Multiple sequence alignment - TraesCS2B01G054800

Loading Multiple Alignment...

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 TraesCS2B01G054800 chr2B 100.000 6067 0 0 1 6067 26712005 26705939 0.000000e+00 11204.0
1 TraesCS2B01G054800 chr2B 98.633 6073 74 5 1 6067 26732652 26726583 0.000000e+00 10746.0
2 TraesCS2B01G054800 chr2B 81.010 495 89 4 3492 3981 26576485 26575991 7.370000e-104 388.0
3 TraesCS2B01G054800 chr2B 82.166 471 67 12 3473 3935 26582976 26582515 7.370000e-104 388.0
4 TraesCS2B01G054800 chr2B 76.402 517 86 19 1439 1929 26577841 26577335 4.700000e-61 246.0
5 TraesCS2B01G054800 chr2B 85.062 241 32 4 3090 3328 26590103 26589865 6.080000e-60 243.0
6 TraesCS2B01G054800 chr2B 82.168 286 43 6 981 1260 26590646 26590363 7.860000e-59 239.0
7 TraesCS2B01G054800 chr2B 81.921 177 23 5 1970 2140 104305923 104306096 2.280000e-29 141.0
8 TraesCS2B01G054800 chr2D 94.733 5905 241 26 1 5858 14829411 14823530 0.000000e+00 9118.0
9 TraesCS2B01G054800 chr2D 93.784 547 30 2 5522 6067 14823521 14822978 0.000000e+00 819.0
10 TraesCS2B01G054800 chr2D 81.399 586 98 9 3424 4000 14787580 14786997 9.210000e-128 468.0
11 TraesCS2B01G054800 chr2D 81.211 479 81 7 3492 3964 14780849 14780374 1.600000e-100 377.0
12 TraesCS2B01G054800 chr2D 80.822 438 51 20 2877 3292 14788086 14787660 4.570000e-81 313.0
13 TraesCS2B01G054800 chr2D 86.957 207 22 4 3090 3294 14781323 14781120 1.700000e-55 228.0
14 TraesCS2B01G054800 chr2D 74.944 443 62 27 1515 1929 14782153 14781732 2.260000e-34 158.0
15 TraesCS2B01G054800 chr2D 100.000 36 0 0 2105 2140 67195935 67195900 3.920000e-07 67.6
16 TraesCS2B01G054800 chr2A 90.569 6150 439 68 1 6067 16990617 16984526 0.000000e+00 8013.0
17 TraesCS2B01G054800 chr2A 80.880 523 86 12 3421 3935 16884204 16883688 3.410000e-107 399.0
18 TraesCS2B01G054800 chr2A 80.213 470 79 12 3498 3964 16874229 16873771 2.090000e-89 340.0
19 TraesCS2B01G054800 chr2A 89.545 220 19 2 3076 3294 16884466 16884250 5.990000e-70 276.0
20 TraesCS2B01G054800 chr2A 76.653 484 72 24 1474 1929 16875541 16875071 4.730000e-56 230.0
21 TraesCS2B01G054800 chr2A 87.129 202 21 3 3090 3289 16874667 16874469 2.200000e-54 224.0
22 TraesCS2B01G054800 chr2A 80.476 210 38 3 2256 2464 27627274 27627481 2.260000e-34 158.0
23 TraesCS2B01G054800 chr2A 79.191 173 33 3 2323 2494 98454688 98454858 3.840000e-22 117.0
24 TraesCS2B01G054800 chr2A 80.142 141 16 10 2322 2457 41650546 41650413 1.800000e-15 95.3
25 TraesCS2B01G054800 chr2A 91.935 62 4 1 2087 2147 114625936 114625997 1.080000e-12 86.1
26 TraesCS2B01G054800 chr6A 78.523 298 53 9 2161 2452 85574080 85574372 1.040000e-42 185.0
27 TraesCS2B01G054800 chr5A 77.778 297 50 12 2170 2463 443732909 443732626 1.050000e-37 169.0
28 TraesCS2B01G054800 chr5A 78.146 151 24 6 2002 2145 558336119 558335971 3.010000e-13 87.9
29 TraesCS2B01G054800 chr5D 80.952 210 31 5 2256 2458 416797929 416798136 2.260000e-34 158.0
