Multiple sequence alignment - TraesCS5D01G207000

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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 TraesCS5D01G207000 chr5D 100.000 3219 0 0 1 3219 313281775 313278557 0.000000e+00 5945
1 TraesCS5D01G207000 chr5D 80.702 342 42 6 1661 2002 313205374 313205057 8.920000e-61 244
2 TraesCS5D01G207000 chr5D 90.361 166 15 1 2030 2194 313205062 313204897 1.940000e-52 217
3 TraesCS5D01G207000 chr5A 95.580 2285 60 10 951 3219 407148005 407145746 0.000000e+00 3622
4 TraesCS5D01G207000 chr5A 89.623 742 53 11 162 900 407148853 407148133 0.000000e+00 922
5 TraesCS5D01G207000 chr5A 82.590 471 50 14 1726 2194 407131015 407130575 1.400000e-103 387
6 TraesCS5D01G207000 chr5A 97.059 102 3 0 1 102 407149276 407149175 4.270000e-39 172
7 TraesCS5D01G207000 chr5B 94.224 1385 57 8 831 2194 360874873 360873491 0.000000e+00 2093
8 TraesCS5D01G207000 chr5B 95.013 782 39 0 1413 2194 360844436 360843655 0.000000e+00 1229
9 TraesCS5D01G207000 chr5B 92.707 617 27 6 823 1422 360854666 360854051 0.000000e+00 874
10 TraesCS5D01G207000 chr5B 88.982 717 40 23 1 684 360876192 360875482 0.000000e+00 850
11 TraesCS5D01G207000 chr5B 92.513 187 8 5 503 684 360856724 360856539 2.460000e-66 263
12 TraesCS5D01G207000 chr5B 84.733 131 9 7 690 818 360875435 360875314 1.570000e-23 121
13 TraesCS5D01G207000 chr5B 83.969 131 10 7 690 818 360856492 360856371 7.300000e-22 115


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 TraesCS5D01G207000 chr5D 313278557 313281775 3218 True 5945.000000 5945 100.000000 1 3219 1 chr5D.!!$R1 3218
1 TraesCS5D01G207000 chr5A 407145746 407149276 3530 True 1572.000000 3622 94.087333 1 3219 3 chr5A.!!$R2 3218
2 TraesCS5D01G207000 chr5B 360843655 360844436 781 True 1229.000000 1229 95.013000 1413 2194 1 chr5B.!!$R1 781
3 TraesCS5D01G207000 chr5B 360873491 360876192 2701 True 1021.333333 2093 89.313000 1 2194 3 chr5B.!!$R3 2193
4 TraesCS5D01G207000 chr5B 360854051 360856724 2673 True 417.333333 874 89.729667 503 1422 3 chr5B.!!$R2 919

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
797 1153 0.460284 AGGCACTACGAATCCGCTTG 60.460 55.000 0.0 0.0 36.02 4.01 F
1671 3813 1.002134 CTGGGGAAAGATGGTGCGT 60.002 57.895 0.0 0.0 0.00 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 4022 0.671781 CAGTGAACAAGGCTCTCCCG 60.672 60.0 0.00 0.0 39.21 5.14 R
2561 4711 1.337817 CTTTCTGAGTCGCGGACGTG 61.338 60.0 6.13 0.0 41.18 4.49 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
160 161 1.653918 TCTCTTCCAGGAATCCCCTCT 59.346 52.381 1.09 0.00 45.60 3.69
249 512 2.032376 TGTCGCATGAGCAGCCAA 59.968 55.556 0.00 0.00 42.27 4.52
298 565 1.511613 TTCCAGATCATCCAGTCCCC 58.488 55.000 0.00 0.00 0.00 4.81
319 586 1.138047 GCGCTGTGATTGCTGCATTC 61.138 55.000 15.58 15.58 33.72 2.67
344 611 3.386768 TGTGCTGTACAAGAAGAGACC 57.613 47.619 0.00 0.00 36.06 3.85
