Multiple sequence alignment - TraesCS3D01G091400

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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 TraesCS3D01G091400 chr3D 100.000 2420 0 0 1 2420 46250430 46252849 0.000000e+00 4470
1 TraesCS3D01G091400 chr3D 100.000 323 0 0 2732 3054 46253161 46253483 5.640000e-167 597
2 TraesCS3D01G091400 chr3B 94.772 1798 79 7 620 2416 72319475 72321258 0.000000e+00 2785
3 TraesCS3D01G091400 chr3B 84.735 642 64 21 1 629 72318613 72319233 2.010000e-171 612
4 TraesCS3D01G091400 chr3B 88.545 323 36 1 2732 3054 72321331 72321652 1.030000e-104 390
5 TraesCS3D01G091400 chr3A 92.996 1799 91 7 620 2417 57861124 57862888 0.000000e+00 2591
6 TraesCS3D01G091400 chr3A 82.883 666 69 22 3 629 57860223 57860882 9.570000e-155 556
7 TraesCS3D01G091400 chr3A 88.125 320 37 1 2732 3051 57862952 57863270 2.220000e-101 379


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 TraesCS3D01G091400 chr3D 46250430 46253483 3053 False 2533.500000 4470 100.000000 1 3054 2 chr3D.!!$F1 3053
1 TraesCS3D01G091400 chr3B 72318613 72321652 3039 False 1262.333333 2785 89.350667 1 3054 3 chr3B.!!$F1 3053
2 TraesCS3D01G091400 chr3A 57860223 57863270 3047 False 1175.333333 2591 88.001333 3 3051 3 chr3A.!!$F1 3048

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
309 326 0.439985 CTGACACGCCAAATGAGACG 59.56 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2372 1.071385 ACTCAGCTCCAGGAAAGTGTG 59.929 52.381 0.0 0.0 0.0 3.82 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
194 211 6.597562 TCATATATGTGTTACCCCAAACTCC 58.402 40.000 12.42 0.00 0.00 3.85
204 221 1.751924 CCCCAAACTCCGTTGACAAAA 59.248 47.619 0.00 0.00 0.00 2.44
207 224 2.096174 CCAAACTCCGTTGACAAAACGA 59.904 45.455 11.87 0.00 45.64 3.85
248 265 1.293924 CGAAGCCTATGCAGGACAAG 58.706 55.000 0.00 0.00 45.91 3.16
268 285 3.152341 AGCAAGAAATTGTCCACTCCAG 58.848 45.455 0.00 0.00 0.00 3.86
309 326 0.439985 CTGACACGCCAAATGAGACG 59.560 55.000 0.00 0.00 0.00 4.18
390 415 8.408601 ACATGCATGGAACTAAGTATTGAAATC 58.591 33.333 29.41 0.00 0.00 2.17
391 416 7.936496 TGCATGGAACTAAGTATTGAAATCA 57.064 32.000 0.00 0.00 0.00 2.57
395 420 9.655769 CATGGAACTAAGTATTGAAATCAATCG 57.344 33.333 11.69 1.30 44.67 3.34
450 475 9.717942 AGTTGATTATCTTATGGCATCTACTTC 57.282 33.333 1.65 0.00 29.26 3.01
478 503 5.615289 AGTCCTATTCCAGATGTGCAATAC 58.385 41.667 0.00 0.00 0.00 1.89
479 504 5.130975 AGTCCTATTCCAGATGTGCAATACA 59.869 40.000 0.00 0.00 44.87 2.29
480 505 5.468072 GTCCTATTCCAGATGTGCAATACAG 59.532 44.000 0.00 0.00 43.80 2.74
481 506 4.214971 CCTATTCCAGATGTGCAATACAGC 59.785 45.833 0.00 0.00 45.88 4.40
