Multiple sequence alignment - TraesCS7D01G299000

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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 TraesCS7D01G299000 chr7D 100.000 3145 0 0 1 3145 378849327 378852471 0.000000e+00 5808.0
1 TraesCS7D01G299000 chr7D 94.925 335 8 4 1 328 75887935 75888267 1.670000e-142 516.0
2 TraesCS7D01G299000 chr7D 80.308 325 33 22 2711 3016 628735166 628734854 1.900000e-52 217.0
3 TraesCS7D01G299000 chr7B 96.286 2612 73 15 438 3032 374312735 374315339 0.000000e+00 4265.0
4 TraesCS7D01G299000 chr7B 85.294 238 26 5 2780 3013 170507765 170507533 1.460000e-58 237.0
5 TraesCS7D01G299000 chr7B 90.400 125 2 3 328 452 374311342 374311456 4.200000e-34 156.0
6 TraesCS7D01G299000 chr7B 90.566 106 9 1 2533 2637 176697421 176697526 4.230000e-29 139.0
7 TraesCS7D01G299000 chr2A 95.739 1760 64 5 882 2637 338279376 338281128 0.000000e+00 2824.0
8 TraesCS7D01G299000 chr2A 94.014 568 24 5 328 885 338278729 338279296 0.000000e+00 852.0
9 TraesCS7D01G299000 chr2A 89.247 465 30 10 2696 3145 338282378 338282837 5.890000e-157 564.0
10 TraesCS7D01G299000 chr7A 96.972 1486 38 4 964 2447 427288186 427289666 0.000000e+00 2488.0
11 TraesCS7D01G299000 chr7A 96.881 513 12 4 328 838 427287625 427288135 0.000000e+00 856.0
12 TraesCS7D01G299000 chr7A 97.256 328 7 2 1 328 22155322 22155647 3.540000e-154 555.0
13 TraesCS7D01G299000 chr7A 95.122 328 13 3 1 328 21835548 21835872 6.010000e-142 514.0
14 TraesCS7D01G299000 chr7A 94.512 328 16 2 1 328 22161940 22162265 3.620000e-139 505.0
15 TraesCS7D01G299000 chr7A 90.351 114 9 2 2526 2637 90607669 90607556 7.030000e-32 148.0
16 TraesCS7D01G299000 chr7A 80.288 208 17 9 2533 2720 233339201 233338998 5.470000e-28 135.0
17 TraesCS7D01G299000 chr3D 96.037 328 11 2 1 328 610893871 610893546 1.660000e-147 532.0
18 TraesCS7D01G299000 chr5B 94.864 331 14 3 1 330 439356039 439355711 6.010000e-142 514.0
19 TraesCS7D01G299000 chr5B 84.937 239 26 7 2780 3013 545893091 545893324 1.890000e-57 233.0
20 TraesCS7D01G299000 chr5B 80.573 314 34 21 2716 3013 166646356 166646054 1.900000e-52 217.0
21 TraesCS7D01G299000 chr4A 94.817 328 14 3 7 333 611400839 611401164 2.800000e-140 508.0
22 TraesCS7D01G299000 chr4A 80.268 299 35 15 2723 3013 31396837 31396555 1.480000e-48 204.0
23 TraesCS7D01G299000 chr4A 94.286 105 6 0 2533 2637 613610084 613609980 9.030000e-36 161.0
24 TraesCS7D01G299000 chr4A 77.992 259 21 21 2533 2762 535863919 535863668 2.550000e-26 130.0
25 TraesCS7D01G299000 chr6D 94.545 330 14 3 1 328 132363031 132362704 1.010000e-139 507.0
26 TraesCS7D01G299000 chr6A 94.545 330 15 2 1 328 36144197 36143869 1.010000e-139 507.0
27 TraesCS7D01G299000 chr6A 79.143 350 36 30 2687 3013 600261973 600262308 1.140000e-49 207.0
28 TraesCS7D01G299000 chr6A 93.578 109 6 1 2530 2637 604154316 604154424 9.030000e-36 161.0
29 TraesCS7D01G299000 chr3A 88.208 212 19 4 2818 3026 535080687 535080895 6.740000e-62 248.0
30 TraesCS7D01G299000 chr3B 85.294 238 22 8 2792 3020 39576961 39577194 1.890000e-57 233.0
31 TraesCS7D01G299000 chrUn 92.793 111 8 0 2533 2643 138408427 138408317 9.030000e-36 161.0
32 TraesCS7D01G299000 chrUn 92.793 111 8 0 2533 2643 138477484 138477374 9.030000e-36 161.0
33 TraesCS7D01G299000 chrUn 94.286 105 6 0 2533 2637 171119845 171119949 9.030000e-36 161.0
34 TraesCS7D01G299000 chrUn 94.286 105 6 0 2533 2637 172139501 172139605 9.030000e-36 161.0
35 TraesCS7D01G299000 chrUn 92.793 111 8 0 2533 2643 371414104 371413994 9.030000e-36 161.0
36 TraesCS7D01G299000 chrUn 94.286 105 6 0 2533 2637 390075731 390075835 9.030000e-36 161.0
37 TraesCS7D01G299000 chr5D 79.245 265 25 18 2520 2761 506689238 506689495 1.170000e-34 158.0
38 TraesCS7D01G299000 chr4B 81.152 191 16 6 2533 2704 103548990 103548801 5.470000e-28 135.0
39 TraesCS7D01G299000 chr1A 92.157 51 3 1 2641 2690 506548051 506548101 1.560000e-08 71.3


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 TraesCS7D01G299000 chr7D 378849327 378852471 3144 False 5808.000000 5808 100.0000 1 3145 1 chr7D.!!$F2 3144
1 TraesCS7D01G299000 chr7B 374311342 374315339 3997 False 2210.500000 4265 93.3430 328 3032 2 chr7B.!!$F2 2704
2 TraesCS7D01G299000 chr2A 338278729 338282837 4108 False 1413.333333 2824 93.0000 328 3145 3 chr2A.!!$F1 2817
3 TraesCS7D01G299000 chr7A 427287625 427289666 2041 False 1672.000000 2488 96.9265 328 2447 2 chr7A.!!$F4 2119

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
254 255 0.035343 GTTGAGGTTGAGGCCTACCC 60.035 60.0 19.46 13.07 39.34 3.69 F
291 292 0.395586 GCACCAGCACCCCATCAATA 60.396 55.0 0.00 0.00 41.58 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 3232 1.246056 GCTGCATTGAGTTGCCTGGA 61.246 55.0 0.00 0.0 42.06 3.86 R
2285 3677 4.563580 CCCGGGACTATGATAATCCACAAG 60.564 50.0 18.48 0.0 33.87 3.16 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
21 22 2.912900 GCTCGATATTCACTTCGTGC 57.087 50.000 4.04 4.04 44.24 5.34
22 23 1.188138 GCTCGATATTCACTTCGTGCG 59.812 52.381 4.04 0.00 42.49 5.34
23 24 1.188138 CTCGATATTCACTTCGTGCGC 59.812 52.381 0.00 0.00 36.74 6.09
24 25 0.112137 CGATATTCACTTCGTGCGCG 60.112 55.000 14.79 14.79 39.92 6.86
