Multiple sequence alignment - TraesCS3A01G226100

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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 TraesCS3A01G226100 chr3A 100.000 2708 0 0 1 2708 423670659 423673366 0.000000e+00 5001.0
1 TraesCS3A01G226100 chr3B 93.988 2728 122 19 1 2708 416136962 416134257 0.000000e+00 4091.0
2 TraesCS3A01G226100 chr3D 91.993 2248 89 46 481 2707 305621662 305623839 0.000000e+00 3070.0
3 TraesCS3A01G226100 chr3D 90.672 461 36 7 1 457 305596988 305597445 8.290000e-170 606.0
4 TraesCS3A01G226100 chr2D 80.142 141 25 1 1128 1268 388481930 388481793 4.770000e-18 102.0
5 TraesCS3A01G226100 chr2A 80.142 141 25 1 1128 1268 524953218 524953081 4.770000e-18 102.0
6 TraesCS3A01G226100 chr6B 78.472 144 23 5 1136 1272 539195662 539195520 1.340000e-13 87.9
7 TraesCS3A01G226100 chr6A 78.723 141 22 5 1136 1269 499955058 499955197 1.340000e-13 87.9
8 TraesCS3A01G226100 chr6D 77.778 144 24 5 1136 1272 357592515 357592373 6.210000e-12 82.4
9 TraesCS3A01G226100 chr1D 97.222 36 1 0 1229 1264 74929947 74929912 8.100000e-06 62.1
10 TraesCS3A01G226100 chr1D 90.244 41 3 1 539 579 482230082 482230043 5.000000e-03 52.8
11 TraesCS3A01G226100 chr1A 97.222 36 1 0 1229 1264 75256103 75256068 8.100000e-06 62.1


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 TraesCS3A01G226100 chr3A 423670659 423673366 2707 False 5001 5001 100.000 1 2708 1 chr3A.!!$F1 2707
1 TraesCS3A01G226100 chr3B 416134257 416136962 2705 True 4091 4091 93.988 1 2708 1 chr3B.!!$R1 2707
2 TraesCS3A01G226100 chr3D 305621662 305623839 2177 False 3070 3070 91.993 481 2707 1 chr3D.!!$F2 2226

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
104 107 0.179048 TGGATATGGTCTTGCCGCAG 60.179 55.0 0.00 0.00 41.21 5.18 F
810 824 0.596082 GCAGACTCTATCTCCGGCTC 59.404 60.0 0.00 0.00 34.41 4.70 F
970 986 0.925267 CAGTTTGACAAGCACACGCG 60.925 55.0 3.53 3.53 45.49 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 1718 1.451567 ATGGCTACTGCTGCTGCTG 60.452 57.895 18.66 18.66 42.70 4.41 R
1694 1719 1.451567 CATGGCTACTGCTGCTGCT 60.452 57.895 17.00 0.00 40.48 4.24 R
1854 1881 1.688735 TGCTCCTACCAGGAATGATCG 59.311 52.381 0.00 0.00 45.28 3.69 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
29 30 2.281761 CAGCCCTTCAGCCGTTGT 60.282 61.111 0.00 0.00 0.00 3.32
63 65 1.080329 AGCCTCTCCTTCCTTCTTCCT 59.920 52.381 0.00 0.00 0.00 3.36
65 67 2.355615 GCCTCTCCTTCCTTCTTCCTTG 60.356 54.545 0.00 0.00 0.00 3.61
100 103 2.233271 CATGGTGGATATGGTCTTGCC 58.767 52.381 0.00 0.00 37.90 4.52
104 107 0.179048 TGGATATGGTCTTGCCGCAG 60.179 55.000 0.00 0.00 41.21 5.18
117 120 1.078497 CCGCAGCAATGGAGGTGTA 60.078 57.895 0.00 0.00 39.13 2.90
