Multiple sequence alignment - TraesCS2D01G292300

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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 TraesCS2D01G292300 chr2D 100.000 2480 0 0 1 2480 374143915 374146394 0.000000e+00 4580
1 TraesCS2D01G292300 chr2D 96.682 211 6 1 2271 2480 357894836 357895046 1.410000e-92 350
2 TraesCS2D01G292300 chr2D 94.762 210 11 0 2271 2480 516365392 516365183 6.610000e-86 327
3 TraesCS2D01G292300 chr2A 92.971 2319 91 31 1 2271 507083051 507085345 0.000000e+00 3314
4 TraesCS2D01G292300 chr2A 93.333 210 14 0 2271 2480 42775737 42775946 6.660000e-81 311
5 TraesCS2D01G292300 chr2B 96.036 1791 35 18 439 2217 444844271 444846037 0.000000e+00 2881
6 TraesCS2D01G292300 chr2B 93.333 210 14 0 2271 2480 401668956 401669165 6.660000e-81 311
7 TraesCS2D01G292300 chr2B 91.045 134 11 1 310 443 444843221 444843353 1.960000e-41 180
8 TraesCS2D01G292300 chr2B 94.286 70 3 1 2202 2271 444847261 444847329 3.370000e-19 106
9 TraesCS2D01G292300 chr7D 97.619 210 5 0 2271 2480 592727410 592727619 6.520000e-96 361
10 TraesCS2D01G292300 chr5D 96.313 217 6 2 2266 2480 42063359 42063575 3.030000e-94 355
11 TraesCS2D01G292300 chr3D 95.714 210 5 2 2271 2480 17523262 17523057 3.950000e-88 335
12 TraesCS2D01G292300 chr5A 94.762 210 11 0 2271 2480 597832287 597832078 6.610000e-86 327
13 TraesCS2D01G292300 chr1A 94.712 208 11 0 2273 2480 570922800 570922593 8.550000e-85 324


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 TraesCS2D01G292300 chr2D 374143915 374146394 2479 False 4580.000000 4580 100.000 1 2480 1 chr2D.!!$F2 2479
1 TraesCS2D01G292300 chr2A 507083051 507085345 2294 False 3314.000000 3314 92.971 1 2271 1 chr2A.!!$F2 2270
2 TraesCS2D01G292300 chr2B 444843221 444847329 4108 False 1055.666667 2881 93.789 310 2271 3 chr2B.!!$F2 1961

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
421 444 0.179108 GTCGGGTGGATCTTTCCTCG 60.179 60.0 0.0 0.48 43.07 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 2683 1.446272 GGAGAACAACGCTCCTCGG 60.446 63.158 0.0 0.0 46.7 4.63 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 4.953940 TTTTCCTAAAAACCAGCTGCAT 57.046 36.364 8.66 0.00 29.44 3.96
49 50 4.519540 TTTCCTAAAAACCAGCTGCATC 57.480 40.909 8.66 0.00 0.00 3.91
50 51 2.083774 TCCTAAAAACCAGCTGCATCG 58.916 47.619 8.66 0.00 0.00 3.84
61 66 2.086869 AGCTGCATCGCACTTGTTATT 58.913 42.857 1.02 0.00 33.79 1.40
67 72 4.023279 TGCATCGCACTTGTTATTGACTTT 60.023 37.500 0.00 0.00 31.71 2.66
69 74 5.402270 GCATCGCACTTGTTATTGACTTTTT 59.598 36.000 0.00 0.00 0.00 1.94
102 107 8.840833 ATTTTGTTTTGTTTGGTAAGTCAAGT 57.159 26.923 0.00 0.00 0.00 3.16
103 108 7.876896 TTTGTTTTGTTTGGTAAGTCAAGTC 57.123 32.000 0.00 0.00 0.00 3.01
