Multiple sequence alignment - TraesCS2D01G112300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G112300 chr2D 100.000 2765 0 0 1 2765 62290911 62288147 0.000000e+00 5107.0
1 TraesCS2D01G112300 chr2D 78.010 764 97 43 1061 1768 62553298 62552550 5.510000e-112 414.0
2 TraesCS2D01G112300 chr2D 79.180 317 40 17 1476 1769 62559263 62558950 2.170000e-46 196.0
3 TraesCS2D01G112300 chr2D 76.962 395 56 23 1057 1424 62559800 62559414 2.810000e-45 193.0
4 TraesCS2D01G112300 chr2D 75.064 389 62 24 1055 1415 62565123 62564742 6.170000e-32 148.0
5 TraesCS2D01G112300 chr2D 75.710 317 51 17 1476 1769 62564621 62564308 4.800000e-28 135.0
6 TraesCS2D01G112300 chr2B 91.155 1922 108 30 852 2746 97934072 97932186 0.000000e+00 2551.0
7 TraesCS2D01G112300 chr2B 90.400 375 28 4 382 752 97934479 97934109 1.150000e-133 486.0
8 TraesCS2D01G112300 chr2B 76.645 775 108 49 1055 1769 98264686 98263925 7.280000e-96 361.0
9 TraesCS2D01G112300 chr2B 79.939 329 46 12 1306 1614 98256763 98256435 9.970000e-55 224.0
10 TraesCS2D01G112300 chr2B 86.782 174 14 4 1055 1219 98257055 98256882 4.700000e-43 185.0
11 TraesCS2D01G112300 chr2B 88.060 134 15 1 6 139 97935017 97934885 1.030000e-34 158.0
12 TraesCS2D01G112300 chr2B 77.070 314 44 19 1480 1769 98286301 98285992 3.690000e-34 156.0
13 TraesCS2D01G112300 chr2B 75.128 390 60 28 1055 1415 98286787 98286406 6.170000e-32 148.0
14 TraesCS2D01G112300 chr2A 91.114 1733 100 31 1053 2763 63138197 63136497 0.000000e+00 2298.0
15 TraesCS2D01G112300 chr2A 78.740 762 97 38 1061 1768 63588997 63588247 1.510000e-122 449.0
16 TraesCS2D01G112300 chr2A 84.956 452 35 19 382 819 63138773 63138341 7.080000e-116 427.0
17 TraesCS2D01G112300 chr2A 80.198 303 46 11 1476 1768 63606776 63606478 6.000000e-52 215.0
18 TraesCS2D01G112300 chr2A 77.468 395 56 21 1056 1424 63607261 63606874 3.610000e-49 206.0
19 TraesCS2D01G112300 chr2A 91.791 134 10 1 6 139 63139288 63139156 4.700000e-43 185.0
20 TraesCS2D01G112300 chr1D 94.545 165 9 0 141 305 11799175 11799339 3.530000e-64 255.0
21 TraesCS2D01G112300 chr1A 93.529 170 11 0 136 305 233421511 233421342 1.270000e-63 254.0
22 TraesCS2D01G112300 chrUn 92.135 178 13 1 137 313 382102277 382102454 1.640000e-62 250.0
23 TraesCS2D01G112300 chrUn 89.529 191 18 2 137 326 76787746 76787557 9.900000e-60 241.0
24 TraesCS2D01G112300 chr3A 92.982 171 12 0 135 305 649828303 649828473 1.640000e-62 250.0
25 TraesCS2D01G112300 chr3A 100.000 29 0 0 473 501 616097041 616097013 1.000000e-03 54.7
26 TraesCS2D01G112300 chr7D 92.090 177 13 1 130 305 404245318 404245494 5.910000e-62 248.0
27 TraesCS2D01G112300 chr4D 92.045 176 13 1 136 311 93338211 93338037 2.130000e-61 246.0
28 TraesCS2D01G112300 chr7A 88.945 199 17 5 114 309 115807716 115807520 9.900000e-60 241.0
29 TraesCS2D01G112300 chr6B 89.529 191 16 3 129 319 52217706 52217892 3.560000e-59 239.0
30 TraesCS2D01G112300 chr3B 100.000 31 0 0 471 501 771760017 771759987 1.070000e-04 58.4
31 TraesCS2D01G112300 chr6D 94.118 34 2 0 468 501 470572066 470572099 5.000000e-03 52.8


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 TraesCS2D01G112300 chr2D 62288147 62290911 2764 True 5107.0 5107 100.000000 1 2765 1 chr2D.!!$R1 2764
1 TraesCS2D01G112300 chr2D 62552550 62553298 748 True 414.0 414 78.010000 1061 1768 1 chr2D.!!$R2 707
2 TraesCS2D01G112300 chr2B 97932186 97935017 2831 True 1065.0 2551 89.871667 6 2746 3 chr2B.!!$R2 2740
3 TraesCS2D01G112300 chr2B 98263925 98264686 761 True 361.0 361 76.645000 1055 1769 1 chr2B.!!$R1 714
4 TraesCS2D01G112300 chr2B 98256435 98257055 620 True 204.5 224 83.360500 1055 1614 2 chr2B.!!$R3 559
5 TraesCS2D01G112300 chr2A 63136497 63139288 2791 True 970.0 2298 89.287000 6 2763 3 chr2A.!!$R2 2757
6 TraesCS2D01G112300 chr2A 63588247 63588997 750 True 449.0 449 78.740000 1061 1768 1 chr2A.!!$R1 707
7 TraesCS2D01G112300 chr2A 63606478 63607261 783 True 210.5 215 78.833000 1056 1768 2 chr2A.!!$R3 712

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
877 1255 0.036875 CGGTTTTGGCCCTTCTCTCT 59.963 55.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2732 3292 0.65784 GACTATGACGGCACAATGGC 59.342 55.0 0.0 0.0 39.85 4.4 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
