Multiple sequence alignment - TraesCS5B01G182000

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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 TraesCS5B01G182000 chr5B 100.000 3050 0 0 1 3050 331372959 331376008 0.000000e+00 5633.0
1 TraesCS5B01G182000 chr5D 93.406 3124 109 32 1 3050 291083758 291086858 0.000000e+00 4538.0
2 TraesCS5B01G182000 chr5A 92.357 2342 114 26 81 2399 383417433 383419732 0.000000e+00 3273.0
3 TraesCS5B01G182000 chr5A 85.041 615 27 24 2492 3050 383419852 383420457 1.590000e-157 566.0
4 TraesCS5B01G182000 chr3D 85.535 159 21 2 1772 1929 467750243 467750400 6.770000e-37 165.0
5 TraesCS5B01G182000 chr3D 83.871 124 18 2 1544 1666 329495352 329495474 1.920000e-22 117.0
6 TraesCS5B01G182000 chr3A 85.535 159 21 2 1772 1929 610368482 610368639 6.770000e-37 165.0
7 TraesCS5B01G182000 chr3A 83.065 124 19 2 1544 1666 444534958 444535080 8.940000e-21 111.0
8 TraesCS5B01G182000 chr3B 84.906 159 22 2 1772 1929 621937731 621937888 3.150000e-35 159.0
9 TraesCS5B01G182000 chr3B 83.065 124 19 2 1544 1666 426995428 426995550 8.940000e-21 111.0
10 TraesCS5B01G182000 chr7A 83.065 124 17 4 1545 1666 22543196 22543075 3.220000e-20 110.0
11 TraesCS5B01G182000 chr7D 82.258 124 18 4 1545 1666 21836566 21836445 1.500000e-18 104.0
12 TraesCS5B01G182000 chr4A 83.636 110 13 5 1539 1645 711880571 711880678 6.960000e-17 99.0
13 TraesCS5B01G182000 chr2A 77.439 164 20 16 1513 1666 280198 280354 7.010000e-12 82.4


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 TraesCS5B01G182000 chr5B 331372959 331376008 3049 False 5633.0 5633 100.000 1 3050 1 chr5B.!!$F1 3049
1 TraesCS5B01G182000 chr5D 291083758 291086858 3100 False 4538.0 4538 93.406 1 3050 1 chr5D.!!$F1 3049
2 TraesCS5B01G182000 chr5A 383417433 383420457 3024 False 1919.5 3273 88.699 81 3050 2 chr5A.!!$F1 2969

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
340 355 0.672711 CCGCATCCGCATCATCAGAT 60.673 55.0 0.00 0.0 38.40 2.90 F
1896 1938 0.868602 ACGTGGTCAACAACGAGACG 60.869 55.0 16.52 0.0 35.63 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2064 0.250510 GATTCCTTGGCCGGAGATCC 60.251 60.0 5.05 0.0 33.89 3.36 R
2961 3204 0.388649 GACGCGTCACTCCAATCAGT 60.389 55.0 33.09 0.0 0.00 3.41 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
293 299 4.631740 CCCCCAACCCCCGCTTTT 62.632 66.667 0.00 0.00 0.00 2.27
294 300 2.525629 CCCCAACCCCCGCTTTTT 60.526 61.111 0.00 0.00 0.00 1.94
295 301 2.579657 CCCCAACCCCCGCTTTTTC 61.580 63.158 0.00 0.00 0.00 2.29
296 302 1.834822 CCCAACCCCCGCTTTTTCA 60.835 57.895 0.00 0.00 0.00 2.69
297 303 1.191489 CCCAACCCCCGCTTTTTCAT 61.191 55.000 0.00 0.00 0.00 2.57
