Multiple sequence alignment - TraesCS4D01G065600

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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 TraesCS4D01G065600 chr4D 100.000 4823 0 0 1 4823 40657887 40653065 0.000000e+00 8907
1 TraesCS4D01G065600 chr4A 94.021 4884 178 46 32 4823 559043679 559048540 0.000000e+00 7297
2 TraesCS4D01G065600 chr4B 93.325 4929 195 61 1 4823 59595663 59590763 0.000000e+00 7156
3 TraesCS4D01G065600 chr2B 76.868 281 54 7 1105 1384 528829625 528829895 1.080000e-31 148
4 TraesCS4D01G065600 chr2D 76.596 282 53 9 1105 1384 449556344 449556074 5.030000e-30 143
5 TraesCS4D01G065600 chr2A 76.596 282 53 9 1105 1384 593443486 593443756 5.030000e-30 143


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 TraesCS4D01G065600 chr4D 40653065 40657887 4822 True 8907 8907 100.000 1 4823 1 chr4D.!!$R1 4822
1 TraesCS4D01G065600 chr4A 559043679 559048540 4861 False 7297 7297 94.021 32 4823 1 chr4A.!!$F1 4791
2 TraesCS4D01G065600 chr4B 59590763 59595663 4900 True 7156 7156 93.325 1 4823 1 chr4B.!!$R1 4822

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
206 212 0.106318 CCCCCACGTAGCTACTACCT 60.106 60.0 21.20 0.00 33.79 3.08 F
1460 1566 0.039798 TTCCACCTCTCGTTCGTTCG 60.040 55.0 0.00 0.00 0.00 3.95 F
2175 2295 0.179040 TCGTATCCCGGGAAATTGGC 60.179 55.0 30.84 12.76 37.11 4.52 F
2629 2749 0.396695 CTCCAGGGATGGCAAAGCAT 60.397 55.0 0.00 0.00 0.00 3.79 F
3468 3595 2.555325 GGGTTTTGGAAAGAAGTACCCG 59.445 50.0 0.00 0.00 34.90 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1875 0.601311 GAACTCACAAGGTGCGCTCT 60.601 55.000 9.73 3.07 32.98 4.09 R
2383 2503 0.323302 TGAACACTATGGAAGCCGCA 59.677 50.000 0.00 0.00 0.00 5.69 R
3229 3355 1.153369 CCACCCTGGTGTATCTGCG 60.153 63.158 14.89 0.00 44.02 5.18 R
3651 3778 1.549203 CATTTGCTGCAAGGGTAGGT 58.451 50.000 15.39 0.00 0.00 3.08 R
4729 4869 1.000993 ACTCTGATCGGGAGTGCCT 59.999 57.895 16.86 0.00 41.76 4.75 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
170 176 2.514458 TCTTCCCCTCCAATTCAAGC 57.486 50.000 0.00 0.00 0.00 4.01
186 192 1.187567 AAGCATCCAACCAACCCTGC 61.188 55.000 0.00 0.00 0.00 4.85
205 211 2.423388 CCCCCACGTAGCTACTACC 58.577 63.158 21.20 0.00 33.79 3.18
206 212 0.106318 CCCCCACGTAGCTACTACCT 60.106 60.000 21.20 0.00 33.79 3.08
207 213 1.143684 CCCCCACGTAGCTACTACCTA 59.856 57.143 21.20 0.00 33.79 3.08
208 214 2.502295 CCCCACGTAGCTACTACCTAG 58.498 57.143 21.20 7.42 33.79 3.02
210 216 3.137533 CCCACGTAGCTACTACCTAGAC 58.862 54.545 21.20 0.00 33.79 2.59
211 217 3.181456 CCCACGTAGCTACTACCTAGACT 60.181 52.174 21.20 0.00 33.79 3.24
245 251 4.025858 ACAGAGGCAGGCACGCAT 62.026 61.111 0.00 0.00 0.00 4.73