123 124 1.244816 CATGCTGACCCATGCATAGG 58.755 55.000 9.87 9.87 46.65 2.57
124 125 0.538977 ATGCTGACCCATGCATAGGC 60.539 55.000 11.45 2.72 46.53 3.93
148 149 7.020914 CAATAAGTTTTGCATCTACTCCCTC 57.979 40.000 0.00 0.00 0.00 4.30
149 150 3.636153 AGTTTTGCATCTACTCCCTCC 57.364 47.619 0.00 0.00 0.00 4.30
150 151 2.093447 AGTTTTGCATCTACTCCCTCCG 60.093 50.000 0.00 0.00 0.00 4.63
151 152 1.568504 TTTGCATCTACTCCCTCCGT 58.431 50.000 0.00 0.00 0.00 4.69
152 153 1.568504 TTGCATCTACTCCCTCCGTT 58.431 50.000 0.00 0.00 0.00 4.44
153 154 1.112113 TGCATCTACTCCCTCCGTTC 58.888 55.000 0.00 0.00 0.00 3.95
154 155 0.389757 GCATCTACTCCCTCCGTTCC 59.610 60.000 0.00 0.00 0.00 3.62
155 156 2.030045 GCATCTACTCCCTCCGTTCCT 61.030 57.143 0.00 0.00 0.00 3.36
156 157 2.752154 GCATCTACTCCCTCCGTTCCTA 60.752 54.545 0.00 0.00 0.00 2.94
157 158 3.563223 CATCTACTCCCTCCGTTCCTAA 58.437 50.000 0.00 0.00 0.00 2.69
158 159 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
159 160 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
160 161 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
161 162 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
162 163 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
163 164 6.944862 TCTACTCCCTCCGTTCCTAAATATAC 59.055 42.308 0.00 0.00 0.00 1.47
164 165 4.522022 ACTCCCTCCGTTCCTAAATATACG 59.478 45.833 0.00 0.00 0.00 3.06
165 166 4.473444 TCCCTCCGTTCCTAAATATACGT 58.527 43.478 0.00 0.00 32.45 3.57
166 167 4.520492 TCCCTCCGTTCCTAAATATACGTC 59.480 45.833 0.00 0.00 32.45 4.34
167 168 4.279169 CCCTCCGTTCCTAAATATACGTCA 59.721 45.833 0.00 0.00 32.45 4.35
168 169 5.047519 CCCTCCGTTCCTAAATATACGTCAT 60.048 44.000 0.00 0.00 32.45 3.06
169 170 6.453092 CCTCCGTTCCTAAATATACGTCATT 58.547 40.000 0.00 0.00 32.45 2.57
170 171 6.927381 CCTCCGTTCCTAAATATACGTCATTT 59.073 38.462 11.47 11.47 32.45 2.32
171 172 7.440255 CCTCCGTTCCTAAATATACGTCATTTT 59.560 37.037 11.87 4.58 32.45 1.82
172 173 9.467258 CTCCGTTCCTAAATATACGTCATTTTA 57.533 33.333 11.87 5.36 32.45 1.52
173 174 9.467258 TCCGTTCCTAAATATACGTCATTTTAG 57.533 33.333 11.87 12.60 33.47 1.85
174 175 9.467258 CCGTTCCTAAATATACGTCATTTTAGA 57.533 33.333 18.33 11.38 34.90 2.10
188 189 9.831737 ACGTCATTTTAGAGATTTCAAATGAAG 57.168 29.630 16.12 16.12 43.70 3.02
189 190 9.831737 CGTCATTTTAGAGATTTCAAATGAAGT 57.168 29.630 11.18 0.00 43.70 3.01
199 200 9.855361 GAGATTTCAAATGAAGTATCACATACG 57.145 33.333 7.99 0.00 40.64 3.06
200 201 8.830580 AGATTTCAAATGAAGTATCACATACGG 58.169 33.333 9.37 0.00 40.64 4.02
201 202 8.731275 ATTTCAAATGAAGTATCACATACGGA 57.269 30.769 0.00 0.00 40.64 4.69
202 203 8.731275 TTTCAAATGAAGTATCACATACGGAT 57.269 30.769 0.00 0.00 40.64 4.18
203 204 7.713764 TCAAATGAAGTATCACATACGGATG 57.286 36.000 5.94 5.94 40.64 3.51
205 206 8.417884 TCAAATGAAGTATCACATACGGATGTA 58.582 33.333 14.23 2.61 44.82 2.29
206 207 9.208022 CAAATGAAGTATCACATACGGATGTAT 57.792 33.333 14.23 10.02 44.82 2.29
213 214 9.901172 AGTATCACATACGGATGTATATAGACA 57.099 33.333 14.23 2.07 44.82 3.41
233 234 7.750229 AGACAAATTTTAGAGTGCAGATTCA 57.250 32.000 0.00 0.00 0.00 2.57
234 235 7.588512 AGACAAATTTTAGAGTGCAGATTCAC 58.411 34.615 0.00 0.00 37.24 3.18
243 244 4.170292 AGTGCAGATTCACTCATTTTGC 57.830 40.909 0.00 0.00 43.28 3.68
244 245 3.825014 AGTGCAGATTCACTCATTTTGCT 59.175 39.130 0.00 0.00 43.28 3.91
245 246 4.082895 AGTGCAGATTCACTCATTTTGCTC 60.083 41.667 0.00 0.00 43.28 4.26
246 247 3.192001 TGCAGATTCACTCATTTTGCTCC 59.808 43.478 0.00 0.00 0.00 4.70
247 248 3.730061 GCAGATTCACTCATTTTGCTCCG 60.730 47.826 0.00 0.00 0.00 4.63
248 249 3.438087 CAGATTCACTCATTTTGCTCCGT 59.562 43.478 0.00 0.00 0.00 4.69
249 250 4.631377 CAGATTCACTCATTTTGCTCCGTA 59.369 41.667 0.00 0.00 0.00 4.02
250 251 5.295292 CAGATTCACTCATTTTGCTCCGTAT 59.705 40.000 0.00 0.00 0.00 3.06
251 252 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
252 253 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
253 254 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
254 255 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
