Multiple sequence alignment - TraesCS6A01G197000

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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 TraesCS6A01G197000 chr6A 100.000 2453 0 0 1 2453 290264122 290266574 0.000000e+00 4530
1 TraesCS6A01G197000 chr6A 84.570 1698 216 27 6 1677 66389346 66391023 0.000000e+00 1642
2 TraesCS6A01G197000 chr6A 84.270 1246 184 10 596 1832 454141375 454140133 0.000000e+00 1205
3 TraesCS6A01G197000 chr2D 88.071 1794 179 17 4 1770 552290447 552288662 0.000000e+00 2095
4 TraesCS6A01G197000 chr2D 86.114 857 115 4 977 1832 4661744 4662597 0.000000e+00 920
5 TraesCS6A01G197000 chr5B 87.073 1903 179 35 1 1873 335206121 335204256 0.000000e+00 2089
6 TraesCS6A01G197000 chr6D 97.941 1117 22 1 1337 2453 202967103 202965988 0.000000e+00 1934
7 TraesCS6A01G197000 chr6D 89.008 1028 97 8 856 1879 460404823 460403808 0.000000e+00 1258
8 TraesCS6A01G197000 chr6D 86.486 1073 101 19 1 1053 15646065 15647113 0.000000e+00 1138
9 TraesCS6A01G197000 chr6D 88.202 873 87 9 1 861 460457473 460456605 0.000000e+00 1027
10 TraesCS6A01G197000 chr6D 94.249 626 25 3 1 616 202967847 202967223 0.000000e+00 946
11 TraesCS6A01G197000 chr3A 84.957 1868 230 30 9 1830 707116805 707114943 0.000000e+00 1845
12 TraesCS6A01G197000 chr3A 89.189 1332 100 15 2 1314 215476563 215477869 0.000000e+00 1622
13 TraesCS6A01G197000 chr6B 84.737 1638 175 28 259 1862 640696079 640697675 0.000000e+00 1570
14 TraesCS6A01G197000 chr6B 85.856 1209 140 14 688 1870 640806026 640807229 0.000000e+00 1256
15 TraesCS6A01G197000 chr1D 86.373 1020 114 12 872 1871 363506146 363507160 0.000000e+00 1090
16 TraesCS6A01G197000 chr1D 85.200 1027 96 18 1 993 404496640 404495636 0.000000e+00 1003
17 TraesCS6A01G197000 chr1D 85.078 898 112 8 2 878 363480176 363481072 0.000000e+00 896
18 TraesCS6A01G197000 chr4B 85.319 1049 88 27 1 1006 568421082 568420057 0.000000e+00 1024
19 TraesCS6A01G197000 chr2B 82.966 1180 156 25 333 1471 738209862 738208687 0.000000e+00 1024
20 TraesCS6A01G197000 chr2B 86.644 876 109 7 973 1846 657863674 657862805 0.000000e+00 963
21 TraesCS6A01G197000 chr2B 85.890 326 38 4 7 325 738232703 738232379 8.400000e-90 340
22 TraesCS6A01G197000 chr7A 86.067 890 105 11 9 882 344754510 344755396 0.000000e+00 939
23 TraesCS6A01G197000 chr7A 83.388 909 139 12 970 1873 530935727 530936628 0.000000e+00 832
24 TraesCS6A01G197000 chr7A 88.201 339 36 4 9 344 531182304 531181967 3.800000e-108 401
25 TraesCS6A01G197000 chr5D 87.270 762 94 3 973 1732 300127870 300127110 0.000000e+00 867
26 TraesCS6A01G197000 chr7B 85.502 538 59 7 487 1006 172539994 172540530 5.970000e-151 544
27 TraesCS6A01G197000 chr3B 85.749 414 49 4 6 409 805739752 805740165 1.740000e-116 429
28 TraesCS6A01G197000 chr4D 87.264 212 18 5 1668 1878 495822315 495822518 1.470000e-57 233


