Multiple sequence alignment - TraesCS5D01G029000

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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 TraesCS5D01G029000 chr5D 100.000 2928 0 0 1 2928 27280054 27282981 0.000000e+00 5408
1 TraesCS5D01G029000 chr5D 95.462 1212 41 7 1071 2273 431973345 431974551 0.000000e+00 1921
2 TraesCS5D01G029000 chr5D 98.944 663 6 1 2267 2928 67946804 67946142 0.000000e+00 1184
3 TraesCS5D01G029000 chr5D 99.238 656 5 0 2273 2928 428300725 428301380 0.000000e+00 1184
4 TraesCS5D01G029000 chr5D 98.793 663 7 1 2266 2928 205182147 205182808 0.000000e+00 1179
5 TraesCS5D01G029000 chr5D 98.068 673 12 1 2257 2928 13878378 13877706 0.000000e+00 1170
6 TraesCS5D01G029000 chr5D 90.769 780 39 11 13 765 431972574 431973347 0.000000e+00 1011
7 TraesCS5D01G029000 chr5D 93.665 663 38 2 1614 2273 127940012 127939351 0.000000e+00 989
8 TraesCS5D01G029000 chr2B 95.498 2288 63 19 24 2273 134340616 134342901 0.000000e+00 3618
9 TraesCS5D01G029000 chr4D 94.255 2315 78 18 1 2273 85853528 85851227 0.000000e+00 3487
10 TraesCS5D01G029000 chr4D 99.085 656 6 0 2273 2928 507706914 507706259 0.000000e+00 1179
11 TraesCS5D01G029000 chr6D 96.251 1814 49 9 472 2271 440673101 440674909 0.000000e+00 2955
12 TraesCS5D01G029000 chr6D 90.145 761 39 9 65 796 137153310 137152557 0.000000e+00 957
13 TraesCS5D01G029000 chr6D 90.000 460 14 7 1 433 440672645 440673099 1.520000e-157 566
14 TraesCS5D01G029000 chr4A 93.932 1714 70 11 203 1899 658380920 658382616 0.000000e+00 2558
15 TraesCS5D01G029000 chr4A 84.685 222 8 11 28 223 658380791 658381012 6.400000e-47 198
16 TraesCS5D01G029000 chr2D 95.669 1547 50 8 472 2004 606091670 606090127 0.000000e+00 2470
17 TraesCS5D01G029000 chr2D 92.566 1130 46 12 1 1102 29097472 29096353 0.000000e+00 1587
18 TraesCS5D01G029000 chr2D 99.238 656 5 0 2273 2928 590747511 590746856 0.000000e+00 1184
19 TraesCS5D01G029000 chr2D 97.781 676 11 2 2256 2928 75625507 75624833 0.000000e+00 1162
20 TraesCS5D01G029000 chr2D 89.716 457 18 4 1 433 606092123 606091672 9.170000e-155 556
21 TraesCS5D01G029000 chr6A 95.120 1168 45 6 699 1856 163168206 163167041 0.000000e+00 1831
22 TraesCS5D01G029000 chr6A 89.228 622 37 6 57 651 163168821 163168203 0.000000e+00 750
23 TraesCS5D01G029000 chr7B 92.301 1182 39 12 1 1137 228799893 228801067 0.000000e+00 1631
24 TraesCS5D01G029000 chr7B 97.627 927 21 1 1178 2103 228801066 228801992 0.000000e+00 1589
25 TraesCS5D01G029000 chr1D 99.238 656 5 0 2273 2928 326540141 326539486 0.000000e+00 1184
26 TraesCS5D01G029000 chr1D 93.665 663 38 2 1614 2273 415596550 415597211 0.000000e+00 989
