Multiple sequence alignment - TraesCS5A01G078200

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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 TraesCS5A01G078200 chr5A 100.000 2393 0 0 1 2393 96331145 96333537 0.000000e+00 4420.0
1 TraesCS5A01G078200 chr5A 89.325 993 85 20 1413 2393 441798209 441797226 0.000000e+00 1227.0
2 TraesCS5A01G078200 chr5A 88.632 994 87 23 1413 2393 441790246 441789266 0.000000e+00 1186.0
3 TraesCS5A01G078200 chr5A 94.262 488 28 0 1413 1900 267786209 267785722 0.000000e+00 747.0
4 TraesCS5A01G078200 chr5A 87.500 568 62 7 1832 2393 172458746 172458182 0.000000e+00 647.0
5 TraesCS5A01G078200 chr5A 85.025 601 78 10 1799 2393 433512849 433513443 3.400000e-168 601.0
6 TraesCS5A01G078200 chr5A 85.739 568 72 7 1832 2393 282163921 282163357 2.050000e-165 592.0
7 TraesCS5A01G078200 chr5A 90.385 104 9 1 838 941 484415508 484415406 4.150000e-28 135.0
8 TraesCS5A01G078200 chr3A 94.045 1545 82 10 1 1540 220015031 220016570 0.000000e+00 2335.0
9 TraesCS5A01G078200 chr3A 93.538 1563 89 12 1 1556 220023106 220024663 0.000000e+00 2316.0
10 TraesCS5A01G078200 chr3A 91.633 980 74 7 578 1553 263720887 263719912 0.000000e+00 1349.0
11 TraesCS5A01G078200 chr3A 90.928 981 81 6 578 1553 263712859 263711882 0.000000e+00 1312.0
12 TraesCS5A01G078200 chr3A 87.769 605 54 18 1799 2393 316659140 316659734 0.000000e+00 689.0
13 TraesCS5A01G078200 chr3A 87.500 136 15 2 807 941 626415080 626414946 3.180000e-34 156.0
14 TraesCS5A01G078200 chr2A 93.005 1501 81 9 171 1649 206909811 206911309 0.000000e+00 2169.0
15 TraesCS5A01G078200 chr2A 88.721 993 90 21 1413 2393 156218182 156219164 0.000000e+00 1194.0
16 TraesCS5A01G078200 chr2A 88.419 993 93 21 1413 2393 156226162 156227144 0.000000e+00 1177.0
17 TraesCS5A01G078200 chr2A 97.137 489 14 0 1 489 145736964 145737452 0.000000e+00 826.0
18 TraesCS5A01G078200 chr2A 88.676 680 71 6 895 1572 303844208 303844883 0.000000e+00 824.0
19 TraesCS5A01G078200 chr2A 96.349 493 17 1 1 493 145758802 145759293 0.000000e+00 809.0
20 TraesCS5A01G078200 chr2A 91.416 466 35 3 1930 2393 309564356 309563894 3.360000e-178 634.0
21 TraesCS5A01G078200 chr7A 93.133 1063 65 8 1 1059 394402477 394403535 0.000000e+00 1552.0
22 TraesCS5A01G078200 chr7A 93.133 1063 64 9 1 1059 394423977 394425034 0.000000e+00 1550.0
23 TraesCS5A01G078200 chr7A 86.878 663 68 17 1742 2393 99689005 99688351 0.000000e+00 725.0
24 TraesCS5A01G078200 chr7A 94.828 464 21 2 1930 2393 238028425 238028885 0.000000e+00 721.0
25 TraesCS5A01G078200 chr7A 86.576 663 70 17 1742 2393 99700355 99699701 0.000000e+00 713.0
26 TraesCS5A01G078200 chr7A 91.853 491 35 4 1162 1649 394425025 394425513 0.000000e+00 680.0
27 TraesCS5A01G078200 chr7A 85.191 601 78 9 1799 2393 369432495 369433090 7.320000e-170 606.0
28 TraesCS5A01G078200 chr7A 84.641 599 73 17 1802 2393 665089880 665089294 1.590000e-161 579.0
29 TraesCS5A01G078200 chr7A 90.991 222 16 3 705 925 295070999 295070781 1.800000e-76 296.0
30 TraesCS5A01G078200 chr7A 90.000 100 8 2 489 586 458627928 458627829 6.940000e-26 128.0
