Multiple sequence alignment - TraesCS5B01G406300

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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 TraesCS5B01G406300 chr5B 100.000 3474 0 0 1 3474 582424750 582428223 0.000000e+00 6416.0
1 TraesCS5B01G406300 chr5A 88.312 3234 194 96 325 3471 594350220 594353356 0.000000e+00 3709.0
2 TraesCS5B01G406300 chr5D 89.838 2834 132 75 346 3095 475209146 475211907 0.000000e+00 3494.0
3 TraesCS5B01G406300 chr5D 94.149 376 17 3 3093 3468 475211932 475212302 5.030000e-158 568.0
4 TraesCS5B01G406300 chr5D 92.553 188 10 3 1 184 475208891 475209078 2.060000e-67 267.0
5 TraesCS5B01G406300 chr5D 91.304 46 3 1 2799 2844 486618929 486618885 1.040000e-05 62.1
6 TraesCS5B01G406300 chr2A 83.146 356 32 14 325 674 216291216 216291549 2.030000e-77 300.0
7 TraesCS5B01G406300 chr2A 91.579 95 8 0 2051 2145 420226948 420227042 7.820000e-27 132.0
8 TraesCS5B01G406300 chr2D 85.606 132 14 5 2018 2145 315115264 315115134 2.180000e-27 134.0
9 TraesCS5B01G406300 chr2B 91.579 95 8 0 2051 2145 383057158 383057064 7.820000e-27 132.0
10 TraesCS5B01G406300 chr1A 100.000 29 0 0 271 299 337151304 337151276 2.000000e-03 54.7


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 TraesCS5B01G406300 chr5B 582424750 582428223 3473 False 6416 6416 100.000 1 3474 1 chr5B.!!$F1 3473
1 TraesCS5B01G406300 chr5A 594350220 594353356 3136 False 3709 3709 88.312 325 3471 1 chr5A.!!$F1 3146
2 TraesCS5B01G406300 chr5D 475208891 475212302 3411 False 1443 3494 92.180 1 3468 3 chr5D.!!$F1 3467

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
887 956 0.034896 TCCAACCAGACTTCTTCGGC 59.965 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2477 2616 0.036306 ACGGTAGTCCCAAAGCCTTG 59.964 55.0 0.0 0.0 0.0 3.61 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
46 47 1.953559 AACTCTCTCTTTTGCGTGCA 58.046 45.000 0.00 0.00 0.00 4.57
78 79 3.866910 ACGTGACATAAACTCGTGTTTGT 59.133 39.130 22.25 14.76 45.01 2.83
116 117 4.364415 AAACAAAGCGTGTAAGCAAAGA 57.636 36.364 0.00 0.00 40.60 2.52
117 118 4.364415 AACAAAGCGTGTAAGCAAAGAA 57.636 36.364 0.00 0.00 40.60 2.52
121 122 1.607148 AGCGTGTAAGCAAAGAAACCC 59.393 47.619 0.00 0.00 40.15 4.11
132 133 3.872630 GCAAAGAAACCCCGGTTCTAGAT 60.873 47.826 6.25 0.00 37.35 1.98
158 159 1.338107 TCCACGGAAGAGAAGAGCAA 58.662 50.000 0.00 0.00 0.00 3.91
162 163 1.270358 ACGGAAGAGAAGAGCAACACC 60.270 52.381 0.00 0.00 0.00 4.16
171 176 1.226491 GAGCAACACCGCATGCATC 60.226 57.895 19.57 0.00 44.95 3.91
172 177 1.651240 GAGCAACACCGCATGCATCT 61.651 55.000 19.57 2.90 44.95 2.90
193 198 2.942879 GTGGCAACGCGTGAATCA 59.057 55.556 14.98 6.63 42.51 2.57
196 201 1.129624 GTGGCAACGCGTGAATCAATA 59.870 47.619 14.98 0.00 42.51 1.90
197 202 2.013400 TGGCAACGCGTGAATCAATAT 58.987 42.857 14.98 0.00 42.51 1.28
198 203 2.031560 TGGCAACGCGTGAATCAATATC 59.968 45.455 14.98 0.00 42.51 1.63
199 204 2.031560 GGCAACGCGTGAATCAATATCA 59.968 45.455 14.98 0.00 0.00 2.15
200 205 3.486708 GGCAACGCGTGAATCAATATCAA 60.487 43.478 14.98 0.00 0.00 2.57
201 206 4.094911 GCAACGCGTGAATCAATATCAAA 58.905 39.130 14.98 0.00 0.00 2.69
202 207 4.556912 GCAACGCGTGAATCAATATCAAAA 59.443 37.500 14.98 0.00 0.00 2.44
203 208 5.060323 GCAACGCGTGAATCAATATCAAAAA 59.940 36.000 14.98 0.00 0.00 1.94
204 209 6.676385 CAACGCGTGAATCAATATCAAAAAG 58.324 36.000 14.98 0.00 0.00 2.27
205 210 6.176975 ACGCGTGAATCAATATCAAAAAGA 57.823 33.333 12.93 0.00 0.00 2.52
207 212 6.742718 ACGCGTGAATCAATATCAAAAAGAAG 59.257 34.615 12.93 0.00 0.00 2.85
210 215 8.792538 GCGTGAATCAATATCAAAAAGAAGAAG 58.207 33.333 0.00 0.00 0.00 2.85
211 216 9.831737 CGTGAATCAATATCAAAAAGAAGAAGT 57.168 29.630 0.00 0.00 0.00 3.01
215 220 9.985730 AATCAATATCAAAAAGAAGAAGTTGCA 57.014 25.926 0.00 0.00 0.00 4.08
217 222 9.630098 TCAATATCAAAAAGAAGAAGTTGCATC 57.370 29.630 0.00 0.00 0.00 3.91
218 223 9.635520 CAATATCAAAAAGAAGAAGTTGCATCT 57.364 29.630 0.00 0.00 0.00 2.90
221 226 7.807977 TCAAAAAGAAGAAGTTGCATCTACT 57.192 32.000 0.00 0.00 0.00 2.57
222 227 7.642669 TCAAAAAGAAGAAGTTGCATCTACTG 58.357 34.615 0.00 0.00 0.00 2.74
