Multiple sequence alignment - TraesCS4A01G455200

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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 TraesCS4A01G455200 chr4A 100.000 4391 0 0 1 4391 718899025 718894635 0.000000e+00 8109
1 TraesCS4A01G455200 chr4A 97.869 3894 74 2 506 4391 718464660 718468552 0.000000e+00 6722
2 TraesCS4A01G455200 chr4A 94.578 498 27 0 2625 3122 718249897 718250394 0.000000e+00 771
3 TraesCS4A01G455200 chr4A 89.785 186 15 2 45 228 718458069 718458252 7.340000e-58 235
4 TraesCS4A01G455200 chr7D 88.045 3346 354 27 577 3910 26384610 26381299 0.000000e+00 3921
5 TraesCS4A01G455200 chr7D 87.179 2847 351 11 1072 3910 26449659 26446819 0.000000e+00 3223
6 TraesCS4A01G455200 chr7D 86.729 746 27 23 224 910 16371035 16370303 0.000000e+00 763
7 TraesCS4A01G455200 chr7D 89.583 288 24 3 680 966 26450009 26449727 1.160000e-95 361
8 TraesCS4A01G455200 chr7D 76.361 808 79 46 224 939 26450795 26450008 9.100000e-87 331
9 TraesCS4A01G455200 chr7D 81.590 239 22 7 363 579 26385208 26384970 1.250000e-40 178
10 TraesCS4A01G455200 chr7A 88.697 3123 327 15 791 3910 15276513 15273414 0.000000e+00 3788
11 TraesCS4A01G455200 chr7A 88.804 2733 295 9 1153 3881 15254393 15251668 0.000000e+00 3341
12 TraesCS4A01G455200 chr7A 81.452 372 37 11 401 755 15276998 15276642 4.330000e-70 276


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 TraesCS4A01G455200 chr4A 718894635 718899025 4390 True 8109.0 8109 100.000000 1 4391 1 chr4A.!!$R1 4390
1 TraesCS4A01G455200 chr4A 718464660 718468552 3892 False 6722.0 6722 97.869000 506 4391 1 chr4A.!!$F3 3885
2 TraesCS4A01G455200 chr7D 26381299 26385208 3909 True 2049.5 3921 84.817500 363 3910 2 chr7D.!!$R2 3547
3 TraesCS4A01G455200 chr7D 26446819 26450795 3976 True 1305.0 3223 84.374333 224 3910 3 chr7D.!!$R3 3686
4 TraesCS4A01G455200 chr7D 16370303 16371035 732 True 763.0 763 86.729000 224 910 1 chr7D.!!$R1 686
5 TraesCS4A01G455200 chr7A 15251668 15254393 2725 True 3341.0 3341 88.804000 1153 3881 1 chr7A.!!$R1 2728
6 TraesCS4A01G455200 chr7A 15273414 15276998 3584 True 2032.0 3788 85.074500 401 3910 2 chr7A.!!$R2 3509

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
61 62 0.031043 CCATGTGGTTGCTGTGTGTG 59.969 55.0 0.00 0.00 0.00 3.82 F
1739 2566 0.179108 AATCTTACGGCACTCGAGGC 60.179 55.0 18.41 16.51 42.43 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2801 0.111253 CCCTGAGGTTTGGCTGTCTT 59.889 55.0 0.0 0.0 0.0 3.01 R
3485 4319 2.031258 TAGAGAGGTGAGAGCAGTCG 57.969 55.0 0.0 0.0 0.0 4.18 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
23 24 5.982356 CCTTGTGTTTCTAGATGATGAGGA 58.018 41.667 0.00 0.00 0.00 3.71
24 25 6.590068 CCTTGTGTTTCTAGATGATGAGGAT 58.410 40.000 0.00 0.00 0.00 3.24
25 26 7.730084 CCTTGTGTTTCTAGATGATGAGGATA 58.270 38.462 0.00 0.00 0.00 2.59
26 27 8.373981 CCTTGTGTTTCTAGATGATGAGGATAT 58.626 37.037 0.00 0.00 0.00 1.63
27 28 9.421806 CTTGTGTTTCTAGATGATGAGGATATC 57.578 37.037 0.00 0.00 0.00 1.63
28 29 8.718158 TGTGTTTCTAGATGATGAGGATATCT 57.282 34.615 2.05 0.00 35.49 1.98
29 30 8.583296 TGTGTTTCTAGATGATGAGGATATCTG 58.417 37.037 2.05 0.00 33.51 2.90
30 31 8.584157 GTGTTTCTAGATGATGAGGATATCTGT 58.416 37.037 2.05 0.00 33.51 3.41
31 32 8.801299 TGTTTCTAGATGATGAGGATATCTGTC 58.199 37.037 2.05 0.94 33.51 3.51
32 33 8.801299 GTTTCTAGATGATGAGGATATCTGTCA 58.199 37.037 2.05 6.72 33.51 3.58
33 34 7.936496 TCTAGATGATGAGGATATCTGTCAC 57.064 40.000 9.61 6.11 33.51 3.67
