Multiple sequence alignment - TraesCS7B01G415500

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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 TraesCS7B01G415500 chr7B 100.000 2636 0 0 1 2636 683106284 683108919 0.000000e+00 4868
1 TraesCS7B01G415500 chr7B 89.067 1683 159 12 1 1675 682842722 682844387 0.000000e+00 2065
2 TraesCS7B01G415500 chr7B 88.015 1652 180 9 1 1651 683243255 683241621 0.000000e+00 1938
3 TraesCS7B01G415500 chr7B 90.882 1338 116 4 332 1665 683151371 683152706 0.000000e+00 1790
4 TraesCS7B01G415500 chr7B 89.119 1351 133 7 329 1675 683168440 683167100 0.000000e+00 1668
5 TraesCS7B01G415500 chr7A 94.232 1699 78 5 1 1695 694196988 694198670 0.000000e+00 2577
6 TraesCS7B01G415500 chr7A 86.428 1702 171 30 1 1675 694253801 694252133 0.000000e+00 1808
7 TraesCS7B01G415500 chr7A 86.992 1576 175 8 1 1575 694375340 694373794 0.000000e+00 1748
8 TraesCS7B01G415500 chr7A 85.533 1659 202 19 1 1649 694331372 694329742 0.000000e+00 1700
9 TraesCS7B01G415500 chr7A 90.642 545 29 9 1 542 694141609 694142134 0.000000e+00 704
10 TraesCS7B01G415500 chr7A 82.182 275 43 4 1 269 694297052 694297326 5.670000e-57 231
11 TraesCS7B01G415500 chr7D 88.225 1656 178 11 1 1651 602750966 602749323 0.000000e+00 1962
12 TraesCS7B01G415500 chr7D 85.646 1463 188 13 40 1496 602627066 602628512 0.000000e+00 1519
13 TraesCS7B01G415500 chr3D 90.572 944 85 3 1693 2636 602041625 602042564 0.000000e+00 1247
14 TraesCS7B01G415500 chr3D 90.254 944 87 4 1693 2636 615133384 615134322 0.000000e+00 1229
15 TraesCS7B01G415500 chr6B 89.831 944 92 3 1693 2636 600436627 600437566 0.000000e+00 1208
16 TraesCS7B01G415500 chr6B 89.725 944 93 3 1693 2636 600314569 600315508 0.000000e+00 1203
17 TraesCS7B01G415500 chr6B 89.619 944 93 4 1693 2636 600356422 600357360 0.000000e+00 1195
18 TraesCS7B01G415500 chr3A 89.513 944 91 4 1693 2636 579232293 579233228 0.000000e+00 1188
19 TraesCS7B01G415500 chr3A 89.041 949 93 8 1693 2636 127423916 127422974 0.000000e+00 1166
20 TraesCS7B01G415500 chr2D 89.089 944 97 3 1693 2636 551923514 551922577 0.000000e+00 1168
21 TraesCS7B01G415500 chr5D 88.960 942 99 4 1695 2636 526245243 526246179 0.000000e+00 1158


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 TraesCS7B01G415500 chr7B 683106284 683108919 2635 False 4868 4868 100.000 1 2636 1 chr7B.!!$F2 2635
1 TraesCS7B01G415500 chr7B 682842722 682844387 1665 False 2065 2065 89.067 1 1675 1 chr7B.!!$F1 1674
