Multiple sequence alignment - TraesCS3B01G364000

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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 TraesCS3B01G364000 chr3B 100.000 2276 0 0 1 2276 575768920 575766645 0.000000e+00 4204
1 TraesCS3B01G364000 chr3B 96.926 2277 67 3 1 2276 483372819 483375093 0.000000e+00 3814
2 TraesCS3B01G364000 chr1A 97.453 2277 57 1 1 2276 238154627 238152351 0.000000e+00 3882
3 TraesCS3B01G364000 chr1A 97.365 2277 59 1 1 2276 238109242 238106966 0.000000e+00 3871
4 TraesCS3B01G364000 chr5A 97.320 2276 60 1 2 2276 16577416 16575141 0.000000e+00 3864
5 TraesCS3B01G364000 chr5A 91.926 706 53 4 676 1379 119265250 119265953 0.000000e+00 985
6 TraesCS3B01G364000 chr5A 96.764 309 7 3 118 425 606482921 606482615 1.560000e-141 512
7 TraesCS3B01G364000 chr5A 93.827 243 12 1 1380 1622 16614230 16613991 1.660000e-96 363
8 TraesCS3B01G364000 chr5A 93.416 243 13 1 1380 1622 300057557 300057796 7.730000e-95 357
9 TraesCS3B01G364000 chr5A 85.944 249 31 3 158 406 34975509 34975265 1.730000e-66 263
10 TraesCS3B01G364000 chr5A 98.901 91 1 0 987 1077 454966106 454966016 1.810000e-36 163
11 TraesCS3B01G364000 chr7A 97.189 2277 63 1 1 2276 60328507 60326231 0.000000e+00 3849
12 TraesCS3B01G364000 chr6B 97.014 2277 63 3 1 2276 596656803 596654531 0.000000e+00 3823
13 TraesCS3B01G364000 chr1B 96.750 2277 70 4 1 2276 672508047 672505774 0.000000e+00 3792
14 TraesCS3B01G364000 chr2B 97.350 717 18 1 1560 2276 385135083 385134368 0.000000e+00 1218
15 TraesCS3B01G364000 chr2B 96.070 687 27 0 1590 2276 234505656 234504970 0.000000e+00 1120
16 TraesCS3B01G364000 chr2B 95.796 666 27 1 316 980 357539912 357539247 0.000000e+00 1074
17 TraesCS3B01G364000 chr2B 92.991 214 14 1 1103 1316 78308097 78307885 6.100000e-81 311
18 TraesCS3B01G364000 chr2B 98.837 172 1 1 504 674 357757995 357757824 2.840000e-79 305
19 TraesCS3B01G364000 chr2A 98.182 110 2 0 55 164 24962874 24962983 2.310000e-45 193


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 TraesCS3B01G364000 chr3B 575766645 575768920 2275 True 4204 4204 100.000 1 2276 1 chr3B.!!$R1 2275
1 TraesCS3B01G364000 chr3B 483372819 483375093 2274 False 3814 3814 96.926 1 2276 1 chr3B.!!$F1 2275
2 TraesCS3B01G364000 chr1A 238152351 238154627 2276 True 3882 3882 97.453 1 2276 1 chr1A.!!$R2 2275
3 TraesCS3B01G364000 chr1A 238106966 238109242 2276 True 3871 3871 97.365 1 2276 1 chr1A.!!$R1 2275
4 TraesCS3B01G364000 chr5A 16575141 16577416 2275 True 3864 3864 97.320 2 2276 1 chr5A.!!$R1 2274
5 TraesCS3B01G364000 chr5A 119265250 119265953 703 False 985 985 91.926 676 1379 1 chr5A.!!$F1 703
6 TraesCS3B01G364000 chr7A 60326231 60328507 2276 True 3849 3849 97.189 1 2276 1 chr7A.!!$R1 2275
7 TraesCS3B01G364000 chr6B 596654531 596656803 2272 True 3823 3823 97.014 1 2276 1 chr6B.!!$R1 2275
8 TraesCS3B01G364000 chr1B 672505774 672508047 2273 True 3792 3792 96.750 1 2276 1 chr1B.!!$R1 2275
9 TraesCS3B01G364000 chr2B 385134368 385135083 715 True 1218 1218 97.350 1560 2276 1 chr2B.!!$R5 716
10 TraesCS3B01G364000 chr2B 234504970 234505656 686 True 1120 1120 96.070 1590 2276 1 chr2B.!!$R2 686
11 TraesCS3B01G364000 chr2B 357539247 357539912 665 True 1074 1074 95.796 316 980 1 chr2B.!!$R3 664

