Multiple sequence alignment - TraesCS3D01G162800

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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 TraesCS3D01G162800 chr3D 100.000 3188 0 0 1 3188 134173975 134177162 0 5888
1 TraesCS3D01G162800 chr3A 93.300 3209 128 37 9 3187 147811686 147814837 0 4654
2 TraesCS3D01G162800 chr3B 94.630 2551 82 23 9 2543 190489372 190491883 0 3901
3 TraesCS3D01G162800 chr3B 89.537 669 54 12 2528 3188 190574660 190575320 0 833


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 TraesCS3D01G162800 chr3D 134173975 134177162 3187 False 5888 5888 100.000 1 3188 1 chr3D.!!$F1 3187
1 TraesCS3D01G162800 chr3A 147811686 147814837 3151 False 4654 4654 93.300 9 3187 1 chr3A.!!$F1 3178
2 TraesCS3D01G162800 chr3B 190489372 190491883 2511 False 3901 3901 94.630 9 2543 1 chr3B.!!$F1 2534
3 TraesCS3D01G162800 chr3B 190574660 190575320 660 False 833 833 89.537 2528 3188 1 chr3B.!!$F2 660

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
188 189 2.112190 GACCTAGGCTTAAGCACCTCT 58.888 52.381 27.83 17.62 44.36 3.69 F
1075 1097 0.039256 CCAATAATCAATGGCGCCCG 60.039 55.000 26.77 13.03 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 1935 0.467106 CGGGCTCTGATCCTCTCTCA 60.467 60.0 0.0 0.0 0.00 3.27 R
2412 2451 0.541863 ATAGTTGGCGGGGACAAGAG 59.458 55.0 0.0 0.0 27.77 2.85 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
63 64 2.660553 TTTGCACAGCACGCGAAAGG 62.661 55.000 15.93 1.50 38.71 3.11
170 171 2.479566 TCTCCCAAATCTGCACTGAC 57.520 50.000 0.00 0.00 0.00 3.51
188 189 2.112190 GACCTAGGCTTAAGCACCTCT 58.888 52.381 27.83 17.62 44.36 3.69
1074 1096 3.892200 CCAATAATCAATGGCGCCC 57.108 52.632 26.77 6.44 0.00 6.13
1075 1097 0.039256 CCAATAATCAATGGCGCCCG 60.039 55.000 26.77 13.03 0.00 6.13
1076 1098 0.039256 CAATAATCAATGGCGCCCGG 60.039 55.000 26.77 13.69 0.00 5.73
1490 1516 7.676947 AGCTGTAAGTACCTACTTGAAAATCA 58.323 34.615 7.81 0.00 45.44 2.57
1491 1517 7.819900 AGCTGTAAGTACCTACTTGAAAATCAG 59.180 37.037 7.81 7.50 45.44 2.90
1860 1886 4.202060 TGAGCTTGATAGATCGAAGTGTCC 60.202 45.833 0.00 0.00 39.68 4.02
1925 1953 1.039856 GTGAGAGAGGATCAGAGCCC 58.960 60.000 0.00 0.00 37.82 5.19
1953 1981 7.072961 AGGAAGGCCTTAGAATTAGATTGATCA 59.927 37.037 20.54 0.00 43.90 2.92
1956 1984 9.652114 AAGGCCTTAGAATTAGATTGATCAATT 57.348 29.630 18.87 13.62 0.00 2.32
