Multiple sequence alignment - TraesCS3B01G204100

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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 TraesCS3B01G204100 chr3B 100.000 2180 0 0 949 3128 238113778 238111599 0.000000e+00 4026.0
1 TraesCS3B01G204100 chr3B 86.469 2121 178 55 1057 3123 237734317 237732252 0.000000e+00 2226.0
2 TraesCS3B01G204100 chr3B 88.733 1571 144 26 1571 3123 237972969 237971414 0.000000e+00 1890.0
3 TraesCS3B01G204100 chr3B 100.000 708 0 0 1 708 238114726 238114019 0.000000e+00 1308.0
4 TraesCS3B01G204100 chr3B 85.057 522 46 17 1057 1562 237973528 237973023 1.290000e-138 503.0
5 TraesCS3B01G204100 chr3B 82.292 96 5 2 952 1035 237973764 237973669 4.330000e-09 73.1
6 TraesCS3B01G204100 chr3B 93.182 44 3 0 988 1031 237734506 237734463 7.240000e-07 65.8
7 TraesCS3B01G204100 chr3D 96.036 2195 55 12 949 3128 161596852 161594675 0.000000e+00 3542.0
8 TraesCS3B01G204100 chr3D 88.119 2121 176 42 1057 3123 161401867 161399769 0.000000e+00 2451.0
9 TraesCS3B01G204100 chr3D 93.048 1568 84 13 1571 3128 161497956 161496404 0.000000e+00 2268.0
10 TraesCS3B01G204100 chr3D 85.249 522 45 16 1057 1562 161498524 161498019 2.780000e-140 508.0
11 TraesCS3B01G204100 chr3D 84.211 76 10 2 952 1025 161402732 161402657 4.330000e-09 73.1
12 TraesCS3B01G204100 chr3D 84.211 76 10 2 952 1025 161498751 161498676 4.330000e-09 73.1
13 TraesCS3B01G204100 chr3A 94.887 2210 64 17 949 3128 190229151 190226961 0.000000e+00 3410.0
14 TraesCS3B01G204100 chr3A 95.138 2180 61 16 949 3100 191254133 191251971 0.000000e+00 3397.0
15 TraesCS3B01G204100 chr3A 86.563 2121 209 44 1057 3123 190094658 190092560 0.000000e+00 2268.0
16 TraesCS3B01G204100 chr3A 92.430 1572 90 12 1571 3128 191006605 191005049 0.000000e+00 2217.0
17 TraesCS3B01G204100 chr3A 89.000 1100 79 23 1319 2393 188112420 188113502 0.000000e+00 1323.0
18 TraesCS3B01G204100 chr3A 89.076 476 39 8 949 1415 190583080 190582609 2.090000e-161 579.0
19 TraesCS3B01G204100 chr3A 84.483 522 49 17 1057 1562 191007622 191007117 1.300000e-133 486.0
20 TraesCS3B01G204100 chr3A 86.861 274 33 2 1057 1327 188101483 188101756 1.410000e-78 303.0
21 TraesCS3B01G204100 chr3A 81.013 79 13 2 949 1025 188101253 188101331 9.370000e-06 62.1
22 TraesCS3B01G204100 chr3A 100.000 32 0 0 3097 3128 191251868 191251837 3.370000e-05 60.2
23 TraesCS3B01G204100 chr6B 89.333 675 64 5 8 675 656528619 656527946 0.000000e+00 841.0
24 TraesCS3B01G204100 chr6B 91.781 511 37 1 170 675 89169617 89170127 0.000000e+00 706.0
