Multiple sequence alignment - TraesCS7A01G093400

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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 TraesCS7A01G093400 chr7A 100.000 2870 0 0 1 2870 56801391 56804260 0.000000e+00 5301.0
1 TraesCS7A01G093400 chr7A 88.965 1894 161 23 998 2870 56354004 56355870 0.000000e+00 2296.0
2 TraesCS7A01G093400 chr7A 89.264 1779 131 24 998 2730 56450817 56452581 0.000000e+00 2172.0
3 TraesCS7A01G093400 chr7A 90.560 1017 79 10 1839 2840 56258396 56259410 0.000000e+00 1330.0
4 TraesCS7A01G093400 chr7A 87.368 855 68 13 1018 1845 56248027 56248868 0.000000e+00 944.0
5 TraesCS7A01G093400 chr7A 95.085 468 22 1 1 467 457499369 457498902 0.000000e+00 736.0
6 TraesCS7A01G093400 chr7A 91.635 526 42 2 474 998 450040754 450041278 0.000000e+00 726.0
7 TraesCS7A01G093400 chr7A 94.635 466 23 2 3 467 609096406 609095942 0.000000e+00 721.0
8 TraesCS7A01G093400 chr7A 83.958 667 83 15 1478 2138 57198108 57198756 4.060000e-173 617.0
9 TraesCS7A01G093400 chr7A 82.727 660 94 10 1478 2129 56927685 56928332 1.150000e-158 569.0
10 TraesCS7A01G093400 chr4A 89.071 1894 143 23 998 2849 668312603 668314474 0.000000e+00 2292.0
11 TraesCS7A01G093400 chr4A 92.030 527 40 2 474 999 472514748 472515273 0.000000e+00 739.0
12 TraesCS7A01G093400 chr4A 91.651 527 42 2 474 999 341848960 341848435 0.000000e+00 728.0
13 TraesCS7A01G093400 chr4A 94.670 469 23 2 1 467 418081977 418081509 0.000000e+00 726.0
14 TraesCS7A01G093400 chr4A 80.330 910 124 30 1508 2384 668334370 668335257 3.120000e-179 638.0
15 TraesCS7A01G093400 chr4A 80.044 912 130 28 1508 2384 668357642 668358536 1.880000e-176 628.0
16 TraesCS7A01G093400 chr7D 89.739 1803 116 23 1107 2870 53569128 53570900 0.000000e+00 2241.0
17 TraesCS7A01G093400 chr7D 85.983 585 68 8 1536 2118 53600770 53601342 5.260000e-172 614.0
18 TraesCS7A01G093400 chr7D 83.609 665 91 12 1478 2138 53747114 53747764 2.450000e-170 608.0
19 TraesCS7A01G093400 chr7D 84.112 642 86 10 1478 2118 53696760 53697386 8.790000e-170 606.0
20 TraesCS7A01G093400 chr7D 78.761 113 21 3 2655 2765 25997580 25997691 3.970000e-09 73.1
21 TraesCS7A01G093400 chr7D 78.761 113 21 3 2655 2765 26054379 26054490 3.970000e-09 73.1
22 TraesCS7A01G093400 chr2A 92.075 530 41 1 474 1002 646877010 646876481 0.000000e+00 745.0
23 TraesCS7A01G093400 chr2A 95.299 468 20 2 1 467 182921031 182921497 0.000000e+00 741.0
24 TraesCS7A01G093400 chr2A 92.176 524 39 2 475 997 693450523 693450001 0.000000e+00 739.0
25 TraesCS7A01G093400 chr2A 91.635 526 42 2 474 997 178570316 178570841 0.000000e+00 726.0
26 TraesCS7A01G093400 chr2A 94.456 469 24 2 1 467 671963693 671963225 0.000000e+00 721.0
