Multiple sequence alignment - TraesCS7D01G227200

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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 TraesCS7D01G227200 chr7D 100.000 2417 0 0 1 2417 187113730 187111314 0.000000e+00 4464
1 TraesCS7D01G227200 chr7A 92.703 2453 109 26 2 2414 197989952 197992374 0.000000e+00 3474
2 TraesCS7D01G227200 chr7B 92.910 1890 83 24 1 1858 329926763 329924893 0.000000e+00 2700
3 TraesCS7D01G227200 chr7B 93.182 308 18 2 1853 2157 329924814 329924507 1.320000e-122 449


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 TraesCS7D01G227200 chr7D 187111314 187113730 2416 True 4464.0 4464 100.000 1 2417 1 chr7D.!!$R1 2416
1 TraesCS7D01G227200 chr7A 197989952 197992374 2422 False 3474.0 3474 92.703 2 2414 1 chr7A.!!$F1 2412
2 TraesCS7D01G227200 chr7B 329924507 329926763 2256 True 1574.5 2700 93.046 1 2157 2 chr7B.!!$R1 2156

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
458 475 0.173481 CTCTGAATCCGGAGTTCGCA 59.827 55.0 11.34 0.22 40.21 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2312 2466 0.035725 CATCAGGAGAGCTGGTGCAA 60.036 55.0 0.0 0.0 42.74 4.08 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
95 98 2.595463 TCAGGCCAGTTGCACTGC 60.595 61.111 5.01 0.00 44.63 4.40
96 99 4.034258 CAGGCCAGTTGCACTGCG 62.034 66.667 5.01 5.89 44.63 5.18
99 102 3.049674 GCCAGTTGCACTGCGCTA 61.050 61.111 9.73 0.00 44.63 4.26
249 263 4.363990 CTCTCCTGCGCGTGGTGT 62.364 66.667 17.00 0.00 0.00 4.16
453 470 1.110442 CTCTGCTCTGAATCCGGAGT 58.890 55.000 11.34 7.44 45.49 3.85
458 475 0.173481 CTCTGAATCCGGAGTTCGCA 59.827 55.000 11.34 0.22 40.21 5.10
572 593 1.536766 TGCTTCTTTGATGCAAGGTCG 59.463 47.619 0.00 0.00 39.22 4.79
576 597 1.277842 TCTTTGATGCAAGGTCGGCTA 59.722 47.619 0.00 0.00 0.00 3.93
586 607 0.617820 AGGTCGGCTACACCATCCTT 60.618 55.000 0.00 0.00 37.76 3.36
587 608 0.179081 GGTCGGCTACACCATCCTTC 60.179 60.000 0.00 0.00 39.03 3.46
588 609 0.179081 GTCGGCTACACCATCCTTCC 60.179 60.000 0.00 0.00 39.03 3.46
589 610 0.325296 TCGGCTACACCATCCTTCCT 60.325 55.000 0.00 0.00 39.03 3.36
631 659 5.451103 GGATGCTTCCTTTTTCCTGATTAGC 60.451 44.000 11.34 0.00 39.14 3.09
713 750 4.402155 TGATGGGGATATTTGTTGCTTCAC 59.598 41.667 0.00 0.00 0.00 3.18
718 755 4.142160 GGGATATTTGTTGCTTCACCTTCC 60.142 45.833 0.00 0.00 0.00 3.46
719 756 4.142160 GGATATTTGTTGCTTCACCTTCCC 60.142 45.833 0.00 0.00 0.00 3.97
740 777 3.493272 CGATTCCTACGGATCTCATTCG 58.507 50.000 0.00 0.00 0.00 3.34
746 783 1.909376 ACGGATCTCATTCGAACACG 58.091 50.000 0.00 0.28 0.00 4.49
756 796 2.273370 TTCGAACACGGAGATACTGC 57.727 50.000 0.00 0.00 0.00 4.40
