Multiple sequence alignment - TraesCS5B01G088600

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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 TraesCS5B01G088600 chr5B 100.000 2687 0 0 1 2687 113824463 113821777 0.000000e+00 4963.0
1 TraesCS5B01G088600 chr5B 91.702 952 58 13 894 1837 113805884 113804946 0.000000e+00 1301.0
2 TraesCS5B01G088600 chr5D 95.654 2715 62 19 1 2687 104448074 104445388 0.000000e+00 4309.0
3 TraesCS5B01G088600 chr5D 92.537 871 51 9 894 1758 104398467 104397605 0.000000e+00 1236.0
4 TraesCS5B01G088600 chr5D 82.031 256 36 8 357 603 14026050 14026304 2.710000e-50 209.0
5 TraesCS5B01G088600 chr5A 90.859 1827 90 30 1 1795 106856818 106855037 0.000000e+00 2377.0
6 TraesCS5B01G088600 chr5A 92.720 728 45 6 894 1616 93188350 93189074 0.000000e+00 1044.0
7 TraesCS5B01G088600 chr5A 86.382 492 41 7 1937 2408 93066210 93066695 5.130000e-142 514.0
8 TraesCS5B01G088600 chr5A 90.253 277 27 0 2410 2686 93066655 93066931 1.970000e-96 363.0
9 TraesCS5B01G088600 chr5A 90.066 151 9 4 1791 1941 106854900 106854756 9.820000e-45 191.0
10 TraesCS5B01G088600 chr7A 82.857 245 32 7 368 603 96146874 96147117 7.540000e-51 211.0
11 TraesCS5B01G088600 chr1D 83.550 231 32 5 357 582 437843473 437843702 7.540000e-51 211.0
12 TraesCS5B01G088600 chr2B 82.329 249 32 9 366 603 63848257 63848010 3.510000e-49 206.0
13 TraesCS5B01G088600 chr1A 82.377 244 36 7 365 603 463926634 463926393 3.510000e-49 206.0
14 TraesCS5B01G088600 chr3D 82.186 247 34 7 366 603 251397635 251397390 1.260000e-48 204.0
15 TraesCS5B01G088600 chr3D 85.981 107 12 3 42 145 425145855 425145749 7.860000e-21 111.0
16 TraesCS5B01G088600 chr1B 81.712 257 35 9 357 603 409675809 409676063 1.260000e-48 204.0
17 TraesCS5B01G088600 chr1B 82.400 125 16 4 42 161 513973251 513973128 1.320000e-18 104.0
18 TraesCS5B01G088600 chr3A 83.200 125 16 4 42 161 563400498 563400622 2.830000e-20 110.0
19 TraesCS5B01G088600 chr6A 92.982 57 2 1 2149 2205 99971813 99971867 6.170000e-12 82.4
20 TraesCS5B01G088600 chr2A 91.071 56 3 2 2149 2203 1549055 1549001 1.030000e-09 75.0
21 TraesCS5B01G088600 chr3B 81.429 70 10 2 2116 2184 819649767 819649700 1.000000e-03 54.7


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 TraesCS5B01G088600 chr5B 113821777 113824463 2686 True 4963.0 4963 100.0000 1 2687 1 chr5B.!!$R2 2686
1 TraesCS5B01G088600 chr5B 113804946 113805884 938 True 1301.0 1301 91.7020 894 1837 1 chr5B.!!$R1 943
2 TraesCS5B01G088600 chr5D 104445388 104448074 2686 True 4309.0 4309 95.6540 1 2687 1 chr5D.!!$R2 2686
3 TraesCS5B01G088600 chr5D 104397605 104398467 862 True 1236.0 1236 92.5370 894 1758 1 chr5D.!!$R1 864
