Multiple sequence alignment - TraesCS2D01G362400

Loading Multiple Alignment...

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 TraesCS2D01G362400 chr2D 100.000 2289 0 0 1 2289 468362635 468360347 0.000000e+00 4228
1 TraesCS2D01G362400 chr2D 97.823 827 18 0 1080 1906 152092129 152092955 0.000000e+00 1428
2 TraesCS2D01G362400 chr2D 95.954 865 32 1 1045 1909 607668341 607667480 0.000000e+00 1400
3 TraesCS2D01G362400 chr2D 93.212 604 39 1 1 602 445945844 445946447 0.000000e+00 887
4 TraesCS2D01G362400 chr2D 95.202 396 17 2 598 991 607669406 607669011 1.930000e-175 625
5 TraesCS2D01G362400 chr2D 92.708 384 26 2 1908 2289 289691389 289691006 9.240000e-154 553
6 TraesCS2D01G362400 chr7D 94.499 1327 59 12 595 1913 574232602 574233922 0.000000e+00 2034
7 TraesCS2D01G362400 chr7D 94.041 386 18 4 1908 2289 223297310 223297694 4.240000e-162 580
8 TraesCS2D01G362400 chr7D 92.969 384 25 2 1908 2289 333310473 333310090 1.990000e-155 558
9 TraesCS2D01G362400 chr5D 94.558 1323 60 10 598 1913 435542893 435541576 0.000000e+00 2034
10 TraesCS2D01G362400 chr5D 93.554 605 35 3 1 602 315074553 315075156 0.000000e+00 898
11 TraesCS2D01G362400 chr5D 93.532 603 38 1 1 602 199421985 199422587 0.000000e+00 896
12 TraesCS2D01G362400 chr5D 93.377 604 38 1 1 602 152707180 152706577 0.000000e+00 893
13 TraesCS2D01G362400 chr5D 92.881 604 41 1 1 602 516845382 516844779 0.000000e+00 876
14 TraesCS2D01G362400 chr5D 93.473 383 23 2 1908 2289 291735368 291734987 3.300000e-158 568
15 TraesCS2D01G362400 chr6D 94.466 1319 61 8 598 1909 392885266 392886579 0.000000e+00 2021
16 TraesCS2D01G362400 chr6D 91.541 993 44 16 601 1583 72195351 72194389 0.000000e+00 1332
17 TraesCS2D01G362400 chr6D 93.201 603 36 3 3 602 168584447 168583847 0.000000e+00 881
18 TraesCS2D01G362400 chr6D 93.046 604 40 2 1 602 232679384 232679987 0.000000e+00 881
19 TraesCS2D01G362400 chr6D 93.194 382 25 1 1908 2289 233831191 233830811 5.520000e-156 560
20 TraesCS2D01G362400 chr6D 92.969 384 22 4 1908 2289 232679983 232680363 2.570000e-154 555
21 TraesCS2D01G362400 chr6D 92.727 385 22 5 1908 2289 28918805 28918424 3.320000e-153 551
22 TraesCS2D01G362400 chr6D 92.689 383 27 1 1908 2289 37943266 37943648 3.320000e-153 551
23 TraesCS2D01G362400 chr4D 92.515 1336 61 10 598 1912 414509590 414508273 0.000000e+00 1877
24 TraesCS2D01G362400 chr1A 92.498 1333 52 9 601 1907 577043560 577042250 0.000000e+00 1864
25 TraesCS2D01G362400 chr1A 91.704 1338 64 7 601 1913 485018716 485017401 0.000000e+00 1812
26 TraesCS2D01G362400 chr5A 90.814 1339 86 12 598 1909 599254832 599256160 0.000000e+00 1757
27 TraesCS2D01G362400 chr5A 88.209 1340 120 17 597 1909 653279832 653281160 0.000000e+00 1565
28 TraesCS2D01G362400 chr5A 92.203 513 18 5 600 1091 666947937 666947426 0.000000e+00 706
29 TraesCS2D01G362400 chr3D 90.075 1340 97 12 601 1913 189003951 189002621 0.000000e+00 1705
