Multiple sequence alignment - TraesCS3D01G169100

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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 TraesCS3D01G169100 chr3D 100.000 4531 0 0 1 4531 144778767 144783297 0.000000e+00 8368.0
1 TraesCS3D01G169100 chr3D 97.563 2052 20 5 608 2636 145201682 145199638 0.000000e+00 3485.0
2 TraesCS3D01G169100 chr3D 94.190 568 21 4 2634 3194 145199364 145198802 0.000000e+00 856.0
3 TraesCS3D01G169100 chr3D 97.449 392 6 3 3197 3586 145198716 145198327 0.000000e+00 665.0
4 TraesCS3D01G169100 chr3B 97.013 2712 63 6 608 3309 205465661 205462958 0.000000e+00 4543.0
5 TraesCS3D01G169100 chr3B 96.617 1685 39 7 1914 3586 205686215 205684537 0.000000e+00 2780.0
6 TraesCS3D01G169100 chr3B 97.420 659 16 1 608 1265 205692217 205691559 0.000000e+00 1122.0
7 TraesCS3D01G169100 chr3B 96.347 219 7 1 3368 3586 205462970 205462753 4.310000e-95 359.0
8 TraesCS3D01G169100 chr7D 98.638 881 8 2 3655 4531 184577859 184578739 0.000000e+00 1557.0
9 TraesCS3D01G169100 chr7D 97.893 807 8 4 3654 4457 93949572 93950372 0.000000e+00 1387.0
10 TraesCS3D01G169100 chr7D 97.767 806 15 2 3655 4457 95101951 95101146 0.000000e+00 1386.0
11 TraesCS3D01G169100 chr7D 80.174 575 92 12 3649 4210 412125414 412125979 1.170000e-110 411.0
12 TraesCS3D01G169100 chr7D 98.039 51 1 0 4481 4531 93950372 93950422 6.240000e-14 89.8
13 TraesCS3D01G169100 chr7D 98.039 51 1 0 4481 4531 95101146 95101096 6.240000e-14 89.8
14 TraesCS3D01G169100 chr1D 98.521 879 7 2 3654 4531 224139812 224140685 0.000000e+00 1546.0
15 TraesCS3D01G169100 chr1D 96.760 679 20 2 3652 4328 197521065 197520387 0.000000e+00 1131.0
16 TraesCS3D01G169100 chr1D 95.694 209 8 1 4324 4531 197510982 197510774 7.260000e-88 335.0
17 TraesCS3D01G169100 chr2A 95.795 880 30 4 3659 4531 11029979 11030858 0.000000e+00 1413.0
18 TraesCS3D01G169100 chr5B 97.209 609 17 0 1 609 426624213 426624821 0.000000e+00 1031.0
19 TraesCS3D01G169100 chr5B 95.292 616 21 3 1 609 468892386 468893000 0.000000e+00 970.0
20 TraesCS3D01G169100 chrUn 94.272 611 27 4 1 609 342225253 342224649 0.000000e+00 928.0
21 TraesCS3D01G169100 chr6B 93.954 612 28 5 1 609 704701341 704700736 0.000000e+00 917.0
22 TraesCS3D01G169100 chr6B 79.412 340 44 16 3842 4161 32289410 32289743 2.740000e-52 217.0
23 TraesCS3D01G169100 chr6B 97.414 116 3 0 494 609 704704271 704704386 9.940000e-47 198.0
24 TraesCS3D01G169100 chr2B 93.257 608 39 2 3654 4259 788523936 788523329 0.000000e+00 894.0
25 TraesCS3D01G169100 chr2B 90.141 284 23 4 4251 4531 788522601 788522320 9.260000e-97 364.0
26 TraesCS3D01G169100 chr4A 93.506 539 21 7 1 539 631135301 631134777 0.000000e+00 789.0
27 TraesCS3D01G169100 chr4A 92.153 548 30 3 1 548 631161169 631160635 0.000000e+00 761.0
28 TraesCS3D01G169100 chr4A 85.714 371 24 13 1 371 9906253 9905912 9.260000e-97 364.0
