Multiple sequence alignment - TraesCS5B01G340000

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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 TraesCS5B01G340000 chr5B 100.000 3200 0 0 1 3200 524453198 524449999 0.000000e+00 5910.0
1 TraesCS5B01G340000 chr5B 89.855 1863 100 50 1 1816 524555063 524553243 0.000000e+00 2311.0
2 TraesCS5B01G340000 chr5B 83.007 459 44 16 873 1305 704121065 704120615 5.010000e-103 385.0
3 TraesCS5B01G340000 chr5B 88.327 257 20 5 1703 1958 524451415 524451168 1.870000e-77 300.0
4 TraesCS5B01G340000 chr5B 88.327 257 20 5 1784 2031 524451496 524451241 1.870000e-77 300.0
5 TraesCS5B01G340000 chr5D 95.086 1811 64 10 761 2554 431826694 431828496 0.000000e+00 2828.0
6 TraesCS5B01G340000 chr5D 94.398 1803 75 8 770 2554 513381753 513383547 0.000000e+00 2747.0
7 TraesCS5B01G340000 chr5D 96.302 649 14 2 2562 3200 431828545 431829193 0.000000e+00 1057.0
8 TraesCS5B01G340000 chr5D 96.302 649 14 2 2562 3200 513383596 513384244 0.000000e+00 1057.0
9 TraesCS5B01G340000 chr5D 83.372 872 83 27 995 1847 558584926 558584098 0.000000e+00 750.0
10 TraesCS5B01G340000 chr5D 86.572 633 58 20 1890 2504 558584267 558583644 0.000000e+00 673.0
11 TraesCS5B01G340000 chr5D 78.347 1113 127 60 763 1818 558614585 558615640 1.630000e-172 616.0
12 TraesCS5B01G340000 chr5D 83.989 356 48 8 72 423 534098561 534098211 1.840000e-87 333.0
13 TraesCS5B01G340000 chr5D 88.583 254 17 6 1703 1955 431827728 431827970 6.710000e-77 298.0
14 TraesCS5B01G340000 chr5D 88.583 254 17 6 1703 1955 513382778 513383020 6.710000e-77 298.0
15 TraesCS5B01G340000 chr5D 87.008 254 21 6 1784 2028 431827647 431827897 3.140000e-70 276.0
16 TraesCS5B01G340000 chr5D 86.614 254 22 6 1784 2028 513382697 513382947 1.460000e-68 270.0
17 TraesCS5B01G340000 chr5D 89.855 138 11 3 1784 1919 558584234 558584098 1.180000e-39 174.0
18 TraesCS5B01G340000 chr5D 86.232 138 17 2 1856 1991 558584235 558584098 7.150000e-32 148.0
19 TraesCS5B01G340000 chrUn 100.000 401 0 0 598 998 478696242 478695842 0.000000e+00 741.0
20 TraesCS5B01G340000 chrUn 79.661 118 20 4 306 423 41529423 41529310 7.360000e-12 82.4
21 TraesCS5B01G340000 chr4A 83.817 482 46 17 872 1329 611918542 611919015 2.280000e-116 429.0
22 TraesCS5B01G340000 chr4A 84.848 363 51 4 62 423 165413716 165414075 2.350000e-96 363.0
23 TraesCS5B01G340000 chr4A 82.991 341 51 7 61 397 639192332 639191995 5.190000e-78 302.0
24 TraesCS5B01G340000 chr4A 76.169 449 61 25 1387 1818 611920384 611920803 9.060000e-46 195.0
25 TraesCS5B01G340000 chr4A 92.308 117 8 1 761 877 611916987 611917102 7.100000e-37 165.0
26 TraesCS5B01G340000 chr4A 92.105 38 3 0 2875 2912 639181605 639181642 2.000000e-03 54.7
27 TraesCS5B01G340000 chr1D 84.167 360 50 6 69 425 221023261 221023616 3.060000e-90 342.0
28 TraesCS5B01G340000 chr1D 84.590 305 43 4 61 363 205085586 205085284 1.870000e-77 300.0
29 TraesCS5B01G340000 chr4B 83.014 365 55 6 62 423 386465594 386465234 1.110000e-84 324.0
30 TraesCS5B01G340000 chr4D 82.609 368 51 10 61 423 434281205 434281564 2.400000e-81 313.0
31 TraesCS5B01G340000 chr3B 81.818 363 53 11 65 425 736309527 736309878 3.120000e-75 292.0
32 TraesCS5B01G340000 chr1B 76.253 379 40 31 839 1178 683995487 683995854 4.270000e-34 156.0
33 TraesCS5B01G340000 chr1B 78.601 243 22 14 829 1049 683310727 683310961 2.000000e-27 134.0
34 TraesCS5B01G340000 chr1B 79.894 189 19 5 943 1112 683240391 683240579 1.560000e-23 121.0
35 TraesCS5B01G340000 chr1B 75.940 266 36 10 1000 1256 683236208 683236454 9.380000e-21 111.0
36 TraesCS5B01G340000 chr1B 78.571 154 22 8 1430 1573 683236854 683237006 1.220000e-14 91.6
37 TraesCS5B01G340000 chr5A 94.231 52 2 1 3044 3095 546772223 546772273 9.520000e-11 78.7
38 TraesCS5B01G340000 chr5A 100.000 37 0 0 2911 2947 546772101 546772137 5.730000e-08 69.4
39 TraesCS5B01G340000 chr7A 97.368 38 1 0 2863 2900 735856416 735856453 7.410000e-07 65.8