30 TraesCS2D01G362400 chr3D 92.881 604 41 1 1 602 134214940 134215543 0.000000e+00 876
31 TraesCS2D01G362400 chr2A 93.234 606 34 4 1 602 485681813 485681211 0.000000e+00 885
32 TraesCS2D01G362400 chr1D 92.689 383 27 1 1908 2289 93298636 93299018 3.320000e-153 551


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 TraesCS2D01G362400 chr2D 468360347 468362635 2288 True 4228.0 4228 100.0000 1 2289 1 chr2D.!!$R2 2288
1 TraesCS2D01G362400 chr2D 152092129 152092955 826 False 1428.0 1428 97.8230 1080 1906 1 chr2D.!!$F1 826
2 TraesCS2D01G362400 chr2D 607667480 607669406 1926 True 1012.5 1400 95.5780 598 1909 2 chr2D.!!$R3 1311
3 TraesCS2D01G362400 chr2D 445945844 445946447 603 False 887.0 887 93.2120 1 602 1 chr2D.!!$F2 601
4 TraesCS2D01G362400 chr7D 574232602 574233922 1320 False 2034.0 2034 94.4990 595 1913 1 chr7D.!!$F2 1318
5 TraesCS2D01G362400 chr5D 435541576 435542893 1317 True 2034.0 2034 94.5580 598 1913 1 chr5D.!!$R3 1315
6 TraesCS2D01G362400 chr5D 315074553 315075156 603 False 898.0 898 93.5540 1 602 1 chr5D.!!$F2 601
7 TraesCS2D01G362400 chr5D 199421985 199422587 602 False 896.0 896 93.5320 1 602 1 chr5D.!!$F1 601
8 TraesCS2D01G362400 chr5D 152706577 152707180 603 True 893.0 893 93.3770 1 602 1 chr5D.!!$R1 601
9 TraesCS2D01G362400 chr5D 516844779 516845382 603 True 876.0 876 92.8810 1 602 1 chr5D.!!$R4 601
10 TraesCS2D01G362400 chr6D 392885266 392886579 1313 False 2021.0 2021 94.4660 598 1909 1 chr6D.!!$F2 1311
11 TraesCS2D01G362400 chr6D 72194389 72195351 962 True 1332.0 1332 91.5410 601 1583 1 chr6D.!!$R2 982
12 TraesCS2D01G362400 chr6D 168583847 168584447 600 True 881.0 881 93.2010 3 602 1 chr6D.!!$R3 599
13 TraesCS2D01G362400 chr6D 232679384 232680363 979 False 718.0 881 93.0075 1 2289 2 chr6D.!!$F3 2288
14 TraesCS2D01G362400 chr4D 414508273 414509590 1317 True 1877.0 1877 92.5150 598 1912 1 chr4D.!!$R1 1314
15 TraesCS2D01G362400 chr1A 577042250 577043560 1310 True 1864.0 1864 92.4980 601 1907 1 chr1A.!!$R2 1306
16 TraesCS2D01G362400 chr1A 485017401 485018716 1315 True 1812.0 1812 91.7040 601 1913 1 chr1A.!!$R1 1312
17 TraesCS2D01G362400 chr5A 599254832 599256160 1328 False 1757.0 1757 90.8140 598 1909 1 chr5A.!!$F1 1311
18 TraesCS2D01G362400 chr5A 653279832 653281160 1328 False 1565.0 1565 88.2090 597 1909 1 chr5A.!!$F2 1312
19 TraesCS2D01G362400 chr5A 666947426 666947937 511 True 706.0 706 92.2030 600 1091 1 chr5A.!!$R1 491
20 TraesCS2D01G362400 chr3D 189002621 189003951 1330 True 1705.0 1705 90.0750 601 1913 1 chr3D.!!$R1 1312
21 TraesCS2D01G362400 chr3D 134214940 134215543 603 False 876.0 876 92.8810 1 602 1 chr3D.!!$F1 601
22 TraesCS2D01G362400 chr2A 485681211 485681813 602 True 885.0 885 93.2340 1 602 1 chr2A.!!$R1 601

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
353 356 0.038159 GCTTCGGCTGTAGTGTGAGT 60.038 55.0 0.8 0.0 38.08 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2129 2804 0.314935 CGGCTGCACACAAGGAAATT 59.685 50.0 0.5 0.0 0.0 1.82 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
