Multiple sequence alignment - TraesCS7D01G296700

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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 TraesCS7D01G296700 chr7D 100.000 5209 0 0 1 5209 373582341 373587549 0.000000e+00 9620.0
1 TraesCS7D01G296700 chr7D 84.503 342 45 4 210 551 164403380 164403713 1.080000e-86 331.0
2 TraesCS7D01G296700 chr7B 96.188 4565 130 18 440 4976 368621101 368625649 0.000000e+00 7426.0
3 TraesCS7D01G296700 chr7B 88.664 247 20 3 9 255 368616746 368616984 1.420000e-75 294.0
4 TraesCS7D01G296700 chr7B 87.560 209 21 2 4995 5199 368652817 368653024 2.420000e-58 237.0
5 TraesCS7D01G296700 chr7A 97.916 4078 73 8 548 4618 419564559 419568631 0.000000e+00 7049.0
6 TraesCS7D01G296700 chr7A 93.686 586 19 8 4624 5209 419569073 419569640 0.000000e+00 861.0
7 TraesCS7D01G296700 chr7A 88.203 551 57 6 21 571 419561373 419561915 0.000000e+00 651.0
8 TraesCS7D01G296700 chr7A 88.128 219 16 5 1 215 34052542 34052330 8.660000e-63 252.0
9 TraesCS7D01G296700 chr1A 85.674 356 42 3 204 559 330148066 330148412 2.960000e-97 366.0
10 TraesCS7D01G296700 chr1D 86.127 346 36 6 206 551 256794624 256794957 3.830000e-96 363.0
11 TraesCS7D01G296700 chr1D 84.726 347 44 5 205 551 253189328 253188991 6.460000e-89 339.0
12 TraesCS7D01G296700 chr1D 84.503 342 45 4 210 551 431817559 431817892 1.080000e-86 331.0
13 TraesCS7D01G296700 chrUn 84.503 342 45 4 210 551 296437528 296437861 1.080000e-86 331.0
14 TraesCS7D01G296700 chr5D 84.211 342 46 4 210 551 339719440 339719773 5.030000e-85 326.0
15 TraesCS7D01G296700 chr5D 87.442 215 20 6 1 212 67589196 67588986 1.870000e-59 241.0
16 TraesCS7D01G296700 chr1B 86.093 302 38 4 210 511 356448487 356448190 6.510000e-84 322.0
17 TraesCS7D01G296700 chr1B 88.517 209 13 6 1 206 634236936 634236736 5.210000e-60 243.0
18 TraesCS7D01G296700 chr6B 88.372 215 17 5 2 214 520427983 520428191 8.660000e-63 252.0
19 TraesCS7D01G296700 chr5A 88.780 205 21 2 2 204 521014087 521014291 3.110000e-62 250.0
20 TraesCS7D01G296700 chr3A 88.038 209 20 3 1 207 587584818 587585023 5.210000e-60 243.0
21 TraesCS7D01G296700 chr2B 87.156 218 16 7 1 214 63796071 63795862 2.420000e-58 237.0
22 TraesCS7D01G296700 chr2A 81.006 179 28 6 4555 4730 471810082 471810257 2.530000e-28 137.0
23 TraesCS7D01G296700 chr5B 78.571 154 18 11 4582 4730 631891363 631891506 2.580000e-13 87.9


