Multiple sequence alignment - TraesCS5B01G230200

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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 TraesCS5B01G230200 chr5B 100.000 3140 0 0 1 3140 407124773 407127912 0.000000e+00 5799
1 TraesCS5B01G230200 chr5D 93.864 3178 119 16 1 3140 344695270 344692131 0.000000e+00 4719
2 TraesCS5B01G230200 chr5A 93.523 3196 116 21 1 3140 447366626 447369786 0.000000e+00 4671
3 TraesCS5B01G230200 chr1D 89.600 125 11 2 3017 3140 457876138 457876015 1.170000e-34 158


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 TraesCS5B01G230200 chr5B 407124773 407127912 3139 False 5799 5799 100.000 1 3140 1 chr5B.!!$F1 3139
1 TraesCS5B01G230200 chr5D 344692131 344695270 3139 True 4719 4719 93.864 1 3140 1 chr5D.!!$R1 3139
2 TraesCS5B01G230200 chr5A 447366626 447369786 3160 False 4671 4671 93.523 1 3140 1 chr5A.!!$F1 3139

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
29 30 0.370273 GCATCATCGTGTTCACGACC 59.630 55.0 26.16 11.39 45.30 4.79 F
1590 1616 0.034380 TCCTCATCGGAGAAGACGGT 60.034 55.0 0.00 0.00 44.26 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1956 0.456221 AGCTCTCGTAACCGGTCATG 59.544 55.0 8.04 0.00 33.95 3.07 R
2612 2670 0.445436 GTGATTTCAGGCTGCAGACG 59.555 55.0 20.43 11.72 0.00 4.18 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
29 30 0.370273 GCATCATCGTGTTCACGACC 59.630 55.000 26.16 11.39 45.30 4.79
173 174 2.821366 GGCGACCAGGACATGCTG 60.821 66.667 0.00 0.00 0.00 4.41
508 509 2.031857 CGTGCGTTTTAGGTTAGGCAAA 60.032 45.455 0.00 0.00 36.97 3.68
510 511 4.552355 GTGCGTTTTAGGTTAGGCAAAAT 58.448 39.130 0.00 0.00 36.97 1.82
513 514 6.471198 GTGCGTTTTAGGTTAGGCAAAATATC 59.529 38.462 0.00 0.00 36.97 1.63
515 516 6.196571 CGTTTTAGGTTAGGCAAAATATCGG 58.803 40.000 0.00 0.00 0.00 4.18
540 542 6.197096 GGCGCATCTTCAAAGTTTAATGTATG 59.803 38.462 10.83 0.00 0.00 2.39
590 592 1.605457 GCCATGATCGACGGCTTCATA 60.605 52.381 11.51 0.00 42.78 2.15
772 792 2.282110 CCGGTTGCACCATGACCA 60.282 61.111 5.40 0.00 38.47 4.02
834 854 0.875059 GTTCCTTTCGAACCTGCAGG 59.125 55.000 31.60 31.60 44.46 4.85
925 945 1.962822 TTGGCAGAAGCACAGCTCG 60.963 57.895 0.00 0.00 44.61 5.03
1010 1030 2.030274 ACATATTCGCCATGATCGACGA 60.030 45.455 0.00 0.00 35.51 4.20
1015 1035 1.153647 GCCATGATCGACGACCACA 60.154 57.895 0.00 1.45 0.00 4.17
1081 1101 1.018910 CATGATCAACGATGCCTGCA 58.981 50.000 0.00 0.00 0.00 4.41
1097 1120 2.549282 CAACGACGACGCAAAGGG 59.451 61.111 7.30 0.00 43.96 3.95
1359 1382 2.683933 AACCTCGTCGGCCTCCAT 60.684 61.111 0.00 0.00 35.61 3.41
1590 1616 0.034380 TCCTCATCGGAGAAGACGGT 60.034 55.000 0.00 0.00 44.26 4.83
