Multiple sequence alignment - TraesCS7D01G272200

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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 TraesCS7D01G272200 chr7D 100.000 3280 0 0 1 3280 262353254 262356533 0.000000e+00 6058.0
1 TraesCS7D01G272200 chr7D 88.152 633 47 15 2670 3280 480048717 480048091 0.000000e+00 728.0
2 TraesCS7D01G272200 chr7D 86.443 627 59 15 2675 3280 47500729 47501350 0.000000e+00 664.0
3 TraesCS7D01G272200 chr7B 96.499 2685 77 12 1 2675 241579457 241576780 0.000000e+00 4421.0
4 TraesCS7D01G272200 chr7A 93.189 2687 119 23 1 2675 285424176 285426810 0.000000e+00 3890.0
5 TraesCS7D01G272200 chr7A 87.153 576 46 12 2729 3280 17302249 17301678 2.150000e-176 628.0
6 TraesCS7D01G272200 chr4A 84.834 1932 172 47 715 2592 5832700 5834564 0.000000e+00 1832.0
7 TraesCS7D01G272200 chr4A 90.499 621 46 6 2672 3280 387090961 387091580 0.000000e+00 808.0
8 TraesCS7D01G272200 chr3D 91.368 614 43 6 2671 3274 552621859 552622472 0.000000e+00 832.0
9 TraesCS7D01G272200 chr3D 87.658 632 52 13 2670 3279 70683497 70684124 0.000000e+00 712.0
10 TraesCS7D01G272200 chr3D 89.674 184 7 2 3106 3280 83688452 83688272 1.180000e-54 224.0
11 TraesCS7D01G272200 chr6D 88.925 614 56 4 2678 3280 368059383 368058771 0.000000e+00 747.0
12 TraesCS7D01G272200 chr6D 88.754 578 53 4 2714 3280 368143232 368142656 0.000000e+00 697.0
13 TraesCS7D01G272200 chr5A 88.160 625 52 6 2675 3280 325742362 325742983 0.000000e+00 725.0
14 TraesCS7D01G272200 chr5A 87.480 615 59 12 2672 3274 279574163 279574771 0.000000e+00 693.0
15 TraesCS7D01G272200 chr5A 84.051 627 75 13 2673 3280 362754612 362755232 6.100000e-162 580.0
16 TraesCS7D01G272200 chr5A 88.940 434 28 8 2866 3280 487768617 487768185 4.850000e-143 518.0
17 TraesCS7D01G272200 chr1D 87.797 631 48 19 2673 3280 461271336 461270712 0.000000e+00 712.0
18 TraesCS7D01G272200 chr2A 85.692 629 45 13 2673 3280 526072243 526071639 3.590000e-174 621.0
19 TraesCS7D01G272200 chr2B 85.167 627 67 15 2675 3280 539382341 539382962 1.290000e-173 619.0
20 TraesCS7D01G272200 chr3B 82.919 644 71 15 2672 3280 399314596 399313957 8.000000e-151 544.0
21 TraesCS7D01G272200 chr4D 90.026 391 38 1 966 1355 464178039 464177649 3.780000e-139 505.0
22 TraesCS7D01G272200 chr4B 85.542 83 9 2 2370 2452 580037727 580037648 2.100000e-12 84.2


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 TraesCS7D01G272200 chr7D 262353254 262356533 3279 False 6058 6058 100.000 1 3280 1 chr7D.!!$F2 3279
1 TraesCS7D01G272200 chr7D 480048091 480048717 626 True 728 728 88.152 2670 3280 1 chr7D.!!$R1 610
2 TraesCS7D01G272200 chr7D 47500729 47501350 621 False 664 664 86.443 2675 3280 1 chr7D.!!$F1 605
3 TraesCS7D01G272200 chr7B 241576780 241579457 2677 True 4421 4421 96.499 1 2675 1 chr7B.!!$R1 2674
4 TraesCS7D01G272200 chr7A 285424176 285426810 2634 False 3890 3890 93.189 1 2675 1 chr7A.!!$F1 2674
5 TraesCS7D01G272200 chr7A 17301678 17302249 571 True 628 628 87.153 2729 3280 1 chr7A.!!$R1 551
6 TraesCS7D01G272200 chr4A 5832700 5834564 1864 False 1832 1832 84.834 715 2592 1 chr4A.!!$F1 1877
7 TraesCS7D01G272200 chr4A 387090961 387091580 619 False 808 808 90.499 2672 3280 1 chr4A.!!$F2 608
8 TraesCS7D01G272200 chr3D 552621859 552622472 613 False 832 832 91.368 2671 3274 1 chr3D.!!$F2 603
9 TraesCS7D01G272200 chr3D 70683497 70684124 627 False 712 712 87.658 2670 3279 1 chr3D.!!$F1 609
10 TraesCS7D01G272200 chr6D 368058771 368059383 612 True 747 747 88.925 2678 3280 1 chr6D.!!$R1 602
11 TraesCS7D01G272200 chr6D 368142656 368143232 576 True 697 697 88.754 2714 3280 1 chr6D.!!$R2 566
12 TraesCS7D01G272200 chr5A 325742362 325742983 621 False 725 725 88.160 2675 3280 1 chr5A.!!$F2 605
13 TraesCS7D01G272200 chr5A 279574163 279574771 608 False 693 693 87.480 2672 3274 1 chr5A.!!$F1 602
14 TraesCS7D01G272200 chr5A 362754612 362755232 620 False 580 580 84.051 2673 3280 1 chr5A.!!$F3 607
15 TraesCS7D01G272200 chr1D 461270712 461271336 624 True 712 712 87.797 2673 3280 1 chr1D.!!$R1 607
16 TraesCS7D01G272200 chr2A 526071639 526072243 604 True 621 621 85.692 2673 3280 1 chr2A.!!$R1 607
17 TraesCS7D01G272200 chr2B 539382341 539382962 621 False 619 619 85.167 2675 3280 1 chr2B.!!$F1 605
18 TraesCS7D01G272200 chr3B 399313957 399314596 639 True 544 544 82.919 2672 3280 1 chr3B.!!$R1 608