86 89 1.608336 CGTCCAGTGGGTCCCTACA 60.608 63.158 9.92 0.00 34.93 2.74
272 275 3.162154 GGCCTAGGAAGGGGACGG 61.162 72.222 14.75 0.00 43.87 4.79
353 356 0.038159 GCTTCGGCTGTAGTGTGAGT 60.038 55.000 0.80 0.00 38.08 3.41
373 376 0.668706 CTGCCATCGCCGGAGAATAG 60.669 60.000 13.28 5.01 0.00 1.73
473 476 1.599518 ATGGCCGACGCTTGTTTGA 60.600 52.632 0.00 0.00 34.44 2.69
492 495 2.105466 GCGGCTGGAGCAAGAAGAG 61.105 63.158 0.20 0.00 44.36 2.85
622 625 2.884639 GGGTGTGTTTAGTTGCTGTCAT 59.115 45.455 0.00 0.00 0.00 3.06
637 640 3.493350 GCTGTCATCGGGTAGAATGTCAT 60.493 47.826 0.00 0.00 0.00 3.06
793 798 1.687493 CGAGCCCTCTTCCCCTCTT 60.687 63.158 0.00 0.00 0.00 2.85
800 805 2.032528 CTTCCCCTCTTGCACGCA 59.967 61.111 0.00 0.00 0.00 5.24
834 846 3.071206 TCCCCTGTCTCAGCGCTC 61.071 66.667 7.13 0.00 0.00 5.03
843 855 4.704103 TCAGCGCTCCCACCCTCT 62.704 66.667 7.13 0.00 0.00 3.69
1244 1907 3.950794 GACGCCATGCTCCCGTTCA 62.951 63.158 0.00 0.00 35.06 3.18
1527 2191 0.792640 ATGAACGACGCAGCAAAGAG 59.207 50.000 0.00 0.00 0.00 2.85
1536 2200 2.221169 CGCAGCAAAGAGGCCAATATA 58.779 47.619 5.01 0.00 0.00 0.86
1538 2202 3.365666 CGCAGCAAAGAGGCCAATATATG 60.366 47.826 5.01 0.00 0.00 1.78
1769 2433 8.600449 TTATGTGGTTTCATTTTTCATTCCAC 57.400 30.769 0.00 0.00 42.72 4.02
1776 2440 6.824305 TTCATTTTTCATTCCACCTCTCTC 57.176 37.500 0.00 0.00 0.00 3.20
1793 2457 3.118920 TCTCTCACCAAACACAAGAACGA 60.119 43.478 0.00 0.00 0.00 3.85
1815 2479 1.301423 CCGACCCGTTTCACTTTTCA 58.699 50.000 0.00 0.00 0.00 2.69
1848 2518 1.553248 CACAGGAATGGAACGGACCTA 59.447 52.381 0.00 0.00 0.00 3.08
1852 2522 3.134804 CAGGAATGGAACGGACCTATTCT 59.865 47.826 16.16 4.36 32.97 2.40
1861 2531 5.537674 GGAACGGACCTATTCTAGTGGAATA 59.462 44.000 8.48 8.48 43.59 1.75
1927 2602 2.505819 CCTTAGTAGGCCCACAAGTCAT 59.494 50.000 3.54 0.00 33.99 3.06
1953 2628 0.836400 ATATGGTGGGTCCCGGCTAG 60.836 60.000 2.65 0.00 34.77 3.42
1972 2647 4.202151 GCTAGCAGGGGGTATTCATTTTTG 60.202 45.833 10.63 0.00 0.00 2.44
1978 2653 3.260632 GGGGGTATTCATTTTTGTGTGCT 59.739 43.478 0.00 0.00 0.00 4.40
2000 2675 5.802451 GCTTAATAAGGAAGCACTTTCTTGC 59.198 40.000 13.21 4.91 46.97 4.01
2091 2766 0.323629 TTCGGTTGGTCCCAGATGTC 59.676 55.000 0.00 0.00 0.00 3.06
2113 2788 6.377996 TGTCAGGTGGAGGAATCATTATTTTG 59.622 38.462 0.00 0.00 0.00 2.44
2115 2790 5.127519 CAGGTGGAGGAATCATTATTTTGCA 59.872 40.000 0.00 0.00 0.00 4.08
2129 2804 7.771361 TCATTATTTTGCACGTAATAAGGAGGA 59.229 33.333 10.32 3.13 34.19 3.71
2173 2848 1.624479 CCAGCTGTCAGCCTCTCCAT 61.624 60.000 21.32 0.00 43.77 3.41
2247 2922 3.746949 GAGAGCACCAGGGCGATGG 62.747 68.421 5.87 5.87 46.47 3.51
2259 2934 1.138247 GCGATGGACGACGGTTAGT 59.862 57.895 0.00 0.00 45.77 2.24
2276 2951 4.809513 TCCTAGGAAGGGGACAGC 57.190 61.111 9.71 0.00 43.84 4.40
