Multiple sequence alignment - TraesCS5B01G077000

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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 TraesCS5B01G077000 chr5B 100.000 3268 0 0 1 3268 92697329 92700596 0.000000e+00 6035
1 TraesCS5B01G077000 chr5B 93.529 1190 62 5 3 1192 230901284 230902458 0.000000e+00 1757
2 TraesCS5B01G077000 chr1B 96.083 3268 124 4 5 3268 400394455 400397722 0.000000e+00 5323
3 TraesCS5B01G077000 chr1B 94.602 2816 114 10 469 3268 647447094 647444301 0.000000e+00 4324
4 TraesCS5B01G077000 chr1B 92.713 3019 167 10 289 3268 37412716 37415720 0.000000e+00 4307
5 TraesCS5B01G077000 chr1B 94.233 2809 129 14 469 3268 554955605 554952821 0.000000e+00 4259
6 TraesCS5B01G077000 chr6B 95.606 3277 133 3 3 3268 692863583 692866859 0.000000e+00 5243
7 TraesCS5B01G077000 chr4B 94.825 3285 128 9 3 3268 16567564 16570825 0.000000e+00 5086
8 TraesCS5B01G077000 chr4B 93.537 1408 75 4 1877 3268 560073062 560074469 0.000000e+00 2082
9 TraesCS5B01G077000 chr4B 94.764 382 19 1 3 383 560068875 560069256 7.810000e-166 593
10 TraesCS5B01G077000 chr4A 94.578 3283 161 5 3 3268 656355390 656358672 0.000000e+00 5060
11 TraesCS5B01G077000 chr4A 94.455 3282 165 8 3 3268 656148094 656151374 0.000000e+00 5036
12 TraesCS5B01G077000 chr4A 94.085 2908 151 8 378 3268 655846675 655849578 0.000000e+00 4397
13 TraesCS5B01G077000 chr4A 93.913 2908 156 8 378 3268 655893826 655896729 0.000000e+00 4370
14 TraesCS5B01G077000 chr4A 94.517 383 19 2 3 383 655846392 655846774 1.010000e-164 590
15 TraesCS5B01G077000 chr2B 94.001 3284 175 11 3 3268 177236730 177240009 0.000000e+00 4953
16 TraesCS5B01G077000 chr2B 93.702 2842 162 5 377 3201 791334312 791331471 0.000000e+00 4241
17 TraesCS5B01G077000 chr3B 94.083 2907 156 4 378 3268 729227105 729230011 0.000000e+00 4401
18 TraesCS5B01G077000 chr3B 94.284 1697 72 10 1589 3268 746767970 746766282 0.000000e+00 2573


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 TraesCS5B01G077000 chr5B 92697329 92700596 3267 False 6035.0 6035 100.0000 1 3268 1 chr5B.!!$F1 3267
1 TraesCS5B01G077000 chr5B 230901284 230902458 1174 False 1757.0 1757 93.5290 3 1192 1 chr5B.!!$F2 1189
2 TraesCS5B01G077000 chr1B 400394455 400397722 3267 False 5323.0 5323 96.0830 5 3268 1 chr1B.!!$F2 3263
3 TraesCS5B01G077000 chr1B 647444301 647447094 2793 True 4324.0 4324 94.6020 469 3268 1 chr1B.!!$R2 2799
4 TraesCS5B01G077000 chr1B 37412716 37415720 3004 False 4307.0 4307 92.7130 289 3268 1 chr1B.!!$F1 2979
5 TraesCS5B01G077000 chr1B 554952821 554955605 2784 True 4259.0 4259 94.2330 469 3268 1 chr1B.!!$R1 2799
6 TraesCS5B01G077000 chr6B 692863583 692866859 3276 False 5243.0 5243 95.6060 3 3268 1 chr6B.!!$F1 3265
7 TraesCS5B01G077000 chr4B 16567564 16570825 3261 False 5086.0 5086 94.8250 3 3268 1 chr4B.!!$F1 3265
8 TraesCS5B01G077000 chr4B 560068875 560074469 5594 False 1337.5 2082 94.1505 3 3268 2 chr4B.!!$F2 3265
