Multiple sequence alignment - TraesCS5B01G532200

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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 TraesCS5B01G532200 chr5B 100.000 3844 0 0 1 3844 689901870 689898027 0.000000e+00 7099.0
1 TraesCS5B01G532200 chr5B 100.000 131 0 0 4140 4270 689897731 689897601 4.270000e-60 243.0
2 TraesCS5B01G532200 chr5B 79.237 236 18 16 972 1197 689879137 689878923 7.450000e-28 135.0
3 TraesCS5B01G532200 chr5D 94.466 3867 164 16 1 3844 546824485 546828324 0.000000e+00 5910.0
4 TraesCS5B01G532200 chr5D 77.951 449 31 25 334 779 546683017 546682634 7.190000e-53 219.0
5 TraesCS5B01G532200 chr5D 96.183 131 5 0 4140 4270 546828759 546828889 9.300000e-52 215.0
6 TraesCS5B01G532200 chr4A 93.700 3857 197 22 1 3826 622176404 622172563 0.000000e+00 5734.0
7 TraesCS5B01G532200 chr4A 93.115 305 21 0 3488 3792 53767606 53767302 8.420000e-122 448.0
8 TraesCS5B01G532200 chr4A 87.766 188 15 5 3658 3837 461675130 461674943 3.340000e-51 213.0
9 TraesCS5B01G532200 chr4A 84.579 214 18 3 235 448 622245899 622246097 9.370000e-47 198.0
10 TraesCS5B01G532200 chr4A 82.677 254 13 15 529 779 622248010 622248235 3.370000e-46 196.0
11 TraesCS5B01G532200 chr4A 90.789 76 1 2 4147 4216 622172535 622172460 3.510000e-16 97.1
12 TraesCS5B01G532200 chr3D 93.506 308 20 0 3485 3792 97984604 97984911 3.890000e-125 459.0
13 TraesCS5B01G532200 chr2D 94.314 299 17 0 3494 3792 411766120 411765822 3.890000e-125 459.0
14 TraesCS5B01G532200 chr6D 93.311 299 20 0 3494 3792 38963688 38963390 3.920000e-120 442.0
15 TraesCS5B01G532200 chr2A 88.360 189 12 7 3658 3837 574011867 574012054 7.190000e-53 219.0
16 TraesCS5B01G532200 chr2A 87.766 188 15 5 3658 3837 266791952 266791765 3.340000e-51 213.0


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 TraesCS5B01G532200 chr5B 689897601 689901870 4269 True 3671.00 7099 100.0000 1 4270 2 chr5B.!!$R2 4269
1 TraesCS5B01G532200 chr5D 546824485 546828889 4404 False 3062.50 5910 95.3245 1 4270 2 chr5D.!!$F1 4269
2 TraesCS5B01G532200 chr4A 622172460 622176404 3944 True 2915.55 5734 92.2445 1 4216 2 chr4A.!!$R3 4215

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
106 107 0.183492 TCACTTTGTGCTCCTGGCTT 59.817 50.000 0.00 0.0 42.39 4.35 F
229 233 0.532115 ATGCCCAAATGAGCCGAAAC 59.468 50.000 0.00 0.0 0.00 2.78 F
772 776 0.600518 CTCCATCTCCATCGCTGCTG 60.601 60.000 0.00 0.0 0.00 4.41 F
