Multiple sequence alignment - TraesCS4A01G309000

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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 TraesCS4A01G309000 chr4A 100.000 3419 0 0 1 3419 602308929 602305511 0.000000e+00 6314.0
1 TraesCS4A01G309000 chr4A 81.302 1444 229 26 993 2414 602272649 602274073 0.000000e+00 1133.0
2 TraesCS4A01G309000 chr4D 93.547 1937 115 7 844 2771 3241447 3243382 0.000000e+00 2876.0
3 TraesCS4A01G309000 chr4D 81.874 1462 216 35 993 2422 3250757 3249313 0.000000e+00 1186.0
4 TraesCS4A01G309000 chr4D 90.649 385 25 4 2814 3198 3243383 3243756 5.090000e-138 501.0
5 TraesCS4A01G309000 chr4D 97.959 147 3 0 3273 3419 3243808 3243954 4.380000e-64 255.0
6 TraesCS4A01G309000 chr4D 82.857 315 18 11 297 602 3241026 3241313 2.040000e-62 250.0
7 TraesCS4A01G309000 chr4D 83.846 130 10 8 684 811 3241327 3241447 2.790000e-21 113.0
8 TraesCS4A01G309000 chr4D 81.061 132 15 8 692 813 300312107 300311976 2.810000e-16 97.1
9 TraesCS4A01G309000 chr4B 89.162 1873 182 14 818 2685 3820645 3822501 0.000000e+00 2314.0
10 TraesCS4A01G309000 chr4B 83.309 1390 206 17 1046 2422 3831214 3829838 0.000000e+00 1258.0
11 TraesCS4A01G309000 chr4B 84.844 640 77 9 2618 3253 3825320 3825943 8.050000e-176 627.0
12 TraesCS4A01G309000 chr4B 89.542 459 23 13 308 754 3820205 3820650 2.980000e-155 558.0
13 TraesCS4A01G309000 chr4B 89.683 252 23 2 2277 2526 3825068 3825318 5.510000e-83 318.0
14 TraesCS4A01G309000 chr4B 89.831 177 15 3 1 175 3816771 3816946 1.230000e-54 224.0
15 TraesCS4A01G309000 chr7B 86.477 281 37 1 2982 3261 498485307 498485027 1.190000e-79 307.0
16 TraesCS4A01G309000 chrUn 84.586 266 40 1 2989 3253 74808492 74808227 2.620000e-66 263.0
17 TraesCS4A01G309000 chr6A 86.139 202 26 2 3061 3261 91668931 91669131 2.070000e-52 217.0
18 TraesCS4A01G309000 chr6A 88.966 145 16 0 3275 3419 91669177 91669321 2.710000e-41 180.0
19 TraesCS4A01G309000 chr7D 93.220 59 3 1 762 819 115414642 115414584 6.080000e-13 86.1
20 TraesCS4A01G309000 chr7D 85.185 81 7 5 738 816 39223564 39223487 1.020000e-10 78.7
21 TraesCS4A01G309000 chr6D 86.585 82 6 5 738 816 3733605 3733684 6.080000e-13 86.1
22 TraesCS4A01G309000 chr2D 93.220 59 2 2 760 817 32026921 32026978 6.080000e-13 86.1
23 TraesCS4A01G309000 chr2B 89.394 66 7 0 752 817 710728467 710728402 2.190000e-12 84.2
24 TraesCS4A01G309000 chr3B 94.118 51 3 0 766 816 370148159 370148209 1.020000e-10 78.7
25 TraesCS4A01G309000 chr1A 91.071 56 3 2 763 817 555643893 555643839 1.320000e-09 75.0
26 TraesCS4A01G309000 chr1A 91.071 56 3 2 763 817 555644723 555644669 1.320000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G309000 chr4A 602305511 602308929 3418 True 6314.0 6314 100.0000 1 3419 1 chr4A.!!$R1 3418
1 TraesCS4A01G309000 chr4A 602272649 602274073 1424 False 1133.0 1133 81.3020 993 2414 1 chr4A.!!$F1 1421
2 TraesCS4A01G309000 chr4D 3249313 3250757 1444 True 1186.0 1186 81.8740 993 2422 1 chr4D.!!$R1 1429
3 TraesCS4A01G309000 chr4D 3241026 3243954 2928 False 799.0 2876 89.7716 297 3419 5 chr4D.!!$F1 3122
4 TraesCS4A01G309000 chr4B 3829838 3831214 1376 True 1258.0 1258 83.3090 1046 2422 1 chr4B.!!$R1 1376
5 TraesCS4A01G309000 chr4B 3816771 3825943 9172 False 808.2 2314 88.6124 1 3253 5 chr4B.!!$F1 3252

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
574 3736 0.035725 CTTCACTGATCAGCCAGCCA 60.036 55.0 22.83 0.4 37.68 4.75 F
1459 4641 0.250295 CTTCTTCCACGTGCCTTCCA 60.250 55.0 10.91 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 5333 0.033504 TGAGGAACTGGTCGCTGAAC 59.966 55.0 0.00 0.0 41.55 3.18 R
3080 9185 0.177836 CTGCATGACGTGATGGGGTA 59.822 55.0 16.87 0.0 0.00 3.69 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
30 31 8.543774 AGGAAGTGAAGAGTATACATGAATTGT 58.456 33.333 5.50 0.00 42.62 2.71
31 32 9.817809 GGAAGTGAAGAGTATACATGAATTGTA 57.182 33.333 5.50 0.00 44.71 2.41
81 83 1.512230 CATGAATTGCCACACCGGG 59.488 57.895 6.32 0.00 34.06 5.73
123 125 6.657966 ACAGTATCTGCTGCAATATTATGCAT 59.342 34.615 3.79 3.79 43.79 3.96
154 156 2.545537 GAAACCCTTTCCACTCTCGT 57.454 50.000 0.00 0.00 33.56 4.18
167 169 0.743688 CTCTCGTCCACCCTCATCAG 59.256 60.000 0.00 0.00 0.00 2.90
169 171 0.174389 CTCGTCCACCCTCATCAGTG 59.826 60.000 0.00 0.00 0.00 3.66
175 177 3.099905 TCCACCCTCATCAGTGTAAGAG 58.900 50.000 0.00 0.00 31.88 2.85
177 179 1.834263 ACCCTCATCAGTGTAAGAGCC 59.166 52.381 0.00 0.00 0.00 4.70
178 180 1.202463 CCCTCATCAGTGTAAGAGCCG 60.202 57.143 0.00 0.00 0.00 5.52
179 181 1.751351 CCTCATCAGTGTAAGAGCCGA 59.249 52.381 0.00 0.00 0.00 5.54
180 182 2.223688 CCTCATCAGTGTAAGAGCCGAG 60.224 54.545 0.00 0.00 0.00 4.63
182 184 3.617284 TCATCAGTGTAAGAGCCGAGTA 58.383 45.455 0.00 0.00 0.00 2.59
183 185 3.377485 TCATCAGTGTAAGAGCCGAGTAC 59.623 47.826 0.00 0.00 0.00 2.73
184 186 2.786777 TCAGTGTAAGAGCCGAGTACA 58.213 47.619 0.00 0.00 0.00 2.90
185 187 3.151554 TCAGTGTAAGAGCCGAGTACAA 58.848 45.455 0.00 0.00 29.93 2.41
186 188 3.057736 TCAGTGTAAGAGCCGAGTACAAC 60.058 47.826 0.00 0.00 29.93 3.32
187 189 2.889045 AGTGTAAGAGCCGAGTACAACA 59.111 45.455 0.00 0.00 29.93 3.33
