Multiple sequence alignment - TraesCS2A01G308400

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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 TraesCS2A01G308400 chr2A 100.000 4394 0 0 1 4394 530378020 530382413 0.000000e+00 8115
1 TraesCS2A01G308400 chr2B 93.790 3446 143 22 245 3650 464464231 464467645 0.000000e+00 5112
2 TraesCS2A01G308400 chr2B 88.402 388 28 6 4002 4389 464505813 464506183 6.700000e-123 451
3 TraesCS2A01G308400 chr2B 87.234 141 15 3 1 140 464464054 464464192 1.640000e-34 158
4 TraesCS2A01G308400 chr2B 91.358 81 7 0 3919 3999 464503681 464503761 1.290000e-20 111
5 TraesCS2A01G308400 chr2D 95.866 2782 80 17 756 3510 392524116 392526889 0.000000e+00 4468
6 TraesCS2A01G308400 chr2D 89.506 324 33 1 335 658 392523390 392523712 4.090000e-110 409
7 TraesCS2A01G308400 chr2D 89.342 319 17 8 4074 4389 392527952 392528256 6.890000e-103 385
8 TraesCS2A01G308400 chr2D 87.117 163 10 3 3546 3704 392526881 392527036 1.620000e-39 174
9 TraesCS2A01G308400 chr4B 76.695 811 131 46 2544 3316 119823420 119822630 8.850000e-107 398
10 TraesCS2A01G308400 chr4D 75.050 1006 170 60 2362 3316 84546411 84545436 4.120000e-105 392
11 TraesCS2A01G308400 chr4A 75.025 1001 173 60 2362 3316 497441237 497440268 4.120000e-105 392
12 TraesCS2A01G308400 chr7B 76.408 657 119 19 2434 3081 418049662 418049033 5.480000e-84 322
13 TraesCS2A01G308400 chr7D 76.067 656 123 17 2434 3081 407072262 407071633 1.190000e-80 311
14 TraesCS2A01G308400 chr7A 75.951 657 122 20 2434 3081 464573268 464572639 5.520000e-79 305
15 TraesCS2A01G308400 chr1D 74.902 510 86 34 2594 3067 53965223 53964720 1.250000e-45 195
16 TraesCS2A01G308400 chr1A 84.932 73 11 0 2426 2498 53455519 53455447 1.690000e-09 75


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 TraesCS2A01G308400 chr2A 530378020 530382413 4393 False 8115 8115 100.00000 1 4394 1 chr2A.!!$F1 4393
1 TraesCS2A01G308400 chr2B 464464054 464467645 3591 False 2635 5112 90.51200 1 3650 2 chr2B.!!$F1 3649
2 TraesCS2A01G308400 chr2B 464503681 464506183 2502 False 281 451 89.88000 3919 4389 2 chr2B.!!$F2 470
3 TraesCS2A01G308400 chr2D 392523390 392528256 4866 False 1359 4468 90.45775 335 4389 4 chr2D.!!$F1 4054
4 TraesCS2A01G308400 chr4B 119822630 119823420 790 True 398 398 76.69500 2544 3316 1 chr4B.!!$R1 772
5 TraesCS2A01G308400 chr4D 84545436 84546411 975 True 392 392 75.05000 2362 3316 1 chr4D.!!$R1 954
6 TraesCS2A01G308400 chr4A 497440268 497441237 969 True 392 392 75.02500 2362 3316 1 chr4A.!!$R1 954
7 TraesCS2A01G308400 chr7B 418049033 418049662 629 True 322 322 76.40800 2434 3081 1 chr7B.!!$R1 647
8 TraesCS2A01G308400 chr7D 407071633 407072262 629 True 311 311 76.06700 2434 3081 1 chr7D.!!$R1 647
9 TraesCS2A01G308400 chr7A 464572639 464573268 629 True 305 305 75.95100 2434 3081 1 chr7A.!!$R1 647

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
229 231 0.449388 GCCAAGATCACTGGAAAGCG 59.551 55.000 16.06 0.0 0.00 4.68 F
902 1216 0.584396 CCGTTCTCTCCTCGATCTCG 59.416 60.000 0.00 0.0 41.45 4.04 F
1578 1892 1.152984 CTATGGCAATGGGGACGCA 60.153 57.895 0.00 0.0 0.00 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 2139 1.373497 CGACGAACTGCTCCTGCTT 60.373 57.895 0.0 0.0 40.48 3.91 R
2120 2437 1.448540 CGCCGCTTCTTCCTCATGT 60.449 57.895 0.0 0.0 0.00 3.21 R
3517 3913 2.362077 GACTTCATTTGCCCAACACAGT 59.638 45.455 0.0 0.0 0.00 3.55 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
23 24 3.032265 AGCAAGACCAAAGAAAACCCT 57.968 42.857 0.00 0.00 0.00 4.34
31 33 4.212716 ACCAAAGAAAACCCTGAGTAACC 58.787 43.478 0.00 0.00 0.00 2.85
37 39 1.188863 AACCCTGAGTAACCGCGTAT 58.811 50.000 4.92 0.00 0.00 3.06
40 42 2.224606 CCCTGAGTAACCGCGTATCTA 58.775 52.381 4.92 0.00 0.00 1.98
76 78 8.593945 AAAAACAATGGTAGTGTGATATGGAT 57.406 30.769 0.00 0.00 0.00 3.41
81 83 5.791336 TGGTAGTGTGATATGGATGTCTC 57.209 43.478 0.00 0.00 0.00 3.36
82 84 5.208121 TGGTAGTGTGATATGGATGTCTCA 58.792 41.667 0.00 0.00 0.00 3.27
95 97 5.194432 TGGATGTCTCACTAGTCCTAACTC 58.806 45.833 0.00 0.00 36.92 3.01
98 100 6.409464 GGATGTCTCACTAGTCCTAACTCCTA 60.409 46.154 0.00 0.00 36.92 2.94
103 105 6.444493 TCTCACTAGTCCTAACTCCTAAGTCT 59.556 42.308 0.00 0.00 36.92 3.24
133 135 7.537306 GTGTTGTTAACATGTTATGTGATCACC 59.463 37.037 22.85 8.07 44.07 4.02
136 138 9.454859 TTGTTAACATGTTATGTGATCACCATA 57.545 29.630 22.85 16.23 44.07 2.74
137 139 8.888716 TGTTAACATGTTATGTGATCACCATAC 58.111 33.333 22.85 16.55 44.07 2.39
138 140 9.109393 GTTAACATGTTATGTGATCACCATACT 57.891 33.333 22.85 10.84 44.07 2.12
141 143 9.679661 AACATGTTATGTGATCACCATACTAAA 57.320 29.630 22.85 1.92 44.07 1.85
142 144 9.330063 ACATGTTATGTGATCACCATACTAAAG 57.670 33.333 22.85 8.26 43.01 1.85
