Multiple sequence alignment - TraesCS2D01G042800

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 TraesCS2D01G042800 chr2D 100.000 2533 0 0 1 2533 15459333 15456801 0.000000e+00 4678.0
1 TraesCS2D01G042800 chr2D 81.870 1572 204 53 1006 2533 15471361 15469827 0.000000e+00 1249.0
2 TraesCS2D01G042800 chr2D 84.079 961 106 31 1510 2436 15505223 15504276 0.000000e+00 883.0
3 TraesCS2D01G042800 chr2D 80.298 1274 155 42 1007 2242 15515536 15514321 0.000000e+00 874.0
4 TraesCS2D01G042800 chr2D 84.892 556 56 8 454 984 15472297 15471745 1.030000e-148 536.0
5 TraesCS2D01G042800 chr2D 87.013 462 52 7 1 459 15473369 15472913 4.830000e-142 514.0
6 TraesCS2D01G042800 chr2D 83.686 331 30 10 2088 2396 15496582 15496254 8.860000e-75 291.0
7 TraesCS2D01G042800 chr2A 96.007 1077 28 7 1006 2071 17597828 17596756 0.000000e+00 1736.0
8 TraesCS2D01G042800 chr2A 83.241 1259 142 41 1007 2242 17474085 17472873 0.000000e+00 1092.0
9 TraesCS2D01G042800 chr2A 82.129 1259 146 39 1007 2242 17533306 17532104 0.000000e+00 1005.0
10 TraesCS2D01G042800 chr2A 86.079 783 76 13 1006 1763 17419027 17418253 0.000000e+00 811.0
11 TraesCS2D01G042800 chr2A 92.973 555 29 3 1006 1560 17548640 17548096 0.000000e+00 800.0
12 TraesCS2D01G042800 chr2A 86.358 755 76 8 1007 1754 17502241 17501507 0.000000e+00 798.0
13 TraesCS2D01G042800 chr2A 88.256 579 40 3 453 1009 17475017 17474445 0.000000e+00 667.0
14 TraesCS2D01G042800 chr2A 92.050 478 17 9 2056 2533 17596737 17596281 0.000000e+00 652.0
15 TraesCS2D01G042800 chr2A 79.543 1007 127 38 1007 1989 17412293 17411342 0.000000e+00 645.0
16 TraesCS2D01G042800 chr2A 85.640 578 55 13 454 1009 17549570 17548999 1.310000e-162 582.0
17 TraesCS2D01G042800 chr2A 88.136 472 49 5 1 470 17426452 17425986 2.850000e-154 555.0
18 TraesCS2D01G042800 chr2A 84.509 581 60 17 454 1012 17598758 17598186 4.760000e-152 547.0
19 TraesCS2D01G042800 chr2A 87.526 473 50 7 1 470 17414263 17413797 2.870000e-149 538.0
20 TraesCS2D01G042800 chr2A 83.592 579 66 13 454 1009 17503173 17502601 1.340000e-142 516.0
21 TraesCS2D01G042800 chr2A 85.593 472 60 5 3 470 17550642 17550175 2.930000e-134 488.0
22 TraesCS2D01G042800 chr2A 82.609 575 70 12 454 1005 17425359 17424792 4.900000e-132 481.0
23 TraesCS2D01G042800 chr2A 84.778 473 63 8 1 470 17535309 17534843 1.370000e-127 466.0
24 TraesCS2D01G042800 chr2A 84.200 481 60 12 1 470 17504254 17503779 1.070000e-123 453.0
25 TraesCS2D01G042800 chr2A 84.944 445 58 7 29 470 17542648 17542210 2.310000e-120 442.0
26 TraesCS2D01G042800 chr2A 79.084 655 72 21 1465 2112 17507911 17507315 8.500000e-105 390.0
27 TraesCS2D01G042800 chr2A 80.354 565 48 31 1425 1963 17559176 17558649 1.110000e-98 370.0
28 TraesCS2D01G042800 chr2A 85.209 311 25 6 2107 2396 17507280 17506970 1.470000e-77 300.0
29 TraesCS2D01G042800 chr2A 83.125 320 30 7 2100 2396 17544865 17544547 1.150000e-68 270.0