194 199 8.345724 AGAAGGTAAATCAGAGACTAACGTAA 57.654 34.615 0.00 0.00 0.00 3.18
204 209 5.050227 CAGAGACTAACGTAATACTCCCTCG 60.050 48.000 0.00 0.00 0.00 4.63
208 213 6.204495 AGACTAACGTAATACTCCCTCGAATC 59.796 42.308 0.00 0.00 0.00 2.52
210 215 3.470709 ACGTAATACTCCCTCGAATCGA 58.529 45.455 4.91 4.91 0.00 3.59
259 265 5.136828 TGGTTGAACCTCAGCTTTGAATAA 58.863 37.500 16.33 0.00 39.58 1.40
271 277 6.267471 TCAGCTTTGAATAAGGTTGGTTCAAT 59.733 34.615 0.00 0.00 40.37 2.57
283 290 7.654022 AGGTTGGTTCAATCTTAGTTCAAAA 57.346 32.000 0.00 0.00 29.62 2.44
284 291 7.489160 AGGTTGGTTCAATCTTAGTTCAAAAC 58.511 34.615 0.00 0.00 29.62 2.43
418 441 1.223763 GGGTCGGGTGGATCTTTCC 59.776 63.158 0.00 0.00 42.94 3.13
421 444 0.179108 GTCGGGTGGATCTTTCCTCG 60.179 60.000 0.00 0.48 43.07 4.63
427 450 1.115467 TGGATCTTTCCTCGCTCCTC 58.885 55.000 0.00 0.00 43.07 3.71
549 1493 1.336609 GGTATCTACCGATTGGCCGTC 60.337 57.143 0.00 0.00 39.70 4.79
866 1811 3.971468 CCCCCATCTTTTAATCTCCCA 57.029 47.619 0.00 0.00 0.00 4.37
982 1928 1.014352 GGCCTGCGTAATTAGTGTGG 58.986 55.000 0.00 0.00 0.00 4.17
1501 2458 3.712187 GCTACTGCTTCACCTCTACATC 58.288 50.000 0.00 0.00 36.03 3.06
1502 2459 3.383185 GCTACTGCTTCACCTCTACATCT 59.617 47.826 0.00 0.00 36.03 2.90
1505 2462 4.344978 ACTGCTTCACCTCTACATCTACA 58.655 43.478 0.00 0.00 0.00 2.74
1506 2463 4.959210 ACTGCTTCACCTCTACATCTACAT 59.041 41.667 0.00 0.00 0.00 2.29
1507 2464 5.163468 ACTGCTTCACCTCTACATCTACATG 60.163 44.000 0.00 0.00 35.92 3.21
1508 2465 4.054671 GCTTCACCTCTACATCTACATGC 58.945 47.826 0.00 0.00 32.57 4.06
1509 2466 4.442052 GCTTCACCTCTACATCTACATGCA 60.442 45.833 0.00 0.00 32.57 3.96
1510 2467 4.655762 TCACCTCTACATCTACATGCAC 57.344 45.455 0.00 0.00 32.57 4.57
1511 2468 4.023291 TCACCTCTACATCTACATGCACA 58.977 43.478 0.00 0.00 32.57 4.57
1512 2469 4.651045 TCACCTCTACATCTACATGCACAT 59.349 41.667 0.00 0.00 32.57 3.21
1679 2646 1.062587 GAAACAACCATCTCGATGCGG 59.937 52.381 1.37 0.00 37.49 5.69
1716 2683 7.374491 GCAAAATTTTAGCTAGTGATGATCGAC 59.626 37.037 2.44 0.00 0.00 4.20
1885 2860 3.270877 GAGTCAATACGATTGGGTTGCT 58.729 45.455 0.00 0.00 0.00 3.91
2114 3090 1.068741 GCGCATACCCTTGCTAGTACT 59.931 52.381 0.30 0.00 40.54 2.73
2115 3091 2.295349 GCGCATACCCTTGCTAGTACTA 59.705 50.000 0.30 1.89 40.54 1.82
2116 3092 3.856267 GCGCATACCCTTGCTAGTACTAC 60.856 52.174 0.30 0.00 40.54 2.73
2117 3093 3.305199 CGCATACCCTTGCTAGTACTACC 60.305 52.174 0.00 0.00 40.54 3.18
2121 3097 4.877436 ACCCTTGCTAGTACTACCTAGT 57.123 45.455 0.00 0.00 37.37 2.57
2122 3098 5.983333 ACCCTTGCTAGTACTACCTAGTA 57.017 43.478 0.00 0.00 37.37 1.82
2123 3099 5.939447 ACCCTTGCTAGTACTACCTAGTAG 58.061 45.833 0.00 0.23 39.29 2.57
