Multiple sequence alignment - TraesCS5A01G427300

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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 TraesCS5A01G427300 chr5A 100.000 3584 0 0 1 3584 611981815 611978232 0.000000e+00 6619
1 TraesCS5A01G427300 chr5A 94.936 1402 59 6 1040 2431 124618323 124619722 0.000000e+00 2185
2 TraesCS5A01G427300 chr5A 91.959 883 48 6 2723 3584 124621662 124622542 0.000000e+00 1216
3 TraesCS5A01G427300 chr5A 89.912 912 55 15 1 884 124612714 124613616 0.000000e+00 1140
4 TraesCS5A01G427300 chr5A 89.632 897 57 13 1 869 124602355 124603243 0.000000e+00 1109
5 TraesCS5A01G427300 chr5A 90.398 854 44 18 1 826 124600245 124601088 0.000000e+00 1088
6 TraesCS5A01G427300 chr5A 89.061 905 59 17 9 884 124605230 124606123 0.000000e+00 1086
7 TraesCS5A01G427300 chr5A 93.352 722 38 8 9 726 124615580 124616295 0.000000e+00 1059
8 TraesCS5A01G427300 chr6D 91.227 3659 223 41 9 3584 420231943 420228300 0.000000e+00 4889
9 TraesCS5A01G427300 chr6D 89.519 582 39 11 2588 3164 28311336 28310772 0.000000e+00 717
10 TraesCS5A01G427300 chr6D 94.949 396 19 1 3120 3514 28310772 28310377 1.410000e-173 619
11 TraesCS5A01G427300 chr4A 90.591 3656 246 43 9 3584 581496532 581492895 0.000000e+00 4756
12 TraesCS5A01G427300 chr4A 86.943 1930 180 32 9 1882 15921418 15919505 0.000000e+00 2102
13 TraesCS5A01G427300 chr4A 89.563 939 66 19 7 918 581497065 581496132 0.000000e+00 1162
14 TraesCS5A01G427300 chr4A 90.066 916 52 24 1 887 581499204 581498299 0.000000e+00 1151
15 TraesCS5A01G427300 chr4A 89.978 908 51 25 9 887 581502050 581501154 0.000000e+00 1136
16 TraesCS5A01G427300 chr5D 89.921 3274 201 46 327 3514 441572655 441569425 0.000000e+00 4098
17 TraesCS5A01G427300 chr5D 92.769 2337 118 21 1216 3513 490439523 490437199 0.000000e+00 3332
18 TraesCS5A01G427300 chr5D 84.089 949 92 28 327 1224 490440487 490439547 0.000000e+00 861
19 TraesCS5A01G427300 chr7A 92.447 1933 89 19 1616 3512 47296922 47295011 0.000000e+00 2708
20 TraesCS5A01G427300 chr7A 85.679 1606 162 43 16 1577 47298498 47296917 0.000000e+00 1629
21 TraesCS5A01G427300 chr7A 86.964 1235 123 29 1398 2617 213100428 213101639 0.000000e+00 1354
22 TraesCS5A01G427300 chr7A 82.830 530 58 12 2615 3118 213101817 213102339 9.130000e-121 444
23 TraesCS5A01G427300 chr7D 91.441 1998 99 24 960 2921 44719598 44717637 0.000000e+00 2676
24 TraesCS5A01G427300 chr7D 89.683 853 60 10 1 827 44722974 44722124 0.000000e+00 1062
25 TraesCS5A01G427300 chr7D 94.085 541 25 5 2978 3514 44717494 44716957 0.000000e+00 815
26 TraesCS5A01G427300 chr5B 88.129 2207 160 46 327 2460 604869372 604871549 0.000000e+00 2531
27 TraesCS5A01G427300 chr5B 87.945 365 19 6 2765 3106 604871548 604871910 1.200000e-109 407
28 TraesCS5A01G427300 chr4D 87.366 1963 189 34 10 1928 472683724 472681777 0.000000e+00 2196
29 TraesCS5A01G427300 chr1D 87.506 1929 168 36 195 2064 439791941 439790027 0.000000e+00 2159
30 TraesCS5A01G427300 chr2B 89.768 1378 95 29 724 2077 733161485 733162840 0.000000e+00 1722
31 TraesCS5A01G427300 chr2B 82.863 531 64 13 2615 3121 270742537 270742010 5.460000e-123 451
32 TraesCS5A01G427300 chr6A 89.619 578 34 13 2588 3161 29576716 29577271 0.000000e+00 712
33 TraesCS5A01G427300 chr6A 94.832 387 19 1 3120 3505 29577274 29577660 1.420000e-168 603
34 TraesCS5A01G427300 chr7B 84.837 521 51 10 2622 3118 433801125 433801641 1.920000e-137 499
