Multiple sequence alignment - TraesCS1D01G171700

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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 TraesCS1D01G171700 chr1D 100.000 2696 0 0 1 2696 244953100 244950405 0 4979
1 TraesCS1D01G171700 chr1D 95.441 2698 115 7 1 2696 244362896 244360205 0 4294
2 TraesCS1D01G171700 chr1D 94.027 1172 59 7 680 1843 254481580 254480412 0 1766
3 TraesCS1D01G171700 chr1D 94.317 827 46 1 1871 2696 244224759 244223933 0 1266
4 TraesCS1D01G171700 chr1D 94.082 828 47 2 1871 2696 244816696 244815869 0 1256
5 TraesCS1D01G171700 chr1D 95.455 682 30 1 1 682 40849429 40848749 0 1086
6 TraesCS1D01G171700 chr2D 95.218 1171 49 4 677 1840 359630289 359631459 0 1845
7 TraesCS1D01G171700 chr2D 95.205 1168 52 3 677 1840 628291908 628293075 0 1844
8 TraesCS1D01G171700 chr2D 95.214 1170 49 4 680 1843 643857943 643856775 0 1844
9 TraesCS1D01G171700 chr2D 92.541 858 56 8 1843 2696 137874009 137874862 0 1223
10 TraesCS1D01G171700 chr2D 92.065 857 61 6 1844 2696 214008676 214007823 0 1199
11 TraesCS1D01G171700 chr2D 95.051 687 33 1 1 687 294880606 294879921 0 1079
12 TraesCS1D01G171700 chr5D 95.132 1171 50 3 677 1840 483803171 483804341 0 1840
13 TraesCS1D01G171700 chr5D 91.958 858 60 9 1843 2696 233403191 233404043 0 1194
14 TraesCS1D01G171700 chr5D 95.716 677 28 1 2 678 418099868 418099193 0 1088
15 TraesCS1D01G171700 chr5D 95.315 683 31 1 1 682 418261175 418260493 0 1083
16 TraesCS1D01G171700 chr2B 94.602 1167 60 2 680 1843 474939449 474938283 0 1803
17 TraesCS1D01G171700 chr3B 94.430 1167 61 4 680 1843 201497600 201496435 0 1792
18 TraesCS1D01G171700 chr3D 93.643 1164 69 2 677 1840 451862658 451863816 0 1735
19 TraesCS1D01G171700 chr3D 92.657 858 59 4 1841 2695 314523213 314524069 0 1232
20 TraesCS1D01G171700 chr3D 95.582 679 27 3 1 678 451645725 451645049 0 1085
21 TraesCS1D01G171700 chr7D 92.558 860 54 9 1844 2696 312646779 312645923 0 1225
22 TraesCS1D01G171700 chr7D 95.729 679 27 2 1 679 236281864 236281188 0 1092
23 TraesCS1D01G171700 chr7D 95.455 682 31 0 1 682 236287102 236286421 0 1088
24 TraesCS1D01G171700 chr6D 92.290 856 60 6 1844 2696 299347360 299346508 0 1210
25 TraesCS1D01G171700 chr4D 95.742 681 28 1 1 681 391057069 391056390 0 1096


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 TraesCS1D01G171700 chr1D 244950405 244953100 2695 True 4979 4979 100.000 1 2696 1 chr1D.!!$R5 2695
1 TraesCS1D01G171700 chr1D 244360205 244362896 2691 True 4294 4294 95.441 1 2696 1 chr1D.!!$R3 2695
2 TraesCS1D01G171700 chr1D 254480412 254481580 1168 True 1766 1766 94.027 680 1843 1 chr1D.!!$R6 1163
3 TraesCS1D01G171700 chr1D 244223933 244224759 826 True 1266 1266 94.317 1871 2696 1 chr1D.!!$R2 825
4 TraesCS1D01G171700 chr1D 244815869 244816696 827 True 1256 1256 94.082 1871 2696 1 chr1D.!!$R4 825
