Multiple sequence alignment - TraesCS6A01G102900

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 TraesCS6A01G102900 chr6A 100.000 3311 0 0 1 3311 71947665 71950975 0.000000e+00 6115.0
1 TraesCS6A01G102900 chr6A 88.143 2488 246 26 834 3311 71924549 71926997 0.000000e+00 2915.0
2 TraesCS6A01G102900 chr6A 77.139 1461 289 37 988 2429 72429421 72430855 0.000000e+00 806.0
3 TraesCS6A01G102900 chr6A 94.872 39 2 0 3 41 586606227 586606189 9.920000e-06 62.1
4 TraesCS6A01G102900 chr6D 94.211 2885 119 19 436 3311 57170731 57173576 0.000000e+00 4359.0
5 TraesCS6A01G102900 chr6D 88.298 2333 213 32 992 3308 57158831 57161119 0.000000e+00 2741.0
6 TraesCS6A01G102900 chr6D 80.878 638 109 12 988 1619 57215898 57216528 1.070000e-134 490.0
7 TraesCS6A01G102900 chr6D 81.188 505 66 16 938 1431 57482346 57482832 2.410000e-101 379.0
8 TraesCS6A01G102900 chr6D 89.796 49 5 0 2 50 404514418 404514466 2.760000e-06 63.9
9 TraesCS6A01G102900 chr6D 87.500 56 3 4 2 54 207984345 207984291 9.920000e-06 62.1
10 TraesCS6A01G102900 chr6B 93.407 2882 138 22 436 3311 129236624 129239459 0.000000e+00 4222.0
11 TraesCS6A01G102900 chr6B 92.199 2346 135 21 436 2775 128015999 128018302 0.000000e+00 3275.0
12 TraesCS6A01G102900 chr6B 96.462 537 17 1 2777 3311 128018562 128019098 0.000000e+00 885.0
13 TraesCS6A01G102900 chr6B 77.854 1463 275 39 988 2429 129268681 129270115 0.000000e+00 861.0
14 TraesCS6A01G102900 chr6B 78.754 626 107 16 998 1607 129512959 129513574 2.390000e-106 396.0
15 TraesCS6A01G102900 chr6B 83.733 375 44 13 68 436 33095064 33095427 4.090000e-89 339.0
16 TraesCS6A01G102900 chr6B 83.646 373 44 13 71 437 5055276 5054915 5.290000e-88 335.0
17 TraesCS6A01G102900 chr6B 94.872 39 2 0 3 41 712974807 712974845 9.920000e-06 62.1
18 TraesCS6A01G102900 chr1A 94.335 406 20 2 32 436 298514979 298515382 1.310000e-173 619.0
19 TraesCS6A01G102900 chr1A 89.268 410 32 9 32 437 238796871 238797272 1.370000e-138 503.0
20 TraesCS6A01G102900 chr1B 91.597 357 27 1 32 388 624692248 624692601 1.070000e-134 490.0
21 TraesCS6A01G102900 chr1B 83.777 376 44 14 68 437 217548326 217548690 1.140000e-89 340.0
22 TraesCS6A01G102900 chr5B 83.690 374 44 13 71 438 644956507 644956145 1.470000e-88 337.0
23 TraesCS6A01G102900 chr5A 83.646 373 44 13 71 437 655492585 655492224 5.290000e-88 335.0
24 TraesCS6A01G102900 chr3B 83.602 372 44 13 71 436 692973914 692973554 1.900000e-87 333.0
25 TraesCS6A01G102900 chr7A 95.238 42 0 2 2 41 611197326 611197367 7.670000e-07 65.8
26 TraesCS6A01G102900 chr1D 94.872 39 2 0 2 40 144066101 144066139 9.920000e-06 62.1
27 TraesCS6A01G102900 chr1D 91.489 47 0 4 3 49 481056589 481056547 9.920000e-06 62.1
28 TraesCS6A01G102900 chr2D 85.484 62 4 5 2 60 514289385 514289326 3.570000e-05 60.2
29 TraesCS6A01G102900 chr3A 85.965 57 4 3 3 57 413404448 413404394 1.280000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G102900 chr6A 71947665 71950975 3310 False 6115 6115 100.0000 1 3311 1 chr6A.!!$F2 3310
1 TraesCS6A01G102900 chr6A 71924549 71926997 2448 False 2915 2915 88.1430 834 3311 1 chr6A.!!$F1 2477
2 TraesCS6A01G102900 chr6A 72429421 72430855 1434 False 806 806 77.1390 988 2429 1 chr6A.!!$F3 1441
3 TraesCS6A01G102900 chr6D 57170731 57173576 2845 False 4359 4359 94.2110 436 3311 1 chr6D.!!$F2 2875
4 TraesCS6A01G102900 chr6D 57158831 57161119 2288 False 2741 2741 88.2980 992 3308 1 chr6D.!!$F1 2316
5 TraesCS6A01G102900 chr6D 57215898 57216528 630 False 490 490 80.8780 988 1619 1 chr6D.!!$F3 631
6 TraesCS6A01G102900 chr6B 129236624 129239459 2835 False 4222 4222 93.4070 436 3311 1 chr6B.!!$F2 2875
7 TraesCS6A01G102900 chr6B 128015999 128019098 3099 False 2080 3275 94.3305 436 3311 2 chr6B.!!$F6 2875
8 TraesCS6A01G102900 chr6B 129268681 129270115 1434 False 861 861 77.8540 988 2429 1 chr6B.!!$F3 1441
9 TraesCS6A01G102900 chr6B 129512959 129513574 615 False 396 396 78.7540 998 1607 1 chr6B.!!$F4 609

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
234 235 0.037326 TCTTGCCGATGAACTCGCTT 60.037 50.0 0.00 0.00 46.25 4.68 F
614 623 0.093026 GAATACGATACATGCGGCGC 59.907 55.0 27.44 27.44 0.00 6.53 F
920 963 0.397941 TTGGCTCACTCCCTGACAAG 59.602 55.0 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1899 1.302832 GATTATCCGGCCAGGCAGG 60.303 63.158 24.17 24.17 44.93 4.85 R
2097 2178 1.623811 TCTGTAGTGGCTCCAAGGAAC 59.376 52.381 0.00 0.00 0.00 3.62 R
2508 2594 1.967066 TGTTATGCAAACTTGGTGGGG 59.033 47.619 11.34 0.00 0.00 4.96 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
19 20 1.262417 TTAGGACATCTGCCGTGACA 58.738 50.000 0.00 0.00 0.00 3.58
20 21 1.262417 TAGGACATCTGCCGTGACAA 58.738 50.000 0.00 0.00 0.00 3.18
21 22 0.396435 AGGACATCTGCCGTGACAAA 59.604 50.000 0.00 0.00 0.00 2.83
22 23 1.202758 AGGACATCTGCCGTGACAAAA 60.203 47.619 0.00 0.00 0.00 2.44
23 24 1.069227 GGACATCTGCCGTGACAAAAC 60.069 52.381 0.00 0.00 0.00 2.43
