Multiple sequence alignment - TraesCS5B01G104400

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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 TraesCS5B01G104400 chr5B 100.000 3491 0 0 1 3491 139264943 139261453 0.000000e+00 6447
1 TraesCS5B01G104400 chr7B 93.534 3418 210 10 79 3491 560848553 560845142 0.000000e+00 5077
2 TraesCS5B01G104400 chr1B 92.378 3503 240 14 1 3491 409880864 409884351 0.000000e+00 4964
3 TraesCS5B01G104400 chr1B 92.362 3260 230 16 242 3491 497611700 497614950 0.000000e+00 4623
4 TraesCS5B01G104400 chr2D 92.388 3429 232 23 81 3491 376028662 376025245 0.000000e+00 4859
5 TraesCS5B01G104400 chr2D 92.010 388 14 2 1 387 172099462 172099091 2.390000e-146 529
6 TraesCS5B01G104400 chr3D 92.367 3354 221 23 79 3409 364943189 364939848 0.000000e+00 4743
7 TraesCS5B01G104400 chr3D 93.089 3198 202 14 308 3491 110958404 110961596 0.000000e+00 4663
8 TraesCS5B01G104400 chr4D 91.562 3425 272 12 79 3491 148264741 148268160 0.000000e+00 4708
9 TraesCS5B01G104400 chr7D 91.468 3434 258 27 79 3491 341105477 341108896 0.000000e+00 4686
10 TraesCS5B01G104400 chr7A 91.105 3429 277 19 80 3491 469517486 469520903 0.000000e+00 4617
11 TraesCS5B01G104400 chr7A 84.163 3435 393 77 1 3389 333028675 333025346 0.000000e+00 3190


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 TraesCS5B01G104400 chr5B 139261453 139264943 3490 True 6447 6447 100.000 1 3491 1 chr5B.!!$R1 3490
1 TraesCS5B01G104400 chr7B 560845142 560848553 3411 True 5077 5077 93.534 79 3491 1 chr7B.!!$R1 3412
2 TraesCS5B01G104400 chr1B 409880864 409884351 3487 False 4964 4964 92.378 1 3491 1 chr1B.!!$F1 3490
3 TraesCS5B01G104400 chr1B 497611700 497614950 3250 False 4623 4623 92.362 242 3491 1 chr1B.!!$F2 3249
4 TraesCS5B01G104400 chr2D 376025245 376028662 3417 True 4859 4859 92.388 81 3491 1 chr2D.!!$R2 3410
5 TraesCS5B01G104400 chr3D 364939848 364943189 3341 True 4743 4743 92.367 79 3409 1 chr3D.!!$R1 3330
6 TraesCS5B01G104400 chr3D 110958404 110961596 3192 False 4663 4663 93.089 308 3491 1 chr3D.!!$F1 3183
7 TraesCS5B01G104400 chr4D 148264741 148268160 3419 False 4708 4708 91.562 79 3491 1 chr4D.!!$F1 3412
8 TraesCS5B01G104400 chr7D 341105477 341108896 3419 False 4686 4686 91.468 79 3491 1 chr7D.!!$F1 3412
9 TraesCS5B01G104400 chr7A 469517486 469520903 3417 False 4617 4617 91.105 80 3491 1 chr7A.!!$F1 3411
10 TraesCS5B01G104400 chr7A 333025346 333028675 3329 True 3190 3190 84.163 1 3389 1 chr7A.!!$R1 3388

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
944 978 0.184451 ATTGCCGCTTCCATCTCCAT 59.816 50.000 0.00 0.0 0.0 3.41 F
