Multiple sequence alignment - TraesCS2D01G458800

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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 TraesCS2D01G458800 chr2D 100.000 3563 0 0 1 3563 565530784 565534346 0.000000e+00 6580.0
1 TraesCS2D01G458800 chr2D 78.345 411 54 22 268 649 624148604 624149008 2.140000e-57 233.0
2 TraesCS2D01G458800 chr2D 77.546 432 63 24 247 649 612897925 612897499 2.770000e-56 230.0
3 TraesCS2D01G458800 chr2D 87.075 147 18 1 650 795 612897389 612897243 7.910000e-37 165.0
4 TraesCS2D01G458800 chr2D 84.354 147 12 7 106 251 6465308 6465172 2.230000e-27 134.0
5 TraesCS2D01G458800 chr2A 98.250 2743 44 1 1 2739 182858689 182861431 0.000000e+00 4796.0
6 TraesCS2D01G458800 chr2A 91.143 350 5 3 3215 3563 182861426 182861750 5.420000e-123 451.0
7 TraesCS2D01G458800 chr2A 94.286 280 13 3 650 928 679001960 679002237 3.290000e-115 425.0
8 TraesCS2D01G458800 chr2A 83.708 356 38 9 1228 1572 679012786 679013132 5.740000e-83 318.0
9 TraesCS2D01G458800 chr2A 96.040 101 4 0 3463 3563 304809201 304809101 7.910000e-37 165.0
10 TraesCS2D01G458800 chr2A 93.220 59 4 0 1786 1844 424506885 424506827 1.760000e-13 87.9
11 TraesCS2D01G458800 chr2A 94.444 36 2 0 1749 1784 679014776 679014811 4.970000e-04 56.5
12 TraesCS2D01G458800 chr7A 97.961 2747 48 1 1 2739 577680168 577677422 0.000000e+00 4756.0
13 TraesCS2D01G458800 chr7A 98.077 1664 30 1 1 1662 471965983 471964320 0.000000e+00 2894.0
14 TraesCS2D01G458800 chr7A 97.434 1676 29 1 1 1662 499901128 499899453 0.000000e+00 2844.0
15 TraesCS2D01G458800 chr7A 97.318 932 25 0 1 932 499852769 499851838 0.000000e+00 1583.0
16 TraesCS2D01G458800 chr7A 96.173 392 11 1 930 1317 499847821 499847430 3.880000e-179 638.0
17 TraesCS2D01G458800 chr7A 99.313 291 2 0 1372 1662 499847431 499847141 8.760000e-146 527.0
18 TraesCS2D01G458800 chr7A 91.404 349 5 2 3215 3563 577677427 577677104 4.190000e-124 455.0
19 TraesCS2D01G458800 chr3D 98.290 2690 38 2 874 3563 301739647 301736966 0.000000e+00 4706.0
20 TraesCS2D01G458800 chr3D 94.545 55 3 0 2857 2911 452551842 452551896 6.340000e-13 86.1
21 TraesCS2D01G458800 chr1A 97.396 2458 56 6 283 2739 450978456 450980906 0.000000e+00 4178.0
22 TraesCS2D01G458800 chr1A 90.857 350 7 2 3215 3563 450980901 450981226 2.520000e-121 446.0
23 TraesCS2D01G458800 chr1A 96.203 237 9 0 1 237 450978223 450978459 4.310000e-104 388.0
24 TraesCS2D01G458800 chr1A 81.567 217 34 5 1471 1683 325872910 325872696 1.310000e-39 174.0
25 TraesCS2D01G458800 chr1A 81.564 179 10 13 10 173 11060400 11060230 3.730000e-25 126.0
26 TraesCS2D01G458800 chr3A 97.653 1662 35 1 1 1662 493274819 493276476 0.000000e+00 2850.0
27 TraesCS2D01G458800 chr3A 95.077 325 15 1 3137 3461 56089809 56090132 8.820000e-141 510.0
28 TraesCS2D01G458800 chr3A 98.020 101 2 0 3463 3563 56086197 56086297 3.660000e-40 176.0
