Multiple sequence alignment - TraesCS1B01G220500

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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 TraesCS1B01G220500 chr1B 100.000 2423 0 0 1 2423 397457657 397455235 0.000000e+00 4475.0
1 TraesCS1B01G220500 chr1B 94.203 276 12 3 1009 1284 626422252 626421981 3.730000e-113 418.0
2 TraesCS1B01G220500 chr3B 98.584 777 11 0 1647 2423 52833111 52832335 0.000000e+00 1375.0
3 TraesCS1B01G220500 chr3B 85.990 207 21 8 635 839 697457031 697457231 5.250000e-52 215.0
4 TraesCS1B01G220500 chr3B 90.909 110 9 1 1644 1752 400329799 400329908 1.940000e-31 147.0
5 TraesCS1B01G220500 chr1D 95.808 811 18 6 841 1644 295974109 295973308 0.000000e+00 1295.0
6 TraesCS1B01G220500 chr1D 91.914 841 59 8 1 839 295976284 295975451 0.000000e+00 1168.0
7 TraesCS1B01G220500 chr1D 87.940 199 21 2 643 839 282409992 282410189 5.210000e-57 231.0
8 TraesCS1B01G220500 chr1A 92.243 838 58 6 1 835 368834525 368833692 0.000000e+00 1181.0
9 TraesCS1B01G220500 chr1A 92.374 813 23 9 841 1647 368832470 368831691 0.000000e+00 1122.0
10 TraesCS1B01G220500 chr1A 88.021 192 21 2 632 823 161823213 161823402 2.420000e-55 226.0
11 TraesCS1B01G220500 chr7A 92.356 798 28 6 1647 2423 508021296 508022081 0.000000e+00 1105.0
12 TraesCS1B01G220500 chr7A 84.318 440 27 13 1647 2077 38918818 38918412 2.260000e-105 392.0
13 TraesCS1B01G220500 chr7A 89.873 158 11 5 2063 2216 38918384 38918228 5.280000e-47 198.0
14 TraesCS1B01G220500 chr7A 96.809 94 3 0 2330 2423 38918213 38918120 8.970000e-35 158.0
15 TraesCS1B01G220500 chr6A 92.491 799 16 8 1647 2423 176997708 176996932 0.000000e+00 1103.0
16 TraesCS1B01G220500 chr5A 90.482 809 30 15 1646 2423 611836551 611837343 0.000000e+00 1024.0
17 TraesCS1B01G220500 chr5A 86.767 665 35 17 1789 2423 6560886 6560245 0.000000e+00 691.0
18 TraesCS1B01G220500 chr6D 94.184 533 8 4 1646 2177 410079487 410079997 0.000000e+00 791.0
19 TraesCS1B01G220500 chr7B 94.977 219 11 0 1066 1284 643383731 643383513 6.410000e-91 344.0
20 TraesCS1B01G220500 chr3D 89.020 255 6 9 2190 2423 575139115 575139368 1.820000e-76 296.0
21 TraesCS1B01G220500 chr3A 87.374 198 22 3 631 828 68145999 68146193 8.720000e-55 224.0
22 TraesCS1B01G220500 chr3A 85.990 207 22 7 635 839 247695343 247695544 5.250000e-52 215.0
23 TraesCS1B01G220500 chr3A 86.000 200 25 3 619 817 262533353 262533550 6.790000e-51 211.0
24 TraesCS1B01G220500 chr7D 95.035 141 7 0 1647 1787 495329357 495329217 3.140000e-54 222.0
25 TraesCS1B01G220500 chr4B 87.831 189 20 3 635 823 581785128 581784943 4.060000e-53 219.0
26 TraesCS1B01G220500 chr4A 94.318 88 5 0 2336 2423 580138679 580138592 4.200000e-28 135.0
27 TraesCS1B01G220500 chr5B 88.889 108 11 1 1647 1754 309359524 309359630 5.440000e-27 132.0
