Multiple sequence alignment - TraesCS3D01G277200

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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 TraesCS3D01G277200 chr3D 100.000 2968 0 0 1 2968 384568901 384565934 0.000000e+00 5481.0
1 TraesCS3D01G277200 chr3D 88.846 260 8 4 32 270 4501914 4502173 1.730000e-77 300.0
2 TraesCS3D01G277200 chr3D 85.965 228 11 4 64 270 73714642 73714869 1.070000e-54 224.0
3 TraesCS3D01G277200 chr3B 91.898 1728 65 30 624 2310 499806605 499804912 0.000000e+00 2346.0
4 TraesCS3D01G277200 chr3B 84.700 634 61 14 2357 2967 499804571 499803951 4.230000e-168 601.0
5 TraesCS3D01G277200 chr3B 94.101 356 13 5 273 623 499806991 499806639 4.350000e-148 534.0
6 TraesCS3D01G277200 chr3B 90.769 65 6 0 653 717 499806641 499806577 1.470000e-13 87.9
7 TraesCS3D01G277200 chr3A 91.603 1560 54 36 759 2290 507121252 507119742 0.000000e+00 2084.0
8 TraesCS3D01G277200 chr3A 90.620 597 25 13 2357 2927 507119384 507118793 0.000000e+00 763.0
9 TraesCS3D01G277200 chr3A 95.189 291 8 2 273 557 507126127 507125837 3.490000e-124 455.0
10 TraesCS3D01G277200 chr2D 89.310 290 11 1 1 270 374070720 374071009 2.190000e-91 346.0
11 TraesCS3D01G277200 chr2D 88.699 292 13 1 1 272 364971141 364970850 3.660000e-89 339.0
12 TraesCS3D01G277200 chr2D 88.621 290 12 9 1 270 506400949 506401237 1.700000e-87 333.0
13 TraesCS3D01G277200 chr2D 88.276 290 14 1 1 270 600431809 600431520 2.210000e-86 329.0
14 TraesCS3D01G277200 chr2D 87.838 296 9 3 1 270 121363767 121363473 3.690000e-84 322.0
15 TraesCS3D01G277200 chr1D 89.310 290 10 6 1 270 300024256 300024544 7.880000e-91 344.0
16 TraesCS3D01G277200 chr1D 89.189 259 7 4 33 270 55033405 55033663 1.340000e-78 303.0
17 TraesCS3D01G277200 chr1D 96.753 154 5 0 33 186 403943797 403943950 1.060000e-64 257.0
18 TraesCS3D01G277200 chr1D 96.825 126 4 0 1110 1235 433464228 433464103 8.330000e-51 211.0
19 TraesCS3D01G277200 chr1D 83.544 158 26 0 1331 1488 433463990 433463833 6.630000e-32 148.0
20 TraesCS3D01G277200 chr5D 93.421 228 6 1 52 270 33024336 33024109 2.210000e-86 329.0
21 TraesCS3D01G277200 chr5D 96.471 85 3 0 186 270 371054347 371054431 1.110000e-29 141.0
22 TraesCS3D01G277200 chr5D 85.135 74 7 2 2606 2675 337390558 337390631 4.100000e-09 73.1
23 TraesCS3D01G277200 chr5D 85.294 68 10 0 2871 2938 106939464 106939397 1.480000e-08 71.3
24 TraesCS3D01G277200 chr5D 85.294 68 10 0 2871 2938 107011802 107011735 1.480000e-08 71.3
25 TraesCS3D01G277200 chr7D 88.462 260 9 5 32 270 33043305 33043564 8.050000e-76 294.0
26 TraesCS3D01G277200 chr7D 88.077 260 9 6 33 270 585313843 585313584 3.740000e-74 289.0
27 TraesCS3D01G277200 chr7D 86.525 141 16 3 1097 1235 60700006 60700145 5.120000e-33 152.0
28 TraesCS3D01G277200 chr6D 88.462 260 9 3 33 271 421064038 421063779 8.050000e-76 294.0
29 TraesCS3D01G277200 chr6D 87.984 258 11 7 33 270 355877371 355877114 1.350000e-73 287.0
30 TraesCS3D01G277200 chr6D 86.058 208 8 3 84 270 23736397 23736604 1.390000e-48 204.0
31 TraesCS3D01G277200 chr1B 98.361 122 2 0 1114 1235 585680431 585680310 6.440000e-52 215.0
32 TraesCS3D01G277200 chr1B 83.544 158 26 0 1331 1488 585680201 585680044 6.630000e-32 148.0
33 TraesCS3D01G277200 chr1A 96.825 126 4 0 1110 1235 531986748 531986623 8.330000e-51 211.0
34 TraesCS3D01G277200 chr1A 89.928 139 14 0 1581 1719 531986238 531986100 2.350000e-41 180.0
35 TraesCS3D01G277200 chr1A 82.911 158 27 0 1331 1488 531986507 531986350 3.080000e-30 143.0
36 TraesCS3D01G277200 chr4D 86.316 190 5 4 102 270 418852933 418852744 1.400000e-43 187.0
37 TraesCS3D01G277200 chr7B 86.525 141 16 3 1097 1235 3336847 3336986 5.120000e-33 152.0
38 TraesCS3D01G277200 chr7A 86.525 141 16 3 1097 1235 65005993 65006132 5.120000e-33 152.0
39 TraesCS3D01G277200 chr2B 84.211 114 17 1 2807 2919 699204296 699204409 3.130000e-20 110.0
40 TraesCS3D01G277200 chr5B 82.927 82 14 0 2857 2938 115870168 115870087 1.140000e-09 75.0
41 TraesCS3D01G277200 chr5B 97.059 34 0 1 2606 2639 456334972 456334940 4.130000e-04 56.5
42 TraesCS3D01G277200 chr4B 84.615 65 7 3 2611 2672 636778027 636777963 8.880000e-06 62.1


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 TraesCS3D01G277200 chr3D 384565934 384568901 2967 True 5481.000 5481 100.0000 1 2968 1 chr3D.!!$R1 2967
1 TraesCS3D01G277200 chr3B 499803951 499806991 3040 True 892.225 2346 90.3670 273 2967 4 chr3B.!!$R1 2694
2 TraesCS3D01G277200 chr3A 507118793 507121252 2459 True 1423.500 2084 91.1115 759 2927 2 chr3A.!!$R2 2168

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
170 171 0.107703 CCTATCTGGAAGGCGTTGCA 60.108 55.0 12.85 12.85 38.35 4.08 F
410 411 0.108585 TCAACTCACTGGCTTGGGTC 59.891 55.0 0.00 0.00 26.58 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1594 0.662085 TTACGTTTGGTTTGGTCGGC 59.338 50.0 0.0 0.0 0.0 5.54 R
2324 2452 0.179004 TCGATCCAGGAGAGGAGAGC 60.179 60.0 0.0 0.0 41.9 4.09 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 3.518992 TTCACTCCCCTAACCCTTTTG 57.481 47.619 0.00 0.00 0.00 2.44
22 23 2.424793 TCACTCCCCTAACCCTTTTGT 58.575 47.619 0.00 0.00 0.00 2.83
23 24 2.107552 TCACTCCCCTAACCCTTTTGTG 59.892 50.000 0.00 0.00 0.00 3.33
24 25 1.203013 ACTCCCCTAACCCTTTTGTGC 60.203 52.381 0.00 0.00 0.00 4.57
25 26 0.854218 TCCCCTAACCCTTTTGTGCA 59.146 50.000 0.00 0.00 0.00 4.57
26 27 1.203001 TCCCCTAACCCTTTTGTGCAG 60.203 52.381 0.00 0.00 0.00 4.41
27 28 0.603065 CCCTAACCCTTTTGTGCAGC 59.397 55.000 0.00 0.00 0.00 5.25
