Multiple sequence alignment - TraesCS7D01G164300

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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 TraesCS7D01G164300 chr7D 100.000 3432 0 0 1 3432 113582075 113585506 0.000000e+00 6338.0
1 TraesCS7D01G164300 chr7D 88.430 1573 130 25 991 2523 500776216 500777776 0.000000e+00 1849.0
2 TraesCS7D01G164300 chr7D 93.875 751 43 2 5 754 500774287 500775035 0.000000e+00 1129.0
3 TraesCS7D01G164300 chr7D 89.081 751 77 4 5 753 523127613 523126866 0.000000e+00 928.0
4 TraesCS7D01G164300 chr7D 89.452 730 73 4 26 754 523056458 523055732 0.000000e+00 918.0
5 TraesCS7D01G164300 chr7D 88.431 752 84 2 5 755 523133270 523132521 0.000000e+00 904.0
6 TraesCS7D01G164300 chr7D 95.610 205 6 1 787 991 500775981 500776182 3.300000e-85 326.0
7 TraesCS7D01G164300 chr7D 98.182 55 1 0 2539 2593 113584558 113584612 2.820000e-16 97.1
8 TraesCS7D01G164300 chr7B 94.540 2271 88 15 1040 3293 73176689 73178940 0.000000e+00 3474.0
9 TraesCS7D01G164300 chr7B 91.465 1570 100 14 991 2538 528873874 528875431 0.000000e+00 2126.0
10 TraesCS7D01G164300 chr7B 88.336 1689 148 20 887 2538 664398977 664397301 0.000000e+00 1982.0
11 TraesCS7D01G164300 chr7B 95.916 759 15 5 3 753 73174708 73175458 0.000000e+00 1216.0
12 TraesCS7D01G164300 chr7B 94.290 753 37 6 5 755 528872183 528872931 0.000000e+00 1147.0
13 TraesCS7D01G164300 chr7B 89.096 752 79 2 5 755 557491063 557490314 0.000000e+00 931.0
14 TraesCS7D01G164300 chr7B 98.008 251 4 1 787 1036 73176251 73176501 5.260000e-118 435.0
15 TraesCS7D01G164300 chr7B 92.248 258 16 2 2538 2795 528875376 528875629 2.520000e-96 363.0
16 TraesCS7D01G164300 chr7B 90.347 259 17 3 2537 2795 73140246 73140496 1.970000e-87 333.0
17 TraesCS7D01G164300 chr7B 92.683 205 6 4 787 991 528873645 528873840 1.560000e-73 287.0
18 TraesCS7D01G164300 chr7B 88.816 152 8 3 2795 2946 73140539 73140681 9.790000e-41 178.0
19 TraesCS7D01G164300 chr7B 90.385 104 6 1 2538 2641 664397356 664397257 2.150000e-27 134.0
20 TraesCS7D01G164300 chr7B 98.182 55 1 0 2539 2593 73178131 73178185 2.820000e-16 97.1
21 TraesCS7D01G164300 chr7B 97.436 39 1 0 2795 2833 528875672 528875710 2.210000e-07 67.6
22 TraesCS7D01G164300 chr7A 95.359 1659 63 8 1261 2913 619305129 619306779 0.000000e+00 2625.0
23 TraesCS7D01G164300 chr7A 88.345 1776 159 32 787 2538 566790298 566792049 0.000000e+00 2089.0
24 TraesCS7D01G164300 chr7A 86.857 1575 150 25 991 2523 566989673 566991232 0.000000e+00 1709.0
25 TraesCS7D01G164300 chr7A 94.800 750 36 2 7 755 566788785 566789532 0.000000e+00 1166.0
26 TraesCS7D01G164300 chr7A 89.589 730 72 4 26 754 603331099 603330373 0.000000e+00 924.0
27 TraesCS7D01G164300 chr7A 94.048 420 18 2 2811 3223 619306779 619307198 6.250000e-177 630.0
28 TraesCS7D01G164300 chr7A 91.532 248 13 6 2538 2783 566791994 566792235 5.490000e-88 335.0
29 TraesCS7D01G164300 chr7A 88.048 251 20 5 2538 2783 566911924 566912169 4.330000e-74 289.0
30 TraesCS7D01G164300 chr7A 89.873 158 9 2 817 974 566910176 566910326 2.700000e-46 196.0
