Multiple sequence alignment - TraesCS1D01G314100

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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 TraesCS1D01G314100 chr1D 100.000 2888 0 0 1 2888 409350033 409347146 0.000000e+00 5334.0
1 TraesCS1D01G314100 chr1D 76.355 203 37 7 2394 2595 121307513 121307321 6.590000e-17 99.0
2 TraesCS1D01G314100 chr1A 93.709 2925 131 23 1 2888 505339982 505337074 0.000000e+00 4333.0
3 TraesCS1D01G314100 chr1B 92.025 2934 152 48 1 2888 551118178 551115281 0.000000e+00 4047.0
4 TraesCS1D01G314100 chr3A 76.136 176 34 5 2408 2582 147794410 147794242 5.130000e-13 86.1
5 TraesCS1D01G314100 chr5A 83.696 92 10 3 2414 2503 679878237 679878149 6.630000e-12 82.4
6 TraesCS1D01G314100 chr5A 75.410 183 30 12 2402 2582 395924029 395924198 1.110000e-09 75.0
7 TraesCS1D01G314100 chr5A 75.926 162 27 10 2406 2561 471478322 471478167 3.990000e-09 73.1
8 TraesCS1D01G314100 chr5B 74.312 218 37 14 2390 2604 247675359 247675158 1.110000e-09 75.0
9 TraesCS1D01G314100 chr2B 84.615 65 9 1 2393 2457 470521109 470521172 2.400000e-06 63.9


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 TraesCS1D01G314100 chr1D 409347146 409350033 2887 True 5334 5334 100.000 1 2888 1 chr1D.!!$R2 2887
1 TraesCS1D01G314100 chr1A 505337074 505339982 2908 True 4333 4333 93.709 1 2888 1 chr1A.!!$R1 2887
2 TraesCS1D01G314100 chr1B 551115281 551118178 2897 True 4047 4047 92.025 1 2888 1 chr1B.!!$R1 2887

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
221 224 0.953727 TTCGACCTTTCCGACTTCGA 59.046 50.0 0.00 0.00 43.02 3.71 F
1350 1368 0.554305 TCCATGGCATGCCTCTTCAT 59.446 50.0 35.53 18.84 36.94 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1575 0.093026 CGTCGCGAAGAAACACATCC 59.907 55.0 17.47 0.00 0.0 3.51 R
2270 2294 0.530744 TGCAACCTCTAGTAGTGCGG 59.469 55.0 6.13 4.37 0.0 5.69 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
24 25 4.582656 TCCAACATGTCATTTCGACCTTTT 59.417 37.500 0.00 0.00 44.71 2.27
56 59 2.843545 GAACCCCTGGTCTTGGCA 59.156 61.111 0.00 0.00 33.12 4.92
72 75 1.768275 TGGCACATGGATCCGACTATT 59.232 47.619 7.39 0.00 0.00 1.73
150 153 6.159398 ACATCAGGGATCTTGAATCCTTAGTT 59.841 38.462 4.20 0.00 38.26 2.24
188 191 2.507944 GAGCATCAGCCGTCCCAT 59.492 61.111 0.00 0.00 43.56 4.00
190 193 2.037620 GAGCATCAGCCGTCCCATCT 62.038 60.000 0.00 0.00 43.56 2.90
220 223 1.774639 TTTCGACCTTTCCGACTTCG 58.225 50.000 0.00 0.00 35.61 3.79
221 224 0.953727 TTCGACCTTTCCGACTTCGA 59.046 50.000 0.00 0.00 43.02 3.71
288 291 1.521457 TGAGCATCATTCGTCCCGC 60.521 57.895 0.00 0.00 42.56 6.13
313 316 3.587923 ACATGGGCATTTTGACATTTCG 58.412 40.909 0.00 0.00 0.00 3.46
447 450 1.077930 CCTGGTGCTGGACTGGATG 60.078 63.158 0.00 0.00 0.00 3.51
