Multiple sequence alignment - TraesCS2D01G049600

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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 TraesCS2D01G049600 chr2D 100.000 2695 0 0 1 2695 18236241 18233547 0.000000e+00 4977
1 TraesCS2D01G049600 chr2A 93.162 1755 81 19 1 1730 19348067 19346327 0.000000e+00 2540
2 TraesCS2D01G049600 chr2B 90.391 1561 100 23 863 2393 30160471 30158931 0.000000e+00 2006
3 TraesCS2D01G049600 chr2B 89.919 982 82 10 863 1831 30230077 30229100 0.000000e+00 1249
4 TraesCS2D01G049600 chr2B 89.817 982 83 10 863 1831 30173808 30172831 0.000000e+00 1243
5 TraesCS2D01G049600 chr2B 89.511 982 86 10 863 1831 30187527 30186550 0.000000e+00 1227
6 TraesCS2D01G049600 chr2B 89.409 982 84 11 863 1831 30209038 30208064 0.000000e+00 1219
7 TraesCS2D01G049600 chr2B 91.858 872 54 7 1 867 30221103 30220244 0.000000e+00 1201
8 TraesCS2D01G049600 chr2B 91.858 872 52 7 1 867 30165158 30164301 0.000000e+00 1199
9 TraesCS2D01G049600 chr2B 91.506 883 57 10 1 877 30200124 30199254 0.000000e+00 1199
10 TraesCS2D01G049600 chr2B 91.743 872 53 7 1 867 30178553 30177696 0.000000e+00 1194
11 TraesCS2D01G049600 chr2B 88.211 246 26 3 2453 2695 30158934 30158689 9.440000e-75 291
12 TraesCS2D01G049600 chrUn 92.271 1035 53 17 721 1730 12595578 12594546 0.000000e+00 1443
13 TraesCS2D01G049600 chrUn 92.245 980 63 7 1722 2695 12594442 12593470 0.000000e+00 1376
14 TraesCS2D01G049600 chrUn 90.020 982 81 10 863 1831 178511310 178512287 0.000000e+00 1254
15 TraesCS2D01G049600 chrUn 89.318 983 86 12 863 1831 178476385 178477362 0.000000e+00 1216
16 TraesCS2D01G049600 chrUn 91.982 873 51 9 1 867 178464529 178465388 0.000000e+00 1206
17 TraesCS2D01G049600 chrUn 91.858 872 54 7 1 867 178503228 178504087 0.000000e+00 1201
18 TraesCS2D01G049600 chrUn 91.284 872 59 7 1 867 178520285 178521144 0.000000e+00 1173
19 TraesCS2D01G049600 chrUn 90.487 883 60 9 1 877 178482663 178483527 0.000000e+00 1144
20 TraesCS2D01G049600 chr3B 88.183 897 64 18 1022 1898 557608607 557609481 0.000000e+00 1031


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 TraesCS2D01G049600 chr2D 18233547 18236241 2694 True 4977.000000 4977 100.000000 1 2695 1 chr2D.!!$R1 2694
1 TraesCS2D01G049600 chr2A 19346327 19348067 1740 True 2540.000000 2540 93.162000 1 1730 1 chr2A.!!$R1 1729
2 TraesCS2D01G049600 chr2B 30229100 30230077 977 True 1249.000000 1249 89.919000 863 1831 1 chr2B.!!$R5 968
3 TraesCS2D01G049600 chr2B 30186550 30187527 977 True 1227.000000 1227 89.511000 863 1831 1 chr2B.!!$R1 968
