Multiple sequence alignment - TraesCS2D01G271700

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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 TraesCS2D01G271700 chr2D 100.000 2771 0 0 1 2771 335409324 335412094 0.000000e+00 5118
1 TraesCS2D01G271700 chr2D 82.514 183 32 0 2432 2614 285340709 285340527 7.940000e-36 161
2 TraesCS2D01G271700 chr2A 93.566 2378 87 29 1 2343 445997203 445999549 0.000000e+00 3483
3 TraesCS2D01G271700 chr2A 86.600 403 44 4 2367 2768 445999542 445999935 1.180000e-118 436
4 TraesCS2D01G271700 chr2B 96.184 1520 26 9 505 2003 403556451 403557959 0.000000e+00 2457
5 TraesCS2D01G271700 chr2B 91.691 337 19 4 2067 2395 403557959 403558294 2.510000e-125 459
6 TraesCS2D01G271700 chr2B 87.234 376 42 4 1 376 403555760 403556129 9.170000e-115 424
7 TraesCS2D01G271700 chr2B 96.667 150 5 0 374 523 403556290 403556439 1.650000e-62 250
8 TraesCS2D01G271700 chr1B 87.395 357 43 2 2417 2771 355158769 355159125 2.570000e-110 409


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 TraesCS2D01G271700 chr2D 335409324 335412094 2770 False 5118.0 5118 100.000 1 2771 1 chr2D.!!$F1 2770
1 TraesCS2D01G271700 chr2A 445997203 445999935 2732 False 1959.5 3483 90.083 1 2768 2 chr2A.!!$F1 2767
2 TraesCS2D01G271700 chr2B 403555760 403558294 2534 False 897.5 2457 92.944 1 2395 4 chr2B.!!$F1 2394

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
656 854 0.100682 GAATCATGGCACTGCAGCAG 59.899 55.0 21.54 21.54 37.52 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2557 2797 0.931005 GAACTGATTCGGGTGATCGC 59.069 55.0 0.0 0.0 0.0 4.58 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
26 27 4.138290 TCTATGAACATCTCCGAGAGACC 58.862 47.826 4.07 0.00 41.76 3.85
30 31 0.464735 ACATCTCCGAGAGACCGAGG 60.465 60.000 4.07 0.00 41.76 4.63
34 35 0.677098 CTCCGAGAGACCGAGGTGAA 60.677 60.000 0.00 0.00 0.00 3.18
38 39 2.623889 CCGAGAGACCGAGGTGAAATAT 59.376 50.000 0.00 0.00 0.00 1.28
86 87 1.290955 CGCTTCGTACCTTCCACCA 59.709 57.895 0.00 0.00 0.00 4.17
161 162 3.504906 GCAAAGGTTAGTACTTGAACCCC 59.495 47.826 19.66 6.64 45.33 4.95
163 164 1.904537 AGGTTAGTACTTGAACCCCGG 59.095 52.381 19.66 0.00 45.33 5.73
192 193 3.394606 AGTTCCAGTAGAAGGAAGCCAAA 59.605 43.478 0.00 0.00 45.27 3.28
