Multiple sequence alignment - TraesCS7B01G046500

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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 TraesCS7B01G046500 chr7B 100.000 2132 0 0 1 2132 45213998 45216129 0.000000e+00 3901
1 TraesCS7B01G046500 chr7B 94.503 764 42 0 1 764 45258201 45258964 0.000000e+00 1179
2 TraesCS7B01G046500 chr7B 93.099 768 49 3 1 765 178129290 178130056 0.000000e+00 1122
3 TraesCS7B01G046500 chr7B 93.081 766 49 3 1 764 350640958 350641721 0.000000e+00 1118
4 TraesCS7B01G046500 chr7B 96.728 489 13 3 1646 2132 45258968 45259455 0.000000e+00 811
5 TraesCS7B01G046500 chr7B 95.902 488 19 1 1646 2132 45251561 45252048 0.000000e+00 789
6 TraesCS7B01G046500 chr7B 94.082 490 26 2 1646 2132 146104648 146104159 0.000000e+00 741
7 TraesCS7B01G046500 chr7B 100.000 185 0 0 775 959 45215237 45215421 2.030000e-90 342
8 TraesCS7B01G046500 chrUn 99.112 676 6 0 970 1645 445811841 445812516 0.000000e+00 1216
9 TraesCS7B01G046500 chrUn 98.919 185 2 0 775 959 445812111 445812295 4.390000e-87 331
10 TraesCS7B01G046500 chr3B 99.112 676 6 0 970 1645 201514323 201513648 0.000000e+00 1216
11 TraesCS7B01G046500 chr3B 93.368 769 45 5 3 770 132726516 132727279 0.000000e+00 1133
12 TraesCS7B01G046500 chr3B 92.987 770 48 6 1 765 238532358 238531590 0.000000e+00 1118
13 TraesCS7B01G046500 chr3B 94.297 491 24 4 1646 2132 548381036 548380546 0.000000e+00 749
14 TraesCS7B01G046500 chr3B 99.459 185 1 0 775 959 201514590 201514406 9.430000e-89 337
15 TraesCS7B01G046500 chr3B 99.454 183 1 0 777 959 201514051 201513869 1.220000e-87 333
16 TraesCS7B01G046500 chr5D 97.932 677 12 2 970 1645 560873690 560873015 0.000000e+00 1171
17 TraesCS7B01G046500 chr5D 97.198 678 15 4 970 1645 6200060 6200735 0.000000e+00 1144
18 TraesCS7B01G046500 chr5D 96.898 677 19 2 970 1645 329163399 329162724 0.000000e+00 1133
19 TraesCS7B01G046500 chr5D 98.913 184 2 0 776 959 560873419 560873236 1.580000e-86 329
20 TraesCS7B01G046500 chr5D 98.907 183 2 0 777 959 6200333 6200515 5.670000e-86 327
21 TraesCS7B01G046500 chr5D 97.838 185 4 0 775 959 329163129 329162945 9.490000e-84 320
22 TraesCS7B01G046500 chr6B 97.337 676 18 0 970 1645 22427166 22426491 0.000000e+00 1149
23 TraesCS7B01G046500 chr6B 93.072 765 52 1 1 764 295785690 295786454 0.000000e+00 1118
24 TraesCS7B01G046500 chr1D 97.341 677 16 2 970 1645 254499220 254498545 0.000000e+00 1149
25 TraesCS7B01G046500 chr1D 98.919 185 2 0 775 959 254498950 254498766 4.390000e-87 331
26 TraesCS7B01G046500 chr1D 98.919 185 2 0 775 959 318665432 318665248 4.390000e-87 331
27 TraesCS7B01G046500 chr2B 93.464 765 50 0 1 765 697499186 697498422 0.000000e+00 1136
28 TraesCS7B01G046500 chr2B 92.996 771 51 3 1 769 154885758 154884989 0.000000e+00 1122