826 866 4.440940 CCAACCCCGGATTAAATTGTAAGC 60.441 45.833 0.73 0.00 0.00 3.09
827 867 3.293337 ACCCCGGATTAAATTGTAAGCC 58.707 45.455 0.73 0.00 0.00 4.35
872 912 6.743575 TTTCTAGATCAAGGTTTTAGCAGC 57.256 37.500 0.00 0.00 0.00 5.25
889 929 2.331194 CAGCCAAAAATCTTGCTTCCG 58.669 47.619 0.00 0.00 30.08 4.30
900 940 2.028385 TCTTGCTTCCGAGAAGTAACCC 60.028 50.000 11.19 0.00 0.00 4.11
936 976 3.435590 GCACCAAGCAGTTGAGCA 58.564 55.556 0.00 0.00 44.79 4.26
941 981 0.725686 CCAAGCAGTTGAGCATCGAG 59.274 55.000 0.00 0.00 38.61 4.04
945 985 1.802960 AGCAGTTGAGCATCGAGTTTG 59.197 47.619 0.00 0.00 38.61 2.93
948 988 2.158449 CAGTTGAGCATCGAGTTTGTCC 59.842 50.000 0.00 0.00 38.61 4.02
949 989 1.126846 GTTGAGCATCGAGTTTGTCCG 59.873 52.381 0.00 0.00 38.61 4.79
950 990 0.389817 TGAGCATCGAGTTTGTCCGG 60.390 55.000 0.00 0.00 38.61 5.14
951 991 0.389948 GAGCATCGAGTTTGTCCGGT 60.390 55.000 0.00 0.00 0.00 5.28
953 994 1.274167 AGCATCGAGTTTGTCCGGTAA 59.726 47.619 0.00 0.00 0.00 2.85
961 1002 6.400568 TCGAGTTTGTCCGGTAATAATTTCT 58.599 36.000 0.00 0.00 0.00 2.52
969 1010 9.621629 TTGTCCGGTAATAATTTCTCAATACAT 57.378 29.630 0.00 0.00 0.00 2.29
1041 1082 1.657751 GAAGGAAGCCCATCGCCAAC 61.658 60.000 0.00 0.00 38.78 3.77
1581 1635 7.420184 TGGATGTAAACATATACTCATTGCG 57.580 36.000 0.00 0.00 36.57 4.85
1609 1663 8.806146 ACTATTGAAGTTTTGCTTATGGTGATT 58.194 29.630 0.00 0.00 37.59 2.57
1622 1676 4.897509 ATGGTGATTGAGAAGAGTGTGA 57.102 40.909 0.00 0.00 0.00 3.58
1626 1680 2.035832 TGATTGAGAAGAGTGTGACGCA 59.964 45.455 0.00 0.00 0.00 5.24
1733 1797 2.106511 AGCTCTTGGCAAGTTTAGTCCA 59.893 45.455 25.39 4.09 44.79 4.02
1778 1845 5.012458 CCTATTCATCACAGCTAATCCTCCA 59.988 44.000 0.00 0.00 0.00 3.86
1841 1908 2.568623 ACCAAGACTGTTGGCTTAGG 57.431 50.000 4.84 0.00 43.23 2.69
1855 1922 9.654663 CTGTTGGCTTAGGTATTATCTATTACC 57.345 37.037 0.00 0.00 0.00 2.85
1915 2066 8.528044 AACTAAAACCACTCAACTTATTTCCA 57.472 30.769 0.00 0.00 0.00 3.53
1942 2093 2.004733 GGGAGTATTTACGTGTGGTGC 58.995 52.381 0.00 0.00 0.00 5.01
2029 2181 5.021033 ACTGGATTCAGATGATCTGTGTC 57.979 43.478 20.82 18.04 44.58 3.67
2035 2189 4.831674 TCAGATGATCTGTGTCCAACAT 57.168 40.909 20.82 0.00 44.58 2.71
2078 2232 4.480115 TCGGGATACATACTCTTGGATGT 58.520 43.478 0.00 0.00 39.57 3.06
2110 2264 3.784511 AGATACTCCCTCCATTGCATG 57.215 47.619 0.00 0.00 0.00 4.06
2171 2325 2.662866 ACGGAGGGAGTATCGATTCAA 58.337 47.619 1.71 0.00 34.37 2.69
2229 2383 1.566703 TCGGGACATCTCTCTCCTCTT 59.433 52.381 0.00 0.00 0.00 2.85
2288 2442 3.000819 CCACACCCTCCTACGCCA 61.001 66.667 0.00 0.00 0.00 5.69
