Multiple sequence alignment - TraesCS3B01G606300

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 TraesCS3B01G606300 chr3B 100.000 2973 0 0 1 2973 825494597 825497569 0.000000e+00 5491
1 TraesCS3B01G606300 chr3B 96.739 2975 88 9 1 2973 825315119 825312152 0.000000e+00 4948
2 TraesCS3B01G606300 chr3B 93.237 2011 92 12 607 2578 823985454 823983449 0.000000e+00 2920
3 TraesCS3B01G606300 chr3B 91.246 594 43 6 1 588 824006295 824005705 0.000000e+00 800
4 TraesCS3B01G606300 chr3B 88.776 588 42 12 1 588 824048030 824047467 0.000000e+00 699
5 TraesCS3B01G606300 chr3B 94.604 278 12 3 706 982 824027504 824027229 7.620000e-116 427
6 TraesCS3B01G606300 chr3B 86.012 336 31 9 2640 2973 823982330 823982009 2.190000e-91 346
7 TraesCS3B01G606300 chrUn 97.344 2974 62 8 1 2973 43084612 43081655 0.000000e+00 5038


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 TraesCS3B01G606300 chr3B 825494597 825497569 2972 False 5491 5491 100.0000 1 2973 1 chr3B.!!$F1 2972
1 TraesCS3B01G606300 chr3B 825312152 825315119 2967 True 4948 4948 96.7390 1 2973 1 chr3B.!!$R4 2972
2 TraesCS3B01G606300 chr3B 823982009 823985454 3445 True 1633 2920 89.6245 607 2973 2 chr3B.!!$R5 2366
3 TraesCS3B01G606300 chr3B 824005705 824006295 590 True 800 800 91.2460 1 588 1 chr3B.!!$R1 587
4 TraesCS3B01G606300 chr3B 824047467 824048030 563 True 699 699 88.7760 1 588 1 chr3B.!!$R3 587
5 TraesCS3B01G606300 chrUn 43081655 43084612 2957 True 5038 5038 97.3440 1 2973 1 chrUn.!!$R1 2972