24 25 0.951558 ACATCTGCCGTGACAAAACC 59.048 50.000 0.00 0.00 0.00 3.27
25 26 0.950836 CATCTGCCGTGACAAAACCA 59.049 50.000 0.00 0.00 0.00 3.67
26 27 0.951558 ATCTGCCGTGACAAAACCAC 59.048 50.000 0.00 0.00 0.00 4.16
34 35 3.183237 GTGACAAAACCACGACATAGC 57.817 47.619 0.00 0.00 0.00 2.97
35 36 2.095919 GTGACAAAACCACGACATAGCC 60.096 50.000 0.00 0.00 0.00 3.93
36 37 2.224426 TGACAAAACCACGACATAGCCT 60.224 45.455 0.00 0.00 0.00 4.58
37 38 2.151202 ACAAAACCACGACATAGCCTG 58.849 47.619 0.00 0.00 0.00 4.85
38 39 2.151202 CAAAACCACGACATAGCCTGT 58.849 47.619 0.00 0.00 42.15 4.00
39 40 1.808411 AAACCACGACATAGCCTGTG 58.192 50.000 0.00 0.00 38.54 3.66
40 41 0.673644 AACCACGACATAGCCTGTGC 60.674 55.000 0.00 0.00 38.54 4.57
104 105 6.591935 TGTTTATACAGAGCTCTTATTGGGG 58.408 40.000 15.27 3.18 0.00 4.96
105 106 3.778954 ATACAGAGCTCTTATTGGGGC 57.221 47.619 15.27 0.00 0.00 5.80
106 107 1.589414 ACAGAGCTCTTATTGGGGCT 58.411 50.000 15.27 0.00 37.77 5.19
107 108 2.764269 ACAGAGCTCTTATTGGGGCTA 58.236 47.619 15.27 0.00 35.01 3.93
108 109 3.321950 ACAGAGCTCTTATTGGGGCTAT 58.678 45.455 15.27 0.00 35.01 2.97
109 110 3.326297 ACAGAGCTCTTATTGGGGCTATC 59.674 47.826 15.27 0.00 35.01 2.08
110 111 3.326006 CAGAGCTCTTATTGGGGCTATCA 59.674 47.826 15.27 0.00 35.01 2.15
111 112 3.976654 AGAGCTCTTATTGGGGCTATCAA 59.023 43.478 11.45 0.00 35.01 2.57
112 113 4.600983 AGAGCTCTTATTGGGGCTATCAAT 59.399 41.667 11.45 0.00 38.29 2.57
113 114 5.074239 AGAGCTCTTATTGGGGCTATCAATT 59.926 40.000 11.45 0.00 36.40 2.32
114 115 5.709594 AGCTCTTATTGGGGCTATCAATTT 58.290 37.500 6.59 0.00 36.40 1.82
115 116 6.138967 AGCTCTTATTGGGGCTATCAATTTT 58.861 36.000 6.59 0.00 36.40 1.82
116 117 6.612863 AGCTCTTATTGGGGCTATCAATTTTT 59.387 34.615 6.59 0.00 36.40 1.94
145 146 4.542662 GCGATATGCTGACTGTTGAAAT 57.457 40.909 0.00 0.00 41.73 2.17
146 147 4.277258 GCGATATGCTGACTGTTGAAATG 58.723 43.478 0.00 0.00 41.73 2.32
147 148 4.787563 GCGATATGCTGACTGTTGAAATGG 60.788 45.833 0.00 0.00 41.73 3.16
148 149 4.571984 CGATATGCTGACTGTTGAAATGGA 59.428 41.667 0.00 0.00 0.00 3.41
149 150 5.277202 CGATATGCTGACTGTTGAAATGGAG 60.277 44.000 0.00 0.00 0.00 3.86
150 151 2.507484 TGCTGACTGTTGAAATGGAGG 58.493 47.619 0.00 0.00 0.00 4.30
151 152 2.106338 TGCTGACTGTTGAAATGGAGGA 59.894 45.455 0.00 0.00 0.00 3.71
152 153 3.149196 GCTGACTGTTGAAATGGAGGAA 58.851 45.455 0.00 0.00 0.00 3.36
153 154 3.760684 GCTGACTGTTGAAATGGAGGAAT 59.239 43.478 0.00 0.00 0.00 3.01
154 155 4.943705 GCTGACTGTTGAAATGGAGGAATA 59.056 41.667 0.00 0.00 0.00 1.75
155 156 5.415701 GCTGACTGTTGAAATGGAGGAATAA 59.584 40.000 0.00 0.00 0.00 1.40
156 157 6.404074 GCTGACTGTTGAAATGGAGGAATAAG 60.404 42.308 0.00 0.00 0.00 1.73
157 158 6.542821 TGACTGTTGAAATGGAGGAATAAGT 58.457 36.000 0.00 0.00 0.00 2.24
158 159 6.655003 TGACTGTTGAAATGGAGGAATAAGTC 59.345 38.462 0.00 0.00 0.00 3.01
159 160 5.643777 ACTGTTGAAATGGAGGAATAAGTCG 59.356 40.000 0.00 0.00 0.00 4.18
160 161 5.800296 TGTTGAAATGGAGGAATAAGTCGA 58.200 37.500 0.00 0.00 0.00 4.20
161 162 5.874810 TGTTGAAATGGAGGAATAAGTCGAG 59.125 40.000 0.00 0.00 0.00 4.04
162 163 5.932619 TGAAATGGAGGAATAAGTCGAGA 57.067 39.130 0.00 0.00 0.00 4.04
163 164 5.907207 TGAAATGGAGGAATAAGTCGAGAG 58.093 41.667 0.00 0.00 0.00 3.20
164 165 5.656859 TGAAATGGAGGAATAAGTCGAGAGA 59.343 40.000 0.00 0.00 38.16 3.10
183 184 8.630037 TCGAGAGACTTTATACATATCAAAGCA 58.370 33.333 0.00 0.00 33.50 3.91
184 185 9.249457 CGAGAGACTTTATACATATCAAAGCAA 57.751 33.333 0.00 0.00 33.50 3.91
188 189 9.890629 AGACTTTATACATATCAAAGCAAGTGA 57.109 29.630 0.00 0.00 33.50 3.41
196 197 8.375608 ACATATCAAAGCAAGTGATCATAGAC 57.624 34.615 0.00 0.00 37.01 2.59
197 198 7.989170 ACATATCAAAGCAAGTGATCATAGACA 59.011 33.333 0.00 0.00 37.01 3.41
198 199 6.674694 ATCAAAGCAAGTGATCATAGACAC 57.325 37.500 0.00 0.00 37.30 3.67
210 211 9.761504 AGTGATCATAGACACTTAAATCATCTG 57.238 33.333 0.00 0.00 43.52 2.90
211 212 8.494347 GTGATCATAGACACTTAAATCATCTGC 58.506 37.037 0.00 0.00 34.65 4.26
212 213 8.427276 TGATCATAGACACTTAAATCATCTGCT 58.573 33.333 0.00 0.00 0.00 4.24
213 214 9.920133 GATCATAGACACTTAAATCATCTGCTA 57.080 33.333 0.00 0.00 0.00 3.49
214 215 9.926158 ATCATAGACACTTAAATCATCTGCTAG 57.074 33.333 0.00 0.00 0.00 3.42
215 216 8.918116 TCATAGACACTTAAATCATCTGCTAGT 58.082 33.333 0.00 0.00 0.00 2.57
216 217 9.190858 CATAGACACTTAAATCATCTGCTAGTC 57.809 37.037 0.00 0.00 0.00 2.59
217 218 7.416964 AGACACTTAAATCATCTGCTAGTCT 57.583 36.000 0.00 0.00 0.00 3.24
218 219 7.846066 AGACACTTAAATCATCTGCTAGTCTT 58.154 34.615 0.00 0.00 0.00 3.01
219 220 7.763528 AGACACTTAAATCATCTGCTAGTCTTG 59.236 37.037 0.00 0.00 0.00 3.02
220 221 6.314896 ACACTTAAATCATCTGCTAGTCTTGC 59.685 38.462 0.00 0.00 0.00 4.01
221 222 5.819901 ACTTAAATCATCTGCTAGTCTTGCC 59.180 40.000 3.76 0.00 0.00 4.52
222 223 2.522836 ATCATCTGCTAGTCTTGCCG 57.477 50.000 3.76 0.00 0.00 5.69
