Multiple sequence alignment - TraesCS2A01G298700

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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 TraesCS2A01G298700 chr2A 100.000 3161 0 0 1 3161 514662935 514666095 0.000000e+00 5838.0
1 TraesCS2A01G298700 chr2A 91.678 1466 92 9 764 2220 534605463 534604019 0.000000e+00 2004.0
2 TraesCS2A01G298700 chr2A 92.049 981 62 5 852 1832 489635783 489634819 0.000000e+00 1365.0
3 TraesCS2A01G298700 chr2A 92.213 809 52 5 842 1646 196080501 196079700 0.000000e+00 1134.0
4 TraesCS2A01G298700 chr2A 92.593 297 18 4 554 849 196081585 196081292 1.050000e-114 424.0
5 TraesCS2A01G298700 chr2A 97.414 116 3 0 2905 3020 196079437 196079322 6.920000e-47 198.0
6 TraesCS2A01G298700 chr2A 95.868 121 5 0 3016 3136 534603571 534603451 2.490000e-46 196.0
7 TraesCS2A01G298700 chr2A 95.614 114 5 0 2907 3020 534604013 534603900 1.940000e-42 183.0
8 TraesCS2A01G298700 chr5D 94.575 2212 88 10 821 3020 79741348 79743539 0.000000e+00 3391.0
9 TraesCS2A01G298700 chr5D 94.636 261 14 0 568 828 79715959 79716219 3.800000e-109 405.0
10 TraesCS2A01G298700 chr5D 97.458 118 3 0 3016 3133 79743850 79743967 5.350000e-48 202.0
11 TraesCS2A01G298700 chr5D 100.000 28 0 0 3131 3158 79743994 79744021 6.000000e-03 52.8
12 TraesCS2A01G298700 chr7A 95.223 1612 73 4 965 2573 688771595 688769985 0.000000e+00 2547.0
13 TraesCS2A01G298700 chr7A 95.591 567 25 0 1 567 353821097 353820531 0.000000e+00 909.0
14 TraesCS2A01G298700 chr7A 92.079 404 30 1 567 970 688781850 688781449 4.580000e-158 568.0
15 TraesCS2A01G298700 chr2D 93.366 1658 98 7 568 2219 430733878 430735529 0.000000e+00 2442.0
16 TraesCS2A01G298700 chr2D 93.254 1601 82 9 627 2220 651123930 651122349 0.000000e+00 2335.0
17 TraesCS2A01G298700 chr2D 98.276 116 2 0 2905 3020 651122345 651122230 1.490000e-48 204.0
18 TraesCS2A01G298700 chr2D 97.414 116 3 0 2905 3020 430735534 430735649 6.920000e-47 198.0
19 TraesCS2A01G298700 chr2D 95.868 121 5 0 3016 3136 651121901 651121781 2.490000e-46 196.0
20 TraesCS2A01G298700 chr6A 92.744 1323 72 14 568 1887 257020759 257019458 0.000000e+00 1890.0
21 TraesCS2A01G298700 chr6A 95.412 741 31 1 2283 3020 257019462 257018722 0.000000e+00 1177.0
22 TraesCS2A01G298700 chr6A 95.501 689 25 3 2221 2903 280597072 280597760 0.000000e+00 1096.0
23 TraesCS2A01G298700 chr6A 95.070 568 26 2 1 567 293207914 293208480 0.000000e+00 893.0
24 TraesCS2A01G298700 chr6A 95.868 121 5 0 3016 3136 257018364 257018244 2.490000e-46 196.0
25 TraesCS2A01G298700 chr6A 96.774 31 1 0 3131 3161 257018220 257018190 6.000000e-03 52.8
26 TraesCS2A01G298700 chr1D 90.037 1365 119 7 872 2220 381612982 381614345 0.000000e+00 1751.0
27 TraesCS2A01G298700 chr1D 92.473 279 20 1 568 846 299566292 299566569 6.350000e-107 398.0
28 TraesCS2A01G298700 chr4D 88.553 1389 116 13 872 2220 451880332 451881717 0.000000e+00 1644.0