193 194 4.043435 AGTTCCAGTAGAAGGAAGCCAAAT 59.957 41.667 0.00 0.00 45.27 2.32
194 195 3.955471 TCCAGTAGAAGGAAGCCAAATG 58.045 45.455 0.00 0.00 30.71 2.32
195 196 3.019564 CCAGTAGAAGGAAGCCAAATGG 58.980 50.000 0.00 0.00 38.53 3.16
292 294 5.413309 ACCTTGAAACAAAACCATGTCAA 57.587 34.783 0.00 0.00 31.81 3.18
334 336 9.521841 TGGAATTGTATTTTACAGGATTACACA 57.478 29.630 0.00 0.00 40.24 3.72
492 657 2.359214 TCATATCTGACACAGTCTCGCC 59.641 50.000 0.00 0.00 33.15 5.54
510 675 2.740714 CGTGGCAGCGGTAGAAAGC 61.741 63.158 0.00 0.00 0.00 3.51
516 711 0.674895 CAGCGGTAGAAAGCTTGCCT 60.675 55.000 0.00 3.07 42.52 4.75
654 852 0.179145 GTGAATCATGGCACTGCAGC 60.179 55.000 15.27 0.33 32.44 5.25
655 853 0.609681 TGAATCATGGCACTGCAGCA 60.610 50.000 15.27 4.00 35.83 4.41
656 854 0.100682 GAATCATGGCACTGCAGCAG 59.899 55.000 21.54 21.54 37.52 4.24
657 855 0.611062 AATCATGGCACTGCAGCAGT 60.611 50.000 23.11 23.11 46.51 4.40
679 877 0.394565 AAGCAACGGAGAGAAGTGCT 59.605 50.000 0.00 0.00 0.00 4.40
699 897 2.544685 TGTACGTAGCGTAGAGAGGAC 58.455 52.381 0.00 0.00 43.06 3.85
700 898 2.094026 TGTACGTAGCGTAGAGAGGACA 60.094 50.000 0.00 0.00 43.06 4.02
701 899 1.367659 ACGTAGCGTAGAGAGGACAC 58.632 55.000 0.00 0.00 38.73 3.67
702 900 0.656785 CGTAGCGTAGAGAGGACACC 59.343 60.000 0.00 0.00 0.00 4.16
703 901 1.747709 GTAGCGTAGAGAGGACACCA 58.252 55.000 0.00 0.00 0.00 4.17
704 902 2.089980 GTAGCGTAGAGAGGACACCAA 58.910 52.381 0.00 0.00 0.00 3.67
776 975 1.169577 GCGTCAGGTCAGAGAGAGAA 58.830 55.000 0.00 0.00 0.00 2.87
867 1072 3.625897 CCACACGCTCCACCTCCA 61.626 66.667 0.00 0.00 0.00 3.86
925 1130 6.884187 TCTACACAAAGATTCGTAGCAAAAC 58.116 36.000 0.00 0.00 33.01 2.43
926 1131 5.751243 ACACAAAGATTCGTAGCAAAACT 57.249 34.783 0.00 0.00 0.00 2.66
1558 1776 2.391724 GACCGTCAAGTCCAAGGCCA 62.392 60.000 5.01 0.00 0.00 5.36
1564 1782 3.553095 AAGTCCAAGGCCAGCGACC 62.553 63.158 5.01 0.00 0.00 4.79
2005 2231 5.221422 CCAATTTTGACTCCTTGTTTAGGCA 60.221 40.000 0.00 0.00 44.37 4.75
2007 2233 7.309744 CCAATTTTGACTCCTTGTTTAGGCATA 60.310 37.037 0.00 0.00 44.37 3.14
2008 2234 7.961326 ATTTTGACTCCTTGTTTAGGCATAT 57.039 32.000 0.00 0.00 44.37 1.78
2009 2235 9.474313 AATTTTGACTCCTTGTTTAGGCATATA 57.526 29.630 0.00 0.00 44.37 0.86
2010 2236 9.646522 ATTTTGACTCCTTGTTTAGGCATATAT 57.353 29.630 0.00 0.00 44.37 0.86