2027 2055 1.097232 CGGAATGGCTGATGCTTTCA 58.903 50.000 0.00 0.00 39.59 2.69
2045 2073 5.500234 CTTTCATTCTGGAACTGTGGGATA 58.500 41.667 0.00 0.00 0.00 2.59
2054 2082 5.989477 TGGAACTGTGGGATAACTGATAAG 58.011 41.667 0.00 0.00 0.00 1.73
2226 2262 0.036010 GGCTGTGATGTGCCTGTACT 60.036 55.000 0.00 0.00 45.26 2.73
2227 2263 1.611673 GGCTGTGATGTGCCTGTACTT 60.612 52.381 0.00 0.00 45.26 2.24
2228 2264 1.466167 GCTGTGATGTGCCTGTACTTG 59.534 52.381 0.00 0.00 0.00 3.16
2229 2265 2.079158 CTGTGATGTGCCTGTACTTGG 58.921 52.381 0.00 0.00 0.00 3.61
2292 2328 3.606153 GCAAACATGTCTGTCCGTTGTAC 60.606 47.826 0.00 0.00 33.36 2.90
2301 2337 2.180017 CCGTTGTACCGGGAGTCG 59.820 66.667 6.32 1.81 44.32 4.18
2303 2339 1.136147 CGTTGTACCGGGAGTCGAG 59.864 63.158 6.32 0.00 42.43 4.04
2356 2395 3.459969 AGTCCAATACCCTCCTTCCAATC 59.540 47.826 0.00 0.00 0.00 2.67
2357 2396 3.202151 GTCCAATACCCTCCTTCCAATCA 59.798 47.826 0.00 0.00 0.00 2.57
2358 2397 3.459598 TCCAATACCCTCCTTCCAATCAG 59.540 47.826 0.00 0.00 0.00 2.90
2362 2401 1.279271 ACCCTCCTTCCAATCAGTTCG 59.721 52.381 0.00 0.00 0.00 3.95
2372 2411 7.548075 TCCTTCCAATCAGTTCGTATTCTTTAC 59.452 37.037 0.00 0.00 0.00 2.01
2378 2417 9.530129 CAATCAGTTCGTATTCTTTACTGAAAC 57.470 33.333 7.25 0.00 45.67 2.78
2412 2451 1.546834 GTGTCGTCGCTTATCCTCAC 58.453 55.000 0.00 0.00 0.00 3.51
2416 2455 2.097791 GTCGTCGCTTATCCTCACTCTT 59.902 50.000 0.00 0.00 0.00 2.85
2426 2465 2.525629 TCACTCTTGTCCCCGCCA 60.526 61.111 0.00 0.00 0.00 5.69
2447 2496 5.687441 GCCAACTATGACCAAGGTATCATCA 60.687 44.000 0.00 0.00 36.87 3.07
2448 2497 5.760253 CCAACTATGACCAAGGTATCATCAC 59.240 44.000 0.00 0.00 36.87 3.06
2451 2500 6.349300 ACTATGACCAAGGTATCATCACAAC 58.651 40.000 0.00 0.00 36.87 3.32
2452 2501 4.632327 TGACCAAGGTATCATCACAACA 57.368 40.909 0.00 0.00 0.00 3.33
2453 2502 4.323417 TGACCAAGGTATCATCACAACAC 58.677 43.478 0.00 0.00 0.00 3.32
2454 2503 3.334691 ACCAAGGTATCATCACAACACG 58.665 45.455 0.00 0.00 0.00 4.49
2455 2504 3.244422 ACCAAGGTATCATCACAACACGT 60.244 43.478 0.00 0.00 0.00 4.49
2456 2505 3.370978 CCAAGGTATCATCACAACACGTC 59.629 47.826 0.00 0.00 0.00 4.34
2457 2506 3.247006 AGGTATCATCACAACACGTCC 57.753 47.619 0.00 0.00 0.00 4.79
2458 2507 1.924524 GGTATCATCACAACACGTCCG 59.075 52.381 0.00 0.00 0.00 4.79
2459 2508 2.416296 GGTATCATCACAACACGTCCGA 60.416 50.000 0.00 0.00 0.00 4.55
