Multiple sequence alignment - TraesCS6B01G453000

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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 TraesCS6B01G453000 chr6B 100.000 3552 0 0 1 3552 711664352 711667903 0.000000e+00 6560.0
1 TraesCS6B01G453000 chr6B 92.176 1815 126 10 794 2597 711695145 711693336 0.000000e+00 2551.0
2 TraesCS6B01G453000 chr6B 99.857 698 0 1 2856 3552 626660592 626659895 0.000000e+00 1282.0
3 TraesCS6B01G453000 chr6B 85.767 1082 120 13 1518 2577 142099024 142097955 0.000000e+00 1114.0
4 TraesCS6B01G453000 chr6B 89.646 367 25 5 2365 2722 711496362 711496000 4.180000e-124 455.0
5 TraesCS6B01G453000 chr6B 85.511 421 40 13 49 460 711695818 711695410 1.520000e-113 420.0
6 TraesCS6B01G453000 chr6B 95.652 69 2 1 487 555 711695410 711695343 3.750000e-20 110.0
7 TraesCS6B01G453000 chr6D 95.835 1969 72 4 897 2856 466544004 466545971 0.000000e+00 3173.0
8 TraesCS6B01G453000 chr6D 91.004 1812 129 14 797 2597 466551955 466550167 0.000000e+00 2412.0
9 TraesCS6B01G453000 chr6D 87.049 1637 168 20 1093 2696 466528255 466526630 0.000000e+00 1808.0
10 TraesCS6B01G453000 chr6D 85.218 1813 198 32 810 2573 67326881 67325090 0.000000e+00 1799.0
11 TraesCS6B01G453000 chr6D 89.629 916 44 12 1 898 466541326 466542208 0.000000e+00 1118.0
12 TraesCS6B01G453000 chr6D 80.105 191 25 10 282 465 466552937 466552753 2.880000e-26 130.0
13 TraesCS6B01G453000 chr6D 92.405 79 6 0 204 282 466552971 466552893 2.900000e-21 113.0
14 TraesCS6B01G453000 chr6D 91.892 74 6 0 2646 2719 67325061 67324988 1.740000e-18 104.0
15 TraesCS6B01G453000 chr6A 83.530 1949 248 34 654 2566 84700129 84698218 0.000000e+00 1753.0
16 TraesCS6B01G453000 chr6A 84.298 484 40 12 2213 2694 612578285 612577836 1.170000e-119 440.0
17 TraesCS6B01G453000 chr5A 90.909 1166 96 7 584 1739 46959204 46960369 0.000000e+00 1557.0
18 TraesCS6B01G453000 chr5A 88.843 242 19 4 12 247 46720111 46720350 1.250000e-74 291.0
19 TraesCS6B01G453000 chr5A 85.171 263 16 6 272 511 46882912 46883174 7.610000e-62 248.0
20 TraesCS6B01G453000 chr7A 80.652 1964 311 49 794 2722 219396792 219398721 0.000000e+00 1458.0
21 TraesCS6B01G453000 chr7A 84.658 1271 158 23 677 1923 668061902 668063159 0.000000e+00 1232.0
22 TraesCS6B01G453000 chr2D 83.106 1610 227 21 857 2444 493883369 493881783 0.000000e+00 1424.0
23 TraesCS6B01G453000 chr2D 85.897 78 9 2 282 359 414974286 414974211 8.170000e-12 82.4
24 TraesCS6B01G453000 chr2A 82.921 1616 234 20 851 2444 639694681 639696276 0.000000e+00 1417.0
