Multiple sequence alignment - TraesCS5D01G257800

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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 TraesCS5D01G257800 chr5D 100.000 3206 0 0 1 3206 364399643 364402848 0.000000e+00 5921.0
1 TraesCS5D01G257800 chr5B 97.465 2485 46 5 1 2473 430471129 430473608 0.000000e+00 4224.0
2 TraesCS5D01G257800 chr5B 90.661 696 45 5 2513 3206 430473680 430474357 0.000000e+00 907.0
3 TraesCS5D01G257800 chr5B 100.000 37 0 0 2541 2577 430473642 430473678 5.740000e-08 69.4
4 TraesCS5D01G257800 chr5A 96.966 2439 64 5 1 2435 465546248 465548680 0.000000e+00 4085.0
5 TraesCS5D01G257800 chr5A 91.870 738 56 4 2472 3206 465548763 465549499 0.000000e+00 1027.0
6 TraesCS5D01G257800 chr7D 87.875 833 99 2 1046 1877 318252546 318251715 0.000000e+00 977.0
7 TraesCS5D01G257800 chr7B 86.058 832 113 3 1047 1877 302512497 302513326 0.000000e+00 891.0
8 TraesCS5D01G257800 chr7B 86.186 818 110 3 1046 1862 302545711 302546526 0.000000e+00 881.0


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 TraesCS5D01G257800 chr5D 364399643 364402848 3205 False 5921.000000 5921 100.000 1 3206 1 chr5D.!!$F1 3205
1 TraesCS5D01G257800 chr5B 430471129 430474357 3228 False 1733.466667 4224 96.042 1 3206 3 chr5B.!!$F1 3205
2 TraesCS5D01G257800 chr5A 465546248 465549499 3251 False 2556.000000 4085 94.418 1 3206 2 chr5A.!!$F1 3205
3 TraesCS5D01G257800 chr7D 318251715 318252546 831 True 977.000000 977 87.875 1046 1877 1 chr7D.!!$R1 831
4 TraesCS5D01G257800 chr7B 302512497 302513326 829 False 891.000000 891 86.058 1047 1877 1 chr7B.!!$F1 830
5 TraesCS5D01G257800 chr7B 302545711 302546526 815 False 881.000000 881 86.186 1046 1862 1 chr7B.!!$F2 816