488 493 1.553248 TGGCAGTGACCGTAATTAGCT 59.447 47.619 0.00 0.00 0.00 3.32
970 988 5.304614 AGCACTTTGTAGTAGTCAAGAGGAA 59.695 40.000 0.00 0.00 31.96 3.36
1266 1284 2.953821 GGTGGGCACATGAACGTG 59.046 61.111 0.00 0.00 40.00 4.49
1314 1332 1.460305 CTCCGGGATGGTGGAGGAT 60.460 63.158 0.00 0.00 46.55 3.24
1347 1365 1.452651 CGTCCATGGCATGCCTCTT 60.453 57.895 35.53 18.68 36.94 2.85
1350 1368 0.554305 TCCATGGCATGCCTCTTCAT 59.446 50.000 35.53 18.84 36.94 2.57
1377 1395 3.800833 ATGATCCAGCCGCTGCCA 61.801 61.111 15.36 12.00 38.69 4.92
1457 1475 2.618045 GCTTTCTTTCGGATCCAGGGAA 60.618 50.000 13.41 4.44 0.00 3.97
1458 1476 3.274288 CTTTCTTTCGGATCCAGGGAAG 58.726 50.000 13.41 6.95 0.00 3.46
1470 1488 0.602905 CAGGGAAGTCGTTGGTGGAC 60.603 60.000 0.00 0.00 34.62 4.02
1557 1575 3.146104 ACCCAAGAACATGGTGAGAAG 57.854 47.619 0.00 0.00 38.91 2.85
1560 1578 3.308688 CCCAAGAACATGGTGAGAAGGAT 60.309 47.826 0.00 0.00 38.91 3.24
1571 1589 3.433615 GGTGAGAAGGATGTGTTTCTTCG 59.566 47.826 0.00 0.00 41.07 3.79
1575 1593 1.429463 AGGATGTGTTTCTTCGCGAC 58.571 50.000 9.15 0.00 0.00 5.19
1658 1676 2.556287 CCGCCGAACAAGAAGTGC 59.444 61.111 0.00 0.00 0.00 4.40
1666 1684 2.031682 CGAACAAGAAGTGCCTTTGAGG 60.032 50.000 0.00 0.00 38.80 3.86
1667 1685 3.214328 GAACAAGAAGTGCCTTTGAGGA 58.786 45.455 0.00 0.00 37.67 3.71
1668 1686 3.515602 ACAAGAAGTGCCTTTGAGGAT 57.484 42.857 0.00 0.00 37.67 3.24
2005 2027 4.109766 GCTTTTTAGAAACGTTGGCTTGT 58.890 39.130 0.00 0.00 0.00 3.16
2007 2029 5.744819 GCTTTTTAGAAACGTTGGCTTGTTA 59.255 36.000 0.00 0.00 0.00 2.41
2240 2264 3.679980 CACCTAGTTGTTTCATCGGACTG 59.320 47.826 0.00 0.00 0.00 3.51
2248 2272 5.233957 TGTTTCATCGGACTGCATTTATG 57.766 39.130 0.00 0.00 0.00 1.90
2319 2343 0.033601 ATCCCCTGCGTAAATGGCAA 60.034 50.000 0.00 0.00 40.39 4.52
2329 2353 4.212214 TGCGTAAATGGCAAAAATGTTTCC 59.788 37.500 0.00 0.00 37.49 3.13
2339 2363 5.506649 GGCAAAAATGTTTCCGACTCTTGTA 60.507 40.000 0.00 0.00 0.00 2.41
2477 2514 3.569277 CCAACATGATCCTTTGTGTGTGA 59.431 43.478 0.00 0.00 0.00 3.58
2503 2544 1.401409 GGTGTTGAATGTGTGCATCCG 60.401 52.381 0.00 0.00 33.50 4.18
2504 2545 0.240678 TGTTGAATGTGTGCATCCGC 59.759 50.000 0.00 0.00 33.50 5.54
2505 2546 0.456653 GTTGAATGTGTGCATCCGCC 60.457 55.000 0.00 0.00 37.32 6.13
2511 2552 0.251634 TGTGTGCATCCGCCTAATCA 59.748 50.000 0.00 0.00 37.32 2.57
2526 2567 3.181462 CCTAATCATGCAGAGGCTGTGTA 60.181 47.826 13.65 9.40 41.91 2.90
2527 2568 3.572632 AATCATGCAGAGGCTGTGTAT 57.427 42.857 13.65 11.52 41.91 2.29
2528 2569 2.320745 TCATGCAGAGGCTGTGTATG 57.679 50.000 28.76 28.76 41.91 2.39
2540 2581 5.363101 AGGCTGTGTATGTACTTGATCATG 58.637 41.667 7.04 7.04 0.00 3.07
2541 2582 4.024556 GGCTGTGTATGTACTTGATCATGC 60.025 45.833 8.45 0.00 0.00 4.06