255 256 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
256 257 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
257 258 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
258 259 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
259 260 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
260 261 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
261 262 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
262 263 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
263 264 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
264 265 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
265 266 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
266 267 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
267 268 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
268 269 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
269 270 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
270 271 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
271 272 7.117812 CCGTATGTAGTCACTTGTTGAAATCTT 59.882 37.037 0.00 0.00 35.39 2.40
272 273 8.495949 CGTATGTAGTCACTTGTTGAAATCTTT 58.504 33.333 0.00 0.00 35.39 2.52
275 276 9.778741 ATGTAGTCACTTGTTGAAATCTTTAGA 57.221 29.630 0.00 0.00 35.39 2.10
276 277 9.607988 TGTAGTCACTTGTTGAAATCTTTAGAA 57.392 29.630 0.00 0.00 35.39 2.10
279 280 9.396022 AGTCACTTGTTGAAATCTTTAGAAAGA 57.604 29.630 7.15 7.15 41.72 2.52
280 281 9.439537 GTCACTTGTTGAAATCTTTAGAAAGAC 57.560 33.333 6.85 0.00 40.95 3.01
281 282 8.621286 TCACTTGTTGAAATCTTTAGAAAGACC 58.379 33.333 6.85 1.49 46.80 3.85
282 283 8.624776 CACTTGTTGAAATCTTTAGAAAGACCT 58.375 33.333 6.85 0.00 46.80 3.85
283 284 9.847224 ACTTGTTGAAATCTTTAGAAAGACCTA 57.153 29.630 6.85 0.00 46.80 3.08
299 300 8.422566 AGAAAGACCTATATTTAGAAACGGAGG 58.577 37.037 0.00 0.00 0.00 4.30
300 301 6.667558 AGACCTATATTTAGAAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
301 302 6.379579 AGACCTATATTTAGAAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
302 303 6.494146 AGACCTATATTTAGAAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
303 304 6.141790 ACCTATATTTAGAAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
304 305 7.300658 ACCTATATTTAGAAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
305 306 7.786464 ACCTATATTTAGAAACGGAGGGAGTAA 59.214 37.037 0.00 0.00 0.00 2.24
306 307 8.813951 CCTATATTTAGAAACGGAGGGAGTAAT 58.186 37.037 0.00 0.00 0.00 1.89
344 345 8.190784 ACAACTTTAAACAAGAGAAACATCTGG 58.809 33.333 0.00 0.00 0.00 3.86
347 348 7.556275 ACTTTAAACAAGAGAAACATCTGGACA 59.444 33.333 0.00 0.00 0.00 4.02
358 359 5.568620 AACATCTGGACAAGAAAGGTACT 57.431 39.130 0.00 0.00 38.79 2.73
359 360 4.899502 ACATCTGGACAAGAAAGGTACTG 58.100 43.478 0.00 0.00 38.79 2.74
360 361 4.348168 ACATCTGGACAAGAAAGGTACTGT 59.652 41.667 0.00 0.00 38.79 3.55
374 375 5.359194 AGGTACTGTGCAGCTATTAACAT 57.641 39.130 0.00 0.00 37.18 2.71
405 770 2.289547 GCTTGTAACCTTCGTTTCTGCA 59.710 45.455 0.00 0.00 33.17 4.41
428 793 2.218759 CCGTGTTATTACTGATCGCTGC 59.781 50.000 0.00 0.00 0.00 5.25
429 794 3.116300 CGTGTTATTACTGATCGCTGCT 58.884 45.455 0.00 0.00 0.00 4.24
430 795 4.287720 CGTGTTATTACTGATCGCTGCTA 58.712 43.478 0.00 0.00 0.00 3.49
431 796 4.917998 CGTGTTATTACTGATCGCTGCTAT 59.082 41.667 0.00 0.00 0.00 2.97
432 797 6.084277 CGTGTTATTACTGATCGCTGCTATA 58.916 40.000 0.00 0.00 0.00 1.31
433 798 6.581166 CGTGTTATTACTGATCGCTGCTATAA 59.419 38.462 0.00 0.00 0.00 0.98
503 873 2.795329 GGGATCAAAAGAGCACTTCCA 58.205 47.619 0.00 0.00 35.05 3.53
588 958 5.597806 TGACCAGCAATTATCTTACTACGG 58.402 41.667 0.00 0.00 0.00 4.02
605 978 1.071699 ACGGTTGTGGCTAATCACAGT 59.928 47.619 0.00 0.00 46.61 3.55
630 1003 2.618709 CGGGAGCAGAAACTGAAAAACT 59.381 45.455 2.81 0.00 32.44 2.66
631 1004 3.813166 CGGGAGCAGAAACTGAAAAACTA 59.187 43.478 2.81 0.00 32.44 2.24
685 1058 2.034066 GGCTGGGCTGTTGCTGTA 59.966 61.111 0.00 0.00 39.59 2.74
730 1106 0.796312 CGCAGGACGTTAGTTGCAAT 59.204 50.000 0.59 0.00 34.64 3.56
756 1132 3.181470 GGAGCTAAAACCAACAGCCAAAA 60.181 43.478 0.00 0.00 35.88 2.44
757 1133 3.792401 AGCTAAAACCAACAGCCAAAAC 58.208 40.909 0.00 0.00 35.88 2.43
