Multiple sequence alignment - TraesCS5B01G216100

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 TraesCS5B01G216100 chr5B 100.000 2904 0 0 1 2904 389022034 389019131 0 5363
1 TraesCS5B01G216100 chr6D 93.425 2920 167 15 3 2904 84777635 84780547 0 4305
2 TraesCS5B01G216100 chr6D 93.228 2909 186 9 1 2904 358093464 358096366 0 4270
3 TraesCS5B01G216100 chr4A 93.123 2879 171 14 31 2904 632977048 632974192 0 4194
4 TraesCS5B01G216100 chr2D 92.802 2862 176 21 47 2904 324340452 324343287 0 4117
5 TraesCS5B01G216100 chr4D 92.300 2896 213 10 13 2902 328179079 328176188 0 4104
6 TraesCS5B01G216100 chr7A 92.471 2829 207 6 33 2859 90122377 90119553 0 4039
7 TraesCS5B01G216100 chr5D 91.022 2896 242 14 17 2904 538211300 538208415 0 3892
8 TraesCS5B01G216100 chr5D 92.280 2746 198 11 13 2753 440708341 440705605 0 3884
9 TraesCS5B01G216100 chr5A 90.652 2899 248 16 17 2904 459318417 459321303 0 3831
10 TraesCS5B01G216100 chr7B 89.196 2277 201 23 17 2286 565989004 565991242 0 2800
11 TraesCS5B01G216100 chr7B 89.509 1325 120 8 17 1338 367333428 367332120 0 1659


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 TraesCS5B01G216100 chr5B 389019131 389022034 2903 True 5363 5363 100.000 1 2904 1 chr5B.!!$R1 2903
1 TraesCS5B01G216100 chr6D 84777635 84780547 2912 False 4305 4305 93.425 3 2904 1 chr6D.!!$F1 2901
2 TraesCS5B01G216100 chr6D 358093464 358096366 2902 False 4270 4270 93.228 1 2904 1 chr6D.!!$F2 2903
3 TraesCS5B01G216100 chr4A 632974192 632977048 2856 True 4194 4194 93.123 31 2904 1 chr4A.!!$R1 2873
4 TraesCS5B01G216100 chr2D 324340452 324343287 2835 False 4117 4117 92.802 47 2904 1 chr2D.!!$F1 2857
5 TraesCS5B01G216100 chr4D 328176188 328179079 2891 True 4104 4104 92.300 13 2902 1 chr4D.!!$R1 2889
6 TraesCS5B01G216100 chr7A 90119553 90122377 2824 True 4039 4039 92.471 33 2859 1 chr7A.!!$R1 2826
7 TraesCS5B01G216100 chr5D 538208415 538211300 2885 True 3892 3892 91.022 17 2904 1 chr5D.!!$R2 2887
8 TraesCS5B01G216100 chr5D 440705605 440708341 2736 True 3884 3884 92.280 13 2753 1 chr5D.!!$R1 2740
9 TraesCS5B01G216100 chr5A 459318417 459321303 2886 False 3831 3831 90.652 17 2904 1 chr5A.!!$F1 2887
10 TraesCS5B01G216100 chr7B 565989004 565991242 2238 False 2800 2800 89.196 17 2286 1 chr7B.!!$F1 2269
11 TraesCS5B01G216100 chr7B 367332120 367333428 1308 True 1659 1659 89.509 17 1338 1 chr7B.!!$R1 1321

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
28 36 1.602377 GCACCACCAGTTACAGAACAC 59.398 52.381 0.0 0.0 38.10 3.32 F
29 37 1.864711 CACCACCAGTTACAGAACACG 59.135 52.381 0.0 0.0 38.10 4.49 F
