Multiple sequence alignment - TraesCS4A01G345200

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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 TraesCS4A01G345200 chr4A 100.000 3029 0 0 1 3029 624835614 624832586 0.000000e+00 5594.0
1 TraesCS4A01G345200 chr4A 94.309 123 6 1 2855 2977 702898366 702898487 1.430000e-43 187.0
2 TraesCS4A01G345200 chr1A 97.731 3041 47 6 1 3029 569254688 569257718 0.000000e+00 5214.0
3 TraesCS4A01G345200 chr1A 81.219 1395 234 23 997 2377 125150289 125151669 0.000000e+00 1099.0
4 TraesCS4A01G345200 chr5D 91.383 1822 118 18 849 2641 545113067 545111256 0.000000e+00 2459.0
5 TraesCS4A01G345200 chr5D 91.797 1475 107 7 980 2442 544896766 544895294 0.000000e+00 2041.0
6 TraesCS4A01G345200 chr5D 87.043 602 61 11 1850 2442 544890646 544890053 0.000000e+00 664.0
7 TraesCS4A01G345200 chr5B 90.386 1737 122 22 854 2559 687694594 687696316 0.000000e+00 2241.0
8 TraesCS4A01G345200 chr5B 92.158 1288 83 5 944 2213 687469769 687468482 0.000000e+00 1803.0
9 TraesCS4A01G345200 chr5B 97.727 44 1 0 2974 3017 687696389 687696432 3.240000e-10 76.8
10 TraesCS4A01G345200 chr5A 88.896 1468 152 5 996 2455 624708253 624706789 0.000000e+00 1797.0
11 TraesCS4A01G345200 chr5A 91.667 132 10 1 2840 2970 364977593 364977462 6.670000e-42 182.0
12 TraesCS4A01G345200 chr7A 95.573 768 25 2 1 759 90023699 90022932 0.000000e+00 1221.0
13 TraesCS4A01G345200 chr7A 84.615 52 8 0 5 56 94293051 94293000 5.000000e-03 52.8
14 TraesCS4A01G345200 chr2A 96.643 715 12 5 59 762 755071640 755070927 0.000000e+00 1177.0
15 TraesCS4A01G345200 chr2A 95.775 710 17 6 59 756 739851721 739851013 0.000000e+00 1133.0
16 TraesCS4A01G345200 chr2A 89.286 56 5 1 5 60 27327285 27327339 5.420000e-08 69.4
17 TraesCS4A01G345200 chr1D 81.031 1397 234 25 997 2377 114645756 114647137 0.000000e+00 1083.0
18 TraesCS4A01G345200 chr1B 80.617 1393 239 25 1001 2377 175661158 175662535 0.000000e+00 1048.0
19 TraesCS4A01G345200 chr1B 78.832 274 36 11 2682 2937 306061908 306062177 6.720000e-37 165.0
20 TraesCS4A01G345200 chr7B 84.142 309 31 11 2685 2975 199792643 199792951 1.780000e-72 283.0
21 TraesCS4A01G345200 chr7B 82.895 304 35 11 2685 2971 35138454 35138757 1.080000e-64 257.0
22 TraesCS4A01G345200 chr7B 82.468 308 36 10 2681 2970 637303970 637304277 1.390000e-63 254.0
23 TraesCS4A01G345200 chr7B 89.796 147 8 7 2855 2999 39465787 39465928 6.670000e-42 182.0
24 TraesCS4A01G345200 chr4B 84.231 260 39 1 2716 2973 579398892 579399151 5.010000e-63 252.0
25 TraesCS4A01G345200 chr3D 82.508 303 35 8 2685 2970 299692337 299692638 1.800000e-62 250.0
26 TraesCS4A01G345200 chr3D 95.000 120 6 0 2852 2971 25580613 25580732 3.990000e-44 189.0
27 TraesCS4A01G345200 chr6B 81.587 315 38 13 2677 2973 423232502 423232814 3.020000e-60 243.0
28 TraesCS4A01G345200 chr3B 81.759 307 36 11 2682 2970 119950004 119949700 3.900000e-59 239.0
29 TraesCS4A01G345200 chr3B 82.397 267 42 4 2708 2970 811699370 811699105 8.450000e-56 228.0
30 TraesCS4A01G345200 chr3B 80.843 261 50 0 1962 2222 133000454 133000714 3.960000e-49 206.0
31 TraesCS4A01G345200 chr3B 85.714 56 8 0 5 60 585408598 585408543 3.260000e-05 60.2
32 TraesCS4A01G345200 chrUn 83.125 160 27 0 2685 2844 47685811 47685652 2.430000e-31 147.0
33 TraesCS4A01G345200 chr2D 82.456 171 25 4 2673 2841 191049378 191049545 8.750000e-31 145.0
34 TraesCS4A01G345200 chr2B 90.000 60 2 4 5 61 364961699 364961641 1.160000e-09 75.0


