Multiple sequence alignment - TraesCS4A01G033000

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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 TraesCS4A01G033000 chr4A 100.000 3502 0 0 1 3502 25198669 25202170 0.000000e+00 6468
1 TraesCS4A01G033000 chrUn 96.650 3522 97 11 1 3502 289577104 289580624 0.000000e+00 5830
2 TraesCS4A01G033000 chrUn 96.593 3522 100 10 1 3502 47723844 47720323 0.000000e+00 5821
3 TraesCS4A01G033000 chr7A 96.538 3524 100 11 1 3502 709868315 709871838 0.000000e+00 5812
4 TraesCS4A01G033000 chr7A 81.208 1325 186 37 491 1758 522245640 522246958 0.000000e+00 1009
5 TraesCS4A01G033000 chr7A 77.963 481 90 14 1827 2294 522247051 522247528 1.590000e-73 287
6 TraesCS4A01G033000 chr1A 93.608 1799 104 9 1337 3126 497228157 497226361 0.000000e+00 2675
7 TraesCS4A01G033000 chr1A 91.940 1340 89 14 4 1339 497229604 497228280 0.000000e+00 1858
8 TraesCS4A01G033000 chr1A 93.803 355 17 3 3152 3502 497225905 497225552 2.390000e-146 529
9 TraesCS4A01G033000 chr7D 82.897 1298 190 25 491 1762 532953983 532955274 0.000000e+00 1138
10 TraesCS4A01G033000 chr7D 83.289 1125 150 23 2409 3502 532955949 532957066 0.000000e+00 1002
11 TraesCS4A01G033000 chr3D 82.910 1299 186 27 491 1762 515702438 515701149 0.000000e+00 1136
12 TraesCS4A01G033000 chr3D 82.817 1292 191 24 497 1762 546583718 546582432 0.000000e+00 1127
13 TraesCS4A01G033000 chr3D 83.762 1127 143 22 2409 3502 515700474 515699355 0.000000e+00 1031
14 TraesCS4A01G033000 chr3D 83.556 1125 149 18 2409 3502 546581757 546580638 0.000000e+00 1020
15 TraesCS4A01G033000 chr2D 88.889 126 13 1 581 705 640260588 640260713 1.680000e-33 154


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 TraesCS4A01G033000 chr4A 25198669 25202170 3501 False 6468.000000 6468 100.0000 1 3502 1 chr4A.!!$F1 3501
1 TraesCS4A01G033000 chrUn 289577104 289580624 3520 False 5830.000000 5830 96.6500 1 3502 1 chrUn.!!$F1 3501
2 TraesCS4A01G033000 chrUn 47720323 47723844 3521 True 5821.000000 5821 96.5930 1 3502 1 chrUn.!!$R1 3501
3 TraesCS4A01G033000 chr7A 709868315 709871838 3523 False 5812.000000 5812 96.5380 1 3502 1 chr7A.!!$F1 3501
4 TraesCS4A01G033000 chr7A 522245640 522247528 1888 False 648.000000 1009 79.5855 491 2294 2 chr7A.!!$F2 1803
5 TraesCS4A01G033000 chr1A 497225552 497229604 4052 True 1687.333333 2675 93.1170 4 3502 3 chr1A.!!$R1 3498
6 TraesCS4A01G033000 chr7D 532953983 532957066 3083 False 1070.000000 1138 83.0930 491 3502 2 chr7D.!!$F1 3011