2012 2238 9.555727 TTTGACTCCTTGTTTAGGCATATATAC 57.444 33.333 0.00 0.00 44.37 1.47
2014 2240 8.934697 TGACTCCTTGTTTAGGCATATATACTT 58.065 33.333 0.00 0.00 44.37 2.24
2053 2282 0.902531 GTTCCCTCCCGATTCAGTGA 59.097 55.000 0.00 0.00 0.00 3.41
2054 2283 1.486726 GTTCCCTCCCGATTCAGTGAT 59.513 52.381 0.00 0.00 0.00 3.06
2097 2327 3.765381 TGTGTTCACCAATCCATGACAT 58.235 40.909 0.00 0.00 0.00 3.06
2177 2414 3.308438 AGAATGTGCATGCCAGTTTTC 57.692 42.857 16.68 12.66 0.00 2.29
2181 2420 3.540314 TGTGCATGCCAGTTTTCTTTT 57.460 38.095 16.68 0.00 0.00 2.27
2182 2421 3.871485 TGTGCATGCCAGTTTTCTTTTT 58.129 36.364 16.68 0.00 0.00 1.94
2222 2461 2.094182 TCAGTGCACCGGATTTCTAGAC 60.094 50.000 14.63 0.00 0.00 2.59
2296 2536 1.686052 TCCAAATGCGCCACTCTTTTT 59.314 42.857 4.18 0.00 0.00 1.94
2400 2640 7.012894 CCTCTAAGAACATCTCGAGAATGTACT 59.987 40.741 20.91 12.18 30.27 2.73
2409 2649 8.088981 ACATCTCGAGAATGTACTGTAAAAACT 58.911 33.333 20.91 0.00 0.00 2.66
2414 2654 7.811236 TCGAGAATGTACTGTAAAAACTAGTGG 59.189 37.037 0.00 0.00 0.00 4.00
2428 2668 3.310193 ACTAGTGGAGATTTAGGCCTCC 58.690 50.000 9.68 3.40 46.99 4.30
2451 2691 3.454812 ACGAATTAGATAGGGTTGGTGCT 59.545 43.478 0.00 0.00 0.00 4.40
2462 2702 3.054361 AGGGTTGGTGCTAGATTTACCTG 60.054 47.826 0.00 0.00 35.51 4.00
2472 2712 1.092348 GATTTACCTGGACCAACCGC 58.908 55.000 0.00 0.00 42.61 5.68
2499 2739 4.180946 CCGACTCGCTCCGTCCTG 62.181 72.222 0.00 0.00 0.00 3.86
2500 2740 4.180946 CGACTCGCTCCGTCCTGG 62.181 72.222 0.00 0.00 40.09 4.45
2502 2742 3.053849 GACTCGCTCCGTCCTGGAC 62.054 68.421 16.99 16.99 43.74 4.02
2503 2743 2.752238 CTCGCTCCGTCCTGGACT 60.752 66.667 23.49 0.00 43.74 3.85
2544 2784 2.502492 GGAGCTGCGATGCCCTCTA 61.502 63.158 0.00 0.00 0.00 2.43
2568 2808 4.847516 CTTCGCGCGATCACCCGA 62.848 66.667 35.21 16.03 0.00 5.14
2571 2811 3.692367 CGCGCGATCACCCGAATC 61.692 66.667 28.94 0.00 0.00 2.52
2572 2812 2.584970 GCGCGATCACCCGAATCA 60.585 61.111 12.10 0.00 0.00 2.57
2573 2813 2.589492 GCGCGATCACCCGAATCAG 61.589 63.158 12.10 0.00 0.00 2.90
2576 2816 0.931005 GCGATCACCCGAATCAGTTC 59.069 55.000 0.00 0.00 0.00 3.01
2590 2830 0.962356 CAGTTCTGACCATGTGCCCC 60.962 60.000 0.00 0.00 0.00 5.80
2595 2835 2.036256 GACCATGTGCCCCTGCTT 59.964 61.111 0.00 0.00 38.71 3.91
2621 2861 0.959372 TCTGAGAACGACCGTCCTCC 60.959 60.000 6.35 0.00 0.00 4.30
