Multiple sequence alignment - TraesCS3D01G529000

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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 TraesCS3D01G529000 chr3D 100.000 2390 0 0 1 2390 606797524 606795135 0.000000e+00 4414.0
1 TraesCS3D01G529000 chrUn 97.919 817 14 1 1 817 42477635 42478448 0.000000e+00 1411.0
2 TraesCS3D01G529000 chrUn 95.647 873 31 1 814 1686 42479395 42480260 0.000000e+00 1395.0
3 TraesCS3D01G529000 chrUn 84.793 651 80 10 793 1437 146317380 146318017 9.320000e-179 636.0
4 TraesCS3D01G529000 chrUn 84.722 648 86 9 793 1437 146406284 146406921 9.320000e-179 636.0
5 TraesCS3D01G529000 chrUn 94.907 216 8 2 1473 1686 42485577 42485791 3.810000e-88 335.0
6 TraesCS3D01G529000 chrUn 92.754 138 8 2 1467 1603 146318004 146318140 5.210000e-47 198.0
7 TraesCS3D01G529000 chrUn 92.029 138 9 2 1467 1603 146371162 146371298 2.420000e-45 193.0
8 TraesCS3D01G529000 chr3A 95.828 791 33 0 861 1651 738958537 738957747 0.000000e+00 1279.0
9 TraesCS3D01G529000 chr3A 100.000 37 0 0 1650 1686 738953456 738953420 4.260000e-08 69.4
10 TraesCS3D01G529000 chr1D 95.198 708 27 5 1689 2390 436094142 436093436 0.000000e+00 1112.0
11 TraesCS3D01G529000 chr1D 94.250 713 36 3 1683 2390 457085875 457085163 0.000000e+00 1085.0
12 TraesCS3D01G529000 chr2A 94.530 713 31 5 1683 2390 113932690 113931981 0.000000e+00 1094.0
13 TraesCS3D01G529000 chr1B 94.530 713 32 5 1683 2390 655840367 655841077 0.000000e+00 1094.0
14 TraesCS3D01G529000 chr1B 77.707 785 131 29 11 785 10313848 10314598 7.840000e-120 440.0
15 TraesCS3D01G529000 chr1B 78.522 433 74 18 352 776 71977413 71976992 1.410000e-67 267.0
16 TraesCS3D01G529000 chr1B 83.626 171 23 1 835 1005 604096661 604096496 3.180000e-34 156.0
17 TraesCS3D01G529000 chr6B 94.507 710 31 5 1686 2390 163547259 163546553 0.000000e+00 1088.0
18 TraesCS3D01G529000 chr2D 94.374 711 35 3 1685 2390 174448908 174449618 0.000000e+00 1086.0
19 TraesCS3D01G529000 chr7D 94.233 711 36 3 1685 2390 504124907 504125617 0.000000e+00 1081.0
20 TraesCS3D01G529000 chr7D 81.748 389 56 11 366 747 538028109 538027729 6.420000e-81 311.0
21 TraesCS3D01G529000 chr6D 93.986 715 33 8 1682 2390 71517866 71518576 0.000000e+00 1074.0
22 TraesCS3D01G529000 chr7B 93.969 713 36 5 1683 2390 115234266 115233556 0.000000e+00 1072.0
23 TraesCS3D01G529000 chr5B 86.414 817 97 9 793 1606 509671487 509670682 0.000000e+00 881.0
24 TraesCS3D01G529000 chr5B 86.902 794 91 8 793 1583 509677333 509676550 0.000000e+00 878.0
