Multiple sequence alignment - TraesCS5D01G212700

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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 TraesCS5D01G212700 chr5D 100.000 2459 0 0 1 2459 321899121 321901579 0.000000e+00 4542
1 TraesCS5D01G212700 chr5D 81.031 543 40 28 10 504 321888884 321889411 8.300000e-100 374
2 TraesCS5D01G212700 chr5B 92.267 2289 109 32 49 2300 373042289 373044546 0.000000e+00 3184
3 TraesCS5D01G212700 chr5B 84.950 299 25 7 40 318 372867242 372867540 4.000000e-73 285
4 TraesCS5D01G212700 chr5A 86.913 1895 142 50 442 2287 417044080 417045917 0.000000e+00 2028
5 TraesCS5D01G212700 chr5A 81.584 543 43 23 1 499 417029347 417029876 1.770000e-106 396
6 TraesCS5D01G212700 chr5A 79.355 310 31 15 143 419 417043452 417043761 1.160000e-43 187
7 TraesCS5D01G212700 chr3B 90.594 1297 60 32 49 1327 585727738 585728990 0.000000e+00 1663
8 TraesCS5D01G212700 chr3B 92.857 756 51 3 1702 2457 585729018 585729770 0.000000e+00 1094
9 TraesCS5D01G212700 chr4A 85.054 736 50 24 1132 1840 374661865 374661163 0.000000e+00 695
10 TraesCS5D01G212700 chr7A 85.294 714 50 24 1148 1840 3419746 3419067 0.000000e+00 686
11 TraesCS5D01G212700 chrUn 83.910 578 39 18 1285 1840 82536247 82536792 1.010000e-138 503


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 TraesCS5D01G212700 chr5D 321899121 321901579 2458 False 4542.0 4542 100.0000 1 2459 1 chr5D.!!$F2 2458
1 TraesCS5D01G212700 chr5D 321888884 321889411 527 False 374.0 374 81.0310 10 504 1 chr5D.!!$F1 494
2 TraesCS5D01G212700 chr5B 373042289 373044546 2257 False 3184.0 3184 92.2670 49 2300 1 chr5B.!!$F2 2251
3 TraesCS5D01G212700 chr5A 417043452 417045917 2465 False 1107.5 2028 83.1340 143 2287 2 chr5A.!!$F2 2144
4 TraesCS5D01G212700 chr5A 417029347 417029876 529 False 396.0 396 81.5840 1 499 1 chr5A.!!$F1 498
5 TraesCS5D01G212700 chr3B 585727738 585729770 2032 False 1378.5 1663 91.7255 49 2457 2 chr3B.!!$F1 2408
6 TraesCS5D01G212700 chr4A 374661163 374661865 702 True 695.0 695 85.0540 1132 1840 1 chr4A.!!$R1 708
7 TraesCS5D01G212700 chr7A 3419067 3419746 679 True 686.0 686 85.2940 1148 1840 1 chr7A.!!$R1 692
8 TraesCS5D01G212700 chrUn 82536247 82536792 545 False 503.0 503 83.9100 1285 1840 1 chrUn.!!$F1 555

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
956 1361 0.108756 AGCTTTCTCCGGTAAGTCGC 60.109 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2588 2.437651 TCCTTGAGTTGTGACACCATGA 59.562 45.455 2.45 0.0 0.0 3.07 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