2279 2954 2.038975 TAGGAAGGGGACAGCGCT 59.961 61.111 2.64 2.64 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 76 0.252284 CCTGACTGTAGGGACCCACT 60.252 60.000 14.60 0.00 34.06 4.00
86 89 5.983333 AATAATGATTCCTCCACCTGACT 57.017 39.130 0.00 0.00 0.00 3.41
140 143 4.051167 CAGCTGGGTCCATGGCCA 62.051 66.667 21.92 8.56 0.00 5.36
253 256 1.689582 CGTCCCCTTCCTAGGCCTT 60.690 63.158 12.58 0.00 40.50 4.35
324 327 2.032681 GCCGAAGCAGTCAACCCT 59.967 61.111 0.00 0.00 39.53 4.34
344 347 0.173481 GCGATGGCAGACTCACACTA 59.827 55.000 0.00 0.00 39.62 2.74
345 348 1.079543 GCGATGGCAGACTCACACT 60.080 57.895 0.00 0.00 39.62 3.55
353 356 1.112916 TATTCTCCGGCGATGGCAGA 61.113 55.000 9.30 0.00 42.47 4.26
373 376 1.192146 TACTCACCCACACCTCCTGC 61.192 60.000 0.00 0.00 0.00 4.85
473 476 2.046507 CTTCTTGCTCCAGCCGCT 60.047 61.111 0.00 0.00 41.18 5.52
492 495 2.849294 AGTGCTTCTTCAACCTCTCC 57.151 50.000 0.00 0.00 0.00 3.71
622 625 1.760613 GACCCATGACATTCTACCCGA 59.239 52.381 0.00 0.00 0.00 5.14
649 653 0.107017 CGAGAATGGGCTGTGGGAAT 60.107 55.000 0.00 0.00 0.00 3.01
793 798 3.240134 GAGGGAAGAGGTGCGTGCA 62.240 63.158 0.00 0.00 0.00 4.57
800 805 0.612453 GGAGTCACGAGGGAAGAGGT 60.612 60.000 0.00 0.00 0.00 3.85
834 846 2.750657 GGGAGATGCAGAGGGTGGG 61.751 68.421 0.00 0.00 0.00 4.61
843 855 1.456518 CGAGAGGGAGGGAGATGCA 60.457 63.158 0.00 0.00 0.00 3.96
1154 1817 4.201679 CGGTGTATCTCCGGCGCA 62.202 66.667 10.83 0.00 43.68 6.09
1536 2200 9.716531 CATACTCAGTCATACAACAATATCCAT 57.283 33.333 0.00 0.00 0.00 3.41
1538 2202 9.935241 ATCATACTCAGTCATACAACAATATCC 57.065 33.333 0.00 0.00 0.00 2.59
1769 2433 3.475566 TCTTGTGTTTGGTGAGAGAGG 57.524 47.619 0.00 0.00 0.00 3.69
1776 2440 3.175929 GGTTTCGTTCTTGTGTTTGGTG 58.824 45.455 0.00 0.00 0.00 4.17
1793 2457 1.753930 AAAGTGAAACGGGTCGGTTT 58.246 45.000 6.39 6.39 45.86 3.27
1861 2531 2.041081 TGGAACGGAATGGAATGGTTCT 59.959 45.455 2.74 0.00 37.66 3.01
1948 2623 1.068121 ATGAATACCCCCTGCTAGCC 58.932 55.000 13.29 0.00 0.00 3.93
1953 2628 3.260632 ACACAAAAATGAATACCCCCTGC 59.739 43.478 0.00 0.00 0.00 4.85
1978 2653 5.472137 ACGCAAGAAAGTGCTTCCTTATTAA 59.528 36.000 0.00 0.00 42.62 1.40
1995 2670 2.034685 AGCTATATCTTCGCACGCAAGA 59.965 45.455 0.00 7.17 43.62 3.02
2000 2675 2.054363 CACCAGCTATATCTTCGCACG 58.946 52.381 0.00 0.00 0.00 5.34
2091 2766 5.127519 TGCAAAATAATGATTCCTCCACCTG 59.872 40.000 0.00 0.00 0.00 4.00
2113 2788 5.123936 AGGAAATTCCTCCTTATTACGTGC 58.876 41.667 9.08 0.00 45.66 5.34
2129 2804 0.314935 CGGCTGCACACAAGGAAATT 59.685 50.000 0.50 0.00 0.00 1.82
2173 2848 0.524414 CATCGGACGTGGACTGTACA 59.476 55.000 0.00 0.00 0.00 2.90
2223 2898 4.007644 CCTGGTGCTCTCGGTGCA 62.008 66.667 0.00 0.00 38.19 4.57
2225 2900 4.767255 GCCCTGGTGCTCTCGGTG 62.767 72.222 0.00 0.00 0.00 4.94
2247 2922 2.029838 TCCTAGGACTAACCGTCGTC 57.970 55.000 7.62 0.00 43.79 4.20
2259 2934 1.381327 CGCTGTCCCCTTCCTAGGA 60.381 63.158 7.62 7.62 45.05 2.94


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

AutoCloner maintained by Alex Coulton.