1827 1853 2.120232 GTCGGCAAGATACTCGATGTG 58.880 52.381 0.00 0.00 34.13 3.21
1863 1889 1.342174 AGGAAAACATGGCAGCACTTG 59.658 47.619 0.00 0.00 0.00 3.16
1941 1967 4.823419 CGGCGCCATGACCGGTTA 62.823 66.667 28.98 4.40 45.74 2.85
2169 2217 2.295070 GCCACACCGGAAAAACAACTAT 59.705 45.455 9.46 0.00 36.56 2.12
2171 2219 4.157105 GCCACACCGGAAAAACAACTATAT 59.843 41.667 9.46 0.00 36.56 0.86
2178 2226 6.091713 ACCGGAAAAACAACTATATTGACGAG 59.908 38.462 9.46 0.00 0.00 4.18
2184 2232 8.928844 AAAACAACTATATTGACGAGAAAACG 57.071 30.769 0.00 0.00 39.31 3.60
2192 2240 1.623973 GACGAGAAAACGGCGAAGGG 61.624 60.000 16.62 0.00 37.61 3.95
2229 2277 8.583810 TGTGTATAGCTTGTTTATTACGATCC 57.416 34.615 0.00 0.00 0.00 3.36
2282 2330 4.161565 AGTGGATTGTACAATCTAGGCGAA 59.838 41.667 35.55 17.24 44.90 4.70
2308 2359 9.878599 ATACTTCAATTAAAGTGTCAAAACGAG 57.121 29.630 4.10 0.00 39.74 4.18
2336 2387 3.061831 TGCATGTGAAAAACGCAAAAGTG 59.938 39.130 0.00 0.00 42.43 3.16
2341 2392 5.277825 TGTGAAAAACGCAAAAGTGGATAG 58.722 37.500 0.00 0.00 35.99 2.08
2344 2395 2.989422 AACGCAAAAGTGGATAGCAC 57.011 45.000 0.00 0.00 0.00 4.40
2449 2507 7.707104 ACAGAGTAAATTTTTCCTTGACAGTG 58.293 34.615 0.00 0.00 0.00 3.66
2452 2510 6.273071 AGTAAATTTTTCCTTGACAGTGCAC 58.727 36.000 9.40 9.40 0.00 4.57
2453 2511 4.734398 AATTTTTCCTTGACAGTGCACA 57.266 36.364 21.04 0.00 0.00 4.57
2454 2512 3.781079 TTTTTCCTTGACAGTGCACAG 57.219 42.857 21.04 14.44 0.00 3.66
2455 2513 1.679139 TTTCCTTGACAGTGCACAGG 58.321 50.000 21.04 16.40 0.00 4.00
2456 2514 0.836606 TTCCTTGACAGTGCACAGGA 59.163 50.000 21.04 18.54 0.00 3.86
2457 2515 0.106708 TCCTTGACAGTGCACAGGAC 59.893 55.000 21.04 11.49 0.00 3.85
2458 2516 0.179048 CCTTGACAGTGCACAGGACA 60.179 55.000 21.04 14.00 0.00 4.02
2459 2517 1.224075 CTTGACAGTGCACAGGACAG 58.776 55.000 21.04 5.30 0.00 3.51
2460 2518 0.829990 TTGACAGTGCACAGGACAGA 59.170 50.000 21.04 5.87 0.00 3.41
2461 2519 0.390492 TGACAGTGCACAGGACAGAG 59.610 55.000 21.04 0.62 0.00 3.35
2462 2520 0.320247 GACAGTGCACAGGACAGAGG 60.320 60.000 21.04 0.00 0.00 3.69
2463 2521 0.760567 ACAGTGCACAGGACAGAGGA 60.761 55.000 21.04 0.00 0.00 3.71
2464 2522 0.394192 CAGTGCACAGGACAGAGGAA 59.606 55.000 21.04 0.00 0.00 3.36
2465 2523 0.683973 AGTGCACAGGACAGAGGAAG 59.316 55.000 21.04 0.00 0.00 3.46
2466 2524 0.394565 GTGCACAGGACAGAGGAAGT 59.605 55.000 13.17 0.00 0.00 3.01
2467 2525 0.394192 TGCACAGGACAGAGGAAGTG 59.606 55.000 0.00 0.00 0.00 3.16
2468 2526 0.952984 GCACAGGACAGAGGAAGTGC 60.953 60.000 0.00 0.00 44.31 4.40
2469 2527 0.668706 CACAGGACAGAGGAAGTGCG 60.669 60.000 0.00 0.00 32.12 5.34
2470 2528 1.739562 CAGGACAGAGGAAGTGCGC 60.740 63.158 0.00 0.00 32.12 6.09
