Multiple sequence alignment - TraesCS7D01G217200

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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 TraesCS7D01G217200 chr7D 100.000 3266 0 0 1 3266 177168198 177171463 0.000000e+00 6032
1 TraesCS7D01G217200 chr7D 93.216 855 49 8 1 849 241594035 241593184 0.000000e+00 1249
2 TraesCS7D01G217200 chr7A 94.271 2339 123 5 844 3172 181168913 181171250 0.000000e+00 3567
3 TraesCS7D01G217200 chr7A 94.150 2342 122 4 844 3172 181014834 181017173 0.000000e+00 3552
4 TraesCS7D01G217200 chr7A 94.042 2333 125 5 844 3165 180984812 180987141 0.000000e+00 3526
5 TraesCS7D01G217200 chr7A 93.713 2338 124 9 844 3171 180843780 180846104 0.000000e+00 3482
6 TraesCS7D01G217200 chr7A 94.573 1603 75 3 848 2439 181050400 181052001 0.000000e+00 2468
7 TraesCS7D01G217200 chr7A 94.166 857 39 9 1 849 180753599 180754452 0.000000e+00 1295
8 TraesCS7D01G217200 chr7A 93.494 830 52 2 2438 3266 181134904 181135732 0.000000e+00 1232
9 TraesCS7D01G217200 chr3D 93.580 1433 91 1 844 2276 77999163 78000594 0.000000e+00 2135
10 TraesCS7D01G217200 chr3D 93.510 1433 92 1 844 2276 78096856 78098287 0.000000e+00 2130
11 TraesCS7D01G217200 chr3D 91.964 1008 63 2 2269 3266 78001129 78002128 0.000000e+00 1397
12 TraesCS7D01G217200 chr3D 92.531 964 64 1 2303 3266 78098868 78099823 0.000000e+00 1375
13 TraesCS7D01G217200 chr3A 93.450 1313 84 2 965 2276 91285685 91284374 0.000000e+00 1947
14 TraesCS7D01G217200 chr3A 93.684 855 46 6 1 849 424594210 424593358 0.000000e+00 1273
15 TraesCS7D01G217200 chr3A 89.693 1009 76 7 2268 3266 91283863 91282873 0.000000e+00 1262
16 TraesCS7D01G217200 chr3A 89.683 126 13 0 844 969 91288274 91288149 9.380000e-36 161
17 TraesCS7D01G217200 chr3B 90.693 1429 98 15 848 2276 124120487 124119094 0.000000e+00 1869
18 TraesCS7D01G217200 chr3B 91.881 1010 70 8 2268 3266 124118561 124117553 0.000000e+00 1400
19 TraesCS7D01G217200 chr4D 91.170 1359 95 10 930 2276 388250912 388249567 0.000000e+00 1821
20 TraesCS7D01G217200 chr4D 92.523 856 54 8 1 849 206089185 206090037 0.000000e+00 1218
21 TraesCS7D01G217200 chr6D 92.640 856 55 5 1 849 139164213 139165067 0.000000e+00 1225
22 TraesCS7D01G217200 chr6B 92.714 851 55 5 4 849 300646751 300645903 0.000000e+00 1221
23 TraesCS7D01G217200 chr5D 92.380 853 59 4 1 849 136279450 136278600 0.000000e+00 1210
24 TraesCS7D01G217200 chr2D 92.290 856 59 5 1 849 400629674 400630529 0.000000e+00 1208
25 TraesCS7D01G217200 chr2D 92.281 855 58 7 1 849 310069875 310070727 0.000000e+00 1206


