Multiple sequence alignment - TraesCS2D01G239900

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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 TraesCS2D01G239900 chr2D 100.000 4306 0 0 1 4306 256890547 256886242 0.000000e+00 7952
1 TraesCS2D01G239900 chrUn 97.517 2658 64 1 1 2658 31366063 31363408 0.000000e+00 4542
2 TraesCS2D01G239900 chrUn 93.910 1642 79 13 2654 4283 31363339 31361707 0.000000e+00 2459
3 TraesCS2D01G239900 chr7A 96.352 2659 90 4 1 2658 117642303 117644955 0.000000e+00 4366
4 TraesCS2D01G239900 chr7A 93.992 1548 77 11 2741 4283 117669654 117671190 0.000000e+00 2329
5 TraesCS2D01G239900 chr2B 96.087 2658 104 0 1 2658 710034338 710036995 0.000000e+00 4333
6 TraesCS2D01G239900 chr2B 89.947 945 83 9 2722 3662 710036977 710037913 0.000000e+00 1208
7 TraesCS2D01G239900 chr2B 91.627 633 42 5 3661 4285 710038172 710038801 0.000000e+00 865
8 TraesCS2D01G239900 chr5B 94.361 2660 146 2 1 2658 159690065 159687408 0.000000e+00 4078
9 TraesCS2D01G239900 chr5B 87.943 2654 295 16 3 2638 465528992 465526346 0.000000e+00 3105
10 TraesCS2D01G239900 chr5B 85.894 1673 171 39 2654 4285 159687339 159685691 0.000000e+00 1722
11 TraesCS2D01G239900 chr3B 94.328 2662 143 6 1 2658 61994674 61997331 0.000000e+00 4072
12 TraesCS2D01G239900 chr3B 86.116 1671 171 36 2654 4283 61997400 61999050 0.000000e+00 1744
13 TraesCS2D01G239900 chr4B 93.797 2660 161 2 1 2658 66638259 66635602 0.000000e+00 3995
14 TraesCS2D01G239900 chr4B 85.236 1612 172 44 2654 4220 66635534 66633944 0.000000e+00 1598
15 TraesCS2D01G239900 chr5A 93.034 2670 171 5 1 2658 145672188 145674854 0.000000e+00 3886
16 TraesCS2D01G239900 chr5A 86.597 761 82 15 2722 3476 145674836 145675582 0.000000e+00 822
17 TraesCS2D01G239900 chr6A 92.769 2669 179 5 1 2658 272151458 272148793 0.000000e+00 3847
18 TraesCS2D01G239900 chr4A 85.364 1674 181 44 2656 4286 528939966 528941618 0.000000e+00 1676
19 TraesCS2D01G239900 chr1D 88.351 764 72 15 2666 3421 59630315 59631069 0.000000e+00 902
20 TraesCS2D01G239900 chr1D 89.294 411 39 5 3406 3813 59631085 59631493 1.070000e-140 510
21 TraesCS2D01G239900 chr1D 84.096 459 63 10 3829 4282 291777499 291777046 6.610000e-118 435
22 TraesCS2D01G239900 chr1A 81.423 1012 146 29 3282 4283 558028745 558027766 0.000000e+00 789
23 TraesCS2D01G239900 chr1A 91.081 370 24 3 1 361 558029114 558028745 3.870000e-135 492
