Multiple sequence alignment - TraesCS7D01G309100

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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 TraesCS7D01G309100 chr7D 100.000 7901 0 0 1 7901 392254658 392262558 0.000000e+00 14591.0
1 TraesCS7D01G309100 chr7D 87.651 413 39 3 3169 3571 573109241 573109651 3.340000e-128 470.0
2 TraesCS7D01G309100 chr7D 95.804 143 6 0 2872 3014 517335599 517335741 1.710000e-56 231.0
3 TraesCS7D01G309100 chr7D 91.720 157 6 3 6 155 511939884 511940040 2.230000e-50 211.0
4 TraesCS7D01G309100 chr7D 93.590 78 5 0 3085 3162 566960715 566960792 5.010000e-22 117.0
5 TraesCS7D01G309100 chr7A 97.707 4449 66 14 3146 7565 443957892 443962333 0.000000e+00 7618.0
6 TraesCS7D01G309100 chr7A 98.483 2702 35 4 178 2875 443954978 443957677 0.000000e+00 4758.0
7 TraesCS7D01G309100 chr7A 98.198 111 2 0 3016 3126 443957675 443957785 2.250000e-45 195.0
8 TraesCS7D01G309100 chr7B 92.947 4381 173 45 3574 7901 388591306 388595603 0.000000e+00 6253.0
9 TraesCS7D01G309100 chr7B 97.083 2708 56 12 179 2875 388588528 388591223 0.000000e+00 4542.0
10 TraesCS7D01G309100 chr7B 85.000 420 50 4 3167 3576 570462366 570461950 1.590000e-111 414.0
11 TraesCS7D01G309100 chr7B 84.185 411 54 2 3167 3568 64495156 64495564 9.610000e-104 388.0
12 TraesCS7D01G309100 chr7B 91.463 164 7 5 1 157 662648614 662648451 1.330000e-52 219.0
13 TraesCS7D01G309100 chr7B 98.649 74 1 0 3016 3089 388591221 388591294 1.790000e-26 132.0
14 TraesCS7D01G309100 chr7B 88.235 85 10 0 5564 5648 388593156 388593240 1.400000e-17 102.0
15 TraesCS7D01G309100 chr7B 88.312 77 9 0 6471 6547 734775873 734775797 8.440000e-15 93.5
16 TraesCS7D01G309100 chr1D 87.019 416 39 8 3171 3576 308461992 308462402 9.350000e-124 455.0
17 TraesCS7D01G309100 chr1D 90.909 165 6 5 1 156 257424770 257424606 6.210000e-51 213.0
18 TraesCS7D01G309100 chr1D 90.625 160 8 3 2 154 433907865 433907706 1.040000e-48 206.0
19 TraesCS7D01G309100 chr4B 84.964 419 51 3 3168 3577 33626159 33625744 1.590000e-111 414.0
20 TraesCS7D01G309100 chr4B 97.315 149 4 0 2872 3020 398790178 398790326 3.660000e-63 254.0
21 TraesCS7D01G309100 chr2A 85.194 412 46 6 3172 3571 584516390 584516798 7.380000e-110 409.0
22 TraesCS7D01G309100 chr2A 96.429 140 4 1 2875 3014 70056865 70056727 6.170000e-56 230.0
23 TraesCS7D01G309100 chr2A 85.075 67 8 2 3413 3478 34320536 34320471 5.120000e-07 67.6
24 TraesCS7D01G309100 chr2A 92.105 38 2 1 3541 3577 367647793 367647830 1.400000e-02 52.8
25 TraesCS7D01G309100 chr5D 84.010 419 49 10 3170 3575 490931122 490931535 3.460000e-103 387.0
26 TraesCS7D01G309100 chr5D 96.622 148 5 0 2875 3022 37189328 37189181 6.120000e-61 246.0
27 TraesCS7D01G309100 chr5D 89.091 165 10 4 2 158 135516805 135516969 1.740000e-46 198.0
28 TraesCS7D01G309100 chr5D 82.424 165 26 2 3413 3577 112344543 112344382 2.970000e-29 141.0
29 TraesCS7D01G309100 chr4D 84.772 394 42 8 3153 3536 496612670 496613055 5.790000e-101 379.0
30 TraesCS7D01G309100 chr4D 97.987 149 3 0 2870 3018 14942055 14941907 7.870000e-65 259.0
31 TraesCS7D01G309100 chr4D 91.195 159 7 3 2 153 73211779 73211937 8.030000e-50 209.0
32 TraesCS7D01G309100 chr5A 79.717 424 63 7 3171 3577 115247325 115246908 1.300000e-72 285.0
33 TraesCS7D01G309100 chr2D 98.582 141 2 0 2875 3015 135316972 135317112 4.730000e-62 250.0
34 TraesCS7D01G309100 chr2D 92.157 153 7 1 6 153 367987382 367987230 2.230000e-50 211.0
35 TraesCS7D01G309100 chr2D 96.000 75 3 0 3086 3160 376701261 376701187 1.080000e-23 122.0
36 TraesCS7D01G309100 chr2D 94.595 74 4 0 3087 3160 8495904 8495977 1.800000e-21 115.0
37 TraesCS7D01G309100 chr2D 76.364 165 31 6 3413 3574 32180899 32180740 1.830000e-11 82.4
38 TraesCS7D01G309100 chr2D 100.000 28 0 0 3550 3577 15851809 15851782 1.400000e-02 52.8
39 TraesCS7D01G309100 chr2D 92.105 38 2 1 3541 3577 296362677 296362714 1.400000e-02 52.8
40 TraesCS7D01G309100 chr4A 97.203 143 2 2 2873 3014 36371016 36371157 2.850000e-59 241.0
41 TraesCS7D01G309100 chr4A 100.000 29 0 0 3550 3578 78321376 78321348 4.000000e-03 54.7
42 TraesCS7D01G309100 chr5B 98.519 135 2 0 2872 3006 2580306 2580440 1.020000e-58 239.0
43 TraesCS7D01G309100 chr5B 91.720 157 7 2 1 151 448291704 448291548 6.210000e-51 213.0
44 TraesCS7D01G309100 chr1A 94.595 148 8 0 2871 3018 547944618 547944471 6.170000e-56 230.0
45 TraesCS7D01G309100 chr1A 91.083 157 6 4 6 154 232089198 232089042 1.040000e-48 206.0
46 TraesCS7D01G309100 chr6B 76.540 341 48 21 3212 3525 85789528 85789193 2.950000e-34 158.0
47 TraesCS7D01G309100 chr6B 89.888 89 6 2 3085 3170 553057203 553057115 2.330000e-20 111.0
48 TraesCS7D01G309100 chr3D 94.872 78 4 0 3085 3162 555598244 555598321 1.080000e-23 122.0
49 TraesCS7D01G309100 chrUn 94.667 75 4 0 3086 3160 31324798 31324872 5.010000e-22 117.0
50 TraesCS7D01G309100 chr6D 93.421 76 4 1 3085 3159 368365284 368365359 2.330000e-20 111.0
51 TraesCS7D01G309100 chr6A 93.421 76 4 1 3085 3159 509279057 509279132 2.330000e-20 111.0
52 TraesCS7D01G309100 chr2B 92.105 38 2 1 3541 3577 366019067 366019030 1.400000e-02 52.8


