Multiple sequence alignment - TraesCS3D01G061800

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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 TraesCS3D01G061800 chr3D 100.000 2489 0 0 1 2489 27053173 27055661 0.000000e+00 4597.0
1 TraesCS3D01G061800 chr3D 93.728 1674 81 12 1 1658 26688196 26686531 0.000000e+00 2488.0
2 TraesCS3D01G061800 chr3D 84.287 2272 225 67 1 2223 26808761 26810949 0.000000e+00 2097.0
3 TraesCS3D01G061800 chr3D 89.311 421 33 10 1818 2232 26686481 26686067 3.670000e-143 518.0
4 TraesCS3D01G061800 chr3D 94.937 237 11 1 2253 2489 26683943 26683708 1.090000e-98 370.0
5 TraesCS3D01G061800 chr3D 89.340 197 17 2 2293 2489 26813733 26813925 6.880000e-61 244.0
6 TraesCS3D01G061800 chr3D 81.061 132 16 2 2048 2171 284814191 284814321 2.040000e-16 97.1
7 TraesCS3D01G061800 chrUn 91.111 1980 116 17 529 2489 336342460 336344398 0.000000e+00 2627.0
8 TraesCS3D01G061800 chrUn 91.010 1980 118 17 529 2489 39212308 39210370 0.000000e+00 2615.0
9 TraesCS3D01G061800 chrUn 91.010 1980 118 17 529 2489 336353128 336355066 0.000000e+00 2615.0
10 TraesCS3D01G061800 chrUn 92.548 1570 92 12 1 1558 38655190 38656746 0.000000e+00 2228.0
11 TraesCS3D01G061800 chrUn 90.625 960 55 9 1535 2489 311241690 311242619 0.000000e+00 1242.0
12 TraesCS3D01G061800 chrUn 91.885 382 27 4 1848 2229 38657077 38657454 4.710000e-147 531.0
13 TraesCS3D01G061800 chrUn 80.000 510 93 7 1 504 434813893 434814399 3.910000e-98 368.0
14 TraesCS3D01G061800 chrUn 89.723 253 22 4 1556 1807 38656828 38657077 1.110000e-83 320.0
15 TraesCS3D01G061800 chrUn 96.178 157 6 0 2333 2489 38669255 38669411 8.830000e-65 257.0
16 TraesCS3D01G061800 chr3A 91.243 1770 112 28 478 2223 36946255 36944505 0.000000e+00 2370.0
17 TraesCS3D01G061800 chr3A 91.478 1502 84 26 637 2121 37305749 37304275 0.000000e+00 2025.0
18 TraesCS3D01G061800 chr3A 92.314 1249 60 18 741 1977 37242805 37241581 0.000000e+00 1742.0
19 TraesCS3D01G061800 chr3A 94.565 184 6 2 478 659 37243016 37242835 5.240000e-72 281.0
20 TraesCS3D01G061800 chr3A 90.367 218 16 1 2277 2489 37304092 37303875 5.240000e-72 281.0
21 TraesCS3D01G061800 chr3A 88.995 209 22 1 623 830 37308775 37308567 8.830000e-65 257.0
22 TraesCS3D01G061800 chr3A 89.881 168 12 1 2277 2439 37241375 37241208 6.970000e-51 211.0
23 TraesCS3D01G061800 chr3A 89.333 75 8 0 2149 2223 37241554 37241480 7.330000e-16 95.3
24 TraesCS3D01G061800 chr3A 90.625 64 4 1 2162 2223 37304258 37304195 1.590000e-12 84.2
25 TraesCS3D01G061800 chr1D 80.273 512 88 9 4 508 418405316 418404811 8.410000e-100 374.0
26 TraesCS3D01G061800 chr1D 79.921 508 90 8 4 504 469610639 469610137 1.820000e-96 363.0
27 TraesCS3D01G061800 chr7A 79.804 510 95 6 1 504 670686119 670686626 5.060000e-97 364.0
28 TraesCS3D01G061800 chr2D 79.719 498 93 8 1 492 14023419 14022924 1.100000e-93 353.0
29 TraesCS3D01G061800 chr2D 79.877 487 89 7 4 484 313801143 313800660 5.090000e-92 348.0
30 TraesCS3D01G061800 chr5D 79.794 485 90 5 4 482 485603816 485603334 1.830000e-91 346.0
31 TraesCS3D01G061800 chr3B 82.237 152 16 7 2048 2190 378496789 378496640 1.210000e-23 121.0