31 TraesCS5A01G078200 chr6A 94.882 508 20 6 1 504 87026344 87026849 0.000000e+00 789.0
32 TraesCS5A01G078200 chr6A 91.297 563 43 5 1307 1867 346131110 346131668 0.000000e+00 763.0
33 TraesCS5A01G078200 chr6A 90.764 563 46 5 1307 1867 346160146 346160704 0.000000e+00 747.0
34 TraesCS5A01G078200 chr6A 92.857 98 7 0 819 916 347164520 347164617 2.480000e-30 143.0
35 TraesCS5A01G078200 chr6A 87.129 101 13 0 819 919 264791473 264791373 5.410000e-22 115.0
36 TraesCS5A01G078200 chr1A 94.882 508 21 5 1 504 124997494 124996988 0.000000e+00 789.0
37 TraesCS5A01G078200 chr1A 90.432 533 41 10 1027 1553 163669336 163668808 0.000000e+00 693.0
38 TraesCS5A01G078200 chr1A 89.423 520 49 5 1027 1542 428859046 428859563 0.000000e+00 651.0
39 TraesCS5A01G078200 chr1A 84.514 607 78 14 1798 2393 133518626 133519227 9.530000e-164 586.0
40 TraesCS5A01G078200 chr1A 93.878 98 6 0 819 916 206350578 206350675 5.330000e-32 148.0
41 TraesCS5A01G078200 chr4A 93.661 489 31 0 1413 1901 302615882 302615394 0.000000e+00 732.0
42 TraesCS5A01G078200 chr4A 91.493 529 42 3 1374 1901 323785310 323784784 0.000000e+00 725.0
43 TraesCS5A01G078200 chr4A 90.196 255 21 3 688 942 378958765 378958515 1.770000e-86 329.0
44 TraesCS5A01G078200 chr4A 88.618 246 19 2 688 933 378951116 378950880 8.370000e-75 291.0
45 TraesCS5A01G078200 chr4A 83.654 104 11 5 940 1039 469070825 469070926 2.530000e-15 93.5


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 TraesCS5A01G078200 chr5A 96331145 96333537 2392 False 4420 4420 100.000 1 2393 1 chr5A.!!$F1 2392
1 TraesCS5A01G078200 chr5A 441797226 441798209 983 True 1227 1227 89.325 1413 2393 1 chr5A.!!$R5 980
2 TraesCS5A01G078200 chr5A 441789266 441790246 980 True 1186 1186 88.632 1413 2393 1 chr5A.!!$R4 980
3 TraesCS5A01G078200 chr5A 172458182 172458746 564 True 647 647 87.500 1832 2393 1 chr5A.!!$R1 561
4 TraesCS5A01G078200 chr5A 433512849 433513443 594 False 601 601 85.025 1799 2393 1 chr5A.!!$F2 594
5 TraesCS5A01G078200 chr5A 282163357 282163921 564 True 592 592 85.739 1832 2393 1 chr5A.!!$R3 561
6 TraesCS5A01G078200 chr3A 220015031 220016570 1539 False 2335 2335 94.045 1 1540 1 chr3A.!!$F1 1539
7 TraesCS5A01G078200 chr3A 220023106 220024663 1557 False 2316 2316 93.538 1 1556 1 chr3A.!!$F2 1555
8 TraesCS5A01G078200 chr3A 263719912 263720887 975 True 1349 1349 91.633 578 1553 1 chr3A.!!$R2 975
9 TraesCS5A01G078200 chr3A 263711882 263712859 977 True 1312 1312 90.928 578 1553 1 chr3A.!!$R1 975
10 TraesCS5A01G078200 chr3A 316659140 316659734 594 False 689 689 87.769 1799 2393 1 chr3A.!!$F3 594
11 TraesCS5A01G078200 chr2A 206909811 206911309 1498 False 2169 2169 93.005 171 1649 1 chr2A.!!$F5 1478
12 TraesCS5A01G078200 chr2A 156218182 156219164 982 False 1194 1194 88.721 1413 2393 1 chr2A.!!$F3 980
13 TraesCS5A01G078200 chr2A 156226162 156227144 982 False 1177 1177 88.419 1413 2393 1 chr2A.!!$F4 980
14 TraesCS5A01G078200 chr2A 303844208 303844883 675 False 824 824 88.676 895 1572 1 chr2A.!!$F6 677
15 TraesCS5A01G078200 chr7A 394402477 394403535 1058 False 1552 1552 93.133 1 1059 1 chr7A.!!$F3 1058