4 TraesCS2D01G049600 chr2B 30208064 30209038 974 True 1219.000000 1219 89.409000 863 1831 1 chr2B.!!$R3 968
5 TraesCS2D01G049600 chr2B 30172831 30178553 5722 True 1218.500000 1243 90.780000 1 1831 2 chr2B.!!$R7 1830
6 TraesCS2D01G049600 chr2B 30220244 30221103 859 True 1201.000000 1201 91.858000 1 867 1 chr2B.!!$R4 866
7 TraesCS2D01G049600 chr2B 30199254 30200124 870 True 1199.000000 1199 91.506000 1 877 1 chr2B.!!$R2 876
8 TraesCS2D01G049600 chr2B 30158689 30165158 6469 True 1165.333333 2006 90.153333 1 2695 3 chr2B.!!$R6 2694
9 TraesCS2D01G049600 chrUn 12593470 12595578 2108 True 1409.500000 1443 92.258000 721 2695 2 chrUn.!!$R1 1974
10 TraesCS2D01G049600 chrUn 178511310 178512287 977 False 1254.000000 1254 90.020000 863 1831 1 chrUn.!!$F5 968
11 TraesCS2D01G049600 chrUn 178476385 178477362 977 False 1216.000000 1216 89.318000 863 1831 1 chrUn.!!$F2 968
12 TraesCS2D01G049600 chrUn 178464529 178465388 859 False 1206.000000 1206 91.982000 1 867 1 chrUn.!!$F1 866
13 TraesCS2D01G049600 chrUn 178503228 178504087 859 False 1201.000000 1201 91.858000 1 867 1 chrUn.!!$F4 866
14 TraesCS2D01G049600 chrUn 178520285 178521144 859 False 1173.000000 1173 91.284000 1 867 1 chrUn.!!$F6 866
15 TraesCS2D01G049600 chrUn 178482663 178483527 864 False 1144.000000 1144 90.487000 1 877 1 chrUn.!!$F3 876
16 TraesCS2D01G049600 chr3B 557608607 557609481 874 False 1031.000000 1031 88.183000 1022 1898 1 chr3B.!!$F1 876

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
291 292 1.308069 CGAGGAGGCAACAACCATGG 61.308 60.0 11.19 11.19 37.68 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 6042 1.519719 GGCAGCTCTCCGTCTGATT 59.48 57.895 0.0 0.0 32.26 2.57 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
28 29 6.388814 AGATCTATTTCCCCTCAATCTCTGA 58.611 40.000 0.00 0.00 0.00 3.27
29 30 6.848631 AGATCTATTTCCCCTCAATCTCTGAA 59.151 38.462 0.00 0.00 32.17 3.02
291 292 1.308069 CGAGGAGGCAACAACCATGG 61.308 60.000 11.19 11.19 37.68 3.66
628 634 6.316140 TGATCGGTGAATGGTTTCTCTAATTG 59.684 38.462 0.00 0.00 32.78 2.32
714 720 4.065321 CTGAACCAAGTCTCAGTCAAGT 57.935 45.455 0.00 0.00 35.38 3.16
715 721 3.797039 TGAACCAAGTCTCAGTCAAGTG 58.203 45.455 0.00 0.00 0.00 3.16
716 722 3.450817 TGAACCAAGTCTCAGTCAAGTGA 59.549 43.478 0.00 0.00 0.00 3.41
717 723 4.101585 TGAACCAAGTCTCAGTCAAGTGAT 59.898 41.667 0.00 0.00 0.00 3.06
718 724 5.304357 TGAACCAAGTCTCAGTCAAGTGATA 59.696 40.000 0.00 0.00 0.00 2.15
719 725 6.014242 TGAACCAAGTCTCAGTCAAGTGATAT 60.014 38.462 0.00 0.00 0.00 1.63
