Multiple sequence alignment - TraesCS3A01G016000

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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 TraesCS3A01G016000 chr3A 100.000 4285 0 0 1 4285 10475771 10471487 0.000000e+00 7914.0
1 TraesCS3A01G016000 chr3A 98.951 2098 19 3 1104 3198 10441466 10439369 0.000000e+00 3749.0
2 TraesCS3A01G016000 chr3A 95.667 877 34 4 1 876 614543239 614544112 0.000000e+00 1406.0
3 TraesCS3A01G016000 chr3A 95.455 880 38 2 1 879 682736174 682737052 0.000000e+00 1402.0
4 TraesCS3A01G016000 chr3A 95.543 875 37 2 1 874 708643607 708644480 0.000000e+00 1399.0
5 TraesCS3A01G016000 chr3A 83.937 635 60 23 3687 4285 10422038 10421410 1.730000e-158 569.0
6 TraesCS3A01G016000 chr3A 81.292 449 54 14 3261 3691 10438524 10438088 1.910000e-88 337.0
7 TraesCS3A01G016000 chr3A 86.400 250 22 8 1188 1425 10441555 10441306 3.290000e-66 263.0
8 TraesCS3A01G016000 chr3A 81.988 161 16 7 1104 1263 10441292 10441144 1.620000e-24 124.0
9 TraesCS3A01G016000 chr3A 81.988 161 16 7 1104 1263 10474495 10474347 1.620000e-24 124.0
10 TraesCS3A01G016000 chr3A 81.988 161 16 7 1277 1425 10474668 10474509 1.620000e-24 124.0
11 TraesCS3A01G016000 chr3D 93.823 2137 73 20 1104 3225 4819307 4817215 0.000000e+00 3160.0
12 TraesCS3A01G016000 chr3D 97.485 1511 38 0 2775 4285 4674525 4673015 0.000000e+00 2580.0
13 TraesCS3A01G016000 chr3D 82.284 1445 144 57 2931 4285 4817172 4815750 0.000000e+00 1147.0
14 TraesCS3A01G016000 chr3D 84.615 481 49 9 960 1425 4819620 4819150 5.050000e-124 455.0
15 TraesCS3A01G016000 chr3D 86.335 161 18 2 1104 1263 4819136 4818979 5.700000e-39 172.0
16 TraesCS3A01G016000 chr3D 93.333 90 5 1 2905 2993 9761604 9761693 9.670000e-27 132.0
17 TraesCS3A01G016000 chrUn 90.750 1719 108 23 2308 4008 35985889 35984204 0.000000e+00 2246.0
18 TraesCS3A01G016000 chrUn 91.533 1429 77 12 1104 2492 236970321 236971745 0.000000e+00 1929.0
19 TraesCS3A01G016000 chrUn 88.394 1077 80 26 3253 4285 35390351 35389276 0.000000e+00 1254.0
20 TraesCS3A01G016000 chrUn 88.266 963 78 22 2308 3252 35391339 35390394 0.000000e+00 1120.0
21 TraesCS3A01G016000 chrUn 93.264 772 27 14 1880 2629 35392178 35391410 0.000000e+00 1114.0
22 TraesCS3A01G016000 chrUn 81.194 1441 161 60 2931 4285 35588807 35590223 0.000000e+00 1059.0
23 TraesCS3A01G016000 chrUn 90.461 629 47 9 2544 3168 35389033 35388414 0.000000e+00 817.0
24 TraesCS3A01G016000 chrUn 91.358 567 29 4 876 1425 236969915 236970478 0.000000e+00 758.0
25 TraesCS3A01G016000 chrUn 83.528 771 94 14 3256 4008 322863660 322862905 0.000000e+00 689.0
26 TraesCS3A01G016000 chrUn 83.333 774 96 15 3253 4008 34641054 34640296 0.000000e+00 684.0
27 TraesCS3A01G016000 chrUn 87.654 486 44 8 3539 4008 392314122 392313637 6.260000e-153 551.0
28 TraesCS3A01G016000 chrUn 89.019 428 43 3 3585 4008 257312865 257313292 1.060000e-145 527.0
