Multiple sequence alignment - TraesCS5A01G089700

Loading Multiple Alignment...

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 TraesCS5A01G089700 chr5A 100.000 2665 0 0 1 2665 119862366 119865030 0.000000e+00 4922.0
1 TraesCS5A01G089700 chr5A 95.975 323 13 0 129 451 94158847 94159169 2.350000e-145 525.0
2 TraesCS5A01G089700 chr5A 78.441 603 96 17 1058 1647 639213484 639212903 1.950000e-96 363.0
3 TraesCS5A01G089700 chr5B 87.948 2091 201 29 596 2665 125828587 125830647 0.000000e+00 2418.0
4 TraesCS5A01G089700 chr5B 83.792 654 94 7 993 1635 652820177 652820829 6.310000e-171 610.0
5 TraesCS5A01G089700 chr5B 76.453 998 211 20 1654 2635 425012749 425013738 1.090000e-143 520.0
6 TraesCS5A01G089700 chr5B 76.361 643 113 25 1025 1647 10086341 10086964 2.580000e-80 309.0
7 TraesCS5A01G089700 chr5B 97.692 130 3 0 1 130 125798139 125798268 9.600000e-55 224.0
8 TraesCS5A01G089700 chr5D 90.268 1603 140 9 454 2048 114600317 114601911 0.000000e+00 2082.0
9 TraesCS5A01G089700 chr5D 90.143 629 55 5 2044 2665 114603487 114604115 0.000000e+00 811.0
10 TraesCS5A01G089700 chr5D 99.231 130 1 0 1 130 114600189 114600318 4.440000e-58 235.0
11 TraesCS5A01G089700 chr4A 83.433 670 103 3 984 1647 617363827 617364494 1.360000e-172 616.0
12 TraesCS5A01G089700 chr4A 96.375 331 12 0 125 455 158289670 158290000 1.800000e-151 545.0
13 TraesCS5A01G089700 chr4A 75.688 909 155 40 1786 2665 339194843 339193972 6.910000e-106 394.0
14 TraesCS5A01G089700 chr2B 77.500 1000 200 20 1671 2657 278021101 278020114 6.400000e-161 577.0
15 TraesCS5A01G089700 chr2B 78.901 455 70 15 1201 1647 751317767 751317331 4.340000e-73 285.0
16 TraesCS5A01G089700 chr7B 77.324 979 205 14 1698 2664 425509717 425508744 1.790000e-156 562.0
17 TraesCS5A01G089700 chr7A 97.256 328 9 0 128 455 142300214 142300541 8.330000e-155 556.0
18 TraesCS5A01G089700 chr7A 96.657 329 11 0 127 455 731254414 731254742 5.020000e-152 547.0
19 TraesCS5A01G089700 chr3A 96.942 327 10 0 129 455 659863415 659863741 1.390000e-152 549.0
20 TraesCS5A01G089700 chr3A 78.340 494 83 15 1167 1647 663728417 663728899 5.580000e-77 298.0
21 TraesCS5A01G089700 chr3A 90.722 97 8 1 1551 1647 573693263 573693358 7.740000e-26 128.0
22 TraesCS5A01G089700 chr1A 96.636 327 11 0 129 455 305208541 305208867 6.490000e-151 544.0
23 TraesCS5A01G089700 chr1A 94.382 356 14 3 129 482 94006571 94006220 2.330000e-150 542.0
24 TraesCS5A01G089700 chr2A 93.855 358 16 3 129 484 434365956 434366309 3.900000e-148 534.0
25 TraesCS5A01G089700 chr2A 93.820 356 16 3 129 482 269794406 269794055 5.050000e-147 531.0
26 TraesCS5A01G089700 chr2A 76.015 542 92 21 1128 1647 359445112 359444587 2.050000e-61 246.0
27 TraesCS5A01G089700 chr2A 76.699 412 83 7 1654 2063 640219872 640219472 1.610000e-52 217.0
28 TraesCS5A01G089700 chr3D 78.878 606 89 27 1059 1649 423844821 423845402 9.010000e-100 374.0
29 TraesCS5A01G089700 chr4B 75.931 698 149 17 1915 2599 340729450 340730141 9.140000e-90 340.0
30 TraesCS5A01G089700 chr2D 79.198 524 79 23 1132 1650 26941668 26941170 1.180000e-88 337.0
31 TraesCS5A01G089700 chr2D 78.740 508 85 12 1150 1647 578335325 578334831 4.280000e-83 318.0
32 TraesCS5A01G089700 chr7D 76.498 634 108 23 1027 1647 162837609 162837004 9.270000e-80 307.0
33 TraesCS5A01G089700 chr7D 77.154 499 87 9 1159 1647 602174684 602174203 5.660000e-67 265.0
34 TraesCS5A01G089700 chr7D 77.282 471 81 11 1176 1635 33224086 33224541 1.220000e-63 254.0
35 TraesCS5A01G089700 chr3B 78.156 499 93 14 1647 2140 140235822 140236309 1.200000e-78 303.0
36 TraesCS5A01G089700 chr1B 80.368 326 54 4 1151 1466 498059176 498059501 3.430000e-59 239.0
37 TraesCS5A01G089700 chr1B 83.942 137 22 0 2529 2665 195029341 195029477 5.990000e-27 132.0
38 TraesCS5A01G089700 chr1B 90.110 91 9 0 2571 2661 301114526 301114616 4.660000e-23 119.0
39 TraesCS5A01G089700 chr1B 80.645 93 16 2 1692 1783 314152789 314152698 1.320000e-08 71.3
40 TraesCS5A01G089700 chr4D 84.795 171 19 4 2084 2248 320592484 320592315 5.900000e-37 165.0
41 TraesCS5A01G089700 chr1D 92.473 93 7 0 2569 2661 146470422 146470514 1.660000e-27 134.0
42 TraesCS5A01G089700 chr1D 100.000 31 0 0 2631 2661 205299014 205299044 1.030000e-04 58.4


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 TraesCS5A01G089700 chr5A 119862366 119865030 2664 False 4922.000000 4922 100.000 1 2665 1 chr5A.!!$F2 2664
1 TraesCS5A01G089700 chr5A 639212903 639213484 581 True 363.000000 363 78.441 1058 1647 1 chr5A.!!$R1 589
2 TraesCS5A01G089700 chr5B 125828587 125830647 2060 False 2418.000000 2418 87.948 596 2665 1 chr5B.!!$F3 2069
3 TraesCS5A01G089700 chr5B 652820177 652820829 652 False 610.000000 610 83.792 993 1635 1 chr5B.!!$F5 642
4 TraesCS5A01G089700 chr5B 425012749 425013738 989 False 520.000000 520 76.453 1654 2635 1 chr5B.!!$F4 981
5 TraesCS5A01G089700 chr5B 10086341 10086964 623 False 309.000000 309 76.361 1025 1647 1 chr5B.!!$F1 622
6 TraesCS5A01G089700 chr5D 114600189 114604115 3926 False 1042.666667 2082 93.214 1 2665 3 chr5D.!!$F1 2664
7 TraesCS5A01G089700 chr4A 617363827 617364494 667 False 616.000000 616 83.433 984 1647 1 chr4A.!!$F2 663
8 TraesCS5A01G089700 chr4A 339193972 339194843 871 True 394.000000 394 75.688 1786 2665 1 chr4A.!!$R1 879
9 TraesCS5A01G089700 chr2B 278020114 278021101 987 True 577.000000 577 77.500 1671 2657 1 chr2B.!!$R1 986
10 TraesCS5A01G089700 chr7B 425508744 425509717 973 True 562.000000 562 77.324 1698 2664 1 chr7B.!!$R1 966
