Multiple sequence alignment - TraesCS4A01G394400

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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 TraesCS4A01G394400 chr4A 100.000 2953 0 0 1 2953 669671899 669674851 0 5454
1 TraesCS4A01G394400 chr7A 92.438 2486 110 34 1 2459 57619005 57621439 0 3478
2 TraesCS4A01G394400 chr7D 94.275 2131 91 18 822 2938 53989083 53991196 0 3230
3 TraesCS4A01G394400 chr7D 98.688 762 8 2 1 762 53988324 53989083 0 1351


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 TraesCS4A01G394400 chr4A 669671899 669674851 2952 False 5454.0 5454 100.0000 1 2953 1 chr4A.!!$F1 2952
1 TraesCS4A01G394400 chr7A 57619005 57621439 2434 False 3478.0 3478 92.4380 1 2459 1 chr7A.!!$F1 2458
2 TraesCS4A01G394400 chr7D 53988324 53991196 2872 False 2290.5 3230 96.4815 1 2938 2 chr7D.!!$F1 2937

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
38 45 3.652057 TCTCCATTCACCCTTCAATCC 57.348 47.619 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2006 0.030908 GGTCTCGTCCTAAGCCATCG 59.969 60.0 0.0 0.0 0.0 3.84 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
38 45 3.652057 TCTCCATTCACCCTTCAATCC 57.348 47.619 0.00 0.00 0.00 3.01
314 321 6.490381 AGACCAAGTTCCTTTATTGTTCTTCC 59.510 38.462 0.00 0.00 0.00 3.46
975 985 9.862149 TTATGTCTAGTTCTTTTCTTCCCTTTT 57.138 29.630 0.00 0.00 0.00 2.27
988 998 6.693315 TCTTCCCTTTTTGTCACTAACTTG 57.307 37.500 0.00 0.00 0.00 3.16
994 1004 5.737290 CCTTTTTGTCACTAACTTGTTGACG 59.263 40.000 0.00 0.00 32.68 4.35
1605 1615 1.820519 CCTGGCTGTAATGTGCACAAT 59.179 47.619 25.72 19.05 0.00 2.71
1700 1713 6.924111 ACTTATATGTTCTTTTGGTGCCTTG 58.076 36.000 0.00 0.00 0.00 3.61
1740 1756 7.509050 TTGATCAAATACATGCATGTTTTCG 57.491 32.000 35.45 23.38 41.97 3.46
1743 1759 6.926280 TCAAATACATGCATGTTTTCGAAC 57.074 33.333 35.45 0.00 41.97 3.95
1755 1771 1.028130 TTTCGAACCTGCATGCAACA 58.972 45.000 22.88 0.00 0.00 3.33
1773 1789 4.557296 GCAACACTCAATGCAAAAGAGCTA 60.557 41.667 11.84 0.00 42.12 3.32
1774 1790 5.522456 CAACACTCAATGCAAAAGAGCTAA 58.478 37.500 11.84 0.00 34.99 3.09
1775 1791 5.772825 ACACTCAATGCAAAAGAGCTAAA 57.227 34.783 11.84 0.00 34.99 1.85
1807 1823 7.392494 TGTTTGACAACAGTTAATTGTGGTA 57.608 32.000 10.84 0.00 40.36 3.25
1885 1901 4.456566 GCAATTTGCAAACCTTCATCCAAT 59.543 37.500 15.41 0.00 44.26 3.16
1913 1929 3.686016 TCTCTGTGCCCTAAAATGGAAC 58.314 45.455 0.00 0.00 0.00 3.62