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 TraesCS7D01G217200 chr7D 177168198 177171463 3265 False 6032.000000 6032 100.0000 1 3266 1 chr7D.!!$F1 3265
1 TraesCS7D01G217200 chr7D 241593184 241594035 851 True 1249.000000 1249 93.2160 1 849 1 chr7D.!!$R1 848
2 TraesCS7D01G217200 chr7A 181168913 181171250 2337 False 3567.000000 3567 94.2710 844 3172 1 chr7A.!!$F7 2328
3 TraesCS7D01G217200 chr7A 181014834 181017173 2339 False 3552.000000 3552 94.1500 844 3172 1 chr7A.!!$F4 2328
4 TraesCS7D01G217200 chr7A 180984812 180987141 2329 False 3526.000000 3526 94.0420 844 3165 1 chr7A.!!$F3 2321
5 TraesCS7D01G217200 chr7A 180843780 180846104 2324 False 3482.000000 3482 93.7130 844 3171 1 chr7A.!!$F2 2327
6 TraesCS7D01G217200 chr7A 181050400 181052001 1601 False 2468.000000 2468 94.5730 848 2439 1 chr7A.!!$F5 1591
7 TraesCS7D01G217200 chr7A 180753599 180754452 853 False 1295.000000 1295 94.1660 1 849 1 chr7A.!!$F1 848
8 TraesCS7D01G217200 chr7A 181134904 181135732 828 False 1232.000000 1232 93.4940 2438 3266 1 chr7A.!!$F6 828
9 TraesCS7D01G217200 chr3D 77999163 78002128 2965 False 1766.000000 2135 92.7720 844 3266 2 chr3D.!!$F1 2422
10 TraesCS7D01G217200 chr3D 78096856 78099823 2967 False 1752.500000 2130 93.0205 844 3266 2 chr3D.!!$F2 2422
11 TraesCS7D01G217200 chr3A 424593358 424594210 852 True 1273.000000 1273 93.6840 1 849 1 chr3A.!!$R1 848
12 TraesCS7D01G217200 chr3A 91282873 91288274 5401 True 1123.333333 1947 90.9420 844 3266 3 chr3A.!!$R2 2422
13 TraesCS7D01G217200 chr3B 124117553 124120487 2934 True 1634.500000 1869 91.2870 848 3266 2 chr3B.!!$R1 2418
14 TraesCS7D01G217200 chr4D 388249567 388250912 1345 True 1821.000000 1821 91.1700 930 2276 1 chr4D.!!$R1 1346
15 TraesCS7D01G217200 chr4D 206089185 206090037 852 False 1218.000000 1218 92.5230 1 849 1 chr4D.!!$F1 848
16 TraesCS7D01G217200 chr6D 139164213 139165067 854 False 1225.000000 1225 92.6400 1 849 1 chr6D.!!$F1 848
17 TraesCS7D01G217200 chr6B 300645903 300646751 848 True 1221.000000 1221 92.7140 4 849 1 chr6B.!!$R1 845
18 TraesCS7D01G217200 chr5D 136278600 136279450 850 True 1210.000000 1210 92.3800 1 849 1 chr5D.!!$R1 848
19 TraesCS7D01G217200 chr2D 400629674 400630529 855 False 1208.000000 1208 92.2900 1 849 1 chr2D.!!$F2 848
20 TraesCS7D01G217200 chr2D 310069875 310070727 852 False 1206.000000 1206 92.2810 1 849 1 chr2D.!!$F1 848

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
641 657 0.100325 TTTTTGCTGCTGTGGTGACG 59.9 50.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 5375 0.455295 GACGAGACCAGACAAGAGCG 60.455 60.0 0.0 0.0 0.0 5.03 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
