Multiple sequence alignment - TraesCS3D01G041200

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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 TraesCS3D01G041200 chr3D 100.000 7976 0 0 1 7976 15915764 15923739 0.000000e+00 14729.0
1 TraesCS3D01G041200 chr3D 79.739 918 165 11 843 1749 15331546 15332453 0.000000e+00 645.0
2 TraesCS3D01G041200 chr3D 84.211 171 22 2 7093 7258 15909858 15910028 2.300000e-35 161.0
3 TraesCS3D01G041200 chr3B 87.934 2420 242 26 761 3151 22674847 22677245 0.000000e+00 2806.0
4 TraesCS3D01G041200 chr3B 91.144 1976 163 10 5015 6981 22837034 22839006 0.000000e+00 2669.0
5 TraesCS3D01G041200 chr3B 85.614 2141 280 18 4916 7046 22699178 22701300 0.000000e+00 2222.0
6 TraesCS3D01G041200 chr3B 86.674 1891 236 13 5222 7102 22788351 22790235 0.000000e+00 2082.0
7 TraesCS3D01G041200 chr3B 84.839 1926 224 40 838 2732 22831292 22833180 0.000000e+00 1877.0
8 TraesCS3D01G041200 chr3B 84.992 1779 231 18 5064 6829 22804739 22806494 0.000000e+00 1773.0
9 TraesCS3D01G041200 chr3B 79.672 1953 327 45 761 2669 22802632 22804558 0.000000e+00 1343.0
10 TraesCS3D01G041200 chr3B 81.152 1146 179 21 853 1977 22784747 22785876 0.000000e+00 885.0
11 TraesCS3D01G041200 chr3B 91.749 303 21 4 3140 3441 22677272 22677571 1.240000e-112 418.0
12 TraesCS3D01G041200 chr3B 86.325 351 27 12 3142 3491 22835336 22835666 5.880000e-96 363.0
13 TraesCS3D01G041200 chr3B 89.011 273 21 3 6825 7097 22824015 22824278 5.970000e-86 329.0
14 TraesCS3D01G041200 chr3B 82.456 228 26 6 7090 7313 22701402 22701619 3.800000e-43 187.0
15 TraesCS3D01G041200 chr3B 87.349 166 18 2 7090 7252 22839167 22839332 3.800000e-43 187.0
16 TraesCS3D01G041200 chr3B 88.889 153 10 3 181 326 22672139 22672291 1.770000e-41 182.0
17 TraesCS3D01G041200 chr3B 81.900 221 27 5 7096 7313 22826170 22826380 2.960000e-39 174.0
18 TraesCS3D01G041200 chr3B 95.327 107 5 0 49 155 22672040 22672146 3.830000e-38 171.0
19 TraesCS3D01G041200 chr3B 80.000 100 16 3 2282 2379 22804075 22804172 3.990000e-08 71.3
20 TraesCS3D01G041200 chr3A 87.144 2038 231 22 5073 7102 20720209 20718195 0.000000e+00 2283.0
21 TraesCS3D01G041200 chr3A 90.365 1588 130 17 761 2339 20727327 20725754 0.000000e+00 2063.0
22 TraesCS3D01G041200 chr3A 84.878 1931 223 42 838 2738 20745874 20743983 0.000000e+00 1884.0
23 TraesCS3D01G041200 chr3A 92.237 1314 93 4 5670 6981 20739032 20737726 0.000000e+00 1853.0
24 TraesCS3D01G041200 chr3A 84.492 1251 178 11 5859 7102 20735114 20733873 0.000000e+00 1221.0
25 TraesCS3D01G041200 chr3A 91.927 768 45 8 1 766 20728373 20727621 0.000000e+00 1059.0
26 TraesCS3D01G041200 chr3A 89.067 686 68 5 5015 5695 20739892 20739209 0.000000e+00 845.0
27 TraesCS3D01G041200 chr3A 83.461 786 114 14 5042 5818 20735894 20735116 0.000000e+00 717.0
28 TraesCS3D01G041200 chr3A 79.006 905 165 16 843 1732 20966249 20965355 5.330000e-166 595.0
29 TraesCS3D01G041200 chr3A 79.572 842 153 12 884 1712 21066099 21065264 1.150000e-162 584.0
30 TraesCS3D01G041200 chr3A 83.051 531 77 5 843 1369 20989773 20989252 3.370000e-128 470.0
31 TraesCS3D01G041200 chr3A 90.040 251 25 0 7269 7519 20715759 20715509 7.720000e-85 326.0
32 TraesCS3D01G041200 chr3A 90.722 194 16 2 7089 7281 20718172 20717980 2.860000e-64 257.0
33 TraesCS3D01G041200 chr3A 86.364 242 16 7 3142 3382 20741904 20741679 1.720000e-61 248.0
34 TraesCS3D01G041200 chr3A 89.908 109 6 4 3385 3491 20741350 20741245 1.400000e-27 135.0
35 TraesCS3D01G041200 chr6B 84.100 478 66 3 838 1315 707804092 707804559 3.390000e-123 453.0
36 TraesCS3D01G041200 chr6D 82.151 465 71 4 4062 4516 312685064 312684602 9.710000e-104 388.0
37 TraesCS3D01G041200 chr5B 93.182 44 3 0 7437 7480 673630018 673629975 1.860000e-06 65.8
38 TraesCS3D01G041200 chr4D 92.500 40 3 0 4253 4292 483619628 483619667 3.110000e-04 58.4


