Multiple sequence alignment - TraesCS2D01G224200

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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 TraesCS2D01G224200 chr2D 100.000 4025 0 0 1 4025 191240455 191236431 0 7433
1 TraesCS2D01G224200 chr2B 93.315 4084 164 42 1 4025 248654411 248658444 0 5928
2 TraesCS2D01G224200 chr2A 95.055 3276 127 18 1 3250 206403158 206406424 0 5120
3 TraesCS2D01G224200 chr2A 92.777 803 18 16 3236 4025 206409432 206410207 0 1125


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 TraesCS2D01G224200 chr2D 191236431 191240455 4024 True 7433.0 7433 100.000 1 4025 1 chr2D.!!$R1 4024
1 TraesCS2D01G224200 chr2B 248654411 248658444 4033 False 5928.0 5928 93.315 1 4025 1 chr2B.!!$F1 4024
2 TraesCS2D01G224200 chr2A 206403158 206410207 7049 False 3122.5 5120 93.916 1 4025 2 chr2A.!!$F1 4024

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
25 26 0.179023 GGTGTTGGGGTGTTCGGTTA 60.179 55.0 0.0 0.0 0.0 2.85 F
1384 1436 0.321996 GCTATCCCCTCATCCGTTCC 59.678 60.0 0.0 0.0 0.0 3.62 F
1883 1940 0.036388 AGTTCGACATCATGGGCGTT 60.036 50.0 0.0 0.0 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1476 0.816825 GCCATCATCGTCACCTGCAT 60.817 55.000 0.0 0.0 0.00 3.96 R
2732 2789 0.321671 GCACAGTCTTGAGCACCCTA 59.678 55.000 0.0 0.0 40.18 3.53 R
3229 3297 1.067846 TGACGACCTGAAAGACATCGG 60.068 52.381 0.0 0.0 37.74 4.18 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
25 26 0.179023 GGTGTTGGGGTGTTCGGTTA 60.179 55.000 0.00 0.00 0.00 2.85
63 64 7.177041 TGGTTTGTCTTTATTTATAAAGCGGGT 59.823 33.333 14.54 0.00 45.46 5.28
130 132 2.167398 TTTTGGGGAGAGTCTCGGCG 62.167 60.000 13.97 0.00 0.00 6.46
194 196 2.093921 GTCTGCTTCTACCACTTCCTCC 60.094 54.545 0.00 0.00 0.00 4.30
199 201 2.283388 TACCACTTCCTCCGCGGT 60.283 61.111 27.15 4.43 0.00 5.68
215 217 1.274447 GCGGTAGACCAGTACCTTGTT 59.726 52.381 0.00 0.00 40.49 2.83
247 249 1.006832 GTTGACGACAGTGTTGCACT 58.993 50.000 10.62 0.00 46.51 4.40
256 258 2.717639 AGTGTTGCACTGGAGTTTCT 57.282 45.000 0.53 0.00 43.63 2.52
349 351 4.725556 TTTCTTGTCTGTTACATGCGAC 57.274 40.909 0.00 0.00 38.10 5.19
378 380 7.066284 GCCATGTTAGTAAACTTCTGATGATGT 59.934 37.037 0.00 0.00 36.51 3.06
466 468 6.752815 GGTACAATCTGCTACAGACTTTCTAC 59.247 42.308 0.00 0.00 43.63 2.59
474 476 4.861462 GCTACAGACTTTCTACGGGTAAAC 59.139 45.833 0.00 0.00 0.00 2.01
