Multiple sequence alignment - TraesCS2D01G247600

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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 TraesCS2D01G247600 chr2D 100.000 2487 0 0 1 2487 291731000 291728514 0.000000e+00 4593
1 TraesCS2D01G247600 chr2D 90.839 775 54 8 1715 2487 288213297 288214056 0.000000e+00 1022
2 TraesCS2D01G247600 chr2D 89.075 778 63 11 1715 2487 288197404 288198164 0.000000e+00 946
3 TraesCS2D01G247600 chr2D 83.259 448 48 18 1701 2137 270175789 270175358 1.080000e-103 387
4 TraesCS2D01G247600 chrUn 96.232 1725 53 7 1 1714 282364700 282362977 0.000000e+00 2815
5 TraesCS2D01G247600 chrUn 95.826 1725 60 7 1 1714 86510016 86508293 0.000000e+00 2776
6 TraesCS2D01G247600 chrUn 95.478 1725 66 7 1 1714 260203731 260202008 0.000000e+00 2743
7 TraesCS2D01G247600 chr4D 96.279 1720 56 8 1 1714 123423711 123425428 0.000000e+00 2815
8 TraesCS2D01G247600 chr4D 88.645 775 71 9 1714 2485 219500671 219499911 0.000000e+00 928
9 TraesCS2D01G247600 chr4D 87.677 779 77 11 1715 2487 364673085 364673850 0.000000e+00 889
10 TraesCS2D01G247600 chr3D 96.056 1724 57 7 1 1714 154704964 154703242 0.000000e+00 2796
11 TraesCS2D01G247600 chr3D 87.708 781 59 14 1715 2487 244710274 244709523 0.000000e+00 876
12 TraesCS2D01G247600 chr6A 95.768 1725 61 7 1 1714 84434140 84435863 0.000000e+00 2771
13 TraesCS2D01G247600 chr1D 95.758 1721 64 9 1 1714 351079424 351077706 0.000000e+00 2765
14 TraesCS2D01G247600 chr1D 85.967 791 81 25 1715 2486 152901610 152900831 0.000000e+00 819
15 TraesCS2D01G247600 chr1D 85.841 791 83 25 1715 2486 153087070 153086290 0.000000e+00 813
16 TraesCS2D01G247600 chr2B 95.705 1723 62 8 1 1714 30670615 30668896 0.000000e+00 2761
17 TraesCS2D01G247600 chr5B 95.581 1720 69 7 1 1714 567270599 567268881 0.000000e+00 2748
18 TraesCS2D01G247600 chr5A 84.772 788 95 22 1713 2487 247348930 247348155 0.000000e+00 767
19 TraesCS2D01G247600 chr7D 85.619 751 79 25 1754 2486 312751051 312750312 0.000000e+00 761
20 TraesCS2D01G247600 chr7A 84.233 463 38 20 1715 2161 383650848 383650405 3.830000e-113 418
21 TraesCS2D01G247600 chr1A 81.957 460 50 22 1714 2161 135986524 135986962 2.350000e-95 359
22 TraesCS2D01G247600 chr1A 81.304 460 50 22 1715 2161 196764447 196764011 8.520000e-90 340


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 TraesCS2D01G247600 chr2D 291728514 291731000 2486 True 4593 4593 100.000 1 2487 1 chr2D.!!$R2 2486
1 TraesCS2D01G247600 chr2D 288213297 288214056 759 False 1022 1022 90.839 1715 2487 1 chr2D.!!$F2 772
2 TraesCS2D01G247600 chr2D 288197404 288198164 760 False 946 946 89.075 1715 2487 1 chr2D.!!$F1 772
