Multiple sequence alignment - TraesCS2B01G556400

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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 TraesCS2B01G556400 chr2B 100.000 3125 0 0 1 3125 751298996 751295872 0.000000e+00 5771.0
1 TraesCS2B01G556400 chr2B 89.965 1156 112 3 1001 2153 115909506 115908352 0.000000e+00 1489.0
2 TraesCS2B01G556400 chr2B 94.881 879 38 7 1 876 751288352 751287478 0.000000e+00 1367.0
3 TraesCS2B01G556400 chr2B 85.997 657 68 10 19 653 751282594 751281940 0.000000e+00 682.0
4 TraesCS2B01G556400 chr2B 86.996 546 58 9 10 551 751316164 751315628 1.240000e-168 603.0
5 TraesCS2B01G556400 chr2B 79.545 440 49 18 23 428 751284019 751283587 3.070000e-70 276.0
6 TraesCS2B01G556400 chr2B 86.466 133 16 2 874 1005 115966022 115965891 9.030000e-31 145.0
7 TraesCS2B01G556400 chr2B 82.424 165 18 4 646 806 751281781 751281624 1.960000e-27 134.0
8 TraesCS2B01G556400 chr2B 95.556 45 2 0 15 59 751278615 751278571 4.320000e-09 73.1
9 TraesCS2B01G556400 chr2B 95.000 40 2 0 837 876 751315425 751315386 2.600000e-06 63.9
10 TraesCS2B01G556400 chr5B 92.470 2231 157 9 871 3092 281238656 281240884 0.000000e+00 3179.0
11 TraesCS2B01G556400 chr6B 91.191 2225 187 8 877 3094 478890193 478887971 0.000000e+00 3014.0
12 TraesCS2B01G556400 chr1B 92.062 1751 132 3 1344 3091 533807916 533809662 0.000000e+00 2457.0
13 TraesCS2B01G556400 chr1B 96.240 1383 49 2 1718 3098 510817964 510816583 0.000000e+00 2263.0
14 TraesCS2B01G556400 chr1D 85.907 2228 294 16 877 3094 442404185 442401968 0.000000e+00 2357.0
15 TraesCS2B01G556400 chr7B 97.088 1305 36 1 876 2180 74322791 74321489 0.000000e+00 2198.0
16 TraesCS2B01G556400 chr7B 84.432 2229 332 11 874 3094 621915987 621913766 0.000000e+00 2180.0
17 TraesCS2B01G556400 chr7B 97.413 889 23 0 2204 3092 74321278 74320390 0.000000e+00 1515.0
18 TraesCS2B01G556400 chr7B 83.320 1277 200 8 1823 3094 120466875 120468143 0.000000e+00 1166.0
19 TraesCS2B01G556400 chr7B 83.862 378 49 9 467 834 60458088 60457713 1.780000e-92 350.0
20 TraesCS2B01G556400 chr7B 100.000 36 0 0 3090 3125 74320377 74320342 2.010000e-07 67.6
21 TraesCS2B01G556400 chr2A 91.365 1297 107 4 877 2169 48199150 48200445 0.000000e+00 1770.0
22 TraesCS2B01G556400 chr2A 89.020 847 74 9 1 830 746632603 746631759 0.000000e+00 1031.0
23 TraesCS2B01G556400 chr2A 85.135 592 66 11 99 671 746616307 746615719 1.250000e-163 586.0
24 TraesCS2B01G556400 chr6A 91.446 1286 105 4 877 2158 511532056 511533340 0.000000e+00 1760.0
25 TraesCS2B01G556400 chr4A 90.169 1302 121 5 1796 3092 493997173 493998472 0.000000e+00 1688.0
26 TraesCS2B01G556400 chr4D 84.238 387 45 11 458 834 40758802 40758422 2.290000e-96 363.0
27 TraesCS2B01G556400 chr4D 83.896 385 46 9 458 830 334964319 334964699 1.380000e-93 353.0
28 TraesCS2B01G556400 chr7D 83.979 387 48 7 458 834 611009097 611009479 2.960000e-95 359.0
29 TraesCS2B01G556400 chr5D 83.929 392 46 11 458 834 341240342 341239953 2.960000e-95 359.0
