Multiple sequence alignment - TraesCS4B01G233200

Loading Multiple Alignment...

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 TraesCS4B01G233200 chr4B 100.000 3128 0 0 1 3128 484764175 484761048 0.000000e+00 5777.0
1 TraesCS4B01G233200 chr4B 96.610 59 2 0 2 60 66179908 66179966 7.140000e-17 99.0
2 TraesCS4B01G233200 chr4B 88.158 76 9 0 168 243 430981003 430980928 1.190000e-14 91.6
3 TraesCS4B01G233200 chr3B 95.018 2770 113 12 377 3123 769411304 769414071 0.000000e+00 4327.0
4 TraesCS4B01G233200 chr3B 93.939 165 9 1 85 248 769410848 769411012 6.700000e-62 248.0
5 TraesCS4B01G233200 chr3B 98.333 60 1 0 2 61 769410794 769410853 4.270000e-19 106.0
6 TraesCS4B01G233200 chr2B 95.613 2690 111 5 437 3123 103466647 103469332 0.000000e+00 4307.0
7 TraesCS4B01G233200 chr2B 90.582 361 31 1 2 359 103465860 103466220 2.820000e-130 475.0
8 TraesCS4B01G233200 chr2B 88.288 222 14 10 380 593 683146849 683146632 4.000000e-64 255.0
9 TraesCS4B01G233200 chr6B 94.780 2701 122 16 437 3126 664454375 664451683 0.000000e+00 4189.0
10 TraesCS4B01G233200 chr3D 96.348 2492 85 4 631 3121 58419940 58422426 0.000000e+00 4093.0
11 TraesCS4B01G233200 chr3D 96.046 2504 91 6 620 3121 557718118 557715621 0.000000e+00 4069.0
12 TraesCS4B01G233200 chr4D 96.148 2492 90 4 631 3121 461817745 461820231 0.000000e+00 4065.0
13 TraesCS4B01G233200 chr4D 92.423 1201 70 14 498 1680 67448445 67449642 0.000000e+00 1694.0
14 TraesCS4B01G233200 chr7D 95.949 2493 95 4 631 3121 468270972 468273460 0.000000e+00 4039.0
15 TraesCS4B01G233200 chr7D 85.393 89 12 1 165 253 598440942 598441029 1.190000e-14 91.6
16 TraesCS4B01G233200 chr7D 82.418 91 9 6 168 257 632616510 632616426 4.330000e-09 73.1
17 TraesCS4B01G233200 chr2D 95.735 2509 96 6 620 3121 422069382 422071886 0.000000e+00 4030.0
18 TraesCS4B01G233200 chr2D 93.935 2638 137 15 498 3121 10438901 10441529 0.000000e+00 3964.0
19 TraesCS4B01G233200 chr2D 92.952 2724 153 28 432 3121 548732405 548735123 0.000000e+00 3930.0
20 TraesCS4B01G233200 chr2D 85.000 100 9 4 498 591 575237062 575236963 2.570000e-16 97.1
21 TraesCS4B01G233200 chr1D 94.872 2574 117 11 555 3121 467392236 467394801 0.000000e+00 4008.0
22 TraesCS4B01G233200 chr1D 90.789 76 7 0 168 243 471655419 471655494 5.520000e-18 102.0
23 TraesCS4B01G233200 chr5D 93.279 2723 145 27 427 3121 265953495 265956207 0.000000e+00 3980.0
24 TraesCS4B01G233200 chr5D 88.312 77 8 1 168 243 361414578 361414502 1.190000e-14 91.6
25 TraesCS4B01G233200 chr5B 86.290 248 28 2 2 243 689648760 689649007 6.650000e-67 265.0
26 TraesCS4B01G233200 chr7A 87.129 101 13 0 135 235 82953636 82953736 7.090000e-22 115.0
27 TraesCS4B01G233200 chr1B 93.333 75 2 1 6 77 498731218 498731292 1.190000e-19 108.0


