Multiple sequence alignment - TraesCS5A01G058700

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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 TraesCS5A01G058700 chr5A 100.000 3067 0 0 1 3067 57562056 57565122 0.000000e+00 5664.0
1 TraesCS5A01G058700 chr5A 82.456 228 22 7 1424 1633 575612944 575612717 1.880000e-42 183.0
2 TraesCS5A01G058700 chr5A 75.455 220 45 8 1419 1632 622558150 622557934 7.000000e-17 99.0
3 TraesCS5A01G058700 chr5D 92.513 3112 94 45 1 3067 66670226 66667209 0.000000e+00 4327.0
4 TraesCS5A01G058700 chr5D 82.667 225 24 8 1424 1633 457680290 457680066 5.220000e-43 185.0
5 TraesCS5A01G058700 chr5D 75.115 217 45 8 1422 1632 498404344 498404131 3.260000e-15 93.5
6 TraesCS5A01G058700 chr5B 93.074 2570 90 33 1 2519 64417892 64420424 0.000000e+00 3679.0
7 TraesCS5A01G058700 chr5B 91.408 547 19 8 2516 3056 64420708 64421232 0.000000e+00 725.0
8 TraesCS5A01G058700 chr5B 82.008 239 23 11 1424 1644 559778623 559778387 5.220000e-43 185.0
9 TraesCS5A01G058700 chr5B 75.926 216 45 7 1419 1632 617712015 617711805 1.500000e-18 104.0
10 TraesCS5A01G058700 chr2D 87.302 63 6 2 1571 1632 633785331 633785270 1.530000e-08 71.3


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 TraesCS5A01G058700 chr5A 57562056 57565122 3066 False 5664 5664 100.000 1 3067 1 chr5A.!!$F1 3066
1 TraesCS5A01G058700 chr5D 66667209 66670226 3017 True 4327 4327 92.513 1 3067 1 chr5D.!!$R1 3066
2 TraesCS5A01G058700 chr5B 64417892 64421232 3340 False 2202 3679 92.241 1 3056 2 chr5B.!!$F1 3055

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
619 624 0.388134 GTGCAGCAATCCAGCAACTG 60.388 55.0 0.0 0.0 40.35 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2362 2433 1.113788 AATTGGACGCATTCCCCATG 58.886 50.0 0.0 0.0 45.17 3.66 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
195 198 5.382664 AGAAGAAACAAAAGGTAGTGGGA 57.617 39.130 0.00 0.00 0.00 4.37
266 269 8.559536 CATATACTCCATGTTACATTGTTCCAC 58.440 37.037 0.00 0.00 0.00 4.02
377 380 3.758715 GCATTGGCGCCCTATTTTT 57.241 47.368 26.77 0.00 0.00 1.94
383 386 5.065859 GCATTGGCGCCCTATTTTTATTTTT 59.934 36.000 26.77 0.00 0.00 1.94
438 441 5.239525 GTGCTGTTTGAACCTTTCTAGATGT 59.760 40.000 0.00 0.00 0.00 3.06
451 454 4.832608 GATGTCGGGTCCGGGCAC 62.833 72.222 9.07 1.59 40.25 5.01
