Multiple sequence alignment - TraesCS5B01G192300

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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 TraesCS5B01G192300 chr5B 100.000 3134 0 0 1 3134 345974172 345971039 0.000000e+00 5788.0
1 TraesCS5B01G192300 chr5B 99.512 1845 6 1 549 2393 345816455 345818296 0.000000e+00 3354.0
2 TraesCS5B01G192300 chr5B 84.709 1890 177 55 573 2399 344533588 344531748 0.000000e+00 1786.0
3 TraesCS5B01G192300 chr5B 94.737 190 10 0 2945 3134 206098994 206099183 2.360000e-76 296.0
4 TraesCS5B01G192300 chr5B 98.000 150 3 0 2799 2948 206098883 206099032 8.620000e-66 261.0
5 TraesCS5B01G192300 chr5B 91.908 173 9 5 2799 2967 75746660 75746489 1.450000e-58 237.0
6 TraesCS5B01G192300 chr5D 96.822 1605 30 2 573 2177 300756994 300758577 0.000000e+00 2662.0
7 TraesCS5B01G192300 chr5D 86.443 1726 162 33 568 2264 301440445 301438763 0.000000e+00 1825.0
8 TraesCS5B01G192300 chr5D 92.139 547 27 6 1 546 365308406 365307875 0.000000e+00 758.0
9 TraesCS5B01G192300 chr5D 98.049 410 6 1 2321 2728 300760064 300760473 0.000000e+00 712.0
10 TraesCS5B01G192300 chr5D 84.000 575 47 20 1 548 219762878 219762322 7.750000e-141 510.0
11 TraesCS5B01G192300 chr5D 98.206 223 4 0 2726 2948 300760633 300760855 1.050000e-104 390.0
12 TraesCS5B01G192300 chr5D 95.263 190 5 1 2945 3134 300760817 300761002 6.570000e-77 298.0
13 TraesCS5B01G192300 chr5D 94.444 90 4 1 2186 2275 300758662 300758750 1.520000e-28 137.0
14 TraesCS5B01G192300 chr5A 90.413 751 55 10 1517 2261 398445755 398446494 0.000000e+00 972.0
15 TraesCS5B01G192300 chr5A 87.741 571 67 1 960 1527 398445112 398445682 0.000000e+00 664.0
16 TraesCS5B01G192300 chr5A 93.717 191 12 0 2944 3134 695848180 695848370 1.420000e-73 287.0
17 TraesCS5B01G192300 chr5A 83.154 279 35 9 571 839 398444749 398445025 8.680000e-61 244.0
18 TraesCS5B01G192300 chr1A 96.000 550 21 1 1 549 10811810 10811261 0.000000e+00 893.0
19 TraesCS5B01G192300 chr4B 95.620 548 6 1 1 548 456376248 456375719 0.000000e+00 863.0
20 TraesCS5B01G192300 chr6D 92.322 547 28 5 1 546 421060839 421060306 0.000000e+00 765.0
21 TraesCS5B01G192300 chr6D 92.157 102 5 3 2396 2494 403053111 403053212 1.170000e-29 141.0
22 TraesCS5B01G192300 chr3B 94.926 473 22 2 1 472 631519532 631519061 0.000000e+00 739.0
23 TraesCS5B01G192300 chr3B 86.164 477 31 12 25 473 7078126 7077657 1.690000e-132 483.0
24 TraesCS5B01G192300 chr3B 94.737 190 10 0 2945 3134 774808064 774808253 2.360000e-76 296.0
25 TraesCS5B01G192300 chr7A 86.458 576 42 17 1 547 94705776 94706344 1.610000e-167 599.0
26 TraesCS5B01G192300 chr7A 84.575 577 52 19 1 550 82162676 82163242 3.560000e-149 538.0
27 TraesCS5B01G192300 chr7B 84.000 575 55 21 1 548 606793634 606794198 4.630000e-143 518.0