2471 2529 2.210013 AGGACAGAGGAAGTGCGCA 61.210 57.895 5.66 5.66 32.12 6.09
2472 2530 1.301716 GGACAGAGGAAGTGCGCAA 60.302 57.895 14.00 0.00 0.00 4.85
2473 2531 0.884704 GGACAGAGGAAGTGCGCAAA 60.885 55.000 14.00 0.00 0.00 3.68
2474 2532 0.514691 GACAGAGGAAGTGCGCAAAG 59.485 55.000 14.00 0.00 0.00 2.77
2590 2648 1.151221 TGGCAGCATGGTCTGTTGT 59.849 52.632 0.00 0.00 38.27 3.32
2599 2657 3.678289 CATGGTCTGTTGTCTCCATCAA 58.322 45.455 0.00 0.00 38.43 2.57
2612 2670 4.759183 GTCTCCATCAATTCTAATCCAGGC 59.241 45.833 0.00 0.00 0.00 4.85
2637 2695 1.736681 GCAGCCTGAAATCACTCAGAC 59.263 52.381 0.00 0.00 44.82 3.51
2644 2702 7.496920 CAGCCTGAAATCACTCAGACATAAATA 59.503 37.037 2.18 0.00 44.82 1.40
2695 2753 2.787601 CCAAATCTGGCAATCCGATG 57.212 50.000 0.00 0.00 35.39 3.84
2718 2776 7.873719 TGTTATACCCATTCTTAACCACATG 57.126 36.000 0.00 0.00 0.00 3.21
2731 2789 8.684386 TCTTAACCACATGTGAACTGAAATTA 57.316 30.769 27.46 8.94 0.00 1.40
2732 2790 8.783093 TCTTAACCACATGTGAACTGAAATTAG 58.217 33.333 27.46 8.00 0.00 1.73
2744 2802 6.881065 TGAACTGAAATTAGCTAGTCTGCATT 59.119 34.615 0.00 0.00 34.99 3.56
2745 2803 7.391554 TGAACTGAAATTAGCTAGTCTGCATTT 59.608 33.333 0.00 0.00 34.99 2.32
2746 2804 8.792830 AACTGAAATTAGCTAGTCTGCATTTA 57.207 30.769 0.00 0.00 34.99 1.40
2787 2845 1.899142 ACCACAGCACAAACCAAAACT 59.101 42.857 0.00 0.00 0.00 2.66
2795 2853 5.294060 CAGCACAAACCAAAACTTTTATGCT 59.706 36.000 0.00 0.00 40.16 3.79
2858 2926 1.599542 GCATAAGAACCACCGATCAGC 59.400 52.381 0.00 0.00 0.00 4.26
2929 2997 5.126545 GGGTTCCAATTATTTACCCTGTCAC 59.873 44.000 10.65 0.00 44.10 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.668212 ATGCCGTCCACGTGGTTG 60.668 61.111 32.74 24.60 37.74 3.77
221 222 3.241530 AGCACTTCGCCCACCTCA 61.242 61.111 0.00 0.00 44.04 3.86
287 288 3.334054 ACCCTGGCCTTCAGCTCC 61.334 66.667 3.32 0.00 42.05 4.70
402 403 0.622665 CCCAAGATCCTGACCTTGCT 59.377 55.000 0.00 0.00 38.65 3.91
508 509 2.254546 TTGAAGATGCGCCCGATATT 57.745 45.000 4.18 0.00 0.00 1.28
510 511 1.134521 ACTTTGAAGATGCGCCCGATA 60.135 47.619 4.18 0.00 0.00 2.92
513 514 0.240945 AAACTTTGAAGATGCGCCCG 59.759 50.000 4.18 0.00 0.00 6.13
515 516 4.485163 ACATTAAACTTTGAAGATGCGCC 58.515 39.130 4.18 0.00 0.00 6.53
540 542 4.280929 AGCTTACAAGAAACCATCAAACCC 59.719 41.667 0.00 0.00 0.00 4.11
590 592 1.139058 AGGTTCGAATATTGCTCGGCT 59.861 47.619 0.00 0.00 36.93 5.52
649 651 3.002277 GGCAAGTATAAGCCGTCCC 57.998 57.895 0.00 0.00 41.70 4.46
676 686 1.768077 GTGGGATGGGAGGAGAGGG 60.768 68.421 0.00 0.00 0.00 4.30
681 701 1.502039 AGTATACGTGGGATGGGAGGA 59.498 52.381 0.00 0.00 0.00 3.71
734 754 2.415608 CCAGCTCCCGTAAGCGAGA 61.416 63.158 0.00 0.00 45.01 4.04
