Multiple sequence alignment - TraesCS2D01G301700

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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 TraesCS2D01G301700 chr2D 100.000 4316 0 0 1 4316 385158750 385163065 0.000000e+00 7971.0
1 TraesCS2D01G301700 chr2D 78.327 263 37 15 23 269 25325311 25325053 7.480000e-33 152.0
2 TraesCS2D01G301700 chr2B 95.036 4069 144 26 267 4304 456016454 456020495 0.000000e+00 6342.0
3 TraesCS2D01G301700 chr2B 82.584 178 28 2 95 272 131838747 131838573 2.080000e-33 154.0
4 TraesCS2D01G301700 chr2A 94.384 3757 150 26 267 3991 520297776 520301503 0.000000e+00 5712.0
5 TraesCS2D01G301700 chr3D 87.124 233 25 5 6 235 12885942 12885712 4.280000e-65 259.0
6 TraesCS2D01G301700 chrUn 78.030 264 41 12 16 272 93026808 93026555 2.690000e-32 150.0
7 TraesCS2D01G301700 chrUn 77.108 166 36 2 109 272 410417286 410417121 1.280000e-15 95.3
8 TraesCS2D01G301700 chr7A 77.574 272 44 11 9 269 128824434 128824699 9.670000e-32 148.0
9 TraesCS2D01G301700 chr1D 73.131 495 96 25 1393 1879 366874271 366874736 4.500000e-30 143.0
10 TraesCS2D01G301700 chr5D 81.169 154 24 4 95 245 1888040 1887889 7.580000e-23 119.0
11 TraesCS2D01G301700 chr5B 81.507 146 22 5 109 253 664726440 664726581 9.810000e-22 115.0
12 TraesCS2D01G301700 chr3B 80.000 150 30 0 123 272 742982320 742982171 1.270000e-20 111.0
13 TraesCS2D01G301700 chr6D 85.393 89 5 5 1227 1315 419271975 419272055 7.690000e-13 86.1


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 TraesCS2D01G301700 chr2D 385158750 385163065 4315 False 7971 7971 100.000 1 4316 1 chr2D.!!$F1 4315
1 TraesCS2D01G301700 chr2B 456016454 456020495 4041 False 6342 6342 95.036 267 4304 1 chr2B.!!$F1 4037
2 TraesCS2D01G301700 chr2A 520297776 520301503 3727 False 5712 5712 94.384 267 3991 1 chr2A.!!$F1 3724

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
174 175 0.040514 CATTTTGCAACGACCGCTGA 60.041 50.0 0.0 0.0 0.0 4.26 F
955 970 0.107703 CCTCGCTTCAACCCTGCATA 60.108 55.0 0.0 0.0 0.0 3.14 F
2055 2071 0.108138 CCATCGACAGGGAGTTCACC 60.108 60.0 0.0 0.0 0.0 4.02 F
2773 2789 0.385473 CAACGCCAACAACGTCATCC 60.385 55.0 0.0 0.0 44.3 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 1945 0.627451 AGATTCCCTTCTGCATGGCA 59.373 50.0 0.0 0.0 36.92 4.92 R
2739 2755 0.038526 CGTTGTCCTTCACGTAGGCT 60.039 55.0 0.0 0.0 35.15 4.58 R
3006 3022 0.319555 ACGTCGTGTGGTTGAGGATG 60.320 55.0 0.0 0.0 0.00 3.51 R
4278 4323 0.390866 CAGCTGCTCCTACAGTGGTG 60.391 60.0 0.0 0.0 39.96 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.909550 CTATTGTAGAGGAGGCTATGAACT 57.090 41.667 0.00 0.00 0.00 3.01
25 26 8.588290 CTATTGTAGAGGAGGCTATGAACTAT 57.412 38.462 0.00 0.00 0.00 2.12
26 27 6.902771 TTGTAGAGGAGGCTATGAACTATC 57.097 41.667 0.00 0.00 0.00 2.08
27 28 6.207509 TGTAGAGGAGGCTATGAACTATCT 57.792 41.667 0.00 0.00 0.00 1.98
28 29 7.331089 TGTAGAGGAGGCTATGAACTATCTA 57.669 40.000 0.00 0.00 0.00 1.98
29 30 7.934313 TGTAGAGGAGGCTATGAACTATCTAT 58.066 38.462 0.00 0.00 0.00 1.98
30 31 7.831690 TGTAGAGGAGGCTATGAACTATCTATG 59.168 40.741 0.00 0.00 0.00 2.23
31 32 6.799827 AGAGGAGGCTATGAACTATCTATGT 58.200 40.000 0.00 0.00 0.00 2.29
32 33 7.934313 AGAGGAGGCTATGAACTATCTATGTA 58.066 38.462 0.00 0.00 0.00 2.29
33 34 7.832187 AGAGGAGGCTATGAACTATCTATGTAC 59.168 40.741 0.00 0.00 0.00 2.90
34 35 6.893005 AGGAGGCTATGAACTATCTATGTACC 59.107 42.308 0.00 0.00 0.00 3.34
35 36 6.183360 GGAGGCTATGAACTATCTATGTACCG 60.183 46.154 0.00 0.00 0.00 4.02
36 37 6.246919 AGGCTATGAACTATCTATGTACCGT 58.753 40.000 0.00 0.00 0.00 4.83
37 38 6.720288 AGGCTATGAACTATCTATGTACCGTT 59.280 38.462 0.00 0.00 0.00 4.44
38 39 7.232941 AGGCTATGAACTATCTATGTACCGTTT 59.767 37.037 0.00 0.00 0.00 3.60
39 40 7.871463 GGCTATGAACTATCTATGTACCGTTTT 59.129 37.037 0.00 0.00 0.00 2.43
40 41 9.903682 GCTATGAACTATCTATGTACCGTTTTA 57.096 33.333 0.00 0.00 0.00 1.52
96 97 8.613482 TCTATCGTTTTATCTATCTATGCCTCG 58.387 37.037 0.00 0.00 0.00 4.63
97 98 6.812879 TCGTTTTATCTATCTATGCCTCGA 57.187 37.500 0.00 0.00 0.00 4.04
98 99 6.843208 TCGTTTTATCTATCTATGCCTCGAG 58.157 40.000 5.13 5.13 0.00 4.04
99 100 6.430308 TCGTTTTATCTATCTATGCCTCGAGT 59.570 38.462 12.31 0.00 0.00 4.18
100 101 6.743627 CGTTTTATCTATCTATGCCTCGAGTC 59.256 42.308 12.31 0.00 0.00 3.36
101 102 7.573283 CGTTTTATCTATCTATGCCTCGAGTCA 60.573 40.741 12.31 4.80 0.00 3.41
