Multiple sequence alignment - TraesCS5A01G077800

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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 TraesCS5A01G077800 chr5A 100.000 2375 0 0 1 2375 94783467 94781093 0.000000e+00 4386.0
1 TraesCS5A01G077800 chr5A 95.947 1357 54 1 423 1778 94795504 94794148 0.000000e+00 2200.0
2 TraesCS5A01G077800 chr5A 93.610 1158 68 5 420 1572 433069204 433068048 0.000000e+00 1724.0
3 TraesCS5A01G077800 chr5A 93.980 598 33 1 1778 2375 94764587 94763993 0.000000e+00 902.0
4 TraesCS5A01G077800 chr5A 84.587 545 74 10 1 541 502877190 502877728 1.250000e-147 532.0
5 TraesCS5A01G077800 chr5A 80.696 632 104 13 13 633 36725063 36725687 2.140000e-130 475.0
6 TraesCS5A01G077800 chr5A 88.579 394 41 4 1778 2169 146435793 146435402 2.140000e-130 475.0
7 TraesCS5A01G077800 chr5A 80.573 628 107 13 12 630 218845274 218844653 9.940000e-129 470.0
8 TraesCS5A01G077800 chr5A 88.710 372 42 0 1037 1408 295687381 295687752 2.780000e-124 455.0
9 TraesCS5A01G077800 chr5A 85.151 431 59 5 1778 2205 146298200 146297772 1.010000e-118 436.0
10 TraesCS5A01G077800 chr3A 93.010 1359 90 5 423 1778 195156760 195155404 0.000000e+00 1978.0
11 TraesCS5A01G077800 chr3A 95.297 893 41 1 11 902 195148918 195148026 0.000000e+00 1415.0
12 TraesCS5A01G077800 chr3A 92.382 827 62 1 942 1767 195148028 195147202 0.000000e+00 1177.0
13 TraesCS5A01G077800 chr3A 83.158 570 86 9 21 585 623011447 623010883 1.630000e-141 512.0
14 TraesCS5A01G077800 chr3A 85.401 137 14 4 2234 2367 119912145 119912012 1.140000e-28 137.0
15 TraesCS5A01G077800 chr1A 86.510 682 74 16 259 934 340353277 340353946 0.000000e+00 734.0
16 TraesCS5A01G077800 chr1A 80.485 907 144 23 23 916 446742979 446743865 0.000000e+00 664.0
17 TraesCS5A01G077800 chr1A 79.017 834 152 17 36 857 196741494 196740672 1.240000e-152 549.0
18 TraesCS5A01G077800 chr2A 89.980 489 35 11 1778 2256 310856679 310857163 9.330000e-174 619.0
19 TraesCS5A01G077800 chr2A 89.300 486 34 13 1778 2254 310848207 310848683 5.650000e-166 593.0
20 TraesCS5A01G077800 chr2A 83.019 583 86 13 11 585 150660021 150660598 1.260000e-142 516.0
21 TraesCS5A01G077800 chr2A 75.718 383 59 26 1972 2334 323973943 323974311 6.790000e-36 161.0
22 TraesCS5A01G077800 chr4A 91.549 426 29 7 512 934 309517403 309517824 4.400000e-162 580.0
23 TraesCS5A01G077800 chr7D 82.753 632 91 16 12 633 406002203 406001580 4.460000e-152 547.0
24 TraesCS5A01G077800 chr2D 83.306 605 88 12 11 606 252161700 252162300 1.610000e-151 545.0
25 TraesCS5A01G077800 chr2D 82.537 607 94 11 1 603 570175762 570176360 7.520000e-145 523.0
26 TraesCS5A01G077800 chr2D 93.220 59 4 0 1076 1134 414415780 414415838 1.170000e-13 87.9
27 TraesCS5A01G077800 chr2D 82.418 91 8 7 2287 2375 264318402 264318318 3.270000e-09 73.1
