Multiple sequence alignment - TraesCS4D01G001000

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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 TraesCS4D01G001000 chr4D 100.000 4673 0 0 1 4673 627521 632193 0.000000e+00 8630.0
1 TraesCS4D01G001000 chr4D 78.837 860 161 17 2629 3479 349190359 349189512 1.140000e-155 560.0
2 TraesCS4D01G001000 chr4D 96.066 305 12 0 1 305 109549378 109549682 9.030000e-137 497.0
3 TraesCS4D01G001000 chr4D 95.779 308 11 2 1 307 380926474 380926780 3.250000e-136 496.0
4 TraesCS4D01G001000 chr4D 95.738 305 12 1 1 305 31380365 31380062 1.510000e-134 490.0
5 TraesCS4D01G001000 chr4B 92.470 3891 129 40 311 4166 1246811 1243050 0.000000e+00 5411.0
6 TraesCS4D01G001000 chr4B 78.679 863 157 22 2629 3479 431796128 431795281 2.460000e-152 549.0
7 TraesCS4D01G001000 chr4B 76.796 849 133 48 2660 3477 654125473 654126288 7.230000e-113 418.0
8 TraesCS4D01G001000 chr4B 82.022 445 54 21 4195 4626 1242915 1242484 5.750000e-94 355.0
9 TraesCS4D01G001000 chr4B 75.688 436 81 21 3056 3480 638987968 638988389 1.330000e-45 195.0
10 TraesCS4D01G001000 chr4A 92.839 3505 126 57 476 3933 898536 901962 0.000000e+00 4966.0
11 TraesCS4D01G001000 chr4A 79.282 864 150 24 2629 3479 115788280 115789127 1.130000e-160 577.0
12 TraesCS4D01G001000 chr4A 86.456 443 39 18 4197 4628 902342 902774 2.550000e-127 466.0
13 TraesCS4D01G001000 chr4A 90.722 194 7 5 337 529 895328 895511 1.000000e-61 248.0
14 TraesCS4D01G001000 chr4A 85.926 135 18 1 4495 4628 537537337 537537471 4.870000e-30 143.0
15 TraesCS4D01G001000 chr4A 78.088 251 26 15 3936 4166 901993 902234 1.060000e-26 132.0
16 TraesCS4D01G001000 chr4A 80.576 139 13 5 4526 4663 152758567 152758442 1.380000e-15 95.3
17 TraesCS4D01G001000 chr4A 98.077 52 1 0 515 566 898135 898186 1.790000e-14 91.6
18 TraesCS4D01G001000 chr3A 81.298 1294 187 34 2216 3489 186041507 186040249 0.000000e+00 998.0
19 TraesCS4D01G001000 chr3A 74.008 958 224 21 1094 2034 186042596 186041647 2.660000e-97 366.0
20 TraesCS4D01G001000 chr3D 81.206 1293 190 32 2216 3489 159787154 159785896 0.000000e+00 992.0
21 TraesCS4D01G001000 chr3D 73.895 950 231 15 1095 2034 159788236 159787294 9.560000e-97 364.0
22 TraesCS4D01G001000 chr3D 79.167 120 23 2 4503 4620 610165237 610165356 1.080000e-11 82.4
23 TraesCS4D01G001000 chr3B 80.820 1293 195 34 2216 3489 236496818 236495560 0.000000e+00 965.0
24 TraesCS4D01G001000 chr3B 73.739 952 229 19 1095 2034 236497900 236496958 2.070000e-93 353.0
25 TraesCS4D01G001000 chr3B 80.000 150 29 1 4480 4628 823197309 823197458 4.940000e-20 110.0
26 TraesCS4D01G001000 chr3B 78.000 100 16 6 4523 4620 712585971 712585876 1.820000e-04 58.4
27 TraesCS4D01G001000 chr5A 84.625 813 120 4 2669 3480 540053618 540054426 0.000000e+00 804.0
28 TraesCS4D01G001000 chr5A 81.034 116 19 3 4515 4628 593276604 593276490 6.440000e-14 89.8
29 TraesCS4D01G001000 chr2D 96.393 305 10 1 1 305 423246436 423246739 6.980000e-138 501.0
30 TraesCS4D01G001000 chr2D 96.066 305 11 1 1 305 576148490 576148187 3.250000e-136 496.0
31 TraesCS4D01G001000 chr2D 87.368 95 11 1 4523 4616 33709547 33709453 1.780000e-19 108.0
32 TraesCS4D01G001000 chr2D 80.882 136 24 2 4487 4621 634080936 634081070 6.390000e-19 106.0
33 TraesCS4D01G001000 chr7D 95.765 307 12 1 1 307 228340407 228340102 1.170000e-135 494.0
34 TraesCS4D01G001000 chr7D 77.901 181 26 9 4494 4673 597408148 597408315 2.980000e-17 100.0
35 TraesCS4D01G001000 chr7D 84.211 95 14 1 4535 4628 623266322 623266416 1.790000e-14 91.6
36 TraesCS4D01G001000 chr7D 77.401 177 19 9 4495 4663 508896604 508896767 8.330000e-13 86.1
37 TraesCS4D01G001000 chr1D 95.752 306 12 1 1 305 222675461 222675766 4.200000e-135 492.0
38 TraesCS4D01G001000 chr6D 95.738 305 12 1 1 305 290586726 290586423 1.510000e-134 490.0
39 TraesCS4D01G001000 chr6D 95.425 306 14 0 1 306 265800296 265800601 5.430000e-134 488.0
40 TraesCS4D01G001000 chr6D 75.956 183 28 9 4483 4663 319251260 319251092 3.880000e-11 80.5
41 TraesCS4D01G001000 chr6D 96.970 33 1 0 4628 4660 436467887 436467919 6.530000e-04 56.5
42 TraesCS4D01G001000 chr6A 85.938 128 17 1 4495 4621 562139851 562139724 8.160000e-28 135.0
43 TraesCS4D01G001000 chr5D 78.919 185 25 9 4480 4663 348499960 348499789 3.820000e-21 113.0
44 TraesCS4D01G001000 chr5D 79.259 135 17 2 4530 4663 298865288 298865164 3.000000e-12 84.2
45 TraesCS4D01G001000 chr2A 80.142 141 27 1 4491 4630 27641072 27641212 2.300000e-18 104.0
46 TraesCS4D01G001000 chr7A 100.000 29 0 0 4637 4665 166657254 166657226 2.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G001000 chr4D 627521 632193 4672 False 8630.00 8630 100.0000 1 4673 1 chr4D.!!$F1 4672
1 TraesCS4D01G001000 chr4D 349189512 349190359 847 True 560.00 560 78.8370 2629 3479 1 chr4D.!!$R2 850
2 TraesCS4D01G001000 chr4B 1242484 1246811 4327 True 2883.00 5411 87.2460 311 4626 2 chr4B.!!$R2 4315
3 TraesCS4D01G001000 chr4B 431795281 431796128 847 True 549.00 549 78.6790 2629 3479 1 chr4B.!!$R1 850
4 TraesCS4D01G001000 chr4B 654125473 654126288 815 False 418.00 418 76.7960 2660 3477 1 chr4B.!!$F2 817
5 TraesCS4D01G001000 chr4A 895328 902774 7446 False 1180.72 4966 89.2364 337 4628 5 chr4A.!!$F3 4291
6 TraesCS4D01G001000 chr4A 115788280 115789127 847 False 577.00 577 79.2820 2629 3479 1 chr4A.!!$F1 850
