Multiple sequence alignment - TraesCS3D01G396600

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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 TraesCS3D01G396600 chr3D 100.000 3246 0 0 1 3246 511394987 511398232 0.000000e+00 5995.0
1 TraesCS3D01G396600 chr3D 87.194 898 94 16 980 1864 511941715 511940826 0.000000e+00 1002.0
2 TraesCS3D01G396600 chr3D 98.148 54 1 0 555 608 511395488 511395541 9.590000e-16 95.3
3 TraesCS3D01G396600 chr3D 98.148 54 1 0 502 555 511395541 511395594 9.590000e-16 95.3
4 TraesCS3D01G396600 chr2D 96.714 1339 26 1 1926 3246 608633411 608634749 0.000000e+00 2213.0
5 TraesCS3D01G396600 chr2D 82.408 1279 173 37 2005 3246 80747608 80748871 0.000000e+00 1068.0
6 TraesCS3D01G396600 chr2D 94.745 647 10 3 2618 3246 644042757 644042117 0.000000e+00 985.0
7 TraesCS3D01G396600 chr2D 84.000 175 26 2 556 729 648089314 648089487 2.000000e-37 167.0
8 TraesCS3D01G396600 chr6D 96.490 1339 29 1 1926 3246 37522370 37523708 0.000000e+00 2196.0
9 TraesCS3D01G396600 chr6D 79.225 1136 187 24 1993 3087 409752971 409751844 0.000000e+00 745.0
10 TraesCS3D01G396600 chr6D 87.689 528 35 2 2749 3246 80696190 80696717 3.610000e-164 588.0
11 TraesCS3D01G396600 chr3B 96.639 952 32 0 918 1869 672961130 672962081 0.000000e+00 1581.0
12 TraesCS3D01G396600 chr3B 96.853 572 18 0 1298 1869 673061358 673061929 0.000000e+00 957.0
13 TraesCS3D01G396600 chr3B 85.045 896 107 19 980 1864 674280694 674279815 0.000000e+00 887.0
14 TraesCS3D01G396600 chr3B 96.570 379 13 0 918 1296 673060812 673061190 2.130000e-176 628.0
15 TraesCS3D01G396600 chr3B 90.184 163 11 2 1 163 673058077 673058234 1.180000e-49 207.0
16 TraesCS3D01G396600 chr3B 100.000 44 0 0 773 816 672961098 672961141 7.460000e-12 82.4
17 TraesCS3D01G396600 chr3B 100.000 44 0 0 773 816 673060780 673060823 7.460000e-12 82.4
18 TraesCS3D01G396600 chr3B 95.918 49 1 1 765 812 673058595 673058643 9.660000e-11 78.7
19 TraesCS3D01G396600 chr3A 95.417 960 33 3 918 1869 647490728 647491684 0.000000e+00 1519.0
20 TraesCS3D01G396600 chr3A 93.885 556 31 3 1 555 647486196 647486749 0.000000e+00 835.0
21 TraesCS3D01G396600 chr3A 84.419 430 50 9 1451 1864 647803014 647802586 1.080000e-109 407.0
22 TraesCS3D01G396600 chr3A 94.898 196 9 1 556 751 647486697 647486891 4.070000e-79 305.0
23 TraesCS3D01G396600 chr3A 83.983 231 27 5 1086 1316 647804561 647804341 2.540000e-51 213.0
24 TraesCS3D01G396600 chr3A 98.039 51 1 0 766 816 647490689 647490739 4.460000e-14 89.8
25 TraesCS3D01G396600 chr3A 100.000 30 0 0 744 773 647490406 647490435 4.520000e-04 56.5
26 TraesCS3D01G396600 chr1D 97.932 822 16 1 1926 2747 10649273 10650093 0.000000e+00 1423.0
27 TraesCS3D01G396600 chr1D 81.206 1293 181 27 2002 3246 471936444 471935166 0.000000e+00 985.0