28 TraesCS5A01G077800 chr2D 81.818 88 8 7 2287 2372 144954067 144954148 1.520000e-07 67.6
29 TraesCS5A01G077800 chr2D 80.952 84 7 6 2234 2316 344575449 344575374 9.170000e-05 58.4
30 TraesCS5A01G077800 chr5D 85.150 532 62 17 411 934 82880142 82879620 1.620000e-146 529.0
31 TraesCS5A01G077800 chr5D 90.588 85 8 0 1481 1565 78427039 78426955 1.930000e-21 113.0
32 TraesCS5A01G077800 chr1B 81.150 626 107 9 12 631 211259735 211259115 2.120000e-135 492.0
33 TraesCS5A01G077800 chr1B 86.131 411 52 3 1778 2186 248440701 248441108 2.800000e-119 438.0
34 TraesCS5A01G077800 chr1B 83.885 453 63 9 1779 2226 248424872 248425319 7.850000e-115 424.0
35 TraesCS5A01G077800 chr1B 85.330 409 56 3 1778 2186 446984171 446983767 1.020000e-113 420.0
36 TraesCS5A01G077800 chr1B 92.784 97 6 1 2237 2333 169315637 169315542 3.180000e-29 139.0
37 TraesCS5A01G077800 chr3D 85.649 439 47 12 1779 2205 168370515 168370949 4.660000e-122 448.0
38 TraesCS5A01G077800 chr3D 85.577 416 51 9 1817 2226 164998287 164998699 6.070000e-116 427.0
39 TraesCS5A01G077800 chr3D 81.818 88 8 7 2287 2372 197958631 197958712 1.520000e-07 67.6
40 TraesCS5A01G077800 chr3D 97.059 34 1 0 2342 2375 405201385 405201352 9.170000e-05 58.4
41 TraesCS5A01G077800 chr6D 89.683 126 9 4 2231 2354 325429162 325429039 8.790000e-35 158.0
42 TraesCS5A01G077800 chr4B 85.714 126 13 5 2231 2354 353832136 353832014 6.890000e-26 128.0


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 TraesCS5A01G077800 chr5A 94781093 94783467 2374 True 4386 4386 100.0000 1 2375 1 chr5A.!!$R2 2374
1 TraesCS5A01G077800 chr5A 94794148 94795504 1356 True 2200 2200 95.9470 423 1778 1 chr5A.!!$R3 1355
2 TraesCS5A01G077800 chr5A 433068048 433069204 1156 True 1724 1724 93.6100 420 1572 1 chr5A.!!$R7 1152
3 TraesCS5A01G077800 chr5A 94763993 94764587 594 True 902 902 93.9800 1778 2375 1 chr5A.!!$R1 597
4 TraesCS5A01G077800 chr5A 502877190 502877728 538 False 532 532 84.5870 1 541 1 chr5A.!!$F3 540
5 TraesCS5A01G077800 chr5A 36725063 36725687 624 False 475 475 80.6960 13 633 1 chr5A.!!$F1 620
6 TraesCS5A01G077800 chr5A 218844653 218845274 621 True 470 470 80.5730 12 630 1 chr5A.!!$R6 618
7 TraesCS5A01G077800 chr3A 195155404 195156760 1356 True 1978 1978 93.0100 423 1778 1 chr3A.!!$R2 1355
8 TraesCS5A01G077800 chr3A 195147202 195148918 1716 True 1296 1415 93.8395 11 1767 2 chr3A.!!$R4 1756
9 TraesCS5A01G077800 chr3A 623010883 623011447 564 True 512 512 83.1580 21 585 1 chr3A.!!$R3 564
10 TraesCS5A01G077800 chr1A 340353277 340353946 669 False 734 734 86.5100 259 934 1 chr1A.!!$F1 675
11 TraesCS5A01G077800 chr1A 446742979 446743865 886 False 664 664 80.4850 23 916 1 chr1A.!!$F2 893
12 TraesCS5A01G077800 chr1A 196740672 196741494 822 True 549 549 79.0170 36 857 1 chr1A.!!$R1 821
