Multiple sequence alignment - TraesCS1B01G358500

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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 TraesCS1B01G358500 chr1B 100.000 3221 0 0 1 3221 588004994 588008214 0.000000e+00 5949
1 TraesCS1B01G358500 chr1B 83.680 2212 315 27 105 2287 587991098 587993292 0.000000e+00 2043
2 TraesCS1B01G358500 chr1D 95.805 1788 62 8 1 1780 434337315 434339097 0.000000e+00 2874
3 TraesCS1B01G358500 chr1D 94.572 1437 74 3 1785 3219 434339136 434340570 0.000000e+00 2218
4 TraesCS1B01G358500 chr1D 80.299 2005 321 48 700 2659 434284612 434286587 0.000000e+00 1447
5 TraesCS1B01G358500 chr1D 86.271 539 66 8 105 637 434283786 434284322 2.150000e-161 579
6 TraesCS1B01G358500 chr1A 81.863 2619 381 57 105 2659 532477033 532479621 0.000000e+00 2119
7 TraesCS1B01G358500 chr1A 75.807 2261 425 68 1 2210 532487803 532489992 0.000000e+00 1033
8 TraesCS1B01G358500 chr7A 76.572 1272 249 32 961 2206 77562658 77561410 0.000000e+00 652


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 TraesCS1B01G358500 chr1B 588004994 588008214 3220 False 5949 5949 100.0000 1 3221 1 chr1B.!!$F2 3220
1 TraesCS1B01G358500 chr1B 587991098 587993292 2194 False 2043 2043 83.6800 105 2287 1 chr1B.!!$F1 2182
2 TraesCS1B01G358500 chr1D 434337315 434340570 3255 False 2546 2874 95.1885 1 3219 2 chr1D.!!$F2 3218
3 TraesCS1B01G358500 chr1D 434283786 434286587 2801 False 1013 1447 83.2850 105 2659 2 chr1D.!!$F1 2554
4 TraesCS1B01G358500 chr1A 532477033 532479621 2588 False 2119 2119 81.8630 105 2659 1 chr1A.!!$F1 2554
5 TraesCS1B01G358500 chr1A 532487803 532489992 2189 False 1033 1033 75.8070 1 2210 1 chr1A.!!$F2 2209
6 TraesCS1B01G358500 chr7A 77561410 77562658 1248 True 652 652 76.5720 961 2206 1 chr7A.!!$R1 1245

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
816 1075 0.177141 TGCCGTCCCTATAGTTGTGC 59.823 55.000 0.0 0.0 0.0 4.57 F
1410 1694 3.202818 AGATGGGAAATACATGGCACTCA 59.797 43.478 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 2113 1.021390 CAAGCCGAAGTCCGCAATCT 61.021 55.0 0.0 0.0 36.84 2.40 R
3193 3564 0.609662 ATGCAAAAGATGGCACCCAC 59.390 50.0 0.0 0.0 43.75 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
99 100 1.632965 GGGCCCCAAGGATTAGACGT 61.633 60.000 12.23 0.00 33.47 4.34
188 190 2.038557 TGGAGAAAGGGTTACACTGCTC 59.961 50.000 8.63 8.63 0.00 4.26