102 103 6.993786 TTATCTATCTATGCCTCGAGTCAG 57.006 41.667 12.31 2.77 0.00 3.51
103 104 4.625607 TCTATCTATGCCTCGAGTCAGA 57.374 45.455 12.31 0.10 0.00 3.27
104 105 4.574892 TCTATCTATGCCTCGAGTCAGAG 58.425 47.826 11.71 11.71 37.97 3.35
105 106 2.719531 TCTATGCCTCGAGTCAGAGT 57.280 50.000 16.75 0.00 36.56 3.24
106 107 3.840124 TCTATGCCTCGAGTCAGAGTA 57.160 47.619 16.75 2.64 36.56 2.59
107 108 3.734463 TCTATGCCTCGAGTCAGAGTAG 58.266 50.000 16.75 7.06 36.56 2.57
108 109 2.719531 ATGCCTCGAGTCAGAGTAGA 57.280 50.000 12.31 0.00 36.56 2.59
109 110 2.491675 TGCCTCGAGTCAGAGTAGAA 57.508 50.000 12.31 0.00 36.56 2.10
110 111 2.360844 TGCCTCGAGTCAGAGTAGAAG 58.639 52.381 12.31 0.00 36.56 2.85
111 112 1.673920 GCCTCGAGTCAGAGTAGAAGG 59.326 57.143 12.31 0.00 36.56 3.46
112 113 2.681390 GCCTCGAGTCAGAGTAGAAGGA 60.681 54.545 12.31 0.00 36.56 3.36
113 114 3.202906 CCTCGAGTCAGAGTAGAAGGAG 58.797 54.545 12.31 0.00 36.56 3.69
114 115 3.118555 CCTCGAGTCAGAGTAGAAGGAGA 60.119 52.174 12.31 0.00 36.56 3.71
115 116 4.509616 CTCGAGTCAGAGTAGAAGGAGAA 58.490 47.826 3.62 0.00 33.75 2.87
116 117 4.509616 TCGAGTCAGAGTAGAAGGAGAAG 58.490 47.826 0.00 0.00 0.00 2.85
117 118 4.223255 TCGAGTCAGAGTAGAAGGAGAAGA 59.777 45.833 0.00 0.00 0.00 2.87
118 119 4.938832 CGAGTCAGAGTAGAAGGAGAAGAA 59.061 45.833 0.00 0.00 0.00 2.52
119 120 5.413213 CGAGTCAGAGTAGAAGGAGAAGAAA 59.587 44.000 0.00 0.00 0.00 2.52
120 121 6.094881 CGAGTCAGAGTAGAAGGAGAAGAAAT 59.905 42.308 0.00 0.00 0.00 2.17
121 122 7.281324 CGAGTCAGAGTAGAAGGAGAAGAAATA 59.719 40.741 0.00 0.00 0.00 1.40
122 123 9.131791 GAGTCAGAGTAGAAGGAGAAGAAATAT 57.868 37.037 0.00 0.00 0.00 1.28
125 126 9.073475 TCAGAGTAGAAGGAGAAGAAATATAGC 57.927 37.037 0.00 0.00 0.00 2.97
126 127 8.020819 CAGAGTAGAAGGAGAAGAAATATAGCG 58.979 40.741 0.00 0.00 0.00 4.26
127 128 6.683715 AGTAGAAGGAGAAGAAATATAGCGC 58.316 40.000 0.00 0.00 0.00 5.92
128 129 4.551388 AGAAGGAGAAGAAATATAGCGCG 58.449 43.478 0.00 0.00 0.00 6.86
129 130 4.038162 AGAAGGAGAAGAAATATAGCGCGT 59.962 41.667 8.43 0.00 0.00 6.01
130 131 3.903360 AGGAGAAGAAATATAGCGCGTC 58.097 45.455 8.43 0.00 0.00 5.19
131 132 3.570550 AGGAGAAGAAATATAGCGCGTCT 59.429 43.478 8.43 8.22 0.00 4.18
132 133 3.670991 GGAGAAGAAATATAGCGCGTCTG 59.329 47.826 8.43 0.00 0.00 3.51
133 134 3.053455 AGAAGAAATATAGCGCGTCTGC 58.947 45.455 8.43 0.00 37.91 4.26
135 136 2.398498 AGAAATATAGCGCGTCTGCTG 58.602 47.619 8.43 0.00 46.70 4.41
136 137 1.457303 GAAATATAGCGCGTCTGCTGG 59.543 52.381 8.43 0.00 46.70 4.85
137 138 0.673985 AATATAGCGCGTCTGCTGGA 59.326 50.000 8.43 0.00 46.70 3.86
138 139 0.242286 ATATAGCGCGTCTGCTGGAG 59.758 55.000 8.43 0.00 46.70 3.86
139 140 2.407846 TATAGCGCGTCTGCTGGAGC 62.408 60.000 8.43 0.00 46.70 4.70
159 160 3.913573 CTCGCGCGCGCTACATTT 61.914 61.111 45.97 0.00 39.59 2.32
160 161 3.420222 CTCGCGCGCGCTACATTTT 62.420 57.895 45.97 0.00 39.59 1.82
161 162 3.296923 CGCGCGCGCTACATTTTG 61.297 61.111 45.97 27.76 39.32 2.44
162 163 3.597626 GCGCGCGCTACATTTTGC 61.598 61.111 44.38 18.46 38.26 3.68
163 164 2.202285 CGCGCGCTACATTTTGCA 60.202 55.556 30.48 0.00 0.00 4.08
164 165 1.795569 CGCGCGCTACATTTTGCAA 60.796 52.632 30.48 0.00 0.00 4.08
165 166 1.696083 GCGCGCTACATTTTGCAAC 59.304 52.632 26.67 0.00 0.00 4.17
166 167 1.972801 CGCGCTACATTTTGCAACG 59.027 52.632 5.56 0.00 0.00 4.10
167 168 0.451957 CGCGCTACATTTTGCAACGA 60.452 50.000 5.56 0.00 32.53 3.85
168 169 0.974836 GCGCTACATTTTGCAACGAC 59.025 50.000 0.00 0.00 0.00 4.34
169 170 1.602191 CGCTACATTTTGCAACGACC 58.398 50.000 0.00 0.00 0.00 4.79
170 171 1.602191 GCTACATTTTGCAACGACCG 58.398 50.000 0.00 0.00 0.00 4.79
171 172 1.602191 CTACATTTTGCAACGACCGC 58.398 50.000 0.00 0.00 0.00 5.68
172 173 1.196808 CTACATTTTGCAACGACCGCT 59.803 47.619 0.00 0.00 0.00 5.52
173 174 0.317770 ACATTTTGCAACGACCGCTG 60.318 50.000 0.00 0.00 0.00 5.18
174 175 0.040514 CATTTTGCAACGACCGCTGA 60.041 50.000 0.00 0.00 0.00 4.26
175 176 0.665835 ATTTTGCAACGACCGCTGAA 59.334 45.000 0.00 0.00 0.00 3.02
176 177 0.452184 TTTTGCAACGACCGCTGAAA 59.548 45.000 0.00 0.00 0.00 2.69
177 178 0.248296 TTTGCAACGACCGCTGAAAC 60.248 50.000 0.00 0.00 0.00 2.78
178 179 2.054140 TTGCAACGACCGCTGAAACC 62.054 55.000 0.00 0.00 0.00 3.27
179 180 2.549282 CAACGACCGCTGAAACCG 59.451 61.111 0.00 0.00 0.00 4.44
