Multiple sequence alignment - TraesCS1D01G140900

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 TraesCS1D01G140900 chr1D 100.000 2360 0 0 1 2360 194203124 194200765 0.000000e+00 4359.0
1 TraesCS1D01G140900 chr1D 95.195 666 19 7 1 662 273565428 273566084 0.000000e+00 1040.0
2 TraesCS1D01G140900 chr1D 92.544 684 25 15 1 659 48465068 48464386 0.000000e+00 957.0
3 TraesCS1D01G140900 chr1D 85.806 155 19 2 686 840 484544085 484543934 6.750000e-36 161.0
4 TraesCS1D01G140900 chr1A 91.461 1745 81 21 658 2354 241377890 241376166 0.000000e+00 2335.0
5 TraesCS1D01G140900 chr1B 92.657 926 36 9 1442 2359 268898911 268898010 0.000000e+00 1304.0
6 TraesCS1D01G140900 chr1B 91.783 791 42 9 658 1427 268899780 268898992 0.000000e+00 1079.0
7 TraesCS1D01G140900 chr7D 97.428 661 14 3 1 659 58202273 58202932 0.000000e+00 1123.0
8 TraesCS1D01G140900 chr7D 97.143 665 16 3 1 662 548099156 548098492 0.000000e+00 1120.0
9 TraesCS1D01G140900 chr7D 94.737 38 2 0 2321 2358 156034402 156034439 2.530000e-05 60.2
10 TraesCS1D01G140900 chr4D 97.428 661 13 4 1 659 470144203 470143545 0.000000e+00 1123.0
11 TraesCS1D01G140900 chr4D 96.375 662 13 5 1 660 503851326 503851978 0.000000e+00 1079.0
12 TraesCS1D01G140900 chr4D 85.897 156 17 3 686 840 459818951 459819102 6.750000e-36 161.0
13 TraesCS1D01G140900 chr4D 94.286 35 2 0 2325 2359 69399529 69399563 1.000000e-03 54.7
14 TraesCS1D01G140900 chr2D 97.281 662 14 4 1 660 9559276 9559935 0.000000e+00 1120.0
15 TraesCS1D01G140900 chr2D 97.321 560 13 2 1 558 539237406 539236847 0.000000e+00 950.0
16 TraesCS1D01G140900 chr5D 96.823 661 17 4 1 659 417445651 417444993 0.000000e+00 1101.0
17 TraesCS1D01G140900 chr3D 92.398 684 26 12 1 659 545826981 545826299 0.000000e+00 952.0
18 TraesCS1D01G140900 chr3D 92.105 684 27 14 1 659 2283703 2284384 0.000000e+00 939.0
19 TraesCS1D01G140900 chr6A 85.465 172 21 4 675 844 64321679 64321510 2.410000e-40 176.0
20 TraesCS1D01G140900 chr6D 85.714 168 20 2 675 841 141974329 141974493 8.670000e-40 174.0
21 TraesCS1D01G140900 chr5B 85.897 156 20 2 687 841 247347997 247348151 5.220000e-37 165.0
22 TraesCS1D01G140900 chr5B 100.000 28 0 0 2331 2358 40753229 40753202 4.000000e-03 52.8
23 TraesCS1D01G140900 chr2B 85.897 156 19 1 685 840 727715103 727714951 1.880000e-36 163.0
24 TraesCS1D01G140900 chrUn 85.806 155 19 1 686 840 320881588 320881739 6.750000e-36 161.0
25 TraesCS1D01G140900 chr3B 81.579 190 26 5 660 844 629587706 629587891 5.260000e-32 148.0


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 TraesCS1D01G140900 chr1D 194200765 194203124 2359 True 4359.0 4359 100.000 1 2360 1 chr1D.!!$R2 2359
1 TraesCS1D01G140900 chr1D 273565428 273566084 656 False 1040.0 1040 95.195 1 662 1 chr1D.!!$F1 661
2 TraesCS1D01G140900 chr1D 48464386 48465068 682 True 957.0 957 92.544 1 659 1 chr1D.!!$R1 658
3 TraesCS1D01G140900 chr1A 241376166 241377890 1724 True 2335.0 2335 91.461 658 2354 1 chr1A.!!$R1 1696
4 TraesCS1D01G140900 chr1B 268898010 268899780 1770 True 1191.5 1304 92.220 658 2359 2 chr1B.!!$R1 1701
5 TraesCS1D01G140900 chr7D 58202273 58202932 659 False 1123.0 1123 97.428 1 659 1 chr7D.!!$F1 658
6 TraesCS1D01G140900 chr7D 548098492 548099156 664 True 1120.0 1120 97.143 1 662 1 chr7D.!!$R1 661
7 TraesCS1D01G140900 chr4D 470143545 470144203 658 True 1123.0 1123 97.428 1 659 1 chr4D.!!$R1 658
8 TraesCS1D01G140900 chr4D 503851326 503851978 652 False 1079.0 1079 96.375 1 660 1 chr4D.!!$F3 659
9 TraesCS1D01G140900 chr2D 9559276 9559935 659 False 1120.0 1120 97.281 1 660 1 chr2D.!!$F1 659
10 TraesCS1D01G140900 chr2D 539236847 539237406 559 True 950.0 950 97.321 1 558 1 chr2D.!!$R1 557
11 TraesCS1D01G140900 chr5D 417444993 417445651 658 True 1101.0 1101 96.823 1 659 1 chr5D.!!$R1 658
12 TraesCS1D01G140900 chr3D 545826299 545826981 682 True 952.0 952 92.398 1 659 1 chr3D.!!$R1 658
13 TraesCS1D01G140900 chr3D 2283703 2284384 681 False 939.0 939 92.105 1 659 1 chr3D.!!$F1 658

