Multiple sequence alignment - TraesCS7D01G169600

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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 TraesCS7D01G169600 chr7D 100.000 3044 0 0 1 3044 121120464 121123507 0.000000e+00 5622.0
1 TraesCS7D01G169600 chr7D 97.126 1322 32 3 921 2241 121049906 121051222 0.000000e+00 2226.0
2 TraesCS7D01G169600 chr7D 96.028 705 22 3 142 846 121033967 121034665 0.000000e+00 1142.0
3 TraesCS7D01G169600 chr7D 91.407 803 51 14 2254 3044 630922851 630923647 0.000000e+00 1085.0
4 TraesCS7D01G169600 chr7D 90.440 795 43 9 2253 3044 529994265 529993501 0.000000e+00 1016.0
5 TraesCS7D01G169600 chr7D 93.215 619 25 2 2252 2861 412701841 412702451 0.000000e+00 894.0
6 TraesCS7D01G169600 chr7D 94.702 151 8 0 1 151 121031217 121031367 5.070000e-58 235.0
7 TraesCS7D01G169600 chr7D 96.203 79 3 0 844 922 121037104 121037182 2.460000e-26 130.0
8 TraesCS7D01G169600 chr7D 100.000 31 0 0 1774 1804 8214672 8214702 1.180000e-04 58.4
9 TraesCS7D01G169600 chr2A 90.596 872 67 11 868 1726 23426315 23427184 0.000000e+00 1142.0
10 TraesCS7D01G169600 chr2A 78.310 355 72 5 32 382 50443462 50443109 1.100000e-54 224.0
11 TraesCS7D01G169600 chr2A 88.108 185 13 2 1864 2048 23431652 23431827 8.550000e-51 211.0
12 TraesCS7D01G169600 chr2A 84.834 211 14 7 2040 2244 23445283 23445481 2.390000e-46 196.0
13 TraesCS7D01G169600 chr2D 91.717 821 38 14 2254 3044 21713124 21712304 0.000000e+00 1112.0
14 TraesCS7D01G169600 chr2D 92.867 757 16 5 2254 2985 628849824 628849081 0.000000e+00 1064.0
15 TraesCS7D01G169600 chr2D 92.657 749 12 8 2254 2969 597938495 597937757 0.000000e+00 1038.0
16 TraesCS7D01G169600 chr2D 89.612 722 29 14 2254 2938 545028176 545027464 0.000000e+00 876.0
17 TraesCS7D01G169600 chr2D 88.959 317 18 11 2730 3044 611130988 611131289 2.870000e-100 375.0
18 TraesCS7D01G169600 chr2D 98.113 212 2 2 2834 3044 47708620 47708410 4.790000e-98 368.0
19 TraesCS7D01G169600 chr2D 96.818 220 3 4 2825 3044 642047934 642047719 6.200000e-97 364.0
20 TraesCS7D01G169600 chr2D 96.380 221 7 1 2825 3044 68751086 68750866 2.230000e-96 363.0
21 TraesCS7D01G169600 chr2D 96.380 221 6 2 2825 3044 69948840 69949059 2.230000e-96 363.0
22 TraesCS7D01G169600 chr2D 96.380 221 6 2 2825 3044 597936582 597936363 2.230000e-96 363.0
23 TraesCS7D01G169600 chr2D 100.000 30 0 0 1776 1805 650063848 650063819 4.240000e-04 56.5
24 TraesCS7D01G169600 chr3D 92.886 745 13 7 2254 2967 586015498 586016233 0.000000e+00 1046.0
25 TraesCS7D01G169600 chr3D 90.403 719 25 9 2254 2938 586315465 586316173 0.000000e+00 905.0
26 TraesCS7D01G169600 chr3D 96.875 32 1 0 1774 1805 556016203 556016234 2.000000e-03 54.7
27 TraesCS7D01G169600 chr6D 91.903 741 23 5 2254 2969 86754271 86753543 0.000000e+00 1002.0