25 26 1.197055 GATATTCACTTCGTGCGCGA 58.803 50.000 20.10 20.10 46.36 5.87
39 40 3.741476 GCGAGCAGGTTGCCCTTG 61.741 66.667 0.00 0.00 46.52 3.61
40 41 3.058160 CGAGCAGGTTGCCCTTGG 61.058 66.667 0.00 0.00 46.52 3.61
60 61 1.850640 CGTGTTCGGGTTCTTCACG 59.149 57.895 0.00 0.00 45.33 4.35
61 62 0.872881 CGTGTTCGGGTTCTTCACGT 60.873 55.000 7.65 0.00 44.19 4.49
62 63 0.580104 GTGTTCGGGTTCTTCACGTG 59.420 55.000 9.94 9.94 44.19 4.49
63 64 1.155424 TGTTCGGGTTCTTCACGTGC 61.155 55.000 11.67 0.00 44.19 5.34
64 65 1.595929 TTCGGGTTCTTCACGTGCC 60.596 57.895 11.67 5.56 44.19 5.01
65 66 3.411351 CGGGTTCTTCACGTGCCG 61.411 66.667 11.67 13.15 38.27 5.69
66 67 2.029964 GGGTTCTTCACGTGCCGA 59.970 61.111 11.67 6.60 0.00 5.54
67 68 2.315386 GGGTTCTTCACGTGCCGAC 61.315 63.158 11.67 6.65 0.00 4.79
77 78 4.059459 GTGCCGACGTCGCAACAG 62.059 66.667 31.73 18.63 38.18 3.16
78 79 4.578898 TGCCGACGTCGCAACAGT 62.579 61.111 31.73 0.00 38.18 3.55
79 80 3.335534 GCCGACGTCGCAACAGTT 61.336 61.111 31.73 0.00 38.18 3.16
80 81 2.877974 GCCGACGTCGCAACAGTTT 61.878 57.895 31.73 0.00 38.18 2.66
81 82 1.083657 CCGACGTCGCAACAGTTTG 60.084 57.895 31.73 11.40 38.18 2.93
93 94 4.492791 CAACAGTTTGCTGATGTGATGA 57.507 40.909 1.30 0.00 45.28 2.92
94 95 4.224433 CAACAGTTTGCTGATGTGATGAC 58.776 43.478 1.30 0.00 45.28 3.06
95 96 3.748083 ACAGTTTGCTGATGTGATGACT 58.252 40.909 1.30 0.00 45.28 3.41
96 97 4.898320 ACAGTTTGCTGATGTGATGACTA 58.102 39.130 1.30 0.00 45.28 2.59
97 98 5.308014 ACAGTTTGCTGATGTGATGACTAA 58.692 37.500 1.30 0.00 45.28 2.24
98 99 5.410746 ACAGTTTGCTGATGTGATGACTAAG 59.589 40.000 1.30 0.00 45.28 2.18
99 100 4.940046 AGTTTGCTGATGTGATGACTAAGG 59.060 41.667 0.00 0.00 0.00 2.69
100 101 3.548745 TGCTGATGTGATGACTAAGGG 57.451 47.619 0.00 0.00 0.00 3.95
101 102 3.106827 TGCTGATGTGATGACTAAGGGA 58.893 45.455 0.00 0.00 0.00 4.20
102 103 3.713248 TGCTGATGTGATGACTAAGGGAT 59.287 43.478 0.00 0.00 0.00 3.85
103 104 4.164796 TGCTGATGTGATGACTAAGGGATT 59.835 41.667 0.00 0.00 0.00 3.01
104 105 4.514441 GCTGATGTGATGACTAAGGGATTG 59.486 45.833 0.00 0.00 0.00 2.67
105 106 4.454678 TGATGTGATGACTAAGGGATTGC 58.545 43.478 0.00 0.00 0.00 3.56
106 107 3.281727 TGTGATGACTAAGGGATTGCC 57.718 47.619 0.00 0.00 0.00 4.52
107 108 2.846206 TGTGATGACTAAGGGATTGCCT 59.154 45.455 0.00 0.00 0.00 4.75
108 109 4.037222 TGTGATGACTAAGGGATTGCCTA 58.963 43.478 0.00 0.00 0.00 3.93
109 110 4.141711 TGTGATGACTAAGGGATTGCCTAC 60.142 45.833 0.00 0.00 0.00 3.18
110 111 4.101741 GTGATGACTAAGGGATTGCCTACT 59.898 45.833 0.00 0.00 0.00 2.57
111 112 4.721776 TGATGACTAAGGGATTGCCTACTT 59.278 41.667 0.00 0.00 0.00 2.24
112 113 4.755266 TGACTAAGGGATTGCCTACTTC 57.245 45.455 0.00 0.00 0.00 3.01
113 114 3.454812 TGACTAAGGGATTGCCTACTTCC 59.545 47.826 0.00 0.00 0.00 3.46
114 115 2.434702 ACTAAGGGATTGCCTACTTCCG 59.565 50.000 0.00 0.00 0.00 4.30
115 116 1.286248 AAGGGATTGCCTACTTCCGT 58.714 50.000 0.00 0.00 0.00 4.69
116 117 0.831307 AGGGATTGCCTACTTCCGTC 59.169 55.000 0.00 0.00 0.00 4.79
117 118 0.831307 GGGATTGCCTACTTCCGTCT 59.169 55.000 0.00 0.00 0.00 4.18
118 119 1.209747 GGGATTGCCTACTTCCGTCTT 59.790 52.381 0.00 0.00 0.00 3.01
119 120 2.552031 GGATTGCCTACTTCCGTCTTC 58.448 52.381 0.00 0.00 0.00 2.87
120 121 2.194271 GATTGCCTACTTCCGTCTTCG 58.806 52.381 0.00 0.00 0.00 3.79
121 122 1.250328 TTGCCTACTTCCGTCTTCGA 58.750 50.000 0.00 0.00 39.71 3.71
122 123 0.809385 TGCCTACTTCCGTCTTCGAG 59.191 55.000 0.00 0.00 39.71 4.04
123 124 0.100861 GCCTACTTCCGTCTTCGAGG 59.899 60.000 0.00 0.00 39.71 4.63
124 125 1.747709 CCTACTTCCGTCTTCGAGGA 58.252 55.000 0.00 0.00 39.71 3.71
125 126 1.671845 CCTACTTCCGTCTTCGAGGAG 59.328 57.143 0.00 0.00 37.88 3.69
126 127 2.358015 CTACTTCCGTCTTCGAGGAGT 58.642 52.381 0.00 0.00 37.88 3.85
127 128 1.618487 ACTTCCGTCTTCGAGGAGTT 58.382 50.000 0.00 0.00 37.88 3.01
128 129 1.962100 ACTTCCGTCTTCGAGGAGTTT 59.038 47.619 0.00 0.00 37.88 2.66
129 130 2.030096 ACTTCCGTCTTCGAGGAGTTTC 60.030 50.000 0.00 0.00 37.88 2.78
130 131 0.520404 TCCGTCTTCGAGGAGTTTCG 59.480 55.000 0.00 0.00 41.79 3.46
131 132 0.456312 CCGTCTTCGAGGAGTTTCGG 60.456 60.000 9.38 9.38 40.83 4.30
132 133 0.240411 CGTCTTCGAGGAGTTTCGGT 59.760 55.000 0.00 0.00 40.83 4.69
133 134 1.728502 CGTCTTCGAGGAGTTTCGGTC 60.729 57.143 0.00 0.00 40.83 4.79
134 135 0.886563 TCTTCGAGGAGTTTCGGTCC 59.113 55.000 0.00 0.00 40.83 4.46
135 136 0.601558 CTTCGAGGAGTTTCGGTCCA 59.398 55.000 0.00 0.00 40.83 4.02
136 137 0.601558 TTCGAGGAGTTTCGGTCCAG 59.398 55.000 0.00 0.00 40.83 3.86
137 138 0.538977 TCGAGGAGTTTCGGTCCAGT 60.539 55.000 0.00 0.00 40.83 4.00
138 139 0.109226 CGAGGAGTTTCGGTCCAGTC 60.109 60.000 0.00 0.00 36.43 3.51
139 140 1.258676 GAGGAGTTTCGGTCCAGTCT 58.741 55.000 0.00 0.00 36.43 3.24
140 141 1.202817 GAGGAGTTTCGGTCCAGTCTC 59.797 57.143 0.00 0.00 36.43 3.36
141 142 1.203075 AGGAGTTTCGGTCCAGTCTCT 60.203 52.381 0.00 0.00 36.43 3.10
142 143 1.067495 GGAGTTTCGGTCCAGTCTCTG 60.067 57.143 0.00 0.00 33.84 3.35
143 144 1.614413 GAGTTTCGGTCCAGTCTCTGT 59.386 52.381 0.00 0.00 0.00 3.41
144 145 1.341531 AGTTTCGGTCCAGTCTCTGTG 59.658 52.381 0.00 0.00 0.00 3.66
145 146 1.068741 GTTTCGGTCCAGTCTCTGTGT 59.931 52.381 0.00 0.00 0.00 3.72
146 147 0.959553 TTCGGTCCAGTCTCTGTGTC 59.040 55.000 0.00 0.00 0.00 3.67
