Multiple sequence alignment - TraesCS1A01G406900

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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 TraesCS1A01G406900 chr1A 100.000 2492 0 0 1 2492 569378316 569375825 0.000000e+00 4602.0
1 TraesCS1A01G406900 chr1A 89.700 767 73 4 1249 2013 569355566 569354804 0.000000e+00 974.0
2 TraesCS1A01G406900 chr1A 100.000 303 0 0 2584 2886 569375733 569375431 6.980000e-156 560.0
3 TraesCS1A01G406900 chr1A 88.571 105 8 4 1 102 20709907 20709804 1.090000e-24 124.0
4 TraesCS1A01G406900 chr1A 88.571 105 8 4 1 102 269753584 269753481 1.090000e-24 124.0
5 TraesCS1A01G406900 chr4A 98.219 2246 28 8 207 2450 624732498 624734733 0.000000e+00 3916.0
6 TraesCS1A01G406900 chr4A 88.831 770 80 4 1246 2013 624747298 624748063 0.000000e+00 941.0
7 TraesCS1A01G406900 chr4A 79.507 1298 183 47 621 1886 24935208 24936454 0.000000e+00 846.0
8 TraesCS1A01G406900 chr4A 79.467 1276 192 31 643 1886 24919803 24918566 0.000000e+00 841.0
9 TraesCS1A01G406900 chr4A 86.168 535 36 22 621 1141 624746491 624747001 7.030000e-151 544.0
10 TraesCS1A01G406900 chr4A 98.350 303 5 0 2584 2886 624734856 624735158 1.520000e-147 532.0
11 TraesCS1A01G406900 chr4A 82.530 166 22 3 257 422 26325396 26325238 3.880000e-29 139.0
12 TraesCS1A01G406900 chr5D 90.321 2490 166 39 3 2464 544798129 544800571 0.000000e+00 3193.0
13 TraesCS1A01G406900 chr5D 89.109 808 76 8 1210 2013 544817245 544818044 0.000000e+00 994.0
14 TraesCS1A01G406900 chr5D 87.759 531 36 18 621 1141 544816470 544816981 6.890000e-166 593.0
15 TraesCS1A01G406900 chr5D 91.722 302 25 0 2584 2885 544800849 544801150 1.240000e-113 420.0
16 TraesCS1A01G406900 chr5D 88.571 105 8 4 1 102 563631596 563631699 1.090000e-24 124.0
17 TraesCS1A01G406900 chr5D 88.462 104 9 3 1 102 72929333 72929435 3.910000e-24 122.0
18 TraesCS1A01G406900 chr5B 88.260 2172 161 51 1 2147 687222768 687224870 0.000000e+00 2512.0
19 TraesCS1A01G406900 chr5B 89.132 1739 118 26 726 2448 687212492 687214175 0.000000e+00 2098.0
20 TraesCS1A01G406900 chr5B 87.995 808 78 12 1210 2013 687326390 687327182 0.000000e+00 937.0
21 TraesCS1A01G406900 chr5B 86.749 566 30 21 620 1162 687325609 687326152 3.200000e-164 588.0
22 TraesCS1A01G406900 chr5B 87.617 533 29 17 621 1139 687259261 687259770 4.140000e-163 584.0
23 TraesCS1A01G406900 chr5B 87.738 473 38 11 1 471 687211892 687212346 4.230000e-148 534.0
24 TraesCS1A01G406900 chr5B 84.929 491 34 17 680 1152 687342057 687342525 7.290000e-126 460.0
25 TraesCS1A01G406900 chr5B 89.527 296 29 2 2591 2885 687233034 687233328 9.760000e-100 374.0