574 580 3.059884 TCGTTCTGCAACTTGATGTCTC 58.940 45.455 0.00 0.00 0.00 3.36
580 586 1.792949 GCAACTTGATGTCTCGACGTT 59.207 47.619 0.00 0.00 0.00 3.99
619 625 4.217118 AGCATGGATCACAGTTCAGTTTTC 59.783 41.667 0.00 0.00 0.00 2.29
627 633 4.507756 TCACAGTTCAGTTTTCAGACGATG 59.492 41.667 0.00 0.00 0.00 3.84
633 639 2.738846 CAGTTTTCAGACGATGGGAGTG 59.261 50.000 0.00 0.00 0.00 3.51
738 744 1.407721 TTGCGCGTAACCGATCGAAG 61.408 55.000 18.66 2.80 35.63 3.79
745 751 1.747355 GTAACCGATCGAAGTCCTGGA 59.253 52.381 18.66 0.00 0.00 3.86
854 873 2.435418 ATCGGAGAGATCAGGCCAC 58.565 57.895 5.01 0.00 43.63 5.01
1055 1082 2.544267 GTGTTGCTACCTTGTCAGTGAC 59.456 50.000 16.68 16.68 0.00 3.67
1056 1083 2.143925 GTTGCTACCTTGTCAGTGACC 58.856 52.381 20.43 3.79 0.00 4.02
1375 1427 2.533318 CGCAATTCGCTATCCCCTC 58.467 57.895 0.00 0.00 39.08 4.30
1384 1436 0.321996 GCTATCCCCTCATCCGTTCC 59.678 60.000 0.00 0.00 0.00 3.62
1406 1462 1.062294 CCTGTACTGTACGTCTCGCTC 59.938 57.143 12.87 0.00 0.00 5.03
1416 1472 4.748102 TGTACGTCTCGCTCAAGAATTTTT 59.252 37.500 0.00 0.00 0.00 1.94
1419 1476 3.186409 CGTCTCGCTCAAGAATTTTTCCA 59.814 43.478 0.00 0.00 0.00 3.53
1439 1496 1.450134 GCAGGTGACGATGATGGCA 60.450 57.895 0.00 0.00 0.00 4.92
1496 1553 4.337060 TCGTCCACGCACACCTCG 62.337 66.667 0.00 0.00 39.60 4.63
1883 1940 0.036388 AGTTCGACATCATGGGCGTT 60.036 50.000 0.00 0.00 0.00 4.84
1970 2027 0.741221 GCGACCACCAGTTCATCCTC 60.741 60.000 0.00 0.00 0.00 3.71
2732 2789 1.837439 TCGGGTGCCAACTTCTATGAT 59.163 47.619 0.00 0.00 0.00 2.45
2747 2804 4.809193 TCTATGATAGGGTGCTCAAGACT 58.191 43.478 0.00 0.00 0.00 3.24
2796 2853 1.693606 CCATGGGAAAAGGCAAGTTGT 59.306 47.619 2.85 0.00 0.00 3.32
2973 3035 4.887748 CTGAAGAGCAGTTCTGGACTAAA 58.112 43.478 1.97 0.00 39.85 1.85
3091 3158 7.885399 AGATAATTGGATAGAATAAAAGCGGCT 59.115 33.333 0.00 0.00 0.00 5.52
3116 3183 1.404391 GGCACATCAGCTCTGGAAATG 59.596 52.381 0.00 0.00 34.17 2.32
3122 3189 4.411540 ACATCAGCTCTGGAAATGGATACT 59.588 41.667 0.00 0.00 37.61 2.12
3123 3190 5.104193 ACATCAGCTCTGGAAATGGATACTT 60.104 40.000 0.00 0.00 37.61 2.24
3124 3191 5.441718 TCAGCTCTGGAAATGGATACTTT 57.558 39.130 0.00 0.00 35.05 2.66
3125 3192 6.560003 TCAGCTCTGGAAATGGATACTTTA 57.440 37.500 0.00 0.00 32.90 1.85
3126 3193 6.349300 TCAGCTCTGGAAATGGATACTTTAC 58.651 40.000 0.00 0.00 32.90 2.01
3131 3198 7.307455 GCTCTGGAAATGGATACTTTACGAATC 60.307 40.741 0.00 0.00 32.90 2.52