189 191 3.427863 GTGTAAGAGCCGAGTACAACAAC 59.572 47.826 0.00 0.00 29.93 3.32
190 192 2.165319 AAGAGCCGAGTACAACAACC 57.835 50.000 0.00 0.00 0.00 3.77
192 194 1.623811 AGAGCCGAGTACAACAACCAT 59.376 47.619 0.00 0.00 0.00 3.55
193 195 2.038557 AGAGCCGAGTACAACAACCATT 59.961 45.455 0.00 0.00 0.00 3.16
196 198 2.550606 GCCGAGTACAACAACCATTGAA 59.449 45.455 0.00 0.00 33.57 2.69
198 200 3.813166 CCGAGTACAACAACCATTGAAGT 59.187 43.478 0.00 0.00 33.57 3.01
199 201 4.084013 CCGAGTACAACAACCATTGAAGTC 60.084 45.833 0.00 0.00 33.57 3.01
200 202 4.084013 CGAGTACAACAACCATTGAAGTCC 60.084 45.833 0.00 0.00 33.57 3.85
201 203 5.048846 AGTACAACAACCATTGAAGTCCT 57.951 39.130 0.00 0.00 33.57 3.85
202 204 4.821805 AGTACAACAACCATTGAAGTCCTG 59.178 41.667 0.00 0.00 33.57 3.86
204 206 2.361757 CAACAACCATTGAAGTCCTGCA 59.638 45.455 0.00 0.00 0.00 4.41
205 207 2.665165 ACAACCATTGAAGTCCTGCAA 58.335 42.857 0.00 0.00 0.00 4.08
206 208 3.233507 ACAACCATTGAAGTCCTGCAAT 58.766 40.909 0.00 0.00 35.24 3.56
207 209 3.006110 ACAACCATTGAAGTCCTGCAATG 59.994 43.478 17.65 17.65 46.71 2.82
209 211 2.953466 CATTGAAGTCCTGCAATGGG 57.047 50.000 17.04 0.00 44.62 4.00
210 212 2.173519 CATTGAAGTCCTGCAATGGGT 58.826 47.619 17.04 0.00 44.62 4.51
211 213 1.909700 TTGAAGTCCTGCAATGGGTC 58.090 50.000 0.00 0.00 0.00 4.46
212 214 1.067295 TGAAGTCCTGCAATGGGTCT 58.933 50.000 0.00 0.00 0.00 3.85
214 216 2.087646 GAAGTCCTGCAATGGGTCTTC 58.912 52.381 12.37 12.37 34.44 2.87
215 217 1.366319 AGTCCTGCAATGGGTCTTCT 58.634 50.000 0.00 0.00 0.00 2.85
216 218 1.280421 AGTCCTGCAATGGGTCTTCTC 59.720 52.381 0.00 0.00 0.00 2.87
218 220 1.280133 TCCTGCAATGGGTCTTCTCTG 59.720 52.381 0.00 0.00 0.00 3.35
220 222 2.553904 CCTGCAATGGGTCTTCTCTGTT 60.554 50.000 0.00 0.00 0.00 3.16
221 223 2.486982 CTGCAATGGGTCTTCTCTGTTG 59.513 50.000 0.00 0.00 0.00 3.33
223 225 2.553028 GCAATGGGTCTTCTCTGTTGGA 60.553 50.000 0.00 0.00 0.00 3.53
224 226 3.341823 CAATGGGTCTTCTCTGTTGGAG 58.658 50.000 0.00 0.00 43.12 3.86
225 227 0.687354 TGGGTCTTCTCTGTTGGAGC 59.313 55.000 0.00 0.00 41.60 4.70
226 228 0.035915 GGGTCTTCTCTGTTGGAGCC 60.036 60.000 0.00 0.00 41.60 4.70
227 229 0.687354 GGTCTTCTCTGTTGGAGCCA 59.313 55.000 0.00 0.00 41.60 4.75
228 230 1.338579 GGTCTTCTCTGTTGGAGCCAG 60.339 57.143 0.00 0.00 41.60 4.85
230 232 0.324285 CTTCTCTGTTGGAGCCAGCT 59.676 55.000 4.99 0.00 41.60 4.24
231 233 0.035881 TTCTCTGTTGGAGCCAGCTG 59.964 55.000 6.78 6.78 41.60 4.24
232 234 2.033141 TCTGTTGGAGCCAGCTGC 59.967 61.111 8.66 3.95 41.71 5.25
241 243 3.200593 GCCAGCTGCGATGAGGTG 61.201 66.667 8.66 0.00 40.49 4.00
242 244 2.580815 CCAGCTGCGATGAGGTGA 59.419 61.111 8.66 0.00 42.92 4.02
244 246 0.879400 CCAGCTGCGATGAGGTGATC 60.879 60.000 8.66 0.00 42.92 2.92
245 247 0.879400 CAGCTGCGATGAGGTGATCC 60.879 60.000 0.00 0.00 42.92 3.36
246 248 1.144716 GCTGCGATGAGGTGATCCA 59.855 57.895 0.00 0.00 35.89 3.41
247 249 0.250209 GCTGCGATGAGGTGATCCAT 60.250 55.000 0.00 0.00 35.89 3.41
248 250 1.793258 CTGCGATGAGGTGATCCATC 58.207 55.000 0.00 0.00 36.67 3.51
249 251 1.343789 CTGCGATGAGGTGATCCATCT 59.656 52.381 7.72 0.00 37.58 2.90
250 252 1.069668 TGCGATGAGGTGATCCATCTG 59.930 52.381 7.72 3.91 37.58 2.90
251 253 1.342496 GCGATGAGGTGATCCATCTGA 59.658 52.381 7.72 0.00 37.58 3.27
252 254 2.609984 GCGATGAGGTGATCCATCTGAG 60.610 54.545 7.72 0.00 37.58 3.35
253 255 2.609984 CGATGAGGTGATCCATCTGAGC 60.610 54.545 7.72 0.00 37.58 4.26
255 257 2.405559 TGAGGTGATCCATCTGAGCAT 58.594 47.619 0.00 0.00 42.25 3.79
257 259 2.104451 GAGGTGATCCATCTGAGCATGT 59.896 50.000 0.00 0.00 42.25 3.21
258 260 3.311990 AGGTGATCCATCTGAGCATGTA 58.688 45.455 0.00 0.00 42.25 2.29
259 261 3.070734 AGGTGATCCATCTGAGCATGTAC 59.929 47.826 0.00 0.00 42.25 2.90
260 262 3.070734 GGTGATCCATCTGAGCATGTACT 59.929 47.826 0.00 0.00 42.25 2.73
263 265 2.379005 TCCATCTGAGCATGTACTCGT 58.621 47.619 0.00 0.00 39.68 4.18
264 266 2.359214 TCCATCTGAGCATGTACTCGTC 59.641 50.000 0.00 0.00 39.68 4.20
265 267 2.379732 CATCTGAGCATGTACTCGTCG 58.620 52.381 0.00 0.00 39.68 5.12
266 268 1.734163 TCTGAGCATGTACTCGTCGA 58.266 50.000 0.00 0.00 39.68 4.20
267 269 1.397343 TCTGAGCATGTACTCGTCGAC 59.603 52.381 5.18 5.18 39.68 4.20
268 270 0.450583 TGAGCATGTACTCGTCGACC 59.549 55.000 10.58 0.00 39.68 4.79
269 271 0.450583 GAGCATGTACTCGTCGACCA 59.549 55.000 10.58 1.52 0.00 4.02
271 273 1.200483 GCATGTACTCGTCGACCATG 58.800 55.000 20.70 20.70 36.77 3.66
273 275 1.103803 ATGTACTCGTCGACCATGCT 58.896 50.000 10.58 0.00 0.00 3.79
274 276 0.170339 TGTACTCGTCGACCATGCTG 59.830 55.000 10.58 0.00 0.00 4.41
276 278 0.733150 TACTCGTCGACCATGCTGAG 59.267 55.000 10.58 11.76 0.00 3.35
277 279 1.244697 ACTCGTCGACCATGCTGAGT 61.245 55.000 10.58 12.41 32.19 3.41
279 3385 1.807165 CGTCGACCATGCTGAGTGG 60.807 63.158 10.58 0.00 42.55 4.00
281 3387 2.124983 CGACCATGCTGAGTGGGG 60.125 66.667 4.20 0.00 41.14 4.96
284 3390 2.439701 CCATGCTGAGTGGGGCAG 60.440 66.667 0.00 0.00 41.88 4.85
290 3396 0.322816 GCTGAGTGGGGCAGATTCAA 60.323 55.000 0.00 0.00 35.39 2.69
293 3399 1.144708 TGAGTGGGGCAGATTCAAACA 59.855 47.619 0.00 0.00 0.00 2.83
