Multiple sequence alignment - TraesCS2D01G012100

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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 TraesCS2D01G012100 chr2D 100.000 3266 0 0 1 3266 5746582 5749847 0.000000e+00 6032.0
1 TraesCS2D01G012100 chr2D 82.864 1243 196 14 1031 2266 618288572 618287340 0.000000e+00 1099.0
2 TraesCS2D01G012100 chr2B 87.964 3207 173 91 207 3266 5627507 5630647 0.000000e+00 3587.0
3 TraesCS2D01G012100 chr2B 82.254 1251 209 11 1021 2266 754928657 754927415 0.000000e+00 1068.0
4 TraesCS2D01G012100 chr2A 94.273 2008 67 19 791 2772 4294025 4292040 0.000000e+00 3027.0
5 TraesCS2D01G012100 chr2A 82.602 1253 201 14 1021 2266 749104597 749103355 0.000000e+00 1090.0
6 TraesCS2D01G012100 chr2A 87.740 416 15 13 2829 3233 4292026 4291636 1.380000e-123 453.0
7 TraesCS2D01G012100 chr2A 96.970 33 1 0 3234 3266 4291619 4291587 4.550000e-04 56.5
8 TraesCS2D01G012100 chr4A 79.316 643 114 16 1053 1681 603981896 603981259 1.800000e-117 433.0
9 TraesCS2D01G012100 chr4A 93.519 108 6 1 2524 2631 656045843 656045737 3.370000e-35 159.0
10 TraesCS2D01G012100 chr7D 91.803 61 5 0 149 209 212359657 212359717 5.810000e-13 86.1
11 TraesCS2D01G012100 chr7A 75.429 175 41 2 1445 1618 32701482 32701309 2.090000e-12 84.2
12 TraesCS2D01G012100 chr7B 91.667 60 4 1 150 209 531683736 531683794 7.510000e-12 82.4
13 TraesCS2D01G012100 chr6D 90.164 61 6 0 149 209 121403805 121403865 2.700000e-11 80.5
14 TraesCS2D01G012100 chr6D 90.164 61 6 0 149 209 192916965 192916905 2.700000e-11 80.5
15 TraesCS2D01G012100 chr6D 90.164 61 6 0 149 209 217373244 217373304 2.700000e-11 80.5
16 TraesCS2D01G012100 chr4D 90.164 61 6 0 149 209 149168294 149168354 2.700000e-11 80.5
17 TraesCS2D01G012100 chr3D 90.164 61 6 0 149 209 35154345 35154285 2.700000e-11 80.5
18 TraesCS2D01G012100 chr3D 90.164 61 6 0 149 209 514611784 514611724 2.700000e-11 80.5
19 TraesCS2D01G012100 chr1D 90.164 61 6 0 149 209 165694567 165694627 2.700000e-11 80.5


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 TraesCS2D01G012100 chr2D 5746582 5749847 3265 False 6032.000000 6032 100.000000 1 3266 1 chr2D.!!$F1 3265
1 TraesCS2D01G012100 chr2D 618287340 618288572 1232 True 1099.000000 1099 82.864000 1031 2266 1 chr2D.!!$R1 1235
2 TraesCS2D01G012100 chr2B 5627507 5630647 3140 False 3587.000000 3587 87.964000 207 3266 1 chr2B.!!$F1 3059
3 TraesCS2D01G012100 chr2B 754927415 754928657 1242 True 1068.000000 1068 82.254000 1021 2266 1 chr2B.!!$R1 1245
4 TraesCS2D01G012100 chr2A 4291587 4294025 2438 True 1178.833333 3027 92.994333 791 3266 3 chr2A.!!$R2 2475
5 TraesCS2D01G012100 chr2A 749103355 749104597 1242 True 1090.000000 1090 82.602000 1021 2266 1 chr2A.!!$R1 1245
6 TraesCS2D01G012100 chr4A 603981259 603981896 637 True 433.000000 433 79.316000 1053 1681 1 chr4A.!!$R1 628

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
917 993 0.101759 AGCAACAACAACAGCAGCAG 59.898 50.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2303 2420 0.168788 TTGGTTAGTAGTCGCCGTCG 59.831 55.0 0.0 0.0 0.0 5.12 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
22 23 5.695851 TCATGCTTCCTTTCAAAGAGTTC 57.304 39.130 0.00 0.00 0.00 3.01
23 24 5.132502 TCATGCTTCCTTTCAAAGAGTTCA 58.867 37.500 0.00 0.00 0.00 3.18
24 25 5.771666 TCATGCTTCCTTTCAAAGAGTTCAT 59.228 36.000 0.00 0.00 0.00 2.57
25 26 6.266103 TCATGCTTCCTTTCAAAGAGTTCATT 59.734 34.615 0.00 0.00 0.00 2.57
26 27 6.076981 TGCTTCCTTTCAAAGAGTTCATTC 57.923 37.500 0.00 0.00 0.00 2.67
27 28 5.829924 TGCTTCCTTTCAAAGAGTTCATTCT 59.170 36.000 0.00 0.00 0.00 2.40
28 29 6.998074 TGCTTCCTTTCAAAGAGTTCATTCTA 59.002 34.615 0.00 0.00 0.00 2.10
29 30 7.173907 TGCTTCCTTTCAAAGAGTTCATTCTAG 59.826 37.037 0.00 0.00 0.00 2.43
30 31 7.174080 GCTTCCTTTCAAAGAGTTCATTCTAGT 59.826 37.037 0.00 0.00 0.00 2.57
31 32 8.980481 TTCCTTTCAAAGAGTTCATTCTAGTT 57.020 30.769 0.00 0.00 0.00 2.24
32 33 8.980481 TCCTTTCAAAGAGTTCATTCTAGTTT 57.020 30.769 0.00 0.00 0.00 2.66
33 34 9.408648 TCCTTTCAAAGAGTTCATTCTAGTTTT 57.591 29.630 0.00 0.00 0.00 2.43
37 38 8.617290 TCAAAGAGTTCATTCTAGTTTTACCC 57.383 34.615 0.00 0.00 0.00 3.69
38 39 8.437575 TCAAAGAGTTCATTCTAGTTTTACCCT 58.562 33.333 0.00 0.00 0.00 4.34
39 40 9.067986 CAAAGAGTTCATTCTAGTTTTACCCTT 57.932 33.333 0.00 0.00 0.00 3.95
44 45 9.011095 AGTTCATTCTAGTTTTACCCTTAAAGC 57.989 33.333 0.00 0.00 0.00 3.51
45 46 9.011095 GTTCATTCTAGTTTTACCCTTAAAGCT 57.989 33.333 0.00 0.21 40.62 3.74
46 47 9.582648 TTCATTCTAGTTTTACCCTTAAAGCTT 57.417 29.630 0.00 0.00 38.99 3.74
47 48 9.582648 TCATTCTAGTTTTACCCTTAAAGCTTT 57.417 29.630 17.30 17.30 38.99 3.51
