Multiple sequence alignment - TraesCS2B01G554100

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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 TraesCS2B01G554100 chr2B 100.000 3095 0 0 1 3095 749229828 749232922 0.000000e+00 5716.0
1 TraesCS2B01G554100 chr2B 86.783 628 77 3 1473 2094 749238549 749237922 0.000000e+00 695.0
2 TraesCS2B01G554100 chr2B 81.609 348 52 5 1474 1818 749302482 749302820 8.450000e-71 278.0
3 TraesCS2B01G554100 chr2B 80.556 180 29 3 999 1175 749302028 749302204 1.940000e-27 134.0
4 TraesCS2B01G554100 chr2D 95.323 2566 71 15 1 2518 614842818 614845382 0.000000e+00 4028.0
5 TraesCS2B01G554100 chr2D 94.313 633 18 5 2480 3095 614845370 614846001 0.000000e+00 953.0
6 TraesCS2B01G554100 chr2D 86.465 628 79 3 1473 2094 614853908 614853281 0.000000e+00 684.0
7 TraesCS2B01G554100 chr2D 83.176 743 108 13 1473 2212 649677318 649678046 0.000000e+00 664.0
8 TraesCS2B01G554100 chr7D 90.731 1327 105 10 1000 2310 511213210 511214534 0.000000e+00 1753.0
9 TraesCS2B01G554100 chr7D 84.495 574 79 7 8 572 159709688 159709116 2.700000e-155 558.0
10 TraesCS2B01G554100 chr7D 90.000 90 8 1 570 659 511192721 511192809 7.010000e-22 115.0
11 TraesCS2B01G554100 chr7D 93.478 46 3 0 768 813 511192861 511192906 5.540000e-08 69.4
12 TraesCS2B01G554100 chr7D 84.000 75 4 2 892 958 511192946 511193020 7.160000e-07 65.8
13 TraesCS2B01G554100 chrUn 87.068 781 58 19 2333 3094 100333695 100332939 0.000000e+00 843.0
14 TraesCS2B01G554100 chr2A 82.427 717 116 7 1473 2188 775186657 775185950 4.380000e-173 617.0
15 TraesCS2B01G554100 chr5B 84.817 573 81 4 3 570 659710573 659711144 3.460000e-159 571.0
16 TraesCS2B01G554100 chr5B 83.421 573 86 6 7 574 390551525 390550957 9.830000e-145 523.0
17 TraesCS2B01G554100 chr5B 80.831 313 56 4 1770 2080 610868137 610868447 3.080000e-60 243.0
18 TraesCS2B01G554100 chr6A 86.719 512 58 7 3 509 66277042 66277548 7.500000e-156 560.0
19 TraesCS2B01G554100 chr6A 83.421 573 85 9 7 570 212030945 212031516 9.830000e-145 523.0
20 TraesCS2B01G554100 chr6B 83.882 577 79 12 11 575 717912029 717911455 3.510000e-149 538.0
21 TraesCS2B01G554100 chr4B 83.705 583 82 7 1 570 577009623 577010205 3.510000e-149 538.0
22 TraesCS2B01G554100 chr3D 83.854 576 82 8 3 576 514849970 514850536 3.510000e-149 538.0
23 TraesCS2B01G554100 chr5D 75.567 573 124 10 1473 2043 43092570 43093128 5.090000e-68 268.0
24 TraesCS2B01G554100 chr5A 76.285 253 55 3 1474 1722 618464200 618464451 2.500000e-26 130.0
25 TraesCS2B01G554100 chr5A 81.176 85 12 4 2015 2097 618303887 618303969 7.160000e-07 65.8


