Multiple sequence alignment - TraesCS1D01G009900

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 TraesCS1D01G009900 chr1D 100.000 3068 0 0 1 3068 5355684 5358751 0.000000e+00 5666.0
1 TraesCS1D01G009900 chr1D 88.053 3097 248 64 3 3068 3711581 3708576 0.000000e+00 3557.0
2 TraesCS1D01G009900 chr1D 85.714 1904 187 45 1208 3068 5139396 5141257 0.000000e+00 1930.0
3 TraesCS1D01G009900 chr1D 86.159 1734 159 35 1013 2732 3826365 3824699 0.000000e+00 1797.0
4 TraesCS1D01G009900 chr1D 87.130 1352 108 24 480 1767 84072 85421 0.000000e+00 1472.0
5 TraesCS1D01G009900 chr1D 90.049 1025 76 20 3 1020 3842327 3841322 0.000000e+00 1304.0
6 TraesCS1D01G009900 chr1D 83.889 1409 157 39 1216 2575 7156339 7154952 0.000000e+00 1280.0
7 TraesCS1D01G009900 chr1D 83.031 1432 174 35 1193 2575 4342032 4343443 0.000000e+00 1234.0
8 TraesCS1D01G009900 chr1D 86.404 1015 102 24 430 1414 98698 99706 0.000000e+00 1077.0
9 TraesCS1D01G009900 chr1D 82.789 796 89 24 1786 2573 100219 100974 0.000000e+00 667.0
10 TraesCS1D01G009900 chr1D 83.475 587 59 20 1215 1767 99654 100236 2.110000e-141 512.0
11 TraesCS1D01G009900 chr1D 79.333 300 35 10 2795 3068 4347183 4347481 5.220000e-43 185.0
12 TraesCS1D01G009900 chr1D 100.000 31 0 0 2759 2789 4347036 4347066 1.190000e-04 58.4
13 TraesCS1D01G009900 chr1A 92.707 3099 172 20 5 3068 6516342 6519421 0.000000e+00 4421.0
14 TraesCS1D01G009900 chr1A 93.478 1748 76 14 486 2224 6561199 6562917 0.000000e+00 2562.0
15 TraesCS1D01G009900 chr1A 89.118 726 64 11 430 1142 4204250 4203527 0.000000e+00 889.0
16 TraesCS1D01G009900 chr1A 88.703 717 69 6 435 1142 4097477 4096764 0.000000e+00 865.0
17 TraesCS1D01G009900 chr1A 94.661 487 23 2 5 488 6560632 6561118 0.000000e+00 752.0
18 TraesCS1D01G009900 chr1A 87.409 548 61 5 1777 2322 4095936 4095395 9.340000e-175 623.0
19 TraesCS1D01G009900 chr1B 84.577 1407 151 37 1215 2575 6437233 6435847 0.000000e+00 1336.0
20 TraesCS1D01G009900 chr1B 83.065 1429 162 35 1179 2575 22185993 22187373 0.000000e+00 1225.0
21 TraesCS1D01G009900 chr1B 85.918 980 114 16 430 1390 5688349 5687375 0.000000e+00 1024.0
22 TraesCS1D01G009900 chr1B 88.092 697 63 12 671 1348 5585887 5585192 0.000000e+00 809.0
23 TraesCS1D01G009900 chr1B 84.173 695 82 17 735 1414 22185385 22186066 0.000000e+00 649.0
24 TraesCS1D01G009900 chr1B 82.218 568 80 15 1215 1767 5584908 5584347 1.290000e-128 470.0
25 TraesCS1D01G009900 chr1B 96.154 208 6 2 240 446 8159462 8159668 3.790000e-89 339.0
26 TraesCS1D01G009900 chr1B 94.444 180 7 1 72 248 8156579 8156758 1.080000e-69 274.0
27 TraesCS1D01G009900 chr1B 83.959 293 27 13 2795 3068 7314097 7313806 2.350000e-66 263.0
28 TraesCS1D01G009900 chr1B 80.537 298 34 12 2795 3068 22191156 22191453 1.110000e-49 207.0
