Multiple sequence alignment - TraesCS5B01G371500

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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 TraesCS5B01G371500 chr5B 100.000 2417 0 0 1 2417 550192335 550194751 0.000000e+00 4464.0
1 TraesCS5B01G371500 chr5B 97.302 1927 35 8 447 2358 550175497 550177421 0.000000e+00 3254.0
2 TraesCS5B01G371500 chr5B 87.459 1228 103 28 740 1949 550161663 550162857 0.000000e+00 1367.0
3 TraesCS5B01G371500 chr5B 85.739 1143 116 27 627 1749 550155868 550156983 0.000000e+00 1164.0
4 TraesCS5B01G371500 chr5B 87.919 596 51 13 1783 2363 550157324 550157913 0.000000e+00 682.0
5 TraesCS5B01G371500 chr5B 93.850 439 17 4 1934 2363 550163793 550164230 0.000000e+00 652.0
6 TraesCS5B01G371500 chr5B 79.922 513 50 22 127 626 550155510 550155982 6.440000e-86 327.0
7 TraesCS5B01G371500 chr5B 91.089 202 14 2 1 199 550171437 550171637 1.100000e-68 270.0
8 TraesCS5B01G371500 chr5B 79.784 371 39 22 68 432 550160736 550161076 1.120000e-58 237.0
9 TraesCS5B01G371500 chr5B 93.893 131 8 0 429 559 550161158 550161288 5.270000e-47 198.0
10 TraesCS5B01G371500 chr5B 87.850 107 10 2 521 626 550161281 550161385 3.260000e-24 122.0
11 TraesCS5B01G371500 chr5B 97.436 39 1 0 2371 2409 550177454 550177492 1.550000e-07 67.6
12 TraesCS5B01G371500 chr5D 85.383 2196 181 64 213 2363 450158336 450160436 0.000000e+00 2148.0
13 TraesCS5B01G371500 chr5D 87.046 1073 89 21 627 1681 450148855 450149895 0.000000e+00 1166.0
14 TraesCS5B01G371500 chr5D 85.092 1147 117 25 627 1729 450163872 450165008 0.000000e+00 1122.0
15 TraesCS5B01G371500 chr5D 88.110 942 92 14 831 1761 450153282 450154214 0.000000e+00 1101.0
16 TraesCS5B01G371500 chr5D 90.937 651 30 15 1790 2413 450154591 450155239 0.000000e+00 848.0
17 TraesCS5B01G371500 chr5D 86.424 302 24 8 331 623 450152802 450153095 5.020000e-82 315.0
18 TraesCS5B01G371500 chr5D 88.776 196 22 0 1833 2028 450149914 450150109 8.630000e-60 241.0
19 TraesCS5B01G371500 chr5D 88.265 196 18 3 78 270 450163327 450163520 1.870000e-56 230.0
20 TraesCS5B01G371500 chr5D 79.144 374 35 23 257 626 450163649 450163983 4.050000e-53 219.0
21 TraesCS5B01G371500 chr5A 86.574 1795 163 39 627 2363 569451821 569453595 0.000000e+00 1908.0
22 TraesCS5B01G371500 chr5A 88.832 1558 105 20 213 1750 569462931 569464439 0.000000e+00 1849.0
23 TraesCS5B01G371500 chr5A 86.465 1123 115 23 627 1723 569455922 569457033 0.000000e+00 1197.0
24 TraesCS5B01G371500 chr5A 87.676 641 53 15 1 626 569455405 569456034 0.000000e+00 723.0
25 TraesCS5B01G371500 chr5A 93.229 384 15 6 1990 2363 569458268 569458650 2.710000e-154 555.0
26 TraesCS5B01G371500 chr4D 83.164 1081 128 26 622 1675 5275676 5276729 0.000000e+00 939.0
27 TraesCS5B01G371500 chr1A 77.778 135 16 9 2146 2272 430603020 430603148 1.200000e-08 71.3


