Multiple sequence alignment - TraesCS3A01G180300

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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 TraesCS3A01G180300 chr3A 100.000 3651 0 0 1 3651 208233220 208236870 0.000000e+00 6743
1 TraesCS3A01G180300 chr3A 85.421 878 115 7 1777 2653 208086396 208085531 0.000000e+00 900
2 TraesCS3A01G180300 chr3A 88.782 624 70 0 2037 2660 208089595 208088972 0.000000e+00 765
3 TraesCS3A01G180300 chr3A 91.411 163 14 0 33 195 204885395 204885557 1.320000e-54 224
4 TraesCS3A01G180300 chr3A 82.051 234 36 3 1000 1227 208090513 208090280 1.030000e-45 195
5 TraesCS3A01G180300 chr3D 96.381 3675 83 15 1 3651 170667054 170670702 0.000000e+00 6004
6 TraesCS3A01G180300 chr3D 85.063 877 112 7 1777 2653 170558160 170557303 0.000000e+00 876
7 TraesCS3A01G180300 chr3D 88.339 626 71 2 2036 2660 170564257 170563633 0.000000e+00 750
8 TraesCS3A01G180300 chr3D 86.942 582 76 0 2062 2643 170659786 170660367 0.000000e+00 654
9 TraesCS3A01G180300 chr3D 81.590 239 32 8 1001 1230 170558776 170558541 1.730000e-43 187
10 TraesCS3A01G180300 chr3D 86.310 168 13 3 572 734 391318916 391318754 1.350000e-39 174
11 TraesCS3A01G180300 chr3B 95.816 2629 77 12 727 3337 246145239 246147852 0.000000e+00 4215
12 TraesCS3A01G180300 chr3B 83.854 960 124 18 1777 2732 245964146 245963214 0.000000e+00 885
13 TraesCS3A01G180300 chr3B 91.910 581 25 4 1 575 246144683 246145247 0.000000e+00 793
14 TraesCS3A01G180300 chr3B 88.160 625 74 0 2036 2660 245969607 245968983 0.000000e+00 745
15 TraesCS3A01G180300 chr3B 87.801 582 71 0 2062 2643 246129338 246129919 0.000000e+00 682
16 TraesCS3A01G180300 chr3B 98.182 330 6 0 3322 3651 246148029 246148358 8.790000e-161 577
17 TraesCS3A01G180300 chr3B 81.172 239 29 12 1000 1227 245970513 245970280 1.040000e-40 178
18 TraesCS3A01G180300 chr3B 80.169 237 39 5 1001 1230 245964727 245964492 1.740000e-38 171
19 TraesCS3A01G180300 chr7A 91.176 170 15 0 26 195 83784825 83784994 7.880000e-57 231
20 TraesCS3A01G180300 chr5B 91.925 161 13 0 35 195 574956445 574956605 3.670000e-55 226
21 TraesCS3A01G180300 chr4D 91.463 164 14 0 32 195 482703628 482703465 3.670000e-55 226
22 TraesCS3A01G180300 chr4D 86.747 166 12 3 572 732 427269514 427269674 3.750000e-40 176
23 TraesCS3A01G180300 chr2B 91.463 164 14 0 34 197 248148226 248148063 3.670000e-55 226
24 TraesCS3A01G180300 chr2B 85.000 180 16 7 572 745 215832712 215832538 4.850000e-39 172
25 TraesCS3A01G180300 chr2A 90.964 166 12 3 32 195 231352954 231352790 1.710000e-53 220
26 TraesCS3A01G180300 chr2A 89.157 166 8 5 572 732 696850717 696850877 8.000000e-47 198
