137 780744062 925 True 499.500000 828 86.473000 1047 3295 2 chr2A.!!$R1 2248
7 TraesCS1B01G343700 chr2D 633592211 633593982 1771 False 472.000000 785 88.223000 1084 3280 2 chr2D.!!$F2 2196
8 TraesCS1B01G343700 chr5A 565940308 565940987 679 True 645.000000 645 84.257000 2615 3280 1 chr5A.!!$R2 665

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
500 511 0.035152 TGCACTGAGGGGCATACAAG 60.035 55.000 0.00 0.00 34.58 3.16 F
1210 1924 0.322456 ACATGCATGCAGGTACGGTT 60.322 50.000 34.44 10.70 39.28 4.44 F
1319 2049 0.318445 CGGACACCGGATTCGTATCC 60.318 60.000 9.46 10.86 45.89 2.59 F
1496 2241 4.940046 AGCAGTTCATCCTCATGTTAACAG 59.060 41.667 14.65 6.58 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1319 2049 1.733526 GAATCCCCGCCCAATTTCG 59.266 57.895 0.0 0.0 0.0 3.46 R
2690 3561 9.061435 TCATAATGAAGTCAACAACATACAACA 57.939 29.630 0.0 0.0 0.0 3.33 R
2691 3562 9.546909 CTCATAATGAAGTCAACAACATACAAC 57.453 33.333 0.0 0.0 0.0 3.32 R
4195 5173 4.324254 CCAAAATCACTAAGGGGCACTAGA 60.324 45.833 0.0 0.0 0.0 2.43 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
19 20 2.951457 TACATCCATTTCAGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
20 21 1.645034 ACATCCATTTCAGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
21 22 1.066858 ACATCCATTTCAGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
22 23 2.165641 ACATCCATTTCAGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
23 24 3.186909 CATCCATTTCAGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
24 25 3.520290 TCCATTTCAGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
25 26 3.857052 TCCATTTCAGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
26 27 4.250464 TCCATTTCAGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
27 28 4.092821 TCCATTTCAGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
28 29 4.092821 CCATTTCAGCGACGAGTAATTTGA 59.907 41.667 0.00 0.00 0.00 2.69
29 30 5.390461 CCATTTCAGCGACGAGTAATTTGAA 60.390 40.000 0.00 0.00 0.00 2.69
30 31 5.660629 TTTCAGCGACGAGTAATTTGAAA 57.339 34.783 0.00 0.31 32.52 2.69
31 32 4.640805 TCAGCGACGAGTAATTTGAAAC 57.359 40.909 0.00 0.00 0.00 2.78
32 33 3.120616 TCAGCGACGAGTAATTTGAAACG 59.879 43.478 0.00 0.00 0.00 3.60
33 34 2.410730 AGCGACGAGTAATTTGAAACGG 59.589 45.455 0.00 0.00 0.00 4.44
34 35 2.409378 GCGACGAGTAATTTGAAACGGA 59.591 45.455 0.00 0.00 0.00 4.69
35 36 3.481467 GCGACGAGTAATTTGAAACGGAG 60.481 47.826 0.00 0.00 0.00 4.63
36 37 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
37 38 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
38 39 3.007182 ACGAGTAATTTGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
39 40 3.617263 CGAGTAATTTGAAACGGAGGGAG 59.383 47.826 0.00 0.00 0.00 4.30
69 77 4.157656 ACAACTTGCACACACTTACAACAT 59.842 37.500 0.00 0.00 0.00 2.71
82 90 0.185901 ACAACATTGGCCCACTGTCT 59.814 50.000 7.24 0.00 0.00 3.41
88 96 0.322456 TTGGCCCACTGTCTGTATGC 60.322 55.000 0.00 0.00 0.00 3.14
121 130 0.880278 CCGGCGTATCACTTGGATGG 60.880 60.000 6.01 0.00 36.72 3.51
122 131 0.104120 CGGCGTATCACTTGGATGGA 59.896 55.000 0.00 0.00 36.72 3.41
123 132 1.472552 CGGCGTATCACTTGGATGGAA 60.473 52.381 0.00 0.00 36.72 3.53
126 136 2.549754 GCGTATCACTTGGATGGAATGG 59.450 50.000 0.00 0.00 36.72 3.16
135 145 0.183731 GGATGGAATGGTGGTCTCCC 59.816 60.000 0.00 0.00 0.00 4.30
143 153 1.003233 GGTGGTCTCCCTGACTTGC 60.003 63.158 0.00 0.00 44.74 4.01
176 186 6.294955 GCCATCTTGTTCTTTCTCTTTGGATT 60.295 38.462 0.00 0.00 0.00 3.01
185 195 4.982241 TTCTCTTTGGATTCAGTGACCT 57.018 40.909 0.00 0.00 0.00 3.85
216 226 1.312815 AGTGTTGCCTGCACTTTCTC 58.687 50.000 0.00 0.00 43.87 2.87
218 228 0.106769 TGTTGCCTGCACTTTCTCCA 60.107 50.000 0.00 0.00 0.00 3.86
219 229 0.595095 GTTGCCTGCACTTTCTCCAG 59.405 55.000 0.00 0.00 0.00 3.86
220 230 0.183492 TTGCCTGCACTTTCTCCAGT 59.817 50.000 0.00 0.00 0.00 4.00
221 231 0.183492 TGCCTGCACTTTCTCCAGTT 59.817 50.000 0.00 0.00 0.00 3.16
222 232 1.322442 GCCTGCACTTTCTCCAGTTT 58.678 50.000 0.00 0.00 0.00 2.66
223 233 1.268079 GCCTGCACTTTCTCCAGTTTC 59.732 52.381 0.00 0.00 0.00 2.78
224 234 2.575532 CCTGCACTTTCTCCAGTTTCA 58.424 47.619 0.00 0.00 0.00 2.69
225 235 3.152341 CCTGCACTTTCTCCAGTTTCAT 58.848 45.455 0.00 0.00 0.00 2.57
226 236 3.190118 CCTGCACTTTCTCCAGTTTCATC 59.810 47.826 0.00 0.00 0.00 2.92
227 237 3.817084 CTGCACTTTCTCCAGTTTCATCA 59.183 43.478 0.00 0.00 0.00 3.07
228 238 3.817084 TGCACTTTCTCCAGTTTCATCAG 59.183 43.478 0.00 0.00 0.00 2.90
