Multiple sequence alignment - TraesCS7A01G451400

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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 TraesCS7A01G451400 chr7A 100.000 2627 0 0 1 2627 644615699 644618325 0.000000e+00 4852
1 TraesCS7A01G451400 chr2A 96.133 2638 69 3 1 2627 612400883 612398268 0.000000e+00 4276
2 TraesCS7A01G451400 chr7B 75.322 932 190 30 532 1442 603342893 603343805 6.770000e-111 411


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 TraesCS7A01G451400 chr7A 644615699 644618325 2626 False 4852 4852 100.000 1 2627 1 chr7A.!!$F1 2626
1 TraesCS7A01G451400 chr2A 612398268 612400883 2615 True 4276 4276 96.133 1 2627 1 chr2A.!!$R1 2626
2 TraesCS7A01G451400 chr7B 603342893 603343805 912 False 411 411 75.322 532 1442 1 chr7B.!!$F1 910

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
388 389 0.87439 GCATGAAGAGCCGACAACAA 59.126 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1751 0.323629 ATGGAACCACTACCACACGG 59.676 55.0 0.0 0.0 39.06 4.94 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
85 86 6.294361 TGTAATACAGTTACTGCATCTGGT 57.706 37.500 12.80 0.00 34.37 4.00
96 97 1.841919 TGCATCTGGTGGATCATCAGT 59.158 47.619 7.88 0.00 42.61 3.41
331 332 6.573664 TGGTTAGGACATTTGTGAAGAATG 57.426 37.500 0.00 0.00 39.73 2.67
332 333 6.303054 TGGTTAGGACATTTGTGAAGAATGA 58.697 36.000 4.05 0.00 37.79 2.57
385 386 1.270785 TGAAGCATGAAGAGCCGACAA 60.271 47.619 0.00 0.00 0.00 3.18
388 389 0.874390 GCATGAAGAGCCGACAACAA 59.126 50.000 0.00 0.00 0.00 2.83
433 434 1.081892 AATGCTGACATGCACGAGAC 58.918 50.000 0.00 0.00 46.33 3.36
455 456 2.891580 AGGAGCTCGACAAGTAAGTTCA 59.108 45.455 7.83 0.00 0.00 3.18
460 461 4.024809 AGCTCGACAAGTAAGTTCAAAAGC 60.025 41.667 0.00 0.00 0.00 3.51
486 487 4.225942 AGACATTAGAAGAAGGTGCATCCA 59.774 41.667 0.00 0.00 39.02 3.41
535 536 5.239525 ACTTACCACTTGCTGAACTCATTTC 59.760 40.000 0.00 0.00 34.41 2.17
562 563 2.086610 ATGGTTCAAACACCTTGCCT 57.913 45.000 0.00 0.00 37.75 4.75
639 640 4.380550 GGAAGGCTAACAATTACTGGTTGC 60.381 45.833 0.00 0.00 42.11 4.17
714 715 2.124570 ATCAGGTGGCGCCATGTC 60.125 61.111 35.23 24.09 40.61 3.06
739 740 1.279840 GTGCGCTTTGTGGTGAGTC 59.720 57.895 9.73 0.00 0.00 3.36
744 745 1.295792 GCTTTGTGGTGAGTCGTTGA 58.704 50.000 0.00 0.00 0.00 3.18
803 805 4.497291 TGACCCGCTAACTGGAAATATT 57.503 40.909 0.00 0.00 0.00 1.28
849 851 9.020731 TGTACAACTCATACAGTCTAGATTTCA 57.979 33.333 0.00 0.00 32.30 2.69
894 896 1.717032 TGAGGCGCTTGGATATAGGT 58.283 50.000 7.64 0.00 0.00 3.08
1073 1081 4.470462 GACGAGAAGACGCTACTTGTTAA 58.530 43.478 0.00 0.00 36.70 2.01
1254 1262 1.080569 CCCCAACAGCGAAATGTGC 60.081 57.895 0.00 0.00 32.52 4.57
