Multiple sequence alignment - TraesCS1D01G167200

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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 TraesCS1D01G167200 chr1D 100.000 2568 0 0 1 2568 238327482 238330049 0.000000e+00 4743.0
1 TraesCS1D01G167200 chr1D 100.000 29 0 0 1898 1926 372835961 372835989 1.000000e-03 54.7
2 TraesCS1D01G167200 chr1A 90.172 1221 55 25 636 1806 301893781 301894986 0.000000e+00 1530.0
3 TraesCS1D01G167200 chr1A 95.652 644 20 3 1927 2568 301895981 301896618 0.000000e+00 1027.0
4 TraesCS1D01G167200 chr1A 85.567 679 51 18 1 639 301892808 301893479 0.000000e+00 667.0
5 TraesCS1D01G167200 chr1B 93.515 956 33 11 876 1822 335976900 335975965 0.000000e+00 1395.0
6 TraesCS1D01G167200 chr1B 94.696 641 24 5 1930 2568 335975922 335975290 0.000000e+00 987.0
7 TraesCS1D01G167200 chr1B 86.691 819 59 19 1 779 335978380 335977572 0.000000e+00 863.0
8 TraesCS1D01G167200 chr1B 95.146 103 5 0 779 881 335977207 335977105 2.040000e-36 163.0
9 TraesCS1D01G167200 chr2D 97.222 36 1 0 1902 1937 644287742 644287777 7.670000e-06 62.1


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 TraesCS1D01G167200 chr1D 238327482 238330049 2567 False 4743.000000 4743 100.000000 1 2568 1 chr1D.!!$F1 2567
1 TraesCS1D01G167200 chr1A 301892808 301896618 3810 False 1074.666667 1530 90.463667 1 2568 3 chr1A.!!$F1 2567
2 TraesCS1D01G167200 chr1B 335975290 335978380 3090 True 852.000000 1395 92.512000 1 2568 4 chr1B.!!$R1 2567

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
978 1913 0.038159 AAAGAGAGCTCCACGTTCGG 60.038 55.0 10.93 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2297 4140 0.038166 CCAAGTGCCCAGCTCCTAAA 59.962 55.0 0.0 0.0 0.0 1.85 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
17 18 2.750350 AACCAACAGCCTCCCTCG 59.250 61.111 0.00 0.00 0.00 4.63
39 40 2.079158 CACACTCCATGCAATTCTCGT 58.921 47.619 0.00 0.00 0.00 4.18
47 48 5.125356 TCCATGCAATTCTCGTCACAATAT 58.875 37.500 0.00 0.00 0.00 1.28
50 51 7.019418 CCATGCAATTCTCGTCACAATATATG 58.981 38.462 0.00 0.00 0.00 1.78
51 52 7.308169 CCATGCAATTCTCGTCACAATATATGT 60.308 37.037 0.00 0.00 45.34 2.29
52 53 8.711457 CATGCAATTCTCGTCACAATATATGTA 58.289 33.333 0.00 0.00 41.46 2.29
73 74 2.086054 AGAGAATGTGGTCGCAGTTC 57.914 50.000 0.00 0.00 0.00 3.01