3 TraesCS2D01G247600 chrUn 282362977 282364700 1723 True 2815 2815 96.232 1 1714 1 chrUn.!!$R3 1713
4 TraesCS2D01G247600 chrUn 86508293 86510016 1723 True 2776 2776 95.826 1 1714 1 chrUn.!!$R1 1713
5 TraesCS2D01G247600 chrUn 260202008 260203731 1723 True 2743 2743 95.478 1 1714 1 chrUn.!!$R2 1713
6 TraesCS2D01G247600 chr4D 123423711 123425428 1717 False 2815 2815 96.279 1 1714 1 chr4D.!!$F1 1713
7 TraesCS2D01G247600 chr4D 219499911 219500671 760 True 928 928 88.645 1714 2485 1 chr4D.!!$R1 771
8 TraesCS2D01G247600 chr4D 364673085 364673850 765 False 889 889 87.677 1715 2487 1 chr4D.!!$F2 772
9 TraesCS2D01G247600 chr3D 154703242 154704964 1722 True 2796 2796 96.056 1 1714 1 chr3D.!!$R1 1713
10 TraesCS2D01G247600 chr3D 244709523 244710274 751 True 876 876 87.708 1715 2487 1 chr3D.!!$R2 772
11 TraesCS2D01G247600 chr6A 84434140 84435863 1723 False 2771 2771 95.768 1 1714 1 chr6A.!!$F1 1713
12 TraesCS2D01G247600 chr1D 351077706 351079424 1718 True 2765 2765 95.758 1 1714 1 chr1D.!!$R3 1713
13 TraesCS2D01G247600 chr1D 152900831 152901610 779 True 819 819 85.967 1715 2486 1 chr1D.!!$R1 771
14 TraesCS2D01G247600 chr1D 153086290 153087070 780 True 813 813 85.841 1715 2486 1 chr1D.!!$R2 771
15 TraesCS2D01G247600 chr2B 30668896 30670615 1719 True 2761 2761 95.705 1 1714 1 chr2B.!!$R1 1713
16 TraesCS2D01G247600 chr5B 567268881 567270599 1718 True 2748 2748 95.581 1 1714 1 chr5B.!!$R1 1713
17 TraesCS2D01G247600 chr5A 247348155 247348930 775 True 767 767 84.772 1713 2487 1 chr5A.!!$R1 774
18 TraesCS2D01G247600 chr7D 312750312 312751051 739 True 761 761 85.619 1754 2486 1 chr7D.!!$R1 732

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
842 846 0.185901 ATTGTGTCAACCAGGCCAGT 59.814 50.0 5.01 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 2043 0.115152 TGCTCCTCCAAGAGAGACCA 59.885 55.0 0.0 0.0 46.5 4.02 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
59 60 5.304686 TGGAACAGTTTAGGACAGAACAT 57.695 39.130 0.00 0.00 0.00 2.71
65 66 3.584848 AGTTTAGGACAGAACATGCCTCT 59.415 43.478 0.00 0.00 36.93 3.69
115 116 0.618458 ACCTCGAAGCCCAATTAGCA 59.382 50.000 2.79 0.00 0.00 3.49
141 142 2.067932 CTGCCCCCTCAACTCAACCA 62.068 60.000 0.00 0.00 0.00 3.67
165 166 1.862201 CGAGTACGCAAACTTGGTCAA 59.138 47.619 0.00 0.00 0.00 3.18
168 169 1.265905 GTACGCAAACTTGGTCAAGGG 59.734 52.381 14.29 5.57 42.53 3.95
343 346 7.921214 CACCTTACAATAACATACGAGAGACAT 59.079 37.037 0.00 0.00 0.00 3.06
359 362 6.528423 CGAGAGACATCTTTCTATTTTGTCGT 59.472 38.462 0.00 0.00 41.15 4.34
370 373 7.773864 TTCTATTTTGTCGTACAACAAGTCA 57.226 32.000 0.00 0.00 37.90 3.41
572 575 3.119743 TCGATACACCGAAAACGAGTCAT 60.120 43.478 0.00 0.00 35.42 3.06
