Multiple sequence alignment - TraesCS6A01G138700

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 TraesCS6A01G138700 chr6A 100.000 3420 0 0 1 3420 110127316 110130735 0.000000e+00 6316
1 TraesCS6A01G138700 chr6A 94.778 3428 145 10 1 3420 110135486 110138887 0.000000e+00 5308
2 TraesCS6A01G138700 chr6A 90.259 2669 210 39 770 3420 398693577 398690941 0.000000e+00 3443
3 TraesCS6A01G138700 chr6A 89.858 2672 220 40 768 3420 408351769 408349130 0.000000e+00 3386
4 TraesCS6A01G138700 chr6A 89.775 2670 222 40 770 3420 408343651 408341014 0.000000e+00 3371
5 TraesCS6A01G138700 chr6A 94.417 806 44 1 771 1576 398713517 398712713 0.000000e+00 1238
6 TraesCS6A01G138700 chr6A 94.236 798 38 3 1 790 408344382 408343585 0.000000e+00 1212
7 TraesCS6A01G138700 chr6A 94.110 798 39 4 1 790 398694308 398693511 0.000000e+00 1206
8 TraesCS6A01G138700 chr6A 93.099 797 48 3 1 790 398714248 398713452 0.000000e+00 1160
9 TraesCS6A01G138700 chr6A 91.751 691 42 5 107 790 408352383 408351701 0.000000e+00 946
10 TraesCS6A01G138700 chr4A 92.845 1705 116 6 776 2479 402926071 402924372 0.000000e+00 2468
11 TraesCS6A01G138700 chr4A 91.905 803 54 5 1 792 402926811 402926009 0.000000e+00 1112
12 TraesCS6A01G138700 chr4A 90.427 773 72 2 770 1542 441787660 441786890 0.000000e+00 1016
13 TraesCS6A01G138700 chr4A 88.497 765 86 2 768 1532 272733870 272734632 0.000000e+00 924
14 TraesCS6A01G138700 chr4A 92.424 198 12 3 1 195 536011192 536011389 2.600000e-71 279
15 TraesCS6A01G138700 chr3A 90.235 1874 152 29 1564 3420 578862584 578860725 0.000000e+00 2418
16 TraesCS6A01G138700 chr3A 90.080 1875 153 31 1564 3420 374413790 374415649 0.000000e+00 2401
17 TraesCS6A01G138700 chr3A 89.600 1875 162 31 1564 3420 349854545 349856404 0.000000e+00 2351
18 TraesCS6A01G138700 chr3A 89.276 1893 167 29 1552 3420 210120209 210122089 0.000000e+00 2338
19 TraesCS6A01G138700 chr3A 89.135 1896 174 30 1538 3420 257696971 257695095 0.000000e+00 2331
20 TraesCS6A01G138700 chr3A 88.636 1936 182 36 1501 3420 379798092 379796179 0.000000e+00 2322
21 TraesCS6A01G138700 chr3A 91.593 797 49 6 1 790 395217745 395216960 0.000000e+00 1085
22 TraesCS6A01G138700 chr3A 91.217 797 53 5 1 790 395225790 395225004 0.000000e+00 1068
23 TraesCS6A01G138700 chr2A 89.701 1874 156 31 1564 3420 131570132 131568279 0.000000e+00 2357
24 TraesCS6A01G138700 chr2A 92.127 724 55 2 819 1542 542342851 542342130 0.000000e+00 1020
25 TraesCS6A01G138700 chr2A 90.840 393 36 0 1328 1720 424495004 424494612 8.410000e-146 527
26 TraesCS6A01G138700 chr7A 93.593 796 45 1 1 790 26814407 26815202 0.000000e+00 1182


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 TraesCS6A01G138700 chr6A 110127316 110130735 3419 False 6316.0 6316 100.0000 1 3420 1 chr6A.!!$F1 3419