29 TraesCS2D01G458800 chr4A 96.873 1471 34 2 150 1610 702698044 702699512 0.000000e+00 2451.0
30 TraesCS2D01G458800 chr4A 94.887 1154 36 7 1800 2941 702700276 702701418 0.000000e+00 1783.0
31 TraesCS2D01G458800 chr4A 94.569 626 28 3 2939 3563 702702508 702703128 0.000000e+00 963.0
32 TraesCS2D01G458800 chr4A 90.501 379 26 4 1786 2155 298169535 298169158 3.200000e-135 492.0
33 TraesCS2D01G458800 chr4A 96.739 92 3 0 1601 1692 702700185 702700276 1.710000e-33 154.0
34 TraesCS2D01G458800 chr3B 88.986 1026 94 6 1831 2838 706921544 706920520 0.000000e+00 1251.0
35 TraesCS2D01G458800 chr3B 85.475 179 16 5 2963 3141 706920434 706920266 1.020000e-40 178.0
36 TraesCS2D01G458800 chr5D 85.893 1042 103 22 1829 2833 521483874 521484908 0.000000e+00 1070.0
37 TraesCS2D01G458800 chr5D 84.694 196 22 3 2946 3141 108541601 108541414 4.700000e-44 189.0
38 TraesCS2D01G458800 chr5D 94.545 55 3 0 2857 2911 367190032 367190086 6.340000e-13 86.1
39 TraesCS2D01G458800 chr5B 83.786 1067 109 27 1806 2833 657729777 657730818 0.000000e+00 953.0
40 TraesCS2D01G458800 chr5B 85.951 783 88 13 2068 2833 657880140 657880917 0.000000e+00 817.0
41 TraesCS2D01G458800 chr5B 91.497 588 41 3 1 583 166676713 166676130 0.000000e+00 800.0
42 TraesCS2D01G458800 chr7B 94.168 583 30 2 1 583 647150791 647150213 0.000000e+00 885.0
43 TraesCS2D01G458800 chr7B 98.020 101 2 0 3463 3563 687182387 687182287 3.660000e-40 176.0
44 TraesCS2D01G458800 chr5A 83.673 833 74 21 2018 2833 649806475 649807262 0.000000e+00 728.0
45 TraesCS2D01G458800 chr5A 83.417 199 25 4 2943 3141 294614886 294615076 1.020000e-40 178.0
46 TraesCS2D01G458800 chr7D 90.426 282 15 6 1819 2089 336236021 336236301 9.400000e-96 361.0
47 TraesCS2D01G458800 chr1B 89.328 253 16 7 10 262 368167978 368167737 1.240000e-79 307.0
48 TraesCS2D01G458800 chr1B 87.747 253 21 6 10 262 368098312 368098070 1.620000e-73 287.0
49 TraesCS2D01G458800 chr2B 91.089 202 12 4 1596 1792 46418814 46418614 5.860000e-68 268.0
50 TraesCS2D01G458800 chr6D 84.422 199 23 3 2943 3141 291688098 291688288 4.700000e-44 189.0
51 TraesCS2D01G458800 chr4D 83.920 199 24 3 2943 3141 24096905 24097095 2.180000e-42 183.0
52 TraesCS2D01G458800 chr4D 83.673 196 24 3 2946 3141 215176477 215176290 1.020000e-40 178.0
53 TraesCS2D01G458800 chr1D 83.838 198 18 4 2944 3141 428193165 428192982 3.660000e-40 176.0
54 TraesCS2D01G458800 chr1D 95.050 101 5 0 3463 3563 136503662 136503762 3.680000e-35 159.0
55 TraesCS2D01G458800 chr1D 86.239 109 15 0 687 795 108108407 108108515 6.250000e-23 119.0
56 TraesCS2D01G458800 chr1D 94.545 55 3 0 2857 2911 454246855 454246801 6.340000e-13 86.1
57 TraesCS2D01G458800 chr1D 94.545 55 3 0 2857 2911 454246891 454246837 6.340000e-13 86.1
58 TraesCS2D01G458800 chr6B 93.651 63 3 1 2857 2919 503547934 503547873 3.790000e-15 93.5
