Multiple sequence alignment - TraesCS7B01G074000

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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 TraesCS7B01G074000 chr7B 100.000 2939 0 0 1 2939 83922237 83919299 0.000000e+00 5428
1 TraesCS7B01G074000 chr7B 85.153 229 29 3 2224 2452 83919786 83919563 2.280000e-56 230
2 TraesCS7B01G074000 chr7B 85.153 229 29 3 2452 2675 83920014 83919786 2.280000e-56 230
3 TraesCS7B01G074000 chr7D 90.547 2412 96 45 34 2372 122682466 122684818 0.000000e+00 3070
4 TraesCS7B01G074000 chr7D 91.594 571 35 4 2371 2939 122684901 122685460 0.000000e+00 776
5 TraesCS7B01G074000 chr7D 86.900 229 23 1 2224 2452 122684975 122685196 1.750000e-62 250
6 TraesCS7B01G074000 chr7D 87.662 154 15 3 2447 2598 122684667 122684818 3.010000e-40 176
7 TraesCS7B01G074000 chr7D 83.158 190 29 2 2747 2935 122685077 122685264 1.400000e-38 171
8 TraesCS7B01G074000 chr7A 94.156 1831 86 9 1113 2939 125677923 125679736 0.000000e+00 2769
9 TraesCS7B01G074000 chr7A 86.123 908 54 29 34 885 125676660 125677551 0.000000e+00 913
10 TraesCS7B01G074000 chr7A 86.307 241 19 7 1 231 125915449 125915213 1.750000e-62 250
11 TraesCS7B01G074000 chr7A 86.463 229 26 2 2224 2452 125679249 125679472 2.260000e-61 246
12 TraesCS7B01G074000 chr7A 82.986 288 18 7 221 507 125913814 125913557 6.330000e-57 231
13 TraesCS7B01G074000 chr7A 82.741 197 27 5 2747 2939 125679351 125679544 5.040000e-38 169


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 TraesCS7B01G074000 chr7B 83919299 83922237 2938 True 1962.666667 5428 90.10200 1 2939 3 chr7B.!!$R1 2938
1 TraesCS7B01G074000 chr7D 122682466 122685460 2994 False 888.600000 3070 87.97220 34 2939 5 chr7D.!!$F1 2905
2 TraesCS7B01G074000 chr7A 125676660 125679736 3076 False 1024.250000 2769 87.37075 34 2939 4 chr7A.!!$F1 2905
3 TraesCS7B01G074000 chr7A 125913557 125915449 1892 True 240.500000 250 84.64650 1 507 2 chr7A.!!$R1 506

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
730 2200 0.660488 TCGGCATGTGTGTTGTGAAC 59.340 50.0 0.00 0.00 0.0 3.18 F
1679 3341 0.317479 GAGGAATATACTGGCGCGGT 59.683 55.0 8.83 5.51 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 3390 0.034380 TCCTCCTCCAGTACTCACCG 60.034 60.0 0.0 0.0 0.00 4.94 R
