Multiple sequence alignment - TraesCS4B01G027700

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 TraesCS4B01G027700 chr4B 100.000 3420 0 0 1 3420 20731881 20735300 0.000000e+00 6316.0
1 TraesCS4B01G027700 chr4B 85.973 442 45 10 978 1411 20724366 20724798 1.120000e-124 457.0
2 TraesCS4B01G027700 chr4B 83.588 262 27 10 2170 2426 20726160 20726410 7.380000e-57 231.0
3 TraesCS4B01G027700 chr4B 80.782 307 44 9 1717 2019 20725354 20725649 3.430000e-55 226.0
4 TraesCS4B01G027700 chr4A 89.397 2273 163 27 1169 3420 591865153 591867368 0.000000e+00 2791.0
5 TraesCS4B01G027700 chr4A 95.092 326 3 4 852 1176 591863897 591864210 5.100000e-138 501.0
6 TraesCS4B01G027700 chr4A 82.824 425 47 14 1029 1451 591854885 591855285 1.170000e-94 357.0
7 TraesCS4B01G027700 chr4A 87.192 203 19 5 2231 2426 591856708 591856910 1.240000e-54 224.0
8 TraesCS4B01G027700 chr4A 86.154 130 18 0 1717 1846 591855967 591856096 1.280000e-29 141.0
9 TraesCS4B01G027700 chr3A 96.933 489 11 2 330 817 588541129 588540644 0.000000e+00 817.0
10 TraesCS4B01G027700 chr3A 99.310 145 0 1 1 145 588541263 588541120 9.410000e-66 261.0
11 TraesCS4B01G027700 chr3A 85.106 188 24 4 143 329 13363282 13363466 4.510000e-44 189.0
12 TraesCS4B01G027700 chr3A 82.178 202 25 7 134 329 11754289 11754093 2.730000e-36 163.0
13 TraesCS4B01G027700 chr7A 97.993 299 6 0 330 628 40368128 40368426 1.410000e-143 520.0
14 TraesCS4B01G027700 chr7A 97.449 196 4 1 623 817 40368615 40368810 1.970000e-87 333.0
15 TraesCS4B01G027700 chr7A 90.233 215 14 7 124 337 155567828 155568036 1.210000e-69 274.0
16 TraesCS4B01G027700 chr7A 97.260 146 1 3 2 145 40367993 40368137 9.480000e-61 244.0
17 TraesCS4B01G027700 chr4D 85.934 455 40 15 962 1405 10976482 10976923 6.680000e-127 464.0
18 TraesCS4B01G027700 chr4D 84.848 264 25 6 2170 2426 10978618 10978873 5.670000e-63 252.0
19 TraesCS4B01G027700 chr5A 90.286 350 22 6 330 673 18750635 18750292 6.730000e-122 448.0
20 TraesCS4B01G027700 chr5A 85.263 190 25 2 143 330 451757726 451757538 3.480000e-45 193.0
21 TraesCS4B01G027700 chr5A 94.915 118 6 0 24 141 18750746 18750629 5.830000e-43 185.0
22 TraesCS4B01G027700 chr2B 97.340 188 4 1 143 329 799144057 799144244 5.510000e-83 318.0
23 TraesCS4B01G027700 chr2B 92.553 188 11 2 143 328 732618656 732618470 2.020000e-67 267.0
24 TraesCS4B01G027700 chr2A 94.681 188 7 3 144 330 162726279 162726094 4.320000e-74 289.0
25 TraesCS4B01G027700 chr7B 93.122 189 9 2 142 329 712882391 712882206 1.210000e-69 274.0
26 TraesCS4B01G027700 chr1D 79.843 382 44 15 1041 1414 21451199 21450843 7.330000e-62 248.0
27 TraesCS4B01G027700 chr1D 80.635 315 38 11 2179 2488 21414607 21414311 4.440000e-54 222.0
28 TraesCS4B01G027700 chr1B 84.314 255 24 10 2179 2428 35681534 35681291 5.710000e-58 235.0
29 TraesCS4B01G027700 chr1B 80.247 324 42 11 2170 2488 35359681 35359987 1.240000e-54 224.0
30 TraesCS4B01G027700 chr1B 79.630 324 43 11 2170 2488 35254103 35254408 9.620000e-51 211.0
31 TraesCS4B01G027700 chr1B 88.158 152 14 2 1261 1411 433455243 433455095 9.750000e-41 178.0
32 TraesCS4B01G027700 chr1B 76.503 366 40 16 1041 1405 35134975 35135295 1.270000e-34 158.0
33 TraesCS4B01G027700 chr1B 90.526 95 9 0 1311 1405 363218927 363219021 3.580000e-25 126.0
34 TraesCS4B01G027700 chr1B 84.426 122 19 0 1725 1846 35145811 35145932 1.670000e-23 121.0
35 TraesCS4B01G027700 chr1B 87.129 101 4 4 1049 1149 35687544 35687453 4.670000e-19 106.0
36 TraesCS4B01G027700 chr6A 86.702 188 23 2 143 329 454642270 454642084 1.240000e-49 207.0
37 TraesCS4B01G027700 chr5B 85.526 152 18 2 1261 1411 645875402 645875254 4.570000e-34 156.0
38 TraesCS4B01G027700 chr6B 83.333 168 24 2 1245 1411 122512697 122512533 5.910000e-33 152.0
39 TraesCS4B01G027700 chr1A 90.385 52 5 0 1717 1768 22999334 22999283 6.120000e-08 69.4


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 TraesCS4B01G027700 chr4B 20731881 20735300 3419 False 6316.000000 6316 100.000000 1 3420 1 chr4B.!!$F1 3419
1 TraesCS4B01G027700 chr4B 20724366 20726410 2044 False 304.666667 457 83.447667 978 2426 3 chr4B.!!$F2 1448
2 TraesCS4B01G027700 chr4A 591863897 591867368 3471 False 1646.000000 2791 92.244500 852 3420 2 chr4A.!!$F2 2568
3 TraesCS4B01G027700 chr4A 591854885 591856910 2025 False 240.666667 357 85.390000 1029 2426 3 chr4A.!!$F1 1397
4 TraesCS4B01G027700 chr3A 588540644 588541263 619 True 539.000000 817 98.121500 1 817 2 chr3A.!!$R2 816
5 TraesCS4B01G027700 chr7A 40367993 40368810 817 False 365.666667 520 97.567333 2 817 3 chr7A.!!$F2 815
6 TraesCS4B01G027700 chr4D 10976482 10978873 2391 False 358.000000 464 85.391000 962 2426 2 chr4D.!!$F1 1464

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
333 336 0.036952 CTGTCTCCGCCACTGAACAT 60.037 55.0 0.0 0.0 0.00 2.71 F
334 337 0.037326 TGTCTCCGCCACTGAACATC 60.037 55.0 0.0 0.0 0.00 3.06 F
774 975 0.468585 ACACGGGTAGTCAGTGGTCA 60.469 55.0 0.0 0.0 39.95 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 3629 0.610232 CAAAGAGTGCAAGGGAGGGG 60.610 60.000 0.00 0.00 0.00 4.79 R
