Multiple sequence alignment - TraesCS4A01G419600

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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 TraesCS4A01G419600 chr4A 100.000 6102 0 0 1 6102 690408648 690414749 0.000000e+00 11269.0
1 TraesCS4A01G419600 chr4A 94.014 3458 132 25 2695 6102 690621655 690618223 0.000000e+00 5169.0
2 TraesCS4A01G419600 chr4A 91.230 878 38 21 878 1742 690623586 690622735 0.000000e+00 1158.0
3 TraesCS4A01G419600 chr4A 93.320 509 32 2 2185 2692 690622257 690621750 0.000000e+00 750.0
4 TraesCS4A01G419600 chr4A 91.469 422 18 6 1742 2145 690622681 690622260 1.150000e-156 564.0
5 TraesCS4A01G419600 chr4A 91.795 195 16 0 1888 2082 690620232 690620038 7.790000e-69 272.0
6 TraesCS4A01G419600 chr4A 92.228 193 11 4 267 457 670838470 670838280 2.800000e-68 270.0
7 TraesCS4A01G419600 chr4A 75.207 242 56 4 3048 3288 294121064 294121302 1.800000e-20 111.0
8 TraesCS4A01G419600 chr4A 74.380 242 57 5 3048 3288 741112214 741112451 1.400000e-16 99.0
9 TraesCS4A01G419600 chr4A 97.059 34 1 0 183 216 123256706 123256739 2.380000e-04 58.4
10 TraesCS4A01G419600 chr7D 93.357 3869 182 26 1741 5553 34372401 34376250 0.000000e+00 5651.0
11 TraesCS4A01G419600 chr7D 90.251 1836 118 19 4166 5954 34471631 34473452 0.000000e+00 2342.0
12 TraesCS4A01G419600 chr7D 92.160 1620 80 22 913 2507 34758896 34757299 0.000000e+00 2244.0
13 TraesCS4A01G419600 chr7D 97.480 1230 22 3 2786 4006 34756490 34755261 0.000000e+00 2091.0
14 TraesCS4A01G419600 chr7D 92.889 1111 51 4 4046 5131 34755262 34754155 0.000000e+00 1589.0
15 TraesCS4A01G419600 chr7D 94.854 855 41 2 5129 5981 34754071 34753218 0.000000e+00 1332.0
16 TraesCS4A01G419600 chr7D 86.629 875 64 32 898 1742 34470486 34471337 0.000000e+00 918.0
17 TraesCS4A01G419600 chr7D 90.000 730 37 22 929 1637 34371596 34372310 0.000000e+00 911.0
18 TraesCS4A01G419600 chr7D 91.803 610 29 5 5481 6077 34376251 34376852 0.000000e+00 830.0
19 TraesCS4A01G419600 chr7D 96.694 242 7 1 2564 2804 34757097 34756856 9.530000e-108 401.0
20 TraesCS4A01G419600 chr7D 90.508 295 24 1 1784 2078 34471450 34471740 2.670000e-103 387.0
21 TraesCS4A01G419600 chr7D 92.857 196 13 1 1888 2082 34755200 34755005 3.600000e-72 283.0
22 TraesCS4A01G419600 chr7D 92.308 195 15 0 1888 2082 34374779 34374973 1.680000e-70 278.0
23 TraesCS4A01G419600 chr7D 89.781 137 6 5 5966 6102 34753129 34753001 1.050000e-37 169.0
24 TraesCS4A01G419600 chr7D 100.000 32 0 0 883 914 34470458 34470489 6.610000e-05 60.2
25 TraesCS4A01G419600 chr7A 91.996 2024 79 30 4090 6077 35001823 34999847 0.000000e+00 2763.0
26 TraesCS4A01G419600 chr7A 92.002 1813 103 24 4268 6077 34744682 34746455 0.000000e+00 2507.0