1265 1275 0.598065 GAAATGTGCGTGCCCTTCTT 59.402 50.000 0.00 0.00 0.00 2.52
1347 1357 2.736144 AATTTGTGCAGCCATGACAG 57.264 45.000 0.00 0.00 0.00 3.51
1442 1452 3.208594 GCAGTGTTCATGATGCTCCATA 58.791 45.455 11.01 0.00 35.78 2.74
1507 1528 8.926092 ACTAGTGATGCTGACATAGATTACTA 57.074 34.615 0.00 0.00 36.35 1.82
1511 1532 6.364706 GTGATGCTGACATAGATTACTACTGC 59.635 42.308 0.00 0.00 36.35 4.40
1540 1561 3.380637 TCAGAATCGCCTACACTACTTCC 59.619 47.826 0.00 0.00 0.00 3.46
1612 1633 3.817647 GCTACCTGATTTTATGCTGGAGG 59.182 47.826 0.00 0.00 0.00 4.30
1667 1688 1.079503 GCAAGACGTCTGGATTCACC 58.920 55.000 24.45 0.42 39.54 4.02
1688 1709 3.865745 CCAGCTCCATCAAGTAGTAAACG 59.134 47.826 0.00 0.00 0.00 3.60
1730 1751 3.763057 ACCATCCCAAAGTACTTCAACC 58.237 45.455 8.95 0.00 0.00 3.77
1731 1752 3.089284 CCATCCCAAAGTACTTCAACCC 58.911 50.000 8.95 0.00 0.00 4.11
1869 1890 1.400494 CCCCTGCGGTTCGAATTAAAG 59.600 52.381 0.00 0.00 0.00 1.85
1878 1899 5.111293 CGGTTCGAATTAAAGCCCTAACTA 58.889 41.667 0.00 0.00 0.00 2.24
1915 1936 9.912634 CATGAAATAGACATGTTTAAGTTTGGT 57.087 29.630 0.00 0.00 39.84 3.67
1921 1942 7.687941 AGACATGTTTAAGTTTGGTATCAGG 57.312 36.000 0.00 0.00 0.00 3.86
1922 1943 6.151144 AGACATGTTTAAGTTTGGTATCAGGC 59.849 38.462 0.00 0.00 0.00 4.85
1923 1944 6.010219 ACATGTTTAAGTTTGGTATCAGGCT 58.990 36.000 0.00 0.00 0.00 4.58
1924 1945 5.957842 TGTTTAAGTTTGGTATCAGGCTG 57.042 39.130 8.58 8.58 0.00 4.85
1925 1946 5.626142 TGTTTAAGTTTGGTATCAGGCTGA 58.374 37.500 21.19 21.19 0.00 4.26
1926 1947 6.065374 TGTTTAAGTTTGGTATCAGGCTGAA 58.935 36.000 22.84 8.26 0.00 3.02
1957 1978 8.488651 AACCCTATATGTAGAACTTTCGTTTG 57.511 34.615 0.00 0.00 32.39 2.93
1958 1979 7.046033 ACCCTATATGTAGAACTTTCGTTTGG 58.954 38.462 0.00 0.00 32.39 3.28
2163 2184 9.607333 AACCTATCCTCACAGAATGATAGATTA 57.393 33.333 6.89 0.00 39.21 1.75
2170 2191 7.655328 CCTCACAGAATGATAGATTAAGACCAC 59.345 40.741 0.00 0.00 39.69 4.16
2196 2217 5.743636 TGATATACTGCCTGCATGTATCA 57.256 39.130 13.66 13.30 0.00 2.15
2222 2243 1.786937 TGGGAGGTGTTTGTTGCAAT 58.213 45.000 0.59 0.00 0.00 3.56
2256 2277 5.836705 TGAATATTTGGAAGGGTTCATCCA 58.163 37.500 0.00 0.00 43.84 3.41
2293 2314 7.973944 GGGGATGAATTAATGTTCACTTTGTAC 59.026 37.037 0.00 0.00 40.60 2.90
2308 2329 2.823924 TGTACGTGCCTGAAAGCTTA 57.176 45.000 0.00 0.00 0.00 3.09
2357 2378 8.687824 AAAATTAATTGTCAATCCTTGCTACG 57.312 30.769 0.39 0.00 0.00 3.51
2397 2418 6.330278 GGCTAGAAATGGTAAATTGGTTCAC 58.670 40.000 0.00 0.00 0.00 3.18
2464 2485 1.200519 ACAGCTAGGGCCACGAATTA 58.799 50.000 6.18 0.00 39.73 1.40
2466 2487 0.759346 AGCTAGGGCCACGAATTAGG 59.241 55.000 6.18 0.00 39.73 2.69
2572 2593 8.786826 TTTAGTGGGATTACATGACTTTACTG 57.213 34.615 0.00 0.00 0.00 2.74