4 TraesCS5B01G088600 chr5A 106854756 106856818 2062 True 1284.0 2377 90.4625 1 1941 2 chr5A.!!$R1 1940
5 TraesCS5B01G088600 chr5A 93188350 93189074 724 False 1044.0 1044 92.7200 894 1616 1 chr5A.!!$F1 722
6 TraesCS5B01G088600 chr5A 93066210 93066931 721 False 438.5 514 88.3175 1937 2686 2 chr5A.!!$F2 749

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
744 755 0.884704 AACATCTGGTGCACCGACAC 60.885 55.0 30.07 7.26 39.43 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2558 2787 0.108472 CTGCAGCGATGGAGTTGAGA 60.108 55.0 14.58 0.0 0.0 3.27 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
38 39 7.201617 GCCAATAGACATGAGTTTACAACCTAC 60.202 40.741 0.00 0.00 0.00 3.18
236 238 1.630878 AGGTCTTGTCCTGGGAACATC 59.369 52.381 0.00 0.00 41.51 3.06
245 247 4.283212 TGTCCTGGGAACATCCAATTTTTC 59.717 41.667 0.00 0.00 41.51 2.29
250 252 5.062528 TGGGAACATCCAATTTTTCTTTGC 58.937 37.500 0.00 0.00 38.64 3.68
310 312 4.767578 AGCATGTGAGAGTTGGTATCAT 57.232 40.909 0.00 0.00 0.00 2.45
352 354 3.508012 CCACGAGGGAGAATATCTAGTGG 59.492 52.174 7.28 7.28 43.81 4.00
574 583 5.795972 TCACATTGATGCCAAATTTGTCAT 58.204 33.333 14.19 14.19 35.67 3.06
582 591 8.030744 TGATGCCAAATTTGTCATTTTGTATG 57.969 30.769 15.30 0.00 32.23 2.39
744 755 0.884704 AACATCTGGTGCACCGACAC 60.885 55.000 30.07 7.26 39.43 3.67
960 1015 1.391157 CCGCTCCTCTCTCTTCCCTG 61.391 65.000 0.00 0.00 0.00 4.45
1143 1198 2.288643 GGCCTCCCCTCCATCTCT 59.711 66.667 0.00 0.00 0.00 3.10
1707 1765 2.049063 ACAGAGCTTCCGTGTCGC 60.049 61.111 0.00 0.00 0.00 5.19
1741 1799 0.108992 TTGCCGTACTTCTACGCCAG 60.109 55.000 0.00 0.00 43.82 4.85
1772 1833 4.318332 CCGTCGTACTACGTTTCAGTTAAC 59.682 45.833 17.39 0.00 43.14 2.01
1776 1837 6.085588 GTCGTACTACGTTTCAGTTAACAGTC 59.914 42.308 8.61 0.00 43.14 3.51
1794 1996 3.306166 CAGTCCGTGAGCGTTAATTAAGG 59.694 47.826 12.51 12.51 36.15 2.69
2012 2214 7.508687 TCTTCTTCTTTATGTGCTATGCCATA 58.491 34.615 0.00 0.00 0.00 2.74
2018 2220 6.707608 TCTTTATGTGCTATGCCATAAGTCAG 59.292 38.462 10.72 8.00 35.19 3.51
2019 2221 4.694760 ATGTGCTATGCCATAAGTCAGA 57.305 40.909 0.00 0.00 0.00 3.27
2020 2222 3.797039 TGTGCTATGCCATAAGTCAGAC 58.203 45.455 0.00 0.00 0.00 3.51
2021 2223 3.452264 TGTGCTATGCCATAAGTCAGACT 59.548 43.478 0.00 0.00 0.00 3.24
2022 2224 4.080919 TGTGCTATGCCATAAGTCAGACTT 60.081 41.667 19.81 19.81 41.97 3.01
2190 2397 6.557568 TCAGTTAATGGAAAAGGGGTTATGT 58.442 36.000 0.00 0.00 0.00 2.29
2279 2507 3.101437 TGGTCCTAAATAAGCCGAGACA 58.899 45.455 0.00 0.00 0.00 3.41
2356 2585 3.954258 AGATTTTTCATTTAGGCCCTCCG 59.046 43.478 0.00 0.00 37.47 4.63