34 35 7.697946 TCTAGATGATGAGGATATCTGTCACT 58.302 38.462 9.61 6.25 33.51 3.41
35 36 8.169393 TCTAGATGATGAGGATATCTGTCACTT 58.831 37.037 9.61 0.00 33.51 3.16
36 37 9.460019 CTAGATGATGAGGATATCTGTCACTTA 57.540 37.037 9.61 2.39 33.51 2.24
37 38 8.121305 AGATGATGAGGATATCTGTCACTTAC 57.879 38.462 9.61 4.59 30.41 2.34
38 39 7.949565 AGATGATGAGGATATCTGTCACTTACT 59.050 37.037 9.61 6.17 30.41 2.24
39 40 7.282332 TGATGAGGATATCTGTCACTTACTG 57.718 40.000 9.61 0.00 0.00 2.74
40 41 6.836007 TGATGAGGATATCTGTCACTTACTGT 59.164 38.462 9.61 0.00 0.00 3.55
42 43 5.163509 TGAGGATATCTGTCACTTACTGTGC 60.164 44.000 2.05 0.00 45.81 4.57
43 44 4.100189 AGGATATCTGTCACTTACTGTGCC 59.900 45.833 2.05 0.00 45.81 5.01
44 45 4.141937 GGATATCTGTCACTTACTGTGCCA 60.142 45.833 2.05 0.00 45.81 4.92
45 46 3.988976 ATCTGTCACTTACTGTGCCAT 57.011 42.857 0.00 0.00 45.81 4.40
46 47 3.044235 TCTGTCACTTACTGTGCCATG 57.956 47.619 0.00 0.00 45.81 3.66
47 48 2.368548 TCTGTCACTTACTGTGCCATGT 59.631 45.455 0.00 0.00 45.81 3.21
48 49 2.481568 CTGTCACTTACTGTGCCATGTG 59.518 50.000 0.00 0.00 45.81 3.21
49 50 1.806542 GTCACTTACTGTGCCATGTGG 59.193 52.381 0.00 0.00 45.81 4.17
50 51 1.419762 TCACTTACTGTGCCATGTGGT 59.580 47.619 0.35 0.00 45.81 4.16
51 52 2.158682 TCACTTACTGTGCCATGTGGTT 60.159 45.455 0.35 0.00 45.81 3.67
52 53 2.030893 CACTTACTGTGCCATGTGGTTG 60.031 50.000 0.35 0.00 40.06 3.77
53 54 0.958091 TTACTGTGCCATGTGGTTGC 59.042 50.000 0.35 0.00 37.57 4.17
54 55 0.110295 TACTGTGCCATGTGGTTGCT 59.890 50.000 0.35 0.00 37.57 3.91
55 56 1.287815 CTGTGCCATGTGGTTGCTG 59.712 57.895 0.35 0.00 37.57 4.41
56 57 1.455402 TGTGCCATGTGGTTGCTGT 60.455 52.632 0.35 0.00 37.57 4.40
57 58 1.007038 GTGCCATGTGGTTGCTGTG 60.007 57.895 0.35 0.00 37.57 3.66
58 59 1.455402 TGCCATGTGGTTGCTGTGT 60.455 52.632 0.35 0.00 37.57 3.72
59 60 1.007038 GCCATGTGGTTGCTGTGTG 60.007 57.895 0.35 0.00 37.57 3.82
60 61 1.737355 GCCATGTGGTTGCTGTGTGT 61.737 55.000 0.35 0.00 37.57 3.72
61 62 0.031043 CCATGTGGTTGCTGTGTGTG 59.969 55.000 0.00 0.00 0.00 3.82
62 63 0.740149 CATGTGGTTGCTGTGTGTGT 59.260 50.000 0.00 0.00 0.00 3.72
63 64 1.134753 CATGTGGTTGCTGTGTGTGTT 59.865 47.619 0.00 0.00 0.00 3.32
64 65 2.115343 TGTGGTTGCTGTGTGTGTTA 57.885 45.000 0.00 0.00 0.00 2.41
65 66 2.013400 TGTGGTTGCTGTGTGTGTTAG 58.987 47.619 0.00 0.00 0.00 2.34
66 67 2.014128 GTGGTTGCTGTGTGTGTTAGT 58.986 47.619 0.00 0.00 0.00 2.24
67 68 2.013400 TGGTTGCTGTGTGTGTTAGTG 58.987 47.619 0.00 0.00 0.00 2.74
68 69 2.014128 GGTTGCTGTGTGTGTTAGTGT 58.986 47.619 0.00 0.00 0.00 3.55
69 70 2.422127 GGTTGCTGTGTGTGTTAGTGTT 59.578 45.455 0.00 0.00 0.00 3.32
70 71 3.623960 GGTTGCTGTGTGTGTTAGTGTTA 59.376 43.478 0.00 0.00 0.00 2.41
71 72 4.260620 GGTTGCTGTGTGTGTTAGTGTTAG 60.261 45.833 0.00 0.00 0.00 2.34
72 73 3.462982 TGCTGTGTGTGTTAGTGTTAGG 58.537 45.455 0.00 0.00 0.00 2.69
73 74 3.133183 TGCTGTGTGTGTTAGTGTTAGGA 59.867 43.478 0.00 0.00 0.00 2.94
74 75 3.493503 GCTGTGTGTGTTAGTGTTAGGAC 59.506 47.826 0.00 0.00 0.00 3.85
75 76 4.056050 CTGTGTGTGTTAGTGTTAGGACC 58.944 47.826 0.00 0.00 0.00 4.46
76 77 3.181463 TGTGTGTGTTAGTGTTAGGACCC 60.181 47.826 0.00 0.00 0.00 4.46
77 78 3.039743 TGTGTGTTAGTGTTAGGACCCA 58.960 45.455 0.00 0.00 0.00 4.51
78 79 3.070446 TGTGTGTTAGTGTTAGGACCCAG 59.930 47.826 0.00 0.00 0.00 4.45
79 80 3.070590 GTGTGTTAGTGTTAGGACCCAGT 59.929 47.826 0.00 0.00 0.00 4.00
80 81 4.281688 GTGTGTTAGTGTTAGGACCCAGTA 59.718 45.833 0.00 0.00 0.00 2.74
81 82 4.900652 TGTGTTAGTGTTAGGACCCAGTAA 59.099 41.667 0.00 0.00 0.00 2.24