75 78 7.343357 TGTTTTTCTTCTTCTTCCTGGAGTAA 58.657 34.615 0.00 0.00 0.00 2.24
84 87 0.323629 TCCTGGAGTAAACCAAGCGG 59.676 55.000 0.00 0.00 39.59 5.52
182 186 1.978454 GGAATCTGATCCTGCCCAAG 58.022 55.000 0.00 0.00 36.50 3.61
209 213 1.284982 CGGGTTGTGAGCAGTTCTCG 61.285 60.000 0.00 0.00 44.86 4.04
290 336 1.228245 TCCTGGTGAAACTGGCAGC 60.228 57.895 15.89 0.00 36.74 5.25
349 413 1.026182 TTCCACCATCATCAGCGCAC 61.026 55.000 11.47 0.00 0.00 5.34
350 414 1.746239 CCACCATCATCAGCGCACA 60.746 57.895 11.47 0.00 0.00 4.57
392 463 5.340803 TGTAAAGATGAACTCGGATTCTCG 58.659 41.667 2.03 0.00 0.00 4.04
405 476 2.449031 ATTCTCGGCGCACACAAGGA 62.449 55.000 10.83 0.00 0.00 3.36
427 505 4.564782 TGGAAGAGTCAAGATTGATGCT 57.435 40.909 0.00 0.00 39.73 3.79
437 515 9.495754 GAGTCAAGATTGATGCTATGTAAAAAC 57.504 33.333 0.00 0.00 39.73 2.43
689 1088 2.712057 ATGCAGAACTTTTTGCCTCG 57.288 45.000 2.33 0.00 39.54 4.63
719 1119 9.694137 AACTTATAAAATAGATACCGAGAGCAC 57.306 33.333 0.00 0.00 0.00 4.40
757 1158 4.818546 CCAGCAACTGATAAAGATCCGAAT 59.181 41.667 0.00 0.00 32.44 3.34
901 1306 2.224793 ACTTTCTGCACCTAAGGTTCCC 60.225 50.000 0.00 0.00 31.02 3.97
950 1355 0.901580 ACCCGAAGCTTTCTCCGGTA 60.902 55.000 19.42 0.00 40.30 4.02
954 1359 2.260481 CGAAGCTTTCTCCGGTAAGTC 58.740 52.381 0.00 1.47 0.00 3.01
955 1360 2.260481 GAAGCTTTCTCCGGTAAGTCG 58.740 52.381 0.00 0.00 0.00 4.18
956 1361 0.108756 AGCTTTCTCCGGTAAGTCGC 60.109 55.000 0.00 0.00 0.00 5.19
957 1362 1.082679 GCTTTCTCCGGTAAGTCGCC 61.083 60.000 0.00 0.00 0.00 5.54
990 1403 4.847444 GCCGAGGAAGAGCAGCCC 62.847 72.222 0.00 0.00 0.00 5.19
991 1404 3.080121 CCGAGGAAGAGCAGCCCT 61.080 66.667 0.00 0.00 0.00 5.19
992 1405 2.498726 CGAGGAAGAGCAGCCCTC 59.501 66.667 5.55 5.55 42.24 4.30
1090 1513 1.257743 TACTCTGTGTCTCCTGTGCC 58.742 55.000 0.00 0.00 0.00 5.01
1189 1618 2.810650 CTCCAGATGCAAGGTACGTAC 58.189 52.381 17.56 17.56 0.00 3.67
1463 1896 0.190815 ATGCCCCCAAACTGAAACCT 59.809 50.000 0.00 0.00 0.00 3.50
1471 1904 3.317993 CCCAAACTGAAACCTACCTTGTG 59.682 47.826 0.00 0.00 0.00 3.33
1516 1957 0.460311 GCTCCCGCTAGCTTCTGTAA 59.540 55.000 13.93 0.00 39.50 2.41
1558 2002 1.371183 CCCCTTCTTGTGTGCGAGA 59.629 57.895 0.00 0.00 33.47 4.04
1559 2003 0.671781 CCCCTTCTTGTGTGCGAGAG 60.672 60.000 0.00 0.00 36.56 3.20
1579 2024 8.945758 CGAGAGCTTATAAATCATCATTTTGG 57.054 34.615 0.00 0.00 33.95 3.28