474 477 3.782443 GCCAGACCCGGATCCGTT 61.782 66.667 31.22 18.73 37.81 4.44
508 511 4.039245 CCGAGCTATAAGGTCTTCATTCCA 59.961 45.833 4.77 0.00 40.38 3.53
510 513 5.636965 CGAGCTATAAGGTCTTCATTCCATG 59.363 44.000 4.77 0.00 40.38 3.66
511 514 5.312079 AGCTATAAGGTCTTCATTCCATGC 58.688 41.667 0.00 0.00 0.00 4.06
513 516 2.787473 AAGGTCTTCATTCCATGCGA 57.213 45.000 0.00 0.00 0.00 5.10
514 517 2.787473 AGGTCTTCATTCCATGCGAA 57.213 45.000 0.00 0.00 34.14 4.70
515 518 2.359900 AGGTCTTCATTCCATGCGAAC 58.640 47.619 0.00 0.00 31.79 3.95
516 519 2.026822 AGGTCTTCATTCCATGCGAACT 60.027 45.455 0.00 0.00 31.79 3.01
517 520 3.197766 AGGTCTTCATTCCATGCGAACTA 59.802 43.478 0.00 0.00 31.79 2.24
518 521 3.309954 GGTCTTCATTCCATGCGAACTAC 59.690 47.826 0.00 0.00 31.79 2.73
519 522 3.932710 GTCTTCATTCCATGCGAACTACA 59.067 43.478 0.00 0.00 31.79 2.74
520 523 3.932710 TCTTCATTCCATGCGAACTACAC 59.067 43.478 0.00 0.00 31.79 2.90
521 524 3.610040 TCATTCCATGCGAACTACACT 57.390 42.857 0.00 0.00 31.79 3.55
544 547 9.726232 CACTGTACATTTTGAGGATAATTGATG 57.274 33.333 0.00 0.00 0.00 3.07
570 575 7.221452 GTGGTCCAATTAGTAATGTACACGTAG 59.779 40.741 0.00 0.00 0.00 3.51
618 623 0.538977 AGTGCAGCAATCCAGCAACT 60.539 50.000 0.00 0.00 40.35 3.16
619 624 0.388134 GTGCAGCAATCCAGCAACTG 60.388 55.000 0.00 0.00 40.35 3.16
860 865 1.001641 GCATGTGGAGTTGGAGCCT 60.002 57.895 0.00 0.00 0.00 4.58
861 866 1.028868 GCATGTGGAGTTGGAGCCTC 61.029 60.000 0.00 0.00 0.00 4.70
863 868 1.566298 ATGTGGAGTTGGAGCCTCCC 61.566 60.000 8.62 0.00 46.64 4.30
864 869 1.920835 GTGGAGTTGGAGCCTCCCT 60.921 63.158 8.62 0.00 46.64 4.20
956 973 6.765989 CGTCCTCTATAAAACATTTCCATGGA 59.234 38.462 11.44 11.44 34.27 3.41
957 974 7.254795 CGTCCTCTATAAAACATTTCCATGGAC 60.255 40.741 15.91 0.00 34.27 4.02
958 975 7.013369 GTCCTCTATAAAACATTTCCATGGACC 59.987 40.741 15.91 0.00 34.27 4.46
959 976 6.833416 CCTCTATAAAACATTTCCATGGACCA 59.167 38.462 15.91 4.33 34.27 4.02
960 977 7.506938 CCTCTATAAAACATTTCCATGGACCAT 59.493 37.037 15.91 6.88 34.27 3.55
961 978 8.236585 TCTATAAAACATTTCCATGGACCATG 57.763 34.615 25.27 25.27 41.10 3.66
1026 1043 1.342819 AGCTGAGAAGAACGACTTGCT 59.657 47.619 0.00 0.00 39.13 3.91
1032 1049 3.060602 AGAAGAACGACTTGCTAGTTGC 58.939 45.455 14.58 0.95 39.08 4.17
1447 1486 2.265739 GTGAGCATGGACGGAGCA 59.734 61.111 0.00 0.00 0.00 4.26
