Multiple sequence alignment - TraesCS2B01G551000

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 TraesCS2B01G551000 chr2B 100.000 4349 0 0 1 4349 747112893 747117241 0 8032
1 TraesCS2B01G551000 chr1B 95.369 4362 176 15 1 4349 588831658 588836006 0 6913
2 TraesCS2B01G551000 chr4D 94.999 4379 178 21 1 4349 65867803 65872170 0 6835
3 TraesCS2B01G551000 chr3B 94.928 4377 191 19 1 4349 694798194 694802567 0 6824
4 TraesCS2B01G551000 chr2D 94.789 4356 206 17 1 4349 594636246 594640587 0 6767
5 TraesCS2B01G551000 chr7B 94.677 4377 193 19 1 4349 99703367 99707731 0 6756
6 TraesCS2B01G551000 chr5B 94.656 4379 187 28 1 4349 12564756 12560395 0 6746
7 TraesCS2B01G551000 chr1D 94.677 4377 173 28 1 4347 10795618 10799964 0 6737
8 TraesCS2B01G551000 chr1D 94.605 4356 182 24 24 4349 108780794 108785126 0 6693
9 TraesCS2B01G551000 chr1D 94.849 1592 50 15 2784 4349 58471147 58472732 0 2457
10 TraesCS2B01G551000 chr7D 94.450 4378 197 25 1 4349 54981407 54977047 0 6697
11 TraesCS2B01G551000 chr7D 93.836 4364 240 21 1 4349 607570345 607574694 0 6541
12 TraesCS2B01G551000 chr5D 94.452 4362 201 21 1 4349 65973509 65969176 0 6676
13 TraesCS2B01G551000 chrUn 94.252 4349 227 21 10 4349 52481944 52477610 0 6625


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 TraesCS2B01G551000 chr2B 747112893 747117241 4348 False 8032 8032 100.000 1 4349 1 chr2B.!!$F1 4348
1 TraesCS2B01G551000 chr1B 588831658 588836006 4348 False 6913 6913 95.369 1 4349 1 chr1B.!!$F1 4348
2 TraesCS2B01G551000 chr4D 65867803 65872170 4367 False 6835 6835 94.999 1 4349 1 chr4D.!!$F1 4348
3 TraesCS2B01G551000 chr3B 694798194 694802567 4373 False 6824 6824 94.928 1 4349 1 chr3B.!!$F1 4348
4 TraesCS2B01G551000 chr2D 594636246 594640587 4341 False 6767 6767 94.789 1 4349 1 chr2D.!!$F1 4348
5 TraesCS2B01G551000 chr7B 99703367 99707731 4364 False 6756 6756 94.677 1 4349 1 chr7B.!!$F1 4348
6 TraesCS2B01G551000 chr5B 12560395 12564756 4361 True 6746 6746 94.656 1 4349 1 chr5B.!!$R1 4348
7 TraesCS2B01G551000 chr1D 10795618 10799964 4346 False 6737 6737 94.677 1 4347 1 chr1D.!!$F1 4346
8 TraesCS2B01G551000 chr1D 108780794 108785126 4332 False 6693 6693 94.605 24 4349 1 chr1D.!!$F3 4325
9 TraesCS2B01G551000 chr1D 58471147 58472732 1585 False 2457 2457 94.849 2784 4349 1 chr1D.!!$F2 1565
10 TraesCS2B01G551000 chr7D 54977047 54981407 4360 True 6697 6697 94.450 1 4349 1 chr7D.!!$R1 4348
11 TraesCS2B01G551000 chr7D 607570345 607574694 4349 False 6541 6541 93.836 1 4349 1 chr7D.!!$F1 4348
12 TraesCS2B01G551000 chr5D 65969176 65973509 4333 True 6676 6676 94.452 1 4349 1 chr5D.!!$R1 4348
13 TraesCS2B01G551000 chrUn 52477610 52481944 4334 True 6625 6625 94.252 10 4349 1 chrUn.!!$R1 4339