2290 2444 1.602237 CACACCCTCCTACGCCATT 59.398 57.895 0.00 0.00 0.00 3.16
2300 2454 0.379669 CTACGCCATTAGGTCGTCGT 59.620 55.000 7.13 0.00 43.28 4.34
2312 2466 4.065281 CGTCGTCCCGCCTCCTTT 62.065 66.667 0.00 0.00 0.00 3.11
2326 2480 0.250901 TCCTTTTGCACCAGCTCTCC 60.251 55.000 0.00 0.00 42.74 3.71
2383 2537 4.501743 GGATAGAGCTCTAGTTTTTCCCCG 60.502 50.000 26.64 0.00 0.00 5.73
2384 2538 1.066071 AGAGCTCTAGTTTTTCCCCGC 60.066 52.381 16.50 0.00 0.00 6.13
2414 2569 6.071784 GGGTTTTTAGTAGGGTTACACAATGG 60.072 42.308 0.00 0.00 31.96 3.16
2415 2570 6.491062 GGTTTTTAGTAGGGTTACACAATGGT 59.509 38.462 0.00 0.00 31.96 3.55
2416 2571 7.014518 GGTTTTTAGTAGGGTTACACAATGGTT 59.985 37.037 0.00 0.00 31.96 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 98 3.112075 CCGTGGTGCAGTGTAGCG 61.112 66.667 5.93 0.04 37.31 4.26
96 99 3.423154 GCCGTGGTGCAGTGTAGC 61.423 66.667 3.19 3.19 0.00 3.58
97 100 3.112075 CGCCGTGGTGCAGTGTAG 61.112 66.667 0.00 0.00 0.00 2.74
98 101 4.673298 CCGCCGTGGTGCAGTGTA 62.673 66.667 0.00 0.00 0.00 2.90
229 241 3.443925 CCACGCGCAGGAGAGAGA 61.444 66.667 12.47 0.00 0.00 3.10
453 470 0.108709 GCAAATGGATTGGCTGCGAA 60.109 50.000 0.00 0.00 39.54 4.70
572 593 0.470341 GGAGGAAGGATGGTGTAGCC 59.530 60.000 0.00 0.00 37.90 3.93
576 597 0.621862 GGAGGGAGGAAGGATGGTGT 60.622 60.000 0.00 0.00 0.00 4.16
586 607 3.048600 CAATCCAATACAGGAGGGAGGA 58.951 50.000 0.00 0.00 41.90 3.71
587 608 2.107204 CCAATCCAATACAGGAGGGAGG 59.893 54.545 0.00 0.00 41.90 4.30
588 609 3.048600 TCCAATCCAATACAGGAGGGAG 58.951 50.000 0.00 0.00 41.90 4.30
589 610 3.144068 TCCAATCCAATACAGGAGGGA 57.856 47.619 0.00 0.00 41.90 4.20
740 777 7.948278 AATAATAAGCAGTATCTCCGTGTTC 57.052 36.000 0.00 0.00 0.00 3.18
792 832 2.239402 TCCGGGGTTGGATTTAAGTACC 59.761 50.000 0.00 0.00 31.53 3.34
826 866 1.885887 TGCAAGAAAAAGGACCGATGG 59.114 47.619 0.00 0.00 0.00 3.51
827 867 2.813754 TCTGCAAGAAAAAGGACCGATG 59.186 45.455 0.00 0.00 42.31 3.84
872 912 4.022849 ACTTCTCGGAAGCAAGATTTTTGG 60.023 41.667 11.97 0.00 0.00 3.28
889 929 1.544691 TGCTCGTCTGGGTTACTTCTC 59.455 52.381 0.00 0.00 0.00 2.87
900 940 1.079956 AGCTGCTTCTGCTCGTCTG 60.080 57.895 0.00 0.00 40.48 3.51
922 962 0.725686 CTCGATGCTCAACTGCTTGG 59.274 55.000 0.00 0.00 0.00 3.61
936 976 7.046033 AGAAATTATTACCGGACAAACTCGAT 58.954 34.615 9.46 0.00 0.00 3.59
941 981 9.712359 GTATTGAGAAATTATTACCGGACAAAC 57.288 33.333 9.46 0.00 0.00 2.93
945 985 9.490379 AGATGTATTGAGAAATTATTACCGGAC 57.510 33.333 9.46 0.00 0.00 4.79
961 1002 4.342378 GTGCCTCCTCTGTAGATGTATTGA 59.658 45.833 0.00 0.00 0.00 2.57
969 1010 0.040351 AGCAGTGCCTCCTCTGTAGA 59.960 55.000 12.58 0.00 35.53 2.59
