Multiple sequence alignment - TraesCS7D01G270100

Loading Multiple Alignment...

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 TraesCS7D01G270100 chr7D 100.000 3088 0 0 1 3088 255785739 255782652 0 5703
1 TraesCS7D01G270100 chr7B 93.806 3148 79 45 1 3088 234015061 234011970 0 4626
2 TraesCS7D01G270100 chr7A 92.018 3107 103 55 36 3088 275547629 275544614 0 4229


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 TraesCS7D01G270100 chr7D 255782652 255785739 3087 True 5703 5703 100.000 1 3088 1 chr7D.!!$R1 3087
1 TraesCS7D01G270100 chr7B 234011970 234015061 3091 True 4626 4626 93.806 1 3088 1 chr7B.!!$R1 3087
2 TraesCS7D01G270100 chr7A 275544614 275547629 3015 True 4229 4229 92.018 36 3088 1 chr7A.!!$R1 3052


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
606 641 0.108186 TTACAGCCAGATCAGGTGCG 60.108 55.000 13.13 2.38 36.18 5.34 F
891 929 1.002990 TGCACAGCTGCTAGCACAT 60.003 52.632 20.88 1.64 45.56 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1894 0.607762 TTATTGGCCGTTGCAGCAGA 60.608 50.0 0.0 0.0 40.13 4.26 R
2127 2197 0.948623 TCGAGCCAATGAACGTGTGG 60.949 55.0 0.0 0.0 35.39 4.17 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
51 56 2.359214 TGTAAACACCCACGTACGTACA 59.641 45.455 22.34 15.89 0.00 2.90
140 146 1.796017 TATACCGATCCTTGGTGCCA 58.204 50.000 1.35 0.00 40.73 4.92
297 312 2.892425 GGCAACGATGGCGAGGAG 60.892 66.667 2.89 0.00 42.73 3.69
298 313 2.892425 GCAACGATGGCGAGGAGG 60.892 66.667 0.00 0.00 41.64 4.30
299 314 2.892640 CAACGATGGCGAGGAGGA 59.107 61.111 0.00 0.00 41.64 3.71
490 515 1.199558 GCGGTTACTGTCTCTTCTCGT 59.800 52.381 0.00 0.00 0.00 4.18
491 516 2.417933 GCGGTTACTGTCTCTTCTCGTA 59.582 50.000 0.00 0.00 0.00 3.43
492 517 3.727376 GCGGTTACTGTCTCTTCTCGTAC 60.727 52.174 0.00 0.00 0.00 3.67
606 641 0.108186 TTACAGCCAGATCAGGTGCG 60.108 55.000 13.13 2.38 36.18 5.34
629 664 2.556534 GTGCAATCCACAGATCTTGC 57.443 50.000 7.70 7.70 44.06 4.01
669 704 4.026968 CACACCAACAGTTGTTTTATTGCG 60.027 41.667 12.42 0.00 35.83 4.85
891 929 1.002990 TGCACAGCTGCTAGCACAT 60.003 52.632 20.88 1.64 45.56 3.21
1525 1590 1.343069 ACCGCTCCTCCTCCATATTC 58.657 55.000 0.00 0.00 0.00 1.75
1819 1889 1.946768 CAAGACGGCCAAGAGAAACAA 59.053 47.619 2.24 0.00 0.00 2.83
1820 1890 1.594331 AGACGGCCAAGAGAAACAAC 58.406 50.000 2.24 0.00 0.00 3.32
