Multiple sequence alignment - TraesCS6A01G021700

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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 TraesCS6A01G021700 chr6A 100.000 2882 0 0 1 2882 10917614 10920495 0.000000e+00 5323
1 TraesCS6A01G021700 chr6A 93.642 2894 158 8 1 2882 10559031 10561910 0.000000e+00 4301
2 TraesCS6A01G021700 chr6A 93.642 2894 157 9 1 2882 10516469 10519347 0.000000e+00 4300
3 TraesCS6A01G021700 chr6A 94.481 2283 118 2 1 2275 10600166 10602448 0.000000e+00 3511
4 TraesCS6A01G021700 chr6A 91.326 611 36 5 2274 2882 10609521 10610116 0.000000e+00 819
5 TraesCS6A01G021700 chr6A 91.589 321 22 3 2508 2826 588602430 588602113 3.410000e-119 438
6 TraesCS6A01G021700 chr6D 96.022 2891 93 7 1 2882 9792513 9795390 0.000000e+00 4682
7 TraesCS6A01G021700 chr6D 93.944 2906 136 9 1 2882 9586911 9589800 0.000000e+00 4355
8 TraesCS6A01G021700 chr6D 78.286 175 38 0 1119 1293 9588617 9588791 2.350000e-21 113
9 TraesCS6A01G021700 chr6B 92.644 2148 126 9 151 2270 17532962 17535105 0.000000e+00 3062
10 TraesCS6A01G021700 chr6B 90.494 2167 165 17 132 2270 17704939 17702786 0.000000e+00 2822
11 TraesCS6A01G021700 chr6B 92.938 1501 76 12 738 2209 17685747 17687246 0.000000e+00 2158
12 TraesCS6A01G021700 chr6B 79.063 363 70 4 1173 1532 17534179 17534538 7.980000e-61 244
13 TraesCS6A01G021700 chr6B 86.266 233 21 8 2011 2236 17535067 17535295 2.870000e-60 243
14 TraesCS6A01G021700 chr6B 88.095 210 12 3 2304 2510 17687248 17687447 1.330000e-58 237
15 TraesCS6A01G021700 chr6B 94.355 124 7 0 1 124 17532841 17532964 1.050000e-44 191
16 TraesCS6A01G021700 chr6B 79.508 244 48 2 1551 1793 17703908 17703666 3.820000e-39 172
17 TraesCS6A01G021700 chr5A 92.744 317 20 2 2504 2819 549204648 549204334 3.390000e-124 455
18 TraesCS6A01G021700 chr1D 92.834 307 20 2 2509 2814 276505100 276504795 7.330000e-121 444
19 TraesCS6A01G021700 chr3D 92.557 309 21 2 2509 2816 22573667 22573974 2.640000e-120 442


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 TraesCS6A01G021700 chr6A 10917614 10920495 2881 False 5323.0 5323 100.0000 1 2882 1 chr6A.!!$F5 2881
1 TraesCS6A01G021700 chr6A 10559031 10561910 2879 False 4301.0 4301 93.6420 1 2882 1 chr6A.!!$F2 2881
2 TraesCS6A01G021700 chr6A 10516469 10519347 2878 False 4300.0 4300 93.6420 1 2882 1 chr6A.!!$F1 2881
3 TraesCS6A01G021700 chr6A 10600166 10602448 2282 False 3511.0 3511 94.4810 1 2275 1 chr6A.!!$F3 2274
