Multiple sequence alignment - TraesCS4B01G368300

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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 TraesCS4B01G368300 chr4B 100.000 2432 0 0 1 2432 654721109 654718678 0.000000e+00 4492.0
1 TraesCS4B01G368300 chr4B 95.147 2452 78 14 1 2432 654594022 654591592 0.000000e+00 3831.0
2 TraesCS4B01G368300 chr4B 88.493 982 87 19 782 1754 654794104 654793140 0.000000e+00 1164.0
3 TraesCS4B01G368300 chr4B 92.991 585 34 7 782 1362 654676599 654676018 0.000000e+00 846.0
4 TraesCS4B01G368300 chr4B 91.313 495 26 5 1941 2432 654781233 654780753 0.000000e+00 660.0
5 TraesCS4B01G368300 chr4B 90.688 494 31 3 1941 2432 654649507 654649027 0.000000e+00 643.0
6 TraesCS4B01G368300 chr4B 83.259 675 89 15 779 1443 654752245 654751585 1.240000e-167 599.0
7 TraesCS4B01G368300 chr4B 82.963 675 91 15 779 1443 654762484 654761824 2.690000e-164 588.0
8 TraesCS4B01G368300 chr4B 82.815 675 92 15 779 1443 654774690 654774030 1.250000e-162 582.0
9 TraesCS4B01G368300 chr4B 82.615 650 92 13 802 1443 654699726 654699090 2.730000e-154 555.0
10 TraesCS4B01G368300 chr4B 81.387 548 71 19 99 618 654794661 654794117 3.740000e-113 418.0
11 TraesCS4B01G368300 chr4B 83.827 371 46 10 99 461 654677165 654676801 8.330000e-90 340.0
12 TraesCS4B01G368300 chr4B 86.413 184 22 3 437 618 654676794 654676612 5.300000e-47 198.0
13 TraesCS4B01G368300 chrUn 85.751 1544 130 40 435 1909 154586302 154587824 0.000000e+00 1550.0
14 TraesCS4B01G368300 chrUn 87.579 475 39 11 1956 2426 154619219 154619677 1.280000e-147 532.0
15 TraesCS4B01G368300 chrUn 87.589 419 35 10 2017 2425 154588472 154588883 1.020000e-128 470.0
16 TraesCS4B01G368300 chrUn 85.845 219 16 7 99 308 154585918 154586130 4.070000e-53 219.0
17 TraesCS4B01G368300 chr5A 88.994 1272 83 22 719 1943 692180082 692178821 0.000000e+00 1520.0
18 TraesCS4B01G368300 chr5A 80.654 765 77 32 1 714 692181194 692180450 5.960000e-146 527.0
19 TraesCS4B01G368300 chr5A 90.610 213 15 2 2220 2427 692178573 692178361 6.620000e-71 278.0
20 TraesCS4B01G368300 chr5A 91.111 180 13 2 1941 2118 692178764 692178586 8.690000e-60 241.0
21 TraesCS4B01G368300 chr1B 74.074 297 41 26 330 600 65709065 65708779 3.330000e-14 89.8


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 TraesCS4B01G368300 chr4B 654718678 654721109 2431 True 4492.000000 4492 100.000000 1 2432 1 chr4B.!!$R4 2431
1 TraesCS4B01G368300 chr4B 654591592 654594022 2430 True 3831.000000 3831 95.147000 1 2432 1 chr4B.!!$R1 2431
2 TraesCS4B01G368300 chr4B 654793140 654794661 1521 True 791.000000 1164 84.940000 99 1754 2 chr4B.!!$R10 1655
3 TraesCS4B01G368300 chr4B 654751585 654752245 660 True 599.000000 599 83.259000 779 1443 1 chr4B.!!$R5 664