29 TraesCS2A01G298700 chr4D 85.714 119 16 1 931 1049 46140064 46139947 1.190000e-24 124.0
30 TraesCS2A01G298700 chr2B 85.427 1393 152 12 864 2220 126755404 126756781 0.000000e+00 1400.0
31 TraesCS2A01G298700 chr2B 95.868 121 5 0 3016 3136 13436447 13436327 2.490000e-46 196.0
32 TraesCS2A01G298700 chr6B 90.939 927 78 4 568 1494 665316208 665317128 0.000000e+00 1242.0
33 TraesCS2A01G298700 chr6B 95.627 686 27 1 2221 2903 390635664 390634979 0.000000e+00 1098.0
34 TraesCS2A01G298700 chr6B 95.380 671 29 2 1552 2220 665317127 665317797 0.000000e+00 1066.0
35 TraesCS2A01G298700 chr6B 95.633 229 4 1 2905 3133 665317801 665318023 2.320000e-96 363.0
36 TraesCS2A01G298700 chr4A 92.450 808 52 5 842 1646 586021069 586020268 0.000000e+00 1146.0
37 TraesCS2A01G298700 chr4A 95.544 561 23 2 8 567 557345337 557345896 0.000000e+00 896.0
38 TraesCS2A01G298700 chr4A 94.894 568 28 1 1 567 314832073 314831506 0.000000e+00 887.0
39 TraesCS2A01G298700 chr4A 90.447 649 60 2 8 656 305424096 305424742 0.000000e+00 854.0
40 TraesCS2A01G298700 chr4A 91.582 297 21 4 554 849 586022153 586021860 1.060000e-109 407.0
41 TraesCS2A01G298700 chr4A 98.276 116 2 0 2905 3020 586020005 586019890 1.490000e-48 204.0
42 TraesCS2A01G298700 chr6D 96.064 686 24 1 2221 2903 214542377 214543062 0.000000e+00 1114.0
43 TraesCS2A01G298700 chr1A 95.238 567 27 0 1 567 220151232 220151798 0.000000e+00 898.0
44 TraesCS2A01G298700 chr1A 79.079 521 74 22 921 1430 544450259 544449763 3.040000e-85 326.0
45 TraesCS2A01G298700 chr1A 94.737 114 6 0 2905 3018 168047537 168047424 9.010000e-41 178.0
46 TraesCS2A01G298700 chr3A 95.062 567 28 0 1 567 305730052 305730618 0.000000e+00 893.0
47 TraesCS2A01G298700 chr3A 95.062 567 27 1 1 567 310585552 310584987 0.000000e+00 891.0
48 TraesCS2A01G298700 chr3A 94.885 567 29 0 1 567 335077182 335076616 0.000000e+00 887.0
49 TraesCS2A01G298700 chrUn 92.126 381 28 2 1842 2220 37758600 37758220 1.290000e-148 536.0
50 TraesCS2A01G298700 chrUn 92.126 381 28 2 1842 2220 322369457 322369837 1.290000e-148 536.0
51 TraesCS2A01G298700 chrUn 95.868 121 5 0 3016 3136 37757893 37757773 2.490000e-46 196.0
52 TraesCS2A01G298700 chrUn 96.610 118 4 0 3016 3133 322370164 322370281 2.490000e-46 196.0
53 TraesCS2A01G298700 chr3D 89.933 298 30 0 567 864 578665200 578665497 4.950000e-103 385.0
54 TraesCS2A01G298700 chr7B 93.671 237 14 1 1047 1282 611347705 611347469 1.390000e-93 353.0
55 TraesCS2A01G298700 chr7B 84.472 161 18 5 921 1075 138611537 138611378 5.460000e-33 152.0
56 TraesCS2A01G298700 chr5A 95.868 121 5 0 3016 3136 560417464 560417584 2.490000e-46 196.0


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 TraesCS2A01G298700 chr2A 514662935 514666095 3160 False 5838.000000 5838 100.000000 1 3161 1 chr2A.!!$F1 3160
1 TraesCS2A01G298700 chr2A 489634819 489635783 964 True 1365.000000 1365 92.049000 852 1832 1 chr2A.!!$R1 980
