Multiple sequence alignment - TraesCS2B01G015400

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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 TraesCS2B01G015400 chr2B 100.000 3643 0 0 1 3643 7159621 7163263 0.000000e+00 6728.0
1 TraesCS2B01G015400 chr2B 98.633 3658 35 8 1 3643 7085372 7089029 0.000000e+00 6464.0
2 TraesCS2B01G015400 chr2B 97.722 3555 65 9 1 3540 454721433 454717880 0.000000e+00 6102.0
3 TraesCS2B01G015400 chr2B 95.731 2717 89 13 849 3540 454694628 454691914 0.000000e+00 4349.0
4 TraesCS2B01G015400 chr2B 95.774 2603 86 15 955 3540 6958905 6956310 0.000000e+00 4176.0
5 TraesCS2B01G015400 chr2B 97.924 2360 48 1 1 2360 7047561 7049919 0.000000e+00 4085.0
6 TraesCS2B01G015400 chr2B 95.582 1969 58 12 1587 3540 7000938 7002892 0.000000e+00 3127.0
7 TraesCS2B01G015400 chr2B 96.354 1618 41 10 1938 3540 6871299 6869685 0.000000e+00 2645.0
8 TraesCS2B01G015400 chr2B 98.557 1317 18 1 1 1316 454785562 454784246 0.000000e+00 2326.0
9 TraesCS2B01G015400 chr2B 94.650 1028 48 4 955 1980 6872321 6871299 0.000000e+00 1587.0
10 TraesCS2B01G015400 chr2B 100.000 100 0 0 3544 3643 454797311 454797212 6.210000e-43 185.0
11 TraesCS2B01G015400 chr2B 99.000 100 1 0 3544 3643 7049934 7050033 2.890000e-41 180.0
12 TraesCS2B01G015400 chr2B 96.117 103 4 0 851 953 6959057 6958955 6.260000e-38 169.0
13 TraesCS2B01G015400 chr2B 95.146 103 5 0 851 953 6872473 6872371 2.910000e-36 163.0
14 TraesCS2B01G015400 chr2B 100.000 83 0 0 3559 3641 7198470 7198552 1.750000e-33 154.0
15 TraesCS2B01G015400 chr2B 100.000 56 0 0 3588 3643 454783729 454783674 1.790000e-18 104.0
16 TraesCS2B01G015400 chrUn 97.344 1393 23 1 1 1393 268872289 268870911 0.000000e+00 2355.0
17 TraesCS2B01G015400 chrUn 98.396 1122 18 0 1 1122 385832158 385833279 0.000000e+00 1973.0
18 TraesCS2B01G015400 chrUn 88.320 625 54 11 2930 3538 11589947 11589326 0.000000e+00 732.0
19 TraesCS2B01G015400 chrUn 99.000 100 1 0 3544 3643 268870905 268870806 2.890000e-41 180.0
20 TraesCS2B01G015400 chrUn 100.000 83 0 0 3559 3641 365226190 365226108 1.750000e-33 154.0
21 TraesCS2B01G015400 chrUn 97.619 84 1 1 3559 3641 196972167 196972084 3.790000e-30 143.0
22 TraesCS2B01G015400 chr2D 92.552 1356 79 14 2202 3540 4027132 4025782 0.000000e+00 1925.0
23 TraesCS2B01G015400 chr2D 92.336 1357 80 15 2202 3540 3969540 3968190 0.000000e+00 1908.0
24 TraesCS2B01G015400 chr2D 89.374 1261 101 15 955 2207 4029629 4028394 0.000000e+00 1555.0
25 TraesCS2B01G015400 chr2D 89.277 1259 104 12 955 2207 3972032 3970799 0.000000e+00 1548.0
26 TraesCS2B01G015400 chr4D 93.355 602 35 3 229 826 27473484 27472884 0.000000e+00 885.0
27 TraesCS2B01G015400 chr4D 88.217 645 48 8 229 847 366732320 366732962 0.000000e+00 745.0
28 TraesCS2B01G015400 chr4D 88.112 143 7 1 715 847 441178225 441178367 1.050000e-35 161.0
29 TraesCS2B01G015400 chr5D 93.189 602 36 3 229 826 264727791 264727191 0.000000e+00 880.0
30 TraesCS2B01G015400 chr6D 93.023 602 37 3 229 826 409405310 409404710 0.000000e+00 874.0
31 TraesCS2B01G015400 chr4B 88.300 641 47 6 233 847 522603160 522603798 0.000000e+00 743.0
32 TraesCS2B01G015400 chr4B 95.408 196 9 0 40 235 428477675 428477480 2.730000e-81 313.0
33 TraesCS2B01G015400 chr4B 90.909 55 3 2 1 53 428477772 428477718 5.050000e-09 73.1
34 TraesCS2B01G015400 chr6A 94.146 205 11 1 40 243 602183674 602183470 9.820000e-81 311.0
35 TraesCS2B01G015400 chr6A 90.909 55 3 2 1 53 602183771 602183717 5.050000e-09 73.1


