Multiple sequence alignment - TraesCS7D01G468200

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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 TraesCS7D01G468200 chr7D 100.000 2876 0 0 1 2876 581451646 581454521 0.000000e+00 5312.0
1 TraesCS7D01G468200 chr7D 85.714 2380 221 49 590 2876 581289597 581291950 0.000000e+00 2401.0
2 TraesCS7D01G468200 chr7D 92.575 1468 59 11 476 1894 581384395 581385861 0.000000e+00 2061.0
3 TraesCS7D01G468200 chr7D 83.258 1105 136 25 1491 2565 581431517 581432602 0.000000e+00 970.0
4 TraesCS7D01G468200 chr7D 95.167 538 24 2 2341 2876 581389604 581390141 0.000000e+00 848.0
5 TraesCS7D01G468200 chr7D 82.812 960 131 21 1626 2565 581297667 581298612 0.000000e+00 828.0
6 TraesCS7D01G468200 chr7D 85.980 592 52 12 1186 1753 581297090 581297674 3.170000e-169 604.0
7 TraesCS7D01G468200 chr7D 94.536 366 15 4 2401 2765 581386447 581386808 6.960000e-156 560.0
8 TraesCS7D01G468200 chr7D 93.458 107 6 1 1 107 581384259 581384364 1.070000e-34 158.0
9 TraesCS7D01G468200 chr7D 96.203 79 3 0 2798 2876 581690342 581690420 2.330000e-26 130.0
10 TraesCS7D01G468200 chr7A 96.972 2510 45 5 397 2876 673243639 673246147 0.000000e+00 4185.0
11 TraesCS7D01G468200 chr7A 86.113 2362 226 49 592 2864 673126438 673128786 0.000000e+00 2451.0
12 TraesCS7D01G468200 chr7A 85.144 626 41 21 1186 1774 673133168 673133778 6.860000e-166 593.0
13 TraesCS7D01G468200 chr7A 92.523 107 8 0 1 107 673243547 673243653 1.380000e-33 154.0
14 TraesCS7D01G468200 chr7A 92.405 79 6 0 2798 2876 673315536 673315614 2.340000e-21 113.0
15 TraesCS7D01G468200 chr7B 85.364 2364 249 47 590 2876 648916557 648918900 0.000000e+00 2359.0
16 TraesCS7D01G468200 chr7B 92.842 1453 54 15 491 1894 649013322 649014773 0.000000e+00 2061.0
17 TraesCS7D01G468200 chr7B 94.499 1127 47 6 1761 2876 649212603 649213725 0.000000e+00 1724.0
18 TraesCS7D01G468200 chr7B 94.400 1125 50 4 1761 2876 649014765 649015885 0.000000e+00 1716.0
19 TraesCS7D01G468200 chr7B 92.633 923 52 6 1762 2674 649098348 649099264 0.000000e+00 1314.0
20 TraesCS7D01G468200 chr7B 86.140 1140 122 15 719 1831 648783030 648784160 0.000000e+00 1197.0
21 TraesCS7D01G468200 chr7B 76.694 2111 320 99 611 2599 649247349 649249409 0.000000e+00 1014.0
22 TraesCS7D01G468200 chr7B 90.934 739 40 8 1174 1894 649097626 649098355 0.000000e+00 968.0
23 TraesCS7D01G468200 chr7B 94.797 615 31 1 587 1201 649211317 649211930 0.000000e+00 957.0
24 TraesCS7D01G468200 chr7B 94.003 617 34 1 1278 1894 649211998 649212611 0.000000e+00 931.0
25 TraesCS7D01G468200 chr7B 87.717 635 51 12 1369 1988 648925942 648926564 0.000000e+00 715.0
26 TraesCS7D01G468200 chr7B 90.722 291 27 0 106 396 634277385 634277095 3.480000e-104 388.0
27 TraesCS7D01G468200 chr7B 96.835 158 5 0 2719 2876 649099260 649099417 6.110000e-67 265.0
28 TraesCS7D01G468200 chr7B 98.734 79 1 0 2798 2876 649319789 649319867 1.070000e-29 141.0
29 TraesCS7D01G468200 chr7B 89.189 111 8 3 1 107 649013175 649013285 5.000000e-28 135.0
30 TraesCS7D01G468200 chr7B 93.617 47 3 0 1232 1278 649211934 649211980 1.430000e-08 71.3
31 TraesCS7D01G468200 chr2D 89.967 299 28 2 107 403 611247961 611247663 4.500000e-103 385.0
32 TraesCS7D01G468200 chr1D 90.657 289 27 0 107 395 326788263 326787975 4.500000e-103 385.0
33 TraesCS7D01G468200 chr5D 90.411 292 25 3 107 396 339717242 339716952 5.810000e-102 381.0
34 TraesCS7D01G468200 chr5D 88.776 294 31 2 107 399 483234411 483234119 2.720000e-95 359.0
35 TraesCS7D01G468200 chr3D 90.681 279 24 2 102 380 8384855 8384579 1.260000e-98 370.0
36 TraesCS7D01G468200 chr3B 89.003 291 30 1 108 396 723513337 723513047 2.720000e-95 359.0
37 TraesCS7D01G468200 chr3B 89.003 291 29 3 107 396 598993791 598993503 9.800000e-95 357.0
38 TraesCS7D01G468200 chr2A 88.079 302 33 3 104 404 750552242 750552541 3.520000e-94 355.0


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 TraesCS7D01G468200 chr7D 581451646 581454521 2875 False 5312.000 5312 100.000000 1 2876 1 chr7D.!!$F3 2875
1 TraesCS7D01G468200 chr7D 581289597 581291950 2353 False 2401.000 2401 85.714000 590 2876 1 chr7D.!!$F1 2286
2 TraesCS7D01G468200 chr7D 581431517 581432602 1085 False 970.000 970 83.258000 1491 2565 1 chr7D.!!$F2 1074
3 TraesCS7D01G468200 chr7D 581384259 581390141 5882 False 906.750 2061 93.934000 1 2876 4 chr7D.!!$F6 2875
4 TraesCS7D01G468200 chr7D 581297090 581298612 1522 False 716.000 828 84.396000 1186 2565 2 chr7D.!!$F5 1379
5 TraesCS7D01G468200 chr7A 673126438 673128786 2348 False 2451.000 2451 86.113000 592 2864 1 chr7A.!!$F1 2272
6 TraesCS7D01G468200 chr7A 673243547 673246147 2600 False 2169.500 4185 94.747500 1 2876 2 chr7A.!!$F4 2875
7 TraesCS7D01G468200 chr7A 673133168 673133778 610 False 593.000 593 85.144000 1186 1774 1 chr7A.!!$F2 588
8 TraesCS7D01G468200 chr7B 648916557 648918900 2343 False 2359.000 2359 85.364000 590 2876 1 chr7B.!!$F2 2286
9 TraesCS7D01G468200 chr7B 649013175 649015885 2710 False 1304.000 2061 92.143667 1 2876 3 chr7B.!!$F6 2875
10 TraesCS7D01G468200 chr7B 648783030 648784160 1130 False 1197.000 1197 86.140000 719 1831 1 chr7B.!!$F1 1112
11 TraesCS7D01G468200 chr7B 649247349 649249409 2060 False 1014.000 1014 76.694000 611 2599 1 chr7B.!!$F4 1988
