Multiple sequence alignment - TraesCS2D01G177100

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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 TraesCS2D01G177100 chr2D 100.000 3084 0 0 1 3084 120564102 120567185 0 5696
1 TraesCS2D01G177100 chr2A 93.730 3062 152 24 1 3043 124389631 124392671 0 4554
2 TraesCS2D01G177100 chr2B 92.701 3110 150 30 1 3084 173483990 173487048 0 4414


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 TraesCS2D01G177100 chr2D 120564102 120567185 3083 False 5696 5696 100.000 1 3084 1 chr2D.!!$F1 3083
1 TraesCS2D01G177100 chr2A 124389631 124392671 3040 False 4554 4554 93.730 1 3043 1 chr2A.!!$F1 3042
2 TraesCS2D01G177100 chr2B 173483990 173487048 3058 False 4414 4414 92.701 1 3084 1 chr2B.!!$F1 3083

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
125 130 0.036765 ACGGTGCATAAGCCTTCGAA 60.037 50.0 0.0 0.0 41.13 3.71 F
1042 1069 0.461961 GTCACCATCCTCTTCCTCCG 59.538 60.0 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 1232 0.032678 AGATCGGCAGCTGGTAATCG 59.967 55.000 17.12 0.0 0.0 3.34 R
2774 2816 1.548269 TGAATCCCCAACCAAAATCGC 59.452 47.619 0.00 0.0 0.0 4.58 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
34 36 2.094675 GCTACGTCCACACCCTACTTA 58.905 52.381 0.00 0.00 0.00 2.24
36 38 0.893447 ACGTCCACACCCTACTTAGC 59.107 55.000 0.00 0.00 0.00 3.09
58 61 2.290960 CCCCTCTAACTTGGGTTTCCAG 60.291 54.545 0.00 0.00 45.04 3.86
123 128 0.460284 AGACGGTGCATAAGCCTTCG 60.460 55.000 0.00 0.00 41.13 3.79
125 130 0.036765 ACGGTGCATAAGCCTTCGAA 60.037 50.000 0.00 0.00 41.13 3.71
133 138 5.117135 GTGCATAAGCCTTCGAAAGTTTTTC 59.883 40.000 1.02 0.00 41.13 2.29
134 139 5.219633 GCATAAGCCTTCGAAAGTTTTTCA 58.780 37.500 1.02 0.00 33.58 2.69
154 159 5.759506 TCAATTTTTCCTAACGAGTGCAA 57.240 34.783 0.00 0.00 0.00 4.08
164 169 1.102978 ACGAGTGCAAAAGCCTTTGT 58.897 45.000 9.45 0.00 43.34 2.83
173 178 3.260740 CAAAAGCCTTTGTCAGTTTGCA 58.739 40.909 0.00 0.00 37.69 4.08
183 188 3.544684 TGTCAGTTTGCACATGAGAGTT 58.455 40.909 0.00 0.00 0.00 3.01
189 194 2.885135 TGCACATGAGAGTTCCCATT 57.115 45.000 0.00 0.00 0.00 3.16
289 300 6.677913 ACAAAAACCATCTGTACAAGTATGC 58.322 36.000 0.00 0.00 0.00 3.14
292 303 4.568072 ACCATCTGTACAAGTATGCCAA 57.432 40.909 0.00 0.00 0.00 4.52
335 346 1.134995 GCCCATAAGCTCAAAGTTGCC 60.135 52.381 0.00 0.00 0.00 4.52
370 381 1.208259 GCCCGCAAAGTTTCAAACAG 58.792 50.000 2.41 0.00 0.00 3.16
413 424 5.924825 AGTGTAAACGTGAGGTTGAATAGTC 59.075 40.000 0.00 0.00 43.76 2.59
420 431 9.661563 AAACGTGAGGTTGAATAGTCAAATATA 57.338 29.630 7.26 0.00 45.29 0.86
480 492 1.919600 ATGCCCAGAGTTGCTCCTCC 61.920 60.000 0.34 0.00 31.53 4.30
531 543 7.440523 AATTCAAACTACTCTGTGGACAATC 57.559 36.000 0.00 0.00 0.00 2.67
543 555 6.377080 TCTGTGGACAATCTATAGTCTGGAT 58.623 40.000 0.00 0.00 35.18 3.41