27 TraesCS4A01G419600 chr7A 89.419 860 46 15 5232 6077 34963750 34962922 0.000000e+00 1042.0
28 TraesCS4A01G419600 chr7A 89.034 766 57 14 884 1637 35003033 35002283 0.000000e+00 924.0
29 TraesCS4A01G419600 chr7A 86.220 820 65 22 879 1688 34743402 34744183 0.000000e+00 845.0
30 TraesCS4A01G419600 chr7A 87.458 295 30 4 1784 2078 34744376 34744663 3.520000e-87 333.0
31 TraesCS4A01G419600 chr7A 81.292 449 43 29 429 870 34742896 34743310 5.900000e-85 326.0
32 TraesCS4A01G419600 chr7A 92.308 195 15 0 1888 2082 35001806 35001612 1.680000e-70 278.0
33 TraesCS4A01G419600 chr7A 85.217 230 18 10 21 235 34742581 34742809 7.960000e-54 222.0
34 TraesCS4A01G419600 chr7A 84.358 179 12 6 1741 1903 35002019 35001841 1.760000e-35 161.0
35 TraesCS4A01G419600 chr7A 75.207 242 56 4 3048 3288 694787522 694787760 1.800000e-20 111.0
36 TraesCS4A01G419600 chr7A 74.486 243 56 6 3048 3288 605159971 605160209 3.890000e-17 100.0
37 TraesCS4A01G419600 chr2B 95.262 401 18 1 4268 4668 704812733 704813132 8.630000e-178 634.0
38 TraesCS4A01G419600 chr2B 86.765 272 27 4 1205 1469 704812365 704812634 1.660000e-75 294.0
39 TraesCS4A01G419600 chr2B 98.171 164 3 0 283 446 548626817 548626654 2.780000e-73 287.0
40 TraesCS4A01G419600 chr7B 96.067 178 7 0 280 457 705310600 705310777 2.150000e-74 291.0
41 TraesCS4A01G419600 chr6B 96.045 177 7 0 280 456 606434020 606433844 7.740000e-74 289.0
42 TraesCS4A01G419600 chr6B 96.045 177 6 1 275 451 160905311 160905136 2.780000e-73 287.0
43 TraesCS4A01G419600 chr6B 77.143 175 29 10 69 236 349466366 349466196 2.340000e-14 91.6
44 TraesCS4A01G419600 chr5B 97.041 169 5 0 278 446 497454794 497454962 1.000000e-72 285.0
45 TraesCS4A01G419600 chr5B 95.506 178 7 1 282 458 221204313 221204136 3.600000e-72 283.0
46 TraesCS4A01G419600 chr5A 95.000 180 6 3 276 453 290391868 290391690 4.660000e-71 279.0
47 TraesCS4A01G419600 chr6A 87.168 226 22 7 280 499 85270642 85270418 3.650000e-62 250.0
48 TraesCS4A01G419600 chr6A 97.059 34 0 1 186 218 15634282 15634315 8.540000e-04 56.5
49 TraesCS4A01G419600 chr4B 95.513 156 6 1 2642 2796 106227408 106227563 1.310000e-61 248.0
50 TraesCS4A01G419600 chr4B 93.711 159 9 1 2637 2794 438375175 438375333 2.840000e-58 237.0
51 TraesCS4A01G419600 chr4D 94.268 157 7 2 2642 2796 74079350 74079506 7.900000e-59 239.0
52 TraesCS4A01G419600 chr4D 76.871 147 24 9 136 276 1674533 1674675 2.360000e-09 75.0
53 TraesCS4A01G419600 chr6D 94.156 154 8 1 2643 2795 392273074 392273227 3.680000e-57 233.0
54 TraesCS4A01G419600 chr2A 93.168 161 8 3 2643 2801 141506470 141506311 3.680000e-57 233.0
55 TraesCS4A01G419600 chr2A 78.889 90 15 4 133 218 43498146 43498235 2.380000e-04 58.4
56 TraesCS4A01G419600 chr2A 89.362 47 1 4 186 228 496464891 496464845 8.540000e-04 56.5