143 145 7.786178 TGTTATGTGATCACCATACTAAAGC 57.214 36.000 22.85 4.69 0.00 3.51
144 146 7.564793 TGTTATGTGATCACCATACTAAAGCT 58.435 34.615 22.85 0.00 0.00 3.74
145 147 8.700973 TGTTATGTGATCACCATACTAAAGCTA 58.299 33.333 22.85 0.00 0.00 3.32
146 148 9.542462 GTTATGTGATCACCATACTAAAGCTAA 57.458 33.333 22.85 0.00 0.00 3.09
147 149 9.764363 TTATGTGATCACCATACTAAAGCTAAG 57.236 33.333 22.85 0.00 0.00 2.18
148 150 6.582636 TGTGATCACCATACTAAAGCTAAGG 58.417 40.000 22.85 0.00 0.00 2.69
149 151 5.992217 GTGATCACCATACTAAAGCTAAGGG 59.008 44.000 15.31 0.00 0.00 3.95
150 152 5.903010 TGATCACCATACTAAAGCTAAGGGA 59.097 40.000 0.00 0.00 0.00 4.20
151 153 6.558775 TGATCACCATACTAAAGCTAAGGGAT 59.441 38.462 0.00 0.00 0.00 3.85
152 154 6.420913 TCACCATACTAAAGCTAAGGGATC 57.579 41.667 0.00 0.00 0.00 3.36
153 155 5.903010 TCACCATACTAAAGCTAAGGGATCA 59.097 40.000 0.00 0.00 0.00 2.92
154 156 5.992217 CACCATACTAAAGCTAAGGGATCAC 59.008 44.000 0.00 0.00 0.00 3.06
155 157 5.071923 ACCATACTAAAGCTAAGGGATCACC 59.928 44.000 0.00 0.00 40.67 4.02
167 169 3.477210 GGGATCACCTAGGACACATTC 57.523 52.381 17.98 3.29 35.85 2.67
168 170 2.771943 GGGATCACCTAGGACACATTCA 59.228 50.000 17.98 0.00 35.85 2.57
169 171 3.199946 GGGATCACCTAGGACACATTCAA 59.800 47.826 17.98 0.00 35.85 2.69
170 172 4.141390 GGGATCACCTAGGACACATTCAAT 60.141 45.833 17.98 0.00 35.85 2.57
171 173 4.818546 GGATCACCTAGGACACATTCAATG 59.181 45.833 17.98 0.00 0.00 2.82
172 174 5.396772 GGATCACCTAGGACACATTCAATGA 60.397 44.000 17.98 4.72 0.00 2.57
173 175 5.089970 TCACCTAGGACACATTCAATGAG 57.910 43.478 17.98 0.00 0.00 2.90
174 176 4.777366 TCACCTAGGACACATTCAATGAGA 59.223 41.667 17.98 0.00 0.00 3.27
175 177 5.248248 TCACCTAGGACACATTCAATGAGAA 59.752 40.000 17.98 0.00 41.28 2.87
177 179 6.600822 CACCTAGGACACATTCAATGAGAATT 59.399 38.462 17.98 0.00 44.48 2.17
178 180 7.121759 CACCTAGGACACATTCAATGAGAATTT 59.878 37.037 17.98 0.00 44.48 1.82
179 181 7.671398 ACCTAGGACACATTCAATGAGAATTTT 59.329 33.333 17.98 0.00 44.48 1.82
180 182 8.186821 CCTAGGACACATTCAATGAGAATTTTC 58.813 37.037 1.05 0.00 44.48 2.29
181 183 7.771927 AGGACACATTCAATGAGAATTTTCT 57.228 32.000 3.79 0.00 44.48 2.52
182 184 8.868522 AGGACACATTCAATGAGAATTTTCTA 57.131 30.769 3.79 0.00 44.48 2.10
183 185 8.954350 AGGACACATTCAATGAGAATTTTCTAG 58.046 33.333 3.79 0.00 44.48 2.43
184 186 8.950210 GGACACATTCAATGAGAATTTTCTAGA 58.050 33.333 3.79 0.00 44.48 2.43
215 217 2.770164 ACTAGCTAGTGTTGGCCAAG 57.230 50.000 25.52 7.88 34.72 3.61
216 218 2.257207 ACTAGCTAGTGTTGGCCAAGA 58.743 47.619 25.52 16.53 34.72 3.02
219 221 1.630369 AGCTAGTGTTGGCCAAGATCA 59.370 47.619 21.21 11.18 0.00 2.92
220 222 1.740025 GCTAGTGTTGGCCAAGATCAC 59.260 52.381 21.21 22.66 0.00 3.06
221 223 2.616510 GCTAGTGTTGGCCAAGATCACT 60.617 50.000 31.36 31.36 41.32 3.41
222 224 1.901591 AGTGTTGGCCAAGATCACTG 58.098 50.000 29.55 0.00 37.85 3.66
223 225 0.883833 GTGTTGGCCAAGATCACTGG 59.116 55.000 21.21 9.06 0.00 4.00
224 226 0.770499 TGTTGGCCAAGATCACTGGA 59.230 50.000 21.21 0.00 0.00 3.86
225 227 1.144708 TGTTGGCCAAGATCACTGGAA 59.855 47.619 21.21 0.00 0.00 3.53
226 228 2.238521 GTTGGCCAAGATCACTGGAAA 58.761 47.619 21.21 7.80 0.00 3.13
227 229 2.205022 TGGCCAAGATCACTGGAAAG 57.795 50.000 16.06 0.00 0.00 2.62
228 230 0.813821 GGCCAAGATCACTGGAAAGC 59.186 55.000 16.06 2.62 0.00 3.51
229 231 0.449388 GCCAAGATCACTGGAAAGCG 59.551 55.000 16.06 0.00 0.00 4.68
230 232 1.813513 CCAAGATCACTGGAAAGCGT 58.186 50.000 7.90 0.00 0.00 5.07
231 233 2.154462 CCAAGATCACTGGAAAGCGTT 58.846 47.619 7.90 0.00 0.00 4.84
232 234 2.554032 CCAAGATCACTGGAAAGCGTTT 59.446 45.455 7.90 0.00 0.00 3.60
233 235 3.558505 CAAGATCACTGGAAAGCGTTTG 58.441 45.455 0.00 0.00 0.00 2.93
234 236 2.851195 AGATCACTGGAAAGCGTTTGT 58.149 42.857 0.00 0.00 0.00 2.83
235 237 2.808543 AGATCACTGGAAAGCGTTTGTC 59.191 45.455 0.00 0.00 0.00 3.18
236 238 2.325583 TCACTGGAAAGCGTTTGTCT 57.674 45.000 0.00 0.00 0.00 3.41
237 239 1.939934 TCACTGGAAAGCGTTTGTCTG 59.060 47.619 0.00 0.00 0.00 3.51
238 240 1.939934 CACTGGAAAGCGTTTGTCTGA 59.060 47.619 0.00 0.00 0.00 3.27
239 241 2.354510 CACTGGAAAGCGTTTGTCTGAA 59.645 45.455 0.00 0.00 0.00 3.02
240 242 3.013921 ACTGGAAAGCGTTTGTCTGAAA 58.986 40.909 0.00 0.00 0.00 2.69
241 243 3.632145 ACTGGAAAGCGTTTGTCTGAAAT 59.368 39.130 0.00 0.00 0.00 2.17
242 244 4.097892 ACTGGAAAGCGTTTGTCTGAAATT 59.902 37.500 0.00 0.00 0.00 1.82
243 245 4.358851 TGGAAAGCGTTTGTCTGAAATTG 58.641 39.130 0.00 0.00 0.00 2.32
249 251 4.037923 AGCGTTTGTCTGAAATTGGTTGAT 59.962 37.500 0.00 0.00 0.00 2.57
261 263 1.255882 TGGTTGATCCCACATGCAAC 58.744 50.000 0.00 0.00 39.76 4.17
266 268 2.710377 TGATCCCACATGCAACAGTAC 58.290 47.619 0.00 0.00 0.00 2.73
287 289 5.861222 ACTTTCTGGTTTGTTTGCTTTTG 57.139 34.783 0.00 0.00 0.00 2.44