7 TraesCS4D01G001000 chr3A 186040249 186042596 2347 True 682.00 998 77.6530 1094 3489 2 chr3A.!!$R1 2395
8 TraesCS4D01G001000 chr3D 159785896 159788236 2340 True 678.00 992 77.5505 1095 3489 2 chr3D.!!$R1 2394
9 TraesCS4D01G001000 chr3B 236495560 236497900 2340 True 659.00 965 77.2795 1095 3489 2 chr3B.!!$R2 2394
10 TraesCS4D01G001000 chr5A 540053618 540054426 808 False 804.00 804 84.6250 2669 3480 1 chr5A.!!$F1 811

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
364 366 0.109723 AGCGGTTTTCAGCCTACCAA 59.890 50.0 0.0 0.0 41.74 3.67 F
1059 4216 0.178767 TCCTCTTGATGATGGTGGCG 59.821 55.0 0.0 0.0 0.00 5.69 F
1752 4918 0.387929 GTGAGTGGTTCTCCGACACA 59.612 55.0 0.0 0.0 42.12 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 5377 0.179094 AAGCGTTGACGAACTGTGGA 60.179 50.0 7.85 0.0 43.02 4.02 R
2763 5938 2.350057 TCTCGATCTCCGTCTGGAAT 57.650 50.0 0.00 0.0 45.87 3.01 R
3695 6888 0.249699 ACGTCCGTGCATCAAGTGAA 60.250 50.0 0.00 0.0 0.00 3.18 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
77 78 6.849085 GAGAAGCCATATTATCTCCTCTCA 57.151 41.667 0.00 0.00 33.75 3.27
78 79 7.422465 GAGAAGCCATATTATCTCCTCTCAT 57.578 40.000 0.00 0.00 33.75 2.90
79 80 8.532186 GAGAAGCCATATTATCTCCTCTCATA 57.468 38.462 0.00 0.00 33.75 2.15
80 81 9.146586 GAGAAGCCATATTATCTCCTCTCATAT 57.853 37.037 0.00 0.00 33.75 1.78
139 140 8.447787 AATTAAAACAAATGATCCTCGTTTCG 57.552 30.769 0.00 0.00 33.65 3.46
140 141 5.682943 AAAACAAATGATCCTCGTTTCGA 57.317 34.783 0.00 0.00 33.65 3.71
141 142 5.880054 AAACAAATGATCCTCGTTTCGAT 57.120 34.783 0.00 0.00 33.65 3.59
142 143 6.978343 AAACAAATGATCCTCGTTTCGATA 57.022 33.333 0.00 0.00 33.65 2.92
143 144 7.553881 AAACAAATGATCCTCGTTTCGATAT 57.446 32.000 0.00 0.00 33.65 1.63
144 145 7.553881 AACAAATGATCCTCGTTTCGATATT 57.446 32.000 0.00 0.00 33.65 1.28
145 146 7.553881 ACAAATGATCCTCGTTTCGATATTT 57.446 32.000 0.00 0.00 33.65 1.40
146 147 7.409697 ACAAATGATCCTCGTTTCGATATTTG 58.590 34.615 0.00 0.00 33.65 2.32
147 148 7.279981 ACAAATGATCCTCGTTTCGATATTTGA 59.720 33.333 19.20 5.93 33.65 2.69
148 149 7.969536 AATGATCCTCGTTTCGATATTTGAT 57.030 32.000 0.00 0.00 34.61 2.57
149 150 9.489084 AAATGATCCTCGTTTCGATATTTGATA 57.511 29.630 0.00 0.00 30.29 2.15
150 151 9.489084 AATGATCCTCGTTTCGATATTTGATAA 57.511 29.630 0.00 0.00 34.61 1.75
151 152 8.880878 TGATCCTCGTTTCGATATTTGATAAA 57.119 30.769 0.00 0.00 34.61 1.40
152 153 9.320352 TGATCCTCGTTTCGATATTTGATAAAA 57.680 29.630 0.00 0.00 34.61 1.52
180 181 7.610865 TCAAATATGAAAACAGTGAAATCCCC 58.389 34.615 0.00 0.00 30.99 4.81
181 182 7.234371 TCAAATATGAAAACAGTGAAATCCCCA 59.766 33.333 0.00 0.00 30.99 4.96
182 183 7.552050 AATATGAAAACAGTGAAATCCCCAA 57.448 32.000 0.00 0.00 0.00 4.12
183 184 4.664150 TGAAAACAGTGAAATCCCCAAC 57.336 40.909 0.00 0.00 0.00 3.77
184 185 4.285863 TGAAAACAGTGAAATCCCCAACT 58.714 39.130 0.00 0.00 0.00 3.16
185 186 4.340950 TGAAAACAGTGAAATCCCCAACTC 59.659 41.667 0.00 0.00 0.00 3.01
186 187 3.884037 AACAGTGAAATCCCCAACTCT 57.116 42.857 0.00 0.00 0.00 3.24
187 188 3.425162 ACAGTGAAATCCCCAACTCTC 57.575 47.619 0.00 0.00 0.00 3.20
188 189 2.982488 ACAGTGAAATCCCCAACTCTCT 59.018 45.455 0.00 0.00 0.00 3.10
189 190 3.008485 ACAGTGAAATCCCCAACTCTCTC 59.992 47.826 0.00 0.00 0.00 3.20
190 191 2.573915 AGTGAAATCCCCAACTCTCTCC 59.426 50.000 0.00 0.00 0.00 3.71
191 192 1.555075 TGAAATCCCCAACTCTCTCCG 59.445 52.381 0.00 0.00 0.00 4.63
192 193 1.555533 GAAATCCCCAACTCTCTCCGT 59.444 52.381 0.00 0.00 0.00 4.69
193 194 0.905357 AATCCCCAACTCTCTCCGTG 59.095 55.000 0.00 0.00 0.00 4.94
194 195 0.978146 ATCCCCAACTCTCTCCGTGG 60.978 60.000 0.00 0.00 0.00 4.94
195 196 2.660064 CCCCAACTCTCTCCGTGGG 61.660 68.421 0.30 0.30 36.40 4.61
196 197 1.913762 CCCAACTCTCTCCGTGGGT 60.914 63.158 0.00 0.00 32.22 4.51
197 198 1.592223 CCAACTCTCTCCGTGGGTC 59.408 63.158 0.00 0.00 0.00 4.46
198 199 1.592223 CAACTCTCTCCGTGGGTCC 59.408 63.158 0.00 0.00 0.00 4.46
199 200 0.900647 CAACTCTCTCCGTGGGTCCT 60.901 60.000 0.00 0.00 0.00 3.85
200 201 0.178929 AACTCTCTCCGTGGGTCCTT 60.179 55.000 0.00 0.00 0.00 3.36
201 202 0.900647 ACTCTCTCCGTGGGTCCTTG 60.901 60.000 0.00 0.00 0.00 3.61
202 203 0.612174 CTCTCTCCGTGGGTCCTTGA 60.612 60.000 0.00 0.00 0.00 3.02
203 204 0.612174 TCTCTCCGTGGGTCCTTGAG 60.612 60.000 0.00 0.00 0.00 3.02
204 205 0.900647 CTCTCCGTGGGTCCTTGAGT 60.901 60.000 0.00 0.00 0.00 3.41
205 206 0.471211 TCTCCGTGGGTCCTTGAGTT 60.471 55.000 0.00 0.00 0.00 3.01
206 207 0.320771 CTCCGTGGGTCCTTGAGTTG 60.321 60.000 0.00 0.00 0.00 3.16
207 208 0.761323 TCCGTGGGTCCTTGAGTTGA 60.761 55.000 0.00 0.00 0.00 3.18
208 209 0.324943 CCGTGGGTCCTTGAGTTGAT 59.675 55.000 0.00 0.00 0.00 2.57
209 210 1.271379 CCGTGGGTCCTTGAGTTGATT 60.271 52.381 0.00 0.00 0.00 2.57
210 211 2.027561 CCGTGGGTCCTTGAGTTGATTA 60.028 50.000 0.00 0.00 0.00 1.75
211 212 3.262420 CGTGGGTCCTTGAGTTGATTAG 58.738 50.000 0.00 0.00 0.00 1.73
212 213 3.056107 CGTGGGTCCTTGAGTTGATTAGA 60.056 47.826 0.00 0.00 0.00 2.10
213 214 4.562757 CGTGGGTCCTTGAGTTGATTAGAA 60.563 45.833 0.00 0.00 0.00 2.10
214 215 5.501156 GTGGGTCCTTGAGTTGATTAGAAT 58.499 41.667 0.00 0.00 0.00 2.40
215 216 5.946377 GTGGGTCCTTGAGTTGATTAGAATT 59.054 40.000 0.00 0.00 0.00 2.17
216 217 6.434340 GTGGGTCCTTGAGTTGATTAGAATTT 59.566 38.462 0.00 0.00 0.00 1.82
217 218 6.659242 TGGGTCCTTGAGTTGATTAGAATTTC 59.341 38.462 0.00 0.00 0.00 2.17
218 219 6.183360 GGGTCCTTGAGTTGATTAGAATTTCG 60.183 42.308 0.00 0.00 0.00 3.46
