Multiple sequence alignment - TraesCS5A01G249400

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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 TraesCS5A01G249400 chr5A 100.000 3188 0 0 1 3188 464178215 464175028 0.000000e+00 5888.0
1 TraesCS5A01G249400 chr5A 83.367 2471 338 36 49 2505 464160697 464158286 0.000000e+00 2218.0
2 TraesCS5A01G249400 chr5A 80.527 1176 221 5 1011 2185 474928644 474929812 0.000000e+00 896.0
3 TraesCS5A01G249400 chr5D 93.849 1837 103 5 670 2503 362887119 362885290 0.000000e+00 2758.0
4 TraesCS5A01G249400 chr5D 89.886 1493 140 11 1015 2503 362869069 362867584 0.000000e+00 1910.0
5 TraesCS5A01G249400 chr5D 96.499 657 23 0 1 657 362887762 362887106 0.000000e+00 1086.0
6 TraesCS5A01G249400 chr5D 81.224 1209 202 16 1014 2211 362969322 362968128 0.000000e+00 952.0
7 TraesCS5A01G249400 chr5D 89.419 671 53 7 2521 3188 362884912 362884257 0.000000e+00 830.0
8 TraesCS5A01G249400 chr5D 83.866 719 64 33 2503 3188 362867093 362866394 3.470000e-179 638.0
9 TraesCS5A01G249400 chr5B 83.273 2475 329 48 49 2503 429069142 429066733 0.000000e+00 2198.0
10 TraesCS5A01G249400 chr5B 90.577 1560 133 8 928 2482 429094503 429092953 0.000000e+00 2054.0
11 TraesCS5A01G249400 chr5B 87.518 1378 166 5 1130 2505 429177628 429176255 0.000000e+00 1587.0
12 TraesCS5A01G249400 chr5B 86.975 691 53 18 2502 3188 429092510 429091853 0.000000e+00 743.0
13 TraesCS5A01G249400 chr5B 92.308 104 7 1 2502 2605 429175885 429175783 2.560000e-31 147.0
14 TraesCS5A01G249400 chr5B 90.291 103 9 1 2503 2605 429066356 429066255 2.000000e-27 134.0
15 TraesCS5A01G249400 chr7B 89.130 92 4 5 2772 2861 506228135 506228222 3.360000e-20 110.0
16 TraesCS5A01G249400 chr3B 79.874 159 20 11 2702 2857 4499065 4499214 4.350000e-19 106.0
17 TraesCS5A01G249400 chr6B 83.838 99 16 0 2876 2974 66737906 66738004 9.410000e-16 95.3
18 TraesCS5A01G249400 chr2B 87.719 57 7 0 373 429 793972432 793972488 2.050000e-07 67.6
19 TraesCS5A01G249400 chr1B 80.220 91 9 8 2590 2674 623457203 623457116 3.430000e-05 60.2


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 TraesCS5A01G249400 chr5A 464175028 464178215 3187 True 5888.0 5888 100.000000 1 3188 1 chr5A.!!$R2 3187
1 TraesCS5A01G249400 chr5A 464158286 464160697 2411 True 2218.0 2218 83.367000 49 2505 1 chr5A.!!$R1 2456
2 TraesCS5A01G249400 chr5A 474928644 474929812 1168 False 896.0 896 80.527000 1011 2185 1 chr5A.!!$F1 1174
3 TraesCS5A01G249400 chr5D 362884257 362887762 3505 True 1558.0 2758 93.255667 1 3188 3 chr5D.!!$R3 3187
4 TraesCS5A01G249400 chr5D 362866394 362869069 2675 True 1274.0 1910 86.876000 1015 3188 2 chr5D.!!$R2 2173
5 TraesCS5A01G249400 chr5D 362968128 362969322 1194 True 952.0 952 81.224000 1014 2211 1 chr5D.!!$R1 1197
