Multiple sequence alignment - TraesCS5B01G332100

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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 TraesCS5B01G332100 chr5B 100.000 3248 0 0 1 3248 516094580 516091333 0.000000e+00 5999
1 TraesCS5B01G332100 chr5D 96.459 2457 65 13 1 2445 426297507 426295061 0.000000e+00 4036
2 TraesCS5B01G332100 chr5D 87.821 624 28 16 2651 3248 426294879 426294278 0.000000e+00 688
3 TraesCS5B01G332100 chr5D 95.909 220 9 0 2484 2703 426295078 426294859 1.110000e-94 357
4 TraesCS5B01G332100 chr5A 95.883 2453 66 15 1 2445 540395957 540393532 0.000000e+00 3938
5 TraesCS5B01G332100 chr5A 89.984 619 40 14 2651 3248 540393350 540392733 0.000000e+00 780
6 TraesCS5B01G332100 chr5A 94.091 220 13 0 2484 2703 540393549 540393330 5.190000e-88 335
7 TraesCS5B01G332100 chr4D 87.667 600 37 13 2678 3248 24334555 24333964 0.000000e+00 664
8 TraesCS5B01G332100 chr4D 90.367 436 20 13 2026 2445 24335268 24334839 1.320000e-153 553
9 TraesCS5B01G332100 chr4D 94.086 186 9 2 2484 2668 24334856 24334672 6.860000e-72 281
10 TraesCS5B01G332100 chr3A 85.373 335 39 3 311 645 382372191 382372515 4.010000e-89 339
11 TraesCS5B01G332100 chr3A 88.608 158 18 0 31 188 382372004 382372161 3.310000e-45 193
12 TraesCS5B01G332100 chr7D 89.241 158 16 1 31 188 8974543 8974699 2.560000e-46 196


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 TraesCS5B01G332100 chr5B 516091333 516094580 3247 True 5999.000000 5999 100.000000 1 3248 1 chr5B.!!$R1 3247
1 TraesCS5B01G332100 chr5D 426294278 426297507 3229 True 1693.666667 4036 93.396333 1 3248 3 chr5D.!!$R1 3247
2 TraesCS5B01G332100 chr5A 540392733 540395957 3224 True 1684.333333 3938 93.319333 1 3248 3 chr5A.!!$R1 3247
3 TraesCS5B01G332100 chr4D 24333964 24335268 1304 True 499.333333 664 90.706667 2026 3248 3 chr4D.!!$R1 1222
4 TraesCS5B01G332100 chr3A 382372004 382372515 511 False 266.000000 339 86.990500 31 645 2 chr3A.!!$F1 614

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
980 991 0.248907 TCGCGTTGGATTCCTCGATC 60.249 55.0 19.31 6.69 0.00 3.69 F
1270 1284 0.179150 CTCCAACCTCTTCGAGCTCG 60.179 60.0 30.03 30.03 41.45 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 1805 0.108138 GCAGCTCGTTATCCTGTGGT 60.108 55.0 0.0 0.0 0.0 4.16 R
2456 2487 0.907837 CTCGAATACGCACGAGTGTG 59.092 55.0 14.4 14.4 46.9 3.82 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
46 47 1.878522 CGGCACAGGAGCATACGTC 60.879 63.158 0.00 0.00 35.83 4.34
69 70 2.488153 GGACATTACCTCAAACACCTGC 59.512 50.000 0.00 0.00 0.00 4.85
