Multiple sequence alignment - TraesCS2D01G099600

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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 TraesCS2D01G099600 chr2D 100.000 4353 0 0 1 4353 51252237 51256589 0.000000e+00 8039
1 TraesCS2D01G099600 chr2D 86.814 2351 284 14 918 3256 51160287 51157951 0.000000e+00 2601
2 TraesCS2D01G099600 chr2D 87.209 688 77 8 920 1596 51137892 51137205 0.000000e+00 773
3 TraesCS2D01G099600 chr2D 97.101 69 2 0 918 986 51253090 51253158 2.750000e-22 117
4 TraesCS2D01G099600 chr2D 97.101 69 2 0 854 922 51253154 51253222 2.750000e-22 117
5 TraesCS2D01G099600 chr2A 96.015 3814 105 22 551 4353 52756180 52759957 0.000000e+00 6157
6 TraesCS2D01G099600 chr2A 87.123 2353 282 16 918 3256 52573270 52570925 0.000000e+00 2647
7 TraesCS2D01G099600 chr2A 84.475 2087 306 11 1108 3184 52427833 52425755 0.000000e+00 2043
8 TraesCS2D01G099600 chr2A 82.322 1731 274 21 919 2634 52540943 52539230 0.000000e+00 1472
9 TraesCS2D01G099600 chr2A 93.085 376 25 1 20 394 52749375 52749750 2.290000e-152 549
10 TraesCS2D01G099600 chr2A 98.276 174 3 0 379 552 52755929 52756102 5.470000e-79 305
11 TraesCS2D01G099600 chr2A 83.163 196 22 5 3497 3689 52570622 52570435 7.490000e-38 169
12 TraesCS2D01G099600 chr2A 95.714 70 2 1 854 922 52756522 52756591 1.280000e-20 111
13 TraesCS2D01G099600 chr2B 95.751 3224 101 19 548 3754 80200070 80203274 0.000000e+00 5162
14 TraesCS2D01G099600 chr2B 86.431 2351 302 11 918 3256 79709220 79706875 0.000000e+00 2558
15 TraesCS2D01G099600 chr2B 84.282 2284 333 16 918 3184 79671883 79669609 0.000000e+00 2206
16 TraesCS2D01G099600 chr2B 89.127 607 34 8 3751 4353 80203337 80203915 0.000000e+00 726
17 TraesCS2D01G099600 chr2B 86.301 584 27 11 1 566 80199507 80200055 1.740000e-163 586
18 TraesCS2D01G099600 chr2B 95.652 69 3 0 854 922 80200438 80200506 1.280000e-20 111
19 TraesCS2D01G099600 chr7D 82.697 2410 397 16 918 3320 76396820 76399216 0.000000e+00 2122
20 TraesCS2D01G099600 chr7A 82.710 2111 347 10 1232 3339 82155452 82153357 0.000000e+00 1860


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 TraesCS2D01G099600 chr2D 51252237 51256589 4352 False 2757.666667 8039 98.067333 1 4353 3 chr2D.!!$F1 4352
1 TraesCS2D01G099600 chr2D 51157951 51160287 2336 True 2601.000000 2601 86.814000 918 3256 1 chr2D.!!$R2 2338
2 TraesCS2D01G099600 chr2D 51137205 51137892 687 True 773.000000 773 87.209000 920 1596 1 chr2D.!!$R1 676
3 TraesCS2D01G099600 chr2A 52755929 52759957 4028 False 2191.000000 6157 96.668333 379 4353 3 chr2A.!!$F2 3974
4 TraesCS2D01G099600 chr2A 52425755 52427833 2078 True 2043.000000 2043 84.475000 1108 3184 1 chr2A.!!$R1 2076