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 TraesCS6A01G197000 chr6A 290264122 290266574 2452 False 4530 4530 100.000 1 2453 1 chr6A.!!$F2 2452
1 TraesCS6A01G197000 chr6A 66389346 66391023 1677 False 1642 1642 84.570 6 1677 1 chr6A.!!$F1 1671
2 TraesCS6A01G197000 chr6A 454140133 454141375 1242 True 1205 1205 84.270 596 1832 1 chr6A.!!$R1 1236
3 TraesCS6A01G197000 chr2D 552288662 552290447 1785 True 2095 2095 88.071 4 1770 1 chr2D.!!$R1 1766
4 TraesCS6A01G197000 chr2D 4661744 4662597 853 False 920 920 86.114 977 1832 1 chr2D.!!$F1 855
5 TraesCS6A01G197000 chr5B 335204256 335206121 1865 True 2089 2089 87.073 1 1873 1 chr5B.!!$R1 1872
6 TraesCS6A01G197000 chr6D 202965988 202967847 1859 True 1440 1934 96.095 1 2453 2 chr6D.!!$R3 2452
7 TraesCS6A01G197000 chr6D 460403808 460404823 1015 True 1258 1258 89.008 856 1879 1 chr6D.!!$R1 1023
8 TraesCS6A01G197000 chr6D 15646065 15647113 1048 False 1138 1138 86.486 1 1053 1 chr6D.!!$F1 1052
9 TraesCS6A01G197000 chr6D 460456605 460457473 868 True 1027 1027 88.202 1 861 1 chr6D.!!$R2 860
10 TraesCS6A01G197000 chr3A 707114943 707116805 1862 True 1845 1845 84.957 9 1830 1 chr3A.!!$R1 1821
11 TraesCS6A01G197000 chr3A 215476563 215477869 1306 False 1622 1622 89.189 2 1314 1 chr3A.!!$F1 1312
12 TraesCS6A01G197000 chr6B 640696079 640697675 1596 False 1570 1570 84.737 259 1862 1 chr6B.!!$F1 1603
13 TraesCS6A01G197000 chr6B 640806026 640807229 1203 False 1256 1256 85.856 688 1870 1 chr6B.!!$F2 1182
14 TraesCS6A01G197000 chr1D 363506146 363507160 1014 False 1090 1090 86.373 872 1871 1 chr1D.!!$F2 999
15 TraesCS6A01G197000 chr1D 404495636 404496640 1004 True 1003 1003 85.200 1 993 1 chr1D.!!$R1 992
16 TraesCS6A01G197000 chr1D 363480176 363481072 896 False 896 896 85.078 2 878 1 chr1D.!!$F1 876
17 TraesCS6A01G197000 chr4B 568420057 568421082 1025 True 1024 1024 85.319 1 1006 1 chr4B.!!$R1 1005
18 TraesCS6A01G197000 chr2B 738208687 738209862 1175 True 1024 1024 82.966 333 1471 1 chr2B.!!$R2 1138
19 TraesCS6A01G197000 chr2B 657862805 657863674 869 True 963 963 86.644 973 1846 1 chr2B.!!$R1 873
20 TraesCS6A01G197000 chr7A 344754510 344755396 886 False 939 939 86.067 9 882 1 chr7A.!!$F1 873
21 TraesCS6A01G197000 chr7A 530935727 530936628 901 False 832 832 83.388 970 1873 1 chr7A.!!$F2 903
22 TraesCS6A01G197000 chr5D 300127110 300127870 760 True 867 867 87.270 973 1732 1 chr5D.!!$R1 759
23 TraesCS6A01G197000 chr7B 172539994 172540530 536 False 544 544 85.502 487 1006 1 chr7B.!!$F1 519

