Multiple sequence alignment - TraesCS7D01G359900

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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 TraesCS7D01G359900 chr7D 100.000 3293 0 0 1 3293 462283196 462279904 0.000000e+00 6082.0
1 TraesCS7D01G359900 chr7B 94.836 2866 94 29 448 3293 485431714 485428883 0.000000e+00 4423.0
2 TraesCS7D01G359900 chr7B 93.933 445 26 1 1 444 485432222 485431778 0.000000e+00 671.0
3 TraesCS7D01G359900 chr7A 91.414 2108 95 52 858 2930 537662373 537664429 0.000000e+00 2811.0
4 TraesCS7D01G359900 chr7A 90.146 822 49 14 1 808 537661384 537662187 0.000000e+00 1040.0
5 TraesCS7D01G359900 chr7A 80.759 395 24 20 2928 3293 537664543 537664914 9.060000e-66 261.0
6 TraesCS7D01G359900 chr6A 96.774 62 2 0 1639 1700 219561938 219561877 1.620000e-18 104.0
7 TraesCS7D01G359900 chr6D 95.161 62 3 0 1639 1700 160429219 160429158 7.520000e-17 99.0
8 TraesCS7D01G359900 chrUn 93.548 62 4 0 1639 1700 453960274 453960335 3.500000e-15 93.5
9 TraesCS7D01G359900 chrUn 93.548 62 4 0 1639 1700 466322510 466322571 3.500000e-15 93.5
10 TraesCS7D01G359900 chr6B 93.548 62 4 0 1639 1700 290596899 290596838 3.500000e-15 93.5
11 TraesCS7D01G359900 chr6B 93.548 62 4 0 1639 1700 290628457 290628396 3.500000e-15 93.5


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 TraesCS7D01G359900 chr7D 462279904 462283196 3292 True 6082.000000 6082 100.000000 1 3293 1 chr7D.!!$R1 3292
1 TraesCS7D01G359900 chr7B 485428883 485432222 3339 True 2547.000000 4423 94.384500 1 3293 2 chr7B.!!$R1 3292
2 TraesCS7D01G359900 chr7A 537661384 537664914 3530 False 1370.666667 2811 87.439667 1 3293 3 chr7A.!!$F1 3292

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
829 905 0.106217 GACCCCTCCCTCTCTCTCTG 60.106 65.0 0.0 0.00 0.00 3.35 F
2020 2263 0.391661 CAAGGTGGTCCAGGATCACG 60.392 60.0 24.2 9.06 43.85 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2393 1.130054 AGGGCTCTTGCTCCAGTTGA 61.13 55.000 0.0 0.0 41.57 3.18 R
3266 3698 1.129811 GTTTGTGGGATAAGTTCGCCG 59.87 52.381 0.0 0.0 36.49 6.46 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
78 79 4.736307 ACCGTTTAAAATCTTGTTTGACGC 59.264 37.500 0.00 0.00 33.62 5.19
96 97 5.302360 TGACGCTTACAAACCAAGAACTAT 58.698 37.500 0.00 0.00 0.00 2.12
97 98 5.178623 TGACGCTTACAAACCAAGAACTATG 59.821 40.000 0.00 0.00 0.00 2.23
106 108 4.650972 ACCAAGAACTATGCCCTACAAA 57.349 40.909 0.00 0.00 0.00 2.83