5 TraesCS2D01G099600 chr2A 52539230 52540943 1713 True 1472.000000 1472 82.322000 919 2634 1 chr2A.!!$R2 1715
6 TraesCS2D01G099600 chr2A 52570435 52573270 2835 True 1408.000000 2647 85.143000 918 3689 2 chr2A.!!$R3 2771
7 TraesCS2D01G099600 chr2B 79706875 79709220 2345 True 2558.000000 2558 86.431000 918 3256 1 chr2B.!!$R2 2338
8 TraesCS2D01G099600 chr2B 79669609 79671883 2274 True 2206.000000 2206 84.282000 918 3184 1 chr2B.!!$R1 2266
9 TraesCS2D01G099600 chr2B 80199507 80203915 4408 False 1646.250000 5162 91.707750 1 4353 4 chr2B.!!$F1 4352
10 TraesCS2D01G099600 chr7D 76396820 76399216 2396 False 2122.000000 2122 82.697000 918 3320 1 chr7D.!!$F1 2402
11 TraesCS2D01G099600 chr7A 82153357 82155452 2095 True 1860.000000 1860 82.710000 1232 3339 1 chr7A.!!$R1 2107

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
75 76 0.110295 TACATGCTGCCACAGGTGTT 59.890 50.000 0.0 0.0 35.0 3.32 F
165 168 0.179018 GTGCCATGTCCCATACCCTC 60.179 60.000 0.0 0.0 0.0 4.30 F
166 169 0.327480 TGCCATGTCCCATACCCTCT 60.327 55.000 0.0 0.0 0.0 3.69 F
208 211 0.613777 AGGTACAGCTTTCTTCCCCG 59.386 55.000 0.0 0.0 0.0 5.73 F
374 393 1.136329 ACCTTCCATGCACCCACTCT 61.136 55.000 0.0 0.0 0.0 3.24 F
774 872 1.339631 CGTTCCTGCCATCCCAGTAAA 60.340 52.381 0.0 0.0 0.0 2.01 F
1059 1175 1.395954 GGAATGGCGTCGTTTAGGAAC 59.604 52.381 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1158 1274 0.037790 AAGCACGAGAAGCAGAGGAC 60.038 55.000 0.00 0.00 0.00 3.85 R
1338 1454 0.953960 TAGTGTCGAGCTCAGCGTCA 60.954 55.000 15.40 1.65 0.00 4.35 R
2050 2183 1.712977 GCAGCAAAGCTCCGATCCAG 61.713 60.000 0.00 0.00 36.40 3.86 R
2327 2462 2.722094 TGTAATCCTGAACCATGGTGC 58.278 47.619 20.60 18.68 0.00 5.01 R
2517 2654 4.142780 GGCTTTAGGATGCCGACC 57.857 61.111 0.00 0.00 39.71 4.79 R
2706 2844 1.067212 GACGTCGTTAGGATGGCAGAT 59.933 52.381 0.00 0.00 39.68 2.90 R
3932 4223 7.568199 AGACCAAATAATGCATTGTACTACC 57.432 36.000 22.27 6.60 0.00 3.18 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
48 49 8.142994 TCACAACTTATCTTTCTCAGTGTTTC 57.857 34.615 0.00 0.00 0.00 2.78
51 52 7.442666 ACAACTTATCTTTCTCAGTGTTTCTCC 59.557 37.037 0.00 0.00 0.00 3.71
73 74 0.606130 TGTACATGCTGCCACAGGTG 60.606 55.000 0.00 0.00 35.00 4.00
74 75 0.606401 GTACATGCTGCCACAGGTGT 60.606 55.000 0.00 0.00 35.00 4.16
75 76 0.110295 TACATGCTGCCACAGGTGTT 59.890 50.000 0.00 0.00 35.00 3.32
76 77 1.287815 CATGCTGCCACAGGTGTTG 59.712 57.895 0.00 0.00 31.21 3.33
77 78 1.904865 ATGCTGCCACAGGTGTTGG 60.905 57.895 0.00 0.00 31.21 3.77
78 79 3.297620 GCTGCCACAGGTGTTGGG 61.298 66.667 0.00 0.00 31.21 4.12
