Multiple sequence alignment - TraesCS6A01G062400

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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 TraesCS6A01G062400 chr6A 100.000 2222 0 0 1 2222 33404848 33402627 0.000000e+00 4104.0
1 TraesCS6A01G062400 chr6A 87.191 648 75 7 1 643 33530505 33529861 0.000000e+00 730.0
2 TraesCS6A01G062400 chr6A 92.279 272 17 2 1 271 33305847 33305579 1.240000e-102 383.0
3 TraesCS6A01G062400 chr5B 98.074 1558 28 2 665 2222 640414837 640416392 0.000000e+00 2710.0
4 TraesCS6A01G062400 chr5B 80.465 645 101 19 643 1266 672101060 672101700 9.290000e-129 470.0
5 TraesCS6A01G062400 chr5A 98.072 1556 28 2 667 2222 475377613 475379166 0.000000e+00 2706.0
6 TraesCS6A01G062400 chr5A 82.775 209 25 6 1854 2059 255588758 255588558 2.270000e-40 176.0
7 TraesCS6A01G062400 chr5A 82.775 209 25 6 1854 2059 257331878 257331678 2.270000e-40 176.0
8 TraesCS6A01G062400 chr5A 100.000 29 0 0 992 1020 6207326 6207354 1.000000e-03 54.7
9 TraesCS6A01G062400 chrUn 97.561 1558 32 3 665 2222 62068747 62070298 0.000000e+00 2662.0
10 TraesCS6A01G062400 chrUn 99.030 722 6 1 1501 2222 428748801 428749521 0.000000e+00 1293.0
11 TraesCS6A01G062400 chr6D 87.461 646 77 3 1 642 29093997 29094642 0.000000e+00 741.0
12 TraesCS6A01G062400 chr6D 76.145 524 103 15 108 620 29152370 29152882 2.830000e-64 255.0
13 TraesCS6A01G062400 chr6B 86.822 645 77 7 1 641 60615581 60614941 0.000000e+00 713.0
14 TraesCS6A01G062400 chr6B 85.736 645 84 7 1 641 60632274 60631634 0.000000e+00 675.0
15 TraesCS6A01G062400 chr6B 85.983 585 72 7 64 641 60657724 60657143 3.130000e-173 617.0
16 TraesCS6A01G062400 chr6B 85.484 434 45 8 190 620 59829166 59829584 9.420000e-119 436.0
17 TraesCS6A01G062400 chr6B 74.803 635 126 27 5 620 60584380 60583761 2.830000e-64 255.0
18 TraesCS6A01G062400 chr6B 87.943 141 16 1 1 140 59828718 59828858 4.910000e-37 165.0
19 TraesCS6A01G062400 chr2D 85.857 601 73 8 675 1266 83846736 83847333 1.450000e-176 628.0
20 TraesCS6A01G062400 chr2D 77.992 518 86 13 665 1165 430218607 430219113 1.290000e-77 300.0
21 TraesCS6A01G062400 chr1A 83.010 618 78 19 663 1266 157082957 157083561 3.250000e-148 534.0
22 TraesCS6A01G062400 chr2A 78.116 361 63 11 250 604 762930490 762930840 4.810000e-52 215.0
23 TraesCS6A01G062400 chr7A 91.429 70 6 0 1329 1398 701403688 701403757 1.820000e-16 97.1
24 TraesCS6A01G062400 chr7D 91.176 68 6 0 1331 1398 611348668 611348735 2.350000e-15 93.5