2792 4544 0.106708 AAAGCAGACACGGAAGCTGA 59.893 50.0 0.0 0.0 37.41 4.26 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
25 26 2.270352 AAGTCAATGAGGGCGTGAAA 57.730 45.000 0.00 0.00 0.00 2.69
29 30 2.293399 GTCAATGAGGGCGTGAAACTTT 59.707 45.455 0.00 0.00 31.75 2.66
30 31 2.552315 TCAATGAGGGCGTGAAACTTTC 59.448 45.455 0.00 0.00 31.75 2.62
32 33 0.882927 TGAGGGCGTGAAACTTTCGG 60.883 55.000 0.00 0.00 31.75 4.30
98 111 6.477033 GCAAGAACAGAACAGATACGATACAT 59.523 38.462 0.00 0.00 0.00 2.29
156 175 5.093457 CGTGTATATATAACTCCAGCACGG 58.907 45.833 16.23 0.00 41.97 4.94
157 176 5.408356 GTGTATATATAACTCCAGCACGGG 58.592 45.833 0.00 0.00 34.36 5.28
176 195 1.941812 CAAGGTGCACAAGACGGAC 59.058 57.895 20.43 0.00 0.00 4.79
183 202 1.939934 TGCACAAGACGGACAAAGAAG 59.060 47.619 0.00 0.00 0.00 2.85
185 204 1.939934 CACAAGACGGACAAAGAAGCA 59.060 47.619 0.00 0.00 0.00 3.91
189 208 3.746045 AGACGGACAAAGAAGCAGTAA 57.254 42.857 0.00 0.00 0.00 2.24
562 2026 4.786927 GCAAGATCGATCGATATACTCCCG 60.787 50.000 29.45 14.93 34.60 5.14
563 2027 3.468770 AGATCGATCGATATACTCCCGG 58.531 50.000 29.45 0.00 34.60 5.73
611 2081 2.038689 CTGCATGGCTGGTCTATGAGAT 59.961 50.000 0.00 0.00 35.89 2.75
641 2111 8.809468 ACTATGATGATATGTACTCGTATGGT 57.191 34.615 0.00 0.00 0.00 3.55
642 2112 8.894731 ACTATGATGATATGTACTCGTATGGTC 58.105 37.037 0.00 0.00 0.00 4.02
723 2193 3.803082 GCGCATCGGCATGTGTGT 61.803 61.111 0.30 0.00 41.85 3.72
724 2194 2.869646 CGCATCGGCATGTGTGTT 59.130 55.556 0.00 0.00 41.24 3.32
725 2195 1.512522 CGCATCGGCATGTGTGTTG 60.513 57.895 0.00 0.00 41.24 3.33
726 2196 1.580942 GCATCGGCATGTGTGTTGT 59.419 52.632 0.00 0.00 40.72 3.32
727 2197 0.730155 GCATCGGCATGTGTGTTGTG 60.730 55.000 0.00 0.00 40.72 3.33
728 2198 0.873721 CATCGGCATGTGTGTTGTGA 59.126 50.000 0.00 0.00 0.00 3.58
729 2199 1.266446 CATCGGCATGTGTGTTGTGAA 59.734 47.619 0.00 0.00 0.00 3.18
730 2200 0.660488 TCGGCATGTGTGTTGTGAAC 59.340 50.000 0.00 0.00 0.00 3.18
731 2201 0.662619 CGGCATGTGTGTTGTGAACT 59.337 50.000 0.00 0.00 0.00 3.01
735 2205 2.853594 GCATGTGTGTTGTGAACTTGTG 59.146 45.455 0.00 0.00 0.00 3.33
738 2208 4.354071 TGTGTGTTGTGAACTTGTGATG 57.646 40.909 0.00 0.00 0.00 3.07
756 2226 2.047655 TCCGAACGGATGCACCAC 60.048 61.111 12.04 0.00 39.76 4.16
757 2227 3.124921 CCGAACGGATGCACCACC 61.125 66.667 7.53 0.00 38.90 4.61
759 2229 2.390599 CGAACGGATGCACCACCAG 61.391 63.158 0.00 0.00 38.90 4.00
