Multiple sequence alignment - TraesCS5D01G476500

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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 TraesCS5D01G476500 chr5D 100.000 2919 0 0 1 2919 515425983 515423065 0.000000e+00 5391
1 TraesCS5D01G476500 chr5D 94.924 788 25 10 14 787 450544825 450544039 0.000000e+00 1219
2 TraesCS5D01G476500 chr5D 84.525 1189 158 17 1027 2207 515466210 515465040 0.000000e+00 1153
3 TraesCS5D01G476500 chr5D 86.093 604 80 4 1608 2209 515568278 515567677 0.000000e+00 647
4 TraesCS5D01G476500 chr5D 86.446 605 63 12 986 1582 515568865 515568272 0.000000e+00 645
5 TraesCS5D01G476500 chr5D 85.880 602 82 3 1608 2207 551243507 551242907 3.170000e-179 638
6 TraesCS5D01G476500 chr5D 85.950 605 67 11 986 1582 551244095 551243501 5.310000e-177 630
7 TraesCS5D01G476500 chr5D 82.886 596 87 10 1613 2205 515411857 515411274 3.330000e-144 521
8 TraesCS5D01G476500 chr5B 93.530 1422 69 13 790 2207 648181062 648179660 0.000000e+00 2095
9 TraesCS5D01G476500 chr5B 86.106 1202 136 23 1027 2205 648260541 648259348 0.000000e+00 1266
10 TraesCS5D01G476500 chr5B 81.650 703 104 19 1515 2207 648145429 648144742 7.060000e-156 560
11 TraesCS5D01G476500 chr5B 88.889 441 48 1 986 1425 647994573 647994133 2.560000e-150 542
12 TraesCS5D01G476500 chr5A 85.946 1416 148 24 819 2205 643735252 643733859 0.000000e+00 1465
13 TraesCS5D01G476500 chr5A 86.227 1198 135 17 1027 2209 643855497 643854315 0.000000e+00 1271
14 TraesCS5D01G476500 chr5A 85.158 1233 125 32 788 2004 643652952 643651762 0.000000e+00 1210
15 TraesCS5D01G476500 chr5A 89.535 430 44 1 997 1426 643453876 643453448 7.110000e-151 544
16 TraesCS5D01G476500 chr2D 95.076 792 24 7 11 787 336326803 336326012 0.000000e+00 1232
17 TraesCS5D01G476500 chr2D 96.788 716 23 0 2204 2919 19057273 19057988 0.000000e+00 1195
18 TraesCS5D01G476500 chr3D 95.281 784 23 10 16 788 8557268 8556488 0.000000e+00 1230
19 TraesCS5D01G476500 chr3D 97.486 716 18 0 2204 2919 560043103 560042388 0.000000e+00 1223
20 TraesCS5D01G476500 chr3D 96.653 717 24 0 2203 2919 565088366 565089082 0.000000e+00 1192
21 TraesCS5D01G476500 chr3D 96.523 719 25 0 2201 2919 4447129 4446411 0.000000e+00 1190
22 TraesCS5D01G476500 chr3D 94.081 794 25 13 13 787 280122056 280122846 0.000000e+00 1186
23 TraesCS5D01G476500 chr6D 94.862 798 19 17 15 795 315352609 315351817 0.000000e+00 1227
24 TraesCS5D01G476500 chr6D 93.789 805 23 12 13 797 464841495 464842292 0.000000e+00 1184
25 TraesCS5D01G476500 chr4D 94.541 806 25 11 6 794 108318339 108317536 0.000000e+00 1227
26 TraesCS5D01G476500 chr4D 96.653 717 24 0 2203 2919 471279924 471280640 0.000000e+00 1192
27 TraesCS5D01G476500 chr4D 94.275 786 28 13 15 787 280415625 280416406 0.000000e+00 1186
28 TraesCS5D01G476500 chr1D 96.797 718 23 0 2202 2919 467540867 467541584 0.000000e+00 1199