758 1134 2.869801 GCTAAAACCAACAGCCAAAACC 59.130 45.455 0.00 0.00 0.00 3.27
759 1135 2.017138 AAAACCAACAGCCAAAACCG 57.983 45.000 0.00 0.00 0.00 4.44
761 1137 1.681486 AACCAACAGCCAAAACCGGG 61.681 55.000 6.32 0.00 0.00 5.73
763 1139 2.131067 CAACAGCCAAAACCGGGGT 61.131 57.895 6.32 0.00 36.34 4.95
764 1140 1.830847 AACAGCCAAAACCGGGGTC 60.831 57.895 6.32 0.00 32.88 4.46
765 1141 2.989253 CAGCCAAAACCGGGGTCC 60.989 66.667 6.32 0.00 32.88 4.46
801 1179 2.374525 TGCCGCCACCAGTATCCAT 61.375 57.895 0.00 0.00 0.00 3.41
802 1180 1.598130 GCCGCCACCAGTATCCATC 60.598 63.158 0.00 0.00 0.00 3.51
803 1181 1.071471 CCGCCACCAGTATCCATCC 59.929 63.158 0.00 0.00 0.00 3.51
804 1182 1.300931 CGCCACCAGTATCCATCCG 60.301 63.158 0.00 0.00 0.00 4.18
805 1183 1.744320 CGCCACCAGTATCCATCCGA 61.744 60.000 0.00 0.00 0.00 4.55
806 1184 0.687354 GCCACCAGTATCCATCCGAT 59.313 55.000 0.00 0.00 34.73 4.18
807 1185 1.338200 GCCACCAGTATCCATCCGATC 60.338 57.143 0.00 0.00 31.92 3.69
808 1186 1.276421 CCACCAGTATCCATCCGATCC 59.724 57.143 0.00 0.00 31.92 3.36
809 1187 1.970640 CACCAGTATCCATCCGATCCA 59.029 52.381 0.00 0.00 31.92 3.41
810 1188 2.568956 CACCAGTATCCATCCGATCCAT 59.431 50.000 0.00 0.00 31.92 3.41
811 1189 2.834549 ACCAGTATCCATCCGATCCATC 59.165 50.000 0.00 0.00 31.92 3.51
812 1190 2.833943 CCAGTATCCATCCGATCCATCA 59.166 50.000 0.00 0.00 31.92 3.07
813 1191 3.453717 CCAGTATCCATCCGATCCATCAT 59.546 47.826 0.00 0.00 31.92 2.45
814 1192 4.442612 CCAGTATCCATCCGATCCATCATC 60.443 50.000 0.00 0.00 31.92 2.92
815 1193 4.161001 CAGTATCCATCCGATCCATCATCA 59.839 45.833 0.00 0.00 31.92 3.07
816 1194 4.967442 AGTATCCATCCGATCCATCATCAT 59.033 41.667 0.00 0.00 31.92 2.45
817 1195 3.900966 TCCATCCGATCCATCATCATC 57.099 47.619 0.00 0.00 0.00 2.92
818 1196 2.502947 TCCATCCGATCCATCATCATCC 59.497 50.000 0.00 0.00 0.00 3.51
819 1197 2.547826 CATCCGATCCATCATCATCCG 58.452 52.381 0.00 0.00 0.00 4.18
820 1198 0.247460 TCCGATCCATCATCATCCGC 59.753 55.000 0.00 0.00 0.00 5.54
821 1199 0.742281 CCGATCCATCATCATCCGCC 60.742 60.000 0.00 0.00 0.00 6.13
822 1200 0.742281 CGATCCATCATCATCCGCCC 60.742 60.000 0.00 0.00 0.00 6.13
823 1201 0.617413 GATCCATCATCATCCGCCCT 59.383 55.000 0.00 0.00 0.00 5.19
824 1202 1.004044 GATCCATCATCATCCGCCCTT 59.996 52.381 0.00 0.00 0.00 3.95
825 1203 0.109153 TCCATCATCATCCGCCCTTG 59.891 55.000 0.00 0.00 0.00 3.61
826 1204 0.892358 CCATCATCATCCGCCCTTGG 60.892 60.000 0.00 0.00 0.00 3.61
827 1205 1.228367 ATCATCATCCGCCCTTGGC 60.228 57.895 0.00 0.00 46.75 4.52
870 1248 3.979497 CCCTCCGGTTTTGGCCCT 61.979 66.667 0.00 0.00 0.00 5.19
877 1255 0.036875 CGGTTTTGGCCCTTCTCTCT 59.963 55.000 0.00 0.00 0.00 3.10
879 1257 1.443802 GTTTTGGCCCTTCTCTCTCG 58.556 55.000 0.00 0.00 0.00 4.04
959 1340 1.371183 CAGACCTGCCGACCAAGAA 59.629 57.895 0.00 0.00 0.00 2.52
973 1354 4.322049 CGACCAAGAACCTCTTACATCAGT 60.322 45.833 0.00 0.00 33.78 3.41
976 1357 5.998363 ACCAAGAACCTCTTACATCAGTTTC 59.002 40.000 0.00 0.00 33.78 2.78
1037 1418 3.805928 ACCTGCGATGGTGAAGGA 58.194 55.556 0.00 0.00 39.17 3.36
1041 1422 2.514824 GCGATGGTGAAGGAGGCC 60.515 66.667 0.00 0.00 0.00 5.19
1238 1637 4.402528 CGGTCGCCAACCCCATCA 62.403 66.667 0.00 0.00 46.27 3.07
1259 1658 7.168637 CCATCATTAATTTCCAGCTTTGATTCG 59.831 37.037 0.00 0.00 0.00 3.34
1268 1667 2.420022 CAGCTTTGATTCGGTTCGGAAT 59.580 45.455 5.52 5.52 39.27 3.01
1269 1668 3.621268 CAGCTTTGATTCGGTTCGGAATA 59.379 43.478 5.77 0.00 36.79 1.75
1406 1864 2.817834 GCCTATGCGTCGCCAACA 60.818 61.111 15.88 0.00 0.00 3.33
1426 1897 2.590114 GGTAACAGCCACGACCCCT 61.590 63.158 0.00 0.00 0.00 4.79
1448 1928 2.325857 GCCGCATTGCTCGATCAC 59.674 61.111 7.12 0.00 0.00 3.06
1454 1934 1.592081 GCATTGCTCGATCACAGAGAC 59.408 52.381 0.16 0.00 37.93 3.36
1460 1942 3.194329 TGCTCGATCACAGAGACATTTCT 59.806 43.478 0.75 0.00 37.93 2.52
1470 1960 5.227238 CAGAGACATTTCTGTAACATGCC 57.773 43.478 0.00 0.00 39.76 4.40
1471 1961 4.696877 CAGAGACATTTCTGTAACATGCCA 59.303 41.667 0.00 0.00 39.76 4.92
1625 2145 4.142491 GGTAATTGATGATGTGTTCCGCAA 60.142 41.667 0.00 0.00 0.00 4.85
1765 2317 2.229784 CAGCCCAAGTCCAAGAAATGAC 59.770 50.000 0.00 0.00 0.00 3.06
1801 2353 2.815478 CCGAGCCTGTTGTATCTCTTC 58.185 52.381 0.00 0.00 0.00 2.87