79 80 2.515398 CTGCCACAGGTGTTGGGA 59.485 61.111 0.00 0.00 28.76 4.37
80 81 1.075482 CTGCCACAGGTGTTGGGAT 59.925 57.895 0.00 0.00 28.76 3.85
81 82 0.962356 CTGCCACAGGTGTTGGGATC 60.962 60.000 0.00 0.00 28.76 3.36
82 83 1.074775 GCCACAGGTGTTGGGATCA 59.925 57.895 0.00 0.00 28.76 2.92
83 84 0.323725 GCCACAGGTGTTGGGATCAT 60.324 55.000 0.00 0.00 28.76 2.45
84 85 1.755179 CCACAGGTGTTGGGATCATC 58.245 55.000 0.00 0.00 28.76 2.92
110 113 1.153509 GGCAAGGTGATGGCAATGC 60.154 57.895 0.00 0.00 44.66 3.56
136 139 2.266689 GCGACGGGGCCTAAGAAA 59.733 61.111 0.84 0.00 0.00 2.52
165 168 0.179018 GTGCCATGTCCCATACCCTC 60.179 60.000 0.00 0.00 0.00 4.30
166 169 0.327480 TGCCATGTCCCATACCCTCT 60.327 55.000 0.00 0.00 0.00 3.69
195 198 1.681538 TCGCCAAAGCAAAAGGTACA 58.318 45.000 0.00 0.00 39.83 2.90
198 201 1.341209 GCCAAAGCAAAAGGTACAGCT 59.659 47.619 0.00 0.00 39.53 4.24
207 210 2.881111 AAGGTACAGCTTTCTTCCCC 57.119 50.000 0.00 0.00 0.00 4.81
208 211 0.613777 AGGTACAGCTTTCTTCCCCG 59.386 55.000 0.00 0.00 0.00 5.73
225 228 2.590092 GGCACTAGGAATGGCCGT 59.410 61.111 0.00 0.00 43.43 5.68
299 318 3.625764 TGTGTTTCTGCCTGTTTGTAGAC 59.374 43.478 0.00 0.00 0.00 2.59
315 334 7.652105 TGTTTGTAGACTATAATCTGATTCGCC 59.348 37.037 6.10 0.00 0.00 5.54
328 347 2.859273 ATTCGCCGAGCACCAGAAGG 62.859 60.000 0.00 0.00 42.21 3.46
351 370 2.672996 CCACTGGAACGCCAAGGG 60.673 66.667 0.00 0.00 45.41 3.95
374 393 1.136329 ACCTTCCATGCACCCACTCT 61.136 55.000 0.00 0.00 0.00 3.24
708 806 7.283127 TCAAGAGAATGGAAAATATCTTTCCCG 59.717 37.037 18.67 0.00 45.59 5.14
709 807 6.064717 AGAGAATGGAAAATATCTTTCCCGG 58.935 40.000 18.67 0.00 45.59 5.73
774 872 1.339631 CGTTCCTGCCATCCCAGTAAA 60.340 52.381 0.00 0.00 0.00 2.01
860 958 8.509690 CGCTGGATTTATCAACTGATGATTAAT 58.490 33.333 10.59 10.59 46.85 1.40
872 970 8.810427 CAACTGATGATTAATACATGCCAAAAC 58.190 33.333 0.00 0.00 0.00 2.43
1059 1175 1.395954 GGAATGGCGTCGTTTAGGAAC 59.604 52.381 0.00 0.00 0.00 3.62
1092 1208 2.641815 ACTTCTCTTGCTCACCATCCTT 59.358 45.455 0.00 0.00 0.00 3.36
1158 1274 3.049206 CGTACACCAAAATGCCACAAAG 58.951 45.455 0.00 0.00 0.00 2.77
2517 2654 1.815003 TGGTCCAAGCATCATCGCG 60.815 57.895 0.00 0.00 36.85 5.87
2706 2844 4.713735 TCGCCAGCCGCCATCAAA 62.714 61.111 0.00 0.00 36.73 2.69
2961 3099 1.000396 GAAGCTGCCCAAGGTCCAT 60.000 57.895 0.00 0.00 34.84 3.41
3196 3334 2.738213 CTTGGGCGAGGAACTGCACT 62.738 60.000 0.00 0.00 41.55 4.40
3324 3462 2.157834 ACGTGCCGTGAAATCAGTAA 57.842 45.000 0.00 0.00 39.18 2.24
3432 3616 6.946340 TGCCATTCAAACTAGAGATCAGTAA 58.054 36.000 0.00 0.00 0.00 2.24