223 228 7.283127 TCAAAAAGAAGAAGTTGCATCTACTGT 59.717 33.333 0.00 0.00 0.00 3.55
224 229 8.559536 CAAAAAGAAGAAGTTGCATCTACTGTA 58.440 33.333 0.00 0.00 0.00 2.74
225 230 7.659652 AAAGAAGAAGTTGCATCTACTGTAC 57.340 36.000 0.00 0.00 0.00 2.90
226 231 6.346477 AGAAGAAGTTGCATCTACTGTACA 57.654 37.500 0.00 0.00 0.00 2.90
227 232 6.159988 AGAAGAAGTTGCATCTACTGTACAC 58.840 40.000 0.00 0.00 0.00 2.90
228 233 5.468540 AGAAGTTGCATCTACTGTACACA 57.531 39.130 0.00 0.00 0.00 3.72
229 234 6.042638 AGAAGTTGCATCTACTGTACACAT 57.957 37.500 0.00 0.00 0.00 3.21
230 235 5.871524 AGAAGTTGCATCTACTGTACACATG 59.128 40.000 0.00 0.00 0.00 3.21
231 236 5.152623 AGTTGCATCTACTGTACACATGT 57.847 39.130 0.00 0.00 0.00 3.21
232 237 6.280855 AGTTGCATCTACTGTACACATGTA 57.719 37.500 0.00 0.00 0.00 2.29
233 238 6.878317 AGTTGCATCTACTGTACACATGTAT 58.122 36.000 0.00 0.00 32.54 2.29
234 239 8.007405 AGTTGCATCTACTGTACACATGTATA 57.993 34.615 0.00 0.00 32.54 1.47
235 240 8.474831 AGTTGCATCTACTGTACACATGTATAA 58.525 33.333 0.00 0.00 32.54 0.98
236 241 8.755941 GTTGCATCTACTGTACACATGTATAAG 58.244 37.037 0.00 0.00 32.54 1.73
237 242 8.007405 TGCATCTACTGTACACATGTATAAGT 57.993 34.615 0.00 12.35 35.68 2.24
238 243 7.920682 TGCATCTACTGTACACATGTATAAGTG 59.079 37.037 15.40 0.00 41.40 3.16
240 245 9.452065 CATCTACTGTACACATGTATAAGTGTC 57.548 37.037 3.64 0.00 45.16 3.67
241 246 8.803397 TCTACTGTACACATGTATAAGTGTCT 57.197 34.615 3.64 0.00 45.16 3.41
242 247 8.674607 TCTACTGTACACATGTATAAGTGTCTG 58.325 37.037 3.64 4.09 45.16 3.51
243 248 6.100004 ACTGTACACATGTATAAGTGTCTGC 58.900 40.000 3.64 0.00 45.16 4.26
244 249 5.099575 TGTACACATGTATAAGTGTCTGCG 58.900 41.667 3.64 0.00 45.16 5.18
245 250 4.188247 ACACATGTATAAGTGTCTGCGT 57.812 40.909 0.00 0.00 45.16 5.24
246 251 4.174009 ACACATGTATAAGTGTCTGCGTC 58.826 43.478 0.00 0.00 45.16 5.19
247 252 4.082190 ACACATGTATAAGTGTCTGCGTCT 60.082 41.667 0.00 0.00 45.16 4.18
248 253 5.124936 ACACATGTATAAGTGTCTGCGTCTA 59.875 40.000 0.00 0.00 45.16 2.59
249 254 6.183360 ACACATGTATAAGTGTCTGCGTCTAT 60.183 38.462 0.00 0.00 45.16 1.98
250 255 7.012989 ACACATGTATAAGTGTCTGCGTCTATA 59.987 37.037 0.00 0.00 45.16 1.31
251 256 8.023706 CACATGTATAAGTGTCTGCGTCTATAT 58.976 37.037 0.00 0.00 0.00 0.86
252 257 8.023706 ACATGTATAAGTGTCTGCGTCTATATG 58.976 37.037 0.00 0.00 0.00 1.78
253 258 7.739498 TGTATAAGTGTCTGCGTCTATATGA 57.261 36.000 0.00 0.00 0.00 2.15
254 259 8.336801 TGTATAAGTGTCTGCGTCTATATGAT 57.663 34.615 0.00 0.00 0.00 2.45
255 260 8.793592 TGTATAAGTGTCTGCGTCTATATGATT 58.206 33.333 0.00 0.00 0.00 2.57
256 261 9.279904 GTATAAGTGTCTGCGTCTATATGATTC 57.720 37.037 0.00 0.00 0.00 2.52
257 262 6.398234 AAGTGTCTGCGTCTATATGATTCT 57.602 37.500 0.00 0.00 0.00 2.40
258 263 5.767269 AGTGTCTGCGTCTATATGATTCTG 58.233 41.667 0.00 0.00 0.00 3.02
259 264 5.300539 AGTGTCTGCGTCTATATGATTCTGT 59.699 40.000 0.00 0.00 0.00 3.41
260 265 5.980116 GTGTCTGCGTCTATATGATTCTGTT 59.020 40.000 0.00 0.00 0.00 3.16
261 266 7.013369 AGTGTCTGCGTCTATATGATTCTGTTA 59.987 37.037 0.00 0.00 0.00 2.41
262 267 7.648112 GTGTCTGCGTCTATATGATTCTGTTAA 59.352 37.037 0.00 0.00 0.00 2.01
263 268 7.862873 TGTCTGCGTCTATATGATTCTGTTAAG 59.137 37.037 0.00 0.00 0.00 1.85
264 269 8.076781 GTCTGCGTCTATATGATTCTGTTAAGA 58.923 37.037 0.00 0.00 0.00 2.10
279 284 8.964420 TTCTGTTAAGAAACAACAACAAAGAG 57.036 30.769 0.00 0.00 44.79 2.85
285 290 4.884164 AGAAACAACAACAAAGAGGAGGAG 59.116 41.667 0.00 0.00 0.00 3.69
288 293 3.181450 ACAACAACAAAGAGGAGGAGGAG 60.181 47.826 0.00 0.00 0.00 3.69
299 304 2.385417 AGGAGGAGGAGGAAGAAGAAGT 59.615 50.000 0.00 0.00 0.00 3.01
300 305 2.499693 GGAGGAGGAGGAAGAAGAAGTG 59.500 54.545 0.00 0.00 0.00 3.16
301 306 1.905894 AGGAGGAGGAAGAAGAAGTGC 59.094 52.381 0.00 0.00 0.00 4.40
302 307 1.404851 GGAGGAGGAAGAAGAAGTGCG 60.405 57.143 0.00 0.00 0.00 5.34
303 308 1.273886 GAGGAGGAAGAAGAAGTGCGT 59.726 52.381 0.00 0.00 0.00 5.24
304 309 1.001406 AGGAGGAAGAAGAAGTGCGTG 59.999 52.381 0.00 0.00 0.00 5.34
305 310 1.000955 GGAGGAAGAAGAAGTGCGTGA 59.999 52.381 0.00 0.00 0.00 4.35
306 311 2.333014 GAGGAAGAAGAAGTGCGTGAG 58.667 52.381 0.00 0.00 0.00 3.51
