Multiple sequence alignment - TraesCS3D01G433600

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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 TraesCS3D01G433600 chr3D 100.000 2897 0 0 1 2897 546582672 546579776 0.000000e+00 5350
1 TraesCS3D01G433600 chr3D 97.964 2898 54 5 1 2897 515701389 515698496 0.000000e+00 5020
2 TraesCS3D01G433600 chr7D 97.585 2898 65 5 1 2897 532955034 532957927 0.000000e+00 4959
3 TraesCS3D01G433600 chrUn 82.173 1997 294 48 933 2897 47721416 47719450 0.000000e+00 1659
4 TraesCS3D01G433600 chrUn 81.964 1996 299 46 933 2897 289579531 289581496 0.000000e+00 1635
5 TraesCS3D01G433600 chrUn 90.871 241 22 0 1 241 47722321 47722081 1.000000e-84 324
6 TraesCS3D01G433600 chrUn 90.871 241 22 0 1 241 289578626 289578866 1.000000e-84 324
7 TraesCS3D01G433600 chr7A 83.212 1787 247 37 1139 2895 522256088 522257851 0.000000e+00 1589
8 TraesCS3D01G433600 chr7A 83.445 1643 236 28 933 2560 709870745 709872366 0.000000e+00 1495
9 TraesCS3D01G433600 chr7A 78.848 851 143 26 1 836 522246720 522247548 9.130000e-150 540
10 TraesCS3D01G433600 chr7A 90.456 241 23 0 1 241 709869840 709870080 4.660000e-83 318
11 TraesCS3D01G433600 chr7A 91.124 169 14 1 978 1146 522247677 522247844 8.080000e-56 228
12 TraesCS3D01G433600 chr7A 82.041 245 30 8 2665 2897 709872438 709872680 2.280000e-46 196
13 TraesCS3D01G433600 chr4A 81.470 2013 297 48 916 2897 25201077 25203044 0.000000e+00 1581
14 TraesCS3D01G433600 chr4A 91.701 241 19 1 1 241 25200191 25200430 1.660000e-87 333
15 TraesCS3D01G433600 chr1A 81.768 1097 162 32 1677 2753 497225905 497224827 0.000000e+00 883
16 TraesCS3D01G433600 chr1A 83.469 738 100 15 916 1649 497227082 497226363 0.000000e+00 667
17 TraesCS3D01G433600 chr1A 91.286 241 21 0 1 241 497227971 497227731 2.150000e-86 329
18 TraesCS3D01G433600 chr3B 90.722 97 8 1 2801 2897 615890939 615890844 8.430000e-26 128


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 TraesCS3D01G433600 chr3D 546579776 546582672 2896 True 5350.000000 5350 100.000000 1 2897 1 chr3D.!!$R2 2896
1 TraesCS3D01G433600 chr3D 515698496 515701389 2893 True 5020.000000 5020 97.964000 1 2897 1 chr3D.!!$R1 2896
2 TraesCS3D01G433600 chr7D 532955034 532957927 2893 False 4959.000000 4959 97.585000 1 2897 1 chr7D.!!$F1 2896
3 TraesCS3D01G433600 chrUn 47719450 47722321 2871 True 991.500000 1659 86.522000 1 2897 2 chrUn.!!$R1 2896
4 TraesCS3D01G433600 chrUn 289578626 289581496 2870 False 979.500000 1635 86.417500 1 2897 2 chrUn.!!$F1 2896
5 TraesCS3D01G433600 chr7A 522256088 522257851 1763 False 1589.000000 1589 83.212000 1139 2895 1 chr7A.!!$F1 1756
6 TraesCS3D01G433600 chr7A 709869840 709872680 2840 False 669.666667 1495 85.314000 1 2897 3 chr7A.!!$F3 2896
7 TraesCS3D01G433600 chr7A 522246720 522247844 1124 False 384.000000 540 84.986000 1 1146 2 chr7A.!!$F2 1145
8 TraesCS3D01G433600 chr4A 25200191 25203044 2853 False 957.000000 1581 86.585500 1 2897 2 chr4A.!!$F1 2896
9 TraesCS3D01G433600 chr1A 497224827 497227971 3144 True 626.333333 883 85.507667 1 2753 3 chr1A.!!$R1 2752