180 181 1.952133 CAACGACCGCTGAAACCGA 60.952 57.895 0.00 0.00 0.00 4.69
181 182 1.952635 AACGACCGCTGAAACCGAC 60.953 57.895 0.00 0.00 0.00 4.79
182 183 3.467119 CGACCGCTGAAACCGACG 61.467 66.667 0.00 0.00 0.00 5.12
183 184 3.774702 GACCGCTGAAACCGACGC 61.775 66.667 0.00 0.00 0.00 5.19
184 185 4.295119 ACCGCTGAAACCGACGCT 62.295 61.111 0.00 0.00 0.00 5.07
185 186 3.041940 CCGCTGAAACCGACGCTT 61.042 61.111 0.00 0.00 0.00 4.68
186 187 2.470286 CGCTGAAACCGACGCTTC 59.530 61.111 0.00 0.00 0.00 3.86
187 188 2.470286 GCTGAAACCGACGCTTCG 59.530 61.111 5.49 5.49 45.44 3.79
188 189 2.470286 CTGAAACCGACGCTTCGC 59.530 61.111 7.15 0.00 44.43 4.70
189 190 2.279584 TGAAACCGACGCTTCGCA 60.280 55.556 7.15 0.00 44.43 5.10
190 191 2.215478 CTGAAACCGACGCTTCGCAG 62.215 60.000 7.15 5.40 44.43 5.18
191 192 3.631049 GAAACCGACGCTTCGCAGC 62.631 63.158 7.15 0.00 44.43 5.25
202 203 2.933769 GCTTCGCAGCATGTAAAAACT 58.066 42.857 0.97 0.00 46.49 2.66
203 204 2.658325 GCTTCGCAGCATGTAAAAACTG 59.342 45.455 0.97 0.00 46.49 3.16
204 205 2.987413 TCGCAGCATGTAAAAACTGG 57.013 45.000 0.00 0.00 39.31 4.00
205 206 1.068610 TCGCAGCATGTAAAAACTGGC 60.069 47.619 0.00 0.00 39.31 4.85
206 207 1.068333 CGCAGCATGTAAAAACTGGCT 60.068 47.619 0.00 0.00 39.31 4.75
207 208 2.161410 CGCAGCATGTAAAAACTGGCTA 59.839 45.455 0.00 0.00 39.31 3.93
208 209 3.501950 GCAGCATGTAAAAACTGGCTAC 58.498 45.455 0.00 0.00 39.31 3.58
209 210 3.747193 CAGCATGTAAAAACTGGCTACG 58.253 45.455 0.00 0.00 0.00 3.51
210 211 3.435327 CAGCATGTAAAAACTGGCTACGA 59.565 43.478 0.00 0.00 0.00 3.43
211 212 4.069304 AGCATGTAAAAACTGGCTACGAA 58.931 39.130 0.00 0.00 0.00 3.85
212 213 4.154195 AGCATGTAAAAACTGGCTACGAAG 59.846 41.667 0.00 0.00 0.00 3.79
213 214 4.671766 GCATGTAAAAACTGGCTACGAAGG 60.672 45.833 0.00 0.00 0.00 3.46
220 221 2.493030 GGCTACGAAGGCGCTGTA 59.507 61.111 7.64 4.80 42.48 2.74
221 222 1.153706 GGCTACGAAGGCGCTGTAA 60.154 57.895 7.64 0.00 42.48 2.41
222 223 0.738412 GGCTACGAAGGCGCTGTAAA 60.738 55.000 7.64 0.00 42.48 2.01
223 224 0.369248 GCTACGAAGGCGCTGTAAAC 59.631 55.000 7.64 0.00 42.48 2.01
224 225 0.638746 CTACGAAGGCGCTGTAAACG 59.361 55.000 7.64 7.81 42.48 3.60
258 259 3.378042 CGTGTTGCGCGCTTGTTG 61.378 61.111 33.29 15.44 0.00 3.33
259 260 3.024043 GTGTTGCGCGCTTGTTGG 61.024 61.111 33.29 0.00 0.00 3.77
260 261 3.205536 TGTTGCGCGCTTGTTGGA 61.206 55.556 33.29 6.82 0.00 3.53
261 262 2.427410 GTTGCGCGCTTGTTGGAG 60.427 61.111 33.29 0.00 0.00 3.86
262 263 2.590291 TTGCGCGCTTGTTGGAGA 60.590 55.556 33.29 5.03 0.00 3.71
263 264 1.965930 TTGCGCGCTTGTTGGAGAT 60.966 52.632 33.29 0.00 0.00 2.75
264 265 1.514678 TTGCGCGCTTGTTGGAGATT 61.515 50.000 33.29 0.00 0.00 2.40
265 266 1.226128 GCGCGCTTGTTGGAGATTC 60.226 57.895 26.67 0.00 0.00 2.52
293 294 8.446599 TCAGTACGTGAGAGACATGATAAATA 57.553 34.615 0.00 0.00 38.72 1.40
294 295 8.899771 TCAGTACGTGAGAGACATGATAAATAA 58.100 33.333 0.00 0.00 38.72 1.40
328 330 7.582667 ACAGTACATTTTTCTAGCAAACCTT 57.417 32.000 0.00 0.00 0.00 3.50
329 331 8.685838 ACAGTACATTTTTCTAGCAAACCTTA 57.314 30.769 0.00 0.00 0.00 2.69
389 394 4.514441 CACAAGACAGAGCAGTGAAAAGAT 59.486 41.667 0.00 0.00 32.14 2.40
390 395 4.754114 ACAAGACAGAGCAGTGAAAAGATC 59.246 41.667 0.00 0.00 0.00 2.75
391 396 4.613925 AGACAGAGCAGTGAAAAGATCA 57.386 40.909 0.00 0.00 35.05 2.92
393 398 4.040217 AGACAGAGCAGTGAAAAGATCAGT 59.960 41.667 0.00 0.00 42.62 3.41
413 419 1.073025 CTACCAGTGCAGCACCCAA 59.927 57.895 22.41 4.69 34.49 4.12
415 421 0.537143 TACCAGTGCAGCACCCAAAG 60.537 55.000 22.41 8.90 34.49 2.77
417 423 1.529010 CAGTGCAGCACCCAAAGGA 60.529 57.895 22.41 0.00 34.49 3.36
418 424 1.108727 CAGTGCAGCACCCAAAGGAA 61.109 55.000 22.41 0.00 34.49 3.36
419 425 0.825010 AGTGCAGCACCCAAAGGAAG 60.825 55.000 22.41 0.00 34.49 3.46
446 452 7.659390 GGAGGATAACATATCTTGAGACTTTGG 59.341 40.741 0.00 0.00 0.00 3.28
489 495 2.029073 CGGTGCCACGACTTGACT 59.971 61.111 0.00 0.00 35.47 3.41
605 618 1.299468 CAGCGCAGAGGGTATCGTC 60.299 63.158 11.47 0.00 0.00 4.20
658 671 1.606668 CGCACACCCAACACAACTATT 59.393 47.619 0.00 0.00 0.00 1.73
934 949 2.764007 TGGCATCCACTCACACTCT 58.236 52.632 0.00 0.00 0.00 3.24
936 951 0.107945 GGCATCCACTCACACTCTCC 60.108 60.000 0.00 0.00 0.00 3.71
939 954 1.480137 CATCCACTCACACTCTCCCTC 59.520 57.143 0.00 0.00 0.00 4.30
943 958 0.540830 ACTCACACTCTCCCTCGCTT 60.541 55.000 0.00 0.00 0.00 4.68
