Multiple sequence alignment - TraesCS5D01G239000

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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 TraesCS5D01G239000 chr5D 100.000 3238 0 0 1 3238 347275288 347278525 0.000000 5980.0
1 TraesCS5D01G239000 chr5A 94.805 3253 118 22 1 3238 444597583 444594367 0.000000 5024.0
2 TraesCS5D01G239000 chr5B 92.197 1807 95 24 1 1792 403857578 403855803 0.000000 2514.0
3 TraesCS5D01G239000 chr5B 94.153 496 29 0 1832 2327 403855825 403855330 0.000000 756.0
4 TraesCS5D01G239000 chr5B 100.000 30 0 0 1793 1822 403855840 403855811 0.000451 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 TraesCS5D01G239000 chr5D 347275288 347278525 3237 False 5980.000000 5980 100.000 1 3238 1 chr5D.!!$F1 3237
1 TraesCS5D01G239000 chr5A 444594367 444597583 3216 True 5024.000000 5024 94.805 1 3238 1 chr5A.!!$R1 3237
2 TraesCS5D01G239000 chr5B 403855330 403857578 2248 True 1108.833333 2514 95.450 1 2327 3 chr5B.!!$R1 2326

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
690 699 0.17914 CCAAGCTCTCTCTCTCACGC 60.179 60.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2529 2576 0.391597 CGTATGATTGTAGGGCGGGT 59.608 55.0 0.0 0.0 0.0 5.28 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
161 164 0.469917 ACACCAGACCACTGTGAAGG 59.530 55.000 9.86 7.68 42.05 3.46
162 165 0.250467 CACCAGACCACTGTGAAGGG 60.250 60.000 9.86 7.67 42.05 3.95
163 166 1.302832 CCAGACCACTGTGAAGGGC 60.303 63.158 9.86 0.00 42.05 5.19
194 197 6.849811 CGAATAGATTTGATGACATGCAGTTC 59.150 38.462 0.00 0.00 0.00 3.01
204 208 5.643379 TGACATGCAGTTCCTATTTTTCC 57.357 39.130 0.00 0.00 0.00 3.13
208 212 8.271458 TGACATGCAGTTCCTATTTTTCCTATA 58.729 33.333 0.00 0.00 0.00 1.31
294 298 8.996271 AGAAAAGAAAAGGAAAATGATGAATGC 58.004 29.630 0.00 0.00 0.00 3.56
298 302 8.992835 AGAAAAGGAAAATGATGAATGCTTAC 57.007 30.769 0.00 0.00 0.00 2.34
328 332 7.581011 AACTTGTGTTCTTTTTGTGCTAAAG 57.419 32.000 0.00 0.00 34.63 1.85
343 347 7.147143 TGTGCTAAAGTTGTGTTCTTTGTTA 57.853 32.000 0.00 0.00 36.65 2.41
497 504 0.748005 CCATCGAAAAGCCGTCCCAT 60.748 55.000 0.00 0.00 0.00 4.00
525 532 1.335964 TGATAGTGATCGCCGCTAAGC 60.336 52.381 1.76 0.00 40.83 3.09
526 533 0.962489 ATAGTGATCGCCGCTAAGCT 59.038 50.000 1.76 0.00 40.83 3.74
527 534 1.601166 TAGTGATCGCCGCTAAGCTA 58.399 50.000 1.76 0.00 35.12 3.32
528 535 0.744874 AGTGATCGCCGCTAAGCTAA 59.255 50.000 1.76 0.00 33.01 3.09
529 536 1.132588 GTGATCGCCGCTAAGCTAAG 58.867 55.000 0.00 0.00 0.00 2.18
553 560 6.262496 AGTTGAAAGTGCTTCCTAAACCTAAC 59.738 38.462 0.00 0.00 32.53 2.34
