Multiple sequence alignment - TraesCS5B01G470800

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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 TraesCS5B01G470800 chr5B 100.000 2774 0 0 1 2774 644353550 644356323 0 5123
1 TraesCS5B01G470800 chr5B 92.846 2614 156 15 1 2593 672914246 672911643 0 3762
2 TraesCS5B01G470800 chr3D 94.470 2803 124 18 1 2774 64822375 64819575 0 4289
3 TraesCS5B01G470800 chr3D 93.966 2801 138 18 1 2774 613553133 613555929 0 4207
4 TraesCS5B01G470800 chr3D 92.687 2694 168 15 106 2772 175422134 175419443 0 3856
5 TraesCS5B01G470800 chr3D 94.779 1743 69 11 1 1723 570598941 570597201 0 2695
6 TraesCS5B01G470800 chr6D 94.532 2780 124 16 1 2756 419840773 419843548 0 4266
7 TraesCS5B01G470800 chr7B 94.204 2795 128 19 1 2774 92647789 92650570 0 4233
8 TraesCS5B01G470800 chr1B 93.768 2792 135 14 1 2774 604094659 604091889 0 4156
9 TraesCS5B01G470800 chr2B 93.689 2789 136 14 3 2774 694895771 694898536 0 4139
10 TraesCS5B01G470800 chr2B 93.388 2798 159 12 1 2774 693491951 693494746 0 4119
11 TraesCS5B01G470800 chr4B 93.569 2768 150 13 31 2774 200734706 200731943 0 4100
12 TraesCS5B01G470800 chr7A 90.077 2741 220 37 67 2772 722695935 722693212 0 3507
13 TraesCS5B01G470800 chr3B 92.432 1546 79 10 1 1529 692068791 692070315 0 2172
14 TraesCS5B01G470800 chr6B 92.857 1134 63 8 1 1118 157530941 157529810 0 1629


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 TraesCS5B01G470800 chr5B 644353550 644356323 2773 False 5123 5123 100.000 1 2774 1 chr5B.!!$F1 2773
1 TraesCS5B01G470800 chr5B 672911643 672914246 2603 True 3762 3762 92.846 1 2593 1 chr5B.!!$R1 2592
2 TraesCS5B01G470800 chr3D 64819575 64822375 2800 True 4289 4289 94.470 1 2774 1 chr3D.!!$R1 2773
3 TraesCS5B01G470800 chr3D 613553133 613555929 2796 False 4207 4207 93.966 1 2774 1 chr3D.!!$F1 2773
4 TraesCS5B01G470800 chr3D 175419443 175422134 2691 True 3856 3856 92.687 106 2772 1 chr3D.!!$R2 2666
5 TraesCS5B01G470800 chr3D 570597201 570598941 1740 True 2695 2695 94.779 1 1723 1 chr3D.!!$R3 1722
6 TraesCS5B01G470800 chr6D 419840773 419843548 2775 False 4266 4266 94.532 1 2756 1 chr6D.!!$F1 2755
7 TraesCS5B01G470800 chr7B 92647789 92650570 2781 False 4233 4233 94.204 1 2774 1 chr7B.!!$F1 2773
8 TraesCS5B01G470800 chr1B 604091889 604094659 2770 True 4156 4156 93.768 1 2774 1 chr1B.!!$R1 2773
9 TraesCS5B01G470800 chr2B 694895771 694898536 2765 False 4139 4139 93.689 3 2774 1 chr2B.!!$F2 2771
