Multiple sequence alignment - TraesCS4B01G258100

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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 TraesCS4B01G258100 chr4B 100.000 3835 0 0 1 3835 524150660 524146826 0.000000e+00 7083.0
1 TraesCS4B01G258100 chr4B 92.727 385 26 2 3016 3400 669430142 669430524 4.330000e-154 555.0
2 TraesCS4B01G258100 chr4B 92.112 393 29 2 3008 3400 668306436 668306826 1.560000e-153 553.0
3 TraesCS4B01G258100 chr4B 92.506 387 27 1 3014 3400 669203862 669203478 1.560000e-153 553.0
4 TraesCS4B01G258100 chr4B 96.078 51 2 0 369 419 77073820 77073870 2.460000e-12 84.2
5 TraesCS4B01G258100 chr2B 96.498 3427 105 8 420 3835 651660564 651657142 0.000000e+00 5650.0
6 TraesCS4B01G258100 chr2B 95.682 440 19 0 3396 3835 359115461 359115022 0.000000e+00 708.0
7 TraesCS4B01G258100 chr2B 96.403 417 15 0 3 419 651661023 651660607 0.000000e+00 688.0
8 TraesCS4B01G258100 chr2B 89.506 162 13 1 747 908 359278068 359278225 6.500000e-48 202.0
9 TraesCS4B01G258100 chr2B 85.542 166 10 7 541 706 359277921 359278072 1.100000e-35 161.0
10 TraesCS4B01G258100 chr2B 94.253 87 5 0 425 511 359277511 359277597 2.400000e-27 134.0
11 TraesCS4B01G258100 chr7B 95.247 2567 116 4 420 2985 74776258 74773697 0.000000e+00 4060.0
12 TraesCS4B01G258100 chr7B 94.954 2477 117 6 519 2990 720361565 720359092 0.000000e+00 3875.0
13 TraesCS4B01G258100 chr7B 95.227 440 21 0 3396 3835 494749282 494749721 0.000000e+00 697.0
14 TraesCS4B01G258100 chr7B 95.683 417 17 1 3 419 720362437 720362022 0.000000e+00 669.0
15 TraesCS4B01G258100 chr7B 95.204 417 19 1 3 419 74776716 74776301 0.000000e+00 658.0
16 TraesCS4B01G258100 chr3B 92.896 2759 156 22 1083 3835 685957570 685954846 0.000000e+00 3973.0
17 TraesCS4B01G258100 chr3B 95.231 1384 58 3 730 2113 26466824 26468199 0.000000e+00 2183.0
18 TraesCS4B01G258100 chr3B 96.897 419 11 1 3 419 26466010 26466428 0.000000e+00 701.0
19 TraesCS4B01G258100 chr3B 97.319 373 9 1 420 792 26466471 26466842 1.940000e-177 632.0
20 TraesCS4B01G258100 chr3B 90.506 158 15 0 751 908 750374515 750374358 3.880000e-50 209.0
21 TraesCS4B01G258100 chr3B 91.241 137 10 2 909 1043 685957698 685957562 6.540000e-43 185.0
22 TraesCS4B01G258100 chr5B 92.816 2756 164 15 1083 3835 447871882 447874606 0.000000e+00 3962.0
23 TraesCS4B01G258100 chr1B 92.677 2772 139 17 1083 3835 24033685 24030959 0.000000e+00 3936.0
24 TraesCS4B01G258100 chr1B 94.326 2573 120 5 420 2990 178491812 178489264 0.000000e+00 3919.0
25 TraesCS4B01G258100 chr1B 95.499 2333 97 6 420 2752 653855718 653858042 0.000000e+00 3720.0
26 TraesCS4B01G258100 chr1B 94.659 2153 104 10 1689 3835 328518463 328516316 0.000000e+00 3328.0
27 TraesCS4B01G258100 chr1B 96.163 417 16 0 3 419 178492271 178491855 0.000000e+00 682.0
28 TraesCS4B01G258100 chr1B 94.885 391 20 0 29 419 653855285 653855675 2.530000e-171 612.0
29 TraesCS4B01G258100 chr4A 92.033 2774 157 17 1083 3835 711858567 711861297 0.000000e+00 3840.0