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 TraesCS4B01G233200 chr4B 484761048 484764175 3127 True 5777.000000 5777 100.000000 1 3128 1 chr4B.!!$R2 3127
1 TraesCS4B01G233200 chr3B 769410794 769414071 3277 False 1560.333333 4327 95.763333 2 3123 3 chr3B.!!$F1 3121
2 TraesCS4B01G233200 chr2B 103465860 103469332 3472 False 2391.000000 4307 93.097500 2 3123 2 chr2B.!!$F1 3121
3 TraesCS4B01G233200 chr6B 664451683 664454375 2692 True 4189.000000 4189 94.780000 437 3126 1 chr6B.!!$R1 2689
4 TraesCS4B01G233200 chr3D 58419940 58422426 2486 False 4093.000000 4093 96.348000 631 3121 1 chr3D.!!$F1 2490
5 TraesCS4B01G233200 chr3D 557715621 557718118 2497 True 4069.000000 4069 96.046000 620 3121 1 chr3D.!!$R1 2501
6 TraesCS4B01G233200 chr4D 461817745 461820231 2486 False 4065.000000 4065 96.148000 631 3121 1 chr4D.!!$F2 2490
7 TraesCS4B01G233200 chr4D 67448445 67449642 1197 False 1694.000000 1694 92.423000 498 1680 1 chr4D.!!$F1 1182
8 TraesCS4B01G233200 chr7D 468270972 468273460 2488 False 4039.000000 4039 95.949000 631 3121 1 chr7D.!!$F1 2490
9 TraesCS4B01G233200 chr2D 422069382 422071886 2504 False 4030.000000 4030 95.735000 620 3121 1 chr2D.!!$F2 2501
10 TraesCS4B01G233200 chr2D 10438901 10441529 2628 False 3964.000000 3964 93.935000 498 3121 1 chr2D.!!$F1 2623
11 TraesCS4B01G233200 chr2D 548732405 548735123 2718 False 3930.000000 3930 92.952000 432 3121 1 chr2D.!!$F3 2689
12 TraesCS4B01G233200 chr1D 467392236 467394801 2565 False 4008.000000 4008 94.872000 555 3121 1 chr1D.!!$F1 2566
13 TraesCS4B01G233200 chr5D 265953495 265956207 2712 False 3980.000000 3980 93.279000 427 3121 1 chr5D.!!$F1 2694

