Multiple sequence alignment - TraesCS1D01G110100

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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 TraesCS1D01G110100 chr1D 100.000 3162 0 0 1 3162 103502227 103505388 0.000000e+00 5840.0
1 TraesCS1D01G110100 chr1A 95.532 3178 117 12 1 3162 100917147 100913979 0.000000e+00 5059.0
2 TraesCS1D01G110100 chr1B 94.725 2256 97 12 1 2239 162346753 162344503 0.000000e+00 3487.0
3 TraesCS1D01G110100 chr1B 94.481 761 40 2 2403 3162 162344504 162343745 0.000000e+00 1171.0
4 TraesCS1D01G110100 chr7D 78.188 298 52 11 2873 3159 249038180 249037885 9.010000e-41 178.0
5 TraesCS1D01G110100 chr7B 77.465 284 49 9 2889 3159 226146168 226145887 4.220000e-34 156.0
6 TraesCS1D01G110100 chr3D 78.226 248 42 10 2895 3131 32817882 32818128 7.070000e-32 148.0
7 TraesCS1D01G110100 chr2D 89.831 59 6 0 2767 2825 531254267 531254209 3.380000e-10 76.8


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 TraesCS1D01G110100 chr1D 103502227 103505388 3161 False 5840 5840 100.000 1 3162 1 chr1D.!!$F1 3161
1 TraesCS1D01G110100 chr1A 100913979 100917147 3168 True 5059 5059 95.532 1 3162 1 chr1A.!!$R1 3161
2 TraesCS1D01G110100 chr1B 162343745 162346753 3008 True 2329 3487 94.603 1 3162 2 chr1B.!!$R1 3161