25 TraesCS6B01G453000 chr2A 88.160 625 63 8 1969 2590 581963984 581963368 0.000000e+00 734.0
26 TraesCS6B01G453000 chr2A 84.722 144 12 5 2723 2856 2616072 2615929 6.190000e-28 135.0
27 TraesCS6B01G453000 chr2A 82.550 149 14 6 2719 2856 2614229 2614376 1.730000e-23 121.0
28 TraesCS6B01G453000 chr2A 82.639 144 14 5 2724 2856 23941100 23941243 2.240000e-22 117.0
29 TraesCS6B01G453000 chr2A 85.714 70 8 2 290 359 581966257 581966190 4.920000e-09 73.1
30 TraesCS6B01G453000 chr7D 88.319 1190 124 11 758 1936 576658036 576659221 0.000000e+00 1413.0
31 TraesCS6B01G453000 chr7D 86.262 626 76 8 1969 2590 576661160 576661779 0.000000e+00 671.0
32 TraesCS6B01G453000 chr7D 93.103 87 6 0 204 290 576657406 576657492 1.040000e-25 128.0
33 TraesCS6B01G453000 chr3B 100.000 698 0 0 2855 3552 292383483 292384180 0.000000e+00 1290.0
34 TraesCS6B01G453000 chr3B 99.857 700 1 0 2853 3552 292391560 292392259 0.000000e+00 1288.0
35 TraesCS6B01G453000 chr2B 99.857 700 1 0 2853 3552 451176083 451176782 0.000000e+00 1288.0
36 TraesCS6B01G453000 chr2B 99.857 697 1 0 2856 3552 443046355 443047051 0.000000e+00 1282.0
37 TraesCS6B01G453000 chr2B 99.715 701 1 1 2853 3552 443054430 443055130 0.000000e+00 1282.0
38 TraesCS6B01G453000 chr2B 81.079 1390 226 25 583 1947 246574409 246575786 0.000000e+00 1075.0
39 TraesCS6B01G453000 chr2B 82.857 140 20 4 237 374 246569990 246570127 4.820000e-24 122.0
40 TraesCS6B01G453000 chrUn 99.857 697 1 0 2856 3552 245665600 245664904 0.000000e+00 1282.0
41 TraesCS6B01G453000 chr5B 99.428 699 3 1 2855 3552 37237225 37236527 0.000000e+00 1267.0
42 TraesCS6B01G453000 chr5B 99.287 701 1 1 2856 3552 37229140 37228440 0.000000e+00 1264.0
43 TraesCS6B01G453000 chr1A 82.993 147 16 3 2722 2859 533777439 533777293 1.340000e-24 124.0
44 TraesCS6B01G453000 chr1A 82.069 145 15 6 2723 2856 533772558 533772702 2.900000e-21 113.0
45 TraesCS6B01G453000 chr1B 80.128 156 17 7 2717 2859 54923812 54923658 1.740000e-18 104.0
46 TraesCS6B01G453000 chr1B 90.278 72 7 0 2788 2859 54940643 54940572 1.050000e-15 95.3
47 TraesCS6B01G453000 chr7B 79.167 144 20 6 2726 2859 630605620 630605477 1.360000e-14 91.6


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 TraesCS6B01G453000 chr6B 711664352 711667903 3551 False 6560.000000 6560 100.000 1 3552 1 chr6B.!!$F1 3551
1 TraesCS6B01G453000 chr6B 626659895 626660592 697 True 1282.000000 1282 99.857 2856 3552 1 chr6B.!!$R2 696
2 TraesCS6B01G453000 chr6B 142097955 142099024 1069 True 1114.000000 1114 85.767 1518 2577 1 chr6B.!!$R1 1059
