Multiple sequence alignment - TraesCS3A01G092400

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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 TraesCS3A01G092400 chr3A 100.000 4006 0 0 1 4006 57961372 57957367 0.000000e+00 7398.0
1 TraesCS3A01G092400 chr3B 95.077 3169 75 20 892 4006 72935457 72938598 0.000000e+00 4913.0
2 TraesCS3A01G092400 chr3B 88.449 909 52 13 1 869 72934572 72935467 0.000000e+00 1048.0
3 TraesCS3A01G092400 chr3D 94.029 3182 98 25 892 4006 46554080 46557236 0.000000e+00 4739.0
4 TraesCS3A01G092400 chr3D 87.015 670 34 15 1 657 46553218 46553847 0.000000e+00 706.0
5 TraesCS3A01G092400 chr3D 94.170 223 7 4 653 872 46553874 46554093 6.420000e-88 335.0
6 TraesCS3A01G092400 chr3D 87.086 302 32 6 2527 2822 369413408 369413708 6.420000e-88 335.0
7 TraesCS3A01G092400 chr7B 89.869 306 27 2 2521 2822 13823711 13823406 1.350000e-104 390.0
8 TraesCS3A01G092400 chr7B 86.688 308 34 5 2522 2823 616539803 616540109 6.420000e-88 335.0
9 TraesCS3A01G092400 chr7B 92.216 167 13 0 1012 1178 147586614 147586448 1.860000e-58 237.0
10 TraesCS3A01G092400 chr5D 89.542 306 27 3 2522 2822 115401775 115401470 2.260000e-102 383.0
11 TraesCS3A01G092400 chr5B 89.542 306 27 3 2522 2822 126598771 126598466 2.260000e-102 383.0
12 TraesCS3A01G092400 chr5A 88.925 307 28 3 2522 2822 121412055 121411749 1.360000e-99 374.0
13 TraesCS3A01G092400 chr4D 85.759 316 36 9 2517 2826 421335522 421335210 3.860000e-85 326.0
14 TraesCS3A01G092400 chr2D 90.950 221 18 1 1012 1232 196365211 196365429 3.030000e-76 296.0
15 TraesCS3A01G092400 chr6A 91.617 167 14 0 1012 1178 576945102 576944936 8.660000e-57 231.0
16 TraesCS3A01G092400 chrUn 91.018 167 15 0 1012 1178 50316819 50316653 4.030000e-55 226.0
17 TraesCS3A01G092400 chrUn 91.018 167 15 0 1012 1178 307457563 307457397 4.030000e-55 226.0
18 TraesCS3A01G092400 chr6B 83.333 228 32 5 281 504 157774322 157774547 5.250000e-49 206.0
19 TraesCS3A01G092400 chr7A 80.435 92 13 5 281 370 25858208 25858120 9.290000e-07 65.8


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 TraesCS3A01G092400 chr3A 57957367 57961372 4005 True 7398.000000 7398 100.000 1 4006 1 chr3A.!!$R1 4005
1 TraesCS3A01G092400 chr3B 72934572 72938598 4026 False 2980.500000 4913 91.763 1 4006 2 chr3B.!!$F1 4005
2 TraesCS3A01G092400 chr3D 46553218 46557236 4018 False 1926.666667 4739 91.738 1 4006 3 chr3D.!!$F2 4005

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
72 76 0.323360 GGTTCAGGGGTTAGCATGCA 60.323 55.000 21.98 2.77 0.0 3.96 F
469 487 1.341156 CCCCACACCTCATCTCTCCC 61.341 65.000 0.00 0.00 0.0 4.30 F
