Multiple sequence alignment - TraesCS1A01G406700

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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 TraesCS1A01G406700 chr1A 100.000 3029 0 0 1 3029 569254699 569257727 0.000000e+00 5594.0
1 TraesCS1A01G406700 chr1A 81.075 1395 236 24 997 2377 125150289 125151669 0.000000e+00 1088.0
2 TraesCS1A01G406700 chr4A 97.730 3039 47 6 1 3029 624835603 624832577 0.000000e+00 5210.0
3 TraesCS1A01G406700 chr4A 79.934 304 41 8 2676 2961 152575963 152575662 3.960000e-49 206.0
4 TraesCS1A01G406700 chr5D 91.244 1816 122 18 850 2632 545113067 545111256 0.000000e+00 2438.0
5 TraesCS1A01G406700 chr5D 91.390 1475 113 7 980 2442 544896766 544895294 0.000000e+00 2008.0
6 TraesCS1A01G406700 chr5D 86.877 602 62 11 1850 2442 544890646 544890053 0.000000e+00 658.0
7 TraesCS1A01G406700 chr5B 89.622 1773 132 21 855 2597 687694594 687696344 0.000000e+00 2207.0
8 TraesCS1A01G406700 chr5B 92.003 1288 85 5 944 2213 687469769 687468482 0.000000e+00 1792.0
9 TraesCS1A01G406700 chr5B 80.456 307 42 13 2672 2961 505606459 505606764 5.080000e-53 219.0
10 TraesCS1A01G406700 chr5B 79.538 303 43 14 2676 2961 635804254 635803954 6.620000e-47 198.0
11 TraesCS1A01G406700 chr5B 91.176 68 3 3 2965 3029 687696389 687696456 4.160000e-14 89.8
12 TraesCS1A01G406700 chr5A 88.624 1468 156 5 996 2455 624708253 624706789 0.000000e+00 1775.0
13 TraesCS1A01G406700 chr5A 80.062 321 44 10 2676 2977 524008379 524008698 1.410000e-53 220.0
14 TraesCS1A01G406700 chr5A 79.276 304 46 12 2672 2958 522114000 522113697 2.380000e-46 196.0
15 TraesCS1A01G406700 chr5A 88.636 132 14 1 2831 2961 364977593 364977462 3.130000e-35 159.0
16 TraesCS1A01G406700 chr7A 96.711 760 22 2 1 760 90023688 90022932 0.000000e+00 1262.0
17 TraesCS1A01G406700 chr2A 98.462 715 9 2 50 763 755071640 755070927 0.000000e+00 1258.0
18 TraesCS1A01G406700 chr2A 97.606 710 14 3 50 757 739851721 739851013 0.000000e+00 1214.0
19 TraesCS1A01G406700 chr1D 80.888 1397 236 27 997 2377 114645756 114647137 0.000000e+00 1072.0
20 TraesCS1A01G406700 chr1B 80.474 1393 241 26 1001 2377 175661158 175662535 0.000000e+00 1037.0
21 TraesCS1A01G406700 chr6B 82.178 303 37 6 2676 2961 680182303 680182605 8.390000e-61 244.0
22 TraesCS1A01G406700 chr6B 88.710 62 7 0 2522 2583 246678496 246678435 3.240000e-10 76.8
23 TraesCS1A01G406700 chr6B 90.566 53 5 0 2531 2583 246514769 246514717 1.510000e-08 71.3
24 TraesCS1A01G406700 chr4B 82.692 260 43 1 2707 2964 579398892 579399151 2.350000e-56 230.0
25 TraesCS1A01G406700 chr3D 81.188 303 39 8 2676 2961 299692337 299692638 8.450000e-56 228.0
26 TraesCS1A01G406700 chr3D 80.328 305 40 14 2676 2962 561831436 561831738 2.370000e-51 213.0
27 TraesCS1A01G406700 chr2D 81.126 302 37 14 2676 2959 81245094 81244795 1.090000e-54 224.0
28 TraesCS1A01G406700 chr2D 80.392 306 40 11 2676 2963 649373526 649373829 6.580000e-52 215.0
29 TraesCS1A01G406700 chr2D 79.070 301 45 7 2676 2959 37051634 37051335 1.110000e-44 191.0