2 TraesCS2A01G298700 chr2A 534603451 534605463 2012 True 794.333333 2004 94.386667 764 3136 3 chr2A.!!$R3 2372
3 TraesCS2A01G298700 chr2A 196079322 196081585 2263 True 585.333333 1134 94.073333 554 3020 3 chr2A.!!$R2 2466
4 TraesCS2A01G298700 chr5D 79741348 79744021 2673 False 1215.266667 3391 97.344333 821 3158 3 chr5D.!!$F2 2337
5 TraesCS2A01G298700 chr7A 688769985 688771595 1610 True 2547.000000 2547 95.223000 965 2573 1 chr7A.!!$R2 1608
6 TraesCS2A01G298700 chr7A 353820531 353821097 566 True 909.000000 909 95.591000 1 567 1 chr7A.!!$R1 566
7 TraesCS2A01G298700 chr2D 430733878 430735649 1771 False 1320.000000 2442 95.390000 568 3020 2 chr2D.!!$F1 2452
8 TraesCS2A01G298700 chr2D 651121781 651123930 2149 True 911.666667 2335 95.799333 627 3136 3 chr2D.!!$R1 2509
9 TraesCS2A01G298700 chr6A 280597072 280597760 688 False 1096.000000 1096 95.501000 2221 2903 1 chr6A.!!$F1 682
10 TraesCS2A01G298700 chr6A 293207914 293208480 566 False 893.000000 893 95.070000 1 567 1 chr6A.!!$F2 566
11 TraesCS2A01G298700 chr6A 257018190 257020759 2569 True 828.950000 1890 95.199500 568 3161 4 chr6A.!!$R1 2593
12 TraesCS2A01G298700 chr1D 381612982 381614345 1363 False 1751.000000 1751 90.037000 872 2220 1 chr1D.!!$F2 1348
13 TraesCS2A01G298700 chr4D 451880332 451881717 1385 False 1644.000000 1644 88.553000 872 2220 1 chr4D.!!$F1 1348
14 TraesCS2A01G298700 chr2B 126755404 126756781 1377 False 1400.000000 1400 85.427000 864 2220 1 chr2B.!!$F1 1356
15 TraesCS2A01G298700 chr6B 390634979 390635664 685 True 1098.000000 1098 95.627000 2221 2903 1 chr6B.!!$R1 682
16 TraesCS2A01G298700 chr6B 665316208 665318023 1815 False 890.333333 1242 93.984000 568 3133 3 chr6B.!!$F1 2565
17 TraesCS2A01G298700 chr4A 557345337 557345896 559 False 896.000000 896 95.544000 8 567 1 chr4A.!!$F2 559
18 TraesCS2A01G298700 chr4A 314831506 314832073 567 True 887.000000 887 94.894000 1 567 1 chr4A.!!$R1 566
19 TraesCS2A01G298700 chr4A 305424096 305424742 646 False 854.000000 854 90.447000 8 656 1 chr4A.!!$F1 648
20 TraesCS2A01G298700 chr4A 586019890 586022153 2263 True 585.666667 1146 94.102667 554 3020 3 chr4A.!!$R2 2466
21 TraesCS2A01G298700 chr6D 214542377 214543062 685 False 1114.000000 1114 96.064000 2221 2903 1 chr6D.!!$F1 682
22 TraesCS2A01G298700 chr1A 220151232 220151798 566 False 898.000000 898 95.238000 1 567 1 chr1A.!!$F1 566
23 TraesCS2A01G298700 chr3A 305730052 305730618 566 False 893.000000 893 95.062000 1 567 1 chr3A.!!$F1 566
24 TraesCS2A01G298700 chr3A 310584987 310585552 565 True 891.000000 891 95.062000 1 567 1 chr3A.!!$R1 566
25 TraesCS2A01G298700 chr3A 335076616 335077182 566 True 887.000000 887 94.885000 1 567 1 chr3A.!!$R2 566
26 TraesCS2A01G298700 chrUn 37757773 37758600 827 True 366.000000 536 93.997000 1842 3136 2 chrUn.!!$R1 1294