461 462 2.401766 CGAGCATGAGGTGGTTGGC 61.402 63.158 0.00 0.00 39.00 4.52
696 697 1.013596 CGCCGTCCATTGCTGATTTA 58.986 50.000 0.00 0.00 0.00 1.40
803 805 2.614983 GGCGAGGTTTTATTGCGGATTA 59.385 45.455 0.00 0.00 0.00 1.75
886 888 4.861102 AAAAGAAAGTCATCAAGCCCAG 57.139 40.909 0.00 0.00 0.00 4.45
893 895 2.575279 AGTCATCAAGCCCAGATTCACT 59.425 45.455 0.00 0.00 0.00 3.41
895 897 2.842496 TCATCAAGCCCAGATTCACTCT 59.158 45.455 0.00 0.00 33.14 3.24
975 986 0.970937 TCTCCTCGCGTTGGATTCCT 60.971 55.000 19.97 0.00 32.56 3.36
977 988 1.878522 CCTCGCGTTGGATTCCTCG 60.879 63.158 5.77 9.88 0.00 4.63
980 991 0.248907 TCGCGTTGGATTCCTCGATC 60.249 55.000 19.31 6.69 0.00 3.69
981 992 0.249073 CGCGTTGGATTCCTCGATCT 60.249 55.000 19.31 0.00 0.00 2.75
982 993 1.212616 GCGTTGGATTCCTCGATCTG 58.787 55.000 19.31 0.12 0.00 2.90
1242 1256 1.903294 GCTGCTCCACCTCATCTCA 59.097 57.895 0.00 0.00 0.00 3.27
1270 1284 0.179150 CTCCAACCTCTTCGAGCTCG 60.179 60.000 30.03 30.03 41.45 5.03
1302 1316 1.516365 CCGCCTGGATCTCGTCGTAT 61.516 60.000 0.00 0.00 37.49 3.06
1740 1754 1.705256 TAAGCTACACGACCTTTGCG 58.295 50.000 0.00 0.00 0.00 4.85
1818 1832 0.595053 ATAACGAGCTGCGGATGTCG 60.595 55.000 0.00 3.58 46.49 4.35
1875 1889 1.412361 CCCAAGAAACCCCTGGAAACA 60.412 52.381 0.00 0.00 39.59 2.83
2367 2398 4.037690 GTCTGTTTAAACTGCTGCAACAG 58.962 43.478 18.91 18.91 43.79 3.16
2429 2460 6.377429 TGCTAGTTTAGTACAGCAGTCACTAT 59.623 38.462 0.00 0.00 36.58 2.12
2430 2461 7.555195 TGCTAGTTTAGTACAGCAGTCACTATA 59.445 37.037 0.00 0.00 36.58 1.31
2431 2462 8.569641 GCTAGTTTAGTACAGCAGTCACTATAT 58.430 37.037 0.00 0.00 33.69 0.86
2433 2464 8.521170 AGTTTAGTACAGCAGTCACTATATCA 57.479 34.615 0.00 0.00 0.00 2.15
2434 2465 8.407064 AGTTTAGTACAGCAGTCACTATATCAC 58.593 37.037 0.00 0.00 0.00 3.06
2435 2466 8.407064 GTTTAGTACAGCAGTCACTATATCACT 58.593 37.037 0.00 0.00 0.00 3.41
2436 2467 8.521170 TTAGTACAGCAGTCACTATATCACTT 57.479 34.615 0.00 0.00 0.00 3.16
2437 2468 7.411486 AGTACAGCAGTCACTATATCACTTT 57.589 36.000 0.00 0.00 0.00 2.66
2438 2469 7.484975 AGTACAGCAGTCACTATATCACTTTC 58.515 38.462 0.00 0.00 0.00 2.62
2439 2470 6.537453 ACAGCAGTCACTATATCACTTTCT 57.463 37.500 0.00 0.00 0.00 2.52
2440 2471 6.336566 ACAGCAGTCACTATATCACTTTCTG 58.663 40.000 0.00 0.00 0.00 3.02
2441 2472 6.071108 ACAGCAGTCACTATATCACTTTCTGT 60.071 38.462 0.00 0.00 31.51 3.41
2457 2488 7.117285 ACTTTCTGTGATCTAGTGATATGCA 57.883 36.000 0.00 0.00 32.19 3.96
2474 2505 3.010088 CACACTCGTGCGTATTCGA 57.990 52.632 0.00 0.00 36.06 3.71