12 TraesCS7D01G468200 chr7B 649211317 649213725 2408 False 920.825 1724 94.229000 587 2876 4 chr7B.!!$F8 2289
13 TraesCS7D01G468200 chr7B 649097626 649099417 1791 False 849.000 1314 93.467333 1174 2876 3 chr7B.!!$F7 1702
14 TraesCS7D01G468200 chr7B 648925942 648926564 622 False 715.000 715 87.717000 1369 1988 1 chr7B.!!$F3 619

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
300 305 0.040692 CTCCCATTGAATGCGCATCG 60.041 55.0 25.53 9.81 0.0 3.84 F
364 369 0.109342 GTGGGCTGGGGATATCACAG 59.891 60.0 17.64 17.64 35.4 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1459 1648 1.628846 GAAGTTAGTCCTTGCTCCCCA 59.371 52.381 0.0 0.0 0.00 4.96 R
2078 2889 2.835156 TGTATCACAATCTCCCGTTGGA 59.165 45.455 0.0 0.0 38.75 3.53 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
29 30 1.343465 GGTTCCCTCAAGAACGACTCA 59.657 52.381 0.00 0.00 45.82 3.41
41 42 5.890424 AGAACGACTCAAAAACTCCAAAA 57.110 34.783 0.00 0.00 0.00 2.44
91 96 8.630037 ACGAAATCTGTAAAAACAAAGGATCTT 58.370 29.630 0.00 0.00 0.00 2.40
92 97 9.118236 CGAAATCTGTAAAAACAAAGGATCTTC 57.882 33.333 0.00 0.00 0.00 2.87
93 98 9.411801 GAAATCTGTAAAAACAAAGGATCTTCC 57.588 33.333 0.00 0.00 36.58 3.46
94 99 8.477419 AATCTGTAAAAACAAAGGATCTTCCA 57.523 30.769 0.00 0.00 39.61 3.53
95 100 8.655935 ATCTGTAAAAACAAAGGATCTTCCAT 57.344 30.769 0.00 0.00 39.61 3.41
96 101 8.477419 TCTGTAAAAACAAAGGATCTTCCATT 57.523 30.769 0.00 0.00 39.61 3.16
97 102 8.923270 TCTGTAAAAACAAAGGATCTTCCATTT 58.077 29.630 0.00 0.00 39.61 2.32
102 107 7.709149 AAACAAAGGATCTTCCATTTAGAGG 57.291 36.000 0.00 0.00 39.61 3.69
103 108 6.642733 ACAAAGGATCTTCCATTTAGAGGA 57.357 37.500 0.00 0.00 39.61 3.71
104 109 7.218314 ACAAAGGATCTTCCATTTAGAGGAT 57.782 36.000 0.00 0.00 39.61 3.24
105 110 7.286313 ACAAAGGATCTTCCATTTAGAGGATC 58.714 38.462 5.38 5.38 44.50 3.36
106 111 7.128573 ACAAAGGATCTTCCATTTAGAGGATCT 59.871 37.037 11.81 0.00 44.58 2.75
107 112 7.704359 AAGGATCTTCCATTTAGAGGATCTT 57.296 36.000 11.81 3.73 40.77 2.40
108 113 7.704359 AGGATCTTCCATTTAGAGGATCTTT 57.296 36.000 11.81 1.44 40.77 2.52
109 114 8.111928 AGGATCTTCCATTTAGAGGATCTTTT 57.888 34.615 11.81 0.00 40.77 2.27
110 115 8.564370 AGGATCTTCCATTTAGAGGATCTTTTT 58.436 33.333 11.81 0.00 40.77 1.94
134 139 5.673337 TTAACATCAGTTCTGACACAAGC 57.327 39.130 4.58 0.00 39.15 4.01
135 140 2.138320 ACATCAGTTCTGACACAAGCG 58.862 47.619 4.58 0.00 0.00 4.68
136 141 1.136141 CATCAGTTCTGACACAAGCGC 60.136 52.381 0.00 0.00 0.00 5.92
137 142 0.104855 TCAGTTCTGACACAAGCGCT 59.895 50.000 2.64 2.64 0.00 5.92
138 143 0.510359 CAGTTCTGACACAAGCGCTC 59.490 55.000 12.06 0.00 0.00 5.03
139 144 0.104855 AGTTCTGACACAAGCGCTCA 59.895 50.000 12.06 2.61 0.00 4.26
140 145 1.151668 GTTCTGACACAAGCGCTCAT 58.848 50.000 12.06 0.00 0.00 2.90
141 146 2.029020 AGTTCTGACACAAGCGCTCATA 60.029 45.455 12.06 0.00 0.00 2.15
142 147 2.932614 GTTCTGACACAAGCGCTCATAT 59.067 45.455 12.06 0.00 0.00 1.78
143 148 4.112634 GTTCTGACACAAGCGCTCATATA 58.887 43.478 12.06 0.00 0.00 0.86
144 149 3.706698 TCTGACACAAGCGCTCATATAC 58.293 45.455 12.06 1.70 0.00 1.47
145 150 3.130340 TCTGACACAAGCGCTCATATACA 59.870 43.478 12.06 6.68 0.00 2.29
146 151 3.186909 TGACACAAGCGCTCATATACAC 58.813 45.455 12.06 0.00 0.00 2.90
147 152 2.193447 ACACAAGCGCTCATATACACG 58.807 47.619 12.06 0.00 0.00 4.49
151 156 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
152 157 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
153 158 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
154 159 1.317611 CGCTCATATACACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
155 160 2.324860 GCTCATATACACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
156 161 2.090658 GCTCATATACACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
157 162 3.565516 CTCATATACACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
158 163 3.561503 TCATATACACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
159 164 3.003897 TCATATACACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
160 165 2.509052 ATACACGCGCATACACTCAT 57.491 45.000 5.73 0.00 0.00 2.90
161 166 2.287393 TACACGCGCATACACTCATT 57.713 45.000 5.73 0.00 0.00 2.57
162 167 0.999406 ACACGCGCATACACTCATTC 59.001 50.000 5.73 0.00 0.00 2.67
163 168 0.301687 CACGCGCATACACTCATTCC 59.698 55.000 5.73 0.00 0.00 3.01
164 169 0.175760 ACGCGCATACACTCATTCCT 59.824 50.000 5.73 0.00 0.00 3.36
165 170 1.407618 ACGCGCATACACTCATTCCTA 59.592 47.619 5.73 0.00 0.00 2.94
166 171 2.035961 ACGCGCATACACTCATTCCTAT 59.964 45.455 5.73 0.00 0.00 2.57
167 172 2.409715 CGCGCATACACTCATTCCTATG 59.590 50.000 8.75 0.00 0.00 2.23
168 173 3.653344 GCGCATACACTCATTCCTATGA 58.347 45.455 0.30 0.00 38.45 2.15
169 174 4.058124 GCGCATACACTCATTCCTATGAA 58.942 43.478 0.30 0.00 40.17 2.57
170 175 4.084328 GCGCATACACTCATTCCTATGAAC 60.084 45.833 0.30 0.00 40.17 3.18
171 176 4.148871 CGCATACACTCATTCCTATGAACG 59.851 45.833 0.00 0.00 40.17 3.95
172 177 4.084328 GCATACACTCATTCCTATGAACGC 60.084 45.833 0.00 0.00 40.17 4.84
173 178 3.610040 ACACTCATTCCTATGAACGCA 57.390 42.857 0.00 0.00 40.17 5.24
174 179 3.262420 ACACTCATTCCTATGAACGCAC 58.738 45.455 0.00 0.00 40.17 5.34
175 180 3.261580 CACTCATTCCTATGAACGCACA 58.738 45.455 0.00 0.00 40.17 4.57
176 181 3.873361 CACTCATTCCTATGAACGCACAT 59.127 43.478 0.94 0.94 40.17 3.21