4 TraesCS6A01G021700 chr6A 10609521 10610116 595 False 819.0 819 91.3260 2274 2882 1 chr6A.!!$F4 608
5 TraesCS6A01G021700 chr6D 9792513 9795390 2877 False 4682.0 4682 96.0220 1 2882 1 chr6D.!!$F1 2881
6 TraesCS6A01G021700 chr6D 9586911 9589800 2889 False 2234.0 4355 86.1150 1 2882 2 chr6D.!!$F2 2881
7 TraesCS6A01G021700 chr6B 17702786 17704939 2153 True 1497.0 2822 85.0010 132 2270 2 chr6B.!!$R1 2138
8 TraesCS6A01G021700 chr6B 17685747 17687447 1700 False 1197.5 2158 90.5165 738 2510 2 chr6B.!!$F2 1772
9 TraesCS6A01G021700 chr6B 17532841 17535295 2454 False 935.0 3062 88.0820 1 2270 4 chr6B.!!$F1 2269

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
290 293 1.071542 ACACACCGAATGTCATCCACA 59.928 47.619 0.0 0.0 40.64 4.17 F
452 455 1.079750 GGAGACGACTTCTGGTGGC 60.080 63.158 0.0 0.0 33.22 5.01 F
1337 1340 1.280421 CCTAGGCAGGAAAGAAGCAGT 59.720 52.381 0.0 0.0 45.91 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1226 1229 0.540133 TGCTCCATCTTGCTTGGCAA 60.540 50.000 0.0 0.0 46.80 4.52 R
1440 1443 1.400242 GCATCGTCAACAGACTTTGCC 60.400 52.381 0.0 0.0 34.48 4.52 R
2302 2492 2.574006 ATCATTATGCCGCTCCATGT 57.426 45.000 0.0 0.0 0.00 3.21 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
251 254 3.970410 CTCCAGTTGGGGCCTGCA 61.970 66.667 0.84 0.00 37.22 4.41
290 293 1.071542 ACACACCGAATGTCATCCACA 59.928 47.619 0.00 0.00 40.64 4.17
452 455 1.079750 GGAGACGACTTCTGGTGGC 60.080 63.158 0.00 0.00 33.22 5.01
554 557 2.169832 GGATACGCATGCACCTACAT 57.830 50.000 19.57 0.43 0.00 2.29
556 559 2.878406 GGATACGCATGCACCTACATTT 59.122 45.455 19.57 0.00 0.00 2.32
624 627 2.439409 TCCATTACGACGAGAAGGACA 58.561 47.619 0.00 0.00 0.00 4.02
645 648 2.696775 TCCTGGTCTGGGTTTGAAGTA 58.303 47.619 0.00 0.00 0.00 2.24
681 684 7.439381 ACCTACAACAATCTCGAAAAGAGTAA 58.561 34.615 0.00 0.00 46.86 2.24
732 735 5.143916 TCGCGCTCAGAAATCTATTTTTC 57.856 39.130 5.56 0.00 36.13 2.29
885 888 3.873361 CGCTTATGACCTCACATTCATGT 59.127 43.478 0.00 0.00 42.84 3.21
1050 1053 5.957842 TGTTATTTCTCACCACCATTGTC 57.042 39.130 0.00 0.00 0.00 3.18
1337 1340 1.280421 CCTAGGCAGGAAAGAAGCAGT 59.720 52.381 0.00 0.00 45.91 4.40
1468 1471 5.530519 GTCTGTTGACGATGCATTAAAGA 57.469 39.130 0.00 0.00 33.15 2.52
1484 1487 3.726557 AAAGAATGGTGCCATCTCTCA 57.273 42.857 3.96 0.00 35.31 3.27
1489 1492 3.726557 ATGGTGCCATCTCTCAGAAAA 57.273 42.857 0.00 0.00 29.42 2.29
1541 1544 0.538287 AGGAAAGAAGGCACCACTGC 60.538 55.000 0.00 0.00 43.41 4.40