30 TraesCS4B01G258100 chr4A 91.997 2774 158 17 1083 3835 711810498 711813228 0.000000e+00 3834.0
31 TraesCS4B01G258100 chr4A 93.455 382 23 2 3017 3398 687958042 687957663 2.000000e-157 566.0
32 TraesCS4B01G258100 chr4A 79.133 369 37 15 541 908 718711712 718712041 6.450000e-53 219.0
33 TraesCS4B01G258100 chr4A 84.337 166 12 7 541 706 675001555 675001706 2.390000e-32 150.0
34 TraesCS4B01G258100 chr4A 94.253 87 5 0 425 511 675001145 675001231 2.400000e-27 134.0
35 TraesCS4B01G258100 chr6B 94.280 2325 121 9 1083 3400 55638794 55636475 0.000000e+00 3546.0
36 TraesCS4B01G258100 chr6B 95.444 417 19 0 3 419 113021989 113022405 0.000000e+00 665.0
37 TraesCS4B01G258100 chr3A 94.170 223 13 0 82 304 562953348 562953126 1.320000e-89 340.0
38 TraesCS4B01G258100 chr6D 93.750 224 14 0 78 301 413797168 413797391 1.710000e-88 337.0
39 TraesCS4B01G258100 chr6D 81.250 368 30 12 541 908 413799289 413799617 1.060000e-65 261.0
40 TraesCS4B01G258100 chr6D 81.919 271 24 5 639 908 364859953 364859707 5.020000e-49 206.0
41 TraesCS4B01G258100 chr6D 97.436 78 2 0 3 80 413793669 413793746 2.400000e-27 134.0
42 TraesCS4B01G258100 chr6D 93.103 87 6 0 425 511 413798788 413798874 1.120000e-25 128.0
43 TraesCS4B01G258100 chr6D 96.078 51 2 0 369 419 413798690 413798740 2.460000e-12 84.2
44 TraesCS4B01G258100 chr4D 82.288 271 23 5 639 908 502958695 502958941 1.080000e-50 211.0
45 TraesCS4B01G258100 chr4D 97.436 78 2 0 3 80 129498511 129498434 2.400000e-27 134.0
46 TraesCS4B01G258100 chr6A 81.132 212 20 15 541 750 35121981 35121788 6.640000e-33 152.0
47 TraesCS4B01G258100 chr6A 94.253 87 5 0 425 511 35122391 35122305 2.400000e-27 134.0


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 TraesCS4B01G258100 chr4B 524146826 524150660 3834 True 7083.0 7083 100.000000 1 3835 1 chr4B.!!$R1 3834
1 TraesCS4B01G258100 chr2B 651657142 651661023 3881 True 3169.0 5650 96.450500 3 3835 2 chr2B.!!$R2 3832
2 TraesCS4B01G258100 chr7B 74773697 74776716 3019 True 2359.0 4060 95.225500 3 2985 2 chr7B.!!$R1 2982
3 TraesCS4B01G258100 chr7B 720359092 720362437 3345 True 2272.0 3875 95.318500 3 2990 2 chr7B.!!$R2 2987
4 TraesCS4B01G258100 chr3B 685954846 685957698 2852 True 2079.0 3973 92.068500 909 3835 2 chr3B.!!$R2 2926
5 TraesCS4B01G258100 chr3B 26466010 26468199 2189 False 1172.0 2183 96.482333 3 2113 3 chr3B.!!$F1 2110
6 TraesCS4B01G258100 chr5B 447871882 447874606 2724 False 3962.0 3962 92.816000 1083 3835 1 chr5B.!!$F1 2752
7 TraesCS4B01G258100 chr1B 24030959 24033685 2726 True 3936.0 3936 92.677000 1083 3835 1 chr1B.!!$R1 2752
8 TraesCS4B01G258100 chr1B 328516316 328518463 2147 True 3328.0 3328 94.659000 1689 3835 1 chr1B.!!$R2 2146
9 TraesCS4B01G258100 chr1B 178489264 178492271 3007 True 2300.5 3919 95.244500 3 2990 2 chr1B.!!$R3 2987
10 TraesCS4B01G258100 chr1B 653855285 653858042 2757 False 2166.0 3720 95.192000 29 2752 2 chr1B.!!$F1 2723
11 TraesCS4B01G258100 chr4A 711858567 711861297 2730 False 3840.0 3840 92.033000 1083 3835 1 chr4A.!!$F2 2752