2246 5101 1.278699 TGTATCTGACAGCATGCACCA 59.721 47.619 21.98 12.98 42.53 4.17 R
2426 5288 0.774491 AGGAGGGGGCAAGGTGTTAA 60.774 55.000 0.00 0.00 0.00 2.01 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
147 150 8.929827 TTATTTTATTGCAACATCATCAGTGG 57.070 30.769 0.00 0.00 0.00 4.00
148 151 2.953466 ATTGCAACATCATCAGTGGC 57.047 45.000 0.00 0.00 36.45 5.01
149 152 0.522626 TTGCAACATCATCAGTGGCG 59.477 50.000 0.00 0.00 38.79 5.69
150 153 1.307355 TGCAACATCATCAGTGGCGG 61.307 55.000 0.00 0.00 38.79 6.13
151 154 1.026182 GCAACATCATCAGTGGCGGA 61.026 55.000 0.00 0.00 0.00 5.54
152 155 1.012086 CAACATCATCAGTGGCGGAG 58.988 55.000 0.00 0.00 0.00 4.63
171 174 6.846325 CGGAGCTAGGAAAAAGTATTAAGG 57.154 41.667 0.00 0.00 0.00 2.69
172 175 5.758784 CGGAGCTAGGAAAAAGTATTAAGGG 59.241 44.000 0.00 0.00 0.00 3.95
173 176 6.062749 GGAGCTAGGAAAAAGTATTAAGGGG 58.937 44.000 0.00 0.00 0.00 4.79
174 177 6.126565 GGAGCTAGGAAAAAGTATTAAGGGGA 60.127 42.308 0.00 0.00 0.00 4.81
175 178 6.901300 AGCTAGGAAAAAGTATTAAGGGGAG 58.099 40.000 0.00 0.00 0.00 4.30
176 179 5.531659 GCTAGGAAAAAGTATTAAGGGGAGC 59.468 44.000 0.00 0.00 0.00 4.70
177 180 4.868268 AGGAAAAAGTATTAAGGGGAGCC 58.132 43.478 0.00 0.00 0.00 4.70
178 181 4.293901 AGGAAAAAGTATTAAGGGGAGCCA 59.706 41.667 0.00 0.00 0.00 4.75
179 182 5.020795 GGAAAAAGTATTAAGGGGAGCCAA 58.979 41.667 0.00 0.00 0.00 4.52
180 183 5.127194 GGAAAAAGTATTAAGGGGAGCCAAG 59.873 44.000 0.00 0.00 0.00 3.61
181 184 4.948062 AAAGTATTAAGGGGAGCCAAGT 57.052 40.909 0.00 0.00 0.00 3.16
182 185 3.933861 AGTATTAAGGGGAGCCAAGTG 57.066 47.619 0.00 0.00 0.00 3.16
183 186 3.190439 AGTATTAAGGGGAGCCAAGTGT 58.810 45.455 0.00 0.00 0.00 3.55
184 187 3.591977 AGTATTAAGGGGAGCCAAGTGTT 59.408 43.478 0.00 0.00 0.00 3.32
185 188 2.286365 TTAAGGGGAGCCAAGTGTTG 57.714 50.000 0.00 0.00 0.00 3.33
186 189 0.251165 TAAGGGGAGCCAAGTGTTGC 60.251 55.000 0.00 0.00 0.00 4.17
187 190 2.011617 AAGGGGAGCCAAGTGTTGCT 62.012 55.000 0.00 0.00 41.42 3.91
188 191 1.531602 GGGGAGCCAAGTGTTGCTT 60.532 57.895 0.00 0.00 38.11 3.91
189 192 0.251165 GGGGAGCCAAGTGTTGCTTA 60.251 55.000 0.00 0.00 38.11 3.09
190 193 1.616994 GGGGAGCCAAGTGTTGCTTAT 60.617 52.381 0.00 0.00 38.11 1.73
191 194 1.745653 GGGAGCCAAGTGTTGCTTATC 59.254 52.381 0.00 0.00 38.11 1.75
192 195 1.745653 GGAGCCAAGTGTTGCTTATCC 59.254 52.381 0.00 0.00 38.11 2.59
193 196 2.619074 GGAGCCAAGTGTTGCTTATCCT 60.619 50.000 0.00 0.00 38.11 3.24
194 197 3.084786 GAGCCAAGTGTTGCTTATCCTT 58.915 45.455 0.00 0.00 38.11 3.36
195 198 2.821969 AGCCAAGTGTTGCTTATCCTTG 59.178 45.455 0.00 0.00 35.27 3.61
196 199 3.855689 CCAAGTGTTGCTTATCCTTGG 57.144 47.619 0.00 0.00 44.29 3.61
197 200 2.094545 CCAAGTGTTGCTTATCCTTGGC 60.095 50.000 4.00 0.00 43.90 4.52
198 201 2.557924 CAAGTGTTGCTTATCCTTGGCA 59.442 45.455 0.00 0.00 35.27 4.92
199 202 2.440409 AGTGTTGCTTATCCTTGGCAG 58.560 47.619 0.00 0.00 37.28 4.85
200 203 1.474077 GTGTTGCTTATCCTTGGCAGG 59.526 52.381 0.00 0.00 42.50 4.85
201 204 1.106285 GTTGCTTATCCTTGGCAGGG 58.894 55.000 9.81 9.81 41.25 4.45
202 205 0.998928 TTGCTTATCCTTGGCAGGGA 59.001 50.000 21.53 21.53 41.25 4.20
203 206 0.548031 TGCTTATCCTTGGCAGGGAG 59.452 55.000 23.44 11.38 41.25 4.30
204 207 0.179006 GCTTATCCTTGGCAGGGAGG 60.179 60.000 23.44 15.96 41.25 4.30
205 208 0.475906 CTTATCCTTGGCAGGGAGGG 59.524 60.000 23.44 11.81 41.25 4.30
206 209 1.645402 TTATCCTTGGCAGGGAGGGC 61.645 60.000 23.44 0.00 41.25 5.19
223 226 2.137810 GGCCAGCCCACTAAAATACA 57.862 50.000 0.00 0.00 0.00 2.29
224 227 2.666317 GGCCAGCCCACTAAAATACAT 58.334 47.619 0.00 0.00 0.00 2.29
225 228 2.623416 GGCCAGCCCACTAAAATACATC 59.377 50.000 0.00 0.00 0.00 3.06
226 229 3.287222 GCCAGCCCACTAAAATACATCA 58.713 45.455 0.00 0.00 0.00 3.07
227 230 3.891366 GCCAGCCCACTAAAATACATCAT 59.109 43.478 0.00 0.00 0.00 2.45
228 231 4.342092 GCCAGCCCACTAAAATACATCATT 59.658 41.667 0.00 0.00 0.00 2.57
229 232 5.163416 GCCAGCCCACTAAAATACATCATTT 60.163 40.000 0.00 0.00 38.54 2.32
230 233 6.630188 GCCAGCCCACTAAAATACATCATTTT 60.630 38.462 1.12 1.12 46.31 1.82
231 234 6.980397 CCAGCCCACTAAAATACATCATTTTC 59.020 38.462 0.00 0.00 44.08 2.29
232 235 7.363705 CCAGCCCACTAAAATACATCATTTTCA 60.364 37.037 0.00 0.00 44.08 2.69
233 236 7.489113 CAGCCCACTAAAATACATCATTTTCAC 59.511 37.037 0.00 0.00 44.08 3.18
234 237 7.397192 AGCCCACTAAAATACATCATTTTCACT 59.603 33.333 0.00 0.00 44.08 3.41
235 238 7.489113 GCCCACTAAAATACATCATTTTCACTG 59.511 37.037 0.00 0.00 44.08 3.66
236 239 8.522830 CCCACTAAAATACATCATTTTCACTGT 58.477 33.333 0.00 0.00 44.08 3.55
245 248 7.994425 ACATCATTTTCACTGTACATAACCA 57.006 32.000 0.00 0.00 0.00 3.67
246 249 7.816640 ACATCATTTTCACTGTACATAACCAC 58.183 34.615 0.00 0.00 0.00 4.16
247 250 7.665559 ACATCATTTTCACTGTACATAACCACT 59.334 33.333 0.00 0.00 0.00 4.00
248 251 8.514594 CATCATTTTCACTGTACATAACCACTT 58.485 33.333 0.00 0.00 0.00 3.16
249 252 7.870826 TCATTTTCACTGTACATAACCACTTG 58.129 34.615 0.00 0.00 0.00 3.16
250 253 7.500892 TCATTTTCACTGTACATAACCACTTGT 59.499 33.333 0.00 0.00 0.00 3.16
