Multiple sequence alignment - TraesCS5A01G004300

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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 TraesCS5A01G004300 chr5A 100.000 7756 0 0 1 7756 2977325 2969570 0.000000e+00 14323.0
1 TraesCS5A01G004300 chr5A 98.835 3520 18 3 3179 6693 2897390 2893889 0.000000e+00 6252.0
2 TraesCS5A01G004300 chr5A 99.792 2406 5 0 789 3194 2899813 2897408 0.000000e+00 4416.0
3 TraesCS5A01G004300 chr5A 97.637 1058 17 4 6704 7756 24348047 24346993 0.000000e+00 1808.0
4 TraesCS5A01G004300 chr5A 97.450 1059 18 5 6704 7756 704856657 704855602 0.000000e+00 1797.0
5 TraesCS5A01G004300 chr5A 96.742 890 27 1 1 888 2984293 2983404 0.000000e+00 1482.0
6 TraesCS5A01G004300 chr5A 95.833 96 4 0 4961 5056 605313485 605313390 1.040000e-33 156.0
7 TraesCS5A01G004300 chr5A 94.000 100 6 0 1458 1557 699483282 699483183 1.350000e-32 152.0
8 TraesCS5A01G004300 chr5D 92.924 2459 102 31 4250 6693 7016637 7014236 0.000000e+00 3511.0
9 TraesCS5A01G004300 chr5D 92.528 1606 88 20 2214 3795 7018743 7017146 0.000000e+00 2272.0
10 TraesCS5A01G004300 chr5D 85.138 942 56 43 899 1803 7019971 7019077 0.000000e+00 887.0
11 TraesCS5A01G004300 chr5D 87.569 362 28 8 3798 4142 7017069 7016708 3.370000e-108 403.0
12 TraesCS5A01G004300 chr5D 93.796 274 8 4 1913 2183 7019094 7018827 3.370000e-108 403.0
13 TraesCS5A01G004300 chr5D 82.787 122 1 9 903 1024 7031214 7031113 2.980000e-14 91.6
14 TraesCS5A01G004300 chrUn 91.368 1842 102 31 1986 3795 65426681 65428497 0.000000e+00 2468.0
15 TraesCS5A01G004300 chrUn 91.228 1482 87 29 5024 6488 65429580 65431035 0.000000e+00 1977.0
16 TraesCS5A01G004300 chrUn 96.742 890 27 1 1 888 358494697 358495586 0.000000e+00 1482.0
17 TraesCS5A01G004300 chrUn 96.629 890 28 1 1 888 358496813 358497702 0.000000e+00 1476.0
18 TraesCS5A01G004300 chrUn 95.338 665 26 1 4262 4921 65428923 65429587 0.000000e+00 1051.0
19 TraesCS5A01G004300 chrUn 84.668 587 53 19 6090 6657 146275919 146276487 1.140000e-152 551.0
20 TraesCS5A01G004300 chrUn 95.273 275 9 1 1291 1561 65426056 65426330 4.300000e-117 433.0
21 TraesCS5A01G004300 chrUn 83.696 460 24 22 899 1337 65425536 65425965 3.390000e-103 387.0
22 TraesCS5A01G004300 chrUn 92.126 254 13 2 3896 4142 65428630 65428883 1.240000e-92 351.0
23 TraesCS5A01G004300 chrUn 88.776 196 5 4 1560 1755 65426364 65426542 2.820000e-54 224.0
24 TraesCS5A01G004300 chr3A 97.545 1059 17 5 6704 7756 670643349 670642294 0.000000e+00 1803.0
25 TraesCS5A01G004300 chr3A 96.875 96 3 0 4961 5056 11851851 11851946 2.240000e-35 161.0
26 TraesCS5A01G004300 chr2A 97.450 1059 19 5 6704 7756 79528213 79529269 0.000000e+00 1799.0
27 TraesCS5A01G004300 chr2A 97.538 1056 17 5 6707 7756 11210931 11209879 0.000000e+00 1797.0
