Multiple sequence alignment - TraesCS7A01G433300

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 TraesCS7A01G433300 chr7A 100.000 3407 0 0 1 3407 626955148 626958554 0.000000e+00 6292
1 TraesCS7A01G433300 chr7A 97.297 1073 29 0 1338 2410 670889856 670888784 0.000000e+00 1821
2 TraesCS7A01G433300 chr7A 91.273 1100 47 24 259 1342 670905225 670904159 0.000000e+00 1454
3 TraesCS7A01G433300 chr7A 93.902 164 9 1 17 179 670905386 670905223 2.630000e-61 246
4 TraesCS7A01G433300 chr7B 93.695 3172 150 31 261 3407 643128948 643125802 0.000000e+00 4704
5 TraesCS7A01G433300 chr7B 91.411 163 12 2 17 177 643129112 643128950 4.430000e-54 222
6 TraesCS7A01G433300 chr2D 86.232 1627 185 25 792 2398 17830197 17831804 0.000000e+00 1727
7 TraesCS7A01G433300 chr2D 85.268 1663 199 31 792 2430 17954809 17956449 0.000000e+00 1672
8 TraesCS7A01G433300 chr2D 81.287 1010 163 21 1171 2165 18185835 18186833 0.000000e+00 795
9 TraesCS7A01G433300 chr2D 75.212 827 174 24 1077 1886 620399290 620398478 2.500000e-96 363
10 TraesCS7A01G433300 chr2D 91.509 212 17 1 533 743 17954450 17954661 1.200000e-74 291
11 TraesCS7A01G433300 chr2D 81.690 213 20 8 548 743 17829839 17830049 3.520000e-35 159
12 TraesCS7A01G433300 chr2A 85.766 1665 191 30 792 2430 19124831 19126475 0.000000e+00 1720
13 TraesCS7A01G433300 chr2A 81.006 179 16 6 582 743 19124523 19124700 3.570000e-25 126
14 TraesCS7A01G433300 chr2B 83.787 1653 233 25 792 2430 508737368 508738999 0.000000e+00 1535
15 TraesCS7A01G433300 chr2B 88.832 788 54 10 795 1562 29141694 29140921 0.000000e+00 937
16 TraesCS7A01G433300 chr6D 83.734 1082 150 20 1340 2408 395370786 395369718 0.000000e+00 1000
17 TraesCS7A01G433300 chr6D 93.732 351 22 0 997 1347 395371488 395371138 8.370000e-146 527
18 TraesCS7A01G433300 chr6D 91.787 207 10 3 792 998 395374868 395374669 7.200000e-72 281
19 TraesCS7A01G433300 chr6D 88.298 188 20 2 557 743 395375202 395375016 1.230000e-54 224
20 TraesCS7A01G433300 chr6D 94.118 85 4 1 177 260 48464503 48464587 9.920000e-26 128
21 TraesCS7A01G433300 chr3A 89.831 177 8 3 3 178 574312282 574312449 5.720000e-53 219
22 TraesCS7A01G433300 chr3B 91.411 163 6 4 17 178 43340333 43340488 2.060000e-52 217
23 TraesCS7A01G433300 chr5A 91.954 87 6 1 175 260 622203850 622203936 1.660000e-23 121
24 TraesCS7A01G433300 chr5B 91.765 85 6 1 177 260 462138986 462139070 2.150000e-22 117
25 TraesCS7A01G433300 chr5B 88.172 93 10 1 177 268 13704962 13704870 3.590000e-20 110
26 TraesCS7A01G433300 chr1B 90.698 86 8 0 175 260 53802225 53802310 7.730000e-22 115
27 TraesCS7A01G433300 chr7D 89.412 85 8 1 177 260 602187324 602187240 4.650000e-19 106
28 TraesCS7A01G433300 chr3D 88.636 88 8 2 169 254 504069142 504069055 4.650000e-19 106
29 TraesCS7A01G433300 chr1A 89.286 84 9 0 177 260 513118186 513118103 4.650000e-19 106
30 TraesCS7A01G433300 chr5D 85.714 98 8 5 175 271 463131404 463131312 7.780000e-17 99


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 TraesCS7A01G433300 chr7A 626955148 626958554 3406 False 6292.0 6292 100.00000 1 3407 1 chr7A.!!$F1 3406
1 TraesCS7A01G433300 chr7A 670888784 670889856 1072 True 1821.0 1821 97.29700 1338 2410 1 chr7A.!!$R1 1072
2 TraesCS7A01G433300 chr7A 670904159 670905386 1227 True 850.0 1454 92.58750 17 1342 2 chr7A.!!$R2 1325
