Multiple sequence alignment - TraesCS1D01G089500

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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 TraesCS1D01G089500 chr1D 100.000 6688 0 0 1 6688 75672428 75665741 0.000000e+00 12351.0
1 TraesCS1D01G089500 chr1D 100.000 521 0 0 6939 7459 75665490 75664970 0.000000e+00 963.0
2 TraesCS1D01G089500 chr1D 93.156 263 16 2 7198 7459 304333325 304333586 1.170000e-102 385.0
3 TraesCS1D01G089500 chr1D 83.422 374 52 5 2121 2487 79103606 79103976 9.270000e-89 339.0
4 TraesCS1D01G089500 chr1A 95.995 3745 97 18 755 4470 76501511 76497791 0.000000e+00 6035.0
5 TraesCS1D01G089500 chr1A 95.494 1598 55 9 5099 6686 76496963 76495373 0.000000e+00 2536.0
6 TraesCS1D01G089500 chr1A 96.626 652 10 6 4464 5105 76497691 76497042 0.000000e+00 1072.0
7 TraesCS1D01G089500 chr1A 88.426 432 33 14 341 761 76504460 76504035 8.640000e-139 505.0
8 TraesCS1D01G089500 chr1A 92.720 261 16 3 7195 7453 376212296 376212555 2.540000e-99 374.0
9 TraesCS1D01G089500 chr1B 94.590 2680 89 11 818 3484 119129184 119126548 0.000000e+00 4095.0
10 TraesCS1D01G089500 chr1B 95.118 1188 39 11 4343 5517 119122976 119121795 0.000000e+00 1855.0
11 TraesCS1D01G089500 chr1B 94.366 852 36 3 3475 4326 119124185 119123346 0.000000e+00 1297.0
12 TraesCS1D01G089500 chr1B 93.690 840 42 7 5854 6686 119121732 119120897 0.000000e+00 1247.0
13 TraesCS1D01G089500 chr5B 95.019 522 24 2 6939 7459 10359358 10359878 0.000000e+00 819.0
14 TraesCS1D01G089500 chr3D 94.444 522 27 2 6939 7459 157760321 157759801 0.000000e+00 802.0
15 TraesCS1D01G089500 chr3D 82.900 269 33 11 1 267 177615058 177614801 5.820000e-56 230.0
16 TraesCS1D01G089500 chr3D 96.875 32 1 0 4629 4660 190315247 190315216 4.000000e-03 54.7
17 TraesCS1D01G089500 chr5D 95.821 335 14 0 6939 7273 11427263 11426929 6.580000e-150 542.0
18 TraesCS1D01G089500 chr5D 92.776 263 17 2 7198 7459 427566291 427566030 5.460000e-101 379.0
19 TraesCS1D01G089500 chr5D 96.330 109 4 0 6939 7047 353691620 353691512 5.950000e-41 180.0
20 TraesCS1D01G089500 chr2D 94.643 280 15 0 6994 7273 389694553 389694274 1.150000e-117 435.0
21 TraesCS1D01G089500 chr2D 83.271 269 33 10 1 267 334925937 334926195 3.480000e-58 237.0
22 TraesCS1D01G089500 chr2D 82.836 268 35 10 1 267 634175006 634175263 5.820000e-56 230.0
23 TraesCS1D01G089500 chr6D 93.536 263 14 3 7198 7459 461370342 461370602 9.080000e-104 388.0
24 TraesCS1D01G089500 chr6D 92.776 263 15 4 7198 7459 435976708 435976449 1.960000e-100 377.0
25 TraesCS1D01G089500 chr6D 84.015 269 31 10 1 267 81701846 81701588 1.610000e-61 248.0
26 TraesCS1D01G089500 chr6D 83.643 269 32 10 1 267 466599026 466598768 7.480000e-60 243.0
27 TraesCS1D01G089500 chr6D 82.042 284 39 10 1 282 196195155 196194882 1.620000e-56 231.0
28 TraesCS1D01G089500 chr7D 92.776 263 17 2 7198 7459 156773548 156773809 5.460000e-101 379.0
29 TraesCS1D01G089500 chr2A 92.395 263 18 2 7198 7459 251082825 251082564 2.540000e-99 374.0
30 TraesCS1D01G089500 chr4D 83.271 269 33 10 1 267 298875942 298875684 3.480000e-58 237.0
31 TraesCS1D01G089500 chr4D 82.900 269 34 10 1 267 121825565 121825307 1.620000e-56 231.0
32 TraesCS1D01G089500 chr4D 82.900 269 34 10 1 267 207040574 207040832 1.620000e-56 231.0
33 TraesCS1D01G089500 chr7A 78.548 303 51 12 1 296 29916203 29916498 3.550000e-43 187.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G089500 chr1D 75664970 75672428 7458 True 6657.0 12351 100.00000 1 7459 2 chr1D.!!$R1 7458
1 TraesCS1D01G089500 chr1A 76495373 76504460 9087 True 2537.0 6035 94.13525 341 6686 4 chr1A.!!$R1 6345
2 TraesCS1D01G089500 chr1B 119120897 119129184 8287 True 2123.5 4095 94.44100 818 6686 4 chr1B.!!$R1 5868
3 TraesCS1D01G089500 chr5B 10359358 10359878 520 False 819.0 819 95.01900 6939 7459 1 chr5B.!!$F1 520
4 TraesCS1D01G089500 chr3D 157759801 157760321 520 True 802.0 802 94.44400 6939 7459 1 chr3D.!!$R1 520

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
766 3305 0.109179 AACTGTATCGCGCAACCGTA 60.109 50.000 8.75 0.00 36.67 4.02 F
786 3325 0.179006 GAGAAATAGCCCTGGCCCAG 60.179 60.000 2.91 2.91 43.17 4.45 F
788 3327 0.480252 GAAATAGCCCTGGCCCAGAT 59.520 55.000 13.74 0.00 43.17 2.90 F
859 3405 0.902516 GCCAGTCCAGAGTCCAGACT 60.903 60.000 0.00 0.00 45.84 3.24 F
1251 3809 1.407258 CACGAGATGGAGAAGACCCTC 59.593 57.143 0.00 0.00 0.00 4.30 F
1275 3833 2.055042 GCTCCGCCTCCTCTTCTCA 61.055 63.158 0.00 0.00 0.00 3.27 F
2465 5023 2.224113 TGGAACCTACTCACGTGGTTTC 60.224 50.000 17.00 10.80 43.28 2.78 F
3771 8703 2.122783 TTAGTCCCCAAAGAATGCCG 57.877 50.000 0.00 0.00 0.00 5.69 F
3780 8712 3.304928 CCCAAAGAATGCCGATCTTATGC 60.305 47.826 0.00 0.00 36.14 3.14 F
5568 11063 3.181446 TGAACATGTGATGGACTTGTGGA 60.181 43.478 0.00 0.00 41.01 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2680 5238 0.539051 CGATTGGGCTGAGAGTTCCT 59.461 55.000 0.00 0.0 0.00 3.36 R
2812 5370 7.838884 TGAAATATGAAAGCACAAATGGATCA 58.161 30.769 0.00 0.0 0.00 2.92 R
2870 5428 7.040617 TCGTGTTATTCTACTAGCATAAGGAGG 60.041 40.741 0.00 0.0 0.00 4.30 R
3033 5591 0.741927 CAGGATCACTGCGCATGTCA 60.742 55.000 12.24 0.0 40.97 3.58 R
3269 5827 3.499338 TGCTTGTCCAATTGAGATGGTT 58.501 40.909 7.12 0.0 39.09 3.67 R
3395 5953 3.793559 ACCATCCACTGCTTAACGATAC 58.206 45.455 0.00 0.0 0.00 2.24 R
4201 9133 0.043788 GTTACCACCCCTAGTCCCCT 59.956 60.000 0.00 0.0 0.00 4.79 R
5423 10917 1.269998 ACTCTCACGTCAAGGCAGTAC 59.730 52.381 0.00 0.0 0.00 2.73 R