9 TraesCS5B01G077000 chr4A 656355390 656358672 3282 False 5060.0 5060 94.5780 3 3268 1 chr4A.!!$F3 3265
10 TraesCS5B01G077000 chr4A 656148094 656151374 3280 False 5036.0 5036 94.4550 3 3268 1 chr4A.!!$F2 3265
11 TraesCS5B01G077000 chr4A 655893826 655896729 2903 False 4370.0 4370 93.9130 378 3268 1 chr4A.!!$F1 2890
12 TraesCS5B01G077000 chr4A 655846392 655849578 3186 False 2493.5 4397 94.3010 3 3268 2 chr4A.!!$F4 3265
13 TraesCS5B01G077000 chr2B 177236730 177240009 3279 False 4953.0 4953 94.0010 3 3268 1 chr2B.!!$F1 3265
14 TraesCS5B01G077000 chr2B 791331471 791334312 2841 True 4241.0 4241 93.7020 377 3201 1 chr2B.!!$R1 2824
15 TraesCS5B01G077000 chr3B 729227105 729230011 2906 False 4401.0 4401 94.0830 378 3268 1 chr3B.!!$F1 2890
16 TraesCS5B01G077000 chr3B 746766282 746767970 1688 True 2573.0 2573 94.2840 1589 3268 1 chr3B.!!$R1 1679

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
987 1182 0.107508 CATGTCAAGGCCTCCATCGT 60.108 55.0 5.23 0.0 0.0 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2797 5456 0.235926 GTCGCACAACCTTTGCTCTC 59.764 55.0 0.0 0.0 37.87 3.2 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
79 82 5.480772 CCTAAGAGGAGACCTTTTGTGAGTA 59.519 44.000 0.00 0.00 37.67 2.59
155 158 3.054139 TGGGAGAGTTGGAAATGATGGAG 60.054 47.826 0.00 0.00 0.00 3.86
169 172 2.362397 TGATGGAGCCGTCTGTTATCTC 59.638 50.000 9.92 0.00 33.41 2.75
203 206 2.689553 TAGCATCAAGATTCGTGCCA 57.310 45.000 0.00 0.00 38.31 4.92
304 310 4.161565 ACGTTGGAATTATAGAGGCACTGA 59.838 41.667 0.00 0.00 41.55 3.41
369 375 4.081972 TGCATCTGAAGACTTACTCAGACC 60.082 45.833 7.36 3.81 41.29 3.85
374 380 4.079970 TGAAGACTTACTCAGACCGTCAT 58.920 43.478 0.40 0.00 0.00 3.06
461 653 5.321959 TGCATCTGAAGACTTACTCAGAG 57.678 43.478 10.34 0.00 41.69 3.35
746 940 5.890334 TGATTAATTGGACGATTTGAAGGC 58.110 37.500 0.00 0.00 0.00 4.35
758 952 1.786937 TTGAAGGCTGCTTTTTCCCA 58.213 45.000 0.00 0.00 0.00 4.37
772 966 2.360350 CCCAGCAACCGTGAGCAT 60.360 61.111 0.00 0.00 0.00 3.79
812 1006 2.100631 GCACATAGCAACCGCGAGT 61.101 57.895 8.23 0.00 45.49 4.18
917 1111 2.780595 GCTTCCATAGCCGCTCAAA 58.219 52.632 0.00 0.00 44.48 2.69
939 1133 2.762745 ACGGAAACACTATTGTCGCTT 58.237 42.857 0.00 0.00 33.55 4.68
968 1163 3.996480 ACTAGCAACTCTCACAAACTCC 58.004 45.455 0.00 0.00 0.00 3.85
987 1182 0.107508 CATGTCAAGGCCTCCATCGT 60.108 55.000 5.23 0.00 0.00 3.73
1130 1325 2.351276 GGAGGTTGGCATCCACGT 59.649 61.111 16.58 0.00 44.42 4.49
1337 1532 1.411246 GGTATACCACATCACCGCTGA 59.589 52.381 17.44 0.00 35.64 4.26
1474 1669 9.601217 GTTTCTGAAGTAGATAAAGCAGGATAA 57.399 33.333 0.00 0.00 34.80 1.75
1959 4563 1.075374 CTGGTTTGGAGATCAACCCCA 59.925 52.381 9.53 7.43 37.15 4.96
2045 4650 1.001641 GGCTGATGTTGCAGGGAGT 60.002 57.895 0.00 0.00 36.41 3.85
2075 4680 7.174413 TCCATCCATTCTACAAACAGATGAAA 58.826 34.615 0.00 0.00 33.16 2.69
2293 4899 5.103290 TGACGAAAACATAGAAAACTGGC 57.897 39.130 0.00 0.00 0.00 4.85
2669 5316 1.202651 AGCCACCAGTGTGTGTTAGTC 60.203 52.381 9.85 0.00 41.09 2.59