35 TraesCS5A01G427300 chr4B 89.873 316 29 3 721 1034 564150938 564151252 1.550000e-108 403


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 TraesCS5A01G427300 chr5A 611978232 611981815 3583 True 6619.000000 6619 100.000000 1 3584 1 chr5A.!!$R1 3583
1 TraesCS5A01G427300 chr5A 124612714 124622542 9828 False 1400.000000 2185 92.539750 1 3584 4 chr5A.!!$F2 3583
2 TraesCS5A01G427300 chr5A 124600245 124606123 5878 False 1094.333333 1109 89.697000 1 884 3 chr5A.!!$F1 883
3 TraesCS5A01G427300 chr6D 420228300 420231943 3643 True 4889.000000 4889 91.227000 9 3584 1 chr6D.!!$R1 3575
4 TraesCS5A01G427300 chr6D 28310377 28311336 959 True 668.000000 717 92.234000 2588 3514 2 chr6D.!!$R2 926
5 TraesCS5A01G427300 chr4A 15919505 15921418 1913 True 2102.000000 2102 86.943000 9 1882 1 chr4A.!!$R1 1873
6 TraesCS5A01G427300 chr4A 581492895 581502050 9155 True 2051.250000 4756 90.049500 1 3584 4 chr4A.!!$R2 3583
7 TraesCS5A01G427300 chr5D 441569425 441572655 3230 True 4098.000000 4098 89.921000 327 3514 1 chr5D.!!$R1 3187
8 TraesCS5A01G427300 chr5D 490437199 490440487 3288 True 2096.500000 3332 88.429000 327 3513 2 chr5D.!!$R2 3186
9 TraesCS5A01G427300 chr7A 47295011 47298498 3487 True 2168.500000 2708 89.063000 16 3512 2 chr7A.!!$R1 3496
10 TraesCS5A01G427300 chr7A 213100428 213102339 1911 False 899.000000 1354 84.897000 1398 3118 2 chr7A.!!$F1 1720
11 TraesCS5A01G427300 chr7D 44716957 44722974 6017 True 1517.666667 2676 91.736333 1 3514 3 chr7D.!!$R1 3513
12 TraesCS5A01G427300 chr5B 604869372 604871910 2538 False 1469.000000 2531 88.037000 327 3106 2 chr5B.!!$F1 2779
13 TraesCS5A01G427300 chr4D 472681777 472683724 1947 True 2196.000000 2196 87.366000 10 1928 1 chr4D.!!$R1 1918
14 TraesCS5A01G427300 chr1D 439790027 439791941 1914 True 2159.000000 2159 87.506000 195 2064 1 chr1D.!!$R1 1869
15 TraesCS5A01G427300 chr2B 733161485 733162840 1355 False 1722.000000 1722 89.768000 724 2077 1 chr2B.!!$F1 1353
16 TraesCS5A01G427300 chr2B 270742010 270742537 527 True 451.000000 451 82.863000 2615 3121 1 chr2B.!!$R1 506
17 TraesCS5A01G427300 chr6A 29576716 29577660 944 False 657.500000 712 92.225500 2588 3505 2 chr6A.!!$F1 917
18 TraesCS5A01G427300 chr7B 433801125 433801641 516 False 499.000000 499 84.837000 2622 3118 1 chr7B.!!$F1 496

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
552 8546 1.619827 ACATGGAGCAATTTGGGTGTG 59.380 47.619 0.0 0.0 0.0 3.82 F
1926 14349 0.106819 GGCTGGCTCATTCATGGACT 60.107 55.000 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 14493 0.036732 CCCTGCAGTAGCCAACAGAA 59.963 55.0 13.81 0.0 41.13 3.02 R
3408 17925 0.482446 TGAGCAACCCCAATGGACTT 59.518 50.0 0.00 0.0 38.00 3.01 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
40 43 3.678056 AGTTCAGCGATTGTGACCTTA 57.322 42.857 0.00 0.00 0.00 2.69
48 51 4.339814 AGCGATTGTGACCTTAAACCAAAA 59.660 37.500 0.00 0.00 0.00 2.44
179 723 3.861840 AGGTGATTGTGATACTGAACCG 58.138 45.455 0.00 0.00 0.00 4.44
185 729 7.305474 GTGATTGTGATACTGAACCGAATTTT 58.695 34.615 0.00 0.00 0.00 1.82
199 5660 5.120399 ACCGAATTTTACGCTGGATTATGA 58.880 37.500 0.00 0.00 0.00 2.15
200 5661 5.236478 ACCGAATTTTACGCTGGATTATGAG 59.764 40.000 0.00 0.00 0.00 2.90
201 5662 5.465390 CCGAATTTTACGCTGGATTATGAGA 59.535 40.000 0.00 0.00 0.00 3.27
202 5663 6.147821 CCGAATTTTACGCTGGATTATGAGAT 59.852 38.462 0.00 0.00 0.00 2.75
203 5664 7.307989 CCGAATTTTACGCTGGATTATGAGATT 60.308 37.037 0.00 0.00 0.00 2.40