2460 2509 2.448926 ATCATCACAACACGTCCGAA 57.551 45.000 0.00 0.00 0.00 4.30
2461 2510 1.493772 TCATCACAACACGTCCGAAC 58.506 50.000 0.00 0.00 0.00 3.95
2502 2551 3.108289 CTCAGCCAGCACACGACG 61.108 66.667 0.00 0.00 0.00 5.12
2525 2574 1.609061 CCTGTCATTGAACCGAGCTGT 60.609 52.381 0.00 0.00 0.00 4.40
2574 2623 6.932356 ATTAATCTAGTCGAGTTGGACGTA 57.068 37.500 0.00 0.00 41.81 3.57
2600 2649 2.124236 CCCCGACGAGCTACTCCT 60.124 66.667 0.00 0.00 0.00 3.69
2689 2738 2.414994 ATGAGACATGGAGCAGTTGG 57.585 50.000 0.00 0.00 0.00 3.77
2752 2801 1.630369 CTGAAATGGTGGAGGTGAGGA 59.370 52.381 0.00 0.00 0.00 3.71
2762 2811 0.629058 GAGGTGAGGAGGGAGAGAGT 59.371 60.000 0.00 0.00 0.00 3.24
2789 2838 2.481952 CCGAGGAAAGAAAGAAGCACAG 59.518 50.000 0.00 0.00 0.00 3.66
2798 2847 5.753721 AGAAAGAAGCACAGGATAGAACT 57.246 39.130 0.00 0.00 0.00 3.01
2799 2848 6.120507 AGAAAGAAGCACAGGATAGAACTT 57.879 37.500 0.00 0.00 0.00 2.66
2892 2950 3.204158 TGCCCCCATTACTTCACACATAT 59.796 43.478 0.00 0.00 0.00 1.78
2893 2951 4.413851 TGCCCCCATTACTTCACACATATA 59.586 41.667 0.00 0.00 0.00 0.86
2934 2992 3.316308 GCAACATAACTCTTATGGGCCAG 59.684 47.826 13.78 0.00 45.67 4.85
2938 2996 5.826643 ACATAACTCTTATGGGCCAGAAAA 58.173 37.500 15.40 0.00 45.67 2.29
2958 3016 3.319198 GGAGGCAGTCCAACCCGA 61.319 66.667 0.00 0.00 46.10 5.14
3067 3125 5.351233 TTTTGTCGCCATGTAGTACAAAG 57.649 39.130 7.16 2.88 40.13 2.77
3093 3151 5.984233 TTATTTTGATACTGTGGCTAGCG 57.016 39.130 9.00 0.00 0.00 4.26
3117 3175 3.837213 ATGCTCGATTTTCAACACAGG 57.163 42.857 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 171 1.067821 CGAGAGGTGCTTAAGCCTAGG 59.932 57.143 24.30 3.67 41.18 3.02
188 189 4.944962 ATGCGTTGAAAAATGAGATCGA 57.055 36.364 0.00 0.00 0.00 3.59
371 372 6.325919 GCAGATGAGTAAGTACTGCTAGAT 57.674 41.667 0.00 0.00 46.66 1.98
372 373 5.759506 GCAGATGAGTAAGTACTGCTAGA 57.240 43.478 0.00 0.00 46.66 2.43
537 544 3.969117 ACTCGTGTAGTTTGACGTACA 57.031 42.857 0.00 0.00 33.35 2.90
545 552 2.450609 ATCGCCAACTCGTGTAGTTT 57.549 45.000 0.00 0.00 46.61 2.66
1073 1095 1.457643 TAGGAGTCCATGAGGCCGG 60.458 63.158 12.86 0.00 33.74 6.13
1074 1096 0.757188 AGTAGGAGTCCATGAGGCCG 60.757 60.000 12.86 0.00 33.74 6.13
1075 1097 1.139853 CAAGTAGGAGTCCATGAGGCC 59.860 57.143 12.86 0.00 33.74 5.19
1076 1098 1.834263 ACAAGTAGGAGTCCATGAGGC 59.166 52.381 12.86 0.00 33.74 4.70