25 TraesCS6A01G062400 chr7B 85.714 77 11 0 1190 1266 501559515 501559439 5.090000e-12 82.4


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 TraesCS6A01G062400 chr6A 33402627 33404848 2221 True 4104.0 4104 100.0000 1 2222 1 chr6A.!!$R2 2221
1 TraesCS6A01G062400 chr6A 33529861 33530505 644 True 730.0 730 87.1910 1 643 1 chr6A.!!$R3 642
2 TraesCS6A01G062400 chr5B 640414837 640416392 1555 False 2710.0 2710 98.0740 665 2222 1 chr5B.!!$F1 1557
3 TraesCS6A01G062400 chr5B 672101060 672101700 640 False 470.0 470 80.4650 643 1266 1 chr5B.!!$F2 623
4 TraesCS6A01G062400 chr5A 475377613 475379166 1553 False 2706.0 2706 98.0720 667 2222 1 chr5A.!!$F2 1555
5 TraesCS6A01G062400 chrUn 62068747 62070298 1551 False 2662.0 2662 97.5610 665 2222 1 chrUn.!!$F1 1557
6 TraesCS6A01G062400 chrUn 428748801 428749521 720 False 1293.0 1293 99.0300 1501 2222 1 chrUn.!!$F2 721
7 TraesCS6A01G062400 chr6D 29093997 29094642 645 False 741.0 741 87.4610 1 642 1 chr6D.!!$F1 641
8 TraesCS6A01G062400 chr6D 29152370 29152882 512 False 255.0 255 76.1450 108 620 1 chr6D.!!$F2 512
9 TraesCS6A01G062400 chr6B 60614941 60615581 640 True 713.0 713 86.8220 1 641 1 chr6B.!!$R2 640
10 TraesCS6A01G062400 chr6B 60631634 60632274 640 True 675.0 675 85.7360 1 641 1 chr6B.!!$R3 640
11 TraesCS6A01G062400 chr6B 60657143 60657724 581 True 617.0 617 85.9830 64 641 1 chr6B.!!$R4 577
12 TraesCS6A01G062400 chr6B 59828718 59829584 866 False 300.5 436 86.7135 1 620 2 chr6B.!!$F1 619
13 TraesCS6A01G062400 chr6B 60583761 60584380 619 True 255.0 255 74.8030 5 620 1 chr6B.!!$R1 615
14 TraesCS6A01G062400 chr2D 83846736 83847333 597 False 628.0 628 85.8570 675 1266 1 chr2D.!!$F1 591
15 TraesCS6A01G062400 chr2D 430218607 430219113 506 False 300.0 300 77.9920 665 1165 1 chr2D.!!$F2 500
16 TraesCS6A01G062400 chr1A 157082957 157083561 604 False 534.0 534 83.0100 663 1266 1 chr1A.!!$F1 603

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
294 560 0.03213 TCCAAGATAGACGATGCGCC 59.968 55.0 4.18 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2344 0.876342 AGCTCTTATTGTAGCGCGCC 60.876 55.0 30.33 14.69 43.63 6.53 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
60 62 1.342082 CGACGAGTAAACACAGGCGG 61.342 60.000 0.00 0.00 0.00 6.13
80 82 1.401018 GCCGCTTGCGTAATTTGTCTT 60.401 47.619 13.97 0.00 0.00 3.01
87 89 5.743026 TTGCGTAATTTGTCTTTCACTGA 57.257 34.783 0.00 0.00 0.00 3.41
101 109 1.350684 TCACTGATGCCTACCAAAGCA 59.649 47.619 0.00 0.00 44.45 3.91
114 122 1.962807 CCAAAGCAACATGGAAGTGGA 59.037 47.619 0.00 0.00 39.12 4.02
