Multiple sequence alignment - TraesCS2D01G461900

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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 TraesCS2D01G461900 chr2D 100.000 2976 0 0 1 2976 568104983 568107958 0.000000e+00 5496
1 TraesCS2D01G461900 chr2D 98.720 1953 19 2 1 1953 568090221 568092167 0.000000e+00 3463
2 TraesCS2D01G461900 chr2D 100.000 145 0 0 1955 2099 568093535 568093679 4.890000e-68 268
3 TraesCS2D01G461900 chr2B 88.762 2011 136 40 1 1953 680596731 680598709 0.000000e+00 2379
4 TraesCS2D01G461900 chr2B 96.985 199 5 1 2777 2975 680600944 680601141 1.710000e-87 333
5 TraesCS2D01G461900 chr2B 80.851 282 45 8 2176 2451 781114673 781114395 2.320000e-51 213
6 TraesCS2D01G461900 chr2A 87.914 1721 90 57 295 1953 707567096 707568760 0.000000e+00 1917
7 TraesCS2D01G461900 chr2A 97.160 1021 26 3 1955 2975 707570127 707571144 0.000000e+00 1722
8 TraesCS2D01G461900 chr2A 80.142 282 46 7 2176 2451 516088154 516087877 5.030000e-48 202
9 TraesCS2D01G461900 chr2A 80.756 291 28 9 1 288 707565042 707565307 5.030000e-48 202
10 TraesCS2D01G461900 chrUn 100.000 414 0 0 984 1397 477382456 477382043 0.000000e+00 765
11 TraesCS2D01G461900 chr7D 81.625 283 43 9 2176 2452 74570374 74570653 2.980000e-55 226
12 TraesCS2D01G461900 chr7D 80.702 285 46 8 2176 2454 614030872 614030591 2.320000e-51 213
13 TraesCS2D01G461900 chr6D 81.272 283 42 10 2176 2451 463456341 463456063 4.990000e-53 219
14 TraesCS2D01G461900 chr5A 81.404 285 38 11 2176 2451 698485184 698485462 4.990000e-53 219
15 TraesCS2D01G461900 chr3A 80.000 285 48 8 2176 2454 52365047 52364766 5.030000e-48 202
16 TraesCS2D01G461900 chr7A 79.649 285 49 8 2176 2454 680712218 680711937 2.340000e-46 196


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 TraesCS2D01G461900 chr2D 568104983 568107958 2975 False 5496.000000 5496 100.0000 1 2976 1 chr2D.!!$F1 2975
1 TraesCS2D01G461900 chr2D 568090221 568093679 3458 False 1865.500000 3463 99.3600 1 2099 2 chr2D.!!$F2 2098
2 TraesCS2D01G461900 chr2B 680596731 680601141 4410 False 1356.000000 2379 92.8735 1 2975 2 chr2B.!!$F1 2974
3 TraesCS2D01G461900 chr2A 707565042 707571144 6102 False 1280.333333 1917 88.6100 1 2975 3 chr2A.!!$F1 2974

