Multiple sequence alignment - TraesCS4A01G433300

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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 TraesCS4A01G433300 chr4A 100.000 2964 0 0 1 2964 704155010 704152047 0.000000e+00 5474
1 TraesCS4A01G433300 chr4A 88.662 979 74 23 739 1698 703942262 703941302 0.000000e+00 1158
2 TraesCS4A01G433300 chr4A 83.654 624 74 17 1045 1654 703932186 703932795 1.990000e-156 562
3 TraesCS4A01G433300 chr5B 96.663 1019 30 4 1948 2964 376339229 376338213 0.000000e+00 1690
4 TraesCS4A01G433300 chr5B 96.464 1018 32 3 1948 2964 17559606 17560620 0.000000e+00 1677
5 TraesCS4A01G433300 chr2B 96.562 1018 28 4 1948 2964 639521829 639520818 0.000000e+00 1679
6 TraesCS4A01G433300 chr2B 96.169 1018 37 2 1948 2964 754002546 754003562 0.000000e+00 1663
7 TraesCS4A01G433300 chr1B 96.464 1018 30 4 1948 2964 9728763 9729775 0.000000e+00 1676
8 TraesCS4A01G433300 chr1B 96.365 1018 31 4 1948 2964 646837844 646836832 0.000000e+00 1670
9 TraesCS4A01G433300 chr1B 96.271 1019 32 4 1948 2964 646851392 646850378 0.000000e+00 1666
10 TraesCS4A01G433300 chr1B 81.176 255 45 3 1054 1305 562433785 562433531 5.010000e-48 202
11 TraesCS4A01G433300 chr4B 96.278 1021 28 8 1948 2964 389774388 389773374 0.000000e+00 1666
12 TraesCS4A01G433300 chr3B 96.267 1018 34 3 1948 2964 12124845 12125859 0.000000e+00 1666
13 TraesCS4A01G433300 chr7D 86.282 1509 119 48 353 1829 27472078 27470626 0.000000e+00 1559
14 TraesCS4A01G433300 chr7D 84.709 1321 123 31 579 1856 27468645 27467361 0.000000e+00 1247
15 TraesCS4A01G433300 chr7D 85.263 570 65 11 1045 1609 27453193 27453748 1.190000e-158 569
16 TraesCS4A01G433300 chr7A 83.480 1368 142 51 571 1905 27905819 27904503 0.000000e+00 1197
17 TraesCS4A01G433300 chr7A 82.555 642 72 21 1045 1654 27901383 27902016 2.020000e-146 529
18 TraesCS4A01G433300 chr7A 89.130 230 22 3 1 229 27906607 27906380 1.740000e-72 283
19 TraesCS4A01G433300 chr7A 93.662 142 6 3 365 503 27906047 27905906 2.990000e-50 209
20 TraesCS4A01G433300 chr2D 79.575 612 72 34 1046 1654 7228077 7227516 3.580000e-104 388
21 TraesCS4A01G433300 chr2D 78.889 180 33 4 1115 1293 527272553 527272378 1.870000e-22 117
22 TraesCS4A01G433300 chrUn 88.646 229 23 3 1 228 326787401 326787175 2.910000e-70 276
23 TraesCS4A01G433300 chr5D 82.353 272 37 10 1058 1320 411845881 411845612 2.970000e-55 226
24 TraesCS4A01G433300 chr5A 80.952 252 45 3 1054 1302 522425292 522425543 2.330000e-46 196
25 TraesCS4A01G433300 chr3D 81.690 142 17 8 1123 1261 103621545 103621680 3.120000e-20 110


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 TraesCS4A01G433300 chr4A 704152047 704155010 2963 True 5474 5474 100.000000 1 2964 1 chr4A.!!$R2 2963
1 TraesCS4A01G433300 chr4A 703941302 703942262 960 True 1158 1158 88.662000 739 1698 1 chr4A.!!$R1 959
2 TraesCS4A01G433300 chr4A 703932186 703932795 609 False 562 562 83.654000 1045 1654 1 chr4A.!!$F1 609
3 TraesCS4A01G433300 chr5B 376338213 376339229 1016 True 1690 1690 96.663000 1948 2964 1 chr5B.!!$R1 1016
4 TraesCS4A01G433300 chr5B 17559606 17560620 1014 False 1677 1677 96.464000 1948 2964 1 chr5B.!!$F1 1016
5 TraesCS4A01G433300 chr2B 639520818 639521829 1011 True 1679 1679 96.562000 1948 2964 1 chr2B.!!$R1 1016
6 TraesCS4A01G433300 chr2B 754002546 754003562 1016 False 1663 1663 96.169000 1948 2964 1 chr2B.!!$F1 1016
7 TraesCS4A01G433300 chr1B 9728763 9729775 1012 False 1676 1676 96.464000 1948 2964 1 chr1B.!!$F1 1016
8 TraesCS4A01G433300 chr1B 646836832 646837844 1012 True 1670 1670 96.365000 1948 2964 1 chr1B.!!$R2 1016
