Multiple sequence alignment - TraesCS7D01G423500

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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 TraesCS7D01G423500 chr7D 100.000 3672 0 0 1 3672 543732627 543728956 0.000000e+00 6782
1 TraesCS7D01G423500 chr7D 82.695 861 128 10 1055 1913 548551106 548550265 0.000000e+00 745
2 TraesCS7D01G423500 chr7D 84.571 525 64 11 1475 1997 548324514 548324005 4.230000e-139 505
3 TraesCS7D01G423500 chr6B 91.894 2973 127 47 752 3670 694681409 694678497 0.000000e+00 4050
4 TraesCS7D01G423500 chr6B 95.618 753 30 1 1 750 694682206 694681454 0.000000e+00 1205
5 TraesCS7D01G423500 chr7A 95.693 1393 28 17 2307 3672 625641121 625639734 0.000000e+00 2211
6 TraesCS7D01G423500 chr7A 91.483 1409 76 21 752 2150 625642616 625641242 0.000000e+00 1897
7 TraesCS7D01G423500 chr7A 91.753 1067 58 14 752 1814 625675394 625674354 0.000000e+00 1456
8 TraesCS7D01G423500 chr7A 93.984 748 45 0 1 748 625643406 625642659 0.000000e+00 1133
9 TraesCS7D01G423500 chr7A 92.176 818 31 20 2224 3014 625673890 625673079 0.000000e+00 1125
10 TraesCS7D01G423500 chr7A 93.359 768 33 5 1 750 625676202 625675435 0.000000e+00 1120
11 TraesCS7D01G423500 chr7A 84.520 1053 120 25 1016 2058 631652538 631653557 0.000000e+00 1002
12 TraesCS7D01G423500 chr7A 85.906 298 35 2 1016 1309 617552007 617552301 9.900000e-81 311
13 TraesCS7D01G423500 chr1D 91.673 1369 73 21 752 2102 110905622 110904277 0.000000e+00 1858
14 TraesCS7D01G423500 chr7B 90.909 1155 59 26 1 1133 587102725 587101595 0.000000e+00 1509
15 TraesCS7D01G423500 chr7B 90.390 1155 56 27 1 1133 587267932 587266811 0.000000e+00 1467
16 TraesCS7D01G423500 chr7B 94.841 756 33 4 1 750 587441656 587440901 0.000000e+00 1175
17 TraesCS7D01G423500 chr7B 94.203 759 35 5 1 750 587480661 587479903 0.000000e+00 1149
18 TraesCS7D01G423500 chr7B 92.857 756 34 3 1 750 587519905 587519164 0.000000e+00 1079
19 TraesCS7D01G423500 chr7B 86.490 792 88 11 1066 1840 569439964 569440753 0.000000e+00 852
20 TraesCS7D01G423500 chr7B 94.820 444 23 0 307 750 587615877 587615434 0.000000e+00 693
21 TraesCS7D01G423500 chr7B 94.322 317 15 2 1 314 587620889 587620573 1.980000e-132 483
22 TraesCS7D01G423500 chr7B 87.467 383 22 15 752 1131 587479858 587479499 5.670000e-113 418
23 TraesCS7D01G423500 chr7B 87.139 381 23 15 754 1131 587519117 587518760 3.410000e-110 409
24 TraesCS7D01G423500 chr7B 87.736 212 9 11 752 963 587440856 587440662 7.930000e-57 231
25 TraesCS7D01G423500 chr7B 83.133 166 11 9 752 917 587615389 587615241 6.400000e-28 135
26 TraesCS7D01G423500 chr1B 91.636 1088 61 17 794 1876 169025361 169024299 0.000000e+00 1478
27 TraesCS7D01G423500 chr1B 88.073 327 15 9 1869 2171 169013846 169013520 2.080000e-97 366