29 TraesCS3D01G169100 chr1A 88.033 610 36 18 1 609 531691717 531691144 0.000000e+00 688.0
30 TraesCS3D01G169100 chr6D 87.643 437 23 3 175 610 3833330 3833736 3.170000e-131 479.0
31 TraesCS3D01G169100 chr6D 93.536 263 17 0 144 406 430310162 430309900 4.250000e-105 392.0
32 TraesCS3D01G169100 chr6D 97.357 227 6 0 1 227 430310336 430310110 1.980000e-103 387.0
33 TraesCS3D01G169100 chr6D 96.216 185 7 0 1 185 3833187 3833371 2.050000e-78 303.0
34 TraesCS3D01G169100 chr6D 97.661 171 4 0 425 595 430309689 430309519 1.230000e-75 294.0
35 TraesCS3D01G169100 chr1B 86.031 451 30 13 1 451 435184857 435184440 1.920000e-123 453.0
36 TraesCS3D01G169100 chr1B 92.073 164 13 0 447 610 435175738 435175575 9.800000e-57 231.0
37 TraesCS3D01G169100 chr6A 100.000 29 0 0 3585 3613 502527944 502527972 2.000000e-03 54.7


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 TraesCS3D01G169100 chr3D 144778767 144783297 4530 False 8368.000000 8368 100.000000 1 4531 1 chr3D.!!$F1 4530
1 TraesCS3D01G169100 chr3D 145198327 145201682 3355 True 1668.666667 3485 96.400667 608 3586 3 chr3D.!!$R1 2978
2 TraesCS3D01G169100 chr3B 205684537 205686215 1678 True 2780.000000 2780 96.617000 1914 3586 1 chr3B.!!$R1 1672
3 TraesCS3D01G169100 chr3B 205462753 205465661 2908 True 2451.000000 4543 96.680000 608 3586 2 chr3B.!!$R3 2978
4 TraesCS3D01G169100 chr3B 205691559 205692217 658 True 1122.000000 1122 97.420000 608 1265 1 chr3B.!!$R2 657
5 TraesCS3D01G169100 chr7D 184577859 184578739 880 False 1557.000000 1557 98.638000 3655 4531 1 chr7D.!!$F1 876
6 TraesCS3D01G169100 chr7D 93949572 93950422 850 False 738.400000 1387 97.966000 3654 4531 2 chr7D.!!$F3 877
7 TraesCS3D01G169100 chr7D 95101096 95101951 855 True 737.900000 1386 97.903000 3655 4531 2 chr7D.!!$R1 876
8 TraesCS3D01G169100 chr7D 412125414 412125979 565 False 411.000000 411 80.174000 3649 4210 1 chr7D.!!$F2 561
9 TraesCS3D01G169100 chr1D 224139812 224140685 873 False 1546.000000 1546 98.521000 3654 4531 1 chr1D.!!$F1 877
10 TraesCS3D01G169100 chr1D 197520387 197521065 678 True 1131.000000 1131 96.760000 3652 4328 1 chr1D.!!$R2 676
11 TraesCS3D01G169100 chr2A 11029979 11030858 879 False 1413.000000 1413 95.795000 3659 4531 1 chr2A.!!$F1 872
12 TraesCS3D01G169100 chr5B 426624213 426624821 608 False 1031.000000 1031 97.209000 1 609 1 chr5B.!!$F1 608
13 TraesCS3D01G169100 chr5B 468892386 468893000 614 False 970.000000 970 95.292000 1 609 1 chr5B.!!$F2 608
14 TraesCS3D01G169100 chrUn 342224649 342225253 604 True 928.000000 928 94.272000 1 609 1 chrUn.!!$R1 608
15 TraesCS3D01G169100 chr6B 704700736 704701341 605 True 917.000000 917 93.954000 1 609 1 chr6B.!!$R1 608
16 TraesCS3D01G169100 chr2B 788522320 788523936 1616 True 629.000000 894 91.699000 3654 4531 2 chr2B.!!$R1 877
