Multiple sequence alignment - TraesCS3B01G339500

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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 TraesCS3B01G339500 chr3B 100.000 3194 0 0 1 3194 545431662 545434855 0.000000e+00 5899.0
1 TraesCS3B01G339500 chr3B 95.412 2223 55 19 366 2545 545561711 545563929 0.000000e+00 3496.0
2 TraesCS3B01G339500 chr3B 97.376 1486 38 1 833 2318 545667688 545669172 0.000000e+00 2527.0
3 TraesCS3B01G339500 chr3B 97.445 1370 30 2 1177 2546 545494443 545495807 0.000000e+00 2331.0
4 TraesCS3B01G339500 chr3B 96.203 869 16 5 1 855 545484398 545485263 0.000000e+00 1406.0
5 TraesCS3B01G339500 chr3B 95.378 649 26 3 2547 3193 344729945 344729299 0.000000e+00 1029.0
6 TraesCS3B01G339500 chr3B 85.366 902 106 15 1441 2326 545384559 545385450 0.000000e+00 911.0
7 TraesCS3B01G339500 chr3B 94.154 325 13 6 46 366 116083205 116082883 1.030000e-134 490.0
8 TraesCS3B01G339500 chr3B 94.099 322 9 8 49 365 521475226 521474910 6.200000e-132 481.0
9 TraesCS3B01G339500 chr3B 96.981 265 7 1 851 1115 545493494 545493757 8.130000e-121 444.0
10 TraesCS3B01G339500 chr3B 86.555 119 14 2 2334 2451 54544368 54544485 2.590000e-26 130.0
11 TraesCS3B01G339500 chr3A 91.429 1785 110 27 540 2303 531945314 531943552 0.000000e+00 2409.0
12 TraesCS3B01G339500 chr3A 84.621 1463 157 34 880 2331 531702706 531701301 0.000000e+00 1393.0
13 TraesCS3B01G339500 chr3A 88.845 251 12 8 366 603 531946154 531945907 8.660000e-76 294.0
14 TraesCS3B01G339500 chr3A 92.727 110 6 2 406 514 531945593 531945485 1.190000e-34 158.0
15 TraesCS3B01G339500 chr3A 100.000 44 0 0 602 645 531945633 531945590 7.340000e-12 82.4
16 TraesCS3B01G339500 chr3D 92.393 1525 65 28 756 2271 419386363 419387845 0.000000e+00 2126.0
17 TraesCS3B01G339500 chr3D 86.980 937 109 7 1400 2331 419515900 419516828 0.000000e+00 1042.0
18 TraesCS3B01G339500 chr3D 93.093 333 15 6 46 374 23155899 23155571 6.200000e-132 481.0
19 TraesCS3B01G339500 chr3D 81.869 535 54 23 816 1346 419515264 419515759 8.250000e-111 411.0
20 TraesCS3B01G339500 chr3D 94.203 207 12 0 2338 2544 419388133 419388339 1.850000e-82 316.0
21 TraesCS3B01G339500 chr3D 94.667 150 5 2 366 514 419385841 419385988 2.480000e-56 230.0
22 TraesCS3B01G339500 chr3D 90.667 75 1 1 651 719 419386286 419386360 9.430000e-16 95.3
23 TraesCS3B01G339500 chr5D 87.311 1521 142 35 816 2326 442012143 442010664 0.000000e+00 1692.0
24 TraesCS3B01G339500 chr5B 87.509 1409 120 25 904 2301 538039243 538037880 0.000000e+00 1576.0
25 TraesCS3B01G339500 chr5B 94.931 651 29 3 2545 3194 637989288 637989935 0.000000e+00 1016.0
26 TraesCS3B01G339500 chr4A 89.695 951 80 11 1374 2316 544381397 544382337 0.000000e+00 1197.0
27 TraesCS3B01G339500 chr4A 84.256 578 47 27 816 1375 544380764 544381315 1.020000e-144 523.0
28 TraesCS3B01G339500 chr1B 95.399 652 26 3 2545 3194 30770495 30769846 0.000000e+00 1035.0