28 TraesCS7D01G423500 chr1B 93.143 175 10 2 2387 2559 169011430 169011256 4.710000e-64 255
29 TraesCS7D01G423500 chr2B 86.910 741 69 10 1074 1814 671009888 671010600 0.000000e+00 806
30 TraesCS7D01G423500 chr2A 86.229 777 55 16 1 750 701781707 701782458 0.000000e+00 795
31 TraesCS7D01G423500 chr2A 83.073 449 39 17 757 1187 701782672 701783101 1.250000e-99 374
32 TraesCS7D01G423500 chr6A 80.730 794 153 0 2871 3664 93814881 93814088 1.450000e-173 619


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 TraesCS7D01G423500 chr7D 543728956 543732627 3671 True 6782.000000 6782 100.000000 1 3672 1 chr7D.!!$R1 3671
1 TraesCS7D01G423500 chr7D 548550265 548551106 841 True 745.000000 745 82.695000 1055 1913 1 chr7D.!!$R3 858
2 TraesCS7D01G423500 chr7D 548324005 548324514 509 True 505.000000 505 84.571000 1475 1997 1 chr7D.!!$R2 522
3 TraesCS7D01G423500 chr6B 694678497 694682206 3709 True 2627.500000 4050 93.756000 1 3670 2 chr6B.!!$R1 3669
4 TraesCS7D01G423500 chr7A 625639734 625643406 3672 True 1747.000000 2211 93.720000 1 3672 3 chr7A.!!$R1 3671
5 TraesCS7D01G423500 chr7A 625673079 625676202 3123 True 1233.666667 1456 92.429333 1 3014 3 chr7A.!!$R2 3013
6 TraesCS7D01G423500 chr7A 631652538 631653557 1019 False 1002.000000 1002 84.520000 1016 2058 1 chr7A.!!$F2 1042
7 TraesCS7D01G423500 chr1D 110904277 110905622 1345 True 1858.000000 1858 91.673000 752 2102 1 chr1D.!!$R1 1350
8 TraesCS7D01G423500 chr7B 587101595 587102725 1130 True 1509.000000 1509 90.909000 1 1133 1 chr7B.!!$R1 1132
9 TraesCS7D01G423500 chr7B 587266811 587267932 1121 True 1467.000000 1467 90.390000 1 1133 1 chr7B.!!$R2 1132
10 TraesCS7D01G423500 chr7B 569439964 569440753 789 False 852.000000 852 86.490000 1066 1840 1 chr7B.!!$F1 774
11 TraesCS7D01G423500 chr7B 587479499 587480661 1162 True 783.500000 1149 90.835000 1 1131 2 chr7B.!!$R5 1130
12 TraesCS7D01G423500 chr7B 587518760 587519905 1145 True 744.000000 1079 89.998000 1 1131 2 chr7B.!!$R6 1130
13 TraesCS7D01G423500 chr7B 587440662 587441656 994 True 703.000000 1175 91.288500 1 963 2 chr7B.!!$R4 962
14 TraesCS7D01G423500 chr7B 587615241 587615877 636 True 414.000000 693 88.976500 307 917 2 chr7B.!!$R7 610
15 TraesCS7D01G423500 chr1B 169024299 169025361 1062 True 1478.000000 1478 91.636000 794 1876 1 chr1B.!!$R1 1082
16 TraesCS7D01G423500 chr1B 169011256 169013846 2590 True 310.500000 366 90.608000 1869 2559 2 chr1B.!!$R2 690
17 TraesCS7D01G423500 chr2B 671009888 671010600 712 False 806.000000 806 86.910000 1074 1814 1 chr2B.!!$F1 740
18 TraesCS7D01G423500 chr2A 701781707 701783101 1394 False 584.500000 795 84.651000 1 1187 2 chr2A.!!$F1 1186
19 TraesCS7D01G423500 chr6A 93814088 93814881 793 True 619.000000 619 80.730000 2871 3664 1 chr6A.!!$R1 793

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