3221 3289 5.947663 TGGATATGTCAAATCGGGGTAAAT 58.052 37.500 0.00 0.00 0.00 1.40
3229 3297 5.746721 GTCAAATCGGGGTAAATTGTATTGC 59.253 40.000 0.00 0.00 0.00 3.56
3293 6384 9.665719 TTGCTATTGAAACTCTTATGTATGTCA 57.334 29.630 0.00 0.00 0.00 3.58
3294 6385 9.665719 TGCTATTGAAACTCTTATGTATGTCAA 57.334 29.630 0.00 0.00 0.00 3.18
3295 6386 9.922305 GCTATTGAAACTCTTATGTATGTCAAC 57.078 33.333 0.00 0.00 0.00 3.18
3310 6401 6.597672 TGTATGTCAACTCAACTCAAACAAGT 59.402 34.615 0.00 0.00 0.00 3.16
3409 6501 1.676006 AGCAACTGTTTCTTGGTTCCG 59.324 47.619 0.00 0.00 0.00 4.30
3417 6509 4.850680 TGTTTCTTGGTTCCGCCTTATAT 58.149 39.130 0.00 0.00 38.35 0.86
3418 6510 5.991861 TGTTTCTTGGTTCCGCCTTATATA 58.008 37.500 0.00 0.00 38.35 0.86
3421 6513 6.488769 TTCTTGGTTCCGCCTTATATAGAA 57.511 37.500 0.00 0.00 38.35 2.10
3448 6540 2.255994 CTGTCGCATGCCAAATCGCA 62.256 55.000 13.15 0.10 44.35 5.10
3454 6546 2.187707 GCATGCCAAATCGCAACTTAG 58.812 47.619 6.36 0.00 43.24 2.18
3460 6552 3.181491 GCCAAATCGCAACTTAGCCATAA 60.181 43.478 0.00 0.00 0.00 1.90
3637 6739 3.961480 GCCCAAGGCTTTAAAACTGAT 57.039 42.857 0.00 0.00 46.69 2.90
3697 6799 1.530293 GCGATCATCATGCACTTCCTC 59.470 52.381 0.00 0.00 0.00 3.71
3709 6811 2.029828 GCACTTCCTCGACTTCTTCTGA 60.030 50.000 0.00 0.00 0.00 3.27
3775 6877 3.821033 GGTTTACAGCATTCTGAACCTGT 59.179 43.478 21.59 21.59 40.92 4.00
3886 6991 5.543507 AATAGACCTGGCTCTCTATGTTG 57.456 43.478 6.19 0.00 31.35 3.33
3970 7075 6.629128 CAATGTTAGATGCCATTGGTAAACA 58.371 36.000 10.64 10.64 42.58 2.83
3971 7076 5.895636 TGTTAGATGCCATTGGTAAACAG 57.104 39.130 4.26 0.00 0.00 3.16
4007 7112 1.808411 TGTGAAATCGCTGGAGGTTC 58.192 50.000 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.916360 AAAGACAAACCATGATACAACCAT 57.084 33.333 0.00 0.00 0.00 3.55
63 64 6.594159 CAGGTTCTATCGAAAAAGGCTTCTTA 59.406 38.462 0.00 0.00 0.00 2.10
93 95 5.069516 CCCAAAACTCTTATAGCCATTGCAT 59.930 40.000 0.00 0.00 41.13 3.96
99 101 4.108570 TCTCCCCAAAACTCTTATAGCCA 58.891 43.478 0.00 0.00 0.00 4.75
109 111 0.977395 CCGAGACTCTCCCCAAAACT 59.023 55.000 0.03 0.00 0.00 2.66
194 196 0.179145 CAAGGTACTGGTCTACCGCG 60.179 60.000 0.00 0.00 41.18 6.46
199 201 4.903049 TGGAGAAAACAAGGTACTGGTCTA 59.097 41.667 0.00 0.00 39.17 2.59
238 240 2.288666 TCAGAAACTCCAGTGCAACAC 58.711 47.619 0.00 0.00 41.43 3.32
247 249 7.009179 ACATAAGAGTTCATCAGAAACTCCA 57.991 36.000 10.30 1.89 34.89 3.86