28 TraesCS5B01G192300 chr1B 91.738 351 10 1 2799 3130 562143894 562144244 1.320000e-128 470.0
29 TraesCS5B01G192300 chr1B 97.333 150 4 0 2799 2948 182046807 182046658 4.010000e-64 255.0
30 TraesCS5B01G192300 chr1B 96.667 150 5 0 2799 2948 604306391 604306540 1.870000e-62 250.0
31 TraesCS5B01G192300 chr2D 87.847 288 22 5 1 282 465338220 465337940 3.010000e-85 326.0
32 TraesCS5B01G192300 chr1D 87.500 288 23 5 1 282 415874562 415874842 1.400000e-83 320.0
33 TraesCS5B01G192300 chr4D 96.316 190 7 0 2945 3134 491458965 491458776 2.350000e-81 313.0
34 TraesCS5B01G192300 chr4D 95.789 190 8 0 2945 3134 418353659 418353848 1.090000e-79 307.0
35 TraesCS5B01G192300 chr4D 94.839 155 7 1 2795 2948 418353543 418353697 1.120000e-59 241.0
36 TraesCS5B01G192300 chr7D 95.699 186 8 0 2945 3130 188158878 188159063 1.830000e-77 300.0
37 TraesCS5B01G192300 chr7D 98.000 150 3 0 2799 2948 188158767 188158916 8.620000e-66 261.0
38 TraesCS5B01G192300 chr7D 97.561 41 1 0 1022 1062 478780220 478780260 1.560000e-08 71.3
39 TraesCS5B01G192300 chr4A 94.737 190 10 0 2945 3134 698792390 698792201 2.360000e-76 296.0
40 TraesCS5B01G192300 chr4A 98.000 150 3 0 2799 2948 698792501 698792352 8.620000e-66 261.0
41 TraesCS5B01G192300 chr6B 88.406 207 23 1 358 563 687243977 687243771 6.710000e-62 248.0
42 TraesCS5B01G192300 chr6B 89.796 98 7 3 2396 2490 603901223 603901320 4.240000e-24 122.0
43 TraesCS5B01G192300 chr6A 90.000 100 9 1 2396 2494 549529954 549530053 9.120000e-26 128.0


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 TraesCS5B01G192300 chr5B 345971039 345974172 3133 True 5788.000000 5788 100.000000 1 3134 1 chr5B.!!$R3 3133
1 TraesCS5B01G192300 chr5B 345816455 345818296 1841 False 3354.000000 3354 99.512000 549 2393 1 chr5B.!!$F1 1844
2 TraesCS5B01G192300 chr5B 344531748 344533588 1840 True 1786.000000 1786 84.709000 573 2399 1 chr5B.!!$R2 1826
3 TraesCS5B01G192300 chr5D 301438763 301440445 1682 True 1825.000000 1825 86.443000 568 2264 1 chr5D.!!$R2 1696
4 TraesCS5B01G192300 chr5D 300756994 300761002 4008 False 839.800000 2662 96.556800 573 3134 5 chr5D.!!$F1 2561
5 TraesCS5B01G192300 chr5D 365307875 365308406 531 True 758.000000 758 92.139000 1 546 1 chr5D.!!$R3 545
6 TraesCS5B01G192300 chr5D 219762322 219762878 556 True 510.000000 510 84.000000 1 548 1 chr5D.!!$R1 547
7 TraesCS5B01G192300 chr5A 398444749 398446494 1745 False 626.666667 972 87.102667 571 2261 3 chr5A.!!$F2 1690
8 TraesCS5B01G192300 chr1A 10811261 10811810 549 True 893.000000 893 96.000000 1 549 1 chr1A.!!$R1 548
9 TraesCS5B01G192300 chr4B 456375719 456376248 529 True 863.000000 863 95.620000 1 548 1 chr4B.!!$R1 547
10 TraesCS5B01G192300 chr6D 421060306 421060839 533 True 765.000000 765 92.322000 1 546 1 chr6D.!!$R1 545
