Multiple sequence alignment - TraesCS5A01G140800

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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 TraesCS5A01G140800 chr5A 100.000 4208 0 0 1 4208 312918344 312922551 0.000000e+00 7771.0
1 TraesCS5A01G140800 chr5D 95.787 4225 149 16 1 4208 240851461 240847249 0.000000e+00 6789.0
2 TraesCS5A01G140800 chr5D 83.448 145 22 2 1869 2012 550577841 550577698 2.640000e-27 134.0
3 TraesCS5A01G140800 chr5B 94.467 1717 64 13 1 1706 262821282 262822978 0.000000e+00 2615.0
4 TraesCS5A01G140800 chr5B 96.805 1064 26 2 2170 3233 262823349 262824404 0.000000e+00 1770.0
5 TraesCS5A01G140800 chr5B 95.842 986 33 3 3229 4208 262824602 262825585 0.000000e+00 1587.0
6 TraesCS5A01G140800 chr5B 95.664 369 15 1 1769 2137 262822984 262823351 3.620000e-165 592.0
7 TraesCS5A01G140800 chr5B 82.305 243 33 7 1774 2012 111200342 111200106 7.130000e-48 202.0
8 TraesCS5A01G140800 chr5B 81.893 243 38 5 1774 2012 355609939 355610179 2.570000e-47 200.0
9 TraesCS5A01G140800 chr2B 80.083 241 43 5 1776 2012 750016755 750016994 1.560000e-39 174.0
10 TraesCS5A01G140800 chr2B 73.494 249 52 12 1772 2012 733461335 733461577 9.700000e-12 82.4
11 TraesCS5A01G140800 chr4A 77.941 272 30 19 1780 2026 576154404 576154138 4.390000e-30 143.0
12 TraesCS5A01G140800 chr6D 81.818 110 16 4 1905 2012 204682924 204682817 5.790000e-14 89.8


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 TraesCS5A01G140800 chr5A 312918344 312922551 4207 False 7771 7771 100.0000 1 4208 1 chr5A.!!$F1 4207
1 TraesCS5A01G140800 chr5D 240847249 240851461 4212 True 6789 6789 95.7870 1 4208 1 chr5D.!!$R1 4207
2 TraesCS5A01G140800 chr5B 262821282 262825585 4303 False 1641 2615 95.6945 1 4208 4 chr5B.!!$F2 4207

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
710 713 0.109086 ACGACATCTCGCCTTCACAG 60.109 55.000 0.00 0.00 44.33 3.66 F
1363 1366 0.397675 TGGGTGTGTTGAAATGGCCA 60.398 50.000 8.56 8.56 0.00 5.36 F
1535 1538 1.884928 GCATGGGTTCGGTAGTGGTTT 60.885 52.381 0.00 0.00 0.00 3.27 F
2716 2729 0.250295 TTGTCTCCTTGCCCAGTTCG 60.250 55.000 0.00 0.00 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 2307 0.321387 TCACGTCTGCTCGTCCTAGT 60.321 55.000 0.0 0.0 42.27 2.57 R
2295 2308 0.803117 TTCACGTCTGCTCGTCCTAG 59.197 55.000 0.0 0.0 42.27 3.02 R
2817 2830 2.658807 AGGGTTTTGAGAGGGTTGAC 57.341 50.000 0.0 0.0 0.00 3.18 R
3958 4174 1.543429 GCACCTTTAGCACCAGTCAGT 60.543 52.381 0.0 0.0 0.00 3.41 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
122 123 6.949352 ATTTGGATCGAGCATAACTGAAAT 57.051 33.333 1.84 0.00 0.00 2.17
151 154 6.511416 TGACAGATTTAACATTTTGGTGTGG 58.489 36.000 0.00 0.00 31.49 4.17
274 277 2.939103 CAGTTCGCTCTAGAAAATGGGG 59.061 50.000 0.00 0.00 0.00 4.96
