Multiple sequence alignment - TraesCS5D01G207300

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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 TraesCS5D01G207300 chr5D 100.000 2943 0 0 1 2943 313332203 313335145 0.000000e+00 5435
1 TraesCS5D01G207300 chr5D 87.450 1004 114 8 1046 2042 313151647 313150649 0.000000e+00 1146
2 TraesCS5D01G207300 chr5D 86.157 1033 73 29 1 977 313152776 313151758 0.000000e+00 1051
3 TraesCS5D01G207300 chr5D 92.089 493 37 2 1551 2042 313284296 313284787 0.000000e+00 693
4 TraesCS5D01G207300 chr5B 89.358 2086 146 27 1 2042 360862177 360860124 0.000000e+00 2553
5 TraesCS5D01G207300 chr5B 90.330 848 73 4 1196 2042 360925005 360925844 0.000000e+00 1103
6 TraesCS5D01G207300 chr5B 93.596 203 11 1 2 204 360922388 360922588 4.770000e-78 302
7 TraesCS5D01G207300 chr1D 97.351 906 19 1 2043 2943 200313793 200312888 0.000000e+00 1535
8 TraesCS5D01G207300 chr1D 97.003 901 23 2 2043 2943 39535820 39536716 0.000000e+00 1511
9 TraesCS5D01G207300 chr3D 97.336 901 21 3 2043 2943 248008771 248007874 0.000000e+00 1528
10 TraesCS5D01G207300 chr3D 96.678 903 25 5 2043 2943 25590504 25589605 0.000000e+00 1496
11 TraesCS5D01G207300 chr2D 97.118 902 23 3 2043 2943 41494511 41493612 0.000000e+00 1519
12 TraesCS5D01G207300 chr2D 96.563 902 30 1 2043 2943 44293029 44293930 0.000000e+00 1493
13 TraesCS5D01G207300 chr7D 96.920 909 18 5 2043 2943 106054195 106055101 0.000000e+00 1515
14 TraesCS5D01G207300 chr6D 97.007 902 24 3 2043 2943 443306023 443306922 0.000000e+00 1513
15 TraesCS5D01G207300 chr6D 96.785 902 26 3 2043 2943 443313042 443313941 0.000000e+00 1502
16 TraesCS5D01G207300 chr5A 88.749 1191 92 23 883 2042 407125286 407124107 0.000000e+00 1419
17 TraesCS5D01G207300 chr5A 88.783 1150 73 12 930 2042 407156511 407157641 0.000000e+00 1358
18 TraesCS5D01G207300 chr5A 92.164 804 46 2 1 787 407153761 407154564 0.000000e+00 1120
19 TraesCS5D01G207300 chr5A 89.325 815 63 7 1 800 407126128 407125323 0.000000e+00 1002


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 TraesCS5D01G207300 chr5D 313332203 313335145 2942 False 5435.0 5435 100.0000 1 2943 1 chr5D.!!$F2 2942
1 TraesCS5D01G207300 chr5D 313150649 313152776 2127 True 1098.5 1146 86.8035 1 2042 2 chr5D.!!$R1 2041
2 TraesCS5D01G207300 chr5B 360860124 360862177 2053 True 2553.0 2553 89.3580 1 2042 1 chr5B.!!$R1 2041
3 TraesCS5D01G207300 chr5B 360922388 360925844 3456 False 702.5 1103 91.9630 2 2042 2 chr5B.!!$F1 2040
4 TraesCS5D01G207300 chr1D 200312888 200313793 905 True 1535.0 1535 97.3510 2043 2943 1 chr1D.!!$R1 900
5 TraesCS5D01G207300 chr1D 39535820 39536716 896 False 1511.0 1511 97.0030 2043 2943 1 chr1D.!!$F1 900
6 TraesCS5D01G207300 chr3D 248007874 248008771 897 True 1528.0 1528 97.3360 2043 2943 1 chr3D.!!$R2 900
