Multiple sequence alignment - TraesCS5B01G105300

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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 TraesCS5B01G105300 chr5B 100.000 2867 0 0 1 2867 141149334 141146468 0.000000e+00 5295.0
1 TraesCS5B01G105300 chr5A 97.515 2012 44 5 1 2010 143660103 143658096 0.000000e+00 3434.0
2 TraesCS5B01G105300 chr5A 89.531 277 10 3 2183 2441 143657850 143657575 1.650000e-87 333.0
3 TraesCS5B01G105300 chr5A 98.286 175 3 0 2010 2184 143658057 143657883 9.980000e-80 307.0
4 TraesCS5B01G105300 chr5A 78.298 235 46 5 2603 2834 567208337 567208569 2.300000e-31 147.0
5 TraesCS5B01G105300 chr5D 98.397 1809 26 2 1 1808 128643817 128642011 0.000000e+00 3177.0
6 TraesCS5B01G105300 chr5D 92.736 413 26 3 2457 2867 128641236 128640826 6.840000e-166 593.0
7 TraesCS5B01G105300 chr5D 95.620 274 5 2 2183 2456 128641531 128641265 1.580000e-117 433.0
8 TraesCS5B01G105300 chr5D 98.718 234 2 1 1777 2010 128642009 128641777 5.720000e-112 414.0
9 TraesCS5B01G105300 chr5D 99.429 175 1 0 2010 2184 128641738 128641564 4.610000e-83 318.0
10 TraesCS5B01G105300 chr5D 77.239 268 50 10 2604 2866 367653330 367653069 2.300000e-31 147.0
11 TraesCS5B01G105300 chr3B 77.001 1387 285 30 398 1762 72715464 72716838 0.000000e+00 763.0
12 TraesCS5B01G105300 chr3B 80.890 607 103 10 1161 1762 72923375 72923973 1.560000e-127 466.0
13 TraesCS5B01G105300 chr3D 75.764 1473 319 34 314 1762 46485703 46487161 0.000000e+00 708.0
14 TraesCS5B01G105300 chr3D 75.200 1375 299 29 389 1731 560024577 560023213 1.890000e-171 612.0
15 TraesCS5B01G105300 chr3D 82.043 607 99 9 1161 1762 46525744 46526345 2.550000e-140 508.0
16 TraesCS5B01G105300 chr3D 94.872 39 2 0 1963 2001 4061086 4061048 8.580000e-06 62.1
17 TraesCS5B01G105300 chr6A 73.497 1381 316 41 401 1758 556038300 556036947 7.190000e-131 477.0
18 TraesCS5B01G105300 chr6D 73.348 1407 326 39 401 1785 411470789 411469410 2.580000e-130 475.0
19 TraesCS5B01G105300 chr6D 87.500 72 7 2 2718 2788 457279887 457279957 6.580000e-12 82.4
20 TraesCS5B01G105300 chr3A 80.592 608 106 10 1161 1762 57905489 57906090 2.600000e-125 459.0
21 TraesCS5B01G105300 chr6B 72.299 1379 333 39 401 1758 618670090 618668740 4.480000e-103 385.0
22 TraesCS5B01G105300 chr6B 79.623 265 50 4 2603 2866 609839985 609839724 1.360000e-43 187.0
23 TraesCS5B01G105300 chr7A 78.365 208 42 3 2628 2834 324948683 324948888 6.450000e-27 132.0
24 TraesCS5B01G105300 chr7A 74.812 266 56 11 2605 2866 680261910 680261652 3.020000e-20 110.0
25 TraesCS5B01G105300 chr7A 89.552 67 5 2 2718 2783 143381503 143381438 1.830000e-12 84.2


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 TraesCS5B01G105300 chr5B 141146468 141149334 2866 True 5295 5295 100.000000 1 2867 1 chr5B.!!$R1 2866
1 TraesCS5B01G105300 chr5A 143657575 143660103 2528 True 1358 3434 95.110667 1 2441 3 chr5A.!!$R1 2440
2 TraesCS5B01G105300 chr5D 128640826 128643817 2991 True 987 3177 96.980000 1 2867 5 chr5D.!!$R2 2866
3 TraesCS5B01G105300 chr3B 72715464 72716838 1374 False 763 763 77.001000 398 1762 1 chr3B.!!$F1 1364
4 TraesCS5B01G105300 chr3B 72923375 72923973 598 False 466 466 80.890000 1161 1762 1 chr3B.!!$F2 601
5 TraesCS5B01G105300 chr3D 46485703 46487161 1458 False 708 708 75.764000 314 1762 1 chr3D.!!$F1 1448
6 TraesCS5B01G105300 chr3D 560023213 560024577 1364 True 612 612 75.200000 389 1731 1 chr3D.!!$R2 1342
7 TraesCS5B01G105300 chr3D 46525744 46526345 601 False 508 508 82.043000 1161 1762 1 chr3D.!!$F2 601
8 TraesCS5B01G105300 chr6A 556036947 556038300 1353 True 477 477 73.497000 401 1758 1 chr6A.!!$R1 1357
9 TraesCS5B01G105300 chr6D 411469410 411470789 1379 True 475 475 73.348000 401 1785 1 chr6D.!!$R1 1384
10 TraesCS5B01G105300 chr3A 57905489 57906090 601 False 459 459 80.592000 1161 1762 1 chr3A.!!$F1 601
11 TraesCS5B01G105300 chr6B 618668740 618670090 1350 True 385 385 72.299000 401 1758 1 chr6B.!!$R2 1357