251 254 7.633193 TTTTCACTGTACATAACCACTTGTT 57.367 32.000 0.00 0.00 41.11 2.83
252 255 7.633193 TTTCACTGTACATAACCACTTGTTT 57.367 32.000 0.00 0.00 38.42 2.83
253 256 8.734218 TTTCACTGTACATAACCACTTGTTTA 57.266 30.769 0.00 0.00 38.42 2.01
254 257 8.911918 TTCACTGTACATAACCACTTGTTTAT 57.088 30.769 0.00 0.00 38.42 1.40
255 258 9.999660 TTCACTGTACATAACCACTTGTTTATA 57.000 29.630 0.00 0.00 38.42 0.98
258 261 9.953565 ACTGTACATAACCACTTGTTTATATGT 57.046 29.630 0.00 0.00 37.41 2.29
288 291 6.946340 AGGCTTAAATCAATTTTGTTAGGGG 58.054 36.000 0.00 0.00 0.00 4.79
289 292 6.070251 AGGCTTAAATCAATTTTGTTAGGGGG 60.070 38.462 0.00 0.00 0.00 5.40
328 331 4.087892 CCCCTGTCTCCGCCACTG 62.088 72.222 0.00 0.00 0.00 3.66
329 332 2.997315 CCCTGTCTCCGCCACTGA 60.997 66.667 0.00 0.00 0.00 3.41
330 333 2.583441 CCCTGTCTCCGCCACTGAA 61.583 63.158 0.00 0.00 0.00 3.02
331 334 1.374758 CCTGTCTCCGCCACTGAAC 60.375 63.158 0.00 0.00 0.00 3.18
332 335 1.367471 CTGTCTCCGCCACTGAACA 59.633 57.895 0.00 0.00 0.00 3.18
333 336 0.036952 CTGTCTCCGCCACTGAACAT 60.037 55.000 0.00 0.00 0.00 2.71
334 337 0.037326 TGTCTCCGCCACTGAACATC 60.037 55.000 0.00 0.00 0.00 3.06
335 338 0.037326 GTCTCCGCCACTGAACATCA 60.037 55.000 0.00 0.00 0.00 3.07
336 339 0.904649 TCTCCGCCACTGAACATCAT 59.095 50.000 0.00 0.00 0.00 2.45
494 500 0.664166 GGTGTCCAAGCGCATTTGTG 60.664 55.000 11.47 0.95 0.00 3.33
503 509 4.143347 CCAAGCGCATTTGTGATTTGTAAC 60.143 41.667 11.47 0.00 31.17 2.50
519 525 8.093927 TGATTTGTAACCCTGAAATTTGAATCC 58.906 33.333 0.00 0.00 0.00 3.01
544 550 2.529151 GTTTGCCATTGATAACCTGCG 58.471 47.619 0.00 0.00 0.00 5.18
628 634 3.567478 AGCAATCACATCCTAACCTCC 57.433 47.619 0.00 0.00 0.00 4.30
759 960 6.018994 GTGGCTAGTAAATTATCCAGAACACG 60.019 42.308 0.00 0.00 0.00 4.49
761 962 5.465724 GCTAGTAAATTATCCAGAACACGGG 59.534 44.000 0.00 0.00 0.00 5.28
774 975 0.468585 ACACGGGTAGTCAGTGGTCA 60.469 55.000 0.00 0.00 39.95 4.02
817 1018 6.506538 AATCAGCCCATACTTAGTTGAGAT 57.493 37.500 0.00 0.00 0.00 2.75
818 1019 7.618019 AATCAGCCCATACTTAGTTGAGATA 57.382 36.000 0.00 0.00 0.00 1.98
819 1020 7.805083 ATCAGCCCATACTTAGTTGAGATAT 57.195 36.000 0.00 0.00 0.00 1.63
820 1021 8.901472 ATCAGCCCATACTTAGTTGAGATATA 57.099 34.615 0.00 0.00 0.00 0.86
821 1022 8.721133 TCAGCCCATACTTAGTTGAGATATAA 57.279 34.615 0.00 0.00 0.00 0.98
822 1023 9.154632 TCAGCCCATACTTAGTTGAGATATAAA 57.845 33.333 0.00 0.00 0.00 1.40
823 1024 9.209175 CAGCCCATACTTAGTTGAGATATAAAC 57.791 37.037 0.00 0.00 0.00 2.01
824 1025 8.376270 AGCCCATACTTAGTTGAGATATAAACC 58.624 37.037 0.00 0.00 0.00 3.27
825 1026 7.331193 GCCCATACTTAGTTGAGATATAAACCG 59.669 40.741 0.00 0.00 0.00 4.44
826 1027 7.331193 CCCATACTTAGTTGAGATATAAACCGC 59.669 40.741 0.00 0.00 0.00 5.68
827 1028 7.331193 CCATACTTAGTTGAGATATAAACCGCC 59.669 40.741 0.00 0.00 0.00 6.13
828 1029 6.229936 ACTTAGTTGAGATATAAACCGCCA 57.770 37.500 0.00 0.00 0.00 5.69
829 1030 6.827727 ACTTAGTTGAGATATAAACCGCCAT 58.172 36.000 0.00 0.00 0.00 4.40
830 1031 7.280356 ACTTAGTTGAGATATAAACCGCCATT 58.720 34.615 0.00 0.00 0.00 3.16
831 1032 8.426489 ACTTAGTTGAGATATAAACCGCCATTA 58.574 33.333 0.00 0.00 0.00 1.90
832 1033 9.436957 CTTAGTTGAGATATAAACCGCCATTAT 57.563 33.333 0.00 0.00 0.00 1.28
833 1034 7.672983 AGTTGAGATATAAACCGCCATTATG 57.327 36.000 0.00 0.00 0.00 1.90
834 1035 6.655003 AGTTGAGATATAAACCGCCATTATGG 59.345 38.462 6.92 6.92 41.55 2.74
1219 2382 0.698886 CCCATCCCATCTTCTCCCCA 60.699 60.000 0.00 0.00 0.00 4.96
1360 2535 1.215382 CACCGAGTTCATGCTCCGA 59.785 57.895 0.00 0.00 32.11 4.55
1511 2922 1.191096 CACGTGTTGTTTTGCTGCTC 58.809 50.000 7.58 0.00 0.00 4.26
1550 3009 5.231991 CGAAACTGCTTGCAAAAATAAGTGT 59.768 36.000 0.00 0.00 0.00 3.55
1564 3023 9.810545 CAAAAATAAGTGTGGAAAACCTAGAAA 57.189 29.630 0.00 0.00 0.00 2.52
1630 3249 2.747446 CCTGGCAAAGTGGTACATACAC 59.253 50.000 0.00 0.00 44.52 2.90
1706 3507 5.048434 GCTTCTTTTTCAGGCTAGTTCATGT 60.048 40.000 0.00 0.00 0.00 3.21
1710 3512 8.458573 TCTTTTTCAGGCTAGTTCATGTTTTA 57.541 30.769 0.00 0.00 0.00 1.52
1816 3629 1.026718 CAGCGGTCAAGGTTCCATCC 61.027 60.000 0.00 0.00 0.00 3.51
1826 3639 1.615262 GTTCCATCCCCCTCCCTTG 59.385 63.158 0.00 0.00 0.00 3.61
1857 4195 4.263462 TGTCCATCCTTGTCTGCTTACATT 60.263 41.667 0.00 0.00 0.00 2.71
1858 4196 4.333926 GTCCATCCTTGTCTGCTTACATTC 59.666 45.833 0.00 0.00 0.00 2.67
1859 4197 4.019411 TCCATCCTTGTCTGCTTACATTCA 60.019 41.667 0.00 0.00 0.00 2.57
1860 4198 4.885907 CCATCCTTGTCTGCTTACATTCAT 59.114 41.667 0.00 0.00 0.00 2.57
1861 4199 6.057533 CCATCCTTGTCTGCTTACATTCATA 58.942 40.000 0.00 0.00 0.00 2.15
2044 4491 4.879104 ATGTCTGCTCGTAGTACACTAC 57.121 45.455 9.11 9.11 44.00 2.73
2047 4494 5.107824 TGTCTGCTCGTAGTACACTACTAG 58.892 45.833 15.57 14.67 44.97 2.57
2049 4496 6.127619 TGTCTGCTCGTAGTACACTACTAGTA 60.128 42.308 17.46 13.85 44.97 1.82
2050 4497 6.198216 GTCTGCTCGTAGTACACTACTAGTAC 59.802 46.154 17.46 11.88 44.97 2.73
2052 4499 6.269315 TGCTCGTAGTACACTACTAGTACTC 58.731 44.000 17.46 6.34 46.80 2.59
2060 4514 8.945481 AGTACACTACTAGTACTCATGTACAG 57.055 38.462 25.59 9.98 46.80 2.74
