Multiple sequence alignment - TraesCS2D01G488400

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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 TraesCS2D01G488400 chr2D 100.000 1828 0 0 1 1828 587740754 587738927 0.000000e+00 3376.0
1 TraesCS2D01G488400 chr2D 98.553 622 9 0 31 652 37298183 37298804 0.000000e+00 1099.0
2 TraesCS2D01G488400 chr2D 98.232 622 11 0 31 652 57150888 57150267 0.000000e+00 1088.0
3 TraesCS2D01G488400 chr2D 97.760 625 14 0 28 652 15816385 15817009 0.000000e+00 1077.0
4 TraesCS2D01G488400 chr2D 100.000 487 0 0 2215 2701 587738540 587738054 0.000000e+00 900.0
5 TraesCS2D01G488400 chr2D 82.500 80 12 1 2446 2523 225272431 225272352 4.830000e-08 69.4
6 TraesCS2D01G488400 chr2A 94.271 1187 47 8 652 1828 722565712 722564537 0.000000e+00 1796.0
7 TraesCS2D01G488400 chr2A 97.746 621 14 0 32 652 214445637 214445017 0.000000e+00 1070.0
8 TraesCS2D01G488400 chr2A 97.251 291 6 1 2411 2701 722564093 722563805 2.420000e-135 492.0
9 TraesCS2D01G488400 chr2A 98.507 201 3 0 2218 2418 722564485 722564285 3.310000e-94 355.0
10 TraesCS2D01G488400 chr2B 92.649 993 49 13 855 1828 710325384 710324397 0.000000e+00 1408.0
11 TraesCS2D01G488400 chr2B 92.008 488 31 5 2218 2701 710324303 710323820 0.000000e+00 678.0
12 TraesCS2D01G488400 chr2B 90.566 53 5 0 2496 2548 37012528 37012580 1.340000e-08 71.3
13 TraesCS2D01G488400 chr5D 98.248 628 9 2 27 652 327998103 327998730 0.000000e+00 1098.0
14 TraesCS2D01G488400 chr5D 97.581 620 15 0 33 652 495032749 495033368 0.000000e+00 1062.0
15 TraesCS2D01G488400 chr3D 98.068 621 12 0 32 652 478139201 478138581 0.000000e+00 1081.0
16 TraesCS2D01G488400 chr6D 97.749 622 14 0 31 652 390247868 390248489 0.000000e+00 1072.0
17 TraesCS2D01G488400 chr6D 97.746 621 14 0 32 652 169577395 169578015 0.000000e+00 1070.0
18 TraesCS2D01G488400 chr1B 78.431 204 29 11 2441 2639 111663736 111663929 4.720000e-23 119.0
19 TraesCS2D01G488400 chr6B 92.308 39 3 0 2511 2549 143462183 143462145 3.760000e-04 56.5


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 TraesCS2D01G488400 chr2D 587738054 587740754 2700 True 2138 3376 100.000000 1 2701 2 chr2D.!!$R3 2700
1 TraesCS2D01G488400 chr2D 37298183 37298804 621 False 1099 1099 98.553000 31 652 1 chr2D.!!$F2 621
2 TraesCS2D01G488400 chr2D 57150267 57150888 621 True 1088 1088 98.232000 31 652 1 chr2D.!!$R1 621
3 TraesCS2D01G488400 chr2D 15816385 15817009 624 False 1077 1077 97.760000 28 652 1 chr2D.!!$F1 624
