Multiple sequence alignment - TraesCS3A01G219400

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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 TraesCS3A01G219400 chr3A 100.000 2954 0 0 1 2954 403005600 403008553 0.000000e+00 5456
1 TraesCS3A01G219400 chr3B 96.078 2652 66 20 1 2633 398590846 398588214 0.000000e+00 4287
2 TraesCS3A01G219400 chr3B 94.099 322 18 1 2634 2954 398588185 398587864 3.420000e-134 488
3 TraesCS3A01G219400 chr3D 95.848 2577 58 17 1 2558 321718003 321720549 0.000000e+00 4120
4 TraesCS3A01G219400 chr3D 88.315 368 27 6 2587 2954 321720548 321720899 7.570000e-116 427
5 TraesCS3A01G219400 chr1B 81.193 218 34 6 2634 2845 555054570 555054786 5.060000e-38 169
6 TraesCS3A01G219400 chr1B 85.821 134 17 2 2661 2793 615750097 615750229 1.100000e-29 141
7 TraesCS3A01G219400 chr2A 79.638 221 34 8 2634 2845 589538343 589538561 6.600000e-32 148
8 TraesCS3A01G219400 chr7D 87.597 129 12 4 2672 2799 458052265 458052390 2.370000e-31 147


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 TraesCS3A01G219400 chr3A 403005600 403008553 2953 False 5456.0 5456 100.0000 1 2954 1 chr3A.!!$F1 2953
1 TraesCS3A01G219400 chr3B 398587864 398590846 2982 True 2387.5 4287 95.0885 1 2954 2 chr3B.!!$R1 2953
2 TraesCS3A01G219400 chr3D 321718003 321720899 2896 False 2273.5 4120 92.0815 1 2954 2 chr3D.!!$F1 2953

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
274 276 0.034896 CGCTGTTACCCCTGACTGTT 59.965 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 1970 0.392729 CCAAGAGAGCAAGGGAGCTG 60.393 60.0 0.0 0.0 46.75 4.24 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
274 276 0.034896 CGCTGTTACCCCTGACTGTT 59.965 55.000 0.00 0.00 0.00 3.16
419 422 1.811266 CGGACCATGTCTCTTGCGG 60.811 63.158 0.00 0.00 32.47 5.69
442 445 2.778299 TCTGTGGGAGAATTTGTTCGG 58.222 47.619 0.00 0.00 0.00 4.30
582 585 0.307760 GTGAACCAACACTTCTGCCG 59.692 55.000 0.00 0.00 37.73 5.69
680 683 1.165270 GTGTTCATTTCCAGACGGGG 58.835 55.000 0.00 0.00 37.22 5.73
681 684 0.037590 TGTTCATTTCCAGACGGGGG 59.962 55.000 0.00 0.00 37.22 5.40
745 748 3.304928 CCAGACTTGTGAATTGCTTGTCC 60.305 47.826 0.00 0.00 0.00 4.02
851 854 5.385617 CGACCTGATTAAACTCTTGCTTTG 58.614 41.667 0.00 0.00 0.00 2.77
969 972 7.674705 GCAGAGAATTTTCAAACAAACCAACAG 60.675 37.037 0.00 0.00 0.00 3.16
1098 1101 0.603569 GTTCTCGCAGGTCAGAGGAA 59.396 55.000 0.00 0.00 35.34 3.36
1101 1104 2.125350 CGCAGGTCAGAGGAAGCC 60.125 66.667 0.00 0.00 0.00 4.35