299 301 5.397326 TGTTTGCTTTTGTTTTGGATTTGC 58.603 33.333 0.00 0.00 0.00 3.68
323 325 9.723601 TGCACATACTTTGCTATATATCAATGA 57.276 29.630 15.31 0.00 40.86 2.57
351 353 3.334881 ACTTCCTTTCCACCATTCCATCT 59.665 43.478 0.00 0.00 0.00 2.90
388 390 4.412796 TTCTCATGTCCATGATCACTCC 57.587 45.455 10.22 0.00 45.74 3.85
403 405 2.584965 TCACTCCTCTTCATCTCCTCCT 59.415 50.000 0.00 0.00 0.00 3.69
404 406 3.012274 TCACTCCTCTTCATCTCCTCCTT 59.988 47.826 0.00 0.00 0.00 3.36
408 410 4.541705 TCCTCTTCATCTCCTCCTTAGTG 58.458 47.826 0.00 0.00 0.00 2.74
430 432 3.305744 GCTCAGTATCGATCTTTCTCCCC 60.306 52.174 0.00 0.00 0.00 4.81
450 452 4.141181 CCCCACTCAATCTCATCCCAATTA 60.141 45.833 0.00 0.00 0.00 1.40
524 528 4.282703 TCCGTTGGCTATACTTCTATTCCC 59.717 45.833 0.00 0.00 0.00 3.97
525 529 4.283722 CCGTTGGCTATACTTCTATTCCCT 59.716 45.833 0.00 0.00 0.00 4.20
537 541 1.760613 CTATTCCCTAGCACCGGTGAA 59.239 52.381 38.30 21.78 0.00 3.18
544 548 1.195442 TAGCACCGGTGAATGACCCA 61.195 55.000 38.30 5.12 42.62 4.51
572 576 3.920231 ATCGAACCTTAACCTAACCCC 57.080 47.619 0.00 0.00 0.00 4.95
592 596 3.006537 CCCATATATCTTCACCCGTCGTT 59.993 47.826 0.00 0.00 0.00 3.85
622 626 0.809385 TGTTCGTCGCTAGAGAAGGG 59.191 55.000 9.31 0.00 39.48 3.95
628 632 2.359531 CGTCGCTAGAGAAGGGAGAAAT 59.640 50.000 0.00 0.00 46.85 2.17
633 637 3.198853 GCTAGAGAAGGGAGAAATGTGGT 59.801 47.826 0.00 0.00 0.00 4.16
739 1016 4.392047 ACACAGTGAATCAAGCATGAGAA 58.608 39.130 7.81 0.00 39.39 2.87
787 1101 9.965824 AAATCTAACAGTTTTCCACTACAAATG 57.034 29.630 0.00 0.00 32.76 2.32
801 1115 6.231211 CACTACAAATGTGGGTCTAAGACTT 58.769 40.000 1.94 0.00 32.47 3.01
802 1116 6.369065 CACTACAAATGTGGGTCTAAGACTTC 59.631 42.308 1.94 0.00 32.47 3.01
845 1159 7.558161 AGAAAAAGAAAAAGGGCAATGAAAG 57.442 32.000 0.00 0.00 0.00 2.62
895 1209 1.720694 CTCGCTCCCGTTCTCTCCTC 61.721 65.000 0.00 0.00 35.54 3.71
896 1210 2.802106 GCTCCCGTTCTCTCCTCG 59.198 66.667 0.00 0.00 0.00 4.63
897 1211 1.749638 GCTCCCGTTCTCTCCTCGA 60.750 63.158 0.00 0.00 0.00 4.04
898 1212 1.104577 GCTCCCGTTCTCTCCTCGAT 61.105 60.000 0.00 0.00 0.00 3.59
902 1216 0.584396 CCGTTCTCTCCTCGATCTCG 59.416 60.000 0.00 0.00 41.45 4.04
959 1273 4.382040 CGACAATGGTCTACACAATCTCCT 60.382 45.833 0.00 0.00 42.05 3.69
1249 1563 3.349006 GATATGGCGGCGGCAGTG 61.349 66.667 37.95 0.00 42.43 3.66
1578 1892 1.152984 CTATGGCAATGGGGACGCA 60.153 57.895 0.00 0.00 0.00 5.24
2030 2347 4.898002 GATGCTCTGTGACAGCGA 57.102 55.556 7.93 0.00 40.01 4.93
2119 2436 4.131088 GGGCGTCGACCTCTCACC 62.131 72.222 10.81 2.08 0.00 4.02
2120 2437 3.371063 GGCGTCGACCTCTCACCA 61.371 66.667 10.58 0.00 0.00 4.17
2121 2438 2.126424 GCGTCGACCTCTCACCAC 60.126 66.667 10.58 0.00 0.00 4.16
2122 2439 2.916052 GCGTCGACCTCTCACCACA 61.916 63.158 10.58 0.00 0.00 4.17
2123 2440 1.883732 CGTCGACCTCTCACCACAT 59.116 57.895 10.58 0.00 0.00 3.21
2204 2521 3.664223 GACTCGTGGTCCTCGTCGC 62.664 68.421 12.76 0.79 38.93 5.19
2302 2619 4.147449 CCGAGCCGATGACAGCCA 62.147 66.667 0.00 0.00 0.00 4.75
2886 3209 3.649277 CTGGTCCGCCAAGGTCTCG 62.649 68.421 0.00 0.00 45.51 4.04
3336 3704 4.554036 GAGCACGAGGATGGCCCC 62.554 72.222 0.00 0.00 34.66 5.80
3435 3829 1.001641 CCTCCCTGGTGGCAAGAAG 60.002 63.158 0.00 0.00 0.00 2.85
3471 3865 8.027440 TCTTGAGGATTTTGTTTGTTTGTTTG 57.973 30.769 0.00 0.00 0.00 2.93
3533 3929 3.255395 TGACATACTGTGTTGGGCAAATG 59.745 43.478 0.00 0.00 42.36 2.32
3534 3930 3.495331 ACATACTGTGTTGGGCAAATGA 58.505 40.909 0.00 0.00 38.01 2.57
3535 3931 3.894427 ACATACTGTGTTGGGCAAATGAA 59.106 39.130 0.00 0.00 38.01 2.57
3571 3967 9.475620 TGTAGAGTAGATCATTTAGTGAAAGGA 57.524 33.333 0.00 0.00 40.97 3.36
3572 3968 9.738832 GTAGAGTAGATCATTTAGTGAAAGGAC 57.261 37.037 0.00 0.00 38.12 3.85
3597 3993 5.469760 ACATTTTTGCTTTGCCTAATTGGAC 59.530 36.000 0.00 0.00 38.35 4.02
3677 4074 4.701651 TGGAGCTCCAAGTGTTATTGAATG 59.298 41.667 33.41 0.00 44.35 2.67
3682 4079 5.449177 GCTCCAAGTGTTATTGAATGGCTAC 60.449 44.000 0.00 0.00 31.55 3.58
3684 4081 6.186957 TCCAAGTGTTATTGAATGGCTACAT 58.813 36.000 0.00 0.00 39.54 2.29
3688 4085 5.945784 AGTGTTATTGAATGGCTACATGTGT 59.054 36.000 9.11 0.00 37.40 3.72
3693 4090 4.898829 TGAATGGCTACATGTGTAATGC 57.101 40.909 9.11 4.97 37.40 3.56
3695 4092 1.662517 TGGCTACATGTGTAATGCCG 58.337 50.000 9.11 0.00 41.85 5.69
3703 4100 1.225908 GTGTAATGCCGGCGTTTCG 60.226 57.895 36.97 0.00 0.00 3.46
3712 4109 4.430765 GGCGTTTCGGAGCTCGGA 62.431 66.667 19.12 19.12 39.77 4.55
3713 4110 2.202756 GCGTTTCGGAGCTCGGAT 60.203 61.111 22.92 0.00 39.77 4.18
3719 4116 1.395045 TTCGGAGCTCGGATGCATCT 61.395 55.000 25.28 5.84 39.77 2.90
3721 4118 1.960250 GGAGCTCGGATGCATCTGC 60.960 63.158 27.68 24.74 42.50 4.26
3788 4200 6.603237 TCTGAAATTTGTACGCATCATAGG 57.397 37.500 0.00 0.00 0.00 2.57
