Multiple sequence alignment - TraesCS5D01G400700

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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 TraesCS5D01G400700 chr5D 100.000 6676 0 0 1 6676 465713703 465720378 0.000000e+00 12329
1 TraesCS5D01G400700 chr5D 89.840 187 15 2 5594 5779 399222956 399222773 3.110000e-58 237
2 TraesCS5D01G400700 chr5B 96.757 6722 150 23 1 6676 572946055 572952754 0.000000e+00 11143
3 TraesCS5D01G400700 chr5A 96.290 6711 202 18 1 6676 586144088 586150786 0.000000e+00 10970
4 TraesCS5D01G400700 chr5A 88.298 188 17 4 5594 5779 504869322 504869138 3.130000e-53 220


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 TraesCS5D01G400700 chr5D 465713703 465720378 6675 False 12329 12329 100.000 1 6676 1 chr5D.!!$F1 6675
1 TraesCS5D01G400700 chr5B 572946055 572952754 6699 False 11143 11143 96.757 1 6676 1 chr5B.!!$F1 6675
2 TraesCS5D01G400700 chr5A 586144088 586150786 6698 False 10970 10970 96.290 1 6676 1 chr5A.!!$F1 6675

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
968 978 2.726351 CCTCTGCTTCCCGTCCCTC 61.726 68.421 0.00 0.00 0.00 4.30 F
1705 1715 1.019278 GGTGCATATATGGGGACGCG 61.019 60.000 14.51 3.53 0.00 6.01 F
1830 1840 1.950630 GGTTGCTTGTGCTTTGGCG 60.951 57.895 0.00 0.00 42.25 5.69 F
3612 3642 3.309954 GGCGTGATAATGTGGAGAAAGTC 59.690 47.826 0.00 0.00 0.00 3.01 F
5090 5120 0.536460 TGGAAGACCGAAAAGTGCCC 60.536 55.000 0.00 0.00 39.42 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3027 3051 4.298332 CAAAACTTCCTTCATTTCCACCG 58.702 43.478 0.00 0.0 0.00 4.94 R
3612 3642 1.007271 AGCACGTCTCCTTGTGTCG 60.007 57.895 0.00 0.0 38.36 4.35 R
3619 3649 2.031163 GGCAACAGCACGTCTCCT 59.969 61.111 0.00 0.0 0.00 3.69 R
5390 5420 0.248661 CGTACATGGCTGAGGAGTCG 60.249 60.000 0.00 0.0 0.00 4.18 R
6063 6126 0.248498 GCGATCGTCGTCTGGATTGA 60.248 55.000 17.81 0.0 42.81 2.57 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
63 64 5.677319 AAGTAGCAGTATCAGCCTTGTTA 57.323 39.130 0.00 0.00 0.00 2.41
132 133 6.661377 TGGTGGTAAGTATGTATGCATTTTGT 59.339 34.615 3.54 0.00 36.58 2.83
618 627 8.149647 TCATGGTTGATGCTTTAAAAAGTTGAT 58.850 29.630 4.50 0.00 38.28 2.57
674 684 8.856153 TTTCAGCATACAACTTTGATACCTTA 57.144 30.769 0.00 0.00 0.00 2.69
968 978 2.726351 CCTCTGCTTCCCGTCCCTC 61.726 68.421 0.00 0.00 0.00 4.30
1347 1357 1.376543 CAGGCTCGAATGTGAAGCAT 58.623 50.000 0.00 0.00 40.03 3.79
1705 1715 1.019278 GGTGCATATATGGGGACGCG 61.019 60.000 14.51 3.53 0.00 6.01
1806 1816 5.048921 CAGCAATATCAATTCTACAGGCCTG 60.049 44.000 31.60 31.60 0.00 4.85
1830 1840 1.950630 GGTTGCTTGTGCTTTGGCG 60.951 57.895 0.00 0.00 42.25 5.69
3027 3051 7.842525 CACAAAGTTGACAATGTGTAATCTC 57.157 36.000 10.84 0.00 38.62 2.75