417 420 1.339055 ACCGACAGATGATGTTGTGGG 60.339 52.381 4.44 4.44 44.17 4.61
578 581 4.148825 CGGAAGTGGAGAGGCGGG 62.149 72.222 0.00 0.00 0.00 6.13
661 664 1.068352 AGCCCCTTCACCAGTTTCCT 61.068 55.000 0.00 0.00 0.00 3.36
705 708 1.802880 GCATGTACGACATCTCGCCTT 60.803 52.381 0.00 0.00 44.33 4.35
710 713 0.109086 ACGACATCTCGCCTTCACAG 60.109 55.000 0.00 0.00 44.33 3.66
902 905 2.037847 GGCCCAAATGAGCCCAGT 59.962 61.111 0.00 0.00 43.76 4.00
903 906 2.054453 GGCCCAAATGAGCCCAGTC 61.054 63.158 0.00 0.00 43.76 3.51
905 908 0.613012 GCCCAAATGAGCCCAGTCTT 60.613 55.000 0.00 0.00 0.00 3.01
906 909 1.340991 GCCCAAATGAGCCCAGTCTTA 60.341 52.381 0.00 0.00 0.00 2.10
1006 1009 0.883814 CTCATCCTCTTCCATGGCGC 60.884 60.000 6.96 0.00 0.00 6.53
1041 1044 4.444081 CTCCTCCTCGTCCCCCGT 62.444 72.222 0.00 0.00 37.94 5.28
1204 1207 4.711949 CCTGCTGCAACTCCGCCT 62.712 66.667 3.02 0.00 0.00 5.52
1363 1366 0.397675 TGGGTGTGTTGAAATGGCCA 60.398 50.000 8.56 8.56 0.00 5.36
1535 1538 1.884928 GCATGGGTTCGGTAGTGGTTT 60.885 52.381 0.00 0.00 0.00 3.27
1606 1609 5.471456 AGTTCTGTTTGGAGCTTCTTGTATG 59.529 40.000 0.00 0.00 0.00 2.39
1620 1624 6.543831 GCTTCTTGTATGGTGAATGATTACCT 59.456 38.462 0.00 0.00 37.84 3.08
1664 1675 7.923888 AGATCAGTCAATGTAATATTGCACAC 58.076 34.615 8.50 6.25 0.00 3.82
1665 1676 7.553760 AGATCAGTCAATGTAATATTGCACACA 59.446 33.333 8.50 0.00 0.00 3.72
1668 1679 8.022550 TCAGTCAATGTAATATTGCACACAAAG 58.977 33.333 8.50 0.00 39.77 2.77
1975 1988 5.975693 TTTATGGTCAAACTTTAGCCCAG 57.024 39.130 0.00 0.00 0.00 4.45
2038 2051 2.289565 GTAGTCTGGTAATGGCAAGCC 58.710 52.381 3.61 3.61 0.00 4.35
2073 2086 6.312141 TCATTCAAGAATGGACCAGTATCA 57.688 37.500 19.46 0.00 46.08 2.15
2253 2266 3.242220 GCATGCTTGTGTAAGTCTGATCG 60.242 47.826 11.37 0.00 36.27 3.69
2313 2326 0.321387 ACTAGGACGAGCAGACGTGA 60.321 55.000 8.18 0.00 46.52 4.35
2328 2341 5.385617 CAGACGTGAAATTGACAATCCTTC 58.614 41.667 0.05 3.61 0.00 3.46
2355 2368 8.911247 TCTACTTTTTCTTTTGTTGAAGCTTC 57.089 30.769 19.89 19.89 0.00 3.86
2521 2534 8.946085 GTGTCTGGTCTTGTTTGATTGATAATA 58.054 33.333 0.00 0.00 0.00 0.98
2527 2540 8.416329 GGTCTTGTTTGATTGATAATATGCCTT 58.584 33.333 0.00 0.00 0.00 4.35
2640 2653 8.689061 TCATCATTTCCTTCATATCCTGTTTTG 58.311 33.333 0.00 0.00 0.00 2.44
2656 2669 4.743493 TGTTTTGCCTTCTTGAGTTGTTC 58.257 39.130 0.00 0.00 0.00 3.18
2716 2729 0.250295 TTGTCTCCTTGCCCAGTTCG 60.250 55.000 0.00 0.00 0.00 3.95
2817 2830 3.760684 AGCTTAAGCAGGTGAAAAGGATG 59.239 43.478 28.39 0.00 45.16 3.51
2873 2886 7.334171 TGTGTATGTGTCATTTACTGATGAAGG 59.666 37.037 0.00 0.00 37.75 3.46
2885 2898 8.684386 TTTACTGATGAAGGACATTTACAACA 57.316 30.769 0.00 0.00 39.56 3.33
2889 2902 8.084073 ACTGATGAAGGACATTTACAACAATTG 58.916 33.333 3.24 3.24 39.56 2.32