1224 1227 1.344438 TGCTCGTCACATGAGAAAGGT 59.656 47.619 0.00 0.00 33.07 3.50
1395 1398 2.671070 CCGGTCAGCCATTGGACT 59.329 61.111 6.95 0.00 34.49 3.85
1497 1500 1.597854 CCAGTTGAGGAAGCACGCA 60.598 57.895 0.00 0.00 0.00 5.24
1645 1648 0.905357 AGAAGATGGGGTTGGAGTCG 59.095 55.000 0.00 0.00 0.00 4.18
1677 1680 0.033601 AGGGCGTCAGTGAGAGATCT 60.034 55.000 0.00 0.00 0.00 2.75
1857 1860 0.250234 GTGATGCTGAGGCCACTACA 59.750 55.000 5.01 1.24 37.74 2.74
1875 1878 1.871039 ACAACCGACAATGAGGAAACG 59.129 47.619 6.53 0.00 0.00 3.60
1967 1970 1.661341 CAGTGATGCTGCCTAAGGTC 58.339 55.000 0.00 0.00 38.52 3.85
2120 2123 4.868067 ACAAGCAAGCAAGAAGAAATCAG 58.132 39.130 0.00 0.00 0.00 2.90
2124 2140 2.494870 CAAGCAAGAAGAAATCAGGGGG 59.505 50.000 0.00 0.00 0.00 5.40
2234 2250 0.108520 TTGGTACTCCGGTGAATCGC 60.109 55.000 11.17 0.00 36.30 4.58
2287 2303 1.135315 GCTGAATTCCATTTCGCTGCA 60.135 47.619 2.27 0.00 0.00 4.41
2424 2443 5.559770 TGACAGTGAATGAAATGCTCCTTA 58.440 37.500 0.00 0.00 0.00 2.69
2493 2512 3.599343 TCGGACTGACTGAAATCAATGG 58.401 45.455 0.00 0.00 0.00 3.16
2498 2517 5.163683 GGACTGACTGAAATCAATGGACATG 60.164 44.000 0.00 0.00 0.00 3.21
2578 2630 9.555727 ACAGTATTTGTGAAAAAGCTAGTAGAA 57.444 29.630 0.00 0.00 38.99 2.10
2628 2680 0.888736 CAGCGTGATGGAAACCCACA 60.889 55.000 0.00 0.00 36.36 4.17
2670 2750 7.068226 GCCATCAGTTACTTACATGGGTAAATT 59.932 37.037 13.56 0.00 38.92 1.82
2712 2792 8.522830 ACAGTTGGTAAATTAAAGACCATCATG 58.477 33.333 13.27 11.28 42.71 3.07
2854 2935 5.048643 CACTAGGGAGTATAACATCCACTCG 60.049 48.000 0.00 0.00 39.68 4.18
2919 3000 8.238481 TGAATTTTGCAAAGGTTAATCGATTC 57.762 30.769 15.25 14.38 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 48 1.003718 ACGTGGTTGGCTAAGGCTC 60.004 57.895 0.00 0.00 38.73 4.70
47 49 1.003718 GACGTGGTTGGCTAAGGCT 60.004 57.895 0.00 0.00 38.73 4.58
48 50 1.302192 TGACGTGGTTGGCTAAGGC 60.302 57.895 0.00 0.00 37.82 4.35
49 51 0.034896 AGTGACGTGGTTGGCTAAGG 59.965 55.000 0.00 0.00 0.00 2.69
274 276 0.393820 AGGAAGTTTTACCGTGCCGA 59.606 50.000 0.00 0.00 0.00 5.54
419 422 3.058224 CGAACAAATTCTCCCACAGAACC 60.058 47.826 0.00 0.00 44.28 3.62
560 563 1.334869 GCAGAAGTGTTGGTTCACAGG 59.665 52.381 0.00 0.00 40.37 4.00
563 566 0.307760 CGGCAGAAGTGTTGGTTCAC 59.692 55.000 0.00 0.00 38.46 3.18
745 748 5.163854 ACAAGAAGGCGATTTAATCTTCACG 60.164 40.000 3.34 0.00 38.35 4.35
969 972 2.149578 AGTCAGTCAGATGCAAGTTGC 58.850 47.619 21.17 21.17 45.29 4.17
1224 1227 1.005156 GCAAATGAAAGGGCGGCAA 60.005 52.632 12.47 0.00 0.00 4.52