298 304 0.684535 CCAACCCCCGCTTTTTCATT 59.315 50.000 0.00 0.00 0.00 2.57
299 305 1.071542 CCAACCCCCGCTTTTTCATTT 59.928 47.619 0.00 0.00 0.00 2.32
300 306 2.486370 CCAACCCCCGCTTTTTCATTTT 60.486 45.455 0.00 0.00 0.00 1.82
301 307 2.805671 CAACCCCCGCTTTTTCATTTTC 59.194 45.455 0.00 0.00 0.00 2.29
340 355 0.672711 CCGCATCCGCATCATCAGAT 60.673 55.000 0.00 0.00 38.40 2.90
382 397 3.047877 CCGAGTTGGACCGGCAAC 61.048 66.667 14.95 14.95 42.00 4.17
400 417 2.327200 ACGGAGAATTTCGGGGAATC 57.673 50.000 0.00 0.00 0.00 2.52
511 540 3.366070 CGCATTATTCTATCCGGACGTCT 60.366 47.826 16.46 0.00 0.00 4.18
529 558 4.559386 GCTCGTTCGGCGCGATTG 62.559 66.667 12.10 0.00 41.07 2.67
627 657 3.199891 GGTGTTATCGTGGCCGCC 61.200 66.667 11.56 1.04 0.00 6.13
628 658 2.125269 GTGTTATCGTGGCCGCCT 60.125 61.111 11.56 0.39 0.00 5.52
681 712 2.438434 GGTGAGCCGTTGATGGGG 60.438 66.667 0.00 0.00 0.00 4.96
884 920 2.444388 CTCCTCCATTCCATTCCATCCA 59.556 50.000 0.00 0.00 0.00 3.41
906 942 3.327757 ACCTTCATCTTCTTGTAGCCACA 59.672 43.478 0.00 0.00 0.00 4.17
911 947 1.067565 TCTTCTTGTAGCCACAGAGCG 60.068 52.381 0.00 0.00 35.67 5.03
967 1003 3.653344 TCTCAGAATTCAGACGGTGTTG 58.347 45.455 8.44 0.00 0.00 3.33
1668 1710 2.525629 TCCTCCGACCACAAGCCA 60.526 61.111 0.00 0.00 0.00 4.75
1701 1743 2.866726 GCTGGAGAGGATCGAGGCC 61.867 68.421 0.00 0.00 42.67 5.19
1752 1794 4.715130 AGGGTGCTGGGCGTCCTA 62.715 66.667 7.97 0.00 33.30 2.94
1764 1806 1.226974 CGTCCTAGCCATGTCACGG 60.227 63.158 0.00 0.00 0.00 4.94
1857 1899 1.226802 CGACGAGTGCCTGATCCTG 60.227 63.158 0.00 0.00 0.00 3.86
1896 1938 0.868602 ACGTGGTCAACAACGAGACG 60.869 55.000 16.52 0.00 35.63 4.18
1908 1950 3.807538 GAGACGGCGTGCGAGGTA 61.808 66.667 21.19 0.00 0.00 3.08
2022 2064 0.386858 ACATCTCCGTTGTCGTCGTG 60.387 55.000 0.00 0.00 35.01 4.35
2085 2127 1.202065 CCGTGATCTTCCATTGCAACG 60.202 52.381 0.00 0.00 0.00 4.10
2135 2181 7.333174 GGATCAATCCAAAACTAGCTCTATAGC 59.667 40.741 4.09 0.00 46.73 2.97
2149 2195 5.031578 GCTCTATAGCGATTCTACCGATTG 58.968 45.833 0.00 0.00 39.39 2.67
2174 2220 9.533253 TGGTTTCTCTTCTTCAAAATTCATTTC 57.467 29.630 0.00 0.00 0.00 2.17
2233 2280 7.526142 TCAGTGGAGTACATAGATTATGGTC 57.474 40.000 0.00 0.00 40.47 4.02
2281 2328 5.030874 GTGTAACCAAAGTTCGATCCTTG 57.969 43.478 0.00 0.00 37.42 3.61
2337 2384 5.812127 AGGTCAGTTTTTGTTCAAATTCTGC 59.188 36.000 16.86 13.74 31.83 4.26
2339 2386 6.258507 GGTCAGTTTTTGTTCAAATTCTGCAT 59.741 34.615 16.86 0.00 31.83 3.96
2367 2414 0.725686 CAGATCTGCAGCTTCCGTTG 59.274 55.000 10.38 0.00 0.00 4.10
2375 2422 2.042831 AGCTTCCGTTGGCATCAGC 61.043 57.895 0.00 0.00 41.10 4.26