557 866 1.133294 TGGATCCGGTGGAGCTGTATA 60.133 52.381 7.39 0.00 38.31 1.47
594 903 1.668419 CCATCGGGTTGTGATTCTCC 58.332 55.000 0.00 0.00 0.00 3.71
601 910 0.949105 GTTGTGATTCTCCGGTGCGT 60.949 55.000 0.00 0.00 0.00 5.24
684 998 1.059913 CTCCCTCCAACAAGTGTCCT 58.940 55.000 0.00 0.00 0.00 3.85
685 999 0.764890 TCCCTCCAACAAGTGTCCTG 59.235 55.000 0.00 0.00 0.00 3.86
688 1002 1.597742 CTCCAACAAGTGTCCTGGTG 58.402 55.000 0.00 0.00 30.09 4.17
706 1061 4.400961 GAGTTCCCTGCAGGCGCT 62.401 66.667 28.39 22.29 39.64 5.92
773 1129 0.992072 GACGATGCGCGCACATATAT 59.008 50.000 39.05 20.73 46.04 0.86
774 1130 2.159435 AGACGATGCGCGCACATATATA 60.159 45.455 39.05 11.72 46.04 0.86
775 1131 2.789339 GACGATGCGCGCACATATATAT 59.211 45.455 39.05 18.93 46.04 0.86
776 1132 3.959943 ACGATGCGCGCACATATATATA 58.040 40.909 39.05 9.89 46.04 0.86
777 1133 4.546570 ACGATGCGCGCACATATATATAT 58.453 39.130 39.05 17.15 46.04 0.86
778 1134 5.695818 ACGATGCGCGCACATATATATATA 58.304 37.500 39.05 9.00 46.04 0.86
779 1135 5.795441 ACGATGCGCGCACATATATATATAG 59.205 40.000 39.05 18.67 46.04 1.31
780 1136 5.228012 CGATGCGCGCACATATATATATAGG 59.772 44.000 39.05 11.87 0.00 2.57
797 1153 0.460284 AGGCACTACGAATCCGCTTG 60.460 55.000 0.00 0.00 36.02 4.01
800 1156 1.470285 GCACTACGAATCCGCTTGGTA 60.470 52.381 0.00 0.00 39.95 3.25
825 2881 3.458189 GAAGTCCCCGTTCTGATGTATG 58.542 50.000 0.00 0.00 0.00 2.39
837 2893 2.548480 CTGATGTATGACCGCGTAGAGA 59.452 50.000 4.92 0.00 0.00 3.10
1068 3210 4.944372 CGTACGGGATGGAGGCGC 62.944 72.222 7.57 0.00 0.00 6.53
1100 3242 2.001812 CACGTGATTGGTCCTCTCTG 57.998 55.000 10.90 0.00 0.00 3.35
1427 3569 3.807538 GGCGACGTCCACGAGCTA 61.808 66.667 10.58 0.00 42.38 3.32
1474 3616 2.995482 CGTTGTCTATGACGGCGC 59.005 61.111 6.90 0.00 34.95 6.53
1508 3650 2.235016 CGTCGACACGCAGTTTGGT 61.235 57.895 17.16 0.00 41.61 3.67
1667 3809 1.302907 ATCTGCTGGGGAAAGATGGT 58.697 50.000 0.00 0.00 29.52 3.55
1671 3813 1.002134 CTGGGGAAAGATGGTGCGT 60.002 57.895 0.00 0.00 0.00 5.24
1765 3907 3.081804 ACCACAAACATAGCTACTTGGC 58.918 45.455 13.67 0.00 0.00 4.52
1766 3908 3.081061 CCACAAACATAGCTACTTGGCA 58.919 45.455 13.67 0.00 34.17 4.92
1866 4008 1.003580 ACACGATGCAGTGGGAGAAAT 59.996 47.619 10.49 0.00 45.80 2.17
1880 4022 3.948473 GGGAGAAATTGGAAAGCCTAGAC 59.052 47.826 0.00 0.00 34.31 2.59
1989 4131 3.432749 GCTCTATGATTGGCCTCAGAACA 60.433 47.826 3.32 0.00 0.00 3.18
2077 4219 2.267426 CACGGTGAAGCATGACGATTA 58.733 47.619 0.74 0.00 0.00 1.75
2166 4311 9.277783 CAGAGAGAGTTAATTATGGTATTTGGG 57.722 37.037 0.00 0.00 0.00 4.12
2202 4347 7.254455 GCACGTAGCAGATGATTTTAACAGTAT 60.254 37.037 5.30 0.00 44.79 2.12
2206 4356 7.325660 AGCAGATGATTTTAACAGTATGGTG 57.674 36.000 0.00 0.00 35.42 4.17
2221 4371 8.488651 ACAGTATGGTGTTTTACTACTATTGC 57.511 34.615 0.00 0.00 43.62 3.56
2225 4375 4.931002 TGGTGTTTTACTACTATTGCCGTC 59.069 41.667 0.00 0.00 0.00 4.79