27 TraesCS2A01G298700 chrUn 322369457 322370281 824 False 366.000000 536 94.368000 1842 3133 2 chrUn.!!$F1 1291

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
662 664 0.974383 AGTAGCGCTGGGTACAAAGT 59.026 50.0 22.9 0.0 46.92 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2525 3401 2.352032 GCGTAGGTGTCTGAGGCCT 61.352 63.158 3.86 3.86 36.47 5.19 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
64 65 8.365060 TGGAGAATATTGACAACATCCAAAAT 57.635 30.769 0.00 0.00 32.84 1.82
83 84 7.980662 TCCAAAATAATGCATAGTTGGAACATG 59.019 33.333 21.72 0.00 38.09 3.21
117 118 4.335400 TGGCATAGTAGATGAATTGCGA 57.665 40.909 0.00 0.00 0.00 5.10
207 208 6.376978 GTCATCTATGCCATAAGTGCAAATC 58.623 40.000 0.00 0.00 42.92 2.17
397 398 7.062255 GCAAATCAACATGCTCATCATCATATG 59.938 37.037 0.00 0.00 39.46 1.78
446 447 3.641434 AGAAGTGGCACTAGCATGAAT 57.359 42.857 22.37 1.55 44.61 2.57
463 464 3.554934 TGAATCATGGGAATAGGTGTGC 58.445 45.455 0.00 0.00 0.00 4.57
488 490 2.197792 TCATGCAAGCAATCATTCGC 57.802 45.000 0.00 0.00 0.00 4.70
575 577 6.265876 TCATGTGTTGTAGGTGACACTACTAA 59.734 38.462 5.39 2.19 44.87 2.24
576 578 6.468333 TGTGTTGTAGGTGACACTACTAAA 57.532 37.500 5.39 0.00 44.87 1.85
662 664 0.974383 AGTAGCGCTGGGTACAAAGT 59.026 50.000 22.90 0.00 46.92 2.66
716 718 2.668212 TTGTGGGCACGCTACTGC 60.668 61.111 0.00 0.00 36.33 4.40
741 743 1.106351 GTGCCACACCACACCATCAA 61.106 55.000 0.00 0.00 35.80 2.57
744 746 1.344114 GCCACACCACACCATCAAATT 59.656 47.619 0.00 0.00 0.00 1.82
775 777 2.305009 AGTAGCGCGGGTAGTAAATCT 58.695 47.619 8.83 0.00 0.00 2.40
994 1819 2.267642 CGGTTCCGGCAATCTCCA 59.732 61.111 0.00 0.00 0.00 3.86
997 1822 1.078143 GTTCCGGCAATCTCCAGCT 60.078 57.895 0.00 0.00 0.00 4.24
1014 1839 2.284039 TGCATGCAACATGCCCCT 60.284 55.556 25.14 0.00 44.23 4.79
1018 1843 1.477553 CATGCAACATGCCCCTAAGT 58.522 50.000 0.00 0.00 44.23 2.24
1319 2145 0.175760 GTGAGGCGCTGTCTTCCATA 59.824 55.000 7.64 0.00 0.00 2.74
1378 2213 2.320587 CGCTGGAGCTGCTCGTTTT 61.321 57.895 22.25 0.00 39.32 2.43
1613 2451 1.590932 AGTGCTGCTCAACTTGAGTG 58.409 50.000 18.16 12.90 45.94 3.51
1620 2458 3.381045 TGCTCAACTTGAGTGTAGTTCG 58.619 45.455 18.16 0.00 45.94 3.95
1861 2716 6.605849 CATAAAGGATGTTATGCGATTCAGG 58.394 40.000 0.00 0.00 35.33 3.86
1866 2721 3.627395 TGTTATGCGATTCAGGTTCCT 57.373 42.857 0.00 0.00 0.00 3.36
1937 2802 9.444600 GTCCTACAGTTTTATCCATCAAACTTA 57.555 33.333 0.00 0.00 40.52 2.24
2444 3320 4.225942 ACTGTATGATTGTCACCACTGGAT 59.774 41.667 0.71 0.00 0.00 3.41
2484 3360 1.350310 ACCCCAGTGTCCGGAAAAGT 61.350 55.000 5.23 0.00 0.00 2.66
2496 3372 7.499895 AGTGTCCGGAAAAGTTGTTAAGAATTA 59.500 33.333 5.23 0.00 0.00 1.40
2553 3429 2.147958 GACACCTACGCCAAATGTTGA 58.852 47.619 0.00 0.00 0.00 3.18
2581 3457 5.812127 GTGAAAACTTCTTGAGTGCCATTTT 59.188 36.000 0.00 0.00 39.00 1.82
2642 3518 4.491280 GCTGCAAATGATTAAACATGCACG 60.491 41.667 9.24 7.64 30.19 5.34