51 52 9.192642 TCTAGTTTTACCCTTAAAGCTTTTTGT 57.807 29.630 18.47 11.61 38.99 2.83
52 53 9.244799 CTAGTTTTACCCTTAAAGCTTTTTGTG 57.755 33.333 18.47 6.94 38.99 3.33
53 54 7.842982 AGTTTTACCCTTAAAGCTTTTTGTGA 58.157 30.769 18.47 4.02 35.78 3.58
54 55 7.762615 AGTTTTACCCTTAAAGCTTTTTGTGAC 59.237 33.333 18.47 9.75 35.78 3.67
55 56 6.777213 TTACCCTTAAAGCTTTTTGTGACA 57.223 33.333 18.47 0.00 0.00 3.58
56 57 5.669164 ACCCTTAAAGCTTTTTGTGACAA 57.331 34.783 18.47 2.51 0.00 3.18
57 58 5.660460 ACCCTTAAAGCTTTTTGTGACAAG 58.340 37.500 18.47 12.25 0.00 3.16
58 59 5.186992 ACCCTTAAAGCTTTTTGTGACAAGT 59.813 36.000 18.47 0.73 0.00 3.16
59 60 6.106003 CCCTTAAAGCTTTTTGTGACAAGTT 58.894 36.000 18.47 0.00 0.00 2.66
60 61 6.593770 CCCTTAAAGCTTTTTGTGACAAGTTT 59.406 34.615 18.47 0.00 0.00 2.66
61 62 7.119116 CCCTTAAAGCTTTTTGTGACAAGTTTT 59.881 33.333 18.47 0.75 37.27 2.43
62 63 9.145865 CCTTAAAGCTTTTTGTGACAAGTTTTA 57.854 29.630 18.47 0.00 35.69 1.52
63 64 9.952341 CTTAAAGCTTTTTGTGACAAGTTTTAC 57.048 29.630 18.47 0.00 36.20 2.01
64 65 9.699703 TTAAAGCTTTTTGTGACAAGTTTTACT 57.300 25.926 18.47 0.00 36.20 2.24
65 66 7.812309 AAGCTTTTTGTGACAAGTTTTACTC 57.188 32.000 0.00 0.00 0.00 2.59
66 67 6.330278 AGCTTTTTGTGACAAGTTTTACTCC 58.670 36.000 0.00 0.00 0.00 3.85
67 68 6.071616 AGCTTTTTGTGACAAGTTTTACTCCA 60.072 34.615 0.00 0.00 0.00 3.86
68 69 6.756542 GCTTTTTGTGACAAGTTTTACTCCAT 59.243 34.615 0.00 0.00 0.00 3.41
69 70 7.277760 GCTTTTTGTGACAAGTTTTACTCCATT 59.722 33.333 0.00 0.00 0.00 3.16
70 71 9.150348 CTTTTTGTGACAAGTTTTACTCCATTT 57.850 29.630 0.00 0.00 0.00 2.32
72 73 9.796120 TTTTGTGACAAGTTTTACTCCATTTAG 57.204 29.630 0.00 0.00 0.00 1.85
73 74 8.514330 TTGTGACAAGTTTTACTCCATTTAGT 57.486 30.769 0.00 0.00 0.00 2.24
74 75 9.616156 TTGTGACAAGTTTTACTCCATTTAGTA 57.384 29.630 0.00 0.00 0.00 1.82
75 76 9.268268 TGTGACAAGTTTTACTCCATTTAGTAG 57.732 33.333 0.00 0.00 33.62 2.57
76 77 9.485206 GTGACAAGTTTTACTCCATTTAGTAGA 57.515 33.333 0.00 0.00 33.62 2.59
107 108 9.512435 TCTTCTATTTTACTCAATGTACGTAGC 57.488 33.333 0.00 0.00 0.00 3.58
108 109 8.638685 TTCTATTTTACTCAATGTACGTAGCC 57.361 34.615 0.00 0.00 0.00 3.93
109 110 7.774134 TCTATTTTACTCAATGTACGTAGCCA 58.226 34.615 0.00 0.00 0.00 4.75
110 111 8.252417 TCTATTTTACTCAATGTACGTAGCCAA 58.748 33.333 0.00 0.00 0.00 4.52
111 112 6.470557 TTTTACTCAATGTACGTAGCCAAC 57.529 37.500 0.00 0.00 0.00 3.77
112 113 3.955650 ACTCAATGTACGTAGCCAACT 57.044 42.857 0.00 0.00 0.00 3.16
113 114 3.846360 ACTCAATGTACGTAGCCAACTC 58.154 45.455 0.00 0.00 0.00 3.01
114 115 3.510360 ACTCAATGTACGTAGCCAACTCT 59.490 43.478 0.00 0.00 0.00 3.24
115 116 4.106029 TCAATGTACGTAGCCAACTCTC 57.894 45.455 0.00 0.00 0.00 3.20
116 117 3.762288 TCAATGTACGTAGCCAACTCTCT 59.238 43.478 0.00 0.00 0.00 3.10
117 118 4.106197 CAATGTACGTAGCCAACTCTCTC 58.894 47.826 0.00 0.00 0.00 3.20
118 119 2.786777 TGTACGTAGCCAACTCTCTCA 58.213 47.619 0.00 0.00 0.00 3.27
119 120 2.486982 TGTACGTAGCCAACTCTCTCAC 59.513 50.000 0.00 0.00 0.00 3.51
120 121 1.912417 ACGTAGCCAACTCTCTCACT 58.088 50.000 0.00 0.00 0.00 3.41
121 122 2.240279 ACGTAGCCAACTCTCTCACTT 58.760 47.619 0.00 0.00 0.00 3.16
122 123 2.628657 ACGTAGCCAACTCTCTCACTTT 59.371 45.455 0.00 0.00 0.00 2.66
123 124 3.069729 ACGTAGCCAACTCTCTCACTTTT 59.930 43.478 0.00 0.00 0.00 2.27
124 125 4.280174 ACGTAGCCAACTCTCTCACTTTTA 59.720 41.667 0.00 0.00 0.00 1.52
125 126 5.221382 ACGTAGCCAACTCTCTCACTTTTAA 60.221 40.000 0.00 0.00 0.00 1.52
126 127 5.694910 CGTAGCCAACTCTCTCACTTTTAAA 59.305 40.000 0.00 0.00 0.00 1.52
127 128 6.128795 CGTAGCCAACTCTCTCACTTTTAAAG 60.129 42.308 2.81 2.81 0.00 1.85
128 129 4.517075 AGCCAACTCTCTCACTTTTAAAGC 59.483 41.667 4.42 0.00 0.00 3.51
129 130 4.517075 GCCAACTCTCTCACTTTTAAAGCT 59.483 41.667 4.42 0.00 0.00 3.74
130 131 5.009110 GCCAACTCTCTCACTTTTAAAGCTT 59.991 40.000 4.42 0.00 0.00 3.74
131 132 6.663565 CCAACTCTCTCACTTTTAAAGCTTC 58.336 40.000 0.00 0.00 0.00 3.86
132 133 6.484977 CCAACTCTCTCACTTTTAAAGCTTCT 59.515 38.462 0.00 0.00 0.00 2.85
133 134 7.657761 CCAACTCTCTCACTTTTAAAGCTTCTA 59.342 37.037 0.00 0.00 0.00 2.10
134 135 9.046296 CAACTCTCTCACTTTTAAAGCTTCTAA 57.954 33.333 0.00 0.00 0.00 2.10
135 136 9.614792 AACTCTCTCACTTTTAAAGCTTCTAAA 57.385 29.630 0.00 4.71 0.00 1.85
136 137 9.614792 ACTCTCTCACTTTTAAAGCTTCTAAAA 57.385 29.630 17.71 17.71 0.00 1.52
160 161 6.619329 AAAATATGTTATGCCAACCAACCT 57.381 33.333 0.00 0.00 0.00 3.50
161 162 7.726033 AAAATATGTTATGCCAACCAACCTA 57.274 32.000 0.00 0.00 0.00 3.08
162 163 7.912778 AAATATGTTATGCCAACCAACCTAT 57.087 32.000 0.00 0.00 0.00 2.57
163 164 6.899393 ATATGTTATGCCAACCAACCTATG 57.101 37.500 0.00 0.00 0.00 2.23
177 178 4.519906 AACCTATGGTTGGATGGTTAGG 57.480 45.455 0.71 0.00 45.07 2.69