223 224 1.474330 TCATCTGCTAGTCTTGCCGA 58.526 50.000 3.76 3.46 0.00 5.54
224 225 2.034878 TCATCTGCTAGTCTTGCCGAT 58.965 47.619 7.24 7.24 35.35 4.18
225 226 2.133553 CATCTGCTAGTCTTGCCGATG 58.866 52.381 20.04 20.04 42.44 3.84
226 227 1.474330 TCTGCTAGTCTTGCCGATGA 58.526 50.000 3.76 0.00 0.00 2.92
227 228 1.824852 TCTGCTAGTCTTGCCGATGAA 59.175 47.619 3.76 0.00 0.00 2.57
228 229 1.929836 CTGCTAGTCTTGCCGATGAAC 59.070 52.381 3.76 0.00 0.00 3.18
229 230 1.550524 TGCTAGTCTTGCCGATGAACT 59.449 47.619 3.76 0.00 0.00 3.01
230 231 2.197577 GCTAGTCTTGCCGATGAACTC 58.802 52.381 0.00 0.00 0.00 3.01
232 233 0.737715 AGTCTTGCCGATGAACTCGC 60.738 55.000 0.00 0.00 46.25 5.03
233 234 0.737715 GTCTTGCCGATGAACTCGCT 60.738 55.000 0.00 0.00 46.25 4.93
234 235 0.037326 TCTTGCCGATGAACTCGCTT 60.037 50.000 0.00 0.00 46.25 4.68
235 236 0.371645 CTTGCCGATGAACTCGCTTC 59.628 55.000 0.00 0.00 46.25 3.86
236 237 0.037326 TTGCCGATGAACTCGCTTCT 60.037 50.000 0.00 0.00 46.25 2.85
237 238 0.815095 TGCCGATGAACTCGCTTCTA 59.185 50.000 0.00 0.00 46.25 2.10
238 239 1.202302 TGCCGATGAACTCGCTTCTAG 60.202 52.381 0.00 0.00 46.25 2.43
239 240 1.065701 GCCGATGAACTCGCTTCTAGA 59.934 52.381 0.00 0.00 46.25 2.43
240 241 2.287909 GCCGATGAACTCGCTTCTAGAT 60.288 50.000 0.00 0.00 46.25 1.98
241 242 3.797184 GCCGATGAACTCGCTTCTAGATT 60.797 47.826 0.00 0.00 46.25 2.40
242 243 3.733224 CCGATGAACTCGCTTCTAGATTG 59.267 47.826 0.00 0.00 46.25 2.67
243 244 4.355437 CGATGAACTCGCTTCTAGATTGT 58.645 43.478 0.00 0.00 41.14 2.71
244 245 4.205996 CGATGAACTCGCTTCTAGATTGTG 59.794 45.833 0.00 0.00 41.14 3.33
245 246 4.783764 TGAACTCGCTTCTAGATTGTGA 57.216 40.909 0.00 1.42 0.00 3.58
246 247 5.330455 TGAACTCGCTTCTAGATTGTGAT 57.670 39.130 9.11 0.00 0.00 3.06
247 248 5.344066 TGAACTCGCTTCTAGATTGTGATC 58.656 41.667 9.11 6.69 0.00 2.92
248 249 4.314740 ACTCGCTTCTAGATTGTGATCC 57.685 45.455 9.11 0.00 32.44 3.36
249 250 3.701542 ACTCGCTTCTAGATTGTGATCCA 59.298 43.478 9.11 0.00 32.44 3.41
250 251 4.160439 ACTCGCTTCTAGATTGTGATCCAA 59.840 41.667 9.11 0.00 37.49 3.53
251 252 5.084818 TCGCTTCTAGATTGTGATCCAAA 57.915 39.130 0.00 0.00 36.44 3.28
252 253 5.487433 TCGCTTCTAGATTGTGATCCAAAA 58.513 37.500 0.00 0.00 36.44 2.44
253 254 6.115446 TCGCTTCTAGATTGTGATCCAAAAT 58.885 36.000 0.00 0.00 36.44 1.82
254 255 6.599244 TCGCTTCTAGATTGTGATCCAAAATT 59.401 34.615 0.00 0.00 36.44 1.82
255 256 7.768582 TCGCTTCTAGATTGTGATCCAAAATTA 59.231 33.333 0.00 0.00 36.44 1.40
256 257 8.066595 CGCTTCTAGATTGTGATCCAAAATTAG 58.933 37.037 0.00 4.58 36.44 1.73
257 258 8.348507 GCTTCTAGATTGTGATCCAAAATTAGG 58.651 37.037 0.00 0.00 36.44 2.69
258 259 9.401058 CTTCTAGATTGTGATCCAAAATTAGGT 57.599 33.333 0.00 0.00 36.44 3.08
259 260 9.753674 TTCTAGATTGTGATCCAAAATTAGGTT 57.246 29.630 0.00 0.00 36.44 3.50
328 329 9.453325 GAAAAACTATATTTTCGTTGGTTGACA 57.547 29.630 0.00 0.00 38.92 3.58
329 330 9.974980 AAAAACTATATTTTCGTTGGTTGACAT 57.025 25.926 0.00 0.00 0.00 3.06
330 331 9.974980 AAAACTATATTTTCGTTGGTTGACATT 57.025 25.926 0.00 0.00 0.00 2.71
331 332 9.974980 AAACTATATTTTCGTTGGTTGACATTT 57.025 25.926 0.00 0.00 0.00 2.32
336 337 9.921637 ATATTTTCGTTGGTTGACATTTAACAT 57.078 25.926 0.00 0.00 0.00 2.71
338 339 9.921637 ATTTTCGTTGGTTGACATTTAACATAT 57.078 25.926 0.00 0.00 0.00 1.78
339 340 9.751542 TTTTCGTTGGTTGACATTTAACATATT 57.248 25.926 0.00 0.00 0.00 1.28
340 341 9.751542 TTTCGTTGGTTGACATTTAACATATTT 57.248 25.926 0.00 0.00 0.00 1.40
341 342 9.751542 TTCGTTGGTTGACATTTAACATATTTT 57.248 25.926 0.00 0.00 0.00 1.82
342 343 9.400638 TCGTTGGTTGACATTTAACATATTTTC 57.599 29.630 0.00 0.00 0.00 2.29
343 344 9.405587 CGTTGGTTGACATTTAACATATTTTCT 57.594 29.630 0.00 0.00 0.00 2.52
374 375 9.536510 TTTTTACTATGTTTATGTTAAGGCCCT 57.463 29.630 0.00 0.00 0.00 5.19
375 376 9.536510 TTTTACTATGTTTATGTTAAGGCCCTT 57.463 29.630 0.00 0.00 0.00 3.95
376 377 8.514330 TTACTATGTTTATGTTAAGGCCCTTG 57.486 34.615 6.16 0.00 0.00 3.61
377 378 6.727394 ACTATGTTTATGTTAAGGCCCTTGA 58.273 36.000 6.16 0.00 0.00 3.02
378 379 6.828785 ACTATGTTTATGTTAAGGCCCTTGAG 59.171 38.462 6.16 0.00 0.00 3.02
379 380 5.249780 TGTTTATGTTAAGGCCCTTGAGA 57.750 39.130 6.16 0.00 0.00 3.27
380 381 5.826643 TGTTTATGTTAAGGCCCTTGAGAT 58.173 37.500 6.16 4.55 0.00 2.75
381 382 6.252995 TGTTTATGTTAAGGCCCTTGAGATT 58.747 36.000 6.16 0.00 0.00 2.40
382 383 6.152661 TGTTTATGTTAAGGCCCTTGAGATTG 59.847 38.462 6.16 0.00 0.00 2.67
383 384 3.085952 TGTTAAGGCCCTTGAGATTGG 57.914 47.619 6.16 0.00 0.00 3.16
384 385 2.291540 TGTTAAGGCCCTTGAGATTGGG 60.292 50.000 6.16 0.00 46.00 4.12
385 386 1.979809 TAAGGCCCTTGAGATTGGGA 58.020 50.000 6.16 0.00 46.15 4.37
386 387 1.312884 AAGGCCCTTGAGATTGGGAT 58.687 50.000 0.00 0.00 46.15 3.85
387 388 0.849417 AGGCCCTTGAGATTGGGATC 59.151 55.000 0.00 0.00 46.15 3.36
388 389 0.849417 GGCCCTTGAGATTGGGATCT 59.151 55.000 1.75 0.00 46.15 2.75
