Multiple sequence alignment - TraesCS2B01G266300

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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 TraesCS2B01G266300 chr2B 100.000 2909 0 0 1 2909 358757315 358760223 0.000000e+00 5373
1 TraesCS2B01G266300 chr2B 91.767 583 39 6 1 577 579976613 579977192 0.000000e+00 802
2 TraesCS2B01G266300 chr4B 96.756 1819 55 3 576 2394 535285992 535287806 0.000000e+00 3029
3 TraesCS2B01G266300 chr4B 95.934 1648 45 7 753 2398 449518704 449520331 0.000000e+00 2652
4 TraesCS2B01G266300 chr4B 97.751 578 12 1 1 577 449517740 449518317 0.000000e+00 994
5 TraesCS2B01G266300 chr4B 97.405 578 14 1 1 577 535285285 535285862 0.000000e+00 983
6 TraesCS2B01G266300 chr4B 96.837 411 13 0 576 986 449518447 449518857 0.000000e+00 688
7 TraesCS2B01G266300 chr5D 93.538 1625 81 7 750 2362 420019286 420020898 0.000000e+00 2398
8 TraesCS2B01G266300 chr5D 87.590 1523 120 35 576 2059 538686853 538688345 0.000000e+00 1701
9 TraesCS2B01G266300 chr5D 96.532 519 16 2 60 577 420018388 420018905 0.000000e+00 857
10 TraesCS2B01G266300 chr5D 89.060 585 50 9 1 577 538686145 538686723 0.000000e+00 713
11 TraesCS2B01G266300 chr5D 93.917 411 21 3 576 986 420019035 420019441 4.120000e-173 617
12 TraesCS2B01G266300 chr6A 92.479 1662 106 6 751 2396 571574684 571576342 0.000000e+00 2359
13 TraesCS2B01G266300 chr6A 92.388 578 22 10 1 577 571573743 571574299 0.000000e+00 804
14 TraesCS2B01G266300 chr6A 93.333 405 27 0 576 980 571574429 571574833 1.490000e-167 599
15 TraesCS2B01G266300 chr6A 90.909 407 35 2 1989 2394 554477586 554477991 1.970000e-151 545
16 TraesCS2B01G266300 chr3B 97.289 1254 34 0 1144 2397 604141017 604139764 0.000000e+00 2128
17 TraesCS2B01G266300 chr3B 94.293 771 31 3 1635 2393 576053728 576052959 0.000000e+00 1168
18 TraesCS2B01G266300 chr7A 93.704 1366 69 11 1041 2393 297775891 297774530 0.000000e+00 2030
19 TraesCS2B01G266300 chr7A 95.329 578 25 2 1 577 297785846 297785270 0.000000e+00 917
20 TraesCS2B01G266300 chr7A 94.203 414 24 0 576 989 297785140 297784727 1.470000e-177 632
21 TraesCS2B01G266300 chr7A 87.927 439 32 13 576 993 62735909 62736347 5.600000e-137 497
22 TraesCS2B01G266300 chr7A 95.604 273 12 0 751 1023 297784885 297784613 3.440000e-119 438
23 TraesCS2B01G266300 chr3D 86.110 1843 173 39 576 2396 339816902 339818683 0.000000e+00 1908
24 TraesCS2B01G266300 chr3D 92.096 582 37 4 1 576 148504617 148504039 0.000000e+00 811
25 TraesCS2B01G266300 chr1A 87.837 1447 138 17 576 1988 80284102 80282660 0.000000e+00 1663
26 TraesCS2B01G266300 chr1B 93.602 1016 49 6 1392 2394 400360003 400361015 0.000000e+00 1502
27 TraesCS2B01G266300 chr4A 86.777 1331 126 25 750 2059 629935544 629936845 0.000000e+00 1437
28 TraesCS2B01G266300 chr2A 96.325 517 14 3 2394 2909 377126351 377126863 0.000000e+00 845
29 TraesCS2B01G266300 chr2A 89.384 584 49 10 1 577 57825427 57826004 0.000000e+00 723
30 TraesCS2B01G266300 chr2D 96.132 517 12 4 2394 2909 300878731 300879240 0.000000e+00 837
31 TraesCS2B01G266300 chr5A 89.498 438 25 10 576 993 78449133 78449569 4.270000e-148 534


