Multiple sequence alignment - TraesCS6D01G312300

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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 TraesCS6D01G312300 chr6D 100.000 2585 0 0 1 2585 421665583 421662999 0.000000e+00 4774
1 TraesCS6D01G312300 chr6D 97.007 2105 62 1 482 2585 421683076 421680972 0.000000e+00 3537
2 TraesCS6D01G312300 chr6D 94.546 1797 85 9 793 2585 421697225 421695438 0.000000e+00 2763
3 TraesCS6D01G312300 chr6D 91.573 1068 80 10 768 1832 421463127 421464187 0.000000e+00 1465
4 TraesCS6D01G312300 chr6D 90.757 1017 65 15 1582 2582 420968137 420969140 0.000000e+00 1330
5 TraesCS6D01G312300 chr6D 92.247 761 47 7 1833 2585 421466041 421466797 0.000000e+00 1068
6 TraesCS6D01G312300 chr6D 89.251 828 51 17 769 1591 420966159 420966953 0.000000e+00 1002
7 TraesCS6D01G312300 chr6D 98.117 478 9 0 1 478 421674184 421673707 0.000000e+00 833
8 TraesCS6D01G312300 chr6D 87.884 619 58 6 994 1611 422604039 422603437 0.000000e+00 712
9 TraesCS6D01G312300 chr6D 99.162 358 3 0 121 478 421683766 421683409 0.000000e+00 645
10 TraesCS6D01G312300 chr6D 95.822 359 15 0 120 478 308897693 308898051 4.790000e-162 580
11 TraesCS6D01G312300 chr6D 81.477 745 98 28 1849 2585 422603191 422602479 2.230000e-160 575
12 TraesCS6D01G312300 chr6D 88.537 410 41 5 1206 1611 422217928 422217521 2.310000e-135 492
13 TraesCS6D01G312300 chr6D 83.173 416 37 16 2162 2573 422216952 422216566 1.470000e-92 350
14 TraesCS6D01G312300 chr6D 87.027 185 19 4 1839 2022 422217285 422217105 1.210000e-48 204
15 TraesCS6D01G312300 chr6B 92.995 828 52 5 787 1611 634501423 634502247 0.000000e+00 1203
16 TraesCS6D01G312300 chr6B 88.331 617 62 3 994 1610 636767678 636767072 0.000000e+00 732
17 TraesCS6D01G312300 chr6B 95.822 359 15 0 120 478 675447743 675448101 4.790000e-162 580
18 TraesCS6D01G312300 chr6B 95.265 359 17 0 120 478 278149672 278150030 1.040000e-158 569
19 TraesCS6D01G312300 chr6B 80.526 760 106 30 1839 2585 636748036 636747306 1.750000e-151 545
20 TraesCS6D01G312300 chr6B 93.939 198 12 0 480 677 31941513 31941316 1.500000e-77 300
21 TraesCS6D01G312300 chr6A 90.836 622 43 7 778 1392 564275973 564276587 0.000000e+00 821
22 TraesCS6D01G312300 chr6A 80.840 762 86 38 1839 2585 565342259 565341543 6.290000e-151 544
23 TraesCS6D01G312300 chr6A 91.667 312 24 2 2276 2585 564277359 564277670 5.110000e-117 431
24 TraesCS6D01G312300 chr4A 84.921 630 80 8 972 1594 11817262 11816641 7.860000e-175 623
25 TraesCS6D01G312300 chr3A 94.486 399 17 3 83 478 649574761 649574365 6.120000e-171 610
26 TraesCS6D01G312300 chr7D 96.379 359 13 0 120 478 28797034 28797392 2.220000e-165 592
27 TraesCS6D01G312300 chr7D 94.118 204 9 2 481 683 563502698 563502899 8.990000e-80 307
28 TraesCS6D01G312300 chr7D 99.213 127 1 0 1 127 392196071 392196197 2.000000e-56 230
29 TraesCS6D01G312300 chr7D 97.059 136 3 1 1 136 498148188 498148054 7.200000e-56 228
