Multiple sequence alignment - TraesCS5B01G562900

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 TraesCS5B01G562900 chr5B 100.000 2974 0 0 1 2974 708529562 708532535 0.000000e+00 5493
1 TraesCS5B01G562900 chr5B 97.472 2650 64 3 1 2648 708606125 708608773 0.000000e+00 4519
2 TraesCS5B01G562900 chr5B 97.365 2277 51 3 1 2275 708567521 708569790 0.000000e+00 3864
3 TraesCS5B01G562900 chr5B 96.623 1925 45 4 1051 2974 708451198 708453103 0.000000e+00 3177
4 TraesCS5B01G562900 chr5B 96.929 977 28 1 1 975 708450185 708451161 0.000000e+00 1637
5 TraesCS5B01G562900 chr5B 96.543 781 25 1 1 779 708432263 708433043 0.000000e+00 1291
6 TraesCS5B01G562900 chr5B 98.788 330 4 0 2645 2974 708610283 708610612 3.300000e-164 588
7 TraesCS5B01G562900 chr5B 97.902 286 6 0 2689 2974 708569836 708570121 2.060000e-136 496
8 TraesCS5B01G562900 chr5B 75.714 350 70 11 2638 2974 708408155 708408502 8.530000e-36 161
9 TraesCS5B01G562900 chr5B 100.000 59 0 0 2516 2574 708569789 708569847 3.130000e-20 110
10 TraesCS5B01G562900 chrUn 96.287 781 27 1 1 779 319360237 319359457 0.000000e+00 1280
11 TraesCS5B01G562900 chrUn 96.287 781 27 1 1 779 350486209 350486989 0.000000e+00 1280
12 TraesCS5B01G562900 chrUn 92.025 815 62 3 1103 1915 414798990 414798177 0.000000e+00 1142
13 TraesCS5B01G562900 chrUn 79.500 200 41 0 2724 2923 376646048 376646247 3.090000e-30 143
14 TraesCS5B01G562900 chrUn 79.500 200 41 0 2724 2923 404506006 404506205 3.090000e-30 143
15 TraesCS5B01G562900 chrUn 89.474 95 10 0 2388 2482 455531600 455531694 1.450000e-23 121
16 TraesCS5B01G562900 chr5D 92.044 817 60 5 1103 1915 557397288 557398103 0.000000e+00 1144
17 TraesCS5B01G562900 chr5D 92.025 815 62 3 1103 1915 564737706 564738519 0.000000e+00 1142
18 TraesCS5B01G562900 chr5D 91.789 816 63 3 1103 1915 557335158 557335972 0.000000e+00 1133
19 TraesCS5B01G562900 chr5D 88.732 284 30 2 2119 2401 557349808 557349526 2.190000e-91 346
20 TraesCS5B01G562900 chr5D 88.462 286 31 2 2117 2401 557341087 557340803 7.890000e-91 344
21 TraesCS5B01G562900 chr5D 88.462 286 31 2 2117 2401 557371177 557370893 7.890000e-91 344
22 TraesCS5B01G562900 chr5D 88.462 286 31 2 2117 2401 564743633 564743349 7.890000e-91 344
23 TraesCS5B01G562900 chr5D 86.063 287 36 4 2117 2401 557319884 557319600 3.720000e-79 305
24 TraesCS5B01G562900 chr5D 91.628 215 18 0 2388 2602 557340458 557340672 6.230000e-77 298
25 TraesCS5B01G562900 chr5D 91.628 215 18 0 2388 2602 557349181 557349395 6.230000e-77 298
26 TraesCS5B01G562900 chr5D 91.628 215 18 0 2388 2602 557370549 557370763 6.230000e-77 298
27 TraesCS5B01G562900 chr5D 91.628 215 18 0 2388 2602 564743005 564743219 6.230000e-77 298
28 TraesCS5B01G562900 chr5D 91.163 215 18 1 2388 2602 557319257 557319470 1.040000e-74 291
29 TraesCS5B01G562900 chr5D 79.500 200 41 0 2724 2923 557323942 557324141 3.090000e-30 143
30 TraesCS5B01G562900 chr5D 79.500 200 41 0 2724 2923 557354792 557354991 3.090000e-30 143
31 TraesCS5B01G562900 chr5D 79.500 200 41 0 2724 2923 557375230 557375429 3.090000e-30 143
32 TraesCS5B01G562900 chr4A 91.862 811 65 1 1103 1912 606333483 606334293 0.000000e+00 1131
33 TraesCS5B01G562900 chr4A 91.739 811 66 1 1103 1912 606262551 606263361 0.000000e+00 1125
34 TraesCS5B01G562900 chr4A 87.888 644 61 11 1 642 606332495 606333123 0.000000e+00 741
35 TraesCS5B01G562900 chr4A 87.422 644 64 11 1 642 605892169 605892797 0.000000e+00 725
36 TraesCS5B01G562900 chr4A 87.267 644 65 11 1 642 606196661 606197289 0.000000e+00 719