3 TraesCS7A01G433300 chr7B 643125802 643129112 3310 True 2463.0 4704 92.55300 17 3407 2 chr7B.!!$R1 3390
4 TraesCS7A01G433300 chr2D 17954450 17956449 1999 False 981.5 1672 88.38850 533 2430 2 chr2D.!!$F3 1897
5 TraesCS7A01G433300 chr2D 17829839 17831804 1965 False 943.0 1727 83.96100 548 2398 2 chr2D.!!$F2 1850
6 TraesCS7A01G433300 chr2D 18185835 18186833 998 False 795.0 795 81.28700 1171 2165 1 chr2D.!!$F1 994
7 TraesCS7A01G433300 chr2D 620398478 620399290 812 True 363.0 363 75.21200 1077 1886 1 chr2D.!!$R1 809
8 TraesCS7A01G433300 chr2A 19124523 19126475 1952 False 923.0 1720 83.38600 582 2430 2 chr2A.!!$F1 1848
9 TraesCS7A01G433300 chr2B 508737368 508738999 1631 False 1535.0 1535 83.78700 792 2430 1 chr2B.!!$F1 1638
10 TraesCS7A01G433300 chr2B 29140921 29141694 773 True 937.0 937 88.83200 795 1562 1 chr2B.!!$R1 767
11 TraesCS7A01G433300 chr6D 395369718 395375202 5484 True 508.0 1000 89.38775 557 2408 4 chr6D.!!$R1 1851

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
440 447 0.112995 TGAGAGCAAAATGGGCCAGT 59.887 50.0 13.78 6.48 0.00 4.00 F
442 449 0.407139 AGAGCAAAATGGGCCAGTCT 59.593 50.0 13.78 2.23 0.00 3.24 F
937 1119 0.678048 ATCAGTTTGGCCGAAGCTCC 60.678 55.0 5.37 0.00 39.73 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1363 5098 0.399454 AGGCATGCAACACTCTCACT 59.601 50.000 21.36 0.0 0.00 3.41 R
1525 5260 1.280421 AGGGAGAGCAATCTGTTCACC 59.720 52.381 0.00 0.0 37.55 4.02 R
2476 6228 0.458025 GCCACGCACAGTCCTAGTAC 60.458 60.000 0.00 0.0 0.00 2.73 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
44 45 0.671472 TGCATGTGACTGAGCCTTCG 60.671 55.000 0.00 0.00 0.00 3.79
83 84 8.799367 GTGTTGGACCCAATTAAGTAAACTAAT 58.201 33.333 4.63 0.00 38.28 1.73
178 181 7.681939 TTTTATTGAGGTTCATGTCCACTAC 57.318 36.000 11.03 0.00 0.00 2.73
179 182 6.620877 TTATTGAGGTTCATGTCCACTACT 57.379 37.500 11.03 0.00 0.00 2.57
180 183 4.537135 TTGAGGTTCATGTCCACTACTC 57.463 45.455 11.03 0.00 0.00 2.59
181 184 2.832129 TGAGGTTCATGTCCACTACTCC 59.168 50.000 11.03 0.00 0.00 3.85
182 185 2.168728 GAGGTTCATGTCCACTACTCCC 59.831 54.545 11.03 0.00 0.00 4.30
183 186 2.188817 GGTTCATGTCCACTACTCCCT 58.811 52.381 0.00 0.00 0.00 4.20
184 187 2.168728 GGTTCATGTCCACTACTCCCTC 59.831 54.545 0.00 0.00 0.00 4.30
185 188 3.100671 GTTCATGTCCACTACTCCCTCT 58.899 50.000 0.00 0.00 0.00 3.69
186 189 2.739943 TCATGTCCACTACTCCCTCTG 58.260 52.381 0.00 0.00 0.00 3.35
187 190 2.043115 TCATGTCCACTACTCCCTCTGT 59.957 50.000 0.00 0.00 0.00 3.41
188 191 3.268595 TCATGTCCACTACTCCCTCTGTA 59.731 47.826 0.00 0.00 0.00 2.74
189 192 3.083122 TGTCCACTACTCCCTCTGTAC 57.917 52.381 0.00 0.00 0.00 2.90
190 193 2.291411 TGTCCACTACTCCCTCTGTACC 60.291 54.545 0.00 0.00 0.00 3.34
191 194 1.997791 TCCACTACTCCCTCTGTACCA 59.002 52.381 0.00 0.00 0.00 3.25
192 195 2.380932 TCCACTACTCCCTCTGTACCAA 59.619 50.000 0.00 0.00 0.00 3.67
193 196 3.170717 CCACTACTCCCTCTGTACCAAA 58.829 50.000 0.00 0.00 0.00 3.28
194 197 3.581332 CCACTACTCCCTCTGTACCAAAA 59.419 47.826 0.00 0.00 0.00 2.44
195 198 4.225267 CCACTACTCCCTCTGTACCAAAAT 59.775 45.833 0.00 0.00 0.00 1.82
196 199 5.424252 CCACTACTCCCTCTGTACCAAAATA 59.576 44.000 0.00 0.00 0.00 1.40
197 200 6.338937 CACTACTCCCTCTGTACCAAAATAC 58.661 44.000 0.00 0.00 0.00 1.89
198 201 6.154706 CACTACTCCCTCTGTACCAAAATACT 59.845 42.308 0.00 0.00 0.00 2.12
