Multiple sequence alignment - TraesCS5D01G127400

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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 TraesCS5D01G127400 chr5D 100.000 2378 0 0 1 2378 197839498 197837121 0 4392
1 TraesCS5D01G127400 chr5D 93.378 2386 148 10 1 2378 79865655 79868038 0 3522
2 TraesCS5D01G127400 chr4D 94.263 2388 122 12 1 2378 483696759 483699141 0 3637
3 TraesCS5D01G127400 chr4D 93.923 2386 134 11 1 2378 135005821 135003439 0 3592
4 TraesCS5D01G127400 chr4D 93.219 2389 146 15 1 2378 241142845 241140462 0 3500
5 TraesCS5D01G127400 chr1B 92.830 2385 148 14 1 2376 286167000 286169370 0 3435
6 TraesCS5D01G127400 chr1B 92.850 2028 133 11 361 2378 286025634 286023609 0 2931
7 TraesCS5D01G127400 chr7A 93.026 2194 142 9 195 2378 571648029 571650221 0 3193
8 TraesCS5D01G127400 chr6B 93.219 1637 93 9 1 1627 53079407 53081035 0 2392
9 TraesCS5D01G127400 chr3A 95.400 1500 65 4 1 1497 191855949 191857447 0 2385
10 TraesCS5D01G127400 chr1D 94.176 1219 66 5 1165 2378 185763599 185764817 0 1853
11 TraesCS5D01G127400 chr7B 94.595 925 44 6 1460 2378 743080627 743081551 0 1426


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 TraesCS5D01G127400 chr5D 197837121 197839498 2377 True 4392 4392 100.000 1 2378 1 chr5D.!!$R1 2377
1 TraesCS5D01G127400 chr5D 79865655 79868038 2383 False 3522 3522 93.378 1 2378 1 chr5D.!!$F1 2377
2 TraesCS5D01G127400 chr4D 483696759 483699141 2382 False 3637 3637 94.263 1 2378 1 chr4D.!!$F1 2377
3 TraesCS5D01G127400 chr4D 135003439 135005821 2382 True 3592 3592 93.923 1 2378 1 chr4D.!!$R1 2377
4 TraesCS5D01G127400 chr4D 241140462 241142845 2383 True 3500 3500 93.219 1 2378 1 chr4D.!!$R2 2377
5 TraesCS5D01G127400 chr1B 286167000 286169370 2370 False 3435 3435 92.830 1 2376 1 chr1B.!!$F1 2375
6 TraesCS5D01G127400 chr1B 286023609 286025634 2025 True 2931 2931 92.850 361 2378 1 chr1B.!!$R1 2017
7 TraesCS5D01G127400 chr7A 571648029 571650221 2192 False 3193 3193 93.026 195 2378 1 chr7A.!!$F1 2183
8 TraesCS5D01G127400 chr6B 53079407 53081035 1628 False 2392 2392 93.219 1 1627 1 chr6B.!!$F1 1626
9 TraesCS5D01G127400 chr3A 191855949 191857447 1498 False 2385 2385 95.400 1 1497 1 chr3A.!!$F1 1496
10 TraesCS5D01G127400 chr1D 185763599 185764817 1218 False 1853 1853 94.176 1165 2378 1 chr1D.!!$F1 1213
11 TraesCS5D01G127400 chr7B 743080627 743081551 924 False 1426 1426 94.595 1460 2378 1 chr7B.!!$F1 918

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
