Multiple sequence alignment - TraesCS1A01G284700

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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 TraesCS1A01G284700 chr1A 100.000 3623 0 0 1 3623 482247621 482251243 0.000000e+00 6691
1 TraesCS1A01G284700 chr1A 82.558 2299 323 52 836 3080 124897914 124895640 0.000000e+00 1953
2 TraesCS1A01G284700 chr1D 92.574 3030 157 23 631 3623 381973570 381976568 0.000000e+00 4287
3 TraesCS1A01G284700 chr1D 83.333 2298 302 47 836 3078 114366058 114363787 0.000000e+00 2047
4 TraesCS1A01G284700 chr1D 89.679 717 40 21 1 703 381972976 381973672 0.000000e+00 883
5 TraesCS1A01G284700 chr1B 91.454 3089 175 43 1 3051 511972301 511975338 0.000000e+00 4159
6 TraesCS1A01G284700 chr1B 83.185 2248 306 39 877 3078 175429776 175427555 0.000000e+00 1991
7 TraesCS1A01G284700 chr1B 94.217 415 22 1 3048 3462 511977563 511977975 1.840000e-177 632
8 TraesCS1A01G284700 chr5D 78.847 1631 273 34 882 2455 40929133 40927518 0.000000e+00 1035


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 TraesCS1A01G284700 chr1A 482247621 482251243 3622 False 6691.0 6691 100.0000 1 3623 1 chr1A.!!$F1 3622
1 TraesCS1A01G284700 chr1A 124895640 124897914 2274 True 1953.0 1953 82.5580 836 3080 1 chr1A.!!$R1 2244
2 TraesCS1A01G284700 chr1D 381972976 381976568 3592 False 2585.0 4287 91.1265 1 3623 2 chr1D.!!$F1 3622
3 TraesCS1A01G284700 chr1D 114363787 114366058 2271 True 2047.0 2047 83.3330 836 3078 1 chr1D.!!$R1 2242
4 TraesCS1A01G284700 chr1B 511972301 511977975 5674 False 2395.5 4159 92.8355 1 3462 2 chr1B.!!$F1 3461
5 TraesCS1A01G284700 chr1B 175427555 175429776 2221 True 1991.0 1991 83.1850 877 3078 1 chr1B.!!$R1 2201
6 TraesCS1A01G284700 chr5D 40927518 40929133 1615 True 1035.0 1035 78.8470 882 2455 1 chr5D.!!$R1 1573

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
148 149 2.306847 TGTGTCAAAAGGGGAAAGAGC 58.693 47.619 0.00 0.0 0.00 4.09 F
1345 1458 0.231279 GTTCGACGAAATGTGTGCGT 59.769 50.000 12.67 0.0 41.45 5.24 F
1553 1669 0.321919 GGTCTGCTTGAGTGGATGCA 60.322 55.000 0.00 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 1601 0.398696 ACAGCCCCGTGACAATTGTA 59.601 50.000 11.95 0.00 0.00 2.41 R
2455 2580 3.572682 TGGAATATGCGAATAGTCTCCGT 59.427 43.478 10.54 0.00 0.00 4.69 R
3367 5723 1.066303 TGTTTCGTGCAAACCATGGAC 59.934 47.619 21.47 4.36 46.05 4.02 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
83 84 7.661437 TGTAATTTAGAAGATGCACTGTCAGTT 59.339 33.333 1.67 0.00 0.00 3.16
85 86 8.798859 AATTTAGAAGATGCACTGTCAGTTAT 57.201 30.769 1.67 0.81 0.00 1.89
