Multiple sequence alignment - TraesCS2D01G089600

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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 TraesCS2D01G089600 chr2D 100.000 2723 0 0 1 2723 39534502 39531780 0.000000e+00 5029
1 TraesCS2D01G089600 chr2D 98.864 88 1 0 1 88 17996161 17996248 1.010000e-34 158
2 TraesCS2D01G089600 chr5A 96.849 2444 56 5 295 2723 19245665 19248102 0.000000e+00 4067
3 TraesCS2D01G089600 chr7D 96.768 2444 58 5 295 2723 382053257 382050820 0.000000e+00 4056
4 TraesCS2D01G089600 chr7D 96.727 2444 61 5 295 2723 381970587 381973026 0.000000e+00 4052
5 TraesCS2D01G089600 chr7D 96.686 2444 60 5 295 2723 203503177 203500740 0.000000e+00 4045
6 TraesCS2D01G089600 chr7D 96.686 2444 60 5 295 2723 381927179 381924742 0.000000e+00 4045
7 TraesCS2D01G089600 chr7D 96.244 213 8 0 97 309 579003035 579003247 1.550000e-92 350
8 TraesCS2D01G089600 chr6D 96.442 2445 65 6 295 2723 124520701 124518263 0.000000e+00 4013
9 TraesCS2D01G089600 chr6D 98.864 88 1 0 1 88 283199268 283199355 1.010000e-34 158
10 TraesCS2D01G089600 chr7B 96.399 2444 66 6 295 2723 716835393 716837829 0.000000e+00 4006
11 TraesCS2D01G089600 chr7B 96.399 2444 62 6 295 2723 716875608 716878040 0.000000e+00 4002
12 TraesCS2D01G089600 chr7B 96.399 2444 63 6 295 2723 742992619 742990186 0.000000e+00 4002
13 TraesCS2D01G089600 chrUn 96.318 2444 64 6 295 2723 186205248 186207680 0.000000e+00 3991
14 TraesCS2D01G089600 chrUn 96.244 213 8 0 97 309 209404860 209404648 1.550000e-92 350
15 TraesCS2D01G089600 chrUn 96.244 213 8 0 97 309 378215017 378215229 1.550000e-92 350
16 TraesCS2D01G089600 chrUn 96.244 213 8 0 97 309 438448248 438448036 1.550000e-92 350
17 TraesCS2D01G089600 chrUn 95.775 213 9 0 97 309 267893448 267893660 7.220000e-91 344
18 TraesCS2D01G089600 chrUn 98.864 88 1 0 1 88 267893029 267893116 1.010000e-34 158
19 TraesCS2D01G089600 chrUn 98.864 88 1 0 1 88 438448667 438448580 1.010000e-34 158
20 TraesCS2D01G089600 chr4D 96.349 2438 66 6 301 2723 123338642 123336213 0.000000e+00 3988
21 TraesCS2D01G089600 chr4D 98.864 88 1 0 1 88 241065804 241065891 1.010000e-34 158
22 TraesCS2D01G089600 chr7A 96.277 2444 65 6 295 2723 60282486 60280054 0.000000e+00 3986
23 TraesCS2D01G089600 chr1A 96.277 2444 65 6 295 2723 498688054 498690486 0.000000e+00 3986
24 TraesCS2D01G089600 chr1A 98.864 88 1 0 1 88 94589405 94589492 1.010000e-34 158
25 TraesCS2D01G089600 chr1A 98.864 88 1 0 1 88 94732191 94732104 1.010000e-34 158
