Multiple sequence alignment - TraesCS7B01G147300

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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 TraesCS7B01G147300 chr7B 100.000 3394 0 0 1 3394 193199930 193203323 0.000000e+00 6268
1 TraesCS7B01G147300 chr7B 92.699 452 30 1 497 945 73564930 73565381 0.000000e+00 649
2 TraesCS7B01G147300 chr7B 98.182 275 4 1 2 276 717108199 717107926 2.370000e-131 479
3 TraesCS7B01G147300 chr7B 94.966 298 12 1 107 404 242512015 242512309 6.630000e-127 464
4 TraesCS7B01G147300 chr7B 91.265 332 25 2 618 945 439174276 439173945 1.860000e-122 449
5 TraesCS7B01G147300 chr5D 96.268 3403 111 6 2 3394 489745816 489742420 0.000000e+00 5566
6 TraesCS7B01G147300 chr4D 95.616 3399 137 7 2 3394 200716416 200713024 0.000000e+00 5441
7 TraesCS7B01G147300 chr2D 95.529 3400 125 6 2 3394 232181106 232177727 0.000000e+00 5411
8 TraesCS7B01G147300 chr3D 95.369 3412 122 12 2 3394 497287766 497291160 0.000000e+00 5393
9 TraesCS7B01G147300 chr3D 95.861 1788 68 1 1613 3394 172531322 172529535 0.000000e+00 2887
10 TraesCS7B01G147300 chr3D 95.692 441 16 3 1065 1503 71520939 71520500 0.000000e+00 706
11 TraesCS7B01G147300 chr3D 90.863 197 14 2 723 916 415924736 415924931 9.340000e-66 261
12 TraesCS7B01G147300 chr2A 95.002 2501 118 3 899 3394 299510669 299508171 0.000000e+00 3919
13 TraesCS7B01G147300 chr2A 94.882 2501 121 2 900 3394 460473426 460470927 0.000000e+00 3903
14 TraesCS7B01G147300 chr2A 89.415 359 33 4 107 461 82159397 82159754 6.680000e-122 448
15 TraesCS7B01G147300 chr2A 93.367 196 10 1 727 919 482751938 482751743 1.540000e-73 287
16 TraesCS7B01G147300 chr6D 92.963 2359 137 10 1061 3392 219292805 219290449 0.000000e+00 3410
17 TraesCS7B01G147300 chr6D 91.270 126 10 1 940 1065 219292974 219292850 1.620000e-38 171
18 TraesCS7B01G147300 chr7D 91.838 1899 147 4 1503 3394 72785637 72787534 0.000000e+00 2641
19 TraesCS7B01G147300 chr7A 90.792 1401 79 24 1061 2438 540916364 540917737 0.000000e+00 1827
20 TraesCS7B01G147300 chr7A 90.046 432 37 2 341 767 667805239 667805669 3.830000e-154 555
21 TraesCS7B01G147300 chr7A 89.888 356 31 4 107 458 709715015 709715369 1.440000e-123 453
22 TraesCS7B01G147300 chr4B 88.212 509 46 5 269 768 112879747 112880250 2.250000e-166 595
23 TraesCS7B01G147300 chr4B 93.093 333 23 0 613 945 275417052 275416720 3.940000e-134 488
24 TraesCS7B01G147300 chr4B 92.562 121 9 0 940 1060 213964789 213964909 1.250000e-39 174
25 TraesCS7B01G147300 chr5B 87.154 506 46 6 269 765 528735725 528736220 1.060000e-154 556
26 TraesCS7B01G147300 chr5A 90.692 419 38 1 350 768 677630293 677629876 1.060000e-154 556
27 TraesCS7B01G147300 chr4A 89.694 359 32 4 107 461 471922525 471922882 1.440000e-123 453


