Multiple sequence alignment - TraesCS5A01G260000

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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 TraesCS5A01G260000 chr5A 100.000 3107 0 0 1 3107 474195792 474192686 0.000000e+00 5738.0
1 TraesCS5A01G260000 chr5A 99.324 3107 13 1 1 3107 474062257 474059159 0.000000e+00 5614.0
2 TraesCS5A01G260000 chr5A 99.523 2933 13 1 176 3107 474327562 474324630 0.000000e+00 5337.0
3 TraesCS5A01G260000 chr5A 96.667 210 6 1 2898 3107 474383068 474382860 6.380000e-92 348.0
4 TraesCS5A01G260000 chr5A 78.056 360 67 8 1589 1945 474026204 474026554 1.880000e-52 217.0
5 TraesCS5A01G260000 chr5A 78.056 360 67 8 1589 1945 474159531 474159881 1.880000e-52 217.0
6 TraesCS5A01G260000 chr5A 78.056 360 67 8 1589 1945 474291839 474292189 1.880000e-52 217.0
7 TraesCS5A01G260000 chr5A 86.792 159 12 4 712 868 382336308 382336459 5.330000e-38 169.0
8 TraesCS5A01G260000 chr5D 93.443 2684 137 10 222 2899 371267307 371269957 0.000000e+00 3945.0
9 TraesCS5A01G260000 chr5D 96.283 1614 54 3 906 2514 371023184 371021572 0.000000e+00 2643.0
10 TraesCS5A01G260000 chr5D 92.857 154 9 2 72 224 329780451 329780603 4.030000e-54 222.0
11 TraesCS5A01G260000 chr5D 76.441 399 80 12 1550 1940 52365589 52365981 1.460000e-48 204.0
12 TraesCS5A01G260000 chr5D 94.366 71 4 0 1 71 371267247 371267317 3.280000e-20 110.0
13 TraesCS5A01G260000 chr5B 93.034 2699 136 13 222 2899 440533426 440536093 0.000000e+00 3895.0
14 TraesCS5A01G260000 chr5B 92.775 2699 141 13 222 2899 440513760 440516425 0.000000e+00 3855.0
15 TraesCS5A01G260000 chr5B 88.506 435 26 13 879 1293 441124340 441123910 3.580000e-139 505.0
16 TraesCS5A01G260000 chr5B 89.744 156 5 3 69 224 617706270 617706414 4.090000e-44 189.0
17 TraesCS5A01G260000 chr5B 85.714 154 8 6 72 225 577607771 577607632 1.930000e-32 150.0
18 TraesCS5A01G260000 chr5B 83.439 157 11 5 72 225 235766633 235766777 6.990000e-27 132.0
19 TraesCS5A01G260000 chr5B 97.183 71 2 0 1 71 440533366 440533436 1.510000e-23 121.0
20 TraesCS5A01G260000 chrUn 96.458 960 22 2 222 1177 371166267 371167218 0.000000e+00 1574.0
21 TraesCS5A01G260000 chrUn 90.293 1092 65 11 1825 2899 272196412 272195345 0.000000e+00 1391.0
22 TraesCS5A01G260000 chrUn 90.830 807 51 8 1825 2622 465607523 465606731 0.000000e+00 1059.0
23 TraesCS5A01G260000 chrUn 97.183 71 2 0 1 71 371166207 371166277 1.510000e-23 121.0
24 TraesCS5A01G260000 chr7D 87.924 472 38 6 222 688 184517511 184517968 3.530000e-149 538.0
25 TraesCS5A01G260000 chr7D 90.909 66 4 2 2883 2947 105221645 105221709 1.530000e-13 87.9
26 TraesCS5A01G260000 chr7B 86.875 480 44 6 222 696 173302949 173303414 1.280000e-143 520.0
27 TraesCS5A01G260000 chr7B 82.500 120 15 6 69 184 516467988 516468105 1.970000e-17 100.0
28 TraesCS5A01G260000 chr6D 87.886 421 36 5 272 691 460765586 460765180 6.030000e-132 481.0
29 TraesCS5A01G260000 chr6D 86.740 181 16 5 2888 3066 380043738 380043564 8.790000e-46 195.0
30 TraesCS5A01G260000 chr6D 85.535 159 14 4 712 868 73497393 73497242 1.150000e-34 158.0
31 TraesCS5A01G260000 chr1B 96.347 219 8 0 2889 3107 228760194 228760412 8.190000e-96 361.0
32 TraesCS5A01G260000 chr4A 95.890 219 9 0 2889 3107 552885199 552885417 3.810000e-94 355.0
33 TraesCS5A01G260000 chr2D 91.333 150 2 2 72 221 185386107 185386245 8.790000e-46 195.0
34 TraesCS5A01G260000 chr1A 96.512 86 2 1 140 224 583933291 583933376 1.160000e-29 141.0
35 TraesCS5A01G260000 chr3D 82.209 163 19 6 72 224 40010400 40010238 6.990000e-27 132.0
36 TraesCS5A01G260000 chr7A 82.278 158 21 4 712 868 539543828 539543677 2.510000e-26 130.0
37 TraesCS5A01G260000 chr7A 92.982 57 3 1 2887 2943 524850944 524850999 7.140000e-12 82.4
38 TraesCS5A01G260000 chr6B 79.121 182 14 13 72 230 438927625 438927445 1.520000e-18 104.0
39 TraesCS5A01G260000 chr6B 82.114 123 16 6 69 187 434635274 434635154 1.970000e-17 100.0
40 TraesCS5A01G260000 chr6B 78.977 176 13 13 72 224 239363626 239363452 7.090000e-17 99.0
41 TraesCS5A01G260000 chr6B 77.228 202 17 15 61 236 438924747 438924945 1.190000e-14 91.6
42 TraesCS5A01G260000 chr6A 78.977 176 13 13 72 224 111742545 111742719 7.090000e-17 99.0
43 TraesCS5A01G260000 chr4D 91.667 72 2 3 2869 2937 456265010 456265080 2.550000e-16 97.1