25 TraesCS3B01G204100 chr6B 92.929 99 6 1 35 132 89169219 89169317 3.250000e-30 143.0
26 TraesCS3B01G204100 chr1A 85.294 680 88 7 4 674 579797525 579796849 0.000000e+00 691.0
27 TraesCS3B01G204100 chr4A 84.503 684 95 7 4 679 622580277 622579597 0.000000e+00 665.0


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 TraesCS3B01G204100 chr3B 238111599 238114726 3127 True 2667.000000 4026 100.000000 1 3128 2 chr3B.!!$R3 3127
1 TraesCS3B01G204100 chr3B 237732252 237734506 2254 True 1145.900000 2226 89.825500 988 3123 2 chr3B.!!$R1 2135
2 TraesCS3B01G204100 chr3B 237971414 237973764 2350 True 822.033333 1890 85.360667 952 3123 3 chr3B.!!$R2 2171
3 TraesCS3B01G204100 chr3D 161594675 161596852 2177 True 3542.000000 3542 96.036000 949 3128 1 chr3D.!!$R1 2179
4 TraesCS3B01G204100 chr3D 161399769 161402732 2963 True 1262.050000 2451 86.165000 952 3123 2 chr3D.!!$R2 2171
5 TraesCS3B01G204100 chr3D 161496404 161498751 2347 True 949.700000 2268 87.502667 952 3128 3 chr3D.!!$R3 2176
6 TraesCS3B01G204100 chr3A 190226961 190229151 2190 True 3410.000000 3410 94.887000 949 3128 1 chr3A.!!$R2 2179
7 TraesCS3B01G204100 chr3A 190092560 190094658 2098 True 2268.000000 2268 86.563000 1057 3123 1 chr3A.!!$R1 2066
8 TraesCS3B01G204100 chr3A 191251837 191254133 2296 True 1728.600000 3397 97.569000 949 3128 2 chr3A.!!$R5 2179
9 TraesCS3B01G204100 chr3A 191005049 191007622 2573 True 1351.500000 2217 88.456500 1057 3128 2 chr3A.!!$R4 2071
10 TraesCS3B01G204100 chr3A 188112420 188113502 1082 False 1323.000000 1323 89.000000 1319 2393 1 chr3A.!!$F1 1074
11 TraesCS3B01G204100 chr6B 656527946 656528619 673 True 841.000000 841 89.333000 8 675 1 chr6B.!!$R1 667
12 TraesCS3B01G204100 chr6B 89169219 89170127 908 False 424.500000 706 92.355000 35 675 2 chr6B.!!$F1 640
13 TraesCS3B01G204100 chr1A 579796849 579797525 676 True 691.000000 691 85.294000 4 674 1 chr1A.!!$R1 670
14 TraesCS3B01G204100 chr4A 622579597 622580277 680 True 665.000000 665 84.503000 4 679 1 chr4A.!!$R1 675

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
557 826 0.250467 AACGTTGAGCAGCATGGAGT 60.250 50.0 0.00 0.0 35.86 3.85 F
1416 2473 0.730840 GTAAAATCCTTCACGCCGGG 59.269 55.0 2.18 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 3513 0.722848 GCATTGCCGCAATTTTCAGG 59.277 50.0 16.1 5.28 31.05 3.86 R
2515 4130 2.201921 ACCGAGAAGAGACAGTAGCA 57.798 50.0 0.0 0.00 0.00 3.49 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