205 210 3.937706 CTGCTCCTATCAACTGAAACTGG 59.062 47.826 0.00 0.00 0.00 4.00
218 223 3.674997 TGAAACTGGTCCACTGCTTATC 58.325 45.455 0.00 0.00 0.00 1.75
260 265 1.213013 CGAGAGGTCTGAACGGTGG 59.787 63.158 0.00 0.00 0.00 4.61
341 346 2.113860 TCTGCCTTAATGTCCACTGC 57.886 50.000 0.00 0.00 0.00 4.40
512 519 5.505286 CCATTCGCATGAATTACTTCTGAC 58.495 41.667 0.00 0.00 42.14 3.51
595 603 5.363868 TGGAGTAATCCCATCTAGACTTGTG 59.636 44.000 6.78 0.00 0.00 3.33
599 607 7.560368 AGTAATCCCATCTAGACTTGTGAAAG 58.440 38.462 0.00 0.00 0.00 2.62
689 916 8.437360 TCTATCTACCGTTATAGTCGACAAAA 57.563 34.615 19.50 5.74 0.00 2.44
786 1033 5.273170 CAAACAAACGAAAGAGCAATCTGA 58.727 37.500 0.00 0.00 0.00 3.27
788 1035 4.130118 ACAAACGAAAGAGCAATCTGACT 58.870 39.130 0.00 0.00 0.00 3.41
816 1075 0.177141 TGCCGTCCCTATAGTTGTGC 59.823 55.000 0.00 0.00 0.00 4.57
1004 1268 4.403432 GGATCCACACAATGAAACCATGAT 59.597 41.667 6.95 0.00 0.00 2.45
1008 1272 4.460034 CCACACAATGAAACCATGATGAGA 59.540 41.667 0.00 0.00 0.00 3.27
1160 1424 4.678574 CGGGTACGTCTATGATGGTTTTCA 60.679 45.833 0.00 0.00 34.81 2.69
1355 1639 7.859377 GCTCATATTTTGACACGAATTCATCAT 59.141 33.333 6.22 0.00 0.00 2.45
1395 1679 3.517296 TTGGTTACTGCAAAGATGGGA 57.483 42.857 0.00 0.00 0.00 4.37
1397 1681 3.838565 TGGTTACTGCAAAGATGGGAAA 58.161 40.909 0.00 0.00 0.00 3.13
1410 1694 3.202818 AGATGGGAAATACATGGCACTCA 59.797 43.478 0.00 0.00 0.00 3.41
1621 1908 3.348119 TGCACAAGGTACACACTTCAAA 58.652 40.909 0.00 0.00 0.00 2.69
1625 1914 3.214328 CAAGGTACACACTTCAAAGCCT 58.786 45.455 0.00 0.00 0.00 4.58
1875 2201 2.670592 GTTGGCACACCCGGGTAC 60.671 66.667 29.72 16.77 39.29 3.34
1892 2218 1.899437 TACGTCGACCCCGAGTACCT 61.899 60.000 10.58 0.00 46.52 3.08
1912 2238 2.965147 GCGACGATGCAGCCAACAA 61.965 57.895 0.00 0.00 34.15 2.83
1917 2243 2.225491 GACGATGCAGCCAACAACTAAA 59.775 45.455 0.00 0.00 0.00 1.85
1931 2257 7.523219 CCAACAACTAAAAGCGATGTGTATAA 58.477 34.615 0.00 0.00 0.00 0.98
2062 2388 1.674359 TGAAAGTGTGGTTGATGCGT 58.326 45.000 0.00 0.00 0.00 5.24
2101 2427 6.707440 ATGATGTTAACAGTGTGTGGAAAA 57.293 33.333 14.65 0.00 0.00 2.29
2112 2438 4.057432 GTGTGTGGAAAATGGTGGAAATG 58.943 43.478 0.00 0.00 0.00 2.32
2211 2537 1.045350 AGCTCGAGGAAGGCAGCATA 61.045 55.000 15.58 0.00 34.08 3.14
2212 2538 0.034616 GCTCGAGGAAGGCAGCATAT 59.965 55.000 15.58 0.00 0.00 1.78
