Multiple sequence alignment - TraesCS7A01G520600

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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 TraesCS7A01G520600 chr7A 100.000 3302 0 0 1 3302 704791223 704794524 0.000000e+00 6098
1 TraesCS7A01G520600 chr7A 88.922 1002 95 8 1112 2110 704776826 704777814 0.000000e+00 1221
2 TraesCS7A01G520600 chr7A 86.885 183 13 7 2107 2286 704778366 704778540 9.350000e-46 195
3 TraesCS7A01G520600 chr7A 90.909 77 6 1 248 323 704691559 704691635 5.830000e-18 102
4 TraesCS7A01G520600 chr7D 96.098 3306 95 14 1 3302 613405311 613408586 0.000000e+00 5360
5 TraesCS7A01G520600 chr7D 88.922 1002 95 8 1112 2110 613394582 613395570 0.000000e+00 1221
6 TraesCS7A01G520600 chr7D 79.862 581 77 29 248 811 613393761 613394318 4.000000e-104 388
7 TraesCS7A01G520600 chr7D 86.885 183 13 7 2107 2286 613396122 613396296 9.350000e-46 195
8 TraesCS7A01G520600 chr7B 94.566 3165 144 8 159 3302 703245198 703248355 0.000000e+00 4867
9 TraesCS7A01G520600 chr7B 89.022 1002 94 7 1112 2110 703165853 703166841 0.000000e+00 1227
10 TraesCS7A01G520600 chr7B 89.571 163 8 3 2124 2284 703167411 703167566 7.230000e-47 198


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 TraesCS7A01G520600 chr7A 704791223 704794524 3301 False 6098.000000 6098 100.0000 1 3302 1 chr7A.!!$F2 3301
1 TraesCS7A01G520600 chr7A 704776826 704778540 1714 False 708.000000 1221 87.9035 1112 2286 2 chr7A.!!$F3 1174
2 TraesCS7A01G520600 chr7D 613405311 613408586 3275 False 5360.000000 5360 96.0980 1 3302 1 chr7D.!!$F1 3301
3 TraesCS7A01G520600 chr7D 613393761 613396296 2535 False 601.333333 1221 85.2230 248 2286 3 chr7D.!!$F2 2038
4 TraesCS7A01G520600 chr7B 703245198 703248355 3157 False 4867.000000 4867 94.5660 159 3302 1 chr7B.!!$F1 3143
5 TraesCS7A01G520600 chr7B 703165853 703167566 1713 False 712.500000 1227 89.2965 1112 2284 2 chr7B.!!$F2 1172

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
733 771 0.306533 CTGACCGGGTTTTGTTCACG 59.693 55.0 6.32 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 2961 0.401356 TCCAGCTCACATTTCTGGCA 59.599 50.0 2.8 0.0 45.25 4.92 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 2.168521 CCTTCCGCATTTGAGTCTAGGA 59.831 50.000 0.00 0.00 0.00 2.94
27 28 1.666189 GCATTTGAGTCTAGGAACGGC 59.334 52.381 0.00 0.00 0.00 5.68
45 46 2.552599 GCCTTAGCCCATCTTCTACC 57.447 55.000 0.00 0.00 0.00 3.18
46 47 1.270358 GCCTTAGCCCATCTTCTACCG 60.270 57.143 0.00 0.00 0.00 4.02
47 48 2.040178 CCTTAGCCCATCTTCTACCGT 58.960 52.381 0.00 0.00 0.00 4.83
48 49 3.228453 CCTTAGCCCATCTTCTACCGTA 58.772 50.000 0.00 0.00 0.00 4.02
49 50 3.005578 CCTTAGCCCATCTTCTACCGTAC 59.994 52.174 0.00 0.00 0.00 3.67