199 202 6.729569 ACTACTCCCTCTGTACCAAAATACTT 59.270 38.462 0.00 0.00 0.00 2.24
200 203 5.805728 ACTCCCTCTGTACCAAAATACTTG 58.194 41.667 0.00 0.00 0.00 3.16
201 204 5.309806 ACTCCCTCTGTACCAAAATACTTGT 59.690 40.000 0.00 0.00 0.00 3.16
202 205 6.499350 ACTCCCTCTGTACCAAAATACTTGTA 59.501 38.462 0.00 0.00 0.00 2.41
203 206 6.942976 TCCCTCTGTACCAAAATACTTGTAG 58.057 40.000 0.00 0.00 0.00 2.74
204 207 6.499350 TCCCTCTGTACCAAAATACTTGTAGT 59.501 38.462 0.00 0.00 0.00 2.73
205 208 7.016858 TCCCTCTGTACCAAAATACTTGTAGTT 59.983 37.037 0.00 0.00 0.00 2.24
206 209 7.119262 CCCTCTGTACCAAAATACTTGTAGTTG 59.881 40.741 0.00 0.00 0.00 3.16
207 210 7.119262 CCTCTGTACCAAAATACTTGTAGTTGG 59.881 40.741 17.42 17.42 43.60 3.77
208 211 6.938030 TCTGTACCAAAATACTTGTAGTTGGG 59.062 38.462 20.55 16.74 42.52 4.12
209 212 6.005198 TGTACCAAAATACTTGTAGTTGGGG 58.995 40.000 20.55 15.16 42.52 4.96
210 213 5.327737 ACCAAAATACTTGTAGTTGGGGA 57.672 39.130 20.55 0.00 42.52 4.81
211 214 5.707495 ACCAAAATACTTGTAGTTGGGGAA 58.293 37.500 20.55 0.00 42.52 3.97
212 215 6.137559 ACCAAAATACTTGTAGTTGGGGAAA 58.862 36.000 20.55 0.00 42.52 3.13
213 216 6.041182 ACCAAAATACTTGTAGTTGGGGAAAC 59.959 38.462 20.55 0.00 42.52 2.78
225 228 5.936686 GTTGGGGAAACTAGTACAAGTTC 57.063 43.478 0.00 0.00 38.76 3.01
226 229 4.628963 TGGGGAAACTAGTACAAGTTCC 57.371 45.455 12.95 12.95 38.76 3.62
227 230 3.328637 TGGGGAAACTAGTACAAGTTCCC 59.671 47.826 25.26 25.26 41.07 3.97
228 231 3.586174 GGGGAAACTAGTACAAGTTCCCT 59.414 47.826 29.13 0.00 41.59 4.20
229 232 4.323333 GGGGAAACTAGTACAAGTTCCCTC 60.323 50.000 29.13 20.26 41.59 4.30
230 233 4.285260 GGGAAACTAGTACAAGTTCCCTCA 59.715 45.833 25.69 0.00 40.27 3.86
231 234 5.221783 GGGAAACTAGTACAAGTTCCCTCAA 60.222 44.000 25.69 0.00 40.27 3.02
232 235 5.699915 GGAAACTAGTACAAGTTCCCTCAAC 59.300 44.000 10.93 0.00 38.76 3.18
234 237 7.256083 GGAAACTAGTACAAGTTCCCTCAACTA 60.256 40.741 10.93 0.00 45.32 2.24
235 238 6.587206 ACTAGTACAAGTTCCCTCAACTAC 57.413 41.667 0.00 0.00 45.32 2.73
236 239 6.073314 ACTAGTACAAGTTCCCTCAACTACA 58.927 40.000 0.00 0.00 45.32 2.74
237 240 5.881923 AGTACAAGTTCCCTCAACTACAA 57.118 39.130 0.00 0.00 45.32 2.41
238 241 5.855045 AGTACAAGTTCCCTCAACTACAAG 58.145 41.667 0.00 0.00 45.32 3.16
239 242 4.772886 ACAAGTTCCCTCAACTACAAGT 57.227 40.909 0.00 0.00 45.32 3.16
240 243 5.881923 ACAAGTTCCCTCAACTACAAGTA 57.118 39.130 0.00 0.00 45.32 2.24
241 244 6.435292 ACAAGTTCCCTCAACTACAAGTAT 57.565 37.500 0.00 0.00 45.32 2.12
242 245 6.838382 ACAAGTTCCCTCAACTACAAGTATT 58.162 36.000 0.00 0.00 45.32 1.89
243 246 7.287810 ACAAGTTCCCTCAACTACAAGTATTT 58.712 34.615 0.00 0.00 45.32 1.40
244 247 7.444487 ACAAGTTCCCTCAACTACAAGTATTTC 59.556 37.037 0.00 0.00 45.32 2.17
245 248 6.164176 AGTTCCCTCAACTACAAGTATTTCG 58.836 40.000 0.00 0.00 44.13 3.46
246 249 5.080969 TCCCTCAACTACAAGTATTTCGG 57.919 43.478 0.00 0.00 0.00 4.30
247 250 4.529377 TCCCTCAACTACAAGTATTTCGGT 59.471 41.667 0.00 0.00 0.00 4.69
248 251 5.716228 TCCCTCAACTACAAGTATTTCGGTA 59.284 40.000 0.00 0.00 0.00 4.02
249 252 5.809051 CCCTCAACTACAAGTATTTCGGTAC 59.191 44.000 0.00 0.00 0.00 3.34
250 253 6.392354 CCTCAACTACAAGTATTTCGGTACA 58.608 40.000 0.00 0.00 0.00 2.90
251 254 7.039882 CCTCAACTACAAGTATTTCGGTACAT 58.960 38.462 0.00 0.00 0.00 2.29
252 255 8.192774 CCTCAACTACAAGTATTTCGGTACATA 58.807 37.037 0.00 0.00 0.00 2.29
