Multiple sequence alignment - TraesCS4B01G077200

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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 TraesCS4B01G077200 chr4B 100.000 3050 0 0 1 3050 73927729 73930778 0.000000e+00 5633
1 TraesCS4B01G077200 chr4D 94.591 3069 128 22 1 3050 50150378 50153427 0.000000e+00 4713
2 TraesCS4B01G077200 chr4D 84.241 514 53 8 1835 2322 50156419 50156930 2.750000e-130 475
3 TraesCS4B01G077200 chr4D 88.485 165 12 3 1 161 50150114 50150275 3.100000e-45 193
4 TraesCS4B01G077200 chr4A 95.177 2861 108 17 196 3050 546797542 546794706 0.000000e+00 4492
5 TraesCS4B01G077200 chr4A 85.000 360 33 4 1835 2173 546791733 546791374 2.250000e-91 346


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 TraesCS4B01G077200 chr4B 73927729 73930778 3049 False 5633.000000 5633 100.000000 1 3050 1 chr4B.!!$F1 3049
1 TraesCS4B01G077200 chr4D 50150114 50156930 6816 False 1793.666667 4713 89.105667 1 3050 3 chr4D.!!$F1 3049
2 TraesCS4B01G077200 chr4A 546791374 546797542 6168 True 2419.000000 4492 90.088500 196 3050 2 chr4A.!!$R1 2854

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
776 1056 0.105039 GATCGGGAGGCAATCTTCGT 59.895 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 2408 0.53109 AACTGTAGTTTCGCGGCACA 60.531 50.0 6.13 2.65 33.93 4.57 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
20 21 3.422417 TGATCGCAACACTCTACTAGC 57.578 47.619 0.00 0.00 0.00 3.42
22 23 2.631418 TCGCAACACTCTACTAGCAC 57.369 50.000 0.00 0.00 0.00 4.40
23 24 1.883926 TCGCAACACTCTACTAGCACA 59.116 47.619 0.00 0.00 0.00 4.57
24 25 2.492088 TCGCAACACTCTACTAGCACAT 59.508 45.455 0.00 0.00 0.00 3.21
25 26 3.692593 TCGCAACACTCTACTAGCACATA 59.307 43.478 0.00 0.00 0.00 2.29
31 35 7.867909 GCAACACTCTACTAGCACATAATGATA 59.132 37.037 0.00 0.00 0.00 2.15
34 38 8.914011 ACACTCTACTAGCACATAATGATACAA 58.086 33.333 0.00 0.00 0.00 2.41
54 58 2.706339 AGTTATCAAGCAGCCTCCAG 57.294 50.000 0.00 0.00 0.00 3.86
66 70 0.322008 GCCTCCAGCACTGTTTAGCT 60.322 55.000 0.00 0.00 42.97 3.32
67 71 1.066143 GCCTCCAGCACTGTTTAGCTA 60.066 52.381 0.00 0.00 42.97 3.32
68 72 2.615493 GCCTCCAGCACTGTTTAGCTAA 60.615 50.000 0.86 0.86 42.97 3.09
121 125 2.313643 TGGAGTCCCATGTCACCTAGTA 59.686 50.000 6.74 0.00 37.58 1.82
140 144 9.959721 ACCTAGTATATCTTTTGAAACACACAT 57.040 29.630 0.00 0.00 0.00 3.21
156 417 1.731709 CACATCTTGCCGTTCATTCGA 59.268 47.619 0.00 0.00 0.00 3.71