154 162 3.050166 GCACCGCGCCATTGATTGA 62.050 57.895 0.00 0.00 32.94 2.57
176 184 3.744660 GGATTTATCCATGTCGAAGCCT 58.255 45.455 3.87 0.00 46.38 4.58
187 453 3.647771 GAAGCCTGGGGGAACGGT 61.648 66.667 0.00 0.00 33.58 4.83
188 454 3.182996 AAGCCTGGGGGAACGGTT 61.183 61.111 0.00 0.00 33.58 4.44
198 464 2.757056 GGAACGGTTATGCGGTGCC 61.757 63.158 0.00 0.00 38.70 5.01
215 481 4.444838 CGGTCGCCAATGACGGGA 62.445 66.667 0.00 0.00 39.83 5.14
221 487 1.077068 GCCAATGACGGGATCCCAA 60.077 57.895 30.42 15.56 35.37 4.12
230 496 0.328258 CGGGATCCCAAACAAGGAGT 59.672 55.000 30.42 0.00 36.67 3.85
260 526 4.690748 CGCTTCCAAAGAAAGATGAGTACA 59.309 41.667 0.00 0.00 0.00 2.90
281 547 2.124193 CCATGGCGGCATCCAAGA 60.124 61.111 23.19 0.00 39.96 3.02
282 548 1.529948 CCATGGCGGCATCCAAGAT 60.530 57.895 23.19 0.00 39.96 2.40
289 555 1.337260 GCGGCATCCAAGATAGACGAT 60.337 52.381 0.00 0.00 0.00 3.73
293 559 1.723542 CATCCAAGATAGACGATGCGC 59.276 52.381 0.00 0.00 0.00 6.09
294 560 0.032130 TCCAAGATAGACGATGCGCC 59.968 55.000 4.18 0.00 0.00 6.53
296 562 0.946221 CAAGATAGACGATGCGCCCC 60.946 60.000 4.18 0.00 0.00 5.80
312 593 3.411351 CCCCGTCTTCGTGTTGCG 61.411 66.667 0.00 0.00 43.01 4.85
387 668 1.956297 GAGCCTGTCGTCTAGCTCTA 58.044 55.000 13.91 0.00 46.50 2.43
426 707 2.282180 GGTTGTGGCGATGGTGGT 60.282 61.111 0.00 0.00 0.00 4.16
620 907 0.394565 GGTTGCTCATCTCGCCCTAT 59.605 55.000 0.00 0.00 0.00 2.57
624 911 2.807676 TGCTCATCTCGCCCTATGATA 58.192 47.619 0.00 0.00 31.95 2.15
742 1031 6.017192 CCACAAAGTGTACACAGAATCATCAA 60.017 38.462 27.06 0.00 0.00 2.57
807 1096 7.092712 CCATATTACATCAGGGGTCTATCACAT 60.093 40.741 0.00 0.00 0.00 3.21
830 1119 9.669353 ACATAAATGAACGATGCAGATTAAATC 57.331 29.630 0.00 0.00 0.00 2.17
901 1201 6.399743 GGATTTCTATCCCGTAATCTTCTCC 58.600 44.000 0.00 0.00 43.98 3.71
915 1217 1.912043 CTTCTCCCTCCCTCACAACAT 59.088 52.381 0.00 0.00 0.00 2.71
1334 1653 1.169661 TTGCTGCCGATTTTCGTGGT 61.170 50.000 0.00 0.00 38.40 4.16
1344 1663 3.621794 GATTTTCGTGGTGAGCATATGC 58.378 45.455 20.36 20.36 42.49 3.14
1654 1973 9.496710 TCCCCTGTACTGATTTACTATCTTTTA 57.503 33.333 0.60 0.00 0.00 1.52
1848 2167 1.853963 ATGGGAAGTAGCGAGAGTGT 58.146 50.000 0.00 0.00 0.00 3.55
1929 2248 7.398332 AGTTTCTGATCCTGATGGCTAAAAATT 59.602 33.333 0.00 0.00 0.00 1.82
2025 2344 5.089970 TCCATGTGTAAGAGGATCAGTTG 57.910 43.478 0.00 0.00 37.82 3.16
2125 2444 2.359848 TCCTCGGTCATATGGTTACACG 59.640 50.000 2.13 1.10 0.00 4.49
