Multiple sequence alignment - TraesCS5B01G218200

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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 TraesCS5B01G218200 chr5B 100.000 2851 0 0 1 2851 392047537 392050387 0.000000e+00 5265.0
1 TraesCS5B01G218200 chr5B 99.346 2754 14 2 1 2751 392106275 392109027 0.000000e+00 4983.0
2 TraesCS5B01G218200 chr5B 99.670 1516 5 0 1336 2851 392064533 392066048 0.000000e+00 2772.0
3 TraesCS5B01G218200 chr5B 99.670 1516 5 0 1336 2851 392071925 392073440 0.000000e+00 2772.0
4 TraesCS5B01G218200 chr5B 99.604 1516 6 0 1336 2851 392112349 392113864 0.000000e+00 2767.0
5 TraesCS5B01G218200 chr5B 100.000 750 0 0 585 1334 392063106 392063855 0.000000e+00 1386.0
6 TraesCS5B01G218200 chr5B 97.374 495 10 1 3 494 78311512 78312006 0.000000e+00 839.0
7 TraesCS5B01G218200 chr5B 94.030 402 20 3 1380 1777 391866989 391867390 8.740000e-170 606.0
8 TraesCS5B01G218200 chr5B 84.142 536 40 16 764 1285 391866488 391866992 7.150000e-131 477.0
9 TraesCS5B01G218200 chrUn 99.102 1337 8 2 1 1334 341235549 341236884 0.000000e+00 2399.0
10 TraesCS5B01G218200 chrUn 90.110 91 8 1 498 588 298565245 298565334 1.790000e-22 117.0
11 TraesCS5B01G218200 chr5A 91.499 1294 73 16 604 1888 436374008 436375273 0.000000e+00 1746.0
12 TraesCS5B01G218200 chr5A 88.066 486 38 11 1421 1888 436590852 436591335 2.480000e-155 558.0
13 TraesCS5B01G218200 chr5A 84.803 533 68 6 2325 2851 436549692 436550217 9.050000e-145 523.0
14 TraesCS5B01G218200 chr5A 82.642 530 75 9 2325 2851 436382539 436383054 1.200000e-123 453.0
15 TraesCS5B01G218200 chr5A 89.645 338 28 6 1976 2309 436576956 436577290 9.440000e-115 424.0
16 TraesCS5B01G218200 chr5A 84.977 426 28 14 866 1282 436548621 436549019 1.590000e-107 399.0
17 TraesCS5B01G218200 chr5A 82.213 506 42 16 2325 2819 436577662 436578130 2.660000e-105 392.0
18 TraesCS5B01G218200 chr5A 87.578 322 34 4 2530 2847 436378522 436378841 4.490000e-98 368.0
19 TraesCS5B01G218200 chr5A 90.514 253 21 3 2046 2296 436377741 436377992 5.890000e-87 331.0
20 TraesCS5B01G218200 chr5A 93.500 200 10 1 1716 1912 436377425 436377624 7.720000e-76 294.0
21 TraesCS5B01G218200 chr5A 90.361 166 10 2 2325 2485 436376324 436376488 2.230000e-51 213.0
22 TraesCS5B01G218200 chr5A 82.075 106 13 4 741 846 436548529 436548628 5.060000e-13 86.1
23 TraesCS5B01G218200 chr5D 89.790 1283 90 19 604 1878 335083584 335084833 0.000000e+00 1605.0
24 TraesCS5B01G218200 chr5D 93.227 753 49 2 1081 1831 335103493 335104245 0.000000e+00 1107.0
25 TraesCS5B01G218200 chr5D 97.159 528 14 1 2325 2851 335105228 335105755 0.000000e+00 891.0
26 TraesCS5B01G218200 chr5D 83.631 953 113 32 839 1773 335079237 335080164 0.000000e+00 856.0