307 312 1.689273 AGGAAGAAGAAGTGCGTGAGT 59.311 47.619 0.00 0.00 0.00 3.41
308 313 1.795286 GGAAGAAGAAGTGCGTGAGTG 59.205 52.381 0.00 0.00 0.00 3.51
309 314 2.545952 GGAAGAAGAAGTGCGTGAGTGA 60.546 50.000 0.00 0.00 0.00 3.41
310 315 2.430546 AGAAGAAGTGCGTGAGTGAG 57.569 50.000 0.00 0.00 0.00 3.51
311 316 1.683917 AGAAGAAGTGCGTGAGTGAGT 59.316 47.619 0.00 0.00 0.00 3.41
312 317 1.789464 GAAGAAGTGCGTGAGTGAGTG 59.211 52.381 0.00 0.00 0.00 3.51
313 318 0.598680 AGAAGTGCGTGAGTGAGTGC 60.599 55.000 0.00 0.00 0.00 4.40
314 319 1.880601 GAAGTGCGTGAGTGAGTGCG 61.881 60.000 0.00 0.00 0.00 5.34
315 320 2.629050 AAGTGCGTGAGTGAGTGCGT 62.629 55.000 0.00 0.00 0.00 5.24
316 321 2.658268 TGCGTGAGTGAGTGCGTG 60.658 61.111 0.00 0.00 0.00 5.34
317 322 4.064491 GCGTGAGTGAGTGCGTGC 62.064 66.667 0.00 0.00 0.00 5.34
318 323 2.658268 CGTGAGTGAGTGCGTGCA 60.658 61.111 0.00 0.00 0.00 4.57
319 324 2.023771 CGTGAGTGAGTGCGTGCAT 61.024 57.895 0.00 0.00 0.00 3.96
320 325 1.494628 GTGAGTGAGTGCGTGCATG 59.505 57.895 0.09 0.09 0.00 4.06
321 326 2.319841 TGAGTGAGTGCGTGCATGC 61.320 57.895 24.20 24.20 0.00 4.06
322 327 2.281002 AGTGAGTGCGTGCATGCA 60.281 55.556 29.30 29.30 43.95 3.96
548 566 4.735132 CCAGGCGGCTCGAACGAA 62.735 66.667 9.32 0.00 0.00 3.85
549 567 3.479269 CAGGCGGCTCGAACGAAC 61.479 66.667 9.32 5.11 0.00 3.95
552 570 3.101428 GCGGCTCGAACGAACGAA 61.101 61.111 19.23 0.00 41.67 3.85
553 571 2.761354 CGGCTCGAACGAACGAAC 59.239 61.111 12.92 5.76 41.67 3.95
554 572 2.761354 GGCTCGAACGAACGAACG 59.239 61.111 0.14 6.37 41.67 3.95
556 574 0.725784 GGCTCGAACGAACGAACGTA 60.726 55.000 11.14 0.00 45.83 3.57
557 575 1.044725 GCTCGAACGAACGAACGTAA 58.955 50.000 11.14 1.98 45.83 3.18
720 785 1.546961 TCACGGTTCCTTCTCTCTCC 58.453 55.000 0.00 0.00 0.00 3.71
734 799 3.041211 CTCTCTCCCTCTCTCTCTCTCA 58.959 54.545 0.00 0.00 0.00 3.27
794 861 2.366167 AGCTCGCAGATTCCCCCT 60.366 61.111 0.00 0.00 33.89 4.79
859 928 2.800788 ACATTCCTATCCTCCTCCTCCT 59.199 50.000 0.00 0.00 0.00 3.69
860 929 3.181412 ACATTCCTATCCTCCTCCTCCTC 60.181 52.174 0.00 0.00 0.00 3.71
861 930 2.542257 TCCTATCCTCCTCCTCCTCT 57.458 55.000 0.00 0.00 0.00 3.69
862 931 2.808355 TCCTATCCTCCTCCTCCTCTT 58.192 52.381 0.00 0.00 0.00 2.85
863 932 2.719705 TCCTATCCTCCTCCTCCTCTTC 59.280 54.545 0.00 0.00 0.00 2.87
864 933 2.225267 CCTATCCTCCTCCTCCTCTTCC 60.225 59.091 0.00 0.00 0.00 3.46
865 934 1.631536 ATCCTCCTCCTCCTCTTCCT 58.368 55.000 0.00 0.00 0.00 3.36
866 935 0.930726 TCCTCCTCCTCCTCTTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
867 936 0.105709 CCTCCTCCTCCTCTTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
868 937 0.933700 CTCCTCCTCCTCTTCCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
869 938 0.930726 TCCTCCTCCTCTTCCTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
870 939 0.105709 CCTCCTCCTCTTCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
881 950 1.645710 TCCTCCTCCAACCAGACTTC 58.354 55.000 0.00 0.00 0.00 3.01
882 951 1.150135 TCCTCCTCCAACCAGACTTCT 59.850 52.381 0.00 0.00 0.00 2.85
883 952 1.981495 CCTCCTCCAACCAGACTTCTT 59.019 52.381 0.00 0.00 0.00 2.52
884 953 2.027653 CCTCCTCCAACCAGACTTCTTC 60.028 54.545 0.00 0.00 0.00 2.87
885 954 1.618837 TCCTCCAACCAGACTTCTTCG 59.381 52.381 0.00 0.00 0.00 3.79
886 955 1.338200 CCTCCAACCAGACTTCTTCGG 60.338 57.143 0.00 0.00 0.00 4.30
887 956 0.034896 TCCAACCAGACTTCTTCGGC 59.965 55.000 0.00 0.00 0.00 5.54
913 982 1.901085 CGCTACCAGCTTCCTTCCT 59.099 57.895 0.00 0.00 39.60 3.36
928 1007 2.180276 CTTCCTTCCTTCCTTCCTCGA 58.820 52.381 0.00 0.00 0.00 4.04
929 1008 1.853963 TCCTTCCTTCCTTCCTCGAG 58.146 55.000 5.13 5.13 0.00 4.04
930 1009 1.358103 TCCTTCCTTCCTTCCTCGAGA 59.642 52.381 15.71 0.00 0.00 4.04
931 1010 2.180276 CCTTCCTTCCTTCCTCGAGAA 58.820 52.381 15.71 5.59 0.00 2.87
932 1011 2.567615 CCTTCCTTCCTTCCTCGAGAAA 59.432 50.000 15.71 0.00 32.88 2.52
935 1014 3.714144 TCCTTCCTTCCTCGAGAAAGAT 58.286 45.455 13.66 0.00 32.88 2.40
947 1032 3.129813 TCGAGAAAGATTTCGATCGGGAA 59.870 43.478 16.41 11.07 40.55 3.97
961 1046 2.589442 GGAACGGTGGCGTGTTCA 60.589 61.111 15.18 0.00 44.85 3.18