11 TraesCS5A01G089700 chr2A 359444587 359445112 525 True 246.000000 246 76.015 1128 1647 1 chr2A.!!$R2 519
12 TraesCS5A01G089700 chr3D 423844821 423845402 581 False 374.000000 374 78.878 1059 1649 1 chr3D.!!$F1 590
13 TraesCS5A01G089700 chr4B 340729450 340730141 691 False 340.000000 340 75.931 1915 2599 1 chr4B.!!$F1 684
14 TraesCS5A01G089700 chr7D 162837004 162837609 605 True 307.000000 307 76.498 1027 1647 1 chr7D.!!$R1 620

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
584 585 0.913876 GCGCGTTTGATTGGTATTGC 59.086 50.0 8.43 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2523 4216 1.358152 AGGGCTACTGTGGCACTTAA 58.642 50.0 15.7 2.76 40.99 1.85 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
52 53 1.307866 AGTGGGGTGGTGGGGATAG 60.308 63.158 0.00 0.00 0.00 2.08
128 129 2.722094 TGCGTTTTAGCCCTTGATGAT 58.278 42.857 0.00 0.00 36.02 2.45
129 130 3.879998 TGCGTTTTAGCCCTTGATGATA 58.120 40.909 0.00 0.00 36.02 2.15
130 131 3.625764 TGCGTTTTAGCCCTTGATGATAC 59.374 43.478 0.00 0.00 36.02 2.24
131 132 3.877508 GCGTTTTAGCCCTTGATGATACT 59.122 43.478 0.00 0.00 0.00 2.12
132 133 4.335594 GCGTTTTAGCCCTTGATGATACTT 59.664 41.667 0.00 0.00 0.00 2.24
133 134 5.504173 GCGTTTTAGCCCTTGATGATACTTC 60.504 44.000 0.00 0.00 0.00 3.01
134 135 5.007724 CGTTTTAGCCCTTGATGATACTTCC 59.992 44.000 0.00 0.00 0.00 3.46
135 136 5.975988 TTTAGCCCTTGATGATACTTCCT 57.024 39.130 0.00 0.00 0.00 3.36
136 137 5.552870 TTAGCCCTTGATGATACTTCCTC 57.447 43.478 0.00 0.00 0.00 3.71
137 138 2.708325 AGCCCTTGATGATACTTCCTCC 59.292 50.000 0.00 0.00 0.00 4.30
138 139 2.708325 GCCCTTGATGATACTTCCTCCT 59.292 50.000 0.00 0.00 0.00 3.69
139 140 3.137360 GCCCTTGATGATACTTCCTCCTT 59.863 47.826 0.00 0.00 0.00 3.36
140 141 4.385754 GCCCTTGATGATACTTCCTCCTTT 60.386 45.833 0.00 0.00 0.00 3.11
141 142 5.372373 CCCTTGATGATACTTCCTCCTTTC 58.628 45.833 0.00 0.00 0.00 2.62
142 143 5.131809 CCCTTGATGATACTTCCTCCTTTCT 59.868 44.000 0.00 0.00 0.00 2.52
143 144 6.054295 CCTTGATGATACTTCCTCCTTTCTG 58.946 44.000 0.00 0.00 0.00 3.02
144 145 5.620738 TGATGATACTTCCTCCTTTCTGG 57.379 43.478 0.00 0.00 37.10 3.86
145 146 5.032846 TGATGATACTTCCTCCTTTCTGGT 58.967 41.667 0.00 0.00 37.07 4.00
146 147 5.488919 TGATGATACTTCCTCCTTTCTGGTT 59.511 40.000 0.00 0.00 37.07 3.67
147 148 5.843019 TGATACTTCCTCCTTTCTGGTTT 57.157 39.130 0.00 0.00 37.07 3.27
148 149 6.945636 TGATACTTCCTCCTTTCTGGTTTA 57.054 37.500 0.00 0.00 37.07 2.01
149 150 7.510675 TGATACTTCCTCCTTTCTGGTTTAT 57.489 36.000 0.00 0.00 37.07 1.40
150 151 8.618240 TGATACTTCCTCCTTTCTGGTTTATA 57.382 34.615 0.00 0.00 37.07 0.98
151 152 8.705594 TGATACTTCCTCCTTTCTGGTTTATAG 58.294 37.037 0.00 0.00 37.07 1.31
152 153 6.314899 ACTTCCTCCTTTCTGGTTTATAGG 57.685 41.667 0.00 0.00 37.07 2.57
153 154 5.191921 ACTTCCTCCTTTCTGGTTTATAGGG 59.808 44.000 0.00 0.00 37.07 3.53
154 155 3.458487 TCCTCCTTTCTGGTTTATAGGGC 59.542 47.826 0.00 0.00 37.07 5.19
155 156 3.459969 CCTCCTTTCTGGTTTATAGGGCT 59.540 47.826 0.00 0.00 37.07 5.19
156 157 4.079730 CCTCCTTTCTGGTTTATAGGGCTT 60.080 45.833 0.00 0.00 37.07 4.35
157 158 5.132144 CCTCCTTTCTGGTTTATAGGGCTTA 59.868 44.000 0.00 0.00 37.07 3.09
158 159 6.183361 CCTCCTTTCTGGTTTATAGGGCTTAT 60.183 42.308 0.00 0.00 37.07 1.73
159 160 6.838382 TCCTTTCTGGTTTATAGGGCTTATC 58.162 40.000 0.00 0.00 37.07 1.75
160 161 6.619852 TCCTTTCTGGTTTATAGGGCTTATCT 59.380 38.462 0.00 0.00 37.07 1.98
161 162 6.937465 CCTTTCTGGTTTATAGGGCTTATCTC 59.063 42.308 0.00 0.00 0.00 2.75
162 163 7.420214 CCTTTCTGGTTTATAGGGCTTATCTCA 60.420 40.741 0.00 0.00 0.00 3.27
163 164 7.446106 TTCTGGTTTATAGGGCTTATCTCAA 57.554 36.000 0.00 0.00 0.00 3.02
164 165 7.446106 TCTGGTTTATAGGGCTTATCTCAAA 57.554 36.000 0.00 0.00 0.00 2.69
165 166 7.867921 TCTGGTTTATAGGGCTTATCTCAAAA 58.132 34.615 0.00 0.00 0.00 2.44
166 167 8.502738 TCTGGTTTATAGGGCTTATCTCAAAAT 58.497 33.333 0.00 0.00 0.00 1.82
167 168 9.136323 CTGGTTTATAGGGCTTATCTCAAAATT 57.864 33.333 0.00 0.00 0.00 1.82
168 169 9.487442 TGGTTTATAGGGCTTATCTCAAAATTT 57.513 29.630 0.00 0.00 0.00 1.82
199 200 9.447157 TTTTCCATTTTATAAGGCTCAATTTGG 57.553 29.630 0.00 0.00 0.00 3.28
200 201 7.732222 TCCATTTTATAAGGCTCAATTTGGT 57.268 32.000 0.00 0.00 0.00 3.67
201 202 8.144862 TCCATTTTATAAGGCTCAATTTGGTT 57.855 30.769 0.00 0.00 0.00 3.67
202 203 8.040132 TCCATTTTATAAGGCTCAATTTGGTTG 58.960 33.333 0.00 0.00 39.25 3.77
203 204 7.823799 CCATTTTATAAGGCTCAATTTGGTTGT 59.176 33.333 0.00 0.00 38.95 3.32
204 205 9.218440 CATTTTATAAGGCTCAATTTGGTTGTT 57.782 29.630 0.00 0.00 38.95 2.83
205 206 8.825667 TTTTATAAGGCTCAATTTGGTTGTTC 57.174 30.769 0.00 0.00 38.95 3.18
206 207 3.751479 AAGGCTCAATTTGGTTGTTCC 57.249 42.857 0.00 0.00 38.95 3.62
207 208 1.970640 AGGCTCAATTTGGTTGTTCCC 59.029 47.619 0.00 0.00 38.95 3.97
208 209 1.001974 GGCTCAATTTGGTTGTTCCCC 59.998 52.381 0.00 0.00 38.95 4.81
209 210 1.691434 GCTCAATTTGGTTGTTCCCCA 59.309 47.619 0.00 0.00 38.95 4.96
210 211 2.302733 GCTCAATTTGGTTGTTCCCCAT 59.697 45.455 0.00 0.00 38.95 4.00
211 212 3.617288 GCTCAATTTGGTTGTTCCCCATC 60.617 47.826 0.00 0.00 38.95 3.51
212 213 3.577848 CTCAATTTGGTTGTTCCCCATCA 59.422 43.478 0.00 0.00 38.95 3.07
213 214 3.323403 TCAATTTGGTTGTTCCCCATCAC 59.677 43.478 0.00 0.00 38.95 3.06
214 215 2.461300 TTTGGTTGTTCCCCATCACA 57.539 45.000 0.00 0.00 34.77 3.58
215 216 2.692709 TTGGTTGTTCCCCATCACAT 57.307 45.000 0.00 0.00 34.77 3.21
216 217 1.921982 TGGTTGTTCCCCATCACATG 58.078 50.000 0.00 0.00 34.77 3.21
217 218 1.146774 TGGTTGTTCCCCATCACATGT 59.853 47.619 0.00 0.00 34.77 3.21