577 580 1.732259 ACCGAAAACGAGTCATGATGC 59.268 47.619 0.00 0.00 0.00 3.91
595 598 7.940688 TCATGATGCATACATAAAATGGAGACT 59.059 33.333 0.00 0.00 36.35 3.24
596 599 7.734924 TGATGCATACATAAAATGGAGACTC 57.265 36.000 0.00 0.00 36.35 3.36
628 631 3.149196 CCAAATTGGGATGACGATAGGG 58.851 50.000 3.60 0.00 34.91 3.53
725 728 6.307031 TGTTTTCGCTTATGCTTAGTCAAA 57.693 33.333 0.00 0.00 36.97 2.69
827 831 6.718454 GTCCCATCCTTCAATATCATGATTGT 59.282 38.462 14.65 0.15 37.92 2.71
842 846 0.185901 ATTGTGTCAACCAGGCCAGT 59.814 50.000 5.01 0.00 0.00 4.00
1044 1049 2.398588 GGTCCTGATGTAGTGGGATCA 58.601 52.381 0.00 0.00 0.00 2.92
1129 1135 5.946377 CCAAGTAGTGCTAATTTCTCCCTTT 59.054 40.000 0.00 0.00 0.00 3.11
1361 1368 1.139853 GGTCAAAATGGGTTTGTGCCA 59.860 47.619 0.00 0.00 45.83 4.92
1387 1394 5.652891 AGGTGTTGAACGATCTACTCTACAT 59.347 40.000 8.53 0.00 33.23 2.29
1401 1408 4.557705 ACTCTACATAGGTGTGGGCTTAT 58.442 43.478 0.00 0.00 39.39 1.73
1517 1524 4.183865 TGTTTCTCTTCGCACCTCATATG 58.816 43.478 0.00 0.00 0.00 1.78
1562 1569 5.574188 AGCTGGTCTCACTATTGGAAATTT 58.426 37.500 0.00 0.00 0.00 1.82
1614 1637 4.716784 TGTCAATGCTACTAAGGACCTGAT 59.283 41.667 0.00 0.00 0.00 2.90
1644 1667 5.940470 ACCTACTTGATGGATGAAAGAACAC 59.060 40.000 0.00 0.00 0.00 3.32
1702 1725 9.165035 GTCTACTGTAGTATAGTCAAAGTCAGT 57.835 37.037 14.11 0.00 37.40 3.41
1704 1727 7.997773 ACTGTAGTATAGTCAAAGTCAGTGA 57.002 36.000 0.00 0.00 33.37 3.41
1897 1926 3.770666 ACACAAAGAGATACACGATCCG 58.229 45.455 0.00 0.00 34.80 4.18
2008 2043 2.359531 GGATCTTCTCCGAAGACGTGAT 59.640 50.000 8.34 0.00 37.88 3.06
2100 2137 0.558712 ACCCTAGCTAGGAGGAGGTG 59.441 60.000 36.80 21.75 46.63 4.00
2145 2182 1.204941 CACGAAGGGGTAAGTGAGAGG 59.795 57.143 0.00 0.00 36.79 3.69
2200 2238 3.078836 GGCAGGGCGGTAGTACCA 61.079 66.667 19.41 0.00 38.47 3.25
2211 2249 3.427705 GGTAGTACCAGACCCTCGGGT 62.428 61.905 14.82 7.50 46.52 5.28
2221 2259 1.309006 CCCTCGGGTGGTAGTACCT 59.691 63.158 20.07 0.00 39.58 3.08
2402 2440 1.450312 GTTCCGGACTGGGCAGATG 60.450 63.158 1.83 0.00 38.76 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 2.251818 AGCTCACTTTCTACAGAGGCA 58.748 47.619 0.00 0.00 0.00 4.75
141 142 2.066262 CCAAGTTTGCGTACTCGTCAT 58.934 47.619 0.00 0.00 39.49 3.06
165 166 1.077716 GCACCGTCTAAATGCCCCT 60.078 57.895 0.00 0.00 33.06 4.79
168 169 1.165270 AACTGCACCGTCTAAATGCC 58.835 50.000 0.00 0.00 38.63 4.40
343 346 8.428186 ACTTGTTGTACGACAAAATAGAAAGA 57.572 30.769 25.22 3.90 40.15 2.52
359 362 5.419155 TGTTCATTGGGTTTGACTTGTTGTA 59.581 36.000 0.00 0.00 0.00 2.41
370 373 6.185114 TGAATGGAATTGTTCATTGGGTTT 57.815 33.333 0.00 0.00 36.07 3.27
