Multiple sequence alignment - TraesCS4B01G143700

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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 TraesCS4B01G143700 chr4B 100.000 2935 0 0 1 2935 191662093 191665027 0.000000e+00 5421.0
1 TraesCS4B01G143700 chr4B 91.509 106 9 0 2820 2925 191664816 191664921 2.360000e-31 147.0
2 TraesCS4B01G143700 chr4B 91.509 106 9 0 2724 2829 191664912 191665017 2.360000e-31 147.0
3 TraesCS4B01G143700 chr4D 98.642 2578 33 2 359 2935 127565502 127568078 0.000000e+00 4566.0
4 TraesCS4B01G143700 chr4D 96.121 232 3 1 1 232 127559212 127559437 9.930000e-100 374.0
5 TraesCS4B01G143700 chr4D 91.509 106 9 0 2820 2925 127567867 127567972 2.360000e-31 147.0
6 TraesCS4B01G143700 chr4D 91.509 106 9 0 2724 2829 127567963 127568068 2.360000e-31 147.0
7 TraesCS4B01G143700 chr4D 98.462 65 0 1 244 308 127559422 127559485 2.390000e-21 113.0
8 TraesCS4B01G143700 chr4A 96.561 2588 74 7 359 2935 440869902 440867319 0.000000e+00 4272.0
9 TraesCS4B01G143700 chr4A 88.169 355 16 11 1 355 440870281 440869953 1.640000e-107 399.0
10 TraesCS4B01G143700 chr4A 89.423 104 11 0 2726 2829 440867432 440867329 6.600000e-27 132.0
11 TraesCS4B01G143700 chr4A 87.736 106 13 0 2820 2925 440867530 440867425 1.100000e-24 124.0
12 TraesCS4B01G143700 chr3B 82.895 76 9 4 1468 1541 653152434 653152507 6.790000e-07 65.8
13 TraesCS4B01G143700 chr6D 89.796 49 4 1 1483 1531 90869470 90869423 8.780000e-06 62.1
14 TraesCS4B01G143700 chr6B 89.796 49 4 1 1483 1531 172990136 172990089 8.780000e-06 62.1
15 TraesCS4B01G143700 chr6A 89.796 49 4 1 1483 1531 109114240 109114193 8.780000e-06 62.1
16 TraesCS4B01G143700 chr2B 89.362 47 5 0 1504 1550 663180748 663180702 3.160000e-05 60.2


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 TraesCS4B01G143700 chr4B 191662093 191665027 2934 False 1905.00 5421 94.339333 1 2935 3 chr4B.!!$F1 2934
1 TraesCS4B01G143700 chr4D 127565502 127568078 2576 False 1620.00 4566 93.886667 359 2935 3 chr4D.!!$F2 2576
2 TraesCS4B01G143700 chr4A 440867319 440870281 2962 True 1231.75 4272 90.472250 1 2935 4 chr4A.!!$R1 2934