229 239 3.190118 GCACTTTCTCCAGTTTCATCAGG 59.810 47.826 0.00 0.00 0.00 3.86
230 240 4.392940 CACTTTCTCCAGTTTCATCAGGT 58.607 43.478 0.00 0.00 0.00 4.00
231 241 5.551233 CACTTTCTCCAGTTTCATCAGGTA 58.449 41.667 0.00 0.00 0.00 3.08
232 242 5.997746 CACTTTCTCCAGTTTCATCAGGTAA 59.002 40.000 0.00 0.00 0.00 2.85
233 243 6.486657 CACTTTCTCCAGTTTCATCAGGTAAA 59.513 38.462 0.00 0.00 0.00 2.01
234 244 7.013274 CACTTTCTCCAGTTTCATCAGGTAAAA 59.987 37.037 0.00 0.00 0.00 1.52
235 245 6.877611 TTCTCCAGTTTCATCAGGTAAAAC 57.122 37.500 0.00 0.00 33.98 2.43
236 246 5.935945 TCTCCAGTTTCATCAGGTAAAACA 58.064 37.500 0.00 0.00 35.77 2.83
237 247 5.763204 TCTCCAGTTTCATCAGGTAAAACAC 59.237 40.000 0.00 0.00 35.77 3.32
238 248 5.441500 TCCAGTTTCATCAGGTAAAACACA 58.558 37.500 0.00 0.00 35.77 3.72
239 249 6.068010 TCCAGTTTCATCAGGTAAAACACAT 58.932 36.000 0.00 0.00 35.77 3.21
240 250 6.549364 TCCAGTTTCATCAGGTAAAACACATT 59.451 34.615 0.00 0.00 35.77 2.71
241 251 6.863126 CCAGTTTCATCAGGTAAAACACATTC 59.137 38.462 0.00 0.00 35.77 2.67
242 252 7.255590 CCAGTTTCATCAGGTAAAACACATTCT 60.256 37.037 0.00 0.00 35.77 2.40
243 253 8.137437 CAGTTTCATCAGGTAAAACACATTCTT 58.863 33.333 0.00 0.00 35.77 2.52
244 254 8.352942 AGTTTCATCAGGTAAAACACATTCTTC 58.647 33.333 0.00 0.00 35.77 2.87
245 255 7.815840 TTCATCAGGTAAAACACATTCTTCA 57.184 32.000 0.00 0.00 0.00 3.02
246 256 7.439157 TCATCAGGTAAAACACATTCTTCAG 57.561 36.000 0.00 0.00 0.00 3.02
247 257 6.998074 TCATCAGGTAAAACACATTCTTCAGT 59.002 34.615 0.00 0.00 0.00 3.41
248 258 7.502226 TCATCAGGTAAAACACATTCTTCAGTT 59.498 33.333 0.00 0.00 0.00 3.16
249 259 7.639113 TCAGGTAAAACACATTCTTCAGTTT 57.361 32.000 0.00 0.00 35.87 2.66
250 260 7.703328 TCAGGTAAAACACATTCTTCAGTTTC 58.297 34.615 0.00 0.00 33.45 2.78
251 261 7.338196 TCAGGTAAAACACATTCTTCAGTTTCA 59.662 33.333 0.00 0.00 33.45 2.69
252 262 8.137437 CAGGTAAAACACATTCTTCAGTTTCAT 58.863 33.333 0.00 0.00 33.45 2.57
253 263 8.352942 AGGTAAAACACATTCTTCAGTTTCATC 58.647 33.333 0.00 0.00 33.45 2.92
254 264 8.134895 GGTAAAACACATTCTTCAGTTTCATCA 58.865 33.333 0.00 0.00 33.45 3.07
255 265 9.173939 GTAAAACACATTCTTCAGTTTCATCAG 57.826 33.333 0.00 0.00 33.45 2.90
256 266 5.954296 ACACATTCTTCAGTTTCATCAGG 57.046 39.130 0.00 0.00 0.00 3.86
257 267 5.380043 ACACATTCTTCAGTTTCATCAGGT 58.620 37.500 0.00 0.00 0.00 4.00
258 268 6.533730 ACACATTCTTCAGTTTCATCAGGTA 58.466 36.000 0.00 0.00 0.00 3.08
259 269 6.998074 ACACATTCTTCAGTTTCATCAGGTAA 59.002 34.615 0.00 0.00 0.00 2.85
260 270 7.041098 ACACATTCTTCAGTTTCATCAGGTAAC 60.041 37.037 0.00 0.00 0.00 2.50
261 271 6.998074 ACATTCTTCAGTTTCATCAGGTAACA 59.002 34.615 0.00 0.00 41.41 2.41
262 272 6.861065 TTCTTCAGTTTCATCAGGTAACAC 57.139 37.500 0.00 0.00 41.41 3.32
263 273 5.924356 TCTTCAGTTTCATCAGGTAACACA 58.076 37.500 0.00 0.00 41.41 3.72
264 274 5.758296 TCTTCAGTTTCATCAGGTAACACAC 59.242 40.000 0.00 0.00 41.41 3.82
265 275 5.290493 TCAGTTTCATCAGGTAACACACT 57.710 39.130 0.00 0.00 41.41 3.55
266 276 5.680619 TCAGTTTCATCAGGTAACACACTT 58.319 37.500 0.00 0.00 41.41 3.16
267 277 6.119536 TCAGTTTCATCAGGTAACACACTTT 58.880 36.000 0.00 0.00 41.41 2.66
268 278 6.260050 TCAGTTTCATCAGGTAACACACTTTC 59.740 38.462 0.00 0.00 41.41 2.62
269 279 6.260936 CAGTTTCATCAGGTAACACACTTTCT 59.739 38.462 0.00 0.00 41.41 2.52
270 280 6.828785 AGTTTCATCAGGTAACACACTTTCTT 59.171 34.615 0.00 0.00 41.41 2.52
271 281 7.990886 AGTTTCATCAGGTAACACACTTTCTTA 59.009 33.333 0.00 0.00 41.41 2.10
293 303 8.514594 TCTTAAGTTTCATCAATTAGCACCTTG 58.485 33.333 1.63 0.00 0.00 3.61
296 306 6.006449 AGTTTCATCAATTAGCACCTTGAGT 58.994 36.000 0.00 0.00 35.04 3.41
297 307 6.491403 AGTTTCATCAATTAGCACCTTGAGTT 59.509 34.615 0.00 0.00 35.04 3.01
304 314 1.889545 AGCACCTTGAGTTTGCTCTC 58.110 50.000 0.00 0.00 43.14 3.20
316 326 8.918202 TTGAGTTTGCTCTCCTTTTCTTATTA 57.082 30.769 0.00 0.00 42.13 0.98
321 331 9.914131 GTTTGCTCTCCTTTTCTTATTATTTGT 57.086 29.630 0.00 0.00 0.00 2.83
324 335 8.028938 TGCTCTCCTTTTCTTATTATTTGTTGC 58.971 33.333 0.00 0.00 0.00 4.17
329 340 8.313292 TCCTTTTCTTATTATTTGTTGCTGCAT 58.687 29.630 1.84 0.00 0.00 3.96
378 389 3.250323 CGAGTGTCGCTGCATCCG 61.250 66.667 0.00 0.00 31.14 4.18
396 407 1.871039 CCGGGGCGTTACAATTATCAG 59.129 52.381 0.00 0.00 0.00 2.90
408 419 5.991328 ACAATTATCAGTATGTCCAAGCG 57.009 39.130 0.00 0.00 37.40 4.68
436 447 1.516386 CACCAGACGGATCGAACGG 60.516 63.158 15.74 8.11 35.59 4.44
464 475 3.969117 TTGTGCTGCAACTTCTAAGTG 57.031 42.857 2.77 0.00 39.66 3.16
