Multiple sequence alignment - TraesCS5A01G287800

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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 TraesCS5A01G287800 chr5A 100.000 3524 0 0 1 3524 495729803 495726280 0.000000e+00 6508.0
1 TraesCS5A01G287800 chr5A 95.464 3549 110 14 19 3518 663335644 663339190 0.000000e+00 5614.0
2 TraesCS5A01G287800 chr5A 95.275 2222 99 3 436 2652 495820403 495818183 0.000000e+00 3517.0
3 TraesCS5A01G287800 chr5A 88.720 1844 150 19 923 2709 495397518 495395676 0.000000e+00 2200.0
4 TraesCS5A01G287800 chr5A 97.400 1077 22 3 2452 3522 495586964 495585888 0.000000e+00 1829.0
5 TraesCS5A01G287800 chr5A 93.414 1245 43 15 1 1208 495589120 495587878 0.000000e+00 1808.0
6 TraesCS5A01G287800 chr5A 96.275 886 33 0 1476 2361 495587857 495586972 0.000000e+00 1454.0
7 TraesCS5A01G287800 chr5A 84.976 619 55 19 1 583 495820619 495820003 8.420000e-166 593.0
8 TraesCS5A01G287800 chr5A 83.088 680 73 18 61 708 495588920 495588251 6.560000e-162 580.0
9 TraesCS5A01G287800 chr5A 84.211 551 52 17 61 583 495588794 495588251 1.460000e-138 503.0
10 TraesCS5A01G287800 chr5A 83.906 553 53 14 61 583 663335950 663336496 2.440000e-136 496.0
11 TraesCS5A01G287800 chr5A 88.529 401 43 3 436 835 495588901 495588503 1.900000e-132 483.0
12 TraesCS5A01G287800 chr5A 82.944 557 53 9 317 835 663335691 663336243 6.890000e-127 464.0
13 TraesCS5A01G287800 chr5D 92.714 2745 135 18 1 2709 393740137 393737422 0.000000e+00 3901.0
14 TraesCS5A01G287800 chr5D 89.213 1854 143 20 912 2709 393619554 393617702 0.000000e+00 2263.0
15 TraesCS5A01G287800 chr5D 86.676 1501 196 4 1019 2517 549324009 549325507 0.000000e+00 1661.0
16 TraesCS5A01G287800 chr5D 85.630 675 67 8 188 835 393740076 393739405 0.000000e+00 682.0
17 TraesCS5A01G287800 chr5D 89.154 544 34 9 317 835 393740074 393739531 0.000000e+00 654.0
18 TraesCS5A01G287800 chr5D 84.366 678 70 14 61 708 393739950 393739279 1.780000e-177 632.0
19 TraesCS5A01G287800 chr5D 83.848 551 52 14 63 583 393739822 393739279 1.140000e-134 490.0
20 TraesCS5A01G287800 chr5D 88.131 396 43 4 442 835 393740051 393739658 5.330000e-128 468.0
21 TraesCS5A01G287800 chr5D 84.197 386 49 7 61 441 393739698 393739320 7.190000e-97 364.0
22 TraesCS5A01G287800 chr5D 94.828 58 3 0 2652 2709 393737005 393736948 1.350000e-14 91.6
23 TraesCS5A01G287800 chr5B 92.810 1808 106 5 920 2709 473610438 473608637 0.000000e+00 2597.0
24 TraesCS5A01G287800 chr5B 88.943 1854 149 18 912 2709 473520260 473518407 0.000000e+00 2237.0
