Multiple sequence alignment - TraesCS3B01G500100

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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 TraesCS3B01G500100 chr3B 100.000 3217 0 0 1 3217 744542262 744539046 0.000000e+00 5941
1 TraesCS3B01G500100 chr3B 97.042 1724 34 3 765 2477 747099095 747100812 0.000000e+00 2885
2 TraesCS3B01G500100 chr3B 91.904 667 29 12 2477 3142 747102619 747103261 0.000000e+00 909
3 TraesCS3B01G500100 chr3B 86.656 637 50 14 100 722 747098480 747099095 0.000000e+00 673
4 TraesCS3B01G500100 chr3A 93.350 3248 134 20 1 3216 696349228 696346031 0.000000e+00 4726
5 TraesCS3B01G500100 chr3A 93.664 2920 131 24 1 2901 629062768 629065652 0.000000e+00 4318
6 TraesCS3B01G500100 chr3A 96.330 218 8 0 2999 3216 629065759 629065976 3.050000e-95 359
7 TraesCS3B01G500100 chr3D 92.761 2901 120 25 34 2893 560281916 560279065 0.000000e+00 4111
8 TraesCS3B01G500100 chr3D 96.899 129 3 1 2963 3091 560279046 560278919 6.990000e-52 215
9 TraesCS3B01G500100 chr3D 94.203 69 4 0 3147 3215 560273839 560273771 4.390000e-19 106
10 TraesCS3B01G500100 chrUn 89.857 1814 149 21 586 2375 221377115 221378917 0.000000e+00 2298
11 TraesCS3B01G500100 chrUn 89.659 1818 151 23 586 2378 225550240 225552045 0.000000e+00 2281
12 TraesCS3B01G500100 chrUn 89.543 1817 155 21 586 2378 306578663 306576858 0.000000e+00 2270
13 TraesCS3B01G500100 chrUn 91.391 1301 92 11 1090 2378 285617361 285618653 0.000000e+00 1764
14 TraesCS3B01G500100 chrUn 89.436 1382 117 15 586 1945 228681984 228683358 0.000000e+00 1716
15 TraesCS3B01G500100 chrUn 90.562 943 70 10 1448 2378 387971966 387971031 0.000000e+00 1230
16 TraesCS3B01G500100 chr7A 89.857 1814 149 21 586 2375 5794649 5796451 0.000000e+00 2298
17 TraesCS3B01G500100 chr7A 81.345 922 94 31 1 886 5524068 5524947 0.000000e+00 678
18 TraesCS3B01G500100 chr4A 90.965 1129 73 12 659 1767 737716703 737715584 0.000000e+00 1493
19 TraesCS3B01G500100 chr4A 83.158 665 65 27 1 647 737717485 737716850 6.020000e-157 564
20 TraesCS3B01G500100 chr4A 91.176 238 17 3 2665 2901 738079319 738079553 1.440000e-83 320
21 TraesCS3B01G500100 chr7B 81.375 800 108 23 1877 2653 705892411 705893192 5.900000e-172 614
22 TraesCS3B01G500100 chr6A 78.060 670 93 29 2236 2889 17945774 17945143 1.090000e-99 374
23 TraesCS3B01G500100 chr1D 94.712 208 7 2 2801 3008 20478632 20478835 1.440000e-83 320


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 TraesCS3B01G500100 chr3B 744539046 744542262 3216 True 5941.0 5941 100.000000 1 3217 1 chr3B.!!$R1 3216
1 TraesCS3B01G500100 chr3B 747098480 747103261 4781 False 1489.0 2885 91.867333 100 3142 3 chr3B.!!$F1 3042
2 TraesCS3B01G500100 chr3A 696346031 696349228 3197 True 4726.0 4726 93.350000 1 3216 1 chr3A.!!$R1 3215
3 TraesCS3B01G500100 chr3A 629062768 629065976 3208 False 2338.5 4318 94.997000 1 3216 2 chr3A.!!$F1 3215
4 TraesCS3B01G500100 chr3D 560278919 560281916 2997 True 2163.0 4111 94.830000 34 3091 2 chr3D.!!$R2 3057
5 TraesCS3B01G500100 chrUn 221377115 221378917 1802 False 2298.0 2298 89.857000 586 2375 1 chrUn.!!$F1 1789
6 TraesCS3B01G500100 chrUn 225550240 225552045 1805 False 2281.0 2281 89.659000 586 2378 1 chrUn.!!$F2 1792
