Multiple sequence alignment - TraesCS5B01G090100

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 TraesCS5B01G090100 chr5B 100.000 2510 0 0 1 2510 115869980 115872489 0.000000e+00 4636.0
1 TraesCS5B01G090100 chr5B 94.941 593 29 1 1919 2510 701870804 701870212 0.000000e+00 928.0
2 TraesCS5B01G090100 chr5B 91.282 390 22 3 921 1298 114446484 114446873 2.860000e-144 521.0
3 TraesCS5B01G090100 chr5B 85.548 429 37 13 1293 1714 114452344 114452754 2.310000e-115 425.0
4 TraesCS5B01G090100 chr5B 81.250 192 36 0 1208 1399 115654909 115654718 3.340000e-34 156.0
5 TraesCS5B01G090100 chr5A 96.900 1000 27 3 921 1918 136644071 136645068 0.000000e+00 1672.0
6 TraesCS5B01G090100 chr5A 89.506 486 23 8 459 926 136643564 136644039 7.730000e-165 590.0
7 TraesCS5B01G090100 chr5A 89.944 179 13 4 109 285 136642324 136642499 2.510000e-55 226.0
8 TraesCS5B01G090100 chr5A 92.143 140 7 4 86 223 136642251 136642388 7.080000e-46 195.0
9 TraesCS5B01G090100 chr5D 97.050 983 25 3 921 1901 107012475 107013455 0.000000e+00 1652.0
10 TraesCS5B01G090100 chr5D 95.626 1006 31 5 921 1913 106940135 106941140 0.000000e+00 1602.0
11 TraesCS5B01G090100 chr5D 90.992 655 12 11 290 926 107011818 107012443 0.000000e+00 839.0
12 TraesCS5B01G090100 chr5D 87.287 763 58 10 921 1661 104579960 104579215 0.000000e+00 835.0
13 TraesCS5B01G090100 chr5D 87.105 760 59 10 921 1658 104826032 104826774 0.000000e+00 824.0
14 TraesCS5B01G090100 chr5D 90.091 656 14 11 290 926 106939480 106940103 0.000000e+00 804.0
15 TraesCS5B01G090100 chr5D 98.837 172 2 0 1 172 106939290 106939461 8.720000e-80 307.0
16 TraesCS5B01G090100 chr5D 98.837 172 1 1 1 172 107011629 107011799 3.140000e-79 305.0
17 TraesCS5B01G090100 chr5D 96.774 155 4 1 1764 1918 107030629 107030782 8.910000e-65 257.0
18 TraesCS5B01G090100 chr5D 82.474 194 30 4 1208 1399 105620277 105620086 1.540000e-37 167.0
19 TraesCS5B01G090100 chr3B 95.000 600 30 0 1909 2508 1633009 1633608 0.000000e+00 942.0
20 TraesCS5B01G090100 chr3B 95.286 594 27 1 1918 2510 637645137 637644544 0.000000e+00 941.0
21 TraesCS5B01G090100 chr3B 88.889 603 44 11 1919 2510 84778472 84777882 0.000000e+00 721.0
22 TraesCS5B01G090100 chr2B 94.604 593 31 1 1918 2510 731626581 731625990 0.000000e+00 917.0
23 TraesCS5B01G090100 chr2B 86.371 609 54 17 1919 2510 98450931 98450335 2.720000e-179 638.0
24 TraesCS5B01G090100 chr2B 82.963 135 14 8 4 136 463359894 463359767 2.040000e-21 113.0
25 TraesCS5B01G090100 chrUn 94.955 555 27 1 1956 2510 8326232 8325679 0.000000e+00 869.0