30 TraesCS2B01G556400 chr4B 84.115 384 44 8 467 834 122566539 122566157 3.830000e-94 355.0
31 TraesCS2B01G556400 chr2D 83.763 388 49 11 458 834 351288792 351288408 3.830000e-94 355.0
32 TraesCS2B01G556400 chr2D 90.045 221 21 1 15 234 616522635 616522415 5.100000e-73 285.0


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 TraesCS2B01G556400 chr2B 751295872 751298996 3124 True 5771.00 5771 100.0000 1 3125 1 chr2B.!!$R3 3124
1 TraesCS2B01G556400 chr2B 115908352 115909506 1154 True 1489.00 1489 89.9650 1001 2153 1 chr2B.!!$R1 1152
2 TraesCS2B01G556400 chr2B 751278571 751288352 9781 True 506.42 1367 87.6806 1 876 5 chr2B.!!$R4 875
3 TraesCS2B01G556400 chr2B 751315386 751316164 778 True 333.45 603 90.9980 10 876 2 chr2B.!!$R5 866
4 TraesCS2B01G556400 chr5B 281238656 281240884 2228 False 3179.00 3179 92.4700 871 3092 1 chr5B.!!$F1 2221
5 TraesCS2B01G556400 chr6B 478887971 478890193 2222 True 3014.00 3014 91.1910 877 3094 1 chr6B.!!$R1 2217
6 TraesCS2B01G556400 chr1B 533807916 533809662 1746 False 2457.00 2457 92.0620 1344 3091 1 chr1B.!!$F1 1747
7 TraesCS2B01G556400 chr1B 510816583 510817964 1381 True 2263.00 2263 96.2400 1718 3098 1 chr1B.!!$R1 1380
8 TraesCS2B01G556400 chr1D 442401968 442404185 2217 True 2357.00 2357 85.9070 877 3094 1 chr1D.!!$R1 2217
9 TraesCS2B01G556400 chr7B 621913766 621915987 2221 True 2180.00 2180 84.4320 874 3094 1 chr7B.!!$R2 2220
10 TraesCS2B01G556400 chr7B 74320342 74322791 2449 True 1260.20 2198 98.1670 876 3125 3 chr7B.!!$R3 2249
11 TraesCS2B01G556400 chr7B 120466875 120468143 1268 False 1166.00 1166 83.3200 1823 3094 1 chr7B.!!$F1 1271
12 TraesCS2B01G556400 chr2A 48199150 48200445 1295 False 1770.00 1770 91.3650 877 2169 1 chr2A.!!$F1 1292
13 TraesCS2B01G556400 chr2A 746631759 746632603 844 True 1031.00 1031 89.0200 1 830 1 chr2A.!!$R2 829
14 TraesCS2B01G556400 chr2A 746615719 746616307 588 True 586.00 586 85.1350 99 671 1 chr2A.!!$R1 572
15 TraesCS2B01G556400 chr6A 511532056 511533340 1284 False 1760.00 1760 91.4460 877 2158 1 chr6A.!!$F1 1281
16 TraesCS2B01G556400 chr4A 493997173 493998472 1299 False 1688.00 1688 90.1690 1796 3092 1 chr4A.!!$F1 1296

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
64 65 0.685097 TCTAAAGCGGCTTCAGTGGT 59.315 50.000 16.70 1.36 0.0 4.16 F
716 751 2.929641 TGCACAGTCCTCATTTCAACA 58.070 42.857 0.00 0.00 0.0 3.33 F
1926 7912 1.221021 GAACCCGGGGACAGTCATC 59.779 63.158 27.92 5.78 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 7912 2.332104 CTCGCATCCCTATCAACATCG 58.668 52.381 0.0 0.0 0.0 3.84 R
2122 8329 0.183014 AGGGAAGCCGACGATCTCTA 59.817 55.000 0.0 0.0 0.0 2.43 R
2961 10644 0.040425 GCCGCCTGTAGTTTTGTGTG 60.040 55.000 0.0 0.0 0.0 3.82 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
64 65 0.685097 TCTAAAGCGGCTTCAGTGGT 59.315 50.000 16.70 1.36 0.00 4.16
143 145 4.010349 GGTAACTAAATGCTTCCACTGCT 58.990 43.478 0.00 0.00 0.00 4.24