834 854 8.918961 ATATTTCGACGAAGATCCATAGAATC 57.081 34.615 10.61 0.00 0.00 2.52
1043 1063 1.595382 GCGCATATTGCCTCGACCT 60.595 57.895 0.30 0.00 41.12 3.85
1081 1101 3.343421 GCCCTTTGCGTCGTCGTT 61.343 61.111 3.66 0.00 39.49 3.85
1108 1131 1.450491 GCCGCCTTCTCCCTTTCTC 60.450 63.158 0.00 0.00 0.00 2.87
1296 1319 2.271497 CAGGCCTCCTTGAGCAGG 59.729 66.667 0.00 0.00 45.64 4.85
1590 1616 1.866237 GCAGAATTTCACGACGCCA 59.134 52.632 0.00 0.00 0.00 5.69
1725 1751 2.573869 CCGAGCGACCACATGTCT 59.426 61.111 0.00 0.00 42.13 3.41
1844 1870 1.606224 CCAAGTGCTGCCATGTTTTCC 60.606 52.381 0.00 0.00 0.00 3.13
1851 1877 1.001641 GGACTCCAAGTGCTGCCAT 60.002 57.895 0.00 0.00 33.44 4.40
1905 1931 2.126850 CGCACTTCTCGCTGTCGA 60.127 61.111 0.00 0.00 43.28 4.20
1926 1952 3.560278 CGTAACCGGTCATGGCGC 61.560 66.667 8.04 0.00 0.00 6.53
1928 1954 0.527817 CTCTCGTAACCGGTCATGGC 60.528 60.000 8.04 0.00 33.95 4.40
1930 1956 0.456221 AGCTCTCGTAACCGGTCATG 59.544 55.000 8.04 0.00 33.95 3.07
1931 1957 0.456221 CAGCTCTCGTAACCGGTCAT 59.544 55.000 8.04 0.00 33.95 3.06
1932 1958 0.892358 ACAGCTCTCGTAACCGGTCA 60.892 55.000 8.04 0.00 33.95 4.02
1939 1965 0.609957 TCGGGGAACAGCTCTCGTAA 60.610 55.000 0.00 0.00 0.00 3.18
1941 1967 2.282958 TCGGGGAACAGCTCTCGT 60.283 61.111 0.00 0.00 0.00 4.18
1962 1988 4.969196 CCGTGCCACGACAGCAGT 62.969 66.667 20.57 0.00 46.05 4.40
2169 2217 2.350899 TCGCCGTTTTCTCGTCAATA 57.649 45.000 0.00 0.00 0.00 1.90
2171 2219 0.856641 CTTCGCCGTTTTCTCGTCAA 59.143 50.000 0.00 0.00 0.00 3.18
2178 2226 1.161843 TTCATCCCTTCGCCGTTTTC 58.838 50.000 0.00 0.00 0.00 2.29
2184 2232 4.023707 CACATTCTTATTCATCCCTTCGCC 60.024 45.833 0.00 0.00 0.00 5.54
2282 2330 9.878599 CTCGTTTTGACACTTTAATTGAAGTAT 57.121 29.630 14.58 4.40 37.76 2.12
2336 2387 6.749139 TCATATGTAAGTGACTGTGCTATCC 58.251 40.000 1.90 0.00 0.00 2.59
2341 2392 7.584987 AGTTTTTCATATGTAAGTGACTGTGC 58.415 34.615 1.90 0.00 0.00 4.57
2344 2395 9.950680 ACAAAGTTTTTCATATGTAAGTGACTG 57.049 29.630 1.90 0.00 0.00 3.51
2388 2446 6.127591 CCCTCTCATTCGAAGTTAGAGAAGAA 60.128 42.308 24.72 7.00 36.60 2.52
2392 2450 4.601084 ACCCTCTCATTCGAAGTTAGAGA 58.399 43.478 24.72 20.62 36.60 3.10
2393 2451 4.993029 ACCCTCTCATTCGAAGTTAGAG 57.007 45.455 19.68 19.68 34.71 2.43
2410 2468 3.390175 ACTCTGTCTGCAGTATACCCT 57.610 47.619 14.67 0.00 43.05 4.34
2449 2507 0.952984 GCACTTCCTCTGTCCTGTGC 60.953 60.000 0.00 0.00 42.69 4.57
2452 2510 1.739562 GCGCACTTCCTCTGTCCTG 60.740 63.158 0.30 0.00 0.00 3.86
2453 2511 1.758440 TTGCGCACTTCCTCTGTCCT 61.758 55.000 11.12 0.00 0.00 3.85
2454 2512 0.884704 TTTGCGCACTTCCTCTGTCC 60.885 55.000 11.12 0.00 0.00 4.02
2455 2513 0.514691 CTTTGCGCACTTCCTCTGTC 59.485 55.000 11.12 0.00 0.00 3.51
