Multiple sequence alignment - TraesCS6D01G055500

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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 TraesCS6D01G055500 chr6D 100.000 2849 0 0 1 2849 26349920 26352768 0.000000e+00 5262
1 TraesCS6D01G055500 chr6D 86.858 487 57 6 1180 1661 462422963 462423447 3.230000e-149 538
2 TraesCS6D01G055500 chr6A 89.538 2705 125 57 1 2615 27771646 27774282 0.000000e+00 3282
3 TraesCS6D01G055500 chr6A 87.654 486 55 4 1180 1661 609176277 609176761 6.890000e-156 560
4 TraesCS6D01G055500 chr6A 94.758 248 7 2 2601 2846 27775706 27775949 5.760000e-102 381
5 TraesCS6D01G055500 chr6B 92.187 2291 83 34 13 2253 48550816 48553060 0.000000e+00 3151
6 TraesCS6D01G055500 chr6B 87.654 486 55 4 1180 1661 704890658 704891142 6.890000e-156 560
7 TraesCS6D01G055500 chr6B 93.182 176 12 0 2391 2566 48553117 48553292 2.820000e-65 259
8 TraesCS6D01G055500 chr6B 92.481 133 9 1 2704 2836 48553294 48553425 3.750000e-44 189
9 TraesCS6D01G055500 chr6B 95.652 46 2 0 2287 2332 48553072 48553117 1.090000e-09 75
10 TraesCS6D01G055500 chr4D 81.131 2104 154 128 156 2117 1229857 1231859 0.000000e+00 1461
11 TraesCS6D01G055500 chr4B 84.631 1477 103 67 792 2208 653977 652565 0.000000e+00 1356
12 TraesCS6D01G055500 chr4B 78.079 406 40 33 156 524 654735 654342 8.000000e-51 211
13 TraesCS6D01G055500 chr4B 95.775 71 2 1 2572 2642 32960995 32961064 2.320000e-21 113
14 TraesCS6D01G055500 chr4A 86.810 1213 97 34 937 2117 603540617 603539436 0.000000e+00 1295
15 TraesCS6D01G055500 chr4A 83.932 473 70 5 1204 1670 103068740 103069212 5.600000e-122 448
16 TraesCS6D01G055500 chr4A 77.590 415 36 32 156 524 603541432 603541029 6.230000e-47 198
17 TraesCS6D01G055500 chr4A 84.146 82 7 4 571 651 603540913 603540837 1.090000e-09 75
18 TraesCS6D01G055500 chr7B 93.182 88 6 0 2572 2659 479997009 479996922 2.300000e-26 130
19 TraesCS6D01G055500 chr5D 91.398 93 7 1 2567 2658 303718393 303718301 2.980000e-25 126
20 TraesCS6D01G055500 chr1D 91.860 86 7 0 2573 2658 245089474 245089389 1.390000e-23 121
21 TraesCS6D01G055500 chr2A 91.765 85 6 1 2571 2655 80227300 80227383 1.790000e-22 117
22 TraesCS6D01G055500 chr2B 94.203 69 3 1 2572 2640 785751310 785751243 1.400000e-18 104
23 TraesCS6D01G055500 chr1A 92.754 69 5 0 2573 2641 204826161 204826093 1.810000e-17 100


