Multiple sequence alignment - TraesCS3B01G476400

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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 TraesCS3B01G476400 chr3B 100.000 2565 0 0 1 2565 725074539 725077103 0 4737
1 TraesCS3B01G476400 chr1D 95.173 2569 118 5 1 2565 490702073 490704639 0 4052
2 TraesCS3B01G476400 chr3D 95.107 2575 110 10 1 2565 41338658 41336090 0 4043
3 TraesCS3B01G476400 chr5D 95.092 2567 120 4 1 2565 236312503 236309941 0 4037
4 TraesCS3B01G476400 chr4D 94.981 2570 120 7 1 2565 85404872 85407437 0 4023
5 TraesCS3B01G476400 chr4D 94.786 2570 123 8 1 2565 417185083 417187646 0 3993
6 TraesCS3B01G476400 chr2A 94.994 2557 127 1 10 2565 509480720 509483276 0 4012
7 TraesCS3B01G476400 chr2D 94.827 2571 125 5 1 2565 68240666 68238098 0 4004
8 TraesCS3B01G476400 chr2D 94.780 2567 128 4 1 2565 163793146 163795708 0 3993
9 TraesCS3B01G476400 chr5A 94.821 2568 122 6 1 2565 468547185 468544626 0 3995


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 TraesCS3B01G476400 chr3B 725074539 725077103 2564 False 4737 4737 100.000 1 2565 1 chr3B.!!$F1 2564
1 TraesCS3B01G476400 chr1D 490702073 490704639 2566 False 4052 4052 95.173 1 2565 1 chr1D.!!$F1 2564
2 TraesCS3B01G476400 chr3D 41336090 41338658 2568 True 4043 4043 95.107 1 2565 1 chr3D.!!$R1 2564
3 TraesCS3B01G476400 chr5D 236309941 236312503 2562 True 4037 4037 95.092 1 2565 1 chr5D.!!$R1 2564
4 TraesCS3B01G476400 chr4D 85404872 85407437 2565 False 4023 4023 94.981 1 2565 1 chr4D.!!$F1 2564
5 TraesCS3B01G476400 chr4D 417185083 417187646 2563 False 3993 3993 94.786 1 2565 1 chr4D.!!$F2 2564
6 TraesCS3B01G476400 chr2A 509480720 509483276 2556 False 4012 4012 94.994 10 2565 1 chr2A.!!$F1 2555
7 TraesCS3B01G476400 chr2D 68238098 68240666 2568 True 4004 4004 94.827 1 2565 1 chr2D.!!$R1 2564
8 TraesCS3B01G476400 chr2D 163793146 163795708 2562 False 3993 3993 94.780 1 2565 1 chr2D.!!$F1 2564
9 TraesCS3B01G476400 chr5A 468544626 468547185 2559 True 3995 3995 94.821 1 2565 1 chr5A.!!$R1 2564