26 TraesCS2D01G089600 chr3B 96.714 213 7 0 97 309 759911526 759911314 3.330000e-94 355
27 TraesCS2D01G089600 chr6B 96.244 213 8 0 97 309 596595120 596595332 1.550000e-92 350
28 TraesCS2D01G089600 chr2B 96.244 213 8 0 97 309 391151540 391151328 1.550000e-92 350
29 TraesCS2D01G089600 chr1D 96.244 213 8 0 97 309 212441122 212441334 1.550000e-92 350
30 TraesCS2D01G089600 chr1D 98.864 88 1 0 1 88 212440704 212440791 1.010000e-34 158
31 TraesCS2D01G089600 chr5D 98.864 88 1 0 1 88 562909248 562909335 1.010000e-34 158


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 TraesCS2D01G089600 chr2D 39531780 39534502 2722 True 5029 5029 100.0000 1 2723 1 chr2D.!!$R1 2722
1 TraesCS2D01G089600 chr5A 19245665 19248102 2437 False 4067 4067 96.8490 295 2723 1 chr5A.!!$F1 2428
2 TraesCS2D01G089600 chr7D 382050820 382053257 2437 True 4056 4056 96.7680 295 2723 1 chr7D.!!$R3 2428
3 TraesCS2D01G089600 chr7D 381970587 381973026 2439 False 4052 4052 96.7270 295 2723 1 chr7D.!!$F1 2428
4 TraesCS2D01G089600 chr7D 203500740 203503177 2437 True 4045 4045 96.6860 295 2723 1 chr7D.!!$R1 2428
5 TraesCS2D01G089600 chr7D 381924742 381927179 2437 True 4045 4045 96.6860 295 2723 1 chr7D.!!$R2 2428
6 TraesCS2D01G089600 chr6D 124518263 124520701 2438 True 4013 4013 96.4420 295 2723 1 chr6D.!!$R1 2428
7 TraesCS2D01G089600 chr7B 716835393 716837829 2436 False 4006 4006 96.3990 295 2723 1 chr7B.!!$F1 2428
8 TraesCS2D01G089600 chr7B 716875608 716878040 2432 False 4002 4002 96.3990 295 2723 1 chr7B.!!$F2 2428
9 TraesCS2D01G089600 chr7B 742990186 742992619 2433 True 4002 4002 96.3990 295 2723 1 chr7B.!!$R1 2428
10 TraesCS2D01G089600 chrUn 186205248 186207680 2432 False 3991 3991 96.3180 295 2723 1 chrUn.!!$F1 2428
11 TraesCS2D01G089600 chrUn 438448036 438448667 631 True 254 350 97.5540 1 309 2 chrUn.!!$R2 308
12 TraesCS2D01G089600 chrUn 267893029 267893660 631 False 251 344 97.3195 1 309 2 chrUn.!!$F3 308
13 TraesCS2D01G089600 chr4D 123336213 123338642 2429 True 3988 3988 96.3490 301 2723 1 chr4D.!!$R1 2422
14 TraesCS2D01G089600 chr7A 60280054 60282486 2432 True 3986 3986 96.2770 295 2723 1 chr7A.!!$R1 2428
15 TraesCS2D01G089600 chr1A 498688054 498690486 2432 False 3986 3986 96.2770 295 2723 1 chr1A.!!$F2 2428
16 TraesCS2D01G089600 chr1D 212440704 212441334 630 False 254 350 97.5540 1 309 2 chr1D.!!$F1 308

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