945 960 0.539669 TCACACTCTCCCTCGCTTCA 60.540 55.000 0.00 0.00 0.00 3.02
946 961 0.318441 CACACTCTCCCTCGCTTCAA 59.682 55.000 0.00 0.00 0.00 2.69
947 962 0.318762 ACACTCTCCCTCGCTTCAAC 59.681 55.000 0.00 0.00 0.00 3.18
949 964 1.219393 CTCTCCCTCGCTTCAACCC 59.781 63.158 0.00 0.00 0.00 4.11
950 965 1.229209 TCTCCCTCGCTTCAACCCT 60.229 57.895 0.00 0.00 0.00 4.34
951 966 1.078848 CTCCCTCGCTTCAACCCTG 60.079 63.158 0.00 0.00 0.00 4.45
953 968 2.032528 CCTCGCTTCAACCCTGCA 59.967 61.111 0.00 0.00 0.00 4.41
954 969 1.377725 CCTCGCTTCAACCCTGCAT 60.378 57.895 0.00 0.00 0.00 3.96
955 970 0.107703 CCTCGCTTCAACCCTGCATA 60.108 55.000 0.00 0.00 0.00 3.14
957 972 2.083774 CTCGCTTCAACCCTGCATAAA 58.916 47.619 0.00 0.00 0.00 1.40
958 973 2.083774 TCGCTTCAACCCTGCATAAAG 58.916 47.619 0.00 0.00 0.00 1.85
961 976 2.424956 GCTTCAACCCTGCATAAAGAGG 59.575 50.000 0.00 0.00 0.00 3.69
962 977 3.873801 GCTTCAACCCTGCATAAAGAGGA 60.874 47.826 0.00 0.00 0.00 3.71
991 1007 0.250467 TCTGGCCTGAGCTGAAACAC 60.250 55.000 8.48 0.00 39.73 3.32
1150 1166 3.760035 CGCACGAGGGCTGGTACT 61.760 66.667 0.00 0.00 0.00 2.73
1189 1205 2.364317 CCGGCAAGGAGGAGGAGA 60.364 66.667 0.00 0.00 45.00 3.71
1275 1291 1.226974 GCAGCTCGCGGAGATACAA 60.227 57.895 6.13 0.00 0.00 2.41
1569 1585 1.218047 CAACGGGAAGCTCATCGGA 59.782 57.895 7.31 0.00 0.00 4.55
1581 1597 3.771160 ATCGGAGCGCGGTCCTTT 61.771 61.111 43.42 31.53 34.00 3.11
1809 1825 4.988716 ACCCTGGAGTCCGCGTCA 62.989 66.667 4.92 0.00 0.00 4.35
1983 1999 3.834799 GGGAACGACGGCTCCGAT 61.835 66.667 15.95 0.00 42.83 4.18
2055 2071 0.108138 CCATCGACAGGGAGTTCACC 60.108 60.000 0.00 0.00 0.00 4.02
2058 2074 2.741092 GACAGGGAGTTCACCGCA 59.259 61.111 0.00 0.00 0.00 5.69
2118 2134 0.398696 ACGGCAAATCTGTGTACCCA 59.601 50.000 0.00 0.00 31.81 4.51
2361 2377 2.125147 GTCATGCCGCTGGTGCTA 60.125 61.111 0.00 0.00 36.97 3.49
2488 2504 2.202570 CCGTGGCGTACTTCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
2730 2746 4.314440 GCCATCCGCTCGGCCATA 62.314 66.667 2.24 0.00 42.82 2.74
2739 2755 0.463654 GCTCGGCCATAATGACCACA 60.464 55.000 2.24 0.00 0.00 4.17
2773 2789 0.385473 CAACGCCAACAACGTCATCC 60.385 55.000 0.00 0.00 44.30 3.51
2820 2836 2.754658 CCCCTCGACTACGGCAGT 60.755 66.667 0.00 0.00 41.47 4.40
3144 3160 1.079543 GACGCCATCAGCACTGTCT 60.080 57.895 0.00 0.00 44.04 3.41
3224 3240 3.974719 AGAGAGCAGGAGATGACTACAA 58.025 45.455 0.00 0.00 0.00 2.41
3379 3395 9.492730 AGGATGACCATAGGAAAACAATAAATT 57.507 29.630 0.00 0.00 38.94 1.82
3474 3495 6.108687 TGATGTCAAGTGTATTTAGCCTCTG 58.891 40.000 0.00 0.00 0.00 3.35
3534 3559 4.098501 ACATTTGGCCTAAAATGAGCTAGC 59.901 41.667 26.90 6.62 46.13 3.42
3647 3672 1.826720 TGGAAATCTCAAATGGCTGGC 59.173 47.619 0.00 0.00 0.00 4.85
3650 3675 3.638160 GGAAATCTCAAATGGCTGGCATA 59.362 43.478 17.59 1.36 0.00 3.14
3662 3687 4.903054 TGGCTGGCATATTCTCTATCAAG 58.097 43.478 0.00 0.00 0.00 3.02
3771 3800 9.857656 AGATGTTATTGATATTTCCATGACAGT 57.142 29.630 0.00 0.00 30.35 3.55
3815 3846 4.082245 AGGGCAAAGTGGATGATTTTTACG 60.082 41.667 0.00 0.00 0.00 3.18
3825 3856 9.219603 AGTGGATGATTTTTACGATACATATGG 57.780 33.333 7.80 0.00 0.00 2.74
3848 3879 2.371841 TGATCCATGTCCTAAATCCGGG 59.628 50.000 0.00 0.00 0.00 5.73
3849 3880 2.184088 TCCATGTCCTAAATCCGGGA 57.816 50.000 0.00 0.00 0.00 5.14
3850 3881 2.483547 TCCATGTCCTAAATCCGGGAA 58.516 47.619 0.00 0.00 33.01 3.97
3902 3933 2.610727 GCGTCTAAAGCTTCACTCCAGT 60.611 50.000 0.00 0.00 0.00 4.00
3908 3939 4.439253 AAAGCTTCACTCCAGTACCTTT 57.561 40.909 0.00 0.00 0.00 3.11
3941 3980 8.995220 ACGTGTAGCATTAGACTGAATTTTAAA 58.005 29.630 0.00 0.00 0.00 1.52
4113 4153 3.868077 CAGACGATCCCAGAACTTTGATC 59.132 47.826 0.00 0.00 0.00 2.92
4220 4265 5.068215 ACTGTGCTATACCTCCTCACTAT 57.932 43.478 0.00 0.00 0.00 2.12
4239 4284 8.526667 TCACTATTCTACATAGCTCAAACTCT 57.473 34.615 0.00 0.00 0.00 3.24
4240 4285 8.409371 TCACTATTCTACATAGCTCAAACTCTG 58.591 37.037 0.00 0.00 0.00 3.35
4245 4290 7.468141 TCTACATAGCTCAAACTCTGAAAGA 57.532 36.000 0.00 0.00 43.69 2.52
4257 4302 4.315803 ACTCTGAAAGACACGGTAAATGG 58.684 43.478 0.00 0.00 38.67 3.16
4278 4323 0.036388 TGTAGCCACTAGCCAACAGC 60.036 55.000 0.00 0.00 45.47 4.40
4298 4343 1.449246 CCACTGTAGGAGCAGCTGC 60.449 63.158 31.53 31.53 39.96 5.25
4304 4349 0.801251 GTAGGAGCAGCTGCAACTTG 59.199 55.000 38.24 1.33 45.16 3.16