24 TraesCS2D01G239900 chr2A 84.948 764 101 13 3525 4282 193546013 193546768 0.000000e+00 761


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 TraesCS2D01G239900 chr2D 256886242 256890547 4305 True 7952.000000 7952 100.000000 1 4306 1 chr2D.!!$R1 4305
1 TraesCS2D01G239900 chrUn 31361707 31366063 4356 True 3500.500000 4542 95.713500 1 4283 2 chrUn.!!$R1 4282
2 TraesCS2D01G239900 chr7A 117642303 117644955 2652 False 4366.000000 4366 96.352000 1 2658 1 chr7A.!!$F1 2657
3 TraesCS2D01G239900 chr7A 117669654 117671190 1536 False 2329.000000 2329 93.992000 2741 4283 1 chr7A.!!$F2 1542
4 TraesCS2D01G239900 chr2B 710034338 710038801 4463 False 2135.333333 4333 92.553667 1 4285 3 chr2B.!!$F1 4284
5 TraesCS2D01G239900 chr5B 465526346 465528992 2646 True 3105.000000 3105 87.943000 3 2638 1 chr5B.!!$R1 2635
6 TraesCS2D01G239900 chr5B 159685691 159690065 4374 True 2900.000000 4078 90.127500 1 4285 2 chr5B.!!$R2 4284
7 TraesCS2D01G239900 chr3B 61994674 61999050 4376 False 2908.000000 4072 90.222000 1 4283 2 chr3B.!!$F1 4282
8 TraesCS2D01G239900 chr4B 66633944 66638259 4315 True 2796.500000 3995 89.516500 1 4220 2 chr4B.!!$R1 4219
9 TraesCS2D01G239900 chr5A 145672188 145675582 3394 False 2354.000000 3886 89.815500 1 3476 2 chr5A.!!$F1 3475
10 TraesCS2D01G239900 chr6A 272148793 272151458 2665 True 3847.000000 3847 92.769000 1 2658 1 chr6A.!!$R1 2657
11 TraesCS2D01G239900 chr4A 528939966 528941618 1652 False 1676.000000 1676 85.364000 2656 4286 1 chr4A.!!$F1 1630
12 TraesCS2D01G239900 chr1D 59630315 59631493 1178 False 706.000000 902 88.822500 2666 3813 2 chr1D.!!$F1 1147
13 TraesCS2D01G239900 chr1A 558027766 558029114 1348 True 640.500000 789 86.252000 1 4283 2 chr1A.!!$R1 4282
14 TraesCS2D01G239900 chr2A 193546013 193546768 755 False 761.000000 761 84.948000 3525 4282 1 chr2A.!!$F1 757

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
252 264 5.161358 TGATTCTAATGCGCTCCGTAATAG 58.839 41.667 9.73 0.0 0.00 1.73 F
1013 1030 2.169352 CACACTGTATGGAAGGGGAGAG 59.831 54.545 0.00 0.0 0.00 3.20 F
1725 1745 2.291741 CCTTGCAGAGACCTTCAACAAC 59.708 50.000 0.00 0.0 0.00 3.32 F
2564 2586 1.153823 CAGCCCTCGTCCTGTTACG 60.154 63.158 0.00 0.0 44.19 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 1892 1.246737 GCCCAAGCCCTCTTGTTCTG 61.247 60.000 4.6 0.0 46.33 3.02 R
2139 2159 2.735663 CCATTGCGATCTATCTGTGAGC 59.264 50.000 0.0 0.0 0.00 4.26 R
