Multiple sequence alignment - TraesCS7A01G326900

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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 TraesCS7A01G326900 chr7A 100.000 2768 0 0 1 2768 475167708 475164941 0.000000e+00 5112.0
1 TraesCS7A01G326900 chr7D 94.530 2468 92 17 320 2768 413443151 413440708 0.000000e+00 3770.0
2 TraesCS7A01G326900 chr7D 88.338 343 18 11 1 335 413443501 413443173 2.580000e-105 392.0
3 TraesCS7A01G326900 chr7B 91.274 1845 82 33 638 2442 427823051 427821246 0.000000e+00 2442.0
4 TraesCS7A01G326900 chr7B 92.436 661 25 5 1 646 427823793 427823143 0.000000e+00 920.0
5 TraesCS7A01G326900 chr7B 87.097 341 33 4 2429 2759 427814381 427814042 2.600000e-100 375.0
6 TraesCS7A01G326900 chr7B 75.686 255 40 15 2512 2757 577202904 577203145 1.050000e-19 108.0
7 TraesCS7A01G326900 chr3D 78.919 370 51 17 2405 2759 171131641 171131284 2.770000e-55 226.0
8 TraesCS7A01G326900 chr3A 78.378 370 46 18 2404 2759 208644582 208644233 2.790000e-50 209.0
9 TraesCS7A01G326900 chr2D 77.695 269 39 13 2507 2765 547154493 547154750 7.990000e-31 145.0
10 TraesCS7A01G326900 chr2D 74.608 319 51 22 2435 2742 431928461 431928760 2.250000e-21 113.0
11 TraesCS7A01G326900 chr5B 78.166 229 31 10 2507 2726 696724842 696725060 8.050000e-26 128.0
12 TraesCS7A01G326900 chr4A 77.366 243 36 15 2514 2748 477053219 477053450 2.890000e-25 126.0
13 TraesCS7A01G326900 chr3B 76.923 247 36 11 2507 2743 492571794 492572029 1.350000e-23 121.0
14 TraesCS7A01G326900 chr1D 77.880 217 29 16 2435 2648 308448544 308448744 1.740000e-22 117.0
15 TraesCS7A01G326900 chr2A 75.833 240 39 9 2512 2742 554095340 554095569 1.360000e-18 104.0
16 TraesCS7A01G326900 chr5A 77.311 119 20 7 2428 2542 375574912 375574797 2.300000e-06 63.9


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 TraesCS7A01G326900 chr7A 475164941 475167708 2767 True 5112 5112 100.000 1 2768 1 chr7A.!!$R1 2767
1 TraesCS7A01G326900 chr7D 413440708 413443501 2793 True 2081 3770 91.434 1 2768 2 chr7D.!!$R1 2767
2 TraesCS7A01G326900 chr7B 427821246 427823793 2547 True 1681 2442 91.855 1 2442 2 chr7B.!!$R2 2441

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
509 569 0.035056 AGAAACAGAGGGGGATTGCG 60.035 55.0 0.0 0.0 0.00 4.85 F
916 1086 0.039617 CGGTCGATCCATCTCTGCTC 60.040 60.0 0.0 0.0 35.57 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1763 1.139734 GATCAGCTCGCCGAACAGA 59.86 57.895 0.0 0.00 0.00 3.41 R