155 164 0.178767 CAGATTGATGGAGTCCGCCA 59.821 55.0 4.3 1.7 43.23 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2105 0.043334 TCCTCCCTCTTTGCCTAGCT 59.957 55.0 0.0 0.0 0.0 3.32 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
24 25 2.289565 GGTATGGCTGAGTGGCTTAAC 58.710 52.381 0.00 0.00 42.34 2.01
26 27 0.613260 ATGGCTGAGTGGCTTAACGA 59.387 50.000 0.00 0.00 42.34 3.85
28 29 0.796927 GGCTGAGTGGCTTAACGAAC 59.203 55.000 0.00 0.00 38.32 3.95
37 38 1.335597 GGCTTAACGAACTGGTTTGCC 60.336 52.381 0.00 0.00 39.37 4.52
57 58 4.391830 TGCCAAATCGACATACAAGAAGAC 59.608 41.667 0.00 0.00 0.00 3.01
66 67 7.418408 TCGACATACAAGAAGACTGTATCATC 58.582 38.462 0.00 0.00 0.00 2.92
86 87 2.026636 TCGGTTCGAATCCCATTTCCTT 60.027 45.455 0.00 0.00 31.06 3.36
130 131 4.273480 CGGGCGAAATTACATGAGAGAAAT 59.727 41.667 0.00 0.00 0.00 2.17
155 164 0.178767 CAGATTGATGGAGTCCGCCA 59.821 55.000 4.30 1.70 43.23 5.69
204 213 2.359975 CGGAGCGCCCCTTTCTTT 60.360 61.111 6.33 0.00 0.00 2.52
218 227 3.430236 CCTTTCTTTTTCTTGGTGGCGTT 60.430 43.478 0.00 0.00 0.00 4.84
220 229 3.878160 TCTTTTTCTTGGTGGCGTTTT 57.122 38.095 0.00 0.00 0.00 2.43
240 249 1.933021 TAGCGAAGAAGACCTTCCCA 58.067 50.000 6.17 0.00 46.65 4.37
292 301 1.163554 GGTTCTTGAGCAAGCTCCTG 58.836 55.000 18.54 11.37 42.09 3.86
300 309 2.341101 GCAAGCTCCTGCACTGCAT 61.341 57.895 3.64 0.00 44.49 3.96
480 489 4.657814 ATTTTAGTGGGAAGAGCAAGGA 57.342 40.909 0.00 0.00 0.00 3.36
503 512 3.853475 CATTGCCCTTGAAATCCTTCAC 58.147 45.455 0.00 0.00 41.34 3.18
522 531 3.767131 TCACTGGTTCGAATCCACATCTA 59.233 43.478 5.84 0.00 0.00 1.98
652 663 3.238108 AGTGATCAGTCCGCTAGTTTG 57.762 47.619 0.00 0.00 0.00 2.93
684 695 3.568430 ACTCGGTGTTCCTTTTCCATTTC 59.432 43.478 0.00 0.00 0.00 2.17
757 768 1.983119 GATCCCTCCGGTGATGCCAA 61.983 60.000 4.76 0.00 36.97 4.52
905 917 7.546667 CCATGATGACCTTTTTACTGATTTTGG 59.453 37.037 0.00 0.00 0.00 3.28
907 919 5.860941 TGACCTTTTTACTGATTTTGGCA 57.139 34.783 0.00 0.00 0.00 4.92
918 930 4.161001 ACTGATTTTGGCAATTGGATCTCC 59.839 41.667 7.72 0.00 0.00 3.71
942 954 2.688477 TGAATGGAAAAGGGGTGCTTT 58.312 42.857 0.00 0.00 0.00 3.51
943 955 2.632512 TGAATGGAAAAGGGGTGCTTTC 59.367 45.455 0.00 0.00 0.00 2.62
1105 1117 2.435805 CCAGAAGCAAGGAGTATGCCTA 59.564 50.000 0.00 0.00 44.91 3.93
1117 1129 2.229543 AGTATGCCTACGTGTTTCGACA 59.770 45.455 0.00 0.00 42.86 4.35
1221 1234 4.314522 TCCAGGCAAAGGTCATAATTCA 57.685 40.909 0.00 0.00 0.00 2.57