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 TraesCS7B01G147300 chr7B 193199930 193203323 3393 False 6268.0 6268 100.0000 1 3394 1 chr7B.!!$F2 3393
1 TraesCS7B01G147300 chr5D 489742420 489745816 3396 True 5566.0 5566 96.2680 2 3394 1 chr5D.!!$R1 3392
2 TraesCS7B01G147300 chr4D 200713024 200716416 3392 True 5441.0 5441 95.6160 2 3394 1 chr4D.!!$R1 3392
3 TraesCS7B01G147300 chr2D 232177727 232181106 3379 True 5411.0 5411 95.5290 2 3394 1 chr2D.!!$R1 3392
4 TraesCS7B01G147300 chr3D 497287766 497291160 3394 False 5393.0 5393 95.3690 2 3394 1 chr3D.!!$F2 3392
5 TraesCS7B01G147300 chr3D 172529535 172531322 1787 True 2887.0 2887 95.8610 1613 3394 1 chr3D.!!$R2 1781
6 TraesCS7B01G147300 chr2A 299508171 299510669 2498 True 3919.0 3919 95.0020 899 3394 1 chr2A.!!$R1 2495
7 TraesCS7B01G147300 chr2A 460470927 460473426 2499 True 3903.0 3903 94.8820 900 3394 1 chr2A.!!$R2 2494
8 TraesCS7B01G147300 chr6D 219290449 219292974 2525 True 1790.5 3410 92.1165 940 3392 2 chr6D.!!$R1 2452
9 TraesCS7B01G147300 chr7D 72785637 72787534 1897 False 2641.0 2641 91.8380 1503 3394 1 chr7D.!!$F1 1891
10 TraesCS7B01G147300 chr7A 540916364 540917737 1373 False 1827.0 1827 90.7920 1061 2438 1 chr7A.!!$F1 1377
11 TraesCS7B01G147300 chr4B 112879747 112880250 503 False 595.0 595 88.2120 269 768 1 chr4B.!!$F1 499

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
443 446 0.248565 GAGACTGCCAGTGATGAGCA 59.751 55.000 0.00 0.0 34.79 4.26 F
655 671 1.226542 CCAGCAGGGAGATGTGCAT 59.773 57.895 0.00 0.0 42.47 3.96 F
2005 2098 1.264749 CGGGTGGTGATTCTCCTGGA 61.265 60.000 6.35 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2071 1.276989 GAATCACCACCCGTACCTTGA 59.723 52.381 0.00 0.00 0.0 3.02 R
2050 2143 2.205022 TTTGCCTTCCCAGATGACAG 57.795 50.000 0.00 0.00 0.0 3.51 R
2816 2918 0.102481 GCATCAAGCAGAAGGCCATG 59.898 55.000 5.01 1.11 46.5 3.66 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
156 158 9.739276 TTTCATTCCTTGATACAGAAAGTACAT 57.261 29.630 0.00 0.00 35.05 2.29
395 398 2.587194 GATCAGCGAGCGCATGGT 60.587 61.111 17.68 3.46 44.88 3.55
443 446 0.248565 GAGACTGCCAGTGATGAGCA 59.751 55.000 0.00 0.00 34.79 4.26
480 483 2.261671 CAGCAAGTAGGCGACGGT 59.738 61.111 0.00 0.00 39.27 4.83
491 494 2.100631 GCGACGGTGACCTCATTGG 61.101 63.158 0.00 0.00 42.93 3.16
499 502 1.351017 GTGACCTCATTGGGAAGTGGA 59.649 52.381 0.00 0.00 41.11 4.02
595 606 8.493547 GTTTCATACTGAAGTTTACTGGTACAC 58.506 37.037 0.00 0.00 37.70 2.90
598 609 5.772825 ACTGAAGTTTACTGGTACACGTA 57.227 39.130 0.00 0.00 0.00 3.57
655 671 1.226542 CCAGCAGGGAGATGTGCAT 59.773 57.895 0.00 0.00 42.47 3.96
707 723 4.371417 CCAGCCAGCCACCACCAT 62.371 66.667 0.00 0.00 0.00 3.55
713 729 1.626686 CCAGCCACCACCATGTAAAA 58.373 50.000 0.00 0.00 0.00 1.52
719 735 5.650266 CAGCCACCACCATGTAAAAGTAATA 59.350 40.000 0.00 0.00 0.00 0.98
909 926 8.563732 AGCAGAACTGAAGTTTTCTCTAATTTC 58.436 33.333 5.97 0.00 38.56 2.17