4 TraesCS2D01G488400 chr2A 214445017 214445637 620 True 1070 1070 97.746000 32 652 1 chr2A.!!$R1 620
5 TraesCS2D01G488400 chr2A 722563805 722565712 1907 True 881 1796 96.676333 652 2701 3 chr2A.!!$R2 2049
6 TraesCS2D01G488400 chr2B 710323820 710325384 1564 True 1043 1408 92.328500 855 2701 2 chr2B.!!$R1 1846
7 TraesCS2D01G488400 chr5D 327998103 327998730 627 False 1098 1098 98.248000 27 652 1 chr5D.!!$F1 625
8 TraesCS2D01G488400 chr5D 495032749 495033368 619 False 1062 1062 97.581000 33 652 1 chr5D.!!$F2 619
9 TraesCS2D01G488400 chr3D 478138581 478139201 620 True 1081 1081 98.068000 32 652 1 chr3D.!!$R1 620
10 TraesCS2D01G488400 chr6D 390247868 390248489 621 False 1072 1072 97.749000 31 652 1 chr6D.!!$F2 621
11 TraesCS2D01G488400 chr6D 169577395 169578015 620 False 1070 1070 97.746000 32 652 1 chr6D.!!$F1 620

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
473 474 0.321564 CCACAAGATGAAGACCGGCA 60.322 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 1764 0.678684 TCACGCAGTACTCCGGATGA 60.679 55.0 11.57 3.21 41.61 2.92 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
19 20 2.427232 GCAGCAGCTGTGATTTTTGA 57.573 45.000 23.60 0.00 37.91 2.69
20 21 2.955614 GCAGCAGCTGTGATTTTTGAT 58.044 42.857 23.60 0.00 37.91 2.57
21 22 2.666508 GCAGCAGCTGTGATTTTTGATG 59.333 45.455 23.60 0.00 37.91 3.07
22 23 3.613193 GCAGCAGCTGTGATTTTTGATGA 60.613 43.478 23.60 0.00 37.91 2.92
23 24 4.744570 CAGCAGCTGTGATTTTTGATGAT 58.255 39.130 16.64 0.00 0.00 2.45
24 25 5.168569 CAGCAGCTGTGATTTTTGATGATT 58.831 37.500 16.64 0.00 0.00 2.57
25 26 5.062183 CAGCAGCTGTGATTTTTGATGATTG 59.938 40.000 16.64 0.00 0.00 2.67
26 27 4.201685 GCAGCTGTGATTTTTGATGATTGC 60.202 41.667 16.64 0.00 0.00 3.56
27 28 5.168569 CAGCTGTGATTTTTGATGATTGCT 58.831 37.500 5.25 0.00 0.00 3.91
28 29 6.327154 CAGCTGTGATTTTTGATGATTGCTA 58.673 36.000 5.25 0.00 0.00 3.49
29 30 6.252869 CAGCTGTGATTTTTGATGATTGCTAC 59.747 38.462 5.25 0.00 0.00 3.58
473 474 0.321564 CCACAAGATGAAGACCGGCA 60.322 55.000 0.00 0.00 0.00 5.69
661 662 3.529533 AGAGCACAGTGATGATTGCTAC 58.470 45.455 4.15 1.10 45.32 3.58
662 663 3.197333 AGAGCACAGTGATGATTGCTACT 59.803 43.478 4.15 3.04 45.32 2.57
663 664 3.937706 GAGCACAGTGATGATTGCTACTT 59.062 43.478 4.15 0.00 45.32 2.24
664 665 5.089970 AGCACAGTGATGATTGCTACTTA 57.910 39.130 4.15 0.00 43.51 2.24
