Multiple sequence alignment - TraesCS1B01G229500

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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 TraesCS1B01G229500 chr1B 100.000 2954 0 0 1 2954 412242057 412245010 0.000000e+00 5456.0
1 TraesCS1B01G229500 chr1D 94.367 3000 92 30 1 2954 305230964 305227996 0.000000e+00 4532.0
2 TraesCS1B01G229500 chr1A 93.621 2273 67 31 716 2953 382253426 382251197 0.000000e+00 3323.0
3 TraesCS1B01G229500 chr1A 92.800 250 11 4 249 493 382253962 382253715 3.620000e-94 355.0
4 TraesCS1B01G229500 chr7A 88.732 71 5 3 97 165 584204152 584204221 1.890000e-12 84.2
5 TraesCS1B01G229500 chr6B 87.931 58 7 0 96 153 12593054 12592997 5.280000e-08 69.4


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 TraesCS1B01G229500 chr1B 412242057 412245010 2953 False 5456 5456 100.0000 1 2954 1 chr1B.!!$F1 2953
1 TraesCS1B01G229500 chr1D 305227996 305230964 2968 True 4532 4532 94.3670 1 2954 1 chr1D.!!$R1 2953
2 TraesCS1B01G229500 chr1A 382251197 382253962 2765 True 1839 3323 93.2105 249 2953 2 chr1A.!!$R1 2704

