Multiple sequence alignment - TraesCS4D01G161200

Loading Multiple Alignment...

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 TraesCS4D01G161200 chr4D 100.000 2342 0 0 1 2342 241053884 241056225 0 4325
1 TraesCS4D01G161200 chr4D 95.403 2371 80 3 1 2342 123689138 123691508 0 3747
2 TraesCS4D01G161200 chrUn 95.993 2371 65 4 1 2342 257944289 257946658 0 3825
3 TraesCS4D01G161200 chrUn 95.740 2371 66 5 1 2342 233525091 233522727 0 3786
4 TraesCS4D01G161200 chrUn 95.544 1683 49 1 686 2342 369795034 369796716 0 2669
5 TraesCS4D01G161200 chr1D 95.868 2372 67 5 1 2342 212429045 212431415 0 3808
6 TraesCS4D01G161200 chr7B 95.571 2371 70 5 1 2342 698126757 698124393 0 3764
7 TraesCS4D01G161200 chr7B 95.445 2371 70 6 1 2342 742937658 742940019 0 3746
8 TraesCS4D01G161200 chr7A 95.445 2371 74 4 1 2342 60096022 60093657 0 3749
9 TraesCS4D01G161200 chr7A 95.278 2372 81 11 1 2342 211237958 211235588 0 3731
10 TraesCS4D01G161200 chr2D 95.405 2372 76 7 1 2342 637308529 637306161 0 3746
11 TraesCS4D01G161200 chr2D 95.308 2195 75 2 176 2342 200957774 200955580 0 3458
12 TraesCS4D01G161200 chr7D 95.192 2371 65 5 1 2342 578990942 578993292 0 3701
13 TraesCS4D01G161200 chr7D 94.897 2371 91 4 1 2342 307089671 307092040 0 3681


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 TraesCS4D01G161200 chr4D 241053884 241056225 2341 False 4325 4325 100.000 1 2342 1 chr4D.!!$F2 2341
1 TraesCS4D01G161200 chr4D 123689138 123691508 2370 False 3747 3747 95.403 1 2342 1 chr4D.!!$F1 2341
2 TraesCS4D01G161200 chrUn 257944289 257946658 2369 False 3825 3825 95.993 1 2342 1 chrUn.!!$F1 2341
3 TraesCS4D01G161200 chrUn 233522727 233525091 2364 True 3786 3786 95.740 1 2342 1 chrUn.!!$R1 2341
4 TraesCS4D01G161200 chrUn 369795034 369796716 1682 False 2669 2669 95.544 686 2342 1 chrUn.!!$F2 1656
5 TraesCS4D01G161200 chr1D 212429045 212431415 2370 False 3808 3808 95.868 1 2342 1 chr1D.!!$F1 2341
6 TraesCS4D01G161200 chr7B 698124393 698126757 2364 True 3764 3764 95.571 1 2342 1 chr7B.!!$R1 2341
7 TraesCS4D01G161200 chr7B 742937658 742940019 2361 False 3746 3746 95.445 1 2342 1 chr7B.!!$F1 2341
8 TraesCS4D01G161200 chr7A 60093657 60096022 2365 True 3749 3749 95.445 1 2342 1 chr7A.!!$R1 2341
9 TraesCS4D01G161200 chr7A 211235588 211237958 2370 True 3731 3731 95.278 1 2342 1 chr7A.!!$R2 2341
10 TraesCS4D01G161200 chr2D 637306161 637308529 2368 True 3746 3746 95.405 1 2342 1 chr2D.!!$R2 2341