177 182 5.049828 CACTCATTCCTATGAACGCACATA 58.950 41.667 2.94 2.94 40.17 2.29
178 183 5.698089 CACTCATTCCTATGAACGCACATAT 59.302 40.000 3.29 0.00 40.17 1.78
179 184 5.698089 ACTCATTCCTATGAACGCACATATG 59.302 40.000 0.00 0.00 40.17 1.78
180 185 4.452114 TCATTCCTATGAACGCACATATGC 59.548 41.667 1.58 0.00 41.96 3.14
181 186 4.213906 CATTCCTATGAACGCACATATGCA 59.786 41.667 1.58 0.00 42.17 3.96
182 187 4.214119 ATTCCTATGAACGCACATATGCAC 59.786 41.667 1.58 0.00 41.74 4.57
183 188 6.202969 ATTCCTATGAACGCACATATGCACA 61.203 40.000 1.58 0.00 41.74 4.57
184 189 7.464769 ATTCCTATGAACGCACATATGCACAT 61.465 38.462 1.58 1.34 41.74 3.21
185 190 9.165287 ATTCCTATGAACGCACATATGCACATC 62.165 40.741 1.58 0.00 41.74 3.06
192 197 1.800586 CACATATGCACATCCTACCGC 59.199 52.381 1.58 0.00 0.00 5.68
193 198 1.694150 ACATATGCACATCCTACCGCT 59.306 47.619 1.58 0.00 0.00 5.52
194 199 2.897326 ACATATGCACATCCTACCGCTA 59.103 45.455 1.58 0.00 0.00 4.26
195 200 3.515502 ACATATGCACATCCTACCGCTAT 59.484 43.478 1.58 0.00 0.00 2.97
196 201 2.462456 ATGCACATCCTACCGCTATG 57.538 50.000 0.00 0.00 0.00 2.23
197 202 1.408969 TGCACATCCTACCGCTATGA 58.591 50.000 0.00 0.00 0.00 2.15
198 203 1.341209 TGCACATCCTACCGCTATGAG 59.659 52.381 0.00 0.00 0.00 2.90
199 204 1.937108 GCACATCCTACCGCTATGAGC 60.937 57.143 0.00 0.00 38.02 4.26
200 205 1.341209 CACATCCTACCGCTATGAGCA 59.659 52.381 0.00 0.00 42.58 4.26
201 206 2.028658 CACATCCTACCGCTATGAGCAT 60.029 50.000 0.00 0.00 42.58 3.79
202 207 2.232452 ACATCCTACCGCTATGAGCATC 59.768 50.000 0.00 0.00 42.58 3.91
203 208 2.294449 TCCTACCGCTATGAGCATCT 57.706 50.000 0.00 0.00 42.58 2.90
204 209 2.163509 TCCTACCGCTATGAGCATCTC 58.836 52.381 0.00 0.00 42.58 2.75
205 210 1.203523 CCTACCGCTATGAGCATCTCC 59.796 57.143 0.00 0.00 42.58 3.71
206 211 0.881796 TACCGCTATGAGCATCTCCG 59.118 55.000 0.00 0.00 42.58 4.63
207 212 0.823769 ACCGCTATGAGCATCTCCGA 60.824 55.000 0.00 0.00 42.58 4.55
208 213 0.315251 CCGCTATGAGCATCTCCGAA 59.685 55.000 0.00 0.00 42.58 4.30
209 214 1.269778 CCGCTATGAGCATCTCCGAAA 60.270 52.381 0.00 0.00 42.58 3.46
210 215 2.057316 CGCTATGAGCATCTCCGAAAG 58.943 52.381 0.00 0.00 42.58 2.62
211 216 2.287849 CGCTATGAGCATCTCCGAAAGA 60.288 50.000 0.00 0.00 42.58 2.52
212 217 3.056304 GCTATGAGCATCTCCGAAAGAC 58.944 50.000 0.00 0.00 41.89 3.01
213 218 3.243704 GCTATGAGCATCTCCGAAAGACT 60.244 47.826 0.00 0.00 41.89 3.24
214 219 2.662006 TGAGCATCTCCGAAAGACTG 57.338 50.000 0.00 0.00 36.65 3.51
215 220 2.171003 TGAGCATCTCCGAAAGACTGA 58.829 47.619 0.00 0.00 36.65 3.41
216 221 2.165234 TGAGCATCTCCGAAAGACTGAG 59.835 50.000 0.00 0.00 36.65 3.35
217 222 1.134848 AGCATCTCCGAAAGACTGAGC 60.135 52.381 0.00 0.00 36.65 4.26
218 223 1.134848 GCATCTCCGAAAGACTGAGCT 60.135 52.381 0.00 0.00 36.65 4.09
219 224 2.538437 CATCTCCGAAAGACTGAGCTG 58.462 52.381 0.00 0.00 36.65 4.24
220 225 0.891373 TCTCCGAAAGACTGAGCTGG 59.109 55.000 0.00 0.00 31.43 4.85
221 226 0.739112 CTCCGAAAGACTGAGCTGGC 60.739 60.000 0.00 0.00 0.00 4.85
222 227 1.004560 CCGAAAGACTGAGCTGGCA 60.005 57.895 0.00 0.00 0.00 4.92
223 228 0.392193 CCGAAAGACTGAGCTGGCAT 60.392 55.000 0.00 0.00 0.00 4.40
224 229 1.134699 CCGAAAGACTGAGCTGGCATA 60.135 52.381 0.00 0.00 0.00 3.14
225 230 2.484417 CCGAAAGACTGAGCTGGCATAT 60.484 50.000 0.00 0.00 0.00 1.78
226 231 2.799412 CGAAAGACTGAGCTGGCATATC 59.201 50.000 0.00 0.00 0.00 1.63
227 232 3.739209 CGAAAGACTGAGCTGGCATATCA 60.739 47.826 0.00 0.00 0.00 2.15
228 233 4.387598 GAAAGACTGAGCTGGCATATCAT 58.612 43.478 0.00 0.00 0.00 2.45
229 234 3.681593 AGACTGAGCTGGCATATCATC 57.318 47.619 0.00 3.89 0.00 2.92
230 235 3.241156 AGACTGAGCTGGCATATCATCT 58.759 45.455 0.00 5.63 0.00 2.90
231 236 3.647113 AGACTGAGCTGGCATATCATCTT 59.353 43.478 0.00 0.00 0.00 2.40
232 237 3.741249 ACTGAGCTGGCATATCATCTTG 58.259 45.455 0.00 0.00 0.00 3.02
233 238 3.390311 ACTGAGCTGGCATATCATCTTGA 59.610 43.478 0.00 0.00 0.00 3.02
234 239 3.997681 CTGAGCTGGCATATCATCTTGAG 59.002 47.826 0.00 0.00 0.00 3.02
235 240 3.644738 TGAGCTGGCATATCATCTTGAGA 59.355 43.478 0.00 0.00 0.00 3.27
236 241 4.286291 TGAGCTGGCATATCATCTTGAGAT 59.714 41.667 0.00 0.00 34.56 2.75
237 242 5.221864 TGAGCTGGCATATCATCTTGAGATT 60.222 40.000 0.00 0.00 31.21 2.40
238 243 5.632118 AGCTGGCATATCATCTTGAGATTT 58.368 37.500 0.00 0.00 31.21 2.17
239 244 6.776744 AGCTGGCATATCATCTTGAGATTTA 58.223 36.000 0.00 0.00 31.21 1.40
240 245 6.654161 AGCTGGCATATCATCTTGAGATTTAC 59.346 38.462 0.00 0.00 31.21 2.01
241 246 6.401903 GCTGGCATATCATCTTGAGATTTACG 60.402 42.308 0.00 0.00 31.21 3.18
242 247 6.758254 TGGCATATCATCTTGAGATTTACGA 58.242 36.000 0.00 0.00 31.21 3.43
243 248 7.216494 TGGCATATCATCTTGAGATTTACGAA 58.784 34.615 0.00 0.00 31.21 3.85
244 249 7.386025 TGGCATATCATCTTGAGATTTACGAAG 59.614 37.037 0.00 0.00 31.21 3.79
245 250 7.386299 GGCATATCATCTTGAGATTTACGAAGT 59.614 37.037 0.00 0.00 37.29 3.01
246 251 8.431593 GCATATCATCTTGAGATTTACGAAGTC 58.568 37.037 0.00 0.00 35.39 3.01
247 252 9.468532 CATATCATCTTGAGATTTACGAAGTCA 57.531 33.333 0.00 0.00 35.39 3.41
248 253 7.763172 ATCATCTTGAGATTTACGAAGTCAC 57.237 36.000 0.00 0.00 35.39 3.67
249 254 6.925211 TCATCTTGAGATTTACGAAGTCACT 58.075 36.000 0.00 0.00 35.39 3.41
250 255 6.808704 TCATCTTGAGATTTACGAAGTCACTG 59.191 38.462 0.00 0.00 35.39 3.66
251 256 6.085555 TCTTGAGATTTACGAAGTCACTGT 57.914 37.500 0.00 0.00 43.93 3.55
