Multiple sequence alignment - TraesCS5D01G370800

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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 TraesCS5D01G370800 chr5D 100.000 4766 0 0 1 4766 445406746 445401981 0.000000e+00 8802.0
1 TraesCS5D01G370800 chr5D 84.105 648 94 3 2375 3016 445490906 445490262 6.780000e-173 617.0
2 TraesCS5D01G370800 chr5D 81.412 694 101 17 852 1536 445486178 445485504 4.200000e-150 542.0
3 TraesCS5D01G370800 chr5D 83.689 515 73 8 1000 1513 437015194 437015698 4.320000e-130 475.0
4 TraesCS5D01G370800 chr5D 84.943 352 39 10 3172 3514 445489986 445489640 1.270000e-90 344.0
5 TraesCS5D01G370800 chr5D 77.500 480 87 10 3074 3544 436983203 436983670 7.860000e-68 268.0
6 TraesCS5D01G370800 chr5A 96.509 4154 115 16 1 4141 563257419 563253283 0.000000e+00 6841.0
7 TraesCS5D01G370800 chr5A 82.972 646 110 0 2373 3018 552268803 552269448 6.870000e-163 584.0
8 TraesCS5D01G370800 chr5A 82.576 528 81 8 1000 1526 552298393 552298910 5.620000e-124 455.0
9 TraesCS5D01G370800 chr5B 96.494 3936 99 11 852 4766 543246501 543242584 0.000000e+00 6468.0
10 TraesCS5D01G370800 chr5B 89.153 590 34 16 134 712 543247133 543246563 0.000000e+00 708.0
11 TraesCS5D01G370800 chr5B 84.462 650 92 5 2373 3016 543298640 543297994 2.420000e-177 632.0
12 TraesCS5D01G370800 chr5B 84.000 650 81 12 985 1627 543282521 543281888 1.900000e-168 603.0
13 TraesCS5D01G370800 chr5B 83.462 647 105 2 2373 3018 531193753 531194398 6.820000e-168 601.0
14 TraesCS5D01G370800 chr5B 82.353 595 88 13 1010 1600 543275902 543275321 7.120000e-138 501.0
15 TraesCS5D01G370800 chr5B 82.765 528 80 8 1000 1526 531204685 531205202 1.210000e-125 460.0
16 TraesCS5D01G370800 chr5B 89.179 268 23 5 3252 3514 543297683 543297417 3.560000e-86 329.0
17 TraesCS5D01G370800 chr5B 78.085 470 82 10 3095 3555 531194625 531195082 1.310000e-70 278.0
18 TraesCS5D01G370800 chr5B 85.317 252 34 2 3246 3494 543270125 543269874 1.700000e-64 257.0
19 TraesCS5D01G370800 chr5B 90.351 114 10 1 24 137 543248257 543248145 1.070000e-31 148.0
20 TraesCS5D01G370800 chr5B 89.000 100 11 0 2186 2285 531205826 531205925 1.800000e-24 124.0
21 TraesCS5D01G370800 chr5B 88.660 97 11 0 2178 2274 543281415 543281319 8.380000e-23 119.0
22 TraesCS5D01G370800 chr5B 80.420 143 23 5 1954 2094 543281663 543281524 2.350000e-18 104.0
23 TraesCS5D01G370800 chr1B 82.243 749 116 13 1002 1746 553015703 553014968 8.700000e-177 630.0
24 TraesCS5D01G370800 chr1B 81.604 636 115 2 2358 2992 553014263 553013629 4.230000e-145 525.0