29 TraesCS3B01G339500 chr1B 95.231 650 26 4 2546 3193 61337383 61336737 0.000000e+00 1024.0
30 TraesCS3B01G339500 chr1B 89.646 367 23 11 7 364 465368348 465367988 1.350000e-123 453.0
31 TraesCS3B01G339500 chr4B 94.923 650 30 2 2546 3194 672056675 672057322 0.000000e+00 1014.0
32 TraesCS3B01G339500 chr4B 94.640 653 30 4 2544 3194 642324517 642323868 0.000000e+00 1007.0
33 TraesCS3B01G339500 chr6B 94.915 649 29 3 2547 3194 674341269 674340624 0.000000e+00 1013.0
34 TraesCS3B01G339500 chr2B 94.761 649 30 3 2547 3194 270761976 270762621 0.000000e+00 1007.0
35 TraesCS3B01G339500 chr2B 94.624 651 32 2 2545 3194 305884667 305885315 0.000000e+00 1005.0
36 TraesCS3B01G339500 chr2B 92.814 334 17 7 46 375 35127503 35127833 8.020000e-131 477.0
37 TraesCS3B01G339500 chr5A 95.356 323 10 5 46 365 510497431 510497751 2.840000e-140 508.0
38 TraesCS3B01G339500 chr7B 94.190 327 12 6 46 369 2379962 2379640 2.860000e-135 492.0
39 TraesCS3B01G339500 chr1A 94.154 325 13 6 46 365 511219325 511219648 1.030000e-134 490.0
40 TraesCS3B01G339500 chr7D 93.846 325 14 6 46 365 534653905 534654228 4.790000e-133 484.0
41 TraesCS3B01G339500 chr7D 78.923 650 81 39 746 1364 577703242 577703866 1.070000e-104 390.0
42 TraesCS3B01G339500 chr7D 81.818 220 28 5 2327 2546 572685321 572685114 1.180000e-39 174.0
43 TraesCS3B01G339500 chr7A 80.673 683 67 43 746 1375 669771225 669771895 1.340000e-128 470.0
44 TraesCS3B01G339500 chr7A 92.063 63 5 0 2484 2546 661846117 661846055 4.390000e-14 89.8


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 TraesCS3B01G339500 chr3B 545431662 545434855 3193 False 5899.000 5899 100.00000 1 3194 1 chr3B.!!$F3 3193
1 TraesCS3B01G339500 chr3B 545561711 545563929 2218 False 3496.000 3496 95.41200 366 2545 1 chr3B.!!$F5 2179
2 TraesCS3B01G339500 chr3B 545667688 545669172 1484 False 2527.000 2527 97.37600 833 2318 1 chr3B.!!$F6 1485
3 TraesCS3B01G339500 chr3B 545484398 545485263 865 False 1406.000 1406 96.20300 1 855 1 chr3B.!!$F4 854
4 TraesCS3B01G339500 chr3B 545493494 545495807 2313 False 1387.500 2331 97.21300 851 2546 2 chr3B.!!$F7 1695
5 TraesCS3B01G339500 chr3B 344729299 344729945 646 True 1029.000 1029 95.37800 2547 3193 1 chr3B.!!$R2 646
6 TraesCS3B01G339500 chr3B 545384559 545385450 891 False 911.000 911 85.36600 1441 2326 1 chr3B.!!$F2 885
7 TraesCS3B01G339500 chr3A 531701301 531702706 1405 True 1393.000 1393 84.62100 880 2331 1 chr3A.!!$R1 1451
8 TraesCS3B01G339500 chr3A 531943552 531946154 2602 True 735.850 2409 93.25025 366 2303 4 chr3A.!!$R2 1937
9 TraesCS3B01G339500 chr3D 419515264 419516828 1564 False 726.500 1042 84.42450 816 2331 2 chr3D.!!$F2 1515
10 TraesCS3B01G339500 chr3D 419385841 419388339 2498 False 691.825 2126 92.98250 366 2544 4 chr3D.!!$F1 2178
11 TraesCS3B01G339500 chr5D 442010664 442012143 1479 True 1692.000 1692 87.31100 816 2326 1 chr5D.!!$R1 1510