6 TraesCS5A01G249400 chr5B 429091853 429094503 2650 True 1398.5 2054 88.776000 928 3188 2 chr5B.!!$R2 2260
7 TraesCS5A01G249400 chr5B 429066255 429069142 2887 True 1166.0 2198 86.782000 49 2605 2 chr5B.!!$R1 2556
8 TraesCS5A01G249400 chr5B 429175783 429177628 1845 True 867.0 1587 89.913000 1130 2605 2 chr5B.!!$R3 1475


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
592 604 1.376424 CTGCGGCTCTGGAATGTGT 60.376 57.895 0.0 0.0 0.00 3.72 F
1425 1447 1.134220 TGTTGCCTCGAAGTGGAAGTT 60.134 47.619 0.0 0.0 45.27 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 1866 1.831106 TCGCTAGGCTCTTTTCATGGA 59.169 47.619 0.0 0.0 0.0 3.41 R
3016 3685 5.681337 TCGTATTCATGTGCTTTTTGTCA 57.319 34.783 0.0 0.0 0.0 3.58 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
121 122 3.955771 TTTCGACCAAAGCTACAACAC 57.044 42.857 0.00 0.00 0.00 3.32
175 176 5.827797 GCTACATGGTATTGATGGAAAAGGA 59.172 40.000 0.00 0.00 0.00 3.36
226 229 4.094294 CGAATCCACGGTGTTTTATGATGT 59.906 41.667 7.45 0.00 0.00 3.06
317 320 1.893544 ACATGAGCTCCTATGCATGC 58.106 50.000 11.82 11.82 41.25 4.06
376 379 3.127533 GCCAGGTTACCGCTGCAG 61.128 66.667 10.11 10.11 0.00 4.41
592 604 1.376424 CTGCGGCTCTGGAATGTGT 60.376 57.895 0.00 0.00 0.00 3.72
698 710 3.306019 GGCAATTGTCAATCCCGTTTTCT 60.306 43.478 4.85 0.00 0.00 2.52
1125 1141 1.469940 CGAGACTACTTTCGGCAGCAT 60.470 52.381 0.00 0.00 33.39 3.79
1182 1198 9.558396 TCAAAGCAAGGTATTTCATTCAAAATT 57.442 25.926 0.00 0.00 31.50 1.82
1425 1447 1.134220 TGTTGCCTCGAAGTGGAAGTT 60.134 47.619 0.00 0.00 45.27 2.66
1699 1721 9.500785 TTGATAAGTCACAATTCATCACACTTA 57.499 29.630 0.00 0.00 33.11 2.24
1815 1837 1.203994 GAGCTACTCACGGGCAAGTTA 59.796 52.381 0.00 0.00 0.00 2.24
1818 1840 1.549170 CTACTCACGGGCAAGTTACCT 59.451 52.381 0.00 0.00 0.00 3.08
1844 1866 3.433306 TTTCAATCCGGATGTCCTTGT 57.567 42.857 19.95 0.00 0.00 3.16
1851 1873 1.065491 CCGGATGTCCTTGTCCATGAA 60.065 52.381 0.00 0.00 34.05 2.57
1861 1883 3.944015 CCTTGTCCATGAAAAGAGCCTAG 59.056 47.826 0.00 0.00 28.86 3.02
1986 2008 2.193447 CTAGCGATGCGTTGCTTAGAA 58.807 47.619 25.46 7.06 42.59 2.10
2025 2047 2.636830 CCATCGATGAAGGAAGTTGCT 58.363 47.619 26.86 0.00 0.00 3.91
2028 2050 3.401033 TCGATGAAGGAAGTTGCTGAA 57.599 42.857 0.00 0.00 0.00 3.02
2105 2133 3.205784 AGAGATGGAATGCCTACTTGC 57.794 47.619 0.00 0.00 34.31 4.01
2185 2213 6.613153 AGAAGGAAGCTGTTAATAGTCTGT 57.387 37.500 0.90 0.00 0.00 3.41
2378 2407 8.416329 GGTTATGTATCTTCTGGAAAAATGCAT 58.584 33.333 0.00 0.00 0.00 3.96
2454 2483 7.701539 TGATTTAGTGTGGTAAATGCTTGAT 57.298 32.000 0.00 0.00 33.60 2.57
2459 2488 8.574251 TTAGTGTGGTAAATGCTTGATACATT 57.426 30.769 0.00 0.00 39.38 2.71
2460 2489 6.855836 AGTGTGGTAAATGCTTGATACATTG 58.144 36.000 0.00 0.00 37.78 2.82