2041 2234 1.160137 GGATGAAGCTTCGTTGCAGT 58.84 50.000 21.8 1.89 34.99 4.40 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
64 67 3.257873 AGAATCTGCAGGTAGATCCATCG 59.742 47.826 15.13 0.00 36.42 3.84
65 68 2.364972 TCTGCAGGTAGATCCATCGA 57.635 50.000 15.13 0.00 39.02 3.59
66 69 2.881734 TCTGCAGGTAGATCCATCGAT 58.118 47.619 15.13 0.00 39.02 3.59
67 70 4.034285 TCTGCAGGTAGATCCATCGATA 57.966 45.455 15.13 0.00 39.02 2.92
68 71 4.604156 TCTGCAGGTAGATCCATCGATAT 58.396 43.478 15.13 0.00 39.02 1.63
118 125 2.507854 GCTAGCTACATGGGCCCGA 61.508 63.158 19.37 6.86 0.00 5.14
123 130 2.056906 GCTACATGGGCCCGATCCTT 62.057 60.000 19.37 0.00 0.00 3.36
158 165 5.981088 TTCATAATCCTGCAACAACACAT 57.019 34.783 0.00 0.00 0.00 3.21
159 166 5.313520 TCATAATCCTGCAACAACACATG 57.686 39.130 0.00 0.00 0.00 3.21
179 186 9.689976 ACACATGTTCGATTCAAAAATTAATCA 57.310 25.926 0.00 0.00 32.70 2.57
185 192 7.504922 TCGATTCAAAAATTAATCAAAGCCG 57.495 32.000 0.00 0.00 32.70 5.52
197 204 2.104967 TCAAAGCCGCTTAGCTAGGTA 58.895 47.619 5.94 0.00 44.11 3.08
332 341 0.539986 TGCCCGACTAATCCTGGAAC 59.460 55.000 0.00 0.00 0.00 3.62
398 444 2.290387 TGGAGCTAGAGAACGACAGAGT 60.290 50.000 0.00 0.00 0.00 3.24
407 453 1.000506 GAACGACAGAGTAACCAGCCA 59.999 52.381 0.00 0.00 0.00 4.75
456 516 6.494666 TGAATATATCTGACCCGGTTCTTT 57.505 37.500 0.00 0.00 0.00 2.52
509 569 0.035056 AGAAACAGAGGGGGATTGCG 60.035 55.000 0.00 0.00 0.00 4.85
618 678 6.610741 AACTTCAAAGTTAGCTTGTGAGAG 57.389 37.500 6.35 3.60 46.75 3.20
625 685 3.007398 AGTTAGCTTGTGAGAGGGTGAAG 59.993 47.826 0.00 0.00 0.00 3.02
693 853 1.292061 TACACGCCCATAATTCGCAC 58.708 50.000 0.00 0.00 0.00 5.34
743 903 5.726980 TTAGTAGTTTTTGCGTCTCCCTA 57.273 39.130 0.00 0.00 0.00 3.53
744 904 4.820894 AGTAGTTTTTGCGTCTCCCTAT 57.179 40.909 0.00 0.00 0.00 2.57
748 914 2.413310 TTTTGCGTCTCCCTATTCCC 57.587 50.000 0.00 0.00 0.00 3.97
794 964 1.562942 TGATCTCCTTTCAGCTGCCAT 59.437 47.619 9.47 0.00 0.00 4.40
823 993 9.634021 CTATATATACATGGCTCCACTAGAGAA 57.366 37.037 0.00 0.00 46.50 2.87
824 994 6.849085 ATATACATGGCTCCACTAGAGAAG 57.151 41.667 0.00 0.00 46.50 2.85
825 995 3.107402 ACATGGCTCCACTAGAGAAGA 57.893 47.619 0.00 0.00 46.50 2.87
826 996 3.030291 ACATGGCTCCACTAGAGAAGAG 58.970 50.000 0.00 0.00 46.50 2.85
827 997 3.295093 CATGGCTCCACTAGAGAAGAGA 58.705 50.000 0.00 0.00 46.50 3.10
894 1064 2.135664 AGAACGTTTCTCACTGACCG 57.864 50.000 0.46 0.00 34.07 4.79
916 1086 0.039617 CGGTCGATCCATCTCTGCTC 60.040 60.000 0.00 0.00 35.57 4.26