28 TraesCS7D01G169600 chrUn 91.386 743 18 12 2250 2966 9884538 9885260 0.000000e+00 976.0
29 TraesCS7D01G169600 chr6B 79.412 408 75 7 1 404 697807884 697808286 2.310000e-71 279.0
30 TraesCS7D01G169600 chr5B 80.319 376 68 6 8 379 597195731 597196104 2.310000e-71 279.0
31 TraesCS7D01G169600 chr5B 89.130 46 4 1 1776 1821 320386328 320386284 4.240000e-04 56.5
32 TraesCS7D01G169600 chr5A 82.209 326 47 9 79 396 606881082 606881404 1.390000e-68 270.0
33 TraesCS7D01G169600 chr5A 81.272 283 49 4 1 280 606878992 606879273 3.050000e-55 226.0
34 TraesCS7D01G169600 chr1D 79.947 374 68 5 35 404 353553977 353553607 5.000000e-68 268.0
35 TraesCS7D01G169600 chr1D 100.000 32 0 0 1774 1805 291574193 291574162 3.280000e-05 60.2
36 TraesCS7D01G169600 chr4A 79.661 354 57 12 1 342 637964303 637964653 1.090000e-59 241.0
37 TraesCS7D01G169600 chr3B 96.970 33 1 0 1773 1805 770246874 770246906 4.240000e-04 56.5
38 TraesCS7D01G169600 chr4B 96.875 32 1 0 1774 1805 188177847 188177816 2.000000e-03 54.7
39 TraesCS7D01G169600 chr3A 96.875 32 1 0 1774 1805 559864288 559864257 2.000000e-03 54.7
40 TraesCS7D01G169600 chr6A 100.000 28 0 0 1777 1804 239459570 239459543 5.000000e-03 52.8


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 TraesCS7D01G169600 chr7D 121120464 121123507 3043 False 5622.000000 5622 100.000000 1 3044 1 chr7D.!!$F3 3043
1 TraesCS7D01G169600 chr7D 121049906 121051222 1316 False 2226.000000 2226 97.126000 921 2241 1 chr7D.!!$F2 1320
2 TraesCS7D01G169600 chr7D 630922851 630923647 796 False 1085.000000 1085 91.407000 2254 3044 1 chr7D.!!$F5 790
3 TraesCS7D01G169600 chr7D 529993501 529994265 764 True 1016.000000 1016 90.440000 2253 3044 1 chr7D.!!$R1 791
4 TraesCS7D01G169600 chr7D 412701841 412702451 610 False 894.000000 894 93.215000 2252 2861 1 chr7D.!!$F4 609
5 TraesCS7D01G169600 chr7D 121031217 121037182 5965 False 502.333333 1142 95.644333 1 922 3 chr7D.!!$F6 921
6 TraesCS7D01G169600 chr2A 23426315 23427184 869 False 1142.000000 1142 90.596000 868 1726 1 chr2A.!!$F1 858
7 TraesCS7D01G169600 chr2D 21712304 21713124 820 True 1112.000000 1112 91.717000 2254 3044 1 chr2D.!!$R1 790
8 TraesCS7D01G169600 chr2D 628849081 628849824 743 True 1064.000000 1064 92.867000 2254 2985 1 chr2D.!!$R5 731
9 TraesCS7D01G169600 chr2D 545027464 545028176 712 True 876.000000 876 89.612000 2254 2938 1 chr2D.!!$R4 684
10 TraesCS7D01G169600 chr2D 597936363 597938495 2132 True 700.500000 1038 94.518500 2254 3044 2 chr2D.!!$R8 790
11 TraesCS7D01G169600 chr3D 586015498 586016233 735 False 1046.000000 1046 92.886000 2254 2967 1 chr3D.!!$F2 713
12 TraesCS7D01G169600 chr3D 586315465 586316173 708 False 905.000000 905 90.403000 2254 2938 1 chr3D.!!$F3 684