1811 2363 7.042335 CCTGTTGTATCTCTTCGTAAAATCCT 58.958 38.462 0.00 0.00 0.00 3.24
1816 2368 7.481642 TGTATCTCTTCGTAAAATCCTGAGTC 58.518 38.462 0.00 0.00 0.00 3.36
1913 2470 6.770785 TCCAGGTTATATTTCCAGCATTACAC 59.229 38.462 0.00 0.00 0.00 2.90
1947 2504 9.878667 TGTTACTGTATTCAAATATCTTCCGAA 57.121 29.630 0.00 0.00 0.00 4.30
1956 2513 2.660189 TATCTTCCGAACCAACGACC 57.340 50.000 0.00 0.00 35.09 4.79
1957 2514 0.682852 ATCTTCCGAACCAACGACCA 59.317 50.000 0.00 0.00 35.09 4.02
1958 2515 0.682852 TCTTCCGAACCAACGACCAT 59.317 50.000 0.00 0.00 35.09 3.55
1959 2516 0.796312 CTTCCGAACCAACGACCATG 59.204 55.000 0.00 0.00 35.09 3.66
2046 2604 7.710475 CCATCCAAACAAGTTTTACAGAAACAT 59.290 33.333 4.68 0.00 32.81 2.71
2047 2605 8.755018 CATCCAAACAAGTTTTACAGAAACATC 58.245 33.333 4.68 0.00 32.81 3.06
2091 2651 6.939132 ACACAGATAGTACTATAACAGCGT 57.061 37.500 15.42 5.98 0.00 5.07
2210 2770 5.045872 GCCTGAAAATGCAATTGGATACTC 58.954 41.667 13.27 12.43 36.10 2.59
2211 2771 5.163478 GCCTGAAAATGCAATTGGATACTCT 60.163 40.000 13.27 0.00 36.10 3.24
2233 2793 8.531982 ACTCTTAGTATAAGAGCAATGAACACA 58.468 33.333 21.04 0.00 45.78 3.72
2242 2802 5.255687 AGAGCAATGAACACATACCAATCA 58.744 37.500 0.00 0.00 0.00 2.57
2252 2812 8.511321 TGAACACATACCAATCAACAATAAGTC 58.489 33.333 0.00 0.00 0.00 3.01
2263 2823 9.897744 CAATCAACAATAAGTCAACACAAGTAT 57.102 29.630 0.00 0.00 0.00 2.12
2368 2928 0.102120 CGGGCTGAGCAAAAACAACA 59.898 50.000 6.82 0.00 0.00 3.33
2388 2948 9.581099 AACAACAAAGGTAAGTTTCATAAACAG 57.419 29.630 5.42 0.00 43.79 3.16
2390 2950 9.965824 CAACAAAGGTAAGTTTCATAAACAGAT 57.034 29.630 5.42 0.00 43.79 2.90
2441 3001 1.153086 GATGCAGCGACAGGGGATT 60.153 57.895 0.00 0.00 0.00 3.01
2472 3032 3.243501 GCTGGTGATCTGCAAAAAGTTCA 60.244 43.478 0.00 0.00 39.69 3.18
2572 3132 4.450419 CCAATCGCCAAATGCAAGTAAAAA 59.550 37.500 0.00 0.00 41.33 1.94
2580 3140 5.240121 CAAATGCAAGTAAAAAGGGCTCAT 58.760 37.500 0.00 0.00 0.00 2.90
2581 3141 3.940209 TGCAAGTAAAAAGGGCTCATG 57.060 42.857 0.00 0.00 0.00 3.07
2592 3152 9.448438 GTAAAAAGGGCTCATGGAAATTAAAAT 57.552 29.630 0.00 0.00 0.00 1.82
2653 3213 3.064271 AGCGTTTTGTGTCAATGTTACGT 59.936 39.130 0.00 0.00 0.00 3.57
2654 3214 3.176867 GCGTTTTGTGTCAATGTTACGTG 59.823 43.478 0.00 0.00 0.00 4.49
2655 3215 4.579564 CGTTTTGTGTCAATGTTACGTGA 58.420 39.130 0.00 0.00 0.00 4.35
2664 3224 6.254804 GTGTCAATGTTACGTGAGCATATACA 59.745 38.462 0.00 5.42 0.00 2.29
2675 3235 5.506483 CGTGAGCATATACACTAGAACAGCT 60.506 44.000 0.00 0.00 35.23 4.24
2763 3323 3.061322 CGTCATAGTCCAAACCGTCAAA 58.939 45.455 0.00 0.00 0.00 2.69
2764 3324 3.682858 CGTCATAGTCCAAACCGTCAAAT 59.317 43.478 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.087750 AGAATTCATGTGATTTTTAAAAGCGGA 58.912 29.630 8.44 0.00 0.00 5.54
1 2 8.164153 CAGAATTCATGTGATTTTTAAAAGCGG 58.836 33.333 8.44 0.00 0.00 5.52
2 3 8.702438 ACAGAATTCATGTGATTTTTAAAAGCG 58.298 29.630 8.44 0.00 0.00 4.68
56 57 7.540745 GGCGTACATGTCAAACATAAAAATCTT 59.459 33.333 0.00 0.00 36.53 2.40
59 60 6.806249 CAGGCGTACATGTCAAACATAAAAAT 59.194 34.615 0.00 0.00 36.53 1.82
124 125 6.038714 GGAGGGAGTAGATGCAAAACTTATTG 59.961 42.308 0.00 0.00 0.00 1.90
126 127 5.685075 CGGAGGGAGTAGATGCAAAACTTAT 60.685 44.000 0.00 0.00 0.00 1.73
127 128 4.382685 CGGAGGGAGTAGATGCAAAACTTA 60.383 45.833 0.00 0.00 0.00 2.24
128 129 3.619979 CGGAGGGAGTAGATGCAAAACTT 60.620 47.826 0.00 0.00 0.00 2.66
129 130 2.093447 CGGAGGGAGTAGATGCAAAACT 60.093 50.000 0.00 0.00 0.00 2.66
130 131 2.280628 CGGAGGGAGTAGATGCAAAAC 58.719 52.381 0.00 0.00 0.00 2.43
134 135 1.112113 GAACGGAGGGAGTAGATGCA 58.888 55.000 0.00 0.00 0.00 3.96
136 137 2.074729 AGGAACGGAGGGAGTAGATG 57.925 55.000 0.00 0.00 0.00 2.90
137 138 3.967467 TTAGGAACGGAGGGAGTAGAT 57.033 47.619 0.00 0.00 0.00 1.98
138 139 3.744940 TTTAGGAACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
140 141 5.707298 CGTATATTTAGGAACGGAGGGAGTA 59.293 44.000 0.00 0.00 0.00 2.59
141 142 4.522022 CGTATATTTAGGAACGGAGGGAGT 59.478 45.833 0.00 0.00 0.00 3.85
142 143 4.522022 ACGTATATTTAGGAACGGAGGGAG 59.478 45.833 0.00 0.00 39.57 4.30
143 144 4.473444 ACGTATATTTAGGAACGGAGGGA 58.527 43.478 0.00 0.00 39.57 4.20