224 548 0.68566 TGCTGGCATGGCATTTTTCA 59.314 45.0 23.59 12.35 34.56 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 2484 0.250945 TCCAGCATTACGGCAAACCA 60.251 50.0 0.0 0.0 35.83 3.67 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
61 62 7.779326 TGCCTATGATTTTTCCAACTGATATGA 59.221 33.333 0.00 0.00 0.00 2.15
134 458 6.294361 TGTTCCTCAATCTTCGGAGAATAA 57.706 37.500 0.00 0.00 45.90 1.40
138 462 4.443457 CCTCAATCTTCGGAGAATAAGGCA 60.443 45.833 0.00 0.00 45.90 4.75
191 515 2.281539 TCCTGGAAGTAGACGACACA 57.718 50.000 0.00 0.00 0.00 3.72
224 548 0.685660 TGCTGGCATGGCATTTTTCA 59.314 45.000 23.59 12.35 34.56 2.69
365 689 5.587844 ACAGATATGAACTGAGTGCCATTTC 59.412 40.000 6.15 7.85 38.55 2.17
438 762 6.437477 TGAAAGAGGAAGTCATTGCTAGTAGA 59.563 38.462 0.00 0.00 37.20 2.59
462 786 2.673893 CGACTTGTCACGATCCATTGGA 60.674 50.000 8.08 8.08 35.55 3.53
666 991 4.394712 CTCGCTCCGGGCAGGTTT 62.395 66.667 14.17 0.00 41.91 3.27
677 1002 2.683742 CGGGCAGGTTTGGATCACTTAT 60.684 50.000 0.00 0.00 0.00 1.73
691 1016 4.330944 TCACTTATTATACACGGCCCTG 57.669 45.455 0.00 0.00 0.00 4.45
864 1189 7.792032 TCTTATTCCCGTGTTTGATCTTATCT 58.208 34.615 0.00 0.00 0.00 1.98
909 1234 5.715434 GGTAGAGACCCATGTAGAGAATC 57.285 47.826 0.00 0.00 40.23 2.52
910 1235 5.390387 GGTAGAGACCCATGTAGAGAATCT 58.610 45.833 0.00 0.00 44.62 2.40
962 1287 1.265635 CTTCGATAGGCTCCACTCTCG 59.734 57.143 0.00 0.00 38.11 4.04
1009 1334 1.630878 CCTGGGCTAAGATGGGGATAC 59.369 57.143 0.00 0.00 0.00 2.24
1075 1400 4.781087 ACAGGGGTAAGCTCTGTAAATGTA 59.219 41.667 3.32 0.00 39.63 2.29
1076 1401 5.116882 CAGGGGTAAGCTCTGTAAATGTAC 58.883 45.833 0.00 0.00 0.00 2.90
1089 1414 4.754618 TGTAAATGTACAGAGCCAAGTGTG 59.245 41.667 0.33 0.00 35.23 3.82
1128 1453 3.087906 TTCTAGGCCCCTTCCCGC 61.088 66.667 0.00 0.00 0.00 6.13
1134 1459 2.445274 GCCCCTTCCCGCCTACTA 60.445 66.667 0.00 0.00 0.00 1.82
1189 1514 1.035932 GCCATCCATTGCAGCAGAGT 61.036 55.000 0.00 0.00 0.00 3.24
1772 2111 5.161358 GTTCATCTCGTGTAGTGATTGTGA 58.839 41.667 0.00 0.00 31.32 3.58
1799 2138 2.651455 ACAAGGATATGGAGTCGACGA 58.349 47.619 10.46 0.00 0.00 4.20
1849 2188 2.579873 GTAGCATGCATTCCCATCTGT 58.420 47.619 21.98 0.00 0.00 3.41
1907 2246 2.367567 ACAGAAAACTGCCTTCGGTCTA 59.632 45.455 0.00 0.00 0.00 2.59
1984 2338 0.404426 GGAAGTAAGCCCCACAACCT 59.596 55.000 0.00 0.00 0.00 3.50
1992 2346 1.377229 CCCCACAACCTAAAGCGGA 59.623 57.895 0.00 0.00 0.00 5.54
2130 2484 6.655003 CCCAAATCCGCTATATATTTGACACT 59.345 38.462 8.75 0.00 41.14 3.55
2157 2511 2.745152 GCCGTAATGCTGGAACTATGGT 60.745 50.000 0.00 0.00 0.00 3.55