1593 1619 2.049433 GCTGTACTGCACGTCGGT 60.049 61.111 18.75 0.00 38.08 4.69
1790 1816 3.117550 TCAGCTCCAGATCTAGCTCTTCT 60.118 47.826 15.72 0.00 45.92 2.85
1843 1869 6.961360 ATTAGTGGACACTTCGATCTATCA 57.039 37.500 10.57 0.00 42.54 2.15
1860 1886 5.064579 TGCACGGACACATGATTAATTAGTG 59.935 40.000 0.00 11.83 36.34 2.74
1907 1935 0.467106 CGGGCTCTGATCCTCTCTCA 60.467 60.000 0.00 0.00 0.00 3.27
1925 1953 4.939052 TCTAATTCTAAGGCCTTCCTCG 57.061 45.455 24.49 9.43 43.40 4.63
1953 1981 5.057149 CCGCCAGTTTGATAGCTAGTAATT 58.943 41.667 0.00 0.00 0.00 1.40
1956 1984 3.028850 ACCGCCAGTTTGATAGCTAGTA 58.971 45.455 0.00 0.00 0.00 1.82
1957 1985 1.831736 ACCGCCAGTTTGATAGCTAGT 59.168 47.619 0.00 0.00 0.00 2.57
1958 1986 2.205074 CACCGCCAGTTTGATAGCTAG 58.795 52.381 0.00 0.00 0.00 3.42
2027 2055 4.536090 TCAGTTATCCCACAGTTCCAGAAT 59.464 41.667 0.00 0.00 0.00 2.40
2071 2099 8.097038 ACAAGATTTACATGCATATATCGGTCT 58.903 33.333 0.00 0.00 0.00 3.85
2130 2158 9.330063 CAACACATGTATATGTTTCCTCTACAT 57.670 33.333 1.82 0.00 45.01 2.29
2226 2262 1.444933 AGAGTCATGGACCCAACCAA 58.555 50.000 0.00 0.00 43.47 3.67
2227 2263 1.444933 AAGAGTCATGGACCCAACCA 58.555 50.000 0.00 0.00 44.41 3.67
2228 2264 2.586648 AAAGAGTCATGGACCCAACC 57.413 50.000 0.00 0.00 32.18 3.77
2229 2265 2.820197 GGAAAAGAGTCATGGACCCAAC 59.180 50.000 0.00 0.00 32.18 3.77
2269 2305 0.951558 AACGGACAGACATGTTTGCC 59.048 50.000 15.86 15.59 40.68 4.52
2292 2328 2.505405 TGAGATAATCTCGACTCCCGG 58.495 52.381 0.00 0.00 46.25 5.73
2299 2335 2.894731 AGGGGCATGAGATAATCTCGA 58.105 47.619 0.00 0.00 46.25 4.04
2300 2336 3.430098 GCTAGGGGCATGAGATAATCTCG 60.430 52.174 0.00 0.00 42.57 4.04
2301 2337 3.774216 AGCTAGGGGCATGAGATAATCTC 59.226 47.826 0.00 0.00 42.75 2.75
2303 2339 3.118445 GGAGCTAGGGGCATGAGATAATC 60.118 52.174 0.00 0.00 44.79 1.75
2337 2376 3.203040 ACTGATTGGAAGGAGGGTATTGG 59.797 47.826 0.00 0.00 0.00 3.16
2356 2395 9.878599 ATTTGTTTCAGTAAAGAATACGAACTG 57.121 29.630 0.00 0.00 39.10 3.16
2358 2397 9.037417 CGATTTGTTTCAGTAAAGAATACGAAC 57.963 33.333 0.00 0.00 33.29 3.95
2362 2401 7.961283 GGGACGATTTGTTTCAGTAAAGAATAC 59.039 37.037 0.00 0.00 28.99 1.89
2372 2411 2.157668 CGAGTGGGACGATTTGTTTCAG 59.842 50.000 0.00 0.00 0.00 3.02
2378 2417 1.068474 GACACGAGTGGGACGATTTG 58.932 55.000 8.19 0.00 34.19 2.32