1 TraesCS6A01G138700 chr6A 110135486 110138887 3401 False 5308.0 5308 94.7780 1 3420 1 chr6A.!!$F2 3419
2 TraesCS6A01G138700 chr6A 398690941 398694308 3367 True 2324.5 3443 92.1845 1 3420 2 chr6A.!!$R1 3419
3 TraesCS6A01G138700 chr6A 408341014 408344382 3368 True 2291.5 3371 92.0055 1 3420 2 chr6A.!!$R3 3419
4 TraesCS6A01G138700 chr6A 408349130 408352383 3253 True 2166.0 3386 90.8045 107 3420 2 chr6A.!!$R4 3313
5 TraesCS6A01G138700 chr6A 398712713 398714248 1535 True 1199.0 1238 93.7580 1 1576 2 chr6A.!!$R2 1575
6 TraesCS6A01G138700 chr4A 402924372 402926811 2439 True 1790.0 2468 92.3750 1 2479 2 chr4A.!!$R2 2478
7 TraesCS6A01G138700 chr4A 441786890 441787660 770 True 1016.0 1016 90.4270 770 1542 1 chr4A.!!$R1 772
8 TraesCS6A01G138700 chr4A 272733870 272734632 762 False 924.0 924 88.4970 768 1532 1 chr4A.!!$F1 764
9 TraesCS6A01G138700 chr3A 578860725 578862584 1859 True 2418.0 2418 90.2350 1564 3420 1 chr3A.!!$R5 1856
10 TraesCS6A01G138700 chr3A 374413790 374415649 1859 False 2401.0 2401 90.0800 1564 3420 1 chr3A.!!$F3 1856
11 TraesCS6A01G138700 chr3A 349854545 349856404 1859 False 2351.0 2351 89.6000 1564 3420 1 chr3A.!!$F2 1856
12 TraesCS6A01G138700 chr3A 210120209 210122089 1880 False 2338.0 2338 89.2760 1552 3420 1 chr3A.!!$F1 1868
13 TraesCS6A01G138700 chr3A 257695095 257696971 1876 True 2331.0 2331 89.1350 1538 3420 1 chr3A.!!$R1 1882
14 TraesCS6A01G138700 chr3A 379796179 379798092 1913 True 2322.0 2322 88.6360 1501 3420 1 chr3A.!!$R2 1919
15 TraesCS6A01G138700 chr3A 395216960 395217745 785 True 1085.0 1085 91.5930 1 790 1 chr3A.!!$R3 789
16 TraesCS6A01G138700 chr3A 395225004 395225790 786 True 1068.0 1068 91.2170 1 790 1 chr3A.!!$R4 789
17 TraesCS6A01G138700 chr2A 131568279 131570132 1853 True 2357.0 2357 89.7010 1564 3420 1 chr2A.!!$R1 1856
18 TraesCS6A01G138700 chr2A 542342130 542342851 721 True 1020.0 1020 92.1270 819 1542 1 chr2A.!!$R3 723
19 TraesCS6A01G138700 chr7A 26814407 26815202 795 False 1182.0 1182 93.5930 1 790 1 chr7A.!!$F1 789

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
341 353 0.033991 CTCTCTCGTTCCCCTCCTCA 60.034 60.0 0.00 0.00 0.0 3.86 F
1315 1336 0.246635 CAGACCCCAAACGATCGACT 59.753 55.0 24.34 5.28 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 2392 0.106918 AACCCGAAGAAGCAACACCA 60.107 50.000 0.0 0.0 0.0 4.17 R
2479 2582 1.341531 AGTGGTAGGTATCGCAGCATC 59.658 52.381 0.0 0.0 0.0 3.91 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
54 55 9.698309 TTGAATTTAGATCGTTTAATTTTGGCA 57.302 25.926 0.00 0.00 0.00 4.92
72 73 6.773976 TTGGCATTTTTCTATTTCTCGGAT 57.226 33.333 0.00 0.00 0.00 4.18