147 148 0.110678 TCGGTCCAGTCTCTGTGTCT 59.889 55.000 0.00 0.00 0.00 3.41
148 149 0.523966 CGGTCCAGTCTCTGTGTCTC 59.476 60.000 0.00 0.00 0.00 3.36
149 150 1.884497 CGGTCCAGTCTCTGTGTCTCT 60.884 57.143 0.00 0.00 0.00 3.10
150 151 1.543802 GGTCCAGTCTCTGTGTCTCTG 59.456 57.143 0.00 0.00 0.00 3.35
151 152 1.543802 GTCCAGTCTCTGTGTCTCTGG 59.456 57.143 0.00 0.00 44.69 3.86
152 153 0.246086 CCAGTCTCTGTGTCTCTGGC 59.754 60.000 0.00 0.00 39.02 4.85
153 154 0.109365 CAGTCTCTGTGTCTCTGGCG 60.109 60.000 0.00 0.00 0.00 5.69
154 155 0.250945 AGTCTCTGTGTCTCTGGCGA 60.251 55.000 0.00 0.00 0.00 5.54
155 156 0.109504 GTCTCTGTGTCTCTGGCGAC 60.110 60.000 0.00 0.00 34.52 5.19
156 157 1.154131 CTCTGTGTCTCTGGCGACG 60.154 63.158 0.00 0.00 36.71 5.12
157 158 2.807045 CTGTGTCTCTGGCGACGC 60.807 66.667 12.43 12.43 43.02 5.19
158 159 3.274455 CTGTGTCTCTGGCGACGCT 62.274 63.158 20.77 0.00 43.10 5.07
159 160 2.049063 GTGTCTCTGGCGACGCTT 60.049 61.111 20.77 0.00 40.36 4.68
160 161 2.089349 GTGTCTCTGGCGACGCTTC 61.089 63.158 20.77 4.29 40.36 3.86
189 190 4.251543 GGGGGTGTTGAGTTGTATTTTG 57.748 45.455 0.00 0.00 0.00 2.44
190 191 3.639561 GGGGGTGTTGAGTTGTATTTTGT 59.360 43.478 0.00 0.00 0.00 2.83
191 192 4.500716 GGGGGTGTTGAGTTGTATTTTGTG 60.501 45.833 0.00 0.00 0.00 3.33
192 193 4.098807 GGGGTGTTGAGTTGTATTTTGTGT 59.901 41.667 0.00 0.00 0.00 3.72
193 194 5.394773 GGGGTGTTGAGTTGTATTTTGTGTT 60.395 40.000 0.00 0.00 0.00 3.32
194 195 5.518487 GGGTGTTGAGTTGTATTTTGTGTTG 59.482 40.000 0.00 0.00 0.00 3.33
195 196 5.005299 GGTGTTGAGTTGTATTTTGTGTTGC 59.995 40.000 0.00 0.00 0.00 4.17
196 197 5.574830 GTGTTGAGTTGTATTTTGTGTTGCA 59.425 36.000 0.00 0.00 0.00 4.08
197 198 6.255453 GTGTTGAGTTGTATTTTGTGTTGCAT 59.745 34.615 0.00 0.00 0.00 3.96
198 199 6.255237 TGTTGAGTTGTATTTTGTGTTGCATG 59.745 34.615 0.00 0.00 0.00 4.06
199 200 5.900425 TGAGTTGTATTTTGTGTTGCATGT 58.100 33.333 0.00 0.00 0.00 3.21
200 201 7.032377 TGAGTTGTATTTTGTGTTGCATGTA 57.968 32.000 0.00 0.00 0.00 2.29
201 202 7.656412 TGAGTTGTATTTTGTGTTGCATGTAT 58.344 30.769 0.00 0.00 0.00 2.29
202 203 8.140628 TGAGTTGTATTTTGTGTTGCATGTATT 58.859 29.630 0.00 0.00 0.00 1.89
203 204 9.619316 GAGTTGTATTTTGTGTTGCATGTATTA 57.381 29.630 0.00 0.00 0.00 0.98
204 205 9.624697 AGTTGTATTTTGTGTTGCATGTATTAG 57.375 29.630 0.00 0.00 0.00 1.73
205 206 9.619316 GTTGTATTTTGTGTTGCATGTATTAGA 57.381 29.630 0.00 0.00 0.00 2.10
207 208 9.786105 TGTATTTTGTGTTGCATGTATTAGATG 57.214 29.630 0.00 0.00 0.00 2.90
208 209 9.787532 GTATTTTGTGTTGCATGTATTAGATGT 57.212 29.630 3.10 0.00 0.00 3.06
210 211 8.518151 TTTTGTGTTGCATGTATTAGATGTTG 57.482 30.769 3.10 0.00 0.00 3.33
211 212 6.816134 TGTGTTGCATGTATTAGATGTTGT 57.184 33.333 3.10 0.00 0.00 3.32
212 213 6.610456 TGTGTTGCATGTATTAGATGTTGTG 58.390 36.000 3.10 0.00 0.00 3.33
213 214 6.029607 GTGTTGCATGTATTAGATGTTGTGG 58.970 40.000 3.10 0.00 0.00 4.17
214 215 4.898829 TGCATGTATTAGATGTTGTGGC 57.101 40.909 3.10 0.00 0.00 5.01
215 216 3.631686 TGCATGTATTAGATGTTGTGGCC 59.368 43.478 0.00 0.00 0.00 5.36
216 217 3.004734 GCATGTATTAGATGTTGTGGCCC 59.995 47.826 0.00 0.00 0.00 5.80
217 218 4.206375 CATGTATTAGATGTTGTGGCCCA 58.794 43.478 0.00 0.00 0.00 5.36
218 219 3.616219 TGTATTAGATGTTGTGGCCCAC 58.384 45.455 7.01 7.01 34.56 4.61
219 220 2.143876 ATTAGATGTTGTGGCCCACC 57.856 50.000 12.25 0.00 32.73 4.61
220 221 1.072266 TTAGATGTTGTGGCCCACCT 58.928 50.000 12.25 2.96 36.63 4.00
221 222 0.618458 TAGATGTTGTGGCCCACCTC 59.382 55.000 12.25 4.93 36.63 3.85
222 223 1.678970 GATGTTGTGGCCCACCTCC 60.679 63.158 12.25 0.00 36.63 4.30
223 224 2.142292 GATGTTGTGGCCCACCTCCT 62.142 60.000 12.25 0.00 36.63 3.69
224 225 0.844661 ATGTTGTGGCCCACCTCCTA 60.845 55.000 12.25 0.00 36.63 2.94
225 226 1.299976 GTTGTGGCCCACCTCCTAG 59.700 63.158 12.25 0.00 36.63 3.02
226 227 1.151899 TTGTGGCCCACCTCCTAGT 60.152 57.895 12.25 0.00 36.63 2.57
227 228 0.770557 TTGTGGCCCACCTCCTAGTT 60.771 55.000 12.25 0.00 36.63 2.24
228 229 1.299976 GTGGCCCACCTCCTAGTTG 59.700 63.158 1.17 0.00 36.63 3.16
229 230 1.151899 TGGCCCACCTCCTAGTTGT 60.152 57.895 0.00 0.00 36.63 3.32
230 231 1.299976 GGCCCACCTCCTAGTTGTG 59.700 63.158 0.00 0.00 0.00 3.33
231 232 1.489560 GGCCCACCTCCTAGTTGTGT 61.490 60.000 0.00 0.00 0.00 3.72
232 233 1.272807 GCCCACCTCCTAGTTGTGTA 58.727 55.000 0.00 0.00 0.00 2.90
233 234 1.838077 GCCCACCTCCTAGTTGTGTAT 59.162 52.381 0.00 0.00 0.00 2.29
234 235 3.036091 GCCCACCTCCTAGTTGTGTATA 58.964 50.000 0.00 0.00 0.00 1.47
235 236 3.069729 GCCCACCTCCTAGTTGTGTATAG 59.930 52.174 0.00 0.00 0.00 1.31
236 237 4.287552 CCCACCTCCTAGTTGTGTATAGT 58.712 47.826 0.00 0.00 0.00 2.12
237 238 4.715297 CCCACCTCCTAGTTGTGTATAGTT 59.285 45.833 0.00 0.00 0.00 2.24
238 239 5.395324 CCCACCTCCTAGTTGTGTATAGTTG 60.395 48.000 0.00 0.00 0.00 3.16
239 240 5.421056 CCACCTCCTAGTTGTGTATAGTTGA 59.579 44.000 0.00 0.00 0.00 3.18
240 241 6.405953 CCACCTCCTAGTTGTGTATAGTTGAG 60.406 46.154 0.00 0.00 0.00 3.02
241 242 5.657302 ACCTCCTAGTTGTGTATAGTTGAGG 59.343 44.000 0.00 0.00 41.08 3.86
242 243 5.657302 CCTCCTAGTTGTGTATAGTTGAGGT 59.343 44.000 0.00 0.00 32.82 3.85
243 244 6.154706 CCTCCTAGTTGTGTATAGTTGAGGTT 59.845 42.308 0.00 0.00 32.82 3.50