27 TraesCS7A01G093400 chr5D 92.205 526 37 4 474 997 243900109 243900632 0.000000e+00 741.0
28 TraesCS7A01G093400 chr5D 90.909 44 4 0 2722 2765 539474531 539474574 3.090000e-05 60.2
29 TraesCS7A01G093400 chr3D 92.015 526 40 2 474 998 160999323 160998799 0.000000e+00 737.0
30 TraesCS7A01G093400 chr3A 94.692 471 24 1 1 470 59835629 59835159 0.000000e+00 730.0
31 TraesCS7A01G093400 chr3A 94.692 471 24 1 1 470 59857325 59856855 0.000000e+00 730.0
32 TraesCS7A01G093400 chr3A 94.304 474 25 2 1 472 169923685 169923212 0.000000e+00 725.0
33 TraesCS7A01G093400 chr3A 91.477 528 43 2 474 1000 249724259 249723733 0.000000e+00 725.0
34 TraesCS7A01G093400 chr5A 94.456 469 24 2 1 467 68384046 68384514 0.000000e+00 721.0
35 TraesCS7A01G093400 chr7B 79.788 1039 152 34 1 995 459225422 459224398 0.000000e+00 702.0
36 TraesCS7A01G093400 chr1D 80.702 114 18 4 2655 2765 51443049 51443161 5.090000e-13 86.1
37 TraesCS7A01G093400 chr1D 80.702 114 16 5 2655 2765 51324539 51324649 1.830000e-12 84.2
38 TraesCS7A01G093400 chr1D 90.909 44 4 0 2722 2765 7282914 7282957 3.090000e-05 60.2
39 TraesCS7A01G093400 chr1D 100.000 32 0 0 2734 2765 19079643 19079674 3.090000e-05 60.2
40 TraesCS7A01G093400 chr1D 92.308 39 3 0 2722 2760 17830861 17830823 3.990000e-04 56.5
41 TraesCS7A01G093400 chr1A 81.915 94 15 2 2667 2759 68786300 68786392 8.530000e-11 78.7
42 TraesCS7A01G093400 chr1A 80.000 100 18 2 2667 2765 95691774 95691676 3.970000e-09 73.1
43 TraesCS7A01G093400 chr1A 78.788 99 19 2 2668 2765 45039314 45039411 6.640000e-07 65.8
44 TraesCS7A01G093400 chr3B 78.947 114 18 6 2655 2765 36381358 36381468 3.970000e-09 73.1
45 TraesCS7A01G093400 chrUn 79.245 106 18 3 2655 2759 340424655 340424757 1.430000e-08 71.3
46 TraesCS7A01G093400 chrUn 97.059 34 1 0 2732 2765 466643805 466643838 1.110000e-04 58.4
47 TraesCS7A01G093400 chrUn 97.059 34 1 0 2732 2765 472304187 472304220 1.110000e-04 58.4
48 TraesCS7A01G093400 chrUn 94.118 34 2 0 2732 2765 131278366 131278333 5.000000e-03 52.8
49 TraesCS7A01G093400 chr1B 78.571 112 20 3 2655 2765 41317016 41316908 1.430000e-08 71.3
50 TraesCS7A01G093400 chr1B 78.182 110 20 4 2658 2765 78206581 78206474 1.850000e-07 67.6
51 TraesCS7A01G093400 chr6D 77.679 112 23 2 2655 2765 22252449 22252559 1.850000e-07 67.6
52 TraesCS7A01G093400 chr6A 76.147 109 24 2 2655 2762 13449436 13449329 3.990000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G093400 chr7A 56801391 56804260 2869 False 5301 5301 100.000 1 2870 1 chr7A.!!$F5 2869
1 TraesCS7A01G093400 chr7A 56354004 56355870 1866 False 2296 2296 88.965 998 2870 1 chr7A.!!$F3 1872
2 TraesCS7A01G093400 chr7A 56450817 56452581 1764 False 2172 2172 89.264 998 2730 1 chr7A.!!$F4 1732
3 TraesCS7A01G093400 chr7A 56258396 56259410 1014 False 1330 1330 90.560 1839 2840 1 chr7A.!!$F2 1001