2935 2948 3.550639 CGCGAATTGGCAATTGTGGATAT 60.551 43.478 28.78 3.16 0.00 1.63
3011 3024 5.786401 AGTTGCACATTTCGATAGTCTTC 57.214 39.130 0.00 0.00 37.40 2.87
3013 3026 5.877012 AGTTGCACATTTCGATAGTCTTCAT 59.123 36.000 0.00 0.00 37.40 2.57
3258 3473 2.479566 ACATGTAACAGTCCTGCCTG 57.520 50.000 0.00 0.00 38.45 4.85
3278 3493 4.282195 CCTGTAGTTCTTCAGTCCTCTTGT 59.718 45.833 5.90 0.00 0.00 3.16
3355 3571 8.503196 CATCACATAGTAACAAAAGTGCACTTA 58.497 33.333 31.31 13.63 34.61 2.24
3445 3661 7.639113 TCCTGAAACAAACTACTTTGACAAT 57.361 32.000 2.34 0.00 39.43 2.71
3604 3820 4.848660 AGGTGGCCATCTGTTATGATATCT 59.151 41.667 20.51 0.00 0.00 1.98
3732 3948 3.199289 TCAAGTCAGATGATGCCTCATGT 59.801 43.478 9.39 2.25 42.27 3.21
3747 3963 3.329386 CTCATGTCGATGTGGTTGAAGT 58.671 45.455 0.00 0.00 0.00 3.01
3768 3984 2.068837 ATTGCATTTGTGGTCTTGCG 57.931 45.000 0.00 0.00 37.92 4.85
4043 4259 7.391148 AACACAAGTGAGTAAATGAAACAGT 57.609 32.000 7.28 0.00 0.00 3.55
4132 4348 3.859061 TGGTAACATTGGTGTGTGGTA 57.141 42.857 0.00 0.00 46.17 3.25
4141 4360 4.757019 TTGGTGTGTGGTACTGAACTTA 57.243 40.909 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.239654 CTGCCCTACCTTTTCATCTGGA 59.760 50.000 0.00 0.00 0.00 3.86
151 154 3.059352 TCCTAGGCAAGCTTCAAACTC 57.941 47.619 2.96 0.00 0.00 3.01
274 277 9.734620 TGCAGAATTATTGTAAATCAATGTAGC 57.265 29.630 3.73 0.00 45.14 3.58
417 420 8.520351 AGTTGGTAAAACTAGATTTGGTATTGC 58.480 33.333 8.15 0.00 0.00 3.56
578 581 2.039348 AGTACTCTCTCGATCCCTAGCC 59.961 54.545 0.00 0.00 0.00 3.93
661 664 1.579932 GACCTGCTGACGAAGACGA 59.420 57.895 0.00 0.00 42.66 4.20
745 748 2.291043 ATTTCCTCCCACTCGCGGT 61.291 57.895 6.13 0.00 0.00 5.68
750 753 1.452108 CCGGCATTTCCTCCCACTC 60.452 63.158 0.00 0.00 0.00 3.51
902 905 7.773690 GGGGCAGTGAAAGAATAAACTATAAGA 59.226 37.037 0.00 0.00 0.00 2.10
903 906 7.775561 AGGGGCAGTGAAAGAATAAACTATAAG 59.224 37.037 0.00 0.00 0.00 1.73
905 908 7.127339 AGAGGGGCAGTGAAAGAATAAACTATA 59.873 37.037 0.00 0.00 0.00 1.31
906 909 6.069381 AGAGGGGCAGTGAAAGAATAAACTAT 60.069 38.462 0.00 0.00 0.00 2.12
1204 1207 3.381333 CTCCAGATGCTGCTGCGGA 62.381 63.158 13.72 9.99 43.34 5.54
1310 1313 3.231734 TGAAGCATCAGAACCCACG 57.768 52.632 0.00 0.00 0.00 4.94
1535 1538 0.885196 GGCTCGGCAATTAACCAACA 59.115 50.000 0.00 0.00 0.00 3.33
1606 1609 7.121168 TGAAGAATTGTGAGGTAATCATTCACC 59.879 37.037 1.87 0.00 40.92 4.02
1620 1624 7.038729 ACTGATCTAGTTCCTGAAGAATTGTGA 60.039 37.037 0.00 0.00 35.67 3.58
1664 1675 9.390795 CATGTTTAACATTCAGACTCTTCTTTG 57.609 33.333 7.97 0.00 36.53 2.77
1665 1676 8.078596 GCATGTTTAACATTCAGACTCTTCTTT 58.921 33.333 7.97 0.00 36.53 2.52
1668 1679 7.020010 CAGCATGTTTAACATTCAGACTCTTC 58.980 38.462 7.97 0.00 36.53 2.87
1739 1752 3.010250 ACTCTTCCACCCTGATTTTACCC 59.990 47.826 0.00 0.00 0.00 3.69
