Multiple sequence alignment - TraesCS5D01G137800

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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 TraesCS5D01G137800 chr5D 100.000 3500 0 0 1 3500 218696309 218692810 0.000000e+00 6464.0
1 TraesCS5D01G137800 chr5A 94.035 3487 152 15 56 3500 291931040 291927568 0.000000e+00 5236.0
2 TraesCS5D01G137800 chr5A 96.610 59 1 1 1 58 291931122 291931064 2.880000e-16 97.1
3 TraesCS5D01G137800 chr5B 96.818 1603 51 0 942 2544 241518376 241516774 0.000000e+00 2678.0
4 TraesCS5D01G137800 chr5B 89.430 965 63 13 2572 3500 241516776 241515815 0.000000e+00 1181.0
5 TraesCS5D01G137800 chr5B 89.860 572 37 14 373 939 241518976 241518421 0.000000e+00 715.0
6 TraesCS5D01G137800 chr5B 91.613 310 25 1 56 365 241519846 241519538 8.980000e-116 427.0
7 TraesCS5D01G137800 chr5B 93.220 59 2 1 1 57 241520494 241520436 6.220000e-13 86.1
8 TraesCS5D01G137800 chr2B 81.470 626 48 27 2419 3020 726670993 726671574 5.330000e-123 451.0
9 TraesCS5D01G137800 chr2B 89.956 229 21 2 3053 3281 726684276 726684502 9.500000e-76 294.0
10 TraesCS5D01G137800 chr7B 79.747 237 37 7 371 604 570362517 570362745 1.010000e-35 161.0
11 TraesCS5D01G137800 chr7B 79.832 238 33 11 371 604 570280769 570280995 3.620000e-35 159.0


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 TraesCS5D01G137800 chr5D 218692810 218696309 3499 True 6464.00 6464 100.0000 1 3500 1 chr5D.!!$R1 3499
1 TraesCS5D01G137800 chr5A 291927568 291931122 3554 True 2666.55 5236 95.3225 1 3500 2 chr5A.!!$R1 3499
2 TraesCS5D01G137800 chr5B 241515815 241520494 4679 True 1017.42 2678 92.1882 1 3500 5 chr5B.!!$R1 3499
3 TraesCS5D01G137800 chr2B 726670993 726671574 581 False 451.00 451 81.4700 2419 3020 1 chr2B.!!$F1 601