465 476 2.917933 TGTGCTGCAACTTCTAAGTGT 58.082 42.857 2.77 0.00 39.66 3.55
466 477 2.613595 TGTGCTGCAACTTCTAAGTGTG 59.386 45.455 2.77 0.00 39.66 3.82
468 479 1.603802 GCTGCAACTTCTAAGTGTGCA 59.396 47.619 20.87 20.87 43.67 4.57
475 486 5.215160 CAACTTCTAAGTGTGCAATTGTCC 58.785 41.667 7.40 0.00 39.66 4.02
477 488 2.422597 TCTAAGTGTGCAATTGTCCCG 58.577 47.619 7.40 0.00 0.00 5.14
478 489 2.037902 TCTAAGTGTGCAATTGTCCCGA 59.962 45.455 7.40 0.00 0.00 5.14
485 496 0.099436 GCAATTGTCCCGAGATGCAC 59.901 55.000 7.40 0.00 34.10 4.57
488 499 0.904649 ATTGTCCCGAGATGCACTGA 59.095 50.000 0.00 0.00 0.00 3.41
489 500 0.247460 TTGTCCCGAGATGCACTGAG 59.753 55.000 0.00 0.00 0.00 3.35
490 501 1.142748 GTCCCGAGATGCACTGAGG 59.857 63.158 0.00 0.00 0.00 3.86
493 504 2.202987 CGAGATGCACTGAGGGGC 60.203 66.667 0.00 0.00 0.00 5.80
494 505 2.993008 GAGATGCACTGAGGGGCA 59.007 61.111 3.61 3.61 45.23 5.36
498 509 3.818965 TGCACTGAGGGGCATACA 58.181 55.556 0.00 0.00 34.58 2.29
500 511 0.035152 TGCACTGAGGGGCATACAAG 60.035 55.000 0.00 0.00 34.58 3.16
532 543 3.118261 TCAACCATCATGTCTAAGGGCTC 60.118 47.826 0.00 0.00 0.00 4.70
533 544 1.771255 ACCATCATGTCTAAGGGCTCC 59.229 52.381 0.00 0.00 0.00 4.70
567 578 2.498078 GAGCTAGGTAGAAACTGCTGGT 59.502 50.000 0.00 0.00 30.92 4.00
568 579 2.234908 AGCTAGGTAGAAACTGCTGGTG 59.765 50.000 0.00 0.00 0.00 4.17
569 580 2.678190 GCTAGGTAGAAACTGCTGGTGG 60.678 54.545 0.00 0.00 0.00 4.61
570 581 0.693049 AGGTAGAAACTGCTGGTGGG 59.307 55.000 0.00 0.00 0.00 4.61
571 582 0.400594 GGTAGAAACTGCTGGTGGGT 59.599 55.000 0.00 0.00 0.00 4.51
572 583 1.523758 GTAGAAACTGCTGGTGGGTG 58.476 55.000 0.00 0.00 0.00 4.61
573 584 0.400213 TAGAAACTGCTGGTGGGTGG 59.600 55.000 0.00 0.00 0.00 4.61
574 585 1.903404 GAAACTGCTGGTGGGTGGG 60.903 63.158 0.00 0.00 0.00 4.61
575 586 3.451056 AAACTGCTGGTGGGTGGGG 62.451 63.158 0.00 0.00 0.00 4.96
577 588 4.666253 CTGCTGGTGGGTGGGGTG 62.666 72.222 0.00 0.00 0.00 4.61
600 611 4.952102 GGGGTGGGGCAAGGCAAA 62.952 66.667 0.00 0.00 0.00 3.68
601 612 2.846754 GGGTGGGGCAAGGCAAAA 60.847 61.111 0.00 0.00 0.00 2.44
602 613 2.447714 GGGTGGGGCAAGGCAAAAA 61.448 57.895 0.00 0.00 0.00 1.94
603 614 1.760527 GGTGGGGCAAGGCAAAAAT 59.239 52.632 0.00 0.00 0.00 1.82
604 615 0.980423 GGTGGGGCAAGGCAAAAATA 59.020 50.000 0.00 0.00 0.00 1.40
605 616 1.559219 GGTGGGGCAAGGCAAAAATAT 59.441 47.619 0.00 0.00 0.00 1.28
606 617 2.631267 GTGGGGCAAGGCAAAAATATG 58.369 47.619 0.00 0.00 0.00 1.78
607 618 2.235898 GTGGGGCAAGGCAAAAATATGA 59.764 45.455 0.00 0.00 0.00 2.15
608 619 2.500910 TGGGGCAAGGCAAAAATATGAG 59.499 45.455 0.00 0.00 0.00 2.90
609 620 2.501316 GGGGCAAGGCAAAAATATGAGT 59.499 45.455 0.00 0.00 0.00 3.41
610 621 3.524541 GGGCAAGGCAAAAATATGAGTG 58.475 45.455 0.00 0.00 0.00 3.51
611 622 3.055891 GGGCAAGGCAAAAATATGAGTGT 60.056 43.478 0.00 0.00 0.00 3.55
612 623 4.563374 GGGCAAGGCAAAAATATGAGTGTT 60.563 41.667 0.00 0.00 0.00 3.32
613 624 4.996758 GGCAAGGCAAAAATATGAGTGTTT 59.003 37.500 0.00 0.00 0.00 2.83
614 625 5.106987 GGCAAGGCAAAAATATGAGTGTTTG 60.107 40.000 0.00 0.00 34.74 2.93
623 634 2.363306 ATGAGTGTTTGGGAGTGCAA 57.637 45.000 0.00 0.00 0.00 4.08
644 655 6.748658 TGCAAAATGCTAAAAGAATCTCATCG 59.251 34.615 3.78 0.00 45.31 3.84
648 659 5.725110 TGCTAAAAGAATCTCATCGAAGC 57.275 39.130 0.00 0.00 0.00 3.86
650 943 4.024472 GCTAAAAGAATCTCATCGAAGCCC 60.024 45.833 0.00 0.00 0.00 5.19
656 949 0.757188 TCTCATCGAAGCCCTCCCTC 60.757 60.000 0.00 0.00 0.00 4.30
657 950 1.001631 TCATCGAAGCCCTCCCTCA 59.998 57.895 0.00 0.00 0.00 3.86
661 954 0.991920 TCGAAGCCCTCCCTCAAAAT 59.008 50.000 0.00 0.00 0.00 1.82
667 960 4.888626 AGCCCTCCCTCAAAATATTTCT 57.111 40.909 0.10 0.00 0.00 2.52
669 962 5.204292 AGCCCTCCCTCAAAATATTTCTTC 58.796 41.667 0.10 0.00 0.00 2.87
670 963 4.956075 GCCCTCCCTCAAAATATTTCTTCA 59.044 41.667 0.10 0.00 0.00 3.02
672 965 6.190587 CCCTCCCTCAAAATATTTCTTCACT 58.809 40.000 0.10 0.00 0.00 3.41
673 966 6.096001 CCCTCCCTCAAAATATTTCTTCACTG 59.904 42.308 0.10 0.00 0.00 3.66
674 967 6.405176 CCTCCCTCAAAATATTTCTTCACTGC 60.405 42.308 0.10 0.00 0.00 4.40
675 968 6.248433 TCCCTCAAAATATTTCTTCACTGCT 58.752 36.000 0.10 0.00 0.00 4.24
676 969 6.375455 TCCCTCAAAATATTTCTTCACTGCTC 59.625 38.462 0.10 0.00 0.00 4.26
677 970 6.405176 CCCTCAAAATATTTCTTCACTGCTCC 60.405 42.308 0.10 0.00 0.00 4.70
678 971 6.376581 CCTCAAAATATTTCTTCACTGCTCCT 59.623 38.462 0.10 0.00 0.00 3.69
679 972 7.094032 CCTCAAAATATTTCTTCACTGCTCCTT 60.094 37.037 0.10 0.00 0.00 3.36