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
86 87 2.377193 TGGTAAGTGCCACATTTAGGGT 59.623 45.455 0.0 0.0 32.81 4.34 F
1221 1294 1.358046 GCTAATCGAGGCGTACCGT 59.642 57.895 0.0 0.0 42.76 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1263 1336 3.063084 GCGACCTCGTCCCAGTCT 61.063 66.667 0.00 0.00 42.22 3.24 R
2877 2998 0.323629 TCGTGAATTCACACCCTCCC 59.676 55.000 32.06 8.58 46.75 4.30 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 5.015733 CGAAGGAAAACGAGATTCATTTCG 58.984 41.667 15.61 15.61 42.26 3.46
83 84 4.079253 ACCTTGGTAAGTGCCACATTTAG 58.921 43.478 0.00 0.00 38.42 1.85
86 87 2.377193 TGGTAAGTGCCACATTTAGGGT 59.623 45.455 0.00 0.00 32.81 4.34
96 97 6.490040 GTGCCACATTTAGGGTATGAACATAT 59.510 38.462 0.00 0.00 0.00 1.78
97 98 6.489700 TGCCACATTTAGGGTATGAACATATG 59.510 38.462 0.00 0.00 0.00 1.78
99 100 6.071952 CCACATTTAGGGTATGAACATATGGC 60.072 42.308 7.80 0.00 0.00 4.40
102 103 7.729881 ACATTTAGGGTATGAACATATGGCAAT 59.270 33.333 7.80 0.00 0.00 3.56
103 104 8.587608 CATTTAGGGTATGAACATATGGCAATT 58.412 33.333 7.80 0.00 0.00 2.32
147 148 8.607459 CAAGTTTAGTGATATGAGGATGACAAC 58.393 37.037 0.00 0.00 0.00 3.32
150 151 9.167311 GTTTAGTGATATGAGGATGACAACTTT 57.833 33.333 0.00 0.00 0.00 2.66
280 281 3.961729 GGTGCTTCGTACCACACC 58.038 61.111 5.74 5.74 45.22 4.16
303 304 7.592533 CACCTGTGTCACTTATCATTTGAAAAG 59.407 37.037 4.27 0.00 0.00 2.27
932 1005 2.633481 GCCTCCTTATATGACCGGTTCT 59.367 50.000 9.42 0.99 0.00 3.01
1044 1117 3.507009 GACGACGTCCCCTCCTCG 61.507 72.222 17.25 0.00 0.00 4.63
1221 1294 1.358046 GCTAATCGAGGCGTACCGT 59.642 57.895 0.00 0.00 42.76 4.83
2025 2110 5.432885 TTGCTGGCTTTGTTAGTTAACTC 57.567 39.130 12.39 0.00 37.12 3.01
2027 2112 3.120304 GCTGGCTTTGTTAGTTAACTCCG 60.120 47.826 12.39 3.60 37.12 4.63
2028 2113 4.062991 CTGGCTTTGTTAGTTAACTCCGT 58.937 43.478 12.39 0.00 37.12 4.69
2029 2114 3.810941 TGGCTTTGTTAGTTAACTCCGTG 59.189 43.478 12.39 0.57 37.12 4.94
2031 2116 4.274214 GGCTTTGTTAGTTAACTCCGTGTT 59.726 41.667 12.39 0.00 42.31 3.32
2032 2117 5.202640 GCTTTGTTAGTTAACTCCGTGTTG 58.797 41.667 12.39 0.15 39.55 3.33
2033 2118 5.006941 GCTTTGTTAGTTAACTCCGTGTTGA 59.993 40.000 12.39 0.00 39.55 3.18
2208 2314 4.140536 AGAAAAGAGTGCAGCTTAGCTTT 58.859 39.130 3.00 0.00 36.40 3.51
2217 2323 2.292828 AGCTTAGCTTTGCTGGGAAA 57.707 45.000 0.00 0.00 40.10 3.13
2263 2369 3.213506 TCTTTGTCTTGCTGCTGCTTTA 58.786 40.909 17.00 1.71 40.48 1.85
2271 2377 4.393062 TCTTGCTGCTGCTTTACTATTGTC 59.607 41.667 17.00 0.00 40.48 3.18
2366 2472 0.751277 TGTTATGGATGGCCCTTGCG 60.751 55.000 0.00 0.00 38.85 4.85
2386 2492 4.221262 TGCGTAACTATCAACTGGGTACTT 59.779 41.667 0.00 0.00 0.00 2.24
2497 2604 2.565841 GTGAGTTTCACAGTTCCTGCT 58.434 47.619 4.42 0.00 46.22 4.24
2651 2768 9.557338 GTAACTAATGTCACTGGATACGATATC 57.443 37.037 0.00 0.00 42.51 1.63
2674 2791 6.180472 TCTGTTCTTCTCAACCTTGAACTTT 58.820 36.000 0.00 0.00 38.17 2.66
2688 2805 1.472878 GAACTTTTCCATTCCCTCCGC 59.527 52.381 0.00 0.00 0.00 5.54
2689 2806 0.323451 ACTTTTCCATTCCCTCCGCC 60.323 55.000 0.00 0.00 0.00 6.13
2690 2807 1.000145 TTTTCCATTCCCTCCGCCC 60.000 57.895 0.00 0.00 0.00 6.13
2691 2808 2.508407 TTTTCCATTCCCTCCGCCCC 62.508 60.000 0.00 0.00 0.00 5.80
2694 2811 3.158648 CATTCCCTCCGCCCCGTA 61.159 66.667 0.00 0.00 0.00 4.02
2695 2812 2.842936 ATTCCCTCCGCCCCGTAG 60.843 66.667 0.00 0.00 0.00 3.51
2751 2868 6.149807 GGTCGGTAATTTGATTGACTAACCAA 59.850 38.462 0.00 0.00 0.00 3.67
2866 2987 0.248907 ATCAACGACCGTCCTATGCG 60.249 55.000 0.00 0.00 0.00 4.73
2873 2994 4.944372 CGTCCTATGCGCCGGACC 62.944 72.222 25.40 13.71 45.41 4.46
2877 2998 2.028190 CTATGCGCCGGACCTGAG 59.972 66.667 5.05 0.00 0.00 3.35
2894 3015 1.351017 TGAGGGAGGGTGTGAATTCAC 59.649 52.381 28.10 28.10 46.59 3.18
2930 3055 4.778213 AAAGCACCATAGCCAGAAGATA 57.222 40.909 0.00 0.00 34.23 1.98