29 TraesCS3A01G016000 chrUn 89.019 428 43 3 3585 4008 270690907 270690480 1.060000e-145 527.0
30 TraesCS3A01G016000 chrUn 88.785 428 42 3 3585 4008 226966926 226967351 1.770000e-143 520.0
31 TraesCS3A01G016000 chrUn 88.785 428 42 3 3585 4008 250248100 250248525 1.770000e-143 520.0
32 TraesCS3A01G016000 chrUn 92.958 284 19 1 4002 4285 35984180 35983898 3.080000e-111 412.0
33 TraesCS3A01G016000 chrUn 88.070 285 28 4 4006 4285 226967378 226967661 2.470000e-87 333.0
34 TraesCS3A01G016000 chrUn 88.070 285 28 4 4006 4285 250248552 250248835 2.470000e-87 333.0
35 TraesCS3A01G016000 chrUn 87.368 285 30 4 4006 4285 392313610 392313327 5.350000e-84 322.0
36 TraesCS3A01G016000 chrUn 95.946 148 6 0 2433 2580 236971993 236972140 1.540000e-59 241.0
37 TraesCS3A01G016000 chrUn 85.714 161 19 4 1104 1263 236970492 236970649 2.650000e-37 167.0
38 TraesCS3A01G016000 chrUn 91.549 71 6 0 2556 2626 236971758 236971828 9.810000e-17 99.0
39 TraesCS3A01G016000 chrUn 96.000 50 2 0 3286 3335 303517898 303517947 9.880000e-12 82.4
40 TraesCS3A01G016000 chrUn 86.250 80 2 1 3256 3335 356144378 356144308 1.280000e-10 78.7
41 TraesCS3A01G016000 chrUn 92.308 52 4 0 3537 3588 34640812 34640761 1.650000e-09 75.0
42 TraesCS3A01G016000 chrUn 92.308 52 4 0 3537 3588 257312776 257312827 1.650000e-09 75.0
43 TraesCS3A01G016000 chrUn 92.308 52 4 0 3537 3588 270690996 270690945 1.650000e-09 75.0
44 TraesCS3A01G016000 chrUn 92.308 52 4 0 3537 3588 315977765 315977714 1.650000e-09 75.0
45 TraesCS3A01G016000 chrUn 92.308 52 4 0 3537 3588 322863421 322863370 1.650000e-09 75.0
46 TraesCS3A01G016000 chrUn 100.000 32 0 0 3253 3284 236971967 236971998 4.630000e-05 60.2
47 TraesCS3A01G016000 chr1A 95.895 877 35 1 1 876 504402761 504403637 0.000000e+00 1419.0
48 TraesCS3A01G016000 chr1A 95.667 877 36 2 1 876 534887836 534886961 0.000000e+00 1408.0
49 TraesCS3A01G016000 chr1A 95.444 878 37 3 1 876 552497422 552498298 0.000000e+00 1397.0
50 TraesCS3A01G016000 chr2A 95.657 875 36 2 1 873 507163212 507162338 0.000000e+00 1404.0
51 TraesCS3A01G016000 chr2A 90.588 85 6 2 3145 3228 402688279 402688362 1.260000e-20 111.0
52 TraesCS3A01G016000 chr2A 90.588 85 6 2 3145 3228 404607201 404607284 1.260000e-20 111.0
53 TraesCS3A01G016000 chr4A 95.553 877 37 2 1 876 441779190 441778315 0.000000e+00 1402.0
54 TraesCS3A01G016000 chr4A 91.765 85 5 2 3145 3228 737235902 737235985 2.710000e-22 117.0
55 TraesCS3A01G016000 chr5A 95.254 885 39 3 1 883 290726729 290725846 0.000000e+00 1399.0
56 TraesCS3A01G016000 chr5D 91.667 84 5 2 3149 3231 66974052 66973970 9.740000e-22 115.0


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 TraesCS3A01G016000 chr3A 10471487 10475771 4284 True 2720.666667 7914 87.992000 1 4285 3 chr3A.!!$R3 4284
1 TraesCS3A01G016000 chr3A 614543239 614544112 873 False 1406.000000 1406 95.667000 1 876 1 chr3A.!!$F1 875
2 TraesCS3A01G016000 chr3A 682736174 682737052 878 False 1402.000000 1402 95.455000 1 879 1 chr3A.!!$F2 878