29 TraesCS5D01G476500 chr1D 96.547 724 24 1 2196 2919 462312972 462313694 0.000000e+00 1197
30 TraesCS5D01G476500 chr7D 96.788 716 22 1 2204 2919 596907329 596908043 0.000000e+00 1194
31 TraesCS5D01G476500 chr7D 93.569 793 20 17 13 787 364260673 364259894 0.000000e+00 1153
32 TraesCS5D01G476500 chrUn 96.779 714 22 1 2207 2919 95414989 95414276 0.000000e+00 1190


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 TraesCS5D01G476500 chr5D 515423065 515425983 2918 True 5391 5391 100.0000 1 2919 1 chr5D.!!$R3 2918
1 TraesCS5D01G476500 chr5D 450544039 450544825 786 True 1219 1219 94.9240 14 787 1 chr5D.!!$R1 773
2 TraesCS5D01G476500 chr5D 515465040 515466210 1170 True 1153 1153 84.5250 1027 2207 1 chr5D.!!$R4 1180
3 TraesCS5D01G476500 chr5D 515567677 515568865 1188 True 646 647 86.2695 986 2209 2 chr5D.!!$R5 1223
4 TraesCS5D01G476500 chr5D 551242907 551244095 1188 True 634 638 85.9150 986 2207 2 chr5D.!!$R6 1221
5 TraesCS5D01G476500 chr5D 515411274 515411857 583 True 521 521 82.8860 1613 2205 1 chr5D.!!$R2 592
6 TraesCS5D01G476500 chr5B 648179660 648181062 1402 True 2095 2095 93.5300 790 2207 1 chr5B.!!$R3 1417
7 TraesCS5D01G476500 chr5B 648259348 648260541 1193 True 1266 1266 86.1060 1027 2205 1 chr5B.!!$R4 1178
8 TraesCS5D01G476500 chr5B 648144742 648145429 687 True 560 560 81.6500 1515 2207 1 chr5B.!!$R2 692
9 TraesCS5D01G476500 chr5A 643733859 643735252 1393 True 1465 1465 85.9460 819 2205 1 chr5A.!!$R3 1386
10 TraesCS5D01G476500 chr5A 643854315 643855497 1182 True 1271 1271 86.2270 1027 2209 1 chr5A.!!$R4 1182
11 TraesCS5D01G476500 chr5A 643651762 643652952 1190 True 1210 1210 85.1580 788 2004 1 chr5A.!!$R2 1216
12 TraesCS5D01G476500 chr2D 336326012 336326803 791 True 1232 1232 95.0760 11 787 1 chr2D.!!$R1 776
13 TraesCS5D01G476500 chr2D 19057273 19057988 715 False 1195 1195 96.7880 2204 2919 1 chr2D.!!$F1 715
14 TraesCS5D01G476500 chr3D 8556488 8557268 780 True 1230 1230 95.2810 16 788 1 chr3D.!!$R2 772
15 TraesCS5D01G476500 chr3D 560042388 560043103 715 True 1223 1223 97.4860 2204 2919 1 chr3D.!!$R3 715
16 TraesCS5D01G476500 chr3D 565088366 565089082 716 False 1192 1192 96.6530 2203 2919 1 chr3D.!!$F2 716
17 TraesCS5D01G476500 chr3D 4446411 4447129 718 True 1190 1190 96.5230 2201 2919 1 chr3D.!!$R1 718
18 TraesCS5D01G476500 chr3D 280122056 280122846 790 False 1186 1186 94.0810 13 787 1 chr3D.!!$F1 774
19 TraesCS5D01G476500 chr6D 315351817 315352609 792 True 1227 1227 94.8620 15 795 1 chr6D.!!$R1 780
20 TraesCS5D01G476500 chr6D 464841495 464842292 797 False 1184 1184 93.7890 13 797 1 chr6D.!!$F1 784
21 TraesCS5D01G476500 chr4D 108317536 108318339 803 True 1227 1227 94.5410 6 794 1 chr4D.!!$R1 788
22 TraesCS5D01G476500 chr4D 471279924 471280640 716 False 1192 1192 96.6530 2203 2919 1 chr4D.!!$F2 716
23 TraesCS5D01G476500 chr4D 280415625 280416406 781 False 1186 1186 94.2750 15 787 1 chr4D.!!$F1 772