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 TraesCS2B01G266300 chr2B 358757315 358760223 2908 False 5373.000000 5373 100.000000 1 2909 1 chr2B.!!$F1 2908
1 TraesCS2B01G266300 chr2B 579976613 579977192 579 False 802.000000 802 91.767000 1 577 1 chr2B.!!$F2 576
2 TraesCS2B01G266300 chr4B 535285285 535287806 2521 False 2006.000000 3029 97.080500 1 2394 2 chr4B.!!$F2 2393
3 TraesCS2B01G266300 chr4B 449517740 449520331 2591 False 1444.666667 2652 96.840667 1 2398 3 chr4B.!!$F1 2397
4 TraesCS2B01G266300 chr5D 420018388 420020898 2510 False 1290.666667 2398 94.662333 60 2362 3 chr5D.!!$F1 2302
5 TraesCS2B01G266300 chr5D 538686145 538688345 2200 False 1207.000000 1701 88.325000 1 2059 2 chr5D.!!$F2 2058
6 TraesCS2B01G266300 chr6A 571573743 571576342 2599 False 1254.000000 2359 92.733333 1 2396 3 chr6A.!!$F2 2395
7 TraesCS2B01G266300 chr3B 604139764 604141017 1253 True 2128.000000 2128 97.289000 1144 2397 1 chr3B.!!$R2 1253
8 TraesCS2B01G266300 chr3B 576052959 576053728 769 True 1168.000000 1168 94.293000 1635 2393 1 chr3B.!!$R1 758
9 TraesCS2B01G266300 chr7A 297774530 297775891 1361 True 2030.000000 2030 93.704000 1041 2393 1 chr7A.!!$R1 1352
10 TraesCS2B01G266300 chr7A 297784613 297785846 1233 True 662.333333 917 95.045333 1 1023 3 chr7A.!!$R2 1022
11 TraesCS2B01G266300 chr3D 339816902 339818683 1781 False 1908.000000 1908 86.110000 576 2396 1 chr3D.!!$F1 1820
12 TraesCS2B01G266300 chr3D 148504039 148504617 578 True 811.000000 811 92.096000 1 576 1 chr3D.!!$R1 575
13 TraesCS2B01G266300 chr1A 80282660 80284102 1442 True 1663.000000 1663 87.837000 576 1988 1 chr1A.!!$R1 1412
14 TraesCS2B01G266300 chr1B 400360003 400361015 1012 False 1502.000000 1502 93.602000 1392 2394 1 chr1B.!!$F1 1002
15 TraesCS2B01G266300 chr4A 629935544 629936845 1301 False 1437.000000 1437 86.777000 750 2059 1 chr4A.!!$F1 1309
16 TraesCS2B01G266300 chr2A 377126351 377126863 512 False 845.000000 845 96.325000 2394 2909 1 chr2A.!!$F2 515
17 TraesCS2B01G266300 chr2A 57825427 57826004 577 False 723.000000 723 89.384000 1 577 1 chr2A.!!$F1 576
18 TraesCS2B01G266300 chr2D 300878731 300879240 509 False 837.000000 837 96.132000 2394 2909 1 chr2D.!!$F1 515

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
272 274 1.152830 GCTGGTTGGGAAGGGTCAA 59.847 57.895 0.0 0.0 0.0 3.18 F
1121 1440 3.726557 TGTTGCTGATGGGAAGAGAAT 57.273 42.857 0.0 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1564 1884 0.104304 GGTGACGTGTTGACCTCACT 59.896 55.0 0.0 0.0 37.9 3.41 R
2484 2836 0.744414 CAGGAACACCATCGCCGATT 60.744 55.0 0.0 0.0 0.0 3.34 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
28 29 2.700897 AGGAAATCATCGATTCGACCCT 59.299 45.455 11.56 8.21 39.18 4.34
272 274 1.152830 GCTGGTTGGGAAGGGTCAA 59.847 57.895 0.00 0.00 0.00 3.18
504 517 4.062991 GTGAGGTACCATTTGAACGAGTT 58.937 43.478 15.94 0.00 0.00 3.01
608 752 9.268268 GAATTTATTATACCGGAAGTGACATGA 57.732 33.333 9.46 0.00 0.00 3.07
761 905 5.414454 GCACACTCCATGTATTTGAACCTTA 59.586 40.000 0.00 0.00 40.64 2.69
