Multiple sequence alignment - TraesCS2D01G139400

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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 TraesCS2D01G139400 chr2D 100.000 6056 0 0 1 6056 82186194 82180139 0.000000e+00 11184
1 TraesCS2D01G139400 chr2D 83.077 1430 148 38 1672 3028 82189287 82187879 0.000000e+00 1214
2 TraesCS2D01G139400 chr2D 85.014 694 61 17 4607 5284 82186300 82185634 0.000000e+00 665
3 TraesCS2D01G139400 chr2D 85.026 581 50 13 6 561 82181479 82180911 1.910000e-154 556
4 TraesCS2D01G139400 chr2D 87.810 443 49 5 3684 4122 82187159 82186718 1.160000e-141 514
5 TraesCS2D01G139400 chr2D 78.059 711 67 39 934 1594 82189993 82189322 3.450000e-97 366
6 TraesCS2D01G139400 chr2D 88.421 95 7 4 4179 4271 96798682 96798774 1.780000e-20 111
7 TraesCS2D01G139400 chr2A 94.064 4801 165 47 698 5468 82349742 82345032 0.000000e+00 7177
8 TraesCS2D01G139400 chr2A 82.463 1437 155 43 1672 3028 82353740 82352321 0.000000e+00 1168
9 TraesCS2D01G139400 chr2A 91.453 702 23 4 1 699 82350507 82349840 0.000000e+00 929
10 TraesCS2D01G139400 chr2A 85.754 723 74 12 4600 5315 82350620 82349920 0.000000e+00 737
11 TraesCS2D01G139400 chr2A 86.043 652 68 15 3043 3680 82352334 82351692 0.000000e+00 678
12 TraesCS2D01G139400 chr2A 92.841 447 17 10 5549 5981 82344896 82344451 8.560000e-178 634
13 TraesCS2D01G139400 chr2A 87.945 506 58 3 3684 4186 82351582 82351077 1.450000e-165 593
14 TraesCS2D01G139400 chr2A 82.961 716 59 39 962 1654 82354811 82354136 6.760000e-164 588
15 TraesCS2D01G139400 chr2A 83.681 576 58 14 6 557 82345785 82345222 1.510000e-140 510
16 TraesCS2D01G139400 chr2A 94.667 75 4 0 5982 6056 82344415 82344341 3.840000e-22 117
17 TraesCS2D01G139400 chr2B 92.189 2010 88 30 3978 5981 134045749 134043803 0.000000e+00 2778
18 TraesCS2D01G139400 chr2B 94.281 1836 72 12 1201 3005 134049017 134047184 0.000000e+00 2778
19 TraesCS2D01G139400 chr2B 96.472 992 26 2 2996 3980 134046899 134045910 0.000000e+00 1629
20 TraesCS2D01G139400 chr2B 87.828 723 61 10 4600 5314 134090703 134090000 0.000000e+00 822
21 TraesCS2D01G139400 chr2B 91.930 570 30 6 1 561 134090591 134090029 0.000000e+00 784
22 TraesCS2D01G139400 chr2B 85.423 686 74 14 3043 3710 134092351 134091674 0.000000e+00 689
23 TraesCS2D01G139400 chr2B 86.823 554 55 12 1672 2214 134093715 134093169 2.410000e-168 603
24 TraesCS2D01G139400 chr2B 80.220 819 92 37 2269 3028 134093145 134092338 8.870000e-153 551
25 TraesCS2D01G139400 chr2B 84.201 576 55 14 6 557 134045032 134044469 1.500000e-145 527
26 TraesCS2D01G139400 chr2B 81.006 716 66 37 973 1655 134094834 134094156 7.010000e-139 505
27 TraesCS2D01G139400 chr4D 91.579 95 3 5 4186 4278 34660035 34659944 6.370000e-25 126
28 TraesCS2D01G139400 chr6B 91.954 87 7 0 4185 4271 124550588 124550502 8.240000e-24 122
29 TraesCS2D01G139400 chr1A 91.765 85 6 1 4192 4275 343398331 343398415 3.840000e-22 117
30 TraesCS2D01G139400 chr5D 89.888 89 5 4 4186 4272 278271122 278271036 1.780000e-20 111
31 TraesCS2D01G139400 chr1B 89.888 89 5 4 4186 4272 288805396 288805482 1.780000e-20 111
32 TraesCS2D01G139400 chr1B 93.878 49 3 0 722 770 578093855 578093807 2.340000e-09 75
33 TraesCS2D01G139400 chr4A 87.234 94 8 4 4180 4271 581944255 581944346 2.990000e-18 104


