Multiple sequence alignment - TraesCS2D01G070900

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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 TraesCS2D01G070900 chr2D 100.000 2514 0 0 1 2514 29886110 29883597 0.000000e+00 4643
1 TraesCS2D01G070900 chr2D 90.909 1892 140 14 84 1963 30098007 30096136 0.000000e+00 2512
2 TraesCS2D01G070900 chr2D 90.693 1891 145 12 84 1963 30159658 30157788 0.000000e+00 2488
3 TraesCS2D01G070900 chr2D 90.534 1891 146 10 84 1963 30239247 30237379 0.000000e+00 2470
4 TraesCS2D01G070900 chr2D 90.481 1891 143 18 84 1963 30231639 30229775 0.000000e+00 2460
5 TraesCS2D01G070900 chr2D 93.863 554 32 2 1962 2514 30047588 30047036 0.000000e+00 833
6 TraesCS2D01G070900 chr2D 90.072 554 43 6 1965 2513 30165210 30164664 0.000000e+00 708
7 TraesCS2D01G070900 chr2D 89.531 554 46 8 1965 2513 30121362 30120816 0.000000e+00 691
8 TraesCS2D01G070900 chr2D 89.531 554 46 6 1965 2513 30237220 30236674 0.000000e+00 691
9 TraesCS2D01G070900 chr2D 88.070 285 29 4 1965 2247 30229616 30229335 1.440000e-87 333
10 TraesCS2D01G070900 chr2B 96.125 2013 72 5 503 2514 49285440 49287447 0.000000e+00 3280
11 TraesCS2D01G070900 chr2B 91.950 1913 120 15 80 1963 48216863 48214956 0.000000e+00 2649
12 TraesCS2D01G070900 chr2B 90.653 1915 144 14 80 1963 48181531 48179621 0.000000e+00 2512
13 TraesCS2D01G070900 chr2B 90.444 1894 148 15 81 1963 49115198 49117069 0.000000e+00 2464
14 TraesCS2D01G070900 chr2B 95.152 825 38 2 503 1327 48148611 48147789 0.000000e+00 1301
15 TraesCS2D01G070900 chr2B 94.278 769 33 4 1747 2514 48147778 48147020 0.000000e+00 1166
16 TraesCS2D01G070900 chr2B 92.506 774 50 7 503 1274 48305000 48304233 0.000000e+00 1101
17 TraesCS2D01G070900 chr2B 92.362 707 52 1 1259 1963 48304214 48303508 0.000000e+00 1005
18 TraesCS2D01G070900 chr2B 88.179 829 81 6 155 972 49153849 49154671 0.000000e+00 972
19 TraesCS2D01G070900 chr2B 92.430 502 35 3 1962 2462 49255717 49256216 0.000000e+00 713
20 TraesCS2D01G070900 chr2A 91.527 1971 106 23 50 1963 32101745 32099779 0.000000e+00 2658
21 TraesCS2D01G070900 chr2A 94.029 1189 68 2 775 1963 32017857 32016672 0.000000e+00 1799
22 TraesCS2D01G070900 chr2A 92.023 351 26 2 2161 2510 32097437 32097088 2.250000e-135 492
23 TraesCS2D01G070900 chrUn 90.919 1894 142 12 81 1963 311530785 311532659 0.000000e+00 2518
24 TraesCS2D01G070900 chrUn 90.741 1890 146 14 84 1963 335402634 335400764 0.000000e+00 2494
