Multiple sequence alignment - TraesCS5D01G243500

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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 TraesCS5D01G243500 chr5D 100.000 2503 0 0 975 3477 351785775 351788277 0.000000e+00 4623.0
1 TraesCS5D01G243500 chr5D 100.000 162 0 0 1 162 351784801 351784962 2.030000e-77 300.0
2 TraesCS5D01G243500 chr5D 91.975 162 11 2 1 162 351774476 351774635 3.490000e-55 226.0
3 TraesCS5D01G243500 chr5D 77.778 153 26 7 3248 3396 141424783 141424931 1.720000e-13 87.9
4 TraesCS5D01G243500 chr5B 95.784 2467 80 11 975 3423 414827896 414830356 0.000000e+00 3958.0
5 TraesCS5D01G243500 chr5B 94.444 162 8 1 1 162 414826784 414826944 7.450000e-62 248.0
6 TraesCS5D01G243500 chr5A 95.282 2268 78 11 975 3235 452109258 452111503 0.000000e+00 3568.0
7 TraesCS5D01G243500 chr5A 96.045 177 7 0 3247 3423 452111762 452111938 4.390000e-74 289.0
8 TraesCS5D01G243500 chr2B 77.600 250 48 8 3158 3404 508959634 508959390 1.010000e-30 145.0
9 TraesCS5D01G243500 chr3D 78.390 236 40 11 3172 3404 400694619 400694392 3.620000e-30 143.0
10 TraesCS5D01G243500 chr3D 80.571 175 31 3 3232 3404 39927984 39928157 7.830000e-27 132.0
11 TraesCS5D01G243500 chr3D 96.774 62 0 2 3415 3475 58053601 58053541 6.140000e-18 102.0
12 TraesCS5D01G243500 chr1B 82.692 156 23 2 2220 2375 24350213 24350364 6.050000e-28 135.0
13 TraesCS5D01G243500 chr2D 76.190 252 49 11 3158 3404 430625755 430625510 4.710000e-24 122.0
14 TraesCS5D01G243500 chr2D 98.276 58 1 0 3418 3475 571223173 571223230 6.140000e-18 102.0
15 TraesCS5D01G243500 chr6A 78.453 181 34 5 3227 3405 446898054 446898231 2.840000e-21 113.0
16 TraesCS5D01G243500 chr2A 85.437 103 14 1 3319 3420 161954741 161954843 4.750000e-19 106.0
17 TraesCS5D01G243500 chr7B 100.000 56 0 0 3420 3475 726848614 726848669 1.710000e-18 104.0
18 TraesCS5D01G243500 chr6B 100.000 56 0 0 3420 3475 550785915 550785970 1.710000e-18 104.0
19 TraesCS5D01G243500 chr3B 100.000 56 0 0 3420 3475 760601608 760601553 1.710000e-18 104.0
20 TraesCS5D01G243500 chr7D 96.721 61 2 0 3415 3475 599696627 599696687 6.140000e-18 102.0
21 TraesCS5D01G243500 chr6D 96.721 61 2 0 3415 3475 437424743 437424683 6.140000e-18 102.0
22 TraesCS5D01G243500 chr4A 93.846 65 4 0 3411 3475 210939902 210939838 7.940000e-17 99.0
23 TraesCS5D01G243500 chr1D 95.238 63 1 2 3413 3475 311900847 311900907 7.940000e-17 99.0
24 TraesCS5D01G243500 chr1D 91.304 46 4 0 1057 1102 426595153 426595198 2.900000e-06 63.9
25 TraesCS5D01G243500 chr1A 91.304 46 4 0 1057 1102 521639874 521639919 2.900000e-06 63.9