28 29 0.240945 CCTAACCCTTTTGTGCAGCG 59.759 55.000 0.00 0.00 0.00 5.18
29 30 0.387239 CTAACCCTTTTGTGCAGCGC 60.387 55.000 0.00 0.00 0.00 5.92
30 31 1.801309 TAACCCTTTTGTGCAGCGCC 61.801 55.000 2.29 0.00 0.00 6.53
31 32 4.362476 CCCTTTTGTGCAGCGCCC 62.362 66.667 2.29 0.00 0.00 6.13
32 33 3.604667 CCTTTTGTGCAGCGCCCA 61.605 61.111 2.29 0.00 0.00 5.36
33 34 2.049802 CTTTTGTGCAGCGCCCAG 60.050 61.111 2.29 0.00 0.00 4.45
34 35 3.562779 CTTTTGTGCAGCGCCCAGG 62.563 63.158 2.29 0.00 0.00 4.45
46 47 4.087892 CCCAGGCGCTGCACTAGT 62.088 66.667 7.64 0.00 0.00 2.57
47 48 2.816958 CCAGGCGCTGCACTAGTG 60.817 66.667 18.93 18.93 39.95 2.74
57 58 3.566261 CACTAGTGCAACGCCCAG 58.434 61.111 10.54 0.00 45.86 4.45
58 59 2.034879 CACTAGTGCAACGCCCAGG 61.035 63.158 10.54 0.00 45.86 4.45
59 60 2.214216 ACTAGTGCAACGCCCAGGA 61.214 57.895 0.00 0.00 45.86 3.86
60 61 1.448540 CTAGTGCAACGCCCAGGAG 60.449 63.158 0.00 0.00 45.86 3.69
61 62 3.605749 TAGTGCAACGCCCAGGAGC 62.606 63.158 0.00 0.00 45.86 4.70
63 64 3.318384 TGCAACGCCCAGGAGCTA 61.318 61.111 0.00 0.00 0.00 3.32
64 65 2.512515 GCAACGCCCAGGAGCTAG 60.513 66.667 0.00 0.00 0.00 3.42
65 66 2.187946 CAACGCCCAGGAGCTAGG 59.812 66.667 0.00 0.00 0.00 3.02
66 67 3.787001 AACGCCCAGGAGCTAGGC 61.787 66.667 6.50 6.50 43.53 3.93
77 78 3.494336 GCTAGGCGCTGCACTGTG 61.494 66.667 7.64 2.76 35.14 3.66
78 79 2.047844 CTAGGCGCTGCACTGTGT 60.048 61.111 7.64 0.00 0.00 3.72
79 80 1.215382 CTAGGCGCTGCACTGTGTA 59.785 57.895 7.64 3.78 0.00 2.90
80 81 0.803768 CTAGGCGCTGCACTGTGTAG 60.804 60.000 19.77 19.77 33.01 2.74
81 82 1.532604 TAGGCGCTGCACTGTGTAGT 61.533 55.000 23.60 9.32 37.75 2.73
89 90 2.030562 ACTGTGTAGTGTGGCGCC 59.969 61.111 22.73 22.73 35.34 6.53
90 91 2.343758 CTGTGTAGTGTGGCGCCT 59.656 61.111 29.70 9.99 0.00 5.52
91 92 1.183030 ACTGTGTAGTGTGGCGCCTA 61.183 55.000 29.70 14.39 35.34 3.93
92 93 0.458543 CTGTGTAGTGTGGCGCCTAG 60.459 60.000 29.70 7.79 0.00 3.02
102 103 4.615834 GCGCCTAGCTCTCGGACG 62.616 72.222 0.00 0.00 44.04 4.79
103 104 4.615834 CGCCTAGCTCTCGGACGC 62.616 72.222 0.00 0.00 0.00 5.19
104 105 3.213402 GCCTAGCTCTCGGACGCT 61.213 66.667 0.00 3.02 40.15 5.07
105 106 2.718731 CCTAGCTCTCGGACGCTG 59.281 66.667 0.00 0.00 37.05 5.18
106 107 2.025441 CTAGCTCTCGGACGCTGC 59.975 66.667 0.00 0.00 37.05 5.25
107 108 2.750237 TAGCTCTCGGACGCTGCA 60.750 61.111 0.00 0.00 37.05 4.41
108 109 2.928313 CTAGCTCTCGGACGCTGCAC 62.928 65.000 0.00 0.00 37.05 4.57
118 119 4.081030 CGCTGCACGCTGACTTGG 62.081 66.667 0.00 0.00 36.13 3.61
119 120 3.730761 GCTGCACGCTGACTTGGG 61.731 66.667 0.00 0.00 35.14 4.12
120 121 3.730761 CTGCACGCTGACTTGGGC 61.731 66.667 0.00 0.00 0.00 5.36
121 122 4.560743 TGCACGCTGACTTGGGCA 62.561 61.111 0.00 0.00 0.00 5.36
122 123 4.030452 GCACGCTGACTTGGGCAC 62.030 66.667 0.00 0.00 0.00 5.01
123 124 2.591429 CACGCTGACTTGGGCACA 60.591 61.111 0.00 0.00 0.00 4.57
124 125 1.968017 CACGCTGACTTGGGCACAT 60.968 57.895 0.00 0.00 0.00 3.21
125 126 0.673333 CACGCTGACTTGGGCACATA 60.673 55.000 0.00 0.00 0.00 2.29
126 127 0.253044 ACGCTGACTTGGGCACATAT 59.747 50.000 0.00 0.00 0.00 1.78
127 128 0.659427 CGCTGACTTGGGCACATATG 59.341 55.000 0.00 0.00 0.00 1.78
128 129 1.027357 GCTGACTTGGGCACATATGG 58.973 55.000 7.80 0.00 0.00 2.74
129 130 1.683943 CTGACTTGGGCACATATGGG 58.316 55.000 7.80 3.61 0.00 4.00
130 131 0.998928 TGACTTGGGCACATATGGGT 59.001 50.000 6.86 0.00 0.00 4.51
131 132 1.340893 TGACTTGGGCACATATGGGTG 60.341 52.381 6.86 0.00 41.72 4.61
137 138 3.014036 CACATATGGGTGCGACGC 58.986 61.111 14.19 14.19 31.10 5.19
138 139 1.521457 CACATATGGGTGCGACGCT 60.521 57.895 22.08 2.17 31.67 5.07
139 140 1.521457 ACATATGGGTGCGACGCTG 60.521 57.895 22.08 11.28 31.67 5.18
140 141 2.108976 ATATGGGTGCGACGCTGG 59.891 61.111 22.08 0.00 31.67 4.85
141 142 4.830765 TATGGGTGCGACGCTGGC 62.831 66.667 22.08 10.89 31.67 4.85
154 155 3.833645 CTGGCCGTGTAGCGCCTA 61.834 66.667 2.29 0.00 39.71 3.93
155 156 3.151710 TGGCCGTGTAGCGCCTAT 61.152 61.111 2.29 0.00 39.71 2.57
156 157 2.355956 GGCCGTGTAGCGCCTATC 60.356 66.667 2.29 0.00 39.71 2.08
157 158 2.728817 GCCGTGTAGCGCCTATCT 59.271 61.111 2.29 0.00 39.71 1.98
158 159 1.661821 GCCGTGTAGCGCCTATCTG 60.662 63.158 2.29 0.00 39.71 2.90
159 160 1.007271 CCGTGTAGCGCCTATCTGG 60.007 63.158 2.29 0.00 39.71 3.86
160 161 1.452953 CCGTGTAGCGCCTATCTGGA 61.453 60.000 2.29 0.00 39.71 3.86
161 162 0.384309 CGTGTAGCGCCTATCTGGAA 59.616 55.000 2.29 0.00 38.35 3.53
162 163 1.600663 CGTGTAGCGCCTATCTGGAAG 60.601 57.143 2.29 0.00 38.35 3.46
163 164 1.040646 TGTAGCGCCTATCTGGAAGG 58.959 55.000 2.29 0.00 38.35 3.46
169 170 2.695314 CCTATCTGGAAGGCGTTGC 58.305 57.895 3.45 3.45 38.35 4.17
170 171 0.107703 CCTATCTGGAAGGCGTTGCA 60.108 55.000 12.85 12.85 38.35 4.08
171 172 1.009829 CTATCTGGAAGGCGTTGCAC 58.990 55.000 9.41 0.00 29.74 4.57
172 173 0.323302 TATCTGGAAGGCGTTGCACA 59.677 50.000 9.41 0.00 29.74 4.57
173 174 0.957395 ATCTGGAAGGCGTTGCACAG 60.957 55.000 9.41 8.64 29.74 3.66
174 175 1.893808 CTGGAAGGCGTTGCACAGT 60.894 57.895 9.41 0.00 29.74 3.55
175 176 0.602638 CTGGAAGGCGTTGCACAGTA 60.603 55.000 9.41 0.00 29.74 2.74
176 177 0.602638 TGGAAGGCGTTGCACAGTAG 60.603 55.000 9.41 0.00 0.00 2.57
177 178 0.320421 GGAAGGCGTTGCACAGTAGA 60.320 55.000 5.73 0.00 0.00 2.59
178 179 1.676014 GGAAGGCGTTGCACAGTAGAT 60.676 52.381 5.73 0.00 0.00 1.98
179 180 1.394917 GAAGGCGTTGCACAGTAGATG 59.605 52.381 0.00 0.00 0.00 2.90
