Multiple sequence alignment - TraesCS1D01G070400

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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 TraesCS1D01G070400 chr1D 100.000 3209 0 0 1 3209 51831152 51827944 0.000000e+00 5927
1 TraesCS1D01G070400 chr1D 96.527 3225 81 10 1 3209 254460222 254463431 0.000000e+00 5306
2 TraesCS1D01G070400 chr5D 97.049 3219 81 8 1 3209 6252463 6249249 0.000000e+00 5406
3 TraesCS1D01G070400 chr5D 97.020 3222 71 11 1 3209 503340251 503343460 0.000000e+00 5395
4 TraesCS1D01G070400 chr5D 96.864 3221 86 9 1 3209 503314312 503317529 0.000000e+00 5374
5 TraesCS1D01G070400 chr1A 96.970 3234 66 12 1 3209 554482824 554486050 0.000000e+00 5400
6 TraesCS1D01G070400 chr3A 96.836 3224 76 9 1 3209 105556144 105552932 0.000000e+00 5365
7 TraesCS1D01G070400 chr3A 94.719 303 8 5 182 478 659158944 659158644 6.270000e-127 464
8 TraesCS1D01G070400 chr5A 97.228 3103 56 11 1 3085 559031136 559028046 0.000000e+00 5227
9 TraesCS1D01G070400 chr5A 92.647 204 7 2 1 202 167504962 167505159 1.460000e-73 287
10 TraesCS1D01G070400 chr7A 95.745 3220 111 14 1 3209 537840598 537837394 0.000000e+00 5164
11 TraesCS1D01G070400 chr4D 95.555 3217 121 14 1 3206 19901536 19904741 0.000000e+00 5129
12 TraesCS1D01G070400 chr2A 89.351 385 24 8 1 384 719803128 719803496 4.850000e-128 468
13 TraesCS1D01G070400 chr3B 95.425 153 4 3 1 152 12664258 12664408 1.150000e-59 241
14 TraesCS1D01G070400 chr7D 97.561 123 3 0 3087 3209 231599523 231599401 9.020000e-51 211


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 TraesCS1D01G070400 chr1D 51827944 51831152 3208 True 5927 5927 100.000 1 3209 1 chr1D.!!$R1 3208
1 TraesCS1D01G070400 chr1D 254460222 254463431 3209 False 5306 5306 96.527 1 3209 1 chr1D.!!$F1 3208
2 TraesCS1D01G070400 chr5D 6249249 6252463 3214 True 5406 5406 97.049 1 3209 1 chr5D.!!$R1 3208
3 TraesCS1D01G070400 chr5D 503340251 503343460 3209 False 5395 5395 97.020 1 3209 1 chr5D.!!$F2 3208
4 TraesCS1D01G070400 chr5D 503314312 503317529 3217 False 5374 5374 96.864 1 3209 1 chr5D.!!$F1 3208
5 TraesCS1D01G070400 chr1A 554482824 554486050 3226 False 5400 5400 96.970 1 3209 1 chr1A.!!$F1 3208
6 TraesCS1D01G070400 chr3A 105552932 105556144 3212 True 5365 5365 96.836 1 3209 1 chr3A.!!$R1 3208
7 TraesCS1D01G070400 chr5A 559028046 559031136 3090 True 5227 5227 97.228 1 3085 1 chr5A.!!$R1 3084
8 TraesCS1D01G070400 chr7A 537837394 537840598 3204 True 5164 5164 95.745 1 3209 1 chr7A.!!$R1 3208
9 TraesCS1D01G070400 chr4D 19901536 19904741 3205 False 5129 5129 95.555 1 3206 1 chr4D.!!$F1 3205