5620 11115 4.020573 AGCAGTAAAGCCCAATTTTAACCC 60.021 41.667 0.00 0.0 34.23 4.11 R
7118 12672 0.404426 GGACAAAGGGCAGGGTTAGT 59.596 55.000 0.00 0.0 0.00 2.24 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
27 28 8.420374 AGTTACATTCATATTGGTTCACTACG 57.580 34.615 0.00 0.00 0.00 3.51
28 29 8.038944 AGTTACATTCATATTGGTTCACTACGT 58.961 33.333 0.00 0.00 0.00 3.57
29 30 9.304731 GTTACATTCATATTGGTTCACTACGTA 57.695 33.333 0.00 0.00 0.00 3.57
30 31 9.872721 TTACATTCATATTGGTTCACTACGTAA 57.127 29.630 0.00 0.00 0.00 3.18
31 32 8.780846 ACATTCATATTGGTTCACTACGTAAA 57.219 30.769 0.00 0.00 0.00 2.01
32 33 9.221933 ACATTCATATTGGTTCACTACGTAAAA 57.778 29.630 0.00 0.00 0.00 1.52
37 38 9.284594 CATATTGGTTCACTACGTAAAAATTGG 57.715 33.333 0.00 0.00 0.00 3.16
38 39 5.110940 TGGTTCACTACGTAAAAATTGGC 57.889 39.130 0.00 0.00 0.00 4.52
39 40 4.579340 TGGTTCACTACGTAAAAATTGGCA 59.421 37.500 0.00 0.00 0.00 4.92
40 41 5.241949 TGGTTCACTACGTAAAAATTGGCAT 59.758 36.000 0.00 0.00 0.00 4.40
41 42 6.430308 TGGTTCACTACGTAAAAATTGGCATA 59.570 34.615 0.00 0.00 0.00 3.14
42 43 6.744082 GGTTCACTACGTAAAAATTGGCATAC 59.256 38.462 0.00 0.00 0.00 2.39
43 44 6.097156 TCACTACGTAAAAATTGGCATACG 57.903 37.500 14.14 14.14 44.82 3.06
44 45 5.868258 TCACTACGTAAAAATTGGCATACGA 59.132 36.000 20.60 6.96 42.66 3.43
45 46 6.368243 TCACTACGTAAAAATTGGCATACGAA 59.632 34.615 20.60 0.00 42.66 3.85
46 47 7.016466 CACTACGTAAAAATTGGCATACGAAA 58.984 34.615 20.60 9.70 42.66 3.46
47 48 7.534578 CACTACGTAAAAATTGGCATACGAAAA 59.465 33.333 20.60 7.77 42.66 2.29
48 49 6.678540 ACGTAAAAATTGGCATACGAAAAC 57.321 33.333 20.60 0.51 42.66 2.43
49 50 6.207213 ACGTAAAAATTGGCATACGAAAACA 58.793 32.000 20.60 0.00 42.66 2.83
50 51 6.696148 ACGTAAAAATTGGCATACGAAAACAA 59.304 30.769 20.60 0.00 42.66 2.83
51 52 7.222224 ACGTAAAAATTGGCATACGAAAACAAA 59.778 29.630 20.60 0.00 42.66 2.83
52 53 8.056571 CGTAAAAATTGGCATACGAAAACAAAA 58.943 29.630 11.12 0.00 42.66 2.44
53 54 9.704098 GTAAAAATTGGCATACGAAAACAAAAA 57.296 25.926 0.00 0.00 0.00 1.94
60 61 9.862371 TTGGCATACGAAAACAAAAATATATGT 57.138 25.926 0.00 0.00 0.00 2.29
61 62 9.509855 TGGCATACGAAAACAAAAATATATGTC 57.490 29.630 0.00 0.00 0.00 3.06
62 63 9.509855 GGCATACGAAAACAAAAATATATGTCA 57.490 29.630 0.00 0.00 0.00 3.58
115 116 9.748708 TTACACTATGTTTTTACGTCTGTAACT 57.251 29.630 0.00 0.00 40.19 2.24
116 117 8.652810 ACACTATGTTTTTACGTCTGTAACTT 57.347 30.769 0.00 0.00 40.19 2.66
117 118 9.101655 ACACTATGTTTTTACGTCTGTAACTTT 57.898 29.630 0.00 0.00 40.19 2.66
120 121 9.717844 CTATGTTTTTACGTCTGTAACTTTACG 57.282 33.333 0.00 0.00 40.19 3.18
122 123 8.621921 TGTTTTTACGTCTGTAACTTTACGTA 57.378 30.769 0.00 0.00 45.85 3.57
129 130 8.795786 ACGTCTGTAACTTTACGTAACATAAA 57.204 30.769 7.70 0.00 45.85 1.40
130 131 9.243637 ACGTCTGTAACTTTACGTAACATAAAA 57.756 29.630 7.70 0.00 45.85 1.52
179 180 9.483916 TTTCTTACATTCTCTTTTCACGTATGA 57.516 29.630 0.00 0.00 0.00 2.15
180 181 9.483916 TTCTTACATTCTCTTTTCACGTATGAA 57.516 29.630 0.00 0.00 43.28 2.57
237 238 8.463607 ACGGTACATTGATGTTAAAATAAAGGG 58.536 33.333 1.46 0.00 41.97 3.95
238 239 7.918562 CGGTACATTGATGTTAAAATAAAGGGG 59.081 37.037 1.46 0.00 41.97 4.79
239 240 8.201464 GGTACATTGATGTTAAAATAAAGGGGG 58.799 37.037 1.46 0.00 41.97 5.40
240 241 8.973182 GTACATTGATGTTAAAATAAAGGGGGA 58.027 33.333 1.46 0.00 41.97 4.81
241 242 8.078060 ACATTGATGTTAAAATAAAGGGGGAG 57.922 34.615 0.00 0.00 37.90 4.30
242 243 7.125659 ACATTGATGTTAAAATAAAGGGGGAGG 59.874 37.037 0.00 0.00 37.90 4.30
243 244 5.524535 TGATGTTAAAATAAAGGGGGAGGG 58.475 41.667 0.00 0.00 0.00 4.30
244 245 3.715287 TGTTAAAATAAAGGGGGAGGGC 58.285 45.455 0.00 0.00 0.00 5.19
245 246 2.691526 GTTAAAATAAAGGGGGAGGGCG 59.308 50.000 0.00 0.00 0.00 6.13
246 247 1.004436 AAAATAAAGGGGGAGGGCGA 58.996 50.000 0.00 0.00 0.00 5.54
247 248 1.004436 AAATAAAGGGGGAGGGCGAA 58.996 50.000 0.00 0.00 0.00 4.70
248 249 0.551396 AATAAAGGGGGAGGGCGAAG 59.449 55.000 0.00 0.00 0.00 3.79
249 250 0.327191 ATAAAGGGGGAGGGCGAAGA 60.327 55.000 0.00 0.00 0.00 2.87
250 251 0.548197 TAAAGGGGGAGGGCGAAGAA 60.548 55.000 0.00 0.00 0.00 2.52
251 252 1.214992 AAAGGGGGAGGGCGAAGAAT 61.215 55.000 0.00 0.00 0.00 2.40
252 253 0.327191 AAGGGGGAGGGCGAAGAATA 60.327 55.000 0.00 0.00 0.00 1.75
253 254 0.327191 AGGGGGAGGGCGAAGAATAA 60.327 55.000 0.00 0.00 0.00 1.40
254 255 0.179026 GGGGGAGGGCGAAGAATAAC 60.179 60.000 0.00 0.00 0.00 1.89
255 256 0.837940 GGGGAGGGCGAAGAATAACT 59.162 55.000 0.00 0.00 0.00 2.24
256 257 2.044758 GGGGAGGGCGAAGAATAACTA 58.955 52.381 0.00 0.00 0.00 2.24
257 258 2.638363 GGGGAGGGCGAAGAATAACTAT 59.362 50.000 0.00 0.00 0.00 2.12
258 259 3.072622 GGGGAGGGCGAAGAATAACTATT 59.927 47.826 0.00 0.00 0.00 1.73
259 260 4.316645 GGGAGGGCGAAGAATAACTATTC 58.683 47.826 1.83 1.83 41.78 1.75
260 261 4.316645 GGAGGGCGAAGAATAACTATTCC 58.683 47.826 5.95 0.00 42.29 3.01
261 262 4.040584 GGAGGGCGAAGAATAACTATTCCT 59.959 45.833 5.95 0.00 42.29 3.36
262 263 5.216614 AGGGCGAAGAATAACTATTCCTC 57.783 43.478 5.95 2.77 42.29 3.71
263 264 4.654262 AGGGCGAAGAATAACTATTCCTCA 59.346 41.667 5.95 0.00 42.29 3.86
264 265 4.750598 GGGCGAAGAATAACTATTCCTCAC 59.249 45.833 5.95 0.00 42.29 3.51
265 266 4.750598 GGCGAAGAATAACTATTCCTCACC 59.249 45.833 5.95 3.44 42.29 4.02
266 267 4.750598 GCGAAGAATAACTATTCCTCACCC 59.249 45.833 5.95 0.00 42.29 4.61
267 268 5.298347 CGAAGAATAACTATTCCTCACCCC 58.702 45.833 5.95 0.00 42.29 4.95
268 269 5.163343 CGAAGAATAACTATTCCTCACCCCA 60.163 44.000 5.95 0.00 42.29 4.96