681 974 8.084073 TCAAAATATTTCTTCACTGCTCCTTTG 58.916 33.333 0.10 0.00 0.00 2.77
682 975 7.765695 AAATATTTCTTCACTGCTCCTTTGA 57.234 32.000 0.00 0.00 0.00 2.69
683 976 7.951347 AATATTTCTTCACTGCTCCTTTGAT 57.049 32.000 0.00 0.00 0.00 2.57
684 977 7.951347 ATATTTCTTCACTGCTCCTTTGATT 57.049 32.000 0.00 0.00 0.00 2.57
685 978 5.695851 TTTCTTCACTGCTCCTTTGATTC 57.304 39.130 0.00 0.00 0.00 2.52
686 979 4.356405 TCTTCACTGCTCCTTTGATTCA 57.644 40.909 0.00 0.00 0.00 2.57
687 980 4.717877 TCTTCACTGCTCCTTTGATTCAA 58.282 39.130 0.00 0.00 0.00 2.69
689 982 3.415212 TCACTGCTCCTTTGATTCAAGG 58.585 45.455 1.69 1.69 0.00 3.61
691 984 4.015084 CACTGCTCCTTTGATTCAAGGAT 58.985 43.478 9.88 0.00 0.00 3.24
692 985 5.045651 TCACTGCTCCTTTGATTCAAGGATA 60.046 40.000 9.88 6.15 0.00 2.59
693 986 5.826737 CACTGCTCCTTTGATTCAAGGATAT 59.173 40.000 9.88 0.00 0.00 1.63
695 988 6.545298 ACTGCTCCTTTGATTCAAGGATATTC 59.455 38.462 9.88 5.45 0.00 1.75
696 989 6.425735 TGCTCCTTTGATTCAAGGATATTCA 58.574 36.000 9.88 7.29 0.00 2.57
697 990 7.064866 TGCTCCTTTGATTCAAGGATATTCAT 58.935 34.615 9.88 0.00 0.00 2.57
742 1456 7.891183 TTTGAGGAAATTAGAAGTTCTCTCG 57.109 36.000 9.12 0.00 35.27 4.04
779 1493 7.413767 GCGGTAATTAGAAGTTTTCTCGGAAAT 60.414 37.037 0.00 0.00 41.14 2.17
806 1520 6.911250 AAAAACTCCCGATCCAACTAATTT 57.089 33.333 0.00 0.00 0.00 1.82
807 1521 6.911250 AAAACTCCCGATCCAACTAATTTT 57.089 33.333 0.00 0.00 0.00 1.82
808 1522 6.911250 AAACTCCCGATCCAACTAATTTTT 57.089 33.333 0.00 0.00 0.00 1.94
840 1554 3.054361 AGCAACTCCCGATCCAACTAAAT 60.054 43.478 0.00 0.00 0.00 1.40
852 1566 2.470821 CAACTAAATAGGACCGCCTCG 58.529 52.381 0.00 0.00 45.54 4.63
888 1602 1.073897 AGGCCAGCAGTGACTTTCC 59.926 57.895 5.01 0.00 0.00 3.13
891 1605 1.322442 GCCAGCAGTGACTTTCCTTT 58.678 50.000 0.00 0.00 0.00 3.11
892 1606 1.000938 GCCAGCAGTGACTTTCCTTTG 60.001 52.381 0.00 0.00 0.00 2.77
988 1702 2.070399 TTTTAACCAGGCCCAGGCGA 62.070 55.000 11.64 0.00 43.06 5.54
1166 1880 0.760567 AGGAGCGGCTGGTCATGATA 60.761 55.000 25.17 0.00 44.47 2.15
1193 1907 2.265904 CCACGACTGGGACGAGACA 61.266 63.158 0.00 0.00 33.23 3.41
1210 1924 0.322456 ACATGCATGCAGGTACGGTT 60.322 50.000 34.44 10.70 39.28 4.44
1247 1977 6.166982 CGAAACCCTAACTTCTTGATTCTCT 58.833 40.000 0.00 0.00 0.00 3.10
1261 1991 2.949451 TTCTCTCTCGATCCAACTGC 57.051 50.000 0.00 0.00 0.00 4.40
1291 2021 1.301479 GTTTGAGGCCGTTCGGTCT 60.301 57.895 18.31 18.31 43.80 3.85
1298 2028 3.622826 CCGTTCGGTCTGGGGTGT 61.623 66.667 2.82 0.00 0.00 4.16
1319 2049 0.318445 CGGACACCGGATTCGTATCC 60.318 60.000 9.46 10.86 45.89 2.59
1384 2127 5.104067 ACCAGGCTAGATTTAGTTTTAGGGG 60.104 44.000 0.00 0.00 0.00 4.79
1496 2241 4.940046 AGCAGTTCATCCTCATGTTAACAG 59.060 41.667 14.65 6.58 0.00 3.16
2689 3560 5.130975 TGGTTCTACATCAATCTAGCATGGT 59.869 40.000 1.62 1.62 0.00 3.55
2690 3561 6.058183 GGTTCTACATCAATCTAGCATGGTT 58.942 40.000 1.12 0.00 0.00 3.67
2691 3562 6.017605 GGTTCTACATCAATCTAGCATGGTTG 60.018 42.308 1.12 0.20 0.00 3.77
3462 4397 3.416156 GCCCTGTGTCTCTGATTTTCTT 58.584 45.455 0.00 0.00 0.00 2.52
3463 4398 3.190118 GCCCTGTGTCTCTGATTTTCTTG 59.810 47.826 0.00 0.00 0.00 3.02
3464 4399 4.645535 CCCTGTGTCTCTGATTTTCTTGA 58.354 43.478 0.00 0.00 0.00 3.02
4187 5165 9.862371 TTTATACTTTGTTGTGTTTCACATTGT 57.138 25.926 3.43 0.00 44.16 2.71
4190 5168 7.810766 ACTTTGTTGTGTTTCACATTGTAAG 57.189 32.000 3.43 7.75 44.16 2.34
4191 5169 7.375053 ACTTTGTTGTGTTTCACATTGTAAGT 58.625 30.769 3.43 8.24 44.16 2.24
4192 5170 7.328249 ACTTTGTTGTGTTTCACATTGTAAGTG 59.672 33.333 3.43 0.00 44.16 3.16
4193 5171 5.098893 TGTTGTGTTTCACATTGTAAGTGC 58.901 37.500 3.43 0.00 44.16 4.40
4194 5172 4.972514 TGTGTTTCACATTGTAAGTGCA 57.027 36.364 0.00 0.00 39.62 4.57
4195 5173 5.512753 TGTGTTTCACATTGTAAGTGCAT 57.487 34.783 0.00 0.00 39.62 3.96
4196 5174 5.518812 TGTGTTTCACATTGTAAGTGCATC 58.481 37.500 0.00 0.00 39.62 3.91
4197 5175 5.299028 TGTGTTTCACATTGTAAGTGCATCT 59.701 36.000 0.00 0.00 39.62 2.90
4198 5176 6.484977 TGTGTTTCACATTGTAAGTGCATCTA 59.515 34.615 0.00 0.00 39.62 1.98
4199 5177 7.017645 GTGTTTCACATTGTAAGTGCATCTAG 58.982 38.462 0.00 0.00 36.93 2.43
4200 5178 6.710295 TGTTTCACATTGTAAGTGCATCTAGT 59.290 34.615 0.00 0.00 36.93 2.57
4201 5179 6.726258 TTCACATTGTAAGTGCATCTAGTG 57.274 37.500 0.00 0.00 36.93 2.74
4214 5192 4.696479 CATCTAGTGCCCCTTAGTGATT 57.304 45.455 0.00 0.00 0.00 2.57
4215 5193 5.041191 CATCTAGTGCCCCTTAGTGATTT 57.959 43.478 0.00 0.00 0.00 2.17