760 2230 1.003839 GAACGGATGCACCACCAGA 60.004 57.895 0.00 0.00 38.90 3.86
761 2231 1.298859 GAACGGATGCACCACCAGAC 61.299 60.000 0.00 0.00 38.90 3.51
1639 3301 1.449246 CCAGAAGCAGAAGAGCCCG 60.449 63.158 0.00 0.00 34.23 6.13
1640 3302 1.593787 CAGAAGCAGAAGAGCCCGA 59.406 57.895 0.00 0.00 34.23 5.14
1641 3303 0.459934 CAGAAGCAGAAGAGCCCGAG 60.460 60.000 0.00 0.00 34.23 4.63
1653 3315 2.197324 CCCGAGGAGGAGGAGGAG 59.803 72.222 0.00 0.00 45.00 3.69
1679 3341 0.317479 GAGGAATATACTGGCGCGGT 59.683 55.000 8.83 5.51 0.00 5.68
1749 3411 2.753247 GGTGAGTACTGGAGGAGGAAT 58.247 52.381 0.00 0.00 0.00 3.01
1821 3483 0.835941 CAGAGGAGGGCAATGTAGCT 59.164 55.000 0.00 0.00 34.17 3.32
1955 3617 0.326808 TAGCCCGGGGTACAAATCCT 60.327 55.000 28.49 12.37 0.00 3.24
2017 3680 4.202010 TGCACTTTAACTTGCCTTGAACTC 60.202 41.667 5.27 0.00 38.00 3.01
2097 3760 7.784790 TTTGTTCAAACTTAAAGTCGTGAAC 57.215 32.000 17.33 17.33 44.71 3.18
2122 3785 3.796165 GCATGTTGATTGAAGTGCACACA 60.796 43.478 21.04 15.68 33.09 3.72
2154 3817 9.997482 GATTAAACTCGAAAATAAGCATGGTTA 57.003 29.630 18.95 18.95 0.00 2.85
2221 3884 7.337938 CCCATTGGTTAAATAGCCATTTTCTT 58.662 34.615 1.20 0.00 36.43 2.52
2274 3938 8.752005 TGGCATATTCTTGATAAGCTAGTTTT 57.248 30.769 0.00 0.00 35.72 2.43
2307 3971 2.076100 CGTAAGCATTGAAGCCACTGA 58.924 47.619 0.00 0.00 34.23 3.41
2351 4015 5.245531 AGTATGGTGTGTTCACTATTGTGG 58.754 41.667 7.45 0.00 41.76 4.17
2362 4026 5.029807 TCACTATTGTGGTTCAGTTGTCA 57.970 39.130 7.45 0.00 43.94 3.58
2366 4030 5.938125 ACTATTGTGGTTCAGTTGTCATACC 59.062 40.000 0.00 0.00 0.00 2.73
2401 4149 9.389755 TGCATGTCTATTTTGCTATACTTAACA 57.610 29.630 0.00 0.00 37.28 2.41
2457 4205 5.860941 TTCTTGCAGTCCTATCTCTAAGG 57.139 43.478 0.00 0.00 35.26 2.69
2503 4251 9.502091 TGGCATATTTTCGATAAGCTAGTTTAT 57.498 29.630 11.22 11.22 0.00 1.40
2609 4359 2.927028 TGCATGATAGCTTGCATGTCT 58.073 42.857 16.60 2.21 46.38 3.41
2683 4435 1.269988 CCAGTCCTATCTGTGGCATCG 60.270 57.143 0.00 0.00 34.02 3.84
2684 4436 1.683385 CAGTCCTATCTGTGGCATCGA 59.317 52.381 0.00 0.00 0.00 3.59
2712 4464 3.364366 CCAACTTACTTTTCTGCGAGCAG 60.364 47.826 18.20 18.20 44.86 4.24
2724 4476 0.868406 GCGAGCAGTAAGTTTGCACT 59.132 50.000 2.54 0.00 43.92 4.40
2725 4477 1.264288 GCGAGCAGTAAGTTTGCACTT 59.736 47.619 2.54 0.00 45.73 3.16