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
77 81 0.038526 GACACCGACCAGATGACGTT 60.039 55.0 0.0 0.0 0.0 3.99 F
1193 1590 0.392327 GCTCTGCACTTTCTCCCTCC 60.392 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2368 0.176449 TGGACGTCGGTAGAGATCGA 59.824 55.000 9.92 0.00 35.28 3.59 R
2759 3181 1.228956 AGGGTAGTGTACACGGGCA 60.229 57.895 19.93 4.61 37.12 5.36 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
61 62 3.659786 ACGATGTTTTGAGATTCCGACA 58.340 40.909 0.00 0.00 0.00 4.35
76 80 1.585006 GACACCGACCAGATGACGT 59.415 57.895 0.00 0.00 0.00 4.34
77 81 0.038526 GACACCGACCAGATGACGTT 60.039 55.000 0.00 0.00 0.00 3.99
113 117 4.994201 GTCACGAGCACCGCGTCA 62.994 66.667 4.92 0.00 37.87 4.35
114 118 4.050934 TCACGAGCACCGCGTCAT 62.051 61.111 4.92 0.00 37.87 3.06
126 130 3.240203 CGTCATGTCGCCGTTGTT 58.760 55.556 0.00 0.00 0.00 2.83
616 1003 2.087462 AAAAAGGGTTGCTGCGGCTC 62.087 55.000 20.27 11.66 39.59 4.70
732 1122 1.952990 TCTGTTTTCGCTGGAAATGCA 59.047 42.857 0.00 0.00 41.54 3.96
738 1128 6.625362 TGTTTTCGCTGGAAATGCATATTTA 58.375 32.000 0.00 0.00 41.54 1.40
786 1177 6.285790 CAATTTTTGGGCTAGTTTTCACAC 57.714 37.500 0.00 0.00 0.00 3.82
1155 1552 0.609131 CCGCCACTGATCCCAAGTTT 60.609 55.000 0.00 0.00 0.00 2.66
1190 1587 0.676151 CAGGCTCTGCACTTTCTCCC 60.676 60.000 0.00 0.00 0.00 4.30
1193 1590 0.392327 GCTCTGCACTTTCTCCCTCC 60.392 60.000 0.00 0.00 0.00 4.30
1325 1723 1.336632 GCAGAGGCAGAGTGGATCCT 61.337 60.000 14.23 0.00 40.72 3.24
1349 1747 2.224523 TGAGGTTTGCGGACTTCAAGAT 60.225 45.455 0.00 0.00 33.39 2.40
1714 2124 1.135523 GCTAAGCAGAACAAGCCGC 59.864 57.895 0.00 0.00 0.00 6.53
1751 2161 2.421952 GGCCTCATGACTGCTTCCATTA 60.422 50.000 11.22 0.00 0.00 1.90
1836 2246 4.717629 CGGAAGGCGCGTGAGACA 62.718 66.667 8.43 0.00 0.00 3.41
1957 2368 3.434319 CCATCGCGGCAGCTTTGT 61.434 61.111 6.13 0.00 42.32 2.83
1960 2371 3.932580 ATCGCGGCAGCTTTGTCGA 62.933 57.895 6.13 2.42 39.54 4.20
2105 2523 1.470098 GATTGCGGCTGAAGTGAATGT 59.530 47.619 0.00 0.00 0.00 2.71
2123 2541 1.613925 TGTCTTCTTCACCGAGTCCAG 59.386 52.381 0.00 0.00 0.00 3.86
2140 2559 4.532521 AGTCCAGTTAGCATACCTCTTTGT 59.467 41.667 0.00 0.00 0.00 2.83
2236 2655 9.490663 CATAAACTTATTCTTTACTTTGGCGAG 57.509 33.333 0.00 0.00 0.00 5.03
2299 2718 7.729116 TGATAGCATGTTATGTTCTGAGATGA 58.271 34.615 6.82 0.00 0.00 2.92
2512 2931 2.497675 GTCTCTCACATAGTTGGCTCCA 59.502 50.000 0.00 0.00 0.00 3.86
2759 3181 9.439500 GCTATACTACACTAAGATAGTAGCACT 57.561 37.037 0.00 0.00 38.98 4.40
3107 3529 6.295292 GCTTCCTCTAAATGGTCCAATGTTTT 60.295 38.462 0.00 0.00 0.00 2.43
3123 3545 1.668751 GTTTTCCTGCTGTCAACACGA 59.331 47.619 0.00 0.00 0.00 4.35
3126 3548 2.254546 TCCTGCTGTCAACACGAAAT 57.745 45.000 0.00 0.00 0.00 2.17
3127 3549 2.143122 TCCTGCTGTCAACACGAAATC 58.857 47.619 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 0.319555 CACAACGTCATCTGGTCGGT 60.320 55.000 0.00 0.00 0.00 4.69
110 114 1.440353 GCAACAACGGCGACATGAC 60.440 57.895 16.62 0.00 0.00 3.06
111 115 2.612567 GGCAACAACGGCGACATGA 61.613 57.895 16.62 0.00 0.00 3.07
616 1003 1.662122 ACGTAAAAATTCCCGCGCTAG 59.338 47.619 5.56 0.00 0.00 3.42
786 1177 2.868583 AGCATGTTAAGCGCATCTAGTG 59.131 45.455 11.47 2.56 37.01 2.74
1053 1445 1.191535 CCGAGGACCATGACAGGTAA 58.808 55.000 0.00 0.00 43.38 2.85
1155 1552 1.159285 CCTGCGCATTCTCAGTTTCA 58.841 50.000 12.24 0.00 0.00 2.69
1190 1587 2.096248 GAGTAGGTGACAGGTGAGGAG 58.904 57.143 0.00 0.00 0.00 3.69
1193 1590 2.796557 TCAGAGTAGGTGACAGGTGAG 58.203 52.381 0.00 0.00 0.00 3.51
1325 1723 1.140052 TGAAGTCCGCAAACCTCAGAA 59.860 47.619 0.00 0.00 0.00 3.02
1349 1747 1.003812 CCGAATTGTACTCCCCAACCA 59.996 52.381 0.00 0.00 0.00 3.67
1714 2124 4.479993 CCTCTGCCCTCCCTTGCG 62.480 72.222 0.00 0.00 0.00 4.85
1737 2147 2.742856 CGAGCCATAATGGAAGCAGTCA 60.743 50.000 0.00 0.00 40.96 3.41
1836 2246 0.474184 CCTGAACCAAGGTGAGGTGT 59.526 55.000 8.71 0.00 39.86 4.16
1957 2368 0.176449 TGGACGTCGGTAGAGATCGA 59.824 55.000 9.92 0.00 35.28 3.59
1960 2371 2.391469 CGTGGACGTCGGTAGAGAT 58.609 57.895 9.92 0.00 34.11 2.75
2105 2523 1.996798 ACTGGACTCGGTGAAGAAGA 58.003 50.000 0.00 0.00 0.00 2.87
2123 2541 6.401153 CGTGAGAAACAAAGAGGTATGCTAAC 60.401 42.308 0.00 0.00 0.00 2.34
2184 2603 6.946340 TCTCATAGAGCTTACAACCAAATCA 58.054 36.000 0.00 0.00 0.00 2.57
2461 2880 4.819630 GGCGATTGTCATAATACTTCCCAA 59.180 41.667 0.00 0.00 0.00 4.12
2462 2881 4.385825 GGCGATTGTCATAATACTTCCCA 58.614 43.478 0.00 0.00 0.00 4.37
2492 2911 2.762887 CTGGAGCCAACTATGTGAGAGA 59.237 50.000 0.00 0.00 0.00 3.10
2493 2912 2.762887 TCTGGAGCCAACTATGTGAGAG 59.237 50.000 0.00 0.00 0.00 3.20
2512 2931 4.080687 GGGAGTATAATAGTGGCTCGTCT 58.919 47.826 0.00 0.00 0.00 4.18
2759 3181 1.228956 AGGGTAGTGTACACGGGCA 60.229 57.895 19.93 4.61 37.12 5.36
2821 3243 1.350310 CCGGGGTGGCCTAACCTATT 61.350 60.000 11.83 0.00 40.35 1.73
2879 3301 7.094933 GGAAGTTCTTCACGTTAACATTATGGT 60.095 37.037 13.44 0.00 0.00 3.55
3066 3488 3.117776 AGGAAGCATCAATGAGCACCATA 60.118 43.478 15.88 0.00 34.45 2.74
3107 3529 2.143122 GATTTCGTGTTGACAGCAGGA 58.857 47.619 10.19 10.19 0.00 3.86


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

AutoCloner maintained by Alex Coulton.