Multiple sequence alignment - TraesCS2B01G488900

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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 TraesCS2B01G488900 chr2B 100.000 1440 0 0 1 1440 686329212 686330651 0.000000e+00 2660
1 TraesCS2B01G488900 chr2B 95.000 1440 69 2 1 1440 752245793 752244357 0.000000e+00 2257
2 TraesCS2B01G488900 chr2B 94.656 1441 75 2 1 1440 747922157 747920718 0.000000e+00 2233
3 TraesCS2B01G488900 chr2B 100.000 566 0 0 1711 2276 686330922 686331487 0.000000e+00 1046
4 TraesCS2B01G488900 chr6B 95.347 1440 62 4 1 1440 568678612 568677178 0.000000e+00 2283
5 TraesCS2B01G488900 chr6B 95.142 1441 65 4 1 1440 533238318 533239754 0.000000e+00 2268
6 TraesCS2B01G488900 chr6B 95.080 1443 64 6 1 1440 593121553 593122991 0.000000e+00 2265
7 TraesCS2B01G488900 chr7B 95.284 1442 61 3 1 1440 115033329 115031893 0.000000e+00 2279
8 TraesCS2B01G488900 chr7B 94.730 1442 70 4 1 1440 35584175 35582738 0.000000e+00 2237
9 TraesCS2B01G488900 chr5B 95.281 1441 62 3 1 1440 122800522 122801957 0.000000e+00 2279
10 TraesCS2B01G488900 chr5B 97.143 140 1 2 1301 1440 353149641 353149777 1.360000e-57 233
11 TraesCS2B01G488900 chr1B 95.139 1440 65 5 1 1440 518058718 518057284 0.000000e+00 2266
12 TraesCS2B01G488900 chr6D 96.820 566 18 0 1711 2276 68406188 68406753 0.000000e+00 946
13 TraesCS2B01G488900 chr5D 96.643 566 19 0 1711 2276 370872880 370872315 0.000000e+00 941
14 TraesCS2B01G488900 chr3B 96.643 566 19 0 1711 2276 275235264 275235829 0.000000e+00 941
15 TraesCS2B01G488900 chr7D 96.466 566 20 0 1711 2276 236150574 236151139 0.000000e+00 935
16 TraesCS2B01G488900 chr7D 96.466 566 20 0 1711 2276 247007849 247008414 0.000000e+00 935
17 TraesCS2B01G488900 chr4D 96.466 566 20 0 1711 2276 111195563 111196128 0.000000e+00 935
18 TraesCS2B01G488900 chr3D 96.466 566 20 0 1711 2276 263917344 263917909 0.000000e+00 935
19 TraesCS2B01G488900 chr2D 96.466 566 20 0 1711 2276 589054514 589055079 0.000000e+00 935
20 TraesCS2B01G488900 chr1D 96.466 566 20 0 1711 2276 221396833 221397398 0.000000e+00 935


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 TraesCS2B01G488900 chr2B 686329212 686331487 2275 False 1853 2660 100.000 1 2276 2 chr2B.!!$F1 2275
1 TraesCS2B01G488900 chr2B 752244357 752245793 1436 True 2257 2257 95.000 1 1440 1 chr2B.!!$R2 1439
2 TraesCS2B01G488900 chr2B 747920718 747922157 1439 True 2233 2233 94.656 1 1440 1 chr2B.!!$R1 1439
3 TraesCS2B01G488900 chr6B 568677178 568678612 1434 True 2283 2283 95.347 1 1440 1 chr6B.!!$R1 1439
4 TraesCS2B01G488900 chr6B 533238318 533239754 1436 False 2268 2268 95.142 1 1440 1 chr6B.!!$F1 1439
5 TraesCS2B01G488900 chr6B 593121553 593122991 1438 False 2265 2265 95.080 1 1440 1 chr6B.!!$F2 1439
6 TraesCS2B01G488900 chr7B 115031893 115033329 1436 True 2279 2279 95.284 1 1440 1 chr7B.!!$R2 1439
7 TraesCS2B01G488900 chr7B 35582738 35584175 1437 True 2237 2237 94.730 1 1440 1 chr7B.!!$R1 1439
8 TraesCS2B01G488900 chr5B 122800522 122801957 1435 False 2279 2279 95.281 1 1440 1 chr5B.!!$F1 1439
9 TraesCS2B01G488900 chr1B 518057284 518058718 1434 True 2266 2266 95.139 1 1440 1 chr1B.!!$R1 1439
10 TraesCS2B01G488900 chr6D 68406188 68406753 565 False 946 946 96.820 1711 2276 1 chr6D.!!$F1 565
11 TraesCS2B01G488900 chr5D 370872315 370872880 565 True 941 941 96.643 1711 2276 1 chr5D.!!$R1 565
12 TraesCS2B01G488900 chr3B 275235264 275235829 565 False 941 941 96.643 1711 2276 1 chr3B.!!$F1 565
13 TraesCS2B01G488900 chr7D 236150574 236151139 565 False 935 935 96.466 1711 2276 1 chr7D.!!$F1 565
14 TraesCS2B01G488900 chr7D 247007849 247008414 565 False 935 935 96.466 1711 2276 1 chr7D.!!$F2 565
15 TraesCS2B01G488900 chr4D 111195563 111196128 565 False 935 935 96.466 1711 2276 1 chr4D.!!$F1 565
16 TraesCS2B01G488900 chr3D 263917344 263917909 565 False 935 935 96.466 1711 2276 1 chr3D.!!$F1 565
17 TraesCS2B01G488900 chr2D 589054514 589055079 565 False 935 935 96.466 1711 2276 1 chr2D.!!$F1 565
18 TraesCS2B01G488900 chr1D 221396833 221397398 565 False 935 935 96.466 1711 2276 1 chr1D.!!$F1 565