2549 2581 9.545611 CAATTTTCTTGACCTTTGTTCAAAAAG 57.454 29.630 0.00 1.53 36.99 2.27
2592 2624 4.097892 AGGTTTGACTTAAACTTGTGCCAG 59.902 41.667 0.00 0.00 46.26 4.85
2600 2632 7.005709 ACTTAAACTTGTGCCAGTCTAGTAT 57.994 36.000 0.00 0.00 0.00 2.12
2647 2679 7.112122 TGTGATAAATACAGCCAATCTTGACT 58.888 34.615 0.00 0.00 0.00 3.41
2690 2829 7.012421 ACCTTTGTAGTTCAAGATGTTCAGTTC 59.988 37.037 0.00 0.00 37.35 3.01
2709 2848 1.133199 TCCCTTGACCTTTGCAACCAT 60.133 47.619 0.00 0.00 0.00 3.55
2711 2850 2.548493 CCCTTGACCTTTGCAACCATTG 60.548 50.000 0.00 0.00 0.00 2.82
2737 2876 4.341487 ACCCAAAACCTGGCTTCTATTAC 58.659 43.478 0.00 0.00 44.90 1.89
2814 2954 2.586258 ATTGCCTGCTAGTGTAGTCG 57.414 50.000 0.00 0.00 0.00 4.18
2816 2956 1.254026 TGCCTGCTAGTGTAGTCGTT 58.746 50.000 0.00 0.00 0.00 3.85
2818 2958 1.067776 GCCTGCTAGTGTAGTCGTTGT 60.068 52.381 0.00 0.00 0.00 3.32
2859 3000 6.882140 TGAGTAAATCATTCCGTGTTTATGGT 59.118 34.615 0.00 0.00 31.65 3.55
2860 3001 7.083875 AGTAAATCATTCCGTGTTTATGGTG 57.916 36.000 0.00 0.00 34.41 4.17
2907 3073 1.733360 GCCTTCGTTAATGGCGTGTTA 59.267 47.619 0.00 0.00 37.11 2.41
2909 3075 3.545426 GCCTTCGTTAATGGCGTGTTATC 60.545 47.826 0.00 0.00 37.11 1.75
2910 3076 3.001939 CCTTCGTTAATGGCGTGTTATCC 59.998 47.826 0.00 0.00 0.00 2.59
2911 3077 2.553086 TCGTTAATGGCGTGTTATCCC 58.447 47.619 0.00 0.00 0.00 3.85
2912 3078 2.093606 TCGTTAATGGCGTGTTATCCCA 60.094 45.455 0.00 0.00 0.00 4.37
2913 3079 2.875933 CGTTAATGGCGTGTTATCCCAT 59.124 45.455 0.00 0.00 40.94 4.00
2958 3126 6.388100 TCCTTTACATGATTCCTCTCCATCTT 59.612 38.462 0.00 0.00 0.00 2.40
3038 3206 1.002659 GGGTGGGCATTTGGTTAAACC 59.997 52.381 0.00 0.00 39.22 3.27
3168 3336 1.080298 TGTAACCATGTAAAGCGCCG 58.920 50.000 2.29 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.081462 GGTGTTTGAGGTAATGTCCCG 58.919 52.381 0.00 0.00 0.00 5.14
231 232 3.141488 CTCGGGGAGGACGGTGAG 61.141 72.222 0.00 0.00 0.00 3.51
651 652 1.381327 CTCCTCCTTCCAGGCCGTA 60.381 63.158 0.00 0.00 34.61 4.02
696 697 2.357517 CACTTTCCCGCGCAGAGT 60.358 61.111 8.75 0.00 0.00 3.24
803 805 1.304713 CAGCCCAACAAGCCCATCT 60.305 57.895 0.00 0.00 0.00 2.90
886 888 1.794714 TCCTGGGCCTAGAGTGAATC 58.205 55.000 19.36 0.00 0.00 2.52
893 895 1.074471 GTGGGATCCTGGGCCTAGA 60.074 63.158 19.36 4.91 0.00 2.43
895 897 0.645496 TTAGTGGGATCCTGGGCCTA 59.355 55.000 12.58 0.00 0.00 3.93
1242 1256 2.041265 AGGTTGGAGGCGAGGGAT 59.959 61.111 0.00 0.00 0.00 3.85
1791 1805 0.108138 GCAGCTCGTTATCCTGTGGT 60.108 55.000 0.00 0.00 0.00 4.16
1875 1889 1.611851 CTCTGCTGTGACCCCCTCT 60.612 63.158 0.00 0.00 0.00 3.69