256 258 7.987458 GGAGGTTCATAACATAAGAGTTCATCA 59.013 37.037 0.00 0.00 33.07 3.07
341 343 1.739466 CTAACATGGCAAGTCGCATGT 59.261 47.619 0.00 0.00 45.17 3.21
349 351 6.801539 TCAGAAGTTTACTAACATGGCAAG 57.198 37.500 0.00 0.00 36.70 4.01
466 468 5.844301 ATTACTGTTTACACGTTTACCCG 57.156 39.130 0.00 0.00 0.00 5.28
474 476 6.092944 TGCCTCCAAATATTACTGTTTACACG 59.907 38.462 0.00 0.00 0.00 4.49
574 580 1.262882 GGCTTCGGTAACTAACGTCG 58.737 55.000 0.00 0.00 0.00 5.12
580 586 3.244078 CCATGCTATGGCTTCGGTAACTA 60.244 47.826 1.68 0.00 44.70 2.24
619 625 1.448540 GTGCCACTCCCATCGTCTG 60.449 63.158 0.00 0.00 0.00 3.51
738 744 2.342648 GACGGTGGTGTCCAGGAC 59.657 66.667 13.35 13.35 32.34 3.85
745 751 2.949106 CTACGTCGACGGTGGTGT 59.051 61.111 37.89 20.67 44.95 4.16
801 815 2.414594 GGGATTTCGCATGCAGCC 59.585 61.111 19.57 10.52 41.38 4.85
840 859 1.520342 GCGTGTGGCCTGATCTCTC 60.520 63.158 3.32 0.00 34.80 3.20
847 866 2.108514 CATGGTAGCGTGTGGCCTG 61.109 63.158 3.32 0.00 45.17 4.85
850 869 2.745884 TGCATGGTAGCGTGTGGC 60.746 61.111 15.20 2.25 44.05 5.01
854 873 1.723273 CATGGTGCATGGTAGCGTG 59.277 57.895 9.83 9.83 38.11 5.34
1019 1046 3.117663 AGCAACACTAACCAAAGAAGGGA 60.118 43.478 0.00 0.00 0.00 4.20
1361 1410 0.898320 CGGATGAGGGGATAGCGAAT 59.102 55.000 0.00 0.00 0.00 3.34
1366 1416 1.344763 GTGGAACGGATGAGGGGATAG 59.655 57.143 0.00 0.00 0.00 2.08
1373 1425 1.825474 AGTACAGGTGGAACGGATGAG 59.175 52.381 0.00 0.00 38.12 2.90
1375 1427 1.275291 ACAGTACAGGTGGAACGGATG 59.725 52.381 0.00 0.00 38.12 3.51
1384 1436 1.465354 GCGAGACGTACAGTACAGGTG 60.465 57.143 11.37 0.00 0.00 4.00
1406 1462 4.687483 GTCACCTGCATGGAAAAATTCTTG 59.313 41.667 8.91 0.00 39.71 3.02
1416 1472 0.832626 ATCATCGTCACCTGCATGGA 59.167 50.000 8.91 0.00 39.71 3.41
1419 1476 0.816825 GCCATCATCGTCACCTGCAT 60.817 55.000 0.00 0.00 0.00 3.96
1439 1496 3.679917 CGTAGATGGTGTCCAGATGCTTT 60.680 47.826 0.00 0.00 36.75 3.51
1556 1613 1.448717 GGCGAAGAAGAGGTGCTCC 60.449 63.158 0.00 0.00 0.00 4.70
1860 1917 1.452110 CCCATGATGTCGAACTGCAA 58.548 50.000 0.00 0.00 0.00 4.08
1883 1940 2.649034 GCAACGAGGACGGTCTCA 59.351 61.111 8.23 0.00 44.46 3.27
2249 2306 2.048503 CAGAACACGGACCCGACC 60.049 66.667 16.07 1.34 42.83 4.79
2732 2789 0.321671 GCACAGTCTTGAGCACCCTA 59.678 55.000 0.00 0.00 40.18 3.53
2826 2883 6.563422 TGAACAATTGAGACAAAAACTCTGG 58.437 36.000 13.59 0.00 35.66 3.86