26 TraesCS5B01G090100 chr1B 90.894 604 41 7 1920 2510 39831946 39832548 0.000000e+00 798.0
27 TraesCS5B01G090100 chr1B 90.280 607 40 7 1919 2510 603222816 603223418 0.000000e+00 776.0
28 TraesCS5B01G090100 chr2D 87.047 193 17 8 1 189 637604157 637604345 7.030000e-51 211.0
29 TraesCS5B01G090100 chr3A 84.865 185 20 6 4 181 507118605 507118788 1.980000e-41 180.0
30 TraesCS5B01G090100 chr2A 85.526 76 8 3 61 136 762413653 762413581 2.680000e-10 76.8
31 TraesCS5B01G090100 chr3D 82.927 82 14 0 108 189 384565964 384566045 9.630000e-10 75.0


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 TraesCS5B01G090100 chr5B 115869980 115872489 2509 False 4636.000000 4636 100.000000 1 2510 1 chr5B.!!$F3 2509
1 TraesCS5B01G090100 chr5B 701870212 701870804 592 True 928.000000 928 94.941000 1919 2510 1 chr5B.!!$R2 591
2 TraesCS5B01G090100 chr5A 136642251 136645068 2817 False 670.750000 1672 92.123250 86 1918 4 chr5A.!!$F1 1832
3 TraesCS5B01G090100 chr5D 107011629 107013455 1826 False 932.000000 1652 95.626333 1 1901 3 chr5D.!!$F4 1900
4 TraesCS5B01G090100 chr5D 106939290 106941140 1850 False 904.333333 1602 94.851333 1 1913 3 chr5D.!!$F3 1912
5 TraesCS5B01G090100 chr5D 104579215 104579960 745 True 835.000000 835 87.287000 921 1661 1 chr5D.!!$R1 740
6 TraesCS5B01G090100 chr5D 104826032 104826774 742 False 824.000000 824 87.105000 921 1658 1 chr5D.!!$F1 737
7 TraesCS5B01G090100 chr3B 1633009 1633608 599 False 942.000000 942 95.000000 1909 2508 1 chr3B.!!$F1 599
8 TraesCS5B01G090100 chr3B 637644544 637645137 593 True 941.000000 941 95.286000 1918 2510 1 chr3B.!!$R2 592
9 TraesCS5B01G090100 chr3B 84777882 84778472 590 True 721.000000 721 88.889000 1919 2510 1 chr3B.!!$R1 591
10 TraesCS5B01G090100 chr2B 731625990 731626581 591 True 917.000000 917 94.604000 1918 2510 1 chr2B.!!$R3 592
11 TraesCS5B01G090100 chr2B 98450335 98450931 596 True 638.000000 638 86.371000 1919 2510 1 chr2B.!!$R1 591
12 TraesCS5B01G090100 chrUn 8325679 8326232 553 True 869.000000 869 94.955000 1956 2510 1 chrUn.!!$R1 554
13 TraesCS5B01G090100 chr1B 39831946 39832548 602 False 798.000000 798 90.894000 1920 2510 1 chr1B.!!$F1 590
14 TraesCS5B01G090100 chr1B 603222816 603223418 602 False 776.000000 776 90.280000 1919 2510 1 chr1B.!!$F2 591

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
383 452 0.323957 GGTAATACGATGGGGGAGGC 59.676 60.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 3181 0.10741 AACAGTGAGCCAACGGACAA 60.107 50.0 0.0 0.0 0.0 3.18 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
