Multiple sequence alignment - TraesCS5D01G127500

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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 TraesCS5D01G127500 chr5D 100.000 2356 0 0 1 2356 197839898 197837543 0 4351
1 TraesCS5D01G127500 chr5D 93.260 2359 152 6 1 2356 79865257 79867611 0 3469
2 TraesCS5D01G127500 chr4D 94.534 2360 121 7 1 2356 483696361 483698716 0 3637
3 TraesCS5D01G127500 chr4D 93.896 2359 136 7 1 2356 135006219 135003866 0 3552
4 TraesCS5D01G127500 chr4D 93.184 2362 148 11 1 2356 241143243 241140889 0 3458
5 TraesCS5D01G127500 chr7D 95.380 1883 81 5 1 1880 579015580 579017459 0 2990
6 TraesCS5D01G127500 chr3A 95.105 1900 87 5 1 1897 191855551 191857447 0 2988
7 TraesCS5D01G127500 chr1A 95.228 1886 84 5 1 1883 238109743 238107861 0 2979
8 TraesCS5D01G127500 chr1A 94.950 1901 89 6 1 1897 278506348 278508245 0 2972
9 TraesCS5D01G127500 chr6B 93.029 2037 122 10 1 2027 53079009 53081035 0 2957
10 TraesCS5D01G127500 chr1D 94.956 793 39 1 1565 2356 185763599 185764391 0 1242
11 TraesCS5D01G127500 chr5B 93.367 799 52 1 1559 2356 87747596 87748394 0 1181
12 TraesCS5D01G127500 chr2A 95.382 498 22 1 1860 2356 735187105 735187602 0 791
13 TraesCS5D01G127500 chr7B 95.181 498 23 1 1860 2356 743080627 743081124 0 785
14 TraesCS5D01G127500 chr3B 95.181 498 23 1 1860 2356 92194034 92194531 0 785


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 TraesCS5D01G127500 chr5D 197837543 197839898 2355 True 4351 4351 100.000 1 2356 1 chr5D.!!$R1 2355
1 TraesCS5D01G127500 chr5D 79865257 79867611 2354 False 3469 3469 93.260 1 2356 1 chr5D.!!$F1 2355
2 TraesCS5D01G127500 chr4D 483696361 483698716 2355 False 3637 3637 94.534 1 2356 1 chr4D.!!$F1 2355
3 TraesCS5D01G127500 chr4D 135003866 135006219 2353 True 3552 3552 93.896 1 2356 1 chr4D.!!$R1 2355
4 TraesCS5D01G127500 chr4D 241140889 241143243 2354 True 3458 3458 93.184 1 2356 1 chr4D.!!$R2 2355
5 TraesCS5D01G127500 chr7D 579015580 579017459 1879 False 2990 2990 95.380 1 1880 1 chr7D.!!$F1 1879
6 TraesCS5D01G127500 chr3A 191855551 191857447 1896 False 2988 2988 95.105 1 1897 1 chr3A.!!$F1 1896
7 TraesCS5D01G127500 chr1A 238107861 238109743 1882 True 2979 2979 95.228 1 1883 1 chr1A.!!$R1 1882
8 TraesCS5D01G127500 chr1A 278506348 278508245 1897 False 2972 2972 94.950 1 1897 1 chr1A.!!$F1 1896
9 TraesCS5D01G127500 chr6B 53079009 53081035 2026 False 2957 2957 93.029 1 2027 1 chr6B.!!$F1 2026
10 TraesCS5D01G127500 chr1D 185763599 185764391 792 False 1242 1242 94.956 1565 2356 1 chr1D.!!$F1 791
11 TraesCS5D01G127500 chr5B 87747596 87748394 798 False 1181 1181 93.367 1559 2356 1 chr5B.!!$F1 797