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
391 400 0.104855 TAGCTTGGCGCATGAGTAGG 59.895 55.000 10.83 0.0 42.61 3.18 F
737 750 1.152830 ATCCAACGGCCCAACAGTT 59.847 52.632 0.00 0.0 37.12 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1451 0.026803 GCTTGCACGCATAGTAGCAC 59.973 55.0 10.77 0.0 36.89 4.40 R
2360 2416 0.534873 GAGAGAGGCTCAACCAGGAC 59.465 60.0 18.26 0.0 43.38 3.85 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
36 38 7.706281 AGCTCGACATTTGATAAGTTGATAG 57.294 36.000 0.00 0.00 0.00 2.08
123 127 3.124636 GGCAAACTTGGATGTAGTACACG 59.875 47.826 4.80 0.00 0.00 4.49
136 140 0.381089 GTACACGCGAGATAGCCACT 59.619 55.000 15.93 0.00 0.00 4.00
243 251 3.995048 GCTAAAGACTCTACGCTGGTTTT 59.005 43.478 0.00 0.00 0.00 2.43
277 286 2.354704 CGGACATTGGAGCTCAAAGGTA 60.355 50.000 20.59 0.00 39.05 3.08
285 294 1.936547 GAGCTCAAAGGTATTCGCAGG 59.063 52.381 9.40 0.00 0.00 4.85
353 362 1.001633 TCACTTTTGCTAGGTCCGGTC 59.998 52.381 0.00 0.00 0.00 4.79
354 363 0.323957 ACTTTTGCTAGGTCCGGTCC 59.676 55.000 10.05 10.05 0.00 4.46
391 400 0.104855 TAGCTTGGCGCATGAGTAGG 59.895 55.000 10.83 0.00 42.61 3.18
579 588 1.672881 CATCTTTTCTTAGGCCTGCGG 59.327 52.381 17.99 5.23 0.00 5.69
686 699 4.569676 TTTGGGGGATAGATAGACTGGA 57.430 45.455 0.00 0.00 0.00 3.86
737 750 1.152830 ATCCAACGGCCCAACAGTT 59.847 52.632 0.00 0.00 37.12 3.16
913 933 1.637086 CGTTGTTTAATTGACGCAGCG 59.363 47.619 14.82 14.82 0.00 5.18
1170 1190 3.057548 TACGAGCCGGCGTTCTCA 61.058 61.111 23.20 2.19 42.71 3.27
1251 1271 4.796231 CGCAACCGCTACTCCGCT 62.796 66.667 0.00 0.00 35.30 5.52
2052 2081 2.349817 GGTCGCATTCTTCAACAGTGTG 60.350 50.000 0.00 0.00 0.00 3.82
2123 2167 9.396022 ACATCTTCGTTACAATCTCCATTATTT 57.604 29.630 0.00 0.00 0.00 1.40
2225 2273 6.554419 GCATCACAAATGCATACAAGAAGTA 58.446 36.000 0.00 0.00 44.00 2.24
2251 2299 3.375699 AGTATGAGTCGGATTTGGTCCT 58.624 45.455 0.00 0.00 45.46 3.85
2299 2348 4.607293 AGACTGATGACACTGCAAAGTA 57.393 40.909 0.00 0.00 0.00 2.24
2360 2416 1.107114 AGTGGCATCTACTCTCCGTG 58.893 55.000 0.00 0.00 0.00 4.94
2404 2460 4.402056 TTCGTGAGAGAAGGAAACAACT 57.598 40.909 0.00 0.00 43.69 3.16
2496 2558 9.747898 TTATTAACACCACTTCAGGTCAATAAT 57.252 29.630 0.00 0.00 40.77 1.28
2650 2720 7.411480 CGTTAAACTCGTGATCATTAAAGCTCA 60.411 37.037 0.00 0.00 0.00 4.26
2655 2725 4.870426 TCGTGATCATTAAAGCTCAGTTCC 59.130 41.667 0.00 0.00 0.00 3.62
2782 2856 4.623814 CTGAAATCCGCCAGCTCA 57.376 55.556 0.00 0.00 0.00 4.26
3041 3138 1.152247 AGACAGCCTCTCCACCACA 60.152 57.895 0.00 0.00 0.00 4.17
3091 3190 3.391382 GAGGGGCAGTGTAGCGGT 61.391 66.667 0.00 0.00 34.64 5.68