26 27 1.450134 TCGCTGCACCATTAGCCAG 60.450 57.895 0.00 0.00 36.60 4.85
95 96 1.674057 CCACTGCGAAGTCCTTCCT 59.326 57.895 0.00 0.00 36.27 3.36
104 105 0.830866 AAGTCCTTCCTCCGAACCGT 60.831 55.000 0.00 0.00 0.00 4.83
134 136 3.129287 GGTATGTTTTGCAGATGACAGGG 59.871 47.826 0.00 0.00 0.00 4.45
135 137 0.961019 TGTTTTGCAGATGACAGGGC 59.039 50.000 0.00 0.00 0.00 5.19
140 142 3.016971 CAGATGACAGGGCCCCCA 61.017 66.667 21.43 15.29 38.92 4.96
141 143 2.045132 AGATGACAGGGCCCCCAT 59.955 61.111 21.43 19.69 38.92 4.00
142 144 2.081161 AGATGACAGGGCCCCCATC 61.081 63.158 28.64 28.64 38.92 3.51
298 562 2.644212 CGCTCTCACCTGCCAGACT 61.644 63.158 0.00 0.00 0.00 3.24
404 668 1.648467 GGAGACAGTGCGGCCATTTC 61.648 60.000 2.24 0.00 0.00 2.17
415 679 0.947244 GGCCATTTCTAGCATCCACG 59.053 55.000 0.00 0.00 0.00 4.94
474 738 4.767255 CACGCCCTGCTCTCCCAC 62.767 72.222 0.00 0.00 0.00 4.61
493 762 1.912763 GGCCACCATTCCCAAGCAA 60.913 57.895 0.00 0.00 0.00 3.91
513 782 1.779025 CGATCGCCCATTTGCCTCTG 61.779 60.000 0.26 0.00 0.00 3.35
524 793 3.415087 GCCTCTGCCCAGACCCAT 61.415 66.667 0.00 0.00 33.22 4.00
527 796 2.934932 TCTGCCCAGACCCATGCA 60.935 61.111 0.00 0.00 31.41 3.96
533 802 2.277737 CAGACCCATGCAGCCCAT 59.722 61.111 0.00 0.00 33.39 4.00
535 804 2.903855 GACCCATGCAGCCCATCG 60.904 66.667 0.00 0.00 29.71 3.84
549 818 1.057822 CATCGCGAACGTTGAGCAG 59.942 57.895 15.24 14.58 40.63 4.24
557 826 0.250467 AACGTTGAGCAGCATGGAGT 60.250 50.000 0.00 0.00 35.86 3.85
590 859 6.530534 CCATTTTCAGCAAGAGACATTCATTC 59.469 38.462 0.00 0.00 0.00 2.67
593 862 5.156608 TCAGCAAGAGACATTCATTCTGA 57.843 39.130 0.00 0.00 0.00 3.27
595 864 4.936411 CAGCAAGAGACATTCATTCTGAGT 59.064 41.667 0.00 0.00 0.00 3.41
617 886 2.298661 AAGGCTACGAACCCCCAGG 61.299 63.158 0.00 0.00 40.04 4.45
645 914 4.980805 TCTTCGCGCGGCAAACCT 62.981 61.111 31.69 0.00 0.00 3.50
653 922 2.409870 GCGGCAAACCTGATCCCAG 61.410 63.158 0.00 0.00 40.09 4.45
679 948 3.277133 GCATTGCGCTCCCAGAAA 58.723 55.556 9.73 0.00 37.77 2.52
680 949 1.138247 GCATTGCGCTCCCAGAAAG 59.862 57.895 9.73 0.00 37.77 2.62
681 950 1.805254 CATTGCGCTCCCAGAAAGG 59.195 57.895 9.73 0.00 37.03 3.11
682 951 2.048603 ATTGCGCTCCCAGAAAGGC 61.049 57.895 9.73 0.00 35.39 4.35
683 952 4.722700 TGCGCTCCCAGAAAGGCC 62.723 66.667 9.73 0.00 35.39 5.19
685 954 3.721706 CGCTCCCAGAAAGGCCCT 61.722 66.667 0.00 0.00 35.39 5.19
686 955 2.273776 GCTCCCAGAAAGGCCCTC 59.726 66.667 0.00 0.00 35.39 4.30
687 956 3.002371 CTCCCAGAAAGGCCCTCC 58.998 66.667 0.00 0.00 35.39 4.30
688 957 3.009115 TCCCAGAAAGGCCCTCCG 61.009 66.667 0.00 0.00 37.47 4.63