2 TraesCS7B01G415500 chr7B 683241621 683243255 1634 True 1938 1938 88.015 1 1651 1 chr7B.!!$R2 1650
3 TraesCS7B01G415500 chr7B 683151371 683152706 1335 False 1790 1790 90.882 332 1665 1 chr7B.!!$F3 1333
4 TraesCS7B01G415500 chr7B 683167100 683168440 1340 True 1668 1668 89.119 329 1675 1 chr7B.!!$R1 1346
5 TraesCS7B01G415500 chr7A 694196988 694198670 1682 False 2577 2577 94.232 1 1695 1 chr7A.!!$F2 1694
6 TraesCS7B01G415500 chr7A 694252133 694253801 1668 True 1808 1808 86.428 1 1675 1 chr7A.!!$R1 1674
7 TraesCS7B01G415500 chr7A 694373794 694375340 1546 True 1748 1748 86.992 1 1575 1 chr7A.!!$R3 1574
8 TraesCS7B01G415500 chr7A 694329742 694331372 1630 True 1700 1700 85.533 1 1649 1 chr7A.!!$R2 1648
9 TraesCS7B01G415500 chr7A 694141609 694142134 525 False 704 704 90.642 1 542 1 chr7A.!!$F1 541
10 TraesCS7B01G415500 chr7D 602749323 602750966 1643 True 1962 1962 88.225 1 1651 1 chr7D.!!$R1 1650
11 TraesCS7B01G415500 chr7D 602627066 602628512 1446 False 1519 1519 85.646 40 1496 1 chr7D.!!$F1 1456
12 TraesCS7B01G415500 chr3D 602041625 602042564 939 False 1247 1247 90.572 1693 2636 1 chr3D.!!$F1 943
13 TraesCS7B01G415500 chr3D 615133384 615134322 938 False 1229 1229 90.254 1693 2636 1 chr3D.!!$F2 943
14 TraesCS7B01G415500 chr6B 600436627 600437566 939 False 1208 1208 89.831 1693 2636 1 chr6B.!!$F3 943
15 TraesCS7B01G415500 chr6B 600314569 600315508 939 False 1203 1203 89.725 1693 2636 1 chr6B.!!$F1 943
16 TraesCS7B01G415500 chr6B 600356422 600357360 938 False 1195 1195 89.619 1693 2636 1 chr6B.!!$F2 943
17 TraesCS7B01G415500 chr3A 579232293 579233228 935 False 1188 1188 89.513 1693 2636 1 chr3A.!!$F1 943
18 TraesCS7B01G415500 chr3A 127422974 127423916 942 True 1166 1166 89.041 1693 2636 1 chr3A.!!$R1 943
19 TraesCS7B01G415500 chr2D 551922577 551923514 937 True 1168 1168 89.089 1693 2636 1 chr2D.!!$R1 943
20 TraesCS7B01G415500 chr5D 526245243 526246179 936 False 1158 1158 88.960 1695 2636 1 chr5D.!!$F1 941

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
631 663 0.616891 GTTTACCGGGGTCACCTCAT 59.383 55.0 6.32 0.0 36.97 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1904 0.034337 CGACCGGGACTTGGAAGAAA 59.966 55.0 6.32 0.0 0.0 2.52 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
136 146 1.025812 GACCTCCTCATCGACGATGT 58.974 55.000 31.06 15.41 40.55 3.06
147 164 1.135489 TCGACGATGTCTTGTACCAGC 60.135 52.381 0.00 0.00 0.00 4.85
151 168 2.497675 ACGATGTCTTGTACCAGCTCAT 59.502 45.455 0.00 0.00 0.00 2.90