982 1152 4.498520 CGAGCTCGTGGCATCGGT 62.499 66.667 27.79 0.00 44.79 4.69
983 1153 2.583593 GAGCTCGTGGCATCGGTC 60.584 66.667 0.00 3.96 44.79 4.79
984 1154 4.498520 AGCTCGTGGCATCGGTCG 62.499 66.667 9.05 0.00 44.79 4.79
1251 1421 0.684479 CGTCATCCTCCTCACTCCCA 60.684 60.000 0.00 0.00 0.00 4.37
1359 1529 1.376037 GTTCCCGTTCCAGCTCCAG 60.376 63.158 0.00 0.00 0.00 3.86
1360 1530 3.254024 TTCCCGTTCCAGCTCCAGC 62.254 63.158 0.00 0.00 42.49 4.85
1361 1531 4.020617 CCCGTTCCAGCTCCAGCA 62.021 66.667 0.48 0.00 45.16 4.41
1545 1715 3.452621 ATCTCTCCCGGCGATCCCA 62.453 63.158 9.30 0.00 0.00 4.37
1567 1737 2.202810 GCTTCTTCTCTCCGCCGG 60.203 66.667 0.00 0.00 0.00 6.13
1593 1763 3.142838 GCTGGCGGTGGCATCAAT 61.143 61.111 0.00 0.00 42.47 2.57
1680 1853 2.105649 TGCAAGTCCTACACCAATGTCA 59.894 45.455 0.00 0.00 40.48 3.58
1895 2075 0.716108 GTCGCCGTCTGACAGAATTG 59.284 55.000 6.76 0.17 36.37 2.32
2041 2234 1.134250 TGCTGATTACCCGCATGCTAA 60.134 47.619 17.13 8.23 0.00 3.09
2091 2284 0.522286 CTCGTGTCTGCTCTGCTACG 60.522 60.000 0.00 0.00 0.00 3.51
2262 2462 7.765307 AGTATGCCATTCATTTGTAACAGAAG 58.235 34.615 0.00 0.00 36.63 2.85
2265 2465 5.301551 TGCCATTCATTTGTAACAGAAGTGT 59.698 36.000 0.00 0.00 39.19 3.55
2341 2541 2.810852 TGTTTAAGCGTGCATGATCACA 59.189 40.909 10.93 4.92 36.80 3.58
2418 2618 9.167311 GCCCCTTACATCTTAACTCATTATATG 57.833 37.037 0.00 0.00 0.00 1.78
2506 2707 6.647067 GCCAATTCGTCTTAGCTTCTGTATAT 59.353 38.462 0.00 0.00 0.00 0.86
2507 2708 7.813148 GCCAATTCGTCTTAGCTTCTGTATATA 59.187 37.037 0.00 0.00 0.00 0.86
2653 2854 4.040461 TCAAACACACAAAAGGGTCCAAAA 59.960 37.500 0.00 0.00 0.00 2.44
2656 2857 3.447229 ACACACAAAAGGGTCCAAAAGAG 59.553 43.478 0.00 0.00 0.00 2.85
2657 2858 2.430694 ACACAAAAGGGTCCAAAAGAGC 59.569 45.455 0.00 0.00 42.55 4.09
2658 2859 2.430332 CACAAAAGGGTCCAAAAGAGCA 59.570 45.455 0.00 0.00 45.21 4.26
2659 2860 2.430694 ACAAAAGGGTCCAAAAGAGCAC 59.569 45.455 0.00 0.00 45.21 4.40
2714 2924 1.212616 GCTACTAATGCTCAGCACGG 58.787 55.000 0.00 0.00 43.04 4.94
2726 2936 0.036952 CAGCACGGTCATCTTGGAGT 60.037 55.000 0.00 0.00 0.00 3.85
2744 2954 3.194968 GGAGTTGGGTATGAACTTCTCGA 59.805 47.826 0.00 0.00 33.71 4.04
2748 2958 5.046591 AGTTGGGTATGAACTTCTCGATTCA 60.047 40.000 1.91 1.91 39.09 2.57
2750 2960 4.221924 TGGGTATGAACTTCTCGATTCACA 59.778 41.667 1.45 0.00 37.64 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 67 9.828039 TGTATCTTCTGGAATATGCATCATATC 57.172 33.333 0.19 0.00 36.20 1.63