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 TraesCS4A01G345200 chr4A 624832586 624835614 3028 True 5594.0 5594 100.0000 1 3029 1 chr4A.!!$R1 3028
1 TraesCS4A01G345200 chr1A 569254688 569257718 3030 False 5214.0 5214 97.7310 1 3029 1 chr1A.!!$F2 3028
2 TraesCS4A01G345200 chr1A 125150289 125151669 1380 False 1099.0 1099 81.2190 997 2377 1 chr1A.!!$F1 1380
3 TraesCS4A01G345200 chr5D 545111256 545113067 1811 True 2459.0 2459 91.3830 849 2641 1 chr5D.!!$R3 1792
4 TraesCS4A01G345200 chr5D 544895294 544896766 1472 True 2041.0 2041 91.7970 980 2442 1 chr5D.!!$R2 1462
5 TraesCS4A01G345200 chr5D 544890053 544890646 593 True 664.0 664 87.0430 1850 2442 1 chr5D.!!$R1 592
6 TraesCS4A01G345200 chr5B 687468482 687469769 1287 True 1803.0 1803 92.1580 944 2213 1 chr5B.!!$R1 1269
7 TraesCS4A01G345200 chr5B 687694594 687696432 1838 False 1158.9 2241 94.0565 854 3017 2 chr5B.!!$F1 2163
8 TraesCS4A01G345200 chr5A 624706789 624708253 1464 True 1797.0 1797 88.8960 996 2455 1 chr5A.!!$R2 1459
9 TraesCS4A01G345200 chr7A 90022932 90023699 767 True 1221.0 1221 95.5730 1 759 1 chr7A.!!$R1 758
10 TraesCS4A01G345200 chr2A 755070927 755071640 713 True 1177.0 1177 96.6430 59 762 1 chr2A.!!$R2 703
11 TraesCS4A01G345200 chr2A 739851013 739851721 708 True 1133.0 1133 95.7750 59 756 1 chr2A.!!$R1 697
12 TraesCS4A01G345200 chr1D 114645756 114647137 1381 False 1083.0 1083 81.0310 997 2377 1 chr1D.!!$F1 1380
13 TraesCS4A01G345200 chr1B 175661158 175662535 1377 False 1048.0 1048 80.6170 1001 2377 1 chr1B.!!$F1 1376