973 1058 0.315869 CGTGTTCACTTGTTGTCCGC 60.316 55.000 1.53 0.00 0.00 5.54
974 1059 0.315869 GTGTTCACTTGTTGTCCGCG 60.316 55.000 0.00 0.00 0.00 6.46
975 1060 0.741574 TGTTCACTTGTTGTCCGCGT 60.742 50.000 4.92 0.00 0.00 6.01
976 1061 0.315869 GTTCACTTGTTGTCCGCGTG 60.316 55.000 4.92 0.00 0.00 5.34
977 1062 2.042520 TTCACTTGTTGTCCGCGTGC 62.043 55.000 4.92 0.00 0.00 5.34
978 1063 3.636043 ACTTGTTGTCCGCGTGCG 61.636 61.111 4.92 7.38 39.44 5.34
1312 1430 1.291184 CGCCTTGTGCAGTGATCGAA 61.291 55.000 0.00 0.00 41.33 3.71
1410 1528 2.433318 GCAGCTCTGGGTCGACAC 60.433 66.667 18.91 15.66 0.00 3.67
1480 1602 7.481275 TCCGTTTCTATTTGTTTACTTTCGT 57.519 32.000 0.00 0.00 0.00 3.85
1487 1609 8.080083 TCTATTTGTTTACTTTCGTTCTGGTC 57.920 34.615 0.00 0.00 0.00 4.02
1503 1625 8.138074 TCGTTCTGGTCTGATCTTTATTATCTG 58.862 37.037 0.00 0.00 0.00 2.90
1567 1694 2.734175 CGATCCTGACCGAAACGAATCA 60.734 50.000 0.00 0.00 0.00 2.57
1605 1736 1.194218 GGAGCAGAAGAAGGAGAGCT 58.806 55.000 0.00 0.00 34.61 4.09
1607 1738 0.817013 AGCAGAAGAAGGAGAGCTCG 59.183 55.000 8.37 0.00 0.00 5.03
1892 2023 1.179814 AGTCGAGGAAGACAAGGCGT 61.180 55.000 0.00 0.00 43.24 5.68
2012 2151 6.430000 GCTTTAGGTTCTAGTTGGAACATTCA 59.570 38.462 10.00 0.00 45.07 2.57
2013 2152 7.361286 GCTTTAGGTTCTAGTTGGAACATTCAG 60.361 40.741 10.00 4.50 45.07 3.02
2014 2153 5.825593 AGGTTCTAGTTGGAACATTCAGA 57.174 39.130 10.00 0.00 45.07 3.27
2015 2154 6.187727 AGGTTCTAGTTGGAACATTCAGAA 57.812 37.500 10.00 0.00 45.07 3.02
2064 2203 2.730382 TCCATGATGATTGCAGTTGCT 58.270 42.857 5.62 0.00 42.66 3.91
2160 2299 6.553476 AGGTTAGCAACAGTTTTATCCCTTTT 59.447 34.615 0.00 0.00 0.00 2.27
2165 2304 5.236263 GCAACAGTTTTATCCCTTTTTGTGG 59.764 40.000 0.00 0.00 0.00 4.17
2173 2312 9.944663 GTTTTATCCCTTTTTGTGGAAATTTTC 57.055 29.630 0.24 0.24 33.54 2.29
2187 2326 6.863126 GTGGAAATTTTCGTGAACAATCATCT 59.137 34.615 3.17 0.00 38.01 2.90
2236 2375 9.155975 ACATCTTATGTTGAGACTGATTTGTAC 57.844 33.333 0.00 0.00 41.63 2.90
2240 2379 9.599866 CTTATGTTGAGACTGATTTGTACCATA 57.400 33.333 0.00 0.00 0.00 2.74
2277 2416 0.946221 CGTCTGCACAACCAGAGGTC 60.946 60.000 4.27 0.00 42.14 3.85
2281 2420 2.347490 CACAACCAGAGGTCCCCG 59.653 66.667 0.00 0.00 33.12 5.73
2306 2445 1.552799 TTCTTCAGCCAGCCATCCGA 61.553 55.000 0.00 0.00 0.00 4.55
2320 2459 1.072173 CATCCGATTATGCTGGTGGGA 59.928 52.381 0.00 0.00 0.00 4.37
2517 2656 5.335935 CGTCGAAGATTTTCATGAGAGAGA 58.664 41.667 0.00 0.00 40.67 3.10
2518 2657 5.455201 CGTCGAAGATTTTCATGAGAGAGAG 59.545 44.000 0.00 0.00 40.67 3.20
2545 2684 1.102809 TAGCTTTGCGGCATGGATGG 61.103 55.000 2.28 0.00 34.17 3.51
2614 2753 0.472471 TCCAGGGATATTGGGCGTTC 59.528 55.000 0.00 0.00 36.34 3.95
2862 3012 1.045407 AGCGTCAACCTTGTACCTGA 58.955 50.000 0.00 0.00 0.00 3.86
2864 3014 2.000447 GCGTCAACCTTGTACCTGATC 59.000 52.381 0.00 0.00 0.00 2.92
2876 3026 2.206576 ACCTGATCAACTGCCCTTTC 57.793 50.000 0.00 0.00 0.00 2.62
2900 3050 2.938956 CCAGGAGTTGGTTCTGAACT 57.061 50.000 19.05 0.00 42.41 3.01
2901 3051 3.214696 CCAGGAGTTGGTTCTGAACTT 57.785 47.619 19.05 4.21 42.41 2.66
2902 3052 3.142174 CCAGGAGTTGGTTCTGAACTTC 58.858 50.000 19.05 11.71 42.41 3.01
2903 3053 3.181450 CCAGGAGTTGGTTCTGAACTTCT 60.181 47.826 19.05 14.13 39.48 2.85
2904 3054 4.061596 CAGGAGTTGGTTCTGAACTTCTC 58.938 47.826 19.05 19.82 37.19 2.87
2905 3055 3.711704 AGGAGTTGGTTCTGAACTTCTCA 59.288 43.478 24.85 13.84 34.67 3.27
2912 3062 5.192927 TGGTTCTGAACTTCTCACATGTTT 58.807 37.500 19.05 0.00 0.00 2.83
2946 3104 1.342082 GCAACAGCATCGCAGCAAAG 61.342 55.000 0.00 0.00 36.85 2.77
3015 3173 2.028930 TGCTCTCTCCGTTTTCTCCTTC 60.029 50.000 0.00 0.00 0.00 3.46
3016 3174 2.869897 CTCTCTCCGTTTTCTCCTTCG 58.130 52.381 0.00 0.00 0.00 3.79
3017 3175 1.067776 TCTCTCCGTTTTCTCCTTCGC 60.068 52.381 0.00 0.00 0.00 4.70
3018 3176 0.677288 TCTCCGTTTTCTCCTTCGCA 59.323 50.000 0.00 0.00 0.00 5.10
3041 3199 2.963371 GGCGACCTCGACTGAACT 59.037 61.111 0.00 0.00 45.57 3.01
3045 3203 1.444553 GACCTCGACTGAACTGCGG 60.445 63.158 0.00 0.00 0.00 5.69
3112 3297 0.586802 GTCCAGGCGACAGACAAAAC 59.413 55.000 6.58 0.00 41.54 2.43
3155 3340 1.269723 GGAAGGAAAGAAGCAAACCGG 59.730 52.381 0.00 0.00 0.00 5.28
