Multiple sequence alignment - TraesCS1B01G044700

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 TraesCS1B01G044700 chr1B 100.000 2552 0 0 1 2552 24708524 24711075 0.000000e+00 4713
1 TraesCS1B01G044700 chr1B 94.381 1744 53 17 669 2389 594055748 594057469 0.000000e+00 2636
2 TraesCS1B01G044700 chr1B 93.478 1748 66 10 669 2389 7580683 7578957 0.000000e+00 2553
3 TraesCS1B01G044700 chr1B 93.988 682 27 8 1 668 24695239 24695920 0.000000e+00 1020
4 TraesCS1B01G044700 chr3D 97.513 1729 35 6 669 2389 4843174 4841446 0.000000e+00 2948
5 TraesCS1B01G044700 chr3D 97.222 1728 37 4 669 2389 578771567 578769844 0.000000e+00 2915
6 TraesCS1B01G044700 chr3D 100.000 135 0 0 2393 2527 4838354 4838220 1.520000e-62 250
7 TraesCS1B01G044700 chr3B 96.827 1702 41 8 669 2364 542146895 542145201 0.000000e+00 2832
8 TraesCS1B01G044700 chr3B 94.518 1587 56 12 831 2389 513952837 513954420 0.000000e+00 2420
9 TraesCS1B01G044700 chr3B 90.616 682 53 4 1 672 776300896 776300216 0.000000e+00 894
10 TraesCS1B01G044700 chr3A 95.083 1749 56 13 669 2389 65762256 65760510 0.000000e+00 2726
11 TraesCS1B01G044700 chr3A 95.157 1590 49 7 831 2395 47065892 47067478 0.000000e+00 2484
12 TraesCS1B01G044700 chr3A 100.000 135 0 0 2393 2527 65748687 65748553 1.520000e-62 250
13 TraesCS1B01G044700 chr4A 95.011 1744 46 18 671 2389 49220330 49218603 0.000000e+00 2700
14 TraesCS1B01G044700 chr4A 95.503 1601 45 11 815 2389 676497809 676499408 0.000000e+00 2532
15 TraesCS1B01G044700 chr2D 94.333 1747 54 9 669 2389 381049090 381047363 0.000000e+00 2636
16 TraesCS1B01G044700 chr5B 93.188 1747 69 21 669 2389 358002761 358004483 0.000000e+00 2521
17 TraesCS1B01G044700 chr5B 99.275 138 1 0 2390 2527 358007640 358007777 1.520000e-62 250
18 TraesCS1B01G044700 chr7A 95.409 1590 48 11 831 2395 563484874 563483285 0.000000e+00 2508
19 TraesCS1B01G044700 chr7B 91.137 677 50 5 1 668 220528572 220529247 0.000000e+00 909
20 TraesCS1B01G044700 chr7B 91.029 680 46 12 1 669 380656111 380656786 0.000000e+00 904
21 TraesCS1B01G044700 chr2B 91.137 677 50 7 1 668 46488604 46487929 0.000000e+00 909
22 TraesCS1B01G044700 chr2B 91.952 497 22 5 1911 2389 82348824 82348328 0.000000e+00 680
23 TraesCS1B01G044700 chr4B 91.003 678 51 3 1 668 150727766 150727089 0.000000e+00 905
24 TraesCS1B01G044700 chr4B 90.133 679 55 5 1 668 197660723 197660046 0.000000e+00 872
25 TraesCS1B01G044700 chr6B 90.560 678 55 3 1 669 270451686 270452363 0.000000e+00 889
26 TraesCS1B01G044700 chr6B 90.029 682 54 7 1 668 409177136 409176455 0.000000e+00 870
27 TraesCS1B01G044700 chr6A 100.000 135 0 0 2393 2527 47962323 47962189 1.520000e-62 250
28 TraesCS1B01G044700 chr5D 99.275 138 1 0 2390 2527 404031189 404031326 1.520000e-62 250
29 TraesCS1B01G044700 chr5D 98.551 138 2 0 2390 2527 9322890 9323027 7.050000e-61 244
30 TraesCS1B01G044700 chr4D 99.259 135 1 0 2393 2527 493007115 493006981 7.050000e-61 244