30 TraesCS1A01G406700 chr6D 80.488 287 34 10 2676 2962 424770314 424770050 1.840000e-47 200.0
31 TraesCS1A01G406700 chr6D 88.710 62 7 0 2522 2583 139320808 139320747 3.240000e-10 76.8
32 TraesCS1A01G406700 chr7B 92.437 119 8 1 2847 2964 384361138 384361256 5.190000e-38 169.0
33 TraesCS1A01G406700 chr7B 87.755 147 11 7 2846 2990 39465787 39465928 6.720000e-37 165.0
34 TraesCS1A01G406700 chr7B 89.062 64 7 0 2520 2583 697931285 697931222 2.500000e-11 80.5
35 TraesCS1A01G406700 chr3B 88.406 138 13 3 2846 2983 702862848 702862714 2.420000e-36 163.0
36 TraesCS1A01G406700 chr2B 88.806 134 12 2 2831 2961 53455831 53455698 8.690000e-36 161.0
37 TraesCS1A01G406700 chrUn 90.566 53 5 0 2531 2583 190888291 190888239 1.510000e-08 71.3
38 TraesCS1A01G406700 chrUn 85.294 68 10 0 2516 2583 355878533 355878600 1.510000e-08 71.3


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 TraesCS1A01G406700 chr1A 569254699 569257727 3028 False 5594.0 5594 100.000 1 3029 1 chr1A.!!$F2 3028
1 TraesCS1A01G406700 chr1A 125150289 125151669 1380 False 1088.0 1088 81.075 997 2377 1 chr1A.!!$F1 1380
2 TraesCS1A01G406700 chr4A 624832577 624835603 3026 True 5210.0 5210 97.730 1 3029 1 chr4A.!!$R2 3028
3 TraesCS1A01G406700 chr5D 545111256 545113067 1811 True 2438.0 2438 91.244 850 2632 1 chr5D.!!$R3 1782
4 TraesCS1A01G406700 chr5D 544895294 544896766 1472 True 2008.0 2008 91.390 980 2442 1 chr5D.!!$R2 1462
5 TraesCS1A01G406700 chr5D 544890053 544890646 593 True 658.0 658 86.877 1850 2442 1 chr5D.!!$R1 592
6 TraesCS1A01G406700 chr5B 687468482 687469769 1287 True 1792.0 1792 92.003 944 2213 1 chr5B.!!$R2 1269
7 TraesCS1A01G406700 chr5B 687694594 687696456 1862 False 1148.4 2207 90.399 855 3029 2 chr5B.!!$F2 2174
8 TraesCS1A01G406700 chr5A 624706789 624708253 1464 True 1775.0 1775 88.624 996 2455 1 chr5A.!!$R3 1459
9 TraesCS1A01G406700 chr7A 90022932 90023688 756 True 1262.0 1262 96.711 1 760 1 chr7A.!!$R1 759
10 TraesCS1A01G406700 chr2A 755070927 755071640 713 True 1258.0 1258 98.462 50 763 1 chr2A.!!$R2 713
11 TraesCS1A01G406700 chr2A 739851013 739851721 708 True 1214.0 1214 97.606 50 757 1 chr2A.!!$R1 707
12 TraesCS1A01G406700 chr1D 114645756 114647137 1381 False 1072.0 1072 80.888 997 2377 1 chr1D.!!$F1 1380
13 TraesCS1A01G406700 chr1B 175661158 175662535 1377 False 1037.0 1037 80.474 1001 2377 1 chr1B.!!$F1 1376

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
42 43 0.169672 CTCCGGCGTCTTCGTTCTAA 59.830 55.0 6.01 0.0 39.49 2.10 F
720 723 0.384309 CATCGACGGGGAGAATTCGA 59.616 55.0 0.00 0.0 44.06 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1432 4.778143 GGGATGTCAAGCCGGCGT 62.778 66.667 23.2 16.9 30.11 5.68 R
2295 2349 0.682852 CGTATTTCCGCCCCCTCATA 59.317 55.000 0.0 0.0 0.00 2.15 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
41 42 1.651240 CCTCCGGCGTCTTCGTTCTA 61.651 60.000 6.01 0.00 39.49 2.10
42 43 0.169672 CTCCGGCGTCTTCGTTCTAA 59.830 55.000 6.01 0.00 39.49 2.10
218 219 0.674581 CTTGGTGAAGCGCTGATGGA 60.675 55.000 12.58 0.00 0.00 3.41