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
527 530 0.251341 GAGGCATCACAAAGGGGTGT 60.251 55.0 0.0 0.0 39.76 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2498 2680 0.179023 ACCTCCTCGATAGTCCCGTC 60.179 60.0 0.0 0.0 37.4 4.79 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
527 530 0.251341 GAGGCATCACAAAGGGGTGT 60.251 55.000 0.00 0.00 39.76 4.16
687 690 3.433314 GCCTCCTTGTGATCTCATCATGT 60.433 47.826 0.00 0.00 42.04 3.21
696 699 1.288188 TCTCATCATGTTGCCCCTCA 58.712 50.000 0.00 0.00 0.00 3.86
799 802 2.109774 CTCTGAGGCTGAACTCCATCT 58.890 52.381 0.00 0.00 36.66 2.90
1404 1433 4.237724 TGCTTGAGTCTATTGAACTCACG 58.762 43.478 5.51 5.58 39.83 4.35
1668 1697 0.738762 CACTCCGGATCTGTGCACAG 60.739 60.000 36.07 36.07 45.08 3.66
1972 2035 3.676324 CGTTGCTACTCCCTTTGTCCTAG 60.676 52.174 0.00 0.00 0.00 3.02
2262 2415 5.201713 TCGATGATTCCCATAGTCTGTTC 57.798 43.478 0.00 0.00 35.17 3.18
2307 2460 5.822204 TGAAGGCCTAGCTGGTTTTAAATA 58.178 37.500 5.16 0.00 38.35 1.40
2402 2556 7.337938 TGCAAAAGATTGACTCCAGATACATA 58.662 34.615 0.00 0.00 38.94 2.29
2414 2568 3.878699 CCAGATACATACATGCTGCAACA 59.121 43.478 6.36 0.00 0.00 3.33
2449 2603 6.363088 ACGCAGTGTTCATATGTTTCAAAATG 59.637 34.615 1.90 3.16 42.51 2.32
2498 2680 9.512588 AGGCCAGATAAAAGACAATATCATAAG 57.487 33.333 5.01 0.00 32.17 1.73
2516 2698 0.108963 AGACGGGACTATCGAGGAGG 59.891 60.000 0.00 0.00 0.00 4.30
2565 2747 6.210584 TGAGGTTGACTTTTCCTTTGACTTTT 59.789 34.615 0.00 0.00 0.00 2.27
2566 2748 6.398095 AGGTTGACTTTTCCTTTGACTTTTG 58.602 36.000 0.00 0.00 0.00 2.44
2572 2754 5.425217 ACTTTTCCTTTGACTTTTGGGTGAT 59.575 36.000 0.00 0.00 0.00 3.06
2590 2772 5.154932 GGTGATCATCTATCGAGGTTTACG 58.845 45.833 0.00 0.00 37.42 3.18
2658 2840 1.604693 CGTCACCACAGTTACAGGGAC 60.605 57.143 0.00 0.00 0.00 4.46
2667 2849 4.573201 CACAGTTACAGGGACGAAAGAAAA 59.427 41.667 0.00 0.00 0.00 2.29
2672 2854 8.347035 CAGTTACAGGGACGAAAGAAAAATTAA 58.653 33.333 0.00 0.00 0.00 1.40
2673 2855 8.347771 AGTTACAGGGACGAAAGAAAAATTAAC 58.652 33.333 0.00 0.00 0.00 2.01
2675 2857 5.297527 ACAGGGACGAAAGAAAAATTAACGT 59.702 36.000 0.00 0.00 35.31 3.99
2676 2858 6.482973 ACAGGGACGAAAGAAAAATTAACGTA 59.517 34.615 0.00 0.00 32.88 3.57
2687 2869 5.885230 AAAATTAACGTAGTGGCCTAACC 57.115 39.130 3.32 0.00 45.00 2.85
2698 2880 1.375523 GCCTAACCAGACACGGTGG 60.376 63.158 13.48 0.00 39.95 4.61
2715 2897 1.303948 GGCCCGCCCCTAACTTTAA 59.696 57.895 0.00 0.00 0.00 1.52
2724 2906 3.429410 GCCCCTAACTTTAAAGCATGCTG 60.429 47.826 23.48 10.93 0.00 4.41
2725 2907 3.429410 CCCCTAACTTTAAAGCATGCTGC 60.429 47.826 23.48 0.00 45.46 5.25
2740 2923 2.287769 TGCTGCGCTAAATTATGAGCA 58.712 42.857 9.73 9.26 38.69 4.26
2749 2932 6.011879 CGCTAAATTATGAGCATCGACATTC 58.988 40.000 0.00 0.00 38.69 2.67