25 TraesCS2D01G070900 chrUn 90.956 1747 128 12 84 1819 338699824 338698097 0.000000e+00 2324
26 TraesCS2D01G070900 chrUn 90.979 1164 86 8 81 1233 363756492 363757647 0.000000e+00 1550
27 TraesCS2D01G070900 chrUn 89.408 557 47 8 1962 2513 295795823 295796372 0.000000e+00 691


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 TraesCS2D01G070900 chr2D 29883597 29886110 2513 True 4643.0 4643 100.0000 1 2514 1 chr2D.!!$R1 2513
1 TraesCS2D01G070900 chr2D 30096136 30098007 1871 True 2512.0 2512 90.9090 84 1963 1 chr2D.!!$R3 1879
2 TraesCS2D01G070900 chr2D 30157788 30159658 1870 True 2488.0 2488 90.6930 84 1963 1 chr2D.!!$R5 1879
3 TraesCS2D01G070900 chr2D 30236674 30239247 2573 True 1580.5 2470 90.0325 84 2513 2 chr2D.!!$R8 2429
4 TraesCS2D01G070900 chr2D 30229335 30231639 2304 True 1396.5 2460 89.2755 84 2247 2 chr2D.!!$R7 2163
5 TraesCS2D01G070900 chr2D 30047036 30047588 552 True 833.0 833 93.8630 1962 2514 1 chr2D.!!$R2 552
6 TraesCS2D01G070900 chr2D 30164664 30165210 546 True 708.0 708 90.0720 1965 2513 1 chr2D.!!$R6 548
7 TraesCS2D01G070900 chr2D 30120816 30121362 546 True 691.0 691 89.5310 1965 2513 1 chr2D.!!$R4 548
8 TraesCS2D01G070900 chr2B 49285440 49287447 2007 False 3280.0 3280 96.1250 503 2514 1 chr2B.!!$F4 2011
9 TraesCS2D01G070900 chr2B 48214956 48216863 1907 True 2649.0 2649 91.9500 80 1963 1 chr2B.!!$R2 1883
10 TraesCS2D01G070900 chr2B 48179621 48181531 1910 True 2512.0 2512 90.6530 80 1963 1 chr2B.!!$R1 1883
11 TraesCS2D01G070900 chr2B 49115198 49117069 1871 False 2464.0 2464 90.4440 81 1963 1 chr2B.!!$F1 1882
12 TraesCS2D01G070900 chr2B 48147020 48148611 1591 True 1233.5 1301 94.7150 503 2514 2 chr2B.!!$R3 2011
13 TraesCS2D01G070900 chr2B 48303508 48305000 1492 True 1053.0 1101 92.4340 503 1963 2 chr2B.!!$R4 1460
14 TraesCS2D01G070900 chr2B 49153849 49154671 822 False 972.0 972 88.1790 155 972 1 chr2B.!!$F2 817
15 TraesCS2D01G070900 chr2A 32016672 32017857 1185 True 1799.0 1799 94.0290 775 1963 1 chr2A.!!$R1 1188
16 TraesCS2D01G070900 chr2A 32097088 32101745 4657 True 1575.0 2658 91.7750 50 2510 2 chr2A.!!$R2 2460
17 TraesCS2D01G070900 chrUn 311530785 311532659 1874 False 2518.0 2518 90.9190 81 1963 1 chrUn.!!$F2 1882
18 TraesCS2D01G070900 chrUn 335400764 335402634 1870 True 2494.0 2494 90.7410 84 1963 1 chrUn.!!$R1 1879
19 TraesCS2D01G070900 chrUn 338698097 338699824 1727 True 2324.0 2324 90.9560 84 1819 1 chrUn.!!$R2 1735
