Multiple sequence alignment - TraesCS6A01G037500

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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 TraesCS6A01G037500 chr6A 100.000 2873 0 0 1 2873 18533777 18536649 0.000000e+00 5306
1 TraesCS6A01G037500 chr6A 95.050 101 4 1 2251 2350 493557698 493557598 1.070000e-34 158
2 TraesCS6A01G037500 chr4A 98.225 2873 45 4 1 2873 515458190 515455324 0.000000e+00 5018
3 TraesCS6A01G037500 chr1A 81.445 1024 135 26 1182 2171 535728829 535729831 0.000000e+00 787
4 TraesCS6A01G037500 chr1A 91.954 261 19 2 1 259 32407393 32407653 5.850000e-97 364
5 TraesCS6A01G037500 chr1A 92.105 76 6 0 1116 1191 535728663 535728738 1.090000e-19 108
6 TraesCS6A01G037500 chr7D 78.922 1058 185 24 1188 2219 74459827 74458782 0.000000e+00 684
7 TraesCS6A01G037500 chr7D 87.903 124 15 0 994 1117 609606857 609606734 2.310000e-31 147
8 TraesCS6A01G037500 chr7D 92.233 103 4 1 2248 2350 25322313 25322411 2.980000e-30 143
9 TraesCS6A01G037500 chr2D 78.190 1050 193 24 1188 2212 15445812 15446850 3.120000e-179 638
10 TraesCS6A01G037500 chr2D 89.256 121 13 0 994 1114 15445322 15445442 4.960000e-33 152
11 TraesCS6A01G037500 chr2D 92.523 107 5 2 2247 2350 18197546 18197440 1.780000e-32 150
12 TraesCS6A01G037500 chr2D 91.667 108 5 2 2247 2350 33554441 33554334 2.310000e-31 147
13 TraesCS6A01G037500 chr2D 91.589 107 6 2 2247 2350 18197439 18197545 8.300000e-31 145
14 TraesCS6A01G037500 chr2A 80.485 825 118 27 1445 2234 46343181 46343997 2.470000e-165 592
15 TraesCS6A01G037500 chr5A 97.701 261 4 2 1 259 275123174 275123434 5.650000e-122 448
16 TraesCS6A01G037500 chr5A 97.701 261 4 2 1 259 330508141 330508401 5.650000e-122 448
17 TraesCS6A01G037500 chr5A 96.226 106 3 1 2245 2350 618190316 618190212 3.810000e-39 172
18 TraesCS6A01G037500 chr3A 97.701 261 1 3 1 259 698257795 698258052 7.300000e-121 444
19 TraesCS6A01G037500 chr3A 77.500 320 55 13 777 1091 743691691 743691998 2.940000e-40 176
20 TraesCS6A01G037500 chr2B 95.785 261 9 2 1 259 519703207 519703467 1.230000e-113 420
21 TraesCS6A01G037500 chr2B 84.076 157 22 2 959 1114 797768782 797768936 6.410000e-32 148
22 TraesCS6A01G037500 chr2B 83.439 157 23 2 959 1114 797808395 797808549 2.980000e-30 143
23 TraesCS6A01G037500 chr3D 80.680 559 91 15 1630 2180 31049369 31049918 4.430000e-113 418
24 TraesCS6A01G037500 chr3D 79.427 593 102 17 1630 2213 31000115 31000696 4.460000e-108 401
25 TraesCS6A01G037500 chr3D 78.235 510 94 15 1712 2213 31023894 31024394 7.730000e-81 311
26 TraesCS6A01G037500 chr3B 90.588 255 22 1 1 253 492623462 492623208 1.280000e-88 337
27 TraesCS6A01G037500 chr7B 82.201 309 50 1 1178 1481 121783420 121783728 7.900000e-66 261
28 TraesCS6A01G037500 chr4D 92.308 104 6 1 2247 2350 192289400 192289501 2.310000e-31 147
29 TraesCS6A01G037500 chr6B 90.000 110 8 2 2244 2350 46138489 46138598 3.860000e-29 139