31 TraesCS1B01G044700 chr1A 99.259 135 1 0 2393 2527 242719565 242719431 7.050000e-61 244
32 TraesCS1B01G044700 chr1A 99.259 135 1 0 2393 2527 381105590 381105456 7.050000e-61 244


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 TraesCS1B01G044700 chr1B 24708524 24711075 2551 False 4713.0 4713 100.0000 1 2552 1 chr1B.!!$F2 2551
1 TraesCS1B01G044700 chr1B 594055748 594057469 1721 False 2636.0 2636 94.3810 669 2389 1 chr1B.!!$F3 1720
2 TraesCS1B01G044700 chr1B 7578957 7580683 1726 True 2553.0 2553 93.4780 669 2389 1 chr1B.!!$R1 1720
3 TraesCS1B01G044700 chr1B 24695239 24695920 681 False 1020.0 1020 93.9880 1 668 1 chr1B.!!$F1 667
4 TraesCS1B01G044700 chr3D 578769844 578771567 1723 True 2915.0 2915 97.2220 669 2389 1 chr3D.!!$R1 1720
5 TraesCS1B01G044700 chr3D 4838220 4843174 4954 True 1599.0 2948 98.7565 669 2527 2 chr3D.!!$R2 1858
6 TraesCS1B01G044700 chr3B 542145201 542146895 1694 True 2832.0 2832 96.8270 669 2364 1 chr3B.!!$R1 1695
7 TraesCS1B01G044700 chr3B 513952837 513954420 1583 False 2420.0 2420 94.5180 831 2389 1 chr3B.!!$F1 1558
8 TraesCS1B01G044700 chr3B 776300216 776300896 680 True 894.0 894 90.6160 1 672 1 chr3B.!!$R2 671
9 TraesCS1B01G044700 chr3A 65760510 65762256 1746 True 2726.0 2726 95.0830 669 2389 1 chr3A.!!$R2 1720
10 TraesCS1B01G044700 chr3A 47065892 47067478 1586 False 2484.0 2484 95.1570 831 2395 1 chr3A.!!$F1 1564
11 TraesCS1B01G044700 chr4A 49218603 49220330 1727 True 2700.0 2700 95.0110 671 2389 1 chr4A.!!$R1 1718
12 TraesCS1B01G044700 chr4A 676497809 676499408 1599 False 2532.0 2532 95.5030 815 2389 1 chr4A.!!$F1 1574
13 TraesCS1B01G044700 chr2D 381047363 381049090 1727 True 2636.0 2636 94.3330 669 2389 1 chr2D.!!$R1 1720
14 TraesCS1B01G044700 chr5B 358002761 358007777 5016 False 1385.5 2521 96.2315 669 2527 2 chr5B.!!$F1 1858
15 TraesCS1B01G044700 chr7A 563483285 563484874 1589 True 2508.0 2508 95.4090 831 2395 1 chr7A.!!$R1 1564
16 TraesCS1B01G044700 chr7B 220528572 220529247 675 False 909.0 909 91.1370 1 668 1 chr7B.!!$F1 667
17 TraesCS1B01G044700 chr7B 380656111 380656786 675 False 904.0 904 91.0290 1 669 1 chr7B.!!$F2 668
18 TraesCS1B01G044700 chr2B 46487929 46488604 675 True 909.0 909 91.1370 1 668 1 chr2B.!!$R1 667
19 TraesCS1B01G044700 chr4B 150727089 150727766 677 True 905.0 905 91.0030 1 668 1 chr4B.!!$R1 667
20 TraesCS1B01G044700 chr4B 197660046 197660723 677 True 872.0 872 90.1330 1 668 1 chr4B.!!$R2 667
21 TraesCS1B01G044700 chr6B 270451686 270452363 677 False 889.0 889 90.5600 1 669 1 chr6B.!!$F1 668
22 TraesCS1B01G044700 chr6B 409176455 409177136 681 True 870.0 870 90.0290 1 668 1 chr6B.!!$R1 667

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
123 136 1.063867 ACTCGTACATACCCTCAGCCT 60.064 52.381 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2129 1.329906 GATCATCTCAGCAAGTTGCCG 59.67 52.381 24.02 14.69 46.52 5.69 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