59 TraesCS2D01G458800 chr6B 96.226 53 1 1 2863 2914 257272570 257272622 6.340000e-13 86.1
60 TraesCS2D01G458800 chr6B 94.444 54 3 0 3408 3461 649824358 649824411 2.280000e-12 84.2
61 TraesCS2D01G458800 chr4B 94.643 56 3 0 2857 2912 454040349 454040294 1.760000e-13 87.9
62 TraesCS2D01G458800 chr6A 94.444 54 3 0 3408 3461 577717582 577717635 2.280000e-12 84.2
63 TraesCS2D01G458800 chr6A 94.444 54 3 0 3408 3461 577718386 577718439 2.280000e-12 84.2


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 TraesCS2D01G458800 chr2D 565530784 565534346 3562 False 6580.000000 6580 100.000000 1 3563 1 chr2D.!!$F1 3562
1 TraesCS2D01G458800 chr2A 182858689 182861750 3061 False 2623.500000 4796 94.696500 1 3563 2 chr2A.!!$F2 3562
2 TraesCS2D01G458800 chr7A 471964320 471965983 1663 True 2894.000000 2894 98.077000 1 1662 1 chr7A.!!$R1 1661
3 TraesCS2D01G458800 chr7A 499899453 499901128 1675 True 2844.000000 2844 97.434000 1 1662 1 chr7A.!!$R3 1661
4 TraesCS2D01G458800 chr7A 577677104 577680168 3064 True 2605.500000 4756 94.682500 1 3563 2 chr7A.!!$R5 3562
5 TraesCS2D01G458800 chr7A 499851838 499852769 931 True 1583.000000 1583 97.318000 1 932 1 chr7A.!!$R2 931
6 TraesCS2D01G458800 chr7A 499847141 499847821 680 True 582.500000 638 97.743000 930 1662 2 chr7A.!!$R4 732
7 TraesCS2D01G458800 chr3D 301736966 301739647 2681 True 4706.000000 4706 98.290000 874 3563 1 chr3D.!!$R1 2689
8 TraesCS2D01G458800 chr1A 450978223 450981226 3003 False 1670.666667 4178 94.818667 1 3563 3 chr1A.!!$F1 3562
9 TraesCS2D01G458800 chr3A 493274819 493276476 1657 False 2850.000000 2850 97.653000 1 1662 1 chr3A.!!$F1 1661
10 TraesCS2D01G458800 chr3A 56086197 56090132 3935 False 343.000000 510 96.548500 3137 3563 2 chr3A.!!$F2 426
11 TraesCS2D01G458800 chr4A 702698044 702703128 5084 False 1337.750000 2451 95.767000 150 3563 4 chr4A.!!$F1 3413
12 TraesCS2D01G458800 chr3B 706920266 706921544 1278 True 714.500000 1251 87.230500 1831 3141 2 chr3B.!!$R1 1310
13 TraesCS2D01G458800 chr5D 521483874 521484908 1034 False 1070.000000 1070 85.893000 1829 2833 1 chr5D.!!$F2 1004
14 TraesCS2D01G458800 chr5B 657729777 657730818 1041 False 953.000000 953 83.786000 1806 2833 1 chr5B.!!$F1 1027
15 TraesCS2D01G458800 chr5B 657880140 657880917 777 False 817.000000 817 85.951000 2068 2833 1 chr5B.!!$F2 765
16 TraesCS2D01G458800 chr5B 166676130 166676713 583 True 800.000000 800 91.497000 1 583 1 chr5B.!!$R1 582
17 TraesCS2D01G458800 chr7B 647150213 647150791 578 True 885.000000 885 94.168000 1 583 1 chr7B.!!$R1 582
18 TraesCS2D01G458800 chr5A 649806475 649807262 787 False 728.000000 728 83.673000 2018 2833 1 chr5A.!!$F2 815

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
201 202 4.819783 TGCTACCTGGCACCAAAG 57.180 55.556 0.00 0.0 37.29 2.77 F