2093 4547 2.989824 CGTGGGAGTGGACGAGGT 60.990 66.667 0.00 0.00 37.81 3.85
2105 4559 2.076863 GGACGAGGTGTTCATCCTTTG 58.923 52.381 0.00 0.00 35.20 2.77
2163 5018 9.646427 AAATTACAGTTTTTGTCTTAAGTGCAA 57.354 25.926 1.63 6.74 41.29 4.08
2165 5020 9.816354 ATTACAGTTTTTGTCTTAAGTGCAAAT 57.184 25.926 20.08 12.26 41.29 2.32
2177 5032 3.806625 AGTGCAAATTTCAGCAGTTGT 57.193 38.095 3.59 0.00 41.35 3.32
2202 5057 8.905702 GTTTACTGTTTGTATTCTCAATGCTTG 58.094 33.333 0.00 0.00 0.00 4.01
2207 5062 3.689347 TGTATTCTCAATGCTTGCCACT 58.311 40.909 0.00 0.00 0.00 4.00
2211 5066 1.908619 TCTCAATGCTTGCCACTCCTA 59.091 47.619 0.00 0.00 0.00 2.94
2246 5101 5.555017 AGAAGCCGTTATATCTTGCATCAT 58.445 37.500 0.00 0.00 0.00 2.45
2389 5251 2.745515 ACAACTTCTTCTACGAGGCC 57.254 50.000 0.00 0.00 0.00 5.19
2426 5288 0.529833 CTCACCGTCATGAGCACTCT 59.470 55.000 0.00 0.00 39.77 3.24
2431 5293 2.299013 ACCGTCATGAGCACTCTTAACA 59.701 45.455 0.00 0.00 0.00 2.41
2438 5300 1.807142 GAGCACTCTTAACACCTTGCC 59.193 52.381 0.00 0.00 0.00 4.52
2450 5312 2.599597 CTTGCCCCCTCCTGATGG 59.400 66.667 0.00 0.00 0.00 3.51
2460 5322 1.673033 CCTCCTGATGGTTCGTGTCAC 60.673 57.143 0.00 0.00 34.23 3.67
2471 5333 0.237498 TCGTGTCACTGTAGCACTCG 59.763 55.000 0.65 6.95 0.00 4.18
2477 5339 1.199327 TCACTGTAGCACTCGTAGCAC 59.801 52.381 0.00 0.00 0.00 4.40
2492 5354 1.004560 GCACTGCTGCCACTCTGTA 60.005 57.895 0.00 0.00 37.45 2.74
2513 5375 0.788391 CCGTGCTCGTTACCTTGTTC 59.212 55.000 7.47 0.00 35.01 3.18
2517 5379 3.251571 GTGCTCGTTACCTTGTTCTAGG 58.748 50.000 0.00 0.00 41.31 3.02
2518 5380 2.269172 GCTCGTTACCTTGTTCTAGGC 58.731 52.381 0.60 0.00 38.99 3.93
2555 5417 1.228675 AGAGGCCCTTTTGGTGCTG 60.229 57.895 0.00 0.00 38.10 4.41
2566 5428 2.132740 TTGGTGCTGCGAATTGTTTC 57.867 45.000 0.00 0.00 0.00 2.78
2578 5440 4.494199 GCGAATTGTTTCAGGGTTATCTCG 60.494 45.833 0.00 0.00 0.00 4.04
2588 5450 2.764572 AGGGTTATCTCGGATGAACGTT 59.235 45.455 0.00 0.00 34.94 3.99
2619 5481 3.634448 TCCAAATTCCAACAGCGAGAAAA 59.366 39.130 0.00 0.00 0.00 2.29
2634 5496 4.201861 GCGAGAAAATTGACTGGAATCTCC 60.202 45.833 0.00 0.00 36.96 3.71
2657 5520 4.142534 CCAACATTTCATGCGACTGATTCT 60.143 41.667 0.00 0.00 0.00 2.40
2661 5524 5.356190 ACATTTCATGCGACTGATTCTTGAT 59.644 36.000 0.00 0.00 0.00 2.57
2662 5525 4.870221 TTCATGCGACTGATTCTTGATG 57.130 40.909 0.00 0.00 0.00 3.07
2667 5530 3.194329 TGCGACTGATTCTTGATGTCTCT 59.806 43.478 0.00 0.00 0.00 3.10
2715 5586 6.595716 GCTAGTGGTTCTGTTGATGACTTAAT 59.404 38.462 0.00 0.00 0.00 1.40
2716 5587 6.808008 AGTGGTTCTGTTGATGACTTAATG 57.192 37.500 0.00 0.00 0.00 1.90
2718 5589 6.772716 AGTGGTTCTGTTGATGACTTAATGTT 59.227 34.615 0.00 0.00 0.00 2.71
2719 5590 7.285401 AGTGGTTCTGTTGATGACTTAATGTTT 59.715 33.333 0.00 0.00 0.00 2.83
2720 5591 7.591426 GTGGTTCTGTTGATGACTTAATGTTTC 59.409 37.037 0.00 0.00 0.00 2.78
2721 5592 7.502226 TGGTTCTGTTGATGACTTAATGTTTCT 59.498 33.333 0.00 0.00 0.00 2.52
2737 5613 2.408271 TTCTTGCATCAGGATTCGCT 57.592 45.000 0.00 0.00 0.00 4.93
2738 5614 2.408271 TCTTGCATCAGGATTCGCTT 57.592 45.000 0.00 0.00 0.00 4.68
2739 5615 2.011947 TCTTGCATCAGGATTCGCTTG 58.988 47.619 0.00 0.00 0.00 4.01
2754 5630 2.036992 TCGCTTGGGTTGCATCAATTTT 59.963 40.909 0.00 0.00 0.00 1.82
2761 5637 3.498018 GGGTTGCATCAATTTTGTGAACC 59.502 43.478 0.00 0.00 0.00 3.62
2848 5724 2.404186 GGCGTCCCCGGAAACATTC 61.404 63.158 0.73 0.00 33.68 2.67
2851 5727 1.530323 CGTCCCCGGAAACATTCTTT 58.470 50.000 0.73 0.00 0.00 2.52
2871 5747 4.993029 TTTTGTCAGACCCAATCGTTTT 57.007 36.364 0.00 0.00 0.00 2.43
2915 5791 4.355543 TGTTGTCAGACTCTTGCAAAAC 57.644 40.909 0.00 0.00 0.00 2.43
2917 5793 2.997980 TGTCAGACTCTTGCAAAACCA 58.002 42.857 0.00 0.00 0.00 3.67
2918 5794 3.554934 TGTCAGACTCTTGCAAAACCAT 58.445 40.909 0.00 0.00 0.00 3.55
2958 5838 4.976987 GACGGAAAGTCTGAAACAAACAA 58.023 39.130 0.00 0.00 46.13 2.83
2959 5839 5.379732 ACGGAAAGTCTGAAACAAACAAA 57.620 34.783 0.00 0.00 0.00 2.83
2960 5840 5.774630 ACGGAAAGTCTGAAACAAACAAAA 58.225 33.333 0.00 0.00 0.00 2.44
2961 5841 6.217294 ACGGAAAGTCTGAAACAAACAAAAA 58.783 32.000 0.00 0.00 0.00 1.94
2986 5866 1.874562 GCAACTGGCAGAAGCTCTG 59.125 57.895 23.66 8.97 46.90 3.35
3054 5934 9.674068 TTATATAAGGAAAATTGGCCAAAAACC 57.326 29.630 24.71 21.50 0.00 3.27
3073 5953 2.101783 CCAATACATGCCCACACACAT 58.898 47.619 0.00 0.00 0.00 3.21
3080 5960 2.282674 CCCACACACATGCCAGCT 60.283 61.111 0.00 0.00 0.00 4.24
3112 5992 0.173708 CCCAAGTGAGCCGACTACTC 59.826 60.000 0.00 0.00 34.62 2.59
3118 5998 2.361357 AGCCGACTACTCTGCCGT 60.361 61.111 0.00 0.00 0.00 5.68
3127 6007 0.613260 TACTCTGCCGTCCAAGCAAT 59.387 50.000 0.00 0.00 40.35 3.56
3129 6009 1.003118 ACTCTGCCGTCCAAGCAATTA 59.997 47.619 0.00 0.00 40.35 1.40
3132 6012 1.667724 CTGCCGTCCAAGCAATTAGAG 59.332 52.381 0.00 0.00 40.35 2.43
3149 6029 7.446625 GCAATTAGAGATGACACCCTATCAAAT 59.553 37.037 0.00 0.00 0.00 2.32
3154 6034 4.723789 AGATGACACCCTATCAAATGACCT 59.276 41.667 0.00 0.00 0.00 3.85
3157 6037 2.242196 ACACCCTATCAAATGACCTGGG 59.758 50.000 12.73 12.73 37.27 4.45