3210 3399 4.827087 CGCGCTGCACTGATCCCT 62.827 66.667 5.56 0.00 0.00 4.20
3319 3508 8.839310 AATAATAACTGCTGGTATCACATCTC 57.161 34.615 1.18 0.00 0.00 2.75
3322 3511 4.134379 ACTGCTGGTATCACATCTCTTG 57.866 45.455 0.00 0.00 0.00 3.02
3326 3515 3.464907 CTGGTATCACATCTCTTGGCTG 58.535 50.000 0.00 0.00 0.00 4.85
3327 3516 2.840038 TGGTATCACATCTCTTGGCTGT 59.160 45.455 0.00 0.00 0.00 4.40
3328 3517 3.118629 TGGTATCACATCTCTTGGCTGTC 60.119 47.826 0.00 0.00 0.00 3.51
3329 3518 3.133721 GGTATCACATCTCTTGGCTGTCT 59.866 47.826 0.00 0.00 0.00 3.41
3346 3535 2.632512 TGTCTGTCTGTGCTTATCCACA 59.367 45.455 0.00 0.00 42.99 4.17
3370 3559 9.388506 ACAGCCTAATATAATGCAGTATTGATC 57.611 33.333 12.49 0.00 0.00 2.92
3398 3587 1.943693 GCTGCTCGATCGCTCTGAC 60.944 63.158 11.09 0.00 0.00 3.51
3410 3599 1.812922 CTCTGACGAGCATGTGCCC 60.813 63.158 0.57 0.00 43.38 5.36
3471 3660 3.407252 CGCATAATTTATGTGATCGGCG 58.593 45.455 20.39 0.00 46.77 6.46
3472 3661 3.724716 CGCATAATTTATGTGATCGGCGG 60.725 47.826 20.39 0.00 46.77 6.13
3473 3662 3.747193 CATAATTTATGTGATCGGCGGC 58.253 45.455 7.21 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.020333 GTAATTACGTGCGCCACCCA 61.020 55.000 4.18 0.00 0.00 4.51
13 14 4.857588 AGAGAGAGTTTGTAATTACGTGCG 59.142 41.667 10.92 0.00 0.00 5.34
46 47 0.323302 TATGTCACGTGGTGGTGCAT 59.677 50.000 17.00 12.37 37.89 3.96
78 79 7.271653 CGCTTTGTTTTGTTTCTTACTGTACAA 59.728 33.333 0.00 0.00 0.00 2.41
116 117 1.209747 GCTGATCTAGAACCGGGGTTT 59.790 52.381 6.32 0.00 38.60 3.27
117 118 0.831307 GCTGATCTAGAACCGGGGTT 59.169 55.000 6.32 2.01 41.54 4.11
121 122 1.536284 GGAACGCTGATCTAGAACCGG 60.536 57.143 0.00 0.00 0.00 5.28
158 159 1.521457 CGGTAGATGCATGCGGTGT 60.521 57.895 14.09 5.48 0.00 4.16
162 163 2.885676 GCCACGGTAGATGCATGCG 61.886 63.158 14.09 0.00 0.00 4.73
184 189 8.673626 TTCTTCTTTTTGATATTGATTCACGC 57.326 30.769 0.00 0.00 0.00 5.34
185 190 9.831737 ACTTCTTCTTTTTGATATTGATTCACG 57.168 29.630 0.00 0.00 0.00 4.35
189 194 9.985730 TGCAACTTCTTCTTTTTGATATTGATT 57.014 25.926 0.00 0.00 0.00 2.57
192 197 9.635520 AGATGCAACTTCTTCTTTTTGATATTG 57.364 29.630 0.00 0.00 0.00 1.90
196 201 8.295288 CAGTAGATGCAACTTCTTCTTTTTGAT 58.705 33.333 0.30 0.00 0.00 2.57
197 202 7.283127 ACAGTAGATGCAACTTCTTCTTTTTGA 59.717 33.333 0.30 0.00 0.00 2.69
198 203 7.420800 ACAGTAGATGCAACTTCTTCTTTTTG 58.579 34.615 0.30 0.00 0.00 2.44
199 204 7.573968 ACAGTAGATGCAACTTCTTCTTTTT 57.426 32.000 0.30 0.00 0.00 1.94
200 205 7.715249 TGTACAGTAGATGCAACTTCTTCTTTT 59.285 33.333 0.30 0.00 0.00 2.27
201 206 7.171678 GTGTACAGTAGATGCAACTTCTTCTTT 59.828 37.037 0.30 0.00 0.00 2.52
202 207 6.647067 GTGTACAGTAGATGCAACTTCTTCTT 59.353 38.462 0.30 0.00 0.00 2.52
203 208 6.159988 GTGTACAGTAGATGCAACTTCTTCT 58.840 40.000 0.30 0.00 0.00 2.85
204 209 5.926542 TGTGTACAGTAGATGCAACTTCTTC 59.073 40.000 0.30 0.00 0.00 2.87
205 210 5.853936 TGTGTACAGTAGATGCAACTTCTT 58.146 37.500 0.30 0.00 0.00 2.52
207 212 5.639506 ACATGTGTACAGTAGATGCAACTTC 59.360 40.000 0.30 0.00 0.00 3.01
210 215 8.642908 TTATACATGTGTACAGTAGATGCAAC 57.357 34.615 9.11 0.00 32.72 4.17
211 216 8.474831 ACTTATACATGTGTACAGTAGATGCAA 58.525 33.333 9.11 0.00 32.72 4.08
212 217 7.920682 CACTTATACATGTGTACAGTAGATGCA 59.079 37.037 9.11 0.00 32.72 3.96
213 218 7.921214 ACACTTATACATGTGTACAGTAGATGC 59.079 37.037 9.11 0.00 44.40 3.91
214 219 9.452065 GACACTTATACATGTGTACAGTAGATG 57.548 37.037 9.11 0.00 45.94 2.90
215 220 9.409918 AGACACTTATACATGTGTACAGTAGAT 57.590 33.333 9.11 0.00 45.94 1.98
216 221 8.674607 CAGACACTTATACATGTGTACAGTAGA 58.325 37.037 9.11 0.00 45.94 2.59
217 222 7.432545 GCAGACACTTATACATGTGTACAGTAG 59.567 40.741 9.11 3.13 45.94 2.57
218 223 7.255569 GCAGACACTTATACATGTGTACAGTA 58.744 38.462 9.11 0.00 45.94 2.74
219 224 6.100004 GCAGACACTTATACATGTGTACAGT 58.900 40.000 9.11 9.58 45.94 3.55
220 225 5.230097 CGCAGACACTTATACATGTGTACAG 59.770 44.000 9.11 9.00 45.94 2.74
221 226 5.099575 CGCAGACACTTATACATGTGTACA 58.900 41.667 9.11 0.00 45.94 2.90
222 227 5.100259 ACGCAGACACTTATACATGTGTAC 58.900 41.667 9.11 0.00 45.94 2.90
