Multiple sequence alignment - TraesCS5B01G285900

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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 TraesCS5B01G285900 chr5B 100.000 3385 0 0 1 3385 471305622 471309006 0.000000e+00 6252
1 TraesCS5B01G285900 chr5D 93.711 2894 116 23 31 2914 391047958 391050795 0.000000e+00 4276
2 TraesCS5B01G285900 chr5D 95.643 482 16 5 2908 3385 391051598 391052078 0.000000e+00 769
3 TraesCS5B01G285900 chr5D 86.869 99 6 2 1020 1111 521494837 521494739 1.660000e-18 104
4 TraesCS5B01G285900 chr5A 95.261 2490 83 17 916 3385 494388153 494390627 0.000000e+00 3912
5 TraesCS5B01G285900 chr5A 81.702 705 55 30 1 685 494386512 494387162 1.390000e-143 520
6 TraesCS5B01G285900 chr5A 80.663 181 15 13 968 1140 649848891 649848723 4.590000e-24 122
7 TraesCS5B01G285900 chr5A 91.954 87 1 1 732 818 494387249 494387329 2.130000e-22 117


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 TraesCS5B01G285900 chr5B 471305622 471309006 3384 False 6252.000000 6252 100.000 1 3385 1 chr5B.!!$F1 3384
1 TraesCS5B01G285900 chr5D 391047958 391052078 4120 False 2522.500000 4276 94.677 31 3385 2 chr5D.!!$F1 3354
2 TraesCS5B01G285900 chr5A 494386512 494390627 4115 False 1516.333333 3912 89.639 1 3385 3 chr5A.!!$F1 3384

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
901 1746 0.251787 GCACCTCCCCCAAATCTGTT 60.252 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
2526 3386 0.950836 CACTCCCATTTGTCGTTGCA 59.049 50.0 0.0 0.0 0.0 4.08 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
48 49 5.697473 TTTGCCTGAATGATGAAACGTAA 57.303 34.783 0.00 0.00 0.00 3.18
131 141 0.666274 TTTGTACTGAGCAGCGACGG 60.666 55.000 0.00 0.00 0.00 4.79
180 190 1.276421 CTTGGGTGCTGTAGCTGTAGT 59.724 52.381 5.38 0.00 42.66 2.73
196 206 4.500887 GCTGTAGTTACTGTTCTGTGGTCA 60.501 45.833 0.00 0.00 0.00 4.02
428 461 3.077359 ACTGTAGCAGTTCATTCCTTGC 58.923 45.455 0.00 0.00 42.59 4.01
472 505 2.987547 GTGGTCACGTCTCCCGGA 60.988 66.667 0.73 0.00 42.24 5.14
511 544 1.102978 CCTCCGGCCGATGAAATTTT 58.897 50.000 30.73 0.00 0.00 1.82
520 553 3.609409 GCCGATGAAATTTTATCCGGAGC 60.609 47.826 24.43 15.99 0.00 4.70
525 561 3.372822 TGAAATTTTATCCGGAGCACGTC 59.627 43.478 11.34 1.86 42.24 4.34
597 633 1.366030 GTGTTTGTGCGACACGACG 60.366 57.895 0.00 0.00 38.15 5.12