26 TraesCS1A01G406900 chr5B 89.080 174 9 5 2258 2430 687232767 687232931 1.050000e-49 207.0
27 TraesCS1A01G406900 chr5B 92.537 67 4 1 2421 2486 687232974 687233040 8.510000e-16 95.3
28 TraesCS1A01G406900 chr4B 83.730 1469 162 43 621 2049 547309113 547310544 0.000000e+00 1317.0
29 TraesCS1A01G406900 chr4B 80.769 312 41 15 853 1154 550488104 550487802 2.890000e-55 226.0
30 TraesCS1A01G406900 chr4B 81.609 174 25 4 249 422 547308329 547308495 1.390000e-28 137.0
31 TraesCS1A01G406900 chr4D 83.676 1458 153 44 621 2035 441255523 441256938 0.000000e+00 1295.0
32 TraesCS1A01G406900 chr4D 80.031 1297 176 50 623 1886 442223382 442222136 0.000000e+00 883.0
33 TraesCS1A01G406900 chrUn 100.000 390 0 0 923 1312 480040813 480040424 0.000000e+00 721.0
34 TraesCS1A01G406900 chr2D 90.476 105 6 4 1 102 243672403 243672506 5.020000e-28 135.0
35 TraesCS1A01G406900 chr5A 89.524 105 7 4 1 102 693948577 693948680 2.330000e-26 130.0


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 TraesCS1A01G406900 chr1A 569375431 569378316 2885 True 2581.000000 4602 100.000000 1 2886 2 chr1A.!!$R4 2885
1 TraesCS1A01G406900 chr1A 569354804 569355566 762 True 974.000000 974 89.700000 1249 2013 1 chr1A.!!$R3 764
2 TraesCS1A01G406900 chr4A 624732498 624735158 2660 False 2224.000000 3916 98.284500 207 2886 2 chr4A.!!$F2 2679
3 TraesCS1A01G406900 chr4A 24935208 24936454 1246 False 846.000000 846 79.507000 621 1886 1 chr4A.!!$F1 1265
4 TraesCS1A01G406900 chr4A 24918566 24919803 1237 True 841.000000 841 79.467000 643 1886 1 chr4A.!!$R1 1243
5 TraesCS1A01G406900 chr4A 624746491 624748063 1572 False 742.500000 941 87.499500 621 2013 2 chr4A.!!$F3 1392
6 TraesCS1A01G406900 chr5D 544798129 544801150 3021 False 1806.500000 3193 91.021500 3 2885 2 chr5D.!!$F3 2882
7 TraesCS1A01G406900 chr5D 544816470 544818044 1574 False 793.500000 994 88.434000 621 2013 2 chr5D.!!$F4 1392
8 TraesCS1A01G406900 chr5B 687222768 687224870 2102 False 2512.000000 2512 88.260000 1 2147 1 chr5B.!!$F1 2146
9 TraesCS1A01G406900 chr5B 687211892 687214175 2283 False 1316.000000 2098 88.435000 1 2448 2 chr5B.!!$F4 2447
10 TraesCS1A01G406900 chr5B 687325609 687327182 1573 False 762.500000 937 87.372000 620 2013 2 chr5B.!!$F6 1393
11 TraesCS1A01G406900 chr5B 687259261 687259770 509 False 584.000000 584 87.617000 621 1139 1 chr5B.!!$F2 518
12 TraesCS1A01G406900 chr5B 687232767 687233328 561 False 225.433333 374 90.381333 2258 2885 3 chr5B.!!$F5 627
13 TraesCS1A01G406900 chr4B 547308329 547310544 2215 False 727.000000 1317 82.669500 249 2049 2 chr4B.!!$F1 1800