4 TraesCS4B01G368300 chr4B 654761824 654762484 660 True 588.000000 588 82.963000 779 1443 1 chr4B.!!$R6 664
5 TraesCS4B01G368300 chr4B 654774030 654774690 660 True 582.000000 582 82.815000 779 1443 1 chr4B.!!$R7 664
6 TraesCS4B01G368300 chr4B 654699090 654699726 636 True 555.000000 555 82.615000 802 1443 1 chr4B.!!$R3 641
7 TraesCS4B01G368300 chr4B 654676018 654677165 1147 True 461.333333 846 87.743667 99 1362 3 chr4B.!!$R9 1263
8 TraesCS4B01G368300 chrUn 154585918 154588883 2965 False 746.333333 1550 86.395000 99 2425 3 chrUn.!!$F2 2326
9 TraesCS4B01G368300 chr5A 692178361 692181194 2833 True 641.500000 1520 87.842250 1 2427 4 chr5A.!!$R1 2426

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
918 1437 1.127343 CCCAAGCAACCCAGGAAAAA 58.873 50.0 0.0 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 2466 3.726291 ACACGTGGCAAGCTTAAAAAT 57.274 38.095 21.57 0.0 0.0 1.82 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
25 26 3.733443 AATTCCTTTGTCAGTGTTGGC 57.267 42.857 0.00 0.00 0.00 4.52
174 211 7.233144 TGCATTTGTATGGCTACATGGAATAAT 59.767 33.333 0.00 0.00 37.68 1.28
309 377 2.613977 GGAGAATGATCGCCTACCCATG 60.614 54.545 0.00 0.00 41.86 3.66
319 387 1.212375 CCTACCCATGGTCCATGTCA 58.788 55.000 26.73 12.59 39.94 3.58
431 506 5.935206 TGTATCACCATGTTTCGTTGTGTAT 59.065 36.000 0.00 0.00 0.00 2.29
439 514 7.012515 ACCATGTTTCGTTGTGTATAGACAAAA 59.987 33.333 16.30 6.42 37.58 2.44
538 648 3.579147 CGTAACACGCTGAAACAAGAA 57.421 42.857 0.00 0.00 33.65 2.52
567 679 4.156922 TGTCAAAACGAGGAAACACAACAT 59.843 37.500 0.00 0.00 0.00 2.71
590 703 1.686355 TTCAAAGCAATGGTGGACGT 58.314 45.000 0.00 0.00 0.00 4.34
604 717 3.653539 TGGACGTTGGATCCATATACG 57.346 47.619 27.80 27.80 41.47 3.06
746 1231 4.747540 TGGTACGCACGTAATATCGTAT 57.252 40.909 4.20 0.00 42.27 3.06
784 1278 1.153745 GTAGCAGCAGCGCTAGTGT 60.154 57.895 10.99 4.24 44.92 3.55
918 1437 1.127343 CCCAAGCAACCCAGGAAAAA 58.873 50.000 0.00 0.00 0.00 1.94
1288 1823 3.393970 CCCTTCTGAGCGGCCTCA 61.394 66.667 0.00 0.00 45.54 3.86
1566 2111 4.841443 ATGGTATATGTTAGTCGCGTGA 57.159 40.909 5.77 0.00 0.00 4.35
1615 2168 5.005740 TGCATGCTTCAGTTAGTCATTTCT 58.994 37.500 20.33 0.00 0.00 2.52
1680 2246 8.599774 CGTGGAATAAAAAGTTTGTTCATGTTT 58.400 29.630 10.92 0.00 0.00 2.83
1714 2282 1.098712 TTTGTGCGGGTGTTCTGGTC 61.099 55.000 0.00 0.00 0.00 4.02
1730 2298 1.887854 TGGTCGTGTTAACTCGATCCA 59.112 47.619 29.95 29.62 40.88 3.41
1855 2457 0.584876 GTCAGTTACAAAAGCGCGGT 59.415 50.000 4.23 4.23 0.00 5.68
1856 2458 1.794116 GTCAGTTACAAAAGCGCGGTA 59.206 47.619 12.91 0.00 0.00 4.02
1857 2459 2.414138 GTCAGTTACAAAAGCGCGGTAT 59.586 45.455 12.91 0.00 0.00 2.73
1858 2460 2.669434 TCAGTTACAAAAGCGCGGTATC 59.331 45.455 12.91 1.80 0.00 2.24
1859 2461 2.413796 CAGTTACAAAAGCGCGGTATCA 59.586 45.455 12.91 0.00 0.00 2.15