65 68 9.833917 CTGTATCTTCTGGAATATGCATCATAT 57.166 33.333 0.19 0.00 38.52 1.78
66 69 8.819845 ACTGTATCTTCTGGAATATGCATCATA 58.180 33.333 0.19 0.00 0.00 2.15
67 70 7.687388 ACTGTATCTTCTGGAATATGCATCAT 58.313 34.615 0.19 0.00 0.00 2.45
68 71 7.071069 ACTGTATCTTCTGGAATATGCATCA 57.929 36.000 0.19 0.00 0.00 3.07
118 125 3.565307 TGAAAGTGCAAAGGTGAAGGAT 58.435 40.909 0.00 0.00 0.00 3.24
123 130 5.183713 CAGGATTATGAAAGTGCAAAGGTGA 59.816 40.000 0.00 0.00 0.00 4.02
158 165 8.707839 GGCTTTGATTAATTTTTGAATCGAACA 58.292 29.630 0.00 0.00 35.25 3.18
159 166 7.892731 CGGCTTTGATTAATTTTTGAATCGAAC 59.107 33.333 0.00 0.00 35.25 3.95
165 172 7.148656 GCTAAGCGGCTTTGATTAATTTTTGAA 60.149 33.333 24.68 0.01 0.00 2.69
179 186 2.235402 TGTTACCTAGCTAAGCGGCTTT 59.765 45.455 21.72 5.54 42.97 3.51
197 204 6.540438 TTCCAGATACTCTCGGTATTTGTT 57.460 37.500 0.00 0.00 40.82 2.83
305 314 2.213499 GATTAGTCGGGCATGGACTTG 58.787 52.381 8.18 0.00 41.83 3.16
398 444 6.890293 TGTGTATGTATATTGTGGCTGGTTA 58.110 36.000 0.00 0.00 0.00 2.85
407 453 8.166422 TGTCTCTCGATGTGTATGTATATTGT 57.834 34.615 0.00 0.00 0.00 2.71
456 516 1.324383 TTGACTAGCACTGACGACCA 58.676 50.000 0.00 0.00 0.00 4.02
611 671 2.777692 ACCTTTTCTTCACCCTCTCACA 59.222 45.455 0.00 0.00 0.00 3.58
618 678 9.020731 TCATATAAAGAAACCTTTTCTTCACCC 57.979 33.333 13.00 0.00 37.75 4.61
733 893 1.473497 GGGAGGGAATAGGGAGACGC 61.473 65.000 0.00 0.00 0.00 5.19
743 903 0.618981 GACCAAGTTCGGGAGGGAAT 59.381 55.000 0.00 0.00 0.00 3.01
744 904 1.823169 CGACCAAGTTCGGGAGGGAA 61.823 60.000 0.00 0.00 35.26 3.97
748 914 2.434359 GGCGACCAAGTTCGGGAG 60.434 66.667 0.00 0.00 39.50 4.30
794 964 9.004231 TCTAGTGGAGCCATGTATATATAGAGA 57.996 37.037 0.00 0.00 0.00 3.10
823 993 0.988832 ACGTGTCTCCTCTCCTCTCT 59.011 55.000 0.00 0.00 0.00 3.10
824 994 2.282407 GTACGTGTCTCCTCTCCTCTC 58.718 57.143 0.00 0.00 0.00 3.20
825 995 1.405797 CGTACGTGTCTCCTCTCCTCT 60.406 57.143 7.22 0.00 0.00 3.69
826 996 1.008329 CGTACGTGTCTCCTCTCCTC 58.992 60.000 7.22 0.00 0.00 3.71
827 997 0.324285 ACGTACGTGTCTCCTCTCCT 59.676 55.000 22.14 0.00 0.00 3.69
962 1132 2.959071 GATGCCACGAGCTCGCTC 60.959 66.667 34.83 23.06 44.23 5.03
1295 1465 0.802607 GAGCATGGAAGACGACGACC 60.803 60.000 0.00 0.00 0.00 4.79
1360 1530 3.515286 CTGCGGCCCAGATGCTTG 61.515 66.667 14.21 0.00 44.64 4.01
1361 1531 4.809496 CCTGCGGCCCAGATGCTT 62.809 66.667 19.43 0.00 44.64 3.91