255 263 2.801063 CAGGCACGCATAATGGAAAAG 58.199 47.619 0.00 0.00 0.00 2.27
261 269 4.731773 GCACGCATAATGGAAAAGAGAAGG 60.732 45.833 0.00 0.00 0.00 3.46
262 270 3.947834 ACGCATAATGGAAAAGAGAAGGG 59.052 43.478 0.00 0.00 0.00 3.95
264 272 4.823989 CGCATAATGGAAAAGAGAAGGGAT 59.176 41.667 0.00 0.00 0.00 3.85
266 274 6.486657 CGCATAATGGAAAAGAGAAGGGATTA 59.513 38.462 0.00 0.00 0.00 1.75
378 395 3.037833 GCCAAGCAAAGCAACGGC 61.038 61.111 0.00 0.00 41.61 5.68
413 442 1.003331 CTAGCTAGGAGAACTGTCGCG 60.003 57.143 13.32 0.00 0.00 5.87
432 461 2.800629 GCGCTCTTTGCATTATTGGCAT 60.801 45.455 0.00 0.00 41.58 4.40
502 534 2.587522 CCATCCATCTAGAGACGACCA 58.412 52.381 0.00 0.00 0.00 4.02
586 628 1.402325 GGCCGGACAGTAACAAAATGC 60.402 52.381 5.05 0.00 0.00 3.56
702 762 1.222113 GCACCTAGAACCAGAGCCC 59.778 63.158 0.00 0.00 0.00 5.19
703 763 1.517832 CACCTAGAACCAGAGCCCG 59.482 63.158 0.00 0.00 0.00 6.13
704 764 2.359967 ACCTAGAACCAGAGCCCGC 61.360 63.158 0.00 0.00 0.00 6.13
705 765 2.501610 CTAGAACCAGAGCCCGCC 59.498 66.667 0.00 0.00 0.00 6.13
762 826 1.977009 GAAAAGACGGGCCAAGGGG 60.977 63.158 4.39 0.00 37.18 4.79
763 827 2.420466 GAAAAGACGGGCCAAGGGGA 62.420 60.000 4.39 0.00 35.59 4.81
1308 1397 3.056328 GTCCCGCACAAGAAGCCC 61.056 66.667 0.00 0.00 0.00 5.19
1344 1433 2.507102 CAGTACACCCTCGCGCTG 60.507 66.667 5.56 0.00 0.00 5.18
1458 1564 2.685100 GATTTCCACCTCTCGTTCGTT 58.315 47.619 0.00 0.00 0.00 3.85
1460 1566 0.039798 TTCCACCTCTCGTTCGTTCG 60.040 55.000 0.00 0.00 0.00 3.95
1462 1568 0.728466 CCACCTCTCGTTCGTTCGTC 60.728 60.000 2.67 0.00 0.00 4.20
1670 1783 4.204012 TGCCCATATTTTACCGGAAGAAG 58.796 43.478 9.46 0.00 0.00 2.85
2147 2261 0.462581 GGCTGATCATCTCGGTTGCA 60.463 55.000 0.00 0.00 32.34 4.08
2175 2295 0.179040 TCGTATCCCGGGAAATTGGC 60.179 55.000 30.84 12.76 37.11 4.52
2299 2419 1.137872 GACCACTACTGCTGGATGAGG 59.862 57.143 0.00 0.00 32.55 3.86
2437 2557 1.261480 ACTCTGACAAGCTCGTCCAT 58.739 50.000 1.52 0.00 34.88 3.41
2581 2701 1.514087 GATGTACTTCGCCACGGGA 59.486 57.895 0.00 0.00 0.00 5.14
2590 2710 2.867472 GCCACGGGAAACACATCG 59.133 61.111 0.00 0.00 0.00 3.84
2596 2716 1.337447 ACGGGAAACACATCGTACCTG 60.337 52.381 0.00 0.00 36.91 4.00
2629 2749 0.396695 CTCCAGGGATGGCAAAGCAT 60.397 55.000 0.00 0.00 0.00 3.79
2650 2770 4.179579 GGCGCGTTCTGGATTGGC 62.180 66.667 8.43 0.00 0.00 4.52
2741 2862 6.407202 ACCTATGTTCAGTTAACTGGATGTC 58.593 40.000 30.35 14.42 43.91 3.06
2887 3012 7.506328 TCAATGCTAATGAAGAATGATCCAG 57.494 36.000 0.00 0.00 0.00 3.86
2894 3019 7.806960 GCTAATGAAGAATGATCCAGCATTAAC 59.193 37.037 0.00 0.00 38.53 2.01
2895 3020 5.739752 TGAAGAATGATCCAGCATTAACG 57.260 39.130 0.00 0.00 38.53 3.18
