Multiple sequence alignment - TraesCS5D01G138700

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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 TraesCS5D01G138700 chr5D 100.000 3616 0 0 1 3616 220756842 220753227 0.000000e+00 6678.0
1 TraesCS5D01G138700 chr5D 92.508 2149 138 20 648 2781 544604751 544602611 0.000000e+00 3055.0
2 TraesCS5D01G138700 chr5D 77.168 784 130 40 511 1270 48594228 48594986 9.340000e-111 411.0
3 TraesCS5D01G138700 chr6D 94.308 2811 105 25 1 2783 384231628 384228845 0.000000e+00 4253.0
4 TraesCS5D01G138700 chr6D 90.459 283 10 7 1 266 384268232 384267950 1.230000e-94 357.0
5 TraesCS5D01G138700 chr1D 93.063 2148 123 19 649 2781 385635708 385637844 0.000000e+00 3118.0
6 TraesCS5D01G138700 chr1D 92.499 2133 140 14 664 2781 246425804 246423677 0.000000e+00 3035.0
7 TraesCS5D01G138700 chr1D 90.311 836 79 2 2782 3616 188575061 188574227 0.000000e+00 1094.0
8 TraesCS5D01G138700 chr1D 91.116 439 16 13 1 418 250412095 250411659 1.130000e-159 573.0
9 TraesCS5D01G138700 chr1D 88.000 175 16 3 510 679 268870545 268870719 6.120000e-48 202.0
10 TraesCS5D01G138700 chr2D 93.065 2134 133 13 657 2781 619068327 619070454 0.000000e+00 3107.0
11 TraesCS5D01G138700 chr2D 92.412 2148 145 15 646 2781 131433797 131435938 0.000000e+00 3048.0
12 TraesCS5D01G138700 chr2D 93.660 836 49 3 2782 3614 290468977 290469811 0.000000e+00 1247.0
13 TraesCS5D01G138700 chr2D 90.580 828 75 3 2781 3606 410434168 410433342 0.000000e+00 1094.0
14 TraesCS5D01G138700 chr2D 90.311 836 78 3 2782 3616 546770328 546769495 0.000000e+00 1092.0
15 TraesCS5D01G138700 chr3D 92.891 2138 133 15 652 2781 102693239 102691113 0.000000e+00 3088.0
16 TraesCS5D01G138700 chr3D 92.797 2138 136 13 652 2781 102701184 102699057 0.000000e+00 3079.0
17 TraesCS5D01G138700 chr3D 92.601 2149 136 16 649 2781 123343271 123341130 0.000000e+00 3066.0
18 TraesCS5D01G138700 chr3D 92.519 2152 137 19 648 2781 1600707 1598562 0.000000e+00 3061.0
19 TraesCS5D01G138700 chr3D 94.705 831 42 2 2782 3611 463627767 463626938 0.000000e+00 1290.0
20 TraesCS5D01G138700 chr3D 91.606 822 67 2 2796 3616 404056391 404057211 0.000000e+00 1134.0
21 TraesCS5D01G138700 chr4B 85.592 2332 245 68 510 2782 299798733 299801032 0.000000e+00 2361.0
22 TraesCS5D01G138700 chr4D 93.622 831 50 3 2782 3611 251937904 251938732 0.000000e+00 1238.0
23 TraesCS5D01G138700 chr7D 90.323 837 76 5 2782 3616 477460880 477460047 0.000000e+00 1092.0
24 TraesCS5D01G138700 chr7D 90.385 832 76 3 2781 3611 163092201 163091373 0.000000e+00 1090.0
25 TraesCS5D01G138700 chr3A 91.429 490 33 5 255 739 252652238 252651753 0.000000e+00 664.0
26 TraesCS5D01G138700 chr3A 81.633 98 6 3 430 515 567500555 567500652 1.800000e-08 71.3
27 TraesCS5D01G138700 chr5A 94.182 275 9 4 249 521 229159900 229159631 2.600000e-111 412.0
28 TraesCS5D01G138700 chr5A 93.091 275 10 5 249 521 229151693 229151426 9.410000e-106 394.0