9 TraesCS4A01G433300 chr1B 646850378 646851392 1014 True 1666 1666 96.271000 1948 2964 1 chr1B.!!$R3 1016
10 TraesCS4A01G433300 chr4B 389773374 389774388 1014 True 1666 1666 96.278000 1948 2964 1 chr4B.!!$R1 1016
11 TraesCS4A01G433300 chr3B 12124845 12125859 1014 False 1666 1666 96.267000 1948 2964 1 chr3B.!!$F1 1016
12 TraesCS4A01G433300 chr7D 27467361 27472078 4717 True 1403 1559 85.495500 353 1856 2 chr7D.!!$R1 1503
13 TraesCS4A01G433300 chr7D 27453193 27453748 555 False 569 569 85.263000 1045 1609 1 chr7D.!!$F1 564
14 TraesCS4A01G433300 chr7A 27904503 27906607 2104 True 563 1197 88.757333 1 1905 3 chr7A.!!$R1 1904
15 TraesCS4A01G433300 chr7A 27901383 27902016 633 False 529 529 82.555000 1045 1654 1 chr7A.!!$F1 609
16 TraesCS4A01G433300 chr2D 7227516 7228077 561 True 388 388 79.575000 1046 1654 1 chr2D.!!$R1 608

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
280 469 0.035152 TTCTACAGGGCGTCTACGGA 60.035 55.0 4.49 0.0 40.23 4.69 F
774 1026 0.037697 ACGGACGACTGCTTTGCATA 60.038 50.0 0.00 0.0 38.13 3.14 F
1700 5309 0.458543 TCTGGATTCGCTTGCTCGTC 60.459 55.0 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 5382 0.034059 AGCAGAGTATATGGCGTGCC 59.966 55.000 3.30 3.3 0.00 5.01 R
1960 5590 0.035247 TTTTAATACGCGCCTGGGGT 60.035 50.000 5.73 0.0 44.91 4.95 R
2583 6224 3.449227 CGCACTCCTCCGGCACTA 61.449 66.667 0.00 0.0 0.00 2.74 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.337703 CGAGAAGATGCAGAGGGAGAG 59.662 57.143 0.00 0.00 0.00 3.20
47 48 3.418995 AGCTTGATGATGGATGTATGGC 58.581 45.455 0.00 0.00 0.00 4.40
48 49 3.151554 GCTTGATGATGGATGTATGGCA 58.848 45.455 0.00 0.00 0.00 4.92
75 76 0.800012 TCGTCTTTTTGTATGCCGGC 59.200 50.000 22.73 22.73 0.00 6.13
120 121 2.747135 CGTGGTTGAACTACCCCTTTGT 60.747 50.000 6.24 0.00 37.39 2.83
126 127 4.986054 TGAACTACCCCTTTGTATGTGT 57.014 40.909 0.00 0.00 0.00 3.72
130 131 1.627864 ACCCCTTTGTATGTGTTGGC 58.372 50.000 0.00 0.00 0.00 4.52
138 139 4.662468 TTGTATGTGTTGGCAATTGTGT 57.338 36.364 1.92 0.00 0.00 3.72
145 146 2.258286 GGCAATTGTGTCGGCCAC 59.742 61.111 2.24 0.25 45.70 5.01
171 172 3.829886 AATGTGCCAACATGAACTACG 57.170 42.857 0.00 0.00 46.58 3.51
176 177 1.369625 CCAACATGAACTACGAGCCC 58.630 55.000 0.00 0.00 0.00 5.19
182 183 3.502211 ACATGAACTACGAGCCCTTTTTG 59.498 43.478 0.00 0.00 0.00 2.44
183 184 3.202829 TGAACTACGAGCCCTTTTTGT 57.797 42.857 0.00 0.00 0.00 2.83
184 185 4.339872 TGAACTACGAGCCCTTTTTGTA 57.660 40.909 0.00 0.00 0.00 2.41
185 186 4.312443 TGAACTACGAGCCCTTTTTGTAG 58.688 43.478 0.00 0.00 38.14 2.74
186 187 4.039488 TGAACTACGAGCCCTTTTTGTAGA 59.961 41.667 4.84 0.00 36.46 2.59
188 189 2.474410 ACGAGCCCTTTTTGTAGAGG 57.526 50.000 0.00 0.00 0.00 3.69
189 190 1.087501 CGAGCCCTTTTTGTAGAGGC 58.912 55.000 0.00 0.00 44.20 4.70
196 197 3.620488 CCTTTTTGTAGAGGCTGGCATA 58.380 45.455 3.38 0.00 0.00 3.14
218 219 2.555547 GCCGGCATGAACTATGGGC 61.556 63.158 24.80 0.00 37.09 5.36
229 230 1.152984 CTATGGGCGTTGGCATGGA 60.153 57.895 0.00 0.00 42.47 3.41
230 231 1.152984 TATGGGCGTTGGCATGGAG 60.153 57.895 0.00 0.00 42.47 3.86
231 232 1.920734 TATGGGCGTTGGCATGGAGT 61.921 55.000 0.00 0.00 42.47 3.85
232 233 2.676471 GGGCGTTGGCATGGAGTT 60.676 61.111 0.00 0.00 42.47 3.01
234 235 1.212751 GGCGTTGGCATGGAGTTTC 59.787 57.895 0.00 0.00 42.47 2.78
235 236 1.244019 GGCGTTGGCATGGAGTTTCT 61.244 55.000 0.00 0.00 42.47 2.52
236 237 1.448985 GCGTTGGCATGGAGTTTCTA 58.551 50.000 0.00 0.00 39.62 2.10
238 239 2.422597 CGTTGGCATGGAGTTTCTACA 58.577 47.619 0.00 0.00 0.00 2.74
239 240 2.416547 CGTTGGCATGGAGTTTCTACAG 59.583 50.000 0.00 0.00 0.00 2.74
240 241 2.749621 GTTGGCATGGAGTTTCTACAGG 59.250 50.000 0.00 0.00 0.00 4.00