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
982 2805 0.322008 GGTGGCAGGAAGGTGAAGAG 60.322 60.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 6042 0.598065 GGGAGTTGTGTCATGGCAAC 59.402 55.0 0.0 10.7 43.63 4.17 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
97 100 3.548415 CGCTCGAACCCATCTTCTAGTAC 60.548 52.174 0.00 0.00 0.00 2.73
289 293 5.546621 AACCCATACGACATTGCTACTAT 57.453 39.130 0.00 0.00 0.00 2.12
982 2805 0.322008 GGTGGCAGGAAGGTGAAGAG 60.322 60.000 0.00 0.00 0.00 2.85
1746 3629 4.440829 GGGGAAAGGGATGGCGCA 62.441 66.667 10.83 0.00 0.00 6.09
1953 3836 1.841302 ATCAACTTCCTCAGGCCGCA 61.841 55.000 0.00 0.00 0.00 5.69
2102 5735 2.043953 GGCCAAGGACATGACCCC 60.044 66.667 10.77 1.13 0.00 4.95
2127 5760 5.297776 CACAAGATACCCAAAGCTATCCAAG 59.702 44.000 0.00 0.00 0.00 3.61
2133 5766 3.332485 ACCCAAAGCTATCCAAGGTACAA 59.668 43.478 0.00 0.00 33.87 2.41
2170 5803 1.823899 CCTTAATGGGCGTGGGCTC 60.824 63.158 0.00 0.00 41.28 4.70
2185 5818 0.674895 GGCTCGGCTTCACAACATCT 60.675 55.000 0.00 0.00 0.00 2.90
2192 5825 2.352960 GGCTTCACAACATCTCGAATCC 59.647 50.000 0.00 0.00 0.00 3.01
2223 5856 1.167851 ACATCAATGTGCTTGGTCCG 58.832 50.000 0.00 0.00 40.03 4.79
2230 5863 1.374758 GTGCTTGGTCCGAGAGTGG 60.375 63.158 10.67 0.00 0.00 4.00
2280 5913 4.121317 ACACTTCGACGTCCACAAAATAA 58.879 39.130 10.58 0.00 0.00 1.40
2281 5914 4.025480 ACACTTCGACGTCCACAAAATAAC 60.025 41.667 10.58 0.00 0.00 1.89
2284 5917 2.981805 TCGACGTCCACAAAATAACGAG 59.018 45.455 10.58 0.00 38.44 4.18
2409 6042 9.512435 TTTTGAAACACATTTATGCAATTTTGG 57.488 25.926 0.00 0.00 0.00 3.28
2498 6131 1.000163 CGCTATCAGCTATCCAACGGT 60.000 52.381 0.00 0.00 39.60 4.83
2624 6257 1.203125 CCACAATTGTAGGGGGTGGTT 60.203 52.381 11.53 0.00 43.08 3.67
2853 7000 0.259938 GCTTGGTGGGAGGAATGGAT 59.740 55.000 0.00 0.00 0.00 3.41
2907 7054 3.637911 ATGTGTGGCGATTAGGGTTTA 57.362 42.857 0.00 0.00 0.00 2.01
2975 7122 0.987294 CCACTCTCACATCCAAGGGT 59.013 55.000 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 100 4.665833 AATGTGATTGATCAATGGCTGG 57.334 40.909 25.37 0.00 38.75 4.85
289 293 8.915036 GGTGTCATTTCTTCTCTAGGTATTAGA 58.085 37.037 0.00 0.00 36.91 2.10
735 2523 2.754012 AGAGAGGATGGAGACTCAGG 57.246 55.000 4.53 0.00 36.20 3.86
982 2805 1.799403 CATCAGCGATCTTGATGAGCC 59.201 52.381 22.74 0.00 41.20 4.70
1397 3238 2.688446 AGCGATTTCAGGTAGTCGATCA 59.312 45.455 0.00 0.00 36.25 2.92
1675 3555 3.696051 GACATGACCAACCAGCATAATGT 59.304 43.478 0.00 0.00 0.00 2.71
1882 3765 1.282738 TGCATCTGGCTGAGGAAATCA 59.717 47.619 10.31 0.00 45.15 2.57
1953 3836 4.883585 GTCACCACATACATGGATGAACAT 59.116 41.667 25.07 4.05 43.02 2.71
2102 5735 4.137543 GGATAGCTTTGGGTATCTTGTGG 58.862 47.826 12.72 0.00 46.33 4.17
2127 5760 7.973944 GGTCATCACCTATGAAAATTTTGTACC 59.026 37.037 8.47 0.94 46.17 3.34
2170 5803 1.428448 TTCGAGATGTTGTGAAGCCG 58.572 50.000 0.00 0.00 0.00 5.52
2185 5818 5.070313 TGATGTGAGGTATCATTGGATTCGA 59.930 40.000 0.00 0.00 37.87 3.71
2223 5856 7.826690 TGCCAGTAATTAAAATTTCCACTCTC 58.173 34.615 0.00 0.00 0.00 3.20
2280 5913 4.270834 TGAGGCAAGAGAAGTATACTCGT 58.729 43.478 5.70 0.00 39.12 4.18
2281 5914 4.902443 TGAGGCAAGAGAAGTATACTCG 57.098 45.455 5.70 0.00 39.12 4.18
2318 5951 5.712152 AATGTTGTGGATGAAGAACTTCC 57.288 39.130 11.30 0.00 41.46 3.46
2409 6042 0.598065 GGGAGTTGTGTCATGGCAAC 59.402 55.000 0.00 10.70 43.63 4.17
2456 6089 7.736893 AGCGATAGGGATTTTAGTTAGTCAAT 58.263 34.615 0.00 0.00 0.00 2.57
2498 6131 7.685481 TGGTGATAGTGATTTTAGGAAGTTCA 58.315 34.615 5.01 0.00 0.00 3.18
2624 6257 7.514721 ACTCTTACTTATTGAAAAGGGTGACA 58.485 34.615 0.00 0.00 31.54 3.58
2708 6341 6.018751 CCACTATGACATTATTCAACACCTCG 60.019 42.308 0.00 0.00 0.00 4.63
2709 6342 6.823689 ACCACTATGACATTATTCAACACCTC 59.176 38.462 0.00 0.00 0.00 3.85
2853 7000 7.226441 CAGTCCAAGGTCATGAATTCCATATA 58.774 38.462 2.27 0.00 33.31 0.86
2907 7054 9.247861 GAAGCAATGTGGATTTATAATCCCTAT 57.752 33.333 14.20 7.16 37.40 2.57


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

AutoCloner maintained by Alex Coulton.