Multiple sequence alignment - TraesCS3D01G504400

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 TraesCS3D01G504400 chr3D 100.000 3123 0 0 1 3123 591972912 591976034 0.000000e+00 5768.0
1 TraesCS3D01G504400 chr2D 97.059 3162 42 19 1 3123 5276063 5272914 0.000000e+00 5276.0
2 TraesCS3D01G504400 chr2D 84.255 1791 158 73 250 1958 610716313 610718061 0.000000e+00 1631.0
3 TraesCS3D01G504400 chr6D 97.102 3140 37 22 17 3123 131657311 131660429 0.000000e+00 5245.0
4 TraesCS3D01G504400 chr6D 95.236 1994 47 21 271 2225 38522088 38524072 0.000000e+00 3112.0
5 TraesCS3D01G504400 chr6D 95.620 411 7 10 2230 2637 38524120 38524522 0.000000e+00 649.0
6 TraesCS3D01G504400 chr6D 97.541 122 3 0 1 122 38521968 38522089 3.160000e-50 209.0
7 TraesCS3D01G504400 chr3A 90.034 2057 107 53 250 2225 202617731 202619770 0.000000e+00 2573.0
8 TraesCS3D01G504400 chr3A 89.212 241 17 7 22 258 202616978 202617213 3.050000e-75 292.0
9 TraesCS3D01G504400 chr1D 96.278 1585 18 12 677 2225 49544957 49543378 0.000000e+00 2562.0
10 TraesCS3D01G504400 chr1D 84.185 1821 143 73 250 1958 481572278 481574065 0.000000e+00 1633.0
11 TraesCS3D01G504400 chr1D 96.325 898 21 10 2229 3123 49543330 49542442 0.000000e+00 1465.0
12 TraesCS3D01G504400 chr6A 93.214 1739 67 28 535 2225 194789792 194788057 0.000000e+00 2510.0
13 TraesCS3D01G504400 chr6A 92.478 678 32 16 1563 2225 194773430 194772757 0.000000e+00 952.0
14 TraesCS3D01G504400 chr6A 92.319 677 35 14 1563 2225 194745571 194744898 0.000000e+00 946.0
15 TraesCS3D01G504400 chr6A 90.102 394 26 12 2229 2619 194744850 194744467 1.670000e-137 499.0
16 TraesCS3D01G504400 chr6A 90.981 377 23 11 2229 2602 194788009 194787641 6.010000e-137 497.0
17 TraesCS3D01G504400 chr6A 90.078 383 26 10 2229 2608 194772709 194772336 1.300000e-133 486.0
18 TraesCS3D01G504400 chr6A 92.420 343 20 6 2691 3031 194735067 194734729 4.680000e-133 484.0
19 TraesCS3D01G504400 chr6A 91.545 343 23 6 2691 3031 194762699 194762361 4.720000e-128 468.0
20 TraesCS3D01G504400 chr6A 83.121 314 38 13 2815 3123 194785421 194785118 3.970000e-69 272.0
21 TraesCS3D01G504400 chr7A 93.539 1687 54 26 1 1637 107639392 107637711 0.000000e+00 2460.0
22 TraesCS3D01G504400 chr7A 89.354 1766 99 39 534 2225 84784517 84782767 0.000000e+00 2137.0
23 TraesCS3D01G504400 chr7A 94.643 560 24 5 1670 2225 107637623 107637066 0.000000e+00 863.0
24 TraesCS3D01G504400 chr7A 91.837 392 24 8 2642 3031 107636641 107636256 9.850000e-150 540.0
25 TraesCS3D01G504400 chr7A 90.863 394 23 10 2229 2619 107637018 107636635 1.660000e-142 516.0
26 TraesCS3D01G504400 chr7A 94.208 259 8 7 2229 2487 84782719 84782468 3.780000e-104 388.0
27 TraesCS3D01G504400 chr7A 88.797 241 18 6 22 258 84785905 84785670 1.420000e-73 287.0
28 TraesCS3D01G504400 chr7A 90.233 215 10 5 2629 2841 84782342 84782137 1.430000e-68 270.0
29 TraesCS3D01G504400 chr7A 82.410 307 42 12 2821 3123 107635019 107634721 1.110000e-64 257.0
30 TraesCS3D01G504400 chr7A 88.660 194 15 6 2933 3123 84779853 84779664 2.420000e-56 230.0
31 TraesCS3D01G504400 chr1A 84.628 1815 148 73 242 1958 127097517 127099298 0.000000e+00 1685.0
32 TraesCS3D01G504400 chr7D 83.901 1820 144 78 250 1958 223970802 223972583 0.000000e+00 1600.0
33 TraesCS3D01G504400 chr7D 98.214 56 1 0 173 228 514757342 514757287 7.130000e-17 99.0
34 TraesCS3D01G504400 chr2B 88.034 117 8 5 35 147 578584630 578584516 1.950000e-27 134.0
35 TraesCS3D01G504400 chr4A 81.513 119 19 3 2870 2988 705769953 705770068 9.220000e-16 95.3
36 TraesCS3D01G504400 chr5A 97.059 34 1 0 262 295 436073439 436073406 1.210000e-04 58.4