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 TraesCS2B01G554100 chr2B 749229828 749232922 3094 False 5716.0 5716 100.0000 1 3095 1 chr2B.!!$F1 3094
1 TraesCS2B01G554100 chr2B 749237922 749238549 627 True 695.0 695 86.7830 1473 2094 1 chr2B.!!$R1 621
2 TraesCS2B01G554100 chr2B 749302028 749302820 792 False 206.0 278 81.0825 999 1818 2 chr2B.!!$F2 819
3 TraesCS2B01G554100 chr2D 614842818 614846001 3183 False 2490.5 4028 94.8180 1 3095 2 chr2D.!!$F2 3094
4 TraesCS2B01G554100 chr2D 614853281 614853908 627 True 684.0 684 86.4650 1473 2094 1 chr2D.!!$R1 621
5 TraesCS2B01G554100 chr2D 649677318 649678046 728 False 664.0 664 83.1760 1473 2212 1 chr2D.!!$F1 739
6 TraesCS2B01G554100 chr7D 511213210 511214534 1324 False 1753.0 1753 90.7310 1000 2310 1 chr7D.!!$F1 1310
7 TraesCS2B01G554100 chr7D 159709116 159709688 572 True 558.0 558 84.4950 8 572 1 chr7D.!!$R1 564
8 TraesCS2B01G554100 chrUn 100332939 100333695 756 True 843.0 843 87.0680 2333 3094 1 chrUn.!!$R1 761
9 TraesCS2B01G554100 chr2A 775185950 775186657 707 True 617.0 617 82.4270 1473 2188 1 chr2A.!!$R1 715
10 TraesCS2B01G554100 chr5B 659710573 659711144 571 False 571.0 571 84.8170 3 570 1 chr5B.!!$F2 567
11 TraesCS2B01G554100 chr5B 390550957 390551525 568 True 523.0 523 83.4210 7 574 1 chr5B.!!$R1 567
12 TraesCS2B01G554100 chr6A 66277042 66277548 506 False 560.0 560 86.7190 3 509 1 chr6A.!!$F1 506
13 TraesCS2B01G554100 chr6A 212030945 212031516 571 False 523.0 523 83.4210 7 570 1 chr6A.!!$F2 563
14 TraesCS2B01G554100 chr6B 717911455 717912029 574 True 538.0 538 83.8820 11 575 1 chr6B.!!$R1 564
15 TraesCS2B01G554100 chr4B 577009623 577010205 582 False 538.0 538 83.7050 1 570 1 chr4B.!!$F1 569
16 TraesCS2B01G554100 chr3D 514849970 514850536 566 False 538.0 538 83.8540 3 576 1 chr3D.!!$F1 573
17 TraesCS2B01G554100 chr5D 43092570 43093128 558 False 268.0 268 75.5670 1473 2043 1 chr5D.!!$F1 570