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 TraesCS5B01G562900 chr5B 708529562 708532535 2973 False 5493.0 5493 100.000000 1 2974 1 chr5B.!!$F3 2973
1 TraesCS5B01G562900 chr5B 708606125 708610612 4487 False 2553.5 4519 98.130000 1 2974 2 chr5B.!!$F6 2973
2 TraesCS5B01G562900 chr5B 708450185 708453103 2918 False 2407.0 3177 96.776000 1 2974 2 chr5B.!!$F4 2973
3 TraesCS5B01G562900 chr5B 708567521 708570121 2600 False 1490.0 3864 98.422333 1 2974 3 chr5B.!!$F5 2973
4 TraesCS5B01G562900 chr5B 708432263 708433043 780 False 1291.0 1291 96.543000 1 779 1 chr5B.!!$F2 778
5 TraesCS5B01G562900 chrUn 319359457 319360237 780 True 1280.0 1280 96.287000 1 779 1 chrUn.!!$R1 778
6 TraesCS5B01G562900 chrUn 350486209 350486989 780 False 1280.0 1280 96.287000 1 779 1 chrUn.!!$F1 778
7 TraesCS5B01G562900 chrUn 414798177 414798990 813 True 1142.0 1142 92.025000 1103 1915 1 chrUn.!!$R2 812
8 TraesCS5B01G562900 chr5D 557397288 557398103 815 False 1144.0 1144 92.044000 1103 1915 1 chr5D.!!$F9 812
9 TraesCS5B01G562900 chr5D 564737706 564738519 813 False 1142.0 1142 92.025000 1103 1915 1 chr5D.!!$F10 812
10 TraesCS5B01G562900 chr5D 557335158 557335972 814 False 1133.0 1133 91.789000 1103 1915 1 chr5D.!!$F3 812
11 TraesCS5B01G562900 chr4A 606262551 606263361 810 False 1125.0 1125 91.739000 1103 1912 1 chr4A.!!$F3 809
12 TraesCS5B01G562900 chr4A 606332495 606334293 1798 False 936.0 1131 89.875000 1 1912 2 chr4A.!!$F4 1911
13 TraesCS5B01G562900 chr4A 605892169 605892797 628 False 725.0 725 87.422000 1 642 1 chr4A.!!$F1 641
14 TraesCS5B01G562900 chr4A 606196661 606197289 628 False 719.0 719 87.267000 1 642 1 chr4A.!!$F2 641