144 145 4.279169 TGACGTATATTTAGGAACGGAGGG 59.721 45.833 0.00 0.00 39.57 4.30
145 146 5.443185 TGACGTATATTTAGGAACGGAGG 57.557 43.478 0.00 0.00 39.57 4.30
146 147 7.941795 AAATGACGTATATTTAGGAACGGAG 57.058 36.000 8.12 0.00 39.57 4.63
147 148 9.467258 CTAAAATGACGTATATTTAGGAACGGA 57.533 33.333 14.20 0.00 39.57 4.69
148 149 9.467258 TCTAAAATGACGTATATTTAGGAACGG 57.533 33.333 18.61 2.79 39.57 4.44
162 163 9.831737 CTTCATTTGAAATCTCTAAAATGACGT 57.168 29.630 8.70 0.00 44.46 4.34
163 164 9.831737 ACTTCATTTGAAATCTCTAAAATGACG 57.168 29.630 8.70 9.53 44.46 4.35
173 174 9.855361 CGTATGTGATACTTCATTTGAAATCTC 57.145 33.333 6.56 4.41 33.56 2.75
174 175 8.830580 CCGTATGTGATACTTCATTTGAAATCT 58.169 33.333 6.56 0.00 33.56 2.40
175 176 8.826710 TCCGTATGTGATACTTCATTTGAAATC 58.173 33.333 0.00 0.00 33.56 2.17
176 177 8.731275 TCCGTATGTGATACTTCATTTGAAAT 57.269 30.769 0.00 0.00 33.56 2.17
177 178 8.611757 CATCCGTATGTGATACTTCATTTGAAA 58.388 33.333 0.00 0.00 33.56 2.69
178 179 7.768582 ACATCCGTATGTGATACTTCATTTGAA 59.231 33.333 0.00 0.00 44.79 2.69
179 180 7.272244 ACATCCGTATGTGATACTTCATTTGA 58.728 34.615 0.00 0.00 44.79 2.69
180 181 7.482654 ACATCCGTATGTGATACTTCATTTG 57.517 36.000 0.00 0.00 44.79 2.32
187 188 9.901172 TGTCTATATACATCCGTATGTGATACT 57.099 33.333 3.56 0.00 45.99 2.12
207 208 9.453572 TGAATCTGCACTCTAAAATTTGTCTAT 57.546 29.630 0.00 0.00 0.00 1.98
208 209 8.721478 GTGAATCTGCACTCTAAAATTTGTCTA 58.279 33.333 0.00 0.00 35.91 2.59
209 210 7.446625 AGTGAATCTGCACTCTAAAATTTGTCT 59.553 33.333 0.00 0.00 45.54 3.41
210 211 7.588512 AGTGAATCTGCACTCTAAAATTTGTC 58.411 34.615 0.00 0.00 45.54 3.18
211 212 7.516198 AGTGAATCTGCACTCTAAAATTTGT 57.484 32.000 0.00 0.00 45.54 2.83
223 224 4.164294 GAGCAAAATGAGTGAATCTGCAC 58.836 43.478 0.00 0.00 39.05 4.57
224 225 3.192001 GGAGCAAAATGAGTGAATCTGCA 59.808 43.478 0.00 0.00 0.00 4.41
225 226 3.730061 CGGAGCAAAATGAGTGAATCTGC 60.730 47.826 0.00 0.00 0.00 4.26
226 227 3.438087 ACGGAGCAAAATGAGTGAATCTG 59.562 43.478 0.00 0.00 0.00 2.90
227 228 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
228 229 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
229 230 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
230 231 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
231 232 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
232 233 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
233 234 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
234 235 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
235 236 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
236 237 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
237 238 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
238 239 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
239 240 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
240 241 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
241 242 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
242 243 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
243 244 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
244 245 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
245 246 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
246 247 7.582435 AGATTTCAACAAGTGACTACATACG 57.418 36.000 0.00 0.00 35.39 3.06
249 250 9.778741 TCTAAAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
250 251 9.607988 TTCTAAAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
253 254 9.396022 TCTTTCTAAAGATTTCAACAAGTGACT 57.604 29.630 1.00 0.00 39.95 3.41
254 255 9.439537 GTCTTTCTAAAGATTTCAACAAGTGAC 57.560 33.333 8.31 0.00 45.83 3.67
255 256 8.621286 GGTCTTTCTAAAGATTTCAACAAGTGA 58.379 33.333 8.31 0.00 45.83 3.41
256 257 8.624776 AGGTCTTTCTAAAGATTTCAACAAGTG 58.375 33.333 8.31 0.00 45.83 3.16
257 258 8.753497 AGGTCTTTCTAAAGATTTCAACAAGT 57.247 30.769 8.31 0.00 45.83 3.16
273 274 8.422566 CCTCCGTTTCTAAATATAGGTCTTTCT 58.577 37.037 0.00 0.00 0.00 2.52
274 275 7.656542 CCCTCCGTTTCTAAATATAGGTCTTTC 59.343 40.741 0.00 0.00 0.00 2.62
275 276 7.346436 TCCCTCCGTTTCTAAATATAGGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
