Multiple sequence alignment - TraesCS5A01G061900

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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 TraesCS5A01G061900 chr5A 100.000 2465 0 0 1 2465 65995745 65998209 0.000000e+00 4553
1 TraesCS5A01G061900 chr5A 94.786 1400 49 4 659 2038 427855285 427853890 0.000000e+00 2159
2 TraesCS5A01G061900 chr5A 96.178 628 17 6 1 628 427855897 427855277 0.000000e+00 1020
3 TraesCS5A01G061900 chr5A 98.282 582 9 1 1884 2465 66045698 66046278 0.000000e+00 1018
4 TraesCS5A01G061900 chr5A 87.433 374 34 6 2080 2440 139249236 139249609 3.790000e-113 418
5 TraesCS5A01G061900 chr3B 90.991 2109 120 21 385 2465 17318238 17320304 0.000000e+00 2778
6 TraesCS5A01G061900 chr3B 92.724 1663 90 9 700 2343 679712657 679711007 0.000000e+00 2372
7 TraesCS5A01G061900 chr4A 92.420 1926 113 11 569 2465 96105158 96107079 0.000000e+00 2717
8 TraesCS5A01G061900 chr4A 91.446 1777 113 17 478 2227 588546967 588548731 0.000000e+00 2403
9 TraesCS5A01G061900 chr4A 94.437 1402 51 13 659 2037 679660953 679659556 0.000000e+00 2132
10 TraesCS5A01G061900 chr4A 96.178 628 17 6 1 628 679661565 679660945 0.000000e+00 1020
11 TraesCS5A01G061900 chr4A 78.808 302 33 22 1573 1870 665073475 665073749 9.060000e-40 174
12 TraesCS5A01G061900 chrUn 94.504 1765 55 9 294 2037 19134910 19136653 0.000000e+00 2684
13 TraesCS5A01G061900 chr2D 94.397 1767 54 11 294 2037 142214584 142216328 0.000000e+00 2673
14 TraesCS5A01G061900 chr7D 94.337 1766 57 9 294 2037 292321173 292322917 0.000000e+00 2667
15 TraesCS5A01G061900 chr7D 85.407 1350 150 20 753 2073 69829438 69828107 0.000000e+00 1358
16 TraesCS5A01G061900 chr7D 94.415 376 15 3 1 374 627191147 627190776 7.650000e-160 573
17 TraesCS5A01G061900 chr7D 94.022 368 18 2 1 368 399054687 399055050 2.770000e-154 555
18 TraesCS5A01G061900 chr1D 94.330 1746 58 8 294 2018 460576136 460574411 0.000000e+00 2638
19 TraesCS5A01G061900 chr6A 93.781 1399 49 7 659 2037 517541511 517540131 0.000000e+00 2067
20 TraesCS5A01G061900 chr6A 96.184 629 16 8 1 628 517542124 517541503 0.000000e+00 1022
21 TraesCS5A01G061900 chr6A 94.118 374 15 2 1 374 600375050 600374684 1.660000e-156 562
22 TraesCS5A01G061900 chr6A 87.533 377 33 7 2080 2443 464935182 464935557 8.150000e-115 424
23 TraesCS5A01G061900 chr4D 95.823 1245 45 6 294 1535 215030015 215028775 0.000000e+00 2004
24 TraesCS5A01G061900 chr4D 94.057 387 9 1 1651 2037 215025841 215025469 2.130000e-160 575
25 TraesCS5A01G061900 chr7B 92.212 565 38 5 373 936 78142357 78141798 0.000000e+00 795