218 219 2.247358 GGTTGTTCCCCATCACATGTT 58.753 47.619 0.00 0.00 0.00 2.71
219 220 2.231235 GGTTGTTCCCCATCACATGTTC 59.769 50.000 0.00 0.00 0.00 3.18
220 221 2.890311 GTTGTTCCCCATCACATGTTCA 59.110 45.455 0.00 0.00 0.00 3.18
221 222 2.794103 TGTTCCCCATCACATGTTCAG 58.206 47.619 0.00 0.00 0.00 3.02
222 223 2.374839 TGTTCCCCATCACATGTTCAGA 59.625 45.455 0.00 0.00 0.00 3.27
223 224 2.749621 GTTCCCCATCACATGTTCAGAC 59.250 50.000 0.00 0.00 0.00 3.51
224 225 2.269023 TCCCCATCACATGTTCAGACT 58.731 47.619 0.00 0.00 0.00 3.24
225 226 2.644299 TCCCCATCACATGTTCAGACTT 59.356 45.455 0.00 0.00 0.00 3.01
226 227 3.074390 TCCCCATCACATGTTCAGACTTT 59.926 43.478 0.00 0.00 0.00 2.66
227 228 4.288366 TCCCCATCACATGTTCAGACTTTA 59.712 41.667 0.00 0.00 0.00 1.85
228 229 5.009631 CCCCATCACATGTTCAGACTTTAA 58.990 41.667 0.00 0.00 0.00 1.52
229 230 5.124457 CCCCATCACATGTTCAGACTTTAAG 59.876 44.000 0.00 0.00 0.00 1.85
230 231 5.124457 CCCATCACATGTTCAGACTTTAAGG 59.876 44.000 0.00 0.00 0.00 2.69
231 232 5.707298 CCATCACATGTTCAGACTTTAAGGT 59.293 40.000 0.00 0.00 0.00 3.50
232 233 6.348786 CCATCACATGTTCAGACTTTAAGGTG 60.349 42.308 0.00 0.00 0.00 4.00
233 234 4.515191 TCACATGTTCAGACTTTAAGGTGC 59.485 41.667 0.00 0.00 0.00 5.01
234 235 4.275689 CACATGTTCAGACTTTAAGGTGCA 59.724 41.667 0.00 0.00 0.00 4.57
235 236 5.048504 CACATGTTCAGACTTTAAGGTGCAT 60.049 40.000 0.00 0.00 0.00 3.96
236 237 5.536161 ACATGTTCAGACTTTAAGGTGCATT 59.464 36.000 0.00 0.00 0.00 3.56
237 238 6.714810 ACATGTTCAGACTTTAAGGTGCATTA 59.285 34.615 0.00 0.00 0.00 1.90
238 239 7.230510 ACATGTTCAGACTTTAAGGTGCATTAA 59.769 33.333 0.00 0.00 0.00 1.40
239 240 7.575414 TGTTCAGACTTTAAGGTGCATTAAA 57.425 32.000 0.00 5.39 34.38 1.52
240 241 8.177119 TGTTCAGACTTTAAGGTGCATTAAAT 57.823 30.769 5.86 0.00 34.89 1.40
241 242 8.296713 TGTTCAGACTTTAAGGTGCATTAAATC 58.703 33.333 5.86 6.39 34.89 2.17
242 243 7.994425 TCAGACTTTAAGGTGCATTAAATCA 57.006 32.000 5.86 0.00 34.89 2.57
243 244 8.579850 TCAGACTTTAAGGTGCATTAAATCAT 57.420 30.769 5.86 0.00 34.89 2.45
244 245 9.023962 TCAGACTTTAAGGTGCATTAAATCATT 57.976 29.630 5.86 0.00 34.89 2.57
245 246 9.079833 CAGACTTTAAGGTGCATTAAATCATTG 57.920 33.333 5.86 0.00 34.89 2.82
246 247 7.761249 AGACTTTAAGGTGCATTAAATCATTGC 59.239 33.333 5.86 0.00 34.89 3.56
247 248 7.385267 ACTTTAAGGTGCATTAAATCATTGCA 58.615 30.769 5.86 0.00 43.63 4.08
248 249 8.042515 ACTTTAAGGTGCATTAAATCATTGCAT 58.957 29.630 4.14 0.00 46.90 3.96
249 250 7.773864 TTAAGGTGCATTAAATCATTGCATG 57.226 32.000 4.14 0.00 46.90 4.06
250 251 4.124238 AGGTGCATTAAATCATTGCATGC 58.876 39.130 11.82 11.82 46.90 4.06
251 252 3.872182 GGTGCATTAAATCATTGCATGCA 59.128 39.130 18.46 18.46 46.90 3.96
252 253 4.333095 GGTGCATTAAATCATTGCATGCAA 59.667 37.500 33.57 33.57 46.90 4.08
253 254 5.498159 GTGCATTAAATCATTGCATGCAAG 58.502 37.500 34.15 25.40 46.90 4.01
254 255 5.064198 GTGCATTAAATCATTGCATGCAAGT 59.936 36.000 34.15 21.32 46.90 3.16
255 256 6.256104 GTGCATTAAATCATTGCATGCAAGTA 59.744 34.615 34.15 25.25 46.90 2.24
256 257 6.987404 TGCATTAAATCATTGCATGCAAGTAT 59.013 30.769 34.15 26.18 40.64 2.12
257 258 7.496263 TGCATTAAATCATTGCATGCAAGTATT 59.504 29.630 34.15 29.40 40.64 1.89
258 259 8.980610 GCATTAAATCATTGCATGCAAGTATTA 58.019 29.630 34.15 25.22 39.47 0.98
262 263 8.867112 AAATCATTGCATGCAAGTATTAAGAG 57.133 30.769 34.15 16.39 39.47 2.85
263 264 7.812690 ATCATTGCATGCAAGTATTAAGAGA 57.187 32.000 34.15 20.12 39.47 3.10
264 265 7.628769 TCATTGCATGCAAGTATTAAGAGAA 57.371 32.000 34.15 10.64 39.47 2.87
265 266 8.054152 TCATTGCATGCAAGTATTAAGAGAAA 57.946 30.769 34.15 10.19 39.47 2.52
266 267 8.522003 TCATTGCATGCAAGTATTAAGAGAAAA 58.478 29.630 34.15 9.52 39.47 2.29
267 268 8.589629 CATTGCATGCAAGTATTAAGAGAAAAC 58.410 33.333 34.15 0.00 39.47 2.43
268 269 7.452880 TGCATGCAAGTATTAAGAGAAAACT 57.547 32.000 20.30 0.00 0.00 2.66
269 270 7.307694 TGCATGCAAGTATTAAGAGAAAACTG 58.692 34.615 20.30 0.00 0.00 3.16
270 271 7.174772 TGCATGCAAGTATTAAGAGAAAACTGA 59.825 33.333 20.30 0.00 0.00 3.41
271 272 7.483059 GCATGCAAGTATTAAGAGAAAACTGAC 59.517 37.037 14.21 0.00 0.00 3.51
272 273 7.435068 TGCAAGTATTAAGAGAAAACTGACC 57.565 36.000 0.00 0.00 0.00 4.02
273 274 6.995686 TGCAAGTATTAAGAGAAAACTGACCA 59.004 34.615 0.00 0.00 0.00 4.02
274 275 7.500892 TGCAAGTATTAAGAGAAAACTGACCAA 59.499 33.333 0.00 0.00 0.00 3.67
275 276 8.515414 GCAAGTATTAAGAGAAAACTGACCAAT 58.485 33.333 0.00 0.00 0.00 3.16
276 277 9.831737 CAAGTATTAAGAGAAAACTGACCAATG 57.168 33.333 0.00 0.00 0.00 2.82
277 278 8.045176 AGTATTAAGAGAAAACTGACCAATGC 57.955 34.615 0.00 0.00 0.00 3.56
278 279 6.899393 ATTAAGAGAAAACTGACCAATGCA 57.101 33.333 0.00 0.00 0.00 3.96
279 280 6.899393 TTAAGAGAAAACTGACCAATGCAT 57.101 33.333 0.00 0.00 0.00 3.96
280 281 4.778534 AGAGAAAACTGACCAATGCATG 57.221 40.909 0.00 0.00 0.00 4.06
281 282 3.057033 AGAGAAAACTGACCAATGCATGC 60.057 43.478 11.82 11.82 0.00 4.06
282 283 2.629137 AGAAAACTGACCAATGCATGCA 59.371 40.909 25.04 25.04 0.00 3.96
283 284 2.443887 AAACTGACCAATGCATGCAC 57.556 45.000 25.37 10.66 0.00 4.57
284 285 1.624336 AACTGACCAATGCATGCACT 58.376 45.000 25.37 10.02 0.00 4.40
285 286 1.624336 ACTGACCAATGCATGCACTT 58.376 45.000 25.37 15.39 0.00 3.16
286 287 1.965643 ACTGACCAATGCATGCACTTT 59.034 42.857 25.37 12.10 0.00 2.66
287 288 3.156293 ACTGACCAATGCATGCACTTTA 58.844 40.909 25.37 6.77 0.00 1.85
288 289 3.765511 ACTGACCAATGCATGCACTTTAT 59.234 39.130 25.37 7.83 0.00 1.40
289 290 4.109766 CTGACCAATGCATGCACTTTATG 58.890 43.478 25.37 16.06 0.00 1.90