660 696 3.245284 GCTTCGCATCGTTAGCTTGATAA 59.755 43.478 0.00 0.00 34.71 1.75
662 698 4.772046 TCGCATCGTTAGCTTGATAAAC 57.228 40.909 0.00 0.00 0.00 2.01
663 699 3.242016 TCGCATCGTTAGCTTGATAAACG 59.758 43.478 11.56 11.56 45.46 3.60
673 710 7.515371 CGTTAGCTTGATAAACGAAAGAGATCC 60.515 40.741 12.27 0.00 46.66 3.36
685 722 6.574350 ACGAAAGAGATCCATAACGAAATCT 58.426 36.000 0.00 0.00 0.00 2.40
686 723 7.713750 ACGAAAGAGATCCATAACGAAATCTA 58.286 34.615 0.00 0.00 0.00 1.98
687 724 8.195436 ACGAAAGAGATCCATAACGAAATCTAA 58.805 33.333 0.00 0.00 0.00 2.10
688 725 8.695284 CGAAAGAGATCCATAACGAAATCTAAG 58.305 37.037 0.00 0.00 0.00 2.18
689 726 9.535878 GAAAGAGATCCATAACGAAATCTAAGT 57.464 33.333 0.00 0.00 0.00 2.24
692 729 9.357161 AGAGATCCATAACGAAATCTAAGTAGT 57.643 33.333 0.00 0.00 0.00 2.73
698 735 9.591404 CCATAACGAAATCTAAGTAGTAGTACG 57.409 37.037 2.04 0.00 33.97 3.67
704 741 9.708222 CGAAATCTAAGTAGTAGTACGCTAAAA 57.292 33.333 2.04 0.00 33.97 1.52
866 1711 7.623268 ATCAAAACTAACACAAATTCGAAGC 57.377 32.000 3.35 0.00 0.00 3.86
899 1744 0.682209 CAGCACCTCCCCCAAATCTG 60.682 60.000 0.00 0.00 0.00 2.90
901 1746 0.251787 GCACCTCCCCCAAATCTGTT 60.252 55.000 0.00 0.00 0.00 3.16
1281 2138 1.611519 CTCCGCCTACTTCTCCTAGG 58.388 60.000 0.82 0.82 34.81 3.02
1397 2254 1.138859 CTGGTAGCACATCGGGATCAA 59.861 52.381 0.00 0.00 0.00 2.57
1398 2255 1.138859 TGGTAGCACATCGGGATCAAG 59.861 52.381 0.00 0.00 0.00 3.02
1399 2256 1.221414 GTAGCACATCGGGATCAAGC 58.779 55.000 0.00 0.00 0.00 4.01
1400 2257 0.829990 TAGCACATCGGGATCAAGCA 59.170 50.000 0.00 0.00 0.00 3.91
1417 2274 2.041153 CAGGGGTTGTTGGAAGCAC 58.959 57.895 0.00 0.00 0.00 4.40
1472 2329 8.539544 TCTGGACTTTGTGTGAATGATATAAGA 58.460 33.333 0.00 0.00 0.00 2.10
1659 2518 1.340017 TGTGCCTGTATTTCCTCCTGC 60.340 52.381 0.00 0.00 0.00 4.85
1693 2552 3.287312 TGTGCTTATTTTCACAGCTGC 57.713 42.857 15.27 0.00 38.18 5.25
1717 2576 7.176515 TGCAGTTATATCAAATGGTCTGTTTGT 59.823 33.333 0.00 0.00 37.70 2.83
1815 2674 6.206438 TGCACTGCTGATCTGTTATGTTTTTA 59.794 34.615 1.98 0.00 0.00 1.52
2053 2912 0.172803 CCCCACTAGTACAGCGTGTC 59.827 60.000 0.00 0.00 0.00 3.67
2157 3016 1.143481 CATGGACATCAGGGTATGCCA 59.857 52.381 1.04 0.00 37.41 4.92
2204 3063 1.340889 TGCACAAATGAAAGGTGAGCC 59.659 47.619 0.00 0.00 34.52 4.70
2300 3160 2.952978 TGGTTGGTACGTTGCTGATTTT 59.047 40.909 0.00 0.00 0.00 1.82