142 143 2.441375 TGTCTGATGTGTCAAAAGGGGA 59.559 45.455 0.00 0.00 33.05 4.81
148 149 2.306847 TGTGTCAAAAGGGGAAAGAGC 58.693 47.619 0.00 0.00 0.00 4.09
167 168 5.336945 AGAGCTGCAGATATATGACCCTAA 58.663 41.667 20.43 0.00 0.00 2.69
221 225 8.789825 TTGGGACATATTTTCCATGAAATTTG 57.210 30.769 0.00 1.80 39.30 2.32
252 256 9.658475 TTCAAGTTCACGTATTTGTTATTCTTG 57.342 29.630 0.00 0.00 0.00 3.02
392 396 5.221126 CCACAAGGAGCATTTTTAGGATAGC 60.221 44.000 0.00 0.00 36.89 2.97
395 399 7.446625 CACAAGGAGCATTTTTAGGATAGCTAT 59.553 37.037 5.76 5.76 31.61 2.97
396 400 8.660435 ACAAGGAGCATTTTTAGGATAGCTATA 58.340 33.333 6.13 0.00 31.61 1.31
397 401 9.507329 CAAGGAGCATTTTTAGGATAGCTATAA 57.493 33.333 6.13 0.00 31.61 0.98
398 402 9.732130 AAGGAGCATTTTTAGGATAGCTATAAG 57.268 33.333 6.13 0.00 31.61 1.73
399 403 8.885346 AGGAGCATTTTTAGGATAGCTATAAGT 58.115 33.333 6.13 0.00 31.61 2.24
401 405 9.712305 GAGCATTTTTAGGATAGCTATAAGTGA 57.288 33.333 6.13 0.00 31.61 3.41
406 410 9.832445 TTTTTAGGATAGCTATAAGTGAAGTGG 57.168 33.333 6.13 0.00 0.00 4.00
407 411 8.777578 TTTAGGATAGCTATAAGTGAAGTGGA 57.222 34.615 6.13 0.00 0.00 4.02
408 412 8.777578 TTAGGATAGCTATAAGTGAAGTGGAA 57.222 34.615 6.13 0.00 0.00 3.53
424 428 7.652909 GTGAAGTGGAATGAAATGAAATGTGAA 59.347 33.333 0.00 0.00 0.00 3.18
433 438 8.767478 ATGAAATGAAATGTGAATTCCTGTTC 57.233 30.769 2.27 2.62 0.00 3.18
487 495 8.040716 ACATGAGCTTGTGTTTACTAATTACC 57.959 34.615 0.00 0.00 0.00 2.85
523 531 9.131791 GCTCTAATTTTATATTTTCCTCCCACA 57.868 33.333 0.00 0.00 0.00 4.17
570 578 4.823989 ACTTTGGACAAGGTCAAATCTCTG 59.176 41.667 0.00 0.00 33.68 3.35
595 603 7.882791 TGTTGGATATGCTCTGTTTTTCTTCTA 59.117 33.333 0.00 0.00 0.00 2.10
772 785 3.515901 AGCACTTTAGGGTCCTCTGTTAG 59.484 47.826 0.00 0.00 0.00 2.34
858 893 3.864686 CGCCGTTTCAGCCCATCG 61.865 66.667 0.00 0.00 0.00 3.84
1104 1178 1.742768 GCCTCTACCCACATCGGAG 59.257 63.158 0.00 0.00 36.56 4.63
1173 1265 2.803670 GAGCGCGACTGCAACGTA 60.804 61.111 12.10 0.00 42.97 3.57
1240 1332 2.361230 TCTTCGCCGAGCTCAGGA 60.361 61.111 23.26 10.73 0.00 3.86
1279 1392 1.273606 TGCTCTGCTACAACACTCTCC 59.726 52.381 0.00 0.00 0.00 3.71
1306 1419 1.880340 CTCGTCGAAGCTGGCCATC 60.880 63.158 5.51 0.31 0.00 3.51
1319 1432 3.174265 CCATCTGGAGGAGGCCCC 61.174 72.222 0.00 0.00 37.39 5.80
1323 1436 3.415087 CTGGAGGAGGCCCCCAAG 61.415 72.222 5.89 0.00 34.01 3.61
1339 1452 1.871039 CCAAGGTGTTCGACGAAATGT 59.129 47.619 12.67 0.00 0.00 2.71
1340 1453 2.349438 CCAAGGTGTTCGACGAAATGTG 60.349 50.000 12.67 6.46 0.00 3.21
1345 1458 0.231279 GTTCGACGAAATGTGTGCGT 59.769 50.000 12.67 0.00 41.45 5.24