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 TraesCS2D01G139400 chr2D 82180139 82186194 6055 True 11184.000000 11184 100.000000 1 6056 1 chr2D.!!$R1 6055
1 TraesCS2D01G139400 chr2D 82185634 82189993 4359 True 689.750000 1214 83.490000 934 5284 4 chr2D.!!$R3 4350
2 TraesCS2D01G139400 chr2D 82180911 82181479 568 True 556.000000 556 85.026000 6 561 1 chr2D.!!$R2 555
3 TraesCS2D01G139400 chr2A 82344341 82349742 5401 True 2642.666667 7177 93.857333 698 6056 3 chr2A.!!$R2 5358
4 TraesCS2D01G139400 chr2A 82349840 82354811 4971 True 782.166667 1168 86.103167 1 5315 6 chr2A.!!$R3 5314
5 TraesCS2D01G139400 chr2A 82345222 82345785 563 True 510.000000 510 83.681000 6 557 1 chr2A.!!$R1 551
6 TraesCS2D01G139400 chr2B 134043803 134049017 5214 True 1928.000000 2778 91.785750 6 5981 4 chr2B.!!$R1 5975
7 TraesCS2D01G139400 chr2B 134090000 134094834 4834 True 659.000000 822 85.538333 1 5314 6 chr2B.!!$R2 5313


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
169 170 0.036010 AGTTCCACCATCCGCAAGAG 60.036 55.000 0.00 0.0 43.02 2.85 F
1114 1124 0.036164 CCATCGAACCAACTGACCCA 59.964 55.000 0.00 0.0 0.00 4.51 F
1654 1723 0.254462 TCCCGCAGCCATGAATGTTA 59.746 50.000 0.00 0.0 0.00 2.41 F
1821 1890 3.119602 TCAAGGACTGCTGTGACGTATAC 60.120 47.826 0.00 0.0 0.00 1.47 F
3319 3775 1.145803 GCACGTTTAGTCAGTGGTCC 58.854 55.000 0.00 0.0 36.48 4.46 F
3451 3918 2.511600 GATTGCGAGGGTCGTGGG 60.512 66.667 0.00 0.0 42.81 4.61 F
3961 4512 4.221703 AGACAAGTGACCACAGAATAGAGG 59.778 45.833 2.78 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1375 1412 1.675641 GCAGCAGTTGACGGGGATT 60.676 57.895 0.00 0.00 0.00 3.01 R
2609 2731 2.375509 GGAAAGGAACTCCAGGGAGAAA 59.624 50.000 21.73 0.00 44.53 2.52 R
2943 3090 2.928334 ACTGGTCCATGAGATGAATGC 58.072 47.619 0.00 0.00 0.00 3.56 R
3451 3918 3.055385 TGCAAGTAGGACATGGTACCTTC 60.055 47.826 14.36 6.82 37.68 3.46 R
4437 5256 3.128764 GCCCTACTGGTTTGCTGATAAAC 59.871 47.826 0.00 0.00 39.28 2.01 R
4639 5512 4.276926 AGAAATTGCAAGTCAGACCAAGAC 59.723 41.667 4.94 0.00 36.26 3.01 R
5838 6827 0.442699 GACGATTCTTGGCCGTGTTC 59.557 55.000 0.00 0.00 36.60 3.18 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)



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

AutoCloner maintained by Alex Coulton.