Multiple sequence alignment - TraesCS5D01G368800

Loading Multiple Alignment...

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 TraesCS5D01G368800 chr5D 100.000 3638 0 0 892 4529 444550856 444547219 0.000000e+00 6719
1 TraesCS5D01G368800 chr5D 100.000 503 0 0 1 503 444551747 444551245 0.000000e+00 929
2 TraesCS5D01G368800 chr5D 80.319 188 17 6 3667 3853 444540924 444540756 1.710000e-24 124
3 TraesCS5D01G368800 chr5A 95.706 3330 107 10 925 4225 561534888 561531566 0.000000e+00 5325
4 TraesCS5D01G368800 chr5A 90.845 284 19 2 4248 4525 561531455 561531173 1.540000e-99 374
5 TraesCS5D01G368800 chr5A 85.852 311 13 9 224 503 561535260 561534950 7.360000e-78 302
6 TraesCS5D01G368800 chr5B 97.980 3070 39 8 925 3976 541344636 541341572 0.000000e+00 5304
7 TraesCS5D01G368800 chr5B 93.510 339 13 3 62 392 541345465 541345128 3.150000e-136 496
8 TraesCS5D01G368800 chr5B 90.604 149 11 2 3671 3819 541336119 541335974 1.290000e-45 195


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 TraesCS5D01G368800 chr5D 444547219 444551747 4528 True 3824.000000 6719 100.000 1 4529 2 chr5D.!!$R2 4528
1 TraesCS5D01G368800 chr5A 561531173 561535260 4087 True 2000.333333 5325 90.801 224 4525 3 chr5A.!!$R1 4301
2 TraesCS5D01G368800 chr5B 541341572 541345465 3893 True 2900.000000 5304 95.745 62 3976 2 chr5B.!!$R2 3914

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
109 110 1.193650 CGTTTTCATTTCGGCTCGACA 59.806 47.619 0.0 0.0 34.89 4.35 F
1560 1929 1.153429 GGAAGGTATGCCGTTCGCT 60.153 57.895 0.0 0.0 40.50 4.93 F
1971 2340 0.179000 AGGACAGGATCATTGCCGAC 59.821 55.000 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 2016 0.102481 AATCGTTCCTCCCGTCATCG 59.898 55.0 0.00 0.0 0.0 3.84 R
3207 3576 0.716108 CGACGACAATTGCTGACCTC 59.284 55.0 5.05 0.0 0.0 3.85 R
3579 3948 0.618458 AGGACTTGGTGTGTGTGTGT 59.382 50.0 0.00 0.0 0.0 3.72 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
28 29 7.964666 AAAAACCCGGATATTTTCCATCTAA 57.035 32.000 0.73 0.00 45.78 2.10
29 30 7.582667 AAAACCCGGATATTTTCCATCTAAG 57.417 36.000 0.73 0.00 45.78 2.18
30 31 6.509523 AACCCGGATATTTTCCATCTAAGA 57.490 37.500 0.73 0.00 45.78 2.10
31 32 6.704056 ACCCGGATATTTTCCATCTAAGAT 57.296 37.500 0.73 0.00 45.78 2.40
32 33 7.091533 ACCCGGATATTTTCCATCTAAGATT 57.908 36.000 0.73 0.00 45.78 2.40
33 34 7.168905 ACCCGGATATTTTCCATCTAAGATTC 58.831 38.462 0.73 0.00 45.78 2.52
34 35 7.168219 CCCGGATATTTTCCATCTAAGATTCA 58.832 38.462 0.73 0.00 45.78 2.57
35 36 7.119846 CCCGGATATTTTCCATCTAAGATTCAC 59.880 40.741 0.73 0.00 45.78 3.18
36 37 7.880195 CCGGATATTTTCCATCTAAGATTCACT 59.120 37.037 0.00 0.00 45.78 3.41
37 38 9.929180 CGGATATTTTCCATCTAAGATTCACTA 57.071 33.333 0.00 0.00 45.78 2.74