27 TraesCS5B01G218200 chr5D 91.054 503 33 7 1828 2328 335104325 335104817 0.000000e+00 669.0
28 TraesCS5B01G218200 chr5D 87.743 514 55 4 1380 1887 335087486 335087997 6.800000e-166 593.0
29 TraesCS5B01G218200 chr5D 86.330 534 58 7 2325 2851 335084995 335085520 4.120000e-158 568.0
30 TraesCS5B01G218200 chr5D 79.472 682 79 38 634 1284 335120966 335121617 7.300000e-116 427.0
31 TraesCS5B01G218200 chr5D 77.859 682 104 30 632 1284 334970255 334969592 2.070000e-101 379.0
32 TraesCS5B01G218200 chr5D 75.596 545 70 33 772 1283 334991115 334990601 8.000000e-51 211.0
33 TraesCS5B01G218200 chr5D 80.060 331 29 14 635 956 335103050 335103352 8.000000e-51 211.0
34 TraesCS5B01G218200 chr3B 97.782 496 7 2 3 494 687469788 687470283 0.000000e+00 852.0
35 TraesCS5B01G218200 chr3B 86.957 92 10 2 501 592 821404993 821404904 5.030000e-18 102.0
36 TraesCS5B01G218200 chr7A 82.314 1046 121 33 838 1847 177344750 177343733 0.000000e+00 848.0
37 TraesCS5B01G218200 chr2B 97.400 500 9 2 3 499 37769316 37768818 0.000000e+00 848.0
38 TraesCS5B01G218200 chr7B 97.576 495 9 1 3 494 649467430 649467924 0.000000e+00 845.0
39 TraesCS5B01G218200 chr7B 97.189 498 10 2 3 496 110319058 110318561 0.000000e+00 839.0
40 TraesCS5B01G218200 chr7B 90.526 95 7 1 498 592 742470231 742470323 1.070000e-24 124.0
41 TraesCS5B01G218200 chr7B 89.011 91 10 0 501 591 125361444 125361354 2.320000e-21 113.0
42 TraesCS5B01G218200 chr1B 97.379 496 9 2 3 494 161398488 161397993 0.000000e+00 841.0
43 TraesCS5B01G218200 chr1B 97.000 500 12 1 3 499 42060994 42060495 0.000000e+00 837.0
44 TraesCS5B01G218200 chr4D 89.888 89 8 1 501 589 118238503 118238416 2.320000e-21 113.0
45 TraesCS5B01G218200 chr1A 88.298 94 9 2 498 591 42117893 42117984 8.350000e-21 111.0
46 TraesCS5B01G218200 chr2D 88.506 87 9 1 503 589 380046722 380046637 1.400000e-18 104.0


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 TraesCS5B01G218200 chr5B 392047537 392050387 2850 False 5265.000000 5265 100.000000 1 2851 1 chr5B.!!$F2 2850
1 TraesCS5B01G218200 chr5B 392106275 392113864 7589 False 3875.000000 4983 99.475000 1 2851 2 chr5B.!!$F6 2850
2 TraesCS5B01G218200 chr5B 392071925 392073440 1515 False 2772.000000 2772 99.670000 1336 2851 1 chr5B.!!$F3 1515
3 TraesCS5B01G218200 chr5B 392063106 392066048 2942 False 2079.000000 2772 99.835000 585 2851 2 chr5B.!!$F5 2266
4 TraesCS5B01G218200 chr5B 391866488 391867390 902 False 541.500000 606 89.086000 764 1777 2 chr5B.!!$F4 1013
5 TraesCS5B01G218200 chrUn 341235549 341236884 1335 False 2399.000000 2399 99.102000 1 1334 1 chrUn.!!$F2 1333
6 TraesCS5B01G218200 chr5A 436374008 436383054 9046 False 567.500000 1746 89.349000 604 2851 6 chr5A.!!$F2 2247