965 1285 1.334054 GCACCTCGTGTACGTAACTG 58.666 55.0 0.00 0.00 40.8 3.16 F
1667 2054 0.318762 GGTACATGGCTCCGGAGATC 59.681 60.0 35.69 24.38 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2670 5147 0.109723 TAAACTGGGGTTGCTCGCTT 59.890 50.000 0.0 0.0 35.63 4.68 R
3380 5876 3.421919 TCTTGATGTGAGCATGGACAA 57.578 42.857 0.0 0.0 35.07 3.18 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
448 508 2.962569 CTCGGACTCGTGCTTCCA 59.037 61.111 0.00 0.00 37.69 3.53
661 721 4.082523 CATGTCAGGGTCGGCGGT 62.083 66.667 7.21 0.00 0.00 5.68
965 1285 1.334054 GCACCTCGTGTACGTAACTG 58.666 55.000 0.00 0.00 40.80 3.16
1224 1559 1.831652 CGCCCTCAAGTTCCTGGTCT 61.832 60.000 0.00 0.00 0.00 3.85
1667 2054 0.318762 GGTACATGGCTCCGGAGATC 59.681 60.000 35.69 24.38 0.00 2.75
1781 2168 0.669318 GACAGAATGCGGTCGACCAA 60.669 55.000 32.80 21.22 42.53 3.67
1960 2348 1.405661 GGTTTTAGACGGGCTCCTCAG 60.406 57.143 0.00 0.00 0.00 3.35
2150 2593 9.575868 TTTAGTCAGTAATGGAATTGTACCAAA 57.424 29.630 0.00 0.00 40.93 3.28
2245 4101 6.072286 ACAGAAGTAATGCAATCTTGGAAGTG 60.072 38.462 0.00 0.00 30.51 3.16
2268 4124 5.219633 GTCAAAATGTTACAGAAATGGCGT 58.780 37.500 0.00 0.00 0.00 5.68
2324 4781 8.468349 CACAAAACGAACTGTACATTATTTGTG 58.532 33.333 21.57 21.57 44.57 3.33
2364 4831 5.086058 CAGACAAAGTTAACACACACACAC 58.914 41.667 8.61 0.00 0.00 3.82
2366 4833 4.789784 ACAAAGTTAACACACACACACAC 58.210 39.130 8.61 0.00 0.00 3.82
2369 4836 4.413495 AGTTAACACACACACACACAAC 57.587 40.909 8.61 0.00 0.00 3.32
2370 4837 4.069304 AGTTAACACACACACACACAACT 58.931 39.130 8.61 0.00 0.00 3.16
2371 4838 5.239351 AGTTAACACACACACACACAACTA 58.761 37.500 8.61 0.00 0.00 2.24
2372 4839 5.701750 AGTTAACACACACACACACAACTAA 59.298 36.000 8.61 0.00 0.00 2.24
2455 4926 6.762077 TTGATCCAAGACCATCCATACATA 57.238 37.500 0.00 0.00 0.00 2.29
2640 5117 4.107622 CCAAACAAACAGCAACAAGAGAG 58.892 43.478 0.00 0.00 0.00 3.20
2656 5133 8.376203 CAACAAGAGAGAAAACATATCACTACG 58.624 37.037 0.00 0.00 0.00 3.51
2666 5143 8.657074 AAAACATATCACTACGCATTAGCTAA 57.343 30.769 8.99 8.99 39.10 3.09
2670 5147 9.923143 ACATATCACTACGCATTAGCTAAATAA 57.077 29.630 10.85 0.00 39.10 1.40
2684 5163 1.917872 AAATAAAGCGAGCAACCCCA 58.082 45.000 0.00 0.00 0.00 4.96
2805 5301 2.922740 AACGCCACTTGAAAGGTCTA 57.077 45.000 0.00 0.00 0.00 2.59
2824 5320 6.494835 AGGTCTAATTTGTTTTCATGGAAGCT 59.505 34.615 1.98 0.00 0.00 3.74
3193 5689 2.231380 AGGCATTCCACTCCCGGTT 61.231 57.895 0.00 0.00 33.74 4.44
3225 5721 1.205893 ACAGGGCTCTTCTTCGCTTAG 59.794 52.381 0.00 0.00 0.00 2.18
3380 5876 3.113043 GGTACTTCCCTCCATACAGGTT 58.887 50.000 0.00 0.00 39.02 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
503 563 2.049063 ACGCTGCGGTTGACTCTC 60.049 61.111 26.95 0.00 0.00 3.20
504 564 2.049063 GACGCTGCGGTTGACTCT 60.049 61.111 26.95 1.54 0.00 3.24
