Multiple sequence alignment - TraesCS5D01G007400

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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 TraesCS5D01G007400 chr5D 100.000 6461 0 0 1 6461 6104345 6097885 0.000000e+00 11932.0
1 TraesCS5D01G007400 chr5D 98.167 3492 61 3 2970 6461 6088508 6085020 0.000000e+00 6091.0
2 TraesCS5D01G007400 chr5D 98.513 2959 40 3 1 2955 6091738 6088780 0.000000e+00 5217.0
3 TraesCS5D01G007400 chr5D 76.986 365 78 5 83 444 437743620 437743981 3.050000e-48 204.0
4 TraesCS5D01G007400 chr5A 94.025 2544 92 25 3353 5850 3348634 3351163 0.000000e+00 3801.0
5 TraesCS5D01G007400 chr5A 95.530 1141 31 10 590 1722 3345605 3346733 0.000000e+00 1807.0
6 TraesCS5D01G007400 chr5A 93.178 1246 60 15 1720 2955 3346777 3348007 0.000000e+00 1807.0
7 TraesCS5D01G007400 chr5A 95.580 362 15 1 2970 3331 3348284 3348644 4.340000e-161 579.0
8 TraesCS5D01G007400 chr5A 88.221 416 30 8 5846 6251 3352308 3352714 4.530000e-131 479.0
9 TraesCS5D01G007400 chr5A 76.562 384 86 4 4491 4872 442282991 442283372 2.360000e-49 207.0
10 TraesCS5D01G007400 chr5A 93.939 66 4 0 6385 6450 3352764 3352829 4.120000e-17 100.0
11 TraesCS5D01G007400 chr5A 91.837 49 1 2 1908 1953 529364178 529364226 1.500000e-06 65.8
12 TraesCS5D01G007400 chr5B 93.897 1573 59 14 3449 4989 6215927 6217494 0.000000e+00 2338.0
13 TraesCS5D01G007400 chr5B 91.297 1264 57 10 1730 2955 6214594 6215842 0.000000e+00 1676.0
14 TraesCS5D01G007400 chr5B 94.139 819 32 8 916 1722 6213726 6214540 0.000000e+00 1232.0
15 TraesCS5D01G007400 chr5B 96.259 401 13 2 529 927 6212033 6212433 0.000000e+00 656.0
16 TraesCS5D01G007400 chr5B 88.025 476 53 3 57 528 6210422 6210897 1.570000e-155 560.0
17 TraesCS5D01G007400 chr5B 90.312 320 29 2 5985 6303 6217503 6217821 1.000000e-112 418.0
18 TraesCS5D01G007400 chr5B 75.448 391 88 7 4491 4878 400522817 400523202 3.980000e-42 183.0
19 TraesCS5D01G007400 chr5B 81.818 231 25 9 5697 5918 6207425 6207647 1.850000e-40 178.0
20 TraesCS5D01G007400 chr5B 81.532 222 36 3 6044 6265 6208071 6208287 1.850000e-40 178.0
21 TraesCS5D01G007400 chr5B 75.603 373 81 10 62 428 679802220 679802588 6.660000e-40 176.0
22 TraesCS5D01G007400 chr5B 89.474 76 7 1 6386 6461 6217835 6217909 1.920000e-15 95.3
23 TraesCS5D01G007400 chr5B 74.477 239 52 8 4492 4726 400467840 400468073 1.920000e-15 95.3
24 TraesCS5D01G007400 chr5B 77.358 159 29 6 1798 1952 641921614 641921459 3.210000e-13 87.9
25 TraesCS5D01G007400 chr6A 79.692 389 72 6 57 441 611294413 611294798 2.300000e-69 274.0
26 TraesCS5D01G007400 chr6A 92.208 77 2 3 2 76 256988937 256989011 8.860000e-19 106.0