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
879 898 0.260230 TTGTCAAGTTTGCCAGGGGA 59.740 50.0 0.00 0.0 0.0 4.81 F
1080 1099 0.395586 AAACCACCACAGCTGCTCAA 60.396 50.0 15.27 0.0 0.0 3.02 F
1572 1593 0.815095 CTGATGCTGATGCTGGCAAA 59.185 50.0 0.00 0.0 41.9 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2412 2444 0.106268 TGGGCACAACACTCACCAAT 60.106 50.000 0.00 0.0 0.00 3.16 R
3007 3054 0.392193 CCACTCTGCAACTGGCTAGG 60.392 60.000 0.85 0.0 45.15 3.02 R
3361 3498 1.691976 TCCGTGGAGCAGAGAAAGAAA 59.308 47.619 0.00 0.0 0.00 2.52 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
75 76 1.625818 GGCAGTGAGAGGGAAGAAGAA 59.374 52.381 0.00 0.00 0.00 2.52
91 92 5.713792 AGAAGAAGACGATGAAGAAGACA 57.286 39.130 0.00 0.00 0.00 3.41
120 121 0.397535 ATGGTGATGATGTTGGGGGC 60.398 55.000 0.00 0.00 0.00 5.80
165 173 3.431233 GCGATGATGACGATGATGACAAT 59.569 43.478 0.00 0.00 0.00 2.71
410 418 1.692411 GCAACCACCTTTCCTGTTCT 58.308 50.000 0.00 0.00 0.00 3.01
635 644 1.959226 CAAACCCTCACGTGGTCCG 60.959 63.158 17.00 3.54 44.03 4.79
682 691 2.157738 AGAATCTGCAGTTGCCTCAAC 58.842 47.619 14.67 1.71 43.83 3.18
772 781 1.404717 CGCCAACTGTAGTGAGCAGAT 60.405 52.381 0.00 0.00 37.40 2.90
879 898 0.260230 TTGTCAAGTTTGCCAGGGGA 59.740 50.000 0.00 0.00 0.00 4.81
999 1018 1.876156 CTGCCAACTCAGACTGGAAAC 59.124 52.381 1.81 0.00 36.19 2.78
1080 1099 0.395586 AAACCACCACAGCTGCTCAA 60.396 50.000 15.27 0.00 0.00 3.02
1289 1308 5.131142 ACATTATAAGTAGGTGCAAGCCTCT 59.869 40.000 0.00 0.00 39.94 3.69
1389 1409 2.629051 GTCCTTGAACCCATACGAAGG 58.371 52.381 0.00 0.00 35.46 3.46
1430 1450 2.475466 GGGTCTGCGATGCACCATG 61.475 63.158 0.00 0.00 33.79 3.66
1463 1483 2.224475 GCATAGATGGTCATGCTCCAGT 60.224 50.000 13.28 7.32 43.38 4.00
1527 1548 4.929211 CGTATTGATGAGTGTGAGTTGGAA 59.071 41.667 0.00 0.00 0.00 3.53
1556 1577 1.338960 TGTGAATGAAGGATGCGCTGA 60.339 47.619 9.73 0.00 0.00 4.26
1572 1593 0.815095 CTGATGCTGATGCTGGCAAA 59.185 50.000 0.00 0.00 41.90 3.68
1661 1682 1.510480 GCTGGCACGAGCAGTTCTTT 61.510 55.000 7.26 0.00 44.61 2.52
1798 1819 1.796796 CTTTACGCTGCCCTCTTGC 59.203 57.895 0.00 0.00 0.00 4.01
1962 1983 4.440112 GGCTTTTAGTTGCACACTGTTCTT 60.440 41.667 10.59 0.00 35.97 2.52
2172 2198 6.154203 TCTTACACATCATGGAGAGCTTAG 57.846 41.667 0.00 0.00 0.00 2.18
2317 2345 2.191400 ACTAAGGAGCTTGAGCCATGA 58.809 47.619 0.00 0.00 43.38 3.07
2318 2346 2.776536 ACTAAGGAGCTTGAGCCATGAT 59.223 45.455 0.00 0.00 43.38 2.45
2334 2363 7.503230 TGAGCCATGATTTTATAATCTCTGCAA 59.497 33.333 7.32 0.00 40.68 4.08
2715 2750 4.150627 CGCTTCGAAGTTCTTGATTCAAGA 59.849 41.667 25.24 22.26 46.93 3.02
2831 2877 3.797039 TCGAGCACTTCCAGATTATTGG 58.203 45.455 0.00 0.00 39.70 3.16
3047 3138 4.250464 GGCACATAAGTAGTTGCACAGTA 58.750 43.478 0.00 0.00 0.00 2.74
3048 3139 4.092968 GGCACATAAGTAGTTGCACAGTAC 59.907 45.833 0.00 0.00 0.00 2.73
3062 3175 4.578516 TGCACAGTACAACATAAGCAGTTT 59.421 37.500 0.00 0.00 0.00 2.66
3413 3550 5.448360 GCTGGTTTGCACAATTTTTAAGCAA 60.448 36.000 0.00 0.00 42.74 3.91
3491 3628 8.100791 ACTTTTGTTGATACATTAGGAGCACTA 58.899 33.333 0.00 0.00 33.44 2.74
3824 3975 0.460311 CCGTCGACTCTTTGCCCTAT 59.540 55.000 14.70 0.00 0.00 2.57
3997 4152 3.079578 CTGATGTTCTCTGCAACCACAT 58.920 45.455 0.00 0.00 0.00 3.21