3516 3546 5.065731 GCATGACTGGAGGTTGAAGAATAAG 59.934 44.000 0.00 0.00 0.00 1.73
3612 3642 3.309954 GGCGTGATAATGTGGAGAAAGTC 59.690 47.826 0.00 0.00 0.00 3.01
3619 3649 2.971660 TGTGGAGAAAGTCGACACAA 57.028 45.000 19.50 0.00 38.84 3.33
3664 3694 4.704540 CACTGCATACCTTGGGTGAAATAA 59.295 41.667 0.00 0.00 36.19 1.40
3804 3834 3.055240 ACAAAGAGGAGCTGGAGAAGATG 60.055 47.826 0.00 0.00 0.00 2.90
4151 4181 5.375773 TGTAGCTGCCAATATATTGCAAGA 58.624 37.500 18.40 0.00 36.48 3.02
4472 4502 2.704464 TAGATGTGCTTGCATGCTCT 57.296 45.000 23.31 19.22 0.00 4.09
4601 4631 6.273071 TGACTGTGTGAAATATCTCATACCG 58.727 40.000 3.76 0.45 36.81 4.02
4745 4775 5.153675 AGGCTCATCTTAAGATCAGGATCA 58.846 41.667 16.99 0.00 40.22 2.92
4991 5021 2.238395 GGACCTGAAGGAAGAGATTGCT 59.762 50.000 2.62 0.00 38.94 3.91
4995 5025 3.465871 CTGAAGGAAGAGATTGCTAGCC 58.534 50.000 13.29 0.00 0.00 3.93
5079 5109 2.508526 ACAGCATTCAACTGGAAGACC 58.491 47.619 0.00 0.00 39.30 3.85
5090 5120 0.536460 TGGAAGACCGAAAAGTGCCC 60.536 55.000 0.00 0.00 39.42 5.36
5128 5158 1.192146 AGCCTAGACAACCGCTCCAA 61.192 55.000 0.00 0.00 0.00 3.53
5144 5174 1.768275 TCCAAGAAGCTGGTCACAAGA 59.232 47.619 0.00 0.00 37.74 3.02
5228 5258 0.760567 TGGTGGAGGATCAGATCGGG 60.761 60.000 4.23 0.00 36.25 5.14
5303 5333 4.080969 GAGCAAGTTCATGAAGCTCTTG 57.919 45.455 28.05 25.68 46.06 3.02
5339 5369 1.296867 CGGCGCACATTTCATCGTC 60.297 57.895 10.83 0.00 0.00 4.20
5399 5429 2.640302 GCACCTGCTCGACTCCTCA 61.640 63.158 0.00 0.00 38.21 3.86
5477 5513 4.722700 AGGAACAGCGGCGCCAAT 62.723 61.111 30.40 14.98 0.00 3.16
5534 5570 2.103373 CTCGTGGATTTCCTGAGAGGA 58.897 52.381 11.66 0.00 44.10 3.71
5546 5582 3.333980 TCCTGAGAGGACAAGGAGTTCTA 59.666 47.826 0.00 0.00 40.06 2.10
5807 5861 7.548780 GCTCTGTTCTTATCATTCTCTTCTGTT 59.451 37.037 0.00 0.00 0.00 3.16
5914 5968 1.270550 GTGAAGGGTGTGATTTGCCTG 59.729 52.381 0.00 0.00 0.00 4.85
6007 6066 2.849942 TGTTCACAATGTGACTCAGGG 58.150 47.619 16.50 0.00 42.60 4.45
6063 6126 3.726557 TGAATTCATGGCTTCCTCTGT 57.273 42.857 3.38 0.00 0.00 3.41
6076 6139 1.819288 TCCTCTGTCAATCCAGACGAC 59.181 52.381 0.00 0.00 41.41 4.34
6137 6200 4.094684 CTCCGGCGAGCTTAGTTG 57.905 61.111 9.30 0.00 0.00 3.16
6568 6631 2.918802 TTCCGGTACAGCCCGTGT 60.919 61.111 0.00 0.00 46.66 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.269178 GCTATCTGAAGAAGCAAGCAGT 58.731 45.455 0.00 0.00 36.26 4.40
132 133 7.015877 TGTTAAGGTGCTAGGAGTAGAAAGAAA 59.984 37.037 0.00 0.00 0.00 2.52
674 684 1.610522 ACTTGCGTAGTTCCACGTACT 59.389 47.619 0.00 0.00 43.79 2.73
968 978 3.681417 TGTCGATGAAGAGCAGTTGAATG 59.319 43.478 0.00 0.00 0.00 2.67
1705 1715 1.739371 GCCACCTCTTGTATCACGACC 60.739 57.143 0.00 0.00 0.00 4.79
3027 3051 4.298332 CAAAACTTCCTTCATTTCCACCG 58.702 43.478 0.00 0.00 0.00 4.94