29 TraesCS7B01G046500 chr2B 94.309 492 21 6 1646 2132 66497310 66496821 0.000000e+00 747
30 TraesCS7B01G046500 chr1B 93.333 765 50 1 1 765 489051011 489051774 0.000000e+00 1129
31 TraesCS7B01G046500 chr1B 94.898 490 21 3 1646 2132 455345055 455345543 0.000000e+00 763
32 TraesCS7B01G046500 chr1B 94.286 490 25 2 1646 2132 82399862 82400351 0.000000e+00 747
33 TraesCS7B01G046500 chr4D 96.750 677 18 4 970 1645 19917715 19917042 0.000000e+00 1125
34 TraesCS7B01G046500 chr1A 96.603 677 20 3 970 1645 168449346 168450020 0.000000e+00 1120
35 TraesCS7B01G046500 chr4B 92.075 795 56 6 1 791 487847993 487848784 0.000000e+00 1112
36 TraesCS7B01G046500 chr5B 95.643 482 19 2 1652 2132 159636420 159635940 0.000000e+00 773
37 TraesCS7B01G046500 chr5B 94.262 488 26 2 1646 2132 316167872 316167386 0.000000e+00 745
38 TraesCS7B01G046500 chr3D 98.919 185 2 0 775 959 21905579 21905395 4.390000e-87 331


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 TraesCS7B01G046500 chr7B 45213998 45216129 2131 False 2121.500000 3901 100.000000 1 2132 2 chr7B.!!$F4 2131
1 TraesCS7B01G046500 chr7B 178129290 178130056 766 False 1122.000000 1122 93.099000 1 765 1 chr7B.!!$F2 764
2 TraesCS7B01G046500 chr7B 350640958 350641721 763 False 1118.000000 1118 93.081000 1 764 1 chr7B.!!$F3 763
3 TraesCS7B01G046500 chr7B 45258201 45259455 1254 False 995.000000 1179 95.615500 1 2132 2 chr7B.!!$F5 2131
4 TraesCS7B01G046500 chrUn 445811841 445812516 675 False 773.500000 1216 99.015500 775 1645 2 chrUn.!!$F1 870
5 TraesCS7B01G046500 chr3B 132726516 132727279 763 False 1133.000000 1133 93.368000 3 770 1 chr3B.!!$F1 767
6 TraesCS7B01G046500 chr3B 238531590 238532358 768 True 1118.000000 1118 92.987000 1 765 1 chr3B.!!$R1 764
7 TraesCS7B01G046500 chr3B 201513648 201514590 942 True 628.666667 1216 99.341667 775 1645 3 chr3B.!!$R3 870
8 TraesCS7B01G046500 chr5D 560873015 560873690 675 True 750.000000 1171 98.422500 776 1645 2 chr5D.!!$R2 869
9 TraesCS7B01G046500 chr5D 6200060 6200735 675 False 735.500000 1144 98.052500 777 1645 2 chr5D.!!$F1 868
10 TraesCS7B01G046500 chr5D 329162724 329163399 675 True 726.500000 1133 97.368000 775 1645 2 chr5D.!!$R1 870
11 TraesCS7B01G046500 chr6B 22426491 22427166 675 True 1149.000000 1149 97.337000 970 1645 1 chr6B.!!$R1 675
12 TraesCS7B01G046500 chr6B 295785690 295786454 764 False 1118.000000 1118 93.072000 1 764 1 chr6B.!!$F1 763
13 TraesCS7B01G046500 chr1D 254498545 254499220 675 True 740.000000 1149 98.130000 775 1645 2 chr1D.!!$R2 870
14 TraesCS7B01G046500 chr2B 697498422 697499186 764 True 1136.000000 1136 93.464000 1 765 1 chr2B.!!$R3 764
15 TraesCS7B01G046500 chr2B 154884989 154885758 769 True 1122.000000 1122 92.996000 1 769 1 chr2B.!!$R2 768