947 959 1.098050 ATCCATTTCCAGCTCGTTGC 58.902 50.000 0.00 0.0 43.29 4.17 F
2143 2166 1.153289 AAGGCCATAGCACTGCTCG 60.153 57.895 6.86 0.0 42.56 5.03 F
2928 2951 0.178955 TGGAGGTCAGGAACGTGGTA 60.179 55.000 0.00 0.0 0.00 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1772 0.249868 TGCACTGGAGGTTGTCGAAG 60.250 55.000 0.00 0.00 0.00 3.79 R
2064 2087 0.325933 TCCAGCTGACAATGTCTGGG 59.674 55.000 17.39 13.64 44.62 4.45 R
2353 2376 0.172578 TCACGGTGATCCATGACGTC 59.827 55.000 9.11 9.11 30.56 4.34 R
2433 2456 0.249699 TCTCGCTGAACGCCTTCAAA 60.250 50.000 0.00 0.00 43.23 2.69 R
2997 3020 2.301009 TGTATCTCGCATGGCATCAGAT 59.699 45.455 14.43 14.43 0.00 2.90 R
3800 3837 3.311106 TCAGTAACTTCGTGTTTAGGCG 58.689 45.455 2.43 0.00 39.89 5.52 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
47 48 2.441164 ACACAAAACCGGCAGGCA 60.441 55.556 0.00 0.00 42.76 4.75
49 50 1.080569 CACAAAACCGGCAGGCATC 60.081 57.895 0.00 0.00 42.76 3.91
106 107 0.183492 TCACTTTGTGCTCCTGGCTT 59.817 50.000 0.00 0.00 42.39 4.35
144 145 0.611896 AGTGCCCTGCCAAACCATAC 60.612 55.000 0.00 0.00 0.00 2.39
146 147 0.611618 TGCCCTGCCAAACCATACAG 60.612 55.000 0.00 0.00 0.00 2.74
229 233 0.532115 ATGCCCAAATGAGCCGAAAC 59.468 50.000 0.00 0.00 0.00 2.78
765 769 2.356793 CGCGCCTCCATCTCCATC 60.357 66.667 0.00 0.00 0.00 3.51
772 776 0.600518 CTCCATCTCCATCGCTGCTG 60.601 60.000 0.00 0.00 0.00 4.41
773 777 2.252346 CCATCTCCATCGCTGCTGC 61.252 63.158 5.34 5.34 0.00 5.25
774 778 1.227586 CATCTCCATCGCTGCTGCT 60.228 57.895 14.03 0.00 36.97 4.24
775 779 1.227586 ATCTCCATCGCTGCTGCTG 60.228 57.895 14.03 5.96 36.97 4.41
779 783 3.574445 CATCGCTGCTGCTGCTCC 61.574 66.667 25.43 6.56 40.48 4.70
864 872 2.630580 TGTGTATTCTTTTGTTGGGCCC 59.369 45.455 17.59 17.59 0.00 5.80
866 874 2.630580 TGTATTCTTTTGTTGGGCCCAC 59.369 45.455 28.70 20.43 0.00 4.61
867 875 2.101640 ATTCTTTTGTTGGGCCCACT 57.898 45.000 28.70 0.00 0.00 4.00
947 959 1.098050 ATCCATTTCCAGCTCGTTGC 58.902 50.000 0.00 0.00 43.29 4.17
964 976 2.498726 CTTCCTCTCTGCGGCTCC 59.501 66.667 0.00 0.00 0.00 4.70
1250 1273 3.124921 GTTCGCGGACATGGTGGG 61.125 66.667 14.01 0.00 0.00 4.61
1566 1589 4.802051 CAGATGGTGGTGCGGGGG 62.802 72.222 0.00 0.00 0.00 5.40
1605 1628 2.512515 GTGACGAGCATCCTGGCC 60.513 66.667 0.00 0.00 0.00 5.36
1716 1739 1.711298 GCGCTGATCGATTTCTACTCG 59.289 52.381 0.00 0.00 41.67 4.18
1742 1765 2.508891 GCGAGTTCGACATGGCGAG 61.509 63.158 24.88 13.76 41.79 5.03