30 TraesCS2B01G054800 chr3D 91.667 108 9 0 5753 5860 536330683 536330576 3.790000e-32 150.0
31 TraesCS2B01G054800 chr4A 81.421 183 31 3 2146 2328 556254661 556254482 4.900000e-31 147.0
32 TraesCS2B01G054800 chr4A 86.916 107 14 0 5753 5859 362103033 362103139 2.970000e-23 121.0
33 TraesCS2B01G054800 chr7D 90.179 112 10 1 5742 5852 607955400 607955289 1.760000e-30 145.0
34 TraesCS2B01G054800 chr4D 75.986 279 52 9 2183 2459 466732396 466732661 4.930000e-26 130.0
35 TraesCS2B01G054800 chr4D 87.037 108 13 1 5745 5852 46030483 46030589 2.970000e-23 121.0
36 TraesCS2B01G054800 chr4B 86.916 107 14 0 5753 5859 28196882 28196988 2.970000e-23 121.0
37 TraesCS2B01G054800 chr4B 87.719 57 5 2 2090 2146 414256679 414256625 1.410000e-06 65.8
38 TraesCS2B01G054800 chr6B 81.818 88 12 4 222 307 46071637 46071552 3.030000e-08 71.3


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 TraesCS2B01G054800 chr2B 26705939 26712005 6066 True 11204.000000 11204 100.000000 1 6067 1 chr2B.!!$R2 6066
1 TraesCS2B01G054800 chr2B 26726583 26732652 6069 True 10746.000000 10746 98.633000 1 6067 1 chr2B.!!$R3 6066
2 TraesCS2B01G054800 chr2B 26575991 26577841 1850 True 317.000000 388 78.706000 1439 3981 2 chr2B.!!$R4 2542
3 TraesCS2B01G054800 chr2B 26589865 26590646 781 True 241.000000 243 83.615000 981 3328 2 chr2B.!!$R5 2347
4 TraesCS2B01G054800 chr2D 14822978 14829411 6433 True 4968.500000 9118 94.258500 1 6067 2 chr2D.!!$R4 6066
5 TraesCS2B01G054800 chr2D 14786997 14788086 1089 True 390.500000 468 81.110500 2877 4000 2 chr2D.!!$R3 1123
6 TraesCS2B01G054800 chr2D 14780374 14782153 1779 True 254.333333 377 81.037333 1515 3964 3 chr2D.!!$R2 2449
7 TraesCS2B01G054800 chr2A 16984526 16990617 6091 True 8013.000000 8013 90.569000 1 6067 1 chr2A.!!$R1 6066
8 TraesCS2B01G054800 chr2A 16883688 16884466 778 True 337.500000 399 85.212500 3076 3935 2 chr2A.!!$R4 859
9 TraesCS2B01G054800 chr2A 16873771 16875541 1770 True 264.666667 340 81.331667 1474 3964 3 chr2A.!!$R3 2490

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
1036 1085 2.035193 CGCACTGCTATGTATCCTCAGT 59.965 50.000 0.00 0.00 38.40 3.41 F
1916 2004 3.265737 ACCATGTGTTAGCATGAACCCTA 59.734 43.478 0.00 0.00 46.65 3.53 F
2676 2825 4.822685 TTTAGCATTCCCAATTGCATGT 57.177 36.364 0.00 0.00 0.00 3.21 F
4050 4358 4.279169 GCCTTAACACATGCATGGACATAT 59.721 41.667 29.41 12.18 0.00 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2577 2673 1.795768 TCAAATGAGCTCACGACCAC 58.204 50.000 20.97 0.00 0.00 4.16 R
3011 3175 2.028130 ACCTCAGCATAGGAGTTCTCG 58.972 52.381 11.07 0.00 39.15 4.04 R
4445 4753 0.036448 CCTCTGCTATGGCTGGATGG 59.964 60.000 8.06 4.99 39.59 3.51 R
5224 5546 1.273327 GCCAGAAGTGGGGTTTGATTG 59.727 52.381 0.00 0.00 45.17 2.67 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
1036 1085 2.035193 CGCACTGCTATGTATCCTCAGT 59.965 50.000 0.00 0.00 38.40 3.41