31 TraesCS7D01G164300 chr7A 83.761 117 10 6 3290 3400 619307509 619307622 6.060000e-18 102.0
32 TraesCS7D01G164300 chr7A 100.000 32 0 0 3031 3062 619307236 619307267 3.700000e-05 60.2
33 TraesCS7D01G164300 chr3A 89.086 1576 136 17 992 2538 732404542 732402974 0.000000e+00 1925.0
34 TraesCS7D01G164300 chr3A 82.424 165 14 10 817 975 732404762 732404607 2.780000e-26 130.0
35 TraesCS7D01G164300 chrUn 87.861 1557 153 15 991 2522 86612154 86613699 0.000000e+00 1796.0
36 TraesCS7D01G164300 chrUn 87.302 189 11 5 787 969 86611915 86612096 1.610000e-48 204.0
37 TraesCS7D01G164300 chr3B 87.642 1586 145 22 991 2537 810194225 810192652 0.000000e+00 1796.0
38 TraesCS7D01G164300 chr3B 86.234 1155 118 19 991 2122 806058477 806057341 0.000000e+00 1214.0
39 TraesCS7D01G164300 chr3D 86.904 1153 111 21 991 2122 598726091 598724958 0.000000e+00 1256.0


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 TraesCS7D01G164300 chr7D 113582075 113585506 3431 False 3217.550000 6338 99.091000 1 3432 2 chr7D.!!$F1 3431
1 TraesCS7D01G164300 chr7D 500774287 500777776 3489 False 1101.333333 1849 92.638333 5 2523 3 chr7D.!!$F2 2518
2 TraesCS7D01G164300 chr7D 523126866 523127613 747 True 928.000000 928 89.081000 5 753 1 chr7D.!!$R2 748
3 TraesCS7D01G164300 chr7D 523055732 523056458 726 True 918.000000 918 89.452000 26 754 1 chr7D.!!$R1 728
4 TraesCS7D01G164300 chr7D 523132521 523133270 749 True 904.000000 904 88.431000 5 755 1 chr7D.!!$R3 750
5 TraesCS7D01G164300 chr7B 73174708 73178940 4232 False 1305.525000 3474 96.661500 3 3293 4 chr7B.!!$F2 3290
6 TraesCS7D01G164300 chr7B 664397257 664398977 1720 True 1058.000000 1982 89.360500 887 2641 2 chr7B.!!$R2 1754
7 TraesCS7D01G164300 chr7B 557490314 557491063 749 True 931.000000 931 89.096000 5 755 1 chr7B.!!$R1 750
8 TraesCS7D01G164300 chr7B 528872183 528875710 3527 False 798.120000 2126 93.624400 5 2833 5 chr7B.!!$F3 2828
9 TraesCS7D01G164300 chr7A 566989673 566991232 1559 False 1709.000000 1709 86.857000 991 2523 1 chr7A.!!$F1 1532
10 TraesCS7D01G164300 chr7A 566788785 566792235 3450 False 1196.666667 2089 91.559000 7 2783 3 chr7A.!!$F2 2776
11 TraesCS7D01G164300 chr7A 603330373 603331099 726 True 924.000000 924 89.589000 26 754 1 chr7A.!!$R1 728
12 TraesCS7D01G164300 chr7A 619305129 619307622 2493 False 854.300000 2625 93.292000 1261 3400 4 chr7A.!!$F4 2139
13 TraesCS7D01G164300 chr7A 566910176 566912169 1993 False 242.500000 289 88.960500 817 2783 2 chr7A.!!$F3 1966
14 TraesCS7D01G164300 chr3A 732402974 732404762 1788 True 1027.500000 1925 85.755000 817 2538 2 chr3A.!!$R1 1721
15 TraesCS7D01G164300 chrUn 86611915 86613699 1784 False 1000.000000 1796 87.581500 787 2522 2 chrUn.!!$F1 1735
16 TraesCS7D01G164300 chr3B 810192652 810194225 1573 True 1796.000000 1796 87.642000 991 2537 1 chr3B.!!$R2 1546
17 TraesCS7D01G164300 chr3B 806057341 806058477 1136 True 1214.000000 1214 86.234000 991 2122 1 chr3B.!!$R1 1131