17 TraesCS3D01G169100 chr4A 631134777 631135301 524 True 789.000000 789 93.506000 1 539 1 chr4A.!!$R2 538
18 TraesCS3D01G169100 chr4A 631160635 631161169 534 True 761.000000 761 92.153000 1 548 1 chr4A.!!$R3 547
19 TraesCS3D01G169100 chr1A 531691144 531691717 573 True 688.000000 688 88.033000 1 609 1 chr1A.!!$R1 608
20 TraesCS3D01G169100 chr6D 3833187 3833736 549 False 391.000000 479 91.929500 1 610 2 chr6D.!!$F1 609
21 TraesCS3D01G169100 chr6D 430309519 430310336 817 True 357.666667 392 96.184667 1 595 3 chr6D.!!$R1 594

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
229 301 1.756950 AGCTCCACGGCCTCGATAA 60.757 57.895 0.00 0.0 40.11 1.75 F
1098 1387 1.789523 CCCCCTTCGTTGGAGATAGA 58.210 55.000 0.00 0.0 0.00 1.98 F
1597 1887 3.270433 ACCTGATGGTCTGGATTCCAATT 59.730 43.478 6.88 0.0 44.78 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1887 0.250858 CCTGGGTCAATGCACAGACA 60.251 55.0 18.71 2.55 42.22 3.41 R
2051 2341 0.536460 GAACGGGCTGGGAACAAAGA 60.536 55.0 0.00 0.00 42.06 2.52 R
3587 4244 0.461961 AGTCTGATTCCTAGCGGTGC 59.538 55.0 0.00 0.00 0.00 5.01 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
229 301 1.756950 AGCTCCACGGCCTCGATAA 60.757 57.895 0.00 0.00 40.11 1.75
994 1283 3.233919 TACCTCCACTGGCCCGAGT 62.234 63.158 0.00 0.00 0.00 4.18
1098 1387 1.789523 CCCCCTTCGTTGGAGATAGA 58.210 55.000 0.00 0.00 0.00 1.98
1597 1887 3.270433 ACCTGATGGTCTGGATTCCAATT 59.730 43.478 6.88 0.00 44.78 2.32
1987 2277 6.367422 GTCAACCAGTCTCTACATCTTTGAAG 59.633 42.308 0.00 0.00 0.00 3.02
1988 2278 6.267699 TCAACCAGTCTCTACATCTTTGAAGA 59.732 38.462 0.00 0.00 39.78 2.87
1989 2279 6.672266 ACCAGTCTCTACATCTTTGAAGAA 57.328 37.500 0.00 0.00 38.77 2.52
2051 2341 3.782523 TGGAGATCATTTCCTGGCTACTT 59.217 43.478 0.00 0.00 35.67 2.24
2603 2893 5.583061 TCATGCCGTTGAACTATATTCGTTT 59.417 36.000 0.00 0.00 0.00 3.60
2621 2911 3.548818 CGTTTTGACTTTGGAGAGGCAAG 60.549 47.826 0.00 0.00 44.95 4.01
2622 2912 1.609208 TTGACTTTGGAGAGGCAAGC 58.391 50.000 0.00 0.00 39.68 4.01
2695 3260 3.194329 TCAGAGCCGCCAGAATATGATAG 59.806 47.826 0.00 0.00 0.00 2.08
2974 3546 3.044894 TGAAGGGCTTGGGAAATTTTGT 58.955 40.909 0.00 0.00 0.00 2.83
3056 3628 1.098050 GCATCAATCGAAACAGCCCT 58.902 50.000 0.00 0.00 0.00 5.19
3223 3878 4.469227 AGGTTCTGAACTAGTCATGCAGAT 59.531 41.667 19.05 2.91 35.73 2.90
3376 4033 3.181443 GCCTAGGGTTGTATATTGGTGCT 60.181 47.826 11.72 0.00 0.00 4.40
3514 4171 6.204495 AGACTTGAGCAAGCTAAAGAAAAGAG 59.796 38.462 22.80 0.00 41.99 2.85
3586 4243 8.637196 AGAAGAAACCAGGAATACTTTTTAGG 57.363 34.615 0.00 0.00 0.00 2.69
3587 4244 7.670140 AGAAGAAACCAGGAATACTTTTTAGGG 59.330 37.037 0.00 0.00 0.00 3.53
3588 4245 5.715279 AGAAACCAGGAATACTTTTTAGGGC 59.285 40.000 0.00 0.00 0.00 5.19
3589 4246 4.668138 ACCAGGAATACTTTTTAGGGCA 57.332 40.909 0.00 0.00 0.00 5.36