26 TraesCS5A01G061900 chr7B 91.281 562 43 5 373 933 85846503 85847059 0.000000e+00 761
27 TraesCS5A01G061900 chr4B 94.149 376 17 3 1 374 646860554 646860182 3.560000e-158 568
28 TraesCS5A01G061900 chr4B 86.737 377 33 7 2080 2443 545091732 545091360 1.060000e-108 403
29 TraesCS5A01G061900 chr6D 94.149 376 13 3 1 374 239298516 239298148 4.600000e-157 564
30 TraesCS5A01G061900 chr3D 94.054 370 18 3 2 371 122966344 122966709 2.140000e-155 558
31 TraesCS5A01G061900 chr7A 78.261 851 106 44 837 1659 31040994 31040195 7.980000e-130 473
32 TraesCS5A01G061900 chr1B 96.154 286 11 0 2180 2465 28802961 28803246 3.710000e-128 468
33 TraesCS5A01G061900 chr2A 78.147 842 105 40 837 1650 108026318 108027108 1.730000e-126 462
34 TraesCS5A01G061900 chr5B 89.028 319 33 2 2127 2443 593463527 593463209 6.390000e-106 394


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 TraesCS5A01G061900 chr5A 65995745 65998209 2464 False 4553.0 4553 100.0000 1 2465 1 chr5A.!!$F1 2464
1 TraesCS5A01G061900 chr5A 427853890 427855897 2007 True 1589.5 2159 95.4820 1 2038 2 chr5A.!!$R1 2037
2 TraesCS5A01G061900 chr5A 66045698 66046278 580 False 1018.0 1018 98.2820 1884 2465 1 chr5A.!!$F2 581
3 TraesCS5A01G061900 chr3B 17318238 17320304 2066 False 2778.0 2778 90.9910 385 2465 1 chr3B.!!$F1 2080
4 TraesCS5A01G061900 chr3B 679711007 679712657 1650 True 2372.0 2372 92.7240 700 2343 1 chr3B.!!$R1 1643
5 TraesCS5A01G061900 chr4A 96105158 96107079 1921 False 2717.0 2717 92.4200 569 2465 1 chr4A.!!$F1 1896
6 TraesCS5A01G061900 chr4A 588546967 588548731 1764 False 2403.0 2403 91.4460 478 2227 1 chr4A.!!$F2 1749
7 TraesCS5A01G061900 chr4A 679659556 679661565 2009 True 1576.0 2132 95.3075 1 2037 2 chr4A.!!$R1 2036
8 TraesCS5A01G061900 chrUn 19134910 19136653 1743 False 2684.0 2684 94.5040 294 2037 1 chrUn.!!$F1 1743
9 TraesCS5A01G061900 chr2D 142214584 142216328 1744 False 2673.0 2673 94.3970 294 2037 1 chr2D.!!$F1 1743
10 TraesCS5A01G061900 chr7D 292321173 292322917 1744 False 2667.0 2667 94.3370 294 2037 1 chr7D.!!$F1 1743
11 TraesCS5A01G061900 chr7D 69828107 69829438 1331 True 1358.0 1358 85.4070 753 2073 1 chr7D.!!$R1 1320
12 TraesCS5A01G061900 chr1D 460574411 460576136 1725 True 2638.0 2638 94.3300 294 2018 1 chr1D.!!$R1 1724
13 TraesCS5A01G061900 chr6A 517540131 517542124 1993 True 1544.5 2067 94.9825 1 2037 2 chr6A.!!$R2 2036
14 TraesCS5A01G061900 chr4D 215025469 215030015 4546 True 1289.5 2004 94.9400 294 2037 2 chr4D.!!$R1 1743
15 TraesCS5A01G061900 chr7B 78141798 78142357 559 True 795.0 795 92.2120 373 936 1 chr7B.!!$R1 563