269 270 6.464465 CGAAGAATAACTATTCCTCACCCCAT 60.464 42.308 5.95 0.00 42.29 4.00
270 271 6.192970 AGAATAACTATTCCTCACCCCATG 57.807 41.667 5.95 0.00 42.29 3.66
271 272 5.672194 AGAATAACTATTCCTCACCCCATGT 59.328 40.000 5.95 0.00 42.29 3.21
272 273 3.652057 AACTATTCCTCACCCCATGTG 57.348 47.619 0.00 0.00 46.88 3.21
273 274 6.409234 GAATAACTATTCCTCACCCCATGTGA 60.409 42.308 0.00 0.00 42.27 3.58
274 275 8.384104 GAATAACTATTCCTCACCCCATGTGAC 61.384 44.444 0.00 0.00 41.11 3.67
282 283 1.981256 ACCCCATGTGACAAACAGTC 58.019 50.000 0.00 0.00 43.64 3.51
302 303 8.451908 ACAGTCAATCCCTATTTTTATACTGC 57.548 34.615 0.00 0.00 35.24 4.40
303 304 7.502561 ACAGTCAATCCCTATTTTTATACTGCC 59.497 37.037 0.00 0.00 35.24 4.85
304 305 7.721399 CAGTCAATCCCTATTTTTATACTGCCT 59.279 37.037 0.00 0.00 0.00 4.75
305 306 7.939588 AGTCAATCCCTATTTTTATACTGCCTC 59.060 37.037 0.00 0.00 0.00 4.70
306 307 7.175119 GTCAATCCCTATTTTTATACTGCCTCC 59.825 40.741 0.00 0.00 0.00 4.30
307 308 5.578157 TCCCTATTTTTATACTGCCTCCC 57.422 43.478 0.00 0.00 0.00 4.30
308 309 4.352893 TCCCTATTTTTATACTGCCTCCCC 59.647 45.833 0.00 0.00 0.00 4.81
309 310 4.324267 CCTATTTTTATACTGCCTCCCCG 58.676 47.826 0.00 0.00 0.00 5.73
310 311 3.945640 ATTTTTATACTGCCTCCCCGT 57.054 42.857 0.00 0.00 0.00 5.28
311 312 2.702592 TTTTATACTGCCTCCCCGTG 57.297 50.000 0.00 0.00 0.00 4.94
312 313 1.575419 TTTATACTGCCTCCCCGTGT 58.425 50.000 0.00 0.00 0.00 4.49
313 314 1.575419 TTATACTGCCTCCCCGTGTT 58.425 50.000 0.00 0.00 0.00 3.32
314 315 2.457813 TATACTGCCTCCCCGTGTTA 57.542 50.000 0.00 0.00 0.00 2.41
315 316 1.575419 ATACTGCCTCCCCGTGTTAA 58.425 50.000 0.00 0.00 0.00 2.01
316 317 1.350071 TACTGCCTCCCCGTGTTAAA 58.650 50.000 0.00 0.00 0.00 1.52
317 318 0.475044 ACTGCCTCCCCGTGTTAAAA 59.525 50.000 0.00 0.00 0.00 1.52
318 319 1.074889 ACTGCCTCCCCGTGTTAAAAT 59.925 47.619 0.00 0.00 0.00 1.82
319 320 2.306512 ACTGCCTCCCCGTGTTAAAATA 59.693 45.455 0.00 0.00 0.00 1.40
320 321 2.943033 CTGCCTCCCCGTGTTAAAATAG 59.057 50.000 0.00 0.00 0.00 1.73
321 322 2.572556 TGCCTCCCCGTGTTAAAATAGA 59.427 45.455 0.00 0.00 0.00 1.98
322 323 3.203716 GCCTCCCCGTGTTAAAATAGAG 58.796 50.000 0.00 0.00 0.00 2.43
323 324 3.805207 CCTCCCCGTGTTAAAATAGAGG 58.195 50.000 0.00 0.00 34.20 3.69
324 325 3.433173 CCTCCCCGTGTTAAAATAGAGGG 60.433 52.174 0.00 0.00 36.76 4.30
326 327 2.927028 CCCGTGTTAAAATAGAGGGGG 58.073 52.381 0.00 0.00 33.97 5.40
327 328 2.506644 CCCGTGTTAAAATAGAGGGGGA 59.493 50.000 0.00 0.00 34.00 4.81
328 329 3.433173 CCCGTGTTAAAATAGAGGGGGAG 60.433 52.174 0.00 0.00 34.00 4.30
329 330 3.433173 CCGTGTTAAAATAGAGGGGGAGG 60.433 52.174 0.00 0.00 0.00 4.30
330 331 3.453353 CGTGTTAAAATAGAGGGGGAGGA 59.547 47.826 0.00 0.00 0.00 3.71
331 332 4.102681 CGTGTTAAAATAGAGGGGGAGGAT 59.897 45.833 0.00 0.00 0.00 3.24
332 333 5.377478 GTGTTAAAATAGAGGGGGAGGATG 58.623 45.833 0.00 0.00 0.00 3.51
333 334 4.415512 TGTTAAAATAGAGGGGGAGGATGG 59.584 45.833 0.00 0.00 0.00 3.51
334 335 3.455085 AAAATAGAGGGGGAGGATGGA 57.545 47.619 0.00 0.00 0.00 3.41
335 336 2.731339 AATAGAGGGGGAGGATGGAG 57.269 55.000 0.00 0.00 0.00 3.86
336 337 0.796255 ATAGAGGGGGAGGATGGAGG 59.204 60.000 0.00 0.00 0.00 4.30
337 338 1.380280 TAGAGGGGGAGGATGGAGGG 61.380 65.000 0.00 0.00 0.00 4.30
338 339 4.523282 AGGGGGAGGATGGAGGGC 62.523 72.222 0.00 0.00 0.00 5.19
354 355 2.218603 AGGGCGTATTATGAAAAGGCG 58.781 47.619 0.00 0.00 0.00 5.52
355 356 1.334689 GGGCGTATTATGAAAAGGCGC 60.335 52.381 0.00 0.00 42.20 6.53
359 360 4.041723 GCGTATTATGAAAAGGCGCAAAT 58.958 39.130 10.83 0.00 42.44 2.32
360 361 4.502645 GCGTATTATGAAAAGGCGCAAATT 59.497 37.500 10.83 0.00 42.44 1.82
361 362 5.005299 GCGTATTATGAAAAGGCGCAAATTT 59.995 36.000 10.83 6.89 42.44 1.82
362 363 6.627274 CGTATTATGAAAAGGCGCAAATTTC 58.373 36.000 10.83 16.25 34.45 2.17
377 379 6.569693 GCGCAAATTTCTGTTAAAAACATGTC 59.430 34.615 0.30 0.00 41.26 3.06
378 380 7.616673 CGCAAATTTCTGTTAAAAACATGTCA 58.383 30.769 0.00 0.00 41.26 3.58
379 381 8.113062 CGCAAATTTCTGTTAAAAACATGTCAA 58.887 29.630 0.00 0.00 41.26 3.18
380 382 9.766277 GCAAATTTCTGTTAAAAACATGTCAAA 57.234 25.926 0.00 0.00 41.26 2.69
494 500 7.230849 ACAGGCATCAAAAGATATGTTTGAA 57.769 32.000 12.76 0.41 45.43 2.69
496 502 7.816031 ACAGGCATCAAAAGATATGTTTGAAAG 59.184 33.333 12.76 10.38 45.43 2.62
566 572 6.935741 TGTAAGTTGTGTATGAAAAGTGCT 57.064 33.333 0.00 0.00 0.00 4.40
607 613 7.495135 AATAAAAAGAGACGTAAAAACCCGA 57.505 32.000 0.00 0.00 0.00 5.14
633 639 1.963747 CCGGTGAAATGCGAAGAAAC 58.036 50.000 0.00 0.00 0.00 2.78
634 640 1.265635 CCGGTGAAATGCGAAGAAACA 59.734 47.619 0.00 0.00 0.00 2.83
637 643 3.421888 CGGTGAAATGCGAAGAAACAAAG 59.578 43.478 0.00 0.00 0.00 2.77
655 663 7.812309 AACAAAGAAAAGAGAAAGAAAACCG 57.188 32.000 0.00 0.00 0.00 4.44
723 733 0.953960 GTGTGGTTTCGGCCCAGTAG 60.954 60.000 0.00 0.00 31.13 2.57
753 763 1.751351 CAGAGGCGAGATGGAACTGTA 59.249 52.381 0.00 0.00 0.00 2.74
766 3305 0.109179 AACTGTATCGCGCAACCGTA 60.109 50.000 8.75 0.00 36.67 4.02
782 3321 1.270358 CCGTAGAGAAATAGCCCTGGC 60.270 57.143 0.00 0.00 42.33 4.85
783 3322 1.270358 CGTAGAGAAATAGCCCTGGCC 60.270 57.143 4.13 0.00 43.17 5.36
785 3324 0.624500 AGAGAAATAGCCCTGGCCCA 60.625 55.000 4.13 0.00 43.17 5.36
786 3325 0.179006 GAGAAATAGCCCTGGCCCAG 60.179 60.000 2.91 2.91 43.17 4.45
787 3326 0.624500 AGAAATAGCCCTGGCCCAGA 60.625 55.000 13.74 0.00 43.17 3.86
788 3327 0.480252 GAAATAGCCCTGGCCCAGAT 59.520 55.000 13.74 0.00 43.17 2.90