544 556 6.266330 TCTGTGGACAATCTATAGTCTGGATG 59.734 42.308 0.00 0.00 35.18 3.51
551 563 4.944619 TCTATAGTCTGGATGCAAGGTG 57.055 45.455 0.00 0.00 0.00 4.00
586 598 6.992063 ACTGATGCTTTATGAAACCTACTG 57.008 37.500 0.00 0.00 0.00 2.74
656 669 2.988493 CGGACAATGCTGGTCAAATTTG 59.012 45.455 12.15 12.15 37.00 2.32
679 692 7.076842 TGAGATGATTTCGAGTGAATTTTCC 57.923 36.000 0.00 0.00 33.20 3.13
765 778 5.631929 TCGTGCGACATCCATACATAAATAC 59.368 40.000 0.00 0.00 0.00 1.89
886 900 4.639310 TGAGAGACAAACGAGATACTACCC 59.361 45.833 0.00 0.00 0.00 3.69
931 949 2.808202 GCAGAGCAGAAGGTTCTCAACA 60.808 50.000 0.00 0.00 34.49 3.33
932 950 2.805099 CAGAGCAGAAGGTTCTCAACAC 59.195 50.000 0.00 0.00 34.49 3.32
1022 1040 7.530010 CATATGCCGGTAAATATTCCAAGAAG 58.470 38.462 1.90 0.00 0.00 2.85
1042 1069 0.461961 GTCACCATCCTCTTCCTCCG 59.538 60.000 0.00 0.00 0.00 4.63
1073 1100 3.146066 ACCTCACTAACCACGTACGTAA 58.854 45.455 22.34 6.19 0.00 3.18
1078 1107 2.253603 CTAACCACGTACGTAAGGTGC 58.746 52.381 25.75 0.00 41.62 5.01
1096 1125 1.017701 GCCCGCGCCTATATTACCAC 61.018 60.000 0.00 0.00 0.00 4.16
1100 1129 1.804601 GCGCCTATATTACCACCACC 58.195 55.000 0.00 0.00 0.00 4.61
1102 1131 1.975680 CGCCTATATTACCACCACCCT 59.024 52.381 0.00 0.00 0.00 4.34
1116 1145 4.394712 CCCTTCGCCGCTTCACCT 62.395 66.667 0.00 0.00 0.00 4.00
1129 1158 3.557595 CGCTTCACCTCTCATTAATCCAC 59.442 47.826 0.00 0.00 0.00 4.02
1182 1211 2.070783 GATTGTTGTTGCATTGCCCTG 58.929 47.619 6.12 0.00 0.00 4.45
1203 1232 2.619646 GGAGGAGACGAGGTCATTAGTC 59.380 54.545 0.00 0.00 34.60 2.59
1222 1251 0.032678 CGATTACCAGCTGCCGATCT 59.967 55.000 8.66 0.00 0.00 2.75
1273 1302 4.333649 TCGGTGATCTCTTGATTGATTTGC 59.666 41.667 0.00 0.00 32.19 3.68
1274 1303 4.595116 GGTGATCTCTTGATTGATTTGCG 58.405 43.478 0.00 0.00 32.19 4.85
1276 1305 3.690628 TGATCTCTTGATTGATTTGCGCA 59.309 39.130 5.66 5.66 32.19 6.09
1344 1373 1.301479 GGCGTGGAAGGACGAGTTT 60.301 57.895 0.00 0.00 42.10 2.66
1550 1583 4.994852 CCTGTGAATTTCTCTGACGGTTTA 59.005 41.667 6.85 0.00 0.00 2.01
1562 1595 0.519961 ACGGTTTATGCGTTCTTGGC 59.480 50.000 0.00 0.00 0.00 4.52
1576 1609 0.669318 CTTGGCGGTGTGTGTACGAT 60.669 55.000 0.00 0.00 0.00 3.73
2090 2123 4.593864 GCTCCTTCTAGCCGCCGG 62.594 72.222 0.00 0.00 36.45 6.13
2091 2124 3.917760 CTCCTTCTAGCCGCCGGG 61.918 72.222 4.77 0.00 0.00 5.73
2112 2145 2.127232 CCCATTCCCCGTCCAATGC 61.127 63.158 0.00 0.00 0.00 3.56
2180 2213 4.079787 ACAGCCCACAGATATGTAATTGGT 60.080 41.667 0.00 0.00 0.00 3.67
2304 2344 6.602803 TGCATTATGCTCCTAAATCTTTGTCA 59.397 34.615 18.44 0.00 45.31 3.58
2353 2393 9.167311 CTACTTGAGTTTCTGCTTAAATATGGT 57.833 33.333 0.00 0.00 0.00 3.55
2412 2452 9.635520 AAACTGTCATGATGATCAAGAAAAATC 57.364 29.630 1.52 0.00 0.00 2.17
