Multiple sequence alignment - TraesCS1A01G214300

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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 TraesCS1A01G214300 chr1A 100.000 4072 0 0 1 4072 377426552 377430623 0.000000e+00 7520
1 TraesCS1A01G214300 chr1B 95.312 4032 132 21 68 4072 409626980 409630981 0.000000e+00 6346
2 TraesCS1A01G214300 chr1D 93.509 4067 162 46 67 4072 302816512 302820537 0.000000e+00 5954
3 TraesCS1A01G214300 chr1D 95.775 71 2 1 3 72 302816408 302816478 3.330000e-21 113


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 TraesCS1A01G214300 chr1A 377426552 377430623 4071 False 7520.0 7520 100.000 1 4072 1 chr1A.!!$F1 4071
1 TraesCS1A01G214300 chr1B 409626980 409630981 4001 False 6346.0 6346 95.312 68 4072 1 chr1B.!!$F1 4004
2 TraesCS1A01G214300 chr1D 302816408 302820537 4129 False 3033.5 5954 94.642 3 4072 2 chr1D.!!$F1 4069

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
360 401 0.028770 CGTCAACGTTGCCAACATGT 59.971 50.0 23.47 0.00 34.11 3.21 F
832 898 0.106268 TTGGTCCAGCTTCAGCCAAA 60.106 50.0 6.39 0.00 43.38 3.28 F
1417 1483 0.673022 GCCAGCACCTGAGTCTTCTG 60.673 60.0 0.00 0.00 32.44 3.02 F
1587 1653 1.321474 TGCTTTCCTGCAGGTTGAAG 58.679 50.0 31.58 28.83 38.12 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2066 0.557729 ATAGCCCAAATCCCTGGTGG 59.442 55.000 0.00 0.0 34.33 4.61 R
2756 2840 1.019278 ATACCGCTTTGGCAGTCACG 61.019 55.000 0.00 0.0 43.94 4.35 R
2964 3048 1.972588 AAGGCCCTACCAATCTGTCT 58.027 50.000 0.00 0.0 43.14 3.41 R
3548 3641 3.434299 CAGCAAGGAAATGTGATTTTGCC 59.566 43.478 3.65 0.0 35.28 4.52 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
50 51 1.345176 CGATCGACAAAGAAGCCGC 59.655 57.895 10.26 0.00 0.00 6.53
59 60 3.347216 ACAAAGAAGCCGCAAGATACAT 58.653 40.909 0.00 0.00 43.02 2.29
264 305 5.971763 TCACTAGCTTCTCTTCTGGAAATC 58.028 41.667 0.00 0.00 0.00 2.17
311 352 1.155889 TAGCAGACGCCACATGTTTG 58.844 50.000 0.00 0.00 39.83 2.93
346 387 2.228582 CTGATTGAAATGGTGCCGTCAA 59.771 45.455 4.89 4.89 34.68 3.18
349 390 0.816018 TGAAATGGTGCCGTCAACGT 60.816 50.000 1.48 0.00 37.74 3.99
350 391 0.309612 GAAATGGTGCCGTCAACGTT 59.690 50.000 0.00 0.00 40.66 3.99
351 392 0.030101 AAATGGTGCCGTCAACGTTG 59.970 50.000 22.35 22.35 38.12 4.10
352 393 2.400896 AATGGTGCCGTCAACGTTGC 62.401 55.000 23.47 16.53 37.71 4.17
353 394 4.322385 GGTGCCGTCAACGTTGCC 62.322 66.667 23.47 11.79 37.74 4.52
354 395 3.578272 GTGCCGTCAACGTTGCCA 61.578 61.111 23.47 13.75 37.74 4.92
355 396 2.824489 TGCCGTCAACGTTGCCAA 60.824 55.556 23.47 3.51 37.74 4.52
356 397 2.353030 GCCGTCAACGTTGCCAAC 60.353 61.111 23.47 15.09 37.74 3.77
