Multiple sequence alignment - TraesCS6D01G003500

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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 TraesCS6D01G003500 chr6D 100.000 2930 0 0 1 2930 1904404 1901475 0.000000e+00 5411.0
1 TraesCS6D01G003500 chr6D 92.338 1775 89 23 716 2452 1760333 1762098 0.000000e+00 2481.0
2 TraesCS6D01G003500 chr6D 90.927 1554 107 23 715 2260 1850277 1848750 0.000000e+00 2058.0
3 TraesCS6D01G003500 chr6D 86.350 1304 152 18 975 2261 1799996 1798702 0.000000e+00 1399.0
4 TraesCS6D01G003500 chr6D 84.637 1406 169 27 868 2261 1635624 1636994 0.000000e+00 1356.0
5 TraesCS6D01G003500 chr6D 98.039 714 11 3 1 713 369860941 369861652 0.000000e+00 1238.0
6 TraesCS6D01G003500 chr6D 83.918 1026 118 26 1251 2257 1809409 1808412 0.000000e+00 937.0
7 TraesCS6D01G003500 chr6D 86.690 571 50 13 2224 2774 1848730 1848166 6.940000e-171 610.0
8 TraesCS6D01G003500 chr6D 90.638 235 10 5 2552 2774 1762102 1762336 4.750000e-78 302.0
9 TraesCS6D01G003500 chr6D 89.109 202 19 3 2487 2687 1798473 1798274 6.270000e-62 248.0
10 TraesCS6D01G003500 chr6D 82.879 257 41 3 2487 2742 1637233 1637487 8.170000e-56 228.0
11 TraesCS6D01G003500 chr6D 89.831 59 5 1 897 955 1800140 1800083 1.130000e-09 75.0
12 TraesCS6D01G003500 chr6A 91.682 2212 120 29 759 2930 932011 934198 0.000000e+00 3007.0
13 TraesCS6D01G003500 chr6A 85.714 1302 157 17 982 2261 968811 967517 0.000000e+00 1347.0
14 TraesCS6D01G003500 chr6A 82.069 290 45 4 2487 2774 967278 966994 1.050000e-59 241.0
15 TraesCS6D01G003500 chr6A 91.525 59 4 1 897 955 968961 968904 2.420000e-11 80.5
16 TraesCS6D01G003500 chr6B 90.869 1588 87 31 715 2272 4856218 4857777 0.000000e+00 2076.0
17 TraesCS6D01G003500 chr6B 90.025 1584 111 24 715 2272 4885582 4884020 0.000000e+00 2006.0
18 TraesCS6D01G003500 chr6B 87.037 162 15 4 715 872 4847793 4847952 8.340000e-41 178.0
19 TraesCS6D01G003500 chr6B 95.960 99 3 1 2224 2321 4884010 4883912 3.020000e-35 159.0
20 TraesCS6D01G003500 chr2D 98.315 712 11 1 1 711 80211422 80210711 0.000000e+00 1247.0
21 TraesCS6D01G003500 chr2D 97.759 714 15 1 1 713 602235568 602236281 0.000000e+00 1229.0
22 TraesCS6D01G003500 chr3D 98.172 711 12 1 1 710 613548403 613547693 0.000000e+00 1240.0
23 TraesCS6D01G003500 chr3D 98.036 713 13 1 1 712 604675 603963 0.000000e+00 1238.0
24 TraesCS6D01G003500 chr3D 82.590 919 128 22 1016 1928 582909598 582908706 0.000000e+00 782.0
25 TraesCS6D01G003500 chr1D 98.172 711 12 1 1 710 288843937 288844647 0.000000e+00 1240.0