10 TraesCS5B01G470800 chr2B 693491951 693494746 2795 False 4119 4119 93.388 1 2774 1 chr2B.!!$F1 2773
11 TraesCS5B01G470800 chr4B 200731943 200734706 2763 True 4100 4100 93.569 31 2774 1 chr4B.!!$R1 2743
12 TraesCS5B01G470800 chr7A 722693212 722695935 2723 True 3507 3507 90.077 67 2772 1 chr7A.!!$R1 2705
13 TraesCS5B01G470800 chr3B 692068791 692070315 1524 False 2172 2172 92.432 1 1529 1 chr3B.!!$F1 1528
14 TraesCS5B01G470800 chr6B 157529810 157530941 1131 True 1629 1629 92.857 1 1118 1 chr6B.!!$R1 1117

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
370 390 5.065988 GGCAATCTATTCTAGCGAAAACCAA 59.934 40.0 0.0 0.0 31.91 3.67 F
1200 1265 1.856629 GTGGTGCCCCTGTAGTAGTA 58.143 55.0 0.0 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 1309 0.187117 TGGACCAGGAACATTTGCCA 59.813 50.000 0.00 0.0 0.0 4.92 R
2731 2818 1.270785 ACATCGATGCACAGTGGTTGA 60.271 47.619 25.11 0.0 0.0 3.18 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
76 78 6.037500 CACATGTACTGGATATTTGTGAGTGG 59.962 42.308 0.00 0.00 33.50 4.00
197 203 6.239543 CCAACTGAGACATCTATTCTAGCCAT 60.240 42.308 0.00 0.00 0.00 4.40
370 390 5.065988 GGCAATCTATTCTAGCGAAAACCAA 59.934 40.000 0.00 0.00 31.91 3.67
483 503 5.708736 TGTCCCACACATATATTCTGGTT 57.291 39.130 0.00 0.00 0.00 3.67
567 601 6.431198 AAACGGCGATGAAAACATATAACT 57.569 33.333 16.62 0.00 0.00 2.24
568 602 7.542534 AAACGGCGATGAAAACATATAACTA 57.457 32.000 16.62 0.00 0.00 2.24
569 603 7.724305 AACGGCGATGAAAACATATAACTAT 57.276 32.000 16.62 0.00 0.00 2.12
570 604 8.821147 AACGGCGATGAAAACATATAACTATA 57.179 30.769 16.62 0.00 0.00 1.31
571 605 8.821147 ACGGCGATGAAAACATATAACTATAA 57.179 30.769 16.62 0.00 0.00 0.98
572 606 9.431887 ACGGCGATGAAAACATATAACTATAAT 57.568 29.630 16.62 0.00 0.00 1.28
573 607 9.901724 CGGCGATGAAAACATATAACTATAATC 57.098 33.333 0.00 0.00 0.00 1.75
783 827 7.928908 CAAACTGTGCAACTAACATAACAAT 57.071 32.000 0.00 0.00 38.04 2.71
895 946 6.801862 GTGCAACTGCCTATTTACTAAGTTTG 59.198 38.462 0.00 0.00 41.18 2.93
1059 1124 5.308759 TGAGCTTCCTCATGATATGGATCAA 59.691 40.000 3.19 0.00 42.98 2.57
1197 1262 1.985662 CCGTGGTGCCCCTGTAGTA 60.986 63.158 0.00 0.00 0.00 1.82
1200 1265 1.856629 GTGGTGCCCCTGTAGTAGTA 58.143 55.000 0.00 0.00 0.00 1.82
1300 1366 3.691342 CTGGGGCTGTCGACGGAA 61.691 66.667 28.38 8.74 0.00 4.30
1323 1389 2.705658 TGTGCAAGGAGAAGAAGGAGAA 59.294 45.455 0.00 0.00 0.00 2.87
1580 1647 3.633986 CCTATTCCAGATCCAAAACCTGC 59.366 47.826 0.00 0.00 0.00 4.85
1585 1652 1.815003 CAGATCCAAAACCTGCTGACC 59.185 52.381 0.00 0.00 0.00 4.02