129 131 0.250166 AACGTGGAACCTCGGGAAAG 60.250 55.000 17.27 0.00 37.27 2.62
161 163 6.966637 ATAGGCATCAATTCCTAGATTCCT 57.033 37.500 0.00 0.00 40.30 3.36
407 413 9.843334 GATCTAAGAAGACCTAATTACATACCG 57.157 37.037 0.00 0.00 33.57 4.02
477 543 6.017605 CCACAAACTATGGATGATGAGCTAAC 60.018 42.308 0.00 0.00 39.87 2.34
507 573 5.850046 ACATAGGATTAGCTAGGCCAAAT 57.150 39.130 5.01 0.00 0.00 2.32
510 576 4.526438 AGGATTAGCTAGGCCAAATGTT 57.474 40.909 5.01 0.00 0.00 2.71
519 585 1.202830 AGGCCAAATGTTCGTACCACA 60.203 47.619 5.01 0.00 0.00 4.17
524 590 2.074547 AATGTTCGTACCACAGGTCG 57.925 50.000 0.00 0.00 37.09 4.79
668 736 1.153349 GACCCTGATCCTTGTCGGC 60.153 63.158 0.00 0.00 0.00 5.54
731 799 2.287457 TTACTGTTCCCCGCCGATCG 62.287 60.000 8.51 8.51 38.08 3.69
733 801 3.151710 TGTTCCCCGCCGATCGAT 61.152 61.111 18.66 0.00 41.67 3.59
737 805 1.241990 TTCCCCGCCGATCGATCTAG 61.242 60.000 22.43 14.64 41.67 2.43
738 806 2.179517 CCCGCCGATCGATCTAGC 59.820 66.667 22.43 21.71 41.67 3.42
747 815 0.449786 ATCGATCTAGCGCTCATCCG 59.550 55.000 16.34 14.51 0.00 4.18
762 830 0.976641 ATCCGTTTCCTGTGCTCTCA 59.023 50.000 0.00 0.00 0.00 3.27
763 831 0.976641 TCCGTTTCCTGTGCTCTCAT 59.023 50.000 0.00 0.00 0.00 2.90
812 888 2.622436 GTGATCACACAAGGCCTAGAC 58.378 52.381 21.07 0.00 45.32 2.59
813 889 1.555075 TGATCACACAAGGCCTAGACC 59.445 52.381 5.16 0.00 0.00 3.85
829 905 0.106217 GACCCCTCCCTCTCTCTCTG 60.106 65.000 0.00 0.00 0.00 3.35
830 906 1.457455 CCCCTCCCTCTCTCTCTGC 60.457 68.421 0.00 0.00 0.00 4.26
831 907 1.457455 CCCTCCCTCTCTCTCTGCC 60.457 68.421 0.00 0.00 0.00 4.85
853 931 4.498894 CCTTTATAAAAGGGACCCGACT 57.501 45.455 4.40 0.00 33.69 4.18
953 1169 2.453991 TCCCCATCTCATCCTGATCTCT 59.546 50.000 0.00 0.00 0.00 3.10
1142 1366 2.886523 TGTTCCCTTTTGTGATCAGCAG 59.113 45.455 0.00 0.00 0.00 4.24
1462 1694 2.401568 TGATATGGAGAAGCTGCAGGA 58.598 47.619 17.12 0.00 34.87 3.86
1715 1950 5.346522 CCCAAGGTAGTACTACGATTTGTC 58.653 45.833 23.40 10.24 36.94 3.18
1726 1961 9.570488 AGTACTACGATTTGTCTGTTAATTCTC 57.430 33.333 0.00 0.00 0.00 2.87
1783 2026 4.664891 GCGTAACGGTAACTAACTTTGCTG 60.665 45.833 0.00 0.00 0.00 4.41
1815 2058 2.327592 CAGTCGCTTTGCAACGCA 59.672 55.556 25.29 11.43 36.47 5.24
1957 2200 2.342179 CGAAGGTGAAGAAGGAGAAGC 58.658 52.381 0.00 0.00 0.00 3.86
2020 2263 0.391661 CAAGGTGGTCCAGGATCACG 60.392 60.000 24.20 9.06 43.85 4.35