1355 1368 7.643123 ACAAAGGGAAGATCTAAATATGGTGT 58.357 34.615 0.00 0.00 0.00 4.16
1397 1410 3.203710 TGAATGGAAGATGCCTCTGGAAT 59.796 43.478 0.00 0.00 0.00 3.01
1402 1415 5.579047 TGGAAGATGCCTCTGGAATTTTTA 58.421 37.500 0.00 0.00 0.00 1.52
1480 1493 7.278868 CGTTACCATTTCTCTCTGCTATTCTTT 59.721 37.037 0.00 0.00 0.00 2.52
1507 1520 4.566987 AGAAGGGCTTGACTTACTTAACG 58.433 43.478 0.00 0.00 0.00 3.18
1535 1548 5.391449 GCTTTCCCGAAACTAGCTAAAAAG 58.609 41.667 0.00 0.00 0.00 2.27
1568 1581 0.671251 CTGCCTGACGAGATAGGGTC 59.329 60.000 0.00 0.00 34.58 4.46
1588 1601 4.505039 GGTCTTTTCTAAAGTGGGAGCTGA 60.505 45.833 0.00 0.00 0.00 4.26
1607 1620 3.360867 TGATGTCGGTATGGGCAATTTT 58.639 40.909 0.00 0.00 0.00 1.82
1608 1621 3.130164 TGATGTCGGTATGGGCAATTTTG 59.870 43.478 0.00 0.00 0.00 2.44
1638 1652 3.981071 TGATTGATTCTGTCCCGAGTT 57.019 42.857 0.00 0.00 0.00 3.01
1644 1658 1.171308 TTCTGTCCCGAGTTCTACCG 58.829 55.000 0.00 0.00 0.00 4.02
1674 1688 6.212388 TCCTCTAATTCCTCAGCCAGATATTC 59.788 42.308 0.00 0.00 0.00 1.75
1677 1691 2.494888 TCCTCAGCCAGATATTCCCA 57.505 50.000 0.00 0.00 0.00 4.37
1754 1768 4.151883 AGCAACCTTCATTCCTGCTTTTA 58.848 39.130 0.00 0.00 40.36 1.52
1899 1913 3.611025 ATTTCCTTGTTTCCCACCTCA 57.389 42.857 0.00 0.00 0.00 3.86
1907 1921 1.700186 GTTTCCCACCTCAGACCTTCT 59.300 52.381 0.00 0.00 0.00 2.85
1915 1929 3.030291 ACCTCAGACCTTCTGCTATGAG 58.970 50.000 0.00 0.00 43.95 2.90
1923 1937 3.776969 ACCTTCTGCTATGAGATGACCAA 59.223 43.478 0.00 0.00 0.00 3.67
1930 1944 4.063689 GCTATGAGATGACCAATCCACTG 58.936 47.826 0.00 0.00 35.72 3.66
1996 2010 5.419542 TCATCAATAGAAGAACTCCAACCG 58.580 41.667 0.00 0.00 0.00 4.44
2016 2031 5.169295 ACCGTGCTTCTTGAAATAGTAGTC 58.831 41.667 0.00 0.00 0.00 2.59
2056 2073 1.269102 CGACGAGTGACTCTTGGTTGT 60.269 52.381 11.26 0.00 32.04 3.32
2062 2079 1.352622 TGACTCTTGGTTGTGGGGCT 61.353 55.000 0.00 0.00 0.00 5.19
2085 2104 5.635133 AGGGGGCCTACTATCTACTTAAT 57.365 43.478 0.84 0.00 28.47 1.40
2086 2105 6.748111 AGGGGGCCTACTATCTACTTAATA 57.252 41.667 0.84 0.00 28.47 0.98
2111 2130 1.557269 GCAAAGAGGGAGGAGCCAGA 61.557 60.000 0.00 0.00 38.95 3.86
2135 2154 2.354805 GCGGGTGTTTAGTGAGGAAGAT 60.355 50.000 0.00 0.00 0.00 2.40
2185 2204 1.730064 GTGCTTTCGATCGGCTTGTTA 59.270 47.619 16.41 0.00 0.00 2.41
2194 2213 3.924686 CGATCGGCTTGTTACACTAAAGT 59.075 43.478 7.38 0.00 0.00 2.66
2208 2227 4.272748 ACACTAAAGTTGCGAGGTTCTTTC 59.727 41.667 0.00 0.00 33.22 2.62