4 TraesCS7A01G093400 chr7A 56248027 56248868 841 False 944 944 87.368 1018 1845 1 chr7A.!!$F1 827
5 TraesCS7A01G093400 chr7A 450040754 450041278 524 False 726 726 91.635 474 998 1 chr7A.!!$F8 524
6 TraesCS7A01G093400 chr7A 57198108 57198756 648 False 617 617 83.958 1478 2138 1 chr7A.!!$F7 660
7 TraesCS7A01G093400 chr7A 56927685 56928332 647 False 569 569 82.727 1478 2129 1 chr7A.!!$F6 651
8 TraesCS7A01G093400 chr4A 668312603 668314474 1871 False 2292 2292 89.071 998 2849 1 chr4A.!!$F2 1851
9 TraesCS7A01G093400 chr4A 472514748 472515273 525 False 739 739 92.030 474 999 1 chr4A.!!$F1 525
10 TraesCS7A01G093400 chr4A 341848435 341848960 525 True 728 728 91.651 474 999 1 chr4A.!!$R1 525
11 TraesCS7A01G093400 chr4A 668334370 668335257 887 False 638 638 80.330 1508 2384 1 chr4A.!!$F3 876
12 TraesCS7A01G093400 chr4A 668357642 668358536 894 False 628 628 80.044 1508 2384 1 chr4A.!!$F4 876
13 TraesCS7A01G093400 chr7D 53569128 53570900 1772 False 2241 2241 89.739 1107 2870 1 chr7D.!!$F3 1763
14 TraesCS7A01G093400 chr7D 53600770 53601342 572 False 614 614 85.983 1536 2118 1 chr7D.!!$F4 582
15 TraesCS7A01G093400 chr7D 53747114 53747764 650 False 608 608 83.609 1478 2138 1 chr7D.!!$F6 660
16 TraesCS7A01G093400 chr7D 53696760 53697386 626 False 606 606 84.112 1478 2118 1 chr7D.!!$F5 640
17 TraesCS7A01G093400 chr2A 646876481 646877010 529 True 745 745 92.075 474 1002 1 chr2A.!!$R1 528
18 TraesCS7A01G093400 chr2A 693450001 693450523 522 True 739 739 92.176 475 997 1 chr2A.!!$R3 522
19 TraesCS7A01G093400 chr2A 178570316 178570841 525 False 726 726 91.635 474 997 1 chr2A.!!$F1 523
20 TraesCS7A01G093400 chr5D 243900109 243900632 523 False 741 741 92.205 474 997 1 chr5D.!!$F1 523
21 TraesCS7A01G093400 chr3D 160998799 160999323 524 True 737 737 92.015 474 998 1 chr3D.!!$R1 524
22 TraesCS7A01G093400 chr3A 249723733 249724259 526 True 725 725 91.477 474 1000 1 chr3A.!!$R4 526
23 TraesCS7A01G093400 chr7B 459224398 459225422 1024 True 702 702 79.788 1 995 1 chr7B.!!$R1 994

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
264 286 0.041684 CCCCCTGGCCTTCATCTTTT 59.958 55.0 3.32 0.0 0.00 2.27 F
303 325 0.464870 TCCGAAAAGGTGTTCCGTGA 59.535 50.0 0.00 0.0 41.99 4.35 F
1096 1139 0.943835 CGTCGCTGTGGTTGACATGA 60.944 55.0 0.00 0.0 32.74 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1097 1140 1.079490 TCCATCTGGGACTCACCTTCT 59.921 52.381 0.00 0.00 42.15 2.85 R
1129 1174 1.963515 GAATTGGATGTATGCCCCACC 59.036 52.381 0.00 0.00 0.00 4.61 R
2351 2505 0.178924 ACATGGCCTTGGCCTTCTTT 60.179 50.000 28.37 8.69 0.00 2.52 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
21 22 4.000331 GAGGATGGTTGATGATGACGAT 58.000 45.455 0.00 0.00 0.00 3.73
