Multiple sequence alignment - TraesCS1D01G313600

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 TraesCS1D01G313600 chr1D 100.000 2731 0 0 1 2731 408889413 408892143 0.000000e+00 5044
1 TraesCS1D01G313600 chr1D 95.029 342 13 1 370 707 408884675 408885016 4.000000e-148 534
2 TraesCS1D01G313600 chr3D 96.747 2029 61 3 706 2731 577373109 577375135 0.000000e+00 3376
3 TraesCS1D01G313600 chr3D 96.624 711 20 1 1 707 529492484 529493194 0.000000e+00 1177
4 TraesCS1D01G313600 chr3D 95.044 343 11 1 371 707 529487898 529488240 4.000000e-148 534
5 TraesCS1D01G313600 chr7B 96.740 1043 32 1 1689 2731 712627316 712626276 0.000000e+00 1736
6 TraesCS1D01G313600 chr7B 96.069 1043 31 1 1689 2731 693286268 693287300 0.000000e+00 1690
7 TraesCS1D01G313600 chr2A 96.740 1043 32 1 1689 2731 1110027 1111067 0.000000e+00 1736
8 TraesCS1D01G313600 chr2A 91.120 259 22 1 710 968 1968428 1968171 1.560000e-92 350
9 TraesCS1D01G313600 chr2A 91.120 259 22 1 710 968 2007415 2007158 1.560000e-92 350
10 TraesCS1D01G313600 chr2A 91.120 259 22 1 710 968 2043371 2043114 1.560000e-92 350
11 TraesCS1D01G313600 chr2A 91.120 259 22 1 710 968 2135880 2135623 1.560000e-92 350
12 TraesCS1D01G313600 chr2A 90.347 259 24 1 710 968 2098369 2098112 3.370000e-89 339
13 TraesCS1D01G313600 chr2A 92.982 114 8 0 1450 1563 777292366 777292253 1.680000e-37 167
14 TraesCS1D01G313600 chr1B 97.228 1010 27 1 1723 2731 8847404 8848413 0.000000e+00 1709
15 TraesCS1D01G313600 chr1B 90.625 256 23 1 710 965 685907747 685908001 3.370000e-89 339
16 TraesCS1D01G313600 chr1A 96.819 1006 32 0 1726 2731 507227384 507226379 0.000000e+00 1681
17 TraesCS1D01G313600 chrUn 96.531 1009 25 1 1723 2731 225683766 225684764 0.000000e+00 1661
18 TraesCS1D01G313600 chrUn 96.421 1006 25 2 1726 2731 195643650 195642656 0.000000e+00 1648
19 TraesCS1D01G313600 chrUn 91.406 256 21 1 710 965 268624617 268624871 1.560000e-92 350
20 TraesCS1D01G313600 chr3A 97.185 888 25 0 1842 2729 48643222 48642335 0.000000e+00 1502
21 TraesCS1D01G313600 chr3A 79.003 381 72 8 3 379 220645849 220646225 1.260000e-63 254
22 TraesCS1D01G313600 chr3B 95.445 922 25 2 1813 2731 43530547 43529640 0.000000e+00 1454
23 TraesCS1D01G313600 chr3B 83.176 636 93 13 3 633 83489048 83489674 1.100000e-158 569
24 TraesCS1D01G313600 chr5B 93.597 937 53 5 1580 2513 430135875 430134943 0.000000e+00 1391
25 TraesCS1D01G313600 chr5B 86.676 698 65 15 781 1450 535566808 535567505 0.000000e+00 749
26 TraesCS1D01G313600 chr5B 81.678 715 114 14 3 706 548394838 548395546 1.820000e-161 579
27 TraesCS1D01G313600 chr5B 81.302 722 112 18 1 704 70922663 70921947 5.110000e-157 564