5 TraesCS1D01G171700 chr1D 40848749 40849429 680 True 1086 1086 95.455 1 682 1 chr1D.!!$R1 681
6 TraesCS1D01G171700 chr2D 359630289 359631459 1170 False 1845 1845 95.218 677 1840 1 chr2D.!!$F2 1163
7 TraesCS1D01G171700 chr2D 628291908 628293075 1167 False 1844 1844 95.205 677 1840 1 chr2D.!!$F3 1163
8 TraesCS1D01G171700 chr2D 643856775 643857943 1168 True 1844 1844 95.214 680 1843 1 chr2D.!!$R3 1163
9 TraesCS1D01G171700 chr2D 137874009 137874862 853 False 1223 1223 92.541 1843 2696 1 chr2D.!!$F1 853
10 TraesCS1D01G171700 chr2D 214007823 214008676 853 True 1199 1199 92.065 1844 2696 1 chr2D.!!$R1 852
11 TraesCS1D01G171700 chr2D 294879921 294880606 685 True 1079 1079 95.051 1 687 1 chr2D.!!$R2 686
12 TraesCS1D01G171700 chr5D 483803171 483804341 1170 False 1840 1840 95.132 677 1840 1 chr5D.!!$F2 1163
13 TraesCS1D01G171700 chr5D 233403191 233404043 852 False 1194 1194 91.958 1843 2696 1 chr5D.!!$F1 853
14 TraesCS1D01G171700 chr5D 418099193 418099868 675 True 1088 1088 95.716 2 678 1 chr5D.!!$R1 676
15 TraesCS1D01G171700 chr5D 418260493 418261175 682 True 1083 1083 95.315 1 682 1 chr5D.!!$R2 681
16 TraesCS1D01G171700 chr2B 474938283 474939449 1166 True 1803 1803 94.602 680 1843 1 chr2B.!!$R1 1163
17 TraesCS1D01G171700 chr3B 201496435 201497600 1165 True 1792 1792 94.430 680 1843 1 chr3B.!!$R1 1163
18 TraesCS1D01G171700 chr3D 451862658 451863816 1158 False 1735 1735 93.643 677 1840 1 chr3D.!!$F2 1163
19 TraesCS1D01G171700 chr3D 314523213 314524069 856 False 1232 1232 92.657 1841 2695 1 chr3D.!!$F1 854
20 TraesCS1D01G171700 chr3D 451645049 451645725 676 True 1085 1085 95.582 1 678 1 chr3D.!!$R1 677
21 TraesCS1D01G171700 chr7D 312645923 312646779 856 True 1225 1225 92.558 1844 2696 1 chr7D.!!$R3 852
22 TraesCS1D01G171700 chr7D 236281188 236281864 676 True 1092 1092 95.729 1 679 1 chr7D.!!$R1 678
23 TraesCS1D01G171700 chr7D 236286421 236287102 681 True 1088 1088 95.455 1 682 1 chr7D.!!$R2 681
24 TraesCS1D01G171700 chr6D 299346508 299347360 852 True 1210 1210 92.290 1844 2696 1 chr6D.!!$R1 852
25 TraesCS1D01G171700 chr4D 391056390 391057069 679 True 1096 1096 95.742 1 681 1 chr4D.!!$R1 680

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
649 652 1.073923 TCACCCTTTCCTCTTCAAGGC 59.926 52.381 0.0 0.0 45.78 4.35 F
1354 1369 0.110486 TGTTCTTGGGGAGCCTGTTC 59.890 55.000 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1573 1591 0.031515 ACGGATACACCCCCATGAGA 60.032 55.0 0.0 0.0 34.64 3.27 R
2477 2512 1.835494 TCAACGGAGGAGATCGAGTT 58.165 50.0 0.0 0.0 32.02 3.01 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
176 177 8.581057 AATAGTAGTAGATGCAGAATCGTTTG 57.419 34.615 0.00 0.00 40.54 2.93
178 179 4.471904 AGTAGATGCAGAATCGTTTGGA 57.528 40.909 0.00 0.00 40.54 3.53
213 214 4.573607 CGGATGTGATGCCTATATTCATGG 59.426 45.833 0.00 0.00 0.00 3.66