1101 1141 1.066430 GGTGCTCCTTTCACGTGGATA 60.066 52.381 17.0 0.0 35.39 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1028 1068 0.040646 TTCTGGTTCCCGAGGCTCTA 59.959 55.0 13.50 0.0 0.00 2.43 R
1218 1258 0.387929 GCCACATCCATGGAGCATTG 59.612 55.0 21.33 15.6 43.02 2.82 R
2664 2713 0.174845 CGCCGACCTAGACCATTCAA 59.825 55.0 0.00 0.0 0.00 2.69 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
25 33 2.719531 TTGCACCACCAGTTACAGAA 57.280 45.000 0.00 0.00 0.00 3.02
28 36 1.602377 GCACCACCAGTTACAGAACAC 59.398 52.381 0.00 0.00 38.10 3.32
29 37 1.864711 CACCACCAGTTACAGAACACG 59.135 52.381 0.00 0.00 38.10 4.49
139 147 5.604650 CCAATCCATCCTAGAAGGTACTCTT 59.395 44.000 0.00 0.00 38.49 2.85
394 426 9.803507 AAGTAGGCCTAGTTTAGTTTATTTGTT 57.196 29.630 24.69 0.20 0.00 2.83
538 570 8.655651 TTGTTTCAAATTGTTAGGATGGTTTC 57.344 30.769 0.00 0.00 0.00 2.78
703 741 2.231716 TGTAGGAGCTTGCACCTCTA 57.768 50.000 14.46 3.47 37.68 2.43
825 865 2.202878 CGGTCGACGCCATCCAAT 60.203 61.111 9.92 0.00 34.82 3.16
912 952 2.348104 CGGGGAGATGACCGTGACA 61.348 63.158 0.00 0.00 44.85 3.58
975 1015 5.308237 GGGGAATCCTCTATGTATGAACACT 59.692 44.000 0.00 0.00 38.78 3.55
1028 1068 3.240302 CCCTTATCGGTATGGTTCCTCT 58.760 50.000 6.85 0.00 0.00 3.69
1101 1141 1.066430 GGTGCTCCTTTCACGTGGATA 60.066 52.381 17.00 0.00 35.39 2.59
1106 1146 4.081365 TGCTCCTTTCACGTGGATAACATA 60.081 41.667 17.00 0.00 0.00 2.29
1107 1147 5.057149 GCTCCTTTCACGTGGATAACATAT 58.943 41.667 17.00 0.00 0.00 1.78
1121 1161 9.826574 GTGGATAACATATCACTTTGGTACTTA 57.173 33.333 0.00 0.00 0.00 2.24
1152 1192 4.414337 AGCTAATGAGGATGAGGTCAAC 57.586 45.455 0.00 0.00 0.00 3.18
1156 1196 2.839486 TGAGGATGAGGTCAACACAC 57.161 50.000 0.00 0.00 0.00 3.82
1159 1199 3.837731 TGAGGATGAGGTCAACACACATA 59.162 43.478 0.00 0.00 0.00 2.29
1191 1231 3.958147 ACATGTGGTACGTGATATCCAGA 59.042 43.478 0.00 0.00 37.29 3.86
1248 1288 1.648467 GGATGTGGCTGAAGGCGTTC 61.648 60.000 12.18 12.18 44.42 3.95
1250 1290 0.537143 ATGTGGCTGAAGGCGTTCAA 60.537 50.000 21.17 7.97 42.27 2.69
1381 1421 6.815089 TCTTGCTGTTAATTCAACCATGTTT 58.185 32.000 0.00 0.00 36.20 2.83
1519 1559 1.829222 TGAAGTACGAGGATTGGGACC 59.171 52.381 0.00 0.00 0.00 4.46
1619 1659 4.216257 GGTCATGCACAAGTTGTACAAGAT 59.784 41.667 15.21 0.00 26.32 2.40
1629 1669 3.119316 AGTTGTACAAGATCGAGCTGGAG 60.119 47.826 13.06 4.23 0.00 3.86
1658 1698 1.154131 CTGAGCAGGTGACTCGACG 60.154 63.158 0.00 0.00 40.21 5.12
1756 1798 0.326238 AGCCGTATGGAAGAGGGGAA 60.326 55.000 4.73 0.00 37.49 3.97
1757 1799 0.544697 GCCGTATGGAAGAGGGGAAA 59.455 55.000 4.73 0.00 37.49 3.13
1815 1858 1.546476 GTGCACTAGGGATAGGGATCG 59.454 57.143 10.32 0.00 32.28 3.69
1816 1859 0.533032 GCACTAGGGATAGGGATCGC 59.467 60.000 0.00 0.54 43.65 4.58