30 TraesCS2D01G042800 chr2A 81.818 198 18 5 2296 2478 17410983 17410789 1.570000e-32 150.0
31 TraesCS2D01G042800 chr2A 97.561 41 1 0 2437 2477 17417706 17417666 1.260000e-08 71.3
32 TraesCS2D01G042800 chr2B 83.050 1469 179 39 1006 2446 27616345 27614919 0.000000e+00 1269.0
33 TraesCS2D01G042800 chr2B 91.212 751 46 6 1006 1754 27543927 27543195 0.000000e+00 1003.0
34 TraesCS2D01G042800 chr2B 86.332 578 51 5 453 1008 27544858 27544287 2.790000e-169 604.0
35 TraesCS2D01G042800 chr2B 86.151 556 49 11 473 1006 27617256 27616707 2.190000e-160 575.0
36 TraesCS2D01G042800 chr2B 87.949 473 48 7 1 470 27583364 27582898 1.320000e-152 549.0
37 TraesCS2D01G042800 chr2B 87.500 472 45 8 1 469 27619594 27619134 1.330000e-147 532.0
38 TraesCS2D01G042800 chr2B 86.920 474 54 5 1 470 27545932 27545463 2.230000e-145 525.0
39 TraesCS2D01G042800 chr2B 86.310 336 26 11 2197 2523 27627632 27627308 5.190000e-92 348.0
40 TraesCS2D01G042800 chr2B 88.660 97 9 2 2428 2523 27587734 27587639 1.590000e-22 117.0
41 TraesCS2D01G042800 chr4A 78.302 106 21 2 1231 1335 722931334 722931438 1.630000e-07 67.6


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 TraesCS2D01G042800 chr2D 15456801 15459333 2532 True 4678.000000 4678 100.000000 1 2533 1 chr2D.!!$R1 2532
1 TraesCS2D01G042800 chr2D 15504276 15505223 947 True 883.000000 883 84.079000 1510 2436 1 chr2D.!!$R3 926
2 TraesCS2D01G042800 chr2D 15514321 15515536 1215 True 874.000000 874 80.298000 1007 2242 1 chr2D.!!$R4 1235
3 TraesCS2D01G042800 chr2D 15469827 15473369 3542 True 766.333333 1249 84.591667 1 2533 3 chr2D.!!$R5 2532
4 TraesCS2D01G042800 chr2A 17596281 17598758 2477 True 978.333333 1736 90.855333 454 2533 3 chr2A.!!$R8 2079
5 TraesCS2D01G042800 chr2A 17472873 17475017 2144 True 879.500000 1092 85.748500 453 2242 2 chr2A.!!$R4 1789
6 TraesCS2D01G042800 chr2A 17532104 17535309 3205 True 735.500000 1005 83.453500 1 2242 2 chr2A.!!$R6 2241
7 TraesCS2D01G042800 chr2A 17424792 17426452 1660 True 518.000000 555 85.372500 1 1005 2 chr2A.!!$R3 1004
8 TraesCS2D01G042800 chr2A 17542210 17550642 8432 True 516.400000 800 86.455000 3 2396 5 chr2A.!!$R7 2393
9 TraesCS2D01G042800 chr2A 17501507 17507911 6404 True 491.400000 798 83.688600 1 2396 5 chr2A.!!$R5 2395
10 TraesCS2D01G042800 chr2A 17410789 17419027 8238 True 443.060000 811 86.505400 1 2478 5 chr2A.!!$R2 2477
11 TraesCS2D01G042800 chr2A 17558649 17559176 527 True 370.000000 370 80.354000 1425 1963 1 chr2A.!!$R1 538
12 TraesCS2D01G042800 chr2B 27614919 27619594 4675 True 792.000000 1269 85.567000 1 2446 3 chr2B.!!$R5 2445
13 TraesCS2D01G042800 chr2B 27543195 27545932 2737 True 710.666667 1003 88.154667 1 1754 3 chr2B.!!$R4 1753

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
