Multiple sequence alignment - TraesCS3B01G006500

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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 TraesCS3B01G006500 chr3B 100.000 3483 0 0 1 3483 3406299 3409781 0.000000e+00 6433.0
1 TraesCS3B01G006500 chr3B 90.273 1357 85 21 55 1379 5324512 5323171 0.000000e+00 1731.0
2 TraesCS3B01G006500 chr3B 87.628 1269 91 27 854 2108 3667380 3666164 0.000000e+00 1413.0
3 TraesCS3B01G006500 chr3B 89.003 1164 73 16 959 2108 5169064 5170186 0.000000e+00 1389.0
4 TraesCS3B01G006500 chr3B 91.088 965 64 13 1899 2862 5322652 5321709 0.000000e+00 1286.0
5 TraesCS3B01G006500 chr3B 82.579 442 69 7 106 543 3610485 3610922 1.960000e-102 383.0
6 TraesCS3B01G006500 chr3B 82.500 440 73 4 106 543 5226207 5225770 1.960000e-102 383.0
7 TraesCS3B01G006500 chr3B 92.647 204 15 0 3280 3483 5321306 5321103 9.450000e-76 294.0
8 TraesCS3B01G006500 chr3B 88.177 203 17 3 2414 2616 3625833 3626028 5.810000e-58 235.0
9 TraesCS3B01G006500 chr3B 83.475 236 23 14 2310 2538 3665866 3665640 4.560000e-49 206.0
10 TraesCS3B01G006500 chr3B 83.404 235 23 14 2311 2538 5170484 5170709 1.640000e-48 204.0
11 TraesCS3B01G006500 chr3B 83.408 223 28 4 540 762 3610958 3611171 7.630000e-47 198.0
12 TraesCS3B01G006500 chr3B 83.636 220 27 4 543 762 5225731 5225521 7.630000e-47 198.0
13 TraesCS3B01G006500 chr3B 81.250 288 15 11 2906 3184 5321594 5321337 2.740000e-46 196.0
14 TraesCS3B01G006500 chr3D 91.109 1136 74 12 937 2071 1337531 1338640 0.000000e+00 1513.0
15 TraesCS3B01G006500 chr3D 95.672 439 13 5 937 1374 1640646 1640213 0.000000e+00 701.0
16 TraesCS3B01G006500 chr3D 85.735 687 69 11 1422 2103 1591396 1592058 0.000000e+00 699.0
17 TraesCS3B01G006500 chr3D 93.925 428 25 1 2983 3409 1339816 1340243 0.000000e+00 645.0
18 TraesCS3B01G006500 chr3D 89.139 488 50 3 57 543 1641539 1641054 3.850000e-169 604.0
19 TraesCS3B01G006500 chr3D 89.234 483 49 3 62 543 1336629 1337109 4.970000e-168 601.0
20 TraesCS3B01G006500 chr3D 90.974 421 22 9 853 1273 1644239 1643835 1.410000e-153 553.0
21 TraesCS3B01G006500 chr3D 90.339 383 22 7 543 915 1641015 1640638 4.040000e-134 488.0
22 TraesCS3B01G006500 chr3D 89.421 397 19 4 540 915 1337145 1337539 2.430000e-131 479.0
23 TraesCS3B01G006500 chr3D 86.455 347 31 11 2215 2553 1338984 1339322 1.980000e-97 366.0
24 TraesCS3B01G006500 chr3D 87.687 268 22 3 2590 2857 1339323 1339579 5.650000e-78 302.0
25 TraesCS3B01G006500 chr3D 87.435 191 19 4 2351 2538 1639106 1638918 7.570000e-52 215.0
26 TraesCS3B01G006500 chr3D 82.353 221 30 1 543 763 1523587 1523798 2.140000e-42 183.0
27 TraesCS3B01G006500 chr3A 90.521 844 42 13 588 1422 7477206 7476392 0.000000e+00 1081.0
28 TraesCS3B01G006500 chr3A 92.926 311 19 3 224 532 7477528 7477219 1.910000e-122 449.0
29 TraesCS3B01G006500 chr3A 90.909 209 14 4 1899 2107 7475900 7475697 3.420000e-70 276.0
30 TraesCS3B01G006500 chr3A 85.864 191 22 4 2351 2538 7475373 7475185 7.630000e-47 198.0
31 TraesCS3B01G006500 chr7D 96.783 373 12 0 994 1366 7302269 7301897 1.060000e-174 623.0
32 TraesCS3B01G006500 chr7D 86.719 128 17 0 1939 2066 7301777 7301650 3.620000e-30 143.0
33 TraesCS3B01G006500 chr7D 93.333 90 6 0 2397 2486 7300734 7300645 2.180000e-27 134.0
34 TraesCS3B01G006500 chr7A 96.515 373 13 0 994 1366 8262589 8262217 4.940000e-173 617.0
35 TraesCS3B01G006500 chr7A 83.509 285 44 3 3111 3393 725193620 725193903 2.670000e-66 263.0