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 TraesCS6D01G055500 chr6D 26349920 26352768 2848 False 5262.000000 5262 100.000000 1 2849 1 chr6D.!!$F1 2848
1 TraesCS6D01G055500 chr6A 27771646 27775949 4303 False 1831.500000 3282 92.148000 1 2846 2 chr6A.!!$F2 2845
2 TraesCS6D01G055500 chr6B 48550816 48553425 2609 False 918.500000 3151 93.375500 13 2836 4 chr6B.!!$F2 2823
3 TraesCS6D01G055500 chr4D 1229857 1231859 2002 False 1461.000000 1461 81.131000 156 2117 1 chr4D.!!$F1 1961
4 TraesCS6D01G055500 chr4B 652565 654735 2170 True 783.500000 1356 81.355000 156 2208 2 chr4B.!!$R1 2052
5 TraesCS6D01G055500 chr4A 603539436 603541432 1996 True 522.666667 1295 82.848667 156 2117 3 chr4A.!!$R1 1961

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
874 1150 0.033796 CCAGGGCATCATGGTGAAGT 60.034 55.0 11.02 0.0 39.78 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2642 4523 0.743097 GCCACCTCCAGATTGCATTC 59.257 55.0 0.16 0.16 0.0 2.67 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
92 98 8.841300 GCAGGATAGCTAGCTTAATTTTTAAGT 58.159 33.333 24.88 0.00 0.00 2.24
312 333 7.111247 TGTCATCATGTACACATACTGATCA 57.889 36.000 0.00 0.00 34.26 2.92
316 337 9.865321 TCATCATGTACACATACTGATCATATG 57.135 33.333 16.89 16.89 34.26 1.78
406 477 2.808543 GGCAGGTGTTGAACAAGTAGAG 59.191 50.000 0.00 0.00 0.00 2.43
604 793 2.510594 GCTGCAATTTCATGGCGCG 61.511 57.895 0.00 0.00 0.00 6.86
608 797 1.133982 TGCAATTTCATGGCGCGTAAT 59.866 42.857 8.43 0.00 0.00 1.89
609 798 2.192624 GCAATTTCATGGCGCGTAATT 58.807 42.857 8.43 0.00 0.00 1.40
610 799 3.181496 TGCAATTTCATGGCGCGTAATTA 60.181 39.130 8.43 0.00 0.00 1.40
612 801 4.085619 GCAATTTCATGGCGCGTAATTAAG 60.086 41.667 8.43 0.00 0.00 1.85
614 803 2.319136 TCATGGCGCGTAATTAAGGT 57.681 45.000 8.43 0.00 0.00 3.50
616 805 3.125316 TCATGGCGCGTAATTAAGGTAC 58.875 45.455 8.43 0.00 0.00 3.34
618 807 2.542597 TGGCGCGTAATTAAGGTACTG 58.457 47.619 8.43 0.00 40.86 2.74
620 809 2.537214 GGCGCGTAATTAAGGTACTGAC 59.463 50.000 8.43 0.00 40.86 3.51
624 813 5.116680 GCGCGTAATTAAGGTACTGACATAG 59.883 44.000 8.43 0.00 40.86 2.23
656 868 4.196626 TCTCCTAGCTAGCTAGATCGAC 57.803 50.000 40.98 6.07 46.56 4.20
781 1043 8.944029 GCTGAATCACATCTATATTTGTAGCAT 58.056 33.333 0.00 0.00 0.00 3.79
783 1045 9.783081 TGAATCACATCTATATTTGTAGCATGT 57.217 29.630 0.00 0.00 0.00 3.21
839 1115 6.148976 TGAAGCTTCTCTGATCTTCATTTGTG 59.851 38.462 26.09 0.00 39.70 3.33