26 TraesCS6D01G003500 chr4D 98.031 711 12 2 1 710 59077230 59077939 0.000000e+00 1234.0
27 TraesCS6D01G003500 chr5D 97.890 711 14 1 1 710 247320046 247319336 0.000000e+00 1229.0
28 TraesCS6D01G003500 chr5D 97.490 717 14 4 1 715 380177452 380176738 0.000000e+00 1221.0


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 TraesCS6D01G003500 chr6D 1901475 1904404 2929 True 5411.000000 5411 100.0000 1 2930 1 chr6D.!!$R2 2929
1 TraesCS6D01G003500 chr6D 1760333 1762336 2003 False 1391.500000 2481 91.4880 716 2774 2 chr6D.!!$F3 2058
2 TraesCS6D01G003500 chr6D 1848166 1850277 2111 True 1334.000000 2058 88.8085 715 2774 2 chr6D.!!$R4 2059
3 TraesCS6D01G003500 chr6D 369860941 369861652 711 False 1238.000000 1238 98.0390 1 713 1 chr6D.!!$F1 712
4 TraesCS6D01G003500 chr6D 1808412 1809409 997 True 937.000000 937 83.9180 1251 2257 1 chr6D.!!$R1 1006
5 TraesCS6D01G003500 chr6D 1635624 1637487 1863 False 792.000000 1356 83.7580 868 2742 2 chr6D.!!$F2 1874
6 TraesCS6D01G003500 chr6D 1798274 1800140 1866 True 574.000000 1399 88.4300 897 2687 3 chr6D.!!$R3 1790
7 TraesCS6D01G003500 chr6A 932011 934198 2187 False 3007.000000 3007 91.6820 759 2930 1 chr6A.!!$F1 2171
8 TraesCS6D01G003500 chr6A 966994 968961 1967 True 556.166667 1347 86.4360 897 2774 3 chr6A.!!$R1 1877
9 TraesCS6D01G003500 chr6B 4856218 4857777 1559 False 2076.000000 2076 90.8690 715 2272 1 chr6B.!!$F2 1557
10 TraesCS6D01G003500 chr6B 4883912 4885582 1670 True 1082.500000 2006 92.9925 715 2321 2 chr6B.!!$R1 1606
11 TraesCS6D01G003500 chr2D 80210711 80211422 711 True 1247.000000 1247 98.3150 1 711 1 chr2D.!!$R1 710
12 TraesCS6D01G003500 chr2D 602235568 602236281 713 False 1229.000000 1229 97.7590 1 713 1 chr2D.!!$F1 712
13 TraesCS6D01G003500 chr3D 613547693 613548403 710 True 1240.000000 1240 98.1720 1 710 1 chr3D.!!$R3 709
14 TraesCS6D01G003500 chr3D 603963 604675 712 True 1238.000000 1238 98.0360 1 712 1 chr3D.!!$R1 711
15 TraesCS6D01G003500 chr3D 582908706 582909598 892 True 782.000000 782 82.5900 1016 1928 1 chr3D.!!$R2 912
16 TraesCS6D01G003500 chr1D 288843937 288844647 710 False 1240.000000 1240 98.1720 1 710 1 chr1D.!!$F1 709
17 TraesCS6D01G003500 chr4D 59077230 59077939 709 False 1234.000000 1234 98.0310 1 710 1 chr4D.!!$F1 709
18 TraesCS6D01G003500 chr5D 247319336 247320046 710 True 1229.000000 1229 97.8900 1 710 1 chr5D.!!$R1 709
19 TraesCS6D01G003500 chr5D 380176738 380177452 714 True 1221.000000 1221 97.4900 1 715 1 chr5D.!!$R2 714