1739 1807 1.771746 ATGGGCGATGGGAGGTGAT 60.772 57.895 0.00 0.00 0.00 3.06
1870 1939 9.102757 CATCTTGTATAACTGCAACTTGACTAT 57.897 33.333 0.00 0.00 0.00 2.12
1923 1995 5.640189 TTAAGTTTCCCTCTAGACAGTCG 57.360 43.478 0.00 0.00 0.00 4.18
1933 2005 2.820197 TCTAGACAGTCGAGTGTGCAAT 59.180 45.455 29.81 14.77 0.00 3.56
1937 2009 1.867233 ACAGTCGAGTGTGCAATTGTC 59.133 47.619 24.71 0.07 0.00 3.18
1962 2034 6.104146 TGGTACTACTGTGCAACTGAAATA 57.896 37.500 0.00 0.00 39.30 1.40
1970 2042 7.145932 ACTGTGCAACTGAAATATCTTAACC 57.854 36.000 0.00 0.00 39.30 2.85
2072 2145 4.935205 GCAACTACACAATGTCCTGTATGA 59.065 41.667 0.00 0.00 0.00 2.15
2104 2181 6.372659 TGCAAAGTGATTTTAAAAAGGTGCAA 59.627 30.769 16.15 6.56 0.00 4.08
2180 2257 1.377594 AGCTGGATGTGCGCATTCA 60.378 52.632 19.97 19.97 38.23 2.57
2252 2330 6.019237 CGTATGATGCATATAATGGCAGAGTC 60.019 42.308 0.00 0.00 44.24 3.36
2253 2331 5.494390 TGATGCATATAATGGCAGAGTCT 57.506 39.130 0.00 0.00 44.24 3.24
2496 2580 1.640428 CTGATGCGTACCACGATTGT 58.360 50.000 2.35 0.00 46.05 2.71
2571 2658 4.849518 TCATTGGAATAAACCGACATGGA 58.150 39.130 0.00 0.00 42.00 3.41
2605 2692 2.713154 GTTGCGCGTTTGTGAGGT 59.287 55.556 8.43 0.00 0.00 3.85
2706 2793 3.558931 ACCGATCAAGATGGTGCAATA 57.441 42.857 0.00 0.00 33.91 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 169 2.481441 TGTCTCAGTTGGCCAGGATAT 58.519 47.619 5.11 0.00 0.00 1.63
197 203 5.527214 CAGTTGGACAGTTAATGTGTTCAGA 59.473 40.000 0.00 0.00 44.17 3.27
370 390 7.755822 TGTTTTTGCTGTCGTACTACAAATTTT 59.244 29.630 1.54 0.00 30.95 1.82
483 503 1.202989 TGGCTTTGCAATAGGTGTGGA 60.203 47.619 0.00 0.00 0.00 4.02
531 553 6.670233 TCATCGCCGTTTATGTTTTTACTTT 58.330 32.000 0.00 0.00 0.00 2.66
570 604 9.176460 GAAAGAAGAAGAATTGGATGAGAGATT 57.824 33.333 0.00 0.00 0.00 2.40
571 605 8.327271 TGAAAGAAGAAGAATTGGATGAGAGAT 58.673 33.333 0.00 0.00 0.00 2.75
572 606 7.605691 GTGAAAGAAGAAGAATTGGATGAGAGA 59.394 37.037 0.00 0.00 0.00 3.10
573 607 7.148272 GGTGAAAGAAGAAGAATTGGATGAGAG 60.148 40.741 0.00 0.00 0.00 3.20
574 608 6.656693 GGTGAAAGAAGAAGAATTGGATGAGA 59.343 38.462 0.00 0.00 0.00 3.27
575 609 6.658391 AGGTGAAAGAAGAAGAATTGGATGAG 59.342 38.462 0.00 0.00 0.00 2.90
576 610 6.432162 CAGGTGAAAGAAGAAGAATTGGATGA 59.568 38.462 0.00 0.00 0.00 2.92
577 611 6.349944 CCAGGTGAAAGAAGAAGAATTGGATG 60.350 42.308 0.00 0.00 0.00 3.51
833 882 6.952773 TCTTAGTTGCAAAAGTTACATGGT 57.047 33.333 0.00 0.00 0.00 3.55
895 946 5.963586 CGAAAGAGTGTTTGAAACAACCTAC 59.036 40.000 12.89 9.21 44.16 3.18