354 355 9.612066 TTTTTGAGGAAAACAAGAGCATTAATT 57.388 25.926 0.00 0.00 32.44 1.40
356 357 9.912634 TTTGAGGAAAACAAGAGCATTAATTAG 57.087 29.630 0.00 0.00 0.00 1.73
357 358 8.055279 TGAGGAAAACAAGAGCATTAATTAGG 57.945 34.615 0.00 0.00 0.00 2.69
358 359 7.669722 TGAGGAAAACAAGAGCATTAATTAGGT 59.330 33.333 0.00 0.00 0.00 3.08
359 360 7.830739 AGGAAAACAAGAGCATTAATTAGGTG 58.169 34.615 0.00 0.00 0.00 4.00
360 361 7.451566 AGGAAAACAAGAGCATTAATTAGGTGT 59.548 33.333 0.00 0.00 0.00 4.16
361 362 8.088365 GGAAAACAAGAGCATTAATTAGGTGTT 58.912 33.333 0.00 0.00 0.00 3.32
362 363 9.476202 GAAAACAAGAGCATTAATTAGGTGTTT 57.524 29.630 7.63 7.63 38.06 2.83
363 364 9.830975 AAAACAAGAGCATTAATTAGGTGTTTT 57.169 25.926 14.78 14.78 40.15 2.43
364 365 9.830975 AAACAAGAGCATTAATTAGGTGTTTTT 57.169 25.926 7.63 0.00 34.04 1.94
365 366 8.816640 ACAAGAGCATTAATTAGGTGTTTTTG 57.183 30.769 13.29 13.29 0.00 2.44
366 367 7.384932 ACAAGAGCATTAATTAGGTGTTTTTGC 59.615 33.333 14.10 0.00 0.00 3.68
367 368 6.991938 AGAGCATTAATTAGGTGTTTTTGCA 58.008 32.000 0.00 0.00 0.00 4.08
368 369 7.441017 AGAGCATTAATTAGGTGTTTTTGCAA 58.559 30.769 0.00 0.00 0.00 4.08
369 370 7.930865 AGAGCATTAATTAGGTGTTTTTGCAAA 59.069 29.630 8.05 8.05 0.00 3.68
370 371 7.860613 AGCATTAATTAGGTGTTTTTGCAAAC 58.139 30.769 12.39 2.38 42.49 2.93
371 372 7.714813 AGCATTAATTAGGTGTTTTTGCAAACT 59.285 29.630 12.39 7.91 42.61 2.66
372 373 8.983724 GCATTAATTAGGTGTTTTTGCAAACTA 58.016 29.630 12.39 6.86 42.61 2.24
375 376 9.871238 TTAATTAGGTGTTTTTGCAAACTACAA 57.129 25.926 21.46 8.51 42.61 2.41
376 377 8.779354 AATTAGGTGTTTTTGCAAACTACAAA 57.221 26.923 21.46 15.22 42.61 2.83
377 378 8.779354 ATTAGGTGTTTTTGCAAACTACAAAA 57.221 26.923 21.46 17.05 43.33 2.44
401 402 8.915057 AAAATATTCCACCACTCATCATCTAG 57.085 34.615 0.00 0.00 0.00 2.43
402 403 3.827008 TTCCACCACTCATCATCTAGC 57.173 47.619 0.00 0.00 0.00 3.42
403 404 3.037851 TCCACCACTCATCATCTAGCT 57.962 47.619 0.00 0.00 0.00 3.32
404 405 3.378512 TCCACCACTCATCATCTAGCTT 58.621 45.455 0.00 0.00 0.00 3.74
405 406 3.133542 TCCACCACTCATCATCTAGCTTG 59.866 47.826 0.00 0.00 0.00 4.01
406 407 3.464907 CACCACTCATCATCTAGCTTGG 58.535 50.000 0.00 0.00 0.00 3.61
407 408 3.110705 ACCACTCATCATCTAGCTTGGT 58.889 45.455 0.00 0.00 0.00 3.67
408 409 3.521126 ACCACTCATCATCTAGCTTGGTT 59.479 43.478 0.00 0.00 0.00 3.67
409 410 3.875727 CCACTCATCATCTAGCTTGGTTG 59.124 47.826 0.00 0.00 0.00 3.77
410 411 4.383444 CCACTCATCATCTAGCTTGGTTGA 60.383 45.833 0.00 0.00 0.00 3.18
411 412 5.366460 CACTCATCATCTAGCTTGGTTGAT 58.634 41.667 0.00 0.00 0.00 2.57
412 413 5.236695 CACTCATCATCTAGCTTGGTTGATG 59.763 44.000 23.02 23.02 43.10 3.07
413 414 5.129980 ACTCATCATCTAGCTTGGTTGATGA 59.870 40.000 26.32 26.32 46.22 2.92
414 415 5.608449 TCATCATCTAGCTTGGTTGATGAG 58.392 41.667 25.36 17.19 44.56 2.90
415 416 5.364735 TCATCATCTAGCTTGGTTGATGAGA 59.635 40.000 25.36 18.45 44.56 3.27
416 417 5.883685 TCATCTAGCTTGGTTGATGAGAT 57.116 39.130 17.81 0.00 39.91 2.75
417 418 6.244552 TCATCTAGCTTGGTTGATGAGATT 57.755 37.500 17.81 0.00 39.91 2.40
418 419 6.656902 TCATCTAGCTTGGTTGATGAGATTT 58.343 36.000 17.81 0.00 39.91 2.17
419 420 7.114754 TCATCTAGCTTGGTTGATGAGATTTT 58.885 34.615 17.81 0.00 39.91 1.82
420 421 7.613022 TCATCTAGCTTGGTTGATGAGATTTTT 59.387 33.333 17.81 0.00 39.91 1.94
421 422 7.149569 TCTAGCTTGGTTGATGAGATTTTTG 57.850 36.000 0.00 0.00 0.00 2.44
422 423 6.942005 TCTAGCTTGGTTGATGAGATTTTTGA 59.058 34.615 0.00 0.00 0.00 2.69
423 424 6.409524 AGCTTGGTTGATGAGATTTTTGAA 57.590 33.333 0.00 0.00 0.00 2.69
424 425 7.001099 AGCTTGGTTGATGAGATTTTTGAAT 57.999 32.000 0.00 0.00 0.00 2.57
425 426 7.447594 AGCTTGGTTGATGAGATTTTTGAATT 58.552 30.769 0.00 0.00 0.00 2.17
426 427 7.386848 AGCTTGGTTGATGAGATTTTTGAATTG 59.613 33.333 0.00 0.00 0.00 2.32
427 428 7.385752 GCTTGGTTGATGAGATTTTTGAATTGA 59.614 33.333 0.00 0.00 0.00 2.57
428 429 8.821147 TTGGTTGATGAGATTTTTGAATTGAG 57.179 30.769 0.00 0.00 0.00 3.02
429 430 6.869913 TGGTTGATGAGATTTTTGAATTGAGC 59.130 34.615 0.00 0.00 0.00 4.26
430 431 6.312180 GGTTGATGAGATTTTTGAATTGAGCC 59.688 38.462 0.00 0.00 0.00 4.70
431 432 6.845758 TGATGAGATTTTTGAATTGAGCCT 57.154 33.333 0.00 0.00 0.00 4.58
432 433 7.235935 TGATGAGATTTTTGAATTGAGCCTT 57.764 32.000 0.00 0.00 0.00 4.35
433 434 8.352137 TGATGAGATTTTTGAATTGAGCCTTA 57.648 30.769 0.00 0.00 0.00 2.69
434 435 8.974238 TGATGAGATTTTTGAATTGAGCCTTAT 58.026 29.630 0.00 0.00 0.00 1.73
439 440 9.875691 AGATTTTTGAATTGAGCCTTATAAACC 57.124 29.630 0.00 0.00 0.00 3.27
440 441 8.702163 ATTTTTGAATTGAGCCTTATAAACCG 57.298 30.769 0.00 0.00 0.00 4.44
441 442 7.455641 TTTTGAATTGAGCCTTATAAACCGA 57.544 32.000 0.00 0.00 0.00 4.69
442 443 7.455641 TTTGAATTGAGCCTTATAAACCGAA 57.544 32.000 0.00 0.00 0.00 4.30
443 444 7.455641 TTGAATTGAGCCTTATAAACCGAAA 57.544 32.000 0.00 0.00 0.00 3.46
444 445 7.455641 TGAATTGAGCCTTATAAACCGAAAA 57.544 32.000 0.00 0.00 0.00 2.29
445 446 7.535139 TGAATTGAGCCTTATAAACCGAAAAG 58.465 34.615 0.00 0.00 0.00 2.27
447 448 5.168647 TGAGCCTTATAAACCGAAAAGGA 57.831 39.130 4.19 0.00 45.00 3.36
448 449 5.183228 TGAGCCTTATAAACCGAAAAGGAG 58.817 41.667 4.19 0.00 45.00 3.69
449 450 4.524053 AGCCTTATAAACCGAAAAGGAGG 58.476 43.478 4.19 0.00 45.00 4.30
450 451 3.630769 GCCTTATAAACCGAAAAGGAGGG 59.369 47.826 4.19 0.00 45.00 4.30
451 452 4.627013 GCCTTATAAACCGAAAAGGAGGGA 60.627 45.833 4.19 0.00 45.00 4.20
452 453 5.123936 CCTTATAAACCGAAAAGGAGGGAG 58.876 45.833 0.00 0.00 45.00 4.30
469 470 6.443849 AGGAGGGAGTAAATGTGAATGAACTA 59.556 38.462 0.00 0.00 0.00 2.24