252 257 7.210718 TCTTGAGATTTACGAAGTCACTGTA 57.789 36.000 0.00 0.00 43.93 2.74
253 258 7.306213 TCTTGAGATTTACGAAGTCACTGTAG 58.694 38.462 0.00 0.00 43.93 2.74
254 259 5.950883 TGAGATTTACGAAGTCACTGTAGG 58.049 41.667 0.00 0.00 43.93 3.18
255 260 4.745649 AGATTTACGAAGTCACTGTAGGC 58.254 43.478 0.00 0.00 43.93 3.93
256 261 2.624316 TTACGAAGTCACTGTAGGCG 57.376 50.000 0.00 0.00 43.93 5.52
257 262 0.169672 TACGAAGTCACTGTAGGCGC 59.830 55.000 0.00 0.00 43.93 6.53
258 263 1.805945 CGAAGTCACTGTAGGCGCC 60.806 63.158 21.89 21.89 0.00 6.53
259 264 1.592223 GAAGTCACTGTAGGCGCCT 59.408 57.895 34.85 34.85 0.00 5.52
260 265 0.458716 GAAGTCACTGTAGGCGCCTC 60.459 60.000 36.73 24.38 0.00 4.70
261 266 2.202623 GTCACTGTAGGCGCCTCG 60.203 66.667 36.73 24.39 0.00 4.63
262 267 2.675423 TCACTGTAGGCGCCTCGT 60.675 61.111 36.73 25.10 0.00 4.18
263 268 2.202623 CACTGTAGGCGCCTCGTC 60.203 66.667 36.73 24.11 0.00 4.20
264 269 3.812019 ACTGTAGGCGCCTCGTCG 61.812 66.667 36.73 21.73 36.23 5.12
265 270 3.812019 CTGTAGGCGCCTCGTCGT 61.812 66.667 36.73 11.27 36.23 4.34
266 271 3.736482 CTGTAGGCGCCTCGTCGTC 62.736 68.421 36.73 17.21 36.23 4.20
267 272 4.883300 GTAGGCGCCTCGTCGTCG 62.883 72.222 36.73 0.00 39.34 5.12
278 283 4.068302 GTCGTCGACGGGAACATC 57.932 61.111 35.05 14.32 40.29 3.06
279 284 1.505353 GTCGTCGACGGGAACATCT 59.495 57.895 35.05 0.00 40.29 2.90
280 285 0.522915 GTCGTCGACGGGAACATCTC 60.523 60.000 35.05 12.17 40.29 2.75
281 286 1.226603 CGTCGACGGGAACATCTCC 60.227 63.158 29.70 0.00 44.54 3.71
282 287 1.654954 CGTCGACGGGAACATCTCCT 61.655 60.000 29.70 0.00 44.68 3.69
283 288 0.100861 GTCGACGGGAACATCTCCTC 59.899 60.000 0.00 0.00 44.68 3.71
284 289 1.035932 TCGACGGGAACATCTCCTCC 61.036 60.000 0.00 0.00 44.68 4.30
285 290 1.823976 GACGGGAACATCTCCTCCC 59.176 63.158 0.00 0.00 46.97 4.30
291 296 3.652057 GGAACATCTCCTCCCATTGAA 57.348 47.619 0.00 0.00 41.61 2.69
292 297 4.176120 GGAACATCTCCTCCCATTGAAT 57.824 45.455 0.00 0.00 41.61 2.57
293 298 3.887716 GGAACATCTCCTCCCATTGAATG 59.112 47.826 0.00 0.00 41.61 2.67
294 299 2.941480 ACATCTCCTCCCATTGAATGC 58.059 47.619 0.00 0.00 0.00 3.56
295 300 1.878088 CATCTCCTCCCATTGAATGCG 59.122 52.381 0.00 0.00 0.00 4.73
296 301 0.464373 TCTCCTCCCATTGAATGCGC 60.464 55.000 0.00 0.00 0.00 6.09
297 302 0.749091 CTCCTCCCATTGAATGCGCA 60.749 55.000 14.96 14.96 0.00 6.09
298 303 0.106569 TCCTCCCATTGAATGCGCAT 60.107 50.000 19.28 19.28 0.00 4.73
299 304 0.313043 CCTCCCATTGAATGCGCATC 59.687 55.000 25.53 17.12 0.00 3.91
300 305 0.040692 CTCCCATTGAATGCGCATCG 60.041 55.000 25.53 9.81 0.00 3.84
311 316 3.576356 CGCATCGCCGGAAATGCT 61.576 61.111 28.18 0.00 44.81 3.79
312 317 2.025156 GCATCGCCGGAAATGCTG 59.975 61.111 25.75 8.14 43.87 4.41
313 318 2.472059 GCATCGCCGGAAATGCTGA 61.472 57.895 25.75 6.07 43.87 4.26
314 319 1.992233 GCATCGCCGGAAATGCTGAA 61.992 55.000 25.75 0.00 43.87 3.02
315 320 0.451383 CATCGCCGGAAATGCTGAAA 59.549 50.000 5.05 0.00 0.00 2.69
316 321 1.066002 CATCGCCGGAAATGCTGAAAT 59.934 47.619 5.05 0.00 0.00 2.17
317 322 2.031258 TCGCCGGAAATGCTGAAATA 57.969 45.000 5.05 0.00 0.00 1.40
318 323 2.360844 TCGCCGGAAATGCTGAAATAA 58.639 42.857 5.05 0.00 0.00 1.40
319 324 2.750166 TCGCCGGAAATGCTGAAATAAA 59.250 40.909 5.05 0.00 0.00 1.40
320 325 3.380004 TCGCCGGAAATGCTGAAATAAAT 59.620 39.130 5.05 0.00 0.00 1.40
321 326 3.486841 CGCCGGAAATGCTGAAATAAATG 59.513 43.478 5.05 0.00 0.00 2.32
322 327 3.245990 GCCGGAAATGCTGAAATAAATGC 59.754 43.478 5.05 0.00 0.00 3.56
323 328 3.486841 CCGGAAATGCTGAAATAAATGCG 59.513 43.478 0.00 0.00 0.00 4.73
324 329 4.350346 CGGAAATGCTGAAATAAATGCGA 58.650 39.130 0.00 0.00 0.00 5.10
325 330 4.438797 CGGAAATGCTGAAATAAATGCGAG 59.561 41.667 0.00 0.00 0.00 5.03
326 331 4.207841 GGAAATGCTGAAATAAATGCGAGC 59.792 41.667 0.00 0.00 0.00 5.03
327 332 4.374843 AATGCTGAAATAAATGCGAGCA 57.625 36.364 0.00 0.00 40.50 4.26
328 333 3.135414 TGCTGAAATAAATGCGAGCAC 57.865 42.857 0.00 0.00 31.66 4.40
329 334 2.159393 TGCTGAAATAAATGCGAGCACC 60.159 45.455 0.00 0.00 31.66 5.01
330 335 2.159393 GCTGAAATAAATGCGAGCACCA 60.159 45.455 0.00 0.00 0.00 4.17
331 336 3.688272 CTGAAATAAATGCGAGCACCAG 58.312 45.455 0.00 0.00 0.00 4.00
332 337 3.342719 TGAAATAAATGCGAGCACCAGA 58.657 40.909 0.00 0.00 0.00 3.86
333 338 3.755905 TGAAATAAATGCGAGCACCAGAA 59.244 39.130 0.00 0.00 0.00 3.02
334 339 4.398988 TGAAATAAATGCGAGCACCAGAAT 59.601 37.500 0.00 0.00 0.00 2.40
335 340 4.989279 AATAAATGCGAGCACCAGAATT 57.011 36.364 0.00 0.00 0.00 2.17
336 341 4.989279 ATAAATGCGAGCACCAGAATTT 57.011 36.364 0.00 0.00 0.00 1.82
337 342 2.642139 AATGCGAGCACCAGAATTTG 57.358 45.000 0.00 0.00 0.00 2.32
338 343 1.825090 ATGCGAGCACCAGAATTTGA 58.175 45.000 0.00 0.00 0.00 2.69
339 344 1.603456 TGCGAGCACCAGAATTTGAA 58.397 45.000 0.00 0.00 0.00 2.69
340 345 1.266718 TGCGAGCACCAGAATTTGAAC 59.733 47.619 0.00 0.00 0.00 3.18
341 346 1.401539 GCGAGCACCAGAATTTGAACC 60.402 52.381 0.00 0.00 0.00 3.62
342 347 1.200020 CGAGCACCAGAATTTGAACCC 59.800 52.381 0.00 0.00 0.00 4.11
343 348 2.519013 GAGCACCAGAATTTGAACCCT 58.481 47.619 0.00 0.00 0.00 4.34
344 349 2.229784 GAGCACCAGAATTTGAACCCTG 59.770 50.000 0.00 0.00 0.00 4.45
348 353 1.895131 CCAGAATTTGAACCCTGGTGG 59.105 52.381 0.00 0.00 40.84 4.61
358 363 2.368192 CCTGGTGGGCTGGGGATA 60.368 66.667 0.00 0.00 0.00 2.59