82 83 0.039437 GGTCGCAGTTCTCGTCAAGA 60.039 55.000 0.00 0.00 0.00 3.02
97 98 1.211703 TCAAGACCACACCACACACAT 59.788 47.619 0.00 0.00 0.00 3.21
100 101 2.023673 AGACCACACCACACACATTTG 58.976 47.619 0.00 0.00 0.00 2.32
118 120 2.124983 CCATCACCTGGCTCGTGG 60.125 66.667 0.00 0.00 38.47 4.94
124 133 2.513204 CCTGGCTCGTGGCTCATG 60.513 66.667 12.46 0.00 41.46 3.07
355 370 5.576447 TTTCCTCAAAAGAAGGTCACAAC 57.424 39.130 0.00 0.00 35.29 3.32
367 382 2.550830 GTCACAACCAGAGACCATGT 57.449 50.000 0.00 0.00 32.43 3.21
386 401 5.107530 CCATGTTTGAGTGGTTATTTTTGCG 60.108 40.000 0.00 0.00 0.00 4.85
397 412 5.126222 TGGTTATTTTTGCGGCAATCAGATA 59.874 36.000 17.19 9.42 0.00 1.98
495 535 1.272781 GGAGCTCAACTTCACGATCG 58.727 55.000 17.19 14.88 0.00 3.69
499 539 1.914700 GCTCAACTTCACGATCGAGAC 59.085 52.381 24.34 1.56 0.00 3.36
521 561 3.243367 CGATCGAGAAGCTGAGAAAGGAT 60.243 47.826 10.26 0.00 0.00 3.24
565 613 8.363390 TCACATTATGGAGATTAGATCACTGTC 58.637 37.037 0.00 0.00 0.00 3.51
566 614 8.146412 CACATTATGGAGATTAGATCACTGTCA 58.854 37.037 0.00 0.00 0.00 3.58
580 628 5.462530 TCACTGTCATCGGTTAGAAAAGA 57.537 39.130 0.00 0.00 0.00 2.52
589 637 6.592607 TCATCGGTTAGAAAAGATTAAGCGTT 59.407 34.615 13.27 5.14 45.62 4.84
615 663 2.751166 ATGTAGCCGGTCATAGCATC 57.249 50.000 1.90 0.00 0.00 3.91
641 692 4.795080 TCTACGGGTAGATCGCAAGAACC 61.795 52.174 4.47 0.00 42.69 3.62
794 1518 4.820716 CCAACTGGGATTTTGCAAATTCAA 59.179 37.500 26.69 17.11 40.01 2.69
860 1584 4.926860 AAAAAGTTCACAAGTTGCTTGC 57.073 36.364 1.81 0.00 44.43 4.01
879 1814 8.292444 TGCTTGCCAAAATTACTGATATAGTT 57.708 30.769 0.00 0.00 40.89 2.24
910 1845 4.256110 GCAATTTCCCTTTTTGCTGCTAT 58.744 39.130 0.00 0.00 41.86 2.97
911 1846 5.418676 GCAATTTCCCTTTTTGCTGCTATA 58.581 37.500 0.00 0.00 41.86 1.31
978 1913 0.038159 AAAGAGAGCTCCACGTTCGG 60.038 55.000 10.93 0.00 0.00 4.30
981 1916 2.126031 GAGCTCCACGTTCGGTCC 60.126 66.667 0.87 0.00 0.00 4.46
1291 2227 2.930682 GAGACCCTCGCACTGATTTTAC 59.069 50.000 0.00 0.00 0.00 2.01
1302 2238 0.780637 TGATTTTACCACCCTGCCCA 59.219 50.000 0.00 0.00 0.00 5.36
1331 2291 0.110486 TTTGGTCTGAACTCCTGGCC 59.890 55.000 0.00 0.00 38.77 5.36
1588 2548 2.540265 AATCATCAGGATCGGAGCAC 57.460 50.000 0.00 0.00 34.28 4.40
1698 2663 2.557924 TGAAATGTCTGCGCTCCAAATT 59.442 40.909 9.73 0.00 0.00 1.82
1718 2683 7.069331 CCAAATTGCCCCAAATAACAGTATCTA 59.931 37.037 0.00 0.00 0.00 1.98