2908 3034 6.036735 TCCAGCATTAACGCTTTCTACATTAC 59.963 38.462 0.00 0.00 41.38 1.89
3229 3355 4.960938 TGTATGCTGATTATCTGGACACC 58.039 43.478 0.41 0.00 0.00 4.16
3365 3492 9.555727 AATGTATAATGTACGTTAGCAGGAATT 57.444 29.630 12.83 5.00 0.00 2.17
3411 3538 6.255020 CCTTCAATTTGCAGCTTGATTACATC 59.745 38.462 12.20 0.00 31.83 3.06
3468 3595 2.555325 GGGTTTTGGAAAGAAGTACCCG 59.445 50.000 0.00 0.00 34.90 5.28
3651 3778 6.017026 TCCGCACAAATTACAATTACACAGAA 60.017 34.615 0.00 0.00 0.00 3.02
3657 3784 8.789762 ACAAATTACAATTACACAGAACCTACC 58.210 33.333 0.00 0.00 0.00 3.18
4147 4275 3.250762 TGTGTGACTTTCATACAGCTTGC 59.749 43.478 1.99 0.00 42.30 4.01
4199 4327 2.063156 TGCGCATGTTCACCAAATTC 57.937 45.000 5.66 0.00 0.00 2.17
4200 4328 1.336702 TGCGCATGTTCACCAAATTCC 60.337 47.619 5.66 0.00 0.00 3.01
4219 4347 9.814899 CAAATTCCCAAACATTATATAGCAACA 57.185 29.630 0.00 0.00 0.00 3.33
4225 4353 8.562892 CCCAAACATTATATAGCAACAGAGAAG 58.437 37.037 0.00 0.00 0.00 2.85
4321 4449 5.866633 TGAACAGAAAACACACAATTTCACC 59.133 36.000 0.00 0.00 37.87 4.02
4362 4490 6.413783 TCTGGTAAACTGAACATGTGTAGA 57.586 37.500 14.53 0.00 0.00 2.59
4370 4498 3.512496 TGAACATGTGTAGACCTGGGTA 58.488 45.455 0.00 0.00 0.00 3.69
4377 4505 5.223449 TGTGTAGACCTGGGTAAGAAAAG 57.777 43.478 0.00 0.00 0.00 2.27
4396 4524 7.274447 AGAAAAGCAAATTCCTTGTGATGAAA 58.726 30.769 0.00 0.00 37.36 2.69
4452 4580 1.879380 TGGTCATGCTGCAAACTACAC 59.121 47.619 6.36 0.00 0.00 2.90
4506 4634 4.083565 ACCACTTGTAAACAACAACAGGT 58.916 39.130 0.00 4.51 43.22 4.00
4603 4742 2.099141 TCCACTTCATCTTTGCCTCG 57.901 50.000 0.00 0.00 0.00 4.63
4608 4747 2.224523 ACTTCATCTTTGCCTCGGAACA 60.225 45.455 0.00 0.00 0.00 3.18
4645 4784 0.539051 TTGGTGGTGTTTTGGGCTTG 59.461 50.000 0.00 0.00 0.00 4.01
4656 4795 5.406477 GTGTTTTGGGCTTGAATCTCATTTC 59.594 40.000 0.00 0.00 0.00 2.17
4657 4796 5.070180 TGTTTTGGGCTTGAATCTCATTTCA 59.930 36.000 0.00 0.00 33.89 2.69
4658 4797 6.168389 GTTTTGGGCTTGAATCTCATTTCAT 58.832 36.000 0.00 0.00 35.64 2.57
4665 4805 6.474751 GGCTTGAATCTCATTTCATTAAGTGC 59.525 38.462 0.00 0.00 35.64 4.40
4721 4861 3.998099 AGGCTCTTTCAACAAAGCTTC 57.002 42.857 0.00 0.00 39.23 3.86
4729 4869 3.586470 TCAACAAAGCTTCCTACCCAA 57.414 42.857 0.00 0.00 0.00 4.12
4744 4884 1.153289 CCAAGGCACTCCCGATCAG 60.153 63.158 0.00 0.00 38.49 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 176 1.984026 GGGCAGGGTTGGTTGGATG 60.984 63.158 0.00 0.00 0.00 3.51
206 212 9.877222 TCTGTGGAATGGATAATAGTTAGTCTA 57.123 33.333 0.00 0.00 0.00 2.59
207 213 8.783660 TCTGTGGAATGGATAATAGTTAGTCT 57.216 34.615 0.00 0.00 0.00 3.24
208 214 8.091449 CCTCTGTGGAATGGATAATAGTTAGTC 58.909 40.741 0.00 0.00 38.35 2.59