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 TraesCS3D01G504400 chr3D 591972912 591976034 3122 False 5768.000000 5768 100.000000 1 3123 1 chr3D.!!$F1 3122
1 TraesCS3D01G504400 chr2D 5272914 5276063 3149 True 5276.000000 5276 97.059000 1 3123 1 chr2D.!!$R1 3122
2 TraesCS3D01G504400 chr2D 610716313 610718061 1748 False 1631.000000 1631 84.255000 250 1958 1 chr2D.!!$F1 1708
3 TraesCS3D01G504400 chr6D 131657311 131660429 3118 False 5245.000000 5245 97.102000 17 3123 1 chr6D.!!$F1 3106
4 TraesCS3D01G504400 chr6D 38521968 38524522 2554 False 1323.333333 3112 96.132333 1 2637 3 chr6D.!!$F2 2636
5 TraesCS3D01G504400 chr3A 202616978 202619770 2792 False 1432.500000 2573 89.623000 22 2225 2 chr3A.!!$F1 2203
6 TraesCS3D01G504400 chr1D 49542442 49544957 2515 True 2013.500000 2562 96.301500 677 3123 2 chr1D.!!$R1 2446
7 TraesCS3D01G504400 chr1D 481572278 481574065 1787 False 1633.000000 1633 84.185000 250 1958 1 chr1D.!!$F1 1708
8 TraesCS3D01G504400 chr6A 194785118 194789792 4674 True 1093.000000 2510 89.105333 535 3123 3 chr6A.!!$R5 2588
9 TraesCS3D01G504400 chr6A 194744467 194745571 1104 True 722.500000 946 91.210500 1563 2619 2 chr6A.!!$R3 1056
10 TraesCS3D01G504400 chr6A 194772336 194773430 1094 True 719.000000 952 91.278000 1563 2608 2 chr6A.!!$R4 1045
11 TraesCS3D01G504400 chr7A 107634721 107639392 4671 True 927.200000 2460 90.658400 1 3123 5 chr7A.!!$R2 3122
12 TraesCS3D01G504400 chr7A 84779664 84785905 6241 True 662.400000 2137 90.250400 22 3123 5 chr7A.!!$R1 3101
13 TraesCS3D01G504400 chr1A 127097517 127099298 1781 False 1685.000000 1685 84.628000 242 1958 1 chr1A.!!$F1 1716
14 TraesCS3D01G504400 chr7D 223970802 223972583 1781 False 1600.000000 1600 83.901000 250 1958 1 chr7D.!!$F1 1708