7 TraesCS5B01G218200 chr5A 436576956 436578130 1174 False 408.000000 424 85.929000 1976 2819 2 chr5A.!!$F4 843
8 TraesCS5B01G218200 chr5A 436548529 436550217 1688 False 336.033333 523 83.951667 741 2851 3 chr5A.!!$F3 2110
9 TraesCS5B01G218200 chr5D 335079237 335087997 8760 False 905.500000 1605 86.873500 604 2851 4 chr5D.!!$F2 2247
10 TraesCS5B01G218200 chr5D 335103050 335105755 2705 False 719.500000 1107 90.375000 635 2851 4 chr5D.!!$F3 2216
11 TraesCS5B01G218200 chr5D 335120966 335121617 651 False 427.000000 427 79.472000 634 1284 1 chr5D.!!$F1 650
12 TraesCS5B01G218200 chr5D 334969592 334970255 663 True 379.000000 379 77.859000 632 1284 1 chr5D.!!$R1 652
13 TraesCS5B01G218200 chr5D 334990601 334991115 514 True 211.000000 211 75.596000 772 1283 1 chr5D.!!$R2 511
14 TraesCS5B01G218200 chr7A 177343733 177344750 1017 True 848.000000 848 82.314000 838 1847 1 chr7A.!!$R1 1009

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
64 65 1.734655 AGGGAGAGCAAGAAAGTGGA 58.265 50.000 0.00 0.0 0.00 4.02 F
289 290 2.014018 GCGGAATGCGCGTGTTTTT 61.014 52.632 8.43 0.0 0.00 1.94 F
1325 5234 3.058914 CACAGTGCAGTGTTAGTTAAGCC 60.059 47.826 24.56 0.0 34.83 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 5246 0.470766 ACCTGGCACAAACCGAGTAA 59.529 50.000 0.0 0.0 38.70 2.24 R
1497 6102 4.742649 TGCGAGAGGAGCCCGTCT 62.743 66.667 0.0 0.0 39.94 4.18 R
2576 10082 5.253330 TCAACCTGGAACATGAACTTATCC 58.747 41.667 0.0 0.0 38.20 2.59 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
64 65 1.734655 AGGGAGAGCAAGAAAGTGGA 58.265 50.000 0.00 0.0 0.00 4.02
153 154 5.046014 GGCTTCATCATATGGACACCTCTAT 60.046 44.000 2.13 0.0 0.00 1.98
289 290 2.014018 GCGGAATGCGCGTGTTTTT 61.014 52.632 8.43 0.0 0.00 1.94
327 331 3.320541 CCACCACCAATCTTGCTAAACAA 59.679 43.478 0.00 0.0 36.62 2.83
440 444 4.024302 GTGTGCCCTTGTAACAAACTCTAC 60.024 45.833 0.00 0.0 0.00 2.59
442 446 3.079578 GCCCTTGTAACAAACTCTACCC 58.920 50.000 0.00 0.0 0.00 3.69
444 448 4.576879 CCCTTGTAACAAACTCTACCCTC 58.423 47.826 0.00 0.0 0.00 4.30
522 526 4.566987 ACTTTGTGATACTTCGGGACTTC 58.433 43.478 0.00 0.0 0.00 3.01
1300 5209 4.056050 CCAAGGTACGTATCCACATAAGC 58.944 47.826 1.21 0.0 0.00 3.09
1301 5210 4.442332 CCAAGGTACGTATCCACATAAGCA 60.442 45.833 1.21 0.0 0.00 3.91
1303 5212 4.690122 AGGTACGTATCCACATAAGCAAC 58.310 43.478 1.21 0.0 0.00 4.17
1304 5213 4.160814 AGGTACGTATCCACATAAGCAACA 59.839 41.667 1.21 0.0 0.00 3.33
1306 5215 3.932822 ACGTATCCACATAAGCAACACA 58.067 40.909 0.00 0.0 0.00 3.72
1309 5218 4.201714 CGTATCCACATAAGCAACACAGTG 60.202 45.833 0.00 0.0 0.00 3.66
1325 5234 3.058914 CACAGTGCAGTGTTAGTTAAGCC 60.059 47.826 24.56 0.0 34.83 4.35