20 TraesCS2D01G070900 chrUn 363756492 363757647 1155 False 1550.0 1550 90.9790 81 1233 1 chrUn.!!$F3 1152
21 TraesCS2D01G070900 chrUn 295795823 295796372 549 False 691.0 691 89.4080 1962 2513 1 chrUn.!!$F1 551

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
332 333 0.252197 GGCGGTGGAGATAGGTTGTT 59.748 55.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2475 1.201647 CGTCCCTCTTTCTTCTGCGTA 59.798 52.381 0.0 0.0 0.0 4.42 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
21 22 3.628008 TCATAGGGATGAGTACGTGTGT 58.372 45.455 0.00 0.00 37.15 3.72
22 23 3.380320 TCATAGGGATGAGTACGTGTGTG 59.620 47.826 0.00 0.00 37.15 3.82
23 24 1.629043 AGGGATGAGTACGTGTGTGT 58.371 50.000 0.00 0.00 0.00 3.72
24 25 1.272490 AGGGATGAGTACGTGTGTGTG 59.728 52.381 0.00 0.00 0.00 3.82
25 26 1.000506 GGGATGAGTACGTGTGTGTGT 59.999 52.381 0.00 0.00 0.00 3.72
26 27 2.058798 GGATGAGTACGTGTGTGTGTG 58.941 52.381 0.00 0.00 0.00 3.82
27 28 2.545113 GGATGAGTACGTGTGTGTGTGT 60.545 50.000 0.00 0.00 0.00 3.72
28 29 1.915952 TGAGTACGTGTGTGTGTGTG 58.084 50.000 0.00 0.00 0.00 3.82
29 30 1.202817 TGAGTACGTGTGTGTGTGTGT 59.797 47.619 0.00 0.00 0.00 3.72
30 31 1.850441 GAGTACGTGTGTGTGTGTGTC 59.150 52.381 0.00 0.00 0.00 3.67
31 32 0.568888 GTACGTGTGTGTGTGTGTCG 59.431 55.000 0.00 0.00 0.00 4.35
32 33 1.140999 TACGTGTGTGTGTGTGTCGC 61.141 55.000 0.00 0.00 0.00 5.19
33 34 2.319707 GTGTGTGTGTGTGTCGCG 59.680 61.111 0.00 0.00 0.00 5.87
34 35 2.162120 GTGTGTGTGTGTGTCGCGA 61.162 57.895 3.71 3.71 0.00 5.87
35 36 1.876263 TGTGTGTGTGTGTCGCGAG 60.876 57.895 10.24 0.00 0.00 5.03
36 37 1.876714 GTGTGTGTGTGTCGCGAGT 60.877 57.895 10.24 0.00 0.00 4.18
37 38 1.153726 TGTGTGTGTGTCGCGAGTT 60.154 52.632 10.24 0.00 0.00 3.01
38 39 0.738063 TGTGTGTGTGTCGCGAGTTT 60.738 50.000 10.24 0.00 0.00 2.66
39 40 1.202203 GTGTGTGTGTCGCGAGTTTA 58.798 50.000 10.24 0.00 0.00 2.01
40 41 1.790623 GTGTGTGTGTCGCGAGTTTAT 59.209 47.619 10.24 0.00 0.00 1.40
41 42 1.790043 TGTGTGTGTCGCGAGTTTATG 59.210 47.619 10.24 0.00 0.00 1.90
42 43 0.787787 TGTGTGTCGCGAGTTTATGC 59.212 50.000 10.24 0.00 0.00 3.14
58 59 5.932303 AGTTTATGCGTTGTAACATGTCTCT 59.068 36.000 0.00 0.00 0.00 3.10
97 98 6.942532 ACTATAGTGTATTGGCCAACATTG 57.057 37.500 23.27 10.36 0.00 2.82
332 333 0.252197 GGCGGTGGAGATAGGTTGTT 59.748 55.000 0.00 0.00 0.00 2.83
333 334 1.339727 GGCGGTGGAGATAGGTTGTTT 60.340 52.381 0.00 0.00 0.00 2.83
723 763 4.143115 CCATGTTAATGTTATCTAGGCGCG 60.143 45.833 0.00 0.00 31.27 6.86