1525 1564 1.693640 CCTGGAGGCCATGTTCCTT 59.306 57.895 5.01 0.00 33.24 3.36
1665 1707 9.645128 ATCCAAGATACATATGATTTGGTTTGA 57.355 29.630 10.38 2.73 37.09 2.69
1685 1728 8.839343 GGTTTGATTGGAGTTTGAAAAATTCAT 58.161 29.630 0.00 0.00 39.84 2.57
1713 1756 6.410540 GGTGTCTTATGAGGATCTCTTTGTT 58.589 40.000 0.00 0.00 34.92 2.83
1774 1817 0.104855 TCATGAAGGGATCCGAAGCG 59.895 55.000 5.45 0.00 0.00 4.68
1804 1847 5.819901 CCTAGGATCATCAAAGGAGTGAAAC 59.180 44.000 1.05 0.00 0.00 2.78
1805 1848 4.256920 AGGATCATCAAAGGAGTGAAACG 58.743 43.478 0.00 0.00 45.86 3.60
1807 1850 3.762407 TCATCAAAGGAGTGAAACGGA 57.238 42.857 0.00 0.00 45.86 4.69
1959 2003 6.524586 GCTGATTCGAGTGGAGTTTTATTTTG 59.475 38.462 0.00 0.00 0.00 2.44
1960 2004 7.504924 TGATTCGAGTGGAGTTTTATTTTGT 57.495 32.000 0.00 0.00 0.00 2.83
2076 2120 3.251004 CAGCTTTCTTTCCGTGTTAAGCT 59.749 43.478 0.00 0.00 46.53 3.74
2173 2217 6.570571 GCATCAGCTATTTGCAATCATCTCAT 60.571 38.462 0.00 0.00 45.94 2.90
2174 2218 6.555812 TCAGCTATTTGCAATCATCTCATC 57.444 37.500 0.00 0.00 45.94 2.92
2196 2240 5.674525 TCCCATACTAAGCATGAACTTGAG 58.325 41.667 0.00 0.00 0.00 3.02
2245 2291 8.814038 AAAAGAGACCAAAATGCTATACAGAT 57.186 30.769 0.00 0.00 0.00 2.90
2262 2329 5.883685 ACAGATTCCTCTCAGCATCAATA 57.116 39.130 0.00 0.00 0.00 1.90
2268 2335 4.194640 TCCTCTCAGCATCAATAACTTGC 58.805 43.478 0.00 0.00 36.63 4.01
2269 2336 3.943381 CCTCTCAGCATCAATAACTTGCA 59.057 43.478 0.00 0.00 38.84 4.08
2270 2337 4.397103 CCTCTCAGCATCAATAACTTGCAA 59.603 41.667 0.00 0.00 38.84 4.08
2271 2338 5.067413 CCTCTCAGCATCAATAACTTGCAAT 59.933 40.000 0.00 0.00 38.84 3.56
2362 2433 4.445452 AATGAATGATGTGAACACAGGC 57.555 40.909 12.97 8.29 45.48 4.85
2469 2540 1.133199 ACAGGAACAAGATTGGGCCAA 60.133 47.619 23.33 23.33 0.00 4.52
2707 3071 4.058817 GAGGTTGTGGTCAAGACTAGTTG 58.941 47.826 0.00 0.00 33.97 3.16
2754 3118 2.555757 AGCATCCAAAGCAACTCAAGAC 59.444 45.455 0.00 0.00 0.00 3.01
2756 3120 3.365767 GCATCCAAAGCAACTCAAGACTC 60.366 47.826 0.00 0.00 0.00 3.36
2757 3121 3.558931 TCCAAAGCAACTCAAGACTCA 57.441 42.857 0.00 0.00 0.00 3.41
2758 3122 3.884895 TCCAAAGCAACTCAAGACTCAA 58.115 40.909 0.00 0.00 0.00 3.02
2759 3123 3.879295 TCCAAAGCAACTCAAGACTCAAG 59.121 43.478 0.00 0.00 0.00 3.02
2760 3124 3.879295 CCAAAGCAACTCAAGACTCAAGA 59.121 43.478 0.00 0.00 0.00 3.02