13 TraesCS7D01G169600 chr6D 86753543 86754271 728 True 1002.000000 1002 91.903000 2254 2969 1 chr6D.!!$R1 715
14 TraesCS7D01G169600 chrUn 9884538 9885260 722 False 976.000000 976 91.386000 2250 2966 1 chrUn.!!$F1 716
15 TraesCS7D01G169600 chr5A 606878992 606881404 2412 False 248.000000 270 81.740500 1 396 2 chr5A.!!$F1 395

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
772 4788 0.179043 TGCAAGTTTAGTCGGTGGCA 60.179 50.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2518 8990 0.109723 GTGGGACTAAACACTGGCCA 59.89 55.0 4.71 4.71 34.84 5.36 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
56 57 0.389948 GATGGAGCGGAACTTCGTGT 60.390 55.000 0.00 0.00 0.00 4.49
116 1518 9.829507 TCACAAACCAATTAATTTGAAACTGAT 57.170 25.926 16.53 0.00 38.82 2.90
247 4258 4.842531 TTGTGAAGATTGATAGGCAGGA 57.157 40.909 0.00 0.00 0.00 3.86
263 4275 1.344438 CAGGATAACAGGAGGCGCATA 59.656 52.381 10.83 0.00 0.00 3.14
294 4306 6.688813 GCGAAATTTAGATTTGCTAACAGGAG 59.311 38.462 2.11 0.00 38.76 3.69
373 4389 7.206687 ACGATTGCAAGAATCTTGGTTTTTAA 58.793 30.769 22.73 0.33 0.00 1.52
407 4423 6.168270 TGGGTTGGGTTTAAAAGAAATCAG 57.832 37.500 0.00 0.00 0.00 2.90
432 4448 4.278419 CAGGGAAAAAGAAAAGTGACCGAT 59.722 41.667 0.00 0.00 0.00 4.18
437 4453 7.120138 GGGAAAAAGAAAAGTGACCGATACATA 59.880 37.037 0.00 0.00 0.00 2.29
478 4494 2.052468 AGGCATGCATAGATGGTCTCA 58.948 47.619 21.36 0.00 0.00 3.27
510 4526 5.528870 TCATATCTTCATGTTGACGCGTAT 58.471 37.500 13.97 0.00 0.00 3.06
684 4700 7.928307 ATCTGTACTAGTGTTCGTTAACCTA 57.072 36.000 5.39 0.00 34.49 3.08
772 4788 0.179043 TGCAAGTTTAGTCGGTGGCA 60.179 50.000 0.00 0.00 0.00 4.92
799 4815 4.833380 TCGGAGTTGGAATAGGAATAGGAG 59.167 45.833 0.00 0.00 0.00 3.69
899 7356 2.035832 ACCCTCATCAAAAGCCAAAACG 59.964 45.455 0.00 0.00 0.00 3.60
918 7375 1.948145 CGTATAAGGCTCCTCGTGTCT 59.052 52.381 0.00 0.00 0.00 3.41
926 7383 1.433534 CTCCTCGTGTCTCTTTTGCC 58.566 55.000 0.00 0.00 0.00 4.52
945 7402 1.709147 CTGGGAAGCGAAATCAGGCG 61.709 60.000 0.00 0.00 0.00 5.52
1009 7466 3.112075 CGAACGTGATGGCGCTGT 61.112 61.111 7.64 0.00 34.88 4.40
1053 7510 2.031012 CTTGCACTCAGGTCGCCA 59.969 61.111 0.00 0.00 0.00 5.69
1160 7617 6.072673 AGCTATTTGGTTCAGGTTCTTTTACG 60.073 38.462 0.00 0.00 0.00 3.18
1258 7723 4.390297 GCAATTTAGATCTGATACCCGCTC 59.610 45.833 5.18 0.00 0.00 5.03
1310 7779 7.284820 TCATCATCAATCAGCAGAAATTAGGA 58.715 34.615 0.00 0.00 0.00 2.94
1488 7958 9.423061 GCTGTTCAGATTTAACATAAACCAAAT 57.577 29.630 3.84 0.00 36.33 2.32
1597 8067 7.059156 AGACAGATGATTTATCCTGAAAAGGG 58.941 38.462 0.00 0.00 36.40 3.95
1710 8180 4.184629 ACTTCAGAGGTAAATGACATCGC 58.815 43.478 0.00 0.00 43.78 4.58
1773 8243 9.605275 TTGAATCTATCTCTCACCTTTTATGTG 57.395 33.333 0.00 0.00 35.01 3.21
2011 8481 7.841282 ATAGCTCTTTTGATACTAGTGCCTA 57.159 36.000 5.39 0.00 0.00 3.93