28 TraesCS3D01G396600 chr4A 93.200 750 48 3 1999 2747 604200507 604201254 0.000000e+00 1099.0
29 TraesCS3D01G396600 chr4A 90.389 822 75 3 1929 2747 734367600 734368420 0.000000e+00 1077.0
30 TraesCS3D01G396600 chr4A 89.562 776 69 3 1974 2746 606676436 606677202 0.000000e+00 974.0
31 TraesCS3D01G396600 chr7D 82.081 1278 184 31 2002 3246 69863547 69862282 0.000000e+00 1050.0
32 TraesCS3D01G396600 chr7D 85.682 880 113 8 1929 2800 553473441 553474315 0.000000e+00 915.0
33 TraesCS3D01G396600 chr5D 81.321 1317 196 17 1970 3246 57212579 57211273 0.000000e+00 1024.0
34 TraesCS3D01G396600 chr5D 88.091 529 32 3 2749 3246 301622267 301621739 1.670000e-167 599.0
35 TraesCS3D01G396600 chr6A 89.091 825 80 6 1935 2756 8377799 8376982 0.000000e+00 1016.0
36 TraesCS3D01G396600 chr4D 85.140 895 121 7 1929 2816 481183349 481184238 0.000000e+00 905.0
37 TraesCS3D01G396600 chrUn 96.570 379 13 0 918 1296 386103999 386103621 2.130000e-176 628.0
38 TraesCS3D01G396600 chrUn 97.872 47 1 0 773 819 386104031 386103985 7.460000e-12 82.4
39 TraesCS3D01G396600 chr2B 82.051 195 29 6 580 772 384338894 384338704 9.320000e-36 161.0
40 TraesCS3D01G396600 chr1A 80.000 125 22 3 650 772 59073856 59073979 4.460000e-14 89.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G396600 chr3D 511394987 511398232 3245 False 2061.866667 5995 98.765333 1 3246 3 chr3D.!!$F1 3245
1 TraesCS3D01G396600 chr3D 511940826 511941715 889 True 1002.000000 1002 87.194000 980 1864 1 chr3D.!!$R1 884
2 TraesCS3D01G396600 chr2D 608633411 608634749 1338 False 2213.000000 2213 96.714000 1926 3246 1 chr2D.!!$F2 1320
3 TraesCS3D01G396600 chr2D 80747608 80748871 1263 False 1068.000000 1068 82.408000 2005 3246 1 chr2D.!!$F1 1241
4 TraesCS3D01G396600 chr2D 644042117 644042757 640 True 985.000000 985 94.745000 2618 3246 1 chr2D.!!$R1 628
5 TraesCS3D01G396600 chr6D 37522370 37523708 1338 False 2196.000000 2196 96.490000 1926 3246 1 chr6D.!!$F1 1320
6 TraesCS3D01G396600 chr6D 409751844 409752971 1127 True 745.000000 745 79.225000 1993 3087 1 chr6D.!!$R1 1094
7 TraesCS3D01G396600 chr6D 80696190 80696717 527 False 588.000000 588 87.689000 2749 3246 1 chr6D.!!$F2 497
8 TraesCS3D01G396600 chr3B 674279815 674280694 879 True 887.000000 887 85.045000 980 1864 1 chr3B.!!$R1 884
9 TraesCS3D01G396600 chr3B 672961098 672962081 983 False 831.700000 1581 98.319500 773 1869 2 chr3B.!!$F1 1096
10 TraesCS3D01G396600 chr3B 673058077 673061929 3852 False 390.620000 957 95.905000 1 1869 5 chr3B.!!$F2 1868
11 TraesCS3D01G396600 chr3A 647486196 647491684 5488 False 561.060000 1519 96.447800 1 1869 5 chr3A.!!$F1 1868
12 TraesCS3D01G396600 chr3A 647802586 647804561 1975 True 310.000000 407 84.201000 1086 1864 2 chr3A.!!$R1 778
13 TraesCS3D01G396600 chr1D 10649273 10650093 820 False 1423.000000 1423 97.932000 1926 2747 1 chr1D.!!$F1 821