28 TraesCS1B01G220500 chr6B 90.698 43 2 2 1129 1171 656486550 656486510 3.370000e-04 56.5


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 TraesCS1B01G220500 chr1B 397455235 397457657 2422 True 4475.000000 4475 100.000000 1 2423 1 chr1B.!!$R1 2422
1 TraesCS1B01G220500 chr3B 52832335 52833111 776 True 1375.000000 1375 98.584000 1647 2423 1 chr3B.!!$R1 776
2 TraesCS1B01G220500 chr1D 295973308 295976284 2976 True 1231.500000 1295 93.861000 1 1644 2 chr1D.!!$R1 1643
3 TraesCS1B01G220500 chr1A 368831691 368834525 2834 True 1151.500000 1181 92.308500 1 1647 2 chr1A.!!$R1 1646
4 TraesCS1B01G220500 chr7A 508021296 508022081 785 False 1105.000000 1105 92.356000 1647 2423 1 chr7A.!!$F1 776
5 TraesCS1B01G220500 chr7A 38918120 38918818 698 True 249.333333 392 90.333333 1647 2423 3 chr7A.!!$R1 776
6 TraesCS1B01G220500 chr6A 176996932 176997708 776 True 1103.000000 1103 92.491000 1647 2423 1 chr6A.!!$R1 776
7 TraesCS1B01G220500 chr5A 611836551 611837343 792 False 1024.000000 1024 90.482000 1646 2423 1 chr5A.!!$F1 777
8 TraesCS1B01G220500 chr5A 6560245 6560886 641 True 691.000000 691 86.767000 1789 2423 1 chr5A.!!$R1 634
9 TraesCS1B01G220500 chr6D 410079487 410079997 510 False 791.000000 791 94.184000 1646 2177 1 chr6D.!!$F1 531

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
916 2585 0.322906 CCAACCCAAGAAGCTCCCTC 60.323 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 3825 1.688269 GGCAGCAGCTCCTCATCTCT 61.688 60.0 0.0 0.0 41.7 3.1 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
41 42 7.081349 CCTCAACGCAAACTGTATCAAAATTA 58.919 34.615 0.00 0.00 0.00 1.40
96 97 2.663188 CGGCTTCAGCTATCGCCC 60.663 66.667 12.17 0.00 39.34 6.13
107 108 2.088674 CTATCGCCCCTTGGACCTCG 62.089 65.000 0.00 0.00 0.00 4.63
111 112 3.330720 CCCCTTGGACCTCGCCTT 61.331 66.667 0.00 0.00 0.00 4.35
112 113 2.757077 CCCTTGGACCTCGCCTTT 59.243 61.111 0.00 0.00 0.00 3.11
146 148 4.526970 ACAATTACATTTCGAGGATGGCT 58.473 39.130 13.36 0.00 0.00 4.75
158 160 0.811616 GGATGGCTCGTGCTAGGTTG 60.812 60.000 9.61 0.00 39.59 3.77
166 168 3.390135 CTCGTGCTAGGTTGAAAGACAA 58.610 45.455 0.00 0.00 36.02 3.18
284 286 3.576982 CCAACACAACACTACTCCCTCTA 59.423 47.826 0.00 0.00 0.00 2.43
298 301 5.574188 ACTCCCTCTATGTTTGAAATGCTT 58.426 37.500 0.00 0.00 0.00 3.91
323 326 9.902684 TTGTTTTTGGGATATTTATACGGTCTA 57.097 29.630 0.00 0.00 0.00 2.59
377 380 9.357652 ACATTGCAATATTGTAAGTTTGATGTC 57.642 29.630 21.12 0.60 36.26 3.06
446 449 5.405269 GGTTGACCAATGCAATTTCTACAAC 59.595 40.000 0.00 0.00 31.22 3.32
473 476 9.185192 GAGTAACATTTTGAAAAGGAATGAGTG 57.815 33.333 9.45 0.00 35.36 3.51
477 480 8.017418 ACATTTTGAAAAGGAATGAGTGGTAA 57.983 30.769 9.45 0.00 35.36 2.85