2295 2649 6.859112 ACTATGAGCTAGAGGTCTTTTGAA 57.141 37.500 9.92 0.00 42.60 2.69
2299 2653 9.171877 CTATGAGCTAGAGGTCTTTTGAATTTT 57.828 33.333 9.92 0.00 42.60 1.82
2345 2699 6.183361 TGCTCCTAAGATCATAGAAGCAATGT 60.183 38.462 15.41 0.00 35.73 2.71
2534 2888 0.387565 GATTGAGTCCGAGGGAGAGC 59.612 60.000 0.00 0.00 29.39 4.09
2546 2900 0.616891 GGGAGAGCGGGGTTTTCTTA 59.383 55.000 0.00 0.00 0.00 2.10
2595 2949 2.294791 CCCACAAGTTGTTAATTCGCCA 59.705 45.455 5.57 0.00 0.00 5.69
2598 2952 4.214545 CCACAAGTTGTTAATTCGCCACTA 59.785 41.667 5.57 0.00 0.00 2.74
2615 2969 4.220602 GCCACTAGGGAATTCACACAAAAT 59.779 41.667 11.02 0.00 40.01 1.82
2635 2989 7.505585 ACAAAATGGAAGGACTTATTCTCAACA 59.494 33.333 0.00 0.00 0.00 3.33
2669 3023 4.044336 TCTGAACCGAACGTGAAAGTTA 57.956 40.909 0.00 0.00 34.00 2.24
2685 3039 6.001460 TGAAAGTTATTTTCCATCAGACGGT 58.999 36.000 0.00 0.00 43.72 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 8.337118 ACAAGAGGAGATCCATTATTCCTAAA 57.663 34.615 0.92 0.00 40.07 1.85
89 90 7.937700 ACAAGAGGAGATCCATTATTCCTAA 57.062 36.000 0.92 0.00 40.07 2.69
90 91 7.016661 GGAACAAGAGGAGATCCATTATTCCTA 59.983 40.741 14.83 0.00 40.07 2.94
91 92 6.183361 GGAACAAGAGGAGATCCATTATTCCT 60.183 42.308 14.83 0.00 42.60 3.36
92 93 6.000840 GGAACAAGAGGAGATCCATTATTCC 58.999 44.000 9.72 9.72 35.13 3.01
94 95 6.388100 TGAGGAACAAGAGGAGATCCATTATT 59.612 38.462 0.92 0.00 38.89 1.40
95 96 5.907662 TGAGGAACAAGAGGAGATCCATTAT 59.092 40.000 0.92 0.00 38.89 1.28
134 458 6.072199 AGAACTTTCTCTAATCCAATGCCT 57.928 37.500 0.00 0.00 29.94 4.75
165 489 4.995487 GTCGTCTACTTCCAGGAAATGTTT 59.005 41.667 2.72 0.00 0.00 2.83
191 515 6.484308 GCCATGCCAGCATTAAGATTTAAAAT 59.516 34.615 1.47 0.00 33.90 1.82
219 543 6.420604 GGCGAAAAAGACTGATTCAATGAAAA 59.579 34.615 0.00 0.00 0.00 2.29
224 548 4.278170 TGTGGCGAAAAAGACTGATTCAAT 59.722 37.500 0.00 0.00 0.00 2.57
293 617 0.252239 AAGAAAGGGTGGGCCATTCC 60.252 55.000 10.70 15.27 37.87 3.01
365 689 5.011090 TCCCTTGTTCGATCTTACTCATG 57.989 43.478 0.00 0.00 0.00 3.07
438 762 2.519377 TGGATCGTGACAAGTCGTTT 57.481 45.000 0.00 0.00 0.00 3.60
462 786 8.350648 AGACCTAGGACATGGATTCTATATGAT 58.649 37.037 17.98 0.00 0.00 2.45
666 991 4.262721 GGGCCGTGTATAATAAGTGATCCA 60.263 45.833 0.00 0.00 0.00 3.41
677 1002 1.208535 CCTTCACAGGGCCGTGTATAA 59.791 52.381 29.43 23.27 38.12 0.98
691 1016 0.323957 AACGCTCCTAACCCCTTCAC 59.676 55.000 0.00 0.00 0.00 3.18
779 1104 3.711190 GGGATGGATAAAGTGGGCAAAAT 59.289 43.478 0.00 0.00 0.00 1.82