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 TraesCS3D01G041200 chr3D 15915764 15923739 7975 False 14729.000000 14729 100.000000 1 7976 1 chr3D.!!$F3 7975
1 TraesCS3D01G041200 chr3D 15331546 15332453 907 False 645.000000 645 79.739000 843 1749 1 chr3D.!!$F1 906
2 TraesCS3D01G041200 chr3B 22784747 22790235 5488 False 1483.500000 2082 83.913000 853 7102 2 chr3B.!!$F3 6249
3 TraesCS3D01G041200 chr3B 22831292 22839332 8040 False 1274.000000 2669 87.414250 838 7252 4 chr3B.!!$F6 6414
4 TraesCS3D01G041200 chr3B 22699178 22701619 2441 False 1204.500000 2222 84.035000 4916 7313 2 chr3B.!!$F2 2397
5 TraesCS3D01G041200 chr3B 22802632 22806494 3862 False 1062.433333 1773 81.554667 761 6829 3 chr3B.!!$F4 6068
6 TraesCS3D01G041200 chr3B 22672040 22677571 5531 False 894.250000 2806 90.974750 49 3441 4 chr3B.!!$F1 3392
7 TraesCS3D01G041200 chr3B 22824015 22826380 2365 False 251.500000 329 85.455500 6825 7313 2 chr3B.!!$F5 488
8 TraesCS3D01G041200 chr3A 20725754 20728373 2619 True 1561.000000 2063 91.146000 1 2339 2 chr3A.!!$R5 2338
9 TraesCS3D01G041200 chr3A 20733873 20745874 12001 True 986.142857 1884 87.201000 838 7102 7 chr3A.!!$R6 6264
10 TraesCS3D01G041200 chr3A 20715509 20720209 4700 True 955.333333 2283 89.302000 5073 7519 3 chr3A.!!$R4 2446
11 TraesCS3D01G041200 chr3A 20965355 20966249 894 True 595.000000 595 79.006000 843 1732 1 chr3A.!!$R1 889
12 TraesCS3D01G041200 chr3A 21065264 21066099 835 True 584.000000 584 79.572000 884 1712 1 chr3A.!!$R3 828
13 TraesCS3D01G041200 chr3A 20989252 20989773 521 True 470.000000 470 83.051000 843 1369 1 chr3A.!!$R2 526


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
421 2245 0.038159 CCGAGTGTCCTCCTTCACAC 60.038 60.0 0.00 0.0 42.84 3.82 F
2158 4723 0.099436 GCCATCACTGTCGGCAATTC 59.901 55.0 7.37 0.0 45.52 2.17 F
3498 8338 0.393537 ACCGTCGGTCTAGTAGGGTG 60.394 60.0 12.23 0.0 0.00 4.61 F
3536 8376 0.104304 GTTCCTATCCGACGTGGCAT 59.896 55.0 0.00 0.0 37.80 4.40 F
4025 9394 0.106708 TCAGCCAAACTCGAACAGCT 59.893 50.0 0.00 0.0 0.00 4.24 F
4741 10732 0.106894 GAGGAGGGCGGAAATACAGG 59.893 60.0 0.00 0.0 0.00 4.00 F
5700 12115 0.700564 AGCTTCAAGGGCAGATTCCA 59.299 50.0 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2414 5078 1.344114 GCATTGGCCCAGAAAACTCAA 59.656 47.619 0.00 0.0 0.00 3.02 R
3518 8358 0.104120 CATGCCACGTCGGATAGGAA 59.896 55.000 8.04 0.0 36.56 3.36 R
5469 11680 0.030235 GTGCCAACGAAACTGGGAAC 59.970 55.000 0.00 0.0 35.88 3.62 R
5623 11834 7.561251 TCGAAAGGGAGAACATATGATGTAAA 58.439 34.615 10.38 0.0 44.07 2.01 R
5700 12115 2.999063 GCTGGTGGGCTTGGCATT 60.999 61.111 0.00 0.0 0.00 3.56 R
6485 12911 1.097547 CGATCCAGGAATGGTGCCAC 61.098 60.000 0.00 0.0 0.00 5.01 R
7368 21713 0.178873 ACTAGCAGGGAGTTGGGGAA 60.179 55.000 0.00 0.0 0.00 3.97 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.