27 TraesCS5D01G007400 chr7D 78.149 389 79 5 62 447 251355337 251354952 6.470000e-60 243.0
28 TraesCS5D01G007400 chr7D 87.121 132 17 0 3716 3847 632121134 632121003 4.040000e-32 150.0
29 TraesCS5D01G007400 chr3B 75.897 390 85 8 62 447 809343961 809343577 2.380000e-44 191.0
30 TraesCS5D01G007400 chr3B 74.123 228 46 11 1720 1941 781474579 781474799 1.490000e-11 82.4
31 TraesCS5D01G007400 chr3B 97.059 34 1 0 403 436 495814356 495814323 2.520000e-04 58.4
32 TraesCS5D01G007400 chr3D 76.620 355 65 15 58 403 7588194 7587849 5.150000e-41 180.0
33 TraesCS5D01G007400 chr6D 87.313 134 16 1 3714 3847 816329 816197 1.120000e-32 152.0
34 TraesCS5D01G007400 chr2B 88.000 125 15 0 3716 3840 162860511 162860635 1.450000e-31 148.0
35 TraesCS5D01G007400 chr2B 93.056 72 3 2 2 71 281342939 281343010 3.190000e-18 104.0
36 TraesCS5D01G007400 chr2B 93.478 46 3 0 6319 6364 755584174 755584219 1.160000e-07 69.4
37 TraesCS5D01G007400 chr2D 86.822 129 17 0 3716 3844 112538491 112538619 1.880000e-30 145.0
38 TraesCS5D01G007400 chr2D 88.235 51 5 1 6315 6364 639728508 639728458 7.000000e-05 60.2
39 TraesCS5D01G007400 chr2A 86.822 129 17 0 3716 3844 55953014 55953142 1.880000e-30 145.0
40 TraesCS5D01G007400 chr2A 77.193 171 37 2 57 226 441609567 441609736 1.480000e-16 99.0
41 TraesCS5D01G007400 chr2A 76.398 161 35 3 268 428 779500905 779500748 4.150000e-12 84.2
42 TraesCS5D01G007400 chr6B 79.695 197 37 2 1761 1957 204445747 204445554 8.740000e-29 139.0
43 TraesCS5D01G007400 chr4D 85.294 136 18 2 3711 3844 3306148 3306283 8.740000e-29 139.0
44 TraesCS5D01G007400 chr4A 94.444 72 1 3 2 72 686858508 686858577 2.460000e-19 108.0
45 TraesCS5D01G007400 chr1B 94.286 70 3 1 2 70 314401791 314401722 8.860000e-19 106.0
46 TraesCS5D01G007400 chr1B 94.118 68 2 2 2 68 461987216 461987282 1.150000e-17 102.0
47 TraesCS5D01G007400 chr3A 90.123 81 4 3 2 78 627368030 627368110 1.150000e-17 102.0
48 TraesCS5D01G007400 chr3A 90.789 76 5 2 2 75 625456285 625456360 4.120000e-17 100.0
49 TraesCS5D01G007400 chr3A 73.707 232 54 7 1720 1948 303100097 303099870 4.150000e-12 84.2
50 TraesCS5D01G007400 chr3A 100.000 28 0 0 6318 6345 696313894 696313921 1.200000e-02 52.8
51 TraesCS5D01G007400 chr4B 89.744 78 6 2 2 78 130093501 130093577 1.480000e-16 99.0
52 TraesCS5D01G007400 chr4B 93.478 46 3 0 6319 6364 661648346 661648301 1.160000e-07 69.4
53 TraesCS5D01G007400 chr4B 87.755 49 6 0 6316 6364 466787730 466787778 2.520000e-04 58.4
54 TraesCS5D01G007400 chr1A 91.304 46 4 0 6319 6364 20890135 20890180 5.410000e-06 63.9
55 TraesCS5D01G007400 chr1A 94.444 36 2 0 6311 6346 13940182 13940217 1.000000e-03 56.5