2953 3078 2.876079 GCCTCATGGAAGAAACGAACCT 60.876 50.000 0.00 0.00 34.57 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.249155 TCGTTTTCCTTCGCTCGTGT 60.249 50.000 0.00 0.00 0.00 4.49
21 22 2.993899 TGAATCTCGTTTTCCTTCGCTC 59.006 45.455 0.00 0.00 0.00 5.03
67 68 5.433526 TCATACCCTAAATGTGGCACTTAC 58.566 41.667 19.83 0.00 0.00 2.34
83 84 4.082787 CGGAATTGCCATATGTTCATACCC 60.083 45.833 1.24 1.13 35.94 3.69
86 87 5.825151 TGTTCGGAATTGCCATATGTTCATA 59.175 36.000 1.24 0.00 35.94 2.15
118 119 7.439655 GTCATCCTCATATCACTAAACTTGTCC 59.560 40.741 0.00 0.00 0.00 4.02
120 121 7.851228 TGTCATCCTCATATCACTAAACTTGT 58.149 34.615 0.00 0.00 0.00 3.16
171 172 5.828299 ACTGAAACTTGTCATCCGAAAAA 57.172 34.783 0.00 0.00 0.00 1.94
177 178 8.141268 TCCAATAAAAACTGAAACTTGTCATCC 58.859 33.333 0.00 0.00 0.00 3.51
215 216 9.528018 CTAAATAAAGTTGCTGTCCAAAAAGAA 57.472 29.630 0.00 0.00 34.68 2.52
216 217 8.691797 ACTAAATAAAGTTGCTGTCCAAAAAGA 58.308 29.630 0.00 0.00 34.68 2.52
252 253 2.852075 AAGCACCCCGGTCCTGAA 60.852 61.111 0.00 0.00 0.00 3.02
457 464 0.984995 CGTCTCCTTTCCTTTCCCCT 59.015 55.000 0.00 0.00 0.00 4.79
932 1005 2.997584 CGGAGGAGGAGGAGGTGGA 61.998 68.421 0.00 0.00 0.00 4.02
1221 1294 3.240134 GAGCGCCTCCCACTTGTCA 62.240 63.158 2.29 0.00 0.00 3.58
1263 1336 3.063084 GCGACCTCGTCCCAGTCT 61.063 66.667 0.00 0.00 42.22 3.24
2025 2110 4.690748 AGTAGAAACATCACATCAACACGG 59.309 41.667 0.00 0.00 0.00 4.94
2027 2112 7.386299 AGAAGAGTAGAAACATCACATCAACAC 59.614 37.037 0.00 0.00 0.00 3.32
2028 2113 7.445121 AGAAGAGTAGAAACATCACATCAACA 58.555 34.615 0.00 0.00 0.00 3.33
2029 2114 7.897575 AGAAGAGTAGAAACATCACATCAAC 57.102 36.000 0.00 0.00 0.00 3.18
2031 2116 7.386025 CACAAGAAGAGTAGAAACATCACATCA 59.614 37.037 0.00 0.00 0.00 3.07
2032 2117 7.386299 ACACAAGAAGAGTAGAAACATCACATC 59.614 37.037 0.00 0.00 0.00 3.06
2033 2118 7.220030 ACACAAGAAGAGTAGAAACATCACAT 58.780 34.615 0.00 0.00 0.00 3.21
2208 2314 3.293337 CCAGATGATGATTTTCCCAGCA 58.707 45.455 0.00 0.00 34.26 4.41
2217 2323 3.928005 AGCAGTGACCAGATGATGATT 57.072 42.857 0.00 0.00 0.00 2.57
2263 2369 6.648310 CACTGTGAGACAATCTTGACAATAGT 59.352 38.462 0.32 0.00 0.00 2.12
2366 2472 8.788325 ATTCAAAGTACCCAGTTGATAGTTAC 57.212 34.615 0.00 0.00 31.66 2.50
2386 2492 3.491276 CCTGCAGCAACTGTGAAATTCAA 60.491 43.478 8.66 0.00 33.43 2.69
2425 2531 3.065371 GCAACTGTAAAACTCACAGCACT 59.935 43.478 2.51 0.00 45.96 4.40
2428 2534 3.621794 CAGCAACTGTAAAACTCACAGC 58.378 45.455 2.51 0.00 45.96 4.40
2497 2604 8.684386 TTCATACTACAAACAGTTCAATTCCA 57.316 30.769 0.00 0.00 0.00 3.53
2651 2768 6.442513 AAAGTTCAAGGTTGAGAAGAACAG 57.557 37.500 0.00 0.00 40.63 3.16
2674 2791 3.416880 GGGGCGGAGGGAATGGAA 61.417 66.667 0.00 0.00 0.00 3.53
2690 2807 1.530013 CCGCCCTATACACCCTACGG 61.530 65.000 0.00 0.00 0.00 4.02
2691 2808 1.530013 CCCGCCCTATACACCCTACG 61.530 65.000 0.00 0.00 0.00 3.51
2692 2809 1.190178 CCCCGCCCTATACACCCTAC 61.190 65.000 0.00 0.00 0.00 3.18
2693 2810 1.156803 CCCCGCCCTATACACCCTA 59.843 63.158 0.00 0.00 0.00 3.53
2694 2811 2.122547 CCCCGCCCTATACACCCT 60.123 66.667 0.00 0.00 0.00 4.34
2695 2812 2.447186 ACCCCGCCCTATACACCC 60.447 66.667 0.00 0.00 0.00 4.61
2696 2813 2.826702 CACCCCGCCCTATACACC 59.173 66.667 0.00 0.00 0.00 4.16
2697 2814 2.110420 GCACCCCGCCCTATACAC 59.890 66.667 0.00 0.00 32.94 2.90
2698 2815 3.542676 CGCACCCCGCCCTATACA 61.543 66.667 0.00 0.00 37.30 2.29
2699 2816 4.309950 CCGCACCCCGCCCTATAC 62.310 72.222 0.00 0.00 37.30 1.47
2722 2839 5.671493 AGTCAATCAAATTACCGACCTAGG 58.329 41.667 7.41 7.41 37.30 3.02
2873 2994 1.630369 TGAATTCACACCCTCCCTCAG 59.370 52.381 3.38 0.00 0.00 3.35
2877 2998 0.323629 TCGTGAATTCACACCCTCCC 59.676 55.000 32.06 8.58 46.75 4.30
2894 3015 1.946768 TGCTTTTGTTCTGAACCCTCG 59.053 47.619 17.26 5.56 0.00 4.63
2930 3055 2.814336 GTTCGTTTCTTCCATGAGGCTT 59.186 45.455 0.00 0.00 33.74 4.35


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

AutoCloner maintained by Alex Coulton.