3590 4247 4.341487 ACCAGGAATACTTTTTAGGGCAC 58.659 43.478 0.00 0.00 0.00 5.01
3602 4259 2.908015 GGGCACCGCTAGGAATCA 59.092 61.111 0.00 0.00 40.86 2.57
3603 4260 1.227674 GGGCACCGCTAGGAATCAG 60.228 63.158 0.00 0.00 40.86 2.90
3604 4261 1.686325 GGGCACCGCTAGGAATCAGA 61.686 60.000 0.00 0.00 40.86 3.27
3605 4262 0.530870 GGCACCGCTAGGAATCAGAC 60.531 60.000 0.00 0.00 41.02 3.51
3606 4263 0.461961 GCACCGCTAGGAATCAGACT 59.538 55.000 0.00 0.00 41.02 3.24
3607 4264 1.681793 GCACCGCTAGGAATCAGACTA 59.318 52.381 0.00 0.00 41.02 2.59
3608 4265 2.544069 GCACCGCTAGGAATCAGACTAC 60.544 54.545 0.00 0.00 41.02 2.73
3609 4266 2.952978 CACCGCTAGGAATCAGACTACT 59.047 50.000 0.00 0.00 41.02 2.57
3610 4267 2.952978 ACCGCTAGGAATCAGACTACTG 59.047 50.000 0.00 0.00 41.84 2.74
3633 4290 7.150447 TGATAGTCTACTTCCTATCAGACCA 57.850 40.000 5.49 0.00 42.71 4.02
3634 4291 7.227873 TGATAGTCTACTTCCTATCAGACCAG 58.772 42.308 5.49 0.00 42.71 4.00
3635 4292 5.459982 AGTCTACTTCCTATCAGACCAGT 57.540 43.478 0.00 0.00 38.53 4.00
3636 4293 5.442391 AGTCTACTTCCTATCAGACCAGTC 58.558 45.833 0.00 0.00 38.53 3.51
3637 4294 4.273969 GTCTACTTCCTATCAGACCAGTCG 59.726 50.000 0.00 0.00 32.93 4.18
3638 4295 2.379972 ACTTCCTATCAGACCAGTCGG 58.620 52.381 0.00 0.00 38.77 4.79
3650 4307 1.755380 ACCAGTCGGTAGCCATTAGAC 59.245 52.381 0.00 0.00 46.71 2.59
3675 4332 9.965902 ACTAAAGAGACAATATCAGGTGAAAAT 57.034 29.630 0.00 0.00 0.00 1.82
3931 4588 4.487714 TCTATCAAAATCTTGGGCGACT 57.512 40.909 0.00 0.00 33.01 4.18
4206 4883 4.943705 ACACAAAGACAAGACTTGATGTGT 59.056 37.500 27.69 27.69 39.84 3.72
4410 5826 6.381133 CCTAGCTGTTAATGGGGAAGAAATTT 59.619 38.462 0.00 0.00 0.00 1.82
4501 5941 3.596214 ACCGATGTACAGGATTGTTGTC 58.404 45.455 8.09 0.00 38.76 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
315 387 2.281484 GTGGAGGCGGCAGACAAA 60.281 61.111 13.08 0.00 0.00 2.83
650 916 4.934797 TTTTGATGATTCAGGGGAGAGT 57.065 40.909 0.00 0.00 32.27 3.24
994 1283 4.086860 CGACGCCGTCATGAATCA 57.913 55.556 18.40 0.00 32.09 2.57
1098 1387 4.020485 GGGTAATAGTAGAATGCCGGACAT 60.020 45.833 5.05 5.44 42.30 3.06
1597 1887 0.250858 CCTGGGTCAATGCACAGACA 60.251 55.000 18.71 2.55 42.22 3.41
1987 2277 7.148423 GGAGCATTTCTCTTCTTCTTCTTCTTC 60.148 40.741 0.00 0.00 41.60 2.87
1988 2278 6.654582 GGAGCATTTCTCTTCTTCTTCTTCTT 59.345 38.462 0.00 0.00 41.60 2.52
1989 2279 6.172630 GGAGCATTTCTCTTCTTCTTCTTCT 58.827 40.000 0.00 0.00 41.60 2.85
2051 2341 0.536460 GAACGGGCTGGGAACAAAGA 60.536 55.000 0.00 0.00 42.06 2.52
2603 2893 1.133823 TGCTTGCCTCTCCAAAGTCAA 60.134 47.619 0.00 0.00 0.00 3.18
2974 3546 4.141413 CCTGGTACTCATTTGGATGGATGA 60.141 45.833 0.00 0.00 33.93 2.92
3056 3628 7.481642 ACATTAACGGTGTTGTCAATTTGTAA 58.518 30.769 0.00 0.00 0.00 2.41
3194 3766 6.455647 CATGACTAGTTCAGAACCTACAACA 58.544 40.000 9.85 4.23 37.77 3.33
3195 3767 5.348997 GCATGACTAGTTCAGAACCTACAAC 59.651 44.000 9.85 0.00 37.77 3.32