2131 3107 8.931385 GCTAGTACTACCTAGTAGCTAGTATG 57.069 42.308 13.20 8.78 45.61 2.39
2132 3108 8.531146 GCTAGTACTACCTAGTAGCTAGTATGT 58.469 40.741 17.36 17.36 45.61 2.29
2271 4491 4.673841 GCCAATTGCTGCTTCTAGAAGTTC 60.674 45.833 28.72 19.23 37.61 3.01
2272 4492 4.142513 CCAATTGCTGCTTCTAGAAGTTCC 60.143 45.833 28.72 18.47 40.45 3.62
2273 4493 2.770164 TGCTGCTTCTAGAAGTTCCC 57.230 50.000 28.72 15.45 40.45 3.97
2274 4494 2.260822 TGCTGCTTCTAGAAGTTCCCT 58.739 47.619 28.72 0.00 40.45 4.20
2275 4495 2.234908 TGCTGCTTCTAGAAGTTCCCTC 59.765 50.000 28.72 14.50 40.45 4.30
2276 4496 2.419436 GCTGCTTCTAGAAGTTCCCTCC 60.419 54.545 28.72 13.88 40.45 4.30
2277 4497 1.825474 TGCTTCTAGAAGTTCCCTCCG 59.175 52.381 28.72 6.32 40.45 4.63
2278 4498 1.826096 GCTTCTAGAAGTTCCCTCCGT 59.174 52.381 28.72 0.00 40.45 4.69
2279 4499 2.234168 GCTTCTAGAAGTTCCCTCCGTT 59.766 50.000 28.72 0.00 40.45 4.44
2280 4500 3.306849 GCTTCTAGAAGTTCCCTCCGTTT 60.307 47.826 28.72 0.00 40.45 3.60
2281 4501 4.803253 GCTTCTAGAAGTTCCCTCCGTTTT 60.803 45.833 28.72 0.00 40.45 2.43
2282 4502 4.968971 TCTAGAAGTTCCCTCCGTTTTT 57.031 40.909 0.00 0.00 0.00 1.94
2283 4503 6.423776 TTCTAGAAGTTCCCTCCGTTTTTA 57.576 37.500 0.00 0.00 0.00 1.52
2284 4504 6.616237 TCTAGAAGTTCCCTCCGTTTTTAT 57.384 37.500 0.00 0.00 0.00 1.40
2285 4505 7.012661 TCTAGAAGTTCCCTCCGTTTTTATT 57.987 36.000 0.00 0.00 0.00 1.40
2286 4506 7.455891 TCTAGAAGTTCCCTCCGTTTTTATTT 58.544 34.615 0.00 0.00 0.00 1.40
2287 4507 8.596293 TCTAGAAGTTCCCTCCGTTTTTATTTA 58.404 33.333 0.00 0.00 0.00 1.40
2288 4508 7.444629 AGAAGTTCCCTCCGTTTTTATTTAC 57.555 36.000 0.00 0.00 0.00 2.01
2289 4509 7.229308 AGAAGTTCCCTCCGTTTTTATTTACT 58.771 34.615 0.00 0.00 0.00 2.24
2290 4510 7.389884 AGAAGTTCCCTCCGTTTTTATTTACTC 59.610 37.037 0.00 0.00 0.00 2.59
2291 4511 6.776744 AGTTCCCTCCGTTTTTATTTACTCT 58.223 36.000 0.00 0.00 0.00 3.24
2292 4512 6.653740 AGTTCCCTCCGTTTTTATTTACTCTG 59.346 38.462 0.00 0.00 0.00 3.35
2293 4513 4.939439 TCCCTCCGTTTTTATTTACTCTGC 59.061 41.667 0.00 0.00 0.00 4.26
2294 4514 4.698304 CCCTCCGTTTTTATTTACTCTGCA 59.302 41.667 0.00 0.00 0.00 4.41
2295 4515 5.357032 CCCTCCGTTTTTATTTACTCTGCAT 59.643 40.000 0.00 0.00 0.00 3.96
2296 4516 6.540914 CCCTCCGTTTTTATTTACTCTGCATA 59.459 38.462 0.00 0.00 0.00 3.14
2297 4517 7.228706 CCCTCCGTTTTTATTTACTCTGCATAT 59.771 37.037 0.00 0.00 0.00 1.78
2298 4518 8.621286 CCTCCGTTTTTATTTACTCTGCATATT 58.379 33.333 0.00 0.00 0.00 1.28
2312 4532 7.697352 CTCTGCATATTAGAGTTGACTGAAG 57.303 40.000 5.84 0.00 37.48 3.02
2313 4533 7.175347 TCTGCATATTAGAGTTGACTGAAGT 57.825 36.000 0.00 0.00 0.00 3.01
2314 4534 7.261325 TCTGCATATTAGAGTTGACTGAAGTC 58.739 38.462 3.41 3.41 44.97 3.01