24 TraesCS5D01G476500 chr1D 467540867 467541584 717 False 1199 1199 96.7970 2202 2919 1 chr1D.!!$F2 717
25 TraesCS5D01G476500 chr1D 462312972 462313694 722 False 1197 1197 96.5470 2196 2919 1 chr1D.!!$F1 723
26 TraesCS5D01G476500 chr7D 596907329 596908043 714 False 1194 1194 96.7880 2204 2919 1 chr7D.!!$F1 715
27 TraesCS5D01G476500 chr7D 364259894 364260673 779 True 1153 1153 93.5690 13 787 1 chr7D.!!$R1 774
28 TraesCS5D01G476500 chrUn 95414276 95414989 713 True 1190 1190 96.7790 2207 2919 1 chrUn.!!$R1 712

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
638 674 1.115467 TTCATTGGGCGGTTTTGTGT 58.885 45.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 2446 0.461961 AGCTAACGAGGGCATCAGTC 59.538 55.0 0.0 0.0 0.0 3.51 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
69 70 4.574828 CCCACAAAGTATAGAATTGGTCCG 59.425 45.833 0.00 0.00 0.00 4.79
637 673 1.202463 TGTTCATTGGGCGGTTTTGTG 60.202 47.619 0.00 0.00 0.00 3.33
638 674 1.115467 TTCATTGGGCGGTTTTGTGT 58.885 45.000 0.00 0.00 0.00 3.72
699 736 4.278919 GGACCAAACTTATCCGGTTTTGAA 59.721 41.667 0.00 0.00 35.09 2.69
809 848 7.915397 TCTCAAACTAAAAAGAAGTTCACATGC 59.085 33.333 5.50 0.00 36.17 4.06
919 958 2.664081 GCCTGAGCACCACCTAGCT 61.664 63.158 0.00 0.00 45.25 3.32
1016 1079 4.402528 CATGGACGCCGGTTCCCA 62.403 66.667 18.56 15.37 0.00 4.37
1025 1088 2.267642 CGGTTCCCAATCCTCGCA 59.732 61.111 0.00 0.00 0.00 5.10
1434 1497 0.976641 ACAAGGTTCGGCAGATCTGA 59.023 50.000 27.04 2.29 0.00 3.27
1467 1557 3.023832 CCGCTTGGTTCCATTAATTCCT 58.976 45.455 0.00 0.00 0.00 3.36
1473 1563 4.349365 TGGTTCCATTAATTCCTTCCCAC 58.651 43.478 0.00 0.00 0.00 4.61
1482 1575 2.019807 TTCCTTCCCACGTAGGAGTT 57.980 50.000 2.20 0.00 41.38 3.01
1734 1845 4.845580 CGCGGCCATCAGGAGCTT 62.846 66.667 2.24 0.00 37.76 3.74
1761 1872 3.839432 GGAGCCCGAGTCCTTCCG 61.839 72.222 0.00 0.00 0.00 4.30
1915 2027 2.319841 GCGGGTTCGGTTGTGTACC 61.320 63.158 0.00 0.00 44.03 3.34
2025 2137 0.250513 CTCTTAGGAAGCCAAGCGGT 59.749 55.000 0.00 0.00 33.28 5.68
2073 2188 1.377333 GCTTCCTCCCGGTTTCCAG 60.377 63.158 0.00 0.00 0.00 3.86
2162 2277 4.323477 CGTGGGCGGGTTCCTGAA 62.323 66.667 1.37 0.00 0.00 3.02
2168 2283 1.295423 GCGGGTTCCTGAAGCACTA 59.705 57.895 10.84 0.00 40.33 2.74
2224 2339 0.533755 GCCAATAGCTCCTGTGCGAT 60.534 55.000 0.00 0.00 38.99 4.58
2283 2398 2.108514 CGAATGGCTGTGGTGCGAT 61.109 57.895 0.00 0.00 32.89 4.58
2331 2446 2.066262 ACGACATGGCTGTTAAACTCG 58.934 47.619 0.00 0.00 35.14 4.18
2445 2560 0.730265 CGCAGCTAGAAGAGACGAGT 59.270 55.000 0.00 0.00 0.00 4.18
2509 2624 2.237392 CCCAATCTTTCTCTTCTCCGGT 59.763 50.000 0.00 0.00 0.00 5.28
2592 2707 1.521450 CTGCTCACAAAGTGCCCTGG 61.521 60.000 0.00 0.00 35.92 4.45
2707 2822 1.305213 GGCAGGAAGGGATGGCAAA 60.305 57.895 0.00 0.00 41.35 3.68