504 529 5.277250 GCAATAAGCTCTCACTGCTAATGTC 60.277 44.000 0.00 0.00 40.22 3.06
509 535 5.982356 AGCTCTCACTGCTAATGTCAATAA 58.018 37.500 0.00 0.00 39.21 1.40
510 536 6.409704 AGCTCTCACTGCTAATGTCAATAAA 58.590 36.000 0.00 0.00 39.21 1.40
553 607 4.632538 AAACACAAAAGTTCCTTCCGAG 57.367 40.909 0.00 0.00 0.00 4.63
561 615 2.610873 AGTTCCTTCCGAGGTTCTTCT 58.389 47.619 0.00 0.00 43.97 2.85
573 627 1.134670 GGTTCTTCTCCGAGGATGGTG 60.135 57.143 0.00 0.00 0.00 4.17
757 1062 4.650972 TGTTACAAGTGCCCCTCTTAAT 57.349 40.909 0.00 0.00 0.00 1.40
758 1063 4.993028 TGTTACAAGTGCCCCTCTTAATT 58.007 39.130 0.00 0.00 0.00 1.40
759 1064 6.129414 TGTTACAAGTGCCCCTCTTAATTA 57.871 37.500 0.00 0.00 0.00 1.40
760 1065 6.544650 TGTTACAAGTGCCCCTCTTAATTAA 58.455 36.000 0.00 0.00 0.00 1.40
887 1193 9.643693 TTTTTCCATTGATTCTGAAGCTATTTC 57.356 29.630 7.22 0.00 36.29 2.17
1194 1500 4.644685 AGTCTTGAGAAGGTAGAGCTCATC 59.355 45.833 17.77 8.05 38.35 2.92
1248 1554 1.210478 CCCATCCCTCTTGTCGACATT 59.790 52.381 20.80 0.00 0.00 2.71
1317 1623 0.461870 CGGATGCTGGAACCATCGAA 60.462 55.000 0.00 0.00 39.92 3.71
1338 1644 1.610102 GCACATGGCTCAGAGACTGTT 60.610 52.381 4.45 0.00 40.25 3.16
1497 1803 0.909610 AGAAAGCCGGTGAGATCCCA 60.910 55.000 1.90 0.00 0.00 4.37
1924 2230 8.235226 ACGATAACGATGAGGTATACTATGTTG 58.765 37.037 2.25 0.00 42.66 3.33
2032 2338 7.303182 TCCATATCACTTGTATCTTACCCAG 57.697 40.000 0.00 0.00 0.00 4.45
2082 2388 2.576615 GAAACACACTTTCCTGGAGCT 58.423 47.619 0.00 0.00 0.00 4.09
2089 2395 3.584848 ACACTTTCCTGGAGCTGAGTTAT 59.415 43.478 0.00 0.00 0.00 1.89
2102 2409 6.396829 AGCTGAGTTATTGCTTTGAAGTTT 57.603 33.333 0.00 0.00 32.61 2.66
2113 2420 8.729805 ATTGCTTTGAAGTTTTAACAAATGGA 57.270 26.923 0.00 0.00 33.97 3.41
2117 2424 5.860941 TGAAGTTTTAACAAATGGAGCCA 57.139 34.783 0.00 0.00 0.00 4.75
2254 2561 8.879342 TTTTTGTATTTGTGATTCCAATTCGT 57.121 26.923 0.00 0.00 0.00 3.85
2277 2584 7.544566 TCGTGGTCAAGAAGTAATTAAGATGTC 59.455 37.037 0.00 0.00 0.00 3.06
2310 2617 6.992766 CAAAGTCATTGTTGTTTGGAGTTTC 58.007 36.000 0.00 0.00 34.16 2.78
2311 2618 6.530019 AAGTCATTGTTGTTTGGAGTTTCT 57.470 33.333 0.00 0.00 0.00 2.52
2312 2619 6.136541 AGTCATTGTTGTTTGGAGTTTCTC 57.863 37.500 0.00 0.00 0.00 2.87
2313 2620 5.888161 AGTCATTGTTGTTTGGAGTTTCTCT 59.112 36.000 0.00 0.00 0.00 3.10
2314 2621 7.054124 AGTCATTGTTGTTTGGAGTTTCTCTA 58.946 34.615 0.00 0.00 0.00 2.43
2315 2622 7.227512 AGTCATTGTTGTTTGGAGTTTCTCTAG 59.772 37.037 0.00 0.00 0.00 2.43
2316 2623 7.012421 GTCATTGTTGTTTGGAGTTTCTCTAGT 59.988 37.037 0.00 0.00 0.00 2.57
2329 2636 7.254227 AGTTTCTCTAGTCTCTACTATTGCG 57.746 40.000 0.00 0.00 37.57 4.85