82 83 5.366186 TGTGTTAGTGTTAGGACCCAGTAAA 59.634 40.000 0.00 0.00 30.52 2.01
83 84 6.126825 TGTGTTAGTGTTAGGACCCAGTAAAA 60.127 38.462 0.00 0.00 30.52 1.52
84 85 6.203530 GTGTTAGTGTTAGGACCCAGTAAAAC 59.796 42.308 2.95 2.95 31.19 2.43
85 86 6.126825 TGTTAGTGTTAGGACCCAGTAAAACA 60.127 38.462 0.00 0.00 30.52 2.83
86 87 5.376756 AGTGTTAGGACCCAGTAAAACAA 57.623 39.130 0.00 0.00 0.00 2.83
87 88 5.374071 AGTGTTAGGACCCAGTAAAACAAG 58.626 41.667 0.00 0.00 0.00 3.16
88 89 5.104235 AGTGTTAGGACCCAGTAAAACAAGT 60.104 40.000 0.00 0.00 0.00 3.16
89 90 5.591472 GTGTTAGGACCCAGTAAAACAAGTT 59.409 40.000 0.00 0.00 0.00 2.66
90 91 5.824097 TGTTAGGACCCAGTAAAACAAGTTC 59.176 40.000 0.00 0.00 0.00 3.01
91 92 4.513406 AGGACCCAGTAAAACAAGTTCA 57.487 40.909 0.00 0.00 0.00 3.18
92 93 4.461198 AGGACCCAGTAAAACAAGTTCAG 58.539 43.478 0.00 0.00 0.00 3.02
93 94 4.079958 AGGACCCAGTAAAACAAGTTCAGT 60.080 41.667 0.00 0.00 0.00 3.41
94 95 4.643334 GGACCCAGTAAAACAAGTTCAGTT 59.357 41.667 0.00 0.00 0.00 3.16
95 96 5.824097 GGACCCAGTAAAACAAGTTCAGTTA 59.176 40.000 0.00 0.00 0.00 2.24
96 97 6.319405 GGACCCAGTAAAACAAGTTCAGTTAA 59.681 38.462 0.00 0.00 0.00 2.01
97 98 7.329588 ACCCAGTAAAACAAGTTCAGTTAAG 57.670 36.000 0.00 0.00 0.00 1.85
98 99 6.320418 ACCCAGTAAAACAAGTTCAGTTAAGG 59.680 38.462 0.00 0.00 0.00 2.69
99 100 6.544564 CCCAGTAAAACAAGTTCAGTTAAGGA 59.455 38.462 0.00 0.00 0.00 3.36
100 101 7.415229 CCAGTAAAACAAGTTCAGTTAAGGAC 58.585 38.462 0.00 0.00 0.00 3.85
101 102 7.282450 CCAGTAAAACAAGTTCAGTTAAGGACT 59.718 37.037 0.00 0.00 39.89 3.85
102 103 8.674607 CAGTAAAACAAGTTCAGTTAAGGACTT 58.325 33.333 0.00 0.00 36.10 3.01
103 104 9.895138 AGTAAAACAAGTTCAGTTAAGGACTTA 57.105 29.630 0.00 0.00 36.10 2.24
106 107 6.862711 ACAAGTTCAGTTAAGGACTTAAGC 57.137 37.500 1.29 0.00 36.10 3.09
107 108 6.592870 ACAAGTTCAGTTAAGGACTTAAGCT 58.407 36.000 1.29 3.73 36.10 3.74
108 109 7.054751 ACAAGTTCAGTTAAGGACTTAAGCTT 58.945 34.615 3.48 3.48 36.10 3.74
109 110 7.556635 ACAAGTTCAGTTAAGGACTTAAGCTTT 59.443 33.333 3.20 1.30 36.10 3.51
110 111 7.731882 AGTTCAGTTAAGGACTTAAGCTTTC 57.268 36.000 3.20 0.00 36.10 2.62
111 112 7.280356 AGTTCAGTTAAGGACTTAAGCTTTCA 58.720 34.615 3.20 0.00 36.10 2.69
112 113 7.773690 AGTTCAGTTAAGGACTTAAGCTTTCAA 59.226 33.333 3.20 0.00 36.10 2.69
113 114 8.403236 GTTCAGTTAAGGACTTAAGCTTTCAAA 58.597 33.333 3.20 0.00 36.10 2.69
114 115 8.154649 TCAGTTAAGGACTTAAGCTTTCAAAG 57.845 34.615 3.20 4.96 36.10 2.77
115 116 7.990886 TCAGTTAAGGACTTAAGCTTTCAAAGA 59.009 33.333 13.21 0.00 36.10 2.52
116 117 8.286097 CAGTTAAGGACTTAAGCTTTCAAAGAG 58.714 37.037 13.21 0.00 36.10 2.85
117 118 8.211629 AGTTAAGGACTTAAGCTTTCAAAGAGA 58.788 33.333 13.21 0.00 35.90 3.10
118 119 8.837389 GTTAAGGACTTAAGCTTTCAAAGAGAA 58.163 33.333 13.21 0.00 35.90 2.87
119 120 7.881775 AAGGACTTAAGCTTTCAAAGAGAAA 57.118 32.000 13.21 0.00 43.71 2.52
120 121 7.881775 AGGACTTAAGCTTTCAAAGAGAAAA 57.118 32.000 13.21 0.00 45.11 2.29
121 122 8.293699 AGGACTTAAGCTTTCAAAGAGAAAAA 57.706 30.769 13.21 0.00 45.11 1.94
122 123 8.918116 AGGACTTAAGCTTTCAAAGAGAAAAAT 58.082 29.630 13.21 0.00 45.11 1.82
135 136 9.868277 TCAAAGAGAAAAATAAAAGTGAAAGCA 57.132 25.926 0.00 0.00 0.00 3.91
141 142 8.699749 AGAAAAATAAAAGTGAAAGCAATACGC 58.300 29.630 0.00 0.00 42.91 4.42
158 159 7.384124 GCAATACGCTGTATATATTCAAGTCG 58.616 38.462 0.00 0.00 37.77 4.18
159 160 7.462856 GCAATACGCTGTATATATTCAAGTCGG 60.463 40.741 0.00 0.00 37.77 4.79
160 161 4.235360 ACGCTGTATATATTCAAGTCGGC 58.765 43.478 0.00 0.00 0.00 5.54
161 162 3.612860 CGCTGTATATATTCAAGTCGGCC 59.387 47.826 0.00 0.00 0.00 6.13