28 TraesCS5A01G004300 chr2A 96.738 889 27 1 1 887 337886689 337887577 0.000000e+00 1480.0
29 TraesCS5A01G004300 chr6A 97.450 1059 18 5 6704 7756 3110133 3109078 0.000000e+00 1797.0
30 TraesCS5A01G004300 chr6A 96.850 889 26 1 2 888 287127401 287128289 0.000000e+00 1485.0
31 TraesCS5A01G004300 chr1A 97.450 1059 18 6 6704 7756 507679179 507678124 0.000000e+00 1797.0
32 TraesCS5A01G004300 chr1A 96.742 890 27 1 1 888 215577274 215578163 0.000000e+00 1482.0
33 TraesCS5A01G004300 chr1A 96.536 895 28 2 1 892 214382977 214383871 0.000000e+00 1478.0
34 TraesCS5A01G004300 chr1A 96.629 890 28 1 1 888 216498958 216499847 0.000000e+00 1476.0
35 TraesCS5A01G004300 chr7A 97.356 1059 20 5 6704 7756 28127040 28128096 0.000000e+00 1794.0
36 TraesCS5A01G004300 chr7A 93.846 130 8 0 1428 1557 96570438 96570309 6.140000e-46 196.0
37 TraesCS5A01G004300 chr4A 97.353 1058 20 5 6704 7756 623381499 623380445 0.000000e+00 1792.0
38 TraesCS5A01G004300 chr4A 96.742 890 27 1 1 888 38018037 38018926 0.000000e+00 1482.0
39 TraesCS5A01G004300 chr4A 77.415 735 126 26 2261 2968 590185337 590184616 1.210000e-107 401.0
40 TraesCS5A01G004300 chr4A 76.396 788 132 34 5698 6435 590181905 590181122 7.350000e-100 375.0
41 TraesCS5A01G004300 chr4A 78.016 373 58 16 5206 5565 590114276 590113915 6.100000e-51 213.0
42 TraesCS5A01G004300 chr4A 79.897 194 39 0 5705 5898 590113802 590113609 8.110000e-30 143.0
43 TraesCS5A01G004300 chr4A 88.043 92 11 0 5206 5297 590182400 590182309 8.230000e-20 110.0
44 TraesCS5A01G004300 chr4D 75.386 1361 237 74 2263 3580 12460006 12461311 1.130000e-157 568.0
45 TraesCS5A01G004300 chr4D 87.075 147 19 0 1988 2134 12459746 12459892 4.810000e-37 167.0
46 TraesCS5A01G004300 chr4D 80.597 201 39 0 5698 5898 12463464 12463664 1.040000e-33 156.0
47 TraesCS5A01G004300 chr4D 87.778 90 11 0 5208 5297 12462942 12463031 1.060000e-18 106.0
48 TraesCS5A01G004300 chr4B 75.321 778 144 31 5698 6435 22734077 22733308 5.800000e-86 329.0
49 TraesCS5A01G004300 chr4B 85.887 248 35 0 4546 4793 23011354 23011107 1.660000e-66 265.0
50 TraesCS5A01G004300 chr4B 80.597 201 39 0 5698 5898 23010199 23009999 1.040000e-33 156.0
51 TraesCS5A01G004300 chr4B 94.505 91 5 0 1458 1548 660120276 660120186 2.920000e-29 141.0
52 TraesCS5A01G004300 chr7D 93.077 130 9 0 1428 1557 93791602 93791473 2.860000e-44 191.0
53 TraesCS5A01G004300 chr7B 93.077 130 9 0 1428 1557 47003574 47003445 2.860000e-44 191.0
54 TraesCS5A01G004300 chr7B 96.875 96 3 0 4961 5056 11439020 11439115 2.240000e-35 161.0
55 TraesCS5A01G004300 chr2D 96.875 96 3 0 4961 5056 220629259 220629354 2.240000e-35 161.0
56 TraesCS5A01G004300 chr2B 96.875 96 3 0 4961 5056 73978959 73979054 2.240000e-35 161.0
57 TraesCS5A01G004300 chr1D 96.875 96 3 0 4961 5056 4547597 4547502 2.240000e-35 161.0