178 179 3.743132 ACCTATGGTTGGATGGTTAGGA 58.257 45.455 0.00 0.00 27.29 2.94
179 180 3.716872 ACCTATGGTTGGATGGTTAGGAG 59.283 47.826 0.00 0.00 27.29 3.69
180 181 3.073062 CCTATGGTTGGATGGTTAGGAGG 59.927 52.174 0.00 0.00 0.00 4.30
181 182 2.352561 TGGTTGGATGGTTAGGAGGA 57.647 50.000 0.00 0.00 0.00 3.71
182 183 1.913419 TGGTTGGATGGTTAGGAGGAC 59.087 52.381 0.00 0.00 0.00 3.85
183 184 1.913419 GGTTGGATGGTTAGGAGGACA 59.087 52.381 0.00 0.00 0.00 4.02
184 185 2.092914 GGTTGGATGGTTAGGAGGACAG 60.093 54.545 0.00 0.00 0.00 3.51
185 186 2.572104 GTTGGATGGTTAGGAGGACAGT 59.428 50.000 0.00 0.00 0.00 3.55
186 187 2.187958 TGGATGGTTAGGAGGACAGTG 58.812 52.381 0.00 0.00 0.00 3.66
187 188 1.486726 GGATGGTTAGGAGGACAGTGG 59.513 57.143 0.00 0.00 0.00 4.00
188 189 0.912486 ATGGTTAGGAGGACAGTGGC 59.088 55.000 0.00 0.00 0.00 5.01
189 190 0.472925 TGGTTAGGAGGACAGTGGCA 60.473 55.000 0.00 0.00 0.00 4.92
190 191 0.912486 GGTTAGGAGGACAGTGGCAT 59.088 55.000 0.00 0.00 0.00 4.40
191 192 1.134371 GGTTAGGAGGACAGTGGCATC 60.134 57.143 0.79 0.79 0.00 3.91
192 193 1.555075 GTTAGGAGGACAGTGGCATCA 59.445 52.381 13.55 0.00 0.00 3.07
193 194 1.195115 TAGGAGGACAGTGGCATCAC 58.805 55.000 13.55 1.92 43.93 3.06
201 202 3.876300 GTGGCATCACGAGTCCAC 58.124 61.111 0.00 5.18 41.66 4.02
202 203 1.741770 GTGGCATCACGAGTCCACC 60.742 63.158 8.52 0.00 42.25 4.61
203 204 2.213513 TGGCATCACGAGTCCACCA 61.214 57.895 0.00 0.00 0.00 4.17
204 205 1.448540 GGCATCACGAGTCCACCAG 60.449 63.158 0.00 0.00 0.00 4.00
205 206 1.591703 GCATCACGAGTCCACCAGA 59.408 57.895 0.00 0.00 0.00 3.86
212 213 1.070289 ACGAGTCCACCAGAGTTTTCC 59.930 52.381 0.00 0.00 0.00 3.13
215 216 2.368875 GAGTCCACCAGAGTTTTCCTCA 59.631 50.000 0.00 0.00 43.12 3.86
219 220 2.158608 CCACCAGAGTTTTCCTCAAGGT 60.159 50.000 0.00 0.00 46.03 3.50
245 246 1.145819 GTCATCCTCCTCTGCTGCC 59.854 63.158 0.00 0.00 0.00 4.85
261 262 1.212688 CTGCCCCCACATGTAAGATGA 59.787 52.381 0.00 0.00 0.00 2.92
281 282 7.320399 AGATGACAGTCGTAATTAATGACACA 58.680 34.615 16.96 14.05 45.20 3.72
320 321 1.002900 CTTGACGTCGTGCATGGTTTT 60.003 47.619 11.62 0.00 0.00 2.43
321 322 1.018148 TGACGTCGTGCATGGTTTTT 58.982 45.000 11.62 0.00 0.00 1.94
347 348 6.183360 CCCTTAATTGACCAGATTAGTCCGTA 60.183 42.308 0.00 0.00 33.09 4.02
357 358 3.961408 AGATTAGTCCGTAATGCCAGTCT 59.039 43.478 0.00 0.00 30.93 3.24
362 363 1.138859 TCCGTAATGCCAGTCTCATGG 59.861 52.381 0.00 0.00 43.72 3.66
369 370 1.672030 CCAGTCTCATGGCGTGCAA 60.672 57.895 0.65 0.00 32.48 4.08
370 371 1.642037 CCAGTCTCATGGCGTGCAAG 61.642 60.000 0.65 0.00 32.48 4.01
371 372 1.376424 AGTCTCATGGCGTGCAAGG 60.376 57.895 0.65 0.00 0.00 3.61
372 373 2.046023 TCTCATGGCGTGCAAGGG 60.046 61.111 0.65 0.00 0.00 3.95
388 389 1.953138 GGGCACAGATCTCGATGCG 60.953 63.158 14.08 0.00 39.02 4.73
391 392 1.227060 CACAGATCTCGATGCGGCA 60.227 57.895 4.58 4.58 0.00 5.69
528 539 1.670811 GCATGTTCTCCACGGGTAATG 59.329 52.381 0.00 0.00 0.00 1.90
530 541 1.354101 TGTTCTCCACGGGTAATGGT 58.646 50.000 0.00 0.00 38.47 3.55
588 603 2.439156 GCACCATGCAGTCCCCTC 60.439 66.667 0.00 0.00 44.26 4.30
589 604 2.976490 GCACCATGCAGTCCCCTCT 61.976 63.158 0.00 0.00 44.26 3.69
590 605 1.077930 CACCATGCAGTCCCCTCTG 60.078 63.158 0.00 0.00 38.35 3.35
591 606 1.229625 ACCATGCAGTCCCCTCTGA 60.230 57.895 0.00 0.00 37.61 3.27
592 607 0.622738 ACCATGCAGTCCCCTCTGAT 60.623 55.000 0.00 0.00 37.61 2.90
593 608 0.108207 CCATGCAGTCCCCTCTGATC 59.892 60.000 0.00 0.00 37.61 2.92
594 609 1.129917 CATGCAGTCCCCTCTGATCT 58.870 55.000 0.00 0.00 37.61 2.75
596 611 0.337773 TGCAGTCCCCTCTGATCTCT 59.662 55.000 0.00 0.00 37.61 3.10
597 612 1.570979 TGCAGTCCCCTCTGATCTCTA 59.429 52.381 0.00 0.00 37.61 2.43
598 613 2.238521 GCAGTCCCCTCTGATCTCTAG 58.761 57.143 0.00 0.00 37.61 2.43
640 665 8.792830 AACCAAAATCGAATTTCTCTCTCATA 57.207 30.769 0.00 0.00 0.00 2.15
741 781 6.993288 TCCTATCAATCCCCCAATATCATT 57.007 37.500 0.00 0.00 0.00 2.57
744 784 5.750352 ATCAATCCCCCAATATCATTTGC 57.250 39.130 0.00 0.00 0.00 3.68
752 792 3.436906 CCCAATATCATTTGCTCCCTCCA 60.437 47.826 0.00 0.00 0.00 3.86
754 794 4.219944 CCAATATCATTTGCTCCCTCCATG 59.780 45.833 0.00 0.00 0.00 3.66
755 795 5.074804 CAATATCATTTGCTCCCTCCATGA 58.925 41.667 0.00 0.00 0.00 3.07
756 796 3.897657 ATCATTTGCTCCCTCCATGAT 57.102 42.857 0.00 0.00 31.10 2.45
758 798 3.559069 TCATTTGCTCCCTCCATGATTC 58.441 45.455 0.00 0.00 0.00 2.52
759 799 3.203710 TCATTTGCTCCCTCCATGATTCT 59.796 43.478 0.00 0.00 0.00 2.40
771 831 6.070881 CCCTCCATGATTCTTCTACCTATCAG 60.071 46.154 0.00 0.00 31.20 2.90
772 832 6.352016 TCCATGATTCTTCTACCTATCAGC 57.648 41.667 0.00 0.00 31.20 4.26