276 277 6.842807 TCCCTCCGTTTCTAAATATAGGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
277 278 6.379579 TCCCTCCGTTTCTAAATATAGGTCT 58.620 40.000 0.00 0.00 0.00 3.85
278 279 6.267242 ACTCCCTCCGTTTCTAAATATAGGTC 59.733 42.308 0.00 0.00 0.00 3.85
279 280 6.141790 ACTCCCTCCGTTTCTAAATATAGGT 58.858 40.000 0.00 0.00 0.00 3.08
280 281 6.667558 ACTCCCTCCGTTTCTAAATATAGG 57.332 41.667 0.00 0.00 0.00 2.57
287 288 8.964772 GCTATATATTACTCCCTCCGTTTCTAA 58.035 37.037 0.00 0.00 0.00 2.10
288 289 8.334734 AGCTATATATTACTCCCTCCGTTTCTA 58.665 37.037 0.00 0.00 0.00 2.10
289 290 7.122948 CAGCTATATATTACTCCCTCCGTTTCT 59.877 40.741 0.00 0.00 0.00 2.52
290 291 7.122353 TCAGCTATATATTACTCCCTCCGTTTC 59.878 40.741 0.00 0.00 0.00 2.78
291 292 6.952358 TCAGCTATATATTACTCCCTCCGTTT 59.048 38.462 0.00 0.00 0.00 3.60
292 293 6.491383 TCAGCTATATATTACTCCCTCCGTT 58.509 40.000 0.00 0.00 0.00 4.44
293 294 6.075949 TCAGCTATATATTACTCCCTCCGT 57.924 41.667 0.00 0.00 0.00 4.69
294 295 7.093902 TGTTTCAGCTATATATTACTCCCTCCG 60.094 40.741 0.00 0.00 0.00 4.63
295 296 8.135382 TGTTTCAGCTATATATTACTCCCTCC 57.865 38.462 0.00 0.00 0.00 4.30
296 297 9.425577 GTTGTTTCAGCTATATATTACTCCCTC 57.574 37.037 0.00 0.00 0.00 4.30
297 298 9.160412 AGTTGTTTCAGCTATATATTACTCCCT 57.840 33.333 0.00 0.00 0.00 4.20
298 299 9.780186 AAGTTGTTTCAGCTATATATTACTCCC 57.220 33.333 0.00 0.00 0.00 4.30
334 335 5.998363 AGTACCTTTCTTGTCCAGATGTTTC 59.002 40.000 0.00 0.00 0.00 2.78
344 345 2.224314 GCTGCACAGTACCTTTCTTGTC 59.776 50.000 0.00 0.00 0.00 3.18
347 348 2.938956 AGCTGCACAGTACCTTTCTT 57.061 45.000 1.02 0.00 0.00 2.52
358 359 5.163723 GCTTCTCAATGTTAATAGCTGCACA 60.164 40.000 1.02 0.00 0.00 4.57
359 360 5.065731 AGCTTCTCAATGTTAATAGCTGCAC 59.934 40.000 1.02 0.00 36.25 4.57
360 361 5.065602 CAGCTTCTCAATGTTAATAGCTGCA 59.934 40.000 1.02 0.00 44.94 4.41
374 375 3.492102 AGGTTACAAGCAGCTTCTCAA 57.508 42.857 4.07 0.00 0.00 3.02
405 770 3.863424 CAGCGATCAGTAATAACACGGTT 59.137 43.478 0.00 0.00 0.00 4.44
428 793 5.751990 AGTAACACCGCTTCCGATTTTATAG 59.248 40.000 0.00 0.00 36.29 1.31
429 794 5.521010 CAGTAACACCGCTTCCGATTTTATA 59.479 40.000 0.00 0.00 36.29 0.98
430 795 4.331717 CAGTAACACCGCTTCCGATTTTAT 59.668 41.667 0.00 0.00 36.29 1.40
431 796 3.680937 CAGTAACACCGCTTCCGATTTTA 59.319 43.478 0.00 0.00 36.29 1.52
432 797 2.482721 CAGTAACACCGCTTCCGATTTT 59.517 45.455 0.00 0.00 36.29 1.82
433 798 2.073816 CAGTAACACCGCTTCCGATTT 58.926 47.619 0.00 0.00 36.29 2.17
463 833 2.360852 GCTCACATGCTGCCACCT 60.361 61.111 0.00 0.00 0.00 4.00
464 834 2.360852 AGCTCACATGCTGCCACC 60.361 61.111 0.00 0.00 42.33 4.61
466 836 2.435410 CGAGCTCACATGCTGCCA 60.435 61.111 15.40 0.00 44.17 4.92
469 839 0.879400 GATCCCGAGCTCACATGCTG 60.879 60.000 15.40 0.00 44.17 4.41
503 873 7.603404 AGAAGATTACATAGTCTCGTATAGCGT 59.397 37.037 0.00 0.00 42.13 5.07
588 958 3.123621 CGAAGACTGTGATTAGCCACAAC 59.876 47.826 0.00 0.00 45.27 3.32
605 978 1.338107 TCAGTTTCTGCTCCCGAAGA 58.662 50.000 0.00 0.00 0.00 2.87
630 1003 1.135315 GTGCTGACCGTGACCGTTATA 60.135 52.381 0.00 0.00 0.00 0.98
631 1004 0.389426 GTGCTGACCGTGACCGTTAT 60.389 55.000 0.00 0.00 0.00 1.89
720 1096 2.205022 AGCTCCAGCATTGCAACTAA 57.795 45.000 11.91 0.00 45.16 2.24
721 1097 3.348647 TTAGCTCCAGCATTGCAACTA 57.651 42.857 11.91 2.18 45.16 2.24
730 1106 2.229792 CTGTTGGTTTTAGCTCCAGCA 58.770 47.619 8.18 8.18 45.16 4.41
801 1179 0.247460 GCGGATGATGATGGATCGGA 59.753 55.000 0.00 0.00 33.17 4.55
802 1180 0.742281 GGCGGATGATGATGGATCGG 60.742 60.000 0.00 0.00 33.17 4.18
803 1181 0.742281 GGGCGGATGATGATGGATCG 60.742 60.000 0.00 0.00 33.17 3.69
804 1182 0.617413 AGGGCGGATGATGATGGATC 59.383 55.000 0.00 0.00 0.00 3.36
805 1183 1.070604 AAGGGCGGATGATGATGGAT 58.929 50.000 0.00 0.00 0.00 3.41
806 1184 0.109153 CAAGGGCGGATGATGATGGA 59.891 55.000 0.00 0.00 0.00 3.41
807 1185 0.892358 CCAAGGGCGGATGATGATGG 60.892 60.000 0.00 0.00 0.00 3.51
808 1186 1.521450 GCCAAGGGCGGATGATGATG 61.521 60.000 0.00 0.00 39.62 3.07
809 1187 1.228367 GCCAAGGGCGGATGATGAT 60.228 57.895 0.00 0.00 39.62 2.45
810 1188 2.192979 GCCAAGGGCGGATGATGA 59.807 61.111 0.00 0.00 39.62 2.92