897 4811 9.591792 TCAATTTTGTTCAATGTGATTGTAACA 57.408 25.926 0.00 0.00 41.02 2.41
1056 4982 3.866582 GACCATGGCCCCTCTCCG 61.867 72.222 13.04 0.00 0.00 4.63
1076 5002 1.826487 GCTCTCTCCTCCGTCCTCC 60.826 68.421 0.00 0.00 0.00 4.30
1084 5010 2.043852 TCCGTCCTCCTCCTGCTC 60.044 66.667 0.00 0.00 0.00 4.26
1088 5014 2.124693 GTCCTCCTCCTGCTCCTCG 61.125 68.421 0.00 0.00 0.00 4.63
1174 5103 1.080025 GGCGCAGGACTACGACTTT 60.080 57.895 10.83 0.00 33.47 2.66
1370 5299 1.514087 GATTACGCCTGGACCGTGA 59.486 57.895 9.23 2.19 39.54 4.35
1488 5429 0.179240 CGCTGTGACAAGATGTTCGC 60.179 55.000 0.00 0.00 0.00 4.70
1490 5431 1.800805 CTGTGACAAGATGTTCGCCT 58.199 50.000 0.00 0.00 0.00 5.52
1654 5596 7.315142 CGGAAGAAAAATGATCATCTTTTCCA 58.685 34.615 28.85 1.46 39.02 3.53
1821 5882 1.065854 CAGATCAGGCGAGGAAGGTTT 60.066 52.381 0.00 0.00 0.00 3.27
1831 5892 2.603953 GAGGAAGGTTTACCGTTCGAG 58.396 52.381 0.00 0.00 42.08 4.04
1912 5975 2.887151 AATTCTACTGCTTGGCCTGT 57.113 45.000 3.32 0.00 0.00 4.00
1934 6001 6.959361 TGTCTGAACTGAAGCATCTAAAAAC 58.041 36.000 0.00 0.00 0.00 2.43
1955 6022 0.758685 CGGAGGAGGCCTGAAGAGAT 60.759 60.000 12.00 0.00 31.76 2.75
1971 6042 7.410120 TGAAGAGATCTTTACATACAGCTCA 57.590 36.000 0.00 0.00 36.11 4.26
2012 6083 4.143333 GCTGGCTCGGCGACCTTA 62.143 66.667 22.60 8.50 0.00 2.69
2018 6089 1.227002 CTCGGCGACCTTAGGCTTC 60.227 63.158 4.99 0.00 0.00 3.86
2190 6261 1.456705 ATCTCCCACTCGCTCTCCC 60.457 63.158 0.00 0.00 0.00 4.30
2267 6338 2.628696 CGGTGCTTGCAATGCCTGA 61.629 57.895 15.29 0.00 35.91 3.86
2280 6351 4.676196 GCAATGCCTGAAGAATCGACAAAT 60.676 41.667 0.00 0.00 0.00 2.32
2283 6354 6.757897 ATGCCTGAAGAATCGACAAATTAA 57.242 33.333 0.00 0.00 0.00 1.40
2335 6406 8.816894 TCCACATTTCTAGAGATATACAATCCC 58.183 37.037 0.00 0.00 0.00 3.85
2348 6419 9.139734 AGATATACAATCCCGACAAGTACTAAA 57.860 33.333 0.00 0.00 0.00 1.85
2349 6420 9.408069 GATATACAATCCCGACAAGTACTAAAG 57.592 37.037 0.00 0.00 0.00 1.85
2350 6421 5.479124 ACAATCCCGACAAGTACTAAAGT 57.521 39.130 0.00 0.00 0.00 2.66
2351 6422 6.594788 ACAATCCCGACAAGTACTAAAGTA 57.405 37.500 0.00 0.00 0.00 2.24
2353 6424 7.618137 ACAATCCCGACAAGTACTAAAGTATT 58.382 34.615 0.00 0.00 32.54 1.89
2354 6425 7.548075 ACAATCCCGACAAGTACTAAAGTATTG 59.452 37.037 0.00 5.50 32.54 1.90
2355 6426 6.594788 TCCCGACAAGTACTAAAGTATTGT 57.405 37.500 0.00 13.19 36.22 2.71
2356 6427 6.392354 TCCCGACAAGTACTAAAGTATTGTG 58.608 40.000 16.02 8.39 35.01 3.33
2357 6428 5.579511 CCCGACAAGTACTAAAGTATTGTGG 59.420 44.000 16.02 14.83 35.01 4.17