4305 4350 0.397941 TAGGAGCAGCTGCAACTTGT 59.602 50.000 38.24 18.66 45.16 3.16
4306 4351 1.170919 AGGAGCAGCTGCAACTTGTG 61.171 55.000 38.24 0.00 45.16 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.909550 AGTTCATAGCCTCCTCTACAATAG 57.090 41.667 0.00 0.00 0.00 1.73
1 2 8.394822 AGATAGTTCATAGCCTCCTCTACAATA 58.605 37.037 0.00 0.00 0.00 1.90
2 3 7.245292 AGATAGTTCATAGCCTCCTCTACAAT 58.755 38.462 0.00 0.00 0.00 2.71
3 4 6.615617 AGATAGTTCATAGCCTCCTCTACAA 58.384 40.000 0.00 0.00 0.00 2.41
4 5 6.207509 AGATAGTTCATAGCCTCCTCTACA 57.792 41.667 0.00 0.00 0.00 2.74
5 6 7.832187 ACATAGATAGTTCATAGCCTCCTCTAC 59.168 40.741 0.00 0.00 0.00 2.59
6 7 7.934313 ACATAGATAGTTCATAGCCTCCTCTA 58.066 38.462 0.00 0.00 0.00 2.43
7 8 6.799827 ACATAGATAGTTCATAGCCTCCTCT 58.200 40.000 0.00 0.00 0.00 3.69
8 9 7.067737 GGTACATAGATAGTTCATAGCCTCCTC 59.932 44.444 0.00 0.00 0.00 3.71
9 10 6.893005 GGTACATAGATAGTTCATAGCCTCCT 59.107 42.308 0.00 0.00 0.00 3.69
10 11 6.183360 CGGTACATAGATAGTTCATAGCCTCC 60.183 46.154 0.00 0.00 0.00 4.30
11 12 6.374894 ACGGTACATAGATAGTTCATAGCCTC 59.625 42.308 0.00 0.00 0.00 4.70
12 13 6.246919 ACGGTACATAGATAGTTCATAGCCT 58.753 40.000 0.00 0.00 0.00 4.58
13 14 6.512342 ACGGTACATAGATAGTTCATAGCC 57.488 41.667 0.00 0.00 0.00 3.93
14 15 8.813643 AAAACGGTACATAGATAGTTCATAGC 57.186 34.615 0.00 0.00 0.00 2.97
70 71 8.613482 CGAGGCATAGATAGATAAAACGATAGA 58.387 37.037 0.00 0.00 41.38 1.98
71 72 8.613482 TCGAGGCATAGATAGATAAAACGATAG 58.387 37.037 0.00 0.00 46.19 2.08
72 73 8.502105 TCGAGGCATAGATAGATAAAACGATA 57.498 34.615 0.00 0.00 0.00 2.92
73 74 7.121463 ACTCGAGGCATAGATAGATAAAACGAT 59.879 37.037 18.41 0.00 0.00 3.73
74 75 6.430308 ACTCGAGGCATAGATAGATAAAACGA 59.570 38.462 18.41 0.00 0.00 3.85
75 76 6.613233 ACTCGAGGCATAGATAGATAAAACG 58.387 40.000 18.41 0.00 0.00 3.60
76 77 7.594714 TGACTCGAGGCATAGATAGATAAAAC 58.405 38.462 19.45 0.00 0.00 2.43
77 78 7.665974 TCTGACTCGAGGCATAGATAGATAAAA 59.334 37.037 23.99 0.00 0.00 1.52
78 79 7.168905 TCTGACTCGAGGCATAGATAGATAAA 58.831 38.462 23.99 0.00 0.00 1.40
79 80 6.712276 TCTGACTCGAGGCATAGATAGATAA 58.288 40.000 23.99 0.00 0.00 1.75
80 81 6.070481 ACTCTGACTCGAGGCATAGATAGATA 60.070 42.308 33.40 4.12 35.33 1.98
81 82 5.172687 TCTGACTCGAGGCATAGATAGAT 57.827 43.478 23.99 0.00 0.00 1.98
82 83 4.041075 ACTCTGACTCGAGGCATAGATAGA 59.959 45.833 33.40 20.23 35.33 1.98
83 84 4.323417 ACTCTGACTCGAGGCATAGATAG 58.677 47.826 33.40 21.53 35.33 2.08
84 85 4.359434 ACTCTGACTCGAGGCATAGATA 57.641 45.455 33.40 12.61 35.33 1.98
85 86 3.222173 ACTCTGACTCGAGGCATAGAT 57.778 47.619 33.40 18.25 35.33 1.98
86 87 2.719531 ACTCTGACTCGAGGCATAGA 57.280 50.000 33.40 22.23 35.33 1.98
87 88 3.734463 TCTACTCTGACTCGAGGCATAG 58.266 50.000 27.21 27.21 35.33 2.23
88 89 3.840124 TCTACTCTGACTCGAGGCATA 57.160 47.619 23.99 14.54 35.33 3.14
89 90 2.719531 TCTACTCTGACTCGAGGCAT 57.280 50.000 23.99 10.12 35.33 4.40
90 91 2.360844 CTTCTACTCTGACTCGAGGCA 58.639 52.381 22.21 22.21 35.33 4.75
91 92 1.673920 CCTTCTACTCTGACTCGAGGC 59.326 57.143 18.41 15.78 35.33 4.70
92 93 3.118555 TCTCCTTCTACTCTGACTCGAGG 60.119 52.174 18.41 0.17 35.33 4.63
93 94 4.131649 TCTCCTTCTACTCTGACTCGAG 57.868 50.000 11.84 11.84 37.07 4.04
94 95 4.223255 TCTTCTCCTTCTACTCTGACTCGA 59.777 45.833 0.00 0.00 0.00 4.04
95 96 4.509616 TCTTCTCCTTCTACTCTGACTCG 58.490 47.826 0.00 0.00 0.00 4.18
96 97 6.827586 TTTCTTCTCCTTCTACTCTGACTC 57.172 41.667 0.00 0.00 0.00 3.36
99 100 9.073475 GCTATATTTCTTCTCCTTCTACTCTGA 57.927 37.037 0.00 0.00 0.00 3.27
100 101 8.020819 CGCTATATTTCTTCTCCTTCTACTCTG 58.979 40.741 0.00 0.00 0.00 3.35
101 102 7.308951 GCGCTATATTTCTTCTCCTTCTACTCT 60.309 40.741 0.00 0.00 0.00 3.24
102 103 6.804783 GCGCTATATTTCTTCTCCTTCTACTC 59.195 42.308 0.00 0.00 0.00 2.59
103 104 6.568844 CGCGCTATATTTCTTCTCCTTCTACT 60.569 42.308 5.56 0.00 0.00 2.57
104 105 5.569823 CGCGCTATATTTCTTCTCCTTCTAC 59.430 44.000 5.56 0.00 0.00 2.59
105 106 5.241064 ACGCGCTATATTTCTTCTCCTTCTA 59.759 40.000 5.73 0.00 0.00 2.10
106 107 4.038162 ACGCGCTATATTTCTTCTCCTTCT 59.962 41.667 5.73 0.00 0.00 2.85
107 108 4.299978 ACGCGCTATATTTCTTCTCCTTC 58.700 43.478 5.73 0.00 0.00 3.46
108 109 4.038162 AGACGCGCTATATTTCTTCTCCTT 59.962 41.667 5.73 0.00 0.00 3.36
109 110 3.570550 AGACGCGCTATATTTCTTCTCCT 59.429 43.478 5.73 0.00 0.00 3.69