29 TraesCS1D01G009900 chr1B 100.000 31 0 0 2759 2789 22191009 22191039 1.190000e-04 58.4
30 TraesCS1D01G009900 chr1B 96.875 32 1 0 2661 2692 8159944 8159975 2.000000e-03 54.7
31 TraesCS1D01G009900 chrUn 93.985 399 21 1 5 400 374223862 374224260 4.380000e-168 601.0
32 TraesCS1D01G009900 chrUn 93.734 399 22 1 5 400 349408926 349409324 2.040000e-166 595.0


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 TraesCS1D01G009900 chr1D 5355684 5358751 3067 False 5666.000000 5666 100.000000 1 3068 1 chr1D.!!$F3 3067
1 TraesCS1D01G009900 chr1D 3708576 3711581 3005 True 3557.000000 3557 88.053000 3 3068 1 chr1D.!!$R1 3065
2 TraesCS1D01G009900 chr1D 5139396 5141257 1861 False 1930.000000 1930 85.714000 1208 3068 1 chr1D.!!$F2 1860
3 TraesCS1D01G009900 chr1D 3824699 3826365 1666 True 1797.000000 1797 86.159000 1013 2732 1 chr1D.!!$R2 1719
4 TraesCS1D01G009900 chr1D 84072 85421 1349 False 1472.000000 1472 87.130000 480 1767 1 chr1D.!!$F1 1287
5 TraesCS1D01G009900 chr1D 3841322 3842327 1005 True 1304.000000 1304 90.049000 3 1020 1 chr1D.!!$R3 1017
6 TraesCS1D01G009900 chr1D 7154952 7156339 1387 True 1280.000000 1280 83.889000 1216 2575 1 chr1D.!!$R4 1359
7 TraesCS1D01G009900 chr1D 98698 100974 2276 False 752.000000 1077 84.222667 430 2573 3 chr1D.!!$F4 2143
8 TraesCS1D01G009900 chr1D 4342032 4347481 5449 False 492.466667 1234 87.454667 1193 3068 3 chr1D.!!$F5 1875
9 TraesCS1D01G009900 chr1A 6516342 6519421 3079 False 4421.000000 4421 92.707000 5 3068 1 chr1A.!!$F1 3063
10 TraesCS1D01G009900 chr1A 6560632 6562917 2285 False 1657.000000 2562 94.069500 5 2224 2 chr1A.!!$F2 2219
11 TraesCS1D01G009900 chr1A 4203527 4204250 723 True 889.000000 889 89.118000 430 1142 1 chr1A.!!$R1 712
12 TraesCS1D01G009900 chr1A 4095395 4097477 2082 True 744.000000 865 88.056000 435 2322 2 chr1A.!!$R2 1887
13 TraesCS1D01G009900 chr1B 6435847 6437233 1386 True 1336.000000 1336 84.577000 1215 2575 1 chr1B.!!$R2 1360
14 TraesCS1D01G009900 chr1B 5687375 5688349 974 True 1024.000000 1024 85.918000 430 1390 1 chr1B.!!$R1 960
15 TraesCS1D01G009900 chr1B 5584347 5585887 1540 True 639.500000 809 85.155000 671 1767 2 chr1B.!!$R4 1096
16 TraesCS1D01G009900 chr1B 22185385 22191453 6068 False 534.850000 1225 86.943750 735 3068 4 chr1B.!!$F2 2333
17 TraesCS1D01G009900 chr1B 8156579 8159975 3396 False 222.566667 339 95.824333 72 2692 3 chr1B.!!$F1 2620


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
22 24 3.556423 GGTCTAGAACTTCTTTTGCGGGA 60.556 47.826 0.0 0.0 0.0 5.14 F
1107 3936 0.321671 CTTCCTCGTCTTTGCCCTCA 59.678 55.000 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1514 5301 0.311790 CAAGACGTTGTGGCATTGCT 59.688 50.000 8.82 0.0 0.0 3.91 R