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
686 1840 0.393537 GTTCTGACCAGCTGGGATGG 60.394 60.0 35.42 21.34 43.87 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2550 3777 0.670546 GGGCATGGTACCGATCGATG 60.671 60.0 18.66 12.83 0.0 3.84 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
106 700 2.614057 CTCAAGGTCAACGCTCAAAACT 59.386 45.455 0.00 0.00 0.00 2.66
182 776 2.549754 CGCTTATCCCAGCCAATACTTG 59.450 50.000 0.00 0.00 36.31 3.16
307 901 8.201554 TGATTATGAATCTCACTTGTTAGCAC 57.798 34.615 1.24 0.00 38.72 4.40
325 919 3.904339 AGCACCGATCTAGGAATGGTTAT 59.096 43.478 0.00 0.00 34.73 1.89
391 1539 5.903764 TTGGAAATGCAAAAATTCTGACG 57.096 34.783 0.00 0.00 0.00 4.35
403 1551 7.616514 GCAAAAATTCTGACGTCGGATTTTTAC 60.617 37.037 36.25 30.47 40.76 2.01
413 1561 3.369756 GTCGGATTTTTACGCATGTCAGA 59.630 43.478 0.00 0.00 0.00 3.27
415 1563 4.634004 TCGGATTTTTACGCATGTCAGATT 59.366 37.500 0.00 0.00 0.00 2.40
460 1608 0.468226 ATGTCGCGGGTATGGACAAT 59.532 50.000 6.13 0.00 43.21 2.71
488 1637 2.827322 AGCACAAGCATGGCAAATTCTA 59.173 40.909 0.00 0.00 45.49 2.10
523 1676 0.683828 ATGCCGGGATTTGACATGCA 60.684 50.000 0.92 0.00 0.00 3.96
550 1703 2.025156 GAATTGCCATGCTCGCGG 59.975 61.111 6.13 0.00 0.00 6.46
621 1775 1.338973 CATCATATTTGCAGCGGGCTT 59.661 47.619 5.05 0.00 45.15 4.35
622 1776 1.473258 TCATATTTGCAGCGGGCTTT 58.527 45.000 5.05 0.00 45.15 3.51
684 1838 2.254152 TAGTTCTGACCAGCTGGGAT 57.746 50.000 35.42 17.17 41.15 3.85
685 1839 0.617413 AGTTCTGACCAGCTGGGATG 59.383 55.000 35.42 23.14 41.15 3.51
686 1840 0.393537 GTTCTGACCAGCTGGGATGG 60.394 60.000 35.42 21.34 43.87 3.51
687 1841 1.565390 TTCTGACCAGCTGGGATGGG 61.565 60.000 35.42 19.68 42.48 4.00
688 1842 1.997311 CTGACCAGCTGGGATGGGA 60.997 63.158 35.42 11.89 42.48 4.37
789 1943 1.523154 GCGGGTGATGCAAAGTTCCA 61.523 55.000 0.00 0.00 0.00 3.53
1092 2288 3.352338 GATTGACGGAGCCGACGGT 62.352 63.158 16.73 1.83 42.83 4.83
1122 2318 4.235762 ACGCAGCTGTCCAACGGT 62.236 61.111 16.64 0.00 0.00 4.83
1444 2640 1.084370 CGTCATCCGGCTCTTCAACC 61.084 60.000 0.00 0.00 0.00 3.77
1752 2948 3.088500 GAGCGTCGACATGCTTGCC 62.089 63.158 17.36 3.70 45.56 4.52
1788 2984 4.699522 AACCTCACCGGCGCCTTC 62.700 66.667 26.68 0.00 35.61 3.46
1878 3074 0.105039 CCTCCGACTACAAGGCCATC 59.895 60.000 5.01 0.00 0.00 3.51
1879 3075 0.824109 CTCCGACTACAAGGCCATCA 59.176 55.000 5.01 0.00 0.00 3.07
1880 3076 1.207089 CTCCGACTACAAGGCCATCAA 59.793 52.381 5.01 0.00 0.00 2.57
2767 4004 6.510536 TCTCTGTATCTGAACATGTATGCTG 58.489 40.000 0.00 0.00 0.00 4.41
2954 4222 6.749036 AAATCTAGTATGTCCTAAGTGGGG 57.251 41.667 0.00 0.00 36.20 4.96
2967 4235 3.603965 AAGTGGGGTTTTGGTGTGATA 57.396 42.857 0.00 0.00 0.00 2.15
2983 4251 4.335594 GTGTGATAACAAGTGATTAGGGGC 59.664 45.833 0.00 0.00 0.00 5.80
3368 4642 1.640670 TCTTAAAAGAGGCCAGGGCAT 59.359 47.619 16.94 6.70 44.11 4.40
3437 4731 6.551227 ACAGAGCAATACATAGGTGATACTCA 59.449 38.462 0.00 0.00 0.00 3.41
3453 4747 5.724370 TGATACTCAAATCCTTAGGGACACA 59.276 40.000 0.00 0.00 45.43 3.72
3479 4774 1.337823 ACACTTCCTAGTTCGCGCATT 60.338 47.619 8.75 0.00 30.26 3.56
3480 4775 1.061131 CACTTCCTAGTTCGCGCATTG 59.939 52.381 8.75 0.00 30.26 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 700 3.056536 TGCTGCTGGTTGTTTGTTTGTTA 60.057 39.130 0.00 0.00 0.00 2.41
182 776 0.391130 TCACCCTGCGATGTAACTGC 60.391 55.000 0.00 0.00 0.00 4.40
300 894 3.069729 ACCATTCCTAGATCGGTGCTAAC 59.930 47.826 0.00 0.00 0.00 2.34
325 919 6.174720 ACTTGTTCTGAATAGTGAGGTTCA 57.825 37.500 7.16 0.00 33.63 3.18
354 948 6.642950 TGCATTTCCAAAAATTAAATCGACGT 59.357 30.769 0.00 0.00 32.69 4.34
356 950 9.657121 TTTTGCATTTCCAAAAATTAAATCGAC 57.343 25.926 0.00 0.00 40.57 4.20