27 TraesCS3A01G180300 chr1A 90.419 167 16 0 29 195 398450751 398450585 1.710000e-53 220
28 TraesCS3A01G180300 chr1A 86.905 168 11 3 572 733 181769427 181769589 1.040000e-40 178
29 TraesCS3A01G180300 chr1D 87.952 166 8 5 572 732 379456352 379456510 6.230000e-43 185
30 TraesCS3A01G180300 chr6D 85.965 171 11 5 571 735 178849198 178849361 1.740000e-38 171
31 TraesCS3A01G180300 chr4A 85.882 170 13 4 572 735 80142935 80142771 1.740000e-38 171


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 TraesCS3A01G180300 chr3A 208233220 208236870 3650 False 6743.000000 6743 100.000000 1 3651 1 chr3A.!!$F2 3650
1 TraesCS3A01G180300 chr3A 208085531 208090513 4982 True 620.000000 900 85.418000 1000 2660 3 chr3A.!!$R1 1660
2 TraesCS3A01G180300 chr3D 170667054 170670702 3648 False 6004.000000 6004 96.381000 1 3651 1 chr3D.!!$F2 3650
3 TraesCS3A01G180300 chr3D 170563633 170564257 624 True 750.000000 750 88.339000 2036 2660 1 chr3D.!!$R1 624
4 TraesCS3A01G180300 chr3D 170659786 170660367 581 False 654.000000 654 86.942000 2062 2643 1 chr3D.!!$F1 581
5 TraesCS3A01G180300 chr3D 170557303 170558776 1473 True 531.500000 876 83.326500 1001 2653 2 chr3D.!!$R3 1652
6 TraesCS3A01G180300 chr3B 246144683 246148358 3675 False 1861.666667 4215 95.302667 1 3651 3 chr3B.!!$F2 3650
7 TraesCS3A01G180300 chr3B 246129338 246129919 581 False 682.000000 682 87.801000 2062 2643 1 chr3B.!!$F1 581
8 TraesCS3A01G180300 chr3B 245963214 245964727 1513 True 528.000000 885 82.011500 1001 2732 2 chr3B.!!$R1 1731
9 TraesCS3A01G180300 chr3B 245968983 245970513 1530 True 461.500000 745 84.666000 1000 2660 2 chr3B.!!$R2 1660

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
98 99 0.178301 GGGAAGGGTCCGATCACTTC 59.822 60.000 11.51 11.51 46.04 3.01 F
926 946 1.702401 TCTGCACCTCATAACCCACAA 59.298 47.619 0.00 0.00 0.00 3.33 F
927 947 2.086869 CTGCACCTCATAACCCACAAG 58.913 52.381 0.00 0.00 0.00 3.16 F
2295 5985 0.830444 AGGCTGTACAACCAGTCGGA 60.830 55.000 17.41 0.00 41.93 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 5394 1.133598 CACAGATTCGGCACATGCAAT 59.866 47.619 6.15 0.00 44.36 3.56 R
2116 5806 0.332293 TTGATCCCTGGATGCTTGCA 59.668 50.000 2.75 0.00 34.60 4.08 R
2620 6310 1.123861 TGTTGAGCCTCCTGCAGTCT 61.124 55.000 13.81 3.86 44.83 3.24 R
3313 7019 1.841302 TTCCGATGAGCAAGGCAGGT 61.841 55.000 0.00 0.00 0.00 4.00 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
98 99 0.178301 GGGAAGGGTCCGATCACTTC 59.822 60.000 11.51 11.51 46.04 3.01
153 154 3.225104 TGCAAGAGGCTGTTTTCAAGAT 58.775 40.909 0.00 0.00 45.15 2.40
352 358 2.622942 GTTCTTCAAGTGGTGATGGCAA 59.377 45.455 0.00 0.00 35.70 4.52
393 399 6.917477 AGTGTTACAGTGTGCATTTGTATTTG 59.083 34.615 5.88 0.00 0.00 2.32