25 TraesCS5A01G287800 chr5B 88.534 846 40 7 2706 3523 673462532 673461716 0.000000e+00 972.0
26 TraesCS5A01G287800 chr5B 94.000 50 3 0 3 52 473610933 473610884 3.770000e-10 76.8
27 TraesCS5A01G287800 chr5B 97.436 39 1 0 3 41 357915217 357915255 2.270000e-07 67.6
28 TraesCS5A01G287800 chr5B 95.349 43 1 1 5 46 547331174 547331216 2.270000e-07 67.6
29 TraesCS5A01G287800 chr4A 82.503 1526 238 15 1018 2515 620934108 620932584 0.000000e+00 1312.0
30 TraesCS5A01G287800 chr4A 97.436 39 1 0 3 41 662590597 662590559 2.270000e-07 67.6
31 TraesCS5A01G287800 chr7D 83.413 627 98 6 1894 2517 162789710 162789087 8.480000e-161 577.0
32 TraesCS5A01G287800 chr7D 76.398 483 59 22 3064 3523 616927785 616927335 3.560000e-50 209.0
33 TraesCS5A01G287800 chr7A 75.328 839 106 39 2727 3495 257360397 257361204 3.420000e-80 309.0
34 TraesCS5A01G287800 chr1A 95.349 43 1 1 5 46 262015901 262015943 2.270000e-07 67.6


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 TraesCS5A01G287800 chr5A 495726280 495729803 3523 True 6508.000000 6508 100.000000 1 3524 1 chr5A.!!$R2 3523
1 TraesCS5A01G287800 chr5A 495395676 495397518 1842 True 2200.000000 2200 88.720000 923 2709 1 chr5A.!!$R1 1786
2 TraesCS5A01G287800 chr5A 663335644 663339190 3546 False 2191.333333 5614 87.438000 19 3518 3 chr5A.!!$F1 3499
3 TraesCS5A01G287800 chr5A 495818183 495820619 2436 True 2055.000000 3517 90.125500 1 2652 2 chr5A.!!$R4 2651
4 TraesCS5A01G287800 chr5A 495585888 495589120 3232 True 1109.500000 1829 90.486167 1 3522 6 chr5A.!!$R3 3521
5 TraesCS5A01G287800 chr5D 393617702 393619554 1852 True 2263.000000 2263 89.213000 912 2709 1 chr5D.!!$R1 1797
6 TraesCS5A01G287800 chr5D 549324009 549325507 1498 False 1661.000000 1661 86.676000 1019 2517 1 chr5D.!!$F1 1498
7 TraesCS5A01G287800 chr5D 393736948 393740137 3189 True 910.325000 3901 87.858500 1 2709 8 chr5D.!!$R2 2708
8 TraesCS5A01G287800 chr5B 473518407 473520260 1853 True 2237.000000 2237 88.943000 912 2709 1 chr5B.!!$R1 1797
9 TraesCS5A01G287800 chr5B 473608637 473610933 2296 True 1336.900000 2597 93.405000 3 2709 2 chr5B.!!$R3 2706
10 TraesCS5A01G287800 chr5B 673461716 673462532 816 True 972.000000 972 88.534000 2706 3523 1 chr5B.!!$R2 817
11 TraesCS5A01G287800 chr4A 620932584 620934108 1524 True 1312.000000 1312 82.503000 1018 2515 1 chr4A.!!$R1 1497
12 TraesCS5A01G287800 chr7D 162789087 162789710 623 True 577.000000 577 83.413000 1894 2517 1 chr7D.!!$R1 623
13 TraesCS5A01G287800 chr7A 257360397 257361204 807 False 309.000000 309 75.328000 2727 3495 1 chr7A.!!$F1 768

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