1773 2738 4.211164 TGATGTTGCAGTTTCAGACTAACG 59.789 41.667 0.00 0.00 36.65 3.18
1813 3088 1.032014 TTGTTGCTGAAGAGCCAACC 58.968 50.000 0.00 0.00 45.57 3.77
1821 3096 1.490490 TGAAGAGCCAACCTCACTGTT 59.510 47.619 0.00 0.00 43.31 3.16
1826 3101 3.003480 GAGCCAACCTCACTGTTGTATC 58.997 50.000 3.54 0.00 43.22 2.24
1828 3103 2.484264 GCCAACCTCACTGTTGTATCAC 59.516 50.000 3.54 0.00 43.22 3.06
1829 3104 3.807209 GCCAACCTCACTGTTGTATCACT 60.807 47.826 3.54 0.00 43.22 3.41
1830 3105 4.389374 CCAACCTCACTGTTGTATCACTT 58.611 43.478 3.54 0.00 43.22 3.16
1831 3106 4.821805 CCAACCTCACTGTTGTATCACTTT 59.178 41.667 3.54 0.00 43.22 2.66
1832 3107 5.277974 CCAACCTCACTGTTGTATCACTTTG 60.278 44.000 3.54 0.00 43.22 2.77
1848 3125 9.534565 GTATCACTTTGTCAGCAAGAGAATATA 57.465 33.333 0.00 0.00 35.82 0.86
1900 3503 9.282247 GTCAATTTCACAAGCATTAATCAGTAG 57.718 33.333 0.00 0.00 0.00 2.57
1908 3511 3.322254 AGCATTAATCAGTAGTCCCTCCG 59.678 47.826 0.00 0.00 0.00 4.63
1909 3512 3.321111 GCATTAATCAGTAGTCCCTCCGA 59.679 47.826 0.00 0.00 0.00 4.55
1922 3525 6.704056 AGTCCCTCCGATCCATATTAATTT 57.296 37.500 0.00 0.00 0.00 1.82
1925 3528 6.092259 GTCCCTCCGATCCATATTAATTTTCG 59.908 42.308 0.00 0.00 0.00 3.46
1933 3536 7.149080 CGATCCATATTAATTTTCGCAGCTTTG 60.149 37.037 0.00 0.00 0.00 2.77
2062 3901 3.500471 GGGGGAAAACATGGGAGGATATC 60.500 52.174 0.00 0.00 0.00 1.63
2240 4081 0.759346 AGTTCAGGCACTTCGAAGGT 59.241 50.000 27.86 11.72 34.60 3.50
2265 4106 1.271926 GGTACAGGCATGGAAACCAGT 60.272 52.381 12.98 0.00 36.75 4.00
2295 4138 6.682537 TGGGAGCTTTGGGAATAGATTAAAT 58.317 36.000 0.00 0.00 0.00 1.40
2296 4139 7.821566 TGGGAGCTTTGGGAATAGATTAAATA 58.178 34.615 0.00 0.00 0.00 1.40
2297 4140 8.456124 TGGGAGCTTTGGGAATAGATTAAATAT 58.544 33.333 0.00 0.00 0.00 1.28
2298 4141 9.314133 GGGAGCTTTGGGAATAGATTAAATATT 57.686 33.333 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.133790 GAGAATTGCATGGAGTGTGCC 59.866 52.381 0.00 0.00 41.83 5.01
47 48 5.079689 TGCGACCACATTCTCTTTACATA 57.920 39.130 0.00 0.00 0.00 2.29
50 51 3.326747 ACTGCGACCACATTCTCTTTAC 58.673 45.455 0.00 0.00 0.00 2.01
51 52 3.678056 ACTGCGACCACATTCTCTTTA 57.322 42.857 0.00 0.00 0.00 1.85
52 53 2.550830 ACTGCGACCACATTCTCTTT 57.449 45.000 0.00 0.00 0.00 2.52
73 74 0.104120 TGTGGTGTGGTCTTGACGAG 59.896 55.000 0.00 0.00 0.00 4.18