11 TraesCS5B01G192300 chr7A 94705776 94706344 568 False 599.000000 599 86.458000 1 547 1 chr7A.!!$F2 546
12 TraesCS5B01G192300 chr7A 82162676 82163242 566 False 538.000000 538 84.575000 1 550 1 chr7A.!!$F1 549
13 TraesCS5B01G192300 chr7B 606793634 606794198 564 False 518.000000 518 84.000000 1 548 1 chr7B.!!$F1 547

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
539 580 0.961857 TGCGCTCGGGACTAGTTACA 60.962 55.0 9.73 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2462 4003 1.15283 GCCCCTGGGTTTCTGTCAA 59.847 57.895 12.71 0.0 37.65 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
248 265 1.095807 GCTACCAAATGACCCTCGGC 61.096 60.000 0.00 0.00 0.00 5.54
539 580 0.961857 TGCGCTCGGGACTAGTTACA 60.962 55.000 9.73 0.00 0.00 2.41
1112 1199 0.238289 CCGACAGCAAAAGACGCAAT 59.762 50.000 0.00 0.00 0.00 3.56
2221 2489 0.622136 TGGCTGGATGCATCACTCTT 59.378 50.000 27.25 0.00 45.15 2.85
2503 4044 7.143340 GGCTACATAGTCATATTACACACGAA 58.857 38.462 0.00 0.00 0.00 3.85
2567 4108 9.590088 CAAAATTAACTTTCCTACTCACGTAAC 57.410 33.333 0.00 0.00 0.00 2.50
2737 4440 4.635223 TCTTGCCATATACACAGCATCTC 58.365 43.478 0.00 0.00 34.72 2.75
2766 4469 5.474876 AGCAAACAACTCAGAGAATTAAGGG 59.525 40.000 3.79 0.00 0.00 3.95
2790 4493 1.277842 AGTCACGCCCAATATGACACA 59.722 47.619 6.40 0.00 44.26 3.72
2858 4561 0.398318 ACACTTCTCAACCCAGCCTC 59.602 55.000 0.00 0.00 0.00 4.70
2928 4631 2.107750 CATCGAGGGTCGCTGCAT 59.892 61.111 0.00 0.00 40.21 3.96
2929 4632 1.522355 CATCGAGGGTCGCTGCATT 60.522 57.895 0.00 0.00 40.21 3.56
2930 4633 0.249447 CATCGAGGGTCGCTGCATTA 60.249 55.000 0.00 0.00 40.21 1.90
2931 4634 0.032678 ATCGAGGGTCGCTGCATTAG 59.967 55.000 0.00 0.00 40.21 1.73
2932 4635 1.592669 CGAGGGTCGCTGCATTAGG 60.593 63.158 0.00 0.00 31.14 2.69
2933 4636 1.522569 GAGGGTCGCTGCATTAGGT 59.477 57.895 0.00 0.00 0.00 3.08
2934 4637 0.750850 GAGGGTCGCTGCATTAGGTA 59.249 55.000 0.00 0.00 0.00 3.08
2935 4638 1.138266 GAGGGTCGCTGCATTAGGTAA 59.862 52.381 0.00 0.00 0.00 2.85
2936 4639 1.768870 AGGGTCGCTGCATTAGGTAAT 59.231 47.619 0.00 0.00 0.00 1.89
2937 4640 2.969950 AGGGTCGCTGCATTAGGTAATA 59.030 45.455 0.00 0.00 0.00 0.98
2938 4641 3.064931 GGGTCGCTGCATTAGGTAATAC 58.935 50.000 0.00 0.00 0.00 1.89
2939 4642 3.064931 GGTCGCTGCATTAGGTAATACC 58.935 50.000 0.07 0.07 38.99 2.73
2940 4643 3.064931 GTCGCTGCATTAGGTAATACCC 58.935 50.000 5.71 0.00 39.75 3.69
2941 4644 2.701423 TCGCTGCATTAGGTAATACCCA 59.299 45.455 5.71 0.00 39.75 4.51
2942 4645 3.134985 TCGCTGCATTAGGTAATACCCAA 59.865 43.478 5.71 0.00 39.75 4.12
2943 4646 3.498397 CGCTGCATTAGGTAATACCCAAG 59.502 47.826 5.71 0.00 39.75 3.61
2944 4647 4.461198 GCTGCATTAGGTAATACCCAAGT 58.539 43.478 5.71 0.00 39.75 3.16
2945 4648 4.275936 GCTGCATTAGGTAATACCCAAGTG 59.724 45.833 5.71 3.47 39.75 3.16