241 242 1.281867 TGGCATGGAGTTTCTACAGGG 59.718 52.381 0.00 0.00 0.00 4.45
248 437 3.259902 GGAGTTTCTACAGGGCGTTAAG 58.740 50.000 0.00 0.00 0.00 1.85
260 449 4.091939 GTTAAGCCGGGCGGGAGT 62.092 66.667 16.19 3.74 38.47 3.85
261 450 3.324108 TTAAGCCGGGCGGGAGTT 61.324 61.111 16.19 9.56 38.47 3.01
262 451 2.897762 TTAAGCCGGGCGGGAGTTT 61.898 57.895 16.19 3.64 38.47 2.66
263 452 2.808181 TTAAGCCGGGCGGGAGTTTC 62.808 60.000 16.19 0.00 38.47 2.78
265 454 3.777910 GCCGGGCGGGAGTTTCTA 61.778 66.667 16.19 0.00 38.47 2.10
267 456 2.652095 CCGGGCGGGAGTTTCTACA 61.652 63.158 4.88 0.00 38.47 2.74
270 459 1.221021 GGCGGGAGTTTCTACAGGG 59.779 63.158 0.00 0.00 0.00 4.45
271 460 1.449778 GCGGGAGTTTCTACAGGGC 60.450 63.158 0.00 0.00 0.00 5.19
273 462 1.885163 CGGGAGTTTCTACAGGGCGT 61.885 60.000 0.00 0.00 0.00 5.68
274 463 0.108281 GGGAGTTTCTACAGGGCGTC 60.108 60.000 0.00 0.00 0.00 5.19
275 464 0.896226 GGAGTTTCTACAGGGCGTCT 59.104 55.000 0.00 0.00 0.00 4.18
277 466 2.159268 GGAGTTTCTACAGGGCGTCTAC 60.159 54.545 0.00 0.00 0.00 2.59
280 469 0.035152 TTCTACAGGGCGTCTACGGA 60.035 55.000 4.49 0.00 40.23 4.69
281 470 0.463295 TCTACAGGGCGTCTACGGAG 60.463 60.000 4.49 0.00 40.23 4.63
283 472 1.028330 TACAGGGCGTCTACGGAGTG 61.028 60.000 4.49 0.00 45.73 3.51
284 473 2.754658 AGGGCGTCTACGGAGTGG 60.755 66.667 4.49 0.00 45.73 4.00
285 474 3.066814 GGGCGTCTACGGAGTGGT 61.067 66.667 4.49 0.00 45.73 4.16
286 475 2.643232 GGGCGTCTACGGAGTGGTT 61.643 63.158 4.49 0.00 45.73 3.67
287 476 1.315257 GGGCGTCTACGGAGTGGTTA 61.315 60.000 4.49 0.00 45.73 2.85
288 477 0.527565 GGCGTCTACGGAGTGGTTAA 59.472 55.000 4.49 0.00 45.73 2.01
290 479 2.358898 GGCGTCTACGGAGTGGTTAATA 59.641 50.000 4.49 0.00 45.73 0.98
292 481 3.065925 GCGTCTACGGAGTGGTTAATAGT 59.934 47.826 4.49 0.00 45.73 2.12
293 482 4.595116 CGTCTACGGAGTGGTTAATAGTG 58.405 47.826 0.00 0.00 45.73 2.74
295 484 5.008415 CGTCTACGGAGTGGTTAATAGTGAT 59.992 44.000 0.00 0.00 45.73 3.06
296 485 6.459298 CGTCTACGGAGTGGTTAATAGTGATT 60.459 42.308 0.00 0.00 45.73 2.57
297 486 6.696148 GTCTACGGAGTGGTTAATAGTGATTG 59.304 42.308 0.00 0.00 45.73 2.67
298 487 4.766375 ACGGAGTGGTTAATAGTGATTGG 58.234 43.478 0.00 0.00 42.51 3.16
299 488 4.224370 ACGGAGTGGTTAATAGTGATTGGT 59.776 41.667 0.00 0.00 42.51 3.67
303 492 6.134535 AGTGGTTAATAGTGATTGGTTGGA 57.865 37.500 0.00 0.00 0.00 3.53
305 494 7.182060 AGTGGTTAATAGTGATTGGTTGGAAT 58.818 34.615 0.00 0.00 0.00 3.01
306 495 7.673926 AGTGGTTAATAGTGATTGGTTGGAATT 59.326 33.333 0.00 0.00 0.00 2.17
307 496 8.311109 GTGGTTAATAGTGATTGGTTGGAATTT 58.689 33.333 0.00 0.00 0.00 1.82
308 497 8.310382 TGGTTAATAGTGATTGGTTGGAATTTG 58.690 33.333 0.00 0.00 0.00 2.32
315 504 8.193953 AGTGATTGGTTGGAATTTGATTAAGT 57.806 30.769 0.00 0.00 0.00 2.24
316 505 8.090214 AGTGATTGGTTGGAATTTGATTAAGTG 58.910 33.333 0.00 0.00 0.00 3.16
324 525 7.149569 TGGAATTTGATTAAGTGAAGAGCAG 57.850 36.000 0.00 0.00 0.00 4.24
328 529 3.603532 TGATTAAGTGAAGAGCAGGCAG 58.396 45.455 0.00 0.00 0.00 4.85
329 530 1.813513 TTAAGTGAAGAGCAGGCAGC 58.186 50.000 0.00 0.00 46.19 5.25
369 570 1.957186 TGTTAACCTGACGTGCGCC 60.957 57.895 4.18 0.00 0.00 6.53
423 629 2.661537 CGCGCAGTCAGTGGACAA 60.662 61.111 8.75 0.00 46.80 3.18
428 634 1.669115 CAGTCAGTGGACAAGCCGG 60.669 63.158 0.00 0.00 46.80 6.13
466 675 4.447989 GCTGCTCTGCTCTGCGGA 62.448 66.667 0.00 0.00 42.08 5.54
501 731 0.609662 TAGGATAATAACGGCGGGCC 59.390 55.000 13.24 0.00 0.00 5.80
537 783 3.284449 GCCGCACGTGGTTTCCTT 61.284 61.111 18.88 0.00 0.00 3.36
543 789 2.695359 GCACGTGGTTTCCTTGAGATA 58.305 47.619 18.88 0.00 0.00 1.98