26 27 1.570813 GTTGATGATGACGATGGCGA 58.429 50.000 0.00 0.00 41.64 5.54
29 30 1.278172 GATGATGACGATGGCGACGG 61.278 60.000 0.00 0.00 41.64 4.79
32 33 0.597637 GATGACGATGGCGACGGATT 60.598 55.000 0.00 0.00 41.64 3.01
60 61 4.144703 GAGCCCCGAACGGACTCC 62.145 72.222 15.07 0.30 37.50 3.85
74 75 0.398381 GACTCCAGATCAGCCCTCCT 60.398 60.000 0.00 0.00 0.00 3.69
75 76 0.937441 ACTCCAGATCAGCCCTCCTA 59.063 55.000 0.00 0.00 0.00 2.94
92 93 4.518249 CTCCTAAGAGGTTTTAGGGCTTG 58.482 47.826 10.91 0.00 46.39 4.01
117 118 1.913403 CGGCTTCGTATCGTAAAACGT 59.087 47.619 0.00 0.00 43.14 3.99
123 124 5.051907 GCTTCGTATCGTAAAACGTGATGAT 60.052 40.000 0.00 0.00 43.14 2.45
124 125 6.507456 GCTTCGTATCGTAAAACGTGATGATT 60.507 38.462 0.00 0.00 43.14 2.57
125 126 6.874297 TCGTATCGTAAAACGTGATGATTT 57.126 33.333 0.00 0.00 43.14 2.17
126 127 6.914935 TCGTATCGTAAAACGTGATGATTTC 58.085 36.000 0.00 0.00 43.14 2.17
133 134 8.024865 TCGTAAAACGTGATGATTTCTTCTCTA 58.975 33.333 0.00 0.00 43.14 2.43
134 135 8.808529 CGTAAAACGTGATGATTTCTTCTCTAT 58.191 33.333 0.00 0.00 36.74 1.98
163 165 8.754991 TTTTTCTCCCCGAAAGCAAATATATA 57.245 30.769 0.00 0.00 42.22 0.86
171 173 6.710744 CCCGAAAGCAAATATATAGAGTTGGT 59.289 38.462 6.44 6.44 33.37 3.67
172 174 7.095187 CCCGAAAGCAAATATATAGAGTTGGTC 60.095 40.741 12.01 1.52 31.68 4.02
176 178 9.905713 AAAGCAAATATATAGAGTTGGTCTTGA 57.094 29.630 12.01 0.00 36.64 3.02
177 179 9.553064 AAGCAAATATATAGAGTTGGTCTTGAG 57.447 33.333 12.01 0.00 36.64 3.02
186 188 0.178944 TTGGTCTTGAGGTCGGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
187 189 0.612174 TGGTCTTGAGGTCGGAGGAG 60.612 60.000 0.00 0.00 0.00 3.69
239 261 2.343758 CACCCTCGTGGACAGGTG 59.656 66.667 4.76 0.63 43.50 4.00
264 286 0.041684 CCCCCTGGCCTTCATCTTTT 59.958 55.000 3.32 0.00 0.00 2.27
267 289 1.259609 CCTGGCCTTCATCTTTTGCA 58.740 50.000 3.32 0.00 0.00 4.08
303 325 0.464870 TCCGAAAAGGTGTTCCGTGA 59.535 50.000 0.00 0.00 41.99 4.35
304 326 1.071071 TCCGAAAAGGTGTTCCGTGAT 59.929 47.619 0.00 0.00 41.99 3.06
319 341 3.007940 TCCGTGATGTTTCAGGTCATTCT 59.992 43.478 0.00 0.00 36.28 2.40
334 356 6.914757 CAGGTCATTCTGAGAACTTTTGTTTC 59.085 38.462 0.00 0.00 38.67 2.78
335 357 6.830838 AGGTCATTCTGAGAACTTTTGTTTCT 59.169 34.615 0.00 0.00 43.66 2.52
336 358 6.914757 GGTCATTCTGAGAACTTTTGTTTCTG 59.085 38.462 0.00 0.00 43.66 3.02
337 359 6.416161 GTCATTCTGAGAACTTTTGTTTCTGC 59.584 38.462 0.00 0.00 43.66 4.26
338 360 5.895636 TTCTGAGAACTTTTGTTTCTGCA 57.104 34.783 0.00 0.00 43.66 4.41
339 361 5.235305 TCTGAGAACTTTTGTTTCTGCAC 57.765 39.130 0.00 0.00 43.66 4.57
340 362 4.699735 TCTGAGAACTTTTGTTTCTGCACA 59.300 37.500 0.00 0.00 43.66 4.57
341 363 5.357878 TCTGAGAACTTTTGTTTCTGCACAT 59.642 36.000 0.00 0.00 43.66 3.21