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
388 389 0.039618 AACCCGGCACATCCAATTCT 59.96 50.0 0.0 0.0 34.01 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2089 1.315257 CGGGAAAGTCTGGCAATGGG 61.315 60.0 0.0 0.0 0.0 4.0 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
58 59 7.064728 GTCATGTAATGGTTTAGAAGAGTCACC 59.935 40.741 0.00 0.00 46.73 4.02
70 71 1.152312 AGTCACCGTCCTGTTCCCT 60.152 57.895 0.00 0.00 0.00 4.20
73 74 2.526873 ACCGTCCTGTTCCCTGCT 60.527 61.111 0.00 0.00 0.00 4.24
90 91 1.342074 GCTGGGCTTTTTCCCTTCTT 58.658 50.000 0.12 0.00 46.67 2.52
109 110 6.680874 TTCTTGACTAGACGAAGGAGATAC 57.319 41.667 0.00 0.00 30.90 2.24
126 127 5.371526 GAGATACTCATTCCATTCAGGCAA 58.628 41.667 0.00 0.00 37.29 4.52
142 143 1.455849 CAAGTGAGGAAGGGTGGCA 59.544 57.895 0.00 0.00 0.00 4.92
170 171 2.158310 TGACCCTGTCTTCTCTCTTGGA 60.158 50.000 0.00 0.00 33.15 3.53
249 250 2.253513 CCAACGAGTGGCGGATTTT 58.746 52.632 0.00 0.00 46.49 1.82
250 251 0.596082 CCAACGAGTGGCGGATTTTT 59.404 50.000 0.00 0.00 46.49 1.94
292 293 1.270907 GACGCTGGGGAGATCCATAT 58.729 55.000 0.47 0.00 36.05 1.78
298 299 4.036518 GCTGGGGAGATCCATATATCTGT 58.963 47.826 0.47 0.00 36.33 3.41
301 302 6.239543 GCTGGGGAGATCCATATATCTGTATG 60.240 46.154 0.47 0.00 36.33 2.39
326 327 7.147724 TGGAGTCTTTCTCACTCAGTAAAGAAA 60.148 37.037 11.98 11.98 44.40 2.52
388 389 0.039618 AACCCGGCACATCCAATTCT 59.960 50.000 0.00 0.00 34.01 2.40
403 404 5.139727 TCCAATTCTGATCAACAACTTGGT 58.860 37.500 15.33 0.00 34.79 3.67
424 425 2.289565 GGTATGGCTGAGTGGCTTAAC 58.710 52.381 0.00 0.00 42.34 2.01
426 427 0.613260 ATGGCTGAGTGGCTTAACGA 59.387 50.000 0.00 0.00 42.34 3.85
428 429 0.796927 GGCTGAGTGGCTTAACGAAC 59.203 55.000 0.00 0.00 38.32 3.95
437 438 1.335597 GGCTTAACGAACTGGTTTGCC 60.336 52.381 0.00 0.00 39.37 4.52
457 458 4.391830 TGCCAAATCGACATACAAGAAGAC 59.608 41.667 0.00 0.00 0.00 3.01
466 467 7.418408 TCGACATACAAGAAGACTGTATCATC 58.582 38.462 0.00 0.00 0.00 2.92
486 487 2.026636 TCGGTTCGAATCCCATTTCCTT 60.027 45.455 0.00 0.00 31.06 3.36
530 531 4.273480 CGGGCGAAATTACATGAGAGAAAT 59.727 41.667 0.00 0.00 0.00 2.17
604 613 2.359975 CGGAGCGCCCCTTTCTTT 60.360 61.111 6.33 0.00 0.00 2.52
618 627 3.430236 CCTTTCTTTTTCTTGGTGGCGTT 60.430 43.478 0.00 0.00 0.00 4.84
620 629 3.878160 TCTTTTTCTTGGTGGCGTTTT 57.122 38.095 0.00 0.00 0.00 2.43
640 649 1.933021 TAGCGAAGAAGACCTTCCCA 58.067 50.000 6.17 0.00 46.65 4.37
692 701 1.163554 GGTTCTTGAGCAAGCTCCTG 58.836 55.000 18.54 11.37 42.09 3.86
700 709 2.341101 GCAAGCTCCTGCACTGCAT 61.341 57.895 3.64 0.00 44.49 3.96
880 889 4.657814 ATTTTAGTGGGAAGAGCAAGGA 57.342 40.909 0.00 0.00 0.00 3.36