2420 2460 8.124808 TGATGATCAAGAAAAATCATGGTTCA 57.875 30.769 0.00 0.00 41.51 3.18
2536 2578 4.644685 CCCCAATGGTTATACTGTTTCAGG 59.355 45.833 0.00 0.00 35.51 3.86
2588 2630 6.731292 TTAGTCTGAGGCTGATAATGCTAA 57.269 37.500 0.00 0.00 0.00 3.09
2774 2816 0.669619 TTGTCAATGTGCACAGCCTG 59.330 50.000 25.84 20.37 0.00 4.85
2788 2830 1.079888 GCCTGCGATTTTGGTTGGG 60.080 57.895 0.00 0.00 0.00 4.12
2795 2837 2.673893 GCGATTTTGGTTGGGGATTCAC 60.674 50.000 0.00 0.00 0.00 3.18
2798 2840 2.478872 TTTGGTTGGGGATTCACCAA 57.521 45.000 16.57 16.57 45.25 3.67
2810 2852 4.250464 GGATTCACCAACTCGTTGTCATA 58.750 43.478 8.77 0.00 38.85 2.15
2989 3031 4.402155 TGCAAGGCAATTCCGAATTTCTAT 59.598 37.500 3.48 0.00 40.77 1.98
3033 3076 4.118410 CTCGAACAATGAGATAGCAAGCT 58.882 43.478 0.00 0.00 35.43 3.74
3046 3089 6.467677 AGATAGCAAGCTGAGTCTGTTTTTA 58.532 36.000 4.53 0.00 0.00 1.52
3053 3096 7.517259 GCAAGCTGAGTCTGTTTTTATTTTTGG 60.517 37.037 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 4.171186 CCCAAGTTAGAGGGGGCT 57.829 61.111 0.00 0.00 41.58 5.19
86 91 4.976116 CCGTCTGGAAAAACATTGAACTTC 59.024 41.667 0.00 0.00 37.49 3.01
125 130 9.083080 CACTCGTTAGGAAAAATTGAAAAACTT 57.917 29.630 0.00 0.00 0.00 2.66
133 138 6.562086 GCTTTTGCACTCGTTAGGAAAAATTG 60.562 38.462 0.00 0.00 46.58 2.32
134 139 5.462068 GCTTTTGCACTCGTTAGGAAAAATT 59.538 36.000 0.00 0.00 46.58 1.82
154 159 2.233431 TGTGCAAACTGACAAAGGCTTT 59.767 40.909 6.68 6.68 0.00 3.51
164 169 3.141398 GGAACTCTCATGTGCAAACTGA 58.859 45.455 0.00 0.00 0.00 3.41
173 178 7.184862 AGGAATTTTAATGGGAACTCTCATGT 58.815 34.615 0.00 0.00 0.00 3.21
225 236 7.668525 AGATGTTTAACCTTGCAGTTACTAC 57.331 36.000 0.00 2.11 32.05 2.73
226 237 9.781633 TTTAGATGTTTAACCTTGCAGTTACTA 57.218 29.630 0.00 0.00 32.05 1.82
227 238 8.685838 TTTAGATGTTTAACCTTGCAGTTACT 57.314 30.769 0.00 0.00 32.05 2.24
335 346 1.924524 CGGGCACTATTGACGTACAAG 59.075 52.381 0.00 0.00 42.02 3.16
413 424 9.927668 ATTGAGTCCCACAAACTTTTATATTTG 57.072 29.630 0.00 0.00 40.83 2.32
420 431 4.081198 TGCAATTGAGTCCCACAAACTTTT 60.081 37.500 10.34 0.00 0.00 2.27
520 532 6.453943 CATCCAGACTATAGATTGTCCACAG 58.546 44.000 6.78 0.00 33.89 3.66
531 543 4.679373 ACACCTTGCATCCAGACTATAG 57.321 45.455 0.00 0.00 0.00 1.31
543 555 9.853555 CATCAGTATTTAAATTTACACCTTGCA 57.146 29.630 5.91 0.00 0.00 4.08
544 556 8.807581 GCATCAGTATTTAAATTTACACCTTGC 58.192 33.333 5.91 4.72 0.00 4.01
568 580 5.070001 ACAAGCAGTAGGTTTCATAAAGCA 58.930 37.500 4.61 0.00 41.18 3.91
586 598 1.019805 GTAGGCCGAACCAGACAAGC 61.020 60.000 0.00 0.00 43.14 4.01
616 628 2.092211 CCGCGTACAAAGAAGCTACTTG 59.908 50.000 4.92 0.00 0.00 3.16
656 669 6.183360 ACGGAAAATTCACTCGAAATCATCTC 60.183 38.462 0.00 0.00 34.01 2.75
679 692 6.668323 AGAATTTGAACCTTGTATTCACACG 58.332 36.000 0.00 0.00 35.82 4.49