11 TraesCS4D01G161200 chr2D 200955580 200957774 2194 True 3458 3458 95.308 176 2342 1 chr2D.!!$R1 2166
12 TraesCS4D01G161200 chr7D 578990942 578993292 2350 False 3701 3701 95.192 1 2342 1 chr7D.!!$F2 2341
13 TraesCS4D01G161200 chr7D 307089671 307092040 2369 False 3681 3681 94.897 1 2342 1 chr7D.!!$F1 2341

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
541 545 1.29985 CGTCCGTCAAGTGACAGCA 60.3 57.895 11.77 0.0 44.99 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2123 0.10212 CCTCTGACAGTCCATCTCGC 59.898 60.0 1.59 0.0 0.0 5.03 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
63 64 4.222124 AGGTATCAGTGGGAACATCAAC 57.778 45.455 0.00 0.0 46.14 3.18
111 112 7.543172 CAGATCGACCAAATTGAACAAATGATT 59.457 33.333 0.00 0.0 0.00 2.57
256 260 5.460419 CGAACTCATACTAATGCAAGGACTC 59.540 44.000 0.00 0.0 32.76 3.36
272 276 1.806542 GACTCCTCGCAAGCAAATTCA 59.193 47.619 0.00 0.0 37.18 2.57
307 311 2.289547 GCTACCGAAAGAACAAGCAACA 59.710 45.455 0.00 0.0 0.00 3.33
314 318 5.273170 CGAAAGAACAAGCAACAGATTTCA 58.727 37.500 0.00 0.0 0.00 2.69
315 319 5.916883 CGAAAGAACAAGCAACAGATTTCAT 59.083 36.000 0.00 0.0 0.00 2.57
387 391 6.148315 TGTCTGATCAATCACACTGTTCATTC 59.852 38.462 0.00 0.0 32.50 2.67
534 538 2.049433 CGGCTTCGTCCGTCAAGT 60.049 61.111 5.59 0.0 44.18 3.16
541 545 1.299850 CGTCCGTCAAGTGACAGCA 60.300 57.895 11.77 0.0 44.99 4.41
798 802 2.283460 GCCCTTCCTGCCTGCTTT 60.283 61.111 0.00 0.0 0.00 3.51
990 1020 7.147373 CCACTAGATTTTTATAGGGGTCAGGAA 60.147 40.741 0.00 0.0 37.73 3.36
1005 1035 5.163195 GGGTCAGGAAGGAAAAGATATGCTA 60.163 44.000 0.00 0.0 0.00 3.49
1056 1086 1.590147 CTTCCACGGTCCGCTTACT 59.410 57.895 12.28 0.0 0.00 2.24
1071 1101 2.099921 GCTTACTGAGGAAGAGATGCGA 59.900 50.000 9.01 0.0 0.00 5.10
1180 1210 4.632153 AGTTGGGTATGATATTCTCGTGC 58.368 43.478 0.00 0.0 0.00 5.34
1192 1222 2.198827 TCTCGTGCATTGTTGGGAAT 57.801 45.000 0.00 0.0 0.00 3.01
1220 1250 8.041323 TCCTCTATATTCGAAATATGCCTTTCC 58.959 37.037 0.00 0.0 32.60 3.13
1237 1267 4.039245 CCTTTCCAGGAGCATTACGATCTA 59.961 45.833 0.00 0.0 44.19 1.98
1251 1281 4.207891 ACGATCTACAGCTCAAATGGTT 57.792 40.909 0.00 0.0 0.00 3.67
1325 1355 0.886490 GGATCCGCGAAGGCAATCAT 60.886 55.000 8.23 0.0 40.77 2.45
1326 1356 0.236711 GATCCGCGAAGGCAATCATG 59.763 55.000 8.23 0.0 40.77 3.07
1327 1357 0.464373 ATCCGCGAAGGCAATCATGT 60.464 50.000 8.23 0.0 40.77 3.21