18 TraesCS7D01G164300 chr3D 598724958 598726091 1133 True 1256.000000 1256 86.904000 991 2122 1 chr3D.!!$R1 1131

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
654 656 0.039437 GAAGGACGTCTGCGACAGAA 60.039 55.0 16.46 0.0 42.46 3.02 F
1906 3200 0.179059 TATCGGTTGCACGCCATCAT 60.179 50.0 7.21 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2293 3595 1.225855 CAGTGTACAAAAGCTCCGCA 58.774 50.000 0.00 0.0 0.00 5.69 R
3361 5149 1.604593 TGGCCTCCTGCAAAAGCTC 60.605 57.895 3.32 0.0 43.89 4.09 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
22 23 1.283793 CGCTGAACAAGGCCACAAG 59.716 57.895 5.01 0.00 0.00 3.16
135 137 1.284297 CGCTCGCTCACATTGTGTCA 61.284 55.000 16.06 0.00 34.79 3.58
586 588 1.153745 CCTTCTTCTCCGACCAGCG 60.154 63.158 0.00 0.00 40.47 5.18
654 656 0.039437 GAAGGACGTCTGCGACAGAA 60.039 55.000 16.46 0.00 42.46 3.02
767 1555 1.538512 GCGGAGGTTAACTGAAAACCC 59.461 52.381 5.42 4.91 46.33 4.11
774 1562 3.995048 GGTTAACTGAAAACCCGAGAGAG 59.005 47.826 5.42 0.00 40.49 3.20
1053 2273 2.622436 CTCCTCGTTCTGAATCCCAAC 58.378 52.381 0.00 0.00 0.00 3.77
1906 3200 0.179059 TATCGGTTGCACGCCATCAT 60.179 50.000 7.21 0.00 0.00 2.45
1963 3257 3.451141 TTGAAAACTTGGGTGCATCAC 57.549 42.857 0.00 0.00 0.00 3.06
1980 3274 7.090808 GTGCATCACTCCATAACGATAATCTA 58.909 38.462 0.00 0.00 0.00 1.98
2140 3442 3.722908 TTCGATGGGGGTTTGATTGTA 57.277 42.857 0.00 0.00 0.00 2.41
2293 3595 0.108424 GACAGCAAGGCGAGTCATCT 60.108 55.000 10.48 0.00 37.98 2.90
2580 3940 7.004086 AGTTTCATGTATTTCAAAGACTGGGA 58.996 34.615 0.00 0.00 0.00 4.37
2685 4046 7.828508 AATGTCATATGCCACATCTACAATT 57.171 32.000 9.73 0.00 31.79 2.32
2686 4047 7.828508 ATGTCATATGCCACATCTACAATTT 57.171 32.000 4.59 0.00 0.00 1.82
2766 4136 3.196469 TGGCAATTTCACACCTGTTGAAA 59.804 39.130 0.31 0.31 36.23 2.69
2790 4161 7.690952 ATTTTTGTTGTCGGCTTATAGGTAA 57.309 32.000 0.00 0.00 0.00 2.85
3025 4550 4.037923 TGCTGAGTTTCAGTTTTGGAATCC 59.962 41.667 7.80 0.00 45.94 3.01
3082 4607 4.565166 CACTATGCACAAAATTCAGCCATG 59.435 41.667 0.00 0.00 0.00 3.66
3139 4670 9.683069 AGATTCAATTGTATTGAACACAGAAAC 57.317 29.630 14.93 0.00 40.70 2.78
3144 4675 5.651172 TGTATTGAACACAGAAACGACAG 57.349 39.130 0.00 0.00 31.43 3.51
3153 4684 5.784177 ACACAGAAACGACAGATACTCAAT 58.216 37.500 0.00 0.00 0.00 2.57
3226 4770 3.646715 TTCCTTGGGCCACCTCGG 61.647 66.667 5.23 4.71 37.76 4.63
3249 4793 1.439353 CCATTGGGTTCGCAGGATCG 61.439 60.000 0.00 0.00 0.00 3.69
3302 5077 1.134965 CAGGTGATTGTCCTCTCCGTC 60.135 57.143 0.00 0.00 34.66 4.79
3326 5101 1.811679 GTTGGTAGCCTGCTCGCTC 60.812 63.158 0.00 0.00 40.39 5.03
3327 5102 3.356639 TTGGTAGCCTGCTCGCTCG 62.357 63.158 0.00 0.00 40.39 5.03
3328 5103 4.577246 GGTAGCCTGCTCGCTCGG 62.577 72.222 0.00 0.00 40.39 4.63
3401 5189 4.899239 GATGCGGCGAGGGTGGAG 62.899 72.222 12.98 0.00 0.00 3.86
3407 5195 4.779733 GCGAGGGTGGAGAGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
3408 5196 2.443016 CGAGGGTGGAGAGGGGAG 60.443 72.222 0.00 0.00 0.00 4.30
3409 5197 2.781406 GAGGGTGGAGAGGGGAGT 59.219 66.667 0.00 0.00 0.00 3.85