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 TraesCS5B01G340000 chr5B 524449999 524453198 3199 True 2170.00 5910 92.21800 1 3200 3 chr5B.!!$R3 3199
1 TraesCS5B01G340000 chr5B 524553243 524555063 1820 True 2311.00 2311 89.85500 1 1816 1 chr5B.!!$R1 1815
2 TraesCS5B01G340000 chr5D 431826694 431829193 2499 False 1114.75 2828 91.74475 761 3200 4 chr5D.!!$F2 2439
3 TraesCS5B01G340000 chr5D 513381753 513384244 2491 False 1093.00 2747 91.47425 770 3200 4 chr5D.!!$F3 2430
4 TraesCS5B01G340000 chr5D 558614585 558615640 1055 False 616.00 616 78.34700 763 1818 1 chr5D.!!$F1 1055
5 TraesCS5B01G340000 chr5D 558583644 558584926 1282 True 436.25 750 86.50775 995 2504 4 chr5D.!!$R2 1509
6 TraesCS5B01G340000 chr4A 611916987 611920803 3816 False 263.00 429 84.09800 761 1818 3 chr4A.!!$F3 1057

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
1097 2570 3.581101 CCCAGGAGGTATCTTGATCTCA 58.419 50.0 0.0 0.0 34.53 3.27 F
2069 4915 0.252696 ACTGCCTCATCCCACCTACA 60.253 55.0 0.0 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 4919 0.539518 TAGTTATCCAGCGCCTGCAA 59.46 50.0 2.29 0.0 46.23 4.08 R
2921 5817 0.850100 ACACCAACAAGGATGACCCA 59.15 50.0 0.00 0.0 41.22 4.51 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
1097 2570 3.581101 CCCAGGAGGTATCTTGATCTCA 58.419 50.000 0.00 0.0 34.53 3.27
1569 4401 4.491675 AGGAGGAGCTGTATGATCTCATT 58.508 43.478 0.00 0.0 37.76 2.57
1604 4436 6.940298 CAGTCCAAGAAGGTTGGTCTATTTTA 59.060 38.462 3.77 0.0 40.40 1.52
1612 4444 3.126343 GGTTGGTCTATTTTACACGGCTG 59.874 47.826 0.00 0.0 0.00 4.85
1628 4460 1.611851 CTGCCCAGGGAGACAGACT 60.612 63.158 10.89 0.0 35.50 3.24
1810 4646 4.256920 GCTCTGATTTTCCTCTGCTACAA 58.743 43.478 0.00 0.0 0.00 2.41
2069 4915 0.252696 ACTGCCTCATCCCACCTACA 60.253 55.000 0.00 0.0 0.00 2.74
2073 4919 2.330216 GCCTCATCCCACCTACATACT 58.670 52.381 0.00 0.0 0.00 2.12
2114 4960 3.005554 CAGCCAAGAAGGTGACTATGTG 58.994 50.000 0.00 0.0 42.68 3.21
2115 4961 2.639839 AGCCAAGAAGGTGACTATGTGT 59.360 45.455 0.00 0.0 42.68 3.72
2117 4963 3.437049 GCCAAGAAGGTGACTATGTGTTC 59.563 47.826 0.00 0.0 42.68 3.18
2554 5406 7.222999 GGTTAGTGCTAGATACATCTGTTTGAC 59.777 40.741 1.88 0.0 37.76 3.18
2555 5407 6.537453 AGTGCTAGATACATCTGTTTGACT 57.463 37.500 1.88 0.0 37.76 3.41
2556 5408 6.940739 AGTGCTAGATACATCTGTTTGACTT 58.059 36.000 1.88 0.0 37.76 3.01
2557 5409 6.815641 AGTGCTAGATACATCTGTTTGACTTG 59.184 38.462 1.88 0.0 37.76 3.16
2558 5410 6.591834 GTGCTAGATACATCTGTTTGACTTGT 59.408 38.462 1.88 0.0 37.76 3.16
2559 5411 6.591448 TGCTAGATACATCTGTTTGACTTGTG 59.409 38.462 1.88 0.0 37.76 3.33
2560 5412 5.869753 AGATACATCTGTTTGACTTGTGC 57.130 39.130 0.00 0.0 35.42 4.57
2614 5507 5.045578 ACCTCATACCAAACAGTGCTCTAAT 60.046 40.000 0.00 0.0 0.00 1.73
2648 5541 3.119849 GCCACTCGCACAGACAAATTATT 60.120 43.478 0.00 0.0 37.47 1.40