334 351 4.518970 TCTTCCGATTCCAAGTTTTCCAAG 59.481 41.667 0.00 0.00 0.00 3.61
347 364 1.042003 TTCCAAGCACCAGCAGCAAA 61.042 50.000 0.00 0.00 45.49 3.68
435 452 3.716195 CGGTGGTGCTGGGATGGA 61.716 66.667 0.00 0.00 0.00 3.41
631 663 0.616891 GTTTACCGGGGTCACCTCAT 59.383 55.000 6.32 0.00 36.97 2.90
716 748 2.872001 GCAGAGTCGTCGTCGCAG 60.872 66.667 0.00 0.00 36.96 5.18
1076 1108 3.514362 CCATGGCGCCGGGTTAAC 61.514 66.667 24.70 0.00 0.00 2.01
1224 1256 4.907034 CGGCCGGTGATCGAGACG 62.907 72.222 20.10 0.00 42.43 4.18
1558 1594 0.959553 TGTTCGCTCTTCTTCGGTCT 59.040 50.000 0.00 0.00 0.00 3.85
1659 1699 5.125100 TCATCCAGATTTGTTGTTCTTGC 57.875 39.130 0.00 0.00 0.00 4.01
1703 1743 2.304180 GTCCAGTATGCATATCTGGGCT 59.696 50.000 31.45 15.64 46.55 5.19
1741 1781 3.736740 GCAAGGTTTCCAACAACGAATGT 60.737 43.478 0.00 0.00 46.82 2.71
1749 1789 5.910637 TCCAACAACGAATGTAAGTGTAC 57.089 39.130 0.00 0.00 42.99 2.90
1789 1829 3.589288 AGAATCTTAGTTGCTGGAAGGGT 59.411 43.478 0.00 0.00 0.00 4.34
1822 1862 4.593206 TCATATGGAGGCCGACTAATTCTT 59.407 41.667 2.13 0.00 0.00 2.52
1843 1883 7.031226 TCTTATTAATTTGGTGCTGATGAGC 57.969 36.000 0.00 0.00 46.44 4.26
1855 1895 2.798499 GCTGATGAGCATGCCAATGTTC 60.798 50.000 15.66 4.60 45.46 3.18
1864 1904 4.060205 GCATGCCAATGTTCTTTTTGTCT 58.940 39.130 6.36 0.00 36.08 3.41
1871 1911 6.018751 GCCAATGTTCTTTTTGTCTTTCTTCC 60.019 38.462 0.00 0.00 0.00 3.46
1882 1922 1.346722 TCTTTCTTCCAAGTCCCGGTC 59.653 52.381 0.00 0.00 0.00 4.79
1923 1963 6.455246 GGTTGGACTTTTATCGATCTCGTTTC 60.455 42.308 0.00 0.00 40.80 2.78
1953 1993 6.374578 GCAGAGTGATGAGTTAAAAAGGAAC 58.625 40.000 0.00 0.00 0.00 3.62
1971 2011 9.959721 AAAAGGAACTATAGACTTGCTAAATGA 57.040 29.630 6.78 0.00 38.49 2.57
1975 2015 9.202273 GGAACTATAGACTTGCTAAATGAGATG 57.798 37.037 6.78 0.00 31.66 2.90
1999 2041 3.586470 TCTGTAGGCCAAAAGACCAAA 57.414 42.857 5.01 0.00 0.00 3.28
2092 2134 1.194781 AGAGACCGATGCCACTTGGT 61.195 55.000 0.00 0.00 35.49 3.67
2154 2196 1.152631 TCAGGTGACGGTCAGACCA 60.153 57.895 20.13 0.00 38.47 4.02
2172 2214 1.292061 CAACCGACTCACCGTTTTGA 58.708 50.000 0.00 0.00 0.00 2.69
2183 2225 5.648960 ACTCACCGTTTTGAAAAGGACTAAA 59.351 36.000 14.04 0.00 39.50 1.85
2187 2229 5.298527 ACCGTTTTGAAAAGGACTAAAGAGG 59.701 40.000 14.04 0.00 39.50 3.69
2256 2298 2.257207 ACTTCCACGAGATTCTGGGAA 58.743 47.619 9.48 9.48 36.31 3.97
2272 2314 3.973973 CTGGGAAGATACATGGTTAGGGA 59.026 47.826 0.00 0.00 0.00 4.20
2284 2326 2.105766 GGTTAGGGAAGACGCCTCTAA 58.894 52.381 0.00 0.00 0.00 2.10
