Multiple sequence alignment - TraesCS5D01G174800

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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 TraesCS5D01G174800 chr5D 100.000 2619 0 0 1 2619 274216563 274213945 0.000000e+00 4837
1 TraesCS5D01G174800 chr5D 85.314 749 100 9 1 743 220004694 220005438 0.000000e+00 765
2 TraesCS5D01G174800 chr5D 87.034 671 81 5 33 698 97895871 97896540 0.000000e+00 752
3 TraesCS5D01G174800 chr5D 84.878 205 29 2 2042 2245 25489513 25489716 3.420000e-49 206
4 TraesCS5D01G174800 chr6A 91.556 2629 198 11 1 2619 388961520 388958906 0.000000e+00 3603
5 TraesCS5D01G174800 chr1B 89.260 2635 257 19 1 2619 497019111 497021735 0.000000e+00 3275
6 TraesCS5D01G174800 chr3D 91.389 1440 89 16 443 1874 409898860 409897448 0.000000e+00 1940
7 TraesCS5D01G174800 chr3D 91.679 697 57 1 1924 2619 409897455 409896759 0.000000e+00 965
8 TraesCS5D01G174800 chr3D 89.604 606 58 4 1181 1785 315453458 315454059 0.000000e+00 765
9 TraesCS5D01G174800 chr3A 85.467 1211 126 21 1428 2619 161146219 161147398 0.000000e+00 1216
10 TraesCS5D01G174800 chr3A 81.910 691 112 9 1 681 254896258 254895571 2.920000e-159 571
11 TraesCS5D01G174800 chr5A 85.173 1214 123 30 1428 2619 451057421 451058599 0.000000e+00 1192
12 TraesCS5D01G174800 chr7D 87.741 1036 105 13 1592 2619 95941645 95942666 0.000000e+00 1190
13 TraesCS5D01G174800 chr7D 85.185 1026 106 18 1592 2598 132241642 132242640 0.000000e+00 1011
14 TraesCS5D01G174800 chr7D 88.671 715 59 5 1437 2151 111145134 111144442 0.000000e+00 852
15 TraesCS5D01G174800 chr7D 86.450 738 89 9 1 731 407134421 407133688 0.000000e+00 798
16 TraesCS5D01G174800 chr7D 89.590 586 57 3 1181 1765 594503230 594503812 0.000000e+00 741
17 TraesCS5D01G174800 chr7D 90.226 399 37 2 2222 2619 111144441 111144044 1.070000e-143 520
18 TraesCS5D01G174800 chr4D 89.837 797 62 12 443 1230 199652622 199653408 0.000000e+00 1005
19 TraesCS5D01G174800 chr4B 88.466 841 74 17 517 1342 631926477 631927309 0.000000e+00 994
20 TraesCS5D01G174800 chr7B 88.292 837 74 13 523 1342 42251013 42251842 0.000000e+00 981
21 TraesCS5D01G174800 chr7B 91.304 391 32 2 556 944 181997547 181997157 1.380000e-147 532
22 TraesCS5D01G174800 chr2B 87.603 847 72 21 517 1346 512641315 512640485 0.000000e+00 952
23 TraesCS5D01G174800 chr2B 87.022 601 70 6 87 681 622284472 622285070 0.000000e+00 671
24 TraesCS5D01G174800 chr2B 90.227 440 38 3 519 954 114380636 114381074 1.050000e-158 569
25 TraesCS5D01G174800 chr2B 89.431 369 31 6 982 1342 114393043 114393411 2.380000e-125 459
26 TraesCS5D01G174800 chr2A 88.011 709 70 7 1924 2619 527444398 527445104 0.000000e+00 824