25 TraesCS5D01G370800 chr1D 80.798 802 142 11 2358 3150 410458693 410457895 6.780000e-173 617.0
26 TraesCS5D01G370800 chr4D 80.401 847 106 35 3061 3893 2975631 2976431 1.480000e-164 590.0
27 TraesCS5D01G370800 chr4D 84.241 514 71 6 2470 2977 2975080 2975589 4.290000e-135 492.0
28 TraesCS5D01G370800 chr4D 80.238 420 77 2 3072 3485 1689482 1689901 1.290000e-80 311.0
29 TraesCS5D01G370800 chr7A 83.463 641 88 10 985 1624 7817244 7817867 8.890000e-162 580.0
30 TraesCS5D01G370800 chr7A 90.411 73 7 0 2189 2261 7818561 7818633 3.930000e-16 97.1
31 TraesCS5D01G370800 chr3A 83.333 162 24 2 3766 3927 13553334 13553492 3.840000e-31 147.0
32 TraesCS5D01G370800 chr3B 72.281 469 120 9 4171 4634 586757423 586757886 2.310000e-28 137.0
33 TraesCS5D01G370800 chr2B 72.816 206 47 8 4209 4409 657548034 657548235 1.430000e-05 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 TraesCS5D01G370800 chr5D 445401981 445406746 4765 True 8802.000000 8802 100.000000 1 4766 1 chr5D.!!$R1 4765
1 TraesCS5D01G370800 chr5D 445485504 445490906 5402 True 501.000000 617 83.486667 852 3514 3 chr5D.!!$R2 2662
2 TraesCS5D01G370800 chr5D 437015194 437015698 504 False 475.000000 475 83.689000 1000 1513 1 chr5D.!!$F2 513
3 TraesCS5D01G370800 chr5A 563253283 563257419 4136 True 6841.000000 6841 96.509000 1 4141 1 chr5A.!!$R1 4140
4 TraesCS5D01G370800 chr5A 552268803 552269448 645 False 584.000000 584 82.972000 2373 3018 1 chr5A.!!$F1 645
5 TraesCS5D01G370800 chr5A 552298393 552298910 517 False 455.000000 455 82.576000 1000 1526 1 chr5A.!!$F2 526
6 TraesCS5D01G370800 chr5B 543242584 543248257 5673 True 2441.333333 6468 91.999333 24 4766 3 chr5B.!!$R3 4742
7 TraesCS5D01G370800 chr5B 543275321 543275902 581 True 501.000000 501 82.353000 1010 1600 1 chr5B.!!$R2 590
8 TraesCS5D01G370800 chr5B 543297417 543298640 1223 True 480.500000 632 86.820500 2373 3514 2 chr5B.!!$R5 1141
9 TraesCS5D01G370800 chr5B 531193753 531195082 1329 False 439.500000 601 80.773500 2373 3555 2 chr5B.!!$F1 1182
10 TraesCS5D01G370800 chr5B 531204685 531205925 1240 False 292.000000 460 85.882500 1000 2285 2 chr5B.!!$F2 1285
11 TraesCS5D01G370800 chr5B 543281319 543282521 1202 True 275.333333 603 84.360000 985 2274 3 chr5B.!!$R4 1289
12 TraesCS5D01G370800 chr1B 553013629 553015703 2074 True 577.500000 630 81.923500 1002 2992 2 chr1B.!!$R1 1990
13 TraesCS5D01G370800 chr1D 410457895 410458693 798 True 617.000000 617 80.798000 2358 3150 1 chr1D.!!$R1 792
14 TraesCS5D01G370800 chr4D 2975080 2976431 1351 False 541.000000 590 82.321000 2470 3893 2 chr4D.!!$F2 1423