2300 2342 6.270231 ACGCCTCTAACTATCCAATATCCTTT 59.730 38.462 0.00 0.00 0.00 3.11
2344 2386 2.480419 AGAGATGCTTACGTTGCAACAC 59.520 45.455 28.01 12.42 44.01 3.32
2354 2396 3.788937 ACGTTGCAACACTACTACAGTT 58.211 40.909 28.01 0.00 34.26 3.16
2379 2424 5.009410 CACTCCCCTCAATATTCAATTCAGC 59.991 44.000 0.00 0.00 0.00 4.26
2442 2488 6.111382 TCTTGTGAGAAGATTGATGGATGTC 58.889 40.000 0.00 0.00 0.00 3.06
2461 2507 4.802307 TGTCCATCTCTCTCTCAATAGCT 58.198 43.478 0.00 0.00 0.00 3.32
2473 2519 3.769300 TCTCAATAGCTAGACCAGTTGCA 59.231 43.478 0.00 0.00 0.00 4.08
2512 2558 8.673711 TCAGAATGGAGTATTTTCGGTAAAATG 58.326 33.333 6.39 0.00 40.09 2.32
2524 2570 3.629855 TCGGTAAAATGCATGTATGTGGG 59.370 43.478 0.00 0.00 0.00 4.61
2526 2572 4.681744 GGTAAAATGCATGTATGTGGGTG 58.318 43.478 0.00 0.00 0.00 4.61
2530 2576 4.981806 AATGCATGTATGTGGGTGTTAC 57.018 40.909 0.00 0.00 0.00 2.50
2547 2593 6.998673 GGGTGTTACTAATTCTGGCATTATCT 59.001 38.462 0.00 0.00 0.00 1.98
2615 2661 8.918961 TTAAAGTGTTTATGTGGTTTGTTCAG 57.081 30.769 0.00 0.00 0.00 3.02
2619 2665 6.601613 AGTGTTTATGTGGTTTGTTCAGAAGA 59.398 34.615 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.569049 CTTGCCCGGTCTCGTCGTT 62.569 63.158 0.00 0.00 33.95 3.85
136 146 2.813754 GTTGCAATGAGCTGGTACAAGA 59.186 45.455 0.59 0.00 45.94 3.02
147 164 1.325640 CAGATCGACGGTTGCAATGAG 59.674 52.381 0.59 0.00 0.00 2.90
151 168 0.601057 TCTCAGATCGACGGTTGCAA 59.399 50.000 0.00 0.00 0.00 4.08
231 248 2.305635 ACCATGACAGTATCTGGTGCAA 59.694 45.455 0.00 0.00 37.42 4.08
334 351 1.143620 TGGTTTTTGCTGCTGGTGC 59.856 52.632 0.00 0.00 40.20 5.01
347 364 2.824341 TGGTACCAACGTTTTGTGGTTT 59.176 40.909 13.60 0.00 34.90 3.27
631 663 2.566529 CGCCTGCGAGTGTGAGTA 59.433 61.111 5.43 0.00 42.83 2.59
716 748 1.305887 TCGAACTCCTTCCTCCCCC 60.306 63.158 0.00 0.00 0.00 5.40
807 839 0.417841 AGACAAGGAGGAGCCCCTTA 59.582 55.000 8.39 0.00 44.53 2.69
852 884 1.219393 GCTGTAGAGGTGCCTGTCC 59.781 63.158 0.00 0.00 0.00 4.02
1149 1181 0.320334 TGTACACGTCGGACTCGGTA 60.320 55.000 6.57 3.34 36.95 4.02
1224 1256 2.579738 GTGAAGGACCTCTCCGCC 59.420 66.667 0.00 0.00 42.22 6.13
1676 1716 5.394802 CAGATATGCATACTGGACGTACTC 58.605 45.833 20.01 7.96 0.00 2.59
1677 1717 5.378292 CAGATATGCATACTGGACGTACT 57.622 43.478 20.01 0.05 0.00 2.73
1741 1781 6.769134 TCAAATCGATCCTCAGTACACTTA 57.231 37.500 0.00 0.00 0.00 2.24
1749 1789 7.551035 AGATTCTTTTCAAATCGATCCTCAG 57.449 36.000 0.00 0.00 38.02 3.35
1789 1829 5.305902 TCGGCCTCCATATGACATTAGTTTA 59.694 40.000 3.65 0.00 0.00 2.01