482 500 1.653918 TCTCTCCCCCTCTTCCATTCT 59.346 52.381 0.00 0.00 0.0 2.40 F
2015 2095 2.072298 GCAAATCGAGAGCTTCACAGT 58.928 47.619 0.00 0.00 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1917 1.467734 CAGTGCAGACTTTCAGCATCC 59.532 52.381 0.0 0.0 40.92 3.51 R
2082 2163 0.179009 AACATGTGCCAGTGCTCAGT 60.179 50.000 0.0 0.0 43.52 3.41 R
2093 2174 4.516698 CACCAGATAATCCCTAACATGTGC 59.483 45.833 0.0 0.0 0.00 4.57 R
3005 3100 1.377856 GCTTGGGTTCCTCAGCCTC 60.378 63.158 0.0 0.0 44.37 4.70 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
43 47 6.771267 GGGCTGGTAGTTAGTAGCAAATTTAT 59.229 38.462 0.57 0.00 38.67 1.40
70 74 0.625849 AGGGTTCAGGGGTTAGCATG 59.374 55.000 0.00 0.00 0.00 4.06
71 75 1.037579 GGGTTCAGGGGTTAGCATGC 61.038 60.000 10.51 10.51 0.00 4.06
72 76 0.323360 GGTTCAGGGGTTAGCATGCA 60.323 55.000 21.98 2.77 0.00 3.96
73 77 1.686115 GGTTCAGGGGTTAGCATGCAT 60.686 52.381 21.98 7.68 0.00 3.96
266 280 5.636837 CAGTAAGAGTCTAAGAGAGCACAC 58.363 45.833 0.00 0.00 0.00 3.82
311 325 7.363880 GCATCTCTAACCGATCCCTTATAATCA 60.364 40.741 0.00 0.00 0.00 2.57
337 352 9.620259 AGTTAGAGGAGGATAAAATCATGTTTC 57.380 33.333 0.00 0.00 0.00 2.78
458 476 2.490509 CGGAGTAAAAATTCCCCACACC 59.509 50.000 0.00 0.00 0.00 4.16
459 477 3.774734 GGAGTAAAAATTCCCCACACCT 58.225 45.455 0.00 0.00 0.00 4.00
462 480 5.010708 AGTAAAAATTCCCCACACCTCAT 57.989 39.130 0.00 0.00 0.00 2.90
469 487 1.341156 CCCCACACCTCATCTCTCCC 61.341 65.000 0.00 0.00 0.00 4.30
482 500 1.653918 TCTCTCCCCCTCTTCCATTCT 59.346 52.381 0.00 0.00 0.00 2.40
559 577 3.377759 CCCCGCCGCCAAAAATGA 61.378 61.111 0.00 0.00 0.00 2.57
567 585 2.094675 CCGCCAAAAATGACTGGATCT 58.905 47.619 0.00 0.00 34.35 2.75
592 610 6.721208 TGGCCATTTTAAGTGAAGAAATCTCT 59.279 34.615 0.00 0.00 33.37 3.10
627 645 4.136796 AGTCTAGCTGTGTTGATTTTGCA 58.863 39.130 0.00 0.00 0.00 4.08
666 715 8.654997 AGTGGTCTGCTAATTATGATAATCACT 58.345 33.333 0.00 2.78 0.00 3.41
699 748 6.925165 CCTTTTTGACTGTGCAAATACTTCAT 59.075 34.615 0.00 0.00 37.57 2.57
751 803 7.613022 ACAGAGTTTGGATGATTTATGTCACAT 59.387 33.333 0.00 0.00 0.00 3.21
772 824 7.714813 TCACATTCACTTCATTCTTCAACAGTA 59.285 33.333 0.00 0.00 0.00 2.74
903 955 2.311124 GCTACGGCTTTGGATACAGT 57.689 50.000 0.00 0.00 41.47 3.55
904 956 2.629051 GCTACGGCTTTGGATACAGTT 58.371 47.619 0.00 0.00 41.47 3.16
905 957 2.608090 GCTACGGCTTTGGATACAGTTC 59.392 50.000 0.00 0.00 41.47 3.01
906 958 3.925530 GCTACGGCTTTGGATACAGTTCA 60.926 47.826 0.00 0.00 41.47 3.18
907 959 5.216363 GCTACGGCTTTGGATACAGTTCAT 61.216 45.833 0.00 0.00 41.47 2.57
908 960 6.653987 GCTACGGCTTTGGATACAGTTCATT 61.654 44.000 0.00 0.00 41.47 2.57