4216 5194 5.440610 CATCTAGTGCCCCTTAGTGATTTT 58.559 41.667 0.00 0.00 0.00 1.82
4217 5195 4.843728 TCTAGTGCCCCTTAGTGATTTTG 58.156 43.478 0.00 0.00 0.00 2.44
4218 5196 2.807676 AGTGCCCCTTAGTGATTTTGG 58.192 47.619 0.00 0.00 0.00 3.28
4220 5198 2.231235 GTGCCCCTTAGTGATTTTGGTG 59.769 50.000 0.00 0.00 0.00 4.17
4221 5199 2.158385 TGCCCCTTAGTGATTTTGGTGT 60.158 45.455 0.00 0.00 0.00 4.16
4226 5329 5.949354 CCCCTTAGTGATTTTGGTGTATTGA 59.051 40.000 0.00 0.00 0.00 2.57
4233 5336 8.918202 AGTGATTTTGGTGTATTGAAGACTTA 57.082 30.769 0.00 0.00 0.00 2.24
4234 5337 9.520515 AGTGATTTTGGTGTATTGAAGACTTAT 57.479 29.630 0.00 0.00 0.00 1.73
4243 5346 9.543783 GGTGTATTGAAGACTTATAGGTTAAGG 57.456 37.037 0.00 0.00 0.00 2.69
4244 5347 9.543783 GTGTATTGAAGACTTATAGGTTAAGGG 57.456 37.037 0.00 0.00 0.00 3.95
4245 5348 9.496710 TGTATTGAAGACTTATAGGTTAAGGGA 57.503 33.333 0.00 0.00 0.00 4.20
4246 5349 9.761504 GTATTGAAGACTTATAGGTTAAGGGAC 57.238 37.037 0.00 0.00 0.00 4.46
4249 5352 9.551339 TTGAAGACTTATAGGTTAAGGGACTAA 57.449 33.333 0.00 0.00 38.49 2.24
4250 5353 9.725206 TGAAGACTTATAGGTTAAGGGACTAAT 57.275 33.333 0.00 0.00 38.49 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.165641 ACTCGTCGCTGAAATGGATGTA 59.834 45.455 0.00 0.00 0.00 2.29
1 2 1.066858 ACTCGTCGCTGAAATGGATGT 60.067 47.619 0.00 0.00 0.00 3.06
2 3 1.645034 ACTCGTCGCTGAAATGGATG 58.355 50.000 0.00 0.00 0.00 3.51
3 4 3.520290 TTACTCGTCGCTGAAATGGAT 57.480 42.857 0.00 0.00 0.00 3.41
4 5 3.520290 ATTACTCGTCGCTGAAATGGA 57.480 42.857 0.00 0.00 0.00 3.41
6 7 5.203358 TCAAATTACTCGTCGCTGAAATG 57.797 39.130 0.00 0.00 0.00 2.32
7 8 5.856126 TTCAAATTACTCGTCGCTGAAAT 57.144 34.783 0.00 0.00 0.00 2.17
8 9 5.437263 GTTTCAAATTACTCGTCGCTGAAA 58.563 37.500 0.00 0.00 0.00 2.69
9 10 4.375606 CGTTTCAAATTACTCGTCGCTGAA 60.376 41.667 0.00 0.00 0.00 3.02
10 11 3.120616 CGTTTCAAATTACTCGTCGCTGA 59.879 43.478 0.00 0.00 0.00 4.26
11 12 3.395671 CGTTTCAAATTACTCGTCGCTG 58.604 45.455 0.00 0.00 0.00 5.18
12 13 2.410730 CCGTTTCAAATTACTCGTCGCT 59.589 45.455 0.00 0.00 0.00 4.93
13 14 2.409378 TCCGTTTCAAATTACTCGTCGC 59.591 45.455 0.00 0.00 0.00 5.19
14 15 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
15 16 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
16 17 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
17 18 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
18 19 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
19 20 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
20 21 5.878669 ACATACTCCCTCCGTTTCAAATTAC 59.121 40.000 0.00 0.00 0.00 1.89
21 22 6.057321 ACATACTCCCTCCGTTTCAAATTA 57.943 37.500 0.00 0.00 0.00 1.40
22 23 4.918588 ACATACTCCCTCCGTTTCAAATT 58.081 39.130 0.00 0.00 0.00 1.82
23 24 4.569719 ACATACTCCCTCCGTTTCAAAT 57.430 40.909 0.00 0.00 0.00 2.32
24 25 4.360951 AACATACTCCCTCCGTTTCAAA 57.639 40.909 0.00 0.00 0.00 2.69
25 26 4.283978 TGTAACATACTCCCTCCGTTTCAA 59.716 41.667 0.00 0.00 0.00 2.69
26 27 3.833650 TGTAACATACTCCCTCCGTTTCA 59.166 43.478 0.00 0.00 0.00 2.69
27 28 4.460948 TGTAACATACTCCCTCCGTTTC 57.539 45.455 0.00 0.00 0.00 2.78
28 29 4.285260 AGTTGTAACATACTCCCTCCGTTT 59.715 41.667 0.00 0.00 0.00 3.60
29 30 3.836562 AGTTGTAACATACTCCCTCCGTT 59.163 43.478 0.00 0.00 0.00 4.44
30 31 3.438183 AGTTGTAACATACTCCCTCCGT 58.562 45.455 0.00 0.00 0.00 4.69
31 32 4.181578 CAAGTTGTAACATACTCCCTCCG 58.818 47.826 0.00 0.00 0.00 4.63
32 33 3.939592 GCAAGTTGTAACATACTCCCTCC 59.060 47.826 4.48 0.00 0.00 4.30
33 34 4.392138 GTGCAAGTTGTAACATACTCCCTC 59.608 45.833 4.48 0.00 0.00 4.30
34 35 4.202419 TGTGCAAGTTGTAACATACTCCCT 60.202 41.667 4.48 0.00 0.00 4.20
35 36 4.069304 TGTGCAAGTTGTAACATACTCCC 58.931 43.478 4.48 0.00 0.00 4.30
36 37 4.513692 TGTGTGCAAGTTGTAACATACTCC 59.486 41.667 14.14 4.86 0.00 3.85
37 38 5.236478 AGTGTGTGCAAGTTGTAACATACTC 59.764 40.000 24.27 14.88 0.00 2.59
38 39 5.123227 AGTGTGTGCAAGTTGTAACATACT 58.877 37.500 24.27 24.27 0.00 2.12
39 40 5.418310 AGTGTGTGCAAGTTGTAACATAC 57.582 39.130 21.87 21.87 0.00 2.39
69 77 0.322456 GCATACAGACAGTGGGCCAA 60.322 55.000 8.40 0.00 0.00 4.52
82 90 2.438868 CGAGGAATGGATCGCATACA 57.561 50.000 0.00 0.00 31.42 2.29
88 96 2.356313 CCGGCGAGGAATGGATCG 60.356 66.667 9.30 0.00 45.00 3.69
103 111 0.104120 TCCATCCAAGTGATACGCCG 59.896 55.000 0.00 0.00 30.56 6.46
151 161 4.520492 TCCAAAGAGAAAGAACAAGATGGC 59.480 41.667 0.00 0.00 0.00 4.40
176 186 0.534203 GTGCGGGAAAAGGTCACTGA 60.534 55.000 0.00 0.00 0.00 3.41