94 95 3.868661 GGTTCAAGAAAATGCCACGTTTT 59.131 39.130 0.00 0.00 0.00 2.43
95 96 4.026062 GGTTCAAGAAAATGCCACGTTTTC 60.026 41.667 14.32 14.32 42.84 2.29
109 110 1.193650 CGTTTTCATTTCGGCTCGACA 59.806 47.619 0.00 0.00 34.89 4.35
127 128 6.129352 GCTCGACAAAATGACACATCTTTTTC 60.129 38.462 0.00 0.00 39.13 2.29
133 134 8.348507 ACAAAATGACACATCTTTTTCTCTCTC 58.651 33.333 0.00 0.00 39.13 3.20
139 140 7.989741 TGACACATCTTTTTCTCTCTCTCTTTT 59.010 33.333 0.00 0.00 0.00 2.27
418 449 4.696805 GAACCCAGCCCCAACCCC 62.697 72.222 0.00 0.00 0.00 4.95
427 458 2.117423 CCCAACCCCACTCCAACC 59.883 66.667 0.00 0.00 0.00 3.77
478 835 2.203082 CGGGCCAGATCTCGATCCA 61.203 63.158 4.39 0.00 38.58 3.41
479 836 1.748329 CGGGCCAGATCTCGATCCAA 61.748 60.000 4.39 0.00 38.58 3.53
1560 1929 1.153429 GGAAGGTATGCCGTTCGCT 60.153 57.895 0.00 0.00 40.50 4.93
1647 2016 2.033194 GTGCCCGGACAGTGCTTAC 61.033 63.158 0.73 0.00 0.00 2.34
1905 2274 2.555123 GCTCAATTTGTCCGAGGCA 58.445 52.632 0.00 0.00 0.00 4.75
1971 2340 0.179000 AGGACAGGATCATTGCCGAC 59.821 55.000 0.00 0.00 0.00 4.79
2244 2613 2.520458 CCAGCAACCCCCACAGAA 59.480 61.111 0.00 0.00 0.00 3.02
2721 3090 3.814504 ATTGATCCAACCACACCTCTT 57.185 42.857 0.00 0.00 0.00 2.85
3150 3519 2.919043 CCCAAGAGGCCCGCTAAT 59.081 61.111 0.00 0.00 0.00 1.73
3207 3576 3.706594 AGTACCTACATGTCATCACAGGG 59.293 47.826 13.40 3.30 38.70 4.45
3327 3696 0.111061 TGATGCTGTGGGTGCTTTCT 59.889 50.000 0.00 0.00 0.00 2.52
3522 3891 1.744741 GCAGCTTGAGCCTCTCACC 60.745 63.158 0.00 0.00 40.46 4.02
3594 3963 1.135717 CACACACACACACACACCAAG 60.136 52.381 0.00 0.00 0.00 3.61
3643 4012 2.203153 GGTGTCCACAAGCACGGT 60.203 61.111 0.00 0.00 36.54 4.83
3858 4229 5.948162 TCTTTTCCCCATCAGATTTTGAGAG 59.052 40.000 0.00 0.00 39.68 3.20
3859 4230 5.519183 TTTCCCCATCAGATTTTGAGAGA 57.481 39.130 0.00 0.00 39.68 3.10
3860 4231 4.767578 TCCCCATCAGATTTTGAGAGAG 57.232 45.455 0.00 0.00 39.68 3.20
3900 4288 1.604604 TTGTTAACTGGGCAGAGCAC 58.395 50.000 7.22 0.00 0.00 4.40
4001 4389 9.624697 TGTAATGTGCTTAGAATTTTGAACATC 57.375 29.630 0.00 0.00 0.00 3.06
4017 4405 6.867519 TGAACATCTCCATAACTACTGGAA 57.132 37.500 0.00 0.00 42.12 3.53
4030 4418 6.727824 AACTACTGGAACATCTTCAATTCG 57.272 37.500 0.00 0.00 38.20 3.34
4038 4426 5.362556 AACATCTTCAATTCGTTGACTGG 57.637 39.130 0.00 0.00 0.00 4.00
4052 4440 5.765677 TCGTTGACTGGTCATTCCATTAAAA 59.234 36.000 4.19 0.00 46.12 1.52
4088 4476 8.489676 AGAATATCACTGATGAGTGGTAAGAT 57.510 34.615 9.45 0.00 46.63 2.40
4135 4523 3.679980 GCGCCAATGTGATAATATCGTCT 59.320 43.478 0.00 0.00 0.00 4.18
4137 4525 4.030641 CGCCAATGTGATAATATCGTCTCG 59.969 45.833 0.00 0.00 0.00 4.04
4148 4536 5.769967 AATATCGTCTCGATGCTATTTGC 57.230 39.130 13.70 0.00 46.43 3.68