172 223 2.008242 TTACTTTTGCCATGCCACCT 57.992 45.000 0.00 0.00 0.00 4.00
178 229 4.530161 ACTTTTGCCATGCCACCTATAAAA 59.470 37.500 0.00 0.00 0.00 1.52
179 230 5.189539 ACTTTTGCCATGCCACCTATAAAAT 59.810 36.000 0.00 0.00 0.00 1.82
181 232 4.669206 TGCCATGCCACCTATAAAATTG 57.331 40.909 0.00 0.00 0.00 2.32
183 234 4.469227 TGCCATGCCACCTATAAAATTGTT 59.531 37.500 0.00 0.00 0.00 2.83
222 273 4.586421 TCATTACTTTTTGTCATGCCACCA 59.414 37.500 0.00 0.00 32.04 4.17
238 289 6.068461 TGCCACCAGTTTTTGTAGGATATA 57.932 37.500 0.00 0.00 0.00 0.86
283 335 9.855021 ATTATTTTTATAGCAAGCGTTTCTGTT 57.145 25.926 0.00 0.00 0.00 3.16
284 336 9.685828 TTATTTTTATAGCAAGCGTTTCTGTTT 57.314 25.926 0.00 0.00 0.00 2.83
285 337 7.995463 TTTTTATAGCAAGCGTTTCTGTTTT 57.005 28.000 0.00 0.00 0.00 2.43
286 338 9.685828 ATTTTTATAGCAAGCGTTTCTGTTTTA 57.314 25.926 0.00 0.00 0.00 1.52
287 339 9.685828 TTTTTATAGCAAGCGTTTCTGTTTTAT 57.314 25.926 0.00 0.00 0.00 1.40
288 340 9.685828 TTTTATAGCAAGCGTTTCTGTTTTATT 57.314 25.926 0.00 0.00 0.00 1.40
289 341 9.685828 TTTATAGCAAGCGTTTCTGTTTTATTT 57.314 25.926 0.00 0.00 0.00 1.40
290 342 9.685828 TTATAGCAAGCGTTTCTGTTTTATTTT 57.314 25.926 0.00 0.00 0.00 1.82
291 343 6.902224 AGCAAGCGTTTCTGTTTTATTTTT 57.098 29.167 0.00 0.00 0.00 1.94
292 344 7.995463 AGCAAGCGTTTCTGTTTTATTTTTA 57.005 28.000 0.00 0.00 0.00 1.52
293 345 7.837505 AGCAAGCGTTTCTGTTTTATTTTTAC 58.162 30.769 0.00 0.00 0.00 2.01
294 346 7.704899 AGCAAGCGTTTCTGTTTTATTTTTACT 59.295 29.630 0.00 0.00 0.00 2.24
295 347 8.325282 GCAAGCGTTTCTGTTTTATTTTTACTT 58.675 29.630 0.00 0.00 0.00 2.24
343 404 7.639113 TTACTGACTGTCTGTTTTTGGATTT 57.361 32.000 22.54 0.12 31.00 2.17
344 405 8.740123 TTACTGACTGTCTGTTTTTGGATTTA 57.260 30.769 22.54 1.40 31.00 1.40
382 451 2.025636 AGGTAATACGATGGGGGAGG 57.974 55.000 0.00 0.00 0.00 4.30
383 452 0.323957 GGTAATACGATGGGGGAGGC 59.676 60.000 0.00 0.00 0.00 4.70
384 453 0.323957 GTAATACGATGGGGGAGGCC 59.676 60.000 0.00 0.00 0.00 5.19
385 454 0.838987 TAATACGATGGGGGAGGCCC 60.839 60.000 0.00 0.00 44.51 5.80
733 1741 6.719365 CGACAGGAAATTTCAGGATATCAAC 58.281 40.000 19.49 0.00 0.00 3.18
782 1790 8.018695 GGATTCAATCCCCTCTGTTAAAGAGTT 61.019 40.741 4.89 0.00 44.28 3.01
1011 2068 5.971763 ACAAGTCTAGACATGGATTCTGTC 58.028 41.667 26.83 0.00 42.68 3.51
1256 2313 1.534729 GGCGAGACAAGGGAACAAAT 58.465 50.000 0.00 0.00 0.00 2.32
1542 2609 3.512680 CCAGTGAATTAGACTCGACACC 58.487 50.000 0.00 0.00 0.00 4.16
1560 2627 3.259374 ACACCTGTGATCTGAAGACGATT 59.741 43.478 3.94 0.00 0.00 3.34
1686 2757 4.538089 GGGAGATTAAGGCTAAGATGGGAT 59.462 45.833 0.00 0.00 0.00 3.85