544 545 6.735510 GCAATGATAAATCAAGATCGTCATCG 59.264 38.462 0.00 0.00 40.69 3.84
567 568 4.783242 CCTAACATTTTCCGATTATGGCG 58.217 43.478 0.00 0.00 0.00 5.69
569 570 1.002900 ACATTTTCCGATTATGGCGCG 60.003 47.619 0.00 0.00 0.00 6.86
584 585 0.913876 GCGCGTTTGATTGGTATTGC 59.086 50.000 8.43 0.00 0.00 3.56
585 586 1.179332 CGCGTTTGATTGGTATTGCG 58.821 50.000 0.00 0.00 38.28 4.85
605 606 2.611971 CGGTGTTGTTGCTAAGGCTAGA 60.612 50.000 0.00 0.00 39.59 2.43
606 607 3.610911 GGTGTTGTTGCTAAGGCTAGAT 58.389 45.455 0.00 0.00 39.59 1.98
684 685 5.082425 TCTCTAGTCGAACCCTTAAAAGGT 58.918 41.667 7.94 0.00 44.98 3.50
730 731 5.765576 TTACACCTCTAATTGGCACCTAA 57.234 39.130 0.00 0.00 0.00 2.69
787 788 2.295253 AATTACTCCTTGACTCCGCG 57.705 50.000 0.00 0.00 0.00 6.46
790 791 4.821589 CTCCTTGACTCCGCGGGC 62.822 72.222 27.83 15.78 0.00 6.13
835 840 5.652518 GAGCGGTAGACTAACAAATCTTCT 58.347 41.667 0.00 0.00 0.00 2.85
847 852 0.914417 AATCTTCTCCCCCTTCGGCA 60.914 55.000 0.00 0.00 0.00 5.69
852 857 4.722535 TCCCCCTTCGGCAGCTCT 62.723 66.667 0.00 0.00 0.00 4.09
858 863 2.604686 TTCGGCAGCTCTCACCCT 60.605 61.111 0.00 0.00 0.00 4.34
970 975 2.760477 CACCCACCCGGATTTGGA 59.240 61.111 16.08 0.00 34.46 3.53
998 1003 1.573829 ATCGGCGACATTGCGTTTGT 61.574 50.000 13.76 0.00 35.06 2.83
1011 1016 1.463056 GCGTTTGTGATGGATTCGACA 59.537 47.619 0.00 0.00 0.00 4.35
1017 1022 2.829120 TGTGATGGATTCGACAGGTACA 59.171 45.455 0.00 0.00 0.00 2.90
1018 1023 3.119137 TGTGATGGATTCGACAGGTACAG 60.119 47.826 0.00 0.00 0.00 2.74
1070 1076 1.051812 CATCTCGGTATGGCCTCCTT 58.948 55.000 3.32 0.00 34.25 3.36
1100 1106 0.393132 TCGGAGCTCAGTCATCGACT 60.393 55.000 17.19 0.00 44.44 4.18
1124 1130 0.462937 ACTGGCACAACTACGCACAA 60.463 50.000 0.00 0.00 38.70 3.33
1126 1132 0.871722 TGGCACAACTACGCACAATC 59.128 50.000 0.00 0.00 31.92 2.67
1235 1244 2.032634 GCCGAGTTTCGACCATGCA 61.033 57.895 0.00 0.00 43.74 3.96
1376 1399 4.162131 GGATGCAAGTTTTGGTATTGGGAT 59.838 41.667 0.00 0.00 0.00 3.85
1738 1792 3.213206 TGGGGCATGCTAGTTTCTATG 57.787 47.619 18.92 0.00 0.00 2.23
1765 1819 8.687242 GGAGGTTTATTAAAGATTTCTCCAAGG 58.313 37.037 0.00 0.00 38.40 3.61
1817 1871 7.917505 GCAGAAAGATGTACCATATTCTTTTGG 59.082 37.037 0.00 0.00 38.25 3.28
1964 2020 0.945813 GTCCTAGGACGACGAGATGG 59.054 60.000 25.83 0.00 35.30 3.51
1966 2022 1.764723 TCCTAGGACGACGAGATGGTA 59.235 52.381 7.62 0.00 0.00 3.25
2002 2059 4.073293 TGCCTTTTATGCTAGTAGGAGC 57.927 45.455 0.00 0.00 43.16 4.70
2178 3842 2.930826 AGCCCCGTTTGATTCGATAT 57.069 45.000 0.00 0.00 0.00 1.63
2233 3901 1.072505 GAAGGGGCGAAGACAACCA 59.927 57.895 0.00 0.00 37.00 3.67
2254 3922 1.765314 AGTGGCAGATCACCTATCACC 59.235 52.381 6.38 0.00 38.34 4.02
2284 3952 4.296056 AGGATACCTTACGAACCCATTCT 58.704 43.478 0.00 0.00 31.54 2.40
2388 4059 7.624360 TTTGTAGGAAAGTACATGCCATAAG 57.376 36.000 0.00 0.00 32.92 1.73
2399 4085 7.093354 AGTACATGCCATAAGATGAACTATCG 58.907 38.462 0.00 0.00 40.86 2.92
2400 4086 4.692625 ACATGCCATAAGATGAACTATCGC 59.307 41.667 0.00 0.00 40.86 4.58
2449 4137 8.265764 AGTTAAAATACTACTTCTGGGATGACC 58.734 37.037 0.00 0.00 40.81 4.02
2453 4141 6.893020 ATACTACTTCTGGGATGACCTTTT 57.107 37.500 0.00 0.00 41.11 2.27
2523 4216 3.675225 CACGAGATGAACGTCATTCTTGT 59.325 43.478 8.07 8.07 42.07 3.16
2565 4258 1.039233 GCAGGACATCATGTTGGGGG 61.039 60.000 8.58 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 3.604582 CTTTCTCACCTTCCCATCTCAC 58.395 50.000 0.00 0.00 0.00 3.51
128 129 6.386050 CCCTATAAACCAGAAAGGAGGAAGTA 59.614 42.308 0.00 0.00 41.22 2.24
129 130 5.191921 CCCTATAAACCAGAAAGGAGGAAGT 59.808 44.000 0.00 0.00 41.22 3.01
130 131 5.685728 CCCTATAAACCAGAAAGGAGGAAG 58.314 45.833 0.00 0.00 41.22 3.46
131 132 4.079958 GCCCTATAAACCAGAAAGGAGGAA 60.080 45.833 0.00 0.00 41.22 3.36
132 133 3.458487 GCCCTATAAACCAGAAAGGAGGA 59.542 47.826 0.00 0.00 41.22 3.71
133 134 3.459969 AGCCCTATAAACCAGAAAGGAGG 59.540 47.826 0.00 0.00 41.22 4.30
134 135 4.779993 AGCCCTATAAACCAGAAAGGAG 57.220 45.455 0.00 0.00 41.22 3.69
135 136 6.619852 AGATAAGCCCTATAAACCAGAAAGGA 59.380 38.462 0.00 0.00 41.22 3.36
136 137 6.842676 AGATAAGCCCTATAAACCAGAAAGG 58.157 40.000 0.00 0.00 45.67 3.11
137 138 7.509546 TGAGATAAGCCCTATAAACCAGAAAG 58.490 38.462 0.00 0.00 0.00 2.62
138 139 7.446106 TGAGATAAGCCCTATAAACCAGAAA 57.554 36.000 0.00 0.00 0.00 2.52
139 140 7.446106 TTGAGATAAGCCCTATAAACCAGAA 57.554 36.000 0.00 0.00 0.00 3.02
140 141 7.446106 TTTGAGATAAGCCCTATAAACCAGA 57.554 36.000 0.00 0.00 0.00 3.86
141 142 8.697507 ATTTTGAGATAAGCCCTATAAACCAG 57.302 34.615 0.00 0.00 0.00 4.00
142 143 9.487442 AAATTTTGAGATAAGCCCTATAAACCA 57.513 29.630 0.00 0.00 0.00 3.67
173 174 9.447157 CCAAATTGAGCCTTATAAAATGGAAAA 57.553 29.630 0.00 0.00 0.00 2.29
174 175 8.601546 ACCAAATTGAGCCTTATAAAATGGAAA 58.398 29.630 0.00 0.00 0.00 3.13
175 176 8.144862 ACCAAATTGAGCCTTATAAAATGGAA 57.855 30.769 0.00 0.00 0.00 3.53
176 177 7.732222 ACCAAATTGAGCCTTATAAAATGGA 57.268 32.000 0.00 0.00 0.00 3.41
177 178 7.823799 ACAACCAAATTGAGCCTTATAAAATGG 59.176 33.333 0.00 0.00 41.23 3.16
178 179 8.776376 ACAACCAAATTGAGCCTTATAAAATG 57.224 30.769 0.00 0.00 41.23 2.32
179 180 9.435688 GAACAACCAAATTGAGCCTTATAAAAT 57.564 29.630 0.00 0.00 41.23 1.82
180 181 7.875554 GGAACAACCAAATTGAGCCTTATAAAA 59.124 33.333 0.00 0.00 41.23 1.52
181 182 7.382898 GGAACAACCAAATTGAGCCTTATAAA 58.617 34.615 0.00 0.00 41.23 1.40
182 183 6.071051 GGGAACAACCAAATTGAGCCTTATAA 60.071 38.462 0.00 0.00 41.23 0.98
183 184 5.420739 GGGAACAACCAAATTGAGCCTTATA 59.579 40.000 0.00 0.00 41.23 0.98