28 TraesCS1D01G313600 chr5B 94.529 329 18 0 1237 1565 430136321 430135993 2.430000e-140 508
29 TraesCS1D01G313600 chr5B 77.980 713 145 9 1 706 72236040 72236747 1.160000e-118 436
30 TraesCS1D01G313600 chr6A 86.247 778 70 17 710 1450 510236913 510236136 0.000000e+00 809
31 TraesCS1D01G313600 chr6A 86.207 696 64 17 781 1450 441297092 441296403 0.000000e+00 725
32 TraesCS1D01G313600 chr6A 93.548 93 5 1 1359 1450 478523759 478523667 1.320000e-28 137
33 TraesCS1D01G313600 chr2B 87.661 697 59 14 781 1450 765735273 765735969 0.000000e+00 785
34 TraesCS1D01G313600 chr2B 95.614 114 5 0 1450 1563 779850792 779850905 1.670000e-42 183
35 TraesCS1D01G313600 chr5A 85.190 709 99 5 2 706 359989955 359990661 0.000000e+00 723
36 TraesCS1D01G313600 chr4B 80.618 712 128 8 3 706 665472605 665473314 2.390000e-150 542
37 TraesCS1D01G313600 chr4B 81.481 378 68 2 3 379 473855861 473856237 2.640000e-80 309
38 TraesCS1D01G313600 chr7A 95.570 316 14 0 2416 2731 714818094 714818409 8.730000e-140 507
39 TraesCS1D01G313600 chr4A 82.254 355 37 13 790 1118 395317225 395316871 1.600000e-72 283
40 TraesCS1D01G313600 chr4A 91.743 109 8 1 710 817 395317338 395317230 1.690000e-32 150
41 TraesCS1D01G313600 chr2D 94.737 114 6 0 1450 1563 650857186 650857299 7.770000e-41 178


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 TraesCS1D01G313600 chr1D 408889413 408892143 2730 False 5044.0 5044 100.000 1 2731 1 chr1D.!!$F2 2730
1 TraesCS1D01G313600 chr3D 577373109 577375135 2026 False 3376.0 3376 96.747 706 2731 1 chr3D.!!$F3 2025
2 TraesCS1D01G313600 chr3D 529492484 529493194 710 False 1177.0 1177 96.624 1 707 1 chr3D.!!$F2 706
3 TraesCS1D01G313600 chr7B 712626276 712627316 1040 True 1736.0 1736 96.740 1689 2731 1 chr7B.!!$R1 1042
4 TraesCS1D01G313600 chr7B 693286268 693287300 1032 False 1690.0 1690 96.069 1689 2731 1 chr7B.!!$F1 1042
5 TraesCS1D01G313600 chr2A 1110027 1111067 1040 False 1736.0 1736 96.740 1689 2731 1 chr2A.!!$F1 1042
6 TraesCS1D01G313600 chr1B 8847404 8848413 1009 False 1709.0 1709 97.228 1723 2731 1 chr1B.!!$F1 1008
7 TraesCS1D01G313600 chr1A 507226379 507227384 1005 True 1681.0 1681 96.819 1726 2731 1 chr1A.!!$R1 1005
8 TraesCS1D01G313600 chrUn 225683766 225684764 998 False 1661.0 1661 96.531 1723 2731 1 chrUn.!!$F1 1008
9 TraesCS1D01G313600 chrUn 195642656 195643650 994 True 1648.0 1648 96.421 1726 2731 1 chrUn.!!$R1 1005
10 TraesCS1D01G313600 chr3A 48642335 48643222 887 True 1502.0 1502 97.185 1842 2729 1 chr3A.!!$R1 887
11 TraesCS1D01G313600 chr3B 43529640 43530547 907 True 1454.0 1454 95.445 1813 2731 1 chr3B.!!$R1 918
12 TraesCS1D01G313600 chr3B 83489048 83489674 626 False 569.0 569 83.176 3 633 1 chr3B.!!$F1 630