180 181 0.321671 AGGCGTTGCACAGTAGATGT 59.678 50.000 0.00 0.00 45.43 3.06
188 189 3.623848 ACAGTAGATGTGGCGCAAA 57.376 47.368 10.83 0.00 41.91 3.68
189 190 1.890876 ACAGTAGATGTGGCGCAAAA 58.109 45.000 10.83 0.00 41.91 2.44
190 191 1.806542 ACAGTAGATGTGGCGCAAAAG 59.193 47.619 10.83 0.00 41.91 2.27
191 192 1.131126 CAGTAGATGTGGCGCAAAAGG 59.869 52.381 10.83 0.00 0.00 3.11
192 193 1.003118 AGTAGATGTGGCGCAAAAGGA 59.997 47.619 10.83 0.00 0.00 3.36
193 194 2.017049 GTAGATGTGGCGCAAAAGGAT 58.983 47.619 10.83 0.00 0.00 3.24
194 195 1.098050 AGATGTGGCGCAAAAGGATC 58.902 50.000 10.83 0.00 0.00 3.36
195 196 0.810648 GATGTGGCGCAAAAGGATCA 59.189 50.000 10.83 0.00 0.00 2.92
196 197 0.813184 ATGTGGCGCAAAAGGATCAG 59.187 50.000 10.83 0.00 0.00 2.90
197 198 1.243342 TGTGGCGCAAAAGGATCAGG 61.243 55.000 10.83 0.00 0.00 3.86
198 199 1.678635 TGGCGCAAAAGGATCAGGG 60.679 57.895 10.83 0.00 0.00 4.45
199 200 1.378514 GGCGCAAAAGGATCAGGGA 60.379 57.895 10.83 0.00 0.00 4.20
200 201 0.965363 GGCGCAAAAGGATCAGGGAA 60.965 55.000 10.83 0.00 0.00 3.97
201 202 0.453390 GCGCAAAAGGATCAGGGAAG 59.547 55.000 0.30 0.00 0.00 3.46
202 203 1.826385 CGCAAAAGGATCAGGGAAGT 58.174 50.000 0.00 0.00 0.00 3.01
203 204 1.470098 CGCAAAAGGATCAGGGAAGTG 59.530 52.381 0.00 0.00 0.00 3.16
204 205 2.795329 GCAAAAGGATCAGGGAAGTGA 58.205 47.619 0.00 0.00 0.00 3.41
205 206 3.157087 GCAAAAGGATCAGGGAAGTGAA 58.843 45.455 0.00 0.00 0.00 3.18
206 207 3.573967 GCAAAAGGATCAGGGAAGTGAAA 59.426 43.478 0.00 0.00 0.00 2.69
207 208 4.221482 GCAAAAGGATCAGGGAAGTGAAAT 59.779 41.667 0.00 0.00 0.00 2.17
208 209 5.418840 GCAAAAGGATCAGGGAAGTGAAATA 59.581 40.000 0.00 0.00 0.00 1.40
209 210 6.405176 GCAAAAGGATCAGGGAAGTGAAATAG 60.405 42.308 0.00 0.00 0.00 1.73
210 211 6.394345 AAAGGATCAGGGAAGTGAAATAGT 57.606 37.500 0.00 0.00 0.00 2.12
211 212 6.394345 AAGGATCAGGGAAGTGAAATAGTT 57.606 37.500 0.00 0.00 0.00 2.24
212 213 6.394345 AGGATCAGGGAAGTGAAATAGTTT 57.606 37.500 0.00 0.00 0.00 2.66
213 214 6.418946 AGGATCAGGGAAGTGAAATAGTTTC 58.581 40.000 0.00 0.00 40.08 2.78
214 215 5.294552 GGATCAGGGAAGTGAAATAGTTTCG 59.705 44.000 0.00 0.00 42.55 3.46
222 223 4.483476 GTGAAATAGTTTCGCAACCAGT 57.517 40.909 10.21 0.00 46.56 4.00
223 224 4.464112 GTGAAATAGTTTCGCAACCAGTC 58.536 43.478 10.21 0.00 46.56 3.51
224 225 3.500680 TGAAATAGTTTCGCAACCAGTCC 59.499 43.478 0.00 0.00 42.55 3.85
225 226 2.851263 ATAGTTTCGCAACCAGTCCA 57.149 45.000 0.00 0.00 32.70 4.02
226 227 2.851263 TAGTTTCGCAACCAGTCCAT 57.149 45.000 0.00 0.00 32.70 3.41
227 228 1.981256 AGTTTCGCAACCAGTCCATT 58.019 45.000 0.00 0.00 32.70 3.16
228 229 1.880027 AGTTTCGCAACCAGTCCATTC 59.120 47.619 0.00 0.00 32.70 2.67
229 230 1.880027 GTTTCGCAACCAGTCCATTCT 59.120 47.619 0.00 0.00 0.00 2.40
230 231 1.522668 TTCGCAACCAGTCCATTCTG 58.477 50.000 0.00 0.00 35.45 3.02
231 232 0.396435 TCGCAACCAGTCCATTCTGT 59.604 50.000 0.00 0.00 34.02 3.41
232 233 0.518636 CGCAACCAGTCCATTCTGTG 59.481 55.000 0.00 0.00 34.02 3.66
233 234 1.877680 CGCAACCAGTCCATTCTGTGA 60.878 52.381 0.00 0.00 34.02 3.58
234 235 2.440409 GCAACCAGTCCATTCTGTGAT 58.560 47.619 0.00 0.00 34.02 3.06
235 236 2.821969 GCAACCAGTCCATTCTGTGATT 59.178 45.455 0.00 0.00 34.02 2.57
236 237 3.256631 GCAACCAGTCCATTCTGTGATTT 59.743 43.478 0.00 0.00 34.02 2.17
237 238 4.801891 CAACCAGTCCATTCTGTGATTTG 58.198 43.478 0.00 0.00 34.02 2.32
238 239 4.371624 ACCAGTCCATTCTGTGATTTGA 57.628 40.909 0.00 0.00 34.02 2.69
239 240 4.927049 ACCAGTCCATTCTGTGATTTGAT 58.073 39.130 0.00 0.00 34.02 2.57
240 241 5.327732 ACCAGTCCATTCTGTGATTTGATT 58.672 37.500 0.00 0.00 34.02 2.57
241 242 5.776716 ACCAGTCCATTCTGTGATTTGATTT 59.223 36.000 0.00 0.00 34.02 2.17
242 243 6.071728 ACCAGTCCATTCTGTGATTTGATTTC 60.072 38.462 0.00 0.00 34.02 2.17
243 244 6.025896 CAGTCCATTCTGTGATTTGATTTCG 58.974 40.000 0.00 0.00 0.00 3.46
244 245 5.939883 AGTCCATTCTGTGATTTGATTTCGA 59.060 36.000 0.00 0.00 0.00 3.71
245 246 6.600822 AGTCCATTCTGTGATTTGATTTCGAT 59.399 34.615 0.00 0.00 0.00 3.59
246 247 7.121759 AGTCCATTCTGTGATTTGATTTCGATT 59.878 33.333 0.00 0.00 0.00 3.34
247 248 8.397906 GTCCATTCTGTGATTTGATTTCGATTA 58.602 33.333 0.00 0.00 0.00 1.75
248 249 9.123902 TCCATTCTGTGATTTGATTTCGATTAT 57.876 29.630 0.00 0.00 0.00 1.28
252 253 9.613428 TTCTGTGATTTGATTTCGATTATAGGT 57.387 29.630 0.00 0.00 0.00 3.08
253 254 9.261180 TCTGTGATTTGATTTCGATTATAGGTC 57.739 33.333 0.00 0.00 0.00 3.85
254 255 8.956533 TGTGATTTGATTTCGATTATAGGTCA 57.043 30.769 0.00 0.00 0.00 4.02
255 256 9.389755 TGTGATTTGATTTCGATTATAGGTCAA 57.610 29.630 0.00 0.00 0.00 3.18
365 366 3.509659 GGTACGAATTGCAGGCCC 58.490 61.111 0.00 0.00 0.00 5.80
366 367 1.377987 GGTACGAATTGCAGGCCCA 60.378 57.895 0.00 0.00 0.00 5.36
367 368 1.376609 GGTACGAATTGCAGGCCCAG 61.377 60.000 0.00 0.00 0.00 4.45
368 369 0.676782 GTACGAATTGCAGGCCCAGT 60.677 55.000 0.00 0.00 0.00 4.00
369 370 0.676466 TACGAATTGCAGGCCCAGTG 60.676 55.000 0.00 0.00 0.00 3.66
370 371 1.973281 CGAATTGCAGGCCCAGTGT 60.973 57.895 0.00 0.00 0.00 3.55
371 372 0.676466 CGAATTGCAGGCCCAGTGTA 60.676 55.000 0.00 0.00 0.00 2.90
372 373 0.811281 GAATTGCAGGCCCAGTGTAC 59.189 55.000 0.00 0.00 0.00 2.90
410 411 0.108585 TCAACTCACTGGCTTGGGTC 59.891 55.000 0.00 0.00 26.58 4.46
439 440 7.378995 CACCTTACTCATCACGTTATTACTAGC 59.621 40.741 0.00 0.00 0.00 3.42
518 520 7.877612 CCCATGCTTATTGTAAACCTTTTCTTT 59.122 33.333 0.00 0.00 0.00 2.52
525 527 5.862678 TGTAAACCTTTTCTTTCAAGGGG 57.137 39.130 3.81 0.00 44.70 4.79