253 256 9.234384 CTCAACTACAAGTATTTCGGTACATAG 57.766 37.037 0.00 0.00 0.00 2.23
254 257 8.742777 TCAACTACAAGTATTTCGGTACATAGT 58.257 33.333 0.00 0.00 0.00 2.12
255 258 8.804743 CAACTACAAGTATTTCGGTACATAGTG 58.195 37.037 0.00 0.00 0.00 2.74
256 259 8.284945 ACTACAAGTATTTCGGTACATAGTGA 57.715 34.615 0.00 0.00 0.00 3.41
257 260 8.404000 ACTACAAGTATTTCGGTACATAGTGAG 58.596 37.037 0.00 0.00 0.00 3.51
335 338 9.847224 TTTACAGTCCTTTGAAGAGTAGAATTT 57.153 29.630 0.00 0.00 0.00 1.82
336 339 7.736447 ACAGTCCTTTGAAGAGTAGAATTTG 57.264 36.000 0.00 0.00 0.00 2.32
429 436 2.530151 AGGGGCCTGTGAGAGCAA 60.530 61.111 0.84 0.00 0.00 3.91
430 437 2.156098 AGGGGCCTGTGAGAGCAAA 61.156 57.895 0.84 0.00 0.00 3.68
434 441 0.529378 GGCCTGTGAGAGCAAAATGG 59.471 55.000 0.00 0.00 0.00 3.16
435 442 0.529378 GCCTGTGAGAGCAAAATGGG 59.471 55.000 0.00 0.00 0.00 4.00
436 443 0.529378 CCTGTGAGAGCAAAATGGGC 59.471 55.000 0.00 0.00 0.00 5.36
437 444 0.529378 CTGTGAGAGCAAAATGGGCC 59.471 55.000 0.00 0.00 0.00 5.80
438 445 0.178967 TGTGAGAGCAAAATGGGCCA 60.179 50.000 9.61 9.61 0.00 5.36
439 446 0.529378 GTGAGAGCAAAATGGGCCAG 59.471 55.000 13.78 0.00 0.00 4.85
440 447 0.112995 TGAGAGCAAAATGGGCCAGT 59.887 50.000 13.78 6.48 0.00 4.00
441 448 0.813821 GAGAGCAAAATGGGCCAGTC 59.186 55.000 13.78 0.00 0.00 3.51
442 449 0.407139 AGAGCAAAATGGGCCAGTCT 59.593 50.000 13.78 2.23 0.00 3.24
443 450 1.635487 AGAGCAAAATGGGCCAGTCTA 59.365 47.619 13.78 0.00 0.00 2.59
444 451 1.745653 GAGCAAAATGGGCCAGTCTAC 59.254 52.381 13.78 1.85 0.00 2.59
445 452 1.075374 AGCAAAATGGGCCAGTCTACA 59.925 47.619 13.78 0.00 0.00 2.74
446 453 1.474077 GCAAAATGGGCCAGTCTACAG 59.526 52.381 13.78 0.00 0.00 2.74
447 454 2.879756 GCAAAATGGGCCAGTCTACAGA 60.880 50.000 13.78 0.00 0.00 3.41
448 455 3.420893 CAAAATGGGCCAGTCTACAGAA 58.579 45.455 13.78 0.00 0.00 3.02
449 456 3.806949 AAATGGGCCAGTCTACAGAAA 57.193 42.857 13.78 0.00 0.00 2.52
450 457 4.322057 AAATGGGCCAGTCTACAGAAAT 57.678 40.909 13.78 0.00 0.00 2.17
451 458 5.450818 AAATGGGCCAGTCTACAGAAATA 57.549 39.130 13.78 0.00 0.00 1.40
456 463 4.938226 GGGCCAGTCTACAGAAATATATGC 59.062 45.833 4.39 0.00 0.00 3.14
465 472 7.826252 GTCTACAGAAATATATGCATGATGGGT 59.174 37.037 10.16 0.23 0.00 4.51
643 686 3.723348 GTTCGCACGAACCAGCCC 61.723 66.667 22.02 0.00 46.21 5.19
819 981 2.827652 CTCGGATTTGCTTCTCCTACC 58.172 52.381 0.00 0.00 0.00 3.18
936 1118 2.024176 TATCAGTTTGGCCGAAGCTC 57.976 50.000 5.37 0.00 39.73 4.09
937 1119 0.678048 ATCAGTTTGGCCGAAGCTCC 60.678 55.000 5.37 0.00 39.73 4.70
938 1120 1.302832 CAGTTTGGCCGAAGCTCCT 60.303 57.895 5.37 0.00 39.73 3.69
1119 4484 2.704572 CTAGGCTTCACTCCCAGTTTG 58.295 52.381 0.00 0.00 0.00 2.93
1363 5098 2.571653 CTCTACACCTCCAAATCCACCA 59.428 50.000 0.00 0.00 0.00 4.17
1525 5260 0.458543 CCTCGTCAATCCGGTCACAG 60.459 60.000 0.00 0.00 0.00 3.66
1649 5384 5.189928 TGGAATGCACGATGGTTATAACTT 58.810 37.500 15.05 3.69 0.00 2.66
1664 5405 6.128117 GGTTATAACTTGCCGTCAATCTTTGA 60.128 38.462 15.05 0.00 37.33 2.69
2020 5764 5.332743 TGCTTATTTGGAGAATCTTTGGGT 58.667 37.500 0.00 0.00 33.73 4.51
2343 6092 3.822735 CTCATCTTTGCTCCAACTTTCCA 59.177 43.478 0.00 0.00 0.00 3.53
2414 6163 3.847671 AGGGGTAGCTTGAATAAGAGC 57.152 47.619 0.00 0.00 35.92 4.09
2470 6222 3.990318 GCAAGGTTATTGCAGATACCC 57.010 47.619 7.67 3.00 44.34 3.69