314 3442 2.563179 ACAAAGACCTGATCGCACTACT 59.437 45.455 0.00 0.00 0.00 2.57
340 3468 3.119849 GCAGCTCAACGACACCATTTATT 60.120 43.478 0.00 0.00 0.00 1.40
353 3489 6.248433 ACACCATTTATTGACAGAAGATGGT 58.752 36.000 7.93 7.93 44.73 3.55
365 3501 0.245539 AAGATGGTGTACCGTGACCG 59.754 55.000 0.00 0.00 39.43 4.79
443 3579 4.939439 CAGCGGTACTAAAACAAGGGTAAT 59.061 41.667 0.00 0.00 0.00 1.89
462 3624 2.568623 TGGACTCCCAGAAAAAGCTC 57.431 50.000 0.00 0.00 37.58 4.09
463 3625 1.270839 TGGACTCCCAGAAAAAGCTCG 60.271 52.381 0.00 0.00 37.58 5.03
464 3626 1.002087 GGACTCCCAGAAAAAGCTCGA 59.998 52.381 0.00 0.00 0.00 4.04
465 3627 2.070028 GACTCCCAGAAAAAGCTCGAC 58.930 52.381 0.00 0.00 0.00 4.20
466 3628 1.416401 ACTCCCAGAAAAAGCTCGACA 59.584 47.619 0.00 0.00 0.00 4.35
467 3629 2.158813 ACTCCCAGAAAAAGCTCGACAA 60.159 45.455 0.00 0.00 0.00 3.18
468 3630 2.481952 CTCCCAGAAAAAGCTCGACAAG 59.518 50.000 0.00 0.00 0.00 3.16
469 3631 2.158813 TCCCAGAAAAAGCTCGACAAGT 60.159 45.455 0.00 0.00 0.00 3.16
470 3632 2.618709 CCCAGAAAAAGCTCGACAAGTT 59.381 45.455 0.00 0.00 0.00 2.66
471 3633 3.066760 CCCAGAAAAAGCTCGACAAGTTT 59.933 43.478 0.00 0.00 0.00 2.66
472 3634 4.440112 CCCAGAAAAAGCTCGACAAGTTTT 60.440 41.667 0.00 0.00 39.79 2.43
473 3635 4.500477 CCAGAAAAAGCTCGACAAGTTTTG 59.500 41.667 0.00 0.00 38.30 2.44
474 3636 4.500477 CAGAAAAAGCTCGACAAGTTTTGG 59.500 41.667 0.00 0.00 38.30 3.28
475 3637 2.492019 AAAGCTCGACAAGTTTTGGC 57.508 45.000 0.00 0.00 37.08 4.52
476 3638 1.680338 AAGCTCGACAAGTTTTGGCT 58.320 45.000 0.00 0.00 36.19 4.75
477 3639 0.947244 AGCTCGACAAGTTTTGGCTG 59.053 50.000 0.00 0.00 36.19 4.85
478 3640 0.944386 GCTCGACAAGTTTTGGCTGA 59.056 50.000 0.00 0.00 36.19 4.26
479 3641 1.069636 GCTCGACAAGTTTTGGCTGAG 60.070 52.381 10.22 10.22 40.14 3.35
480 3642 2.483876 CTCGACAAGTTTTGGCTGAGA 58.516 47.619 9.41 0.00 39.82 3.27
481 3643 3.070018 CTCGACAAGTTTTGGCTGAGAT 58.930 45.455 9.41 0.00 39.82 2.75
482 3644 4.245660 CTCGACAAGTTTTGGCTGAGATA 58.754 43.478 9.41 0.00 39.82 1.98
483 3645 4.245660 TCGACAAGTTTTGGCTGAGATAG 58.754 43.478 0.00 0.00 36.19 2.08
484 3646 4.021456 TCGACAAGTTTTGGCTGAGATAGA 60.021 41.667 0.00 0.00 36.19 1.98
529 3691 7.363268 GGTCTTAATTTTGATCAGGTGCAGATT 60.363 37.037 0.00 0.00 0.00 2.40
569 3731 3.195396 AGAGAAGACTTCACTGATCAGCC 59.805 47.826 22.83 5.34 0.00 4.85
574 3736 0.035725 CTTCACTGATCAGCCAGCCA 60.036 55.000 22.83 0.40 37.68 4.75
596 3758 2.412089 GTGGTGCTTAGACATGACGAAC 59.588 50.000 0.00 0.00 0.00 3.95
602 3764 3.059570 GCTTAGACATGACGAACAACGAG 59.940 47.826 0.00 0.00 45.77 4.18
603 3765 2.065993 AGACATGACGAACAACGAGG 57.934 50.000 0.00 0.00 45.77 4.63
606 3768 2.798283 GACATGACGAACAACGAGGAAA 59.202 45.455 0.00 0.00 45.77 3.13
613 3775 3.493503 ACGAACAACGAGGAAAAGTGATC 59.506 43.478 0.00 0.00 45.77 2.92
614 3776 3.493129 CGAACAACGAGGAAAAGTGATCA 59.507 43.478 0.00 0.00 45.77 2.92
615 3777 4.025229 CGAACAACGAGGAAAAGTGATCAA 60.025 41.667 0.00 0.00 45.77 2.57
616 3778 5.424121 AACAACGAGGAAAAGTGATCAAG 57.576 39.130 0.00 0.00 0.00 3.02
617 3779 4.451900 ACAACGAGGAAAAGTGATCAAGT 58.548 39.130 0.00 0.00 0.00 3.16
618 3780 4.881850 ACAACGAGGAAAAGTGATCAAGTT 59.118 37.500 0.00 0.00 0.00 2.66
619 3781 6.053005 ACAACGAGGAAAAGTGATCAAGTTA 58.947 36.000 0.00 0.00 0.00 2.24
620 3782 6.710744 ACAACGAGGAAAAGTGATCAAGTTAT 59.289 34.615 0.00 0.00 0.00 1.89
621 3783 7.228706 ACAACGAGGAAAAGTGATCAAGTTATT 59.771 33.333 0.00 0.00 0.00 1.40
622 3784 7.133891 ACGAGGAAAAGTGATCAAGTTATTG 57.866 36.000 0.00 0.00 37.80 1.90
623 3785 6.149474 ACGAGGAAAAGTGATCAAGTTATTGG 59.851 38.462 0.00 0.00 37.02 3.16
624 3786 6.149474 CGAGGAAAAGTGATCAAGTTATTGGT 59.851 38.462 0.00 0.00 37.02 3.67
660 3822 0.384309 CGTAGATCTACCAAGCGCCA 59.616 55.000 24.01 0.00 32.61 5.69
669 3831 0.962356 ACCAAGCGCCATGAAAGGAG 60.962 55.000 2.29 0.00 0.00 3.69
672 3834 0.393537 AAGCGCCATGAAAGGAGAGG 60.394 55.000 2.29 0.00 0.00 3.69
724 3887 5.263599 TGTTTTCAGCATCCTTGTATCCAT 58.736 37.500 0.00 0.00 0.00 3.41
729 3892 3.756963 CAGCATCCTTGTATCCATCCATG 59.243 47.826 0.00 0.00 0.00 3.66
756 3933 2.812011 GAGTGTTTGTATCGGCTGGTTT 59.188 45.455 0.00 0.00 0.00 3.27
757 3934 3.219281 AGTGTTTGTATCGGCTGGTTTT 58.781 40.909 0.00 0.00 0.00 2.43
758 3935 4.391155 AGTGTTTGTATCGGCTGGTTTTA 58.609 39.130 0.00 0.00 0.00 1.52
759 3936 4.454504 AGTGTTTGTATCGGCTGGTTTTAG 59.545 41.667 0.00 0.00 0.00 1.85
760 3937 4.214758 GTGTTTGTATCGGCTGGTTTTAGT 59.785 41.667 0.00 0.00 0.00 2.24
761 3938 5.409214 GTGTTTGTATCGGCTGGTTTTAGTA 59.591 40.000 0.00 0.00 0.00 1.82
762 3939 6.093082 GTGTTTGTATCGGCTGGTTTTAGTAT 59.907 38.462 0.00 0.00 0.00 2.12
763 3940 6.092944 TGTTTGTATCGGCTGGTTTTAGTATG 59.907 38.462 0.00 0.00 0.00 2.39
764 3941 5.347620 TGTATCGGCTGGTTTTAGTATGT 57.652 39.130 0.00 0.00 0.00 2.29
765 3942 5.736813 TGTATCGGCTGGTTTTAGTATGTT 58.263 37.500 0.00 0.00 0.00 2.71
766 3943 5.813672 TGTATCGGCTGGTTTTAGTATGTTC 59.186 40.000 0.00 0.00 0.00 3.18
767 3944 3.255725 TCGGCTGGTTTTAGTATGTTCG 58.744 45.455 0.00 0.00 0.00 3.95
768 3945 2.350498 CGGCTGGTTTTAGTATGTTCGG 59.650 50.000 0.00 0.00 0.00 4.30