16 TraesCS7B01G046500 chr1B 489051011 489051774 763 False 1129.000000 1129 93.333000 1 765 1 chr1B.!!$F3 764
17 TraesCS7B01G046500 chr4D 19917042 19917715 673 True 1125.000000 1125 96.750000 970 1645 1 chr4D.!!$R1 675
18 TraesCS7B01G046500 chr1A 168449346 168450020 674 False 1120.000000 1120 96.603000 970 1645 1 chr1A.!!$F1 675
19 TraesCS7B01G046500 chr4B 487847993 487848784 791 False 1112.000000 1112 92.075000 1 791 1 chr4B.!!$F1 790

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
322 330 1.269621 CGTGTTCACTTTCCGGACTCT 60.27 52.381 1.83 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2142 0.24445 CAAATTGCCATGTCAGCCGT 59.756 50.0 0.0 0.0 0.0 5.68 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
103 104 1.338200 GCCACGAGGACTCAACAATCT 60.338 52.381 1.86 0.00 36.89 2.40
125 126 7.194112 TCTCATTACCATGGTTATCAAGACA 57.806 36.000 25.38 0.00 0.00 3.41
289 295 7.876068 TGATCCTGAAACTACTTACGTTCAAAT 59.124 33.333 0.00 0.00 0.00 2.32
322 330 1.269621 CGTGTTCACTTTCCGGACTCT 60.270 52.381 1.83 0.00 0.00 3.24
399 407 4.649674 TCTGGTGTCAAGTTCTCTACAACT 59.350 41.667 0.00 0.00 38.30 3.16
642 650 4.185467 CGATAGGAGCTGCACATATCTT 57.815 45.455 22.52 3.57 31.60 2.40
687 695 5.651139 TGAGACTAGCTACGAGTAAAACCAT 59.349 40.000 0.00 0.00 0.00 3.55
1469 1550 2.495155 ACAATGTGTATCAGGCTGCA 57.505 45.000 10.34 1.42 0.00 4.41
1530 1611 3.094572 CCAAATTCCACTTGAGCATCCT 58.905 45.455 0.00 0.00 0.00 3.24
1562 1643 5.000591 TCAATACCAGCAAAAACATCTCGA 58.999 37.500 0.00 0.00 0.00 4.04
1664 1745 5.022787 CCCCAAATAAAGATGACCCTCAAA 58.977 41.667 0.00 0.00 0.00 2.69
1679 1760 1.207593 CAAAAGCGCGACTCCCAAG 59.792 57.895 12.10 0.00 0.00 3.61
1733 1814 2.677875 GTTGGGCCTTGCTGGAGG 60.678 66.667 4.53 0.00 39.93 4.30
1786 1867 1.091537 CATAAATCACCCAACCGCGT 58.908 50.000 4.92 0.00 0.00 6.01
1816 1897 4.621034 CGCAAAATCAAGGAACATAACACC 59.379 41.667 0.00 0.00 0.00 4.16
1835 1916 4.529377 ACACCGGTATGAAAGAAACTAGGA 59.471 41.667 6.87 0.00 0.00 2.94
1977 2058 4.580167 TGGAACAATCTTCAACTTCACCTG 59.420 41.667 0.00 0.00 31.92 4.00
1998 2079 5.005779 CCTGCAACTAACAACGCTATAAGAG 59.994 44.000 0.00 0.00 0.00 2.85
2000 2081 4.270325 GCAACTAACAACGCTATAAGAGGG 59.730 45.833 0.00 0.00 43.73 4.30
2002 2083 4.284178 ACTAACAACGCTATAAGAGGGGA 58.716 43.478 0.00 0.00 42.42 4.81
2003 2084 4.900054 ACTAACAACGCTATAAGAGGGGAT 59.100 41.667 0.00 0.00 42.42 3.85
2004 2085 3.753294 ACAACGCTATAAGAGGGGATG 57.247 47.619 0.00 0.00 42.42 3.51
2005 2086 3.305720 ACAACGCTATAAGAGGGGATGA 58.694 45.455 0.00 0.00 42.42 2.92
2006 2087 3.322254 ACAACGCTATAAGAGGGGATGAG 59.678 47.826 0.00 0.00 42.42 2.90
2007 2088 1.896465 ACGCTATAAGAGGGGATGAGC 59.104 52.381 0.00 0.00 42.42 4.26