750 813 1.972660 ATCGCTTTCTTCCTCCCCCG 61.973 60.000 0.00 0.00 0.00 5.73
953 1270 4.151258 TGTAGACTGCAGTTACGTACAC 57.849 45.455 22.65 11.26 0.00 2.90
965 1285 3.001330 GCGTGTTGGAATATGTAGACTGC 59.999 47.826 0.00 0.00 0.00 4.40
994 1314 3.799755 CGGGTAACGCTTGCTGCC 61.800 66.667 0.00 0.00 38.78 4.85
1004 1324 2.193536 GGCCATGGATGCGGGTAAC 61.194 63.158 18.40 0.00 0.00 2.50
1005 1325 2.194597 GGCCATGGATGCGGGTAA 59.805 61.111 18.40 0.00 0.00 2.85
1006 1326 3.093172 TGGCCATGGATGCGGGTA 61.093 61.111 18.40 0.00 0.00 3.69
1376 1750 2.601666 AGGACGAGGCTGCACTGA 60.602 61.111 0.50 0.00 0.00 3.41
1569 1956 2.748605 GAGGTCGCATATCTTCACCAG 58.251 52.381 0.00 0.00 0.00 4.00
1643 2030 2.203070 GGAGCCATGTACCAGCGG 60.203 66.667 0.00 0.00 0.00 5.52
1781 2168 0.179134 CGCGGAAGATTCGGAAGAGT 60.179 55.000 0.00 0.00 43.69 3.24
1810 2197 3.117589 GTGAATCCTACACACGCGT 57.882 52.632 5.58 5.58 38.05 6.01
1898 2286 1.684049 CTCCTCCGGGAACAGCTCT 60.684 63.158 0.00 0.00 41.69 4.09
2009 2397 2.904866 GCGGTGCCAGTGAACCAA 60.905 61.111 13.46 0.00 36.14 3.67
2150 2593 7.341805 AGATCTACAATTCCATTACAGCAAGT 58.658 34.615 0.00 0.00 0.00 3.16
2198 2671 5.001232 GTGTAACAGGGAAATTGCTGTCTA 58.999 41.667 0.00 0.00 36.32 2.59
2199 2672 3.821033 GTGTAACAGGGAAATTGCTGTCT 59.179 43.478 0.00 0.00 36.32 3.41
2229 2788 5.534207 TTTTGACACTTCCAAGATTGCAT 57.466 34.783 0.00 0.00 0.00 3.96
2245 4101 5.219633 ACGCCATTTCTGTAACATTTTGAC 58.780 37.500 0.00 0.00 0.00 3.18
2268 4124 6.262944 ACAATGCTGAACTGTCATGTTCTAAA 59.737 34.615 13.05 3.57 44.63 1.85
2324 4781 6.431198 TTGTCTGTTTTCCTCTTGTTGTAC 57.569 37.500 0.00 0.00 0.00 2.90
2364 4831 5.409826 CCTCTCAGGTAAGCTTTTAGTTGTG 59.590 44.000 3.20 0.00 0.00 3.33
2366 4833 5.794894 TCCTCTCAGGTAAGCTTTTAGTTG 58.205 41.667 3.20 0.00 36.53 3.16
2369 4836 6.937465 AGTTTTCCTCTCAGGTAAGCTTTTAG 59.063 38.462 3.20 0.00 33.67 1.85
2370 4837 6.838382 AGTTTTCCTCTCAGGTAAGCTTTTA 58.162 36.000 3.20 0.00 33.67 1.52
2371 4838 5.696030 AGTTTTCCTCTCAGGTAAGCTTTT 58.304 37.500 3.20 0.00 33.67 2.27
2372 4839 5.311844 AGTTTTCCTCTCAGGTAAGCTTT 57.688 39.130 3.20 0.00 33.67 3.51
2455 4926 6.873997 TCTGTGAAACCGTGATAGTTATGAT 58.126 36.000 0.00 0.00 34.36 2.45
2640 5117 7.178712 AGCTAATGCGTAGTGATATGTTTTC 57.821 36.000 0.00 0.00 45.42 2.29
2656 5133 5.095691 TGCTCGCTTTATTTAGCTAATGC 57.904 39.130 7.08 6.46 39.03 3.56
2666 5143 1.271926 ACTGGGGTTGCTCGCTTTATT 60.272 47.619 0.00 0.00 0.00 1.40
2670 5147 0.109723 TAAACTGGGGTTGCTCGCTT 59.890 50.000 0.00 0.00 35.63 4.68
2805 5301 6.121590 ACCAAAGCTTCCATGAAAACAAATT 58.878 32.000 0.00 0.00 0.00 1.82
3380 5876 3.421919 TCTTGATGTGAGCATGGACAA 57.578 42.857 0.00 0.00 35.07 3.18


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

AutoCloner maintained by Alex Coulton.