389 390 2.057922 GGCCCTTGAGATTGGGATCTA 58.942 52.381 1.75 0.00 46.15 1.98
390 391 2.039613 GGCCCTTGAGATTGGGATCTAG 59.960 54.545 1.75 0.00 46.15 2.43
391 392 2.708325 GCCCTTGAGATTGGGATCTAGT 59.292 50.000 1.75 0.00 46.15 2.57
392 393 3.904339 GCCCTTGAGATTGGGATCTAGTA 59.096 47.826 1.75 0.00 46.15 1.82
393 394 4.534103 GCCCTTGAGATTGGGATCTAGTAT 59.466 45.833 1.75 0.00 46.15 2.12
394 395 5.013599 GCCCTTGAGATTGGGATCTAGTATT 59.986 44.000 1.75 0.00 46.15 1.89
395 396 6.706295 CCCTTGAGATTGGGATCTAGTATTC 58.294 44.000 0.00 0.00 46.15 1.75
396 397 6.500049 CCCTTGAGATTGGGATCTAGTATTCT 59.500 42.308 0.00 0.00 46.15 2.40
397 398 7.676043 CCCTTGAGATTGGGATCTAGTATTCTA 59.324 40.741 0.00 0.00 46.15 2.10
398 399 8.748412 CCTTGAGATTGGGATCTAGTATTCTAG 58.252 40.741 0.05 0.05 42.66 2.43
399 400 9.308000 CTTGAGATTGGGATCTAGTATTCTAGT 57.692 37.037 6.31 0.00 42.66 2.57
400 401 9.661954 TTGAGATTGGGATCTAGTATTCTAGTT 57.338 33.333 6.31 0.00 42.66 2.24
401 402 9.661954 TGAGATTGGGATCTAGTATTCTAGTTT 57.338 33.333 6.31 0.00 42.66 2.66
403 404 8.798402 AGATTGGGATCTAGTATTCTAGTTTCG 58.202 37.037 6.31 0.00 40.84 3.46
404 405 7.893124 TTGGGATCTAGTATTCTAGTTTCGT 57.107 36.000 6.31 0.00 42.88 3.85
405 406 7.507733 TGGGATCTAGTATTCTAGTTTCGTC 57.492 40.000 6.31 3.32 42.88 4.20
406 407 7.288560 TGGGATCTAGTATTCTAGTTTCGTCT 58.711 38.462 6.31 0.00 42.88 4.18
407 408 7.444792 TGGGATCTAGTATTCTAGTTTCGTCTC 59.555 40.741 6.31 0.93 42.88 3.36
408 409 7.360269 GGGATCTAGTATTCTAGTTTCGTCTCG 60.360 44.444 6.31 0.00 42.88 4.04
409 410 6.841443 TCTAGTATTCTAGTTTCGTCTCGG 57.159 41.667 6.31 0.00 42.88 4.63
410 411 6.577103 TCTAGTATTCTAGTTTCGTCTCGGA 58.423 40.000 6.31 0.00 42.88 4.55
411 412 5.482686 AGTATTCTAGTTTCGTCTCGGAC 57.517 43.478 0.00 0.00 0.00 4.79
412 413 3.779271 ATTCTAGTTTCGTCTCGGACC 57.221 47.619 0.00 0.00 0.00 4.46
413 414 1.457346 TCTAGTTTCGTCTCGGACCC 58.543 55.000 0.00 0.00 0.00 4.46
414 415 0.455005 CTAGTTTCGTCTCGGACCCC 59.545 60.000 0.00 0.00 0.00 4.95
426 427 2.604118 GGACCCCGAAATCTCAGGA 58.396 57.895 0.00 0.00 0.00 3.86
427 428 0.178301 GGACCCCGAAATCTCAGGAC 59.822 60.000 0.00 0.00 0.00 3.85
428 429 0.178301 GACCCCGAAATCTCAGGACC 59.822 60.000 0.00 0.00 0.00 4.46
429 430 1.144057 CCCCGAAATCTCAGGACCG 59.856 63.158 0.00 0.00 0.00 4.79
430 431 1.614241 CCCCGAAATCTCAGGACCGT 61.614 60.000 0.00 0.00 0.00 4.83
431 432 0.179108 CCCGAAATCTCAGGACCGTC 60.179 60.000 0.00 0.00 0.00 4.79
432 433 0.179108 CCGAAATCTCAGGACCGTCC 60.179 60.000 9.81 9.81 36.58 4.79
433 434 0.179108 CGAAATCTCAGGACCGTCCC 60.179 60.000 14.32 0.00 37.19 4.46
434 435 1.196012 GAAATCTCAGGACCGTCCCT 58.804 55.000 14.32 0.00 37.19 4.20
547 548 0.458197 CTCTGCTCTCACTCGCTTGG 60.458 60.000 0.00 0.00 0.00 3.61
556 557 2.348998 CTCGCTTGGAGGCCAACT 59.651 61.111 5.01 0.00 38.75 3.16
577 578 5.003804 ACTAATGAAAATGAGAAGCGGTGT 58.996 37.500 0.00 0.00 0.00 4.16
579 580 2.844946 TGAAAATGAGAAGCGGTGTGA 58.155 42.857 0.00 0.00 0.00 3.58
585 586 1.569479 GAGAAGCGGTGTGAAGTGGC 61.569 60.000 0.00 0.00 0.00 5.01
587 596 2.117941 GAAGCGGTGTGAAGTGGCAC 62.118 60.000 10.29 10.29 39.22 5.01
606 615 3.738899 GCACGGAAAGGGAATACGATACA 60.739 47.826 0.00 0.00 0.00 2.29
614 623 0.093026 GAATACGATACATGCGGCGC 59.907 55.000 27.44 27.44 0.00 6.53
638 647 3.291383 CGGGGCGTTGCTTTTCCA 61.291 61.111 0.00 0.00 0.00 3.53
648 657 3.482110 CGTTGCTTTTCCAAACGAGAAAG 59.518 43.478 1.14 0.00 34.84 2.62
702 711 1.942657 CGTGCTAATGATCCAAGGGTG 59.057 52.381 0.00 0.00 0.00 4.61
717 726 1.766496 AGGGTGGAAAAGACGTTCAGA 59.234 47.619 0.00 0.00 0.00 3.27
726 735 0.469331 AGACGTTCAGACTGGGGTCA 60.469 55.000 17.64 0.00 44.36 4.02
733 742 1.351017 TCAGACTGGGGTCATGGAAAC 59.649 52.381 1.81 0.00 44.36 2.78
759 768 3.329814 ACATTCGGGGGTTATAGATTCCC 59.670 47.826 0.00 0.00 40.41 3.97
827 861 3.737172 CGGCAGCAAACGAAGGGG 61.737 66.667 0.00 0.00 0.00 4.79
847 881 4.043435 GGGGGATAGAATTAGCAACCTCAT 59.957 45.833 0.00 0.00 0.00 2.90
864 898 2.288666 TCATGCTAAATTCCGTGAGCC 58.711 47.619 0.00 0.00 33.87 4.70
865 899 1.003545 CATGCTAAATTCCGTGAGCCG 60.004 52.381 0.00 0.00 33.87 5.52
866 900 1.352056 GCTAAATTCCGTGAGCCGC 59.648 57.895 0.00 0.00 34.38 6.53
902 936 5.180492 TCTCGCTTAATTCCGTGAACAATTT 59.820 36.000 0.00 0.00 0.00 1.82
915 958 1.915141 ACAATTTGGCTCACTCCCTG 58.085 50.000 0.78 0.00 0.00 4.45
916 959 1.425066 ACAATTTGGCTCACTCCCTGA 59.575 47.619 0.78 0.00 0.00 3.86
917 960 1.815003 CAATTTGGCTCACTCCCTGAC 59.185 52.381 0.00 0.00 0.00 3.51
918 961 1.067295 ATTTGGCTCACTCCCTGACA 58.933 50.000 0.00 0.00 0.00 3.58
919 962 0.843309 TTTGGCTCACTCCCTGACAA 59.157 50.000 0.00 0.00 0.00 3.18
920 963 0.397941 TTGGCTCACTCCCTGACAAG 59.602 55.000 0.00 0.00 0.00 3.16
921 964 0.764369 TGGCTCACTCCCTGACAAGT 60.764 55.000 0.00 0.00 0.00 3.16
948 991 0.967887 TAGCTGCTCTGAACTCCGCT 60.968 55.000 4.91 0.00 0.00 5.52
987 1030 0.699231 ATCATCCCCTTCCTCCCACC 60.699 60.000 0.00 0.00 0.00 4.61