219 220 6.594159 GGTCCTTGAGTTGATTAGAATTTCGA 59.406 38.462 0.00 0.00 0.00 3.71
220 221 7.201565 GGTCCTTGAGTTGATTAGAATTTCGAG 60.202 40.741 0.00 0.00 0.00 4.04
221 222 6.818644 TCCTTGAGTTGATTAGAATTTCGAGG 59.181 38.462 0.00 0.00 36.50 4.63
222 223 6.818644 CCTTGAGTTGATTAGAATTTCGAGGA 59.181 38.462 0.00 0.00 37.05 3.71
223 224 7.497249 CCTTGAGTTGATTAGAATTTCGAGGAT 59.503 37.037 0.00 0.00 37.05 3.24
224 225 8.425577 TTGAGTTGATTAGAATTTCGAGGATC 57.574 34.615 0.00 0.00 0.00 3.36
244 245 9.515020 GAGGATCGCAAATTGAAATGTAATAAA 57.485 29.630 0.00 0.00 0.00 1.40
245 246 9.868277 AGGATCGCAAATTGAAATGTAATAAAA 57.132 25.926 0.00 0.00 0.00 1.52
305 306 8.876275 CAAATTGGATATTTGGGATGTTACAG 57.124 34.615 0.00 0.00 35.87 2.74
306 307 8.477256 CAAATTGGATATTTGGGATGTTACAGT 58.523 33.333 0.00 0.00 35.87 3.55
307 308 7.587037 ATTGGATATTTGGGATGTTACAGTG 57.413 36.000 0.00 0.00 0.00 3.66
308 309 5.445069 TGGATATTTGGGATGTTACAGTGG 58.555 41.667 0.00 0.00 0.00 4.00
309 310 4.278419 GGATATTTGGGATGTTACAGTGGC 59.722 45.833 0.00 0.00 0.00 5.01
314 315 1.812571 GGGATGTTACAGTGGCTGTTG 59.187 52.381 7.11 0.00 42.59 3.33
322 323 2.912025 GTGGCTGTTGGGTGGTGG 60.912 66.667 0.00 0.00 0.00 4.61
325 327 4.994756 GCTGTTGGGTGGTGGGGG 62.995 72.222 0.00 0.00 0.00 5.40
360 362 2.264005 TTCAAGCGGTTTTCAGCCTA 57.736 45.000 0.00 0.00 41.74 3.93
364 366 0.109723 AGCGGTTTTCAGCCTACCAA 59.890 50.000 0.00 0.00 41.74 3.67
365 367 0.955905 GCGGTTTTCAGCCTACCAAA 59.044 50.000 0.00 0.00 35.07 3.28
366 368 1.544246 GCGGTTTTCAGCCTACCAAAT 59.456 47.619 0.00 0.00 35.07 2.32
367 369 2.415491 GCGGTTTTCAGCCTACCAAATC 60.415 50.000 0.00 0.00 35.07 2.17
368 370 2.817258 CGGTTTTCAGCCTACCAAATCA 59.183 45.455 0.00 0.00 32.12 2.57
409 411 2.631062 TCTTGCCGTAAAAGTGAGAGGA 59.369 45.455 0.00 0.00 0.00 3.71
466 468 2.492088 GTTGGGTTTATGGGAGCTGTTC 59.508 50.000 0.00 0.00 0.00 3.18
488 490 9.296400 TGTTCAAGTGCTATTTTTGTCTTAAAC 57.704 29.630 0.00 0.00 0.00 2.01
512 3586 8.747538 ACAACCCATAGTTTATTCAAGGATAC 57.252 34.615 0.00 0.00 36.18 2.24
564 3638 3.728385 CCATTGAAAAGGGTCCTCTCT 57.272 47.619 0.00 0.00 44.18 3.10
598 3672 2.457813 TGGCATGGCATGGTCTAAAT 57.542 45.000 27.48 0.00 0.00 1.40
599 3673 2.749600 TGGCATGGCATGGTCTAAATT 58.250 42.857 27.48 0.00 0.00 1.82
600 3674 3.908476 TGGCATGGCATGGTCTAAATTA 58.092 40.909 27.48 0.00 0.00 1.40
601 3675 4.285020 TGGCATGGCATGGTCTAAATTAA 58.715 39.130 27.48 0.00 0.00 1.40
602 3676 4.713814 TGGCATGGCATGGTCTAAATTAAA 59.286 37.500 27.48 0.00 0.00 1.52
705 3784 2.183300 CCACACATGGCATGCAGC 59.817 61.111 26.70 3.15 39.82 5.25
803 3900 3.855853 GAAGCTCCCTCCCTCCGC 61.856 72.222 0.00 0.00 0.00 5.54
938 4057 8.260114 ACATCCTTCCATCCATTCAATTTAAAC 58.740 33.333 0.00 0.00 0.00 2.01
940 4059 7.839907 TCCTTCCATCCATTCAATTTAAACTG 58.160 34.615 0.00 0.00 0.00 3.16
954 4075 2.435372 AAACTGAAGTTGCCACCTCA 57.565 45.000 0.00 0.00 38.44 3.86
981 4117 3.940640 CATCGCCGTGATTGCCCG 61.941 66.667 0.00 0.00 34.13 6.13
984 4120 4.823419 CGCCGTGATTGCCCGGTA 62.823 66.667 0.00 0.00 45.91 4.02
985 4121 3.199891 GCCGTGATTGCCCGGTAC 61.200 66.667 0.00 0.00 45.91 3.34
1049 4206 1.379977 TCGCCGTCCTCCTCTTGAT 60.380 57.895 0.00 0.00 0.00 2.57
1052 4209 0.755686 GCCGTCCTCCTCTTGATGAT 59.244 55.000 0.00 0.00 0.00 2.45
1059 4216 0.178767 TCCTCTTGATGATGGTGGCG 59.821 55.000 0.00 0.00 0.00 5.69
1062 4219 2.086869 CTCTTGATGATGGTGGCGTTT 58.913 47.619 0.00 0.00 0.00 3.60
1137 4294 3.235481 TCGGACAAGGACGGGCAA 61.235 61.111 0.00 0.00 0.00 4.52
1504 4664 4.024984 CCCTCCCTCCCTCCACCA 62.025 72.222 0.00 0.00 0.00 4.17
1707 4873 2.844839 GGCGGCTCCTACATCCCT 60.845 66.667 0.00 0.00 0.00 4.20
1752 4918 0.387929 GTGAGTGGTTCTCCGACACA 59.612 55.000 0.00 0.00 42.12 3.72
1839 5005 4.828296 ACCCCCGCCGACGAGTAT 62.828 66.667 0.00 0.00 43.93 2.12
1901 5067 1.361668 CGCGACCCCAAGATGAACAG 61.362 60.000 0.00 0.00 0.00 3.16
2211 5377 2.034066 CCAGACACCGCCACCAAT 59.966 61.111 0.00 0.00 0.00 3.16
3675 6868 0.976073 AACCCACCGGACGATGATCT 60.976 55.000 9.46 0.00 0.00 2.75
3677 6870 0.249489 CCCACCGGACGATGATCTTC 60.249 60.000 9.46 0.00 0.00 2.87
3678 6871 0.459899 CCACCGGACGATGATCTTCA 59.540 55.000 9.46 0.00 0.00 3.02
3679 6872 1.560923 CACCGGACGATGATCTTCAC 58.439 55.000 9.46 2.70 0.00 3.18
3681 6874 1.405821 ACCGGACGATGATCTTCACTC 59.594 52.381 9.46 2.91 0.00 3.51
3682 6875 1.269309 CCGGACGATGATCTTCACTCC 60.269 57.143 0.00 9.81 0.00 3.85
3683 6876 1.405463 CGGACGATGATCTTCACTCCA 59.595 52.381 16.62 0.00 0.00 3.86
3685 6878 2.428890 GGACGATGATCTTCACTCCACT 59.571 50.000 13.60 0.00 0.00 4.00
3688 6881 3.111838 CGATGATCTTCACTCCACTTCG 58.888 50.000 9.10 0.00 0.00 3.79
3695 6888 1.040646 TCACTCCACTTCGCTTCACT 58.959 50.000 0.00 0.00 0.00 3.41
3700 6893 1.412710 TCCACTTCGCTTCACTTCACT 59.587 47.619 0.00 0.00 0.00 3.41
3703 6896 2.866156 CACTTCGCTTCACTTCACTTGA 59.134 45.455 0.00 0.00 0.00 3.02
3704 6897 3.496130 CACTTCGCTTCACTTCACTTGAT 59.504 43.478 0.00 0.00 0.00 2.57
3705 6898 3.496130 ACTTCGCTTCACTTCACTTGATG 59.504 43.478 0.00 0.00 0.00 3.07
3707 6900 1.532437 CGCTTCACTTCACTTGATGCA 59.468 47.619 9.90 0.00 41.80 3.96
3708 6901 2.663879 CGCTTCACTTCACTTGATGCAC 60.664 50.000 9.90 0.00 41.80 4.57
3709 6902 2.663879 GCTTCACTTCACTTGATGCACG 60.664 50.000 0.00 0.00 41.50 5.34
3710 6903 1.511850 TCACTTCACTTGATGCACGG 58.488 50.000 0.00 0.00 0.00 4.94