2392 2621 4.109050 GCATTTTGTAGTCCTCTCTCTCG 58.891 47.826 0.00 0.00 0.00 4.04
2404 2633 2.363680 CTCTCTCTCGCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
2407 2636 2.362397 TCTCTCGCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
2408 2637 2.363680 CTCTCGCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
2409 2638 2.766263 TCTCGCTCTCTCTCTCTCTCTT 59.234 50.000 0.00 0.00 0.00 2.85
2410 2639 3.197766 TCTCGCTCTCTCTCTCTCTCTTT 59.802 47.826 0.00 0.00 0.00 2.52
2411 2640 4.404394 TCTCGCTCTCTCTCTCTCTCTTTA 59.596 45.833 0.00 0.00 0.00 1.85
2412 2641 4.693283 TCGCTCTCTCTCTCTCTCTTTAG 58.307 47.826 0.00 0.00 0.00 1.85
2413 2642 3.248602 CGCTCTCTCTCTCTCTCTTTAGC 59.751 52.174 0.00 0.00 0.00 3.09
2414 2643 4.199310 GCTCTCTCTCTCTCTCTTTAGCA 58.801 47.826 0.00 0.00 0.00 3.49
2415 2644 4.823989 GCTCTCTCTCTCTCTCTTTAGCAT 59.176 45.833 0.00 0.00 0.00 3.79
2416 2645 5.300286 GCTCTCTCTCTCTCTCTTTAGCATT 59.700 44.000 0.00 0.00 0.00 3.56
2417 2646 6.183360 GCTCTCTCTCTCTCTCTTTAGCATTT 60.183 42.308 0.00 0.00 0.00 2.32
2418 2647 7.631377 GCTCTCTCTCTCTCTCTTTAGCATTTT 60.631 40.741 0.00 0.00 0.00 1.82
2419 2648 7.546358 TCTCTCTCTCTCTCTTTAGCATTTTG 58.454 38.462 0.00 0.00 0.00 2.44
2420 2649 7.178274 TCTCTCTCTCTCTCTTTAGCATTTTGT 59.822 37.037 0.00 0.00 0.00 2.83
2421 2650 8.354711 TCTCTCTCTCTCTTTAGCATTTTGTA 57.645 34.615 0.00 0.00 0.00 2.41
2422 2651 8.465999 TCTCTCTCTCTCTTTAGCATTTTGTAG 58.534 37.037 0.00 0.00 0.00 2.74
2423 2652 8.128322 TCTCTCTCTCTTTAGCATTTTGTAGT 57.872 34.615 0.00 0.00 0.00 2.73
2424 2653 8.247562 TCTCTCTCTCTTTAGCATTTTGTAGTC 58.752 37.037 0.00 0.00 0.00 2.59
2461 2690 2.155279 CTCTCTCTCAGTTCGACCACA 58.845 52.381 0.00 0.00 0.00 4.17
2491 2720 0.397941 CAGGAGAACTGGAGGCAACA 59.602 55.000 0.00 0.00 43.70 3.33
2520 2749 3.280920 GCTACTGGCGAGGAAGATG 57.719 57.895 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
310 312 3.325425 TGGGAAGGTGTGAAAGTATCGAA 59.675 43.478 0.00 0.0 0.00 3.71
352 354 3.660111 GCACCACAAGCACCGGTC 61.660 66.667 2.59 0.0 0.00 4.79
574 583 6.796426 TCAAAACATTGACCGACATACAAAA 58.204 32.000 0.00 0.0 0.00 2.44
582 591 4.684242 GGGAAATTCAAAACATTGACCGAC 59.316 41.667 0.00 0.0 0.00 4.79
684 695 9.676195 AAATGTTTGAAAAACAGGAAACAAAAG 57.324 25.926 10.90 0.0 32.78 2.27
744 755 0.038067 TGGTGTTATCGGTGACCACG 60.038 55.000 1.11 0.0 33.44 4.94
960 1015 4.303282 GCTATAGCTTGTGTCTTAGAGGC 58.697 47.826 17.75 0.0 38.21 4.70
1707 1765 0.449388 GGCAAAGCGAGAAGGACATG 59.551 55.000 0.00 0.0 0.00 3.21
1772 1833 3.306166 CCTTAATTAACGCTCACGGACTG 59.694 47.826 0.00 0.0 46.04 3.51
1776 1837 1.937899 CCCCTTAATTAACGCTCACGG 59.062 52.381 0.00 0.0 46.04 4.94