13 TraesCS5A01G077800 chr2A 150660021 150660598 577 False 516 516 83.0190 11 585 1 chr2A.!!$F1 574
14 TraesCS5A01G077800 chr7D 406001580 406002203 623 True 547 547 82.7530 12 633 1 chr7D.!!$R1 621
15 TraesCS5A01G077800 chr2D 252161700 252162300 600 False 545 545 83.3060 11 606 1 chr2D.!!$F2 595
16 TraesCS5A01G077800 chr2D 570175762 570176360 598 False 523 523 82.5370 1 603 1 chr2D.!!$F4 602
17 TraesCS5A01G077800 chr5D 82879620 82880142 522 True 529 529 85.1500 411 934 1 chr5D.!!$R2 523
18 TraesCS5A01G077800 chr1B 211259115 211259735 620 True 492 492 81.1500 12 631 1 chr1B.!!$R2 619

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
436 454 0.323087 AGATTTGTAACACCCCGGGC 60.323 55.000 17.73 0.0 0.00 6.13 F
1226 1270 2.880879 CCATCACGGTCGTCTGCG 60.881 66.667 0.00 0.0 39.92 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1276 1320 0.329261 CATGGTGGAGGAAGAAGGCA 59.671 55.0 0.0 0.0 0.0 4.75 R
2290 2338 0.637195 TAAGGAGAGGGAGAGGTGGG 59.363 60.0 0.0 0.0 0.0 4.61 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
87 91 7.809806 CCTGCTTGAAACTTCTTATTTACCTTG 59.190 37.037 0.00 0.00 0.00 3.61
152 158 4.873746 ACTATCGATCACATTTCCCGAT 57.126 40.909 0.00 0.00 41.88 4.18
183 190 4.080863 CCAGATAGCCACCTTGTAGAGTTT 60.081 45.833 0.00 0.00 0.00 2.66
246 260 5.492855 TTGGAGTTTCCGAAGAAAGGATA 57.507 39.130 0.00 0.00 42.60 2.59
393 411 5.105473 CCTTACACCACCTCTTAAATCTCGA 60.105 44.000 0.00 0.00 0.00 4.04
436 454 0.323087 AGATTTGTAACACCCCGGGC 60.323 55.000 17.73 0.00 0.00 6.13
1214 1258 3.549900 TTGTGCGGCAGCTCCATCA 62.550 57.895 10.92 0.00 45.42 3.07
1226 1270 2.880879 CCATCACGGTCGTCTGCG 60.881 66.667 0.00 0.00 39.92 5.18
1276 1320 1.662760 CATCATCCGCGACGCTCAT 60.663 57.895 19.02 6.41 0.00 2.90
1290 1334 0.254178 GCTCATGCCTTCTTCCTCCA 59.746 55.000 0.00 0.00 0.00 3.86
1329 1373 2.205074 GTCGTTCAATCCGCATCATCT 58.795 47.619 0.00 0.00 0.00 2.90
1392 1436 2.026822 GTGAGCTCCTCTTTGGATTCCA 60.027 50.000 12.15 0.00 45.16 3.53
1393 1437 2.238144 TGAGCTCCTCTTTGGATTCCAG 59.762 50.000 12.15 0.00 45.16 3.86
1395 1439 1.661341 CTCCTCTTTGGATTCCAGCG 58.339 55.000 5.36 1.47 45.16 5.18
1409 1456 4.048470 AGCGCTTTCCCCCTTCCC 62.048 66.667 2.64 0.00 0.00 3.97
1788 1836 2.813908 GCCTACTTGTGACGCCCG 60.814 66.667 0.00 0.00 0.00 6.13
1804 1852 2.549349 CGCCCGGGTAATTAAGCTACAT 60.549 50.000 24.63 0.00 0.00 2.29
1805 1853 2.812011 GCCCGGGTAATTAAGCTACATG 59.188 50.000 24.63 0.00 0.00 3.21
1814 1862 8.639761 GGGTAATTAAGCTACATGAACTCTCTA 58.360 37.037 0.00 0.00 0.00 2.43
1836 1884 3.684788 ACTAATGATGCCACGTCACTTTC 59.315 43.478 0.00 0.00 0.00 2.62
1848 1896 3.250040 ACGTCACTTTCATTACTGTTGCC 59.750 43.478 0.00 0.00 0.00 4.52
1857 1905 3.825585 TCATTACTGTTGCCAATCTTGCA 59.174 39.130 0.00 0.00 36.84 4.08
1871 1919 6.148948 CCAATCTTGCATTAGTTCGAAAACA 58.851 36.000 0.00 0.00 37.88 2.83