2776 5435 2.101582 GAGGTGAGCTCCGAATACACAT 59.898 50.000 12.15 0.00 33.82 3.21
2797 5456 0.661020 GTCACGGTTTGGAAGTGTGG 59.339 55.000 0.00 0.00 37.20 4.17
2899 5558 2.056223 AAGCCATGGGATGCACTGC 61.056 57.895 15.13 0.00 0.00 4.40
2964 5623 3.621805 TGTCGCGGGGTGTCACAT 61.622 61.111 6.13 0.00 0.00 3.21
2974 5633 2.303600 GGGGTGTCACATGTTAGGTACA 59.696 50.000 5.12 0.00 41.97 2.90
3085 5744 5.163184 TGGATGTTCTAAAGTGTGGTACCAA 60.163 40.000 18.31 4.31 0.00 3.67
3097 5757 2.625790 GTGGTACCAAAAGCATGTTCCA 59.374 45.455 18.31 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.322816 TGCCTCCTGTGCCTTCAATC 60.323 55.000 0.00 0.00 0.00 2.67
79 82 6.403200 CCACAATAAATCTCGAAACATTCCGT 60.403 38.462 0.00 0.00 0.00 4.69
155 158 0.739561 AGTCGGAGATAACAGACGGC 59.260 55.000 0.00 0.00 40.67 5.68
169 172 4.183865 TGATGCTAAAATCAGACAGTCGG 58.816 43.478 0.00 0.00 32.75 4.79
304 310 4.492494 TGTGCATCCACAGAGTTGATAT 57.508 40.909 0.00 0.00 46.51 1.63
369 375 4.452455 GCCTCTATAATTCCAACCATGACG 59.548 45.833 0.00 0.00 0.00 4.35
374 380 4.385199 CCAGTGCCTCTATAATTCCAACCA 60.385 45.833 0.00 0.00 0.00 3.67
461 653 6.223852 TCTAAAGACTTCACAACCATGACTC 58.776 40.000 0.00 0.00 0.00 3.36
758 952 2.629656 GGCAATGCTCACGGTTGCT 61.630 57.895 4.82 0.00 45.56 3.91
796 990 2.100631 GCACTCGCGGTTGCTATGT 61.101 57.895 21.11 0.67 39.65 2.29
799 993 2.100031 CATGCACTCGCGGTTGCTA 61.100 57.895 26.09 16.41 42.97 3.49
812 1006 1.206878 ATGAGGGCAGTAGACATGCA 58.793 50.000 0.00 0.00 45.68 3.96
917 1111 4.119442 AGCGACAATAGTGTTTCCGTAT 57.881 40.909 0.00 0.00 38.41 3.06
939 1133 4.524328 TGTGAGAGTTGCTAGTTGAGATGA 59.476 41.667 0.00 0.00 0.00 2.92
968 1163 0.107508 ACGATGGAGGCCTTGACATG 60.108 55.000 19.39 14.41 0.00 3.21
987 1182 1.153449 CGCCATTACGCTCCTCCAA 60.153 57.895 0.00 0.00 0.00 3.53
1130 1325 3.565307 ACAACATCCAGCTTTTCCTTGA 58.435 40.909 0.00 0.00 0.00 3.02
1474 1669 6.547141 TGATCTGGTGAGTCAAGTTCAAAATT 59.453 34.615 0.00 0.00 0.00 1.82
1925 4529 2.472695 AACCAGAACTTCGCAGCATA 57.527 45.000 0.00 0.00 0.00 3.14
1959 4563 3.262420 GCTGGATGTCGATGTACTTGTT 58.738 45.455 0.00 0.00 0.00 2.83
2045 4650 5.814481 TGTTTGTAGAATGGATGGATCACA 58.186 37.500 0.00 0.00 0.00 3.58
2075 4680 6.410540 GTCTTCAACCCTGTCAATCTTATCT 58.589 40.000 0.00 0.00 0.00 1.98
2293 4899 2.684881 AGAAACACAAGCAACTCCACAG 59.315 45.455 0.00 0.00 0.00 3.66
2669 5316 2.490217 CGTGCCTCCGACACCTAG 59.510 66.667 0.00 0.00 34.45 3.02
2776 5435 0.253610 ACACTTCCAAACCGTGACCA 59.746 50.000 0.00 0.00 33.13 4.02
2797 5456 0.235926 GTCGCACAACCTTTGCTCTC 59.764 55.000 0.00 0.00 37.87 3.20
2899 5558 1.521423 GTCTCTTCACAAACGTCACGG 59.479 52.381 0.35 0.00 0.00 4.94
2964 5623 2.421388 GCCTGCATCCATGTACCTAACA 60.421 50.000 0.00 0.00 43.86 2.41
2974 5633 3.319972 GTGATTTATGTGCCTGCATCCAT 59.680 43.478 0.00 0.00 0.00 3.41
3085 5744 3.255642 ACTGCGTATTTGGAACATGCTTT 59.744 39.130 0.00 0.00 39.30 3.51
3097 5757 3.259876 TGTGACTCCCTAACTGCGTATTT 59.740 43.478 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.