535 537 4.974438 TCAAGGGGTCGGGCCAGT 62.974 66.667 4.39 0.00 39.65 4.00
551 553 4.102035 GCCAGTTCTTTTGATGGCTTAG 57.898 45.455 7.78 0.00 46.07 2.18
569 571 8.324163 TGGCTTAGAAAATAAGTTGTCTTCTC 57.676 34.615 0.00 0.00 35.36 2.87
570 572 7.936847 TGGCTTAGAAAATAAGTTGTCTTCTCA 59.063 33.333 0.00 0.00 35.36 3.27
571 573 8.447053 GGCTTAGAAAATAAGTTGTCTTCTCAG 58.553 37.037 0.00 0.00 35.36 3.35
573 575 9.213799 CTTAGAAAATAAGTTGTCTTCTCAGCT 57.786 33.333 0.00 0.00 35.36 4.24
574 576 9.561069 TTAGAAAATAAGTTGTCTTCTCAGCTT 57.439 29.630 0.00 0.00 40.72 3.74
584 589 8.270744 AGTTGTCTTCTCAGCTTATTCCATAAT 58.729 33.333 0.00 0.00 0.00 1.28
586 591 9.466497 TTGTCTTCTCAGCTTATTCCATAATTT 57.534 29.630 0.00 0.00 0.00 1.82
604 609 8.295288 CCATAATTTGCCTCTCTCATTCATTAC 58.705 37.037 0.00 0.00 0.00 1.89
629 634 9.632638 ACAGCTACACTAATTATGGAATGATTT 57.367 29.630 0.00 0.00 34.14 2.17
658 663 2.883026 AGCTACAGAGAGGCGGATAAT 58.117 47.619 0.00 0.00 0.00 1.28
727 796 4.260825 GCTAAAGAGAGGCGGCTTATTTTC 60.261 45.833 14.76 6.61 0.00 2.29
730 799 4.755266 AGAGAGGCGGCTTATTTTCTAA 57.245 40.909 14.76 0.00 0.00 2.10
731 800 4.698575 AGAGAGGCGGCTTATTTTCTAAG 58.301 43.478 14.76 0.00 0.00 2.18
732 801 3.206964 AGAGGCGGCTTATTTTCTAAGC 58.793 45.455 14.76 8.17 46.64 3.09
733 802 3.118223 AGAGGCGGCTTATTTTCTAAGCT 60.118 43.478 14.76 0.00 46.58 3.74
738 807 5.067021 CGGCTTATTTTCTAAGCTGTACG 57.933 43.478 14.72 7.84 46.42 3.67
739 808 4.025979 CGGCTTATTTTCTAAGCTGTACGG 60.026 45.833 14.72 0.00 46.42 4.02
740 809 5.114081 GGCTTATTTTCTAAGCTGTACGGA 58.886 41.667 5.68 0.00 46.58 4.69
741 810 5.234543 GGCTTATTTTCTAAGCTGTACGGAG 59.765 44.000 5.68 0.00 46.58 4.63
756 825 1.852067 CGGAGAAAACTGGCCCAACG 61.852 60.000 0.00 0.00 0.00 4.10
921 994 2.435586 CGAAGCAGCAGTGGGGAG 60.436 66.667 0.00 0.00 0.00 4.30
922 995 2.045536 GAAGCAGCAGTGGGGAGG 60.046 66.667 0.00 0.00 0.00 4.30
923 996 3.635268 GAAGCAGCAGTGGGGAGGG 62.635 68.421 0.00 0.00 0.00 4.30
924 997 4.664267 AGCAGCAGTGGGGAGGGA 62.664 66.667 0.00 0.00 0.00 4.20
925 998 3.415087 GCAGCAGTGGGGAGGGAT 61.415 66.667 0.00 0.00 0.00 3.85
926 999 2.593978 CAGCAGTGGGGAGGGATG 59.406 66.667 0.00 0.00 0.00 3.51
1093 1166 3.837570 GACCCCGTTTCCTTGCCGT 62.838 63.158 0.00 0.00 0.00 5.68
1495 1574 2.182181 CCATGCATGCACGTCGGAT 61.182 57.895 25.37 1.29 0.00 4.18
1515 1594 0.388659 CCTTCTCATCTCTGCCCTCG 59.611 60.000 0.00 0.00 0.00 4.63
1546 1625 3.504520 ACCAAACGTAAAATCAATCGCCT 59.495 39.130 0.00 0.00 0.00 5.52
1728 1807 1.585521 GGCATGTAGACGACGACGG 60.586 63.158 12.58 0.00 44.46 4.79
1757 1839 2.050168 CGCCGCAGCAACAACAAT 60.050 55.556 0.00 0.00 39.83 2.71
1867 1971 1.677552 CCTGTCCCGGCAACTACTT 59.322 57.895 0.00 0.00 0.00 2.24
2066 2174 6.472163 CCATTGGTTTTGCAATATACGAGAAC 59.528 38.462 0.00 0.00 0.00 3.01
2141 2253 6.326323 TGGTCTGCTTCAACTCCATATACATA 59.674 38.462 0.00 0.00 0.00 2.29
2157 2269 8.753133 CCATATACATAGTTCCTATTCTGCTCA 58.247 37.037 0.00 0.00 0.00 4.26
2161 2273 7.372260 ACATAGTTCCTATTCTGCTCATTCT 57.628 36.000 0.00 0.00 0.00 2.40
2163 2275 4.450053 AGTTCCTATTCTGCTCATTCTGC 58.550 43.478 0.00 0.00 0.00 4.26
2165 2277 5.365025 AGTTCCTATTCTGCTCATTCTGCTA 59.635 40.000 0.00 0.00 0.00 3.49
2177 2289 6.128090 TGCTCATTCTGCTACATTTGAAGAAG 60.128 38.462 0.00 0.00 30.90 2.85
2181 2293 8.849168 TCATTCTGCTACATTTGAAGAAGAAAA 58.151 29.630 0.00 0.00 30.90 2.29
2182 2294 9.467258 CATTCTGCTACATTTGAAGAAGAAAAA 57.533 29.630 0.00 0.00 30.90 1.94
2310 2438 1.364269 TTGGACCCCAATACCGAACT 58.636 50.000 0.00 0.00 38.75 3.01
2314 2442 3.524380 TGGACCCCAATACCGAACTAAAT 59.476 43.478 0.00 0.00 0.00 1.40
2315 2443 4.018233 TGGACCCCAATACCGAACTAAATT 60.018 41.667 0.00 0.00 0.00 1.82
2318 2446 4.264038 ACCCCAATACCGAACTAAATTGGT 60.264 41.667 10.98 0.00 44.51 3.67
2319 2447 4.707934 CCCCAATACCGAACTAAATTGGTT 59.292 41.667 10.98 0.00 44.51 3.67
2320 2448 5.393678 CCCCAATACCGAACTAAATTGGTTG 60.394 44.000 0.00 0.00 44.51 3.77
2322 2450 6.294843 CCCAATACCGAACTAAATTGGTTGTT 60.295 38.462 0.00 0.00 44.51 2.83
2323 2451 7.149307 CCAATACCGAACTAAATTGGTTGTTT 58.851 34.615 0.00 0.00 42.18 2.83
2324 2452 7.115663 CCAATACCGAACTAAATTGGTTGTTTG 59.884 37.037 0.00 1.71 42.18 2.93
2325 2453 4.364860 ACCGAACTAAATTGGTTGTTTGC 58.635 39.130 0.00 0.00 0.00 3.68
2327 2455 4.679654 CCGAACTAAATTGGTTGTTTGCTC 59.320 41.667 0.00 0.00 0.00 4.26
2328 2456 5.507315 CCGAACTAAATTGGTTGTTTGCTCT 60.507 40.000 0.00 0.00 0.00 4.09
2329 2457 5.625311 CGAACTAAATTGGTTGTTTGCTCTC 59.375 40.000 0.00 0.00 0.00 3.20
2331 2459 5.140454 ACTAAATTGGTTGTTTGCTCTCCT 58.860 37.500 0.00 0.00 0.00 3.69
2334 2462 2.550830 TGGTTGTTTGCTCTCCTCTC 57.449 50.000 0.00 0.00 0.00 3.20
2336 2464 1.349357 GGTTGTTTGCTCTCCTCTCCT 59.651 52.381 0.00 0.00 0.00 3.69
2339 2467 1.270907 GTTTGCTCTCCTCTCCTGGA 58.729 55.000 0.00 0.00 34.52 3.86
2340 2468 1.836802 GTTTGCTCTCCTCTCCTGGAT 59.163 52.381 0.00 0.00 35.30 3.41
2346 2474 0.665835 CTCCTCTCCTGGATCGAACG 59.334 60.000 0.00 0.00 35.30 3.95
2348 2476 1.103803 CCTCTCCTGGATCGAACGAA 58.896 55.000 0.00 0.00 0.00 3.85
2349 2477 1.683917 CCTCTCCTGGATCGAACGAAT 59.316 52.381 0.00 0.00 0.00 3.34
2350 2478 2.287909 CCTCTCCTGGATCGAACGAATC 60.288 54.545 0.00 0.44 0.00 2.52
2352 2480 3.024547 TCTCCTGGATCGAACGAATCTT 58.975 45.455 0.00 0.00 0.00 2.40
2353 2481 3.066900 TCTCCTGGATCGAACGAATCTTC 59.933 47.826 0.00 0.00 0.00 2.87
2354 2482 2.100916 TCCTGGATCGAACGAATCTTCC 59.899 50.000 0.12 4.50 0.00 3.46