1177 1212 1.902508 CCAGTGAACTAGAGAAGGCCA 59.097 52.381 5.01 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2450 2517 0.759812 GTAGTAGGGGTCAGCCTCCC 60.760 65.0 0.0 0.4 43.90 4.30 R
2829 2929 0.815734 TGAGCGTCCAAGGCTACTAC 59.184 55.0 0.0 0.0 39.71 2.73 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
196 198 9.362539 CTGCTAAAATGCAAGAAGTTCAAATAT 57.637 29.630 5.50 0.00 42.83 1.28
292 305 6.770785 TCGTAAATAATCTCAATCCCCCAAAG 59.229 38.462 0.00 0.00 0.00 2.77
341 355 6.995686 TGACATCAGTACTAAAAAGCAGGAAA 59.004 34.615 0.00 0.00 0.00 3.13
444 461 8.502161 CACTAAACCATAAGTGCACTAAAAAC 57.498 34.615 22.01 0.00 36.96 2.43
445 462 8.349983 CACTAAACCATAAGTGCACTAAAAACT 58.650 33.333 22.01 5.66 36.96 2.66
547 570 3.807553 AGGGCACTGAAAAATGTTTTGG 58.192 40.909 0.00 0.00 0.00 3.28
571 594 7.140048 GGGATCAACTAGTGTATAAGACTTCG 58.860 42.308 0.00 0.00 0.00 3.79
679 705 2.619849 CCTGAGACATGCAAGTGGGATT 60.620 50.000 0.00 0.00 0.00 3.01
691 717 3.760580 AGTGGGATTAGCAGCTGATAC 57.239 47.619 20.43 4.86 0.00 2.24
704 730 3.300853 CAGCTGATACGTACAACTTGACG 59.699 47.826 8.42 10.37 44.57 4.35
718 744 5.163540 ACAACTTGACGAGACTACTCAGTTT 60.164 40.000 0.00 0.00 42.72 2.66
871 899 2.184322 CCACACATCCCCGTCGAG 59.816 66.667 0.00 0.00 0.00 4.04
907 936 2.092538 CCCATTGTCTTCCATCTCTGCT 60.093 50.000 0.00 0.00 0.00 4.24
944 978 0.184451 ATTGCCGCTTCCATCTCCAT 59.816 50.000 0.00 0.00 0.00 3.41
961 995 2.361757 TCCATTGCAGACAAACCACAAG 59.638 45.455 0.00 0.00 39.77 3.16
1092 1127 4.117661 GTCTCCGGCGAGAAGCGT 62.118 66.667 9.30 0.00 46.74 5.07
1170 1205 4.001652 TCGTCTACACCAGTGAACTAGAG 58.998 47.826 4.48 0.00 0.00 2.43
1177 1212 1.902508 CCAGTGAACTAGAGAAGGCCA 59.097 52.381 5.01 0.00 0.00 5.36
1325 1360 2.299297 AGGAACTCTTCTTGGTGTACCG 59.701 50.000 0.00 0.00 39.43 4.02
1335 1370 2.813474 GTGTACCGCATCGCAGCA 60.813 61.111 0.00 0.00 0.00 4.41
1369 1405 7.736881 TGGTAACCCATACTACTGTTCATTA 57.263 36.000 0.00 0.00 35.17 1.90
1372 1408 9.623000 GGTAACCCATACTACTGTTCATTAATT 57.377 33.333 0.00 0.00 34.74 1.40
1763 1823 7.010771 AGATGTATCAAGCACTGGTATAGGTA 58.989 38.462 0.00 0.00 0.00 3.08
1963 2028 8.100164 TGAACTACATTCATCCATGACTTGTAA 58.900 33.333 0.00 0.00 42.62 2.41
2001 2066 9.784531 CTACCTCATGGATTATCACTTGTAAAT 57.215 33.333 0.00 0.00 37.04 1.40
2027 2093 7.387948 TCAAAAAGAGGGAGAACTAAATCTTCG 59.612 37.037 0.00 0.00 0.00 3.79
2062 2128 5.983333 AATCTTCAATATGTGTCTCCCCT 57.017 39.130 0.00 0.00 0.00 4.79
2180 2246 2.076863 GTCTGGTTTGGAGATCAACCG 58.923 52.381 7.87 4.13 34.67 4.44
2248 2315 3.335579 ACCAAATTCTACGACTCCTTGC 58.664 45.455 0.00 0.00 0.00 4.01