27 TraesCS5D01G174800 chr3B 87.591 685 80 4 1 681 169945037 169945720 0.000000e+00 789
28 TraesCS5D01G174800 chr3B 86.463 687 85 7 2 681 160456735 160456050 0.000000e+00 747
29 TraesCS5D01G174800 chr7A 85.019 781 98 9 1844 2619 491817106 491816340 0.000000e+00 776
30 TraesCS5D01G174800 chr7A 84.264 197 27 2 2042 2237 685013034 685012841 3.440000e-44 189
31 TraesCS5D01G174800 chr1D 86.212 689 85 10 1 681 471204296 471204982 0.000000e+00 737
32 TraesCS5D01G174800 chr2D 90.451 377 36 0 2243 2619 482922175 482922551 5.030000e-137 497
33 TraesCS5D01G174800 chr6B 88.583 254 22 4 940 1187 226077222 226077474 4.240000e-78 302
34 TraesCS5D01G174800 chr4A 84.247 146 20 3 2476 2619 220711791 220711647 3.510000e-29 139


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 TraesCS5D01G174800 chr5D 274213945 274216563 2618 True 4837.0 4837 100.0000 1 2619 1 chr5D.!!$R1 2618
1 TraesCS5D01G174800 chr5D 220004694 220005438 744 False 765.0 765 85.3140 1 743 1 chr5D.!!$F3 742
2 TraesCS5D01G174800 chr5D 97895871 97896540 669 False 752.0 752 87.0340 33 698 1 chr5D.!!$F2 665
3 TraesCS5D01G174800 chr6A 388958906 388961520 2614 True 3603.0 3603 91.5560 1 2619 1 chr6A.!!$R1 2618
4 TraesCS5D01G174800 chr1B 497019111 497021735 2624 False 3275.0 3275 89.2600 1 2619 1 chr1B.!!$F1 2618
5 TraesCS5D01G174800 chr3D 409896759 409898860 2101 True 1452.5 1940 91.5340 443 2619 2 chr3D.!!$R1 2176
6 TraesCS5D01G174800 chr3D 315453458 315454059 601 False 765.0 765 89.6040 1181 1785 1 chr3D.!!$F1 604
7 TraesCS5D01G174800 chr3A 161146219 161147398 1179 False 1216.0 1216 85.4670 1428 2619 1 chr3A.!!$F1 1191
8 TraesCS5D01G174800 chr3A 254895571 254896258 687 True 571.0 571 81.9100 1 681 1 chr3A.!!$R1 680
9 TraesCS5D01G174800 chr5A 451057421 451058599 1178 False 1192.0 1192 85.1730 1428 2619 1 chr5A.!!$F1 1191
10 TraesCS5D01G174800 chr7D 95941645 95942666 1021 False 1190.0 1190 87.7410 1592 2619 1 chr7D.!!$F1 1027
11 TraesCS5D01G174800 chr7D 132241642 132242640 998 False 1011.0 1011 85.1850 1592 2598 1 chr7D.!!$F2 1006
12 TraesCS5D01G174800 chr7D 407133688 407134421 733 True 798.0 798 86.4500 1 731 1 chr7D.!!$R1 730
13 TraesCS5D01G174800 chr7D 594503230 594503812 582 False 741.0 741 89.5900 1181 1765 1 chr7D.!!$F3 584
14 TraesCS5D01G174800 chr7D 111144044 111145134 1090 True 686.0 852 89.4485 1437 2619 2 chr7D.!!$R2 1182
15 TraesCS5D01G174800 chr4D 199652622 199653408 786 False 1005.0 1005 89.8370 443 1230 1 chr4D.!!$F1 787
16 TraesCS5D01G174800 chr4B 631926477 631927309 832 False 994.0 994 88.4660 517 1342 1 chr4B.!!$F1 825
17 TraesCS5D01G174800 chr7B 42251013 42251842 829 False 981.0 981 88.2920 523 1342 1 chr7B.!!$F1 819