552 798 2.738587 TCCTTGAGATACGGAGCTCT 57.261 50.000 15.12 0.00 38.98 4.09
553 799 3.859061 TCCTTGAGATACGGAGCTCTA 57.141 47.619 15.12 5.57 38.98 2.43
554 800 3.745799 TCCTTGAGATACGGAGCTCTAG 58.254 50.000 16.22 16.22 39.67 2.43
555 801 2.227865 CCTTGAGATACGGAGCTCTAGC 59.772 54.545 17.51 1.59 38.95 3.42
556 802 1.898902 TGAGATACGGAGCTCTAGCC 58.101 55.000 15.12 0.00 43.38 3.93
557 803 1.422024 TGAGATACGGAGCTCTAGCCT 59.578 52.381 15.12 4.88 43.38 4.58
558 804 2.081462 GAGATACGGAGCTCTAGCCTC 58.919 57.143 14.64 10.19 43.38 4.70
559 805 1.702957 AGATACGGAGCTCTAGCCTCT 59.297 52.381 14.64 10.38 43.38 3.69
560 806 2.907696 AGATACGGAGCTCTAGCCTCTA 59.092 50.000 14.64 0.00 43.38 2.43
561 807 2.843401 TACGGAGCTCTAGCCTCTAG 57.157 55.000 14.64 0.00 43.38 2.43
562 808 0.536460 ACGGAGCTCTAGCCTCTAGC 60.536 60.000 14.64 1.99 43.38 3.42
774 1026 0.037697 ACGGACGACTGCTTTGCATA 60.038 50.000 0.00 0.00 38.13 3.14
775 1027 1.075542 CGGACGACTGCTTTGCATAA 58.924 50.000 0.00 0.00 38.13 1.90
776 1028 1.665679 CGGACGACTGCTTTGCATAAT 59.334 47.619 0.00 0.00 38.13 1.28
777 1029 2.095853 CGGACGACTGCTTTGCATAATT 59.904 45.455 0.00 0.00 38.13 1.40
778 1030 3.429085 GGACGACTGCTTTGCATAATTG 58.571 45.455 0.00 0.00 38.13 2.32
875 1151 3.503365 CCCCGGCCGAATCCTATATATA 58.497 50.000 30.73 0.00 0.00 0.86
876 1152 3.899360 CCCCGGCCGAATCCTATATATAA 59.101 47.826 30.73 0.00 0.00 0.98
877 1153 4.530946 CCCCGGCCGAATCCTATATATAAT 59.469 45.833 30.73 0.00 0.00 1.28
878 1154 5.718130 CCCCGGCCGAATCCTATATATAATA 59.282 44.000 30.73 0.00 0.00 0.98
879 1155 6.383147 CCCCGGCCGAATCCTATATATAATAT 59.617 42.308 30.73 0.00 0.00 1.28
951 1234 3.323751 AGCCAGCACCATTGATTTTTC 57.676 42.857 0.00 0.00 0.00 2.29
970 1264 2.842810 TCCTAGCAAGCTGCAGAGGAC 61.843 57.143 20.43 3.28 46.33 3.85
1327 1634 3.109612 CTTCTCGCCGTCGATCCGT 62.110 63.158 0.00 0.00 44.56 4.69
1406 1728 2.356553 CCCCAAAGACGCGACGAA 60.357 61.111 15.93 0.00 0.00 3.85
1407 1729 1.740296 CCCCAAAGACGCGACGAAT 60.740 57.895 15.93 0.00 0.00 3.34
1667 5276 0.463620 TGATCGCGTGGGATTGATCA 59.536 50.000 5.77 1.93 43.50 2.92
1679 5288 3.119352 GGGATTGATCAGGCAGTTTGTTC 60.119 47.826 0.00 0.00 0.00 3.18
1681 5290 4.159135 GGATTGATCAGGCAGTTTGTTCAT 59.841 41.667 0.00 0.00 0.00 2.57
1684 5293 3.754850 TGATCAGGCAGTTTGTTCATCTG 59.245 43.478 0.00 0.00 0.00 2.90
1698 5307 0.580578 CATCTGGATTCGCTTGCTCG 59.419 55.000 0.00 0.00 0.00 5.03
1700 5309 0.458543 TCTGGATTCGCTTGCTCGTC 60.459 55.000 0.00 0.00 0.00 4.20
1708 5317 1.803519 GCTTGCTCGTCAGTCCTCG 60.804 63.158 0.00 0.00 0.00 4.63
1713 5322 0.733223 GCTCGTCAGTCCTCGGAAAC 60.733 60.000 0.00 0.00 0.00 2.78
1737 5346 0.892063 GATCTATCGGGGAGGTCAGC 59.108 60.000 0.00 0.00 0.00 4.26
1762 5371 4.436998 CGGAGGGGAGTGTCGTGC 62.437 72.222 0.00 0.00 0.00 5.34
1766 5375 2.227089 GAGGGGAGTGTCGTGCGAAT 62.227 60.000 0.00 0.00 0.00 3.34
1814 5444 3.662759 TCCCTGTTCTTGAAAAGTGGT 57.337 42.857 0.55 0.00 46.34 4.16
1843 5473 5.051891 ACTGCACATATGAGCAAGTTTTC 57.948 39.130 24.85 0.00 40.86 2.29
1847 5477 5.180304 TGCACATATGAGCAAGTTTTCGTAA 59.820 36.000 23.16 0.00 38.62 3.18
1849 5479 6.620733 GCACATATGAGCAAGTTTTCGTAAGT 60.621 38.462 18.76 0.00 39.48 2.24
1858 5488 6.927381 AGCAAGTTTTCGTAAGTGTATAGTGT 59.073 34.615 0.00 0.00 39.48 3.55
1859 5489 7.115947 AGCAAGTTTTCGTAAGTGTATAGTGTC 59.884 37.037 0.00 0.00 39.48 3.67
1866 5496 6.849502 TCGTAAGTGTATAGTGTCAGGAAAG 58.150 40.000 0.00 0.00 39.48 2.62
1870 5500 9.733219 GTAAGTGTATAGTGTCAGGAAAGATAC 57.267 37.037 0.00 0.00 0.00 2.24
1873 5503 2.674796 AGTGTCAGGAAAGATACGCC 57.325 50.000 0.00 0.00 35.15 5.68
1874 5504 1.899814 AGTGTCAGGAAAGATACGCCA 59.100 47.619 0.00 0.00 35.15 5.69