58 TraesCS5A01G004300 chr5B 84.615 78 9 3 1296 1371 702243819 702243743 3.000000e-09 75.0


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 TraesCS5A01G004300 chr5A 2969570 2977325 7755 True 14323.000000 14323 100.0000 1 7756 1 chr5A.!!$R1 7755
1 TraesCS5A01G004300 chr5A 2893889 2899813 5924 True 5334.000000 6252 99.3135 789 6693 2 chr5A.!!$R7 5904
2 TraesCS5A01G004300 chr5A 24346993 24348047 1054 True 1808.000000 1808 97.6370 6704 7756 1 chr5A.!!$R3 1052
3 TraesCS5A01G004300 chr5A 704855602 704856657 1055 True 1797.000000 1797 97.4500 6704 7756 1 chr5A.!!$R6 1052
4 TraesCS5A01G004300 chr5A 2983404 2984293 889 True 1482.000000 1482 96.7420 1 888 1 chr5A.!!$R2 887
5 TraesCS5A01G004300 chr5D 7014236 7019971 5735 True 1495.200000 3511 90.3910 899 6693 5 chr5D.!!$R2 5794
6 TraesCS5A01G004300 chrUn 358494697 358497702 3005 False 1479.000000 1482 96.6855 1 888 2 chrUn.!!$F3 887
7 TraesCS5A01G004300 chrUn 65425536 65431035 5499 False 984.428571 2468 91.1150 899 6488 7 chrUn.!!$F2 5589
8 TraesCS5A01G004300 chrUn 146275919 146276487 568 False 551.000000 551 84.6680 6090 6657 1 chrUn.!!$F1 567
9 TraesCS5A01G004300 chr3A 670642294 670643349 1055 True 1803.000000 1803 97.5450 6704 7756 1 chr3A.!!$R1 1052
10 TraesCS5A01G004300 chr2A 79528213 79529269 1056 False 1799.000000 1799 97.4500 6704 7756 1 chr2A.!!$F1 1052
11 TraesCS5A01G004300 chr2A 11209879 11210931 1052 True 1797.000000 1797 97.5380 6707 7756 1 chr2A.!!$R1 1049
12 TraesCS5A01G004300 chr2A 337886689 337887577 888 False 1480.000000 1480 96.7380 1 887 1 chr2A.!!$F2 886
13 TraesCS5A01G004300 chr6A 3109078 3110133 1055 True 1797.000000 1797 97.4500 6704 7756 1 chr6A.!!$R1 1052
14 TraesCS5A01G004300 chr6A 287127401 287128289 888 False 1485.000000 1485 96.8500 2 888 1 chr6A.!!$F1 886
15 TraesCS5A01G004300 chr1A 507678124 507679179 1055 True 1797.000000 1797 97.4500 6704 7756 1 chr1A.!!$R1 1052
16 TraesCS5A01G004300 chr1A 215577274 215578163 889 False 1482.000000 1482 96.7420 1 888 1 chr1A.!!$F2 887
17 TraesCS5A01G004300 chr1A 214382977 214383871 894 False 1478.000000 1478 96.5360 1 892 1 chr1A.!!$F1 891
18 TraesCS5A01G004300 chr1A 216498958 216499847 889 False 1476.000000 1476 96.6290 1 888 1 chr1A.!!$F3 887
19 TraesCS5A01G004300 chr7A 28127040 28128096 1056 False 1794.000000 1794 97.3560 6704 7756 1 chr7A.!!$F1 1052
20 TraesCS5A01G004300 chr4A 623380445 623381499 1054 True 1792.000000 1792 97.3530 6704 7756 1 chr4A.!!$R1 1052
21 TraesCS5A01G004300 chr4A 38018037 38018926 889 False 1482.000000 1482 96.7420 1 888 1 chr4A.!!$F1 887
22 TraesCS5A01G004300 chr4A 590181122 590185337 4215 True 295.333333 401 80.6180 2261 6435 3 chr4A.!!$R3 4174
23 TraesCS5A01G004300 chr4D 12459746 12463664 3918 False 249.250000 568 82.7090 1988 5898 4 chr4D.!!$F1 3910