65 66 5.656213 ACCGTACTAGTTTGTCAAGCTAT 57.344 39.130 9.31 3.95 0.00 2.97
68 69 5.408356 CGTACTAGTTTGTCAAGCTATGGT 58.592 41.667 9.31 7.77 0.00 3.55
101 102 8.820933 GCTTCTTTCTTTTTCTTTTTACAGCAT 58.179 29.630 0.00 0.00 0.00 3.79
121 122 5.288543 CATGTCCTGCTCTTGTTTTAGTC 57.711 43.478 0.00 0.00 0.00 2.59
122 123 4.689612 TGTCCTGCTCTTGTTTTAGTCT 57.310 40.909 0.00 0.00 0.00 3.24
132 133 7.497579 TGCTCTTGTTTTAGTCTCACATTGTTA 59.502 33.333 0.00 0.00 0.00 2.41
134 135 8.149973 TCTTGTTTTAGTCTCACATTGTTACC 57.850 34.615 0.00 0.00 0.00 2.85
135 136 7.771361 TCTTGTTTTAGTCTCACATTGTTACCA 59.229 33.333 0.00 0.00 0.00 3.25
136 137 7.867305 TGTTTTAGTCTCACATTGTTACCAA 57.133 32.000 0.00 0.00 34.45 3.67
139 140 9.180678 GTTTTAGTCTCACATTGTTACCAAATG 57.819 33.333 0.00 0.00 33.44 2.32
140 141 5.964958 AGTCTCACATTGTTACCAAATGG 57.035 39.130 0.00 0.00 42.17 3.16
141 142 4.218417 AGTCTCACATTGTTACCAAATGGC 59.782 41.667 0.00 0.00 39.32 4.40
142 143 3.190327 TCTCACATTGTTACCAAATGGCG 59.810 43.478 0.00 0.00 39.32 5.69
143 144 1.991965 CACATTGTTACCAAATGGCGC 59.008 47.619 0.00 0.00 39.32 6.53
144 145 1.267365 CATTGTTACCAAATGGCGCG 58.733 50.000 0.00 0.00 39.32 6.86
145 146 0.457681 ATTGTTACCAAATGGCGCGC 60.458 50.000 25.94 25.94 39.32 6.86
146 147 1.796190 TTGTTACCAAATGGCGCGCA 61.796 50.000 34.42 19.50 39.32 6.09
147 148 1.514014 GTTACCAAATGGCGCGCAG 60.514 57.895 34.42 15.96 39.32 5.18
148 149 2.695759 TTACCAAATGGCGCGCAGG 61.696 57.895 34.42 25.55 39.32 4.85
149 150 3.613877 TACCAAATGGCGCGCAGGA 62.614 57.895 34.42 16.66 39.32 3.86
150 151 3.746889 CCAAATGGCGCGCAGGAA 61.747 61.111 34.42 15.57 0.00 3.36
151 152 2.202518 CAAATGGCGCGCAGGAAG 60.203 61.111 34.42 15.52 0.00 3.46
152 153 4.120331 AAATGGCGCGCAGGAAGC 62.120 61.111 34.42 14.98 40.87 3.86
176 177 1.724623 GCACTTGTCTGCATTGCAATG 59.275 47.619 30.92 30.92 38.41 2.82
214 215 6.252281 TCTACAAAAAGTTGCTACGTTGTTG 58.748 36.000 17.56 15.99 38.39 3.33
215 216 4.800784 ACAAAAAGTTGCTACGTTGTTGT 58.199 34.783 15.02 15.02 38.39 3.32
216 217 4.619336 ACAAAAAGTTGCTACGTTGTTGTG 59.381 37.500 17.64 10.23 38.39 3.33
217 218 2.468532 AAGTTGCTACGTTGTTGTGC 57.531 45.000 0.00 0.00 0.00 4.57
237 239 0.530870 GTGGCGAATAGAGTGGCTCC 60.531 60.000 0.00 0.00 0.00 4.70
239 241 1.329256 GGCGAATAGAGTGGCTCCTA 58.671 55.000 0.00 0.00 0.00 2.94
242 244 2.544069 GCGAATAGAGTGGCTCCTACAC 60.544 54.545 0.00 0.00 39.10 2.90
258 260 4.038763 TCCTACACGAACTTGTCATGAAGT 59.961 41.667 0.00 0.00 37.81 3.01
323 326 3.329386 TCTTGCTATTGTGCTGACTGAC 58.671 45.455 0.00 0.00 0.00 3.51
325 328 2.691927 TGCTATTGTGCTGACTGACTG 58.308 47.619 0.00 0.00 0.00 3.51
327 330 2.928757 GCTATTGTGCTGACTGACTGAG 59.071 50.000 0.00 0.00 0.00 3.35