7 TraesCS5D01G207300 chr3D 25589605 25590504 899 True 1496.0 1496 96.6780 2043 2943 1 chr3D.!!$R1 900
8 TraesCS5D01G207300 chr2D 41493612 41494511 899 True 1519.0 1519 97.1180 2043 2943 1 chr2D.!!$R1 900
9 TraesCS5D01G207300 chr2D 44293029 44293930 901 False 1493.0 1493 96.5630 2043 2943 1 chr2D.!!$F1 900
10 TraesCS5D01G207300 chr7D 106054195 106055101 906 False 1515.0 1515 96.9200 2043 2943 1 chr7D.!!$F1 900
11 TraesCS5D01G207300 chr6D 443306023 443306922 899 False 1513.0 1513 97.0070 2043 2943 1 chr6D.!!$F1 900
12 TraesCS5D01G207300 chr6D 443313042 443313941 899 False 1502.0 1502 96.7850 2043 2943 1 chr6D.!!$F2 900
13 TraesCS5D01G207300 chr5A 407153761 407157641 3880 False 1239.0 1358 90.4735 1 2042 2 chr5A.!!$F1 2041
14 TraesCS5D01G207300 chr5A 407124107 407126128 2021 True 1210.5 1419 89.0370 1 2042 2 chr5A.!!$R1 2041

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
887 2749 0.035317 GTTTAGGTTTCGGGTCGGGT 59.965 55.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2606 6858 0.111134 CGTACCGCAATGCATGATCG 60.111 55.0 5.91 4.17 0.0 3.69 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
211 212 1.134907 ACGCTGGGTATGGTAAGAACG 60.135 52.381 0.00 0.00 0.00 3.95
396 399 3.241059 GCTACGAGCACGACGCAG 61.241 66.667 11.40 2.97 46.13 5.18
433 436 1.599606 GAGCGAGAGAAGGCACCTGA 61.600 60.000 0.00 0.00 0.00 3.86
518 521 1.978580 TGGGTTCCAGAGGAAAGAGTC 59.021 52.381 0.00 0.00 43.86 3.36
642 645 5.426833 AGGGATGCTATACAGGAATATGGTC 59.573 44.000 0.00 0.00 0.00 4.02
739 757 1.377333 CCCTTCAAGTTCTCCGCCC 60.377 63.158 0.00 0.00 0.00 6.13
802 928 3.821841 AGTTTTCTTAATTTCCTGCGCG 58.178 40.909 0.00 0.00 0.00 6.86
803 929 3.500680 AGTTTTCTTAATTTCCTGCGCGA 59.499 39.130 12.10 0.00 0.00 5.87
804 930 3.740044 TTTCTTAATTTCCTGCGCGAG 57.260 42.857 12.10 4.18 0.00 5.03
809 935 1.639298 AATTTCCTGCGCGAGACTGC 61.639 55.000 12.10 0.00 0.00 4.40
814 940 3.713205 CTGCGCGAGACTGCCAGAT 62.713 63.158 12.10 0.00 36.11 2.90
817 943 2.107953 GCGAGACTGCCAGATCCC 59.892 66.667 0.00 0.00 0.00 3.85
818 944 2.725312 GCGAGACTGCCAGATCCCA 61.725 63.158 0.00 0.00 0.00 4.37
819 945 2.037620 GCGAGACTGCCAGATCCCAT 62.038 60.000 0.00 0.00 0.00 4.00
820 946 1.332195 CGAGACTGCCAGATCCCATA 58.668 55.000 0.00 0.00 0.00 2.74
822 948 2.094286 CGAGACTGCCAGATCCCATATC 60.094 54.545 0.00 0.00 0.00 1.63
823 949 1.898472 AGACTGCCAGATCCCATATCG 59.102 52.381 0.00 0.00 0.00 2.92
833 2683 6.296026 CCAGATCCCATATCGTTTCCTTTTA 58.704 40.000 0.00 0.00 0.00 1.52
886 2748 0.322648 AGTTTAGGTTTCGGGTCGGG 59.677 55.000 0.00 0.00 0.00 5.14
887 2749 0.035317 GTTTAGGTTTCGGGTCGGGT 59.965 55.000 0.00 0.00 0.00 5.28
888 2750 0.321346 TTTAGGTTTCGGGTCGGGTC 59.679 55.000 0.00 0.00 0.00 4.46
889 2751 1.876497 TTAGGTTTCGGGTCGGGTCG 61.876 60.000 0.00 0.00 0.00 4.79