773 833 5.840693 TCCATGATTCTTCTACCTATCAGCA 59.159 40.000 0.00 0.00 31.20 4.41
774 834 5.931146 CCATGATTCTTCTACCTATCAGCAC 59.069 44.000 0.00 0.00 31.20 4.40
775 835 6.463472 CCATGATTCTTCTACCTATCAGCACA 60.463 42.308 0.00 0.00 31.20 4.57
779 839 3.447586 TCTTCTACCTATCAGCACACACC 59.552 47.826 0.00 0.00 0.00 4.16
782 842 1.064003 ACCTATCAGCACACACCCAA 58.936 50.000 0.00 0.00 0.00 4.12
825 889 3.856206 ACCTCCTCTCTCTAACCTCTCTT 59.144 47.826 0.00 0.00 0.00 2.85
826 890 4.293901 ACCTCCTCTCTCTAACCTCTCTTT 59.706 45.833 0.00 0.00 0.00 2.52
827 891 4.887655 CCTCCTCTCTCTAACCTCTCTTTC 59.112 50.000 0.00 0.00 0.00 2.62
828 892 5.340027 CCTCCTCTCTCTAACCTCTCTTTCT 60.340 48.000 0.00 0.00 0.00 2.52
834 898 3.958147 CTCTAACCTCTCTTTCTCCTCCC 59.042 52.174 0.00 0.00 0.00 4.30
836 900 1.097722 ACCTCTCTTTCTCCTCCCCT 58.902 55.000 0.00 0.00 0.00 4.79
839 903 1.290732 CTCTCTTTCTCCTCCCCTCCT 59.709 57.143 0.00 0.00 0.00 3.69
857 921 3.395941 CTCCTCCCCTATTTAAGCACCAT 59.604 47.826 0.00 0.00 0.00 3.55
860 924 4.392940 CTCCCCTATTTAAGCACCATCAG 58.607 47.826 0.00 0.00 0.00 2.90
861 925 2.887152 CCCCTATTTAAGCACCATCAGC 59.113 50.000 0.00 0.00 0.00 4.26
899 963 2.542205 CCAACACACAACACATCAGCAG 60.542 50.000 0.00 0.00 0.00 4.24
917 993 0.101759 AGCAACAACAACAGCAGCAG 59.898 50.000 0.00 0.00 0.00 4.24
935 1011 2.799562 GCAGCAAACACCTTCTTCAACC 60.800 50.000 0.00 0.00 0.00 3.77
936 1012 2.689983 CAGCAAACACCTTCTTCAACCT 59.310 45.455 0.00 0.00 0.00 3.50
986 1076 2.051941 CAGCACCAAAGCAACCCAT 58.948 52.632 0.00 0.00 36.85 4.00
995 1090 0.541296 AAGCAACCCATCAAGCAGCT 60.541 50.000 0.00 0.00 0.00 4.24
1014 1109 4.512914 GCCATGGTGCTCCTCCCC 62.513 72.222 14.67 0.00 34.23 4.81
1017 1112 3.415087 ATGGTGCTCCTCCCCAGC 61.415 66.667 6.34 0.00 37.40 4.85
1542 1658 0.949397 ACGTCAGCGAGTACAAGTCA 59.051 50.000 0.00 0.00 42.00 3.41
1785 1901 1.456518 CTCCTGGCTCATCCTCGGA 60.457 63.158 0.00 0.00 35.09 4.55
1860 1976 0.250166 ACAAGTACGGCAAGACACCC 60.250 55.000 0.00 0.00 0.00 4.61
1965 2081 4.057428 GAGCTCACCGACGGCACT 62.057 66.667 15.39 6.00 0.00 4.40
2745 2895 9.209175 GTTAGTAACATGTTCTTCTTGTCTCAT 57.791 33.333 15.85 0.00 34.10 2.90
2758 2908 8.730680 TCTTCTTGTCTCATAATTTTTACAGCC 58.269 33.333 0.00 0.00 0.00 4.85
2760 2910 8.635765 TCTTGTCTCATAATTTTTACAGCCTT 57.364 30.769 0.00 0.00 0.00 4.35
2772 2922 4.561735 TTACAGCCTTTCTTTTTCACCG 57.438 40.909 0.00 0.00 0.00 4.94
2775 2925 3.636764 ACAGCCTTTCTTTTTCACCGATT 59.363 39.130 0.00 0.00 0.00 3.34
2790 2940 8.582433 TTTCACCGATTATTTTCCTTGAAAAC 57.418 30.769 4.28 0.00 42.98 2.43
2806 2956 6.256321 CCTTGAAAACAATTCACAGTTCCTTG 59.744 38.462 0.00 0.00 0.00 3.61
2811 2983 7.595311 AAACAATTCACAGTTCCTTGAAAAC 57.405 32.000 0.00 0.00 35.42 2.43
2848 3040 6.339587 TCCTTTTCGCCAATAATTTTCTGT 57.660 33.333 0.00 0.00 0.00 3.41
2850 3042 5.286082 CCTTTTCGCCAATAATTTTCTGTCG 59.714 40.000 0.00 0.00 0.00 4.35
2901 3093 6.377080 TCTCTCTCTAGATCTCAGTCTCTCT 58.623 44.000 0.00 0.00 0.00 3.10
2902 3094 6.491745 TCTCTCTCTAGATCTCAGTCTCTCTC 59.508 46.154 0.00 0.00 0.00 3.20
2903 3095 6.377080 TCTCTCTAGATCTCAGTCTCTCTCT 58.623 44.000 0.00 0.00 0.00 3.10
2904 3096 6.491745 TCTCTCTAGATCTCAGTCTCTCTCTC 59.508 46.154 0.00 0.00 0.00 3.20
2905 3097 6.377080 TCTCTAGATCTCAGTCTCTCTCTCT 58.623 44.000 0.00 0.00 0.00 3.10
2906 3098 6.491745 TCTCTAGATCTCAGTCTCTCTCTCTC 59.508 46.154 0.00 0.00 0.00 3.20
2907 3099 6.377080 TCTAGATCTCAGTCTCTCTCTCTCT 58.623 44.000 0.00 0.00 0.00 3.10
2908 3100 5.543507 AGATCTCAGTCTCTCTCTCTCTC 57.456 47.826 0.00 0.00 0.00 3.20
2909 3101 5.215069 AGATCTCAGTCTCTCTCTCTCTCT 58.785 45.833 0.00 0.00 0.00 3.10
2910 3102 5.304101 AGATCTCAGTCTCTCTCTCTCTCTC 59.696 48.000 0.00 0.00 0.00 3.20
2911 3103 4.614475 TCTCAGTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
2949 3144 5.477510 ACTAGTAGCATTAGCATCAGCATC 58.522 41.667 0.00 0.00 45.49 3.91
3029 3229 2.244769 GGAATTCATTGGGGGAAGAGGA 59.755 50.000 7.93 0.00 0.00 3.71
3031 3231 3.677156 ATTCATTGGGGGAAGAGGAAG 57.323 47.619 0.00 0.00 0.00 3.46
3037 3237 1.223211 GGGGAAGAGGAAGCAGAGC 59.777 63.158 0.00 0.00 0.00 4.09
3040 3240 0.107752 GGAAGAGGAAGCAGAGCAGG 60.108 60.000 0.00 0.00 0.00 4.85
3041 3241 0.107752 GAAGAGGAAGCAGAGCAGGG 60.108 60.000 0.00 0.00 0.00 4.45
3042 3242 0.839853 AAGAGGAAGCAGAGCAGGGT 60.840 55.000 0.00 0.00 0.00 4.34
3122 3338 4.380945 TGGCCATCCCAGTTGCCC 62.381 66.667 0.00 0.00 43.35 5.36
3123 3339 4.066139 GGCCATCCCAGTTGCCCT 62.066 66.667 0.00 0.00 37.94 5.19
3124 3340 2.757099 GCCATCCCAGTTGCCCTG 60.757 66.667 0.00 0.00 41.15 4.45
3190 3412 1.188219 TCACTCACTCTCACCCTGCC 61.188 60.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.492772 AGAATGAACTCTTTGAAAGGAAGCAT 59.507 34.615 4.94 2.42 0.00 3.79