3789 4201 6.345298 TCTGAAATTTGTACGCATCATAGGA 58.655 36.000 0.00 0.00 0.00 2.94
3790 4202 6.479990 TCTGAAATTTGTACGCATCATAGGAG 59.520 38.462 0.00 0.00 0.00 3.69
3791 4203 5.527214 TGAAATTTGTACGCATCATAGGAGG 59.473 40.000 0.00 0.00 0.00 4.30
3804 4216 3.134804 TCATAGGAGGCTCTTTTAGGTGC 59.865 47.826 15.23 0.00 0.00 5.01
3833 4245 3.056250 AGCTTCACGTTGAGATGACATCT 60.056 43.478 17.98 17.98 43.70 2.90
3837 4249 3.758554 TCACGTTGAGATGACATCTGAGA 59.241 43.478 22.64 9.21 40.38 3.27
3840 4252 4.460731 ACGTTGAGATGACATCTGAGAAGA 59.539 41.667 22.64 0.00 40.38 2.87
3842 4254 6.041511 CGTTGAGATGACATCTGAGAAGATT 58.958 40.000 22.64 0.00 40.38 2.40
3867 4279 2.863401 AAAAACAAAGCTCGGGTGTC 57.137 45.000 0.00 0.00 0.00 3.67
3868 4280 0.661020 AAAACAAAGCTCGGGTGTCG 59.339 50.000 0.00 0.00 40.90 4.35
3869 4281 1.164041 AAACAAAGCTCGGGTGTCGG 61.164 55.000 0.00 0.00 39.77 4.79
3871 4283 1.597027 CAAAGCTCGGGTGTCGGTT 60.597 57.895 0.00 0.00 39.77 4.44
3872 4284 0.320073 CAAAGCTCGGGTGTCGGTTA 60.320 55.000 0.00 0.00 39.77 2.85
3873 4285 0.037605 AAAGCTCGGGTGTCGGTTAG 60.038 55.000 0.00 0.00 39.77 2.34
3874 4286 1.183676 AAGCTCGGGTGTCGGTTAGT 61.184 55.000 0.00 0.00 39.77 2.24
3875 4287 1.183676 AGCTCGGGTGTCGGTTAGTT 61.184 55.000 0.00 0.00 39.77 2.24
3876 4288 1.012486 GCTCGGGTGTCGGTTAGTTG 61.012 60.000 0.00 0.00 39.77 3.16
3877 4289 0.389426 CTCGGGTGTCGGTTAGTTGG 60.389 60.000 0.00 0.00 39.77 3.77
3878 4290 0.827089 TCGGGTGTCGGTTAGTTGGA 60.827 55.000 0.00 0.00 39.77 3.53
3881 4398 2.353323 GGGTGTCGGTTAGTTGGATTC 58.647 52.381 0.00 0.00 0.00 2.52
3889 4406 3.119990 CGGTTAGTTGGATTCGCAATGTT 60.120 43.478 0.00 0.00 0.00 2.71
3890 4407 4.165779 GGTTAGTTGGATTCGCAATGTTG 58.834 43.478 0.00 0.00 0.00 3.33
3898 4415 4.037327 TGGATTCGCAATGTTGAAACTGAA 59.963 37.500 0.00 0.00 0.00 3.02
3907 4424 7.689812 CGCAATGTTGAAACTGAATAAGTAGAG 59.310 37.037 0.00 0.00 38.56 2.43
3912 4429 9.778741 TGTTGAAACTGAATAAGTAGAGAACAT 57.221 29.630 0.00 0.00 38.56 2.71
3914 4431 8.256611 TGAAACTGAATAAGTAGAGAACATGC 57.743 34.615 0.00 0.00 38.56 4.06
3916 4433 5.352284 ACTGAATAAGTAGAGAACATGCCG 58.648 41.667 0.00 0.00 37.36 5.69
3918 4435 4.161565 TGAATAAGTAGAGAACATGCCGGT 59.838 41.667 1.90 0.00 0.00 5.28
3920 4437 2.674796 AGTAGAGAACATGCCGGTTC 57.325 50.000 1.90 8.99 45.87 3.62
3927 4473 2.632512 AGAACATGCCGGTTCCAAATTT 59.367 40.909 1.90 0.00 46.52 1.82
3944 4490 5.509840 CCAAATTTCATTTTGACGGTGGGTA 60.510 40.000 0.00 0.00 38.58 3.69
3945 4491 4.776795 ATTTCATTTTGACGGTGGGTAC 57.223 40.909 0.00 0.00 0.00 3.34
3955 4501 0.528924 CGGTGGGTACGTTCTCATCA 59.471 55.000 6.12 0.00 0.00 3.07
4000 4546 9.691362 GCACCTTAAACTCATATCAAAAGAAAA 57.309 29.630 0.00 0.00 0.00 2.29
4020 6617 7.547227 AGAAAACTACCAACCATTCATTATGC 58.453 34.615 0.00 0.00 32.60 3.14
4024 6621 2.951642 ACCAACCATTCATTATGCGAGG 59.048 45.455 0.00 0.00 32.60 4.63
4060 6657 1.073199 AGGCCTGCAACCAGTACAC 59.927 57.895 3.11 0.00 37.38 2.90
4088 7102 7.554118 TGTAAGTAGTACGCTATCCTACACTTT 59.446 37.037 0.00 0.00 35.23 2.66
4120 7134 1.068741 CCTGGTGCGATTCTAGTACCC 59.931 57.143 1.32 0.00 42.57 3.69
4213 7230 1.297012 CAGCGCGTCTCTCTCGTAC 60.297 63.158 8.43 0.00 0.00 3.67
4214 7231 1.448189 AGCGCGTCTCTCTCGTACT 60.448 57.895 8.43 0.00 0.00 2.73
4215 7232 1.297012 GCGCGTCTCTCTCGTACTG 60.297 63.158 8.43 0.00 0.00 2.74
4216 7233 1.297012 CGCGTCTCTCTCGTACTGC 60.297 63.158 0.00 0.00 0.00 4.40
4217 7234 1.697772 CGCGTCTCTCTCGTACTGCT 61.698 60.000 0.00 0.00 0.00 4.24
4218 7235 1.288350 GCGTCTCTCTCGTACTGCTA 58.712 55.000 0.00 0.00 0.00 3.49
4219 7236 1.004715 GCGTCTCTCTCGTACTGCTAC 60.005 57.143 0.00 0.00 0.00 3.58
4230 7247 9.241919 TCTCTCGTACTGCTACTACTATACTAT 57.758 37.037 0.00 0.00 0.00 2.12
4285 7302 0.869068 TTGTACCAACCGTGCATTCG 59.131 50.000 0.00 0.00 36.91 3.34
4286 7303 1.133869 GTACCAACCGTGCATTCGC 59.866 57.895 0.00 0.00 39.24 4.70
4302 7319 2.249535 CGCATTCCCTCGCCATCTG 61.250 63.158 0.00 0.00 0.00 2.90
4303 7320 1.146930 GCATTCCCTCGCCATCTGA 59.853 57.895 0.00 0.00 0.00 3.27
4304 7321 0.464373 GCATTCCCTCGCCATCTGAA 60.464 55.000 0.00 0.00 0.00 3.02
4306 7323 1.134280 CATTCCCTCGCCATCTGAACT 60.134 52.381 0.00 0.00 0.00 3.01
4307 7324 0.537188 TTCCCTCGCCATCTGAACTC 59.463 55.000 0.00 0.00 0.00 3.01
4308 7325 1.144936 CCCTCGCCATCTGAACTCC 59.855 63.158 0.00 0.00 0.00 3.85
4309 7326 1.333636 CCCTCGCCATCTGAACTCCT 61.334 60.000 0.00 0.00 0.00 3.69
4310 7327 0.103937 CCTCGCCATCTGAACTCCTC 59.896 60.000 0.00 0.00 0.00 3.71
4311 7328 0.248825 CTCGCCATCTGAACTCCTCG 60.249 60.000 0.00 0.00 0.00 4.63
4323 7340 0.543174 ACTCCTCGGCAAACTCCTCT 60.543 55.000 0.00 0.00 0.00 3.69
4352 7369 9.750125 GTTTCCATTCCATACCATTATTTTCTC 57.250 33.333 0.00 0.00 0.00 2.87