2301 3161 4.135306 TGGTTGGTACGTTGCTGATTTTA 58.865 39.130 0.00 0.00 0.00 1.52
2302 3162 4.579340 TGGTTGGTACGTTGCTGATTTTAA 59.421 37.500 0.00 0.00 0.00 1.52
2481 3341 8.231837 TGTATTTTGTTCGTTATTTAGCAGTCC 58.768 33.333 0.00 0.00 0.00 3.85
2491 3351 7.330208 TCGTTATTTAGCAGTCCTTCTGTAAAC 59.670 37.037 0.00 0.00 45.23 2.01
2526 3386 6.645790 AGAAATTTGAAGTGCTGATGAGTT 57.354 33.333 0.00 0.00 0.00 3.01
2572 3432 7.886629 TTCCATTTATGCAAAGAGAAGCTAT 57.113 32.000 0.00 0.00 0.00 2.97
2595 3455 4.577283 TGGTTAGTTAGTGTTGTTTGAGCC 59.423 41.667 0.00 0.00 0.00 4.70
2614 3474 3.947834 AGCCAGTATCACAATGTTTAGGC 59.052 43.478 0.00 0.00 38.65 3.93
2637 3497 8.489489 AGGCATCTTGAATCTGAATAGTAGAAA 58.511 33.333 0.00 0.00 0.00 2.52
2648 3508 8.277490 TCTGAATAGTAGAAAGCTAAACGAGA 57.723 34.615 0.00 0.00 0.00 4.04
2769 3629 7.349598 AGTTTGCAGATATATTTCCTTGGACT 58.650 34.615 0.00 0.00 0.00 3.85
2774 3634 8.494433 TGCAGATATATTTCCTTGGACTAGTTT 58.506 33.333 0.00 0.00 0.00 2.66
2845 3705 4.755266 ATGGTATTGGAGTACACCAGAC 57.245 45.455 12.03 13.38 43.94 3.51
2846 3706 2.835764 TGGTATTGGAGTACACCAGACC 59.164 50.000 25.80 25.80 42.78 3.85
2847 3707 2.835764 GGTATTGGAGTACACCAGACCA 59.164 50.000 26.77 10.91 42.39 4.02
2848 3708 3.118738 GGTATTGGAGTACACCAGACCAG 60.119 52.174 26.77 0.00 42.39 4.00
2849 3709 2.391926 TTGGAGTACACCAGACCAGA 57.608 50.000 12.03 0.00 41.19 3.86
2892 3752 1.775385 TATGTCCTGATCTGTCGCCA 58.225 50.000 0.00 0.00 0.00 5.69
2906 3766 1.593750 CGCCAGCCTCTACTCATGC 60.594 63.158 0.00 0.00 0.00 4.06
2908 3768 1.694133 GCCAGCCTCTACTCATGCCT 61.694 60.000 0.00 0.00 0.00 4.75
2991 4663 7.849804 TTCTTTCTCATATGTTAGCAGAACC 57.150 36.000 1.90 0.00 0.00 3.62
3291 4969 9.851686 TGTATATTTTCCTTGCACTAATCTGAT 57.148 29.630 0.00 0.00 0.00 2.90
3318 4997 0.677288 TGCTGCAGCTTGAGCAAAAT 59.323 45.000 36.61 0.00 42.22 1.82
3319 4998 1.069513 TGCTGCAGCTTGAGCAAAATT 59.930 42.857 36.61 0.00 42.22 1.82
3320 4999 2.140717 GCTGCAGCTTGAGCAAAATTT 58.859 42.857 31.33 0.00 45.16 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.604604 GCAAAAGTGGCCTCACAGTA 58.395 50.000 3.32 0.00 45.91 2.74
96 106 8.251750 TCAGTACAAAAGTTCAAATAGATCCG 57.748 34.615 0.00 0.00 0.00 4.18
180 190 4.498513 CGTACACTGACCACAGAACAGTAA 60.499 45.833 0.00 0.00 46.03 2.24
309 329 3.941188 AGGTGACAGTGTGCCGGG 61.941 66.667 2.18 0.00 0.00 5.73