219 221 7.005902 TGTGATGCCTATATTCATGGTCATTT 58.994 34.615 0.00 0.00 0.00 2.32
303 305 8.764558 ACCCACCGTATTATATGCTATCATTAA 58.235 33.333 0.00 0.00 34.22 1.40
340 342 2.122725 TATGGCCCCCGGGTCTAC 60.123 66.667 21.85 7.28 41.25 2.59
383 385 5.452356 CCTGTCAACTTGCCAATTTCTTTCT 60.452 40.000 0.00 0.00 0.00 2.52
546 549 3.249799 TCTTGATTGTTTGTGCAGGTACG 59.750 43.478 0.00 0.00 0.00 3.67
569 572 1.654105 GTGACTTGCGTGTAATCTCCG 59.346 52.381 0.00 0.00 0.00 4.63
649 652 1.073923 TCACCCTTTCCTCTTCAAGGC 59.926 52.381 0.00 0.00 45.78 4.35
811 822 1.487142 TGAACTTTCCCACGGACTCAA 59.513 47.619 0.00 0.00 0.00 3.02
1170 1185 4.277174 CAGAGTAGAGACACTGCCGATAAT 59.723 45.833 0.00 0.00 37.44 1.28
1251 1266 1.065102 GCTATGAGTGCTACGAACGGA 59.935 52.381 0.00 0.00 0.00 4.69
1293 1308 1.661463 TTGACATGGGAGCTCCTCTT 58.339 50.000 31.36 16.54 36.20 2.85
1306 1321 2.168496 CTCCTCTTAGTGTTCCGGTCA 58.832 52.381 0.00 0.00 0.00 4.02
1354 1369 0.110486 TGTTCTTGGGGAGCCTGTTC 59.890 55.000 0.00 0.00 0.00 3.18
1386 1401 4.401519 GGTCCTGTAGATAGTAGTGCAACA 59.598 45.833 0.00 0.00 41.43 3.33
1437 1452 8.762426 GCCTTTATCGAGTTAGATACGAAATTT 58.238 33.333 0.00 0.00 39.38 1.82
1453 1468 9.927668 ATACGAAATTTTCCATCTTTGAAACAT 57.072 25.926 3.61 0.00 31.78 2.71
1465 1480 8.739039 CCATCTTTGAAACATGTATTAAGGTCA 58.261 33.333 0.00 0.00 0.00 4.02
1475 1490 8.594881 ACATGTATTAAGGTCATCGATCTTTC 57.405 34.615 0.00 0.00 34.57 2.62
1584 1602 3.052642 ACATTGCTAAATCTCATGGGGGT 60.053 43.478 0.00 0.00 0.00 4.95
1665 1683 5.470437 GGAAATGAAGGAATCCGGAGTAATC 59.530 44.000 11.34 7.20 0.00 1.75
1668 1686 4.766375 TGAAGGAATCCGGAGTAATCAAC 58.234 43.478 11.34 0.00 0.00 3.18
1669 1688 3.454371 AGGAATCCGGAGTAATCAACG 57.546 47.619 11.34 0.00 0.00 4.10
1722 1741 7.345691 TCTAGTCTATGGCCAAATGAATGAAA 58.654 34.615 10.96 0.00 0.00 2.69
1737 1756 0.468226 TGAAACACTGGGAGCTCGTT 59.532 50.000 7.83 2.74 0.00 3.85
1769 1788 5.014333 TGGTTTAACTTCCCTAACTATGGCA 59.986 40.000 0.00 0.00 0.00 4.92
1770 1789 5.947566 GGTTTAACTTCCCTAACTATGGCAA 59.052 40.000 0.00 0.00 0.00 4.52
1851 1870 4.795268 TCTTGTTCAAGTAGTGTAGCGAG 58.205 43.478 11.52 0.00 0.00 5.03
1902 1922 1.227674 GTGTCATCCCTGGATCGGC 60.228 63.158 0.00 0.00 31.62 5.54
1992 2013 9.972106 AATACTATTACCTTAGTCCGTATAGCT 57.028 33.333 0.00 0.00 34.35 3.32
2025 2047 3.312736 AACTTGTGGAGTCCCAACAAT 57.687 42.857 13.82 0.32 45.59 2.71
2028 2050 3.137544 ACTTGTGGAGTCCCAACAATACA 59.862 43.478 13.82 4.15 45.59 2.29
2029 2051 3.134574 TGTGGAGTCCCAACAATACAC 57.865 47.619 6.74 0.00 45.59 2.90
2477 2512 1.561643 TGTGCACTTTTCCCCACAAA 58.438 45.000 19.41 0.00 35.48 2.83
2533 2568 3.334691 TGATGTTTGAGAACCGGATGAC 58.665 45.455 9.46 0.00 34.80 3.06
2605 2641 4.503714 ACACCTACAATTCCCCTACATG 57.496 45.455 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 177 3.130516 TCACATCCGTGTCAAGTAGATCC 59.869 47.826 0.00 0.00 44.02 3.36