864 1189 0.764369 ATGGAAGCGGGGCAGAGATA 60.764 55.000 0.00 0.00 0.00 1.98
898 1223 5.332106 TGGCTCCTCTAGATTCTCTACAT 57.668 43.478 0.00 0.00 0.00 2.29
909 1234 4.479158 AGTAAGATCCTTGGCTCCTCTAG 58.521 47.826 0.00 0.00 0.00 2.43
910 1235 4.169068 AGAGTAAGATCCTTGGCTCCTCTA 59.831 45.833 0.00 0.00 0.00 2.43
997 1322 1.133575 TCGACTCGGTATCCCCATCTT 60.134 52.381 0.00 0.00 0.00 2.40
1009 1334 1.140407 GGCTTCAATCGTCGACTCGG 61.140 60.000 14.70 0.00 0.00 4.63
1089 1414 2.094338 GTGCCTACTACTACACCACACC 60.094 54.545 0.00 0.00 0.00 4.16
1128 1453 3.957497 AAGCACTGGAGTGATCTAGTAGG 59.043 47.826 11.06 0.00 44.74 3.18
1134 1459 0.534412 CCGAAGCACTGGAGTGATCT 59.466 55.000 11.06 0.00 44.74 2.75
1189 1514 2.267642 CCCCCGCTCATGAAACGA 59.732 61.111 16.99 0.00 0.00 3.85
1268 1607 7.731235 AGATCCATCCATCTATCCAGATATCTG 59.269 40.741 23.53 23.53 39.62 2.90
1772 2111 4.036498 CGACTCCATATCCTTGTACGAGTT 59.964 45.833 9.32 0.00 0.00 3.01
1799 2138 4.038522 CAGGGTCGAGTCTGATACATCAAT 59.961 45.833 8.75 0.00 36.18 2.57
1849 2188 3.304391 GCTTACCGAATCAGTTGCAACAA 60.304 43.478 30.11 18.43 0.00 2.83
1984 2338 8.561738 AATTCTATTTGTTCTTCTCCGCTTTA 57.438 30.769 0.00 0.00 0.00 1.85
2043 2397 7.770433 CCTTCTCCATTACAATGTTCTCATACA 59.230 37.037 0.00 0.00 34.60 2.29
2130 2484 0.250945 TCCAGCATTACGGCAAACCA 60.251 50.000 0.00 0.00 35.83 3.67
2157 2511 6.476243 CATCAATGACGATAGATGCATTCA 57.524 37.500 0.00 0.00 35.18 2.57
2209 2563 5.500234 TGTGGAACCATAGAAGGAATTCAG 58.500 41.667 7.93 0.00 34.36 3.02
2295 2649 0.321475 CGCCATGGCCCAAACAAAAT 60.321 50.000 30.79 0.00 37.98 1.82
2345 2699 8.994429 TTACAACAAATCTTCTTTTTCTGCAA 57.006 26.923 0.00 0.00 0.00 4.08
2434 2788 4.156556 GTGACAGCATTCCTTTCTATTGCA 59.843 41.667 0.00 0.00 35.79 4.08
2534 2888 0.743345 CGAGCCCTAAGAAAACCCCG 60.743 60.000 0.00 0.00 0.00 5.73
2546 2900 3.838565 TCTATTCAATCTCTCGAGCCCT 58.161 45.455 7.81 0.00 0.00 5.19
2595 2949 5.640147 TCCATTTTGTGTGAATTCCCTAGT 58.360 37.500 2.27 0.00 0.00 2.57
2598 2952 4.284234 CCTTCCATTTTGTGTGAATTCCCT 59.716 41.667 2.27 0.00 0.00 4.20
2615 2969 7.889873 TTTTTGTTGAGAATAAGTCCTTCCA 57.110 32.000 0.00 0.00 0.00 3.53
2641 2995 1.337817 CGTTCGGTTCAGAGAGCACG 61.338 60.000 0.00 0.00 0.00 5.34
2669 3023 4.023193 GTGAACAACCGTCTGATGGAAAAT 60.023 41.667 22.36 5.91 0.00 1.82
2685 3039 3.549423 CGAGAGTGGAGTTACGTGAACAA 60.549 47.826 0.00 0.00 40.86 2.83


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

AutoCloner maintained by Alex Coulton.