210 216 6.876257 GCCTCTGTGGAATGGATAATAGTTAG 59.124 42.308 0.00 0.00 38.35 2.34
211 217 6.328934 TGCCTCTGTGGAATGGATAATAGTTA 59.671 38.462 0.00 0.00 38.35 2.24
255 263 5.411669 TGCGTCTTTCTTTTAATCCCTTCTC 59.588 40.000 0.00 0.00 0.00 2.87
261 269 4.105486 GCCATGCGTCTTTCTTTTAATCC 58.895 43.478 0.00 0.00 0.00 3.01
262 270 4.732784 TGCCATGCGTCTTTCTTTTAATC 58.267 39.130 0.00 0.00 0.00 1.75
264 272 4.484236 CATGCCATGCGTCTTTCTTTTAA 58.516 39.130 0.00 0.00 0.00 1.52
266 274 2.950433 CATGCCATGCGTCTTTCTTTT 58.050 42.857 0.00 0.00 0.00 2.27
359 367 1.950630 CCGTTGCTTTGCTTGGCAC 60.951 57.895 0.00 0.00 38.71 5.01
413 442 4.049186 CAGATGCCAATAATGCAAAGAGC 58.951 43.478 0.00 0.00 42.92 4.09
432 461 3.732169 CGAGAGAGATTTTACTGCGCAGA 60.732 47.826 42.03 23.26 0.00 4.26
702 762 2.825836 GATGGGTTGGCTCTGGCG 60.826 66.667 0.00 0.00 39.81 5.69
703 763 2.440980 GGATGGGTTGGCTCTGGC 60.441 66.667 0.00 0.00 37.82 4.85
704 764 1.987807 ATCGGATGGGTTGGCTCTGG 61.988 60.000 0.00 0.00 0.00 3.86
705 765 0.758734 TATCGGATGGGTTGGCTCTG 59.241 55.000 0.00 0.00 0.00 3.35
762 826 2.170273 GGCGTTGCTTTCGTCGTC 59.830 61.111 0.00 0.00 0.00 4.20
763 827 3.343421 GGGCGTTGCTTTCGTCGT 61.343 61.111 0.00 0.00 33.53 4.34
998 1087 3.782443 GGTCCCGCCCGAACATCT 61.782 66.667 0.00 0.00 0.00 2.90
1320 1409 3.001406 AGGGTGTACTGGTCCGGC 61.001 66.667 0.00 0.00 0.00 6.13
1323 1412 2.577593 GCGAGGGTGTACTGGTCC 59.422 66.667 0.00 0.00 0.00 4.46
1344 1433 1.154150 GAACATGAGCGCCTTGTGC 60.154 57.895 2.29 5.47 39.59 4.57
1458 1564 0.614979 CAGGGAGAGGAAAGGGACGA 60.615 60.000 0.00 0.00 0.00 4.20
1460 1566 1.201429 TGCAGGGAGAGGAAAGGGAC 61.201 60.000 0.00 0.00 0.00 4.46
1462 1568 1.204113 AGTGCAGGGAGAGGAAAGGG 61.204 60.000 0.00 0.00 0.00 3.95
1670 1783 5.515797 AGTTACTTTTTCCAAGGTGAAGC 57.484 39.130 0.00 0.00 0.00 3.86
1724 1837 8.938883 TCCTATGAATAGATAGTTCCTTTTGCT 58.061 33.333 0.00 0.00 32.05 3.91
1748 1861 2.009774 TGCGCTCTATTTTTGCTCTCC 58.990 47.619 9.73 0.00 0.00 3.71
1761 1875 0.601311 GAACTCACAAGGTGCGCTCT 60.601 55.000 9.73 3.07 32.98 4.09
2160 2277 1.381191 GTGGCCAATTTCCCGGGAT 60.381 57.895 27.48 7.61 0.00 3.85
2175 2295 3.276857 CTCAATTGAGTGGATCTGGTGG 58.723 50.000 24.65 0.00 37.40 4.61
2211 2331 7.470079 CAACAAGAAGTTCATATGACATCAGG 58.530 38.462 4.48 3.62 38.74 3.86
2299 2419 4.517285 TCTTGTAATCAATGTCCTCTGGC 58.483 43.478 0.00 0.00 32.82 4.85
2377 2497 2.355445 CTATGGAAGCCGCAGCGAGA 62.355 60.000 18.75 0.00 46.67 4.04
2383 2503 0.323302 TGAACACTATGGAAGCCGCA 59.677 50.000 0.00 0.00 0.00 5.69
2386 2506 3.010420 GTCCTTGAACACTATGGAAGCC 58.990 50.000 0.00 0.00 0.00 4.35
2437 2557 3.947459 TACAGCGCCTTGGCACCA 61.947 61.111 2.29 0.00 34.64 4.17
2590 2710 0.525668 CTGTGGCGATCGTCAGGTAC 60.526 60.000 24.93 12.03 0.00 3.34