26 TraesCS5D01G243500 chr3A 100.000 30 0 0 1073 1102 498229371 498229400 4.850000e-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 TraesCS5D01G243500 chr5D 351784801 351788277 3476 False 2461.5 4623 100.0000 1 3477 2 chr5D.!!$F3 3476
1 TraesCS5D01G243500 chr5B 414826784 414830356 3572 False 2103.0 3958 95.1140 1 3423 2 chr5B.!!$F1 3422
2 TraesCS5D01G243500 chr5A 452109258 452111938 2680 False 1928.5 3568 95.6635 975 3423 2 chr5A.!!$F1 2448

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
129 130 0.888619 TCTGTCGTGCGATCTCCTTT 59.111 50.000 0.0 0.0 0.0 3.11 F
148 149 2.721425 TGTCACTTTCCCTTTCCGTT 57.279 45.000 0.0 0.0 0.0 4.44 F
154 155 4.097286 TCACTTTCCCTTTCCGTTTTTCTG 59.903 41.667 0.0 0.0 0.0 3.02 F
1527 1667 4.947147 GCGTGCCCCAACCTCACA 62.947 66.667 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 1997 0.393077 CCTTATACACCCTCCCTGCG 59.607 60.000 0.00 0.00 0.00 5.18 R
2006 2147 0.810648 GGAGCACATCAAAATCGCCA 59.189 50.000 0.00 0.00 0.00 5.69 R
2009 2150 1.202222 GGCTGGAGCACATCAAAATCG 60.202 52.381 0.20 0.00 44.36 3.34 R
2858 3010 1.561542 AGGAGCTTCCAAGTACATGGG 59.438 52.381 16.76 3.35 39.61 4.00 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
22 23 5.482686 AAATTCACAAAACCAACACATGC 57.517 34.783 0.00 0.00 0.00 4.06
129 130 0.888619 TCTGTCGTGCGATCTCCTTT 59.111 50.000 0.00 0.00 0.00 3.11
144 145 4.461198 TCTCCTTTGTCACTTTCCCTTTC 58.539 43.478 0.00 0.00 0.00 2.62
145 146 3.562182 TCCTTTGTCACTTTCCCTTTCC 58.438 45.455 0.00 0.00 0.00 3.13
148 149 2.721425 TGTCACTTTCCCTTTCCGTT 57.279 45.000 0.00 0.00 0.00 4.44
154 155 4.097286 TCACTTTCCCTTTCCGTTTTTCTG 59.903 41.667 0.00 0.00 0.00 3.02
1527 1667 4.947147 GCGTGCCCCAACCTCACA 62.947 66.667 0.00 0.00 0.00 3.58
1828 1969 5.357878 AGATTGTGTTGTCGGATGCAATAAT 59.642 36.000 0.00 0.00 0.00 1.28
1856 1997 6.086765 GTGTCGTGAATTGTGATGAAAATGAC 59.913 38.462 0.00 0.00 0.00 3.06
2006 2147 6.718454 ACCTTGTGATGAAGATTGAATTCTGT 59.282 34.615 7.05 0.00 0.00 3.41
2009 2150 5.106038 TGTGATGAAGATTGAATTCTGTGGC 60.106 40.000 7.05 0.00 0.00 5.01
2230 2373 6.071447 TGACCATGGTTAATTCCTGTGATTTG 60.071 38.462 20.85 0.00 0.00 2.32
2351 2494 5.128992 TGAATCGCTTGTGAAGTACAGTA 57.871 39.130 0.00 0.00 41.10 2.74
2377 2520 3.085208 CCAGTCAATGGTCATCCGG 57.915 57.895 0.00 0.00 44.91 5.14
2553 2697 6.518208 TTTTACCGTATTCCCTGATTTTGG 57.482 37.500 0.00 0.00 0.00 3.28
2567 2711 5.925969 CCTGATTTTGGTTGTTGTCATTACC 59.074 40.000 0.00 0.00 0.00 2.85
2568 2712 6.462207 CCTGATTTTGGTTGTTGTCATTACCA 60.462 38.462 0.00 0.00 38.82 3.25
2628 2772 7.379529 GGAGTTGTGTTGTTTAGTTGATTGATG 59.620 37.037 0.00 0.00 0.00 3.07