18 TraesCS5D01G174800 chr2B 512640485 512641315 830 True 952.0 952 87.6030 517 1346 1 chr2B.!!$R1 829
19 TraesCS5D01G174800 chr2B 622284472 622285070 598 False 671.0 671 87.0220 87 681 1 chr2B.!!$F3 594
20 TraesCS5D01G174800 chr2A 527444398 527445104 706 False 824.0 824 88.0110 1924 2619 1 chr2A.!!$F1 695
21 TraesCS5D01G174800 chr3B 169945037 169945720 683 False 789.0 789 87.5910 1 681 1 chr3B.!!$F1 680
22 TraesCS5D01G174800 chr3B 160456050 160456735 685 True 747.0 747 86.4630 2 681 1 chr3B.!!$R1 679
23 TraesCS5D01G174800 chr7A 491816340 491817106 766 True 776.0 776 85.0190 1844 2619 1 chr7A.!!$R1 775
24 TraesCS5D01G174800 chr1D 471204296 471204982 686 False 737.0 737 86.2120 1 681 1 chr1D.!!$F1 680

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
856 907 0.608856 ATTGCCTGGCATCGTTGACA 60.609 50.0 24.03 4.87 39.06 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2343 2475 1.30062 CCGAGACGTCAAGTGCCAA 60.301 57.895 19.5 0.0 0.0 4.52 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
258 265 2.162681 AGACAACTTGCCCTGCATTAC 58.837 47.619 0.00 0.00 38.76 1.89
293 301 7.709149 AGCCAGAGTAATTGCTCTTTTAAAT 57.291 32.000 21.85 4.43 42.69 1.40
385 395 2.927477 GCGAAGTTGATGATTACCACGA 59.073 45.455 0.00 0.00 0.00 4.35
404 414 3.935203 ACGATGAAGCTGAAATCAATCGT 59.065 39.130 12.03 12.03 36.23 3.73
438 448 1.674764 CGGGAGCAGACAGATGAGCT 61.675 60.000 0.00 0.00 40.60 4.09
540 551 0.673333 CGTGTTGATGTAGCAGGGCA 60.673 55.000 0.00 0.00 0.00 5.36
764 808 2.969628 ATAAACAGAGACGGAGCAGG 57.030 50.000 0.00 0.00 0.00 4.85
775 819 1.580845 CGGAGCAGGCCAAGTTTCAG 61.581 60.000 5.01 0.00 0.00 3.02
856 907 0.608856 ATTGCCTGGCATCGTTGACA 60.609 50.000 24.03 4.87 39.06 3.58
869 920 4.406648 TCGTTGACATGATTCTAGGCAT 57.593 40.909 0.00 0.00 0.00 4.40
1011 1068 2.565645 CCCGCGGATGGAGGTAGAG 61.566 68.421 30.73 0.00 32.98 2.43
1050 1108 1.165270 CACACCCGAAAATCCCTGAC 58.835 55.000 0.00 0.00 0.00 3.51
1113 1181 0.040425 CCGCCGAAACTGAAACTTGG 60.040 55.000 0.00 0.00 0.00 3.61
1184 1252 1.227249 TTCAGAAACCCCCACCTCAA 58.773 50.000 0.00 0.00 0.00 3.02
1208 1277 5.182001 ACAGCAATTTAACTTGAGCACTAGG 59.818 40.000 9.55 0.00 0.00 3.02
1265 1335 3.843619 TCTCCAACATGTACATCCTTCCA 59.156 43.478 5.07 0.00 0.00 3.53
1326 1397 0.457851 TGGTCCTTTGGTTTGTTGCG 59.542 50.000 0.00 0.00 0.00 4.85
1353 1424 9.736023 GTTTATCTTCAGTTTCTGTTGTTTGAT 57.264 29.630 0.00 0.00 32.61 2.57
1414 1486 4.280019 GGACAACGGGGGCAGGTT 62.280 66.667 0.00 0.00 0.00 3.50
1520 1593 3.379445 GACGGGTGCGGAAGAGGA 61.379 66.667 0.00 0.00 0.00 3.71
1598 1674 2.126031 GACGACTTCAGGCCGGTC 60.126 66.667 0.00 0.00 0.00 4.79
1600 1676 4.052229 CGACTTCAGGCCGGTCGT 62.052 66.667 24.37 14.54 44.93 4.34