3216 3331 2.485479 CGGGAGTCCATGTTTCCATAGG 60.485 54.545 12.3 0.0 32.50 2.57 R
4285 4733 0.107214 CGGGGTGTGGCTATGTCATT 60.107 55.000 0.0 0.0 0.00 2.57 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
58 60 6.293407 GGAAGTTGTTGACATCATTTCTCGAA 60.293 38.462 0.00 0.00 0.00 3.71
252 264 5.161358 TGATTCTAATGCGCTCCGTAATAG 58.839 41.667 9.73 0.00 0.00 1.73
709 721 6.650427 TGTCGTATTATGGCTGATAAGACT 57.350 37.500 15.71 0.00 36.83 3.24
738 750 7.960262 ACCAGGGTACTAACATAGCTATTTAC 58.040 38.462 2.64 1.31 0.00 2.01
741 756 9.477484 CAGGGTACTAACATAGCTATTTACTTG 57.523 37.037 2.64 0.00 0.00 3.16
1012 1029 2.187958 CACACTGTATGGAAGGGGAGA 58.812 52.381 0.00 0.00 0.00 3.71
1013 1030 2.169352 CACACTGTATGGAAGGGGAGAG 59.831 54.545 0.00 0.00 0.00 3.20
1059 1078 2.983898 TGGTTCTTGGGGTAGTAGCTTT 59.016 45.455 0.00 0.00 0.00 3.51
1419 1439 4.573900 AGCTTGCTATATGTACTGATGCC 58.426 43.478 0.00 0.00 0.00 4.40
1590 1610 4.988540 TCAATGTTTGAGTACCACTTCTCG 59.011 41.667 0.00 0.00 34.08 4.04
1612 1632 5.044558 CGAAGGTTCTAGAATCTAGCCAAC 58.955 45.833 18.59 11.72 30.24 3.77
1725 1745 2.291741 CCTTGCAGAGACCTTCAACAAC 59.708 50.000 0.00 0.00 0.00 3.32
1766 1786 3.657398 TCTCCCCGTAGATGTGTTAGA 57.343 47.619 0.00 0.00 0.00 2.10
1772 1792 4.039245 CCCCGTAGATGTGTTAGATGACAT 59.961 45.833 0.00 0.00 35.46 3.06
1795 1815 9.807649 ACATGCTTAATGGAAAGATAATGAAAC 57.192 29.630 0.00 0.00 40.94 2.78
1907 1927 3.019799 TGGGCACTTGAAAGTTACCAA 57.980 42.857 11.33 0.54 38.53 3.67
2172 2192 4.516698 AGATCGCAATGGCCTAATGTTAAG 59.483 41.667 3.32 0.00 36.38 1.85
2443 2463 9.959749 TTTTCTTTTATATTGCTCGAGTTTGTT 57.040 25.926 15.13 0.00 0.00 2.83
2564 2586 1.153823 CAGCCCTCGTCCTGTTACG 60.154 63.158 0.00 0.00 44.19 3.18
2573 2595 1.399791 CGTCCTGTTACGAGGAGGTAC 59.600 57.143 12.18 0.00 43.11 3.34
2647 2671 7.436933 TCTCATACTACATATTGTTCAGCCAG 58.563 38.462 0.00 0.00 0.00 4.85
2689 2791 9.985318 GCTTATCATCAATATCTCTACAAATGC 57.015 33.333 0.00 0.00 0.00 3.56
2797 2903 2.097791 CACAAGCTAGTCCTCGACCTAC 59.902 54.545 0.00 0.00 32.18 3.18
2871 2979 7.533561 GGTGCATGTTTTTACATTAAACAATGC 59.466 33.333 18.20 18.20 45.46 3.56
3013 3122 7.710907 TCTTCAATATATCTACAAGTGTGGCAC 59.289 37.037 11.55 11.55 34.10 5.01
3014 3123 6.883744 TCAATATATCTACAAGTGTGGCACA 58.116 36.000 17.96 17.96 36.74 4.57
3033 3145 7.064490 GTGGCACATTTTTATCCTAAACAATGG 59.936 37.037 13.86 0.00 44.52 3.16