2495 2571 7.862741 TGTATTATATTACCAGTCTTTCGCG 57.137 36.000 0.00 0.00 0.00 5.87
2637 3280 2.238245 GCACAAAGCAGACATCGAAG 57.762 50.000 0.00 0.00 44.79 3.79
2845 3512 8.462811 GTGTATGAGAAGAAAGTAGACATCAGA 58.537 37.037 0.00 0.00 0.00 3.27
2848 3515 6.382608 TGAGAAGAAAGTAGACATCAGAACG 58.617 40.000 0.00 0.00 0.00 3.95
3030 3699 6.073657 CCGATGAAAATTGACAAAAAGCACAT 60.074 34.615 0.00 0.00 0.00 3.21
3048 3717 5.088739 GCACATGAATACGAAGAAAACCAG 58.911 41.667 0.00 0.00 0.00 4.00
3050 3719 6.128391 GCACATGAATACGAAGAAAACCAGTA 60.128 38.462 0.00 0.00 0.00 2.74
3051 3720 7.572353 GCACATGAATACGAAGAAAACCAGTAA 60.572 37.037 0.00 0.00 0.00 2.24
3052 3721 8.286800 CACATGAATACGAAGAAAACCAGTAAA 58.713 33.333 0.00 0.00 0.00 2.01
3053 3722 8.842280 ACATGAATACGAAGAAAACCAGTAAAA 58.158 29.630 0.00 0.00 0.00 1.52
3054 3723 9.672086 CATGAATACGAAGAAAACCAGTAAAAA 57.328 29.630 0.00 0.00 0.00 1.94
3055 3724 9.673454 ATGAATACGAAGAAAACCAGTAAAAAC 57.327 29.630 0.00 0.00 0.00 2.43
3056 3725 8.130469 TGAATACGAAGAAAACCAGTAAAAACC 58.870 33.333 0.00 0.00 0.00 3.27
3057 3726 5.900865 ACGAAGAAAACCAGTAAAAACCA 57.099 34.783 0.00 0.00 0.00 3.67
3058 3727 6.270156 ACGAAGAAAACCAGTAAAAACCAA 57.730 33.333 0.00 0.00 0.00 3.67
3059 3728 6.689554 ACGAAGAAAACCAGTAAAAACCAAA 58.310 32.000 0.00 0.00 0.00 3.28
3080 3757 9.508642 ACCAAAAGAGAAAAACAAATAAAACCA 57.491 25.926 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 3.304659 GCTGTAATGCCATATTTCCGTGG 60.305 47.826 0.00 0.00 38.55 4.94
175 176 0.179018 AGTGCGGAAGTTGAAAGCCT 60.179 50.000 0.00 0.00 0.00 4.58
277 280 0.436531 CTTCTGAGCTTCGTCGCAAC 59.563 55.000 0.00 0.00 0.00 4.17
376 379 0.387929 TTCGTATCCATCGGAGCACC 59.612 55.000 0.00 0.00 34.05 5.01
535 547 2.285256 GCACTCGTCAATATCTGCAACG 60.285 50.000 0.00 0.00 34.80 4.10
592 604 2.410322 AATGCCCTGCCGTGTTCTCA 62.410 55.000 0.00 0.00 0.00 3.27
656 668 4.580995 TGCCATTAGTCTTCGGTTCAAAAA 59.419 37.500 0.00 0.00 0.00 1.94
657 669 4.138290 TGCCATTAGTCTTCGGTTCAAAA 58.862 39.130 0.00 0.00 0.00 2.44
658 670 3.745799 TGCCATTAGTCTTCGGTTCAAA 58.254 40.909 0.00 0.00 0.00 2.69
659 671 3.410631 TGCCATTAGTCTTCGGTTCAA 57.589 42.857 0.00 0.00 0.00 2.69
660 672 3.410631 TTGCCATTAGTCTTCGGTTCA 57.589 42.857 0.00 0.00 0.00 3.18
661 673 4.156008 ACAATTGCCATTAGTCTTCGGTTC 59.844 41.667 5.05 0.00 0.00 3.62
662 674 4.079253 ACAATTGCCATTAGTCTTCGGTT 58.921 39.130 5.05 0.00 0.00 4.44
663 675 3.686016 ACAATTGCCATTAGTCTTCGGT 58.314 40.909 5.05 0.00 0.00 4.69
664 676 3.689161 TGACAATTGCCATTAGTCTTCGG 59.311 43.478 5.05 0.00 0.00 4.30
665 677 4.944962 TGACAATTGCCATTAGTCTTCG 57.055 40.909 5.05 0.00 0.00 3.79
666 678 6.268566 GGATTGACAATTGCCATTAGTCTTC 58.731 40.000 5.05 0.00 0.00 2.87