4368 7385 0.172803 TCTCTCTTTTAGGCGGCGAC 59.827 55.000 12.98 8.50 0.00 5.19
4369 7386 0.108804 CTCTCTTTTAGGCGGCGACA 60.109 55.000 18.30 0.00 0.00 4.35
4375 7392 3.583276 TTAGGCGGCGACACACCAG 62.583 63.158 18.30 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 6.528321 AGACATCCATATCACACTACCATTG 58.472 40.000 0.00 0.00 0.00 2.82
65 67 5.536538 GGACTAGTGAGACATCCATATCACA 59.463 44.000 0.00 0.00 43.55 3.58
69 71 7.531317 AGTTAGGACTAGTGAGACATCCATAT 58.469 38.462 0.00 0.00 33.32 1.78
71 73 5.772004 AGTTAGGACTAGTGAGACATCCAT 58.228 41.667 0.00 0.00 33.32 3.41
76 78 4.931027 AGGAGTTAGGACTAGTGAGACA 57.069 45.455 0.00 0.00 35.88 3.41
81 83 7.706100 AAAGACTTAGGAGTTAGGACTAGTG 57.294 40.000 0.00 0.00 35.88 2.74
82 84 7.729431 ACAAAAGACTTAGGAGTTAGGACTAGT 59.271 37.037 0.00 0.00 35.88 2.57
95 97 8.188139 ACATGTTAACAACACAAAAGACTTAGG 58.812 33.333 13.23 0.00 45.50 2.69
103 105 9.809096 ATCACATAACATGTTAACAACACAAAA 57.191 25.926 21.57 0.00 45.50 2.44
133 135 6.426646 AGGTGATCCCTTAGCTTTAGTATG 57.573 41.667 0.00 0.00 42.73 2.39
136 138 4.902448 CCTAGGTGATCCCTTAGCTTTAGT 59.098 45.833 0.00 0.00 42.73 2.24
137 139 5.011227 GTCCTAGGTGATCCCTTAGCTTTAG 59.989 48.000 9.08 0.00 42.73 1.85
138 140 4.900054 GTCCTAGGTGATCCCTTAGCTTTA 59.100 45.833 9.08 0.00 42.73 1.85
139 141 3.712218 GTCCTAGGTGATCCCTTAGCTTT 59.288 47.826 9.08 0.00 42.73 3.51
140 142 3.310193 GTCCTAGGTGATCCCTTAGCTT 58.690 50.000 9.08 0.00 42.73 3.74
141 143 2.247635 TGTCCTAGGTGATCCCTTAGCT 59.752 50.000 9.08 0.00 42.73 3.32
142 144 2.365941 GTGTCCTAGGTGATCCCTTAGC 59.634 54.545 9.08 0.00 42.73 3.09
143 145 3.643237 TGTGTCCTAGGTGATCCCTTAG 58.357 50.000 9.08 0.00 42.73 2.18
144 146 3.769189 TGTGTCCTAGGTGATCCCTTA 57.231 47.619 9.08 0.00 42.73 2.69
145 147 2.642171 TGTGTCCTAGGTGATCCCTT 57.358 50.000 9.08 0.00 42.73 3.95
147 149 2.771943 TGAATGTGTCCTAGGTGATCCC 59.228 50.000 9.08 0.00 0.00 3.85
148 150 4.487714 TTGAATGTGTCCTAGGTGATCC 57.512 45.455 9.08 0.00 0.00 3.36
149 151 5.674525 TCATTGAATGTGTCCTAGGTGATC 58.325 41.667 9.08 1.22 0.00 2.92
150 152 5.426509 TCTCATTGAATGTGTCCTAGGTGAT 59.573 40.000 9.08 0.00 0.00 3.06
151 153 4.777366 TCTCATTGAATGTGTCCTAGGTGA 59.223 41.667 9.08 0.00 0.00 4.02
152 154 5.089970 TCTCATTGAATGTGTCCTAGGTG 57.910 43.478 9.08 0.00 0.00 4.00
153 155 5.762179 TTCTCATTGAATGTGTCCTAGGT 57.238 39.130 9.08 0.00 0.00 3.08
154 156 7.636150 AAATTCTCATTGAATGTGTCCTAGG 57.364 36.000 0.82 0.82 43.99 3.02
155 157 8.954350 AGAAAATTCTCATTGAATGTGTCCTAG 58.046 33.333 4.93 0.00 43.99 3.02
156 158 8.868522 AGAAAATTCTCATTGAATGTGTCCTA 57.131 30.769 4.93 0.00 43.99 2.94
157 159 7.771927 AGAAAATTCTCATTGAATGTGTCCT 57.228 32.000 4.93 0.00 43.99 3.85
158 160 8.950210 TCTAGAAAATTCTCATTGAATGTGTCC 58.050 33.333 4.93 0.00 43.99 4.02
165 167 9.435688 TCACGATTCTAGAAAATTCTCATTGAA 57.564 29.630 9.71 2.12 38.70 2.69
166 168 9.605275 ATCACGATTCTAGAAAATTCTCATTGA 57.395 29.630 9.71 7.77 38.70 2.57
167 169 9.861138 GATCACGATTCTAGAAAATTCTCATTG 57.139 33.333 9.71 2.89 38.70 2.82
168 170 9.829507 AGATCACGATTCTAGAAAATTCTCATT 57.170 29.630 9.71 0.00 38.70 2.57
175 177 9.685828 GCTAGTTAGATCACGATTCTAGAAAAT 57.314 33.333 9.71 0.00 0.00 1.82
176 178 8.904834 AGCTAGTTAGATCACGATTCTAGAAAA 58.095 33.333 9.71 0.00 0.00 2.29
177 179 8.453238 AGCTAGTTAGATCACGATTCTAGAAA 57.547 34.615 9.71 0.00 0.00 2.52
178 180 9.210329 CTAGCTAGTTAGATCACGATTCTAGAA 57.790 37.037 12.92 7.82 0.00 2.10
179 181 8.369424 ACTAGCTAGTTAGATCACGATTCTAGA 58.631 37.037 20.95 0.00 31.13 2.43
180 182 8.440059 CACTAGCTAGTTAGATCACGATTCTAG 58.560 40.741 23.94 2.78 33.46 2.43
181 183 7.932491 ACACTAGCTAGTTAGATCACGATTCTA 59.068 37.037 23.94 0.00 33.46 2.10
182 184 6.768861 ACACTAGCTAGTTAGATCACGATTCT 59.231 38.462 23.94 0.00 33.46 2.40
183 185 6.961576 ACACTAGCTAGTTAGATCACGATTC 58.038 40.000 23.94 0.00 33.46 2.52
184 186 6.945938 ACACTAGCTAGTTAGATCACGATT 57.054 37.500 23.94 0.00 33.46 3.34
185 187 6.238786 CCAACACTAGCTAGTTAGATCACGAT 60.239 42.308 23.94 2.29 33.46 3.73
186 188 5.066117 CCAACACTAGCTAGTTAGATCACGA 59.934 44.000 23.94 0.00 33.46 4.35
187 189 5.274718 CCAACACTAGCTAGTTAGATCACG 58.725 45.833 23.94 12.25 33.46 4.35
190 192 4.099573 TGGCCAACACTAGCTAGTTAGATC 59.900 45.833 23.94 12.56 33.46 2.75
200 202 1.740025 GTGATCTTGGCCAACACTAGC 59.260 52.381 23.62 10.81 0.00 3.42
215 217 2.808543 AGACAAACGCTTTCCAGTGATC 59.191 45.455 0.00 0.00 34.31 2.92
216 218 2.549754 CAGACAAACGCTTTCCAGTGAT 59.450 45.455 0.00 0.00 34.31 3.06
219 221 2.325583 TCAGACAAACGCTTTCCAGT 57.674 45.000 0.00 0.00 0.00 4.00
220 222 3.691049 TTTCAGACAAACGCTTTCCAG 57.309 42.857 0.00 0.00 0.00 3.86
221 223 4.358851 CAATTTCAGACAAACGCTTTCCA 58.641 39.130 0.00 0.00 0.00 3.53
222 224 3.735746 CCAATTTCAGACAAACGCTTTCC 59.264 43.478 0.00 0.00 0.00 3.13