2011 2094 2.947127 ATAAGAGGGGATGAGCAAGC 57.053 50.000 0.00 0.00 0.00 4.01
2024 2107 2.232696 TGAGCAAGCGGTAACATAGTCA 59.767 45.455 0.00 0.00 0.00 3.41
2030 2113 3.873910 AGCGGTAACATAGTCAAGCAAT 58.126 40.909 0.00 0.00 0.00 3.56
2059 2142 5.074804 GCTAGGAAGGGTGAAAAAGGTTAA 58.925 41.667 0.00 0.00 0.00 2.01
2062 2145 3.005050 GGAAGGGTGAAAAAGGTTAACGG 59.995 47.826 0.00 0.00 0.00 4.44
2083 2166 2.675889 GCTGACATGGCAATTTGGAAGG 60.676 50.000 1.11 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 6.318648 GCTTGTCTTGATAACCATGGTAATGA 59.681 38.462 20.12 9.20 35.67 2.57
175 178 3.652057 AGCCACCACATATGCTTAGTT 57.348 42.857 1.58 0.00 0.00 2.24
236 240 4.063998 TGATCATTGCTAGCTTCACGAT 57.936 40.909 17.23 10.37 0.00 3.73
322 330 0.904865 ATGGTGGTCTCTTCTCGGCA 60.905 55.000 0.00 0.00 0.00 5.69
399 407 8.324306 TGGCAAATGGAAATTTGTTAATATCCA 58.676 29.630 11.60 0.00 42.02 3.41
427 435 4.430765 AGTCGTGCCCGCGGTTAG 62.431 66.667 26.12 10.30 0.00 2.34
642 650 0.321564 CCGATGTTGCCCTGAGAACA 60.322 55.000 0.00 0.00 36.54 3.18
687 695 1.198759 CCTCGGGGAAACTTGAGGGA 61.199 60.000 0.00 0.00 43.53 4.20
1469 1550 5.501156 GGAGATCCAACTACAAGGAAACAT 58.499 41.667 0.00 0.00 37.48 2.71
1562 1643 2.415893 GCATGGCGCTAGAACATTGTTT 60.416 45.455 7.64 0.00 37.77 2.83
1664 1745 4.394712 CCCTTGGGAGTCGCGCTT 62.395 66.667 5.56 0.00 0.00 4.68
1679 1760 1.955683 GCCTCACCTAGCCTTTTTCCC 60.956 57.143 0.00 0.00 0.00 3.97
1733 1814 6.427150 TGACAGTTCGCTTTGAATAAAACTC 58.573 36.000 0.00 0.00 39.21 3.01
1786 1867 3.426787 TCCTTGATTTTGCGTCCCTTA 57.573 42.857 0.00 0.00 0.00 2.69
1816 1897 4.110482 CCGTCCTAGTTTCTTTCATACCG 58.890 47.826 0.00 0.00 0.00 4.02
1835 1916 1.404035 GTTTTGTTCCACTCTTGCCGT 59.596 47.619 0.00 0.00 0.00 5.68
1977 2058 4.270325 CCCTCTTATAGCGTTGTTAGTTGC 59.730 45.833 0.00 0.00 0.00 4.17
1998 2079 1.095807 GTTACCGCTTGCTCATCCCC 61.096 60.000 0.00 0.00 0.00 4.81
2000 2081 1.668419 ATGTTACCGCTTGCTCATCC 58.332 50.000 0.00 0.00 0.00 3.51
2002 2083 3.118775 TGACTATGTTACCGCTTGCTCAT 60.119 43.478 0.00 0.00 0.00 2.90
2003 2084 2.232696 TGACTATGTTACCGCTTGCTCA 59.767 45.455 0.00 0.00 0.00 4.26
2004 2085 2.888594 TGACTATGTTACCGCTTGCTC 58.111 47.619 0.00 0.00 0.00 4.26
2005 2086 3.262420 CTTGACTATGTTACCGCTTGCT 58.738 45.455 0.00 0.00 0.00 3.91
2006 2087 2.223044 GCTTGACTATGTTACCGCTTGC 60.223 50.000 0.00 0.00 0.00 4.01
2007 2088 3.000041 TGCTTGACTATGTTACCGCTTG 59.000 45.455 0.00 0.00 0.00 4.01
2011 2094 3.938963 ACCATTGCTTGACTATGTTACCG 59.061 43.478 0.00 0.00 30.48 4.02
2030 2113 1.440618 TCACCCTTCCTAGCAAACCA 58.559 50.000 0.00 0.00 0.00 3.67
2059 2142 0.244450 CAAATTGCCATGTCAGCCGT 59.756 50.000 0.00 0.00 0.00 5.68
2062 2145 2.613691 CTTCCAAATTGCCATGTCAGC 58.386 47.619 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.