7 TraesCS4A01G033000 chr3D 515699355 515702438 3083 True 1083.500000 1136 83.3360 491 3502 2 chr3D.!!$R1 3011
8 TraesCS4A01G033000 chr3D 546580638 546583718 3080 True 1073.500000 1127 83.1865 497 3502 2 chr3D.!!$R2 3005

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
886 926 0.589223 CACTTAGTTTTTCGCCGCCA 59.411 50.0 0.00 0.0 0.0 5.69 F
1065 1125 0.387929 GGAATAGCGACGGTGATGGA 59.612 55.0 10.33 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2265 0.036164 TCTTGTGGGTTGCGTATGCT 59.964 50.0 8.69 0.0 43.34 3.79 R
3060 3330 0.888619 CTTCACAGGTGCTCCGTCTA 59.111 55.0 0.00 0.0 39.05 2.59 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
203 206 1.608055 CACTCCAACTGGATGTGCAA 58.392 50.000 12.41 0.00 44.46 4.08
271 274 0.807667 CTTCGTGGCGAATCCCTGAG 60.808 60.000 4.41 0.00 44.85 3.35
295 298 6.071334 AGCAGATAAAACAGACACTAGTGCTA 60.071 38.462 22.90 6.07 34.72 3.49
435 438 5.115480 ACCGCAACATTTCAACATTTTCTT 58.885 33.333 0.00 0.00 0.00 2.52
462 465 8.613482 GTCTTTACACTTGAAGTTTTAGAAGCT 58.387 33.333 0.00 0.00 0.00 3.74
589 595 1.290955 GTGGTACAGCTACACGCCA 59.709 57.895 0.00 0.00 41.80 5.69
595 601 3.391382 AGCTACACGCCACCCTCC 61.391 66.667 0.00 0.00 40.39 4.30
629 635 1.880675 AGAGTCGTGTCACGTCTTCAT 59.119 47.619 22.76 11.71 39.83 2.57
695 705 0.618981 CCCCACCCAACCTAGTTCTC 59.381 60.000 0.00 0.00 0.00 2.87
747 761 2.417516 CGACGCATCTAGGTGGGG 59.582 66.667 22.62 3.67 36.46 4.96
886 926 0.589223 CACTTAGTTTTTCGCCGCCA 59.411 50.000 0.00 0.00 0.00 5.69
1065 1125 0.387929 GGAATAGCGACGGTGATGGA 59.612 55.000 10.33 0.00 0.00 3.41
1084 1144 0.476771 ATCAGGTTGTTCAACGGGGT 59.523 50.000 9.15 0.00 0.00 4.95
1118 1178 0.818938 TGCTTCACCTCGCGGTTATA 59.181 50.000 6.13 0.00 42.13 0.98
1373 1558 4.661222 TGTGGCAATCTAACCATTCAAGA 58.339 39.130 0.00 0.00 38.46 3.02
1852 2083 4.244862 CTGCAAAACAGGTGTTTGTTCTT 58.755 39.130 8.82 0.00 46.47 2.52
2139 2381 3.245229 TGCAAGGGGTATTGAGTCACATT 60.245 43.478 0.00 0.00 31.55 2.71
2149 2391 8.303876 GGGTATTGAGTCACATTTAAATGTTGT 58.696 33.333 27.33 16.31 46.95 3.32
2182 2424 2.699846 AGATTGCCAAACCAGCTTTCAA 59.300 40.909 0.00 0.00 0.00 2.69
2313 2560 8.927675 AGTAAGTACCATCCACAATTTTGTTA 57.072 30.769 0.00 0.00 39.91 2.41
2396 2644 2.673368 GGTCGGAACTTGCTAACATGAG 59.327 50.000 0.00 0.00 0.00 2.90
2499 2747 2.223479 GCAAACATATCGGAAATGCGGT 60.223 45.455 0.00 0.00 0.00 5.68
2625 2873 4.690748 TCAAGAGCGAAGACAAAACCATAG 59.309 41.667 0.00 0.00 0.00 2.23
2811 3081 4.589374 AGGTCAAGTGTCTGCTACTAGTTT 59.411 41.667 0.00 0.00 0.00 2.66