2596 2716 2.583593 GGAGCTGTGGCGATCGTC 60.584 66.667 13.98 13.98 44.37 4.20
2599 2719 2.202987 CCTGGAGCTGTGGCGATC 60.203 66.667 0.00 0.00 44.37 3.69
2629 2749 3.899981 AATCCAGAACGCGCCTGCA 62.900 57.895 19.80 9.06 42.97 4.41
2650 2770 2.496899 ACACTCCATAGTTTGGGCTG 57.503 50.000 0.00 0.00 46.45 4.85
2762 2883 5.105146 TGCTTGTTTGTTATTCCTTTGGTGT 60.105 36.000 0.00 0.00 0.00 4.16
2887 3012 4.664851 GCGTAATGTAGAAAGCGTTAATGC 59.335 41.667 11.89 11.89 0.00 3.56
2894 3019 2.268298 ACCTGCGTAATGTAGAAAGCG 58.732 47.619 0.00 0.00 30.84 4.68
2895 3020 3.933332 AGAACCTGCGTAATGTAGAAAGC 59.067 43.478 0.00 0.00 30.84 3.51
2908 3034 1.018226 CCTGCTGAGAAGAACCTGCG 61.018 60.000 0.00 0.00 0.00 5.18
3229 3355 1.153369 CCACCCTGGTGTATCTGCG 60.153 63.158 14.89 0.00 44.02 5.18
3362 3489 6.431234 GGGTTCTGAGTGTCAATTGACTAATT 59.569 38.462 32.57 18.42 44.99 1.40
3365 3492 4.593206 AGGGTTCTGAGTGTCAATTGACTA 59.407 41.667 32.57 19.57 44.99 2.59
3382 3509 3.062042 CAAGCTGCAAATTGAAGGGTTC 58.938 45.455 2.74 0.00 0.00 3.62
3411 3538 2.286365 TTTGTGGGTTCTTGCCTAGG 57.714 50.000 3.67 3.67 0.00 3.02
3651 3778 1.549203 CATTTGCTGCAAGGGTAGGT 58.451 50.000 15.39 0.00 0.00 3.08
3676 3803 3.575256 AGAGAAATCAATGCTGCAACCAA 59.425 39.130 6.36 0.00 0.00 3.67
4011 4139 5.535030 GGAATATGGATAACAACAAGGACCC 59.465 44.000 0.00 0.00 0.00 4.46
4199 4327 8.450578 TTCTCTGTTGCTATATAATGTTTGGG 57.549 34.615 0.00 0.00 0.00 4.12
4200 4328 8.562892 CCTTCTCTGTTGCTATATAATGTTTGG 58.437 37.037 0.00 0.00 0.00 3.28
4219 4347 8.001875 TCTATATTAGAAGTCACTGCCTTCTCT 58.998 37.037 5.61 0.00 44.00 3.10
4321 4449 5.540911 ACCAGAATTGCCAGTAAATTGTTG 58.459 37.500 0.00 0.00 0.00 3.33
4362 4490 4.283467 GGAATTTGCTTTTCTTACCCAGGT 59.717 41.667 0.00 0.00 0.00 4.00
4370 4498 6.819284 TCATCACAAGGAATTTGCTTTTCTT 58.181 32.000 0.00 0.00 40.59 2.52
4452 4580 5.416083 TGTTACTGTACATTTCTGGGATCG 58.584 41.667 0.00 0.00 0.00 3.69
4506 4634 1.737355 GCAACAGCCAACAAGCCTGA 61.737 55.000 0.00 0.00 0.00 3.86
4603 4742 4.389374 TCAGAACTCACAGGATTTGTTCC 58.611 43.478 0.00 0.00 45.85 3.62
4608 4747 4.763793 CACCAATCAGAACTCACAGGATTT 59.236 41.667 0.00 0.00 0.00 2.17
4645 4784 9.080915 GGAAAAGCACTTAATGAAATGAGATTC 57.919 33.333 0.00 0.00 0.00 2.52
4656 4795 2.497273 CCCAGGGGAAAAGCACTTAATG 59.503 50.000 0.00 0.00 37.50 1.90
4657 4796 2.381961 TCCCAGGGGAAAAGCACTTAAT 59.618 45.455 5.33 0.00 42.05 1.40
4658 4797 1.783979 TCCCAGGGGAAAAGCACTTAA 59.216 47.619 5.33 0.00 42.05 1.85
4729 4869 1.000993 ACTCTGATCGGGAGTGCCT 59.999 57.895 16.86 0.00 41.76 4.75
4744 4884 4.377841 GCATGTGTAAGCTGTTGAAGACTC 60.378 45.833 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.