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
786 810 0.684535 TGAATCAGGTCCGACAGCAA 59.315 50.000 0.00 0.00 0.00 3.91 F
827 851 3.297134 AGGAGCTCTAGGAACTCTGAG 57.703 52.381 14.64 2.45 41.75 3.35 F
1702 1727 1.090052 GGCGGATTCACCTGCTACAC 61.090 60.000 0.00 0.00 37.93 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1703 0.532115 GCAGGTGAATCCGCCATTTT 59.468 50.000 0.00 0.0 45.32 1.82 R
2088 2114 1.536284 GCGGATCCTACTCTGGAAACG 60.536 57.143 10.75 0.0 39.85 3.60 R
2853 2892 1.202580 CCGGCTCCATACTCCTTCTTG 60.203 57.143 0.00 0.0 0.00 3.02 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
112 118 1.276145 GCCGAATCGACGACCTATGC 61.276 60.000 3.36 0.00 35.09 3.14
385 394 6.842676 AGAGGATAGGCCCATTACTTAAAAG 58.157 40.000 0.00 0.00 37.37 2.27
436 459 1.739466 GCGTGAGAGCCAAATGAATCA 59.261 47.619 0.00 0.00 0.00 2.57
736 760 8.314751 TGGAACAATTGGAAAAGTCTAAAAACA 58.685 29.630 10.83 0.00 31.92 2.83
785 809 0.904649 ATGAATCAGGTCCGACAGCA 59.095 50.000 0.00 0.00 0.00 4.41
786 810 0.684535 TGAATCAGGTCCGACAGCAA 59.315 50.000 0.00 0.00 0.00 3.91
827 851 3.297134 AGGAGCTCTAGGAACTCTGAG 57.703 52.381 14.64 2.45 41.75 3.35
886 910 4.702831 TCGTGCTAATATTGGCATTCTCA 58.297 39.130 26.54 8.84 46.33 3.27
962 986 9.698617 ACTTTCGTTTAGAATTTACGCATTATC 57.301 29.630 0.00 0.00 38.86 1.75
1040 1065 7.549488 AGTCGACGAAATTCATAAAATTCTCCT 59.451 33.333 10.46 0.00 0.00 3.69
1128 1153 4.567747 GGGGATGGGATTGCTCGTATTATT 60.568 45.833 0.00 0.00 0.00 1.40
1259 1284 4.290985 TGGGTTGATGATACAAGAGGGAAA 59.709 41.667 0.00 0.00 0.00 3.13
1547 1572 4.494091 AAACAGCAGTAGCCACAGATAT 57.506 40.909 0.00 0.00 43.56 1.63
1678 1703 8.803235 CCATGGAATACACTATTGTAGTAGCTA 58.197 37.037 5.56 0.00 41.62 3.32
1702 1727 1.090052 GGCGGATTCACCTGCTACAC 61.090 60.000 0.00 0.00 37.93 2.90
1717 1742 4.201657 TGCTACACTACAATACCTCGCTA 58.798 43.478 0.00 0.00 0.00 4.26
1835 1860 4.879545 TCGCCAAATGTCCCTTCTATTAAC 59.120 41.667 0.00 0.00 0.00 2.01
1850 1875 1.128809 TTAACAAGACCTCCCGGCCA 61.129 55.000 2.24 0.00 0.00 5.36
1899 1925 3.829886 TTGCATTCACGCCTTTTAGAG 57.170 42.857 0.00 0.00 0.00 2.43
1978 2004 4.155709 AGTTGAGACTCAATCTGGAGACA 58.844 43.478 20.43 0.00 38.79 3.41
2072 2098 1.590792 CCGGAATTCGACCCGCTAC 60.591 63.158 12.93 0.00 44.07 3.58
2088 2114 4.062991 CCGCTACTAATGTGGGTATTTCC 58.937 47.826 0.00 0.00 0.00 3.13
2271 2302 4.466015 GGAATTGCTTAAACAATCCCAGGA 59.534 41.667 2.25 0.00 39.32 3.86
2451 2482 2.146342 CAAGACATTCACCGAGCAAGT 58.854 47.619 0.00 0.00 0.00 3.16