15 TraesCS5D01G370800 chr7A 7817244 7818633 1389 False 338.550000 580 86.937000 985 2261 2 chr7A.!!$F1 1276

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
283 1301 0.107654 ACGCCCTAAATCACTGCTCC 60.108 55.000 0.00 0.00 0.0 4.70 F
615 1637 0.684535 TTCGAGTTCATCCACCTGCA 59.315 50.000 0.00 0.00 0.0 4.41 F
1230 2300 2.298729 GAGGAGTCAGGATCATGGTAGC 59.701 54.545 7.64 0.00 0.0 3.58 F
1663 2868 0.396435 ACAAGAAGGTGATGCGGTCA 59.604 50.000 0.00 0.00 0.0 4.02 F
2727 4525 1.704641 TCTACTACATGGGCGCATCT 58.295 50.000 14.18 4.87 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 2613 0.532573 GTTCTCCTCGGAGCATGACA 59.467 55.000 8.11 0.0 41.71 3.58 R
1663 2868 2.917713 TAATTGTCAGCCCCATGGTT 57.082 45.000 11.73 0.0 0.00 3.67 R
2730 4528 1.133025 GCAGTGGCACATTGGTGATAC 59.867 52.381 21.41 0.0 46.54 2.24 R
3387 5448 0.253347 AGGTCTCCATCCCCATGTGT 60.253 55.000 0.00 0.0 0.00 3.72 R
4091 6191 0.323725 GGCGGGCATCCATGGAATAT 60.324 55.000 20.67 0.0 0.00 1.28 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
42 43 1.880340 CGCGCCAGAAGATCAGTCC 60.880 63.158 0.00 0.00 0.00 3.85
107 109 6.584185 TTGCACTCTAGGGTTTATTTTTCC 57.416 37.500 0.00 0.00 0.00 3.13
226 1242 3.213402 CTCTCCGACGGCCTCCTC 61.213 72.222 9.66 0.00 0.00 3.71
282 1300 1.134670 AGACGCCCTAAATCACTGCTC 60.135 52.381 0.00 0.00 0.00 4.26
283 1301 0.107654 ACGCCCTAAATCACTGCTCC 60.108 55.000 0.00 0.00 0.00 4.70
285 1303 1.440145 GCCCTAAATCACTGCTCCGC 61.440 60.000 0.00 0.00 0.00 5.54
375 1393 4.694233 AGCGGCAGCCACAGAGTG 62.694 66.667 13.30 0.00 46.67 3.51
615 1637 0.684535 TTCGAGTTCATCCACCTGCA 59.315 50.000 0.00 0.00 0.00 4.41
637 1663 8.956533 TGCAACTGCTAGTATTAACAATATCA 57.043 30.769 2.95 0.00 42.66 2.15
663 1689 3.858503 GCATTGCTCCACCTTTCTGAAAC 60.859 47.826 0.16 0.00 0.00 2.78
744 1797 8.837788 TTATAACAATGCAGATCATCTAGGTG 57.162 34.615 0.00 0.00 33.40 4.00
835 1888 3.950395 AGAGCAAAAGATATGGTTGAGCC 59.050 43.478 0.00 0.00 37.90 4.70
1230 2300 2.298729 GAGGAGTCAGGATCATGGTAGC 59.701 54.545 7.64 0.00 0.00 3.58
1537 2613 3.108847 ACAGCCTAGTAAGCTCTTCCT 57.891 47.619 0.00 0.00 38.95 3.36
1663 2868 0.396435 ACAAGAAGGTGATGCGGTCA 59.604 50.000 0.00 0.00 0.00 4.02
2701 4499 2.040213 CTGGCACATCGCAACGGATC 62.040 60.000 0.00 0.00 45.17 3.36
2727 4525 1.704641 TCTACTACATGGGCGCATCT 58.295 50.000 14.18 4.87 0.00 2.90
3387 5448 4.948004 ACGTATATCTGTCTCCTGTTGTCA 59.052 41.667 0.00 0.00 0.00 3.58
3568 5635 4.340381 ACTCTGCATTCCATCTTTATTGCC 59.660 41.667 0.00 0.00 0.00 4.52
3764 5834 0.251916 CCGCCACCCTTGAGACATTA 59.748 55.000 0.00 0.00 0.00 1.90