843 1119 4.644498 TCTCTGATCTTCATTTGTGTGCA 58.356 39.130 0.00 0.00 0.00 4.57
873 1149 0.256752 TCCAGGGCATCATGGTGAAG 59.743 55.000 11.02 0.00 44.55 3.02
874 1150 0.033796 CCAGGGCATCATGGTGAAGT 60.034 55.000 11.02 0.00 39.78 3.01
875 1151 1.212688 CCAGGGCATCATGGTGAAGTA 59.787 52.381 11.02 0.00 39.78 2.24
878 1154 1.133976 GGGCATCATGGTGAAGTAGCT 60.134 52.381 11.02 0.00 0.00 3.32
879 1155 2.216898 GGCATCATGGTGAAGTAGCTC 58.783 52.381 11.02 0.00 0.00 4.09
923 1220 2.268920 CTTGCTAGCCGCCCTTGA 59.731 61.111 13.29 0.00 38.05 3.02
956 1253 3.181480 GGAAGAAGAAGACCAGATCGAGG 60.181 52.174 5.78 5.78 0.00 4.63
957 1254 3.374042 AGAAGAAGACCAGATCGAGGA 57.626 47.619 13.34 0.00 0.00 3.71
958 1255 3.702792 AGAAGAAGACCAGATCGAGGAA 58.297 45.455 13.34 0.00 0.00 3.36
959 1256 3.699038 AGAAGAAGACCAGATCGAGGAAG 59.301 47.826 13.34 0.00 0.00 3.46
960 1257 2.383855 AGAAGACCAGATCGAGGAAGG 58.616 52.381 13.34 0.00 0.00 3.46
961 1258 2.024846 AGAAGACCAGATCGAGGAAGGA 60.025 50.000 13.34 0.00 0.00 3.36
962 1259 2.534042 AGACCAGATCGAGGAAGGAA 57.466 50.000 13.34 0.00 0.00 3.36
963 1260 2.383855 AGACCAGATCGAGGAAGGAAG 58.616 52.381 13.34 0.00 0.00 3.46
978 1275 3.191078 AGGAAGCAAGCTATAGCACAG 57.809 47.619 26.07 15.56 45.16 3.66
1822 2169 4.488136 ATGCAGCGCCGGAATGGA 62.488 61.111 5.05 0.67 42.00 3.41
1885 2243 5.705397 TCAATCAATCAGGACTTCAGGAT 57.295 39.130 0.00 0.00 0.00 3.24
1889 2247 4.356436 TCAATCAGGACTTCAGGATCAGA 58.644 43.478 0.00 0.00 0.00 3.27
1892 2250 3.986435 TCAGGACTTCAGGATCAGATCA 58.014 45.455 12.66 0.00 0.00 2.92
1893 2251 3.959449 TCAGGACTTCAGGATCAGATCAG 59.041 47.826 12.66 3.58 0.00 2.90
1894 2252 3.705579 CAGGACTTCAGGATCAGATCAGT 59.294 47.826 12.66 6.77 0.00 3.41
1895 2253 3.705579 AGGACTTCAGGATCAGATCAGTG 59.294 47.826 12.66 8.88 0.00 3.66
1896 2254 3.181467 GGACTTCAGGATCAGATCAGTGG 60.181 52.174 12.66 1.29 0.00 4.00
1897 2255 2.170187 ACTTCAGGATCAGATCAGTGGC 59.830 50.000 12.66 0.00 0.00 5.01
1898 2256 1.126488 TCAGGATCAGATCAGTGGCC 58.874 55.000 12.66 0.00 0.00 5.36
1951 2310 1.643310 CTCTCCCCTCATCCTCATCC 58.357 60.000 0.00 0.00 0.00 3.51
1963 2325 3.870538 TCCTCATCCAAATCCATCCTG 57.129 47.619 0.00 0.00 0.00 3.86
1981 2349 2.609459 CCTGCCAATAACTAGACTTGCG 59.391 50.000 0.00 0.00 0.00 4.85
2017 2395 8.529424 TTAGCAGCTGGTAAGTAACTAGAATA 57.471 34.615 29.54 7.54 38.95 1.75