2476 6228 3.496870 GGTTATTGCAGATACCCAGGGAG 60.497 52.174 14.54 0.00 0.00 4.30
2477 6229 1.898863 ATTGCAGATACCCAGGGAGT 58.101 50.000 14.54 0.00 0.00 3.85
2479 6231 1.789523 TGCAGATACCCAGGGAGTAC 58.210 55.000 14.54 0.28 0.00 2.73
2492 6244 1.461559 GGAGTACTAGGACTGTGCGT 58.538 55.000 13.86 0.00 0.00 5.24
2537 6289 7.282450 GCTAATAATGCCCTTAGTTTGTACACT 59.718 37.037 0.00 0.00 0.00 3.55
2551 6303 3.268330 TGTACACTCGACTAGCTTCGAT 58.732 45.455 10.74 0.00 46.53 3.59
2615 6367 9.730420 GTTTACTCATGTTGTTTACTCAATGTT 57.270 29.630 0.00 0.00 0.00 2.71
2620 6372 7.776107 TCATGTTGTTTACTCAATGTTCCAAA 58.224 30.769 0.00 0.00 0.00 3.28
2682 6434 5.103771 AGGAATACCAAATTGCTCTCTCCAT 60.104 40.000 0.00 0.00 38.94 3.41
2686 6438 5.813513 ACCAAATTGCTCTCTCCATTTTT 57.186 34.783 0.00 0.00 0.00 1.94
2748 6503 1.922135 CTGGGGCGGAATCAACAACG 61.922 60.000 0.00 0.00 0.00 4.10
2762 6517 4.847633 TCAACAACGAAATCTTGCTGAAG 58.152 39.130 0.00 0.00 0.00 3.02
2763 6518 4.335315 TCAACAACGAAATCTTGCTGAAGT 59.665 37.500 0.00 0.00 0.00 3.01
2768 6523 6.260050 ACAACGAAATCTTGCTGAAGTAGAAA 59.740 34.615 0.00 0.00 0.00 2.52
2771 6526 6.073548 ACGAAATCTTGCTGAAGTAGAAACAG 60.074 38.462 0.00 0.00 35.14 3.16
2772 6527 6.146184 CGAAATCTTGCTGAAGTAGAAACAGA 59.854 38.462 0.00 0.00 34.07 3.41
2777 6532 8.225603 TCTTGCTGAAGTAGAAACAGATTTTT 57.774 30.769 0.00 0.00 34.07 1.94
2829 6584 4.280929 GCATACAAACAAGGGAAAAGGTCT 59.719 41.667 0.00 0.00 0.00 3.85
2893 6648 7.373493 AGTTGATCATGAAATTTGTTCCAGAC 58.627 34.615 0.00 0.00 0.00 3.51
2896 6651 7.596494 TGATCATGAAATTTGTTCCAGACTTC 58.404 34.615 0.00 0.00 0.00 3.01
2912 6667 5.126384 CCAGACTTCTCTACCACCTAGAAAG 59.874 48.000 0.00 0.00 30.58 2.62
2995 6750 0.037232 GTGACTGGCCACTCTACACC 60.037 60.000 0.00 0.00 34.38 4.16
3042 6797 2.415512 GTCCAGTAGAATGCCGAACAAC 59.584 50.000 0.00 0.00 0.00 3.32
3044 6799 3.009723 CCAGTAGAATGCCGAACAACAT 58.990 45.455 0.00 0.00 0.00 2.71
3046 6801 3.684305 CAGTAGAATGCCGAACAACATGA 59.316 43.478 0.00 0.00 0.00 3.07
3050 6805 1.233950 ATGCCGAACAACATGACGCA 61.234 50.000 0.00 0.00 0.00 5.24
3069 6824 1.812571 CATAGTTGCCGCCTCTTTTGT 59.187 47.619 0.00 0.00 0.00 2.83
3072 6827 0.102300 GTTGCCGCCTCTTTTGTTGT 59.898 50.000 0.00 0.00 0.00 3.32
3076 6831 1.208259 CCGCCTCTTTTGTTGTTTGC 58.792 50.000 0.00 0.00 0.00 3.68
3080 6835 2.866156 GCCTCTTTTGTTGTTTGCCTTC 59.134 45.455 0.00 0.00 0.00 3.46
3166 6921 6.678568 ATATAGCTATTCACAGGAGCAACT 57.321 37.500 12.39 0.00 38.73 3.16
3355 7116 4.514441 CCTACTTGATGCAAATAGGAGCAG 59.486 45.833 8.56 0.00 43.45 4.24
3378 7139 3.584406 TGCCTGATCATCTATGGTTAGGG 59.416 47.826 14.06 2.22 43.00 3.53
3399 7160 5.105063 GGGCATTTCAAAATTAGCTGACTC 58.895 41.667 0.00 0.00 0.00 3.36
3400 7161 5.336690 GGGCATTTCAAAATTAGCTGACTCA 60.337 40.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.219070 GGGTCCAACACAAAGGTAATTACC 59.781 45.833 24.71 24.71 46.82 2.85
83 84 8.190122 CAGTGGCAAGCAAATAGATATGTTTAA 58.810 33.333 0.00 0.00 0.00 1.52
176 179 6.499350 ACAAGTATTTTGGTACAGAGGGAGTA 59.501 38.462 0.00 0.00 42.39 2.59
177 180 5.309806 ACAAGTATTTTGGTACAGAGGGAGT 59.690 40.000 0.00 0.00 42.39 3.85
178 181 5.805728 ACAAGTATTTTGGTACAGAGGGAG 58.194 41.667 0.00 0.00 42.39 4.30
179 182 5.836024 ACAAGTATTTTGGTACAGAGGGA 57.164 39.130 0.00 0.00 42.39 4.20