988 1031 2.044620 ATCCCCTTCCTCCCACCC 59.955 66.667 0.00 0.00 0.00 4.61
989 1032 3.677689 ATCCCCTTCCTCCCACCCC 62.678 68.421 0.00 0.00 0.00 4.95
1286 1336 2.783288 CCTACTCCTTCGTCCCCGC 61.783 68.421 0.00 0.00 0.00 6.13
1384 1448 1.648467 GACCCTCAAAGACATGGCGC 61.648 60.000 0.00 0.00 0.00 6.53
1625 1702 5.988310 TCTATCGGTTGGAGTTTGTTAGA 57.012 39.130 0.00 0.00 0.00 2.10
1632 1709 1.076332 GGAGTTTGTTAGACGCGCAT 58.924 50.000 5.73 0.00 0.00 4.73
1684 1761 1.474077 CTTATGGGTTCTGTGGCTTGC 59.526 52.381 0.00 0.00 0.00 4.01
1785 1866 6.773976 AAAATGGAGTTTCTCACTGTCAAA 57.226 33.333 0.00 0.00 35.01 2.69
1810 1891 5.728637 TCACACTGGCTATGATATACTGG 57.271 43.478 0.00 0.00 0.00 4.00
1818 1899 5.243954 TGGCTATGATATACTGGTCAGACAC 59.756 44.000 2.17 0.00 0.00 3.67
1834 1915 2.690881 ACCTGCCTGGCCGGATAA 60.691 61.111 32.33 5.01 40.22 1.75
1856 1937 1.787155 CGAATTTCTCGCCAGATACGG 59.213 52.381 0.00 0.00 41.49 4.02
1868 1949 3.107601 CCAGATACGGTGATCCCCATAT 58.892 50.000 0.00 0.00 0.00 1.78
1898 1979 0.811616 GGCCAGGACAGAAGTATGCG 60.812 60.000 0.00 0.00 0.00 4.73
2094 2175 0.975556 TGAGTGCGGCTGAGGGATTA 60.976 55.000 0.00 0.00 0.00 1.75
2097 2178 0.947244 GTGCGGCTGAGGGATTATTG 59.053 55.000 0.00 0.00 0.00 1.90
2165 2246 2.124151 GCCGCCATTGTCCAGGAT 60.124 61.111 0.00 0.00 0.00 3.24
2392 2478 7.578310 AGATGTGATTGCTTTATGCTGTTAT 57.422 32.000 0.00 0.00 43.37 1.89
2393 2479 8.681486 AGATGTGATTGCTTTATGCTGTTATA 57.319 30.769 0.00 0.00 43.37 0.98
2625 2712 6.966021 TCTGCTACATTTTGTTAACTGGAAC 58.034 36.000 7.22 0.00 0.00 3.62
2626 2713 6.016610 TCTGCTACATTTTGTTAACTGGAACC 60.017 38.462 7.22 0.00 0.00 3.62
2735 2824 7.221259 ACTCTTGTTTAAATTTTTGTGCGTACC 59.779 33.333 0.00 0.00 0.00 3.34
2919 3268 0.466189 CAGTTGTGGTGAAGCCTGGT 60.466 55.000 0.00 0.00 38.35 4.00
3113 3464 0.955919 GCCTAGAAACCGTGCAGCTT 60.956 55.000 0.00 0.00 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.262417 TGTCACGGCAGATGTCCTAA 58.738 50.000 0.00 0.00 0.00 2.69
1 2 1.262417 TTGTCACGGCAGATGTCCTA 58.738 50.000 0.00 0.00 0.00 2.94
2 3 0.396435 TTTGTCACGGCAGATGTCCT 59.604 50.000 0.00 0.00 0.00 3.85
3 4 1.069227 GTTTTGTCACGGCAGATGTCC 60.069 52.381 0.00 0.00 0.00 4.02
4 5 1.069227 GGTTTTGTCACGGCAGATGTC 60.069 52.381 0.00 0.00 0.00 3.06
5 6 0.951558 GGTTTTGTCACGGCAGATGT 59.048 50.000 0.00 0.00 0.00 3.06
6 7 0.950836 TGGTTTTGTCACGGCAGATG 59.049 50.000 0.00 0.00 0.00 2.90
7 8 0.951558 GTGGTTTTGTCACGGCAGAT 59.048 50.000 0.00 0.00 0.00 2.90
8 9 2.399856 GTGGTTTTGTCACGGCAGA 58.600 52.632 0.00 0.00 0.00 4.26
14 15 2.095919 GGCTATGTCGTGGTTTTGTCAC 60.096 50.000 0.00 0.00 0.00 3.67
15 16 2.147958 GGCTATGTCGTGGTTTTGTCA 58.852 47.619 0.00 0.00 0.00 3.58
16 17 2.159627 CAGGCTATGTCGTGGTTTTGTC 59.840 50.000 0.00 0.00 0.00 3.18
17 18 2.151202 CAGGCTATGTCGTGGTTTTGT 58.849 47.619 0.00 0.00 0.00 2.83
18 19 2.095768 CACAGGCTATGTCGTGGTTTTG 60.096 50.000 0.00 0.00 41.41 2.44
19 20 2.151202 CACAGGCTATGTCGTGGTTTT 58.849 47.619 0.00 0.00 41.41 2.43
20 21 1.808411 CACAGGCTATGTCGTGGTTT 58.192 50.000 0.00 0.00 41.41 3.27
21 22 0.673644 GCACAGGCTATGTCGTGGTT 60.674 55.000 0.00 0.00 41.41 3.67
22 23 1.079127 GCACAGGCTATGTCGTGGT 60.079 57.895 0.00 0.00 41.41 4.16
23 24 3.799753 GCACAGGCTATGTCGTGG 58.200 61.111 0.00 0.00 41.41 4.94
80 81 6.591935 CCCCAATAAGAGCTCTGTATAAACA 58.408 40.000 19.06 0.00 0.00 2.83
81 82 5.470437 GCCCCAATAAGAGCTCTGTATAAAC 59.530 44.000 19.06 0.18 0.00 2.01
82 83 5.369699 AGCCCCAATAAGAGCTCTGTATAAA 59.630 40.000 19.06 0.00 0.00 1.40
83 84 4.907875 AGCCCCAATAAGAGCTCTGTATAA 59.092 41.667 19.06 1.08 0.00 0.98
84 85 4.493618 AGCCCCAATAAGAGCTCTGTATA 58.506 43.478 19.06 6.54 0.00 1.47
85 86 3.321950 AGCCCCAATAAGAGCTCTGTAT 58.678 45.455 19.06 13.77 0.00 2.29
86 87 2.764269 AGCCCCAATAAGAGCTCTGTA 58.236 47.619 19.06 12.07 0.00 2.74
87 88 1.589414 AGCCCCAATAAGAGCTCTGT 58.411 50.000 19.06 10.16 0.00 3.41
88 89 3.326006 TGATAGCCCCAATAAGAGCTCTG 59.674 47.826 19.06 5.25 36.79 3.35
89 90 3.591789 TGATAGCCCCAATAAGAGCTCT 58.408 45.455 11.45 11.45 36.79 4.09
90 91 4.357918 TTGATAGCCCCAATAAGAGCTC 57.642 45.455 5.27 5.27 36.79 4.09
91 92 5.330648 AATTGATAGCCCCAATAAGAGCT 57.669 39.130 0.00 0.00 39.37 4.09
92 93 6.410942 AAAATTGATAGCCCCAATAAGAGC 57.589 37.500 0.00 0.00 33.51 4.09
124 125 4.277258 CATTTCAACAGTCAGCATATCGC 58.723 43.478 0.00 0.00 42.91 4.58
125 126 4.571984 TCCATTTCAACAGTCAGCATATCG 59.428 41.667 0.00 0.00 0.00 2.92
126 127 5.008415 CCTCCATTTCAACAGTCAGCATATC 59.992 44.000 0.00 0.00 0.00 1.63
127 128 4.885907 CCTCCATTTCAACAGTCAGCATAT 59.114 41.667 0.00 0.00 0.00 1.78
128 129 4.019411 TCCTCCATTTCAACAGTCAGCATA 60.019 41.667 0.00 0.00 0.00 3.14
129 130 3.087031 CCTCCATTTCAACAGTCAGCAT 58.913 45.455 0.00 0.00 0.00 3.79
130 131 2.106338 TCCTCCATTTCAACAGTCAGCA 59.894 45.455 0.00 0.00 0.00 4.41
131 132 2.783135 TCCTCCATTTCAACAGTCAGC 58.217 47.619 0.00 0.00 0.00 4.26