30 TraesCS6D01G312300 chr3D 95.787 356 15 0 123 478 564940921 564940566 2.230000e-160 575
31 TraesCS6D01G312300 chr3D 95.050 202 10 0 480 681 568225648 568225447 4.150000e-83 318
32 TraesCS6D01G312300 chr3D 95.000 200 9 1 480 679 32190380 32190578 1.930000e-81 313
33 TraesCS6D01G312300 chr3D 100.000 120 0 0 1 120 832400 832519 3.350000e-54 222
34 TraesCS6D01G312300 chr3D 95.652 138 2 2 1 138 608062633 608062766 4.330000e-53 219
35 TraesCS6D01G312300 chr3D 95.652 138 2 2 1 138 608063646 608063779 4.330000e-53 219
36 TraesCS6D01G312300 chr5D 95.265 359 17 0 120 478 411847751 411847393 1.040000e-158 569
37 TraesCS6D01G312300 chr5D 94.949 198 9 1 480 677 11211579 11211383 2.500000e-80 309
38 TraesCS6D01G312300 chr5D 94.416 197 10 1 480 676 411847046 411846851 4.180000e-78 302
39 TraesCS6D01G312300 chr2D 95.960 198 8 0 480 677 587252363 587252560 3.210000e-84 322
40 TraesCS6D01G312300 chr2D 98.473 131 1 1 1 130 522061946 522062076 2.000000e-56 230
41 TraesCS6D01G312300 chr2D 92.715 151 6 4 1 150 274889085 274888939 2.010000e-51 213
42 TraesCS6D01G312300 chrUn 94.444 198 11 0 480 677 284608493 284608690 3.230000e-79 305
43 TraesCS6D01G312300 chr4B 96.296 135 3 2 1 135 621375363 621375495 1.200000e-53 220


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 TraesCS6D01G312300 chr6D 421662999 421665583 2584 True 4774.000000 4774 100.000000 1 2585 1 chr6D.!!$R1 2584
1 TraesCS6D01G312300 chr6D 421695438 421697225 1787 True 2763.000000 2763 94.546000 793 2585 1 chr6D.!!$R3 1792
2 TraesCS6D01G312300 chr6D 421680972 421683766 2794 True 2091.000000 3537 98.084500 121 2585 2 chr6D.!!$R4 2464
3 TraesCS6D01G312300 chr6D 421463127 421466797 3670 False 1266.500000 1465 91.910000 768 2585 2 chr6D.!!$F3 1817
4 TraesCS6D01G312300 chr6D 420966159 420969140 2981 False 1166.000000 1330 90.004000 769 2582 2 chr6D.!!$F2 1813
5 TraesCS6D01G312300 chr6D 422602479 422604039 1560 True 643.500000 712 84.680500 994 2585 2 chr6D.!!$R6 1591
6 TraesCS6D01G312300 chr6D 422216566 422217928 1362 True 348.666667 492 86.245667 1206 2573 3 chr6D.!!$R5 1367
7 TraesCS6D01G312300 chr6B 634501423 634502247 824 False 1203.000000 1203 92.995000 787 1611 1 chr6B.!!$F2 824
8 TraesCS6D01G312300 chr6B 636767072 636767678 606 True 732.000000 732 88.331000 994 1610 1 chr6B.!!$R3 616
9 TraesCS6D01G312300 chr6B 636747306 636748036 730 True 545.000000 545 80.526000 1839 2585 1 chr6B.!!$R2 746
10 TraesCS6D01G312300 chr6A 564275973 564277670 1697 False 626.000000 821 91.251500 778 2585 2 chr6A.!!$F1 1807
11 TraesCS6D01G312300 chr6A 565341543 565342259 716 True 544.000000 544 80.840000 1839 2585 1 chr6A.!!$R1 746
12 TraesCS6D01G312300 chr4A 11816641 11817262 621 True 623.000000 623 84.921000 972 1594 1 chr4A.!!$R1 622
13 TraesCS6D01G312300 chr3D 608062633 608063779 1146 False 219.000000 219 95.652000 1 138 2 chr3D.!!$F3 137