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
27 28 0.322636 GGTCTCTCGGGTCTGTCTCA 60.323 60.0 0.0 0.0 0.0 3.27 F
849 860 0.682852 TGTTACACCCTCCGTTCCAG 59.317 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1267 1284 1.537202 GGTGCAGGACTCAACAATGTC 59.463 52.381 0.0 0.0 0.00 3.06 R
2843 2863 0.621082 TGTTCCACTGGTGTTCACCA 59.379 50.000 21.2 21.2 38.25 4.17 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
27 28 0.322636 GGTCTCTCGGGTCTGTCTCA 60.323 60.000 0.00 0.00 0.00 3.27
89 94 3.511934 CCCTAAGCTCTAGTGAAGTGTGT 59.488 47.826 0.00 0.00 0.00 3.72
285 293 5.731678 ACATATCCCTCCACTTAAAGGTTCT 59.268 40.000 0.00 0.00 0.00 3.01
294 302 7.178805 CCTCCACTTAAAGGTTCTACTCTACTT 59.821 40.741 0.00 0.00 0.00 2.24
313 321 7.840931 TCTACTTGCTCTTCACATTGAGAATA 58.159 34.615 0.00 0.00 32.44 1.75
355 363 4.651503 TCCTACTTTTGATTTGTTGGCCAA 59.348 37.500 16.05 16.05 0.00 4.52
453 462 7.364851 GGACCCATAAGTAGGATTAGCTATTCC 60.365 44.444 22.02 22.02 0.00 3.01
479 488 7.254898 CGTCAACAATATGTATGCCTCTTTCAT 60.255 37.037 0.00 0.00 0.00 2.57
672 681 7.125356 GTCTAACCAAGGGAGTATAGAAAGGAA 59.875 40.741 0.00 0.00 0.00 3.36
849 860 0.682852 TGTTACACCCTCCGTTCCAG 59.317 55.000 0.00 0.00 0.00 3.86
1137 1148 5.867174 GGTAAACATGTTGCCCAAATTCTAC 59.133 40.000 12.82 6.53 0.00 2.59
1171 1182 7.732222 TTATCCTCTTGCATTTATTTTGGGT 57.268 32.000 0.00 0.00 0.00 4.51
1192 1209 0.698238 TGGGGAGCAGTGCATTTACT 59.302 50.000 19.20 0.00 0.00 2.24
1261 1278 3.600388 AGAACTAGCCGGAATCAAACTG 58.400 45.455 5.05 0.00 0.00 3.16
1267 1284 1.335872 GCCGGAATCAAACTGTTGTGG 60.336 52.381 5.05 0.00 36.07 4.17
1334 1351 6.446318 TCAAAATCTCGCATAAAGCTTTTGT 58.554 32.000 18.47 3.89 41.56 2.83
1359 1376 1.069513 TGTACTTGTTGGACCGACCTG 59.930 52.381 9.52 4.73 39.86 4.00
1466 1483 8.961092 GCATGCATGTTATGTAGTAAAAATCTG 58.039 33.333 26.79 0.00 0.00 2.90
1542 1559 3.099619 CTACGGCTGGCAATGCACG 62.100 63.158 7.79 8.36 0.00 5.34
1879 1896 3.576550 TCAAACCAGTTGGCTATTTTCCC 59.423 43.478 0.00 0.00 37.85 3.97
1930 1947 9.449719 GATAGGAAAGTTGAGATTAGTTTTGGA 57.550 33.333 0.00 0.00 0.00 3.53
2017 2034 0.039256 GCAATGCTGCGTCCTTCAAA 60.039 50.000 0.00 0.00 39.20 2.69
2248 2267 7.098477 TGCCTTCAATTGATAAGGACAATTTG 58.902 34.615 24.48 0.00 44.27 2.32
2250 2269 6.536224 CCTTCAATTGATAAGGACAATTTGGC 59.464 38.462 17.95 0.00 44.27 4.52
2337 2356 7.195839 GGTAACTAGGTATTACTAGACACGG 57.804 44.000 7.20 0.00 42.40 4.94
2338 2357 6.768381 GGTAACTAGGTATTACTAGACACGGT 59.232 42.308 7.20 0.00 42.40 4.83
2359 2378 2.361737 GTCCAAGCTTGAGCCCCC 60.362 66.667 28.05 4.81 43.38 5.40
2372 2391 1.208165 AGCCCCCAGGGTTGAGTAAG 61.208 60.000 4.22 0.00 46.51 2.34
2382 2401 3.579151 AGGGTTGAGTAAGAGACAAGACC 59.421 47.826 0.00 0.00 0.00 3.85
2546 2565 2.607187 CAGAGCTTGTACAACCTACCG 58.393 52.381 3.59 0.00 0.00 4.02
2664 2684 5.369685 TTTTTGAGAGCATGCAAATCGTA 57.630 34.783 21.98 4.18 34.36 3.43
2729 2749 4.291249 ACCAGTATGTTCCCACAATAGGTT 59.709 41.667 0.00 0.00 36.16 3.50
2765 2785 0.320683 CACCAGATGGCGAGACACAA 60.321 55.000 0.00 0.00 39.32 3.33
2801 2821 2.237143 GTCATCATCTTGGAGTCACCCA 59.763 50.000 0.00 0.00 38.00 4.51
2843 2863 4.504858 CTTGGCGAAAACTCTAGTACCAT 58.495 43.478 0.00 0.00 0.00 3.55
2889 2909 1.215655 GGATGTCATCACGCGTAGGC 61.216 60.000 13.44 7.37 0.00 3.93
2898 2918 1.014044 CACGCGTAGGCAGAACACAT 61.014 55.000 13.44 0.00 39.92 3.21
2992 3012 3.628769 GGGGAGAAGTGTAGAGAGGACAT 60.629 52.174 0.00 0.00 0.00 3.06
2994 3014 3.314080 GGAGAAGTGTAGAGAGGACATCG 59.686 52.174 0.00 0.00 0.00 3.84
