Multiple sequence alignment - TraesCS5A01G471500

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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 TraesCS5A01G471500 chr5A 100.000 3333 0 0 1 3333 648362722 648359390 0.000000e+00 6156.0
1 TraesCS5A01G471500 chr5A 96.110 2031 55 10 1067 3090 648228523 648226510 0.000000e+00 3291.0
2 TraesCS5A01G471500 chr5A 97.570 1070 23 3 1 1069 648239097 648238030 0.000000e+00 1829.0
3 TraesCS5A01G471500 chr5A 89.404 1293 114 14 1062 2333 647967239 647965949 0.000000e+00 1607.0
4 TraesCS5A01G471500 chr5A 89.934 914 70 11 1446 2349 648175170 648174269 0.000000e+00 1158.0
5 TraesCS5A01G471500 chr5A 85.816 564 53 10 1800 2349 648193822 648193272 1.040000e-159 573.0
6 TraesCS5A01G471500 chr5A 84.820 527 47 10 2391 2894 647975621 647975105 1.790000e-137 499.0
7 TraesCS5A01G471500 chr5A 93.827 243 9 5 3096 3333 648226098 648225857 8.790000e-96 361.0
8 TraesCS5A01G471500 chr5A 88.433 268 27 4 2628 2894 648178964 648178700 1.490000e-83 320.0
9 TraesCS5A01G471500 chr5A 81.013 395 47 11 1 368 648177645 648177252 4.210000e-74 289.0
10 TraesCS5A01G471500 chr5A 80.506 395 43 18 1 368 647974093 647973706 4.240000e-69 272.0
11 TraesCS5A01G471500 chr5A 85.774 239 25 6 2387 2622 648192984 648192752 9.240000e-61 244.0
12 TraesCS5A01G471500 chr5A 80.000 345 43 14 2563 2891 647955676 647955342 7.190000e-57 231.0
13 TraesCS5A01G471500 chr5A 96.610 59 2 0 750 808 647967435 647967377 7.610000e-17 99.0
14 TraesCS5A01G471500 chr5A 94.828 58 2 1 2456 2512 648313389 648313332 4.580000e-14 89.8
15 TraesCS5A01G471500 chr5B 94.018 2006 102 12 901 2896 655278731 655280728 0.000000e+00 3024.0
16 TraesCS5A01G471500 chr5B 93.509 1633 91 8 722 2349 655391248 655392870 0.000000e+00 2414.0
17 TraesCS5A01G471500 chr5B 92.871 1501 90 9 854 2349 655321968 655323456 0.000000e+00 2163.0
18 TraesCS5A01G471500 chr5B 84.416 1155 136 20 1197 2341 655560708 655559588 0.000000e+00 1096.0
19 TraesCS5A01G471500 chr5B 84.601 539 54 7 2359 2877 655393156 655393685 2.970000e-140 508.0
20 TraesCS5A01G471500 chr5B 89.544 373 32 5 1 368 655373869 655374239 1.810000e-127 466.0
21 TraesCS5A01G471500 chr5B 86.765 272 22 9 1 261 655278078 655278346 1.170000e-74 291.0
22 TraesCS5A01G471500 chr5B 82.072 251 23 12 3102 3332 705432666 705432914 9.440000e-46 195.0
23 TraesCS5A01G471500 chr5B 88.344 163 16 3 367 527 59906869 59907030 3.390000e-45 193.0
24 TraesCS5A01G471500 chr5B 96.262 107 4 0 262 368 655278384 655278490 3.420000e-40 176.0
25 TraesCS5A01G471500 chr5B 95.876 97 4 0 612 708 655391167 655391263 1.240000e-34 158.0
26 TraesCS5A01G471500 chr5B 91.509 106 6 1 526 628 655278489 655278594 3.470000e-30 143.0
27 TraesCS5A01G471500 chr5B 92.391 92 7 0 526 617 655374238 655374329 7.500000e-27 132.0
28 TraesCS5A01G471500 chr5D 93.200 1500 79 10 844 2334 520302187 520300702 0.000000e+00 2183.0