2630 2870 1.605971 GACCGTCCTCCTCAACCTCC 61.606 65.000 0.00 0.00 0.00 4.30
2631 2871 1.305381 CCGTCCTCCTCAACCTCCT 60.305 63.158 0.00 0.00 0.00 3.69
2632 2872 1.324005 CCGTCCTCCTCAACCTCCTC 61.324 65.000 0.00 0.00 0.00 3.71
2633 2873 1.658686 CGTCCTCCTCAACCTCCTCG 61.659 65.000 0.00 0.00 0.00 4.63
2638 2878 1.896465 CTCCTCAACCTCCTCGTTTCT 59.104 52.381 0.00 0.00 0.00 2.52
2662 2902 3.795688 TTGAGGAATTCTGGCTCAACT 57.204 42.857 16.87 0.09 0.00 3.16
2676 2916 2.251893 CTCAACTAGCTCGGTTTCGTC 58.748 52.381 0.00 0.00 37.69 4.20
2685 2925 2.356673 GGTTTCGTCGAGGCCGTT 60.357 61.111 0.00 0.00 37.05 4.44
2689 2929 3.672255 TTCGTCGAGGCCGTTAGCG 62.672 63.158 0.00 0.00 45.17 4.26
2739 2980 2.819550 GCCCCTTCTCGGCGATTA 59.180 61.111 11.27 0.00 36.47 1.75
2750 2991 1.066071 TCGGCGATTAACACCATCCAA 60.066 47.619 4.99 0.00 0.00 3.53
2756 2997 4.032786 GCGATTAACACCATCCAATTTTGC 59.967 41.667 0.00 0.00 0.00 3.68
2763 3004 4.183101 CACCATCCAATTTTGCGCTAAAT 58.817 39.130 21.50 21.50 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.818296 ATTTCACCTCGGTCTCTCGG 59.182 55.000 0.00 0.00 0.00 4.63
18 19 3.315470 TGATATTTCACCTCGGTCTCTCG 59.685 47.826 0.00 0.00 0.00 4.04
59 60 0.101759 GGTACGAAGCGGCTGTGATA 59.898 55.000 1.81 0.00 0.00 2.15
134 135 7.040271 GGGTTCAAGTACTAACCTTTGCAATAA 60.040 37.037 21.54 0.00 43.87 1.40
136 137 5.243060 GGGTTCAAGTACTAACCTTTGCAAT 59.757 40.000 21.54 0.00 43.87 3.56
137 138 4.581409 GGGTTCAAGTACTAACCTTTGCAA 59.419 41.667 21.54 0.00 43.87 4.08
141 142 3.244665 CCGGGGTTCAAGTACTAACCTTT 60.245 47.826 21.54 0.00 43.87 3.11
145 146 2.299867 TCACCGGGGTTCAAGTACTAAC 59.700 50.000 2.12 0.00 0.00 2.34
161 162 2.366533 TCTACTGGAACTAGCTCACCG 58.633 52.381 0.00 0.00 0.00 4.94
163 164 4.017808 TCCTTCTACTGGAACTAGCTCAC 58.982 47.826 0.00 0.00 0.00 3.51
192 193 2.158769 TCAGCGTATCTCAAATGGCCAT 60.159 45.455 14.09 14.09 0.00 4.40
193 194 1.209261 TCAGCGTATCTCAAATGGCCA 59.791 47.619 8.56 8.56 0.00 5.36
194 195 1.953559 TCAGCGTATCTCAAATGGCC 58.046 50.000 0.00 0.00 0.00 5.36
195 196 4.035558 TGAATTCAGCGTATCTCAAATGGC 59.964 41.667 3.38 0.00 0.00 4.40
208 209 4.572389 AGCCTACAAATAGTGAATTCAGCG 59.428 41.667 8.80 0.00 0.00 5.18
492 657 2.740714 GCTTTCTACCGCTGCCACG 61.741 63.158 0.00 0.00 0.00 4.94