2355 2483 2.159099 CCTGGATCGAACGAATCTTCCA 60.159 50.000 13.88 13.88 36.31 3.53
2424 2857 8.474831 GCCATCTTTAATACACCAATTTACCTT 58.525 33.333 0.00 0.00 0.00 3.50
2449 2882 6.039270 TCAATTTTCTTACACACAACCAGGAG 59.961 38.462 0.00 0.00 0.00 3.69
2461 2894 4.642885 CACAACCAGGAGAGGTAAAAACAA 59.357 41.667 0.00 0.00 42.25 2.83
2708 3158 8.383318 TGTTTCAAAATGGTTTTCTGTTTTGA 57.617 26.923 7.74 7.74 44.29 2.69
2709 3159 9.007901 TGTTTCAAAATGGTTTTCTGTTTTGAT 57.992 25.926 11.45 0.00 44.90 2.57
2726 3176 6.870965 TGTTTTGATGGTTTTATGTACATGGC 59.129 34.615 18.81 5.57 0.00 4.40
2796 3254 3.892918 TTTTCGCCATGGCAAAAATTG 57.107 38.095 34.93 17.59 42.06 2.32
2802 3260 4.999950 TCGCCATGGCAAAAATTGTTTTAT 59.000 33.333 34.93 0.00 42.06 1.40
2851 3309 2.877168 GCCATGGCAAAAATTGTGTTGA 59.123 40.909 32.08 0.00 41.49 3.18
2860 3318 5.626132 GCAAAAATTGTGTTGATGAAATGGC 59.374 36.000 1.94 0.00 0.00 4.40
2928 3386 4.508662 TGGAAAAATTTGTGTTGGTGACC 58.491 39.130 0.00 0.00 0.00 4.02
2930 3388 4.570369 GGAAAAATTTGTGTTGGTGACCTG 59.430 41.667 2.11 0.00 0.00 4.00
2944 3402 3.392882 GTGACCTGGCAAAAATCCTTTG 58.607 45.455 0.00 0.00 0.00 2.77
2955 3413 6.820470 CAAAAATCCTTTGCTACGACAAAA 57.180 33.333 0.00 0.00 38.96 2.44
2956 3414 7.227992 CAAAAATCCTTTGCTACGACAAAAA 57.772 32.000 0.00 0.00 38.96 1.94
2959 3417 7.406799 AAATCCTTTGCTACGACAAAAATTG 57.593 32.000 0.00 0.00 38.96 2.32
2967 3425 5.066117 TGCTACGACAAAAATTGTGTTGGTA 59.934 36.000 8.31 5.12 45.52 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.205733 ACAAAAGGGTTAGGGGAGTGAAA 59.794 43.478 0.00 0.00 0.00 2.69
1 2 2.787035 ACAAAAGGGTTAGGGGAGTGAA 59.213 45.455 0.00 0.00 0.00 3.18
2 3 2.107552 CACAAAAGGGTTAGGGGAGTGA 59.892 50.000 0.00 0.00 0.00 3.41
3 4 2.514803 CACAAAAGGGTTAGGGGAGTG 58.485 52.381 0.00 0.00 0.00 3.51
4 5 1.203013 GCACAAAAGGGTTAGGGGAGT 60.203 52.381 0.00 0.00 0.00 3.85
5 6 1.203001 TGCACAAAAGGGTTAGGGGAG 60.203 52.381 0.00 0.00 0.00 4.30
6 7 0.854218 TGCACAAAAGGGTTAGGGGA 59.146 50.000 0.00 0.00 0.00 4.81
7 8 1.256812 CTGCACAAAAGGGTTAGGGG 58.743 55.000 0.00 0.00 0.00 4.79
8 9 0.603065 GCTGCACAAAAGGGTTAGGG 59.397 55.000 0.00 0.00 0.00 3.53
9 10 0.240945 CGCTGCACAAAAGGGTTAGG 59.759 55.000 0.00 0.00 0.00 2.69
10 11 0.387239 GCGCTGCACAAAAGGGTTAG 60.387 55.000 0.00 0.00 0.00 2.34
11 12 1.657556 GCGCTGCACAAAAGGGTTA 59.342 52.632 0.00 0.00 0.00 2.85
12 13 2.417097 GCGCTGCACAAAAGGGTT 59.583 55.556 0.00 0.00 0.00 4.11
13 14 3.605664 GGCGCTGCACAAAAGGGT 61.606 61.111 7.64 0.00 0.00 4.34
14 15 4.362476 GGGCGCTGCACAAAAGGG 62.362 66.667 7.64 0.00 0.00 3.95
15 16 3.562779 CTGGGCGCTGCACAAAAGG 62.563 63.158 7.64 0.00 43.23 3.11
16 17 2.049802 CTGGGCGCTGCACAAAAG 60.050 61.111 7.64 0.00 43.23 2.27
17 18 3.604667 CCTGGGCGCTGCACAAAA 61.605 61.111 7.64 0.00 43.23 2.44
29 30 4.087892 ACTAGTGCAGCGCCTGGG 62.088 66.667 2.29 0.00 31.21 4.45
30 31 2.816958 CACTAGTGCAGCGCCTGG 60.817 66.667 10.54 0.00 31.21 4.45
40 41 2.034879 CCTGGGCGTTGCACTAGTG 61.035 63.158 18.93 18.93 30.56 2.74
41 42 2.172483 CTCCTGGGCGTTGCACTAGT 62.172 60.000 0.00 0.00 30.56 2.57
42 43 1.448540 CTCCTGGGCGTTGCACTAG 60.449 63.158 0.00 0.00 30.56 2.57
43 44 2.662596 CTCCTGGGCGTTGCACTA 59.337 61.111 0.00 0.00 30.56 2.74
45 46 3.605749 TAGCTCCTGGGCGTTGCAC 62.606 63.158 0.00 0.00 37.29 4.57
46 47 3.315142 CTAGCTCCTGGGCGTTGCA 62.315 63.158 0.00 0.00 37.29 4.08
47 48 2.512515 CTAGCTCCTGGGCGTTGC 60.513 66.667 0.00 0.00 37.29 4.17
48 49 2.187946 CCTAGCTCCTGGGCGTTG 59.812 66.667 0.00 0.00 37.29 4.10
61 62 0.803768 CTACACAGTGCAGCGCCTAG 60.804 60.000 2.29 0.00 0.00 3.02
62 63 1.215382 CTACACAGTGCAGCGCCTA 59.785 57.895 2.29 0.00 0.00 3.93
63 64 2.047844 CTACACAGTGCAGCGCCT 60.048 61.111 2.29 0.00 0.00 5.52
64 65 2.357517 ACTACACAGTGCAGCGCC 60.358 61.111 2.29 0.00 32.25 6.53
65 66 2.856032 CACTACACAGTGCAGCGC 59.144 61.111 0.00 0.00 45.44 5.92
72 73 1.183030 TAGGCGCCACACTACACAGT 61.183 55.000 31.54 5.27 34.42 3.55
73 74 0.458543 CTAGGCGCCACACTACACAG 60.459 60.000 31.54 6.91 0.00 3.66
74 75 1.589630 CTAGGCGCCACACTACACA 59.410 57.895 31.54 0.33 0.00 3.72
75 76 1.810030 GCTAGGCGCCACACTACAC 60.810 63.158 31.54 4.76 0.00 2.90
76 77 1.945354 GAGCTAGGCGCCACACTACA 61.945 60.000 31.54 2.99 40.39 2.74
77 78 1.227002 GAGCTAGGCGCCACACTAC 60.227 63.158 31.54 11.53 40.39 2.73
78 79 1.379977 AGAGCTAGGCGCCACACTA 60.380 57.895 31.54 11.42 40.39 2.74
79 80 2.681778 AGAGCTAGGCGCCACACT 60.682 61.111 31.54 21.99 40.39 3.55
80 81 2.202810 GAGAGCTAGGCGCCACAC 60.203 66.667 31.54 17.11 40.39 3.82
81 82 3.826754 CGAGAGCTAGGCGCCACA 61.827 66.667 31.54 15.42 40.39 4.17
82 83 4.577246 CCGAGAGCTAGGCGCCAC 62.577 72.222 31.54 17.93 40.39 5.01
83 84 4.815108 TCCGAGAGCTAGGCGCCA 62.815 66.667 31.54 14.00 40.39 5.69
84 85 4.273257 GTCCGAGAGCTAGGCGCC 62.273 72.222 21.89 21.89 40.39 6.53
85 86 4.615834 CGTCCGAGAGCTAGGCGC 62.616 72.222 0.00 0.00 39.57 6.53
86 87 4.615834 GCGTCCGAGAGCTAGGCG 62.616 72.222 11.71 11.71 0.00 5.52
87 88 3.213402 AGCGTCCGAGAGCTAGGC 61.213 66.667 0.00 0.00 42.60 3.93
88 89 2.718731 CAGCGTCCGAGAGCTAGG 59.281 66.667 0.00 0.00 42.52 3.02
89 90 2.025441 GCAGCGTCCGAGAGCTAG 59.975 66.667 0.00 0.00 42.52 3.42
90 91 2.750237 TGCAGCGTCCGAGAGCTA 60.750 61.111 0.00 0.00 42.52 3.32
91 92 4.427661 GTGCAGCGTCCGAGAGCT 62.428 66.667 0.00 0.00 45.74 4.09
103 104 3.730761 GCCCAAGTCAGCGTGCAG 61.731 66.667 0.00 0.00 0.00 4.41
104 105 4.560743 TGCCCAAGTCAGCGTGCA 62.561 61.111 0.00 0.00 0.00 4.57