2574 2605 7.148902 GGAATCGTTGAGAAAGCTTTTTCATTC 60.149 37.037 27.33 24.85 32.30 2.67
2695 2726 7.604461 ACCAAAGGTTTAGAAGACCTCTGTCT 61.604 42.308 0.00 0.00 46.60 3.41
2890 2929 0.822164 CGGTAGTGGGAATCGAACCT 59.178 55.000 10.93 0.00 0.00 3.50
2898 2937 0.322546 GGAATCGAACCTGCAACCCT 60.323 55.000 0.00 0.00 0.00 4.34
3088 3127 8.746052 TTCCAGAAATCCATACAAATACGAAT 57.254 30.769 0.00 0.00 0.00 3.34
3128 3167 0.321564 CTGGATCTTGTTGCACCCGA 60.322 55.000 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
436 459 4.586841 TCCCGAACCAAACATGAATCTTTT 59.413 37.500 0.00 0.00 0.00 2.27
785 809 1.951602 GTACGGCCTGTTGGAAAACTT 59.048 47.619 0.00 0.00 34.57 2.66
786 810 1.134037 TGTACGGCCTGTTGGAAAACT 60.134 47.619 0.00 0.00 34.57 2.66
827 851 7.642071 TGTAACTCGGTATTCAAACAACTAC 57.358 36.000 0.00 0.00 0.00 2.73
886 910 1.081174 TCTCTTCCATTCCAGGGACCT 59.919 52.381 0.00 0.00 33.18 3.85
954 978 2.301346 AGCAAGGGGAAAGATAATGCG 58.699 47.619 0.00 0.00 37.40 4.73
962 986 1.616159 TTTCGGAAGCAAGGGGAAAG 58.384 50.000 0.00 0.00 0.00 2.62
1128 1153 5.009631 CCTGACATTATTTCACCAAGACCA 58.990 41.667 0.00 0.00 0.00 4.02
1259 1284 8.829612 CAATTCTTCCTGTTGCTTTTACAAAAT 58.170 29.630 0.00 0.00 0.00 1.82
1289 1314 1.400737 AGCCTCACTCACGGGTATAC 58.599 55.000 0.00 0.00 0.00 1.47
1290 1315 2.154567 AAGCCTCACTCACGGGTATA 57.845 50.000 0.00 0.00 0.00 1.47
1547 1572 6.269769 ACCTTGCCCTTTTTGATTGAGAATTA 59.730 34.615 0.00 0.00 0.00 1.40
1678 1703 0.532115 GCAGGTGAATCCGCCATTTT 59.468 50.000 0.00 0.00 45.32 1.82
1702 1727 6.402983 CCCGTATAAGTAGCGAGGTATTGTAG 60.403 46.154 0.00 0.00 0.00 2.74
1850 1875 1.991070 CATCCCCTGGATAAGCCTCAT 59.009 52.381 0.00 0.00 40.98 2.90
1899 1925 6.852858 AGAGAATTTAATTTAGCGGCTCTC 57.147 37.500 5.39 2.99 0.00 3.20
1978 2004 8.147244 ACATTAGTAGGAATATAGGCGGAAAT 57.853 34.615 0.00 0.00 0.00 2.17
2072 2098 4.944930 TGGAAACGGAAATACCCACATTAG 59.055 41.667 0.00 0.00 34.64 1.73
2088 2114 1.536284 GCGGATCCTACTCTGGAAACG 60.536 57.143 10.75 0.00 39.85 3.60
2271 2302 3.260205 TCTTCCACTGGGAGAGGATTTT 58.740 45.455 1.29 0.00 46.01 1.82
2625 2656 9.424319 GGACGCAATCTTATTTCTATCTATTCA 57.576 33.333 0.00 0.00 0.00 2.57
2853 2892 1.202580 CCGGCTCCATACTCCTTCTTG 60.203 57.143 0.00 0.00 0.00 3.02
3028 3067 3.967987 GAGGAGCCCTCTTTACCATTCTA 59.032 47.826 12.53 0.00 46.41 2.10
3088 3127 6.217900 TCCAGTTGGTAAGGATAAAATACCCA 59.782 38.462 0.00 0.00 38.64 4.51


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

AutoCloner maintained by Alex Coulton.