3 4 5.829924 AGAATGAACTCTTTGAAAGGAAGCA 59.170 36.000 4.94 0.15 0.00 3.91
4 5 6.324561 AGAATGAACTCTTTGAAAGGAAGC 57.675 37.500 4.94 0.00 0.00 3.86
7 8 8.980481 AAACTAGAATGAACTCTTTGAAAGGA 57.020 30.769 4.94 0.00 0.00 3.36
11 12 9.063615 GGGTAAAACTAGAATGAACTCTTTGAA 57.936 33.333 0.00 0.00 0.00 2.69
12 13 8.437575 AGGGTAAAACTAGAATGAACTCTTTGA 58.562 33.333 0.00 0.00 0.00 2.69
13 14 8.622948 AGGGTAAAACTAGAATGAACTCTTTG 57.377 34.615 0.00 0.00 0.00 2.77
18 19 9.011095 GCTTTAAGGGTAAAACTAGAATGAACT 57.989 33.333 0.00 0.00 0.00 3.01
19 20 9.011095 AGCTTTAAGGGTAAAACTAGAATGAAC 57.989 33.333 0.00 0.00 0.00 3.18
20 21 9.582648 AAGCTTTAAGGGTAAAACTAGAATGAA 57.417 29.630 0.00 0.00 27.88 2.57
21 22 9.582648 AAAGCTTTAAGGGTAAAACTAGAATGA 57.417 29.630 10.72 0.00 27.88 2.57
25 26 9.192642 ACAAAAAGCTTTAAGGGTAAAACTAGA 57.807 29.630 13.10 0.00 27.88 2.43
26 27 9.244799 CACAAAAAGCTTTAAGGGTAAAACTAG 57.755 33.333 13.10 0.00 27.88 2.57
27 28 8.968969 TCACAAAAAGCTTTAAGGGTAAAACTA 58.031 29.630 13.10 0.00 27.88 2.24
28 29 7.762615 GTCACAAAAAGCTTTAAGGGTAAAACT 59.237 33.333 13.10 0.00 28.82 2.66
29 30 7.546316 TGTCACAAAAAGCTTTAAGGGTAAAAC 59.454 33.333 13.10 4.24 0.00 2.43
30 31 7.612677 TGTCACAAAAAGCTTTAAGGGTAAAA 58.387 30.769 13.10 0.00 0.00 1.52
31 32 7.171630 TGTCACAAAAAGCTTTAAGGGTAAA 57.828 32.000 13.10 0.00 0.00 2.01
32 33 6.777213 TGTCACAAAAAGCTTTAAGGGTAA 57.223 33.333 13.10 0.00 0.00 2.85
33 34 6.378848 ACTTGTCACAAAAAGCTTTAAGGGTA 59.621 34.615 13.10 1.11 0.00 3.69
34 35 5.186992 ACTTGTCACAAAAAGCTTTAAGGGT 59.813 36.000 13.10 5.69 0.00 4.34
35 36 5.660460 ACTTGTCACAAAAAGCTTTAAGGG 58.340 37.500 13.10 9.36 0.00 3.95
36 37 7.595311 AAACTTGTCACAAAAAGCTTTAAGG 57.405 32.000 13.10 7.57 0.00 2.69
37 38 9.952341 GTAAAACTTGTCACAAAAAGCTTTAAG 57.048 29.630 13.10 12.47 30.13 1.85
38 39 9.699703 AGTAAAACTTGTCACAAAAAGCTTTAA 57.300 25.926 13.10 0.00 30.13 1.52
39 40 9.349145 GAGTAAAACTTGTCACAAAAAGCTTTA 57.651 29.630 13.10 0.00 0.00 1.85
40 41 7.330946 GGAGTAAAACTTGTCACAAAAAGCTTT 59.669 33.333 5.69 5.69 0.00 3.51
41 42 6.811665 GGAGTAAAACTTGTCACAAAAAGCTT 59.188 34.615 0.00 0.00 0.00 3.74
42 43 6.071616 TGGAGTAAAACTTGTCACAAAAAGCT 60.072 34.615 0.00 0.00 0.00 3.74
43 44 6.096695 TGGAGTAAAACTTGTCACAAAAAGC 58.903 36.000 0.00 0.00 0.00 3.51
44 45 8.702163 AATGGAGTAAAACTTGTCACAAAAAG 57.298 30.769 0.00 0.00 0.00 2.27
46 47 9.796120 CTAAATGGAGTAAAACTTGTCACAAAA 57.204 29.630 0.00 0.00 0.00 2.44
47 48 8.962679 ACTAAATGGAGTAAAACTTGTCACAAA 58.037 29.630 0.00 0.00 0.00 2.83
48 49 8.514330 ACTAAATGGAGTAAAACTTGTCACAA 57.486 30.769 0.00 0.00 0.00 3.33
49 50 9.268268 CTACTAAATGGAGTAAAACTTGTCACA 57.732 33.333 0.00 0.00 31.57 3.58
50 51 9.485206 TCTACTAAATGGAGTAAAACTTGTCAC 57.515 33.333 0.00 0.00 31.57 3.67
81 82 9.512435 GCTACGTACATTGAGTAAAATAGAAGA 57.488 33.333 0.00 0.00 33.72 2.87
82 83 8.753175 GGCTACGTACATTGAGTAAAATAGAAG 58.247 37.037 0.00 0.00 33.72 2.85
83 84 8.252417 TGGCTACGTACATTGAGTAAAATAGAA 58.748 33.333 0.00 0.00 33.72 2.10
84 85 7.774134 TGGCTACGTACATTGAGTAAAATAGA 58.226 34.615 0.00 0.00 33.72 1.98
85 86 7.997107 TGGCTACGTACATTGAGTAAAATAG 57.003 36.000 0.00 0.00 33.72 1.73
86 87 8.036575 AGTTGGCTACGTACATTGAGTAAAATA 58.963 33.333 0.00 0.00 33.72 1.40
87 88 6.877322 AGTTGGCTACGTACATTGAGTAAAAT 59.123 34.615 0.00 0.00 33.72 1.82
88 89 6.225318 AGTTGGCTACGTACATTGAGTAAAA 58.775 36.000 0.00 0.00 33.72 1.52
89 90 5.786311 AGTTGGCTACGTACATTGAGTAAA 58.214 37.500 0.00 0.00 33.72 2.01
90 91 5.184479 AGAGTTGGCTACGTACATTGAGTAA 59.816 40.000 0.00 0.00 33.72 2.24
91 92 4.703575 AGAGTTGGCTACGTACATTGAGTA 59.296 41.667 0.00 0.00 0.00 2.59
92 93 3.510360 AGAGTTGGCTACGTACATTGAGT 59.490 43.478 0.00 0.00 0.00 3.41
93 94 4.106197 GAGAGTTGGCTACGTACATTGAG 58.894 47.826 0.00 0.00 0.00 3.02
94 95 3.762288 AGAGAGTTGGCTACGTACATTGA 59.238 43.478 0.00 0.00 0.00 2.57
95 96 4.106197 GAGAGAGTTGGCTACGTACATTG 58.894 47.826 0.00 0.00 0.00 2.82
96 97 3.762288 TGAGAGAGTTGGCTACGTACATT 59.238 43.478 0.00 0.00 0.00 2.71
97 98 3.128938 GTGAGAGAGTTGGCTACGTACAT 59.871 47.826 0.00 0.00 0.00 2.29
98 99 2.486982 GTGAGAGAGTTGGCTACGTACA 59.513 50.000 0.00 0.00 0.00 2.90
99 100 2.748532 AGTGAGAGAGTTGGCTACGTAC 59.251 50.000 0.00 0.00 0.00 3.67
100 101 3.069079 AGTGAGAGAGTTGGCTACGTA 57.931 47.619 0.00 0.00 0.00 3.57
101 102 1.912417 AGTGAGAGAGTTGGCTACGT 58.088 50.000 0.00 0.00 0.00 3.57
102 103 3.305398 AAAGTGAGAGAGTTGGCTACG 57.695 47.619 0.00 0.00 0.00 3.51
103 104 6.347806 GCTTTAAAAGTGAGAGAGTTGGCTAC 60.348 42.308 0.00 0.00 0.00 3.58
104 105 5.701290 GCTTTAAAAGTGAGAGAGTTGGCTA 59.299 40.000 0.00 0.00 0.00 3.93