24 TraesCS5A01G004300 chr4B 22733308 22734077 769 True 329.000000 329 75.3210 5698 6435 1 chr4B.!!$R1 737
25 TraesCS5A01G004300 chr4B 23009999 23011354 1355 True 210.500000 265 83.2420 4546 5898 2 chr4B.!!$R3 1352

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
583 584 1.251251 GTCCAAGGCTTCATGCACTT 58.749 50.000 0.00 0.0 45.15 3.16 F
639 640 3.170717 TGTAACTCCGTTCTTGATCCCT 58.829 45.455 0.00 0.0 0.00 4.20 F
722 723 4.286808 AGGCCCTTCATTTGTAAGCAAAAT 59.713 37.500 0.00 0.0 46.23 1.82 F
4297 6085 0.036732 TCAGCTCGCCATTGGAAAGT 59.963 50.000 6.95 0.0 0.00 2.66 F
4298 6086 0.449388 CAGCTCGCCATTGGAAAGTC 59.551 55.000 6.95 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2747 4137 2.031163 GCCGTCAGAACCTGCACT 59.969 61.111 0.00 0.0 0.00 4.40 R
3928 5520 7.918562 ACAACACATACCAAAAACAGATACAAC 59.081 33.333 0.00 0.0 0.00 3.32 R
5898 7858 1.276622 GGACAGGGAGTTAGGAGCAA 58.723 55.000 0.00 0.0 0.00 3.91 R
6717 8744 0.100503 CGGTTGGCATTTCCGATTCC 59.899 55.000 17.16 0.0 46.05 3.01 R
7503 9537 1.893808 CAGCTTCACCCGTTGCAGT 60.894 57.895 0.00 0.0 0.00 4.40 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
194 195 4.762956 AGAAAGAAGCTGAGATTGCAAC 57.237 40.909 0.00 0.00 0.00 4.17
241 242 4.591321 AGCTTTATTGATCAAGGTGGGA 57.409 40.909 14.54 0.00 29.56 4.37
246 247 6.772716 GCTTTATTGATCAAGGTGGGATTCTA 59.227 38.462 14.54 0.00 0.00 2.10
325 326 9.705290 ATGGCGAACTTTTAATCTAAACAAAAT 57.295 25.926 0.00 0.00 0.00 1.82
428 429 5.163591 CGAAACCAACCCTAACTCTTGTTTT 60.164 40.000 0.00 0.00 37.59 2.43
490 491 3.358111 TTCGAAATTACATGGGCCTGA 57.642 42.857 4.53 0.00 0.00 3.86
583 584 1.251251 GTCCAAGGCTTCATGCACTT 58.749 50.000 0.00 0.00 45.15 3.16
639 640 3.170717 TGTAACTCCGTTCTTGATCCCT 58.829 45.455 0.00 0.00 0.00 4.20
722 723 4.286808 AGGCCCTTCATTTGTAAGCAAAAT 59.713 37.500 0.00 0.00 46.23 1.82
758 759 8.953313 CAATTTAGGCAGCATCATAATCTCATA 58.047 33.333 0.00 0.00 0.00 2.15
761 762 9.524496 TTTAGGCAGCATCATAATCTCATAAAT 57.476 29.630 0.00 0.00 0.00 1.40
3928 5520 6.959311 CGTTGGTCGACCTTAATTATTTCTTG 59.041 38.462 33.39 5.36 42.86 3.02
4297 6085 0.036732 TCAGCTCGCCATTGGAAAGT 59.963 50.000 6.95 0.00 0.00 2.66
4298 6086 0.449388 CAGCTCGCCATTGGAAAGTC 59.551 55.000 6.95 0.00 0.00 3.01
5313 7210 2.972153 ACAATCCCTCTACCTCCCTT 57.028 50.000 0.00 0.00 0.00 3.95
6687 8714 2.503356 AGGTTGAGGGAGCTTCATACTG 59.497 50.000 0.00 0.00 0.00 2.74
6689 8716 3.265791 GTTGAGGGAGCTTCATACTGTG 58.734 50.000 0.00 0.00 0.00 3.66
6693 8720 3.935828 GAGGGAGCTTCATACTGTGAAAC 59.064 47.826 0.00 0.00 45.74 2.78
6694 8721 3.584848 AGGGAGCTTCATACTGTGAAACT 59.415 43.478 0.00 0.00 45.74 2.66
6695 8722 3.686726 GGGAGCTTCATACTGTGAAACTG 59.313 47.826 0.00 0.00 45.74 3.16
6717 8744 3.777106 ACTGGCATGTAGGATGTATGG 57.223 47.619 0.00 0.00 0.00 2.74
6786 8818 7.877612 AGTTGAAGAAAACAATTTGTTGAAGGT 59.122 29.630 15.17 0.00 40.14 3.50