178 179 4.686972 CATCACATCCGTGTCAAGTAGAT 58.313 43.478 0.00 0.00 44.02 1.98
219 221 7.558081 AGCGCATAGTTATGAGAATATCTAGGA 59.442 37.037 11.47 0.00 35.84 2.94
303 305 5.491982 CATAGGTTTCACTAGTGGCTTCTT 58.508 41.667 22.48 9.77 0.00 2.52
383 385 9.187455 GAAAGTAAAGATTGCAAAATAAACGGA 57.813 29.630 1.71 0.00 0.00 4.69
569 572 5.104259 AGAACCAAGGTATCAATCCAGTC 57.896 43.478 0.00 0.00 0.00 3.51
649 652 3.655486 TCTTGAGCATGCATTGGTTTTG 58.345 40.909 21.98 0.04 35.82 2.44
811 822 4.758674 CCATTCAATCGCTTACTCATGGAT 59.241 41.667 0.00 0.00 33.08 3.41
1134 1149 3.764434 CTCTACTCTGGACTACCAAAGCA 59.236 47.826 0.00 0.00 46.32 3.91
1170 1185 9.562408 TGTACCTCACAAGTCACATTAATTTTA 57.438 29.630 0.00 0.00 32.95 1.52
1251 1266 5.705397 TCACTTCCATTCCTCTCATCAAT 57.295 39.130 0.00 0.00 0.00 2.57
1293 1308 1.254026 CTCCACTGACCGGAACACTA 58.746 55.000 9.46 0.00 30.33 2.74
1306 1321 0.745128 CGTCCGAGAGTAGCTCCACT 60.745 60.000 0.00 0.00 40.70 4.00
1354 1369 5.745227 ACTATCTACAGGACCCAAATTGTG 58.255 41.667 0.00 0.00 0.00 3.33
1386 1401 4.383552 GGCGCAGATCTATGAATAGGGAAT 60.384 45.833 10.83 0.00 0.00 3.01
1437 1452 9.308000 ACCTTAATACATGTTTCAAAGATGGAA 57.692 29.630 11.70 0.31 36.54 3.53
1453 1468 6.701841 GCTGAAAGATCGATGACCTTAATACA 59.298 38.462 0.54 0.00 34.07 2.29
1475 1490 0.738975 TCCACGTCGATAAGGAGCTG 59.261 55.000 0.00 0.00 0.00 4.24
1573 1591 0.031515 ACGGATACACCCCCATGAGA 60.032 55.000 0.00 0.00 34.64 3.27
1683 1702 8.093927 GCCATAGACTAGAGCTATCTTTGATTT 58.906 37.037 0.00 0.00 36.96 2.17
1722 1741 0.532862 CACAAACGAGCTCCCAGTGT 60.533 55.000 8.47 4.69 0.00 3.55
1755 1774 6.488683 CGGAAATATTTTGCCATAGTTAGGGA 59.511 38.462 1.43 0.00 28.27 4.20
1819 1838 9.832445 ACACTACTTGAACAAGAAGAAAGATAA 57.168 29.630 19.35 0.00 40.79 1.75
1828 1847 5.190992 TCGCTACACTACTTGAACAAGAA 57.809 39.130 19.35 0.03 40.79 2.52
1830 1849 3.365220 GCTCGCTACACTACTTGAACAAG 59.635 47.826 12.22 12.22 43.79 3.16
1902 1922 3.249091 GAGTACTCTGTGTGTCAGCATG 58.751 50.000 15.91 0.00 43.32 4.06
1992 2013 4.265893 TCCACAAGTTTGTTGCTACTTCA 58.734 39.130 0.00 0.00 39.91 3.02
2007 2029 3.502211 GTGTATTGTTGGGACTCCACAAG 59.498 47.826 7.00 0.00 43.94 3.16
2025 2047 1.937223 CACTCAACTTTGCCGTGTGTA 59.063 47.619 0.00 0.00 0.00 2.90
2028 2050 2.159014 TCTACACTCAACTTTGCCGTGT 60.159 45.455 16.05 16.05 41.68 4.49
2029 2051 2.221055 GTCTACACTCAACTTTGCCGTG 59.779 50.000 8.69 8.69 36.26 4.94
2477 2512 1.835494 TCAACGGAGGAGATCGAGTT 58.165 50.000 0.00 0.00 32.02 3.01
2533 2568 6.016943 ACCTCTTCGAAAAGACTATATCTCGG 60.017 42.308 0.00 0.00 36.27 4.63
2539 2574 5.848833 GGGACCTCTTCGAAAAGACTATA 57.151 43.478 0.00 0.00 36.59 1.31
2605 2641 3.181450 ACCTTTCCATGATAGGCTAGCAC 60.181 47.826 15.62 6.06 34.81 4.40


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

AutoCloner maintained by Alex Coulton.