3 TraesCS6B01G453000 chr6B 711693336 711695818 2482 True 1027.000000 2551 91.113 49 2597 3 chr6B.!!$R4 2548
4 TraesCS6B01G453000 chr6D 466541326 466545971 4645 False 2145.500000 3173 92.732 1 2856 2 chr6D.!!$F1 2855
5 TraesCS6B01G453000 chr6D 466526630 466528255 1625 True 1808.000000 1808 87.049 1093 2696 1 chr6D.!!$R1 1603
6 TraesCS6B01G453000 chr6D 67324988 67326881 1893 True 951.500000 1799 88.555 810 2719 2 chr6D.!!$R2 1909
7 TraesCS6B01G453000 chr6D 466550167 466552971 2804 True 885.000000 2412 87.838 204 2597 3 chr6D.!!$R3 2393
8 TraesCS6B01G453000 chr6A 84698218 84700129 1911 True 1753.000000 1753 83.530 654 2566 1 chr6A.!!$R1 1912
9 TraesCS6B01G453000 chr5A 46959204 46960369 1165 False 1557.000000 1557 90.909 584 1739 1 chr5A.!!$F3 1155
10 TraesCS6B01G453000 chr7A 219396792 219398721 1929 False 1458.000000 1458 80.652 794 2722 1 chr7A.!!$F1 1928
11 TraesCS6B01G453000 chr7A 668061902 668063159 1257 False 1232.000000 1232 84.658 677 1923 1 chr7A.!!$F2 1246
12 TraesCS6B01G453000 chr2D 493881783 493883369 1586 True 1424.000000 1424 83.106 857 2444 1 chr2D.!!$R2 1587
13 TraesCS6B01G453000 chr2A 639694681 639696276 1595 False 1417.000000 1417 82.921 851 2444 1 chr2A.!!$F3 1593
14 TraesCS6B01G453000 chr2A 581963368 581966257 2889 True 403.550000 734 86.937 290 2590 2 chr2A.!!$R2 2300
15 TraesCS6B01G453000 chr7D 576657406 576661779 4373 False 737.333333 1413 89.228 204 2590 3 chr7D.!!$F1 2386
16 TraesCS6B01G453000 chr3B 292383483 292384180 697 False 1290.000000 1290 100.000 2855 3552 1 chr3B.!!$F1 697
17 TraesCS6B01G453000 chr3B 292391560 292392259 699 False 1288.000000 1288 99.857 2853 3552 1 chr3B.!!$F2 699
18 TraesCS6B01G453000 chr2B 451176083 451176782 699 False 1288.000000 1288 99.857 2853 3552 1 chr2B.!!$F5 699
19 TraesCS6B01G453000 chr2B 443046355 443047051 696 False 1282.000000 1282 99.857 2856 3552 1 chr2B.!!$F3 696
20 TraesCS6B01G453000 chr2B 443054430 443055130 700 False 1282.000000 1282 99.715 2853 3552 1 chr2B.!!$F4 699
21 TraesCS6B01G453000 chr2B 246574409 246575786 1377 False 1075.000000 1075 81.079 583 1947 1 chr2B.!!$F2 1364
22 TraesCS6B01G453000 chrUn 245664904 245665600 696 True 1282.000000 1282 99.857 2856 3552 1 chrUn.!!$R1 696
23 TraesCS6B01G453000 chr5B 37236527 37237225 698 True 1267.000000 1267 99.428 2855 3552 1 chr5B.!!$R2 697
24 TraesCS6B01G453000 chr5B 37228440 37229140 700 True 1264.000000 1264 99.287 2856 3552 1 chr5B.!!$R1 696