3825 4116 6.155827 TGTTTATAGTGCTTTTGTTCCATGC 58.844 36.000 0.00 0.00 0.00 4.06
3932 4223 0.833287 ATCCAGGATTCCAGGTCGTG 59.167 55.000 13.39 0.00 31.65 4.35
3948 4239 4.160814 AGGTCGTGGTAGTACAATGCATTA 59.839 41.667 12.53 0.00 0.00 1.90
3968 4262 9.023962 TGCATTATTTGGTCTTTCACTAGAAAT 57.976 29.630 0.00 0.00 42.49 2.17
4011 4305 6.804783 AGTTTTACAACAAAAGGACTTGAACG 59.195 34.615 0.00 0.00 35.05 3.95
4019 4313 5.181622 ACAAAAGGACTTGAACGTTGTTACA 59.818 36.000 5.00 0.00 0.00 2.41
4027 4321 7.744715 GGACTTGAACGTTGTTACATTAATCTG 59.255 37.037 5.00 0.00 0.00 2.90
4037 4331 6.115446 TGTTACATTAATCTGCTTCCTCAGG 58.885 40.000 0.00 0.00 34.91 3.86
4059 4353 4.156739 GGGGTGAGATCTTGAACATTGTTC 59.843 45.833 20.27 20.27 0.00 3.18
4076 4370 4.439305 TGTTCTAATTGCAGGATTGTGC 57.561 40.909 0.00 0.00 44.27 4.57
4085 4379 1.945394 GCAGGATTGTGCCACATAGAG 59.055 52.381 0.00 0.00 37.49 2.43
4099 4393 5.585390 CCACATAGAGAAAATTCATGCACC 58.415 41.667 0.00 0.00 0.00 5.01
4281 4581 8.429237 TTGTATTTGGGAAGTTTTCATATGGT 57.571 30.769 2.13 0.00 0.00 3.55
4345 4645 8.243961 TGATCAAACCTATTGAAAGTTTTCCA 57.756 30.769 0.00 0.00 36.36 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.974957 TGATTCGGGTCTTGAACTGGA 59.025 47.619 0.00 0.00 0.00 3.86
48 49 0.538584 TGGCAGCATGTACAGAGGAG 59.461 55.000 0.33 0.00 39.31 3.69
51 52 3.538379 TGTGGCAGCATGTACAGAG 57.462 52.632 0.33 0.00 39.31 3.35
73 74 2.555199 CCAGAAGACGATGATCCCAAC 58.445 52.381 0.00 0.00 0.00 3.77
74 75 1.134401 GCCAGAAGACGATGATCCCAA 60.134 52.381 0.00 0.00 0.00 4.12
75 76 0.465705 GCCAGAAGACGATGATCCCA 59.534 55.000 0.00 0.00 0.00 4.37
76 77 0.465705 TGCCAGAAGACGATGATCCC 59.534 55.000 0.00 0.00 0.00 3.85
77 78 2.208431 CTTGCCAGAAGACGATGATCC 58.792 52.381 0.00 0.00 0.00 3.36
78 79 2.208431 CCTTGCCAGAAGACGATGATC 58.792 52.381 0.00 0.00 0.00 2.92
79 80 1.556911 ACCTTGCCAGAAGACGATGAT 59.443 47.619 0.00 0.00 0.00 2.45
80 81 0.976641 ACCTTGCCAGAAGACGATGA 59.023 50.000 0.00 0.00 0.00 2.92
81 82 1.081892 CACCTTGCCAGAAGACGATG 58.918 55.000 0.00 0.00 0.00 3.84
82 83 0.976641 TCACCTTGCCAGAAGACGAT 59.023 50.000 0.00 0.00 0.00 3.73
83 84 0.976641 ATCACCTTGCCAGAAGACGA 59.023 50.000 0.00 0.00 0.00 4.20
84 85 1.081892 CATCACCTTGCCAGAAGACG 58.918 55.000 0.00 0.00 0.00 4.18
128 131 2.678336 GCACCGGATTCTGTTTCTTAGG 59.322 50.000 9.46 0.00 0.00 2.69
130 133 2.039216 TGGCACCGGATTCTGTTTCTTA 59.961 45.455 9.46 0.00 0.00 2.10
136 139 0.392998 GACATGGCACCGGATTCTGT 60.393 55.000 9.46 4.66 0.00 3.41
165 168 0.718343 CTTTGGCGAAGAAGCTCGAG 59.282 55.000 8.45 8.45 41.44 4.04
166 169 1.291877 GCTTTGGCGAAGAAGCTCGA 61.292 55.000 18.76 0.00 43.69 4.04