2221 2240 5.120830 CGAGGTTCTTTCATCGAATCAACTT 59.879 40.000 0.00 0.00 42.85 2.66
2242 2261 3.546002 TTTGCGTTTACTTTCATCCCG 57.454 42.857 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.578897 TAAGCCACTCAGCCATACCA 58.421 50.000 0.00 0.00 0.00 3.25
37 38 6.712241 ACAGTCTTCTTGTATGTCGATTTG 57.288 37.500 0.00 0.00 0.00 2.32
57 58 3.243737 TGGGATTCGAACCGATGATACAG 60.244 47.826 0.00 0.00 35.23 2.74
66 67 2.038387 AGGAAATGGGATTCGAACCG 57.962 50.000 0.00 0.00 0.00 4.44
86 87 1.601419 CCCTTCTACTTCCGTGCCGA 61.601 60.000 0.00 0.00 0.00 5.54
103 104 1.826487 ATGTAATTTCGCCCGCCCC 60.826 57.895 0.00 0.00 0.00 5.80
130 131 3.384789 CGGACTCCATCAATCTGAGGTTA 59.615 47.826 0.00 0.00 0.00 2.85
155 164 4.572389 CACTAAGCAGCTATTTTGTCCGAT 59.428 41.667 0.00 0.00 0.00 4.18
163 172 5.452636 GCTCCTAGTCACTAAGCAGCTATTT 60.453 44.000 0.00 0.00 33.21 1.40
204 213 2.541999 CGCTAAAAACGCCACCAAGAAA 60.542 45.455 0.00 0.00 0.00 2.52
292 301 0.942962 GAGCATCCTACATGCAGTGC 59.057 55.000 8.58 8.58 46.77 4.40
300 309 6.983906 TTCTTCATCTATGAGCATCCTACA 57.016 37.500 0.00 0.00 38.19 2.74
457 466 6.327386 TCCTTGCTCTTCCCACTAAAATAT 57.673 37.500 0.00 0.00 0.00 1.28
459 468 4.593956 CTCCTTGCTCTTCCCACTAAAAT 58.406 43.478 0.00 0.00 0.00 1.82
480 489 2.242882 AGGATTTCAAGGGCAATGCT 57.757 45.000 4.82 0.00 0.00 3.79
503 512 3.557595 GCTTAGATGTGGATTCGAACCAG 59.442 47.826 16.54 7.33 38.14 4.00
652 663 2.225727 GGAACACCGAGTGGAATCAAAC 59.774 50.000 8.57 0.00 37.94 2.93
684 695 5.793030 AGATAGGTCGAACTATTGGAAGG 57.207 43.478 23.43 0.00 33.95 3.46
716 727 3.745480 CGGAACCACATTCATAGGCTGAT 60.745 47.826 0.00 0.00 39.30 2.90
887 899 6.486320 CCAATTGCCAAAATCAGTAAAAAGGT 59.514 34.615 0.00 0.00 0.00 3.50
896 908 4.442472 GGGAGATCCAATTGCCAAAATCAG 60.442 45.833 0.00 0.00 37.91 2.90
905 917 4.461781 CCATTCATAGGGAGATCCAATTGC 59.538 45.833 0.00 0.00 38.24 3.56
907 919 6.535161 TTCCATTCATAGGGAGATCCAATT 57.465 37.500 0.47 0.00 35.30 2.32
918 930 2.695147 GCACCCCTTTTCCATTCATAGG 59.305 50.000 0.00 0.00 0.00 2.57
942 954 1.843368 AAGTGGTTACTCCCGATCGA 58.157 50.000 18.66 0.00 35.69 3.59
943 955 2.667473 AAAGTGGTTACTCCCGATCG 57.333 50.000 8.51 8.51 35.69 3.69
1045 1057 4.389576 GTACGGTCCGTGCGTCGT 62.390 66.667 27.20 0.00 41.39 4.34
1105 1117 1.662122 GGTGTTCTTGTCGAAACACGT 59.338 47.619 19.31 0.00 43.13 4.49
1117 1129 6.702716 TGAATTAGGTTTTTCGGTGTTCTT 57.297 33.333 0.00 0.00 0.00 2.52
1221 1234 8.824756 TGACTAAGACTATAGAATGTTCCTGT 57.175 34.615 6.78 0.00 0.00 4.00