3345 3460 7.848223 TCATGTTATGTGTTTAGTGATCTGG 57.152 36.000 0.00 0.00 0.00 3.86
3350 3465 9.599866 TGTTATGTGTTTAGTGATCTGGATTAG 57.400 33.333 0.00 0.00 0.00 1.73
3361 3476 3.281727 TCTGGATTAGGTTCATGCCAC 57.718 47.619 0.00 0.00 0.00 5.01
3362 3477 2.846206 TCTGGATTAGGTTCATGCCACT 59.154 45.455 0.00 0.00 0.00 4.00
3363 3478 3.266772 TCTGGATTAGGTTCATGCCACTT 59.733 43.478 0.00 0.00 0.00 3.16
3435 3585 4.758165 TGTGATCTTCTCGTGTGTGTAGTA 59.242 41.667 0.00 0.00 0.00 1.82
3623 3787 7.528182 CGTGAAAATGCTGTTGAAATTTTGATC 59.472 33.333 0.00 0.00 34.51 2.92
3682 4106 8.284945 TGTTAGATCCCAATCTGAATTTTGAG 57.715 34.615 0.00 0.00 42.36 3.02
3813 4242 1.608590 GCTAGCAAACTGAGCAACCAA 59.391 47.619 10.63 0.00 36.20 3.67
3841 4271 3.815401 ACAAACTACAACTGATGGAGCAC 59.185 43.478 0.00 0.00 44.65 4.40
3873 4303 1.220206 CGAGCACTTCTCCAGCCAT 59.780 57.895 0.00 0.00 38.62 4.40
3876 4310 0.917533 AGCACTTCTCCAGCCATCAT 59.082 50.000 0.00 0.00 0.00 2.45
3877 4311 1.134159 AGCACTTCTCCAGCCATCATC 60.134 52.381 0.00 0.00 0.00 2.92
3897 4331 0.731514 GCAACGAGCAGCTACGTACA 60.732 55.000 16.84 0.00 44.79 2.90
4035 4476 2.920912 GGTGGTGGTGTCGGGAGA 60.921 66.667 0.00 0.00 0.00 3.71
4080 4523 3.123621 GCTTCATTCTGTCATCGTTTCGT 59.876 43.478 0.00 0.00 0.00 3.85
4154 4600 2.552373 GGGTCTGGACGTGGAAAAGAAT 60.552 50.000 0.00 0.00 0.00 2.40
4159 4605 3.556999 TGGACGTGGAAAAGAATGGAAA 58.443 40.909 0.00 0.00 0.00 3.13
4285 4733 6.160576 GGCATTTTCTCAATTTGCCCTATA 57.839 37.500 4.04 0.00 45.63 1.31
4286 4734 6.581712 GGCATTTTCTCAATTTGCCCTATAA 58.418 36.000 4.04 0.00 45.63 0.98
4287 4735 7.219322 GGCATTTTCTCAATTTGCCCTATAAT 58.781 34.615 4.04 0.00 45.63 1.28
4288 4736 7.172019 GGCATTTTCTCAATTTGCCCTATAATG 59.828 37.037 4.04 0.00 45.63 1.90
4289 4737 7.927629 GCATTTTCTCAATTTGCCCTATAATGA 59.072 33.333 0.00 0.00 0.00 2.57
4290 4738 9.252962 CATTTTCTCAATTTGCCCTATAATGAC 57.747 33.333 0.00 0.00 0.00 3.06
4291 4739 7.953005 TTTCTCAATTTGCCCTATAATGACA 57.047 32.000 0.00 0.00 0.00 3.58
4292 4740 8.537728 TTTCTCAATTTGCCCTATAATGACAT 57.462 30.769 0.00 0.00 0.00 3.06
4293 4741 9.639563 TTTCTCAATTTGCCCTATAATGACATA 57.360 29.630 0.00 0.00 0.00 2.29
4294 4742 8.853077 TCTCAATTTGCCCTATAATGACATAG 57.147 34.615 0.00 0.00 0.00 2.23
4295 4743 7.391554 TCTCAATTTGCCCTATAATGACATAGC 59.608 37.037 0.00 0.00 0.00 2.97
4296 4744 6.434028 TCAATTTGCCCTATAATGACATAGCC 59.566 38.462 0.00 0.00 0.00 3.93