2340 4560 6.505044 ACTTCGTAAAGTTTGACCAAGTTT 57.495 33.333 0.00 0.00 43.28 2.66
2341 4561 7.614124 ACTTCGTAAAGTTTGACCAAGTTTA 57.386 32.000 0.00 0.00 43.28 2.01
2342 4562 8.217131 ACTTCGTAAAGTTTGACCAAGTTTAT 57.783 30.769 0.00 0.00 43.28 1.40
2343 4563 9.328845 ACTTCGTAAAGTTTGACCAAGTTTATA 57.671 29.630 0.00 0.00 43.28 0.98
2344 4564 9.807386 CTTCGTAAAGTTTGACCAAGTTTATAG 57.193 33.333 0.00 2.48 40.73 1.31
2345 4565 9.545105 TTCGTAAAGTTTGACCAAGTTTATAGA 57.455 29.630 0.00 4.22 40.73 1.98
2346 4566 9.545105 TCGTAAAGTTTGACCAAGTTTATAGAA 57.455 29.630 0.00 0.00 40.73 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.068610 GTGCGATGCAGCTGGTTTTTA 60.069 47.619 17.12 0.00 40.08 1.52
34 35 0.318955 GTGCGATGCAGCTGGTTTTT 60.319 50.000 17.12 0.00 40.08 1.94
39 40 1.859427 AACAAGTGCGATGCAGCTGG 61.859 55.000 17.12 0.00 40.08 4.85
41 42 1.742761 ATAACAAGTGCGATGCAGCT 58.257 45.000 0.00 0.00 40.08 4.24
42 43 2.159531 TCAATAACAAGTGCGATGCAGC 60.160 45.455 0.00 0.00 40.08 5.25
43 44 3.125829 AGTCAATAACAAGTGCGATGCAG 59.874 43.478 0.00 0.00 40.08 4.41
44 45 3.073678 AGTCAATAACAAGTGCGATGCA 58.926 40.909 0.00 0.00 35.60 3.96
45 46 3.747099 AGTCAATAACAAGTGCGATGC 57.253 42.857 0.00 0.00 0.00 3.91
83 88 6.827586 ACTGACTTGACTTACCAAACAAAA 57.172 33.333 0.00 0.00 0.00 2.44
174 179 9.662545 GGAGTATTACGTTAGTCTCTGATTTAC 57.337 37.037 0.00 0.00 0.00 2.01
181 186 5.055812 CGAGGGAGTATTACGTTAGTCTCT 58.944 45.833 4.47 4.47 35.48 3.10
188 193 3.879295 TCGATTCGAGGGAGTATTACGTT 59.121 43.478 4.29 0.00 0.00 3.99
228 233 3.686726 GCTGAGGTTCAACCATAGTTCAG 59.313 47.826 15.44 15.44 41.95 3.02
230 235 3.944087 AGCTGAGGTTCAACCATAGTTC 58.056 45.455 9.90 0.00 41.95 3.01
236 241 2.727123 TCAAAGCTGAGGTTCAACCA 57.273 45.000 9.90 0.00 41.95 3.67
259 265 7.342026 AGTTTTGAACTAAGATTGAACCAACCT 59.658 33.333 0.00 0.00 40.69 3.50
271 277 8.561738 AAAAGTGTCTCAGTTTTGAACTAAGA 57.438 30.769 12.51 0.00 42.88 2.10
308 315 2.159680 TCCACGCTTTTAAATTACGGCG 60.160 45.455 4.80 4.80 46.47 6.46
378 401 5.346822 CCCGAGCAATCAAATTTCTTTTCTG 59.653 40.000 0.00 0.00 0.00 3.02
418 441 2.776913 GGACGAAGGGAGGAGCGAG 61.777 68.421 0.00 0.00 0.00 5.03
421 444 2.034048 GATGGGACGAAGGGAGGAGC 62.034 65.000 0.00 0.00 0.00 4.70
427 450 2.170607 ACATTACTGATGGGACGAAGGG 59.829 50.000 0.00 0.00 40.21 3.95
960 1906 2.486203 CACACTAATTACGCAGGCCAAA 59.514 45.455 5.01 0.00 0.00 3.28
982 1928 0.815734 ATGCAGCAGATCAAGCAACC 59.184 50.000 11.97 1.72 40.76 3.77
1136 2087 3.880846 CTTGATCTTGCGCCGCCC 61.881 66.667 6.63 0.00 0.00 6.13
1501 2458 5.668471 AGCTAGGCATATATGTGCATGTAG 58.332 41.667 23.67 19.61 46.81 2.74
1502 2459 5.682234 AGCTAGGCATATATGTGCATGTA 57.318 39.130 23.67 11.94 46.81 2.29
