Multiple sequence alignment - TraesCS7B01G087100

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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 TraesCS7B01G087100 chr7B 100.000 3048 0 0 1 3048 101498642 101495595 0.000000e+00 5629
1 TraesCS7B01G087100 chr7D 92.767 2129 79 8 953 3048 137293728 137291642 0.000000e+00 3009
2 TraesCS7B01G087100 chr7D 94.479 815 39 4 1 812 137294831 137294020 0.000000e+00 1251
3 TraesCS7B01G087100 chr7A 90.758 2164 88 36 616 2720 137453725 137451615 0.000000e+00 2785
4 TraesCS7B01G087100 chr7A 92.105 608 43 5 1 604 137454412 137453806 0.000000e+00 852
5 TraesCS7B01G087100 chr7A 89.767 215 19 1 2834 3048 137451360 137451149 3.870000e-69 272


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 TraesCS7B01G087100 chr7B 101495595 101498642 3047 True 5629 5629 100.000000 1 3048 1 chr7B.!!$R1 3047
1 TraesCS7B01G087100 chr7D 137291642 137294831 3189 True 2130 3009 93.623000 1 3048 2 chr7D.!!$R1 3047
2 TraesCS7B01G087100 chr7A 137451149 137454412 3263 True 1303 2785 90.876667 1 3048 3 chr7A.!!$R1 3047

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
883 969 0.511221 AAAATCACGGCGTCTGTTCG 59.489 50.0 10.85 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2877 3297 0.251386 TCAAGCTGAGTCGGGAGTCT 60.251 55.0 0.05 0.0 0.0 3.24 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
21 22 4.530857 CATCGTCCCCGTGCCTCC 62.531 72.222 0.00 0.00 35.01 4.30
308 309 5.401550 CAAATTTGGATACTTGCATGACGT 58.598 37.500 10.49 0.00 37.61 4.34
342 343 4.134563 ACGCCGAGCCATAAAATTATTCT 58.865 39.130 0.00 0.00 0.00 2.40
363 364 0.840617 TACCATAGATTTGGCCGCCA 59.159 50.000 8.43 8.43 40.68 5.69
366 367 2.158534 ACCATAGATTTGGCCGCCAATA 60.159 45.455 25.37 15.18 43.55 1.90
593 596 6.039616 GCCAAATAAATCAGTAAAATCGCCA 58.960 36.000 0.00 0.00 0.00 5.69
594 597 6.533367 GCCAAATAAATCAGTAAAATCGCCAA 59.467 34.615 0.00 0.00 0.00 4.52
653 727 6.575162 TTGCTCCTGATAGTTTCTTTTTCC 57.425 37.500 0.00 0.00 0.00 3.13
776 852 2.486592 ACGCCCAGCTGTACATTAAAAC 59.513 45.455 13.81 0.00 0.00 2.43
834 911 2.846550 CAGCTTATCTGTCACACGTACG 59.153 50.000 15.01 15.01 38.02 3.67
835 912 1.582502 GCTTATCTGTCACACGTACGC 59.417 52.381 16.72 0.00 0.00 4.42
836 913 2.731341 GCTTATCTGTCACACGTACGCT 60.731 50.000 16.72 0.00 0.00 5.07
837 914 3.499048 CTTATCTGTCACACGTACGCTT 58.501 45.455 16.72 0.00 0.00 4.68