568 575 8.979534 CCTAAACCTAACAGGAAGAGTTATAGT 58.020 37.037 0.00 0.00 37.67 2.12
682 691 3.008049 TGAAGTTTACCCCAAGCTCTCTC 59.992 47.826 0.00 0.00 0.00 3.20
683 692 2.909217 AGTTTACCCCAAGCTCTCTCT 58.091 47.619 0.00 0.00 0.00 3.10
684 693 2.835156 AGTTTACCCCAAGCTCTCTCTC 59.165 50.000 0.00 0.00 0.00 3.20
685 694 2.835156 GTTTACCCCAAGCTCTCTCTCT 59.165 50.000 0.00 0.00 0.00 3.10
686 695 2.445682 TACCCCAAGCTCTCTCTCTC 57.554 55.000 0.00 0.00 0.00 3.20
687 696 0.411452 ACCCCAAGCTCTCTCTCTCA 59.589 55.000 0.00 0.00 0.00 3.27
688 697 0.823460 CCCCAAGCTCTCTCTCTCAC 59.177 60.000 0.00 0.00 0.00 3.51
689 698 0.455410 CCCAAGCTCTCTCTCTCACG 59.545 60.000 0.00 0.00 0.00 4.35
690 699 0.179140 CCAAGCTCTCTCTCTCACGC 60.179 60.000 0.00 0.00 0.00 5.34
691 700 0.523125 CAAGCTCTCTCTCTCACGCG 60.523 60.000 3.53 3.53 0.00 6.01
692 701 2.265073 AAGCTCTCTCTCTCACGCGC 62.265 60.000 5.73 0.00 0.00 6.86
693 702 2.022623 CTCTCTCTCTCACGCGCG 59.977 66.667 30.96 30.96 0.00 6.86
694 703 4.167359 TCTCTCTCTCACGCGCGC 62.167 66.667 32.58 23.91 0.00 6.86
736 767 0.882927 GTAGTTGCACCAAGACGGCA 60.883 55.000 0.00 0.00 39.03 5.69
937 968 3.308438 TTGGTACCTAGAAACGAGTGC 57.692 47.619 14.36 0.00 0.00 4.40
1059 1097 0.038159 AGCAGTCGAGGCAGTACAAC 60.038 55.000 11.19 0.00 0.00 3.32
1092 1130 2.972713 AGAGAACTTAACAGCCTGGTGA 59.027 45.455 2.95 0.00 0.00 4.02
1121 1159 1.227615 GAGCTCAGCATCCCTCTGC 60.228 63.158 9.40 0.00 42.62 4.26
1137 1175 3.462021 CTCTGCCTAGTTATCACCTTGC 58.538 50.000 0.00 0.00 0.00 4.01
1154 1192 3.760684 CCTTGCTGGCATTCTACTTCTTT 59.239 43.478 0.00 0.00 0.00 2.52
1355 1393 4.382386 AGCCAAAGGTATGGTAGTGTTT 57.618 40.909 0.00 0.00 42.75 2.83
1410 1449 7.600752 AGTGAGCTTTGTTCTAGACTTCATAAC 59.399 37.037 0.00 0.00 0.00 1.89
1713 1758 3.562176 GGAAAAGGAGGAAGCTTCATGGA 60.562 47.826 27.02 0.00 0.00 3.41
1752 1797 4.901250 AGTTCTTTGGGATTCATGTGGTTT 59.099 37.500 0.00 0.00 0.00 3.27
1755 1800 2.692709 TGGGATTCATGTGGTTTGGT 57.307 45.000 0.00 0.00 0.00 3.67
1769 1814 3.580895 TGGTTTGGTGTACTCAGCTATCA 59.419 43.478 0.00 0.00 41.91 2.15
1972 2017 3.141488 CAGGACTACGCGCCCTCT 61.141 66.667 5.73 0.00 0.00 3.69
2017 2062 0.608640 CGGGTTGGAACTGAGCTAGT 59.391 55.000 0.00 0.00 42.89 2.57
2031 2076 2.687200 TAGTGCAGCCCGGGTCAT 60.687 61.111 24.63 5.65 0.00 3.06
2032 2077 2.257409 CTAGTGCAGCCCGGGTCATT 62.257 60.000 24.63 16.28 0.00 2.57
2079 2124 5.412286 GGTTTCATTTAGTTAACCAGCCGTA 59.588 40.000 0.88 0.00 39.80 4.02
2086 2131 1.080298 TTAACCAGCCGTATTGTGCG 58.920 50.000 0.00 0.00 0.00 5.34