263 270 3.425404 CGTGCAATAAAAATGTCCCGAG 58.575 45.455 0.00 0.00 0.00 4.63
356 365 4.599500 ACACCAGGGGGCCTCACT 62.599 66.667 5.99 0.00 37.90 3.41
397 409 3.712907 GCGCCCTACCTTGTGGGA 61.713 66.667 0.00 0.00 46.15 4.37
441 453 1.133181 TCCAGCACCCATCCACTTCA 61.133 55.000 0.00 0.00 0.00 3.02
458 470 5.182760 CCACTTCATCTTCCTCCAGAAAAAG 59.817 44.000 0.00 0.00 32.88 2.27
515 530 1.339920 TGCTGCCATTTTCGATCTCCA 60.340 47.619 0.00 0.00 0.00 3.86
572 587 4.935808 GGATTGTTCTTCGGTATGTGACTT 59.064 41.667 0.00 0.00 0.00 3.01
641 657 0.100325 TTTTTGCTGCTGTGGTGACG 59.900 50.000 0.00 0.00 0.00 4.35
711 727 5.522641 TGATGCATGATATAGCCTCTAGGA 58.477 41.667 2.46 0.00 37.39 2.94
715 731 5.420421 TGCATGATATAGCCTCTAGGAACTC 59.580 44.000 0.00 0.00 41.75 3.01
879 896 2.567169 ACATGATTGGTGGAGAACTCGA 59.433 45.455 0.00 0.00 0.00 4.04
926 944 2.356741 GGGTCGGGAGAAATCCATTTCA 60.357 50.000 13.30 0.00 46.50 2.69
1058 3545 2.957680 TGGTGTGCACAATGAGTTTGAT 59.042 40.909 23.59 0.00 38.76 2.57
1214 3701 3.161067 CGATGGAGAGACCCATAGTGAT 58.839 50.000 0.00 0.00 46.34 3.06
1288 3775 4.530710 TCCTACAACTTGAAGCGTACAT 57.469 40.909 0.00 0.00 0.00 2.29
1699 4188 8.859090 CATACCTGAAATTAATAAATGCAGGGA 58.141 33.333 17.19 10.69 44.74 4.20
1706 4195 9.264719 GAAATTAATAAATGCAGGGAAAGATGG 57.735 33.333 0.00 0.00 0.00 3.51
1772 4261 2.550830 AACTGAACGTCAAGCCATCT 57.449 45.000 0.00 0.00 0.00 2.90
1998 4488 7.987458 TCGATCTTAGCCAATGTTAATTCTTCT 59.013 33.333 0.00 0.00 0.00 2.85
2029 4519 9.498176 GAACTATAGTTTTACTTGGTTCCTCAA 57.502 33.333 18.96 0.00 38.56 3.02
2127 4617 0.748005 GTTGCTACGTGGGATGGCAT 60.748 55.000 0.00 0.00 32.87 4.40
2168 4658 1.475213 GCAATGTAGGGGCAGTAGGAC 60.475 57.143 0.00 0.00 0.00 3.85
2280 5313 6.367983 TGCCAATAAATAGAGAGAAAGGCAT 58.632 36.000 0.00 0.00 42.84 4.40
2332 5375 7.358023 CGGTGAGTTTGTTTAATACATTGCAAC 60.358 37.037 0.00 0.00 36.44 4.17
2577 5621 9.129209 GTGAATTTTTGCTACTAATGGAGAAAC 57.871 33.333 0.00 0.00 0.00 2.78
2618 5662 1.464608 CGTCGCAATCACCTTGACAAT 59.535 47.619 0.00 0.00 36.97 2.71
2822 5867 1.282248 CTCGCAATGAACGACACGGT 61.282 55.000 0.00 0.00 35.35 4.83
3137 6185 2.041081 CCTTGGTATGACCTGGTTTGGA 59.959 50.000 0.00 0.00 39.58 3.53
3151 6199 1.197036 GTTTGGACAAACTAGCGCTCC 59.803 52.381 16.34 8.13 45.26 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.177373 CTAGGTTACCTCAACGGGGC 59.823 60.000 7.39 0.00 38.09 5.80
232 236 8.994429 ACATTTTTATTGCACGGATAATTCAA 57.006 26.923 0.00 0.00 0.00 2.69
263 270 6.071391 TCAGGGCATTTGGAGAACTTTTATTC 60.071 38.462 0.00 0.00 0.00 1.75