769 3946 3.340928 GGCTGGTTTTAGTATGTTCGGT 58.659 45.455 0.00 0.00 0.00 4.69
770 3947 3.126343 GGCTGGTTTTAGTATGTTCGGTG 59.874 47.826 0.00 0.00 0.00 4.94
771 3948 3.998341 GCTGGTTTTAGTATGTTCGGTGA 59.002 43.478 0.00 0.00 0.00 4.02
772 3949 4.634443 GCTGGTTTTAGTATGTTCGGTGAT 59.366 41.667 0.00 0.00 0.00 3.06
773 3950 5.447279 GCTGGTTTTAGTATGTTCGGTGATG 60.447 44.000 0.00 0.00 0.00 3.07
774 3951 4.938832 TGGTTTTAGTATGTTCGGTGATGG 59.061 41.667 0.00 0.00 0.00 3.51
775 3952 4.939439 GGTTTTAGTATGTTCGGTGATGGT 59.061 41.667 0.00 0.00 0.00 3.55
776 3953 5.413523 GGTTTTAGTATGTTCGGTGATGGTT 59.586 40.000 0.00 0.00 0.00 3.67
811 3988 1.197036 GCGAGAGGAAACCCTTTTTCG 59.803 52.381 0.00 0.00 36.46 3.46
813 3990 2.876550 CGAGAGGAAACCCTTTTTCGTT 59.123 45.455 0.00 0.00 33.25 3.85
814 3991 4.060205 CGAGAGGAAACCCTTTTTCGTTA 58.940 43.478 0.00 0.00 33.25 3.18
815 3992 4.512571 CGAGAGGAAACCCTTTTTCGTTAA 59.487 41.667 0.00 0.00 33.25 2.01
816 3993 5.180680 CGAGAGGAAACCCTTTTTCGTTAAT 59.819 40.000 0.00 0.00 33.25 1.40
817 3994 6.327279 AGAGGAAACCCTTTTTCGTTAATG 57.673 37.500 0.00 0.00 33.25 1.90
818 3995 5.243060 AGAGGAAACCCTTTTTCGTTAATGG 59.757 40.000 0.00 0.00 33.25 3.16
819 3996 3.991773 GGAAACCCTTTTTCGTTAATGGC 59.008 43.478 0.00 0.00 0.00 4.40
820 3997 4.262292 GGAAACCCTTTTTCGTTAATGGCT 60.262 41.667 0.00 0.00 0.00 4.75
821 3998 3.934457 ACCCTTTTTCGTTAATGGCTG 57.066 42.857 0.00 0.00 0.00 4.85
822 3999 2.560981 ACCCTTTTTCGTTAATGGCTGG 59.439 45.455 0.00 0.00 0.00 4.85
826 4003 4.923281 CCTTTTTCGTTAATGGCTGGAAAG 59.077 41.667 0.00 0.00 0.00 2.62
835 4012 2.435372 TGGCTGGAAAGTTTGTGAGT 57.565 45.000 0.00 0.00 0.00 3.41
838 4015 2.223805 GGCTGGAAAGTTTGTGAGTTGG 60.224 50.000 0.00 0.00 0.00 3.77
844 4021 3.281727 AAGTTTGTGAGTTGGAGAGCA 57.718 42.857 0.00 0.00 0.00 4.26
918 4095 2.092838 GCTCGACTTGTTGACATACAGC 59.907 50.000 0.00 0.00 0.00 4.40
919 4096 3.317150 CTCGACTTGTTGACATACAGCA 58.683 45.455 0.00 0.00 37.91 4.41
949 4128 6.534934 GCGCTTTGTATATAAATACAGCTCC 58.465 40.000 0.00 0.00 46.58 4.70
969 4148 1.067974 CATACCGGCCGTACATCTCAA 59.932 52.381 26.12 0.00 0.00 3.02
1149 4331 0.315568 GTGTGAGAGTGAGCCTCGTT 59.684 55.000 0.00 0.00 45.44 3.85
1152 4334 1.540267 GTGAGAGTGAGCCTCGTTACA 59.460 52.381 0.00 0.00 45.44 2.41
1155 4337 1.961394 AGAGTGAGCCTCGTTACAACA 59.039 47.619 0.00 0.00 45.44 3.33
1158 4340 1.045407 TGAGCCTCGTTACAACACCT 58.955 50.000 0.00 0.00 0.00 4.00
1323 4505 2.206635 CCTGGACCTCTACAGGCTG 58.793 63.158 14.16 14.16 46.78 4.85
1389 4571 1.067084 CTGCATCATCTCCGACGCT 59.933 57.895 0.00 0.00 0.00 5.07
1459 4641 0.250295 CTTCTTCCACGTGCCTTCCA 60.250 55.000 10.91 0.00 0.00 3.53
1473 4655 2.623889 GCCTTCCATCTTCTACTCGCTA 59.376 50.000 0.00 0.00 0.00 4.26
1488 4670 1.999051 GCTATGCGACCTGAACGTG 59.001 57.895 0.00 0.00 0.00 4.49
1593 4784 3.285484 GTCGTCCTCCTTCTATACCACA 58.715 50.000 0.00 0.00 0.00 4.17
1596 4787 2.699321 GTCCTCCTTCTATACCACACCC 59.301 54.545 0.00 0.00 0.00 4.61
1669 4860 0.948623 CGCCGTGATGAACACCTTCA 60.949 55.000 0.00 0.00 45.73 3.02
1684 4875 1.078214 TTCATGGGCCTCGAGCAAG 60.078 57.895 6.99 0.00 46.50 4.01
1695 4886 2.094286 CCTCGAGCAAGAGTTCATCACT 60.094 50.000 6.99 0.00 39.07 3.41
1704 4895 5.877012 GCAAGAGTTCATCACTTCCTATGAA 59.123 40.000 0.00 0.00 39.24 2.57
1713 4904 2.029838 CTTCCTATGAAGCGGCACTT 57.970 50.000 1.45 0.00 41.45 3.16
1725 4916 2.647297 GCACTTGGCAAGCCTGTC 59.353 61.111 26.45 10.84 43.97 3.51
1746 4937 2.357396 GCGCTTGGGCCCTTTTTG 60.357 61.111 25.70 10.30 34.44 2.44
1782 4976 1.828660 CGAGGAGGCCGTCTACCAT 60.829 63.158 0.00 0.00 0.00 3.55
1884 5078 0.320771 CCAAGCAGCTGTACGAGGTT 60.321 55.000 16.64 0.00 0.00 3.50
1907 5101 2.438614 CGGCCTCGAGGACTCTGA 60.439 66.667 35.69 0.00 42.58 3.27
1938 5132 1.421646 CTTTGGGTGGTGAAGGAGTCT 59.578 52.381 0.00 0.00 0.00 3.24
2019 5213 1.487976 CAGGGACTCATAGTGCATGGT 59.512 52.381 5.46 0.00 43.13 3.55
2139 5333 2.430921 GTCGTGACGTGGCCTCAG 60.431 66.667 3.32 0.00 0.00 3.35
2280 5483 3.882326 CTGATGGGCGATGGGGCT 61.882 66.667 0.00 0.00 41.87 5.19
2292 5495 0.983378 ATGGGGCTGTGGTAGAGGAC 60.983 60.000 0.00 0.00 0.00 3.85
2300 5503 1.431633 TGTGGTAGAGGACAGGAGGAA 59.568 52.381 0.00 0.00 0.00 3.36
2335 5538 1.756408 CGGGGAGAGAGCTCATGCAT 61.756 60.000 17.77 0.00 43.14 3.96
2361 5564 1.140407 CGAAAGGAGGATCGTCGCAC 61.140 60.000 9.20 0.00 34.37 5.34
2459 5662 9.683069 GGTTTCATCATTTTGTAGCATATAAGG 57.317 33.333 0.00 0.00 0.00 2.69
2515 5721 2.200373 TTTCAGCTTTCACCTAGGCC 57.800 50.000 9.30 0.00 0.00 5.19
2525 5731 3.227276 CCTAGGCCGGCTCATCGT 61.227 66.667 28.56 6.79 0.00 3.73
2526 5732 1.901948 CCTAGGCCGGCTCATCGTA 60.902 63.158 28.56 7.61 0.00 3.43
2559 5773 0.965363 GGGATGGCATGGACAAACGT 60.965 55.000 3.81 0.00 0.00 3.99
2567 5781 2.419673 GCATGGACAAACGTGATCATGA 59.580 45.455 21.75 0.00 39.10 3.07
2574 5788 2.595124 AACGTGATCATGATGGCGTA 57.405 45.000 24.92 2.90 31.06 4.42
2605 5819 2.799176 GCAAGGGGCAGTGGAATAG 58.201 57.895 0.00 0.00 43.97 1.73
2607 5821 0.625849 CAAGGGGCAGTGGAATAGGT 59.374 55.000 0.00 0.00 0.00 3.08
2608 5822 0.919710 AAGGGGCAGTGGAATAGGTC 59.080 55.000 0.00 0.00 0.00 3.85