2973 3035 2.175202 CTACTGCTCTCACTTCCAGGT 58.825 52.381 0.00 0.00 0.00 4.00
3091 3158 1.683707 AGAGCTGATGTGCCCTCGA 60.684 57.895 0.00 0.00 0.00 4.04
3122 3189 7.654116 TGCCAATTATAGTGATCGATTCGTAAA 59.346 33.333 5.89 0.00 0.00 2.01
3123 3190 7.149307 TGCCAATTATAGTGATCGATTCGTAA 58.851 34.615 5.89 2.91 0.00 3.18
3124 3191 6.683715 TGCCAATTATAGTGATCGATTCGTA 58.316 36.000 5.89 0.00 0.00 3.43
3125 3192 5.538118 TGCCAATTATAGTGATCGATTCGT 58.462 37.500 5.89 0.00 0.00 3.85
3126 3193 6.456047 CCATGCCAATTATAGTGATCGATTCG 60.456 42.308 0.00 0.00 0.00 3.34
3131 3198 6.748333 ATTCCATGCCAATTATAGTGATCG 57.252 37.500 0.00 0.00 0.00 3.69
3221 3289 3.689161 CCTGAAAGACATCGGCAATACAA 59.311 43.478 0.00 0.00 34.07 2.41
3229 3297 1.067846 TGACGACCTGAAAGACATCGG 60.068 52.381 0.00 0.00 37.74 4.18
3291 6382 5.822519 AGCATACTTGTTTGAGTTGAGTTGA 59.177 36.000 0.00 0.00 0.00 3.18
3292 6383 6.064846 AGCATACTTGTTTGAGTTGAGTTG 57.935 37.500 0.00 0.00 0.00 3.16
3293 6384 6.238759 GGAAGCATACTTGTTTGAGTTGAGTT 60.239 38.462 0.00 0.00 35.82 3.01
3294 6385 5.239525 GGAAGCATACTTGTTTGAGTTGAGT 59.760 40.000 0.00 0.00 35.82 3.41
3295 6386 5.239306 TGGAAGCATACTTGTTTGAGTTGAG 59.761 40.000 0.00 0.00 35.82 3.02
3310 6401 8.535335 GGAGACTCTTATATTGATGGAAGCATA 58.465 37.037 1.74 0.00 23.87 3.14
3409 6501 9.595357 GCGACAGTTTTTAATTCTATATAAGGC 57.405 33.333 0.00 0.00 0.00 4.35
3417 6509 5.182190 TGGCATGCGACAGTTTTTAATTCTA 59.818 36.000 12.44 0.00 0.00 2.10
3418 6510 4.022416 TGGCATGCGACAGTTTTTAATTCT 60.022 37.500 12.44 0.00 0.00 2.40
3421 6513 3.932545 TGGCATGCGACAGTTTTTAAT 57.067 38.095 12.44 0.00 0.00 1.40
3448 6540 8.759782 AGTTACAGTGATACTTATGGCTAAGTT 58.240 33.333 12.42 4.19 44.07 2.66
3454 6546 9.460906 GTACTTAGTTACAGTGATACTTATGGC 57.539 37.037 0.00 0.00 0.00 4.40
3637 6739 1.299089 CGCGGTGATCATCGTGCTA 60.299 57.895 27.10 0.00 38.65 3.49
3775 6877 1.094650 TGCTGCTGCGTTTCAACTCA 61.095 50.000 11.21 0.00 43.34 3.41
3886 6991 4.142609 TGCACAAGGAGAGATATTGGAC 57.857 45.455 0.00 0.00 0.00 4.02
3968 7073 6.524734 TCACATGTTCTTGTTCATAGTCTGT 58.475 36.000 0.00 0.00 0.00 3.41
3969 7074 7.425577 TTCACATGTTCTTGTTCATAGTCTG 57.574 36.000 0.00 0.00 0.00 3.51
3970 7075 8.627208 ATTTCACATGTTCTTGTTCATAGTCT 57.373 30.769 0.00 0.00 0.00 3.24
3971 7076 7.689812 CGATTTCACATGTTCTTGTTCATAGTC 59.310 37.037 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.