345 367 8.196771 TGAGAACTTTTGTTTCTGCACATTAAT 58.803 29.630 0.00 0.00 43.66 1.40
347 369 9.683069 AGAACTTTTGTTTCTGCACATTAATAG 57.317 29.630 0.00 0.00 43.66 1.73
354 378 6.601217 TGTTTCTGCACATTAATAGCACCATA 59.399 34.615 9.88 0.00 34.13 2.74
382 406 1.221414 GCTGAAAACAGCGTCAGTCT 58.779 50.000 6.46 0.00 42.72 3.24
405 429 6.377996 TCTGGGTTAGTTCCATTCAAATCATG 59.622 38.462 0.00 0.00 33.29 3.07
423 447 5.689383 TCATGCAAGTTAGAGTCCAAAAC 57.311 39.130 0.00 0.00 0.00 2.43
461 485 3.379372 TGGAAAAGTAGATACGACGGAGG 59.621 47.826 0.00 0.00 0.00 4.30
462 486 3.370276 GAAAAGTAGATACGACGGAGGC 58.630 50.000 0.00 0.00 0.00 4.70
472 496 1.664306 GACGGAGGCGTATTAGGGG 59.336 63.158 0.00 0.00 0.00 4.79
691 717 7.743116 TGACTTTGATGAGTATAGGGGTTAA 57.257 36.000 0.00 0.00 0.00 2.01
715 741 5.923733 AGAGTTGATCTACCACGAGATTT 57.076 39.130 3.54 0.00 36.27 2.17
727 753 7.990886 TCTACCACGAGATTTTAATGGCTAAAT 59.009 33.333 0.00 0.00 33.46 1.40
766 806 9.875691 GCATGTATGATTATGATTACCTCTACA 57.124 33.333 0.00 0.00 0.00 2.74
776 817 7.973048 ATGATTACCTCTACAGACTAAACCA 57.027 36.000 0.00 0.00 0.00 3.67
812 853 2.590092 CGAAGGGGGCTAGGGTTG 59.410 66.667 0.00 0.00 0.00 3.77
820 861 2.720254 GGGGGCTAGGGTTGGTATAAAT 59.280 50.000 0.00 0.00 0.00 1.40
837 878 9.675464 TGGTATAAATTCGGTTTACAGAGAAAT 57.325 29.630 0.00 0.00 35.23 2.17
879 921 2.855514 GCTTGCCTTCCACGCCAAA 61.856 57.895 0.00 0.00 32.93 3.28
883 925 1.600916 GCCTTCCACGCCAAAGAGT 60.601 57.895 0.00 0.00 0.00 3.24
896 938 1.210478 CAAAGAGTGTCCCATCCGGAT 59.790 52.381 12.38 12.38 44.66 4.18
933 975 4.152647 TCTATCTTGTATCATCACGGCCT 58.847 43.478 0.00 0.00 0.00 5.19
1036 1078 6.371595 AAAATGGAAATTATGGCCTCAACA 57.628 33.333 3.32 0.00 0.00 3.33
1096 1139 0.943835 CGTCGCTGTGGTTGACATGA 60.944 55.000 0.00 0.00 32.74 3.07
1097 1140 1.225855 GTCGCTGTGGTTGACATGAA 58.774 50.000 0.00 0.00 32.74 2.57
1105 1150 3.118075 TGTGGTTGACATGAAGAAGGTGA 60.118 43.478 0.00 0.00 0.00 4.02
1129 1174 2.488528 CCCAGATGGAATGAGATGGTGG 60.489 54.545 0.00 0.00 37.39 4.61
1144 1189 1.152756 GTGGGTGGGGCATACATCC 60.153 63.158 0.00 0.00 39.62 3.51
1226 1271 1.462616 ATATGCAACTTTGGCAGCGA 58.537 45.000 0.00 0.00 45.68 4.93
1463 1534 6.280643 GCATTTATTTGGATAAGGACAACCC 58.719 40.000 0.00 0.00 36.73 4.11
1504 1575 5.831702 AGGATAAGCTTGATGCAAAAGAG 57.168 39.130 9.86 1.76 45.94 2.85
1547 1618 8.469309 AATGACATTAATTGGATAGGGACAAG 57.531 34.615 0.00 0.00 0.00 3.16
1579 1650 6.531948 GCAACCACATCTATATAAGATCGACC 59.468 42.308 0.00 0.00 43.42 4.79
1580 1651 6.777213 ACCACATCTATATAAGATCGACCC 57.223 41.667 0.00 0.00 43.42 4.46
1848 1922 2.993264 GCATTGGCCAGTGCACCT 60.993 61.111 39.37 4.56 42.66 4.00
1879 1954 1.896220 TGAGCCTTGATGTGTGGTTC 58.104 50.000 0.00 0.00 0.00 3.62