223 228 5.124936 AGACGCAGACACTTATACATGTGTA 59.875 40.000 9.11 2.80 45.94 2.90
225 230 4.424626 AGACGCAGACACTTATACATGTG 58.575 43.478 9.11 0.00 39.80 3.21
226 231 4.720649 AGACGCAGACACTTATACATGT 57.279 40.909 2.69 2.69 0.00 3.21
227 232 8.237267 TCATATAGACGCAGACACTTATACATG 58.763 37.037 0.00 0.00 0.00 3.21
228 233 8.336801 TCATATAGACGCAGACACTTATACAT 57.663 34.615 0.00 0.00 0.00 2.29
229 234 7.739498 TCATATAGACGCAGACACTTATACA 57.261 36.000 0.00 0.00 0.00 2.29
230 235 9.279904 GAATCATATAGACGCAGACACTTATAC 57.720 37.037 0.00 0.00 0.00 1.47
231 236 9.232473 AGAATCATATAGACGCAGACACTTATA 57.768 33.333 0.00 0.00 0.00 0.98
232 237 8.026026 CAGAATCATATAGACGCAGACACTTAT 58.974 37.037 0.00 0.00 0.00 1.73
233 238 7.013369 ACAGAATCATATAGACGCAGACACTTA 59.987 37.037 0.00 0.00 0.00 2.24
234 239 6.183360 ACAGAATCATATAGACGCAGACACTT 60.183 38.462 0.00 0.00 0.00 3.16
235 240 5.300539 ACAGAATCATATAGACGCAGACACT 59.699 40.000 0.00 0.00 0.00 3.55
236 241 5.524284 ACAGAATCATATAGACGCAGACAC 58.476 41.667 0.00 0.00 0.00 3.67
237 242 5.774498 ACAGAATCATATAGACGCAGACA 57.226 39.130 0.00 0.00 0.00 3.41
238 243 8.076781 TCTTAACAGAATCATATAGACGCAGAC 58.923 37.037 0.00 0.00 0.00 3.51
239 244 8.166422 TCTTAACAGAATCATATAGACGCAGA 57.834 34.615 0.00 0.00 0.00 4.26
240 245 8.803201 TTCTTAACAGAATCATATAGACGCAG 57.197 34.615 0.00 0.00 33.80 5.18
241 246 9.031360 GTTTCTTAACAGAATCATATAGACGCA 57.969 33.333 0.00 0.00 38.89 5.24
242 247 9.031360 TGTTTCTTAACAGAATCATATAGACGC 57.969 33.333 0.00 0.00 39.29 5.19
250 255 9.868277 TTTGTTGTTGTTTCTTAACAGAATCAT 57.132 25.926 0.00 0.00 44.56 2.45
251 256 9.352784 CTTTGTTGTTGTTTCTTAACAGAATCA 57.647 29.630 0.00 0.00 44.56 2.57
252 257 9.567848 TCTTTGTTGTTGTTTCTTAACAGAATC 57.432 29.630 0.00 0.00 44.56 2.52
253 258 9.573133 CTCTTTGTTGTTGTTTCTTAACAGAAT 57.427 29.630 0.00 0.00 44.56 2.40
254 259 8.026607 CCTCTTTGTTGTTGTTTCTTAACAGAA 58.973 33.333 0.00 0.00 44.56 3.02
255 260 7.392113 TCCTCTTTGTTGTTGTTTCTTAACAGA 59.608 33.333 0.00 0.00 44.56 3.41
256 261 7.535139 TCCTCTTTGTTGTTGTTTCTTAACAG 58.465 34.615 0.00 0.00 44.56 3.16
257 262 7.362574 CCTCCTCTTTGTTGTTGTTTCTTAACA 60.363 37.037 0.00 0.00 42.34 2.41
258 263 6.972901 CCTCCTCTTTGTTGTTGTTTCTTAAC 59.027 38.462 0.00 0.00 34.75 2.01
259 264 6.887545 TCCTCCTCTTTGTTGTTGTTTCTTAA 59.112 34.615 0.00 0.00 0.00 1.85
260 265 6.419791 TCCTCCTCTTTGTTGTTGTTTCTTA 58.580 36.000 0.00 0.00 0.00 2.10
261 266 5.261216 TCCTCCTCTTTGTTGTTGTTTCTT 58.739 37.500 0.00 0.00 0.00 2.52
262 267 4.855340 TCCTCCTCTTTGTTGTTGTTTCT 58.145 39.130 0.00 0.00 0.00 2.52
263 268 4.036852 CCTCCTCCTCTTTGTTGTTGTTTC 59.963 45.833 0.00 0.00 0.00 2.78
264 269 3.954258 CCTCCTCCTCTTTGTTGTTGTTT 59.046 43.478 0.00 0.00 0.00 2.83
273 278 2.826488 TCTTCCTCCTCCTCCTCTTTG 58.174 52.381 0.00 0.00 0.00 2.77
279 284 2.499693 CACTTCTTCTTCCTCCTCCTCC 59.500 54.545 0.00 0.00 0.00 4.30
285 290 1.000955 TCACGCACTTCTTCTTCCTCC 59.999 52.381 0.00 0.00 0.00 4.30
288 293 1.795286 CACTCACGCACTTCTTCTTCC 59.205 52.381 0.00 0.00 0.00 3.46
299 304 2.658268 CACGCACTCACTCACGCA 60.658 61.111 0.00 0.00 0.00 5.24
300 305 4.064491 GCACGCACTCACTCACGC 62.064 66.667 0.00 0.00 0.00 5.34
301 306 2.023771 ATGCACGCACTCACTCACG 61.024 57.895 0.00 0.00 0.00 4.35
302 307 1.494628 CATGCACGCACTCACTCAC 59.505 57.895 0.00 0.00 0.00 3.51
303 308 2.319841 GCATGCACGCACTCACTCA 61.320 57.895 14.21 0.00 0.00 3.41
304 309 2.236803 CTGCATGCACGCACTCACTC 62.237 60.000 18.46 0.00 36.86 3.51
305 310 2.281002 TGCATGCACGCACTCACT 60.281 55.556 18.46 0.00 36.86 3.41
306 311 2.175078 CTGCATGCACGCACTCAC 59.825 61.111 18.46 0.00 36.86 3.51
307 312 3.051479 CCTGCATGCACGCACTCA 61.051 61.111 18.46 0.00 36.86 3.41
308 313 4.471726 GCCTGCATGCACGCACTC 62.472 66.667 29.28 6.55 36.86 3.51
321 326 3.741476 GCTGGTTTCGCAGGCCTG 61.741 66.667 29.34 29.34 0.00 4.85
329 334 4.383602 CGTTGCCCGCTGGTTTCG 62.384 66.667 0.00 0.00 0.00 3.46
532 550 3.479269 GTTCGTTCGAGCCGCCTG 61.479 66.667 0.00 0.00 0.00 4.85
535 553 3.101428 TTCGTTCGTTCGAGCCGC 61.101 61.111 3.77 0.00 40.86 6.53
536 554 2.761354 GTTCGTTCGTTCGAGCCG 59.239 61.111 3.77 6.72 40.86 5.52