165 426 3.195661 GCCGTTCATTCGATTTCTACCT 58.804 45.455 0.00 0.00 0.00 3.08
167 428 4.807304 GCCGTTCATTCGATTTCTACCTAA 59.193 41.667 0.00 0.00 0.00 2.69
170 431 6.198591 CCGTTCATTCGATTTCTACCTAAGTC 59.801 42.308 0.00 0.00 0.00 3.01
172 433 6.446781 TCATTCGATTTCTACCTAAGTCGT 57.553 37.500 0.00 0.00 39.01 4.34
180 441 1.246056 TACCTAAGTCGTGCTGCGGT 61.246 55.000 0.00 0.00 41.72 5.68
205 482 2.712057 ACAAAATTTGAGCTCAGGCG 57.288 45.000 17.43 6.33 44.37 5.52
302 580 0.394565 GCTCTCCATCCTACGCCATT 59.605 55.000 0.00 0.00 0.00 3.16
303 581 1.618837 GCTCTCCATCCTACGCCATTA 59.381 52.381 0.00 0.00 0.00 1.90
351 629 4.932105 GCCCCAAGCCCAACACCA 62.932 66.667 0.00 0.00 34.35 4.17
362 640 3.575247 AACACCATCGCCCCACCA 61.575 61.111 0.00 0.00 0.00 4.17
379 657 5.132144 CCCCACCAGTCAGTTATATAAACCT 59.868 44.000 0.00 0.00 0.00 3.50
636 916 0.530288 ATTTCGCCCCGGATTGTTTG 59.470 50.000 0.73 0.00 0.00 2.93
642 922 1.674322 CCCGGATTGTTTGCCTCGT 60.674 57.895 0.73 0.00 0.00 4.18
729 1009 2.578163 TTCCGAGCAGATTCGCCTGG 62.578 60.000 0.00 0.00 39.19 4.45
772 1052 2.511452 CCGGATCGGGAGGCAATCT 61.511 63.158 13.96 0.00 44.15 2.40
776 1056 0.105039 GATCGGGAGGCAATCTTCGT 59.895 55.000 0.00 0.00 0.00 3.85
794 1074 1.377202 TGCGAGGTGGCCTGAATTC 60.377 57.895 3.32 0.00 31.76 2.17
795 1075 1.078143 GCGAGGTGGCCTGAATTCT 60.078 57.895 3.32 0.00 31.76 2.40
829 1109 3.204827 CTGATTTCGCAGGCGGGG 61.205 66.667 14.24 0.00 40.25 5.73
830 1110 4.794648 TGATTTCGCAGGCGGGGG 62.795 66.667 14.24 0.00 40.25 5.40
858 1138 3.191669 CGACCTCGTGTAATTATTGCCA 58.808 45.455 0.00 0.00 34.11 4.92
878 1158 1.186917 TTTGTCGAGGGTTAGGCGGA 61.187 55.000 0.00 0.00 0.00 5.54
890 1170 1.977056 TAGGCGGAGATTAGCGAAGA 58.023 50.000 0.00 0.00 0.00 2.87
902 1182 3.244105 CGAAGACGCTGGGTGTTG 58.756 61.111 11.90 1.73 31.29 3.33
931 1211 0.741221 CTAGGGTTTGCTCTCCGTGC 60.741 60.000 0.00 0.00 0.00 5.34
974 1254 1.606224 GGTTGCCTGCATTTCTGTTGG 60.606 52.381 0.00 0.00 0.00 3.77
978 1258 1.787012 CCTGCATTTCTGTTGGTTGC 58.213 50.000 0.00 0.00 0.00 4.17
989 1269 1.310904 GTTGGTTGCGTTTGGAGGTA 58.689 50.000 0.00 0.00 0.00 3.08
990 1270 1.883926 GTTGGTTGCGTTTGGAGGTAT 59.116 47.619 0.00 0.00 0.00 2.73
993 1273 1.883926 GGTTGCGTTTGGAGGTATTGT 59.116 47.619 0.00 0.00 0.00 2.71
1057 1337 0.469917 GGAGCTGAAATCCCGGATCA 59.530 55.000 0.73 0.56 29.89 2.92
1263 1543 1.816835 CCTAGTAAGCAGACGGTGACA 59.183 52.381 0.00 0.00 0.00 3.58