12 TraesCS3B01G339500 chr5B 538037880 538039243 1363 True 1576.000 1576 87.50900 904 2301 1 chr5B.!!$R1 1397
13 TraesCS3B01G339500 chr5B 637989288 637989935 647 False 1016.000 1016 94.93100 2545 3194 1 chr5B.!!$F1 649
14 TraesCS3B01G339500 chr4A 544380764 544382337 1573 False 860.000 1197 86.97550 816 2316 2 chr4A.!!$F1 1500
15 TraesCS3B01G339500 chr1B 30769846 30770495 649 True 1035.000 1035 95.39900 2545 3194 1 chr1B.!!$R1 649
16 TraesCS3B01G339500 chr1B 61336737 61337383 646 True 1024.000 1024 95.23100 2546 3193 1 chr1B.!!$R2 647
17 TraesCS3B01G339500 chr4B 672056675 672057322 647 False 1014.000 1014 94.92300 2546 3194 1 chr4B.!!$F1 648
18 TraesCS3B01G339500 chr4B 642323868 642324517 649 True 1007.000 1007 94.64000 2544 3194 1 chr4B.!!$R1 650
19 TraesCS3B01G339500 chr6B 674340624 674341269 645 True 1013.000 1013 94.91500 2547 3194 1 chr6B.!!$R1 647
20 TraesCS3B01G339500 chr2B 270761976 270762621 645 False 1007.000 1007 94.76100 2547 3194 1 chr2B.!!$F2 647
21 TraesCS3B01G339500 chr2B 305884667 305885315 648 False 1005.000 1005 94.62400 2545 3194 1 chr2B.!!$F3 649
22 TraesCS3B01G339500 chr7D 577703242 577703866 624 False 390.000 390 78.92300 746 1364 1 chr7D.!!$F2 618
23 TraesCS3B01G339500 chr7A 669771225 669771895 670 False 470.000 470 80.67300 746 1375 1 chr7A.!!$F1 629

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
128 142 2.684881 ACAAAAGTTGACCTCACAGCAG 59.315 45.455 0.0 0.0 0.0 4.24 F
1981 3696 3.630769 TGTCCTGGATAAGCAGTACTACG 59.369 47.826 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 3748 1.006825 CTGCGTCATCGTTTCCGTCA 61.007 55.000 0.00 0.0 39.49 4.35 R
2877 4840 1.003545 ACGCGCTGCTGCTAAATAATG 60.004 47.619 5.73 0.0 36.97 1.90 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
81 94 8.466798 ACAAAATACTTGACTTACTTTTGCACT 58.533 29.630 0.00 0.0 37.18 4.40
128 142 2.684881 ACAAAAGTTGACCTCACAGCAG 59.315 45.455 0.00 0.0 0.00 4.24
1981 3696 3.630769 TGTCCTGGATAAGCAGTACTACG 59.369 47.826 0.00 0.0 0.00 3.51
2033 3748 2.665185 GGACGCCGTGCTCAACTT 60.665 61.111 0.00 0.0 0.00 2.66
2501 4462 5.168569 TCGATTAGCTCAAACCACAGTAAG 58.831 41.667 0.00 0.0 0.00 2.34
2562 4523 2.838813 GAGGGCACTACTAGGGAAAAGT 59.161 50.000 0.00 0.0 0.00 2.66
2572 4533 8.746530 CACTACTAGGGAAAAGTCTATACACAA 58.253 37.037 0.00 0.0 0.00 3.33
2645 4606 3.290776 GAGTGTGCTGGAAACTCGT 57.709 52.632 3.62 0.0 31.75 4.18
2652 4613 0.235926 GCTGGAAACTCGTTGCTGAC 59.764 55.000 0.00 0.0 0.00 3.51
2703 4664 1.202533 ACCGCGCTGCTACAAATATCT 60.203 47.619 5.56 0.0 0.00 1.98
2769 4730 2.588146 GAACCGCGCTACTGCTACGA 62.588 60.000 5.56 0.0 38.22 3.43
2776 4737 2.651701 CGCTACTGCTACGAATGTAGG 58.348 52.381 4.76 0.0 46.72 3.18
2823 4784 4.813027 CTGCTGCTACATTTCAAATTGGT 58.187 39.130 0.00 0.0 0.00 3.67
2866 4828 3.835790 TAGCGCCGTTGCCCAAAGT 62.836 57.895 2.29 0.0 34.65 2.66
2872 4835 2.829206 CGTTGCCCAAAGTGCGTGA 61.829 57.895 0.00 0.0 0.00 4.35
2877 4840 1.503542 CCCAAAGTGCGTGATGCTC 59.496 57.895 0.00 0.0 46.63 4.26