4195 4595 5.957771 AGAGTAATCTGCATTCAAGGGTA 57.042 39.130 0.00 0.00 0.00 3.69
4206 4606 4.397417 GCATTCAAGGGTATCTGGATATGC 59.603 45.833 0.00 0.00 35.22 3.14
4241 4708 9.708222 CAGAAATACTAATTTGTTCTGAATCCG 57.292 33.333 12.19 0.00 35.41 4.18
4266 4754 4.219288 GGCATCAAAGGAGAGAAATTGTGT 59.781 41.667 0.00 0.00 0.00 3.72
4326 4814 6.248433 AGAATGTGAGATAAAAGGCAAAGGA 58.752 36.000 0.00 0.00 0.00 3.36
4350 4838 6.838198 TGTTGTACTGTCTGTTGTATGTTC 57.162 37.500 0.00 0.00 0.00 3.18
4375 4863 6.203723 CCCAGTGCTATAGCTCTTTAAACATC 59.796 42.308 23.32 2.81 42.25 3.06
4437 4925 9.956720 GATCATTCCATGAAACTTTAACATAGG 57.043 33.333 0.00 0.00 43.50 2.57
4445 4933 9.825972 CATGAAACTTTAACATAGGTACAACAG 57.174 33.333 0.00 0.00 0.00 3.16
4449 4937 6.834107 ACTTTAACATAGGTACAACAGTGGT 58.166 36.000 0.00 0.00 0.00 4.16
4462 4950 6.538945 ACAACAGTGGTAAGATTGGTTTTT 57.461 33.333 0.00 0.00 0.00 1.94
4501 4994 1.000283 GTCGATGATTCATCTCCGCCT 60.000 52.381 21.23 0.00 38.59 5.52
4504 4997 3.511540 TCGATGATTCATCTCCGCCTTAT 59.488 43.478 21.23 0.00 38.59 1.73
4525 5018 0.031857 TGCAAGTTGGGAAATGTGCG 59.968 50.000 4.75 0.00 34.73 5.34
4526 5019 1.284297 GCAAGTTGGGAAATGTGCGC 61.284 55.000 0.00 0.00 0.00 6.09
4527 5020 0.314935 CAAGTTGGGAAATGTGCGCT 59.685 50.000 9.73 0.00 0.00 5.92
4528 5021 1.039856 AAGTTGGGAAATGTGCGCTT 58.960 45.000 9.73 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 5.051106 CGAAATGAAAACGTGGCATTTTCTT 60.051 36.000 20.79 14.65 43.47 2.52
94 95 3.070748 TCATTTTGTCGAGCCGAAATGA 58.929 40.909 19.85 19.85 37.88 2.57
95 96 3.163594 GTCATTTTGTCGAGCCGAAATG 58.836 45.455 16.98 16.98 37.72 2.32
109 110 8.688747 AGAGAGAGAAAAAGATGTGTCATTTT 57.311 30.769 0.00 0.00 37.80 1.82
164 165 0.322277 AGAGAGGCGAGGACGTGTTA 60.322 55.000 0.00 0.00 41.98 2.41
175 176 1.153823 CCCACGTGTTAGAGAGGCG 60.154 63.158 15.65 0.00 0.00 5.52
413 444 2.160853 GGGAGGTTGGAGTGGGGTT 61.161 63.158 0.00 0.00 0.00 4.11
414 445 2.531942 GGGAGGTTGGAGTGGGGT 60.532 66.667 0.00 0.00 0.00 4.95
415 446 3.339093 GGGGAGGTTGGAGTGGGG 61.339 72.222 0.00 0.00 0.00 4.96
463 495 1.043816 TCCTTGGATCGAGATCTGGC 58.956 55.000 0.00 0.00 37.92 4.85
990 1359 1.298993 CTGCAGCATGGTGAGGTCT 59.701 57.895 28.34 0.00 35.86 3.85
1560 1929 5.108187 AGTCGGTAATGTAGTAGTCCTCA 57.892 43.478 0.00 0.00 0.00 3.86
1647 2016 0.102481 AATCGTTCCTCCCGTCATCG 59.898 55.000 0.00 0.00 0.00 3.84
1971 2340 3.530910 AACCAGTGGCGTCTTCCCG 62.531 63.158 9.78 0.00 0.00 5.14
2244 2613 0.698238 TATCAGGCAGCCAAACCAGT 59.302 50.000 15.80 0.00 0.00 4.00
2721 3090 1.638529 CCATGGCCCAAACAACCTTA 58.361 50.000 0.00 0.00 0.00 2.69
3207 3576 0.716108 CGACGACAATTGCTGACCTC 59.284 55.000 5.05 0.00 0.00 3.85