2088 2334 3.667282 CCGGTCGTCGTCACCACT 61.667 66.667 0.00 0.00 37.11 4.00
2107 2353 0.834261 TACCACCACCACTGCTGCTA 60.834 55.000 0.00 0.00 0.00 3.49
2165 2417 1.267574 TGGAGCAAGAGCCCTACTGG 61.268 60.000 0.00 0.00 43.56 4.00
2486 2739 7.950496 GTGATTCGTTTGTGTGTAAGATAAGAC 59.050 37.037 0.00 0.00 0.00 3.01
2646 2908 2.484264 AGTAGCTAGCTTTTTGTTGCCG 59.516 45.455 24.88 0.00 0.00 5.69
2776 3038 4.813027 ACCATGAAATGTTGCTGTTCATC 58.187 39.130 0.00 0.00 44.81 2.92
2883 3145 2.529780 TTCTAACGTTTTCCCGCTGA 57.470 45.000 5.91 0.00 0.00 4.26
2885 3147 2.613691 TCTAACGTTTTCCCGCTGATC 58.386 47.619 5.91 0.00 0.00 2.92
2982 3386 2.099141 TGCTAGTAGCTTTGCACAGG 57.901 50.000 22.34 0.00 42.97 4.00
3266 3698 1.638467 CTATCAGGCGAGCGTTTGC 59.362 57.895 2.31 2.31 43.24 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 7.488322 ACGGTTACCAATGGATTGAAAATATG 58.512 34.615 6.16 0.00 40.14 1.78
36 37 7.469537 AACGGTTACCAATGGATTGAAAATA 57.530 32.000 6.16 0.00 40.14 1.40
38 39 5.793030 AACGGTTACCAATGGATTGAAAA 57.207 34.783 6.16 0.00 40.14 2.29
52 53 7.563827 GCGTCAAACAAGATTTTAAACGGTTAC 60.564 37.037 0.00 0.00 31.99 2.50
78 79 5.010282 AGGGCATAGTTCTTGGTTTGTAAG 58.990 41.667 0.00 0.00 0.00 2.34
89 90 5.624738 CGTTCTCTTTGTAGGGCATAGTTCT 60.625 44.000 0.00 0.00 0.00 3.01
96 97 1.270625 CCACGTTCTCTTTGTAGGGCA 60.271 52.381 0.00 0.00 0.00 5.36
97 98 1.001633 TCCACGTTCTCTTTGTAGGGC 59.998 52.381 0.00 0.00 0.00 5.19
106 108 1.533469 CCCGAGGTTCCACGTTCTCT 61.533 60.000 7.75 0.00 0.00 3.10
129 131 4.202151 GGAATTGATGCCTATTTGGTGGAC 60.202 45.833 0.00 0.00 38.35 4.02
161 163 5.778241 ACCCGATCATATTGGTGTAGATGTA 59.222 40.000 0.00 0.00 31.38 2.29
287 293 2.313909 CCACACGTACACGCATGCA 61.314 57.895 19.57 0.00 44.43 3.96
402 408 4.571919 TCATCAAACCTTCGTTTCGGTAT 58.428 39.130 0.00 0.00 40.28 2.73
407 413 5.607119 TTAGCTCATCAAACCTTCGTTTC 57.393 39.130 0.00 0.00 40.28 2.78
477 543 7.499895 GGCCTAGCTAATCCTATGTACTACTAG 59.500 44.444 0.00 0.00 0.00 2.57
507 573 1.007038 GCGACCTGTGGTACGAACA 60.007 57.895 10.88 0.68 35.25 3.18
510 576 1.287815 CAAGCGACCTGTGGTACGA 59.712 57.895 10.88 0.00 35.25 3.43
519 585 0.319900 CTGTAGCACACAAGCGACCT 60.320 55.000 0.00 0.00 39.06 3.85
540 606 5.701224 TCGAATTAGGGCAAGGGATATTTT 58.299 37.500 0.00 0.00 0.00 1.82
668 736 3.197116 ACACACGTTAGAATTCCTAGGGG 59.803 47.826 9.46 0.00 0.00 4.79
731 799 2.055100 GAAACGGATGAGCGCTAGATC 58.945 52.381 11.50 15.16 0.00 2.75