1960 2047 5.492855 TGGGTTACCTATTCCCGAATATG 57.507 43.478 0.00 0.00 43.75 1.78
2023 2114 9.289782 CTTACCTAATAAAATGGGAGGAGATTG 57.710 37.037 0.00 0.00 0.00 2.67
2170 2319 9.119418 CCTTTGGGAATTTCTGTTTTATTGTTT 57.881 29.630 0.00 0.00 33.58 2.83
2198 2347 3.372206 GTCCTCCATTTGTCGAGATTGTG 59.628 47.826 0.00 0.00 0.00 3.33
2237 2387 9.423061 ACATGCTTTATTTTTCATAAAGGTCAC 57.577 29.630 13.62 1.62 40.25 3.67
2288 2438 7.348080 TGGAGTACATCACCAATTAGTAGAG 57.652 40.000 0.00 0.00 34.04 2.43
2400 2554 4.075963 TGTCTAACCCTTACAACACCAC 57.924 45.455 0.00 0.00 0.00 4.16
2450 2604 8.520119 AACATATACTGGGTTATATCAAGGGT 57.480 34.615 0.00 0.00 0.00 4.34
2460 2614 6.424032 GGTTATATCAAGGGTGTCTTCCTTT 58.576 40.000 0.00 0.00 42.25 3.11
2468 2622 2.414806 GGTGTCTTCCTTTCGGACTTC 58.585 52.381 0.00 0.00 39.60 3.01
2471 2625 4.081586 GGTGTCTTCCTTTCGGACTTCTAT 60.082 45.833 0.00 0.00 39.60 1.98
2634 2801 2.151202 GAGCACGAAGGGATTGTTTGA 58.849 47.619 0.00 0.00 0.00 2.69
2639 2806 2.139917 CGAAGGGATTGTTTGACGTGA 58.860 47.619 0.00 0.00 0.00 4.35
2699 2866 6.286758 TGTACTAATTAGAGACTCCGTCGAT 58.713 40.000 19.38 0.00 37.67 3.59
2704 2871 4.986875 TTAGAGACTCCGTCGATATTCG 57.013 45.455 0.00 0.00 42.10 3.34
2717 2884 5.778825 CGTCGATATTCGCACAATTAATCAC 59.221 40.000 0.00 0.00 40.21 3.06
2840 3008 7.079451 CCATCTGGTGGGACTAAGTTATTAT 57.921 40.000 0.00 0.00 44.79 1.28
2854 3022 8.347771 ACTAAGTTATTATCGCGTAGATCAACA 58.652 33.333 5.77 0.00 40.66 3.33
2855 3023 9.343103 CTAAGTTATTATCGCGTAGATCAACAT 57.657 33.333 5.77 1.03 40.66 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.278172 CCGTCGCCATCGTCATCATC 61.278 60.000 0.00 0.00 36.96 2.92
29 30 2.512355 GGCTCCGGAGAGGGGAATC 61.512 68.421 35.69 14.09 46.06 2.52
74 75 2.617021 CGCCAAGCCCTAAAACCTCTTA 60.617 50.000 0.00 0.00 0.00 2.10
75 76 1.886655 CGCCAAGCCCTAAAACCTCTT 60.887 52.381 0.00 0.00 0.00 2.85
80 81 2.571757 GCCGCCAAGCCCTAAAAC 59.428 61.111 0.00 0.00 0.00 2.43
81 82 3.059386 CGCCGCCAAGCCCTAAAA 61.059 61.111 0.00 0.00 0.00 1.52
102 103 6.748658 AGAAATCATCACGTTTTACGATACGA 59.251 34.615 6.19 0.00 46.05 3.43
106 107 7.545965 AGAGAAGAAATCATCACGTTTTACGAT 59.454 33.333 6.19 0.00 46.05 3.73
155 157 8.361139 CGACCTCAAGACCAACTCTATATATTT 58.639 37.037 0.00 0.00 0.00 1.40
163 165 0.969894 CCGACCTCAAGACCAACTCT 59.030 55.000 0.00 0.00 0.00 3.24
171 173 0.681564 GAGCTCCTCCGACCTCAAGA 60.682 60.000 0.87 0.00 0.00 3.02
172 174 1.671901 GGAGCTCCTCCGACCTCAAG 61.672 65.000 26.25 0.00 41.08 3.02
229 251 4.660938 GGCCCACCACCTGTCCAC 62.661 72.222 0.00 0.00 35.26 4.02
280 302 2.953648 ACGGAACACCTTTTCGGAAAAT 59.046 40.909 15.64 1.42 36.31 1.82
281 303 2.097791 CACGGAACACCTTTTCGGAAAA 59.902 45.455 14.64 14.64 36.31 2.29