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
575 1482 3.125316 CCTGTGTGAAGCTATTCGAAACC 59.875 47.826 0.0 0.0 38.34 3.27 F
1637 2659 0.327259 GAAGGGGCGGGGGTAATATC 59.673 60.000 0.0 0.0 0.00 1.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 3116 1.135257 TCTGCTAGCTGCGAAGTCTTC 60.135 52.381 17.23 2.18 46.63 2.87 R
2494 3654 1.270094 TGTGTAAGGAGCGTGTTCCTG 60.270 52.381 6.00 0.00 46.90 3.86 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
191 196 3.241701 ACTTGTTTGTTCTGTTTGTGCG 58.758 40.909 0.00 0.00 0.00 5.34
575 1482 3.125316 CCTGTGTGAAGCTATTCGAAACC 59.875 47.826 0.00 0.00 38.34 3.27
977 1932 3.690460 AGTTCAAGAATGCAGGGGTAAG 58.310 45.455 0.00 0.00 0.00 2.34
1091 2064 0.968405 GTGCCTTGCAATGAAAGGGA 59.032 50.000 20.99 16.14 43.80 4.20
1317 2296 3.423154 GTGGGCAACGGCTCGAAG 61.423 66.667 1.50 0.00 46.33 3.79
1387 2395 4.201950 GCGATGATAGTGAAGGCATTGTTT 60.202 41.667 0.00 0.00 0.00 2.83
1434 2444 1.755959 ACAGAGGATGCTCAGCTACAG 59.244 52.381 17.24 0.03 0.00 2.74
1637 2659 0.327259 GAAGGGGCGGGGGTAATATC 59.673 60.000 0.00 0.00 0.00 1.63
2009 3116 0.961753 GTTTGGCAGGAAGAAGTGGG 59.038 55.000 0.00 0.00 0.00 4.61
2129 3236 0.609131 GAAGCTTGGCTAGGCACCAA 60.609 55.000 20.09 9.25 44.86 3.67
2468 3628 2.570415 TTTCCACGCTATCCAACCAA 57.430 45.000 0.00 0.00 0.00 3.67
2494 3654 7.923878 ACTTATGTGTTTTTAATTGTGGTGTCC 59.076 33.333 0.00 0.00 0.00 4.02
2552 3712 8.237267 AGAATGTGGACGATGAAACTTTTATTC 58.763 33.333 0.00 0.00 0.00 1.75
2553 3713 5.922546 TGTGGACGATGAAACTTTTATTCG 58.077 37.500 0.00 4.91 33.48 3.34
2554 3714 5.697178 TGTGGACGATGAAACTTTTATTCGA 59.303 36.000 10.89 0.00 32.37 3.71
2555 3715 6.370442 TGTGGACGATGAAACTTTTATTCGAT 59.630 34.615 10.89 0.00 32.37 3.59
2589 3753 5.563842 CCTGTCGTGATCTAATTTTGCTTC 58.436 41.667 0.00 0.00 0.00 3.86
2675 5836 4.041740 GGAGACCTTTGTTTTGTTGGAC 57.958 45.455 0.00 0.00 0.00 4.02
2903 6348 2.494471 ACTAGGCACGTAACTGCATGTA 59.506 45.455 0.00 0.00 39.08 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.766263 TGTACATCTCCAGCACCTTAGG 59.234 50.000 0.00 0.00 0.00 2.69
15 16 4.375272 CATGTACATCTCCAGCACCTTAG 58.625 47.826 5.07 0.00 0.00 2.18
191 196 6.308041 GGTTCATTCTCTAAAAACGGCATTTC 59.692 38.462 0.00 0.00 0.00 2.17
977 1932 9.269453 ACATTAGTACAAAAAGTTAGGAGTGAC 57.731 33.333 0.00 0.00 0.00 3.67
1057 2030 2.438868 GGCACAACCTGATTTGAACC 57.561 50.000 0.00 0.00 34.51 3.62
1091 2064 1.018148 TGTCGCATTGTTGAAACGGT 58.982 45.000 0.00 0.00 0.00 4.83
1314 2293 6.860080 TGAAATCTGAATCTTCAATGGCTTC 58.140 36.000 0.00 0.00 36.64 3.86
1317 2296 5.126707 ACCTGAAATCTGAATCTTCAATGGC 59.873 40.000 0.00 0.00 36.64 4.40
1387 2395 1.606313 GCAAAAGCCCCCTAGTGCA 60.606 57.895 0.00 0.00 33.45 4.57
2009 3116 1.135257 TCTGCTAGCTGCGAAGTCTTC 60.135 52.381 17.23 2.18 46.63 2.87
2129 3236 2.554032 GCTTGTCATTAGTTGCTGTGGT 59.446 45.455 0.00 0.00 0.00 4.16
2468 3628 7.923878 GGACACCACAATTAAAAACACATAAGT 59.076 33.333 0.00 0.00 0.00 2.24
2494 3654 1.270094 TGTGTAAGGAGCGTGTTCCTG 60.270 52.381 6.00 0.00 46.90 3.86
2675 5836 2.356553 TCTTTTGACGTCGCCCCG 60.357 61.111 11.62 0.00 0.00 5.73
2903 6348 4.246458 GAGTTGCGACCAAGTTAGAGAAT 58.754 43.478 0.00 0.00 34.81 2.40


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

AutoCloner maintained by Alex Coulton.