1811 1889 3.041940 CGAGAAAACCCGCAGCGT 61.042 61.111 15.05 0.00 0.00 5.07
2168 2266 3.755628 GGTCGACCACGGCAGCTA 61.756 66.667 29.75 0.00 46.58 3.32
2439 2572 5.215252 TCTCTTGAACCTTTGTCGATCTT 57.785 39.130 0.00 0.00 0.00 2.40
2523 2656 3.423154 CCGCCGCAGAACACTTCC 61.423 66.667 0.00 0.00 0.00 3.46
2579 2714 0.539438 TTTCCATGCCGGTTTGAGCT 60.539 50.000 1.90 0.00 35.57 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
258 265 1.602311 ACTCTGGCTTGCAAGTTCTG 58.398 50.000 26.55 20.61 0.00 3.02
328 337 7.399245 TTTGGCCTAACATATCAGGTAAAAC 57.601 36.000 3.32 0.00 34.18 2.43
385 395 3.181493 GCCACGATTGATTTCAGCTTCAT 60.181 43.478 0.00 0.00 0.00 2.57
418 428 1.954362 GCTCATCTGTCTGCTCCCGT 61.954 60.000 0.00 0.00 0.00 5.28
704 745 8.917088 CAGGTGATATCCATCCAAGTTTATTTT 58.083 33.333 0.00 0.00 0.00 1.82
705 746 7.506938 CCAGGTGATATCCATCCAAGTTTATTT 59.493 37.037 0.00 0.00 0.00 1.40
744 788 2.100916 GCCTGCTCCGTCTCTGTTTATA 59.899 50.000 0.00 0.00 0.00 0.98
764 808 1.508632 TCTGCGTACTGAAACTTGGC 58.491 50.000 0.00 0.00 0.00 4.52
775 819 5.143916 CAACTGTGGATTTATCTGCGTAC 57.856 43.478 0.00 0.00 0.00 3.67
1113 1181 4.762251 ACTCAATTGGCTACTGAAGAAACC 59.238 41.667 5.42 0.00 0.00 3.27
1184 1252 5.182001 CCTAGTGCTCAAGTTAAATTGCTGT 59.818 40.000 10.71 0.00 0.00 4.40
1208 1277 5.415701 TCAGTTTAATGATGCCAGGAAGTTC 59.584 40.000 0.00 0.00 0.00 3.01
1249 1319 8.877864 TTTTAGAAATGGAAGGATGTACATGT 57.122 30.769 14.43 2.69 0.00 3.21
1315 1386 3.632604 TGAAGATAAACCGCAACAAACCA 59.367 39.130 0.00 0.00 0.00 3.67
1326 1397 8.188139 TCAAACAACAGAAACTGAAGATAAACC 58.812 33.333 5.76 0.00 35.18 3.27
1353 1424 4.530553 TGTTTCTGTCACTGAGGCCTATTA 59.469 41.667 4.42 0.00 0.00 0.98
1414 1486 0.245266 TTGCAGCGTAATCCGTCTCA 59.755 50.000 0.00 0.00 39.32 3.27
1429 1501 2.357034 GTCGCCTTCTCCGTTGCA 60.357 61.111 0.00 0.00 0.00 4.08
1502 1575 3.382832 CCTCTTCCGCACCCGTCT 61.383 66.667 0.00 0.00 0.00 4.18
1582 1658 4.052229 CGACCGGCCTGAAGTCGT 62.052 66.667 19.98 1.16 46.23 4.34
1600 1676 3.356639 CTACTGCAAGCCTCCGCGA 62.357 63.158 8.23 0.00 41.18 5.87
1606 1682 3.672295 GAGCCGCTACTGCAAGCCT 62.672 63.158 4.82 0.00 39.43 4.58
1757 1833 2.571757 CCGCGGTTCTAGTCTGCA 59.428 61.111 19.50 0.00 37.06 4.41
1760 1836 3.823330 CGCCCGCGGTTCTAGTCT 61.823 66.667 26.12 0.00 35.56 3.24
1811 1889 1.876664 CTCTCGCCTTGAGTCGTCA 59.123 57.895 0.00 0.00 45.46 4.35
2204 2302 2.225382 TGGATACAGAGTTGACCCGA 57.775 50.000 0.00 0.00 46.17 5.14
2343 2475 1.300620 CCGAGACGTCAAGTGCCAA 60.301 57.895 19.50 0.00 0.00 4.52
2472 2605 9.436957 TGAGATTAAGACTGTTTTGAGTTATCC 57.563 33.333 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.