Multiple sequence alignment - TraesCS2D01G190200

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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 TraesCS2D01G190200 chr2D 100.000 5451 0 0 1 5451 134291778 134297228 0.000000e+00 10067.0
1 TraesCS2D01G190200 chr2D 86.151 2094 250 24 1192 3268 20611386 20609316 0.000000e+00 2224.0
2 TraesCS2D01G190200 chr2D 84.010 2020 303 8 1224 3242 20619601 20617601 0.000000e+00 1923.0
3 TraesCS2D01G190200 chr2D 81.677 1157 166 22 1162 2284 20648552 20647408 0.000000e+00 920.0
4 TraesCS2D01G190200 chr2D 80.525 991 164 13 2286 3268 20636999 20636030 0.000000e+00 734.0
5 TraesCS2D01G190200 chr2D 82.497 817 123 8 2427 3242 20654671 20653874 0.000000e+00 699.0
6 TraesCS2D01G190200 chr2D 80.189 106 15 6 4664 4765 144997940 144998043 2.110000e-09 75.0
7 TraesCS2D01G190200 chr2A 92.925 4820 246 42 49 4822 141880992 141885762 0.000000e+00 6924.0
8 TraesCS2D01G190200 chr2A 83.477 1277 204 4 1419 2689 21209379 21208104 0.000000e+00 1182.0
9 TraesCS2D01G190200 chr2A 86.834 676 74 10 2571 3242 21233310 21232646 0.000000e+00 741.0
10 TraesCS2D01G190200 chr2A 81.835 545 90 5 2677 3221 21208083 21207548 2.990000e-122 449.0
11 TraesCS2D01G190200 chr2A 94.372 231 11 2 5222 5451 141891628 141891857 2.420000e-93 353.0
12 TraesCS2D01G190200 chr2A 82.486 354 26 16 4878 5230 141886026 141886344 1.500000e-70 278.0
13 TraesCS2D01G190200 chr2A 86.864 236 29 2 2291 2525 21233550 21233316 4.190000e-66 263.0
14 TraesCS2D01G190200 chr2B 93.920 4145 190 25 496 4596 190194796 190198922 0.000000e+00 6202.0
15 TraesCS2D01G190200 chr2B 88.710 744 78 3 1529 2271 33771831 33771093 0.000000e+00 904.0
16 TraesCS2D01G190200 chr2B 88.262 443 28 16 50 478 190194060 190194492 4.870000e-140 508.0
17 TraesCS2D01G190200 chr2B 87.259 259 29 4 5072 5327 190232590 190232847 5.340000e-75 292.0
18 TraesCS2D01G190200 chr2B 84.659 176 19 5 1157 1325 33772014 33771840 9.390000e-38 169.0
19 TraesCS2D01G190200 chrUn 83.144 1412 226 10 1159 2561 373122184 373123592 0.000000e+00 1279.0
20 TraesCS2D01G190200 chr4B 84.564 149 15 7 5065 5206 517169961 517170108 2.050000e-29 141.0
21 TraesCS2D01G190200 chr5B 82.787 122 20 1 4606 4726 704167872 704167751 2.080000e-19 108.0
22 TraesCS2D01G190200 chr6B 82.645 121 19 2 4600 4719 46348668 46348549 7.470000e-19 106.0
23 TraesCS2D01G190200 chr1B 80.469 128 23 2 4606 4731 49319117 49318990 4.490000e-16 97.1
24 TraesCS2D01G190200 chr1B 88.571 70 8 0 4664 4733 20044117 20044186 9.730000e-13 86.1
25 TraesCS2D01G190200 chr1B 83.750 80 9 2 3575 3652 603092216 603092139 7.570000e-09 73.1
26 TraesCS2D01G190200 chr1B 82.667 75 9 2 3580 3652 603147907 603147835 4.560000e-06 63.9
27 TraesCS2D01G190200 chr3D 79.839 124 23 2 4606 4728 281905325 281905447 7.520000e-14 89.8
28 TraesCS2D01G190200 chr3D 92.857 56 4 0 4664 4719 11271276 11271331 1.260000e-11 82.4
29 TraesCS2D01G190200 chr3D 97.500 40 1 0 3580 3619 341495006 341495045 9.800000e-08 69.4
30 TraesCS2D01G190200 chr5A 82.292 96 13 4 4282 4375 594972693 594972600 4.530000e-11 80.5
31 TraesCS2D01G190200 chr3A 81.000 100 17 2 4630 4728 368523353 368523451 1.630000e-10 78.7
32 TraesCS2D01G190200 chr3A 84.000 75 8 2 3580 3652 461840113 461840041 9.800000e-08 69.4
33 TraesCS2D01G190200 chr4D 84.211 76 12 0 4282 4357 338011851 338011776 2.110000e-09 75.0
34 TraesCS2D01G190200 chr1D 83.750 80 9 2 3575 3652 443428056 443427979 7.570000e-09 73.1
35 TraesCS2D01G190200 chr1A 83.544 79 11 2 3575 3652 539426727 539426650 7.570000e-09 73.1
36 TraesCS2D01G190200 chr3B 95.000 40 2 0 3580 3619 440230441 440230480 4.560000e-06 63.9