3223 3878 3.008157 TGCCGTAGATTTGGGAACTAACA 59.992 43.478 0.00 0.00 0.00 2.41
3376 4033 3.737559 AATCATTCAGGTAGGTGGCAA 57.262 42.857 0.00 0.00 0.00 4.52
3514 4171 5.938438 AGCTCTTCACTCTTCAACAAATC 57.062 39.130 0.00 0.00 0.00 2.17
3586 4243 0.530870 GTCTGATTCCTAGCGGTGCC 60.531 60.000 0.00 0.00 0.00 5.01
3587 4244 0.461961 AGTCTGATTCCTAGCGGTGC 59.538 55.000 0.00 0.00 0.00 5.01
3588 4245 2.952978 AGTAGTCTGATTCCTAGCGGTG 59.047 50.000 0.00 0.00 0.00 4.94
3589 4246 2.952978 CAGTAGTCTGATTCCTAGCGGT 59.047 50.000 0.00 0.00 43.76 5.68
3590 4247 3.215151 TCAGTAGTCTGATTCCTAGCGG 58.785 50.000 0.00 0.00 44.58 5.52
3610 4267 7.228590 ACTGGTCTGATAGGAAGTAGACTATC 58.771 42.308 0.00 0.00 43.62 2.08
3611 4268 7.156694 ACTGGTCTGATAGGAAGTAGACTAT 57.843 40.000 0.00 0.00 39.50 2.12
3612 4269 6.578313 ACTGGTCTGATAGGAAGTAGACTA 57.422 41.667 0.00 0.00 39.50 2.59
3613 4270 5.442391 GACTGGTCTGATAGGAAGTAGACT 58.558 45.833 0.00 0.00 39.50 3.24
3614 4271 4.273969 CGACTGGTCTGATAGGAAGTAGAC 59.726 50.000 0.00 0.00 38.98 2.59
3615 4272 4.452825 CGACTGGTCTGATAGGAAGTAGA 58.547 47.826 0.00 0.00 0.00 2.59
3616 4273 3.566322 CCGACTGGTCTGATAGGAAGTAG 59.434 52.174 0.00 0.00 0.00 2.57
3617 4274 3.552875 CCGACTGGTCTGATAGGAAGTA 58.447 50.000 0.00 0.00 0.00 2.24
3618 4275 2.379972 CCGACTGGTCTGATAGGAAGT 58.620 52.381 0.00 0.00 0.00 3.01
3631 4288 2.032620 AGTCTAATGGCTACCGACTGG 58.967 52.381 0.00 0.00 42.84 4.00
3632 4289 4.913335 TTAGTCTAATGGCTACCGACTG 57.087 45.455 7.65 0.00 36.46 3.51
3633 4290 5.198965 TCTTTAGTCTAATGGCTACCGACT 58.801 41.667 5.84 0.00 38.40 4.18
3634 4291 5.298777 TCTCTTTAGTCTAATGGCTACCGAC 59.701 44.000 5.84 0.00 0.00 4.79
3635 4292 5.298777 GTCTCTTTAGTCTAATGGCTACCGA 59.701 44.000 5.84 0.00 0.00 4.69
3636 4293 5.067413 TGTCTCTTTAGTCTAATGGCTACCG 59.933 44.000 5.84 0.00 0.00 4.02
3637 4294 6.466885 TGTCTCTTTAGTCTAATGGCTACC 57.533 41.667 5.84 0.00 0.00 3.18
3640 4297 8.928448 TGATATTGTCTCTTTAGTCTAATGGCT 58.072 33.333 5.84 0.00 0.00 4.75
3641 4298 9.202273 CTGATATTGTCTCTTTAGTCTAATGGC 57.798 37.037 5.84 0.00 0.00 4.40
3642 4299 9.703892 CCTGATATTGTCTCTTTAGTCTAATGG 57.296 37.037 5.84 0.00 0.00 3.16
3645 4302 9.475620 TCACCTGATATTGTCTCTTTAGTCTAA 57.524 33.333 0.00 0.00 0.00 2.10
3646 4303 9.475620 TTCACCTGATATTGTCTCTTTAGTCTA 57.524 33.333 0.00 0.00 0.00 2.59
3647 4304 7.962995 TCACCTGATATTGTCTCTTTAGTCT 57.037 36.000 0.00 0.00 0.00 3.24
3931 4588 4.813027 CCTCTGTACTTAAACGTGCCTTA 58.187 43.478 0.00 0.00 0.00 2.69
4206 4883 3.361786 TCATATTGAGTCTGTCCCGTCA 58.638 45.455 0.00 0.00 0.00 4.35
4410 5826 1.453745 GCCAGCCAATCCCGATTCA 60.454 57.895 0.00 0.00 0.00 2.57
4501 5941 6.741992 TGTACAGATTGCAAATAGAACCTG 57.258 37.500 1.71 5.27 0.00 4.00


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

AutoCloner maintained by Alex Coulton.