1527 1807 5.455056 TGGAAGTTGTCTCTGTAGAAGAC 57.545 43.478 0.00 0.00 32.16 3.01
1581 1861 1.567504 CGTGTGTTCAAAGTCGGAGT 58.432 50.000 0.00 0.00 0.00 3.85
1844 2124 1.004277 TGTCGCTAAAGCAAGGGGAAT 59.996 47.619 2.44 0.00 42.21 3.01
1943 2223 1.729586 TCAGGCCAGTTCTACCAAGT 58.270 50.000 5.01 0.00 0.00 3.16
1983 2263 1.541310 TAGCAGTGGAGTCCAACCGG 61.541 60.000 15.09 0.00 34.18 5.28
2124 2404 4.389374 ACCCTGTCTGTTATGTTTCTGTG 58.611 43.478 0.00 0.00 0.00 3.66
2128 2408 3.181445 TGTCTGTTATGTTTCTGTGGGCT 60.181 43.478 0.00 0.00 0.00 5.19
2184 2464 6.995091 AGATGAATGAACTTGGAATAGTAGGC 59.005 38.462 0.00 0.00 0.00 3.93
2342 2622 5.163723 GCTGAAACAAGTAGCTAATGCATCA 60.164 40.000 0.00 5.65 42.74 3.07
2423 2704 8.407832 TGCATTCAGATTTGAAATATCGAATGT 58.592 29.630 23.09 3.04 45.82 2.71
2653 2934 4.038282 TCGACAAACTTGTTACCTAGAGCA 59.962 41.667 0.00 0.00 42.43 4.26
2708 2992 4.019321 AGCTCCTTAAACTCACCATGCTTA 60.019 41.667 0.00 0.00 0.00 3.09
2817 3101 6.742109 AGACATTCATTCAAGTTTCAACCAG 58.258 36.000 0.00 0.00 0.00 4.00
2849 3133 1.578583 ACACGGGAGTTCAAACTTCG 58.421 50.000 13.93 13.93 44.67 3.79
2900 3184 9.689976 ATCTGATATAGTCATCTCAAAACGAAG 57.310 33.333 0.00 0.00 35.97 3.79
2918 3202 5.837437 ACGAAGAATCTGTCTGATATGGTC 58.163 41.667 0.00 0.00 36.40 4.02
2934 3218 3.564053 TGGTCTATGATGCAATGCTGA 57.436 42.857 6.82 0.00 0.00 4.26
2940 3224 1.035385 TGATGCAATGCTGAGCTGGG 61.035 55.000 5.83 0.00 0.00 4.45
2992 3276 1.187087 GCTAGCCTGTGGACTGTAGT 58.813 55.000 2.29 0.00 0.00 2.73
2993 3277 1.135333 GCTAGCCTGTGGACTGTAGTC 59.865 57.143 2.29 3.43 44.04 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.883926 TGTGCTAGTAGAGTGTTGCGA 59.116 47.619 0.00 0.00 0.00 5.10
22 23 9.390795 GCTGCTTGATAACTTTGTATCATTATG 57.609 33.333 0.00 0.00 39.61 1.90
23 24 8.571336 GGCTGCTTGATAACTTTGTATCATTAT 58.429 33.333 0.00 0.00 39.61 1.28
24 25 7.775093 AGGCTGCTTGATAACTTTGTATCATTA 59.225 33.333 0.00 0.00 39.61 1.90
25 26 6.604795 AGGCTGCTTGATAACTTTGTATCATT 59.395 34.615 0.00 0.00 39.61 2.57
31 35 3.084786 GGAGGCTGCTTGATAACTTTGT 58.915 45.455 0.00 0.00 0.00 2.83
34 38 2.943199 GCTGGAGGCTGCTTGATAACTT 60.943 50.000 7.74 0.00 38.06 2.66
44 48 0.606401 TAAACAGTGCTGGAGGCTGC 60.606 55.000 0.00 0.00 42.39 5.25
47 51 0.322008 AGCTAAACAGTGCTGGAGGC 60.322 55.000 4.11 3.12 38.21 4.70
54 58 6.940298 TGGGGATATTATTAGCTAAACAGTGC 59.060 38.462 10.85 1.73 0.00 4.40