3 TraesCS3A01G016000 chr3A 708643607 708644480 873 False 1399.000000 1399 95.543000 1 874 1 chr3A.!!$F3 873
4 TraesCS3A01G016000 chr3A 10438088 10441555 3467 True 1118.250000 3749 87.157750 1104 3691 4 chr3A.!!$R2 2587
5 TraesCS3A01G016000 chr3A 10421410 10422038 628 True 569.000000 569 83.937000 3687 4285 1 chr3A.!!$R1 598
6 TraesCS3A01G016000 chr3D 4673015 4674525 1510 True 2580.000000 2580 97.485000 2775 4285 1 chr3D.!!$R1 1510
7 TraesCS3A01G016000 chr3D 4815750 4819620 3870 True 1233.500000 3160 86.764250 960 4285 4 chr3D.!!$R2 3325
8 TraesCS3A01G016000 chrUn 35983898 35985889 1991 True 1329.000000 2246 91.854000 2308 4285 2 chrUn.!!$R5 1977
9 TraesCS3A01G016000 chrUn 35388414 35392178 3764 True 1076.250000 1254 90.096250 1880 4285 4 chrUn.!!$R4 2405
10 TraesCS3A01G016000 chrUn 35588807 35590223 1416 False 1059.000000 1059 81.194000 2931 4285 1 chrUn.!!$F1 1354
11 TraesCS3A01G016000 chrUn 236969915 236972140 2225 False 542.366667 1929 92.683333 876 3284 6 chrUn.!!$F4 2408
12 TraesCS3A01G016000 chrUn 392313327 392314122 795 True 436.500000 551 87.511000 3539 4285 2 chrUn.!!$R8 746
13 TraesCS3A01G016000 chrUn 226966926 226967661 735 False 426.500000 520 88.427500 3585 4285 2 chrUn.!!$F3 700
14 TraesCS3A01G016000 chrUn 250248100 250248835 735 False 426.500000 520 88.427500 3585 4285 2 chrUn.!!$F5 700
15 TraesCS3A01G016000 chrUn 322862905 322863660 755 True 382.000000 689 87.918000 3256 4008 2 chrUn.!!$R7 752
16 TraesCS3A01G016000 chrUn 34640296 34641054 758 True 379.500000 684 87.820500 3253 4008 2 chrUn.!!$R3 755
17 TraesCS3A01G016000 chrUn 257312776 257313292 516 False 301.000000 527 90.663500 3537 4008 2 chrUn.!!$F6 471
18 TraesCS3A01G016000 chrUn 270690480 270690996 516 True 301.000000 527 90.663500 3537 4008 2 chrUn.!!$R6 471
19 TraesCS3A01G016000 chr1A 504402761 504403637 876 False 1419.000000 1419 95.895000 1 876 1 chr1A.!!$F1 875
20 TraesCS3A01G016000 chr1A 534886961 534887836 875 True 1408.000000 1408 95.667000 1 876 1 chr1A.!!$R1 875
21 TraesCS3A01G016000 chr1A 552497422 552498298 876 False 1397.000000 1397 95.444000 1 876 1 chr1A.!!$F2 875
22 TraesCS3A01G016000 chr2A 507162338 507163212 874 True 1404.000000 1404 95.657000 1 873 1 chr2A.!!$R1 872
23 TraesCS3A01G016000 chr4A 441778315 441779190 875 True 1402.000000 1402 95.553000 1 876 1 chr4A.!!$R1 875
24 TraesCS3A01G016000 chr5A 290725846 290726729 883 True 1399.000000 1399 95.254000 1 883 1 chr5A.!!$R1 882

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
793 796 1.017177 CGATTTTCGGCGTCTTGGGA 61.017 55.000 6.85 0.0 36.0 4.37 F
994 1007 1.153349 GAGTCCAATCCCGAGCACC 60.153 63.158 0.00 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2901 3537 2.691526 AGCAAATCGACATGCCAATGAT 59.308 40.909 17.84 0.0 43.57 2.45 R
3440 5215 2.797156 GCTACGTGGATGTTGCTATGAG 59.203 50.000 1.81 0.0 37.57 2.90 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