835 1157 1.123928 AGCTTCCTAATCTCCACCCG 58.876 55.000 0.00 0.0 0.00 5.28 F
1079 1432 1.302752 TGCTGGTGAAGAAGCGCAT 60.303 52.632 11.47 0.0 42.54 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2676 1.609061 CGGCATCAGTTCCAAGTGAGT 60.609 52.381 3.34 0.0 41.31 3.41 R
2621 3040 1.702401 TCATGTTACCAGCCCAAGACA 59.298 47.619 0.00 0.0 0.00 3.41 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
52 53 7.584987 CATTAAACCAATTAGCCTCCTAATCG 58.415 38.462 0.00 0.0 42.09 3.34
77 83 4.505390 CCCCTGAATTTTTGGCATCAAACT 60.505 41.667 0.00 0.0 41.97 2.66
149 170 5.107143 GCAACGAAAATTGTTATGCAACCAT 60.107 36.000 0.00 0.0 40.28 3.55
150 171 6.524490 CAACGAAAATTGTTATGCAACCATC 58.476 36.000 0.00 0.0 40.28 3.51
151 172 6.024552 ACGAAAATTGTTATGCAACCATCT 57.975 33.333 0.00 0.0 40.28 2.90
152 173 6.092748 ACGAAAATTGTTATGCAACCATCTC 58.907 36.000 0.00 0.0 40.28 2.75
153 174 6.071952 ACGAAAATTGTTATGCAACCATCTCT 60.072 34.615 0.00 0.0 40.28 3.10
154 175 7.120579 ACGAAAATTGTTATGCAACCATCTCTA 59.879 33.333 0.00 0.0 40.28 2.43
200 348 2.158928 GGCATGCTAATTTTGGGCATCA 60.159 45.455 18.92 0.0 43.62 3.07
232 380 3.071747 GCCTCCTAATCTTCACCCCTAAG 59.928 52.174 0.00 0.0 0.00 2.18
250 398 6.208644 CCCTAAGTTTTTGTGTGATTGACAG 58.791 40.000 0.00 0.0 34.28 3.51
251 399 5.687285 CCTAAGTTTTTGTGTGATTGACAGC 59.313 40.000 0.00 0.0 34.28 4.40
252 400 3.694734 AGTTTTTGTGTGATTGACAGCG 58.305 40.909 0.00 0.0 34.28 5.18
354 628 2.775490 TAGCCTCCTAATCTCTGCCA 57.225 50.000 0.00 0.0 0.00 4.92
419 693 6.719370 ACCAATCTCTAGCCAACATTTAACAA 59.281 34.615 0.00 0.0 0.00 2.83
623 945 3.572255 ACAACGAAAATGGGTATGCAACT 59.428 39.130 0.00 0.0 0.00 3.16
835 1157 1.123928 AGCTTCCTAATCTCCACCCG 58.876 55.000 0.00 0.0 0.00 5.28
903 1225 4.054780 CCAATCAATGGCTTCCAATCAG 57.945 45.455 0.00 0.0 43.80 2.90
994 1317 1.968050 GCTAGCTAAACCTCCGGCCA 61.968 60.000 7.70 0.0 0.00 5.36
1079 1432 1.302752 TGCTGGTGAAGAAGCGCAT 60.303 52.632 11.47 0.0 42.54 4.73
1164 1517 1.923395 CCAACTGGGCCCTCTACCA 60.923 63.158 25.70 0.0 35.05 3.25
1751 2113 4.163427 AGGATCTTCAGAGACCTTGACAA 58.837 43.478 0.00 0.0 32.78 3.18
2003 2365 1.760086 CGCAGGAGGAGATCAGGGT 60.760 63.158 0.00 0.0 0.00 4.34
2244 2621 2.125912 CAGGACGCGGAGGAGTTG 60.126 66.667 12.47 0.0 0.00 3.16
2299 2676 2.448582 AAGGTGGACTTCCGTGGCA 61.449 57.895 0.00 0.0 39.43 4.92
2449 2826 4.704103 TGGCCGAGGAGGTGAGCT 62.704 66.667 0.00 0.0 43.70 4.09
2487 2864 1.070786 GACCTTCCACCGCAAGACA 59.929 57.895 0.00 0.0 43.02 3.41
2602 3017 8.902806 TGACTGAAGTTAGTTGAACAAATGAAT 58.097 29.630 0.00 0.0 40.86 2.57