1948 1996 8.827177 AACACTAAAATGTTCGTGAGATAAGA 57.173 30.769 7.26 0.00 38.44 2.10
2106 2154 4.747583 AGTTGCCCAAAAGTTAATAGGGT 58.252 39.130 0.00 0.00 41.67 4.34
2238 2286 2.207229 GGAAAACACCCCCACTGGC 61.207 63.158 0.00 0.00 0.00 4.85
2312 2360 2.604139 CACCTCTCCCTCTCCTTATCC 58.396 57.143 0.00 0.00 0.00 2.59
2327 2375 2.884179 TATCCCCTGGTCCCCGTGAC 62.884 65.000 0.00 0.00 43.67 3.67
2372 2420 2.207924 ACTCGCTCCTCCCACGTTT 61.208 57.895 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.585289 TGAAAGGGGTATAGAGCAACACA 59.415 43.478 0.00 0.00 0.00 3.72
9 10 3.369052 CGTGAAAGGGGTATAGAGCAACA 60.369 47.826 0.00 0.00 0.00 3.33
152 158 6.727394 ACAAGGTGGCTATCTGGTTTATAAA 58.273 36.000 0.00 0.00 0.00 1.40
183 190 1.120530 GGGTAGCTCCGGAAGAATGA 58.879 55.000 5.23 0.00 37.00 2.57
393 411 4.336993 CCTGCACTACTAGAAATCTCGTCT 59.663 45.833 0.00 0.00 0.00 4.18
406 424 5.238583 GTGTTACAAATCTCCTGCACTACT 58.761 41.667 0.00 0.00 0.00 2.57
436 454 4.870426 ACAGGAGTTTATTGTAGCATGACG 59.130 41.667 0.00 0.00 0.00 4.35
1182 1226 1.003839 CACAAGCTCCAAGCCGGTA 60.004 57.895 1.90 0.00 43.77 4.02
1214 1258 0.952497 TAGAAGACGCAGACGACCGT 60.952 55.000 0.00 0.00 43.93 4.83
1226 1270 4.276431 CCTTGATCCGGTAGAGTAGAAGAC 59.724 50.000 0.00 0.00 0.00 3.01
1276 1320 0.329261 CATGGTGGAGGAAGAAGGCA 59.671 55.000 0.00 0.00 0.00 4.75
1290 1334 4.388499 GTGTCGGACGGCCATGGT 62.388 66.667 14.67 0.00 0.00 3.55
1392 1436 4.048470 GGGAAGGGGGAAAGCGCT 62.048 66.667 2.64 2.64 0.00 5.92
1409 1456 2.026879 CGGCAAACAACAACGGGG 59.973 61.111 0.00 0.00 0.00 5.73
1572 1620 3.554692 GAACGGCGACAGATGCGG 61.555 66.667 16.62 0.00 38.48 5.69
1630 1678 2.268280 CAGAGGGCAGCAGAGGTG 59.732 66.667 0.00 0.00 0.00 4.00
1744 1792 1.749638 CGAGTAGGACAGGGCTCGT 60.750 63.158 0.00 0.00 43.79 4.18
1788 1836 7.501844 AGAGAGTTCATGTAGCTTAATTACCC 58.498 38.462 0.00 0.00 0.00 3.69
1804 1852 5.450550 CGTGGCATCATTAGTAGAGAGTTCA 60.451 44.000 0.00 0.00 0.00 3.18
1805 1853 4.979197 CGTGGCATCATTAGTAGAGAGTTC 59.021 45.833 0.00 0.00 0.00 3.01
1814 1862 3.334583 AAGTGACGTGGCATCATTAGT 57.665 42.857 0.00 0.00 0.00 2.24
1848 1896 7.621832 TTGTTTTCGAACTAATGCAAGATTG 57.378 32.000 0.00 0.00 0.00 2.67
1934 1982 7.881643 ATGCATTATCTCTTATCTCACGAAC 57.118 36.000 0.00 0.00 0.00 3.95
2219 2267 1.541672 CCAGTGGGGGTGTTTTCCT 59.458 57.895 0.00 0.00 0.00 3.36
2263 2311 3.842721 TTGGTTGGCCCATGGGGTG 62.843 63.158 32.23 7.58 46.51 4.61
2264 2312 3.526428 TTGGTTGGCCCATGGGGT 61.526 61.111 32.23 0.00 46.51 4.95
2290 2338 0.637195 TAAGGAGAGGGAGAGGTGGG 59.363 60.000 0.00 0.00 0.00 4.61
2327 2375 1.553248 TGGGGTGTCACTCGATTTAGG 59.447 52.381 2.35 0.00 0.00 2.69
2328 2376 2.233922 AGTGGGGTGTCACTCGATTTAG 59.766 50.000 2.35 0.00 43.82 1.85


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

AutoCloner maintained by Alex Coulton.