2718 2862 5.617252 TCATTTTTCCTCGTCATATACCCC 58.383 41.667 0.00 0.00 0.00 4.95
2731 2875 6.814644 CGTCATATACCCCGCTTTGAATTATA 59.185 38.462 0.00 0.00 0.00 0.98
2817 2969 5.530171 ACATCATGTTCATCTGGTTGATAGC 59.470 40.000 0.00 0.00 33.36 2.97
2821 2973 3.056179 TGTTCATCTGGTTGATAGCGTGA 60.056 43.478 0.00 0.00 33.36 4.35
2824 2976 2.602257 TCTGGTTGATAGCGTGATGG 57.398 50.000 0.00 0.00 0.00 3.51
2825 2977 1.831106 TCTGGTTGATAGCGTGATGGT 59.169 47.619 0.00 0.00 0.00 3.55
2858 3010 8.225603 TCCTGATAAGACTATTTTGATTTGGC 57.774 34.615 0.00 0.00 0.00 4.52
2859 3011 7.285401 TCCTGATAAGACTATTTTGATTTGGCC 59.715 37.037 0.00 0.00 0.00 5.36
2943 3095 8.510243 AACTCTTATACATGAACATCAATGCA 57.490 30.769 0.00 0.00 0.00 3.96
3015 3168 7.824289 TGATTTAGATCCGTTGAGATGACTTTT 59.176 33.333 0.00 0.00 0.00 2.27
3016 3169 7.979444 TTTAGATCCGTTGAGATGACTTTTT 57.021 32.000 0.00 0.00 0.00 1.94
3019 3172 5.577164 AGATCCGTTGAGATGACTTTTTACG 59.423 40.000 0.00 0.00 0.00 3.18
3098 3255 1.334160 TAGTTTCTCCGTGGTCTGCA 58.666 50.000 0.00 0.00 0.00 4.41
3130 3287 4.101114 TGCTTACCACTAGGGAAATCTCA 58.899 43.478 0.00 0.00 37.26 3.27
3137 3294 4.564821 CCACTAGGGAAATCTCAACGGAAA 60.565 45.833 0.00 0.00 40.01 3.13
3138 3295 5.001232 CACTAGGGAAATCTCAACGGAAAA 58.999 41.667 0.00 0.00 0.00 2.29
3172 3329 7.015877 AGAGTAATGTGTACTCCCTTTGTTACA 59.984 37.037 9.37 0.00 43.61 2.41
3187 3345 9.030301 CCCTTTGTTACAAAATACTTGAAGTTG 57.970 33.333 11.80 0.00 0.00 3.16
3423 3828 3.497332 TGAGACGGGGGAGTATATTCTG 58.503 50.000 0.00 0.00 0.00 3.02
3424 3829 3.117246 TGAGACGGGGGAGTATATTCTGT 60.117 47.826 0.00 0.00 0.00 3.41
3425 3830 3.896272 GAGACGGGGGAGTATATTCTGTT 59.104 47.826 0.00 0.00 0.00 3.16
3426 3831 3.641906 AGACGGGGGAGTATATTCTGTTG 59.358 47.826 0.00 0.00 0.00 3.33
3427 3832 3.640029 GACGGGGGAGTATATTCTGTTGA 59.360 47.826 0.00 0.00 0.00 3.18
3428 3833 3.641906 ACGGGGGAGTATATTCTGTTGAG 59.358 47.826 0.00 0.00 0.00 3.02
3429 3834 3.641906 CGGGGGAGTATATTCTGTTGAGT 59.358 47.826 0.00 0.00 0.00 3.41
3430 3835 4.831155 CGGGGGAGTATATTCTGTTGAGTA 59.169 45.833 0.00 0.00 0.00 2.59
3431 3836 5.303589 CGGGGGAGTATATTCTGTTGAGTAA 59.696 44.000 0.00 0.00 0.00 2.24
3432 3837 6.183360 CGGGGGAGTATATTCTGTTGAGTAAA 60.183 42.308 0.00 0.00 0.00 2.01
3433 3838 7.472945 CGGGGGAGTATATTCTGTTGAGTAAAT 60.473 40.741 0.00 0.00 0.00 1.40
3434 3839 8.877195 GGGGGAGTATATTCTGTTGAGTAAATA 58.123 37.037 0.00 0.00 0.00 1.40
3435 3840 9.930693 GGGGAGTATATTCTGTTGAGTAAATAG 57.069 37.037 0.00 0.00 0.00 1.73
3436 3841 9.930693 GGGAGTATATTCTGTTGAGTAAATAGG 57.069 37.037 0.00 0.00 0.00 2.57