3765 6963 6.493115 AGATCCTAGATCAGATCGAATGTGTT 59.507 38.462 4.67 0.00 43.03 3.32
3768 6968 6.546034 TCCTAGATCAGATCGAATGTGTTGTA 59.454 38.462 4.67 0.00 0.00 2.41
3773 6973 5.647589 TCAGATCGAATGTGTTGTAGTACC 58.352 41.667 0.00 0.00 0.00 3.34
3805 7005 1.650912 CACCAGCACACAAGACAGC 59.349 57.895 0.00 0.00 0.00 4.40
3806 7006 1.096967 CACCAGCACACAAGACAGCA 61.097 55.000 0.00 0.00 0.00 4.41
3807 7007 0.816825 ACCAGCACACAAGACAGCAG 60.817 55.000 0.00 0.00 0.00 4.24
3808 7008 0.533531 CCAGCACACAAGACAGCAGA 60.534 55.000 0.00 0.00 0.00 4.26
3809 7009 0.585357 CAGCACACAAGACAGCAGAC 59.415 55.000 0.00 0.00 0.00 3.51
3810 7010 0.178767 AGCACACAAGACAGCAGACA 59.821 50.000 0.00 0.00 0.00 3.41
3811 7011 1.202734 AGCACACAAGACAGCAGACAT 60.203 47.619 0.00 0.00 0.00 3.06
3812 7012 1.069432 GCACACAAGACAGCAGACATG 60.069 52.381 0.00 0.00 0.00 3.21
3991 7223 5.420409 ACAAACTCGAGTCTTCTTCAACTT 58.580 37.500 20.33 1.98 0.00 2.66
3992 7224 5.520649 ACAAACTCGAGTCTTCTTCAACTTC 59.479 40.000 20.33 0.00 0.00 3.01
3993 7225 4.920640 ACTCGAGTCTTCTTCAACTTCA 57.079 40.909 13.58 0.00 0.00 3.02
3994 7226 5.263968 ACTCGAGTCTTCTTCAACTTCAA 57.736 39.130 13.58 0.00 0.00 2.69
3995 7227 5.044558 ACTCGAGTCTTCTTCAACTTCAAC 58.955 41.667 13.58 0.00 0.00 3.18
3996 7228 5.163499 ACTCGAGTCTTCTTCAACTTCAACT 60.163 40.000 13.58 0.00 0.00 3.16
3997 7229 5.043903 TCGAGTCTTCTTCAACTTCAACTG 58.956 41.667 0.00 0.00 0.00 3.16
4011 7243 3.767630 AACTGTGGTGTGGCCGACC 62.768 63.158 15.52 15.52 41.21 4.79
4024 7256 3.829044 CGACCGGCGTGGGTGATA 61.829 66.667 6.01 0.00 44.64 2.15
4044 7276 7.505585 GGTGATAGATGTAAATGGAAATGGGAA 59.494 37.037 0.00 0.00 0.00 3.97
4049 7303 4.415596 TGTAAATGGAAATGGGAAGCAGT 58.584 39.130 0.00 0.00 0.00 4.40
4050 7304 4.837860 TGTAAATGGAAATGGGAAGCAGTT 59.162 37.500 0.00 0.00 0.00 3.16
4087 7341 1.153353 TGTTCGAATTTGCTCGGACC 58.847 50.000 0.00 0.00 45.14 4.46
4090 7344 0.320374 TCGAATTTGCTCGGACCTGT 59.680 50.000 0.00 0.00 39.35 4.00
4101 7355 0.600255 CGGACCTGTTTCTTCACGCT 60.600 55.000 0.00 0.00 0.00 5.07
4103 7357 1.540363 GGACCTGTTTCTTCACGCTGA 60.540 52.381 0.00 0.00 0.00 4.26
4106 7360 2.614057 ACCTGTTTCTTCACGCTGAAAG 59.386 45.455 2.82 0.00 35.73 2.62
4110 7364 3.938963 TGTTTCTTCACGCTGAAAGACTT 59.061 39.130 2.82 0.00 35.73 3.01
4145 7399 1.151679 TGGTTGGTTCCGGCAATGA 59.848 52.632 0.00 0.00 0.00 2.57
4166 7420 2.534903 GCGCCTTAGCATCGTTCCC 61.535 63.158 0.00 0.00 39.83 3.97
4171 7460 2.917933 CCTTAGCATCGTTCCCAATCA 58.082 47.619 0.00 0.00 0.00 2.57
4177 7466 2.032549 GCATCGTTCCCAATCATTCTCG 60.033 50.000 0.00 0.00 0.00 4.04
4183 7472 4.570772 CGTTCCCAATCATTCTCGTTGTAT 59.429 41.667 0.00 0.00 0.00 2.29
4189 7478 5.237344 CCAATCATTCTCGTTGTATTCCCTC 59.763 44.000 0.00 0.00 0.00 4.30
4190 7479 5.878406 ATCATTCTCGTTGTATTCCCTCT 57.122 39.130 0.00 0.00 0.00 3.69
4191 7480 5.011090 TCATTCTCGTTGTATTCCCTCTG 57.989 43.478 0.00 0.00 0.00 3.35
4205 7577 1.649664 CCTCTGCAAAGAGATGGTCG 58.350 55.000 4.59 0.00 38.13 4.79
4209 7581 0.684535 TGCAAAGAGATGGTCGGTGA 59.315 50.000 0.00 0.00 0.00 4.02
4222 7594 0.468226 TCGGTGAGCATATGGTTCCC 59.532 55.000 9.14 10.71 0.00 3.97
4230 7602 2.093447 AGCATATGGTTCCCGCTATAGC 60.093 50.000 15.09 15.09 37.78 2.97
4289 7661 4.229582 TCTTTTTACTCCACCAGGGCATAT 59.770 41.667 0.00 0.00 36.21 1.78
4290 7662 4.601406 TTTTACTCCACCAGGGCATATT 57.399 40.909 0.00 0.00 36.21 1.28
4291 7663 4.601406 TTTACTCCACCAGGGCATATTT 57.399 40.909 0.00 0.00 36.21 1.40
4292 7664 4.601406 TTACTCCACCAGGGCATATTTT 57.399 40.909 0.00 0.00 36.21 1.82
4318 7690 9.658799 TTTTTATCTTGTTTGATTTTGGTGTGA 57.341 25.926 0.00 0.00 0.00 3.58
4333 7716 7.881643 TTTGGTGTGATTTTTATGTGTATGC 57.118 32.000 0.00 0.00 0.00 3.14
4346 7729 2.420372 TGTGTATGCGTGTTGTTGTTGT 59.580 40.909 0.00 0.00 0.00 3.32
4347 7730 3.119814 TGTGTATGCGTGTTGTTGTTGTT 60.120 39.130 0.00 0.00 0.00 2.83
4348 7731 3.239483 GTGTATGCGTGTTGTTGTTGTTG 59.761 43.478 0.00 0.00 0.00 3.33
4349 7732 2.645730 ATGCGTGTTGTTGTTGTTGT 57.354 40.000 0.00 0.00 0.00 3.32
4350 7733 2.423926 TGCGTGTTGTTGTTGTTGTT 57.576 40.000 0.00 0.00 0.00 2.83
4351 7734 2.054363 TGCGTGTTGTTGTTGTTGTTG 58.946 42.857 0.00 0.00 0.00 3.33
4352 7735 1.201758 GCGTGTTGTTGTTGTTGTTGC 60.202 47.619 0.00 0.00 0.00 4.17
4357 7740 4.681942 GTGTTGTTGTTGTTGTTGCTTGTA 59.318 37.500 0.00 0.00 0.00 2.41
4363 7746 7.261325 TGTTGTTGTTGTTGCTTGTATGTATT 58.739 30.769 0.00 0.00 0.00 1.89
4373 7756 9.173021 TGTTGCTTGTATGTATTTTAGCTATGT 57.827 29.630 0.00 0.00 0.00 2.29
4407 7792 7.119699 TGTGCTTATTCTGTTTGTATCTCCTTG 59.880 37.037 0.00 0.00 0.00 3.61
4408 7793 7.334421 GTGCTTATTCTGTTTGTATCTCCTTGA 59.666 37.037 0.00 0.00 0.00 3.02
4424 7809 7.437713 TCTCCTTGATGCTCTATTTTAAGGA 57.562 36.000 0.00 0.00 39.71 3.36
4442 7827 5.420725 AAGGAAATAAAATCCACCCTTGC 57.579 39.130 0.00 0.00 39.55 4.01
4443 7828 3.447229 AGGAAATAAAATCCACCCTTGCG 59.553 43.478 0.00 0.00 39.55 4.85
4463 7848 2.558359 CGGGAAAGAAAAGCACCTCAAT 59.442 45.455 0.00 0.00 0.00 2.57
4493 7878 5.095145 AGCATTATGATCACTATCGCCAT 57.905 39.130 0.00 0.00 34.60 4.40
4508 7893 1.675310 CCATCAGAACAAGCCGCCA 60.675 57.895 0.00 0.00 0.00 5.69
4549 7934 0.541863 CCTACCGGAGTTGGCTTGAT 59.458 55.000 9.46 0.00 32.00 2.57
4575 7961 3.914312 TCGATGACAACCAAGAAGTCTC 58.086 45.455 0.00 0.00 33.56 3.36
4598 7985 0.107017 CACATGCCCCTAAGGACCAG 60.107 60.000 0.00 0.00 38.24 4.00
4617 8004 2.409651 GCCCTAGAGTCGCAGTCG 59.590 66.667 0.00 0.00 0.00 4.18