1326 5235 3.181454 ACAGTGCAGTGTTAGTTAAGCCT 60.181 43.478 21.61 0.0 0.00 4.58
1328 5237 3.325135 AGTGCAGTGTTAGTTAAGCCTCT 59.675 43.478 0.00 0.0 0.00 3.69
1329 5238 4.527038 AGTGCAGTGTTAGTTAAGCCTCTA 59.473 41.667 0.00 0.0 0.00 2.43
1331 5240 4.282449 TGCAGTGTTAGTTAAGCCTCTACA 59.718 41.667 0.00 0.0 0.00 2.74
1336 5245 7.702772 CAGTGTTAGTTAAGCCTCTACATAGTG 59.297 40.741 0.00 0.0 0.00 2.74
1337 5246 7.396623 AGTGTTAGTTAAGCCTCTACATAGTGT 59.603 37.037 0.00 0.0 0.00 3.55
1497 6102 4.329545 GTGGAAGCAGGCCGTGGA 62.330 66.667 0.00 0.0 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.578688 GCATTTGAAGAAAAGATGCGGT 58.421 40.909 0.00 0.00 27.36 5.68
153 154 1.511850 CGAACTCTCAACATGCCACA 58.488 50.000 0.00 0.00 0.00 4.17
327 331 0.250901 AAGGTTTGCCTCGCAGATGT 60.251 50.000 0.00 0.00 46.33 3.06
440 444 8.378565 TGCCTCATCTATTAAATAAGAAGAGGG 58.621 37.037 24.04 14.12 42.89 4.30
522 526 5.854866 CGATGCATGCAACCATCTTATTAAG 59.145 40.000 26.68 0.47 36.55 1.85
1303 5212 3.058914 GGCTTAACTAACACTGCACTGTG 60.059 47.826 2.76 2.76 43.07 3.66
1304 5213 3.139077 GGCTTAACTAACACTGCACTGT 58.861 45.455 0.00 0.00 0.00 3.55
1306 5215 3.325135 AGAGGCTTAACTAACACTGCACT 59.675 43.478 0.00 0.00 0.00 4.40
1309 5218 4.817517 TGTAGAGGCTTAACTAACACTGC 58.182 43.478 0.00 0.00 0.00 4.40
1311 5220 7.396623 ACACTATGTAGAGGCTTAACTAACACT 59.603 37.037 0.00 0.00 0.00 3.55
1314 5223 9.513727 GTAACACTATGTAGAGGCTTAACTAAC 57.486 37.037 0.00 0.00 0.00 2.34
1316 5225 9.118300 GAGTAACACTATGTAGAGGCTTAACTA 57.882 37.037 0.00 0.00 0.00 2.24
1319 5228 6.039047 CCGAGTAACACTATGTAGAGGCTTAA 59.961 42.308 0.00 0.00 0.00 1.85
1320 5229 5.530171 CCGAGTAACACTATGTAGAGGCTTA 59.470 44.000 0.00 0.00 0.00 3.09
1322 5231 3.884091 CCGAGTAACACTATGTAGAGGCT 59.116 47.826 0.00 0.00 0.00 4.58
1323 5232 3.631227 ACCGAGTAACACTATGTAGAGGC 59.369 47.826 0.00 0.00 0.00 4.70
1325 5234 6.527023 CACAAACCGAGTAACACTATGTAGAG 59.473 42.308 0.00 0.00 0.00 2.43
1326 5235 6.384224 CACAAACCGAGTAACACTATGTAGA 58.616 40.000 0.00 0.00 0.00 2.59
1328 5237 4.925054 GCACAAACCGAGTAACACTATGTA 59.075 41.667 0.00 0.00 0.00 2.29
1329 5238 3.744426 GCACAAACCGAGTAACACTATGT 59.256 43.478 0.00 0.00 0.00 2.29
1331 5240 3.244284 TGGCACAAACCGAGTAACACTAT 60.244 43.478 0.00 0.00 31.92 2.12
1336 5245 0.872388 CCTGGCACAAACCGAGTAAC 59.128 55.000 0.00 0.00 38.70 2.50
1337 5246 0.470766 ACCTGGCACAAACCGAGTAA 59.529 50.000 0.00 0.00 38.70 2.24
1497 6102 4.742649 TGCGAGAGGAGCCCGTCT 62.743 66.667 0.00 0.00 39.94 4.18
2576 10082 5.253330 TCAACCTGGAACATGAACTTATCC 58.747 41.667 0.00 0.00 38.20 2.59


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

AutoCloner maintained by Alex Coulton.