Multiple sequence alignment - TraesCS6D01G094900

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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 TraesCS6D01G094900 chr6D 100.000 2520 0 0 1 2520 59276688 59274169 0 4654
1 TraesCS6D01G094900 chr2D 96.235 2523 74 10 1 2520 46525258 46527762 0 4113
2 TraesCS6D01G094900 chr3D 96.157 2524 71 13 1 2520 543133958 543131457 0 4100
3 TraesCS6D01G094900 chr3D 96.002 2526 84 10 1 2520 551735205 551732691 0 4089
4 TraesCS6D01G094900 chr3D 95.998 2524 81 11 1 2520 360444210 360441703 0 4084
5 TraesCS6D01G094900 chr3D 95.534 2530 86 15 1 2520 384995261 384997773 0 4021
6 TraesCS6D01G094900 chr5D 96.006 2529 75 16 1 2520 306886166 306883655 0 4087
7 TraesCS6D01G094900 chr7D 95.719 2523 90 9 1 2520 510254738 510257245 0 4045
8 TraesCS6D01G094900 chr1B 95.644 2525 91 11 1 2520 487691521 487689011 0 4036
9 TraesCS6D01G094900 chr1D 95.602 2524 88 12 1 2520 417885908 417883404 0 4024
10 TraesCS6D01G094900 chr4B 94.535 2525 97 19 1 2520 379060561 379063049 0 3860
11 TraesCS6D01G094900 chr5A 94.422 2528 104 18 1 2520 664010955 664008457 0 3853
12 TraesCS6D01G094900 chr2B 93.901 2525 101 21 1 2520 646053806 646051330 0 3760
13 TraesCS6D01G094900 chr2B 95.549 1730 61 11 1 1728 467754941 467753226 0 2754
14 TraesCS6D01G094900 chrUn 92.877 2527 134 19 1 2520 37646431 37643944 0 3627
15 TraesCS6D01G094900 chrUn 92.877 2527 134 19 1 2520 251163542 251166029 0 3627


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 TraesCS6D01G094900 chr6D 59274169 59276688 2519 True 4654 4654 100.000 1 2520 1 chr6D.!!$R1 2519
1 TraesCS6D01G094900 chr2D 46525258 46527762 2504 False 4113 4113 96.235 1 2520 1 chr2D.!!$F1 2519
2 TraesCS6D01G094900 chr3D 543131457 543133958 2501 True 4100 4100 96.157 1 2520 1 chr3D.!!$R2 2519
3 TraesCS6D01G094900 chr3D 551732691 551735205 2514 True 4089 4089 96.002 1 2520 1 chr3D.!!$R3 2519
4 TraesCS6D01G094900 chr3D 360441703 360444210 2507 True 4084 4084 95.998 1 2520 1 chr3D.!!$R1 2519
5 TraesCS6D01G094900 chr3D 384995261 384997773 2512 False 4021 4021 95.534 1 2520 1 chr3D.!!$F1 2519
6 TraesCS6D01G094900 chr5D 306883655 306886166 2511 True 4087 4087 96.006 1 2520 1 chr5D.!!$R1 2519
7 TraesCS6D01G094900 chr7D 510254738 510257245 2507 False 4045 4045 95.719 1 2520 1 chr7D.!!$F1 2519
8 TraesCS6D01G094900 chr1B 487689011 487691521 2510 True 4036 4036 95.644 1 2520 1 chr1B.!!$R1 2519
9 TraesCS6D01G094900 chr1D 417883404 417885908 2504 True 4024 4024 95.602 1 2520 1 chr1D.!!$R1 2519
10 TraesCS6D01G094900 chr4B 379060561 379063049 2488 False 3860 3860 94.535 1 2520 1 chr4B.!!$F1 2519
11 TraesCS6D01G094900 chr5A 664008457 664010955 2498 True 3853 3853 94.422 1 2520 1 chr5A.!!$R1 2519
12 TraesCS6D01G094900 chr2B 646051330 646053806 2476 True 3760 3760 93.901 1 2520 1 chr2B.!!$R2 2519
13 TraesCS6D01G094900 chr2B 467753226 467754941 1715 True 2754 2754 95.549 1 1728 1 chr2B.!!$R1 1727
14 TraesCS6D01G094900 chrUn 37643944 37646431 2487 True 3627 3627 92.877 1 2520 1 chrUn.!!$R1 2519
15 TraesCS6D01G094900 chrUn 251163542 251166029 2487 False 3627 3627 92.877 1 2520 1 chrUn.!!$F1 2519