57 TraesCS4A01G419600 chr1A 94.156 154 8 1 2642 2794 395177602 395177449 3.680000e-57 233.0
58 TraesCS4A01G419600 chr1A 74.525 263 62 5 3051 3312 265913116 265912858 6.470000e-20 110.0
59 TraesCS4A01G419600 chr1D 72.531 557 125 24 2878 3417 18932829 18933374 8.190000e-34 156.0
60 TraesCS4A01G419600 chr3D 76.033 242 54 4 3051 3291 312379609 312379371 8.310000e-24 122.0
61 TraesCS4A01G419600 chr3A 81.746 126 14 6 4169 4287 474433935 474433812 5.030000e-16 97.1
62 TraesCS4A01G419600 chr3A 96.970 33 0 1 186 217 590595731 590595763 3.000000e-03 54.7
63 TraesCS4A01G419600 chr3B 96.970 33 0 1 187 218 508469401 508469433 3.000000e-03 54.7


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 TraesCS4A01G419600 chr4A 690408648 690414749 6101 False 11269.000000 11269 100.000000 1 6102 1 chr4A.!!$F3 6101
1 TraesCS4A01G419600 chr4A 690618223 690623586 5363 True 1582.600000 5169 92.365600 878 6102 5 chr4A.!!$R2 5224
2 TraesCS4A01G419600 chr7D 34371596 34376852 5256 False 1917.500000 5651 91.867000 929 6077 4 chr7D.!!$F1 5148
3 TraesCS4A01G419600 chr7D 34753001 34758896 5895 True 1158.428571 2244 93.816429 913 6102 7 chr7D.!!$R1 5189
4 TraesCS4A01G419600 chr7D 34470458 34473452 2994 False 926.800000 2342 91.847000 883 5954 4 chr7D.!!$F2 5071
5 TraesCS4A01G419600 chr7A 34962922 34963750 828 True 1042.000000 1042 89.419000 5232 6077 1 chr7A.!!$R1 845
6 TraesCS4A01G419600 chr7A 34999847 35003033 3186 True 1031.500000 2763 89.424000 884 6077 4 chr7A.!!$R2 5193
7 TraesCS4A01G419600 chr7A 34742581 34746455 3874 False 846.600000 2507 86.437800 21 6077 5 chr7A.!!$F3 6056
8 TraesCS4A01G419600 chr2B 704812365 704813132 767 False 464.000000 634 91.013500 1205 4668 2 chr2B.!!$F1 3463


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
22 23 0.108992 GACCGTCCAGTATTGTCGCA 60.109 55.000 0.00 0.00 0.00 5.10 F
873 893 0.668535 CGTCTGGATGGCGTCATCTA 59.331 55.000 27.71 21.90 46.70 1.98 F
2316 2948 0.322098 TACGCAACCACCCTCCATTG 60.322 55.000 0.00 0.00 0.00 2.82 F
3621 4885 0.391597 TCCAGTTGACACCGGTTCTC 59.608 55.000 2.97 2.64 0.00 2.87 F
4208 5497 1.000607 TCAGTACACGTCTGGTTCTGC 60.001 52.381 6.35 0.00 34.15 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1568 1.281960 CCCGTAGTCATACTCCGCG 59.718 63.158 0.00 0.00 0.00 6.46 R
2507 3140 1.199615 GGGAGAGGAGGGTGAAGAAG 58.800 60.000 0.00 0.00 0.00 2.85 R
4167 5432 0.179076 TCGTGCATCATGGGCTAGTG 60.179 55.000 10.83 0.62 0.00 2.74 R
4999 6315 1.041437 AGGATTGCGTACCTAGCCTC 58.959 55.000 0.00 0.00 28.72 4.70 R
5774 7294 0.332632 TTGCTTGGGAATGGCTAGCT 59.667 50.000 15.72 0.00 33.15 3.32 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)



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AutoCloner maintained by Alex Coulton.