3768 5838 2.501723 GCCACCCTTGAGACATTAGAGA 59.498 50.000 0.00 0.00 0.00 3.10
3951 6029 2.415893 CCGGATTGTTTCATGCTTGTCC 60.416 50.000 0.00 0.00 0.00 4.02
4053 6137 5.042593 TGTGTTGTTAGAGCTGCAAAATTG 58.957 37.500 1.02 0.00 0.00 2.32
4091 6191 7.238710 TCTGTAGTATAGTATGGATGCCAGAA 58.761 38.462 0.00 0.00 36.75 3.02
4094 6194 9.715119 TGTAGTATAGTATGGATGCCAGAATAT 57.285 33.333 6.35 6.35 39.01 1.28
4204 7782 7.363268 GGAGGTGAAGAATATTTTGCAAGTCAT 60.363 37.037 0.00 0.00 0.00 3.06
4227 7805 2.065799 AGGAGGTGTTTGATCCCAAGT 58.934 47.619 0.00 0.00 33.30 3.16
4231 7809 4.200092 GAGGTGTTTGATCCCAAGTATCC 58.800 47.826 0.00 0.00 33.23 2.59
4274 7852 5.045066 GGGTAGAGTCCATAAAGGGAAGTTT 60.045 44.000 0.00 0.00 39.05 2.66
4283 7861 6.490040 TCCATAAAGGGAAGTTTCAGACTTTG 59.510 38.462 13.71 4.63 41.81 2.77
4342 7920 4.711846 TGAACGCTATATGGCCTCATCTAT 59.288 41.667 3.32 0.00 34.96 1.98
4371 7949 9.699410 AGGAAATATTGATTAAATCTGTGGTCA 57.301 29.630 0.00 0.00 0.00 4.02
4428 8010 6.627690 AACTTTCGTATTCTATGTGTGACG 57.372 37.500 0.00 0.00 0.00 4.35
4474 8056 0.698238 TGGTGGGGAGTTGAGAATGG 59.302 55.000 0.00 0.00 0.00 3.16
4589 8965 1.180029 CATTGCTGGCTAAACAGGCT 58.820 50.000 0.00 0.00 38.90 4.58
4718 9094 2.230266 GGTTTGGCGTGGTATTGAACAT 59.770 45.455 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.080093 CGCGCCTCCTTGTCTGTTA 60.080 57.895 0.00 0.00 0.00 2.41
226 1242 1.263356 TGGGTAGGACAAGACGGAAG 58.737 55.000 0.00 0.00 0.00 3.46
260 1276 1.398390 GCAGTGATTTAGGGCGTCTTG 59.602 52.381 0.00 0.00 0.00 3.02
265 1283 1.154205 CGGAGCAGTGATTTAGGGCG 61.154 60.000 0.00 0.00 0.00 6.13
334 1352 4.845580 ATCCGCTTGCTCCCTGCG 62.846 66.667 0.00 0.00 46.63 5.18
335 1353 3.207669 CATCCGCTTGCTCCCTGC 61.208 66.667 0.00 0.00 43.25 4.85
336 1354 2.515523 CCATCCGCTTGCTCCCTG 60.516 66.667 0.00 0.00 0.00 4.45
337 1355 3.801997 CCCATCCGCTTGCTCCCT 61.802 66.667 0.00 0.00 0.00 4.20
339 1357 2.203126 CTCCCATCCGCTTGCTCC 60.203 66.667 0.00 0.00 0.00 4.70
340 1358 2.203126 CCTCCCATCCGCTTGCTC 60.203 66.667 0.00 0.00 0.00 4.26
375 1393 0.106217 CTGGAGAGAGAGGAGTCCCC 60.106 65.000 5.25 0.00 0.00 4.81
500 1518 2.685380 CCTCCTTGCTCCGTCCCT 60.685 66.667 0.00 0.00 0.00 4.20
637 1663 3.698040 CAGAAAGGTGGAGCAATGCTATT 59.302 43.478 8.12 0.00 39.88 1.73
642 1668 3.305608 GGTTTCAGAAAGGTGGAGCAATG 60.306 47.826 0.00 0.00 0.00 2.82
663 1689 7.492020 TGAAAAAGATGCATATTTCCAATTCGG 59.508 33.333 18.93 0.00 32.21 4.30
744 1797 7.136772 ACCAAATTACTCGTTAAAAGCTTCAC 58.863 34.615 0.00 0.00 0.00 3.18