14 TraesCS1A01G406900 chr4D 441255523 441256938 1415 False 1295.000000 1295 83.676000 621 2035 1 chr4D.!!$F1 1414
15 TraesCS1A01G406900 chr4D 442222136 442223382 1246 True 883.000000 883 80.031000 623 1886 1 chr4D.!!$R1 1263

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
563 751 0.03601 GGCTTGCAGTTAGAGGCTGA 60.036 55.0 0.0 0.0 36.12 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2862 3894 4.202441 CGTTCCATTTCCTTCATCCTCAT 58.798 43.478 0.0 0.0 0.0 2.9 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
38 40 9.945904 CCTTGATAGGTTAAAGATAGTTATCCC 57.054 37.037 0.00 0.00 36.74 3.85
39 41 9.640963 CTTGATAGGTTAAAGATAGTTATCCCG 57.359 37.037 0.00 0.00 33.17 5.14
98 100 0.815615 GATGTGAAGATCGGGCCACC 60.816 60.000 4.39 0.00 0.00 4.61
130 132 7.525360 GCTTAAAGAATCTTTCCATGGGTTTGA 60.525 37.037 11.97 6.03 0.00 2.69
158 160 5.939883 TCAGGTTTCATCGATGATTTCAGTT 59.060 36.000 27.75 8.37 36.56 3.16
171 173 9.708222 CGATGATTTCAGTTATTTTACAAGGAG 57.292 33.333 0.00 0.00 0.00 3.69
173 175 9.753674 ATGATTTCAGTTATTTTACAAGGAGGA 57.246 29.630 0.00 0.00 0.00 3.71
179 181 8.483758 TCAGTTATTTTACAAGGAGGAGATACC 58.516 37.037 0.00 0.00 39.35 2.73
180 182 7.438459 CAGTTATTTTACAAGGAGGAGATACCG 59.562 40.741 0.00 0.00 44.74 4.02
189 191 4.400120 AGGAGGAGATACCGAAGTATGTC 58.600 47.826 2.61 2.61 44.63 3.06
193 195 6.239345 GGAGGAGATACCGAAGTATGTCAATT 60.239 42.308 11.16 0.00 46.27 2.32
211 214 7.106239 TGTCAATTAGAGAGATCAAAGGGTTC 58.894 38.462 0.00 0.00 0.00 3.62
229 232 3.755378 GGTTCAATCAGTCAGCAGTGAAT 59.245 43.478 0.00 0.00 35.50 2.57
277 280 8.110860 TCACAAAGAAAACTCTGAAGACTTTT 57.889 30.769 0.00 0.00 0.00 2.27
282 285 6.357367 AGAAAACTCTGAAGACTTTTGCCTA 58.643 36.000 3.39 0.00 0.00 3.93
322 325 0.317479 AGCGGCCGTATTCCTGTATC 59.683 55.000 28.70 4.79 0.00 2.24
353 356 2.975732 TCACATGGCTGACTCAGATC 57.024 50.000 10.45 1.98 32.44 2.75
354 357 2.181975 TCACATGGCTGACTCAGATCA 58.818 47.619 10.45 7.49 32.44 2.92
367 370 5.301298 TGACTCAGATCAGATGACGATGATT 59.699 40.000 0.00 0.00 36.30 2.57
368 371 6.488006 TGACTCAGATCAGATGACGATGATTA 59.512 38.462 0.00 0.00 36.30 1.75
563 751 0.036010 GGCTTGCAGTTAGAGGCTGA 60.036 55.000 0.00 0.00 36.12 4.26
595 783 2.738013 ACTAGTTGGTGGCTAACGTC 57.262 50.000 0.00 0.00 33.39 4.34
733 1216 2.565841 GCGTTGGATGATTAGAAGGCT 58.434 47.619 0.00 0.00 0.00 4.58
921 1446 0.395312 AACCAAACCCACTCGATCGT 59.605 50.000 15.94 0.00 0.00 3.73
1312 2098 2.324330 CGGGATCAACAACGCTGCA 61.324 57.895 0.00 0.00 0.00 4.41
2480 3354 5.753744 TGATCAACGTGTTTGTACATTTCC 58.246 37.500 0.00 0.00 36.50 3.13