1184 1261 7.332678 TCTCAATGTATCATTGTCTTGTGTGAG 59.667 37.037 17.93 8.39 0.00 3.51
1278 1355 4.731313 AGTTTCCTGGAATCCTCTTGTT 57.269 40.909 10.45 0.00 0.00 2.83
1528 1606 6.710744 AGTCTTTGTAACAGTTGGTATTGGAG 59.289 38.462 0.00 0.00 0.00 3.86
1541 1619 6.114187 TGGTATTGGAGAGATAATGCGATT 57.886 37.500 0.00 0.00 0.00 3.34
1542 1620 6.533730 TGGTATTGGAGAGATAATGCGATTT 58.466 36.000 0.00 0.00 0.00 2.17
1543 1621 6.998074 TGGTATTGGAGAGATAATGCGATTTT 59.002 34.615 0.00 0.00 0.00 1.82
1686 1766 6.012658 TCTTTTGCGCTTGATTCTGTTATT 57.987 33.333 9.73 0.00 0.00 1.40
1831 1911 3.821033 CTGTTTTCCCCTACCTTCTTGTG 59.179 47.826 0.00 0.00 0.00 3.33
1837 1917 2.504367 CCCTACCTTCTTGTGTTGTGG 58.496 52.381 0.00 0.00 0.00 4.17
1907 1987 2.094854 CAGAGGAAGGCAAAAGTGATGC 60.095 50.000 0.00 0.00 43.08 3.91
1917 1997 3.732721 GCAAAAGTGATGCAGTTGAGAAC 59.267 43.478 0.00 0.00 43.29 3.01
1947 2027 2.401583 ACGTGGCTTCAGATAATGCA 57.598 45.000 0.00 0.00 0.00 3.96
2015 2095 2.072298 GCAAATCGAGAGCTTCACAGT 58.928 47.619 0.00 0.00 0.00 3.55
2093 2174 5.482908 AGTTACTGAAATACTGAGCACTGG 58.517 41.667 0.00 0.00 0.00 4.00
2498 2579 1.062587 CGCTCTTTTGATACCAAGGCG 59.937 52.381 0.00 0.00 35.03 5.52
2642 2723 2.504175 TCCTCTTTAATTCCCCACCTCG 59.496 50.000 0.00 0.00 0.00 4.63
2715 2799 3.314635 GCTTGATTCCCATGTGATGAGAC 59.685 47.826 0.00 0.00 0.00 3.36
2724 2808 4.334759 CCCATGTGATGAGACAGAAACATC 59.665 45.833 0.00 0.00 40.22 3.06
2811 2895 5.585047 GCTAAACGTCCACTTATTTGAGGAT 59.415 40.000 0.00 0.00 31.91 3.24
3005 3100 6.227298 ACTCATGTATCAGGGAAGTTGTAG 57.773 41.667 0.00 0.00 0.00 2.74
3311 3406 6.735556 AGTCAAACCCATTTGGAGATCTATT 58.264 36.000 0.00 0.00 44.61 1.73
3313 3408 8.336235 AGTCAAACCCATTTGGAGATCTATTTA 58.664 33.333 0.00 0.00 44.61 1.40
3315 3410 8.336235 TCAAACCCATTTGGAGATCTATTTACT 58.664 33.333 0.00 0.00 44.61 2.24
3316 3411 8.408601 CAAACCCATTTGGAGATCTATTTACTG 58.591 37.037 0.00 0.00 41.39 2.74
3318 3413 7.872138 ACCCATTTGGAGATCTATTTACTGAA 58.128 34.615 0.00 0.00 37.39 3.02
3436 3556 3.005472 GCATTGGAGATCATGTGATTGGG 59.995 47.826 0.00 0.00 34.37 4.12
3536 3656 9.392259 ACTACTCCTAGGTAACAATTTAAATGC 57.608 33.333 9.08 0.00 41.41 3.56
3555 3675 3.280295 TGCCCAACGTTAAACTCAAGAA 58.720 40.909 0.00 0.00 0.00 2.52
3702 3822 9.579768 GGTGTTTTAAACAATGTATATGCATGA 57.420 29.630 12.37 0.00 44.16 3.07
3856 3985 6.266168 TGTTTCCTTATACAGCCACATTTG 57.734 37.500 0.00 0.00 0.00 2.32
3922 4052 9.065798 TGATGTTCTTGACAACAATATTCTGAA 57.934 29.630 0.00 0.00 42.62 3.02
3925 4055 9.681692 TGTTCTTGACAACAATATTCTGAAATG 57.318 29.630 0.00 0.00 34.69 2.32