689 958 4.803908 CCCAGAAAGGCCCTCCGC 62.804 72.222 0.00 0.00 37.47 5.54
690 959 4.033776 CCAGAAAGGCCCTCCGCA 62.034 66.667 0.00 0.00 40.31 5.69
691 960 2.747855 CAGAAAGGCCCTCCGCAC 60.748 66.667 0.00 0.00 40.31 5.34
692 961 4.394712 AGAAAGGCCCTCCGCACG 62.395 66.667 0.00 0.00 40.31 5.34
705 974 2.515523 GCACGGCATCCAGCTCAT 60.516 61.111 0.00 0.00 44.79 2.90
706 975 2.117156 GCACGGCATCCAGCTCATT 61.117 57.895 0.00 0.00 44.79 2.57
707 976 1.725665 CACGGCATCCAGCTCATTG 59.274 57.895 0.00 0.00 44.79 2.82
1323 2365 2.434185 CTCGCGCTGCTAAACCCA 60.434 61.111 5.56 0.00 0.00 4.51
1416 2473 0.730840 GTAAAATCCTTCACGCCGGG 59.269 55.000 2.18 0.00 0.00 5.73
1908 3513 0.861837 CGCAATCACCCGAGAATAGC 59.138 55.000 0.00 0.00 0.00 2.97
1945 3550 1.746517 CGGGGTAGCATCCTGTACC 59.253 63.158 0.00 0.00 38.43 3.34
2291 3899 7.044181 TGATATTCAGGATTCAGTGACAAGTC 58.956 38.462 0.00 0.00 0.00 3.01
2292 3900 4.687901 TTCAGGATTCAGTGACAAGTCA 57.312 40.909 0.00 0.00 37.24 3.41
2293 3901 4.687901 TCAGGATTCAGTGACAAGTCAA 57.312 40.909 4.20 0.00 41.85 3.18
2294 3902 5.233083 TCAGGATTCAGTGACAAGTCAAT 57.767 39.130 4.20 0.20 41.85 2.57
2515 4130 7.947890 TGAATTACTTATCTGTTCCTTGGGTTT 59.052 33.333 0.00 0.00 0.00 3.27
2630 4252 2.972021 AGCCTGTTTACCCATTTTGCTT 59.028 40.909 0.00 0.00 0.00 3.91
2723 4346 5.928839 AGAATGATGGCGTGTTCTATATGAC 59.071 40.000 2.94 0.00 0.00 3.06
2824 4452 8.202137 TGAACTGTATTAATAGGTTGGCTAGTC 58.798 37.037 14.63 0.00 0.00 2.59
2862 4490 7.921786 TGTAAATTTACACATCTCTTCAGGG 57.078 36.000 23.91 0.00 38.64 4.45
3088 4785 3.278574 TCTGTATACATGCCCAGCAAAC 58.721 45.455 5.91 0.00 43.62 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.428370 TAATGGTGCAGCGACGCATC 61.428 55.000 23.70 13.26 45.26 3.91
26 27 1.620819 TCCAGAGTCAGGTTCTTCTGC 59.379 52.381 0.95 0.00 34.91 4.26
95 96 4.124351 CGGCTGCTACGGTTCGGA 62.124 66.667 0.00 0.00 0.00 4.55
104 105 1.091537 GCAAAACATACCGGCTGCTA 58.908 50.000 0.00 0.00 0.00 3.49
150 152 1.714414 CGGTCTCTCCTACACGTCG 59.286 63.158 0.00 0.00 0.00 5.12
153 155 1.722677 GAGCGGTCTCTCCTACACG 59.277 63.158 7.51 0.00 36.42 4.49
157 159 1.153208 GGACGAGCGGTCTCTCCTA 60.153 63.158 13.48 0.00 45.35 2.94
193 457 1.165270 CAACCCTGATTTCGACCACC 58.835 55.000 0.00 0.00 0.00 4.61
280 544 2.125753 GTCTGGCAGGTGAGAGCG 60.126 66.667 15.73 0.00 0.00 5.03
298 562 0.673985 CCGTCTCTGTTGAGGTGACA 59.326 55.000 0.00 0.00 40.58 3.58
377 641 0.318441 CGCACTGTCTCCTTCTGGAA 59.682 55.000 0.00 0.00 42.66 3.53