7 TraesCS3B01G500100 chrUn 306576858 306578663 1805 True 2270.0 2270 89.543000 586 2378 1 chrUn.!!$R1 1792
8 TraesCS3B01G500100 chrUn 285617361 285618653 1292 False 1764.0 1764 91.391000 1090 2378 1 chrUn.!!$F4 1288
9 TraesCS3B01G500100 chrUn 228681984 228683358 1374 False 1716.0 1716 89.436000 586 1945 1 chrUn.!!$F3 1359
10 TraesCS3B01G500100 chrUn 387971031 387971966 935 True 1230.0 1230 90.562000 1448 2378 1 chrUn.!!$R2 930
11 TraesCS3B01G500100 chr7A 5794649 5796451 1802 False 2298.0 2298 89.857000 586 2375 1 chr7A.!!$F2 1789
12 TraesCS3B01G500100 chr7A 5524068 5524947 879 False 678.0 678 81.345000 1 886 1 chr7A.!!$F1 885
13 TraesCS3B01G500100 chr4A 737715584 737717485 1901 True 1028.5 1493 87.061500 1 1767 2 chr4A.!!$R1 1766
14 TraesCS3B01G500100 chr7B 705892411 705893192 781 False 614.0 614 81.375000 1877 2653 1 chr7B.!!$F1 776
15 TraesCS3B01G500100 chr6A 17945143 17945774 631 True 374.0 374 78.060000 2236 2889 1 chr6A.!!$R1 653

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
558 602 0.255890 ACAGTGTTGTGAGCCCAGTT 59.744 50.000 0.0 0.0 35.83 3.16 F
1125 1379 1.153823 CGTGGTCAAGGGCTACTCG 60.154 63.158 0.0 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1652 1.101049 ACTTGTCGCAACCCCAACAG 61.101 55.000 0.0 0.0 0.0 3.16 R
2504 4610 1.544246 GGGAATGCACAAAGGTACACC 59.456 52.381 0.0 0.0 0.0 4.16 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
42 43 4.461081 AGGGCAAAAATGTGCGTAGATTTA 59.539 37.500 8.96 0.00 45.91 1.40
96 108 4.499183 TCAAAAGAATGTTTGCACCGTTT 58.501 34.783 0.00 0.00 38.20 3.60
392 432 8.285776 ACTTGTCAAAATGTCATCGATTTTTC 57.714 30.769 0.00 0.00 31.96 2.29
405 445 7.542130 GTCATCGATTTTTCAAAACCTGCTATT 59.458 33.333 0.00 0.00 0.00 1.73
556 600 1.392589 AAACAGTGTTGTGAGCCCAG 58.607 50.000 9.79 0.00 37.67 4.45
558 602 0.255890 ACAGTGTTGTGAGCCCAGTT 59.744 50.000 0.00 0.00 35.83 3.16
652 710 1.424493 CGGCGCAAACTCTCCATCTC 61.424 60.000 10.83 0.00 0.00 2.75
841 1053 4.966787 TGTTTCTGGGGTGGCGCC 62.967 66.667 22.73 22.73 36.97 6.53
931 1153 2.203070 CCTCGATCCAAAGCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
1125 1379 1.153823 CGTGGTCAAGGGCTACTCG 60.154 63.158 0.00 0.00 0.00 4.18
1398 1652 0.179000 ACTTCCGCAGATGTGATCCC 59.821 55.000 0.00 0.00 0.00 3.85
1440 1694 3.520721 TCATGAGAAGAGATGCCCTTGAA 59.479 43.478 0.00 0.00 0.00 2.69
1802 2072 2.172293 GGAGAAGAACAGCATGGAGGAT 59.828 50.000 0.00 0.00 43.62 3.24
1822 2092 1.820519 TGATGAAATGCCAGGAGTTGC 59.179 47.619 0.00 0.00 0.00 4.17
2168 2439 0.742505 TAGCAACGACATACCCCTCG 59.257 55.000 0.00 0.00 35.96 4.63
2258 2548 4.556942 TCAAGTGACACTCTTTTGCATG 57.443 40.909 8.93 0.84 0.00 4.06
2263 2554 7.443879 TCAAGTGACACTCTTTTGCATGTATAA 59.556 33.333 8.93 0.00 0.00 0.98
2265 2558 7.755591 AGTGACACTCTTTTGCATGTATAATG 58.244 34.615 1.07 0.00 0.00 1.90
2315 2611 6.183360 TGTGTTCTGCTTTTAATTGTCTCGTT 60.183 34.615 0.00 0.00 0.00 3.85
2353 2649 5.750352 ATGCTGAATCAGAAAAACCCAAT 57.250 34.783 15.38 0.00 32.44 3.16
2380 2676 3.252701 GGGCATATTGTCTCTTCATGCAG 59.747 47.826 7.12 0.00 42.94 4.41
2504 4610 1.124297 GTCTGTGCATTGTGTCGTACG 59.876 52.381 9.53 9.53 0.00 3.67