966 1027 0.467844 TTGGATGCTGCCACACACTT 60.468 50.000 0.00 0.00 37.75 3.16
1059 1124 0.609131 GTGGTATGCTGGGTTGCTGT 60.609 55.000 0.00 0.00 0.00 4.40
1197 1262 3.118811 GGCTCTCTGACTGCAAAGATACT 60.119 47.826 0.00 0.00 0.00 2.12
1200 1265 1.627329 TGGCTCTCTGACTGCAAAGAT 59.373 47.619 0.00 0.00 0.00 2.40
1244 1309 0.187117 TGGACCAGGAACATTTGCCA 59.813 50.000 0.00 0.00 0.00 4.92
1293 1359 1.284982 CTCCTTGCACAGTTCCGTCG 61.285 60.000 0.00 0.00 0.00 5.12
1300 1366 2.038295 CTCCTTCTTCTCCTTGCACAGT 59.962 50.000 0.00 0.00 0.00 3.55
1323 1389 2.777832 GTTGAGAACCAGCCTCATCT 57.222 50.000 0.00 0.00 40.02 2.90
1381 1447 7.575720 GCTGTTGTAGTGATCCTTAGCAATTTT 60.576 37.037 0.00 0.00 0.00 1.82
1580 1647 4.160642 TCCATTTCCTCATCATGGTCAG 57.839 45.455 0.00 0.00 38.93 3.51
1585 1652 6.238953 GGTTCATCTTCCATTTCCTCATCATG 60.239 42.308 0.00 0.00 0.00 3.07
1680 1747 3.540314 TTTGCCTTGCATTGAGTTTGT 57.460 38.095 0.00 0.00 38.76 2.83
1683 1750 4.453751 ACATTTTTGCCTTGCATTGAGTT 58.546 34.783 0.00 0.00 38.76 3.01
1739 1807 0.730265 GTGGTCACGAACAAAGTGCA 59.270 50.000 0.00 0.00 39.31 4.57
1870 1939 5.535029 AGGGATATAGAAACACCACACCTA 58.465 41.667 0.00 0.00 0.00 3.08
1917 1989 1.867233 GACAATTGCACACTCGACTGT 59.133 47.619 5.05 0.00 0.00 3.55
1923 1995 3.753272 AGTACCATGACAATTGCACACTC 59.247 43.478 5.05 0.00 0.00 3.51
1933 2005 4.062293 GTTGCACAGTAGTACCATGACAA 58.938 43.478 0.00 6.44 0.00 3.18
1937 2009 3.925379 TCAGTTGCACAGTAGTACCATG 58.075 45.455 0.00 0.00 0.00 3.66
1970 2042 1.321474 AGTTGGACACCAGTTGCATG 58.679 50.000 0.00 0.00 33.81 4.06
2088 2164 7.119709 ACACCTAGTTGCACCTTTTTAAAAT 57.880 32.000 0.55 0.00 0.00 1.82
2104 2181 1.985159 TGCAGGAAATGGACACCTAGT 59.015 47.619 0.00 0.00 32.35 2.57
2252 2330 4.554292 CACCATCATCTCAGATCCGTAAG 58.446 47.826 0.00 0.00 0.00 2.34
2253 2331 3.243873 GCACCATCATCTCAGATCCGTAA 60.244 47.826 0.00 0.00 0.00 3.18
2428 2506 5.153513 CACCCAAAATATGTTGACAACTCG 58.846 41.667 18.73 0.77 0.00 4.18
2481 2559 3.557508 CGATATACAATCGTGGTACGCA 58.442 45.455 0.00 0.00 42.21 5.24
2496 2580 8.347771 GTCATGTAGGTAGTGTCAAACGATATA 58.652 37.037 0.00 0.00 0.00 0.86
2571 2658 2.095059 GCAACCGAGCATGAAAGATTGT 60.095 45.455 0.00 0.00 0.00 2.71
2605 2692 3.084039 CAAAGCTTGATGCCAACTCCTA 58.916 45.455 0.00 0.00 44.23 2.94
2706 2793 3.199508 AGATGCTCTGTATTGACTGCCTT 59.800 43.478 0.00 0.00 0.00 4.35
2731 2818 1.270785 ACATCGATGCACAGTGGTTGA 60.271 47.619 25.11 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.