415 679 1.008309 GTACCGCGCTCTCTCATCC 60.008 63.158 5.56 0.00 0.00 3.51
474 738 3.451894 GCTTGGGAATGGTGGCCG 61.452 66.667 0.00 0.00 0.00 6.13
527 796 3.118454 CAACGTTCGCGATGGGCT 61.118 61.111 10.88 0.00 44.71 5.19
533 802 3.403057 GCTGCTCAACGTTCGCGA 61.403 61.111 3.71 3.71 44.71 5.87
535 804 1.510623 CATGCTGCTCAACGTTCGC 60.511 57.895 11.16 11.16 0.00 4.70
549 818 5.357878 TGAAAATGGTTCATAGACTCCATGC 59.642 40.000 0.00 0.00 40.08 4.06
557 826 6.372659 GTCTCTTGCTGAAAATGGTTCATAGA 59.627 38.462 0.00 0.00 0.00 1.98
590 859 0.109272 TTCGTAGCCTTGCGACTCAG 60.109 55.000 0.00 0.00 41.15 3.35
593 862 1.080025 GGTTCGTAGCCTTGCGACT 60.080 57.895 0.00 0.00 41.15 4.18
595 864 2.263540 GGGTTCGTAGCCTTGCGA 59.736 61.111 2.65 0.00 39.70 5.10
617 886 4.882396 GCGAAGAGCGAGGGAGGC 62.882 72.222 0.00 0.00 44.57 4.70
629 898 4.741781 CAGGTTTGCCGCGCGAAG 62.742 66.667 34.63 17.45 40.50 3.79
645 914 1.304381 GCTTGGTTGCCTGGGATCA 60.304 57.895 0.00 0.00 0.00 2.92
647 916 0.252375 AATGCTTGGTTGCCTGGGAT 60.252 50.000 0.00 0.00 0.00 3.85
653 922 3.113979 GCGCAATGCTTGGTTGCC 61.114 61.111 0.30 0.00 46.97 4.52
674 943 2.747855 GTGCGGAGGGCCTTTCTG 60.748 66.667 7.89 7.50 42.61 3.02
675 944 4.394712 CGTGCGGAGGGCCTTTCT 62.395 66.667 7.89 0.00 42.61 2.52
688 957 2.117156 AATGAGCTGGATGCCGTGC 61.117 57.895 0.00 0.00 44.23 5.34
689 958 1.725665 CAATGAGCTGGATGCCGTG 59.274 57.895 0.00 0.00 44.23 4.94
690 959 4.230603 CAATGAGCTGGATGCCGT 57.769 55.556 0.00 0.00 44.23 5.68
1051 1332 1.072505 GGTGGTGGTCGATGTTGGT 59.927 57.895 0.00 0.00 0.00 3.67
1416 2473 1.640428 TTTCGTCATCGCAGATCACC 58.360 50.000 0.00 0.00 45.12 4.02
1908 3513 0.722848 GCATTGCCGCAATTTTCAGG 59.277 50.000 16.10 5.28 31.05 3.86
1945 3550 2.287644 TGAACATCGCTGTTGTTGTCAG 59.712 45.455 9.74 0.00 45.57 3.51
2291 3899 7.475015 ACGATCAAATTACAGGATTGACATTG 58.525 34.615 0.00 0.00 36.03 2.82
2292 3900 7.630242 ACGATCAAATTACAGGATTGACATT 57.370 32.000 0.00 0.00 36.03 2.71
2293 3901 7.630242 AACGATCAAATTACAGGATTGACAT 57.370 32.000 0.00 0.00 36.03 3.06
2294 3902 7.447374 AAACGATCAAATTACAGGATTGACA 57.553 32.000 0.00 0.00 36.03 3.58
2295 3903 9.438291 CATAAACGATCAAATTACAGGATTGAC 57.562 33.333 0.00 0.00 36.03 3.18
2296 3904 8.620416 CCATAAACGATCAAATTACAGGATTGA 58.380 33.333 0.00 0.00 37.47 2.57
2515 4130 2.201921 ACCGAGAAGAGACAGTAGCA 57.798 50.000 0.00 0.00 0.00 3.49
2862 4490 5.232838 CCTGTTTCAGCTTTTGACACAAATC 59.767 40.000 0.00 0.00 43.75 2.17


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

AutoCloner maintained by Alex Coulton.