153 154 7.583625 ACCTTTTCTTTTCTCTCCTTCCTTTA 58.416 34.615 0.00 0.00 0.00 1.85
193 202 3.626222 GCTGGGTTAAGAGAGGAGAGAGA 60.626 52.174 0.00 0.00 0.00 3.10
341 353 0.033991 CTCTCTCGTTCCCCTCCTCA 60.034 60.000 0.00 0.00 0.00 3.86
358 370 2.289882 CCTCATTGACTCCTTGCTCACA 60.290 50.000 0.00 0.00 0.00 3.58
407 419 1.897201 GCCATCTCCCTCGATCCCATA 60.897 57.143 0.00 0.00 0.00 2.74
437 449 1.574339 TCGATACCTCTCCCTTCCCTT 59.426 52.381 0.00 0.00 0.00 3.95
456 468 1.675641 GTTTCCTCAGCACCGCCAT 60.676 57.895 0.00 0.00 0.00 4.40
484 503 1.306226 CTCGACCCCTTTCCCCTCT 60.306 63.158 0.00 0.00 0.00 3.69
564 583 0.745845 GTGCACCTCTACCATGGCTG 60.746 60.000 13.04 4.79 0.00 4.85
645 664 1.304952 CTCTCCTCCGTCCCTCTGT 59.695 63.158 0.00 0.00 0.00 3.41
676 696 3.532155 AGCGCCCATCTCCTCGAC 61.532 66.667 2.29 0.00 0.00 4.20
890 910 2.581354 GAGACGCCATCCAGCAGT 59.419 61.111 0.00 0.00 0.00 4.40
1020 1040 2.439701 ACCTTCGATCCCGCGAGA 60.440 61.111 8.23 0.00 41.79 4.04
1149 1169 1.616865 TCGTTTCGGACCATCAAGACT 59.383 47.619 0.00 0.00 0.00 3.24
1215 1236 1.751924 CCGGACTTCACCAAAAACCAA 59.248 47.619 0.00 0.00 0.00 3.67
1297 1318 2.281484 GGCAAGACCCGCAAGTCA 60.281 61.111 5.95 0.00 39.34 3.41
1315 1336 0.246635 CAGACCCCAAACGATCGACT 59.753 55.000 24.34 5.28 0.00 4.18
1345 1366 0.972717 CGTGTACAACTACTGTCGCG 59.027 55.000 0.00 0.00 39.64 5.87
1381 1402 4.691860 TTCGTTAAGTACCTCTCCGAAG 57.308 45.455 0.00 0.00 31.84 3.79
1405 1426 1.473258 AACGTATACCGCTACCACCA 58.527 50.000 0.00 0.00 41.42 4.17
1420 1441 2.226330 CCACCACAAAAATCGAGACCA 58.774 47.619 0.00 0.00 0.00 4.02
1459 1480 3.995636 AGTACCACTCCAGACCATGTAT 58.004 45.455 0.00 0.00 0.00 2.29
1473 1494 1.040646 ATGTATGATGACCGTCGCCT 58.959 50.000 0.00 0.00 0.00 5.52
1479 1500 0.454600 GATGACCGTCGCCTAAGACA 59.545 55.000 0.00 0.00 40.98 3.41
1534 1555 2.681097 GCGAGAAATGCCTACTTCCCTT 60.681 50.000 0.00 0.00 0.00 3.95
1726 1792 3.485764 GGAGCACCCCATCTTCTTC 57.514 57.895 0.00 0.00 0.00 2.87
1747 1815 0.389025 ATGACACACTCGCACTCACA 59.611 50.000 0.00 0.00 0.00 3.58
1884 1962 4.565022 TCATCACGCTCATGTCAACTTTA 58.435 39.130 0.00 0.00 0.00 1.85
2182 2269 5.010922 TGCATGTTGAGCTCCACTAAATTTT 59.989 36.000 17.93 0.00 0.00 1.82
2300 2392 7.518370 CGTTTACTATGTTGTGTGCTTCTTTCT 60.518 37.037 0.00 0.00 0.00 2.52
2371 2473 1.757574 TTCGTCTACGTCCGTTTGTG 58.242 50.000 0.00 0.00 40.80 3.33
2389 2491 6.457663 CGTTTGTGTTCTTCATGGACTTGTTA 60.458 38.462 0.00 0.00 0.00 2.41
2479 2582 1.267932 GCTCGCTCTTTTGCTATGCTG 60.268 52.381 0.00 0.00 0.00 4.41
2600 2704 1.743996 CTTTGCTCAGCCCCTCTTAC 58.256 55.000 0.00 0.00 0.00 2.34
2604 2708 1.903877 GCTCAGCCCCTCTTACAGCA 61.904 60.000 0.00 0.00 0.00 4.41