1951 1967 1.350071 TAAACAGGCACCGGGAAGTA 58.650 50.000 6.32 0.00 0.00 2.24
1956 1972 0.620700 AGGCACCGGGAAGTAAGGAT 60.621 55.000 6.32 0.00 0.00 3.24
2033 2049 0.870393 ATTGTCACACTCGCAAGCTG 59.130 50.000 0.00 0.00 37.18 4.24
2058 2074 6.018669 GCGATCCAGGAAGAATAAAACTACAG 60.019 42.308 0.00 0.00 0.00 2.74
2459 2494 7.388437 ACTTGTGAAAAATAATCCATGCATGT 58.612 30.769 24.58 9.62 0.00 3.21
2476 2526 6.788598 TGCATGTCCATTGTAAATATTGGT 57.211 33.333 0.00 0.00 0.00 3.67
2477 2527 7.888250 TGCATGTCCATTGTAAATATTGGTA 57.112 32.000 0.00 0.00 0.00 3.25
2478 2528 7.939782 TGCATGTCCATTGTAAATATTGGTAG 58.060 34.615 0.00 0.00 0.00 3.18
2479 2529 7.014134 TGCATGTCCATTGTAAATATTGGTAGG 59.986 37.037 0.00 0.00 0.00 3.18
2480 2530 7.230510 GCATGTCCATTGTAAATATTGGTAGGA 59.769 37.037 0.00 0.00 0.00 2.94
2481 2531 9.130661 CATGTCCATTGTAAATATTGGTAGGAA 57.869 33.333 0.00 0.00 0.00 3.36
2482 2532 8.746052 TGTCCATTGTAAATATTGGTAGGAAG 57.254 34.615 0.00 0.00 0.00 3.46
2483 2533 8.553153 TGTCCATTGTAAATATTGGTAGGAAGA 58.447 33.333 0.00 0.00 0.00 2.87
2484 2534 9.574516 GTCCATTGTAAATATTGGTAGGAAGAT 57.425 33.333 0.00 0.00 0.00 2.40
2494 2544 9.745018 AATATTGGTAGGAAGATATGTCCATTG 57.255 33.333 5.11 0.00 37.65 2.82
2495 2545 5.567037 TGGTAGGAAGATATGTCCATTGG 57.433 43.478 0.00 0.00 37.65 3.16
2514 2564 1.431496 GCAACTGGCGCAAAATTCAT 58.569 45.000 10.83 0.00 0.00 2.57
2521 2571 4.984161 ACTGGCGCAAAATTCATATATTGC 59.016 37.500 10.83 1.04 43.51 3.56
2677 2727 8.981659 TCTAGTTGAATTCTCAGGATTGACATA 58.018 33.333 7.05 0.00 31.69 2.29
2693 2743 9.450807 GGATTGACATACAAATTTGCATACTAC 57.549 33.333 18.12 5.06 42.03 2.73
2806 2858 9.739276 ATTAGAACTCATTTCATCCTGTGTAAA 57.261 29.630 0.00 0.00 36.57 2.01
2821 2873 8.141298 TCCTGTGTAAAACTAATGACTATCCA 57.859 34.615 0.00 0.00 0.00 3.41
2881 2933 3.250762 TCCAAGATTTGCAAGTTCGTCTG 59.749 43.478 0.00 2.60 0.00 3.51
2903 2955 9.262358 GTCTGGGTACATTAATATCTTCTGTTC 57.738 37.037 0.00 0.00 0.00 3.18
2925 2977 8.206867 TGTTCTTATACATGAAGCTTAGAGCAT 58.793 33.333 0.00 0.00 45.56 3.79
2932 2984 6.125029 ACATGAAGCTTAGAGCATGGTTAAT 58.875 36.000 22.64 5.77 45.56 1.40
2939 2991 8.709386 AGCTTAGAGCATGGTTAATAATATCG 57.291 34.615 0.00 0.00 45.56 2.92
2940 2992 7.766278 AGCTTAGAGCATGGTTAATAATATCGG 59.234 37.037 0.00 0.00 45.56 4.18
2941 2993 7.011482 GCTTAGAGCATGGTTAATAATATCGGG 59.989 40.741 0.00 0.00 41.89 5.14