3160 6040 1.479389 CCTATCAAATGACCTGGGGCC 60.479 57.143 0.00 0.00 0.00 5.80
3195 6075 4.609691 ACAAACCTTAAGAACACACACG 57.390 40.909 3.36 0.00 0.00 4.49
3199 6079 0.110823 CTTAAGAACACACACGCCGC 60.111 55.000 0.00 0.00 0.00 6.53
3217 6097 1.876714 CCCTCGATGTTGCGTACCG 60.877 63.158 0.00 0.00 0.00 4.02
3220 6100 1.138047 CTCGATGTTGCGTACCGGAC 61.138 60.000 9.46 0.32 0.00 4.79
3231 6111 0.669077 GTACCGGACGAGCTGATGAT 59.331 55.000 9.46 0.00 0.00 2.45
3233 6113 0.537188 ACCGGACGAGCTGATGATTT 59.463 50.000 9.46 0.00 0.00 2.17
3234 6114 0.933097 CCGGACGAGCTGATGATTTG 59.067 55.000 0.00 0.00 0.00 2.32
3244 6125 2.881403 GCTGATGATTTGTCACCCAGGT 60.881 50.000 9.92 0.00 0.00 4.00
3265 6146 4.768968 GGTAACTAGAGTCAACACCCTACA 59.231 45.833 0.00 0.00 0.00 2.74
3269 6150 3.470645 AGAGTCAACACCCTACAACAC 57.529 47.619 0.00 0.00 0.00 3.32
3272 6153 1.862827 GTCAACACCCTACAACACGAC 59.137 52.381 0.00 0.00 0.00 4.34
3273 6154 0.856641 CAACACCCTACAACACGACG 59.143 55.000 0.00 0.00 0.00 5.12
3274 6155 0.746063 AACACCCTACAACACGACGA 59.254 50.000 0.00 0.00 0.00 4.20
3275 6156 0.963962 ACACCCTACAACACGACGAT 59.036 50.000 0.00 0.00 0.00 3.73
3276 6157 1.336517 ACACCCTACAACACGACGATG 60.337 52.381 0.00 0.00 0.00 3.84
3282 6163 1.374125 CAACACGACGATGGAGCCA 60.374 57.895 0.00 0.00 0.00 4.75
3284 6165 2.509336 CACGACGATGGAGCCACC 60.509 66.667 0.00 0.00 39.54 4.61
3285 6166 3.771160 ACGACGATGGAGCCACCC 61.771 66.667 0.00 0.00 38.00 4.61
3289 6170 2.190578 CGATGGAGCCACCCCTTC 59.809 66.667 0.00 0.00 38.00 3.46
3301 6182 0.763223 ACCCCTTCGTCTTCCACACT 60.763 55.000 0.00 0.00 0.00 3.55
3302 6183 0.320771 CCCCTTCGTCTTCCACACTG 60.321 60.000 0.00 0.00 0.00 3.66
3322 6203 1.807226 CCACGAGGTCGCATGTCTA 59.193 57.895 0.00 0.00 44.43 2.59
3361 6242 6.243216 TCTAAGGTGACAGTACCAAAAACT 57.757 37.500 0.00 0.00 43.37 2.66
3362 6243 7.364149 TCTAAGGTGACAGTACCAAAAACTA 57.636 36.000 0.00 0.00 43.37 2.24
3363 6244 7.970102 TCTAAGGTGACAGTACCAAAAACTAT 58.030 34.615 0.00 0.00 43.37 2.12
3374 6255 4.315803 ACCAAAAACTATCAGTGTCCTCG 58.684 43.478 0.00 0.00 0.00 4.63
3389 6270 1.379977 CTCGGTAGGGTGGAGAGCA 60.380 63.158 0.00 0.00 0.00 4.26
3390 6271 0.757188 CTCGGTAGGGTGGAGAGCAT 60.757 60.000 0.00 0.00 0.00 3.79
3391 6272 0.755698 TCGGTAGGGTGGAGAGCATC 60.756 60.000 0.00 0.00 0.00 3.91
3393 6274 1.043673 GGTAGGGTGGAGAGCATCGT 61.044 60.000 0.00 0.00 42.67 3.73
3394 6275 0.386113 GTAGGGTGGAGAGCATCGTC 59.614 60.000 0.00 0.00 42.67 4.20
3411 6292 0.464452 GTCGGATGTACCAGAAGGGG 59.536 60.000 0.00 0.00 42.91 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 144 0.902984 TTTCCTAGCTCCGCCACTGA 60.903 55.000 0.00 0.00 0.00 3.41
142 145 0.036388 TTTTCCTAGCTCCGCCACTG 60.036 55.000 0.00 0.00 0.00 3.66
143 146 0.690762 TTTTTCCTAGCTCCGCCACT 59.309 50.000 0.00 0.00 0.00 4.00
144 147 1.087501 CTTTTTCCTAGCTCCGCCAC 58.912 55.000 0.00 0.00 0.00 5.01
145 148 0.690762 ACTTTTTCCTAGCTCCGCCA 59.309 50.000 0.00 0.00 0.00 5.69
146 149 2.685850 TACTTTTTCCTAGCTCCGCC 57.314 50.000 0.00 0.00 0.00 6.13
147 150 5.236695 CCTTAATACTTTTTCCTAGCTCCGC 59.763 44.000 0.00 0.00 0.00 5.54
148 151 5.758784 CCCTTAATACTTTTTCCTAGCTCCG 59.241 44.000 0.00 0.00 0.00 4.63
149 152 6.062749 CCCCTTAATACTTTTTCCTAGCTCC 58.937 44.000 0.00 0.00 0.00 4.70
150 153 6.896883 TCCCCTTAATACTTTTTCCTAGCTC 58.103 40.000 0.00 0.00 0.00 4.09
151 154 6.635185 GCTCCCCTTAATACTTTTTCCTAGCT 60.635 42.308 0.00 0.00 0.00 3.32
152 155 5.531659 GCTCCCCTTAATACTTTTTCCTAGC 59.468 44.000 0.00 0.00 0.00 3.42
153 156 6.062749 GGCTCCCCTTAATACTTTTTCCTAG 58.937 44.000 0.00 0.00 0.00 3.02
154 157 5.493250 TGGCTCCCCTTAATACTTTTTCCTA 59.507 40.000 0.00 0.00 0.00 2.94
155 158 4.293901 TGGCTCCCCTTAATACTTTTTCCT 59.706 41.667 0.00 0.00 0.00 3.36
156 159 4.606210 TGGCTCCCCTTAATACTTTTTCC 58.394 43.478 0.00 0.00 0.00 3.13
157 160 5.715279 ACTTGGCTCCCCTTAATACTTTTTC 59.285 40.000 0.00 0.00 0.00 2.29
158 161 5.480422 CACTTGGCTCCCCTTAATACTTTTT 59.520 40.000 0.00 0.00 0.00 1.94
159 162 5.016831 CACTTGGCTCCCCTTAATACTTTT 58.983 41.667 0.00 0.00 0.00 2.27
160 163 4.044191 ACACTTGGCTCCCCTTAATACTTT 59.956 41.667 0.00 0.00 0.00 2.66
161 164 3.591977 ACACTTGGCTCCCCTTAATACTT 59.408 43.478 0.00 0.00 0.00 2.24
162 165 3.190439 ACACTTGGCTCCCCTTAATACT 58.810 45.455 0.00 0.00 0.00 2.12
163 166 3.646736 ACACTTGGCTCCCCTTAATAC 57.353 47.619 0.00 0.00 0.00 1.89
164 167 3.876156 GCAACACTTGGCTCCCCTTAATA 60.876 47.826 0.00 0.00 0.00 0.98
165 168 2.807676 CAACACTTGGCTCCCCTTAAT 58.192 47.619 0.00 0.00 0.00 1.40
166 169 1.821666 GCAACACTTGGCTCCCCTTAA 60.822 52.381 0.00 0.00 0.00 1.85
167 170 0.251165 GCAACACTTGGCTCCCCTTA 60.251 55.000 0.00 0.00 0.00 2.69
168 171 1.531602 GCAACACTTGGCTCCCCTT 60.532 57.895 0.00 0.00 0.00 3.95
169 172 2.011617 AAGCAACACTTGGCTCCCCT 62.012 55.000 0.00 0.00 40.01 4.79
170 173 0.251165 TAAGCAACACTTGGCTCCCC 60.251 55.000 0.00 0.00 40.01 4.81
171 174 1.745653 GATAAGCAACACTTGGCTCCC 59.254 52.381 0.00 0.00 40.01 4.30
172 175 1.745653 GGATAAGCAACACTTGGCTCC 59.254 52.381 0.00 0.00 40.01 4.70
173 176 2.716217 AGGATAAGCAACACTTGGCTC 58.284 47.619 0.00 0.00 40.01 4.70