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 TraesCS3D01G061800 chr3D 27053173 27055661 2488 False 4597.000000 4597 100.000000 1 2489 1 chr3D.!!$F1 2488
1 TraesCS3D01G061800 chr3D 26808761 26813925 5164 False 1170.500000 2097 86.813500 1 2489 2 chr3D.!!$F3 2488
2 TraesCS3D01G061800 chr3D 26683708 26688196 4488 True 1125.333333 2488 92.658667 1 2489 3 chr3D.!!$R1 2488
3 TraesCS3D01G061800 chrUn 336342460 336344398 1938 False 2627.000000 2627 91.111000 529 2489 1 chrUn.!!$F3 1960
4 TraesCS3D01G061800 chrUn 39210370 39212308 1938 True 2615.000000 2615 91.010000 529 2489 1 chrUn.!!$R1 1960
5 TraesCS3D01G061800 chrUn 336353128 336355066 1938 False 2615.000000 2615 91.010000 529 2489 1 chrUn.!!$F4 1960
6 TraesCS3D01G061800 chrUn 311241690 311242619 929 False 1242.000000 1242 90.625000 1535 2489 1 chrUn.!!$F2 954
7 TraesCS3D01G061800 chrUn 38655190 38657454 2264 False 1026.333333 2228 91.385333 1 2229 3 chrUn.!!$F6 2228
8 TraesCS3D01G061800 chrUn 434813893 434814399 506 False 368.000000 368 80.000000 1 504 1 chrUn.!!$F5 503
9 TraesCS3D01G061800 chr3A 36944505 36946255 1750 True 2370.000000 2370 91.243000 478 2223 1 chr3A.!!$R1 1745
10 TraesCS3D01G061800 chr3A 37303875 37308775 4900 True 661.800000 2025 90.366250 623 2489 4 chr3A.!!$R3 1866
11 TraesCS3D01G061800 chr3A 37241208 37243016 1808 True 582.325000 1742 91.523250 478 2439 4 chr3A.!!$R2 1961
12 TraesCS3D01G061800 chr1D 418404811 418405316 505 True 374.000000 374 80.273000 4 508 1 chr1D.!!$R1 504
13 TraesCS3D01G061800 chr1D 469610137 469610639 502 True 363.000000 363 79.921000 4 504 1 chr1D.!!$R2 500
14 TraesCS3D01G061800 chr7A 670686119 670686626 507 False 364.000000 364 79.804000 1 504 1 chr7A.!!$F1 503