369 387 7.572724 GCATTTATCTGAGCTAATAACTGGCTG 60.573 40.741 11.78 0.00 36.37 4.85
412 432 1.827681 GTTGCCTCTTTTCTCCCTCC 58.172 55.000 0.00 0.00 0.00 4.30
569 607 3.333680 TCCCTCTTTGCTGGTAAGGAAAT 59.666 43.478 0.00 0.00 42.12 2.17
575 613 4.365514 TTGCTGGTAAGGAAATCTGTCA 57.634 40.909 0.00 0.00 29.72 3.58
602 640 2.186076 GATCGCTGTTCGTTCGATTCT 58.814 47.619 0.00 0.00 42.20 2.40
692 730 2.371386 ATCCCATCCCATGCCCCA 60.371 61.111 0.00 0.00 0.00 4.96
713 751 6.149633 CCCAGTTTTGCAACTTCAATACTAC 58.850 40.000 0.00 0.00 40.66 2.73
733 771 0.306533 CTGACCGGGTTTTGTTCACG 59.693 55.000 6.32 0.00 0.00 4.35
734 772 0.392729 TGACCGGGTTTTGTTCACGT 60.393 50.000 6.32 0.00 0.00 4.49
937 977 5.047802 CCCCAGTTCCATTATGCATGATTAC 60.048 44.000 10.16 4.90 34.31 1.89
946 986 8.605065 TCCATTATGCATGATTACTTGATCCTA 58.395 33.333 10.16 0.00 34.31 2.94
969 1009 3.433615 GTCCTGACTATGTTGCTTGTCAC 59.566 47.826 0.00 0.00 35.83 3.67
1166 1242 1.672881 GGATCTTCCAGTTGCCAATCG 59.327 52.381 0.00 0.00 36.28 3.34
1206 1282 1.842920 TCAGCTTCTCCAGTGCCCA 60.843 57.895 0.00 0.00 0.00 5.36
1485 1561 2.029728 GGATGATTTCAGTCGCACGAAG 59.970 50.000 0.00 0.00 0.00 3.79
2119 2752 4.527816 TCACTGCCCTCTTATTTGCATTTT 59.472 37.500 0.00 0.00 32.53 1.82
2120 2753 4.628333 CACTGCCCTCTTATTTGCATTTTG 59.372 41.667 0.00 0.00 32.53 2.44
2122 2755 4.567971 TGCCCTCTTATTTGCATTTTGTG 58.432 39.130 0.00 0.00 0.00 3.33
2213 2850 4.342378 TCTGTACTTTCTGCAGTCTGAAGT 59.658 41.667 14.67 19.27 34.34 3.01
2431 3068 8.731275 TTTGAGTCTTTCTGTCACATCTTTTA 57.269 30.769 0.00 0.00 0.00 1.52
2438 3075 9.663904 TCTTTCTGTCACATCTTTTATTTTTCG 57.336 29.630 0.00 0.00 0.00 3.46
2440 3077 9.796120 TTTCTGTCACATCTTTTATTTTTCGTT 57.204 25.926 0.00 0.00 0.00 3.85
2587 3224 9.896645 ATGTAACAAGAAGTACATGAGATGATT 57.103 29.630 0.00 0.00 32.56 2.57
2659 3296 2.367567 GTGTTCTAGTTCCTGGTGGTCA 59.632 50.000 0.00 0.00 34.23 4.02
2748 3385 5.518812 TCGTGATCATTCAACCAAAAACTG 58.481 37.500 0.00 0.00 32.48 3.16
2816 3453 4.142773 CCAGCCAAACATTCAAAATGCATC 60.143 41.667 0.00 0.00 0.00 3.91
2893 3530 5.570205 TGTCCATGAAAGGTGGTAAACTA 57.430 39.130 0.00 0.00 37.96 2.24
2920 3557 2.238521 GGGATGCAGTGTTTTTCCTCA 58.761 47.619 0.00 0.00 0.00 3.86
3284 3922 6.716628 ACTAGAATTCTTGCCAAATCTTGTGA 59.283 34.615 14.36 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.040178 ACGGTAGAAGATGGGCTAAGG 58.960 52.381 0.00 0.00 0.00 2.69
44 45 4.804139 CCATAGCTTGACAAACTAGTACGG 59.196 45.833 0.00 0.00 0.00 4.02
45 46 5.408356 ACCATAGCTTGACAAACTAGTACG 58.592 41.667 0.00 0.00 0.00 3.67
46 47 6.755607 GGTACCATAGCTTGACAAACTAGTAC 59.244 42.308 7.15 14.18 0.00 2.73