2744 4496 7.370383 TGCACTTCTTTTCTAAAATCATGTCC 58.630 34.615 0.00 0.00 0.00 4.02
2745 4497 7.231317 TGCACTTCTTTTCTAAAATCATGTCCT 59.769 33.333 0.00 0.00 0.00 3.85
2755 4507 9.982651 TTCTAAAATCATGTCCTACTAGTATGC 57.017 33.333 2.33 0.00 0.00 3.14
2756 4508 9.143155 TCTAAAATCATGTCCTACTAGTATGCA 57.857 33.333 2.33 3.62 0.00 3.96
2792 4544 7.915293 TGTGATTAAATTGTCCTACGTGATT 57.085 32.000 0.00 0.00 0.00 2.57
2799 4551 3.232213 TGTCCTACGTGATTCAGCTTC 57.768 47.619 0.00 0.00 0.00 3.86
2848 4600 7.042523 GCAAAGTAGAATTGTGTCTGCAATTTT 60.043 33.333 5.66 3.41 45.68 1.82
2862 4614 4.692228 TGCAATTTTGTTTCTTCCAGTCC 58.308 39.130 0.00 0.00 0.00 3.85
2910 4662 1.129437 CCTTTTCTGCGAGCAGTAAGC 59.871 52.381 22.47 0.00 43.96 3.09
2924 4676 4.545610 GCAGTAAGCATGCACAACTTTTA 58.454 39.130 21.98 4.79 43.31 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.254350 GGCCCGAAAGTTTCACGC 59.746 61.111 15.67 14.26 0.00 5.34
25 26 3.860930 ATGGTTGCGGCCCGAAAGT 62.861 57.895 7.68 0.00 0.00 2.66
32 33 4.133796 GCTTGGATGGTTGCGGCC 62.134 66.667 0.00 0.00 0.00 6.13
156 175 2.639286 CGTCTTGTGCACCTTGCC 59.361 61.111 15.69 0.00 44.23 4.52
157 176 1.891919 TCCGTCTTGTGCACCTTGC 60.892 57.895 15.69 1.38 45.29 4.01
176 195 4.611355 CGTCCATGTGTTACTGCTTCTTTG 60.611 45.833 0.00 0.00 0.00 2.77
183 202 1.419922 CGCGTCCATGTGTTACTGC 59.580 57.895 0.00 0.00 0.00 4.40
185 204 0.736325 GAGCGCGTCCATGTGTTACT 60.736 55.000 8.43 0.00 0.00 2.24
189 208 1.738099 GAAGAGCGCGTCCATGTGT 60.738 57.895 8.43 0.00 0.00 3.72
452 1907 3.952675 CCAAATCCATCGCCGCCG 61.953 66.667 0.00 0.00 0.00 6.46
453 1908 4.270376 GCCAAATCCATCGCCGCC 62.270 66.667 0.00 0.00 0.00 6.13
454 1909 4.270376 GGCCAAATCCATCGCCGC 62.270 66.667 0.00 0.00 0.00 6.53
455 1910 2.063541 GAAGGCCAAATCCATCGCCG 62.064 60.000 5.01 0.00 46.36 6.46
456 1911 1.037030 TGAAGGCCAAATCCATCGCC 61.037 55.000 5.01 0.00 41.96 5.54
457 1912 0.817013 TTGAAGGCCAAATCCATCGC 59.183 50.000 5.01 0.00 0.00 4.58
458 1913 1.406539 CCTTGAAGGCCAAATCCATCG 59.593 52.381 5.01 0.00 33.76 3.84
507 1971 0.941463 CATCGATCTTTCCCGCTCGG 60.941 60.000 0.00 0.48 0.00 4.63
562 2026 3.189910 CACATACATACATGCTCATGGCC 59.810 47.826 13.69 0.00 42.91 5.36
563 2027 3.365666 GCACATACATACATGCTCATGGC 60.366 47.826 13.69 0.00 42.91 4.40