1144 1211 5.063880 CAGTTAGCTCTAACAACCCAGTTT 58.936 41.667 18.63 0.00 45.79 2.66
1576 1669 2.029470 CCTCTCTCTGTTTGACTCGCTT 60.029 50.000 0.00 0.00 0.00 4.68
1604 1697 5.811190 TCTCTCTATCTTTCTATAGGCGCT 58.189 41.667 7.64 0.00 31.50 5.92
1624 1717 2.797278 CCCGATTCGAGGGTGGAGG 61.797 68.421 7.83 0.00 43.89 4.30
1686 1779 1.301244 GCTCCGCATGGATCACGAT 60.301 57.895 0.00 0.00 45.33 3.73
1720 1813 2.122768 GGGTCTGGATCATCAAGTCCT 58.877 52.381 5.40 0.00 35.49 3.85
1919 2012 1.369625 ATTTCGATGCCAAGACGGAC 58.630 50.000 0.00 0.00 36.56 4.79
1922 2015 1.399714 TCGATGCCAAGACGGACTAT 58.600 50.000 0.00 0.00 36.56 2.12
1977 2070 6.349611 GGATGTGTTCAACAAGTTGCAGATAT 60.350 38.462 8.04 0.38 43.61 1.63
1978 2071 6.389830 TGTGTTCAACAAGTTGCAGATATT 57.610 33.333 8.04 0.00 40.24 1.28
2005 2098 1.264749 CGGGTGGTGATTCTCCTGGA 61.265 60.000 6.35 0.00 0.00 3.86
2050 2143 4.754372 TCTGTGATTGTGTCTTGCATTC 57.246 40.909 0.00 0.00 0.00 2.67
2064 2157 2.995283 TGCATTCTGTCATCTGGGAAG 58.005 47.619 0.00 0.00 0.00 3.46
2108 2201 6.973843 ACAGTAGTTCGGTTTATATATGCGA 58.026 36.000 0.00 0.00 0.00 5.10
2133 2226 5.222027 TGTGTGGGGATTCAATCTAGAACAA 60.222 40.000 0.00 0.00 0.00 2.83
2199 2292 8.175069 GTGATTCGATAACTGACTAAATTTGCA 58.825 33.333 0.00 0.00 0.00 4.08
2249 2342 9.820725 TTGTTGTGTACAGTACTAAACTTGTAT 57.179 29.630 20.57 0.00 38.19 2.29
2270 2363 7.802738 TGTATAATTCTTGTCTTGTTTCCACG 58.197 34.615 0.00 0.00 0.00 4.94
2455 2548 7.763071 TCAATCGATATTTATCTCATCCAGCAG 59.237 37.037 0.00 0.00 0.00 4.24
2516 2615 6.814954 AGTATGAAGTGGACACCATATTCT 57.185 37.500 14.80 0.00 35.28 2.40
2557 2656 9.699410 AGGAATAATTTGTTTCATCATGTCCTA 57.301 29.630 0.00 0.00 0.00 2.94
2590 2689 2.493278 CCAGATTTGTTGCTTCCGGAAT 59.507 45.455 19.21 0.00 0.00 3.01
2721 2820 1.601914 CGGCGTCCATCATCAACGATA 60.602 52.381 0.00 0.00 38.65 2.92
2733 2833 2.536365 TCAACGATAATGCGGACTGAC 58.464 47.619 0.00 0.00 35.12 3.51
2753 2855 1.872952 CGTTCAACTGCAGAACCATCA 59.127 47.619 23.35 0.00 41.72 3.07
2816 2918 3.484407 ACAGATAAGGGCATGATGCTTC 58.516 45.455 17.84 9.99 44.28 3.86
3336 3448 3.820467 CCAACACCTGAATGCTTGACTAA 59.180 43.478 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.992835 AGATTTAACAATTGCTTTCAGATTCC 57.007 30.769 5.05 0.00 0.00 3.01
156 158 7.597386 CAGGATCGATGTATATCAGAACTTGA 58.403 38.462 0.54 0.00 40.85 3.02
380 383 3.120385 CAACCATGCGCTCGCTGA 61.120 61.111 9.73 0.00 42.51 4.26
443 446 2.185350 CTCGAGGTTGCCATCGCT 59.815 61.111 3.91 0.00 38.79 4.93
480 483 1.741028 TCCACTTCCCAATGAGGTCA 58.259 50.000 0.00 0.00 29.41 4.02
491 494 3.861840 TCAAGTCGATTCATCCACTTCC 58.138 45.455 0.00 0.00 36.35 3.46
499 502 0.537188 ACCGCCTCAAGTCGATTCAT 59.463 50.000 0.00 0.00 0.00 2.57
595 606 6.182634 CGAAACAATAGTAGCAAACCATACG 58.817 40.000 0.00 0.00 0.00 3.06