110 111 3.670991 CAGACGCGCTATATTTCTTCTCC 59.329 47.826 5.73 0.00 0.00 3.71
111 112 3.120451 GCAGACGCGCTATATTTCTTCTC 59.880 47.826 5.73 0.00 0.00 2.87
112 113 3.053455 GCAGACGCGCTATATTTCTTCT 58.947 45.455 5.73 0.00 0.00 2.85
113 114 3.053455 AGCAGACGCGCTATATTTCTTC 58.947 45.455 5.73 0.00 45.49 2.87
114 115 2.797156 CAGCAGACGCGCTATATTTCTT 59.203 45.455 5.73 0.00 45.49 2.52
115 116 2.398498 CAGCAGACGCGCTATATTTCT 58.602 47.619 5.73 0.00 45.49 2.52
116 117 1.457303 CCAGCAGACGCGCTATATTTC 59.543 52.381 5.73 0.00 45.49 2.17
117 118 1.068588 TCCAGCAGACGCGCTATATTT 59.931 47.619 5.73 0.00 45.49 1.40
118 119 0.673985 TCCAGCAGACGCGCTATATT 59.326 50.000 5.73 0.00 45.49 1.28
119 120 0.242286 CTCCAGCAGACGCGCTATAT 59.758 55.000 5.73 0.00 45.49 0.86
120 121 1.654774 CTCCAGCAGACGCGCTATA 59.345 57.895 5.73 0.00 45.49 1.31
121 122 2.415010 CTCCAGCAGACGCGCTAT 59.585 61.111 5.73 0.00 45.49 2.97
122 123 4.498520 GCTCCAGCAGACGCGCTA 62.499 66.667 5.73 0.00 45.49 4.26
145 146 3.597626 GCAAAATGTAGCGCGCGC 61.598 61.111 45.10 45.10 42.33 6.86
146 147 1.795569 TTGCAAAATGTAGCGCGCG 60.796 52.632 28.44 28.44 0.00 6.86
147 148 1.696083 GTTGCAAAATGTAGCGCGC 59.304 52.632 26.66 26.66 0.00 6.86
148 149 0.451957 TCGTTGCAAAATGTAGCGCG 60.452 50.000 0.00 0.00 36.73 6.86
149 150 0.974836 GTCGTTGCAAAATGTAGCGC 59.025 50.000 0.00 0.00 36.73 5.92
150 151 1.602191 GGTCGTTGCAAAATGTAGCG 58.398 50.000 0.00 0.00 37.94 4.26
151 152 1.602191 CGGTCGTTGCAAAATGTAGC 58.398 50.000 0.00 0.00 0.00 3.58
152 153 1.196808 AGCGGTCGTTGCAAAATGTAG 59.803 47.619 0.00 0.00 33.85 2.74
153 154 1.069568 CAGCGGTCGTTGCAAAATGTA 60.070 47.619 0.00 0.00 33.85 2.29
154 155 0.317770 CAGCGGTCGTTGCAAAATGT 60.318 50.000 0.00 0.00 33.85 2.71
155 156 0.040514 TCAGCGGTCGTTGCAAAATG 60.041 50.000 0.00 0.00 33.85 2.32
156 157 0.665835 TTCAGCGGTCGTTGCAAAAT 59.334 45.000 0.00 0.00 33.85 1.82
157 158 0.452184 TTTCAGCGGTCGTTGCAAAA 59.548 45.000 0.00 0.00 33.85 2.44
158 159 0.248296 GTTTCAGCGGTCGTTGCAAA 60.248 50.000 0.00 2.62 33.85 3.68
159 160 1.353804 GTTTCAGCGGTCGTTGCAA 59.646 52.632 0.00 0.00 33.85 4.08
160 161 2.539338 GGTTTCAGCGGTCGTTGCA 61.539 57.895 2.40 0.00 33.85 4.08
161 162 2.251371 GGTTTCAGCGGTCGTTGC 59.749 61.111 2.40 0.00 0.00 4.17
162 163 1.952133 TCGGTTTCAGCGGTCGTTG 60.952 57.895 0.83 0.83 39.89 4.10
163 164 1.952635 GTCGGTTTCAGCGGTCGTT 60.953 57.895 0.00 0.00 39.89 3.85
164 165 2.355481 GTCGGTTTCAGCGGTCGT 60.355 61.111 0.00 0.00 39.89 4.34
165 166 3.467119 CGTCGGTTTCAGCGGTCG 61.467 66.667 0.00 0.00 39.89 4.79
166 167 3.774702 GCGTCGGTTTCAGCGGTC 61.775 66.667 0.00 0.00 39.89 4.79
167 168 3.802418 AAGCGTCGGTTTCAGCGGT 62.802 57.895 3.34 0.00 39.89 5.68
168 169 3.011760 GAAGCGTCGGTTTCAGCGG 62.012 63.158 11.49 0.00 39.89 5.52
169 170 2.470286 GAAGCGTCGGTTTCAGCG 59.530 61.111 11.49 0.00 40.97 5.18
170 171 2.470286 CGAAGCGTCGGTTTCAGC 59.530 61.111 14.59 0.00 43.81 4.26
183 184 3.236816 CCAGTTTTTACATGCTGCGAAG 58.763 45.455 0.00 0.00 0.00 3.79
184 185 2.606795 GCCAGTTTTTACATGCTGCGAA 60.607 45.455 0.00 0.00 0.00 4.70
185 186 1.068610 GCCAGTTTTTACATGCTGCGA 60.069 47.619 0.00 0.00 0.00 5.10
186 187 1.068333 AGCCAGTTTTTACATGCTGCG 60.068 47.619 0.00 0.00 0.00 5.18
187 188 2.730550 AGCCAGTTTTTACATGCTGC 57.269 45.000 0.00 0.00 0.00 5.25
188 189 3.435327 TCGTAGCCAGTTTTTACATGCTG 59.565 43.478 0.00 0.00 0.00 4.41
189 190 3.670625 TCGTAGCCAGTTTTTACATGCT 58.329 40.909 0.00 0.00 0.00 3.79
190 191 4.403453 CTTCGTAGCCAGTTTTTACATGC 58.597 43.478 0.00 0.00 0.00 4.06
191 192 4.671766 GCCTTCGTAGCCAGTTTTTACATG 60.672 45.833 0.00 0.00 0.00 3.21
192 193 3.439129 GCCTTCGTAGCCAGTTTTTACAT 59.561 43.478 0.00 0.00 0.00 2.29
193 194 2.809696 GCCTTCGTAGCCAGTTTTTACA 59.190 45.455 0.00 0.00 0.00 2.41
194 195 2.159747 CGCCTTCGTAGCCAGTTTTTAC 60.160 50.000 0.00 0.00 0.00 2.01
195 196 2.070783 CGCCTTCGTAGCCAGTTTTTA 58.929 47.619 0.00 0.00 0.00 1.52
196 197 0.872388 CGCCTTCGTAGCCAGTTTTT 59.128 50.000 0.00 0.00 0.00 1.94
197 198 1.574702 GCGCCTTCGTAGCCAGTTTT 61.575 55.000 0.00 0.00 38.14 2.43
198 199 2.033194 GCGCCTTCGTAGCCAGTTT 61.033 57.895 0.00 0.00 38.14 2.66
199 200 2.434359 GCGCCTTCGTAGCCAGTT 60.434 61.111 0.00 0.00 38.14 3.16
200 201 3.382832 AGCGCCTTCGTAGCCAGT 61.383 61.111 2.29 0.00 38.14 4.00
201 202 2.279502 TACAGCGCCTTCGTAGCCAG 62.280 60.000 2.29 0.00 38.14 4.85