2015 8485 6.036191 GCTCTTTTGATACTAGTGCCTACAAC 59.964 42.308 5.39 0.00 0.00 3.32
2234 8704 8.607441 ATTATTGATGCTATATGAACGTGTGT 57.393 30.769 0.00 0.00 0.00 3.72
2237 8707 6.144078 TGATGCTATATGAACGTGTGTACT 57.856 37.500 0.00 0.00 0.00 2.73
2238 8708 6.206498 TGATGCTATATGAACGTGTGTACTC 58.794 40.000 0.00 0.00 0.00 2.59
2240 8710 6.203808 TGCTATATGAACGTGTGTACTCTT 57.796 37.500 0.00 0.00 0.00 2.85
2241 8711 7.324354 TGCTATATGAACGTGTGTACTCTTA 57.676 36.000 0.00 0.00 0.00 2.10
2242 8712 7.937649 TGCTATATGAACGTGTGTACTCTTAT 58.062 34.615 0.00 0.00 0.00 1.73
2243 8713 9.059260 TGCTATATGAACGTGTGTACTCTTATA 57.941 33.333 0.00 0.00 0.00 0.98
2244 8714 9.544314 GCTATATGAACGTGTGTACTCTTATAG 57.456 37.037 14.95 14.95 0.00 1.31
2245 8715 9.544314 CTATATGAACGTGTGTACTCTTATAGC 57.456 37.037 10.31 0.00 0.00 2.97
2246 8716 4.990257 TGAACGTGTGTACTCTTATAGCC 58.010 43.478 0.00 0.00 0.00 3.93
2247 8717 4.460034 TGAACGTGTGTACTCTTATAGCCA 59.540 41.667 0.00 0.00 0.00 4.75
2248 8718 5.047872 TGAACGTGTGTACTCTTATAGCCAA 60.048 40.000 0.00 0.00 0.00 4.52
2269 8739 5.179555 CCAACCTTCACTAGTAGAAAACTGC 59.820 44.000 3.59 0.00 39.39 4.40
2433 8905 1.152839 CGGTTGGTGGGACAAACCT 60.153 57.895 10.60 0.00 44.16 3.50
2437 8909 0.856982 TTGGTGGGACAAACCTGGAT 59.143 50.000 0.00 0.00 44.16 3.41
2518 8990 1.446016 AAAGGGCTGGTCCTAGTTGT 58.554 50.000 0.00 0.00 35.80 3.32
2624 9096 7.539712 TCTCTTAAAGTGAAAATAGATGCCG 57.460 36.000 0.00 0.00 0.00 5.69
3001 10841 3.646715 GCCACCTACTGGGCCACA 61.647 66.667 0.00 0.00 44.53 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 0.645868 GCATACACGAAGTTCCGCTC 59.354 55.000 0.00 0.00 41.61 5.03
56 57 1.271982 TGTTAAACCCGGCAAGGCATA 60.272 47.619 0.00 0.00 39.21 3.14
116 1518 2.071778 AGGAAGCAACAAAGGAGCAA 57.928 45.000 0.00 0.00 0.00 3.91
247 4258 4.067896 CAATCTTATGCGCCTCCTGTTAT 58.932 43.478 4.18 0.00 0.00 1.89
263 4275 9.076596 GTTAGCAAATCTAAATTTCGCAATCTT 57.923 29.630 0.00 0.00 38.86 2.40
271 4283 6.688813 CGCTCCTGTTAGCAAATCTAAATTTC 59.311 38.462 0.00 0.00 42.91 2.17
294 4306 3.190535 ACCATTACAAAACACTCCATCGC 59.809 43.478 0.00 0.00 0.00 4.58
373 4389 9.771140 TTTTAAACCCAACCCATGTATATTAGT 57.229 29.630 0.00 0.00 0.00 2.24
407 4423 4.497507 CGGTCACTTTTCTTTTTCCCTGTC 60.498 45.833 0.00 0.00 0.00 3.51
487 4503 3.780902 ACGCGTCAACATGAAGATATGA 58.219 40.909 5.58 0.00 0.00 2.15
528 4544 6.389869 AGTGGACATCCTCCCAATTTTATCTA 59.610 38.462 0.00 0.00 38.49 1.98
529 4545 5.194537 AGTGGACATCCTCCCAATTTTATCT 59.805 40.000 0.00 0.00 38.49 1.98
724 4740 2.742116 ATACACGGCCCGGCTTGAT 61.742 57.895 8.57 1.05 0.00 2.57
772 4788 5.896073 ATTCCTATTCCAACTCCGATTCT 57.104 39.130 0.00 0.00 0.00 2.40
799 4815 3.934962 GCTCTCCGGCCCTCATCC 61.935 72.222 0.00 0.00 0.00 3.51