359 364 1.775877 CCTGGTGGGCTGGGGATAT 60.776 63.158 0.00 0.00 0.00 1.63
360 365 1.763770 CTGGTGGGCTGGGGATATC 59.236 63.158 0.00 0.00 0.00 1.63
361 366 1.005423 TGGTGGGCTGGGGATATCA 59.995 57.895 4.83 0.00 0.00 2.15
362 367 1.352622 TGGTGGGCTGGGGATATCAC 61.353 60.000 4.83 0.00 0.00 3.06
363 368 1.352622 GGTGGGCTGGGGATATCACA 61.353 60.000 7.40 3.31 0.00 3.58
364 369 0.109342 GTGGGCTGGGGATATCACAG 59.891 60.000 17.64 17.64 35.40 3.66
365 370 0.327480 TGGGCTGGGGATATCACAGT 60.327 55.000 20.90 0.00 34.79 3.55
366 371 0.398318 GGGCTGGGGATATCACAGTC 59.602 60.000 20.90 19.49 36.17 3.51
367 372 0.398318 GGCTGGGGATATCACAGTCC 59.602 60.000 20.90 18.51 34.79 3.85
375 380 4.875561 GGATATCACAGTCCCTCTAACC 57.124 50.000 4.83 0.00 0.00 2.85
376 381 4.223953 GGATATCACAGTCCCTCTAACCA 58.776 47.826 4.83 0.00 0.00 3.67
377 382 4.841246 GGATATCACAGTCCCTCTAACCAT 59.159 45.833 4.83 0.00 0.00 3.55
378 383 5.046950 GGATATCACAGTCCCTCTAACCATC 60.047 48.000 4.83 0.00 0.00 3.51
379 384 2.467880 TCACAGTCCCTCTAACCATCC 58.532 52.381 0.00 0.00 0.00 3.51
380 385 2.187958 CACAGTCCCTCTAACCATCCA 58.812 52.381 0.00 0.00 0.00 3.41
381 386 2.571653 CACAGTCCCTCTAACCATCCAA 59.428 50.000 0.00 0.00 0.00 3.53
382 387 2.572104 ACAGTCCCTCTAACCATCCAAC 59.428 50.000 0.00 0.00 0.00 3.77
383 388 2.092914 CAGTCCCTCTAACCATCCAACC 60.093 54.545 0.00 0.00 0.00 3.77
384 389 1.913419 GTCCCTCTAACCATCCAACCA 59.087 52.381 0.00 0.00 0.00 3.67
385 390 1.913419 TCCCTCTAACCATCCAACCAC 59.087 52.381 0.00 0.00 0.00 4.16
386 391 1.633432 CCCTCTAACCATCCAACCACA 59.367 52.381 0.00 0.00 0.00 4.17
387 392 2.242196 CCCTCTAACCATCCAACCACAT 59.758 50.000 0.00 0.00 0.00 3.21
388 393 3.282021 CCTCTAACCATCCAACCACATG 58.718 50.000 0.00 0.00 0.00 3.21
389 394 3.308402 CCTCTAACCATCCAACCACATGT 60.308 47.826 0.00 0.00 0.00 3.21
390 395 4.335416 CTCTAACCATCCAACCACATGTT 58.665 43.478 0.00 0.00 37.80 2.71
437 442 5.517054 TCGGTGTGTTTTCTGCAAATTTAAC 59.483 36.000 0.00 0.00 0.00 2.01
459 501 4.794278 GGTTTGACCGGGATATTTGTTT 57.206 40.909 6.32 0.00 0.00 2.83
460 502 5.142061 GGTTTGACCGGGATATTTGTTTT 57.858 39.130 6.32 0.00 0.00 2.43
461 503 5.543714 GGTTTGACCGGGATATTTGTTTTT 58.456 37.500 6.32 0.00 0.00 1.94
683 791 1.002684 GACGCATCAGGTACGTAGAGG 60.003 57.143 0.00 0.00 40.69 3.69
824 933 1.090625 CCGAGAGACTCACCGACGAT 61.091 60.000 15.85 0.00 0.00 3.73
890 999 0.235926 GCTTCAAGTGCGTCTCCAAC 59.764 55.000 0.00 0.00 0.00 3.77
925 1034 1.055551 ACCAACGACCCCAACTACCA 61.056 55.000 0.00 0.00 0.00 3.25
1105 1226 2.092375 TCCTTCTCTGCTCCTCATACGA 60.092 50.000 0.00 0.00 0.00 3.43
1107 1228 3.057596 CCTTCTCTGCTCCTCATACGATC 60.058 52.174 0.00 0.00 0.00 3.69
1349 1527 1.859302 AAGGAGAAGAGATGGAGCGT 58.141 50.000 0.00 0.00 0.00 5.07
1357 1535 5.133941 AGAAGAGATGGAGCGTCACTATTA 58.866 41.667 0.00 0.00 0.00 0.98
1459 1648 1.072159 GCTGCAGTGGACAAGGAGT 59.928 57.895 16.64 0.00 0.00 3.85
1832 2153 5.699143 AGATAGCAACCAGGCATATTTTCT 58.301 37.500 0.00 0.00 35.83 2.52
1886 2453 3.064207 TGCACAAGTGACGTCTTATTCC 58.936 45.455 17.92 0.73 0.00 3.01
2529 6572 7.746475 CGAAACTAATTTCTTTAGCTGGTCAAG 59.254 37.037 0.00 0.00 41.88 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.065235 CCATGCCTCATTTTTGGAGTTTTT 58.935 37.500 0.00 0.00 0.00 1.94
109 114 6.972328 GCTTGTGTCAGAACTGATGTTAAAAA 59.028 34.615 7.77 0.00 42.18 1.94
110 115 6.494842 GCTTGTGTCAGAACTGATGTTAAAA 58.505 36.000 7.77 0.00 42.18 1.52
111 116 5.277297 CGCTTGTGTCAGAACTGATGTTAAA 60.277 40.000 7.77 0.00 42.18 1.52
112 117 4.211164 CGCTTGTGTCAGAACTGATGTTAA 59.789 41.667 7.77 1.99 42.18 2.01
113 118 3.740832 CGCTTGTGTCAGAACTGATGTTA 59.259 43.478 7.77 0.00 42.18 2.41
114 119 2.545526 CGCTTGTGTCAGAACTGATGTT 59.454 45.455 7.77 0.00 42.18 2.71
115 120 2.138320 CGCTTGTGTCAGAACTGATGT 58.862 47.619 7.77 0.00 42.18 3.06
116 121 1.136141 GCGCTTGTGTCAGAACTGATG 60.136 52.381 0.00 0.00 42.18 3.07
117 122 1.151668 GCGCTTGTGTCAGAACTGAT 58.848 50.000 0.00 0.00 42.18 2.90
118 123 0.104855 AGCGCTTGTGTCAGAACTGA 59.895 50.000 2.64 0.00 37.24 3.41
119 124 0.510359 GAGCGCTTGTGTCAGAACTG 59.490 55.000 13.26 0.00 0.00 3.16
120 125 0.104855 TGAGCGCTTGTGTCAGAACT 59.895 50.000 13.26 0.00 0.00 3.01
121 126 1.151668 ATGAGCGCTTGTGTCAGAAC 58.848 50.000 13.26 0.00 0.00 3.01
122 127 2.741759 TATGAGCGCTTGTGTCAGAA 57.258 45.000 13.26 0.00 0.00 3.02
123 128 2.967599 ATATGAGCGCTTGTGTCAGA 57.032 45.000 13.26 1.56 0.00 3.27
124 129 3.243877 GTGTATATGAGCGCTTGTGTCAG 59.756 47.826 13.26 0.00 0.00 3.51
125 130 3.186909 GTGTATATGAGCGCTTGTGTCA 58.813 45.455 13.26 4.74 0.00 3.58
126 131 2.216488 CGTGTATATGAGCGCTTGTGTC 59.784 50.000 13.26 0.00 0.00 3.67
127 132 2.193447 CGTGTATATGAGCGCTTGTGT 58.807 47.619 13.26 4.27 0.00 3.72
128 133 1.071239 GCGTGTATATGAGCGCTTGTG 60.071 52.381 13.26 0.00 45.48 3.33
129 134 1.209128 GCGTGTATATGAGCGCTTGT 58.791 50.000 13.26 5.98 45.48 3.16
130 135 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
131 136 2.506544 CGCGTGTATATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
132 137 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
135 140 2.090658 GTGTATGCGCGTGTATATGAGC 59.909 50.000 13.61 0.41 38.85 4.26
136 141 3.565516 AGTGTATGCGCGTGTATATGAG 58.434 45.455 13.61 0.00 0.00 2.90
137 142 3.003897 TGAGTGTATGCGCGTGTATATGA 59.996 43.478 13.61 0.00 0.00 2.15