14 TraesCS6D01G312300 chr5D 411846851 411847751 900 True 435.500000 569 94.840500 120 676 2 chr5D.!!$R2 556

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
791 1121 0.109342 CACTTGTGCCTTCTCCTGGT 59.891 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 7179 3.458163 CGTGGAGCTTAGCCCGGA 61.458 66.667 0.73 0.0 0.0 5.14 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
488 818 1.451936 GTGCCGGCTAAGATGGGAT 59.548 57.895 29.70 0.00 0.00 3.85
708 1038 3.140519 ACTGGTACCATAGACTAGAGGGG 59.859 52.174 16.75 0.90 0.00 4.79
764 1094 2.964464 TGGGCTGTTGTGATTGTGAAAT 59.036 40.909 0.00 0.00 0.00 2.17
791 1121 0.109342 CACTTGTGCCTTCTCCTGGT 59.891 55.000 0.00 0.00 0.00 4.00
812 1142 3.454573 CGGGATTGGGGTCGACGA 61.455 66.667 9.92 0.00 0.00 4.20
891 1222 0.526211 CCTCCGTTGTGATCGAGTCA 59.474 55.000 0.00 0.00 0.00 3.41
935 1269 3.423154 GCACTCTTCCGGCGTTGG 61.423 66.667 6.01 0.00 0.00 3.77
1479 2992 1.731613 CGCCGAGCACAACTACGAA 60.732 57.895 0.00 0.00 0.00 3.85
1545 3378 2.844839 GCCCTAGGCCTCGACCAT 60.845 66.667 9.68 0.00 44.06 3.55
1547 3380 0.905337 GCCCTAGGCCTCGACCATAT 60.905 60.000 9.68 0.00 44.06 1.78
1586 3419 4.532126 TGTCACCTGGTCTGATGAGTAAAT 59.468 41.667 0.00 0.00 0.00 1.40
1956 6939 4.592997 AAGAAGTGGGCCTTAAGCTAAT 57.407 40.909 4.53 0.00 43.05 1.73
2015 7002 5.108517 CAATTGCTTCTCTCTCCTCTACAC 58.891 45.833 0.00 0.00 0.00 2.90
2085 7072 1.439228 CCGGATCGCTCACAGTCAT 59.561 57.895 0.00 0.00 0.00 3.06
2134 7124 0.988832 TTCACCACCGCTATTCCCTT 59.011 50.000 0.00 0.00 0.00 3.95
2477 7505 1.135489 TGTTAGAGTCATGTCGACCGC 60.135 52.381 14.12 0.00 46.69 5.68
2501 7530 6.128956 GCGCAAATAAATGTAAGACTTTTGCA 60.129 34.615 0.30 4.28 44.57 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.036388 ACGTACCCTCGTAGACCGAA 60.036 55.000 0.00 0.00 46.75 4.30
478 479 1.754745 GCTGCCCGATCCCATCTTA 59.245 57.895 0.00 0.00 0.00 2.10
480 481 3.933722 CGCTGCCCGATCCCATCT 61.934 66.667 0.00 0.00 40.02 2.90
524 854 2.027192 TCAACTTGGTATCAGCCAGGTC 60.027 50.000 0.47 0.00 46.25 3.85
724 1054 3.381272 CCCAAATGACACTTCACACAAGT 59.619 43.478 0.00 0.00 33.38 3.16
738 1068 2.964464 ACAATCACAACAGCCCAAATGA 59.036 40.909 0.00 0.00 0.00 2.57
764 1094 0.105964 AAGGCACAAGTGACGTAGCA 59.894 50.000 4.04 0.00 45.19 3.49
791 1121 4.418328 CGACCCCAATCCCGCCAA 62.418 66.667 0.00 0.00 0.00 4.52
812 1142 1.834263 AGCTTAGAAACCTCCGCTGAT 59.166 47.619 0.00 0.00 0.00 2.90
891 1222 3.740128 CTCCGCGGGCATAAGCAGT 62.740 63.158 27.83 0.00 44.61 4.40
920 1254 4.016706 CCCCAACGCCGGAAGAGT 62.017 66.667 5.05 0.00 0.00 3.24
1545 3378 3.118445 TGACATCCTGCAAACCGATGATA 60.118 43.478 15.69 5.33 37.44 2.15
1547 3380 1.003003 TGACATCCTGCAAACCGATGA 59.997 47.619 15.69 0.00 37.44 2.92
1956 6939 6.093219 GCTATGGACTCGGTCTTATACGATTA 59.907 42.308 0.00 0.00 38.56 1.75
2157 7179 3.458163 CGTGGAGCTTAGCCCGGA 61.458 66.667 0.73 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.