3396 3514 1.095600 CCGTGATGGTCTCTTCTCGA 58.904 55.000 0.00 0.00 36.68 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 7.121168 TGTGCTTGATCCGAGAAATAGAAAAAT 59.879 33.333 0.00 0.0 0.00 1.82
153 154 6.298361 ACCCAGCAGAAAAATAAAAGCAAAT 58.702 32.000 0.00 0.0 0.00 2.32
193 202 1.380302 CTACTGGGCTGTTGGGCTT 59.620 57.895 0.00 0.0 40.65 4.35
341 353 1.609061 CGGTGTGAGCAAGGAGTCAAT 60.609 52.381 0.00 0.0 0.00 2.57
407 419 1.790157 AGAGGTATCGAGGGAGGGAAT 59.210 52.381 0.00 0.0 0.00 3.01
437 449 2.281484 GGCGGTGCTGAGGAAACA 60.281 61.111 0.00 0.0 0.00 2.83
484 503 4.029520 CAGAGGGAGGAGAAGATTGAGAA 58.970 47.826 0.00 0.0 0.00 2.87
555 574 3.987404 GCGAAGAACAGCCATGGT 58.013 55.556 14.67 0.0 0.00 3.55
564 583 3.047877 CGGTGGGTGGCGAAGAAC 61.048 66.667 0.00 0.0 0.00 3.01
676 696 3.570638 CGCTGGCGATGAAGCAGG 61.571 66.667 9.51 0.0 42.83 4.85
730 750 3.402681 CAGTGGCGGGGATGGACT 61.403 66.667 0.00 0.0 0.00 3.85
850 870 1.176619 TGAGAACCGAGTCGAGGCAA 61.177 55.000 15.64 0.0 0.00 4.52
1020 1040 1.832912 GAGGTTGATGCCTCGGGAT 59.167 57.895 0.00 0.0 44.64 3.85
1149 1169 2.107366 TCCATGTAGTCGATCTTGCCA 58.893 47.619 0.00 0.0 0.00 4.92
1215 1236 2.558795 CATCCGAAGGGTCATCGAGTAT 59.441 50.000 0.00 0.0 28.78 2.12
1297 1318 0.974383 AAGTCGATCGTTTGGGGTCT 59.026 50.000 15.94 0.0 0.00 3.85
1345 1366 2.165301 CGAATCCAACGTCCTCGGC 61.165 63.158 0.00 0.0 41.85 5.54
1381 1402 2.223249 TGGTAGCGGTATACGTTTCGTC 60.223 50.000 0.00 0.0 46.52 4.20
1405 1426 4.881850 AGACTTGTTGGTCTCGATTTTTGT 59.118 37.500 0.00 0.0 42.15 2.83
1420 1441 4.757149 GGTACTTGCATCTTCAGACTTGTT 59.243 41.667 0.00 0.0 0.00 2.83
1459 1480 0.454600 GTCTTAGGCGACGGTCATCA 59.545 55.000 9.10 0.0 0.00 3.07
1473 1494 2.126467 GTTGGCGTTACACGTGTCTTA 58.874 47.619 27.16 9.3 44.73 2.10
1490 1511 2.861935 ACGGTAGTTGAACTTGACGTTG 59.138 45.455 1.97 0.0 35.56 4.10
1726 1792 0.319813 TGAGTGCGAGTGTGTCATGG 60.320 55.000 0.00 0.0 0.00 3.66
1747 1815 2.052782 GGATACCGGTGCAAAAGGAT 57.947 50.000 19.93 0.0 0.00 3.24
2053 2139 1.729267 AACATGGCAAGAGGTGGGGT 61.729 55.000 0.00 0.0 0.00 4.95
2182 2269 5.921004 GCAAAATGCACAAACAATCCTAA 57.079 34.783 0.00 0.0 44.26 2.69
2300 2392 0.106918 AACCCGAAGAAGCAACACCA 60.107 50.000 0.00 0.0 0.00 4.17
2371 2473 7.391833 AGGAAGAATAACAAGTCCATGAAGAAC 59.608 37.037 0.00 0.0 0.00 3.01
2479 2582 1.341531 AGTGGTAGGTATCGCAGCATC 59.658 52.381 0.00 0.0 0.00 3.91
2600 2704 2.553602 TCACCTGCAACTAACAATGCTG 59.446 45.455 0.00 0.0 42.97 4.41
2604 2708 5.047802 CCAATCTTCACCTGCAACTAACAAT 60.048 40.000 0.00 0.0 0.00 2.71
2884 2991 2.579410 AGGTGGCGAATGGTAAAACT 57.421 45.000 0.00 0.0 0.00 2.66
3396 3514 1.532316 TTCACTTCCCGGACTCCGT 60.532 57.895 16.35 0.0 46.80 4.69


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

AutoCloner maintained by Alex Coulton.