36 37 1.376543 CAAGCATCCTCATCGCTGTT 58.623 50.000 0.00 0.00 35.79 3.16
87 88 1.667236 CGCCAGTGCAATCCATCTTA 58.333 50.000 0.00 0.00 37.32 2.10
185 186 2.096819 GCCGAAATGTTTTCTCGCCATA 59.903 45.455 0.00 0.00 0.00 2.74
449 450 1.658686 AAAACGCCGAACACCTTGCA 61.659 50.000 0.00 0.00 0.00 4.08
657 659 1.073284 TCGGGGGAAGAAAACCTTGAG 59.927 52.381 0.00 0.00 34.68 3.02
670 672 1.145119 ACCTTGAGTTTTCCCCTGTCC 59.855 52.381 0.00 0.00 0.00 4.02
793 796 1.017177 CGATTTTCGGCGTCTTGGGA 61.017 55.000 6.85 0.00 36.00 4.37
844 848 1.228429 CGAAAAAGTGGCCTGGGGA 60.228 57.895 3.32 0.00 0.00 4.81
994 1007 1.153349 GAGTCCAATCCCGAGCACC 60.153 63.158 0.00 0.00 0.00 5.01
1138 1157 1.762460 TGGATCTTCCGGCTCCTCC 60.762 63.158 0.00 0.84 40.17 4.30
1156 1346 2.507324 GCGGGAGAAGAGCACGAC 60.507 66.667 0.00 0.00 0.00 4.34
2901 3537 7.809331 GCAATGTGTATGAAGAAATTCACTTGA 59.191 33.333 0.00 0.00 33.23 3.02
3198 3839 8.554528 CGCATATAAGATTTGTCTGAAGTCAAT 58.445 33.333 0.00 0.00 0.00 2.57
3440 5215 4.346129 GTGCGAGAATTTGTCATGGATTC 58.654 43.478 0.00 0.00 0.00 2.52
3650 5468 7.360946 CCAAGTGTATGCATGTATCATCTCATG 60.361 40.741 10.16 0.00 42.71 3.07
3832 5651 4.142403 ACACATTCATCGGCATTTCGAAAT 60.142 37.500 17.60 17.60 42.69 2.17
4169 6058 4.991153 TGTGTTTTGTGCTAATCAACCA 57.009 36.364 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.325933 CCTCCATCCAGAAGTGCACA 59.674 55.000 21.04 0.00 0.00 4.57
87 88 5.007385 AGTTCGACAACTACTTCAAGTGT 57.993 39.130 0.00 0.00 41.39 3.55
156 157 0.110101 AAACATTTCGGCGCCGTTAC 60.110 50.000 44.16 9.92 40.74 2.50
185 186 1.003839 TTCGCCGATGCTCCACTTT 60.004 52.632 0.00 0.00 34.43 2.66
449 450 3.688159 GGTACACGCCCACCGAGT 61.688 66.667 0.00 0.00 43.15 4.18
657 659 1.170290 CCACACGGACAGGGGAAAAC 61.170 60.000 0.00 0.00 0.00 2.43
863 868 7.846311 AGTATATATACATCAGGGCATCTCCAA 59.154 37.037 22.00 0.00 35.74 3.53
899 904 2.382305 TCCTCTCCTCCAAGAACCTACA 59.618 50.000 0.00 0.00 0.00 2.74
948 961 8.030106 CGGGATTATATAAAGACCAGAGACTTC 58.970 40.741 0.00 0.00 0.00 3.01
994 1007 1.369091 CGGCGGAAGGAGATGGTTTG 61.369 60.000 0.00 0.00 0.00 2.93
1035 1048 0.165944 CGGTGCTGTGGATTTCGAAC 59.834 55.000 0.00 0.00 0.00 3.95
1138 1157 4.116328 TCGTGCTCTTCTCCCGCG 62.116 66.667 0.00 0.00 0.00 6.46
2901 3537 2.691526 AGCAAATCGACATGCCAATGAT 59.308 40.909 17.84 0.00 43.57 2.45
3440 5215 2.797156 GCTACGTGGATGTTGCTATGAG 59.203 50.000 1.81 0.00 37.57 2.90
3582 5400 1.514014 GGCCAGCGCATTTTGTACG 60.514 57.895 11.47 0.00 36.38 3.67
3592 5410 0.808453 TTACAGTAATCGGCCAGCGC 60.808 55.000 2.24 0.00 0.00 5.92
3650 5468 7.539366 GTCCTATTCTAACGTGATCATAAGAGC 59.461 40.741 0.00 0.00 0.00 4.09
3656 5474 6.716934 ACTGTCCTATTCTAACGTGATCAT 57.283 37.500 0.00 0.00 0.00 2.45
4169 6058 5.279256 GGCCACATGGTTGTAACAGTTTTAT 60.279 40.000 0.00 0.00 37.57 1.40


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

AutoCloner maintained by Alex Coulton.