Multiple sequence alignment - TraesCS2A01G194800

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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 TraesCS2A01G194800 chr2A 100.000 3150 0 0 696 3845 164266604 164269753 0.000000e+00 5818.0
1 TraesCS2A01G194800 chr2A 100.000 425 0 0 1 425 164265909 164266333 0.000000e+00 785.0
2 TraesCS2A01G194800 chr2D 96.784 3172 80 10 696 3845 137592456 137589285 0.000000e+00 5273.0
3 TraesCS2A01G194800 chr2D 96.215 317 11 1 109 425 137592861 137592546 5.690000e-143 518.0
4 TraesCS2A01G194800 chr2B 97.375 2248 59 0 696 2943 195693469 195691222 0.000000e+00 3825.0
5 TraesCS2A01G194800 chr2B 96.546 579 13 2 2942 3514 195691098 195690521 0.000000e+00 952.0
6 TraesCS2A01G194800 chr2B 90.073 413 24 9 1 397 195694212 195693801 1.580000e-143 520.0
7 TraesCS2A01G194800 chr2B 94.578 332 17 1 3514 3845 195690489 195690159 2.650000e-141 512.0
8 TraesCS2A01G194800 chrUn 100.000 403 0 0 2469 2871 478410716 478410314 0.000000e+00 745.0
9 TraesCS2A01G194800 chr5B 79.433 141 21 4 3579 3711 482323118 482323258 4.090000e-15 93.5


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 TraesCS2A01G194800 chr2A 164265909 164269753 3844 False 3301.50 5818 100.0000 1 3845 2 chr2A.!!$F1 3844
1 TraesCS2A01G194800 chr2D 137589285 137592861 3576 True 2895.50 5273 96.4995 109 3845 2 chr2D.!!$R1 3736
2 TraesCS2A01G194800 chr2B 195690159 195694212 4053 True 1452.25 3825 94.6430 1 3845 4 chr2B.!!$R1 3844

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
362 379 1.228124 CAAGACCTTCCGCCACCAA 60.228 57.895 0.0 0.0 0.00 3.67 F
1133 1364 1.343142 TGTCGTGCTCCATGTGTACTT 59.657 47.619 0.0 0.0 0.00 2.24 F
1501 1732 1.485895 AGCTCAAAGAGGAGATGGAGC 59.514 52.381 0.0 0.0 46.01 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 2218 0.106268 TTTTCTGCCTGCTCCCAACA 60.106 50.0 0.0 0.0 0.0 3.33 R
2348 2579 0.391130 TGCGGTGCTGAGGTTGATAC 60.391 55.0 0.0 0.0 0.0 2.24 R
3289 3645 0.106918 TCAAAACCGAGCCCACAACT 60.107 50.0 0.0 0.0 0.0 3.16 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
24 25 6.820470 TTCGGTGAACATTTTTGTTGAATC 57.180 33.333 0.00 0.00 31.35 2.52
25 26 5.895928 TCGGTGAACATTTTTGTTGAATCA 58.104 33.333 0.00 0.00 31.35 2.57
26 27 6.511416 TCGGTGAACATTTTTGTTGAATCAT 58.489 32.000 0.00 0.00 31.35 2.45
32 34 8.326713 TGAACATTTTTGTTGAATCATTGAACG 58.673 29.630 0.00 0.00 31.35 3.95
34 36 7.840489 ACATTTTTGTTGAATCATTGAACGTC 58.160 30.769 0.00 0.00 0.00 4.34
44 46 6.417635 TGAATCATTGAACGTCTTTTGAAAGC 59.582 34.615 0.00 0.00 35.99 3.51
99 102 3.068881 CACCTCGACCCCACATGT 58.931 61.111 0.00 0.00 0.00 3.21
100 103 1.375908 CACCTCGACCCCACATGTG 60.376 63.158 19.31 19.31 0.00 3.21
101 104 1.841556 ACCTCGACCCCACATGTGT 60.842 57.895 23.79 6.10 0.00 3.72
106 109 4.697756 ACCCCACATGTGTCGGCG 62.698 66.667 23.79 14.22 0.00 6.46
111 114 4.357947 ACATGTGTCGGCGAGCGT 62.358 61.111 11.20 4.91 0.00 5.07