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
945 958 0.166814 GTGCGCTCCACTGATCAAAC 59.833 55.0 9.73 0.0 41.35 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2773 2843 0.387202 CGATGAGCCTTCCGAGACAT 59.613 55.0 0.0 0.0 0.0 3.06 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
122 123 1.523758 CTTCCACAAACTTCCTCCGG 58.476 55.000 0.00 0.00 0.00 5.14
143 144 3.077556 CTCCGACTCCCCCACTGG 61.078 72.222 0.00 0.00 0.00 4.00
487 488 0.755698 TTCTCGGAATCCTCCTCGGG 60.756 60.000 0.00 0.00 39.93 5.14
538 539 1.879575 CTAGGGGTGAGATTGTGGGA 58.120 55.000 0.00 0.00 0.00 4.37
913 926 2.125106 GATCGAACGGCTGCCCTT 60.125 61.111 14.12 7.99 0.00 3.95
945 958 0.166814 GTGCGCTCCACTGATCAAAC 59.833 55.000 9.73 0.00 41.35 2.93
2124 2138 1.374758 CGTGCTCAGGGACAAGGAC 60.375 63.158 0.00 0.00 33.21 3.85
2189 2203 2.341543 CGAGATGGATCCCAGGCG 59.658 66.667 9.90 4.52 36.75 5.52
2227 2241 1.233285 GCTGATGGGTGATCGATGCC 61.233 60.000 0.54 4.71 33.17 4.40
2354 2372 8.433893 CGAGTCATATGCTAGATCTTGAAAATG 58.566 37.037 8.45 7.36 0.00 2.32
2367 2385 0.686789 GAAAATGCAGGTTTGGGGCT 59.313 50.000 3.04 0.00 0.00 5.19
2371 2389 3.376918 GCAGGTTTGGGGCTGCTC 61.377 66.667 0.00 0.00 39.48 4.26
2378 2396 2.501316 GGTTTGGGGCTGCTCAAAATAT 59.499 45.455 5.18 0.00 35.08 1.28
2380 2398 2.530460 TGGGGCTGCTCAAAATATGT 57.470 45.000 0.21 0.00 0.00 2.29
2448 2483 0.458543 GGCTCGCTCGTTGATCTTCA 60.459 55.000 0.00 0.00 0.00 3.02
2461 2496 2.261430 ATCTTCAGCAGGGCGCATCA 62.261 55.000 10.83 0.00 46.13 3.07
2528 2595 2.511600 GGTTCGGCGTCAGATGGG 60.512 66.667 6.85 0.00 0.00 4.00
2529 2596 2.577059 GTTCGGCGTCAGATGGGA 59.423 61.111 6.85 0.00 0.00 4.37
2532 2599 1.667154 TTCGGCGTCAGATGGGAGAG 61.667 60.000 6.85 0.00 0.00 3.20
2538 2605 0.108207 GTCAGATGGGAGAGGCCATG 59.892 60.000 5.01 0.00 38.95 3.66
2577 2644 1.134175 GAGGAAGAAGCGACTCCTCTG 59.866 57.143 15.73 0.00 42.58 3.35
2586 2653 1.137872 GCGACTCCTCTGGTGATTGAT 59.862 52.381 0.00 0.00 0.00 2.57
2618 2685 1.404035 GTGTTCAAAACCGAAGTGGCT 59.596 47.619 0.00 0.00 43.94 4.75
2623 2690 4.339872 TCAAAACCGAAGTGGCTACTAA 57.660 40.909 1.97 0.00 43.94 2.24
2630 2697 3.251571 CGAAGTGGCTACTAACAGGAAC 58.748 50.000 1.97 0.00 35.69 3.62
2697 2766 3.023832 CCTTCGTTAGCATGGGGAAATT 58.976 45.455 0.00 0.00 0.00 1.82
2725 2794 1.070134 TCTGGTGTTTCGTCCTCTTGG 59.930 52.381 0.00 0.00 0.00 3.61
2773 2843 0.740737 TCTCAGCGCGATCAAGATCA 59.259 50.000 12.10 0.00 37.69 2.92
2779 2849 1.455030 GCGCGATCAAGATCATGTCTC 59.545 52.381 12.10 0.00 35.67 3.36
2853 2924 3.379865 AATGTACGCGGCCATCGGT 62.380 57.895 12.47 4.97 39.69 4.69
2957 3028 2.005451 GATCGACAAGCATGCAACTCT 58.995 47.619 21.98 0.00 0.00 3.24
2958 3029 1.150827 TCGACAAGCATGCAACTCTG 58.849 50.000 21.98 10.89 0.00 3.35
2959 3030 0.167470 CGACAAGCATGCAACTCTGG 59.833 55.000 21.98 0.00 0.00 3.86
2964 3035 1.211969 GCATGCAACTCTGGTGCAG 59.788 57.895 14.21 8.96 42.11 4.41
3019 3090 4.117685 GTCACCACTGACGTAAAGAAACT 58.882 43.478 4.81 0.00 37.67 2.66
3063 3134 1.468914 GATTCGGCAAGAAGGAACCAC 59.531 52.381 0.62 0.00 42.92 4.16
3064 3135 0.181587 TTCGGCAAGAAGGAACCACA 59.818 50.000 0.00 0.00 34.26 4.17
3083 3154 5.428457 ACCACAAGTGATTGGTAGGATATCA 59.572 40.000 4.83 0.00 44.68 2.15
3084 3155 6.101734 ACCACAAGTGATTGGTAGGATATCAT 59.898 38.462 4.83 0.00 44.68 2.45
3112 3183 6.503524 TGAACAAATACCTCACTTTTGCTTC 58.496 36.000 0.00 0.00 34.47 3.86