1824 1894 1.608590 CGGCCAAGAGAAACAACACAT 59.391 47.619 2.24 0.00 0.00 3.21
2012 2082 2.881352 GCGCCCTCTTCTTCGTCG 60.881 66.667 0.00 0.00 0.00 5.12
2013 2083 2.567049 CGCCCTCTTCTTCGTCGT 59.433 61.111 0.00 0.00 0.00 4.34
2015 2085 1.585006 GCCCTCTTCTTCGTCGTCA 59.415 57.895 0.00 0.00 0.00 4.35
2018 2088 0.241213 CCTCTTCTTCGTCGTCAGCA 59.759 55.000 0.00 0.00 0.00 4.41
2027 2097 2.910479 TCGTCAGCACCGGTGTCT 60.910 61.111 33.92 26.98 32.43 3.41
2140 2210 4.942090 GTGGCCACACGTTCATTG 57.058 55.556 31.23 0.00 37.94 2.82
2141 2211 1.285641 GTGGCCACACGTTCATTGG 59.714 57.895 31.23 0.00 37.94 3.16
2145 2215 1.497278 CCACACGTTCATTGGCTCG 59.503 57.895 0.00 0.00 0.00 5.03
2312 2403 1.452108 CCAGCGACTCCCAAATCCC 60.452 63.158 0.00 0.00 0.00 3.85
2364 2460 1.819208 GCATGCATCGGGTGTGCTA 60.819 57.895 14.21 0.00 42.92 3.49
2400 2496 2.689983 GGTGGCCTTATGTTGATGAAGG 59.310 50.000 3.32 0.00 42.32 3.46
2418 2514 1.133869 GTTCGGAATTTCCACGGCG 59.866 57.895 15.58 4.80 35.91 6.46
2440 2536 7.278629 GGCGAATTTGTGTATAGTATTGTACG 58.721 38.462 0.00 0.00 0.00 3.67
2462 2561 7.156876 ACGGTGTACATCAAATCATCAATTT 57.843 32.000 6.97 0.00 38.11 1.82
2692 2808 4.827284 TCTCTTCAAAAGGTTCCATTCACC 59.173 41.667 0.00 0.00 34.06 4.02
2854 2974 1.035139 GGCATCATTAGCTGTTGGGG 58.965 55.000 0.00 0.00 0.00 4.96
2867 2987 1.229951 TTGGGGACTCAGGGCTGAT 60.230 57.895 0.00 0.00 39.13 2.90
2873 2993 2.603021 GGACTCAGGGCTGATGAGATA 58.397 52.381 17.57 0.00 45.80 1.98
2874 2994 3.172339 GGACTCAGGGCTGATGAGATAT 58.828 50.000 17.57 0.81 45.80 1.63
2875 2995 4.348486 GGACTCAGGGCTGATGAGATATA 58.652 47.826 17.57 0.00 45.80 0.86
2876 2996 4.159506 GGACTCAGGGCTGATGAGATATAC 59.840 50.000 17.57 6.91 45.80 1.47
2877 2997 5.009436 ACTCAGGGCTGATGAGATATACT 57.991 43.478 17.57 0.00 45.80 2.12
2878 2998 5.016173 ACTCAGGGCTGATGAGATATACTC 58.984 45.833 17.57 0.00 45.80 2.59
2905 3025 5.627499 ACATACATTTGTGTGCTTGGTAG 57.373 39.130 7.28 0.00 40.25 3.18
2963 3087 0.599991 TGCTAGGTCAGTGCGTGTTG 60.600 55.000 0.00 0.00 0.00 3.33
3004 3128 6.146898 ACGGCAAAAACAACAATACTCATAC 58.853 36.000 0.00 0.00 0.00 2.39
3005 3129 6.146216 CGGCAAAAACAACAATACTCATACA 58.854 36.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.986817 AGAAATGTGGCGTATATATATCCAGC 59.013 38.462 13.76 3.79 0.00 4.85
11 12 9.984190 TGTTTACAGAAATGTGGCGTATATATA 57.016 29.630 0.00 0.00 0.00 0.86