357 398 3.102985 CCGTCAACGTTGCCAACA 58.897 55.556 23.47 2.69 37.74 3.33
358 399 1.652012 CCGTCAACGTTGCCAACAT 59.348 52.632 23.47 0.00 37.74 2.71
359 400 0.660005 CCGTCAACGTTGCCAACATG 60.660 55.000 23.47 10.87 37.74 3.21
360 401 0.028770 CGTCAACGTTGCCAACATGT 59.971 50.000 23.47 0.00 34.11 3.21
361 402 1.532921 CGTCAACGTTGCCAACATGTT 60.533 47.619 23.47 4.92 34.11 2.71
362 403 2.116366 GTCAACGTTGCCAACATGTTC 58.884 47.619 23.47 0.00 0.00 3.18
363 404 2.020720 TCAACGTTGCCAACATGTTCT 58.979 42.857 23.47 0.00 0.00 3.01
390 431 8.817100 TGTCTGCATCTACTTAATTATTTCACG 58.183 33.333 0.00 0.00 0.00 4.35
402 443 8.789825 TTAATTATTTCACGGGTTAGTTAGCA 57.210 30.769 0.00 0.00 0.00 3.49
407 448 2.028748 TCACGGGTTAGTTAGCACTTCC 60.029 50.000 0.00 0.00 34.06 3.46
417 458 5.874895 AGTTAGCACTTCCGTTAAATTCC 57.125 39.130 0.00 0.00 0.00 3.01
426 467 1.611148 CCGTTAAATTCCGGTGGTGGA 60.611 52.381 0.00 0.00 39.38 4.02
473 514 2.425143 TTGATCCCACTGATTGGCTC 57.575 50.000 0.00 0.00 45.37 4.70
476 517 2.092753 TGATCCCACTGATTGGCTCTTC 60.093 50.000 0.00 0.00 45.37 2.87
477 518 0.620556 TCCCACTGATTGGCTCTTCC 59.379 55.000 0.00 0.00 45.37 3.46
493 534 0.401738 TTCCTGTCTTGGGCTCTTGG 59.598 55.000 0.00 0.00 0.00 3.61
500 541 1.228552 TTGGGCTCTTGGTCTTGCC 60.229 57.895 0.00 0.00 44.22 4.52
620 671 7.329717 CAGAGTTCTTTATGTGTCCTTCAGTAC 59.670 40.741 0.00 0.00 0.00 2.73
707 773 0.313043 CTGAACTTTGCTGGGCACTG 59.687 55.000 0.00 0.00 38.71 3.66
753 819 5.300539 GGGATTGGCTAGAGAAAGGAATTTC 59.699 44.000 0.00 0.00 0.00 2.17
756 822 5.762179 TGGCTAGAGAAAGGAATTTCTGA 57.238 39.130 7.91 0.00 41.02 3.27
832 898 0.106268 TTGGTCCAGCTTCAGCCAAA 60.106 50.000 6.39 0.00 43.38 3.28
887 953 4.517285 TCATTGTCTGGTTCCTATTGCTC 58.483 43.478 0.00 0.00 0.00 4.26
907 973 4.829492 GCTCCCTGATTTTATAAGGCATGT 59.171 41.667 0.00 0.00 28.41 3.21
999 1065 0.961019 TGGAAAAGCGAGCTTGCATT 59.039 45.000 27.59 19.37 36.26 3.56
1005 1071 1.303309 AGCGAGCTTGCATTATGGAC 58.697 50.000 27.59 0.00 37.31 4.02
1155 1221 2.834638 CCAGTTCAAGGGGATCCATT 57.165 50.000 15.23 4.73 34.83 3.16
1188 1254 1.175983 AGATGGGCGACTCGATCCTC 61.176 60.000 1.63 3.44 0.00 3.71
1243 1309 2.612672 CAGTTGCTAGGTGATGCTGATG 59.387 50.000 0.00 0.00 0.00 3.07
1304 1370 1.765314 GCTAGCCTTGGAAGATGAGGA 59.235 52.381 2.29 0.00 32.11 3.71
1305 1371 2.371510 GCTAGCCTTGGAAGATGAGGAT 59.628 50.000 2.29 0.00 33.13 3.24
1316 1382 7.002250 TGGAAGATGAGGATGATGAAGATAC 57.998 40.000 0.00 0.00 0.00 2.24
1417 1483 0.673022 GCCAGCACCTGAGTCTTCTG 60.673 60.000 0.00 0.00 32.44 3.02
1492 1558 6.694447 AGTTCAGTGATTGCTTGCAATTATT 58.306 32.000 19.90 11.32 0.00 1.40
1534 1600 1.871080 GCACTATTGCGAGGCTGTAT 58.129 50.000 0.00 0.00 39.50 2.29