195 198 1.198759 TAGTGCCGGGGAAGAAAGCT 61.199 55.000 2.18 0.00 0.00 3.74
198 201 0.545787 TCCTAGTGCCGGGGAAGAAA 60.546 55.000 2.18 0.00 0.00 2.52
208 211 1.523938 GACGGCCATTCCTAGTGCC 60.524 63.158 2.24 0.00 40.54 5.01
225 228 0.887387 CTTGGAAAAGGAACCCGCGA 60.887 55.000 8.23 0.00 0.00 5.87
246 249 1.967779 TGAACCAAGATGAGACGACCA 59.032 47.619 0.00 0.00 0.00 4.02
299 318 3.610242 GTGCTCGGCGAATCAGATTATAG 59.390 47.826 12.13 0.00 0.00 1.31
328 347 2.258726 GGCGTTCCAGTGGACCAAC 61.259 63.158 12.69 6.90 0.00 3.77
351 370 2.048603 GGGTGCATGGAAGGTCTGC 61.049 63.158 0.00 0.00 36.45 4.26
357 376 0.037303 ACAGAGTGGGTGCATGGAAG 59.963 55.000 0.00 0.00 0.00 3.46
374 393 3.855255 TGGGAGAAAATGACACTGACA 57.145 42.857 0.00 0.00 0.00 3.58
583 681 4.777896 GCTGGTTCTGTATCCCCAGATATA 59.222 45.833 8.65 0.00 45.97 0.86
709 807 0.834687 TGGTGCGGGATAGGGGATAC 60.835 60.000 0.00 0.00 0.00 2.24
872 970 4.905866 CGAATGATTAATGCGTTGCCTTAG 59.094 41.667 0.08 0.00 32.06 2.18
1059 1175 1.216710 GAGAAGTGGCACGGAGAGG 59.783 63.158 12.71 0.00 0.00 3.69
1092 1208 2.621338 CAGAGTGCGAGCATAGGAAAA 58.379 47.619 0.00 0.00 0.00 2.29
1158 1274 0.037790 AAGCACGAGAAGCAGAGGAC 60.038 55.000 0.00 0.00 0.00 3.85
1338 1454 0.953960 TAGTGTCGAGCTCAGCGTCA 60.954 55.000 15.40 1.65 0.00 4.35
1440 1556 1.743995 CCCGGTGCCGTTCTTTAGG 60.744 63.158 9.90 0.00 37.81 2.69
2050 2183 1.712977 GCAGCAAAGCTCCGATCCAG 61.713 60.000 0.00 0.00 36.40 3.86
2327 2462 2.722094 TGTAATCCTGAACCATGGTGC 58.278 47.619 20.60 18.68 0.00 5.01
2517 2654 4.142780 GGCTTTAGGATGCCGACC 57.857 61.111 0.00 0.00 39.71 4.79
2706 2844 1.067212 GACGTCGTTAGGATGGCAGAT 59.933 52.381 0.00 0.00 39.68 2.90
3932 4223 7.568199 AGACCAAATAATGCATTGTACTACC 57.432 36.000 22.27 6.60 0.00 3.18
3948 4239 8.463930 TGTCAATTTCTAGTGAAAGACCAAAT 57.536 30.769 0.00 0.00 44.25 2.32
4011 4305 7.377766 TGAGGAAGCAGATTAATGTAACAAC 57.622 36.000 0.00 0.00 0.00 3.32
4019 4313 3.117738 CACCCCTGAGGAAGCAGATTAAT 60.118 47.826 0.00 0.00 38.14 1.40
4027 4321 0.467804 GATCTCACCCCTGAGGAAGC 59.532 60.000 0.00 0.00 43.87 3.86
4037 4331 5.006386 AGAACAATGTTCAAGATCTCACCC 58.994 41.667 25.63 0.00 0.00 4.61
4059 4353 2.492881 TGTGGCACAATCCTGCAATTAG 59.507 45.455 19.74 0.00 44.16 1.73
4076 4370 5.585390 GGTGCATGAATTTTCTCTATGTGG 58.415 41.667 0.00 0.00 0.00 4.17
4099 4393 4.116961 TGGAAACTCGGTAATAGAATGCG 58.883 43.478 0.00 0.00 0.00 4.73
4306 4606 5.786975 AGGTTTGATCATGAAATTTTCCCCT 59.213 36.000 0.00 0.00 0.00 4.79
4307 4607 6.053632 AGGTTTGATCATGAAATTTTCCCC 57.946 37.500 0.00 0.00 0.00 4.81
4308 4608 9.101655 CAATAGGTTTGATCATGAAATTTTCCC 57.898 33.333 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.