25 TraesCS3D01G529000 chr5D 98.529 476 7 0 1 476 417373494 417373969 0.000000e+00 841.0
26 TraesCS3D01G529000 chr5D 98.339 301 1 2 518 817 417373966 417374263 2.100000e-145 525.0
27 TraesCS3D01G529000 chr7A 78.507 442 76 16 352 785 26798522 26798092 3.030000e-69 272.0
28 TraesCS3D01G529000 chr6A 77.368 190 23 13 558 744 262509429 262509601 7.030000e-16 95.3


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 TraesCS3D01G529000 chr3D 606795135 606797524 2389 True 4414 4414 100.0000 1 2390 1 chr3D.!!$R1 2389
1 TraesCS3D01G529000 chrUn 42477635 42480260 2625 False 1403 1411 96.7830 1 1686 2 chrUn.!!$F4 1685
2 TraesCS3D01G529000 chrUn 146406284 146406921 637 False 636 636 84.7220 793 1437 1 chrUn.!!$F3 644
3 TraesCS3D01G529000 chrUn 146317380 146318140 760 False 417 636 88.7735 793 1603 2 chrUn.!!$F5 810
4 TraesCS3D01G529000 chr3A 738957747 738958537 790 True 1279 1279 95.8280 861 1651 1 chr3A.!!$R2 790
5 TraesCS3D01G529000 chr1D 436093436 436094142 706 True 1112 1112 95.1980 1689 2390 1 chr1D.!!$R1 701
6 TraesCS3D01G529000 chr1D 457085163 457085875 712 True 1085 1085 94.2500 1683 2390 1 chr1D.!!$R2 707
7 TraesCS3D01G529000 chr2A 113931981 113932690 709 True 1094 1094 94.5300 1683 2390 1 chr2A.!!$R1 707
8 TraesCS3D01G529000 chr1B 655840367 655841077 710 False 1094 1094 94.5300 1683 2390 1 chr1B.!!$F2 707
9 TraesCS3D01G529000 chr1B 10313848 10314598 750 False 440 440 77.7070 11 785 1 chr1B.!!$F1 774
10 TraesCS3D01G529000 chr6B 163546553 163547259 706 True 1088 1088 94.5070 1686 2390 1 chr6B.!!$R1 704
11 TraesCS3D01G529000 chr2D 174448908 174449618 710 False 1086 1086 94.3740 1685 2390 1 chr2D.!!$F1 705
12 TraesCS3D01G529000 chr7D 504124907 504125617 710 False 1081 1081 94.2330 1685 2390 1 chr7D.!!$F1 705
13 TraesCS3D01G529000 chr6D 71517866 71518576 710 False 1074 1074 93.9860 1682 2390 1 chr6D.!!$F1 708
14 TraesCS3D01G529000 chr7B 115233556 115234266 710 True 1072 1072 93.9690 1683 2390 1 chr7B.!!$R1 707
15 TraesCS3D01G529000 chr5B 509670682 509671487 805 True 881 881 86.4140 793 1606 1 chr5B.!!$R1 813
16 TraesCS3D01G529000 chr5B 509676550 509677333 783 True 878 878 86.9020 793 1583 1 chr5B.!!$R2 790
17 TraesCS3D01G529000 chr5D 417373494 417374263 769 False 683 841 98.4340 1 817 2 chr5D.!!$F1 816

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