3516 3546 1.142748 CCACCTGATCACGGCTCTC 59.857 63.158 10.15 0.00 0.00 3.20
3612 3642 1.007271 AGCACGTCTCCTTGTGTCG 60.007 57.895 0.00 0.00 38.36 4.35
3619 3649 2.031163 GGCAACAGCACGTCTCCT 59.969 61.111 0.00 0.00 0.00 3.69
3804 3834 2.479650 CGCAGCTTCTCTTGCAGC 59.520 61.111 0.00 0.00 39.13 5.25
4472 4502 7.958088 TCACCATGTCCGTAATATTTCTATCA 58.042 34.615 0.00 0.00 0.00 2.15
4601 4631 2.171489 GAGTTGCACGGAACCTTCGC 62.171 60.000 0.00 0.00 0.00 4.70
4643 4673 4.695455 GGCAGTGACAGTAGAATTTGCTTA 59.305 41.667 0.00 0.00 0.00 3.09
4745 4775 0.469070 GCAGATCTCTGGCATGGTCT 59.531 55.000 9.15 0.00 43.94 3.85
4991 5021 4.346127 TGATACTCGTAGTACCTCAGGCTA 59.654 45.833 0.00 0.00 32.84 3.93
4995 5025 4.706035 AGGTGATACTCGTAGTACCTCAG 58.294 47.826 8.43 0.00 32.84 3.35
5079 5109 1.200020 GAACATCTGGGGCACTTTTCG 59.800 52.381 0.00 0.00 0.00 3.46
5090 5120 3.265791 GCTGACAAGGTAGAACATCTGG 58.734 50.000 0.00 0.00 0.00 3.86
5128 5158 2.641815 AGGATTCTTGTGACCAGCTTCT 59.358 45.455 0.00 0.00 0.00 2.85
5144 5174 2.635787 ATCGCATGCCAGGCAGGATT 62.636 55.000 30.35 10.06 43.36 3.01
5228 5258 0.531532 CCACCTGGATCAGATCGCAC 60.532 60.000 0.00 0.00 37.39 5.34
5303 5333 1.212616 CGATCTTCAGGGCGAATGTC 58.787 55.000 0.00 0.00 31.69 3.06
5339 5369 1.557269 GGATCATCTCCCCCATCCCG 61.557 65.000 0.00 0.00 38.19 5.14
5390 5420 0.248661 CGTACATGGCTGAGGAGTCG 60.249 60.000 0.00 0.00 0.00 4.18
5443 5479 1.227263 CTCGCCCTCCCGTACATTG 60.227 63.158 0.00 0.00 0.00 2.82
5444 5480 2.432300 CCTCGCCCTCCCGTACATT 61.432 63.158 0.00 0.00 0.00 2.71
5477 5513 0.253113 TCATGTCCTCCCCCATGTCA 60.253 55.000 0.00 0.00 39.53 3.58
5534 5570 3.264450 CCATCCCTGTTAGAACTCCTTGT 59.736 47.826 0.00 0.00 0.00 3.16
5546 5582 1.315257 GCGCAATGTCCATCCCTGTT 61.315 55.000 0.30 0.00 0.00 3.16
5588 5624 1.428620 GCCGTCGTCTCTGTACCTC 59.571 63.158 0.00 0.00 0.00 3.85
5589 5625 2.045131 GGCCGTCGTCTCTGTACCT 61.045 63.158 0.00 0.00 0.00 3.08
5709 5746 3.249189 GGGAGGCACCTGTGGTCA 61.249 66.667 0.00 0.00 38.98 4.02
5832 5886 3.698040 AGTAGCAAGCAAATCAATCCCAG 59.302 43.478 0.00 0.00 0.00 4.45
5914 5968 7.881643 AAATCATCGCTCTGAATATACTCAC 57.118 36.000 0.00 0.00 0.00 3.51
6063 6126 0.248498 GCGATCGTCGTCTGGATTGA 60.248 55.000 17.81 0.00 42.81 2.57
6132 6195 1.272490 CGGTCTTCTGAGCACCAACTA 59.728 52.381 7.61 0.00 40.44 2.24
6134 6197 0.951040 CCGGTCTTCTGAGCACCAAC 60.951 60.000 0.00 0.00 40.44 3.77
6135 6198 1.371183 CCGGTCTTCTGAGCACCAA 59.629 57.895 0.00 0.00 40.44 3.67
6136 6199 2.583441 CCCGGTCTTCTGAGCACCA 61.583 63.158 0.00 0.00 40.44 4.17
6137 6200 2.266055 CCCGGTCTTCTGAGCACC 59.734 66.667 0.00 0.00 40.44 5.01
6529 6592 2.542907 GGTGTGGCTGTTCGTGGTG 61.543 63.158 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.