1887 5517 0.882927 TACGCCACCAGTTTGCTGAC 60.883 55.000 0.00 0.00 45.28 3.51
1888 5518 1.893808 CGCCACCAGTTTGCTGACT 60.894 57.895 0.00 0.00 45.28 3.41
1896 5526 3.781079 CAGTTTGCTGACTGGTTTGAA 57.219 42.857 10.91 0.00 45.28 2.69
1902 5532 4.305989 TGCTGACTGGTTTGAAACAATC 57.694 40.909 10.53 4.68 0.00 2.67
1905 5535 5.592282 TGCTGACTGGTTTGAAACAATCTAA 59.408 36.000 10.53 0.00 0.00 2.10
1906 5536 6.145535 GCTGACTGGTTTGAAACAATCTAAG 58.854 40.000 10.53 1.66 0.00 2.18
1907 5537 6.633500 TGACTGGTTTGAAACAATCTAAGG 57.367 37.500 10.53 0.00 0.00 2.69
1908 5538 5.534654 TGACTGGTTTGAAACAATCTAAGGG 59.465 40.000 10.53 0.00 0.00 3.95
1909 5539 4.280929 ACTGGTTTGAAACAATCTAAGGGC 59.719 41.667 10.53 0.00 0.00 5.19
1910 5540 4.219115 TGGTTTGAAACAATCTAAGGGCA 58.781 39.130 10.53 0.00 0.00 5.36
1911 5541 4.837860 TGGTTTGAAACAATCTAAGGGCAT 59.162 37.500 10.53 0.00 0.00 4.40
1912 5542 5.047377 TGGTTTGAAACAATCTAAGGGCATC 60.047 40.000 10.53 0.00 0.00 3.91
1913 5543 5.185828 GGTTTGAAACAATCTAAGGGCATCT 59.814 40.000 10.53 0.00 0.00 2.90
1914 5544 6.377146 GGTTTGAAACAATCTAAGGGCATCTA 59.623 38.462 10.53 0.00 0.00 1.98
1915 5545 7.251281 GTTTGAAACAATCTAAGGGCATCTAC 58.749 38.462 2.68 0.00 0.00 2.59
1916 5546 6.061022 TGAAACAATCTAAGGGCATCTACA 57.939 37.500 0.00 0.00 0.00 2.74
1917 5547 6.115446 TGAAACAATCTAAGGGCATCTACAG 58.885 40.000 0.00 0.00 0.00 2.74
1918 5548 4.078639 ACAATCTAAGGGCATCTACAGC 57.921 45.455 0.00 0.00 0.00 4.40
1924 5554 3.813596 GGCATCTACAGCCGTTGG 58.186 61.111 0.00 0.00 43.15 3.77
1950 5580 2.822701 GGGGGTCTAAAAGCGCCG 60.823 66.667 2.29 0.00 46.85 6.46
2239 5880 4.213666 TCGCATAGGACGACGACT 57.786 55.556 0.00 1.61 33.96 4.18
2905 6547 1.081092 CTGGGGGAGGGAGAGTTGA 59.919 63.158 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.687700 TCATCAAGCTTGAGCCTCTC 57.312 50.000 31.14 0.00 41.08 3.20
20 21 2.048444 TCCATCATCAAGCTTGAGCC 57.952 50.000 31.14 0.00 41.08 4.70
47 48 2.128035 ACAAAAAGACGACGCTCTCTG 58.872 47.619 0.00 0.00 0.00 3.35
48 49 2.510768 ACAAAAAGACGACGCTCTCT 57.489 45.000 0.00 0.00 0.00 3.10
58 59 2.163412 TCATGCCGGCATACAAAAAGAC 59.837 45.455 39.94 0.00 34.91 3.01
59 60 2.163412 GTCATGCCGGCATACAAAAAGA 59.837 45.455 39.94 27.40 34.91 2.52
60 61 2.529151 GTCATGCCGGCATACAAAAAG 58.471 47.619 39.94 25.60 34.91 2.27
62 63 0.814457 GGTCATGCCGGCATACAAAA 59.186 50.000 39.94 20.38 34.91 2.44
75 76 0.179127 ACATCTCTGTCGCGGTCATG 60.179 55.000 6.13 4.31 0.00 3.07
85 86 3.509967 TCAACCACGTCATACATCTCTGT 59.490 43.478 0.00 0.00 39.49 3.41
120 121 2.227626 CCGACACAATTGCCAACACATA 59.772 45.455 5.05 0.00 0.00 2.29
126 127 3.046870 GGCCGACACAATTGCCAA 58.953 55.556 5.05 0.00 43.46 4.52
153 154 2.412870 CTCGTAGTTCATGTTGGCACA 58.587 47.619 0.00 0.00 37.31 4.57
160 161 3.418684 AAAAGGGCTCGTAGTTCATGT 57.581 42.857 0.00 0.00 0.00 3.21
176 177 3.065925 GCTATGCCAGCCTCTACAAAAAG 59.934 47.826 0.00 0.00 45.23 2.27
196 197 0.816825 CATAGTTCATGCCGGCAGCT 60.817 55.000 35.36 27.79 44.23 4.24
198 199 1.168407 CCCATAGTTCATGCCGGCAG 61.168 60.000 35.36 25.00 32.84 4.85
201 202 2.253758 CGCCCATAGTTCATGCCGG 61.254 63.158 0.00 0.00 32.84 6.13
218 219 2.416547 CTGTAGAAACTCCATGCCAACG 59.583 50.000 0.00 0.00 0.00 4.10
229 230 2.696506 GCTTAACGCCCTGTAGAAACT 58.303 47.619 0.00 0.00 0.00 2.66
248 437 3.777910 TAGAAACTCCCGCCCGGC 61.778 66.667 0.00 0.00 0.00 6.13
258 447 1.471684 CGTAGACGCCCTGTAGAAACT 59.528 52.381 0.00 0.00 0.00 2.66
260 449 0.813184 CCGTAGACGCCCTGTAGAAA 59.187 55.000 0.00 0.00 38.18 2.52
261 450 0.035152 TCCGTAGACGCCCTGTAGAA 60.035 55.000 0.00 0.00 38.18 2.10