838 915 4.655027 CTTATCTGTCACACGTACGCTTA 58.345 43.478 16.72 0.00 0.00 3.09
839 916 3.564235 ATCTGTCACACGTACGCTTAA 57.436 42.857 16.72 0.00 0.00 1.85
840 917 2.924903 TCTGTCACACGTACGCTTAAG 58.075 47.619 16.72 6.08 0.00 1.85
841 918 2.549329 TCTGTCACACGTACGCTTAAGA 59.451 45.455 16.72 8.41 0.00 2.10
842 919 2.909244 CTGTCACACGTACGCTTAAGAG 59.091 50.000 16.72 5.51 0.00 2.85
844 921 3.003585 TGTCACACGTACGCTTAAGAGAA 59.996 43.478 16.72 0.00 0.00 2.87
845 922 3.602915 GTCACACGTACGCTTAAGAGAAG 59.397 47.826 16.72 6.09 0.00 2.85
883 969 0.511221 AAAATCACGGCGTCTGTTCG 59.489 50.000 10.85 0.00 0.00 3.95
1007 1236 1.338105 CGCATCTCCACAGAACCTCAA 60.338 52.381 0.00 0.00 30.24 3.02
1241 1493 4.130255 CGGAGGTCTTTGAGGGGA 57.870 61.111 0.00 0.00 0.00 4.81
1602 1854 3.532155 ATCAGACGCGGAGGAGGC 61.532 66.667 12.47 0.00 0.00 4.70
1819 2071 8.033626 GTGCACTGAGATTATATGAGATCATGA 58.966 37.037 10.32 0.00 37.15 3.07
1865 2117 8.339247 TGAGATTCAAGAAAATCTAGGGGAAAT 58.661 33.333 0.00 0.00 44.16 2.17
1921 2173 8.673275 CATTAATATTGTGCGTCGAAGAATTTC 58.327 33.333 0.20 0.00 39.69 2.17
1955 2207 5.932303 TCTTTGGAGAAAGAAATCTGTACCG 59.068 40.000 0.00 0.00 43.79 4.02
1981 2233 2.489329 CCGTATGATCAAATCCATGCCC 59.511 50.000 0.00 0.00 0.00 5.36
1987 2239 2.425143 TCAAATCCATGCCCAGAGAC 57.575 50.000 0.00 0.00 0.00 3.36
2030 2282 2.874701 GAGAGTACATGCATTGCCGAAT 59.125 45.455 6.12 0.00 0.00 3.34
2092 2367 8.709646 CAGTACTGTACTAAACTTTTGTGATCC 58.290 37.037 19.32 0.00 37.23 3.36
2129 2404 3.596214 GTCTCCTTTAACTCAATGGCGA 58.404 45.455 0.00 0.00 32.60 5.54
2256 2535 1.602327 GACTTTACCTCCGGCCGAGT 61.602 60.000 30.73 20.54 36.82 4.18
2266 2545 0.813184 CCGGCCGAGTAACTTACTGA 59.187 55.000 30.73 0.00 39.59 3.41
2280 2559 0.970427 TACTGATGACAGCCGGCTCA 60.970 55.000 30.29 24.07 46.95 4.26
2288 2567 1.166531 ACAGCCGGCTCACTCAAAAC 61.167 55.000 30.29 0.00 0.00 2.43
2289 2568 1.961277 AGCCGGCTCACTCAAAACG 60.961 57.895 27.08 0.00 0.00 3.60
2290 2569 1.959226 GCCGGCTCACTCAAAACGA 60.959 57.895 22.15 0.00 0.00 3.85
2292 2571 0.319555 CCGGCTCACTCAAAACGAGA 60.320 55.000 0.00 0.00 45.45 4.04
2293 2572 1.063806 CGGCTCACTCAAAACGAGAG 58.936 55.000 0.00 0.00 45.45 3.20
2294 2573 1.335964 CGGCTCACTCAAAACGAGAGA 60.336 52.381 0.00 0.00 45.45 3.10
2299 2578 4.757799 TCACTCAAAACGAGAGAGAGAG 57.242 45.455 0.00 0.00 45.45 3.20
2300 2579 4.390264 TCACTCAAAACGAGAGAGAGAGA 58.610 43.478 0.00 0.00 45.45 3.10