2610 5824 1.623542 GGGGCAGTGGAATAGGTCGT 61.624 60.000 0.00 0.00 0.00 4.34
2611 5825 1.117150 GGGCAGTGGAATAGGTCGTA 58.883 55.000 0.00 0.00 0.00 3.43
2612 5826 1.483415 GGGCAGTGGAATAGGTCGTAA 59.517 52.381 0.00 0.00 0.00 3.18
2613 5827 2.547826 GGCAGTGGAATAGGTCGTAAC 58.452 52.381 0.00 0.00 0.00 2.50
2615 5829 3.445857 GCAGTGGAATAGGTCGTAACTC 58.554 50.000 0.00 0.00 0.00 3.01
2619 8719 4.398673 AGTGGAATAGGTCGTAACTCAGTC 59.601 45.833 0.00 0.00 0.00 3.51
2695 8795 2.686602 GCTCATTGCAGCGAGATCA 58.313 52.632 16.33 0.00 42.31 2.92
2794 8899 7.943413 AATTCAGTTGATCATACTCGAGATG 57.057 36.000 21.68 17.39 0.00 2.90
2888 8993 7.934855 AAGACTGCTCACAATGAAGAATAAT 57.065 32.000 0.00 0.00 0.00 1.28
3005 9110 0.532573 TCGCTAAAGTGAGCCAGAGG 59.467 55.000 0.00 0.00 39.43 3.69
3063 9168 0.036875 ACCTGGTTGCCTGCTTAGTC 59.963 55.000 0.00 0.00 0.00 2.59
3077 9182 3.117046 GCTTAGTCACGCCATTCTCTAC 58.883 50.000 0.00 0.00 0.00 2.59
3080 9185 3.963428 AGTCACGCCATTCTCTACTTT 57.037 42.857 0.00 0.00 0.00 2.66
3208 9313 9.237846 GCATGCTTATGGTAAATCTTTTAGTTC 57.762 33.333 11.37 0.00 0.00 3.01
3263 9368 2.540931 GGAAACGAAAACGCTACACAGA 59.459 45.455 0.00 0.00 0.00 3.41
3264 9369 3.185797 GGAAACGAAAACGCTACACAGAT 59.814 43.478 0.00 0.00 0.00 2.90
3265 9370 3.788434 AACGAAAACGCTACACAGATG 57.212 42.857 0.00 0.00 0.00 2.90
3267 9372 2.729882 ACGAAAACGCTACACAGATGAC 59.270 45.455 0.00 0.00 0.00 3.06
3268 9373 2.222289 CGAAAACGCTACACAGATGACG 60.222 50.000 0.00 0.00 0.00 4.35
3269 9374 1.068474 AAACGCTACACAGATGACGC 58.932 50.000 0.00 0.00 0.00 5.19
3270 9375 0.243907 AACGCTACACAGATGACGCT 59.756 50.000 0.00 0.00 0.00 5.07
3271 9376 0.456824 ACGCTACACAGATGACGCTG 60.457 55.000 0.00 0.00 41.63 5.18
3326 9457 1.207593 GGTGACGCTGCATGTTGAC 59.792 57.895 0.00 0.00 0.00 3.18
3365 9496 9.871238 AGTTCTGTTACTATATGTACCAAGTTG 57.129 33.333 0.00 0.00 0.00 3.16
3392 9523 5.987953 TCTCTAGCATGAGTAATGTGAATGC 59.012 40.000 0.00 0.00 43.10 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.606631 AATTCATGTATACTCTTCACTTCCTTC 57.393 33.333 4.17 0.00 0.00 3.46
31 32 9.265901 GCAACAATACTATCAGTCTGTCATTAT 57.734 33.333 0.00 0.00 0.00 1.28
32 33 8.257306 TGCAACAATACTATCAGTCTGTCATTA 58.743 33.333 0.00 0.00 0.00 1.90
33 34 7.105588 TGCAACAATACTATCAGTCTGTCATT 58.894 34.615 0.00 0.00 0.00 2.57
38 40 6.674037 GCAACTGCAACAATACTATCAGTCTG 60.674 42.308 0.00 0.00 41.59 3.51
123 125 1.836604 GGGTTTCCCTGCTGGCAAA 60.837 57.895 3.63 0.00 41.34 3.68
148 150 0.743688 CTGATGAGGGTGGACGAGAG 59.256 60.000 0.00 0.00 0.00 3.20
150 152 0.174389 CACTGATGAGGGTGGACGAG 59.826 60.000 0.00 0.00 0.00 4.18
154 156 3.099905 CTCTTACACTGATGAGGGTGGA 58.900 50.000 0.00 0.00 36.14 4.02
167 169 3.293311 TGTTGTACTCGGCTCTTACAC 57.707 47.619 0.00 0.00 0.00 2.90
169 171 2.991866 GGTTGTTGTACTCGGCTCTTAC 59.008 50.000 0.00 0.00 0.00 2.34
175 177 2.147958 TCAATGGTTGTTGTACTCGGC 58.852 47.619 0.00 0.00 0.00 5.54
177 179 4.084013 GGACTTCAATGGTTGTTGTACTCG 60.084 45.833 0.00 0.00 0.00 4.18
178 180 5.049405 CAGGACTTCAATGGTTGTTGTACTC 60.049 44.000 0.00 0.00 30.33 2.59
179 181 4.821805 CAGGACTTCAATGGTTGTTGTACT 59.178 41.667 0.00 0.00 31.90 2.73
180 182 4.556699 GCAGGACTTCAATGGTTGTTGTAC 60.557 45.833 0.00 0.00 0.00 2.90
182 184 2.362077 GCAGGACTTCAATGGTTGTTGT 59.638 45.455 0.00 0.00 0.00 3.32
183 185 2.361757 TGCAGGACTTCAATGGTTGTTG 59.638 45.455 0.00 0.00 0.00 3.33
184 186 2.665165 TGCAGGACTTCAATGGTTGTT 58.335 42.857 0.00 0.00 0.00 2.83
185 187 2.363306 TGCAGGACTTCAATGGTTGT 57.637 45.000 0.00 0.00 0.00 3.32
186 188 3.581755 CATTGCAGGACTTCAATGGTTG 58.418 45.455 14.28 0.00 43.36 3.77
187 189 3.947910 CATTGCAGGACTTCAATGGTT 57.052 42.857 14.28 0.00 43.36 3.67
190 192 2.165030 GACCCATTGCAGGACTTCAATG 59.835 50.000 14.90 14.90 45.42 2.82
192 194 1.425066 AGACCCATTGCAGGACTTCAA 59.575 47.619 0.00 0.00 0.00 2.69
193 195 1.067295 AGACCCATTGCAGGACTTCA 58.933 50.000 0.00 0.00 0.00 3.02
196 198 1.280421 GAGAAGACCCATTGCAGGACT 59.720 52.381 0.00 0.00 0.00 3.85
198 200 1.280133 CAGAGAAGACCCATTGCAGGA 59.720 52.381 0.00 0.00 0.00 3.86
199 201 1.004044 ACAGAGAAGACCCATTGCAGG 59.996 52.381 0.00 0.00 0.00 4.85
200 202 2.486472 ACAGAGAAGACCCATTGCAG 57.514 50.000 0.00 0.00 0.00 4.41
201 203 2.507484 CAACAGAGAAGACCCATTGCA 58.493 47.619 0.00 0.00 0.00 4.08
202 204 1.815003 CCAACAGAGAAGACCCATTGC 59.185 52.381 0.00 0.00 0.00 3.56
204 206 2.290577 GCTCCAACAGAGAAGACCCATT 60.291 50.000 0.00 0.00 46.50 3.16
205 207 1.280421 GCTCCAACAGAGAAGACCCAT 59.720 52.381 0.00 0.00 46.50 4.00
206 208 0.687354 GCTCCAACAGAGAAGACCCA 59.313 55.000 0.00 0.00 46.50 4.51
207 209 0.035915 GGCTCCAACAGAGAAGACCC 60.036 60.000 0.00 0.00 46.50 4.46
209 211 1.943507 GCTGGCTCCAACAGAGAAGAC 60.944 57.143 0.00 0.00 46.50 3.01
210 212 0.322975 GCTGGCTCCAACAGAGAAGA 59.677 55.000 0.00 0.00 46.50 2.87
211 213 0.324285 AGCTGGCTCCAACAGAGAAG 59.676 55.000 0.00 0.00 46.50 2.85
212 214 0.035881 CAGCTGGCTCCAACAGAGAA 59.964 55.000 5.57 0.00 46.50 2.87
214 216 2.039405 GCAGCTGGCTCCAACAGAG 61.039 63.158 17.12 0.00 46.29 3.35
215 217 2.033141 GCAGCTGGCTCCAACAGA 59.967 61.111 17.12 0.00 38.20 3.41