890 2752 4.747529 GGTTTCGGGTCGGGTCGG 62.748 72.222 0.00 0.00 0.00 4.79
891 2753 4.747529 GTTTCGGGTCGGGTCGGG 62.748 72.222 0.00 0.00 0.00 5.14
925 2793 0.671781 ACGTGACATCTGCTGCTTCC 60.672 55.000 0.00 0.00 0.00 3.46
926 2794 0.390866 CGTGACATCTGCTGCTTCCT 60.391 55.000 0.00 0.00 0.00 3.36
927 2795 1.367659 GTGACATCTGCTGCTTCCTC 58.632 55.000 0.00 0.00 0.00 3.71
928 2796 0.251354 TGACATCTGCTGCTTCCTCC 59.749 55.000 0.00 0.00 0.00 4.30
984 2855 9.985318 CAAGAGAGAAATTTTAGCAAGATACAG 57.015 33.333 0.00 0.00 0.00 2.74
985 2856 9.732130 AAGAGAGAAATTTTAGCAAGATACAGT 57.268 29.630 0.00 0.00 0.00 3.55
1108 3085 0.105039 CGGTGGACCTGCTTATCCTC 59.895 60.000 0.00 0.00 0.00 3.71
1169 3146 0.888736 CTTGGTGTGCCGACAATGGA 60.889 55.000 0.00 0.00 37.67 3.41
1174 3151 2.125552 TGCCGACAATGGAGCTCG 60.126 61.111 7.83 0.00 0.00 5.03
1375 5601 4.202233 TGCATGTCAAAGCAAATCCTCAAA 60.202 37.500 1.23 0.00 37.90 2.69
1482 5714 1.358725 TTCGGCATCAGTACGCTTGC 61.359 55.000 8.02 8.02 0.00 4.01
1809 6041 1.391485 CGACGTCTTCAAGCTCAATGG 59.609 52.381 14.70 0.00 0.00 3.16
1812 6044 1.734465 CGTCTTCAAGCTCAATGGACC 59.266 52.381 0.00 0.00 0.00 4.46
1867 6100 1.584495 CAGGGCTTTGTTTACGGGC 59.416 57.895 0.00 0.00 0.00 6.13
1895 6128 6.377429 ACTCACGACCATAATGAAGAAGACTA 59.623 38.462 0.00 0.00 0.00 2.59
1900 6133 6.642950 CGACCATAATGAAGAAGACTACCATC 59.357 42.308 0.00 0.00 0.00 3.51
1906 6139 6.611613 ATGAAGAAGACTACCATCAAGTCA 57.388 37.500 6.06 0.00 44.77 3.41
1949 6182 2.487934 CCAAGACTCTATGATTGGCCG 58.512 52.381 0.00 0.00 36.12 6.13
1955 6188 2.439507 ACTCTATGATTGGCCGGACATT 59.560 45.455 13.08 7.99 0.00 2.71
1986 6219 1.202440 ACTTTGTTCTGTGCGACGGTA 60.202 47.619 0.00 0.00 0.00 4.02
1988 6221 2.157834 TTGTTCTGTGCGACGGTAAT 57.842 45.000 0.00 0.00 0.00 1.89
1991 6224 2.222213 TGTTCTGTGCGACGGTAATTTG 59.778 45.455 0.00 0.00 0.00 2.32
2273 6524 7.387673 TCATTGATAACGGGATCACATCATTAC 59.612 37.037 0.00 0.00 35.56 1.89
2350 6602 5.500645 AGTTTCGTTTGCTAGAGCTTTTT 57.499 34.783 2.72 0.00 42.66 1.94
2599 6851 2.159653 GCTCAATGTGACTAAGGCGTTG 60.160 50.000 0.97 0.00 0.00 4.10
2724 6976 5.074115 ACCGATTGACAAAGGGAATTGTAA 58.926 37.500 13.19 0.00 43.31 2.41
2912 7164 0.175073 GGTGACGCTAGGGTTGTAGG 59.825 60.000 14.33 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 212 3.549471 CACGATCAGATTGTCACACTAGC 59.451 47.826 0.00 0.00 0.00 3.42
396 399 0.532573 TCAAGCCGACAGATCCAGAC 59.467 55.000 0.00 0.00 0.00 3.51
405 408 1.524008 TTCTCTCGCTCAAGCCGACA 61.524 55.000 0.00 0.00 37.91 4.35
518 521 1.556958 CTGCATCTCGAATCGCACG 59.443 57.895 0.00 0.00 0.00 5.34
642 645 2.444624 CGACCAACATGACGGCGAG 61.445 63.158 16.62 2.56 0.00 5.03
739 757 0.387878 GAGATGGATACGAGCTGCGG 60.388 60.000 0.00 0.00 46.49 5.69
746 764 1.224075 GGACGACGAGATGGATACGA 58.776 55.000 0.00 0.00 42.51 3.43