204 5665 8.070171 CGAATTTTACGCTGGATTATGAGATTT 58.930 33.333 0.00 0.00 0.00 2.17
205 5666 9.736023 GAATTTTACGCTGGATTATGAGATTTT 57.264 29.630 0.00 0.00 0.00 1.82
208 5669 7.962964 TTACGCTGGATTATGAGATTTTAGG 57.037 36.000 0.00 0.00 0.00 2.69
209 5670 5.930135 ACGCTGGATTATGAGATTTTAGGT 58.070 37.500 0.00 0.00 0.00 3.08
210 5671 5.760253 ACGCTGGATTATGAGATTTTAGGTG 59.240 40.000 0.00 0.00 0.00 4.00
211 5672 5.180117 CGCTGGATTATGAGATTTTAGGTGG 59.820 44.000 0.00 0.00 0.00 4.61
212 5673 6.299141 GCTGGATTATGAGATTTTAGGTGGA 58.701 40.000 0.00 0.00 0.00 4.02
213 5674 6.944862 GCTGGATTATGAGATTTTAGGTGGAT 59.055 38.462 0.00 0.00 0.00 3.41
214 5675 7.449704 GCTGGATTATGAGATTTTAGGTGGATT 59.550 37.037 0.00 0.00 0.00 3.01
215 5676 9.359653 CTGGATTATGAGATTTTAGGTGGATTT 57.640 33.333 0.00 0.00 0.00 2.17
222 5683 9.853177 ATGAGATTTTAGGTGGATTTAGTTAGG 57.147 33.333 0.00 0.00 0.00 2.69
223 5684 8.832735 TGAGATTTTAGGTGGATTTAGTTAGGT 58.167 33.333 0.00 0.00 0.00 3.08
224 5685 9.110502 GAGATTTTAGGTGGATTTAGTTAGGTG 57.889 37.037 0.00 0.00 0.00 4.00
225 5686 8.832735 AGATTTTAGGTGGATTTAGTTAGGTGA 58.167 33.333 0.00 0.00 0.00 4.02
226 5687 9.628500 GATTTTAGGTGGATTTAGTTAGGTGAT 57.372 33.333 0.00 0.00 0.00 3.06
227 5688 9.990868 ATTTTAGGTGGATTTAGTTAGGTGATT 57.009 29.630 0.00 0.00 0.00 2.57
228 5689 8.801882 TTTAGGTGGATTTAGTTAGGTGATTG 57.198 34.615 0.00 0.00 0.00 2.67
229 5690 6.388619 AGGTGGATTTAGTTAGGTGATTGT 57.611 37.500 0.00 0.00 0.00 2.71
230 5691 6.180472 AGGTGGATTTAGTTAGGTGATTGTG 58.820 40.000 0.00 0.00 0.00 3.33
231 5692 5.944007 GGTGGATTTAGTTAGGTGATTGTGT 59.056 40.000 0.00 0.00 0.00 3.72
232 5693 6.093633 GGTGGATTTAGTTAGGTGATTGTGTC 59.906 42.308 0.00 0.00 0.00 3.67
233 5694 6.879458 GTGGATTTAGTTAGGTGATTGTGTCT 59.121 38.462 0.00 0.00 0.00 3.41
234 5695 7.390718 GTGGATTTAGTTAGGTGATTGTGTCTT 59.609 37.037 0.00 0.00 0.00 3.01
235 5696 7.390440 TGGATTTAGTTAGGTGATTGTGTCTTG 59.610 37.037 0.00 0.00 0.00 3.02
236 5697 7.606456 GGATTTAGTTAGGTGATTGTGTCTTGA 59.394 37.037 0.00 0.00 0.00 3.02
237 5698 7.962964 TTTAGTTAGGTGATTGTGTCTTGAG 57.037 36.000 0.00 0.00 0.00 3.02
238 5699 5.808366 AGTTAGGTGATTGTGTCTTGAGA 57.192 39.130 0.00 0.00 0.00 3.27
239 5700 6.174720 AGTTAGGTGATTGTGTCTTGAGAA 57.825 37.500 0.00 0.00 0.00 2.87
240 5701 6.773638 AGTTAGGTGATTGTGTCTTGAGAAT 58.226 36.000 0.00 0.00 0.00 2.40
241 5702 7.907389 AGTTAGGTGATTGTGTCTTGAGAATA 58.093 34.615 0.00 0.00 0.00 1.75
242 5703 8.543774 AGTTAGGTGATTGTGTCTTGAGAATAT 58.456 33.333 0.00 0.00 0.00 1.28
243 5704 9.817809 GTTAGGTGATTGTGTCTTGAGAATATA 57.182 33.333 0.00 0.00 0.00 0.86
245 5706 8.083828 AGGTGATTGTGTCTTGAGAATATAGT 57.916 34.615 0.00 0.00 0.00 2.12
246 5707 8.200792 AGGTGATTGTGTCTTGAGAATATAGTC 58.799 37.037 0.00 0.00 0.00 2.59
247 5708 7.981789 GGTGATTGTGTCTTGAGAATATAGTCA 59.018 37.037 2.62 0.00 0.00 3.41
248 5709 9.371136 GTGATTGTGTCTTGAGAATATAGTCAA 57.629 33.333 2.62 0.00 0.00 3.18
249 5710 9.942850 TGATTGTGTCTTGAGAATATAGTCAAA 57.057 29.630 2.62 0.00 32.36 2.69
253 5714 9.591792 TGTGTCTTGAGAATATAGTCAAAGATG 57.408 33.333 16.45 0.00 32.36 2.90
254 5715 9.593134 GTGTCTTGAGAATATAGTCAAAGATGT 57.407 33.333 16.45 0.00 32.36 3.06
261 5722 9.994432 GAGAATATAGTCAAAGATGTTTGTTGG 57.006 33.333 14.36 0.00 43.22 3.77
262 5723 9.739276 AGAATATAGTCAAAGATGTTTGTTGGA 57.261 29.630 14.36 0.92 43.22 3.53
263 5724 9.774742 GAATATAGTCAAAGATGTTTGTTGGAC 57.225 33.333 14.36 6.09 43.22 4.02
264 5725 9.520515 AATATAGTCAAAGATGTTTGTTGGACT 57.479 29.630 14.36 12.36 43.22 3.85