903 912 3.853475 CATTGCCCTTGAAATCCTTCAC 58.147 45.455 0.00 0.00 41.34 3.18
922 931 3.767131 TCACTGGTTCGAATCCACATCTA 59.233 43.478 5.84 0.00 0.00 1.98
1052 1064 3.238108 AGTGATCAGTCCGCTAGTTTG 57.762 47.619 0.00 0.00 0.00 2.93
1084 1096 3.568430 ACTCGGTGTTCCTTTTCCATTTC 59.432 43.478 0.00 0.00 0.00 2.17
1106 1118 5.455872 TCCTTCCAATAGTTCGACCTATCT 58.544 41.667 2.67 0.00 0.00 1.98
1157 1169 1.983119 GATCCCTCCGGTGATGCCAA 61.983 60.000 4.76 0.00 36.97 4.52
1305 1318 7.546667 CCATGATGACCTTTTTACTGATTTTGG 59.453 37.037 0.00 0.00 0.00 3.28
1307 1320 5.860941 TGACCTTTTTACTGATTTTGGCA 57.139 34.783 0.00 0.00 0.00 4.92
1318 1331 4.161001 ACTGATTTTGGCAATTGGATCTCC 59.839 41.667 7.72 0.00 0.00 3.71
1342 1355 2.688477 TGAATGGAAAAGGGGTGCTTT 58.312 42.857 0.00 0.00 0.00 3.51
1343 1356 2.632512 TGAATGGAAAAGGGGTGCTTTC 59.367 45.455 0.00 0.00 0.00 2.62
1505 1518 2.435805 CCAGAAGCAAGGAGTATGCCTA 59.564 50.000 0.00 0.00 44.91 3.93
1517 1530 2.229543 AGTATGCCTACGTGTTTCGACA 59.770 45.455 0.00 0.00 42.86 4.35
1607 1621 1.927487 ATTTGCTCACATTCCAGGCA 58.073 45.000 0.00 0.00 0.00 4.75
1621 1635 4.314522 TCCAGGCAAAGGTCATAATTCA 57.685 40.909 0.00 0.00 0.00 2.57
1755 1769 7.643123 ACAAAGGGAAGATCTAAATATGGTGT 58.357 34.615 0.00 0.00 0.00 4.16
1797 1811 3.203710 TGAATGGAAGATGCCTCTGGAAT 59.796 43.478 0.00 0.00 0.00 3.01
1802 1816 5.579047 TGGAAGATGCCTCTGGAATTTTTA 58.421 37.500 0.00 0.00 0.00 1.52
1880 1894 7.278868 CGTTACCATTTCTCTCTGCTATTCTTT 59.721 37.037 0.00 0.00 0.00 2.52
1907 1921 4.566987 AGAAGGGCTTGACTTACTTAACG 58.433 43.478 0.00 0.00 0.00 3.18
1935 1949 5.391449 GCTTTCCCGAAACTAGCTAAAAAG 58.609 41.667 0.00 0.00 0.00 2.27
1968 1982 0.671251 CTGCCTGACGAGATAGGGTC 59.329 60.000 0.00 0.00 34.58 4.46
1988 2002 4.505039 GGTCTTTTCTAAAGTGGGAGCTGA 60.505 45.833 0.00 0.00 0.00 4.26
2007 2021 3.360867 TGATGTCGGTATGGGCAATTTT 58.639 40.909 0.00 0.00 0.00 1.82
2008 2022 3.130164 TGATGTCGGTATGGGCAATTTTG 59.870 43.478 0.00 0.00 0.00 2.44
2038 2053 3.981071 TGATTGATTCTGTCCCGAGTT 57.019 42.857 0.00 0.00 0.00 3.01
2044 2059 1.171308 TTCTGTCCCGAGTTCTACCG 58.829 55.000 0.00 0.00 0.00 4.02
2074 2089 6.212388 TCCTCTAATTCCTCAGCCAGATATTC 59.788 42.308 0.00 0.00 0.00 1.75
2077 2092 2.494888 TCCTCAGCCAGATATTCCCA 57.505 50.000 0.00 0.00 0.00 4.37
2154 2169 4.151883 AGCAACCTTCATTCCTGCTTTTA 58.848 39.130 0.00 0.00 40.36 1.52
2299 2314 3.611025 ATTTCCTTGTTTCCCACCTCA 57.389 42.857 0.00 0.00 0.00 3.86
2307 2322 1.700186 GTTTCCCACCTCAGACCTTCT 59.300 52.381 0.00 0.00 0.00 2.85
2315 2330 3.030291 ACCTCAGACCTTCTGCTATGAG 58.970 50.000 0.00 0.00 43.95 2.90
2323 2338 3.776969 ACCTTCTGCTATGAGATGACCAA 59.223 43.478 0.00 0.00 0.00 3.67