16 TraesCS5A01G061900 chr7B 85846503 85847059 556 False 761.0 761 91.2810 373 933 1 chr7B.!!$F1 560
17 TraesCS5A01G061900 chr7A 31040195 31040994 799 True 473.0 473 78.2610 837 1659 1 chr7A.!!$R1 822
18 TraesCS5A01G061900 chr2A 108026318 108027108 790 False 462.0 462 78.1470 837 1650 1 chr2A.!!$F1 813

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
922 957 0.252742 CCCTCCCCTTAGTCACCAGT 60.253 60.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 4688 1.625818 GCACCTCCTTCTTCTCCTTCA 59.374 52.381 0.0 0.0 0.0 3.02 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
47 48 1.846439 CACCATGGTCAAGGGTCCTAT 59.154 52.381 16.53 0.00 31.03 2.57
143 144 2.414612 TCCTCCTCCTACTCCTCTCTC 58.585 57.143 0.00 0.00 0.00 3.20
191 192 9.631452 AATAATTTTCTCTTCTTTTGTAGCAGC 57.369 29.630 0.00 0.00 0.00 5.25
192 193 6.639632 ATTTTCTCTTCTTTTGTAGCAGCA 57.360 33.333 0.00 0.00 0.00 4.41
193 194 6.449635 TTTTCTCTTCTTTTGTAGCAGCAA 57.550 33.333 0.00 0.00 0.00 3.91
194 195 6.639632 TTTCTCTTCTTTTGTAGCAGCAAT 57.360 33.333 0.00 0.00 0.00 3.56
204 205 5.859205 TTGTAGCAGCAATAGATGAGAGA 57.141 39.130 0.00 0.00 31.30 3.10
260 261 2.044793 TGGACAACTTCATCCCCTCT 57.955 50.000 0.00 0.00 33.69 3.69
389 390 7.039714 GGGGCCCTAACAATCTTCTTAATAATG 60.040 40.741 24.38 0.00 0.00 1.90
412 413 6.048257 GAAGGAAACGTCAAAGCTTTTGCG 62.048 45.833 22.76 22.76 43.87 4.85
615 624 2.070783 TCAGACACGGCCGATAAAAAC 58.929 47.619 35.90 14.80 0.00 2.43
654 663 2.126071 CGGACAACGCCGTGATCT 60.126 61.111 0.00 0.00 46.07 2.75
913 948 2.692368 CAGGCTGCCCTCCCCTTA 60.692 66.667 16.57 0.00 40.33 2.69
922 957 0.252742 CCCTCCCCTTAGTCACCAGT 60.253 60.000 0.00 0.00 0.00 4.00
1073 1113 0.466922 GCACGCCCTACTCTACCCTA 60.467 60.000 0.00 0.00 0.00 3.53
1170 1214 2.537714 ATCCTCCTGGTTCCCTCGCT 62.538 60.000 0.00 0.00 34.23 4.93
1236 1288 3.791545 AGGTCCAGGTAATCTCTCTCTCT 59.208 47.826 0.00 0.00 0.00 3.10
1237 1289 4.141251 AGGTCCAGGTAATCTCTCTCTCTC 60.141 50.000 0.00 0.00 0.00 3.20
1238 1290 4.141251 GGTCCAGGTAATCTCTCTCTCTCT 60.141 50.000 0.00 0.00 0.00 3.10
1239 1291 5.063880 GTCCAGGTAATCTCTCTCTCTCTC 58.936 50.000 0.00 0.00 0.00 3.20
1240 1292 4.975147 TCCAGGTAATCTCTCTCTCTCTCT 59.025 45.833 0.00 0.00 0.00 3.10
1293 1347 0.177141 GGTTAGTCGCCAGGTGCATA 59.823 55.000 0.00 0.00 41.33 3.14
1467 1526 8.525316 TCACATGATGCAGTATCTTTTTGAAAT 58.475 29.630 0.00 0.00 36.71 2.17
1587 2842 5.759963 CCTACACTAACTAATCAGGTAGCG 58.240 45.833 0.00 0.00 44.73 4.26
1616 2871 9.853555 TGCAAATTTTTAACCATACTACATCTG 57.146 29.630 0.00 0.00 0.00 2.90