3437 3842 9.425577 GGAGTATATTCTGTTGAGTAAATAGGC 57.574 37.037 0.00 0.00 0.00 3.93
3438 3843 9.982651 GAGTATATTCTGTTGAGTAAATAGGCA 57.017 33.333 0.00 0.00 0.00 4.75
3444 3849 8.635765 TTCTGTTGAGTAAATAGGCAATTTCT 57.364 30.769 0.00 0.00 38.71 2.52
3445 3850 8.268850 TCTGTTGAGTAAATAGGCAATTTCTC 57.731 34.615 0.00 7.49 38.71 2.87
3446 3851 7.064609 TCTGTTGAGTAAATAGGCAATTTCTCG 59.935 37.037 0.00 0.00 38.71 4.04
3447 3852 6.876789 TGTTGAGTAAATAGGCAATTTCTCGA 59.123 34.615 0.00 5.03 38.71 4.04
3448 3853 7.552687 TGTTGAGTAAATAGGCAATTTCTCGAT 59.447 33.333 0.00 0.00 38.71 3.59
3449 3854 8.398665 GTTGAGTAAATAGGCAATTTCTCGATT 58.601 33.333 0.00 0.00 38.71 3.34
3450 3855 9.607988 TTGAGTAAATAGGCAATTTCTCGATTA 57.392 29.630 0.00 0.00 38.71 1.75
3451 3856 9.607988 TGAGTAAATAGGCAATTTCTCGATTAA 57.392 29.630 0.00 0.00 38.71 1.40
3460 3865 8.912988 AGGCAATTTCTCGATTAAATTAATCCA 58.087 29.630 17.23 6.53 41.10 3.41
3461 3866 8.968242 GGCAATTTCTCGATTAAATTAATCCAC 58.032 33.333 17.23 0.00 41.10 4.02
3462 3867 8.682016 GCAATTTCTCGATTAAATTAATCCACG 58.318 33.333 17.23 8.92 41.10 4.94
3463 3868 9.929722 CAATTTCTCGATTAAATTAATCCACGA 57.070 29.630 17.23 12.07 41.10 4.35
3465 3870 8.712285 TTTCTCGATTAAATTAATCCACGAGT 57.288 30.769 22.80 0.00 41.10 4.18
3466 3871 9.806203 TTTCTCGATTAAATTAATCCACGAGTA 57.194 29.630 22.80 16.29 41.10 2.59
3467 3872 9.806203 TTCTCGATTAAATTAATCCACGAGTAA 57.194 29.630 22.80 16.72 41.10 2.24
3468 3873 9.806203 TCTCGATTAAATTAATCCACGAGTAAA 57.194 29.630 22.80 10.58 41.10 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.118482 TGATGTTTTGGCATGTGTTGGTT 60.118 39.130 0.00 0.00 0.00 3.67
81 82 7.503566 GGATATGAACAAGGATGGATGAGAAAA 59.496 37.037 0.00 0.00 0.00 2.29
121 122 4.731313 AAGGGAAAGTGACAAAGGAGAT 57.269 40.909 0.00 0.00 0.00 2.75
129 130 2.721425 AACGGAAAGGGAAAGTGACA 57.279 45.000 0.00 0.00 0.00 3.58
1527 1667 2.345244 CCAAGCAGCGACAGGTCT 59.655 61.111 0.00 0.00 0.00 3.85
1828 1969 5.491635 TTCATCACAATTCACGACACAAA 57.508 34.783 0.00 0.00 0.00 2.83
1856 1997 0.393077 CCTTATACACCCTCCCTGCG 59.607 60.000 0.00 0.00 0.00 5.18
2006 2147 0.810648 GGAGCACATCAAAATCGCCA 59.189 50.000 0.00 0.00 0.00 5.69
2009 2150 1.202222 GGCTGGAGCACATCAAAATCG 60.202 52.381 0.20 0.00 44.36 3.34
2079 2220 2.165030 CACCATGGATCTCAAACTTGGC 59.835 50.000 21.47 0.00 33.96 4.52
2230 2373 4.771590 TCTTGAATCCAACTGCATTGAC 57.228 40.909 9.56 1.85 41.23 3.18
2377 2520 4.880120 TGGCAATTCTTCATCTGTGAGATC 59.120 41.667 0.00 0.00 31.32 2.75
2537 2681 6.096673 ACAACAACCAAAATCAGGGAATAC 57.903 37.500 0.00 0.00 0.00 1.89
2553 2697 4.142600 GCATCCTCTGGTAATGACAACAAC 60.143 45.833 0.00 0.00 0.00 3.32