1648 2112 2.884639 TGCTTAACCTTGACTTCTTGCC 59.115 45.455 0.00 0.00 0.00 4.52
1649 2113 2.095718 GCTTAACCTTGACTTCTTGCCG 60.096 50.000 0.00 0.00 0.00 5.69
1670 2158 1.721664 CCAGCATCATCCAAGCCACG 61.722 60.000 0.00 0.00 0.00 4.94
1687 2175 4.295051 GCCACGAGCAATCTTTGTTTTTA 58.705 39.130 0.00 0.00 42.97 1.52
1693 2181 6.183360 ACGAGCAATCTTTGTTTTTAGGTTGA 60.183 34.615 0.00 0.00 35.05 3.18
1840 2330 7.094118 TGGCTATTCTACATTTTTAACGCCTTT 60.094 33.333 0.00 0.00 33.99 3.11
1843 2333 5.440234 TCTACATTTTTAACGCCTTTGCA 57.560 34.783 0.00 0.00 37.32 4.08
2037 2527 4.518970 GCAGTAACATTGACCTGAAAAGGA 59.481 41.667 0.00 0.00 0.00 3.36
2077 2567 3.254827 CTCATGAGCTGCATTTCGATG 57.745 47.619 10.38 0.00 34.15 3.84
2079 2569 1.944709 CATGAGCTGCATTTCGATGGA 59.055 47.619 1.02 0.00 34.15 3.41
2086 2576 3.242188 GCTGCATTTCGATGGAATTTTGC 60.242 43.478 11.22 11.22 35.33 3.68
2089 2579 5.101628 TGCATTTCGATGGAATTTTGCTAC 58.898 37.500 16.04 0.00 35.57 3.58
2093 2583 6.567687 TTTCGATGGAATTTTGCTACTTCA 57.432 33.333 0.00 0.00 30.88 3.02
2095 2585 6.567687 TCGATGGAATTTTGCTACTTCAAA 57.432 33.333 0.00 0.00 34.47 2.69
2098 2588 8.087750 TCGATGGAATTTTGCTACTTCAAAAAT 58.912 29.630 5.87 0.00 45.50 1.82
2100 2590 9.206870 GATGGAATTTTGCTACTTCAAAAATCA 57.793 29.630 14.85 9.98 45.50 2.57
2107 2597 6.012658 TGCTACTTCAAAAATCATGGTGTC 57.987 37.500 0.00 0.00 0.00 3.67
2108 2598 5.534278 TGCTACTTCAAAAATCATGGTGTCA 59.466 36.000 0.00 0.00 0.00 3.58
2114 2604 5.830912 TCAAAAATCATGGTGTCACAACTC 58.169 37.500 5.12 0.00 0.00 3.01
2143 2634 2.867109 AGGTCTAACAGCTGCATGTT 57.133 45.000 15.27 17.22 45.19 2.71
2152 2643 9.046296 GTCTAACAGCTGCATGTTATAATACTT 57.954 33.333 15.27 0.00 42.97 2.24
2158 2649 7.377928 CAGCTGCATGTTATAATACTTTGAAGC 59.622 37.037 0.00 6.28 35.50 3.86
2161 2652 8.049655 TGCATGTTATAATACTTTGAAGCACA 57.950 30.769 0.00 0.00 0.00 4.57
2225 2716 5.984695 AGCACTTAGAATGTACAGTCTGA 57.015 39.130 30.63 23.28 36.34 3.27
2242 2733 6.171921 CAGTCTGAAAAGAATCAGGAGACAT 58.828 40.000 0.00 0.00 45.55 3.06
2333 2824 8.944212 AATAGTAATGTCACAAACTAAAACGC 57.056 30.769 7.30 0.00 0.00 4.84
2334 2825 5.437263 AGTAATGTCACAAACTAAAACGCG 58.563 37.500 3.53 3.53 0.00 6.01
2368 2859 7.663043 ATAGAACCAAACCAAACTTTACCAA 57.337 32.000 0.00 0.00 0.00 3.67
2376 2867 8.300286 CCAAACCAAACTTTACCAAATTGTTTT 58.700 29.630 0.00 0.00 0.00 2.43
2420 2911 3.931907 ACATCCTGCAGCCATACTTAA 57.068 42.857 8.66 0.00 0.00 1.85