184 185 4.222810 GGGAACAACCAAATTGAGCCTTAT 59.777 41.667 0.00 0.00 41.23 1.73
185 186 3.576550 GGGAACAACCAAATTGAGCCTTA 59.423 43.478 0.00 0.00 41.23 2.69
186 187 2.368548 GGGAACAACCAAATTGAGCCTT 59.631 45.455 0.00 0.00 41.23 4.35
187 188 1.970640 GGGAACAACCAAATTGAGCCT 59.029 47.619 0.00 0.00 41.23 4.58
188 189 1.001974 GGGGAACAACCAAATTGAGCC 59.998 52.381 0.00 0.00 41.23 4.70
189 190 1.691434 TGGGGAACAACCAAATTGAGC 59.309 47.619 0.00 0.00 41.23 4.26
190 191 3.577848 TGATGGGGAACAACCAAATTGAG 59.422 43.478 0.00 0.00 42.17 3.02
191 192 3.323403 GTGATGGGGAACAACCAAATTGA 59.677 43.478 0.00 0.00 42.17 2.57
192 193 3.070734 TGTGATGGGGAACAACCAAATTG 59.929 43.478 0.00 0.00 42.17 2.32
193 194 3.312890 TGTGATGGGGAACAACCAAATT 58.687 40.909 0.00 0.00 42.17 1.82
194 195 2.969628 TGTGATGGGGAACAACCAAAT 58.030 42.857 0.00 0.00 42.17 2.32
195 196 2.461300 TGTGATGGGGAACAACCAAA 57.539 45.000 0.00 0.00 42.17 3.28
196 197 2.246469 CATGTGATGGGGAACAACCAA 58.754 47.619 0.00 0.00 42.17 3.67
197 198 1.146774 ACATGTGATGGGGAACAACCA 59.853 47.619 0.00 0.00 43.22 3.67
198 199 1.923356 ACATGTGATGGGGAACAACC 58.077 50.000 0.00 0.00 38.08 3.77
199 200 2.890311 TGAACATGTGATGGGGAACAAC 59.110 45.455 0.00 0.00 33.60 3.32
200 201 3.156293 CTGAACATGTGATGGGGAACAA 58.844 45.455 0.00 0.00 33.60 2.83
201 202 2.374839 TCTGAACATGTGATGGGGAACA 59.625 45.455 0.00 0.00 33.60 3.18
202 203 2.749621 GTCTGAACATGTGATGGGGAAC 59.250 50.000 0.00 0.00 33.60 3.62
203 204 2.644299 AGTCTGAACATGTGATGGGGAA 59.356 45.455 0.00 0.00 33.60 3.97
204 205 2.269023 AGTCTGAACATGTGATGGGGA 58.731 47.619 0.00 0.00 33.60 4.81
205 206 2.795231 AGTCTGAACATGTGATGGGG 57.205 50.000 0.00 0.00 33.60 4.96
206 207 5.124457 CCTTAAAGTCTGAACATGTGATGGG 59.876 44.000 0.00 0.00 33.60 4.00
207 208 5.707298 ACCTTAAAGTCTGAACATGTGATGG 59.293 40.000 0.00 0.00 33.60 3.51
208 209 6.605849 CACCTTAAAGTCTGAACATGTGATG 58.394 40.000 0.00 0.00 0.00 3.07
209 210 5.182001 GCACCTTAAAGTCTGAACATGTGAT 59.818 40.000 0.00 0.00 0.00 3.06
210 211 4.515191 GCACCTTAAAGTCTGAACATGTGA 59.485 41.667 0.00 0.00 0.00 3.58
211 212 4.275689 TGCACCTTAAAGTCTGAACATGTG 59.724 41.667 0.00 0.00 0.00 3.21
212 213 4.460263 TGCACCTTAAAGTCTGAACATGT 58.540 39.130 0.00 0.00 0.00 3.21
213 214 5.633830 ATGCACCTTAAAGTCTGAACATG 57.366 39.130 0.00 0.00 0.00 3.21
214 215 7.759489 TTAATGCACCTTAAAGTCTGAACAT 57.241 32.000 0.00 0.00 0.00 2.71
215 216 7.575414 TTTAATGCACCTTAAAGTCTGAACA 57.425 32.000 0.00 0.00 0.00 3.18
216 217 8.296713 TGATTTAATGCACCTTAAAGTCTGAAC 58.703 33.333 10.19 0.16 34.89 3.18
217 218 8.402798 TGATTTAATGCACCTTAAAGTCTGAA 57.597 30.769 10.19 0.00 34.89 3.02
218 219 7.994425 TGATTTAATGCACCTTAAAGTCTGA 57.006 32.000 10.19 0.00 34.89 3.27
219 220 9.079833 CAATGATTTAATGCACCTTAAAGTCTG 57.920 33.333 10.19 3.40 34.89 3.51
220 221 7.761249 GCAATGATTTAATGCACCTTAAAGTCT 59.239 33.333 10.19 0.00 39.81 3.24
221 222 7.545265 TGCAATGATTTAATGCACCTTAAAGTC 59.455 33.333 10.19 8.58 44.52 3.01
222 223 7.385267 TGCAATGATTTAATGCACCTTAAAGT 58.615 30.769 10.19 1.37 44.52 2.66
223 224 7.830940 TGCAATGATTTAATGCACCTTAAAG 57.169 32.000 10.19 0.16 44.52 1.85
242 243 8.526147 AGTTTTCTCTTAATACTTGCATGCAAT 58.474 29.630 31.96 22.79 35.20 3.56
243 244 7.809331 CAGTTTTCTCTTAATACTTGCATGCAA 59.191 33.333 30.12 30.12 0.00 4.08
244 245 7.174772 TCAGTTTTCTCTTAATACTTGCATGCA 59.825 33.333 18.46 18.46 0.00 3.96
245 246 7.483059 GTCAGTTTTCTCTTAATACTTGCATGC 59.517 37.037 11.82 11.82 0.00 4.06
246 247 7.965107 GGTCAGTTTTCTCTTAATACTTGCATG 59.035 37.037 0.00 0.00 0.00 4.06
247 248 7.665559 TGGTCAGTTTTCTCTTAATACTTGCAT 59.334 33.333 0.00 0.00 0.00 3.96
248 249 6.995686 TGGTCAGTTTTCTCTTAATACTTGCA 59.004 34.615 0.00 0.00 0.00 4.08
249 250 7.435068 TGGTCAGTTTTCTCTTAATACTTGC 57.565 36.000 0.00 0.00 0.00 4.01
250 251 9.831737 CATTGGTCAGTTTTCTCTTAATACTTG 57.168 33.333 0.00 0.00 0.00 3.16
251 252 8.515414 GCATTGGTCAGTTTTCTCTTAATACTT 58.485 33.333 0.00 0.00 0.00 2.24
252 253 7.665559 TGCATTGGTCAGTTTTCTCTTAATACT 59.334 33.333 0.00 0.00 0.00 2.12
253 254 7.816640 TGCATTGGTCAGTTTTCTCTTAATAC 58.183 34.615 0.00 0.00 0.00 1.89
254 255 7.994425 TGCATTGGTCAGTTTTCTCTTAATA 57.006 32.000 0.00 0.00 0.00 0.98
255 256 6.899393 TGCATTGGTCAGTTTTCTCTTAAT 57.101 33.333 0.00 0.00 0.00 1.40
256 257 6.680810 CATGCATTGGTCAGTTTTCTCTTAA 58.319 36.000 0.00 0.00 0.00 1.85
257 258 5.335897 GCATGCATTGGTCAGTTTTCTCTTA 60.336 40.000 14.21 0.00 0.00 2.10
258 259 4.560108 GCATGCATTGGTCAGTTTTCTCTT 60.560 41.667 14.21 0.00 0.00 2.85
259 260 3.057033 GCATGCATTGGTCAGTTTTCTCT 60.057 43.478 14.21 0.00 0.00 3.10
260 261 3.248266 GCATGCATTGGTCAGTTTTCTC 58.752 45.455 14.21 0.00 0.00 2.87
261 262 2.629137 TGCATGCATTGGTCAGTTTTCT 59.371 40.909 18.46 0.00 0.00 2.52
262 263 2.733026 GTGCATGCATTGGTCAGTTTTC 59.267 45.455 25.64 1.60 0.00 2.29
263 264 2.366266 AGTGCATGCATTGGTCAGTTTT 59.634 40.909 25.64 0.00 0.00 2.43
264 265 1.965643 AGTGCATGCATTGGTCAGTTT 59.034 42.857 25.64 0.00 0.00 2.66
265 266 1.624336 AGTGCATGCATTGGTCAGTT 58.376 45.000 25.64 0.00 0.00 3.16
266 267 1.624336 AAGTGCATGCATTGGTCAGT 58.376 45.000 25.64 0.00 0.00 3.41
267 268 2.736144 AAAGTGCATGCATTGGTCAG 57.264 45.000 25.64 0.00 0.00 3.51
268 269 4.112716 CATAAAGTGCATGCATTGGTCA 57.887 40.909 25.64 7.86 0.00 4.02
328 329 9.612066 AATTAATGCTCTTGTTTTCCTCAAAAA 57.388 25.926 0.00 0.00 33.17 1.94
330 331 9.912634 CTAATTAATGCTCTTGTTTTCCTCAAA 57.087 29.630 0.00 0.00 0.00 2.69
331 332 8.522830 CCTAATTAATGCTCTTGTTTTCCTCAA 58.477 33.333 0.00 0.00 0.00 3.02