4297 4745 4.991789 TTGCCCTATAATGACATAGCCA 57.008 40.909 0.00 0.00 0.00 4.75
4298 4746 4.286297 TGCCCTATAATGACATAGCCAC 57.714 45.455 0.00 0.00 0.00 5.01
4299 4747 3.650461 TGCCCTATAATGACATAGCCACA 59.350 43.478 0.00 0.00 0.00 4.17
4300 4748 4.003648 GCCCTATAATGACATAGCCACAC 58.996 47.826 0.00 0.00 0.00 3.82
4301 4749 4.579869 CCCTATAATGACATAGCCACACC 58.420 47.826 0.00 0.00 0.00 4.16
4302 4750 4.565652 CCCTATAATGACATAGCCACACCC 60.566 50.000 0.00 0.00 0.00 4.61
4303 4751 3.508845 ATAATGACATAGCCACACCCC 57.491 47.619 0.00 0.00 0.00 4.95
4304 4752 0.107214 AATGACATAGCCACACCCCG 60.107 55.000 0.00 0.00 0.00 5.73
4305 4753 1.983119 ATGACATAGCCACACCCCGG 61.983 60.000 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 60 5.578073 AGCAATTCTTTCTCTTCCCATCTT 58.422 37.500 0.00 0.00 0.00 2.40
252 264 5.408909 CCATCAGATTGCACATATCTCTCAC 59.591 44.000 0.00 0.00 30.05 3.51
611 623 1.070758 GTCAGCTCTGTGAGTCCCAAA 59.929 52.381 0.00 0.00 31.39 3.28
709 721 5.774179 AGCTATGTTAGTACCCTGGTCTTA 58.226 41.667 0.00 0.00 0.00 2.10
1012 1029 0.251832 TCGTCCTTTGCTCTCTCCCT 60.252 55.000 0.00 0.00 0.00 4.20
1013 1030 0.174617 CTCGTCCTTTGCTCTCTCCC 59.825 60.000 0.00 0.00 0.00 4.30
1059 1078 7.389330 TCTGCTTTGAAATTGAATAGGTAACGA 59.611 33.333 0.00 0.00 46.39 3.85
1386 1406 7.408756 ACATATAGCAAGCTTTGAAATTGGA 57.591 32.000 0.00 0.00 0.00 3.53
1419 1439 4.702131 ACTGCATTTTCTAGGCCTTTACAG 59.298 41.667 12.58 10.33 0.00 2.74
1515 1535 3.128415 TGCGTCCAATTATGTCACCATTG 59.872 43.478 0.50 0.50 32.29 2.82
1590 1610 5.129650 AGGTTGGCTAGATTCTAGAACCTTC 59.870 44.000 26.45 15.56 38.86 3.46
1725 1745 6.319911 GGAGATCTTTGGTTCCTTTTATCCAG 59.680 42.308 0.00 0.00 0.00 3.86
1766 1786 9.358406 TCATTATCTTTCCATTAAGCATGTCAT 57.642 29.630 0.00 0.00 0.00 3.06
1772 1792 8.469200 CCAGTTTCATTATCTTTCCATTAAGCA 58.531 33.333 0.00 0.00 0.00 3.91
1795 1815 2.951642 TCTTTCTCCTTGTTGCAACCAG 59.048 45.455 26.14 23.32 0.00 4.00
1872 1892 1.246737 GCCCAAGCCCTCTTGTTCTG 61.247 60.000 4.60 0.00 46.33 3.02
1907 1927 6.314917 ACCTCACCTTTCCAATTACTTGATT 58.685 36.000 0.00 0.00 34.04 2.57
2139 2159 2.735663 CCATTGCGATCTATCTGTGAGC 59.264 50.000 0.00 0.00 0.00 4.26
2172 2192 5.095490 GGTGCATGCAATACAAAGTCTAAC 58.905 41.667 24.58 4.16 0.00 2.34
2426 2446 8.511321 TCAAACAATAACAAACTCGAGCAATAT 58.489 29.630 13.61 1.85 0.00 1.28
