Multiple sequence alignment - TraesCS3B01G398800

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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 TraesCS3B01G398800 chr3B 100.000 2336 0 0 1 2336 629908992 629911327 0 4314
1 TraesCS3B01G398800 chr3B 96.520 661 23 0 1669 2329 629918594 629919254 0 1094
2 TraesCS3B01G398800 chr3B 90.732 669 55 7 1669 2335 643674338 643675001 0 885
3 TraesCS3B01G398800 chr3B 89.686 669 64 5 1669 2335 324599634 324600299 0 848
4 TraesCS3B01G398800 chr3B 89.254 670 63 9 1669 2335 643681055 643681718 0 830
5 TraesCS3B01G398800 chr4A 95.332 1671 78 0 2 1672 700975955 700977625 0 2654
6 TraesCS3B01G398800 chr4A 90.240 1670 160 3 2 1671 632630872 632632538 0 2178
7 TraesCS3B01G398800 chr5B 94.365 1668 93 1 2 1669 364099710 364098044 0 2558
8 TraesCS3B01G398800 chr5B 91.382 673 48 10 1669 2335 257824275 257824943 0 913
9 TraesCS3B01G398800 chr5B 90.490 673 51 12 1669 2335 257803862 257804527 0 876
10 TraesCS3B01G398800 chr6B 90.078 1673 156 10 2 1669 18600448 18598781 0 2161
11 TraesCS3B01G398800 chr6B 88.975 1678 171 12 2 1670 573347664 573349336 0 2061
12 TraesCS3B01G398800 chr3A 89.102 1670 178 4 2 1670 702515841 702514175 0 2073
13 TraesCS3B01G398800 chr2A 88.597 1675 183 8 2 1672 179276105 179277775 0 2028
14 TraesCS3B01G398800 chr2A 86.423 1672 221 6 2 1669 673275405 673273736 0 1825
15 TraesCS3B01G398800 chr7B 88.571 1680 178 13 2 1672 484928863 484927189 0 2026
16 TraesCS3B01G398800 chr1B 89.732 672 60 9 1669 2336 603392669 603393335 0 850
17 TraesCS3B01G398800 chr4B 89.537 669 66 4 1669 2335 332166621 332167287 0 845
18 TraesCS3B01G398800 chr2B 89.686 669 58 11 1669 2333 144104120 144104781 0 843


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 TraesCS3B01G398800 chr3B 629908992 629911327 2335 False 4314 4314 100.000 1 2336 1 chr3B.!!$F2 2335
1 TraesCS3B01G398800 chr3B 629918594 629919254 660 False 1094 1094 96.520 1669 2329 1 chr3B.!!$F3 660
2 TraesCS3B01G398800 chr3B 643674338 643675001 663 False 885 885 90.732 1669 2335 1 chr3B.!!$F4 666
3 TraesCS3B01G398800 chr3B 324599634 324600299 665 False 848 848 89.686 1669 2335 1 chr3B.!!$F1 666
4 TraesCS3B01G398800 chr3B 643681055 643681718 663 False 830 830 89.254 1669 2335 1 chr3B.!!$F5 666
5 TraesCS3B01G398800 chr4A 700975955 700977625 1670 False 2654 2654 95.332 2 1672 1 chr4A.!!$F2 1670
6 TraesCS3B01G398800 chr4A 632630872 632632538 1666 False 2178 2178 90.240 2 1671 1 chr4A.!!$F1 1669
7 TraesCS3B01G398800 chr5B 364098044 364099710 1666 True 2558 2558 94.365 2 1669 1 chr5B.!!$R1 1667