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
80 81 0.178964 CCCAACTTCACCACCACCAT 60.179 55.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 1697 0.6603 GGGCACGAAACAAAAGCGAG 60.66 55.0 0.0 0.0 0.0 5.03 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
80 81 0.178964 CCCAACTTCACCACCACCAT 60.179 55.000 0.00 0.00 0.00 3.55
585 614 1.589727 CGGGCCGACGGTGTATTAC 60.590 63.158 24.41 0.00 0.00 1.89
683 713 5.248477 GGTTGTAGATGCTCTTATATCCCCA 59.752 44.000 0.00 0.00 0.00 4.96
684 714 6.069963 GGTTGTAGATGCTCTTATATCCCCAT 60.070 42.308 0.00 0.00 0.00 4.00
770 801 8.021973 ACGTAGTTTAGAGTGTAGATTGACTTG 58.978 37.037 0.00 0.00 37.78 3.16
778 809 6.203723 AGAGTGTAGATTGACTTGTTTTGCTC 59.796 38.462 0.00 0.00 0.00 4.26
783 814 6.305693 AGATTGACTTGTTTTGCTCTGTAC 57.694 37.500 0.00 0.00 0.00 2.90
795 831 5.847111 TTGCTCTGTACGTAGTCCATATT 57.153 39.130 0.00 0.00 43.93 1.28
796 832 6.947644 TTGCTCTGTACGTAGTCCATATTA 57.052 37.500 0.00 0.00 43.93 0.98
797 833 6.947644 TGCTCTGTACGTAGTCCATATTAA 57.052 37.500 0.00 0.00 43.93 1.40
841 881 9.520204 TTTATATTTAGAAACGAAGGGAGTACG 57.480 33.333 0.00 0.00 0.00 3.67
842 882 4.853924 TTTAGAAACGAAGGGAGTACGT 57.146 40.909 0.00 0.00 41.97 3.57
854 894 6.311445 CGAAGGGAGTACGTACGTATATGTAT 59.689 42.308 29.05 15.47 35.66 2.29
905 945 6.878389 GCCTGATCTTTCTATAAATAGCTGCT 59.122 38.462 7.57 7.57 0.00 4.24
970 1010 3.235195 GTCACTGCTTACTAGACACACG 58.765 50.000 0.00 0.00 0.00 4.49
1062 1114 2.361610 CCATGGGGCAAGTTCGCT 60.362 61.111 2.85 0.00 0.00 4.93
1433 1487 6.536224 GGCCTACACAAATACATACGTAAACT 59.464 38.462 0.00 0.00 0.00 2.66
1434 1488 7.706179 GGCCTACACAAATACATACGTAAACTA 59.294 37.037 0.00 0.00 0.00 2.24
1536 1658 3.367630 GCATTTAGTTGCAATTTCCACCG 59.632 43.478 0.59 0.00 42.31 4.94
1563 1685 6.936335 TGGACCAATGTCATATATGCTACAAG 59.064 38.462 7.92 5.83 43.65 3.16
1655 1778 6.807230 ACGTACTTCTGTGATGAATGAACTAC 59.193 38.462 0.00 0.00 0.00 2.73
1697 1824 5.107133 AGGCAATATGTACGTGTTACTGTC 58.893 41.667 0.00 0.00 0.00 3.51
1824 1951 0.455410 TTGAGCCGCCATTGTAATGC 59.545 50.000 0.00 0.00 35.08 3.56
2161 2300 7.553044 ACCATTGGCTAGATCTAGTAAACAAAC 59.447 37.037 26.73 10.51 35.65 2.93
2195 2335 0.370273 CGGCTGCTCACGTGATTAAC 59.630 55.000 20.40 9.69 0.00 2.01
2211 2351 9.968870 ACGTGATTAACTATTAAGGAATCTCTC 57.031 33.333 0.00 0.00 33.50 3.20
2214 2354 9.967346 TGATTAACTATTAAGGAATCTCTCGTG 57.033 33.333 0.00 0.00 33.50 4.35
2224 2364 4.039730 AGGAATCTCTCGTGGGTTCATATG 59.960 45.833 0.00 0.00 0.00 1.78
