Multiple sequence alignment - TraesCS2D01G332400

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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 TraesCS2D01G332400 chr2D 100.000 3006 0 0 1 3006 425495605 425492600 0.000000e+00 5552
1 TraesCS2D01G332400 chr2B 92.925 2926 142 35 108 3006 500839356 500836469 0.000000e+00 4196
2 TraesCS2D01G332400 chr2B 94.118 119 5 2 1 117 500840807 500840689 2.380000e-41 180
3 TraesCS2D01G332400 chr2A 92.308 1937 100 21 1 1921 562680293 562682196 0.000000e+00 2706
4 TraesCS2D01G332400 chr2A 91.667 780 29 9 1991 2762 562685939 562686690 0.000000e+00 1048
5 TraesCS2D01G332400 chr2A 96.053 76 3 0 1913 1988 562685808 562685883 1.130000e-24 124
6 TraesCS2D01G332400 chr2A 89.655 87 9 0 2920 3006 562687121 562687207 8.810000e-21 111


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 TraesCS2D01G332400 chr2D 425492600 425495605 3005 True 5552.00 5552 100.00000 1 3006 1 chr2D.!!$R1 3005
1 TraesCS2D01G332400 chr2B 500836469 500840807 4338 True 2188.00 4196 93.52150 1 3006 2 chr2B.!!$R1 3005
2 TraesCS2D01G332400 chr2A 562680293 562687207 6914 False 997.25 2706 92.42075 1 3006 4 chr2A.!!$F1 3005

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
192 1537 0.382515 AGTAGCGCCGAGACAGAATC 59.617 55.0 2.29 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 7144 0.036858 AAAGACGGAGGCAAGAGAGC 60.037 55.0 0.0 0.0 0.0 4.09 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
22 23 1.617947 ATGGGGAGACAGAACGAGGC 61.618 60.000 0.00 0.00 0.00 4.70
23 24 2.283529 GGGGAGACAGAACGAGGCA 61.284 63.158 0.00 0.00 0.00 4.75
24 25 1.216710 GGGAGACAGAACGAGGCAG 59.783 63.158 0.00 0.00 0.00 4.85
26 27 1.251527 GGAGACAGAACGAGGCAGGA 61.252 60.000 0.00 0.00 0.00 3.86
192 1537 0.382515 AGTAGCGCCGAGACAGAATC 59.617 55.000 2.29 0.00 0.00 2.52
198 1543 4.719997 CGAGACAGAATCCTCGCC 57.280 61.111 0.00 0.00 44.35 5.54
202 1547 3.411418 GACAGAATCCTCGCCGCGA 62.411 63.158 15.90 15.90 0.00 5.87
224 1569 2.048127 GTCTCCAGCTTTCGCCGT 60.048 61.111 0.00 0.00 36.60 5.68
281 1633 6.208988 ACTACGTGCATAAGAGATTCAGAA 57.791 37.500 0.00 0.00 0.00 3.02
283 1635 7.268586 ACTACGTGCATAAGAGATTCAGAATT 58.731 34.615 0.00 0.00 0.00 2.17
284 1636 6.355397 ACGTGCATAAGAGATTCAGAATTG 57.645 37.500 0.00 0.00 0.00 2.32
285 1637 5.877012 ACGTGCATAAGAGATTCAGAATTGT 59.123 36.000 0.00 0.00 0.00 2.71
286 1638 7.041721 ACGTGCATAAGAGATTCAGAATTGTA 58.958 34.615 0.00 0.00 0.00 2.41
287 1639 7.010552 ACGTGCATAAGAGATTCAGAATTGTAC 59.989 37.037 0.00 0.00 0.00 2.90