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
807 819 0.178941 TCTTATCCCCCGCCCTAGAC 60.179 60.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 2444 0.036732 AGATTTTGGCACCGCTCTCA 59.963 50.0 0.0 0.0 0.0 3.27 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
25 26 4.576463 GGAGTAGCTCTTTCTCTCTCTCTG 59.424 50.000 0.00 0.0 0.00 3.35
71 76 5.354842 TCTCACTCGAACTCTCTATACCA 57.645 43.478 0.00 0.0 0.00 3.25
74 79 5.250982 TCACTCGAACTCTCTATACCAACA 58.749 41.667 0.00 0.0 0.00 3.33
180 188 3.004002 TCGTGTTCTGTATCTTCGTGTGT 59.996 43.478 0.00 0.0 0.00 3.72
345 355 1.011968 GGACGCACTCACGCACAATA 61.012 55.000 0.00 0.0 36.19 1.90
346 356 0.787787 GACGCACTCACGCACAATAA 59.212 50.000 0.00 0.0 36.19 1.40
353 363 3.743911 CACTCACGCACAATAAACCACTA 59.256 43.478 0.00 0.0 0.00 2.74
434 444 1.007734 CGTGTACACCAGCGTCACT 60.008 57.895 20.11 0.0 0.00 3.41
447 457 1.404181 GCGTCACTGCTGGTTGAGATA 60.404 52.381 0.00 0.0 0.00 1.98
579 589 1.606313 CCCCACCAAATCTGCCGTT 60.606 57.895 0.00 0.0 0.00 4.44
580 590 1.184970 CCCCACCAAATCTGCCGTTT 61.185 55.000 0.00 0.0 0.00 3.60
594 604 2.597510 GTTTGGACCGCCCTGCTT 60.598 61.111 0.00 0.0 35.38 3.91
645 656 2.526046 CCCCCTCAACCTCACCGTT 61.526 63.158 0.00 0.0 0.00 4.44
707 718 4.268359 GCAGTCTCCAAGATCCTTTCATT 58.732 43.478 0.00 0.0 0.00 2.57
780 791 1.064825 AGGTCCAACCCAAGTTCGAT 58.935 50.000 0.00 0.0 39.75 3.59
807 819 0.178941 TCTTATCCCCCGCCCTAGAC 60.179 60.000 0.00 0.0 0.00 2.59
811 823 4.475444 CCCCCGCCCTAGACCAGA 62.475 72.222 0.00 0.0 0.00 3.86
882 894 3.059982 CTCCTCCTCACGCCAACA 58.940 61.111 0.00 0.0 0.00 3.33
937 949 0.813610 CCAGATTAATGTCGCGCCCA 60.814 55.000 0.00 0.0 0.00 5.36
994 1006 3.818961 TCGACGTTGTTATCTCGAAGT 57.181 42.857 1.96 0.0 32.41 3.01
1051 1063 3.001414 CTCGAGTACCTTCGTCTTGAGA 58.999 50.000 3.62 0.0 40.31 3.27
1060 1072 3.056536 CCTTCGTCTTGAGAAGATCCACA 60.057 47.826 7.45 0.0 45.78 4.17
1125 1137 4.643387 GTGTCTTGCTGGCCCCGT 62.643 66.667 0.00 0.0 0.00 5.28
1142 1154 3.756434 CCCCGTAACAAGACATCAATTGT 59.244 43.478 5.13 0.0 41.28 2.71
1583 1596 8.814235 CCTATTAGTAAACCGTAATCACAACAG 58.186 37.037 0.00 0.0 0.00 3.16
1797 1816 5.128991 ACTCTATGGTTACCCTAAGAGCAAC 59.871 44.000 18.54 0.0 40.85 4.17
1901 1920 9.650539 ATGCATGTCACTAAGAACTATATCATC 57.349 33.333 0.00 0.0 0.00 2.92
2128 2149 8.434589 TTTAAGACAAGAATTTTGGGATGGAT 57.565 30.769 5.68 0.0 0.00 3.41
2137 2158 6.552350 AGAATTTTGGGATGGATGGAATACAG 59.448 38.462 0.00 0.0 43.16 2.74
2240 2261 1.072965 GCCCCAATCTGGATCACCTAG 59.927 57.143 0.00 0.0 40.96 3.02
2253 2274 0.034896 CACCTAGTTTGCTCCGGTGT 59.965 55.000 0.00 0.0 39.54 4.16
2319 2345 5.249420 AGAGAGGACTGAGGCAATAAAAAC 58.751 41.667 0.00 0.0 0.00 2.43
2331 2359 5.073008 AGGCAATAAAAACCTTGTTTGGGAT 59.927 36.000 0.00 0.0 0.00 3.85
2382 2410 9.467796 TGATTGATTTGTTTATACATGTGGGTA 57.532 29.630 9.11 0.0 33.44 3.69
2416 2444 0.969149 TGCCAACTCTCTCACATCGT 59.031 50.000 0.00 0.0 0.00 3.73
2437 2465 1.131315 GAGAGCGGTGCCAAAATCTTC 59.869 52.381 0.00 0.0 0.00 2.87