138 143 3.305110 TGAGTGTATGCGCGTGTATATG 58.695 45.455 13.61 0.00 0.00 1.78
139 144 3.636282 TGAGTGTATGCGCGTGTATAT 57.364 42.857 13.61 0.00 0.00 0.86
140 145 3.636282 ATGAGTGTATGCGCGTGTATA 57.364 42.857 13.61 2.40 0.00 1.47
141 146 2.509052 ATGAGTGTATGCGCGTGTAT 57.491 45.000 13.61 4.63 0.00 2.29
142 147 2.190161 GAATGAGTGTATGCGCGTGTA 58.810 47.619 13.61 0.00 0.00 2.90
143 148 0.999406 GAATGAGTGTATGCGCGTGT 59.001 50.000 13.61 0.00 0.00 4.49
144 149 0.301687 GGAATGAGTGTATGCGCGTG 59.698 55.000 13.61 0.00 0.00 5.34
145 150 0.175760 AGGAATGAGTGTATGCGCGT 59.824 50.000 8.43 7.55 0.00 6.01
146 151 2.134201 TAGGAATGAGTGTATGCGCG 57.866 50.000 0.00 0.00 0.00 6.86
147 152 3.653344 TCATAGGAATGAGTGTATGCGC 58.347 45.455 0.00 0.00 37.20 6.09
148 153 4.148871 CGTTCATAGGAATGAGTGTATGCG 59.851 45.833 3.19 0.00 42.97 4.73
149 154 4.084328 GCGTTCATAGGAATGAGTGTATGC 60.084 45.833 13.33 0.00 42.97 3.14
150 155 5.049828 TGCGTTCATAGGAATGAGTGTATG 58.950 41.667 13.33 0.00 42.97 2.39
151 156 5.050490 GTGCGTTCATAGGAATGAGTGTAT 58.950 41.667 13.33 0.00 42.97 2.29
152 157 4.081917 TGTGCGTTCATAGGAATGAGTGTA 60.082 41.667 13.33 0.00 42.97 2.90
153 158 3.262420 GTGCGTTCATAGGAATGAGTGT 58.738 45.455 13.33 0.00 42.97 3.55
154 159 3.261580 TGTGCGTTCATAGGAATGAGTG 58.738 45.455 13.33 0.00 42.97 3.51
155 160 3.610040 TGTGCGTTCATAGGAATGAGT 57.390 42.857 13.33 0.00 42.97 3.41
156 161 5.390251 GCATATGTGCGTTCATAGGAATGAG 60.390 44.000 13.33 0.26 41.32 2.90
157 162 4.452114 GCATATGTGCGTTCATAGGAATGA 59.548 41.667 13.33 0.00 41.62 2.57
158 163 4.715896 GCATATGTGCGTTCATAGGAATG 58.284 43.478 14.22 4.97 42.28 2.67
172 177 1.800586 GCGGTAGGATGTGCATATGTG 59.199 52.381 0.00 0.00 0.00 3.21
173 178 1.694150 AGCGGTAGGATGTGCATATGT 59.306 47.619 0.00 0.00 0.00 2.29
174 179 2.462456 AGCGGTAGGATGTGCATATG 57.538 50.000 0.00 0.00 0.00 1.78
175 180 3.769300 TCATAGCGGTAGGATGTGCATAT 59.231 43.478 4.66 0.00 0.00 1.78
176 181 3.161866 TCATAGCGGTAGGATGTGCATA 58.838 45.455 4.66 0.00 0.00 3.14
177 182 1.970640 TCATAGCGGTAGGATGTGCAT 59.029 47.619 4.66 0.00 0.00 3.96
178 183 1.341209 CTCATAGCGGTAGGATGTGCA 59.659 52.381 9.65 0.00 0.00 4.57
179 184 1.937108 GCTCATAGCGGTAGGATGTGC 60.937 57.143 9.65 8.13 34.21 4.57
180 185 1.341209 TGCTCATAGCGGTAGGATGTG 59.659 52.381 9.65 1.81 46.26 3.21
181 186 1.704641 TGCTCATAGCGGTAGGATGT 58.295 50.000 9.65 0.00 46.26 3.06
182 187 2.495270 AGATGCTCATAGCGGTAGGATG 59.505 50.000 9.65 5.57 46.26 3.51
183 188 2.757868 GAGATGCTCATAGCGGTAGGAT 59.242 50.000 9.65 0.00 46.26 3.24
184 189 2.163509 GAGATGCTCATAGCGGTAGGA 58.836 52.381 8.84 8.84 46.26 2.94
185 190 1.203523 GGAGATGCTCATAGCGGTAGG 59.796 57.143 0.00 0.00 46.26 3.18
186 191 1.135546 CGGAGATGCTCATAGCGGTAG 60.136 57.143 0.00 0.00 46.26 3.18
187 192 0.881796 CGGAGATGCTCATAGCGGTA 59.118 55.000 0.00 0.00 46.26 4.02
188 193 0.823769 TCGGAGATGCTCATAGCGGT 60.824 55.000 0.00 0.00 46.26 5.68
189 194 0.315251 TTCGGAGATGCTCATAGCGG 59.685 55.000 0.00 0.00 46.26 5.52
190 195 2.057316 CTTTCGGAGATGCTCATAGCG 58.943 52.381 0.00 0.00 46.26 4.26
191 196 3.056304 GTCTTTCGGAGATGCTCATAGC 58.944 50.000 0.00 0.00 42.82 2.97
192 197 4.037327 TCAGTCTTTCGGAGATGCTCATAG 59.963 45.833 0.00 0.00 36.61 2.23
193 198 3.954258 TCAGTCTTTCGGAGATGCTCATA 59.046 43.478 0.00 0.00 36.61 2.15
194 199 2.762887 TCAGTCTTTCGGAGATGCTCAT 59.237 45.455 0.00 0.00 36.61 2.90
195 200 2.165234 CTCAGTCTTTCGGAGATGCTCA 59.835 50.000 0.00 0.00 40.01 4.26
196 201 2.808244 CTCAGTCTTTCGGAGATGCTC 58.192 52.381 0.00 0.00 40.01 4.26
197 202 1.134848 GCTCAGTCTTTCGGAGATGCT 60.135 52.381 0.00 0.00 40.01 3.79
198 203 1.134848 AGCTCAGTCTTTCGGAGATGC 60.135 52.381 0.00 0.00 40.01 3.91
199 204 2.538437 CAGCTCAGTCTTTCGGAGATG 58.462 52.381 0.00 0.00 44.80 2.90
200 205 1.480137 CCAGCTCAGTCTTTCGGAGAT 59.520 52.381 0.00 0.00 40.01 2.75
201 206 0.891373 CCAGCTCAGTCTTTCGGAGA 59.109 55.000 0.00 0.00 40.01 3.71
202 207 0.739112 GCCAGCTCAGTCTTTCGGAG 60.739 60.000 0.00 0.00 40.44 4.63
203 208 1.293498 GCCAGCTCAGTCTTTCGGA 59.707 57.895 0.00 0.00 0.00 4.55
204 209 0.392193 ATGCCAGCTCAGTCTTTCGG 60.392 55.000 0.00 0.00 0.00 4.30
205 210 2.299993 TATGCCAGCTCAGTCTTTCG 57.700 50.000 0.00 0.00 0.00 3.46
206 211 3.801698 TGATATGCCAGCTCAGTCTTTC 58.198 45.455 0.00 0.00 0.00 2.62
207 212 3.920231 TGATATGCCAGCTCAGTCTTT 57.080 42.857 0.00 0.00 0.00 2.52
208 213 3.647113 AGATGATATGCCAGCTCAGTCTT 59.353 43.478 0.00 0.00 0.00 3.01
209 214 3.241156 AGATGATATGCCAGCTCAGTCT 58.759 45.455 0.00 0.00 0.00 3.24
210 215 3.681593 AGATGATATGCCAGCTCAGTC 57.318 47.619 0.00 0.00 0.00 3.51
211 216 3.390311 TCAAGATGATATGCCAGCTCAGT 59.610 43.478 0.00 0.00 30.67 3.41
212 217 3.997681 CTCAAGATGATATGCCAGCTCAG 59.002 47.826 0.00 0.00 30.67 3.35
213 218 3.644738 TCTCAAGATGATATGCCAGCTCA 59.355 43.478 0.00 0.00 30.67 4.26
214 219 4.268797 TCTCAAGATGATATGCCAGCTC 57.731 45.455 0.00 0.00 30.67 4.09
215 220 4.912317 ATCTCAAGATGATATGCCAGCT 57.088 40.909 0.00 0.00 33.74 4.24
216 221 5.961396 AAATCTCAAGATGATATGCCAGC 57.039 39.130 0.00 0.00 34.49 4.85
217 222 6.870439 TCGTAAATCTCAAGATGATATGCCAG 59.130 38.462 0.00 0.00 34.49 4.85
218 223 6.758254 TCGTAAATCTCAAGATGATATGCCA 58.242 36.000 0.00 0.00 34.49 4.92
219 224 7.386299 ACTTCGTAAATCTCAAGATGATATGCC 59.614 37.037 0.00 0.00 34.49 4.40