332 333 7.669722 ACCTAATTAATGCTCTTGTTTTCCTCA 59.330 33.333 0.00 0.00 0.00 3.86
333 334 7.970614 CACCTAATTAATGCTCTTGTTTTCCTC 59.029 37.037 0.00 0.00 0.00 3.71
334 335 7.451566 ACACCTAATTAATGCTCTTGTTTTCCT 59.548 33.333 0.00 0.00 0.00 3.36
335 336 7.602753 ACACCTAATTAATGCTCTTGTTTTCC 58.397 34.615 0.00 0.00 0.00 3.13
336 337 9.476202 AAACACCTAATTAATGCTCTTGTTTTC 57.524 29.630 8.52 0.00 32.21 2.29
337 338 9.830975 AAAACACCTAATTAATGCTCTTGTTTT 57.169 25.926 15.51 15.51 38.92 2.43
338 339 9.830975 AAAAACACCTAATTAATGCTCTTGTTT 57.169 25.926 8.52 8.52 36.48 2.83
339 340 9.260002 CAAAAACACCTAATTAATGCTCTTGTT 57.740 29.630 0.00 0.00 0.00 2.83
340 341 7.384932 GCAAAAACACCTAATTAATGCTCTTGT 59.615 33.333 0.00 0.00 0.00 3.16
341 342 7.384660 TGCAAAAACACCTAATTAATGCTCTTG 59.615 33.333 0.00 0.00 32.74 3.02
342 343 7.441017 TGCAAAAACACCTAATTAATGCTCTT 58.559 30.769 0.00 0.00 32.74 2.85
343 344 6.991938 TGCAAAAACACCTAATTAATGCTCT 58.008 32.000 0.00 0.00 32.74 4.09
344 345 7.650834 TTGCAAAAACACCTAATTAATGCTC 57.349 32.000 0.00 0.00 32.74 4.26
345 346 7.714813 AGTTTGCAAAAACACCTAATTAATGCT 59.285 29.630 14.67 0.00 35.20 3.79
346 347 7.860613 AGTTTGCAAAAACACCTAATTAATGC 58.139 30.769 14.67 0.00 35.20 3.56
349 350 9.871238 TTGTAGTTTGCAAAAACACCTAATTAA 57.129 25.926 21.86 9.92 35.20 1.40
350 351 9.871238 TTTGTAGTTTGCAAAAACACCTAATTA 57.129 25.926 21.86 8.40 33.51 1.40
351 352 8.779354 TTTGTAGTTTGCAAAAACACCTAATT 57.221 26.923 21.86 0.00 33.51 1.40
352 353 8.779354 TTTTGTAGTTTGCAAAAACACCTAAT 57.221 26.923 21.86 0.00 41.18 1.73
353 354 8.603242 TTTTTGTAGTTTGCAAAAACACCTAA 57.397 26.923 21.86 14.12 45.24 2.69
375 376 9.347240 CTAGATGATGAGTGGTGGAATATTTTT 57.653 33.333 0.00 0.00 0.00 1.94
376 377 7.446625 GCTAGATGATGAGTGGTGGAATATTTT 59.553 37.037 0.00 0.00 0.00 1.82
377 378 6.939163 GCTAGATGATGAGTGGTGGAATATTT 59.061 38.462 0.00 0.00 0.00 1.40
378 379 6.271857 AGCTAGATGATGAGTGGTGGAATATT 59.728 38.462 0.00 0.00 0.00 1.28
379 380 5.784390 AGCTAGATGATGAGTGGTGGAATAT 59.216 40.000 0.00 0.00 0.00 1.28
380 381 5.150715 AGCTAGATGATGAGTGGTGGAATA 58.849 41.667 0.00 0.00 0.00 1.75
381 382 3.972638 AGCTAGATGATGAGTGGTGGAAT 59.027 43.478 0.00 0.00 0.00 3.01
382 383 3.378512 AGCTAGATGATGAGTGGTGGAA 58.621 45.455 0.00 0.00 0.00 3.53
383 384 3.037851 AGCTAGATGATGAGTGGTGGA 57.962 47.619 0.00 0.00 0.00 4.02
384 385 3.464907 CAAGCTAGATGATGAGTGGTGG 58.535 50.000 0.00 0.00 0.00 4.61
385 386 3.118482 ACCAAGCTAGATGATGAGTGGTG 60.118 47.826 0.00 0.00 36.77 4.17
386 387 3.110705 ACCAAGCTAGATGATGAGTGGT 58.889 45.455 0.00 0.00 33.31 4.16
387 388 3.834489 ACCAAGCTAGATGATGAGTGG 57.166 47.619 0.00 0.00 0.00 4.00
388 389 4.763073 TCAACCAAGCTAGATGATGAGTG 58.237 43.478 0.00 0.00 0.00 3.51
389 390 5.129980 TCATCAACCAAGCTAGATGATGAGT 59.870 40.000 24.13 3.46 46.77 3.41
390 391 5.608449 TCATCAACCAAGCTAGATGATGAG 58.392 41.667 24.13 9.92 46.77 2.90
392 393 5.608449 TCTCATCAACCAAGCTAGATGATG 58.392 41.667 21.52 21.52 43.99 3.07
393 394 5.883685 TCTCATCAACCAAGCTAGATGAT 57.116 39.130 12.87 8.97 43.99 2.45
394 395 5.883685 ATCTCATCAACCAAGCTAGATGA 57.116 39.130 12.25 12.25 43.14 2.92
395 396 6.939132 AAATCTCATCAACCAAGCTAGATG 57.061 37.500 0.00 0.00 39.29 2.90
396 397 7.613022 TCAAAAATCTCATCAACCAAGCTAGAT 59.387 33.333 0.00 0.00 0.00 1.98
397 398 6.942005 TCAAAAATCTCATCAACCAAGCTAGA 59.058 34.615 0.00 0.00 0.00 2.43
398 399 7.149569 TCAAAAATCTCATCAACCAAGCTAG 57.850 36.000 0.00 0.00 0.00 3.42
399 400 7.523293 TTCAAAAATCTCATCAACCAAGCTA 57.477 32.000 0.00 0.00 0.00 3.32
400 401 6.409524 TTCAAAAATCTCATCAACCAAGCT 57.590 33.333 0.00 0.00 0.00 3.74
401 402 7.385752 TCAATTCAAAAATCTCATCAACCAAGC 59.614 33.333 0.00 0.00 0.00 4.01
402 403 8.821147 TCAATTCAAAAATCTCATCAACCAAG 57.179 30.769 0.00 0.00 0.00 3.61
403 404 7.385752 GCTCAATTCAAAAATCTCATCAACCAA 59.614 33.333 0.00 0.00 0.00 3.67
404 405 6.869913 GCTCAATTCAAAAATCTCATCAACCA 59.130 34.615 0.00 0.00 0.00 3.67
405 406 6.312180 GGCTCAATTCAAAAATCTCATCAACC 59.688 38.462 0.00 0.00 0.00 3.77
406 407 7.095270 AGGCTCAATTCAAAAATCTCATCAAC 58.905 34.615 0.00 0.00 0.00 3.18
407 408 7.235935 AGGCTCAATTCAAAAATCTCATCAA 57.764 32.000 0.00 0.00 0.00 2.57
408 409 6.845758 AGGCTCAATTCAAAAATCTCATCA 57.154 33.333 0.00 0.00 0.00 3.07
413 414 9.875691 GGTTTATAAGGCTCAATTCAAAAATCT 57.124 29.630 0.00 0.00 0.00 2.40
414 415 8.807581 CGGTTTATAAGGCTCAATTCAAAAATC 58.192 33.333 0.00 0.00 0.00 2.17
415 416 8.527810 TCGGTTTATAAGGCTCAATTCAAAAAT 58.472 29.630 0.00 0.00 0.00 1.82
416 417 7.887381 TCGGTTTATAAGGCTCAATTCAAAAA 58.113 30.769 0.00 0.00 0.00 1.94
417 418 7.455641 TCGGTTTATAAGGCTCAATTCAAAA 57.544 32.000 0.00 0.00 0.00 2.44
418 419 7.455641 TTCGGTTTATAAGGCTCAATTCAAA 57.544 32.000 0.00 0.00 0.00 2.69
419 420 7.455641 TTTCGGTTTATAAGGCTCAATTCAA 57.544 32.000 0.00 0.00 0.00 2.69
420 421 7.362574 CCTTTTCGGTTTATAAGGCTCAATTCA 60.363 37.037 0.00 0.00 31.59 2.57
421 422 6.972901 CCTTTTCGGTTTATAAGGCTCAATTC 59.027 38.462 0.00 0.00 31.59 2.17
422 423 6.661805 TCCTTTTCGGTTTATAAGGCTCAATT 59.338 34.615 0.00 0.00 37.62 2.32
423 424 6.184789 TCCTTTTCGGTTTATAAGGCTCAAT 58.815 36.000 0.00 0.00 37.62 2.57
424 425 5.562635 TCCTTTTCGGTTTATAAGGCTCAA 58.437 37.500 0.00 0.00 37.62 3.02
425 426 5.168647 TCCTTTTCGGTTTATAAGGCTCA 57.831 39.130 0.00 0.00 37.62 4.26
426 427 4.575236 CCTCCTTTTCGGTTTATAAGGCTC 59.425 45.833 0.00 0.00 37.62 4.70
427 428 4.524053 CCTCCTTTTCGGTTTATAAGGCT 58.476 43.478 0.00 0.00 37.62 4.58
428 429 3.630769 CCCTCCTTTTCGGTTTATAAGGC 59.369 47.826 0.00 0.00 37.62 4.35