1839 1879 4.059511 CAAAAAGAACATTGGCATGCTCA 58.940 39.130 18.92 11.22 33.05 4.26
1843 1883 6.480981 AGAAAGACAAAAAGAACATTGGCATG 59.519 34.615 0.00 0.00 37.01 4.06
1855 1895 5.592054 GGGACTTGGAAGAAAGACAAAAAG 58.408 41.667 0.00 0.00 0.00 2.27
1864 1904 0.034337 CGACCGGGACTTGGAAGAAA 59.966 55.000 6.32 0.00 0.00 2.52
1899 1939 6.310711 AGAAACGAGATCGATAAAAGTCCAAC 59.689 38.462 9.58 0.00 43.02 3.77
1923 1963 3.331478 AACTCATCACTCTGCCAGAAG 57.669 47.619 0.00 0.00 0.00 2.85
1971 2011 6.116126 GTCTTTTGGCCTACAGATAACATCT 58.884 40.000 3.32 0.00 41.15 2.90
1975 2015 4.585879 TGGTCTTTTGGCCTACAGATAAC 58.414 43.478 3.32 0.32 46.45 1.89
1999 2041 7.734942 TCTAAATTTTCAATTCAAAGCCCACT 58.265 30.769 0.00 0.00 0.00 4.00
2008 2050 9.965824 GTTCTTCACCTCTAAATTTTCAATTCA 57.034 29.630 0.00 0.00 0.00 2.57
2036 2078 5.316167 ACAACCATTTGCTGAGAAGACATA 58.684 37.500 0.00 0.00 36.00 2.29
2092 2134 5.221382 GGTACTTATTACGCAGAATCTGGGA 60.221 44.000 29.93 12.11 45.41 4.37
2154 2196 2.027003 TTCAAAACGGTGAGTCGGTT 57.973 45.000 0.00 0.00 42.32 4.44
2172 2214 8.857098 GTTGATTTAACCCTCTTTAGTCCTTTT 58.143 33.333 0.00 0.00 33.01 2.27
2183 2225 6.552008 TGGAAGAATGTTGATTTAACCCTCT 58.448 36.000 0.00 0.00 38.55 3.69
2187 2229 7.684428 GCCCTATGGAAGAATGTTGATTTAACC 60.684 40.741 0.00 0.00 38.55 2.85
2256 2298 3.069729 GCGTCTTCCCTAACCATGTATCT 59.930 47.826 0.00 0.00 0.00 1.98
2272 2314 6.071278 GGATATTGGATAGTTAGAGGCGTCTT 60.071 42.308 15.09 0.00 33.84 3.01
2344 2386 3.698289 TGAGGGGAGTGAACTGTAGTAG 58.302 50.000 0.00 0.00 0.00 2.57
2354 2396 6.325993 TGAATTGAATATTGAGGGGAGTGA 57.674 37.500 0.00 0.00 0.00 3.41
2379 2424 1.450025 GGTTTCCCGCTAAAGTCCTG 58.550 55.000 0.00 0.00 0.00 3.86
2442 2488 5.415701 GGTCTAGCTATTGAGAGAGAGATGG 59.584 48.000 0.00 0.00 0.00 3.51
2445 2491 5.131977 ACTGGTCTAGCTATTGAGAGAGAGA 59.868 44.000 0.00 0.00 0.00 3.10
2446 2492 5.376625 ACTGGTCTAGCTATTGAGAGAGAG 58.623 45.833 0.00 0.00 0.00 3.20
2447 2493 5.381184 ACTGGTCTAGCTATTGAGAGAGA 57.619 43.478 0.00 0.00 0.00 3.10
2473 2519 5.308237 ACTCCATTCTGAGTAAGTTTCCAGT 59.692 40.000 0.00 0.00 43.65 4.00
2512 2558 6.542370 AGAATTAGTAACACCCACATACATGC 59.458 38.462 0.00 0.00 0.00 4.06
2524 2570 8.894768 AGAGATAATGCCAGAATTAGTAACAC 57.105 34.615 0.00 0.00 0.00 3.32
2526 2572 8.082852 TCGAGAGATAATGCCAGAATTAGTAAC 58.917 37.037 0.00 0.00 33.31 2.50
2547 2593 5.535753 TTCCAGATATGCAAAGATCGAGA 57.464 39.130 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.