12 TraesCS4B01G258100 chr4A 711810498 711813228 2730 False 3834.0 3834 91.997000 1083 3835 1 chr4A.!!$F1 2752
13 TraesCS4B01G258100 chr6B 55636475 55638794 2319 True 3546.0 3546 94.280000 1083 3400 1 chr6B.!!$R1 2317

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
183 184 0.321741 TTTACATCCTTCGGCGGCAA 60.322 50.000 10.53 1.56 0.00 4.52 F
1138 1539 1.395045 CCTCCAGCTCCACGATGCTA 61.395 60.000 0.00 0.00 37.81 3.49 F
1894 2297 1.077858 GCCTCAGGAAGCTGAAGGG 60.078 63.158 0.00 0.00 32.43 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1182 1583 1.229177 GAAATGCCTTGGTGGGGGT 60.229 57.895 0.0 0.0 36.00 4.95 R
2432 2837 1.271325 TGTCTTGTCGCCAATCCATGT 60.271 47.619 0.0 0.0 0.00 3.21 R
3182 3610 1.206371 CGGTTGAATCCTCGTAGGGTT 59.794 52.381 0.0 0.0 42.59 4.11 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
35 36 2.030007 TGTACTATAATACCCGTGCGGC 60.030 50.000 4.91 0.00 33.26 6.53
91 92 3.181450 GGCATTCTGTAGTAGGGCTTGAT 60.181 47.826 0.00 0.00 0.00 2.57
183 184 0.321741 TTTACATCCTTCGGCGGCAA 60.322 50.000 10.53 1.56 0.00 4.52
206 207 5.690865 ACATTGTTCCTCCAACTGTTTCTA 58.309 37.500 0.00 0.00 35.79 2.10
323 326 2.978824 GCCCGCTGTTCTGACCTA 59.021 61.111 0.00 0.00 0.00 3.08
359 362 5.975988 ATTAGGGATGAGCAGGAAAACTA 57.024 39.130 0.00 0.00 0.00 2.24
594 954 2.809696 GGCATGCAAGCAATGAAAAGTT 59.190 40.909 21.36 0.00 35.83 2.66
718 1078 9.538508 CATTTGATGGAAAAAGGAAATAGATCC 57.461 33.333 0.00 0.00 39.96 3.36
834 1233 1.477553 ACCCAGTTATTCTCCGCGTA 58.522 50.000 4.92 0.00 0.00 4.42
899 1298 2.047274 TTGCTCTTCCTTCGGCCG 60.047 61.111 22.12 22.12 0.00 6.13
900 1299 4.760047 TGCTCTTCCTTCGGCCGC 62.760 66.667 23.51 2.86 0.00 6.53
1138 1539 1.395045 CCTCCAGCTCCACGATGCTA 61.395 60.000 0.00 0.00 37.81 3.49
1261 1662 1.326852 GCGTTCATGATGAGCAGACAG 59.673 52.381 9.88 0.00 0.00 3.51
1691 2093 1.881973 TGCTAGAAGGTGCTGCAAAAG 59.118 47.619 2.77 0.00 0.00 2.27
1883 2286 1.871408 CGGATCGAAATCAGCCTCAGG 60.871 57.143 0.00 0.00 33.21 3.86
1894 2297 1.077858 GCCTCAGGAAGCTGAAGGG 60.078 63.158 0.00 0.00 32.43 3.95
1950 2353 3.425359 CGAATGCTTCAATCTCGCTGTTT 60.425 43.478 0.00 0.00 0.00 2.83
2250 2654 1.687123 CCGTTGTCTATCCCGGATTCT 59.313 52.381 0.73 0.00 43.01 2.40
2251 2655 2.889045 CCGTTGTCTATCCCGGATTCTA 59.111 50.000 0.73 0.00 43.01 2.10
2628 3033 2.012673 GCATGACCTGGATGAACACTC 58.987 52.381 0.00 0.00 0.00 3.51
2631 3036 2.054021 TGACCTGGATGAACACTCCAA 58.946 47.619 0.00 0.00 42.12 3.53
2763 3172 2.169352 GTGGTAGTCCAGATGCTCATGT 59.831 50.000 0.00 0.00 45.24 3.21
2911 3320 9.881773 ATGTTTGGTTATGGATGGAAACTATAT 57.118 29.630 0.00 0.00 0.00 0.86
2987 3414 7.383843 ACAAGTTGGTTTCGCTTTTATATTTGG 59.616 33.333 7.96 0.00 0.00 3.28
2996 3423 5.635700 TCGCTTTTATATTTGGTGTTTTGGC 59.364 36.000 0.00 0.00 0.00 4.52
3106 3534 4.574674 AAGCTAACATCCATGTCCTTCA 57.425 40.909 0.00 0.00 40.80 3.02
3125 3553 7.984617 GTCCTTCAGAGATAAATCAGCTTAACT 59.015 37.037 0.00 0.00 0.00 2.24