2391 2699 2.158813 AGAGTCCAAGCAACGAGGAAAA 60.159 45.455 0.00 0.00 32.30 2.29
2401 2709 4.395231 AGCAACGAGGAAAATAACTAAGGC 59.605 41.667 0.00 0.00 0.00 4.35
2402 2710 4.155280 GCAACGAGGAAAATAACTAAGGCA 59.845 41.667 0.00 0.00 0.00 4.75
2405 2713 3.938963 CGAGGAAAATAACTAAGGCAGCA 59.061 43.478 0.00 0.00 0.00 4.41
2409 2717 4.700213 GGAAAATAACTAAGGCAGCACTGA 59.300 41.667 0.81 0.00 0.00 3.41
2417 2725 0.177604 AGGCAGCACTGACATAGAGC 59.822 55.000 6.23 0.00 42.32 4.09
2757 3065 2.632028 AGCAAATGTTATTGGTGTGCCA 59.368 40.909 0.00 0.00 44.38 4.92
2764 3072 0.538516 TATTGGTGTGCCACGGCTTT 60.539 50.000 9.92 0.00 46.01 3.51
2810 3118 4.713824 ACTAGTGTACGCTGCTCAATTA 57.286 40.909 19.20 0.00 0.00 1.40
2821 3129 5.820423 ACGCTGCTCAATTATATTGTGGTAA 59.180 36.000 0.00 0.00 0.00 2.85
2843 3151 6.743575 AACCTTGTATTCTTGTGTAGATGC 57.256 37.500 0.00 0.00 31.54 3.91
2852 3160 6.706055 TTCTTGTGTAGATGCTTAGAAACG 57.294 37.500 0.00 0.00 31.54 3.60
2857 3165 5.169295 GTGTAGATGCTTAGAAACGGTCTT 58.831 41.667 0.00 0.00 37.84 3.01
2866 3174 7.426410 TGCTTAGAAACGGTCTTATCATAGAG 58.574 38.462 0.00 0.00 37.84 2.43
2912 3220 9.661187 GCTTGTGTTCATAGATAGATGAATTTG 57.339 33.333 2.43 0.00 45.21 2.32
2936 3244 9.541884 TTGCCTAAATTAGAAAAGGGAATACTT 57.458 29.630 0.83 0.00 34.90 2.24
2937 3245 8.966868 TGCCTAAATTAGAAAAGGGAATACTTG 58.033 33.333 0.83 0.00 0.00 3.16
2962 3270 3.009473 ACATGCAAGTGTAGGTTGAGGAT 59.991 43.478 0.00 0.00 0.00 3.24
2970 3278 4.223032 AGTGTAGGTTGAGGATTGGTACTG 59.777 45.833 0.00 0.00 0.00 2.74
2984 3292 5.464030 TTGGTACTGGACTTCACTTCTAC 57.536 43.478 0.00 0.00 0.00 2.59
2993 3301 4.264849 GGACTTCACTTCTACGCGATAAAC 59.735 45.833 15.93 0.00 0.00 2.01
2996 3304 6.558009 ACTTCACTTCTACGCGATAAACATA 58.442 36.000 15.93 0.00 0.00 2.29
3006 3314 4.849383 ACGCGATAAACATACAAAGTTTGC 59.151 37.500 15.93 0.00 39.36 3.68
3041 3349 5.538849 TGGTACACAACATAGACACAAGA 57.461 39.130 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.241430 AGGCCAATCCCTAACTTACACC 59.759 50.000 5.01 0.00 32.11 4.16
44 45 3.279434 CAGGCCAATCCCTAACTTACAC 58.721 50.000 5.01 0.00 32.78 2.90
190 207 2.542595 GACATCGTTTTGTCAACGGAGT 59.457 45.455 7.23 6.25 44.38 3.85
194 211 5.444613 CCATCTAGACATCGTTTTGTCAACG 60.445 44.000 14.86 0.63 46.81 4.10
204 221 3.319405 CCTAAGCACCATCTAGACATCGT 59.681 47.826 0.00 0.00 0.00 3.73
207 224 3.041211 TGCCTAAGCACCATCTAGACAT 58.959 45.455 0.00 0.00 46.52 3.06
230 247 1.020437 GCTTGTCCTGCATAGGCTTC 58.980 55.000 0.00 0.00 44.22 3.86
248 265 3.149196 TCTGGAGTGGACAATTTCTTGC 58.851 45.455 0.00 0.00 35.69 4.01
293 310 2.380084 ATACGTCTCATTTGGCGTGT 57.620 45.000 4.39 0.00 38.10 4.49