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
997 1110 0.174617 AGCTAACGAGAGCAAGCTCC 59.825 55.0 17.81 9.04 45.9 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 2615 0.914417 AATCGGTGATGGGACCAGGT 60.914 55.0 0.0 0.0 35.5 4.0 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
290 291 2.292292 GAGTTTGTGCGTTGTTATGGGT 59.708 45.455 0.00 0.00 0.00 4.51
303 304 6.294286 CGTTGTTATGGGTAATTTGGAACTGT 60.294 38.462 0.00 0.00 0.00 3.55
502 503 5.338056 GGATGGCGGTCATGTAATAGGATTA 60.338 44.000 0.00 0.00 35.97 1.75
569 571 6.923508 GCTTTATGGCCTTTTATTGTGTATCC 59.076 38.462 3.32 0.00 0.00 2.59
577 579 6.414732 CCTTTTATTGTGTATCCTCCTGACA 58.585 40.000 0.00 0.00 0.00 3.58
955 1008 1.330655 TTCATCCCAGTCTCGCTCCC 61.331 60.000 0.00 0.00 0.00 4.30
996 1109 3.731295 AGCTAACGAGAGCAAGCTC 57.269 52.632 14.00 14.00 45.90 4.09
997 1110 0.174617 AGCTAACGAGAGCAAGCTCC 59.825 55.000 17.81 9.04 45.90 4.70
999 1112 0.526524 CTAACGAGAGCAAGCTCCGG 60.527 60.000 25.35 17.79 43.70 5.14
1000 1113 0.963856 TAACGAGAGCAAGCTCCGGA 60.964 55.000 25.35 2.93 43.70 5.14
1001 1114 1.608717 AACGAGAGCAAGCTCCGGAT 61.609 55.000 25.35 16.41 43.70 4.18
1088 1204 2.577059 GTTCATCTCCGTGGGCGA 59.423 61.111 0.00 0.00 41.33 5.54
1094 1210 4.003788 CTCCGTGGGCGACAACCT 62.004 66.667 0.00 0.00 41.33 3.50
1592 1710 5.536916 GGGAGTAAGTGCACTACTGAGATAT 59.463 44.000 22.01 3.16 40.26 1.63
1711 1833 7.747155 TTGATGTTTGATGATTGGCAATTTT 57.253 28.000 14.93 4.86 0.00 1.82
2004 2135 4.163458 TGTTAGCCAGATCTACCGGATTTT 59.837 41.667 9.46 0.00 34.33 1.82
2069 2202 5.772393 TGGAGCCAAATTAGGAGAAACTA 57.228 39.130 0.00 0.00 0.00 2.24
2102 2238 5.546526 TGACAAAAAGTTTGTTGCTCCTTT 58.453 33.333 7.72 0.00 31.96 3.11
2117 2253 4.512571 TGCTCCTTTCGTTTGGTACTAAAC 59.487 41.667 21.29 21.29 37.23 2.01
2236 2487 1.448922 AACCTTGGCGCGCAAAAGTA 61.449 50.000 34.42 5.20 0.00 2.24
2357 2613 0.958382 TCCTTCACGCAATTTCCCCG 60.958 55.000 0.00 0.00 0.00 5.73
2359 2615 0.878416 CTTCACGCAATTTCCCCGAA 59.122 50.000 0.00 0.00 0.00 4.30
2361 2617 1.211709 CACGCAATTTCCCCGAACC 59.788 57.895 0.00 0.00 0.00 3.62
2390 2646 6.010219 CCCATCACCGATTATTTTCCCTATT 58.990 40.000 0.00 0.00 0.00 1.73
2477 2733 1.266989 TGAGCATGTACTATCTCCGCG 59.733 52.381 0.00 0.00 0.00 6.46
2481 2737 0.598562 ATGTACTATCTCCGCGCTGG 59.401 55.000 5.56 9.07 40.09 4.85
2503 2759 7.569599 TGGAAGGGGTAGATATTCCTAATTC 57.430 40.000 4.60 0.00 41.49 2.17
2523 2779 1.755395 GCTTCATGCTCCCATGCCA 60.755 57.895 0.00 0.00 46.69 4.92