2126 2171 6.347881 GTGATGCTCACGATCTTAATTTACG 58.652 40.000 0.00 0.00 37.67 3.18
2161 2206 8.313292 TGCTTGAAAGATGCCAACTTATTTTAT 58.687 29.630 0.00 0.00 0.00 1.40
2245 2290 8.156820 TCAACCATGACCATTCTATCGATAAAT 58.843 33.333 6.58 6.77 0.00 1.40
2274 2319 1.730612 CGAACGGTTTTTCTCCCTAGC 59.269 52.381 0.00 0.00 0.00 3.42
2286 2331 0.691078 TCCCTAGCGCTTCCTTCCAT 60.691 55.000 18.68 0.00 0.00 3.41
2309 2354 3.087031 CAACGTTGTCTCCCCTACTCTA 58.913 50.000 20.21 0.00 0.00 2.43
2337 2382 2.855180 CTGCCAATAGCTTGTTGTTCG 58.145 47.619 0.00 0.00 44.23 3.95
2389 2436 2.813179 GCACTAACCATCGCTGCGG 61.813 63.158 23.03 8.78 0.00 5.69
2412 2459 0.393537 CCACTGATGCCACCTTCTCC 60.394 60.000 0.00 0.00 0.00 3.71
2435 2482 1.133809 ACCCCTAGCAGCAGTTTCCA 61.134 55.000 0.00 0.00 0.00 3.53
2445 2492 2.030562 AGTTTCCAGCGGGTGTCG 59.969 61.111 1.81 0.00 42.76 4.35
2500 2547 4.006319 CGCCTTTTCTTCCTCTTCTTCAT 58.994 43.478 0.00 0.00 0.00 2.57
2529 2576 2.560981 TCGCTTGAGTTGTATGTCTCCA 59.439 45.455 0.00 0.00 0.00 3.86
2530 2577 2.668457 CGCTTGAGTTGTATGTCTCCAC 59.332 50.000 0.00 0.00 0.00 4.02
2552 2599 2.124903 CGCCCTACAATCATACGTCAC 58.875 52.381 0.00 0.00 0.00 3.67
2565 2612 0.171455 ACGTCACTGAATCTCTCGCC 59.829 55.000 0.00 0.00 0.00 5.54
2572 2619 5.918011 GTCACTGAATCTCTCGCCTATTAAG 59.082 44.000 0.00 0.00 0.00 1.85
2582 2629 1.940613 CGCCTATTAAGACCAACTGGC 59.059 52.381 0.00 0.00 39.32 4.85
2587 2634 4.273480 CCTATTAAGACCAACTGGCGAATG 59.727 45.833 0.00 0.00 39.32 2.67
2697 2744 6.136541 AGGAGCTCAAAACTGTAACAAAAG 57.863 37.500 17.19 0.00 0.00 2.27
2854 2902 6.647067 GTGGCGACTTAAGCAATCTATTATCT 59.353 38.462 1.29 0.00 36.08 1.98
3022 3070 8.474006 AAATATTCCTGCGAACAAAAATAACC 57.526 30.769 0.00 0.00 0.00 2.85
3087 3135 6.417930 CGTATATGTGGGAATATATGCTCGTG 59.582 42.308 0.00 0.00 29.59 4.35
3162 3210 9.532697 GTGAAAACAATAAGCAAAAATGCTATG 57.467 29.630 3.44 6.68 45.54 2.23
3191 3239 6.409704 AGTATGTGAGCACAACTAACATCAT 58.590 36.000 7.46 0.00 46.16 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 132 1.686052 TCTGGTGTCAAAACCCAATGC 59.314 47.619 0.00 0.00 39.70 3.56
161 164 0.868406 CAAATCTATTCGGAGCCGCC 59.132 55.000 3.59 0.00 39.59 6.13
162 165 1.865865 TCAAATCTATTCGGAGCCGC 58.134 50.000 3.59 0.00 39.59 6.53
163 166 3.430218 GTCATCAAATCTATTCGGAGCCG 59.570 47.826 1.74 1.74 41.35 5.52
208 212 9.458727 AGTGAATCTGAACATGAAATCTAATGT 57.541 29.630 0.00 0.00 38.66 2.71
254 258 7.656948 CCTTTTCTTTTCTGATTTATGCCAACA 59.343 33.333 0.00 0.00 0.00 3.33
255 259 7.872483 TCCTTTTCTTTTCTGATTTATGCCAAC 59.128 33.333 0.00 0.00 0.00 3.77