223 225 4.359706 ACCAATTTCAGACAAACGCTTTC 58.640 39.130 0.00 0.00 0.00 2.62
224 226 4.385358 ACCAATTTCAGACAAACGCTTT 57.615 36.364 0.00 0.00 0.00 3.51
225 227 4.111916 CAACCAATTTCAGACAAACGCTT 58.888 39.130 0.00 0.00 0.00 4.68
226 228 3.380004 TCAACCAATTTCAGACAAACGCT 59.620 39.130 0.00 0.00 0.00 5.07
227 229 3.701241 TCAACCAATTTCAGACAAACGC 58.299 40.909 0.00 0.00 0.00 4.84
228 230 4.917415 GGATCAACCAATTTCAGACAAACG 59.083 41.667 0.00 0.00 38.79 3.60
229 231 5.221422 TGGGATCAACCAATTTCAGACAAAC 60.221 40.000 0.00 0.00 41.20 2.93
230 232 4.898265 TGGGATCAACCAATTTCAGACAAA 59.102 37.500 0.00 0.00 41.20 2.83
231 233 4.280677 GTGGGATCAACCAATTTCAGACAA 59.719 41.667 0.00 0.00 43.34 3.18
232 234 3.826157 GTGGGATCAACCAATTTCAGACA 59.174 43.478 0.00 0.00 43.34 3.41
233 235 3.826157 TGTGGGATCAACCAATTTCAGAC 59.174 43.478 0.00 0.00 43.34 3.51
234 236 4.111255 TGTGGGATCAACCAATTTCAGA 57.889 40.909 0.00 0.00 43.34 3.27
235 237 4.751060 CATGTGGGATCAACCAATTTCAG 58.249 43.478 0.00 0.00 43.34 3.02
236 238 3.055963 GCATGTGGGATCAACCAATTTCA 60.056 43.478 0.00 0.00 43.34 2.69
237 239 3.055963 TGCATGTGGGATCAACCAATTTC 60.056 43.478 0.00 0.00 43.34 2.17
238 240 2.905085 TGCATGTGGGATCAACCAATTT 59.095 40.909 0.00 0.00 43.34 1.82
239 241 2.538222 TGCATGTGGGATCAACCAATT 58.462 42.857 0.00 0.00 43.34 2.32
240 242 2.234414 GTTGCATGTGGGATCAACCAAT 59.766 45.455 0.00 0.00 43.34 3.16
241 243 1.617850 GTTGCATGTGGGATCAACCAA 59.382 47.619 0.00 0.00 43.34 3.67
242 244 1.255882 GTTGCATGTGGGATCAACCA 58.744 50.000 0.00 0.00 41.20 3.67
243 245 1.203052 CTGTTGCATGTGGGATCAACC 59.797 52.381 8.53 0.00 38.32 3.77
249 251 2.949177 AAGTACTGTTGCATGTGGGA 57.051 45.000 0.00 0.00 0.00 4.37
261 263 5.248870 AGCAAACAAACCAGAAAGTACTG 57.751 39.130 0.00 0.00 37.61 2.74
266 268 5.861222 ACAAAAGCAAACAAACCAGAAAG 57.139 34.783 0.00 0.00 0.00 2.62
351 353 5.105351 ACATGAGAATGTGATCGGTTAGACA 60.105 40.000 0.00 0.00 32.79 3.41
388 390 3.960102 AGCACTAAGGAGGAGATGAAGAG 59.040 47.826 0.00 0.00 0.00 2.85
403 405 6.238786 GGAGAAAGATCGATACTGAGCACTAA 60.239 42.308 0.00 0.00 0.00 2.24
404 406 5.239744 GGAGAAAGATCGATACTGAGCACTA 59.760 44.000 0.00 0.00 0.00 2.74
408 410 3.305744 GGGGAGAAAGATCGATACTGAGC 60.306 52.174 0.00 0.00 0.00 4.26
430 432 6.604795 ACCTTTAATTGGGATGAGATTGAGTG 59.395 38.462 0.00 0.00 0.00 3.51
450 452 3.171528 GGGTGACACCTAGAGTACCTTT 58.828 50.000 23.72 0.00 38.64 3.11
524 528 3.065575 GGTCATTCACCGGTGCTAG 57.934 57.895 30.25 19.92 34.56 3.42
572 576 4.680110 GTCAACGACGGGTGAAGATATATG 59.320 45.833 0.00 0.00 0.00 1.78
604 608 1.064357 CTCCCTTCTCTAGCGACGAAC 59.936 57.143 0.00 0.00 0.00 3.95
608 612 3.131400 ACATTTCTCCCTTCTCTAGCGAC 59.869 47.826 0.00 0.00 0.00 5.19
622 626 8.447053 GTTATTTCTTCTCAGACCACATTTCTC 58.553 37.037 0.00 0.00 0.00 2.87
716 993 5.151297 TCTCATGCTTGATTCACTGTGTA 57.849 39.130 7.79 0.00 0.00 2.90
746 1023 0.249955 GATTTTGGGGTGCATGTGGG 59.750 55.000 0.00 0.00 0.00 4.61
813 1127 8.039603 TGCCCTTTTTCTTTTTCTTTTTCTTC 57.960 30.769 0.00 0.00 0.00 2.87
845 1159 2.889045 GAGGTTTAAAGGTTGGTGTCCC 59.111 50.000 0.00 0.00 0.00 4.46
895 1209 0.941542 GAGACCAGGAGACGAGATCG 59.058 60.000 0.00 0.00 46.33 3.69
896 1210 1.133915 AGGAGACCAGGAGACGAGATC 60.134 57.143 0.00 0.00 0.00 2.75
897 1211 0.923358 AGGAGACCAGGAGACGAGAT 59.077 55.000 0.00 0.00 0.00 2.75
898 1212 0.699399 AAGGAGACCAGGAGACGAGA 59.301 55.000 0.00 0.00 0.00 4.04
902 1216 0.899019 GTGGAAGGAGACCAGGAGAC 59.101 60.000 0.00 0.00 38.14 3.36
959 1273 1.595058 GGAGGAGGAGGAGAAGGGGA 61.595 65.000 0.00 0.00 0.00 4.81
1068 1382 2.042435 AAGGAGGAGGAGGAGGCG 60.042 66.667 0.00 0.00 0.00 5.52
1825 2139 1.373497 CGACGAACTGCTCCTGCTT 60.373 57.895 0.00 0.00 40.48 3.91
1826 2140 2.259818 CGACGAACTGCTCCTGCT 59.740 61.111 0.00 0.00 40.48 4.24
1854 2168 1.903404 GCACACCACCTTCCCCTTG 60.903 63.158 0.00 0.00 0.00 3.61
1856 2170 3.953775 CGCACACCACCTTCCCCT 61.954 66.667 0.00 0.00 0.00 4.79
2119 2436 1.699656 CGCCGCTTCTTCCTCATGTG 61.700 60.000 0.00 0.00 0.00 3.21
2120 2437 1.448540 CGCCGCTTCTTCCTCATGT 60.449 57.895 0.00 0.00 0.00 3.21
2121 2438 2.176273 CCGCCGCTTCTTCCTCATG 61.176 63.158 0.00 0.00 0.00 3.07
2122 2439 2.187946 CCGCCGCTTCTTCCTCAT 59.812 61.111 0.00 0.00 0.00 2.90
2123 2440 4.760047 GCCGCCGCTTCTTCCTCA 62.760 66.667 0.00 0.00 0.00 3.86
2886 3209 3.453679 AGCGAGAGGCCGAAGTCC 61.454 66.667 0.00 0.00 45.17 3.85
3435 3829 3.990959 ATCCTCAAGAAACTCCCTGTC 57.009 47.619 0.00 0.00 0.00 3.51
3517 3913 2.362077 GACTTCATTTGCCCAACACAGT 59.638 45.455 0.00 0.00 0.00 3.55
3523 3919 3.575805 AGGAAAGACTTCATTTGCCCAA 58.424 40.909 0.00 0.00 32.75 4.12
3533 3929 8.057536 TGATCTACTCTACAAGGAAAGACTTC 57.942 38.462 0.00 0.00 0.00 3.01
3534 3930 8.602472 ATGATCTACTCTACAAGGAAAGACTT 57.398 34.615 0.00 0.00 0.00 3.01