13 TraesCS1D01G313600 chr5B 430134943 430136321 1378 True 949.5 1391 94.063 1237 2513 2 chr5B.!!$R2 1276
14 TraesCS1D01G313600 chr5B 535566808 535567505 697 False 749.0 749 86.676 781 1450 1 chr5B.!!$F2 669
15 TraesCS1D01G313600 chr5B 548394838 548395546 708 False 579.0 579 81.678 3 706 1 chr5B.!!$F3 703
16 TraesCS1D01G313600 chr5B 70921947 70922663 716 True 564.0 564 81.302 1 704 1 chr5B.!!$R1 703
17 TraesCS1D01G313600 chr5B 72236040 72236747 707 False 436.0 436 77.980 1 706 1 chr5B.!!$F1 705
18 TraesCS1D01G313600 chr6A 510236136 510236913 777 True 809.0 809 86.247 710 1450 1 chr6A.!!$R3 740
19 TraesCS1D01G313600 chr6A 441296403 441297092 689 True 725.0 725 86.207 781 1450 1 chr6A.!!$R1 669
20 TraesCS1D01G313600 chr2B 765735273 765735969 696 False 785.0 785 87.661 781 1450 1 chr2B.!!$F1 669
21 TraesCS1D01G313600 chr5A 359989955 359990661 706 False 723.0 723 85.190 2 706 1 chr5A.!!$F1 704
22 TraesCS1D01G313600 chr4B 665472605 665473314 709 False 542.0 542 80.618 3 706 1 chr4B.!!$F2 703

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
969 1027 0.03467 GTGCTTCCTTGCCTCATCCT 60.035 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 2792 4.678309 GCAACTCCTAGTATGAGACGCTTT 60.678 45.833 9.2 0.0 33.95 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
68 69 2.878406 GCAGCTTACAAACTGGAACTGA 59.122 45.455 0.00 0.00 34.38 3.41
298 308 0.107017 CATCCGCAACCTGGGAAGAT 60.107 55.000 0.00 0.00 35.60 2.40
330 340 0.824759 AAGGCTAGATTTCCGAGCGT 59.175 50.000 0.00 0.00 43.36 5.07
360 370 1.072331 GGGACAAGCTGGTTCTTCAGA 59.928 52.381 0.00 0.00 36.93 3.27
415 425 2.094894 CGGTGATGATGCAGTTCAGAAC 59.905 50.000 5.00 5.00 0.00 3.01
433 443 4.351938 ACAAGCGGCGCGTACAGA 62.352 61.111 27.59 0.00 0.00 3.41
496 508 2.606213 TGTGGGCTCGGGTGATGA 60.606 61.111 0.00 0.00 0.00 2.92
569 583 4.549489 CGTGACGGTCACTAACTTTGAAAC 60.549 45.833 31.68 7.85 44.85 2.78
707 734 3.261250 GACCCTAGGTCGTGACAGA 57.739 57.895 8.29 0.00 43.14 3.41
969 1027 0.034670 GTGCTTCCTTGCCTCATCCT 60.035 55.000 0.00 0.00 0.00 3.24
1113 1175 6.899393 TTTCATTCTGCAATAGAGTTTGGT 57.101 33.333 0.00 0.00 36.61 3.67
1352 1416 1.930908 GCCATTCTGTGCAGCCTGTC 61.931 60.000 0.00 0.00 0.00 3.51
1435 1500 5.815222 GCCATTTGTAGTTTTTCAGGTTGTT 59.185 36.000 0.00 0.00 0.00 2.83
1455 1520 0.450184 GTGTGACAACTTTGCGGTGT 59.550 50.000 0.00 0.00 0.00 4.16
1644 1813 3.967393 TTGCTGCCGCTCCGCATTA 62.967 57.895 0.70 0.00 38.30 1.90
1652 1821 1.437986 GCTCCGCATTACTCCGACT 59.562 57.895 0.00 0.00 0.00 4.18
1724 1893 1.369625 GAATTCCCACTGTACTGCCG 58.630 55.000 0.00 0.00 0.00 5.69
1728 1897 3.319198 CCACTGTACTGCCGGGGT 61.319 66.667 2.18 0.00 0.00 4.95