2378 2425 0.597568 CTTCCGTTGGCATCAGCAAA 59.402 50.000 0.00 0.00 44.61 3.68
2384 2431 1.250328 TTGGCATCAGCAAACTCTGG 58.750 50.000 0.00 0.00 44.61 3.86
2386 2433 1.251251 GGCATCAGCAAACTCTGGTT 58.749 50.000 0.00 0.00 44.61 3.67
2387 2434 2.224744 TGGCATCAGCAAACTCTGGTTA 60.225 45.455 0.00 0.00 44.61 2.85
2388 2435 2.421424 GGCATCAGCAAACTCTGGTTAG 59.579 50.000 0.00 0.00 44.61 2.34
2389 2436 3.338249 GCATCAGCAAACTCTGGTTAGA 58.662 45.455 0.00 0.00 41.58 2.10
2390 2437 3.944015 GCATCAGCAAACTCTGGTTAGAT 59.056 43.478 0.00 0.00 41.58 1.98
2414 2463 5.243730 TGGATGATGCGTATCTCATGTCTTA 59.756 40.000 14.76 0.00 32.36 2.10
2415 2464 6.159293 GGATGATGCGTATCTCATGTCTTAA 58.841 40.000 14.76 0.00 32.36 1.85
2416 2465 6.090088 GGATGATGCGTATCTCATGTCTTAAC 59.910 42.308 14.76 0.00 32.36 2.01
2417 2466 6.149129 TGATGCGTATCTCATGTCTTAACT 57.851 37.500 14.76 0.00 34.31 2.24
2418 2467 6.573434 TGATGCGTATCTCATGTCTTAACTT 58.427 36.000 14.76 0.00 34.31 2.66
2419 2468 6.697455 TGATGCGTATCTCATGTCTTAACTTC 59.303 38.462 14.76 0.00 34.31 3.01
2420 2469 5.961272 TGCGTATCTCATGTCTTAACTTCA 58.039 37.500 0.00 0.00 0.00 3.02
2444 2497 7.125659 TCACAAGTTCAGATTAGATGGGTGATA 59.874 37.037 0.00 0.00 0.00 2.15
2447 2500 8.373981 CAAGTTCAGATTAGATGGGTGATATCT 58.626 37.037 3.98 0.00 38.40 1.98
2449 2502 7.955185 AGTTCAGATTAGATGGGTGATATCTCT 59.045 37.037 3.98 0.63 36.38 3.10
2451 2504 7.244558 TCAGATTAGATGGGTGATATCTCTGT 58.755 38.462 3.98 0.00 36.38 3.41
2467 2520 9.638239 GATATCTCTGTATCTTCATCAACTTCC 57.362 37.037 0.00 0.00 0.00 3.46
2505 2686 5.008811 CCGACCTGTTAGTAGGACTCAATAG 59.991 48.000 0.00 0.00 40.42 1.73
2506 2687 5.589452 CGACCTGTTAGTAGGACTCAATAGT 59.411 44.000 0.00 0.00 40.42 2.12
2528 2711 7.426929 AGTGTTCTGATGTGTTCAAATCTAC 57.573 36.000 4.85 2.22 32.78 2.59
2555 2738 6.461110 TTACACTAGGTACTGATGGTTAGC 57.539 41.667 0.00 0.00 41.52 3.09
2748 2959 1.207791 GATCAGAGGCTCCCAAGGAA 58.792 55.000 11.71 0.00 0.00 3.36
2796 3015 3.537206 AAGCACGACACCTGCCCTC 62.537 63.158 0.00 0.00 35.01 4.30
2797 3016 4.008933 GCACGACACCTGCCCTCT 62.009 66.667 0.00 0.00 0.00 3.69
2875 3106 0.462047 CCATTCCGTCCAGCTGGTAC 60.462 60.000 31.58 24.62 36.34 3.34
2930 3173 1.359848 CACCTCGACAAATTCCCTCG 58.640 55.000 0.00 0.00 0.00 4.63
2961 3204 3.662759 AAAGAAGGGGTTTGTCACTCA 57.337 42.857 0.00 0.00 0.00 3.41
3010 3258 5.508825 CCATTGAAAAATCGTCCACTCCAAA 60.509 40.000 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 241 2.124570 CCACCCCATTGGCTCTCG 60.125 66.667 0.00 0.00 37.83 4.04
297 303 8.803799 CGGATTCGAAAAGAAAAGAAAAGAAAA 58.196 29.630 0.00 0.00 42.91 2.29
298 304 7.043656 GCGGATTCGAAAAGAAAAGAAAAGAAA 60.044 33.333 0.00 0.00 42.91 2.52