2903 4866 3.418068 GCAGCAGCGCGTTTCTCT 61.418 61.111 8.43 0.0 0.00 3.10
2904 4867 2.959357 GCAGCAGCGCGTTTCTCTT 61.959 57.895 8.43 0.0 0.00 2.85
2905 4868 1.571460 CAGCAGCGCGTTTCTCTTT 59.429 52.632 8.43 0.0 0.00 2.52
2920 4883 2.031314 TTTTCCCGCGCTACTGCA 59.969 55.556 5.56 0.0 39.64 4.41
2937 4900 2.200092 AAACCCGCACCAACCCAT 59.800 55.556 0.00 0.0 0.00 4.00
2983 4946 0.253394 CCCCCTCCTCTCTTCCCTTT 60.253 60.000 0.00 0.0 0.00 3.11
3048 5011 5.486332 TCCTCAATACTTCTCCCCCATTAT 58.514 41.667 0.00 0.0 0.00 1.28
3059 5022 6.658555 TCTCCCCCATTATTCTTTCTCTTT 57.341 37.500 0.00 0.0 0.00 2.52
3160 5124 4.431378 TCCCCTCCATAGTTGAAGTTGTA 58.569 43.478 0.00 0.0 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 237 8.102676 TGTACTCATGAGAAATGAAATCCAGAA 58.897 33.333 29.27 0.00 0.00 3.02
224 238 7.623630 TGTACTCATGAGAAATGAAATCCAGA 58.376 34.615 29.27 0.00 0.00 3.86
233 247 8.954950 ACCTTCTATTGTACTCATGAGAAATG 57.045 34.615 29.27 16.68 30.03 2.32
314 329 9.551339 ACATATGCATCCTATATGGGAAATTTT 57.449 29.630 12.36 0.00 40.92 1.82
315 330 9.193806 GACATATGCATCCTATATGGGAAATTT 57.806 33.333 12.36 0.00 40.92 1.82
316 331 7.781693 GGACATATGCATCCTATATGGGAAATT 59.218 37.037 12.36 0.75 40.92 1.82
317 332 7.293073 GGACATATGCATCCTATATGGGAAAT 58.707 38.462 12.36 8.84 40.92 2.17
1981 3696 2.631418 TTCCTGTCGATCACGTTCTC 57.369 50.000 0.00 0.00 40.69 2.87
2033 3748 1.006825 CTGCGTCATCGTTTCCGTCA 61.007 55.000 0.00 0.00 39.49 4.35
2436 4397 6.989169 CAGATAAACTAGCTAGAAATGGCTGT 59.011 38.462 27.45 0.39 39.31 4.40
2501 4462 3.870419 GCTTCTCTCCTCACATGATGAAC 59.130 47.826 0.00 0.00 36.69 3.18
2562 4523 6.258727 GCTGCTGCTAAGATTTTGTGTATAGA 59.741 38.462 8.53 0.00 36.03 1.98
2572 4533 1.709147 CCGCGCTGCTGCTAAGATTT 61.709 55.000 14.03 0.00 36.97 2.17
2645 4606 4.981806 ACTGCTAAAAACTTGTCAGCAA 57.018 36.364 0.00 0.00 41.38 3.91
2652 4613 2.495939 CGCGCTACTGCTAAAAACTTG 58.504 47.619 5.56 0.00 36.97 3.16
2769 4730 0.460311 AAGCGCGCTACTCCTACATT 59.540 50.000 36.73 12.02 0.00 2.71
2776 4737 0.645868 CCAGTAAAAGCGCGCTACTC 59.354 55.000 36.73 23.34 0.00 2.59
2877 4840 1.003545 ACGCGCTGCTGCTAAATAATG 60.004 47.619 5.73 0.00 36.97 1.90
2903 4866 1.167155 TTTGCAGTAGCGCGGGAAAA 61.167 50.000 8.83 0.00 46.23 2.29
2904 4867 1.598407 TTTGCAGTAGCGCGGGAAA 60.598 52.632 8.83 0.96 46.23 3.13
2905 4868 2.031314 TTTGCAGTAGCGCGGGAA 59.969 55.556 8.83 0.00 46.23 3.97
2920 4883 1.906333 GATGGGTTGGTGCGGGTTT 60.906 57.895 0.00 0.00 0.00 3.27
2937 4900 2.448931 ACGGGTGGGGAAAGGTGA 60.449 61.111 0.00 0.00 0.00 4.02
2983 4946 2.269040 ATGTGGGGGAGGTAGGGGA 61.269 63.158 0.00 0.00 0.00 4.81
3048 5011 8.440771 AGAGAAAGGTGGATAAAAGAGAAAGAA 58.559 33.333 0.00 0.00 0.00 2.52
3059 5022 7.502060 AATGAAGAGAGAGAAAGGTGGATAA 57.498 36.000 0.00 0.00 0.00 1.75
3160 5124 4.534103 CCTAGCTAGCTAATTTGGGAGGAT 59.466 45.833 24.20 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.