2439 6510 7.213178 ACTATCCTAAATGATTGTCCTTGGT 57.787 36.000 0.00 0.00 0.00 3.67
2525 6597 6.663093 TGGTAAATGCAATTTCTACCATCAGT 59.337 34.615 3.89 0.00 44.81 3.41
2528 6600 9.076596 GTAAATGCAATTTCTACCATCAGTTTC 57.923 33.333 0.00 0.00 44.81 2.78
2542 6615 5.884232 CCATCAGTTTCCATGAAAGAGATCA 59.116 40.000 0.00 0.00 31.87 2.92
2553 6626 7.767659 TCCATGAAAGAGATCAATGTAGTTCAG 59.232 37.037 0.00 0.00 32.06 3.02
2554 6627 7.551974 CCATGAAAGAGATCAATGTAGTTCAGT 59.448 37.037 0.00 0.00 32.06 3.41
2559 6632 6.815089 AGAGATCAATGTAGTTCAGTCCATC 58.185 40.000 0.00 0.00 0.00 3.51
2567 6640 8.554528 CAATGTAGTTCAGTCCATCAACATATC 58.445 37.037 0.00 0.00 0.00 1.63
2571 6644 7.290110 AGTTCAGTCCATCAACATATCGATA 57.710 36.000 7.75 7.75 0.00 2.92
2573 6646 7.816513 AGTTCAGTCCATCAACATATCGATATG 59.183 37.037 33.70 33.70 44.37 1.78
2589 6662 9.998106 ATATCGATATGTAAGCAAGTTACCTTT 57.002 29.630 17.08 0.00 40.49 3.11
2616 6689 3.939939 TCAGCACCAAGGCGCTCA 61.940 61.111 7.64 0.00 35.96 4.26
2619 6692 2.747460 GCACCAAGGCGCTCATCA 60.747 61.111 7.64 0.00 0.00 3.07
2631 6704 1.791204 CGCTCATCATGGTCTTCGATG 59.209 52.381 0.00 0.00 38.29 3.84
2646 6719 1.658596 TCGATGGTTTCTTTGATCGCG 59.341 47.619 0.00 0.00 38.05 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.398044 CGTAGCACACCCCAAAGAATTATT 59.602 41.667 0.00 0.00 0.00 1.40
29 30 3.945285 CGTAGCACACCCCAAAGAATTAT 59.055 43.478 0.00 0.00 0.00 1.28
100 101 2.477825 CCGCGAGATCATGTCAGATTT 58.522 47.619 8.23 0.00 0.00 2.17
142 143 5.196341 TCTCACAACACGACTTCTGTTAT 57.804 39.130 0.00 0.00 30.48 1.89
203 204 0.317160 TGCTAGTGTTGTGCTACGCT 59.683 50.000 5.35 5.35 41.46 5.07
229 230 0.446222 CGCCATAACAACAGTTCCCG 59.554 55.000 0.00 0.00 0.00 5.14
291 292 3.499737 CCGGCGTGGACAAGCATC 61.500 66.667 6.01 0.00 42.00 3.91
674 680 0.733729 GTCGACTGAGACGTAGCCAT 59.266 55.000 8.70 0.00 0.00 4.40
697 703 6.665680 ACTATATCACTTGACTGAGACTTGGT 59.334 38.462 0.00 0.00 0.00 3.67
698 704 6.977502 CACTATATCACTTGACTGAGACTTGG 59.022 42.308 0.00 0.00 0.00 3.61
699 705 7.766283 TCACTATATCACTTGACTGAGACTTG 58.234 38.462 0.00 0.00 0.00 3.16
818 832 3.549423 CCGTCGACTGAGACTTTGTTACA 60.549 47.826 14.70 0.00 38.90 2.41
1056 4982 0.818040 GAGGACGGAGGAGAGAGCTC 60.818 65.000 5.27 5.27 40.54 4.09
1284 5213 4.790962 CCTGCAGCTGGGCGATGT 62.791 66.667 17.12 0.00 36.28 3.06
1327 5256 4.087892 CACTCGTCCAGCCCCAGG 62.088 72.222 0.00 0.00 0.00 4.45
1654 5596 4.011698 TGCACATCACATATTTCACTGCT 58.988 39.130 0.00 0.00 0.00 4.24