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 TraesCS7D01G296700 chr7D 373582341 373587549 5208 False 9620.000000 9620 100.000000 1 5209 1 chr7D.!!$F2 5208
1 TraesCS7D01G296700 chr7B 368621101 368625649 4548 False 7426.000000 7426 96.188000 440 4976 1 chr7B.!!$F2 4536
2 TraesCS7D01G296700 chr7A 419561373 419569640 8267 False 2853.666667 7049 93.268333 21 5209 3 chr7A.!!$F1 5188

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
166 167 1.076727 GGGGTGGTGGGAAGAAAGG 59.923 63.158 0.00 0.0 0.0 3.11 F
773 3444 1.185315 AACTCTGCCTCTCTGCTCTC 58.815 55.000 0.00 0.0 0.0 3.20 F
1600 4294 0.385751 CCGTGTCGACCATATCAGCT 59.614 55.000 14.12 0.0 0.0 4.24 F
2638 5332 1.734465 GAGGATTCACAAGTCGGCAAG 59.266 52.381 0.00 0.0 0.0 4.01 F
3643 6337 0.878523 CGTTTCCAAGCGTGACCTCA 60.879 55.000 0.00 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 4294 0.950836 CACAATTGAACACCGAGCCA 59.049 50.000 13.59 0.00 0.00 4.75 R
2443 5137 0.179179 GGCAATCTCGAAGCTTGTGC 60.179 55.000 2.10 3.55 40.05 4.57 R
3031 5725 1.891919 AACACGCGCATTGTGGTCT 60.892 52.632 16.56 0.00 41.64 3.85 R
4166 6864 0.387622 CCAGTTTGCAGGCGAACATG 60.388 55.000 22.58 17.06 41.50 3.21 R
5072 8208 1.133407 ACGTGACGGTGCAAACAAATT 59.867 42.857 10.66 0.00 0.00 1.82 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
29 30 8.915871 AATAAATGTTCATCAAATTCTGACCG 57.084 30.769 0.00 0.00 36.69 4.79
49 50 8.795842 TGACCGTGAATTACCTTATATTTTGT 57.204 30.769 0.00 0.00 0.00 2.83
158 159 2.033602 GAACGAAGGGGTGGTGGG 59.966 66.667 0.00 0.00 0.00 4.61
166 167 1.076727 GGGGTGGTGGGAAGAAAGG 59.923 63.158 0.00 0.00 0.00 3.11
167 168 1.432023 GGGGTGGTGGGAAGAAAGGA 61.432 60.000 0.00 0.00 0.00 3.36
175 176 3.245264 GGTGGGAAGAAAGGAGAAATGGA 60.245 47.826 0.00 0.00 0.00 3.41
184 185 5.705905 AGAAAGGAGAAATGGAAACCTTACG 59.294 40.000 0.00 0.00 39.59 3.18
185 186 3.951663 AGGAGAAATGGAAACCTTACGG 58.048 45.455 0.00 0.00 0.00 4.02
280 281 3.780850 TGAGTAAGATTTCCTTCCCTCCC 59.219 47.826 0.00 0.00 34.55 4.30
297 298 2.352960 CTCCCGCTGATAGCAGTTTTTC 59.647 50.000 10.15 0.00 42.58 2.29
379 380 1.473258 TCATACCCACATTTGCAGGC 58.527 50.000 0.00 0.00 0.00 4.85
461 462 3.560481 CGCCTTATCTTCTACTCTCGTGA 59.440 47.826 0.00 0.00 0.00 4.35
462 463 4.553156 CGCCTTATCTTCTACTCTCGTGAC 60.553 50.000 0.00 0.00 0.00 3.67