2933 3203 3.119849 CCAAAAACAGAGACCAATAGCCG 60.120 47.826 0.00 0.00 0.00 5.52
2945 3215 4.694339 ACCAATAGCCGAAGATTCTACAC 58.306 43.478 0.00 0.00 0.00 2.90
3060 3330 2.676076 GATCTTGTTTGGCGCAACAAT 58.324 42.857 21.79 11.49 0.00 2.71
3092 3362 2.619849 CCTGTGAAGATTGACCTGGCAT 60.620 50.000 0.00 0.00 0.00 4.40
3134 3404 2.442413 CATGGGTTGTTGGTTCGGTAT 58.558 47.619 0.00 0.00 0.00 2.73
3170 3870 4.697352 CAGAAAATGCGCTTAGGGCTATAT 59.303 41.667 21.33 4.89 42.10 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
271 274 4.932200 AGCACTAGTGTCTGTTTTATCTGC 59.068 41.667 23.44 4.52 0.00 4.26
435 438 8.395633 GCTTCTAAAACTTCAAGTGTAAAGACA 58.604 33.333 0.00 0.00 0.00 3.41
462 465 5.123502 TGGTCAAGTGCGTGTTTAACTAAAA 59.876 36.000 0.00 0.00 0.00 1.52
695 705 3.658709 GGTGAGGAAAACAGAGTGAGAG 58.341 50.000 0.00 0.00 0.00 3.20
886 926 5.560966 ACACAAGAAAGAATGAACACGTT 57.439 34.783 0.00 0.00 0.00 3.99
960 1020 8.527810 CCACTAAAAAGGCCTGACATTTTTATA 58.472 33.333 16.10 1.23 37.59 0.98
1065 1125 0.476771 ACCCCGTTGAACAACCTGAT 59.523 50.000 11.30 0.00 38.03 2.90
1373 1558 2.086869 CAGATGGTTCAACGCCTTCAT 58.913 47.619 0.00 0.00 33.95 2.57
1432 1617 1.065551 GTTGTGTGTGCCTTTCTCACC 59.934 52.381 0.00 0.00 38.15 4.02
1804 2008 6.989155 AAACATATGGGCATGAATGAATCT 57.011 33.333 7.80 0.00 0.00 2.40
1852 2083 2.515854 AGACCGAGCTCTAAGTTGTCA 58.484 47.619 12.85 0.00 0.00 3.58
2029 2265 0.036164 TCTTGTGGGTTGCGTATGCT 59.964 50.000 8.69 0.00 43.34 3.79
2139 2381 2.950781 TCCTGTGCCCACAACATTTAA 58.049 42.857 2.45 0.00 41.33 1.52
2149 2391 2.657297 GCAATCTTTCCTGTGCCCA 58.343 52.632 0.00 0.00 0.00 5.36
2182 2424 2.289506 GGAGTACTTGCTCTTTTCGGGT 60.290 50.000 0.00 0.00 35.89 5.28
2313 2560 9.533253 CAAAGGAAACAAAGATATGACAAAACT 57.467 29.630 0.00 0.00 0.00 2.66
2499 2747 5.009110 TGAACATGTTTGATTGGAACGCTTA 59.991 36.000 13.36 0.00 0.00 3.09
2552 2800 7.521423 GCTTTACAACATGTACACATTTCTCCA 60.521 37.037 0.00 0.00 31.69 3.86
2625 2873 4.324991 AGTTGGGGGCGGTTCGTC 62.325 66.667 0.00 0.00 0.00 4.20
2811 3081 6.578439 GCTTCCATCCCTTTTCCTAGAAACTA 60.578 42.308 0.00 0.00 0.00 2.24
2933 3203 6.144724 GCGATGTCCATAAGTGTAGAATCTTC 59.855 42.308 0.00 0.00 0.00 2.87
2945 3215 2.064762 GCTGCTAGCGATGTCCATAAG 58.935 52.381 10.77 0.00 0.00 1.73
3060 3330 0.888619 CTTCACAGGTGCTCCGTCTA 59.111 55.000 0.00 0.00 39.05 2.59
3092 3362 1.073284 GTCCCTCCCAAAGTTGCACTA 59.927 52.381 0.00 0.00 0.00 2.74
3190 3890 2.165030 CCTCTGCAAATTGGTCATGGAC 59.835 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.