7281 9314 1.203052 CCATGCACTGAATGTGGGAAC 59.797 52.381 0.00 0.00 46.27 3.62
7457 9491 2.672996 GGTGATGCTGCAACGGGT 60.673 61.111 6.36 0.00 0.00 5.28
7503 9537 2.485302 CCAGACGATGTGCCCAATGATA 60.485 50.000 0.00 0.00 0.00 2.15
7718 9807 2.577700 ACCGTACTGGAATTGTTGCAA 58.422 42.857 10.17 0.00 42.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.202604 GGTCGACTCCCACAGAAAACA 60.203 52.381 16.46 0.00 0.00 2.83
194 195 6.280643 TCATCTTATATTCGCAATATCCCGG 58.719 40.000 0.00 0.00 35.72 5.73
241 242 5.450137 CGACCAGACCAAGACGTTATAGAAT 60.450 44.000 0.00 0.00 0.00 2.40
246 247 1.891150 ACGACCAGACCAAGACGTTAT 59.109 47.619 0.00 0.00 0.00 1.89
248 249 0.462789 AACGACCAGACCAAGACGTT 59.537 50.000 0.00 0.00 38.72 3.99
428 429 2.812836 TAGAGTCCGTATGTGTGGGA 57.187 50.000 0.00 0.00 0.00 4.37
490 491 3.954258 GCTGCTTCACCTTATTAATGGGT 59.046 43.478 8.53 8.53 0.00 4.51
583 584 2.356135 GACTTTGAAGCCGCCATAAGA 58.644 47.619 0.00 0.00 0.00 2.10
639 640 0.109179 GAGTTGATGGCATGCGCAAA 60.109 50.000 17.11 0.00 41.24 3.68
2747 4137 2.031163 GCCGTCAGAACCTGCACT 59.969 61.111 0.00 0.00 0.00 4.40
3928 5520 7.918562 ACAACACATACCAAAAACAGATACAAC 59.081 33.333 0.00 0.00 0.00 3.32
5898 7858 1.276622 GGACAGGGAGTTAGGAGCAA 58.723 55.000 0.00 0.00 0.00 3.91
6209 8203 4.338964 GTCATGCATGATACATGGTCCAAA 59.661 41.667 30.89 1.62 44.09 3.28
6687 8714 3.684788 CCTACATGCCAGTACAGTTTCAC 59.315 47.826 0.00 0.00 0.00 3.18
6689 8716 4.202245 TCCTACATGCCAGTACAGTTTC 57.798 45.455 0.00 0.00 0.00 2.78
6693 8720 3.827008 ACATCCTACATGCCAGTACAG 57.173 47.619 0.00 0.00 0.00 2.74
6694 8721 4.040339 CCATACATCCTACATGCCAGTACA 59.960 45.833 0.00 0.00 0.00 2.90
6695 8722 4.563580 CCCATACATCCTACATGCCAGTAC 60.564 50.000 0.00 0.00 0.00 2.73
6696 8723 3.582647 CCCATACATCCTACATGCCAGTA 59.417 47.826 0.00 0.00 0.00 2.74
6697 8724 2.373169 CCCATACATCCTACATGCCAGT 59.627 50.000 0.00 0.00 0.00 4.00
6698 8725 2.639347 TCCCATACATCCTACATGCCAG 59.361 50.000 0.00 0.00 0.00 4.85
6699 8726 2.700354 TCCCATACATCCTACATGCCA 58.300 47.619 0.00 0.00 0.00 4.92
6700 8727 3.788227 TTCCCATACATCCTACATGCC 57.212 47.619 0.00 0.00 0.00 4.40
6701 8728 3.935203 CGATTCCCATACATCCTACATGC 59.065 47.826 0.00 0.00 0.00 4.06
6702 8729 4.222810 TCCGATTCCCATACATCCTACATG 59.777 45.833 0.00 0.00 0.00 3.21
6717 8744 0.100503 CGGTTGGCATTTCCGATTCC 59.899 55.000 17.16 0.00 46.05 3.01
6799 8831 9.933240 AATATCATCTTCTCCTCCTCAATTTTT 57.067 29.630 0.00 0.00 0.00 1.94
6800 8832 9.352191 CAATATCATCTTCTCCTCCTCAATTTT 57.648 33.333 0.00 0.00 0.00 1.82
7281 9314 2.097142 CCGGTTAGAGTAAGACCTCGTG 59.903 54.545 0.00 0.00 36.56 4.35
7457 9491 2.235650 CTCTTGATCTTCACCAGCTCCA 59.764 50.000 0.00 0.00 0.00 3.86
7503 9537 1.893808 CAGCTTCACCCGTTGCAGT 60.894 57.895 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.