180 183 6.708285 ACTACAAGTATTTTGGTACAGAGGG 58.292 40.000 0.00 0.00 42.39 4.30
181 184 7.119262 CCAACTACAAGTATTTTGGTACAGAGG 59.881 40.741 10.48 0.00 42.39 3.69
182 185 7.119262 CCCAACTACAAGTATTTTGGTACAGAG 59.881 40.741 14.71 1.86 42.39 3.35
183 186 6.938030 CCCAACTACAAGTATTTTGGTACAGA 59.062 38.462 14.71 0.00 42.39 3.41
184 187 6.150474 CCCCAACTACAAGTATTTTGGTACAG 59.850 42.308 14.71 4.95 42.39 2.74
185 188 6.005198 CCCCAACTACAAGTATTTTGGTACA 58.995 40.000 14.71 0.00 0.00 2.90
186 189 6.240145 TCCCCAACTACAAGTATTTTGGTAC 58.760 40.000 14.71 0.00 0.00 3.34
187 190 6.451292 TCCCCAACTACAAGTATTTTGGTA 57.549 37.500 14.71 5.30 0.00 3.25
188 191 5.327737 TCCCCAACTACAAGTATTTTGGT 57.672 39.130 14.71 0.00 0.00 3.67
189 192 6.266786 AGTTTCCCCAACTACAAGTATTTTGG 59.733 38.462 11.25 11.25 44.56 3.28
190 193 7.284919 AGTTTCCCCAACTACAAGTATTTTG 57.715 36.000 0.00 0.00 44.56 2.44
191 194 8.222637 ACTAGTTTCCCCAACTACAAGTATTTT 58.777 33.333 0.00 0.00 44.56 1.82
192 195 7.752638 ACTAGTTTCCCCAACTACAAGTATTT 58.247 34.615 0.00 0.00 44.56 1.40
193 196 7.325725 ACTAGTTTCCCCAACTACAAGTATT 57.674 36.000 0.00 0.00 44.56 1.89
194 197 6.947376 ACTAGTTTCCCCAACTACAAGTAT 57.053 37.500 0.00 0.00 44.56 2.12
195 198 6.782000 TGTACTAGTTTCCCCAACTACAAGTA 59.218 38.462 0.00 0.00 44.56 2.24
196 199 5.603813 TGTACTAGTTTCCCCAACTACAAGT 59.396 40.000 0.00 0.00 44.56 3.16
197 200 6.105397 TGTACTAGTTTCCCCAACTACAAG 57.895 41.667 0.00 0.00 44.56 3.16
198 201 6.100134 ACTTGTACTAGTTTCCCCAACTACAA 59.900 38.462 0.00 0.42 44.56 2.41
199 202 5.603813 ACTTGTACTAGTTTCCCCAACTACA 59.396 40.000 0.00 0.00 44.56 2.74
200 203 6.106648 ACTTGTACTAGTTTCCCCAACTAC 57.893 41.667 0.00 0.00 44.56 2.73
201 204 6.239686 GGAACTTGTACTAGTTTCCCCAACTA 60.240 42.308 21.05 0.00 44.56 2.24
202 205 8.385258 GGGAACTTGTACTAGTTTCCCCAACT 62.385 46.154 27.93 4.58 44.78 3.16
203 206 4.758674 GGAACTTGTACTAGTTTCCCCAAC 59.241 45.833 21.05 8.65 38.43 3.77
204 207 4.202493 GGGAACTTGTACTAGTTTCCCCAA 60.202 45.833 27.93 9.90 44.78 4.12
205 208 3.328637 GGGAACTTGTACTAGTTTCCCCA 59.671 47.826 27.93 3.67 44.78 4.96
206 209 3.947868 GGGAACTTGTACTAGTTTCCCC 58.052 50.000 27.93 24.96 44.78 4.81
209 212 6.522946 AGTTGAGGGAACTTGTACTAGTTTC 58.477 40.000 21.05 19.16 42.70 2.78
210 213 6.496144 AGTTGAGGGAACTTGTACTAGTTT 57.504 37.500 21.05 8.12 42.70 2.66
211 214 6.552350 TGTAGTTGAGGGAACTTGTACTAGTT 59.448 38.462 20.40 20.40 42.70 2.24
212 215 6.073314 TGTAGTTGAGGGAACTTGTACTAGT 58.927 40.000 3.98 3.98 42.70 2.57
213 216 6.585695 TGTAGTTGAGGGAACTTGTACTAG 57.414 41.667 2.56 2.56 42.70 2.57
214 217 6.552350 ACTTGTAGTTGAGGGAACTTGTACTA 59.448 38.462 0.00 0.00 42.70 1.82
215 218 5.365895 ACTTGTAGTTGAGGGAACTTGTACT 59.634 40.000 0.00 0.00 42.70 2.73
216 219 5.608449 ACTTGTAGTTGAGGGAACTTGTAC 58.392 41.667 0.00 0.00 42.70 2.90
217 220 5.881923 ACTTGTAGTTGAGGGAACTTGTA 57.118 39.130 0.00 0.00 42.70 2.41
218 221 4.772886 ACTTGTAGTTGAGGGAACTTGT 57.227 40.909 0.00 0.00 42.70 3.16
219 222 7.360101 CGAAATACTTGTAGTTGAGGGAACTTG 60.360 40.741 0.00 0.00 42.70 3.16
220 223 6.649557 CGAAATACTTGTAGTTGAGGGAACTT 59.350 38.462 0.00 0.00 42.70 2.66
222 225 5.350640 CCGAAATACTTGTAGTTGAGGGAAC 59.649 44.000 0.00 0.00 34.40 3.62
223 226 5.012354 ACCGAAATACTTGTAGTTGAGGGAA 59.988 40.000 12.88 0.00 0.00 3.97
224 227 4.529377 ACCGAAATACTTGTAGTTGAGGGA 59.471 41.667 12.88 0.00 0.00 4.20