244 245 6.931838 TCCTAGTTGTGTATAGTTGAGGTTG 58.068 40.000 0.00 0.00 0.00 3.77
245 246 6.722590 TCCTAGTTGTGTATAGTTGAGGTTGA 59.277 38.462 0.00 0.00 0.00 3.18
246 247 7.036220 CCTAGTTGTGTATAGTTGAGGTTGAG 58.964 42.308 0.00 0.00 0.00 3.02
247 248 5.794894 AGTTGTGTATAGTTGAGGTTGAGG 58.205 41.667 0.00 0.00 0.00 3.86
248 249 4.202245 TGTGTATAGTTGAGGTTGAGGC 57.798 45.455 0.00 0.00 0.00 4.70
249 250 3.055385 TGTGTATAGTTGAGGTTGAGGCC 60.055 47.826 0.00 0.00 0.00 5.19
250 251 3.197983 GTGTATAGTTGAGGTTGAGGCCT 59.802 47.826 3.86 3.86 42.53 5.19
251 252 4.404715 GTGTATAGTTGAGGTTGAGGCCTA 59.595 45.833 4.42 0.00 39.34 3.93
252 253 4.404715 TGTATAGTTGAGGTTGAGGCCTAC 59.595 45.833 4.42 0.00 39.34 3.18
253 254 0.984995 AGTTGAGGTTGAGGCCTACC 59.015 55.000 16.00 16.00 39.34 3.18
254 255 0.035343 GTTGAGGTTGAGGCCTACCC 60.035 60.000 19.46 13.07 39.34 3.69
256 257 0.909610 TGAGGTTGAGGCCTACCCTG 60.910 60.000 19.46 0.00 46.60 4.45
257 258 0.910088 GAGGTTGAGGCCTACCCTGT 60.910 60.000 19.46 3.03 46.60 4.00
258 259 0.416231 AGGTTGAGGCCTACCCTGTA 59.584 55.000 19.46 0.00 46.60 2.74
259 260 0.540454 GGTTGAGGCCTACCCTGTAC 59.460 60.000 13.16 0.00 46.60 2.90
260 261 1.569653 GTTGAGGCCTACCCTGTACT 58.430 55.000 4.42 0.00 46.60 2.73
261 262 1.907255 GTTGAGGCCTACCCTGTACTT 59.093 52.381 4.42 0.00 46.60 2.24
262 263 3.102204 GTTGAGGCCTACCCTGTACTTA 58.898 50.000 4.42 0.00 46.60 2.24
263 264 3.700863 TGAGGCCTACCCTGTACTTAT 57.299 47.619 4.42 0.00 46.60 1.73
264 265 4.819702 TGAGGCCTACCCTGTACTTATA 57.180 45.455 4.42 0.00 46.60 0.98
265 266 5.349738 TGAGGCCTACCCTGTACTTATAT 57.650 43.478 4.42 0.00 46.60 0.86
266 267 6.473429 TGAGGCCTACCCTGTACTTATATA 57.527 41.667 4.42 0.00 46.60 0.86
267 268 7.052901 TGAGGCCTACCCTGTACTTATATAT 57.947 40.000 4.42 0.00 46.60 0.86
268 269 8.178662 TGAGGCCTACCCTGTACTTATATATA 57.821 38.462 4.42 0.00 46.60 0.86
269 270 8.057623 TGAGGCCTACCCTGTACTTATATATAC 58.942 40.741 4.42 0.00 46.60 1.47
270 271 7.059156 AGGCCTACCCTGTACTTATATATACG 58.941 42.308 1.29 0.00 44.28 3.06
271 272 6.830838 GGCCTACCCTGTACTTATATATACGT 59.169 42.308 7.04 7.04 0.00 3.57
272 273 7.201767 GGCCTACCCTGTACTTATATATACGTG 60.202 44.444 11.18 0.00 0.00 4.49
273 274 7.680588 GCCTACCCTGTACTTATATATACGTGC 60.681 44.444 11.18 10.35 0.00 5.34
274 275 7.337689 CCTACCCTGTACTTATATATACGTGCA 59.662 40.741 15.88 15.88 0.00 4.57
275 276 6.917533 ACCCTGTACTTATATATACGTGCAC 58.082 40.000 13.70 6.82 0.00 4.57
276 277 6.071728 ACCCTGTACTTATATATACGTGCACC 60.072 42.308 12.15 0.00 0.00 5.01
277 278 6.071784 CCCTGTACTTATATATACGTGCACCA 60.072 42.308 12.15 0.00 0.00 4.17
278 279 7.027760 CCTGTACTTATATATACGTGCACCAG 58.972 42.308 12.15 7.10 0.00 4.00
279 280 6.384224 TGTACTTATATATACGTGCACCAGC 58.616 40.000 12.15 0.00 42.57 4.85
289 290 2.283101 GCACCAGCACCCCATCAA 60.283 61.111 0.00 0.00 41.58 2.57
290 291 1.683365 GCACCAGCACCCCATCAAT 60.683 57.895 0.00 0.00 41.58 2.57
291 292 0.395586 GCACCAGCACCCCATCAATA 60.396 55.000 0.00 0.00 41.58 1.90
292 293 1.392589 CACCAGCACCCCATCAATAC 58.607 55.000 0.00 0.00 0.00 1.89
293 294 0.998928 ACCAGCACCCCATCAATACA 59.001 50.000 0.00 0.00 0.00 2.29
294 295 1.357420 ACCAGCACCCCATCAATACAA 59.643 47.619 0.00 0.00 0.00 2.41
295 296 1.750778 CCAGCACCCCATCAATACAAC 59.249 52.381 0.00 0.00 0.00 3.32
296 297 1.750778 CAGCACCCCATCAATACAACC 59.249 52.381 0.00 0.00 0.00 3.77
297 298 1.357420 AGCACCCCATCAATACAACCA 59.643 47.619 0.00 0.00 0.00 3.67
298 299 2.024080 AGCACCCCATCAATACAACCAT 60.024 45.455 0.00 0.00 0.00 3.55
299 300 2.765699 GCACCCCATCAATACAACCATT 59.234 45.455 0.00 0.00 0.00 3.16
300 301 3.957497 GCACCCCATCAATACAACCATTA 59.043 43.478 0.00 0.00 0.00 1.90
301 302 4.588528 GCACCCCATCAATACAACCATTAT 59.411 41.667 0.00 0.00 0.00 1.28
302 303 5.070313 GCACCCCATCAATACAACCATTATT 59.930 40.000 0.00 0.00 0.00 1.40
303 304 6.514947 CACCCCATCAATACAACCATTATTG 58.485 40.000 0.00 0.00 38.00 1.90
304 305 6.098124 CACCCCATCAATACAACCATTATTGT 59.902 38.462 0.00 0.00 44.87 2.71
305 306 7.286546 CACCCCATCAATACAACCATTATTGTA 59.713 37.037 1.16 1.16 46.33 2.41
315 316 7.665561 ACAACCATTATTGTATTGGCAAAAC 57.334 32.000 3.01 0.00 41.04 2.43
316 317 7.220030 ACAACCATTATTGTATTGGCAAAACA 58.780 30.769 3.01 0.00 41.04 2.83
317 318 7.882271 ACAACCATTATTGTATTGGCAAAACAT 59.118 29.630 3.01 0.00 41.04 2.71
318 319 8.389603 CAACCATTATTGTATTGGCAAAACATC 58.610 33.333 3.01 0.00 33.56 3.06
319 320 7.850193 ACCATTATTGTATTGGCAAAACATCT 58.150 30.769 3.01 0.00 33.56 2.90
320 321 7.981225 ACCATTATTGTATTGGCAAAACATCTC 59.019 33.333 3.01 0.00 33.56 2.75
321 322 8.199449 CCATTATTGTATTGGCAAAACATCTCT 58.801 33.333 3.01 0.00 31.63 3.10
322 323 9.590451 CATTATTGTATTGGCAAAACATCTCTT 57.410 29.630 3.01 0.00 31.63 2.85
323 324 9.807649 ATTATTGTATTGGCAAAACATCTCTTC 57.192 29.630 3.01 0.00 31.63 2.87
324 325 6.899393 TTGTATTGGCAAAACATCTCTTCT 57.101 33.333 3.01 0.00 0.00 2.85
325 326 7.994425 TTGTATTGGCAAAACATCTCTTCTA 57.006 32.000 3.01 0.00 0.00 2.10
326 327 7.377766 TGTATTGGCAAAACATCTCTTCTAC 57.622 36.000 3.01 0.00 0.00 2.59
453 1753 0.412244 TACAGGAGTACCAGGGCTGT 59.588 55.000 0.00 0.00 38.94 4.40
500 1800 3.119849 CCTTCTTTACCAGAATGCAACCG 60.120 47.826 0.00 0.00 40.95 4.44