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
503 504 0.478072 AGTGGGCTTTGGTGATGTCA 59.522 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1879 1.204704 ACGAGAACATTGAGATCCGCA 59.795 47.619 0.0 0.0 0.0 5.69 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
23 24 1.567504 CGGGCGAAATTACGTGAGAT 58.432 50.000 0.00 0.00 35.59 2.75
34 35 7.513196 CGAAATTACGTGAGATAAAGAACCTCG 60.513 40.741 0.00 0.00 0.00 4.63
278 279 3.445450 TGGTTAGAGCAAAACAAGCAACA 59.555 39.130 0.00 0.00 0.00 3.33
406 407 3.500343 CCTGGAAATCCTTCAGTGGTTT 58.500 45.455 0.44 0.00 36.82 3.27
503 504 0.478072 AGTGGGCTTTGGTGATGTCA 59.522 50.000 0.00 0.00 0.00 3.58
666 667 2.143122 GTGATGCCAGAAGTCGTTTCA 58.857 47.619 5.49 0.00 38.31 2.69
763 765 7.506261 GGAGTACCTCCTAACAAGATTGATCTA 59.494 40.741 2.98 0.00 46.41 1.98
788 790 1.144503 GATCTTGGTCCATGATGGCCT 59.855 52.381 21.76 1.73 37.47 5.19
857 860 1.687123 CTTCGGATCGGGAGTAACCAT 59.313 52.381 0.30 0.00 41.20 3.55
901 904 4.014273 AGGACATAGGAAAGAGGGATGT 57.986 45.455 0.00 0.00 33.52 3.06
962 965 2.183300 GCGCACGGACCATACTCA 59.817 61.111 0.30 0.00 0.00 3.41
1084 1087 3.329743 GGTTGAGCAATCGACATGATG 57.670 47.619 0.00 0.00 37.39 3.07
1107 1110 0.035152 TTGCTCACATTCCAGGCGAT 60.035 50.000 0.00 0.00 0.00 4.58
1183 1186 0.400213 TTCGCCAGGTGTGAAATCCT 59.600 50.000 0.00 0.00 40.41 3.24
1193 1196 5.696724 CAGGTGTGAAATCCTATCGTATTCC 59.303 44.000 0.00 0.00 32.26 3.01
1221 1224 2.833338 CAAGGATTTGCTGGGAATTCCA 59.167 45.455 25.67 11.08 44.79 3.53
1328 1331 4.683766 TTTTTGGGGGTGATATGGAAGA 57.316 40.909 0.00 0.00 0.00 2.87
1430 1433 6.712276 AGAAAAGAAATCTTCTACGGGTGAT 58.288 36.000 0.00 0.00 39.61 3.06
1435 1438 3.897657 ATCTTCTACGGGTGATAGGGA 57.102 47.619 0.00 0.00 0.00 4.20
1643 1646 9.142014 TCTTCCTCATTCTTATTTTGGTTTTCA 57.858 29.630 0.00 0.00 0.00 2.69
1786 1789 7.936496 TCTTTTGTTCATTGCTATACCATCA 57.064 32.000 0.00 0.00 0.00 3.07
1805 1808 4.630894 TCATTTGGTCTTGTGTTGACAC 57.369 40.909 7.31 7.31 46.59 3.67
1876 1879 6.154021 CCTTTCATCTTGGGAATGAGAATGTT 59.846 38.462 0.00 0.00 0.00 2.71
1970 1973 0.323542 CGGACTACCAGACCTCCAGT 60.324 60.000 0.00 0.00 35.59 4.00
2086 2089 4.323792 CCTTTAGAGGAAGGTGAATCTGCA 60.324 45.833 0.00 0.00 46.74 4.41