27 TraesCS5D01G029000 chr7D 99.085 656 6 0 2273 2928 262726263 262725608 0.000000e+00 1179
28 TraesCS5D01G029000 chr7D 94.118 663 35 2 1614 2273 530740951 530740290 0.000000e+00 1005
29 TraesCS5D01G029000 chr7A 89.722 827 61 13 814 1625 41464795 41463978 0.000000e+00 1035
30 TraesCS5D01G029000 chr7A 89.769 821 60 14 814 1622 617598489 617599297 0.000000e+00 1029
31 TraesCS5D01G029000 chr7A 88.861 395 16 12 1 371 658271398 658271788 7.390000e-126 460
32 TraesCS5D01G029000 chr2A 89.647 821 61 13 814 1622 756524456 756525264 0.000000e+00 1024
33 TraesCS5D01G029000 chr2A 87.342 395 24 13 1 371 764882245 764882637 2.080000e-116 429
34 TraesCS5D01G029000 chr3D 93.978 465 16 4 787 1239 614089797 614089333 0.000000e+00 693
35 TraesCS5D01G029000 chr3D 91.147 497 26 5 311 796 614099918 614099429 0.000000e+00 658


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 TraesCS5D01G029000 chr5D 27280054 27282981 2927 False 5408.0 5408 100.0000 1 2928 1 chr5D.!!$F1 2927
1 TraesCS5D01G029000 chr5D 431972574 431974551 1977 False 1466.0 1921 93.1155 13 2273 2 chr5D.!!$F4 2260
2 TraesCS5D01G029000 chr5D 67946142 67946804 662 True 1184.0 1184 98.9440 2267 2928 1 chr5D.!!$R2 661
3 TraesCS5D01G029000 chr5D 428300725 428301380 655 False 1184.0 1184 99.2380 2273 2928 1 chr5D.!!$F3 655
4 TraesCS5D01G029000 chr5D 205182147 205182808 661 False 1179.0 1179 98.7930 2266 2928 1 chr5D.!!$F2 662
5 TraesCS5D01G029000 chr5D 13877706 13878378 672 True 1170.0 1170 98.0680 2257 2928 1 chr5D.!!$R1 671
6 TraesCS5D01G029000 chr5D 127939351 127940012 661 True 989.0 989 93.6650 1614 2273 1 chr5D.!!$R3 659
7 TraesCS5D01G029000 chr2B 134340616 134342901 2285 False 3618.0 3618 95.4980 24 2273 1 chr2B.!!$F1 2249
8 TraesCS5D01G029000 chr4D 85851227 85853528 2301 True 3487.0 3487 94.2550 1 2273 1 chr4D.!!$R1 2272
9 TraesCS5D01G029000 chr4D 507706259 507706914 655 True 1179.0 1179 99.0850 2273 2928 1 chr4D.!!$R2 655
10 TraesCS5D01G029000 chr6D 440672645 440674909 2264 False 1760.5 2955 93.1255 1 2271 2 chr6D.!!$F1 2270
11 TraesCS5D01G029000 chr6D 137152557 137153310 753 True 957.0 957 90.1450 65 796 1 chr6D.!!$R1 731
12 TraesCS5D01G029000 chr4A 658380791 658382616 1825 False 1378.0 2558 89.3085 28 1899 2 chr4A.!!$F1 1871
13 TraesCS5D01G029000 chr2D 29096353 29097472 1119 True 1587.0 1587 92.5660 1 1102 1 chr2D.!!$R1 1101
14 TraesCS5D01G029000 chr2D 606090127 606092123 1996 True 1513.0 2470 92.6925 1 2004 2 chr2D.!!$R4 2003
15 TraesCS5D01G029000 chr2D 590746856 590747511 655 True 1184.0 1184 99.2380 2273 2928 1 chr2D.!!$R3 655