1864 2466 3.004171 ACAAAAGCGCGGTATCATAACA 58.996 40.909 12.91 0.00 0.00 2.41
2143 3293 6.365970 AGAACAATATCCTACATAGCCCTG 57.634 41.667 0.00 0.00 0.00 4.45
2428 3584 9.365906 ACAATAATATTTCCCATGCATAGTCAA 57.634 29.630 0.00 0.00 0.00 3.18
2429 3585 9.850628 CAATAATATTTCCCATGCATAGTCAAG 57.149 33.333 0.00 0.00 0.00 3.02
2430 3586 9.812347 AATAATATTTCCCATGCATAGTCAAGA 57.188 29.630 0.00 0.00 0.00 3.02
2431 3587 7.756395 AATATTTCCCATGCATAGTCAAGAG 57.244 36.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.596260 CAGCGGTGCTCACAGATAATG 59.404 52.381 0.00 0.00 36.40 1.90
309 377 2.715046 TCTCAAAGCATGACATGGACC 58.285 47.619 17.03 0.68 33.47 4.46
439 514 4.023193 CGATCTAAAACAAGTGCACCCTTT 60.023 41.667 14.63 10.33 0.00 3.11
502 612 5.202640 GTGTTACGTTAGGTTTTGCTCTTG 58.797 41.667 0.00 0.00 0.00 3.02
503 613 4.025480 CGTGTTACGTTAGGTTTTGCTCTT 60.025 41.667 0.00 0.00 36.74 2.85
538 648 6.647067 TGTGTTTCCTCGTTTTGACAAATTTT 59.353 30.769 0.50 0.00 0.00 1.82
567 679 4.279671 ACGTCCACCATTGCTTTGAAATTA 59.720 37.500 0.00 0.00 0.00 1.40
590 703 5.068591 CGGGATATCACGTATATGGATCCAA 59.931 44.000 20.67 8.82 38.11 3.53
604 717 4.649674 TGATATTCTAGCCCGGGATATCAC 59.350 45.833 26.58 10.77 0.00 3.06
714 836 3.130869 ACGTGCGTACCATTATTGGAGTA 59.869 43.478 10.62 0.00 46.92 2.59
758 1243 1.602851 GCGCTGCTGCTACTACTAGTA 59.397 52.381 14.03 1.89 36.97 1.82
759 1244 0.382515 GCGCTGCTGCTACTACTAGT 59.617 55.000 14.03 0.00 36.97 2.57
760 1245 0.665835 AGCGCTGCTGCTACTACTAG 59.334 55.000 10.39 0.00 45.14 2.57
784 1278 8.499162 CCGTAATTTGAAAACATTATTTGCCAA 58.501 29.630 0.00 0.00 0.00 4.52
918 1437 1.616994 GGGTTTGCTAGCTTGGGATGT 60.617 52.381 17.23 0.00 0.00 3.06
1505 2047 7.709182 GGAAATATATAGGTGCATGCGTATACA 59.291 37.037 14.09 4.26 0.00 2.29
1556 2101 0.809636 CCCATGCATTCACGCGACTA 60.810 55.000 15.93 0.00 33.35 2.59
1566 2111 2.605299 GGAGGGAGCCCATGCATT 59.395 61.111 8.53 0.00 41.13 3.56
1714 2282 4.442403 CAGATCATGGATCGAGTTAACACG 59.558 45.833 17.84 17.84 43.17 4.49
1730 2298 7.400439 ACAATATATACAAGCTGGCAGATCAT 58.600 34.615 20.86 9.07 0.00 2.45
1855 2457 7.700234 CGTGGCAAGCTTAAAAATGTTATGATA 59.300 33.333 0.00 0.00 0.00 2.15
1856 2458 6.531240 CGTGGCAAGCTTAAAAATGTTATGAT 59.469 34.615 0.00 0.00 0.00 2.45
1857 2459 5.861251 CGTGGCAAGCTTAAAAATGTTATGA 59.139 36.000 0.00 0.00 0.00 2.15
1858 2460 5.633182 ACGTGGCAAGCTTAAAAATGTTATG 59.367 36.000 0.00 0.00 0.00 1.90
1859 2461 5.633182 CACGTGGCAAGCTTAAAAATGTTAT 59.367 36.000 7.95 0.00 0.00 1.89
1864 2466 3.726291 ACACGTGGCAAGCTTAAAAAT 57.274 38.095 21.57 0.00 0.00 1.82
2041 3183 8.598924 CGAGAGCCACAAATTATATGCTAATAG 58.401 37.037 0.00 0.00 0.00 1.73
2136 3286 8.034313 AGTAATTCATTCATCTAACAGGGCTA 57.966 34.615 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.