1668 1707 1.135859 GGTGTCATTTCTCAGCAAGCG 60.136 52.381 0.00 0.00 33.12 4.68
1669 1708 0.518636 TGTCATTTCTCAGCAAGCGC 59.481 50.000 0.00 0.00 38.99 5.92
1709 1748 2.192263 CTCCCCTAGCAGGAAAGAAGT 58.808 52.381 4.00 0.00 37.67 3.01
1786 1825 1.122632 TGAAACCGCCACCAGACCTA 61.123 55.000 0.00 0.00 0.00 3.08
1846 1891 2.119029 GCAATGAAGTACGGGGCCC 61.119 63.158 15.76 15.76 0.00 5.80
1916 1961 0.043053 CCTATTCACGCGCAACATCG 60.043 55.000 5.73 0.00 0.00 3.84
2243 2290 1.295792 GGAGCCGCGAATCATGTTTA 58.704 50.000 8.23 0.00 0.00 2.01
2252 2299 5.799936 CCGCGAATCATGTTTAATTGTCTTT 59.200 36.000 8.23 0.00 0.00 2.52
2302 2492 5.208463 TGCTCGTCAATGTATTATGGCTA 57.792 39.130 0.00 0.00 0.00 3.93
2401 2591 3.197983 TCATCCAACCTCCCTACCAATT 58.802 45.455 0.00 0.00 0.00 2.32
2402 2592 3.596046 TCATCCAACCTCCCTACCAATTT 59.404 43.478 0.00 0.00 0.00 1.82
2403 2593 4.045334 TCATCCAACCTCCCTACCAATTTT 59.955 41.667 0.00 0.00 0.00 1.82
2404 2594 4.479156 TCCAACCTCCCTACCAATTTTT 57.521 40.909 0.00 0.00 0.00 1.94
2529 2724 1.285078 GGCCTCCTTTGGTTCATAGGT 59.715 52.381 0.00 0.00 34.84 3.08
2530 2725 2.508300 GGCCTCCTTTGGTTCATAGGTA 59.492 50.000 0.00 0.00 34.84 3.08
2531 2726 3.433740 GGCCTCCTTTGGTTCATAGGTAG 60.434 52.174 0.00 2.42 34.84 3.18
2537 2734 7.615757 CCTCCTTTGGTTCATAGGTAGAAAAAT 59.384 37.037 4.75 0.00 34.84 1.82
2539 2736 7.335924 TCCTTTGGTTCATAGGTAGAAAAATCG 59.664 37.037 4.75 0.00 34.84 3.34
2740 2939 6.730447 TGATTCCATTCCTACAATCCAAAGA 58.270 36.000 0.00 0.00 0.00 2.52
2860 3060 2.669391 GCTGGGCACTTCAGATTTTTCG 60.669 50.000 0.00 0.00 34.36 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.153479 TCGCACTATTCATGCATTTATAGTTT 57.847 30.769 20.28 5.46 43.57 2.66
32 33 5.471116 ACATGTATCGCACTATTCATGCATT 59.529 36.000 0.00 0.00 43.57 3.56
188 190 5.821204 ACTCGGATTCAAAGTTTCAAACTG 58.179 37.500 2.78 0.00 41.91 3.16
251 254 2.012673 GTGTACCGACGATCCTACACT 58.987 52.381 0.00 0.00 37.21 3.55
341 344 3.066621 GCACACAAACTTCATGAAGGACA 59.933 43.478 33.11 2.05 42.53 4.02
452 455 0.603707 AGGTGTGACATGAGCAACGG 60.604 55.000 0.00 0.00 0.00 4.44
608 611 2.422479 CAGGATGTCCTTCTCGTCGTAA 59.578 50.000 0.00 0.00 46.09 3.18
624 627 2.065799 ACTTCAAACCCAGACCAGGAT 58.934 47.619 0.00 0.00 0.00 3.24
645 648 6.704310 AGATTGTTGTAGGTACCATTACGTT 58.296 36.000 15.94 0.00 0.00 3.99
681 684 2.303022 TGCTCTCGAAATCCAGGACTTT 59.697 45.455 0.00 0.00 0.00 2.66
732 735 4.895889 TCTCTATGTATGGACTGTGGGAAG 59.104 45.833 0.00 0.00 0.00 3.46