2692 2955 6.899114 ACTAACCGAAGTTTATTTTCTGCAG 58.101 36.000 7.63 7.63 37.42 4.41
2696 2959 4.023193 CCGAAGTTTATTTTCTGCAGTGGT 60.023 41.667 14.67 1.36 0.00 4.16
2706 2984 1.572085 CTGCAGTGGTTCAAGCCTCG 61.572 60.000 5.25 0.00 0.00 4.63
2708 2986 1.845809 GCAGTGGTTCAAGCCTCGTG 61.846 60.000 0.00 0.00 0.00 4.35
2764 3048 9.565090 TCAATACTTGCATATGCTTTCTCTTAT 57.435 29.630 27.13 11.51 42.66 1.73
2784 3068 6.894654 TCTTATGAAAATGTTTAGGGCATGGA 59.105 34.615 0.00 0.00 0.00 3.41
2801 3085 7.049754 GGGCATGGAAATTCTCACAATTTAAT 58.950 34.615 0.00 0.00 30.68 1.40
2830 3114 7.451255 TGATGTAACATGAAAATTCCCTTCAGT 59.549 33.333 0.00 0.00 36.30 3.41
2835 3119 3.575805 TGAAAATTCCCTTCAGTTGGCT 58.424 40.909 0.00 0.00 0.00 4.75
2844 3128 1.000938 CTTCAGTTGGCTTGGCAAGTC 60.001 52.381 24.39 24.39 0.00 3.01
2845 3129 0.183492 TCAGTTGGCTTGGCAAGTCT 59.817 50.000 29.80 18.32 33.26 3.24
2852 3136 1.795170 GCTTGGCAAGTCTTCGGCAA 61.795 55.000 26.71 17.04 44.41 4.52
2900 3185 1.135199 GTCTGCCAATTGTCCATGCTG 60.135 52.381 4.43 4.64 0.00 4.41
2904 3189 1.717194 CCAATTGTCCATGCTGCAAC 58.283 50.000 6.36 0.44 0.00 4.17
2918 3203 0.040058 TGCAACCATGGCAATCTCCT 59.960 50.000 13.04 0.00 38.54 3.69
2924 3209 2.311542 ACCATGGCAATCTCCTAAACCA 59.688 45.455 13.04 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 153 3.959975 GCACGGAGCGCCACAAAA 61.960 61.111 7.44 0.00 0.00 2.44
200 201 0.975135 TCCAAATAACGACCCGACCA 59.025 50.000 0.00 0.00 0.00 4.02
290 291 9.177608 CCAGATCATTTCTACAGTTCCAAATTA 57.822 33.333 0.00 0.00 31.77 1.40
303 304 8.862325 TTCTGTTAAAAGCCAGATCATTTCTA 57.138 30.769 0.00 0.00 37.54 2.10
502 503 7.978099 AAATTAGGGATGGAAACTAATTGCT 57.022 32.000 8.99 0.00 43.07 3.91
518 519 0.740737 CGGCTGGCAGAAAATTAGGG 59.259 55.000 20.86 0.00 0.00 3.53
569 571 3.430098 GCTCACATAGACCTTGTCAGGAG 60.430 52.174 0.00 0.00 44.19 3.69
577 579 1.402259 CGTCGAGCTCACATAGACCTT 59.598 52.381 15.40 0.00 0.00 3.50
999 1112 1.071471 CATAGTGGCCGACCCCATC 59.929 63.158 0.00 0.00 37.20 3.51
1000 1113 1.383943 TCATAGTGGCCGACCCCAT 60.384 57.895 0.00 0.00 37.20 4.00
1001 1114 2.039787 TCATAGTGGCCGACCCCA 59.960 61.111 0.00 0.00 33.59 4.96
1094 1210 4.020617 CGTTCTGGGCCTGCTCCA 62.021 66.667 4.53 0.00 0.00 3.86
1249 1365 3.492353 CGGGATGGGTGGGAGCAT 61.492 66.667 0.00 0.00 0.00 3.79
1257 1373 0.620410 TGGAGATGAACGGGATGGGT 60.620 55.000 0.00 0.00 0.00 4.51
1267 1383 0.538584 ATGCAGAGCGTGGAGATGAA 59.461 50.000 0.00 0.00 0.00 2.57