1395 1398 5.290493 ACTTCCGTGCATCATAATCCTTA 57.710 39.130 0.00 0.00 0.00 2.69
1497 1500 1.138568 CAGCAGGATGATCCTCCCTT 58.861 55.000 11.91 0.00 45.66 3.95
1645 1648 2.047179 GCCCTCGTCACCTTCACC 60.047 66.667 0.00 0.00 0.00 4.02
1857 1860 1.071071 TCCGTTTCCTCATTGTCGGTT 59.929 47.619 0.00 0.00 39.14 4.44
1875 1878 0.598065 GTGTTGACATTGCCAGGTCC 59.402 55.000 0.00 0.00 33.09 4.46
1967 1970 0.392729 CCAAGAGAGCAAGGGAGCTG 60.393 60.000 0.00 0.00 46.75 4.24
2037 2040 2.415893 GGATGTTTCTTCCCAACATGCG 60.416 50.000 3.07 0.00 43.47 4.73
2124 2140 4.802563 GGATGTAAACGACACTACTTAGCC 59.197 45.833 0.00 0.00 42.17 3.93
2128 2144 4.021368 AGCAGGATGTAAACGACACTACTT 60.021 41.667 0.00 0.00 42.17 2.24
2234 2250 2.668457 AGAGAATTACAACGCAGCGAAG 59.332 45.455 24.65 15.59 0.00 3.79
2287 2303 9.624373 AAAGATCTACTCAGATGCAATTACAAT 57.376 29.630 0.00 0.00 41.78 2.71
2424 2443 3.735237 AACATCTCACGTGTCTGAACT 57.265 42.857 16.51 0.25 0.00 3.01
2493 2512 4.227177 CGTAGACACGTTTTAGCATGTC 57.773 45.455 0.00 0.00 43.31 3.06
2578 2630 9.706691 CCCGTTCACAAATACTGTATTAGATAT 57.293 33.333 13.07 0.00 36.10 1.63
2579 2631 8.145767 CCCCGTTCACAAATACTGTATTAGATA 58.854 37.037 13.07 0.00 36.10 1.98
2580 2632 6.990349 CCCCGTTCACAAATACTGTATTAGAT 59.010 38.462 13.07 0.28 36.10 1.98
2581 2633 6.342906 CCCCGTTCACAAATACTGTATTAGA 58.657 40.000 13.07 9.15 36.10 2.10
2582 2634 5.007332 GCCCCGTTCACAAATACTGTATTAG 59.993 44.000 13.07 7.21 36.10 1.73
2583 2635 4.877251 GCCCCGTTCACAAATACTGTATTA 59.123 41.667 13.07 0.00 36.10 0.98
2584 2636 3.692593 GCCCCGTTCACAAATACTGTATT 59.307 43.478 7.22 7.22 36.10 1.89
2585 2637 3.054655 AGCCCCGTTCACAAATACTGTAT 60.055 43.478 0.00 0.00 36.10 2.29
2586 2638 2.303600 AGCCCCGTTCACAAATACTGTA 59.696 45.455 0.00 0.00 36.10 2.74
2587 2639 1.073284 AGCCCCGTTCACAAATACTGT 59.927 47.619 0.00 0.00 39.56 3.55
2588 2640 1.468520 CAGCCCCGTTCACAAATACTG 59.531 52.381 0.00 0.00 0.00 2.74
2589 2641 1.821216 CAGCCCCGTTCACAAATACT 58.179 50.000 0.00 0.00 0.00 2.12
2628 2680 6.821388 ACTGATGGCTAAGAATTCGACTTAT 58.179 36.000 0.00 0.00 30.96 1.73
2745 2826 8.940768 TTCCGAATCAACTTCTTGAAATTTTT 57.059 26.923 0.00 0.00 39.90 1.94
2764 2845 7.680442 TGAAATTCACACTAATGATTCCGAA 57.320 32.000 0.00 0.00 0.00 4.30
2766 2847 8.915871 ATTTGAAATTCACACTAATGATTCCG 57.084 30.769 0.00 0.00 0.00 4.30
2813 2894 5.415077 CCCTAGTGTTACGGGATATACTCTG 59.585 48.000 0.00 0.00 40.55 3.35
2854 2935 2.230508 TGACACACGACATTAGGAGGAC 59.769 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.