16 TraesCS5A01G078200 chr7A 394423977 394425513 1536 False 1115 1550 92.493 1 1649 2 chr7A.!!$F4 1648
17 TraesCS5A01G078200 chr7A 99688351 99689005 654 True 725 725 86.878 1742 2393 1 chr7A.!!$R1 651
18 TraesCS5A01G078200 chr7A 99699701 99700355 654 True 713 713 86.576 1742 2393 1 chr7A.!!$R2 651
19 TraesCS5A01G078200 chr7A 369432495 369433090 595 False 606 606 85.191 1799 2393 1 chr7A.!!$F2 594
20 TraesCS5A01G078200 chr7A 665089294 665089880 586 True 579 579 84.641 1802 2393 1 chr7A.!!$R5 591
21 TraesCS5A01G078200 chr6A 87026344 87026849 505 False 789 789 94.882 1 504 1 chr6A.!!$F1 503
22 TraesCS5A01G078200 chr6A 346131110 346131668 558 False 763 763 91.297 1307 1867 1 chr6A.!!$F2 560
23 TraesCS5A01G078200 chr6A 346160146 346160704 558 False 747 747 90.764 1307 1867 1 chr6A.!!$F3 560
24 TraesCS5A01G078200 chr1A 124996988 124997494 506 True 789 789 94.882 1 504 1 chr1A.!!$R1 503
25 TraesCS5A01G078200 chr1A 163668808 163669336 528 True 693 693 90.432 1027 1553 1 chr1A.!!$R2 526
26 TraesCS5A01G078200 chr1A 428859046 428859563 517 False 651 651 89.423 1027 1542 1 chr1A.!!$F3 515
27 TraesCS5A01G078200 chr1A 133518626 133519227 601 False 586 586 84.514 1798 2393 1 chr1A.!!$F1 595
28 TraesCS5A01G078200 chr4A 323784784 323785310 526 True 725 725 91.493 1374 1901 1 chr4A.!!$R2 527

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
553 560 0.252835 ATTTTGCCAAGGCCTCCCAT 60.253 50.0 5.23 0.0 41.09 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1838 0.393537 AGGGTCGACGGTAGTGGTAG 60.394 60.0 9.92 0.0 0.0 3.18 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
170 174 7.231519 CCTTTCCTTCTATTTCCTGTCTTTTGT 59.768 37.037 0.00 0.00 0.00 2.83
191 195 4.853276 TGTTAGTCCCATTTTCCCCTTCTA 59.147 41.667 0.00 0.00 0.00 2.10
240 244 0.537188 CTAGACCGTGCCAGGAACAT 59.463 55.000 0.00 0.00 34.73 2.71
289 293 6.037062 GGACTTGTTTTGGTTGGATTCAAAAG 59.963 38.462 0.00 0.00 41.59 2.27
538 545 0.471022 ACTTTCCCGTGGCCCATTTT 60.471 50.000 0.00 0.00 0.00 1.82
553 560 0.252835 ATTTTGCCAAGGCCTCCCAT 60.253 50.000 5.23 0.00 41.09 4.00
554 561 0.473501 TTTTGCCAAGGCCTCCCATT 60.474 50.000 5.23 0.00 41.09 3.16
649 656 1.708551 TCGTTCCCTTCTTTCCCCATT 59.291 47.619 0.00 0.00 0.00 3.16
657 664 3.523564 CCTTCTTTCCCCATTGACCTCTA 59.476 47.826 0.00 0.00 0.00 2.43
786 794 3.691342 CTCCTCCCACGAACGCCA 61.691 66.667 0.00 0.00 0.00 5.69
904 931 4.662961 CAGCGACCGCCACTGTCA 62.663 66.667 11.03 0.00 43.17 3.58
1092 1119 4.996434 GCAGCAGAGCACCACGGT 62.996 66.667 0.00 0.00 0.00 4.83
1405 1440 2.094100 TCCATAGGCCTCTCCAAGAG 57.906 55.000 9.68 0.00 41.96 2.85
1427 1462 1.065491 AGGATGCGCCAAGTCATGTTA 60.065 47.619 4.18 0.00 40.02 2.41
1616 1655 1.844003 CGACGGCCGTTATTCATCG 59.156 57.895 34.65 24.77 0.00 3.84
1689 1728 2.912967 CGAAACGTGTATCACTAACGCT 59.087 45.455 0.00 0.00 40.90 5.07
1720 1759 0.037605 CTACGAGGACCGCCAAGTTT 60.038 55.000 0.00 0.00 43.32 2.66
1725 1764 0.535102 AGGACCGCCAAGTTTGTCTG 60.535 55.000 0.00 0.00 36.29 3.51
1793 1835 1.577328 CCCTCGACGTGCATTTTGCT 61.577 55.000 0.00 0.00 45.31 3.91
1796 1838 2.495939 CTCGACGTGCATTTTGCTAAC 58.504 47.619 0.00 0.00 45.31 2.34