4628 8015 0.318360 TCGCAGTCGTCGTTGTTGAT 60.318 50.000 0.00 0.00 36.96 2.57
4629 8016 0.091344 CGCAGTCGTCGTTGTTGATC 59.909 55.000 0.00 0.00 0.00 2.92
4630 8017 0.091344 GCAGTCGTCGTTGTTGATCG 59.909 55.000 0.00 0.00 0.00 3.69
4631 8018 1.405461 CAGTCGTCGTTGTTGATCGT 58.595 50.000 0.00 0.00 0.00 3.73
4632 8019 1.382419 CAGTCGTCGTTGTTGATCGTC 59.618 52.381 0.00 0.00 0.00 4.20
4633 8020 0.357894 GTCGTCGTTGTTGATCGTCG 59.642 55.000 0.00 0.00 39.11 5.12
4634 8021 0.041047 TCGTCGTTGTTGATCGTCGT 60.041 50.000 0.00 0.00 38.92 4.34
4635 8022 0.774098 CGTCGTTGTTGATCGTCGTT 59.226 50.000 0.00 0.00 35.03 3.85
4636 8023 1.458029 CGTCGTTGTTGATCGTCGTTG 60.458 52.381 0.00 0.00 35.03 4.10
4637 8024 1.519758 GTCGTTGTTGATCGTCGTTGT 59.480 47.619 0.00 0.00 0.00 3.32
4638 8025 2.034339 GTCGTTGTTGATCGTCGTTGTT 60.034 45.455 0.00 0.00 0.00 2.83
4639 8026 2.034423 TCGTTGTTGATCGTCGTTGTTG 60.034 45.455 0.00 0.00 0.00 3.33
4640 8027 2.034423 CGTTGTTGATCGTCGTTGTTGA 60.034 45.455 0.00 0.00 0.00 3.18
4641 8028 3.542485 CGTTGTTGATCGTCGTTGTTGAA 60.542 43.478 0.00 0.00 0.00 2.69
4642 8029 3.579147 TGTTGATCGTCGTTGTTGAAC 57.421 42.857 0.00 0.00 0.00 3.18
4643 8030 2.285756 TGTTGATCGTCGTTGTTGAACC 59.714 45.455 0.00 0.00 0.00 3.62
4644 8031 1.504359 TGATCGTCGTTGTTGAACCC 58.496 50.000 0.00 0.00 0.00 4.11
4645 8032 1.069513 TGATCGTCGTTGTTGAACCCT 59.930 47.619 0.00 0.00 0.00 4.34
4646 8033 2.140717 GATCGTCGTTGTTGAACCCTT 58.859 47.619 0.00 0.00 0.00 3.95
4647 8034 1.292061 TCGTCGTTGTTGAACCCTTG 58.708 50.000 0.00 0.00 0.00 3.61
4648 8035 1.134759 TCGTCGTTGTTGAACCCTTGA 60.135 47.619 0.00 0.00 0.00 3.02
4649 8036 1.666700 CGTCGTTGTTGAACCCTTGAA 59.333 47.619 0.00 0.00 0.00 2.69
4650 8037 2.289547 CGTCGTTGTTGAACCCTTGAAT 59.710 45.455 0.00 0.00 0.00 2.57
4651 8038 3.495377 CGTCGTTGTTGAACCCTTGAATA 59.505 43.478 0.00 0.00 0.00 1.75
4652 8039 4.377022 CGTCGTTGTTGAACCCTTGAATAG 60.377 45.833 0.00 0.00 0.00 1.73
4653 8040 4.753107 GTCGTTGTTGAACCCTTGAATAGA 59.247 41.667 0.00 0.00 0.00 1.98
4654 8041 5.411669 GTCGTTGTTGAACCCTTGAATAGAT 59.588 40.000 0.00 0.00 0.00 1.98
4655 8042 5.642063 TCGTTGTTGAACCCTTGAATAGATC 59.358 40.000 0.00 0.00 0.00 2.75
4656 8043 5.643777 CGTTGTTGAACCCTTGAATAGATCT 59.356 40.000 0.00 0.00 0.00 2.75
4657 8044 6.402550 CGTTGTTGAACCCTTGAATAGATCTG 60.403 42.308 5.18 0.00 0.00 2.90
4658 8045 6.373005 TGTTGAACCCTTGAATAGATCTGA 57.627 37.500 5.18 0.00 0.00 3.27
4659 8046 6.778821 TGTTGAACCCTTGAATAGATCTGAA 58.221 36.000 5.18 0.00 0.00 3.02
4660 8047 7.230747 TGTTGAACCCTTGAATAGATCTGAAA 58.769 34.615 5.18 0.00 0.00 2.69
4661 8048 7.174946 TGTTGAACCCTTGAATAGATCTGAAAC 59.825 37.037 5.18 0.00 0.00 2.78
4662 8049 6.778821 TGAACCCTTGAATAGATCTGAAACA 58.221 36.000 5.18 0.00 0.00 2.83
4663 8050 7.230747 TGAACCCTTGAATAGATCTGAAACAA 58.769 34.615 5.18 5.98 0.00 2.83
4664 8051 7.174946 TGAACCCTTGAATAGATCTGAAACAAC 59.825 37.037 5.18 0.00 0.00 3.32
4665 8052 5.643777 ACCCTTGAATAGATCTGAAACAACG 59.356 40.000 5.18 1.73 0.00 4.10
4666 8053 5.065218 CCCTTGAATAGATCTGAAACAACGG 59.935 44.000 5.18 6.48 0.00 4.44
4667 8054 5.447818 CCTTGAATAGATCTGAAACAACGGC 60.448 44.000 5.18 0.00 0.00 5.68
4668 8055 3.938963 TGAATAGATCTGAAACAACGGCC 59.061 43.478 5.18 0.00 0.00 6.13
4669 8056 3.627395 ATAGATCTGAAACAACGGCCA 57.373 42.857 5.18 0.00 0.00 5.36
4670 8057 2.496899 AGATCTGAAACAACGGCCAT 57.503 45.000 2.24 0.00 0.00 4.40
4671 8058 2.359900 AGATCTGAAACAACGGCCATC 58.640 47.619 2.24 0.00 0.00 3.51
4672 8059 2.083774 GATCTGAAACAACGGCCATCA 58.916 47.619 2.24 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 6.849085 TGAGAGGAGATAATATGGCTTCTC 57.151 41.667 0.00 0.00 35.03 2.87
113 114 9.549509 CGAAACGAGGATCATTTGTTTTAATTA 57.450 29.630 13.16 0.00 33.42 1.40
114 115 8.293867 TCGAAACGAGGATCATTTGTTTTAATT 58.706 29.630 13.16 0.00 33.42 1.40
115 116 7.812648 TCGAAACGAGGATCATTTGTTTTAAT 58.187 30.769 13.16 0.00 33.42 1.40
116 117 7.192148 TCGAAACGAGGATCATTTGTTTTAA 57.808 32.000 13.16 5.49 33.42 1.52
117 118 6.788684 TCGAAACGAGGATCATTTGTTTTA 57.211 33.333 13.16 5.73 33.42 1.52
118 119 5.682943 TCGAAACGAGGATCATTTGTTTT 57.317 34.783 13.16 0.00 33.42 2.43
119 120 5.880054 ATCGAAACGAGGATCATTTGTTT 57.120 34.783 12.25 12.25 39.91 2.83
120 121 7.553881 AATATCGAAACGAGGATCATTTGTT 57.446 32.000 0.00 0.00 39.91 2.83
121 122 7.279981 TCAAATATCGAAACGAGGATCATTTGT 59.720 33.333 16.78 0.00 39.91 2.83
122 123 7.630026 TCAAATATCGAAACGAGGATCATTTG 58.370 34.615 0.00 1.35 39.91 2.32
123 124 7.786178 TCAAATATCGAAACGAGGATCATTT 57.214 32.000 0.00 0.00 39.91 2.32
124 125 7.969536 ATCAAATATCGAAACGAGGATCATT 57.030 32.000 0.00 0.00 39.91 2.57
125 126 9.489084 TTTATCAAATATCGAAACGAGGATCAT 57.511 29.630 0.00 0.00 39.91 2.45
126 127 8.880878 TTTATCAAATATCGAAACGAGGATCA 57.119 30.769 0.00 0.00 39.91 2.92
153 154 9.657419 GGGATTTCACTGTTTTCATATTTGAAT 57.343 29.630 0.00 0.00 41.38 2.57
154 155 8.093927 GGGGATTTCACTGTTTTCATATTTGAA 58.906 33.333 0.00 0.00 40.09 2.69
155 156 7.234371 TGGGGATTTCACTGTTTTCATATTTGA 59.766 33.333 0.00 0.00 0.00 2.69
156 157 7.385267 TGGGGATTTCACTGTTTTCATATTTG 58.615 34.615 0.00 0.00 0.00 2.32
157 158 7.552050 TGGGGATTTCACTGTTTTCATATTT 57.448 32.000 0.00 0.00 0.00 1.40
158 159 7.235399 AGTTGGGGATTTCACTGTTTTCATATT 59.765 33.333 0.00 0.00 0.00 1.28
159 160 6.725834 AGTTGGGGATTTCACTGTTTTCATAT 59.274 34.615 0.00 0.00 0.00 1.78