2255 4405 1.268743 GCCAATGGATTAAGCACGAGC 60.269 52.381 2.05 0.00 42.56 5.03
2268 4418 1.126890 CACGAGCACGAGCATGATAG 58.873 55.000 11.40 0.00 45.49 2.08
2269 4419 0.596083 ACGAGCACGAGCATGATAGC 60.596 55.000 11.40 0.00 45.49 2.97
2271 4421 1.863267 GAGCACGAGCATGATAGCTT 58.137 50.000 7.77 0.00 46.75 3.74
2272 4422 1.791785 GAGCACGAGCATGATAGCTTC 59.208 52.381 7.77 0.00 46.75 3.86
2300 4450 4.137116 TGGATTCTCTTACAATGGTCGG 57.863 45.455 0.00 0.00 0.00 4.79
2307 4457 4.069304 CTCTTACAATGGTCGGTGGAAAA 58.931 43.478 0.00 0.00 0.00 2.29
2345 4495 3.062763 CGAACAGAAGCAGTCAGATTGT 58.937 45.455 0.00 0.00 0.00 2.71
2369 4519 0.035458 CTGGACTTGTCTCCACACCC 59.965 60.000 0.61 0.00 35.23 4.61
2561 4711 1.810030 GATCTTGACCGGCGTGACC 60.810 63.158 6.01 0.00 0.00 4.02
2672 4826 1.510776 GAGCTAGCAGACCATCATGC 58.489 55.000 18.83 0.00 42.87 4.06
2696 4850 3.112709 GCACGTCCGAGGCTGTTC 61.113 66.667 0.00 0.00 0.00 3.18
2715 4869 1.577328 CGCCAAGTTTCCATGTCGCT 61.577 55.000 0.00 0.00 0.00 4.93
3077 5235 0.387622 CAGGAACCAGCATGCGTTTG 60.388 55.000 13.01 5.14 31.27 2.93
3078 5236 1.080569 GGAACCAGCATGCGTTTGG 60.081 57.895 19.91 19.91 37.98 3.28
3079 5237 1.734117 GAACCAGCATGCGTTTGGC 60.734 57.895 21.09 5.55 43.96 4.52
3080 5238 2.146073 GAACCAGCATGCGTTTGGCT 62.146 55.000 21.09 11.57 44.05 4.75
3081 5239 2.146073 AACCAGCATGCGTTTGGCTC 62.146 55.000 21.09 0.00 44.05 4.70
3082 5240 2.202388 CAGCATGCGTTTGGCTCG 60.202 61.111 13.01 0.00 44.05 5.03
3089 5247 4.430423 CGTTTGGCTCGCACGCTC 62.430 66.667 0.00 0.00 0.00 5.03
3090 5248 4.090057 GTTTGGCTCGCACGCTCC 62.090 66.667 0.00 0.00 0.00 4.70
3128 5286 1.296392 CCATCTCCGTTCAGTGCCA 59.704 57.895 0.00 0.00 0.00 4.92
3145 5303 1.339151 GCCACGGGATCCTCCATATTC 60.339 57.143 12.58 0.00 38.64 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.378038 GAGCCCAATGGTTTGAGCATA 58.622 47.619 0.00 0.00 38.91 3.14
158 159 1.689243 CCTGCCATCGGGTCATCAGA 61.689 60.000 0.00 0.00 36.17 3.27
160 161 2.910360 CCTGCCATCGGGTCATCA 59.090 61.111 0.00 0.00 36.17 3.07
298 565 2.202440 GCAGCAATCACAGCGCAG 60.202 61.111 11.47 3.33 37.01 5.18
342 609 2.249413 CTGAGGAGGCAAGCGATGGT 62.249 60.000 0.00 0.00 0.00 3.55
344 611 0.809241 GACTGAGGAGGCAAGCGATG 60.809 60.000 0.00 0.00 0.00 3.84
557 866 1.359459 GGCGACGAAAGGAAGCGAAT 61.359 55.000 0.00 0.00 0.00 3.34
594 903 2.736682 GGAATCCGTTCACGCACCG 61.737 63.158 0.00 0.00 36.01 4.94
601 910 2.303022 AGAAGCTGAAGGAATCCGTTCA 59.697 45.455 11.66 11.66 42.70 3.18
684 998 2.528818 CCTGCAGGGAACTCCACCA 61.529 63.158 26.14 0.00 40.21 4.17
685 999 2.352805 CCTGCAGGGAACTCCACC 59.647 66.667 26.14 0.00 40.21 4.61
706 1061 1.201647 GTGTAGGAGCAGTTCGTAGCA 59.798 52.381 0.00 0.00 0.00 3.49
773 1129 4.267536 AGCGGATTCGTAGTGCCTATATA 58.732 43.478 0.00 0.00 38.89 0.86
774 1130 3.090037 AGCGGATTCGTAGTGCCTATAT 58.910 45.455 0.00 0.00 38.89 0.86
775 1131 2.511659 AGCGGATTCGTAGTGCCTATA 58.488 47.619 0.00 0.00 38.89 1.31