14 TraesCS3D01G396600 chr1D 471935166 471936444 1278 True 985.000000 985 81.206000 2002 3246 1 chr1D.!!$R1 1244
15 TraesCS3D01G396600 chr4A 604200507 604201254 747 False 1099.000000 1099 93.200000 1999 2747 1 chr4A.!!$F1 748
16 TraesCS3D01G396600 chr4A 734367600 734368420 820 False 1077.000000 1077 90.389000 1929 2747 1 chr4A.!!$F3 818
17 TraesCS3D01G396600 chr4A 606676436 606677202 766 False 974.000000 974 89.562000 1974 2746 1 chr4A.!!$F2 772
18 TraesCS3D01G396600 chr7D 69862282 69863547 1265 True 1050.000000 1050 82.081000 2002 3246 1 chr7D.!!$R1 1244
19 TraesCS3D01G396600 chr7D 553473441 553474315 874 False 915.000000 915 85.682000 1929 2800 1 chr7D.!!$F1 871
20 TraesCS3D01G396600 chr5D 57211273 57212579 1306 True 1024.000000 1024 81.321000 1970 3246 1 chr5D.!!$R1 1276
21 TraesCS3D01G396600 chr5D 301621739 301622267 528 True 599.000000 599 88.091000 2749 3246 1 chr5D.!!$R2 497
22 TraesCS3D01G396600 chr6A 8376982 8377799 817 True 1016.000000 1016 89.091000 1935 2756 1 chr6A.!!$R1 821
23 TraesCS3D01G396600 chr4D 481183349 481184238 889 False 905.000000 905 85.140000 1929 2816 1 chr4D.!!$F1 887

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
893 4834 0.177373 GGACGTCCGGCTCCTATTTT 59.823 55.0 20.85 0.0 0.0 1.82 F
1702 9172 1.076332 AGTACAATCTCAAACGCCGC 58.924 50.0 0.00 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 9372 0.107312 CCCTGGTCTCAGCCTGATTG 60.107 60.0 0.0 0.0 39.61 2.67 R
2569 10043 0.404812 GCTACGAGGAGGGATAGGGA 59.595 60.0 0.0 0.0 0.00 4.20 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
116 120 1.151943 AGCGATGGATGGATCCCCT 60.152 57.895 9.90 0.00 46.59 4.79
117 121 1.197430 AGCGATGGATGGATCCCCTC 61.197 60.000 9.90 6.07 46.59 4.30
118 122 1.986413 CGATGGATGGATCCCCTCC 59.014 63.158 19.20 19.20 46.59 4.30
119 123 1.557269 CGATGGATGGATCCCCTCCC 61.557 65.000 21.84 12.87 46.59 4.30
159 316 3.589881 GCCACATGAGCCATCGCC 61.590 66.667 0.00 0.00 34.57 5.54
160 317 2.903855 CCACATGAGCCATCGCCC 60.904 66.667 0.00 0.00 34.57 6.13
161 318 2.124612 CACATGAGCCATCGCCCA 60.125 61.111 0.00 0.00 34.57 5.36
162 319 1.527611 CACATGAGCCATCGCCCAT 60.528 57.895 0.00 0.00 34.57 4.00
163 320 1.228063 ACATGAGCCATCGCCCATC 60.228 57.895 0.00 0.00 34.57 3.51
164 321 2.031616 ATGAGCCATCGCCCATCG 59.968 61.111 0.00 0.00 40.15 3.84
165 322 4.916293 TGAGCCATCGCCCATCGC 62.916 66.667 0.00 0.00 38.27 4.58
166 323 4.916293 GAGCCATCGCCCATCGCA 62.916 66.667 0.00 0.00 37.30 5.10
167 324 4.923942 AGCCATCGCCCATCGCAG 62.924 66.667 0.00 0.00 37.30 5.18
169 326 4.923942 CCATCGCCCATCGCAGCT 62.924 66.667 0.00 0.00 37.30 4.24
170 327 2.029518 CATCGCCCATCGCAGCTA 59.970 61.111 0.00 0.00 37.30 3.32
171 328 2.029666 ATCGCCCATCGCAGCTAC 59.970 61.111 0.00 0.00 37.30 3.58