220 225 8.304202 ACTTCGTAAATCTCAAGATGATATGC 57.696 34.615 0.00 0.00 34.49 3.14
221 226 9.468532 TGACTTCGTAAATCTCAAGATGATATG 57.531 33.333 0.00 0.00 34.49 1.78
222 227 9.469807 GTGACTTCGTAAATCTCAAGATGATAT 57.530 33.333 0.00 0.00 34.49 1.63
223 228 8.687242 AGTGACTTCGTAAATCTCAAGATGATA 58.313 33.333 0.00 0.00 34.49 2.15
224 229 7.490725 CAGTGACTTCGTAAATCTCAAGATGAT 59.509 37.037 0.00 0.00 34.49 2.45
225 230 6.808704 CAGTGACTTCGTAAATCTCAAGATGA 59.191 38.462 0.00 0.00 34.49 2.92
226 231 6.587990 ACAGTGACTTCGTAAATCTCAAGATG 59.412 38.462 0.00 0.00 34.49 2.90
227 232 6.692486 ACAGTGACTTCGTAAATCTCAAGAT 58.308 36.000 0.00 0.00 36.07 2.40
228 233 6.085555 ACAGTGACTTCGTAAATCTCAAGA 57.914 37.500 0.00 0.00 0.00 3.02
229 234 6.528423 CCTACAGTGACTTCGTAAATCTCAAG 59.472 42.308 0.00 0.00 0.00 3.02
230 235 6.387465 CCTACAGTGACTTCGTAAATCTCAA 58.613 40.000 0.00 0.00 0.00 3.02
231 236 5.621555 GCCTACAGTGACTTCGTAAATCTCA 60.622 44.000 0.00 0.00 0.00 3.27
232 237 4.799428 GCCTACAGTGACTTCGTAAATCTC 59.201 45.833 0.00 0.00 0.00 2.75
233 238 4.674623 CGCCTACAGTGACTTCGTAAATCT 60.675 45.833 0.00 0.00 0.00 2.40
234 239 3.546670 CGCCTACAGTGACTTCGTAAATC 59.453 47.826 0.00 0.00 0.00 2.17
235 240 3.508762 CGCCTACAGTGACTTCGTAAAT 58.491 45.455 0.00 0.00 0.00 1.40
236 241 2.923605 GCGCCTACAGTGACTTCGTAAA 60.924 50.000 0.00 0.00 0.00 2.01
237 242 1.401931 GCGCCTACAGTGACTTCGTAA 60.402 52.381 0.00 0.00 0.00 3.18
238 243 0.169672 GCGCCTACAGTGACTTCGTA 59.830 55.000 0.00 0.00 0.00 3.43
239 244 1.080705 GCGCCTACAGTGACTTCGT 60.081 57.895 0.00 0.00 0.00 3.85
240 245 1.805945 GGCGCCTACAGTGACTTCG 60.806 63.158 22.15 0.00 0.00 3.79
241 246 1.592223 AGGCGCCTACAGTGACTTC 59.408 57.895 31.86 0.00 44.04 3.01
242 247 3.793060 AGGCGCCTACAGTGACTT 58.207 55.556 31.86 0.00 44.04 3.01
244 249 2.202623 CGAGGCGCCTACAGTGAC 60.203 66.667 32.97 14.51 0.00 3.67
245 250 2.675423 ACGAGGCGCCTACAGTGA 60.675 61.111 32.97 0.00 0.00 3.41
246 251 2.202623 GACGAGGCGCCTACAGTG 60.203 66.667 32.97 18.94 0.00 3.66
247 252 3.812019 CGACGAGGCGCCTACAGT 61.812 66.667 32.97 28.48 0.00 3.55
248 253 3.736482 GACGACGAGGCGCCTACAG 62.736 68.421 32.97 25.33 33.86 2.74
249 254 3.807538 GACGACGAGGCGCCTACA 61.808 66.667 32.97 0.00 33.86 2.74
261 266 0.522915 GAGATGTTCCCGTCGACGAC 60.523 60.000 37.65 27.09 43.02 4.34
262 267 1.651240 GGAGATGTTCCCGTCGACGA 61.651 60.000 37.65 18.99 40.37 4.20
263 268 1.226603 GGAGATGTTCCCGTCGACG 60.227 63.158 30.33 30.33 40.37 5.12
264 269 4.808649 GGAGATGTTCCCGTCGAC 57.191 61.111 5.18 5.18 40.37 4.20
272 277 3.317430 GCATTCAATGGGAGGAGATGTTC 59.683 47.826 0.00 0.00 0.00 3.18
273 278 3.294214 GCATTCAATGGGAGGAGATGTT 58.706 45.455 0.00 0.00 0.00 2.71
274 279 2.747467 CGCATTCAATGGGAGGAGATGT 60.747 50.000 8.78 0.00 45.09 3.06
275 280 1.878088 CGCATTCAATGGGAGGAGATG 59.122 52.381 8.78 0.00 45.09 2.90
276 281 1.816961 GCGCATTCAATGGGAGGAGAT 60.817 52.381 18.25 0.00 45.09 2.75
277 282 0.464373 GCGCATTCAATGGGAGGAGA 60.464 55.000 18.25 0.00 45.09 3.71
278 283 0.749091 TGCGCATTCAATGGGAGGAG 60.749 55.000 18.25 0.00 45.09 3.69
279 284 0.106569 ATGCGCATTCAATGGGAGGA 60.107 50.000 19.28 1.56 45.09 3.71
280 285 0.313043 GATGCGCATTCAATGGGAGG 59.687 55.000 26.12 0.00 45.09 4.30
281 286 0.040692 CGATGCGCATTCAATGGGAG 60.041 55.000 26.12 4.12 45.09 4.30
282 287 2.024117 CGATGCGCATTCAATGGGA 58.976 52.632 26.12 4.11 45.09 4.37
283 288 4.620437 CGATGCGCATTCAATGGG 57.380 55.556 26.12 10.08 45.06 4.00
295 300 1.992233 TTCAGCATTTCCGGCGATGC 61.992 55.000 25.40 25.40 46.88 3.91
296 301 0.451383 TTTCAGCATTTCCGGCGATG 59.549 50.000 9.30 5.45 36.08 3.84
297 302 1.392589 ATTTCAGCATTTCCGGCGAT 58.607 45.000 9.30 0.00 36.08 4.58
298 303 2.031258 TATTTCAGCATTTCCGGCGA 57.969 45.000 9.30 0.00 36.08 5.54
299 304 2.842208 TTATTTCAGCATTTCCGGCG 57.158 45.000 0.00 0.00 36.08 6.46
300 305 3.245990 GCATTTATTTCAGCATTTCCGGC 59.754 43.478 0.00 0.00 0.00 6.13
301 306 3.486841 CGCATTTATTTCAGCATTTCCGG 59.513 43.478 0.00 0.00 0.00 5.14
302 307 4.350346 TCGCATTTATTTCAGCATTTCCG 58.650 39.130 0.00 0.00 0.00 4.30
303 308 4.207841 GCTCGCATTTATTTCAGCATTTCC 59.792 41.667 0.00 0.00 0.00 3.13
304 309 4.799949 TGCTCGCATTTATTTCAGCATTTC 59.200 37.500 0.00 0.00 32.00 2.17
305 310 4.563976 GTGCTCGCATTTATTTCAGCATTT 59.436 37.500 0.00 0.00 39.01 2.32
306 311 4.107622 GTGCTCGCATTTATTTCAGCATT 58.892 39.130 0.00 0.00 39.01 3.56
307 312 3.489738 GGTGCTCGCATTTATTTCAGCAT 60.490 43.478 0.00 0.00 39.01 3.79
308 313 2.159393 GGTGCTCGCATTTATTTCAGCA 60.159 45.455 0.00 0.00 34.54 4.41
309 314 2.159393 TGGTGCTCGCATTTATTTCAGC 60.159 45.455 0.00 0.00 0.00 4.26
310 315 3.374988 TCTGGTGCTCGCATTTATTTCAG 59.625 43.478 0.00 0.00 0.00 3.02
311 316 3.342719 TCTGGTGCTCGCATTTATTTCA 58.657 40.909 0.00 0.00 0.00 2.69
312 317 4.355543 TTCTGGTGCTCGCATTTATTTC 57.644 40.909 0.00 0.00 0.00 2.17
313 318 4.989279 ATTCTGGTGCTCGCATTTATTT 57.011 36.364 0.00 0.00 0.00 1.40
314 319 4.989279 AATTCTGGTGCTCGCATTTATT 57.011 36.364 0.00 0.00 0.00 1.40
315 320 4.398988 TCAAATTCTGGTGCTCGCATTTAT 59.601 37.500 0.00 0.00 0.00 1.40
316 321 3.755905 TCAAATTCTGGTGCTCGCATTTA 59.244 39.130 0.00 0.00 0.00 1.40
317 322 2.557924 TCAAATTCTGGTGCTCGCATTT 59.442 40.909 0.00 0.00 0.00 2.32
318 323 2.161855 TCAAATTCTGGTGCTCGCATT 58.838 42.857 0.00 0.00 0.00 3.56