1794 1996 4.494484 GACATTTGTATGAAAACTGGCCC 58.506 43.478 0.00 0.0 35.65 5.80
2020 2222 2.593257 GTCGACGGAGACTTAACCAAG 58.407 52.381 0.00 0.0 38.09 3.61
2021 2223 2.712057 GTCGACGGAGACTTAACCAA 57.288 50.000 0.00 0.0 38.09 3.67
2084 2291 5.007234 TGAGTTTTCGTGTCAAGTACAATGG 59.993 40.000 0.00 0.0 40.63 3.16
2180 2387 1.364269 TTGAACCGGACATAACCCCT 58.636 50.000 9.46 0.0 0.00 4.79
2244 2462 0.527817 GGACCAATCGCCGAGTACAG 60.528 60.000 0.00 0.0 0.00 2.74
2356 2585 9.543018 GACTACAAAATGCTAATATAAATCGCC 57.457 33.333 0.00 0.0 0.00 5.54
2389 2618 2.898729 AGAGAGAGAGAGAGAGCGAG 57.101 55.000 0.00 0.0 0.00 5.03
2392 2621 4.199310 TGCTAAAGAGAGAGAGAGAGAGC 58.801 47.826 0.00 0.0 0.00 4.09
2404 2633 7.179338 AGAGAGGACTACAAAATGCTAAAGAGA 59.821 37.037 0.00 0.0 0.00 3.10
2407 2636 7.327214 AGAGAGAGGACTACAAAATGCTAAAG 58.673 38.462 0.00 0.0 0.00 1.85
2408 2637 7.179338 AGAGAGAGAGGACTACAAAATGCTAAA 59.821 37.037 0.00 0.0 0.00 1.85
2409 2638 6.665680 AGAGAGAGAGGACTACAAAATGCTAA 59.334 38.462 0.00 0.0 0.00 3.09
2410 2639 6.191315 AGAGAGAGAGGACTACAAAATGCTA 58.809 40.000 0.00 0.0 0.00 3.49
2411 2640 5.022787 AGAGAGAGAGGACTACAAAATGCT 58.977 41.667 0.00 0.0 0.00 3.79
2412 2641 5.127031 AGAGAGAGAGAGGACTACAAAATGC 59.873 44.000 0.00 0.0 0.00 3.56
2413 2642 6.603201 AGAGAGAGAGAGAGGACTACAAAATG 59.397 42.308 0.00 0.0 0.00 2.32
2414 2643 6.731467 AGAGAGAGAGAGAGGACTACAAAAT 58.269 40.000 0.00 0.0 0.00 1.82
2415 2644 6.012858 AGAGAGAGAGAGAGAGGACTACAAAA 60.013 42.308 0.00 0.0 0.00 2.44
2416 2645 5.487488 AGAGAGAGAGAGAGAGGACTACAAA 59.513 44.000 0.00 0.0 0.00 2.83
2417 2646 5.030147 AGAGAGAGAGAGAGAGGACTACAA 58.970 45.833 0.00 0.0 0.00 2.41
2418 2647 4.620723 AGAGAGAGAGAGAGAGGACTACA 58.379 47.826 0.00 0.0 0.00 2.74
2419 2648 4.896482 AGAGAGAGAGAGAGAGAGGACTAC 59.104 50.000 0.00 0.0 0.00 2.73
2420 2649 5.103473 AGAGAGAGAGAGAGAGAGAGGACTA 60.103 48.000 0.00 0.0 0.00 2.59
2421 2650 3.964031 GAGAGAGAGAGAGAGAGAGGACT 59.036 52.174 0.00 0.0 0.00 3.85
2422 2651 3.964031 AGAGAGAGAGAGAGAGAGAGGAC 59.036 52.174 0.00 0.0 0.00 3.85
2423 2652 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.0 0.00 3.71
2424 2653 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.0 0.00 3.69
2461 2690 1.846124 TTCTCCTGCCCCCTTTCGT 60.846 57.895 0.00 0.0 0.00 3.85
2484 2713 1.446792 CTGCTCGTCGATGTTGCCT 60.447 57.895 17.63 0.0 0.00 4.75
2491 2720 1.730487 CCAGTAGCTGCTCGTCGAT 59.270 57.895 4.91 0.0 0.00 3.59
2520 2749 1.062148 GCTCGTCATTCCCTTTAACGC 59.938 52.381 0.00 0.0 33.58 4.84
2558 2787 0.108472 CTGCAGCGATGGAGTTGAGA 60.108 55.000 14.58 0.0 0.00 3.27


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

AutoCloner maintained by Alex Coulton.