160 161 6.074648 AGTTGGGGATTTCACTGTTTTCATA 58.925 36.000 0.00 0.00 0.00 2.15
161 162 4.901250 AGTTGGGGATTTCACTGTTTTCAT 59.099 37.500 0.00 0.00 0.00 2.57
162 163 4.285863 AGTTGGGGATTTCACTGTTTTCA 58.714 39.130 0.00 0.00 0.00 2.69
163 164 4.584743 AGAGTTGGGGATTTCACTGTTTTC 59.415 41.667 0.00 0.00 0.00 2.29
164 165 4.546674 AGAGTTGGGGATTTCACTGTTTT 58.453 39.130 0.00 0.00 0.00 2.43
165 166 4.141158 AGAGAGTTGGGGATTTCACTGTTT 60.141 41.667 0.00 0.00 0.00 2.83
166 167 3.395941 AGAGAGTTGGGGATTTCACTGTT 59.604 43.478 0.00 0.00 0.00 3.16
167 168 2.982488 AGAGAGTTGGGGATTTCACTGT 59.018 45.455 0.00 0.00 0.00 3.55
168 169 3.604582 GAGAGAGTTGGGGATTTCACTG 58.395 50.000 0.00 0.00 0.00 3.66
169 170 2.573915 GGAGAGAGTTGGGGATTTCACT 59.426 50.000 0.00 0.00 0.00 3.41
170 171 2.678190 CGGAGAGAGTTGGGGATTTCAC 60.678 54.545 0.00 0.00 0.00 3.18
171 172 1.555075 CGGAGAGAGTTGGGGATTTCA 59.445 52.381 0.00 0.00 0.00 2.69
172 173 1.555533 ACGGAGAGAGTTGGGGATTTC 59.444 52.381 0.00 0.00 0.00 2.17
173 174 1.279271 CACGGAGAGAGTTGGGGATTT 59.721 52.381 0.00 0.00 0.00 2.17
174 175 0.905357 CACGGAGAGAGTTGGGGATT 59.095 55.000 0.00 0.00 0.00 3.01
175 176 0.978146 CCACGGAGAGAGTTGGGGAT 60.978 60.000 0.00 0.00 0.00 3.85
176 177 1.609501 CCACGGAGAGAGTTGGGGA 60.610 63.158 0.00 0.00 0.00 4.81
177 178 2.660064 CCCACGGAGAGAGTTGGGG 61.660 68.421 0.00 0.00 33.17 4.96
178 179 1.889530 GACCCACGGAGAGAGTTGGG 61.890 65.000 3.87 3.87 42.05 4.12
179 180 1.592223 GACCCACGGAGAGAGTTGG 59.408 63.158 0.00 0.00 0.00 3.77
180 181 0.900647 AGGACCCACGGAGAGAGTTG 60.901 60.000 0.00 0.00 0.00 3.16
181 182 0.178929 AAGGACCCACGGAGAGAGTT 60.179 55.000 0.00 0.00 0.00 3.01
182 183 0.900647 CAAGGACCCACGGAGAGAGT 60.901 60.000 0.00 0.00 0.00 3.24
183 184 0.612174 TCAAGGACCCACGGAGAGAG 60.612 60.000 0.00 0.00 0.00 3.20
184 185 0.612174 CTCAAGGACCCACGGAGAGA 60.612 60.000 0.00 0.00 0.00 3.10
185 186 0.900647 ACTCAAGGACCCACGGAGAG 60.901 60.000 6.37 0.00 0.00 3.20
186 187 0.471211 AACTCAAGGACCCACGGAGA 60.471 55.000 6.37 0.00 0.00 3.71
187 188 0.320771 CAACTCAAGGACCCACGGAG 60.321 60.000 0.00 0.00 0.00 4.63
188 189 0.761323 TCAACTCAAGGACCCACGGA 60.761 55.000 0.00 0.00 0.00 4.69
189 190 0.324943 ATCAACTCAAGGACCCACGG 59.675 55.000 0.00 0.00 0.00 4.94
190 191 2.185004 AATCAACTCAAGGACCCACG 57.815 50.000 0.00 0.00 0.00 4.94
191 192 4.553330 TCTAATCAACTCAAGGACCCAC 57.447 45.455 0.00 0.00 0.00 4.61
192 193 5.779241 ATTCTAATCAACTCAAGGACCCA 57.221 39.130 0.00 0.00 0.00 4.51
193 194 6.183360 CGAAATTCTAATCAACTCAAGGACCC 60.183 42.308 0.00 0.00 0.00 4.46
194 195 6.594159 TCGAAATTCTAATCAACTCAAGGACC 59.406 38.462 0.00 0.00 0.00 4.46
195 196 7.201565 CCTCGAAATTCTAATCAACTCAAGGAC 60.202 40.741 0.00 0.00 0.00 3.85
196 197 6.818644 CCTCGAAATTCTAATCAACTCAAGGA 59.181 38.462 0.00 0.00 0.00 3.36
197 198 6.818644 TCCTCGAAATTCTAATCAACTCAAGG 59.181 38.462 0.00 0.00 0.00 3.61
198 199 7.834068 TCCTCGAAATTCTAATCAACTCAAG 57.166 36.000 0.00 0.00 0.00 3.02
199 200 7.222805 CGATCCTCGAAATTCTAATCAACTCAA 59.777 37.037 0.00 0.00 43.74 3.02
200 201 6.697455 CGATCCTCGAAATTCTAATCAACTCA 59.303 38.462 0.00 0.00 43.74 3.41
201 202 6.346199 GCGATCCTCGAAATTCTAATCAACTC 60.346 42.308 0.00 0.00 43.74 3.01
202 203 5.463724 GCGATCCTCGAAATTCTAATCAACT 59.536 40.000 0.00 0.00 43.74 3.16
203 204 5.234329 TGCGATCCTCGAAATTCTAATCAAC 59.766 40.000 0.00 0.00 43.74 3.18
204 205 5.356426 TGCGATCCTCGAAATTCTAATCAA 58.644 37.500 0.00 0.00 43.74 2.57
205 206 4.944048 TGCGATCCTCGAAATTCTAATCA 58.056 39.130 0.00 0.00 43.74 2.57
206 207 5.907197 TTGCGATCCTCGAAATTCTAATC 57.093 39.130 0.00 0.00 43.74 1.75
207 208 6.867662 ATTTGCGATCCTCGAAATTCTAAT 57.132 33.333 0.00 0.00 43.74 1.73
208 209 6.315144 TCAATTTGCGATCCTCGAAATTCTAA 59.685 34.615 0.00 0.00 43.74 2.10
209 210 5.815222 TCAATTTGCGATCCTCGAAATTCTA 59.185 36.000 0.00 0.16 43.74 2.10
210 211 4.635765 TCAATTTGCGATCCTCGAAATTCT 59.364 37.500 0.00 0.00 43.74 2.40
211 212 4.908736 TCAATTTGCGATCCTCGAAATTC 58.091 39.130 0.00 0.00 43.74 2.17
212 213 4.963276 TCAATTTGCGATCCTCGAAATT 57.037 36.364 0.00 7.13 43.74 1.82
213 214 4.963276 TTCAATTTGCGATCCTCGAAAT 57.037 36.364 0.00 1.89 43.74 2.17
214 215 4.757799 TTTCAATTTGCGATCCTCGAAA 57.242 36.364 0.00 0.00 43.74 3.46
215 216 4.155826 ACATTTCAATTTGCGATCCTCGAA 59.844 37.500 0.00 0.00 43.74 3.71
216 217 3.689161 ACATTTCAATTTGCGATCCTCGA 59.311 39.130 0.00 0.00 43.74 4.04
217 218 4.019919 ACATTTCAATTTGCGATCCTCG 57.980 40.909 0.00 0.00 43.89 4.63
218 219 9.515020 TTTATTACATTTCAATTTGCGATCCTC 57.485 29.630 0.00 0.00 0.00 3.71
219 220 9.868277 TTTTATTACATTTCAATTTGCGATCCT 57.132 25.926 0.00 0.00 0.00 3.24
280 281 8.477256 ACTGTAACATCCCAAATATCCAATTTG 58.523 33.333 3.94 3.94 38.39 2.32
281 282 8.477256 CACTGTAACATCCCAAATATCCAATTT 58.523 33.333 0.00 0.00 0.00 1.82
282 283 7.069826 CCACTGTAACATCCCAAATATCCAATT 59.930 37.037 0.00 0.00 0.00 2.32
283 284 6.550854 CCACTGTAACATCCCAAATATCCAAT 59.449 38.462 0.00 0.00 0.00 3.16
284 285 5.890985 CCACTGTAACATCCCAAATATCCAA 59.109 40.000 0.00 0.00 0.00 3.53
285 286 5.445069 CCACTGTAACATCCCAAATATCCA 58.555 41.667 0.00 0.00 0.00 3.41
286 287 4.278419 GCCACTGTAACATCCCAAATATCC 59.722 45.833 0.00 0.00 0.00 2.59
287 288 5.009010 CAGCCACTGTAACATCCCAAATATC 59.991 44.000 0.00 0.00 0.00 1.63
288 289 4.889409 CAGCCACTGTAACATCCCAAATAT 59.111 41.667 0.00 0.00 0.00 1.28