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
569 593 1.086634 GCCCAGCGAAGATGTCAGAC 61.087 60.000 0.00 0.0 45.74 3.51 F
1010 1129 2.356278 GCTGCCCATGGAGGTTGA 59.644 61.111 15.22 0.0 34.66 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 1558 1.597027 CGTTGACGGTGAAGGCCTT 60.597 57.895 20.65 20.65 35.37 4.35 R
2191 2351 3.142174 GGCTGGCATAATTACAGAGACC 58.858 50.000 5.91 0.00 34.21 3.85 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
148 152 1.806542 ACATCGTCATGAGTTTGTGGC 59.193 47.619 0.00 0.00 33.72 5.01
200 212 2.225934 TGAGTACAAGGGTATTGGGGGA 60.226 50.000 0.00 0.00 0.00 4.81
208 221 4.710197 AGGGTATTGGGGGAAAATCTTT 57.290 40.909 0.00 0.00 0.00 2.52
567 591 1.817099 GGCCCAGCGAAGATGTCAG 60.817 63.158 0.00 0.00 45.74 3.51
568 592 1.219124 GCCCAGCGAAGATGTCAGA 59.781 57.895 0.00 0.00 45.74 3.27
569 593 1.086634 GCCCAGCGAAGATGTCAGAC 61.087 60.000 0.00 0.00 45.74 3.51
995 1102 3.971702 GGGCAAGGAGGTGGTGCT 61.972 66.667 0.00 0.00 38.36 4.40
1010 1129 2.356278 GCTGCCCATGGAGGTTGA 59.644 61.111 15.22 0.00 34.66 3.18
1056 1175 2.660064 GGATGAGGACGTGGTGCCT 61.660 63.158 0.00 0.00 37.18 4.75
1335 1464 5.163478 CCATCAGATCATGATCGGCTACATA 60.163 44.000 25.61 11.76 46.01 2.29
1585 1719 5.424121 AAACTATCTTCTGTTGTGTGTGC 57.576 39.130 0.00 0.00 0.00 4.57
1665 1805 6.314784 GTTACCAGACAATAGTTGTTGCATC 58.685 40.000 0.00 0.00 45.52 3.91
1735 1875 4.792521 AACGGTATGCCAAAATTGCTAA 57.207 36.364 0.00 0.00 34.09 3.09
1787 1927 3.253921 CCAAACAATGTGCAGATGTCAGA 59.746 43.478 0.00 0.00 0.00 3.27
1838 1998 0.036010 GTTGAGCCAGGCTGAGCTAA 60.036 55.000 22.26 17.41 39.88 3.09
1931 2091 6.605849 AGATCGCATGATAAAATTCATTCGG 58.394 36.000 0.00 0.00 41.20 4.30
1957 2117 7.926555 GGAATTATCTTCGGTCACAAATAGAGA 59.073 37.037 0.00 0.00 0.00 3.10
2058 2218 4.711399 TCAGCATGGATTCAGAATTCGAT 58.289 39.130 0.00 0.00 36.16 3.59
2059 2219 4.514066 TCAGCATGGATTCAGAATTCGATG 59.486 41.667 0.00 3.79 36.16 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 152 2.943033 GGTAACCTCAAATCCATCGGTG 59.057 50.000 0.00 0.00 0.00 4.94
208 221 6.664714 AGGCTAAGATCTAGAACTACTGTGA 58.335 40.000 2.55 0.00 0.00 3.58
506 529 2.982130 CCCGACAGAGGTCAAGGG 59.018 66.667 0.00 0.00 44.54 3.95
540 563 0.323269 TTCGCTGGGCCATGAATCAA 60.323 50.000 6.72 0.00 0.00 2.57
567 591 1.944676 CGAAGGGCGCTATGTCGTC 60.945 63.158 7.64 2.10 0.00 4.20
568 592 2.104331 CGAAGGGCGCTATGTCGT 59.896 61.111 7.64 0.00 0.00 4.34
995 1102 2.356278 GCTCAACCTCCATGGGCA 59.644 61.111 13.02 0.00 43.87 5.36
1069 1188 2.400399 GTAGTTACGACACTTGCTGCA 58.600 47.619 0.00 0.00 0.00 4.41
1335 1464 0.104855 TGAGCAGCTTGAACGTCACT 59.895 50.000 0.00 0.00 0.00 3.41
1429 1558 1.597027 CGTTGACGGTGAAGGCCTT 60.597 57.895 20.65 20.65 35.37 4.35
1585 1719 2.095768 ACGGCGTGAAGAAACAATCATG 60.096 45.455 13.76 0.00 36.00 3.07
1665 1805 2.144482 ACTACTCGGTGTTTGGTTCG 57.856 50.000 0.00 0.00 0.00 3.95
1735 1875 1.789523 TTAGGCCTCTCGCATTAGGT 58.210 50.000 9.68 0.00 40.31 3.08
1787 1927 4.769345 TGAAGGAAAACAGGCCAAAAAT 57.231 36.364 5.01 0.00 0.00 1.82
1931 2091 7.926555 TCTCTATTTGTGACCGAAGATAATTCC 59.073 37.037 0.00 0.00 0.00 3.01
2191 2351 3.142174 GGCTGGCATAATTACAGAGACC 58.858 50.000 5.91 0.00 34.21 3.85
2399 2559 6.357240 GCGGAATATTGCGTTTTTAGAATCTC 59.643 38.462 26.83 5.34 44.21 2.75


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

AutoCloner maintained by Alex Coulton.