2457 2948 8.362464 ACCTGAAATTAGTCTACATCACTACA 57.638 34.615 0.00 0.00 0.00 2.74
2458 2949 8.812972 ACCTGAAATTAGTCTACATCACTACAA 58.187 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.864882 CCAGGAAGAAGAAGAAAAACAAGATTC 59.135 37.037 0.00 0.00 0.00 2.52
84 87 4.383173 TGGATGCATGATGATACACAGAC 58.617 43.478 2.46 0.00 0.00 3.51
85 88 4.693042 TGGATGCATGATGATACACAGA 57.307 40.909 2.46 0.00 0.00 3.41
86 89 5.278315 CCTTTGGATGCATGATGATACACAG 60.278 44.000 2.46 0.00 0.00 3.66
87 90 4.581409 CCTTTGGATGCATGATGATACACA 59.419 41.667 2.46 0.00 0.00 3.72
182 186 3.332493 CTCACAACCCGCTGCATGC 62.332 63.158 11.82 11.82 38.57 4.06
188 192 1.598130 GAACTGCTCACAACCCGCT 60.598 57.895 0.00 0.00 0.00 5.52
290 336 2.126228 TAGCCGGCGAGTTTGACG 60.126 61.111 23.20 0.00 41.03 4.35
392 463 1.926511 CTTCCATCCTTGTGTGCGCC 61.927 60.000 4.18 0.00 0.00 6.53
405 476 5.113446 AGCATCAATCTTGACTCTTCCAT 57.887 39.130 0.00 0.00 40.49 3.41
427 505 5.998981 TCCGAGCTTTTCTGGTTTTTACATA 59.001 36.000 0.00 0.00 0.00 2.29
437 515 4.034510 GTGAACATATCCGAGCTTTTCTGG 59.965 45.833 0.00 0.00 0.00 3.86
582 977 1.068474 CAGTTCACCTTTACGCCTCG 58.932 55.000 0.00 0.00 0.00 4.63
689 1088 9.485206 TCTCGGTATCTATTTTATAAGTTTGGC 57.515 33.333 0.00 0.00 0.00 4.52
719 1119 2.840974 CTGGTAGGACCTGCAAACG 58.159 57.895 12.04 0.00 39.58 3.60
757 1158 6.599244 CCAGATTGTTCCTTTGCTATCTGTTA 59.401 38.462 0.00 0.00 40.63 2.41
807 1208 3.733960 CTCGTGGGCTCGACGTGA 61.734 66.667 0.00 0.00 38.04 4.35
826 1231 2.717809 GCCACTCGCTTCGTCGTTC 61.718 63.158 0.00 0.00 0.00 3.95
832 1237 1.083489 TTTTATGGCCACTCGCTTCG 58.917 50.000 8.16 0.00 37.74 3.79
901 1306 1.335324 CCAAAGTTGCGAGGAAAGCAG 60.335 52.381 0.00 0.00 46.01 4.24
990 1403 2.099921 CCTGTAGTCCATGAAGACGGAG 59.900 54.545 0.00 0.00 41.83 4.63
991 1404 2.100197 CCTGTAGTCCATGAAGACGGA 58.900 52.381 0.00 0.00 41.83 4.69
992 1405 1.137086 CCCTGTAGTCCATGAAGACGG 59.863 57.143 0.00 0.00 41.83 4.79
1189 1618 0.175989 GTGGAAAGAGGAGGGCGTAG 59.824 60.000 0.00 0.00 0.00 3.51
1194 1623 0.615850 GGTCTGTGGAAAGAGGAGGG 59.384 60.000 0.00 0.00 0.00 4.30
1450 1883 3.951680 ACACAAGGTAGGTTTCAGTTTGG 59.048 43.478 0.00 0.00 0.00 3.28
1463 1896 2.281208 GCCGGTGCACACAAGGTA 60.281 61.111 20.43 0.00 37.47 3.08
1504 1945 7.226720 TGAAAAGTTTCAGGTTACAGAAGCTAG 59.773 37.037 2.32 0.00 41.49 3.42
1558 2002 9.193806 ACAGACCAAAATGATGATTTATAAGCT 57.806 29.630 0.00 0.00 31.18 3.74