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
870 885 0.248661 CGATCTCGATCCAACGCTGT 60.249 55.0 1.57 0.0 43.02 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2821 2894 0.878961 GACAAGGTGTCCACGGTGAC 60.879 60.0 10.28 6.73 41.37 3.67 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
443 446 2.355756 CGCATGCAGCCTAAGTAACAAT 59.644 45.455 19.57 0.0 41.38 2.71
519 523 4.261801 GGAGTCTGGGAATCGAAATTTGA 58.738 43.478 0.00 0.0 0.00 2.69
549 553 2.805827 ATCACTGGGGTGGATGGGGT 62.806 60.000 0.00 0.0 43.17 4.95
552 556 0.254107 ACTGGGGTGGATGGGGTAAT 60.254 55.000 0.00 0.0 0.00 1.89
596 600 0.548926 TCAATGGTGTAGGGGCCTGA 60.549 55.000 0.84 0.0 0.00 3.86
623 635 1.822990 ACGATGTGACTGTATCCGGTT 59.177 47.619 0.00 0.0 0.00 4.44
745 760 1.013596 TGCGCAAACGGATAGGATTG 58.986 50.000 8.16 0.0 40.57 2.67
774 789 1.803334 GTGTAAACGGCATCACCTCA 58.197 50.000 0.00 0.0 35.61 3.86
789 804 3.052620 CTCAGCATCGTCCGTCCGT 62.053 63.158 0.00 0.0 0.00 4.69
870 885 0.248661 CGATCTCGATCCAACGCTGT 60.249 55.000 1.57 0.0 43.02 4.40
2725 2798 3.797039 ACACAAGCGCTCATATACACAT 58.203 40.909 12.06 0.0 0.00 3.21
2733 2806 4.330894 GCGCTCATATACACATGCATACAT 59.669 41.667 0.00 0.0 36.79 2.29
2738 2811 7.747799 GCTCATATACACATGCATACATTCAAC 59.252 37.037 0.00 0.0 32.87 3.18
2795 2868 2.601804 GCTTCTCTGAAAGACCGAGTC 58.398 52.381 0.00 0.0 38.67 3.36
2821 2894 7.474332 CGGCATATCATCTTAAAATTTACGACG 59.526 37.037 0.00 0.0 0.00 5.12
2863 2936 4.335082 TCTTGAAATTTACGCATCACCG 57.665 40.909 0.00 0.0 0.00 4.94
2864 2937 3.126171 TCTTGAAATTTACGCATCACCGG 59.874 43.478 0.00 0.0 0.00 5.28
2875 2948 2.680841 CGCATCACCGGAAATCCTAAAA 59.319 45.455 9.46 0.0 0.00 1.52
2881 2954 7.926018 GCATCACCGGAAATCCTAAAATAAATT 59.074 33.333 9.46 0.0 0.00 1.82
2909 2982 2.572191 AATGCGAGCACCATGATTTG 57.428 45.000 0.00 0.0 0.00 2.32
3025 3098 9.877178 AGTACACCTATTATTCTCTTTCTGTTG 57.123 33.333 0.00 0.0 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 222 2.225343 TGCATTTTCTTCCCCCATCAGT 60.225 45.455 0.00 0.00 0.00 3.41
533 537 0.254107 ATTACCCCATCCACCCCAGT 60.254 55.000 0.00 0.00 0.00 4.00
549 553 2.034179 CGCCTACACCATCACTCGATTA 59.966 50.000 0.00 0.00 0.00 1.75
552 556 1.807226 CGCCTACACCATCACTCGA 59.193 57.895 0.00 0.00 0.00 4.04
642 656 3.418047 CCAACCAACGATTCCCTAGTTT 58.582 45.455 0.00 0.00 0.00 2.66
726 741 1.013596 CAATCCTATCCGTTTGCGCA 58.986 50.000 5.66 5.66 36.67 6.09
735 750 3.941483 CACGAATATGGCCAATCCTATCC 59.059 47.826 10.96 0.00 35.26 2.59
774 789 4.175489 CGACGGACGGACGATGCT 62.175 66.667 8.01 0.00 38.46 3.79
789 804 2.666022 CACGTGCATTATCAACAGACGA 59.334 45.455 0.82 0.00 0.00 4.20
870 885 1.966901 ATAGAATCACGGCCACGGCA 61.967 55.000 10.83 0.00 46.48 5.69
2725 2798 5.008217 GCGTTTATAGGGTTGAATGTATGCA 59.992 40.000 0.00 0.00 0.00 3.96
2733 2806 3.499157 GTGTGTGCGTTTATAGGGTTGAA 59.501 43.478 0.00 0.00 0.00 2.69
2738 2811 1.339247 TGGGTGTGTGCGTTTATAGGG 60.339 52.381 0.00 0.00 0.00 3.53
2795 2868 7.474332 CGTCGTAAATTTTAAGATGATATGCCG 59.526 37.037 15.17 6.02 0.00 5.69
2821 2894 0.878961 GACAAGGTGTCCACGGTGAC 60.879 60.000 10.28 6.73 41.37 3.67
2829 2902 5.712152 AATTTCAAGATGACAAGGTGTCC 57.288 39.130 5.96 0.00 46.40 4.02
2875 2948 7.649306 GGTGCTCGCATTTATTTCTGAATTTAT 59.351 33.333 0.00 0.00 0.00 1.40
2881 2954 3.342719 TGGTGCTCGCATTTATTTCTGA 58.657 40.909 0.00 0.00 0.00 3.27
2936 3009 3.244770 TGTGGTTGGATGGTTAGAGGAAC 60.245 47.826 0.00 0.00 37.31 3.62


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

AutoCloner maintained by Alex Coulton.