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 TraesCS6A01G037500 chr6A 18533777 18536649 2872 False 5306.0 5306 100.000 1 2873 1 chr6A.!!$F1 2872
1 TraesCS6A01G037500 chr4A 515455324 515458190 2866 True 5018.0 5018 98.225 1 2873 1 chr4A.!!$R1 2872
2 TraesCS6A01G037500 chr1A 535728663 535729831 1168 False 447.5 787 86.775 1116 2171 2 chr1A.!!$F2 1055
3 TraesCS6A01G037500 chr7D 74458782 74459827 1045 True 684.0 684 78.922 1188 2219 1 chr7D.!!$R1 1031
4 TraesCS6A01G037500 chr2D 15445322 15446850 1528 False 395.0 638 83.723 994 2212 2 chr2D.!!$F2 1218
5 TraesCS6A01G037500 chr2A 46343181 46343997 816 False 592.0 592 80.485 1445 2234 1 chr2A.!!$F1 789
6 TraesCS6A01G037500 chr3D 31049369 31049918 549 False 418.0 418 80.680 1630 2180 1 chr3D.!!$F3 550
7 TraesCS6A01G037500 chr3D 31000115 31000696 581 False 401.0 401 79.427 1630 2213 1 chr3D.!!$F1 583
8 TraesCS6A01G037500 chr3D 31023894 31024394 500 False 311.0 311 78.235 1712 2213 1 chr3D.!!$F2 501

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
380 381 2.157668 CGTTTTACTGCTGAATGTCGCT 59.842 45.455 0.00 0.00 0.0 4.93 F
1378 1682 1.231221 GACCATTGCGTGTACACCAA 58.769 50.000 23.33 23.33 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 2013 1.091771 CGTTACATGGGCTCCTGCAG 61.092 60.0 6.78 6.78 41.91 4.41 R
2444 2812 0.250597 AGGGGTTTCAACTGCGTACC 60.251 55.0 0.00 0.00 0.00 3.34 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
348 349 5.707066 AAGCATTACTCTCTCATTTCCCT 57.293 39.130 0.00 0.00 0.00 4.20
380 381 2.157668 CGTTTTACTGCTGAATGTCGCT 59.842 45.455 0.00 0.00 0.00 4.93
425 426 5.576128 TCATATCATCCATGGTGCATGATT 58.424 37.500 24.71 14.10 43.81 2.57
586 587 9.301153 CTGAGCATATTTTGGTTTATTTACACC 57.699 33.333 0.00 0.00 35.82 4.16
658 659 9.293404 CAAGAGGATGTTCCAAATGATATATGT 57.707 33.333 0.00 0.00 39.61 2.29
798 799 7.233389 TCTCTCTCACCATATACTTATTGCC 57.767 40.000 0.00 0.00 0.00 4.52
836 837 3.913548 ACATGCACGCTCACATAAAAA 57.086 38.095 0.00 0.00 0.00 1.94
914 915 9.730420 ATTGGCGTAGTATAATGATTTGTTTTC 57.270 29.630 0.00 0.00 0.00 2.29
1378 1682 1.231221 GACCATTGCGTGTACACCAA 58.769 50.000 23.33 23.33 0.00 3.67
1387 1691 2.801063 CGTGTACACCAAGGGTATACG 58.199 52.381 20.11 11.05 45.20 3.06
1608 1923 3.910328 CAAACGTGTTGTTGTTTGCATC 58.090 40.909 5.07 0.00 45.64 3.91
1691 2013 3.552273 GGGATCATTCTTGTGCATGATGC 60.552 47.826 11.12 11.12 43.79 3.91
2249 2617 7.147312 CACATGATTGGTTTCAACACTTGTAT 58.853 34.615 0.00 0.00 35.48 2.29
2256 2624 4.217767 GGTTTCAACACTTGTATTCCCTCC 59.782 45.833 0.00 0.00 0.00 4.30
2321 2689 9.945904 ACTAAAACCAAATTTGAACTAAAACCA 57.054 25.926 19.86 0.00 0.00 3.67
2324 2692 9.454859 AAAACCAAATTTGAACTAAAACCATGA 57.545 25.926 19.86 0.00 0.00 3.07
2325 2693 8.432110 AACCAAATTTGAACTAAAACCATGAC 57.568 30.769 19.86 0.00 0.00 3.06
2444 2812 2.163390 CAGATCACGTGCTCGGCAG 61.163 63.158 11.67 0.42 40.08 4.85