2412 2451 0.541863 ATAGTTGGCGGGGACAAGAG 59.458 55.000 0.00 0.00 27.77 2.85
2416 2455 1.600107 GTCATAGTTGGCGGGGACA 59.400 57.895 0.00 0.00 0.00 4.02
2426 2465 6.560003 TGTGATGATACCTTGGTCATAGTT 57.440 37.500 0.00 0.00 35.33 2.24
2454 2503 0.992802 GAGATTGAGCACGTTCGGAC 59.007 55.000 0.00 0.00 0.00 4.79
2455 2504 0.601057 TGAGATTGAGCACGTTCGGA 59.399 50.000 0.00 0.00 0.00 4.55
2456 2505 1.391485 CTTGAGATTGAGCACGTTCGG 59.609 52.381 0.00 0.00 0.00 4.30
2457 2506 1.391485 CCTTGAGATTGAGCACGTTCG 59.609 52.381 0.00 0.00 0.00 3.95
2458 2507 2.158449 CACCTTGAGATTGAGCACGTTC 59.842 50.000 0.00 0.00 0.00 3.95
2459 2508 2.146342 CACCTTGAGATTGAGCACGTT 58.854 47.619 0.00 0.00 0.00 3.99
2460 2509 1.344438 TCACCTTGAGATTGAGCACGT 59.656 47.619 0.00 0.00 0.00 4.49
2461 2510 2.084610 TCACCTTGAGATTGAGCACG 57.915 50.000 0.00 0.00 0.00 5.34
2502 2551 0.798776 CTCGGTTCAATGACAGGTGC 59.201 55.000 0.00 0.00 0.00 5.01
2548 2597 7.765307 ACGTCCAACTCGACTAGATTAATTTA 58.235 34.615 0.00 0.00 0.00 1.40
2581 2630 2.479750 GGAGTAGCTCGTCGGGGAC 61.480 68.421 0.00 0.00 0.00 4.46
2672 2721 2.011046 GCTCCAACTGCTCCATGTCTC 61.011 57.143 0.00 0.00 0.00 3.36
2723 2772 1.415659 CCACCATTTCAGGTTTTGCCA 59.584 47.619 0.00 0.00 40.77 4.92
2752 2801 1.680651 CGGCACTCACTCTCTCCCT 60.681 63.158 0.00 0.00 0.00 4.20
2762 2811 1.691976 TCTTTCTTTCCTCGGCACTCA 59.308 47.619 0.00 0.00 0.00 3.41
2789 2838 8.421673 AAGTAAGAATACGCAAAGTTCTATCC 57.578 34.615 0.00 0.00 37.11 2.59
2864 2921 4.648762 TGTGAAGTAATGGGGGCATAAATG 59.351 41.667 0.00 0.00 0.00 2.32
2872 2929 8.477419 AAATTATATGTGTGAAGTAATGGGGG 57.523 34.615 0.00 0.00 0.00 5.40
2901 2959 2.159366 AGTTATGTTGCGACGGAGAGAG 60.159 50.000 0.00 0.00 0.00 3.20
2910 2968 3.202906 GCCCATAAGAGTTATGTTGCGA 58.797 45.455 6.05 0.00 41.08 5.10
2934 2992 1.001706 GTTGGACTGCCTCCGTTTTTC 60.002 52.381 0.00 0.00 43.03 2.29
2938 2996 2.430367 GGTTGGACTGCCTCCGTT 59.570 61.111 0.00 0.00 43.03 4.44
3067 3125 6.638468 GCTAGCCACAGTATCAAAATAATTGC 59.362 38.462 2.29 0.00 0.00 3.56
3082 3140 1.864862 GCATATGCGCTAGCCACAG 59.135 57.895 12.82 0.00 44.33 3.66
3093 3151 4.661125 TGTGTTGAAAATCGAGCATATGC 58.339 39.130 20.36 20.36 42.49 3.14
3117 3175 1.749063 AAGGCTTTATTACCTTGCCGC 59.251 47.619 0.00 0.00 44.65 6.53


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

AutoCloner maintained by Alex Coulton.