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
530 532 0.679002 CTCCGGGTCGTTCCAGTCTA 60.679 60.0 0.0 0.0 38.11 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2028 1.098712 GGTTCACTGGTTCGGTTGCA 61.099 55.0 0.0 0.0 0.0 4.08 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 4.309950 GCCGTCGTCCACCACCTT 62.310 66.667 0.00 0.00 0.00 3.50
27 28 1.116536 TCGTCCACCACCTTGCTGTA 61.117 55.000 0.00 0.00 0.00 2.74
175 177 1.507140 TGTTTCCTCCACCTGACAGT 58.493 50.000 0.93 0.00 0.00 3.55
185 187 0.772124 ACCTGACAGTTGGGACCCAT 60.772 55.000 15.83 0.00 31.53 4.00
266 268 2.448582 TTGACAGCTGGGACCCGTT 61.449 57.895 19.93 0.00 0.00 4.44
309 311 1.541233 GCCTGCTAAGCGGACATGTAT 60.541 52.381 0.00 0.00 37.02 2.29
411 413 3.239449 TCAACCTCTGTTCTTGCTCCTA 58.761 45.455 0.00 0.00 30.42 2.94
484 486 3.012959 AGTTTCCCACTCCTCTCCATCTA 59.987 47.826 0.00 0.00 0.00 1.98
530 532 0.679002 CTCCGGGTCGTTCCAGTCTA 60.679 60.000 0.00 0.00 38.11 2.59
707 709 3.680642 TCGGAAGTATACTGTACGTGC 57.319 47.619 6.06 0.00 0.00 5.34
762 764 2.027073 CCGCAACGAAGCAGCTGTA 61.027 57.895 16.64 0.00 0.00 2.74
921 924 3.535561 CAAGCCTTTCGGTGACATATCT 58.464 45.455 0.00 0.00 0.00 1.98
1140 1145 7.770801 TGAGATTCAACATGTATTAAGGTCG 57.229 36.000 0.00 0.00 0.00 4.79
1360 1369 2.883828 AACTGACAGCAGGGACCCG 61.884 63.158 4.40 1.05 46.60 5.28
1387 1398 0.179174 GGCCACCGTATTTTGCGAAG 60.179 55.000 0.00 0.00 0.00 3.79
1848 1859 1.567504 CGTACGATGTCCATCCAACC 58.432 55.000 10.44 0.00 34.40 3.77
1849 1860 1.136305 CGTACGATGTCCATCCAACCT 59.864 52.381 10.44 0.00 34.40 3.50
2017 2028 4.363990 CGACGGCAGCCTCACACT 62.364 66.667 10.54 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.019278 CGCACCGAATACAGCAAGGT 61.019 55.000 0.00 0.00 35.24 3.50
21 22 2.817834 GCCGCACCGAATACAGCA 60.818 61.111 0.00 0.00 0.00 4.41
175 177 0.986019 ATACAGCCGATGGGTCCCAA 60.986 55.000 16.55 0.00 36.95 4.12
185 187 1.226575 CGTGCGAAGATACAGCCGA 60.227 57.895 0.00 0.00 0.00 5.54
211 213 1.327303 TTCGCAAAACAAGGAGGCAT 58.673 45.000 0.00 0.00 0.00 4.40
266 268 4.504864 CCCACAAGTCAGTCACCAAATCTA 60.505 45.833 0.00 0.00 0.00 1.98
309 311 1.669604 TAAGTTGACAAAGCCGTGCA 58.330 45.000 0.00 0.00 0.00 4.57
376 378 0.250338 GGTTGAAGAAGGAGCACGGT 60.250 55.000 0.00 0.00 0.00 4.83
707 709 0.902048 TGGACCCAGCTGAGACTCTG 60.902 60.000 17.39 4.41 0.00 3.35
921 924 8.917414 ATAGGGCTTACATTATAAGAGGATCA 57.083 34.615 0.00 0.00 37.82 2.92
937 940 3.244215 CCTTCTCGCATTGATAGGGCTTA 60.244 47.826 0.00 0.00 0.00 3.09
1140 1145 3.385193 AAATGTGCTGGTAAGTTTGCC 57.615 42.857 0.00 0.00 0.00 4.52
1185 1191 2.238521 AGCCAACATTCGGTCACATTT 58.761 42.857 0.00 0.00 0.00 2.32
1298 1306 6.044682 GCGTAATAAGGAGGCACTTACTTTA 58.955 40.000 4.17 0.00 41.55 1.85
1393 1404 1.341080 CAGTCAGGGGGCAAACATTT 58.659 50.000 0.00 0.00 0.00 2.32
1394 1405 1.187567 GCAGTCAGGGGGCAAACATT 61.188 55.000 0.00 0.00 0.00 2.71
1395 1406 1.607467 GCAGTCAGGGGGCAAACAT 60.607 57.895 0.00 0.00 0.00 2.71
1848 1859 2.028930 AGGTTGAAGAAGCACTACGGAG 60.029 50.000 0.00 0.00 31.56 4.63
1849 1860 1.968493 AGGTTGAAGAAGCACTACGGA 59.032 47.619 0.00 0.00 31.56 4.69
2017 2028 1.098712 GGTTCACTGGTTCGGTTGCA 61.099 55.000 0.00 0.00 0.00 4.08
2183 2194 1.402259 CAGCCTCTCCACGTACAGTAG 59.598 57.143 0.00 0.00 0.00 2.57
2245 2256 2.548057 CTGGCAAAGCGACTTACTTGAA 59.452 45.455 0.00 0.00 0.00 2.69
2246 2257 2.143122 CTGGCAAAGCGACTTACTTGA 58.857 47.619 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.