2738 5631 3.544698 TGGGGAACTTGTAGAGAGACT 57.455 47.619 0.00 0.0 0.00 3.24
2888 5781 9.332502 GAGAAGAAGTAGATTAAATCCCCTTTC 57.667 37.037 0.00 0.0 0.00 2.62
2911 5804 5.179368 TCGAGATTGTTTTCTCCATGTGTTC 59.821 40.000 0.00 0.0 39.19 3.18
2921 5817 5.304686 TCTCCATGTGTTCTTGTAAACCT 57.695 39.130 0.00 0.0 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
366 367 1.299541 GCATCCGTCCACATGTAAGG 58.700 55.000 0.00 0.0 0.00 2.69
1097 2570 1.038130 AGCGAGCCGGAGATGTAACT 61.038 55.000 5.05 0.0 0.00 2.24
1216 2696 6.353323 TGTTTTAAGGATAGCGATTCATCCA 58.647 36.000 5.33 0.0 42.78 3.41
1409 4236 3.355626 TGTCTGAGTGCAGCGTATATC 57.644 47.619 0.00 0.0 42.01 1.63
1441 4269 9.865321 CATTGAGAATTGATGACCAAGTAATTT 57.135 29.630 0.00 0.0 38.31 1.82
1442 4270 7.977853 GCATTGAGAATTGATGACCAAGTAATT 59.022 33.333 0.00 0.0 38.31 1.40
1569 4401 3.535629 CTTGGACTGAGCACGGGCA 62.536 63.158 14.57 0.0 44.61 5.36
1612 4444 1.298014 CAAGTCTGTCTCCCTGGGC 59.702 63.158 8.22 0.0 0.00 5.36
1810 4646 3.248024 TGTACCATCAAGGGTCAACTCT 58.752 45.455 0.00 0.0 43.89 3.24
2054 4900 3.495100 GCAAGTATGTAGGTGGGATGAGG 60.495 52.174 0.00 0.0 0.00 3.86
2069 4915 0.758734 TATCCAGCGCCTGCAAGTAT 59.241 50.000 2.29 0.0 46.23 2.12
2073 4919 0.539518 TAGTTATCCAGCGCCTGCAA 59.460 50.000 2.29 0.0 46.23 4.08
2109 4955 2.177394 TTGCAGCCGAAGAACACATA 57.823 45.000 0.00 0.0 0.00 2.29
2114 4960 2.030805 AGAACAATTGCAGCCGAAGAAC 60.031 45.455 5.05 0.0 0.00 3.01
2115 4961 2.229792 AGAACAATTGCAGCCGAAGAA 58.770 42.857 5.05 0.0 0.00 2.52
2117 4963 2.322161 CAAGAACAATTGCAGCCGAAG 58.678 47.619 5.05 0.0 0.00 3.79
2434 5285 2.743928 CCACTGCTCTCGCCAACC 60.744 66.667 0.00 0.0 34.43 3.77
2554 5406 7.606456 TCCCTCTGTAAACTTTTATAGCACAAG 59.394 37.037 1.64 0.0 33.50 3.16
2555 5407 7.455058 TCCCTCTGTAAACTTTTATAGCACAA 58.545 34.615 1.64 0.0 33.50 3.33
2556 5408 7.011499 TCCCTCTGTAAACTTTTATAGCACA 57.989 36.000 1.64 0.0 33.50 4.57
2557 5409 7.104290 ACTCCCTCTGTAAACTTTTATAGCAC 58.896 38.462 1.64 0.0 33.50 4.40
2558 5410 7.253905 ACTCCCTCTGTAAACTTTTATAGCA 57.746 36.000 1.64 0.0 33.50 3.49
2559 5411 8.476447 AGTACTCCCTCTGTAAACTTTTATAGC 58.524 37.037 0.00 0.0 33.50 2.97
2614 5507 1.337823 GCGAGTGGCTCTCCTTTGTTA 60.338 52.381 10.72 0.0 39.84 2.41
2648 5541 8.634335 TTGACTCATTTTCATACAATCCAAGA 57.366 30.769 0.00 0.0 0.00 3.02
2738 5631 1.612442 CCTCCTGGGACCCGAGAAA 60.612 63.158 15.17 0.0 37.23 2.52
2821 5714 3.048600 CCATCAGGGAGGAAAGTATGGA 58.951 50.000 0.00 0.0 40.01 3.41
2888 5781 5.180117 AGAACACATGGAGAAAACAATCTCG 59.820 40.000 0.00 0.0 45.54 4.04
2911 5804 3.721087 AGGATGACCCAGGTTTACAAG 57.279 47.619 0.00 0.0 37.41 3.16
2921 5817 0.850100 ACACCAACAAGGATGACCCA 59.150 50.000 0.00 0.0 41.22 4.51
3015 5911 3.003793 GCAGACAAGGTGTTTTCTCTTCC 59.996 47.826 0.00 0.0 0.00 3.46


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

AutoCloner maintained by Alex Coulton.