3927 4057 9.897744 TTCTTGACAACAATATTCTGAAATGTC 57.102 29.630 0.00 4.07 37.15 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 47 1.207488 CCCCTGAACCCTGATGTCCA 61.207 60.000 0.00 0.00 0.00 4.02
70 74 4.446413 GCACTGGGGCAGCAATGC 62.446 66.667 0.00 0.00 34.37 3.56
71 75 2.992689 TGCACTGGGGCAGCAATG 60.993 61.111 0.00 0.00 39.25 2.82
266 280 6.821388 AGATGCTCTAACATAACTAACCCTG 58.179 40.000 0.00 0.00 0.00 4.45
311 325 9.620259 GAAACATGATTTTATCCTCCTCTAACT 57.380 33.333 0.00 0.00 0.00 2.24
328 343 5.189180 GCACTTTAGAGGAGGAAACATGAT 58.811 41.667 0.00 0.00 0.00 2.45
332 347 3.496160 GGTGCACTTTAGAGGAGGAAACA 60.496 47.826 17.98 0.00 0.00 2.83
337 352 3.369576 GGTTAGGTGCACTTTAGAGGAGG 60.370 52.174 17.98 0.00 0.00 4.30
411 426 2.152016 GGGCGGAGTATATTTGAAGGC 58.848 52.381 0.00 0.00 0.00 4.35
416 431 1.876416 CGGGTGGGCGGAGTATATTTG 60.876 57.143 0.00 0.00 0.00 2.32
420 435 3.228759 GCGGGTGGGCGGAGTATA 61.229 66.667 0.00 0.00 0.00 1.47
458 476 1.062581 TGGAAGAGGGGGAGAGATGAG 60.063 57.143 0.00 0.00 0.00 2.90
459 477 1.018840 TGGAAGAGGGGGAGAGATGA 58.981 55.000 0.00 0.00 0.00 2.92
462 480 1.653918 AGAATGGAAGAGGGGGAGAGA 59.346 52.381 0.00 0.00 0.00 3.10
469 487 1.821332 GCGGCAGAATGGAAGAGGG 60.821 63.158 0.00 0.00 35.86 4.30
559 577 4.019174 CACTTAAAATGGCCAGATCCAGT 58.981 43.478 13.05 7.75 39.89 4.00
567 585 6.721208 AGAGATTTCTTCACTTAAAATGGCCA 59.279 34.615 8.56 8.56 0.00 5.36
592 610 6.183360 ACACAGCTAGACTCACTTAAAACTCA 60.183 38.462 0.00 0.00 0.00 3.41
666 715 1.210967 ACAGTCAAAAAGGTCACCCGA 59.789 47.619 0.00 0.00 35.12 5.14
711 760 8.862325 TCCAAACTCTGTATAACACAATGAAT 57.138 30.769 0.00 0.00 36.48 2.57
751 803 9.119418 TGATTTACTGTTGAAGAATGAAGTGAA 57.881 29.630 0.00 0.00 0.00 3.18
772 824 6.299805 TCAGTATTCTGCACCTACTGATTT 57.700 37.500 17.87 0.00 43.81 2.17
884 936 2.311124 ACTGTATCCAAAGCCGTAGC 57.689 50.000 0.00 0.00 40.32 3.58
885 937 3.857052 TGAACTGTATCCAAAGCCGTAG 58.143 45.455 0.00 0.00 0.00 3.51
886 938 3.965379 TGAACTGTATCCAAAGCCGTA 57.035 42.857 0.00 0.00 0.00 4.02
887 939 2.851263 TGAACTGTATCCAAAGCCGT 57.149 45.000 0.00 0.00 0.00 5.68
888 940 4.701956 AAATGAACTGTATCCAAAGCCG 57.298 40.909 0.00 0.00 0.00 5.52
889 941 9.120538 TCTATAAAATGAACTGTATCCAAAGCC 57.879 33.333 0.00 0.00 0.00 4.35
1184 1261 4.460263 TGAATATGGACATGGGTGTAAGC 58.540 43.478 0.00 0.00 39.09 3.09
1225 1302 4.456280 TCATCACATGGACTCTGTACAC 57.544 45.455 0.00 0.00 0.00 2.90
1278 1355 7.500141 TGCAGCATTATCAACTAATGAGACTA 58.500 34.615 8.71 0.00 46.55 2.59
1425 1503 7.867445 AGAAAAACAAAACTACAACACTGTG 57.133 32.000 6.19 6.19 36.96 3.66