47 48 6.870769 GGTACCATAGCTTGACAAACTAGTA 58.129 40.000 7.15 0.59 0.00 1.82
48 49 5.731591 GGTACCATAGCTTGACAAACTAGT 58.268 41.667 7.15 0.00 0.00 2.57
68 69 7.418337 AAAGAAAAAGAAAGAAGCAAGGGTA 57.582 32.000 0.00 0.00 0.00 3.69
101 102 4.100963 TGAGACTAAAACAAGAGCAGGACA 59.899 41.667 0.00 0.00 0.00 4.02
102 103 4.449405 GTGAGACTAAAACAAGAGCAGGAC 59.551 45.833 0.00 0.00 0.00 3.85
134 135 2.202518 CTTCCTGCGCGCCATTTG 60.203 61.111 30.77 12.39 0.00 2.32
135 136 4.120331 GCTTCCTGCGCGCCATTT 62.120 61.111 30.77 0.00 0.00 2.32
145 146 3.058160 CAAGTGCCCGGCTTCCTG 61.058 66.667 11.61 0.46 0.00 3.86
146 147 3.553095 GACAAGTGCCCGGCTTCCT 62.553 63.158 11.61 0.85 0.00 3.36
147 148 3.056328 GACAAGTGCCCGGCTTCC 61.056 66.667 11.61 0.00 0.00 3.46
148 149 2.032681 AGACAAGTGCCCGGCTTC 59.967 61.111 11.61 4.03 0.00 3.86
149 150 2.281761 CAGACAAGTGCCCGGCTT 60.282 61.111 11.61 0.00 0.00 4.35
152 153 1.973281 AATGCAGACAAGTGCCCGG 60.973 57.895 0.00 0.00 43.28 5.73
153 154 1.210931 CAATGCAGACAAGTGCCCG 59.789 57.895 0.00 0.00 43.28 6.13
154 155 1.080298 GCAATGCAGACAAGTGCCC 60.080 57.895 0.00 0.00 43.28 5.36
155 156 0.032403 TTGCAATGCAGACAAGTGCC 59.968 50.000 8.31 0.00 43.28 5.01
156 157 1.724623 CATTGCAATGCAGACAAGTGC 59.275 47.619 25.50 0.00 40.61 4.40
176 177 8.999220 ACTTTTTGTAGATACTAGTACAAGGC 57.001 34.615 4.31 0.00 39.63 4.35
184 185 8.684973 ACGTAGCAACTTTTTGTAGATACTAG 57.315 34.615 0.00 0.00 34.90 2.57
185 186 8.918658 CAACGTAGCAACTTTTTGTAGATACTA 58.081 33.333 0.00 0.00 34.90 1.82
186 187 7.440255 ACAACGTAGCAACTTTTTGTAGATACT 59.560 33.333 0.00 0.00 34.90 2.12
207 208 2.709629 ATTCGCCACGCACAACAACG 62.710 55.000 0.00 0.00 0.00 4.10
214 215 1.421410 CCACTCTATTCGCCACGCAC 61.421 60.000 0.00 0.00 0.00 5.34
215 216 1.153647 CCACTCTATTCGCCACGCA 60.154 57.895 0.00 0.00 0.00 5.24
216 217 2.526120 GCCACTCTATTCGCCACGC 61.526 63.158 0.00 0.00 0.00 5.34
217 218 0.872021 GAGCCACTCTATTCGCCACG 60.872 60.000 0.00 0.00 0.00 4.94
237 239 5.234329 ACAACTTCATGACAAGTTCGTGTAG 59.766 40.000 9.39 1.92 43.41 2.74
239 241 3.938963 ACAACTTCATGACAAGTTCGTGT 59.061 39.130 9.39 4.23 43.41 4.49
242 244 4.201812 ACACACAACTTCATGACAAGTTCG 60.202 41.667 9.39 7.09 43.41 3.95
258 260 1.608055 CTGAAGCCATGGACACACAA 58.392 50.000 18.40 0.00 0.00 3.33
323 326 2.352225 GCTACACCACTCACTCACTCAG 60.352 54.545 0.00 0.00 0.00 3.35
325 328 1.613925 TGCTACACCACTCACTCACTC 59.386 52.381 0.00 0.00 0.00 3.51
327 330 2.751166 ATGCTACACCACTCACTCAC 57.249 50.000 0.00 0.00 0.00 3.51
369 387 8.366671 ACGTTCAGAATGTTCTATAATTAGCC 57.633 34.615 1.78 0.00 35.34 3.93
569 607 0.538584 AGCGATCCAAGCATGACAGA 59.461 50.000 0.00 0.00 37.01 3.41
575 613 0.391661 ACGAACAGCGATCCAAGCAT 60.392 50.000 0.00 0.00 44.57 3.79