2301 2580 4.454161 TCACTCAAAACGAGAGAGAGAGAG 59.546 45.833 0.00 0.00 45.45 3.20
2302 2581 4.454161 CACTCAAAACGAGAGAGAGAGAGA 59.546 45.833 0.00 0.00 45.45 3.10
2303 2582 4.695455 ACTCAAAACGAGAGAGAGAGAGAG 59.305 45.833 0.00 0.00 45.45 3.20
2304 2583 4.900684 TCAAAACGAGAGAGAGAGAGAGA 58.099 43.478 0.00 0.00 0.00 3.10
2305 2584 4.935205 TCAAAACGAGAGAGAGAGAGAGAG 59.065 45.833 0.00 0.00 0.00 3.20
2306 2585 4.819105 AAACGAGAGAGAGAGAGAGAGA 57.181 45.455 0.00 0.00 0.00 3.10
2307 2586 4.392921 AACGAGAGAGAGAGAGAGAGAG 57.607 50.000 0.00 0.00 0.00 3.20
2308 2587 3.632333 ACGAGAGAGAGAGAGAGAGAGA 58.368 50.000 0.00 0.00 0.00 3.10
2330 2609 3.058777 AGAGAGAGAGAAAACACGTCGAC 60.059 47.826 5.18 5.18 0.00 4.20
2364 2643 8.071368 CGTTACTAAGTTGCCTTGTGAATTAAA 58.929 33.333 0.00 0.00 31.89 1.52
2401 2680 1.021202 GCAGTGGCAGTGTGTGTAAA 58.979 50.000 22.50 0.00 40.72 2.01
2471 2750 1.070038 GATTTTGGTTGCATGCACCG 58.930 50.000 22.58 0.00 0.00 4.94
2535 2814 0.813210 GCCCATCTCGAAGCTTCCTG 60.813 60.000 20.62 13.11 0.00 3.86
2569 2848 2.032681 GTTGCTTCGGCCCTGAGT 59.967 61.111 0.00 0.00 40.91 3.41
2636 2915 9.162764 GTGTGATTTGTAGAGTGTATAATGGTT 57.837 33.333 0.00 0.00 0.00 3.67
2696 2975 3.281727 TTGGAGTCTATGATGGCCAAC 57.718 47.619 10.96 8.17 31.04 3.77
2746 3025 3.073946 TCCAAGGAACCCCTGTCTAAAAG 59.926 47.826 0.00 0.00 43.48 2.27
2767 3046 5.365021 AGTTGGGAAGAAGATTCGATCAT 57.635 39.130 0.00 0.00 0.00 2.45
2807 3086 1.455822 AAGTTTGTGATGGGGGAGGA 58.544 50.000 0.00 0.00 0.00 3.71
2853 3273 4.949856 AGGCATGTTTTATTTCCTCGTGAT 59.050 37.500 0.00 0.00 0.00 3.06
2862 3282 9.968870 GTTTTATTTCCTCGTGATATAGAGAGT 57.031 33.333 4.46 0.00 36.65 3.24
2922 3342 5.408880 TGACTTTGTGGTCCGATATGTAA 57.591 39.130 0.00 0.00 35.54 2.41
2977 3397 4.142403 TGCCTTCATACTTGCTTTGCATAC 60.142 41.667 0.00 0.00 38.76 2.39
2984 3404 7.600960 TCATACTTGCTTTGCATACAAAATCA 58.399 30.769 0.00 0.00 44.90 2.57
2986 3406 6.088016 ACTTGCTTTGCATACAAAATCAGA 57.912 33.333 0.00 0.00 44.90 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 1.880941 AGGTAAGAGGGTTAGGGCTG 58.119 55.000 0.00 0.00 0.00 4.85
248 249 2.675348 CGACAGAAAGGAGGAATGAAGC 59.325 50.000 0.00 0.00 0.00 3.86
299 300 0.102300 ATCGATCCGAACGTCATGCA 59.898 50.000 0.00 0.00 39.99 3.96
308 309 0.040692 CTCGGCGTTATCGATCCGAA 60.041 55.000 21.83 9.94 45.39 4.30
342 343 5.521727 TTGGCGGCCAAATCTATGGTACA 62.522 47.826 31.03 4.41 40.92 2.90