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 TraesCS5B01G371500 chr5B 550192335 550194751 2416 False 4464.000000 4464 100.000000 1 2417 1 chr5B.!!$F1 2416
1 TraesCS5B01G371500 chr5B 550171437 550177492 6055 False 1197.200000 3254 95.275667 1 2409 3 chr5B.!!$F3 2408
2 TraesCS5B01G371500 chr5B 550155510 550164230 8720 False 593.625000 1367 87.052000 68 2363 8 chr5B.!!$F2 2295
3 TraesCS5B01G371500 chr5D 450148855 450165008 16153 False 821.111111 2148 86.575222 78 2413 9 chr5D.!!$F1 2335
4 TraesCS5B01G371500 chr5A 569462931 569464439 1508 False 1849.000000 1849 88.832000 213 1750 1 chr5A.!!$F1 1537
5 TraesCS5B01G371500 chr5A 569451821 569458650 6829 False 1095.750000 1908 88.486000 1 2363 4 chr5A.!!$F2 2362
6 TraesCS5B01G371500 chr4D 5275676 5276729 1053 False 939.000000 939 83.164000 622 1675 1 chr4D.!!$F1 1053

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
397 13535 0.246635 TCCGGAGAGCTTTCCTTTCG 59.753 55.0 20.28 7.57 34.96 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 18823 0.64741 GCAAGTCGTCCACATCATCG 59.353 55.0 0.0 0.0 0.0 3.84 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
48 49 2.291540 CCCCATTAGTTTTGGAGCTCCA 60.292 50.000 32.00 32.00 45.94 3.86
99 11312 8.560355 TCATACATGCATAACTAAAACACACT 57.440 30.769 0.00 0.00 0.00 3.55
200 11421 8.839947 TTGAGACATTACGCATGATAAAATTG 57.160 30.769 0.00 0.00 36.24 2.32
231 11489 6.072175 GGTATCTACCATTTTGAAACTGTGCA 60.072 38.462 1.40 0.00 45.73 4.57
301 11561 4.232221 CGAAAACTCGGTCTACTAAGCAA 58.768 43.478 0.00 0.00 0.00 3.91
354 13486 2.749110 GAAGCTCACGCACGAGGTGA 62.749 60.000 4.96 0.00 42.76 4.02
375 13509 1.675641 GCACAATCGGGCCAGTTCT 60.676 57.895 4.39 0.00 0.00 3.01
386 13520 1.443802 GCCAGTTCTTTTCCGGAGAG 58.556 55.000 3.34 7.45 0.00 3.20
397 13535 0.246635 TCCGGAGAGCTTTCCTTTCG 59.753 55.000 20.28 7.57 34.96 3.46
414 13552 4.618489 CCTTTCGATTGTGAATTGAACTGC 59.382 41.667 0.00 0.00 40.19 4.40
1050 16332 1.069823 CTCATCGGGATAGTTGCAGCT 59.930 52.381 8.54 8.54 0.00 4.24
1539 16872 4.453177 TTGTATTGTTCCATGCATGTGG 57.547 40.909 24.58 13.01 40.76 4.17
1618 16955 3.909776 ATGTGACTCGACTCGTTGTTA 57.090 42.857 0.00 0.00 0.00 2.41
1623 16960 5.174398 TGTGACTCGACTCGTTGTTATTTTC 59.826 40.000 0.00 0.00 0.00 2.29
1705 17044 5.760253 CAGTCTATGTTGTTTTCTCTGTGGT 59.240 40.000 0.00 0.00 0.00 4.16
1734 17074 6.989169 CAGTCTCAGTTATTTTCTCTATGGGG 59.011 42.308 0.00 0.00 0.00 4.96
1912 17499 3.736720 GGTTTTGTTCTCTACCCTTCGT 58.263 45.455 0.00 0.00 0.00 3.85