870 1248 2.410687 CCGGCAGAGCGAGAGAGAA 61.411 63.158 0.00 0.00 0.00 2.87
890 1268 1.280998 AGGGGCGTATATATTGGGCAC 59.719 52.381 10.18 7.28 0.00 5.01
959 1340 4.283722 AGGAACGAAACTGATGTAAGAGGT 59.716 41.667 0.00 0.00 0.00 3.85
973 1354 1.939934 CAGACAGTGCAAGGAACGAAA 59.060 47.619 0.00 0.00 0.00 3.46
1026 1407 1.144936 CTCGGCCTCCTTCACCATC 59.855 63.158 0.00 0.00 0.00 3.51
1028 1409 3.003173 CCTCGGCCTCCTTCACCA 61.003 66.667 0.00 0.00 0.00 4.17
1029 1410 3.787001 CCCTCGGCCTCCTTCACC 61.787 72.222 0.00 0.00 0.00 4.02
1030 1411 4.475135 GCCCTCGGCCTCCTTCAC 62.475 72.222 0.00 0.00 44.06 3.18
1041 1422 3.905678 CTCCTACCGCTGCCCTCG 61.906 72.222 0.00 0.00 0.00 4.63
1224 1620 2.746279 ATTAATGATGGGGTTGGCGA 57.254 45.000 0.00 0.00 0.00 5.54
1235 1634 7.147846 ACCGAATCAAAGCTGGAAATTAATGAT 60.148 33.333 0.00 0.00 0.00 2.45
1238 1637 6.530019 ACCGAATCAAAGCTGGAAATTAAT 57.470 33.333 0.00 0.00 0.00 1.40
1259 1658 1.203052 TCACCACGAGTATTCCGAACC 59.797 52.381 0.00 0.00 0.00 3.62
1268 1667 0.601558 GCTCCAGTTCACCACGAGTA 59.398 55.000 0.00 0.00 0.00 2.59
1269 1668 1.115930 AGCTCCAGTTCACCACGAGT 61.116 55.000 0.00 0.00 0.00 4.18
1393 1851 3.576932 TACCGTGTTGGCGACGCAT 62.577 57.895 23.09 8.13 43.94 4.73
1406 1864 2.341176 GGTCGTGGCTGTTACCGT 59.659 61.111 0.00 0.00 0.00 4.83
1448 1928 4.696877 TGGCATGTTACAGAAATGTCTCTG 59.303 41.667 0.00 0.00 46.94 3.35
1454 1934 8.533965 CGATTTATTTGGCATGTTACAGAAATG 58.466 33.333 0.00 0.00 0.00 2.32
1460 1942 5.316327 TGCGATTTATTTGGCATGTTACA 57.684 34.783 0.00 0.00 0.00 2.41
1463 1945 3.195396 ACCTGCGATTTATTTGGCATGTT 59.805 39.130 0.00 0.00 31.66 2.71
1469 1959 2.937469 TGCACCTGCGATTTATTTGG 57.063 45.000 0.00 0.00 45.83 3.28
1470 1960 3.117794 CCATGCACCTGCGATTTATTTG 58.882 45.455 0.00 0.00 45.83 2.32
1471 1961 2.760092 ACCATGCACCTGCGATTTATTT 59.240 40.909 0.00 0.00 45.83 1.40
1643 2188 4.142687 CGTCCATGTTCAGATAAAACCCAC 60.143 45.833 0.00 0.00 0.00 4.61
1801 2353 3.679980 CACACAGGACTCAGGATTTTACG 59.320 47.826 0.00 0.00 0.00 3.18
1811 2363 2.280119 GCACGCACACAGGACTCA 60.280 61.111 0.00 0.00 0.00 3.41
1816 2368 1.509644 ATCACTTGCACGCACACAGG 61.510 55.000 0.00 0.00 0.00 4.00
1902 2459 0.810648 ATTGCCGTGTGTAATGCTGG 59.189 50.000 0.00 0.00 0.00 4.85
1913 2470 4.937696 TGAATACAGTAACATTGCCGTG 57.062 40.909 0.00 0.00 0.00 4.94
1947 2504 4.415881 TTATCTATGCATGGTCGTTGGT 57.584 40.909 10.16 0.00 0.00 3.67
1948 2505 7.201644 GGATTATTATCTATGCATGGTCGTTGG 60.202 40.741 10.16 0.00 0.00 3.77
2016 2573 8.017418 TCTGTAAAACTTGTTTGGATGGATTT 57.983 30.769 0.00 0.00 0.00 2.17
2046 2604 5.246656 TGTTCGGTTATTCTAGGTTCCTTGA 59.753 40.000 0.00 0.00 0.00 3.02
2047 2605 5.350640 GTGTTCGGTTATTCTAGGTTCCTTG 59.649 44.000 0.00 0.00 0.00 3.61
2091 2651 0.815095 TCTTCGCCGACTTCTGCATA 59.185 50.000 0.00 0.00 0.00 3.14
2211 2771 9.542462 GGTATGTGTTCATTGCTCTTATACTAA 57.458 33.333 0.00 0.00 35.70 2.24
2233 2793 8.402798 TGTGTTGACTTATTGTTGATTGGTAT 57.597 30.769 0.00 0.00 0.00 2.73
2235 2795 6.707440 TGTGTTGACTTATTGTTGATTGGT 57.293 33.333 0.00 0.00 0.00 3.67
2263 2823 9.011095 CGGTCTCCTGATGTAATATAACTCTTA 57.989 37.037 0.00 0.00 0.00 2.10
2403 2963 8.374327 TGCATCTGTAAGTATTCTCAATCATG 57.626 34.615 0.00 0.00 33.76 3.07
2441 3001 2.449464 CAGATCACCAGCAAAATCCCA 58.551 47.619 0.00 0.00 0.00 4.37
2504 3064 7.371159 GTTCTTGGAAGCAAGCTATTAAAACT 58.629 34.615 0.00 0.00 32.52 2.66
2506 3066 6.493458 AGGTTCTTGGAAGCAAGCTATTAAAA 59.507 34.615 11.19 0.00 32.52 1.52
2572 3132 6.872585 TTGATTTTAATTTCCATGAGCCCT 57.127 33.333 0.00 0.00 0.00 5.19
2633 3193 4.579564 TCACGTAACATTGACACAAAACG 58.420 39.130 0.00 0.00 35.38 3.60
2653 3213 5.830457 AGAGCTGTTCTAGTGTATATGCTCA 59.170 40.000 12.56 0.00 44.49 4.26
2654 3214 6.325919 AGAGCTGTTCTAGTGTATATGCTC 57.674 41.667 0.00 0.00 43.01 4.26
2655 3215 5.242838 GGAGAGCTGTTCTAGTGTATATGCT 59.757 44.000 0.00 0.00 35.87 3.79
2664 3224 5.489792 TCAAATTGGAGAGCTGTTCTAGT 57.510 39.130 0.00 0.00 35.87 2.57
2675 3235 3.507162 TCACAGGCTTCAAATTGGAGA 57.493 42.857 5.27 0.00 0.00 3.71
2732 3292 0.657840 GACTATGACGGCACAATGGC 59.342 55.000 0.00 0.00 39.85 4.40


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

AutoCloner maintained by Alex Coulton.