789 3328 1.705186 GAAATAGCCCTGGCCCAGATA 59.295 52.381 13.74 2.41 43.17 1.98
790 3329 1.366319 AATAGCCCTGGCCCAGATAG 58.634 55.000 13.74 1.32 43.17 2.08
792 3331 1.674931 TAGCCCTGGCCCAGATAGGA 61.675 60.000 13.74 0.00 43.17 2.94
793 3332 2.524204 GCCCTGGCCCAGATAGGAG 61.524 68.421 13.74 0.00 41.22 3.69
794 3333 2.524204 CCCTGGCCCAGATAGGAGC 61.524 68.421 13.74 0.00 41.22 4.70
795 3334 1.461075 CCTGGCCCAGATAGGAGCT 60.461 63.158 13.74 0.00 41.22 4.09
796 3335 1.479368 CCTGGCCCAGATAGGAGCTC 61.479 65.000 13.74 4.71 41.22 4.09
829 3375 2.567615 ACGAAGTGCAAAGAGAGGGTAT 59.432 45.455 0.00 0.00 42.51 2.73
859 3405 0.902516 GCCAGTCCAGAGTCCAGACT 60.903 60.000 0.00 0.00 45.84 3.24
860 3406 1.638529 CCAGTCCAGAGTCCAGACTT 58.361 55.000 9.41 0.00 42.66 3.01
1251 3809 1.407258 CACGAGATGGAGAAGACCCTC 59.593 57.143 0.00 0.00 0.00 4.30
1275 3833 2.055042 GCTCCGCCTCCTCTTCTCA 61.055 63.158 0.00 0.00 0.00 3.27
1809 4367 3.899981 AAACCTGCGGCGCATCTCA 62.900 57.895 36.35 12.41 38.13 3.27
1870 4428 4.210331 ACTTGCTCTTTTCAGGATTGTGT 58.790 39.130 0.00 0.00 0.00 3.72
1882 4440 4.338118 TCAGGATTGTGTGTGTTTCCTTTC 59.662 41.667 0.00 0.00 34.59 2.62
2041 4599 3.618690 ACCTGCCAAGTGAGTATCTTC 57.381 47.619 0.00 0.00 34.92 2.87
2046 4604 3.006430 TGCCAAGTGAGTATCTTCGTTCA 59.994 43.478 0.00 0.00 34.92 3.18
2048 4606 5.105513 TGCCAAGTGAGTATCTTCGTTCATA 60.106 40.000 0.00 0.00 34.92 2.15
2064 4622 8.437360 TTCGTTCATAACTATCTGATTTGCAT 57.563 30.769 0.00 0.00 0.00 3.96
2110 4668 7.913297 CCGGGACAGTTTATAATAATGTGTTTG 59.087 37.037 0.00 0.00 0.00 2.93
2438 4996 2.362077 GACCATTTGTGACTTTGCCACT 59.638 45.455 0.00 0.00 35.66 4.00
2450 5008 3.181466 ACTTTGCCACTTTGATTGGAACC 60.181 43.478 0.00 0.00 36.02 3.62
2453 5011 3.153919 TGCCACTTTGATTGGAACCTAC 58.846 45.455 0.00 0.00 36.02 3.18
2456 5014 4.651778 CCACTTTGATTGGAACCTACTCA 58.348 43.478 0.00 0.00 36.02 3.41
2465 5023 2.224113 TGGAACCTACTCACGTGGTTTC 60.224 50.000 17.00 10.80 43.28 2.78
2561 5119 7.944729 ACTCTATAAGATTGTGGTGCAATTT 57.055 32.000 0.00 0.00 46.90 1.82
2575 5133 2.801679 TGCAATTTTTACAAGCTGCAGC 59.198 40.909 31.53 31.53 42.49 5.25
2596 5154 3.747193 CGTCAATGTGCTAATGTGGTTC 58.253 45.455 0.00 0.00 0.00 3.62
2650 5208 2.884639 ACTCGCAATACAGCCTGTTTTT 59.115 40.909 1.02 0.00 0.00 1.94
2680 5238 3.130633 CCAAACTGTCGTCATCACTTCA 58.869 45.455 0.00 0.00 0.00 3.02
2812 5370 4.023980 TGACACGAGGAAGGTATGATCTT 58.976 43.478 0.00 0.00 0.00 2.40
2870 5428 8.931385 ATATTTGGAAACACACTTATTGCATC 57.069 30.769 0.00 0.00 42.67 3.91
2899 5457 7.062371 CCTTATGCTAGTAGAATAACACGATGC 59.938 40.741 6.50 0.00 0.00 3.91
2936 5494 4.773013 ACCGGTTTAGTTGTCTCTCAAAA 58.227 39.130 0.00 0.00 37.81 2.44
2989 5547 5.703592 TGAATCCAGTTGCGTAACATTAACT 59.296 36.000 18.75 0.00 39.30 2.24
3033 5591 5.057149 CAGCTACCTGTGAGTACAAAGTTT 58.943 41.667 0.00 0.00 36.14 2.66
3289 5847 5.183904 AGTTAACCATCTCAATTGGACAAGC 59.816 40.000 5.42 0.00 37.69 4.01
3352 5910 7.743400 GGTGTTTATTGTTTAAGCGTTCTAGTC 59.257 37.037 0.00 0.00 0.00 2.59
3395 5953 3.612479 GCAAAGTTATTCAGGCACCTGTG 60.612 47.826 16.12 6.02 43.96 3.66
3456 6014 8.141298 TGACATTAAAGGGTATCAACTACTCA 57.859 34.615 0.00 0.00 32.76 3.41
3591 8523 3.439825 GTCATGTATGCAATGTGGTCACA 59.560 43.478 6.24 6.24 46.44 3.58
3708 8640 5.422214 TCCATTCCTTCTTCCTCTTGTAC 57.578 43.478 0.00 0.00 0.00 2.90
3715 8647 6.185511 TCCTTCTTCCTCTTGTACGATTCTA 58.814 40.000 0.00 0.00 0.00 2.10
3726 8658 7.637229 TCTTGTACGATTCTATAGTTTCCTCG 58.363 38.462 0.00 5.40 0.00 4.63
3771 8703 2.122783 TTAGTCCCCAAAGAATGCCG 57.877 50.000 0.00 0.00 0.00 5.69
3780 8712 3.304928 CCCAAAGAATGCCGATCTTATGC 60.305 47.826 0.00 0.00 36.14 3.14
3968 8900 6.314917 AGACCACCCTTCAAAATTCACTATT 58.685 36.000 0.00 0.00 0.00 1.73
4055 8987 3.328382 TTGACCCCGATCAAAGTAGTG 57.672 47.619 0.00 0.00 35.65 2.74
4299 9231 6.543465 CCCAGATCAAGCAAACTATCACATTA 59.457 38.462 0.00 0.00 0.00 1.90
4580 9979 8.507249 CCAAACAAATTTTGGTTCAAACACTTA 58.493 29.630 9.44 0.00 38.84 2.24
4623 10023 4.638421 CCATTGTAATCCTGCGTTTTCCTA 59.362 41.667 0.00 0.00 0.00 2.94
5124 10617 6.100004 CCTCCTAACAGCCGTGTTATATATG 58.900 44.000 0.00 0.00 45.95 1.78
5259 10752 4.717279 TTGGTTGTAAGGGAGTAAAGCT 57.283 40.909 0.00 0.00 0.00 3.74
5510 11005 3.434299 GGCCAAGCAATTTTCAATCTGTG 59.566 43.478 0.00 0.00 0.00 3.66
5568 11063 3.181446 TGAACATGTGATGGACTTGTGGA 60.181 43.478 0.00 0.00 41.01 4.02
5583 11078 4.335594 ACTTGTGGACAACTAGCAAGAAAC 59.664 41.667 9.96 0.00 38.90 2.78
5620 11115 7.422465 TCTGATTTAATGAAATTCCCTTGGG 57.578 36.000 0.00 0.00 37.87 4.12
5621 11116 6.383726 TCTGATTTAATGAAATTCCCTTGGGG 59.616 38.462 5.78 0.00 38.67 4.96
5638 11133 3.870559 TGGGGGTTAAAATTGGGCTTTA 58.129 40.909 0.00 0.00 0.00 1.85
5640 11135 3.841845 GGGGGTTAAAATTGGGCTTTACT 59.158 43.478 0.00 0.00 0.00 2.24
5641 11136 4.323180 GGGGGTTAAAATTGGGCTTTACTG 60.323 45.833 0.00 0.00 0.00 2.74
5676 11173 4.404073 ACTTTTAGTCAATGGTTGTGGCAA 59.596 37.500 0.00 0.00 0.00 4.52
5778 11275 9.128404 ACATATAGTGCTCATCAAACATCAATT 57.872 29.630 0.00 0.00 0.00 2.32
6031 11578 2.163818 TGTTCCCTTACGTTGCTCTG 57.836 50.000 0.00 0.00 0.00 3.35
6090 11637 3.981211 TGCTTTTAAAAGAGCAAGCCAG 58.019 40.909 28.11 2.32 45.19 4.85
6157 11705 3.708563 ATGCTAAACACGCACAGTTTT 57.291 38.095 3.89 0.00 40.65 2.43
6159 11707 2.680841 TGCTAAACACGCACAGTTTTCT 59.319 40.909 3.89 0.00 39.65 2.52
6161 11709 3.724257 GCTAAACACGCACAGTTTTCTTC 59.276 43.478 3.89 0.00 39.65 2.87