537 555 0.725784 TACGTTCGTTCGTTCGAGCC 60.726 55.000 11.84 4.51 43.80 4.70
538 556 1.044725 TTACGTTCGTTCGTTCGAGC 58.955 50.000 11.84 8.17 43.80 5.03
539 557 5.406156 TTTATTACGTTCGTTCGTTCGAG 57.594 39.130 11.84 0.00 43.80 4.04
540 558 5.797909 TTTTATTACGTTCGTTCGTTCGA 57.202 34.783 11.84 1.29 43.80 3.71
720 785 2.091541 GGTGTGTGAGAGAGAGAGAGG 58.908 57.143 0.00 0.00 0.00 3.69
734 799 3.889692 CCCTGGCTGGTGGTGTGT 61.890 66.667 9.73 0.00 0.00 3.72
754 819 2.040544 CGCAGGATTTGTTCGGCCT 61.041 57.895 0.00 0.00 0.00 5.19
859 928 1.150135 AGTCTGGTTGGAGGAGGAAGA 59.850 52.381 0.00 0.00 0.00 2.87
860 929 1.650528 AGTCTGGTTGGAGGAGGAAG 58.349 55.000 0.00 0.00 0.00 3.46
861 930 1.978580 GAAGTCTGGTTGGAGGAGGAA 59.021 52.381 0.00 0.00 0.00 3.36
862 931 1.150135 AGAAGTCTGGTTGGAGGAGGA 59.850 52.381 0.00 0.00 0.00 3.71
863 932 1.650528 AGAAGTCTGGTTGGAGGAGG 58.349 55.000 0.00 0.00 0.00 4.30
864 933 2.353208 CGAAGAAGTCTGGTTGGAGGAG 60.353 54.545 0.00 0.00 0.00 3.69
865 934 1.618837 CGAAGAAGTCTGGTTGGAGGA 59.381 52.381 0.00 0.00 0.00 3.71
866 935 1.338200 CCGAAGAAGTCTGGTTGGAGG 60.338 57.143 0.00 0.00 0.00 4.30
867 936 1.941668 GCCGAAGAAGTCTGGTTGGAG 60.942 57.143 0.00 0.00 0.00 3.86
868 937 0.034896 GCCGAAGAAGTCTGGTTGGA 59.965 55.000 0.00 0.00 0.00 3.53
869 938 0.955919 GGCCGAAGAAGTCTGGTTGG 60.956 60.000 0.00 0.00 0.00 3.77
870 939 0.035458 AGGCCGAAGAAGTCTGGTTG 59.965 55.000 0.00 0.00 0.00 3.77
886 955 4.537433 CTGGTAGCGCTGGGAGGC 62.537 72.222 22.90 2.80 0.00 4.70
887 956 4.537433 GCTGGTAGCGCTGGGAGG 62.537 72.222 22.90 7.50 0.00 4.30
913 982 3.507411 TCTTTCTCGAGGAAGGAAGGAA 58.493 45.455 29.13 9.61 37.15 3.36
928 1007 3.187700 CGTTCCCGATCGAAATCTTTCT 58.812 45.455 18.66 0.00 33.74 2.52
929 1008 2.284417 CCGTTCCCGATCGAAATCTTTC 59.716 50.000 18.66 0.00 35.63 2.62
930 1009 2.277084 CCGTTCCCGATCGAAATCTTT 58.723 47.619 18.66 0.00 35.63 2.52
931 1010 1.206371 ACCGTTCCCGATCGAAATCTT 59.794 47.619 18.66 0.00 35.63 2.40
932 1011 0.822164 ACCGTTCCCGATCGAAATCT 59.178 50.000 18.66 0.00 35.63 2.40
935 1014 1.079681 CCACCGTTCCCGATCGAAA 60.080 57.895 18.66 7.77 35.63 3.46
961 1046 3.636043 CGCACGCGGACAACAAGT 61.636 61.111 12.47 0.00 35.56 3.16
982 1067 0.596341 ATGCAAACGCAAACGGGAAC 60.596 50.000 0.00 0.00 44.09 3.62
983 1068 0.596083 CATGCAAACGCAAACGGGAA 60.596 50.000 0.00 0.00 44.09 3.97
984 1069 1.007964 CATGCAAACGCAAACGGGA 60.008 52.632 0.00 0.00 44.09 5.14
985 1070 2.021039 CCATGCAAACGCAAACGGG 61.021 57.895 0.00 0.00 44.09 5.28
1235 1329 9.532697 CAAACAAACAATCAGAAAAACAAGAAG 57.467 29.630 0.00 0.00 0.00 2.85
1238 1332 9.662545 AAACAAACAAACAATCAGAAAAACAAG 57.337 25.926 0.00 0.00 0.00 3.16
1245 1339 8.558973 AAATCCAAACAAACAAACAATCAGAA 57.441 26.923 0.00 0.00 0.00 3.02
1247 1341 8.235905 ACAAAATCCAAACAAACAAACAATCAG 58.764 29.630 0.00 0.00 0.00 2.90
1250 1344 8.235905 CAGACAAAATCCAAACAAACAAACAAT 58.764 29.630 0.00 0.00 0.00 2.71
1296 1414 4.093850 TCATGAATTCGATCACTGCACAAG 59.906 41.667 0.04 0.00 30.82 3.16
1298 1416 3.598299 TCATGAATTCGATCACTGCACA 58.402 40.909 0.04 0.00 30.82 4.57
1306 1424 4.314121 CCTCCTCCTTCATGAATTCGATC 58.686 47.826 8.96 0.00 0.00 3.69
1312 1430 0.471617 CCGCCTCCTCCTTCATGAAT 59.528 55.000 8.96 0.00 0.00 2.57
1480 1602 7.795047 TGCAGATAATAAAGATCAGACCAGAA 58.205 34.615 0.00 0.00 0.00 3.02
1503 1625 6.361481 TCGTATCGTATAGCAACAACTTATGC 59.639 38.462 0.00 0.00 42.87 3.14
1536 1660 3.702548 TCGGTCAGGATCGGATTTCTTTA 59.297 43.478 1.70 0.00 35.26 1.85
1540 1667 2.596904 TTCGGTCAGGATCGGATTTC 57.403 50.000 1.70 0.00 35.26 2.17
1567 1694 4.216472 GCTCCTTCTGAAACCGAAGAAATT 59.784 41.667 0.00 0.00 40.15 1.82
1738 1869 2.372264 GAGAAATCATGGGCAGAGCAA 58.628 47.619 0.00 0.00 0.00 3.91
1980 2111 8.370266 TCCAACTAGAACCTAAAGCTAACATA 57.630 34.615 0.00 0.00 0.00 2.29
1990 2121 7.311092 TCTGAATGTTCCAACTAGAACCTAA 57.689 36.000 0.00 0.00 44.55 2.69
1993 2124 6.877611 TTTCTGAATGTTCCAACTAGAACC 57.122 37.500 0.00 0.00 44.55 3.62
2064 2203 3.308402 CCTCCCTGATTTGCTTTGGAGTA 60.308 47.826 0.00 0.00 38.14 2.59
2145 2284 8.675705 AATTTCCACAAAAAGGGATAAAACTG 57.324 30.769 0.00 0.00 32.15 3.16