1536 1602 2.138320 CACTATTGCGAGGCTGTATGG 58.862 52.381 0.00 0.00 0.00 2.74
1587 1653 1.321474 TGCTTTCCTGCAGGTTGAAG 58.679 50.000 31.58 28.83 38.12 3.02
1616 1682 3.068307 TGCTTTCTCGGAGGCTAGATTAC 59.932 47.826 4.96 0.00 0.00 1.89
1649 1715 1.851304 TCCATTTAGCTGCCTTTGGG 58.149 50.000 0.00 0.00 0.00 4.12
1665 1731 4.841813 CCTTTGGGTTATTTGGGGTAACTT 59.158 41.667 0.00 0.00 33.60 2.66
1770 1849 8.418662 GTTCAGGGGACATTTTTACTTTAAACT 58.581 33.333 0.00 0.00 0.00 2.66
1771 1850 8.173542 TCAGGGGACATTTTTACTTTAAACTC 57.826 34.615 0.00 0.00 0.00 3.01
1772 1851 7.780745 TCAGGGGACATTTTTACTTTAAACTCA 59.219 33.333 0.00 0.00 0.00 3.41
1773 1852 8.585018 CAGGGGACATTTTTACTTTAAACTCAT 58.415 33.333 0.00 0.00 0.00 2.90
1774 1853 8.585018 AGGGGACATTTTTACTTTAAACTCATG 58.415 33.333 0.00 0.00 0.00 3.07
1969 2052 7.302948 ACATGGTATGTTCTATCCTGTACCTA 58.697 38.462 0.00 0.00 41.63 3.08
2150 2234 2.368875 CGGATACATGGGAAGCCTTACT 59.631 50.000 0.00 0.00 0.00 2.24
2284 2368 9.169592 GTGCTATTAGTCCAAAATTAGTTACCA 57.830 33.333 0.00 0.00 0.00 3.25
2839 2923 6.150140 GTGTTGCTATCTCTCTGATTGGTTTT 59.850 38.462 0.00 0.00 36.65 2.43
3133 3217 0.675633 GCTGGTTGCAACATCCAAGT 59.324 50.000 29.55 0.00 42.31 3.16
3266 3358 2.289274 TGTTTGTACACAACATCTGCCG 59.711 45.455 15.24 0.00 38.10 5.69
3268 3360 1.790755 TGTACACAACATCTGCCGTC 58.209 50.000 0.00 0.00 31.43 4.79
3269 3361 1.069358 TGTACACAACATCTGCCGTCA 59.931 47.619 0.00 0.00 31.43 4.35
3280 3372 1.138859 TCTGCCGTCATAATCCTGTGG 59.861 52.381 0.00 0.00 0.00 4.17
3362 3454 8.886719 AGGTATGCATATGAAATGAATGTATCG 58.113 33.333 10.16 0.00 30.19 2.92
3382 3475 4.382291 TCGCCTGTAGTAGCAAAAGAAAA 58.618 39.130 0.00 0.00 0.00 2.29
3548 3641 3.674997 ACACAACTACATGCTAACCTGG 58.325 45.455 0.00 0.00 0.00 4.45
3631 3725 5.994054 ACACAGATGCAGATACAATATGGAC 59.006 40.000 0.00 0.00 0.00 4.02
3738 3854 2.159296 CCATTGGCATGTGACATGACAG 60.159 50.000 30.37 21.06 38.44 3.51
3869 3985 3.560251 ACCACGCCCAGCAGAACT 61.560 61.111 0.00 0.00 0.00 3.01
3871 3987 2.345244 CACGCCCAGCAGAACTCT 59.655 61.111 0.00 0.00 0.00 3.24
3973 4094 6.183360 CCAGTCTCTGTTCACAAAAGAATGTT 60.183 38.462 13.87 0.00 31.93 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.381056 GCAGGAGCAGGAGAGAGGA 60.381 63.158 0.00 0.00 41.58 3.71
1 2 3.219224 GCAGGAGCAGGAGAGAGG 58.781 66.667 0.00 0.00 41.58 3.69
50 51 1.534163 CGGAGCCATGCATGTATCTTG 59.466 52.381 24.58 13.88 0.00 3.02
264 305 4.202050 GGCTGCTACTGGATAAACAAATGG 60.202 45.833 0.00 0.00 0.00 3.16
346 387 1.748493 ACAAGAACATGTTGGCAACGT 59.252 42.857 24.03 21.64 42.51 3.99
349 390 2.223782 GCAGACAAGAACATGTTGGCAA 60.224 45.455 17.58 0.00 35.14 4.52