174 177 2.821969 CAAGGATAAGCAACACTTGGCT 59.178 45.455 0.00 0.00 43.46 4.75
175 178 3.221964 CAAGGATAAGCAACACTTGGC 57.778 47.619 0.00 0.00 39.58 4.52
177 180 2.557924 TGCCAAGGATAAGCAACACTTG 59.442 45.455 0.00 0.00 39.58 3.16
178 181 2.821969 CTGCCAAGGATAAGCAACACTT 59.178 45.455 0.00 0.00 42.76 3.16
179 182 2.440409 CTGCCAAGGATAAGCAACACT 58.560 47.619 0.00 0.00 35.79 3.55
180 183 2.927553 CTGCCAAGGATAAGCAACAC 57.072 50.000 0.00 0.00 35.79 3.32
204 207 2.137810 TGTATTTTAGTGGGCTGGCC 57.862 50.000 14.23 14.23 0.00 5.36
205 208 3.287222 TGATGTATTTTAGTGGGCTGGC 58.713 45.455 0.00 0.00 0.00 4.85
206 209 6.469782 AAATGATGTATTTTAGTGGGCTGG 57.530 37.500 0.00 0.00 35.47 4.85
207 210 7.489113 GTGAAAATGATGTATTTTAGTGGGCTG 59.511 37.037 0.00 0.00 46.27 4.85
208 211 7.397192 AGTGAAAATGATGTATTTTAGTGGGCT 59.603 33.333 0.00 0.00 46.27 5.19
209 212 7.489113 CAGTGAAAATGATGTATTTTAGTGGGC 59.511 37.037 0.00 0.00 46.27 5.36
210 213 8.522830 ACAGTGAAAATGATGTATTTTAGTGGG 58.477 33.333 0.00 0.00 46.27 4.61
219 222 9.679661 TGGTTATGTACAGTGAAAATGATGTAT 57.320 29.630 0.33 0.00 34.17 2.29
220 223 8.941977 GTGGTTATGTACAGTGAAAATGATGTA 58.058 33.333 0.33 0.00 34.17 2.29
221 224 7.665559 AGTGGTTATGTACAGTGAAAATGATGT 59.334 33.333 0.33 0.00 34.17 3.06
222 225 8.044060 AGTGGTTATGTACAGTGAAAATGATG 57.956 34.615 0.33 0.00 34.17 3.07
223 226 8.514594 CAAGTGGTTATGTACAGTGAAAATGAT 58.485 33.333 0.33 0.00 34.17 2.45
224 227 7.500892 ACAAGTGGTTATGTACAGTGAAAATGA 59.499 33.333 0.33 0.00 34.17 2.57
225 228 7.648142 ACAAGTGGTTATGTACAGTGAAAATG 58.352 34.615 0.33 0.00 38.30 2.32
226 229 7.817418 ACAAGTGGTTATGTACAGTGAAAAT 57.183 32.000 0.33 0.00 0.00 1.82
227 230 7.633193 AACAAGTGGTTATGTACAGTGAAAA 57.367 32.000 0.33 0.00 38.15 2.29
228 231 7.633193 AAACAAGTGGTTATGTACAGTGAAA 57.367 32.000 0.33 0.00 39.29 2.69
229 232 8.911918 ATAAACAAGTGGTTATGTACAGTGAA 57.088 30.769 0.33 0.00 39.29 3.18
232 235 9.953565 ACATATAAACAAGTGGTTATGTACAGT 57.046 29.630 11.12 0.00 38.31 3.55
262 265 8.536175 CCCCTAACAAAATTGATTTAAGCCTAA 58.464 33.333 0.00 0.00 0.00 2.69
263 266 7.125053 CCCCCTAACAAAATTGATTTAAGCCTA 59.875 37.037 0.00 0.00 0.00 3.93
264 267 6.070251 CCCCCTAACAAAATTGATTTAAGCCT 60.070 38.462 0.00 0.00 0.00 4.58
265 268 6.112734 CCCCCTAACAAAATTGATTTAAGCC 58.887 40.000 0.00 0.00 0.00 4.35
316 319 0.037326 TGATGTTCAGTGGCGGAGAC 60.037 55.000 0.00 0.00 0.00 3.36
317 320 0.904649 ATGATGTTCAGTGGCGGAGA 59.095 50.000 0.00 0.00 0.00 3.71
318 321 2.477825 CTATGATGTTCAGTGGCGGAG 58.522 52.381 0.00 0.00 0.00 4.63
319 322 1.473257 GCTATGATGTTCAGTGGCGGA 60.473 52.381 0.00 0.00 0.00 5.54
320 323 0.940126 GCTATGATGTTCAGTGGCGG 59.060 55.000 0.00 0.00 0.00 6.13
321 324 1.596260 CAGCTATGATGTTCAGTGGCG 59.404 52.381 0.00 0.00 0.00 5.69
322 325 2.611292 GTCAGCTATGATGTTCAGTGGC 59.389 50.000 0.00 0.00 37.87 5.01
323 326 4.134379 AGTCAGCTATGATGTTCAGTGG 57.866 45.455 0.00 0.00 37.87 4.00
324 327 5.173664 TGAAGTCAGCTATGATGTTCAGTG 58.826 41.667 0.00 0.00 36.81 3.66
325 328 5.411831 TGAAGTCAGCTATGATGTTCAGT 57.588 39.130 0.00 0.00 36.81 3.41
326 329 5.236695 CCATGAAGTCAGCTATGATGTTCAG 59.763 44.000 0.00 5.08 41.14 3.02
327 330 5.104817 TCCATGAAGTCAGCTATGATGTTCA 60.105 40.000 0.00 7.86 41.62 3.18
328 331 5.363101 TCCATGAAGTCAGCTATGATGTTC 58.637 41.667 0.00 0.00 37.87 3.18
329 332 5.363562 TCCATGAAGTCAGCTATGATGTT 57.636 39.130 0.00 0.00 37.87 2.71
330 333 4.743045 GCTCCATGAAGTCAGCTATGATGT 60.743 45.833 0.00 0.00 37.87 3.06
331 334 3.747010 GCTCCATGAAGTCAGCTATGATG 59.253 47.826 0.00 0.00 37.87 3.07
332 335 3.647113 AGCTCCATGAAGTCAGCTATGAT 59.353 43.478 0.00 0.00 37.87 2.45
333 336 3.036819 AGCTCCATGAAGTCAGCTATGA 58.963 45.455 0.00 0.00 0.00 2.15
334 337 3.069872 AGAGCTCCATGAAGTCAGCTATG 59.930 47.826 10.93 0.00 32.34 2.23
335 338 3.307506 AGAGCTCCATGAAGTCAGCTAT 58.692 45.455 10.93 0.00 32.34 2.97
336 339 2.744760 AGAGCTCCATGAAGTCAGCTA 58.255 47.619 10.93 0.00 32.34 3.32
375 381 8.298854 CCATGTGTTCATGTTTCAGATTAGAAA 58.701 33.333 7.30 0.00 46.99 2.52
376 382 7.094248 CCCATGTGTTCATGTTTCAGATTAGAA 60.094 37.037 7.30 0.00 46.99 2.10
377 383 6.375174 CCCATGTGTTCATGTTTCAGATTAGA 59.625 38.462 7.30 0.00 46.99 2.10
494 500 8.093927 TGGATTCAAATTTCAGGGTTACAAATC 58.906 33.333 0.00 0.00 0.00 2.17
503 509 3.834231 ACCACTGGATTCAAATTTCAGGG 59.166 43.478 0.71 4.47 0.00 4.45
544 550 7.750903 GTGATTACCAACTTAACAAGAGAATGC 59.249 37.037 0.00 0.00 0.00 3.56
574 580 8.043113 TCATATATGTTCTGTTTCAAGTCAGCT 58.957 33.333 12.42 0.00 0.00 4.24
628 634 2.298163 AGGATTGGCAAGCTCAAAACAG 59.702 45.455 15.82 0.00 0.00 3.16
759 960 0.905357 AGCATGACCACTGACTACCC 59.095 55.000 0.00 0.00 0.00 3.69
761 962 1.827969 AGGAGCATGACCACTGACTAC 59.172 52.381 0.00 0.00 0.00 2.73
844 1045 2.700722 GTGAAAAGGCCCACCAAAAA 57.299 45.000 0.00 0.00 39.06 1.94
849 1050 2.203437 ACGGTGAAAAGGCCCACC 60.203 61.111 16.63 16.63 46.99 4.61
850 1051 1.228154 AGACGGTGAAAAGGCCCAC 60.228 57.895 0.00 0.00 0.00 4.61
851 1052 1.228124 CAGACGGTGAAAAGGCCCA 60.228 57.895 0.00 0.00 0.00 5.36