172 329 3.521529 ATCGCCCATCGCAGCTACC 62.522 63.158 0.00 0.00 37.30 3.18
173 330 4.529219 CGCCCATCGCAGCTACCA 62.529 66.667 0.00 0.00 37.30 3.25
174 331 2.590007 GCCCATCGCAGCTACCAG 60.590 66.667 0.00 0.00 37.47 4.00
175 332 2.109799 CCCATCGCAGCTACCAGG 59.890 66.667 0.00 0.00 0.00 4.45
176 333 2.434843 CCCATCGCAGCTACCAGGA 61.435 63.158 0.00 0.00 0.00 3.86
177 334 1.522092 CCATCGCAGCTACCAGGAA 59.478 57.895 0.00 0.00 0.00 3.36
178 335 0.531532 CCATCGCAGCTACCAGGAAG 60.532 60.000 0.00 0.00 0.00 3.46
179 336 0.531532 CATCGCAGCTACCAGGAAGG 60.532 60.000 0.00 0.00 45.67 3.46
180 337 0.687757 ATCGCAGCTACCAGGAAGGA 60.688 55.000 0.00 0.00 41.22 3.36
181 338 1.142748 CGCAGCTACCAGGAAGGAG 59.857 63.158 0.00 0.00 41.22 3.69
182 339 1.524482 GCAGCTACCAGGAAGGAGG 59.476 63.158 0.00 0.00 41.22 4.30
183 340 1.524482 CAGCTACCAGGAAGGAGGC 59.476 63.158 0.00 0.00 41.22 4.70
184 341 1.081092 AGCTACCAGGAAGGAGGCA 59.919 57.895 0.00 0.00 41.22 4.75
185 342 0.980231 AGCTACCAGGAAGGAGGCAG 60.980 60.000 0.00 0.00 41.22 4.85
186 343 1.524482 CTACCAGGAAGGAGGCAGC 59.476 63.158 0.00 0.00 41.22 5.25
187 344 1.229496 TACCAGGAAGGAGGCAGCA 60.229 57.895 0.00 0.00 41.22 4.41
188 345 1.553690 TACCAGGAAGGAGGCAGCAC 61.554 60.000 0.00 0.00 41.22 4.40
189 346 2.045536 CAGGAAGGAGGCAGCACC 60.046 66.667 0.00 0.00 39.61 5.01
190 347 3.334054 AGGAAGGAGGCAGCACCC 61.334 66.667 0.00 0.00 40.58 4.61
191 348 3.650950 GGAAGGAGGCAGCACCCA 61.651 66.667 0.00 0.00 40.58 4.51
192 349 2.679716 GAAGGAGGCAGCACCCAT 59.320 61.111 0.00 0.00 40.58 4.00
193 350 1.452833 GAAGGAGGCAGCACCCATC 60.453 63.158 0.00 0.00 40.58 3.51
194 351 3.335356 AAGGAGGCAGCACCCATCG 62.335 63.158 0.00 0.00 40.58 3.84
195 352 4.101448 GGAGGCAGCACCCATCGT 62.101 66.667 0.00 0.00 40.58 3.73
196 353 2.512515 GAGGCAGCACCCATCGTC 60.513 66.667 0.00 0.00 40.58 4.20
197 354 4.457496 AGGCAGCACCCATCGTCG 62.457 66.667 0.00 0.00 40.58 5.12
205 362 2.758327 CCCATCGTCGGGTGGAGA 60.758 66.667 16.15 0.00 41.83 3.71
206 363 2.355986 CCCATCGTCGGGTGGAGAA 61.356 63.158 16.15 0.00 41.83 2.87
207 364 1.141881 CCATCGTCGGGTGGAGAAG 59.858 63.158 10.85 0.00 37.72 2.85
208 365 1.519455 CATCGTCGGGTGGAGAAGC 60.519 63.158 0.00 0.00 0.00 3.86
209 366 2.722201 ATCGTCGGGTGGAGAAGCC 61.722 63.158 0.00 0.00 43.54 4.35
227 384 2.499214 CGGAGGTGGAGAAGAGAGG 58.501 63.158 0.00 0.00 0.00 3.69
228 385 0.323908 CGGAGGTGGAGAAGAGAGGT 60.324 60.000 0.00 0.00 0.00 3.85
229 386 1.480789 GGAGGTGGAGAAGAGAGGTC 58.519 60.000 0.00 0.00 0.00 3.85
230 387 1.099689 GAGGTGGAGAAGAGAGGTCG 58.900 60.000 0.00 0.00 0.00 4.79
231 388 0.968393 AGGTGGAGAAGAGAGGTCGC 60.968 60.000 0.00 0.00 0.00 5.19
232 389 1.137825 GTGGAGAAGAGAGGTCGCG 59.862 63.158 0.00 0.00 0.00 5.87
233 390 2.046864 TGGAGAAGAGAGGTCGCGG 61.047 63.158 6.13 0.00 0.00 6.46