6162 11710 3.840890 AAACACGCACAGTTTTCTTCA 57.159 38.095 0.00 0.00 35.81 3.02
6163 11711 2.825086 ACACGCACAGTTTTCTTCAC 57.175 45.000 0.00 0.00 0.00 3.18
6164 11712 1.062002 ACACGCACAGTTTTCTTCACG 59.938 47.619 0.00 0.00 0.00 4.35
6188 11742 5.163963 GGCTTGCAATGCAACTTGTTATAAC 60.164 40.000 17.55 8.75 43.99 1.89
6206 11760 1.121407 ACTGTAGCCACCTGTCAGCA 61.121 55.000 0.00 0.00 31.90 4.41
6207 11761 0.251354 CTGTAGCCACCTGTCAGCAT 59.749 55.000 0.00 0.00 0.00 3.79
6210 11764 2.505407 TGTAGCCACCTGTCAGCATATT 59.495 45.455 0.00 0.00 0.00 1.28
6232 11786 4.143543 TGTCATTCTTTTCCATGTCTGCA 58.856 39.130 0.00 0.00 0.00 4.41
6262 11816 5.115021 GGATTTCGTTTGAATTTGTCGTGTC 59.885 40.000 0.00 0.00 33.20 3.67
6263 11817 3.595709 TCGTTTGAATTTGTCGTGTCC 57.404 42.857 0.00 0.00 0.00 4.02
6567 12121 9.415544 CTGAAGCATAAATTCAGTTTTTAGCTT 57.584 29.630 7.39 0.00 45.58 3.74
6653 12207 7.975616 ACCATGTTTTCGAAATGAATGAATAGG 59.024 33.333 20.76 11.53 36.22 2.57
6686 12240 9.868277 CAGGGAAAATAAATACACTTGCAAATA 57.132 29.630 0.00 0.00 0.00 1.40
7028 12582 3.316071 TTTGTGTGCAAAGCCCATATG 57.684 42.857 0.00 0.00 39.43 1.78
7036 12590 2.423538 GCAAAGCCCATATGAGTTTCGT 59.576 45.455 3.65 0.00 0.00 3.85
7040 12594 2.238646 AGCCCATATGAGTTTCGTCCAA 59.761 45.455 3.65 0.00 0.00 3.53
7118 12672 2.170166 CAATAGGCAGTTTTCCCAGCA 58.830 47.619 0.00 0.00 0.00 4.41
7174 12728 0.765510 GCCATCCGTCCTATTCCCTT 59.234 55.000 0.00 0.00 0.00 3.95
7176 12730 1.768870 CCATCCGTCCTATTCCCTTGT 59.231 52.381 0.00 0.00 0.00 3.16
7184 12738 3.198853 GTCCTATTCCCTTGTGAGAGCTT 59.801 47.826 0.00 0.00 0.00 3.74
7185 12739 3.846588 TCCTATTCCCTTGTGAGAGCTTT 59.153 43.478 0.00 0.00 0.00 3.51
7313 12868 4.481368 ACTATCTTTGTATTGCACGGGA 57.519 40.909 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.524106 CGTAGTGAACCAATATGAATGTAACTA 57.476 33.333 0.00 0.00 0.00 2.24
3 4 8.193250 ACGTAGTGAACCAATATGAATGTAAC 57.807 34.615 0.00 0.00 42.51 2.50
4 5 9.872721 TTACGTAGTGAACCAATATGAATGTAA 57.127 29.630 0.00 0.00 45.73 2.41
5 6 9.872721 TTTACGTAGTGAACCAATATGAATGTA 57.127 29.630 0.00 0.00 45.73 2.29
11 12 9.284594 CCAATTTTTACGTAGTGAACCAATATG 57.715 33.333 0.00 0.00 45.73 1.78
12 13 7.971722 GCCAATTTTTACGTAGTGAACCAATAT 59.028 33.333 0.00 0.00 45.73 1.28
13 14 7.040617 TGCCAATTTTTACGTAGTGAACCAATA 60.041 33.333 0.00 0.00 45.73 1.90
14 15 6.153756 GCCAATTTTTACGTAGTGAACCAAT 58.846 36.000 0.00 0.00 45.73 3.16
15 16 5.067413 TGCCAATTTTTACGTAGTGAACCAA 59.933 36.000 0.00 0.00 45.73 3.67
16 17 4.579340 TGCCAATTTTTACGTAGTGAACCA 59.421 37.500 0.00 0.00 45.73 3.67
17 18 5.110940 TGCCAATTTTTACGTAGTGAACC 57.889 39.130 0.00 0.00 45.73 3.62
18 19 6.463576 CGTATGCCAATTTTTACGTAGTGAAC 59.536 38.462 0.00 0.00 45.73 3.18
19 20 6.368243 TCGTATGCCAATTTTTACGTAGTGAA 59.632 34.615 0.00 0.00 45.73 3.18
20 21 5.868258 TCGTATGCCAATTTTTACGTAGTGA 59.132 36.000 0.00 0.00 45.73 3.41
21 22 6.097156 TCGTATGCCAATTTTTACGTAGTG 57.903 37.500 0.00 0.00 45.73 2.74
23 24 7.534578 TGTTTTCGTATGCCAATTTTTACGTAG 59.465 33.333 0.00 0.00 38.74 3.51
24 25 7.358066 TGTTTTCGTATGCCAATTTTTACGTA 58.642 30.769 0.00 0.00 38.74 3.57
25 26 6.207213 TGTTTTCGTATGCCAATTTTTACGT 58.793 32.000 0.00 0.00 38.74 3.57
26 27 6.677027 TGTTTTCGTATGCCAATTTTTACG 57.323 33.333 0.00 0.00 38.93 3.18
27 28 9.704098 TTTTTGTTTTCGTATGCCAATTTTTAC 57.296 25.926 0.00 0.00 0.00 2.01
34 35 9.862371 ACATATATTTTTGTTTTCGTATGCCAA 57.138 25.926 0.00 0.00 0.00 4.52
35 36 9.509855 GACATATATTTTTGTTTTCGTATGCCA 57.490 29.630 0.00 0.00 0.00 4.92
36 37 9.509855 TGACATATATTTTTGTTTTCGTATGCC 57.490 29.630 0.00 0.00 0.00 4.40
89 90 9.748708 AGTTACAGACGTAAAAACATAGTGTAA 57.251 29.630 0.00 0.00 39.29 2.41
90 91 9.748708 AAGTTACAGACGTAAAAACATAGTGTA 57.251 29.630 0.00 0.00 39.29 2.90
91 92 8.652810 AAGTTACAGACGTAAAAACATAGTGT 57.347 30.769 0.00 0.00 39.29 3.55
94 95 9.717844 CGTAAAGTTACAGACGTAAAAACATAG 57.282 33.333 0.00 0.00 39.29 2.23
95 96 9.243637 ACGTAAAGTTACAGACGTAAAAACATA 57.756 29.630 7.39 0.00 45.97 2.29
96 97 8.130307 ACGTAAAGTTACAGACGTAAAAACAT 57.870 30.769 7.39 0.00 45.97 2.71
97 98 7.518731 ACGTAAAGTTACAGACGTAAAAACA 57.481 32.000 7.39 0.00 45.97 2.83
103 104 9.885934 TTTATGTTACGTAAAGTTACAGACGTA 57.114 29.630 10.11 10.80 45.97 3.57
104 105 8.795786 TTTATGTTACGTAAAGTTACAGACGT 57.204 30.769 10.11 12.39 44.24 4.34
153 154 9.483916 TCATACGTGAAAAGAGAATGTAAGAAA 57.516 29.630 0.00 0.00 0.00 2.52
154 155 9.483916 TTCATACGTGAAAAGAGAATGTAAGAA 57.516 29.630 0.00 0.00 41.22 2.52
199 200 7.148373 ACATCAATGTACCGTAATTTTACGCTT 60.148 33.333 15.53 8.36 45.53 4.68
200 201 6.314400 ACATCAATGTACCGTAATTTTACGCT 59.686 34.615 15.53 6.62 45.53 5.07
201 202 6.480285 ACATCAATGTACCGTAATTTTACGC 58.520 36.000 15.53 5.07 45.53 4.42
202 203 9.970243 TTAACATCAATGTACCGTAATTTTACG 57.030 29.630 14.32 14.32 46.48 3.18
211 212 8.463607 CCCTTTATTTTAACATCAATGTACCGT 58.536 33.333 0.00 0.00 40.80 4.83
212 213 7.918562 CCCCTTTATTTTAACATCAATGTACCG 59.081 37.037 0.00 0.00 40.80 4.02
213 214 8.201464 CCCCCTTTATTTTAACATCAATGTACC 58.799 37.037 0.00 0.00 40.80 3.34
214 215 8.973182 TCCCCCTTTATTTTAACATCAATGTAC 58.027 33.333 0.00 0.00 40.80 2.90
215 216 9.196139 CTCCCCCTTTATTTTAACATCAATGTA 57.804 33.333 0.00 0.00 40.80 2.29
216 217 7.125659 CCTCCCCCTTTATTTTAACATCAATGT 59.874 37.037 0.00 0.00 44.20 2.71
217 218 7.418942 CCCTCCCCCTTTATTTTAACATCAATG 60.419 40.741 0.00 0.00 0.00 2.82
218 219 6.615316 CCCTCCCCCTTTATTTTAACATCAAT 59.385 38.462 0.00 0.00 0.00 2.57