294 298 4.795970 AGAACACAAGTTTGCGAGTAAG 57.204 40.909 0.00 0.00 38.30 2.34
298 302 4.621034 ACAAAAAGAACACAAGTTTGCGAG 59.379 37.500 0.00 0.00 38.30 5.03
328 332 9.543018 GTGCTAATAGATAACAAAGAACACAAC 57.457 33.333 0.00 0.00 0.00 3.32
412 416 9.594478 GGAATTTCCTTTTTGTTTTTCTACAGA 57.406 29.630 8.25 0.00 32.53 3.41
477 484 1.376812 GGGACGGCTTTTCGATGGT 60.377 57.895 0.00 0.00 0.00 3.55
525 532 6.486993 AGGTTTAGGAAGCACTTTCAACTTAG 59.513 38.462 0.00 0.00 37.54 2.18
526 533 6.362248 AGGTTTAGGAAGCACTTTCAACTTA 58.638 36.000 0.00 0.00 37.54 2.24
527 534 5.201243 AGGTTTAGGAAGCACTTTCAACTT 58.799 37.500 0.00 0.00 37.54 2.66
528 535 4.793201 AGGTTTAGGAAGCACTTTCAACT 58.207 39.130 0.00 0.00 37.54 3.16
529 536 6.038936 TGTTAGGTTTAGGAAGCACTTTCAAC 59.961 38.462 0.00 0.00 37.54 3.18
553 560 6.858993 GCACGATTCTACTATAACTCTTCCTG 59.141 42.308 0.00 0.00 0.00 3.86
559 566 4.379204 GCGTGCACGATTCTACTATAACTC 59.621 45.833 41.19 14.56 43.02 3.01
568 575 2.093625 GTCAAATGCGTGCACGATTCTA 59.906 45.455 41.19 22.53 43.02 2.10
645 654 7.094377 GGGTAAACTTCAATGTATGTGATGTGT 60.094 37.037 0.00 0.00 34.60 3.72
690 699 3.506312 GAGAGAGAGAGAGCGCGCG 62.506 68.421 28.44 28.44 0.00 6.86
691 700 2.105960 GAGAGAGAGAGAGAGCGCGC 62.106 65.000 26.66 26.66 0.00 6.86
692 701 0.530650 AGAGAGAGAGAGAGAGCGCG 60.531 60.000 0.00 0.00 0.00 6.86
693 702 1.221414 GAGAGAGAGAGAGAGAGCGC 58.779 60.000 0.00 0.00 0.00 5.92
694 703 1.202417 ACGAGAGAGAGAGAGAGAGCG 60.202 57.143 0.00 0.00 0.00 5.03
695 704 2.604046 ACGAGAGAGAGAGAGAGAGC 57.396 55.000 0.00 0.00 0.00 4.09
696 705 4.253685 ACAAACGAGAGAGAGAGAGAGAG 58.746 47.826 0.00 0.00 0.00 3.20
697 706 4.280436 ACAAACGAGAGAGAGAGAGAGA 57.720 45.455 0.00 0.00 0.00 3.10
937 968 0.105593 ACATGTCATGCCGCCTAGAG 59.894 55.000 12.91 0.00 0.00 2.43
1059 1097 7.307101 GCTGTTAAGTTCTCTTCTCTTGAACAG 60.307 40.741 0.00 0.00 41.56 3.16
1092 1130 1.302285 CTGAGCTCCCCATTGCACT 59.698 57.895 12.15 0.00 0.00 4.40
1121 1159 2.092968 TGCCAGCAAGGTGATAACTAGG 60.093 50.000 0.03 0.00 40.61 3.02
1137 1175 4.156739 GGGAACAAAGAAGTAGAATGCCAG 59.843 45.833 0.00 0.00 0.00 4.85
1154 1192 1.483415 GGTATAGCGTTGGAGGGAACA 59.517 52.381 0.00 0.00 0.00 3.18
1410 1449 4.582701 TGCTGTAAACACCCTTCAAATG 57.417 40.909 0.00 0.00 0.00 2.32
1463 1502 9.828852 TTACATTTTCACACGAACATTATTACC 57.171 29.630 0.00 0.00 0.00 2.85
1713 1758 9.178758 CCCAAAGAACTAACAAATCTAGCTATT 57.821 33.333 0.00 0.00 0.00 1.73
1752 1797 5.483685 ACTTTTGATAGCTGAGTACACCA 57.516 39.130 0.00 0.00 0.00 4.17
1769 1814 7.094377 ACGCTGTATCACCATAATCAAACTTTT 60.094 33.333 0.00 0.00 0.00 2.27