1774 1894 5.931294 TGTTGTGAGTCATGTACCCTTTTA 58.069 37.500 0.00 0.00 0.00 1.52
1969 2316 9.423061 AGTTAAATTAACTTGCCATGACATTTC 57.577 29.630 12.24 0.00 46.27 2.17
1980 2327 0.179111 TGACATTTCGCTCTAGCCCG 60.179 55.000 0.00 0.00 37.91 6.13
2127 2475 2.306847 GCCATACATCCAATCGGGTTT 58.693 47.619 0.00 0.00 38.11 3.27
2214 4493 6.723298 TGCTTTGGAAATGGAGAAGTAAAA 57.277 33.333 0.00 0.00 0.00 1.52
2338 4617 3.400255 CATCTATGTCACTGCATCTGGG 58.600 50.000 0.00 0.00 0.00 4.45
2359 4638 8.005388 TCTGGGCTCTACTTGAACTATTACTAT 58.995 37.037 0.00 0.00 0.00 2.12
2448 4731 6.937436 AATCGGATATTACAAAGGACAACC 57.063 37.500 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.380320 CACACACGTACTCATCCCTATGA 59.620 47.826 0.00 0.00 39.87 2.15
1 2 3.130516 ACACACACGTACTCATCCCTATG 59.869 47.826 0.00 0.00 0.00 2.23
2 3 3.130516 CACACACACGTACTCATCCCTAT 59.869 47.826 0.00 0.00 0.00 2.57
3 4 2.490509 CACACACACGTACTCATCCCTA 59.509 50.000 0.00 0.00 0.00 3.53
4 5 1.272490 CACACACACGTACTCATCCCT 59.728 52.381 0.00 0.00 0.00 4.20
5 6 1.000506 ACACACACACGTACTCATCCC 59.999 52.381 0.00 0.00 0.00 3.85
6 7 2.058798 CACACACACACGTACTCATCC 58.941 52.381 0.00 0.00 0.00 3.51
7 8 2.471370 CACACACACACACGTACTCATC 59.529 50.000 0.00 0.00 0.00 2.92
8 9 2.159156 ACACACACACACACGTACTCAT 60.159 45.455 0.00 0.00 0.00 2.90
9 10 1.202817 ACACACACACACACGTACTCA 59.797 47.619 0.00 0.00 0.00 3.41
10 11 1.850441 GACACACACACACACGTACTC 59.150 52.381 0.00 0.00 0.00 2.59
11 12 1.796253 CGACACACACACACACGTACT 60.796 52.381 0.00 0.00 0.00 2.73
12 13 0.568888 CGACACACACACACACGTAC 59.431 55.000 0.00 0.00 0.00 3.67
13 14 1.140999 GCGACACACACACACACGTA 61.141 55.000 0.00 0.00 0.00 3.57
14 15 2.449525 GCGACACACACACACACGT 61.450 57.895 0.00 0.00 0.00 4.49
15 16 2.319707 GCGACACACACACACACG 59.680 61.111 0.00 0.00 0.00 4.49
16 17 2.077801 CTCGCGACACACACACACAC 62.078 60.000 3.71 0.00 0.00 3.82
17 18 1.876263 CTCGCGACACACACACACA 60.876 57.895 3.71 0.00 0.00 3.72
18 19 1.418342 AACTCGCGACACACACACAC 61.418 55.000 3.71 0.00 0.00 3.82
19 20 0.738063 AAACTCGCGACACACACACA 60.738 50.000 3.71 0.00 0.00 3.72
20 21 1.202203 TAAACTCGCGACACACACAC 58.798 50.000 3.71 0.00 0.00 3.82
21 22 1.790043 CATAAACTCGCGACACACACA 59.210 47.619 3.71 0.00 0.00 3.72
22 23 1.461888 GCATAAACTCGCGACACACAC 60.462 52.381 3.71 0.00 0.00 3.82
23 24 0.787787 GCATAAACTCGCGACACACA 59.212 50.000 3.71 0.00 0.00 3.72
24 25 3.562869 GCATAAACTCGCGACACAC 57.437 52.632 3.71 0.00 0.00 3.82