118 129 4.889112 TCGGCGAGCGTAGGGGAT 62.889 66.667 4.99 0.00 0.00 3.85
362 379 1.228124 CAAGACCTTCCGCCACCAA 60.228 57.895 0.00 0.00 0.00 3.67
744 975 3.535962 GCGCTCCTCTCCCTCCTG 61.536 72.222 0.00 0.00 0.00 3.86
864 1095 4.127040 CTCGCTGCTCTCCACGCT 62.127 66.667 0.00 0.00 0.00 5.07
897 1128 4.329545 GGCCTGCACGTCCTCCAA 62.330 66.667 0.00 0.00 0.00 3.53
1032 1263 2.432628 GTGTCAGCGTTCTCCCGG 60.433 66.667 0.00 0.00 0.00 5.73
1133 1364 1.343142 TGTCGTGCTCCATGTGTACTT 59.657 47.619 0.00 0.00 0.00 2.24
1272 1503 3.031736 ACTCTATAAGGAGGCAGCGAAA 58.968 45.455 0.00 0.00 37.63 3.46
1353 1584 2.093890 CTTGATGTGTATGGCAAGGCA 58.906 47.619 0.00 0.00 35.34 4.75
1437 1668 3.057315 GTGTGGTAACCTACAACTCGCTA 60.057 47.826 0.00 0.00 33.67 4.26
1501 1732 1.485895 AGCTCAAAGAGGAGATGGAGC 59.514 52.381 0.00 0.00 46.01 4.70
1539 1770 3.420904 CGGATGTCATTACATACACGACG 59.579 47.826 3.20 0.00 45.97 5.12
1854 2085 1.593006 GAGCGGGACACATATGTTTCG 59.407 52.381 14.27 12.25 39.95 3.46
1987 2218 2.943978 GCACTAGCTCGTGGTGGGT 61.944 63.158 18.96 0.00 38.09 4.51
2278 2509 7.717436 TGGATATTAACGTCCTAAATGCAATGA 59.283 33.333 8.86 0.00 35.49 2.57
2467 2698 2.358247 GTGGTGCACGTCCGGATT 60.358 61.111 7.81 0.00 0.00 3.01
2884 3115 8.456904 TTGTATTTGTGATACGACAAGTAGAC 57.543 34.615 0.00 0.00 38.94 2.59
2887 3118 6.944557 TTTGTGATACGACAAGTAGACATG 57.055 37.500 0.00 0.00 38.94 3.21
3289 3645 4.430007 GTGCATCGTGGTATTTAGAGTCA 58.570 43.478 0.00 0.00 0.00 3.41
3371 3733 3.836176 GAGTCGTGGCGGTTCGTGT 62.836 63.158 0.00 0.00 0.00 4.49
3382 3744 0.317854 GGTTCGTGTGAGCCTTTTGC 60.318 55.000 0.00 0.00 41.91 3.68
3399 3761 1.815421 GCCCTATGTGTCAGGTGCG 60.815 63.158 0.00 0.00 0.00 5.34
3435 3797 3.067461 TCGCTGCTTTATTGGTTTTGTGT 59.933 39.130 0.00 0.00 0.00 3.72
3524 3918 0.882042 CTGTGTTCGCTGGTTCTGCT 60.882 55.000 0.00 0.00 0.00 4.24
3530 3924 2.282040 GCTGGTTCTGCTGCTGGT 60.282 61.111 6.69 0.00 0.00 4.00
3555 3949 1.469703 TCGTCTTTCGCATCGGTCTTA 59.530 47.619 0.00 0.00 39.67 2.10
3556 3950 2.095110 TCGTCTTTCGCATCGGTCTTAA 60.095 45.455 0.00 0.00 39.67 1.85
3574 3968 2.417719 AACTGGTCTTCTAGGTGGGT 57.582 50.000 0.00 0.00 0.00 4.51
3615 4009 1.259142 TGGTTACGGGGCTTCATCGA 61.259 55.000 0.00 0.00 0.00 3.59
3736 4130 2.426023 GTGCTGTCCTTGGTCGGT 59.574 61.111 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.379161 CAAAAGACGTTCAATGATTCAACAAAA 58.621 29.630 0.00 0.00 0.00 2.44
17 18 7.678194 TTCAAAAGACGTTCAATGATTCAAC 57.322 32.000 0.00 0.00 0.00 3.18
18 19 7.043458 GCTTTCAAAAGACGTTCAATGATTCAA 60.043 33.333 6.67 0.00 38.28 2.69
19 20 6.417635 GCTTTCAAAAGACGTTCAATGATTCA 59.582 34.615 6.67 0.00 38.28 2.57
20 21 6.129088 GGCTTTCAAAAGACGTTCAATGATTC 60.129 38.462 6.67 0.00 38.28 2.52
21 22 5.691754 GGCTTTCAAAAGACGTTCAATGATT 59.308 36.000 6.67 0.00 38.28 2.57
23 24 4.606961 GGCTTTCAAAAGACGTTCAATGA 58.393 39.130 6.67 0.00 38.28 2.57
24 25 4.954238 GGCTTTCAAAAGACGTTCAATG 57.046 40.909 6.67 0.00 38.28 2.82