2543 2584 5.277202 GCTGTGTATGTACTTGATCATGCTG 60.277 44.000 8.45 0.00 0.00 4.41
2547 2588 7.821846 TGTGTATGTACTTGATCATGCTGTTTA 59.178 33.333 8.45 0.00 0.00 2.01
2565 2615 6.094603 GCTGTTTATATCCCCTTGATGCTATG 59.905 42.308 0.00 0.00 34.76 2.23
2570 2620 3.469008 TCCCCTTGATGCTATGTTACG 57.531 47.619 0.00 0.00 0.00 3.18
2596 2646 7.707104 AGTCAATAAAAATGCCCTTTATCGAG 58.293 34.615 0.00 0.00 30.41 4.04
2671 2722 3.544684 TCATGCATGCTTTAGAATCGGT 58.455 40.909 22.25 0.00 0.00 4.69
2672 2723 3.313249 TCATGCATGCTTTAGAATCGGTG 59.687 43.478 22.25 0.00 0.00 4.94
2808 2873 6.042777 TCTGTAAGCATATGTACACTGAAGC 58.957 40.000 10.64 5.68 0.00 3.86
2813 2878 4.637534 AGCATATGTACACTGAAGCCTTTG 59.362 41.667 10.64 0.00 0.00 2.77
2830 2900 4.392138 GCCTTTGTCTTAACTAAGATGCGT 59.608 41.667 2.62 0.00 43.49 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 59 5.815233 ATGAGAAATAGTCGGATCCATGT 57.185 39.130 13.41 0.00 0.00 3.21
72 75 4.893608 TCGGATGTTCTGTGAAATGAGAA 58.106 39.130 0.00 0.00 0.00 2.87
188 191 2.238646 AGGTCGAAATGCCCATGTTAGA 59.761 45.455 0.00 0.00 0.00 2.10
190 193 2.799126 AGGTCGAAATGCCCATGTTA 57.201 45.000 0.00 0.00 0.00 2.41
220 223 6.495181 TCCATGACTAGGGATTTGATACTCTC 59.505 42.308 0.00 0.00 30.42 3.20
221 224 6.385443 TCCATGACTAGGGATTTGATACTCT 58.615 40.000 0.00 0.00 30.42 3.24
304 307 1.003118 CCCTGGAAGTCCGAAATGTCA 59.997 52.381 0.00 0.00 39.43 3.58
313 316 1.338484 GGTTCGTTACCCTGGAAGTCC 60.338 57.143 0.00 0.00 41.43 3.85
488 493 9.071221 CAATAATTGCGTGTAAAGCTTATTTCA 57.929 29.630 0.00 0.00 43.59 2.69
501 506 2.487762 CTGGGTGTCAATAATTGCGTGT 59.512 45.455 0.00 0.00 0.00 4.49
503 508 2.747446 GACTGGGTGTCAATAATTGCGT 59.253 45.455 0.00 0.00 44.73 5.24
504 509 3.405170 GACTGGGTGTCAATAATTGCG 57.595 47.619 0.00 0.00 44.73 4.85
1285 1303 4.521062 CCCGGAGAGCTTGAGCCG 62.521 72.222 0.73 9.61 43.38 5.52
1347 1365 3.495629 GCTGGATCATGTAGCCTTGATGA 60.496 47.826 0.00 0.00 36.05 2.92
1350 1368 2.627515 GCTGGATCATGTAGCCTTGA 57.372 50.000 0.00 0.00 33.51 3.02
1377 1395 0.343372 TAGGTCTTGGAGGAGGGCAT 59.657 55.000 0.00 0.00 0.00 4.40
1457 1475 2.029073 CAGCGTCCACCAACGACT 59.971 61.111 0.00 0.00 45.37 4.18
1458 1476 3.712881 GCAGCGTCCACCAACGAC 61.713 66.667 0.00 0.00 45.37 4.34
1557 1575 0.093026 CGTCGCGAAGAAACACATCC 59.907 55.000 17.47 0.00 0.00 3.51
1560 1578 2.591311 GGCGTCGCGAAGAAACACA 61.591 57.895 26.19 0.00 0.00 3.72
1571 1589 4.766088 AACGTACCTCGGCGTCGC 62.766 66.667 9.22 9.22 44.69 5.19
1575 1593 1.226323 CTCTGAACGTACCTCGGCG 60.226 63.158 0.00 0.00 44.69 6.46
1632 1650 4.050934 GTTCGGCGGCCCAAAAGG 62.051 66.667 14.55 0.00 39.47 3.11
1658 1676 7.042187 CGTCTTCTTTATCATCATCCTCAAAGG 60.042 40.741 0.00 0.00 36.46 3.11