234 391 2.047443 GGAGAAGAGAGGTCGCGGT 61.047 63.158 6.13 0.00 0.00 5.68
235 392 1.430228 GAGAAGAGAGGTCGCGGTC 59.570 63.158 6.13 0.41 0.00 4.79
236 393 2.100603 GAAGAGAGGTCGCGGTCG 59.899 66.667 6.13 0.00 0.00 4.79
237 394 2.672307 AAGAGAGGTCGCGGTCGT 60.672 61.111 6.13 1.19 36.96 4.34
238 395 2.852431 GAAGAGAGGTCGCGGTCGTG 62.852 65.000 6.13 0.00 36.96 4.35
249 406 3.414700 GGTCGTGCGCCTCTGTTG 61.415 66.667 4.18 0.00 0.00 3.33
250 407 4.077188 GTCGTGCGCCTCTGTTGC 62.077 66.667 4.18 0.00 0.00 4.17
258 415 4.335647 CCTCTGTTGCCGGCTGGT 62.336 66.667 29.70 0.00 37.67 4.00
259 416 2.743928 CTCTGTTGCCGGCTGGTC 60.744 66.667 29.70 15.08 37.67 4.02
260 417 4.329545 TCTGTTGCCGGCTGGTCC 62.330 66.667 29.70 11.01 37.67 4.46
270 427 4.052518 GCTGGTCCCCTGCACCAT 62.053 66.667 7.20 0.00 45.75 3.55
271 428 2.273449 CTGGTCCCCTGCACCATC 59.727 66.667 0.00 0.00 43.21 3.51
272 429 2.204136 TGGTCCCCTGCACCATCT 60.204 61.111 0.00 0.00 39.11 2.90
273 430 2.262774 CTGGTCCCCTGCACCATCTC 62.263 65.000 0.00 0.00 43.21 2.75
274 431 2.592308 GTCCCCTGCACCATCTCC 59.408 66.667 0.00 0.00 0.00 3.71
275 432 2.124768 TCCCCTGCACCATCTCCA 59.875 61.111 0.00 0.00 0.00 3.86
276 433 2.273449 CCCCTGCACCATCTCCAC 59.727 66.667 0.00 0.00 0.00 4.02
277 434 2.273449 CCCTGCACCATCTCCACC 59.727 66.667 0.00 0.00 0.00 4.61
278 435 2.605607 CCCTGCACCATCTCCACCA 61.606 63.158 0.00 0.00 0.00 4.17
279 436 1.377725 CCTGCACCATCTCCACCAC 60.378 63.158 0.00 0.00 0.00 4.16
280 437 1.742880 CTGCACCATCTCCACCACG 60.743 63.158 0.00 0.00 0.00 4.94
281 438 3.127533 GCACCATCTCCACCACGC 61.128 66.667 0.00 0.00 0.00 5.34
282 439 2.815211 CACCATCTCCACCACGCG 60.815 66.667 3.53 3.53 0.00 6.01
283 440 4.082523 ACCATCTCCACCACGCGG 62.083 66.667 12.47 0.00 38.77 6.46
285 442 4.457496 CATCTCCACCACGCGGCT 62.457 66.667 12.47 0.00 34.57 5.52
286 443 4.457496 ATCTCCACCACGCGGCTG 62.457 66.667 12.47 0.00 34.57 4.85
358 515 4.273257 GCCCTCGGCTCTAGCGAC 62.273 72.222 0.00 0.00 46.69 5.19
447 604 7.494922 AAAAATTACAGGGACCATATTGCTT 57.505 32.000 0.00 0.00 0.00 3.91
506 663 2.126142 TGGGGCCCACCTGTCATA 59.874 61.111 24.76 0.00 40.03 2.15
507 664 1.542628 TGGGGCCCACCTGTCATAA 60.543 57.895 24.76 0.00 40.03 1.90
508 665 0.923729 TGGGGCCCACCTGTCATAAT 60.924 55.000 24.76 0.00 40.03 1.28
509 666 1.145571 GGGGCCCACCTGTCATAATA 58.854 55.000 26.86 0.00 40.03 0.98
510 667 1.710809 GGGGCCCACCTGTCATAATAT 59.289 52.381 26.86 0.00 40.03 1.28
511 668 2.555227 GGGGCCCACCTGTCATAATATG 60.555 54.545 26.86 0.00 40.03 1.78
512 669 2.108250 GGGCCCACCTGTCATAATATGT 59.892 50.000 19.95 0.00 35.85 2.29
513 670 3.412386 GGCCCACCTGTCATAATATGTC 58.588 50.000 0.00 0.00 0.00 3.06
514 671 3.181445 GGCCCACCTGTCATAATATGTCA 60.181 47.826 0.00 0.27 0.00 3.58
515 672 4.460263 GCCCACCTGTCATAATATGTCAA 58.540 43.478 0.00 0.00 0.00 3.18