667 679 5.127682 GGGATTGACAATTGCCATTAGTCTT 59.872 40.000 5.05 0.00 0.00 3.01
668 680 4.646492 GGGATTGACAATTGCCATTAGTCT 59.354 41.667 5.05 0.00 0.00 3.24
669 681 4.498009 CGGGATTGACAATTGCCATTAGTC 60.498 45.833 5.05 0.00 0.00 2.59
670 682 3.381272 CGGGATTGACAATTGCCATTAGT 59.619 43.478 5.05 0.00 0.00 2.24
671 683 3.381272 ACGGGATTGACAATTGCCATTAG 59.619 43.478 5.05 0.00 0.00 1.73
672 684 3.360867 ACGGGATTGACAATTGCCATTA 58.639 40.909 5.05 0.00 0.00 1.90
673 685 2.178580 ACGGGATTGACAATTGCCATT 58.821 42.857 5.05 0.00 0.00 3.16
759 771 9.212641 CAGATGTCCGAATAATCATTCATAAGT 57.787 33.333 0.00 0.00 40.61 2.24
774 786 4.884668 AAGTTTCCTACAGATGTCCGAA 57.115 40.909 0.00 0.00 0.00 4.30
1061 1077 2.550180 CTCTCTTGGATCATGCATGCAG 59.450 50.000 26.69 17.32 33.73 4.41
1125 1141 8.033178 TCTCATCAAATAATATCAGACCACCA 57.967 34.615 0.00 0.00 0.00 4.17
1182 1198 4.342951 TCCTGTAGTTCTTCTTCCGTGAAA 59.657 41.667 0.00 0.00 0.00 2.69
1425 1447 5.077564 ACGAACTCATATACTAGCATGGGA 58.922 41.667 6.48 0.00 0.00 4.37
1669 1691 9.012161 TGTGATGAATTGTGACTTATCAATTGA 57.988 29.630 11.26 11.26 42.05 2.57
1673 1695 7.984422 AGTGTGATGAATTGTGACTTATCAA 57.016 32.000 0.00 0.00 36.31 2.57
1699 1721 3.464111 GTACCCGCAAGTACCATGTAT 57.536 47.619 2.53 0.00 37.27 2.29
1815 1837 6.127451 GGACATCCGGATTGAAATTAAAAGGT 60.127 38.462 16.19 4.41 0.00 3.50
1818 1840 7.039363 ACAAGGACATCCGGATTGAAATTAAAA 60.039 33.333 16.19 0.00 42.08 1.52
1844 1866 1.831106 TCGCTAGGCTCTTTTCATGGA 59.169 47.619 0.00 0.00 0.00 3.41
1851 1873 3.550437 AACATCATCGCTAGGCTCTTT 57.450 42.857 0.00 0.00 0.00 2.52
1861 1883 4.747540 TGGCATACATAAACATCATCGC 57.252 40.909 0.00 0.00 0.00 4.58
1986 2008 2.224992 TGGCCTATTGTCACCACACATT 60.225 45.455 3.32 0.00 29.76 2.71
2025 2047 5.745312 TCCTCAGACTATCAAGCTTTTCA 57.255 39.130 0.00 0.00 0.00 2.69
2028 2050 4.534103 ACCTTCCTCAGACTATCAAGCTTT 59.466 41.667 0.00 0.00 0.00 3.51
2083 2111 3.314635 GCAAGTAGGCATTCCATCTCTTG 59.685 47.826 0.00 0.00 34.40 3.02
2105 2133 4.227134 CCACCGATGAGGGCTCCG 62.227 72.222 0.00 0.00 46.96 4.63
2185 2213 5.674569 GCGTGATTACTTAACGACCTGACTA 60.675 44.000 0.00 0.00 39.64 2.59
2292 2321 9.124807 GCAAAATGAACAGTAACATAAAGGTAC 57.875 33.333 0.00 0.00 40.88 3.34
2412 2441 8.755018 ACTAAATCAAATTTGAAAAGCGAACTG 58.245 29.630 23.91 9.04 41.13 3.16
2477 2506 6.730960 TTTTTCGCGAAAGACTGGTAATAT 57.269 33.333 30.60 0.00 0.00 1.28
3016 3685 5.681337 TCGTATTCATGTGCTTTTTGTCA 57.319 34.783 0.00 0.00 0.00 3.58
3030 3699 8.130469 GGTTTTTACTGGTTTTCTTCGTATTCA 58.870 33.333 0.00 0.00 0.00 2.57
3054 3723 9.508642 TGGTTTTATTTGTTTTTCTCTTTTGGT 57.491 25.926 0.00 0.00 0.00 3.67



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

AutoCloner maintained by Alex Coulton.