299 305 6.416750 GCGGATTCGAAAAGAAAAGAAAAGAA 59.583 34.615 0.00 0.00 42.91 2.52
300 306 5.912955 GCGGATTCGAAAAGAAAAGAAAAGA 59.087 36.000 0.00 0.00 42.91 2.52
301 307 5.685511 TGCGGATTCGAAAAGAAAAGAAAAG 59.314 36.000 0.00 0.00 42.91 2.27
340 355 2.031465 GGCAAAGGTTCCGTCGGA 59.969 61.111 10.71 10.71 0.00 4.55
380 395 2.640184 GATTCCCCGAAATTCTCCGTT 58.360 47.619 0.00 0.00 0.00 4.44
382 397 1.594331 GGATTCCCCGAAATTCTCCG 58.406 55.000 0.00 0.00 0.00 4.63
535 564 3.732048 TGAAAGTCCAATCTAACCCCC 57.268 47.619 0.00 0.00 0.00 5.40
588 617 7.506261 ACACCCTCGATAATCAACTAATCTAGT 59.494 37.037 0.00 0.00 41.73 2.57
605 635 1.514087 GCCACGATAACACCCTCGA 59.486 57.895 0.00 0.00 38.24 4.04
627 657 1.954146 CAACCGGGACACGTGACAG 60.954 63.158 25.01 14.61 42.24 3.51
628 658 2.107343 CAACCGGGACACGTGACA 59.893 61.111 25.01 0.00 42.24 3.58
855 886 1.648568 TGGAATGGAGGAGAGGAGTCT 59.351 52.381 0.00 0.00 34.86 3.24
884 920 3.327757 TGTGGCTACAAGAAGATGAAGGT 59.672 43.478 0.00 0.00 32.88 3.50
967 1003 0.253327 CCCCTCTTGCCCTAGACAAC 59.747 60.000 0.00 0.00 0.00 3.32
1376 1418 2.125512 GCTCGTGCATCCGGTCTT 60.126 61.111 0.00 0.00 39.41 3.01
1749 1791 2.203070 GCCCGTGACATGGCTAGG 60.203 66.667 8.32 2.62 44.46 3.02
1782 1824 4.647654 GTCACGAACGGCTTCAGA 57.352 55.556 0.00 0.00 0.00 3.27
1869 1911 1.331399 TGTTGACCACGTCCCACAGA 61.331 55.000 0.00 0.00 0.00 3.41
2022 2064 0.250510 GATTCCTTGGCCGGAGATCC 60.251 60.000 5.05 0.00 33.89 3.36
2144 2190 7.862372 TGAATTTTGAAGAAGAGAAACCAATCG 59.138 33.333 0.00 0.00 0.00 3.34
2149 2195 9.755804 AGAAATGAATTTTGAAGAAGAGAAACC 57.244 29.630 0.00 0.00 0.00 3.27
2181 2227 5.595542 TGATCCAGGGAGAAATATTGCAAAG 59.404 40.000 1.71 0.00 0.00 2.77
2233 2280 5.240844 AGTTGTTATTTCTTTCCTCAACCCG 59.759 40.000 0.00 0.00 35.71 5.28
2267 2314 7.013274 TCTGTTTCAATTCAAGGATCGAACTTT 59.987 33.333 3.27 0.00 0.00 2.66
2280 2327 7.389803 TGAACTGAACTTCTGTTTCAATTCA 57.610 32.000 13.49 5.19 38.41 2.57
2281 2328 8.131100 TGATGAACTGAACTTCTGTTTCAATTC 58.869 33.333 13.49 0.55 38.41 2.17
2337 2384 2.476997 CTGCAGATCTGAATCGAGCATG 59.523 50.000 27.04 5.64 42.67 4.06
2339 2386 1.805495 GCTGCAGATCTGAATCGAGCA 60.805 52.381 27.04 13.67 41.96 4.26
2367 2414 1.251251 AACCAGAGTTTGCTGATGCC 58.749 50.000 0.00 0.00 38.14 4.40
2375 2422 5.008415 GCATCATCCATCTAACCAGAGTTTG 59.992 44.000 0.00 0.00 37.42 2.93
2378 2425 3.244009 CGCATCATCCATCTAACCAGAGT 60.244 47.826 0.00 0.00 33.22 3.24
2380 2427 2.700371 ACGCATCATCCATCTAACCAGA 59.300 45.455 0.00 0.00 34.56 3.86
2381 2428 3.117491 ACGCATCATCCATCTAACCAG 57.883 47.619 0.00 0.00 0.00 4.00
2382 2429 4.528206 AGATACGCATCATCCATCTAACCA 59.472 41.667 0.00 0.00 33.21 3.67