225 228 4.828829 ACCGAAATACTTGTAGTTGAGGG 58.171 43.478 12.88 8.04 0.00 4.30
226 229 6.392354 TGTACCGAAATACTTGTAGTTGAGG 58.608 40.000 0.00 4.85 0.00 3.86
227 230 9.234384 CTATGTACCGAAATACTTGTAGTTGAG 57.766 37.037 0.00 0.00 0.00 3.02
228 231 8.742777 ACTATGTACCGAAATACTTGTAGTTGA 58.257 33.333 0.00 0.00 0.00 3.18
229 232 8.804743 CACTATGTACCGAAATACTTGTAGTTG 58.195 37.037 0.00 0.00 0.00 3.16
230 233 8.742777 TCACTATGTACCGAAATACTTGTAGTT 58.257 33.333 0.00 0.00 0.00 2.24
231 234 8.284945 TCACTATGTACCGAAATACTTGTAGT 57.715 34.615 0.00 0.00 0.00 2.73
232 235 8.404000 ACTCACTATGTACCGAAATACTTGTAG 58.596 37.037 0.00 0.00 0.00 2.74
233 236 8.284945 ACTCACTATGTACCGAAATACTTGTA 57.715 34.615 0.00 0.00 0.00 2.41
234 237 7.166691 ACTCACTATGTACCGAAATACTTGT 57.833 36.000 0.00 0.00 0.00 3.16
235 238 8.186163 TGTACTCACTATGTACCGAAATACTTG 58.814 37.037 0.00 0.00 39.42 3.16
236 239 8.284945 TGTACTCACTATGTACCGAAATACTT 57.715 34.615 0.00 0.00 39.42 2.24
237 240 7.870509 TGTACTCACTATGTACCGAAATACT 57.129 36.000 0.00 0.00 39.42 2.12
242 245 9.740239 GAAATAATGTACTCACTATGTACCGAA 57.260 33.333 0.00 0.00 39.42 4.30
243 246 8.905850 TGAAATAATGTACTCACTATGTACCGA 58.094 33.333 0.00 0.00 39.42 4.69
244 247 9.692749 ATGAAATAATGTACTCACTATGTACCG 57.307 33.333 0.00 0.00 39.42 4.02
251 254 9.936759 TCACAACATGAAATAATGTACTCACTA 57.063 29.630 0.00 0.00 39.89 2.74
252 255 8.846943 TCACAACATGAAATAATGTACTCACT 57.153 30.769 0.00 0.00 39.89 3.41
426 433 1.474077 CTGTAGACTGGCCCATTTTGC 59.526 52.381 0.00 0.00 0.00 3.68
429 436 3.806949 TTTCTGTAGACTGGCCCATTT 57.193 42.857 0.00 0.00 0.00 2.32
430 437 5.653255 ATATTTCTGTAGACTGGCCCATT 57.347 39.130 0.00 0.00 0.00 3.16
434 441 5.551233 TGCATATATTTCTGTAGACTGGCC 58.449 41.667 0.00 0.00 0.00 5.36
435 442 6.875726 TCATGCATATATTTCTGTAGACTGGC 59.124 38.462 0.00 0.00 0.00 4.85
436 443 8.880750 CATCATGCATATATTTCTGTAGACTGG 58.119 37.037 0.00 0.00 0.00 4.00
437 444 8.880750 CCATCATGCATATATTTCTGTAGACTG 58.119 37.037 0.00 0.00 0.00 3.51
438 445 8.045507 CCCATCATGCATATATTTCTGTAGACT 58.954 37.037 0.00 0.00 0.00 3.24
439 446 7.826252 ACCCATCATGCATATATTTCTGTAGAC 59.174 37.037 0.00 0.00 0.00 2.59
440 447 7.921304 ACCCATCATGCATATATTTCTGTAGA 58.079 34.615 0.00 0.00 0.00 2.59
441 448 7.010830 CGACCCATCATGCATATATTTCTGTAG 59.989 40.741 0.00 0.00 0.00 2.74
442 449 6.818142 CGACCCATCATGCATATATTTCTGTA 59.182 38.462 0.00 0.00 0.00 2.74
443 450 5.645067 CGACCCATCATGCATATATTTCTGT 59.355 40.000 0.00 0.00 0.00 3.41
444 451 5.448225 GCGACCCATCATGCATATATTTCTG 60.448 44.000 0.00 0.00 0.00 3.02
445 452 4.637534 GCGACCCATCATGCATATATTTCT 59.362 41.667 0.00 0.00 0.00 2.52
446 453 4.637534 AGCGACCCATCATGCATATATTTC 59.362 41.667 0.00 0.00 0.00 2.17
447 454 4.592942 AGCGACCCATCATGCATATATTT 58.407 39.130 0.00 0.00 0.00 1.40
448 455 4.226427 AGCGACCCATCATGCATATATT 57.774 40.909 0.00 0.00 0.00 1.28
449 456 3.920231 AGCGACCCATCATGCATATAT 57.080 42.857 0.00 0.00 0.00 0.86
450 457 3.337358 CAAGCGACCCATCATGCATATA 58.663 45.455 0.00 0.00 0.00 0.86
451 458 2.156917 CAAGCGACCCATCATGCATAT 58.843 47.619 0.00 0.00 0.00 1.78
456 463 1.314534 TTGGCAAGCGACCCATCATG 61.315 55.000 0.00 0.00 0.00 3.07
465 472 2.976840 GCGGTCAATTGGCAAGCGA 61.977 57.895 18.01 5.09 36.07 4.93
494 501 1.833787 TTCCTGTCCTTGCCGGTACC 61.834 60.000 1.90 0.16 0.00 3.34