665 666 4.872691 AGCACAGTGATGATTGCTACTTAC 59.127 41.667 4.15 0.00 43.51 2.34
675 676 3.449746 TTGCTACTTACCATTTGGCCT 57.550 42.857 3.32 0.00 39.32 5.19
686 687 3.244526 ACCATTTGGCCTGTGATTTTTCC 60.245 43.478 3.32 0.00 39.32 3.13
702 703 9.237846 GTGATTTTTCCTTCACTAGTTTTGAAG 57.762 33.333 12.48 12.48 46.51 3.02
721 732 8.904099 TTTGAAGATAAGCTAATAAGGTAGCC 57.096 34.615 0.70 0.00 46.46 3.93
722 733 7.005709 TGAAGATAAGCTAATAAGGTAGCCC 57.994 40.000 0.70 0.00 46.46 5.19
773 784 5.995282 TCTACGACAAATGATTGGTTTGAGT 59.005 36.000 5.69 7.37 41.01 3.41
807 818 5.577100 TGTTACTGTACCACTCCTACTGAT 58.423 41.667 0.00 0.00 0.00 2.90
811 822 4.646945 ACTGTACCACTCCTACTGATGATG 59.353 45.833 0.00 0.00 0.00 3.07
946 957 1.664016 GCTTGACACATTTCGCCACAG 60.664 52.381 0.00 0.00 0.00 3.66
987 1000 4.903049 TGTATATAAACCCATGGGAGTCGT 59.097 41.667 38.07 19.57 38.96 4.34
1010 1023 2.651361 CGAGCTCACCACCTCGTT 59.349 61.111 15.40 0.00 44.25 3.85
1182 1195 2.097038 CAGCAAGAAGAGGACGGCG 61.097 63.158 4.80 4.80 0.00 6.46
1187 1200 4.162690 GAAGAGGACGGCGGCCAT 62.163 66.667 36.46 20.28 0.00 4.40
1335 1360 4.292178 GCGAGGGATCGGCTGGAG 62.292 72.222 0.00 0.00 0.00 3.86
1494 1519 1.059584 TGTGTTGGCTGGAGGAGGAA 61.060 55.000 0.00 0.00 0.00 3.36
1673 1701 2.224378 CCAGGAGCATATGAACCACGAT 60.224 50.000 6.97 0.00 0.00 3.73
1736 1764 0.898320 CTTGGTGTCCGGACTCTGAT 59.102 55.000 33.39 0.00 0.00 2.90
1783 1811 4.761235 ATTTCATGTTGAGCAGTGAGTG 57.239 40.909 0.00 0.00 0.00 3.51
1784 1812 3.473923 TTCATGTTGAGCAGTGAGTGA 57.526 42.857 0.00 0.00 0.00 3.41
1785 1813 3.690475 TCATGTTGAGCAGTGAGTGAT 57.310 42.857 0.00 0.00 0.00 3.06
1786 1814 4.011966 TCATGTTGAGCAGTGAGTGATT 57.988 40.909 0.00 0.00 0.00 2.57
1807 1835 2.803030 ATTCATGGTGCAGCTCTTCT 57.197 45.000 18.08 0.00 0.00 2.85
2427 2654 6.220881 ACACCCATCTAGAGTCTATACCAT 57.779 41.667 0.00 0.00 0.00 3.55
2658 2888 3.495670 AAAAACACTTTGCGCACTACA 57.504 38.095 11.12 0.00 0.00 2.74
2674 2904 7.273164 TGCGCACTACATTATGAAATGAAAAAG 59.727 33.333 5.66 0.85 44.50 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.427232 TCAAAAATCACAGCTGCTGC 57.573 45.000 28.39 7.62 34.37 5.25
1 2 4.168922 TCATCAAAAATCACAGCTGCTG 57.831 40.909 27.02 27.02 37.52 4.41
3 4 4.201685 GCAATCATCAAAAATCACAGCTGC 60.202 41.667 15.27 0.00 0.00 5.25
4 5 5.168569 AGCAATCATCAAAAATCACAGCTG 58.831 37.500 13.48 13.48 0.00 4.24
6 7 6.327934 AGTAGCAATCATCAAAAATCACAGC 58.672 36.000 0.00 0.00 0.00 4.40