29 TraesCS5A01G471500 chr5D 90.530 264 20 4 1 261 520310125 520309864 8.850000e-91 344.0
30 TraesCS5A01G471500 chr5D 78.700 554 76 18 2366 2891 520300141 520299602 6.890000e-87 331.0
31 TraesCS5A01G471500 chr5D 97.196 107 3 0 262 368 520309826 520309720 7.350000e-42 182.0
32 TraesCS5A01G471500 chr5D 92.000 100 5 1 532 628 520309715 520309616 1.610000e-28 137.0
33 TraesCS5A01G471500 chr5D 94.231 52 3 0 773 824 520302240 520302189 2.760000e-11 80.5
34 TraesCS5A01G471500 chrUn 88.855 1301 110 16 1064 2334 294624926 294623631 0.000000e+00 1567.0
35 TraesCS5A01G471500 chrUn 85.149 707 69 16 1483 2180 67224494 67223815 0.000000e+00 691.0
36 TraesCS5A01G471500 chrUn 85.149 707 69 16 1483 2180 356834017 356833338 0.000000e+00 691.0
37 TraesCS5A01G471500 chrUn 77.617 554 82 18 2366 2891 294623070 294622531 6.990000e-77 298.0
38 TraesCS5A01G471500 chr6D 83.059 1216 167 21 1067 2253 22762729 22761524 0.000000e+00 1068.0
39 TraesCS5A01G471500 chr6D 83.938 193 10 10 3096 3269 277118334 277118524 7.400000e-37 165.0
40 TraesCS5A01G471500 chr3B 84.426 244 17 7 3102 3332 187492289 187492054 1.560000e-53 220.0
41 TraesCS5A01G471500 chr4B 83.468 248 22 9 3102 3331 542188165 542188411 2.600000e-51 213.0
42 TraesCS5A01G471500 chr6A 89.024 164 16 2 366 527 600298782 600298619 5.640000e-48 202.0
43 TraesCS5A01G471500 chr2B 87.059 170 20 1 367 534 562222483 562222652 1.220000e-44 191.0
44 TraesCS5A01G471500 chr2B 84.314 102 12 3 2948 3046 786403376 786403276 2.740000e-16 97.1
45 TraesCS5A01G471500 chr2A 84.236 203 25 7 2893 3089 87868862 87869063 1.220000e-44 191.0
46 TraesCS5A01G471500 chr7B 87.730 163 17 3 367 527 734071471 734071632 1.580000e-43 187.0
47 TraesCS5A01G471500 chr4A 87.117 163 19 2 367 527 714441626 714441788 2.040000e-42 183.0
48 TraesCS5A01G471500 chr4D 87.117 163 18 3 367 527 117421191 117421352 7.350000e-42 182.0
49 TraesCS5A01G471500 chr4D 100.000 29 0 0 1033 1061 375135028 375135000 2.000000e-03 54.7
50 TraesCS5A01G471500 chr1B 87.117 163 18 3 367 527 649337120 649336959 7.350000e-42 182.0
51 TraesCS5A01G471500 chr1B 87.117 163 18 3 367 527 652464767 652464928 7.350000e-42 182.0
52 TraesCS5A01G471500 chr1B 85.795 176 16 4 2921 3089 390837483 390837656 9.500000e-41 178.0
53 TraesCS5A01G471500 chr3A 80.075 266 24 18 3091 3333 198250421 198250680 1.590000e-38 171.0
54 TraesCS5A01G471500 chr3A 84.483 174 20 7 2921 3089 296727643 296727472 7.400000e-37 165.0
55 TraesCS5A01G471500 chr6B 80.000 260 27 14 3096 3332 84675996 84676253 5.720000e-38 169.0
56 TraesCS5A01G471500 chr6B 79.608 255 32 8 3091 3326 41028564 41028817 7.400000e-37 165.0
57 TraesCS5A01G471500 chr6B 79.151 259 32 15 3091 3332 41110001 41110254 3.440000e-35 159.0
58 TraesCS5A01G471500 chr6B 83.030 165 20 8 2937 3093 574894016 574893852 3.470000e-30 143.0