132 133 6.656693 ACTTATTCCTCCATTTCAACAGTCAG 59.343 38.462 0.00 0.00 0.00 3.51
133 134 6.542821 ACTTATTCCTCCATTTCAACAGTCA 58.457 36.000 0.00 0.00 0.00 3.41
134 135 6.183360 CGACTTATTCCTCCATTTCAACAGTC 60.183 42.308 0.00 0.00 0.00 3.51
135 136 5.643777 CGACTTATTCCTCCATTTCAACAGT 59.356 40.000 0.00 0.00 0.00 3.55
136 137 5.874810 TCGACTTATTCCTCCATTTCAACAG 59.125 40.000 0.00 0.00 0.00 3.16
137 138 5.800296 TCGACTTATTCCTCCATTTCAACA 58.200 37.500 0.00 0.00 0.00 3.33
138 139 6.106673 TCTCGACTTATTCCTCCATTTCAAC 58.893 40.000 0.00 0.00 0.00 3.18
139 140 6.154534 TCTCTCGACTTATTCCTCCATTTCAA 59.845 38.462 0.00 0.00 0.00 2.69
140 141 5.656859 TCTCTCGACTTATTCCTCCATTTCA 59.343 40.000 0.00 0.00 0.00 2.69
141 142 5.980715 GTCTCTCGACTTATTCCTCCATTTC 59.019 44.000 0.00 0.00 37.19 2.17
142 143 5.908341 GTCTCTCGACTTATTCCTCCATTT 58.092 41.667 0.00 0.00 37.19 2.32
143 144 5.523438 GTCTCTCGACTTATTCCTCCATT 57.477 43.478 0.00 0.00 37.19 3.16
156 157 8.907685 GCTTTGATATGTATAAAGTCTCTCGAC 58.092 37.037 0.00 0.00 40.54 4.20
157 158 8.630037 TGCTTTGATATGTATAAAGTCTCTCGA 58.370 33.333 0.00 0.00 34.69 4.04
158 159 8.803201 TGCTTTGATATGTATAAAGTCTCTCG 57.197 34.615 0.00 0.00 34.69 4.04
162 163 9.890629 TCACTTGCTTTGATATGTATAAAGTCT 57.109 29.630 0.00 0.00 34.69 3.24
170 171 9.481340 GTCTATGATCACTTGCTTTGATATGTA 57.519 33.333 0.00 0.00 33.70 2.29
171 172 7.989170 TGTCTATGATCACTTGCTTTGATATGT 59.011 33.333 0.00 0.00 33.70 2.29
172 173 8.281194 GTGTCTATGATCACTTGCTTTGATATG 58.719 37.037 0.00 0.00 33.70 1.78
173 174 8.209584 AGTGTCTATGATCACTTGCTTTGATAT 58.790 33.333 0.00 0.00 41.33 1.63
174 175 7.559486 AGTGTCTATGATCACTTGCTTTGATA 58.441 34.615 0.00 0.00 41.33 2.15
175 176 6.413052 AGTGTCTATGATCACTTGCTTTGAT 58.587 36.000 0.00 0.00 41.33 2.57
176 177 5.798132 AGTGTCTATGATCACTTGCTTTGA 58.202 37.500 0.00 0.00 41.33 2.69
184 185 9.761504 CAGATGATTTAAGTGTCTATGATCACT 57.238 33.333 0.00 0.00 45.21 3.41
185 186 8.494347 GCAGATGATTTAAGTGTCTATGATCAC 58.506 37.037 0.00 0.00 35.13 3.06
186 187 8.427276 AGCAGATGATTTAAGTGTCTATGATCA 58.573 33.333 0.00 0.00 0.00 2.92
187 188 8.830201 AGCAGATGATTTAAGTGTCTATGATC 57.170 34.615 0.00 0.00 0.00 2.92
188 189 9.926158 CTAGCAGATGATTTAAGTGTCTATGAT 57.074 33.333 0.00 0.00 0.00 2.45
189 190 8.918116 ACTAGCAGATGATTTAAGTGTCTATGA 58.082 33.333 0.00 0.00 0.00 2.15
190 191 9.190858 GACTAGCAGATGATTTAAGTGTCTATG 57.809 37.037 0.00 0.00 0.00 2.23
191 192 9.142014 AGACTAGCAGATGATTTAAGTGTCTAT 57.858 33.333 0.00 0.00 0.00 1.98
192 193 8.526667 AGACTAGCAGATGATTTAAGTGTCTA 57.473 34.615 0.00 0.00 0.00 2.59
193 194 7.416964 AGACTAGCAGATGATTTAAGTGTCT 57.583 36.000 0.00 0.00 0.00 3.41
194 195 7.465245 GCAAGACTAGCAGATGATTTAAGTGTC 60.465 40.741 0.00 0.00 0.00 3.67
195 196 6.314896 GCAAGACTAGCAGATGATTTAAGTGT 59.685 38.462 0.00 0.00 0.00 3.55
196 197 6.238320 GGCAAGACTAGCAGATGATTTAAGTG 60.238 42.308 0.00 0.00 0.00 3.16
197 198 5.819901 GGCAAGACTAGCAGATGATTTAAGT 59.180 40.000 0.00 0.00 0.00 2.24
198 199 5.050499 CGGCAAGACTAGCAGATGATTTAAG 60.050 44.000 0.00 0.00 0.00 1.85
199 200 4.811024 CGGCAAGACTAGCAGATGATTTAA 59.189 41.667 0.00 0.00 0.00 1.52
200 201 4.099419 TCGGCAAGACTAGCAGATGATTTA 59.901 41.667 0.00 0.00 31.38 1.40
201 202 3.118629 TCGGCAAGACTAGCAGATGATTT 60.119 43.478 0.00 0.00 31.38 2.17
202 203 2.432146 TCGGCAAGACTAGCAGATGATT 59.568 45.455 0.00 0.00 31.38 2.57
203 204 2.034878 TCGGCAAGACTAGCAGATGAT 58.965 47.619 0.00 0.00 31.38 2.45
204 205 1.474330 TCGGCAAGACTAGCAGATGA 58.526 50.000 0.00 0.00 31.38 2.92
205 206 2.522836 ATCGGCAAGACTAGCAGATG 57.477 50.000 0.00 0.00 43.52 2.90
206 207 2.034878 TCATCGGCAAGACTAGCAGAT 58.965 47.619 0.00 0.00 45.51 2.90
207 208 1.474330 TCATCGGCAAGACTAGCAGA 58.526 50.000 0.00 0.00 40.30 4.26
208 209 1.929836 GTTCATCGGCAAGACTAGCAG 59.070 52.381 0.00 0.00 0.00 4.24
209 210 1.550524 AGTTCATCGGCAAGACTAGCA 59.449 47.619 0.00 0.00 0.00 3.49
210 211 2.197577 GAGTTCATCGGCAAGACTAGC 58.802 52.381 0.00 0.00 0.00 3.42
222 223 5.344066 TCACAATCTAGAAGCGAGTTCATC 58.656 41.667 0.00 0.00 37.67 2.92
223 224 5.330455 TCACAATCTAGAAGCGAGTTCAT 57.670 39.130 0.00 0.00 37.67 2.57
224 225 4.783764 TCACAATCTAGAAGCGAGTTCA 57.216 40.909 0.00 0.00 37.67 3.18
225 226 4.742659 GGATCACAATCTAGAAGCGAGTTC 59.257 45.833 0.00 0.00 32.11 3.01
226 227 4.160439 TGGATCACAATCTAGAAGCGAGTT 59.840 41.667 0.00 0.00 32.12 3.01
227 228 3.701542 TGGATCACAATCTAGAAGCGAGT 59.298 43.478 0.00 0.00 32.12 4.18
228 229 4.313277 TGGATCACAATCTAGAAGCGAG 57.687 45.455 0.00 0.00 32.12 5.03
229 230 4.736126 TTGGATCACAATCTAGAAGCGA 57.264 40.909 0.00 0.00 33.18 4.93
230 231 5.801350 TTTTGGATCACAATCTAGAAGCG 57.199 39.130 0.00 0.00 39.21 4.68
231 232 8.348507 CCTAATTTTGGATCACAATCTAGAAGC 58.651 37.037 0.00 0.00 39.21 3.86
232 233 9.401058 ACCTAATTTTGGATCACAATCTAGAAG 57.599 33.333 0.00 0.00 39.21 2.85