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
634 660 0.784778 GCTTCTCACCAAACTCGTCG 59.215 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2520 2640 0.327191 TGGTTATCCACCCCCTCTCC 60.327 60.0 0.0 0.0 46.68 3.71 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
68 72 0.955428 GCAGTGATCCAGGTTTCGCA 60.955 55.000 0.00 0.00 0.00 5.10
411 434 3.238497 CCGACGCCCCCATATCCA 61.238 66.667 0.00 0.00 0.00 3.41
573 599 2.965831 TCCGCCTGTAGATGCTCTTAAT 59.034 45.455 0.00 0.00 0.00 1.40
623 649 1.586564 CCGTCGATCCGCTTCTCAC 60.587 63.158 0.00 0.00 0.00 3.51
634 660 0.784778 GCTTCTCACCAAACTCGTCG 59.215 55.000 0.00 0.00 0.00 5.12
673 699 6.217693 ACATTCCTAATTAGTTTGGAGGTCCT 59.782 38.462 11.50 0.00 39.75 3.85
745 799 2.107204 AGGGGAAATCTTGATCGATGGG 59.893 50.000 0.54 0.00 0.00 4.00
897 951 5.909621 AATCAACACAGCAGAGCAATAAT 57.090 34.783 0.00 0.00 0.00 1.28
1277 1352 7.416326 GGCCCAAGTCAAATTTTGTATACTAGG 60.416 40.741 8.89 10.11 0.00 3.02
1327 1402 3.406361 GTGCCGTCGCTGACTGTG 61.406 66.667 7.03 0.00 35.36 3.66
2228 2317 2.009774 CTATGTTCGTTCCTTGCTGGG 58.990 52.381 0.00 0.00 36.20 4.45
2246 2335 1.676006 GGGTCTGATGTTTATTGGCGG 59.324 52.381 0.00 0.00 0.00 6.13
2357 2446 2.362077 GGTTTGCAATGACTTGGACTGT 59.638 45.455 0.00 0.00 31.84 3.55
2578 2698 2.092429 ACACAAGTGGGAGACATTGTGT 60.092 45.455 14.82 14.82 45.74 3.72
2680 2816 7.410174 AGGTCAAGGGATGTTATTAACAATGA 58.590 34.615 12.96 9.68 45.86 2.57
2738 2876 4.215613 CCAAACTACAAGTGGGTAGAAAGC 59.784 45.833 7.30 0.00 42.68 3.51
2846 2984 2.025887 ACTCACATCCACTTCCCATTCC 60.026 50.000 0.00 0.00 0.00 3.01
3053 3191 4.010349 AGCTCAAAATGCACCTACTAACC 58.990 43.478 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.408309 TCCGGAAGAGTTGGAGGAGA 59.592 55.000 0.00 0.00 0.00 3.71
51 55 1.556911 AGATGCGAAACCTGGATCACT 59.443 47.619 0.00 0.00 36.72 3.41
68 72 0.178950 TGAGCAGATCCGGGCTAGAT 60.179 55.000 0.00 0.00 41.22 1.98
397 413 2.231380 GGGATGGATATGGGGGCGT 61.231 63.158 0.00 0.00 0.00 5.68
411 434 5.797457 TCCATATCCAGTCCAAATATGGGAT 59.203 40.000 16.58 0.00 46.60 3.85
524 547 2.180769 CCGTCTCATGCGTTCGGA 59.819 61.111 13.58 0.00 43.22 4.55
573 599 7.491372 CGTGACCTTAGACTCATTTAATAAGCA 59.509 37.037 0.00 0.00 0.00 3.91
716 770 3.541632 TCAAGATTTCCCCTAACATCGC 58.458 45.455 0.00 0.00 0.00 4.58
717 771 4.449068 CGATCAAGATTTCCCCTAACATCG 59.551 45.833 0.00 0.00 0.00 3.84
745 799 2.237392 ACTCTGGCTATGGAAACCTCAC 59.763 50.000 0.00 0.00 0.00 3.51
897 951 2.477375 GACGAAACACGCTGGTTGATTA 59.523 45.455 0.00 0.00 46.94 1.75
943 997 0.989890 CCACCGATTCTCGACGAAAC 59.010 55.000 0.00 0.00 43.74 2.78
1180 1255 2.099921 TGTGACCAACATGTTTTTCCGG 59.900 45.455 8.77 9.33 32.36 5.14
1277 1352 2.125106 CTGGTAGCCCGTCCTTGC 60.125 66.667 0.00 0.00 0.00 4.01
1327 1402 3.053831 TGAATCTTTCCGTGGGAAGAC 57.946 47.619 11.85 1.55 43.06 3.01
2228 2317 4.695217 TTTCCGCCAATAAACATCAGAC 57.305 40.909 0.00 0.00 0.00 3.51
2520 2640 0.327191 TGGTTATCCACCCCCTCTCC 60.327 60.000 0.00 0.00 46.68 3.71
2578 2698 4.680237 CGAGGCGTGTGCTTCCCA 62.680 66.667 0.00 0.00 43.83 4.37
2680 2816 6.975471 TCCATATGAGGGATAACCATTGAT 57.025 37.500 3.65 0.00 43.89 2.57
2738 2876 9.791820 TTGTCTCATCTTTGCAAATAACATATG 57.208 29.630 13.23 0.00 0.00 1.78
2819 2957 3.609853 GGAAGTGGATGTGAGTATGCAA 58.390 45.455 0.00 0.00 29.97 4.08
2846 2984 9.630098 ATGCAATTTACTGTTGTCAAGATTAAG 57.370 29.630 0.00 0.00 0.00 1.85
3053 3191 2.048597 TGTGTTGCGTAGGCCTCG 60.049 61.111 9.68 14.69 38.85 4.63


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

AutoCloner maintained by Alex Coulton.