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 TraesCS2B01G015400 chr2B 7159621 7163263 3642 False 6728.0 6728 100.000000 1 3643 1 chr2B.!!$F3 3642
1 TraesCS2B01G015400 chr2B 7085372 7089029 3657 False 6464.0 6464 98.633000 1 3643 1 chr2B.!!$F2 3642
2 TraesCS2B01G015400 chr2B 454717880 454721433 3553 True 6102.0 6102 97.722000 1 3540 1 chr2B.!!$R2 3539
3 TraesCS2B01G015400 chr2B 454691914 454694628 2714 True 4349.0 4349 95.731000 849 3540 1 chr2B.!!$R1 2691
4 TraesCS2B01G015400 chr2B 7000938 7002892 1954 False 3127.0 3127 95.582000 1587 3540 1 chr2B.!!$F1 1953
5 TraesCS2B01G015400 chr2B 6956310 6959057 2747 True 2172.5 4176 95.945500 851 3540 2 chr2B.!!$R5 2689
6 TraesCS2B01G015400 chr2B 7047561 7050033 2472 False 2132.5 4085 98.462000 1 3643 2 chr2B.!!$F5 3642
7 TraesCS2B01G015400 chr2B 6869685 6872473 2788 True 1465.0 2645 95.383333 851 3540 3 chr2B.!!$R4 2689
8 TraesCS2B01G015400 chr2B 454783674 454785562 1888 True 1215.0 2326 99.278500 1 3643 2 chr2B.!!$R6 3642
9 TraesCS2B01G015400 chrUn 385832158 385833279 1121 False 1973.0 1973 98.396000 1 1122 1 chrUn.!!$F1 1121
10 TraesCS2B01G015400 chrUn 268870806 268872289 1483 True 1267.5 2355 98.172000 1 3643 2 chrUn.!!$R4 3642
11 TraesCS2B01G015400 chrUn 11589326 11589947 621 True 732.0 732 88.320000 2930 3538 1 chrUn.!!$R1 608
12 TraesCS2B01G015400 chr2D 4025782 4029629 3847 True 1740.0 1925 90.963000 955 3540 2 chr2D.!!$R2 2585
13 TraesCS2B01G015400 chr2D 3968190 3972032 3842 True 1728.0 1908 90.806500 955 3540 2 chr2D.!!$R1 2585
14 TraesCS2B01G015400 chr4D 27472884 27473484 600 True 885.0 885 93.355000 229 826 1 chr4D.!!$R1 597
15 TraesCS2B01G015400 chr4D 366732320 366732962 642 False 745.0 745 88.217000 229 847 1 chr4D.!!$F1 618
16 TraesCS2B01G015400 chr5D 264727191 264727791 600 True 880.0 880 93.189000 229 826 1 chr5D.!!$R1 597
17 TraesCS2B01G015400 chr6D 409404710 409405310 600 True 874.0 874 93.023000 229 826 1 chr6D.!!$R1 597
18 TraesCS2B01G015400 chr4B 522603160 522603798 638 False 743.0 743 88.300000 233 847 1 chr4B.!!$F1 614