3327 3696 3.578716 GGGACAGAGCTATAACTATGGCA 59.421 47.826 5.99 0.00 38.72 4.92
3522 3891 7.892778 TCTACGCTATTCTACTACTCATCTG 57.107 40.000 0.00 0.00 0.00 2.90
3537 3906 6.320164 GGGAGATACAGATTGATCTACGCTAT 59.680 42.308 0.00 0.00 34.30 2.97
3578 3947 0.732571 GGACTTGGTGTGTGTGTGTG 59.267 55.000 0.00 0.00 0.00 3.82
3579 3948 0.618458 AGGACTTGGTGTGTGTGTGT 59.382 50.000 0.00 0.00 0.00 3.72
3594 3963 5.758296 TCTGTTGTATGACTGAAAACAGGAC 59.242 40.000 12.44 0.00 44.94 3.85
3790 4159 5.301551 ACAAATTGTGCCTGTCTATTGTGAA 59.698 36.000 0.00 0.00 0.00 3.18
3887 4258 2.601666 TCGAGTGCTCTGCCCAGT 60.602 61.111 0.00 0.00 0.00 4.00
3888 4259 2.183811 CTCGAGTGCTCTGCCCAG 59.816 66.667 3.62 0.00 0.00 4.45
3890 4261 4.154347 CCCTCGAGTGCTCTGCCC 62.154 72.222 12.31 0.00 0.00 5.36
3900 4288 3.045601 ACACAATTTCTGTCCCTCGAG 57.954 47.619 5.13 5.13 35.47 4.04
3965 4353 7.364522 TCTAAGCACATTACAACATCTGTTC 57.635 36.000 0.00 0.00 39.64 3.18
4017 4405 4.389374 ACCAGTCAACGAATTGAAGATGT 58.611 39.130 0.00 0.00 46.40 3.06
4038 4426 9.294030 CTCTACTGCAAATTTTAATGGAATGAC 57.706 33.333 0.00 0.00 0.00 3.06
4052 4440 8.427276 TCATCAGTGATATTCTCTACTGCAAAT 58.573 33.333 5.03 0.00 40.15 2.32
4160 4548 8.284945 TGCAGATTACTCTAGCATTTTTCAAT 57.715 30.769 4.04 0.00 33.50 2.57
4161 4549 7.686438 TGCAGATTACTCTAGCATTTTTCAA 57.314 32.000 4.04 0.00 33.50 2.69
4171 4571 5.923204 ACCCTTGAATGCAGATTACTCTAG 58.077 41.667 0.00 0.00 0.00 2.43
4195 4595 4.594491 TCTGTACATGGTGCATATCCAGAT 59.406 41.667 0.00 0.00 38.42 2.90
4227 4694 0.886938 TGCCGCGGATTCAGAACAAA 60.887 50.000 33.48 0.00 0.00 2.83
4233 4700 0.028505 CTTTGATGCCGCGGATTCAG 59.971 55.000 33.48 15.08 0.00 3.02
4236 4703 1.077787 TCCTTTGATGCCGCGGATT 60.078 52.632 33.48 15.81 0.00 3.01
4241 4708 1.453155 TTTCTCTCCTTTGATGCCGC 58.547 50.000 0.00 0.00 0.00 6.53
4286 4774 9.613428 TCTCACATTCTCGGAACAAATATATTT 57.387 29.630 4.81 4.81 0.00 1.40
4311 4799 7.029563 CAGTACAACATCCTTTGCCTTTTATC 58.970 38.462 0.00 0.00 0.00 1.75
4326 4814 6.426937 GGAACATACAACAGACAGTACAACAT 59.573 38.462 0.00 0.00 0.00 2.71
4350 4838 5.428253 TGTTTAAAGAGCTATAGCACTGGG 58.572 41.667 26.07 0.00 41.01 4.45
4429 4917 7.779754 TCTTACCACTGTTGTACCTATGTTA 57.220 36.000 0.00 0.00 0.00 2.41
4430 4918 6.675413 TCTTACCACTGTTGTACCTATGTT 57.325 37.500 0.00 0.00 0.00 2.71
4437 4925 6.628919 AAACCAATCTTACCACTGTTGTAC 57.371 37.500 0.00 0.00 0.00 2.90
4491 4984 2.684881 ACTTGCAAATAAGGCGGAGATG 59.315 45.455 0.00 0.00 31.94 2.90
4492 4985 3.004752 ACTTGCAAATAAGGCGGAGAT 57.995 42.857 0.00 0.00 31.94 2.75
4501 4994 4.754114 GCACATTTCCCAACTTGCAAATAA 59.246 37.500 0.00 0.00 0.00 1.40
4504 4997 2.559440 GCACATTTCCCAACTTGCAAA 58.441 42.857 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.