2215 2541 3.131223 GCTCGAGGAAGGCAGCATATATA 59.869 47.826 15.58 0.00 0.00 0.86
2216 2542 4.736168 GCTCGAGGAAGGCAGCATATATAG 60.736 50.000 15.58 0.00 0.00 1.31
2346 2698 2.826428 CATTGTCCATCGGTCCTACTG 58.174 52.381 0.00 0.00 0.00 2.74
2355 2707 0.732880 CGGTCCTACTGCACGTTGAG 60.733 60.000 0.00 0.00 0.00 3.02
2359 2711 1.684450 TCCTACTGCACGTTGAGAACA 59.316 47.619 0.00 0.00 0.00 3.18
2459 2814 2.193447 TCTCGATGGAATTTCGAAGCG 58.807 47.619 0.00 2.96 44.25 4.68
2595 2966 5.826643 AGTAGGCCATTCCTGATTGTTTAA 58.173 37.500 5.01 0.00 46.98 1.52
2738 3109 0.108186 CGCTAATGCAGACCACTCCA 60.108 55.000 0.00 0.00 39.64 3.86
2742 3113 3.683847 GCTAATGCAGACCACTCCATCTT 60.684 47.826 0.00 0.00 39.41 2.40
2756 3127 7.337942 ACCACTCCATCTTTAGTTCATTCATTC 59.662 37.037 0.00 0.00 0.00 2.67
2857 3228 7.187824 AGGACAACTCATGTAATCTACACAT 57.812 36.000 0.00 0.00 44.12 3.21
2886 3257 5.614887 GCACAAAGAAAGAAGATACCACGTC 60.615 44.000 0.00 0.00 0.00 4.34
2894 3265 3.808726 AGAAGATACCACGTCGCTAGTAG 59.191 47.826 0.00 0.00 0.00 2.57
2906 3277 2.615447 TCGCTAGTAGTATGAACCCACG 59.385 50.000 0.00 0.00 0.00 4.94
2929 3300 1.002087 CCTGGGGTCAACTACTCACAC 59.998 57.143 0.00 0.00 0.00 3.82
3002 3373 2.043252 CCCCCTCCTATAGAGTACCAGG 59.957 59.091 0.00 0.00 41.47 4.45
3058 3429 4.263462 TGAATAGCTTGAAGTGGTGATGGT 60.263 41.667 0.00 0.00 0.00 3.55
3092 3463 9.690913 ACAATAGTTAAATAGTTTAGGGTTCCC 57.309 33.333 0.00 0.00 0.00 3.97
3164 3535 2.058705 TGGACCCACATGACCAAAGTA 58.941 47.619 0.00 0.00 0.00 2.24
3175 3546 5.822519 ACATGACCAAAGTATTATGACGCAT 59.177 36.000 0.00 0.00 0.00 4.73
3178 3549 3.882888 ACCAAAGTATTATGACGCATGGG 59.117 43.478 8.44 8.44 0.00 4.00
3181 3552 1.419762 AGTATTATGACGCATGGGCCA 59.580 47.619 9.61 9.61 36.38 5.36
3219 3590 3.193267 GTGCCATCTTTTGCATACTTCCA 59.807 43.478 0.00 0.00 40.07 3.53
3220 3591 3.831333 TGCCATCTTTTGCATACTTCCAA 59.169 39.130 0.00 0.00 31.31 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
183 185 3.937706 CCAGTTTCAGTTGATAGGAGCAG 59.062 47.826 0.00 0.00 0.00 4.24
188 190 4.003648 GTGGACCAGTTTCAGTTGATAGG 58.996 47.826 0.00 0.00 0.00 2.57
205 210 6.459066 TGCATATAGAAGATAAGCAGTGGAC 58.541 40.000 0.00 0.00 0.00 4.02
218 223 6.403866 AGGACAAGTCTCTGCATATAGAAG 57.596 41.667 0.00 0.00 0.00 2.85
260 265 3.735237 TGGCGAAGGAAGATGAGATAC 57.265 47.619 0.00 0.00 0.00 2.24