1280 1306 3.744719 CGGTCGGACTCCAGCGAA 61.745 66.667 8.23 0.0 35.53 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2823 1.330521 CTGTGCAACCTGTGTGTGTAC 59.669 52.381 0.00 0.0 34.36 2.90 R
2936 3738 0.523072 TCGTAAGTGTACTGGACGGC 59.477 55.000 15.43 0.0 37.00 5.68 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
201 202 4.819783 TGCTACCTGGCACCAAAG 57.180 55.556 0.00 0.00 37.29 2.77
252 253 5.105351 TGCAGCTAAGCAGTATAGTCTGAAA 60.105 40.000 0.00 0.00 40.11 2.69
1280 1306 3.744719 CGGTCGGACTCCAGCGAA 61.745 66.667 8.23 0.00 35.53 4.70
1509 1535 9.006839 TGCTAAGCCTATTCAATCATTTCTATG 57.993 33.333 0.00 0.00 0.00 2.23
1673 2381 4.562789 CCAGATACAACGATGCGGTATATG 59.437 45.833 0.00 0.00 36.80 1.78
2093 2823 4.768968 ACATTTCCTCAACCCATCTTTCAG 59.231 41.667 0.00 0.00 0.00 3.02
2772 3572 2.238521 GGGTGTTGCAAGGAAGATCAA 58.761 47.619 0.00 0.00 0.00 2.57
2797 3597 7.509546 ACGATGAATAATTGTCCAGGATAAGT 58.490 34.615 4.76 4.47 0.00 2.24
2826 3628 7.537991 AGAAAACAGTACTCTCGAAATAGAACG 59.462 37.037 0.00 0.00 0.00 3.95
2834 3636 9.116054 GTACTCTCGAAATAGAACGAATAATCC 57.884 37.037 0.00 0.00 38.05 3.01
2941 4835 5.961396 TCTATACCTCATCTTTAGCCGTC 57.039 43.478 0.00 0.00 0.00 4.79
3105 5036 4.222810 AGCCATTGGGTTAAGGATTTGTTC 59.777 41.667 0.36 0.00 36.17 3.18
3340 5271 5.069501 ACGTTGGACACCTTACTATCTTC 57.930 43.478 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 202 2.104963 ACACCCTGACCTGAACTCTTTC 59.895 50.000 0.00 0.00 0.00 2.62
252 253 7.609532 CACTGAAATCCTCCTCAAACTTAGAAT 59.390 37.037 0.00 0.00 0.00 2.40
1280 1306 2.290705 GGGGTATAACAACCACTGCTGT 60.291 50.000 0.00 0.00 40.05 4.40
1509 1535 6.099269 TGGTATGGAGTGAAATCTAGGGTAAC 59.901 42.308 0.00 0.00 0.00 2.50
2093 2823 1.330521 CTGTGCAACCTGTGTGTGTAC 59.669 52.381 0.00 0.00 34.36 2.90
2772 3572 7.442364 CACTTATCCTGGACAATTATTCATCGT 59.558 37.037 0.00 0.00 0.00 3.73
2797 3597 8.573885 TCTATTTCGAGAGTACTGTTTTCTTCA 58.426 33.333 0.00 0.00 0.00 3.02
2826 3628 8.081633 TCGGCATATTTTGTGAATGGATTATTC 58.918 33.333 0.00 0.00 44.45 1.75
2834 3636 4.297299 AGCTCGGCATATTTTGTGAATG 57.703 40.909 0.00 0.00 0.00 2.67
2936 3738 0.523072 TCGTAAGTGTACTGGACGGC 59.477 55.000 15.43 0.00 37.00 5.68
2941 4835 5.872617 TGAATGGATTTCGTAAGTGTACTGG 59.127 40.000 0.00 0.00 37.13 4.00
3112 5043 3.491104 GCCCATGTGTTACAACGGAAAAA 60.491 43.478 0.00 0.00 29.07 1.94
3113 5044 2.034812 GCCCATGTGTTACAACGGAAAA 59.965 45.455 0.00 0.00 29.07 2.29
3114 5045 1.609555 GCCCATGTGTTACAACGGAAA 59.390 47.619 0.00 0.00 29.07 3.13
3123 5054 7.095910 CAGAAATTACAAATGCCCATGTGTTA 58.904 34.615 9.20 1.48 39.76 2.41
3130 5061 4.040217 ACAAGCAGAAATTACAAATGCCCA 59.960 37.500 0.00 0.00 37.61 5.36
3340 5271 4.955925 TTTGTACCGCCTATCATTTGTG 57.044 40.909 0.00 0.00 0.00 3.33
3451 5382 3.778629 GTTGGGAAGAGTACCCCTATGAA 59.221 47.826 6.50 0.00 46.21 2.57
3461 5392 2.488347 GGCTGTTTGGTTGGGAAGAGTA 60.488 50.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.