467 468 5.721876 ATCTTCTACTCTCGTGACGTTAG 57.278 43.478 4.40 6.34 0.00 2.34
505 506 5.300792 TGAATCTTTCAACGCTTACCCTTTT 59.699 36.000 0.00 0.00 36.59 2.27
554 3222 5.712152 ACATCCAAAACTGATTTCACCTC 57.288 39.130 0.00 0.00 0.00 3.85
773 3444 1.185315 AACTCTGCCTCTCTGCTCTC 58.815 55.000 0.00 0.00 0.00 3.20
951 3622 5.027293 AGGTAACCGTTGTACTCTGTTTT 57.973 39.130 0.00 0.00 37.17 2.43
982 3653 2.464865 CCTTTAGCGGAGATTCTGACG 58.535 52.381 0.00 0.00 0.00 4.35
1153 3847 1.559219 TGCTGCCTAATCTTGCTACCA 59.441 47.619 0.00 0.00 0.00 3.25
1237 3931 3.313524 TTCTGCGGCCTCAGCTCA 61.314 61.111 18.27 1.44 39.73 4.26
1485 4179 2.180204 ACCTGTGTGCACTGCGAAC 61.180 57.895 19.41 7.89 0.00 3.95
1486 4180 1.889105 CCTGTGTGCACTGCGAACT 60.889 57.895 19.41 0.00 0.00 3.01
1600 4294 0.385751 CCGTGTCGACCATATCAGCT 59.614 55.000 14.12 0.00 0.00 4.24
2283 4977 1.755959 TGTGTGCCAGTTTGATTGCTT 59.244 42.857 0.00 0.00 0.00 3.91
2443 5137 4.154195 GCCATTTCTTGCCTATATGTACGG 59.846 45.833 0.00 0.00 0.00 4.02
2491 5185 2.376808 AGAGCAAGTTGAGGATGACG 57.623 50.000 7.16 0.00 0.00 4.35
2498 5192 4.618460 GCAAGTTGAGGATGACGAAGAGTA 60.618 45.833 7.16 0.00 0.00 2.59
2638 5332 1.734465 GAGGATTCACAAGTCGGCAAG 59.266 52.381 0.00 0.00 0.00 4.01
3031 5725 8.722480 AGTCTTCAAACATATTGATCGATGAA 57.278 30.769 0.54 0.00 0.00 2.57
3157 5851 2.015587 CCTGAGTACTACCGTCTCCAC 58.984 57.143 0.00 0.00 0.00 4.02
3439 6133 2.189342 GTGACAACATCTCTAGAGCGC 58.811 52.381 15.35 0.00 0.00 5.92
3547 6241 6.176183 CAAAAAGGTATCACAGAGGTCATCT 58.824 40.000 0.00 0.00 39.56 2.90
3643 6337 0.878523 CGTTTCCAAGCGTGACCTCA 60.879 55.000 0.00 0.00 0.00 3.86
3661 6355 1.067669 TCATCGCAGAGGAGGAAATCG 59.932 52.381 0.00 0.00 44.67 3.34
3893 6587 3.821033 ACCTGTTGCTTTGTAGATCAACC 59.179 43.478 0.00 0.00 38.32 3.77
3912 6606 1.227674 GTAGCAGGCCATTCGGGAG 60.228 63.158 5.01 0.00 40.01 4.30
3913 6607 1.382557 TAGCAGGCCATTCGGGAGA 60.383 57.895 5.01 0.00 40.01 3.71
4248 6947 9.362539 AGATCAAATTGCATGTCTAACATTTTC 57.637 29.630 0.00 0.00 36.53 2.29
4250 6949 9.715121 ATCAAATTGCATGTCTAACATTTTCTT 57.285 25.926 0.00 0.00 36.53 2.52
4251 6950 9.195411 TCAAATTGCATGTCTAACATTTTCTTC 57.805 29.630 0.00 0.00 36.53 2.87
4259 6958 9.322776 CATGTCTAACATTTTCTTCTTCTTTCG 57.677 33.333 0.00 0.00 36.53 3.46
4463 7162 7.862372 TGAAAATCAGTTAATGTTGCTGACTTC 59.138 33.333 0.00 0.00 41.33 3.01