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
614 631 1.949525 GCCATCTCGGTAATGCACATT 59.05 47.619 0.94 0.94 36.97 2.71 F
1443 1524 2.629656 GCGCCAGATGCACAAGGTT 61.63 57.895 0.00 0.00 41.33 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 1524 0.537828 TGAGCAGCTCCACAATGCAA 60.538 50.000 20.16 0.00 42.45 4.08 R
3021 4421 4.944317 CGACATAGGCATCTCTATAGTGGA 59.056 45.833 0.00 0.49 0.00 4.02 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
462 464 6.480763 TGAGATTATGCAACTCCCTTTTACA 58.519 36.000 0.00 0.00 0.00 2.41
614 631 1.949525 GCCATCTCGGTAATGCACATT 59.050 47.619 0.94 0.94 36.97 2.71
1443 1524 2.629656 GCGCCAGATGCACAAGGTT 61.630 57.895 0.00 0.00 41.33 3.50
1596 1680 2.885135 TGATGGAGGTCAGCAACAAT 57.115 45.000 0.00 0.00 39.01 2.71
1771 1855 1.134580 GCATGAAGAGGAGCTACAGCA 60.135 52.381 0.00 0.00 45.16 4.41
1863 1947 1.676635 CACCCACGACGAGGACCTA 60.677 63.158 13.31 0.00 0.00 3.08
1908 1992 4.019174 AGAAGGATGATTCGTTGGCATTT 58.981 39.130 0.00 0.00 34.27 2.32
2579 3976 4.229582 ACCATGGCTTTGACCTTAATCCTA 59.770 41.667 13.04 0.00 0.00 2.94
2673 4070 9.182214 CCTTGATGGAGATCTTTTTATTCTTGA 57.818 33.333 0.00 0.00 38.35 3.02
2783 4181 4.900635 AGATTCCATAAACATTGGTCGC 57.099 40.909 0.00 0.00 35.64 5.19
2926 4324 8.706322 AATGGGTTTTTGTAAGTTCTATCACT 57.294 30.769 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
462 464 3.004752 AGCACACAAAGTGTTTCTCCT 57.995 42.857 0.00 0.00 45.08 3.69
614 631 5.192927 ACAATGCTTGCAAGGCTTATAGTA 58.807 37.500 27.10 0.00 0.00 1.82
1436 1517 1.069049 GCTCCACAATGCAAACCTTGT 59.931 47.619 0.00 0.00 36.04 3.16
1443 1524 0.537828 TGAGCAGCTCCACAATGCAA 60.538 50.000 20.16 0.00 42.45 4.08
1794 1878 1.153765 CTTGCGCTCCTCGATCACA 60.154 57.895 9.73 0.00 41.67 3.58
1863 1947 4.363990 CTGAGCAGCACGTCCGGT 62.364 66.667 0.00 0.00 0.00 5.28
1908 1992 2.604912 TGCTCTCTGTGGTTAGAGGA 57.395 50.000 0.00 0.00 43.48 3.71
2579 3976 8.723942 TGTTGGTTGCAATATTAAAACAAAGT 57.276 26.923 0.59 0.00 32.63 2.66
2783 4181 7.083858 ACAATGTAAAGTGAATGTTCATTCCG 58.916 34.615 18.78 3.21 39.73 4.30
2926 4324 6.513884 GCATGATTTCCTCGATTGCTAATGAA 60.514 38.462 0.00 0.00 0.00 2.57
3021 4421 4.944317 CGACATAGGCATCTCTATAGTGGA 59.056 45.833 0.00 0.49 0.00 4.02
3089 4489 9.480053 CATTCAAGTTTATGAGGATGTTTGTTT 57.520 29.630 0.00 0.00 0.00 2.83
3091 4491 8.181904 ACATTCAAGTTTATGAGGATGTTTGT 57.818 30.769 2.53 0.00 30.38 2.83
3097 4497 6.078456 TGGGACATTCAAGTTTATGAGGAT 57.922 37.500 2.53 0.00 0.00 3.24
3415 4832 6.328934 TCTGTGGCACCAGAAAATATATCCTA 59.671 38.462 16.26 0.00 38.49 2.94


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

AutoCloner maintained by Alex Coulton.