219 220 5.961421 CCCTCCCCCTTTATTTTAACATCAA 59.039 40.000 0.00 0.00 0.00 2.57
220 221 5.524535 CCCTCCCCCTTTATTTTAACATCA 58.475 41.667 0.00 0.00 0.00 3.07
221 222 4.344102 GCCCTCCCCCTTTATTTTAACATC 59.656 45.833 0.00 0.00 0.00 3.06
222 223 4.295201 GCCCTCCCCCTTTATTTTAACAT 58.705 43.478 0.00 0.00 0.00 2.71
223 224 3.715287 GCCCTCCCCCTTTATTTTAACA 58.285 45.455 0.00 0.00 0.00 2.41
224 225 2.691526 CGCCCTCCCCCTTTATTTTAAC 59.308 50.000 0.00 0.00 0.00 2.01
225 226 2.581709 TCGCCCTCCCCCTTTATTTTAA 59.418 45.455 0.00 0.00 0.00 1.52
226 227 2.207105 TCGCCCTCCCCCTTTATTTTA 58.793 47.619 0.00 0.00 0.00 1.52
227 228 1.004436 TCGCCCTCCCCCTTTATTTT 58.996 50.000 0.00 0.00 0.00 1.82
228 229 1.004436 TTCGCCCTCCCCCTTTATTT 58.996 50.000 0.00 0.00 0.00 1.40
229 230 0.551396 CTTCGCCCTCCCCCTTTATT 59.449 55.000 0.00 0.00 0.00 1.40
230 231 0.327191 TCTTCGCCCTCCCCCTTTAT 60.327 55.000 0.00 0.00 0.00 1.40
231 232 0.548197 TTCTTCGCCCTCCCCCTTTA 60.548 55.000 0.00 0.00 0.00 1.85
232 233 1.214992 ATTCTTCGCCCTCCCCCTTT 61.215 55.000 0.00 0.00 0.00 3.11
233 234 0.327191 TATTCTTCGCCCTCCCCCTT 60.327 55.000 0.00 0.00 0.00 3.95
234 235 0.327191 TTATTCTTCGCCCTCCCCCT 60.327 55.000 0.00 0.00 0.00 4.79
235 236 0.179026 GTTATTCTTCGCCCTCCCCC 60.179 60.000 0.00 0.00 0.00 5.40
236 237 0.837940 AGTTATTCTTCGCCCTCCCC 59.162 55.000 0.00 0.00 0.00 4.81
237 238 4.316645 GAATAGTTATTCTTCGCCCTCCC 58.683 47.826 4.93 0.00 39.13 4.30
238 239 4.040584 AGGAATAGTTATTCTTCGCCCTCC 59.959 45.833 10.71 0.00 41.33 4.30
239 240 5.216614 AGGAATAGTTATTCTTCGCCCTC 57.783 43.478 10.71 0.00 41.33 4.30
240 241 4.654262 TGAGGAATAGTTATTCTTCGCCCT 59.346 41.667 15.10 4.25 46.01 5.19
241 242 4.750598 GTGAGGAATAGTTATTCTTCGCCC 59.249 45.833 19.01 8.33 46.01 6.13
242 243 5.908916 GTGAGGAATAGTTATTCTTCGCC 57.091 43.478 19.01 10.04 46.01 5.54
244 245 5.163343 TGGGGTGAGGAATAGTTATTCTTCG 60.163 44.000 15.10 0.00 46.01 3.79
245 246 6.248569 TGGGGTGAGGAATAGTTATTCTTC 57.751 41.667 13.90 13.90 44.40 2.87
246 247 6.160459 ACATGGGGTGAGGAATAGTTATTCTT 59.840 38.462 10.71 4.41 41.33 2.52
247 248 5.672194 ACATGGGGTGAGGAATAGTTATTCT 59.328 40.000 10.71 0.00 41.33 2.40
248 249 5.941788 ACATGGGGTGAGGAATAGTTATTC 58.058 41.667 0.00 3.75 40.96 1.75
249 250 5.994416 ACATGGGGTGAGGAATAGTTATT 57.006 39.130 0.00 0.00 0.00 1.40
263 264 1.981256 GACTGTTTGTCACATGGGGT 58.019 50.000 0.00 0.00 44.73 4.95
276 277 8.903820 GCAGTATAAAAATAGGGATTGACTGTT 58.096 33.333 0.00 0.00 34.46 3.16
277 278 7.502561 GGCAGTATAAAAATAGGGATTGACTGT 59.497 37.037 0.00 0.00 34.46 3.55
278 279 7.721399 AGGCAGTATAAAAATAGGGATTGACTG 59.279 37.037 0.00 0.00 34.96 3.51
279 280 7.816411 AGGCAGTATAAAAATAGGGATTGACT 58.184 34.615 0.00 0.00 0.00 3.41
280 281 7.175119 GGAGGCAGTATAAAAATAGGGATTGAC 59.825 40.741 0.00 0.00 0.00 3.18
281 282 7.231467 GGAGGCAGTATAAAAATAGGGATTGA 58.769 38.462 0.00 0.00 0.00 2.57
282 283 6.434340 GGGAGGCAGTATAAAAATAGGGATTG 59.566 42.308 0.00 0.00 0.00 2.67
283 284 6.468798 GGGGAGGCAGTATAAAAATAGGGATT 60.469 42.308 0.00 0.00 0.00 3.01
284 285 5.015284 GGGGAGGCAGTATAAAAATAGGGAT 59.985 44.000 0.00 0.00 0.00 3.85
285 286 4.352893 GGGGAGGCAGTATAAAAATAGGGA 59.647 45.833 0.00 0.00 0.00 4.20
286 287 4.663334 GGGGAGGCAGTATAAAAATAGGG 58.337 47.826 0.00 0.00 0.00 3.53
287 288 4.202430 ACGGGGAGGCAGTATAAAAATAGG 60.202 45.833 0.00 0.00 0.00 2.57
288 289 4.755123 CACGGGGAGGCAGTATAAAAATAG 59.245 45.833 0.00 0.00 0.00 1.73
289 290 4.164604 ACACGGGGAGGCAGTATAAAAATA 59.835 41.667 0.00 0.00 0.00 1.40
290 291 3.053917 ACACGGGGAGGCAGTATAAAAAT 60.054 43.478 0.00 0.00 0.00 1.82
291 292 2.306512 ACACGGGGAGGCAGTATAAAAA 59.693 45.455 0.00 0.00 0.00 1.94
292 293 1.910671 ACACGGGGAGGCAGTATAAAA 59.089 47.619 0.00 0.00 0.00 1.52
293 294 1.575419 ACACGGGGAGGCAGTATAAA 58.425 50.000 0.00 0.00 0.00 1.40
294 295 1.575419 AACACGGGGAGGCAGTATAA 58.425 50.000 0.00 0.00 0.00 0.98
295 296 2.457813 TAACACGGGGAGGCAGTATA 57.542 50.000 0.00 0.00 0.00 1.47
296 297 1.575419 TTAACACGGGGAGGCAGTAT 58.425 50.000 0.00 0.00 0.00 2.12
297 298 1.350071 TTTAACACGGGGAGGCAGTA 58.650 50.000 0.00 0.00 0.00 2.74
298 299 0.475044 TTTTAACACGGGGAGGCAGT 59.525 50.000 0.00 0.00 0.00 4.40
299 300 1.834188 ATTTTAACACGGGGAGGCAG 58.166 50.000 0.00 0.00 0.00 4.85
300 301 2.572556 TCTATTTTAACACGGGGAGGCA 59.427 45.455 0.00 0.00 0.00 4.75
301 302 3.203716 CTCTATTTTAACACGGGGAGGC 58.796 50.000 0.00 0.00 0.00 4.70
302 303 3.433173 CCCTCTATTTTAACACGGGGAGG 60.433 52.174 0.00 0.00 38.87 4.30
303 304 3.805207 CCCTCTATTTTAACACGGGGAG 58.195 50.000 0.00 0.00 34.94 4.30
304 305 3.918294 CCCTCTATTTTAACACGGGGA 57.082 47.619 0.00 0.00 34.94 4.81
305 306 2.927028 CCCCTCTATTTTAACACGGGG 58.073 52.381 0.00 0.00 43.42 5.73
306 307 2.506644 TCCCCCTCTATTTTAACACGGG 59.493 50.000 0.00 0.00 0.00 5.28
307 308 3.433173 CCTCCCCCTCTATTTTAACACGG 60.433 52.174 0.00 0.00 0.00 4.94
308 309 3.453353 TCCTCCCCCTCTATTTTAACACG 59.547 47.826 0.00 0.00 0.00 4.49
309 310 5.377478 CATCCTCCCCCTCTATTTTAACAC 58.623 45.833 0.00 0.00 0.00 3.32
310 311 4.415512 CCATCCTCCCCCTCTATTTTAACA 59.584 45.833 0.00 0.00 0.00 2.41
311 312 4.663592 TCCATCCTCCCCCTCTATTTTAAC 59.336 45.833 0.00 0.00 0.00 2.01
312 313 4.913968 CTCCATCCTCCCCCTCTATTTTAA 59.086 45.833 0.00 0.00 0.00 1.52
313 314 4.503398 CTCCATCCTCCCCCTCTATTTTA 58.497 47.826 0.00 0.00 0.00 1.52
314 315 3.331120 CTCCATCCTCCCCCTCTATTTT 58.669 50.000 0.00 0.00 0.00 1.82
315 316 2.429985 CCTCCATCCTCCCCCTCTATTT 60.430 54.545 0.00 0.00 0.00 1.40