364 371 7.272037 TCCTGTGAGTTATGAAAAACTTTCC 57.728 36.000 0.00 0.00 39.78 3.13
371 378 8.690203 TGAAAGATTCCTGTGAGTTATGAAAA 57.310 30.769 0.00 0.00 0.00 2.29
379 386 6.966534 ATTGTTTGAAAGATTCCTGTGAGT 57.033 33.333 0.00 0.00 0.00 3.41
552 560 1.267806 CATTGAGCTGGTTGTGTGACC 59.732 52.381 0.00 0.00 40.23 4.02
595 603 2.026822 TGAGCCATCTTGGACTCCTTTC 60.027 50.000 12.37 0.00 40.96 2.62
599 607 0.908198 AGTGAGCCATCTTGGACTCC 59.092 55.000 12.37 0.00 40.96 3.85
713 951 2.906354 AGGTCTCGATTGTTGCCATAC 58.094 47.619 0.00 0.00 0.00 2.39
786 1033 2.679082 AGGGACGGCAATGTAGATAGT 58.321 47.619 0.00 0.00 0.00 2.12
788 1035 5.577100 ACTATAGGGACGGCAATGTAGATA 58.423 41.667 4.43 0.00 0.00 1.98
1004 1268 5.105351 ACATCGTTTCCTGACACATATCTCA 60.105 40.000 0.00 0.00 0.00 3.27
1008 1272 5.487433 TGAACATCGTTTCCTGACACATAT 58.513 37.500 0.00 0.00 0.00 1.78
1071 1335 1.460504 TGAGCTCCTCGTACGTGAAT 58.539 50.000 18.29 6.75 32.35 2.57
1160 1424 0.033796 CACATGGGTGCCATCCTCTT 60.034 55.000 0.00 0.00 43.15 2.85
1395 1679 5.276461 TCGTAGATGAGTGCCATGTATTT 57.724 39.130 0.00 0.00 34.15 1.40
1397 1681 4.511617 CTCGTAGATGAGTGCCATGTAT 57.488 45.455 0.00 0.00 34.15 2.29
1410 1694 5.437946 TCCTTCTGACATGTACTCGTAGAT 58.562 41.667 0.00 0.00 33.89 1.98
1621 1908 9.908152 GTTAATTAATCAACAACAAACTAGGCT 57.092 29.630 0.31 0.00 0.00 4.58
1790 2113 1.021390 CAAGCCGAAGTCCGCAATCT 61.021 55.000 0.00 0.00 36.84 2.40
1842 2168 2.426522 CCAACGAGTGTCATTGTGGAT 58.573 47.619 0.00 0.00 0.00 3.41
1875 2201 2.437359 AGGTACTCGGGGTCGACG 60.437 66.667 9.92 0.00 40.88 5.12
1912 2238 6.255020 CCGAAGTTATACACATCGCTTTTAGT 59.745 38.462 6.98 0.00 43.74 2.24
1917 2243 3.863424 CACCGAAGTTATACACATCGCTT 59.137 43.478 6.98 0.00 43.74 4.68
1931 2257 2.661866 GCAGCACGACACCGAAGT 60.662 61.111 0.00 0.00 39.50 3.01
2062 2388 6.772360 AACATCATAAATGCCACACATACA 57.228 33.333 0.00 0.00 38.34 2.29
2101 2427 2.173519 CTTGAGTGCCATTTCCACCAT 58.826 47.619 0.00 0.00 33.75 3.55
2234 2560 2.092103 TGCCACCACTGGTAGAAAAACT 60.092 45.455 0.00 0.00 40.17 2.66
2346 2698 2.413837 ACATAGGTGTTCTCAACGTGC 58.586 47.619 0.00 0.00 34.01 5.34
2359 2711 7.373617 ACCAAATTGGAAAGAAAACATAGGT 57.626 32.000 20.25 0.00 40.96 3.08
2459 2814 5.569413 CACTCACTTTGGTAAACTCAACAC 58.431 41.667 0.00 0.00 0.00 3.32
2522 2880 9.503427 CGAGGCCTTATTCAAATTAAACTTAAG 57.497 33.333 6.77 0.00 0.00 1.85