1331 1344 9.277783 CTACACCATATTTAGATCTTCCCTTTG 57.722 37.037 0.00 0.00 0.00 2.77
1355 1368 9.109393 CCATTCATTTCGATTTAGGTCTTTCTA 57.891 33.333 0.00 0.00 0.00 2.10
1418 1431 2.732412 GCTAGCTGCTTCCATATCGA 57.268 50.000 7.79 0.00 38.95 3.59
1480 1493 3.583086 AGTAAGTCAAGCCCTTCTAAGCA 59.417 43.478 0.00 0.00 0.00 3.91
1507 1520 2.265683 CTAGTTTCGGGAAAGCGGTAC 58.734 52.381 0.00 0.00 0.00 3.34
1557 1570 6.043411 CCACTTTAGAAAAGACCCTATCTCG 58.957 44.000 6.41 0.00 36.27 4.04
1568 1581 5.006386 ACATCAGCTCCCACTTTAGAAAAG 58.994 41.667 0.00 0.00 0.00 2.27
1588 1601 3.096092 ACAAAATTGCCCATACCGACAT 58.904 40.909 0.00 0.00 0.00 3.06
1607 1620 7.174946 GGGACAGAATCAATCAAAGAACTTACA 59.825 37.037 0.00 0.00 0.00 2.41
1608 1621 7.530863 GGGACAGAATCAATCAAAGAACTTAC 58.469 38.462 0.00 0.00 0.00 2.34
1638 1652 5.516984 AGGAATTAGAGGAACTTCGGTAGA 58.483 41.667 0.00 0.00 41.55 2.59
1644 1658 4.080863 TGGCTGAGGAATTAGAGGAACTTC 60.081 45.833 0.00 0.00 41.55 3.01
1674 1688 1.315257 CGGGAAAGTCTGGCAATGGG 61.315 60.000 0.00 0.00 0.00 4.00
1677 1691 2.746472 GCTATCGGGAAAGTCTGGCAAT 60.746 50.000 0.00 0.00 0.00 3.56
1754 1768 1.873591 CAAGTAGCAAAGGCAAGACGT 59.126 47.619 0.00 0.00 44.61 4.34
1899 1913 3.640967 GGTCATCTCATAGCAGAAGGTCT 59.359 47.826 0.00 0.00 0.00 3.85
1907 1921 3.713248 AGTGGATTGGTCATCTCATAGCA 59.287 43.478 0.00 0.00 31.67 3.49
1915 1929 5.674525 TGACTTATCAGTGGATTGGTCATC 58.325 41.667 0.00 0.00 38.09 2.92
1996 2010 8.034058 ACAATGACTACTATTTCAAGAAGCAC 57.966 34.615 0.00 0.00 0.00 4.40
2016 2031 3.742882 TCGAAAGCTGACAGAAGACAATG 59.257 43.478 6.65 0.00 0.00 2.82
2026 2041 0.666374 TCACTCGTCGAAAGCTGACA 59.334 50.000 0.00 0.00 36.11 3.58
2062 2079 6.748111 ATTAAGTAGATAGTAGGCCCCCTA 57.252 41.667 0.00 0.00 34.61 3.53
2085 2104 1.291033 TCCTCCCTCTTTGCCTAGCTA 59.709 52.381 0.00 0.00 0.00 3.32
2086 2105 0.043334 TCCTCCCTCTTTGCCTAGCT 59.957 55.000 0.00 0.00 0.00 3.32
2111 2130 1.418637 TCCTCACTAAACACCCGCTTT 59.581 47.619 0.00 0.00 0.00 3.51
2150 2169 4.800993 CGAAAGCACTCATCTTTATCGACT 59.199 41.667 0.00 0.00 34.24 4.18
2185 2204 3.470645 AGAACCTCGCAACTTTAGTGT 57.529 42.857 0.00 0.00 0.00 3.55
2194 2213 2.448926 TCGATGAAAGAACCTCGCAA 57.551 45.000 0.00 0.00 0.00 4.85
2208 2227 5.559694 AAACGCAAAAAGTTGATTCGATG 57.440 34.783 0.00 0.00 36.83 3.84
2221 2240 3.315749 ACGGGATGAAAGTAAACGCAAAA 59.684 39.130 0.00 0.00 0.00 2.44
2242 2261 3.991121 CGAAAGAAGAAAGAGAGTGGGAC 59.009 47.826 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.