2055 2072 0.681887 CAGCAGGAATGATGCCACCA 60.682 55.000 0.00 0.00 44.97 4.17
2432 2463 7.042858 GTGCATATCACTAGATCACAGAAAGTG 60.043 40.741 0.00 0.00 44.67 3.16
2433 2464 6.983307 GTGCATATCACTAGATCACAGAAAGT 59.017 38.462 0.00 0.00 42.38 2.66
2434 2465 6.982724 TGTGCATATCACTAGATCACAGAAAG 59.017 38.462 0.00 0.00 45.81 2.62
2435 2466 6.758416 GTGTGCATATCACTAGATCACAGAAA 59.242 38.462 0.00 0.00 45.81 2.52
2436 2467 6.097412 AGTGTGCATATCACTAGATCACAGAA 59.903 38.462 6.66 0.00 45.81 3.02
2437 2468 5.595952 AGTGTGCATATCACTAGATCACAGA 59.404 40.000 6.66 0.00 45.81 3.41
2438 2469 5.840715 AGTGTGCATATCACTAGATCACAG 58.159 41.667 6.66 0.00 45.81 3.66
2439 2470 5.506317 CGAGTGTGCATATCACTAGATCACA 60.506 44.000 8.31 0.00 44.68 3.58
2440 2471 4.914504 CGAGTGTGCATATCACTAGATCAC 59.085 45.833 8.31 0.00 44.68 3.06
2441 2472 4.580580 ACGAGTGTGCATATCACTAGATCA 59.419 41.667 18.53 0.00 44.68 2.92
2442 2473 4.914504 CACGAGTGTGCATATCACTAGATC 59.085 45.833 18.53 3.81 44.68 2.75
2443 2474 4.864633 CACGAGTGTGCATATCACTAGAT 58.135 43.478 18.53 4.90 44.68 1.98
2444 2475 4.292977 CACGAGTGTGCATATCACTAGA 57.707 45.455 18.53 0.00 44.68 2.43
2456 2487 0.907837 CTCGAATACGCACGAGTGTG 59.092 55.000 14.40 14.40 46.90 3.82
2457 2488 3.307829 CTCGAATACGCACGAGTGT 57.692 52.632 4.12 4.12 46.90 3.55
2663 2695 6.828785 ACTGAACATCTTGAACTACAAAGGTT 59.171 34.615 0.00 0.00 38.08 3.50
2690 2829 1.341080 ATGGTTGCAAAGGTCAAGGG 58.659 50.000 0.00 0.00 0.00 3.95
2859 3000 1.476085 CCAAAGTCCAAAGTGCACACA 59.524 47.619 21.04 0.00 0.00 3.72
2860 3001 1.748493 TCCAAAGTCCAAAGTGCACAC 59.252 47.619 21.04 7.95 0.00 3.82
2903 3069 3.662148 AGGCATATGGGAATGGGATAACA 59.338 43.478 4.56 0.00 0.00 2.41
2907 3073 6.393740 TGATATTAGGCATATGGGAATGGGAT 59.606 38.462 4.56 0.00 0.00 3.85
2909 3075 6.017211 TGATATTAGGCATATGGGAATGGG 57.983 41.667 4.56 0.00 0.00 4.00
2910 3076 6.718454 GGATGATATTAGGCATATGGGAATGG 59.282 42.308 4.56 0.00 0.00 3.16
2911 3077 7.524290 AGGATGATATTAGGCATATGGGAATG 58.476 38.462 4.56 0.00 0.00 2.67
2912 3078 7.718399 AGGATGATATTAGGCATATGGGAAT 57.282 36.000 4.56 0.00 0.00 3.01
2913 3079 7.529534 AAGGATGATATTAGGCATATGGGAA 57.470 36.000 4.56 0.00 0.00 3.97
2958 3126 9.140286 GAAGTCGCTATATATTACAGCAATCAA 57.860 33.333 6.75 0.00 34.94 2.57
3038 3206 7.117812 TCTCAAATAAGCTGAACCTAACTTTCG 59.882 37.037 0.00 0.00 0.00 3.46
3128 3296 9.855021 GTTACATTTGATTGCACCTAGTATTTT 57.145 29.630 0.00 0.00 0.00 1.82
3168 3336 4.039124 CACCACCCCAATTTATTATCCAGC 59.961 45.833 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.