2196 2515 4.647564 AATCCTAATTCGGATGGAGCAT 57.352 40.909 12.01 0.00 42.89 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.140325 ACCGGTATATGGGCAATCTTG 57.860 47.619 4.49 0.00 0.00 3.02
60 62 0.168128 AGACAAATTACGCAAGCGGC 59.832 50.000 19.30 0.00 44.69 6.53
80 82 2.224744 TGCTTTGGTAGGCATCAGTGAA 60.225 45.455 0.00 0.00 33.23 3.18
87 89 1.826720 CCATGTTGCTTTGGTAGGCAT 59.173 47.619 0.00 0.00 38.30 4.40
101 109 1.002087 GACGTCCTCCACTTCCATGTT 59.998 52.381 3.51 0.00 0.00 2.71
133 141 1.876497 AATCAATGGCGCGGTGCTTT 61.876 50.000 13.85 5.07 45.43 3.51
154 162 7.721088 CCAGGCTTCGACATGGATAAATCCT 62.721 48.000 10.28 0.00 44.28 3.24
165 173 1.923395 TTCCCCCAGGCTTCGACAT 60.923 57.895 0.00 0.00 0.00 3.06
173 181 1.453197 CATAACCGTTCCCCCAGGC 60.453 63.158 0.00 0.00 0.00 4.85
176 184 2.269562 CGCATAACCGTTCCCCCA 59.730 61.111 0.00 0.00 0.00 4.96
198 464 3.733344 ATCCCGTCATTGGCGACCG 62.733 63.158 13.09 0.00 31.91 4.79
206 472 2.446435 CTTGTTTGGGATCCCGTCATT 58.554 47.619 26.03 0.00 39.42 2.57
207 473 1.340991 CCTTGTTTGGGATCCCGTCAT 60.341 52.381 26.03 0.00 39.42 3.06
215 481 2.716424 TCTCCAACTCCTTGTTTGGGAT 59.284 45.455 0.66 0.00 36.63 3.85
221 487 0.759346 AGCGTCTCCAACTCCTTGTT 59.241 50.000 0.00 0.00 39.92 2.83
312 593 2.964389 GCCCGAGCGCTTCTCATC 60.964 66.667 13.26 0.00 41.98 2.92
314 595 3.939837 CTTGCCCGAGCGCTTCTCA 62.940 63.158 13.26 4.83 44.31 3.27
330 611 3.782443 GGCCCCGGATCGTGTCTT 61.782 66.667 0.73 0.00 0.00 3.01
363 644 1.305201 CTAGACGACAGGCTCTCCTC 58.695 60.000 0.00 0.00 41.93 3.71
373 654 3.908643 TCTTCCTAGAGCTAGACGACA 57.091 47.619 6.11 0.00 35.21 4.35
387 668 0.910088 CCCCTCCTCGGTTTCTTCCT 60.910 60.000 0.00 0.00 0.00 3.36
470 751 2.431430 CTCGTCTGCAAGCGCTGA 60.431 61.111 12.58 0.00 43.07 4.26
603 890 1.413118 TCATAGGGCGAGATGAGCAA 58.587 50.000 0.00 0.00 36.08 3.91
696 985 1.806542 CGTGTCTGTTGGGGAATTCAG 59.193 52.381 7.93 0.00 0.00 3.02
807 1096 9.935682 GAAGATTTAATCTGCATCGTTCATTTA 57.064 29.630 8.34 0.00 40.13 1.40
901 1201 1.746615 CGGCATGTTGTGAGGGAGG 60.747 63.158 0.00 0.00 0.00 4.30
915 1217 0.967887 CAAGAGGAGGAGAGACGGCA 60.968 60.000 0.00 0.00 0.00 5.69
1244 1563 1.536943 GGTCAGCAGAGGAGAACGGT 61.537 60.000 0.00 0.00 0.00 4.83
1654 1973 9.474313 TCTTTGGCCACTAATAAATATGAACTT 57.526 29.630 3.88 0.00 0.00 2.66
1848 2167 3.980022 TCCATAGCCAAATCATAGTCCCA 59.020 43.478 0.00 0.00 0.00 4.37
2025 2344 0.876342 AGCTCTTATTGTAGCGCGCC 60.876 55.000 30.33 14.69 43.63 6.53


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

AutoCloner maintained by Alex Coulton.