157 159 3.253838 TGCTACCCACCCCACCAC 61.254 66.667 0.00 0.00 0.00 4.16
224 228 8.833493 CATCATTGTATAGATTTTCTGTGAGCA 58.167 33.333 0.00 0.00 0.00 4.26
311 317 8.682936 AGGGCATAGTTGTCTTTCATAATAAG 57.317 34.615 0.00 0.00 0.00 1.73
391 417 8.700051 TGGTTCATCCATAAAAAGAAAAAGTCA 58.300 29.630 0.00 0.00 41.93 3.41
662 697 6.814043 TCATGGACTTCTGAGATGAATAGTG 58.186 40.000 2.06 0.00 0.00 2.74
682 717 4.099881 AGTGTCATGTGTTGAAAAGCCATT 59.900 37.500 0.00 0.00 35.70 3.16
716 751 2.929641 TGCACAGTCCTCATTTCAACA 58.070 42.857 0.00 0.00 0.00 3.33
767 805 8.094548 GTGTGTTATGCCTCCATGTTCTATATA 58.905 37.037 0.00 0.00 32.85 0.86
841 6817 8.613613 AAATTTTCAAAAACAGGCGAAATTTC 57.386 26.923 8.20 8.20 0.00 2.17
872 6848 7.327032 GGATTGATGCTTGTAAGAAGAAAACAC 59.673 37.037 0.00 0.00 0.00 3.32
1926 7912 1.221021 GAACCCGGGGACAGTCATC 59.779 63.158 27.92 5.78 0.00 2.92
2122 8329 1.611673 CCAAGGATCTTGCGTCCACTT 60.612 52.381 2.38 0.00 38.25 3.16
2131 8338 1.460504 TGCGTCCACTTAGAGATCGT 58.539 50.000 0.00 0.00 0.00 3.73
2247 8641 3.701664 CCCTCTCAAAAGCCAATAACCT 58.298 45.455 0.00 0.00 0.00 3.50
2749 10266 1.203052 GACCGTAATGTTCAGGTCCGA 59.797 52.381 2.29 0.00 45.39 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.370364 TCAAGAGTTGTGCCTTTTCAAC 57.630 40.909 0.00 0.00 42.62 3.18
20 21 4.464008 TGAAAGATTCAAGAGTTGTGCCT 58.536 39.130 0.00 0.00 36.59 4.75
21 22 4.836125 TGAAAGATTCAAGAGTTGTGCC 57.164 40.909 0.00 0.00 36.59 5.01
143 145 1.203453 TGAATAGTGGTGGGGTGGGTA 60.203 52.381 0.00 0.00 0.00 3.69
157 159 2.481952 GCGGCCAAAGAGCTATGAATAG 59.518 50.000 2.24 0.00 0.00 1.73
311 317 7.656707 ACAATGGTAGATTTTGCATGTTTTC 57.343 32.000 0.00 0.00 0.00 2.29
325 335 2.235155 TCTGCGGCTAAACAATGGTAGA 59.765 45.455 0.00 0.00 0.00 2.59
391 417 5.701224 TCCAACCACAAAGAGGTAAGAAAT 58.299 37.500 0.00 0.00 38.76 2.17
456 482 2.618709 CAAGCTCCAAAAGGACGTTCTT 59.381 45.455 2.29 2.29 0.00 2.52
662 697 4.619973 TCAATGGCTTTTCAACACATGAC 58.380 39.130 0.00 0.00 37.92 3.06
806 844 7.641020 CCTGTTTTTGAAAATTTCAGAATGCAC 59.359 33.333 11.62 8.37 41.38 4.57
809 847 6.847289 CGCCTGTTTTTGAAAATTTCAGAATG 59.153 34.615 11.62 6.42 41.38 2.67
813 851 5.964887 TCGCCTGTTTTTGAAAATTTCAG 57.035 34.783 8.51 1.83 41.38 3.02
841 6817 1.667236 TACAAGCATCAATCCTGCGG 58.333 50.000 0.00 0.00 44.38 5.69
872 6848 1.160329 CGCGAGGCATAGGGGAAAAG 61.160 60.000 0.00 0.00 0.00 2.27
1180 7158 5.500931 GCGAGAAATTCTTATCGGTGTGAAG 60.501 44.000 0.00 0.00 44.51 3.02
1709 7690 2.799126 TTGCTTATCATGAACCCCGT 57.201 45.000 0.00 0.00 0.00 5.28
1926 7912 2.332104 CTCGCATCCCTATCAACATCG 58.668 52.381 0.00 0.00 0.00 3.84
2122 8329 0.183014 AGGGAAGCCGACGATCTCTA 59.817 55.000 0.00 0.00 0.00 2.43
2247 8641 1.597742 GCACAGGAAGACAAGCTTGA 58.402 50.000 32.50 0.00 36.83 3.02
2749 10266 0.896940 CAGCACAAGCCTGGTCCAAT 60.897 55.000 0.00 0.00 43.56 3.16
2961 10644 0.040425 GCCGCCTGTAGTTTTGTGTG 60.040 55.000 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.