16 TraesCS5D01G029000 chr2D 75624833 75625507 674 True 1162.0 1162 97.7810 2256 2928 1 chr2D.!!$R2 672
17 TraesCS5D01G029000 chr6A 163167041 163168821 1780 True 1290.5 1831 92.1740 57 1856 2 chr6A.!!$R1 1799
18 TraesCS5D01G029000 chr7B 228799893 228801992 2099 False 1610.0 1631 94.9640 1 2103 2 chr7B.!!$F1 2102
19 TraesCS5D01G029000 chr1D 326539486 326540141 655 True 1184.0 1184 99.2380 2273 2928 1 chr1D.!!$R1 655
20 TraesCS5D01G029000 chr1D 415596550 415597211 661 False 989.0 989 93.6650 1614 2273 1 chr1D.!!$F1 659
21 TraesCS5D01G029000 chr7D 262725608 262726263 655 True 1179.0 1179 99.0850 2273 2928 1 chr7D.!!$R1 655
22 TraesCS5D01G029000 chr7D 530740290 530740951 661 True 1005.0 1005 94.1180 1614 2273 1 chr7D.!!$R2 659
23 TraesCS5D01G029000 chr7A 41463978 41464795 817 True 1035.0 1035 89.7220 814 1625 1 chr7A.!!$R1 811
24 TraesCS5D01G029000 chr7A 617598489 617599297 808 False 1029.0 1029 89.7690 814 1622 1 chr7A.!!$F1 808
25 TraesCS5D01G029000 chr2A 756524456 756525264 808 False 1024.0 1024 89.6470 814 1622 1 chr2A.!!$F1 808

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
135 145 0.531532 CGAAGCAGCAGGGTAGGATG 60.532 60.000 0.0 0.0 0.00 3.51 F
137 147 0.543749 AAGCAGCAGGGTAGGATGAC 59.456 55.000 0.0 0.0 0.00 3.06 F
138 148 1.147153 GCAGCAGGGTAGGATGACC 59.853 63.158 0.0 0.0 38.93 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 2281 0.037326 GATGGTCAGTCTGGTCGCAA 60.037 55.000 0.00 0.00 0.00 4.85 R
1906 2288 2.486472 AAAGCTGGATGGTCAGTCTG 57.514 50.000 0.00 0.00 37.12 3.51 R
2114 2500 4.396166 GCCTAAGCTTTGACAAGATGCTTA 59.604 41.667 20.67 20.67 42.81 3.09 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
41 42 1.893786 GACACATCTGGGTCGCTCT 59.106 57.895 0.00 0.00 38.85 4.09
53 63 4.647611 TGGGTCGCTCTTGATTCTAAAAA 58.352 39.130 0.00 0.00 0.00 1.94
135 145 0.531532 CGAAGCAGCAGGGTAGGATG 60.532 60.000 0.00 0.00 0.00 3.51
136 146 0.833287 GAAGCAGCAGGGTAGGATGA 59.167 55.000 0.00 0.00 0.00 2.92
137 147 0.543749 AAGCAGCAGGGTAGGATGAC 59.456 55.000 0.00 0.00 0.00 3.06
138 148 1.147153 GCAGCAGGGTAGGATGACC 59.853 63.158 0.00 0.00 38.93 4.02
618 813 2.889045 GCACCGTCTACAGGTCCATATA 59.111 50.000 0.00 0.00 40.59 0.86
620 815 4.618460 GCACCGTCTACAGGTCCATATATG 60.618 50.000 5.68 5.68 40.59 1.78
631 826 7.500992 ACAGGTCCATATATGTTACAGTCTTG 58.499 38.462 11.73 3.64 0.00 3.02
645 840 7.178628 TGTTACAGTCTTGCTCTACCTTATTCT 59.821 37.037 0.00 0.00 0.00 2.40
880 1130 4.696877 TGATTCTGCAGTTGTTGATTCGAT 59.303 37.500 14.67 0.00 0.00 3.59
1050 1324 7.119846 GTGGCAATAGAACACTTGAATTCTACT 59.880 37.037 7.05 0.00 39.58 2.57
1073 1347 1.153409 CAGGCGAGATCAAGCTGCT 60.153 57.895 11.35 0.00 0.00 4.24