216 218 3.429141 CGCAGCTGGCTCCAACAG 61.429 66.667 17.12 0.00 41.67 3.16
218 220 2.437359 ATCGCAGCTGGCTCCAAC 60.437 61.111 17.12 0.00 41.67 3.77
220 222 3.381333 CTCATCGCAGCTGGCTCCA 62.381 63.158 17.12 0.00 41.67 3.86
221 223 2.588314 CTCATCGCAGCTGGCTCC 60.588 66.667 17.12 0.00 41.67 4.70
223 225 3.397439 ACCTCATCGCAGCTGGCT 61.397 61.111 17.12 0.00 41.67 4.75
224 226 2.937379 ATCACCTCATCGCAGCTGGC 62.937 60.000 17.12 6.97 39.90 4.85
225 227 0.879400 GATCACCTCATCGCAGCTGG 60.879 60.000 17.12 5.82 0.00 4.85
226 228 0.879400 GGATCACCTCATCGCAGCTG 60.879 60.000 10.11 10.11 0.00 4.24
227 229 1.332889 TGGATCACCTCATCGCAGCT 61.333 55.000 0.00 0.00 37.04 4.24
228 230 0.250209 ATGGATCACCTCATCGCAGC 60.250 55.000 0.00 0.00 37.04 5.25
230 232 1.069668 CAGATGGATCACCTCATCGCA 59.930 52.381 0.00 0.00 43.13 5.10
231 233 1.342496 TCAGATGGATCACCTCATCGC 59.658 52.381 0.00 0.00 43.13 4.58
232 234 2.609984 GCTCAGATGGATCACCTCATCG 60.610 54.545 0.00 0.00 43.13 3.84
233 235 2.367894 TGCTCAGATGGATCACCTCATC 59.632 50.000 0.00 0.00 39.85 2.92
234 236 2.405559 TGCTCAGATGGATCACCTCAT 58.594 47.619 0.00 0.00 37.04 2.90
235 237 1.870064 TGCTCAGATGGATCACCTCA 58.130 50.000 0.00 0.00 37.04 3.86
236 238 2.104451 ACATGCTCAGATGGATCACCTC 59.896 50.000 0.00 0.00 37.04 3.85
237 239 2.125233 ACATGCTCAGATGGATCACCT 58.875 47.619 0.00 0.00 37.04 4.00
238 240 2.634815 ACATGCTCAGATGGATCACC 57.365 50.000 0.00 0.00 0.00 4.02
239 241 4.305769 GAGTACATGCTCAGATGGATCAC 58.694 47.826 0.00 0.00 35.67 3.06
240 242 3.005155 CGAGTACATGCTCAGATGGATCA 59.995 47.826 0.00 0.00 35.33 2.92
241 243 3.005261 ACGAGTACATGCTCAGATGGATC 59.995 47.826 0.00 0.00 35.33 3.36
242 244 2.961741 ACGAGTACATGCTCAGATGGAT 59.038 45.455 0.00 0.00 35.33 3.41
244 246 2.736978 GACGAGTACATGCTCAGATGG 58.263 52.381 0.00 0.00 35.33 3.51
245 247 2.032178 TCGACGAGTACATGCTCAGATG 59.968 50.000 0.00 0.00 35.33 2.90
246 248 2.032302 GTCGACGAGTACATGCTCAGAT 59.968 50.000 0.00 0.00 35.33 2.90
247 249 1.397343 GTCGACGAGTACATGCTCAGA 59.603 52.381 0.00 0.00 35.33 3.27
248 250 1.532090 GGTCGACGAGTACATGCTCAG 60.532 57.143 9.92 0.00 35.33 3.35
249 251 0.450583 GGTCGACGAGTACATGCTCA 59.549 55.000 9.92 0.00 35.33 4.26
250 252 0.450583 TGGTCGACGAGTACATGCTC 59.549 55.000 9.92 0.00 0.00 4.26
251 253 1.103803 ATGGTCGACGAGTACATGCT 58.896 50.000 9.92 0.00 0.00 3.79
252 254 1.200483 CATGGTCGACGAGTACATGC 58.800 55.000 18.29 0.00 33.45 4.06
253 255 1.200483 GCATGGTCGACGAGTACATG 58.800 55.000 22.73 22.73 41.26 3.21
255 257 0.170339 CAGCATGGTCGACGAGTACA 59.830 55.000 9.92 1.29 0.00 2.90
257 259 0.733150 CTCAGCATGGTCGACGAGTA 59.267 55.000 9.92 0.00 36.16 2.59
258 260 1.244697 ACTCAGCATGGTCGACGAGT 61.245 55.000 13.61 13.61 36.16 4.18
259 261 0.799917 CACTCAGCATGGTCGACGAG 60.800 60.000 9.92 11.49 36.16 4.18
260 262 1.212751 CACTCAGCATGGTCGACGA 59.787 57.895 9.92 5.99 36.16 4.20
263 265 2.659063 CCCCACTCAGCATGGTCGA 61.659 63.158 0.00 0.00 35.23 4.20
264 266 2.124983 CCCCACTCAGCATGGTCG 60.125 66.667 0.00 0.00 35.23 4.79
265 267 2.439156 GCCCCACTCAGCATGGTC 60.439 66.667 0.00 0.00 35.23 4.02
266 268 3.259314 TGCCCCACTCAGCATGGT 61.259 61.111 0.00 0.00 35.23 3.55
267 269 2.280404 ATCTGCCCCACTCAGCATGG 62.280 60.000 0.00 0.00 38.56 3.66
268 270 0.395311 AATCTGCCCCACTCAGCATG 60.395 55.000 0.00 0.00 38.56 4.06
269 271 0.106819 GAATCTGCCCCACTCAGCAT 60.107 55.000 0.00 0.00 38.56 3.79
271 273 0.322816 TTGAATCTGCCCCACTCAGC 60.323 55.000 0.00 0.00 0.00 4.26
273 275 1.144708 TGTTTGAATCTGCCCCACTCA 59.855 47.619 0.00 0.00 0.00 3.41
274 276 1.541588 GTGTTTGAATCTGCCCCACTC 59.458 52.381 0.00 0.00 0.00 3.51
276 278 1.327303 TGTGTTTGAATCTGCCCCAC 58.673 50.000 0.00 0.00 0.00 4.61
277 279 2.079170 TTGTGTTTGAATCTGCCCCA 57.921 45.000 0.00 0.00 0.00 4.96
279 3385 3.552890 GGTCTTTGTGTTTGAATCTGCCC 60.553 47.826 0.00 0.00 0.00 5.36
281 3387 4.036734 TCAGGTCTTTGTGTTTGAATCTGC 59.963 41.667 0.00 0.00 0.00 4.26
284 3390 5.385617 CGATCAGGTCTTTGTGTTTGAATC 58.614 41.667 0.00 0.00 0.00 2.52
290 3396 1.873591 GTGCGATCAGGTCTTTGTGTT 59.126 47.619 0.00 0.00 0.00 3.32
293 3399 2.563179 AGTAGTGCGATCAGGTCTTTGT 59.437 45.455 0.00 0.00 0.00 2.83
340 3468 2.029380 CACGGTACACCATCTTCTGTCA 60.029 50.000 0.00 0.00 35.14 3.58
353 3489 1.287815 CTGCTTCGGTCACGGTACA 59.712 57.895 0.00 0.00 41.39 2.90
365 3501 0.957888 GAGTTGACCTGCCCTGCTTC 60.958 60.000 0.00 0.00 0.00 3.86
443 3579 1.270839 CGAGCTTTTTCTGGGAGTCCA 60.271 52.381 12.30 0.00 41.58 4.02
455 3617 2.427095 AGCCAAAACTTGTCGAGCTTTT 59.573 40.909 0.00 0.00 0.00 2.27
457 3619 1.334869 CAGCCAAAACTTGTCGAGCTT 59.665 47.619 0.00 0.00 0.00 3.74
460 3622 2.483876 TCTCAGCCAAAACTTGTCGAG 58.516 47.619 0.00 0.00 0.00 4.04
461 3623 2.613026 TCTCAGCCAAAACTTGTCGA 57.387 45.000 0.00 0.00 0.00 4.20
462 3624 4.245660 TCTATCTCAGCCAAAACTTGTCG 58.754 43.478 0.00 0.00 0.00 4.35
463 3625 4.633565 CCTCTATCTCAGCCAAAACTTGTC 59.366 45.833 0.00 0.00 0.00 3.18
464 3626 4.566488 CCCTCTATCTCAGCCAAAACTTGT 60.566 45.833 0.00 0.00 0.00 3.16
465 3627 3.944015 CCCTCTATCTCAGCCAAAACTTG 59.056 47.826 0.00 0.00 0.00 3.16
466 3628 3.846588 TCCCTCTATCTCAGCCAAAACTT 59.153 43.478 0.00 0.00 0.00 2.66