1902 1944 0.661187 GAACGTGAACGACTACCGCA 60.661 55.000 10.26 0.00 43.32 5.69
2007 2049 1.404986 CGCATCGAACTTGAACCCCTA 60.405 52.381 0.00 0.00 0.00 3.53
2019 2061 2.769663 TGAACCCCTACGATAATGCACT 59.230 45.455 0.00 0.00 0.00 4.40
2025 2067 4.302455 CCCTACGATAATGCACTCTTCAG 58.698 47.826 0.00 0.00 0.00 3.02
2035 2077 4.371855 TGCACTCTTCAGAGGTATAACG 57.628 45.455 8.70 0.00 46.13 3.18
2061 2106 3.927163 GACCGCCGTGGACGAATGT 62.927 63.158 4.58 0.00 42.00 2.71
2062 2107 3.186047 CCGCCGTGGACGAATGTC 61.186 66.667 0.00 0.00 44.72 3.06
2063 2108 3.541831 CGCCGTGGACGAATGTCG 61.542 66.667 0.00 0.00 46.49 4.35
2131 2176 0.174617 CTTGCTCGGTCCTCCTCTTC 59.825 60.000 0.00 0.00 0.00 2.87
2202 2277 2.029288 CACGCATCCGCACACTTCT 61.029 57.895 0.00 0.00 38.40 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.030106 GGGAGGATATGTTATAAAGAGAACTCG 58.970 40.741 0.00 0.00 34.09 4.18
170 174 7.964730 ATATAGAAGGGGAAAATGGGACTAA 57.035 36.000 0.00 0.00 0.00 2.24
206 210 7.444487 GGCACGGTCTAGAATTTATAGGAAAAT 59.556 37.037 0.00 0.00 0.00 1.82
240 244 5.786121 AAGGATCTGAAAATTGGAGGAGA 57.214 39.130 0.00 0.00 0.00 3.71
289 293 6.913170 TGAATTAGATTCAAACTTGAGCCAC 58.087 36.000 1.10 0.00 45.57 5.01
538 545 2.360191 GAATGGGAGGCCTTGGCA 59.640 61.111 6.77 0.00 0.00 4.92
553 560 3.974293 GGAAGGTTGGGCCGGGAA 61.974 66.667 2.18 0.00 43.70 3.97
649 656 2.052690 GCGCAGGAGGTAGAGGTCA 61.053 63.158 0.30 0.00 0.00 4.02
902 929 2.948147 GCAGAGGAAGGAGTAGCTCTGA 60.948 54.545 3.60 0.00 40.26 3.27
904 931 1.006519 TGCAGAGGAAGGAGTAGCTCT 59.993 52.381 0.00 0.00 0.00 4.09
992 1019 1.953231 CTGCGAGGCCATGAGAGACA 61.953 60.000 5.01 0.00 0.00 3.41
1092 1119 3.315142 GAGGCGCAGGTGATGGTCA 62.315 63.158 10.83 0.00 0.00 4.02
1225 1252 1.954927 GGCTCCCGAAACTTGATAGG 58.045 55.000 0.00 0.00 0.00 2.57
1267 1297 3.842923 CAGACGGCCGGAGATGCT 61.843 66.667 31.76 13.21 0.00 3.79
1405 1440 2.117156 ATGACTTGGCGCATCCTGC 61.117 57.895 10.83 0.00 40.69 4.85
1422 1457 5.120208 CGAACTTGACGAAATCCACTAACAT 59.880 40.000 0.00 0.00 0.00 2.71
1427 1462 3.318017 CTCGAACTTGACGAAATCCACT 58.682 45.455 0.00 0.00 39.23 4.00
1689 1728 5.352284 CGGTCCTCGTAGAACTAGTACTTA 58.648 45.833 0.00 0.00 34.09 2.24
1765 1804 1.870993 GCACGTCGAGGGTAGTTGTTT 60.871 52.381 10.27 0.00 0.00 2.83
1793 1835 2.356135 GGTCGACGGTAGTGGTAGTTA 58.644 52.381 9.92 0.00 0.00 2.24
1796 1838 0.393537 AGGGTCGACGGTAGTGGTAG 60.394 60.000 9.92 0.00 0.00 3.18
1902 1944 5.540719 GGTAGAGGTACTAATGATCTTGGCT 59.459 44.000 0.00 0.00 41.55 4.75
2007 2049 3.449018 ACCTCTGAAGAGTGCATTATCGT 59.551 43.478 6.59 0.00 40.48 3.73
2019 2061 4.569966 GTCTCGACGTTATACCTCTGAAGA 59.430 45.833 0.00 0.00 0.00 2.87
2061 2106 2.993220 GTGCAACTCATACATCACACGA 59.007 45.455 0.00 0.00 0.00 4.35
2062 2107 2.094258 GGTGCAACTCATACATCACACG 59.906 50.000 0.00 0.00 36.74 4.49
2063 2108 2.420022 GGGTGCAACTCATACATCACAC 59.580 50.000 0.00 0.00 37.19 3.82
2131 2176 2.509336 CCCACGAGTTAGCGGCAG 60.509 66.667 1.45 0.00 35.12 4.85
2202 2277 0.539986 GGAGATACCGGTGCAAAGGA 59.460 55.000 19.93 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.