202 203 1.879737 TTACAGCGCCTTCGTAGCCA 61.880 55.000 2.29 0.00 38.14 4.75
203 204 0.738412 TTTACAGCGCCTTCGTAGCC 60.738 55.000 2.29 0.00 38.14 3.93
204 205 0.369248 GTTTACAGCGCCTTCGTAGC 59.631 55.000 2.29 0.00 38.14 3.58
205 206 0.638746 CGTTTACAGCGCCTTCGTAG 59.361 55.000 2.29 0.00 38.14 3.51
206 207 2.728132 CGTTTACAGCGCCTTCGTA 58.272 52.632 2.29 0.00 38.14 3.43
207 208 3.545911 CGTTTACAGCGCCTTCGT 58.454 55.556 2.29 0.00 38.14 3.85
242 243 3.024043 CCAACAAGCGCGCAACAC 61.024 61.111 35.10 2.51 0.00 3.32
243 244 3.179869 CTCCAACAAGCGCGCAACA 62.180 57.895 35.10 8.28 0.00 3.33
244 245 2.187599 ATCTCCAACAAGCGCGCAAC 62.188 55.000 35.10 3.43 0.00 4.17
245 246 1.514678 AATCTCCAACAAGCGCGCAA 61.515 50.000 35.10 8.04 0.00 4.85
246 247 1.911293 GAATCTCCAACAAGCGCGCA 61.911 55.000 35.10 9.50 0.00 6.09
247 248 1.226128 GAATCTCCAACAAGCGCGC 60.226 57.895 26.66 26.66 0.00 6.86
248 249 0.371645 GAGAATCTCCAACAAGCGCG 59.628 55.000 0.00 0.00 0.00 6.86
296 297 9.642327 TGCTAGAAAAATGTACTGTACGATTTA 57.358 29.630 19.22 4.00 0.00 1.40
297 298 8.542497 TGCTAGAAAAATGTACTGTACGATTT 57.458 30.769 12.87 14.75 0.00 2.17
298 299 8.542497 TTGCTAGAAAAATGTACTGTACGATT 57.458 30.769 12.87 10.47 0.00 3.34
299 300 8.440833 GTTTGCTAGAAAAATGTACTGTACGAT 58.559 33.333 12.87 5.50 0.00 3.73
300 301 7.095523 GGTTTGCTAGAAAAATGTACTGTACGA 60.096 37.037 12.87 3.48 0.00 3.43
301 302 7.013529 GGTTTGCTAGAAAAATGTACTGTACG 58.986 38.462 12.87 0.00 0.00 3.67
302 303 8.095937 AGGTTTGCTAGAAAAATGTACTGTAC 57.904 34.615 10.98 10.98 0.00 2.90
303 304 8.685838 AAGGTTTGCTAGAAAAATGTACTGTA 57.314 30.769 0.00 0.00 0.00 2.74
304 305 7.582667 AAGGTTTGCTAGAAAAATGTACTGT 57.417 32.000 0.00 0.00 0.00 3.55
305 306 8.784043 ACTAAGGTTTGCTAGAAAAATGTACTG 58.216 33.333 0.00 0.00 0.00 2.74
306 307 8.919777 ACTAAGGTTTGCTAGAAAAATGTACT 57.080 30.769 0.00 0.00 0.00 2.73
395 400 0.537143 TTTGGGTGCTGCACTGGTAG 60.537 55.000 29.54 0.00 34.40 3.18
396 401 0.537143 CTTTGGGTGCTGCACTGGTA 60.537 55.000 29.54 13.68 34.40 3.25
397 402 1.829533 CTTTGGGTGCTGCACTGGT 60.830 57.895 29.54 0.00 34.40 4.00
398 403 2.567497 CCTTTGGGTGCTGCACTGG 61.567 63.158 29.54 19.39 34.40 4.00
399 404 1.108727 TTCCTTTGGGTGCTGCACTG 61.109 55.000 29.54 15.30 34.40 3.66
413 419 6.851836 TCAAGATATGTTATCCTCCCTTCCTT 59.148 38.462 0.00 0.00 0.00 3.36
415 421 6.498651 TCTCAAGATATGTTATCCTCCCTTCC 59.501 42.308 0.00 0.00 0.00 3.46
417 423 7.079048 AGTCTCAAGATATGTTATCCTCCCTT 58.921 38.462 0.00 0.00 0.00 3.95
418 424 6.629156 AGTCTCAAGATATGTTATCCTCCCT 58.371 40.000 0.00 0.00 0.00 4.20
419 425 6.926630 AGTCTCAAGATATGTTATCCTCCC 57.073 41.667 0.00 0.00 0.00 4.30
421 427 7.659390 CCCAAAGTCTCAAGATATGTTATCCTC 59.341 40.741 0.00 0.00 0.00 3.71
422 428 7.348274 TCCCAAAGTCTCAAGATATGTTATCCT 59.652 37.037 0.00 0.00 0.00 3.24
468 474 4.003788 AAGTCGTGGCACCGAGGG 62.004 66.667 12.86 0.00 37.56 4.30
469 475 2.738521 CAAGTCGTGGCACCGAGG 60.739 66.667 12.86 0.00 37.56 4.63
489 495 1.057636 GCACTCGTCATTTCGTTCGA 58.942 50.000 0.00 0.00 0.00 3.71
512 518 5.889425 CGTTAAATCTTACTCGACAATTCGC 59.111 40.000 0.00 0.00 45.46 4.70
593 599 0.549950 TTCCTCCGACGATACCCTCT 59.450 55.000 0.00 0.00 0.00 3.69
605 618 2.034066 TGGCCTTGCTTTCCTCCG 59.966 61.111 3.32 0.00 0.00 4.63
898 913 2.140792 ACAAGTGGAGGGCACTCGT 61.141 57.895 10.51 0.00 44.93 4.18
934 949 3.068881 CAGGGTTGAAGCGAGGGA 58.931 61.111 0.00 0.00 0.00 4.20
936 951 0.107703 TATGCAGGGTTGAAGCGAGG 60.108 55.000 0.00 0.00 0.00 4.63
939 954 2.083774 TCTTTATGCAGGGTTGAAGCG 58.916 47.619 0.00 0.00 0.00 4.68
943 958 2.239654 CCTCCTCTTTATGCAGGGTTGA 59.760 50.000 0.00 0.00 0.00 3.18
945 960 2.562296 TCCTCCTCTTTATGCAGGGTT 58.438 47.619 0.00 0.00 0.00 4.11
946 961 2.270434 TCCTCCTCTTTATGCAGGGT 57.730 50.000 0.00 0.00 0.00 4.34
947 962 2.774234 TCTTCCTCCTCTTTATGCAGGG 59.226 50.000 0.00 0.00 0.00 4.45
949 964 3.452474 CGTCTTCCTCCTCTTTATGCAG 58.548 50.000 0.00 0.00 0.00 4.41
950 965 2.418746 GCGTCTTCCTCCTCTTTATGCA 60.419 50.000 0.00 0.00 0.00 3.96
951 966 2.159028 AGCGTCTTCCTCCTCTTTATGC 60.159 50.000 0.00 0.00 0.00 3.14
953 968 3.383185 CAGAGCGTCTTCCTCCTCTTTAT 59.617 47.826 0.00 0.00 32.65 1.40
954 969 2.755655 CAGAGCGTCTTCCTCCTCTTTA 59.244 50.000 0.00 0.00 32.65 1.85
955 970 1.548269 CAGAGCGTCTTCCTCCTCTTT 59.452 52.381 0.00 0.00 32.65 2.52