2330 2345 4.063689 GCTATGAGATGACCAATCCACTG 58.936 47.826 0.00 0.00 35.72 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.046892 CCAGCAGGGAACAGGACG 60.047 66.667 0.00 0.00 40.01 4.79
90 91 5.354842 TGAGTATCTCCTTCGTCTAGTCA 57.645 43.478 0.00 0.00 34.92 3.41
109 110 3.349927 TCACTTGCCTGAATGGAATGAG 58.650 45.455 0.00 0.00 38.35 2.90
126 127 1.903877 CGATGCCACCCTTCCTCACT 61.904 60.000 0.00 0.00 0.00 3.41
142 143 0.250513 GAAGACAGGGTCAAGCCGAT 59.749 55.000 0.00 0.00 38.44 4.18
170 171 1.190178 AAACTTAGCCTCCGACCCGT 61.190 55.000 0.00 0.00 0.00 5.28
249 250 1.613255 GCGAGAGACCCCATCCAAAAA 60.613 52.381 0.00 0.00 0.00 1.94
250 251 0.035439 GCGAGAGACCCCATCCAAAA 60.035 55.000 0.00 0.00 0.00 2.44
292 293 7.119387 TGAGTGAGAAAGACTCCATACAGATA 58.881 38.462 0.00 0.00 44.34 1.98
298 299 7.670140 TCTTTACTGAGTGAGAAAGACTCCATA 59.330 37.037 5.22 0.00 44.34 2.74
301 302 6.334102 TCTTTACTGAGTGAGAAAGACTCC 57.666 41.667 5.22 0.00 44.34 3.85
313 314 3.427863 GCGCGTACTTTTCTTTACTGAGT 59.572 43.478 8.43 0.00 0.00 3.41
326 327 2.901051 AAGCCATAGCGCGCGTACTT 62.901 55.000 32.35 21.52 46.67 2.24
388 389 4.078537 CCATACCACCAAGTTGTTGATCA 58.921 43.478 1.35 0.00 35.46 2.92
403 404 1.578897 TAAGCCACTCAGCCATACCA 58.421 50.000 0.00 0.00 0.00 3.25
437 438 6.712241 ACAGTCTTCTTGTATGTCGATTTG 57.288 37.500 0.00 0.00 0.00 2.32
457 458 3.243737 TGGGATTCGAACCGATGATACAG 60.244 47.826 0.00 0.00 35.23 2.74
466 467 2.038387 AGGAAATGGGATTCGAACCG 57.962 50.000 0.00 0.00 0.00 4.44
486 487 1.601419 CCCTTCTACTTCCGTGCCGA 61.601 60.000 0.00 0.00 0.00 5.54
503 504 1.826487 ATGTAATTTCGCCCGCCCC 60.826 57.895 0.00 0.00 0.00 5.80
530 531 3.384789 CGGACTCCATCAATCTGAGGTTA 59.615 47.826 0.00 0.00 0.00 2.85
563 572 5.452636 GCTCCTAGTCACTAAGCAGCTATTT 60.453 44.000 0.00 0.00 33.21 1.40
604 613 2.541999 CGCTAAAAACGCCACCAAGAAA 60.542 45.455 0.00 0.00 0.00 2.52
692 701 0.942962 GAGCATCCTACATGCAGTGC 59.057 55.000 8.58 8.58 46.77 4.40
700 709 6.983906 TTCTTCATCTATGAGCATCCTACA 57.016 37.500 0.00 0.00 38.19 2.74
857 866 6.327386 TCCTTGCTCTTCCCACTAAAATAT 57.673 37.500 0.00 0.00 0.00 1.28
859 868 4.593956 CTCCTTGCTCTTCCCACTAAAAT 58.406 43.478 0.00 0.00 0.00 1.82
863 872 0.905357 GCTCCTTGCTCTTCCCACTA 59.095 55.000 0.00 0.00 38.95 2.74
880 889 2.242882 AGGATTTCAAGGGCAATGCT 57.757 45.000 4.82 0.00 0.00 3.79
903 912 3.557595 GCTTAGATGTGGATTCGAACCAG 59.442 47.826 16.54 7.33 38.14 4.00
1052 1064 2.225727 GGAACACCGAGTGGAATCAAAC 59.774 50.000 8.57 0.00 37.94 2.93
1084 1096 5.793030 AGATAGGTCGAACTATTGGAAGG 57.207 43.478 23.43 0.00 33.95 3.46
1116 1128 3.745480 CGGAACCACATTCATAGGCTGAT 60.745 47.826 0.00 0.00 39.30 2.90