267 5728 7.206981 AGTCAAAGATGTTTGTTGGACTATG 57.793 36.000 14.36 0.00 43.22 2.23
268 5729 6.998074 AGTCAAAGATGTTTGTTGGACTATGA 59.002 34.615 14.36 0.00 43.22 2.15
269 5730 7.173907 AGTCAAAGATGTTTGTTGGACTATGAG 59.826 37.037 14.36 0.00 43.22 2.90
270 5731 7.173218 GTCAAAGATGTTTGTTGGACTATGAGA 59.827 37.037 14.36 0.00 43.22 3.27
271 5732 7.884877 TCAAAGATGTTTGTTGGACTATGAGAT 59.115 33.333 14.36 0.00 43.22 2.75
272 5733 8.517878 CAAAGATGTTTGTTGGACTATGAGATT 58.482 33.333 7.15 0.00 38.64 2.40
273 5734 8.641498 AAGATGTTTGTTGGACTATGAGATTT 57.359 30.769 0.00 0.00 0.00 2.17
274 5735 8.641498 AGATGTTTGTTGGACTATGAGATTTT 57.359 30.769 0.00 0.00 0.00 1.82
275 5736 9.739276 AGATGTTTGTTGGACTATGAGATTTTA 57.261 29.630 0.00 0.00 0.00 1.52
276 5737 9.994432 GATGTTTGTTGGACTATGAGATTTTAG 57.006 33.333 0.00 0.00 0.00 1.85
277 5738 8.335532 TGTTTGTTGGACTATGAGATTTTAGG 57.664 34.615 0.00 0.00 0.00 2.69
278 5739 7.942341 TGTTTGTTGGACTATGAGATTTTAGGT 59.058 33.333 0.00 0.00 0.00 3.08
279 5740 8.793592 GTTTGTTGGACTATGAGATTTTAGGTT 58.206 33.333 0.00 0.00 0.00 3.50
280 5741 8.934023 TTGTTGGACTATGAGATTTTAGGTTT 57.066 30.769 0.00 0.00 0.00 3.27
282 5743 9.667107 TGTTGGACTATGAGATTTTAGGTTTAG 57.333 33.333 0.00 0.00 0.00 1.85
283 5744 9.668497 GTTGGACTATGAGATTTTAGGTTTAGT 57.332 33.333 0.00 0.00 0.00 2.24
297 5758 9.667107 TTTTAGGTTTAGTAGATGAGAATGGTG 57.333 33.333 0.00 0.00 0.00 4.17
298 5759 8.603898 TTAGGTTTAGTAGATGAGAATGGTGA 57.396 34.615 0.00 0.00 0.00 4.02
299 5760 7.682787 AGGTTTAGTAGATGAGAATGGTGAT 57.317 36.000 0.00 0.00 0.00 3.06
300 5761 8.095452 AGGTTTAGTAGATGAGAATGGTGATT 57.905 34.615 0.00 0.00 0.00 2.57
301 5762 9.213777 AGGTTTAGTAGATGAGAATGGTGATTA 57.786 33.333 0.00 0.00 0.00 1.75
313 5774 9.519191 TGAGAATGGTGATTATTATATTGGTGG 57.481 33.333 0.00 0.00 0.00 4.61
314 5775 9.739276 GAGAATGGTGATTATTATATTGGTGGA 57.261 33.333 0.00 0.00 0.00 4.02
326 5787 8.990163 ATTATATTGGTGGATAAACCGTTCTT 57.010 30.769 0.00 0.00 43.73 2.52
327 5788 8.810990 TTATATTGGTGGATAAACCGTTCTTT 57.189 30.769 0.00 0.00 43.73 2.52
328 5789 9.902684 TTATATTGGTGGATAAACCGTTCTTTA 57.097 29.630 0.00 0.00 43.73 1.85
329 5790 8.810990 ATATTGGTGGATAAACCGTTCTTTAA 57.189 30.769 0.00 0.00 43.73 1.52
330 5791 7.712204 ATTGGTGGATAAACCGTTCTTTAAT 57.288 32.000 0.00 0.00 43.73 1.40
331 5792 7.527568 TTGGTGGATAAACCGTTCTTTAATT 57.472 32.000 0.00 0.00 43.73 1.40
334 5795 8.732531 TGGTGGATAAACCGTTCTTTAATTTAG 58.267 33.333 0.00 0.00 43.73 1.85
433 8427 8.328758 TGGATTTAGTTAGGTGATTGTGATCTT 58.671 33.333 0.00 0.00 33.28 2.40
439 8433 4.271696 AGGTGATTGTGATCTTGACGAA 57.728 40.909 0.00 0.00 33.28 3.85
521 8515 9.540538 TGGTTATTATATTGGTGGATAAATGGG 57.459 33.333 0.00 0.00 0.00 4.00
548 8542 4.806640 AGTAAACATGGAGCAATTTGGG 57.193 40.909 0.00 0.00 0.00 4.12
552 8546 1.619827 ACATGGAGCAATTTGGGTGTG 59.380 47.619 0.00 0.00 0.00 3.82
575 8569 5.880332 TGGTTAGGCTATTGTGATCTTGAAC 59.120 40.000 0.00 0.00 0.00 3.18
584 8578 9.195411 GCTATTGTGATCTTGAACAAATTTCAA 57.805 29.630 0.98 0.00 39.57 2.69
593 8587 8.422973 TCTTGAACAAATTTCAAAGTGGATTG 57.577 30.769 1.42 0.00 37.89 2.67
595 8589 5.233902 TGAACAAATTTCAAAGTGGATTGCG 59.766 36.000 0.00 0.00 0.00 4.85
596 8590 4.942852 ACAAATTTCAAAGTGGATTGCGA 58.057 34.783 0.00 0.00 0.00 5.10
699 9764 8.462016 ACAATTTGGATTTAGTTAGATGACTGC 58.538 33.333 0.78 0.00 0.00 4.40
716 9781 5.639757 TGACTGCGATATTGAACCAAATTG 58.360 37.500 0.00 0.00 0.00 2.32