539 1839 3.126000 GTCTTCTGCAATTGCTACTGGAC 59.874 47.826 29.37 23.30 42.66 4.02
627 1928 6.349280 GCTAAAATCCACAATCTGTAACTGCA 60.349 38.462 0.00 0.00 0.00 4.41
632 1933 2.810274 CACAATCTGTAACTGCAGTGCT 59.190 45.455 22.49 8.39 37.70 4.40
1842 3232 5.140454 AGTTTTTCCCAACTGCTACAGAAT 58.860 37.500 0.78 0.00 35.57 2.40
2344 3736 8.954950 AAAATGATACATAGTGGTCAAGAGAG 57.045 34.615 0.00 0.00 0.00 3.20
2468 3861 1.002134 CCAAATGCCTCGTGGACCT 60.002 57.895 7.92 0.00 34.05 3.85
2581 3974 7.169982 TGTTTAAATTTTGTGCCCTATTTGACG 59.830 33.333 0.00 0.00 0.00 4.35
2662 5043 4.459337 CCCTAAATGACACCTGAAAAGACC 59.541 45.833 0.00 0.00 0.00 3.85
2670 5051 2.695147 CACCTGAAAAGACCCTTTTGCT 59.305 45.455 9.14 0.00 0.00 3.91
2746 5275 2.935955 GTGCGTGTGTGTACTGCC 59.064 61.111 0.00 0.00 0.00 4.85
2748 5277 4.072088 GCGTGTGTGTACTGCCGC 62.072 66.667 0.00 0.00 34.18 6.53
2752 5281 3.777925 GTGTGTACTGCCGCTGCG 61.778 66.667 16.34 16.34 41.78 5.18
2810 5402 0.539207 TGTGTGCTATTGGCCTGCAA 60.539 50.000 3.32 0.00 40.92 4.08
2830 5422 4.715896 CAATGATGTTGTGTGTGCTACTC 58.284 43.478 0.00 0.00 0.00 2.59
2841 5434 2.376063 TGCTACTCCCTGCACACAT 58.624 52.632 0.00 0.00 33.94 3.21
2848 5441 3.048600 ACTCCCTGCACACATATACCAT 58.951 45.455 0.00 0.00 0.00 3.55
2857 5450 4.517285 CACACATATACCATATGAGGGGC 58.483 47.826 3.65 0.00 0.00 5.80
2863 5456 1.507140 ACCATATGAGGGGCGAAAGA 58.493 50.000 3.65 0.00 0.00 2.52
3047 5644 4.638421 TGTTTGGTCGAAAGTGATGTTCTT 59.362 37.500 0.00 0.00 0.00 2.52
3075 5672 1.568606 CTCATGTGATGTGAGCTCGG 58.431 55.000 9.64 0.00 36.95 4.63
3078 5675 1.865340 CATGTGATGTGAGCTCGGATG 59.135 52.381 9.64 0.00 0.00 3.51
3089 5686 4.631813 GTGAGCTCGGATGAACAGTAAAAT 59.368 41.667 9.64 0.00 0.00 1.82
3096 5693 7.061094 GCTCGGATGAACAGTAAAATCAAAAAG 59.939 37.037 0.00 0.00 0.00 2.27
3099 5696 9.410556 CGGATGAACAGTAAAATCAAAAAGAAT 57.589 29.630 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.636435 ACCCGAACACGGCCAAGG 62.636 66.667 2.24 0.00 44.70 3.61
36 37 2.593436 AACCCGAACACGGCCAAG 60.593 61.111 2.24 0.00 44.70 3.61
37 38 2.592287 GAACCCGAACACGGCCAA 60.592 61.111 2.24 0.00 44.70 4.52
38 39 2.999739 GAAGAACCCGAACACGGCCA 63.000 60.000 2.24 0.00 44.70 5.36
39 40 2.281276 AAGAACCCGAACACGGCC 60.281 61.111 2.97 0.00 44.70 6.13
40 41 1.595929 TGAAGAACCCGAACACGGC 60.596 57.895 2.97 0.00 44.70 5.68
41 42 1.554042 CGTGAAGAACCCGAACACGG 61.554 60.000 0.00 0.00 46.43 4.94
42 43 1.850640 CGTGAAGAACCCGAACACG 59.149 57.895 0.00 0.00 45.46 4.49
43 44 0.580104 CACGTGAAGAACCCGAACAC 59.420 55.000 10.90 0.00 0.00 3.32
44 45 1.155424 GCACGTGAAGAACCCGAACA 61.155 55.000 22.23 0.00 0.00 3.18
45 46 1.568025 GCACGTGAAGAACCCGAAC 59.432 57.895 22.23 0.00 0.00 3.95
46 47 1.595929 GGCACGTGAAGAACCCGAA 60.596 57.895 22.23 0.00 0.00 4.30
47 48 2.029964 GGCACGTGAAGAACCCGA 59.970 61.111 22.23 0.00 0.00 5.14
60 61 4.059459 CTGTTGCGACGTCGGCAC 62.059 66.667 36.13 24.93 40.23 5.01
61 62 4.578898 ACTGTTGCGACGTCGGCA 62.579 61.111 36.13 29.60 40.23 5.69
62 63 2.877974 AAACTGTTGCGACGTCGGC 61.878 57.895 36.13 27.59 40.23 5.54
63 64 1.083657 CAAACTGTTGCGACGTCGG 60.084 57.895 36.13 22.50 40.23 4.79
64 65 4.471814 CAAACTGTTGCGACGTCG 57.528 55.556 32.57 32.57 43.27 5.12
72 73 4.023450 AGTCATCACATCAGCAAACTGTTG 60.023 41.667 0.00 3.25 45.35 3.33
73 74 4.139786 AGTCATCACATCAGCAAACTGTT 58.860 39.130 0.00 0.00 44.77 3.16
74 75 3.748083 AGTCATCACATCAGCAAACTGT 58.252 40.909 0.00 0.00 44.77 3.55
75 76 5.163784 CCTTAGTCATCACATCAGCAAACTG 60.164 44.000 0.00 0.00 45.95 3.16
76 77 4.940046 CCTTAGTCATCACATCAGCAAACT 59.060 41.667 0.00 0.00 0.00 2.66
77 78 4.095483 CCCTTAGTCATCACATCAGCAAAC 59.905 45.833 0.00 0.00 0.00 2.93
78 79 4.019411 TCCCTTAGTCATCACATCAGCAAA 60.019 41.667 0.00 0.00 0.00 3.68
79 80 3.519107 TCCCTTAGTCATCACATCAGCAA 59.481 43.478 0.00 0.00 0.00 3.91
80 81 3.106827 TCCCTTAGTCATCACATCAGCA 58.893 45.455 0.00 0.00 0.00 4.41
81 82 3.827008 TCCCTTAGTCATCACATCAGC 57.173 47.619 0.00 0.00 0.00 4.26
82 83 4.514441 GCAATCCCTTAGTCATCACATCAG 59.486 45.833 0.00 0.00 0.00 2.90
83 84 4.454678 GCAATCCCTTAGTCATCACATCA 58.545 43.478 0.00 0.00 0.00 3.07
84 85 3.817647 GGCAATCCCTTAGTCATCACATC 59.182 47.826 0.00 0.00 0.00 3.06
85 86 3.461085 AGGCAATCCCTTAGTCATCACAT 59.539 43.478 0.00 0.00 43.06 3.21
86 87 2.846206 AGGCAATCCCTTAGTCATCACA 59.154 45.455 0.00 0.00 43.06 3.58
87 88 3.567478 AGGCAATCCCTTAGTCATCAC 57.433 47.619 0.00 0.00 43.06 3.06
88 89 4.298626 AGTAGGCAATCCCTTAGTCATCA 58.701 43.478 0.00 0.00 43.06 3.07
89 90 4.965200 AGTAGGCAATCCCTTAGTCATC 57.035 45.455 0.00 0.00 43.06 2.92
90 91 4.103311 GGAAGTAGGCAATCCCTTAGTCAT 59.897 45.833 0.00 0.00 43.06 3.06
91 92 3.454812 GGAAGTAGGCAATCCCTTAGTCA 59.545 47.826 0.00 0.00 43.06 3.41
92 93 3.492829 CGGAAGTAGGCAATCCCTTAGTC 60.493 52.174 0.00 0.00 43.06 2.59
93 94 2.434702 CGGAAGTAGGCAATCCCTTAGT 59.565 50.000 0.00 0.00 43.06 2.24
94 95 2.434702 ACGGAAGTAGGCAATCCCTTAG 59.565 50.000 0.00 0.00 46.88 2.18
95 96 2.474112 ACGGAAGTAGGCAATCCCTTA 58.526 47.619 0.00 0.00 46.88 2.69
96 97 1.286248 ACGGAAGTAGGCAATCCCTT 58.714 50.000 0.00 0.00 46.88 3.95
97 98 3.007581 ACGGAAGTAGGCAATCCCT 57.992 52.632 0.00 0.00 46.88 4.20