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
587 614 1.227176 GCCGTCGGATCCTACCAAC 60.227 63.158 17.49 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2147 1.059913 ACTAAGCCAGGTTGTGAGCT 58.94 50.0 0.0 0.0 35.04 4.09 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
400 422 5.509498 ACGCCCCTATACCGAGTTTATATA 58.491 41.667 0.00 0.00 0.00 0.86
441 465 6.761714 GGTCTCATAAACGGATGAACTACATT 59.238 38.462 0.00 0.00 39.56 2.71
442 466 7.280205 GGTCTCATAAACGGATGAACTACATTT 59.720 37.037 0.00 0.00 39.56 2.32
557 584 3.690460 CAGAAATGCTCCAAACCCTAGT 58.310 45.455 0.00 0.00 0.00 2.57
587 614 1.227176 GCCGTCGGATCCTACCAAC 60.227 63.158 17.49 0.00 0.00 3.77
625 652 3.667217 GATGTGGGGGCAGGCATGT 62.667 63.158 0.00 0.00 0.00 3.21
681 708 1.548269 GCTACTGCACTGTCCTTCTCT 59.452 52.381 0.00 0.00 39.41 3.10
854 881 1.344438 TGACAGACAAAGGCATCGAGT 59.656 47.619 0.00 0.00 0.00 4.18
896 923 3.010420 GTTTCTTTCCCCATCTTCTCGG 58.990 50.000 0.00 0.00 0.00 4.63
992 1023 2.987125 GTGGCCGGTGTATGGTCT 59.013 61.111 1.90 0.00 30.50 3.85
1189 1221 3.370840 TCTGTCAGATTTGGGATTGGG 57.629 47.619 0.00 0.00 0.00 4.12
1190 1222 2.918934 TCTGTCAGATTTGGGATTGGGA 59.081 45.455 0.00 0.00 0.00 4.37
1191 1223 3.528905 TCTGTCAGATTTGGGATTGGGAT 59.471 43.478 0.00 0.00 0.00 3.85
1192 1224 4.017222 TCTGTCAGATTTGGGATTGGGATT 60.017 41.667 0.00 0.00 0.00 3.01
1440 1473 2.228343 AGAACTTCAAGCAGCTGATTGC 59.772 45.455 34.18 21.86 40.87 3.56
1521 1554 3.234353 TGATGGCCATCTCTCGTTAGAT 58.766 45.455 38.59 6.83 38.60 1.98
1633 1667 7.471721 TGAATGTATGCAGTTTACTGTTATGC 58.528 34.615 11.23 9.87 45.45 3.14
1731 1765 3.643792 GTGTTGGATCATACCCTAGCTCT 59.356 47.826 0.00 0.00 0.00 4.09
1761 1795 3.322254 ACAGTAAGCAGTACTTGAGCAGT 59.678 43.478 6.47 0.00 41.37 4.40
1902 1939 3.319122 GCAATAGGCCCACAAAGGATAAG 59.681 47.826 0.00 0.00 41.22 1.73
2022 2064 8.153550 GCCTAATCTCTTCTATTTCATTGAGGA 58.846 37.037 0.00 0.00 0.00 3.71
2101 2147 4.036971 ACCGTATGTGCTTTTGTTTTGCTA 59.963 37.500 0.00 0.00 0.00 3.49
2126 2172 1.327303 CAACCTGGCTTAGTTTGGCA 58.673 50.000 0.00 0.00 38.31 4.92
2194 2240 4.682778 ATGCCTAGCGAACCAATACTTA 57.317 40.909 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 195 5.343307 AAAAAGGCTTCACACAAATGAGT 57.657 34.783 0.00 0.0 0.00 3.41
587 614 2.600173 ATGGGTGGTGTTTGGCGG 60.600 61.111 0.00 0.0 0.00 6.13
681 708 2.036089 GTGGGGCAAATCGTAAAAACCA 59.964 45.455 0.00 0.0 0.00 3.67
854 881 3.210227 CAGAGGAACTGCTCGAGATCTA 58.790 50.000 18.75 0.0 41.55 1.98
896 923 3.518634 ATTGCTCGAGAGGAAGAAGAC 57.481 47.619 18.75 0.0 41.97 3.01
1187 1219 6.937436 ACGAAATCATGTAACCTAAATCCC 57.063 37.500 0.00 0.0 0.00 3.85
1188 1220 9.285770 GAAAACGAAATCATGTAACCTAAATCC 57.714 33.333 0.00 0.0 0.00 3.01
1189 1221 9.834628 TGAAAACGAAATCATGTAACCTAAATC 57.165 29.630 0.00 0.0 0.00 2.17
1190 1222 9.840427 CTGAAAACGAAATCATGTAACCTAAAT 57.160 29.630 0.00 0.0 0.00 1.40
1191 1223 9.058174 TCTGAAAACGAAATCATGTAACCTAAA 57.942 29.630 0.00 0.0 0.00 1.85
1192 1224 8.610248 TCTGAAAACGAAATCATGTAACCTAA 57.390 30.769 0.00 0.0 0.00 2.69
1440 1473 4.154737 TCAGATTGGATTGCTTCTTCAACG 59.845 41.667 0.00 0.0 0.00 4.10
1521 1554 5.682943 GGCAACAACAGTAGACAAACATA 57.317 39.130 0.00 0.0 0.00 2.29
1731 1765 5.984695 AGTACTGCTTACTGTCATCTGAA 57.015 39.130 0.00 0.0 39.78 3.02
1761 1795 9.159254 AGATGAACTTGATGTATATCCCTTGTA 57.841 33.333 0.00 0.0 32.09 2.41
1902 1939 1.856265 CGCTTGTTTCTGGGCCTCAC 61.856 60.000 4.53 0.0 0.00 3.51
2101 2147 1.059913 ACTAAGCCAGGTTGTGAGCT 58.940 50.000 0.00 0.0 35.04 4.09
2271 2319 6.613755 TGGCTTTAGTCAAAAGTGTACTTC 57.386 37.500 0.00 0.0 45.46 3.01
2373 2421 5.706369 ACATATTGTACACGGCTTTGGTTTA 59.294 36.000 0.00 0.0 0.00 2.01


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

AutoCloner maintained by Alex Coulton.