4601 7301 7.075674 TCAAATACACATGCATGAACAGTAG 57.924 36.000 32.75 16.32 0.00 2.57
4606 7306 5.003160 ACACATGCATGAACAGTAGCTTTA 58.997 37.500 32.75 0.00 0.00 1.85
4611 7311 9.559732 ACATGCATGAACAGTAGCTTTAATATA 57.440 29.630 32.75 0.00 0.00 0.86
4736 7872 5.365314 TGGAGGCCTGTACAAAAAGAAAATT 59.635 36.000 12.00 0.00 0.00 1.82
4745 7881 6.978080 TGTACAAAAAGAAAATTGGAGCTCAC 59.022 34.615 17.19 5.63 0.00 3.51
4765 7901 5.012239 TCACAAAGCCTCATTTTCTAGCAT 58.988 37.500 0.00 0.00 0.00 3.79
5032 8168 1.002900 ACAGTATTTGTGTGTGTGCGC 60.003 47.619 0.00 0.00 38.99 6.09
5061 8197 8.400947 CCTCAGTGATAGTGTAAAATTCAATGG 58.599 37.037 0.00 0.00 34.26 3.16
5072 8208 7.175990 GTGTAAAATTCAATGGTACCCTCTTGA 59.824 37.037 10.07 12.80 0.00 3.02
5089 8225 3.129462 TCTTGAATTTGTTTGCACCGTCA 59.871 39.130 0.00 0.00 0.00 4.35
5142 8278 5.116069 TCGTTTCTTTTCCTATTTGTGGC 57.884 39.130 0.00 0.00 0.00 5.01
5173 8309 2.504367 CCGACTTTGTTGAAGGATGGT 58.496 47.619 0.00 0.00 39.79 3.55
5182 8318 5.042463 TGTTGAAGGATGGTGAAGTACAA 57.958 39.130 0.00 0.00 0.00 2.41
5190 8326 4.695928 GGATGGTGAAGTACAAGGAAAGTC 59.304 45.833 0.00 0.00 0.00 3.01
5197 8333 1.069775 TACAAGGAAAGTCCACCCCC 58.930 55.000 0.00 0.00 39.61 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.357652 CGGTCAGAATTTGATGAACATTTATTT 57.642 29.630 5.49 0.00 38.29 1.40
4 5 8.522830 ACGGTCAGAATTTGATGAACATTTATT 58.477 29.630 5.49 0.00 38.29 1.40
5 6 7.970061 CACGGTCAGAATTTGATGAACATTTAT 59.030 33.333 5.49 0.00 38.29 1.40
6 7 7.174080 TCACGGTCAGAATTTGATGAACATTTA 59.826 33.333 5.49 0.00 38.29 1.40
7 8 6.016360 TCACGGTCAGAATTTGATGAACATTT 60.016 34.615 5.49 0.00 38.29 2.32
8 9 5.473162 TCACGGTCAGAATTTGATGAACATT 59.527 36.000 5.49 0.00 38.29 2.71
9 10 5.003160 TCACGGTCAGAATTTGATGAACAT 58.997 37.500 5.49 0.00 38.29 2.71
10 11 4.384940 TCACGGTCAGAATTTGATGAACA 58.615 39.130 5.49 0.00 38.29 3.18
11 12 5.356882 TTCACGGTCAGAATTTGATGAAC 57.643 39.130 0.00 0.00 38.29 3.18
12 13 6.573664 AATTCACGGTCAGAATTTGATGAA 57.426 33.333 1.75 0.00 41.54 2.57
13 14 6.093495 GGTAATTCACGGTCAGAATTTGATGA 59.907 38.462 10.52 0.00 41.54 2.92
14 15 6.094048 AGGTAATTCACGGTCAGAATTTGATG 59.906 38.462 10.52 0.00 41.54 3.07
15 16 6.180472 AGGTAATTCACGGTCAGAATTTGAT 58.820 36.000 10.52 0.00 41.54 2.57
16 17 5.556915 AGGTAATTCACGGTCAGAATTTGA 58.443 37.500 10.52 0.00 41.54 2.69