2761 3125 4.024218 CCAAAGCAACTCAAGACTCAAGAG 60.024 45.833 0.00 0.00 35.56 2.85
2776 3140 6.836527 AGACTCAAGAGTGTATGTAGCCTAAT 59.163 38.462 7.57 0.00 42.66 1.73
2778 3142 8.534954 ACTCAAGAGTGTATGTAGCCTAATAA 57.465 34.615 1.20 0.00 40.75 1.40
2779 3143 8.414778 ACTCAAGAGTGTATGTAGCCTAATAAC 58.585 37.037 1.20 0.00 40.75 1.89
2780 3144 8.301252 TCAAGAGTGTATGTAGCCTAATAACA 57.699 34.615 0.00 0.00 0.00 2.41
2781 3145 8.195436 TCAAGAGTGTATGTAGCCTAATAACAC 58.805 37.037 0.00 0.00 0.00 3.32
2782 3146 7.655521 AGAGTGTATGTAGCCTAATAACACA 57.344 36.000 11.86 0.00 0.00 3.72
2783 3147 7.717568 AGAGTGTATGTAGCCTAATAACACAG 58.282 38.462 11.86 0.00 0.00 3.66
2784 3148 6.817184 AGTGTATGTAGCCTAATAACACAGG 58.183 40.000 11.86 0.00 34.85 4.00
2826 3190 2.584608 GAGCTTAGCGAGGGCCAA 59.415 61.111 6.18 0.00 41.24 4.52
2891 3255 4.524053 CCCCCTCAACTCTATTTAACACC 58.476 47.826 0.00 0.00 0.00 4.16
2961 3325 4.611366 CAGAGGACGTTTTAAAATTCGCAC 59.389 41.667 3.52 1.49 0.00 5.34
2972 3336 9.786224 GTTTTAAAATTCGCACGTAATCAATTT 57.214 25.926 3.52 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 97 7.371159 AGCTTGTTTAATTAGTCCAAAAGCTC 58.629 34.615 0.00 0.00 43.04 4.09
96 99 6.586463 GGAGCTTGTTTAATTAGTCCAAAAGC 59.414 38.462 0.00 0.00 38.18 3.51
195 198 6.021672 TCCTCATCATATACCTGCATCTCTT 58.978 40.000 0.00 0.00 0.00 2.85
266 269 7.341805 CCTCCTCCCCAATAATAAGATATGTG 58.658 42.308 0.00 0.00 0.00 3.21
391 394 8.347771 GCACTGATGAAATTTAGCTTGATGATA 58.652 33.333 0.00 0.00 0.00 2.15
395 398 6.152323 ACAGCACTGATGAAATTTAGCTTGAT 59.848 34.615 4.31 0.00 0.00 2.57
396 399 5.474532 ACAGCACTGATGAAATTTAGCTTGA 59.525 36.000 4.31 0.00 0.00 3.02
397 400 5.706916 ACAGCACTGATGAAATTTAGCTTG 58.293 37.500 4.31 0.00 0.00 4.01
508 511 5.699001 TCAAAATGTACAGTGTAGTTCGCAT 59.301 36.000 2.39 0.36 0.00 4.73
510 513 5.389516 CCTCAAAATGTACAGTGTAGTTCGC 60.390 44.000 2.39 0.00 0.00 4.70
511 514 5.924254 TCCTCAAAATGTACAGTGTAGTTCG 59.076 40.000 2.39 0.00 0.00 3.95
513 516 9.959721 ATTATCCTCAAAATGTACAGTGTAGTT 57.040 29.630 2.39 0.00 0.00 2.24
514 517 9.959721 AATTATCCTCAAAATGTACAGTGTAGT 57.040 29.630 2.39 0.00 0.00 2.73
516 519 9.952030 TCAATTATCCTCAAAATGTACAGTGTA 57.048 29.630 0.33 0.00 0.00 2.90
517 520 8.862325 TCAATTATCCTCAAAATGTACAGTGT 57.138 30.769 0.33 0.00 0.00 3.55
518 521 9.726232 CATCAATTATCCTCAAAATGTACAGTG 57.274 33.333 0.33 0.00 0.00 3.66