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
413 420 1.004745 TCCAAGGGAAGTTCATGGAGC 59.995 52.381 16.15 0.0 35.33 4.70 F
1605 1637 1.802636 CGGTTTTGGCGCTCATGAT 59.197 52.632 7.64 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1841 2.098770 GCAGATGCATCTTTCTCAACCC 59.901 50.0 26.70 3.43 41.59 4.11 R
2740 3854 0.315251 TAGCATTGGATCGCTCCTCG 59.685 55.0 6.88 0.00 42.59 4.63 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
413 420 1.004745 TCCAAGGGAAGTTCATGGAGC 59.995 52.381 16.15 0.00 35.33 4.70
490 497 6.130298 TGATGACAAAGTACCACAACAAAG 57.870 37.500 0.00 0.00 0.00 2.77
491 498 5.650266 TGATGACAAAGTACCACAACAAAGT 59.350 36.000 0.00 0.00 0.00 2.66
492 499 6.824196 TGATGACAAAGTACCACAACAAAGTA 59.176 34.615 0.00 0.00 0.00 2.24
493 500 6.425577 TGACAAAGTACCACAACAAAGTAC 57.574 37.500 0.00 0.00 37.27 2.73
494 501 5.354792 TGACAAAGTACCACAACAAAGTACC 59.645 40.000 0.00 0.00 37.64 3.34
495 502 5.254901 ACAAAGTACCACAACAAAGTACCA 58.745 37.500 0.00 0.00 37.64 3.25
496 503 5.124297 ACAAAGTACCACAACAAAGTACCAC 59.876 40.000 0.00 0.00 37.64 4.16
506 513 5.105554 ACAACAAAGTACCACAGCAAAATGA 60.106 36.000 0.00 0.00 0.00 2.57
605 612 5.520376 AAGAGTGGAGTTTGGTTTTGATG 57.480 39.130 0.00 0.00 0.00 3.07
896 904 4.160329 AGATAGATATTCACCCGAGGCAA 58.840 43.478 0.00 0.00 0.00 4.52
1013 1021 5.748630 GTCTCTGCAACATGTCGTATTATCA 59.251 40.000 0.00 0.00 0.00 2.15
1105 1137 2.060567 ATGTGTGCAGTCCAGCCTGT 62.061 55.000 0.00 0.00 34.84 4.00
1605 1637 1.802636 CGGTTTTGGCGCTCATGAT 59.197 52.632 7.64 0.00 0.00 2.45
1787 1819 3.714280 TGATTATGGTAAGGTGCAGGCTA 59.286 43.478 0.00 0.00 0.00 3.93
1809 1841 2.348411 AATGATAACCTTCGGCTGGG 57.652 50.000 0.00 0.00 0.00 4.45
2041 2073 2.246719 GCCTCAGGCGAAAGATGTAT 57.753 50.000 0.00 0.00 39.62 2.29
2210 2255 7.511268 AGAATATTTAGCCCGTATTGTTACCA 58.489 34.615 0.00 0.00 0.00 3.25
2520 2565 4.141642 TGGTGATGGTAGACAGATGGAATG 60.142 45.833 0.00 0.00 0.00 2.67
2701 3815 3.128938 GGACTCGCTCACTGTACAAGTAT 59.871 47.826 0.00 0.00 36.83 2.12
2742 3856 4.284123 GCACATCCTGCTCAACGA 57.716 55.556 0.00 0.00 43.33 3.85
2743 3857 2.084844 GCACATCCTGCTCAACGAG 58.915 57.895 0.00 0.00 43.33 4.18
2744 3858 1.364626 GCACATCCTGCTCAACGAGG 61.365 60.000 0.00 0.00 43.33 4.63
2745 3859 0.247460 CACATCCTGCTCAACGAGGA 59.753 55.000 0.00 0.00 42.67 3.71
2746 3860 0.534412 ACATCCTGCTCAACGAGGAG 59.466 55.000 5.61 5.61 45.59 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
413 420 7.639113 TGCATAGTCTTTAATTTAGGGGTTG 57.361 36.000 0.00 0.00 0.00 3.77
490 497 4.829064 TCTGTTCATTTTGCTGTGGTAC 57.171 40.909 0.00 0.00 0.00 3.34
491 498 4.321156 GCATCTGTTCATTTTGCTGTGGTA 60.321 41.667 0.00 0.00 0.00 3.25
492 499 3.553508 GCATCTGTTCATTTTGCTGTGGT 60.554 43.478 0.00 0.00 0.00 4.16
493 500 2.991190 GCATCTGTTCATTTTGCTGTGG 59.009 45.455 0.00 0.00 0.00 4.17
494 501 3.909430 AGCATCTGTTCATTTTGCTGTG 58.091 40.909 0.00 0.00 41.79 3.66
495 502 4.595762 AAGCATCTGTTCATTTTGCTGT 57.404 36.364 0.00 0.00 42.50 4.40
496 503 5.946298 TCTAAGCATCTGTTCATTTTGCTG 58.054 37.500 0.00 0.00 42.50 4.41
545 552 7.039784 TCCCTTATAATTTAATGATGTGCAGCC 60.040 37.037 0.00 0.00 0.00 4.85
580 587 6.693315 TCAAAACCAAACTCCACTCTTTAG 57.307 37.500 0.00 0.00 0.00 1.85
581 588 6.040391 CCATCAAAACCAAACTCCACTCTTTA 59.960 38.462 0.00 0.00 0.00 1.85
588 595 2.962421 GTCCCATCAAAACCAAACTCCA 59.038 45.455 0.00 0.00 0.00 3.86
605 612 5.509832 TTTAAAGGAAACTAGAGGGTCCC 57.490 43.478 0.00 0.00 42.68 4.46
1013 1021 2.888594 CACCTGACCAATACGAACGAT 58.111 47.619 0.14 0.00 0.00 3.73
1105 1137 1.001293 GAGATGCATGGGATCACGCTA 59.999 52.381 2.46 0.00 32.69 4.26
1809 1841 2.098770 GCAGATGCATCTTTCTCAACCC 59.901 50.000 26.70 3.43 41.59 4.11
2041 2073 9.896645 GAGGCATCCTTATTATCTCATGATTTA 57.103 33.333 0.00 0.00 31.76 1.40
2210 2255 6.249911 AGAGGATGTGATGAATGTTCTCAT 57.750 37.500 0.00 0.00 38.79 2.90
2256 2301 4.388485 AGCCCATTTCAAACACCAATTTC 58.612 39.130 0.00 0.00 0.00 2.17
2268 2313 7.716799 AGTTATCAAATGTAAGCCCATTTCA 57.283 32.000 4.20 0.00 41.79 2.69
2367 2412 4.091509 GTGTTCATGTTACATGACTCGGAC 59.908 45.833 25.42 20.08 0.00 4.79
2520 2565 4.336280 ACAAAGAGTTCCCTTTATGCTCC 58.664 43.478 0.00 0.00 34.85 4.70
2593 2638 4.619437 TTTTACGGCTTTTCTCGTTGTT 57.381 36.364 0.00 0.00 40.31 2.83
2595 2640 4.973663 ACATTTTTACGGCTTTTCTCGTTG 59.026 37.500 0.00 0.00 40.31 4.10
2646 3760 3.877951 CAATGCCTGCTCCTCTTCT 57.122 52.632 0.00 0.00 0.00 2.85
2677 3791 0.596577 TGTACAGTGAGCGAGTCCAC 59.403 55.000 0.00 0.00 0.00 4.02
2740 3854 0.315251 TAGCATTGGATCGCTCCTCG 59.685 55.000 6.88 0.00 42.59 4.63
2741 3855 1.069204 TGTAGCATTGGATCGCTCCTC 59.931 52.381 6.88 0.00 42.59 3.71
2742 3856 1.123077 TGTAGCATTGGATCGCTCCT 58.877 50.000 6.88 0.00 42.59 3.69
2743 3857 2.072298 GATGTAGCATTGGATCGCTCC 58.928 52.381 0.00 0.00 42.45 4.70
2744 3858 2.759191 TGATGTAGCATTGGATCGCTC 58.241 47.619 0.00 0.00 39.70 5.03
2745 3859 2.916702 TGATGTAGCATTGGATCGCT 57.083 45.000 0.00 0.00 42.34 4.93
2746 3860 3.561310 TCTTTGATGTAGCATTGGATCGC 59.439 43.478 0.00 0.00 0.00 4.58
2747 3861 5.739752 TTCTTTGATGTAGCATTGGATCG 57.260 39.130 0.00 0.00 0.00 3.69
2748 3862 5.066893 TGCTTCTTTGATGTAGCATTGGATC 59.933 40.000 0.00 0.00 38.61 3.36
2749 3863 4.951715 TGCTTCTTTGATGTAGCATTGGAT 59.048 37.500 0.00 0.00 38.61 3.41
2879 4003 1.140589 CAGAGTCGCCGAGCTTGAT 59.859 57.895 1.22 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.