467 3629 3.454858 TCCCTCTATCTCAGCCAAAACT 58.545 45.455 0.00 0.00 0.00 2.66
468 3630 3.914426 TCCCTCTATCTCAGCCAAAAC 57.086 47.619 0.00 0.00 0.00 2.43
469 3631 3.434167 GCATCCCTCTATCTCAGCCAAAA 60.434 47.826 0.00 0.00 0.00 2.44
470 3632 2.105477 GCATCCCTCTATCTCAGCCAAA 59.895 50.000 0.00 0.00 0.00 3.28
471 3633 1.696336 GCATCCCTCTATCTCAGCCAA 59.304 52.381 0.00 0.00 0.00 4.52
472 3634 1.132913 AGCATCCCTCTATCTCAGCCA 60.133 52.381 0.00 0.00 0.00 4.75
473 3635 1.275856 CAGCATCCCTCTATCTCAGCC 59.724 57.143 0.00 0.00 0.00 4.85
474 3636 2.246469 TCAGCATCCCTCTATCTCAGC 58.754 52.381 0.00 0.00 0.00 4.26
475 3637 4.773674 AGATTCAGCATCCCTCTATCTCAG 59.226 45.833 0.00 0.00 31.20 3.35
476 3638 4.749820 AGATTCAGCATCCCTCTATCTCA 58.250 43.478 0.00 0.00 31.20 3.27
477 3639 5.743636 AAGATTCAGCATCCCTCTATCTC 57.256 43.478 0.00 0.00 31.20 2.75
478 3640 6.213195 CCTTAAGATTCAGCATCCCTCTATCT 59.787 42.308 3.36 0.00 31.20 1.98
479 3641 6.405538 CCTTAAGATTCAGCATCCCTCTATC 58.594 44.000 3.36 0.00 31.20 2.08
480 3642 5.250313 CCCTTAAGATTCAGCATCCCTCTAT 59.750 44.000 3.36 0.00 31.20 1.98
481 3643 4.594920 CCCTTAAGATTCAGCATCCCTCTA 59.405 45.833 3.36 0.00 31.20 2.43
482 3644 3.393941 CCCTTAAGATTCAGCATCCCTCT 59.606 47.826 3.36 0.00 31.20 3.69
483 3645 3.137360 ACCCTTAAGATTCAGCATCCCTC 59.863 47.826 3.36 0.00 31.20 4.30
484 3646 3.126453 ACCCTTAAGATTCAGCATCCCT 58.874 45.455 3.36 0.00 31.20 4.20
569 3731 0.035317 TGTCTAAGCACCACTGGCTG 59.965 55.000 0.00 0.00 41.66 4.85
574 3736 1.893137 TCGTCATGTCTAAGCACCACT 59.107 47.619 0.00 0.00 0.00 4.00
581 3743 3.608506 CCTCGTTGTTCGTCATGTCTAAG 59.391 47.826 0.00 0.00 40.80 2.18
584 3746 1.611977 TCCTCGTTGTTCGTCATGTCT 59.388 47.619 0.00 0.00 40.80 3.41
596 3758 5.424121 AACTTGATCACTTTTCCTCGTTG 57.576 39.130 0.00 0.00 0.00 4.10
602 3764 7.454260 AGACCAATAACTTGATCACTTTTCC 57.546 36.000 0.00 0.00 34.04 3.13
603 3765 7.327032 GCAAGACCAATAACTTGATCACTTTTC 59.673 37.037 0.00 0.00 43.98 2.29
606 3768 5.183904 GGCAAGACCAATAACTTGATCACTT 59.816 40.000 0.00 0.00 43.98 3.16
622 3784 1.518903 GCTTGGTGAGTGGCAAGACC 61.519 60.000 0.00 0.00 39.84 3.85
623 3785 1.845809 CGCTTGGTGAGTGGCAAGAC 61.846 60.000 0.00 0.00 32.09 3.01
624 3786 1.597854 CGCTTGGTGAGTGGCAAGA 60.598 57.895 0.00 0.00 32.09 3.02
660 3822 7.682787 ATACAGTAACATCCTCTCCTTTCAT 57.317 36.000 0.00 0.00 0.00 2.57
724 3887 1.214175 ACAAACACTCACACCCATGGA 59.786 47.619 15.22 0.00 0.00 3.41
729 3892 2.073816 CCGATACAAACACTCACACCC 58.926 52.381 0.00 0.00 0.00 4.61
736 3913 2.561478 AACCAGCCGATACAAACACT 57.439 45.000 0.00 0.00 0.00 3.55
756 3933 3.936453 GCAACCATCACCGAACATACTAA 59.064 43.478 0.00 0.00 0.00 2.24
757 3934 3.196901 AGCAACCATCACCGAACATACTA 59.803 43.478 0.00 0.00 0.00 1.82
758 3935 2.027192 AGCAACCATCACCGAACATACT 60.027 45.455 0.00 0.00 0.00 2.12
759 3936 2.356135 AGCAACCATCACCGAACATAC 58.644 47.619 0.00 0.00 0.00 2.39
760 3937 2.779755 AGCAACCATCACCGAACATA 57.220 45.000 0.00 0.00 0.00 2.29
761 3938 1.909700 AAGCAACCATCACCGAACAT 58.090 45.000 0.00 0.00 0.00 2.71
762 3939 1.686355 AAAGCAACCATCACCGAACA 58.314 45.000 0.00 0.00 0.00 3.18
763 3940 5.751243 ATATAAAGCAACCATCACCGAAC 57.249 39.130 0.00 0.00 0.00 3.95
764 3941 9.562408 TTTATATATAAAGCAACCATCACCGAA 57.438 29.630 12.90 0.00 0.00 4.30
765 3942 9.214957 CTTTATATATAAAGCAACCATCACCGA 57.785 33.333 25.10 0.00 41.69 4.69
793 3970 6.379386 CATTAACGAAAAAGGGTTTCCTCTC 58.621 40.000 0.00 0.00 44.07 3.20
794 3971 5.243060 CCATTAACGAAAAAGGGTTTCCTCT 59.757 40.000 0.00 0.00 44.07 3.69
811 3988 5.195001 TCACAAACTTTCCAGCCATTAAC 57.805 39.130 0.00 0.00 0.00 2.01
813 3990 4.469657 ACTCACAAACTTTCCAGCCATTA 58.530 39.130 0.00 0.00 0.00 1.90
814 3991 3.299503 ACTCACAAACTTTCCAGCCATT 58.700 40.909 0.00 0.00 0.00 3.16
815 3992 2.949447 ACTCACAAACTTTCCAGCCAT 58.051 42.857 0.00 0.00 0.00 4.40
816 3993 2.426738 CAACTCACAAACTTTCCAGCCA 59.573 45.455 0.00 0.00 0.00 4.75
817 3994 2.223805 CCAACTCACAAACTTTCCAGCC 60.224 50.000 0.00 0.00 0.00 4.85
818 3995 2.687935 TCCAACTCACAAACTTTCCAGC 59.312 45.455 0.00 0.00 0.00 4.85
819 3996 4.199310 TCTCCAACTCACAAACTTTCCAG 58.801 43.478 0.00 0.00 0.00 3.86
820 3997 4.199310 CTCTCCAACTCACAAACTTTCCA 58.801 43.478 0.00 0.00 0.00 3.53
821 3998 3.003793 GCTCTCCAACTCACAAACTTTCC 59.996 47.826 0.00 0.00 0.00 3.13
822 3999 3.627577 TGCTCTCCAACTCACAAACTTTC 59.372 43.478 0.00 0.00 0.00 2.62
826 4003 3.141398 TCATGCTCTCCAACTCACAAAC 58.859 45.455 0.00 0.00 0.00 2.93
844 4021 2.806019 GCGATCCACTGAGCTGATTCAT 60.806 50.000 0.00 0.00 0.00 2.57
918 4095 0.300491 ATATACAAAGCGCGCGTGTG 59.700 50.000 37.27 30.95 0.00 3.82
919 4096 1.842720 TATATACAAAGCGCGCGTGT 58.157 45.000 34.55 34.55 0.00 4.49
949 4128 0.671796 TGAGATGTACGGCCGGTATG 59.328 55.000 31.76 0.43 32.74 2.39
969 4148 4.022849 GGTGCAAGAAAAATAGACTGCAGT 60.023 41.667 21.88 21.88 0.00 4.40
1023 4202 7.327214 GTGGAAGGATTATGGATGTCTCTATC 58.673 42.308 0.00 0.00 0.00 2.08
1149 4331 0.876777 CGGCGTTGACAGGTGTTGTA 60.877 55.000 0.00 0.00 41.05 2.41
1152 4334 3.276846 GCGGCGTTGACAGGTGTT 61.277 61.111 9.37 0.00 0.00 3.32