2601 2622 1.614903 ACACAATGCCCATGTTCACAG 59.385 47.619 0.00 0.00 0.00 3.66
2604 2625 1.135603 CAATGCCCATGTTCACAGTCG 60.136 52.381 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 4.321527 CGATTAGCTGCTACTGATGATCCA 60.322 45.833 9.27 0.00 0.00 3.41
96 97 0.527600 CACCACGCGATTAGCTGCTA 60.528 55.000 15.93 5.02 45.59 3.49
142 143 4.899352 ACCTATACCTTGATGGAGATGC 57.101 45.455 0.00 0.00 39.71 3.91
385 386 5.236478 CGAAGAAGTACACCACATTCTTTGT 59.764 40.000 6.90 0.00 40.97 2.83
388 389 4.989168 GTCGAAGAAGTACACCACATTCTT 59.011 41.667 5.49 5.49 42.96 2.52
433 434 3.246619 GAACTTACTTGTCGAGCTCCTG 58.753 50.000 8.47 0.00 0.00 3.86
455 456 6.429385 CACCTTCTTCTAATGTCTCTGCTTTT 59.571 38.462 0.00 0.00 0.00 2.27
460 461 4.825422 TGCACCTTCTTCTAATGTCTCTG 58.175 43.478 0.00 0.00 0.00 3.35
486 487 1.420138 GTAATCCATGTCGGGATGGGT 59.580 52.381 12.14 4.08 46.96 4.51
535 536 2.393764 GTGTTTGAACCATTTCCTGCG 58.606 47.619 0.00 0.00 0.00 5.18
562 563 3.057104 CCACACATCACAACTAGGTACGA 60.057 47.826 0.00 0.00 0.00 3.43
628 629 2.621055 TCAAGCAAACGCAACCAGTAAT 59.379 40.909 0.00 0.00 0.00 1.89
639 640 0.516877 TCATTCGGCTCAAGCAAACG 59.483 50.000 4.13 0.00 44.36 3.60
714 715 1.269206 ACCACAAAGCGCACATCAAAG 60.269 47.619 11.47 0.00 0.00 2.77
739 740 2.318578 AGCGCAAAAATCATGTCAACG 58.681 42.857 11.47 0.00 0.00 4.10
744 745 1.794116 GCACAAGCGCAAAAATCATGT 59.206 42.857 11.47 0.00 0.00 3.21
950 958 0.527565 CCGATTCAGGGCAAACCAAG 59.472 55.000 0.00 0.00 43.89 3.61
1073 1081 4.680537 AGGTCTCGCACGGGTCCT 62.681 66.667 2.73 2.73 0.00 3.85
1254 1262 3.119531 TGCAATTATCAAAGAAGGGCACG 60.120 43.478 0.00 0.00 0.00 5.34
1265 1275 9.008965 TCTGCTAAGTAGTTTTGCAATTATCAA 57.991 29.630 0.00 0.00 44.72 2.57
1318 1328 3.668656 GGCTGCACAAATTTTAGTCGAAC 59.331 43.478 0.50 0.00 0.00 3.95
1507 1528 2.094545 GGCGATTCTGAAATTTGGCAGT 60.095 45.455 0.00 0.00 33.90 4.40
1511 1532 4.396166 AGTGTAGGCGATTCTGAAATTTGG 59.604 41.667 0.00 0.00 0.00 3.28
1540 1561 1.524355 CTCGTAAGCAATCATCTGCCG 59.476 52.381 0.00 0.00 43.73 5.69
1612 1633 2.354259 CTCTCTTCAGAATGGCACCAC 58.646 52.381 0.00 0.00 36.16 4.16
1667 1688 3.307242 GCGTTTACTACTTGATGGAGCTG 59.693 47.826 0.00 0.00 0.00 4.24
1688 1709 1.065126 AGCTAATGTTCCCTGTCCAGC 60.065 52.381 0.00 0.00 0.00 4.85
1730 1751 0.323629 ATGGAACCACTACCACACGG 59.676 55.000 0.00 0.00 39.06 4.94
1731 1752 1.001520 TGATGGAACCACTACCACACG 59.998 52.381 0.00 0.00 39.06 4.49
1878 1899 7.663827 CATGTCTATTTCATGTGCCCATAATT 58.336 34.615 0.00 0.00 38.17 1.40
1905 1926 8.871629 TTAATTCAGCCTGATACCAAACTTAA 57.128 30.769 0.00 0.00 0.00 1.85
1906 1927 8.325787 TCTTAATTCAGCCTGATACCAAACTTA 58.674 33.333 0.00 0.00 0.00 2.24