2913 10571 1.276138 TGGATGTCTATATGGCTGCCG 59.724 52.381 14.98 0.0 0.0 5.69 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
22 24 3.556423 GGTCTAGAACTTCTTTTGCGGGA 60.556 47.826 0.00 0.00 0.00 5.14
25 27 5.008316 GTCTAGAACTTCTTTTGCGGGAAAA 59.992 40.000 7.21 7.21 32.44 2.29
170 172 5.845614 TCCTTTTGGGTAGACAAAGTACCTA 59.154 40.000 0.00 0.00 40.97 3.08
217 219 3.873361 CACCTGAACATGCACCATAGTAG 59.127 47.826 0.00 0.00 0.00 2.57
341 3058 7.532571 CCCAAAAGATTTAGTAAAAGGTACCG 58.467 38.462 6.18 0.00 0.00 4.02
400 3118 7.839680 AACTTAGTCCACCAAAAGAATGATT 57.160 32.000 0.00 0.00 0.00 2.57
537 3347 6.328410 AGGGAATTCTATGAGTCATGTCATGA 59.672 38.462 16.15 11.62 37.72 3.07
547 3359 7.459795 TGAGTCATGTCATGATCTATACCTC 57.540 40.000 18.32 16.59 42.04 3.85
693 3509 4.327357 CGATTGCAACTTAGTCCTACACAG 59.673 45.833 0.00 0.00 0.00 3.66
832 3648 5.772393 ACCACACATCAGGGTTTCTATAA 57.228 39.130 0.00 0.00 0.00 0.98
950 3777 8.801882 AAAAATCATTTCTGATGCATCCAAAT 57.198 26.923 23.67 21.72 41.34 2.32
1060 3889 4.333372 ACAAGCATCAAAACCAAGCAAAAG 59.667 37.500 0.00 0.00 0.00 2.27
1107 3936 0.321671 CTTCCTCGTCTTTGCCCTCA 59.678 55.000 0.00 0.00 0.00 3.86
1206 4080 2.955660 CAACCATTACCACCACAACAGT 59.044 45.455 0.00 0.00 0.00 3.55
1212 4134 5.221422 CCATTACCACCACAACAGTCATTTT 60.221 40.000 0.00 0.00 0.00 1.82
1314 4599 3.081061 TCGCAGCAACAACCAATTCTAT 58.919 40.909 0.00 0.00 0.00 1.98
1425 5209 5.430462 CACAACAACAACAACAACAACTTG 58.570 37.500 0.00 0.00 0.00 3.16
1484 5271 1.273048 CAGCAGCTAAACCCATGCAAA 59.727 47.619 0.00 0.00 41.14 3.68
1514 5301 2.348620 CAGCAGTGCAGCCCTGTA 59.651 61.111 19.20 0.00 34.23 2.74
1600 5387 1.202663 ACAATGTTGCCAGCAATTGCA 60.203 42.857 30.89 9.98 45.16 4.08
1628 5415 1.474320 CCCGAACAATCCCGCTATGAA 60.474 52.381 0.00 0.00 0.00 2.57
1679 5496 0.459489 TGCAAGAACAACAACAGGGC 59.541 50.000 0.00 0.00 0.00 5.19
1810 5642 0.179020 CAACTGGGTCAACAGCCTCA 60.179 55.000 0.00 0.00 42.21 3.86
1811 5643 0.550914 AACTGGGTCAACAGCCTCAA 59.449 50.000 0.00 0.00 42.21 3.02
1812 5644 0.179018 ACTGGGTCAACAGCCTCAAC 60.179 55.000 0.00 0.00 42.21 3.18
1813 5645 0.179020 CTGGGTCAACAGCCTCAACA 60.179 55.000 0.00 0.00 41.28 3.33
1814 5646 0.257328 TGGGTCAACAGCCTCAACAA 59.743 50.000 0.00 0.00 41.28 2.83
1815 5647 0.668535 GGGTCAACAGCCTCAACAAC 59.331 55.000 0.00 0.00 37.19 3.32
1876 5712 1.202627 CCAGATAGCTCACCTTGAGGC 60.203 57.143 5.37 0.00 44.43 4.70
1878 5714 0.249657 GATAGCTCACCTTGAGGCGG 60.250 60.000 5.37 0.00 44.43 6.13
1941 5777 0.452618 CAATGTGCCGTTGTACAGCG 60.453 55.000 23.31 23.31 40.54 5.18
1949 5785 2.281208 TTGTACAGCGCCACCACC 60.281 61.111 2.29 0.00 0.00 4.61
2043 5882 0.304098 CCACCGTCGTCTAGTCGATC 59.696 60.000 14.92 8.23 41.78 3.69