2942 2994 5.186198 AGAGCATGGTTAATAATATCGGGC 58.814 41.667 0.00 0.00 0.00 6.13
2943 2995 4.270008 AGCATGGTTAATAATATCGGGCC 58.730 43.478 0.00 0.00 0.00 5.80
2944 2996 4.018415 AGCATGGTTAATAATATCGGGCCT 60.018 41.667 0.84 0.00 0.00 5.19
2945 2997 4.096382 GCATGGTTAATAATATCGGGCCTG 59.904 45.833 4.71 4.71 0.00 4.85
2946 2998 3.681593 TGGTTAATAATATCGGGCCTGC 58.318 45.455 6.73 0.00 0.00 4.85
2947 2999 3.329520 TGGTTAATAATATCGGGCCTGCT 59.670 43.478 6.73 0.00 0.00 4.24
2948 3000 4.532916 TGGTTAATAATATCGGGCCTGCTA 59.467 41.667 6.73 0.96 0.00 3.49
2949 3001 5.013287 TGGTTAATAATATCGGGCCTGCTAA 59.987 40.000 6.73 0.00 0.00 3.09
2950 3002 5.941647 GGTTAATAATATCGGGCCTGCTAAA 59.058 40.000 6.73 0.00 0.00 1.85
2951 3003 6.431852 GGTTAATAATATCGGGCCTGCTAAAA 59.568 38.462 6.73 0.00 0.00 1.52
2952 3004 7.040271 GGTTAATAATATCGGGCCTGCTAAAAA 60.040 37.037 6.73 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 45 3.068873 AGCCTTTCTAACTGAGCTATCCG 59.931 47.826 0.00 0.00 0.00 4.18
314 321 1.271934 CCCAGTCTGATAGATGAGCCG 59.728 57.143 0.00 0.00 0.00 5.52
966 976 6.451064 ACAAGTTAGTGACAAAAAGGGAAG 57.549 37.500 0.00 0.00 0.00 3.46
975 985 3.263261 TGCGTCAACAAGTTAGTGACAA 58.737 40.909 14.96 3.83 0.00 3.18
1377 1387 6.690194 AAGGATGACATCTATGTTTGAAGC 57.310 37.500 14.95 0.00 41.95 3.86
1431 1441 4.708421 ACTGTTTCTTGCCATGCATAAGAT 59.292 37.500 10.45 0.00 38.76 2.40
1432 1442 4.081406 ACTGTTTCTTGCCATGCATAAGA 58.919 39.130 0.00 2.14 38.76 2.10
1531 1541 9.604626 GTTTTGTGTCAAAACATGATTCAAAAA 57.395 25.926 23.95 0.00 44.62 1.94
1532 1542 8.997323 AGTTTTGTGTCAAAACATGATTCAAAA 58.003 25.926 27.77 11.49 43.10 2.44
1605 1615 3.125316 GCACTCAATTCTGCTTGCAAAA 58.875 40.909 0.00 0.00 32.86 2.44
1740 1756 0.953727 TGAGTGTTGCATGCAGGTTC 59.046 50.000 21.50 16.54 0.00 3.62
1743 1759 1.990799 CATTGAGTGTTGCATGCAGG 58.009 50.000 21.50 0.00 0.00 4.85
1829 1845 0.966179 GGTTTCGGGGTTGCTTGATT 59.034 50.000 0.00 0.00 0.00 2.57
1875 1891 7.333921 GGCACAGAGAATAGATATTGGATGAAG 59.666 40.741 0.00 0.00 0.00 3.02
1885 1901 7.292356 TCCATTTTAGGGCACAGAGAATAGATA 59.708 37.037 0.00 0.00 0.00 1.98
1951 1967 0.394352 GGTCGGCATGGTTGATCCTT 60.394 55.000 0.00 0.00 37.07 3.36
1956 1972 1.613317 ATCTCGGTCGGCATGGTTGA 61.613 55.000 0.00 0.00 0.00 3.18
1990 2006 0.030908 GGTCTCGTCCTAAGCCATCG 59.969 60.000 0.00 0.00 0.00 3.84