56 TraesCS5D01G007400 chr1D 100.000 28 0 0 6319 6346 389214644 389214617 1.200000e-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 TraesCS5D01G007400 chr5D 6097885 6104345 6460 True 11932.000000 11932 100.000000 1 6461 1 chr5D.!!$R1 6460
1 TraesCS5D01G007400 chr5D 6085020 6091738 6718 True 5654.000000 6091 98.340000 1 6461 2 chr5D.!!$R2 6460
2 TraesCS5D01G007400 chr5A 3345605 3352829 7224 False 1428.833333 3801 93.412167 590 6450 6 chr5A.!!$F3 5860
3 TraesCS5D01G007400 chr5B 6207425 6217909 10484 False 814.588889 2338 89.639222 57 6461 9 chr5B.!!$F4 6404

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
165 3107 1.340502 GCTTCTTCTTGCCTAGCCCTT 60.341 52.381 0.00 0.0 0.00 3.95 F
485 3430 1.535833 TTTGGTGGTGTTCGTTGTGT 58.464 45.000 0.00 0.0 0.00 3.72 F
2032 7485 1.165270 ACTTGCGTTGGTCTATTGCC 58.835 50.000 0.00 0.0 0.00 4.52 F
2728 8225 2.335712 GGAGTTCTTTGGGCAGCCG 61.336 63.158 5.00 0.0 0.00 5.52 F
2974 8736 0.242555 CGCACGGGCCAGTTATTTTT 59.757 50.000 5.51 0.0 36.38 1.94 F
4260 10043 2.042930 GAGGATGGGAGGGGTGGT 59.957 66.667 0.00 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2032 7485 2.369629 CCCGTCACGTAGTTGCACG 61.370 63.158 0.00 0.0 41.61 5.34 R
2266 7742 6.207417 AGTTTCTCCAAATCACATACAAGTGG 59.793 38.462 0.00 0.0 39.93 4.00 R
2955 8452 0.242555 AAAAATAACTGGCCCGTGCG 59.757 50.000 0.00 0.0 38.85 5.34 R
4260 10043 2.673775 TTCTCACCAAATCAAGGCCA 57.326 45.000 5.01 0.0 0.00 5.36 R
4748 10542 1.654954 CCACCGACGTTCTCCTCGAT 61.655 60.000 0.00 0.0 31.24 3.59 R
6211 13185 1.150536 GTGCCTCAACCACTCCCAA 59.849 57.895 0.00 0.0 0.00 4.12 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
95 3037 4.844267 TCTTCGAGTTTTGTTAGCTTTGC 58.156 39.130 0.00 0.00 0.00 3.68
165 3107 1.340502 GCTTCTTCTTGCCTAGCCCTT 60.341 52.381 0.00 0.00 0.00 3.95
485 3430 1.535833 TTTGGTGGTGTTCGTTGTGT 58.464 45.000 0.00 0.00 0.00 3.72
1153 6547 4.215742 TTGCGCCTATCCCCGTCG 62.216 66.667 4.18 0.00 0.00 5.12
1843 7291 5.514274 TTTCTTTGTTTTCCCTGTGCTAG 57.486 39.130 0.00 0.00 0.00 3.42
2032 7485 1.165270 ACTTGCGTTGGTCTATTGCC 58.835 50.000 0.00 0.00 0.00 4.52
2266 7742 7.920738 ACCTAGCGATGTTTCATAGAAAAATC 58.079 34.615 11.04 11.04 0.00 2.17
2290 7766 6.206634 TCCACTTGTATGTGATTTGGAGAAAC 59.793 38.462 0.00 0.00 40.12 2.78
2439 7935 5.047802 CAGTGCCATAAACACTTCCAATCTT 60.048 40.000 0.00 0.00 46.01 2.40
2449 7945 6.992063 ACACTTCCAATCTTCACATATGAC 57.008 37.500 10.38 0.00 33.38 3.06
2728 8225 2.335712 GGAGTTCTTTGGGCAGCCG 61.336 63.158 5.00 0.00 0.00 5.52
2955 8452 7.932335 TCAGTAGCTCACTAATAAGTAGAAGC 58.068 38.462 0.00 6.12 39.95 3.86
2956 8453 6.853872 CAGTAGCTCACTAATAAGTAGAAGCG 59.146 42.308 0.00 0.00 42.23 4.68