510 675 2.719046 CGTTCGCTTTTAACAAGGCAAG 59.281 45.455 0.00 0.00 34.64 4.01
516 711 2.220593 CCGTACCGTTCGCTTTTAACAA 59.779 45.455 0.00 0.00 0.00 2.83
543 738 2.901291 AGGCCTATCTTCAGAGGGATC 58.099 52.381 1.29 0.00 33.04 3.36
654 852 0.601046 TCTCTCCGTTGCTTGCACTG 60.601 55.000 0.00 0.00 0.00 3.66
655 853 0.106708 TTCTCTCCGTTGCTTGCACT 59.893 50.000 0.00 0.00 0.00 4.40
656 854 0.514691 CTTCTCTCCGTTGCTTGCAC 59.485 55.000 0.00 0.00 0.00 4.57
657 855 0.106708 ACTTCTCTCCGTTGCTTGCA 59.893 50.000 0.00 0.00 0.00 4.08
658 856 0.514691 CACTTCTCTCCGTTGCTTGC 59.485 55.000 0.00 0.00 0.00 4.01
659 857 0.514691 GCACTTCTCTCCGTTGCTTG 59.485 55.000 0.00 0.00 0.00 4.01
679 877 2.094026 TGTCCTCTCTACGCTACGTACA 60.094 50.000 0.00 0.00 41.54 2.90
695 893 3.326880 ACGGAAATTCTACTTGGTGTCCT 59.673 43.478 0.00 0.00 0.00 3.85
696 894 3.671716 ACGGAAATTCTACTTGGTGTCC 58.328 45.455 0.00 0.00 0.00 4.02
699 897 4.680171 GGAACGGAAATTCTACTTGGTG 57.320 45.455 0.00 0.00 0.00 4.17
776 975 2.746277 GGCGAATCAGGGCGTGTT 60.746 61.111 7.12 1.21 0.00 3.32
867 1072 2.045340 CGGCGGGAAATGGGAAGT 60.045 61.111 0.00 0.00 0.00 3.01
925 1130 1.615262 GAGGTGGGGGATTTGGGAG 59.385 63.158 0.00 0.00 0.00 4.30
926 1131 1.933812 GGAGGTGGGGGATTTGGGA 60.934 63.158 0.00 0.00 0.00 4.37
1564 1782 1.153469 GAAAGAGCTCCTCCTGGCG 60.153 63.158 10.93 0.00 0.00 5.69
2005 2231 8.378565 ACAGCTGATGTAAGCCAAAGTATATAT 58.621 33.333 23.35 0.00 44.68 0.86
2007 2233 6.595682 ACAGCTGATGTAAGCCAAAGTATAT 58.404 36.000 23.35 0.00 44.68 0.86
2008 2234 5.989477 ACAGCTGATGTAAGCCAAAGTATA 58.011 37.500 23.35 0.00 44.68 1.47
2009 2235 4.848357 ACAGCTGATGTAAGCCAAAGTAT 58.152 39.130 23.35 0.00 44.68 2.12
2010 2236 4.253685 GACAGCTGATGTAAGCCAAAGTA 58.746 43.478 23.35 0.00 44.17 2.24
2011 2237 3.077359 GACAGCTGATGTAAGCCAAAGT 58.923 45.455 23.35 0.00 44.17 2.66
2012 2238 2.421424 GGACAGCTGATGTAAGCCAAAG 59.579 50.000 23.35 0.00 44.17 2.77
2014 2240 1.675714 CGGACAGCTGATGTAAGCCAA 60.676 52.381 23.35 0.00 44.17 4.52
2097 2327 2.639065 GACCGTAGCCAATCCATTTCA 58.361 47.619 0.00 0.00 0.00 2.69
2181 2420 7.574217 GCACTGAATCGGACCATTAAACTTAAA 60.574 37.037 0.00 0.00 0.00 1.52
2182 2421 6.128117 GCACTGAATCGGACCATTAAACTTAA 60.128 38.462 0.00 0.00 0.00 1.85
2183 2422 5.353123 GCACTGAATCGGACCATTAAACTTA 59.647 40.000 0.00 0.00 0.00 2.24