2086 2471 2.279741 TGCTTGCTCCGATTCATGTAC 58.720 47.619 0.00 0.00 0.00 2.90
2201 2603 4.701651 TCCTCTCTGATTATTGCATGCT 57.298 40.909 20.33 1.26 0.00 3.79
2256 2699 9.538508 GTTCCTTTAACTTGAACTAGTTACTGA 57.461 33.333 8.42 0.00 39.61 3.41
2278 2721 9.791801 ACTGATATTGGTTATGTATGTATGCAA 57.208 29.630 0.00 0.00 0.00 4.08
2285 2728 8.972458 TGGTTATGTATGTATGCAATTGTAGT 57.028 30.769 7.40 0.00 0.00 2.73
2364 2807 5.376625 TCTTGCAAGATTAACCAGTTCTGT 58.623 37.500 25.16 0.00 0.00 3.41
2375 2818 3.222603 ACCAGTTCTGTTTGGTCCAATC 58.777 45.455 4.80 5.38 44.16 2.67
2383 2826 4.635765 TCTGTTTGGTCCAATCGATCAATC 59.364 41.667 4.80 0.00 41.30 2.67
2423 2866 6.973843 TGAAACTGGATCTTCTGTTTGATTG 58.026 36.000 10.28 0.00 38.36 2.67
2425 2868 7.449395 TGAAACTGGATCTTCTGTTTGATTGAT 59.551 33.333 10.28 0.00 38.36 2.57
2556 2999 0.399833 TGCCATGACTGCACAAGGTA 59.600 50.000 0.00 0.00 32.85 3.08
2557 3000 1.089920 GCCATGACTGCACAAGGTAG 58.910 55.000 0.00 0.00 32.16 3.18
2636 4517 0.935366 GGAATCTCGTCCGCGATCAC 60.935 60.000 8.23 0.00 46.80 3.06
2642 4523 1.946156 CGTCCGCGATCACATCCAG 60.946 63.158 8.23 0.00 41.33 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 16 0.829990 CAGCCCAACCAACCAGTTTT 59.170 50.000 0.00 0.00 0.00 2.43
45 47 4.771577 TGCTACCATCACATGTGGATTTTT 59.228 37.500 25.16 8.17 39.12 1.94
46 48 4.343231 TGCTACCATCACATGTGGATTTT 58.657 39.130 25.16 9.17 39.12 1.82
92 98 7.926674 TTTCAAAGATGCATCTGAGAATGTA 57.073 32.000 29.61 19.49 37.19 2.29
94 100 9.234384 GTATTTTCAAAGATGCATCTGAGAATG 57.766 33.333 29.61 22.55 37.19 2.67
290 311 9.865321 CATATGATCAGTATGTGTACATGATGA 57.135 33.333 12.47 5.94 37.15 2.92
608 797 9.710818 AGAAGGATAACTATGTCAGTACCTTAA 57.289 33.333 0.00 0.00 41.35 1.85
609 798 9.710818 AAGAAGGATAACTATGTCAGTACCTTA 57.289 33.333 0.00 0.00 41.35 2.69
610 799 8.611051 AAGAAGGATAACTATGTCAGTACCTT 57.389 34.615 0.00 0.00 42.63 3.50
612 801 8.240267 AGAAGAAGGATAACTATGTCAGTACC 57.760 38.462 0.00 0.00 36.04 3.34
614 803 8.282982 AGGAGAAGAAGGATAACTATGTCAGTA 58.717 37.037 0.00 0.00 36.04 2.74
616 805 7.595819 AGGAGAAGAAGGATAACTATGTCAG 57.404 40.000 0.00 0.00 0.00 3.51
618 807 7.450323 AGCTAGGAGAAGAAGGATAACTATGTC 59.550 40.741 0.00 0.00 0.00 3.06
620 809 7.775053 AGCTAGGAGAAGAAGGATAACTATG 57.225 40.000 0.00 0.00 0.00 2.23
624 813 5.773176 AGCTAGCTAGGAGAAGAAGGATAAC 59.227 44.000 17.69 0.00 0.00 1.89
785 1047 6.677781 AACACACAAGAGATCGAAGAAAAA 57.322 33.333 0.00 0.00 43.58 1.94