105 106 4.030452 GTGCCCAAGTCAGCGTGC 62.030 66.667 0.00 0.00 0.00 5.34
106 107 0.673333 TATGTGCCCAAGTCAGCGTG 60.673 55.000 0.00 0.00 0.00 5.34
107 108 0.253044 ATATGTGCCCAAGTCAGCGT 59.747 50.000 0.00 0.00 0.00 5.07
108 109 0.659427 CATATGTGCCCAAGTCAGCG 59.341 55.000 0.00 0.00 0.00 5.18
109 110 1.027357 CCATATGTGCCCAAGTCAGC 58.973 55.000 1.24 0.00 0.00 4.26
110 111 1.064463 ACCCATATGTGCCCAAGTCAG 60.064 52.381 1.24 0.00 0.00 3.51
111 112 0.998928 ACCCATATGTGCCCAAGTCA 59.001 50.000 1.24 0.00 0.00 3.41
112 113 1.392589 CACCCATATGTGCCCAAGTC 58.607 55.000 1.24 0.00 0.00 3.01
113 114 3.594453 CACCCATATGTGCCCAAGT 57.406 52.632 1.24 0.00 0.00 3.16
120 121 1.521457 AGCGTCGCACCCATATGTG 60.521 57.895 21.09 0.00 39.29 3.21
121 122 1.521457 CAGCGTCGCACCCATATGT 60.521 57.895 21.09 0.00 0.00 2.29
122 123 2.246739 CCAGCGTCGCACCCATATG 61.247 63.158 21.09 6.70 0.00 1.78
123 124 2.108976 CCAGCGTCGCACCCATAT 59.891 61.111 21.09 0.00 0.00 1.78
124 125 4.830765 GCCAGCGTCGCACCCATA 62.831 66.667 21.09 0.00 0.00 2.74
141 142 1.007271 CCAGATAGGCGCTACACGG 60.007 63.158 7.64 0.00 43.93 4.94
143 144 1.269831 CCTTCCAGATAGGCGCTACAC 60.270 57.143 7.64 0.00 37.29 2.90
144 145 1.040646 CCTTCCAGATAGGCGCTACA 58.959 55.000 7.64 0.00 37.29 2.74
145 146 3.896317 CCTTCCAGATAGGCGCTAC 57.104 57.895 7.64 0.00 37.29 3.58
151 152 0.107703 TGCAACGCCTTCCAGATAGG 60.108 55.000 0.00 0.00 39.47 2.57
152 153 1.009829 GTGCAACGCCTTCCAGATAG 58.990 55.000 0.00 0.00 0.00 2.08
153 154 0.323302 TGTGCAACGCCTTCCAGATA 59.677 50.000 0.00 0.00 42.39 1.98
154 155 0.957395 CTGTGCAACGCCTTCCAGAT 60.957 55.000 0.00 0.00 42.39 2.90
155 156 1.597854 CTGTGCAACGCCTTCCAGA 60.598 57.895 0.00 0.00 42.39 3.86
156 157 0.602638 TACTGTGCAACGCCTTCCAG 60.603 55.000 0.00 0.00 42.39 3.86
157 158 0.602638 CTACTGTGCAACGCCTTCCA 60.603 55.000 0.00 0.00 42.39 3.53
158 159 0.320421 TCTACTGTGCAACGCCTTCC 60.320 55.000 0.00 0.00 42.39 3.46
159 160 1.394917 CATCTACTGTGCAACGCCTTC 59.605 52.381 0.00 0.00 42.39 3.46
160 161 1.270839 ACATCTACTGTGCAACGCCTT 60.271 47.619 0.00 0.00 42.39 4.35
161 162 0.321671 ACATCTACTGTGCAACGCCT 59.678 50.000 0.00 0.00 42.39 5.52
162 163 2.840974 ACATCTACTGTGCAACGCC 58.159 52.632 0.00 0.00 42.39 5.68
170 171 1.806542 CTTTTGCGCCACATCTACTGT 59.193 47.619 4.18 0.00 39.20 3.55
171 172 1.131126 CCTTTTGCGCCACATCTACTG 59.869 52.381 4.18 0.00 0.00 2.74
172 173 1.003118 TCCTTTTGCGCCACATCTACT 59.997 47.619 4.18 0.00 0.00 2.57
173 174 1.448985 TCCTTTTGCGCCACATCTAC 58.551 50.000 4.18 0.00 0.00 2.59
174 175 2.288666 GATCCTTTTGCGCCACATCTA 58.711 47.619 4.18 0.00 0.00 1.98
175 176 1.098050 GATCCTTTTGCGCCACATCT 58.902 50.000 4.18 0.00 0.00 2.90
176 177 0.810648 TGATCCTTTTGCGCCACATC 59.189 50.000 4.18 0.00 0.00 3.06
177 178 0.813184 CTGATCCTTTTGCGCCACAT 59.187 50.000 4.18 0.00 0.00 3.21
178 179 1.243342 CCTGATCCTTTTGCGCCACA 61.243 55.000 4.18 0.00 0.00 4.17
179 180 1.508088 CCTGATCCTTTTGCGCCAC 59.492 57.895 4.18 0.00 0.00 5.01
180 181 1.678635 CCCTGATCCTTTTGCGCCA 60.679 57.895 4.18 0.00 0.00 5.69
181 182 0.965363 TTCCCTGATCCTTTTGCGCC 60.965 55.000 4.18 0.00 0.00 6.53
182 183 0.453390 CTTCCCTGATCCTTTTGCGC 59.547 55.000 0.00 0.00 0.00 6.09
183 184 1.470098 CACTTCCCTGATCCTTTTGCG 59.530 52.381 0.00 0.00 0.00 4.85
184 185 2.795329 TCACTTCCCTGATCCTTTTGC 58.205 47.619 0.00 0.00 0.00 3.68
185 186 5.990120 ATTTCACTTCCCTGATCCTTTTG 57.010 39.130 0.00 0.00 0.00 2.44
186 187 6.794534 ACTATTTCACTTCCCTGATCCTTTT 58.205 36.000 0.00 0.00 0.00 2.27
187 188 6.394345 ACTATTTCACTTCCCTGATCCTTT 57.606 37.500 0.00 0.00 0.00 3.11
188 189 6.394345 AACTATTTCACTTCCCTGATCCTT 57.606 37.500 0.00 0.00 0.00 3.36
189 190 6.394345 AAACTATTTCACTTCCCTGATCCT 57.606 37.500 0.00 0.00 0.00 3.24
190 191 5.294552 CGAAACTATTTCACTTCCCTGATCC 59.705 44.000 2.50 0.00 39.63 3.36
191 192 5.220681 GCGAAACTATTTCACTTCCCTGATC 60.221 44.000 2.50 0.00 39.63 2.92
192 193 4.636206 GCGAAACTATTTCACTTCCCTGAT 59.364 41.667 2.50 0.00 39.63 2.90
193 194 4.000988 GCGAAACTATTTCACTTCCCTGA 58.999 43.478 2.50 0.00 39.63 3.86
194 195 3.751175 TGCGAAACTATTTCACTTCCCTG 59.249 43.478 2.50 0.00 39.63 4.45
195 196 4.015872 TGCGAAACTATTTCACTTCCCT 57.984 40.909 2.50 0.00 39.63 4.20
196 197 4.473199 GTTGCGAAACTATTTCACTTCCC 58.527 43.478 0.00 0.00 39.63 3.97
197 198 4.023536 TGGTTGCGAAACTATTTCACTTCC 60.024 41.667 6.17 1.11 39.63 3.46
198 199 5.103290 TGGTTGCGAAACTATTTCACTTC 57.897 39.130 6.17 0.00 39.63 3.01
199 200 4.578928 ACTGGTTGCGAAACTATTTCACTT 59.421 37.500 6.17 0.00 39.63 3.16
200 201 4.134563 ACTGGTTGCGAAACTATTTCACT 58.865 39.130 6.17 0.00 39.63 3.41
201 202 4.464112 GACTGGTTGCGAAACTATTTCAC 58.536 43.478 6.17 0.00 39.63 3.18
202 203 3.500680 GGACTGGTTGCGAAACTATTTCA 59.499 43.478 6.17 0.00 39.63 2.69
203 204 3.500680 TGGACTGGTTGCGAAACTATTTC 59.499 43.478 6.17 0.00 36.32 2.17
204 205 3.482436 TGGACTGGTTGCGAAACTATTT 58.518 40.909 6.17 0.00 0.00 1.40
205 206 3.134574 TGGACTGGTTGCGAAACTATT 57.865 42.857 6.17 0.00 0.00 1.73
206 207 2.851263 TGGACTGGTTGCGAAACTAT 57.149 45.000 6.17 0.00 0.00 2.12
207 208 2.851263 ATGGACTGGTTGCGAAACTA 57.149 45.000 6.17 0.00 0.00 2.24
208 209 1.880027 GAATGGACTGGTTGCGAAACT 59.120 47.619 6.17 0.00 0.00 2.66
209 210 1.880027 AGAATGGACTGGTTGCGAAAC 59.120 47.619 0.00 0.00 0.00 2.78
210 211 1.879380 CAGAATGGACTGGTTGCGAAA 59.121 47.619 0.00 0.00 34.64 3.46
211 212 1.202758 ACAGAATGGACTGGTTGCGAA 60.203 47.619 0.00 0.00 43.62 4.70