7 8 8.752766 AAAGTAGCAATCATCAAAAATCACAG 57.247 30.769 0.00 0.00 0.00 3.66
8 9 9.545105 AAAAAGTAGCAATCATCAAAAATCACA 57.455 25.926 0.00 0.00 0.00 3.58
254 255 2.767445 CGGTATGTGGCTCGGTCGA 61.767 63.158 0.00 0.00 0.00 4.20
284 285 0.454600 GAGTGCGTCGGACTGGATTA 59.545 55.000 24.84 0.00 0.00 1.75
473 474 6.090898 GTGTGCAACGTTTCATCTATTCTACT 59.909 38.462 3.46 0.00 42.39 2.57
661 662 4.806640 AAATCACAGGCCAAATGGTAAG 57.193 40.909 5.01 0.00 37.57 2.34
662 663 5.512232 GGAAAAATCACAGGCCAAATGGTAA 60.512 40.000 5.01 0.00 37.57 2.85
663 664 4.020662 GGAAAAATCACAGGCCAAATGGTA 60.021 41.667 5.01 0.00 37.57 3.25
664 665 3.244526 GGAAAAATCACAGGCCAAATGGT 60.245 43.478 5.01 0.00 37.57 3.55
665 666 3.008266 AGGAAAAATCACAGGCCAAATGG 59.992 43.478 5.01 0.00 38.53 3.16
675 676 8.287439 TCAAAACTAGTGAAGGAAAAATCACA 57.713 30.769 0.00 0.00 46.55 3.58
702 703 6.947464 TCATGGGCTACCTTATTAGCTTATC 58.053 40.000 0.00 0.00 43.56 1.75
721 732 3.597255 AGCTAATCTCGCATGATCATGG 58.403 45.455 31.62 22.57 39.16 3.66
722 733 4.804665 CCTAGCTAATCTCGCATGATCATG 59.195 45.833 28.04 28.04 41.60 3.07
773 784 5.020795 TGGTACAGTAACATTGAGAGGCTA 58.979 41.667 0.00 0.00 0.00 3.93
789 800 4.646945 ACATCATCAGTAGGAGTGGTACAG 59.353 45.833 0.00 0.00 41.80 2.74
987 1000 4.687215 GTGGTGAGCTCGCCTGCA 62.687 66.667 38.64 21.95 46.36 4.41
1010 1023 0.036732 GAACAGTGGAGCCATGGTGA 59.963 55.000 14.67 0.00 0.00 4.02
1352 1377 5.244025 GTAGTACGAGTACGACGAATAGG 57.756 47.826 18.81 0.00 42.66 2.57
1494 1519 4.309950 GTGCCACCCGACGACCTT 62.310 66.667 0.00 0.00 0.00 3.50
1736 1764 0.678684 TCACGCAGTACTCCGGATGA 60.679 55.000 11.57 3.21 41.61 2.92
1766 1794 5.868043 TTAATCACTCACTGCTCAACATG 57.132 39.130 0.00 0.00 0.00 3.21
1783 1811 5.298777 AGAAGAGCTGCACCATGAATTAATC 59.701 40.000 1.02 0.00 0.00 1.75
1784 1812 5.198965 AGAAGAGCTGCACCATGAATTAAT 58.801 37.500 1.02 0.00 0.00 1.40
1785 1813 4.592942 AGAAGAGCTGCACCATGAATTAA 58.407 39.130 1.02 0.00 0.00 1.40
1786 1814 4.226427 AGAAGAGCTGCACCATGAATTA 57.774 40.909 1.02 0.00 0.00 1.40
2216 2244 4.738740 AGAATAATTTCGCTTCGACCGTAG 59.261 41.667 4.80 0.00 34.89 3.51
2588 2816 7.333528 AGTTTGAGCAATGTTACTGAGAAAA 57.666 32.000 0.00 0.00 0.00 2.29
2657 2887 6.183360 CCGCCAACCTTTTTCATTTCATAATG 60.183 38.462 0.00 0.00 42.06 1.90
2658 2888 5.874261 CCGCCAACCTTTTTCATTTCATAAT 59.126 36.000 0.00 0.00 0.00 1.28
2674 2904 1.375551 CATACACTTACCCGCCAACC 58.624 55.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.