285 307 1.196808 CATCACGGAACACCTTTTCGG 59.803 52.381 0.00 0.00 39.35 4.30
286 308 1.871039 ACATCACGGAACACCTTTTCG 59.129 47.619 0.00 0.00 0.00 3.46
287 309 3.982576 AACATCACGGAACACCTTTTC 57.017 42.857 0.00 0.00 0.00 2.29
288 310 3.697045 TGAAACATCACGGAACACCTTTT 59.303 39.130 0.00 0.00 0.00 2.27
289 311 3.283751 TGAAACATCACGGAACACCTTT 58.716 40.909 0.00 0.00 0.00 3.11
293 315 2.218603 ACCTGAAACATCACGGAACAC 58.781 47.619 0.00 0.00 0.00 3.32
295 317 2.489971 TGACCTGAAACATCACGGAAC 58.510 47.619 0.00 0.00 0.00 3.62
303 325 5.874093 AGTTCTCAGAATGACCTGAAACAT 58.126 37.500 2.39 0.00 42.56 2.71
304 326 5.296151 AGTTCTCAGAATGACCTGAAACA 57.704 39.130 2.39 0.00 42.56 2.83
319 341 5.581126 ATGTGCAGAAACAAAAGTTCTCA 57.419 34.783 0.00 0.00 32.96 3.27
334 356 4.516321 TGCTATGGTGCTATTAATGTGCAG 59.484 41.667 15.23 7.33 37.39 4.41
335 357 4.459330 TGCTATGGTGCTATTAATGTGCA 58.541 39.130 12.07 12.07 0.00 4.57
336 358 5.437289 TTGCTATGGTGCTATTAATGTGC 57.563 39.130 0.00 3.41 0.00 4.57
337 359 7.806487 CAGAATTGCTATGGTGCTATTAATGTG 59.194 37.037 0.00 0.00 38.19 3.21
338 360 7.522725 GCAGAATTGCTATGGTGCTATTAATGT 60.523 37.037 0.00 0.00 46.95 2.71
339 361 6.805271 GCAGAATTGCTATGGTGCTATTAATG 59.195 38.462 0.00 0.00 46.95 1.90
340 362 6.917533 GCAGAATTGCTATGGTGCTATTAAT 58.082 36.000 7.45 0.00 46.95 1.40
341 363 6.317789 GCAGAATTGCTATGGTGCTATTAA 57.682 37.500 7.45 0.00 46.95 1.40
369 393 1.000955 CTAACCCAGACTGACGCTGTT 59.999 52.381 3.32 2.35 0.00 3.16
382 406 5.105392 GCATGATTTGAATGGAACTAACCCA 60.105 40.000 0.00 0.00 38.19 4.51
405 429 4.261614 CCCTTGTTTTGGACTCTAACTTGC 60.262 45.833 0.00 0.00 0.00 4.01
423 447 2.977772 TCCAAACACTTTTGCCCTTG 57.022 45.000 0.00 0.00 40.84 3.61
461 485 1.375523 CGATGGCCCCCTAATACGC 60.376 63.158 0.00 0.00 0.00 4.42
462 486 0.682852 TTCGATGGCCCCCTAATACG 59.317 55.000 0.00 0.00 0.00 3.06
467 491 0.401395 AAGGATTCGATGGCCCCCTA 60.401 55.000 0.00 0.00 0.00 3.53
469 493 0.476771 TAAAGGATTCGATGGCCCCC 59.523 55.000 0.00 0.00 0.00 5.40
472 496 2.737252 GTCGATAAAGGATTCGATGGCC 59.263 50.000 0.00 0.00 45.13 5.36
520 544 1.000717 GGTTTTGACACCGACATTGGG 60.001 52.381 0.00 0.00 0.00 4.12
691 717 5.923733 ATCTCGTGGTAGATCAACTCTTT 57.076 39.130 0.00 0.00 35.28 2.52
715 741 8.314751 GCTAGACATCTAGGATTTAGCCATTAA 58.685 37.037 15.98 0.00 44.63 1.40
758 784 3.171528 GGGTGGTTTAGTCTGTAGAGGT 58.828 50.000 0.00 0.00 0.00 3.85
812 853 9.931210 CATTTCTCTGTAAACCGAATTTATACC 57.069 33.333 0.00 0.00 35.23 2.73
820 861 7.659799 TGAAGATTCATTTCTCTGTAAACCGAA 59.340 33.333 0.00 0.00 31.01 4.30
837 878 4.522114 TGGCGTTTGGATATGAAGATTCA 58.478 39.130 0.00 0.00 42.14 2.57
1036 1078 2.436646 GCTATGTGGCGGCACACT 60.437 61.111 42.18 31.12 41.84 3.55