82 83 0.459489 GCAAATGTGTGTGGTGTGGT 59.541 50.000 0.00 0.00 0.00 4.16
113 115 0.176449 CAGGTCATCATGAGCCACGA 59.824 55.000 13.36 0.00 45.34 4.35
118 120 2.092968 TGGTAACCAGGTCATCATGAGC 60.093 50.000 8.93 8.93 44.62 4.26
124 133 1.822990 TCGAGTGGTAACCAGGTCATC 59.177 52.381 0.00 0.00 32.34 2.92
335 350 3.053991 TGGTTGTGACCTTCTTTTGAGGA 60.054 43.478 0.00 0.00 46.66 3.71
355 370 2.224621 ACCACTCAAACATGGTCTCTGG 60.225 50.000 0.00 0.00 46.62 3.86
367 382 3.181475 TGCCGCAAAAATAACCACTCAAA 60.181 39.130 0.00 0.00 0.00 2.69
386 401 6.555315 ACAAAAATTCGACTATCTGATTGCC 58.445 36.000 0.00 0.00 0.00 4.52
397 412 4.731480 GCGTGTTGTTACAAAAATTCGACT 59.269 37.500 0.00 0.00 35.69 4.18
416 431 4.749310 AGCTCGGCCTCAAGCGTG 62.749 66.667 13.85 0.00 45.17 5.34
495 535 1.937223 TCTCAGCTTCTCGATCGTCTC 59.063 52.381 15.94 1.57 0.00 3.36
499 539 2.098280 TCCTTTCTCAGCTTCTCGATCG 59.902 50.000 9.36 9.36 0.00 3.69
511 551 1.202417 GCATCGACCGATCCTTTCTCA 60.202 52.381 1.46 0.00 31.62 3.27
521 561 1.153389 ATGTGCATGCATCGACCGA 60.153 52.632 25.64 2.53 0.00 4.69
565 613 6.345920 ACGCTTAATCTTTTCTAACCGATG 57.654 37.500 0.00 0.00 0.00 3.84
566 614 6.980051 AACGCTTAATCTTTTCTAACCGAT 57.020 33.333 0.00 0.00 0.00 4.18
580 628 5.464389 CGGCTACATTACCTTAACGCTTAAT 59.536 40.000 0.00 0.00 0.00 1.40
589 637 4.021719 GCTATGACCGGCTACATTACCTTA 60.022 45.833 0.00 0.00 0.00 2.69
615 663 1.867615 CGATCTACCCGTAGAGGCG 59.132 63.158 10.19 11.51 44.47 5.52
641 692 4.974368 TTACACAACCAACAAGAAGTGG 57.026 40.909 0.00 0.00 0.00 4.00
646 1002 4.400120 GGGGTATTACACAACCAACAAGA 58.600 43.478 0.00 0.00 37.51 3.02
749 1105 4.142816 GGTTCATCATTGTGACTTTCTCCG 60.143 45.833 0.00 0.00 0.00 4.63
756 1112 3.822735 CCAGTTGGTTCATCATTGTGACT 59.177 43.478 0.00 0.00 0.00 3.41
794 1518 7.710511 ACATTGTTCATGTGTACCTCGTGGT 62.711 44.000 14.50 14.50 45.12 4.16
860 1584 9.613428 TGGACAGAACTATATCAGTAATTTTGG 57.387 33.333 0.00 0.00 36.04 3.28
879 1814 2.978156 AGGGAAATTGCTTGGACAGA 57.022 45.000 0.00 0.00 0.00 3.41
910 1845 9.021807 CCCGATTAGAAAATCAGTAGACCTATA 57.978 37.037 0.00 0.00 41.44 1.31
911 1846 7.038941 CCCCGATTAGAAAATCAGTAGACCTAT 60.039 40.741 0.00 0.00 41.44 2.57
950 1885 4.625028 GTGGAGCTCTCTTTTGCAATTTT 58.375 39.130 14.64 0.00 0.00 1.82
981 1916 4.530857 GCTCGTCACGGATGGGGG 62.531 72.222 0.00 0.00 0.00 5.40