350 391 1.337703 GCAGACAAGAACATGTTGGCA 59.662 47.619 17.58 0.00 35.14 4.92
351 392 1.337703 TGCAGACAAGAACATGTTGGC 59.662 47.619 17.58 4.52 34.91 4.52
352 393 3.504906 AGATGCAGACAAGAACATGTTGG 59.495 43.478 17.58 7.84 32.57 3.77
353 394 4.761235 AGATGCAGACAAGAACATGTTG 57.239 40.909 17.58 4.99 32.57 3.33
354 395 5.555017 AGTAGATGCAGACAAGAACATGTT 58.445 37.500 11.78 11.78 32.57 2.71
355 396 5.157940 AGTAGATGCAGACAAGAACATGT 57.842 39.130 0.00 0.00 35.90 3.21
356 397 7.601073 TTAAGTAGATGCAGACAAGAACATG 57.399 36.000 0.00 0.00 0.00 3.21
357 398 8.798859 AATTAAGTAGATGCAGACAAGAACAT 57.201 30.769 0.00 0.00 0.00 2.71
358 399 9.890629 ATAATTAAGTAGATGCAGACAAGAACA 57.109 29.630 0.00 0.00 0.00 3.18
390 431 2.756840 ACGGAAGTGCTAACTAACCC 57.243 50.000 0.00 0.00 46.97 4.11
407 448 1.810959 TCCACCACCGGAATTTAACG 58.189 50.000 9.46 0.00 29.93 3.18
432 473 3.923017 ATCCAAAAGAAGAGCCAAACG 57.077 42.857 0.00 0.00 0.00 3.60
473 514 1.612726 CCAAGAGCCCAAGACAGGAAG 60.613 57.143 0.00 0.00 0.00 3.46
476 517 0.322008 GACCAAGAGCCCAAGACAGG 60.322 60.000 0.00 0.00 0.00 4.00
477 518 0.689623 AGACCAAGAGCCCAAGACAG 59.310 55.000 0.00 0.00 0.00 3.51
493 534 0.536006 ACACCAGCTGAAGGCAAGAC 60.536 55.000 17.39 0.00 44.79 3.01
500 541 2.103263 GGATAGGGTACACCAGCTGAAG 59.897 54.545 17.39 9.67 43.89 3.02
547 588 7.567622 ACACATGGGGTACTGAAGTAACTATAT 59.432 37.037 0.00 0.00 38.26 0.86
556 606 4.191544 CACATACACATGGGGTACTGAAG 58.808 47.826 0.00 0.00 36.39 3.02
610 661 7.182817 ACATAGCTGTTTATGTACTGAAGGA 57.817 36.000 0.00 0.00 41.28 3.36
625 676 7.951591 ACAAAAGGTGAAAATAACATAGCTGT 58.048 30.769 0.00 0.00 37.12 4.40
707 773 6.027749 CCCAACGAGTTCAAAACATATTAGC 58.972 40.000 0.00 0.00 0.00 3.09
780 846 6.436843 AAACATATTAGTACTGCACAAGGC 57.563 37.500 5.39 0.00 45.13 4.35
832 898 9.813826 CAAAGAGATAGATTGGGGGTATATTTT 57.186 33.333 0.00 0.00 0.00 1.82
887 953 7.233348 ACCAATACATGCCTTATAAAATCAGGG 59.767 37.037 0.00 0.00 0.00 4.45
907 973 5.651387 TTCAAAATCAATCGCCACCAATA 57.349 34.783 0.00 0.00 0.00 1.90
948 1014 2.168106 AGAGATGTAAGAGCACTGCCAG 59.832 50.000 0.00 0.00 0.00 4.85
999 1065 4.851843 TCCTAGTTGAAGAGTCGTCCATA 58.148 43.478 3.50 0.00 0.00 2.74
1005 1071 1.819288 TGGCTCCTAGTTGAAGAGTCG 59.181 52.381 0.00 0.00 34.96 4.18
1188 1254 2.731572 AGGGAATGCCTCATTGAGTTG 58.268 47.619 12.54 0.00 33.90 3.16
1243 1309 3.130160 CTGAGCCAAAGCCGAGCC 61.130 66.667 0.00 0.00 41.25 4.70
1304 1370 7.308770 CCAATGTATTTGCCGTATCTTCATCAT 60.309 37.037 0.00 0.00 33.73 2.45
1305 1371 6.017192 CCAATGTATTTGCCGTATCTTCATCA 60.017 38.462 0.00 0.00 33.73 3.07
1316 1382 4.368874 TGTTGATCCAATGTATTTGCCG 57.631 40.909 0.00 0.00 33.73 5.69