2519 4625 1.868469 GTACGGTGTACCTTTGTGCA 58.132 50.000 0.00 0.00 34.49 4.57
2612 4720 8.946797 AGGGATTTTATGAATCTGGATTTAGG 57.053 34.615 0.00 0.00 0.00 2.69
2644 4778 2.398588 TGAAGACAAGACAGGTCACCT 58.601 47.619 0.00 0.00 37.74 4.00
2927 5158 9.193133 GTAAATAAAAAGAAGAAAAGAGGTGCC 57.807 33.333 0.00 0.00 0.00 5.01
2958 5189 2.109425 AATCAAGGTACCAACGAGCC 57.891 50.000 15.94 0.00 0.00 4.70
3027 5258 1.270550 CCACATGAAGGAAGTGGCAAC 59.729 52.381 0.00 0.00 45.39 4.17
3052 5283 9.427821 ACAATCTAGATACCAAGTCTTCATACT 57.572 33.333 5.46 0.00 0.00 2.12
3068 5299 3.117625 TCATACTGTCTAGACCCCGACAT 60.118 47.826 20.11 2.59 39.23 3.06
3189 5422 4.337555 GCAATGTGCTTGGAAGTATGAGAT 59.662 41.667 0.00 0.00 40.96 2.75
3216 5449 3.014623 GTTTACTTGAGGGGTATGTGCC 58.985 50.000 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 184 5.890334 ACATTTTTCAACACATGACGAACT 58.110 33.333 0.00 0.00 37.92 3.01
392 432 4.021192 ACCATGGTTGAATAGCAGGTTTTG 60.021 41.667 13.00 0.00 37.73 2.44
405 445 8.049721 AGGAATTAAAAACAAAACCATGGTTGA 58.950 29.630 30.44 3.24 38.47 3.18
501 545 9.305925 CCTGAAATTTAAATGGAGCTCAATTAC 57.694 33.333 16.86 0.00 0.00 1.89
502 546 7.981225 GCCTGAAATTTAAATGGAGCTCAATTA 59.019 33.333 16.86 8.63 0.00 1.40
507 551 4.142381 ACGCCTGAAATTTAAATGGAGCTC 60.142 41.667 4.71 4.71 0.00 4.09
513 557 4.582441 GGCAACGCCTGAAATTTAAATG 57.418 40.909 0.39 0.00 46.69 2.32
556 600 5.521372 CCTACTACACGTTATTGGGCTAAAC 59.479 44.000 0.00 0.00 0.00 2.01
558 602 4.711355 ACCTACTACACGTTATTGGGCTAA 59.289 41.667 0.00 0.00 0.00 3.09
931 1153 3.365220 CACGATTCCGAAGTTTCAGAGTC 59.635 47.826 0.00 0.00 39.50 3.36
1125 1379 2.496070 GGGCAACTCCTTTTTGATACCC 59.504 50.000 0.00 0.00 34.39 3.69
1398 1652 1.101049 ACTTGTCGCAACCCCAACAG 61.101 55.000 0.00 0.00 0.00 3.16
1440 1694 3.093057 AGACTTTAGACTGGCTGATCGT 58.907 45.455 0.00 0.00 0.00 3.73
1537 1797 4.475135 GGGCAGGAGAACCTCGGC 62.475 72.222 0.00 0.00 45.94 5.54
1802 2072 1.820519 GCAACTCCTGGCATTTCATCA 59.179 47.619 0.00 0.00 0.00 3.07
1822 2092 2.561419 TCCTCTACTTGTCCTTGTTCCG 59.439 50.000 0.00 0.00 0.00 4.30
2168 2439 2.414161 GGCAATGAGCTCGTACAAAACC 60.414 50.000 9.33 1.29 44.79 3.27
2265 2558 9.828852 CACAAACTACGATAATCTATAGAGGAC 57.171 37.037 8.70 0.00 0.00 3.85
2353 2649 6.825213 GCATGAAGAGACAATATGCCCATATA 59.175 38.462 0.00 0.00 38.48 0.86
2380 2676 4.782019 TTTACAGACCATCCATTGCAAC 57.218 40.909 0.00 0.00 0.00 4.17
2504 4610 1.544246 GGGAATGCACAAAGGTACACC 59.456 52.381 0.00 0.00 0.00 4.16
2519 4625 8.122481 AGAAAAGGGTATTAAATGACAGGGAAT 58.878 33.333 0.00 0.00 0.00 3.01
2601 4709 7.647827 TCAATATTGTTTCCCCTAAATCCAGA 58.352 34.615 14.97 0.00 0.00 3.86
2612 4720 7.214467 TGTCTTGTCTTCAATATTGTTTCCC 57.786 36.000 14.97 2.46 32.82 3.97
2927 5158 6.061441 TGGTACCTTGATTACTATGCCATTG 58.939 40.000 14.36 0.00 0.00 2.82
2958 5189 3.128415 TGCATCCGTAAAACCATCACATG 59.872 43.478 0.00 0.00 0.00 3.21
3027 5258 9.689976 CAGTATGAAGACTTGGTATCTAGATTG 57.310 37.037 11.25 0.00 39.69 2.67
3157 5390 0.896940 AAGCACATTGCCCTCTGTGG 60.897 55.000 5.00 0.00 46.52 4.17
3189 5422 7.771826 GCACATACCCCTCAAGTAAACTAAATA 59.228 37.037 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.