2621 3040 5.815850 TGAATAAAATTGATACATGCGCGT 58.184 33.333 8.43 0.0 0.00 6.01
3382 4147 7.663043 ACTTTGACAAACCCCAAAACTATAA 57.337 32.000 0.00 0.0 32.63 0.98
3471 4245 1.693467 TGTAACTGCTGCGACTTACG 58.307 50.000 0.00 0.0 45.66 3.18
3476 4250 0.666274 CTGCTGCGACTTACGGTGAA 60.666 55.000 0.00 0.0 42.83 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 0.620030 ATGCCAAAAATTCAGGGGGC 59.380 50.000 0.00 0.00 41.70 5.80
77 83 6.082707 GGGGTGGAGATTAGGAGTCTAATTA 58.917 44.000 0.00 0.00 43.91 1.40
149 170 7.575414 TTGGCAAGTGTTAAATGTTTAGAGA 57.425 32.000 0.00 0.00 0.00 3.10
150 171 8.641499 TTTTGGCAAGTGTTAAATGTTTAGAG 57.359 30.769 0.00 0.00 0.00 2.43
151 172 9.606631 AATTTTGGCAAGTGTTAAATGTTTAGA 57.393 25.926 0.00 0.00 0.00 2.10
153 174 9.994432 CAAATTTTGGCAAGTGTTAAATGTTTA 57.006 25.926 0.00 0.00 0.00 2.01
154 175 7.972832 CCAAATTTTGGCAAGTGTTAAATGTTT 59.027 29.630 14.96 0.00 45.17 2.83
200 348 7.993758 GGTGAAGATTAGGAGGCTAATTAGTTT 59.006 37.037 13.91 2.77 30.47 2.66
232 380 3.690422 TCGCTGTCAATCACACAAAAAC 58.310 40.909 0.00 0.00 0.00 2.43
354 628 2.031120 CCAATCACACAACAGGTTGGT 58.969 47.619 15.84 8.38 44.45 3.67
502 802 4.808364 GCAACTGTTAAATGTTGGCAAGAA 59.192 37.500 17.81 0.00 42.48 2.52
623 945 8.946085 CAACTGTTAAATGTTGGCTAGAGATTA 58.054 33.333 11.73 0.00 39.64 1.75
835 1157 0.977627 CCCCCTGAAAATTGGGAGGC 60.978 60.000 0.04 0.00 46.15 4.70
903 1225 0.398318 AGTGACTGGCAAGGACCTTC 59.602 55.000 2.91 0.00 0.00 3.46
994 1317 4.767928 GGGTAGTGAGATATCCATCGTCTT 59.232 45.833 0.00 0.00 36.20 3.01
1070 1423 1.888436 TTCCTCGGTGATGCGCTTCT 61.888 55.000 22.11 1.01 0.00 2.85
1198 1551 2.435693 GGAGTAGCATGACGGGGCT 61.436 63.158 0.00 0.00 43.94 5.19
1819 2181 2.971598 CGAGGGCATCCACCAGGTT 61.972 63.158 0.00 0.00 35.89 3.50
2244 2621 2.754658 TCGAACCTCTCCGGCTCC 60.755 66.667 0.00 0.00 35.61 4.70
2299 2676 1.609061 CGGCATCAGTTCCAAGTGAGT 60.609 52.381 3.34 0.00 41.31 3.41
2449 2826 2.365105 CCTACCGGCCTCCTCCAA 60.365 66.667 0.00 0.00 0.00 3.53
2602 3017 4.331443 AGACACGCGCATGTATCAATTTTA 59.669 37.500 10.00 0.00 31.24 1.52
2621 3040 1.702401 TCATGTTACCAGCCCAAGACA 59.298 47.619 0.00 0.00 0.00 3.41
3305 4069 4.393834 TGCAAACCTACAGATTTACAGCA 58.606 39.130 0.00 0.00 0.00 4.41
3382 4147 8.482128 TCTTTGTTGGGTAACATCATTTTTCTT 58.518 29.630 0.00 0.00 45.56 2.52
3471 4245 4.232221 CTGTGATTCTTGTGCAATTCACC 58.768 43.478 14.44 0.00 45.03 4.02
3476 4250 6.579666 ATTACACTGTGATTCTTGTGCAAT 57.420 33.333 15.86 0.00 34.14 3.56


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

AutoCloner maintained by Alex Coulton.