1680 1710 8.232913 ACAAAAGAAAATAACAGACTAAGCCA 57.767 30.769 0.00 0.0 0.00 4.75
1778 1808 0.564171 TCCGGGATATACACCAGGGT 59.436 55.000 0.00 0.0 41.76 4.34
1810 1840 0.961857 GCATATGATGATGCCGCCCA 60.962 55.000 6.97 0.0 45.41 5.36
1863 1893 2.125147 GCTGTAGGTGATGGCGCA 60.125 61.111 10.83 0.0 0.00 6.09
1916 1946 2.103042 GGATCGTGTGTGGCAGCTC 61.103 63.158 0.00 0.0 0.00 4.09
1941 1971 3.287867 AGATGATGATGAAAGGCGGTT 57.712 42.857 0.00 0.0 0.00 4.44
2003 2033 2.214201 AGCTAAATAGGAAAGGGGGCA 58.786 47.619 0.00 0.0 0.00 5.36
2029 2059 2.483876 TGACTGCCTTTTTCGTCAGAG 58.516 47.619 0.00 0.0 33.01 3.35
2093 2123 7.830739 ACAAGTATAGCCAAAGAAAAATGAGG 58.169 34.615 0.00 0.0 0.00 3.86
2128 2158 1.304547 AGGACGCAGCAGGACTACT 60.305 57.895 0.00 0.0 0.00 2.57
2178 2208 7.468141 AACATAGATATCTATTCTCGGTGCA 57.532 36.000 20.53 0.0 37.07 4.57
2214 2244 0.984230 AATCTCTTTCCGACCAGGCA 59.016 50.000 0.00 0.0 40.77 4.75
2237 2267 1.674322 CGAATCGGGCCACCACTTT 60.674 57.895 4.39 0.0 36.13 2.66
2274 2304 3.319689 CAGCCCACATGCATCATTTGATA 59.680 43.478 0.00 0.0 32.63 2.15
2284 2314 6.270156 TGCATCATTTGATAAAAGCACTCA 57.730 33.333 0.00 0.0 32.63 3.41
2289 2319 7.750229 TCATTTGATAAAAGCACTCAAGTCT 57.250 32.000 0.00 0.0 31.11 3.24
2305 2335 1.022735 GTCTAGTCGCCTCCGATCAA 58.977 55.000 0.00 0.0 46.38 2.57
2307 2337 2.812591 GTCTAGTCGCCTCCGATCAATA 59.187 50.000 0.00 0.0 46.38 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 5.336134 CCAATGAACAACATGATCTTGAGCA 60.336 40.000 15.03 5.66 39.39 4.26
256 260 2.995466 TTCTGAATTTGCTTGCGAGG 57.005 45.000 2.37 0.00 0.00 4.63
272 276 4.553330 TCGGTAGCCTTCTTTCATTTCT 57.447 40.909 0.00 0.00 0.00 2.52
307 311 2.957006 GCAAGGGATGAGCATGAAATCT 59.043 45.455 0.00 0.00 0.00 2.40
314 318 2.305009 GCTTTAGCAAGGGATGAGCAT 58.695 47.619 0.00 0.00 41.59 3.79
315 319 1.755179 GCTTTAGCAAGGGATGAGCA 58.245 50.000 0.00 0.00 41.59 4.26
403 407 1.144969 GCGGTTCAAGACATCGAACA 58.855 50.000 0.00 0.00 42.67 3.18
464 468 0.811616 CCAAGATGGGCTAGACGTGC 60.812 60.000 0.00 0.00 32.67 5.34
534 538 0.248565 GTCAGAGGCAGATGCTGTCA 59.751 55.000 4.59 0.00 38.73 3.58
643 647 9.733556 TTAATTAGTACAAGAAAGAGGCATTCA 57.266 29.630 0.00 0.00 0.00 2.57
798 802 7.254084 CGAAGACACGATCATTCACATCAATTA 60.254 37.037 0.00 0.00 35.09 1.40
1005 1035 3.199946 TCCGCTTGGGACTGATAGAAAAT 59.800 43.478 0.00 0.00 40.94 1.82
1056 1086 1.064389 TCCTCTCGCATCTCTTCCTCA 60.064 52.381 0.00 0.00 0.00 3.86