733 801 0.102481 GGAAACGGATGAGCGCTAGA 59.898 55.000 11.50 0.00 0.00 2.43
737 805 1.741770 ACAGGAAACGGATGAGCGC 60.742 57.895 0.00 0.00 0.00 5.92
738 806 1.970917 GCACAGGAAACGGATGAGCG 61.971 60.000 0.00 0.00 0.00 5.03
747 815 1.280421 AGGGATGAGAGCACAGGAAAC 59.720 52.381 0.00 0.00 0.00 2.78
762 830 3.587506 GAGAGGTAGCTAGAGAGAGGGAT 59.412 52.174 0.00 0.00 0.00 3.85
763 831 2.976882 GAGAGGTAGCTAGAGAGAGGGA 59.023 54.545 0.00 0.00 0.00 4.20
808 884 1.011545 AGAGAGAGAGGGAGGGGTCTA 59.988 57.143 0.00 0.00 0.00 2.59
809 885 0.254107 AGAGAGAGAGGGAGGGGTCT 60.254 60.000 0.00 0.00 0.00 3.85
810 886 0.106217 CAGAGAGAGAGGGAGGGGTC 60.106 65.000 0.00 0.00 0.00 4.46
811 887 2.015081 CAGAGAGAGAGGGAGGGGT 58.985 63.158 0.00 0.00 0.00 4.95
812 888 1.457455 GCAGAGAGAGAGGGAGGGG 60.457 68.421 0.00 0.00 0.00 4.79
813 889 1.457455 GGCAGAGAGAGAGGGAGGG 60.457 68.421 0.00 0.00 0.00 4.30
853 931 0.976073 GATCACGAACAGGAGGGGGA 60.976 60.000 0.00 0.00 0.00 4.81
953 1169 3.594603 GCTAGGGAGCGCAGATAATTA 57.405 47.619 11.47 0.00 39.39 1.40
1056 1280 1.491754 TGATGGTGATCCTGGTGATGG 59.508 52.381 0.00 0.00 32.41 3.51
1142 1366 3.958147 TTGTCGCTAGGGCTGCTGC 62.958 63.158 7.10 7.10 36.09 5.25
1272 1496 5.916883 CAGAAAGTGACCAAGCAAACTAATG 59.083 40.000 0.00 0.00 0.00 1.90
1625 1860 5.333645 GCAATCAGAGCATGTCCTAATAACG 60.334 44.000 0.00 0.00 0.00 3.18
1715 1950 5.308825 ACCAAGTGACCAGAGAATTAACAG 58.691 41.667 0.00 0.00 0.00 3.16
1725 1960 2.696526 ACTCCTACCAAGTGACCAGA 57.303 50.000 0.00 0.00 0.00 3.86
1726 1961 3.162666 TGTACTCCTACCAAGTGACCAG 58.837 50.000 0.00 0.00 0.00 4.00
2141 2393 1.130054 AGGGCTCTTGCTCCAGTTGA 61.130 55.000 0.00 0.00 41.57 3.18
2315 2567 4.278170 GTGGTGGATAGATCAGAGTCTCTG 59.722 50.000 21.95 21.95 45.59 3.35
2486 2739 5.364778 TCTAGATCTCTCTCTTTCTCACCG 58.635 45.833 0.00 0.00 32.66 4.94
2776 3038 3.747193 CAAAAGTCATGAACGATTCCCG 58.253 45.455 0.00 0.00 45.44 5.14
2871 3133 1.740025 CCTCAAGATCAGCGGGAAAAC 59.260 52.381 0.00 0.00 0.00 2.43
2883 3145 7.613022 TGATAAAGAGAATGTTTGCCTCAAGAT 59.387 33.333 0.00 0.00 32.11 2.40
2885 3147 7.149569 TGATAAAGAGAATGTTTGCCTCAAG 57.850 36.000 0.00 0.00 32.11 3.02
2982 3386 3.561725 CGATGGAAAGTTATGCCTCCTTC 59.438 47.826 0.00 0.00 0.00 3.46
3266 3698 1.129811 GTTTGTGGGATAAGTTCGCCG 59.870 52.381 0.00 0.00 36.49 6.46


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

AutoCloner maintained by Alex Coulton.