2033 2049 5.815740 TGTAGTTTTATTCTTCCTGGATCGC 59.184 40.000 0.00 0.00 0.00 4.58
2058 2074 9.751542 GGTGGCAATACATCATATATACTACTC 57.248 37.037 0.00 0.00 0.00 2.59
2476 2526 5.132648 AGTTGCCAATGGACATATCTTCCTA 59.867 40.000 2.05 0.00 33.84 2.94
2477 2527 4.079558 AGTTGCCAATGGACATATCTTCCT 60.080 41.667 2.05 0.00 33.84 3.36
2478 2528 4.037208 CAGTTGCCAATGGACATATCTTCC 59.963 45.833 2.05 0.00 0.00 3.46
2479 2529 4.037208 CCAGTTGCCAATGGACATATCTTC 59.963 45.833 2.05 0.00 39.02 2.87
2480 2530 3.956199 CCAGTTGCCAATGGACATATCTT 59.044 43.478 2.05 0.00 39.02 2.40
2481 2531 3.559069 CCAGTTGCCAATGGACATATCT 58.441 45.455 2.05 0.00 39.02 1.98
2482 2532 2.035066 GCCAGTTGCCAATGGACATATC 59.965 50.000 8.68 0.00 39.02 1.63
2483 2533 2.034124 GCCAGTTGCCAATGGACATAT 58.966 47.619 8.68 0.00 39.02 1.78
2484 2534 1.473258 GCCAGTTGCCAATGGACATA 58.527 50.000 8.68 0.00 39.02 2.29
2485 2535 1.597797 CGCCAGTTGCCAATGGACAT 61.598 55.000 8.68 0.00 39.02 3.06
2486 2536 2.267351 CGCCAGTTGCCAATGGACA 61.267 57.895 8.68 0.00 39.02 4.02
2487 2537 2.568090 CGCCAGTTGCCAATGGAC 59.432 61.111 8.68 0.00 39.02 4.02
2488 2538 3.372730 GCGCCAGTTGCCAATGGA 61.373 61.111 8.68 0.00 39.02 3.41
2489 2539 2.712325 TTTGCGCCAGTTGCCAATGG 62.712 55.000 4.18 0.00 39.73 3.16
2490 2540 0.879400 TTTTGCGCCAGTTGCCAATG 60.879 50.000 4.18 0.00 36.24 2.82
2491 2541 0.035176 ATTTTGCGCCAGTTGCCAAT 59.965 45.000 4.18 0.00 36.24 3.16
2492 2542 0.179062 AATTTTGCGCCAGTTGCCAA 60.179 45.000 4.18 0.00 36.24 4.52
2493 2543 0.599728 GAATTTTGCGCCAGTTGCCA 60.600 50.000 4.18 0.00 36.24 4.92
2494 2544 0.599728 TGAATTTTGCGCCAGTTGCC 60.600 50.000 4.18 0.00 36.24 4.52
2495 2545 1.431496 ATGAATTTTGCGCCAGTTGC 58.569 45.000 4.18 0.00 0.00 4.17
2514 2564 6.672266 AACTCTAGCAAGCTAGGCAATATA 57.328 37.500 24.40 6.72 44.45 0.86
2521 2571 4.094146 GCTTTCAAACTCTAGCAAGCTAGG 59.906 45.833 24.40 18.12 44.45 3.02
2677 2727 6.569179 AGGAAACGTAGTATGCAAATTTGT 57.431 33.333 19.03 3.40 45.00 2.83
2693 2743 3.263261 GAGGCTTAGAGGAAAGGAAACG 58.737 50.000 0.00 0.00 0.00 3.60
2806 2858 7.872138 TGGAAGGATTTGGATAGTCATTAGTT 58.128 34.615 0.00 0.00 0.00 2.24
2821 2873 4.020839 CACTGGCTTTTGATGGAAGGATTT 60.021 41.667 0.00 0.00 0.00 2.17
2903 2955 6.933521 ACCATGCTCTAAGCTTCATGTATAAG 59.066 38.462 19.04 9.75 42.97 1.73
2925 2977 3.329520 AGCAGGCCCGATATTATTAACCA 59.670 43.478 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.