29 TraesCS5D01G138700 chr4A 92.364 275 14 4 249 521 189473151 189472882 5.660000e-103 385.0
30 TraesCS5D01G138700 chr4A 92.565 269 10 5 255 521 189506789 189506529 9.480000e-101 377.0
31 TraesCS5D01G138700 chr1A 76.995 639 102 34 507 1127 275811921 275811310 1.250000e-84 324.0
32 TraesCS5D01G138700 chr1A 87.619 210 23 3 510 717 250399086 250398878 1.300000e-59 241.0
33 TraesCS5D01G138700 chrUn 85.338 266 32 6 510 770 407649082 407649345 5.950000e-68 268.0
34 TraesCS5D01G138700 chrUn 87.097 155 15 3 510 659 253645406 253645560 1.730000e-38 171.0
35 TraesCS5D01G138700 chr6B 86.283 226 24 6 510 730 470523787 470523564 4.670000e-59 239.0
36 TraesCS5D01G138700 chr3B 86.061 165 16 6 313 473 734785099 734784938 1.730000e-38 171.0
37 TraesCS5D01G138700 chr1B 84.615 169 15 8 313 473 609669126 609669291 1.340000e-34 158.0
38 TraesCS5D01G138700 chr7B 83.133 166 18 8 314 473 69198611 69198450 3.760000e-30 143.0
39 TraesCS5D01G138700 chr7A 86.408 103 13 1 1 102 724682272 724682374 1.060000e-20 111.0


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 TraesCS5D01G138700 chr5D 220753227 220756842 3615 True 6678 6678 100.000 1 3616 1 chr5D.!!$R1 3615
1 TraesCS5D01G138700 chr5D 544602611 544604751 2140 True 3055 3055 92.508 648 2781 1 chr5D.!!$R2 2133
2 TraesCS5D01G138700 chr5D 48594228 48594986 758 False 411 411 77.168 511 1270 1 chr5D.!!$F1 759
3 TraesCS5D01G138700 chr6D 384228845 384231628 2783 True 4253 4253 94.308 1 2783 1 chr6D.!!$R1 2782
4 TraesCS5D01G138700 chr1D 385635708 385637844 2136 False 3118 3118 93.063 649 2781 1 chr1D.!!$F2 2132
5 TraesCS5D01G138700 chr1D 246423677 246425804 2127 True 3035 3035 92.499 664 2781 1 chr1D.!!$R2 2117
6 TraesCS5D01G138700 chr1D 188574227 188575061 834 True 1094 1094 90.311 2782 3616 1 chr1D.!!$R1 834
7 TraesCS5D01G138700 chr2D 619068327 619070454 2127 False 3107 3107 93.065 657 2781 1 chr2D.!!$F3 2124
8 TraesCS5D01G138700 chr2D 131433797 131435938 2141 False 3048 3048 92.412 646 2781 1 chr2D.!!$F1 2135
9 TraesCS5D01G138700 chr2D 290468977 290469811 834 False 1247 1247 93.660 2782 3614 1 chr2D.!!$F2 832
10 TraesCS5D01G138700 chr2D 410433342 410434168 826 True 1094 1094 90.580 2781 3606 1 chr2D.!!$R1 825
11 TraesCS5D01G138700 chr2D 546769495 546770328 833 True 1092 1092 90.311 2782 3616 1 chr2D.!!$R2 834
12 TraesCS5D01G138700 chr3D 102691113 102693239 2126 True 3088 3088 92.891 652 2781 1 chr3D.!!$R2 2129
13 TraesCS5D01G138700 chr3D 102699057 102701184 2127 True 3079 3079 92.797 652 2781 1 chr3D.!!$R3 2129
14 TraesCS5D01G138700 chr3D 123341130 123343271 2141 True 3066 3066 92.601 649 2781 1 chr3D.!!$R4 2132
15 TraesCS5D01G138700 chr3D 1598562 1600707 2145 True 3061 3061 92.519 648 2781 1 chr3D.!!$R1 2133
16 TraesCS5D01G138700 chr3D 463626938 463627767 829 True 1290 1290 94.705 2782 3611 1 chr3D.!!$R5 829
17 TraesCS5D01G138700 chr3D 404056391 404057211 820 False 1134 1134 91.606 2796 3616 1 chr3D.!!$F1 820