66 70 9.099071 CATGGTTCCAATTTGGGGATATTATTA 57.901 33.333 15.37 0.00 38.32 0.98
67 71 7.793709 TCATGGTTCCAATTTGGGGATATTATT 59.206 33.333 15.37 0.00 38.32 1.40
68 72 7.312181 TCATGGTTCCAATTTGGGGATATTAT 58.688 34.615 15.37 0.00 38.32 1.28
121 125 7.092716 GGCAAGATGTGTGTTTCAAAAGATAT 58.907 34.615 0.00 0.00 0.00 1.63
140 144 3.334691 AGAAATCGAATGAACGGCAAGA 58.665 40.909 0.00 0.00 0.00 3.02
156 417 3.522553 GCAGCACGACTTAGGTAGAAAT 58.477 45.455 0.00 0.00 0.00 2.17
170 431 4.059459 GTTCGTCACCGCAGCACG 62.059 66.667 0.00 0.00 43.15 5.34
172 433 1.369839 TTTTGTTCGTCACCGCAGCA 61.370 50.000 0.00 0.00 0.00 4.41
180 441 4.261155 CCTGAGCTCAAATTTTGTTCGTCA 60.261 41.667 18.85 7.30 0.00 4.35
186 447 1.336240 GCGCCTGAGCTCAAATTTTGT 60.336 47.619 18.85 0.00 36.60 2.83
193 454 2.620112 GCTTTGCGCCTGAGCTCAA 61.620 57.895 18.85 0.00 41.77 3.02
194 455 3.052082 GCTTTGCGCCTGAGCTCA 61.052 61.111 17.19 17.19 38.13 4.26
205 482 1.135859 CACATCCGAGTCAAGCTTTGC 60.136 52.381 0.00 0.00 0.00 3.68
294 572 1.122227 GGTGGGTAGGTAATGGCGTA 58.878 55.000 0.00 0.00 0.00 4.42
302 580 1.005805 TGTAAGCGAGGTGGGTAGGTA 59.994 52.381 0.00 0.00 0.00 3.08
303 581 0.251922 TGTAAGCGAGGTGGGTAGGT 60.252 55.000 0.00 0.00 0.00 3.08
339 617 2.676471 GGCGATGGTGTTGGGCTT 60.676 61.111 0.00 0.00 0.00 4.35
351 629 0.907704 TAACTGACTGGTGGGGCGAT 60.908 55.000 0.00 0.00 0.00 4.58
362 640 4.975794 AGGGGCAGGTTTATATAACTGACT 59.024 41.667 13.07 4.84 38.97 3.41
394 672 4.231439 CTAACCCTACCCGCCGCC 62.231 72.222 0.00 0.00 0.00 6.13
636 916 0.161024 CAGAACGAAACGAACGAGGC 59.839 55.000 0.14 0.00 34.70 4.70
642 922 3.537806 GCGAATTTCAGAACGAAACGAA 58.462 40.909 0.00 0.00 46.22 3.85
709 989 0.740868 CAGGCGAATCTGCTCGGAAA 60.741 55.000 0.00 0.00 39.27 3.13
715 995 0.682209 AATTGCCAGGCGAATCTGCT 60.682 50.000 5.12 0.00 33.64 4.24
765 1045 1.741770 ACCTCGCACGAAGATTGCC 60.742 57.895 0.00 0.00 36.57 4.52
772 1052 4.680237 CAGGCCACCTCGCACGAA 62.680 66.667 5.01 0.00 0.00 3.85
776 1056 1.377202 GAATTCAGGCCACCTCGCA 60.377 57.895 5.01 0.00 0.00 5.10
810 1090 1.745115 CCCGCCTGCGAAATCAGAA 60.745 57.895 13.94 0.00 42.83 3.02
858 1138 0.107848 CCGCCTAACCCTCGACAAAT 60.108 55.000 0.00 0.00 0.00 2.32
890 1170 4.619227 CCGACCAACACCCAGCGT 62.619 66.667 0.00 0.00 0.00 5.07
902 1182 0.108945 CAAACCCTAGACGACCGACC 60.109 60.000 0.00 0.00 0.00 4.79
931 1211 2.607771 CCGAAACCCAATCAAACAGCTG 60.608 50.000 13.48 13.48 0.00 4.24
974 1254 2.920647 GCACAATACCTCCAAACGCAAC 60.921 50.000 0.00 0.00 0.00 4.17