2645 3521 4.031652 GCAAATGATTAAACATGCACGTCC 59.968 41.667 6.47 0.00 0.00 4.79
2675 3551 1.067295 AGGCTCACCACTCAATCCAA 58.933 50.000 0.00 0.00 39.06 3.53
2852 3734 4.387598 TGCATTGGCTTGCTTTTGTTATT 58.612 34.783 12.87 0.00 43.18 1.40
2887 3769 8.760735 GTCCCTTCTTATAGGAGAACTAACTTT 58.239 37.037 0.00 0.00 37.50 2.66
2903 3785 4.980339 AACTTTCCCATCAAGGCAAAAT 57.020 36.364 0.00 0.00 35.39 1.82
3000 3882 9.695155 TTGTTCTTTATTAGGAGGAATTAAGGG 57.305 33.333 0.00 0.00 30.15 3.95
3053 4313 6.201044 GGAAGTTGTCATGTCGACTATAATGG 59.799 42.308 17.92 0.00 45.60 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 7.959658 TCTCCATGTGATGTTTCCATTAATT 57.040 32.000 0.00 0.00 0.00 1.40
64 65 5.504853 TCACCATGTTCCAACTATGCATTA 58.495 37.500 3.54 0.00 0.00 1.90
83 84 1.816835 CTATGCCATGCCATGATCACC 59.183 52.381 6.18 0.00 0.00 4.02
117 118 5.046448 TGCCATGCTTCCTTTACATGATTTT 60.046 36.000 0.00 0.00 43.04 1.82
207 208 2.305928 TGCCCCATTCACATAAATCCG 58.694 47.619 0.00 0.00 0.00 4.18
344 345 2.303890 TGTGATGCTATGCTCCATAGGG 59.696 50.000 12.63 0.00 42.71 3.53
397 398 8.607441 TGTCATGACTTACCTATTTATGATGC 57.393 34.615 25.55 0.00 0.00 3.91
446 447 1.294041 TGGCACACCTATTCCCATGA 58.706 50.000 0.00 0.00 36.63 3.07
463 464 3.239587 TGATTGCTTGCATGATGTTGG 57.760 42.857 3.33 0.00 0.00 3.77
510 512 3.133721 ACATAGGTGATGGTGCTTCTCTC 59.866 47.826 0.00 0.00 40.18 3.20
583 585 9.740239 CGCTACTGGTAAACTTCTATGTATAAA 57.260 33.333 0.00 0.00 0.00 1.40
662 664 1.000843 CTATGCCATACCAGTAGCGCA 59.999 52.381 11.47 4.61 0.00 6.09
775 777 7.361457 AGCTATTCACTTGGTAGTAGCATAA 57.639 36.000 2.28 0.00 35.59 1.90
1313 2139 1.140852 CAGCCACCGGAATCTATGGAA 59.859 52.381 9.46 0.00 33.80 3.53
1319 2145 3.011517 AGCCAGCCACCGGAATCT 61.012 61.111 9.46 0.00 0.00 2.40
1378 2213 4.782019 AGCCGCATTACTGAAAATTCAA 57.218 36.364 0.00 0.00 36.64 2.69
1410 2245 8.424731 CACTTACGAAAATTAAGAAAATGCACC 58.575 33.333 0.00 0.00 31.92 5.01
1422 2257 4.276183 TGGCTGTTGCACTTACGAAAATTA 59.724 37.500 0.00 0.00 41.91 1.40
1620 2458 7.937649 AGGCGTGAATAGAAAATTTTATACCC 58.062 34.615 7.40 3.87 0.00 3.69
2170 3045 9.577110 TTTTGAATGCTAAATATTCAGAAGCAG 57.423 29.630 15.50 0.00 45.53 4.24
2326 3202 9.862149 TGTTATATGATGGTAAGACAGACTAGA 57.138 33.333 0.00 0.00 0.00 2.43
2525 3401 2.352032 GCGTAGGTGTCTGAGGCCT 61.352 63.158 3.86 3.86 36.47 5.19
2553 3429 5.827797 TGGCACTCAAGAAGTTTTCACTTAT 59.172 36.000 0.00 0.00 43.79 1.73
2627 3503 4.517075 TGAAAGGACGTGCATGTTTAATCA 59.483 37.500 13.92 12.68 0.00 2.57
2642 3518 3.003480 GTGAGCCTGTACATGAAAGGAC 58.997 50.000 14.59 9.19 32.43 3.85
2645 3521 2.744202 GTGGTGAGCCTGTACATGAAAG 59.256 50.000 0.00 0.00 35.27 2.62
2675 3551 0.034896 CGGCAAGTACCAGGAGTTGT 59.965 55.000 0.00 0.00 33.11 3.32
3053 4313 8.292448 CACTTGGTCATTATAAATATCACTGGC 58.708 37.037 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.