105 106 4.517075 GCTTTAAAAGTGAGAGAGTTGGCT 59.483 41.667 0.00 0.00 0.00 4.75
106 107 4.517075 AGCTTTAAAAGTGAGAGAGTTGGC 59.483 41.667 0.00 0.00 0.00 4.52
107 108 6.484977 AGAAGCTTTAAAAGTGAGAGAGTTGG 59.515 38.462 0.00 0.00 0.00 3.77
108 109 7.489574 AGAAGCTTTAAAAGTGAGAGAGTTG 57.510 36.000 0.00 0.00 0.00 3.16
109 110 9.614792 TTTAGAAGCTTTAAAAGTGAGAGAGTT 57.385 29.630 0.00 0.00 0.00 3.01
110 111 9.614792 TTTTAGAAGCTTTAAAAGTGAGAGAGT 57.385 29.630 16.09 0.00 0.00 3.24
136 137 7.014988 AGGTTGGTTGGCATAACATATTTTT 57.985 32.000 10.55 0.00 0.00 1.94
137 138 6.619329 AGGTTGGTTGGCATAACATATTTT 57.381 33.333 10.55 0.00 0.00 1.82
138 139 7.201992 CCATAGGTTGGTTGGCATAACATATTT 60.202 37.037 11.60 0.00 40.99 1.40
139 140 6.267471 CCATAGGTTGGTTGGCATAACATATT 59.733 38.462 11.60 0.77 40.99 1.28
140 141 5.774690 CCATAGGTTGGTTGGCATAACATAT 59.225 40.000 9.60 9.60 40.99 1.78
141 142 5.136828 CCATAGGTTGGTTGGCATAACATA 58.863 41.667 10.55 8.58 40.99 2.29
142 143 3.960102 CCATAGGTTGGTTGGCATAACAT 59.040 43.478 10.55 7.01 40.99 2.71
143 144 3.360867 CCATAGGTTGGTTGGCATAACA 58.639 45.455 10.55 0.00 40.99 2.41
157 158 3.716872 CTCCTAACCATCCAACCATAGGT 59.283 47.826 0.00 0.00 37.65 3.08
158 159 3.073062 CCTCCTAACCATCCAACCATAGG 59.927 52.174 0.00 0.00 32.90 2.57
159 160 3.973973 TCCTCCTAACCATCCAACCATAG 59.026 47.826 0.00 0.00 0.00 2.23
160 161 3.714798 GTCCTCCTAACCATCCAACCATA 59.285 47.826 0.00 0.00 0.00 2.74
161 162 2.509964 GTCCTCCTAACCATCCAACCAT 59.490 50.000 0.00 0.00 0.00 3.55
162 163 1.913419 GTCCTCCTAACCATCCAACCA 59.087 52.381 0.00 0.00 0.00 3.67
163 164 1.913419 TGTCCTCCTAACCATCCAACC 59.087 52.381 0.00 0.00 0.00 3.77
164 165 2.572104 ACTGTCCTCCTAACCATCCAAC 59.428 50.000 0.00 0.00 0.00 3.77
165 166 2.571653 CACTGTCCTCCTAACCATCCAA 59.428 50.000 0.00 0.00 0.00 3.53
166 167 2.187958 CACTGTCCTCCTAACCATCCA 58.812 52.381 0.00 0.00 0.00 3.41
167 168 1.486726 CCACTGTCCTCCTAACCATCC 59.513 57.143 0.00 0.00 0.00 3.51
168 169 1.134371 GCCACTGTCCTCCTAACCATC 60.134 57.143 0.00 0.00 0.00 3.51
169 170 0.912486 GCCACTGTCCTCCTAACCAT 59.088 55.000 0.00 0.00 0.00 3.55
170 171 0.472925 TGCCACTGTCCTCCTAACCA 60.473 55.000 0.00 0.00 0.00 3.67
171 172 0.912486 ATGCCACTGTCCTCCTAACC 59.088 55.000 0.00 0.00 0.00 2.85
172 173 1.555075 TGATGCCACTGTCCTCCTAAC 59.445 52.381 0.00 0.00 0.00 2.34
173 174 1.555075 GTGATGCCACTGTCCTCCTAA 59.445 52.381 0.00 0.00 40.10 2.69
174 175 1.195115 GTGATGCCACTGTCCTCCTA 58.805 55.000 0.00 0.00 40.10 2.94
175 176 1.892819 CGTGATGCCACTGTCCTCCT 61.893 60.000 0.00 0.00 41.06 3.69
176 177 1.448540 CGTGATGCCACTGTCCTCC 60.449 63.158 0.00 0.00 41.06 4.30
177 178 0.459237 CTCGTGATGCCACTGTCCTC 60.459 60.000 0.00 0.00 41.06 3.71
178 179 1.188219 ACTCGTGATGCCACTGTCCT 61.188 55.000 0.00 0.00 41.06 3.85
179 180 0.737715 GACTCGTGATGCCACTGTCC 60.738 60.000 0.00 0.00 41.06 4.02
180 181 0.737715 GGACTCGTGATGCCACTGTC 60.738 60.000 0.00 0.00 41.06 3.51
181 182 1.293498 GGACTCGTGATGCCACTGT 59.707 57.895 0.00 0.00 41.06 3.55
182 183 1.016130 GTGGACTCGTGATGCCACTG 61.016 60.000 15.99 0.00 45.58 3.66
183 184 1.293498 GTGGACTCGTGATGCCACT 59.707 57.895 15.99 0.00 45.58 4.00
184 185 3.876300 GTGGACTCGTGATGCCAC 58.124 61.111 11.05 11.05 43.34 5.01
185 186 2.171209 CTGGTGGACTCGTGATGCCA 62.171 60.000 0.00 0.00 0.00 4.92
186 187 1.448540 CTGGTGGACTCGTGATGCC 60.449 63.158 0.00 0.00 0.00 4.40
187 188 0.459237 CTCTGGTGGACTCGTGATGC 60.459 60.000 0.00 0.00 0.00 3.91
188 189 0.891373 ACTCTGGTGGACTCGTGATG 59.109 55.000 0.00 0.00 0.00 3.07
189 190 1.633774 AACTCTGGTGGACTCGTGAT 58.366 50.000 0.00 0.00 0.00 3.06
190 191 1.410004 AAACTCTGGTGGACTCGTGA 58.590 50.000 0.00 0.00 0.00 4.35
191 192 2.135933 GAAAACTCTGGTGGACTCGTG 58.864 52.381 0.00 0.00 0.00 4.35
192 193 1.070289 GGAAAACTCTGGTGGACTCGT 59.930 52.381 0.00 0.00 0.00 4.18
193 194 1.344763 AGGAAAACTCTGGTGGACTCG 59.655 52.381 0.00 0.00 0.00 4.18
194 195 2.368875 TGAGGAAAACTCTGGTGGACTC 59.631 50.000 0.00 0.00 46.72 3.36
195 196 2.408565 TGAGGAAAACTCTGGTGGACT 58.591 47.619 0.00 0.00 46.72 3.85
196 197 2.930826 TGAGGAAAACTCTGGTGGAC 57.069 50.000 0.00 0.00 46.72 4.02
197 198 2.106511 CCTTGAGGAAAACTCTGGTGGA 59.893 50.000 0.00 0.00 46.72 4.02
198 199 2.158608 ACCTTGAGGAAAACTCTGGTGG 60.159 50.000 3.59 0.00 45.23 4.61
199 200 3.142174 GACCTTGAGGAAAACTCTGGTG 58.858 50.000 3.59 0.00 46.14 4.17
201 202 2.553247 GGGACCTTGAGGAAAACTCTGG 60.553 54.545 3.59 0.00 46.72 3.86
202 203 2.106511 TGGGACCTTGAGGAAAACTCTG 59.893 50.000 3.59 0.00 46.72 3.35
203 204 2.106684 GTGGGACCTTGAGGAAAACTCT 59.893 50.000 3.59 0.00 46.72 3.24
204 205 2.106684 AGTGGGACCTTGAGGAAAACTC 59.893 50.000 3.59 0.00 46.78 3.01