3182 3610 2.722094 GCACCCACAAACATATCTCCA 58.278 47.619 0.00 0.00 0.00 3.86
3346 3794 3.969312 TGATGCATCAAGGATAGAGGACA 59.031 43.478 26.87 0.00 33.08 4.02
3535 3983 1.633432 AGCTACTTATGTGGTTGGCCA 59.367 47.619 0.00 0.00 43.73 5.36
3819 4267 6.057533 TGACTCTCTTGTCATGTTGATTTGT 58.942 36.000 0.00 0.00 41.43 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.662044 GCAACAAACCTGCTCCTGG 59.338 57.895 0.00 0.00 36.84 4.45
91 92 1.611006 GGCGACTCATCTCATCTAGCA 59.389 52.381 0.00 0.00 0.00 3.49
183 184 4.536765 AGAAACAGTTGGAGGAACAATGT 58.463 39.130 0.00 0.00 36.98 2.71
206 207 6.497259 TCTTAGAGGAAAATGACAGTAGGTGT 59.503 38.462 0.00 0.00 44.49 4.16
241 244 4.808414 TTGAGAGATGTGACGATTTCCT 57.192 40.909 0.00 0.00 0.00 3.36
314 317 1.409064 CTAGCGTGGCATAGGTCAGAA 59.591 52.381 0.00 0.00 0.00 3.02
323 326 1.072331 CCCTAATTCCTAGCGTGGCAT 59.928 52.381 0.00 0.00 0.00 4.40
359 362 7.465116 CACATAGAGATCCCCAAATTCCTTAT 58.535 38.462 0.00 0.00 0.00 1.73
718 1078 1.581934 ATACCATTGTGGATCGTGCG 58.418 50.000 2.45 0.00 40.96 5.34
792 1191 7.039784 GGGTAGCAAATCATGGCTGAATATTTA 60.040 37.037 4.64 0.00 41.25 1.40
793 1192 6.239402 GGGTAGCAAATCATGGCTGAATATTT 60.239 38.462 4.64 0.00 41.25 1.40
794 1193 5.244626 GGGTAGCAAATCATGGCTGAATATT 59.755 40.000 4.64 0.00 41.25 1.28
834 1233 9.196139 GAGGAGAATGACATATATAGTTAGGCT 57.804 37.037 0.00 0.00 0.00 4.58
840 1239 6.956435 TGGCAGAGGAGAATGACATATATAGT 59.044 38.462 0.00 0.00 26.56 2.12
851 1250 0.467384 ACGGATGGCAGAGGAGAATG 59.533 55.000 0.00 0.00 0.00 2.67
899 1298 8.865590 ACGGATATATTTTTAATTGTTGTGGC 57.134 30.769 0.00 0.00 0.00 5.01
1046 1447 2.742372 CCTGGTAAGTGCGCGCTT 60.742 61.111 35.51 35.51 0.00 4.68
1182 1583 1.229177 GAAATGCCTTGGTGGGGGT 60.229 57.895 0.00 0.00 36.00 4.95
1883 2286 2.409948 ATAGTGTGCCCTTCAGCTTC 57.590 50.000 0.00 0.00 0.00 3.86
1894 2297 5.801350 TGCTGAAGTATGAAATAGTGTGC 57.199 39.130 0.00 0.00 31.50 4.57
1950 2353 2.048222 AGCGCTCGCAAGCTTACA 60.048 55.556 16.86 0.00 46.91 2.41
2250 2654 6.832520 TTTACCACAAGTAGACCATACGTA 57.167 37.500 0.00 0.00 30.92 3.57
2251 2655 5.726980 TTTACCACAAGTAGACCATACGT 57.273 39.130 0.00 0.00 30.92 3.57
2428 2833 1.614996 TGTCGCCAATCCATGTGTTT 58.385 45.000 0.00 0.00 0.00 2.83
2432 2837 1.271325 TGTCTTGTCGCCAATCCATGT 60.271 47.619 0.00 0.00 0.00 3.21
2763 3172 4.005650 CCAGCAGCTAGATTGTCTTTCAA 58.994 43.478 0.00 0.00 40.53 2.69
2987 3414 5.544136 ACAAACAGAAATTGCCAAAACAC 57.456 34.783 0.00 0.00 0.00 3.32
2996 3423 4.087085 CGAGCGCTTAACAAACAGAAATTG 59.913 41.667 13.26 0.00 0.00 2.32
3106 3534 8.637986 CCTCACTAGTTAAGCTGATTTATCTCT 58.362 37.037 0.00 0.00 0.00 3.10
3125 3553 2.642311 TGATTTGCTTGACCCCTCACTA 59.358 45.455 0.00 0.00 0.00 2.74
3182 3610 1.206371 CGGTTGAATCCTCGTAGGGTT 59.794 52.381 0.00 0.00 42.59 4.11
3674 4122 5.705905 CCTACCTTGGAAAAGAATTCGAACT 59.294 40.000 0.00 0.00 0.00 3.01
3802 4250 5.835257 ACTCCAACAAATCAACATGACAAG 58.165 37.500 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.