798 801 2.158385 TGGTAACCCATTTGTGGAAGCT 60.158 45.455 0.00 0.00 35.17 3.74
854 857 3.071479 GAGGTCATAAGCGGTCAACAAA 58.929 45.455 0.00 0.00 0.00 2.83
889 892 6.881602 AGAGACAATGTGAGGTTAAGAAATCC 59.118 38.462 0.00 0.00 0.00 3.01
896 899 9.162764 GCTTTTATAGAGACAATGTGAGGTTAA 57.837 33.333 0.00 0.00 0.00 2.01
898 901 6.599638 GGCTTTTATAGAGACAATGTGAGGTT 59.400 38.462 0.00 0.00 0.00 3.50
1170 1173 1.266178 TCTTGATGGACTTCTCGGCA 58.734 50.000 0.00 0.00 0.00 5.69
1204 1207 2.583441 CGGCCTCTTCTGGTGTGGA 61.583 63.158 0.00 0.00 0.00 4.02
1226 1229 0.540133 TGCTCCATCTTGCTTGGCAA 60.540 50.000 0.00 0.00 46.80 4.52
1440 1443 1.400242 GCATCGTCAACAGACTTTGCC 60.400 52.381 0.00 0.00 34.48 4.52
1468 1471 3.726557 TTTCTGAGAGATGGCACCATT 57.273 42.857 3.16 0.00 36.70 3.16
1484 1487 4.781934 AGAACTTGTACCAGCTGTTTTCT 58.218 39.130 13.81 0.94 0.00 2.52
1489 1492 4.884247 GTAGAAGAACTTGTACCAGCTGT 58.116 43.478 13.81 3.45 34.42 4.40
1541 1544 2.703416 TGGTGAACATCTTAGCAGCAG 58.297 47.619 0.00 0.00 34.28 4.24
1786 1825 2.664402 TCCTTCTTTGCTGCCTCTTT 57.336 45.000 0.00 0.00 0.00 2.52
1797 1842 1.401905 GATTTCGCGGCATCCTTCTTT 59.598 47.619 6.13 0.00 0.00 2.52
1846 1891 4.527583 GGCGGCCTGCTGAGAGAG 62.528 72.222 12.87 0.00 45.43 3.20
2049 2094 2.738846 AGCAAGTCAAGCATGTCTTACG 59.261 45.455 1.25 0.00 33.94 3.18
2229 2276 6.742718 AGAAAGACAATTAAACATGATTCGCG 59.257 34.615 0.00 0.00 0.00 5.87
2302 2492 2.574006 ATCATTATGCCGCTCCATGT 57.426 45.000 0.00 0.00 0.00 3.21
2442 2634 7.124750 AGGTAGAATCAATGGGGAGAAAAATTG 59.875 37.037 0.00 0.00 0.00 2.32
2443 2635 7.191918 AGGTAGAATCAATGGGGAGAAAAATT 58.808 34.615 0.00 0.00 0.00 1.82
2529 2724 9.813446 GACTTTCCTATTCCTACGATTTTTCTA 57.187 33.333 0.00 0.00 0.00 2.10
2530 2725 8.319146 TGACTTTCCTATTCCTACGATTTTTCT 58.681 33.333 0.00 0.00 0.00 2.52
2531 2726 8.488651 TGACTTTCCTATTCCTACGATTTTTC 57.511 34.615 0.00 0.00 0.00 2.29
2537 2734 6.607970 TCCTATGACTTTCCTATTCCTACGA 58.392 40.000 0.00 0.00 0.00 3.43
2539 2736 9.495572 CATTTCCTATGACTTTCCTATTCCTAC 57.504 37.037 0.00 0.00 0.00 3.18
2608 2805 4.346730 TGATGTGAATCAAAGGGCATCTT 58.653 39.130 10.68 0.00 37.28 2.40
2716 2915 6.730447 TCTTTGGATTGTAGGAATGGAATCA 58.270 36.000 0.00 0.00 0.00 2.57
2733 2932 8.360390 GGAAAAATTCTTTTAGAGCTCTTTGGA 58.640 33.333 23.84 12.29 34.83 3.53
2775 2974 9.443323 TGGACGAATCTTGTAAGAATTTCATAA 57.557 29.630 0.00 0.00 38.77 1.90


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

AutoCloner maintained by Alex Coulton.