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 TraesCS5A01G260000 chr5A 474192686 474195792 3106 True 5738.0 5738 100.0000 1 3107 1 chr5A.!!$R2 3106
1 TraesCS5A01G260000 chr5A 474059159 474062257 3098 True 5614.0 5614 99.3240 1 3107 1 chr5A.!!$R1 3106
2 TraesCS5A01G260000 chr5A 474324630 474327562 2932 True 5337.0 5337 99.5230 176 3107 1 chr5A.!!$R3 2931
3 TraesCS5A01G260000 chr5D 371021572 371023184 1612 True 2643.0 2643 96.2830 906 2514 1 chr5D.!!$R1 1608
4 TraesCS5A01G260000 chr5D 371267247 371269957 2710 False 2027.5 3945 93.9045 1 2899 2 chr5D.!!$F3 2898
5 TraesCS5A01G260000 chr5B 440513760 440516425 2665 False 3855.0 3855 92.7750 222 2899 1 chr5B.!!$F2 2677
6 TraesCS5A01G260000 chr5B 440533366 440536093 2727 False 2008.0 3895 95.1085 1 2899 2 chr5B.!!$F4 2898
7 TraesCS5A01G260000 chrUn 272195345 272196412 1067 True 1391.0 1391 90.2930 1825 2899 1 chrUn.!!$R1 1074
8 TraesCS5A01G260000 chrUn 465606731 465607523 792 True 1059.0 1059 90.8300 1825 2622 1 chrUn.!!$R2 797
9 TraesCS5A01G260000 chrUn 371166207 371167218 1011 False 847.5 1574 96.8205 1 1177 2 chrUn.!!$F1 1176

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
310 323 0.824109 TCACGATTGCCACCTCTAGG 59.176 55.0 0.0 0.0 42.17 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2613 2643 3.279434 GTTTATTGAGCCCCCTGTACTG 58.721 50.0 0.0 0.0 0.0 2.74 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
310 323 0.824109 TCACGATTGCCACCTCTAGG 59.176 55.000 0.00 0.00 42.17 3.02
311 324 0.824109 CACGATTGCCACCTCTAGGA 59.176 55.000 2.23 0.00 38.94 2.94
312 325 1.115467 ACGATTGCCACCTCTAGGAG 58.885 55.000 2.23 0.00 38.94 3.69
313 326 1.342076 ACGATTGCCACCTCTAGGAGA 60.342 52.381 2.23 0.00 38.94 3.71
314 327 1.067821 CGATTGCCACCTCTAGGAGAC 59.932 57.143 2.23 0.00 38.94 3.36
316 329 3.567397 GATTGCCACCTCTAGGAGACTA 58.433 50.000 2.23 0.00 43.67 2.59
2613 2643 9.760660 CTATTTATGCTCAAAGTTTGACACTAC 57.239 33.333 14.35 3.16 32.94 2.73
2915 2954 8.848182 TCTCTACTATTAAAGGAGAATCGAACC 58.152 37.037 0.00 0.00 45.02 3.62
3015 3054 7.207383 CCCACGATAAAAAGAAAAAGAAACCT 58.793 34.615 0.00 0.00 0.00 3.50
3083 3122 2.380249 TCTCCCGATCCCATCTGTCTAT 59.620 50.000 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
310 323 3.503891 GTCTTCAAAGCGTCCTAGTCTC 58.496 50.000 0.00 0.00 0.00 3.36
311 324 2.095161 CGTCTTCAAAGCGTCCTAGTCT 60.095 50.000 0.00 0.00 0.00 3.24
312 325 2.095364 TCGTCTTCAAAGCGTCCTAGTC 60.095 50.000 0.00 0.00 0.00 2.59
313 326 1.884579 TCGTCTTCAAAGCGTCCTAGT 59.115 47.619 0.00 0.00 0.00 2.57
314 327 2.520979 CTCGTCTTCAAAGCGTCCTAG 58.479 52.381 6.51 0.00 0.00 3.02
315 328 1.402456 GCTCGTCTTCAAAGCGTCCTA 60.402 52.381 6.51 0.00 0.00 2.94
316 329 0.667792 GCTCGTCTTCAAAGCGTCCT 60.668 55.000 6.51 0.00 0.00 3.85
317 330 0.944311 TGCTCGTCTTCAAAGCGTCC 60.944 55.000 6.51 2.01 38.90 4.79
325 338 4.183865 CCACTAATGAATGCTCGTCTTCA 58.816 43.478 0.00 0.00 35.95 3.02
2613 2643 3.279434 GTTTATTGAGCCCCCTGTACTG 58.721 50.000 0.00 0.00 0.00 2.74
2915 2954 0.179134 GGAGGTCGAACCATCACGAG 60.179 60.000 0.00 0.00 41.95 4.18


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

AutoCloner maintained by Alex Coulton.