17 18 5.880054 AGGTAATTCACGGTCAGAATTTG 57.120 39.130 10.52 0.00 41.54 2.32
18 19 9.847224 ATATAAGGTAATTCACGGTCAGAATTT 57.153 29.630 10.52 0.00 41.54 1.82
19 20 9.847224 AATATAAGGTAATTCACGGTCAGAATT 57.153 29.630 10.22 10.22 45.05 2.17
69 70 7.839680 ACCTTCTGAACCAATTTCACTTTAT 57.160 32.000 0.00 0.00 39.45 1.40
133 134 2.034179 CCACCCCTTCGTTCAACTTTTC 59.966 50.000 0.00 0.00 0.00 2.29
137 138 0.179029 CACCACCCCTTCGTTCAACT 60.179 55.000 0.00 0.00 0.00 3.16
140 141 2.824880 CCCACCACCCCTTCGTTCA 61.825 63.158 0.00 0.00 0.00 3.18
142 143 2.064242 CTTCCCACCACCCCTTCGTT 62.064 60.000 0.00 0.00 0.00 3.85
158 159 6.656632 AAGGTTTCCATTTCTCCTTTCTTC 57.343 37.500 0.00 0.00 35.32 2.87
221 222 6.192970 AGCTATCCCAACTTATGCTATGTT 57.807 37.500 0.00 0.00 0.00 2.71
280 281 4.083324 TGAAAGGAAAAACTGCTATCAGCG 60.083 41.667 0.00 0.00 46.26 5.18
419 420 8.801715 AAGGCGCAAATATATAATGTTTTGAG 57.198 30.769 10.83 7.83 33.69 3.02
434 435 5.283457 AGAGTAGAAGATAAGGCGCAAAT 57.717 39.130 10.83 0.00 0.00 2.32
438 439 2.291190 ACGAGAGTAGAAGATAAGGCGC 59.709 50.000 0.00 0.00 46.88 6.53
483 484 5.528870 CAAAAGGGTAAGCGTTGAAAGATT 58.471 37.500 0.00 0.00 0.00 2.40
486 487 3.049912 GCAAAAGGGTAAGCGTTGAAAG 58.950 45.455 0.00 0.00 0.00 2.62
491 492 0.178973 AGGGCAAAAGGGTAAGCGTT 60.179 50.000 0.00 0.00 0.00 4.84
493 494 0.243636 CAAGGGCAAAAGGGTAAGCG 59.756 55.000 0.00 0.00 0.00 4.68
497 498 1.229051 GGGCAAGGGCAAAAGGGTA 60.229 57.895 0.00 0.00 43.71 3.69
505 506 3.949885 CTGCATCAGGGCAAGGGCA 62.950 63.158 0.00 0.00 44.40 5.36
554 3222 4.738740 ACGACTGTTAAACAAAGACGAGAG 59.261 41.667 0.00 0.00 0.00 3.20
754 3424 1.185315 GAGAGCAGAGAGGCAGAGTT 58.815 55.000 0.00 0.00 35.83 3.01
951 3622 1.234821 CGCTAAAGGGCACAGAACAA 58.765 50.000 0.00 0.00 0.00 2.83
1237 3931 2.526873 ACCAAGTGGGAGCCGTCT 60.527 61.111 1.69 0.00 41.15 4.18
1420 4114 3.432051 CTCCACGCCCTCGACCATC 62.432 68.421 0.00 0.00 39.41 3.51
1485 4179 1.589414 AGGAATCCCCTTGTCAGGAG 58.411 55.000 0.00 0.00 44.85 3.69
1486 4180 3.836945 AGGAATCCCCTTGTCAGGA 57.163 52.632 0.00 0.00 44.85 3.86
1506 4200 2.685850 AGTATCAGGGTTAACACCGC 57.314 50.000 3.66 0.00 45.39 5.68
1600 4294 0.950836 CACAATTGAACACCGAGCCA 59.049 50.000 13.59 0.00 0.00 4.75
2283 4977 2.560105 CACTCATCTGAGACACACCTCA 59.440 50.000 13.94 0.00 44.74 3.86