2164 2167 9.098355 CTTCAACAAATCTTCTCCGATTATACA 57.902 33.333 0.00 0.00 33.47 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.469945 ACTCCATCAATCCGAGGTTCTTTA 59.530 41.667 0.00 0.00 0.00 1.85
34 35 1.595382 CGGCGGACTCCATCAATCC 60.595 63.158 0.00 0.00 0.00 3.01
60 61 5.241949 GCTCCTAGTCACTAAGCAGCTATTA 59.758 44.000 0.00 0.00 33.21 0.98
164 165 1.337260 GCTTGCTCAAGAACCGAGAGA 60.337 52.381 13.33 0.00 40.79 3.10
278 279 0.173481 TCGCGCTAGTTGCTCAATCT 59.827 50.000 5.56 0.00 40.11 2.40
406 407 1.827344 AGACGCTCAGATGTGGATTCA 59.173 47.619 0.00 0.00 0.00 2.57
463 464 1.363145 CGTTCTCTCGCTCTCCTCGT 61.363 60.000 0.00 0.00 0.00 4.18
763 765 4.139786 CCATCATGGACCAAGATCGAAAT 58.860 43.478 9.27 0.00 40.96 2.17
767 769 1.233019 GCCATCATGGACCAAGATCG 58.767 55.000 8.30 4.66 40.96 3.69
857 860 2.615391 CCCCCTTTGCCCTTTCTAAAA 58.385 47.619 0.00 0.00 0.00 1.52
922 925 4.994852 CCGTTTTTCTTCTCTACCATGACA 59.005 41.667 0.00 0.00 0.00 3.58
962 965 1.561542 AGGGACATTGATCCGAAGCTT 59.438 47.619 0.00 0.00 39.97 3.74
1084 1087 2.223340 CGCCTGGAATGTGAGCAAATAC 60.223 50.000 0.00 0.00 0.00 1.89
1107 1110 3.342377 TGTTCCTGCGAATTATGACCA 57.658 42.857 0.00 0.00 0.00 4.02
1183 1186 4.800023 TCCTTGACTCCTGGAATACGATA 58.200 43.478 0.00 0.00 0.00 2.92
1193 1196 2.089980 CCAGCAAATCCTTGACTCCTG 58.910 52.381 0.00 0.00 34.14 3.86
1221 1224 7.899648 TTTAGATCTTCCCTTTCTACGATCT 57.100 36.000 0.00 0.00 40.29 2.75
1317 1320 3.580458 GGGAGCTAGCTTCTTCCATATCA 59.420 47.826 22.47 0.00 0.00 2.15
1328 1331 1.675007 AAGGGAAAGGGAGCTAGCTT 58.325 50.000 20.42 1.21 0.00 3.74
1422 1425 3.152400 GGCGTCCCTATCACCCGT 61.152 66.667 0.00 0.00 0.00 5.28
1480 1483 4.963276 TCAGTTACAATAGCACAATGCC 57.037 40.909 0.00 0.00 46.52 4.40
1521 1524 5.419542 CCTGTAGTGATTTCAGAATTCGGA 58.580 41.667 4.00 4.00 0.00 4.55
1643 1646 2.807967 CGCGAACCAACATCCATGATAT 59.192 45.455 0.00 0.00 0.00 1.63
1876 1879 1.204704 ACGAGAACATTGAGATCCGCA 59.795 47.619 0.00 0.00 0.00 5.69
1970 1973 2.822255 GGCGTGCGGCATTTCCTA 60.822 61.111 5.72 0.00 46.16 2.94
2086 2089 4.690748 ACATGATTTTCAGTGAACGATCGT 59.309 37.500 16.60 16.60 0.00 3.73
2164 2167 4.394712 CTTGCGTCCCCGGCTTCT 62.395 66.667 0.00 0.00 33.68 2.85
2226 2229 2.049063 GTTCACCGAGCTCAGCGT 60.049 61.111 15.40 3.25 0.00 5.07


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

AutoCloner maintained by Alex Coulton.