2461 2829 0.872388 CAGGTACGCAGTTGAAACCC 59.128 55.000 0.00 0.00 37.78 4.11
2564 2932 0.459585 CAGGCACATGATTGCAAGGC 60.460 55.000 4.94 2.13 44.94 4.35
2604 2972 3.369576 GGTCCATAGTCCAAACTGAGACC 60.370 52.174 0.00 0.00 40.24 3.85
2657 3025 3.201494 TGTTGCCCAAACACACGG 58.799 55.556 0.00 0.00 43.96 4.94
2737 3105 6.114187 TGATGCCTATATCATCGGAAGTTT 57.886 37.500 9.30 0.00 42.32 2.66
2792 3160 2.223745 ACGAAAACTATGCAACCGGTT 58.776 42.857 15.86 15.86 0.00 4.44
2807 3175 1.190763 CCGGTTGTTCGTAACTTGACG 59.809 52.381 0.00 0.00 44.29 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
348 349 4.393680 CAGCAGTAAAACGCCTAATACCAA 59.606 41.667 0.00 0.00 0.00 3.67
380 381 2.513666 GGGATGCGTTGCCGATCA 60.514 61.111 0.00 0.00 35.63 2.92
425 426 2.348059 GTGTTACACCGAAACACGTTCA 59.652 45.455 3.79 0.00 45.02 3.18
503 504 3.582208 AGCCATGCCCTTTTTGTATCAAA 59.418 39.130 0.00 0.00 0.00 2.69
545 546 1.714794 CTCAGGTTAAGCTGACGTGG 58.285 55.000 28.81 17.55 34.58 4.94
586 587 6.115452 CGAAAACATCGTGATTTTTGTCTG 57.885 37.500 0.00 0.00 46.52 3.51
609 610 5.048782 TGTTATGCACAGGTGAATGTTTCTC 60.049 40.000 3.10 0.00 29.97 2.87
611 612 5.119931 TGTTATGCACAGGTGAATGTTTC 57.880 39.130 3.10 0.00 29.97 2.78
620 621 3.009473 ACATCCTCTTGTTATGCACAGGT 59.991 43.478 0.00 0.00 36.48 4.00
665 666 5.863935 GGCATTCTGAAACTTATGTTTGGAC 59.136 40.000 11.15 0.00 45.36 4.02
798 799 5.466393 TGCATGTTCCAGATTATCGTGTATG 59.534 40.000 0.00 0.00 0.00 2.39
914 915 4.158949 TGTCCAGAATCTTTGCCATGAATG 59.841 41.667 0.00 0.00 0.00 2.67
1378 1682 7.788026 TGAATATTCAAACTGACGTATACCCT 58.212 34.615 15.82 0.00 33.55 4.34
1608 1923 6.430962 TCATTCTTTGGGATCCTCTATCAG 57.569 41.667 12.58 0.00 36.20 2.90
1691 2013 1.091771 CGTTACATGGGCTCCTGCAG 61.092 60.000 6.78 6.78 41.91 4.41
2249 2617 3.618019 CGAGTAATTTGGAACGGAGGGAA 60.618 47.826 0.00 0.00 0.00 3.97
2256 2624 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
2318 2686 3.682858 CGTTCCAAATTACTCGTCATGGT 59.317 43.478 0.00 0.00 0.00 3.55
2320 2688 3.930229 TCCGTTCCAAATTACTCGTCATG 59.070 43.478 0.00 0.00 0.00 3.07
2321 2689 4.181578 CTCCGTTCCAAATTACTCGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2322 2690 3.581755 CTCCGTTCCAAATTACTCGTCA 58.418 45.455 0.00 0.00 0.00 4.35
2323 2691 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2324 2692 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2325 2693 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2444 2812 0.250597 AGGGGTTTCAACTGCGTACC 60.251 55.000 0.00 0.00 0.00 3.34
2719 3087 6.761242 TGTGAACAAACTTCCGATGATATAGG 59.239 38.462 0.00 0.00 0.00 2.57
2737 3105 2.159448 CGTTGAAGCTGGTTTGTGAACA 60.159 45.455 0.00 0.00 37.51 3.18
2792 3160 2.867287 TGGACGTCAAGTTACGAACA 57.133 45.000 18.91 0.00 45.68 3.18
2807 3175 7.352739 CGAAATATAAGTTGCTTGGTATGGAC 58.647 38.462 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.