875 1833 0.246635 GGCCTCACGCTCTCTTTGTA 59.753 55.0 0.0 0.0 37.74 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 2782 0.098025 GTTGTGTTGTCGTGTGTGGG 59.902 55.0 0.0 0.0 0.0 4.61 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
84 88 4.047166 AGGGAATTCTGGATGATGTACCA 58.953 43.478 5.23 0.00 34.81 3.25
223 230 2.264005 TGTGGTAGAAACGGCAACAT 57.736 45.000 0.00 0.00 0.00 2.71
370 377 0.253044 AACGGCATGTGTGGATAGCT 59.747 50.000 0.00 0.00 0.00 3.32
375 382 3.928992 CGGCATGTGTGGATAGCTTATAG 59.071 47.826 0.00 0.00 0.00 1.31
795 803 4.926238 CAGAGTGCACTCCAGTAAAAGTAG 59.074 45.833 37.09 12.93 43.88 2.57
796 804 4.833380 AGAGTGCACTCCAGTAAAAGTAGA 59.167 41.667 37.09 0.00 43.88 2.59
797 805 4.884247 AGTGCACTCCAGTAAAAGTAGAC 58.116 43.478 15.25 0.00 0.00 2.59
826 1784 4.280677 TGGTTCAGCTAAATTTTCACCCAG 59.719 41.667 0.00 0.00 0.00 4.45
875 1833 0.246635 GGCCTCACGCTCTCTTTGTA 59.753 55.000 0.00 0.00 37.74 2.41
920 1878 0.541863 CCACCTTCATAAGCGTCCCT 59.458 55.000 0.00 0.00 0.00 4.20
1098 2061 2.883828 CGCCACCCTCACCAAGTCT 61.884 63.158 0.00 0.00 0.00 3.24
1121 2084 2.354821 GCGAGAACCTGTTCAAGTTTGT 59.645 45.455 12.21 0.00 41.84 2.83
1139 2102 4.598894 CCTCGCCGGGCTCATCAG 62.599 72.222 18.34 0.00 0.00 2.90
1158 2121 2.666190 TCGGTCCTCGACGACGTT 60.666 61.111 0.13 0.00 43.74 3.99
1298 2261 2.375174 TCATGTTGGCCTACAAGAAGGT 59.625 45.455 23.79 3.49 40.38 3.50
1340 2303 1.374758 CGCCCGCTCAGAAGTTCTT 60.375 57.895 1.56 0.00 0.00 2.52
1412 2382 2.029623 GGCACCTCGTTCACCTCTATA 58.970 52.381 0.00 0.00 0.00 1.31
1413 2383 2.628657 GGCACCTCGTTCACCTCTATAT 59.371 50.000 0.00 0.00 0.00 0.86
1414 2384 3.069729 GGCACCTCGTTCACCTCTATATT 59.930 47.826 0.00 0.00 0.00 1.28
1415 2385 4.299978 GCACCTCGTTCACCTCTATATTC 58.700 47.826 0.00 0.00 0.00 1.75
1416 2386 4.537965 CACCTCGTTCACCTCTATATTCG 58.462 47.826 0.00 0.00 0.00 3.34
1417 2387 4.275196 CACCTCGTTCACCTCTATATTCGA 59.725 45.833 0.00 0.00 0.00 3.71
1418 2388 5.048643 CACCTCGTTCACCTCTATATTCGAT 60.049 44.000 0.00 0.00 0.00 3.59
1681 2651 9.171701 GAAATACTGTGTATGATAGACTCGTTC 57.828 37.037 1.35 0.00 0.00 3.95
1799 2770 2.027192 AGCACAACACCATATCCGACTT 60.027 45.455 0.00 0.00 0.00 3.01
1811 2782 0.966920 TCCGACTTTCCTCAGGACAC 59.033 55.000 0.00 0.00 0.00 3.67
1881 2854 4.719369 ACCTCGCCGCGTCTTGAC 62.719 66.667 13.39 0.00 0.00 3.18
1929 2902 3.873801 GCAACTCCAGCTTCCTTTGGATA 60.874 47.826 0.00 0.00 42.32 2.59
2151 3129 1.073216 CGACACACTCGATGTCCAGC 61.073 60.000 11.10 0.00 46.14 4.85
2243 3221 2.885113 CGCATCTCCACTCCGACA 59.115 61.111 0.00 0.00 0.00 4.35