3134 3251 2.639327 GCGATTTGCCTGCCTTGGT 61.639 57.895 0.00 0.00 37.76 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 104 3.424433 GCGTGTACTACATCCAAGTTTGC 60.424 47.826 0.00 0.00 0.00 3.68
103 105 3.181534 CGCGTGTACTACATCCAAGTTTG 60.182 47.826 0.00 0.00 0.00 2.93
107 109 2.096980 TCTCGCGTGTACTACATCCAAG 59.903 50.000 5.77 0.00 0.00 3.61
108 110 2.086094 TCTCGCGTGTACTACATCCAA 58.914 47.619 5.77 0.00 0.00 3.53
109 111 1.741528 TCTCGCGTGTACTACATCCA 58.258 50.000 5.77 0.00 0.00 3.41
123 127 2.678324 GGAATGTAGTGGCTATCTCGC 58.322 52.381 0.00 0.00 0.00 5.03
150 154 7.841282 TTTTCTTTGGTATGTACCCAATGAA 57.159 32.000 18.49 18.49 46.19 2.57
189 196 5.756195 ACCCATGATAATTTGATGTCACG 57.244 39.130 0.00 0.00 0.00 4.35
277 286 0.395311 TCGTCCTCCTACCTGCGAAT 60.395 55.000 0.00 0.00 0.00 3.34
285 294 0.814812 CCTCCTCGTCGTCCTCCTAC 60.815 65.000 0.00 0.00 0.00 3.18
333 342 1.001633 GACCGGACCTAGCAAAAGTGA 59.998 52.381 9.46 0.00 0.00 3.41
391 400 4.511082 ACAATGGCAAAATTTGTACACTGC 59.489 37.500 7.60 2.33 32.09 4.40
412 421 4.024809 TGTTTTGCGTTGAATGATCGTACA 60.025 37.500 0.00 0.00 0.00 2.90
487 496 4.829064 TGAATAAAACTTGCGCTGTCTT 57.171 36.364 9.73 3.34 0.00 3.01
554 563 4.848357 CAGGCCTAAGAAAAGATGGAGAA 58.152 43.478 3.98 0.00 0.00 2.87
686 699 2.671070 CTGCCCAGTCAATCGGGT 59.329 61.111 0.00 0.00 45.07 5.28
737 750 3.294493 GCTGCGACCAAGGGCAAA 61.294 61.111 0.00 0.00 38.94 3.68
913 933 0.810016 AGAAGAGACCGGCTACGTTC 59.190 55.000 0.00 4.45 38.78 3.95
1251 1271 1.414919 GGGTGCATGGATACGAAGGTA 59.585 52.381 0.00 0.00 42.51 3.08
1425 1448 1.518572 GCACGCATAGTAGCACCGT 60.519 57.895 0.00 0.00 0.00 4.83
1428 1451 0.026803 GCTTGCACGCATAGTAGCAC 59.973 55.000 10.77 0.00 36.89 4.40
2052 2081 4.991153 TCATCACCAGATCACTCTGTAC 57.009 45.455 0.00 0.00 46.33 2.90
2123 2167 2.823924 TTAGTACCACTTCGCTTGCA 57.176 45.000 0.00 0.00 0.00 4.08
2225 2273 5.745227 ACCAAATCCGACTCATACTTGAAT 58.255 37.500 0.00 0.00 0.00 2.57
2251 2299 5.521906 TTTGTTTTCATCGATGTCCCAAA 57.478 34.783 24.09 21.81 0.00 3.28
2360 2416 0.534873 GAGAGAGGCTCAACCAGGAC 59.465 60.000 18.26 0.00 43.38 3.85
2404 2460 8.491331 TGAATTTGTCGACATCATCAAGATTA 57.509 30.769 20.80 0.00 33.72 1.75
2766 2840 1.746615 GCTGAGCTGGCGGATTTCA 60.747 57.895 0.00 0.00 0.00 2.69
2846 2924 2.908073 CGTGCTTTTCCCTTGCGCT 61.908 57.895 9.73 0.00 35.36 5.92
3041 3138 2.046285 CCGAAAAATCGCCCAGCCT 61.046 57.895 0.00 0.00 0.00 4.58
3071 3170 3.391382 GCTACACTGCCCCTCCGT 61.391 66.667 0.00 0.00 0.00 4.69
3131 3248 0.813184 GTCGTCCGAGTCCATTACCA 59.187 55.000 0.00 0.00 0.00 3.25
3134 3251 3.157727 TCGTCGTCCGAGTCCATTA 57.842 52.632 0.00 0.00 41.60 1.90


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

AutoCloner maintained by Alex Coulton.