212 213 0.396435 ACAGAATGGACTGGTTGCGA 59.604 50.000 0.00 0.00 43.62 5.10
213 214 0.518636 CACAGAATGGACTGGTTGCG 59.481 55.000 0.00 0.00 43.62 4.85
214 215 1.896220 TCACAGAATGGACTGGTTGC 58.104 50.000 0.00 0.00 43.62 4.17
215 216 4.520111 TCAAATCACAGAATGGACTGGTTG 59.480 41.667 0.00 0.00 43.62 3.77
216 217 4.728772 TCAAATCACAGAATGGACTGGTT 58.271 39.130 0.00 0.00 43.62 3.67
217 218 4.371624 TCAAATCACAGAATGGACTGGT 57.628 40.909 0.00 0.00 43.62 4.00
218 219 5.909621 AATCAAATCACAGAATGGACTGG 57.090 39.130 0.00 0.00 43.62 4.00
219 220 6.025896 CGAAATCAAATCACAGAATGGACTG 58.974 40.000 0.00 0.00 43.62 3.51
220 221 5.939883 TCGAAATCAAATCACAGAATGGACT 59.060 36.000 0.00 0.00 43.62 3.85
221 222 6.182039 TCGAAATCAAATCACAGAATGGAC 57.818 37.500 0.00 0.00 43.62 4.02
222 223 7.395190 AATCGAAATCAAATCACAGAATGGA 57.605 32.000 0.00 0.00 43.62 3.41
226 227 9.613428 ACCTATAATCGAAATCAAATCACAGAA 57.387 29.630 0.00 0.00 0.00 3.02
227 228 9.261180 GACCTATAATCGAAATCAAATCACAGA 57.739 33.333 0.00 0.00 0.00 3.41
228 229 9.045223 TGACCTATAATCGAAATCAAATCACAG 57.955 33.333 0.00 0.00 0.00 3.66
229 230 8.956533 TGACCTATAATCGAAATCAAATCACA 57.043 30.769 0.00 0.00 0.00 3.58
247 248 9.829507 TGAACAAATTTGACAATTTTGACCTAT 57.170 25.926 28.97 15.88 40.09 2.57
248 249 9.658799 TTGAACAAATTTGACAATTTTGACCTA 57.341 25.926 28.97 18.27 40.09 3.08
249 250 8.558973 TTGAACAAATTTGACAATTTTGACCT 57.441 26.923 28.97 18.18 40.09 3.85
250 251 8.663911 TCTTGAACAAATTTGACAATTTTGACC 58.336 29.630 28.97 21.85 40.09 4.02
253 254 9.823098 TGTTCTTGAACAAATTTGACAATTTTG 57.177 25.926 24.64 24.01 40.09 2.44
255 256 9.824534 GTTGTTCTTGAACAAATTTGACAATTT 57.175 25.926 24.64 7.89 43.42 1.82
256 257 9.218440 AGTTGTTCTTGAACAAATTTGACAATT 57.782 25.926 24.64 14.84 43.42 2.32
257 258 8.776376 AGTTGTTCTTGAACAAATTTGACAAT 57.224 26.923 24.64 7.60 43.42 2.71
258 259 8.600449 AAGTTGTTCTTGAACAAATTTGACAA 57.400 26.923 25.92 23.47 45.11 3.18
365 366 2.096268 CAGCAACGTTGGATGTACACTG 60.096 50.000 28.33 19.18 0.00 3.66
366 367 2.143122 CAGCAACGTTGGATGTACACT 58.857 47.619 28.33 12.10 0.00 3.55
367 368 2.096417 GTCAGCAACGTTGGATGTACAC 60.096 50.000 28.33 10.00 0.00 2.90
368 369 2.139917 GTCAGCAACGTTGGATGTACA 58.860 47.619 28.33 0.00 0.00 2.90
369 370 2.412089 GAGTCAGCAACGTTGGATGTAC 59.588 50.000 28.33 16.14 0.00 2.90
370 371 2.299013 AGAGTCAGCAACGTTGGATGTA 59.701 45.455 28.33 7.09 0.00 2.29
371 372 1.070758 AGAGTCAGCAACGTTGGATGT 59.929 47.619 28.33 10.46 0.00 3.06
372 373 1.728971 GAGAGTCAGCAACGTTGGATG 59.271 52.381 28.33 17.74 0.00 3.51
410 411 2.743636 ACGTGATGAGTAAGGTGTGG 57.256 50.000 0.00 0.00 0.00 4.17
470 471 7.699566 TGGGCATAATCGTAAATCTTTGTAAC 58.300 34.615 0.00 0.00 0.00 2.50
518 520 4.974438 ACTGGCCCGACCCCTTGA 62.974 66.667 0.00 0.00 37.83 3.02
525 527 1.200020 CATCAAAAGAACTGGCCCGAC 59.800 52.381 0.00 0.00 0.00 4.79
559 561 7.849804 TTATGGAATAAGCTGAGAAGACAAC 57.150 36.000 0.00 0.00 32.95 3.32
569 571 6.489361 AGAGAGGCAAATTATGGAATAAGCTG 59.511 38.462 0.00 0.00 42.97 4.24
570 572 6.608922 AGAGAGGCAAATTATGGAATAAGCT 58.391 36.000 0.00 0.00 42.97 3.74
571 573 6.488006 TGAGAGAGGCAAATTATGGAATAAGC 59.512 38.462 0.00 0.00 42.97 3.09
573 575 9.071276 GAATGAGAGAGGCAAATTATGGAATAA 57.929 33.333 0.00 0.00 44.01 1.40
574 576 8.219868 TGAATGAGAGAGGCAAATTATGGAATA 58.780 33.333 0.00 0.00 0.00 1.75
575 577 7.064866 TGAATGAGAGAGGCAAATTATGGAAT 58.935 34.615 0.00 0.00 0.00 3.01
578 580 6.896021 ATGAATGAGAGAGGCAAATTATGG 57.104 37.500 0.00 0.00 0.00 2.74
584 589 4.637534 GCTGTAATGAATGAGAGAGGCAAA 59.362 41.667 0.00 0.00 0.00 3.68
586 591 3.453717 AGCTGTAATGAATGAGAGAGGCA 59.546 43.478 0.00 0.00 0.00 4.75
626 631 9.209175 CGCCTCTCTGTAGCTTAAATAATAAAT 57.791 33.333 0.00 0.00 0.00 1.40
627 632 7.656137 CCGCCTCTCTGTAGCTTAAATAATAAA 59.344 37.037 0.00 0.00 0.00 1.40
628 633 7.014905 TCCGCCTCTCTGTAGCTTAAATAATAA 59.985 37.037 0.00 0.00 0.00 1.40
629 634 6.492429 TCCGCCTCTCTGTAGCTTAAATAATA 59.508 38.462 0.00 0.00 0.00 0.98
630 635 5.304614 TCCGCCTCTCTGTAGCTTAAATAAT 59.695 40.000 0.00 0.00 0.00 1.28
631 636 4.647853 TCCGCCTCTCTGTAGCTTAAATAA 59.352 41.667 0.00 0.00 0.00 1.40
632 637 4.212716 TCCGCCTCTCTGTAGCTTAAATA 58.787 43.478 0.00 0.00 0.00 1.40
633 638 3.031736 TCCGCCTCTCTGTAGCTTAAAT 58.968 45.455 0.00 0.00 0.00 1.40
634 639 2.453521 TCCGCCTCTCTGTAGCTTAAA 58.546 47.619 0.00 0.00 0.00 1.52
635 640 2.139323 TCCGCCTCTCTGTAGCTTAA 57.861 50.000 0.00 0.00 0.00 1.85
636 641 2.366640 ATCCGCCTCTCTGTAGCTTA 57.633 50.000 0.00 0.00 0.00 3.09
637 642 2.366640 TATCCGCCTCTCTGTAGCTT 57.633 50.000 0.00 0.00 0.00 3.74
638 643 2.366640 TTATCCGCCTCTCTGTAGCT 57.633 50.000 0.00 0.00 0.00 3.32
639 644 2.558795 TGATTATCCGCCTCTCTGTAGC 59.441 50.000 0.00 0.00 0.00 3.58
640 645 4.855715 TTGATTATCCGCCTCTCTGTAG 57.144 45.455 0.00 0.00 0.00 2.74
641 646 5.808366 AATTGATTATCCGCCTCTCTGTA 57.192 39.130 0.00 0.00 0.00 2.74
642 647 4.696479 AATTGATTATCCGCCTCTCTGT 57.304 40.909 0.00 0.00 0.00 3.41
643 648 6.459066 TCTAAATTGATTATCCGCCTCTCTG 58.541 40.000 0.00 0.00 0.00 3.35
644 649 6.672266 TCTAAATTGATTATCCGCCTCTCT 57.328 37.500 0.00 0.00 0.00 3.10
645 650 7.117092 GTCTTCTAAATTGATTATCCGCCTCTC 59.883 40.741 0.00 0.00 0.00 3.20
646 651 6.931840 GTCTTCTAAATTGATTATCCGCCTCT 59.068 38.462 0.00 0.00 0.00 3.69
647 652 6.931840 AGTCTTCTAAATTGATTATCCGCCTC 59.068 38.462 0.00 0.00 0.00 4.70
648 653 6.831976 AGTCTTCTAAATTGATTATCCGCCT 58.168 36.000 0.00 0.00 0.00 5.52