2274 2341 2.515523 GCAGCCAGCGTCATCCAT 60.516 61.111 0.00 0.00 0.00 3.41
2319 2386 3.772025 AGAACATCGACAAGGAGGAAGAT 59.228 43.478 0.00 0.00 0.00 2.40
2413 2480 8.667076 CATGTACAAGTCATGGAAGATAATCA 57.333 34.615 0.00 0.00 38.97 2.57
2450 2517 4.399303 AGGTTGGGATATTTCAAAAGAGCG 59.601 41.667 0.00 0.00 0.00 5.03
2559 2630 8.567948 TGTCCTTAATCTTGTTGTTTCAGATTC 58.432 33.333 0.00 0.00 32.37 2.52
2611 2707 5.874810 GCTTCCTTATGTTATGTGTGTCAGA 59.125 40.000 0.00 0.00 0.00 3.27
2664 2760 7.377766 AGTACATCATTTGCTTATGTCGTTT 57.622 32.000 0.00 0.00 35.54 3.60
2829 2929 7.078228 GCAAACTAACTAAGGACAACATCAAG 58.922 38.462 0.00 0.00 0.00 3.02
2856 2956 1.269831 CCTTGGACGCTCAGTATAGCC 60.270 57.143 0.00 0.00 39.43 3.93
2944 3047 2.568623 AAGTTTCAGCCGAGGACAAT 57.431 45.000 0.00 0.00 0.00 2.71
3017 3120 4.141869 ACTGCAACAGGAAAAGCAAAGAAT 60.142 37.500 0.00 0.00 36.44 2.40
3082 3188 5.546621 AGTACTGGTACACTTGAACACAT 57.453 39.130 12.54 0.00 38.48 3.21
3120 3230 8.862085 TCTACAAAAATAAAAAGGAACGGGAAT 58.138 29.630 0.00 0.00 0.00 3.01
3163 3273 7.715265 AACACAGTGACACACTAAGAATAAG 57.285 36.000 7.81 0.00 43.43 1.73
3346 3460 0.111061 ACAGAAGCATCAGCCCACAA 59.889 50.000 0.00 0.00 43.56 3.33
3352 3466 0.454600 GCATCAGCCCACAATGACTG 59.545 55.000 0.00 0.00 33.58 3.51
3374 3488 6.182507 TGGTGAGGTACTAGTTTCAAACAT 57.817 37.500 0.00 0.00 41.55 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 152 6.963796 AGCAGTTGAACTTGTCAGATTTTAG 58.036 36.000 0.00 0.00 37.61 1.85
341 355 1.344953 TGGTGTGAGTGGCCTGACTT 61.345 55.000 3.32 0.00 0.00 3.01
547 570 7.140048 CCGAAGTCTTATACACTAGTTGATCC 58.860 42.308 0.00 0.00 0.00 3.36
679 705 4.157105 TCAAGTTGTACGTATCAGCTGCTA 59.843 41.667 9.47 0.00 0.00 3.49
691 717 4.084171 TGAGTAGTCTCGTCAAGTTGTACG 60.084 45.833 16.68 16.68 43.09 3.67
704 730 8.541312 GTTTTTACTGTCAAACTGAGTAGTCTC 58.459 37.037 0.00 0.00 40.79 3.36
718 744 4.642885 CCAAGTCAAGGGTTTTTACTGTCA 59.357 41.667 0.00 0.00 0.00 3.58
782 810 1.898574 CTTCCTTGTGGCAACCGCT 60.899 57.895 0.00 0.00 38.60 5.52
871 899 1.111277 ATGGGTTATTTTCCAGCGCC 58.889 50.000 2.29 0.00 36.38 6.53
907 936 3.164268 CAATGGTGGTTCTGGGAATGAA 58.836 45.455 0.00 0.00 0.00 2.57
944 978 1.473258 AGCTTGTGGTTTGTCTGCAA 58.527 45.000 0.00 0.00 0.00 4.08
961 995 1.223211 GGGCTTGGGAGAGAGAAGC 59.777 63.158 0.00 0.00 41.18 3.86
1017 1051 1.647545 CGCCATGATGACGCTTGGTT 61.648 55.000 0.00 0.00 35.96 3.67
1078 1112 4.116328 CTCACGCTTCTCGCCGGA 62.116 66.667 5.05 0.00 43.23 5.14
1092 1127 2.960384 TGTGAGGGTTTTCGTCTACTCA 59.040 45.455 0.00 0.00 33.05 3.41
1140 1175 1.678627 CTGGTGTAGACGATCTCCAGG 59.321 57.143 10.66 0.00 39.89 4.45