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
744 1580 0.252927 AACAGAAGAGGAGGAGGGGG 60.253 60.0 0.0 0.0 0.0 5.40 F
752 1588 0.269173 AGGAGGAGGGGGATTCGATT 59.731 55.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2469 7223 0.389817 CTCATCAGCGTTCCGTGGAA 60.390 55.0 0.0 0.0 0.00 3.53 R
2740 7495 5.044476 TGAATAGTGTCCCCAATAATGGTGT 60.044 40.0 0.0 0.0 46.01 4.16 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
39 41 4.668289 AGAAAAACGCATCGAACACTTTT 58.332 34.783 0.00 0.00 0.00 2.27
126 143 6.148150 CCCAGTACTATACAGCAAACGAAAAA 59.852 38.462 0.00 0.00 0.00 1.94
130 147 5.928153 ACTATACAGCAAACGAAAAAGCTC 58.072 37.500 0.00 0.00 34.61 4.09
133 150 2.119457 CAGCAAACGAAAAAGCTCCAC 58.881 47.619 0.00 0.00 34.61 4.02
135 152 2.427095 AGCAAACGAAAAAGCTCCACTT 59.573 40.909 0.00 0.00 41.70 3.16
483 536 2.202756 GTGACGGATGCGGGAGAC 60.203 66.667 12.44 0.00 0.00 3.36
511 564 0.322456 TTCCTTGTGCAATCGGGGAG 60.322 55.000 0.00 0.00 0.00 4.30
561 1378 0.856982 GATCCTCCTCCCTCTCCTCA 59.143 60.000 0.00 0.00 0.00 3.86
570 1387 4.170845 TCCTCCCTCTCCTCAAATATCTCA 59.829 45.833 0.00 0.00 0.00 3.27
575 1392 4.224818 CCTCTCCTCAAATATCTCATCCCC 59.775 50.000 0.00 0.00 0.00 4.81
576 1393 4.171234 TCTCCTCAAATATCTCATCCCCC 58.829 47.826 0.00 0.00 0.00 5.40
577 1394 4.140350 TCTCCTCAAATATCTCATCCCCCT 60.140 45.833 0.00 0.00 0.00 4.79
579 1396 4.984268 TCCTCAAATATCTCATCCCCCTTT 59.016 41.667 0.00 0.00 0.00 3.11
580 1397 5.436374 TCCTCAAATATCTCATCCCCCTTTT 59.564 40.000 0.00 0.00 0.00 2.27
581 1398 5.537674 CCTCAAATATCTCATCCCCCTTTTG 59.462 44.000 0.00 0.00 0.00 2.44
687 1504 2.879026 GGCGTCCCTGATCTTATTTTCC 59.121 50.000 0.00 0.00 0.00 3.13
731 1554 2.750712 GTGCCGGCCTAAATAAACAGAA 59.249 45.455 26.77 0.00 0.00 3.02
744 1580 0.252927 AACAGAAGAGGAGGAGGGGG 60.253 60.000 0.00 0.00 0.00 5.40
745 1581 1.156322 ACAGAAGAGGAGGAGGGGGA 61.156 60.000 0.00 0.00 0.00 4.81
747 1583 1.031112 AGAAGAGGAGGAGGGGGATT 58.969 55.000 0.00 0.00 0.00 3.01
748 1584 1.061735 AGAAGAGGAGGAGGGGGATTC 60.062 57.143 0.00 0.00 0.00 2.52
752 1588 0.269173 AGGAGGAGGGGGATTCGATT 59.731 55.000 0.00 0.00 0.00 3.34
753 1589 0.687920 GGAGGAGGGGGATTCGATTC 59.312 60.000 0.00 0.00 0.00 2.52
754 1590 1.424638 GAGGAGGGGGATTCGATTCA 58.575 55.000 9.36 0.00 0.00 2.57
790 1657 0.323302 TCCAAATAGTGCAGGCGTCA 59.677 50.000 0.00 0.00 0.00 4.35
805 1746 3.820467 AGGCGTCACATCATCAAGAAAAA 59.180 39.130 0.00 0.00 0.00 1.94
954 3741 4.329462 TTTGTTGTTCCAGGTAAATGCC 57.671 40.909 0.00 0.00 0.00 4.40