802 928 2.094286 CGATATGGGATCTGGCAGTCTC 60.094 54.545 15.27 11.71 0.00 3.36
803 929 1.898472 CGATATGGGATCTGGCAGTCT 59.102 52.381 15.27 3.01 0.00 3.24
804 930 1.620819 ACGATATGGGATCTGGCAGTC 59.379 52.381 15.27 11.06 0.00 3.51
809 935 4.357918 AAGGAAACGATATGGGATCTGG 57.642 45.455 0.00 0.00 0.00 3.86
812 938 7.745620 ACATAAAAGGAAACGATATGGGATC 57.254 36.000 0.00 0.00 32.71 3.36
814 940 6.183360 GCAACATAAAAGGAAACGATATGGGA 60.183 38.462 0.00 0.00 32.71 4.37
817 943 5.681105 CGGCAACATAAAAGGAAACGATATG 59.319 40.000 0.00 0.00 33.82 1.78
818 944 5.355910 ACGGCAACATAAAAGGAAACGATAT 59.644 36.000 0.00 0.00 0.00 1.63
819 945 4.696402 ACGGCAACATAAAAGGAAACGATA 59.304 37.500 0.00 0.00 0.00 2.92
820 946 3.504520 ACGGCAACATAAAAGGAAACGAT 59.495 39.130 0.00 0.00 0.00 3.73
822 948 3.276882 ACGGCAACATAAAAGGAAACG 57.723 42.857 0.00 0.00 0.00 3.60
823 949 4.318475 GCAAACGGCAACATAAAAGGAAAC 60.318 41.667 0.00 0.00 43.97 2.78
886 2748 2.202974 GTACAATCCCGGCCCGAC 60.203 66.667 3.71 0.00 0.00 4.79
887 2749 3.840594 CGTACAATCCCGGCCCGA 61.841 66.667 3.71 0.00 0.00 5.14
888 2750 2.784356 TACGTACAATCCCGGCCCG 61.784 63.158 0.00 0.00 0.00 6.13
889 2751 1.227350 GTACGTACAATCCCGGCCC 60.227 63.158 20.67 0.00 0.00 5.80
890 2752 1.589727 CGTACGTACAATCCCGGCC 60.590 63.158 24.50 0.00 0.00 6.13
891 2753 1.139520 ACGTACGTACAATCCCGGC 59.860 57.895 21.41 0.00 0.00 6.13
928 2796 3.996480 GAAGAATTCCATCCCGAGTAGG 58.004 50.000 0.65 0.00 39.83 3.18
991 2862 3.670991 GGCTGAATATCTCGAGCTTTACG 59.329 47.826 7.81 0.00 32.18 3.18
1108 3085 2.169789 CCGCAGACGCTTCAGGATG 61.170 63.158 0.00 0.00 38.22 3.51
1375 5601 0.314302 CGTCGGTCAGAAGGTCAACT 59.686 55.000 0.00 0.00 0.00 3.16
1595 5827 0.824109 TAGATCAAGCCGTGGTGGAG 59.176 55.000 0.00 0.00 42.00 3.86
1790 6022 2.413453 GTCCATTGAGCTTGAAGACGTC 59.587 50.000 7.70 7.70 0.00 4.34
1867 6100 4.494484 TCTTCATTATGGTCGTGAGTGTG 58.506 43.478 0.00 0.00 0.00 3.82
1895 6128 3.244665 TGTTCTGCATCTGACTTGATGGT 60.245 43.478 6.62 0.00 42.82 3.55
1900 6133 4.936411 AGATCTTGTTCTGCATCTGACTTG 59.064 41.667 0.00 0.00 0.00 3.16
1906 6139 4.383989 GGAGGAAGATCTTGTTCTGCATCT 60.384 45.833 14.00 0.00 33.46 2.90
1949 6182 5.772521 ACAAAGTCAGCATAAACAATGTCC 58.227 37.500 0.00 0.00 37.93 4.02
1955 6188 5.733091 GCACAGAACAAAGTCAGCATAAACA 60.733 40.000 0.00 0.00 0.00 2.83
2273 6524 4.269603 GTCTTGTCCATCACATCATTCTCG 59.730 45.833 0.00 0.00 33.90 4.04
2350 6602 9.436957 GTCTAAGGAAAAGATACTTGACATTGA 57.563 33.333 0.00 0.00 0.00 2.57
2560 6812 6.496338 TTGAGCTCATTATGATGATGCATC 57.504 37.500 19.04 20.14 41.28 3.91
2599 6851 0.316442 CAATGCATGATCGCGTGACC 60.316 55.000 5.77 0.00 32.63 4.02
2606 6858 0.111134 CGTACCGCAATGCATGATCG 60.111 55.000 5.91 4.17 0.00 3.69
2912 7164 3.335579 GGGTTTCCGCATACTCATATCC 58.664 50.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.