185 195 0.179124 GCAACACTTGTGCGGGAAAA 60.179 50.000 0.10 0.00 0.00 2.29
216 226 5.766150 TGTGTTTTACCTGATGAAACTGG 57.234 39.130 0.00 0.00 37.60 4.00
218 228 7.823745 AGAATGTGTTTTACCTGATGAAACT 57.176 32.000 0.00 0.00 37.60 2.66
219 229 8.134895 TGAAGAATGTGTTTTACCTGATGAAAC 58.865 33.333 0.00 0.00 37.32 2.78
220 230 8.231692 TGAAGAATGTGTTTTACCTGATGAAA 57.768 30.769 0.00 0.00 0.00 2.69
221 231 7.502226 ACTGAAGAATGTGTTTTACCTGATGAA 59.498 33.333 0.00 0.00 0.00 2.57
222 232 6.998074 ACTGAAGAATGTGTTTTACCTGATGA 59.002 34.615 0.00 0.00 0.00 2.92
223 233 7.206981 ACTGAAGAATGTGTTTTACCTGATG 57.793 36.000 0.00 0.00 0.00 3.07
224 234 7.823745 AACTGAAGAATGTGTTTTACCTGAT 57.176 32.000 0.00 0.00 0.00 2.90
225 235 7.338196 TGAAACTGAAGAATGTGTTTTACCTGA 59.662 33.333 0.00 0.00 33.49 3.86
226 236 7.479980 TGAAACTGAAGAATGTGTTTTACCTG 58.520 34.615 0.00 0.00 33.49 4.00
227 237 7.639113 TGAAACTGAAGAATGTGTTTTACCT 57.361 32.000 0.00 0.00 33.49 3.08
228 238 8.134895 TGATGAAACTGAAGAATGTGTTTTACC 58.865 33.333 0.00 0.00 33.49 2.85
229 239 9.173939 CTGATGAAACTGAAGAATGTGTTTTAC 57.826 33.333 0.00 0.00 33.49 2.01
230 240 8.352201 CCTGATGAAACTGAAGAATGTGTTTTA 58.648 33.333 0.00 0.00 33.49 1.52
231 241 7.147846 ACCTGATGAAACTGAAGAATGTGTTTT 60.148 33.333 0.00 0.00 33.49 2.43
232 242 6.322201 ACCTGATGAAACTGAAGAATGTGTTT 59.678 34.615 0.00 0.00 35.64 2.83
233 243 5.829924 ACCTGATGAAACTGAAGAATGTGTT 59.170 36.000 0.00 0.00 0.00 3.32
234 244 5.380043 ACCTGATGAAACTGAAGAATGTGT 58.620 37.500 0.00 0.00 0.00 3.72
235 245 5.954296 ACCTGATGAAACTGAAGAATGTG 57.046 39.130 0.00 0.00 0.00 3.21
236 246 6.998074 TGTTACCTGATGAAACTGAAGAATGT 59.002 34.615 0.00 0.00 0.00 2.71
237 247 7.041167 TGTGTTACCTGATGAAACTGAAGAATG 60.041 37.037 0.00 0.00 0.00 2.67
238 248 6.998074 TGTGTTACCTGATGAAACTGAAGAAT 59.002 34.615 0.00 0.00 0.00 2.40
239 249 6.260050 GTGTGTTACCTGATGAAACTGAAGAA 59.740 38.462 0.00 0.00 0.00 2.52
240 250 5.758296 GTGTGTTACCTGATGAAACTGAAGA 59.242 40.000 0.00 0.00 0.00 2.87
241 251 5.760253 AGTGTGTTACCTGATGAAACTGAAG 59.240 40.000 0.00 0.00 0.00 3.02
242 252 5.680619 AGTGTGTTACCTGATGAAACTGAA 58.319 37.500 0.00 0.00 0.00 3.02
243 253 5.290493 AGTGTGTTACCTGATGAAACTGA 57.710 39.130 0.00 0.00 0.00 3.41
244 254 6.260936 AGAAAGTGTGTTACCTGATGAAACTG 59.739 38.462 0.00 0.00 0.00 3.16
245 255 6.357367 AGAAAGTGTGTTACCTGATGAAACT 58.643 36.000 0.00 0.00 0.00 2.66
246 256 6.619801 AGAAAGTGTGTTACCTGATGAAAC 57.380 37.500 0.00 0.00 0.00 2.78
247 257 8.740123 TTAAGAAAGTGTGTTACCTGATGAAA 57.260 30.769 0.00 0.00 0.00 2.69
248 258 7.990886 ACTTAAGAAAGTGTGTTACCTGATGAA 59.009 33.333 10.09 0.00 44.40 2.57
249 259 7.506114 ACTTAAGAAAGTGTGTTACCTGATGA 58.494 34.615 10.09 0.00 44.40 2.92
250 260 7.730364 ACTTAAGAAAGTGTGTTACCTGATG 57.270 36.000 10.09 0.00 44.40 3.07
251 261 8.747538 AAACTTAAGAAAGTGTGTTACCTGAT 57.252 30.769 10.09 0.00 45.37 2.90
252 262 7.825270 TGAAACTTAAGAAAGTGTGTTACCTGA 59.175 33.333 10.09 0.00 45.37 3.86
253 263 7.981142 TGAAACTTAAGAAAGTGTGTTACCTG 58.019 34.615 10.09 0.00 45.37 4.00
254 264 8.747538 ATGAAACTTAAGAAAGTGTGTTACCT 57.252 30.769 10.09 0.00 45.37 3.08
255 265 8.617809 TGATGAAACTTAAGAAAGTGTGTTACC 58.382 33.333 10.09 0.00 45.37 2.85
256 266 9.997482 TTGATGAAACTTAAGAAAGTGTGTTAC 57.003 29.630 10.09 0.00 45.37 2.50
261 271 9.899226 GCTAATTGATGAAACTTAAGAAAGTGT 57.101 29.630 10.09 0.00 45.37 3.55
262 272 9.897744 TGCTAATTGATGAAACTTAAGAAAGTG 57.102 29.630 10.09 0.00 45.37 3.16
264 274 9.346725 GGTGCTAATTGATGAAACTTAAGAAAG 57.653 33.333 10.09 0.00 38.77 2.62
265 275 9.077885 AGGTGCTAATTGATGAAACTTAAGAAA 57.922 29.630 10.09 0.00 0.00 2.52
266 276 8.635765 AGGTGCTAATTGATGAAACTTAAGAA 57.364 30.769 10.09 0.00 0.00 2.52
267 277 8.514594 CAAGGTGCTAATTGATGAAACTTAAGA 58.485 33.333 10.09 0.00 0.00 2.10
268 278 8.514594 TCAAGGTGCTAATTGATGAAACTTAAG 58.485 33.333 0.00 0.00 30.67 1.85
269 279 8.402798 TCAAGGTGCTAATTGATGAAACTTAA 57.597 30.769 0.00 0.00 30.67 1.85
270 280 7.665559 ACTCAAGGTGCTAATTGATGAAACTTA 59.334 33.333 0.00 0.00 35.04 2.24
271 281 6.491403 ACTCAAGGTGCTAATTGATGAAACTT 59.509 34.615 0.00 0.00 35.04 2.66
297 307 9.912634 CAACAAATAATAAGAAAAGGAGAGCAA 57.087 29.630 0.00 0.00 0.00 3.91
304 314 7.887996 TGCAGCAACAAATAATAAGAAAAGG 57.112 32.000 0.00 0.00 0.00 3.11
324 335 1.317431 TGCCAAGGCTAAGCATGCAG 61.317 55.000 21.98 10.76 42.51 4.41
329 340 0.680921 GACCATGCCAAGGCTAAGCA 60.681 55.000 12.96 13.05 42.51 3.91
362 373 2.887568 CCGGATGCAGCGACACTC 60.888 66.667 0.00 0.00 0.00 3.51