1749 1772 2.202756 GACATGGCGAGGACGGTC 60.203 66.667 0.00 0.00 40.15 4.79
1961 1984 1.202915 TCACTCTTTGGCCATCAAGCA 60.203 47.619 6.09 0.00 36.62 3.91
1989 2012 1.817209 GAGTGATCTCCGGGTGTCC 59.183 63.158 0.00 0.00 34.87 4.02
2064 2087 2.105128 CTCCGTGGCATCGAGGAC 59.895 66.667 0.00 0.00 0.00 3.85
2143 2166 1.153289 AAGGCCATAGCACTGCTCG 60.153 57.895 6.86 0.00 42.56 5.03
2181 2204 2.000447 GGTCTCATGCCAAACGACTAC 59.000 52.381 0.00 0.00 0.00 2.73
2353 2376 4.139420 CAGCGAGGCTTGCGTTCG 62.139 66.667 20.63 7.50 36.40 3.95
2433 2456 2.959484 CGGTGAGGTGGACATGGCT 61.959 63.158 0.00 0.00 0.00 4.75
2458 2481 1.704582 GCGTTCAGCGAGATGTGTC 59.295 57.895 0.00 0.00 44.77 3.67
2628 2651 4.451150 GTCGACATGCTGGGCCGA 62.451 66.667 11.55 0.00 0.00 5.54
2688 2711 2.649129 GCCTTTTGAGCCCGGCATT 61.649 57.895 13.15 0.00 42.06 3.56
2874 2897 3.606662 CGGCGGAGGATGGACGAT 61.607 66.667 0.00 0.00 0.00 3.73
2877 2900 2.029666 CGGAGGATGGACGATGCC 59.970 66.667 0.00 0.00 0.00 4.40
2924 2947 2.214920 GGGTGGAGGTCAGGAACGT 61.215 63.158 0.00 0.00 0.00 3.99
2928 2951 0.178955 TGGAGGTCAGGAACGTGGTA 60.179 55.000 0.00 0.00 0.00 3.25
2931 2954 1.549170 GAGGTCAGGAACGTGGTACAT 59.451 52.381 0.00 0.00 44.52 2.29
2940 2963 2.369870 CGTGGTACATGCCTTCGTC 58.630 57.895 0.00 0.00 44.52 4.20
2945 2968 3.709880 TACATGCCTTCGTCGCCCG 62.710 63.158 0.00 0.00 38.13 6.13
2989 3012 1.826921 TCCATCTACCGGACGCTCC 60.827 63.158 9.46 0.00 0.00 4.70
2990 3013 2.125326 CCATCTACCGGACGCTCCA 61.125 63.158 9.46 0.00 35.91 3.86
2993 3016 3.528370 CTACCGGACGCTCCAGGG 61.528 72.222 9.46 7.60 35.91 4.45
2997 3020 2.131709 CCGGACGCTCCAGGGATTA 61.132 63.158 0.00 0.00 35.91 1.75
3024 3047 1.937108 GCCATGCGAGATACAGCCTAC 60.937 57.143 0.00 0.00 0.00 3.18
3025 3048 1.341209 CCATGCGAGATACAGCCTACA 59.659 52.381 0.00 0.00 0.00 2.74
3029 3052 1.864435 GCGAGATACAGCCTACAACGG 60.864 57.143 0.00 0.00 0.00 4.44
3063 3086 9.358872 GAATTCTTCGATGTACATATGCAGATA 57.641 33.333 8.71 2.52 0.00 1.98
3127 3163 5.358725 GGTAACTGGGTCTTTGTTCTTTTCA 59.641 40.000 0.00 0.00 0.00 2.69
3298 3334 5.979517 GCTGCAGAAAGTTGATTAAAACACT 59.020 36.000 20.43 0.00 32.21 3.55
3366 3402 4.073293 ACCCTATTTGGCATTAGACTCG 57.927 45.455 6.57 0.00 0.00 4.18
3387 3423 7.263496 ACTCGCTAGTAAACTGGGTTTATAAG 58.737 38.462 6.22 7.75 39.64 1.73
3500 3537 9.371136 CACTACACTAACTAATCACATGAACAT 57.629 33.333 0.00 0.00 0.00 2.71