316 317 1.153132 CCTCCATCCTCCCCCTCTATT 59.847 57.143 0.00 0.00 0.00 1.73
317 318 0.796255 CCTCCATCCTCCCCCTCTAT 59.204 60.000 0.00 0.00 0.00 1.98
318 319 1.380280 CCCTCCATCCTCCCCCTCTA 61.380 65.000 0.00 0.00 0.00 2.43
319 320 2.731461 CCCTCCATCCTCCCCCTCT 61.731 68.421 0.00 0.00 0.00 3.69
320 321 2.122189 CCCTCCATCCTCCCCCTC 60.122 72.222 0.00 0.00 0.00 4.30
321 322 4.523282 GCCCTCCATCCTCCCCCT 62.523 72.222 0.00 0.00 0.00 4.79
323 324 3.768833 TACGCCCTCCATCCTCCCC 62.769 68.421 0.00 0.00 0.00 4.81
324 325 1.128188 AATACGCCCTCCATCCTCCC 61.128 60.000 0.00 0.00 0.00 4.30
325 326 1.640917 TAATACGCCCTCCATCCTCC 58.359 55.000 0.00 0.00 0.00 4.30
326 327 2.832129 TCATAATACGCCCTCCATCCTC 59.168 50.000 0.00 0.00 0.00 3.71
327 328 2.902608 TCATAATACGCCCTCCATCCT 58.097 47.619 0.00 0.00 0.00 3.24
328 329 3.695830 TTCATAATACGCCCTCCATCC 57.304 47.619 0.00 0.00 0.00 3.51
329 330 4.455877 CCTTTTCATAATACGCCCTCCATC 59.544 45.833 0.00 0.00 0.00 3.51
330 331 4.398319 CCTTTTCATAATACGCCCTCCAT 58.602 43.478 0.00 0.00 0.00 3.41
331 332 3.815809 CCTTTTCATAATACGCCCTCCA 58.184 45.455 0.00 0.00 0.00 3.86
332 333 2.552743 GCCTTTTCATAATACGCCCTCC 59.447 50.000 0.00 0.00 0.00 4.30
333 334 2.223377 CGCCTTTTCATAATACGCCCTC 59.777 50.000 0.00 0.00 0.00 4.30
334 335 2.218603 CGCCTTTTCATAATACGCCCT 58.781 47.619 0.00 0.00 0.00 5.19
335 336 1.334689 GCGCCTTTTCATAATACGCCC 60.335 52.381 0.00 0.00 39.01 6.13
336 337 1.332375 TGCGCCTTTTCATAATACGCC 59.668 47.619 4.18 0.00 43.89 5.68
337 338 2.748461 TGCGCCTTTTCATAATACGC 57.252 45.000 4.18 0.00 44.70 4.42
338 339 6.472163 AGAAATTTGCGCCTTTTCATAATACG 59.528 34.615 21.34 0.00 32.94 3.06
339 340 7.275560 ACAGAAATTTGCGCCTTTTCATAATAC 59.724 33.333 21.34 2.25 32.94 1.89
354 355 9.766277 TTTGACATGTTTTTAACAGAAATTTGC 57.234 25.926 0.00 0.00 45.95 3.68
469 475 7.230849 TCAAACATATCTTTTGATGCCTGTT 57.769 32.000 5.31 0.00 37.91 3.16
547 553 4.881273 TGTCAGCACTTTTCATACACAACT 59.119 37.500 0.00 0.00 0.00 3.16
548 554 5.168526 TGTCAGCACTTTTCATACACAAC 57.831 39.130 0.00 0.00 0.00 3.32
552 558 5.308014 ACAGATGTCAGCACTTTTCATACA 58.692 37.500 0.00 0.00 0.00 2.29
558 564 3.554934 TCCAACAGATGTCAGCACTTTT 58.445 40.909 0.00 0.00 0.00 2.27
585 591 6.760770 TCTTCGGGTTTTTACGTCTCTTTTTA 59.239 34.615 0.00 0.00 0.00 1.52
586 592 5.585844 TCTTCGGGTTTTTACGTCTCTTTTT 59.414 36.000 0.00 0.00 0.00 1.94
591 597 4.610007 GCTTTCTTCGGGTTTTTACGTCTC 60.610 45.833 0.00 0.00 0.00 3.36
599 605 2.337361 CCGGCTTTCTTCGGGTTTT 58.663 52.632 0.00 0.00 42.32 2.43
605 611 1.729149 GCATTTCACCGGCTTTCTTCG 60.729 52.381 0.00 0.00 0.00 3.79
607 613 0.240945 CGCATTTCACCGGCTTTCTT 59.759 50.000 0.00 0.00 0.00 2.52
633 639 6.237569 GCACGGTTTTCTTTCTCTTTTCTTTG 60.238 38.462 0.00 0.00 0.00 2.77
634 640 5.805486 GCACGGTTTTCTTTCTCTTTTCTTT 59.195 36.000 0.00 0.00 0.00 2.52
637 643 4.499399 GTGCACGGTTTTCTTTCTCTTTTC 59.501 41.667 0.00 0.00 0.00 2.29
692 702 1.774639 AACCACACTGTAGTTACGCG 58.225 50.000 3.53 3.53 0.00 6.01
698 708 0.250166 GGCCGAAACCACACTGTAGT 60.250 55.000 0.00 0.00 0.00 2.73
703 713 1.412453 TACTGGGCCGAAACCACACT 61.412 55.000 0.00 0.00 33.63 3.55
753 763 0.108992 TTTCTCTACGGTTGCGCGAT 60.109 50.000 12.10 0.00 0.00 4.58
766 3305 0.624500 TGGGCCAGGGCTATTTCTCT 60.625 55.000 13.81 0.00 41.60 3.10
782 3321 0.897863 CCCGAGAGCTCCTATCTGGG 60.898 65.000 10.93 12.41 41.08 4.45
783 3322 0.111446 TCCCGAGAGCTCCTATCTGG 59.889 60.000 10.93 7.81 29.42 3.86
785 3324 2.757894 TTTCCCGAGAGCTCCTATCT 57.242 50.000 10.93 0.00 0.00 1.98
786 3325 4.157105 GTCTATTTCCCGAGAGCTCCTATC 59.843 50.000 10.93 0.08 0.00 2.08
787 3326 4.083565 GTCTATTTCCCGAGAGCTCCTAT 58.916 47.826 10.93 0.00 0.00 2.57
788 3327 3.488363 GTCTATTTCCCGAGAGCTCCTA 58.512 50.000 10.93 0.00 0.00 2.94
789 3328 2.312390 GTCTATTTCCCGAGAGCTCCT 58.688 52.381 10.93 0.00 0.00 3.69
790 3329 1.001158 CGTCTATTTCCCGAGAGCTCC 60.001 57.143 10.93 0.68 0.00 4.70
792 3331 2.054232 TCGTCTATTTCCCGAGAGCT 57.946 50.000 0.00 0.00 0.00 4.09
793 3332 2.099427 ACTTCGTCTATTTCCCGAGAGC 59.901 50.000 0.00 0.00 31.54 4.09
794 3333 3.696898 CACTTCGTCTATTTCCCGAGAG 58.303 50.000 0.00 0.00 31.54 3.20
795 3334 2.159282 GCACTTCGTCTATTTCCCGAGA 60.159 50.000 0.00 0.00 31.54 4.04
796 3335 2.194271 GCACTTCGTCTATTTCCCGAG 58.806 52.381 0.00 0.00 31.54 4.63
820 3359 4.721776 TGGCCCATATGATAATACCCTCTC 59.278 45.833 3.65 0.00 0.00 3.20
821 3360 4.709944 TGGCCCATATGATAATACCCTCT 58.290 43.478 3.65 0.00 0.00 3.69
823 3362 4.448431 ACTGGCCCATATGATAATACCCT 58.552 43.478 3.65 0.00 0.00 4.34
824 3363 4.385310 GGACTGGCCCATATGATAATACCC 60.385 50.000 3.65 0.00 0.00 3.69
829 3375 3.584406 CTCTGGACTGGCCCATATGATAA 59.416 47.826 3.65 0.00 35.33 1.75
872 3418 1.597461 GGCTGCCTCGACCTAAGTT 59.403 57.895 12.43 0.00 0.00 2.66
978 3536 3.851128 GCGGCTAGGAGGGTGGAC 61.851 72.222 0.00 0.00 0.00 4.02
1317 3875 1.219393 GTTCTTGCGGGAGGAGAGG 59.781 63.158 0.00 0.00 0.00 3.69
1809 4367 4.517453 GCTCAGTACCTATCGATCTCTTGT 59.483 45.833 0.00 0.00 0.00 3.16
1870 4428 5.568685 TTGACGATTTGAAAGGAAACACA 57.431 34.783 0.00 0.00 0.00 3.72
1882 4440 9.655769 CTATCCATCTACAATTTTGACGATTTG 57.344 33.333 0.00 0.00 0.00 2.32
2041 4599 8.124823 ACAATGCAAATCAGATAGTTATGAACG 58.875 33.333 0.00 0.00 36.23 3.95
2064 4622 3.692101 CGGTAAGGCCACATAATCAACAA 59.308 43.478 5.01 0.00 36.97 2.83
2110 4668 4.122776 AGCATCGGATACTTCATCACAAC 58.877 43.478 0.00 0.00 35.11 3.32
2438 4996 4.345859 ACGTGAGTAGGTTCCAATCAAA 57.654 40.909 0.00 0.00 46.88 2.69