36 TraesCS3B01G006500 chr7A 87.500 128 16 0 1939 2066 8262112 8261985 7.790000e-32 148.0
37 TraesCS3B01G006500 chr4A 95.979 373 15 0 994 1366 732517265 732516893 1.070000e-169 606.0
38 TraesCS3B01G006500 chr5B 80.777 515 77 15 2980 3483 457081716 457082219 1.960000e-102 383.0
39 TraesCS3B01G006500 chr7B 88.189 127 15 0 1940 2066 150374241 150374115 6.020000e-33 152.0
40 TraesCS3B01G006500 chr7B 94.444 36 0 2 7 42 110687169 110687136 2.000000e-03 54.7
41 TraesCS3B01G006500 chr6B 93.333 90 6 0 2397 2486 265677438 265677349 2.180000e-27 134.0
42 TraesCS3B01G006500 chrUn 85.294 68 6 4 55 122 30189147 30189084 2.240000e-07 67.6
43 TraesCS3B01G006500 chr5D 100.000 34 0 0 1 34 259455764 259455797 2.900000e-06 63.9
44 TraesCS3B01G006500 chr2D 100.000 34 0 0 1 34 485994942 485994909 2.900000e-06 63.9
45 TraesCS3B01G006500 chr2B 100.000 33 0 0 2 34 474542100 474542068 1.040000e-05 62.1
46 TraesCS3B01G006500 chr2B 88.679 53 1 1 1 48 11321442 11321390 3.750000e-05 60.2
47 TraesCS3B01G006500 chr6A 88.462 52 2 3 1 48 101544304 101544253 3.750000e-05 60.2
48 TraesCS3B01G006500 chr6D 97.059 34 1 0 1 34 305186081 305186114 1.350000e-04 58.4
49 TraesCS3B01G006500 chr6D 97.059 34 1 0 1 34 377836886 377836853 1.350000e-04 58.4
50 TraesCS3B01G006500 chr6D 97.059 34 1 0 1 34 404335073 404335106 1.350000e-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 TraesCS3B01G006500 chr3B 3406299 3409781 3482 False 6433.00 6433 100.000000 1 3483 1 chr3B.!!$F1 3482
1 TraesCS3B01G006500 chr3B 5321103 5324512 3409 True 876.75 1731 88.814500 55 3483 4 chr3B.!!$R3 3428
2 TraesCS3B01G006500 chr3B 3665640 3667380 1740 True 809.50 1413 85.551500 854 2538 2 chr3B.!!$R1 1684
3 TraesCS3B01G006500 chr3B 5169064 5170709 1645 False 796.50 1389 86.203500 959 2538 2 chr3B.!!$F4 1579
4 TraesCS3B01G006500 chr3B 3610485 3611171 686 False 290.50 383 82.993500 106 762 2 chr3B.!!$F3 656
5 TraesCS3B01G006500 chr3B 5225521 5226207 686 True 290.50 383 83.068000 106 762 2 chr3B.!!$R2 656
6 TraesCS3B01G006500 chr3D 1591396 1592058 662 False 699.00 699 85.735000 1422 2103 1 chr3D.!!$F2 681
7 TraesCS3B01G006500 chr3D 1336629 1340243 3614 False 651.00 1513 89.638500 62 3409 6 chr3D.!!$F3 3347
8 TraesCS3B01G006500 chr3D 1638918 1644239 5321 True 512.20 701 90.711800 57 2538 5 chr3D.!!$R1 2481
9 TraesCS3B01G006500 chr3A 7475185 7477528 2343 True 501.00 1081 90.055000 224 2538 4 chr3A.!!$R1 2314
10 TraesCS3B01G006500 chr7D 7300645 7302269 1624 True 300.00 623 92.278333 994 2486 3 chr7D.!!$R1 1492
11 TraesCS3B01G006500 chr7A 8261985 8262589 604 True 382.50 617 92.007500 994 2066 2 chr7A.!!$R1 1072
12 TraesCS3B01G006500 chr5B 457081716 457082219 503 False 383.00 383 80.777000 2980 3483 1 chr5B.!!$F1 503


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
547 3236 0.033503 TCCAGACATCGGGAGCTACA 60.034 55.0 0.00 0.00 35.30 2.74 F
619 3308 0.814010 AGATGTTAACGCGGGCATCC 60.814 55.0 21.64 10.71 38.67 3.51 F
1497 4269 0.804989 AGCTGCGGCAGAAACATTAC 59.195 50.0 32.72 12.56 41.70 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 4160 0.321564 CCGATCTGACTGTTTGGCCA 60.322 55.0 0.00 0.0 0.00 5.36 R
2300 5676 0.512952 GCGACTGCAACACTTGTAGG 59.487 55.0 5.27 0.0 46.05 3.18 R
2715 6687 0.250295 AACAGCAGGCAAAGTAGCGA 60.250 50.0 0.00 0.0 34.64 4.93 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.