19 20 2.351350 GGGTGTTTACAGAAATGTGGCG 60.351 50.000 0.00 0.00 0.00 5.69
51 56 1.640917 ATCTTGGAGTGTACGTGGGT 58.359 50.000 0.00 0.00 0.00 4.51
117 123 2.549992 GCACCAAGGATCGGTATATGCA 60.550 50.000 0.00 0.00 34.02 3.96
118 124 2.076863 GCACCAAGGATCGGTATATGC 58.923 52.381 0.00 0.00 34.02 3.14
119 125 2.038426 TGGCACCAAGGATCGGTATATG 59.962 50.000 0.00 0.00 34.02 1.78
120 126 2.334977 TGGCACCAAGGATCGGTATAT 58.665 47.619 0.00 0.00 34.02 0.86
255 267 2.968206 GCCTCCAAGCAAAGCCAG 59.032 61.111 0.00 0.00 0.00 4.85
256 268 2.974692 TTCGCCTCCAAGCAAAGCCA 62.975 55.000 0.00 0.00 0.00 4.75
257 269 2.205243 CTTCGCCTCCAAGCAAAGCC 62.205 60.000 0.00 0.00 0.00 4.35
258 270 1.211190 CTTCGCCTCCAAGCAAAGC 59.789 57.895 0.00 0.00 0.00 3.51
259 271 1.878775 CCTTCGCCTCCAAGCAAAG 59.121 57.895 0.00 0.00 0.00 2.77
297 312 1.895131 GATCTCCTCATCTGCTCCTCC 59.105 57.143 0.00 0.00 0.00 4.30
298 313 1.895131 GGATCTCCTCATCTGCTCCTC 59.105 57.143 0.00 0.00 0.00 3.71
299 314 1.219980 TGGATCTCCTCATCTGCTCCT 59.780 52.381 0.00 0.00 36.82 3.69
490 515 2.171448 GACCGGACAGGAGGTAGTAGTA 59.829 54.545 9.46 0.00 45.00 1.82
491 516 0.998145 ACCGGACAGGAGGTAGTAGT 59.002 55.000 9.46 0.00 45.00 2.73
492 517 1.677942 GACCGGACAGGAGGTAGTAG 58.322 60.000 9.46 0.00 45.00 2.57
539 564 2.234661 TCACCCTGTGATCAGTGTCATC 59.765 50.000 11.34 0.00 37.67 2.92
594 629 0.376152 GCACATTCGCACCTGATCTG 59.624 55.000 0.00 0.00 0.00 2.90
606 641 4.669318 CAAGATCTGTGGATTGCACATTC 58.331 43.478 11.62 11.36 31.46 2.67
617 652 2.165167 ACACAATGGCAAGATCTGTGG 58.835 47.619 16.20 0.52 41.32 4.17
618 653 4.256110 TCTACACAATGGCAAGATCTGTG 58.744 43.478 0.00 1.41 42.43 3.66
629 664 0.394352 GTGGGGGCTCTACACAATGG 60.394 60.000 0.00 0.00 35.30 3.16
669 704 1.439365 CGAAGCAAGCGAGCAACAC 60.439 57.895 6.21 0.00 36.85 3.32
891 929 2.104963 TGCTACCGATGCTCTCTCTCTA 59.895 50.000 0.00 0.00 0.00 2.43
1525 1590 2.160219 CGGCCATCCATGAATATCAACG 59.840 50.000 2.24 0.00 0.00 4.10
1806 1876 3.854784 GCAGATGTGTTGTTTCTCTTGGC 60.855 47.826 0.00 0.00 0.00 4.52
1813 1883 2.780065 TGCAGCAGATGTGTTGTTTC 57.220 45.000 8.47 0.00 37.24 2.78
1819 1889 2.620112 GCCGTTGCAGCAGATGTGT 61.620 57.895 0.24 0.00 37.47 3.72
1820 1890 2.177531 GCCGTTGCAGCAGATGTG 59.822 61.111 0.24 0.00 37.47 3.21
1824 1894 0.607762 TTATTGGCCGTTGCAGCAGA 60.608 50.000 0.00 0.00 40.13 4.26
2012 2082 1.080025 GGTAGACACCGGTGCTGAC 60.080 63.158 34.26 25.93 34.36 3.51