289 290 4.263727 ACAGCCACTGTAACATCCCAAATA 60.264 41.667 0.00 0.00 43.46 1.40
290 291 3.091545 CAGCCACTGTAACATCCCAAAT 58.908 45.455 0.00 0.00 0.00 2.32
291 292 2.158534 ACAGCCACTGTAACATCCCAAA 60.159 45.455 0.00 0.00 43.46 3.28
292 293 1.423541 ACAGCCACTGTAACATCCCAA 59.576 47.619 0.00 0.00 43.46 4.12
293 294 1.064003 ACAGCCACTGTAACATCCCA 58.936 50.000 0.00 0.00 43.46 4.37
294 295 1.812571 CAACAGCCACTGTAACATCCC 59.187 52.381 0.00 0.00 44.62 3.85
295 296 1.812571 CCAACAGCCACTGTAACATCC 59.187 52.381 0.00 0.00 44.62 3.51
296 297 1.812571 CCCAACAGCCACTGTAACATC 59.187 52.381 0.00 0.00 44.62 3.06
297 298 1.144913 ACCCAACAGCCACTGTAACAT 59.855 47.619 0.00 0.00 44.62 2.71
298 299 0.548989 ACCCAACAGCCACTGTAACA 59.451 50.000 0.00 0.00 44.62 2.41
299 300 0.951558 CACCCAACAGCCACTGTAAC 59.048 55.000 0.00 0.00 44.62 2.50
300 301 0.179004 CCACCCAACAGCCACTGTAA 60.179 55.000 0.00 0.00 44.62 2.41
301 302 1.349542 ACCACCCAACAGCCACTGTA 61.350 55.000 0.00 0.00 44.62 2.74
303 304 2.195567 CACCACCCAACAGCCACTG 61.196 63.158 0.00 0.00 37.52 3.66
304 305 2.195683 CACCACCCAACAGCCACT 59.804 61.111 0.00 0.00 0.00 4.00
305 306 2.912025 CCACCACCCAACAGCCAC 60.912 66.667 0.00 0.00 0.00 5.01
306 307 4.217210 CCCACCACCCAACAGCCA 62.217 66.667 0.00 0.00 0.00 4.75
307 308 4.994756 CCCCACCACCCAACAGCC 62.995 72.222 0.00 0.00 0.00 4.85
308 309 4.994756 CCCCCACCACCCAACAGC 62.995 72.222 0.00 0.00 0.00 4.40
309 310 4.994756 GCCCCCACCACCCAACAG 62.995 72.222 0.00 0.00 0.00 3.16
322 323 2.751837 CTCCAAGAAAGCGGCCCC 60.752 66.667 0.00 0.00 0.00 5.80
325 327 0.951558 TGAAACTCCAAGAAAGCGGC 59.048 50.000 0.00 0.00 0.00 6.53
334 336 2.755655 TGAAAACCGCTTGAAACTCCAA 59.244 40.909 0.00 0.00 0.00 3.53
409 411 1.133606 CCCGTATAATTGCCCCCAACT 60.134 52.381 0.00 0.00 32.95 3.16
488 490 7.713507 TCGTATCCTTGAATAAACTATGGGTTG 59.286 37.037 0.00 0.00 38.29 3.77
491 3565 8.671384 TTTCGTATCCTTGAATAAACTATGGG 57.329 34.615 0.00 0.00 0.00 4.00
493 3567 9.046296 AGCTTTCGTATCCTTGAATAAACTATG 57.954 33.333 0.00 0.00 0.00 2.23
512 3586 0.947244 AGCAACTCCAACAGCTTTCG 59.053 50.000 0.00 0.00 32.52 3.46
560 3634 3.405831 CCATGCAACACAAGAGAAGAGA 58.594 45.455 0.00 0.00 0.00 3.10
561 3635 2.095364 GCCATGCAACACAAGAGAAGAG 60.095 50.000 0.00 0.00 0.00 2.85
562 3636 1.881973 GCCATGCAACACAAGAGAAGA 59.118 47.619 0.00 0.00 0.00 2.87
563 3637 1.610038 TGCCATGCAACACAAGAGAAG 59.390 47.619 0.00 0.00 34.76 2.85
564 3638 1.689984 TGCCATGCAACACAAGAGAA 58.310 45.000 0.00 0.00 34.76 2.87
803 3900 1.886422 AGAGAAAGCTAGGGGAAGGG 58.114 55.000 0.00 0.00 0.00 3.95
938 4057 3.799281 TTTTTGAGGTGGCAACTTCAG 57.201 42.857 6.46 0.00 42.66 3.02
985 4121 2.931713 GCCATGAGGGACGACGTACG 62.932 65.000 15.01 15.01 42.10 3.67
986 4122 1.226888 GCCATGAGGGACGACGTAC 60.227 63.158 0.10 0.10 40.01 3.67
987 4123 2.767445 CGCCATGAGGGACGACGTA 61.767 63.158 0.00 0.00 40.01 3.57
988 4124 4.129737 CGCCATGAGGGACGACGT 62.130 66.667 0.00 0.00 40.01 4.34
989 4125 4.873129 CCGCCATGAGGGACGACG 62.873 72.222 0.00 0.00 40.01 5.12
1049 4206 2.123988 GAACGCAAACGCCACCATCA 62.124 55.000 0.00 0.00 45.53 3.07
1052 4209 3.943034 CGAACGCAAACGCCACCA 61.943 61.111 0.00 0.00 45.53 4.17
1137 4294 2.282958 TTCCTGCCGTCCTCGTCT 60.283 61.111 0.00 0.00 35.01 4.18
1194 4354 1.450312 CATGACGGAGGACTTGCCC 60.450 63.158 0.00 0.00 37.37 5.36
1626 4792 1.376942 GAGGGACTGGTCGTCGAGA 60.377 63.158 0.00 0.00 43.79 4.04
1734 4900 0.387929 GTGTGTCGGAGAACCACTCA 59.612 55.000 0.00 0.00 46.54 3.41
1752 4918 3.512516 GCGCCGTAGACGTAGGGT 61.513 66.667 0.00 0.00 36.67 4.34
1901 5067 1.318576 CCAGGTGAGGTTGTTGTTCC 58.681 55.000 0.00 0.00 0.00 3.62
2160 5326 3.005539 AGGATGGTGTCGCTGCCT 61.006 61.111 0.00 0.00 0.00 4.75
2211 5377 0.179094 AAGCGTTGACGAACTGTGGA 60.179 50.000 7.85 0.00 43.02 4.02
2763 5938 2.350057 TCTCGATCTCCGTCTGGAAT 57.650 50.000 0.00 0.00 45.87 3.01
3675 6868 1.412710 AGTGAAGCGAAGTGGAGTGAA 59.587 47.619 0.00 0.00 0.00 3.18
3677 6870 1.795286 GAAGTGAAGCGAAGTGGAGTG 59.205 52.381 0.00 0.00 0.00 3.51
3678 6871 1.412710 TGAAGTGAAGCGAAGTGGAGT 59.587 47.619 0.00 0.00 0.00 3.85
3679 6872 1.795286 GTGAAGTGAAGCGAAGTGGAG 59.205 52.381 0.00 0.00 0.00 3.86
3681 6874 1.871080 AGTGAAGTGAAGCGAAGTGG 58.129 50.000 0.00 0.00 0.00 4.00
3682 6875 2.866156 TCAAGTGAAGTGAAGCGAAGTG 59.134 45.455 0.00 0.00 0.00 3.16
3683 6876 3.179443 TCAAGTGAAGTGAAGCGAAGT 57.821 42.857 0.00 0.00 0.00 3.01
3685 6878 2.224079 GCATCAAGTGAAGTGAAGCGAA 59.776 45.455 0.00 0.00 30.95 4.70
3688 6881 2.663879 CGTGCATCAAGTGAAGTGAAGC 60.664 50.000 0.00 0.00 39.54 3.86
3695 6888 0.249699 ACGTCCGTGCATCAAGTGAA 60.250 50.000 0.00 0.00 0.00 3.18
3700 6893 1.443702 CGAGACGTCCGTGCATCAA 60.444 57.895 13.01 0.00 0.00 2.57
3765 6963 1.298953 ACGTAGGGAGGGGTACTACA 58.701 55.000 0.00 0.00 37.52 2.74
3768 6968 0.553333 GGTACGTAGGGAGGGGTACT 59.447 60.000 0.00 0.00 36.41 2.73
3773 6973 1.000739 TGGTGGTACGTAGGGAGGG 59.999 63.158 0.00 0.00 0.00 4.30
3817 7017 4.730600 CATGCATGCATTTCCATGAATG 57.269 40.909 30.32 13.05 46.99 2.67
3860 7064 3.716195 CTCCGATGCACCCACCCA 61.716 66.667 0.00 0.00 0.00 4.51
3991 7223 2.203139 CGGCCACACCACAGTTGA 60.203 61.111 2.24 0.00 39.03 3.18
3992 7224 2.203139 TCGGCCACACCACAGTTG 60.203 61.111 2.24 0.00 39.03 3.16
3993 7225 2.203153 GTCGGCCACACCACAGTT 60.203 61.111 2.24 0.00 39.03 3.16
3994 7226 4.250305 GGTCGGCCACACCACAGT 62.250 66.667 14.91 0.00 39.03 3.55