1398 1568 3.200593 GGCGAGTGCTGATGCTGG 61.201 66.667 0.00 0.00 42.25 4.85
1545 1715 2.352032 CGGAGAGAAGAAGCCCGGT 61.352 63.158 0.00 0.00 36.81 5.28
1593 1763 1.139734 GATCAGCTCGCCGAACAGA 59.860 57.895 0.00 0.00 0.00 3.41
1680 1853 2.092646 TGCAGCGGGGAAATACTGTAAT 60.093 45.455 0.00 0.00 32.65 1.89
1837 2010 7.776933 ATGGAAATCAATCGATCATATACCG 57.223 36.000 0.00 0.00 0.00 4.02
1838 2011 9.994432 GAAATGGAAATCAATCGATCATATACC 57.006 33.333 0.00 0.09 0.00 2.73
1839 2012 9.994432 GGAAATGGAAATCAATCGATCATATAC 57.006 33.333 0.00 0.00 0.00 1.47
1840 2013 9.737844 TGGAAATGGAAATCAATCGATCATATA 57.262 29.630 0.00 0.00 0.00 0.86
1841 2014 8.640063 TGGAAATGGAAATCAATCGATCATAT 57.360 30.769 0.00 0.00 0.00 1.78
1842 2015 8.517056 CATGGAAATGGAAATCAATCGATCATA 58.483 33.333 0.00 0.00 0.00 2.15
1843 2016 6.964807 TGGAAATGGAAATCAATCGATCAT 57.035 33.333 0.00 0.00 0.00 2.45
1844 2017 6.736519 GCATGGAAATGGAAATCAATCGATCA 60.737 38.462 0.00 0.00 0.00 2.92
1906 2087 4.081695 ACTAATCCTGTTTCTCTCCCCT 57.918 45.455 0.00 0.00 0.00 4.79
2025 2214 1.264288 GCAGTTAGCATGCGGGTAATC 59.736 52.381 13.01 0.30 44.79 1.75
2041 2234 1.160137 GGATGAAGCTTCGTTGCAGT 58.840 50.000 21.80 1.89 34.99 4.40
2091 2284 5.006746 GTGCAAACATATACCAGCTGACTAC 59.993 44.000 17.39 0.00 0.00 2.73
2208 2408 9.138062 CACTGAGCATTATGTATGTCTATCTTC 57.862 37.037 0.00 0.00 36.57 2.87
2326 2526 2.086094 TCAATTGTGATCATGCACGCT 58.914 42.857 5.13 0.00 41.63 5.07
2358 2558 3.694072 GTGATCGGCTAGAGATGCTCTAT 59.306 47.826 4.77 0.00 41.49 1.98
2444 2644 4.954202 GGGAGTTAAGTTTTAGGGATTGGG 59.046 45.833 0.00 0.00 0.00 4.12
2446 2646 8.873186 TTTAGGGAGTTAAGTTTTAGGGATTG 57.127 34.615 0.00 0.00 0.00 2.67
2631 2832 3.601443 TTGGACCCTTTTGTGTGTTTG 57.399 42.857 0.00 0.00 0.00 2.93
2640 2841 2.745968 TGTGCTCTTTTGGACCCTTTT 58.254 42.857 0.00 0.00 0.00 2.27
2653 2854 3.407424 TGTTGTGCTTCTATGTGCTCT 57.593 42.857 0.00 0.00 0.00 4.09
2656 2857 4.424061 TGATTGTTGTGCTTCTATGTGC 57.576 40.909 0.00 0.00 0.00 4.57
2657 2858 5.854866 CACTTGATTGTTGTGCTTCTATGTG 59.145 40.000 0.00 0.00 0.00 3.21
2658 2859 5.048504 CCACTTGATTGTTGTGCTTCTATGT 60.049 40.000 0.00 0.00 0.00 2.29
2659 2860 5.048504 ACCACTTGATTGTTGTGCTTCTATG 60.049 40.000 0.00 0.00 0.00 2.23
2714 2924 4.487714 TCATACCCAACTCCAAGATGAC 57.512 45.455 0.00 0.00 0.00 3.06
2726 2936 5.175859 GTGAATCGAGAAGTTCATACCCAA 58.824 41.667 5.50 0.00 36.79 4.12


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

AutoCloner maintained by Alex Coulton.