3510 3547 7.877612 ACTAATCACATGAACATAACAGACACA 59.122 33.333 0.00 0.00 0.00 3.72
3528 3565 6.036844 CAGACACATAGCTACGAGTTACACTA 59.963 42.308 0.00 0.00 0.00 2.74
3725 3762 3.084039 CACTATGGTGCATTGGTTCACT 58.916 45.455 0.00 0.00 36.61 3.41
4251 4442 7.817418 ATCTCTGAAGTCTCTTGGTATCTAC 57.183 40.000 0.00 0.00 0.00 2.59
4256 4447 5.123502 TGAAGTCTCTTGGTATCTACGTGAC 59.876 44.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 2.076100 CTGACTAACAATGCGAGGCAA 58.924 47.619 0.00 0.00 43.62 4.52
144 145 5.069648 TGTTCTTACTGATCTCCTATGCCTG 59.930 44.000 0.00 0.00 0.00 4.85
146 147 5.537188 CTGTTCTTACTGATCTCCTATGCC 58.463 45.833 0.00 0.00 0.00 4.40
229 233 2.868583 CCTTGTTCTCGTATGCCATCAG 59.131 50.000 0.00 0.00 0.00 2.90
468 472 3.379445 TTCTCCGACGTGCTCCCC 61.379 66.667 0.00 0.00 0.00 4.81
772 776 0.106519 AGAGAGAGAGAGGGAGCAGC 60.107 60.000 0.00 0.00 0.00 5.25
773 777 2.172505 TGTAGAGAGAGAGAGGGAGCAG 59.827 54.545 0.00 0.00 0.00 4.24
774 778 2.172505 CTGTAGAGAGAGAGAGGGAGCA 59.827 54.545 0.00 0.00 0.00 4.26
775 779 2.851195 CTGTAGAGAGAGAGAGGGAGC 58.149 57.143 0.00 0.00 0.00 4.70
779 783 3.632145 GGAAAGCTGTAGAGAGAGAGAGG 59.368 52.174 0.00 0.00 0.00 3.69
840 848 4.929211 GGCCCAACAAAAGAATACACATTC 59.071 41.667 0.00 0.00 40.85 2.67
913 921 0.107017 TGGATAAGCTTCAGCCCAGC 60.107 55.000 0.00 0.00 43.38 4.85
947 959 1.892819 TTGGAGCCGCAGAGAGGAAG 61.893 60.000 0.00 0.00 0.00 3.46
955 967 1.673665 AAAGAGCTTGGAGCCGCAG 60.674 57.895 0.00 0.00 43.77 5.18
956 968 1.968017 CAAAGAGCTTGGAGCCGCA 60.968 57.895 0.00 0.00 43.77 5.69
964 976 0.815734 CTCCCATGGCAAAGAGCTTG 59.184 55.000 6.09 0.00 44.79 4.01
1090 1113 2.513204 CATGAGCCCGTCCAGCTG 60.513 66.667 6.78 6.78 41.75 4.24
1091 1114 2.249413 CTTCATGAGCCCGTCCAGCT 62.249 60.000 0.00 0.00 45.23 4.24
1566 1589 4.373116 TGCTCGTTCGGCTCCACC 62.373 66.667 7.06 0.00 0.00 4.61
1716 1739 1.710013 TGTCGAACTCGCCATTTCTC 58.290 50.000 0.00 0.00 39.60 2.87
1729 1752 2.180769 CGTCCTCGCCATGTCGAA 59.819 61.111 0.00 0.00 38.08 3.71
1749 1772 0.249868 TGCACTGGAGGTTGTCGAAG 60.250 55.000 0.00 0.00 0.00 3.79
1807 1830 1.144936 CCGGCCTTCCATCTCTGAC 59.855 63.158 0.00 0.00 0.00 3.51
1961 1984 0.749649 GAGATCACTCGCCAGGTCAT 59.250 55.000 0.00 0.00 33.32 3.06
1989 2012 0.395311 ACATGGAGAGCAGGGCATTG 60.395 55.000 0.00 0.00 0.00 2.82
2064 2087 0.325933 TCCAGCTGACAATGTCTGGG 59.674 55.000 17.39 13.64 44.62 4.45