2456 2514 1.510480 GCTTTGCGCACTTCCTCTGT 61.510 55.000 11.12 0.00 38.92 3.41
2457 2515 1.208614 GCTTTGCGCACTTCCTCTG 59.791 57.895 11.12 0.00 38.92 3.35
2458 2516 1.072159 AGCTTTGCGCACTTCCTCT 59.928 52.632 11.12 0.00 42.61 3.69
2459 2517 1.208614 CAGCTTTGCGCACTTCCTC 59.791 57.895 11.12 0.00 42.61 3.71
2460 2518 2.912624 GCAGCTTTGCGCACTTCCT 61.913 57.895 11.12 0.62 42.61 3.36
2461 2519 2.429739 GCAGCTTTGCGCACTTCC 60.430 61.111 11.12 0.00 42.61 3.46
2462 2520 1.728426 CTGCAGCTTTGCGCACTTC 60.728 57.895 11.12 0.00 42.61 3.01
2463 2521 1.727511 TTCTGCAGCTTTGCGCACTT 61.728 50.000 11.12 0.00 42.61 3.16
2464 2522 2.188829 TTCTGCAGCTTTGCGCACT 61.189 52.632 11.12 0.00 42.61 4.40
2465 2523 2.012948 GTTCTGCAGCTTTGCGCAC 61.013 57.895 11.12 0.00 42.61 5.34
2466 2524 2.002509 TTGTTCTGCAGCTTTGCGCA 62.003 50.000 5.66 5.66 42.61 6.09
2467 2525 0.665369 ATTGTTCTGCAGCTTTGCGC 60.665 50.000 9.47 0.00 37.69 6.09
2468 2526 1.454276 CAATTGTTCTGCAGCTTTGCG 59.546 47.619 9.47 0.00 37.69 4.85
2469 2527 1.193874 GCAATTGTTCTGCAGCTTTGC 59.806 47.619 9.47 14.52 39.69 3.68
2470 2528 2.750948 AGCAATTGTTCTGCAGCTTTG 58.249 42.857 9.47 8.88 42.48 2.77
2471 2529 3.128349 CAAGCAATTGTTCTGCAGCTTT 58.872 40.909 9.47 0.00 42.48 3.51
2472 2530 2.750948 CAAGCAATTGTTCTGCAGCTT 58.249 42.857 9.47 4.10 42.48 3.74
2473 2531 1.604693 GCAAGCAATTGTTCTGCAGCT 60.605 47.619 9.47 0.00 42.48 4.24
2474 2532 0.788391 GCAAGCAATTGTTCTGCAGC 59.212 50.000 9.47 0.00 42.48 5.25
2475 2533 2.058798 CTGCAAGCAATTGTTCTGCAG 58.941 47.619 28.14 28.14 42.48 4.41
2476 2534 1.682323 TCTGCAAGCAATTGTTCTGCA 59.318 42.857 21.78 21.78 42.48 4.41
2477 2535 2.427232 TCTGCAAGCAATTGTTCTGC 57.573 45.000 16.74 16.74 40.24 4.26
2516 2574 5.682862 GTGACAGTGTTGCTTTTGTTATCTG 59.317 40.000 0.00 0.00 0.00 2.90
2590 2648 4.503817 CGCCTGGATTAGAATTGATGGAGA 60.504 45.833 0.00 0.00 0.00 3.71
2599 2657 1.486310 TGCAGACGCCTGGATTAGAAT 59.514 47.619 0.00 0.00 40.72 2.40
2612 2670 0.445436 GTGATTTCAGGCTGCAGACG 59.555 55.000 20.43 11.72 0.00 4.18
2695 2753 7.554835 TCACATGTGGTTAAGAATGGGTATAAC 59.445 37.037 25.16 0.00 0.00 1.89
2718 2776 5.639506 TGCAGACTAGCTAATTTCAGTTCAC 59.360 40.000 0.00 0.00 34.99 3.18
2795 2853 8.752005 ATGTTAGCTTTCTGCCTAATTATCAA 57.248 30.769 0.00 0.00 44.23 2.57
2853 2921 2.833582 GCATGGCAGGCAGCTGAT 60.834 61.111 20.53 1.05 44.79 2.90
2858 2926 0.454600 CTGTAAAGCATGGCAGGCAG 59.545 55.000 27.04 10.50 0.00 4.85
2884 2952 4.286291 CCCTGTATGGAAGGATACCCTAAC 59.714 50.000 0.00 0.00 43.48 2.34
2929 2997 6.363473 GTCTTTGTTCAATCTTGAGTTACCG 58.637 40.000 0.00 0.00 38.61 4.02


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

AutoCloner maintained by Alex Coulton.