Multiple sequence alignment - TraesCS2A01G130000

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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 TraesCS2A01G130000 chr2A 100.000 2355 0 0 989 3343 77797275 77799629 0.000000e+00 4349.0
1 TraesCS2A01G130000 chr2A 96.147 2362 81 7 989 3343 382861185 382858827 0.000000e+00 3849.0
2 TraesCS2A01G130000 chr2A 100.000 698 0 0 1 698 77796287 77796984 0.000000e+00 1290.0
3 TraesCS2A01G130000 chr2A 95.702 698 30 0 1 698 382861917 382861220 0.000000e+00 1123.0
4 TraesCS2A01G130000 chr2B 95.516 2364 91 8 992 3343 325632258 325634618 0.000000e+00 3764.0
5 TraesCS2A01G130000 chr2B 95.619 1164 50 1 1061 2223 484100383 484101546 0.000000e+00 1866.0
6 TraesCS2A01G130000 chr2B 95.412 1177 41 8 2175 3343 484101576 484102747 0.000000e+00 1862.0
7 TraesCS2A01G130000 chr2B 95.272 698 33 0 1 698 325631312 325632009 0.000000e+00 1107.0
8 TraesCS2A01G130000 chr2B 94.409 626 35 0 73 698 484091056 484091681 0.000000e+00 963.0
9 TraesCS2A01G130000 chr1D 93.610 2363 139 8 989 3343 176355599 176357957 0.000000e+00 3517.0
10 TraesCS2A01G130000 chr1D 93.232 2364 132 8 989 3343 356876061 356878405 0.000000e+00 3454.0
11 TraesCS2A01G130000 chr1D 94.971 696 35 0 3 698 356874970 356875665 0.000000e+00 1092.0
12 TraesCS2A01G130000 chr1D 94.540 696 38 0 3 698 176354875 176355570 0.000000e+00 1075.0
13 TraesCS2A01G130000 chr6D 93.837 2093 119 7 1259 3342 452076331 452074240 0.000000e+00 3142.0
14 TraesCS2A01G130000 chr6D 93.038 1106 66 7 1259 2355 462403984 462402881 0.000000e+00 1605.0
15 TraesCS2A01G130000 chr6D 95.648 942 41 0 2402 3343 462402880 462401939 0.000000e+00 1513.0
16 TraesCS2A01G130000 chr6A 94.370 1794 86 11 996 2775 359014226 359012434 0.000000e+00 2739.0
17 TraesCS2A01G130000 chr6A 95.130 575 28 0 112 686 359015081 359014507 0.000000e+00 907.0
18 TraesCS2A01G130000 chr5B 87.759 1789 198 11 1573 3343 543102878 543104663 0.000000e+00 2071.0
19 TraesCS2A01G130000 chr4B 94.643 1176 54 6 2175 3343 364069697 364068524 0.000000e+00 1814.0
20 TraesCS2A01G130000 chr7A 96.562 698 24 0 1 698 439780261 439780958 0.000000e+00 1157.0
21 TraesCS2A01G130000 chr7A 81.034 116 21 1 426 541 198208478 198208592 1.280000e-14 91.6
22 TraesCS2A01G130000 chr3D 80.531 113 21 1 429 541 230760823 230760712 5.940000e-13 86.1


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 TraesCS2A01G130000 chr2A 77796287 77799629 3342 False 2819.5 4349 100.0000 1 3343 2 chr2A.!!$F1 3342
1 TraesCS2A01G130000 chr2A 382858827 382861917 3090 True 2486.0 3849 95.9245 1 3343 2 chr2A.!!$R1 3342