978 1258 1.529226 TGGCACAATACCTCCAAACG 58.471 50.000 0.00 0.00 31.92 3.60
993 1273 0.390340 GACGAGTCTGCATCTTGGCA 60.390 55.000 7.12 0.00 42.53 4.92
1057 1337 1.000396 GATGGCCCAGCTTCTTGGT 60.000 57.895 0.00 0.00 36.45 3.67
1263 1543 3.449018 CCATGCTAGTCTGTGAGTTACCT 59.551 47.826 0.00 0.00 0.00 3.08
1504 1784 5.465935 GTCTTCTACAGAGACAACTTCCAG 58.534 45.833 0.00 0.00 33.20 3.86
1527 1807 2.527951 CTTGCTCAACCTCCTCCCCG 62.528 65.000 0.00 0.00 0.00 5.73
1581 1861 1.617018 CCAACGGAGCTCTGATGGGA 61.617 60.000 33.77 0.00 40.35 4.37
1616 1896 0.689623 AGGAGTGTGAGCCTTTGGAG 59.310 55.000 0.00 0.00 0.00 3.86
1677 1957 2.028130 CGAGTATCTGGCAACTCCTCT 58.972 52.381 11.21 0.00 39.16 3.69
1844 2124 3.073798 TGCTTGAGGTATCCTTGTTCCAA 59.926 43.478 0.00 0.00 31.76 3.53
1884 2164 3.624777 GTTCTGTCCACCATTCCATGAT 58.375 45.455 0.00 0.00 0.00 2.45
1943 2223 6.930164 TGCTACCTTAACATCTTGTAACGAAA 59.070 34.615 0.00 0.00 0.00 3.46
1983 2263 6.127925 TGGAATGATCACAACTCAATAACTGC 60.128 38.462 0.00 0.00 0.00 4.40
2128 2408 0.531090 AACTGTAGTTTCGCGGCACA 60.531 50.000 6.13 2.65 33.93 4.57
2184 2464 7.330454 CCAAGAATCATGGATGTATAACTCGAG 59.670 40.741 11.84 11.84 40.56 4.04
2342 2622 9.709495 ATAACACAATATTGCAAACAGTCATTT 57.291 25.926 15.48 0.00 0.00 2.32
2423 2704 1.775459 TGGTTACCAGGCTAAACCACA 59.225 47.619 18.95 3.81 45.85 4.17
2653 2934 4.762251 AGCTTAAAGACAGGATTTTCGCTT 59.238 37.500 0.00 0.00 0.00 4.68
2817 3101 0.451783 CCCGTGTTAAAGGCTGATGC 59.548 55.000 0.00 0.00 38.76 3.91
2849 3133 2.604614 GGATGTTTGCGGTGTGAACTTC 60.605 50.000 0.00 0.00 0.00 3.01
2860 3144 3.770263 ATCAGATGTTGGATGTTTGCG 57.230 42.857 0.00 0.00 0.00 4.85
2900 3184 7.492020 GCATCATAGACCATATCAGACAGATTC 59.508 40.741 0.00 0.00 38.19 2.52
2918 3202 2.226674 CCAGCTCAGCATTGCATCATAG 59.773 50.000 11.91 1.84 0.00 2.23
2934 3218 3.117738 CCAATCCAATCTAAGTCCCAGCT 60.118 47.826 0.00 0.00 0.00 4.24
2940 3224 9.956720 CACATTAATTCCAATCCAATCTAAGTC 57.043 33.333 0.00 0.00 0.00 3.01
2992 3276 5.006153 TCGATAAGCTTGGAGAATTTCGA 57.994 39.130 9.86 7.24 0.00 3.71
2993 3277 5.321983 CTCGATAAGCTTGGAGAATTTCG 57.678 43.478 9.86 5.13 0.00 3.46
3020 3304 1.915952 GAGCTAACGAGTTGCTCCTC 58.084 55.000 19.79 8.88 45.12 3.71
3026 3310 1.419374 ACAAGCGAGCTAACGAGTTG 58.581 50.000 0.00 4.31 35.99 3.16


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

AutoCloner maintained by Alex Coulton.