1711 1833 3.385314 TTTCCTGCATCCATCCATGAA 57.615 42.857 0.00 0.00 0.00 2.57
2069 2202 7.258022 ACAAACTTTTTGTCAAGCAGTTTTT 57.742 28.000 16.20 10.75 0.00 1.94
2102 2238 7.660617 TCATATGGTTTGTTTAGTACCAAACGA 59.339 33.333 11.47 11.08 44.49 3.85
2117 2253 5.508489 GGCAATGATGTCCTCATATGGTTTG 60.508 44.000 2.13 0.00 44.03 2.93
2183 2376 7.725844 AGGATGATCTAAACCAAGAACTTTTGT 59.274 33.333 0.00 0.00 0.00 2.83
2236 2487 5.525378 TGCGCAATTTCAAAATAAACCAAGT 59.475 32.000 8.16 0.00 0.00 3.16
2345 2599 1.506262 CAGGTTCGGGGAAATTGCG 59.494 57.895 0.00 0.00 0.00 4.85
2357 2613 1.078426 CGGTGATGGGACCAGGTTC 60.078 63.158 0.00 0.00 35.50 3.62
2359 2615 0.914417 AATCGGTGATGGGACCAGGT 60.914 55.000 0.00 0.00 35.50 4.00
2361 2617 3.492102 AATAATCGGTGATGGGACCAG 57.508 47.619 0.00 0.00 35.50 4.00
2432 2688 7.654022 TGTACCAAGAAAAGAAAAGGAACAT 57.346 32.000 0.00 0.00 0.00 2.71
2434 2690 7.712797 TCATGTACCAAGAAAAGAAAAGGAAC 58.287 34.615 0.00 0.00 0.00 3.62
2437 2693 6.152379 GCTCATGTACCAAGAAAAGAAAAGG 58.848 40.000 0.00 0.00 0.00 3.11
2438 2694 6.738114 TGCTCATGTACCAAGAAAAGAAAAG 58.262 36.000 0.00 0.00 0.00 2.27
2439 2695 6.707440 TGCTCATGTACCAAGAAAAGAAAA 57.293 33.333 0.00 0.00 0.00 2.29
2473 2729 4.530857 CTACCCCTTCCAGCGCGG 62.531 72.222 8.83 11.37 0.00 6.46
2474 2730 1.461091 TATCTACCCCTTCCAGCGCG 61.461 60.000 0.00 0.00 0.00 6.86
2477 2733 3.252351 AGGAATATCTACCCCTTCCAGC 58.748 50.000 3.28 0.00 39.71 4.85
2481 2737 7.037945 AGCTGAATTAGGAATATCTACCCCTTC 60.038 40.741 0.00 0.00 0.00 3.46
2523 2779 2.880890 GACACACAGTTTCTTCCATGCT 59.119 45.455 0.00 0.00 0.00 3.79
2682 2941 2.036346 GGCTTGAACCACTGCAGAAAAT 59.964 45.455 23.35 3.40 0.00 1.82
2688 2947 1.597854 CGAGGCTTGAACCACTGCA 60.598 57.895 0.00 0.00 0.00 4.41
2692 2955 2.946762 GCACGAGGCTTGAACCAC 59.053 61.111 9.20 0.00 40.25 4.16
2696 2959 2.357034 GTCCGCACGAGGCTTGAA 60.357 61.111 9.20 0.00 41.67 2.69
2764 3048 5.815233 TTTCCATGCCCTAAACATTTTCA 57.185 34.783 0.00 0.00 0.00 2.69
2830 3114 1.172180 CCGAAGACTTGCCAAGCCAA 61.172 55.000 3.88 0.00 0.00 4.52
2835 3119 1.172180 CCTTGCCGAAGACTTGCCAA 61.172 55.000 0.00 0.00 0.00 4.52
2844 3128 3.254657 TGGTGAAAATTACCTTGCCGAAG 59.745 43.478 0.00 0.00 39.01 3.79
2845 3129 3.223435 TGGTGAAAATTACCTTGCCGAA 58.777 40.909 0.00 0.00 39.01 4.30
2900 3185 2.057137 TAGGAGATTGCCATGGTTGC 57.943 50.000 14.67 0.00 0.00 4.17
2904 3189 3.017048 TGGTTTAGGAGATTGCCATGG 57.983 47.619 7.63 7.63 0.00 3.66


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

AutoCloner maintained by Alex Coulton.