750 12517 4.897509 TGAGGTGATTGTGTCTTGAGAT 57.102 40.909 0.00 0.00 0.00 2.75
755 12522 6.950842 AGGTGATTGTGTCTTGAGATGATAA 58.049 36.000 0.00 0.00 0.00 1.75
1038 13262 1.795170 GCTTGTGCACAATGGTCCGT 61.795 55.000 31.17 0.00 39.41 4.69
1211 13572 4.587684 GCTAGGTATTCCAGGTAGTTAGCA 59.412 45.833 0.00 0.00 35.89 3.49
1212 13573 5.509332 GCTAGGTATTCCAGGTAGTTAGCAC 60.509 48.000 0.00 0.00 35.89 4.40
1213 13574 3.710165 AGGTATTCCAGGTAGTTAGCACC 59.290 47.826 0.00 0.00 35.89 5.01
1214 13575 3.453353 GGTATTCCAGGTAGTTAGCACCA 59.547 47.826 0.00 0.00 38.62 4.17
1233 13626 4.021916 ACCACTATGGACTACACCTACAC 58.978 47.826 0.84 0.00 40.96 2.90
1379 13781 9.588096 AACTTGGTATGGAGAAGTTTTCTTATT 57.412 29.630 0.00 0.00 40.87 1.40
1543 13959 4.555511 GCTTTTCTTTTCATCTGCAGTCGT 60.556 41.667 14.67 0.00 0.00 4.34
1597 14013 6.100668 GGTTTCACATACCTCTTCTACACTC 58.899 44.000 0.00 0.00 32.75 3.51
1686 14102 8.756864 TGTTTTGTCACTTTGTTAAACTTTGTC 58.243 29.630 0.00 0.00 0.00 3.18
1778 14200 3.895232 ACCTACAGATCTTGAATGCGT 57.105 42.857 0.00 0.00 0.00 5.24
1919 14342 2.124983 TCTGCGGCTGGCTCATTC 60.125 61.111 7.03 0.00 44.05 2.67
1923 14346 2.842256 GCGGCTGGCTCATTCATGG 61.842 63.158 0.00 0.00 39.11 3.66
1924 14347 1.153107 CGGCTGGCTCATTCATGGA 60.153 57.895 0.00 0.00 0.00 3.41
1925 14348 1.442526 CGGCTGGCTCATTCATGGAC 61.443 60.000 0.00 0.00 0.00 4.02
1926 14349 0.106819 GGCTGGCTCATTCATGGACT 60.107 55.000 0.00 0.00 0.00 3.85
1927 14350 1.684248 GGCTGGCTCATTCATGGACTT 60.684 52.381 0.00 0.00 0.00 3.01
2053 14493 0.673644 CCGTTTGAGACCCGCTTCAT 60.674 55.000 0.00 0.00 0.00 2.57
2098 14538 4.396357 TTGGATGGTGGTCTTGGTATTT 57.604 40.909 0.00 0.00 0.00 1.40
2122 14562 4.531332 GCACAGTGACAAGAGATTTGTTC 58.469 43.478 4.15 0.00 31.96 3.18
2220 14669 2.859165 TGAAGGTGAGTTGGATCCAC 57.141 50.000 15.91 10.06 0.00 4.02
2262 14724 2.555448 GCCATTTCTATTCCCTAGGGCC 60.555 54.545 24.42 0.00 34.68 5.80
2285 14747 6.972328 GCCATCGTTGTTGTATACATGAATTT 59.028 34.615 6.36 0.00 36.44 1.82
2520 15835 2.283145 ACAAGAAGGTTCATGCTGCT 57.717 45.000 0.00 0.00 29.52 4.24
2563 15878 4.898861 TGGCAAAATCAACTAAGGAACCTT 59.101 37.500 10.97 10.97 39.83 3.50
2702 16198 8.479689 TCCGTTCATTCCTAAACTATATGTTCA 58.520 33.333 0.00 0.00 38.03 3.18
2895 17197 7.514125 GCAATCATTAATGTTCATTGTCTTCGC 60.514 37.037 20.72 8.92 0.00 4.70
2944 17247 3.886044 GTGTCAGACACGATGGACA 57.114 52.632 17.96 0.00 39.53 4.02
3049 17471 5.859495 AGTTCCTCTGTTTTCTTCTACCAG 58.141 41.667 0.00 0.00 0.00 4.00
3060 17482 4.114015 TCTTCTACCAGGAGTTCTGACA 57.886 45.455 0.00 0.00 46.18 3.58
3122 17545 6.325545 TCACCATACGGATAGTGGTAAGAATT 59.674 38.462 6.35 0.00 44.09 2.17
3211 17722 2.427095 GGTTGCAGGTTTGTTCTTCTGT 59.573 45.455 0.00 0.00 0.00 3.41
3213 17724 1.939934 TGCAGGTTTGTTCTTCTGTCG 59.060 47.619 0.00 0.00 0.00 4.35
3367 17884 6.820656 AGAGCTATGGATTTTAATATGCTCCG 59.179 38.462 0.00 0.00 43.51 4.63
3514 18031 3.254657 TGGTTAAGAGCAATTTCCAACGG 59.745 43.478 0.00 0.00 0.00 4.44
3523 18040 1.970092 ATTTCCAACGGGTCGTCAAA 58.030 45.000 0.00 0.00 39.99 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 27 2.811431 TGGTTTAAGGTCACAATCGCTG 59.189 45.455 0.00 0.00 0.00 5.18
25 28 3.134574 TGGTTTAAGGTCACAATCGCT 57.865 42.857 0.00 0.00 0.00 4.93
40 43 9.889128 CTCATAATCCACCATAAATTTTGGTTT 57.111 29.630 17.24 12.46 45.19 3.27
179 723 9.736023 AAAATCTCATAATCCAGCGTAAAATTC 57.264 29.630 0.00 0.00 0.00 2.17
185 729 6.929049 CACCTAAAATCTCATAATCCAGCGTA 59.071 38.462 0.00 0.00 0.00 4.42