3119 3190 4.070716 ACCTCACTTTTGCTTCTCATCTG 58.929 43.478 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 2.425143 TCATGAATGAGTTGGAGGGC 57.575 50.000 0.00 0.00 32.11 5.19
188 189 0.250513 GGAATCGGACTGCAGGACTT 59.749 55.000 19.93 3.85 0.00 3.01
350 351 4.499633 CCCATACCCGCACCCACC 62.500 72.222 0.00 0.00 0.00 4.61
512 513 2.880629 ATCTCACCCCTAGCACCGCT 62.881 60.000 0.00 0.00 43.41 5.52
913 926 2.965147 GCGCACGAACCTTGATGCA 61.965 57.895 0.30 0.00 37.97 3.96
945 958 0.178992 TTGGGGGCTCAGTGTTTCAG 60.179 55.000 0.00 0.00 0.00 3.02
1272 1285 2.455565 CGGGAGGGAGGCCATGAAT 61.456 63.158 5.01 0.00 0.00 2.57
1623 1637 2.652530 CGGAAGTCGTCGGGGAAA 59.347 61.111 0.00 0.00 0.00 3.13
2124 2138 1.376037 GTTGAAGAGCACGAGGGGG 60.376 63.158 0.00 0.00 0.00 5.40
2227 2241 6.863126 AGGTCAAATGAAGCAATTTAGTTTCG 59.137 34.615 0.00 0.00 32.20 3.46
2268 2283 0.898320 GGACTAGCTGAGCCTGAACA 59.102 55.000 0.00 0.00 0.00 3.18
2367 2385 9.624697 GTTTCTAACATGAACATATTTTGAGCA 57.375 29.630 0.00 0.00 0.00 4.26
2378 2396 6.831353 TCAGGGAAAAGTTTCTAACATGAACA 59.169 34.615 0.00 0.00 37.35 3.18
2380 2398 7.889873 TTCAGGGAAAAGTTTCTAACATGAA 57.110 32.000 0.00 4.68 37.35 2.57
2448 2483 0.682209 AAAATCTGATGCGCCCTGCT 60.682 50.000 4.18 0.00 46.63 4.24
2461 2496 3.385755 ACCTTTCTGCTGCAACAAAATCT 59.614 39.130 3.02 0.00 0.00 2.40
2473 2508 1.961277 CGGCGTTCACCTTTCTGCT 60.961 57.895 0.00 0.00 0.00 4.24
2496 2560 3.288308 AACCGAGCTGAGCGAGTGG 62.288 63.158 0.00 2.12 0.00 4.00
2497 2561 1.803519 GAACCGAGCTGAGCGAGTG 60.804 63.158 0.00 0.00 0.00 3.51
2499 2563 2.578178 CGAACCGAGCTGAGCGAG 60.578 66.667 0.00 0.00 0.00 5.03
2528 2595 1.821136 CAAGTTTTCCCATGGCCTCTC 59.179 52.381 6.09 0.00 0.00 3.20
2529 2596 1.428912 TCAAGTTTTCCCATGGCCTCT 59.571 47.619 6.09 0.00 0.00 3.69
2532 2599 3.960102 TGATATCAAGTTTTCCCATGGCC 59.040 43.478 6.09 0.00 0.00 5.36
2538 2605 3.877508 CCTCCGTGATATCAAGTTTTCCC 59.122 47.826 16.05 0.00 0.00 3.97
2577 2644 5.413833 ACACTCAACAGAATCATCAATCACC 59.586 40.000 0.00 0.00 0.00 4.02
2586 2653 5.448496 CGGTTTTGAACACTCAACAGAATCA 60.448 40.000 0.00 0.00 41.34 2.57
2697 2766 1.208535 ACGAAACACCAGACCACAAGA 59.791 47.619 0.00 0.00 0.00 3.02
2725 2794 4.689612 TCAGCCTATAACATGTTCTCCC 57.310 45.455 15.85 1.39 0.00 4.30
2762 2831 3.632855 TCCGAGACATGATCTTGATCG 57.367 47.619 22.10 22.10 40.99 3.69
2773 2843 0.387202 CGATGAGCCTTCCGAGACAT 59.613 55.000 0.00 0.00 0.00 3.06
2779 2849 2.892425 GCCACGATGAGCCTTCCG 60.892 66.667 0.00 0.00 0.00 4.30
2853 2924 2.550978 GCAGCCTATCAAAAGCGAGTA 58.449 47.619 0.00 0.00 0.00 2.59
2909 2980 4.209538 CAAGCCCATGTATCATTCCTCAA 58.790 43.478 0.00 0.00 0.00 3.02
2957 3028 1.302431 CACGGGTCAATCTGCACCA 60.302 57.895 0.00 0.00 33.91 4.17
2958 3029 2.040544 CCACGGGTCAATCTGCACC 61.041 63.158 0.00 0.00 0.00 5.01
2959 3030 2.040544 CCCACGGGTCAATCTGCAC 61.041 63.158 0.00 0.00 0.00 4.57
2964 3035 0.037734 AAACCTCCCACGGGTCAATC 59.962 55.000 1.07 0.00 35.83 2.67
3019 3090 2.507886 TCACAAACCCACCTTCTCAAGA 59.492 45.455 0.00 0.00 0.00 3.02
3084 3155 9.461312 AGCAAAAGTGAGGTATTTGTTCATATA 57.539 29.630 0.00 0.00 36.63 0.86
3112 3183 1.365633 GCCTAGGCGACCAGATGAG 59.634 63.158 20.16 0.00 0.00 2.90
3149 3220 1.043116 ATCCTTCATGCCGGAGTCGA 61.043 55.000 5.05 0.00 39.00 4.20


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

AutoCloner maintained by Alex Coulton.