2 TraesCS2A01G130000 chr2B 325631312 325634618 3306 False 2435.5 3764 95.3940 1 3343 2 chr2B.!!$F2 3342
3 TraesCS2A01G130000 chr2B 484100383 484102747 2364 False 1864.0 1866 95.5155 1061 3343 2 chr2B.!!$F3 2282
4 TraesCS2A01G130000 chr2B 484091056 484091681 625 False 963.0 963 94.4090 73 698 1 chr2B.!!$F1 625
5 TraesCS2A01G130000 chr1D 176354875 176357957 3082 False 2296.0 3517 94.0750 3 3343 2 chr1D.!!$F1 3340
6 TraesCS2A01G130000 chr1D 356874970 356878405 3435 False 2273.0 3454 94.1015 3 3343 2 chr1D.!!$F2 3340
7 TraesCS2A01G130000 chr6D 452074240 452076331 2091 True 3142.0 3142 93.8370 1259 3342 1 chr6D.!!$R1 2083
8 TraesCS2A01G130000 chr6D 462401939 462403984 2045 True 1559.0 1605 94.3430 1259 3343 2 chr6D.!!$R2 2084
9 TraesCS2A01G130000 chr6A 359012434 359015081 2647 True 1823.0 2739 94.7500 112 2775 2 chr6A.!!$R1 2663
10 TraesCS2A01G130000 chr5B 543102878 543104663 1785 False 2071.0 2071 87.7590 1573 3343 1 chr5B.!!$F1 1770
11 TraesCS2A01G130000 chr4B 364068524 364069697 1173 True 1814.0 1814 94.6430 2175 3343 1 chr4B.!!$R1 1168
12 TraesCS2A01G130000 chr7A 439780261 439780958 697 False 1157.0 1157 96.5620 1 698 1 chr7A.!!$F2 697

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
161 162 0.250513 AGATCGGGACCAAGTCTTGC 59.749 55.0 7.09 0.0 32.47 4.01 F
172 173 0.605589 AAGTCTTGCTCTGGTCGAGG 59.394 55.0 0.00 0.0 40.25 4.63 F
1313 1437 0.897621 TCCTCAATCTCGCTGCTGAA 59.102 50.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1683 0.179084 ATATCTTGACACGCACCCGG 60.179 55.0 0.0 0.0 39.22 5.73 R
2076 2203 0.695347 CACCAGAGGCTCTTTCCCTT 59.305 55.0 15.9 0.0 31.41 3.95 R
2790 3012 1.040646 TCCAGAAGCTCACGAACTGT 58.959 50.0 0.0 0.0 0.00 3.55 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
56 57 1.762370 TGCAGAGGCGATTGATTCCTA 59.238 47.619 0.00 0.0 45.35 2.94
161 162 0.250513 AGATCGGGACCAAGTCTTGC 59.749 55.000 7.09 0.0 32.47 4.01
164 165 0.832135 TCGGGACCAAGTCTTGCTCT 60.832 55.000 7.09 0.0 32.47 4.09
172 173 0.605589 AAGTCTTGCTCTGGTCGAGG 59.394 55.000 0.00 0.0 40.25 4.63
196 197 1.953686 AGAGCGAAGGAGATAGCTGAC 59.046 52.381 0.00 0.0 40.39 3.51
1018 1124 2.348888 CGACGGGTACTTGCTCCCT 61.349 63.158 0.00 0.0 41.40 4.20
1088 1194 2.034685 CCAGCCGAGTTCGATGATTCTA 59.965 50.000 2.59 0.0 43.02 2.10
1313 1437 0.897621 TCCTCAATCTCGCTGCTGAA 59.102 50.000 0.00 0.0 0.00 3.02
1559 1683 8.603242 ACCATGTAATCGTTGATAAATACCTC 57.397 34.615 0.00 0.0 0.00 3.85
1708 1832 3.684693 GCATTGTTGGCCACACTTT 57.315 47.368 3.88 0.0 33.98 2.66
1890 2017 4.738998 CCGCCAAGCCCATGGACA 62.739 66.667 15.22 0.0 43.54 4.02
2085 2213 1.885163 GCGAGACGGGAAGGGAAAGA 61.885 60.000 0.00 0.0 0.00 2.52