2204 2443 2.380084 TGTCTAGAAATCCGGTGCAC 57.620 50.000 8.80 8.80 0.00 4.57
2222 2461 3.861840 AGTGTCTCCATACAAACGGATG 58.138 45.455 0.00 0.00 0.00 3.51
2296 2536 2.523245 TGTCCATGCAAATAAGTGCCA 58.477 42.857 0.00 0.00 44.26 4.92
2400 2640 6.882678 GGCCTAAATCTCCACTAGTTTTTACA 59.117 38.462 0.00 0.00 31.19 2.41
2414 2654 2.981859 TTCGTGGAGGCCTAAATCTC 57.018 50.000 4.42 0.00 0.00 2.75
2428 2668 3.560068 GCACCAACCCTATCTAATTCGTG 59.440 47.826 0.00 0.00 0.00 4.35
2429 2669 3.454812 AGCACCAACCCTATCTAATTCGT 59.545 43.478 0.00 0.00 0.00 3.85
2430 2670 4.073293 AGCACCAACCCTATCTAATTCG 57.927 45.455 0.00 0.00 0.00 3.34
2451 2691 2.093341 GCGGTTGGTCCAGGTAAATCTA 60.093 50.000 0.00 0.00 35.57 1.98
2557 2797 0.931005 GAACTGATTCGGGTGATCGC 59.069 55.000 0.00 0.00 0.00 4.58
2558 2798 2.159240 TCAGAACTGATTCGGGTGATCG 60.159 50.000 0.00 0.00 40.04 3.69
2562 2802 1.001974 TGGTCAGAACTGATTCGGGTG 59.998 52.381 7.77 0.00 42.18 4.61
2566 2806 2.094894 GCACATGGTCAGAACTGATTCG 59.905 50.000 7.77 1.05 42.18 3.34
2568 2808 2.440409 GGCACATGGTCAGAACTGATT 58.560 47.619 7.77 0.00 42.18 2.57
2571 2811 0.962356 GGGGCACATGGTCAGAACTG 60.962 60.000 0.00 0.00 0.00 3.16
2572 2812 1.136329 AGGGGCACATGGTCAGAACT 61.136 55.000 0.00 0.00 0.00 3.01
2573 2813 0.962356 CAGGGGCACATGGTCAGAAC 60.962 60.000 0.00 0.00 0.00 3.01
2576 2816 2.753043 GCAGGGGCACATGGTCAG 60.753 66.667 1.37 0.00 40.72 3.51
2610 2850 1.935327 GAGGTTGAGGAGGACGGTCG 61.935 65.000 1.43 0.00 0.00 4.79
2621 2861 1.344763 ACCAGAAACGAGGAGGTTGAG 59.655 52.381 0.00 0.00 0.00 3.02
2630 2870 4.757149 AGAATTCCTCAAACCAGAAACGAG 59.243 41.667 0.65 0.00 0.00 4.18
2631 2871 4.515191 CAGAATTCCTCAAACCAGAAACGA 59.485 41.667 0.65 0.00 0.00 3.85
2632 2872 4.320494 CCAGAATTCCTCAAACCAGAAACG 60.320 45.833 0.65 0.00 0.00 3.60
2633 2873 4.559502 GCCAGAATTCCTCAAACCAGAAAC 60.560 45.833 0.65 0.00 0.00 2.78
2638 2878 2.108075 TGAGCCAGAATTCCTCAAACCA 59.892 45.455 9.61 0.00 33.05 3.67
2666 2906 4.409218 CGGCCTCGACGAAACCGA 62.409 66.667 25.91 0.00 46.71 4.69
2685 2925 4.077184 CTCAACCCACCGGCGCTA 62.077 66.667 7.64 0.00 0.00 4.26
2734 2975 4.265085 CGCAAAATTGGATGGTGTTAATCG 59.735 41.667 0.00 0.00 0.00 3.34
2739 2980 1.344114 AGCGCAAAATTGGATGGTGTT 59.656 42.857 11.47 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.