378 389 5.061179 ACATACTGATAATTGTAACGCCCC 58.939 41.667 0.00 0.00 0.00 5.80
382 393 7.345192 GCTTGGACATACTGATAATTGTAACG 58.655 38.462 0.00 0.00 0.00 3.18
396 407 3.747193 CAAATCACACGCTTGGACATAC 58.253 45.455 0.00 0.00 0.00 2.39
426 437 2.997986 ACAACACAATACCGTTCGATCC 59.002 45.455 0.00 0.00 0.00 3.36
456 467 2.811431 CGGGACAATTGCACACTTAGAA 59.189 45.455 5.05 0.00 0.00 2.10
457 468 2.037902 TCGGGACAATTGCACACTTAGA 59.962 45.455 5.05 0.00 0.00 2.10
458 469 2.416547 CTCGGGACAATTGCACACTTAG 59.583 50.000 5.05 0.00 0.00 2.18
459 470 2.037902 TCTCGGGACAATTGCACACTTA 59.962 45.455 5.05 0.00 0.00 2.24
461 472 0.396435 TCTCGGGACAATTGCACACT 59.604 50.000 5.05 0.00 0.00 3.55
462 473 1.131126 CATCTCGGGACAATTGCACAC 59.869 52.381 5.05 0.10 0.00 3.82
463 474 1.452110 CATCTCGGGACAATTGCACA 58.548 50.000 5.05 0.00 0.00 4.57
464 475 0.099436 GCATCTCGGGACAATTGCAC 59.901 55.000 5.05 0.00 0.00 4.57
465 476 0.322366 TGCATCTCGGGACAATTGCA 60.322 50.000 7.20 7.20 37.73 4.08
466 477 0.099436 GTGCATCTCGGGACAATTGC 59.901 55.000 5.05 1.54 0.00 3.56
468 479 1.278985 TCAGTGCATCTCGGGACAATT 59.721 47.619 0.00 0.00 0.00 2.32
475 486 2.503061 CCCCTCAGTGCATCTCGG 59.497 66.667 0.00 0.00 0.00 4.63
477 488 0.761187 TATGCCCCTCAGTGCATCTC 59.239 55.000 2.33 0.00 44.58 2.75
478 489 0.471617 GTATGCCCCTCAGTGCATCT 59.528 55.000 2.33 0.00 44.58 2.90
485 496 1.099879 GCAGCTTGTATGCCCCTCAG 61.100 60.000 0.00 0.00 37.73 3.35
488 499 1.379044 GTGCAGCTTGTATGCCCCT 60.379 57.895 0.00 0.00 43.18 4.79
489 500 0.967380 AAGTGCAGCTTGTATGCCCC 60.967 55.000 0.00 0.00 43.18 5.80
490 501 0.453390 GAAGTGCAGCTTGTATGCCC 59.547 55.000 6.31 0.00 43.18 5.36
493 504 3.120060 GGTTGAGAAGTGCAGCTTGTATG 60.120 47.826 6.31 0.00 37.59 2.39
494 505 3.077359 GGTTGAGAAGTGCAGCTTGTAT 58.923 45.455 6.31 0.00 37.59 2.29
498 509 2.157738 GATGGTTGAGAAGTGCAGCTT 58.842 47.619 0.00 0.00 40.76 3.74
500 511 1.527034 TGATGGTTGAGAAGTGCAGC 58.473 50.000 0.00 0.00 0.00 5.25
532 543 2.803155 TAGCTCCGCCAGTGCAAAGG 62.803 60.000 0.00 1.35 37.44 3.11
533 544 1.364626 CTAGCTCCGCCAGTGCAAAG 61.365 60.000 0.00 0.00 37.44 2.77
583 594 4.952102 TTTGCCTTGCCCCACCCC 62.952 66.667 0.00 0.00 0.00 4.95
584 595 1.778017 ATTTTTGCCTTGCCCCACCC 61.778 55.000 0.00 0.00 0.00 4.61
585 596 0.980423 TATTTTTGCCTTGCCCCACC 59.020 50.000 0.00 0.00 0.00 4.61
586 597 2.235898 TCATATTTTTGCCTTGCCCCAC 59.764 45.455 0.00 0.00 0.00 4.61
587 598 2.500910 CTCATATTTTTGCCTTGCCCCA 59.499 45.455 0.00 0.00 0.00 4.96
588 599 2.501316 ACTCATATTTTTGCCTTGCCCC 59.499 45.455 0.00 0.00 0.00 5.80
589 600 3.055891 ACACTCATATTTTTGCCTTGCCC 60.056 43.478 0.00 0.00 0.00 5.36
590 601 4.192429 ACACTCATATTTTTGCCTTGCC 57.808 40.909 0.00 0.00 0.00 4.52
591 602 5.106987 CCAAACACTCATATTTTTGCCTTGC 60.107 40.000 0.00 0.00 0.00 4.01
592 603 5.409214 CCCAAACACTCATATTTTTGCCTTG 59.591 40.000 0.00 0.00 0.00 3.61
593 604 5.306678 TCCCAAACACTCATATTTTTGCCTT 59.693 36.000 0.00 0.00 0.00 4.35
594 605 4.837860 TCCCAAACACTCATATTTTTGCCT 59.162 37.500 0.00 0.00 0.00 4.75
595 606 5.146010 TCCCAAACACTCATATTTTTGCC 57.854 39.130 0.00 0.00 0.00 4.52
596 607 5.634859 CACTCCCAAACACTCATATTTTTGC 59.365 40.000 0.00 0.00 0.00 3.68
597 608 5.634859 GCACTCCCAAACACTCATATTTTTG 59.365 40.000 0.00 0.00 0.00 2.44
598 609 5.304101 TGCACTCCCAAACACTCATATTTTT 59.696 36.000 0.00 0.00 0.00 1.94
599 610 4.832266 TGCACTCCCAAACACTCATATTTT 59.168 37.500 0.00 0.00 0.00 1.82
600 611 4.406456 TGCACTCCCAAACACTCATATTT 58.594 39.130 0.00 0.00 0.00 1.40
601 612 4.032960 TGCACTCCCAAACACTCATATT 57.967 40.909 0.00 0.00 0.00 1.28
602 613 3.719268 TGCACTCCCAAACACTCATAT 57.281 42.857 0.00 0.00 0.00 1.78
603 614 3.500448 TTGCACTCCCAAACACTCATA 57.500 42.857 0.00 0.00 0.00 2.15
604 615 2.363306 TTGCACTCCCAAACACTCAT 57.637 45.000 0.00 0.00 0.00 2.90
605 616 2.136298 TTTGCACTCCCAAACACTCA 57.864 45.000 0.00 0.00 30.28 3.41
606 617 3.383761 CATTTTGCACTCCCAAACACTC 58.616 45.455 0.00 0.00 34.68 3.51
607 618 2.483538 GCATTTTGCACTCCCAAACACT 60.484 45.455 0.00 0.00 44.26 3.55
608 619 1.866601 GCATTTTGCACTCCCAAACAC 59.133 47.619 0.00 0.00 44.26 3.32
609 620 2.237393 GCATTTTGCACTCCCAAACA 57.763 45.000 0.00 0.00 44.26 2.83
623 634 7.192232 GCTTCGATGAGATTCTTTTAGCATTT 58.808 34.615 1.89 0.00 0.00 2.32
644 655 5.204292 AGAAATATTTTGAGGGAGGGCTTC 58.796 41.667 1.43 0.00 0.00 3.86
648 659 6.096001 CAGTGAAGAAATATTTTGAGGGAGGG 59.904 42.308 1.43 0.00 0.00 4.30