2383 2430 5.078411 AGATACGCATCATCCATCTAACC 57.922 43.478 0.00 0.00 33.21 2.85
2384 2431 5.714047 TGAGATACGCATCATCCATCTAAC 58.286 41.667 0.00 0.00 33.21 2.34
2386 2433 5.420104 ACATGAGATACGCATCATCCATCTA 59.580 40.000 0.00 0.00 33.91 1.98
2387 2434 4.222366 ACATGAGATACGCATCATCCATCT 59.778 41.667 0.00 0.00 33.91 2.90
2388 2435 4.502016 ACATGAGATACGCATCATCCATC 58.498 43.478 0.00 0.00 33.91 3.51
2389 2436 4.222366 AGACATGAGATACGCATCATCCAT 59.778 41.667 0.00 0.00 33.91 3.41
2390 2437 3.575687 AGACATGAGATACGCATCATCCA 59.424 43.478 0.00 0.00 33.91 3.41
2415 2464 6.176183 CCCATCTAATCTGAACTTGTGAAGT 58.824 40.000 0.00 0.00 45.46 3.01
2416 2465 6.093219 CACCCATCTAATCTGAACTTGTGAAG 59.907 42.308 0.00 0.00 0.00 3.02
2417 2466 5.939883 CACCCATCTAATCTGAACTTGTGAA 59.060 40.000 0.00 0.00 0.00 3.18
2418 2467 5.248248 TCACCCATCTAATCTGAACTTGTGA 59.752 40.000 0.00 0.00 0.00 3.58
2419 2468 5.491070 TCACCCATCTAATCTGAACTTGTG 58.509 41.667 0.00 0.00 0.00 3.33
2420 2469 5.762179 TCACCCATCTAATCTGAACTTGT 57.238 39.130 0.00 0.00 0.00 3.16
2444 2497 7.673641 AGGAAGTTGATGAAGATACAGAGAT 57.326 36.000 0.00 0.00 0.00 2.75
2447 2500 8.367660 ACTTAGGAAGTTGATGAAGATACAGA 57.632 34.615 0.00 0.00 39.04 3.41
2467 2520 2.480419 CAGGTCGGTTTCAGCAACTTAG 59.520 50.000 0.00 0.00 35.46 2.18
2474 2527 2.165319 ACTAACAGGTCGGTTTCAGC 57.835 50.000 0.00 0.00 32.29 4.26
2475 2528 3.508793 TCCTACTAACAGGTCGGTTTCAG 59.491 47.826 0.00 0.00 36.99 3.02
2505 2686 6.073765 ACGTAGATTTGAACACATCAGAACAC 60.074 38.462 0.00 0.00 39.77 3.32
2506 2687 5.989168 ACGTAGATTTGAACACATCAGAACA 59.011 36.000 0.00 0.00 39.77 3.18
2528 2711 6.630444 ACCATCAGTACCTAGTGTAATACG 57.370 41.667 0.00 0.00 0.00 3.06
2555 2738 4.207224 CGATATAGTTTGTGCTTCACCGAG 59.793 45.833 0.00 0.00 32.73 4.63
2667 2868 5.293079 CGGATCTGTTCTCTTTGATTTCCTC 59.707 44.000 0.00 0.00 0.00 3.71
2668 2869 5.181748 CGGATCTGTTCTCTTTGATTTCCT 58.818 41.667 0.00 0.00 0.00 3.36
2669 2870 4.333926 CCGGATCTGTTCTCTTTGATTTCC 59.666 45.833 0.00 0.00 0.00 3.13
2748 2959 4.696479 ATCCCACAAGAAATATCTCGCT 57.304 40.909 0.00 0.00 33.77 4.93
2844 3075 2.124151 GAATGGCCTGGACCGCAT 60.124 61.111 3.32 0.00 0.00 4.73
2875 3106 3.478540 GGGAAGAATGAGAACCCCG 57.521 57.895 0.00 0.00 35.00 5.73
2930 3173 6.097839 ACAAACCCCTTCTTTTAAAGAGGAAC 59.902 38.462 16.74 0.00 39.03 3.62
2961 3204 0.388649 GACGCGTCACTCCAATCAGT 60.389 55.000 33.09 0.00 0.00 3.41
2986 3234 3.505680 TGGAGTGGACGATTTTTCAATGG 59.494 43.478 0.00 0.00 0.00 3.16
3010 3258 2.749865 CGCCGGACGCAAATCATGT 61.750 57.895 5.05 0.00 37.30 3.21


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

AutoCloner maintained by Alex Coulton.