452 455 5.450688 CCGGAACTCTAGAAATCGTGAAGAT 60.451 44.000 0.00 0.00 42.43 2.40
572 575 6.712095 GGAGTCTCCATTTTATGTATGCATCA 59.288 38.462 14.46 1.39 36.28 3.07
577 580 5.466728 CCACGGAGTCTCCATTTTATGTATG 59.533 44.000 19.15 0.44 41.61 2.39
618 621 3.627395 AAGTGAAATGCCCTATCGTCA 57.373 42.857 0.00 0.00 0.00 4.35
628 631 6.875926 ATATTGCGAAAGAAAGTGAAATGC 57.124 33.333 0.00 0.00 27.47 3.56
725 728 5.050490 CGTTACTTCGAATGGAATCCTCAT 58.950 41.667 0.00 0.00 33.26 2.90
827 831 0.478072 ATGAACTGGCCTGGTTGACA 59.522 50.000 16.97 11.10 0.00 3.58
842 846 9.308000 ACCCAATCAAACTATTTCACTTATGAA 57.692 29.630 0.00 0.00 43.28 2.57
864 868 2.603473 CCTGACCTGGTCGACCCA 60.603 66.667 31.19 20.01 42.51 4.51
913 917 4.955811 TTCCGCTGGAACATCTATGTAT 57.044 40.909 6.01 0.00 40.80 2.29
921 925 5.659440 AACAAATATTTCCGCTGGAACAT 57.341 34.783 9.15 8.84 41.87 2.71
982 987 5.484715 AGCCATTACTTTACGTTCAGCTAA 58.515 37.500 0.00 0.00 0.00 3.09
1016 1021 3.133003 CACTACATCAGGACCCTTTCGAT 59.867 47.826 0.00 0.00 0.00 3.59
1044 1049 6.711277 TGCTAGAGGTTGTAACAATCTGAAT 58.289 36.000 5.23 0.00 31.54 2.57
1129 1135 2.041620 AGCCACTGGAGCCATTCTAAAA 59.958 45.455 0.00 0.00 0.00 1.52
1361 1368 3.827302 AGAGTAGATCGTTCAACACCTGT 59.173 43.478 0.00 0.00 0.00 4.00
1387 1394 1.061657 AGCCCTATAAGCCCACACCTA 60.062 52.381 0.00 0.00 0.00 3.08
1401 1408 2.335933 GGTTTATGAGCCCTAGCCCTA 58.664 52.381 0.00 0.00 41.25 3.53
1517 1524 4.803098 TGACAAGCTACCTTACCTCTTC 57.197 45.455 0.00 0.00 0.00 2.87
1577 1600 3.254166 GCATTGACAAAGAAGAAGAGCCA 59.746 43.478 0.00 0.00 0.00 4.75
1614 1637 3.843619 TCATCCATCAAGTAGGTGAACCA 59.156 43.478 1.62 0.00 38.89 3.67
1620 1643 5.940470 GTGTTCTTTCATCCATCAAGTAGGT 59.060 40.000 0.00 0.00 0.00 3.08
1644 1667 7.027760 GCCTTTTATTTTAGAACCCTTTCTCG 58.972 38.462 0.00 0.00 41.48 4.04
1702 1725 3.646162 ACCCTACATCACAAACTCAGTCA 59.354 43.478 0.00 0.00 0.00 3.41
1704 1727 3.244561 CCACCCTACATCACAAACTCAGT 60.245 47.826 0.00 0.00 0.00 3.41
1897 1926 6.202954 CCTATGTATCGTCCTTTGTTGGATTC 59.797 42.308 0.00 0.00 38.52 2.52
2003 2038 1.135915 CCTCCAAGAGAGACCATCACG 59.864 57.143 0.00 0.00 46.50 4.35
2008 2043 0.115152 TGCTCCTCCAAGAGAGACCA 59.885 55.000 0.00 0.00 46.50 4.02
2145 2182 2.091283 AAGGGCCCATGTATCCCCC 61.091 63.158 27.56 3.62 40.97 5.40
2168 2206 2.666190 GCCTGTGCGCAGAGAACA 60.666 61.111 33.82 16.42 45.28 3.18
2211 2249 3.091633 ACCGCTAAAGAGGTACTACCA 57.908 47.619 3.32 0.00 46.49 3.25
2339 2377 1.361632 GGTACTACCGCTAAGCCCG 59.638 63.158 0.00 0.00 0.00 6.13
2359 2397 0.671472 GTACTACCGCCCACACCAAC 60.671 60.000 0.00 0.00 0.00 3.77
2402 2440 2.941720 GGACATCAAGAACATGGAGAGC 59.058 50.000 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.