1102 1391 4.703379 ATGAGGAATGATCTGGAGAACC 57.297 45.455 0.00 0.00 0.00 3.62
1176 1507 6.162777 GGAGTCTATCAAGCATAAGTCCATC 58.837 44.000 0.00 0.00 0.00 3.51
1205 1576 3.084786 GGCTGAAGCAACTTAAGGATGT 58.915 45.455 7.53 0.00 44.36 3.06
1844 2226 2.097825 GTGAAATCCATGGCTGCTTCT 58.902 47.619 6.96 0.00 0.00 2.85
1906 2288 2.124122 GATGGTTGTTGTTTTGCGACC 58.876 47.619 0.00 0.00 39.14 4.79
2114 2500 9.588096 GGTGTTCCCCATTTATAATTTAGAGAT 57.412 33.333 0.00 0.00 0.00 2.75
2188 2574 3.582647 TCCAAAGTTCTGTGCCTGATCTA 59.417 43.478 0.00 0.00 0.00 1.98
2695 3084 3.770933 ACGTAACTGGGTGGCTATAAAGA 59.229 43.478 0.00 0.00 0.00 2.52
2742 3131 0.466372 TGTTGGGTTGGCACGAATCA 60.466 50.000 0.00 0.00 0.00 2.57
2756 3145 2.749621 ACGAATCAAGACTGGGATTTGC 59.250 45.455 13.53 0.00 38.09 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 63 4.226384 AGGAGCAACCCAGATTTTTCTTT 58.774 39.130 0.00 0.00 40.05 2.52
54 64 3.829026 GAGGAGCAACCCAGATTTTTCTT 59.171 43.478 0.00 0.00 40.05 2.52
55 65 3.425659 GAGGAGCAACCCAGATTTTTCT 58.574 45.455 0.00 0.00 40.05 2.52
69 79 1.984570 CGGGAAGAGTGGAGGAGCA 60.985 63.158 0.00 0.00 0.00 4.26
308 477 1.433879 CATCAGACGTCGGTCCTCC 59.566 63.158 15.37 0.00 44.54 4.30
618 813 5.746990 AAGGTAGAGCAAGACTGTAACAT 57.253 39.130 0.00 0.00 34.24 2.71
620 815 7.548967 AGAATAAGGTAGAGCAAGACTGTAAC 58.451 38.462 0.00 0.00 31.90 2.50
631 826 8.657729 GTGAACTTACAAAGAATAAGGTAGAGC 58.342 37.037 0.00 0.00 34.50 4.09
645 840 2.920524 TGGAAGCCGTGAACTTACAAA 58.079 42.857 0.00 0.00 35.02 2.83
730 980 3.780804 TTAGTTACATGGCCACTGTGT 57.219 42.857 23.16 19.46 0.00 3.72
1050 1324 3.461061 CAGCTTGATCTCGCCTGAAATA 58.539 45.455 0.00 0.00 0.00 1.40
1073 1347 6.086775 TCCAGATCATTCCTCATATTCCTGA 58.913 40.000 0.00 0.00 0.00 3.86
1102 1391 1.796982 CGACTCCAGCGTCATCTTCAG 60.797 57.143 0.00 0.00 33.54 3.02
1176 1507 0.595095 GTTGCTTCAGCCACAGAAGG 59.405 55.000 0.00 0.00 42.08 3.46
1591 1968 3.088532 AGGTGCTTGACAAAAACAGTGA 58.911 40.909 0.00 0.00 0.00 3.41
1899 2281 0.037326 GATGGTCAGTCTGGTCGCAA 60.037 55.000 0.00 0.00 0.00 4.85
1906 2288 2.486472 AAAGCTGGATGGTCAGTCTG 57.514 50.000 0.00 0.00 37.12 3.51
2114 2500 4.396166 GCCTAAGCTTTGACAAGATGCTTA 59.604 41.667 20.67 20.67 42.81 3.09
2188 2574 7.570607 AGGTGGGAGATTAGAAAAGATACTGAT 59.429 37.037 0.00 0.00 0.00 2.90
2197 2583 3.581332 ACGTGAGGTGGGAGATTAGAAAA 59.419 43.478 0.00 0.00 0.00 2.29
2695 3084 2.945456 TCGGAGATACCTGTAGTGCAT 58.055 47.619 0.00 0.00 36.31 3.96
2742 3131 2.206576 GAGTGGCAAATCCCAGTCTT 57.793 50.000 8.42 0.00 46.97 3.01


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

AutoCloner maintained by Alex Coulton.