1907 1928 7.175104 TCTTAATTCAGCCTGATACCAAACTT 58.825 34.615 0.00 0.00 0.00 2.66
1908 1929 6.721318 TCTTAATTCAGCCTGATACCAAACT 58.279 36.000 0.00 0.00 0.00 2.66
1909 1930 7.251281 GTTCTTAATTCAGCCTGATACCAAAC 58.749 38.462 0.00 0.00 0.00 2.93
1910 1931 6.377146 GGTTCTTAATTCAGCCTGATACCAAA 59.623 38.462 0.00 0.00 0.00 3.28
1911 1932 5.885912 GGTTCTTAATTCAGCCTGATACCAA 59.114 40.000 0.00 0.00 0.00 3.67
1912 1933 5.437060 GGTTCTTAATTCAGCCTGATACCA 58.563 41.667 0.00 0.00 0.00 3.25
1913 1934 4.822350 GGGTTCTTAATTCAGCCTGATACC 59.178 45.833 0.00 0.00 0.00 2.73
1914 1935 5.685728 AGGGTTCTTAATTCAGCCTGATAC 58.314 41.667 0.00 0.00 37.04 2.24
1915 1936 5.975988 AGGGTTCTTAATTCAGCCTGATA 57.024 39.130 0.00 0.00 37.04 2.15
1916 1937 4.870021 AGGGTTCTTAATTCAGCCTGAT 57.130 40.909 0.00 0.00 37.04 2.90
1917 1938 5.975988 ATAGGGTTCTTAATTCAGCCTGA 57.024 39.130 8.85 0.00 38.86 3.86
1918 1939 7.227156 ACATATAGGGTTCTTAATTCAGCCTG 58.773 38.462 8.85 0.00 38.86 4.85
1919 1940 7.394144 ACATATAGGGTTCTTAATTCAGCCT 57.606 36.000 5.16 5.16 41.39 4.58
1920 1941 8.594550 TCTACATATAGGGTTCTTAATTCAGCC 58.405 37.037 0.00 0.00 0.00 4.85
1921 1942 9.998106 TTCTACATATAGGGTTCTTAATTCAGC 57.002 33.333 0.00 0.00 0.00 4.26
1952 1973 0.673437 AACATTGCTCCCACCAAACG 59.327 50.000 0.00 0.00 0.00 3.60
1957 1978 1.335872 CGAACAAACATTGCTCCCACC 60.336 52.381 0.00 0.00 0.00 4.61
1958 1979 1.335872 CCGAACAAACATTGCTCCCAC 60.336 52.381 0.00 0.00 0.00 4.61
2071 2092 6.825610 TCTTTGCATACCAAATTTTTCAGGT 58.174 32.000 3.66 3.66 42.22 4.00
2163 2184 3.006967 GGCAGTATATCATCCGTGGTCTT 59.993 47.826 0.00 0.00 0.00 3.01
2170 2191 2.749280 TGCAGGCAGTATATCATCCG 57.251 50.000 0.00 0.00 0.00 4.18
2196 2217 2.661718 ACAAACACCTCCCAAATTCGT 58.338 42.857 0.00 0.00 0.00 3.85
2222 2243 6.491062 CCTTCCAAATATTCAGTGATATGCCA 59.509 38.462 0.00 0.00 0.00 4.92
2256 2277 8.550585 ACATTAATTCATCCCCAAATCAACATT 58.449 29.630 0.00 0.00 0.00 2.71
2293 2314 1.079503 GTCCTAAGCTTTCAGGCACG 58.920 55.000 3.20 0.00 34.17 5.34
2308 2329 1.073199 CAAGCCTTGTTCCCGTCCT 59.927 57.895 0.00 0.00 0.00 3.85
2353 2374 1.927174 CGAATGAGCCTGGTTTCGTAG 59.073 52.381 12.04 1.76 36.96 3.51
2357 2378 0.678048 AGCCGAATGAGCCTGGTTTC 60.678 55.000 0.00 0.00 0.00 2.78
2415 2436 3.117851 TGTGTACCTTGGAACCATGTTCA 60.118 43.478 9.01 0.00 0.00 3.18
2469 2490 5.124457 GTCTCATGTTGTGGCAATGAATAGT 59.876 40.000 1.64 0.00 0.00 2.12
2572 2593 1.273048 TGGGCATTGTGTTCATTCAGC 59.727 47.619 0.00 0.00 0.00 4.26
2601 2622 1.670791 TTCCAAGGGTCAACAACGAC 58.329 50.000 0.00 0.00 35.03 4.34
2604 2625 3.878160 TTGTTTCCAAGGGTCAACAAC 57.122 42.857 9.80 0.00 34.54 3.32


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

AutoCloner maintained by Alex Coulton.