1579 2024 3.093057 ACAGGTCATGAGGAGTACAGAC 58.907 50.000 0.00 0.00 0.00 3.51
1648 2112 1.442526 GGCTTGGATGATGCTGGTCG 61.443 60.000 0.00 0.00 0.00 4.79
1649 2113 0.394762 TGGCTTGGATGATGCTGGTC 60.395 55.000 0.00 0.00 0.00 4.02
1670 2158 6.978080 TGTCAACCTAAAAACAAAGATTGCTC 59.022 34.615 0.00 0.00 0.00 4.26
1681 2169 9.612620 CATTCAGAATAGTGTCAACCTAAAAAC 57.387 33.333 0.00 0.00 0.00 2.43
1840 2330 8.537728 AGGAATAATGTTATGGAGAATTTGCA 57.462 30.769 0.00 0.00 0.00 4.08
2037 2527 6.485830 TGAGCCTAACTAAGTTGCTCATAT 57.514 37.500 14.57 0.00 42.45 1.78
2073 2563 7.636259 TTTTTGAAGTAGCAAAATTCCATCG 57.364 32.000 0.00 0.00 44.45 3.84
2074 2564 9.206870 TGATTTTTGAAGTAGCAAAATTCCATC 57.793 29.630 15.74 10.83 44.45 3.51
2077 2567 8.445493 CCATGATTTTTGAAGTAGCAAAATTCC 58.555 33.333 15.74 6.05 44.45 3.01
2079 2569 8.776470 CACCATGATTTTTGAAGTAGCAAAATT 58.224 29.630 0.00 0.00 44.45 1.82
2086 2576 6.969366 TGTGACACCATGATTTTTGAAGTAG 58.031 36.000 2.45 0.00 0.00 2.57
2089 2579 6.275335 AGTTGTGACACCATGATTTTTGAAG 58.725 36.000 2.45 0.00 0.00 3.02
2093 2583 5.850557 TGAGTTGTGACACCATGATTTTT 57.149 34.783 2.45 0.00 0.00 1.94
2095 2585 4.279169 CCTTGAGTTGTGACACCATGATTT 59.721 41.667 2.45 0.00 0.00 2.17
2098 2588 2.437651 TCCTTGAGTTGTGACACCATGA 59.562 45.455 2.45 0.00 0.00 3.07
2100 2590 3.795688 ATCCTTGAGTTGTGACACCAT 57.204 42.857 2.45 0.00 0.00 3.55
2107 2597 7.444183 TGTTAGACCTTTAATCCTTGAGTTGTG 59.556 37.037 0.00 0.00 0.00 3.33
2108 2598 7.514721 TGTTAGACCTTTAATCCTTGAGTTGT 58.485 34.615 0.00 0.00 0.00 3.32
2114 2604 5.163713 GCAGCTGTTAGACCTTTAATCCTTG 60.164 44.000 16.64 0.00 0.00 3.61
2152 2643 9.761504 TGAATTTTTCTTATGATTGTGCTTCAA 57.238 25.926 0.00 0.00 40.53 2.69
2225 2716 8.986991 AGATACTGTATGTCTCCTGATTCTTTT 58.013 33.333 4.79 0.00 0.00 2.27
2242 2733 8.245195 TGTGGCAGTTATCAATAGATACTGTA 57.755 34.615 0.00 0.00 37.72 2.74
2314 2805 4.281525 ACGCGTTTTAGTTTGTGACATT 57.718 36.364 5.58 0.00 0.00 2.71
2333 2824 5.151389 GGTTTGGTTCTATAACTGCAAACG 58.849 41.667 14.09 0.00 42.51 3.60
2334 2825 6.079424 TGGTTTGGTTCTATAACTGCAAAC 57.921 37.500 13.01 13.01 41.76 2.93
2368 2859 6.649155 ACCTGAGCTGGTTTTTAAAACAATT 58.351 32.000 20.17 2.94 36.89 2.32
2376 2867 7.122948 TGTTCTTTTTACCTGAGCTGGTTTTTA 59.877 33.333 0.33 0.00 41.22 1.52
2378 2869 5.420739 TGTTCTTTTTACCTGAGCTGGTTTT 59.579 36.000 0.33 0.00 41.22 2.43
2420 2911 6.476378 ACTAATTTCAGGTTCATGCTACAGT 58.524 36.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.