8 TraesCS3B01G398800 chr5B 257824275 257824943 668 False 913 913 91.382 1669 2335 1 chr5B.!!$F2 666
9 TraesCS3B01G398800 chr5B 257803862 257804527 665 False 876 876 90.490 1669 2335 1 chr5B.!!$F1 666
10 TraesCS3B01G398800 chr6B 18598781 18600448 1667 True 2161 2161 90.078 2 1669 1 chr6B.!!$R1 1667
11 TraesCS3B01G398800 chr6B 573347664 573349336 1672 False 2061 2061 88.975 2 1670 1 chr6B.!!$F1 1668
12 TraesCS3B01G398800 chr3A 702514175 702515841 1666 True 2073 2073 89.102 2 1670 1 chr3A.!!$R1 1668
13 TraesCS3B01G398800 chr2A 179276105 179277775 1670 False 2028 2028 88.597 2 1672 1 chr2A.!!$F1 1670
14 TraesCS3B01G398800 chr2A 673273736 673275405 1669 True 1825 1825 86.423 2 1669 1 chr2A.!!$R1 1667
15 TraesCS3B01G398800 chr7B 484927189 484928863 1674 True 2026 2026 88.571 2 1672 1 chr7B.!!$R1 1670
16 TraesCS3B01G398800 chr1B 603392669 603393335 666 False 850 850 89.732 1669 2336 1 chr1B.!!$F1 667
17 TraesCS3B01G398800 chr4B 332166621 332167287 666 False 845 845 89.537 1669 2335 1 chr4B.!!$F1 666
18 TraesCS3B01G398800 chr2B 144104120 144104781 661 False 843 843 89.686 1669 2333 1 chr2B.!!$F1 664

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
511 512 0.339162 ATGGATGGACCCAATTGGCA 59.661 50.0 19.75 12.16 40.04 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 2223 1.222567 ACTGAGGGGGAACAAACACT 58.777 50.0 0.0 0.0 0.0 3.55 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
439 440 5.324409 AGGCCATTATGAAAGTGAAAGACA 58.676 37.500 5.01 0.00 0.00 3.41
481 482 1.419922 GTCGTGCATGCTGGTAACG 59.580 57.895 20.33 19.20 42.51 3.18
505 506 2.338809 CTAGGCTATGGATGGACCCAA 58.661 52.381 0.00 0.00 40.04 4.12
511 512 0.339162 ATGGATGGACCCAATTGGCA 59.661 50.000 19.75 12.16 40.04 4.92
572 573 4.139786 TCCATCTGCAATAAGCCTGAATC 58.860 43.478 0.00 0.00 44.83 2.52
617 618 7.662258 GGAGGCTAATCTTATAACCTTCTTTCC 59.338 40.741 0.00 0.00 0.00 3.13
718 719 4.280789 AGTGATAGTATCAAGTGGGGGA 57.719 45.455 14.44 0.00 41.69 4.81
752 753 2.230508 CCTACTACACCACGAAAGCTCA 59.769 50.000 0.00 0.00 0.00 4.26
1049 1051 2.965147 ACTTGTGGCAGGCTTATGTTTT 59.035 40.909 0.00 0.00 0.00 2.43
1240 1242 4.842531 TTGATGAAACAGGAGGATGCTA 57.157 40.909 0.00 0.00 29.87 3.49
1408 1417 0.551396 TCTGGTCGAGATGCCTCCTA 59.449 55.000 0.00 0.00 36.04 2.94
1517 1528 1.451567 TGTCGTCGGGTTTTTGCCA 60.452 52.632 0.00 0.00 0.00 4.92
1593 1604 1.378762 CCCGCTTTCCTCTTTCCCA 59.621 57.895 0.00 0.00 0.00 4.37
1597 1608 1.383523 GCTTTCCTCTTTCCCATCCG 58.616 55.000 0.00 0.00 0.00 4.18
1612 1623 2.523015 CATCCGATTTGCTGAACTTGC 58.477 47.619 0.00 0.00 0.00 4.01
1654 1668 2.509964 AGTAATGGAAAGGGGATTCGCT 59.490 45.455 0.40 0.00 37.82 4.93