3535 3931 8.602472 AATGATCTACTCTACAAGGAAAGACT 57.398 34.615 0.00 0.00 0.00 3.24
3569 3965 2.837498 AGGCAAAGCAAAAATGTGTCC 58.163 42.857 0.00 0.00 0.00 4.02
3570 3966 6.365050 CAATTAGGCAAAGCAAAAATGTGTC 58.635 36.000 0.00 0.00 0.00 3.67
3571 3967 5.239087 CCAATTAGGCAAAGCAAAAATGTGT 59.761 36.000 0.00 0.00 0.00 3.72
3572 3968 5.469421 TCCAATTAGGCAAAGCAAAAATGTG 59.531 36.000 0.00 0.00 37.29 3.21
3597 3993 9.612620 GGAATATATACATTTCTTTTCTTGCCG 57.387 33.333 0.00 0.00 0.00 5.69
3626 4022 6.651975 AGTAGTACTAGCAAAGTCACAACT 57.348 37.500 1.87 0.00 39.80 3.16
3632 4028 9.303537 CTCCAAAATAGTAGTACTAGCAAAGTC 57.696 37.037 15.08 0.00 39.80 3.01
3633 4029 7.764901 GCTCCAAAATAGTAGTACTAGCAAAGT 59.235 37.037 15.08 0.00 42.62 2.66
3634 4030 7.982354 AGCTCCAAAATAGTAGTACTAGCAAAG 59.018 37.037 15.08 8.76 33.66 2.77
3635 4031 7.848128 AGCTCCAAAATAGTAGTACTAGCAAA 58.152 34.615 15.08 0.00 33.66 3.68
3636 4032 7.417570 GGAGCTCCAAAATAGTAGTACTAGCAA 60.418 40.741 28.43 0.00 33.09 3.91
3637 4033 6.040616 GGAGCTCCAAAATAGTAGTACTAGCA 59.959 42.308 28.43 0.00 33.09 3.49
3638 4034 6.040616 TGGAGCTCCAAAATAGTAGTACTAGC 59.959 42.308 33.41 12.31 44.35 3.42
3639 4035 7.584122 TGGAGCTCCAAAATAGTAGTACTAG 57.416 40.000 33.41 3.31 44.35 2.57
3673 4070 3.303990 CGGCATTACACATGTAGCCATTC 60.304 47.826 17.65 1.69 40.09 2.67
3677 4074 0.944386 CCGGCATTACACATGTAGCC 59.056 55.000 0.00 10.76 38.05 3.93
3682 4079 0.170116 AAACGCCGGCATTACACATG 59.830 50.000 28.98 9.11 0.00 3.21
3684 4081 1.870383 GAAACGCCGGCATTACACA 59.130 52.632 28.98 0.00 0.00 3.72
3695 4092 3.718210 ATCCGAGCTCCGAAACGCC 62.718 63.158 8.47 0.00 41.76 5.68
3703 4100 1.960250 GCAGATGCATCCGAGCTCC 60.960 63.158 23.06 0.00 41.59 4.70
3704 4101 3.640231 GCAGATGCATCCGAGCTC 58.360 61.111 23.06 2.73 41.59 4.09
3719 4116 3.324846 AGAATACTGTTCACTCAGGTGCA 59.675 43.478 0.00 0.00 42.72 4.57
3721 4118 6.867662 AAAAGAATACTGTTCACTCAGGTG 57.132 37.500 0.00 0.00 44.23 4.00
3763 4175 8.147704 TCCTATGATGCGTACAAATTTCAGATA 58.852 33.333 0.00 0.00 0.00 1.98
3766 4178 6.293081 CCTCCTATGATGCGTACAAATTTCAG 60.293 42.308 0.00 0.00 0.00 3.02
3767 4179 5.527214 CCTCCTATGATGCGTACAAATTTCA 59.473 40.000 0.00 0.00 0.00 2.69
3768 4180 5.560953 GCCTCCTATGATGCGTACAAATTTC 60.561 44.000 0.00 0.00 0.00 2.17
3769 4181 4.275936 GCCTCCTATGATGCGTACAAATTT 59.724 41.667 0.00 0.00 0.00 1.82
3771 4183 3.071602 AGCCTCCTATGATGCGTACAAAT 59.928 43.478 0.00 0.00 37.23 2.32
3772 4184 2.434336 AGCCTCCTATGATGCGTACAAA 59.566 45.455 0.00 0.00 37.23 2.83
3773 4185 2.035961 GAGCCTCCTATGATGCGTACAA 59.964 50.000 0.00 0.00 37.23 2.41
3774 4186 1.613925 GAGCCTCCTATGATGCGTACA 59.386 52.381 0.00 0.00 37.23 2.90
3775 4187 1.889829 AGAGCCTCCTATGATGCGTAC 59.110 52.381 0.00 0.00 37.23 3.67
3776 4188 2.294449 AGAGCCTCCTATGATGCGTA 57.706 50.000 0.00 0.00 37.23 4.42
3777 4189 1.418334 AAGAGCCTCCTATGATGCGT 58.582 50.000 0.00 0.00 37.23 5.24
3778 4190 2.540265 AAAGAGCCTCCTATGATGCG 57.460 50.000 0.00 0.00 37.23 4.73
3780 4192 5.303971 CACCTAAAAGAGCCTCCTATGATG 58.696 45.833 0.00 0.00 0.00 3.07
3781 4193 4.202409 GCACCTAAAAGAGCCTCCTATGAT 60.202 45.833 0.00 0.00 0.00 2.45
3782 4194 3.134804 GCACCTAAAAGAGCCTCCTATGA 59.865 47.826 0.00 0.00 0.00 2.15
3783 4195 3.135530 AGCACCTAAAAGAGCCTCCTATG 59.864 47.826 0.00 0.00 0.00 2.23
3785 4197 2.834113 AGCACCTAAAAGAGCCTCCTA 58.166 47.619 0.00 0.00 0.00 2.94
3786 4198 1.662686 AGCACCTAAAAGAGCCTCCT 58.337 50.000 0.00 0.00 0.00 3.69
3787 4199 2.087646 CAAGCACCTAAAAGAGCCTCC 58.912 52.381 0.00 0.00 0.00 4.30
3788 4200 1.470494 GCAAGCACCTAAAAGAGCCTC 59.530 52.381 0.00 0.00 0.00 4.70
3789 4201 1.202927 TGCAAGCACCTAAAAGAGCCT 60.203 47.619 0.00 0.00 0.00 4.58
3790 4202 1.247567 TGCAAGCACCTAAAAGAGCC 58.752 50.000 0.00 0.00 0.00 4.70
3791 4203 3.311966 CTTTGCAAGCACCTAAAAGAGC 58.688 45.455 0.00 0.00 31.01 4.09
3804 4216 2.032054 TCTCAACGTGAAGCTTTGCAAG 59.968 45.455 0.00 0.00 0.00 4.01
3812 4224 3.061831 CAGATGTCATCTCAACGTGAAGC 59.938 47.826 12.62 0.00 37.58 3.86
3813 4225 4.488879 TCAGATGTCATCTCAACGTGAAG 58.511 43.478 12.62 0.00 37.58 3.02
3817 4229 4.460731 TCTTCTCAGATGTCATCTCAACGT 59.539 41.667 12.62 0.00 37.58 3.99
3819 4231 6.258287 CCAATCTTCTCAGATGTCATCTCAAC 59.742 42.308 12.62 0.00 39.00 3.18
3820 4232 6.070366 ACCAATCTTCTCAGATGTCATCTCAA 60.070 38.462 12.62 5.49 39.00 3.02
3821 4233 5.424573 ACCAATCTTCTCAGATGTCATCTCA 59.575 40.000 12.62 0.00 39.00 3.27
3854 4266 0.037605 CTAACCGACACCCGAGCTTT 60.038 55.000 0.00 0.00 41.76 3.51
3856 4268 1.183676 AACTAACCGACACCCGAGCT 61.184 55.000 0.00 0.00 41.76 4.09
3857 4269 1.012486 CAACTAACCGACACCCGAGC 61.012 60.000 0.00 0.00 41.76 5.03
3858 4270 0.389426 CCAACTAACCGACACCCGAG 60.389 60.000 0.00 0.00 41.76 4.63