429 430 5.106876 TCCCTCCTTTTCGGTTTATAAGG 57.893 43.478 0.00 0.00 38.78 2.69
430 431 5.742063 ACTCCCTCCTTTTCGGTTTATAAG 58.258 41.667 0.00 0.00 0.00 1.73
431 432 5.767277 ACTCCCTCCTTTTCGGTTTATAA 57.233 39.130 0.00 0.00 0.00 0.98
432 433 6.872585 TTACTCCCTCCTTTTCGGTTTATA 57.127 37.500 0.00 0.00 0.00 0.98
433 434 5.767277 TTACTCCCTCCTTTTCGGTTTAT 57.233 39.130 0.00 0.00 0.00 1.40
434 435 5.565455 TTTACTCCCTCCTTTTCGGTTTA 57.435 39.130 0.00 0.00 0.00 2.01
435 436 4.442401 TTTACTCCCTCCTTTTCGGTTT 57.558 40.909 0.00 0.00 0.00 3.27
436 437 4.202535 ACATTTACTCCCTCCTTTTCGGTT 60.203 41.667 0.00 0.00 0.00 4.44
437 438 3.329814 ACATTTACTCCCTCCTTTTCGGT 59.670 43.478 0.00 0.00 0.00 4.69
438 439 3.689649 CACATTTACTCCCTCCTTTTCGG 59.310 47.826 0.00 0.00 0.00 4.30
439 440 4.575885 TCACATTTACTCCCTCCTTTTCG 58.424 43.478 0.00 0.00 0.00 3.46
440 441 6.659242 TCATTCACATTTACTCCCTCCTTTTC 59.341 38.462 0.00 0.00 0.00 2.29
441 442 6.552008 TCATTCACATTTACTCCCTCCTTTT 58.448 36.000 0.00 0.00 0.00 2.27
442 443 6.139679 TCATTCACATTTACTCCCTCCTTT 57.860 37.500 0.00 0.00 0.00 3.11
443 444 5.779241 TCATTCACATTTACTCCCTCCTT 57.221 39.130 0.00 0.00 0.00 3.36
444 445 5.251700 AGTTCATTCACATTTACTCCCTCCT 59.748 40.000 0.00 0.00 0.00 3.69
445 446 5.501156 AGTTCATTCACATTTACTCCCTCC 58.499 41.667 0.00 0.00 0.00 4.30
446 447 7.556844 TCTAGTTCATTCACATTTACTCCCTC 58.443 38.462 0.00 0.00 0.00 4.30
447 448 7.496346 TCTAGTTCATTCACATTTACTCCCT 57.504 36.000 0.00 0.00 0.00 4.20
448 449 7.987458 TCATCTAGTTCATTCACATTTACTCCC 59.013 37.037 0.00 0.00 0.00 4.30
449 450 8.948631 TCATCTAGTTCATTCACATTTACTCC 57.051 34.615 0.00 0.00 0.00 3.85
451 452 8.887717 GCTTCATCTAGTTCATTCACATTTACT 58.112 33.333 0.00 0.00 0.00 2.24
452 453 8.668353 TGCTTCATCTAGTTCATTCACATTTAC 58.332 33.333 0.00 0.00 0.00 2.01
469 470 7.669427 TCCAAAATTAATGTTGTGCTTCATCT 58.331 30.769 15.67 0.00 0.00 2.90
525 526 4.887748 AGGCGATGACGATCTTGATTTAT 58.112 39.130 0.00 0.00 42.66 1.40
531 532 2.809446 TGTTAGGCGATGACGATCTTG 58.191 47.619 0.00 0.00 42.66 3.02
544 545 4.546570 GCCATAATCGGAAAATGTTAGGC 58.453 43.478 0.00 0.00 0.00 3.93
567 568 1.135517 ACCGCAATACCAATCAAACGC 60.136 47.619 0.00 0.00 0.00 4.84
569 570 3.569250 ACACCGCAATACCAATCAAAC 57.431 42.857 0.00 0.00 0.00 2.93
584 585 1.732259 CTAGCCTTAGCAACAACACCG 59.268 52.381 0.00 0.00 43.56 4.94
585 586 3.053831 TCTAGCCTTAGCAACAACACC 57.946 47.619 0.00 0.00 43.56 4.16
650 651 5.357257 GTTCGACTAGAGATGCCCAATAAA 58.643 41.667 0.00 0.00 0.00 1.40
654 655 1.480954 GGTTCGACTAGAGATGCCCAA 59.519 52.381 0.00 0.00 0.00 4.12
655 656 1.112113 GGTTCGACTAGAGATGCCCA 58.888 55.000 0.00 0.00 0.00 5.36
705 706 5.580022 AGGTGCCAATTAGAGGTGTAAAAT 58.420 37.500 0.00 0.00 0.00 1.82
721 722 0.981183 ATGAGTTCGGTTAGGTGCCA 59.019 50.000 0.00 0.00 0.00 4.92
784 785 2.334838 GAGTATATTTAGGTGCCCGCG 58.665 52.381 0.00 0.00 0.00 6.46
787 788 5.306394 GTGAAGGAGTATATTTAGGTGCCC 58.694 45.833 0.00 0.00 0.00 5.36
790 791 6.401047 TCGGTGAAGGAGTATATTTAGGTG 57.599 41.667 0.00 0.00 0.00 4.00
791 792 5.010820 GCTCGGTGAAGGAGTATATTTAGGT 59.989 44.000 0.00 0.00 34.00 3.08
818 819 5.600749 AGGGGGAGAAGATTTGTTAGTCTA 58.399 41.667 0.00 0.00 0.00 2.59
847 852 2.369001 GGGGGTAGGGTGAGAGCT 59.631 66.667 0.00 0.00 0.00 4.09
970 975 0.753479 ATGTCGCCGATGAGAGAGGT 60.753 55.000 0.00 0.00 0.00 3.85
998 1003 3.130516 GTCTGTACCTGTCGAATCCATCA 59.869 47.826 0.00 0.00 0.00 3.07
1011 1016 0.317479 GGTTGCGTGAGTCTGTACCT 59.683 55.000 0.00 0.00 0.00 3.08
1017 1022 4.003788 CGGGGGTTGCGTGAGTCT 62.004 66.667 0.00 0.00 0.00 3.24
1041 1047 1.114627 TACCGAGATGCAGTGCAGAT 58.885 50.000 24.20 14.20 43.65 2.90
1100 1106 0.249699 CGTAGTTGTGCCAGTGGTCA 60.250 55.000 11.74 6.61 0.00 4.02
1235 1244 0.033796 CACCCATCCAGGATGTTGCT 60.034 55.000 25.35 4.45 41.22 3.91
1376 1399 8.454894 GCTATCAATAGATCGATGTACTCTTCA 58.545 37.037 0.54 0.00 35.67 3.02
1586 1639 4.314522 TCCAATTTCCATAAGTGCTCCA 57.685 40.909 0.00 0.00 0.00 3.86
1686 1740 4.023291 GCATTCCTTTTACATCTTGGGGA 58.977 43.478 0.00 0.00 0.00 4.81
1738 1792 8.589701 TTGGAGAAATCTTTAATAAACCTCCC 57.410 34.615 0.00 0.00 37.46 4.30
1765 1819 2.034685 GGCCAGTCAAAGGTTCTGAAAC 59.965 50.000 0.00 0.00 34.46 2.78
1817 1871 7.307493 TCATAAGCATGTGTACAATTCTCAC 57.693 36.000 0.00 0.00 33.57 3.51
2002 2059 5.531122 AATGCTTTTGATCATCATCCAGG 57.469 39.130 0.00 0.00 0.00 4.45
2108 3771 1.432514 GCACGATGATCCGTATGCAT 58.567 50.000 3.79 3.79 41.29 3.96
2199 3867 8.959287 TCGCCCCTTCGATCTACTATCTGTAG 62.959 50.000 0.00 0.00 40.49 2.74
2201 3869 3.158676 GCCCCTTCGATCTACTATCTGT 58.841 50.000 0.00 0.00 0.00 3.41
2233 3901 2.171448 GGTGATAGGTGATCTGCCACTT 59.829 50.000 9.07 0.00 37.24 3.16
2254 3922 3.497332 TCGTAAGGTATCCTCTCCATGG 58.503 50.000 4.97 4.97 30.89 3.66
2284 3952 9.053472 TCTTACCTGGAAAGGACTCATTTATTA 57.947 33.333 0.00 0.00 0.00 0.98
2388 4059 4.938080 TCTTTCTCTGGCGATAGTTCATC 58.062 43.478 0.00 0.00 39.35 2.92
2399 4085 5.471456 TCATTGAAGAACTTCTTTCTCTGGC 59.529 40.000 14.31 0.00 44.41 4.85
2400 4086 6.709846 ACTCATTGAAGAACTTCTTTCTCTGG 59.290 38.462 14.31 0.00 44.41 3.86
2430 4116 6.893020 AAAAGGTCATCCCAGAAGTAGTAT 57.107 37.500 0.00 0.00 34.66 2.12
2476 4164 6.806668 TCTGGAACACACCATCTAATCATA 57.193 37.500 0.00 0.00 39.34 2.15
2523 4216 1.358152 AGGGCTACTGTGGCACTTAA 58.642 50.000 15.70 2.76 40.99 1.85
2565 4258 1.730612 GTACTTTGGTAGCGGTTCAGC 59.269 52.381 0.00 0.00 37.41 4.26


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

AutoCloner maintained by Alex Coulton.