106 107 7.854839 CGAAACTCCTCGAAGACGGAAGTAG 62.855 52.000 0.00 0.00 42.96 2.57
107 108 6.145029 CGAAACTCCTCGAAGACGGAAGTA 62.145 50.000 0.00 0.00 42.96 2.24
108 109 5.448237 CGAAACTCCTCGAAGACGGAAGT 62.448 52.174 0.00 0.00 44.77 3.01
109 110 2.597520 GAAACTCCTCGAAGACGGAAG 58.402 52.381 0.00 0.00 40.21 3.46
110 111 1.068748 CGAAACTCCTCGAAGACGGAA 60.069 52.381 0.00 0.00 41.44 4.30
111 112 0.520404 CGAAACTCCTCGAAGACGGA 59.480 55.000 0.00 0.00 41.44 4.69
112 113 0.456312 CCGAAACTCCTCGAAGACGG 60.456 60.000 0.00 0.00 41.44 4.79
113 114 0.240411 ACCGAAACTCCTCGAAGACG 59.760 55.000 0.00 0.00 41.44 4.18
114 115 1.402588 GGACCGAAACTCCTCGAAGAC 60.403 57.143 0.00 0.00 41.44 3.01
115 116 0.886563 GGACCGAAACTCCTCGAAGA 59.113 55.000 0.00 0.00 41.44 2.87
116 117 0.601558 TGGACCGAAACTCCTCGAAG 59.398 55.000 0.00 0.00 41.44 3.79
117 118 0.601558 CTGGACCGAAACTCCTCGAA 59.398 55.000 0.00 0.00 41.44 3.71
118 119 0.538977 ACTGGACCGAAACTCCTCGA 60.539 55.000 0.00 0.00 41.44 4.04
119 120 0.109226 GACTGGACCGAAACTCCTCG 60.109 60.000 0.00 0.00 38.58 4.63
120 121 1.202817 GAGACTGGACCGAAACTCCTC 59.797 57.143 0.00 0.00 0.00 3.71
121 122 1.203075 AGAGACTGGACCGAAACTCCT 60.203 52.381 0.00 0.00 0.00 3.69
122 123 1.067495 CAGAGACTGGACCGAAACTCC 60.067 57.143 0.00 0.00 0.00 3.85
123 124 1.614413 ACAGAGACTGGACCGAAACTC 59.386 52.381 0.00 0.00 35.51 3.01
124 125 1.341531 CACAGAGACTGGACCGAAACT 59.658 52.381 0.00 0.00 35.51 2.66
125 126 1.068741 ACACAGAGACTGGACCGAAAC 59.931 52.381 0.00 0.00 35.51 2.78
126 127 1.340248 GACACAGAGACTGGACCGAAA 59.660 52.381 0.00 0.00 35.51 3.46
127 128 0.959553 GACACAGAGACTGGACCGAA 59.040 55.000 0.00 0.00 35.51 4.30
128 129 0.110678 AGACACAGAGACTGGACCGA 59.889 55.000 0.00 0.00 35.51 4.69
129 130 0.523966 GAGACACAGAGACTGGACCG 59.476 60.000 0.00 0.00 35.51 4.79
130 131 1.543802 CAGAGACACAGAGACTGGACC 59.456 57.143 0.00 0.00 35.51 4.46
134 135 0.109365 CGCCAGAGACACAGAGACTG 60.109 60.000 0.00 0.00 37.52 3.51
135 136 0.250945 TCGCCAGAGACACAGAGACT 60.251 55.000 0.00 0.00 0.00 3.24
136 137 0.109504 GTCGCCAGAGACACAGAGAC 60.110 60.000 0.00 0.00 40.65 3.36
137 138 1.578206 CGTCGCCAGAGACACAGAGA 61.578 60.000 2.49 0.00 40.98 3.10
138 139 1.154131 CGTCGCCAGAGACACAGAG 60.154 63.158 2.49 0.00 40.98 3.35
139 140 2.954611 CGTCGCCAGAGACACAGA 59.045 61.111 2.49 0.00 40.98 3.41
140 141 2.755542 AAGCGTCGCCAGAGACACAG 62.756 60.000 14.86 0.00 40.98 3.66
141 142 2.749110 GAAGCGTCGCCAGAGACACA 62.749 60.000 14.86 0.00 40.98 3.72
142 143 2.049063 AAGCGTCGCCAGAGACAC 60.049 61.111 14.86 0.00 40.98 3.67
143 144 2.258591 GAAGCGTCGCCAGAGACA 59.741 61.111 14.86 0.00 40.98 3.41
144 145 2.876645 CGAAGCGTCGCCAGAGAC 60.877 66.667 14.86 0.00 41.08 3.36
168 169 3.639561 ACAAAATACAACTCAACACCCCC 59.360 43.478 0.00 0.00 0.00 5.40
169 170 4.098807 ACACAAAATACAACTCAACACCCC 59.901 41.667 0.00 0.00 0.00 4.95
170 171 5.257082 ACACAAAATACAACTCAACACCC 57.743 39.130 0.00 0.00 0.00 4.61
171 172 5.005299 GCAACACAAAATACAACTCAACACC 59.995 40.000 0.00 0.00 0.00 4.16
172 173 5.574830 TGCAACACAAAATACAACTCAACAC 59.425 36.000 0.00 0.00 0.00 3.32
173 174 5.714047 TGCAACACAAAATACAACTCAACA 58.286 33.333 0.00 0.00 0.00 3.33
174 175 6.255453 ACATGCAACACAAAATACAACTCAAC 59.745 34.615 0.00 0.00 0.00 3.18
175 176 6.336566 ACATGCAACACAAAATACAACTCAA 58.663 32.000 0.00 0.00 0.00 3.02
176 177 5.900425 ACATGCAACACAAAATACAACTCA 58.100 33.333 0.00 0.00 0.00 3.41
177 178 8.519492 AATACATGCAACACAAAATACAACTC 57.481 30.769 0.00 0.00 0.00 3.01
178 179 9.624697 CTAATACATGCAACACAAAATACAACT 57.375 29.630 0.00 0.00 0.00 3.16
179 180 9.619316 TCTAATACATGCAACACAAAATACAAC 57.381 29.630 0.00 0.00 0.00 3.32
181 182 9.786105 CATCTAATACATGCAACACAAAATACA 57.214 29.630 0.00 0.00 0.00 2.29
182 183 9.787532 ACATCTAATACATGCAACACAAAATAC 57.212 29.630 0.00 0.00 0.00 1.89
184 185 9.142515 CAACATCTAATACATGCAACACAAAAT 57.857 29.630 0.00 0.00 0.00 1.82
185 186 8.140628 ACAACATCTAATACATGCAACACAAAA 58.859 29.630 0.00 0.00 0.00 2.44
186 187 7.594386 CACAACATCTAATACATGCAACACAAA 59.406 33.333 0.00 0.00 0.00 2.83
187 188 7.083230 CACAACATCTAATACATGCAACACAA 58.917 34.615 0.00 0.00 0.00 3.33
188 189 6.349197 CCACAACATCTAATACATGCAACACA 60.349 38.462 0.00 0.00 0.00 3.72
189 190 6.029607 CCACAACATCTAATACATGCAACAC 58.970 40.000 0.00 0.00 0.00 3.32
190 191 5.392919 GCCACAACATCTAATACATGCAACA 60.393 40.000 0.00 0.00 0.00 3.33
191 192 5.036737 GCCACAACATCTAATACATGCAAC 58.963 41.667 0.00 0.00 0.00 4.17
192 193 4.097741 GGCCACAACATCTAATACATGCAA 59.902 41.667 0.00 0.00 0.00 4.08
193 194 3.631686 GGCCACAACATCTAATACATGCA 59.368 43.478 0.00 0.00 0.00 3.96
194 195 3.004734 GGGCCACAACATCTAATACATGC 59.995 47.826 4.39 0.00 0.00 4.06
195 196 4.036734 GTGGGCCACAACATCTAATACATG 59.963 45.833 31.26 0.00 34.08 3.21
196 197 4.207165 GTGGGCCACAACATCTAATACAT 58.793 43.478 31.26 0.00 34.08 2.29
197 198 3.616219 GTGGGCCACAACATCTAATACA 58.384 45.455 31.26 0.00 34.08 2.29
198 199 2.949644 GGTGGGCCACAACATCTAATAC 59.050 50.000 35.69 11.87 36.56 1.89
199 200 2.849943 AGGTGGGCCACAACATCTAATA 59.150 45.455 35.69 0.00 40.07 0.98
200 201 1.640670 AGGTGGGCCACAACATCTAAT 59.359 47.619 35.69 8.61 40.07 1.73
201 202 1.004277 GAGGTGGGCCACAACATCTAA 59.996 52.381 35.69 0.00 40.07 2.10