1472 1538 8.637281 TGATTAATAATTGCAAGCAATCACTG 57.363 30.769 19.42 0.00 44.86 3.66
1525 1591 2.918712 ATAGCACACCATACAGCCTC 57.081 50.000 0.00 0.00 0.00 4.70
1534 1600 6.591001 TCATTTTAGCATCTATAGCACACCA 58.409 36.000 0.00 0.00 0.00 4.17
1536 1602 7.919690 TGTTCATTTTAGCATCTATAGCACAC 58.080 34.615 0.00 0.00 0.00 3.82
1587 1653 4.826556 AGCCTCCGAGAAAGCATATATTC 58.173 43.478 0.00 0.00 0.00 1.75
1616 1682 4.212214 GCTAAATGGATCAGGTAAGAAGCG 59.788 45.833 0.00 0.00 0.00 4.68
1649 1715 6.644248 ACAGTGAAAGTTACCCCAAATAAC 57.356 37.500 0.00 0.00 33.50 1.89
1665 1731 7.633193 AACACCTAATACAAACAACAGTGAA 57.367 32.000 0.00 0.00 0.00 3.18
1718 1797 5.220381 TCATCGATCTTCCGCTACATTTAC 58.780 41.667 0.00 0.00 0.00 2.01
1770 1849 4.522722 TGTTTTCTGAATGCATGCATGA 57.477 36.364 32.79 22.43 36.68 3.07
1771 1850 5.794687 AATGTTTTCTGAATGCATGCATG 57.205 34.783 32.79 22.70 36.68 4.06
1772 1851 6.314400 GGTAAATGTTTTCTGAATGCATGCAT 59.686 34.615 27.46 27.46 38.46 3.96
1773 1852 5.638657 GGTAAATGTTTTCTGAATGCATGCA 59.361 36.000 25.04 25.04 0.00 3.96
1774 1853 5.220265 CGGTAAATGTTTTCTGAATGCATGC 60.220 40.000 11.82 11.82 0.00 4.06
1983 2066 0.557729 ATAGCCCAAATCCCTGGTGG 59.442 55.000 0.00 0.00 34.33 4.61
2150 2234 2.626785 TGATTCCACCCACTGAAGGTA 58.373 47.619 0.00 0.00 35.24 3.08
2705 2789 1.086696 CATTGGCTACAAGTGTCCCG 58.913 55.000 0.00 0.00 40.49 5.14
2756 2840 1.019278 ATACCGCTTTGGCAGTCACG 61.019 55.000 0.00 0.00 43.94 4.35
2762 2846 3.485463 AGCTATTATACCGCTTTGGCA 57.515 42.857 0.00 0.00 43.94 4.92
2776 2860 7.497909 ACCGTATAAACACATGCTTTAGCTATT 59.502 33.333 3.10 0.00 42.66 1.73
2839 2923 6.428083 TTGTATTCACCTACAGAAAGACCA 57.572 37.500 0.00 0.00 33.38 4.02
2964 3048 1.972588 AAGGCCCTACCAATCTGTCT 58.027 50.000 0.00 0.00 43.14 3.41
3133 3217 3.733443 TGCTGAGAATTGCGCTATCTA 57.267 42.857 9.73 0.00 0.00 1.98
3266 3358 4.113354 GTTCTCGTCCACAGGATTATGAC 58.887 47.826 0.00 0.00 32.73 3.06
3268 3360 4.123497 TGTTCTCGTCCACAGGATTATG 57.877 45.455 0.00 0.00 32.73 1.90
3269 3361 4.202264 GGATGTTCTCGTCCACAGGATTAT 60.202 45.833 2.09 0.00 46.10 1.28
3362 3454 5.827666 TGTTTTTCTTTTGCTACTACAGGC 58.172 37.500 0.00 0.00 0.00 4.85
3548 3641 3.434299 CAGCAAGGAAATGTGATTTTGCC 59.566 43.478 3.65 0.00 35.28 4.52
3738 3854 2.686558 TTGTCAAGCAAACATCGCTC 57.313 45.000 0.00 0.00 39.29 5.03
3869 3985 0.252421 AGGGACCTGCAGACATGAGA 60.252 55.000 17.39 0.00 0.00 3.27
3871 3987 0.615331 GAAGGGACCTGCAGACATGA 59.385 55.000 17.39 0.00 0.00 3.07
3973 4094 3.675775 GCTGTTTGTTCTTTGCACAGGAA 60.676 43.478 0.00 0.00 36.22 3.36


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

AutoCloner maintained by Alex Coulton.