1747 1761 1.077265 CATCCACCCAAACCAGCCT 59.923 57.895 0.00 0.00 0.00 4.58
1754 1768 0.596082 CCCAAACCAGCCTTGTTACG 59.404 55.000 0.00 0.00 0.00 3.18
1983 2000 9.778741 GTAAAATCCAATCTATCCATCTGTACA 57.221 33.333 0.00 0.00 0.00 2.90
1988 2005 8.681486 TCCAATCTATCCATCTGTACAATTTG 57.319 34.615 0.00 0.00 0.00 2.32
2018 2035 8.279103 GCATGTTAGAACAACTTATAGCTGATC 58.721 37.037 0.00 0.00 43.03 2.92
2182 2199 5.586643 TGCATCATATTGTTGCATTGCATTT 59.413 32.000 12.95 0.63 45.05 2.32
2205 2223 2.997980 TGTGTTCTTTCTCTGTTGCCA 58.002 42.857 0.00 0.00 0.00 4.92
2249 2268 1.079405 GGTTCCGGCGATGAGTTCA 60.079 57.895 9.30 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.395426 TCACATCTCTTGACAAATTTTGCT 57.605 33.333 9.04 0.00 0.00 3.91
235 236 4.042435 CACACCTAAACCTCCCTTTTCCTA 59.958 45.833 0.00 0.00 0.00 2.94
337 338 5.633830 AAGTATTTGGCTCTGACAATGTG 57.366 39.130 0.00 0.00 27.33 3.21
439 440 5.399038 CCACTTTCCTCCCAACCATATACAT 60.399 44.000 0.00 0.00 0.00 2.29
481 482 2.498078 GGTCCATCCATAGCCTAGCTAC 59.502 54.545 0.00 0.00 44.24 3.58
520 521 4.665451 TGAGGAAATTGATCAGCAAAGGA 58.335 39.130 0.00 0.00 40.48 3.36
572 573 1.336332 CCAGACAGTCCTTCACGACAG 60.336 57.143 0.00 0.00 35.07 3.51
617 618 1.740025 GTTCCGAAGCCAATCTCCTTG 59.260 52.381 0.00 0.00 34.42 3.61
628 629 3.865224 TTGTTCGTTAAGTTCCGAAGC 57.135 42.857 9.74 6.80 43.02 3.86
630 631 4.378774 TCCATTGTTCGTTAAGTTCCGAA 58.621 39.130 6.28 6.28 40.45 4.30
773 774 5.351948 TCGATAATCACTCCCAACAATGA 57.648 39.130 0.00 0.00 0.00 2.57
779 780 6.352137 CCATATCCATCGATAATCACTCCCAA 60.352 42.308 0.00 0.00 34.63 4.12
1049 1051 3.583966 ACCCGGGAAGAAAGTATAACACA 59.416 43.478 32.02 0.00 0.00 3.72
1240 1242 1.614824 CTCCAGCCCTCAGGGTCTT 60.615 63.158 12.83 0.00 46.51 3.01
1345 1352 6.900186 ACAATAGATCTTCTTCCTTCTCCTCA 59.100 38.462 0.00 0.00 0.00 3.86
1408 1417 1.352017 TGCTCCACAACATCCTCATGT 59.648 47.619 0.00 0.00 45.89 3.21
1517 1528 3.493350 GCCATCGAGATTACTCACCATGT 60.493 47.826 0.00 0.00 42.72 3.21
1593 1604 2.440409 AGCAAGTTCAGCAAATCGGAT 58.560 42.857 0.00 0.00 0.00 4.18
1597 1608 6.089954 GGAAATACAAGCAAGTTCAGCAAATC 59.910 38.462 0.00 0.00 0.00 2.17
1747 1761 1.301087 CCACGGGTCAGCGTAACAA 60.301 57.895 0.00 0.00 0.00 2.83
1983 2000 6.225318 AGTTGTTCTAACATGCATGCAAATT 58.775 32.000 26.68 22.58 38.95 1.82
1988 2005 6.634436 GCTATAAGTTGTTCTAACATGCATGC 59.366 38.462 26.53 11.82 38.95 4.06
2182 2199 5.129634 TGGCAACAGAGAAAGAACACAATA 58.870 37.500 0.00 0.00 46.17 1.90
2205 2223 1.222567 ACTGAGGGGGAACAAACACT 58.777 50.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.