18 TraesCS5D01G138700 chr4B 299798733 299801032 2299 False 2361 2361 85.592 510 2782 1 chr4B.!!$F1 2272
19 TraesCS5D01G138700 chr4D 251937904 251938732 828 False 1238 1238 93.622 2782 3611 1 chr4D.!!$F1 829
20 TraesCS5D01G138700 chr7D 477460047 477460880 833 True 1092 1092 90.323 2782 3616 1 chr7D.!!$R2 834
21 TraesCS5D01G138700 chr7D 163091373 163092201 828 True 1090 1090 90.385 2781 3611 1 chr7D.!!$R1 830
22 TraesCS5D01G138700 chr1A 275811310 275811921 611 True 324 324 76.995 507 1127 1 chr1A.!!$R2 620

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
266 284 1.138671 GGGTTGTGTGTGTGTGTGC 59.861 57.895 0.00 0.0 0.00 4.57 F
1667 1782 0.596082 TCGTGATGTCAGCGACTCAA 59.404 50.000 9.49 0.0 33.15 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2031 0.897863 GCAGGGGTGCACCACATAAA 60.898 55.0 38.54 0.0 43.57 1.40 R
3405 3540 0.620556 GTCCAGCCTCTCCAATCCAA 59.379 55.0 0.00 0.0 0.00 3.53 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
104 105 1.299562 CTGCTGCTGAACTGCTCCTG 61.300 60.000 0.00 0.00 43.25 3.86
133 134 1.731433 CTGCTGTTGGCTGTGTTGCT 61.731 55.000 0.00 0.00 42.39 3.91
134 135 1.321805 TGCTGTTGGCTGTGTTGCTT 61.322 50.000 0.00 0.00 42.39 3.91
159 177 2.408271 TAACTGCTGCTGCTTGCTAT 57.592 45.000 17.00 0.45 43.37 2.97
209 227 4.243008 TCCAACGCCGTTGCCTGA 62.243 61.111 23.84 13.26 41.62 3.86
266 284 1.138671 GGGTTGTGTGTGTGTGTGC 59.861 57.895 0.00 0.00 0.00 4.57
414 438 2.876550 CGGCCCTGTTTAGGTTAATAGC 59.123 50.000 0.00 0.00 42.96 2.97
461 485 8.419442 GCTAATTAGTGGTTAGGTGTAGTGTAT 58.581 37.037 13.91 0.00 31.38 2.29
1271 1350 1.448013 GCCCTACACTCTTGTCCGC 60.448 63.158 0.00 0.00 37.15 5.54
1417 1531 3.023045 ATCCCGGTAGAGGTGGGCT 62.023 63.158 0.00 0.00 42.98 5.19
1471 1585 4.767255 GGAGCGACAGGGCAGGTG 62.767 72.222 0.00 0.00 34.64 4.00
1533 1647 3.307782 CGTCCGCGGTTACTTCAAAATAT 59.692 43.478 27.15 0.00 0.00 1.28
1665 1780 1.263776 CTTCGTGATGTCAGCGACTC 58.736 55.000 9.49 6.00 33.15 3.36
1667 1782 0.596082 TCGTGATGTCAGCGACTCAA 59.404 50.000 9.49 0.00 33.15 3.02
1670 1785 0.596082 TGATGTCAGCGACTCAACGA 59.404 50.000 9.49 0.00 33.15 3.85
1696 1811 2.016604 GCCAGATTGGACCGCATAACA 61.017 52.381 0.00 0.00 40.96 2.41
1723 1838 3.420893 TCCTTTGTAATGGAGGTTGCTG 58.579 45.455 0.00 0.00 32.33 4.41
1915 2031 1.899437 ATGGGATCGAGCGTGTTGGT 61.899 55.000 0.00 0.00 0.00 3.67
2052 2168 0.258774 AACACACCCTTCCAAGTGCT 59.741 50.000 0.00 0.00 37.51 4.40
2079 2195 0.820074 ACCCGGTGATCGCTCTCTAG 60.820 60.000 6.18 0.00 37.59 2.43
2201 2318 1.525596 CAGAAGCGTAGTCTTCGACG 58.474 55.000 2.72 0.00 42.44 5.12
2264 2385 1.697432 TCCACCGATATGGCCCTTTAG 59.303 52.381 0.00 0.00 43.94 1.85
2433 2558 1.587490 CGACGACGACTCCTACTACAG 59.413 57.143 0.00 0.00 42.66 2.74
2447 2572 1.203137 ACTACAGTGGAGGTGCCTACA 60.203 52.381 7.43 0.00 37.63 2.74
2639 2765 1.279271 AGCACTTGTATTCGAGCCCTT 59.721 47.619 0.00 0.00 0.00 3.95
2882 3011 0.456312 CCGAGCGCCGATCCTATTAC 60.456 60.000 17.96 0.00 41.76 1.89