4011 7243 0.671796 TACATCTATCACCCACGCCG 59.328 55.000 0.00 0.00 0.00 6.46
4019 7251 8.463930 TTCCCATTTCCATTTACATCTATCAC 57.536 34.615 0.00 0.00 0.00 3.06
4024 7256 5.271598 TGCTTCCCATTTCCATTTACATCT 58.728 37.500 0.00 0.00 0.00 2.90
4044 7276 2.484264 GCCTTGAACGTTATCAACTGCT 59.516 45.455 0.00 0.00 35.55 4.24
4049 7303 5.446143 AACAATGCCTTGAACGTTATCAA 57.554 34.783 8.84 0.97 37.70 2.57
4050 7304 4.377943 CGAACAATGCCTTGAACGTTATCA 60.378 41.667 8.84 0.00 36.20 2.15
4087 7341 3.557595 AGTCTTTCAGCGTGAAGAAACAG 59.442 43.478 1.21 0.00 37.70 3.16
4090 7344 3.938963 ACAAGTCTTTCAGCGTGAAGAAA 59.061 39.130 1.21 0.00 37.70 2.52
4101 7355 8.822805 ACTAATGGGTAGATAACAAGTCTTTCA 58.177 33.333 0.00 0.00 33.61 2.69
4103 7357 8.047310 CCACTAATGGGTAGATAACAAGTCTTT 58.953 37.037 0.00 0.00 43.04 2.52
4145 7399 3.659089 AACGATGCTAAGGCGCCGT 62.659 57.895 23.20 22.12 45.50 5.68
4152 7406 4.818546 AGAATGATTGGGAACGATGCTAAG 59.181 41.667 0.00 0.00 33.38 2.18
4166 7420 6.018425 CAGAGGGAATACAACGAGAATGATTG 60.018 42.308 0.00 0.00 0.00 2.67
4171 7460 3.197766 TGCAGAGGGAATACAACGAGAAT 59.802 43.478 0.00 0.00 0.00 2.40
4177 7466 4.579869 TCTCTTTGCAGAGGGAATACAAC 58.420 43.478 3.92 0.00 46.17 3.32
4183 7472 1.988107 ACCATCTCTTTGCAGAGGGAA 59.012 47.619 11.38 0.00 45.66 3.97
4189 7478 1.081892 CACCGACCATCTCTTTGCAG 58.918 55.000 0.00 0.00 0.00 4.41
4190 7479 0.684535 TCACCGACCATCTCTTTGCA 59.315 50.000 0.00 0.00 0.00 4.08
4191 7480 1.363744 CTCACCGACCATCTCTTTGC 58.636 55.000 0.00 0.00 0.00 3.68
4238 7610 7.806409 TCAAAGTGATCAAAACAATGAGAGA 57.194 32.000 0.00 0.00 31.76 3.10
4239 7611 8.133627 ACTTCAAAGTGATCAAAACAATGAGAG 58.866 33.333 0.00 1.42 37.98 3.20
4292 7664 9.658799 TCACACCAAAATCAAACAAGATAAAAA 57.341 25.926 0.00 0.00 0.00 1.94
4296 7668 9.829507 AAAATCACACCAAAATCAAACAAGATA 57.170 25.926 0.00 0.00 0.00 1.98
4313 7685 6.083630 ACACGCATACACATAAAAATCACAC 58.916 36.000 0.00 0.00 0.00 3.82
4314 7686 6.247727 ACACGCATACACATAAAAATCACA 57.752 33.333 0.00 0.00 0.00 3.58
4315 7687 6.580791 ACAACACGCATACACATAAAAATCAC 59.419 34.615 0.00 0.00 0.00 3.06
4316 7688 6.673106 ACAACACGCATACACATAAAAATCA 58.327 32.000 0.00 0.00 0.00 2.57
4317 7689 7.114247 ACAACAACACGCATACACATAAAAATC 59.886 33.333 0.00 0.00 0.00 2.17
4318 7690 6.920758 ACAACAACACGCATACACATAAAAAT 59.079 30.769 0.00 0.00 0.00 1.82
4333 7716 2.323959 AGCAACAACAACAACAACACG 58.676 42.857 0.00 0.00 0.00 4.49
4347 7730 9.173021 ACATAGCTAAAATACATACAAGCAACA 57.827 29.630 0.00 0.00 32.42 3.33
4350 7733 8.988934 GCTACATAGCTAAAATACATACAAGCA 58.011 33.333 0.00 0.00 45.62 3.91
4442 7827 1.604604 TGAGGTGCTTTTCTTTCCCG 58.395 50.000 0.00 0.00 0.00 5.14
4443 7828 3.573967 TGATTGAGGTGCTTTTCTTTCCC 59.426 43.478 0.00 0.00 0.00 3.97
4481 7866 3.785486 CTTGTTCTGATGGCGATAGTGA 58.215 45.455 0.00 0.00 39.35 3.41
4487 7872 4.301505 GGCTTGTTCTGATGGCGA 57.698 55.556 0.00 0.00 0.00 5.54
4493 7878 2.250939 CGTTGGCGGCTTGTTCTGA 61.251 57.895 11.43 0.00 0.00 3.27
4539 7924 4.811024 TGTCATCGATAAGATCAAGCCAAC 59.189 41.667 0.00 0.00 37.52 3.77
4549 7934 6.037786 ACTTCTTGGTTGTCATCGATAAGA 57.962 37.500 0.00 0.00 0.00 2.10
4617 8004 1.519758 ACAACGACGATCAACAACGAC 59.480 47.619 0.00 0.00 0.00 4.34
4628 8015 1.134759 TCAAGGGTTCAACAACGACGA 60.135 47.619 0.00 0.00 32.68 4.20
4629 8016 1.292061 TCAAGGGTTCAACAACGACG 58.708 50.000 0.00 0.00 32.68 5.12
4630 8017 3.982576 ATTCAAGGGTTCAACAACGAC 57.017 42.857 0.00 0.00 32.68 4.34
4631 8018 4.963373 TCTATTCAAGGGTTCAACAACGA 58.037 39.130 0.00 0.00 32.68 3.85
4632 8019 5.643777 AGATCTATTCAAGGGTTCAACAACG 59.356 40.000 0.00 0.00 32.68 4.10
4633 8020 6.655003 TCAGATCTATTCAAGGGTTCAACAAC 59.345 38.462 0.00 0.00 0.00 3.32
4634 8021 6.778821 TCAGATCTATTCAAGGGTTCAACAA 58.221 36.000 0.00 0.00 0.00 2.83
4635 8022 6.373005 TCAGATCTATTCAAGGGTTCAACA 57.627 37.500 0.00 0.00 0.00 3.33
4636 8023 7.174946 TGTTTCAGATCTATTCAAGGGTTCAAC 59.825 37.037 0.00 0.00 0.00 3.18
4637 8024 7.230747 TGTTTCAGATCTATTCAAGGGTTCAA 58.769 34.615 0.00 0.00 0.00 2.69
4638 8025 6.778821 TGTTTCAGATCTATTCAAGGGTTCA 58.221 36.000 0.00 0.00 0.00 3.18
4639 8026 7.530863 GTTGTTTCAGATCTATTCAAGGGTTC 58.469 38.462 0.00 0.00 0.00 3.62
4640 8027 6.149474 CGTTGTTTCAGATCTATTCAAGGGTT 59.851 38.462 0.00 0.00 0.00 4.11
4641 8028 5.643777 CGTTGTTTCAGATCTATTCAAGGGT 59.356 40.000 0.00 0.00 0.00 4.34
4642 8029 5.065218 CCGTTGTTTCAGATCTATTCAAGGG 59.935 44.000 17.66 17.66 34.67 3.95
4643 8030 5.447818 GCCGTTGTTTCAGATCTATTCAAGG 60.448 44.000 0.00 5.14 0.00 3.61
4644 8031 5.447818 GGCCGTTGTTTCAGATCTATTCAAG 60.448 44.000 0.00 0.00 0.00 3.02
4645 8032 4.394920 GGCCGTTGTTTCAGATCTATTCAA 59.605 41.667 0.00 0.00 0.00 2.69
4646 8033 3.938963 GGCCGTTGTTTCAGATCTATTCA 59.061 43.478 0.00 0.00 0.00 2.57
4647 8034 3.938963 TGGCCGTTGTTTCAGATCTATTC 59.061 43.478 0.00 0.00 0.00 1.75
4648 8035 3.950397 TGGCCGTTGTTTCAGATCTATT 58.050 40.909 0.00 0.00 0.00 1.73
4649 8036 3.627395 TGGCCGTTGTTTCAGATCTAT 57.373 42.857 0.00 0.00 0.00 1.98
4650 8037 3.055458 TGATGGCCGTTGTTTCAGATCTA 60.055 43.478 0.00 0.00 0.00 1.98
4651 8038 2.290260 TGATGGCCGTTGTTTCAGATCT 60.290 45.455 0.00 0.00 0.00 2.75
4652 8039 2.083774 TGATGGCCGTTGTTTCAGATC 58.916 47.619 0.00 0.00 0.00 2.75
4653 8040 2.198827 TGATGGCCGTTGTTTCAGAT 57.801 45.000 0.00 0.00 0.00 2.90
4654 8041 3.715871 TGATGGCCGTTGTTTCAGA 57.284 47.368 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.