2224 6071 4.002906 AGTTCATAAGTTCGTCTTGCCA 57.997 40.909 6.03 0.00 37.56 4.92
2440 6290 4.390264 TGACAATCACAACCGGTTTCATA 58.610 39.130 19.55 3.82 0.00 2.15
2499 6351 9.793252 AAATACTTCATTGATACTTTGCACATC 57.207 29.630 0.00 0.00 0.00 3.06
2500 6352 6.199937 ACTTCATTGATACTTTGCACATCC 57.800 37.500 0.00 0.00 0.00 3.51
2541 6395 9.992910 GAAAAACAGCTTTTTCTTGAATTTCAT 57.007 25.926 13.91 0.00 46.46 2.57
2604 6463 1.195115 CCCTAGACCAGCTAGCACAA 58.805 55.000 18.83 0.00 44.35 3.33
2653 6596 2.030451 TGTTGCATGCGTATTCTTTGCA 60.030 40.909 14.09 0.00 43.67 4.08
2720 6866 9.862585 CACATTTTTACTTAATGGAAAGCAAAC 57.137 29.630 0.00 0.00 37.32 2.93
2789 10336 5.032846 TCAACTTCACATCCTCCTCCTTAT 58.967 41.667 0.00 0.00 0.00 1.73
2791 10338 4.889780 ACTTCACATCCTCCTCCTTATCT 58.110 43.478 0.00 0.00 0.00 1.98
2792 10339 4.898861 ACTTCACATCCTCCTCCTTATCTC 59.101 45.833 0.00 0.00 0.00 2.75
2793 10340 4.542906 TCACATCCTCCTCCTTATCTCA 57.457 45.455 0.00 0.00 0.00 3.27
2843 10501 1.970640 TCAGACAGCCATACACAGTGT 59.029 47.619 11.87 11.87 0.00 3.55
2844 10502 2.368548 TCAGACAGCCATACACAGTGTT 59.631 45.455 12.53 0.00 0.00 3.32
2848 10506 4.997395 AGACAGCCATACACAGTGTTAAAG 59.003 41.667 12.53 0.00 0.00 1.85
2857 10515 8.832521 CCATACACAGTGTTAAAGTAAACAAGA 58.167 33.333 12.53 0.00 40.85 3.02
2875 10533 4.883585 ACAAGATGATGGCATTAACGATGT 59.116 37.500 0.00 4.96 38.07 3.06
2913 10571 1.378762 TGGCTAAACTGAGGCACCC 59.621 57.895 0.00 0.00 46.22 4.61
2960 10642 6.742109 AGCATGTAATCCAGAATATTGCAAC 58.258 36.000 0.00 0.00 33.56 4.17
3001 10685 6.839124 ATTTATGACAGAAATCCAGTGCAA 57.161 33.333 2.17 0.00 0.00 4.08
3046 10738 4.823442 TGGCTATGACCTTAGCAAATGATG 59.177 41.667 14.26 0.00 45.21 3.07
3047 10739 4.823989 GGCTATGACCTTAGCAAATGATGT 59.176 41.667 14.26 0.00 45.21 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.742589 CCCGCAAAAGAAGTTCTAGACC 59.257 50.000 5.65 0.00 0.00 3.85
1 2 3.660865 TCCCGCAAAAGAAGTTCTAGAC 58.339 45.455 5.65 0.00 0.00 2.59
25 27 7.944554 TGTTGGATTTTGAGAAGGTCTAGATTT 59.055 33.333 0.00 0.00 0.00 2.17
134 136 4.802307 ACCCAAAAGGAAAATTGCCAAAT 58.198 34.783 0.00 0.00 39.89 2.32
188 190 3.065371 GGTGCATGTTCAGGTGTATAAGC 59.935 47.826 0.00 0.00 0.00 3.09
310 3027 8.093927 CCTTTTACTAAATCTTTTGGGCATGAA 58.906 33.333 0.00 0.00 0.00 2.57
400 3118 6.777091 TGTGAAGAAGGATTTTTCTGGATCAA 59.223 34.615 0.00 0.00 37.48 2.57
662 3476 1.674359 AAGTTGCAATCGTGTGTGGA 58.326 45.000 0.59 0.00 0.00 4.02
693 3509 5.364778 ACCATAAACAAGAAAGGCAAAACC 58.635 37.500 0.00 0.00 39.61 3.27
832 3648 5.900865 TGTGCATATGATCACACACAAAT 57.099 34.783 15.56 0.00 38.07 2.32
960 3787 6.207417 CCTCTTTCCTTCTTTGCATCAACTTA 59.793 38.462 0.00 0.00 0.00 2.24