199 5660 8.832735 TCACCTAACTAAATCCACCTAAAATCT 58.167 33.333 0.00 0.00 0.00 2.40
200 5661 9.628500 ATCACCTAACTAAATCCACCTAAAATC 57.372 33.333 0.00 0.00 0.00 2.17
201 5662 9.990868 AATCACCTAACTAAATCCACCTAAAAT 57.009 29.630 0.00 0.00 0.00 1.82
202 5663 9.238368 CAATCACCTAACTAAATCCACCTAAAA 57.762 33.333 0.00 0.00 0.00 1.52
203 5664 8.387813 ACAATCACCTAACTAAATCCACCTAAA 58.612 33.333 0.00 0.00 0.00 1.85
204 5665 7.827236 CACAATCACCTAACTAAATCCACCTAA 59.173 37.037 0.00 0.00 0.00 2.69
205 5666 7.037873 ACACAATCACCTAACTAAATCCACCTA 60.038 37.037 0.00 0.00 0.00 3.08
206 5667 6.180472 CACAATCACCTAACTAAATCCACCT 58.820 40.000 0.00 0.00 0.00 4.00
207 5668 5.944007 ACACAATCACCTAACTAAATCCACC 59.056 40.000 0.00 0.00 0.00 4.61
208 5669 6.879458 AGACACAATCACCTAACTAAATCCAC 59.121 38.462 0.00 0.00 0.00 4.02
209 5670 7.016153 AGACACAATCACCTAACTAAATCCA 57.984 36.000 0.00 0.00 0.00 3.41
210 5671 7.606456 TCAAGACACAATCACCTAACTAAATCC 59.394 37.037 0.00 0.00 0.00 3.01
211 5672 8.547967 TCAAGACACAATCACCTAACTAAATC 57.452 34.615 0.00 0.00 0.00 2.17
212 5673 8.375506 TCTCAAGACACAATCACCTAACTAAAT 58.624 33.333 0.00 0.00 0.00 1.40
213 5674 7.732025 TCTCAAGACACAATCACCTAACTAAA 58.268 34.615 0.00 0.00 0.00 1.85
214 5675 7.297936 TCTCAAGACACAATCACCTAACTAA 57.702 36.000 0.00 0.00 0.00 2.24
215 5676 6.911250 TCTCAAGACACAATCACCTAACTA 57.089 37.500 0.00 0.00 0.00 2.24
216 5677 5.808366 TCTCAAGACACAATCACCTAACT 57.192 39.130 0.00 0.00 0.00 2.24
217 5678 8.723942 ATATTCTCAAGACACAATCACCTAAC 57.276 34.615 0.00 0.00 0.00 2.34
219 5680 9.201989 ACTATATTCTCAAGACACAATCACCTA 57.798 33.333 0.00 0.00 0.00 3.08
220 5681 8.083828 ACTATATTCTCAAGACACAATCACCT 57.916 34.615 0.00 0.00 0.00 4.00
221 5682 7.981789 TGACTATATTCTCAAGACACAATCACC 59.018 37.037 0.00 0.00 0.00 4.02
222 5683 8.932945 TGACTATATTCTCAAGACACAATCAC 57.067 34.615 0.00 0.00 0.00 3.06
223 5684 9.942850 TTTGACTATATTCTCAAGACACAATCA 57.057 29.630 0.00 0.00 0.00 2.57
227 5688 9.591792 CATCTTTGACTATATTCTCAAGACACA 57.408 33.333 7.16 0.00 0.00 3.72
228 5689 9.593134 ACATCTTTGACTATATTCTCAAGACAC 57.407 33.333 7.16 0.00 0.00 3.67
235 5696 9.994432 CCAACAAACATCTTTGACTATATTCTC 57.006 33.333 0.01 0.00 39.43 2.87
236 5697 9.739276 TCCAACAAACATCTTTGACTATATTCT 57.261 29.630 0.01 0.00 39.43 2.40
237 5698 9.774742 GTCCAACAAACATCTTTGACTATATTC 57.225 33.333 0.01 0.00 39.43 1.75
238 5699 9.520515 AGTCCAACAAACATCTTTGACTATATT 57.479 29.630 0.01 0.00 39.43 1.28
241 5702 8.950210 CATAGTCCAACAAACATCTTTGACTAT 58.050 33.333 0.01 0.00 39.43 2.12
242 5703 8.154203 TCATAGTCCAACAAACATCTTTGACTA 58.846 33.333 0.01 0.00 39.43 2.59
243 5704 6.998074 TCATAGTCCAACAAACATCTTTGACT 59.002 34.615 0.01 0.00 39.43 3.41
244 5705 7.173218 TCTCATAGTCCAACAAACATCTTTGAC 59.827 37.037 0.01 0.00 39.43 3.18
245 5706 7.223584 TCTCATAGTCCAACAAACATCTTTGA 58.776 34.615 0.01 0.00 39.43 2.69
246 5707 7.439157 TCTCATAGTCCAACAAACATCTTTG 57.561 36.000 0.00 0.00 42.33 2.77
247 5708 8.641498 AATCTCATAGTCCAACAAACATCTTT 57.359 30.769 0.00 0.00 0.00 2.52
248 5709 8.641498 AAATCTCATAGTCCAACAAACATCTT 57.359 30.769 0.00 0.00 0.00 2.40
249 5710 8.641498 AAAATCTCATAGTCCAACAAACATCT 57.359 30.769 0.00 0.00 0.00 2.90
250 5711 9.994432 CTAAAATCTCATAGTCCAACAAACATC 57.006 33.333 0.00 0.00 0.00 3.06
251 5712 8.960591 CCTAAAATCTCATAGTCCAACAAACAT 58.039 33.333 0.00 0.00 0.00 2.71
252 5713 7.942341 ACCTAAAATCTCATAGTCCAACAAACA 59.058 33.333 0.00 0.00 0.00 2.83