32 34 6.968131 AAAAAGTTCTGGCTTTCAAAAGAC 57.032 33.333 6.67 4.00 44.48 3.01
101 104 4.889112 ATCCCCTACGCTCGCCGA 62.889 66.667 2.37 0.00 41.02 5.54
106 109 3.303928 CCCCGATCCCCTACGCTC 61.304 72.222 0.00 0.00 0.00 5.03
111 114 2.041301 CACACCCCCGATCCCCTA 60.041 66.667 0.00 0.00 0.00 3.53
154 165 1.340248 GGATCTCCTATTCGGCGAACA 59.660 52.381 26.22 13.43 28.63 3.18
179 190 2.297597 GTGGAGAAGAGGACCGGATATG 59.702 54.545 9.46 0.00 0.00 1.78
227 238 1.917336 TTATGGCCGGTGAAGGGGTC 61.917 60.000 1.90 0.00 0.00 4.46
373 390 0.256464 GAAGAGTCGGAGAGGGGAGA 59.744 60.000 0.00 0.00 36.95 3.71
882 1113 1.003355 ATGTTGGAGGACGTGCAGG 60.003 57.895 10.52 4.53 0.00 4.85
883 1114 1.021390 GGATGTTGGAGGACGTGCAG 61.021 60.000 10.52 0.00 0.00 4.41
884 1115 1.003839 GGATGTTGGAGGACGTGCA 60.004 57.895 10.52 0.00 0.00 4.57
1272 1503 1.939838 GCCCTCATTTCGTCGAACACT 60.940 52.381 7.29 0.00 0.00 3.55
1353 1584 0.107066 TTGCCTCATCATGCATCCGT 60.107 50.000 0.00 0.00 37.33 4.69
1367 1598 0.901580 CTTGAGCACCCCAATTGCCT 60.902 55.000 0.00 0.00 41.18 4.75
1437 1668 6.062095 CCCATCCTTTACATAGGACGAAATT 58.938 40.000 0.00 0.00 46.71 1.82
1501 1732 2.710096 TCCGGCTGAATTCCCTTAAG 57.290 50.000 2.27 0.00 0.00 1.85
1539 1770 2.746362 CCTGTCAAGACCAGAAATCAGC 59.254 50.000 0.00 0.00 0.00 4.26
1569 1800 1.406539 GTCCCGATTGCTGCATCAATT 59.593 47.619 16.36 1.62 36.85 2.32
1590 1821 5.183713 TCCATTCCTCAACATTTCATCACAC 59.816 40.000 0.00 0.00 0.00 3.82
1592 1823 5.902613 TCCATTCCTCAACATTTCATCAC 57.097 39.130 0.00 0.00 0.00 3.06
1854 2085 6.363626 CACACCGACTATATGAACTAATGAGC 59.636 42.308 0.00 0.00 0.00 4.26
1987 2218 0.106268 TTTTCTGCCTGCTCCCAACA 60.106 50.000 0.00 0.00 0.00 3.33
2278 2509 9.243105 CATCCTATTTTTCCCATATACGGAAAT 57.757 33.333 13.90 3.37 46.21 2.17
2348 2579 0.391130 TGCGGTGCTGAGGTTGATAC 60.391 55.000 0.00 0.00 0.00 2.24
2884 3115 8.454106 CCAAGGATAACTAAGAAAACAGTCATG 58.546 37.037 0.00 0.00 0.00 3.07
2887 3118 6.430000 TGCCAAGGATAACTAAGAAAACAGTC 59.570 38.462 0.00 0.00 0.00 3.51
2977 3333 7.983307 AGCAGAGAAAACTAAATGCATCTTAG 58.017 34.615 18.87 18.87 36.15 2.18
3289 3645 0.106918 TCAAAACCGAGCCCACAACT 60.107 50.000 0.00 0.00 0.00 3.16
3382 3744 0.740868 CACGCACCTGACACATAGGG 60.741 60.000 0.00 0.00 39.71 3.53
3399 3761 0.732196 CAGCGAGAGAGCAGACACAC 60.732 60.000 0.00 0.00 40.15 3.82
3530 3924 1.351430 CGATGCGAAAGACGAAGCCA 61.351 55.000 0.00 0.00 45.77 4.75
3555 3949 2.417719 ACCCACCTAGAAGACCAGTT 57.582 50.000 0.00 0.00 0.00 3.16
3556 3950 2.292323 CCTACCCACCTAGAAGACCAGT 60.292 54.545 0.00 0.00 0.00 4.00
3574 3968 3.065306 CCGCTGTCAACACCCCTA 58.935 61.111 0.00 0.00 0.00 3.53
3601 3995 1.115930 ATAGCTCGATGAAGCCCCGT 61.116 55.000 0.00 0.00 43.56 5.28
3615 4009 0.179108 GCGGAGGAACACGAATAGCT 60.179 55.000 0.00 0.00 32.99 3.32
3631 4025 1.377725 AAACCCTCAGATGCAGCGG 60.378 57.895 0.00 0.00 0.00 5.52
3736 4130 1.065401 CAGAAACAAAGAAGCACGCCA 59.935 47.619 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.