202 203 0.618458 GAGGTGGGCCACAACATCTA 59.382 55.000 35.69 0.00 40.07 1.98
203 204 1.380302 GAGGTGGGCCACAACATCT 59.620 57.895 35.69 23.59 40.07 2.90
204 205 1.678970 GGAGGTGGGCCACAACATC 60.679 63.158 35.69 25.28 40.07 3.06
205 206 0.844661 TAGGAGGTGGGCCACAACAT 60.845 55.000 35.69 26.60 40.07 2.71
206 207 1.462432 TAGGAGGTGGGCCACAACA 60.462 57.895 35.69 14.43 40.07 3.33
207 208 1.299976 CTAGGAGGTGGGCCACAAC 59.700 63.158 35.69 26.73 35.86 3.32
208 209 0.770557 AACTAGGAGGTGGGCCACAA 60.771 55.000 35.69 15.37 35.86 3.33
209 210 1.151899 AACTAGGAGGTGGGCCACA 60.152 57.895 35.69 15.84 35.86 4.17
210 211 1.299976 CAACTAGGAGGTGGGCCAC 59.700 63.158 28.69 28.69 37.19 5.01
211 212 1.151899 ACAACTAGGAGGTGGGCCA 60.152 57.895 0.00 0.00 37.20 5.36
212 213 1.299976 CACAACTAGGAGGTGGGCC 59.700 63.158 0.00 0.00 37.20 5.80
213 214 1.272807 TACACAACTAGGAGGTGGGC 58.727 55.000 13.12 0.00 40.90 5.36
214 215 4.287552 ACTATACACAACTAGGAGGTGGG 58.712 47.826 13.12 0.00 43.48 4.61
215 216 5.421056 TCAACTATACACAACTAGGAGGTGG 59.579 44.000 13.12 1.40 37.20 4.61
216 217 6.405953 CCTCAACTATACACAACTAGGAGGTG 60.406 46.154 8.57 8.57 39.30 4.00
217 218 5.657302 CCTCAACTATACACAACTAGGAGGT 59.343 44.000 0.00 0.00 34.83 3.85
218 219 5.657302 ACCTCAACTATACACAACTAGGAGG 59.343 44.000 0.00 0.00 42.90 4.30
219 220 6.777213 ACCTCAACTATACACAACTAGGAG 57.223 41.667 0.00 0.00 0.00 3.69
220 221 6.722590 TCAACCTCAACTATACACAACTAGGA 59.277 38.462 0.00 0.00 0.00 2.94
221 222 6.931838 TCAACCTCAACTATACACAACTAGG 58.068 40.000 0.00 0.00 0.00 3.02
222 223 7.036220 CCTCAACCTCAACTATACACAACTAG 58.964 42.308 0.00 0.00 0.00 2.57
223 224 6.573680 GCCTCAACCTCAACTATACACAACTA 60.574 42.308 0.00 0.00 0.00 2.24
224 225 5.794894 CCTCAACCTCAACTATACACAACT 58.205 41.667 0.00 0.00 0.00 3.16
225 226 4.392138 GCCTCAACCTCAACTATACACAAC 59.608 45.833 0.00 0.00 0.00 3.32
226 227 4.564821 GGCCTCAACCTCAACTATACACAA 60.565 45.833 0.00 0.00 0.00 3.33
227 228 3.055385 GGCCTCAACCTCAACTATACACA 60.055 47.826 0.00 0.00 0.00 3.72
228 229 3.197983 AGGCCTCAACCTCAACTATACAC 59.802 47.826 0.00 0.00 33.62 2.90
229 230 3.450904 AGGCCTCAACCTCAACTATACA 58.549 45.455 0.00 0.00 33.62 2.29
230 231 4.202233 GGTAGGCCTCAACCTCAACTATAC 60.202 50.000 9.68 0.00 41.50 1.47
231 232 3.965347 GGTAGGCCTCAACCTCAACTATA 59.035 47.826 9.68 0.00 41.50 1.31
232 233 2.772515 GGTAGGCCTCAACCTCAACTAT 59.227 50.000 9.68 0.00 41.50 2.12
233 234 2.185387 GGTAGGCCTCAACCTCAACTA 58.815 52.381 9.68 0.00 41.50 2.24
234 235 0.984995 GGTAGGCCTCAACCTCAACT 59.015 55.000 9.68 0.00 41.50 3.16
235 236 0.035343 GGGTAGGCCTCAACCTCAAC 60.035 60.000 21.67 7.05 41.50 3.18
236 237 0.178873 AGGGTAGGCCTCAACCTCAA 60.179 55.000 21.67 0.00 41.50 3.02
237 238 0.909610 CAGGGTAGGCCTCAACCTCA 60.910 60.000 21.67 0.00 41.50 3.86
238 239 0.910088 ACAGGGTAGGCCTCAACCTC 60.910 60.000 21.67 13.10 41.50 3.85
239 240 0.416231 TACAGGGTAGGCCTCAACCT 59.584 55.000 21.67 18.39 44.31 3.50
240 241 0.540454 GTACAGGGTAGGCCTCAACC 59.460 60.000 9.68 13.37 34.85 3.77
241 242 1.569653 AGTACAGGGTAGGCCTCAAC 58.430 55.000 9.68 1.64 34.45 3.18
242 243 2.337359 AAGTACAGGGTAGGCCTCAA 57.663 50.000 9.68 0.00 34.45 3.02
243 244 3.700863 ATAAGTACAGGGTAGGCCTCA 57.299 47.619 9.68 0.00 34.45 3.86
244 245 7.228308 CGTATATATAAGTACAGGGTAGGCCTC 59.772 44.444 9.68 0.00 34.45 4.70
245 246 7.059156 CGTATATATAAGTACAGGGTAGGCCT 58.941 42.308 11.78 11.78 34.45 5.19
246 247 6.830838 ACGTATATATAAGTACAGGGTAGGCC 59.169 42.308 9.27 0.00 0.00 5.19
247 248 7.680588 GCACGTATATATAAGTACAGGGTAGGC 60.681 44.444 10.46 4.27 0.00 3.93
248 249 7.337689 TGCACGTATATATAAGTACAGGGTAGG 59.662 40.741 10.46 0.00 0.00 3.18
249 250 8.180267 GTGCACGTATATATAAGTACAGGGTAG 58.820 40.741 10.81 0.04 0.00 3.18
250 251 7.121168 GGTGCACGTATATATAAGTACAGGGTA 59.879 40.741 11.45 0.00 0.00 3.69
251 252 6.071728 GGTGCACGTATATATAAGTACAGGGT 60.072 42.308 11.45 0.00 0.00 4.34
252 253 6.071784 TGGTGCACGTATATATAAGTACAGGG 60.072 42.308 11.45 1.77 0.00 4.45
253 254 6.916440 TGGTGCACGTATATATAAGTACAGG 58.084 40.000 11.45 2.06 0.00 4.00
254 255 6.527023 GCTGGTGCACGTATATATAAGTACAG 59.473 42.308 11.45 14.82 39.41 2.74
255 256 6.016108 TGCTGGTGCACGTATATATAAGTACA 60.016 38.462 11.45 8.87 45.31 2.90
256 257 6.384224 TGCTGGTGCACGTATATATAAGTAC 58.616 40.000 11.45 6.56 45.31 2.73
257 258 6.578163 TGCTGGTGCACGTATATATAAGTA 57.422 37.500 11.45 0.00 45.31 2.24
258 259 5.462530 TGCTGGTGCACGTATATATAAGT 57.537 39.130 11.45 5.59 45.31 2.24
272 273 0.395586 TATTGATGGGGTGCTGGTGC 60.396 55.000 0.00 0.00 40.20 5.01
273 274 1.340893 TGTATTGATGGGGTGCTGGTG 60.341 52.381 0.00 0.00 0.00 4.17
274 275 0.998928 TGTATTGATGGGGTGCTGGT 59.001 50.000 0.00 0.00 0.00 4.00
275 276 1.750778 GTTGTATTGATGGGGTGCTGG 59.249 52.381 0.00 0.00 0.00 4.85
276 277 1.750778 GGTTGTATTGATGGGGTGCTG 59.249 52.381 0.00 0.00 0.00 4.41
277 278 1.357420 TGGTTGTATTGATGGGGTGCT 59.643 47.619 0.00 0.00 0.00 4.40
278 279 1.846007 TGGTTGTATTGATGGGGTGC 58.154 50.000 0.00 0.00 0.00 5.01
279 280 6.098124 ACAATAATGGTTGTATTGATGGGGTG 59.902 38.462 10.33 0.00 40.35 4.61
280 281 6.201591 ACAATAATGGTTGTATTGATGGGGT 58.798 36.000 10.33 0.00 40.35 4.95