3143 3163 4.003648 GTGTCCAACCTTATCCTGAAGTG 58.996 47.826 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.959553 GTGTTGAGACAGACCCGAGA 59.040 55.000 0.00 0.00 36.20 4.04
27 28 2.767505 CCCTTTACAGCTCGAAGTGTT 58.232 47.619 4.75 0.00 0.00 3.32
89 94 3.431626 CCTCCGTGAAGCATGTAACCATA 60.432 47.826 0.00 0.00 0.00 2.74
285 293 6.434340 TCTCAATGTGAAGAGCAAGTAGAGTA 59.566 38.462 0.00 0.00 0.00 2.59
294 302 8.571461 AAGAAATATTCTCAATGTGAAGAGCA 57.429 30.769 4.09 0.00 39.61 4.26
355 363 9.315525 GTCAACAAAAGTCTAAGAAACTAGTCT 57.684 33.333 0.00 0.00 0.00 3.24
453 462 5.991328 AAGAGGCATACATATTGTTGACG 57.009 39.130 0.00 0.00 0.00 4.35
672 681 5.292345 GTGTGCCTTTAAACCGTTCATTTTT 59.708 36.000 0.00 0.00 0.00 1.94
849 860 9.391006 TGGTTTAGTTCACCATGATAAGTATTC 57.609 33.333 0.00 0.00 39.53 1.75
1149 1160 7.202029 CCATACCCAAAATAAATGCAAGAGGAT 60.202 37.037 0.00 0.00 0.00 3.24
1171 1182 2.509548 AGTAAATGCACTGCTCCCCATA 59.490 45.455 1.98 0.00 0.00 2.74
1267 1284 1.537202 GGTGCAGGACTCAACAATGTC 59.463 52.381 0.00 0.00 0.00 3.06
1334 1351 4.756135 GGTCGGTCCAACAAGTACAATTAA 59.244 41.667 0.00 0.00 35.97 1.40
1466 1483 2.292569 TGTGTGAGTCGTAGTCAGGAAC 59.707 50.000 0.00 0.00 0.00 3.62
1476 1493 5.355910 ACAACCTAAAATTTGTGTGAGTCGT 59.644 36.000 0.00 0.00 34.61 4.34
1542 1559 4.095036 GCTGTCACAAGGGCTAATTAAGTC 59.905 45.833 0.00 0.00 0.00 3.01
1678 1695 8.642908 TTGGATAGTCATATCACAAAACTACG 57.357 34.615 0.00 0.00 39.76 3.51
1879 1896 7.340232 TCAATAAGTCCTGGAATCAAGGATTTG 59.660 37.037 20.77 15.81 34.31 2.32
1930 1947 3.679389 CTTTTGGTGAGACACATAGCCT 58.321 45.455 0.00 0.00 35.86 4.58
2049 2066 6.016860 TGGAAGATTTGTGTTCACAAGATGAG 60.017 38.462 16.09 0.00 38.99 2.90
2221 2240 6.455360 TTGTCCTTATCAATTGAAGGCATC 57.545 37.500 17.98 12.27 41.80 3.91
2248 2267 1.687563 AATATTGCAAGGTACCCGCC 58.312 50.000 18.64 4.21 0.00 6.13
2250 2269 5.757886 CAACATAATATTGCAAGGTACCCG 58.242 41.667 8.74 0.68 0.00 5.28
2261 2280 4.857799 TCATGTGCGGCAACATAATATTG 58.142 39.130 3.23 0.36 38.75 1.90
2262 2281 5.710513 ATCATGTGCGGCAACATAATATT 57.289 34.783 3.23 0.00 38.75 1.28
2263 2282 5.710513 AATCATGTGCGGCAACATAATAT 57.289 34.783 3.23 3.51 38.75 1.28
2264 2283 5.512753 AAATCATGTGCGGCAACATAATA 57.487 34.783 3.23 1.42 38.75 0.98
2265 2284 4.389890 AAATCATGTGCGGCAACATAAT 57.610 36.364 3.23 0.00 38.75 1.28
2337 2356 1.745653 GGGCTCAAGCTTGGACAATAC 59.254 52.381 25.73 9.54 41.70 1.89
2338 2357 1.340991 GGGGCTCAAGCTTGGACAATA 60.341 52.381 25.73 4.85 41.70 1.90
2359 2378 4.561105 GTCTTGTCTCTTACTCAACCCTG 58.439 47.826 0.00 0.00 0.00 4.45
2372 2391 5.759506 TTCTCGAGATATGGTCTTGTCTC 57.240 43.478 17.44 0.00 39.12 3.36
2382 2401 5.177142 CCATTGTGCTCTTTCTCGAGATATG 59.823 44.000 17.44 9.52 32.74 1.78
2597 2617 6.959639 ACTTGCACTTTAATCCTCTTTGAA 57.040 33.333 0.00 0.00 0.00 2.69
2661 2681 8.867112 TGACTTCTATAAAGTTAAGGCATACG 57.133 34.615 0.00 0.00 32.09 3.06
2664 2684 9.606631 CTTCTGACTTCTATAAAGTTAAGGCAT 57.393 33.333 0.00 0.00 36.43 4.40
2713 2733 2.443632 TCACCAACCTATTGTGGGAACA 59.556 45.455 0.00 0.00 41.09 3.18
2765 2785 4.437682 TGATGACTTTCTCCTGGTTGTT 57.562 40.909 0.00 0.00 0.00 2.83
2801 2821 1.276421 GGGCTCTATGTATGCCGTCAT 59.724 52.381 0.00 0.00 46.97 3.06
2843 2863 0.621082 TGTTCCACTGGTGTTCACCA 59.379 50.000 21.20 21.20 38.25 4.17
2889 2909 4.687948 CCTTAGTGTCTCACATGTGTTCTG 59.312 45.833 24.63 13.51 36.74 3.02
2898 2918 3.157881 CTCCAGTCCTTAGTGTCTCACA 58.842 50.000 2.80 0.00 36.74 3.58


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

AutoCloner maintained by Alex Coulton.