852 1053 0.955919 CTCAGACGGTGAAAAGGCCC 60.956 60.000 0.00 0.00 33.60 5.80
853 1054 1.578206 GCTCAGACGGTGAAAAGGCC 61.578 60.000 0.00 0.00 33.60 5.19
854 1055 1.578206 GGCTCAGACGGTGAAAAGGC 61.578 60.000 0.00 0.00 33.60 4.35
855 1056 0.955919 GGGCTCAGACGGTGAAAAGG 60.956 60.000 0.00 0.00 33.60 3.11
856 1057 0.250295 TGGGCTCAGACGGTGAAAAG 60.250 55.000 0.00 0.00 33.60 2.27
857 1058 0.250295 CTGGGCTCAGACGGTGAAAA 60.250 55.000 8.28 0.00 43.49 2.29
1038 1251 3.896133 TAGTCCATCGCCGTCCGC 61.896 66.667 0.00 0.00 36.73 5.54
1078 1291 4.834453 CTCCAGCTGCGAGGCCAG 62.834 72.222 19.07 0.00 35.93 4.85
1194 2355 2.682582 GAAGATGGGATGGGTCGGGC 62.683 65.000 0.00 0.00 0.00 6.13
1219 2382 1.991230 CAGAGGAACGGGGAATGGT 59.009 57.895 0.00 0.00 0.00 3.55
1280 2455 3.181967 GCTGTAGTCCACGCGCAG 61.182 66.667 5.73 4.42 0.00 5.18
1360 2535 3.244616 CCCTTGGCATCCTCGGAT 58.755 61.111 0.00 0.00 34.81 4.18
1511 2922 2.738846 AGTTTCGCATCAACAGCACTAG 59.261 45.455 0.00 0.00 0.00 2.57
1550 3009 7.229907 GTCTTGTGGTAATTTCTAGGTTTTCCA 59.770 37.037 0.00 0.00 43.73 3.53
1564 3023 3.356290 GGGCATCTTGTCTTGTGGTAAT 58.644 45.455 0.00 0.00 0.00 1.89
1710 3512 9.071276 CAGCATAAAATAGGGACATCAGTAAAT 57.929 33.333 0.00 0.00 0.00 1.40
1780 3593 1.936547 GCTGGCAGATTTTCCGTAGAG 59.063 52.381 20.86 0.00 0.00 2.43
1816 3629 0.610232 CAAAGAGTGCAAGGGAGGGG 60.610 60.000 0.00 0.00 0.00 4.79
1826 3639 2.485814 GACAAGGATGGACAAAGAGTGC 59.514 50.000 0.00 0.00 39.32 4.40
1886 4224 4.020662 AGCACCAACAGAAAACCTCAAAAA 60.021 37.500 0.00 0.00 0.00 1.94
2049 4496 6.819649 GTGAGACTACTAGACTGTACATGAGT 59.180 42.308 0.00 0.33 0.00 3.41
2050 4497 7.045416 AGTGAGACTACTAGACTGTACATGAG 58.955 42.308 0.00 0.00 0.00 2.90
2051 4498 6.948589 AGTGAGACTACTAGACTGTACATGA 58.051 40.000 0.00 0.00 0.00 3.07
2052 4499 6.019398 CGAGTGAGACTACTAGACTGTACATG 60.019 46.154 0.00 0.00 0.00 3.21
2060 4514 2.937799 CCCACGAGTGAGACTACTAGAC 59.062 54.545 4.59 0.00 0.00 2.59
2062 4516 3.199677 CTCCCACGAGTGAGACTACTAG 58.800 54.545 4.59 0.00 0.00 2.57
2105 4559 5.368256 AATCATGAGTGCTGTTGAAGTTC 57.632 39.130 0.09 0.00 0.00 3.01
2202 5057 4.081420 TCTCTGTGAAATCTTAGGAGTGGC 60.081 45.833 0.00 0.00 0.00 5.01
2207 5062 4.382040 CGGCTTCTCTGTGAAATCTTAGGA 60.382 45.833 0.00 0.00 33.79 2.94
2211 5066 3.409026 ACGGCTTCTCTGTGAAATCTT 57.591 42.857 0.00 0.00 33.79 2.40
2246 5101 1.278699 TGTATCTGACAGCATGCACCA 59.721 47.619 21.98 12.98 42.53 4.17
2389 5251 2.202797 CCGACACCAGAGGCATCG 60.203 66.667 0.00 3.34 34.47 3.84
2426 5288 0.774491 AGGAGGGGGCAAGGTGTTAA 60.774 55.000 0.00 0.00 0.00 2.01
2431 5293 2.128226 ATCAGGAGGGGGCAAGGT 59.872 61.111 0.00 0.00 0.00 3.50
2438 5300 1.221840 CACGAACCATCAGGAGGGG 59.778 63.158 4.87 0.00 36.39 4.79
2450 5312 2.052157 GAGTGCTACAGTGACACGAAC 58.948 52.381 0.00 0.00 39.31 3.95
2460 5322 1.901538 CAGTGCTACGAGTGCTACAG 58.098 55.000 0.00 0.00 0.00 2.74
2477 5339 1.078848 GGGTACAGAGTGGCAGCAG 60.079 63.158 0.00 0.00 0.00 4.24
2492 5354 1.005394 CAAGGTAACGAGCACGGGT 60.005 57.895 8.74 0.00 44.46 5.28
2518 5380 4.077184 TGAGTTACCAGCGGGCGG 62.077 66.667 1.46 0.00 37.90 6.13
2555 5417 4.494199 CGAGATAACCCTGAAACAATTCGC 60.494 45.833 0.00 0.00 38.46 4.70
2566 5428 2.100916 ACGTTCATCCGAGATAACCCTG 59.899 50.000 0.00 0.00 0.00 4.45
2578 5440 1.787847 CGTGCTCCAACGTTCATCC 59.212 57.895 0.00 0.00 38.74 3.51
2619 5481 4.598036 ATGTTGGGAGATTCCAGTCAAT 57.402 40.909 0.00 0.00 38.64 2.57
2657 5520 2.297315 ACGAGACTGCAAGAGACATCAA 59.703 45.455 0.00 0.00 37.43 2.57
2661 5524 1.032794 ACACGAGACTGCAAGAGACA 58.967 50.000 0.00 0.00 37.43 3.41
2662 5525 1.789464 CAACACGAGACTGCAAGAGAC 59.211 52.381 0.00 0.00 37.43 3.36
2667 5530 1.891919 GCCCAACACGAGACTGCAA 60.892 57.895 0.00 0.00 0.00 4.08
2715 5586 2.162208 GCGAATCCTGATGCAAGAAACA 59.838 45.455 0.00 0.00 0.00 2.83
2716 5587 2.421424 AGCGAATCCTGATGCAAGAAAC 59.579 45.455 0.00 0.00 0.00 2.78
2718 5589 2.408271 AGCGAATCCTGATGCAAGAA 57.592 45.000 0.00 0.00 0.00 2.52
2719 5590 2.011947 CAAGCGAATCCTGATGCAAGA 58.988 47.619 0.00 0.00 0.00 3.02
2720 5591 1.065102 CCAAGCGAATCCTGATGCAAG 59.935 52.381 0.00 0.00 0.00 4.01
2721 5592 1.097232 CCAAGCGAATCCTGATGCAA 58.903 50.000 0.00 0.00 0.00 4.08
2737 5613 4.412796 TCACAAAATTGATGCAACCCAA 57.587 36.364 0.00 0.00 0.00 4.12
2738 5614 4.125703 GTTCACAAAATTGATGCAACCCA 58.874 39.130 0.00 0.00 0.00 4.51
2739 5615 3.498018 GGTTCACAAAATTGATGCAACCC 59.502 43.478 0.00 0.00 0.00 4.11
2754 5630 3.142951 CTCAAACCATAACGGGTTCACA 58.857 45.455 0.00 0.00 43.16 3.58
2761 5637 4.992319 TGTAGTGAACTCAAACCATAACGG 59.008 41.667 0.00 0.00 42.50 4.44
2804 5680 7.282224 CCGATTTGATACTAGGTTTCATTTCCA 59.718 37.037 0.00 0.00 0.00 3.53
2810 5686 4.448210 GCCCGATTTGATACTAGGTTTCA 58.552 43.478 0.00 0.00 0.00 2.69
2838 5714 4.976116 GGTCTGACAAAAAGAATGTTTCCG 59.024 41.667 10.38 0.00 0.00 4.30
2844 5720 5.156355 CGATTGGGTCTGACAAAAAGAATG 58.844 41.667 10.38 0.00 0.00 2.67
2848 5724 4.568152 AACGATTGGGTCTGACAAAAAG 57.432 40.909 10.38 4.98 0.00 2.27
2851 5727 6.642707 AATAAAACGATTGGGTCTGACAAA 57.357 33.333 10.38 3.97 0.00 2.83