2443 5137 0.179179 GGCAATCTCGAAGCTTGTGC 60.179 55.000 2.10 3.55 40.05 4.57
2498 5192 8.718734 GTTATCCTTTCGAAAAGAGTATGTTGT 58.281 33.333 14.15 0.00 0.00 3.32
2638 5332 3.193267 TGAATACACATGAAAAGCTGCCC 59.807 43.478 0.00 0.00 0.00 5.36
3031 5725 1.891919 AACACGCGCATTGTGGTCT 60.892 52.632 16.56 0.00 41.64 3.85
3547 6241 4.399303 TCATTCTCTGAGCACGACTGATTA 59.601 41.667 0.00 0.00 0.00 1.75
3643 6337 1.067821 GACGATTTCCTCCTCTGCGAT 59.932 52.381 0.00 0.00 0.00 4.58
3893 6587 2.588877 CCCGAATGGCCTGCTACG 60.589 66.667 3.32 2.84 0.00 3.51
3912 6606 9.988815 CTCTATATAGCTAGATCTTCCTCTCTC 57.011 40.741 3.65 0.00 0.00 3.20
3913 6607 9.507381 ACTCTATATAGCTAGATCTTCCTCTCT 57.493 37.037 3.65 0.00 0.00 3.10
4166 6864 0.387622 CCAGTTTGCAGGCGAACATG 60.388 55.000 22.58 17.06 41.50 3.21
4248 6947 8.641499 ACTCTTAATAGATGCGAAAGAAGAAG 57.359 34.615 0.00 0.00 0.00 2.85
4250 6949 8.251026 TGAACTCTTAATAGATGCGAAAGAAGA 58.749 33.333 0.00 0.00 0.00 2.87
4251 6950 8.412608 TGAACTCTTAATAGATGCGAAAGAAG 57.587 34.615 0.00 0.00 0.00 2.85
4463 7162 7.502177 AGTACTCGTAACAAACATAATGACG 57.498 36.000 0.00 0.00 0.00 4.35
4650 7786 7.499292 AGAAAATTTGTTGATGTTCATCCACA 58.501 30.769 13.27 13.27 0.00 4.17
4745 7881 5.957798 TGAATGCTAGAAAATGAGGCTTTG 58.042 37.500 0.00 0.00 0.00 2.77
4777 7913 3.680937 CGAATGATGCAAGTGCCAATTTT 59.319 39.130 0.00 0.00 41.18 1.82
4778 7914 3.255725 CGAATGATGCAAGTGCCAATTT 58.744 40.909 0.00 0.00 41.18 1.82
4779 7915 2.231964 ACGAATGATGCAAGTGCCAATT 59.768 40.909 0.00 0.00 41.18 2.32
4780 7916 1.820519 ACGAATGATGCAAGTGCCAAT 59.179 42.857 0.00 0.00 41.18 3.16
4930 8066 4.440112 GCTACATGCAGTTTATTGGGGAAC 60.440 45.833 0.00 0.00 42.31 3.62
4998 8134 9.912634 ACACAAATACTGTTTATTGAAGAATGG 57.087 29.630 6.83 0.00 35.47 3.16
5032 8168 6.878923 TGAATTTTACACTATCACTGAGGTGG 59.121 38.462 15.16 3.24 43.17 4.61
5061 8197 4.982295 GTGCAAACAAATTCAAGAGGGTAC 59.018 41.667 0.00 0.00 0.00 3.34
5072 8208 1.133407 ACGTGACGGTGCAAACAAATT 59.867 42.857 10.66 0.00 0.00 1.82
5089 8225 2.357517 CCTTGCCGAAGCTCACGT 60.358 61.111 11.25 0.00 40.80 4.49
5154 8290 3.138304 TCACCATCCTTCAACAAAGTCG 58.862 45.455 0.00 0.00 32.69 4.18
5173 8309 3.181448 GGGTGGACTTTCCTTGTACTTCA 60.181 47.826 0.00 0.00 37.46 3.02


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

AutoCloner maintained by Alex Coulton.