316 325 5.920840 GTGTTCTTAGTGCCAAAATTTCTCC 59.079 40.000 0.00 0.00 0.00 3.71
322 331 3.957497 TGGTGTGTTCTTAGTGCCAAAAT 59.043 39.130 0.00 0.00 0.00 1.82
356 365 3.166434 CACCCTTGTGGCCCACTA 58.834 61.111 16.23 6.64 38.90 2.74
441 453 5.504853 GGATGACTTTTTCTGGAGGAAGAT 58.495 41.667 0.00 0.00 35.16 2.40
458 470 3.126831 CGAGTTTGAGCTATGGGATGAC 58.873 50.000 0.00 0.00 0.00 3.06
515 530 0.737219 GCGAATGGAGCTTTGAGCAT 59.263 50.000 2.47 0.00 45.56 3.79
572 587 6.553100 ACAAAAACTAATTGGACCATTGGAGA 59.447 34.615 10.37 0.00 32.02 3.71
641 657 3.243168 TGACATGCAAGCTCAAGAACAAC 60.243 43.478 0.00 0.00 0.00 3.32
711 727 8.034278 ATTGATAGCAACTACTCCCACGAGTT 62.034 42.308 0.00 0.00 40.73 3.01
715 731 3.520290 TTGATAGCAACTACTCCCACG 57.480 47.619 0.00 0.00 0.00 4.94
879 896 2.612493 CCCACCACCCCGGAGAATT 61.612 63.158 0.73 0.00 38.63 2.17
1058 3545 4.198530 TGTGTTTGCTTGTCATGAAGAGA 58.801 39.130 0.00 0.00 0.00 3.10
1214 3701 3.963733 CCTTGTGGCCATTCTCTGA 57.036 52.632 9.72 0.00 0.00 3.27
1562 4050 5.616270 TGCTACAATGTTCAGTGGAGTTTA 58.384 37.500 12.87 0.00 0.00 2.01
1699 4188 0.909610 TCTCCCACCGCTCCATCTTT 60.910 55.000 0.00 0.00 0.00 2.52
1772 4261 4.099266 AGTCTTGTTTTGCATAGCCAACAA 59.901 37.500 12.91 12.91 37.93 2.83
1998 4488 8.630054 AACCAAGTAAAACTATAGTTCATGCA 57.370 30.769 18.28 0.00 37.25 3.96
2029 4519 3.259064 ACATGTCGCGTTATTTGCTAGT 58.741 40.909 5.77 0.00 0.00 2.57
2127 4617 6.057321 TGCTATCATGATTGCCATATCTCA 57.943 37.500 30.55 13.16 38.48 3.27
2145 4635 2.639839 CCTACTGCCCCTACATTGCTAT 59.360 50.000 0.00 0.00 0.00 2.97
2146 4636 2.047061 CCTACTGCCCCTACATTGCTA 58.953 52.381 0.00 0.00 0.00 3.49
2168 4658 3.204827 CCATCCCAAAGCCGCTCG 61.205 66.667 0.00 0.00 0.00 5.03
2280 5313 6.321435 TCCTGATCTCGAAGTATTTGCTCTTA 59.679 38.462 0.00 0.00 0.00 2.10
2332 5375 0.455295 GACGAGACCAGACAAGAGCG 60.455 60.000 0.00 0.00 0.00 5.03
2577 5621 0.606401 CCCTGTTGTGCCTACCACTG 60.606 60.000 0.00 0.00 44.92 3.66
2618 5662 7.666063 TTGATTGTCTCTATCTCAGGATTGA 57.334 36.000 0.00 0.00 33.90 2.57
2660 5704 3.201487 TGATCTCACCAGATGGCATCTTT 59.799 43.478 26.87 14.31 39.71 2.52
2787 5832 3.537580 TGCGAGGTTTGTGTACTCTTTT 58.462 40.909 0.00 0.00 0.00 2.27
2822 5867 2.116983 GAGCCAGCAGGTTGGTCTCA 62.117 60.000 15.92 0.00 39.30 3.27
3109 6157 3.199946 CCAGGTCATACCAAGGTACACAT 59.800 47.826 0.14 0.00 41.95 3.21
3137 6185 1.512926 CAAGTGGAGCGCTAGTTTGT 58.487 50.000 11.50 0.00 0.00 2.83
3151 6199 2.195922 GCAAAGGACAAAGTGCAAGTG 58.804 47.619 0.00 0.00 36.97 3.16
3215 6263 6.908870 TTTGGATCATCTCAATCTAACGTG 57.091 37.500 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.