1948 1961 8.527810 TGGGCTAAAGTTTGACCATAAATTTAG 58.472 33.333 8.14 9.78 36.14 1.85
1975 1988 5.472478 CGGGTTTATTAGGCCCTCTTTATTC 59.528 44.000 0.00 0.00 40.22 1.75
2038 2051 9.056005 TCCATTCTTGAATGAATAATAGTTCCG 57.944 33.333 20.95 3.86 35.18 4.30
2073 2086 6.942532 ATACAAGACATATGGCAAAATCGT 57.057 33.333 12.11 0.86 0.00 3.73
2107 2120 5.052693 TGGAATAGAAGGCAAGCATGTAT 57.947 39.130 0.00 0.00 0.00 2.29
2294 2307 0.321387 TCACGTCTGCTCGTCCTAGT 60.321 55.000 0.00 0.00 42.27 2.57
2295 2308 0.803117 TTCACGTCTGCTCGTCCTAG 59.197 55.000 0.00 0.00 42.27 3.02
2296 2309 1.241165 TTTCACGTCTGCTCGTCCTA 58.759 50.000 0.00 0.00 42.27 2.94
2328 2341 8.862550 AGCTTCAACAAAAGAAAAAGTAGATG 57.137 30.769 0.00 0.00 0.00 2.90
2355 2368 7.170658 GTCTAGCTCTGGCACTTTATCAATTAG 59.829 40.741 0.00 0.00 41.70 1.73
2521 2534 4.139786 CAAGTACCTGCATATGAAGGCAT 58.860 43.478 27.52 13.23 45.26 4.40
2527 2540 7.564793 ACTCAAATACAAGTACCTGCATATGA 58.435 34.615 6.97 0.00 0.00 2.15
2640 2653 5.106515 GGACATAAGAACAACTCAAGAAGGC 60.107 44.000 0.00 0.00 0.00 4.35
2656 2669 5.587388 AACAGGAATGCAATGGACATAAG 57.413 39.130 0.00 0.00 0.00 1.73
2716 2729 5.049129 CACCAATGAAAACAGGAGAGAAGAC 60.049 44.000 0.00 0.00 0.00 3.01
2817 2830 2.658807 AGGGTTTTGAGAGGGTTGAC 57.341 50.000 0.00 0.00 0.00 3.18
2873 2886 5.630680 CACTCCTGCAATTGTTGTAAATGTC 59.369 40.000 7.40 0.00 0.00 3.06
2885 2898 3.181440 TGAAGAGAACCACTCCTGCAATT 60.181 43.478 0.00 0.00 45.96 2.32
2889 2902 2.746362 CAATGAAGAGAACCACTCCTGC 59.254 50.000 0.00 0.00 45.96 4.85
2935 2948 9.810545 AAAATAGAAATTCAAAAACTGGAACGA 57.189 25.926 0.00 0.00 0.00 3.85
3355 3571 5.163395 GCTAACTGGAAATAGTAGGCAGACT 60.163 44.000 0.00 0.00 32.39 3.24
3445 3661 7.019656 TCATATCTGCCATGGCTAATTTCTA 57.980 36.000 35.53 17.48 42.51 2.10
3604 3820 6.238374 GCTCACAACAAAGCAGTAAAGTCTTA 60.238 38.462 0.00 0.00 38.42 2.10
3732 3948 4.068599 TGCAATTACTTCAACCACATCGA 58.931 39.130 0.00 0.00 0.00 3.59
3747 3963 3.005261 ACGCAAGACCACAAATGCAATTA 59.995 39.130 0.00 0.00 38.69 1.40
3768 3984 6.710597 AGGGAAAAGGAAAACTCAAGTAAC 57.289 37.500 0.00 0.00 0.00 2.50
3957 4173 2.146342 CACCTTTAGCACCAGTCAGTG 58.854 52.381 0.00 0.00 40.88 3.66
3958 4174 1.543429 GCACCTTTAGCACCAGTCAGT 60.543 52.381 0.00 0.00 0.00 3.41
4043 4259 3.253188 GGACAGTGTTTTTAGCAGATGCA 59.747 43.478 7.68 0.00 45.16 3.96
4111 4327 3.019799 ACCACACACCAATGTTACCAA 57.980 42.857 0.00 0.00 36.72 3.67
4124 4340 4.513692 GCACAATAAGTTCAGTACCACACA 59.486 41.667 0.00 0.00 0.00 3.72
4132 4348 7.217200 TCTAAACTCTGCACAATAAGTTCAGT 58.783 34.615 0.00 0.00 41.48 3.41
4141 4360 8.671921 CACAGAAATATCTAAACTCTGCACAAT 58.328 33.333 0.00 0.00 37.60 2.71


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

AutoCloner maintained by Alex Coulton.