1666 1684 9.861138 CTTTTCATCGTCTTCTTTATCATCATC 57.139 33.333 0.00 0.00 0.00 2.92
1667 1685 9.605275 TCTTTTCATCGTCTTCTTTATCATCAT 57.395 29.630 0.00 0.00 0.00 2.45
1668 1686 9.605275 ATCTTTTCATCGTCTTCTTTATCATCA 57.395 29.630 0.00 0.00 0.00 3.07
1891 1909 5.221461 ACGGGCTCTAGTATAGTTTTGGATG 60.221 44.000 0.00 0.00 40.38 3.51
1986 2008 8.705048 AAAATAACAAGCCAACGTTTCTAAAA 57.295 26.923 0.00 0.00 0.00 1.52
1988 2010 8.404000 TGTAAAATAACAAGCCAACGTTTCTAA 58.596 29.630 0.00 0.00 0.00 2.10
2030 2054 4.464244 TGCCCAAATCAATTAAATCGACCA 59.536 37.500 0.00 0.00 0.00 4.02
2240 2264 5.929278 TGCAAAATGCTTGAACATAAATGC 58.071 33.333 3.78 0.00 45.31 3.56
2248 2272 4.350346 GGGTTTTTGCAAAATGCTTGAAC 58.650 39.130 24.39 16.75 45.31 3.18
2270 2294 0.530744 TGCAACCTCTAGTAGTGCGG 59.469 55.000 6.13 4.37 0.00 5.69
2319 2343 7.504924 TGATTACAAGAGTCGGAAACATTTT 57.495 32.000 0.00 0.00 0.00 1.82
2329 2353 5.004821 CCAACGAAGATGATTACAAGAGTCG 59.995 44.000 0.00 0.00 29.10 4.18
2339 2363 2.290260 TGCTGACCCAACGAAGATGATT 60.290 45.455 0.00 0.00 29.10 2.57
2477 2514 2.159254 GCACACATTCAACACCAACACT 60.159 45.455 0.00 0.00 0.00 3.55
2504 2545 2.219458 CACAGCCTCTGCATGATTAGG 58.781 52.381 0.00 0.00 41.13 2.69
2505 2546 2.915349 ACACAGCCTCTGCATGATTAG 58.085 47.619 0.00 0.00 41.13 1.73
2511 2552 2.768527 AGTACATACACAGCCTCTGCAT 59.231 45.455 0.00 0.00 41.13 3.96
2520 2561 5.814188 ACAGCATGATCAAGTACATACACAG 59.186 40.000 0.00 0.00 39.69 3.66
2526 2567 9.224267 GGATATAAACAGCATGATCAAGTACAT 57.776 33.333 0.00 0.00 39.69 2.29
2527 2568 7.661437 GGGATATAAACAGCATGATCAAGTACA 59.339 37.037 0.00 0.00 39.69 2.90
2528 2569 7.119846 GGGGATATAAACAGCATGATCAAGTAC 59.880 40.741 0.00 0.00 39.69 2.73
2540 2581 4.401925 AGCATCAAGGGGATATAAACAGC 58.598 43.478 0.00 0.00 33.95 4.40
2541 2582 7.170965 ACATAGCATCAAGGGGATATAAACAG 58.829 38.462 0.00 0.00 33.95 3.16
2543 2584 8.947115 GTAACATAGCATCAAGGGGATATAAAC 58.053 37.037 0.00 0.00 33.95 2.01
2547 2588 5.483937 TCGTAACATAGCATCAAGGGGATAT 59.516 40.000 0.00 0.00 33.95 1.63
2565 2615 6.190954 AGGGCATTTTTATTGACTCGTAAC 57.809 37.500 0.00 0.00 0.00 2.50
2570 2620 7.703328 TCGATAAAGGGCATTTTTATTGACTC 58.297 34.615 1.20 0.00 36.60 3.36
2613 2663 5.368145 TGTGAGCTTAGTTCAACAGTCATT 58.632 37.500 0.00 0.00 0.00 2.57
2805 2870 5.122396 CGCATCTTAGTTAAGACAAAGGCTT 59.878 40.000 3.84 0.00 44.30 4.35
2806 2871 4.631813 CGCATCTTAGTTAAGACAAAGGCT 59.368 41.667 3.84 0.00 44.30 4.58
2808 2873 6.073222 ACAACGCATCTTAGTTAAGACAAAGG 60.073 38.462 3.84 0.00 44.30 3.11
2813 2878 4.689345 ACCACAACGCATCTTAGTTAAGAC 59.311 41.667 3.84 0.00 44.30 3.01
2830 2900 3.626930 ACTCTTTGCCACTTTACCACAA 58.373 40.909 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.