1071 1101 3.615811 TCTGGCCCTGGGTCCTCT 61.616 66.667 16.18 0.00 0.00 3.69
1180 1210 7.095060 CGAATATAGAGGACATTCCCAACAATG 60.095 40.741 0.00 0.00 37.19 2.82
1192 1222 7.482169 AGGCATATTTCGAATATAGAGGACA 57.518 36.000 0.00 0.00 0.00 4.02
1220 1250 3.005261 AGCTGTAGATCGTAATGCTCCTG 59.995 47.826 0.00 0.00 0.00 3.86
1237 1267 4.922206 TCATAAGGAACCATTTGAGCTGT 58.078 39.130 0.00 0.00 0.00 4.40
1251 1281 7.979786 AAGACCAATAGAGACTTCATAAGGA 57.020 36.000 0.00 0.00 0.00 3.36
1288 1318 1.723608 CCAAACGTGCTCACAAGGCA 61.724 55.000 0.00 0.00 37.36 4.75
1325 1355 1.203505 TGGGTTAGGGGAAGATCCACA 60.204 52.381 0.82 0.00 44.30 4.17
1326 1356 1.591768 TGGGTTAGGGGAAGATCCAC 58.408 55.000 0.00 0.00 41.37 4.02
1327 1357 1.920351 GTTGGGTTAGGGGAAGATCCA 59.080 52.381 0.00 0.00 38.64 3.41
1477 1507 3.702048 CGCCTCCGGGGTTCTTCA 61.702 66.667 0.00 0.00 37.43 3.02
1713 1743 0.929244 ATACATGAAGGCCTTGGCCT 59.071 50.000 26.25 26.23 42.86 5.19
1778 1808 8.693542 CATCATCATATGCTCGACATTAGTTA 57.306 34.615 0.00 0.00 40.38 2.24
1863 1893 2.435805 TCATCGCCCTAAGAAGCAGAAT 59.564 45.455 0.00 0.00 0.00 2.40
1896 1926 2.815211 CTGCCACACACGATCCCG 60.815 66.667 0.00 0.00 42.50 5.14
1906 1936 2.306847 TCATCTATACGAGCTGCCACA 58.693 47.619 0.00 0.00 0.00 4.17
1916 1946 4.564372 CCGCCTTTCATCATCATCTATACG 59.436 45.833 0.00 0.00 0.00 3.06
1941 1971 0.974010 ATAGGTCCCGGTTCAAGCGA 60.974 55.000 11.37 0.00 42.41 4.93
2003 2033 3.214328 ACGAAAAAGGCAGTCATCAGTT 58.786 40.909 0.00 0.00 0.00 3.16
2029 2059 3.831911 TCCACATTCCACCCTTTTTGATC 59.168 43.478 0.00 0.00 0.00 2.92
2087 2117 1.137872 GACAGTCCATCTCGCCTCATT 59.862 52.381 0.00 0.00 0.00 2.57
2093 2123 0.102120 CCTCTGACAGTCCATCTCGC 59.898 60.000 1.59 0.00 0.00 5.03
2120 2150 2.177811 GGCTTTCCCCTAGTAGTCCT 57.822 55.000 0.00 0.00 0.00 3.85
2152 2182 8.459635 TGCACCGAGAATAGATATCTATGTTAC 58.540 37.037 23.03 15.13 39.02 2.50
2237 2267 1.228228 GCTGAGCCATTCCCATCCA 59.772 57.895 0.00 0.00 0.00 3.41
2274 2304 3.060602 GCGACTAGACTTGAGTGCTTTT 58.939 45.455 0.00 0.00 0.00 2.27
2284 2314 1.310904 GATCGGAGGCGACTAGACTT 58.689 55.000 0.00 0.00 44.43 3.01
2289 2319 1.540267 GCTATTGATCGGAGGCGACTA 59.460 52.381 0.00 0.00 44.43 2.59
2305 2335 0.981183 TCCGGTGGTTGACAAGCTAT 59.019 50.000 17.62 0.00 0.00 2.97
2307 2337 1.227853 GTCCGGTGGTTGACAAGCT 60.228 57.895 17.62 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.