1931 1976 1.751927 CCAGAGCCATCCTTGCACC 60.752 63.158 0.00 0.00 0.00 5.01
1972 2017 3.810188 TGGTGGTTGTTCGGGCCA 61.810 61.111 4.39 0.00 0.00 5.36
2017 2062 1.847798 AAGTAATGACCCGGGCTGCA 61.848 55.000 24.08 17.56 0.00 4.41
2079 2124 3.872696 TCACACAATAGATCCGCACAAT 58.127 40.909 0.00 0.00 0.00 2.71
2086 2131 5.061853 AGCATCACATCACACAATAGATCC 58.938 41.667 0.00 0.00 0.00 3.36
2126 2171 4.155644 GGCATCTTTCAAGCATATCCTAGC 59.844 45.833 0.00 0.00 0.00 3.42
2245 2290 3.057315 AGAAAAACCGTTCGGTCGATAGA 60.057 43.478 17.19 0.00 37.57 1.98
2253 2298 2.344025 CTAGGGAGAAAAACCGTTCGG 58.656 52.381 9.81 9.81 32.50 4.30
2259 2304 1.738350 GAAGCGCTAGGGAGAAAAACC 59.262 52.381 12.05 0.00 0.00 3.27
2263 2308 1.207329 GAAGGAAGCGCTAGGGAGAAA 59.793 52.381 12.05 0.00 0.00 2.52
2274 2319 0.673644 ACGTTGGATGGAAGGAAGCG 60.674 55.000 0.00 0.00 0.00 4.68
2286 2331 0.971386 GTAGGGGAGACAACGTTGGA 59.029 55.000 30.34 4.12 0.00 3.53
2337 2382 4.154015 TCAATGACAACAACATCGATGGAC 59.846 41.667 28.09 11.39 0.00 4.02
2389 2436 3.064324 GGTGGCATCAGTGGTGGC 61.064 66.667 22.45 22.45 41.99 5.01
2412 2459 1.557269 AACTGCTGCTAGGGGTGGAG 61.557 60.000 0.00 0.00 0.00 3.86
2435 2482 1.734707 CGACTAAAATCGACACCCGCT 60.735 52.381 0.00 0.00 45.13 5.52
2478 2525 3.403038 TGAAGAAGAGGAAGAAAAGGCG 58.597 45.455 0.00 0.00 0.00 5.52
2510 2557 3.003480 GGTGGAGACATACAACTCAAGC 58.997 50.000 0.00 0.00 46.14 4.01
2529 2576 0.391597 CGTATGATTGTAGGGCGGGT 59.608 55.000 0.00 0.00 0.00 5.28
2530 2577 0.391597 ACGTATGATTGTAGGGCGGG 59.608 55.000 0.00 0.00 0.00 6.13
2552 2599 5.010112 TGGTCTTAATAGGCGAGAGATTCAG 59.990 44.000 0.00 0.00 0.00 3.02
2565 2612 4.876107 ACATTCGCCAGTTGGTCTTAATAG 59.124 41.667 0.00 0.00 37.57 1.73
2572 2619 4.393680 TGTATAAACATTCGCCAGTTGGTC 59.606 41.667 0.00 0.00 37.57 4.02
2631 2678 9.996554 TTACTAATCTTTGTCATCAAGTTCTCA 57.003 29.630 0.00 0.00 34.88 3.27
2675 2722 4.740205 GCTTTTGTTACAGTTTTGAGCTCC 59.260 41.667 12.15 0.00 0.00 4.70
2697 2744 0.742990 TATTGGCCACTAGTGTGCGC 60.743 55.000 21.18 16.56 42.54 6.09
2735 2782 5.182001 ACCTTGATGCAGTTTGCTACTTAAG 59.818 40.000 0.00 0.00 45.31 1.85
3004 3052 5.226396 TGAATGGTTATTTTTGTTCGCAGG 58.774 37.500 0.00 0.00 0.00 4.85
3100 3148 9.311916 CCTTTTTGTTTCTTGAAATACATGACA 57.688 29.630 0.00 0.00 33.44 3.58
3119 3167 8.089115 TGTTTTCACCTTTTGTTACCTTTTTG 57.911 30.769 0.00 0.00 0.00 2.44
3162 3210 4.457834 AGTTGTGCTCACATACTAGGAC 57.542 45.455 3.31 0.00 41.52 3.85


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

AutoCloner maintained by Alex Coulton.