358 359 1.095228 AGCACGTGGATTATTGGCGG 61.095 55.000 18.88 0.00 0.00 6.13
456 457 3.586454 CCGTTTTCCCCCACCCCT 61.586 66.667 0.00 0.00 0.00 4.79
600 603 6.980978 GCACAGAGCTAGTACTCATTGAATTA 59.019 38.462 0.00 0.00 39.26 1.40
604 607 4.377839 GCACAGAGCTAGTACTCATTGA 57.622 45.455 0.00 0.00 39.26 2.57
653 727 4.992951 CAGGAGCAAAATTCCCTCAAAAAG 59.007 41.667 0.00 0.00 35.20 2.27
776 852 2.419198 CTTCTCGATCTGGGCCGG 59.581 66.667 5.83 5.83 0.00 6.13
814 891 2.731341 GCGTACGTGTGACAGATAAGCT 60.731 50.000 17.90 0.00 0.00 3.74
830 907 2.101082 CCCCCTCTTCTCTTAAGCGTAC 59.899 54.545 0.00 0.00 0.00 3.67
957 1186 1.402107 TTATACCCGTTCCGCCTCCC 61.402 60.000 0.00 0.00 0.00 4.30
1241 1493 1.695597 CCTCATCCCAGCCCTCCTT 60.696 63.158 0.00 0.00 0.00 3.36
1742 1994 2.505982 CGGGGAAGTGCGGATCAT 59.494 61.111 0.00 0.00 0.00 2.45
1819 2071 5.014123 TCTCAAATGACTTGGGGTCTTGTAT 59.986 40.000 0.00 0.00 44.74 2.29
1823 2075 4.664688 ATCTCAAATGACTTGGGGTCTT 57.335 40.909 0.00 0.00 44.74 3.01
1865 2117 5.337009 GGAGTTCTACATACGACTGGGAAAA 60.337 44.000 0.00 0.00 0.00 2.29
1921 2173 5.804446 TTCTTTCTCCAAAGATGGCTACAGG 60.804 44.000 0.00 0.00 46.05 4.00
1955 2207 5.687285 GCATGGATTTGATCATACGGTTTTC 59.313 40.000 0.00 0.00 0.00 2.29
1981 2233 4.576053 TGAAACAACTGGTTCATGTCTCTG 59.424 41.667 6.08 0.00 45.85 3.35
2030 2282 5.645929 CCTAGCTCGAGCATATCTTTCTCTA 59.354 44.000 36.87 15.91 45.16 2.43
2092 2367 3.420397 GACCTCGGTCTTCCTTTCG 57.580 57.895 8.82 0.00 41.57 3.46
2106 2381 3.619979 CGCCATTGAGTTAAAGGAGACCT 60.620 47.826 0.00 0.00 29.73 3.85
2203 2478 0.960286 GGAGTTACCGCCCTAGCTAG 59.040 60.000 14.20 14.20 36.60 3.42
2205 2480 1.001248 TGGAGTTACCGCCCTAGCT 59.999 57.895 0.00 0.00 42.61 3.32
2256 2535 2.418197 GCCGGCTGTCATCAGTAAGTTA 60.418 50.000 22.15 0.00 43.05 2.24
2266 2545 1.830587 TTGAGTGAGCCGGCTGTCAT 61.831 55.000 38.41 17.34 0.00 3.06
2280 2559 4.647611 TCTCTCTCTCTCTCGTTTTGAGT 58.352 43.478 0.00 0.00 45.46 3.41
2288 2567 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
2289 2568 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2290 2569 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2291 2570 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2292 2571 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2293 2572 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2294 2573 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2295 2574 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2296 2575 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2297 2576 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