2946 4649 4.204012 TGCATTAGGTAATACCCAAGTGC 58.796 43.478 17.33 17.33 39.75 4.40
2947 4650 4.204012 GCATTAGGTAATACCCAAGTGCA 58.796 43.478 18.52 0.00 39.75 4.57
2948 4651 4.827284 GCATTAGGTAATACCCAAGTGCAT 59.173 41.667 18.52 0.00 39.75 3.96
2949 4652 5.048713 GCATTAGGTAATACCCAAGTGCATC 60.049 44.000 18.52 0.00 39.75 3.91
2950 4653 3.194005 AGGTAATACCCAAGTGCATCG 57.806 47.619 5.71 0.00 39.75 3.84
2951 4654 2.769663 AGGTAATACCCAAGTGCATCGA 59.230 45.455 5.71 0.00 39.75 3.59
2952 4655 3.131396 GGTAATACCCAAGTGCATCGAG 58.869 50.000 0.00 0.00 30.04 4.04
2953 4656 2.332063 AATACCCAAGTGCATCGAGG 57.668 50.000 0.00 0.00 0.00 4.63
2954 4657 0.469917 ATACCCAAGTGCATCGAGGG 59.530 55.000 13.08 13.08 45.20 4.30
2955 4658 2.671070 CCCAAGTGCATCGAGGGT 59.329 61.111 0.00 0.00 34.75 4.34
2956 4659 1.450312 CCCAAGTGCATCGAGGGTC 60.450 63.158 0.00 0.00 34.75 4.46
2957 4660 1.811266 CCAAGTGCATCGAGGGTCG 60.811 63.158 0.00 0.00 42.10 4.79
2958 4661 2.125512 AAGTGCATCGAGGGTCGC 60.126 61.111 0.00 0.00 40.21 5.19
2959 4662 2.650116 AAGTGCATCGAGGGTCGCT 61.650 57.895 0.00 0.00 40.21 4.93
2960 4663 2.842394 AAGTGCATCGAGGGTCGCTG 62.842 60.000 0.00 0.00 40.21 5.18
3074 4777 3.685139 TTAAGAGCTAGCACTTGCACT 57.315 42.857 30.33 12.08 45.16 4.40
3075 4778 2.557920 AAGAGCTAGCACTTGCACTT 57.442 45.000 24.15 10.00 45.16 3.16
3076 4779 3.685139 AAGAGCTAGCACTTGCACTTA 57.315 42.857 24.15 0.00 45.16 2.24
3077 4780 3.244033 AGAGCTAGCACTTGCACTTAG 57.756 47.619 18.83 0.00 45.16 2.18
3089 4792 0.875059 GCACTTAGCACACAGGGTTC 59.125 55.000 0.00 0.00 44.79 3.62
3102 4805 1.552337 CAGGGTTCAGAGCTAGCAGAA 59.448 52.381 18.83 14.59 0.00 3.02
3123 4826 1.005924 GGAGGGGGAGAAGAAATGCAA 59.994 52.381 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 265 1.139947 GGGGCGAGAGTCTTCTTCG 59.860 63.158 0.00 0.00 32.53 3.79
539 580 2.642171 TCTAGGTCAAGGGACATGGT 57.358 50.000 0.00 0.00 46.17 3.55
1112 1199 2.804986 TGCATCTTCATGGGCTGTTA 57.195 45.000 0.00 0.00 0.00 2.41
2221 2489 6.381994 AGTCCCGACTTACAGGTAATCATAAA 59.618 38.462 0.00 0.00 38.83 1.40
2271 2878 9.643693 ACAAAATCTGCAGTCCAATAAATAAAG 57.356 29.630 14.67 0.00 0.00 1.85
2416 3957 8.456471 GCATCTGCTATATGAATAAAATGCTGA 58.544 33.333 0.00 0.00 38.21 4.26
2462 4003 1.152830 GCCCCTGGGTTTCTGTCAA 59.847 57.895 12.71 0.00 37.65 3.18
2567 4108 0.877071 ATGCAGTGGTTTGAGCTTCG 59.123 50.000 0.00 0.00 0.00 3.79
2737 4440 0.662619 TCTGAGTTGTTTGCTTGCCG 59.337 50.000 0.00 0.00 0.00 5.69
2766 4469 1.134521 TCATATTGGGCGTGACTGACC 60.135 52.381 0.00 0.00 37.64 4.02
2858 4561 1.007387 GGGCTGTTTTTGCTCACCG 60.007 57.895 0.00 0.00 0.00 4.94
2927 4630 5.071250 TCGATGCACTTGGGTATTACCTAAT 59.929 40.000 11.59 0.00 38.10 1.73
2928 4631 4.406326 TCGATGCACTTGGGTATTACCTAA 59.594 41.667 12.54 11.63 38.64 2.69
2929 4632 3.962063 TCGATGCACTTGGGTATTACCTA 59.038 43.478 12.54 3.68 38.64 3.08