835 1888 4.130118 GGTAATCACACTTAGGATGGCTG 58.870 47.826 0.00 0.00 0.00 4.85
1230 2300 2.612212 ACTGTTGTTTGCAGAAGTACCG 59.388 45.455 0.00 0.00 37.40 4.02
1537 2613 0.532573 GTTCTCCTCGGAGCATGACA 59.467 55.000 8.11 0.00 41.71 3.58
1663 2868 2.917713 TAATTGTCAGCCCCATGGTT 57.082 45.000 11.73 0.00 0.00 3.67
1852 3147 9.768215 TCTCCTTTTCTCCATTATTTGGTTTAT 57.232 29.630 0.00 0.00 46.52 1.40
2701 4499 2.544694 CGCCCATGTAGTAGAAGCAGAG 60.545 54.545 0.00 0.00 0.00 3.35
2730 4528 1.133025 GCAGTGGCACATTGGTGATAC 59.867 52.381 21.41 0.00 46.54 2.24
2731 4529 1.462616 GCAGTGGCACATTGGTGATA 58.537 50.000 21.41 0.00 46.54 2.15
2965 4768 5.632347 CCTTGACAATTTTCTTGAGTGATGC 59.368 40.000 0.00 0.00 0.00 3.91
3387 5448 0.253347 AGGTCTCCATCCCCATGTGT 60.253 55.000 0.00 0.00 0.00 3.72
3702 5770 6.815641 CCTGGTAGATCACATATTCACATAGC 59.184 42.308 0.00 0.00 0.00 2.97
3747 5817 2.501723 TCTCTAATGTCTCAAGGGTGGC 59.498 50.000 0.00 0.00 0.00 5.01
3764 5834 1.207570 CAGCAGCTTCATGAGGTCTCT 59.792 52.381 6.70 0.00 32.70 3.10
3768 5838 4.315588 GCAGCAGCTTCATGAGGT 57.684 55.556 6.70 0.00 37.91 3.85
3951 6029 8.307483 AGATGGAGATAGGTAATGAACAATACG 58.693 37.037 0.00 0.00 0.00 3.06
4010 6088 5.163237 ACACACAAACAGACTGGTAGGTAAT 60.163 40.000 7.51 0.00 0.00 1.89
4053 6137 7.932335 ACTATACTACAGAGTACAGACATTGC 58.068 38.462 0.00 0.00 41.01 3.56
4091 6191 0.323725 GGCGGGCATCCATGGAATAT 60.324 55.000 20.67 0.00 0.00 1.28
4094 6194 4.521292 GGGCGGGCATCCATGGAA 62.521 66.667 20.67 1.96 0.00 3.53
4204 7782 2.061848 TGGGATCAAACACCTCCTGAA 58.938 47.619 0.00 0.00 0.00 3.02
4257 7835 5.561679 AGTCTGAAACTTCCCTTTATGGAC 58.438 41.667 0.00 0.00 33.78 4.02
4274 7852 3.988976 AGCCTAGATTGCAAAGTCTGA 57.011 42.857 11.96 0.00 0.00 3.27
4305 7883 2.093973 AGCGTTCACTCCAATCCACTAG 60.094 50.000 0.00 0.00 0.00 2.57
4366 7944 1.668826 AGTGGGAATAGCCTTGACCA 58.331 50.000 0.00 0.00 36.66 4.02
4369 7947 5.450818 AACATAAGTGGGAATAGCCTTGA 57.549 39.130 0.00 0.00 36.66 3.02
4371 7949 7.147302 ACTCATAACATAAGTGGGAATAGCCTT 60.147 37.037 0.00 0.00 36.66 4.35
4410 7992 3.943381 AGGTCGTCACACATAGAATACGA 59.057 43.478 0.00 0.00 37.05 3.43
4411 7993 4.201881 TGAGGTCGTCACACATAGAATACG 60.202 45.833 0.00 0.00 0.00 3.06
4428 8010 1.667724 CCGCATCATTCTTGTGAGGTC 59.332 52.381 0.00 0.00 32.79 3.85
4474 8056 2.899900 ACCCAAGCCATTTTCCTTCTTC 59.100 45.455 0.00 0.00 0.00 2.87
4582 8958 4.640771 TCAATAAGTCTCCAAGCCTGTT 57.359 40.909 0.00 0.00 0.00 3.16
4589 8965 4.224147 TCCGGTTGATCAATAAGTCTCCAA 59.776 41.667 12.12 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.