106 119 4.573201 ACGAGAGAGAACACATAGCTACTC 59.427 45.833 0.00 0.0 0.00 2.59
123 136 1.063867 ACTCGTACATACCCTCAGCCT 60.064 52.381 0.00 0.0 0.00 4.58
613 637 2.641815 AGCCCAATATTGCCCAAAACAA 59.358 40.909 10.11 0.0 0.00 2.83
771 795 8.258007 CCTGTTTAGGTGAGTAATTGAGTATGA 58.742 37.037 0.00 0.0 39.39 2.15
801 825 6.328934 TGGATTCAGTTATGCCTAGTGGATTA 59.671 38.462 0.00 0.0 34.57 1.75
1195 1225 7.555554 CCAAGTTGAAGAAGGACTATGATCATT 59.444 37.037 14.65 0.0 0.00 2.57
1312 1342 4.624015 TGCTGAAAAATTTGAGAAGCAGG 58.376 39.130 11.79 0.0 34.46 4.85
1344 1380 3.134262 TGGAGATGAAGATGGAGAAGCTG 59.866 47.826 0.00 0.0 0.00 4.24
2007 2057 1.132913 CCAGGGAGAGATGGATCCTGA 60.133 57.143 14.23 0.0 45.66 3.86
2078 2129 1.194781 TGCAAGGAGGAGGGTGAGAC 61.195 60.000 0.00 0.0 0.00 3.36
2108 2159 2.852449 CTGAGATGATCCTTGCAGCAT 58.148 47.619 0.00 0.0 0.00 3.79
2276 2328 5.714333 ACCCATGATGCTGTTGTTATGTTTA 59.286 36.000 0.00 0.0 0.00 2.01
2389 2458 6.127925 TGCAATGTATGAAGATGGTGAAAGAC 60.128 38.462 0.00 0.0 0.00 3.01
2533 5842 5.195001 GGCACCAAACAATAACTTTCTCA 57.805 39.130 0.00 0.0 0.00 3.27
2534 5843 5.596845 GGCACCAAACAATAACTTTCTCAA 58.403 37.500 0.00 0.0 0.00 3.02
2535 5844 6.045955 GGCACCAAACAATAACTTTCTCAAA 58.954 36.000 0.00 0.0 0.00 2.69
2536 5845 6.200854 GGCACCAAACAATAACTTTCTCAAAG 59.799 38.462 0.00 0.0 44.10 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.739276 TTGTAGTTGGATCTTATGATGTTTCTT 57.261 29.630 0.00 0.00 32.19 2.52
106 119 0.311165 CGAGGCTGAGGGTATGTACG 59.689 60.000 0.00 0.00 0.00 3.67
123 136 3.277962 GGGAGTAGTTCACCCTCGA 57.722 57.895 0.00 0.00 42.53 4.04
227 241 1.339929 CTGTAGCCACCAAAAACCACC 59.660 52.381 0.00 0.00 0.00 4.61
317 332 3.467226 CCGACGTACCCCCTGCAT 61.467 66.667 0.00 0.00 0.00 3.96
367 388 2.032860 CTCACGAGGGTAGGGGCATG 62.033 65.000 0.00 0.00 0.00 4.06
368 389 1.762460 CTCACGAGGGTAGGGGCAT 60.762 63.158 0.00 0.00 0.00 4.40
369 390 2.363795 CTCACGAGGGTAGGGGCA 60.364 66.667 0.00 0.00 0.00 5.36
589 613 3.625649 TTTGGGCAATATTGGGCTTTC 57.374 42.857 17.02 0.00 0.00 2.62
771 795 2.515429 AGGCATAACTGAATCCACCCAT 59.485 45.455 0.00 0.00 0.00 4.00
826 853 6.040955 CACTAGGCATAACTGAATCCACTAGA 59.959 42.308 0.00 0.00 32.11 2.43
1195 1225 7.112122 ACCATTTTATGATACTCAGTGCAGAA 58.888 34.615 0.00 0.00 0.00 3.02
1296 1326 5.388654 TCTTCCTCCTGCTTCTCAAATTTT 58.611 37.500 0.00 0.00 0.00 1.82
1312 1342 3.030291 TCTTCATCTCCAGCTCTTCCTC 58.970 50.000 0.00 0.00 0.00 3.71
1344 1380 4.006319 ACATCTGTTCTTTTGCTAGCCTC 58.994 43.478 13.29 0.00 0.00 4.70
1815 1857 9.640952 ACATTGTATACATAATGGTTTTAGGCT 57.359 29.630 17.71 0.00 37.52 4.58
2007 2057 6.439487 TCTTCTTCTCCATCTATGACCTCTT 58.561 40.000 0.00 0.00 0.00 2.85
2078 2129 1.329906 GATCATCTCAGCAAGTTGCCG 59.670 52.381 24.02 14.69 46.52 5.69
2389 2458 4.037446 GGAGCTTGTGGAGAGAGTACATAG 59.963 50.000 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.