2884 5760 7.463251 GCAAGAGTCTGACAACAAAAATGTTTC 60.463 37.037 10.88 0.00 0.00 2.78
2889 5765 5.581126 TGCAAGAGTCTGACAACAAAAAT 57.419 34.783 10.88 0.00 0.00 1.82
2890 5766 5.384063 TTGCAAGAGTCTGACAACAAAAA 57.616 34.783 10.88 0.00 0.00 1.94
2891 5767 5.384063 TTTGCAAGAGTCTGACAACAAAA 57.616 34.783 10.88 0.69 0.00 2.44
2893 5769 4.380444 GGTTTTGCAAGAGTCTGACAACAA 60.380 41.667 10.88 4.07 0.00 2.83
2894 5770 3.128589 GGTTTTGCAAGAGTCTGACAACA 59.871 43.478 10.88 0.11 0.00 3.33
2895 5771 3.128589 TGGTTTTGCAAGAGTCTGACAAC 59.871 43.478 10.88 3.87 0.00 3.32
2896 5772 3.351740 TGGTTTTGCAAGAGTCTGACAA 58.648 40.909 10.88 0.00 0.00 3.18
2898 5774 4.574599 AATGGTTTTGCAAGAGTCTGAC 57.425 40.909 0.00 0.00 0.00 3.51
2900 5776 5.646467 CAAAATGGTTTTGCAAGAGTCTG 57.354 39.130 0.00 0.00 42.91 3.51
2927 5807 8.410141 TGTTTCAGACTTTCCGTCAAAATTTAT 58.590 29.630 0.00 0.00 45.32 1.40
2930 5810 6.202516 TGTTTCAGACTTTCCGTCAAAATT 57.797 33.333 0.00 0.00 45.32 1.82
2960 5840 4.039609 AGCTTCTGCCAGTTGCTAATTTTT 59.960 37.500 11.23 0.00 42.00 1.94
2961 5841 3.575687 AGCTTCTGCCAGTTGCTAATTTT 59.424 39.130 11.23 0.00 42.00 1.82
2962 5842 3.160269 AGCTTCTGCCAGTTGCTAATTT 58.840 40.909 11.23 0.00 42.00 1.82
2963 5843 2.751806 GAGCTTCTGCCAGTTGCTAATT 59.248 45.455 12.49 0.00 42.00 1.40
2964 5844 2.026449 AGAGCTTCTGCCAGTTGCTAAT 60.026 45.455 12.49 4.43 42.00 1.73
3033 5913 5.373812 TGGTTTTTGGCCAATTTTCCTTA 57.626 34.783 21.26 0.00 32.29 2.69
3054 5934 2.736081 GCATGTGTGTGGGCATGTATTG 60.736 50.000 6.43 0.00 43.04 1.90
3062 5942 4.060038 GCTGGCATGTGTGTGGGC 62.060 66.667 0.00 0.00 0.00 5.36
3099 5979 2.407428 CGGCAGAGTAGTCGGCTCA 61.407 63.158 19.98 0.00 42.93 4.26
3100 5980 2.325666 GACGGCAGAGTAGTCGGCTC 62.326 65.000 19.98 8.95 42.47 4.70
3102 5982 2.102553 GACGGCAGAGTAGTCGGC 59.897 66.667 13.63 13.63 41.73 5.54
3104 5984 0.179161 CTTGGACGGCAGAGTAGTCG 60.179 60.000 0.00 0.00 43.36 4.18
3112 5992 1.667724 CTCTAATTGCTTGGACGGCAG 59.332 52.381 0.00 0.00 40.90 4.85
3118 5998 4.517285 GGTGTCATCTCTAATTGCTTGGA 58.483 43.478 0.00 0.00 0.00 3.53
3127 6007 7.419057 GGTCATTTGATAGGGTGTCATCTCTAA 60.419 40.741 0.00 0.00 0.00 2.10
3129 6009 5.163258 GGTCATTTGATAGGGTGTCATCTCT 60.163 44.000 0.00 0.00 0.00 3.10
3132 6012 4.818546 CAGGTCATTTGATAGGGTGTCATC 59.181 45.833 0.00 0.00 0.00 2.92
3171 6051 6.544622 CGTGTGTGTTCTTAAGGTTTGTAAA 58.455 36.000 1.85 0.00 0.00 2.01
3172 6052 5.447548 GCGTGTGTGTTCTTAAGGTTTGTAA 60.448 40.000 1.85 0.00 0.00 2.41
3182 6062 1.957186 GGCGGCGTGTGTGTTCTTA 60.957 57.895 9.37 0.00 0.00 2.10
3199 6079 4.104143 GGTACGCAACATCGAGGG 57.896 61.111 0.69 0.00 0.00 4.30
3217 6097 2.349886 GTGACAAATCATCAGCTCGTCC 59.650 50.000 0.00 0.00 37.14 4.79
3220 6100 1.667724 GGGTGACAAATCATCAGCTCG 59.332 52.381 4.40 0.00 42.82 5.03
3231 6111 4.228824 ACTCTAGTTACCTGGGTGACAAA 58.771 43.478 15.34 4.19 37.12 2.83
3233 6113 3.181426 TGACTCTAGTTACCTGGGTGACA 60.181 47.826 15.34 3.13 37.12 3.58
3234 6114 3.428532 TGACTCTAGTTACCTGGGTGAC 58.571 50.000 6.58 6.58 35.24 3.67
3244 6125 5.834742 TGTTGTAGGGTGTTGACTCTAGTTA 59.165 40.000 0.00 0.00 35.71 2.24
3255 6136 0.746063 TCGTCGTGTTGTAGGGTGTT 59.254 50.000 0.00 0.00 0.00 3.32
3256 6137 0.963962 ATCGTCGTGTTGTAGGGTGT 59.036 50.000 0.00 0.00 0.00 4.16
3265 6146 1.374252 GTGGCTCCATCGTCGTGTT 60.374 57.895 0.00 0.00 0.00 3.32
3269 6150 4.530857 GGGGTGGCTCCATCGTCG 62.531 72.222 8.03 0.00 38.11 5.12
3272 6153 2.190578 GAAGGGGTGGCTCCATCG 59.809 66.667 8.03 0.00 38.11 3.84
3273 6154 2.190578 CGAAGGGGTGGCTCCATC 59.809 66.667 8.03 2.01 38.11 3.51
3274 6155 2.610859 ACGAAGGGGTGGCTCCAT 60.611 61.111 8.03 0.00 38.11 3.41
3275 6156 3.319198 GACGAAGGGGTGGCTCCA 61.319 66.667 8.03 0.00 38.11 3.86
3276 6157 2.523453 GAAGACGAAGGGGTGGCTCC 62.523 65.000 0.00 0.00 0.00 4.70
3282 6163 0.763223 AGTGTGGAAGACGAAGGGGT 60.763 55.000 0.00 0.00 33.85 4.95
3284 6165 0.679505 TCAGTGTGGAAGACGAAGGG 59.320 55.000 0.00 0.00 33.85 3.95
3285 6166 1.605712 GGTCAGTGTGGAAGACGAAGG 60.606 57.143 0.00 0.00 33.85 3.46
3289 6170 0.939577 CGTGGTCAGTGTGGAAGACG 60.940 60.000 0.00 0.00 33.85 4.18
3312 6193 5.791336 ATGGTCTTCTATTAGACATGCGA 57.209 39.130 6.17 0.00 45.07 5.10
3348 6229 6.231211 AGGACACTGATAGTTTTTGGTACTG 58.769 40.000 0.00 0.00 0.00 2.74
3349 6230 6.435292 AGGACACTGATAGTTTTTGGTACT 57.565 37.500 0.00 0.00 0.00 2.73
3353 6234 3.684788 CCGAGGACACTGATAGTTTTTGG 59.315 47.826 0.00 0.00 0.00 3.28
3355 6236 4.618920 ACCGAGGACACTGATAGTTTTT 57.381 40.909 0.00 0.00 0.00 1.94
3374 6255 1.043673 ACGATGCTCTCCACCCTACC 61.044 60.000 0.00 0.00 0.00 3.18
3389 6270 1.681793 CCTTCTGGTACATCCGACGAT 59.318 52.381 0.00 0.00 38.20 3.73
3390 6271 1.100510 CCTTCTGGTACATCCGACGA 58.899 55.000 0.00 0.00 38.20 4.20
3391 6272 0.102481 CCCTTCTGGTACATCCGACG 59.898 60.000 0.00 0.00 38.20 5.12
3393 6274 0.042131 ACCCCTTCTGGTACATCCGA 59.958 55.000 0.00 0.00 38.20 4.55
3394 6275 0.464452 GACCCCTTCTGGTACATCCG 59.536 60.000 0.00 0.00 39.24 4.18


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

AutoCloner maintained by Alex Coulton.