839 1115 2.165030 CCCTGGATCTGAAATTGTGCAC 59.835 50.000 10.75 10.75 0.00 4.57
843 1119 2.905415 TGCCCTGGATCTGAAATTGT 57.095 45.000 0.00 0.00 0.00 2.71
873 1149 1.727335 GTTGACTTCTTGCCGAGCTAC 59.273 52.381 0.00 0.00 0.00 3.58
874 1150 1.618837 AGTTGACTTCTTGCCGAGCTA 59.381 47.619 0.00 0.00 0.00 3.32
875 1151 0.394565 AGTTGACTTCTTGCCGAGCT 59.605 50.000 0.00 0.00 0.00 4.09
878 1154 4.265904 TGATTAGTTGACTTCTTGCCGA 57.734 40.909 0.00 0.00 0.00 5.54
879 1155 4.690748 TCTTGATTAGTTGACTTCTTGCCG 59.309 41.667 0.00 0.00 0.00 5.69
923 1220 6.056236 GGTCTTCTTCTTCCTTGTGTAGTTT 58.944 40.000 0.00 0.00 0.00 2.66
956 1253 3.535561 TGTGCTATAGCTTGCTTCCTTC 58.464 45.455 24.61 4.36 42.66 3.46
957 1254 3.198635 TCTGTGCTATAGCTTGCTTCCTT 59.801 43.478 24.61 0.00 42.66 3.36
958 1255 2.768527 TCTGTGCTATAGCTTGCTTCCT 59.231 45.455 24.61 0.00 42.66 3.36
959 1256 3.129871 CTCTGTGCTATAGCTTGCTTCC 58.870 50.000 24.61 5.55 42.66 3.46
960 1257 4.050553 CTCTCTGTGCTATAGCTTGCTTC 58.949 47.826 24.61 9.24 42.66 3.86
961 1258 3.450457 ACTCTCTGTGCTATAGCTTGCTT 59.550 43.478 24.61 0.23 42.66 3.91
962 1259 3.030291 ACTCTCTGTGCTATAGCTTGCT 58.970 45.455 24.61 0.00 42.66 3.91
963 1260 3.451141 ACTCTCTGTGCTATAGCTTGC 57.549 47.619 24.61 15.00 42.66 4.01
978 1275 4.857679 TCTCTCCACCTAACCTAACTCTC 58.142 47.826 0.00 0.00 0.00 3.20
1885 2243 1.591703 GACACGGCCACTGATCTGA 59.408 57.895 2.24 0.00 0.00 3.27
1889 2247 2.261671 GTCGACACGGCCACTGAT 59.738 61.111 11.55 0.00 0.00 2.90
1910 2268 2.054232 AGCTGATCTTGATGCTTGGG 57.946 50.000 0.00 0.00 30.96 4.12
1951 2310 6.016777 GTCTAGTTATTGGCAGGATGGATTTG 60.017 42.308 0.00 0.00 35.86 2.32
1981 2349 5.695851 ACCAGCTGCTAAATATATGCAAC 57.304 39.130 8.66 0.00 36.22 4.17
2040 2425 6.096001 ACTCCAAGATGATTTTTGGCAGATAC 59.904 38.462 5.17 0.00 42.82 2.24
2041 2426 6.189859 ACTCCAAGATGATTTTTGGCAGATA 58.810 36.000 5.17 0.00 42.82 1.98
2042 2427 5.021458 ACTCCAAGATGATTTTTGGCAGAT 58.979 37.500 5.17 0.00 42.82 2.90
2086 2471 7.736447 AAAGGAGCTCATTTATAATTCCTCG 57.264 36.000 23.86 0.00 32.66 4.63
2176 2576 5.557866 CATGCAATAATCAGAGAGGATGGA 58.442 41.667 0.00 0.00 0.00 3.41
2201 2603 9.056799 TGTGAATTATGCAGGGAGGATATATAA 57.943 33.333 0.00 0.00 30.09 0.98
2265 2708 9.777297 TCATACACTACAATTGCATACATACAT 57.223 29.630 5.05 0.00 0.00 2.29
2266 2709 9.260002 CTCATACACTACAATTGCATACATACA 57.740 33.333 5.05 0.00 0.00 2.29