205 206 2.136026 AGTGGGACCTTGAGGAAAACT 58.864 47.619 3.59 0.00 38.94 2.66
212 213 2.616510 GGATGACAAGTGGGACCTTGAG 60.617 54.545 7.84 0.00 43.65 3.02
215 216 1.630878 GAGGATGACAAGTGGGACCTT 59.369 52.381 0.00 0.00 0.00 3.50
219 220 1.079490 AGAGGAGGATGACAAGTGGGA 59.921 52.381 0.00 0.00 0.00 4.37
245 246 3.535561 GACTGTCATCTTACATGTGGGG 58.464 50.000 9.11 0.00 0.00 4.96
261 262 7.152645 AGTCTTGTGTCATTAATTACGACTGT 58.847 34.615 12.95 0.00 0.00 3.55
281 282 7.613411 ACGTCAAGGGTTAAGTATACTAGTCTT 59.387 37.037 5.65 0.00 0.00 3.01
320 321 6.631766 CGGACTAATCTGGTCAATTAAGGGAA 60.632 42.308 0.00 0.00 35.61 3.97
321 322 5.163343 CGGACTAATCTGGTCAATTAAGGGA 60.163 44.000 0.00 0.00 35.61 4.20
357 358 4.657408 TGCCCTTGCACGCCATGA 62.657 61.111 0.00 0.00 44.23 3.07
369 370 1.445095 GCATCGAGATCTGTGCCCT 59.555 57.895 0.00 0.00 0.00 5.19
370 371 1.953138 CGCATCGAGATCTGTGCCC 60.953 63.158 0.00 0.00 34.20 5.36
371 372 1.953138 CCGCATCGAGATCTGTGCC 60.953 63.158 0.00 0.00 34.20 5.01
372 373 2.593134 GCCGCATCGAGATCTGTGC 61.593 63.158 0.00 7.11 0.00 4.57
400 401 2.327244 GCGCTTATCTGCTGCTGC 59.673 61.111 8.89 8.89 40.20 5.25
401 402 2.624811 CGCGCTTATCTGCTGCTG 59.375 61.111 5.56 0.00 33.07 4.41
402 403 3.267860 GCGCGCTTATCTGCTGCT 61.268 61.111 26.67 0.00 33.07 4.24
440 441 2.291043 TTTCCAGCTCGGGGAGGTC 61.291 63.158 0.00 0.00 38.40 3.85
484 495 4.947147 CCACACCACCACCACCCG 62.947 72.222 0.00 0.00 0.00 5.28
487 498 4.204028 AGGCCACACCACCACCAC 62.204 66.667 5.01 0.00 43.14 4.16
488 499 3.884774 GAGGCCACACCACCACCA 61.885 66.667 5.01 0.00 43.14 4.17
493 504 3.574074 ATGCAGGAGGCCACACCAC 62.574 63.158 5.01 2.79 43.89 4.16
494 505 3.259314 ATGCAGGAGGCCACACCA 61.259 61.111 5.01 0.00 43.89 4.17
495 506 2.753043 CATGCAGGAGGCCACACC 60.753 66.667 5.01 5.41 43.89 4.16
496 507 1.589716 GAACATGCAGGAGGCCACAC 61.590 60.000 4.84 0.00 43.89 3.82
497 508 1.303561 GAACATGCAGGAGGCCACA 60.304 57.895 4.84 0.00 43.89 4.17
530 541 1.486310 GTGAGGACACATGCAGGGATA 59.514 52.381 2.31 0.00 45.32 2.59
581 596 5.941555 TTTTTCTAGAGATCAGAGGGGAC 57.058 43.478 0.00 0.00 0.00 4.46
608 633 9.546428 AGAGAAATTCGATTTTGGTTTTTGAAT 57.454 25.926 9.85 0.00 31.47 2.57
640 665 8.052621 ACTTCTCTCTAGGGATAGATACACTT 57.947 38.462 8.47 0.00 0.00 3.16
671 696 8.037723 ACCCCAACTTCTTCTTAGTTTACTAA 57.962 34.615 2.63 2.63 33.73 2.24
741 781 2.848694 AGAAGAATCATGGAGGGAGCAA 59.151 45.455 0.00 0.00 0.00 3.91
744 784 4.230455 AGGTAGAAGAATCATGGAGGGAG 58.770 47.826 0.00 0.00 0.00 4.30
752 792 6.098838 TGTGTGCTGATAGGTAGAAGAATCAT 59.901 38.462 0.00 0.00 0.00 2.45
754 794 5.751028 GTGTGTGCTGATAGGTAGAAGAATC 59.249 44.000 0.00 0.00 0.00 2.52
755 795 5.395768 GGTGTGTGCTGATAGGTAGAAGAAT 60.396 44.000 0.00 0.00 0.00 2.40
756 796 4.081642 GGTGTGTGCTGATAGGTAGAAGAA 60.082 45.833 0.00 0.00 0.00 2.52
758 798 3.430929 GGGTGTGTGCTGATAGGTAGAAG 60.431 52.174 0.00 0.00 0.00 2.85
759 799 2.500098 GGGTGTGTGCTGATAGGTAGAA 59.500 50.000 0.00 0.00 0.00 2.10
771 831 1.675720 AAAGCAGGTTGGGTGTGTGC 61.676 55.000 0.00 0.00 0.00 4.57
772 832 0.385390 GAAAGCAGGTTGGGTGTGTG 59.615 55.000 0.00 0.00 0.00 3.82
773 833 0.258774 AGAAAGCAGGTTGGGTGTGT 59.741 50.000 0.00 0.00 0.00 3.72
774 834 0.954452 GAGAAAGCAGGTTGGGTGTG 59.046 55.000 0.00 0.00 0.00 3.82
775 835 0.846693 AGAGAAAGCAGGTTGGGTGT 59.153 50.000 0.00 0.00 0.00 4.16
779 839 1.627834 AGGAGAGAGAAAGCAGGTTGG 59.372 52.381 0.00 0.00 0.00 3.77
782 842 1.899142 GTGAGGAGAGAGAAAGCAGGT 59.101 52.381 0.00 0.00 0.00 4.00
825 889 2.647949 GGGGAGGAGGGGAGGAGAA 61.648 68.421 0.00 0.00 0.00 2.87
826 890 2.237751 TAGGGGAGGAGGGGAGGAGA 62.238 65.000 0.00 0.00 0.00 3.71
827 891 1.083363 ATAGGGGAGGAGGGGAGGAG 61.083 65.000 0.00 0.00 0.00 3.69
828 892 0.636932 AATAGGGGAGGAGGGGAGGA 60.637 60.000 0.00 0.00 0.00 3.71
834 898 2.106684 GGTGCTTAAATAGGGGAGGAGG 59.893 54.545 0.00 0.00 0.00 4.30
836 900 2.853430 TGGTGCTTAAATAGGGGAGGA 58.147 47.619 0.00 0.00 0.00 3.71
839 903 3.435026 GCTGATGGTGCTTAAATAGGGGA 60.435 47.826 0.00 0.00 0.00 4.81
857 921 2.209809 TTTGGGAGGAGGGGCTGA 59.790 61.111 0.00 0.00 0.00 4.26
860 924 3.264845 TGGTTTGGGAGGAGGGGC 61.265 66.667 0.00 0.00 0.00 5.80
861 925 2.763902 GTGGTTTGGGAGGAGGGG 59.236 66.667 0.00 0.00 0.00 4.79
899 963 1.485032 GCTGCTGCTGTTGTTGTTGC 61.485 55.000 8.53 0.00 36.03 4.17
917 993 2.952310 AGAGGTTGAAGAAGGTGTTTGC 59.048 45.455 0.00 0.00 0.00 3.68
935 1011 0.177604 GGTGGTGAGGATGCTGAGAG 59.822 60.000 0.00 0.00 0.00 3.20
936 1012 0.252421 AGGTGGTGAGGATGCTGAGA 60.252 55.000 0.00 0.00 0.00 3.27
986 1076 0.393402 CACCATGGCTAGCTGCTTGA 60.393 55.000 13.04 0.00 42.39 3.02
995 1090 2.072487 GGGAGGAGCACCATGGCTA 61.072 63.158 13.04 0.00 45.99 3.93