530 543 4.202461 ACCGAAACATGACATAGGGCATAT 60.202 41.667 0.00 0.00 0.00 1.78
594 608 9.684702 AGTTACTCCCTCCATTCCTAAATATAA 57.315 33.333 0.00 0.00 0.00 0.98
597 611 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
621 635 9.991388 GTCGAGATTCCAATATAGACTACATAC 57.009 37.037 0.00 0.00 32.07 2.39
622 636 9.734984 TCGAGATTCCAATATAGACTACATACA 57.265 33.333 0.00 0.00 0.00 2.29
658 672 8.057536 AGTGAATCTACACTCTAAAGTAGGTG 57.942 38.462 0.00 0.00 46.36 4.00
659 673 7.889073 AGTGAATCTACACTCTAAAGTAGGTGA 59.111 37.037 0.00 0.00 46.36 4.02
660 674 8.185505 GTGAATCTACACTCTAAAGTAGGTGAG 58.814 40.741 0.00 0.00 38.54 3.51
661 675 7.339721 TGAATCTACACTCTAAAGTAGGTGAGG 59.660 40.741 0.00 0.00 38.54 3.86
662 676 6.137104 TCTACACTCTAAAGTAGGTGAGGT 57.863 41.667 0.00 0.00 38.54 3.85
674 688 8.653036 AAAGTAGGTGAGGTCTATATACATCC 57.347 38.462 1.11 0.00 29.20 3.51
926 946 1.702401 TCTGCACCTCATAACCCACAA 59.298 47.619 0.00 0.00 0.00 3.33
927 947 2.086869 CTGCACCTCATAACCCACAAG 58.913 52.381 0.00 0.00 0.00 3.16
928 948 1.702401 TGCACCTCATAACCCACAAGA 59.298 47.619 0.00 0.00 0.00 3.02
1230 1256 2.147150 GACTGCTTTGTCAAGGTCTCC 58.853 52.381 0.00 0.00 36.97 3.71
1296 1374 6.197276 GCTACAATGATACTTGCTGAACATG 58.803 40.000 0.00 0.00 0.00 3.21
1347 1941 6.763355 ACTATTTCATTGTGAGTCTGTGACT 58.237 36.000 0.00 0.00 46.42 3.41
1348 1942 7.896811 ACTATTTCATTGTGAGTCTGTGACTA 58.103 34.615 0.00 0.00 43.53 2.59
1349 1943 8.367911 ACTATTTCATTGTGAGTCTGTGACTAA 58.632 33.333 0.00 0.00 43.53 2.24
1350 1944 9.376075 CTATTTCATTGTGAGTCTGTGACTAAT 57.624 33.333 0.00 0.00 43.53 1.73
1352 1946 8.763049 TTTCATTGTGAGTCTGTGACTAATAG 57.237 34.615 0.00 0.00 43.53 1.73
1603 5277 3.689649 AGTCCGTACCATGATTGCTTTTC 59.310 43.478 0.00 0.00 0.00 2.29
1725 5406 3.425577 ACTATTTCATTGCATGTGCCG 57.574 42.857 2.07 0.00 41.18 5.69
1743 5424 2.810650 CCGAATCTGTGTAGTACCAGC 58.189 52.381 11.74 0.00 0.00 4.85
1988 5670 3.067461 TCCTTGTATGTGCACACCAAAAC 59.933 43.478 24.37 15.22 0.00 2.43
2034 5716 6.183360 CGAGTTAAACAATGCAGCCAGTATTA 60.183 38.462 0.00 0.00 30.89 0.98
2116 5806 2.681778 CGCAGGGACTCTCTGGGT 60.682 66.667 13.70 0.00 39.41 4.51
2295 5985 0.830444 AGGCTGTACAACCAGTCGGA 60.830 55.000 17.41 0.00 41.93 4.55
2620 6310 1.203428 TCACAGGGGGAGATCAGGAAA 60.203 52.381 0.00 0.00 0.00 3.13
2758 6450 4.493350 CGAAATCGCTTGATCATTTGTGTC 59.507 41.667 0.00 0.00 0.00 3.67
2825 6517 9.890629 ATATAAGATGAGTTCACTTGTTTGCTA 57.109 29.630 0.00 0.00 0.00 3.49
2834 6529 4.456535 TCACTTGTTTGCTAAGCTGGTTA 58.543 39.130 0.00 0.00 0.00 2.85
3317 7023 1.638529 AAGAGGAGTCCAGTCACCTG 58.361 55.000 12.86 0.00 38.50 4.00