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 TraesCS7D01G309100 chr7D 392254658 392262558 7900 False 14591.000000 14591 100.000000 1 7901 1 chr7D.!!$F1 7900
1 TraesCS7D01G309100 chr7A 443954978 443962333 7355 False 4190.333333 7618 98.129333 178 7565 3 chr7A.!!$F1 7387
2 TraesCS7D01G309100 chr7B 388588528 388595603 7075 False 2757.250000 6253 94.228500 179 7901 4 chr7B.!!$F2 7722


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
75 76 0.033228 CAAATGCAAAACTGGGCGGA 59.967 50.000 0.00 0.00 0.00 5.54 F
76 77 0.033366 AAATGCAAAACTGGGCGGAC 59.967 50.000 0.00 0.00 0.00 4.79 F
152 153 0.321298 GCCCGTTGGAGTTGCTCTAA 60.321 55.000 0.00 0.00 0.00 2.10 F
339 340 1.007336 CCTATAATCGCACCGTCCGC 61.007 60.000 0.00 0.00 0.00 5.54 F
1188 1196 1.711060 CCGGATTTAATGTGCCGCGT 61.711 55.000 4.92 0.00 42.29 6.01 F
2900 2912 0.102663 GTTCGGAATCTCTCCCGTCC 59.897 60.000 0.00 0.00 45.48 4.79 F
2951 2963 0.036732 TTGAGCTGCTCCGTGGAAAT 59.963 50.000 25.61 0.00 0.00 2.17 F
2955 2967 0.378610 GCTGCTCCGTGGAAATAAGC 59.621 55.000 0.00 0.00 0.00 3.09 F
2970 2982 0.673644 TAAGCTGCAGTTTCCTCCGC 60.674 55.000 19.79 0.00 0.00 5.54 F
3363 3462 1.002857 AGTGGGGAGAAATGAAGGGG 58.997 55.000 0.00 0.00 0.00 4.79 F
3634 3734 1.065854 ACTCGCCTTGCTAGCAATCTT 60.066 47.619 29.40 9.11 35.20 2.40 F
5248 5357 1.757731 TGTTTGGCTGGCACAAGCT 60.758 52.632 2.29 0.00 38.70 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1196 0.179234 TCGGCAACTCAAAGACCACA 59.821 50.000 0.00 0.00 0.00 4.17 R
1357 1365 3.452264 AGCTTCCCATCCTTTTTATTGCC 59.548 43.478 0.00 0.00 0.00 4.52 R
2261 2269 6.727231 TGTAGGGTTTCCAGACTGATTTACTA 59.273 38.462 3.32 0.00 34.83 1.82 R
2703 2714 9.787435 TGGTAACAGTTAAGTCAAGATACAAAT 57.213 29.630 0.00 0.00 46.17 2.32 R
2932 2944 0.036732 ATTTCCACGGAGCAGCTCAA 59.963 50.000 24.09 8.81 31.08 3.02 R
5064 5172 3.858503 GCAAGAGCTGGTTTGGCTTAAAG 60.859 47.826 0.00 0.00 40.40 1.85 R
5248 5357 7.093068 TGCTCAGATTGTCTATAGTTTGGGTTA 60.093 37.037 0.00 0.00 0.00 2.85 R
5544 5653 2.943036 ACACAGTCCGGGTTGTAATT 57.057 45.000 0.00 0.00 0.00 1.40 R
5555 5664 1.541588 GGCTCCATTTGAACACAGTCC 59.458 52.381 0.00 0.00 0.00 3.85 R
5801 5910 2.159393 GCAAAGCCAATCGATAAGCACA 60.159 45.455 18.60 0.00 0.00 4.57 R
5968 6077 2.671396 AGACCGCATAAAAGTACAAGCG 59.329 45.455 0.00 0.00 44.24 4.68 R
7712 7853 1.338337 AGATCACTGACGCCTATTCCG 59.662 52.381 0.00 0.00 0.00 4.30 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.