2456 5014 9.978044 GGTTCTATTATTATAGAGAAACCACGT 57.022 33.333 12.92 0.00 42.71 4.49
2561 5119 1.304254 TTGACGCTGCAGCTTGTAAA 58.696 45.000 34.22 22.17 39.32 2.01
2575 5133 3.436704 AGAACCACATTAGCACATTGACG 59.563 43.478 0.00 0.00 0.00 4.35
2596 5154 1.019673 AACTCAGCTGCAACACACAG 58.980 50.000 9.47 0.52 38.22 3.66
2650 5208 3.250744 GACGACAGTTTGGAATCGATCA 58.749 45.455 0.00 0.00 37.97 2.92
2680 5238 0.539051 CGATTGGGCTGAGAGTTCCT 59.461 55.000 0.00 0.00 0.00 3.36
2812 5370 7.838884 TGAAATATGAAAGCACAAATGGATCA 58.161 30.769 0.00 0.00 0.00 2.92
2870 5428 7.040617 TCGTGTTATTCTACTAGCATAAGGAGG 60.041 40.741 0.00 0.00 0.00 4.30
3033 5591 0.741927 CAGGATCACTGCGCATGTCA 60.742 55.000 12.24 0.00 40.97 3.58
3261 5819 7.227873 TGTCCAATTGAGATGGTTAACTTACA 58.772 34.615 7.12 0.00 39.09 2.41
3266 5824 5.048083 TGCTTGTCCAATTGAGATGGTTAAC 60.048 40.000 7.12 0.00 39.09 2.01
3269 5827 3.499338 TGCTTGTCCAATTGAGATGGTT 58.501 40.909 7.12 0.00 39.09 3.67
3289 5847 5.184864 ACAGTGTTCCAGAAGATCTAGTCTG 59.815 44.000 14.98 14.98 40.84 3.51
3334 5892 8.997621 AATATGAGACTAGAACGCTTAAACAA 57.002 30.769 0.00 0.00 0.00 2.83
3395 5953 3.793559 ACCATCCACTGCTTAACGATAC 58.206 45.455 0.00 0.00 0.00 2.24
3708 8640 5.051641 GCAACACGAGGAAACTATAGAATCG 60.052 44.000 6.78 10.25 44.43 3.34
3715 8647 2.851263 TGGCAACACGAGGAAACTAT 57.149 45.000 0.00 0.00 46.17 2.12
3771 8703 5.528690 TCCTGCACAATAACAGCATAAGATC 59.471 40.000 0.00 0.00 37.68 2.75
3780 8712 4.732647 GCATGATGTCCTGCACAATAACAG 60.733 45.833 0.00 0.00 38.97 3.16
3941 8873 4.524328 GTGAATTTTGAAGGGTGGTCTCAT 59.476 41.667 0.00 0.00 0.00 2.90
3968 8900 1.134995 CATCGGTTCAGCTGCAGACTA 60.135 52.381 20.43 0.00 0.00 2.59
4055 8987 1.825090 TCACCACCAATGCAGTGATC 58.175 50.000 17.16 0.00 37.42 2.92
4062 8994 5.070770 TCACAATAAATCACCACCAATGC 57.929 39.130 0.00 0.00 0.00 3.56
4123 9055 8.211629 TCTTTCTAATATTCCCTAGGCAGTTTC 58.788 37.037 2.05 0.00 0.00 2.78
4172 9104 7.360113 ACTAGGTCATTCAATTGTTTTGGTT 57.640 32.000 5.13 0.00 0.00 3.67
4201 9133 0.043788 GTTACCACCCCTAGTCCCCT 59.956 60.000 0.00 0.00 0.00 4.79
4202 9134 0.043788 AGTTACCACCCCTAGTCCCC 59.956 60.000 0.00 0.00 0.00 4.81
4203 9135 1.273438 TGAGTTACCACCCCTAGTCCC 60.273 57.143 0.00 0.00 0.00 4.46
4204 9136 2.242882 TGAGTTACCACCCCTAGTCC 57.757 55.000 0.00 0.00 0.00 3.85
4205 9137 3.371965 TGATGAGTTACCACCCCTAGTC 58.628 50.000 0.00 0.00 0.00 2.59
4206 9138 3.484953 TGATGAGTTACCACCCCTAGT 57.515 47.619 0.00 0.00 0.00 2.57
4207 9139 4.030913 TCTTGATGAGTTACCACCCCTAG 58.969 47.826 0.00 0.00 0.00 3.02
4208 9140 4.069312 TCTTGATGAGTTACCACCCCTA 57.931 45.455 0.00 0.00 0.00 3.53
4299 9231 4.081752 TGTTGGTTGCTGTTTGATTGACTT 60.082 37.500 0.00 0.00 0.00 3.01
4576 9975 5.567423 GCATGCCACTTGAATCCTTTTAAGT 60.567 40.000 6.36 0.00 41.01 2.24
4580 9979 2.027837 GGCATGCCACTTGAATCCTTTT 60.028 45.455 32.08 0.00 35.81 2.27
4623 10023 6.388619 ACAGGATTCCTAAAACACAGGTAT 57.611 37.500 4.51 0.00 34.56 2.73
4807 10216 1.961394 ACCGTTAGCAAGAGTGACTCA 59.039 47.619 15.86 0.00 32.06 3.41
5075 10484 6.969993 AACCCTTACAAGCAAGAAACATTA 57.030 33.333 0.00 0.00 0.00 1.90
5103 10596 6.220930 ACACATATATAACACGGCTGTTAGG 58.779 40.000 0.00 0.00 44.36 2.69
5423 10917 1.269998 ACTCTCACGTCAAGGCAGTAC 59.730 52.381 0.00 0.00 0.00 2.73
5519 11014 6.876257 TGCAACAAACTTTGGACTTGTTATTT 59.124 30.769 6.47 0.00 40.40 1.40
5529 11024 4.825422 TGTTCAATGCAACAAACTTTGGA 58.175 34.783 6.47 0.00 33.21 3.53
5620 11115 4.020573 AGCAGTAAAGCCCAATTTTAACCC 60.021 41.667 0.00 0.00 34.23 4.11
5621 11116 5.147330 AGCAGTAAAGCCCAATTTTAACC 57.853 39.130 0.00 0.00 34.23 2.85
5638 11133 9.991906 TTGACTAAAAGTACACTATTTAGCAGT 57.008 29.630 14.89 4.69 39.24 4.40
6090 11637 3.056313 GCCTCATCCGCAACCAAGC 62.056 63.158 0.00 0.00 0.00 4.01
6157 11705 1.171549 TGCATTGCAAGCCGTGAAGA 61.172 50.000 9.33 0.00 34.76 2.87
6159 11707 1.738432 TTGCATTGCAAGCCGTGAA 59.262 47.368 19.77 0.00 43.99 3.18
6188 11742 0.251354 ATGCTGACAGGTGGCTACAG 59.749 55.000 4.26 0.00 0.00 2.74
6206 11760 7.123098 TGCAGACATGGAAAAGAATGACAATAT 59.877 33.333 0.00 0.00 0.00 1.28
6207 11761 6.433716 TGCAGACATGGAAAAGAATGACAATA 59.566 34.615 0.00 0.00 0.00 1.90
6210 11764 4.143543 TGCAGACATGGAAAAGAATGACA 58.856 39.130 0.00 0.00 0.00 3.58
6232 11786 7.062138 CGACAAATTCAAACGAAATCCATGAAT 59.938 33.333 0.00 0.00 41.20 2.57
6239 11793 5.115021 GGACACGACAAATTCAAACGAAATC 59.885 40.000 0.00 0.00 0.00 2.17
6263 11817 7.610865 ACAGAAGTGAGAAAATCCTCTAGAAG 58.389 38.462 0.00 0.00 34.38 2.85
6567 12121 6.349243 AGCCAATGAATTCATGAAAACTGA 57.651 33.333 21.39 0.00 36.56 3.41
6653 12207 5.458779 GTGTATTTATTTTCCCTGCATTCGC 59.541 40.000 0.00 0.00 39.24 4.70
7028 12582 4.024641 ACCACGTAAAATTGGACGAAACTC 60.025 41.667 16.73 0.00 41.60 3.01
7036 12590 4.080469 TGGGCTATACCACGTAAAATTGGA 60.080 41.667 0.00 0.00 42.05 3.53
7040 12594 4.337274 GCTTTGGGCTATACCACGTAAAAT 59.663 41.667 0.00 0.00 41.03 1.82
7118 12672 0.404426 GGACAAAGGGCAGGGTTAGT 59.596 55.000 0.00 0.00 0.00 2.24
7174 12728 0.884704 GCGGAACCAAAGCTCTCACA 60.885 55.000 0.00 0.00 0.00 3.58
7176 12730 1.302511 GGCGGAACCAAAGCTCTCA 60.303 57.895 0.00 0.00 38.86 3.27
7224 12778 8.602424 AGACCGTCCATTATAATTCATAATCCA 58.398 33.333 0.00 0.00 37.67 3.41
7307 12862 1.336440 TGCAAGTCACAATTTCCCGTG 59.664 47.619 0.00 0.00 34.34 4.94
7313 12868 4.082571 GCTAGTCCATGCAAGTCACAATTT 60.083 41.667 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.