162 163 4.566004 GCTGTATATATTCAAGTCGGCCA 58.434 43.478 2.24 0.00 0.00 5.36
163 164 4.627467 GCTGTATATATTCAAGTCGGCCAG 59.373 45.833 2.24 0.00 0.00 4.85
164 165 4.566004 TGTATATATTCAAGTCGGCCAGC 58.434 43.478 2.24 0.00 0.00 4.85
165 166 2.543777 TATATTCAAGTCGGCCAGCC 57.456 50.000 2.24 0.00 0.00 4.85
175 176 4.002797 GGCCAGCCGAATGAAACT 57.997 55.556 0.00 0.00 0.00 2.66
176 177 1.803289 GGCCAGCCGAATGAAACTC 59.197 57.895 0.00 0.00 0.00 3.01
177 178 1.425428 GCCAGCCGAATGAAACTCG 59.575 57.895 0.00 0.00 0.00 4.18
178 179 1.298859 GCCAGCCGAATGAAACTCGT 61.299 55.000 0.00 0.00 0.00 4.18
179 180 2.004583 CCAGCCGAATGAAACTCGTA 57.995 50.000 0.00 0.00 0.00 3.43
180 181 1.659098 CCAGCCGAATGAAACTCGTAC 59.341 52.381 0.00 0.00 0.00 3.67
181 182 2.607187 CAGCCGAATGAAACTCGTACT 58.393 47.619 0.00 0.00 0.00 2.73
182 183 2.599082 CAGCCGAATGAAACTCGTACTC 59.401 50.000 0.00 0.00 0.00 2.59
183 184 2.230508 AGCCGAATGAAACTCGTACTCA 59.769 45.455 0.00 0.00 0.00 3.41
184 185 3.119101 AGCCGAATGAAACTCGTACTCAT 60.119 43.478 0.00 0.00 0.00 2.90
185 186 3.000322 GCCGAATGAAACTCGTACTCATG 60.000 47.826 0.00 0.00 30.28 3.07
186 187 4.174009 CCGAATGAAACTCGTACTCATGT 58.826 43.478 0.00 0.00 30.28 3.21
187 188 4.625742 CCGAATGAAACTCGTACTCATGTT 59.374 41.667 0.00 0.00 30.28 2.71
188 189 5.120208 CCGAATGAAACTCGTACTCATGTTT 59.880 40.000 0.00 0.00 35.64 2.83
189 190 6.347402 CCGAATGAAACTCGTACTCATGTTTT 60.347 38.462 0.00 0.00 33.49 2.43
190 191 7.069569 CGAATGAAACTCGTACTCATGTTTTT 58.930 34.615 0.00 0.00 33.49 1.94
256 257 2.158842 GCCTGATGCCTTGTCTGATAGT 60.159 50.000 0.00 0.00 0.00 2.12
270 275 6.045318 TGTCTGATAGTTAATGAAGCAGAGC 58.955 40.000 0.00 0.00 32.26 4.09
343 348 2.040278 TCATCTTTGACCCCTGAAGGTG 59.960 50.000 0.00 0.00 41.42 4.00
354 359 0.250295 CTGAAGGTGCCTTGGAACGA 60.250 55.000 8.38 0.00 36.26 3.85
355 360 0.250295 TGAAGGTGCCTTGGAACGAG 60.250 55.000 8.38 0.00 36.26 4.18
357 362 0.250338 AAGGTGCCTTGGAACGAGAC 60.250 55.000 2.19 0.00 34.60 3.36
359 364 0.321653 GGTGCCTTGGAACGAGACAT 60.322 55.000 0.00 0.00 0.00 3.06
360 365 1.079503 GTGCCTTGGAACGAGACATC 58.920 55.000 0.00 0.00 0.00 3.06
365 395 3.633235 CCTTGGAACGAGACATCTATCG 58.367 50.000 0.00 0.00 44.36 2.92
406 456 2.391879 GATATCACTTACCGTGCCGTC 58.608 52.381 0.00 0.00 43.46 4.79
423 473 0.321653 GTCTGTGTTAGGGTGCCAGG 60.322 60.000 0.00 0.00 0.00 4.45
438 488 4.306600 GTGCCAGGAAAACCAATTTAGTG 58.693 43.478 0.00 0.00 0.00 2.74
444 494 6.458210 CAGGAAAACCAATTTAGTGAAGCAT 58.542 36.000 0.00 0.00 0.00 3.79
447 497 7.992608 AGGAAAACCAATTTAGTGAAGCATTTT 59.007 29.630 0.00 0.00 0.00 1.82
911 1727 0.322008 CCTCTGAACCCAAGGACAGC 60.322 60.000 0.00 0.00 33.67 4.40
964 1791 7.813645 AGTTCATAAGCATGCATACATACATG 58.186 34.615 21.98 7.59 45.19 3.21
1021 1848 6.821616 ATATGTCTGACCTCAGGATTCTTT 57.178 37.500 0.00 0.00 43.91 2.52
1027 1854 5.060427 TGACCTCAGGATTCTTTTCCAAA 57.940 39.130 0.00 0.00 38.32 3.28
1036 1863 5.772169 AGGATTCTTTTCCAAAGAACTCTGG 59.228 40.000 12.70 0.00 38.88 3.86
1059 1886 0.313043 CTTTGTTGTGCCTGCTCCTG 59.687 55.000 0.00 0.00 0.00 3.86
1068 1895 1.078848 CCTGCTCCTGTCCTTTCCG 60.079 63.158 0.00 0.00 0.00 4.30
1106 1933 1.304713 CCCTCCATGCACCAGCTTT 60.305 57.895 0.00 0.00 42.74 3.51
1128 1955 2.494918 GGGAGCTGTGTCGCGTAT 59.505 61.111 5.77 0.00 34.40 3.06
1135 1962 0.733150 CTGTGTCGCGTATGAGAGGA 59.267 55.000 5.77 0.00 0.00 3.71
1136 1963 1.335182 CTGTGTCGCGTATGAGAGGAT 59.665 52.381 5.77 0.00 0.00 3.24