1014 1109 2.584418 CTGTCCAGGCGATCGCTG 60.584 66.667 36.25 29.16 41.60 5.18
1304 1399 4.430765 CGAAGGTGGCGGCGTAGT 62.431 66.667 9.37 0.00 0.00 2.73
1542 1658 1.192146 TGCCCTTGTACTTCTCGCCT 61.192 55.000 0.00 0.00 0.00 5.52
1836 1952 4.033019 GTGTCTTGCCGTACTTGTTTTTC 58.967 43.478 0.00 0.00 0.00 2.29
1839 1955 1.944709 GGTGTCTTGCCGTACTTGTTT 59.055 47.619 0.00 0.00 0.00 2.83
1875 1991 2.510012 CTGATCTTGGCGAGCGCA 60.510 61.111 17.16 0.13 44.11 6.09
1929 2045 1.228552 GGCCCTGCTCTTGGTGAAA 60.229 57.895 0.00 0.00 0.00 2.69
2064 2180 4.278513 TTGGGGAAGGCGGTGGTG 62.279 66.667 0.00 0.00 0.00 4.17
2302 2419 0.673333 TGGTTAGTAGTCGCCGTCGA 60.673 55.000 0.00 0.00 43.28 4.20
2303 2420 0.168788 TTGGTTAGTAGTCGCCGTCG 59.831 55.000 0.00 0.00 0.00 5.12
2304 2421 2.352503 TTTGGTTAGTAGTCGCCGTC 57.647 50.000 0.00 0.00 0.00 4.79
2305 2422 2.417787 GGATTTGGTTAGTAGTCGCCGT 60.418 50.000 0.00 0.00 0.00 5.68
2306 2423 2.199236 GGATTTGGTTAGTAGTCGCCG 58.801 52.381 0.00 0.00 0.00 6.46
2307 2424 2.558378 GGGATTTGGTTAGTAGTCGCC 58.442 52.381 0.00 0.00 0.00 5.54
2309 2426 4.081309 TCAAGGGGATTTGGTTAGTAGTCG 60.081 45.833 0.00 0.00 0.00 4.18
2313 2434 7.519347 AGTAATCAAGGGGATTTGGTTAGTA 57.481 36.000 0.00 0.00 43.76 1.82
2447 2576 4.894252 TCCTCCTACCCTTACATAGTGT 57.106 45.455 0.00 0.00 0.00 3.55
2448 2577 8.337739 AGTATATCCTCCTACCCTTACATAGTG 58.662 40.741 0.00 0.00 0.00 2.74
2449 2578 8.479601 AGTATATCCTCCTACCCTTACATAGT 57.520 38.462 0.00 0.00 0.00 2.12
2450 2579 9.850198 GTAGTATATCCTCCTACCCTTACATAG 57.150 40.741 0.00 0.00 0.00 2.23
2451 2580 9.355378 TGTAGTATATCCTCCTACCCTTACATA 57.645 37.037 0.00 0.00 32.01 2.29
2668 2817 5.824097 GGAGGGTTACACAAAGACAGTAAAA 59.176 40.000 0.00 0.00 30.39 1.52
2676 2825 2.637872 CTGAGGGAGGGTTACACAAAGA 59.362 50.000 0.00 0.00 0.00 2.52
2745 2895 9.320352 GGTGAAAAAGAAAGGCTGTAAAAATTA 57.680 29.630 0.00 0.00 0.00 1.40
2757 2907 8.088365 AGGAAAATAATCGGTGAAAAAGAAAGG 58.912 33.333 0.00 0.00 0.00 3.11
2758 2908 9.476202 AAGGAAAATAATCGGTGAAAAAGAAAG 57.524 29.630 0.00 0.00 0.00 2.62
2760 2910 8.634444 TCAAGGAAAATAATCGGTGAAAAAGAA 58.366 29.630 0.00 0.00 0.00 2.52
2775 2925 9.883142 AACTGTGAATTGTTTTCAAGGAAAATA 57.117 25.926 7.33 2.60 42.31 1.40
2790 2940 7.593875 TTTGTTTTCAAGGAACTGTGAATTG 57.406 32.000 0.00 0.00 40.86 2.32
2797 2947 9.971744 CTGTAAATTTTTGTTTTCAAGGAACTG 57.028 29.630 0.00 0.00 40.86 3.16
2811 2983 6.256757 TGGCGAAAAGGAACTGTAAATTTTTG 59.743 34.615 0.00 6.94 40.86 2.44
2833 3005 4.083003 TGGTGTCGACAGAAAATTATTGGC 60.083 41.667 20.73 1.67 0.00 4.52
2848 3040 3.071479 GGAGCTGTAAAAATGGTGTCGA 58.929 45.455 0.00 0.00 0.00 4.20
2850 3042 4.762251 AGAAGGAGCTGTAAAAATGGTGTC 59.238 41.667 0.00 0.00 0.00 3.67
2901 3093 4.078571 ACCCTAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
2902 3094 4.227197 ACCCTAGAGAGAGAGAGAGAGAG 58.773 52.174 0.00 0.00 0.00 3.20
2903 3095 4.280789 ACCCTAGAGAGAGAGAGAGAGA 57.719 50.000 0.00 0.00 0.00 3.10
2904 3096 5.602978 AGTAACCCTAGAGAGAGAGAGAGAG 59.397 48.000 0.00 0.00 0.00 3.20
2905 3097 5.535029 AGTAACCCTAGAGAGAGAGAGAGA 58.465 45.833 0.00 0.00 0.00 3.10
2906 3098 5.888982 AGTAACCCTAGAGAGAGAGAGAG 57.111 47.826 0.00 0.00 0.00 3.20
2907 3099 6.446451 ACTAGTAACCCTAGAGAGAGAGAGA 58.554 44.000 0.00 0.00 45.21 3.10
2908 3100 6.742559 ACTAGTAACCCTAGAGAGAGAGAG 57.257 45.833 0.00 0.00 45.21 3.20
2909 3101 6.268387 GCTACTAGTAACCCTAGAGAGAGAGA 59.732 46.154 3.76 0.00 45.21 3.10
2910 3102 6.042322 TGCTACTAGTAACCCTAGAGAGAGAG 59.958 46.154 3.76 0.00 45.21 3.20
2911 3103 5.904169 TGCTACTAGTAACCCTAGAGAGAGA 59.096 44.000 3.76 0.00 45.21 3.10
2949 3144 6.108687 TCAGTAAGTGGTTTATCAGATGCTG 58.891 40.000 0.00 0.00 0.00 4.41
3029 3229 2.433446 CACCACCCTGCTCTGCTT 59.567 61.111 0.00 0.00 0.00 3.91
3031 3231 3.958860 ACCACCACCCTGCTCTGC 61.959 66.667 0.00 0.00 0.00 4.26
3037 3237 2.538141 ATCCCACACCACCACCCTG 61.538 63.158 0.00 0.00 0.00 4.45
3040 3240 1.603455 CACATCCCACACCACCACC 60.603 63.158 0.00 0.00 0.00 4.61
3041 3241 1.603455 CCACATCCCACACCACCAC 60.603 63.158 0.00 0.00 0.00 4.16
3042 3242 1.356494 TTCCACATCCCACACCACCA 61.356 55.000 0.00 0.00 0.00 4.17
3124 3340 4.792804 GAGCACCAGGAGCCAGCC 62.793 72.222 5.06 0.00 0.00 4.85
3125 3341 3.715097 AGAGCACCAGGAGCCAGC 61.715 66.667 5.06 0.00 0.00 4.85
3126 3342 2.268280 CAGAGCACCAGGAGCCAG 59.732 66.667 5.06 0.00 0.00 4.85
3127 3343 3.324930 CCAGAGCACCAGGAGCCA 61.325 66.667 5.06 0.00 0.00 4.75
3128 3344 4.106925 CCCAGAGCACCAGGAGCC 62.107 72.222 5.06 0.00 0.00 4.70
3129 3345 2.533974 CTTCCCAGAGCACCAGGAGC 62.534 65.000 0.00 0.00 0.00 4.70
3130 3346 1.197430 ACTTCCCAGAGCACCAGGAG 61.197 60.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.