1060 3889 5.368145 TCATGATGGATTGGTGCTAACTAC 58.632 41.667 0.00 0.00 0.00 2.73
1206 4080 5.350504 AATGGTGGTTGTTGTGAAAATGA 57.649 34.783 0.00 0.00 0.00 2.57
1212 4134 3.511540 TGTGAAAATGGTGGTTGTTGTGA 59.488 39.130 0.00 0.00 0.00 3.58
1314 4599 0.313672 GAAAATGGTGGTTGCTGCGA 59.686 50.000 0.00 0.00 0.00 5.10
1433 5220 2.760092 TGGCTGAACAATAGGGATTTGC 59.240 45.455 0.00 0.00 0.00 3.68
1484 5271 1.209019 CACTGCTGCTGGAGGAATACT 59.791 52.381 16.21 0.00 35.84 2.12
1514 5301 0.311790 CAAGACGTTGTGGCATTGCT 59.688 50.000 8.82 0.00 0.00 3.91
1600 5387 1.474330 GGATTGTTCGGGGATTTGCT 58.526 50.000 0.00 0.00 0.00 3.91
1679 5496 0.595095 GCTGCTGAGGTTGGACAAAG 59.405 55.000 0.00 0.00 0.00 2.77
1810 5642 5.706369 TGTAGTACCTGTTGTTGTTGTTGTT 59.294 36.000 0.00 0.00 0.00 2.83
1811 5643 5.247084 TGTAGTACCTGTTGTTGTTGTTGT 58.753 37.500 0.00 0.00 0.00 3.32
1812 5644 5.220777 CCTGTAGTACCTGTTGTTGTTGTTG 60.221 44.000 0.00 0.00 0.00 3.33
1813 5645 4.879545 CCTGTAGTACCTGTTGTTGTTGTT 59.120 41.667 0.00 0.00 0.00 2.83
1814 5646 4.448210 CCTGTAGTACCTGTTGTTGTTGT 58.552 43.478 0.00 0.00 0.00 3.32
1815 5647 3.813166 CCCTGTAGTACCTGTTGTTGTTG 59.187 47.826 0.00 0.00 0.00 3.33
1876 5712 0.798776 GAGTGCAATGGAAGTCACCG 59.201 55.000 0.00 0.00 0.00 4.94
1878 5714 0.798776 CGGAGTGCAATGGAAGTCAC 59.201 55.000 0.00 0.00 0.00 3.67
2137 5984 7.897575 ATGAACATTGTCTAGAGAACACTTC 57.102 36.000 4.15 6.63 0.00 3.01
2488 6340 6.815089 TGAAAAATAAGTGGATGTGCAAAGT 58.185 32.000 0.00 0.00 0.00 2.66
2576 6435 1.340017 GCTGGTCTAGGGCATGAACAA 60.340 52.381 0.00 0.00 28.78 2.83
2707 6853 4.298332 CGTTGCTTAGTTTGCTTTCCATT 58.702 39.130 0.00 0.00 0.00 3.16
2720 6866 2.415512 GGTTTCTACCTGCGTTGCTTAG 59.584 50.000 0.00 0.00 41.53 2.18
2743 6890 2.158900 ACACACCCAGTCTCAAGTTCTG 60.159 50.000 0.00 0.00 0.00 3.02
2789 10336 6.040842 GGGCTATTGCTTTCCAATTAATGAGA 59.959 38.462 0.00 0.00 41.29 3.27
2791 10338 5.898972 AGGGCTATTGCTTTCCAATTAATGA 59.101 36.000 0.00 0.00 41.29 2.57
2792 10339 6.165700 AGGGCTATTGCTTTCCAATTAATG 57.834 37.500 0.00 0.00 41.29 1.90
2793 10340 5.898972 TGAGGGCTATTGCTTTCCAATTAAT 59.101 36.000 0.00 0.00 41.29 1.40
2848 10506 6.781138 TCGTTAATGCCATCATCTTGTTTAC 58.219 36.000 0.00 0.00 31.27 2.01
2857 10515 4.973168 ACCTACATCGTTAATGCCATCAT 58.027 39.130 0.00 0.00 39.12 2.45
2913 10571 1.276138 TGGATGTCTATATGGCTGCCG 59.724 52.381 14.98 0.00 0.00 5.69
2985 10668 5.916318 TGAAAAATTGCACTGGATTTCTGT 58.084 33.333 0.00 0.00 0.00 3.41
2990 10674 7.518689 CGTCATTTTGAAAAATTGCACTGGATT 60.519 33.333 0.00 0.00 36.52 3.01
3001 10685 6.293353 GCCAATGGAACGTCATTTTGAAAAAT 60.293 34.615 2.05 0.00 39.07 1.82



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

AutoCloner maintained by Alex Coulton.