519 522 9.466497 ACATCAATTATCCTCAAAATGTACAGT 57.534 29.630 0.33 0.00 0.00 3.55
520 523 9.726232 CACATCAATTATCCTCAAAATGTACAG 57.274 33.333 0.33 0.00 0.00 2.74
521 524 8.685427 CCACATCAATTATCCTCAAAATGTACA 58.315 33.333 0.00 0.00 0.00 2.90
544 547 5.870978 ACGTGTACATTACTAATTGGACCAC 59.129 40.000 0.00 0.00 0.00 4.16
630 635 1.342076 ACTAGAGATTCTCGGGTGCCA 60.342 52.381 8.01 0.00 35.36 4.92
755 760 1.623811 ACACTTACCACAGGTAGCTGG 59.376 52.381 24.84 12.35 39.52 4.85
756 761 2.037251 ACACACTTACCACAGGTAGCTG 59.963 50.000 20.16 20.16 39.52 4.24
805 810 4.697756 TACGTGCCACAGCCCAGC 62.698 66.667 0.00 0.00 38.69 4.85
930 945 6.017109 CCATGGAAATGTTTTATAGAGGACGG 60.017 42.308 5.56 0.00 0.00 4.79
931 946 6.765989 TCCATGGAAATGTTTTATAGAGGACG 59.234 38.462 13.46 0.00 0.00 4.79
932 947 7.013369 GGTCCATGGAAATGTTTTATAGAGGAC 59.987 40.741 18.20 0.00 38.75 3.85
956 973 2.351276 GTGGAGGTTCGCCATGGT 59.649 61.111 14.67 0.00 35.49 3.55
957 974 1.746615 CTGTGGAGGTTCGCCATGG 60.747 63.158 7.63 7.63 35.49 3.66
958 975 2.401766 GCTGTGGAGGTTCGCCATG 61.402 63.158 0.00 0.00 35.49 3.66
959 976 2.045926 GCTGTGGAGGTTCGCCAT 60.046 61.111 0.00 0.00 35.49 4.40
960 977 3.240134 GAGCTGTGGAGGTTCGCCA 62.240 63.158 0.00 0.00 40.60 5.69
961 978 2.435059 GAGCTGTGGAGGTTCGCC 60.435 66.667 0.00 0.00 37.60 5.54
962 979 2.029844 GTGAGCTGTGGAGGTTCGC 61.030 63.158 0.00 0.00 0.00 4.70
1026 1043 1.278127 GGCTAGAGGTGGTTGCAACTA 59.722 52.381 27.64 20.61 0.00 2.24
1032 1049 2.125106 GCCGGCTAGAGGTGGTTG 60.125 66.667 22.15 0.00 0.00 3.77
1069 1108 1.524621 ATGCACGTAGCTCATGGCC 60.525 57.895 0.00 0.00 45.94 5.36
1279 1318 2.104170 CTCTTCCTGTAGGACCTCACC 58.896 57.143 0.00 0.00 45.39 4.02
1447 1486 1.569548 TCGATCTTCCTCAGGTAGGGT 59.430 52.381 0.00 0.00 46.55 4.34
1665 1707 8.147704 ACCGTAATGAATTTTTCAAACTCCAAT 58.852 29.630 0.00 0.00 43.95 3.16
1685 1728 5.446860 AGAGATCCTCATAAGACACCGTAA 58.553 41.667 0.00 0.00 32.06 3.18
1713 1756 3.129813 GCTCATGAACATCCTGCAAATCA 59.870 43.478 0.00 0.00 0.00 2.57
1774 1817 3.007831 CCTTTGATGATCCTAGGCCTCTC 59.992 52.174 9.68 2.73 0.00 3.20
1804 1847 3.797256 GTGTTCTTCGTAGATGGATTCCG 59.203 47.826 0.00 0.00 35.04 4.30
1805 1848 3.797256 CGTGTTCTTCGTAGATGGATTCC 59.203 47.826 0.00 0.00 35.04 3.01
1807 1850 3.187700 GCGTGTTCTTCGTAGATGGATT 58.812 45.455 0.00 0.00 35.04 3.01