526 527 7.531716 TCGAAATTTGGCAAGTTATAAATCGT 58.468 30.769 19.13 0.57 0.00 3.73
612 613 2.036475 GCCTGGACAGATACGATGTGAT 59.964 50.000 0.00 0.00 0.00 3.06
641 643 3.333804 GGTCGTATAACCGTGGGAAAAA 58.666 45.455 0.00 0.00 0.00 1.94
714 717 1.341209 CATGATTCATCGACGGGGAGA 59.659 52.381 0.00 0.00 0.00 3.71
720 723 0.384309 CATCGACGGGGAGAATTCGA 59.616 55.000 0.00 0.00 44.06 3.71
775 778 1.671850 CGTGTAAACGGCATCACCTCT 60.672 52.381 0.00 0.00 35.61 3.69
790 793 4.492160 TCTGCATCGTCCGTCCGC 62.492 66.667 0.00 0.00 0.00 5.54
1578 1618 3.936203 AAGGCCACGTCGCTTGGA 61.936 61.111 5.01 0.00 36.02 3.53
2295 2349 1.078848 GCGTTGAGGGAGCTGATGT 60.079 57.895 0.00 0.00 0.00 3.06
2529 2587 5.069501 ACATGTACTTAGTTCCTTCGTCC 57.930 43.478 0.00 0.00 0.00 4.79
2716 2784 2.930040 ACACAAGCGCTCATATACACAC 59.070 45.455 12.06 0.00 0.00 3.82
2724 2792 3.119628 CGCTCATATACACACGCATACAC 59.880 47.826 0.00 0.00 0.00 2.90
2729 2797 6.512297 TCATATACACACGCATACACTCAAT 58.488 36.000 0.00 0.00 0.00 2.57
2786 2854 2.608261 CGCTTCTCTGAAAGACCGAGTT 60.608 50.000 0.00 0.00 38.67 3.01
2812 2880 9.114952 TGGCATATCATCTTAAAATTTACGACA 57.885 29.630 0.00 0.00 0.00 4.35
2820 2888 8.597227 CATCTTAAAATTTACGACATCACCGTA 58.403 33.333 0.00 0.00 40.95 4.02
2854 2922 5.414144 TCATCTTGAAATTTACGCATCACCA 59.586 36.000 0.00 0.00 0.00 4.17
2855 2923 5.697473 TCTTGAAATTTACGCATCACCAA 57.303 34.783 0.00 0.00 0.00 3.67
2866 2934 4.805219 ACGCATCACCAAAAATCCTAAAC 58.195 39.130 0.00 0.00 0.00 2.01
2872 2940 9.087424 GCATCACCAAAAATCCTAAACTAAATC 57.913 33.333 0.00 0.00 0.00 2.17
2900 2968 6.389830 AATAAATGCGAGCACCATGATTTA 57.610 33.333 0.00 1.06 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 219 3.119495 GCACCGTAATGCATTTTCTTCCT 60.119 43.478 18.75 0.00 45.39 3.36
456 457 5.500234 CTCATGTGAGTTCTTTCCCCAATA 58.500 41.667 1.84 0.00 37.40 1.90
526 527 3.196385 TTGCCCCATCCACCCCAA 61.196 61.111 0.00 0.00 0.00 4.12
641 643 4.324267 CAACCAACGATTCCCTAGTTCTT 58.676 43.478 0.00 0.00 0.00 2.52
677 680 2.822255 GTGGATTAGCGCGCCCAA 60.822 61.111 30.33 22.73 0.00 4.12
714 717 4.794241 GCGCGCGCAACTCGAATT 62.794 61.111 46.11 0.00 41.67 2.17
790 793 1.999735 ACGTGCATTATCAACAGACGG 59.000 47.619 0.00 0.00 0.00 4.79
1398 1432 4.778143 GGGATGTCAAGCCGGCGT 62.778 66.667 23.20 16.90 30.11 5.68
2295 2349 0.682852 CGTATTTCCGCCCCCTCATA 59.317 55.000 0.00 0.00 0.00 2.15
2529 2587 8.667987 TTCATTTTCTTCGACAAATAATTCCG 57.332 30.769 0.00 0.00 0.00 4.30
2716 2784 5.388475 GCGTTTATAGGATTGAGTGTATGCG 60.388 44.000 0.00 0.00 0.00 4.73
2724 2792 4.034048 GGTGTGTGCGTTTATAGGATTGAG 59.966 45.833 0.00 0.00 0.00 3.02
2729 2797 1.624312 TGGGTGTGTGCGTTTATAGGA 59.376 47.619 0.00 0.00 0.00 2.94
2786 2854 9.114952 TGTCGTAAATTTTAAGATGATATGCCA 57.885 29.630 7.83 0.00 0.00 4.92
2866 2934 6.634436 GTGCTCGCATTTATTTCTGGATTTAG 59.366 38.462 0.00 0.00 0.00 1.85
2872 2940 2.423185 TGGTGCTCGCATTTATTTCTGG 59.577 45.455 0.00 0.00 0.00 3.86
2927 2995 3.591527 TGTGGTTGGATGGTTAGAGGAAT 59.408 43.478 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.