125 128 2.259618 CAATGGAGGTGTAACGACTCG 58.740 52.381 0.00 0.00 38.12 4.18
139 142 4.294416 ACGACTCGTGGAAGATAGATTG 57.706 45.455 2.53 0.00 39.18 2.67
170 173 2.886124 GCGACTAGCGTTGGAGGC 60.886 66.667 8.08 0.00 43.41 4.70
181 184 2.415625 GCGTTGGAGGCGTATAGATAGG 60.416 54.545 0.00 0.00 0.00 2.57
185 188 2.025898 GGAGGCGTATAGATAGGAGGC 58.974 57.143 0.00 0.00 0.00 4.70
232 235 3.009473 TGACTTCTCCCCTTTGATCCAAG 59.991 47.826 0.00 0.00 0.00 3.61
237 240 3.597868 TCTCCCCTTTGATCCAAGGATTT 59.402 43.478 23.88 0.00 34.60 2.17
247 250 4.723789 TGATCCAAGGATTTTAGAGGAGCT 59.276 41.667 2.62 0.00 34.60 4.09
254 257 4.103943 AGGATTTTAGAGGAGCTCAATCCC 59.896 45.833 26.10 14.90 42.45 3.85
256 259 2.568546 TTAGAGGAGCTCAATCCCCA 57.431 50.000 17.19 0.00 40.53 4.96
264 267 2.108952 GAGCTCAATCCCCACCCAATAT 59.891 50.000 9.40 0.00 0.00 1.28
267 270 3.437052 GCTCAATCCCCACCCAATATCTT 60.437 47.826 0.00 0.00 0.00 2.40
280 283 6.889722 CACCCAATATCTTCCTTGGTTTCTAA 59.110 38.462 0.00 0.00 40.28 2.10
298 302 7.119407 GGTTTCTAAGGACTCATAGGAACAAAC 59.881 40.741 11.57 0.00 38.74 2.93
299 303 6.295719 TCTAAGGACTCATAGGAACAAACC 57.704 41.667 0.00 0.00 0.00 3.27
304 308 4.254492 GACTCATAGGAACAAACCTGGAC 58.746 47.826 0.00 0.00 40.81 4.02
309 314 6.074648 TCATAGGAACAAACCTGGACAAATT 58.925 36.000 0.00 0.00 40.81 1.82
323 328 6.982141 CCTGGACAAATTGGTGAATAATCATG 59.018 38.462 0.00 0.00 38.01 3.07
324 329 7.147863 CCTGGACAAATTGGTGAATAATCATGA 60.148 37.037 0.00 0.00 38.01 3.07
334 339 7.715657 TGGTGAATAATCATGAAAGTTATGGC 58.284 34.615 0.00 0.00 38.01 4.40
341 346 6.645790 ATCATGAAAGTTATGGCTGATTCC 57.354 37.500 0.00 0.00 0.00 3.01
344 349 5.178096 TGAAAGTTATGGCTGATTCCTCA 57.822 39.130 0.00 0.00 0.00 3.86
389 394 6.257849 CCTGTGCATAGTCGTAAAATACACAT 59.742 38.462 9.80 0.00 35.23 3.21
393 398 9.417284 GTGCATAGTCGTAAAATACACATAAAC 57.583 33.333 0.00 0.00 0.00 2.01
461 466 9.911788 ATGATCTTTTCTTAACATATGGTGACT 57.088 29.630 2.68 0.00 0.00 3.41
583 589 8.207252 CGATGAACATTGTTTTAAACACATGAC 58.793 33.333 24.84 20.02 41.97 3.06
584 590 8.939201 ATGAACATTGTTTTAAACACATGACA 57.061 26.923 24.84 22.64 41.97 3.58
588 594 8.060020 ACATTGTTTTAAACACATGACAATCG 57.940 30.769 24.84 8.65 41.97 3.34
589 595 7.704472 ACATTGTTTTAAACACATGACAATCGT 59.296 29.630 24.84 9.08 41.97 3.73
810 824 0.596082 GCAGACTCTATCTCCGGCTC 59.404 60.000 0.00 0.00 34.41 4.70
883 897 4.060900 CAGAAATATCCCAGACATGACCG 58.939 47.826 0.00 0.00 0.00 4.79
967 983 1.831343 CTGCAGTTTGACAAGCACAC 58.169 50.000 5.25 0.00 32.87 3.82
970 986 0.925267 CAGTTTGACAAGCACACGCG 60.925 55.000 3.53 3.53 45.49 6.01