1354 1467 4.927782 TGTGTGCGTCTGGGGTGC 62.928 66.667 0.00 0.00 0.00 5.01
1373 1486 4.545706 GCCCGATGCGTCATCCCA 62.546 66.667 6.75 0.00 37.57 4.37
1381 1494 0.324614 TGCGTCATCCCACAACATCT 59.675 50.000 0.00 0.00 0.00 2.90
1394 1507 2.225019 ACAACATCTTTCTCAAGCTGCG 59.775 45.455 0.00 0.00 30.42 5.18
1405 1518 3.454587 AAGCTGCGTTCGTGGACCA 62.455 57.895 0.00 0.00 0.00 4.02
1459 1575 1.078214 CGGATGCAAGAGCTTGGGA 60.078 57.895 11.78 0.00 42.74 4.37
1462 1578 1.409241 GGATGCAAGAGCTTGGGATGA 60.409 52.381 11.78 0.00 42.74 2.92
1466 1582 2.165998 GCAAGAGCTTGGGATGAAAGT 58.834 47.619 11.78 0.00 40.74 2.66
1537 1653 2.764128 TCCTCGAGGCATGGGGTC 60.764 66.667 27.39 0.00 34.44 4.46
1553 1669 0.321919 GGTCTGCTTGAGTGGATGCA 60.322 55.000 0.00 0.00 0.00 3.96
1559 1675 1.093159 CTTGAGTGGATGCAGGAAGC 58.907 55.000 0.00 0.00 45.96 3.86
1593 1709 0.321996 TGGTGCATACTTACACGCCA 59.678 50.000 0.00 0.00 40.25 5.69
1761 1880 3.441572 TCAAGCAGCTTTTAATGGAGAGC 59.558 43.478 4.38 0.00 35.42 4.09
1977 2096 1.937278 TGCTAGAGAGGAGTACGTCG 58.063 55.000 0.00 0.00 36.24 5.12
1978 2097 1.206610 TGCTAGAGAGGAGTACGTCGT 59.793 52.381 2.21 2.21 36.24 4.34
2249 2371 2.159612 GGTTTTTCTACCATCGAACGCC 60.160 50.000 0.00 0.00 38.12 5.68
2380 2505 4.367039 AAGGCCAGTAGTTGCTTTCTAA 57.633 40.909 5.01 0.00 0.00 2.10
2455 2580 3.995705 GCTTGCTTACAATGGCAAAATCA 59.004 39.130 0.00 0.00 45.80 2.57
2844 2971 6.262273 ACGGAATCTGAATTTGTAAGTGTGTT 59.738 34.615 0.00 0.00 0.00 3.32
3039 3166 3.763897 GCTTTTGAGGGAAATGGAAGCTA 59.236 43.478 0.00 0.00 36.15 3.32
3064 3956 7.054751 ACCTGTGCCTAAATAGTATTTTCCTC 58.945 38.462 13.20 4.80 0.00 3.71
3070 3962 6.768381 GCCTAAATAGTATTTTCCTCTGTGCT 59.232 38.462 13.20 0.00 0.00 4.40
3304 5660 9.603921 AAATATTTTGGCAACTGAAATATCCTG 57.396 29.630 12.76 0.00 41.14 3.86
3372 5728 1.167851 CACACTGCAATTCGGTCCAT 58.832 50.000 0.00 0.00 30.14 3.41
3456 5812 1.611673 GCTCTGTTTTCTGGCCTGCTA 60.612 52.381 3.32 0.00 0.00 3.49
3492 5849 6.395629 AGGAATTTCTTGAATGCAGACATTG 58.604 36.000 0.00 0.00 46.59 2.82
3496 5853 3.753815 TCTTGAATGCAGACATTGTGGA 58.246 40.909 0.00 0.00 46.59 4.02
3558 5915 3.552294 GCATTACTGTAGCTCCGTTTCTC 59.448 47.826 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 7.602517 ACTGACAGTGCATCTTCTAAATTAC 57.397 36.000 7.47 0.00 0.00 1.89
142 143 4.596643 AGGGTCATATATCTGCAGCTCTTT 59.403 41.667 9.47 0.00 0.00 2.52
148 149 9.708092 CATGATATTAGGGTCATATATCTGCAG 57.292 37.037 7.63 7.63 33.52 4.41
221 225 3.531262 AATACGTGAACTTGAAACCGC 57.469 42.857 0.00 0.00 0.00 5.68
252 256 1.928503 CATTGCGTTCCATTTCCATGC 59.071 47.619 0.00 0.00 0.00 4.06