2275 3253 1.371183 CACCGTTCCTGAAGCCTCA 59.629 57.895 0.00 0.00 0.00 3.86
2287 3265 4.760047 GCCTCACACCGCCGTCAT 62.760 66.667 0.00 0.00 0.00 3.06
2367 3345 2.741092 GCGAACCAGACCTCCACA 59.259 61.111 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 88 1.542492 CTTTGCCATGCCTTCAGACT 58.458 50.000 0.00 0.0 0.00 3.24
170 174 3.431673 TGGTGGACTGCATGATTTACA 57.568 42.857 0.00 0.0 0.00 2.41
370 377 7.072177 CGCAAGTTCAGTTTTCCATCTATAA 57.928 36.000 0.00 0.0 0.00 0.98
795 803 2.380084 TTAGCTGAACCACCATCGTC 57.620 50.000 0.00 0.0 0.00 4.20
796 804 2.851263 TTTAGCTGAACCACCATCGT 57.149 45.000 0.00 0.0 0.00 3.73
797 805 4.701956 AAATTTAGCTGAACCACCATCG 57.298 40.909 0.00 0.0 0.00 3.84
826 1784 2.598632 GCGGACGCCATACTGCATC 61.599 63.158 5.20 0.0 38.17 3.91
875 1833 6.128007 CCGTTGCTTTAAATAGGAGATGTTGT 60.128 38.462 0.00 0.0 0.00 3.32
920 1878 3.990318 ATGAGATCGATGCTTACGTCA 57.010 42.857 0.54 0.0 0.00 4.35
1098 2061 0.468226 ACTTGAACAGGTTCTCGCCA 59.532 50.000 12.86 0.0 40.14 5.69
1298 2261 2.962569 CGAGGACTTGCTCACCGA 59.037 61.111 0.00 0.0 0.00 4.69
1340 2303 2.978156 AAAGCCTTTCTCCATGACCA 57.022 45.000 0.00 0.0 0.00 4.02
1412 2382 8.872845 GCAATGGAAATAAGAAACAAATCGAAT 58.127 29.630 0.00 0.0 0.00 3.34
1413 2383 7.330700 GGCAATGGAAATAAGAAACAAATCGAA 59.669 33.333 0.00 0.0 0.00 3.71
1414 2384 6.811170 GGCAATGGAAATAAGAAACAAATCGA 59.189 34.615 0.00 0.0 0.00 3.59
1415 2385 6.589523 TGGCAATGGAAATAAGAAACAAATCG 59.410 34.615 0.00 0.0 0.00 3.34
1416 2386 7.903995 TGGCAATGGAAATAAGAAACAAATC 57.096 32.000 0.00 0.0 0.00 2.17
1417 2387 7.148205 GCATGGCAATGGAAATAAGAAACAAAT 60.148 33.333 2.54 0.0 34.09 2.32
1418 2388 6.149142 GCATGGCAATGGAAATAAGAAACAAA 59.851 34.615 2.54 0.0 34.09 2.83
1743 2713 2.034685 GCAGCGAGTGGTAGATGTCATA 59.965 50.000 0.00 0.0 0.00 2.15
1790 2761 2.758979 GTGTCCTGAGGAAAGTCGGATA 59.241 50.000 0.96 0.0 31.38 2.59
1799 2770 0.692756 TGTGTGGGTGTCCTGAGGAA 60.693 55.000 0.96 0.0 31.38 3.36
1811 2782 0.098025 GTTGTGTTGTCGTGTGTGGG 59.902 55.000 0.00 0.0 0.00 4.61
1881 2854 2.048503 GGAGGTGTTCGGTGTCGG 60.049 66.667 0.00 0.0 36.95 4.79
1929 2902 1.065273 GTATGGTCGTCGCGGATGT 59.935 57.895 6.13 0.0 0.00 3.06
2144 3117 1.612146 TCATTCCCCTCGCTGGACA 60.612 57.895 0.00 0.0 38.35 4.02
2151 3129 2.186903 CGGGTGTCATTCCCCTCG 59.813 66.667 0.00 0.0 41.78 4.63
2243 3221 4.029809 GGTGCTGCCCGGTACCTT 62.030 66.667 10.90 0.0 38.61 3.50


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

AutoCloner maintained by Alex Coulton.