957 972 0.682855 CCAGAGCGTCTTCCTCCTCT 60.683 60.000 0.00 0.00 35.17 3.69
958 973 1.813192 CCAGAGCGTCTTCCTCCTC 59.187 63.158 0.00 0.00 0.00 3.71
961 976 2.185608 GGCCAGAGCGTCTTCCTC 59.814 66.667 0.00 0.00 41.24 3.71
962 977 2.284258 AGGCCAGAGCGTCTTCCT 60.284 61.111 5.01 0.00 41.24 3.36
991 1007 2.274437 CTGATGGTTCATCGTGTCAGG 58.726 52.381 3.83 0.00 43.14 3.86
1150 1166 4.379143 CGACGACAGCACCGACGA 62.379 66.667 10.34 0.00 44.84 4.20
1173 1189 2.896443 GTCTCCTCCTCCTTGCCG 59.104 66.667 0.00 0.00 0.00 5.69
1197 1213 0.791983 CGTACGTGTACAGGTGCTCG 60.792 60.000 27.04 22.59 37.97 5.03
1275 1291 4.741239 ACGTGCCCCTCCATCCCT 62.741 66.667 0.00 0.00 0.00 4.20
1569 1585 1.741770 CTTGCTAAAGGACCGCGCT 60.742 57.895 5.56 0.00 0.00 5.92
1581 1597 1.300963 CTGCTTGAGGGCCTTGCTA 59.699 57.895 21.57 11.36 0.00 3.49
1776 1792 2.637383 GGTGTCGCCCGAGAAGACT 61.637 63.158 0.00 0.00 36.01 3.24
1929 1945 0.627451 AGATTCCCTTCTGCATGGCA 59.373 50.000 0.00 0.00 36.92 4.92
2088 2104 0.749454 ATTTGCCGTGGATGCTCCTC 60.749 55.000 4.21 0.36 37.46 3.71
2090 2106 0.749454 AGATTTGCCGTGGATGCTCC 60.749 55.000 0.00 0.00 36.96 4.70
2118 2134 2.507992 GCGATCGCTGTGTGCTCT 60.508 61.111 31.94 0.00 40.11 4.09
2187 2203 2.496817 CGGCTCAGGCTGGAGTAC 59.503 66.667 15.73 7.48 40.90 2.73
2246 2262 1.765657 ATCTGCTCCCTGAGGCTCC 60.766 63.158 12.86 0.00 0.00 4.70
2301 2317 0.957395 CCTTCATGTTGCTGGCGACT 60.957 55.000 13.25 0.00 0.00 4.18
2303 2319 0.250684 TTCCTTCATGTTGCTGGCGA 60.251 50.000 0.00 0.00 0.00 5.54
2730 2746 0.973632 TCACGTAGGCTGTGGTCATT 59.026 50.000 0.00 0.00 37.91 2.57
2739 2755 0.038526 CGTTGTCCTTCACGTAGGCT 60.039 55.000 0.00 0.00 35.15 4.58
2773 2789 1.944709 TGATCGATTTGGCATGCTGAG 59.055 47.619 18.92 3.89 0.00 3.35
2805 2821 2.490217 CCACTGCCGTAGTCGAGG 59.510 66.667 0.00 0.00 37.60 4.63
2921 2937 3.147595 TCACGGCCGCTATCTGCT 61.148 61.111 28.58 0.00 40.11 4.24
2973 2989 2.370849 TGGGTAGTTCAGGTCAAGGTTC 59.629 50.000 0.00 0.00 0.00 3.62
3006 3022 0.319555 ACGTCGTGTGGTTGAGGATG 60.320 55.000 0.00 0.00 0.00 3.51
3144 3160 1.047596 TGCTGCCTTTGCCTCCAAAA 61.048 50.000 0.00 0.00 40.21 2.44
3192 3208 0.324285 CTGCTCTCTTCACCTGGCTT 59.676 55.000 0.00 0.00 0.00 4.35
3224 3240 3.825908 ACCCATGGTTTCCAATGTAGT 57.174 42.857 11.73 0.00 36.95 2.73
3494 3518 7.255208 GGCCAAATGTGATTTGTTGAGATTTTT 60.255 33.333 0.00 0.00 46.22 1.94
3496 3520 5.702209 GGCCAAATGTGATTTGTTGAGATTT 59.298 36.000 0.00 0.00 46.22 2.17
3497 3521 5.012354 AGGCCAAATGTGATTTGTTGAGATT 59.988 36.000 5.01 0.00 46.22 2.40
3498 3522 4.529377 AGGCCAAATGTGATTTGTTGAGAT 59.471 37.500 5.01 0.00 46.22 2.75
3534 3559 5.703978 TCAAACTGGTGGAATATGTGTTG 57.296 39.130 0.00 0.00 0.00 3.33
3647 3672 9.127006 CGATCACTGTTCTTGATAGAGAATATG 57.873 37.037 0.00 0.00 37.91 1.78
3650 3675 6.097554 ACCGATCACTGTTCTTGATAGAGAAT 59.902 38.462 0.00 0.00 37.91 2.40
3662 3687 4.650754 ATACTGGTACCGATCACTGTTC 57.349 45.455 7.57 0.00 0.00 3.18
3724 3753 5.620206 TCTGGAAAAGCAGACAATCACTTA 58.380 37.500 0.00 0.00 0.00 2.24
3771 3800 9.303116 TGCCCTTTTCTGAAGTATTATTTGTAA 57.697 29.630 0.00 0.00 0.00 2.41
3825 3856 4.256920 CCGGATTTAGGACATGGATCATC 58.743 47.826 0.00 0.00 0.00 2.92
3868 3899 1.552578 TAGACGCAGGTGGTGTATGT 58.447 50.000 0.00 0.00 41.19 2.29
3869 3900 2.665649 TTAGACGCAGGTGGTGTATG 57.334 50.000 0.00 0.00 41.19 2.39
3872 3903 0.602905 GCTTTAGACGCAGGTGGTGT 60.603 55.000 0.00 0.00 44.56 4.16
3902 3933 3.132925 GCTACACGTGGTTTCAAAGGTA 58.867 45.455 21.57 0.00 0.00 3.08
3908 3939 3.991773 GTCTAATGCTACACGTGGTTTCA 59.008 43.478 21.57 12.04 0.00 2.69
3941 3980 4.074970 CTCTGAAGTTGTGTGGGCTTTAT 58.925 43.478 0.00 0.00 0.00 1.40
4199 4239 5.772672 AGAATAGTGAGGAGGTATAGCACAG 59.227 44.000 4.48 0.00 32.16 3.66
4220 4265 7.815068 GTCTTTCAGAGTTTGAGCTATGTAGAA 59.185 37.037 0.00 0.00 37.07 2.10
4239 4284 4.647611 ACATCCATTTACCGTGTCTTTCA 58.352 39.130 0.00 0.00 0.00 2.69
4240 4285 5.220605 GCTACATCCATTTACCGTGTCTTTC 60.221 44.000 0.00 0.00 0.00 2.62
4245 4290 2.237643 TGGCTACATCCATTTACCGTGT 59.762 45.455 0.00 0.00 0.00 4.49
4257 4302 2.691409 TGTTGGCTAGTGGCTACATC 57.309 50.000 2.02 0.00 45.65 3.06
4278 4323 0.390866 CAGCTGCTCCTACAGTGGTG 60.391 60.000 0.00 0.00 39.96 4.17


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

AutoCloner maintained by Alex Coulton.