288 1640 7.223582 CGTGCATAAGAGATTCAGAATTGTACT 59.776 37.037 0.00 0.00 0.00 2.73
289 1641 9.534565 GTGCATAAGAGATTCAGAATTGTACTA 57.465 33.333 0.00 0.00 0.00 1.82
444 1797 3.821421 AGAGAACAGTTTCCACGTCTT 57.179 42.857 0.00 0.00 31.28 3.01
448 1801 3.308866 AGAACAGTTTCCACGTCTTTTCG 59.691 43.478 0.00 0.00 31.28 3.46
452 1805 1.064357 GTTTCCACGTCTTTTCGGCAA 59.936 47.619 0.00 0.00 34.94 4.52
464 1817 4.825085 TCTTTTCGGCAATTTTGTAGAGGT 59.175 37.500 0.00 0.00 0.00 3.85
521 1875 4.194678 ACTCCCCGGTCTTGATCTATTA 57.805 45.455 0.00 0.00 0.00 0.98
643 1997 2.281761 ACGGCAACTGAAGGGCTG 60.282 61.111 0.00 0.00 39.77 4.85
670 2024 1.995484 CGTGCTCAACTACCATCACAG 59.005 52.381 0.00 0.00 0.00 3.66
702 2056 1.963515 GCCTGAAGGTTTTGACACCAT 59.036 47.619 0.00 0.00 39.62 3.55
720 2074 2.159254 CCATTGTAAAATCACAGCCCCG 60.159 50.000 0.00 0.00 0.00 5.73
757 2111 1.200020 CCAAAGCGGATCCTGTTTGTC 59.800 52.381 23.78 3.60 36.56 3.18
798 2154 6.549952 GTTCCTGCATATCAGAAGAACAAAG 58.450 40.000 13.21 0.00 45.72 2.77
936 2293 4.281182 CCGGCTTGTACTTCCAGACTATAT 59.719 45.833 0.00 0.00 0.00 0.86
947 2304 8.788325 ACTTCCAGACTATATTTTTACACCAC 57.212 34.615 0.00 0.00 0.00 4.16
955 2312 8.288689 ACTATATTTTTACACCACCCATCAAC 57.711 34.615 0.00 0.00 0.00 3.18
957 2314 2.932855 TTTACACCACCCATCAACGA 57.067 45.000 0.00 0.00 0.00 3.85
958 2315 2.172851 TTACACCACCCATCAACGAC 57.827 50.000 0.00 0.00 0.00 4.34
976 2333 5.284861 ACGACCCATGTGCTATAAATACA 57.715 39.130 0.00 0.00 0.00 2.29
1045 2402 4.280174 AGTTGCTCATCATCTGCACTTTTT 59.720 37.500 0.00 0.00 36.37 1.94
1046 2403 5.474532 AGTTGCTCATCATCTGCACTTTTTA 59.525 36.000 0.00 0.00 36.37 1.52
1047 2404 5.556355 TGCTCATCATCTGCACTTTTTAG 57.444 39.130 0.00 0.00 0.00 1.85
1048 2405 4.142534 TGCTCATCATCTGCACTTTTTAGC 60.143 41.667 0.00 0.00 0.00 3.09
1049 2406 4.142534 GCTCATCATCTGCACTTTTTAGCA 60.143 41.667 0.00 0.00 39.25 3.49
1051 2408 5.946298 TCATCATCTGCACTTTTTAGCAAG 58.054 37.500 0.00 0.00 40.73 4.01
1052 2409 5.474532 TCATCATCTGCACTTTTTAGCAAGT 59.525 36.000 0.00 0.00 40.73 3.16
1053 2410 6.654582 TCATCATCTGCACTTTTTAGCAAGTA 59.345 34.615 0.00 0.00 40.73 2.24
1054 2411 6.875948 TCATCTGCACTTTTTAGCAAGTAA 57.124 33.333 0.00 0.00 40.73 2.24
1056 2413 6.262049 TCATCTGCACTTTTTAGCAAGTAACA 59.738 34.615 0.00 0.00 40.73 2.41
1057 2414 5.816919 TCTGCACTTTTTAGCAAGTAACAC 58.183 37.500 0.00 0.00 40.73 3.32
1058 2415 5.355630 TCTGCACTTTTTAGCAAGTAACACA 59.644 36.000 0.00 0.00 40.73 3.72