2481 3355 5.297029 TGATCAACGTGTTTGTACATTTCCA 59.703 36.000 0.00 0.00 36.50 3.53
2482 3356 4.911053 TCAACGTGTTTGTACATTTCCAC 58.089 39.130 0.00 0.76 36.50 4.02
2483 3357 4.395231 TCAACGTGTTTGTACATTTCCACA 59.605 37.500 0.00 0.00 36.50 4.17
2484 3358 4.966965 ACGTGTTTGTACATTTCCACAA 57.033 36.364 0.00 0.00 36.50 3.33
2485 3359 5.508200 ACGTGTTTGTACATTTCCACAAT 57.492 34.783 0.00 0.00 36.50 2.71
2486 3360 5.516090 ACGTGTTTGTACATTTCCACAATC 58.484 37.500 0.00 0.00 36.50 2.67
2487 3361 4.915085 CGTGTTTGTACATTTCCACAATCC 59.085 41.667 0.00 0.00 36.50 3.01
2488 3362 5.227152 GTGTTTGTACATTTCCACAATCCC 58.773 41.667 0.00 0.00 36.50 3.85
2489 3363 4.282195 TGTTTGTACATTTCCACAATCCCC 59.718 41.667 0.00 0.00 34.78 4.81
2490 3364 3.094484 TGTACATTTCCACAATCCCCC 57.906 47.619 0.00 0.00 0.00 5.40
2862 3894 1.039068 CCTTTGGATGTGTTGCACCA 58.961 50.000 0.00 0.00 32.73 4.17
2871 3903 1.073603 TGTGTTGCACCATGAGGATGA 59.926 47.619 0.00 0.00 38.69 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 20 6.080009 AGCCGGGATAACTATCTTTAACCTA 58.920 40.000 2.18 0.0 33.28 3.08
38 40 2.010145 TAACTAGCTGCAAGAAGCCG 57.990 50.000 1.02 0.0 44.68 5.52
39 41 4.698575 AGTATAACTAGCTGCAAGAAGCC 58.301 43.478 1.02 0.0 44.68 4.35
98 100 6.824305 TGGAAAGATTCTTTAAGCAAGAGG 57.176 37.500 11.55 0.0 42.76 3.69
130 132 3.548745 TCATCGATGAAACCTGATGCT 57.451 42.857 25.44 0.0 38.43 3.79
158 160 7.343833 ACTTCGGTATCTCCTCCTTGTAAAATA 59.656 37.037 0.00 0.0 0.00 1.40
171 173 7.883217 TCTAATTGACATACTTCGGTATCTCC 58.117 38.462 0.00 0.0 38.92 3.71
173 175 8.693120 TCTCTAATTGACATACTTCGGTATCT 57.307 34.615 0.00 0.0 38.92 1.98
179 181 9.521503 TTTGATCTCTCTAATTGACATACTTCG 57.478 33.333 0.00 0.0 0.00 3.79
189 191 7.928307 TTGAACCCTTTGATCTCTCTAATTG 57.072 36.000 0.00 0.0 0.00 2.32
193 195 6.441924 ACTGATTGAACCCTTTGATCTCTCTA 59.558 38.462 0.00 0.0 0.00 2.43
211 214 7.137490 TCTTTTATTCACTGCTGACTGATTG 57.863 36.000 0.00 0.0 0.00 2.67
322 325 4.097286 TCAGCCATGTGATCAATGTCAATG 59.903 41.667 0.00 0.0 0.00 2.82
500 505 2.416547 CGCGTGATTCACCTCTTTCATT 59.583 45.455 11.12 0.0 0.00 2.57
563 751 7.942894 AGCCACCAACTAGTTAAAAGTTCTAAT 59.057 33.333 8.04 0.0 34.99 1.73
595 783 4.820897 TGTTCTAGTTAGTGCTGGATGTG 58.179 43.478 0.00 0.0 0.00 3.21
733 1216 3.743521 CAACCTCCACAGATTGACTTGA 58.256 45.455 0.00 0.0 0.00 3.02
921 1446 3.126073 CGCAGCTTGCTAGATATTGTGA 58.874 45.455 0.00 0.0 42.25 3.58
2862 3894 4.202441 CGTTCCATTTCCTTCATCCTCAT 58.798 43.478 0.00 0.0 0.00 2.90


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

AutoCloner maintained by Alex Coulton.