319 324 1.825090 TCAAATTCTGGTGCTCGCAT 58.175 45.000 0.00 0.00 0.00 4.73
320 325 1.266718 GTTCAAATTCTGGTGCTCGCA 59.733 47.619 0.00 0.00 0.00 5.10
321 326 1.401539 GGTTCAAATTCTGGTGCTCGC 60.402 52.381 0.00 0.00 0.00 5.03
322 327 1.200020 GGGTTCAAATTCTGGTGCTCG 59.800 52.381 0.00 0.00 0.00 5.03
323 328 2.229784 CAGGGTTCAAATTCTGGTGCTC 59.770 50.000 0.00 0.00 0.00 4.26
324 329 2.242043 CAGGGTTCAAATTCTGGTGCT 58.758 47.619 0.00 0.00 0.00 4.40
325 330 1.273327 CCAGGGTTCAAATTCTGGTGC 59.727 52.381 0.00 0.00 41.21 5.01
341 346 1.775877 ATATCCCCAGCCCACCAGG 60.776 63.158 0.00 0.00 39.47 4.45
342 347 1.061905 TGATATCCCCAGCCCACCAG 61.062 60.000 0.00 0.00 0.00 4.00
343 348 1.005423 TGATATCCCCAGCCCACCA 59.995 57.895 0.00 0.00 0.00 4.17
344 349 1.352622 TGTGATATCCCCAGCCCACC 61.353 60.000 0.00 0.00 0.00 4.61
345 350 0.109342 CTGTGATATCCCCAGCCCAC 59.891 60.000 0.00 0.00 0.00 4.61
346 351 0.327480 ACTGTGATATCCCCAGCCCA 60.327 55.000 15.72 0.00 0.00 5.36
347 352 0.398318 GACTGTGATATCCCCAGCCC 59.602 60.000 15.72 7.60 0.00 5.19
348 353 0.398318 GGACTGTGATATCCCCAGCC 59.602 60.000 15.72 14.01 0.00 4.85
354 359 4.223953 TGGTTAGAGGGACTGTGATATCC 58.776 47.826 0.00 0.00 41.55 2.59
355 360 5.046950 GGATGGTTAGAGGGACTGTGATATC 60.047 48.000 0.00 0.00 41.55 1.63
356 361 4.841246 GGATGGTTAGAGGGACTGTGATAT 59.159 45.833 0.00 0.00 41.55 1.63
357 362 4.223953 GGATGGTTAGAGGGACTGTGATA 58.776 47.826 0.00 0.00 41.55 2.15
358 363 3.041946 GGATGGTTAGAGGGACTGTGAT 58.958 50.000 0.00 0.00 41.55 3.06
359 364 2.225522 TGGATGGTTAGAGGGACTGTGA 60.226 50.000 0.00 0.00 41.55 3.58
360 365 2.187958 TGGATGGTTAGAGGGACTGTG 58.812 52.381 0.00 0.00 41.55 3.66
361 366 2.572104 GTTGGATGGTTAGAGGGACTGT 59.428 50.000 0.00 0.00 41.55 3.55
362 367 2.092914 GGTTGGATGGTTAGAGGGACTG 60.093 54.545 0.00 0.00 41.55 3.51
364 369 1.913419 TGGTTGGATGGTTAGAGGGAC 59.087 52.381 0.00 0.00 0.00 4.46
365 370 1.913419 GTGGTTGGATGGTTAGAGGGA 59.087 52.381 0.00 0.00 0.00 4.20
366 371 1.633432 TGTGGTTGGATGGTTAGAGGG 59.367 52.381 0.00 0.00 0.00 4.30
367 372 3.282021 CATGTGGTTGGATGGTTAGAGG 58.718 50.000 0.00 0.00 0.00 3.69
368 373 3.955471 ACATGTGGTTGGATGGTTAGAG 58.045 45.455 0.00 0.00 0.00 2.43
369 374 4.380843 AACATGTGGTTGGATGGTTAGA 57.619 40.909 0.00 0.00 38.60 2.10
391 396 6.166982 CGAATAGATCCTCTAAATGGGAACC 58.833 44.000 0.00 0.00 40.25 3.62
392 397 6.166982 CCGAATAGATCCTCTAAATGGGAAC 58.833 44.000 0.00 0.00 31.96 3.62
393 398 5.844516 ACCGAATAGATCCTCTAAATGGGAA 59.155 40.000 0.00 0.00 31.96 3.97
394 399 5.246203 CACCGAATAGATCCTCTAAATGGGA 59.754 44.000 0.00 0.00 31.96 4.37
395 400 5.012148 ACACCGAATAGATCCTCTAAATGGG 59.988 44.000 0.00 0.00 31.96 4.00
419 424 6.590292 TCAAACCGTTAAATTTGCAGAAAACA 59.410 30.769 0.00 0.00 36.06 2.83
459 501 5.106475 CCCCGTCAATCGTAATTCTCAAAAA 60.106 40.000 0.00 0.00 37.94 1.94
460 502 4.393680 CCCCGTCAATCGTAATTCTCAAAA 59.606 41.667 0.00 0.00 37.94 2.44
461 503 3.936453 CCCCGTCAATCGTAATTCTCAAA 59.064 43.478 0.00 0.00 37.94 2.69
462 504 3.196039 TCCCCGTCAATCGTAATTCTCAA 59.804 43.478 0.00 0.00 37.94 3.02
463 505 2.761767 TCCCCGTCAATCGTAATTCTCA 59.238 45.455 0.00 0.00 37.94 3.27
464 506 3.447918 TCCCCGTCAATCGTAATTCTC 57.552 47.619 0.00 0.00 37.94 2.87
465 507 5.245301 TCATATCCCCGTCAATCGTAATTCT 59.755 40.000 0.00 0.00 37.94 2.40
466 508 5.475719 TCATATCCCCGTCAATCGTAATTC 58.524 41.667 0.00 0.00 37.94 2.17
467 509 5.477607 TCATATCCCCGTCAATCGTAATT 57.522 39.130 0.00 0.00 37.94 1.40
468 510 5.419542 CATCATATCCCCGTCAATCGTAAT 58.580 41.667 0.00 0.00 37.94 1.89
469 511 4.816392 CATCATATCCCCGTCAATCGTAA 58.184 43.478 0.00 0.00 37.94 3.18
470 512 3.368013 GCATCATATCCCCGTCAATCGTA 60.368 47.826 0.00 0.00 37.94 3.43
471 513 2.612972 GCATCATATCCCCGTCAATCGT 60.613 50.000 0.00 0.00 37.94 3.73
472 514 2.002586 GCATCATATCCCCGTCAATCG 58.997 52.381 0.00 0.00 39.52 3.34
473 515 3.055530 AGAGCATCATATCCCCGTCAATC 60.056 47.826 0.00 0.00 37.82 2.67
474 516 2.909006 AGAGCATCATATCCCCGTCAAT 59.091 45.455 0.00 0.00 37.82 2.57
475 517 2.329267 AGAGCATCATATCCCCGTCAA 58.671 47.619 0.00 0.00 37.82 3.18
476 518 2.015456 AGAGCATCATATCCCCGTCA 57.985 50.000 0.00 0.00 37.82 4.35
477 519 3.677424 GCTAAGAGCATCATATCCCCGTC 60.677 52.174 0.00 0.00 41.89 4.79
478 520 2.234908 GCTAAGAGCATCATATCCCCGT 59.765 50.000 0.00 0.00 41.89 5.28
479 521 2.419297 GGCTAAGAGCATCATATCCCCG 60.419 54.545 0.21 0.00 44.75 5.73
480 522 2.092699 GGGCTAAGAGCATCATATCCCC 60.093 54.545 0.21 0.00 44.75 4.81
683 791 2.475685 CGATGATTCATGGCGATGCATC 60.476 50.000 17.10 17.10 34.00 3.91
824 933 3.690487 GAGGATCTCGACGAGGAGA 57.310 57.895 23.92 6.38 46.37 3.71
916 1025 0.391263 GAGCTTCCGGTGGTAGTTGG 60.391 60.000 0.00 0.00 0.00 3.77
925 1034 4.332543 TCTGGGGGAGCTTCCGGT 62.333 66.667 4.51 0.00 37.43 5.28
1349 1527 6.806739 CCGATCATTAGCGACATTAATAGTGA 59.193 38.462 0.00 0.00 36.35 3.41
1357 1535 3.452755 TGACCGATCATTAGCGACATT 57.547 42.857 0.00 0.00 36.35 2.71
1459 1648 1.628846 GAAGTTAGTCCTTGCTCCCCA 59.371 52.381 0.00 0.00 0.00 4.96
1832 2153 6.731292 ACTCTTCATATAGTGGCACATACA 57.269 37.500 21.41 1.88 44.52 2.29
2078 2889 2.835156 TGTATCACAATCTCCCGTTGGA 59.165 45.455 0.00 0.00 38.75 3.53
2529 6572 4.107622 TCGAAAAACTAGCCGTACATAGC 58.892 43.478 0.00 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.