2957 8454 4.612943 AGCTCACTAATAAGTAGAAGCGC 58.387 43.478 0.00 0.00 42.23 5.92
2959 8456 4.207429 GCTCACTAATAAGTAGAAGCGCAC 59.793 45.833 11.47 2.78 34.66 5.34
2960 8457 4.348656 TCACTAATAAGTAGAAGCGCACG 58.651 43.478 11.47 0.00 33.48 5.34
2961 8458 3.486108 CACTAATAAGTAGAAGCGCACGG 59.514 47.826 11.47 0.00 33.48 4.94
2962 8459 1.935933 AATAAGTAGAAGCGCACGGG 58.064 50.000 11.47 0.00 0.00 5.28
2963 8460 0.529992 ATAAGTAGAAGCGCACGGGC 60.530 55.000 11.47 0.00 0.00 6.13
2965 8462 4.752879 GTAGAAGCGCACGGGCCA 62.753 66.667 11.47 0.00 36.38 5.36
2966 8463 4.451150 TAGAAGCGCACGGGCCAG 62.451 66.667 11.47 1.85 36.38 4.85
2974 8736 0.242555 CGCACGGGCCAGTTATTTTT 59.757 50.000 5.51 0.00 36.38 1.94
3257 9019 3.450817 GGATTCCCTTTTTGGTACATGGG 59.549 47.826 0.00 0.00 39.30 4.00
3332 9094 4.753186 AGGGTAGGACTCTCTTTTCTTGA 58.247 43.478 0.00 0.00 0.00 3.02
3339 9101 4.443598 GGACTCTCTTTTCTTGAGTGTGGT 60.444 45.833 0.00 0.00 40.63 4.16
3467 9229 3.385755 GCCTTATCTGGTTTGGCATCATT 59.614 43.478 0.00 0.00 42.79 2.57
3468 9230 4.141869 GCCTTATCTGGTTTGGCATCATTT 60.142 41.667 0.00 0.00 42.79 2.32
3991 9771 8.109634 TCTAATTTTGAAGGGCTCAAGTTCTAT 58.890 33.333 0.00 0.00 44.84 1.98
3998 9778 2.290960 GGGCTCAAGTTCTATGTGGGTT 60.291 50.000 0.00 0.00 0.00 4.11
4260 10043 2.042930 GAGGATGGGAGGGGTGGT 59.957 66.667 0.00 0.00 0.00 4.16
4446 10229 5.186409 AGCAAGCAATAGTTCCATGTGAAAT 59.814 36.000 0.00 0.00 33.94 2.17
4519 10313 7.428020 TGAACTTGACTTTTCCAGATCATTTG 58.572 34.615 0.00 0.00 0.00 2.32
4588 10382 2.072298 GATTGTATCATGCGAGCCCTC 58.928 52.381 0.00 0.00 0.00 4.30
4748 10542 1.272212 GCGCCCTTTCAATCCTTTTCA 59.728 47.619 0.00 0.00 0.00 2.69
4818 10612 2.821969 ACAATGTTCTAGCCAAGCCTTG 59.178 45.455 0.00 0.00 0.00 3.61
4993 10788 6.918892 AATCAACAGTAAAACAAAAAGCCC 57.081 33.333 0.00 0.00 0.00 5.19
5185 10980 1.203187 TCCTAGTGTGGCCTCTGAGTT 60.203 52.381 3.32 0.00 0.00 3.01
5206 11001 7.434897 TGAGTTGTCACAAAGTTGCATTTAATC 59.565 33.333 0.00 0.00 0.00 1.75
5414 11211 7.201794 CGAGGATTACTATGGTACTGTCTTTGA 60.202 40.741 0.00 0.00 0.00 2.69
5449 11246 3.009143 AGGAAAAAGGCTTATCGACACCT 59.991 43.478 0.00 0.48 0.00 4.00
5924 12883 5.475909 CCCCATTGGTATCAATCAATCTCTG 59.524 44.000 0.00 0.00 41.29 3.35
6211 13185 2.434884 CACCGGCTGATGTCGCTT 60.435 61.111 0.00 0.00 40.38 4.68
6348 13335 9.878599 CCTTCCGTAAACTAATATAAAAGCATG 57.121 33.333 0.00 0.00 0.00 4.06
6407 13394 6.235231 AGAAGAATGATGGGTACGTACATT 57.765 37.500 26.02 16.38 34.55 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 3107 2.149803 CTAGACGCACCACCGGAACA 62.150 60.000 9.46 0.00 0.00 3.18