384 1532 2.409378 GCGTAAAAATCCGACGTCAGAA 59.591 45.455 17.16 0.00 38.80 3.02
391 1539 3.369756 TCTGACATGCGTAAAAATCCGAC 59.630 43.478 0.00 0.00 0.00 4.79
427 1575 5.585445 ACCCGCGACATGTAATTTTGTTATA 59.415 36.000 8.23 0.00 0.00 0.98
428 1576 4.396790 ACCCGCGACATGTAATTTTGTTAT 59.603 37.500 8.23 0.00 0.00 1.89
429 1577 3.752222 ACCCGCGACATGTAATTTTGTTA 59.248 39.130 8.23 0.00 0.00 2.41
430 1578 2.554893 ACCCGCGACATGTAATTTTGTT 59.445 40.909 8.23 0.00 0.00 2.83
431 1579 2.156098 ACCCGCGACATGTAATTTTGT 58.844 42.857 8.23 0.00 0.00 2.83
432 1580 2.911819 ACCCGCGACATGTAATTTTG 57.088 45.000 8.23 0.00 0.00 2.44
433 1581 3.314080 CCATACCCGCGACATGTAATTTT 59.686 43.478 8.23 0.00 0.00 1.82
493 1642 2.871096 TCCCGGCATGTTTAGTCTTT 57.129 45.000 0.00 0.00 0.00 2.52
496 1645 3.013921 TCAAATCCCGGCATGTTTAGTC 58.986 45.455 0.00 0.00 0.00 2.59
500 1653 1.626686 TGTCAAATCCCGGCATGTTT 58.373 45.000 0.00 0.00 0.00 2.83
509 1662 1.752498 TCAGCATGCATGTCAAATCCC 59.248 47.619 26.79 8.43 34.76 3.85
523 1676 2.100916 GCATGGCAATTCTCTTCAGCAT 59.899 45.455 0.00 0.00 0.00 3.79
577 1730 7.914465 TGTCAGATTTTTAAACATGGCAAAAC 58.086 30.769 0.00 0.00 0.00 2.43
578 1731 8.674263 ATGTCAGATTTTTAAACATGGCAAAA 57.326 26.923 0.00 0.00 29.00 2.44
626 1780 7.525688 TGCTATACTTTTCAGACGATTCAAG 57.474 36.000 0.00 0.00 0.00 3.02
704 1858 5.247110 ACTCTCTGTTCCAGCTCATCTAAAA 59.753 40.000 0.00 0.00 0.00 1.52
789 1943 3.047115 AGGAGATGAACATGCCTGATCT 58.953 45.455 0.00 0.00 0.00 2.75
845 1999 8.522003 TGTTTCCAACTCACGTAATACATAGTA 58.478 33.333 0.00 0.00 0.00 1.82
846 2000 7.380536 TGTTTCCAACTCACGTAATACATAGT 58.619 34.615 0.00 0.00 0.00 2.12
847 2001 7.758076 TCTGTTTCCAACTCACGTAATACATAG 59.242 37.037 0.00 0.00 0.00 2.23
848 2002 7.543172 GTCTGTTTCCAACTCACGTAATACATA 59.457 37.037 0.00 0.00 0.00 2.29
849 2003 6.367969 GTCTGTTTCCAACTCACGTAATACAT 59.632 38.462 0.00 0.00 0.00 2.29
850 2004 5.693104 GTCTGTTTCCAACTCACGTAATACA 59.307 40.000 0.00 0.00 0.00 2.29
851 2005 5.924825 AGTCTGTTTCCAACTCACGTAATAC 59.075 40.000 0.00 0.00 0.00 1.89
940 2136 1.932511 GCTTGAGACAGAGTAGCATGC 59.067 52.381 10.51 10.51 0.00 4.06
1092 2288 3.573772 CTGCGTCACGGGCTCTTCA 62.574 63.158 0.00 0.00 0.00 3.02
1122 2318 3.033764 GAGTGCGTCGCGGTGAAA 61.034 61.111 13.38 0.00 0.00 2.69
1464 2660 1.885887 TCCGATGGGTTTTCAAAGCTG 59.114 47.619 0.00 0.00 36.67 4.24
1677 2873 4.077184 CTGTCCAGGCGGCCGTAA 62.077 66.667 28.70 4.91 0.00 3.18
1812 3008 4.089239 TATGCGCGGAGGTTGCCA 62.089 61.111 8.83 0.00 0.00 4.92
2175 3371 2.838225 TAGCAGTAGCCGCTCCCC 60.838 66.667 0.00 0.00 43.56 4.81
2184 3380 4.498345 GGAAAGTCGATGAGGTAGCAGTAG 60.498 50.000 0.00 0.00 0.00 2.57
2374 3570 4.096003 CCACCGCTTCCACCCGAT 62.096 66.667 0.00 0.00 0.00 4.18
2445 3641 3.983044 GACTTGAGGTCCCTGTAATGT 57.017 47.619 0.00 0.00 38.93 2.71
2550 3777 0.670546 GGGCATGGTACCGATCGATG 60.671 60.000 18.66 12.83 0.00 3.84
2767 4004 5.159209 CCACCGGATACTTATACACGATTC 58.841 45.833 9.46 0.00 0.00 2.52
2954 4222 7.807907 CCTAATCACTTGTTATCACACCAAAAC 59.192 37.037 0.00 0.00 30.32 2.43
2967 4235 4.229582 TCATTAGGCCCCTAATCACTTGTT 59.770 41.667 15.03 0.00 44.61 2.83
2983 4251 7.424803 TCAAACAAGTCAACATGTTCATTAGG 58.575 34.615 8.48 0.00 36.86 2.69
3215 4489 2.896039 AGATCTCTGGGCTGGTATACC 58.104 52.381 15.50 15.50 0.00 2.73
3346 4620 2.302260 GCCCTGGCCTCTTTTAAGATC 58.698 52.381 3.32 0.00 33.93 2.75
3368 4642 4.079844 TCTGATGCCCCATGATTAGTTTGA 60.080 41.667 0.00 0.00 0.00 2.69
3437 4731 3.655777 TCCAACTGTGTCCCTAAGGATTT 59.344 43.478 0.00 0.00 46.41 2.17


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

AutoCloner maintained by Alex Coulton.