1803 4688 3.308473 GCCCTTAATGGTTCAGACTTCCT 60.308 47.826 0.00 0.00 0.00 3.36
1853 4738 3.119352 GGATGGGAGCAACAAATCTGAAC 60.119 47.826 0.00 0.00 0.00 3.18
2172 5058 5.183713 TGTCTTTCACATGGATGTTCATTCC 59.816 40.000 0.00 0.00 39.39 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.047801 TGACCTGCTACTGCTTGTCA 58.952 50.000 8.33 8.33 43.00 3.58
143 144 6.528537 TTTGAATGAGGAAGAGAGAGAGAG 57.471 41.667 0.00 0.00 0.00 3.20
189 190 2.028294 CCCGCATCTCTCATCTATTGCT 60.028 50.000 0.00 0.00 0.00 3.91
190 191 2.028658 TCCCGCATCTCTCATCTATTGC 60.029 50.000 0.00 0.00 0.00 3.56
191 192 3.949842 TCCCGCATCTCTCATCTATTG 57.050 47.619 0.00 0.00 0.00 1.90
192 193 3.305676 CGTTCCCGCATCTCTCATCTATT 60.306 47.826 0.00 0.00 0.00 1.73
193 194 2.230025 CGTTCCCGCATCTCTCATCTAT 59.770 50.000 0.00 0.00 0.00 1.98
194 195 1.609072 CGTTCCCGCATCTCTCATCTA 59.391 52.381 0.00 0.00 0.00 1.98
204 205 2.046314 CCCAACTCGTTCCCGCAT 60.046 61.111 0.00 0.00 0.00 4.73
260 261 1.271871 CCATGGTTGTTGCTGGTCCTA 60.272 52.381 2.57 0.00 0.00 2.94
389 390 3.242944 GCAAAAGCTTTGACGTTTCCTTC 59.757 43.478 13.54 0.00 0.00 3.46
393 394 2.182014 ACGCAAAAGCTTTGACGTTTC 58.818 42.857 25.57 1.51 31.79 2.78
398 399 1.112459 CACGACGCAAAAGCTTTGAC 58.888 50.000 13.54 7.05 0.00 3.18
654 663 2.317040 GACGGGGGAGAGATTGTGATA 58.683 52.381 0.00 0.00 0.00 2.15
913 948 4.664677 GCGGCGACACTGGTGACT 62.665 66.667 12.98 0.00 0.00 3.41
1073 1113 2.680370 GGGCCGGATTGGAAGGAGT 61.680 63.158 5.05 0.00 42.00 3.85
1170 1214 1.375908 GAGGCTCATGTTGGCGACA 60.376 57.895 10.57 10.57 43.71 4.35
1236 1288 1.679305 GACGGCAGGGTCAGAGAGA 60.679 63.158 0.00 0.00 36.91 3.10
1237 1289 1.680651 AGACGGCAGGGTCAGAGAG 60.681 63.158 0.00 0.00 39.42 3.20
1238 1290 1.979155 CAGACGGCAGGGTCAGAGA 60.979 63.158 0.00 0.00 39.42 3.10
1239 1291 2.575993 CAGACGGCAGGGTCAGAG 59.424 66.667 0.00 0.00 39.42 3.35
1240 1292 3.695606 GCAGACGGCAGGGTCAGA 61.696 66.667 0.00 0.00 43.97 3.27
1293 1347 3.037851 TGGTGATATCTCAGTGAGGCT 57.962 47.619 19.99 10.35 30.18 4.58
1803 4688 1.625818 GCACCTCCTTCTTCTCCTTCA 59.374 52.381 0.00 0.00 0.00 3.02
1853 4738 6.142818 TCCACAACAAAACATACTCTTTGG 57.857 37.500 0.00 0.00 36.94 3.28
2046 4932 3.072915 AGTGGTTGATTGTGTCTGGATCA 59.927 43.478 0.00 0.00 0.00 2.92
2172 5058 7.769272 TTTGTCATTTCTAAGCAACCAAAAG 57.231 32.000 0.00 0.00 0.00 2.27
2210 5096 4.566004 ACTGCTATCACTCACGCTTAAAA 58.434 39.130 0.00 0.00 0.00 1.52
2214 5100 1.821753 AGACTGCTATCACTCACGCTT 59.178 47.619 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.