1265 2092 2.658707 GCCACGTCGTCAAGCTCAC 61.659 63.158 0.00 0.00 0.00 3.51
1425 2252 3.321682 TCATTGGTTCTTTTCCAAGCCTG 59.678 43.478 3.86 0.00 46.14 4.85
1739 2566 0.179108 AATCTTACGGCACTCGAGGC 60.179 55.000 18.41 16.51 42.43 4.70
1973 2801 6.381133 TGCAACCTGAAGATACTGAATCTAGA 59.619 38.462 0.00 0.00 44.56 2.43
2053 2881 4.717233 TCAAACAAGATGCAAGTGTTGT 57.283 36.364 12.19 5.56 37.20 3.32
2142 2970 0.250945 TGGCCCTGCGTCACAATAAA 60.251 50.000 0.00 0.00 0.00 1.40
2394 3222 0.673985 TCCCGTCATGGCTTAGATCG 59.326 55.000 0.00 0.00 35.87 3.69
2828 3656 3.535561 AGGATTCTAACTCAACCATGCG 58.464 45.455 0.00 0.00 0.00 4.73
2902 3730 0.890996 AGTCTTTCAAAGCTGCCCCG 60.891 55.000 0.00 0.00 0.00 5.73
3014 3842 4.802039 ACGTCTGCGGTACAATATGTTTAG 59.198 41.667 0.00 0.00 43.45 1.85
3252 4086 5.785940 AGGAGTTCCTGTTCATACTAAAGGT 59.214 40.000 0.00 0.00 46.55 3.50
3389 4223 3.799366 TGAACTTTTCGTGGAACAGCTA 58.201 40.909 0.00 0.00 41.80 3.32
3485 4319 1.092345 GGCGAGATCCCTTCAAGCAC 61.092 60.000 0.00 0.00 32.67 4.40
3505 4339 2.092646 ACGACTGCTCTCACCTCTCTAT 60.093 50.000 0.00 0.00 0.00 1.98
3756 4590 2.615391 TGGGTGGTCTTCTGTGTGATA 58.385 47.619 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.982356 TCCTCATCATCTAGAAACACAAGG 58.018 41.667 0.00 0.43 0.00 3.61
1 2 9.421806 GATATCCTCATCATCTAGAAACACAAG 57.578 37.037 0.00 0.00 0.00 3.16
2 3 9.152327 AGATATCCTCATCATCTAGAAACACAA 57.848 33.333 0.00 0.00 0.00 3.33
3 4 8.583296 CAGATATCCTCATCATCTAGAAACACA 58.417 37.037 0.00 0.00 0.00 3.72
4 5 8.584157 ACAGATATCCTCATCATCTAGAAACAC 58.416 37.037 0.00 0.00 0.00 3.32
5 6 8.718158 ACAGATATCCTCATCATCTAGAAACA 57.282 34.615 0.00 0.00 0.00 2.83
6 7 8.801299 TGACAGATATCCTCATCATCTAGAAAC 58.199 37.037 0.00 0.00 0.00 2.78
7 8 8.801299 GTGACAGATATCCTCATCATCTAGAAA 58.199 37.037 0.00 0.00 0.00 2.52
8 9 8.169393 AGTGACAGATATCCTCATCATCTAGAA 58.831 37.037 0.00 0.00 0.00 2.10
9 10 7.697946 AGTGACAGATATCCTCATCATCTAGA 58.302 38.462 0.00 0.00 0.00 2.43
10 11 7.943079 AGTGACAGATATCCTCATCATCTAG 57.057 40.000 0.00 0.00 0.00 2.43
11 12 9.237187 GTAAGTGACAGATATCCTCATCATCTA 57.763 37.037 0.00 0.00 0.00 1.98
12 13 7.949565 AGTAAGTGACAGATATCCTCATCATCT 59.050 37.037 0.00 0.00 0.00 2.90
13 14 8.028354 CAGTAAGTGACAGATATCCTCATCATC 58.972 40.741 0.00 0.00 0.00 2.92
14 15 7.508636 ACAGTAAGTGACAGATATCCTCATCAT 59.491 37.037 0.00 0.00 0.00 2.45
15 16 6.836007 ACAGTAAGTGACAGATATCCTCATCA 59.164 38.462 0.00 0.00 0.00 3.07
16 17 7.283625 ACAGTAAGTGACAGATATCCTCATC 57.716 40.000 0.00 0.00 0.00 2.92
39 40 1.007038 CACAGCAACCACATGGCAC 60.007 57.895 0.00 0.00 39.32 5.01
40 41 1.455402 ACACAGCAACCACATGGCA 60.455 52.632 0.00 0.00 39.32 4.92
41 42 1.007038 CACACAGCAACCACATGGC 60.007 57.895 0.00 0.00 39.32 4.40
42 43 0.031043 CACACACAGCAACCACATGG 59.969 55.000 0.00 0.00 42.17 3.66
43 44 0.740149 ACACACACAGCAACCACATG 59.260 50.000 0.00 0.00 0.00 3.21
44 45 1.473258 AACACACACAGCAACCACAT 58.527 45.000 0.00 0.00 0.00 3.21
45 46 2.013400 CTAACACACACAGCAACCACA 58.987 47.619 0.00 0.00 0.00 4.17
46 47 2.014128 ACTAACACACACAGCAACCAC 58.986 47.619 0.00 0.00 0.00 4.16
47 48 2.013400 CACTAACACACACAGCAACCA 58.987 47.619 0.00 0.00 0.00 3.67
48 49 2.014128 ACACTAACACACACAGCAACC 58.986 47.619 0.00 0.00 0.00 3.77
49 50 3.757745 AACACTAACACACACAGCAAC 57.242 42.857 0.00 0.00 0.00 4.17
50 51 3.874543 CCTAACACTAACACACACAGCAA 59.125 43.478 0.00 0.00 0.00 3.91
51 52 3.133183 TCCTAACACTAACACACACAGCA 59.867 43.478 0.00 0.00 0.00 4.41
52 53 3.493503 GTCCTAACACTAACACACACAGC 59.506 47.826 0.00 0.00 0.00 4.40