1209 1225 2.586792 GAGTTCATGCCGGCCTCT 59.413 61.111 26.77 14.48 0.00 3.69
1670 1695 2.359602 GCAGCAGGAGAAGCAGCA 60.360 61.111 0.00 0.00 43.05 4.41
1671 1696 2.400158 GCAGCAGGAGAAGCAGCAG 61.400 63.158 0.00 0.00 43.05 4.24
1672 1697 2.046120 AGCAGGAGAAGCAGCAGC 60.046 61.111 0.00 0.00 42.56 5.25
1693 1718 3.456280 CTTCAGGAGCATAGACAAGAGC 58.544 50.000 0.00 0.00 0.00 4.09
1694 1719 2.460669 TCAGGAGCATAGACAAGAGCA 58.539 47.619 0.00 0.00 0.00 4.26
1722 1747 1.227380 GTAGCCATGGCAGGAGACG 60.227 63.158 37.18 0.00 44.88 4.18
1747 1774 4.259933 TCCATAGTAGTAGGAGGCAACA 57.740 45.455 0.00 0.00 41.41 3.33
1779 1806 5.684184 CGCCCTTGTAAAGTTTTTAACTGTC 59.316 40.000 0.00 0.00 44.25 3.51
1854 1881 3.555139 GCTTCTCTGTCATATCAGTGCAC 59.445 47.826 9.40 9.40 36.85 4.57
2185 2220 3.138798 GCCATGGCCAGACAGCAG 61.139 66.667 27.24 0.00 34.56 4.24
2219 2254 2.570302 AGGCTTAATACAAGTGGACGGT 59.430 45.455 0.00 0.00 0.00 4.83
2428 2463 4.005650 TCAACATCTTGAGATCTTGCACC 58.994 43.478 0.00 0.00 32.68 5.01
2495 2530 7.391554 TCTTCATGAGGTGAAAAGGACAAATAG 59.608 37.037 4.57 0.00 45.74 1.73
2504 2539 5.938125 TGAAAAGGACAAATAGCCACTAGTC 59.062 40.000 0.00 0.00 0.00 2.59
2531 2566 9.639601 TTATAAATGTGGATTGAGCTATACGAG 57.360 33.333 0.00 0.00 0.00 4.18
2625 2660 6.482835 CCGTTAATATGAGCACGAAATTGAA 58.517 36.000 0.00 0.00 34.49 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.281761 CACAACGGCTGAAGGGCT 60.282 61.111 0.00 0.00 38.46 5.19
49 50 3.073062 CCAAGACAAGGAAGAAGGAAGGA 59.927 47.826 0.00 0.00 0.00 3.36
63 65 1.075601 ATGGAGGAAGGCCAAGACAA 58.924 50.000 5.01 0.00 39.21 3.18
65 67 0.394899 CCATGGAGGAAGGCCAAGAC 60.395 60.000 5.56 0.00 41.22 3.01
100 103 0.447801 GTTACACCTCCATTGCTGCG 59.552 55.000 0.00 0.00 0.00 5.18
104 107 2.000447 GAGTCGTTACACCTCCATTGC 59.000 52.381 0.00 0.00 0.00 3.56
117 120 4.440250 CCAATCTATCTTCCACGAGTCGTT 60.440 45.833 17.16 2.63 38.32 3.85
125 128 5.815233 TCCATCTCCAATCTATCTTCCAC 57.185 43.478 0.00 0.00 0.00 4.02
139 142 3.928779 TCGCCGGCATCCATCTCC 61.929 66.667 28.98 0.00 0.00 3.71
181 184 0.907230 AGAAGACCTGTGGAGGCCTC 60.907 60.000 25.59 25.59 44.33 4.70
185 188 2.697751 CCATAGAGAAGACCTGTGGAGG 59.302 54.545 0.00 0.00 43.12 4.30
191 194 4.648762 AGTCACATCCATAGAGAAGACCTG 59.351 45.833 0.00 0.00 0.00 4.00
192 195 4.877773 AGTCACATCCATAGAGAAGACCT 58.122 43.478 0.00 0.00 0.00 3.85
195 198 5.596361 GGAGAAGTCACATCCATAGAGAAGA 59.404 44.000 0.00 0.00 33.08 2.87
232 235 4.393834 GGGATTGAGCTCCTCTAAAATCC 58.606 47.826 23.59 23.59 42.20 3.01
237 240 2.119495 GTGGGGATTGAGCTCCTCTAA 58.881 52.381 12.15 0.00 36.67 2.10
247 250 3.140144 GGAAGATATTGGGTGGGGATTGA 59.860 47.826 0.00 0.00 0.00 2.57