2106 2129 1.191489 TCTCACCATGGCCGTTCTGA 61.191 55.000 13.04 5.95 0.00 3.27
2143 2166 1.310933 CCTTGTGAGTGCATCTGGGC 61.311 60.000 0.00 0.00 0.00 5.36
2337 2360 4.357947 TCGAACGCAAGCCTCGCT 62.358 61.111 6.38 0.00 43.37 4.93
2353 2376 0.172578 TCACGGTGATCCATGACGTC 59.827 55.000 9.11 9.11 30.56 4.34
2433 2456 0.249699 TCTCGCTGAACGCCTTCAAA 60.250 50.000 0.00 0.00 43.23 2.69
2628 2651 1.300697 GTCGTCGAACCTGCCACTT 60.301 57.895 0.00 0.00 0.00 3.16
2686 2709 2.563179 ACAGCGTCTTCCACACTAGAAT 59.437 45.455 0.00 0.00 0.00 2.40
2688 2711 1.617322 ACAGCGTCTTCCACACTAGA 58.383 50.000 0.00 0.00 0.00 2.43
2749 2772 4.577246 GAGCTTCTCGGCGGCGAT 62.577 66.667 34.71 19.82 37.29 4.58
2778 2801 3.827898 CTCGCCGAGTCCTGGTCC 61.828 72.222 5.82 0.00 0.00 4.46
2874 2897 2.528127 TCCTTTCTCACCCCGGCA 60.528 61.111 0.00 0.00 0.00 5.69
2877 2900 2.269241 GCCTCCTTTCTCACCCCG 59.731 66.667 0.00 0.00 0.00 5.73
2924 2947 1.447140 GCGACGAAGGCATGTACCA 60.447 57.895 0.00 0.00 0.00 3.25
2951 2974 4.131088 GCGAGTCCGGGTGAGACC 62.131 72.222 0.00 0.00 37.60 3.85
2984 3007 2.934364 GCATCAGATAATCCCTGGAGCG 60.934 54.545 0.00 0.00 32.73 5.03
2989 3012 2.753452 GCATGGCATCAGATAATCCCTG 59.247 50.000 0.00 0.00 0.00 4.45
2990 3013 2.617276 CGCATGGCATCAGATAATCCCT 60.617 50.000 0.00 0.00 0.00 4.20
2993 3016 3.593096 TCTCGCATGGCATCAGATAATC 58.407 45.455 0.00 0.00 0.00 1.75
2997 3020 2.301009 TGTATCTCGCATGGCATCAGAT 59.699 45.455 14.43 14.43 0.00 2.90
3045 3068 9.178427 CACATCTATATCTGCATATGTACATCG 57.822 37.037 12.68 6.23 0.00 3.84
3090 3113 3.181454 CCCAGTTACCTTGACAGAACAGT 60.181 47.826 0.00 0.00 0.00 3.55
3091 3114 3.181454 ACCCAGTTACCTTGACAGAACAG 60.181 47.826 0.00 0.00 0.00 3.16
3092 3115 2.775384 ACCCAGTTACCTTGACAGAACA 59.225 45.455 0.00 0.00 0.00 3.18
3111 3147 5.584251 TGGCAATTTGAAAAGAACAAAGACC 59.416 36.000 0.00 0.00 39.90 3.85
3256 3292 7.377398 TCTGCAGCACATTTTAATTGTTACAT 58.623 30.769 9.47 0.00 0.00 2.29
3298 3334 3.086818 TCGTCGATGTCACACTGAAAA 57.913 42.857 4.21 0.00 0.00 2.29
3366 3402 7.825761 TGGAACTTATAAACCCAGTTTACTAGC 59.174 37.037 2.22 0.00 40.16 3.42
3500 3537 5.892160 AACTCGTAGCTATGTGTCTGTTA 57.108 39.130 18.36 0.00 0.00 2.41
3725 3762 2.821378 CAGTGGCATCAGGAAATCACAA 59.179 45.455 0.00 0.00 0.00 3.33
3800 3837 3.311106 TCAGTAACTTCGTGTTTAGGCG 58.689 45.455 2.43 0.00 39.89 5.52
4229 4420 5.587043 ACGTAGATACCAAGAGACTTCAGAG 59.413 44.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.