2013 2083 3.373226 GGTAGACACCGGTGCTGA 58.627 61.111 34.26 16.46 34.36 4.26
2027 2097 4.830765 GTCGCCAGCGCCATGGTA 62.831 66.667 14.67 3.58 42.75 3.25
2127 2197 0.948623 TCGAGCCAATGAACGTGTGG 60.949 55.000 0.00 0.00 35.39 4.17
2129 2199 1.337728 TGATCGAGCCAATGAACGTGT 60.338 47.619 0.00 0.00 0.00 4.49
2130 2200 1.325640 CTGATCGAGCCAATGAACGTG 59.674 52.381 0.00 0.00 0.00 4.49
2131 2201 1.645034 CTGATCGAGCCAATGAACGT 58.355 50.000 0.00 0.00 0.00 3.99
2141 2211 1.008995 GAGACGAGGCTGATCGAGC 60.009 63.158 12.28 0.00 45.56 5.03
2142 2212 1.278337 CGAGACGAGGCTGATCGAG 59.722 63.158 12.28 0.00 45.56 4.04
2143 2213 2.180862 CCGAGACGAGGCTGATCGA 61.181 63.158 12.28 0.00 45.56 3.59
2145 2215 1.357334 GACCGAGACGAGGCTGATC 59.643 63.158 0.00 0.00 0.00 2.92
2312 2403 3.914312 AGTGTGTGTATCTTCTTCGTGG 58.086 45.455 0.00 0.00 0.00 4.94
2364 2460 1.205417 GCCACCACTTATTTGCAGCAT 59.795 47.619 0.00 0.00 0.00 3.79
2400 2496 1.133869 CGCCGTGGAAATTCCGAAC 59.866 57.895 7.60 0.00 40.17 3.95
2418 2514 9.090692 ACACCGTACAATACTATACACAAATTC 57.909 33.333 0.00 0.00 0.00 2.17
2440 2536 8.465999 TGGTAAATTGATGATTTGATGTACACC 58.534 33.333 0.00 0.00 38.40 4.16
2462 2561 7.817478 CGAATAAGACAGGCACATATAATGGTA 59.183 37.037 0.00 0.00 33.60 3.25
2794 2914 4.527509 ATTCAGCATATACTGGAGGACG 57.472 45.455 3.06 0.00 38.26 4.79
2801 2921 6.684131 CGACACAACAAATTCAGCATATACTG 59.316 38.462 0.00 0.00 39.12 2.74
2854 2974 5.016173 AGTATATCTCATCAGCCCTGAGTC 58.984 45.833 4.16 0.00 43.61 3.36
2874 2994 9.830975 AAGCACACAAATGTATGTATATGAGTA 57.169 29.630 0.00 0.00 36.72 2.59
2875 2995 8.615211 CAAGCACACAAATGTATGTATATGAGT 58.385 33.333 0.00 0.00 36.72 3.41
2876 2996 8.071967 CCAAGCACACAAATGTATGTATATGAG 58.928 37.037 0.00 0.00 36.72 2.90
2877 2997 7.555914 ACCAAGCACACAAATGTATGTATATGA 59.444 33.333 0.00 0.00 36.72 2.15
2878 2998 7.706159 ACCAAGCACACAAATGTATGTATATG 58.294 34.615 0.00 0.00 36.72 1.78
2888 3008 6.258160 GCTTATACTACCAAGCACACAAATG 58.742 40.000 1.62 0.00 45.20 2.32
2963 3087 1.670811 CCGTACCATTCAATCACAGCC 59.329 52.381 0.00 0.00 0.00 4.85
3004 3128 8.682936 AAGGAATCAGCCTGTAATAATAGTTG 57.317 34.615 0.00 0.00 38.58 3.16
3005 3129 9.780186 GTAAGGAATCAGCCTGTAATAATAGTT 57.220 33.333 0.00 0.00 38.58 2.24



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

AutoCloner maintained by Alex Coulton.