2103 2274 6.372937 GGCAGGGCAGTTAAATTAGATATCTC 59.627 42.308 8.95 0.00 0.00 2.75
2181 2355 5.129634 TCTGTTGTTTCATTCCAGCAAGTA 58.870 37.500 0.00 0.00 0.00 2.24
2395 2571 0.905809 ATGCCTCTTTGCCATGCCAA 60.906 50.000 0.00 0.00 0.00 4.52
2396 2572 1.217244 GCCTCTTTGCCATGCCAAG 59.783 57.895 0.00 0.00 33.41 3.61
2397 2573 1.895238 CCTCTTTGCCATGCCAAGG 59.105 57.895 0.00 0.00 33.05 3.61
2459 2635 9.605951 AATATGGGATGGCTATTTTGATTAAGT 57.394 29.630 0.00 0.00 0.00 2.24
2586 2792 4.021104 CCTGACTGTCTTGTGTATCCTTGA 60.021 45.833 9.51 0.00 0.00 3.02
2705 2911 4.037446 GTCACATAAAGACCAAACCTTGCA 59.963 41.667 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 0.463654 TGCACTTGACTTCCTTGCGT 60.464 50.000 0.00 0.00 35.90 5.24
199 209 0.848942 CCAAGCGACGATCGAGAATG 59.151 55.000 24.34 15.48 43.74 2.67
360 370 1.898154 CTGCTTACAGTACCCGCCT 59.102 57.895 0.00 0.00 39.22 5.52
415 425 4.134187 CTGTACGCGCCGCTTGTG 62.134 66.667 5.73 0.00 0.00 3.33
433 443 4.958581 CCCATTTAAATCTCCTTGCCTCTT 59.041 41.667 0.00 0.00 0.00 2.85
496 508 1.890625 TATTACACGGCCCACACGCT 61.891 55.000 0.00 0.00 34.00 5.07
499 511 1.206371 AGTCTATTACACGGCCCACAC 59.794 52.381 0.00 0.00 0.00 3.82
533 545 0.799152 CGTCACGGCATACACGCTTA 60.799 55.000 0.00 0.00 34.00 3.09
561 574 4.853743 GGCTAGAATGCTTTCGTTTCAAAG 59.146 41.667 6.68 0.00 36.93 2.77
569 583 2.123342 CGAGAGGCTAGAATGCTTTCG 58.877 52.381 6.68 0.00 36.93 3.46
778 805 1.905843 CCTCATCCGGATCGAGGCT 60.906 63.158 32.11 7.67 39.95 4.58
887 925 2.636412 CGAACTCGCCCTCAGGTCA 61.636 63.158 0.00 0.00 34.57 4.02
977 1035 4.758251 TGTCGGGCGTGCATCTGG 62.758 66.667 0.00 0.00 0.00 3.86
1113 1175 1.422402 AGTTAAAAGAGACCCGGGCAA 59.578 47.619 24.08 0.00 0.00 4.52
1235 1298 2.738846 CCACAGAGAAACACATCTTCCG 59.261 50.000 0.00 0.00 0.00 4.30
1352 1416 7.511028 ACCATAGGATTCCTAGAACTAAAGAGG 59.489 40.741 17.24 8.52 39.70 3.69
1435 1500 0.449786 CACCGCAAAGTTGTCACACA 59.550 50.000 0.00 0.00 0.00 3.72
1639 1808 2.033662 GCGAATTCAGTCGGAGTAATGC 60.034 50.000 6.22 0.00 41.40 3.56
1644 1813 1.153823 CCGCGAATTCAGTCGGAGT 60.154 57.895 19.87 0.00 44.23 3.85
1652 1821 0.373370 CAGATTTCGCCGCGAATTCA 59.627 50.000 34.26 21.50 45.28 2.57
2024 2193 9.031537 TCTGATTTCTGAACCAGTGTACTATTA 57.968 33.333 14.68 0.00 32.61 0.98
2181 2355 6.702282 GATAAACTATCTTCGGCTGTAAGCTT 59.298 38.462 3.48 3.48 45.17 3.74
2395 2571 8.814448 TTCATAAGAAATCCCTAGAATACCCT 57.186 34.615 0.00 0.00 0.00 4.34
2567 2773 4.757149 GCTTTCAAGGATACACAAGACAGT 59.243 41.667 0.00 0.00 41.41 3.55
2586 2792 4.678309 GCAACTCCTAGTATGAGACGCTTT 60.678 45.833 9.20 0.00 33.95 3.51


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

AutoCloner maintained by Alex Coulton.