262 451 0.463295 CTCCGTAGACGCCCTGTAGA 60.463 60.000 0.00 0.00 38.18 2.59
263 452 0.747283 ACTCCGTAGACGCCCTGTAG 60.747 60.000 0.00 0.00 38.18 2.74
264 453 1.028330 CACTCCGTAGACGCCCTGTA 61.028 60.000 0.00 0.00 38.18 2.74
265 454 2.035312 ACTCCGTAGACGCCCTGT 59.965 61.111 0.00 0.00 38.18 4.00
267 456 2.754658 CCACTCCGTAGACGCCCT 60.755 66.667 0.00 0.00 38.18 5.19
270 459 2.573941 ATTAACCACTCCGTAGACGC 57.426 50.000 0.00 0.00 38.18 5.19
271 460 4.333649 TCACTATTAACCACTCCGTAGACG 59.666 45.833 0.00 0.00 39.44 4.18
273 462 6.183360 CCAATCACTATTAACCACTCCGTAGA 60.183 42.308 0.00 0.00 0.00 2.59
274 463 5.983720 CCAATCACTATTAACCACTCCGTAG 59.016 44.000 0.00 0.00 0.00 3.51
275 464 5.422970 ACCAATCACTATTAACCACTCCGTA 59.577 40.000 0.00 0.00 0.00 4.02
277 466 4.766375 ACCAATCACTATTAACCACTCCG 58.234 43.478 0.00 0.00 0.00 4.63
280 469 6.134535 TCCAACCAATCACTATTAACCACT 57.865 37.500 0.00 0.00 0.00 4.00
281 470 6.827586 TTCCAACCAATCACTATTAACCAC 57.172 37.500 0.00 0.00 0.00 4.16
283 472 8.527810 TCAAATTCCAACCAATCACTATTAACC 58.472 33.333 0.00 0.00 0.00 2.85
290 479 8.090214 CACTTAATCAAATTCCAACCAATCACT 58.910 33.333 0.00 0.00 0.00 3.41
292 481 8.187913 TCACTTAATCAAATTCCAACCAATCA 57.812 30.769 0.00 0.00 0.00 2.57
293 482 9.143631 CTTCACTTAATCAAATTCCAACCAATC 57.856 33.333 0.00 0.00 0.00 2.67
295 484 8.243961 TCTTCACTTAATCAAATTCCAACCAA 57.756 30.769 0.00 0.00 0.00 3.67
296 485 7.523709 GCTCTTCACTTAATCAAATTCCAACCA 60.524 37.037 0.00 0.00 0.00 3.67
297 486 6.808704 GCTCTTCACTTAATCAAATTCCAACC 59.191 38.462 0.00 0.00 0.00 3.77
298 487 7.370383 TGCTCTTCACTTAATCAAATTCCAAC 58.630 34.615 0.00 0.00 0.00 3.77
299 488 7.309377 CCTGCTCTTCACTTAATCAAATTCCAA 60.309 37.037 0.00 0.00 0.00 3.53
303 492 5.477984 TGCCTGCTCTTCACTTAATCAAATT 59.522 36.000 0.00 0.00 0.00 1.82
305 494 4.397420 TGCCTGCTCTTCACTTAATCAAA 58.603 39.130 0.00 0.00 0.00 2.69
306 495 4.005650 CTGCCTGCTCTTCACTTAATCAA 58.994 43.478 0.00 0.00 0.00 2.57
307 496 3.603532 CTGCCTGCTCTTCACTTAATCA 58.396 45.455 0.00 0.00 0.00 2.57
308 497 2.354199 GCTGCCTGCTCTTCACTTAATC 59.646 50.000 0.00 0.00 38.95 1.75
310 499 1.072173 TGCTGCCTGCTCTTCACTTAA 59.928 47.619 0.00 0.00 43.37 1.85
311 500 0.686789 TGCTGCCTGCTCTTCACTTA 59.313 50.000 0.00 0.00 43.37 2.24
313 502 1.003597 CTGCTGCCTGCTCTTCACT 60.004 57.895 0.00 0.00 43.37 3.41
314 503 2.039405 CCTGCTGCCTGCTCTTCAC 61.039 63.158 0.00 0.00 43.37 3.18
315 504 2.181445 CTCCTGCTGCCTGCTCTTCA 62.181 60.000 0.00 0.00 43.37 3.02
316 505 1.449956 CTCCTGCTGCCTGCTCTTC 60.450 63.158 0.00 0.00 43.37 2.87
339 540 3.350612 TTAACACTGCGCGCCCAC 61.351 61.111 30.77 0.47 0.00 4.61
340 541 3.350612 GTTAACACTGCGCGCCCA 61.351 61.111 30.77 10.31 0.00 5.36
341 542 4.097863 GGTTAACACTGCGCGCCC 62.098 66.667 30.77 16.15 0.00 6.13
342 543 3.047877 AGGTTAACACTGCGCGCC 61.048 61.111 30.77 11.42 0.00 6.53
343 544 2.173382 CAGGTTAACACTGCGCGC 59.827 61.111 27.26 27.26 0.00 6.86
344 545 1.491563 GTCAGGTTAACACTGCGCG 59.508 57.895 8.10 0.00 35.94 6.86
350 551 1.203313 GCGCACGTCAGGTTAACAC 59.797 57.895 0.30 0.00 0.00 3.32
351 552 1.957186 GGCGCACGTCAGGTTAACA 60.957 57.895 10.83 0.00 0.00 2.41
428 634 4.736896 GTGGGACGGACGGTGCTC 62.737 72.222 4.72 0.00 37.13 4.26
450 656 2.099431 GTTCCGCAGAGCAGAGCAG 61.099 63.158 0.00 0.00 0.00 4.24
451 657 2.047844 GTTCCGCAGAGCAGAGCA 60.048 61.111 0.00 0.00 0.00 4.26
452 658 2.047844 TGTTCCGCAGAGCAGAGC 60.048 61.111 0.00 0.00 0.00 4.09
518 764 3.361977 GGAAACCACGTGCGGCAT 61.362 61.111 10.91 0.00 0.00 4.40
530 776 3.131400 AGAGCTCCGTATCTCAAGGAAAC 59.869 47.826 10.93 0.00 34.07 2.78
537 783 1.422024 AGGCTAGAGCTCCGTATCTCA 59.578 52.381 10.93 0.00 41.70 3.27