1291 2227 3.612247 CTTCGACTGGGCAGGGTGG 62.612 68.421 0.00 0.00 0.00 4.61
1302 2238 2.872858 GTTCAGACCAAAAGCTTCGACT 59.127 45.455 0.00 0.00 0.00 4.18
1471 2431 2.436115 GCCTTCCGGTAAAGCGCT 60.436 61.111 2.64 2.64 0.00 5.92
1588 2548 0.519077 GCGAAGTGAAGAAGCCTTGG 59.481 55.000 0.00 0.00 31.62 3.61
1649 2609 9.726438 AGTAAATAAGCTCAACTCATGTAAACT 57.274 29.630 0.00 0.00 0.00 2.66
1650 2610 9.760660 CAGTAAATAAGCTCAACTCATGTAAAC 57.239 33.333 0.00 0.00 0.00 2.01
1651 2611 9.502091 ACAGTAAATAAGCTCAACTCATGTAAA 57.498 29.630 0.00 0.00 0.00 2.01
1652 2612 8.935844 CACAGTAAATAAGCTCAACTCATGTAA 58.064 33.333 0.00 0.00 0.00 2.41
1653 2613 8.311109 TCACAGTAAATAAGCTCAACTCATGTA 58.689 33.333 0.00 0.00 0.00 2.29
1654 2614 7.161404 TCACAGTAAATAAGCTCAACTCATGT 58.839 34.615 0.00 0.00 0.00 3.21
1655 2615 7.601073 TCACAGTAAATAAGCTCAACTCATG 57.399 36.000 0.00 0.00 0.00 3.07
1656 2616 8.621532 TTTCACAGTAAATAAGCTCAACTCAT 57.378 30.769 0.00 0.00 0.00 2.90
1657 2617 8.506437 CATTTCACAGTAAATAAGCTCAACTCA 58.494 33.333 0.00 0.00 0.00 3.41
1698 2663 4.724798 ACCTAGATACTGTTATTTGGGGCA 59.275 41.667 0.00 0.00 27.60 5.36
1718 2683 7.280356 AGTAATACATCCGCAGATTTTTACCT 58.720 34.615 0.00 0.00 0.00 3.08
1813 3088 5.333645 GCTGACAAAGTGATACAACAGTGAG 60.334 44.000 0.00 0.00 0.00 3.51
1821 3096 5.213891 TCTCTTGCTGACAAAGTGATACA 57.786 39.130 0.00 0.00 34.74 2.29
1900 3503 6.092259 CGAAAATTAATATGGATCGGAGGGAC 59.908 42.308 0.00 0.00 0.00 4.46
1908 3511 7.115378 CCAAAGCTGCGAAAATTAATATGGATC 59.885 37.037 0.00 0.00 0.00 3.36
1909 3512 6.925165 CCAAAGCTGCGAAAATTAATATGGAT 59.075 34.615 0.00 0.00 0.00 3.41
2047 3886 4.210331 GCTGTTTGATATCCTCCCATGTT 58.790 43.478 0.00 0.00 0.00 2.71
2062 3901 1.526575 AATGGAGGCGGTGCTGTTTG 61.527 55.000 0.00 0.00 0.00 2.93
2199 4040 2.096417 GTCGCATTTGTAGTCGCAAACT 60.096 45.455 0.00 0.00 40.58 2.66
2240 4081 1.367346 TTCCATGCCTGTACCCAAGA 58.633 50.000 0.00 0.00 0.00 3.02
2295 4138 2.092429 CCAAGTGCCCAGCTCCTAAATA 60.092 50.000 0.00 0.00 0.00 1.40
2296 4139 1.341383 CCAAGTGCCCAGCTCCTAAAT 60.341 52.381 0.00 0.00 0.00 1.40
2297 4140 0.038166 CCAAGTGCCCAGCTCCTAAA 59.962 55.000 0.00 0.00 0.00 1.85
2298 4141 1.685224 CCAAGTGCCCAGCTCCTAA 59.315 57.895 0.00 0.00 0.00 2.69
2299 4142 2.971598 GCCAAGTGCCCAGCTCCTA 61.972 63.158 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.