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
768 781 1.626321 TCTTACACGAGAAATGGCCCA 59.374 47.619 0.0 0.0 0.0 5.36 F
1296 1346 1.334869 GTCTGCACAACCCTGACTTTG 59.665 52.381 0.0 0.0 0.0 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 2181 2.202987 GGAGGCTGCTGACATCCG 60.203 66.667 0.00 0.00 37.15 4.18 R
2129 2621 4.437659 GGCGTTTGACAAAACAGTTGTCTA 60.438 41.667 17.42 9.37 46.53 2.59 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
145 149 2.995283 GGGGGCTTACGTACTGAAAAT 58.005 47.619 0.00 0.0 0.00 1.82
364 371 2.660572 TCTGCTGCAACCAGGTTTTTA 58.339 42.857 0.44 0.0 39.54 1.52
469 476 5.540911 TGAAAAAGATGGTTGAGCAAATCC 58.459 37.500 0.00 0.0 0.00 3.01
637 647 2.592102 ACAGGTAAGGAGTGGTACGA 57.408 50.000 0.00 0.0 0.00 3.43
638 648 3.097342 ACAGGTAAGGAGTGGTACGAT 57.903 47.619 0.00 0.0 0.00 3.73
640 650 3.288964 CAGGTAAGGAGTGGTACGATCT 58.711 50.000 0.00 0.0 0.00 2.75
673 686 1.771255 AGTCAGCTGGGAATCATACCC 59.229 52.381 15.13 0.0 46.87 3.69
719 732 2.531522 ATTGCCACCAAAAGAGCAAC 57.468 45.000 0.00 0.0 46.98 4.17
725 738 2.607771 CCACCAAAAGAGCAACCAATCG 60.608 50.000 0.00 0.0 0.00 3.34
768 781 1.626321 TCTTACACGAGAAATGGCCCA 59.374 47.619 0.00 0.0 0.00 5.36
769 782 2.238646 TCTTACACGAGAAATGGCCCAT 59.761 45.455 0.00 0.0 0.00 4.00
780 793 4.342092 AGAAATGGCCCATAGGAATTTTCG 59.658 41.667 0.00 0.0 33.44 3.46
797 810 2.478547 TCGAATTACATACGCTCGCA 57.521 45.000 0.00 0.0 0.00 5.10
1052 1086 3.073062 ACCTTCACTGACAAGCTAATGGT 59.927 43.478 0.00 0.0 0.00 3.55
1296 1346 1.334869 GTCTGCACAACCCTGACTTTG 59.665 52.381 0.00 0.0 0.00 2.77
1390 1440 5.670792 TCAAGTATACAATCTGGTCCGTT 57.329 39.130 5.50 0.0 0.00 4.44
1460 1510 6.701400 GTCAAAAACAGAAACCAATAGCACAT 59.299 34.615 0.00 0.0 0.00 3.21
2097 2589 7.560991 ACCTTTCCATATTTGCATAGTTCATCA 59.439 33.333 0.00 0.0 0.00 3.07
2129 2621 3.941483 GACCCATTTGTTCTCATGATCGT 59.059 43.478 0.00 0.0 0.00 3.73
2226 2718 3.055719 CAACCCGGCTTCGTGCAT 61.056 61.111 0.00 0.0 45.15 3.96
2394 2886 2.627945 GCATCATCGTGTTAGACCCAA 58.372 47.619 0.00 0.0 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
364 371 2.811431 CGAGCTCTAATCTGTCGAGGAT 59.189 50.000 12.85 0.00 32.32 3.24
469 476 1.366111 CCACCAGCGATGTTAACCGG 61.366 60.000 0.00 0.00 0.00 5.28
624 634 1.749634 CCGAAGATCGTACCACTCCTT 59.250 52.381 0.00 0.00 38.40 3.36
719 732 1.268896 GCATTGGTGAGCATCGATTGG 60.269 52.381 0.00 0.00 38.61 3.16
725 738 1.939974 TCGTAGCATTGGTGAGCATC 58.060 50.000 0.00 0.00 0.00 3.91
768 781 8.603242 AGCGTATGTAATTCGAAAATTCCTAT 57.397 30.769 0.00 0.00 39.64 2.57
769 782 7.096353 CGAGCGTATGTAATTCGAAAATTCCTA 60.096 37.037 0.00 0.00 39.64 2.94
780 793 3.424529 GGTACTGCGAGCGTATGTAATTC 59.575 47.826 0.00 0.00 0.00 2.17
797 810 6.492772 CGGAATTCTTACTATGGTAGGGTACT 59.507 42.308 5.23 0.00 0.00 2.73
872 887 2.047560 ACGTACTTGAAGGGCGCC 60.048 61.111 21.18 21.18 0.00 6.53
1052 1086 0.396435 ACACATTTCTCCGAGGCACA 59.604 50.000 0.00 0.00 0.00 4.57
1246 1281 0.250945 TTGCGGTGGTGATAAGGCAA 60.251 50.000 0.00 0.00 37.98 4.52
1390 1440 4.142038 GGAAGGTAAACAAAGCCTCTTCA 58.858 43.478 0.00 0.00 33.07 3.02
1460 1510 4.368315 CAATCTCCATAACCGTCGAATCA 58.632 43.478 0.00 0.00 0.00 2.57
1508 1558 3.046390 GACAAGGATCGCTGTTAGATCG 58.954 50.000 0.36 0.00 43.93 3.69
1701 2181 2.202987 GGAGGCTGCTGACATCCG 60.203 66.667 0.00 0.00 37.15 4.18
2129 2621 4.437659 GGCGTTTGACAAAACAGTTGTCTA 60.438 41.667 17.42 9.37 46.53 2.59
2226 2718 8.100508 TGATGAAAATTTGTGTCGTACCATTA 57.899 30.769 0.00 0.00 0.00 1.90
2394 2886 4.765339 GCTATAACCAAAAGGTCCAACTGT 59.235 41.667 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.