2930 4633 2.769663 TCGATGCACTTGGGTATTACCT 59.230 45.455 12.54 0.00 38.64 3.08
2931 4634 3.131396 CTCGATGCACTTGGGTATTACC 58.869 50.000 4.11 4.11 37.60 2.85
2932 4635 3.131396 CCTCGATGCACTTGGGTATTAC 58.869 50.000 0.00 0.00 0.00 1.89
2933 4636 2.104111 CCCTCGATGCACTTGGGTATTA 59.896 50.000 7.51 0.00 33.49 0.98
2934 4637 1.134098 CCCTCGATGCACTTGGGTATT 60.134 52.381 7.51 0.00 33.49 1.89
2935 4638 0.469917 CCCTCGATGCACTTGGGTAT 59.530 55.000 7.51 0.00 33.49 2.73
2936 4639 1.904771 CCCTCGATGCACTTGGGTA 59.095 57.895 7.51 0.00 33.49 3.69
2937 4640 2.224159 ACCCTCGATGCACTTGGGT 61.224 57.895 13.72 13.72 45.47 4.51
2938 4641 1.450312 GACCCTCGATGCACTTGGG 60.450 63.158 12.61 12.61 43.26 4.12
2939 4642 1.811266 CGACCCTCGATGCACTTGG 60.811 63.158 0.00 0.00 43.74 3.61
2940 4643 2.456119 GCGACCCTCGATGCACTTG 61.456 63.158 0.00 0.00 43.74 3.16
2941 4644 2.125512 GCGACCCTCGATGCACTT 60.126 61.111 0.00 0.00 43.74 3.16
2942 4645 3.071206 AGCGACCCTCGATGCACT 61.071 61.111 0.00 0.00 43.74 4.40
2947 4650 0.032678 CTAATGCAGCGACCCTCGAT 59.967 55.000 0.00 0.00 43.74 3.59
2948 4651 1.437573 CTAATGCAGCGACCCTCGA 59.562 57.895 0.00 0.00 43.74 4.04
2949 4652 1.592669 CCTAATGCAGCGACCCTCG 60.593 63.158 0.00 0.00 43.89 4.63
2950 4653 0.750850 TACCTAATGCAGCGACCCTC 59.249 55.000 0.00 0.00 0.00 4.30
2951 4654 1.200519 TTACCTAATGCAGCGACCCT 58.799 50.000 0.00 0.00 0.00 4.34
2952 4655 2.256117 ATTACCTAATGCAGCGACCC 57.744 50.000 0.00 0.00 0.00 4.46
2953 4656 3.064931 GGTATTACCTAATGCAGCGACC 58.935 50.000 5.56 0.00 34.73 4.79
2954 4657 3.064931 GGGTATTACCTAATGCAGCGAC 58.935 50.000 12.54 0.00 38.64 5.19
2955 4658 2.701423 TGGGTATTACCTAATGCAGCGA 59.299 45.455 12.54 0.00 38.64 4.93
2956 4659 3.120321 TGGGTATTACCTAATGCAGCG 57.880 47.619 12.54 0.00 38.64 5.18
2957 4660 4.275936 CACTTGGGTATTACCTAATGCAGC 59.724 45.833 11.59 0.00 38.10 5.25
2958 4661 4.275936 GCACTTGGGTATTACCTAATGCAG 59.724 45.833 24.53 13.68 38.10 4.41
2959 4662 4.204012 GCACTTGGGTATTACCTAATGCA 58.796 43.478 24.53 10.91 38.10 3.96
2960 4663 4.036380 GTGCACTTGGGTATTACCTAATGC 59.964 45.833 23.66 23.66 38.10 3.56
2961 4664 5.437060 AGTGCACTTGGGTATTACCTAATG 58.563 41.667 15.25 12.26 38.10 1.90
3052 4755 3.937706 AGTGCAAGTGCTAGCTCTTAATG 59.062 43.478 26.76 18.59 42.66 1.90
3074 4777 1.270839 GCTCTGAACCCTGTGTGCTAA 60.271 52.381 0.00 0.00 0.00 3.09
3075 4778 0.321671 GCTCTGAACCCTGTGTGCTA 59.678 55.000 0.00 0.00 0.00 3.49
3076 4779 1.072159 GCTCTGAACCCTGTGTGCT 59.928 57.895 0.00 0.00 0.00 4.40
3077 4780 0.321671 TAGCTCTGAACCCTGTGTGC 59.678 55.000 0.00 0.00 0.00 4.57
3089 4792 0.752054 CCCTCCTTCTGCTAGCTCTG 59.248 60.000 17.23 6.45 0.00 3.35
3102 4805 0.922626 GCATTTCTTCTCCCCCTCCT 59.077 55.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.