53 54 4.056050 GGTCCTAACACTAACACACACAG 58.944 47.826 0.00 0.00 0.00 3.66
54 55 3.181463 GGGTCCTAACACTAACACACACA 60.181 47.826 0.00 0.00 0.00 3.72
55 56 3.181463 TGGGTCCTAACACTAACACACAC 60.181 47.826 0.00 0.00 0.00 3.82
56 57 3.039743 TGGGTCCTAACACTAACACACA 58.960 45.455 0.00 0.00 0.00 3.72
57 58 3.070590 ACTGGGTCCTAACACTAACACAC 59.929 47.826 0.00 0.00 0.00 3.82
58 59 3.311091 ACTGGGTCCTAACACTAACACA 58.689 45.455 0.00 0.00 0.00 3.72
59 60 5.473066 TTACTGGGTCCTAACACTAACAC 57.527 43.478 0.00 0.00 0.00 3.32
60 61 6.126825 TGTTTTACTGGGTCCTAACACTAACA 60.127 38.462 0.00 0.00 0.00 2.41
61 62 6.290605 TGTTTTACTGGGTCCTAACACTAAC 58.709 40.000 0.00 0.00 0.00 2.34
62 63 6.497624 TGTTTTACTGGGTCCTAACACTAA 57.502 37.500 0.00 0.00 0.00 2.24
63 64 6.100134 ACTTGTTTTACTGGGTCCTAACACTA 59.900 38.462 0.00 0.00 0.00 2.74
64 65 5.104235 ACTTGTTTTACTGGGTCCTAACACT 60.104 40.000 0.00 0.00 0.00 3.55
65 66 5.128205 ACTTGTTTTACTGGGTCCTAACAC 58.872 41.667 0.00 0.00 0.00 3.32
66 67 5.376756 ACTTGTTTTACTGGGTCCTAACA 57.623 39.130 0.00 0.00 0.00 2.41
67 68 5.824097 TGAACTTGTTTTACTGGGTCCTAAC 59.176 40.000 0.00 0.00 0.00 2.34
68 69 6.003859 TGAACTTGTTTTACTGGGTCCTAA 57.996 37.500 0.00 0.00 0.00 2.69
69 70 5.131475 ACTGAACTTGTTTTACTGGGTCCTA 59.869 40.000 0.00 0.00 0.00 2.94
70 71 4.079958 ACTGAACTTGTTTTACTGGGTCCT 60.080 41.667 0.00 0.00 0.00 3.85
71 72 4.204799 ACTGAACTTGTTTTACTGGGTCC 58.795 43.478 0.00 0.00 0.00 4.46
72 73 5.830000 AACTGAACTTGTTTTACTGGGTC 57.170 39.130 0.00 0.00 0.00 4.46
73 74 6.320418 CCTTAACTGAACTTGTTTTACTGGGT 59.680 38.462 0.00 0.00 0.00 4.51
74 75 6.544564 TCCTTAACTGAACTTGTTTTACTGGG 59.455 38.462 0.00 0.00 0.00 4.45
75 76 7.282450 AGTCCTTAACTGAACTTGTTTTACTGG 59.718 37.037 0.00 0.00 36.65 4.00
76 77 8.209917 AGTCCTTAACTGAACTTGTTTTACTG 57.790 34.615 0.00 0.00 36.65 2.74
77 78 8.803397 AAGTCCTTAACTGAACTTGTTTTACT 57.197 30.769 0.00 0.00 38.58 2.24
80 81 8.188799 GCTTAAGTCCTTAACTGAACTTGTTTT 58.811 33.333 4.02 0.00 38.58 2.43
81 82 7.556635 AGCTTAAGTCCTTAACTGAACTTGTTT 59.443 33.333 4.02 0.00 38.58 2.83
82 83 7.054751 AGCTTAAGTCCTTAACTGAACTTGTT 58.945 34.615 4.02 0.00 38.58 2.83
83 84 6.592870 AGCTTAAGTCCTTAACTGAACTTGT 58.407 36.000 4.02 0.00 38.58 3.16
84 85 7.497925 AAGCTTAAGTCCTTAACTGAACTTG 57.502 36.000 0.00 0.00 38.58 3.16
85 86 7.773690 TGAAAGCTTAAGTCCTTAACTGAACTT 59.226 33.333 0.00 0.00 38.58 2.66
86 87 7.280356 TGAAAGCTTAAGTCCTTAACTGAACT 58.720 34.615 0.00 0.00 38.58 3.01
87 88 7.492352 TGAAAGCTTAAGTCCTTAACTGAAC 57.508 36.000 0.00 0.00 38.58 3.18
88 89 8.514330 TTTGAAAGCTTAAGTCCTTAACTGAA 57.486 30.769 0.00 0.00 38.58 3.02
89 90 7.990886 TCTTTGAAAGCTTAAGTCCTTAACTGA 59.009 33.333 0.00 0.00 38.58 3.41
90 91 8.154649 TCTTTGAAAGCTTAAGTCCTTAACTG 57.845 34.615 0.00 0.00 38.58 3.16
91 92 8.211629 TCTCTTTGAAAGCTTAAGTCCTTAACT 58.788 33.333 0.00 0.00 41.10 2.24
92 93 8.379457 TCTCTTTGAAAGCTTAAGTCCTTAAC 57.621 34.615 0.00 0.13 32.26 2.01
93 94 8.974060 TTCTCTTTGAAAGCTTAAGTCCTTAA 57.026 30.769 0.00 0.01 34.28 1.85
94 95 8.974060 TTTCTCTTTGAAAGCTTAAGTCCTTA 57.026 30.769 0.00 0.00 39.50 2.69
95 96 7.881775 TTTCTCTTTGAAAGCTTAAGTCCTT 57.118 32.000 0.00 0.00 39.50 3.36
96 97 7.881775 TTTTCTCTTTGAAAGCTTAAGTCCT 57.118 32.000 0.00 0.00 44.40 3.85
109 110 9.868277 TGCTTTCACTTTTATTTTTCTCTTTGA 57.132 25.926 0.00 0.00 0.00 2.69
115 116 8.699749 GCGTATTGCTTTCACTTTTATTTTTCT 58.300 29.630 0.00 0.00 41.73 2.52
116 117 8.844977 GCGTATTGCTTTCACTTTTATTTTTC 57.155 30.769 0.00 0.00 41.73 2.29