3859 4271 0.827089 TCCAACTAACCGACACCCGA 60.827 55.000 0.00 0.00 41.76 5.14
3860 4272 0.248289 ATCCAACTAACCGACACCCG 59.752 55.000 0.00 0.00 38.18 5.28
3862 4274 1.997606 CGAATCCAACTAACCGACACC 59.002 52.381 0.00 0.00 0.00 4.16
3863 4275 1.392510 GCGAATCCAACTAACCGACAC 59.607 52.381 0.00 0.00 0.00 3.67
3864 4276 1.001068 TGCGAATCCAACTAACCGACA 59.999 47.619 0.00 0.00 0.00 4.35
3865 4277 1.717194 TGCGAATCCAACTAACCGAC 58.283 50.000 0.00 0.00 0.00 4.79
3866 4278 2.459060 TTGCGAATCCAACTAACCGA 57.541 45.000 0.00 0.00 0.00 4.69
3867 4279 2.418628 ACATTGCGAATCCAACTAACCG 59.581 45.455 0.00 0.00 0.00 4.44
3868 4280 4.083003 TCAACATTGCGAATCCAACTAACC 60.083 41.667 0.00 0.00 0.00 2.85
3869 4281 5.041951 TCAACATTGCGAATCCAACTAAC 57.958 39.130 0.00 0.00 0.00 2.34
3871 4283 5.240623 AGTTTCAACATTGCGAATCCAACTA 59.759 36.000 0.00 0.00 0.00 2.24
3872 4284 4.037923 AGTTTCAACATTGCGAATCCAACT 59.962 37.500 0.00 0.00 0.00 3.16
3873 4285 4.148696 CAGTTTCAACATTGCGAATCCAAC 59.851 41.667 0.00 0.00 0.00 3.77
3874 4286 4.037327 TCAGTTTCAACATTGCGAATCCAA 59.963 37.500 0.00 0.00 0.00 3.53
3875 4287 3.567585 TCAGTTTCAACATTGCGAATCCA 59.432 39.130 0.00 0.00 0.00 3.41
3876 4288 4.159377 TCAGTTTCAACATTGCGAATCC 57.841 40.909 0.00 0.00 0.00 3.01
3877 4289 7.538678 ACTTATTCAGTTTCAACATTGCGAATC 59.461 33.333 0.00 0.00 27.32 2.52
3878 4290 7.370383 ACTTATTCAGTTTCAACATTGCGAAT 58.630 30.769 0.00 0.00 27.32 3.34
3881 4398 7.518161 TCTACTTATTCAGTTTCAACATTGCG 58.482 34.615 0.00 0.00 36.88 4.85
3889 4406 7.334421 GGCATGTTCTCTACTTATTCAGTTTCA 59.666 37.037 0.00 0.00 36.88 2.69
3890 4407 7.464710 CGGCATGTTCTCTACTTATTCAGTTTC 60.465 40.741 0.00 0.00 36.88 2.78
3898 4415 4.443034 GGAACCGGCATGTTCTCTACTTAT 60.443 45.833 0.00 0.00 43.31 1.73
3907 4424 2.741759 AATTTGGAACCGGCATGTTC 57.258 45.000 0.00 8.62 43.10 3.18
3910 4427 2.739885 TGAAATTTGGAACCGGCATG 57.260 45.000 0.00 0.00 0.00 4.06
3912 4429 3.760580 AAATGAAATTTGGAACCGGCA 57.239 38.095 0.00 0.00 46.55 5.69
3927 4473 1.070445 ACGTACCCACCGTCAAAATGA 59.930 47.619 0.00 0.00 31.97 2.57
3944 4490 2.802816 GACTTGCAACTGATGAGAACGT 59.197 45.455 0.00 0.00 0.00 3.99
3945 4491 3.062763 AGACTTGCAACTGATGAGAACG 58.937 45.455 0.00 0.00 0.00 3.95
4000 4546 4.776349 TCGCATAATGAATGGTTGGTAGT 58.224 39.130 0.00 0.00 35.99 2.73
4001 4547 4.214119 CCTCGCATAATGAATGGTTGGTAG 59.786 45.833 0.00 0.00 35.99 3.18
4024 6621 1.067354 CCTGCAACTTCAAGGAATGCC 60.067 52.381 8.95 0.00 36.20 4.40
4051 6648 5.392380 GCGTACTACTTACATGTGTACTGGT 60.392 44.000 9.11 3.29 33.47 4.00
4060 6657 7.172875 AGTGTAGGATAGCGTACTACTTACATG 59.827 40.741 11.66 0.00 43.57 3.21
4088 7102 2.080693 CGCACCAGGTTGCAGTTTATA 58.919 47.619 12.71 0.00 43.15 0.98
4213 7230 7.540299 GCCAAGGAATAGTATAGTAGTAGCAG 58.460 42.308 0.00 0.00 0.00 4.24
4214 7231 6.150641 CGCCAAGGAATAGTATAGTAGTAGCA 59.849 42.308 0.00 0.00 0.00 3.49
4215 7232 6.373774 TCGCCAAGGAATAGTATAGTAGTAGC 59.626 42.308 0.00 0.00 0.00 3.58
4216 7233 7.918536 TCGCCAAGGAATAGTATAGTAGTAG 57.081 40.000 0.00 0.00 0.00 2.57
4217 7234 7.918536 CTCGCCAAGGAATAGTATAGTAGTA 57.081 40.000 0.00 0.00 0.00 1.82
4218 7235 6.821031 CTCGCCAAGGAATAGTATAGTAGT 57.179 41.667 0.00 0.00 0.00 2.73
4285 7302 0.464373 TTCAGATGGCGAGGGAATGC 60.464 55.000 0.00 0.00 0.00 3.56
4286 7303 1.134280 AGTTCAGATGGCGAGGGAATG 60.134 52.381 0.00 0.00 0.00 2.67
4287 7304 1.139853 GAGTTCAGATGGCGAGGGAAT 59.860 52.381 0.00 0.00 0.00 3.01
4288 7305 0.537188 GAGTTCAGATGGCGAGGGAA 59.463 55.000 0.00 0.00 0.00 3.97
4289 7306 1.330655 GGAGTTCAGATGGCGAGGGA 61.331 60.000 0.00 0.00 0.00 4.20
4290 7307 1.144936 GGAGTTCAGATGGCGAGGG 59.855 63.158 0.00 0.00 0.00 4.30
4302 7319 0.321996 AGGAGTTTGCCGAGGAGTTC 59.678 55.000 0.00 0.00 0.00 3.01
4303 7320 0.321996 GAGGAGTTTGCCGAGGAGTT 59.678 55.000 0.00 0.00 0.00 3.01
4304 7321 0.543174 AGAGGAGTTTGCCGAGGAGT 60.543 55.000 0.00 0.00 0.00 3.85
4306 7323 1.258445 GGAGAGGAGTTTGCCGAGGA 61.258 60.000 0.00 0.00 0.00 3.71
4307 7324 1.219393 GGAGAGGAGTTTGCCGAGG 59.781 63.158 0.00 0.00 0.00 4.63
4308 7325 1.153745 CGGAGAGGAGTTTGCCGAG 60.154 63.158 0.00 0.00 44.43 4.63
4309 7326 1.469335 AACGGAGAGGAGTTTGCCGA 61.469 55.000 0.00 0.00 44.43 5.54
4310 7327 0.602905 AAACGGAGAGGAGTTTGCCG 60.603 55.000 0.00 0.00 46.83 5.69
4311 7328 1.157585 GAAACGGAGAGGAGTTTGCC 58.842 55.000 0.00 0.00 40.24 4.52
4323 7340 3.943671 ATGGTATGGAATGGAAACGGA 57.056 42.857 0.00 0.00 0.00 4.69
4352 7369 0.669318 TGTGTCGCCGCCTAAAAGAG 60.669 55.000 0.00 0.00 0.00 2.85
4368 7385 2.094659 CGGCTACTTCGCTGGTGTG 61.095 63.158 0.00 0.00 32.64 3.82
4369 7386 2.261671 CGGCTACTTCGCTGGTGT 59.738 61.111 0.00 0.00 32.64 4.16


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

AutoCloner maintained by Alex Coulton.