233 234 9.753674 AACCTAATTTTGGATCACAATCTAGAA 57.246 29.630 0.00 0.00 39.21 2.10
299 300 9.893305 CAACCAACGAAAATATAGTTTTTCTCT 57.107 29.630 0.00 0.00 41.38 3.10
300 301 9.887406 TCAACCAACGAAAATATAGTTTTTCTC 57.113 29.630 0.00 0.00 41.38 2.87
301 302 9.673454 GTCAACCAACGAAAATATAGTTTTTCT 57.327 29.630 0.00 0.00 41.38 2.52
302 303 9.453325 TGTCAACCAACGAAAATATAGTTTTTC 57.547 29.630 0.00 1.11 40.56 2.29
303 304 9.974980 ATGTCAACCAACGAAAATATAGTTTTT 57.025 25.926 0.00 0.00 0.00 1.94
304 305 9.974980 AATGTCAACCAACGAAAATATAGTTTT 57.025 25.926 0.00 0.00 0.00 2.43
305 306 9.974980 AAATGTCAACCAACGAAAATATAGTTT 57.025 25.926 0.00 0.00 0.00 2.66
310 311 9.921637 ATGTTAAATGTCAACCAACGAAAATAT 57.078 25.926 0.00 0.00 0.00 1.28
312 313 9.921637 ATATGTTAAATGTCAACCAACGAAAAT 57.078 25.926 0.00 0.00 0.00 1.82
313 314 9.751542 AATATGTTAAATGTCAACCAACGAAAA 57.248 25.926 0.00 0.00 0.00 2.29
314 315 9.751542 AAATATGTTAAATGTCAACCAACGAAA 57.248 25.926 0.00 0.00 0.00 3.46
315 316 9.751542 AAAATATGTTAAATGTCAACCAACGAA 57.248 25.926 0.00 0.00 0.00 3.85
316 317 9.400638 GAAAATATGTTAAATGTCAACCAACGA 57.599 29.630 0.00 0.00 0.00 3.85
317 318 9.405587 AGAAAATATGTTAAATGTCAACCAACG 57.594 29.630 0.00 0.00 0.00 4.10
348 349 9.536510 AGGGCCTTAACATAAACATAGTAAAAA 57.463 29.630 0.00 0.00 0.00 1.94
349 350 9.536510 AAGGGCCTTAACATAAACATAGTAAAA 57.463 29.630 19.37 0.00 0.00 1.52
350 351 8.962679 CAAGGGCCTTAACATAAACATAGTAAA 58.037 33.333 20.44 0.00 0.00 2.01
351 352 8.330247 TCAAGGGCCTTAACATAAACATAGTAA 58.670 33.333 20.44 0.00 0.00 2.24
352 353 7.863722 TCAAGGGCCTTAACATAAACATAGTA 58.136 34.615 20.44 0.00 0.00 1.82
353 354 6.727394 TCAAGGGCCTTAACATAAACATAGT 58.273 36.000 20.44 0.00 0.00 2.12
354 355 7.054124 TCTCAAGGGCCTTAACATAAACATAG 58.946 38.462 20.44 1.47 0.00 2.23
355 356 6.964464 TCTCAAGGGCCTTAACATAAACATA 58.036 36.000 20.44 0.00 0.00 2.29
356 357 5.826643 TCTCAAGGGCCTTAACATAAACAT 58.173 37.500 20.44 0.00 0.00 2.71
357 358 5.249780 TCTCAAGGGCCTTAACATAAACA 57.750 39.130 20.44 0.00 0.00 2.83
358 359 6.405842 CCAATCTCAAGGGCCTTAACATAAAC 60.406 42.308 20.44 0.00 0.00 2.01
359 360 5.656416 CCAATCTCAAGGGCCTTAACATAAA 59.344 40.000 20.44 0.83 0.00 1.40
360 361 5.200483 CCAATCTCAAGGGCCTTAACATAA 58.800 41.667 20.44 1.95 0.00 1.90
361 362 4.386312 CCCAATCTCAAGGGCCTTAACATA 60.386 45.833 20.44 3.43 38.44 2.29
362 363 3.628257 CCCAATCTCAAGGGCCTTAACAT 60.628 47.826 20.44 7.81 38.44 2.71
363 364 2.291540 CCCAATCTCAAGGGCCTTAACA 60.292 50.000 20.44 5.53 38.44 2.41
364 365 2.025321 TCCCAATCTCAAGGGCCTTAAC 60.025 50.000 20.44 0.00 45.07 2.01
365 366 2.283834 TCCCAATCTCAAGGGCCTTAA 58.716 47.619 20.44 2.84 45.07 1.85
366 367 1.979809 TCCCAATCTCAAGGGCCTTA 58.020 50.000 20.44 3.64 45.07 2.69
367 368 1.216427 GATCCCAATCTCAAGGGCCTT 59.784 52.381 14.48 14.48 45.07 4.35
368 369 0.849417 GATCCCAATCTCAAGGGCCT 59.151 55.000 0.00 0.00 45.07 5.19
369 370 0.849417 AGATCCCAATCTCAAGGGCC 59.151 55.000 0.00 0.00 45.07 5.80
370 371 2.708325 ACTAGATCCCAATCTCAAGGGC 59.292 50.000 0.00 0.00 45.07 5.19
371 372 6.500049 AGAATACTAGATCCCAATCTCAAGGG 59.500 42.308 0.00 0.00 46.90 3.95
372 373 7.552050 AGAATACTAGATCCCAATCTCAAGG 57.448 40.000 0.00 0.00 41.46 3.61
373 374 9.308000 ACTAGAATACTAGATCCCAATCTCAAG 57.692 37.037 10.60 0.00 46.34 3.02
374 375 9.661954 AACTAGAATACTAGATCCCAATCTCAA 57.338 33.333 10.60 0.00 46.34 3.02
375 376 9.661954 AAACTAGAATACTAGATCCCAATCTCA 57.338 33.333 10.60 0.00 46.34 3.27
377 378 8.798402 CGAAACTAGAATACTAGATCCCAATCT 58.202 37.037 10.60 0.00 46.34 2.40
378 379 8.578151 ACGAAACTAGAATACTAGATCCCAATC 58.422 37.037 10.60 0.00 46.34 2.67
379 380 8.480133 ACGAAACTAGAATACTAGATCCCAAT 57.520 34.615 10.60 0.00 46.34 3.16
380 381 7.778853 AGACGAAACTAGAATACTAGATCCCAA 59.221 37.037 10.60 0.00 46.34 4.12
381 382 7.288560 AGACGAAACTAGAATACTAGATCCCA 58.711 38.462 10.60 0.00 46.34 4.37
382 383 7.360269 CGAGACGAAACTAGAATACTAGATCCC 60.360 44.444 10.60 3.93 46.34 3.85
383 384 7.360269 CCGAGACGAAACTAGAATACTAGATCC 60.360 44.444 10.60 0.12 46.34 3.36
384 385 7.384660 TCCGAGACGAAACTAGAATACTAGATC 59.615 40.741 10.60 7.61 46.34 2.75
385 386 7.171337 GTCCGAGACGAAACTAGAATACTAGAT 59.829 40.741 10.60 0.00 46.34 1.98
386 387 6.478344 GTCCGAGACGAAACTAGAATACTAGA 59.522 42.308 10.60 0.00 46.34 2.43
387 388 6.292811 GGTCCGAGACGAAACTAGAATACTAG 60.293 46.154 0.00 0.00 41.25 2.57
388 389 5.525378 GGTCCGAGACGAAACTAGAATACTA 59.475 44.000 0.00 0.00 32.65 1.82
389 390 4.335037 GGTCCGAGACGAAACTAGAATACT 59.665 45.833 0.00 0.00 32.65 2.12
390 391 4.497173 GGGTCCGAGACGAAACTAGAATAC 60.497 50.000 0.00 0.00 32.65 1.89
391 392 3.629398 GGGTCCGAGACGAAACTAGAATA 59.371 47.826 0.00 0.00 32.65 1.75
392 393 2.426381 GGGTCCGAGACGAAACTAGAAT 59.574 50.000 0.00 0.00 32.65 2.40
393 394 1.815003 GGGTCCGAGACGAAACTAGAA 59.185 52.381 0.00 0.00 32.65 2.10
394 395 1.457346 GGGTCCGAGACGAAACTAGA 58.543 55.000 0.00 0.00 32.65 2.43