1121 1440 3.726557 TGTTGCTGATGGGAAGAGAAT 57.273 42.857 0.00 0.00 0.00 2.40
1174 1493 6.804677 AGACAATGTGCTATTGTTTTGAACA 58.195 32.000 17.09 0.00 41.76 3.18
1538 1858 5.163540 GCAGATCTGGCAATGATCTTCTTTT 60.164 40.000 23.89 0.00 45.74 2.27
1564 1884 3.826729 TGATCTTGAAGACGAGGAGAACA 59.173 43.478 0.00 0.00 0.00 3.18
1741 2061 5.546887 AGTGGAGATGATGATGACATACCAT 59.453 40.000 0.00 0.00 37.01 3.55
2263 2615 2.851263 TTACACTCCGTGCTTCCAAT 57.149 45.000 0.00 0.00 36.98 3.16
2273 2625 1.606668 GTGCTTCCAATCAAACACCGA 59.393 47.619 0.00 0.00 0.00 4.69
2318 2670 3.569194 TTTGCTCCTACCAAACACAGA 57.431 42.857 0.00 0.00 0.00 3.41
2330 2682 4.840115 ACCAAACACAGAAATGGAATGGAT 59.160 37.500 0.00 0.00 36.75 3.41
2377 2729 3.156293 CATTCCATGACAGTTGGTTCCA 58.844 45.455 0.00 0.00 35.64 3.53
2379 2731 0.874390 CCATGACAGTTGGTTCCACG 59.126 55.000 0.00 0.00 0.00 4.94
2442 2794 2.233676 GCGAAACTTTCATTCCCCCAAT 59.766 45.455 2.49 0.00 0.00 3.16
2443 2795 3.676049 GCGAAACTTTCATTCCCCCAATC 60.676 47.826 2.49 0.00 0.00 2.67
2444 2796 3.763897 CGAAACTTTCATTCCCCCAATCT 59.236 43.478 2.49 0.00 0.00 2.40
2472 2824 4.569719 AAAATCCCGAAGAAGCTTCCTA 57.430 40.909 22.81 2.90 0.00 2.94
2484 2836 1.956629 GCTTCCTAGTGGTAGCGGCA 61.957 60.000 1.45 0.00 44.65 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.169592 TCTGAATTTACCTTAAAATAAGGGTCG 57.830 33.333 17.91 6.45 41.71 4.79
272 274 4.279169 AGCTAAAACAGTTGCATCATGTGT 59.721 37.500 0.00 0.00 0.00 3.72
504 517 0.187117 TTGGACTGGATTGTTGCCCA 59.813 50.000 0.00 0.00 0.00 5.36
579 723 9.051679 TGTCACTTCCGGTATAATAAATTCATG 57.948 33.333 0.00 0.00 0.00 3.07
608 752 1.684450 GTTCGAATTGGTTGGGTGGTT 59.316 47.619 0.00 0.00 0.00 3.67
883 1188 6.219473 AGTAAATGATAGAATCTGTCCAGCG 58.781 40.000 4.57 0.00 0.00 5.18
1093 1412 2.906389 TCCCATCAGCAACAAGACTAGT 59.094 45.455 0.00 0.00 0.00 2.57
1096 1415 2.373169 TCTTCCCATCAGCAACAAGACT 59.627 45.455 0.00 0.00 0.00 3.24
1121 1440 0.108585 GTCCCTGAAGCCACTTGACA 59.891 55.000 0.00 0.00 0.00 3.58
1538 1858 4.706962 TCTCCTCGTCTTCAAGATCAATGA 59.293 41.667 0.00 0.00 0.00 2.57
1564 1884 0.104304 GGTGACGTGTTGACCTCACT 59.896 55.000 0.00 0.00 37.90 3.41
1674 1994 4.038642 GCCACAAGTTTGAACCCATCTTTA 59.961 41.667 0.00 0.00 0.00 1.85
1741 2061 4.654262 GGAGACTACATCCCAAAGGTCATA 59.346 45.833 0.00 0.00 0.00 2.15
2318 2670 4.641989 CAGAAGAACGGATCCATTCCATTT 59.358 41.667 16.74 5.14 45.78 2.32
2337 2689 3.216187 TGAAATGGTTCCGTTCCAGAA 57.784 42.857 0.00 0.00 38.42 3.02
2377 2729 1.209990 TGTTAGGGTGTGTTTGGTCGT 59.790 47.619 0.00 0.00 0.00 4.34
2379 2731 2.034179 GCTTGTTAGGGTGTGTTTGGTC 59.966 50.000 0.00 0.00 0.00 4.02
2442 2794 1.005450 CTTCGGGATTTTTGGGGGAGA 59.995 52.381 0.00 0.00 0.00 3.71
2443 2795 1.005450 TCTTCGGGATTTTTGGGGGAG 59.995 52.381 0.00 0.00 0.00 4.30
2444 2796 1.077276 TCTTCGGGATTTTTGGGGGA 58.923 50.000 0.00 0.00 0.00 4.81
2472 2824 2.186903 CCGATTGCCGCTACCACT 59.813 61.111 0.00 0.00 36.84 4.00
2484 2836 0.744414 CAGGAACACCATCGCCGATT 60.744 55.000 0.00 0.00 0.00 3.34
2698 3050 4.105553 GGTACGAAGGTGGGGGCC 62.106 72.222 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.