983 3779 2.356135 AGCAACTCACAACAAAGACGT 58.644 42.857 0.00 0.00 0.00 4.34
1050 3861 3.668447 TGACCTTCTGCTCAACATTCTC 58.332 45.455 0.00 0.00 0.00 2.87
1080 3891 2.193447 GACACGCTCGATGCAATAAGA 58.807 47.619 0.00 0.00 43.06 2.10
1182 3993 2.094700 TCACCATGTTAGAGCTCGTGTC 60.095 50.000 8.37 1.35 0.00 3.67
1184 3995 2.094494 ACCATGTTAGAGCTCGTGTCTG 60.094 50.000 8.37 4.97 0.00 3.51
1276 4087 1.406065 CCCCGAGATCACCATCAGCT 61.406 60.000 0.00 0.00 0.00 4.24
1414 4225 7.548427 CAGAGAAGATTCATTTGAAGTGCTCTA 59.452 37.037 12.46 0.00 37.48 2.43
1416 4227 6.597280 AGAAGATTCATTTGAAGTGCTCTACC 59.403 38.462 0.00 0.00 37.48 3.18
1546 4361 1.484653 TGGACATACCCAACATCCTCG 59.515 52.381 0.00 0.00 38.00 4.63
1928 4749 5.652014 TGAATCATACCTGTCCATTTTCACC 59.348 40.000 0.00 0.00 0.00 4.02
2202 6948 2.882761 CAGTATGGGATCATTGGTGCAG 59.117 50.000 0.00 0.00 34.96 4.41
2362 7110 3.698040 ACATCTTTGTGGGATTCATCAGC 59.302 43.478 0.00 0.00 33.85 4.26
2446 7200 1.021390 GCTGTGGTGACTTGGATCCG 61.021 60.000 7.39 0.00 0.00 4.18
2469 7223 2.027745 AGGTGAAGTGTGCATCGAGATT 60.028 45.455 0.00 0.00 0.00 2.40
2631 7386 3.288092 GGTCTGTTGTTGGAAGGAGTTT 58.712 45.455 0.00 0.00 0.00 2.66
2774 7530 2.812011 GGACACTATTCACAAAACCGCT 59.188 45.455 0.00 0.00 0.00 5.52
2782 7538 4.657436 TTCACAAAACCGCTACCATTTT 57.343 36.364 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 4.244862 GTGTTCGATACGTTCCCCTTAAA 58.755 43.478 0.00 0.00 0.00 1.52
52 58 1.135489 GCTCAGTCGTGGTGTTCGATA 60.135 52.381 0.00 0.00 39.45 2.92
126 143 1.959282 CAGCCAAAGAAAAGTGGAGCT 59.041 47.619 0.00 0.00 37.03 4.09
130 147 0.033920 GCCCAGCCAAAGAAAAGTGG 59.966 55.000 0.00 0.00 38.00 4.00
135 152 3.549964 TCTTCGGCCCAGCCAAAGAAA 62.550 52.381 6.53 0.00 46.98 2.52
483 536 3.624326 TTGCACAAGGAAATCAACTCG 57.376 42.857 0.00 0.00 0.00 4.18
561 1378 5.709594 CTCCAAAAGGGGGATGAGATATTT 58.290 41.667 0.00 0.00 41.01 1.40
570 1387 1.699752 CAGGCTCCAAAAGGGGGAT 59.300 57.895 0.00 0.00 41.01 3.85
575 1392 3.064324 CCGGCAGGCTCCAAAAGG 61.064 66.667 0.00 0.00 0.00 3.11
627 1444 3.700350 CCCCCTCCCACTCCTCCT 61.700 72.222 0.00 0.00 0.00 3.69
660 1477 0.036010 AGATCAGGGACGCCAACTTG 60.036 55.000 0.00 0.00 0.00 3.16
687 1504 0.462047 AAAGCAGACTAATCGCCGGG 60.462 55.000 2.18 0.00 0.00 5.73
731 1554 1.234529 CGAATCCCCCTCCTCCTCT 59.765 63.158 0.00 0.00 0.00 3.69
744 1580 8.335356 TCGACCTTATTTGAATTGAATCGAATC 58.665 33.333 0.00 0.00 35.51 2.52
745 1581 8.208718 TCGACCTTATTTGAATTGAATCGAAT 57.791 30.769 0.00 0.00 37.26 3.34