472 505 1.384989 CCCTGTACAGCGATCGACCT 61.385 60.000 21.57 4.05 0.00 3.85
511 544 2.125326 CCAGGACGTGCTCCGGATA 61.125 63.158 6.61 0.00 45.10 2.59
520 553 3.198068 CCATTAGTTGATCCAGGACGTG 58.802 50.000 0.00 0.00 0.00 4.49
525 561 3.474600 CAGAGCCATTAGTTGATCCAGG 58.525 50.000 0.00 0.00 0.00 4.45
589 625 3.104014 GGAAGAACTCCGTCGTGTC 57.896 57.895 0.00 0.00 33.37 3.67
597 633 2.386661 TGATTCGCTGGAAGAACTCC 57.613 50.000 0.00 0.00 45.64 3.85
660 696 7.042335 AGATTTCGTTATGGATCTCTTTCGTT 58.958 34.615 0.00 0.00 0.00 3.85
662 698 8.575565 TTAGATTTCGTTATGGATCTCTTTCG 57.424 34.615 0.00 0.00 31.71 3.46
663 699 9.535878 ACTTAGATTTCGTTATGGATCTCTTTC 57.464 33.333 0.00 0.00 31.71 2.62
673 710 9.100895 GCGTACTACTACTTAGATTTCGTTATG 57.899 37.037 0.00 0.00 0.00 1.90
685 722 7.802738 TCAACGTTTTAGCGTACTACTACTTA 58.197 34.615 0.00 0.00 45.00 2.24
686 723 6.668323 TCAACGTTTTAGCGTACTACTACTT 58.332 36.000 0.00 0.00 45.00 2.24
687 724 6.241207 TCAACGTTTTAGCGTACTACTACT 57.759 37.500 0.00 0.00 45.00 2.57
688 725 5.002934 GCTCAACGTTTTAGCGTACTACTAC 59.997 44.000 14.66 0.00 45.00 2.73
689 726 5.088739 GCTCAACGTTTTAGCGTACTACTA 58.911 41.667 14.66 0.00 45.00 1.82
690 727 3.916776 GCTCAACGTTTTAGCGTACTACT 59.083 43.478 14.66 0.00 45.00 2.57
691 728 3.916776 AGCTCAACGTTTTAGCGTACTAC 59.083 43.478 20.81 0.69 45.00 2.73
692 729 3.916172 CAGCTCAACGTTTTAGCGTACTA 59.084 43.478 20.81 0.00 45.00 1.82
698 735 4.985044 TTAGACAGCTCAACGTTTTAGC 57.015 40.909 19.90 19.90 36.48 3.09
704 741 7.656137 TCTTTTTAGATTTAGACAGCTCAACGT 59.344 33.333 0.00 0.00 0.00 3.99
844 1689 5.607359 GCGCTTCGAATTTGTGTTAGTTTTG 60.607 40.000 0.00 0.00 0.00 2.44
881 1726 1.142688 ACAGATTTGGGGGAGGTGCT 61.143 55.000 0.00 0.00 0.00 4.40
882 1727 0.251787 AACAGATTTGGGGGAGGTGC 60.252 55.000 0.00 0.00 0.00 5.01
883 1728 2.309136 AAACAGATTTGGGGGAGGTG 57.691 50.000 0.00 0.00 0.00 4.00
884 1729 3.344535 AAAAACAGATTTGGGGGAGGT 57.655 42.857 0.00 0.00 0.00 3.85
909 1754 1.272704 GCAGATTTGGGGGAGAAACCT 60.273 52.381 0.00 0.00 38.98 3.50
910 1755 1.186200 GCAGATTTGGGGGAGAAACC 58.814 55.000 0.00 0.00 38.08 3.27
912 1757 1.710244 TCAGCAGATTTGGGGGAGAAA 59.290 47.619 0.00 0.00 0.00 2.52
913 1758 1.371467 TCAGCAGATTTGGGGGAGAA 58.629 50.000 0.00 0.00 0.00 2.87
914 1759 1.283029 CTTCAGCAGATTTGGGGGAGA 59.717 52.381 0.00 0.00 0.00 3.71