2827 3010 4.769688 TGATCTCGTGAATAATTGCACCT 58.230 39.130 0.00 0.00 0.00 4.00
2831 3014 6.662414 TCTCGTGAATAATTGCACCTTAAG 57.338 37.500 0.00 0.00 0.00 1.85
2862 3045 6.148976 CCATTAATCTGCTTGATGTCATCGAT 59.851 38.462 8.29 0.00 35.21 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
687 690 2.551270 AGATCAGTTAGTGAGGGGCAA 58.449 47.619 0.00 0.0 39.07 4.52
696 699 8.254508 CAGAAGCTTAAGGTTAGATCAGTTAGT 58.745 37.037 19.35 0.0 35.69 2.24
1404 1433 1.620822 AGGGCTCACAACCATCAAAC 58.379 50.000 0.00 0.0 0.00 2.93
1593 1622 2.224606 CGCATCCCAGCATCTGTTATT 58.775 47.619 0.00 0.0 0.00 1.40
1668 1697 0.392193 CCACTCCAGCATCAGTCACC 60.392 60.000 0.00 0.0 0.00 4.02
1944 2007 2.510928 AGGGAGTAGCAACGTAGAGT 57.489 50.000 0.00 0.0 0.00 3.24
2262 2415 6.801575 TCAAACCCTTTGCTAACTTAAACAG 58.198 36.000 0.00 0.0 40.43 3.16
2414 2568 2.069273 GAACACTGCGTCTATTGCACT 58.931 47.619 0.00 0.0 37.44 4.40
2449 2603 2.135933 CGTATTTGGATTCTCCTCCGC 58.864 52.381 0.00 0.0 38.21 5.54
2473 2655 9.507329 TCTTATGATATTGTCTTTTATCTGGCC 57.493 33.333 0.00 0.0 0.00 5.36
2498 2680 0.179023 ACCTCCTCGATAGTCCCGTC 60.179 60.000 0.00 0.0 37.40 4.79
2525 2707 3.185246 ACCTCAATAGATGCTCAACCG 57.815 47.619 0.00 0.0 0.00 4.44
2607 2789 6.409524 AAAGGCTTCATGAATTGTCTCAAA 57.590 33.333 8.96 0.0 0.00 2.69
2620 2802 5.531287 GGTGACGGATTAATAAAGGCTTCAT 59.469 40.000 0.00 0.0 0.00 2.57
2621 2803 4.879545 GGTGACGGATTAATAAAGGCTTCA 59.120 41.667 0.00 0.0 0.00 3.02
2658 2840 5.566395 GGCCACTACGTTAATTTTTCTTTCG 59.434 40.000 0.00 0.0 0.00 3.46
2667 2849 4.223477 TCTGGTTAGGCCACTACGTTAATT 59.777 41.667 5.01 0.0 43.61 1.40
2672 2854 0.893447 GTCTGGTTAGGCCACTACGT 59.107 55.000 5.01 0.0 43.61 3.57
2673 2855 0.892755 TGTCTGGTTAGGCCACTACG 59.107 55.000 5.01 0.0 43.61 3.51
2675 2857 0.892755 CGTGTCTGGTTAGGCCACTA 59.107 55.000 5.01 0.0 43.61 2.74
2676 2858 1.671742 CGTGTCTGGTTAGGCCACT 59.328 57.895 5.01 0.0 43.61 4.00
2698 2880 1.100510 CTTTAAAGTTAGGGGCGGGC 58.899 55.000 7.07 0.0 0.00 6.13
2724 2906 3.184379 TGTCGATGCTCATAATTTAGCGC 59.816 43.478 0.00 0.0 41.77 5.92
2725 2907 4.972286 TGTCGATGCTCATAATTTAGCG 57.028 40.909 0.00 0.0 41.77 4.26
2726 2908 6.011879 CGAATGTCGATGCTCATAATTTAGC 58.988 40.000 0.00 0.0 43.74 3.09
2727 2909 7.338440 TCGAATGTCGATGCTCATAATTTAG 57.662 36.000 0.00 0.0 44.82 1.85
2749 2932 2.280628 GTTCATGAGTTTAGGGGCTCG 58.719 52.381 0.00 0.0 34.67 5.03
2792 2975 6.699575 TCACGAGATCATAGAACATTCTCA 57.300 37.500 0.00 0.0 38.70 3.27
2827 3010 8.072847 ATCAAGCAGATTAATGGGACAGCTTAA 61.073 37.037 0.00 0.0 38.86 1.85
2831 3014 3.887716 ATCAAGCAGATTAATGGGACAGC 59.112 43.478 0.00 0.0 35.54 4.40


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

AutoCloner maintained by Alex Coulton.