253 5714 8.336801 ACCTAAAATCTCATAGTCCAACAAAC 57.663 34.615 0.00 0.00 0.00 2.93
254 5715 8.934023 AACCTAAAATCTCATAGTCCAACAAA 57.066 30.769 0.00 0.00 0.00 2.83
255 5716 8.934023 AAACCTAAAATCTCATAGTCCAACAA 57.066 30.769 0.00 0.00 0.00 2.83
256 5717 9.667107 CTAAACCTAAAATCTCATAGTCCAACA 57.333 33.333 0.00 0.00 0.00 3.33
257 5718 9.668497 ACTAAACCTAAAATCTCATAGTCCAAC 57.332 33.333 0.00 0.00 0.00 3.77
271 5732 9.667107 CACCATTCTCATCTACTAAACCTAAAA 57.333 33.333 0.00 0.00 0.00 1.52
272 5733 9.042450 TCACCATTCTCATCTACTAAACCTAAA 57.958 33.333 0.00 0.00 0.00 1.85
273 5734 8.603898 TCACCATTCTCATCTACTAAACCTAA 57.396 34.615 0.00 0.00 0.00 2.69
274 5735 8.783660 ATCACCATTCTCATCTACTAAACCTA 57.216 34.615 0.00 0.00 0.00 3.08
275 5736 7.682787 ATCACCATTCTCATCTACTAAACCT 57.317 36.000 0.00 0.00 0.00 3.50
287 5748 9.519191 CCACCAATATAATAATCACCATTCTCA 57.481 33.333 0.00 0.00 0.00 3.27
288 5749 9.739276 TCCACCAATATAATAATCACCATTCTC 57.261 33.333 0.00 0.00 0.00 2.87
301 5762 8.990163 AAGAACGGTTTATCCACCAATATAAT 57.010 30.769 0.00 0.00 36.49 1.28
302 5763 8.810990 AAAGAACGGTTTATCCACCAATATAA 57.189 30.769 0.00 0.00 36.49 0.98
303 5764 9.902684 TTAAAGAACGGTTTATCCACCAATATA 57.097 29.630 0.00 0.00 36.49 0.86
304 5765 8.810990 TTAAAGAACGGTTTATCCACCAATAT 57.189 30.769 0.00 0.00 36.49 1.28
305 5766 8.810990 ATTAAAGAACGGTTTATCCACCAATA 57.189 30.769 0.00 0.00 36.49 1.90
306 5767 7.712204 ATTAAAGAACGGTTTATCCACCAAT 57.288 32.000 0.00 0.00 36.49 3.16
307 5768 7.527568 AATTAAAGAACGGTTTATCCACCAA 57.472 32.000 0.00 0.00 36.49 3.67
308 5769 7.527568 AAATTAAAGAACGGTTTATCCACCA 57.472 32.000 0.00 0.00 36.49 4.17
309 5770 8.733458 ACTAAATTAAAGAACGGTTTATCCACC 58.267 33.333 0.00 0.00 35.57 4.61
317 5778 9.857957 TGTTTCAAACTAAATTAAAGAACGGTT 57.142 25.926 1.10 0.00 0.00 4.44
318 5779 9.857957 TTGTTTCAAACTAAATTAAAGAACGGT 57.142 25.926 1.10 0.00 0.00 4.83
367 5828 5.694006 CCACCGTGAATTTGCTCAAAAATAA 59.306 36.000 0.00 0.00 33.56 1.40
368 5829 5.010112 TCCACCGTGAATTTGCTCAAAAATA 59.990 36.000 0.00 0.00 33.56 1.40
371 5832 2.690497 TCCACCGTGAATTTGCTCAAAA 59.310 40.909 0.00 0.00 33.56 2.44
374 5835 2.198827 ATCCACCGTGAATTTGCTCA 57.801 45.000 0.00 0.00 0.00 4.26
375 5836 3.575965 AAATCCACCGTGAATTTGCTC 57.424 42.857 0.00 0.00 0.00 4.26
377 5838 3.648009 TCAAAATCCACCGTGAATTTGC 58.352 40.909 0.00 0.00 0.00 3.68
433 8427 6.485313 ACCAAACATCTTTGACTAATTCGTCA 59.515 34.615 8.63 8.63 39.43 4.35
521 8515 5.582689 ATTGCTCCATGTTTACTAAAGGC 57.417 39.130 0.00 0.00 0.00 4.35
548 8542 4.770795 AGATCACAATAGCCTAACCACAC 58.229 43.478 0.00 0.00 0.00 3.82
552 8546 5.880332 TGTTCAAGATCACAATAGCCTAACC 59.120 40.000 0.00 0.00 0.00 2.85
575 8569 5.221880 TCTCGCAATCCACTTTGAAATTTG 58.778 37.500 0.00 0.00 0.00 2.32
584 8578 5.649782 ATTGAAAATCTCGCAATCCACTT 57.350 34.783 0.00 0.00 0.00 3.16
692 9624 6.267817 CAATTTGGTTCAATATCGCAGTCAT 58.732 36.000 0.00 0.00 0.00 3.06
696 9761 4.675510 AGCAATTTGGTTCAATATCGCAG 58.324 39.130 0.00 0.00 0.00 5.18
699 9764 5.740569 CACAGAGCAATTTGGTTCAATATCG 59.259 40.000 2.14 0.00 0.00 2.92
716 9781 5.587844 ACAATCACCTCATAAATCACAGAGC 59.412 40.000 0.00 0.00 0.00 4.09
750 12517 7.959658 ATCCACCAAACATCTTTGATTATCA 57.040 32.000 0.00 0.00 39.43 2.15
755 12522 7.835682 TCTCATAATCCACCAAACATCTTTGAT 59.164 33.333 0.00 0.00 39.43 2.57
1038 13262 0.118346 TGCCAGGAAGGAGAGGGTTA 59.882 55.000 0.00 0.00 41.22 2.85
1211 13572 4.021916 GTGTAGGTGTAGTCCATAGTGGT 58.978 47.826 0.00 0.00 39.03 4.16