598 609 6.569179 AACGAAACAATAGTAGCAAACCAT 57.431 33.333 0.00 0.00 0.00 3.55
655 671 1.022982 GCTCATGCTGCTAGTGTGCA 61.023 55.000 16.31 8.41 41.05 4.57
707 723 7.669427 TCGGTTGGAGAAGTATTACTTTTACA 58.331 34.615 10.32 8.94 38.80 2.41
713 729 3.767673 TGCTCGGTTGGAGAAGTATTACT 59.232 43.478 0.00 0.00 46.23 2.24
719 735 1.072331 ACATTGCTCGGTTGGAGAAGT 59.928 47.619 0.00 0.00 46.23 3.01
928 945 8.940952 ACAGCTAAATTGATTAGAGAAGTTCAC 58.059 33.333 5.50 0.00 43.16 3.18
1144 1211 5.129815 AGGCCACTCCGTAATTGAAATACTA 59.870 40.000 5.01 0.00 40.77 1.82
1576 1669 9.607988 CGCCTATAGAAAGATAGAGAGAGATTA 57.392 37.037 0.00 0.00 32.00 1.75
1604 1697 3.781307 CCACCCTCGAATCGGGCA 61.781 66.667 8.11 0.00 46.04 5.36
1608 1701 2.107141 GCCTCCACCCTCGAATCG 59.893 66.667 0.00 0.00 0.00 3.34
1624 1717 4.154347 CTCCAGTGGAGGCTCGGC 62.154 72.222 28.94 3.58 45.43 5.54
1703 1796 3.036819 CCTGAGGACTTGATGATCCAGA 58.963 50.000 0.00 0.00 37.47 3.86
1919 2012 6.266330 TCCTGTAGTTCTGGATCATGTCATAG 59.734 42.308 0.00 0.00 38.86 2.23
1922 2015 4.352893 TCCTGTAGTTCTGGATCATGTCA 58.647 43.478 0.00 0.00 38.86 3.58
1977 2070 1.354101 ATCACCACCCGTACCTTGAA 58.646 50.000 0.00 0.00 0.00 2.69
1978 2071 1.276989 GAATCACCACCCGTACCTTGA 59.723 52.381 0.00 0.00 0.00 3.02
2005 2098 9.805204 AGATAAATCCATGGGTAGATACCTAAT 57.195 33.333 13.02 1.31 45.72 1.73
2050 2143 2.205022 TTTGCCTTCCCAGATGACAG 57.795 50.000 0.00 0.00 0.00 3.51
2064 2157 4.002982 TGTACAGACAGATCACATTTGCC 58.997 43.478 0.00 0.00 0.00 4.52
2108 2201 5.044919 TGTTCTAGATTGAATCCCCACACAT 60.045 40.000 0.75 0.00 0.00 3.21
2133 2226 3.822167 TGCTGACATCAATCACACACAAT 59.178 39.130 0.00 0.00 0.00 2.71
2199 2292 5.491070 TGAGCATAACTTCAATACTGCACT 58.509 37.500 0.00 0.00 32.18 4.40
2249 2342 4.576873 TGCGTGGAAACAAGACAAGAATTA 59.423 37.500 0.00 0.00 46.06 1.40
2270 2363 7.256756 AGCATGACTCTAATCTTAATGTTGC 57.743 36.000 0.00 0.00 0.00 4.17
2455 2548 6.582636 TGGGATTACACATTGATACTCAGAC 58.417 40.000 0.00 0.00 0.00 3.51
2478 2577 6.019559 CACTTCATACTACCACGTCATCATTG 60.020 42.308 0.00 0.00 0.00 2.82
2479 2578 6.042777 CACTTCATACTACCACGTCATCATT 58.957 40.000 0.00 0.00 0.00 2.57
2557 2656 5.625197 GCAACAAATCTGGCATGGATAAACT 60.625 40.000 0.00 0.00 0.00 2.66
2721 2820 0.865769 GTTGAACGTCAGTCCGCATT 59.134 50.000 0.00 0.00 0.00 3.56
2733 2833 1.872952 TGATGGTTCTGCAGTTGAACG 59.127 47.619 14.67 0.00 43.21 3.95
2753 2855 8.896744 CATACCTGACTTTGTGTTGATATGATT 58.103 33.333 0.00 0.00 0.00 2.57
2816 2918 0.102481 GCATCAAGCAGAAGGCCATG 59.898 55.000 5.01 1.11 46.50 3.66
3170 3274 7.768582 TCAAAAGAGAACAAGAAGTATGTCACA 59.231 33.333 0.00 0.00 0.00 3.58
3317 3421 4.887071 TGTTTTAGTCAAGCATTCAGGTGT 59.113 37.500 0.00 0.00 0.00 4.16
3336 3448 2.552315 CCAAGCAACCTACGACATGTTT 59.448 45.455 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.