2982 3113 0.899253 GATAGAGGCGGGGGTAGTCC 60.899 65.000 0.00 0.00 0.00 3.85
3050 3182 3.070159 ACCCCATCATCGAACTCTATGTG 59.930 47.826 0.00 0.00 0.00 3.21
3169 3303 3.888323 TGACTGTTTATGGCAGCAAAGAA 59.112 39.130 0.00 0.00 37.47 2.52
3211 3346 3.492421 ACAGCAATAAAATGACGCAGG 57.508 42.857 0.00 0.00 0.00 4.85
3218 3353 0.729116 AAAATGACGCAGGCGATCAG 59.271 50.000 21.62 0.00 42.83 2.90
3274 3409 1.884928 GCCTTCCCGGAAGTTTAAGCA 60.885 52.381 23.06 0.00 37.92 3.91
3277 3412 3.610911 CTTCCCGGAAGTTTAAGCAGAT 58.389 45.455 17.91 0.00 35.21 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 2.715046 AGCAGCAGCAGTTAAGCATAA 58.285 42.857 3.17 0.00 45.49 1.90
134 135 2.408271 AGCAGCAGCAGTTAAGCATA 57.592 45.000 3.17 0.00 45.49 3.14
159 177 2.892334 GCAGCAAACGACAGCGGAA 61.892 57.895 0.00 0.00 43.17 4.30
209 227 3.254629 CCAACAGCAGTGGCAGTAT 57.745 52.632 0.00 0.00 44.61 2.12
246 264 1.003112 ACACACACACACAACCCGT 60.003 52.632 0.00 0.00 0.00 5.28
515 539 3.893521 ACCTAATTAAATGGGACCCACG 58.106 45.455 17.78 0.00 35.80 4.94
1271 1350 2.027745 CCCAGTAGTATAGCATGGCAGG 60.028 54.545 0.00 0.00 0.00 4.85
1349 1432 7.595502 CCATCTCCGAACAGTATCATAAGTAAC 59.404 40.741 0.00 0.00 0.00 2.50
1471 1585 1.133606 CCTCTCTCCTAGGTGGTCTCC 60.134 61.905 9.08 0.00 37.07 3.71
1533 1647 1.336517 CCCAGAACTCGTTAAGCGTGA 60.337 52.381 6.54 0.00 42.13 4.35
1551 1665 3.471680 GCCAGACTCAGATCAAATACCC 58.528 50.000 0.00 0.00 0.00 3.69
1665 1780 2.667318 AATCTGGCGTGCGTCGTTG 61.667 57.895 0.00 0.00 42.13 4.10
1667 1782 3.112075 CAATCTGGCGTGCGTCGT 61.112 61.111 0.00 0.00 42.13 4.34
1670 1785 2.742372 GTCCAATCTGGCGTGCGT 60.742 61.111 0.00 0.00 37.47 5.24
1674 1789 1.966901 TATGCGGTCCAATCTGGCGT 61.967 55.000 0.00 0.00 37.47 5.68
1696 1811 5.520748 ACCTCCATTACAAAGGAAGTCAT 57.479 39.130 0.00 0.00 34.16 3.06
1915 2031 0.897863 GCAGGGGTGCACCACATAAA 60.898 55.000 38.54 0.00 43.57 1.40
2052 2168 1.338973 GCGATCACCGGGTTGTATCTA 59.661 52.381 6.32 0.00 39.04 1.98
2079 2195 2.420890 CTCTCCTCATCGCCCTGC 59.579 66.667 0.00 0.00 0.00 4.85
2088 2204 2.519541 CCGGCGATCCTCTCCTCA 60.520 66.667 9.30 0.00 0.00 3.86
2154 2271 2.239402 TCCATCTTGCAGCATGTAGGAA 59.761 45.455 16.53 0.00 40.61 3.36
2433 2558 0.955919 GCAGTTGTAGGCACCTCCAC 60.956 60.000 0.00 0.00 37.29 4.02
2639 2765 1.590591 TAATACAAGCCAGGGCCTCA 58.409 50.000 0.95 0.00 43.17 3.86
2768 2896 3.716195 CCTCATGTGACGCCCCCA 61.716 66.667 0.00 0.00 0.00 4.96
2882 3011 5.003160 TGCCCATTATACTGATCCGAATTG 58.997 41.667 0.00 0.00 0.00 2.32
3050 3182 3.587797 TTCGCAAGGATCCGGATATAC 57.412 47.619 19.15 11.03 38.47 1.47
3211 3346 4.380531 TGAATGGGTAAGATTCTGATCGC 58.619 43.478 0.00 0.00 37.37 4.58
3274 3409 4.843516 AGGGTGAGAAAGAAGAGTTCATCT 59.156 41.667 0.00 0.00 41.27 2.90
3277 3412 6.688073 ATAAGGGTGAGAAAGAAGAGTTCA 57.312 37.500 0.00 0.00 0.00 3.18
3405 3540 0.620556 GTCCAGCCTCTCCAATCCAA 59.379 55.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.