2305 2445 1.214062 CCTCTCTCGTCACTGCCAC 59.786 63.158 0.00 0.00 0.00 5.01
2356 2496 7.885399 AGGCTTTCACCCTGCTTTATATATAAG 59.115 37.037 5.36 2.45 0.00 1.73
2359 2499 6.952605 TCACCCTGCTTTATATATAAGGCT 57.047 37.500 29.13 14.17 43.32 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 1.174783 GTAGCTCGTGGAGGTGAAGA 58.825 55.000 7.54 0.00 40.75 2.87
464 493 4.707840 CACTTGTCGCACGCGCAG 62.708 66.667 5.73 0.00 38.40 5.18
765 796 4.743644 ACTACGTACAGAGCAAAACAAGTC 59.256 41.667 0.00 0.00 0.00 3.01
770 801 3.645884 TGGACTACGTACAGAGCAAAAC 58.354 45.455 0.00 0.00 0.00 2.43
831 871 6.936900 ACATACATATACGTACGTACTCCCTT 59.063 38.462 28.99 15.22 33.01 3.95
854 894 0.248012 CCGGGCATGTACAGTGTACA 59.752 55.000 32.40 32.40 0.00 2.90
905 945 0.966179 TGACTAGCTTTGGACAGCGA 59.034 50.000 0.00 0.00 45.24 4.93
970 1010 2.546789 GAGAGAGAGCGAGCTAGGTAAC 59.453 54.545 0.00 0.00 0.00 2.50
1047 1099 3.064324 GCAGCGAACTTGCCCCAT 61.064 61.111 0.00 0.00 35.54 4.00
1062 1114 3.458163 GGGTCACGGATCTCGGCA 61.458 66.667 8.20 0.00 44.45 5.69
1213 1265 4.194720 CGAAGACGAGCCGGAGGG 62.195 72.222 5.05 0.00 46.33 4.30
1433 1487 6.850752 ATGGATGTGGTATGATCGTGTATA 57.149 37.500 0.00 0.00 0.00 1.47
1434 1488 5.745312 ATGGATGTGGTATGATCGTGTAT 57.255 39.130 0.00 0.00 0.00 2.29
1437 1491 4.872124 CCATATGGATGTGGTATGATCGTG 59.128 45.833 17.49 0.00 34.70 4.35
1438 1492 4.080919 CCCATATGGATGTGGTATGATCGT 60.081 45.833 24.00 0.00 37.36 3.73
1439 1493 4.445453 CCCATATGGATGTGGTATGATCG 58.555 47.826 24.00 0.00 37.36 3.69
1440 1494 4.202441 GCCCATATGGATGTGGTATGATC 58.798 47.826 24.00 0.00 37.36 2.92
1536 1658 4.330250 AGCATATATGACATTGGTCCAGC 58.670 43.478 17.10 0.00 43.65 4.85
1574 1697 0.660300 GGGCACGAAACAAAAGCGAG 60.660 55.000 0.00 0.00 0.00 5.03
1655 1778 5.845103 TGCCTTGTTTTGCCATGATATATG 58.155 37.500 0.00 0.00 0.00 1.78
1824 1951 4.330620 GGTTTGCAATTGCCACATTGATAG 59.669 41.667 26.94 0.00 41.18 2.08
2195 2335 5.793030 ACCCACGAGAGATTCCTTAATAG 57.207 43.478 0.00 0.00 0.00 1.73
2211 2351 2.898729 AGCTCTCATATGAACCCACG 57.101 50.000 6.90 0.00 0.00 4.94
2214 2354 3.891049 ACCAAAGCTCTCATATGAACCC 58.109 45.455 6.90 0.00 0.00 4.11
2224 2364 4.496360 GGAGTACTTGTACCAAAGCTCTC 58.504 47.826 0.00 0.86 33.37 3.20
2313 2453 1.754226 GCCTGGTTCGAGAGAGAGAAT 59.246 52.381 0.00 0.00 43.69 2.40
2314 2454 1.178276 GCCTGGTTCGAGAGAGAGAA 58.822 55.000 0.00 0.00 43.69 2.87
2317 2457 1.546476 GAAAGCCTGGTTCGAGAGAGA 59.454 52.381 0.00 0.00 43.69 3.10


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

AutoCloner maintained by Alex Coulton.