395 399 8.859090 ACATTTCATTTCATTCCACTTCACTTA 58.141 29.630 0.00 0.00 0.00 2.24
396 400 7.654520 CACATTTCATTTCATTCCACTTCACTT 59.345 33.333 0.00 0.00 0.00 3.16
397 401 7.014518 TCACATTTCATTTCATTCCACTTCACT 59.985 33.333 0.00 0.00 0.00 3.41
398 402 7.147312 TCACATTTCATTTCATTCCACTTCAC 58.853 34.615 0.00 0.00 0.00 3.18
399 403 7.287512 TCACATTTCATTTCATTCCACTTCA 57.712 32.000 0.00 0.00 0.00 3.02
401 405 9.211485 GAATTCACATTTCATTTCATTCCACTT 57.789 29.630 0.00 0.00 0.00 3.16
402 406 7.820872 GGAATTCACATTTCATTTCATTCCACT 59.179 33.333 7.93 0.00 38.78 4.00
403 407 7.820872 AGGAATTCACATTTCATTTCATTCCAC 59.179 33.333 7.93 0.00 40.59 4.02
404 408 7.820386 CAGGAATTCACATTTCATTTCATTCCA 59.180 33.333 7.93 0.00 40.59 3.53
405 409 7.820872 ACAGGAATTCACATTTCATTTCATTCC 59.179 33.333 7.93 0.00 39.08 3.01
406 410 8.767478 ACAGGAATTCACATTTCATTTCATTC 57.233 30.769 7.93 0.00 0.00 2.67
407 411 9.211485 GAACAGGAATTCACATTTCATTTCATT 57.789 29.630 7.93 0.00 0.00 2.57
408 412 7.820872 GGAACAGGAATTCACATTTCATTTCAT 59.179 33.333 7.93 0.00 0.00 2.57
451 456 4.278170 CACAAGCTCATGTTCTACCCAAAA 59.722 41.667 0.00 0.00 0.00 2.44
452 457 3.820467 CACAAGCTCATGTTCTACCCAAA 59.180 43.478 0.00 0.00 0.00 3.28
453 458 3.181445 ACACAAGCTCATGTTCTACCCAA 60.181 43.478 0.00 0.00 0.00 4.12
454 459 2.371841 ACACAAGCTCATGTTCTACCCA 59.628 45.455 0.00 0.00 0.00 4.51
487 495 9.683069 AAATATAAAATTAGAGCCTGCATTTCG 57.317 29.630 0.00 0.00 0.00 3.46
570 578 7.150783 AGAAGAAAAACAGAGCATATCCAAC 57.849 36.000 0.00 0.00 0.00 3.77
744 757 4.178956 AGGACCCTAAAGTGCTCAAAAA 57.821 40.909 0.00 0.00 32.22 1.94
750 763 2.031495 ACAGAGGACCCTAAAGTGCT 57.969 50.000 0.00 0.00 41.65 4.40
752 765 3.515901 AGCTAACAGAGGACCCTAAAGTG 59.484 47.826 0.00 0.00 0.00 3.16
753 766 3.515901 CAGCTAACAGAGGACCCTAAAGT 59.484 47.826 0.00 0.00 0.00 2.66
754 767 3.118592 CCAGCTAACAGAGGACCCTAAAG 60.119 52.174 0.00 0.00 0.00 1.85
756 769 2.225547 ACCAGCTAACAGAGGACCCTAA 60.226 50.000 0.00 0.00 0.00 2.69
757 770 1.361543 ACCAGCTAACAGAGGACCCTA 59.638 52.381 0.00 0.00 0.00 3.53
758 771 0.117340 ACCAGCTAACAGAGGACCCT 59.883 55.000 0.00 0.00 0.00 4.34
759 772 0.250513 CACCAGCTAACAGAGGACCC 59.749 60.000 0.00 0.00 0.00 4.46
760 773 0.391793 GCACCAGCTAACAGAGGACC 60.392 60.000 0.00 0.00 37.91 4.46
761 774 3.145228 GCACCAGCTAACAGAGGAC 57.855 57.895 0.00 0.00 37.91 3.85
772 785 2.362120 ATTCAGCCCAGCACCAGC 60.362 61.111 0.00 0.00 42.56 4.85
858 893 4.410555 AGAGACTGATTTTGGGATAGGGAC 59.589 45.833 0.00 0.00 0.00 4.46
1240 1332 2.122099 ACTGGGGGTTCCGGAAGT 60.122 61.111 19.50 7.91 44.90 3.01