59 TraesCS5A01G471500 chr7A 81.159 138 20 6 2956 3089 700935049 700935184 4.550000e-19 106.0


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 TraesCS5A01G471500 chr5A 648359390 648362722 3332 True 6156.000000 6156 100.000000 1 3333 1 chr5A.!!$R4 3332
1 TraesCS5A01G471500 chr5A 648238030 648239097 1067 True 1829.000000 1829 97.570000 1 1069 1 chr5A.!!$R2 1068
2 TraesCS5A01G471500 chr5A 648225857 648228523 2666 True 1826.000000 3291 94.968500 1067 3333 2 chr5A.!!$R9 2266
3 TraesCS5A01G471500 chr5A 647965949 647967435 1486 True 853.000000 1607 93.007000 750 2333 2 chr5A.!!$R5 1583
4 TraesCS5A01G471500 chr5A 648174269 648178964 4695 True 589.000000 1158 86.460000 1 2894 3 chr5A.!!$R7 2893
5 TraesCS5A01G471500 chr5A 648192752 648193822 1070 True 408.500000 573 85.795000 1800 2622 2 chr5A.!!$R8 822
6 TraesCS5A01G471500 chr5A 647973706 647975621 1915 True 385.500000 499 82.663000 1 2894 2 chr5A.!!$R6 2893
7 TraesCS5A01G471500 chr5B 655321968 655323456 1488 False 2163.000000 2163 92.871000 854 2349 1 chr5B.!!$F2 1495
8 TraesCS5A01G471500 chr5B 655559588 655560708 1120 True 1096.000000 1096 84.416000 1197 2341 1 chr5B.!!$R1 1144
9 TraesCS5A01G471500 chr5B 655391167 655393685 2518 False 1026.666667 2414 91.328667 612 2877 3 chr5B.!!$F6 2265
10 TraesCS5A01G471500 chr5B 655278078 655280728 2650 False 908.500000 3024 92.138500 1 2896 4 chr5B.!!$F4 2895
11 TraesCS5A01G471500 chr5D 520299602 520302240 2638 True 864.833333 2183 88.710333 773 2891 3 chr5D.!!$R1 2118
12 TraesCS5A01G471500 chr5D 520309616 520310125 509 True 221.000000 344 93.242000 1 628 3 chr5D.!!$R2 627
13 TraesCS5A01G471500 chrUn 294622531 294624926 2395 True 932.500000 1567 83.236000 1064 2891 2 chrUn.!!$R3 1827
14 TraesCS5A01G471500 chrUn 67223815 67224494 679 True 691.000000 691 85.149000 1483 2180 1 chrUn.!!$R1 697
15 TraesCS5A01G471500 chrUn 356833338 356834017 679 True 691.000000 691 85.149000 1483 2180 1 chrUn.!!$R2 697
16 TraesCS5A01G471500 chr6D 22761524 22762729 1205 True 1068.000000 1068 83.059000 1067 2253 1 chr6D.!!$R1 1186

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
866 3009 3.075148 CCTAATCCAGACGCGAGATAGA 58.925 50.0 15.93 2.72 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2456 5789 1.072331 GCAAGAGGTTTGACTGGAGGA 59.928 52.381 0.0 0.0 0.0 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
166 1492 9.449719 ACCCACTCAACTTATTTAGACATAAAG 57.550 33.333 0.00 0.00 34.44 1.85
655 2798 3.463944 GAAGTTGACGTCTGGAAGGAAA 58.536 45.455 17.92 0.00 0.00 3.13
743 2886 6.519679 AAAAGACAAGTCGGTTAAGGTTTT 57.480 33.333 0.00 0.00 34.09 2.43
744 2887 7.628769 AAAAGACAAGTCGGTTAAGGTTTTA 57.371 32.000 0.00 0.00 34.09 1.52
750 2893 9.949174 GACAAGTCGGTTAAGGTTTTATTTTTA 57.051 29.630 0.00 0.00 0.00 1.52
866 3009 3.075148 CCTAATCCAGACGCGAGATAGA 58.925 50.000 15.93 2.72 0.00 1.98