1311 6705 6.739331 ACCATTTGACAAAAATTAGTCCCA 57.261 33.333 4.41 0.00 33.89 4.37
1843 7291 5.186996 TCAGAATTTGGAAGAGTGTTTGC 57.813 39.130 0.00 0.00 0.00 3.68
2032 7485 2.369629 CCCGTCACGTAGTTGCACG 61.370 63.158 0.00 0.00 41.61 5.34
2211 7683 9.167239 GTAACATATCGATGAGTACAAGTGTAC 57.833 37.037 8.54 12.72 42.17 2.90
2266 7742 6.207417 AGTTTCTCCAAATCACATACAAGTGG 59.793 38.462 0.00 0.00 39.93 4.00
2290 7766 7.156876 TGGGCTCAAAATTATTTCACTGTAG 57.843 36.000 0.00 0.00 0.00 2.74
2479 7976 8.044060 TGAGCCAAAACTACTTCAGATAATTG 57.956 34.615 0.00 0.00 0.00 2.32
2728 8225 7.417612 TGTTGTATTTTTGCTTCTCTTCAGTC 58.582 34.615 0.00 0.00 0.00 3.51
2955 8452 0.242555 AAAAATAACTGGCCCGTGCG 59.757 50.000 0.00 0.00 38.85 5.34
2956 8453 2.416296 GGTAAAAATAACTGGCCCGTGC 60.416 50.000 0.00 0.00 0.00 5.34
2957 8454 2.820787 TGGTAAAAATAACTGGCCCGTG 59.179 45.455 0.00 0.00 0.00 4.94
2959 8456 3.697045 TGATGGTAAAAATAACTGGCCCG 59.303 43.478 0.00 0.00 0.00 6.13
2960 8457 5.669164 TTGATGGTAAAAATAACTGGCCC 57.331 39.130 0.00 0.00 0.00 5.80
2961 8458 7.926018 CCTAATTGATGGTAAAAATAACTGGCC 59.074 37.037 0.00 0.00 0.00 5.36
2962 8459 8.691797 TCCTAATTGATGGTAAAAATAACTGGC 58.308 33.333 0.00 0.00 0.00 4.85
2974 8736 6.964464 TGGCTAGTTTTCCTAATTGATGGTA 58.036 36.000 0.00 0.00 0.00 3.25
3175 8937 9.838339 ATCAACAATATTAAACTAGTCTCCCTG 57.162 33.333 0.00 0.00 0.00 4.45
3350 9112 4.433805 GCACCACACGTAAGAAAATAGACG 60.434 45.833 0.00 0.00 43.62 4.18
3354 9116 6.707161 ACTAAAGCACCACACGTAAGAAAATA 59.293 34.615 0.00 0.00 43.62 1.40
3998 9778 8.747666 GCATGTACTCGAAAATGTTGTTAAAAA 58.252 29.630 0.00 0.00 0.00 1.94
4260 10043 2.673775 TTCTCACCAAATCAAGGCCA 57.326 45.000 5.01 0.00 0.00 5.36
4519 10313 3.195825 ACTGAAGTAGCACATCCCTGTAC 59.804 47.826 0.00 0.00 33.14 2.90
4588 10382 3.071786 TCGAGCTCTAGAAGATTTGCG 57.928 47.619 12.85 0.00 0.00 4.85
4748 10542 1.654954 CCACCGACGTTCTCCTCGAT 61.655 60.000 0.00 0.00 31.24 3.59
5185 10980 8.715191 AAAAGATTAAATGCAACTTTGTGACA 57.285 26.923 0.00 0.00 0.00 3.58
5206 11001 7.128331 CCATTACTCATTATCTGCGTGAAAAG 58.872 38.462 0.00 0.00 0.00 2.27
5506 11307 8.040716 ACCGCATCTTTATTACATTTATAGGC 57.959 34.615 0.00 0.00 0.00 3.93
5526 11327 4.811969 TCCTTACATAAGAGAAACCGCA 57.188 40.909 0.00 0.00 35.33 5.69
5527 11328 4.511826 CCATCCTTACATAAGAGAAACCGC 59.488 45.833 0.00 0.00 35.33 5.68
5924 12883 8.801715 TTGATTCATTTGCTCTGTTTTTACTC 57.198 30.769 0.00 0.00 0.00 2.59
6211 13185 1.150536 GTGCCTCAACCACTCCCAA 59.849 57.895 0.00 0.00 0.00 4.12
6269 13256 4.824479 TCTGTATGATGACAGCCAAGAA 57.176 40.909 0.00 0.00 45.44 2.52


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

AutoCloner maintained by Alex Coulton.