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
940 1187 1.332997 CTGGTGCATGCTAGCTAAAGC 59.667 52.381 20.33 14.22 43.08 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2900 4664 1.630878 AGGTCTGCGATTTCCTTCCTT 59.369 47.619 0.0 0.0 0.0 3.36 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
343 346 3.576550 TCACTAACCAAAGGCAATTTCCC 59.423 43.478 0.00 0.00 0.00 3.97
384 387 3.000727 GTGCACTCCGTGTTTAGCTATT 58.999 45.455 10.32 0.00 35.75 1.73
400 403 5.630415 AGCTATTAGTGTTGGCCATCTTA 57.370 39.130 6.09 0.00 0.00 2.10
420 424 9.158233 CATCTTACTTTTTCCACGGACTATTTA 57.842 33.333 0.00 0.00 0.00 1.40
559 563 7.048512 GCTAGTTACCATAACCTCACAAATCT 58.951 38.462 0.00 0.00 0.00 2.40
573 577 7.884877 ACCTCACAAATCTCAAGACAATATGAA 59.115 33.333 0.00 0.00 0.00 2.57
661 905 6.189133 AGGTAGTAATATAGCCAGAGTAGCC 58.811 44.000 0.00 0.00 0.00 3.93
768 1012 5.350091 GGTCTACAGATGCTTCTCAAAAGAC 59.650 44.000 15.12 15.12 0.00 3.01
940 1187 1.332997 CTGGTGCATGCTAGCTAAAGC 59.667 52.381 20.33 14.22 43.08 3.51
1029 1276 3.773560 ACCTATCTACTCCATCTGGCTC 58.226 50.000 0.00 0.00 34.44 4.70
1132 1379 6.183360 CGATCAAACACATCCATCATAACCAA 60.183 38.462 0.00 0.00 0.00 3.67
1243 1490 2.345876 CACAGGACATAACATGCGACA 58.654 47.619 0.00 0.00 0.00 4.35
1301 1548 0.671251 CGCCCCTACTTTTGCAACAA 59.329 50.000 0.00 0.00 0.00 2.83
1407 1654 3.667360 CAGGATCAACTGTGTGTGATCA 58.333 45.455 17.89 0.00 36.18 2.92
1461 1708 0.822811 AGAGTGTCGATGAGCATGCT 59.177 50.000 22.92 22.92 0.00 3.79
1462 1709 2.027385 AGAGTGTCGATGAGCATGCTA 58.973 47.619 22.74 9.75 0.00 3.49
2029 2280 5.639506 GCAATTTACTAAGCAGTCAGTCAGA 59.360 40.000 0.00 0.00 36.14 3.27
2047 2298 4.746115 GTCAGAAAGCAAATTCATGTGCAA 59.254 37.500 8.54 0.00 43.42 4.08
2147 2398 2.161012 CAGCTATTCACAAGCACACAGG 59.839 50.000 0.00 0.00 42.62 4.00
2641 2892 2.029649 CACATGCAACCTGGGAAGAAAG 60.030 50.000 0.00 0.00 0.00 2.62
2887 4651 2.691409 ATATGACTGGTGGTGTTCCG 57.309 50.000 0.00 0.00 36.30 4.30
2900 4664 1.124780 TGTTCCGTCACCTCCTTTGA 58.875 50.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
343 346 1.308998 GCAACCATATGGAGGTTCCG 58.691 55.000 28.77 8.7 45.98 4.30
384 387 5.475564 GGAAAAAGTAAGATGGCCAACACTA 59.524 40.000 10.96 0.0 0.00 2.74
400 403 5.936372 GTCCTAAATAGTCCGTGGAAAAAGT 59.064 40.000 0.00 0.0 0.00 2.66
420 424 3.561143 CACTATGGCTAGTCTGAGTCCT 58.439 50.000 0.00 0.0 35.99 3.85
494 498 4.082190 CACCTCTCCTCATTAACTCGTTGA 60.082 45.833 0.00 0.0 0.00 3.18
593 597 1.270274 TGTGTGATGTCATGCAAAGCC 59.730 47.619 0.00 0.0 0.00 4.35
661 905 7.436933 TGAATGAGACTAGCCATAACATACAG 58.563 38.462 0.00 0.0 0.00 2.74
1132 1379 1.197812 GCCATTTCTTGGGCTGGATT 58.802 50.000 0.00 0.0 46.55 3.01
1243 1490 3.319198 ACATCCCGGTCCGCACTT 61.319 61.111 5.50 0.0 0.00 3.16
1301 1548 2.887152 GTGGGAAAGATGTTGCAGAAGT 59.113 45.455 0.00 0.0 0.00 3.01
1461 1708 5.067153 AGCAAATATAACAATGGCAACGCTA 59.933 36.000 0.00 0.0 42.51 4.26
1462 1709 4.111916 GCAAATATAACAATGGCAACGCT 58.888 39.130 0.00 0.0 42.51 5.07
1540 1787 2.076100 CAAATGCTAAGTCGAGGCACA 58.924 47.619 4.79 0.0 38.83 4.57
1805 2056 2.476185 CCATTCGGTTTGCGTCAAGATC 60.476 50.000 0.00 0.0 0.00 2.75
1924 2175 9.833917 AATTGGCCTATAGTAGTTACTTCTTTC 57.166 33.333 3.32 0.0 37.73 2.62
2029 2280 7.966246 TTATCTTTGCACATGAATTTGCTTT 57.034 28.000 0.00 0.0 39.62 3.51
2047 2298 7.202139 GGATTGGGAGGAGTACATCTTTATCTT 60.202 40.741 0.00 0.0 0.00 2.40
2122 2373 2.622470 TGTGCTTGTGAATAGCTGCAAA 59.378 40.909 1.02 0.0 39.38 3.68
2641 2892 3.452474 TGTGGTGTTTATTGTTTGCTGC 58.548 40.909 0.00 0.0 0.00 5.25
2900 4664 1.630878 AGGTCTGCGATTTCCTTCCTT 59.369 47.619 0.00 0.0 0.00 3.36


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

AutoCloner maintained by Alex Coulton.