747 1583 7.042051 GGATCGACCTTATTTGAATTGAATCGA 60.042 37.037 2.18 2.18 35.41 3.59
748 1584 7.072030 GGATCGACCTTATTTGAATTGAATCG 58.928 38.462 0.00 0.00 35.41 3.34
752 1588 7.695480 TTTGGATCGACCTTATTTGAATTGA 57.305 32.000 0.00 0.00 39.86 2.57
753 1589 9.669353 CTATTTGGATCGACCTTATTTGAATTG 57.331 33.333 0.00 0.00 39.86 2.32
754 1590 9.408648 ACTATTTGGATCGACCTTATTTGAATT 57.591 29.630 0.00 0.00 39.86 2.17
790 1657 7.546358 TCAACAACTGTTTTTCTTGATGATGT 58.454 30.769 0.00 0.00 35.83 3.06
805 1746 2.350522 GCTGATCGGATCAACAACTGT 58.649 47.619 20.29 0.00 39.11 3.55
917 3699 9.435688 GGAACAACAAATAATCAGCCTTTTTAT 57.564 29.630 0.00 0.00 0.00 1.40
954 3741 3.374988 TGTTGTGAGTTGCTTTCTGTGAG 59.625 43.478 0.00 0.00 0.00 3.51
983 3779 1.536766 CATCTTCTTCGCTGCCAACAA 59.463 47.619 0.00 0.00 0.00 2.83
986 3782 0.324614 TCCATCTTCTTCGCTGCCAA 59.675 50.000 0.00 0.00 0.00 4.52
1019 3830 1.000396 AGAAGGTCATTGGGCAGCC 60.000 57.895 1.26 1.26 0.00 4.85
1050 3861 3.343788 GAGCGTGTCCACCCTCTCG 62.344 68.421 5.12 0.00 34.35 4.04
1080 3891 1.294780 CTTGGAGAGGACGCAAGCT 59.705 57.895 0.00 0.00 45.62 3.74
1182 3993 3.242706 TGACAAATTCACTGACGTTGCAG 60.243 43.478 2.88 2.88 41.63 4.41
1184 3995 3.002246 TCTGACAAATTCACTGACGTTGC 59.998 43.478 0.00 0.00 0.00 4.17
1458 4269 2.072874 ATGCACCAGGACAAGCACCT 62.073 55.000 0.00 0.00 40.14 4.00
1546 4361 2.633509 CCAGGAGCTTGCAAGTGCC 61.634 63.158 26.55 25.00 41.18 5.01
1783 4601 3.827302 GTCGATAGGGAGCCAGATTTAGA 59.173 47.826 0.00 0.00 0.00 2.10
1813 4631 4.074970 CCAAGGAGCTGACTTAACACAAT 58.925 43.478 0.00 0.00 0.00 2.71
1897 4718 5.192927 TGGACAGGTATGATTCAAATGACC 58.807 41.667 0.00 0.00 0.00 4.02
2031 6777 1.260544 GCTTTCTGGCAGAACCCAAT 58.739 50.000 28.58 0.00 33.26 3.16
2202 6948 7.897575 AACTCTTTGTCTCTCATCAACATAC 57.102 36.000 0.00 0.00 0.00 2.39
2362 7110 0.448990 CCGCATGTTCCATGACACAG 59.551 55.000 8.34 0.00 31.30 3.66
2446 7200 1.728971 CTCGATGCACACTTCACCTTC 59.271 52.381 0.00 0.00 0.00 3.46
2469 7223 0.389817 CTCATCAGCGTTCCGTGGAA 60.390 55.000 0.00 0.00 0.00 3.53
2740 7495 5.044476 TGAATAGTGTCCCCAATAATGGTGT 60.044 40.000 0.00 0.00 46.01 4.16
2746 7501 6.209788 GGTTTTGTGAATAGTGTCCCCAATAA 59.790 38.462 0.00 0.00 0.00 1.40
2782 7538 4.227527 ACCCCAATGTTGGTGGTTTAAAAA 59.772 37.500 15.12 0.00 44.36 1.94
2842 7606 4.495422 GGATGTGACATCTACTCAAACGT 58.505 43.478 23.28 0.00 0.00 3.99
2843 7607 3.865745 GGGATGTGACATCTACTCAAACG 59.134 47.826 23.28 0.00 0.00 3.60



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

AutoCloner maintained by Alex Coulton.