3410 5198 1.687493 GAGGGTGGAGAGGGGAGTG 60.687 68.421 0.00 0.00 0.00 3.51
3411 5199 2.689034 GGGTGGAGAGGGGAGTGG 60.689 72.222 0.00 0.00 0.00 4.00
3412 5200 2.122954 GGTGGAGAGGGGAGTGGT 59.877 66.667 0.00 0.00 0.00 4.16
3413 5201 2.294078 GGTGGAGAGGGGAGTGGTG 61.294 68.421 0.00 0.00 0.00 4.17
3414 5202 2.607750 TGGAGAGGGGAGTGGTGC 60.608 66.667 0.00 0.00 0.00 5.01
3415 5203 2.284995 GGAGAGGGGAGTGGTGCT 60.285 66.667 0.00 0.00 0.00 4.40
3416 5204 2.363172 GGAGAGGGGAGTGGTGCTC 61.363 68.421 0.00 0.00 43.39 4.26
3424 5212 4.320456 AGTGGTGCTCCCAGTGCG 62.320 66.667 1.59 0.00 46.45 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.602905 GTGGCCTTGTTCAGCGTACT 60.603 55.000 3.32 0.0 0.00 2.73
1 2 0.882927 TGTGGCCTTGTTCAGCGTAC 60.883 55.000 3.32 0.0 0.00 3.67
22 23 1.225704 CTTGAGCATCCAGGGGTCC 59.774 63.158 0.00 0.0 31.96 4.46
586 588 1.741770 ACGAAGCGGCTGTTGATCC 60.742 57.895 1.81 0.0 0.00 3.36
654 656 2.561885 CGTCCTCTCAACGACGCT 59.438 61.111 0.00 0.0 44.54 5.07
848 1807 2.954611 GACCGGCAAAGCAAGTCC 59.045 61.111 0.00 0.0 0.00 3.85
1327 2565 5.664457 ACCGGGGATTACATAGTACTTCTTT 59.336 40.000 6.32 0.0 0.00 2.52
1348 2605 2.557317 AGGGTTAATTACGATGCACCG 58.443 47.619 0.00 0.0 0.00 4.94
1906 3200 2.433604 TGTAGTTGTTGGTTCGGGTGTA 59.566 45.455 0.00 0.0 0.00 2.90
2188 3490 3.056749 ACAACTCTGAGCCTTTACCTACG 60.057 47.826 4.19 0.0 0.00 3.51
2293 3595 1.225855 CAGTGTACAAAAGCTCCGCA 58.774 50.000 0.00 0.0 0.00 5.69
2614 3974 7.077605 TCTTCACAAAAGAAGATGCAAATACG 58.922 34.615 2.50 0.0 46.62 3.06
2744 4113 2.382882 TCAACAGGTGTGAAATTGCCA 58.617 42.857 0.00 0.0 0.00 4.92
2766 4136 7.690952 TTACCTATAAGCCGACAACAAAAAT 57.309 32.000 0.00 0.0 0.00 1.82
2790 4161 4.233287 ACCCTCCTTAGTCCTGAGTTAGAT 59.767 45.833 0.00 0.0 0.00 1.98
2854 4369 3.125487 TGAACACGAACACGAACACAAAT 59.875 39.130 0.00 0.0 0.00 2.32
3025 4550 9.978044 TGATCTTATCATGTGAAGATGAACTAG 57.022 33.333 21.69 0.0 41.43 2.57
3082 4607 6.586082 GTGGTGTTTGAATCATGGATTTGTAC 59.414 38.462 0.00 0.0 31.89 2.90
3139 4670 5.869344 TCCAAACTTCATTGAGTATCTGTCG 59.131 40.000 0.00 0.0 34.92 4.35
3153 4684 8.293867 CGTTTTCCTATGTTTATCCAAACTTCA 58.706 33.333 2.33 0.0 43.73 3.02
3226 4770 3.039202 CTGCGAACCCAATGGCGTC 62.039 63.158 0.00 0.0 33.59 5.19
3355 5143 4.766088 CTGCAAAAGCTCGCCGCC 62.766 66.667 0.00 0.0 40.39 6.13
3356 5144 4.766088 CCTGCAAAAGCTCGCCGC 62.766 66.667 0.00 0.0 39.57 6.53
3357 5145 3.031964 CTCCTGCAAAAGCTCGCCG 62.032 63.158 0.00 0.0 0.00 6.46
3358 5146 2.694760 CCTCCTGCAAAAGCTCGCC 61.695 63.158 0.00 0.0 0.00 5.54
3359 5147 2.873288 CCTCCTGCAAAAGCTCGC 59.127 61.111 0.00 0.0 0.00 5.03
3360 5148 2.694760 GGCCTCCTGCAAAAGCTCG 61.695 63.158 0.00 0.0 43.89 5.03
3361 5149 1.604593 TGGCCTCCTGCAAAAGCTC 60.605 57.895 3.32 0.0 43.89 4.09
3406 5194 2.359230 GCACTGGGAGCACCACTC 60.359 66.667 1.58 0.0 46.80 3.51
3407 5195 4.320456 CGCACTGGGAGCACCACT 62.320 66.667 1.58 0.0 46.80 4.00


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

AutoCloner maintained by Alex Coulton.