543 789 0.536460 GCTAGAGGCTAGAGCTCCGT 60.536 60.000 10.93 0.00 41.70 4.69
552 798 0.758734 TACCCGTACGCTAGAGGCTA 59.241 55.000 10.49 0.00 39.13 3.93
553 799 0.817229 GTACCCGTACGCTAGAGGCT 60.817 60.000 10.49 0.00 39.13 4.58
554 800 1.651461 GTACCCGTACGCTAGAGGC 59.349 63.158 10.49 0.00 37.64 4.70
555 801 0.464373 TGGTACCCGTACGCTAGAGG 60.464 60.000 10.49 7.90 36.94 3.69
556 802 0.942962 CTGGTACCCGTACGCTAGAG 59.057 60.000 10.49 0.00 36.94 2.43
557 803 0.253044 ACTGGTACCCGTACGCTAGA 59.747 55.000 10.49 0.00 36.94 2.43
558 804 1.599542 GTACTGGTACCCGTACGCTAG 59.400 57.143 25.09 9.92 36.94 3.42
559 805 1.065782 TGTACTGGTACCCGTACGCTA 60.066 52.381 30.02 17.30 36.81 4.26
560 806 0.322456 TGTACTGGTACCCGTACGCT 60.322 55.000 30.02 5.58 36.81 5.07
561 807 0.179163 GTGTACTGGTACCCGTACGC 60.179 60.000 31.46 31.46 36.81 4.42
562 808 0.451783 GGTGTACTGGTACCCGTACG 59.548 60.000 30.02 8.69 36.81 3.67
563 809 0.451783 CGGTGTACTGGTACCCGTAC 59.548 60.000 29.74 29.74 41.07 3.67
564 810 2.866872 CGGTGTACTGGTACCCGTA 58.133 57.895 21.32 11.78 41.07 4.02
565 811 3.685435 CGGTGTACTGGTACCCGT 58.315 61.111 13.90 13.90 41.07 5.28
566 812 0.734889 CTACGGTGTACTGGTACCCG 59.265 60.000 24.72 24.72 46.06 5.28
567 813 1.745653 GACTACGGTGTACTGGTACCC 59.254 57.143 10.07 7.94 35.26 3.69
735 982 0.587285 ACGTCGCGATCTCATCCTAC 59.413 55.000 14.06 0.00 0.00 3.18
736 983 1.797046 GTACGTCGCGATCTCATCCTA 59.203 52.381 14.06 0.00 0.00 2.94
737 984 0.587285 GTACGTCGCGATCTCATCCT 59.413 55.000 14.06 0.00 0.00 3.24
774 1026 3.112126 CTTCGCGCGGGATGCAATT 62.112 57.895 31.69 0.00 46.97 2.32
775 1027 3.576356 CTTCGCGCGGGATGCAAT 61.576 61.111 31.69 0.00 46.97 3.56
779 1031 3.321315 TTTTGCTTCGCGCGGGATG 62.321 57.895 31.69 27.45 43.27 3.51
780 1032 3.039202 CTTTTGCTTCGCGCGGGAT 62.039 57.895 31.69 0.00 43.27 3.85
781 1033 3.722295 CTTTTGCTTCGCGCGGGA 61.722 61.111 31.69 23.01 43.27 5.14
875 1151 2.230025 CGAGGAGAGCGACATGGATATT 59.770 50.000 0.00 0.00 0.00 1.28
876 1152 1.815613 CGAGGAGAGCGACATGGATAT 59.184 52.381 0.00 0.00 0.00 1.63
877 1153 1.239347 CGAGGAGAGCGACATGGATA 58.761 55.000 0.00 0.00 0.00 2.59
878 1154 2.037053 CGAGGAGAGCGACATGGAT 58.963 57.895 0.00 0.00 0.00 3.41
879 1155 2.775856 GCGAGGAGAGCGACATGGA 61.776 63.158 0.00 0.00 0.00 3.41
951 1234 0.461693 GTCCTCTGCAGCTTGCTAGG 60.462 60.000 9.47 9.79 45.31 3.02
967 1261 1.702299 CGACGATCGTTTGCTGTCC 59.298 57.895 23.63 5.71 34.72 4.02
968 1262 1.057361 GCGACGATCGTTTGCTGTC 59.943 57.895 28.44 13.22 42.81 3.51
970 1264 1.626654 AAGGCGACGATCGTTTGCTG 61.627 55.000 31.71 18.35 42.81 4.41
1277 1584 0.313987 GGCAAAGTTAAGGCACGCTT 59.686 50.000 0.00 0.00 0.00 4.68
1278 1585 1.852067 CGGCAAAGTTAAGGCACGCT 61.852 55.000 3.31 0.00 0.00 5.07
1393 1700 1.067776 AGAGGAATTCGTCGCGTCTTT 60.068 47.619 19.46 1.05 36.02 2.52
1395 1702 0.179161 CAGAGGAATTCGTCGCGTCT 60.179 55.000 19.46 2.36 36.02 4.18
1406 1728 1.296715 GCCACGGACACAGAGGAAT 59.703 57.895 0.00 0.00 0.00 3.01
1407 1729 2.741092 GCCACGGACACAGAGGAA 59.259 61.111 0.00 0.00 0.00 3.36
1441 1781 0.179103 TGCATCATCAGCATCGTCGT 60.179 50.000 0.00 0.00 37.02 4.34
1442 1782 0.507358 CTGCATCATCAGCATCGTCG 59.493 55.000 0.00 0.00 41.82 5.12
1443 1783 0.866427 CCTGCATCATCAGCATCGTC 59.134 55.000 0.00 0.00 41.82 4.20
1444 1784 0.466963 TCCTGCATCATCAGCATCGT 59.533 50.000 0.00 0.00 41.82 3.73
1450 1790 1.597302 CGGCCTCCTGCATCATCAG 60.597 63.158 0.00 0.00 43.89 2.90
1667 5276 2.957402 TCCAGATGAACAAACTGCCT 57.043 45.000 0.00 0.00 0.00 4.75
1679 5288 0.580578 CGAGCAAGCGAATCCAGATG 59.419 55.000 0.00 0.00 0.00 2.90
1681 5290 0.458543 GACGAGCAAGCGAATCCAGA 60.459 55.000 0.00 0.00 34.83 3.86