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
340 349 1.892474 ACAATACATTTTGCGTGGCCT 59.108 42.857 3.32 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 4983 1.134995 CAAGTGAGAGCTACGATGGCA 60.135 52.381 0.0 0.0 0.0 4.92 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
23 24 5.001232 TGCTAGGGTTTGTATCTTGTTCAC 58.999 41.667 0.00 0.00 0.00 3.18
88 91 2.861472 TGCTTAGGCCCCCAACCA 60.861 61.111 0.00 0.00 37.74 3.67
334 343 6.247582 CGGTGTTTACTACAATACATTTTGCG 59.752 38.462 0.00 0.00 38.80 4.85
340 349 1.892474 ACAATACATTTTGCGTGGCCT 59.108 42.857 3.32 0.00 0.00 5.19
474 483 8.467963 TCATTGTACTGCCATGATTGATAATT 57.532 30.769 0.00 0.00 0.00 1.40
518 533 2.702261 AGAAAAGTATACGCCGGCAAA 58.298 42.857 28.98 14.42 0.00 3.68
826 3874 7.986553 ATACCCCAATTTAATTGTGGAATCA 57.013 32.000 22.42 7.72 39.77 2.57
1116 4196 6.255670 TCGGACGAATCTAATTTTCTCATGTG 59.744 38.462 0.00 0.00 0.00 3.21
1127 4207 9.525409 CTAATTTTCTCATGTGGATTTTGATCC 57.475 33.333 0.00 0.00 41.10 3.36
1176 4257 1.135402 GGTAAAGGCAATGCGGAGTTG 60.135 52.381 0.00 0.00 0.00 3.16
1215 4296 2.258591 CTCCACGTGACCCAGACG 59.741 66.667 19.30 0.00 42.62 4.18
1592 4760 1.135831 CCGCACATGCATGAAACGTTA 60.136 47.619 32.75 0.00 42.21 3.18
1593 4761 2.477694 CCGCACATGCATGAAACGTTAT 60.478 45.455 32.75 4.93 42.21 1.89
1643 4812 2.804572 CGAGGGTGGATGTATCTTGCTG 60.805 54.545 0.00 0.00 0.00 4.41
1671 4840 6.934048 TGGAAAATTTTGTGAAAATCCCAC 57.066 33.333 8.47 0.00 40.05 4.61
1672 4841 5.825151 TGGAAAATTTTGTGAAAATCCCACC 59.175 36.000 8.47 0.00 40.05 4.61
1843 5025 9.073475 ACTTGCTGGAAATTTGTAATTAGTGTA 57.927 29.630 0.00 0.00 0.00 2.90
1870 5054 3.921630 TGTCATGCTGCGAATCAAAATTG 59.078 39.130 0.00 0.00 0.00 2.32
1986 5179 4.450053 CCTTGGCAAGGTTTTCAATTTCA 58.550 39.130 33.43 0.00 43.95 2.69
2036 5229 7.872483 ACCGCAATATCAGAACTTTTGAAAAAT 59.128 29.630 0.00 0.00 0.00 1.82
2217 5418 8.674925 TCCTTGGTATTATCGGTAGGATTTAT 57.325 34.615 0.00 0.00 36.55 1.40
2407 10398 8.645110 AGAAGGAAGAATTGGCCATTATTTATG 58.355 33.333 6.09 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.260206 CCATCGTTGTCTCGTCTTCG 58.740 55.000 0.00 0.00 38.55 3.79
334 343 3.775654 CTCACTCCCCGAGGCCAC 61.776 72.222 5.01 0.00 33.35 5.01
340 349 4.715130 CCACCCCTCACTCCCCGA 62.715 72.222 0.00 0.00 0.00 5.14
381 390 2.095668 CGACGACTAGAAGCACTGAAGT 60.096 50.000 0.00 0.00 0.00 3.01
841 3889 8.111545 TCCCTATTTACCTCTCTATATAACGCA 58.888 37.037 0.00 0.00 0.00 5.24
1009 4078 2.030451 TCGCGAAGATCCTCATCATCTG 60.030 50.000 6.20 0.00 30.62 2.90
1127 4207 8.170553 CACCAACAACAAAAAGAAGAAGAAATG 58.829 33.333 0.00 0.00 0.00 2.32
1215 4296 3.733960 GCGTTCTTTCCCGTGGCC 61.734 66.667 0.00 0.00 0.00 5.36
1290 4371 2.313172 CGCAAGCAGCTTGACGTCT 61.313 57.895 34.93 0.00 43.42 4.18
1308 4389 1.753078 GGAGGATTTGAACCCGGGC 60.753 63.158 24.08 5.60 0.00 6.13
1592 4760 7.507829 TCAACAAACCCATCAATTCTCAAAAT 58.492 30.769 0.00 0.00 0.00 1.82
1593 4761 6.882656 TCAACAAACCCATCAATTCTCAAAA 58.117 32.000 0.00 0.00 0.00 2.44
1643 4812 6.862608 GGATTTTCACAAAATTTTCCAATGGC 59.137 34.615 0.00 0.00 40.97 4.40
1801 4983 1.134995 CAAGTGAGAGCTACGATGGCA 60.135 52.381 0.00 0.00 0.00 4.92
1802 4984 1.565305 CAAGTGAGAGCTACGATGGC 58.435 55.000 0.00 0.00 0.00 4.40
1843 5025 2.488937 TGATTCGCAGCATGACAAACAT 59.511 40.909 0.00 0.00 39.69 2.71
1933 5123 8.939929 CATATCACTAAACTTGTGAACATCTGT 58.060 33.333 0.66 0.00 45.82 3.41
1934 5124 8.939929 ACATATCACTAAACTTGTGAACATCTG 58.060 33.333 0.66 0.00 45.82 2.90
1979 5172 9.379811 CCCGAAATTGTTTTGTTTATGAAATTG 57.620 29.630 0.00 0.00 0.00 2.32
1986 5179 6.921307 GTGAGACCCGAAATTGTTTTGTTTAT 59.079 34.615 0.00 0.00 0.00 1.40
2133 5332 2.050918 TCAAAATTTTGGTGGGGTCCC 58.949 47.619 26.45 0.00 38.66 4.46
2171 5370 7.588497 AGGAGCAGGATTAAAAATATCAACC 57.412 36.000 0.00 0.00 0.00 3.77
2326 10312 6.761099 TGGAGAAGTTTGACTACTAGCTAG 57.239 41.667 19.44 19.44 0.00 3.42
2407 10398 4.663636 GCTATCGGCAATAATGGTACAC 57.336 45.455 0.00 0.00 41.06 2.90
2439 10430 9.920133 TGTTATGTTGCATAATGCTTTTCTTTA 57.080 25.926 5.08 0.00 45.31 1.85


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

AutoCloner maintained by Alex Coulton.