977 1018 1.751927 CCAATCCAGCAGTGCCTCC 60.752 63.158 12.58 0.00 0.00 4.30
978 1019 0.106819 ATCCAATCCAGCAGTGCCTC 60.107 55.000 12.58 0.00 0.00 4.70
1092 1133 1.119684 GCCTTCCTCTCCTCTTCCTC 58.880 60.000 0.00 0.00 0.00 3.71
1137 1178 1.112113 TGGGTTCTGCTAGATCGACC 58.888 55.000 0.00 0.00 0.00 4.79
1185 1229 2.876645 GCGTCGTCTCCTTCTGCG 60.877 66.667 0.00 0.00 0.00 5.18
1581 1635 8.296713 TCACCATAAGCAAAACTTCAATAGTTC 58.703 33.333 0.00 0.00 46.34 3.01
1609 1663 3.569916 GTGCGTCACACTCTTCTCA 57.430 52.632 5.30 0.00 46.41 3.27
1622 1676 4.554723 GCTAATTGTGAACTTCAAGTGCGT 60.555 41.667 0.00 0.00 0.00 5.24
1626 1680 4.823989 AGCAGCTAATTGTGAACTTCAAGT 59.176 37.500 0.00 0.00 0.00 3.16
1733 1797 4.883006 AGGCAAACAAAATGTGCAAAAGAT 59.117 33.333 0.00 0.00 40.12 2.40
1778 1845 4.865905 TGATTACTTGCCAATACCACCAT 58.134 39.130 0.00 0.00 0.00 3.55
1818 1885 2.386661 AGCCAACAGTCTTGGTATCG 57.613 50.000 0.00 0.00 41.53 2.92
1855 1922 4.273480 CACGCCACTTATTTCCTAATGGAG 59.727 45.833 0.00 0.00 44.24 3.86
1862 2013 2.579410 AACCACGCCACTTATTTCCT 57.421 45.000 0.00 0.00 0.00 3.36
1904 2055 4.202535 ACTCCCTCCGTTTGGAAATAAGTT 60.203 41.667 0.00 0.00 45.87 2.66
1915 2066 3.259123 ACACGTAAATACTCCCTCCGTTT 59.741 43.478 0.00 0.00 0.00 3.60
2029 2181 0.599558 CAAGGCACAGTGGATGTTGG 59.400 55.000 1.84 0.00 41.41 3.77
2078 2232 2.279741 GGAGTATCTTGCAATGTCGCA 58.720 47.619 0.00 0.00 41.03 5.10
2171 2325 2.628178 TCTTCGACAAGGTCATCAGTGT 59.372 45.455 0.00 0.00 32.09 3.55
2229 2383 5.502089 TTTTTATCCTCCCTACGGTTTGA 57.498 39.130 0.00 0.00 0.00 2.69
2259 2413 2.616330 GGTGTGGTGACATGGTGCG 61.616 63.158 0.00 0.00 46.14 5.34
2270 2424 3.001406 GGCGTAGGAGGGTGTGGT 61.001 66.667 0.00 0.00 0.00 4.16
2300 2454 2.282180 GTGCAAAAGGAGGCGGGA 60.282 61.111 0.00 0.00 0.00 5.14
2311 2465 0.694771 ATCAGGAGAGCTGGTGCAAA 59.305 50.000 0.00 0.00 42.74 3.68
2312 2466 0.035725 CATCAGGAGAGCTGGTGCAA 60.036 55.000 0.00 0.00 42.74 4.08
2326 2480 2.124983 CCCGCACTCCCACATCAG 60.125 66.667 0.00 0.00 0.00 2.90
2352 2506 5.897851 ACTAGAGCTCTATCCTGTAGACA 57.102 43.478 23.48 0.00 32.33 3.41
2353 2507 7.576861 AAAACTAGAGCTCTATCCTGTAGAC 57.423 40.000 23.48 0.00 32.33 2.59
2360 2514 4.501743 CGGGGAAAAACTAGAGCTCTATCC 60.502 50.000 23.48 23.63 0.00 2.59
2371 2525 1.282738 CCCTAAGGCGGGGAAAAACTA 59.717 52.381 7.32 0.00 46.50 2.24
2383 2537 4.581309 ACCCTACTAAAAACCCTAAGGC 57.419 45.455 0.00 0.00 36.11 4.35
2384 2538 6.881065 GTGTAACCCTACTAAAAACCCTAAGG 59.119 42.308 0.00 0.00 40.04 2.69


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

AutoCloner maintained by Alex Coulton.