Multiple sequence alignment - TraesCS3D01G232200

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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 TraesCS3D01G232200 chr3D 100.000 2978 0 0 1 2978 318772111 318769134 0.000000e+00 5500.0
1 TraesCS3D01G232200 chr3D 98.077 1768 26 5 1217 2978 607244397 607242632 0.000000e+00 3070.0
2 TraesCS3D01G232200 chr7A 94.605 2984 151 7 1 2978 735719081 735716102 0.000000e+00 4610.0
3 TraesCS3D01G232200 chr6B 96.681 2139 63 5 846 2978 158172865 158175001 0.000000e+00 3550.0
4 TraesCS3D01G232200 chr6B 97.481 794 19 1 1 793 158172077 158172870 0.000000e+00 1354.0
5 TraesCS3D01G232200 chr4A 91.959 1480 115 4 12 1490 681887954 681886478 0.000000e+00 2071.0
6 TraesCS3D01G232200 chr4A 90.934 1489 126 6 1496 2978 681838642 681837157 0.000000e+00 1993.0
7 TraesCS3D01G232200 chr1B 85.779 1097 142 11 1855 2947 572324439 572325525 0.000000e+00 1149.0
8 TraesCS3D01G232200 chr1B 88.496 452 46 5 2526 2973 572388366 572388815 2.610000e-150 542.0
9 TraesCS3D01G232200 chr1B 87.154 397 49 2 2135 2530 572358919 572359314 1.630000e-122 449.0
10 TraesCS3D01G232200 chr4D 79.097 598 117 7 890 1483 461386760 461386167 3.570000e-109 405.0
11 TraesCS3D01G232200 chr7B 73.927 606 133 18 887 1486 272759028 272759614 1.390000e-53 220.0
12 TraesCS3D01G232200 chr7D 97.143 35 0 1 536 569 274872014 274871980 1.150000e-04 58.4


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 TraesCS3D01G232200 chr3D 318769134 318772111 2977 True 5500 5500 100.000 1 2978 1 chr3D.!!$R1 2977
1 TraesCS3D01G232200 chr3D 607242632 607244397 1765 True 3070 3070 98.077 1217 2978 1 chr3D.!!$R2 1761
2 TraesCS3D01G232200 chr7A 735716102 735719081 2979 True 4610 4610 94.605 1 2978 1 chr7A.!!$R1 2977
3 TraesCS3D01G232200 chr6B 158172077 158175001 2924 False 2452 3550 97.081 1 2978 2 chr6B.!!$F1 2977
4 TraesCS3D01G232200 chr4A 681886478 681887954 1476 True 2071 2071 91.959 12 1490 1 chr4A.!!$R2 1478
5 TraesCS3D01G232200 chr4A 681837157 681838642 1485 True 1993 1993 90.934 1496 2978 1 chr4A.!!$R1 1482
6 TraesCS3D01G232200 chr1B 572324439 572325525 1086 False 1149 1149 85.779 1855 2947 1 chr1B.!!$F1 1092
7 TraesCS3D01G232200 chr4D 461386167 461386760 593 True 405 405 79.097 890 1483 1 chr4D.!!$R1 593
8 TraesCS3D01G232200 chr7B 272759028 272759614 586 False 220 220 73.927 887 1486 1 chr7B.!!$F1 599


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
119 121 1.000993 GTCCTCCTCCTCTGCCAGA 59.999 63.158 0.0 0.0 0.0 3.86 F
1180 1182 1.468985 CGTCACCATCACTCTCCTCT 58.531 55.000 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1814 2.096248 GAGGAGTTGGAGACATCGACT 58.904 52.381 0.0 0.0 42.32 4.18 R
2508 2515 3.431486 GGCAAGATCACTAGAGGGACAAG 60.431 52.174 0.0 0.0 0.00 3.16 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
119 121 1.000993 GTCCTCCTCCTCTGCCAGA 59.999 63.158 0.00 0.0 0.00 3.86
245 247 2.056985 CTCTCTGCCCTCCCTATGC 58.943 63.158 0.00 0.0 0.00 3.14
364 366 3.129502 CCTCCTACCGCGACGTGA 61.130 66.667 8.23 0.0 0.00 4.35
502 504 4.573201 TCCGTTCTAGACCTTTGTGTTTTG 59.427 41.667 0.00 0.0 0.00 2.44
525 527 1.763770 CCTTGCTCCAGACCACCTT 59.236 57.895 0.00 0.0 0.00 3.50
1180 1182 1.468985 CGTCACCATCACTCTCCTCT 58.531 55.000 0.00 0.0 0.00 3.69
1492 1494 2.569404 GTCTTTGAGGACCTCACCATCT 59.431 50.000 24.24 0.0 40.46 2.90
2121 2128 3.443045 GGCCATGCGTGTCAAGGG 61.443 66.667 4.96 0.0 34.23 3.95
2508 2515 1.050988 TGCTCCCAGGACTATCTGCC 61.051 60.000 0.00 0.0 33.64 4.85
2590 2597 5.581605 TCACAAATTCAGTTTCTGCTGTTC 58.418 37.500 0.00 0.0 37.70 3.18
2693 2701 3.988976 TTGCAAGAGACCAAGCTAGAT 57.011 42.857 0.00 0.0 0.00 1.98
2800 2808 0.329596 ATGCTTTCGGCCTTCTCCTT 59.670 50.000 0.00 0.0 40.92 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 121 6.605995 GGAGGTAGTTAGGTTTGCCATTAATT 59.394 38.462 0.00 0.00 37.19 1.40
245 247 1.304962 GGGTTTGGGGTAGGGCTTG 60.305 63.158 0.00 0.00 0.00 4.01
502 504 1.973812 GGTCTGGAGCAAGGCAACC 60.974 63.158 0.00 0.00 37.17 3.77
525 527 0.955428 GATCACGGCAAGCTTGGACA 60.955 55.000 27.10 4.97 0.00 4.02
730 732 4.742201 GGCAGAGCGAGGCGAACA 62.742 66.667 0.00 0.00 0.00 3.18
876 878 1.866063 GCCGAGGACGAAGCAGATTAG 60.866 57.143 0.00 0.00 42.66 1.73
878 880 1.153549 GCCGAGGACGAAGCAGATT 60.154 57.895 0.00 0.00 42.66 2.40
1783 1785 3.775654 GGTGCCGGAGAGGTCAGG 61.776 72.222 5.05 0.00 43.70 3.86
1812 1814 2.096248 GAGGAGTTGGAGACATCGACT 58.904 52.381 0.00 0.00 42.32 4.18
2508 2515 3.431486 GGCAAGATCACTAGAGGGACAAG 60.431 52.174 0.00 0.00 0.00 3.16
2693 2701 4.202060 CGCTGCTTTAGAGTAGAGATGGAA 60.202 45.833 2.37 0.00 37.55 3.53
2800 2808 4.655963 AGCAATAAGAGAAAAGTGAGCCA 58.344 39.130 0.00 0.00 0.00 4.75



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

AutoCloner maintained by Alex Coulton.