899 7356 3.215975 AGAGACACGAGGAGCCTTATAC 58.784 50.000 0.00 0.00 0.00 1.47
918 7375 0.179004 TTCGCTTCCCAGGCAAAAGA 60.179 50.000 0.00 0.00 0.00 2.52
926 7383 1.709147 CGCCTGATTTCGCTTCCCAG 61.709 60.000 0.00 0.00 0.00 4.45
945 7402 5.179533 GTGGATCTAGGGTTTGTTTCTCTC 58.820 45.833 0.00 0.00 0.00 3.20
1053 7510 4.424711 ATGCGGGTTGCCATCGGT 62.425 61.111 0.00 0.00 45.60 4.69
1160 7617 5.297029 GCAGGGTATCAATCTAACTTGGTTC 59.703 44.000 0.00 0.00 0.00 3.62
1298 7767 2.587522 GGGGGTCATCCTAATTTCTGC 58.412 52.381 0.00 0.00 35.33 4.26
1475 7945 9.866798 AACAAATTGCAAAATTTGGTTTATGTT 57.133 22.222 22.86 9.51 44.97 2.71
1597 8067 2.747855 CCTCGAGCAGTTTGGCCC 60.748 66.667 6.99 0.00 0.00 5.80
1710 8180 7.144722 TGATAAATGCTTGTTGAGTTGGTAG 57.855 36.000 0.00 0.00 0.00 3.18
1763 8233 2.838637 TTAGGCCCCCACATAAAAGG 57.161 50.000 0.00 0.00 0.00 3.11
1773 8243 1.133575 GTCCAGGTTTATTAGGCCCCC 60.134 57.143 0.00 0.00 0.00 5.40
1872 8342 9.047371 GTTAGGAGAGAAGGAATTATTGCTTAC 57.953 37.037 11.53 9.10 41.66 2.34
1889 8359 5.684704 TGGAAGGCAATTATGTTAGGAGAG 58.315 41.667 0.00 0.00 0.00 3.20
2011 8481 6.209391 ACAGCCATAAAAAGCATAAGAGTTGT 59.791 34.615 0.00 0.00 0.00 3.32
2015 8485 7.559590 ACTACAGCCATAAAAAGCATAAGAG 57.440 36.000 0.00 0.00 0.00 2.85
2234 8704 7.124052 ACTAGTGAAGGTTGGCTATAAGAGTA 58.876 38.462 0.00 0.00 0.00 2.59
2237 8707 7.351952 TCTACTAGTGAAGGTTGGCTATAAGA 58.648 38.462 5.39 0.00 0.00 2.10
2238 8708 7.584122 TCTACTAGTGAAGGTTGGCTATAAG 57.416 40.000 5.39 0.00 0.00 1.73
2240 8710 7.966339 TTTCTACTAGTGAAGGTTGGCTATA 57.034 36.000 5.39 0.00 0.00 1.31
2241 8711 6.869206 TTTCTACTAGTGAAGGTTGGCTAT 57.131 37.500 5.39 0.00 0.00 2.97
2242 8712 6.269307 AGTTTTCTACTAGTGAAGGTTGGCTA 59.731 38.462 5.39 0.00 34.56 3.93
2243 8713 5.071923 AGTTTTCTACTAGTGAAGGTTGGCT 59.928 40.000 5.39 0.00 34.56 4.75
2244 8714 5.179555 CAGTTTTCTACTAGTGAAGGTTGGC 59.820 44.000 5.39 0.00 34.56 4.52
2245 8715 5.179555 GCAGTTTTCTACTAGTGAAGGTTGG 59.820 44.000 5.39 0.30 34.56 3.77
2246 8716 5.107453 CGCAGTTTTCTACTAGTGAAGGTTG 60.107 44.000 5.39 7.64 34.56 3.77
2247 8717 4.989168 CGCAGTTTTCTACTAGTGAAGGTT 59.011 41.667 5.39 0.00 34.56 3.50
2248 8718 4.557205 CGCAGTTTTCTACTAGTGAAGGT 58.443 43.478 5.39 0.00 34.56 3.50
2269 8739 1.526575 ATTGCCCTGTGACCAAAGCG 61.527 55.000 0.00 0.00 0.00 4.68
2407 8879 2.596338 CCACCAACCGGGACCAAC 60.596 66.667 6.32 0.00 41.15 3.77
2433 8905 2.440065 GCGTGGCCCATTGATCCA 60.440 61.111 0.00 0.00 0.00 3.41
2437 8909 3.329889 AGGAGCGTGGCCCATTGA 61.330 61.111 0.00 0.00 0.00 2.57
2458 8930 1.486145 CCGGGACTAAAGGGTGGTGT 61.486 60.000 0.00 0.00 0.00 4.16
2518 8990 0.109723 GTGGGACTAAACACTGGCCA 59.890 55.000 4.71 4.71 34.84 5.36
3001 10841 2.372264 TCTAGTCGTATTCAGGCCGTT 58.628 47.619 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.