1212 13573 4.279145 AGTGTAGGTGTAGTCCATAGTGG 58.721 47.826 0.00 0.00 39.43 4.00
1213 13574 5.417894 TCAAGTGTAGGTGTAGTCCATAGTG 59.582 44.000 0.00 0.00 0.00 2.74
1214 13575 5.577100 TCAAGTGTAGGTGTAGTCCATAGT 58.423 41.667 0.00 0.00 0.00 2.12
1348 13750 7.687941 AAACTTCTCCATACCAAGTTGTATG 57.312 36.000 13.91 13.91 44.95 2.39
1379 13781 7.833682 TCTGCATACAAGAATCTTTATTTCCCA 59.166 33.333 0.00 0.00 0.00 4.37
1495 13911 4.081198 GTGAACTTGAGGTCCTGATCTCAT 60.081 45.833 10.74 0.00 46.83 2.90
1503 13919 1.428869 AGCAGTGAACTTGAGGTCCT 58.571 50.000 0.00 0.00 0.00 3.85
1543 13959 4.541705 CCTGATCTTCCTACTCTTCCTCA 58.458 47.826 0.00 0.00 0.00 3.86
1597 14013 2.951642 TCCTGGAAAGCAAAGACTTGTG 59.048 45.455 0.00 0.00 34.79 3.33
1686 14102 8.504815 CACAAATCATAGCATCAGAATAAGAGG 58.495 37.037 0.00 0.00 0.00 3.69
1778 14200 8.537728 AACCTATCCAGCAAAATTATCAATCA 57.462 30.769 0.00 0.00 0.00 2.57
1828 14251 6.177610 TCCATGTTTACCAACTACATCCTTC 58.822 40.000 0.00 0.00 33.58 3.46
1910 14333 3.245016 ACTTCAAGTCCATGAATGAGCCA 60.245 43.478 0.00 0.00 38.55 4.75
1919 14342 6.294473 AGATTAGGCATACTTCAAGTCCATG 58.706 40.000 0.00 0.00 0.00 3.66
1923 14346 6.258947 GTCCAAGATTAGGCATACTTCAAGTC 59.741 42.308 0.00 0.00 0.00 3.01
1924 14347 6.069963 AGTCCAAGATTAGGCATACTTCAAGT 60.070 38.462 0.00 0.00 0.00 3.16
1925 14348 6.259608 CAGTCCAAGATTAGGCATACTTCAAG 59.740 42.308 0.00 0.00 0.00 3.02
1926 14349 6.115446 CAGTCCAAGATTAGGCATACTTCAA 58.885 40.000 0.00 0.00 0.00 2.69
1927 14350 5.674525 CAGTCCAAGATTAGGCATACTTCA 58.325 41.667 0.00 0.00 0.00 3.02
2053 14493 0.036732 CCCTGCAGTAGCCAACAGAA 59.963 55.000 13.81 0.00 41.13 3.02
2098 14538 2.802247 CAAATCTCTTGTCACTGTGCGA 59.198 45.455 2.12 0.00 0.00 5.10
2122 14562 4.528531 GCTTCTTATCCTTCTTGAAGCG 57.471 45.455 9.68 0.00 46.14 4.68
2220 14669 3.684788 GCATTATAATACCACGAGGGCAG 59.315 47.826 3.29 0.00 42.05 4.85
2285 14747 5.612688 AGGCCCAGATATATCTTCCAGAAAA 59.387 40.000 12.75 0.00 34.22 2.29
2340 14809 7.871853 TGCTTCAGAAATAAGAACAAAGTACC 58.128 34.615 0.00 0.00 0.00 3.34
2520 15835 5.070001 GCCATGGTAGGATAAGCACAAATA 58.930 41.667 14.67 0.00 0.00 1.40
2563 15878 4.316205 TCTAACTCTTGTGCGTCTTTGA 57.684 40.909 0.00 0.00 0.00 2.69
2652 16148 8.821894 GGACTACATGAGTATGAGAAAACATTC 58.178 37.037 0.00 0.00 39.06 2.67
2838 17140 9.193806 AGTGCATAGAAAATCCATAGTTTTCAT 57.806 29.630 12.23 3.59 44.19 2.57
2839 17141 8.579850 AGTGCATAGAAAATCCATAGTTTTCA 57.420 30.769 12.23 1.83 44.19 2.69
2840 17142 9.508567 GAAGTGCATAGAAAATCCATAGTTTTC 57.491 33.333 0.00 3.78 42.84 2.29
2895 17197 1.613437 AGGTGCCAAACAAAATCCGAG 59.387 47.619 0.00 0.00 0.00 4.63
2944 17247 4.457496 CGATGCGGACCTGGCAGT 62.457 66.667 14.43 1.17 44.71 4.40
3049 17471 6.430451 CAAGTGTACAAATTGTCAGAACTCC 58.570 40.000 0.22 0.00 0.00 3.85
3060 17482 4.399004 TTTGCAGCCAAGTGTACAAATT 57.601 36.364 0.00 0.00 31.52 1.82
3122 17545 4.080356 ACCTACTATTGGATTTGCTGCTGA 60.080 41.667 0.00 0.00 0.00 4.26
3211 17722 6.646653 GCTATGATGAGAACCATGAATAACGA 59.353 38.462 0.00 0.00 35.17 3.85
3213 17724 6.712095 TGGCTATGATGAGAACCATGAATAAC 59.288 38.462 0.00 0.00 35.17 1.89
3367 17884 6.149640 GGAGTGATAAAAGACCTGAAGGAAAC 59.850 42.308 2.62 0.00 38.94 2.78
3408 17925 0.482446 TGAGCAACCCCAATGGACTT 59.518 50.000 0.00 0.00 38.00 3.01
3514 18031 6.475402 ACATCAGAAAAACAAATTTGACGACC 59.525 34.615 24.64 10.13 0.00 4.79
3523 18040 6.888105 AGACCCAAACATCAGAAAAACAAAT 58.112 32.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.