1170 1205 2.208431 CTCATCATCTCGTTGGCCTTC 58.792 52.381 3.32 0.00 0.00 3.46
1177 1212 0.829333 AGCCTGCTCATCATCTCGTT 59.171 50.000 0.00 0.00 0.00 3.85
1254 1289 3.107601 CTGGGGAGGTTCATCTTCACTA 58.892 50.000 0.00 0.00 0.00 2.74
1257 1292 2.342406 TCTGGGGAGGTTCATCTTCA 57.658 50.000 0.00 0.00 0.00 3.02
1313 1348 1.447140 GCGATGCGGTACACCAAGA 60.447 57.895 0.00 0.00 35.14 3.02
1325 1360 3.678717 CTTGTGGCTGCTGCGATGC 62.679 63.158 9.65 0.00 40.82 3.91
1653 1695 3.930848 GACCTATACCACTTCACCAAACG 59.069 47.826 0.00 0.00 0.00 3.60
1802 1863 6.835174 ACCAGAGTCAATGATATATGTGCTT 58.165 36.000 0.00 0.00 0.00 3.91
2001 2066 7.387948 CGAAGATTTAGTTCTCCCTCTTTTTGA 59.612 37.037 0.00 0.00 0.00 2.69
2009 2075 7.450903 TCTTTTTCGAAGATTTAGTTCTCCCT 58.549 34.615 0.00 0.00 35.04 4.20
2010 2076 7.668525 TCTTTTTCGAAGATTTAGTTCTCCC 57.331 36.000 0.00 0.00 35.04 4.30
2180 2246 3.382855 TGCATGTTGATGAAGTTGTTGC 58.617 40.909 0.00 0.00 0.00 4.17
2228 2295 2.678336 GGCAAGGAGTCGTAGAATTTGG 59.322 50.000 0.00 0.00 39.69 3.28
2248 2315 3.818787 GCTGGCTGCAACATCGGG 61.819 66.667 11.80 0.00 42.31 5.14
2274 2341 5.178096 TCTTCATGCCTTTGTAGAATGGA 57.822 39.130 8.57 0.00 0.00 3.41
2413 2480 1.946768 CCAACCTGTCACGATGTTGTT 59.053 47.619 0.00 0.00 37.08 2.83
2450 2517 0.759812 GTAGTAGGGGTCAGCCTCCC 60.760 65.000 0.00 0.40 43.90 4.30
2528 2595 6.463995 AACAACAAGATTAAGGACAAGCAA 57.536 33.333 0.00 0.00 0.00 3.91
2559 2630 4.209703 TCAACCTAACGAAAGCAAACTACG 59.790 41.667 0.00 0.00 33.83 3.51
2611 2707 5.594317 AGACATAGGCAAACTTGTTCAAACT 59.406 36.000 0.00 0.00 0.00 2.66
2664 2760 3.492102 AGGAAGCTAGCAAACTTGTCA 57.508 42.857 18.83 0.00 0.00 3.58
2798 2897 4.141574 TGTCCTTAGTTAGTTTGCCACAGT 60.142 41.667 0.00 0.00 0.00 3.55
2799 2898 4.385825 TGTCCTTAGTTAGTTTGCCACAG 58.614 43.478 0.00 0.00 0.00 3.66
2800 2899 4.425180 TGTCCTTAGTTAGTTTGCCACA 57.575 40.909 0.00 0.00 0.00 4.17
2807 2906 8.648693 ACTACTTGATGTTGTCCTTAGTTAGTT 58.351 33.333 0.00 0.00 28.98 2.24
2829 2929 0.815734 TGAGCGTCCAAGGCTACTAC 59.184 55.000 0.00 0.00 39.71 2.73
2856 2956 7.654923 TGTGATAGTACTACCGTACATGTCTAG 59.345 40.741 0.00 0.00 46.68 2.43
2905 3007 9.932699 GAAACTTAGTCTTTTTAGTGTTCTTCC 57.067 33.333 0.00 0.00 0.00 3.46
3017 3120 6.827251 AGTGACTAGGAAATACGTACTGATGA 59.173 38.462 0.00 0.00 0.00 2.92
3120 3230 3.007506 TGTTAGGGAATGCGAACTGAAGA 59.992 43.478 0.00 0.00 0.00 2.87
3346 3460 5.084519 TGAAACTAGTACCTCACCAGTCAT 58.915 41.667 0.00 0.00 0.00 3.06
3352 3466 7.658575 TGTTATGTTTGAAACTAGTACCTCACC 59.341 37.037 9.69 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.