776 1132 1.329256 AGCGGATTCGTAGTGCCTAT 58.671 50.000 0.00 0.00 38.89 2.57
777 1133 1.108776 AAGCGGATTCGTAGTGCCTA 58.891 50.000 0.00 0.00 38.89 3.93
778 1134 0.460284 CAAGCGGATTCGTAGTGCCT 60.460 55.000 0.00 0.00 38.89 4.75
779 1135 1.429148 CCAAGCGGATTCGTAGTGCC 61.429 60.000 0.00 0.00 38.89 5.01
780 1136 0.739813 ACCAAGCGGATTCGTAGTGC 60.740 55.000 0.00 0.00 38.89 4.40
797 1153 1.479730 AGAACGGGGACTTCGATTACC 59.520 52.381 0.00 0.00 0.00 2.85
800 1156 1.263356 TCAGAACGGGGACTTCGATT 58.737 50.000 0.00 0.00 0.00 3.34
825 2881 1.009900 CGTCCATCTCTACGCGGTC 60.010 63.158 12.47 0.00 31.66 4.79
979 3113 1.405661 CGGTGTTTCTCTAGGGAAGCC 60.406 57.143 15.75 12.96 0.00 4.35
1124 3266 0.977627 ACCACCGCAGATGATCCAGA 60.978 55.000 0.00 0.00 0.00 3.86
1389 3531 2.507992 CAAGAGCTGGGCGTCGAG 60.508 66.667 0.00 0.00 0.00 4.04
1508 3650 1.185618 AGCGGGCGATTCCTAGCATA 61.186 55.000 0.00 0.00 39.61 3.14
1646 3788 2.173569 ACCATCTTTCCCCAGCAGATAC 59.826 50.000 0.00 0.00 0.00 2.24
1667 3809 4.325304 TCGTACACCGCGAACGCA 62.325 61.111 18.69 0.04 42.06 5.24
1671 3813 2.127270 GTCGTCGTACACCGCGAA 60.127 61.111 8.23 0.00 43.09 4.70
1765 3907 2.094286 AGCTCACCTCGATCAGACTTTG 60.094 50.000 0.00 0.00 0.00 2.77
1766 3908 2.094286 CAGCTCACCTCGATCAGACTTT 60.094 50.000 0.00 0.00 0.00 2.66
1866 4008 0.902531 CTCCCGTCTAGGCTTTCCAA 59.097 55.000 0.00 0.00 39.21 3.53
1880 4022 0.671781 CAGTGAACAAGGCTCTCCCG 60.672 60.000 0.00 0.00 39.21 5.14
1989 4131 4.191544 CGTTGGACCAGATCAACATGTAT 58.808 43.478 0.00 0.00 42.22 2.29
2052 4194 2.480587 CGTCATGCTTCACCGTGGTATA 60.481 50.000 0.00 0.00 0.00 1.47
2090 4235 3.866651 CTGTCCCAACTCATAAGACCAG 58.133 50.000 0.00 0.00 0.00 4.00
2166 4311 3.176708 TCTGCTACGTGCTAAAATCGAC 58.823 45.455 0.00 0.00 43.37 4.20
2202 4347 4.897140 ACGGCAATAGTAGTAAAACACCA 58.103 39.130 0.00 0.00 0.00 4.17
2206 4356 4.569564 CCTGGACGGCAATAGTAGTAAAAC 59.430 45.833 0.00 0.00 0.00 2.43
2269 4419 5.111989 TGTAAGAGAATCCATCAAGCGAAG 58.888 41.667 0.00 0.00 33.66 3.79
2270 4420 5.084818 TGTAAGAGAATCCATCAAGCGAA 57.915 39.130 0.00 0.00 33.66 4.70
2271 4421 4.736126 TGTAAGAGAATCCATCAAGCGA 57.264 40.909 0.00 0.00 33.66 4.93
2272 4422 5.277683 CCATTGTAAGAGAATCCATCAAGCG 60.278 44.000 0.00 0.00 33.66 4.68
2329 4479 2.681706 CGTCACAATCTGACTGCTTCT 58.318 47.619 0.00 0.00 46.50 2.85
2330 4480 1.127582 GCGTCACAATCTGACTGCTTC 59.872 52.381 8.87 0.00 46.50 3.86
2331 4481 1.151668 GCGTCACAATCTGACTGCTT 58.848 50.000 8.87 0.00 46.50 3.91
2345 4495 1.112916 TGGAGACAAGTCCAGCGTCA 61.113 55.000 0.00 0.00 41.99 4.35
2369 4519 2.544359 CGCGTGTCTTGAACGTGG 59.456 61.111 0.00 0.00 45.31 4.94
2561 4711 1.337817 CTTTCTGAGTCGCGGACGTG 61.338 60.000 6.13 0.00 41.18 4.49
2693 4847 2.331809 GACATGGAAACTTGGCGAAC 57.668 50.000 0.00 0.00 39.68 3.95


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

AutoCloner maintained by Alex Coulton.