287 5747 1.827344 TGCCTACTCAGGTGACATCAG 59.173 52.381 0.0 0.0 44.68 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 9442 1.131883 CAGCATGAAGTAAGGCACAGC 59.868 52.381 0.0 0.0 39.69 4.4 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
23 5474 5.680210 GTGCCTCATATACAGGGACCTGC 62.680 56.522 17.96 1.67 44.57 4.85
34 5485 2.239654 CAGGGACCTGCTTTCTATGGAA 59.760 50.000 5.27 0.00 37.24 3.53
152 5603 8.248945 AGAGAAATTTGAGCTTGGATTGTAATG 58.751 33.333 0.00 0.00 0.00 1.90
153 5613 6.815142 AGAAATTTGAGCTTGGATTGTAATGC 59.185 34.615 0.00 0.00 0.00 3.56
154 5614 4.454728 TTTGAGCTTGGATTGTAATGCC 57.545 40.909 0.00 0.00 0.00 4.40
157 5617 3.193267 TGAGCTTGGATTGTAATGCCAAC 59.807 43.478 0.00 0.00 36.80 3.77
164 5624 8.792633 GCTTGGATTGTAATGCCAACTATAATA 58.207 33.333 0.00 0.00 36.80 0.98
212 5672 8.157476 AGGTGTCAGATGATTTACTTGTTAACT 58.843 33.333 7.22 0.00 0.00 2.24
245 5705 2.242708 ACCACCCACAAACAACTCCTTA 59.757 45.455 0.00 0.00 0.00 2.69
246 5706 3.117284 ACCACCCACAAACAACTCCTTAT 60.117 43.478 0.00 0.00 0.00 1.73
247 5707 4.105057 ACCACCCACAAACAACTCCTTATA 59.895 41.667 0.00 0.00 0.00 0.98
272 5732 3.005472 GGATAATAGTCGTGTGCTGCCTA 59.995 47.826 0.00 0.00 0.00 3.93
287 5747 1.827344 TGCCTACTCAGGTGACATCAG 59.173 52.381 0.00 0.00 44.68 2.90
290 5750 2.428890 CCTACTCAGGTGACATCAGTCC 59.571 54.545 0.00 0.00 37.17 3.85
326 5786 5.766150 TGAACCACCAAGAAATACAACAG 57.234 39.130 0.00 0.00 0.00 3.16
697 8053 8.098912 TGTATACATGGAGATTGATTCCTCATG 58.901 37.037 0.08 0.00 39.34 3.07
752 8108 2.203126 GCTCAAGGCATCGGGAGG 60.203 66.667 0.00 0.00 41.35 4.30
797 8157 6.769822 ACTTATATGCAAGGGATGTCTTTCAG 59.230 38.462 0.00 0.00 0.00 3.02
808 8168 2.747855 CTTTCAGGAGCACCCGCC 60.748 66.667 0.00 0.00 40.87 6.13
821 8181 4.994471 CCGCCAGCTGTCAGTGCA 62.994 66.667 13.81 0.00 0.00 4.57
837 8197 2.027745 AGTGCAATCGAAGGTGTGATCT 60.028 45.455 0.00 0.00 0.00 2.75
855 8215 2.677524 GCTGGATGTGGGCTTGCA 60.678 61.111 0.00 0.00 0.00 4.08
879 8239 4.100189 CACCTATTCCTACTCCAAGTCCTG 59.900 50.000 0.00 0.00 0.00 3.86
991 8357 1.960689 TGCTTTAGCCCCTGTTTTCAC 59.039 47.619 0.00 0.00 41.18 3.18
1026 8754 3.325135 ACGGTGATCTGAAGGAAGTCTTT 59.675 43.478 0.00 0.00 35.50 2.52
1068 8796 6.681368 GCCAACAGAAGCAGGAAATTATAAGG 60.681 42.308 0.00 0.00 0.00 2.69
1816 12408 5.660391 CGTCAAAGTAAGTATGCATCATCG 58.340 41.667 0.19 0.00 0.00 3.84
1991 12599 9.429359 GCTACAGACTGATTATTGTAATGCTAT 57.571 33.333 10.08 0.00 0.00 2.97
2136 12909 1.075374 ACTGGCTATTGCTGGAAACCA 59.925 47.619 0.00 0.00 39.59 3.67
2513 15579 4.458951 GCGTGGTGCATCTAAAATCTAG 57.541 45.455 0.00 0.00 45.45 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 5469 5.649831 GTCTTCAATTCCATAGAAAGCAGGT 59.350 40.000 0.00 0.00 35.09 4.00
19 5470 5.649395 TGTCTTCAATTCCATAGAAAGCAGG 59.351 40.000 0.00 0.00 35.09 4.85
23 5474 6.971184 GCATGTGTCTTCAATTCCATAGAAAG 59.029 38.462 0.00 0.00 35.09 2.62