643 686 4.388499 CCACCGACGACAAGGGGG 62.388 72.222 0.00 0.00 45.86 5.40
819 981 0.596082 ACCAACCGCTTCAAATTCCG 59.404 50.000 0.00 0.00 0.00 4.30
936 1118 4.341806 AGTGTCTCTGCAGATATCTTGAGG 59.658 45.833 18.63 1.85 0.00 3.86
937 1119 5.300034 AGAGTGTCTCTGCAGATATCTTGAG 59.700 44.000 18.63 10.91 39.62 3.02
938 1120 5.199723 AGAGTGTCTCTGCAGATATCTTGA 58.800 41.667 18.63 6.95 39.62 3.02
1119 4484 2.748532 AGCTTTGCAGAATCTCTTCAGC 59.251 45.455 0.00 0.00 42.47 4.26
1264 4640 2.110627 GCGCCAGGATGAGCAGAT 59.889 61.111 0.00 0.00 39.69 2.90
1363 5098 0.399454 AGGCATGCAACACTCTCACT 59.601 50.000 21.36 0.00 0.00 3.41
1525 5260 1.280421 AGGGAGAGCAATCTGTTCACC 59.720 52.381 0.00 0.00 37.55 4.02
1649 5384 3.436704 GTCAAGATCAAAGATTGACGGCA 59.563 43.478 8.50 0.00 42.23 5.69
2020 5764 8.217799 CCCAGGTTCAGGTTCTAAATCATAATA 58.782 37.037 0.00 0.00 0.00 0.98
2414 6163 7.309012 CCATTATTAGCTCATTGAACCCATCAG 60.309 40.741 0.00 0.00 39.77 2.90
2469 6221 2.379972 CACAGTCCTAGTACTCCCTGG 58.620 57.143 0.00 0.00 0.00 4.45
2470 6222 1.751924 GCACAGTCCTAGTACTCCCTG 59.248 57.143 0.00 4.15 0.00 4.45
2476 6228 0.458025 GCCACGCACAGTCCTAGTAC 60.458 60.000 0.00 0.00 0.00 2.73
2477 6229 1.601419 GGCCACGCACAGTCCTAGTA 61.601 60.000 0.00 0.00 0.00 1.82
2479 6231 2.125512 GGCCACGCACAGTCCTAG 60.126 66.667 0.00 0.00 0.00 3.02
2492 6244 2.767394 AGCTCATTGCAAATAATGGCCA 59.233 40.909 8.56 8.56 45.94 5.36
2577 6329 6.687081 ACATGAGTAAACAAAGGAAAACGA 57.313 33.333 0.00 0.00 0.00 3.85
2579 6331 8.474006 AACAACATGAGTAAACAAAGGAAAAC 57.526 30.769 0.00 0.00 0.00 2.43
2620 6372 9.739276 TGACACATTAAAATTGGAGAGAGTTAT 57.261 29.630 0.00 0.00 0.00 1.89
2686 6438 2.953284 TGTTCCGAACATACCCCAAA 57.047 45.000 9.99 0.00 36.25 3.28
2748 6503 7.426929 TCTGTTTCTACTTCAGCAAGATTTC 57.573 36.000 0.00 0.00 33.34 2.17
2794 6549 7.148540 CCCTTGTTTGTATGCATGAAAATCTTG 60.149 37.037 10.16 2.87 0.00 3.02
2829 6584 9.847224 GTTGGGAATTCTTCTTCCTTATACATA 57.153 33.333 5.23 0.00 43.59 2.29
2893 6648 7.234661 AGTTTCTTTCTAGGTGGTAGAGAAG 57.765 40.000 0.00 0.00 39.05 2.85
2896 6651 9.372369 CAATTAGTTTCTTTCTAGGTGGTAGAG 57.628 37.037 0.00 0.00 39.05 2.43
2912 6667 9.394477 GTTCAACTACATTGGTCAATTAGTTTC 57.606 33.333 17.87 12.47 38.98 2.78
2995 6750 4.094590 AGAATTCTCTCTTGCGCATCAAAG 59.905 41.667 12.75 5.52 33.65 2.77
3025 6780 3.684788 GTCATGTTGTTCGGCATTCTACT 59.315 43.478 0.00 0.00 0.00 2.57
3050 6805 2.200373 ACAAAAGAGGCGGCAACTAT 57.800 45.000 13.08 0.45 0.00 2.12
3076 6831 1.278238 GAACCGATACTGTGCGAAGG 58.722 55.000 6.48 0.00 0.00 3.46
3080 6835 0.108804 ACAGGAACCGATACTGTGCG 60.109 55.000 5.38 0.00 43.29 5.34
3086 6841 4.824289 TCCAGTTTTACAGGAACCGATAC 58.176 43.478 0.00 0.00 30.32 2.24
3147 6902 2.938756 GCAGTTGCTCCTGTGAATAGCT 60.939 50.000 0.00 0.00 37.16 3.32
3319 7080 2.032071 GTAGGCGGCACTTGGTGT 59.968 61.111 13.08 0.00 35.75 4.16
3328 7089 0.740737 ATTTGCATCAAGTAGGCGGC 59.259 50.000 0.00 0.00 37.84 6.53
3329 7090 2.549754 CCTATTTGCATCAAGTAGGCGG 59.450 50.000 12.92 0.00 43.31 6.13
3331 7092 3.251972 GCTCCTATTTGCATCAAGTAGGC 59.748 47.826 17.91 8.17 46.52 3.93
3355 7116 4.564406 CCCTAACCATAGATGATCAGGCAC 60.564 50.000 0.09 0.00 0.00 5.01
3378 7139 6.866179 CTGAGTCAGCTAATTTTGAAATGC 57.134 37.500 7.33 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.