254 257 3.981212 AACCAAGGAAGATATTGGGTGG 58.019 45.455 8.68 0.00 44.84 4.61
280 283 3.264450 CCAGGTTTGTTCCTATGAGTCCT 59.736 47.826 0.00 0.00 35.87 3.85
287 291 5.245977 CCAATTTGTCCAGGTTTGTTCCTAT 59.754 40.000 0.00 0.00 35.87 2.57
298 302 6.528537 TGATTATTCACCAATTTGTCCAGG 57.471 37.500 0.00 0.00 0.00 4.45
299 303 7.774134 TCATGATTATTCACCAATTTGTCCAG 58.226 34.615 0.00 0.00 33.85 3.86
309 314 7.560991 AGCCATAACTTTCATGATTATTCACCA 59.439 33.333 0.00 0.00 33.85 4.17
323 328 5.747951 CTGAGGAATCAGCCATAACTTTC 57.252 43.478 0.00 0.00 0.00 2.62
334 339 3.118884 CCCATTTTTGGCTGAGGAATCAG 60.119 47.826 0.83 0.83 40.51 2.90
346 351 3.360886 GCATACCGCCCATTTTTGG 57.639 52.632 0.00 0.00 32.94 3.28
366 371 8.705048 TTATGTGTATTTTACGACTATGCACA 57.295 30.769 13.69 13.69 44.77 4.57
435 440 9.911788 AGTCACCATATGTTAAGAAAAGATCAT 57.088 29.630 1.24 0.00 0.00 2.45
729 735 2.093473 CGGTCTCGTCGACTCGTCT 61.093 63.158 14.70 0.00 42.44 4.18
757 764 5.539955 ACACTGCTGATTTTCCTACCATTTT 59.460 36.000 0.00 0.00 0.00 1.82
759 766 4.666512 ACACTGCTGATTTTCCTACCATT 58.333 39.130 0.00 0.00 0.00 3.16
761 768 3.788227 ACACTGCTGATTTTCCTACCA 57.212 42.857 0.00 0.00 0.00 3.25
762 769 5.449177 GCATTACACTGCTGATTTTCCTACC 60.449 44.000 0.00 0.00 39.12 3.18
764 771 5.252547 TGCATTACACTGCTGATTTTCCTA 58.747 37.500 0.00 0.00 42.75 2.94
800 814 3.222855 CCTCAGCGAGCCGGAGAT 61.223 66.667 5.05 0.00 0.00 2.75
822 836 1.443872 GGTCGGGCGCGTCTATATG 60.444 63.158 23.19 0.00 0.00 1.78
1209 1225 3.379445 GCGAGTGGGTCTTCGGGA 61.379 66.667 0.00 0.00 0.00 5.14
1672 1697 3.118847 TGCTCTTGTCTATGCTCCTGAAG 60.119 47.826 0.00 0.00 0.00 3.02
1692 1717 3.507009 GGCTACTGCTGCTGCTGC 61.507 66.667 22.51 22.51 41.07 5.25
1693 1718 1.451567 ATGGCTACTGCTGCTGCTG 60.452 57.895 18.66 18.66 42.70 4.41
1694 1719 1.451567 CATGGCTACTGCTGCTGCT 60.452 57.895 17.00 0.00 40.48 4.24
1722 1747 2.898612 GCCTCCTACTACTATGGAACCC 59.101 54.545 0.00 0.00 0.00 4.11
1747 1774 1.823169 TTTACAAGGGCGCGAGGAGT 61.823 55.000 12.10 3.31 0.00 3.85
1779 1806 6.469275 GTGAAAAAGAACAGAAGAACTTTCCG 59.531 38.462 0.00 0.00 32.52 4.30
1854 1881 1.688735 TGCTCCTACCAGGAATGATCG 59.311 52.381 0.00 0.00 45.28 3.69
2045 2078 7.368198 TGGTTTCTTTAATTTTAAGGGCACT 57.632 32.000 0.00 0.00 0.00 4.40
2428 2463 7.633621 TCTCAAGAATTTATAAGCTGCGAATG 58.366 34.615 0.00 0.00 0.00 2.67
2495 2530 7.715249 TCAATCCACATTTATAAGACTAGTGGC 59.285 37.037 0.00 0.00 43.48 5.01
2504 2539 9.639601 TCGTATAGCTCAATCCACATTTATAAG 57.360 33.333 0.00 0.00 0.00 1.73
2625 2660 6.656632 TCTGATAGCACTTTCTATTCGGAT 57.343 37.500 0.00 0.00 29.93 4.18


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

AutoCloner maintained by Alex Coulton.