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 TraesCS2D01G190200 chr2D 134291778 134297228 5450 False 10067.0 10067 100.0000 1 5451 1 chr2D.!!$F1 5450
1 TraesCS2D01G190200 chr2D 20609316 20611386 2070 True 2224.0 2224 86.1510 1192 3268 1 chr2D.!!$R1 2076
2 TraesCS2D01G190200 chr2D 20617601 20619601 2000 True 1923.0 1923 84.0100 1224 3242 1 chr2D.!!$R2 2018
3 TraesCS2D01G190200 chr2D 20647408 20648552 1144 True 920.0 920 81.6770 1162 2284 1 chr2D.!!$R4 1122
4 TraesCS2D01G190200 chr2D 20636030 20636999 969 True 734.0 734 80.5250 2286 3268 1 chr2D.!!$R3 982
5 TraesCS2D01G190200 chr2D 20653874 20654671 797 True 699.0 699 82.4970 2427 3242 1 chr2D.!!$R5 815
6 TraesCS2D01G190200 chr2A 141880992 141886344 5352 False 3601.0 6924 87.7055 49 5230 2 chr2A.!!$F2 5181
7 TraesCS2D01G190200 chr2A 21207548 21209379 1831 True 815.5 1182 82.6560 1419 3221 2 chr2A.!!$R1 1802
8 TraesCS2D01G190200 chr2A 21232646 21233550 904 True 502.0 741 86.8490 2291 3242 2 chr2A.!!$R2 951
9 TraesCS2D01G190200 chr2B 190194060 190198922 4862 False 3355.0 6202 91.0910 50 4596 2 chr2B.!!$F2 4546
10 TraesCS2D01G190200 chr2B 33771093 33772014 921 True 536.5 904 86.6845 1157 2271 2 chr2B.!!$R1 1114
11 TraesCS2D01G190200 chrUn 373122184 373123592 1408 False 1279.0 1279 83.1440 1159 2561 1 chrUn.!!$F1 1402


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
485 782 0.035439 TGCCGATCCCTTCTTGTTCC 60.035 55.000 0.00 0.00 0.00 3.62 F
1108 1458 0.321671 CTTCTCTTCTTGGGGCGTGA 59.678 55.000 0.00 0.00 0.00 4.35 F
1443 1815 0.250234 CTCTCCGGCAACTCCATCAA 59.750 55.000 0.00 0.00 34.01 2.57 F
2401 2804 1.188219 GGATCCCAGCGAGCATAGGA 61.188 60.000 0.00 0.56 0.00 2.94 F
2689 3095 1.376543 TCGTCTACTCCGTCATGACC 58.623 55.000 20.03 2.51 0.00 4.02 F
3439 3899 2.165301 CGCGTTCGGAATGTCCTCC 61.165 63.158 11.33 0.00 33.30 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1745 0.600255 CGAGAAGTTGCCGAACACCT 60.600 55.000 0.00 0.0 34.17 4.00 R
3094 3548 0.531200 CGGAGAGGAGTGGGTTGTAC 59.469 60.000 0.00 0.0 0.00 2.90 R
3268 3722 0.250081 GCCAGATCCCGATGGTTCTC 60.250 60.000 1.12 0.0 38.41 2.87 R
3523 3983 0.866061 CGATGTCGCGGTAGGTGAAG 60.866 60.000 6.13 0.0 36.80 3.02 R
4132 4592 1.586564 GAGCACGCCGTAGCTGTAG 60.587 63.158 16.65 0.0 42.04 2.74 R
5337 6030 0.033504 TCTTGGTCCAAGACAGCGAC 59.966 55.000 27.39 0.0 44.27 5.19 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)



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AutoCloner maintained by Alex Coulton.