1176 4358 2.283529 CCTGTCGGCTACACCCTGT 61.284 63.158 0.00 0.00 33.45 4.00
1178 4360 2.683933 CCCTGTCGGCTACACCCT 60.684 66.667 0.00 0.00 33.45 4.34
1279 4461 1.522580 GGAGGAAGCTGTCGATGCC 60.523 63.158 9.29 0.00 0.00 4.40
1389 4571 2.904866 GCTGTCCACGGGTTGCAA 60.905 61.111 0.00 0.00 0.00 4.08
1473 4655 2.742372 GCCACGTTCAGGTCGCAT 60.742 61.111 0.00 0.00 0.00 4.73
1488 4670 3.063743 GCCCTTGCCATACGTTGCC 62.064 63.158 0.00 0.00 0.00 4.52
1543 4731 0.459899 TTGGTCATCTCTACGCGCAT 59.540 50.000 5.73 0.00 0.00 4.73
1596 4787 1.185618 TGGTGAACTCCTCCCACTCG 61.186 60.000 0.00 0.00 0.00 4.18
1642 4833 4.889856 CATCACGGCGCCATCGGA 62.890 66.667 28.98 17.59 35.95 4.55
1669 4860 1.557269 AACTCTTGCTCGAGGCCCAT 61.557 55.000 15.58 0.00 40.92 4.00
1695 4886 1.678728 CCAAGTGCCGCTTCATAGGAA 60.679 52.381 0.00 0.00 34.69 3.36
1734 4925 2.070399 TACCGAGCAAAAAGGGCCCA 62.070 55.000 27.56 0.00 0.00 5.36
1764 4955 0.536687 TATGGTAGACGGCCTCCTCG 60.537 60.000 0.00 0.00 0.00 4.63
1777 4971 2.809706 GGTGACCGCGCTATGGTA 59.190 61.111 5.56 0.00 40.63 3.25
1849 5043 2.079088 TTGGGAGGCATCTGCACCAA 62.079 55.000 16.29 16.29 43.44 3.67
1851 5045 1.751927 CTTGGGAGGCATCTGCACC 60.752 63.158 4.33 6.78 44.36 5.01
1884 5078 4.671590 TCCTCGAGGCCGTGTCCA 62.672 66.667 27.39 3.56 37.05 4.02
1907 5101 0.537371 CACCCAAAGGAACGGCTTCT 60.537 55.000 0.00 0.00 36.73 2.85
1958 5152 1.601759 GCTTGGAGCCACTCTTGCA 60.602 57.895 0.00 0.00 34.48 4.08
2004 5198 1.683011 GCCCAACCATGCACTATGAGT 60.683 52.381 0.00 0.00 39.21 3.41
2019 5213 4.704833 GTGAGCTGAGGCGCCCAA 62.705 66.667 26.15 11.19 44.37 4.12
2035 5229 1.741401 CGTGGTGCGACATGATGGT 60.741 57.895 0.00 0.00 44.77 3.55
2139 5333 0.033504 TGAGGAACTGGTCGCTGAAC 59.966 55.000 0.00 0.00 41.55 3.18
2280 5483 1.081481 TCCTCCTGTCCTCTACCACA 58.919 55.000 0.00 0.00 0.00 4.17
2285 5488 3.008049 GCACTTTTTCCTCCTGTCCTCTA 59.992 47.826 0.00 0.00 0.00 2.43
2292 5495 2.586425 TCCTTGCACTTTTTCCTCCTG 58.414 47.619 0.00 0.00 0.00 3.86
2300 5503 2.167662 CCCCGTAATCCTTGCACTTTT 58.832 47.619 0.00 0.00 0.00 2.27
2335 5538 1.030457 GATCCTCCTTTCGCTACGGA 58.970 55.000 0.00 0.00 0.00 4.69
2361 5564 1.082117 ATAGCCGCGTCAGGTTTTCG 61.082 55.000 4.92 0.00 0.00 3.46
2459 5662 3.129113 TGGACATAACTCACAATGCATGC 59.871 43.478 11.82 11.82 0.00 4.06
2515 5721 3.085443 AGAAATCACTACGATGAGCCG 57.915 47.619 0.00 0.00 33.40 5.52
2525 5731 3.681594 GCCATCCCACGAAGAAATCACTA 60.682 47.826 0.00 0.00 0.00 2.74
2526 5732 2.941415 GCCATCCCACGAAGAAATCACT 60.941 50.000 0.00 0.00 0.00 3.41
2559 5773 4.615912 CGACATACTACGCCATCATGATCA 60.616 45.833 4.86 0.00 0.00 2.92
2567 5781 0.309922 CGGTCGACATACTACGCCAT 59.690 55.000 18.91 0.00 0.00 4.40
2574 5788 1.515954 CCTTGCCGGTCGACATACT 59.484 57.895 18.91 0.00 0.00 2.12
2603 5817 2.426024 GGCATGACTGAGTTACGACCTA 59.574 50.000 0.00 0.00 0.00 3.08
2604 5818 1.204941 GGCATGACTGAGTTACGACCT 59.795 52.381 0.00 0.00 0.00 3.85
2605 5819 1.641577 GGCATGACTGAGTTACGACC 58.358 55.000 0.00 0.00 0.00 4.79
2607 5821 1.204704 CAGGGCATGACTGAGTTACGA 59.795 52.381 11.21 0.00 38.20 3.43
2608 5822 1.204704 TCAGGGCATGACTGAGTTACG 59.795 52.381 14.33 0.00 39.87 3.18
2610 5824 3.173151 TCTTCAGGGCATGACTGAGTTA 58.827 45.455 16.71 5.87 44.91 2.24
2611 5825 1.980765 TCTTCAGGGCATGACTGAGTT 59.019 47.619 16.71 0.00 44.91 3.01
2612 5826 1.649321 TCTTCAGGGCATGACTGAGT 58.351 50.000 16.71 0.00 44.91 3.41
2613 5827 2.775911 TTCTTCAGGGCATGACTGAG 57.224 50.000 16.71 0.00 44.91 3.35
2615 5829 3.118112 ACCTATTCTTCAGGGCATGACTG 60.118 47.826 0.00 4.93 37.77 3.51
2619 8719 2.158900 ACGACCTATTCTTCAGGGCATG 60.159 50.000 0.00 0.00 41.83 4.06
2898 9003 7.772292 AGATAGCCTGGTAATATATGCATGTTG 59.228 37.037 10.16 0.00 0.00 3.33
2946 9051 9.368416 ACACTACACATATGTATGATCCTAGTT 57.632 33.333 8.32 0.00 40.57 2.24
2948 9053 9.014297 TGACACTACACATATGTATGATCCTAG 57.986 37.037 8.32 0.00 40.57 3.02
2949 9054 8.934023 TGACACTACACATATGTATGATCCTA 57.066 34.615 8.32 0.00 40.57 2.94
2950 9055 7.839680 TGACACTACACATATGTATGATCCT 57.160 36.000 8.32 0.00 40.57 3.24
2951 9056 9.574458 GTATGACACTACACATATGTATGATCC 57.426 37.037 8.32 0.00 40.57 3.36
2954 9059 9.744468 GTTGTATGACACTACACATATGTATGA 57.256 33.333 8.32 0.00 40.57 2.15
2955 9060 9.750125 AGTTGTATGACACTACACATATGTATG 57.250 33.333 8.32 7.44 40.57 2.39
3005 9110 3.256136 AGCGTAGGATAGACTACAATGCC 59.744 47.826 0.00 0.00 42.68 4.40
3016 9121 1.609555 GTGGGTCTGAGCGTAGGATAG 59.390 57.143 0.18 0.00 0.00 2.08
3063 9168 3.195661 GGGTAAAGTAGAGAATGGCGTG 58.804 50.000 0.00 0.00 0.00 5.34
3077 9182 1.670811 GCATGACGTGATGGGGTAAAG 59.329 52.381 16.87 0.00 0.00 1.85
3080 9185 0.177836 CTGCATGACGTGATGGGGTA 59.822 55.000 16.87 0.00 0.00 3.69
3233 9338 2.680577 GTTTTCGTTTCCTCCGCTAGA 58.319 47.619 0.00 0.00 0.00 2.43
3239 9344 2.096565 GTGTAGCGTTTTCGTTTCCTCC 60.097 50.000 0.00 0.00 46.03 4.30
3240 9345 2.540931 TGTGTAGCGTTTTCGTTTCCTC 59.459 45.455 0.00 0.00 46.03 3.71
3365 9496 5.895928 TCACATTACTCATGCTAGAGACAC 58.104 41.667 12.03 0.00 38.98 3.67
3392 9523 1.079127 ATGCAACGTCTCCTTCCCG 60.079 57.895 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.