861 875 6.349944 GGGTAGTATCTCGTTTGTCTCTCAAA 60.350 42.308 0.00 0.00 42.79 2.69
1022 1040 0.833949 GGAGGAAGAGGATGGTGACC 59.166 60.000 0.00 0.00 0.00 4.02
1042 1069 1.730612 GTTAGTGAGGTAAGCGGTTGC 59.269 52.381 10.73 8.74 43.24 4.17
1078 1107 0.390735 GGTGGTAATATAGGCGCGGG 60.391 60.000 8.83 0.00 0.00 6.13
1096 1125 4.697756 TGAAGCGGCGAAGGGTGG 62.698 66.667 12.98 0.00 0.00 4.61
1100 1129 2.815647 GAGGTGAAGCGGCGAAGG 60.816 66.667 12.98 0.00 0.00 3.46
1102 1131 1.888436 ATGAGAGGTGAAGCGGCGAA 61.888 55.000 12.98 0.00 0.00 4.70
1116 1145 4.331968 GTGGTGTTGGTGGATTAATGAGA 58.668 43.478 0.00 0.00 0.00 3.27
1129 1158 2.906897 AGCAAGCGGTGGTGTTGG 60.907 61.111 0.00 0.00 36.32 3.77
1182 1211 2.619646 GACTAATGACCTCGTCTCCTCC 59.380 54.545 0.00 0.00 33.15 4.30
1203 1232 0.032678 AGATCGGCAGCTGGTAATCG 59.967 55.000 17.12 0.00 0.00 3.34
1222 1251 1.476085 CTGCCCAATTAATCCGCAACA 59.524 47.619 5.79 0.00 0.00 3.33
1273 1302 2.095263 ACTTTCCGAATTTCATGGTGCG 60.095 45.455 0.00 0.00 0.00 5.34
1274 1303 3.244976 CACTTTCCGAATTTCATGGTGC 58.755 45.455 0.00 0.00 0.00 5.01
1276 1305 2.231235 GCCACTTTCCGAATTTCATGGT 59.769 45.455 0.00 0.00 0.00 3.55
1550 1583 2.281484 ACACCGCCAAGAACGCAT 60.281 55.556 0.00 0.00 0.00 4.73
1562 1595 0.524414 TCCTGATCGTACACACACCG 59.476 55.000 0.00 0.00 0.00 4.94
1678 1711 0.174845 CCATCTCGCCGTGGAAGTTA 59.825 55.000 0.00 0.00 37.72 2.24
1795 1828 0.867753 GCACTAGCACGGTCTCGATG 60.868 60.000 0.00 0.00 41.58 3.84
2304 2344 2.597805 ACGCTCGGTCAGTGTCCT 60.598 61.111 4.86 0.00 42.62 3.85
2330 2370 9.132521 CAAACCATATTTAAGCAGAAACTCAAG 57.867 33.333 0.00 0.00 0.00 3.02
2353 2393 6.528014 TTAATTTTCTACGACGCACTCAAA 57.472 33.333 0.00 0.00 0.00 2.69
2499 2540 3.181476 CCATTGGGGAACGATCAATTTCC 60.181 47.826 8.60 8.60 40.67 3.13
2536 2578 5.613358 AACTCGTGATTGGTCTGAAAATC 57.387 39.130 7.17 7.17 34.11 2.17
2588 2630 3.005554 CGATTTGCTTGATCCAGTCACT 58.994 45.455 0.00 0.00 36.32 3.41
2774 2816 1.548269 TGAATCCCCAACCAAAATCGC 59.452 47.619 0.00 0.00 0.00 4.58
2788 2830 2.489971 TGACAACGAGTTGGTGAATCC 58.510 47.619 18.66 1.96 44.45 3.01
2795 2837 7.554732 CAACAATTTTTATGACAACGAGTTGG 58.445 34.615 18.66 3.08 44.45 3.77
2798 2840 6.269315 TGCAACAATTTTTATGACAACGAGT 58.731 32.000 0.00 0.00 0.00 4.18
2801 2843 5.365133 GCTGCAACAATTTTTATGACAACG 58.635 37.500 0.00 0.00 0.00 4.10
2810 2852 5.181690 TCTTACTCGCTGCAACAATTTTT 57.818 34.783 0.00 0.00 0.00 1.94
2989 3031 8.208224 TCGAGTTTTAGCATTTTGGAGGATATA 58.792 33.333 0.00 0.00 0.00 0.86
3033 3076 9.695526 CATCATCCAAAAATAAAAACAGACTCA 57.304 29.630 0.00 0.00 0.00 3.41
3046 3089 7.057894 CCCATTTTCATCCATCATCCAAAAAT 58.942 34.615 0.00 0.00 0.00 1.82
3053 3096 2.967201 TGGCCCATTTTCATCCATCATC 59.033 45.455 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.