489 492 6.940867 GGAATGAGTGGTAATAGATTTACCCC 59.059 42.308 11.05 1.28 42.84 4.95
533 536 8.948631 ATACTAACACAATTCATGAGATTCGT 57.051 30.769 0.00 0.00 0.00 3.85
660 663 9.063615 GGAGAAATTTTGTTTCTACCACTCTAA 57.936 33.333 3.26 0.00 38.73 2.10
675 678 7.495135 ACCACTCTAATTTTTGCCAATTTTG 57.505 32.000 0.00 0.00 0.00 2.44
701 704 4.771590 TGCCACTCTCAAATTTGACATC 57.228 40.909 16.91 4.44 32.90 3.06
750 753 8.108551 TGACAATGTATCACAATTGACATTCA 57.891 30.769 13.59 9.73 33.38 2.57
796 799 5.063180 AGTGGCAATTGTGATACATTGTG 57.937 39.130 7.40 0.00 0.00 3.33
806 809 8.970691 ATTGTGATACATTGTGAAAAGCTAAC 57.029 30.769 0.00 0.00 0.00 2.34
824 828 9.869757 AAAGCTAACAGTGACAAAAGTAAAAAT 57.130 25.926 0.00 0.00 0.00 1.82
865 2534 2.364780 CGTTCCCTCCACTACCCCC 61.365 68.421 0.00 0.00 0.00 5.40
915 2584 1.068352 ACCAACCCAAGAAGCTCCCT 61.068 55.000 0.00 0.00 0.00 4.20
916 2585 0.322906 CCAACCCAAGAAGCTCCCTC 60.323 60.000 0.00 0.00 0.00 4.30
917 2586 0.695347 CAACCCAAGAAGCTCCCTCT 59.305 55.000 0.00 0.00 0.00 3.69
918 2587 0.988063 AACCCAAGAAGCTCCCTCTC 59.012 55.000 0.00 0.00 0.00 3.20
919 2588 0.912006 ACCCAAGAAGCTCCCTCTCC 60.912 60.000 0.00 0.00 0.00 3.71
920 2589 0.620121 CCCAAGAAGCTCCCTCTCCT 60.620 60.000 0.00 0.00 0.00 3.69
921 2590 0.540923 CCAAGAAGCTCCCTCTCCTG 59.459 60.000 0.00 0.00 0.00 3.86
1125 2801 1.412361 GGAGTAGCAGGAGGAGTGGAT 60.412 57.143 0.00 0.00 0.00 3.41
1355 3031 4.083862 GCCGCCCGAGAAGAAGGT 62.084 66.667 0.00 0.00 0.00 3.50
1644 3323 2.626266 CTGTATGTGATACCCCGTAGCA 59.374 50.000 0.00 0.00 34.86 3.49
1784 3465 3.043419 CCCATCTACTCCCGAGCG 58.957 66.667 0.00 0.00 0.00 5.03
1785 3466 1.528542 CCCATCTACTCCCGAGCGA 60.529 63.158 0.00 0.00 0.00 4.93
2018 3725 2.124403 GCCTGGCTGGTGGATCTG 60.124 66.667 12.43 0.00 38.35 2.90
2113 3862 1.553706 CCCAAGCTTCTGAATGGCTT 58.446 50.000 10.15 10.15 45.57 4.35
2152 3901 1.153127 TTCGTGACGCCCTTTGGTT 60.153 52.632 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.608035 GTTTGCGTTGAGGGGGATGA 60.608 55.000 0.00 0.00 0.00 2.92
41 42 6.173339 TCAAACTCTCGAGCAAAAGGATTAT 58.827 36.000 7.81 0.00 0.00 1.28
54 55 2.555325 TCCGTAAAGCTCAAACTCTCGA 59.445 45.455 0.00 0.00 0.00 4.04
55 56 2.942710 TCCGTAAAGCTCAAACTCTCG 58.057 47.619 0.00 0.00 0.00 4.04
96 97 1.675641 CCAAAGGCGAGGTCCAAGG 60.676 63.158 0.00 0.00 0.00 3.61
108 109 0.958091 TTGTCAATCCGTGCCAAAGG 59.042 50.000 0.00 0.00 0.00 3.11
110 111 3.570125 TGTAATTGTCAATCCGTGCCAAA 59.430 39.130 0.00 0.00 0.00 3.28
111 112 3.149981 TGTAATTGTCAATCCGTGCCAA 58.850 40.909 0.00 0.00 0.00 4.52
112 113 2.784347 TGTAATTGTCAATCCGTGCCA 58.216 42.857 0.00 0.00 0.00 4.92
116 117 5.064707 CCTCGAAATGTAATTGTCAATCCGT 59.935 40.000 0.00 0.00 36.10 4.69
124 125 4.526970 AGCCATCCTCGAAATGTAATTGT 58.473 39.130 6.68 0.00 36.10 2.71