602 640 3.255395 CACAGCAGAGAGAACAAGAGAGA 59.745 47.826 0.00 0.00 0.00 3.10
692 730 6.770785 TCAGGTAGTATTGAAGTTGCAAAACT 59.229 34.615 0.00 0.00 33.76 2.66
713 751 0.666374 GTGAACAAAACCCGGTCAGG 59.334 55.000 0.00 0.00 40.63 3.86
759 799 8.713708 TTTCTACCCAGGAATTGTGAATAAAA 57.286 30.769 0.00 0.00 0.00 1.52
811 851 4.916041 TTTGACATTCTGATCTGGAGGT 57.084 40.909 0.00 0.00 0.00 3.85
849 889 3.935315 TGATCAACAAGAGGAGAAGCTG 58.065 45.455 0.00 0.00 0.00 4.24
917 957 8.701908 ATCAAGTAATCATGCATAATGGAACT 57.298 30.769 0.00 0.00 36.86 3.01
937 977 6.511416 CAACATAGTCAGGACTAGGATCAAG 58.489 44.000 23.26 7.85 45.52 3.02
946 986 3.324846 TGACAAGCAACATAGTCAGGACT 59.675 43.478 7.18 7.18 45.02 3.85
969 1009 5.049828 TGTGATCAAACACCTATAGATGCG 58.950 41.667 0.00 0.00 39.69 4.73
1103 1146 5.415701 ACACCTGCAAACATATAACTTGGAG 59.584 40.000 0.00 6.43 38.01 3.86
1114 1190 2.880443 AGATCCAACACCTGCAAACAT 58.120 42.857 0.00 0.00 0.00 2.71
1166 1242 1.550130 TTCATCCCTCACCGGTCCAC 61.550 60.000 2.59 0.00 0.00 4.02
1206 1282 4.338964 TGCATTGCTTCGGAATCACAATAT 59.661 37.500 10.49 0.00 30.16 1.28
1485 1561 2.360165 GACATGGCCAATGATGTTCCTC 59.640 50.000 10.96 0.00 38.72 3.71
2213 2850 2.809696 GCTTTAGCCAGTTTACCACGAA 59.190 45.455 0.00 0.00 34.31 3.85
2324 2961 0.401356 TCCAGCTCACATTTCTGGCA 59.599 50.000 2.80 0.00 45.25 4.92
2431 3068 8.761575 ATTGTCTGCAAATCATAACGAAAAAT 57.238 26.923 0.00 0.00 38.21 1.82
2436 3073 5.643348 ACTGATTGTCTGCAAATCATAACGA 59.357 36.000 11.67 0.00 38.21 3.85
2438 3075 7.912250 CCTAACTGATTGTCTGCAAATCATAAC 59.088 37.037 11.67 0.00 38.21 1.89
2440 3077 7.112122 ACCTAACTGATTGTCTGCAAATCATA 58.888 34.615 11.67 3.68 38.21 2.15
2441 3078 5.948162 ACCTAACTGATTGTCTGCAAATCAT 59.052 36.000 11.67 2.82 38.21 2.45
2442 3079 5.316167 ACCTAACTGATTGTCTGCAAATCA 58.684 37.500 10.95 10.95 38.21 2.57
2443 3080 5.886960 ACCTAACTGATTGTCTGCAAATC 57.113 39.130 3.13 3.13 38.21 2.17
2444 3081 6.655078 AAACCTAACTGATTGTCTGCAAAT 57.345 33.333 0.00 0.00 38.21 2.32
2621 3258 3.838244 ACACACACTCCAAGCTCTAAA 57.162 42.857 0.00 0.00 0.00 1.85
2696 3333 3.195396 GCAAATGGGGCTGATGTAGAAAA 59.805 43.478 0.00 0.00 0.00 2.29
2787 3424 0.179129 GAATGTTTGGCTGGGCATCG 60.179 55.000 0.00 0.00 0.00 3.84
2796 3433 5.179742 TGAAGATGCATTTTGAATGTTTGGC 59.820 36.000 7.28 0.00 0.00 4.52
2816 3453 7.362660 CCATAACAGGATTCATATGGCATGAAG 60.363 40.741 10.98 0.00 40.80 3.02
2893 3530 1.356124 AACACTGCATCCCAGAGACT 58.644 50.000 0.00 0.00 44.64 3.24
2920 3557 6.881065 ACAACATGAGCTACAAATCAGTACAT 59.119 34.615 0.00 0.00 0.00 2.29
3007 3644 7.391148 TCGAATGTCAATATGATCTATCCGA 57.609 36.000 0.00 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.