339 356 6.674694 AAGCACATGTAATTTTGCACAAAA 57.325 29.167 10.70 10.70 43.48 2.44
360 377 8.892723 TCAATACTTAGTTCCATGCATGTAAAG 58.107 33.333 24.58 19.39 0.00 1.85
390 415 9.970395 ATTATATGGCAAATATAATGGCGATTG 57.030 29.630 16.98 0.00 45.56 2.67
450 475 5.536538 TGCACATCTGGAATAGGACTAGTAG 59.463 44.000 0.00 0.00 0.00 2.57
480 505 4.574013 ACATTAGCAGTGAGAGCTTATTGC 59.426 41.667 0.00 2.24 43.25 3.56
481 506 5.814188 TGACATTAGCAGTGAGAGCTTATTG 59.186 40.000 0.00 0.00 43.25 1.90
482 507 5.982356 TGACATTAGCAGTGAGAGCTTATT 58.018 37.500 0.00 0.00 43.25 1.40
483 508 5.604758 TGACATTAGCAGTGAGAGCTTAT 57.395 39.130 0.00 0.00 43.25 1.73
484 509 5.405935 TTGACATTAGCAGTGAGAGCTTA 57.594 39.130 0.00 0.00 43.25 3.09
485 510 3.969287 TGACATTAGCAGTGAGAGCTT 57.031 42.857 0.00 0.00 43.25 3.74
553 607 1.134670 CACCATCCTCGGAGAAGAACC 60.135 57.143 6.58 0.00 34.09 3.62
561 615 2.471815 AATAGTCCACCATCCTCGGA 57.528 50.000 0.00 0.00 0.00 4.55
757 1062 2.516906 CCTACCCCGTTTTGCCTTTAA 58.483 47.619 0.00 0.00 0.00 1.52
758 1063 1.272037 CCCTACCCCGTTTTGCCTTTA 60.272 52.381 0.00 0.00 0.00 1.85
759 1064 0.541063 CCCTACCCCGTTTTGCCTTT 60.541 55.000 0.00 0.00 0.00 3.11
760 1065 1.076014 CCCTACCCCGTTTTGCCTT 59.924 57.895 0.00 0.00 0.00 4.35
819 1125 6.318900 ACCTAGAGCTTGGCAATACATAAAAC 59.681 38.462 0.00 0.00 0.00 2.43
868 1174 6.820656 ACTGACGAAATAGCTTCAGAATCAAT 59.179 34.615 15.94 0.00 37.53 2.57
1018 1324 2.287849 GGTCTTTGTCAGCTTTCTTGGC 60.288 50.000 0.00 0.00 0.00 4.52
1194 1500 4.437390 GGGTTTGTAATCAGAACATCAGCG 60.437 45.833 0.00 0.00 0.00 5.18
1248 1554 5.588648 CCCTTCGCTTTCAATAAGGTATTCA 59.411 40.000 0.00 0.00 37.40 2.57
1338 1644 2.570415 TGAGCAACACGGGGATTTTA 57.430 45.000 0.00 0.00 0.00 1.52
1665 1971 2.159824 TGTAGACTCTTTCGTCTCAGCG 59.840 50.000 0.00 0.00 42.92 5.18
1803 2109 4.202441 GAGTGTTCACATCAATATGCCCT 58.798 43.478 5.74 0.00 36.50 5.19
1876 2182 7.555965 TCGTCATCATCATCTTCCTTCTTTAA 58.444 34.615 0.00 0.00 0.00 1.52
2061 2367 1.609072 GCTCCAGGAAAGTGTGTTTCC 59.391 52.381 8.25 8.25 46.32 3.13
2066 2372 1.071385 ACTCAGCTCCAGGAAAGTGTG 59.929 52.381 0.00 0.00 0.00 3.82
2067 2373 1.428869 ACTCAGCTCCAGGAAAGTGT 58.571 50.000 0.00 0.00 0.00 3.55
2080 2386 8.480066 GTTAAAACTTCAAAGCAATAACTCAGC 58.520 33.333 0.00 0.00 0.00 4.26
2082 2388 9.862371 TTGTTAAAACTTCAAAGCAATAACTCA 57.138 25.926 10.70 0.00 0.00 3.41
2089 2395 7.201600 GCTCCATTTGTTAAAACTTCAAAGCAA 60.202 33.333 0.00 0.00 35.14 3.91
2102 2409 5.527214 CGAGTCATATGGCTCCATTTGTTAA 59.473 40.000 27.39 0.00 43.52 2.01
2113 2420 1.339610 GTGCTCTCGAGTCATATGGCT 59.660 52.381 10.24 10.24 0.00 4.75