2160 2299 6.333416 TGATTGTTCACGAAAATTTCCACAA 58.667 32.000 0.00 5.31 0.00 3.33
2173 2312 7.005380 GCATTTCAAAAAGATGATTGTTCACG 58.995 34.615 0.00 0.00 33.85 4.35
2207 2346 9.376075 CAAATCAGTCTCAACATAAGATGTACT 57.624 33.333 0.00 0.00 44.07 2.73
2211 2350 8.607459 GGTACAAATCAGTCTCAACATAAGATG 58.393 37.037 0.00 0.00 0.00 2.90
2236 2375 7.442364 AGACGGTATTTCTGAACATCAATATGG 59.558 37.037 0.00 0.00 37.43 2.74
2240 2379 5.065218 GCAGACGGTATTTCTGAACATCAAT 59.935 40.000 4.30 0.00 42.81 2.57
2277 2416 1.153469 GCTGAAGAAGAGCTCGGGG 60.153 63.158 8.37 0.00 33.37 5.73
2281 2420 0.744057 GGCTGGCTGAAGAAGAGCTC 60.744 60.000 5.27 5.27 36.63 4.09
2306 2445 3.327172 CAGAGATCTCCCACCAGCATAAT 59.673 47.826 19.30 0.00 0.00 1.28
2320 2459 1.219980 TCCTGATGAGCCCAGAGATCT 59.780 52.381 0.00 0.00 33.65 2.75
2421 2560 1.176619 TTCCTCGGAACTGTCGCTGA 61.177 55.000 0.00 0.00 0.00 4.26
2475 2614 1.065418 CGGTAGTCCCAAAGCCTTGAT 60.065 52.381 0.00 0.00 34.14 2.57
2477 2616 0.036306 ACGGTAGTCCCAAAGCCTTG 59.964 55.000 0.00 0.00 0.00 3.61
2517 2656 1.069358 GCCGCAAAGCTATCTCTACCT 59.931 52.381 0.00 0.00 0.00 3.08
2518 2657 1.202533 TGCCGCAAAGCTATCTCTACC 60.203 52.381 0.00 0.00 0.00 3.18
2545 2684 0.734889 AGAGTGCATGCCGTTATTGC 59.265 50.000 16.68 0.00 36.91 3.56
2862 3012 1.272147 GGTCAGGAAAGGGCAGTTGAT 60.272 52.381 0.00 0.00 0.00 2.57
2864 3014 0.178992 TGGTCAGGAAAGGGCAGTTG 60.179 55.000 0.00 0.00 0.00 3.16
2886 3036 4.487714 TGTGAGAAGTTCAGAACCAACT 57.512 40.909 9.85 6.90 36.21 3.16
2888 3038 4.780815 ACATGTGAGAAGTTCAGAACCAA 58.219 39.130 9.85 0.00 36.21 3.67
2889 3039 4.422073 ACATGTGAGAAGTTCAGAACCA 57.578 40.909 9.85 0.07 36.21 3.67
2890 3040 5.529060 AGAAACATGTGAGAAGTTCAGAACC 59.471 40.000 9.85 0.00 36.21 3.62
2891 3041 6.258727 TCAGAAACATGTGAGAAGTTCAGAAC 59.741 38.462 5.00 5.00 36.21 3.01
2895 3045 7.572523 ATTTCAGAAACATGTGAGAAGTTCA 57.427 32.000 0.00 0.00 0.00 3.18
2896 3046 8.862550 AAATTTCAGAAACATGTGAGAAGTTC 57.137 30.769 0.00 0.00 0.00 3.01
2897 3047 8.469200 TGAAATTTCAGAAACATGTGAGAAGTT 58.531 29.630 16.91 2.33 32.50 2.66
2898 3048 7.999679 TGAAATTTCAGAAACATGTGAGAAGT 58.000 30.769 16.91 0.00 32.50 3.01
2899 3049 9.125906 GATGAAATTTCAGAAACATGTGAGAAG 57.874 33.333 24.17 0.00 41.08 2.85
2900 3050 8.631797 TGATGAAATTTCAGAAACATGTGAGAA 58.368 29.630 24.17 0.00 41.08 2.87
2901 3051 8.168790 TGATGAAATTTCAGAAACATGTGAGA 57.831 30.769 24.17 0.00 41.08 3.27
2902 3052 7.061905 GCTGATGAAATTTCAGAAACATGTGAG 59.938 37.037 24.17 10.72 42.63 3.51
2903 3053 6.864685 GCTGATGAAATTTCAGAAACATGTGA 59.135 34.615 24.17 0.68 42.63 3.58
2904 3054 6.643360 TGCTGATGAAATTTCAGAAACATGTG 59.357 34.615 24.17 11.59 42.63 3.21
2905 3055 6.751157 TGCTGATGAAATTTCAGAAACATGT 58.249 32.000 24.17 6.69 42.63 3.21
2912 3062 4.278919 TGCTGTTGCTGATGAAATTTCAGA 59.721 37.500 24.17 13.31 42.63 3.27
2946 3104 0.034896 TTGGTTCAGAGAACCTCGGC 59.965 55.000 24.53 3.93 40.88 5.54
3041 3199 0.672889 TTGCAGAAAAGAATGCCGCA 59.327 45.000 0.00 0.00 41.85 5.69
3045 3203 3.054878 CACCAGTTGCAGAAAAGAATGC 58.945 45.455 0.00 0.00 42.86 3.56
3210 3399 3.780693 GCGACGTGCAGCTTATCA 58.219 55.556 0.00 0.00 45.45 2.15
3299 3488 5.395657 CCAAGAGATGTGATACCAGCAGTTA 60.396 44.000 0.00 0.00 0.00 2.24
3300 3489 4.511527 CAAGAGATGTGATACCAGCAGTT 58.488 43.478 0.00 0.00 0.00 3.16
3304 3493 2.158842 AGCCAAGAGATGTGATACCAGC 60.159 50.000 0.00 0.00 0.00 4.85
3308 3497 4.118410 CAGACAGCCAAGAGATGTGATAC 58.882 47.826 0.00 0.00 0.00 2.24
3309 3498 3.771479 ACAGACAGCCAAGAGATGTGATA 59.229 43.478 0.00 0.00 0.00 2.15
3311 3500 1.973515 ACAGACAGCCAAGAGATGTGA 59.026 47.619 0.00 0.00 0.00 3.58
3313 3502 2.028294 CAGACAGACAGCCAAGAGATGT 60.028 50.000 0.00 0.00 0.00 3.06
3319 3508 0.250209 AGCACAGACAGACAGCCAAG 60.250 55.000 0.00 0.00 0.00 3.61
3322 3511 2.275318 GATAAGCACAGACAGACAGCC 58.725 52.381 0.00 0.00 0.00 4.85
3326 3515 3.319137 TGTGGATAAGCACAGACAGAC 57.681 47.619 0.00 0.00 0.00 3.51
3346 3535 7.712639 CGGATCAATACTGCATTATATTAGGCT 59.287 37.037 0.00 0.00 0.00 4.58
3410 3599 1.944676 GCGCCAGTCCGTCTAATCG 60.945 63.158 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.