627 2097 3.504906 CCATACGGACCATACGAGTACAT 59.495 47.826 0.00 0.00 34.93 2.29
628 2098 2.880268 CCATACGGACCATACGAGTACA 59.120 50.000 0.00 0.00 34.93 2.90
641 2111 0.324368 AGCTCTGGTGTCCATACGGA 60.324 55.000 0.00 0.00 39.79 4.69
642 2112 1.338337 CTAGCTCTGGTGTCCATACGG 59.662 57.143 0.00 0.00 30.82 4.02
723 2193 3.186702 TCGGACATCACAAGTTCACAA 57.813 42.857 0.00 0.00 0.00 3.33
724 2194 2.869801 GTTCGGACATCACAAGTTCACA 59.130 45.455 0.00 0.00 0.00 3.58
725 2195 2.096909 CGTTCGGACATCACAAGTTCAC 60.097 50.000 0.00 0.00 0.00 3.18
726 2196 2.131972 CGTTCGGACATCACAAGTTCA 58.868 47.619 0.00 0.00 0.00 3.18
727 2197 1.459592 CCGTTCGGACATCACAAGTTC 59.540 52.381 5.19 0.00 0.00 3.01
728 2198 1.069513 TCCGTTCGGACATCACAAGTT 59.930 47.619 10.00 0.00 0.00 2.66
729 2199 0.677288 TCCGTTCGGACATCACAAGT 59.323 50.000 10.00 0.00 0.00 3.16
730 2200 1.660607 CATCCGTTCGGACATCACAAG 59.339 52.381 16.22 0.00 37.10 3.16
731 2201 1.720805 CATCCGTTCGGACATCACAA 58.279 50.000 16.22 0.00 37.10 3.33
735 2205 1.429148 GGTGCATCCGTTCGGACATC 61.429 60.000 16.22 7.62 37.10 3.06
738 2208 2.047655 TGGTGCATCCGTTCGGAC 60.048 61.111 16.22 5.58 37.10 4.79
755 2225 3.991051 CGCACCTGGTCGTCTGGT 61.991 66.667 0.00 4.80 46.82 4.00
756 2226 3.680786 TCGCACCTGGTCGTCTGG 61.681 66.667 15.00 3.76 39.98 3.86
757 2227 2.430921 GTCGCACCTGGTCGTCTG 60.431 66.667 15.00 0.00 0.00 3.51
831 2342 4.056125 GCCGGAAACTGGCAAGGC 62.056 66.667 5.05 0.00 45.41 4.35
1413 3075 3.933048 GAGACCCTCCACGTCGGGA 62.933 68.421 18.31 7.68 43.44 5.14
1450 3112 0.317160 TTGATGTGCGACGAGAGGTT 59.683 50.000 0.00 0.00 0.00 3.50
1451 3113 0.388649 GTTGATGTGCGACGAGAGGT 60.389 55.000 0.00 0.00 0.00 3.85
1500 3162 3.809832 TGTTACAGAACTTGCTCTTGAGC 59.190 43.478 15.01 15.01 36.45 4.26
1602 3264 1.690845 GGGAGATCCTCTGCTGAAGGA 60.691 57.143 12.00 12.00 35.01 3.36
1639 3301 1.457455 CTGCCTCCTCCTCCTCCTC 60.457 68.421 0.00 0.00 0.00 3.71
1640 3302 1.303423 ATCTGCCTCCTCCTCCTCCT 61.303 60.000 0.00 0.00 0.00 3.69
1641 3303 1.120795 CATCTGCCTCCTCCTCCTCC 61.121 65.000 0.00 0.00 0.00 4.30
1653 3315 3.604582 GCCAGTATATTCCTCATCTGCC 58.395 50.000 0.00 0.00 0.00 4.85
1700 3362 4.680237 TCACCAACGGCAGCCTCG 62.680 66.667 10.54 0.00 0.00 4.63
1728 3390 0.034380 TCCTCCTCCAGTACTCACCG 60.034 60.000 0.00 0.00 0.00 4.94
1821 3483 1.570979 TGCCTCCTCCATCTAGTCTCA 59.429 52.381 0.00 0.00 0.00 3.27