2576 2947 8.785329 TTAAAATTAAACAATCAGGAATGGCC 57.215 30.769 0.00 0.00 0.00 5.36
2615 2986 6.966021 ACATATAAAATGACCGCCATACAAC 58.034 36.000 0.00 0.00 34.45 3.32
2617 2988 6.530120 AGACATATAAAATGACCGCCATACA 58.470 36.000 0.00 0.00 34.45 2.29
2618 2989 6.649141 TGAGACATATAAAATGACCGCCATAC 59.351 38.462 0.00 0.00 34.45 2.39
2619 2990 6.764379 TGAGACATATAAAATGACCGCCATA 58.236 36.000 0.00 0.00 34.45 2.74
2620 2991 5.620206 TGAGACATATAAAATGACCGCCAT 58.380 37.500 0.00 0.00 36.99 4.40
2621 2992 5.029807 TGAGACATATAAAATGACCGCCA 57.970 39.130 0.00 0.00 0.00 5.69
2622 2993 6.560253 ATTGAGACATATAAAATGACCGCC 57.440 37.500 0.00 0.00 0.00 6.13
2624 2995 9.225201 CACAAATTGAGACATATAAAATGACCG 57.775 33.333 0.00 0.00 0.00 4.79
2663 3034 8.657729 GTGTGAGTAAGATAAGAAAAGGCTTAC 58.342 37.037 0.00 0.00 40.53 2.34
2668 3039 8.833231 TCTTGTGTGAGTAAGATAAGAAAAGG 57.167 34.615 0.00 0.00 28.10 3.11
2686 3057 7.661437 TGCTTATTTGTGAAGTATCTCTTGTGT 59.339 33.333 0.00 0.00 36.40 3.72
2698 3069 4.260784 GCGGGAGTATGCTTATTTGTGAAG 60.261 45.833 0.00 0.00 0.00 3.02
2756 3127 9.530633 GTATTACTCCAATCACTGGTTAGTTAG 57.469 37.037 0.00 0.00 46.51 2.34
2825 3196 6.762702 TTACATGAGTTGTCCTACGTGATA 57.237 37.500 0.00 0.00 39.87 2.15
2857 3228 5.408604 GGTATCTTCTTTCTTTGTGCTTCGA 59.591 40.000 0.00 0.00 0.00 3.71
2886 3257 2.615447 TCGTGGGTTCATACTACTAGCG 59.385 50.000 0.00 0.00 0.00 4.26
2894 3265 2.240493 CCAGGATCGTGGGTTCATAC 57.760 55.000 24.05 0.00 33.46 2.39
2906 3277 2.168728 GTGAGTAGTTGACCCCAGGATC 59.831 54.545 0.00 0.00 0.00 3.36
2917 3288 3.638484 TCATGTGACGTGTGAGTAGTTG 58.362 45.455 4.52 0.00 0.00 3.16
2929 3300 2.461903 CTCTGATGCTCTCATGTGACG 58.538 52.381 0.00 0.00 32.10 4.35
3002 3373 2.048603 GCCATGCCACAGTTCCTCC 61.049 63.158 0.00 0.00 0.00 4.30
3028 3399 6.750501 CACCACTTCAAGCTATTCATGATTTG 59.249 38.462 0.00 0.00 0.00 2.32
3030 3401 6.182627 TCACCACTTCAAGCTATTCATGATT 58.817 36.000 0.00 0.00 0.00 2.57
3092 3463 6.151817 TGTGCACCAGCTCTATATATACTCTG 59.848 42.308 15.69 0.00 42.74 3.35
3164 3535 0.823356 GGTGGCCCATGCGTCATAAT 60.823 55.000 0.00 0.00 38.85 1.28
3181 3552 4.599500 ACCCACTGGAGCCCTGGT 62.599 66.667 0.00 0.00 34.81 4.00
3193 3564 0.609662 ATGCAAAAGATGGCACCCAC 59.390 50.000 0.00 0.00 43.75 4.61


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

AutoCloner maintained by Alex Coulton.