133 134 7.384124 CGACTTGAATATATACAGCGTATTGC 58.616 38.462 6.54 0.00 46.98 3.56
134 135 7.462856 GCCGACTTGAATATATACAGCGTATTG 60.463 40.741 6.54 0.00 0.00 1.90
135 136 6.530534 GCCGACTTGAATATATACAGCGTATT 59.469 38.462 6.54 0.00 0.00 1.89
136 137 6.034591 GCCGACTTGAATATATACAGCGTAT 58.965 40.000 6.48 6.48 0.00 3.06
137 138 5.396484 GCCGACTTGAATATATACAGCGTA 58.604 41.667 0.00 0.00 0.00 4.42
138 139 4.235360 GCCGACTTGAATATATACAGCGT 58.765 43.478 0.00 0.00 0.00 5.07
139 140 3.612860 GGCCGACTTGAATATATACAGCG 59.387 47.826 0.00 0.00 0.00 5.18
140 141 4.566004 TGGCCGACTTGAATATATACAGC 58.434 43.478 0.00 0.00 0.00 4.40
141 142 4.627467 GCTGGCCGACTTGAATATATACAG 59.373 45.833 0.00 0.00 0.00 2.74
142 143 4.562757 GGCTGGCCGACTTGAATATATACA 60.563 45.833 0.00 0.00 0.00 2.29
143 144 3.933332 GGCTGGCCGACTTGAATATATAC 59.067 47.826 0.00 0.00 0.00 1.47
144 145 4.202245 GGCTGGCCGACTTGAATATATA 57.798 45.455 0.00 0.00 0.00 0.86
145 146 3.059352 GGCTGGCCGACTTGAATATAT 57.941 47.619 0.00 0.00 0.00 0.86
146 147 2.543777 GGCTGGCCGACTTGAATATA 57.456 50.000 0.00 0.00 0.00 0.86
147 148 3.403936 GGCTGGCCGACTTGAATAT 57.596 52.632 0.00 0.00 0.00 1.28
148 149 4.954933 GGCTGGCCGACTTGAATA 57.045 55.556 0.00 0.00 0.00 1.75
158 159 1.803289 GAGTTTCATTCGGCTGGCC 59.197 57.895 0.00 0.00 0.00 5.36
159 160 1.298859 ACGAGTTTCATTCGGCTGGC 61.299 55.000 0.00 0.00 42.12 4.85
160 161 1.659098 GTACGAGTTTCATTCGGCTGG 59.341 52.381 0.00 0.00 42.12 4.85
161 162 2.599082 GAGTACGAGTTTCATTCGGCTG 59.401 50.000 0.00 0.00 42.12 4.85
162 163 2.230508 TGAGTACGAGTTTCATTCGGCT 59.769 45.455 0.00 0.00 42.12 5.52
163 164 2.602878 TGAGTACGAGTTTCATTCGGC 58.397 47.619 0.00 0.00 42.12 5.54
164 165 4.174009 ACATGAGTACGAGTTTCATTCGG 58.826 43.478 0.00 0.00 42.12 4.30
165 166 5.763444 AACATGAGTACGAGTTTCATTCG 57.237 39.130 0.00 0.00 43.38 3.34
198 199 9.770097 GGATTGTGATACAGATAATTGAGAAGA 57.230 33.333 0.00 0.00 0.00 2.87
199 200 8.997323 GGGATTGTGATACAGATAATTGAGAAG 58.003 37.037 0.00 0.00 0.00 2.85
200 201 7.939039 GGGGATTGTGATACAGATAATTGAGAA 59.061 37.037 0.00 0.00 0.00 2.87
201 202 7.453393 GGGGATTGTGATACAGATAATTGAGA 58.547 38.462 0.00 0.00 0.00 3.27
202 203 6.656693 GGGGGATTGTGATACAGATAATTGAG 59.343 42.308 0.00 0.00 0.00 3.02
203 204 6.332635 AGGGGGATTGTGATACAGATAATTGA 59.667 38.462 0.00 0.00 0.00 2.57
204 205 6.432162 CAGGGGGATTGTGATACAGATAATTG 59.568 42.308 0.00 0.00 0.00 2.32
205 206 6.546484 CAGGGGGATTGTGATACAGATAATT 58.454 40.000 0.00 0.00 0.00 1.40
206 207 5.515534 GCAGGGGGATTGTGATACAGATAAT 60.516 44.000 0.00 0.00 0.00 1.28
207 208 4.202461 GCAGGGGGATTGTGATACAGATAA 60.202 45.833 0.00 0.00 0.00 1.75
208 209 3.327757 GCAGGGGGATTGTGATACAGATA 59.672 47.826 0.00 0.00 0.00 1.98
209 210 2.107204 GCAGGGGGATTGTGATACAGAT 59.893 50.000 0.00 0.00 0.00 2.90
210 211 1.490490 GCAGGGGGATTGTGATACAGA 59.510 52.381 0.00 0.00 0.00 3.41
211 212 1.212688 TGCAGGGGGATTGTGATACAG 59.787 52.381 0.00 0.00 0.00 2.74
212 213 1.212688 CTGCAGGGGGATTGTGATACA 59.787 52.381 5.57 0.00 0.00 2.29
213 214 1.477558 CCTGCAGGGGGATTGTGATAC 60.478 57.143 26.14 0.00 0.00 2.24
214 215 0.846015 CCTGCAGGGGGATTGTGATA 59.154 55.000 26.14 0.00 0.00 2.15
215 216 1.217057 ACCTGCAGGGGGATTGTGAT 61.217 55.000 35.42 8.61 40.27 3.06
216 217 1.852157 ACCTGCAGGGGGATTGTGA 60.852 57.895 35.42 0.00 40.27 3.58
217 218 1.679977 CACCTGCAGGGGGATTGTG 60.680 63.158 35.42 19.25 42.32 3.33
218 219 2.765969 CACCTGCAGGGGGATTGT 59.234 61.111 35.42 11.03 42.32 2.71