3496 7394 1.340889 GCATTGCAAACCCTCAGTTCA 59.659 47.619 1.71 0.00 37.88 3.18
3597 7495 6.261826 CCAGCAGAGAGGAATTTATTTGTAGG 59.738 42.308 0.00 0.00 0.00 3.18
3602 7500 7.226325 CAGAGAGGAATTTATTTGTAGGCTCTG 59.774 40.741 0.00 0.00 38.67 3.35
3617 7515 2.289072 GGCTCTGTGCTTGAAGTCACTA 60.289 50.000 16.50 7.68 42.39 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 1.225376 TGCTGCGTACAAAAGACCCG 61.225 55.000 0.00 0.00 0.00 5.28
153 154 0.037697 CATGAGGTCACGGGTTCGAA 60.038 55.000 0.00 0.00 40.11 3.71
352 358 9.453572 ACTGTAACACTGATGAAACATCAATAT 57.546 29.630 13.97 5.50 0.00 1.28
393 399 9.448294 ACTCAGTAAATATTTTATCGACGAGTC 57.552 33.333 5.91 0.00 0.00 3.36
530 543 6.306199 TCATCTGATTTTCTTCCAAAGGTGA 58.694 36.000 0.00 0.00 0.00 4.02
594 608 8.871629 ATGTAGTCTATATTGGAATCTCGACT 57.128 34.615 0.00 0.00 35.06 4.18
597 611 9.995957 CTGTATGTAGTCTATATTGGAATCTCG 57.004 37.037 0.00 0.00 0.00 4.04
621 635 8.994429 AGTGTAGATTCACTCATTTTACTCTG 57.006 34.615 0.00 0.00 44.07 3.35
658 672 8.961294 ACTACATACGGATGTATATAGACCTC 57.039 38.462 20.64 0.00 45.42 3.85
659 673 9.750783 AAACTACATACGGATGTATATAGACCT 57.249 33.333 20.64 0.00 45.42 3.85
660 674 9.784680 CAAACTACATACGGATGTATATAGACC 57.215 37.037 20.64 0.00 45.42 3.85
1230 1256 6.830114 GGATACTACAGGAAAGATGAAACG 57.170 41.667 0.00 0.00 0.00 3.60
1296 1374 4.202245 TCTGTACTACATTGCAGGAACC 57.798 45.455 0.00 0.00 0.00 3.62
1382 5044 4.708726 GCATTGGAACTGCTGTAAGATT 57.291 40.909 0.00 0.00 36.68 2.40
1603 5277 1.202336 GCAATCGCCATCTTTTCAGGG 60.202 52.381 0.00 0.00 0.00 4.45
1713 5394 1.133598 CACAGATTCGGCACATGCAAT 59.866 47.619 6.15 0.00 44.36 3.56
1725 5406 4.822026 AGTTGCTGGTACTACACAGATTC 58.178 43.478 1.51 0.00 36.86 2.52
1988 5670 5.601662 TCGTGCTATCTGGGAAAGAATTAG 58.398 41.667 0.00 0.00 38.79 1.73
2034 5716 3.611025 TTTGGGTCCCAAAGAATCACT 57.389 42.857 29.12 0.00 46.92 3.41
2116 5806 0.332293 TTGATCCCTGGATGCTTGCA 59.668 50.000 2.75 0.00 34.60 4.08
2620 6310 1.123861 TGTTGAGCCTCCTGCAGTCT 61.124 55.000 13.81 3.86 44.83 3.24
2758 6450 9.089601 ACACACATTTCATAATGCAATTACATG 57.910 29.630 0.00 0.00 42.43 3.21
2825 6517 7.668052 TGGTAAGTTATGTCAAATAACCAGCTT 59.332 33.333 0.00 0.00 35.65 3.74
3313 7019 1.841302 TTCCGATGAGCAAGGCAGGT 61.841 55.000 0.00 0.00 0.00 4.00
3317 7023 2.687842 CTCTTCCGATGAGCAAGGC 58.312 57.895 0.00 0.00 0.00 4.35
3496 7394 8.294954 ACAGTACTAGTGTAGTATGAAAGCAT 57.705 34.615 5.39 0.00 42.68 3.79
3597 7495 1.876322 AGTGACTTCAAGCACAGAGC 58.124 50.000 12.60 0.00 46.19 4.09
3602 7500 5.639506 TCAGCTAATTAGTGACTTCAAGCAC 59.360 40.000 13.91 4.35 35.30 4.40


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

AutoCloner maintained by Alex Coulton.