1037 3192 0.320374 CTCAGGGGTTACACGCTTCA 59.680 55.000 0.00 0.00 0.00 3.02
1143 3301 1.674057 CCTCAGCTCGACCCTGTTT 59.326 57.895 7.88 0.00 0.00 2.83
2008 4688 0.992802 GAGTTCGAAGTGTCATCCGC 59.007 55.000 10.94 0.00 0.00 5.54
2231 4929 0.250553 TTGTGGCGGATCGACCTTTT 60.251 50.000 4.46 0.00 31.60 2.27
2257 4955 0.474660 GCCATGGTAGAGGAGGGGAT 60.475 60.000 14.67 0.00 0.00 3.85
2320 5022 8.293157 TCTCGCTCACTAGATGAATAGTAAATG 58.707 37.037 0.00 0.00 36.69 2.32
2545 5879 9.807921 TCCAAATTTCTTTAGTCTTGTAATCCT 57.192 29.630 0.00 0.00 0.00 3.24
2688 6051 9.953697 GTACAACAACAAAACAATTGATAGGTA 57.046 29.630 13.59 0.00 0.00 3.08
3091 6831 3.872603 ACACGCTCTGGCCCACAA 61.873 61.111 0.00 0.00 34.44 3.33
3095 6835 0.037590 ACGCTCTGGCCCACAAAATA 59.962 50.000 0.00 0.00 34.44 1.40
3096 6836 1.173043 CGCTCTGGCCCACAAAATAA 58.827 50.000 0.00 0.00 34.44 1.40
3097 6837 1.750778 CGCTCTGGCCCACAAAATAAT 59.249 47.619 0.00 0.00 34.44 1.28
3098 6838 2.948979 CGCTCTGGCCCACAAAATAATA 59.051 45.455 0.00 0.00 34.44 0.98
3099 6839 3.569701 CGCTCTGGCCCACAAAATAATAT 59.430 43.478 0.00 0.00 34.44 1.28
3327 7674 6.900568 ACAATTGTCGCATCTTTTGAAAAA 57.099 29.167 4.92 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 1474 8.116624 CGACTCGCTTTATGTCTAAATAAGTT 57.883 34.615 0.00 0.00 0.00 2.66
175 1501 3.876914 TGGCAAACACACAACAACAAAAA 59.123 34.783 0.00 0.00 0.00 1.94
655 2798 1.080434 GACTTCAGCCGCTTCTCGT 60.080 57.895 0.00 0.00 36.19 4.18
723 2866 7.812690 AAATAAAACCTTAACCGACTTGTCT 57.187 32.000 0.00 0.00 0.00 3.41
724 2867 8.861033 AAAAATAAAACCTTAACCGACTTGTC 57.139 30.769 0.00 0.00 0.00 3.18
750 2893 6.301486 ACCGACTTAACACTTCCCTAAAAAT 58.699 36.000 0.00 0.00 0.00 1.82
753 2896 4.961438 ACCGACTTAACACTTCCCTAAA 57.039 40.909 0.00 0.00 0.00 1.85
866 3009 5.910614 ACGAGTACAAGTTAAACACCTCTT 58.089 37.500 0.00 0.00 0.00 2.85
1037 3192 1.062428 TGGGACGGAGGGAGTATGATT 60.062 52.381 0.00 0.00 0.00 2.57
2231 4929 4.386312 CCCTCCTCTACCATGGCAAATAAA 60.386 45.833 13.04 0.00 0.00 1.40
2257 4955 5.592282 TGACCAAGAAACAAAACTGCATCTA 59.408 36.000 0.00 0.00 0.00 1.98
2456 5789 1.072331 GCAAGAGGTTTGACTGGAGGA 59.928 52.381 0.00 0.00 0.00 3.71
2458 5791 2.260844 TGCAAGAGGTTTGACTGGAG 57.739 50.000 0.00 0.00 0.00 3.86
2547 5881 9.378551 GTGACATGTCCTTTTGTATTCTGTATA 57.621 33.333 22.85 0.00 0.00 1.47
2548 5882 8.103305 AGTGACATGTCCTTTTGTATTCTGTAT 58.897 33.333 22.85 0.00 0.00 2.29
2766 6131 1.376609 AATTCCGCGGATCAAGCACC 61.377 55.000 31.56 0.00 34.19 5.01
2932 6300 8.578151 TGGAAAAACGCACCTTACTTTATTAAT 58.422 29.630 0.00 0.00 0.00 1.40
2998 6366 4.577283 GCACAAAAGTTTAGTACCACCTCA 59.423 41.667 0.00 0.00 0.00 3.86
3299 7646 6.038985 TCAAAAGATGCGACAATTGTTTTGA 58.961 32.000 20.44 20.44 39.10 2.69


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

AutoCloner maintained by Alex Coulton.