1988 2032 0.390472 GCACTTAGCAGCTTCTCGGT 60.390 55.000 0.00 0.00 44.79 4.69
2024 2068 8.398665 GGTGCTAATATTCTGTTTCTAACTTGG 58.601 37.037 0.00 0.00 0.00 3.61
2054 2098 1.559682 AGGAAAAGGCAGCGGAAGATA 59.440 47.619 0.00 0.00 0.00 1.98
2055 2099 1.671328 GGAAAAGGCAGCGGAAGATAC 59.329 52.381 0.00 0.00 0.00 2.24
2091 2135 4.342378 AGCATCACAGGAAGTATGTCGTAT 59.658 41.667 0.00 0.00 0.00 3.06
2187 2232 7.095397 CGTTCAACAACTATCTCACATGGTTTA 60.095 37.037 0.00 0.00 0.00 2.01
2191 2236 7.630242 ACAACTATCTCACATGGTTTATTGG 57.370 36.000 0.00 0.00 0.00 3.16
2262 2307 6.949143 TGGAAGATCCCACCGTTTTCGATC 62.949 50.000 0.00 0.00 39.96 3.69
2304 2349 1.017387 CGCATTAGTCAGGAAAGGCC 58.983 55.000 0.00 0.00 0.00 5.19
2388 2437 3.618594 TGCACTATTCACATCTTCGCTTC 59.381 43.478 0.00 0.00 0.00 3.86
2528 2577 3.616821 TCGAGCATTCATTAAGGTTCACG 59.383 43.478 0.00 0.00 0.00 4.35
2537 2586 3.293311 TTAAGGTTCACGTCTCCTTCG 57.707 47.619 15.63 0.00 41.17 3.79
2572 2621 3.857665 ACATGTGTTGCTACGTTCGATAG 59.142 43.478 0.00 0.00 0.00 2.08
2664 2713 2.957006 GTGACCCCGAGTATGTATCACT 59.043 50.000 0.00 0.00 33.74 3.41
2669 2718 4.654262 ACCCCGAGTATGTATCACTTGAAT 59.346 41.667 0.00 0.00 30.10 2.57
2725 2777 1.412074 GGCCATGGTGATCCTTTGGAT 60.412 52.381 14.67 0.00 46.28 3.41
2739 2791 3.117776 CCTTTGGATGATGAGGATGTGGA 60.118 47.826 0.00 0.00 0.00 4.02
2753 2805 0.553333 TGTGGATGTGGTCACCCAAA 59.447 50.000 0.00 0.00 44.15 3.28
2768 2820 3.017048 CCCAAAAGGTATGGCATGAGA 57.983 47.619 10.98 0.00 36.58 3.27
2776 2828 9.850628 CAAAAGGTATGGCATGAGAATATATTG 57.149 33.333 10.98 0.74 0.00 1.90
2779 2831 9.812347 AAGGTATGGCATGAGAATATATTGAAA 57.188 29.630 10.98 0.00 0.00 2.69
2832 2884 6.938030 ACACACGGTCTTTTCCATATCTTTTA 59.062 34.615 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 147 2.552093 AGAAAGAAGGGGATCGGAGA 57.448 50.000 0.00 0.00 45.75 3.71
439 471 7.193595 ACGCCTACTATATGCAAAATTCAAAC 58.806 34.615 0.00 0.00 0.00 2.93
489 521 5.302360 AGCTTTCTTGTCAACACGGTTATA 58.698 37.500 0.00 0.00 0.00 0.98
494 526 3.108144 CAAAGCTTTCTTGTCAACACGG 58.892 45.455 9.23 0.00 31.78 4.94
538 570 1.485397 CCAGTGATCATCGAGAAGCG 58.515 55.000 0.00 0.00 42.69 4.68
788 828 2.489329 CGGCTGACCAACTGAATGAAAT 59.511 45.455 0.00 0.00 34.57 2.17
842 882 0.800683 CCAACGATCAGTAAGCGCGA 60.801 55.000 12.10 0.00 0.00 5.87
912 952 5.046014 GGTGATCATAGCAATATCCTGGAGT 60.046 44.000 1.52 0.00 0.00 3.85
975 1015 1.451927 GCGCCACCCATCAGAATCA 60.452 57.895 0.00 0.00 0.00 2.57
997 1037 1.977854 ACCGATAAGGGCATGCATCTA 59.022 47.619 21.36 7.17 46.96 1.98
1028 1068 0.040646 TTCTGGTTCCCGAGGCTCTA 59.959 55.000 13.50 0.00 0.00 2.43
1121 1161 2.122768 CCTCATTAGCTTCCTCAGGGT 58.877 52.381 0.00 0.00 0.00 4.34