395 396 0.455005 GGGGTCCGAGACGAAACTAG 59.545 60.000 0.00 0.00 32.65 2.57
396 397 2.571548 GGGGTCCGAGACGAAACTA 58.428 57.895 0.00 0.00 32.65 2.24
397 398 3.374332 GGGGTCCGAGACGAAACT 58.626 61.111 0.00 0.00 32.65 2.66
413 414 0.179108 GGACGGTCCTGAGATTTCGG 60.179 60.000 19.92 0.00 32.53 4.30
414 415 0.179108 GGGACGGTCCTGAGATTTCG 60.179 60.000 25.39 0.00 36.57 3.46
415 416 1.196012 AGGGACGGTCCTGAGATTTC 58.804 55.000 25.39 7.35 36.57 2.17
416 417 3.401032 AGGGACGGTCCTGAGATTT 57.599 52.632 25.39 1.93 36.57 2.17
429 430 4.760047 ATCACGGCGCACAGGGAC 62.760 66.667 10.83 0.00 0.00 4.46
430 431 4.015406 AATCACGGCGCACAGGGA 62.015 61.111 10.83 7.00 0.00 4.20
431 432 3.803082 CAATCACGGCGCACAGGG 61.803 66.667 10.83 0.14 0.00 4.45
432 433 4.465512 GCAATCACGGCGCACAGG 62.466 66.667 10.83 0.00 0.00 4.00
433 434 4.465512 GGCAATCACGGCGCACAG 62.466 66.667 10.83 1.82 0.00 3.66
463 464 3.593794 GGCGCCTACCGTCTCGAT 61.594 66.667 22.15 0.00 38.83 3.59
547 548 6.515272 TTCTCATTTTCATTAGTTGGCCTC 57.485 37.500 3.32 0.00 0.00 4.70
556 557 5.000591 TCACACCGCTTCTCATTTTCATTA 58.999 37.500 0.00 0.00 0.00 1.90
577 578 1.228124 CCCTTTCCGTGCCACTTCA 60.228 57.895 0.00 0.00 0.00 3.02
579 580 0.112412 ATTCCCTTTCCGTGCCACTT 59.888 50.000 0.00 0.00 0.00 3.16
585 586 4.049546 TGTATCGTATTCCCTTTCCGTG 57.950 45.455 0.00 0.00 0.00 4.94
587 596 3.432252 GCATGTATCGTATTCCCTTTCCG 59.568 47.826 0.00 0.00 0.00 4.30
638 647 3.809832 CCACATCACACTCTTTCTCGTTT 59.190 43.478 0.00 0.00 0.00 3.60
648 657 1.661341 GGATCAGCCACATCACACTC 58.339 55.000 0.00 0.00 36.34 3.51
702 711 2.143925 CCCAGTCTGAACGTCTTTTCC 58.856 52.381 0.00 0.00 0.00 3.13
717 726 0.405585 CAGGTTTCCATGACCCCAGT 59.594 55.000 0.00 0.00 37.93 4.00
726 735 1.340991 CCCCGAATGTCAGGTTTCCAT 60.341 52.381 0.00 0.00 0.00 3.41
733 742 2.969950 TCTATAACCCCCGAATGTCAGG 59.030 50.000 0.00 0.00 0.00 3.86
759 768 5.751680 CGCTGTATCCAACCATTATTCTTG 58.248 41.667 0.00 0.00 0.00 3.02
827 861 5.619625 GCATGAGGTTGCTAATTCTATCC 57.380 43.478 0.00 0.00 39.57 2.59
847 881 1.366111 GCGGCTCACGGAATTTAGCA 61.366 55.000 0.00 0.00 44.51 3.49
864 898 1.930100 CGAGAGGCTGCTAATTGCG 59.070 57.895 0.00 0.00 46.63 4.85
865 899 1.645997 GCGAGAGGCTGCTAATTGC 59.354 57.895 0.00 0.00 43.25 3.56
902 936 0.764369 ACTTGTCAGGGAGTGAGCCA 60.764 55.000 0.00 0.00 35.13 4.75
915 958 1.801178 GCAGCTAGGTTGTCACTTGTC 59.199 52.381 0.00 0.00 0.00 3.18
916 959 1.417890 AGCAGCTAGGTTGTCACTTGT 59.582 47.619 0.00 0.00 0.00 3.16
917 960 2.072298 GAGCAGCTAGGTTGTCACTTG 58.928 52.381 0.00 0.00 0.00 3.16
918 961 1.974236 AGAGCAGCTAGGTTGTCACTT 59.026 47.619 0.00 0.00 0.00 3.16
919 962 1.274728 CAGAGCAGCTAGGTTGTCACT 59.725 52.381 0.00 0.00 0.00 3.41
920 963 1.273606 TCAGAGCAGCTAGGTTGTCAC 59.726 52.381 0.00 0.00 0.00 3.67
921 964 1.632589 TCAGAGCAGCTAGGTTGTCA 58.367 50.000 0.00 0.00 0.00 3.58
948 991 3.777910 GGGCGGCTAGGGTTTCGA 61.778 66.667 9.56 0.00 0.00 3.71
1045 1092 2.283529 TGGTCAGGCGGAGGAAGAC 61.284 63.158 0.00 0.00 0.00 3.01
1182 1229 1.648467 GGAAGCTGCCATCCACGTTC 61.648 60.000 5.59 2.04 35.71 3.95
1356 1420 2.885266 GTCTTTGAGGGTCTCCAAAACC 59.115 50.000 0.00 0.00 35.97 3.27
1384 1448 1.432514 CGTGACAAGGGATCACACAG 58.567 55.000 0.00 0.00 45.64 3.66
1597 1674 2.111384 ACTCCAACCGATAGATGCAGT 58.889 47.619 0.00 0.00 39.76 4.40
1632 1709 1.538876 CAGTCCAAGGGGAGGGTGA 60.539 63.158 0.00 0.00 46.12 4.02
1684 1761 2.025418 CCTCGTTGTCGAAACCGGG 61.025 63.158 6.32 0.00 45.61 5.73
1774 1855 4.093998 GCCAGTGTGATATTTGACAGTGAG 59.906 45.833 11.16 4.25 43.44 3.51
1785 1866 7.621285 ACCAGTATATCATAGCCAGTGTGATAT 59.379 37.037 14.79 14.79 46.34 1.63
1818 1899 1.302832 GATTATCCGGCCAGGCAGG 60.303 63.158 24.17 24.17 44.93 4.85
1856 1937 5.711976 CCAGGTTGAATTATATGGGGATCAC 59.288 44.000 0.00 0.00 0.00 3.06
1898 1979 5.452077 CCTTCTCTACCTACTACAATGCCAC 60.452 48.000 0.00 0.00 0.00 5.01
2094 2175 2.375174 TGTAGTGGCTCCAAGGAACAAT 59.625 45.455 0.00 0.00 0.00 2.71
2097 2178 1.623811 TCTGTAGTGGCTCCAAGGAAC 59.376 52.381 0.00 0.00 0.00 3.62
2129 2210 2.484594 GGCCCAGACTCTCTATCAAAGC 60.485 54.545 0.00 0.00 0.00 3.51
2165 2246 8.134895 GCGAAAAATAATCTACATCCCAATCAA 58.865 33.333 0.00 0.00 0.00 2.57
2392 2478 6.182507 ACCCTACTTTGACAATGTCTTGTA 57.817 37.500 14.97 12.49 45.57 2.41
2508 2594 1.967066 TGTTATGCAAACTTGGTGGGG 59.033 47.619 11.34 0.00 0.00 4.96
2625 2712 3.004734 GGGACAAATGATCATTTAGCCGG 59.995 47.826 28.61 19.59 38.84 6.13
2626 2713 3.885297 AGGGACAAATGATCATTTAGCCG 59.115 43.478 28.61 19.90 38.84 5.52
2707 2795 8.690680 ACGCACAAAAATTTAAACAAGAGTAA 57.309 26.923 0.00 0.00 0.00 2.24
2735 2824 6.238130 GCCTACTAACTAGAAAGGCGAAAATG 60.238 42.308 14.70 0.00 41.96 2.32
2849 3198 5.105310 TGCAAGAGTGTACTCCTATTCCTTC 60.105 44.000 8.34 0.00 43.88 3.46


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

AutoCloner maintained by Alex Coulton.