2443 2463 9.092876 GTTTCCTGTCAACAAATTCAAACAATA 57.907 29.630 0.00 0.00 0.00 1.90
2564 2586 7.631717 AAGAAGCATTATTTTGTACCTCCTC 57.368 36.000 0.00 0.00 0.00 3.71
2627 2651 6.538945 TGACTGGCTGAACAATATGTAGTA 57.461 37.500 0.00 0.00 0.00 1.82
2689 2791 6.295857 GCATTGTTTAAGTAAAAACATGCCG 58.704 36.000 16.90 5.38 45.91 5.69
2842 2950 8.081208 TGTTTAATGTAAAAACATGCACCATG 57.919 30.769 3.80 3.80 46.18 3.66
2846 2954 8.281893 AGCATTGTTTAATGTAAAAACATGCAC 58.718 29.630 22.65 9.25 44.05 4.57
2847 2955 8.375608 AGCATTGTTTAATGTAAAAACATGCA 57.624 26.923 22.65 0.00 44.05 3.96
2997 3106 5.789643 AAAAATGTGCCACACTTGTAGAT 57.210 34.783 0.00 0.00 35.11 1.98
3216 3331 2.485479 CGGGAGTCCATGTTTCCATAGG 60.485 54.545 12.30 0.00 32.50 2.57
3250 3365 2.680913 GCGGCCTGCACAACTACTG 61.681 63.158 13.61 0.00 45.45 2.74
3345 3460 4.943705 TGAAGAAGTGGCATGAACCTAATC 59.056 41.667 0.00 0.00 0.00 1.75
3350 3465 2.622942 TGTTGAAGAAGTGGCATGAACC 59.377 45.455 0.00 0.00 0.00 3.62
3361 3476 8.103924 CGAAAAACATCAACTTTGTTGAAGAAG 58.896 33.333 18.34 11.13 37.38 2.85
3362 3477 7.810282 TCGAAAAACATCAACTTTGTTGAAGAA 59.190 29.630 18.34 0.00 37.38 2.52
3363 3478 7.309177 TCGAAAAACATCAACTTTGTTGAAGA 58.691 30.769 18.34 6.80 37.38 2.87
3435 3585 8.680903 CAGAAGCATAAAGTGAATAACCATCTT 58.319 33.333 0.00 0.00 0.00 2.40
3801 4230 1.140852 TGTAGCTGTTGGTTGCTCAGT 59.859 47.619 0.00 0.00 40.35 3.41
3813 4242 4.997395 CCATCAGTTGTAGTTTGTAGCTGT 59.003 41.667 0.00 0.00 0.00 4.40
3841 4271 0.673333 TGCTCGCTGTACATGTTGGG 60.673 55.000 2.30 3.85 0.00 4.12
3873 4303 0.802222 GTAGCTGCTCGTTGCGATGA 60.802 55.000 4.91 0.00 46.63 2.92
3876 4310 1.914531 TACGTAGCTGCTCGTTGCGA 61.915 55.000 24.22 10.13 46.63 5.10
3877 4311 1.513373 TACGTAGCTGCTCGTTGCG 60.513 57.895 24.22 16.31 46.63 4.85
3897 4331 1.320344 TAGCGCGTTCCTGTCCAGAT 61.320 55.000 8.43 0.00 0.00 2.90
4035 4476 4.736896 GCCGCCTCGTCGTTCCTT 62.737 66.667 0.00 0.00 0.00 3.36
4080 4523 0.988832 AGGCCGTTTCCTGGTCATAA 59.011 50.000 0.00 0.00 34.56 1.90
4109 4554 3.184581 CAGCTCACTTTTGTTAGGACGAC 59.815 47.826 0.00 0.00 0.00 4.34
4285 4733 0.107214 CGGGGTGTGGCTATGTCATT 60.107 55.000 0.00 0.00 0.00 2.57
4286 4734 1.526887 CGGGGTGTGGCTATGTCAT 59.473 57.895 0.00 0.00 0.00 3.06
4287 4735 2.665089 CCGGGGTGTGGCTATGTCA 61.665 63.158 0.00 0.00 0.00 3.58
4288 4736 2.189521 CCGGGGTGTGGCTATGTC 59.810 66.667 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.