1156 1196 4.371855 ACCACATGTAGACACGAGTATG 57.628 45.455 0.00 0.00 0.00 2.39
1159 1199 2.161012 CGTACCACATGTAGACACGAGT 59.839 50.000 14.22 0.00 0.00 4.18
1218 1258 0.387929 GCCACATCCATGGAGCATTG 59.612 55.000 21.33 15.60 43.02 2.82
1248 1288 3.616821 TCCATTTGCTATCGAAGACGTTG 59.383 43.478 0.00 0.00 42.51 4.10
1250 1290 3.119101 ACTCCATTTGCTATCGAAGACGT 60.119 43.478 0.00 0.00 42.51 4.34
1381 1421 4.130857 TCGTCCAACTGCACATAAAAGAA 58.869 39.130 0.00 0.00 0.00 2.52
1519 1559 2.346803 CCGTAGTGGGTCATCTTTGTG 58.653 52.381 0.00 0.00 0.00 3.33
1619 1659 1.706287 CGTGATCGTCTCCAGCTCGA 61.706 60.000 0.00 0.00 37.96 4.04
1629 1669 1.875813 CTGCTCAGCCGTGATCGTC 60.876 63.158 0.00 0.00 35.01 4.20
1658 1698 7.646314 AGAAGCATGATAATCACTTATGCAAC 58.354 34.615 9.76 3.85 44.81 4.17
1706 1746 5.300034 CCACCTGCAAAATAGCATAGAATGA 59.700 40.000 0.00 0.00 44.68 2.57
1756 1798 9.462606 CTGAACTCTATAGGGTTACCAAAAATT 57.537 33.333 18.07 0.00 40.13 1.82
1757 1799 8.053355 CCTGAACTCTATAGGGTTACCAAAAAT 58.947 37.037 18.07 0.00 40.13 1.82
1828 1871 2.093890 CAGTTGCATATGAGTGGGCAA 58.906 47.619 6.97 0.00 43.32 4.52
1988 2032 6.663093 ACAGAATATTAGCACCATCAAAACCA 59.337 34.615 0.00 0.00 0.00 3.67
2024 2068 3.282885 CTGCCTTTTCCTATCCAACCTC 58.717 50.000 0.00 0.00 0.00 3.85
2054 2098 0.685458 GATGCTTGGCCCAATCCTGT 60.685 55.000 0.00 0.00 0.00 4.00
2055 2099 0.685131 TGATGCTTGGCCCAATCCTG 60.685 55.000 0.00 0.00 0.00 3.86
2091 2135 0.883153 TCCACACTAAGCGCGAACTA 59.117 50.000 12.10 0.00 0.00 2.24
2159 2204 3.064207 TGTGAGATAGTTGTTGAACGCC 58.936 45.455 0.00 0.00 37.15 5.68
2187 2232 1.278127 CTCCACACGGGTACTTCCAAT 59.722 52.381 0.00 0.00 38.11 3.16
2191 2236 1.549203 TACCTCCACACGGGTACTTC 58.451 55.000 0.00 0.00 37.07 3.01
2262 2307 2.288579 TGTACTCGTGTTGGGTTAGCTG 60.289 50.000 0.00 0.00 0.00 4.24
2304 2349 1.280133 TGGAGCTGAAGGGATTGAGTG 59.720 52.381 0.00 0.00 0.00 3.51
2388 2437 6.148811 ACAGAAATGACATTAACGTGTTAGGG 59.851 38.462 0.00 0.00 31.16 3.53
2528 2577 3.938289 AAGTGGTAGTTCGAAGGAGAC 57.062 47.619 0.00 0.00 0.00 3.36
2537 2586 5.238650 AGCAACACATGTTAAGTGGTAGTTC 59.761 40.000 0.00 0.00 41.21 3.01
2572 2621 4.161333 GCAACATGTACAAGTGAATGAGC 58.839 43.478 4.21 2.13 0.00 4.26
2664 2713 0.174845 CGCCGACCTAGACCATTCAA 59.825 55.000 0.00 0.00 0.00 2.69
2669 2718 2.034532 TGTCGCCGACCTAGACCA 59.965 61.111 15.60 0.00 34.24 4.02
2725 2777 2.171237 GACCACATCCACATCCTCATCA 59.829 50.000 0.00 0.00 0.00 3.07
2753 2805 9.812347 TTTCAATATATTCTCATGCCATACCTT 57.188 29.630 0.00 0.00 0.00 3.50
2875 2928 0.892755 TCGTATGCAGACCGAACCTT 59.107 50.000 5.78 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.