1505 2462 5.432680 AGAAGCTAGGCATATATGTGCAT 57.567 39.130 23.67 19.90 46.81 3.96
1506 2463 4.897509 AGAAGCTAGGCATATATGTGCA 57.102 40.909 23.67 5.64 46.81 4.57
1507 2464 5.486526 AGAAGAAGCTAGGCATATATGTGC 58.513 41.667 15.52 15.52 44.31 4.57
1508 2465 6.128336 GCAAGAAGAAGCTAGGCATATATGTG 60.128 42.308 14.14 0.00 0.00 3.21
1509 2466 5.936956 GCAAGAAGAAGCTAGGCATATATGT 59.063 40.000 14.14 0.00 0.00 2.29
1510 2467 6.171921 AGCAAGAAGAAGCTAGGCATATATG 58.828 40.000 8.45 8.45 39.78 1.78
1511 2468 6.013898 TGAGCAAGAAGAAGCTAGGCATATAT 60.014 38.462 0.00 0.00 42.04 0.86
1512 2469 5.305386 TGAGCAAGAAGAAGCTAGGCATATA 59.695 40.000 0.00 0.00 42.04 0.86
1654 2621 4.083324 GCATCGAGATGGTTGTTTCTGAAA 60.083 41.667 14.13 0.00 39.16 2.69
1679 2646 7.740519 AGCTAAAATTTTGCATCAATCGTAC 57.259 32.000 13.76 0.00 0.00 3.67
1716 2683 1.446272 GGAGAACAACGCTCCTCGG 60.446 63.158 0.00 0.00 46.70 4.63
1848 2823 7.699391 CGTATTGACTCGTTAAAGTCCATAGAA 59.301 37.037 5.12 0.00 44.17 2.10
1885 2860 4.526650 TGAGCTTTATGGCGATCTATACCA 59.473 41.667 0.00 0.00 37.99 3.25
2121 3097 9.941664 GTTTCGAATTACAGTACATACTAGCTA 57.058 33.333 0.00 0.00 34.13 3.32
2122 3098 8.684520 AGTTTCGAATTACAGTACATACTAGCT 58.315 33.333 0.00 0.00 34.13 3.32
2123 3099 8.853469 AGTTTCGAATTACAGTACATACTAGC 57.147 34.615 0.00 0.00 34.13 3.42
2128 3104 9.999009 CAGAGTAGTTTCGAATTACAGTACATA 57.001 33.333 17.47 0.00 0.00 2.29
2129 3105 7.488471 GCAGAGTAGTTTCGAATTACAGTACAT 59.512 37.037 17.47 4.68 0.00 2.29
2130 3106 6.805271 GCAGAGTAGTTTCGAATTACAGTACA 59.195 38.462 17.47 0.00 0.00 2.90
2131 3107 6.021626 CGCAGAGTAGTTTCGAATTACAGTAC 60.022 42.308 17.47 11.71 0.00 2.73
2132 3108 6.025896 CGCAGAGTAGTTTCGAATTACAGTA 58.974 40.000 17.47 1.72 0.00 2.74
2133 3109 4.857588 CGCAGAGTAGTTTCGAATTACAGT 59.142 41.667 17.47 2.55 0.00 3.55
2134 3110 4.265556 CCGCAGAGTAGTTTCGAATTACAG 59.734 45.833 17.47 10.63 0.00 2.74
2210 3192 2.094752 ACAGTTTGAACCAAGTGTGTGC 60.095 45.455 0.00 0.00 0.00 4.57
2271 4491 4.698304 TGCAGAGTAAATAAAAACGGAGGG 59.302 41.667 0.00 0.00 0.00 4.30
2272 4492 5.873179 TGCAGAGTAAATAAAAACGGAGG 57.127 39.130 0.00 0.00 0.00 4.30
2288 4508 7.264221 ACTTCAGTCAACTCTAATATGCAGAG 58.736 38.462 11.37 11.37 44.28 3.35
2289 4509 7.175347 ACTTCAGTCAACTCTAATATGCAGA 57.825 36.000 0.00 0.00 0.00 4.26
2290 4510 7.462109 GACTTCAGTCAACTCTAATATGCAG 57.538 40.000 1.86 0.00 44.18 4.41
2318 4538 9.807386 CTATAAACTTGGTCAAACTTTACGAAG 57.193 33.333 0.00 0.00 37.43 3.79
2319 4539 9.545105 TCTATAAACTTGGTCAAACTTTACGAA 57.455 29.630 0.00 0.00 0.00 3.85
2320 4540 9.545105 TTCTATAAACTTGGTCAAACTTTACGA 57.455 29.630 0.00 0.00 0.00 3.43


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

AutoCloner maintained by Alex Coulton.