281 282 6.729690 ACAATAATGGTTGTATTGATGGGG 57.270 37.500 10.33 0.00 40.35 4.96
290 291 8.367911 TGTTTTGCCAATACAATAATGGTTGTA 58.632 29.630 0.00 5.86 45.55 2.41
291 292 7.220030 TGTTTTGCCAATACAATAATGGTTGT 58.780 30.769 0.00 2.10 44.09 3.32
292 293 7.664082 TGTTTTGCCAATACAATAATGGTTG 57.336 32.000 0.00 0.00 36.57 3.77
293 294 8.320617 AGATGTTTTGCCAATACAATAATGGTT 58.679 29.630 4.83 0.00 36.57 3.67
294 295 7.850193 AGATGTTTTGCCAATACAATAATGGT 58.150 30.769 4.83 0.00 36.57 3.55
295 296 8.199449 AGAGATGTTTTGCCAATACAATAATGG 58.801 33.333 4.83 0.00 37.29 3.16
296 297 9.590451 AAGAGATGTTTTGCCAATACAATAATG 57.410 29.630 4.83 0.00 0.00 1.90
297 298 9.807649 GAAGAGATGTTTTGCCAATACAATAAT 57.192 29.630 4.83 0.00 0.00 1.28
298 299 9.023962 AGAAGAGATGTTTTGCCAATACAATAA 57.976 29.630 4.83 0.00 0.00 1.40
299 300 8.579850 AGAAGAGATGTTTTGCCAATACAATA 57.420 30.769 4.83 0.00 0.00 1.90
300 301 7.472334 AGAAGAGATGTTTTGCCAATACAAT 57.528 32.000 4.83 0.00 0.00 2.71
301 302 6.899393 AGAAGAGATGTTTTGCCAATACAA 57.101 33.333 4.83 0.00 0.00 2.41
302 303 6.939730 TGTAGAAGAGATGTTTTGCCAATACA 59.060 34.615 3.20 3.20 0.00 2.29
303 304 7.094805 TGTGTAGAAGAGATGTTTTGCCAATAC 60.095 37.037 0.00 0.00 0.00 1.89
304 305 6.939730 TGTGTAGAAGAGATGTTTTGCCAATA 59.060 34.615 0.00 0.00 0.00 1.90
305 306 5.769662 TGTGTAGAAGAGATGTTTTGCCAAT 59.230 36.000 0.00 0.00 0.00 3.16
306 307 5.129634 TGTGTAGAAGAGATGTTTTGCCAA 58.870 37.500 0.00 0.00 0.00 4.52
307 308 4.713553 TGTGTAGAAGAGATGTTTTGCCA 58.286 39.130 0.00 0.00 0.00 4.92
308 309 5.452777 GTTGTGTAGAAGAGATGTTTTGCC 58.547 41.667 0.00 0.00 0.00 4.52
309 310 5.239525 AGGTTGTGTAGAAGAGATGTTTTGC 59.760 40.000 0.00 0.00 0.00 3.68
310 311 6.867662 AGGTTGTGTAGAAGAGATGTTTTG 57.132 37.500 0.00 0.00 0.00 2.44
311 312 9.574516 AATTAGGTTGTGTAGAAGAGATGTTTT 57.425 29.630 0.00 0.00 0.00 2.43
312 313 9.003658 CAATTAGGTTGTGTAGAAGAGATGTTT 57.996 33.333 0.00 0.00 33.01 2.83
313 314 8.375506 TCAATTAGGTTGTGTAGAAGAGATGTT 58.624 33.333 0.00 0.00 38.95 2.71
314 315 7.907389 TCAATTAGGTTGTGTAGAAGAGATGT 58.093 34.615 0.00 0.00 38.95 3.06
315 316 8.824781 CATCAATTAGGTTGTGTAGAAGAGATG 58.175 37.037 0.00 0.00 38.95 2.90
316 317 7.497249 GCATCAATTAGGTTGTGTAGAAGAGAT 59.503 37.037 0.00 0.00 38.95 2.75
317 318 6.818644 GCATCAATTAGGTTGTGTAGAAGAGA 59.181 38.462 0.00 0.00 38.95 3.10
318 319 6.595326 TGCATCAATTAGGTTGTGTAGAAGAG 59.405 38.462 0.00 0.00 38.95 2.85
319 320 6.472016 TGCATCAATTAGGTTGTGTAGAAGA 58.528 36.000 0.00 0.00 38.95 2.87
320 321 6.741992 TGCATCAATTAGGTTGTGTAGAAG 57.258 37.500 0.00 0.00 38.95 2.85
321 322 7.537715 CATTGCATCAATTAGGTTGTGTAGAA 58.462 34.615 0.00 0.00 38.95 2.10
322 323 6.404623 GCATTGCATCAATTAGGTTGTGTAGA 60.405 38.462 3.15 0.00 38.95 2.59
323 324 5.745294 GCATTGCATCAATTAGGTTGTGTAG 59.255 40.000 3.15 0.00 38.95 2.74
324 325 5.184671 TGCATTGCATCAATTAGGTTGTGTA 59.815 36.000 7.38 0.00 34.76 2.90
325 326 4.021280 TGCATTGCATCAATTAGGTTGTGT 60.021 37.500 7.38 0.00 34.76 3.72
326 327 4.496360 TGCATTGCATCAATTAGGTTGTG 58.504 39.130 7.38 0.00 34.76 3.33
453 1753 9.850628 GGAACTGCATTACGATATATACTACAA 57.149 33.333 0.00 0.00 0.00 2.41
500 1800 1.895280 GACGCAGCAGCTCTCACAAC 61.895 60.000 0.00 0.00 39.10 3.32
539 1839 9.594478 AAACTTGAAACTGTAAAAATAAGGGTG 57.406 29.630 0.00 0.00 0.00 4.61
584 1885 7.897575 TTTTAGCAACAACACAGAAACAAAT 57.102 28.000 0.00 0.00 0.00 2.32
958 2345 3.274393 CCGCGGAGGAATAGAACAG 57.726 57.895 24.07 0.00 45.00 3.16
1842 3232 1.246056 GCTGCATTGAGTTGCCTGGA 61.246 55.000 0.00 0.00 42.06 3.86
2283 3675 4.991056 CGGGACTATGATAATCCACAAGTG 59.009 45.833 2.09 0.00 33.87 3.16
2285 3677 4.563580 CCCGGGACTATGATAATCCACAAG 60.564 50.000 18.48 0.00 33.87 3.16
2468 3861 2.289382 TGTAGCTTTTCATCGCACTCCA 60.289 45.455 0.00 0.00 0.00 3.86
2502 3895 9.937175 GTTTAGATGACCTTGAAATAATACTGC 57.063 33.333 0.00 0.00 0.00 4.40
2550 3943 6.334102 AGGGCACAAAATTTAAACACGATA 57.666 33.333 0.00 0.00 0.00 2.92
2552 3945 4.657436 AGGGCACAAAATTTAAACACGA 57.343 36.364 0.00 0.00 0.00 4.35
2567 3960 0.997196 GTCGACGTCAAATAGGGCAC 59.003 55.000 17.16 0.00 0.00 5.01
2581 3974 8.664211 AGATAGGGAAGAAATTATTTGTCGAC 57.336 34.615 9.11 9.11 0.00 4.20
2637 5018 5.048713 GTCTTTTCAGGTGTCATTTAGGGTG 60.049 44.000 0.00 0.00 0.00 4.61
2662 5043 6.966534 AAATACCATATGAGGAGCAAAAGG 57.033 37.500 3.65 0.00 0.00 3.11
2670 5051 4.574421 CGTGCACAAAATACCATATGAGGA 59.426 41.667 18.64 0.00 0.00 3.71
2700 5081 0.385098 CACACAGCATCACAAGCACG 60.385 55.000 0.00 0.00 0.00 5.34
2774 5355 1.233950 ACACACGCATCGGCAATCAA 61.234 50.000 0.00 0.00 41.24 2.57
2784 5376 0.804364 CCAATAGCACACACACGCAT 59.196 50.000 0.00 0.00 0.00 4.73
2810 5402 3.338249 GGAGTAGCACACACAACATCAT 58.662 45.455 0.00 0.00 0.00 2.45
2830 5422 5.164620 TCATATGGTATATGTGTGCAGGG 57.835 43.478 2.13 0.00 0.00 4.45
2841 5434 4.422057 TCTTTCGCCCCTCATATGGTATA 58.578 43.478 2.13 0.00 0.00 1.47
2848 5441 2.160721 AGACTCTTTCGCCCCTCATA 57.839 50.000 0.00 0.00 0.00 2.15
2857 5450 4.119862 TGACACCTGAAAAGACTCTTTCG 58.880 43.478 4.46 0.00 38.00 3.46
3013 5610 5.682943 TTCGACCAAACAATGTTTAGAGG 57.317 39.130 11.33 11.08 0.00 3.69
3047 5644 2.036346 CACATCACATGAGCTCGGGATA 59.964 50.000 9.64 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.