649 654 6.706270 TGAGTCTTCTAAATTGATTATCCGCC 59.294 38.462 0.00 0.00 0.00 6.13
650 655 7.715265 TGAGTCTTCTAAATTGATTATCCGC 57.285 36.000 0.00 0.00 0.00 5.54
651 656 9.098355 TGTTGAGTCTTCTAAATTGATTATCCG 57.902 33.333 0.00 0.00 0.00 4.18
703 772 0.464452 TAAGCCGCCTCTCTTTAGCC 59.536 55.000 0.00 0.00 0.00 3.93
705 774 5.119694 AGAAAATAAGCCGCCTCTCTTTAG 58.880 41.667 0.00 0.00 0.00 1.85
708 777 3.636153 AGAAAATAAGCCGCCTCTCTT 57.364 42.857 0.00 0.00 0.00 2.85
727 796 3.927142 CCAGTTTTCTCCGTACAGCTTAG 59.073 47.826 0.00 0.00 0.00 2.18
730 799 1.608283 GCCAGTTTTCTCCGTACAGCT 60.608 52.381 0.00 0.00 0.00 4.24
731 800 0.796927 GCCAGTTTTCTCCGTACAGC 59.203 55.000 0.00 0.00 0.00 4.40
732 801 1.439679 GGCCAGTTTTCTCCGTACAG 58.560 55.000 0.00 0.00 0.00 2.74
733 802 0.035739 GGGCCAGTTTTCTCCGTACA 59.964 55.000 4.39 0.00 0.00 2.90
734 803 0.035739 TGGGCCAGTTTTCTCCGTAC 59.964 55.000 0.00 0.00 0.00 3.67
735 804 0.766131 TTGGGCCAGTTTTCTCCGTA 59.234 50.000 6.23 0.00 0.00 4.02
736 805 0.822121 GTTGGGCCAGTTTTCTCCGT 60.822 55.000 6.23 0.00 0.00 4.69
737 806 1.852067 CGTTGGGCCAGTTTTCTCCG 61.852 60.000 6.23 0.00 0.00 4.63
738 807 0.536460 TCGTTGGGCCAGTTTTCTCC 60.536 55.000 6.23 0.00 0.00 3.71
739 808 1.001706 GTTCGTTGGGCCAGTTTTCTC 60.002 52.381 6.23 0.00 0.00 2.87
740 809 1.029681 GTTCGTTGGGCCAGTTTTCT 58.970 50.000 6.23 0.00 0.00 2.52
741 810 0.031585 GGTTCGTTGGGCCAGTTTTC 59.968 55.000 6.23 0.00 0.00 2.29
921 994 1.186200 GGGAAAAAGGTCTGCATCCC 58.814 55.000 2.08 2.08 39.74 3.85
922 995 1.186200 GGGGAAAAAGGTCTGCATCC 58.814 55.000 0.00 0.00 0.00 3.51
923 996 0.811281 CGGGGAAAAAGGTCTGCATC 59.189 55.000 0.00 0.00 0.00 3.91
924 997 0.112412 ACGGGGAAAAAGGTCTGCAT 59.888 50.000 0.00 0.00 0.00 3.96
925 998 0.536460 GACGGGGAAAAAGGTCTGCA 60.536 55.000 0.00 0.00 0.00 4.41
926 999 1.241990 GGACGGGGAAAAAGGTCTGC 61.242 60.000 0.00 0.00 0.00 4.26
1060 1133 4.517703 GTCGACCGGTCTCTCGCG 62.518 72.222 30.92 18.19 0.00 5.87
1072 1145 2.322830 GCAAGGAAACGGGGTCGAC 61.323 63.158 7.13 7.13 40.11 4.20
1299 1373 3.120683 GCAAACATGTCAAGATCGTCGAA 60.121 43.478 0.00 0.00 0.00 3.71
1495 1574 1.786937 GAGGGCAGAGATGAGAAGGA 58.213 55.000 0.00 0.00 0.00 3.36
1515 1594 0.662085 TTACGTTTGGTTTGGTCGGC 59.338 50.000 0.00 0.00 0.00 5.54
1757 1839 2.104451 TGTGTCTTTTGGCCGGTAGTAA 59.896 45.455 1.90 0.00 0.00 2.24
1867 1971 2.364579 AGGGGTGGTAATCGGCGA 60.365 61.111 13.87 13.87 0.00 5.54
1984 2089 0.757188 AACGGCAACCCAAATGACCA 60.757 50.000 0.00 0.00 0.00 4.02
2141 2253 4.163839 AGCAGAATGAGCAGAATAGGAACT 59.836 41.667 0.00 0.00 39.69 3.01
2157 2269 9.468532 GTTTTTCTTCTTCAAATGTAGCAGAAT 57.531 29.630 3.78 0.00 28.90 2.40
2159 2271 7.995289 TGTTTTTCTTCTTCAAATGTAGCAGA 58.005 30.769 0.00 0.00 0.00 4.26
2161 2273 8.868916 GTTTGTTTTTCTTCTTCAAATGTAGCA 58.131 29.630 0.00 0.00 32.16 3.49
2165 2277 8.600449 TGTGTTTGTTTTTCTTCTTCAAATGT 57.400 26.923 0.00 0.00 32.16 2.71
2213 2333 5.128663 TGAGTGGATTCTTCGGTGAATATCA 59.871 40.000 4.31 4.28 36.86 2.15
2310 2438 5.385198 AGAGGAGAGCAAACAACCAATTTA 58.615 37.500 0.00 0.00 0.00 1.40
2314 2442 2.487265 GGAGAGGAGAGCAAACAACCAA 60.487 50.000 0.00 0.00 0.00 3.67
2315 2443 1.072331 GGAGAGGAGAGCAAACAACCA 59.928 52.381 0.00 0.00 0.00 3.67
2318 2446 1.349026 CCAGGAGAGGAGAGCAAACAA 59.651 52.381 0.00 0.00 0.00 2.83
2319 2447 0.979665 CCAGGAGAGGAGAGCAAACA 59.020 55.000 0.00 0.00 0.00 2.83
2320 2448 1.270907 TCCAGGAGAGGAGAGCAAAC 58.729 55.000 0.00 0.00 32.77 2.93
2322 2450 1.786937 GATCCAGGAGAGGAGAGCAA 58.213 55.000 0.00 0.00 41.90 3.91
2323 2451 0.467106 CGATCCAGGAGAGGAGAGCA 60.467 60.000 0.00 0.00 41.90 4.26
2324 2452 0.179004 TCGATCCAGGAGAGGAGAGC 60.179 60.000 0.00 0.00 41.90 4.09
2325 2453 1.953686 GTTCGATCCAGGAGAGGAGAG 59.046 57.143 0.00 0.00 41.90 3.20
2327 2455 0.665835 CGTTCGATCCAGGAGAGGAG 59.334 60.000 0.00 0.00 41.90 3.69
2328 2456 0.255033 TCGTTCGATCCAGGAGAGGA 59.745 55.000 0.00 0.00 43.01 3.71
2329 2457 1.103803 TTCGTTCGATCCAGGAGAGG 58.896 55.000 0.00 0.00 0.00 3.69
2331 2459 2.656002 AGATTCGTTCGATCCAGGAGA 58.344 47.619 0.00 0.00 0.00 3.71
2334 2462 2.159099 TGGAAGATTCGTTCGATCCAGG 60.159 50.000 10.06 0.00 39.11 4.45
2336 2464 3.384789 AGATGGAAGATTCGTTCGATCCA 59.615 43.478 14.63 14.63 44.28 3.41
2339 2467 4.655762 TCAGATGGAAGATTCGTTCGAT 57.344 40.909 0.00 0.00 0.00 3.59
2340 2468 4.450082 TTCAGATGGAAGATTCGTTCGA 57.550 40.909 0.00 0.00 0.00 3.71
2349 2477 9.919416 TTGATATGGTATTTTTCAGATGGAAGA 57.081 29.630 0.00 0.00 36.72 2.87
2424 2857 5.888724 TCCTGGTTGTGTGTAAGAAAATTGA 59.111 36.000 0.00 0.00 0.00 2.57
2427 2860 5.690865 TCTCCTGGTTGTGTGTAAGAAAAT 58.309 37.500 0.00 0.00 0.00 1.82
2449 2882 9.581099 TGACAATTTTCTCTTTGTTTTTACCTC 57.419 29.630 0.00 0.00 36.25 3.85
2461 2894 7.951530 AATTTTGCGATGACAATTTTCTCTT 57.048 28.000 0.00 0.00 0.00 2.85
2567 3000 3.305335 CCATGGCAGTTTTTCCTGTGTAC 60.305 47.826 0.00 0.00 34.84 2.90
2700 3150 7.063308 GCCATGTACATAAAACCATCAAAACAG 59.937 37.037 8.32 0.00 0.00 3.16
2708 3158 8.099537 TGATTTTTGCCATGTACATAAAACCAT 58.900 29.630 8.32 4.05 0.00 3.55
2709 3159 7.445121 TGATTTTTGCCATGTACATAAAACCA 58.555 30.769 8.32 6.30 0.00 3.67
2726 3176 5.261209 TGTTCAACACCTCCTGATTTTTG 57.739 39.130 0.00 0.00 0.00 2.44
2780 3238 3.622627 AAAACAATTTTTGCCATGGCG 57.377 38.095 30.87 17.27 45.51 5.69
2944 3402 4.356289 ACCAACACAATTTTTGTCGTAGC 58.644 39.130 0.00 0.00 43.23 3.58


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

AutoCloner maintained by Alex Coulton.