650 943 6.376581 AGCAGTGAAGAAATATTTTGAGGGAG 59.623 38.462 1.43 0.00 0.00 4.30
656 949 8.084073 TCAAAGGAGCAGTGAAGAAATATTTTG 58.916 33.333 1.43 0.00 0.00 2.44
657 950 8.181904 TCAAAGGAGCAGTGAAGAAATATTTT 57.818 30.769 1.43 0.00 0.00 1.82
661 954 6.942005 TGAATCAAAGGAGCAGTGAAGAAATA 59.058 34.615 0.00 0.00 0.00 1.40
750 1464 5.575606 CGAGAAAACTTCTAATTACCGCTCA 59.424 40.000 0.00 0.00 40.87 4.26
751 1465 5.005490 CCGAGAAAACTTCTAATTACCGCTC 59.995 44.000 0.00 0.00 40.87 5.03
753 1467 4.866486 TCCGAGAAAACTTCTAATTACCGC 59.134 41.667 0.00 0.00 40.87 5.68
754 1468 6.956299 TTCCGAGAAAACTTCTAATTACCG 57.044 37.500 0.00 0.00 40.87 4.02
757 1471 9.509956 TTCCATTTCCGAGAAAACTTCTAATTA 57.490 29.630 3.67 0.00 40.87 1.40
807 1521 3.193691 TCGGGAGTTGCTCAAAACAAAAA 59.806 39.130 0.00 0.00 32.21 1.94
808 1522 2.755655 TCGGGAGTTGCTCAAAACAAAA 59.244 40.909 0.00 0.00 32.21 2.44
809 1523 2.370349 TCGGGAGTTGCTCAAAACAAA 58.630 42.857 0.00 0.00 32.21 2.83
810 1524 2.045561 TCGGGAGTTGCTCAAAACAA 57.954 45.000 0.00 0.00 32.21 2.83
811 1525 2.151202 GATCGGGAGTTGCTCAAAACA 58.849 47.619 0.00 0.00 32.21 2.83
812 1526 1.468914 GGATCGGGAGTTGCTCAAAAC 59.531 52.381 0.00 0.00 31.08 2.43
813 1527 1.073125 TGGATCGGGAGTTGCTCAAAA 59.927 47.619 0.00 0.00 31.08 2.44
814 1528 0.690192 TGGATCGGGAGTTGCTCAAA 59.310 50.000 0.00 0.00 31.08 2.69
815 1529 0.690192 TTGGATCGGGAGTTGCTCAA 59.310 50.000 0.00 0.00 31.08 3.02
816 1530 0.036388 GTTGGATCGGGAGTTGCTCA 60.036 55.000 0.00 0.00 31.08 4.26
817 1531 0.250513 AGTTGGATCGGGAGTTGCTC 59.749 55.000 0.00 0.00 0.00 4.26
818 1532 1.568504 TAGTTGGATCGGGAGTTGCT 58.431 50.000 0.00 0.00 0.00 3.91
819 1533 2.396590 TTAGTTGGATCGGGAGTTGC 57.603 50.000 0.00 0.00 0.00 4.17
820 1534 5.057149 CCTATTTAGTTGGATCGGGAGTTG 58.943 45.833 0.00 0.00 0.00 3.16
821 1535 4.966805 TCCTATTTAGTTGGATCGGGAGTT 59.033 41.667 0.00 0.00 0.00 3.01
888 1602 2.985896 TGAGGCGGTCCTATTTCAAAG 58.014 47.619 0.00 0.00 44.46 2.77
891 1605 1.209504 CCTTGAGGCGGTCCTATTTCA 59.790 52.381 0.00 0.00 44.46 2.69
892 1606 1.954927 CCTTGAGGCGGTCCTATTTC 58.045 55.000 0.00 0.00 44.46 2.17
1193 1907 0.748005 GGAACCGTACCTGCATGCAT 60.748 55.000 22.97 10.26 0.00 3.96
1261 1991 3.392882 GGCCTCAAACAATCAAACCAAG 58.607 45.455 0.00 0.00 0.00 3.61
1319 2049 1.733526 GAATCCCCGCCCAATTTCG 59.266 57.895 0.00 0.00 0.00 3.46
1384 2127 2.044123 ATTTCCTTCCGCCTCATGAC 57.956 50.000 0.00 0.00 0.00 3.06
1496 2241 2.159028 CCTTACCAGAGCTTACTCCTGC 60.159 54.545 0.00 0.00 44.65 4.85
2689 3560 9.676195 CATAATGAAGTCAACAACATACAACAA 57.324 29.630 0.00 0.00 0.00 2.83
2690 3561 9.061435 TCATAATGAAGTCAACAACATACAACA 57.939 29.630 0.00 0.00 0.00 3.33
2691 3562 9.546909 CTCATAATGAAGTCAACAACATACAAC 57.453 33.333 0.00 0.00 0.00 3.32
4193 5171 4.696479 AATCACTAAGGGGCACTAGATG 57.304 45.455 0.00 0.00 0.00 2.90
4194 5172 5.440610 CAAAATCACTAAGGGGCACTAGAT 58.559 41.667 0.00 0.00 0.00 1.98
4195 5173 4.324254 CCAAAATCACTAAGGGGCACTAGA 60.324 45.833 0.00 0.00 0.00 2.43
4196 5174 3.947834 CCAAAATCACTAAGGGGCACTAG 59.052 47.826 0.00 0.00 0.00 2.57
4197 5175 3.332485 ACCAAAATCACTAAGGGGCACTA 59.668 43.478 0.00 0.00 0.00 2.74
4198 5176 2.110011 ACCAAAATCACTAAGGGGCACT 59.890 45.455 0.00 0.00 0.00 4.40
4199 5177 2.231235 CACCAAAATCACTAAGGGGCAC 59.769 50.000 0.00 0.00 0.00 5.01
4200 5178 2.158385 ACACCAAAATCACTAAGGGGCA 60.158 45.455 0.00 0.00 0.00 5.36
4201 5179 2.525368 ACACCAAAATCACTAAGGGGC 58.475 47.619 0.00 0.00 0.00 5.80
4202 5180 5.949354 TCAATACACCAAAATCACTAAGGGG 59.051 40.000 0.00 0.00 0.00 4.79
4203 5181 7.393234 TCTTCAATACACCAAAATCACTAAGGG 59.607 37.037 0.00 0.00 0.00 3.95
4204 5182 8.237267 GTCTTCAATACACCAAAATCACTAAGG 58.763 37.037 0.00 0.00 0.00 2.69
4205 5183 9.003658 AGTCTTCAATACACCAAAATCACTAAG 57.996 33.333 0.00 0.00 0.00 2.18
4206 5184 8.918202 AGTCTTCAATACACCAAAATCACTAA 57.082 30.769 0.00 0.00 0.00 2.24
4207 5185 8.918202 AAGTCTTCAATACACCAAAATCACTA 57.082 30.769 0.00 0.00 0.00 2.74
4208 5186 7.823745 AAGTCTTCAATACACCAAAATCACT 57.176 32.000 0.00 0.00 0.00 3.41
4212 5190 9.975218 ACCTATAAGTCTTCAATACACCAAAAT 57.025 29.630 0.00 0.00 0.00 1.82
4217 5195 9.543783 CCTTAACCTATAAGTCTTCAATACACC 57.456 37.037 0.00 0.00 0.00 4.16
4218 5196 9.543783 CCCTTAACCTATAAGTCTTCAATACAC 57.456 37.037 0.00 0.00 0.00 2.90
4220 5198 9.761504 GTCCCTTAACCTATAAGTCTTCAATAC 57.238 37.037 0.00 0.00 0.00 1.89
4221 5199 9.725206 AGTCCCTTAACCTATAAGTCTTCAATA 57.275 33.333 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.