Multiple sequence alignment - TraesCS5A01G304500

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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 TraesCS5A01G304500 chr5A 100.000 3000 0 0 1 3000 513256588 513253589 0.000000e+00 5541.0
1 TraesCS5A01G304500 chr5A 84.259 108 12 3 2575 2682 372247012 372247114 1.900000e-17 100.0
2 TraesCS5A01G304500 chr5A 91.304 46 3 1 1518 1563 513254565 513254609 8.980000e-06 62.1
3 TraesCS5A01G304500 chr5A 91.304 46 3 1 1980 2024 513255026 513255071 8.980000e-06 62.1
4 TraesCS5A01G304500 chr1A 96.220 3016 95 7 1 3000 46358949 46361961 0.000000e+00 4920.0
5 TraesCS5A01G304500 chr1A 90.566 212 19 1 894 1104 561113158 561112947 2.280000e-71 279.0
6 TraesCS5A01G304500 chr1A 84.848 99 14 1 668 765 14481646 14481548 6.840000e-17 99.0
7 TraesCS5A01G304500 chr1A 91.228 57 5 0 2938 2994 532453554 532453498 8.920000e-11 78.7
8 TraesCS5A01G304500 chr1A 93.478 46 2 1 1980 2024 46360524 46360479 1.930000e-07 67.6
9 TraesCS5A01G304500 chr1A 93.478 46 2 1 1518 1563 46360986 46360942 1.930000e-07 67.6
10 TraesCS5A01G304500 chr7B 96.434 2608 69 6 1 2589 88051106 88053708 0.000000e+00 4279.0
11 TraesCS5A01G304500 chr7B 95.789 380 13 3 2624 3000 88053705 88054084 7.110000e-171 610.0
12 TraesCS5A01G304500 chr7B 93.478 46 2 1 1518 1563 88053143 88053099 1.930000e-07 67.6
13 TraesCS5A01G304500 chr7B 91.304 46 3 1 1980 2024 88052679 88052634 8.980000e-06 62.1
14 TraesCS5A01G304500 chr7B 88.235 51 6 0 1008 1058 365368780 365368730 8.980000e-06 62.1
15 TraesCS5A01G304500 chr3A 88.618 246 27 1 120 365 279432924 279432680 6.290000e-77 298.0
16 TraesCS5A01G304500 chr3A 90.659 182 14 3 578 759 279432662 279432484 3.870000e-59 239.0
17 TraesCS5A01G304500 chr3A 87.156 218 17 3 757 973 279432523 279432316 1.390000e-58 237.0
18 TraesCS5A01G304500 chr3A 84.259 108 12 3 2575 2682 509517852 509517954 1.900000e-17 100.0
19 TraesCS5A01G304500 chr3A 83.168 101 13 3 668 765 137909261 137909360 4.120000e-14 89.8
20 TraesCS5A01G304500 chr6A 88.400 250 20 2 1635 1875 21403901 21404150 2.930000e-75 292.0
21 TraesCS5A01G304500 chr1D 91.038 212 18 1 894 1104 468099924 468099713 4.890000e-73 285.0
22 TraesCS5A01G304500 chr5D 90.909 209 19 0 1667 1875 34274546 34274338 6.330000e-72 281.0
23 TraesCS5A01G304500 chr4A 90.610 213 18 1 1665 1875 37972785 37972573 6.330000e-72 281.0
24 TraesCS5A01G304500 chr2D 90.909 209 19 0 1667 1875 433216057 433216265 6.330000e-72 281.0
25 TraesCS5A01G304500 chr2D 87.374 198 20 5 1878 2072 433216308 433216503 3.890000e-54 222.0
26 TraesCS5A01G304500 chr3D 86.694 248 26 2 1635 1875 556073757 556073510 4.930000e-68 268.0
27 TraesCS5A01G304500 chr3D 88.889 63 7 0 2938 3000 95583039 95582977 8.920000e-11 78.7
28 TraesCS5A01G304500 chr7A 89.100 211 21 1 1667 1875 200006962 200007172 8.250000e-66 261.0
29 TraesCS5A01G304500 chr7A 89.394 198 17 4 1878 2072 200007215 200007411 2.310000e-61 246.0
30 TraesCS5A01G304500 chr1B 87.615 218 23 3 1662 1876 661033380 661033596 1.790000e-62 250.0
31 TraesCS5A01G304500 chr5B 80.456 307 55 5 2219 2523 10492809 10492506 2.330000e-56 230.0
32 TraesCS5A01G304500 chr5B 80.000 290 46 8 2227 2511 473506829 473506547 1.410000e-48 204.0
33 TraesCS5A01G304500 chr5B 85.714 77 9 2 2924 3000 15139959 15139885 2.480000e-11 80.5
34 TraesCS5A01G304500 chr5B 86.111 72 10 0 2926 2997 469971432 469971503 8.920000e-11 78.7
35 TraesCS5A01G304500 chr2B 85.787 197 25 3 1878 2072 63275906 63276101 3.920000e-49 206.0
36 TraesCS5A01G304500 chr7D 78.507 335 53 8 394 716 400836079 400836406 5.070000e-48 202.0
37 TraesCS5A01G304500 chr7D 86.667 105 14 0 1207 1311 523079990 523079886 1.890000e-22 117.0
38 TraesCS5A01G304500 chr4B 78.899 327 40 9 394 692 21367290 21367615 8.490000e-46 195.0
39 TraesCS5A01G304500 chr4B 92.727 55 4 0 1031 1085 16551790 16551844 2.480000e-11 80.5
40 TraesCS5A01G304500 chr4B 90.909 55 5 0 1031 1085 550673850 550673904 1.150000e-09 75.0
41 TraesCS5A01G304500 chr2A 83.333 108 13 3 2575 2682 138829499 138829601 8.850000e-16 95.3
42 TraesCS5A01G304500 chr2A 91.228 57 5 0 2938 2994 596413248 596413192 8.920000e-11 78.7
43 TraesCS5A01G304500 chr2A 87.719 57 7 0 2938 2994 431009279 431009335 1.930000e-07 67.6
44 TraesCS5A01G304500 chr6B 88.406 69 8 0 2926 2994 559467753 559467821 1.920000e-12 84.2
45 TraesCS5A01G304500 chr3B 92.593 54 4 0 1031 1084 511031414 511031361 8.920000e-11 78.7