219 220 2.757099 GCACCTGCAGGGGGATTG 60.757 66.667 35.65 24.37 42.32 2.67
220 221 4.066139 GGCACCTGCAGGGGGATT 62.066 66.667 35.65 12.44 42.32 3.01
256 257 3.939740 ATCCAGGCTCTGCTTCATTAA 57.060 42.857 0.00 0.00 0.00 1.40
336 341 0.250295 CTCGTTCCAAGGCACCTTCA 60.250 55.000 0.00 0.00 33.42 3.02
338 343 0.250338 GTCTCGTTCCAAGGCACCTT 60.250 55.000 0.00 0.00 36.60 3.50
343 348 2.961526 TAGATGTCTCGTTCCAAGGC 57.038 50.000 0.00 0.00 0.00 4.35
354 359 8.735315 CATCTAGAAATACCACGATAGATGTCT 58.265 37.037 0.00 0.00 40.44 3.41
355 360 8.731605 TCATCTAGAAATACCACGATAGATGTC 58.268 37.037 15.73 0.00 43.43 3.06
357 362 7.694367 CGTCATCTAGAAATACCACGATAGATG 59.306 40.741 11.86 11.86 43.93 2.90
359 364 6.932960 TCGTCATCTAGAAATACCACGATAGA 59.067 38.462 0.00 0.00 41.38 1.98
360 365 7.130303 TCGTCATCTAGAAATACCACGATAG 57.870 40.000 0.00 0.00 46.19 2.08
365 395 5.769484 TCCTCGTCATCTAGAAATACCAC 57.231 43.478 0.00 0.00 0.00 4.16
406 456 0.400213 TTCCTGGCACCCTAACACAG 59.600 55.000 0.00 0.00 0.00 3.66
480 531 8.846943 TGCCGACTTGAATATATAATGTGAAT 57.153 30.769 0.00 0.00 0.00 2.57
482 533 7.931407 AGTTGCCGACTTGAATATATAATGTGA 59.069 33.333 0.00 0.00 33.92 3.58
911 1727 7.575909 CGGTCTGGATCTTGTTATATAGTGGAG 60.576 44.444 0.00 0.00 0.00 3.86
964 1791 2.614829 TCTCTTACGGCTATTTGGGC 57.385 50.000 0.00 0.00 0.00 5.36
973 1800 2.882761 AGTTTGGGTTTTCTCTTACGGC 59.117 45.455 0.00 0.00 0.00 5.68
1021 1848 4.706842 AAGCTACCAGAGTTCTTTGGAA 57.293 40.909 14.86 0.00 37.89 3.53
1027 1854 4.130118 CACAACAAAGCTACCAGAGTTCT 58.870 43.478 0.00 0.00 0.00 3.01
1036 1863 0.954452 AGCAGGCACAACAAAGCTAC 59.046 50.000 0.00 0.00 0.00 3.58
1059 1886 3.056328 GCTGGTGGCGGAAAGGAC 61.056 66.667 0.00 0.00 0.00 3.85
1106 1933 2.338620 CGACACAGCTCCCGTTCA 59.661 61.111 0.00 0.00 0.00 3.18
1128 1955 0.749818 AGAGAAGCGCGATCCTCTCA 60.750 55.000 23.49 0.00 30.85 3.27
1135 1962 0.461548 TTGATGGAGAGAAGCGCGAT 59.538 50.000 12.10 0.00 0.00 4.58
1136 1963 0.179127 CTTGATGGAGAGAAGCGCGA 60.179 55.000 12.10 0.00 0.00 5.87
1176 2003 1.293924 GCCATGACGAGAGGTTGATG 58.706 55.000 0.00 0.00 0.00 3.07
1265 2092 2.064762 CTTGAGCACTTCCACGAAGAG 58.935 52.381 8.34 1.75 41.71 2.85
1341 2168 5.523438 AGTCTAGATACCTTAGTTGCTGC 57.477 43.478 0.00 0.00 0.00 5.25
1739 2566 2.349590 TGTTCCATGAGATGTCAAGCG 58.650 47.619 0.00 0.00 35.88 4.68
1973 2801 0.111253 CCCTGAGGTTTGGCTGTCTT 59.889 55.000 0.00 0.00 0.00 3.01
2053 2881 7.256012 CCCACCTAACAAATTTTTAGCCAAGTA 60.256 37.037 11.53 0.00 0.00 2.24
2062 2890 3.049344 TGGCCCCACCTAACAAATTTTT 58.951 40.909 0.00 0.00 40.22 1.94
2068 2896 1.304879 GCATGGCCCCACCTAACAA 60.305 57.895 0.00 0.00 40.22 2.83
2132 2960 8.788325 AATAGGTCCTGTAAGTTTATTGTGAC 57.212 34.615 0.00 0.00 0.00 3.67
2142 2970 5.396436 CCATTTCGGAATAGGTCCTGTAAGT 60.396 44.000 0.00 0.00 45.36 2.24
2505 3333 1.677820 GCTGGTAGTGTGCCGGTTATT 60.678 52.381 1.90 0.00 34.91 1.40
2902 3730 9.696917 ATATGAAAGATCAACAAAAACAAGGTC 57.303 29.630 0.00 0.00 39.49 3.85
3014 3842 3.415457 TTTCAATGGGAATTTGGCCAC 57.585 42.857 3.88 0.00 34.91 5.01
3159 3987 2.282407 TGTCTGTGATCGATGGCATTG 58.718 47.619 0.54 8.51 0.00 2.82
3389 4223 2.551270 TCTCAGGGATAGCACCACTTT 58.449 47.619 0.00 0.00 0.00 2.66
3485 4319 2.031258 TAGAGAGGTGAGAGCAGTCG 57.969 55.000 0.00 0.00 0.00 4.18
3505 4339 6.761242 GTGTTGTATGACAGGTTCATATAGCA 59.239 38.462 4.28 4.28 46.73 3.49
3678 4512 6.924060 GGTAAAAGGATATATCATCGGATCCG 59.076 42.308 28.62 28.62 42.34 4.18


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

AutoCloner maintained by Alex Coulton.