2298 2577 6.013379 TGTTTTCTCTCTCTCTCTCTCTCTCT 60.013 42.308 0.00 0.00 0.00 3.10
2299 2578 6.092807 GTGTTTTCTCTCTCTCTCTCTCTCTC 59.907 46.154 0.00 0.00 0.00 3.20
2300 2579 5.940470 GTGTTTTCTCTCTCTCTCTCTCTCT 59.060 44.000 0.00 0.00 0.00 3.10
2301 2580 5.163854 CGTGTTTTCTCTCTCTCTCTCTCTC 60.164 48.000 0.00 0.00 0.00 3.20
2302 2581 4.695455 CGTGTTTTCTCTCTCTCTCTCTCT 59.305 45.833 0.00 0.00 0.00 3.10
2303 2582 4.454504 ACGTGTTTTCTCTCTCTCTCTCTC 59.545 45.833 0.00 0.00 0.00 3.20
2304 2583 4.394729 ACGTGTTTTCTCTCTCTCTCTCT 58.605 43.478 0.00 0.00 0.00 3.10
2305 2584 4.668177 CGACGTGTTTTCTCTCTCTCTCTC 60.668 50.000 0.00 0.00 0.00 3.20
2306 2585 3.187637 CGACGTGTTTTCTCTCTCTCTCT 59.812 47.826 0.00 0.00 0.00 3.10
2307 2586 3.186817 TCGACGTGTTTTCTCTCTCTCTC 59.813 47.826 0.00 0.00 0.00 3.20
2308 2587 3.058777 GTCGACGTGTTTTCTCTCTCTCT 60.059 47.826 0.00 0.00 0.00 3.10
2330 2609 2.159881 GCAACTTAGTAACGGCTTGTCG 60.160 50.000 0.00 0.00 0.00 4.35
2364 2643 6.458070 GCCACTGCAACAAACAACAAATTTAT 60.458 34.615 0.00 0.00 37.47 1.40
2393 2672 5.685511 CCACTGCAACAAGTAATTTACACAC 59.314 40.000 9.15 0.00 0.00 3.82
2471 2750 8.277329 TGTGAAACCATGGATACAACTCATCTC 61.277 40.741 21.47 0.12 45.91 2.75
2535 2814 1.331756 CAACGGAGCACATAAGCCATC 59.668 52.381 0.00 0.00 34.23 3.51
2565 2844 6.350864 CCCATATTTATTGTGTTGCCAACTCA 60.351 38.462 9.30 8.71 33.51 3.41
2569 2848 4.469227 AGCCCATATTTATTGTGTTGCCAA 59.531 37.500 0.00 0.00 0.00 4.52
2580 2859 8.854117 GTTTCAGAAGATCAAGCCCATATTTAT 58.146 33.333 0.00 0.00 0.00 1.40
2585 2864 5.178096 TGTTTCAGAAGATCAAGCCCATA 57.822 39.130 0.00 0.00 0.00 2.74
2746 3025 5.118990 TCATGATCGAATCTTCTTCCCAAC 58.881 41.667 0.00 0.00 0.00 3.77
2807 3086 3.828451 CACCAAGTTTCCATTCCATCACT 59.172 43.478 0.00 0.00 0.00 3.41
2862 3282 4.344102 CGGGAGTCTCATAATAAGGAACCA 59.656 45.833 1.47 0.00 0.00 3.67
2877 3297 0.251386 TCAAGCTGAGTCGGGAGTCT 60.251 55.000 0.05 0.00 0.00 3.24
2922 3342 3.509575 AGAAGCAACAAGATCTCTCGACT 59.490 43.478 0.00 0.00 0.00 4.18
2957 3377 7.872163 TTTTGTATGCAAAGCAAGTATGAAG 57.128 32.000 8.99 0.00 44.32 3.02


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

AutoCloner maintained by Alex Coulton.