31 32 3.443054 TGTTACAACGCATAAACTCGC 57.557 42.857 0.00 0.00 0.00 5.03
32 33 4.953269 ACATGTTACAACGCATAAACTCG 58.047 39.130 0.00 0.00 0.00 4.18
33 34 6.090898 AGAGACATGTTACAACGCATAAACTC 59.909 38.462 0.00 0.00 0.00 3.01
34 35 5.932303 AGAGACATGTTACAACGCATAAACT 59.068 36.000 0.00 0.00 0.00 2.66
35 36 6.128661 TGAGAGACATGTTACAACGCATAAAC 60.129 38.462 0.00 0.00 0.00 2.01
36 37 5.929415 TGAGAGACATGTTACAACGCATAAA 59.071 36.000 0.00 0.00 0.00 1.40
37 38 5.474825 TGAGAGACATGTTACAACGCATAA 58.525 37.500 0.00 0.00 0.00 1.90
38 39 5.066968 TGAGAGACATGTTACAACGCATA 57.933 39.130 0.00 0.00 0.00 3.14
39 40 3.925379 TGAGAGACATGTTACAACGCAT 58.075 40.909 0.00 0.00 0.00 4.73
40 41 3.378911 TGAGAGACATGTTACAACGCA 57.621 42.857 0.00 0.00 0.00 5.24
41 42 4.725556 TTTGAGAGACATGTTACAACGC 57.274 40.909 0.00 0.00 0.00 4.84
42 43 9.658475 TTTTATTTTGAGAGACATGTTACAACG 57.342 29.630 0.00 0.00 0.00 4.10
82 83 6.429385 TCCAAATTTTCAATGTTGGCCAATAC 59.571 34.615 23.66 11.51 40.33 1.89
192 193 6.128172 CCCACCTAAATATTCTCGATTGATGC 60.128 42.308 0.00 0.00 0.00 3.91
212 213 3.644966 TTAATGAGTCATGTCCCCACC 57.355 47.619 6.34 0.00 0.00 4.61
332 333 4.525100 GGAAAAGGTAAGTGTGGCCAATAA 59.475 41.667 7.24 0.00 0.00 1.40
333 334 4.083565 GGAAAAGGTAAGTGTGGCCAATA 58.916 43.478 7.24 0.00 0.00 1.90
458 459 8.331931 ATGGAACATATACCTGAAGGTTAGAA 57.668 34.615 7.43 0.00 46.52 2.10
675 715 8.513774 GGAAAAATAAACAATGAACATGCCAAT 58.486 29.630 0.00 0.00 0.00 3.16
699 739 4.994852 GCGCCTAGATAACATTAACATGGA 59.005 41.667 0.00 0.00 34.27 3.41
707 747 1.066605 ACGACGCGCCTAGATAACATT 59.933 47.619 5.73 0.00 0.00 2.71
749 789 8.921205 AGATTCCCATATTCATTCCTTTTTCTG 58.079 33.333 0.00 0.00 0.00 3.02
984 1036 3.309954 GCTCCATGATCACCTAAACGAAC 59.690 47.826 0.00 0.00 0.00 3.95
1405 1524 2.497138 TCAGCACCAACACTCATGAAG 58.503 47.619 0.00 0.00 0.00 3.02
1805 1926 7.038587 TGCTAATCCGGACCATATAACAGTTAT 60.039 37.037 6.12 10.71 0.00 1.89
1877 1998 9.280174 GTTTTATATAAAGGATCGGTGATGGAA 57.720 33.333 7.91 0.00 0.00 3.53
1914 2035 2.269023 CATGGCAGAGATATGGGGGTA 58.731 52.381 0.00 0.00 0.00 3.69
1969 2316 4.241555 AATGGCCGGGCTAGAGCG 62.242 66.667 29.87 0.00 43.26 5.03
2127 2475 1.201647 CGTCCCTCTTTCTTCTGCGTA 59.798 52.381 0.00 0.00 0.00 4.42
2448 4731 7.498900 TGGTTATCATGTCTATGTAAGCTTTGG 59.501 37.037 3.20 0.00 35.73 3.28


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

AutoCloner maintained by Alex Coulton.