2567 2711 1.952296 GGGCTAAACATGCATCCTCTG 59.048 52.381 0.00 0.00 0.00 3.35
2568 2712 1.849039 AGGGCTAAACATGCATCCTCT 59.151 47.619 0.00 0.00 0.00 3.69
2718 2862 8.525876 CATCAACAATGTGTATAATTCAAAGCG 58.474 33.333 0.00 0.00 0.00 4.68
2731 2875 2.756760 GCATCCTCCATCAACAATGTGT 59.243 45.455 0.00 0.00 33.13 3.72
2824 2976 6.980416 ATAGTCTTATCAGGAGGGTGTAAC 57.020 41.667 0.00 0.00 0.00 2.50
2825 2977 7.989947 AAATAGTCTTATCAGGAGGGTGTAA 57.010 36.000 0.00 0.00 0.00 2.41
2858 3010 1.561542 AGGAGCTTCCAAGTACATGGG 59.438 52.381 16.76 3.35 39.61 4.00
2859 3011 3.356529 AAGGAGCTTCCAAGTACATGG 57.643 47.619 10.98 10.98 39.61 3.66
2989 3141 6.471233 AGTCATCTCAACGGATCTAAATCA 57.529 37.500 0.00 0.00 33.21 2.57
3001 3153 6.295039 TGGAACGTAAAAAGTCATCTCAAC 57.705 37.500 0.00 0.00 0.00 3.18
3015 3168 5.968528 AAATAAACAGCCATGGAACGTAA 57.031 34.783 18.40 1.27 0.00 3.18
3016 3169 5.336055 CCAAAATAAACAGCCATGGAACGTA 60.336 40.000 18.40 0.17 0.00 3.57
3019 3172 5.146010 TCCAAAATAAACAGCCATGGAAC 57.854 39.130 18.40 0.00 32.84 3.62
3098 3255 7.016914 TCCCTAGTGGTAAGCATATACTCATT 58.983 38.462 0.00 0.00 34.77 2.57
3130 3287 8.079809 CACATTACTCTTTTGGTATTTTCCGTT 58.920 33.333 0.00 0.00 0.00 4.44
3137 3294 7.827729 GGGAGTACACATTACTCTTTTGGTATT 59.172 37.037 10.47 0.00 42.54 1.89
3138 3295 7.182206 AGGGAGTACACATTACTCTTTTGGTAT 59.818 37.037 10.47 0.00 42.54 2.73
3172 3329 9.797556 GAACAAACCTACAACTTCAAGTATTTT 57.202 29.630 0.00 0.00 0.00 1.82
3187 3345 6.930667 TGTTTGAGTTAGGAACAAACCTAC 57.069 37.500 15.78 0.00 46.91 3.18
3423 3828 7.303634 TCGAGAAATTGCCTATTTACTCAAC 57.696 36.000 0.00 0.00 36.59 3.18
3424 3829 8.506168 AATCGAGAAATTGCCTATTTACTCAA 57.494 30.769 0.00 0.00 36.59 3.02
3425 3830 9.607988 TTAATCGAGAAATTGCCTATTTACTCA 57.392 29.630 0.00 0.00 36.59 3.41
3434 3839 8.912988 TGGATTAATTTAATCGAGAAATTGCCT 58.087 29.630 22.08 11.75 44.24 4.75
3435 3840 8.968242 GTGGATTAATTTAATCGAGAAATTGCC 58.032 33.333 22.08 19.77 44.24 4.52
3436 3841 8.682016 CGTGGATTAATTTAATCGAGAAATTGC 58.318 33.333 22.08 14.50 44.24 3.56
3437 3842 9.929722 TCGTGGATTAATTTAATCGAGAAATTG 57.070 29.630 22.08 10.11 44.24 2.32
3439 3844 9.326413 ACTCGTGGATTAATTTAATCGAGAAAT 57.674 29.630 27.80 14.36 44.24 2.17
3440 3845 8.712285 ACTCGTGGATTAATTTAATCGAGAAA 57.288 30.769 27.80 13.16 44.24 2.52
3441 3846 9.806203 TTACTCGTGGATTAATTTAATCGAGAA 57.194 29.630 27.80 19.77 44.24 2.87
3442 3847 9.806203 TTTACTCGTGGATTAATTTAATCGAGA 57.194 29.630 27.80 20.93 44.24 4.04


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

AutoCloner maintained by Alex Coulton.