2267 2710 8.223769 GCTCATACACTACAATTGCATACATAC 58.776 37.037 5.05 0.00 0.00 2.39
2268 2711 7.930865 TGCTCATACACTACAATTGCATACATA 59.069 33.333 5.05 0.00 0.00 2.29
2269 2712 6.767423 TGCTCATACACTACAATTGCATACAT 59.233 34.615 5.05 0.00 0.00 2.29
2270 2713 6.037062 GTGCTCATACACTACAATTGCATACA 59.963 38.462 5.05 0.00 37.58 2.29
2271 2714 6.037062 TGTGCTCATACACTACAATTGCATAC 59.963 38.462 5.05 0.00 41.30 2.39
2272 2715 6.112058 TGTGCTCATACACTACAATTGCATA 58.888 36.000 5.05 0.00 41.30 3.14
2273 2716 4.943093 TGTGCTCATACACTACAATTGCAT 59.057 37.500 5.05 0.00 41.30 3.96
2274 2717 4.322567 TGTGCTCATACACTACAATTGCA 58.677 39.130 5.05 0.00 41.30 4.08
2275 2718 4.944962 TGTGCTCATACACTACAATTGC 57.055 40.909 5.05 0.00 41.30 3.56
2276 2719 6.726258 TCTTGTGCTCATACACTACAATTG 57.274 37.500 3.24 3.24 41.30 2.32
2277 2720 6.128172 GCTTCTTGTGCTCATACACTACAATT 60.128 38.462 0.00 0.00 41.30 2.32
2278 2721 5.352569 GCTTCTTGTGCTCATACACTACAAT 59.647 40.000 0.00 0.00 41.30 2.71
2279 2722 4.690748 GCTTCTTGTGCTCATACACTACAA 59.309 41.667 0.00 0.00 41.30 2.41
2280 2723 4.245660 GCTTCTTGTGCTCATACACTACA 58.754 43.478 0.00 0.00 41.30 2.74
2281 2724 3.619038 GGCTTCTTGTGCTCATACACTAC 59.381 47.826 0.00 0.00 41.30 2.73
2282 2725 3.515502 AGGCTTCTTGTGCTCATACACTA 59.484 43.478 0.00 0.00 41.30 2.74
2283 2726 2.304180 AGGCTTCTTGTGCTCATACACT 59.696 45.455 0.00 0.00 41.30 3.55
2284 2727 2.417933 CAGGCTTCTTGTGCTCATACAC 59.582 50.000 0.00 0.00 41.10 2.90
2285 2728 2.302733 TCAGGCTTCTTGTGCTCATACA 59.697 45.455 0.00 0.00 0.00 2.29
2364 2807 7.505258 TGTATAGATTGATCGATTGGACCAAA 58.495 34.615 11.82 0.00 0.00 3.28
2450 2893 4.699735 ACATCCAGCGATTACAATTTGTGA 59.300 37.500 12.30 4.30 0.00 3.58
2459 2902 2.279741 TGAGCAACATCCAGCGATTAC 58.720 47.619 0.00 0.00 35.48 1.89
2630 4511 3.813724 AGATTGCATTCTGGATGTGATCG 59.186 43.478 10.25 0.00 38.07 3.69
2642 4523 0.743097 GCCACCTCCAGATTGCATTC 59.257 55.000 0.16 0.16 0.00 2.67
2706 4587 7.797121 AAAAGTCCCATAAACTTGATGGAAT 57.203 32.000 6.72 0.00 45.89 3.01
2707 4588 7.288852 TCAAAAAGTCCCATAAACTTGATGGAA 59.711 33.333 6.72 0.00 45.89 3.53
2708 4589 6.780031 TCAAAAAGTCCCATAAACTTGATGGA 59.220 34.615 6.72 0.00 45.89 3.41
2709 4590 6.991938 TCAAAAAGTCCCATAAACTTGATGG 58.008 36.000 0.00 0.00 43.12 3.51


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

AutoCloner maintained by Alex Coulton.