2719 2834 4.228210 AGGGATGGCAAAGTTAGATCTCAA 59.772 41.667 0.00 0.00 0.00 3.02
2817 2932 7.595819 TTAGGGTTCATGTTGTTCTTTTCAT 57.404 32.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 1.801771 CCGGTCAACGTGCTCAAAATA 59.198 47.619 0.00 0.00 42.24 1.40
241 257 4.866088 GCAGCTTGCGCATGTAAA 57.134 50.000 22.50 1.61 39.10 2.01
255 271 1.267806 AGCATGAAAAGTTGGTCGCAG 59.732 47.619 0.00 0.00 0.00 5.18
604 640 5.393027 GCCCAATGAACAGTAAATTCGACAT 60.393 40.000 0.00 0.00 0.00 3.06
624 660 2.902846 CCGACACAAAACCGCCCA 60.903 61.111 0.00 0.00 0.00 5.36
699 736 6.134535 TGTATACATTTGGTCCCTCAAGTT 57.865 37.500 0.08 0.00 0.00 2.66
735 773 5.091552 TCCCACAAAGTATAGACTTGGTCT 58.908 41.667 7.32 5.52 45.23 3.85
919 958 1.906105 AAGGACCGGCGGCTTAATGA 61.906 55.000 28.71 0.00 0.00 2.57
1015 1078 1.374343 ATGTGCAGCTGCGAGGATTG 61.374 55.000 32.11 0.00 45.83 2.67
1016 1079 1.077930 ATGTGCAGCTGCGAGGATT 60.078 52.632 32.11 11.87 45.83 3.01
1025 1088 2.433145 CGACCACGATGTGCAGCT 60.433 61.111 0.00 0.00 42.66 4.24
1061 1124 3.001406 GGTACGGGAGCAGGTGGT 61.001 66.667 0.00 0.00 0.00 4.16
1308 1371 1.079127 CATGAACTCCGCGAAGGGT 60.079 57.895 8.23 0.00 41.52 4.34
1347 1410 1.448540 CCAGTGAGGCCTTGTAGCG 60.449 63.158 6.77 0.00 0.00 4.26
1350 1413 0.472925 TGACCCAGTGAGGCCTTGTA 60.473 55.000 6.77 0.00 35.39 2.41
1467 1557 4.346730 TGAGATAAACTCCTACGTGGGAA 58.653 43.478 21.99 7.34 44.34 3.97
1473 1563 6.758886 AGCAAGATTTGAGATAAACTCCTACG 59.241 38.462 0.00 0.00 44.34 3.51
1482 1575 5.663795 GCATCGAGCAAGATTTGAGATAA 57.336 39.130 0.00 0.00 44.79 1.75
1727 1838 2.344203 CCCACTCGACGAAGCTCCT 61.344 63.158 0.00 0.00 0.00 3.69
1844 1955 1.746615 CTGCTGATCCGTTGGTGGG 60.747 63.158 0.00 0.00 0.00 4.61
1915 2027 1.142748 CTTCACTCCCCAGCGCTAG 59.857 63.158 10.99 6.46 0.00 3.42
2019 2131 4.254709 TGGACTGCTGCACCGCTT 62.255 61.111 0.00 0.00 0.00 4.68
2025 2137 3.601685 TCGTCGTGGACTGCTGCA 61.602 61.111 0.88 0.88 0.00 4.41
2073 2188 4.357947 TGGTCACGAGTGCGCTCC 62.358 66.667 21.21 8.31 42.48 4.70
2162 2277 2.995574 AGTTCCGGCCGTAGTGCT 60.996 61.111 26.12 11.55 0.00 4.40
2224 2339 5.076182 TCTTGCCAATTCACCTCAAATGTA 58.924 37.500 0.00 0.00 0.00 2.29
2283 2398 6.191315 TGGGCTATTTACCTGCTCAAAATTA 58.809 36.000 0.00 0.00 33.92 1.40
2331 2446 0.461961 AGCTAACGAGGGCATCAGTC 59.538 55.000 0.00 0.00 0.00 3.51
2509 2624 2.418197 GGTAGACATTTGCGCTAGGTCA 60.418 50.000 22.80 11.07 0.00 4.02
2658 2773 3.365820 GCTCAAGCATTTCACAAATTCCG 59.634 43.478 0.00 0.00 41.59 4.30
2707 2822 5.364157 ACGGGCTAAGAATTGAGATCTAACT 59.636 40.000 0.00 0.00 0.00 2.24
2719 2834 2.007608 GCGAAAGAACGGGCTAAGAAT 58.992 47.619 0.00 0.00 0.00 2.40
2781 2896 6.263754 ACATGAACCCTAAATCCCAAATTCT 58.736 36.000 0.00 0.00 0.00 2.40
2834 2949 4.572985 TCATCAATCCATTCGAAATGGC 57.427 40.909 17.00 0.00 39.01 4.40


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

AutoCloner maintained by Alex Coulton.