1734 2805 7.233553 CCATGATTATCTCTGTAACCTGACCTA 59.766 40.741 0.00 0.00 0.00 3.08
1935 3014 9.948964 AAAATGAATCCTAAATGCTAAAAAGCT 57.051 25.926 0.00 0.00 35.49 3.74
2042 3135 2.678934 CGGTTCGTCCTCCTCCCA 60.679 66.667 0.00 0.00 0.00 4.37
2086 3181 2.525877 ACCACTACCCACACGCCT 60.526 61.111 0.00 0.00 0.00 5.52
2087 3182 2.144738 ACCACTACCCACACGCCTT 61.145 57.895 0.00 0.00 0.00 4.35
2112 3207 1.002792 GTTGGCTCACTGTTCGAAACC 60.003 52.381 0.00 0.00 0.00 3.27
2158 3255 1.133976 CAATCCGCTCCCCATTCTCTT 60.134 52.381 0.00 0.00 0.00 2.85
2415 3526 1.373812 GTCCGGTGGCCTAGTGTTT 59.626 57.895 3.32 0.00 0.00 2.83
2481 3593 2.180131 CTCTGCTTTCTGCGTGTGCC 62.180 60.000 0.00 0.00 46.63 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 7.542130 GGATTCGATACATTGCAAAAGAGTTTT 59.458 33.333 1.71 0.00 0.00 2.43
260 312 8.587952 AAAACAGAAACGCTTGCTATAAAAAT 57.412 26.923 0.00 0.00 0.00 1.82
388 457 2.597217 TTTGCTGGGCGTCCCTTG 60.597 61.111 2.12 4.05 45.70 3.61
389 458 2.282462 CTTTGCTGGGCGTCCCTT 60.282 61.111 2.12 0.00 45.70 3.95
390 459 4.351054 CCTTTGCTGGGCGTCCCT 62.351 66.667 2.12 0.00 45.70 4.20
543 1533 4.143333 ACGTTCGATCTGGGCCCG 62.143 66.667 19.37 12.57 0.00 6.13
733 1741 0.376152 GCATGTGCGTGAAGATCCAG 59.624 55.000 0.00 0.00 0.00 3.86
782 1790 2.658285 CTGCAGGCTAATTCCAATCCA 58.342 47.619 5.57 0.00 0.00 3.41
998 2055 4.743057 TCTTGATCGACAGAATCCATGT 57.257 40.909 0.00 0.00 0.00 3.21
1484 2544 0.542232 AGTAGCCGGGTTGTGTCTCT 60.542 55.000 13.43 0.00 0.00 3.10
1542 2609 3.061831 GTGCAATCGTCTTCAGATCACAG 59.938 47.826 0.00 0.00 0.00 3.66
1560 2627 2.337879 AAAGTCCTTGGCCGAGTGCA 62.338 55.000 19.14 0.00 43.89 4.57
1686 2757 5.175859 GGATCATGTTTACTCCGTCAAAGA 58.824 41.667 0.00 0.00 0.00 2.52
1708 2779 6.042552 AGGTCAGGTTACAGAGATAATCATGG 59.957 42.308 0.00 0.00 0.00 3.66
1734 2805 7.238710 AGGGTCAGGTTACACAGATTAAAAAT 58.761 34.615 0.00 0.00 0.00 1.82
1935 3014 1.269569 CGTGACAACCAGCACTCAGTA 60.270 52.381 0.00 0.00 32.98 2.74
2086 3181 0.107410 AACAGTGAGCCAACGGACAA 60.107 50.000 0.00 0.00 0.00 3.18
2087 3182 0.531974 GAACAGTGAGCCAACGGACA 60.532 55.000 0.00 0.00 0.00 4.02
2158 3255 1.595058 GGAGGGAGGGAGAGAAGGGA 61.595 65.000 0.00 0.00 0.00 4.20
2307 3417 2.076184 CCTTATTCTCCGGGGGCCA 61.076 63.158 4.39 0.00 0.00 5.36
2393 3504 3.379445 CTAGGCCACCGGACACGT 61.379 66.667 9.46 0.04 38.78 4.49
2415 3526 4.141321 CCTCAGGATTCCAGAATCATCCAA 60.141 45.833 19.27 3.00 46.77 3.53


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

AutoCloner maintained by Alex Coulton.