2076 2120 5.569355 AGACATCAACCAACCATTGACATA 58.431 37.500 0.00 0.00 38.84 2.29
2173 2217 5.189736 ACTCAAGTTCATGCTTAGTATGGGA 59.810 40.000 10.23 0.00 0.00 4.37
2174 2218 5.431765 ACTCAAGTTCATGCTTAGTATGGG 58.568 41.667 10.23 0.00 0.00 4.00
2196 2240 7.859325 TTTGTAGCATTAGTGATTAAGGGAC 57.141 36.000 0.00 0.00 0.00 4.46
2236 2282 6.587206 TGATGCTGAGAGGAATCTGTATAG 57.413 41.667 0.00 0.00 0.00 1.31
2239 2285 5.883685 ATTGATGCTGAGAGGAATCTGTA 57.116 39.130 0.00 0.00 0.00 2.74
2245 2291 4.637534 GCAAGTTATTGATGCTGAGAGGAA 59.362 41.667 0.00 0.00 38.83 3.36
2281 2348 1.547901 GGAGCCTTGCTTGGTTAACCT 60.548 52.381 24.78 1.38 39.88 3.50
2362 2433 1.113788 AATTGGACGCATTCCCCATG 58.886 50.000 0.00 0.00 45.17 3.66
2469 2540 1.913778 TGACAAGTGGCTCATGCATT 58.086 45.000 0.00 0.00 41.91 3.56
2568 2932 7.044181 CAGATTTAGCACTACTCATCAAGGAA 58.956 38.462 0.00 0.00 0.00 3.36
2707 3071 4.763793 CCATCTCTCTCATCTTCTCTCTCC 59.236 50.000 0.00 0.00 0.00 3.71
2754 3118 8.414003 TGTTATTAGGCTACATACACTCTTGAG 58.586 37.037 0.00 0.00 0.00 3.02
2756 3120 7.979537 TGTGTTATTAGGCTACATACACTCTTG 59.020 37.037 22.29 0.00 0.00 3.02
2757 3121 8.074613 TGTGTTATTAGGCTACATACACTCTT 57.925 34.615 22.29 0.00 0.00 2.85
2758 3122 7.201920 CCTGTGTTATTAGGCTACATACACTCT 60.202 40.741 22.29 0.00 0.00 3.24
2759 3123 6.924060 CCTGTGTTATTAGGCTACATACACTC 59.076 42.308 22.29 12.93 0.00 3.51
2760 3124 6.817184 CCTGTGTTATTAGGCTACATACACT 58.183 40.000 22.29 0.00 0.00 3.55
2776 3140 2.039746 ACAGTAATGCCTGCCTGTGTTA 59.960 45.455 0.00 0.00 36.82 2.41
2778 3142 0.401738 ACAGTAATGCCTGCCTGTGT 59.598 50.000 0.00 0.00 36.82 3.72
2779 3143 1.089920 GACAGTAATGCCTGCCTGTG 58.910 55.000 3.94 0.00 38.23 3.66
2780 3144 0.692476 TGACAGTAATGCCTGCCTGT 59.308 50.000 0.00 0.00 40.67 4.00
2781 3145 1.376543 CTGACAGTAATGCCTGCCTG 58.623 55.000 0.00 0.00 35.83 4.85
2782 3146 0.393537 GCTGACAGTAATGCCTGCCT 60.394 55.000 3.99 0.00 35.83 4.75
2783 3147 0.677731 TGCTGACAGTAATGCCTGCC 60.678 55.000 5.95 0.00 35.83 4.85
2784 3148 0.731417 CTGCTGACAGTAATGCCTGC 59.269 55.000 3.99 1.57 39.22 4.85
2807 3171 3.470888 GGCCCTCGCTAAGCTCCA 61.471 66.667 0.00 0.00 34.44 3.86
2861 3225 3.372440 AGAGTTGAGGGGGCTAATTTG 57.628 47.619 0.00 0.00 0.00 2.32
2891 3255 3.254166 CGATTCAAGATGGGGCTAAATGG 59.746 47.826 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.