2117 2424 4.727507 ACAAAGTGCTCTCGAGTCATAT 57.272 40.909 13.13 2.90 0.00 1.78
2202 2509 5.992217 GTCAAGATGAGAAAGGTGTTACACT 59.008 40.000 15.44 0.00 34.40 3.55
2212 2519 5.514279 ACAAAAAGCGTCAAGATGAGAAAG 58.486 37.500 0.00 0.00 0.00 2.62
2219 2526 6.734137 TCACAAATACAAAAAGCGTCAAGAT 58.266 32.000 0.00 0.00 0.00 2.40
2254 2561 7.685481 TGGACATCTTAATTACTTCTTGACCA 58.315 34.615 0.00 0.00 0.00 4.02
2277 2584 3.389925 ACAATGACTTTGTGCCATTGG 57.610 42.857 15.75 0.00 46.80 3.16
2310 2617 4.752604 TCAGCGCAATAGTAGAGACTAGAG 59.247 45.833 11.47 0.00 41.50 2.43
2311 2618 4.512198 GTCAGCGCAATAGTAGAGACTAGA 59.488 45.833 11.47 0.00 41.50 2.43
2312 2619 4.273724 TGTCAGCGCAATAGTAGAGACTAG 59.726 45.833 11.47 0.00 41.50 2.57
2313 2620 4.196971 TGTCAGCGCAATAGTAGAGACTA 58.803 43.478 11.47 0.00 42.41 2.59
2314 2621 3.017442 TGTCAGCGCAATAGTAGAGACT 58.983 45.455 11.47 0.00 39.92 3.24
2315 2622 3.422417 TGTCAGCGCAATAGTAGAGAC 57.578 47.619 11.47 3.78 0.00 3.36
2316 2623 4.499865 GGAATGTCAGCGCAATAGTAGAGA 60.500 45.833 11.47 0.00 0.00 3.10
2362 2669 2.952310 GTTGCTTGGACTCTTTGGAAGT 59.048 45.455 0.00 0.00 0.00 3.01
2391 2699 3.981071 TGTCAGTGCTGCCTTAGTTAT 57.019 42.857 0.00 0.00 0.00 1.89
2757 3065 5.049612 GCACTTTCTCTTACTAAAAAGCCGT 60.050 40.000 0.00 0.00 33.10 5.68
2764 3072 9.257651 GTAGACTTTGCACTTTCTCTTACTAAA 57.742 33.333 0.00 0.00 0.00 1.85
2810 3118 8.956426 CACAAGAATACAAGGTTACCACAATAT 58.044 33.333 3.51 0.00 0.00 1.28
2821 3129 6.054860 AGCATCTACACAAGAATACAAGGT 57.945 37.500 0.00 0.00 37.89 3.50
2843 3151 8.622157 TCACTCTATGATAAGACCGTTTCTAAG 58.378 37.037 0.00 0.00 29.45 2.18
2852 3160 6.719370 AGGACATCTCACTCTATGATAAGACC 59.281 42.308 0.00 0.00 36.48 3.85
2857 3165 6.264067 CACACAGGACATCTCACTCTATGATA 59.736 42.308 0.00 0.00 36.48 2.15
2866 3174 2.625737 CCATCACACAGGACATCTCAC 58.374 52.381 0.00 0.00 0.00 3.51
2912 3220 8.414003 CCAAGTATTCCCTTTTCTAATTTAGGC 58.586 37.037 3.66 0.00 0.00 3.93
2919 3227 5.636123 TGTGCCAAGTATTCCCTTTTCTAA 58.364 37.500 0.00 0.00 0.00 2.10
2936 3244 0.110295 ACCTACACTTGCATGTGCCA 59.890 50.000 27.41 16.86 41.30 4.92
2937 3245 1.068333 CAACCTACACTTGCATGTGCC 60.068 52.381 27.41 0.00 41.30 5.01
2962 3270 4.022589 CGTAGAAGTGAAGTCCAGTACCAA 60.023 45.833 0.00 0.00 0.00 3.67
2970 3278 2.563471 ATCGCGTAGAAGTGAAGTCC 57.437 50.000 5.77 0.00 34.06 3.85
2984 3292 5.086058 AGCAAACTTTGTATGTTTATCGCG 58.914 37.500 0.00 0.00 36.07 5.87
3006 3314 2.159296 TGTGTACCACTAGTGCGCATAG 60.159 50.000 15.91 18.00 45.17 2.23
3015 3323 6.020971 TGTGTCTATGTTGTGTACCACTAG 57.979 41.667 0.00 0.00 35.11 2.57


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

AutoCloner maintained by Alex Coulton.