1059 2416 5.336744 TGCACTTTTTAGCAAGTAACACAC 58.663 37.500 0.00 0.00 37.90 3.82
1060 2417 4.436523 GCACTTTTTAGCAAGTAACACACG 59.563 41.667 0.00 0.00 35.10 4.49
1063 2430 3.870723 TTTAGCAAGTAACACACGCAG 57.129 42.857 0.00 0.00 0.00 5.18
1082 2449 2.298163 CAGGTTTTGCAGAAATGGAGCT 59.702 45.455 0.00 0.00 0.00 4.09
1752 3119 1.002257 TGCCAGTGACAATGCGGAT 60.002 52.632 0.00 0.00 0.00 4.18
1969 6959 7.585579 ATGTAAATGGTGCACATCATAATGA 57.414 32.000 20.43 0.52 39.40 2.57
2095 7140 3.136763 CTGAAGAACAAGAGCTCTGCAA 58.863 45.455 19.06 0.00 25.22 4.08
2099 7144 1.458827 GAACAAGAGCTCTGCAACGAG 59.541 52.381 19.06 4.28 0.00 4.18
2285 7340 3.625897 CCGCACTGTCCCTGTCCA 61.626 66.667 0.00 0.00 0.00 4.02
2386 7441 0.322906 GGCCCTTCCAGACCTTCTTG 60.323 60.000 0.00 0.00 34.01 3.02
2793 7854 2.202932 CCAAGATCCTCGGCACCG 60.203 66.667 1.73 1.73 41.35 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.557443 GAAACGTGTGTCCTGCCTCG 61.557 60.000 0.00 0.00 0.00 4.63
18 19 1.557443 CGAAACGTGTGTCCTGCCTC 61.557 60.000 0.00 0.00 0.00 4.70
19 20 1.594293 CGAAACGTGTGTCCTGCCT 60.594 57.895 0.00 0.00 0.00 4.75
20 21 1.433837 AACGAAACGTGTGTCCTGCC 61.434 55.000 0.00 0.00 39.99 4.85
22 23 2.861935 ACTTAACGAAACGTGTGTCCTG 59.138 45.455 0.00 0.00 39.99 3.86
23 24 3.118542 GACTTAACGAAACGTGTGTCCT 58.881 45.455 0.00 0.00 39.99 3.85
24 25 2.097733 CGACTTAACGAAACGTGTGTCC 60.098 50.000 0.00 0.00 39.99 4.02
26 27 2.279659 CACGACTTAACGAAACGTGTGT 59.720 45.455 0.00 0.00 45.57 3.72
202 1547 1.373497 CGAAAGCTGGAGACGTGCT 60.373 57.895 0.00 0.00 43.11 4.40
224 1569 1.064758 AGGTGCACAAACTCTTGTCCA 60.065 47.619 20.43 0.00 44.15 4.02
337 1689 8.991783 AACAGAGGTATGATGAATGAATGATT 57.008 30.769 0.00 0.00 0.00 2.57
444 1797 5.300792 AGAAACCTCTACAAAATTGCCGAAA 59.699 36.000 0.00 0.00 0.00 3.46
448 1801 4.021981 AGCAGAAACCTCTACAAAATTGCC 60.022 41.667 0.00 0.00 0.00 4.52
452 1805 4.022849 GCACAGCAGAAACCTCTACAAAAT 60.023 41.667 0.00 0.00 0.00 1.82
464 1817 0.512518 CGACGAATGCACAGCAGAAA 59.487 50.000 0.00 0.00 43.65 2.52
573 1927 7.640240 GCGACAGATACTCCAATTTATTTGTTC 59.360 37.037 0.00 0.00 33.15 3.18
702 2056 1.074084 TCCGGGGCTGTGATTTTACAA 59.926 47.619 0.00 0.00 0.00 2.41
720 2074 4.745125 GCTTTGGCTTCAGTAAAGTTTTCC 59.255 41.667 0.00 0.00 37.31 3.13
757 2111 3.118454 CGCTGCAGGTACGTTGGG 61.118 66.667 17.12 0.00 0.00 4.12
936 2293 3.315749 GTCGTTGATGGGTGGTGTAAAAA 59.684 43.478 0.00 0.00 0.00 1.94
942 2299 1.674322 GGGTCGTTGATGGGTGGTG 60.674 63.158 0.00 0.00 0.00 4.17