4092 4253 5.588648 CCGTCATGGTACTTGGATTGTAATT 59.411 40.000 0.00 0.00 0.00 1.40
4131 4292 9.936759 AACAGGAAAAACAAGTTAGATTTTCAA 57.063 25.926 15.82 0.00 40.15 2.69
4179 4340 2.632377 GCAACTAGGCAGCATGTTCTA 58.368 47.619 0.00 0.00 39.31 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.833630 CCCTCTCACTGCCATCAACTA 59.166 52.381 0.00 0.00 0.00 2.24
75 76 3.366476 CGTCCTTGTCTTCTTCATCGTCT 60.366 47.826 0.00 0.00 0.00 4.18
91 92 3.199946 ACATCATCACCATAACCGTCCTT 59.800 43.478 0.00 0.00 0.00 3.36
165 173 2.993038 TACCACCAGAACCAGGGGCA 62.993 60.000 0.00 0.00 0.00 5.36
193 201 1.410882 GCTAGTCCTCCTGGATGTGTC 59.589 57.143 0.00 0.00 45.29 3.67
410 418 7.438160 CACACATATCTTGGTCGCTAAAATCTA 59.562 37.037 0.00 0.00 0.00 1.98
635 644 0.030638 TGAAACTGCTTTGCGCTTCC 59.969 50.000 9.73 0.00 40.11 3.46
682 691 1.912043 ACTCACCATCTTCTCCTTGGG 59.088 52.381 0.00 0.00 34.72 4.12
772 781 0.327924 CCTGTGATGGTGGTTGGCTA 59.672 55.000 0.00 0.00 0.00 3.93
879 898 1.152333 GGCCTGTTCCCCCTTTGTT 60.152 57.895 0.00 0.00 0.00 2.83
999 1018 4.883585 ACATTGGTATCTGTAGTTGGCATG 59.116 41.667 0.00 0.00 0.00 4.06
1289 1308 0.397187 TGTTGTAGTTGGCGGCCTTA 59.603 50.000 21.46 5.38 0.00 2.69
1389 1409 3.865745 CGTCACCATGATAGGACTTTGAC 59.134 47.826 0.00 0.00 31.29 3.18
1430 1450 2.614057 CCATCTATGCCGAGGTCAAAAC 59.386 50.000 0.00 0.00 0.00 2.43
1527 1548 1.531423 CTTCATTCACAGCTGCTGGT 58.469 50.000 31.00 15.43 35.51 4.00
1598 1619 2.821969 GTGTGGCAATTCTCTGGTGATT 59.178 45.455 0.00 0.00 0.00 2.57
1661 1682 1.195442 TCGTGCAATAGGTGGTCCCA 61.195 55.000 0.00 0.00 34.66 4.37
1798 1819 1.548081 TTGTGATGCCTGACCCAATG 58.452 50.000 0.00 0.00 0.00 2.82
2039 2064 7.830697 CCATACCTGATTATATCATGGCTGAAA 59.169 37.037 0.00 0.00 38.85 2.69
2172 2198 2.278332 ACCTTCTTTGACCCTTCTGC 57.722 50.000 0.00 0.00 0.00 4.26
2334 2363 5.127682 GTGGATCCCTTGCTGTAAATTCATT 59.872 40.000 9.90 0.00 0.00 2.57
2412 2444 0.106268 TGGGCACAACACTCACCAAT 60.106 50.000 0.00 0.00 0.00 3.16
2560 2594 7.410120 TTCAGACACAGATACATGATGTAGT 57.590 36.000 11.32 3.00 36.14 2.73
2568 2602 6.311445 GTGAACGATTTCAGACACAGATACAT 59.689 38.462 0.00 0.00 42.60 2.29
2715 2750 1.278985 TCAATGTCATCCAGCGTCCTT 59.721 47.619 0.00 0.00 0.00 3.36
2961 3008 9.768662 AAAAATGATAAAACAGATTGCAGACTT 57.231 25.926 0.00 0.00 0.00 3.01
3007 3054 0.392193 CCACTCTGCAACTGGCTAGG 60.392 60.000 0.85 0.00 45.15 3.02
3047 3138 6.288294 TCTACTGTGAAACTGCTTATGTTGT 58.712 36.000 0.00 0.00 39.67 3.32
3048 3139 6.785488 TCTACTGTGAAACTGCTTATGTTG 57.215 37.500 0.00 0.00 39.67 3.33
3062 3175 6.018262 GTGCAACTGTTTATGTTCTACTGTGA 60.018 38.462 0.00 0.00 0.00 3.58
3361 3498 1.691976 TCCGTGGAGCAGAGAAAGAAA 59.308 47.619 0.00 0.00 0.00 2.52
3413 3550 6.485313 TGCTACTAGTGTGCAACTACAAAATT 59.515 34.615 18.74 0.00 40.56 1.82
3530 3675 2.697751 TGCTATTTGTGCCTTTGTTGGT 59.302 40.909 0.00 0.00 0.00 3.67
3824 3975 4.094476 CCTCCAAGGTCTACTACAAAGGA 58.906 47.826 0.00 0.00 0.00 3.36
4065 4226 1.933021 TCCAAGTACCATGACGGACT 58.067 50.000 0.00 0.00 38.63 3.85
4179 4340 2.814805 ATCTTAGTGCCCAGTTGCAT 57.185 45.000 0.00 0.00 44.30 3.96
4195 4356 4.692625 GTGTGACTTCAGTTGCACATATCT 59.307 41.667 0.00 0.00 42.45 1.98


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

AutoCloner maintained by Alex Coulton.