146 148 3.390135 CTTGTCTTTCAACCTAGCACGA 58.610 45.455 0.00 0.00 32.18 4.35
158 160 7.321153 TGTAGTAGATAGTTGCCTTGTCTTTC 58.679 38.462 0.00 0.00 0.00 2.62
166 168 8.100791 TGAACAAATTGTAGTAGATAGTTGCCT 58.899 33.333 0.00 0.00 0.00 4.75
199 201 0.947244 CTTGACGCTTTGCCAGACTT 59.053 50.000 0.00 0.00 0.00 3.01
201 203 0.040958 CACTTGACGCTTTGCCAGAC 60.041 55.000 0.00 0.00 0.00 3.51
257 259 5.250774 AGGGAGTAGTGTTGTGTTGGAATAT 59.749 40.000 0.00 0.00 0.00 1.28
284 286 5.884792 TCCCAAAAACAAGCATTTCAAACAT 59.115 32.000 0.00 0.00 0.00 2.71
298 301 9.328845 GTAGACCGTATAAATATCCCAAAAACA 57.671 33.333 0.00 0.00 0.00 2.83
377 380 5.528690 TCCAGAAGAGTTGTCAACATTGAAG 59.471 40.000 17.78 3.81 39.21 3.02
446 449 8.076178 ACTCATTCCTTTTCAAAATGTTACTCG 58.924 33.333 0.00 0.00 33.22 4.18
619 622 9.118236 CAAAATTTCTCCTTTCAGTTTCGATAC 57.882 33.333 0.00 0.00 0.00 2.24
624 627 9.371136 AGAAACAAAATTTCTCCTTTCAGTTTC 57.629 29.630 0.00 0.00 38.76 2.78
660 663 5.243283 TGGCATAAGCAAAATTGGCAAAAAT 59.757 32.000 3.01 0.00 44.61 1.82
661 664 4.581824 TGGCATAAGCAAAATTGGCAAAAA 59.418 33.333 3.01 0.00 44.61 1.94
675 678 5.098211 GTCAAATTTGAGAGTGGCATAAGC 58.902 41.667 21.05 1.30 37.98 3.09
701 704 8.567948 TCAAAATCTAAGAGTGGCAAAAGTTAG 58.432 33.333 0.00 0.00 0.00 2.34
768 771 6.925610 TGTATCACAATTGCCACTCTAATC 57.074 37.500 5.05 0.00 0.00 1.75
772 775 5.012239 ACAATGTATCACAATTGCCACTCT 58.988 37.500 5.05 0.00 0.00 3.24
796 799 8.905103 TTTACTTTTGTCACTGTTAGCTTTTC 57.095 30.769 0.00 0.00 0.00 2.29
839 843 3.839432 GGAGGGAACGAGGGAGCG 61.839 72.222 0.00 0.00 37.29 5.03
915 2584 2.652348 AGAAGGAAGAGGAGACAGGAGA 59.348 50.000 0.00 0.00 0.00 3.71
916 2585 3.100207 AGAAGGAAGAGGAGACAGGAG 57.900 52.381 0.00 0.00 0.00 3.69
917 2586 3.436243 GAAGAAGGAAGAGGAGACAGGA 58.564 50.000 0.00 0.00 0.00 3.86
918 2587 2.499693 GGAAGAAGGAAGAGGAGACAGG 59.500 54.545 0.00 0.00 0.00 4.00
919 2588 3.440127 AGGAAGAAGGAAGAGGAGACAG 58.560 50.000 0.00 0.00 0.00 3.51
920 2589 3.551635 AGGAAGAAGGAAGAGGAGACA 57.448 47.619 0.00 0.00 0.00 3.41
921 2590 4.093743 AGAAGGAAGAAGGAAGAGGAGAC 58.906 47.826 0.00 0.00 0.00 3.36
1296 2972 3.731653 GAAGAGGCGCTCCAGCTCC 62.732 68.421 7.64 0.00 45.80 4.70
1355 3031 4.986645 TGCGGCGCTTGAGCTTGA 62.987 61.111 33.26 5.98 39.32 3.02
1428 3104 2.566529 CAGACGCACGTCCTGCTA 59.433 61.111 18.81 0.00 45.59 3.49
1644 3323 2.045340 GCTGGGTACGCCAATGGT 60.045 61.111 7.55 0.00 36.17 3.55
1935 3641 1.767692 GGTGGAAGGAGGCAAGGAA 59.232 57.895 0.00 0.00 0.00 3.36
2076 3825 1.688269 GGCAGCAGCTCCTCATCTCT 61.688 60.000 0.00 0.00 41.70 3.10
2113 3862 5.453339 CGAACTAGGAATTCAGCAGGGATTA 60.453 44.000 7.93 0.00 0.00 1.75
2152 3901 2.727123 TGACAGAAGCTCACCCAAAA 57.273 45.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.