1955 3617 1.203441 ACAGAGGGCAGGAGATTGCA 61.203 55.000 0.11 0.00 45.86 4.08
2017 3680 7.329226 ACGATAAGCAGAAAATGAAACCAAATG 59.671 33.333 0.00 0.00 0.00 2.32
2097 3760 2.029739 TGCACTTCAATCAACATGCCAG 60.030 45.455 0.00 0.00 32.02 4.85
2122 3785 8.527810 TGCTTATTTTCGAGTTTAATCCCAAAT 58.472 29.630 0.00 0.00 0.00 2.32
2239 3902 9.693739 TTATCAAGAATATGCCAAAACTTCCTA 57.306 29.630 0.00 0.00 0.00 2.94
2274 3938 3.410631 TGCTTACGAATCCAAACTCCA 57.589 42.857 0.00 0.00 0.00 3.86
2351 4015 5.665459 AGCTATCAGGTATGACAACTGAAC 58.335 41.667 10.61 5.55 43.65 3.18
2362 4026 4.970860 AGACATGCAAGCTATCAGGTAT 57.029 40.909 5.58 0.70 0.00 2.73
2366 4030 5.913514 GCAAAATAGACATGCAAGCTATCAG 59.086 40.000 0.00 0.00 39.81 2.90
2428 4176 6.205658 AGAGATAGGACTGCAAGAAAACAAAC 59.794 38.462 0.00 0.00 37.43 2.93
2433 4181 6.213600 ACCTTAGAGATAGGACTGCAAGAAAA 59.786 38.462 0.00 0.00 35.01 2.29
2457 4205 5.414454 TGCCACAACTTCCTAATGTAATGAC 59.586 40.000 0.00 0.00 0.00 3.06
2606 4356 7.481642 TGCTAAGTATAGTAAAGCAGACAGAC 58.518 38.462 11.61 0.00 38.22 3.51
2607 4357 7.640597 TGCTAAGTATAGTAAAGCAGACAGA 57.359 36.000 11.61 0.00 38.22 3.41
2608 4358 8.703604 TTTGCTAAGTATAGTAAAGCAGACAG 57.296 34.615 14.06 0.00 43.47 3.51
2639 4391 6.366061 GGAAGAAACCAAATTGCAGATACAAC 59.634 38.462 0.00 0.00 31.03 3.32
2683 4435 5.614887 CGCAGAAAAGTAAGTTGGCTACTTC 60.615 44.000 17.35 9.69 43.67 3.01
2684 4436 7.723006 CTCGCAGAAAAGTAAGTTGGCTACTT 61.723 42.308 17.88 17.88 43.24 2.24
2693 4445 3.113260 ACTGCTCGCAGAAAAGTAAGT 57.887 42.857 24.30 0.00 46.30 2.24
2745 4497 9.797556 CACAATAGTAAACACTGCATACTAGTA 57.202 33.333 4.77 4.77 36.05 1.82
2777 4529 3.895232 AGCTGAATCACGTAGGACAAT 57.105 42.857 0.00 0.00 0.00 2.71
2792 4544 0.106708 AAAGCAGACACGGAAGCTGA 59.893 50.000 0.00 0.00 37.41 4.26
2799 4551 3.021269 TGTGTAGTAAAGCAGACACGG 57.979 47.619 0.00 0.00 44.11 4.94
2848 4600 4.020218 CCACAGATAGGACTGGAAGAAACA 60.020 45.833 0.00 0.00 41.59 2.83
2862 4614 6.057533 TGGAATACTTTGATGCCACAGATAG 58.942 40.000 0.00 0.00 28.48 2.08
2910 4662 7.481275 ACAGGATTTTTAAAAGTTGTGCATG 57.519 32.000 0.14 0.00 0.00 4.06
2911 4663 7.467131 GCAACAGGATTTTTAAAAGTTGTGCAT 60.467 33.333 21.42 5.63 37.69 3.96


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

AutoCloner maintained by Alex Coulton.