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 TraesCS5A01G304500 chr5A 513253589 513256588 2999 True 5541.0 5541 100.0000 1 3000 1 chr5A.!!$R1 2999
1 TraesCS5A01G304500 chr1A 46358949 46361961 3012 False 4920.0 4920 96.2200 1 3000 1 chr1A.!!$F1 2999
2 TraesCS5A01G304500 chr7B 88051106 88054084 2978 False 2444.5 4279 96.1115 1 3000 2 chr7B.!!$F1 2999
3 TraesCS5A01G304500 chr3A 279432316 279432924 608 True 258.0 298 88.8110 120 973 3 chr3A.!!$R1 853

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
475 487 1.102978 GCACTTTCCCGCAATACCAT 58.897 50.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2113 1.867166 GCCGCCACTATTAGGACTTC 58.133 55.0 0.0 0.0 0.0 3.01 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
296 297 5.163622 CCAAAGTAGCATTGTTGTGGGATAG 60.164 44.000 0.00 0.00 0.00 2.08
452 464 5.452078 TGCCTTTTAAATGTTGTCTGGAG 57.548 39.130 0.00 0.00 0.00 3.86
475 487 1.102978 GCACTTTCCCGCAATACCAT 58.897 50.000 0.00 0.00 0.00 3.55
773 785 6.551736 TGAGAGTTTACTTTTTGCACTGAAC 58.448 36.000 0.00 0.00 0.00 3.18
787 799 3.476552 CACTGAACCCAAGCAAGACTTA 58.523 45.455 0.00 0.00 36.04 2.24
789 801 3.883489 ACTGAACCCAAGCAAGACTTAAC 59.117 43.478 0.00 0.00 36.04 2.01
1162 1175 5.446143 AAATTGGTTTGCACGAATGTCTA 57.554 34.783 0.00 0.00 32.11 2.59
1507 1524 7.872163 TGTATGATTTGTTCAAAATCTGCAC 57.128 32.000 11.03 7.35 38.03 4.57
1554 1571 6.100424 AGGCTGCATATTCTACTAACTTCCTT 59.900 38.462 0.50 0.00 0.00 3.36
1882 1906 9.839817 TTTCTGGATATGTTATTTTCCGTCATA 57.160 29.630 0.00 0.00 0.00 2.15
1910 1934 6.612863 AGAAAGCTAGGATTTATTTTGGCCAT 59.387 34.615 6.09 0.00 0.00 4.40
1993 2017 8.568794 ACTATTGTTTTTCTTCTAACAGGAAGC 58.431 33.333 0.00 0.00 41.55 3.86
2029 2053 4.022935 CAGCCTTCAAAGCAGATGTTTGTA 60.023 41.667 0.00 0.00 36.47 2.41
2050 2074 1.392589 ATTTTATGCCAGGTGAGCCG 58.607 50.000 0.00 0.00 40.50 5.52
2089 2113 3.501062 TGAGTGCATTTCTCTGAGCTTTG 59.499 43.478 0.00 0.00 33.59 2.77
2100 2124 7.482169 TTCTCTGAGCTTTGAAGTCCTAATA 57.518 36.000 0.00 0.00 0.00 0.98
2427 2451 3.680754 GCGCTTAATTACTGTAGTGGGGT 60.681 47.826 0.00 0.00 0.00 4.95
2454 2478 7.815383 AGGGATATTCAGAATTTGTGGTCATA 58.185 34.615 0.00 0.00 0.00 2.15
2554 2578 4.020378 GGAAAAAGCGGCGCGTCA 62.020 61.111 27.59 0.00 0.00 4.35
2596 2620 6.820656 ACAGGAAGAATACTGTTGTGATGATC 59.179 38.462 0.00 0.00 45.03 2.92
2629 2653 7.891183 ATATATGTATTCCAGTTCGTTGCTC 57.109 36.000 0.00 0.00 0.00 4.26
2630 2654 2.333926 TGTATTCCAGTTCGTTGCTCG 58.666 47.619 0.00 0.00 41.41 5.03