1287 1300 6.486320 CCAATTGCCAAAATCAGTAAAAAGGT 59.514 34.615 0.00 0.00 0.00 3.50
1296 1309 4.442472 GGGAGATCCAATTGCCAAAATCAG 60.442 45.833 0.00 0.00 37.91 2.90
1305 1318 4.461781 CCATTCATAGGGAGATCCAATTGC 59.538 45.833 0.00 0.00 38.24 3.56
1307 1320 6.535161 TTCCATTCATAGGGAGATCCAATT 57.465 37.500 0.47 0.00 35.30 2.32
1318 1331 2.695147 GCACCCCTTTTCCATTCATAGG 59.305 50.000 0.00 0.00 0.00 2.57
1342 1355 1.843368 AAGTGGTTACTCCCGATCGA 58.157 50.000 18.66 0.00 35.69 3.59
1343 1356 2.667473 AAAGTGGTTACTCCCGATCG 57.333 50.000 8.51 8.51 35.69 3.69
1445 1458 4.389576 GTACGGTCCGTGCGTCGT 62.390 66.667 27.20 0.00 41.39 4.34
1446 1459 3.989566 GAGTACGGTCCGTGCGTCG 62.990 68.421 27.20 0.00 46.19 5.12
1448 1461 4.093952 CGAGTACGGTCCGTGCGT 62.094 66.667 27.20 14.75 46.19 5.24
1505 1518 1.662122 GGTGTTCTTGTCGAAACACGT 59.338 47.619 19.31 0.00 43.13 4.49
1517 1530 6.702716 TGAATTAGGTTTTTCGGTGTTCTT 57.297 33.333 0.00 0.00 0.00 2.52
1607 1621 7.671398 AGAATGTTCCTGTGAATTATGACCTTT 59.329 33.333 0.00 0.00 31.98 3.11
1621 1635 8.824756 TGACTAAGACTATAGAATGTTCCTGT 57.175 34.615 6.78 0.00 0.00 4.00
1731 1745 9.277783 CTACACCATATTTAGATCTTCCCTTTG 57.722 37.037 0.00 0.00 0.00 2.77
1755 1769 9.109393 CCATTCATTTCGATTTAGGTCTTTCTA 57.891 33.333 0.00 0.00 0.00 2.10
1818 1832 2.732412 GCTAGCTGCTTCCATATCGA 57.268 50.000 7.79 0.00 38.95 3.59
1880 1894 3.583086 AGTAAGTCAAGCCCTTCTAAGCA 59.417 43.478 0.00 0.00 0.00 3.91
1907 1921 2.265683 CTAGTTTCGGGAAAGCGGTAC 58.734 52.381 0.00 0.00 0.00 3.34
1957 1971 6.043411 CCACTTTAGAAAAGACCCTATCTCG 58.957 44.000 6.41 0.00 36.27 4.04
1968 1982 5.006386 ACATCAGCTCCCACTTTAGAAAAG 58.994 41.667 0.00 0.00 0.00 2.27
1988 2002 3.096092 ACAAAATTGCCCATACCGACAT 58.904 40.909 0.00 0.00 0.00 3.06
2007 2021 7.174946 GGGACAGAATCAATCAAAGAACTTACA 59.825 37.037 0.00 0.00 0.00 2.41
2008 2022 7.530863 GGGACAGAATCAATCAAAGAACTTAC 58.469 38.462 0.00 0.00 0.00 2.34
2038 2053 5.516984 AGGAATTAGAGGAACTTCGGTAGA 58.483 41.667 0.00 0.00 41.55 2.59
2044 2059 4.080863 TGGCTGAGGAATTAGAGGAACTTC 60.081 45.833 0.00 0.00 41.55 3.01
2074 2089 1.315257 CGGGAAAGTCTGGCAATGGG 61.315 60.000 0.00 0.00 0.00 4.00
2077 2092 2.746472 GCTATCGGGAAAGTCTGGCAAT 60.746 50.000 0.00 0.00 0.00 3.56
2154 2169 1.873591 CAAGTAGCAAAGGCAAGACGT 59.126 47.619 0.00 0.00 44.61 4.34
2299 2314 3.640967 GGTCATCTCATAGCAGAAGGTCT 59.359 47.826 0.00 0.00 0.00 3.85
2307 2322 3.713248 AGTGGATTGGTCATCTCATAGCA 59.287 43.478 0.00 0.00 31.67 3.49
2315 2330 5.674525 TGACTTATCAGTGGATTGGTCATC 58.325 41.667 0.00 0.00 38.09 2.92


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

AutoCloner maintained by Alex Coulton.