1938 17525 0.178941 ACTAAGTCCCGACCAGGTGT 60.179 55.000 0.00 0.00 38.74 4.16
2012 18550 3.709987 ACTAGGTAAACGTCACACACAC 58.290 45.455 0.00 0.00 0.00 3.82
2276 18823 3.248602 GTCGAATGATTACATGCACCCTC 59.751 47.826 0.00 0.00 36.79 4.30
2288 18835 0.811616 GCACCCTCGATGATGTGGAC 60.812 60.000 0.00 0.00 0.00 4.02
2363 18911 6.145534 CCTCATGATGTGATTAATTTGCATGC 59.854 38.462 11.82 11.82 35.97 4.06
2364 18912 5.986741 TCATGATGTGATTAATTTGCATGCC 59.013 36.000 16.68 0.00 33.73 4.40
2366 18914 4.406326 TGATGTGATTAATTTGCATGCCCT 59.594 37.500 16.68 0.00 0.00 5.19
2367 18915 4.389890 TGTGATTAATTTGCATGCCCTC 57.610 40.909 16.68 2.07 0.00 4.30
2368 18916 3.768215 TGTGATTAATTTGCATGCCCTCA 59.232 39.130 16.68 4.68 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.340617 CTCCAAAACTAATGGGGTTGCTA 58.659 43.478 0.00 0.0 38.54 3.49
26 27 2.291605 GGAGCTCCAAAACTAATGGGGT 60.292 50.000 28.43 0.0 40.77 4.95
99 11312 0.913924 TTCTCCAGCCTCATGCATGA 59.086 50.000 27.10 27.1 44.83 3.07
183 11404 7.542890 ACCAATGACAATTTTATCATGCGTAA 58.457 30.769 0.00 0.0 35.71 3.18
231 11489 0.759436 CCTCTGGCCCGGTATACTGT 60.759 60.000 10.79 0.0 0.00 3.55
301 11561 2.772924 CCCCAAGGCTCCATGGTT 59.227 61.111 12.58 0.0 33.37 3.67
320 11580 1.348036 AGCTTCACCACCTGTTAGGAC 59.652 52.381 1.13 0.0 37.67 3.85
354 13486 2.360350 CTGGCCCGATTGTGCAGT 60.360 61.111 0.00 0.0 0.00 4.40
375 13509 2.951229 AAGGAAAGCTCTCCGGAAAA 57.049 45.000 5.23 0.0 40.75 2.29
386 13520 5.460646 TCAATTCACAATCGAAAGGAAAGC 58.539 37.500 0.00 0.0 0.00 3.51
397 13535 2.912967 CGCTGCAGTTCAATTCACAATC 59.087 45.455 16.64 0.0 0.00 2.67
581 15561 4.420206 TCCATCTGATGATAGTAGGGTGG 58.580 47.826 18.92 0.0 0.00 4.61
1050 16332 1.956477 GCTGCTTGGTTGAAAGAGGAA 59.044 47.619 0.00 0.0 0.00 3.36
1618 16955 6.291377 ACCATCATGCGTAGATACTGAAAAT 58.709 36.000 0.00 0.0 0.00 1.82
1623 16960 6.389906 TGAATACCATCATGCGTAGATACTG 58.610 40.000 0.00 0.0 0.00 2.74
1660 16997 3.253188 TGCAGTTCACTGACAAAATAGCC 59.747 43.478 11.29 0.0 46.59 3.93
1705 17044 5.858381 AGAGAAAATAACTGAGACTGCACA 58.142 37.500 0.00 0.0 0.00 4.57
1912 17499 3.952323 CTGGTCGGGACTTAGTTCATAGA 59.048 47.826 0.00 0.0 0.00 1.98
1938 17525 7.040201 CGTAGAGCCTGGGTATAAATACTAACA 60.040 40.741 1.23 0.0 33.81 2.41
2012 18550 6.321717 TCATTGCTTTAAATTTCCGTAGCAG 58.678 36.000 12.91 6.6 39.49 4.24
2276 18823 0.647410 GCAAGTCGTCCACATCATCG 59.353 55.000 0.00 0.0 0.00 3.84
2288 18835 4.325204 CCATTTTTCATCACATGCAAGTCG 59.675 41.667 0.00 0.0 0.00 4.18


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

AutoCloner maintained by Alex Coulton.