1271 1325 5.014202 GGAGCCAAGTAAAATCCCTTGTTA 58.986 41.667 0.00 0.00 37.05 2.41
1411 1465 6.934083 TGATGTTGACAAGAGCATTACAACTA 59.066 34.615 0.00 0.00 38.51 2.24
1916 2004 3.265737 ACCATGTGTTAGCATGAACCCTA 59.734 43.478 0.00 0.00 46.65 3.53
2253 2346 5.455056 AATAGGATCACCTCGACATGTAC 57.545 43.478 0.00 0.00 46.43 2.90
2611 2711 8.842358 AGCTCATTTGAAATGTTCATTTTGAT 57.158 26.923 16.62 4.86 39.84 2.57
2676 2825 4.822685 TTTAGCATTCCCAATTGCATGT 57.177 36.364 0.00 0.00 0.00 3.21
2950 3099 8.503196 CCATGTGCGCATAATCTAGTAAAAATA 58.497 33.333 15.91 0.00 33.30 1.40
4050 4358 4.279169 GCCTTAACACATGCATGGACATAT 59.721 41.667 29.41 12.18 0.00 1.78
4445 4753 8.512138 ACTTTAAACATGTATGGTAAAGAGTGC 58.488 33.333 23.95 0.00 39.40 4.40
4468 4776 0.543277 CCAGCCATAGCAGAGGAACA 59.457 55.000 0.00 0.00 43.56 3.18
4472 4780 1.202627 GCCATAGCAGAGGAACAGAGG 60.203 57.143 0.00 0.00 39.53 3.69
4890 5211 1.453155 GCTCAATGGTGTTGGTCGAT 58.547 50.000 0.00 0.00 0.00 3.59
4964 5286 9.463443 GATATTTTATAGCGTGGATTTGCTTTT 57.537 29.630 0.00 0.00 42.48 2.27
5051 5373 5.394663 CGGACTTGATCTTCCTAGTGATGTT 60.395 44.000 0.00 0.00 0.00 2.71
5078 5400 1.930251 AGAAGTGAGCTAGAGCACCA 58.070 50.000 4.01 0.00 45.16 4.17
5224 5546 6.963796 ACCGCATGATTATCTTTGATTCTTC 58.036 36.000 0.00 0.00 0.00 2.87
5810 6481 8.470657 ACAGATGTATCTAGCACTGAAATAGA 57.529 34.615 0.00 0.00 34.85 1.98
5878 6552 6.708054 GGAGTAGCAGCTTGTATGTGAATAAT 59.292 38.462 0.00 0.00 0.00 1.28
5933 6607 5.952387 TGGTGCCCTCTATTGCTTAATAAT 58.048 37.500 0.00 0.00 0.00 1.28
5987 6661 7.795534 TTTGCCCGTCCTACCTAATATTATA 57.204 36.000 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1036 1085 4.334203 CAGGTATATGTTTTTGCAGCGGTA 59.666 41.667 0.00 0.00 0.00 4.02
2577 2673 1.795768 TCAAATGAGCTCACGACCAC 58.204 50.000 20.97 0.00 0.00 4.16
2676 2825 8.256605 ACCTACAAATGCATGCAAATTAACATA 58.743 29.630 26.68 11.56 0.00 2.29
2950 3099 9.880064 GTAAAAGAAGAGCTCGAACTAAATTTT 57.120 29.630 8.37 10.34 0.00 1.82
3011 3175 2.028130 ACCTCAGCATAGGAGTTCTCG 58.972 52.381 11.07 0.00 39.15 4.04
4050 4358 5.811100 TGTCGACACACACAAAGTAACATAA 59.189 36.000 15.76 0.00 0.00 1.90
4445 4753 0.036448 CCTCTGCTATGGCTGGATGG 59.964 60.000 8.06 4.99 39.59 3.51
4468 4776 4.820894 ACAAATACTTACCGCTTCCTCT 57.179 40.909 0.00 0.00 0.00 3.69
4472 4780 5.874895 AGGAAACAAATACTTACCGCTTC 57.125 39.130 0.00 0.00 0.00 3.86
4890 5211 5.130350 AGCAAAACAAGAGCTAACCTTACA 58.870 37.500 0.00 0.00 36.73 2.41
4964 5286 3.485394 TCCAAGCTTACTGCAACATTGA 58.515 40.909 0.00 0.00 45.94 2.57
5051 5373 3.230976 TCTAGCTCACTTCTTGTCCACA 58.769 45.455 0.00 0.00 0.00 4.17
5224 5546 1.273327 GCCAGAAGTGGGGTTTGATTG 59.727 52.381 0.00 0.00 45.17 2.67
5810 6481 2.612471 GCTCAAGCGGATGCATCTAGAT 60.612 50.000 25.28 15.81 46.23 1.98
5878 6552 9.513906 TGATACAATCAAACTTTCTATTGTGGA 57.486 29.630 15.79 4.40 41.38 4.02
5933 6607 5.592688 CAGGAAACAAAAACTAGGAGTCCAA 59.407 40.000 12.86 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.