1030 1878 1.137825 GCTCGCAGTACTCGAAGCT 59.862 57.895 15.11 0.00 35.38 3.74
1281 2138 2.125512 CTAGGTGTGCAGGGACGC 60.126 66.667 0.00 0.00 0.00 5.19
1397 2254 1.531602 GCTTCCAACAACCCCTGCT 60.532 57.895 0.00 0.00 0.00 4.24
1398 2255 1.832167 TGCTTCCAACAACCCCTGC 60.832 57.895 0.00 0.00 0.00 4.85
1399 2256 0.754957 TGTGCTTCCAACAACCCCTG 60.755 55.000 0.00 0.00 0.00 4.45
1400 2257 0.468029 CTGTGCTTCCAACAACCCCT 60.468 55.000 0.00 0.00 0.00 4.79
1815 2674 3.529319 AGCCCTTCTCCCACTGAAATTAT 59.471 43.478 0.00 0.00 0.00 1.28
2157 3016 5.526111 AGCACTATGAAACACGTTTGTACTT 59.474 36.000 0.00 0.00 33.55 2.24
2204 3063 7.102346 AGATCAGTGAGAATTTCAACACTAGG 58.898 38.462 20.48 13.62 40.84 3.02
2300 3160 4.919774 TTGAGCACCTGTAAAGGGATTA 57.080 40.909 3.35 0.00 0.00 1.75
2301 3161 3.806949 TTGAGCACCTGTAAAGGGATT 57.193 42.857 3.35 0.00 0.00 3.01
2302 3162 3.525199 AGATTGAGCACCTGTAAAGGGAT 59.475 43.478 3.35 0.00 0.00 3.85
2381 3241 4.535781 ACATGGGTGTGTGCACATATTAT 58.464 39.130 24.69 12.75 46.95 1.28
2481 3341 8.833231 TTCTTAGTGGATCTTGTTTACAGAAG 57.167 34.615 0.00 0.00 0.00 2.85
2491 3351 7.540055 GCACTTCAAATTTCTTAGTGGATCTTG 59.460 37.037 18.32 0.00 37.33 3.02
2526 3386 0.950836 CACTCCCATTTGTCGTTGCA 59.049 50.000 0.00 0.00 0.00 4.08
2572 3432 4.577283 GGCTCAAACAACACTAACTAACCA 59.423 41.667 0.00 0.00 0.00 3.67
2595 3455 6.932356 AGATGCCTAAACATTGTGATACTG 57.068 37.500 0.00 0.00 0.00 2.74
2614 3474 9.545105 AGCTTTCTACTATTCAGATTCAAGATG 57.455 33.333 0.00 0.00 0.00 2.90
2637 3497 3.321111 TGACAACTTCCTCTCGTTTAGCT 59.679 43.478 0.00 0.00 0.00 3.32
2845 3705 2.398252 AGCACATCTGACATGTCTGG 57.602 50.000 26.61 18.90 0.00 3.86
2846 3706 7.543947 TTTAATAGCACATCTGACATGTCTG 57.456 36.000 25.55 24.12 0.00 3.51
2847 3707 8.743085 AATTTAATAGCACATCTGACATGTCT 57.257 30.769 25.55 3.73 0.00 3.41
2892 3752 1.484240 GTGAAGGCATGAGTAGAGGCT 59.516 52.381 0.00 0.00 40.14 4.58
2906 3766 1.302511 CACCGGGGAACAGTGAAGG 60.303 63.158 6.32 0.00 38.12 3.46
2908 3768 1.052124 AGACACCGGGGAACAGTGAA 61.052 55.000 12.96 0.00 38.93 3.18
3199 4877 2.449518 TGGCCCTGTTGGACCTGA 60.450 61.111 0.00 0.00 44.34 3.86
3291 4969 3.386486 CTCAAGCTGCAGCATTTTCAAA 58.614 40.909 38.24 14.47 45.16 2.69
3331 5011 6.748333 TGCATGGACTGAGAAAGAATTAAG 57.252 37.500 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.