1686 1766 4.142038 GTTTCCTCCAGCCTGTAAAAGAA 58.858 43.478 0.00 0.00 0.00 2.52
1831 1911 2.227388 CAGACTTTCAGCATCCCACAAC 59.773 50.000 0.00 0.00 0.00 3.32
1837 1917 1.467734 CAGTGCAGACTTTCAGCATCC 59.532 52.381 0.00 0.00 40.92 3.51
1907 1987 5.291128 ACGTTACTGAGTTTGTTCTCAACTG 59.709 40.000 0.00 0.00 42.73 3.16
1917 1997 2.869801 TGAAGCCACGTTACTGAGTTTG 59.130 45.455 0.00 0.00 0.00 2.93
2015 2095 4.314522 TCCCCTAAAGATTCATGCACAA 57.685 40.909 0.00 0.00 0.00 3.33
2071 2152 4.093556 GCCAGTGCTCAGTATTTCAGTAAC 59.906 45.833 0.00 0.00 33.53 2.50
2082 2163 0.179009 AACATGTGCCAGTGCTCAGT 60.179 50.000 0.00 0.00 43.52 3.41
2093 2174 4.516698 CACCAGATAATCCCTAACATGTGC 59.483 45.833 0.00 0.00 0.00 4.57
2525 2606 2.500098 CCACTTATTTGAGGACGGAGGA 59.500 50.000 0.00 0.00 0.00 3.71
2642 2723 6.668541 TTTCTACATGCACTTAGCTCATTC 57.331 37.500 0.00 0.00 45.94 2.67
2724 2808 7.657336 TCCCAATGCACTTTAAAGTAGAAAAG 58.343 34.615 20.15 8.43 37.08 2.27
2811 2895 4.141251 AGCAAAAGAAACTTACTCCCTCCA 60.141 41.667 0.00 0.00 0.00 3.86
3005 3100 1.377856 GCTTGGGTTCCTCAGCCTC 60.378 63.158 0.00 0.00 44.37 4.70
3231 3326 7.250569 AGACAATATTTCAGTAAATGGCAACG 58.749 34.615 0.00 0.00 36.02 4.10
3286 3381 5.779241 AGATCTCCAAATGGGTTTGACTA 57.221 39.130 0.00 0.00 46.03 2.59
3311 3406 9.575783 GTCAAAACCAACTTAATGTTTCAGTAA 57.424 29.630 0.00 0.00 36.63 2.24
3313 3408 7.607250 TGTCAAAACCAACTTAATGTTTCAGT 58.393 30.769 0.00 0.00 36.63 3.41
3315 3410 7.543868 CACTGTCAAAACCAACTTAATGTTTCA 59.456 33.333 0.00 0.00 36.63 2.69
3316 3411 7.544217 ACACTGTCAAAACCAACTTAATGTTTC 59.456 33.333 0.00 0.00 36.63 2.78
3318 3413 6.930731 ACACTGTCAAAACCAACTTAATGTT 58.069 32.000 0.00 0.00 39.92 2.71
3536 3656 5.494632 AACTTCTTGAGTTTAACGTTGGG 57.505 39.130 11.99 0.00 46.34 4.12
3598 3718 3.514645 ATTCGATGGAAAGCATTGTTGC 58.485 40.909 0.00 0.00 40.61 4.17
3717 3846 9.259832 TGATATGGCAATATGATACAGTACTCT 57.740 33.333 0.00 0.00 0.00 3.24
3718 3847 9.875691 TTGATATGGCAATATGATACAGTACTC 57.124 33.333 0.00 0.00 0.00 2.59
3755 3884 9.964354 ATTAGAACATGGAGCAATATAGCATTA 57.036 29.630 0.00 0.00 36.85 1.90
3804 3933 2.638363 AGAGGTGGTACTCCAAACTTCC 59.362 50.000 9.52 0.00 45.79 3.46
3894 4024 7.484007 CAGAATATTGTTGTCAAGAACATCAGC 59.516 37.037 0.00 0.00 38.48 4.26
3922 4052 5.887598 TGCTCCTACAAATATTGCAGACATT 59.112 36.000 0.00 0.00 0.00 2.71
3925 4055 4.635765 TGTGCTCCTACAAATATTGCAGAC 59.364 41.667 0.00 0.00 0.00 3.51
3927 4057 5.355071 TCTTGTGCTCCTACAAATATTGCAG 59.645 40.000 0.00 0.00 39.81 4.41


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

AutoCloner maintained by Alex Coulton.