2159 2293 2.612972 CGCCACACTATTGGTCTGAACT 60.613 50.000 0.00 0.0 39.09 3.01
2223 2435 2.750657 GCATGCCCAGCCTAGTCCT 61.751 63.158 6.36 0.0 0.00 3.85
2241 2459 3.840666 GTCCTAGGGGCTAATGATGATGA 59.159 47.826 9.46 0.0 0.00 2.92
2711 2933 4.159135 AGAAAAAGATGAGAATGGCGCATT 59.841 37.500 10.83 7.3 37.13 3.56
2790 3012 1.067142 GTGGTATGCTCTCCAACACGA 60.067 52.381 0.00 0.0 35.38 4.35
2816 3038 2.826128 TCGTGAGCTTCTGGAACTACAT 59.174 45.455 0.00 0.0 0.00 2.29
3070 3300 2.238646 TCACGGGCTTTTATGGTCATCT 59.761 45.455 0.00 0.0 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 3.065925 GCCTCGATCTTTCCTTGATTTGG 59.934 47.826 0.00 0.00 0.00 3.28
161 162 1.734047 CGCTCTTTTCCTCGACCAGAG 60.734 57.143 0.00 0.00 46.44 3.35
164 165 0.677288 TTCGCTCTTTTCCTCGACCA 59.323 50.000 0.00 0.00 0.00 4.02
172 173 3.801594 CAGCTATCTCCTTCGCTCTTTTC 59.198 47.826 0.00 0.00 0.00 2.29
196 197 1.093159 GAATCTCACCTGCCAGCAAG 58.907 55.000 0.00 0.00 0.00 4.01
993 1099 0.108804 CAAGTACCCGTCGATGCAGT 60.109 55.000 0.00 1.40 0.00 4.40
1036 1142 1.821966 TAGGTGGGAGGAGGAGCCAA 61.822 60.000 0.00 0.00 40.02 4.52
1278 1402 2.205691 GGATAAACCTCCCGTCCGT 58.794 57.895 0.00 0.00 35.41 4.69
1313 1437 0.370273 GCACAAATCGACGATCGCTT 59.630 50.000 16.60 0.00 40.21 4.68
1559 1683 0.179084 ATATCTTGACACGCACCCGG 60.179 55.000 0.00 0.00 39.22 5.73
1652 1776 5.514500 ACAGGGGAAGCTTTTCATACTTA 57.486 39.130 0.00 0.00 0.00 2.24
1708 1832 5.472137 CGAGGGATTTTACAAAACCTCTCAA 59.528 40.000 8.96 0.00 38.25 3.02
1817 1941 1.473677 TCGCGAAGATAGTTCCCGAAA 59.526 47.619 6.20 0.00 0.00 3.46
1890 2017 1.003355 CAGTGGCCACCTTGACGAT 60.003 57.895 32.29 8.36 0.00 3.73
1953 2080 2.289072 CCTGGTCGAGTGTCAACTTGAT 60.289 50.000 0.00 0.00 46.38 2.57
2008 2135 1.893808 CCAAGTGTTGCGTCAGCCT 60.894 57.895 0.00 0.00 44.33 4.58
2076 2203 0.695347 CACCAGAGGCTCTTTCCCTT 59.305 55.000 15.90 0.00 31.41 3.95
2077 2204 1.846712 GCACCAGAGGCTCTTTCCCT 61.847 60.000 15.90 0.00 34.77 4.20
2148 2276 4.082845 CAGGAGAGACTAGTTCAGACCAA 58.917 47.826 0.00 0.00 0.00 3.67
2223 2435 7.095183 AGAAATTCATCATCATTAGCCCCTA 57.905 36.000 0.00 0.00 0.00 3.53
2241 2459 2.035832 CACACCGGCTGGAAAAGAAATT 59.964 45.455 21.41 0.00 39.21 1.82
2407 2627 1.817357 CATCCTCAGCTCTGTTTGCA 58.183 50.000 0.00 0.00 0.00 4.08
2628 2850 3.818773 CCTCCTTCTCGTCTATCTCCTTC 59.181 52.174 0.00 0.00 0.00 3.46
2720 2942 4.816984 GGCGGTCCTCCTCCTCGA 62.817 72.222 0.00 0.00 35.82 4.04
2790 3012 1.040646 TCCAGAAGCTCACGAACTGT 58.959 50.000 0.00 0.00 0.00 3.55
2816 3038 1.264749 ACTCCGCCCTTGTATGCTCA 61.265 55.000 0.00 0.00 0.00 4.26
3070 3300 2.768253 ATGATGCTCGTTCCAGTTCA 57.232 45.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.