2735 2760 1.271108 TGCCGCTGGTTTCAAGTCATA 60.271 47.619 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 4.932799 CCTAATGTTACGGACACATTGACA 59.067 41.667 15.52 0.00 43.31 3.58
296 297 0.464452 ACCGCTAGTTCCATGGCTAC 59.536 55.000 6.96 7.82 0.00 3.58
452 464 1.130561 GTATTGCGGGAAAGTGCAGAC 59.869 52.381 0.00 0.00 42.89 3.51
475 487 1.367471 CCACTTGAGCAGTCCGTCA 59.633 57.895 0.00 0.00 30.92 4.35
584 596 6.659242 TGTTAGGGAGAAGGCAAATAAAGAAG 59.341 38.462 0.00 0.00 0.00 2.85
773 785 6.389906 CCTAAAATGTTAAGTCTTGCTTGGG 58.610 40.000 0.00 0.00 38.05 4.12
787 799 6.879400 TGCAAACAAGTAACCCTAAAATGTT 58.121 32.000 0.00 0.00 0.00 2.71
985 998 1.399440 CTTCATCCGTGGCATGTCAAG 59.601 52.381 0.00 3.23 0.00 3.02
1162 1175 5.112686 GTTGTATTCCGCTCTCTTCTCATT 58.887 41.667 0.00 0.00 0.00 2.57
1335 1348 3.405823 TCAGTGAACATGCATCTGTCA 57.594 42.857 10.99 5.95 0.00 3.58
1385 1398 8.185003 TGAATTTTGACATCGACACACTATAG 57.815 34.615 0.00 0.00 0.00 1.31
1389 1402 4.816385 ACTGAATTTTGACATCGACACACT 59.184 37.500 0.00 0.00 0.00 3.55
1507 1524 5.801947 CCTTCAAAGCAGATGGAAATAAACG 59.198 40.000 0.00 0.00 35.44 3.60
1554 1571 5.357742 TTCCTATGAGCATGCTTCTACAA 57.642 39.130 23.61 8.15 0.00 2.41
1845 1868 6.065976 ACATATCCAGAAACAACATGAGGA 57.934 37.500 0.00 0.00 0.00 3.71
1875 1898 9.877178 ATAAATCCTAGCTTTCTTATATGACGG 57.123 33.333 0.00 0.00 0.00 4.79
1882 1906 8.642432 GGCCAAAATAAATCCTAGCTTTCTTAT 58.358 33.333 0.00 0.00 0.00 1.73
1910 1934 7.557724 TCCAGTATATGTTTACGGAAATCACA 58.442 34.615 0.00 0.00 0.00 3.58
1993 2017 4.077300 TGAAGGCTGCATATTCTACCAG 57.923 45.455 0.50 0.00 0.00 4.00
2029 2053 2.166254 CGGCTCACCTGGCATAAAATTT 59.834 45.455 0.00 0.00 0.00 1.82
2050 2074 5.406175 TGCACTCAAGCATTAAAATGAAAGC 59.594 36.000 6.87 1.66 40.11 3.51
2089 2113 1.867166 GCCGCCACTATTAGGACTTC 58.133 55.000 0.00 0.00 0.00 3.01
2100 2124 4.078516 GTTCCTACCGCCGCCACT 62.079 66.667 0.00 0.00 0.00 4.00
2400 2424 6.404293 CCCACTACAGTAATTAAGCGCAAATT 60.404 38.462 20.15 20.15 0.00 1.82
2427 2451 7.638444 TGACCACAAATTCTGAATATCCCTTA 58.362 34.615 2.85 0.00 0.00 2.69
2454 2478 9.479549 AATTATCCCTGATGTTGTTCTACAAAT 57.520 29.630 0.00 0.00 40.15 2.32
2541 2565 3.490759 CTGATGACGCGCCGCTTT 61.491 61.111 5.73 0.00 0.00 3.51
2551 2575 5.506686 TGTAGTCACTGCTATCTGATGAC 57.493 43.478 0.00 0.00 39.99 3.06
2554 2578 4.797743 TCCTGTAGTCACTGCTATCTGAT 58.202 43.478 0.00 0.00 0.00 2.90
2676 2700 6.927416 AGTTATCATCAAAGCATGCTTTCAA 58.073 32.000 36.68 28.21 43.56 2.69


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

AutoCloner maintained by Alex Coulton.