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
70 71 0.481567 ATGGGCCTTATCAGCATGCT 59.518 50.0 16.3 16.3 34.76 3.79 F
328 330 0.782384 GTAACAACACCTGCTCGTCG 59.218 55.0 0.0 0.0 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1860 0.250640 CCCATAGGAGATGGCAGCAC 60.251 60.000 5.19 0.0 37.85 4.40 R
2121 2172 3.620374 CACACATCATAAGCAGACCTGAC 59.380 47.826 0.47 0.0 0.00 3.51 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
70 71 0.481567 ATGGGCCTTATCAGCATGCT 59.518 50.000 16.30 16.30 34.76 3.79
121 122 9.713684 AGATTATATGTTCCCAAGAAAATTCCA 57.286 29.630 0.00 0.00 32.00 3.53
207 208 9.286946 CAAAGAAATTGATGCTAAAGCTAAGAG 57.713 33.333 3.26 0.00 41.85 2.85
218 219 8.455903 TGCTAAAGCTAAGAGCATGAAATTAT 57.544 30.769 11.87 0.00 45.56 1.28
219 220 8.906867 TGCTAAAGCTAAGAGCATGAAATTATT 58.093 29.630 11.87 0.00 45.56 1.40
220 221 9.178427 GCTAAAGCTAAGAGCATGAAATTATTG 57.822 33.333 0.00 0.00 45.56 1.90
221 222 7.998753 AAAGCTAAGAGCATGAAATTATTGC 57.001 32.000 0.00 0.26 45.56 3.56
222 223 6.704289 AGCTAAGAGCATGAAATTATTGCA 57.296 33.333 0.00 0.00 45.56 4.08
223 224 7.286215 AGCTAAGAGCATGAAATTATTGCAT 57.714 32.000 0.00 0.00 45.56 3.96
224 225 7.145985 AGCTAAGAGCATGAAATTATTGCATG 58.854 34.615 18.95 18.95 45.56 4.06
225 226 6.365247 GCTAAGAGCATGAAATTATTGCATGG 59.635 38.462 23.03 9.68 41.89 3.66
226 227 6.474140 AAGAGCATGAAATTATTGCATGGA 57.526 33.333 23.03 0.00 39.71 3.41
227 228 6.474140 AGAGCATGAAATTATTGCATGGAA 57.526 33.333 23.03 0.79 39.71 3.53
228 229 7.062749 AGAGCATGAAATTATTGCATGGAAT 57.937 32.000 23.03 17.08 39.71 3.01
229 230 7.506114 AGAGCATGAAATTATTGCATGGAATT 58.494 30.769 23.03 0.04 39.71 2.17
230 231 8.644216 AGAGCATGAAATTATTGCATGGAATTA 58.356 29.630 23.03 9.50 39.71 1.40
231 232 9.431887 GAGCATGAAATTATTGCATGGAATTAT 57.568 29.630 23.03 11.53 39.71 1.28
232 233 9.787435 AGCATGAAATTATTGCATGGAATTATT 57.213 25.926 23.03 16.74 39.71 1.40
328 330 0.782384 GTAACAACACCTGCTCGTCG 59.218 55.000 0.00 0.00 0.00 5.12
651 700 4.922206 AGTTAGATGCAGTCCAAATCCAA 58.078 39.130 0.00 0.00 0.00 3.53
778 827 1.205460 ACCACGTAAAGAGGCCCCAT 61.205 55.000 0.00 0.00 33.55 4.00
1416 1465 5.491323 AAGAAGACCTTACTAAAGCAGCT 57.509 39.130 0.00 0.00 32.24 4.24
1417 1466 4.826556 AGAAGACCTTACTAAAGCAGCTG 58.173 43.478 10.11 10.11 0.00 4.24
1779 1830 0.828762 GGCCATGCTGCCCATTGATA 60.829 55.000 0.00 0.00 46.11 2.15
1781 1832 1.413445 GCCATGCTGCCCATTGATAAA 59.587 47.619 0.00 0.00 29.71 1.40
1809 1860 1.676746 CAGCAATCTCCCATGTCCTG 58.323 55.000 0.00 0.00 0.00 3.86
2288 2339 7.899178 TTGACACGAATGAACATTGTACTAT 57.101 32.000 4.72 0.00 0.00 2.12
2289 2340 7.520119 TGACACGAATGAACATTGTACTATC 57.480 36.000 4.72 0.00 0.00 2.08
2290 2341 7.093992 TGACACGAATGAACATTGTACTATCA 58.906 34.615 4.72 0.00 0.00 2.15
2347 2408 3.737559 ACAAACAGGGCCATGAGATTA 57.262 42.857 26.87 0.00 0.00 1.75
2411 2472 7.902920 ATGGGTACAGAATCAGCATTATTTT 57.097 32.000 0.00 0.00 0.00 1.82
2451 2512 5.463724 GCTATTACACTCTCATTTCCTTCGG 59.536 44.000 0.00 0.00 0.00 4.30
2470 2531 2.947652 CGGCAGGATGTTGAGATTGAAT 59.052 45.455 0.00 0.00 39.31 2.57
2543 2604 1.444836 TTCTCCAATAAACACGCGGG 58.555 50.000 6.92 6.92 0.00 6.13
2632 2694 4.635223 TCTGAGTGGAATTGACAGACTTG 58.365 43.478 0.00 0.00 33.57 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 3.440173 CGGTGCATGTTTCTTACTGGAAT 59.560 43.478 0.00 0.0 0.00 3.01
120 121 1.135689 GCCGGTGCATGTTTCTTACTG 60.136 52.381 1.90 0.0 37.47 2.74
121 122 1.165270 GCCGGTGCATGTTTCTTACT 58.835 50.000 1.90 0.0 37.47 2.24
203 204 6.474140 TCCATGCAATAATTTCATGCTCTT 57.526 33.333 0.00 0.0 40.66 2.85
235 236 9.936759 TCTATAATTCCATACAATATGCGTCAA 57.063 29.630 0.00 0.0 0.00 3.18
236 237 9.936759 TTCTATAATTCCATACAATATGCGTCA 57.063 29.630 0.00 0.0 0.00 4.35
316 318 3.865929 AAGGCACGACGAGCAGGTG 62.866 63.158 18.77 0.0 34.85 4.00
1293 1342 1.498176 GGCCAGGGTGGAGGTAGTTT 61.498 60.000 0.00 0.0 40.96 2.66
1781 1832 1.206371 GGGAGATTGCTGCATGCTTTT 59.794 47.619 20.33 0.0 43.37 2.27
1809 1860 0.250640 CCCATAGGAGATGGCAGCAC 60.251 60.000 5.19 0.0 37.85 4.40
2121 2172 3.620374 CACACATCATAAGCAGACCTGAC 59.380 47.826 0.47 0.0 0.00 3.51
2257 2308 7.173218 ACAATGTTCATTCGTGTCAATCTAACT 59.827 33.333 0.00 0.0 0.00 2.24
2347 2408 3.906218 TGCTCCTTGAGATACAGCCATAT 59.094 43.478 0.00 0.0 0.00 1.78
2353 2414 5.947228 TTTGTTTGCTCCTTGAGATACAG 57.053 39.130 0.00 0.0 0.00 2.74
2354 2415 6.061441 TCTTTTGTTTGCTCCTTGAGATACA 58.939 36.000 0.00 0.0 0.00 2.29
2411 2472 8.564574 AGTGTAATAGCAAGAACGATTTGAAAA 58.435 29.630 0.00 0.0 0.00 2.29
2451 2512 3.380637 AGCATTCAATCTCAACATCCTGC 59.619 43.478 0.00 0.0 0.00 4.85
2470 2531 4.400251 CCAGAAGCCATTTTATCAAGAGCA 59.600 41.667 0.00 0.0 0.00 4.26
2573 2635 0.605083 TGTCTGTACAGCAGCCTCAG 59.395 55.000 18.45 0.0 44.66 3.35
2632 2694 1.257743 TAGACCACTCACTCTGCACC 58.742 55.000 0.00 0.0 0.00 5.01


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

AutoCloner maintained by Alex Coulton.