1306 1419 3.415087 CTTGGGGGCCTCCTCCAG 61.415 72.222 25.88 12.64 35.68 3.86
1319 1432 1.871039 ACATTTCGTCGAACACCTTGG 59.129 47.619 7.29 0.00 0.00 3.61
1323 1436 1.659211 GCACACATTTCGTCGAACACC 60.659 52.381 7.29 0.00 0.00 4.16
1360 1473 1.331756 GATGTTGTGGGATGACGCATC 59.668 52.381 10.26 10.26 40.82 3.91
1368 1481 3.760684 GCTTGAGAAAGATGTTGTGGGAT 59.239 43.478 0.00 0.00 0.00 3.85
1373 1486 2.225019 CGCAGCTTGAGAAAGATGTTGT 59.775 45.455 5.70 0.00 38.37 3.32
1381 1494 0.581529 CACGAACGCAGCTTGAGAAA 59.418 50.000 0.00 0.00 0.00 2.52
1394 1507 2.356673 GGTCGGTGGTCCACGAAC 60.357 66.667 15.93 14.61 41.17 3.95
1405 1518 2.281345 AGAGTCGTCGTGGTCGGT 60.281 61.111 0.00 0.00 37.69 4.69
1485 1601 0.398696 ACAGCCCCGTGACAATTGTA 59.601 50.000 11.95 0.00 0.00 2.41
1489 1605 2.672996 GCACAGCCCCGTGACAAT 60.673 61.111 2.89 0.00 39.34 2.71
1517 1633 3.160047 CCCATGCCTCGAGGAGCT 61.160 66.667 35.69 15.10 37.39 4.09
1523 1639 3.785859 GCAGACCCCATGCCTCGA 61.786 66.667 0.00 0.00 37.73 4.04
1593 1709 3.882888 CACGGCAATATCCCTGTACAATT 59.117 43.478 0.00 0.00 0.00 2.32
1627 1743 0.625683 ATCAGGTCCATGGCCTCCTT 60.626 55.000 20.88 9.10 33.31 3.36
1803 1922 6.748333 TTCTTGCAGAGACCATTCATAAAG 57.252 37.500 0.00 0.00 33.02 1.85
1850 1969 1.746615 AGCATAACACCCAGCAGCG 60.747 57.895 0.00 0.00 0.00 5.18
1977 2096 2.036475 ACCAGCATACCATCTCGATGAC 59.964 50.000 8.42 0.00 41.20 3.06
1978 2097 2.036346 CACCAGCATACCATCTCGATGA 59.964 50.000 8.42 0.00 41.20 2.92
2249 2371 4.162690 GGCGGCCCACCTCACTAG 62.163 72.222 8.12 0.00 0.00 2.57
2380 2505 4.160439 TGACAGTCCATTCTCTAGCGATTT 59.840 41.667 0.00 0.00 0.00 2.17
2455 2580 3.572682 TGGAATATGCGAATAGTCTCCGT 59.427 43.478 10.54 0.00 0.00 4.69
2518 2643 9.346725 GAATCTTTCAATTGTGAGGTCAAATAC 57.653 33.333 5.13 0.00 34.49 1.89
2844 2971 7.511959 TTACATAGCACAACAATTTGGTACA 57.488 32.000 0.78 0.00 37.00 2.90
3039 3166 6.970191 AGGAAAATACTATTTAGGCACAGGT 58.030 36.000 0.00 0.00 0.00 4.00
3188 5543 7.201574 GGTTCCAAACACCAAAATGAAAACTAC 60.202 37.037 0.00 0.00 34.04 2.73
3367 5723 1.066303 TGTTTCGTGCAAACCATGGAC 59.934 47.619 21.47 4.36 46.05 4.02
3372 5728 1.332375 GCTACTGTTTCGTGCAAACCA 59.668 47.619 0.00 0.00 43.52 3.67
3456 5812 4.937201 AGAAATTCCTTTGTTTTCGGCT 57.063 36.364 0.00 0.00 35.14 5.52
3512 5869 8.977505 TGCTGAACAAAATAAAAAGTATGCTTC 58.022 29.630 0.00 0.00 33.01 3.86
3552 5909 7.282450 TCAAAAGGAAACCTGAGTAAGAGAAAC 59.718 37.037 0.00 0.00 32.13 2.78
3558 5915 6.944234 AACTCAAAAGGAAACCTGAGTAAG 57.056 37.500 10.17 0.96 34.64 2.34


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

AutoCloner maintained by Alex Coulton.