1684 5293 0.737715 ACTGACGAGCAAGCGAATCC 60.738 55.000 0.00 0.00 34.83 3.01
1722 5331 1.457643 CAGGCTGACCTCCCCGATA 60.458 63.158 9.42 0.00 46.34 2.92
1725 5334 3.465403 CTCAGGCTGACCTCCCCG 61.465 72.222 14.43 0.00 46.34 5.73
1726 5335 3.791586 GCTCAGGCTGACCTCCCC 61.792 72.222 14.43 0.00 46.34 4.81
1727 5336 2.686835 AGCTCAGGCTGACCTCCC 60.687 66.667 14.43 0.00 46.34 4.30
1728 5337 2.899505 GAGCTCAGGCTGACCTCC 59.100 66.667 23.54 9.96 46.34 4.30
1729 5338 2.493973 CGAGCTCAGGCTGACCTC 59.506 66.667 23.95 23.95 46.34 3.85
1737 5346 2.837291 CTCCCCTCCGAGCTCAGG 60.837 72.222 15.40 13.64 0.00 3.86
1739 5348 2.363018 CACTCCCCTCCGAGCTCA 60.363 66.667 15.40 0.00 32.79 4.26
1773 5382 0.034059 AGCAGAGTATATGGCGTGCC 59.966 55.000 3.30 3.30 0.00 5.01
1774 5383 1.871080 AAGCAGAGTATATGGCGTGC 58.129 50.000 0.00 0.00 0.00 5.34
1775 5384 2.802816 GGAAAGCAGAGTATATGGCGTG 59.197 50.000 0.00 0.00 0.00 5.34
1777 5386 2.037772 AGGGAAAGCAGAGTATATGGCG 59.962 50.000 0.00 0.00 0.00 5.69
1778 5387 3.181450 ACAGGGAAAGCAGAGTATATGGC 60.181 47.826 0.00 0.00 0.00 4.40
1780 5389 5.923204 AGAACAGGGAAAGCAGAGTATATG 58.077 41.667 0.00 0.00 0.00 1.78
1781 5390 6.156949 TCAAGAACAGGGAAAGCAGAGTATAT 59.843 38.462 0.00 0.00 0.00 0.86
1782 5391 5.483937 TCAAGAACAGGGAAAGCAGAGTATA 59.516 40.000 0.00 0.00 0.00 1.47
1783 5392 4.287067 TCAAGAACAGGGAAAGCAGAGTAT 59.713 41.667 0.00 0.00 0.00 2.12
1814 5444 4.009002 TGCTCATATGTGCAGTTTTAGCA 58.991 39.130 24.59 15.17 39.29 3.49
1829 5459 9.297586 CTATACACTTACGAAAACTTGCTCATA 57.702 33.333 0.00 0.00 0.00 2.15
1843 5473 6.849502 TCTTTCCTGACACTATACACTTACG 58.150 40.000 0.00 0.00 0.00 3.18
1847 5477 6.459848 GCGTATCTTTCCTGACACTATACACT 60.460 42.308 0.00 0.00 0.00 3.55
1849 5479 5.221185 GGCGTATCTTTCCTGACACTATACA 60.221 44.000 0.00 0.00 0.00 2.29
1858 5488 1.207089 CTGGTGGCGTATCTTTCCTGA 59.793 52.381 0.00 0.00 0.00 3.86
1859 5489 1.066143 ACTGGTGGCGTATCTTTCCTG 60.066 52.381 0.00 0.00 0.00 3.86
1866 5496 0.447801 CAGCAAACTGGTGGCGTATC 59.552 55.000 0.00 0.00 41.77 2.24
1870 5500 2.639286 GTCAGCAAACTGGTGGCG 59.361 61.111 6.05 0.00 45.21 5.69
1887 5517 4.280677 TGCCCTTAGATTGTTTCAAACCAG 59.719 41.667 0.00 0.00 0.00 4.00
1888 5518 4.219115 TGCCCTTAGATTGTTTCAAACCA 58.781 39.130 0.00 0.00 0.00 3.67
1893 5523 6.061022 TGTAGATGCCCTTAGATTGTTTCA 57.939 37.500 0.00 0.00 0.00 2.69
1894 5524 5.008118 GCTGTAGATGCCCTTAGATTGTTTC 59.992 44.000 0.00 0.00 0.00 2.78
1896 5526 4.455606 GCTGTAGATGCCCTTAGATTGTT 58.544 43.478 0.00 0.00 0.00 2.83
1907 5537 2.472909 GCCAACGGCTGTAGATGCC 61.473 63.158 0.00 0.00 46.69 4.40
1908 5538 3.102097 GCCAACGGCTGTAGATGC 58.898 61.111 0.00 0.00 46.69 3.91
1933 5563 2.822701 CGGCGCTTTTAGACCCCC 60.823 66.667 7.64 0.00 0.00 5.40
1934 5564 3.506096 GCGGCGCTTTTAGACCCC 61.506 66.667 26.86 0.00 0.00 4.95
1935 5565 3.506096 GGCGGCGCTTTTAGACCC 61.506 66.667 32.30 7.60 0.00 4.46
1936 5566 3.506096 GGGCGGCGCTTTTAGACC 61.506 66.667 32.30 18.43 0.00 3.85
1937 5567 2.744709 TGGGCGGCGCTTTTAGAC 60.745 61.111 32.30 12.84 0.00 2.59
1938 5568 2.435938 CTGGGCGGCGCTTTTAGA 60.436 61.111 32.30 8.23 0.00 2.10
1939 5569 3.508840 CCTGGGCGGCGCTTTTAG 61.509 66.667 32.30 21.81 0.00 1.85
1960 5590 0.035247 TTTTAATACGCGCCTGGGGT 60.035 50.000 5.73 0.00 44.91 4.95
2025 5660 3.296322 TTTGCCATGTTTAGCCGAAAG 57.704 42.857 0.00 0.00 0.00 2.62
2406 6047 3.744719 CGGTGAAGACGGAGCCGA 61.745 66.667 16.83 0.00 44.57 5.54
2490 6131 3.390521 TCATCAACGAGGGCGGCT 61.391 61.111 9.56 0.00 43.17 5.52
2583 6224 3.449227 CGCACTCCTCCGGCACTA 61.449 66.667 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.