947 2304 1.656818 GCACATGGGTCGTTGATGGG 61.657 60.000 0.00 0.00 0.00 4.00
955 2312 6.166279 AGATGTATTTATAGCACATGGGTCG 58.834 40.000 0.00 0.00 33.16 4.79
957 2314 6.207417 GCAAGATGTATTTATAGCACATGGGT 59.793 38.462 0.00 0.00 33.16 4.51
958 2315 6.349611 GGCAAGATGTATTTATAGCACATGGG 60.350 42.308 0.00 0.00 33.16 4.00
976 2333 4.442192 GGTGAATCTCTACGAAGGCAAGAT 60.442 45.833 0.00 0.00 0.00 2.40
1045 2402 1.069513 ACCTGCGTGTGTTACTTGCTA 59.930 47.619 0.00 0.00 0.00 3.49
1046 2403 0.179056 ACCTGCGTGTGTTACTTGCT 60.179 50.000 0.00 0.00 0.00 3.91
1047 2404 0.661020 AACCTGCGTGTGTTACTTGC 59.339 50.000 0.00 0.00 0.00 4.01
1048 2405 3.105203 CAAAACCTGCGTGTGTTACTTG 58.895 45.455 0.00 0.00 0.00 3.16
1049 2406 2.478879 GCAAAACCTGCGTGTGTTACTT 60.479 45.455 0.00 0.00 42.37 2.24
1051 2408 1.472990 GCAAAACCTGCGTGTGTTAC 58.527 50.000 0.00 0.00 42.37 2.50
1052 2409 3.928343 GCAAAACCTGCGTGTGTTA 57.072 47.368 0.00 0.00 42.37 2.41
1053 2410 4.804496 GCAAAACCTGCGTGTGTT 57.196 50.000 0.00 0.00 42.37 3.32
1063 2430 2.297033 TGAGCTCCATTTCTGCAAAACC 59.703 45.455 12.15 0.00 0.00 3.27
1082 2449 0.884704 GACAAGAACAGCCGCCTTGA 60.885 55.000 12.37 0.00 39.55 3.02
1158 2525 2.827642 GGGGTCTCGACGATCGGT 60.828 66.667 20.98 4.89 40.88 4.69
1239 2606 0.391263 GGTACTCCAGGAACTTGCCG 60.391 60.000 0.00 0.00 34.60 5.69
1752 3119 1.301716 GCAGGACGAACTCTTGGCA 60.302 57.895 0.00 0.00 0.00 4.92
1785 3152 2.115910 CCAAGTGCAAGGCTCCCA 59.884 61.111 0.00 0.00 0.00 4.37
1906 3273 6.438259 TTCGGCGGAATAAATGAATTTACA 57.562 33.333 7.21 0.00 35.31 2.41
1969 6959 5.902613 ACAATACATACAAGCAGTGCATT 57.097 34.783 19.20 5.94 0.00 3.56
2006 7051 3.059884 TGTTTGCTCTCAATGTCTCGTC 58.940 45.455 0.00 0.00 31.33 4.20
2008 7053 3.496130 AGTTGTTTGCTCTCAATGTCTCG 59.504 43.478 0.00 0.00 31.33 4.04
2095 7140 2.705821 CGGAGGCAAGAGAGCTCGT 61.706 63.158 8.37 0.00 34.17 4.18
2099 7144 0.036858 AAAGACGGAGGCAAGAGAGC 60.037 55.000 0.00 0.00 0.00 4.09
2344 7399 2.343163 CTGGCGTCAGGATCTCGGTC 62.343 65.000 9.79 0.00 37.36 4.79
2386 7441 3.369576 GGTTGGTCTGATTGAGGTACCTC 60.370 52.174 31.61 31.61 43.01 3.85
2711 7772 2.912967 CGTCACGTTCACCATGTACTAC 59.087 50.000 0.00 0.00 0.00 2.73
2712 7773 2.553602 ACGTCACGTTCACCATGTACTA 59.446 45.455 0.00 0.00 36.35 1.82
2713 7774 1.338973 ACGTCACGTTCACCATGTACT 59.661 47.619 0.00 0.00 36.35 2.73
2952 8286 2.202932 CTTCCCATCCGCCTCACG 60.203 66.667 0.00 0.00 43.15 4.35


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

AutoCloner maintained by Alex Coulton.