26 5477 5.355071 GTGCATGTGTCTTCAATTCCATAGA 59.645 40.000 0.00 0.00 0.00 1.98
34 5485 3.638160 AGTTTGGTGCATGTGTCTTCAAT 59.362 39.130 0.00 0.00 0.00 2.57
133 5584 3.831333 TGGCATTACAATCCAAGCTCAAA 59.169 39.130 0.00 0.00 0.00 2.69
134 5585 3.429492 TGGCATTACAATCCAAGCTCAA 58.571 40.909 0.00 0.00 0.00 3.02
152 5603 2.484264 CTGCGGCCTTATTATAGTTGGC 59.516 50.000 0.00 0.00 42.56 4.52
153 5613 2.484264 GCTGCGGCCTTATTATAGTTGG 59.516 50.000 6.12 0.00 0.00 3.77
154 5614 3.403038 AGCTGCGGCCTTATTATAGTTG 58.597 45.455 15.55 0.00 39.73 3.16
157 5617 2.622436 GGAGCTGCGGCCTTATTATAG 58.378 52.381 15.55 0.00 39.73 1.31
245 5705 5.696724 GCAGCACACGACTATTATCCTTTAT 59.303 40.000 0.00 0.00 0.00 1.40
246 5706 5.047847 GCAGCACACGACTATTATCCTTTA 58.952 41.667 0.00 0.00 0.00 1.85
247 5707 3.871594 GCAGCACACGACTATTATCCTTT 59.128 43.478 0.00 0.00 0.00 3.11
256 5716 0.809385 GAGTAGGCAGCACACGACTA 59.191 55.000 0.00 0.00 0.00 2.59
258 5718 0.734253 CTGAGTAGGCAGCACACGAC 60.734 60.000 0.00 0.00 0.00 4.34
272 5732 2.175202 GAGGACTGATGTCACCTGAGT 58.825 52.381 0.00 0.00 44.61 3.41
287 5747 3.006247 GTTCATCTGCAGAAAGGAGGAC 58.994 50.000 22.50 10.75 36.17 3.85
290 5750 2.746362 GTGGTTCATCTGCAGAAAGGAG 59.254 50.000 22.50 8.68 36.96 3.69
690 8046 0.325933 CCACTTGCAGGACATGAGGA 59.674 55.000 1.40 0.00 36.61 3.71
691 8047 0.325933 TCCACTTGCAGGACATGAGG 59.674 55.000 1.40 0.00 36.06 3.86
692 8048 1.735386 CTCCACTTGCAGGACATGAG 58.265 55.000 1.40 0.00 0.00 2.90
697 8053 2.331132 GCAGCTCCACTTGCAGGAC 61.331 63.158 1.40 0.00 0.00 3.85
769 8126 5.784177 AGACATCCCTTGCATATAAGTACG 58.216 41.667 0.00 0.00 0.00 3.67
770 8127 7.715249 TGAAAGACATCCCTTGCATATAAGTAC 59.285 37.037 0.00 0.00 27.02 2.73
808 8168 1.128136 CTTCGATTGCACTGACAGCTG 59.872 52.381 13.48 13.48 0.00 4.24
821 8181 2.625737 CAGCAGATCACACCTTCGATT 58.374 47.619 0.00 0.00 0.00 3.34
837 8197 2.677524 GCAAGCCCACATCCAGCA 60.678 61.111 0.00 0.00 0.00 4.41
855 8215 4.031611 GGACTTGGAGTAGGAATAGGTGT 58.968 47.826 0.00 0.00 0.00 4.16
1026 8754 1.298667 GCGCTTAGGGTCCAAAGGA 59.701 57.895 0.00 0.00 0.00 3.36
1068 8796 1.616159 TGTGCCTTAGCTTGGGAAAC 58.384 50.000 8.58 6.45 40.80 2.78
1114 8842 2.207501 CTGCTCCCACAGATGCCCTT 62.208 60.000 0.00 0.00 40.25 3.95
1634 9441 1.167851 GCATGAAGTAAGGCACAGCA 58.832 50.000 0.00 0.00 0.00 4.41
1635 9442 1.131883 CAGCATGAAGTAAGGCACAGC 59.868 52.381 0.00 0.00 39.69 4.40
1636 9443 1.131883 GCAGCATGAAGTAAGGCACAG 59.868 52.381 0.00 0.00 39.69 3.66
1816 12408 3.566742 TGCATGCATCATCTATCCAACAC 59.433 43.478 18.46 0.00 0.00 3.32
2054 12700 4.981674 TCAGCGCAGAACAAAATAAAAAGG 59.018 37.500 11.47 0.00 0.00 3.11
2254 13055 3.070018 CAACACCTCCAGTCTTGCTAAG 58.930 50.000 0.00 0.00 0.00 2.18
2513 15579 0.798776 CATGGTCGAAGTTGCCACTC 59.201 55.000 0.00 0.00 34.84 3.51


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

AutoCloner maintained by Alex Coulton.