2533 2565 1.598130 GCCCAAGCTCTTCACGTGT 60.598 57.895 16.51 0.0 35.50 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.068250 GGCCCGTGAGAGATAGCAC 59.932 63.158 0.00 0.00 0.00 4.40
134 142 0.692476 ACAAGGCAGCATGTGGACTA 59.308 50.000 2.45 0.00 39.31 2.59
282 290 4.463891 CCTCAATGCACCCTCAATTTACTT 59.536 41.667 0.00 0.00 0.00 2.24
336 346 2.477375 CGTGTAGTGGTTTATTGTGCGT 59.523 45.455 0.00 0.00 0.00 5.24
345 355 2.667199 GCCGCCGTGTAGTGGTTT 60.667 61.111 0.00 0.00 39.73 3.27
346 356 3.248446 ATGCCGCCGTGTAGTGGTT 62.248 57.895 0.00 0.00 39.73 3.67
434 444 0.175760 GCCGTCTATCTCAACCAGCA 59.824 55.000 0.00 0.00 0.00 4.41
579 589 2.282180 GAAAGCAGGGCGGTCCAA 60.282 61.111 0.00 0.00 38.24 3.53
580 590 4.344865 GGAAAGCAGGGCGGTCCA 62.345 66.667 0.00 0.00 36.72 4.02
617 627 4.954118 TGAGGGGGACGTGGCACT 62.954 66.667 16.72 2.45 0.00 4.40
619 629 3.948719 GTTGAGGGGGACGTGGCA 61.949 66.667 0.00 0.00 0.00 4.92
623 633 2.203182 TGAGGTTGAGGGGGACGT 59.797 61.111 0.00 0.00 0.00 4.34
645 656 1.368950 GTCACAGAGGCAGCTGTCA 59.631 57.895 22.50 0.00 45.54 3.58
780 791 1.200519 CGGGGGATAAGAACCACTCA 58.799 55.000 0.00 0.00 0.00 3.41
807 819 1.108727 AGCTGAGCTCCTCGATCTGG 61.109 60.000 12.15 0.00 30.62 3.86
811 823 1.189752 TCAAAGCTGAGCTCCTCGAT 58.810 50.000 7.72 0.00 38.25 3.59
869 881 1.227527 CACAGTGTTGGCGTGAGGA 60.228 57.895 0.00 0.00 32.23 3.71
937 949 2.261729 GAGTTGAGGGAGAAGAAGGGT 58.738 52.381 0.00 0.00 0.00 4.34
984 996 4.011023 GCTCCATAGCCTACTTCGAGATA 58.989 47.826 0.00 0.00 43.40 1.98
1027 1039 1.062206 GACGAAGGTACTCGAGCGG 59.938 63.158 13.61 0.00 38.49 5.52
1051 1063 3.525199 AGGCTAATGAACCTGTGGATCTT 59.475 43.478 0.00 0.00 34.07 2.40
1060 1072 3.624777 CAATGTGGAGGCTAATGAACCT 58.375 45.455 0.00 0.00 39.65 3.50
1125 1137 8.853077 ATCTCTTCACAATTGATGTCTTGTTA 57.147 30.769 13.59 0.00 41.46 2.41
1142 1154 2.533916 ACAGCTGGAGTGATCTCTTCA 58.466 47.619 19.93 5.66 40.29 3.02
1570 1583 5.536554 AATTGAGCTCTGTTGTGATTACG 57.463 39.130 16.19 0.00 0.00 3.18
1797 1816 5.262804 AGTAAACCAGGACAGAGGTAGTAG 58.737 45.833 0.00 0.00 37.07 2.57
1901 1920 9.497030 TTGAAATTATGTTCAAATACGAATCCG 57.503 29.630 0.00 0.00 42.94 4.18
2010 2030 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2102 2122 8.256356 TCCATCCCAAAATTCTTGTCTTAAAA 57.744 30.769 0.00 0.00 0.00 1.52
2128 2149 3.780294 ACATAGCCCACTTCTGTATTCCA 59.220 43.478 0.00 0.00 0.00 3.53
2137 2158 3.708013 GGCCTACATAGCCCACTTC 57.292 57.895 0.00 0.00 45.16 3.01
2163 2184 3.007074 TGCATCACAAGTGAATTTGGCAT 59.993 39.130 7.02 0.00 43.58 4.40
2240 2261 2.793278 AATTTGACACCGGAGCAAAC 57.207 45.000 9.46 0.00 34.72 2.93
2319 2345 3.878778 CCTCTCACTATCCCAAACAAGG 58.121 50.000 0.00 0.00 0.00 3.61
2331 2359 2.826128 CAACTACACCAGCCTCTCACTA 59.174 50.000 0.00 0.00 0.00 2.74
2416 2444 0.036732 AGATTTTGGCACCGCTCTCA 59.963 50.000 0.00 0.00 0.00 3.27
2437 2465 4.979564 ATACGCATCGATGTCAAATCAG 57.020 40.909 25.47 10.02 0.00 2.90
2533 2565 8.202461 TCTGTTTCCTCTCATTTAACTAGGAA 57.798 34.615 0.00 0.00 42.99 3.36


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

AutoCloner maintained by Alex Coulton.