1051 1093 1.961180 CTCGATTGACCCTTCCGGCT 61.961 60.000 0.00 0.00 33.26 5.52
1085 1128 3.136443 ACTCACCTTCTTCATGTCAACCA 59.864 43.478 0.00 0.00 0.00 3.67
1096 1139 1.912043 CCATCTGGGACTCACCTTCTT 59.088 52.381 0.00 0.00 40.01 2.52
1097 1140 1.079490 TCCATCTGGGACTCACCTTCT 59.921 52.381 0.00 0.00 42.15 2.85
1129 1174 1.963515 GAATTGGATGTATGCCCCACC 59.036 52.381 0.00 0.00 0.00 4.61
1368 1415 5.813383 AGCCATGGTCATGATATAGGAAAG 58.187 41.667 14.67 0.00 41.20 2.62
1369 1416 5.848286 AGCCATGGTCATGATATAGGAAA 57.152 39.130 14.67 0.00 41.20 3.13
1370 1417 7.182568 TCAATAGCCATGGTCATGATATAGGAA 59.817 37.037 14.67 0.00 41.20 3.36
1371 1418 6.673537 TCAATAGCCATGGTCATGATATAGGA 59.326 38.462 14.67 8.47 41.20 2.94
1372 1419 6.892485 TCAATAGCCATGGTCATGATATAGG 58.108 40.000 14.67 0.58 41.20 2.57
1373 1420 8.208903 TCATCAATAGCCATGGTCATGATATAG 58.791 37.037 14.67 7.32 41.20 1.31
1374 1421 8.093118 TCATCAATAGCCATGGTCATGATATA 57.907 34.615 14.67 7.57 41.20 0.86
1463 1534 2.747446 CCTTATCCGACCCACAACAAAG 59.253 50.000 0.00 0.00 0.00 2.77
1547 1618 9.219603 TCTTATATAGATGTGGTTGCATTAAGC 57.780 33.333 0.00 0.00 45.96 3.09
1579 1650 2.026356 TGGTCATGACTGGTACCATTGG 60.026 50.000 24.50 6.57 37.09 3.16
1580 1651 3.009723 GTGGTCATGACTGGTACCATTG 58.990 50.000 24.50 7.39 43.53 2.82
1682 1756 6.906157 AAACAATGATCACTTGGAAGATGT 57.094 33.333 16.89 3.38 0.00 3.06
1848 1922 2.829914 GGCTCAATGGATGGCGCA 60.830 61.111 10.83 0.00 0.00 6.09
1879 1954 5.310451 AGCTTACTACCTCGAGGAGAATAG 58.690 45.833 37.69 27.48 38.94 1.73
1934 2021 3.386063 TCGGGAATAGGTAACCCATGAA 58.614 45.455 0.00 0.00 43.40 2.57
1940 2027 5.699458 CACACATATTCGGGAATAGGTAACC 59.301 44.000 15.73 0.00 43.70 2.85
1960 2047 6.734104 ATCTTCTTGAAAGTAGCATCACAC 57.266 37.500 0.00 0.00 0.00 3.82
2074 2194 9.459640 GTAATCTTGTTTCCAAAAGGACTAAAC 57.540 33.333 0.00 0.00 0.00 2.01
2198 2347 4.101790 CATGTTGCCACGACCCGC 62.102 66.667 0.00 0.00 0.00 6.13
2351 2505 0.178924 ACATGGCCTTGGCCTTCTTT 60.179 50.000 28.37 8.69 0.00 2.52
2432 2586 4.371681 AGACACCCTTGATATAACCCAGT 58.628 43.478 0.00 0.00 0.00 4.00
2460 2614 0.738975 CTCACGCCATAGAAGTCCGA 59.261 55.000 0.00 0.00 0.00 4.55
2468 2622 2.772739 AGCTTTGCTCACGCCATAG 58.227 52.632 0.00 0.00 30.62 2.23
2613 2780 2.154462 CAAACAATCCCTTCGTGCTCT 58.846 47.619 0.00 0.00 0.00 4.09
2694 2861 6.645705 TGTGATTAATTGTGCGAATATCGAC 58.354 36.000 3.61 0.41 43.74 4.20
2699 2866 8.604890 TCGTATTTGTGATTAATTGTGCGAATA 58.395 29.630 0.00 0.00 0.00 1.75
2704 2871 7.461416 GCAGTTCGTATTTGTGATTAATTGTGC 60.461 37.037 0.00 0.00 0.00 4.57
2717 2884 3.935203 ACCAGATGAGCAGTTCGTATTTG 59.065 43.478 0.00 0.00 0.00 2.32
2840 3008 6.016527 AGGACTATTTATGTTGATCTACGCGA 60.017 38.462 15.93 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.