1732 5787 8.807948 AAATAAATACTGATAACACCACAGCT 57.192 30.769 0.00 0.00 35.38 4.24
1774 5829 8.729805 ACTCTTGTGAATCAGAGAAATATTCC 57.270 34.615 5.20 0.00 33.09 3.01
1778 5833 8.588472 TCTGAACTCTTGTGAATCAGAGAAATA 58.412 33.333 5.20 0.00 38.86 1.40
1821 5882 1.850377 TTTTTGCGACTCGAACGGTA 58.150 45.000 1.63 0.00 0.00 4.02
1831 5892 2.368655 AGGATTGCCATTTTTGCGAC 57.631 45.000 0.00 0.00 36.29 5.19
1912 5975 6.292865 CGTGTTTTTAGATGCTTCAGTTCAGA 60.293 38.462 2.07 0.00 0.00 3.27
1934 6001 1.954362 CTCTTCAGGCCTCCTCCGTG 61.954 65.000 0.00 0.00 0.00 4.94
1955 6022 6.036470 CGTCTGATTGAGCTGTATGTAAAGA 58.964 40.000 0.00 0.00 0.00 2.52
1971 6042 1.519719 GGCAGCTCTCCGTCTGATT 59.480 57.895 0.00 0.00 32.26 2.57
2012 6083 3.927481 GAAGCCCAAGCCGAAGCCT 62.927 63.158 0.00 0.00 41.25 4.58
2018 6089 2.815647 GTCGAGAAGCCCAAGCCG 60.816 66.667 0.00 0.00 41.25 5.52
2280 6351 7.954835 ACACCTGTGTACAGTACTTACATTAA 58.045 34.615 12.07 8.38 42.90 1.40
2283 6354 6.415206 AACACCTGTGTACAGTACTTACAT 57.585 37.500 12.07 3.68 44.13 2.29
2290 6361 5.304871 TGTGGAATAACACCTGTGTACAGTA 59.695 40.000 10.80 0.00 44.13 2.74
2293 6364 4.691326 TGTGGAATAACACCTGTGTACA 57.309 40.909 2.92 0.00 44.13 2.90
2335 6406 5.867716 AGCCACAATACTTTAGTACTTGTCG 59.132 40.000 0.00 0.00 33.87 4.35
2357 6428 2.680339 GTTTCAGGCTAAGGATGTGAGC 59.320 50.000 0.00 0.00 35.39 4.26
2430 6501 2.957402 AGAGAATGCAACCAAGGACA 57.043 45.000 0.00 0.00 0.00 4.02
2437 6508 7.661968 TGTCTATACTGATAGAGAATGCAACC 58.338 38.462 0.00 0.00 43.84 3.77
2439 6510 7.869937 GCTTGTCTATACTGATAGAGAATGCAA 59.130 37.037 0.00 7.47 43.38 4.08
2523 6595 8.105829 ACTACATTGATCTCTTTCATGGAAACT 58.894 33.333 0.00 0.00 0.00 2.66
2525 6597 8.868522 AACTACATTGATCTCTTTCATGGAAA 57.131 30.769 0.00 0.00 0.00 3.13
2528 6600 7.551974 ACTGAACTACATTGATCTCTTTCATGG 59.448 37.037 0.00 0.00 0.00 3.66
2542 6615 7.439356 CGATATGTTGATGGACTGAACTACATT 59.561 37.037 0.00 0.00 32.97 2.71
2589 6662 2.821378 CCTTGGTGCTGACATCATTCAA 59.179 45.455 0.00 0.00 36.60 2.69
2616 6689 4.494091 AGAAACCATCGAAGACCATGAT 57.506 40.909 0.00 0.00 42.51 2.45
2619 6692 4.651778 TCAAAGAAACCATCGAAGACCAT 58.348 39.130 0.00 0.00 42.51 3.55
2631 6704 0.675522 TCCCCGCGATCAAAGAAACC 60.676 55.000 8.23 0.00 0.00 3.27
2646 6719 1.475682 CACCTGTCTACTTACGTCCCC 59.524 57.143 0.00 0.00 0.00 4.81
2652 6725 4.103357 CGTATGTGCACCTGTCTACTTAC 58.897 47.826 15.69 0.00 0.00 2.34
2655 6728 1.135083 GCGTATGTGCACCTGTCTACT 60.135 52.381 15.69 0.00 34.15 2.57


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

AutoCloner maintained by Alex Coulton.