516 673 4.275936 GCCCACCTGTCATAATATGTCAAC 59.724 45.833 0.00 0.00 0.00 3.18
517 674 4.511454 CCCACCTGTCATAATATGTCAACG 59.489 45.833 0.00 0.00 0.00 4.10
518 675 4.511454 CCACCTGTCATAATATGTCAACGG 59.489 45.833 0.00 2.85 0.00 4.44
519 676 5.116180 CACCTGTCATAATATGTCAACGGT 58.884 41.667 0.00 3.42 30.91 4.83
520 677 5.234329 CACCTGTCATAATATGTCAACGGTC 59.766 44.000 7.90 0.00 29.29 4.79
521 678 5.105106 ACCTGTCATAATATGTCAACGGTCA 60.105 40.000 0.00 0.00 26.72 4.02
522 679 5.815222 CCTGTCATAATATGTCAACGGTCAA 59.185 40.000 0.00 0.00 0.00 3.18
523 680 6.238103 CCTGTCATAATATGTCAACGGTCAAC 60.238 42.308 0.00 0.00 0.00 3.18
524 681 6.403049 TGTCATAATATGTCAACGGTCAACT 58.597 36.000 0.00 0.00 0.00 3.16
525 682 7.548967 TGTCATAATATGTCAACGGTCAACTA 58.451 34.615 0.00 0.00 0.00 2.24
526 683 8.035984 TGTCATAATATGTCAACGGTCAACTAA 58.964 33.333 0.00 0.00 0.00 2.24
527 684 8.875803 GTCATAATATGTCAACGGTCAACTAAA 58.124 33.333 0.00 0.00 0.00 1.85
528 685 8.875803 TCATAATATGTCAACGGTCAACTAAAC 58.124 33.333 0.00 0.00 0.00 2.01
529 686 8.661257 CATAATATGTCAACGGTCAACTAAACA 58.339 33.333 0.00 0.00 0.00 2.83
530 687 6.721571 ATATGTCAACGGTCAACTAAACAG 57.278 37.500 0.00 0.00 0.00 3.16
531 688 3.864243 TGTCAACGGTCAACTAAACAGT 58.136 40.909 0.00 0.00 0.00 3.55
532 689 3.866910 TGTCAACGGTCAACTAAACAGTC 59.133 43.478 0.00 0.00 0.00 3.51
533 690 3.866910 GTCAACGGTCAACTAAACAGTCA 59.133 43.478 0.00 0.00 0.00 3.41
534 691 4.330620 GTCAACGGTCAACTAAACAGTCAA 59.669 41.667 0.00 0.00 0.00 3.18
535 692 4.936411 TCAACGGTCAACTAAACAGTCAAA 59.064 37.500 0.00 0.00 0.00 2.69
536 693 5.587043 TCAACGGTCAACTAAACAGTCAAAT 59.413 36.000 0.00 0.00 0.00 2.32
537 694 5.668558 ACGGTCAACTAAACAGTCAAATC 57.331 39.130 0.00 0.00 0.00 2.17
538 695 5.365619 ACGGTCAACTAAACAGTCAAATCT 58.634 37.500 0.00 0.00 0.00 2.40
539 696 6.518493 ACGGTCAACTAAACAGTCAAATCTA 58.482 36.000 0.00 0.00 0.00 1.98
540 697 6.987992 ACGGTCAACTAAACAGTCAAATCTAA 59.012 34.615 0.00 0.00 0.00 2.10
541 698 7.496591 ACGGTCAACTAAACAGTCAAATCTAAA 59.503 33.333 0.00 0.00 0.00 1.85
542 699 8.339714 CGGTCAACTAAACAGTCAAATCTAAAA 58.660 33.333 0.00 0.00 0.00 1.52
543 700 9.665264 GGTCAACTAAACAGTCAAATCTAAAAG 57.335 33.333 0.00 0.00 0.00 2.27
549 706 9.665264 CTAAACAGTCAAATCTAAAAGTCAACC 57.335 33.333 0.00 0.00 0.00 3.77
550 707 7.881775 AACAGTCAAATCTAAAAGTCAACCT 57.118 32.000 0.00 0.00 0.00 3.50
551 708 7.264373 ACAGTCAAATCTAAAAGTCAACCTG 57.736 36.000 0.00 0.00 0.00 4.00
552 709 7.054124 ACAGTCAAATCTAAAAGTCAACCTGA 58.946 34.615 0.00 0.00 0.00 3.86
578 735 5.636121 GTCATAACATGTCAACGGTCAACTA 59.364 40.000 0.00 0.00 0.00 2.24
594 751 7.496591 ACGGTCAACTAAACAGTCAAATCTAAA 59.503 33.333 0.00 0.00 0.00 1.85
668 825 3.733684 CGGTTCAGTCACTTGGGTTTTTG 60.734 47.826 0.00 0.00 0.00 2.44
740 898 7.876896 TTGGTAATATTTTGAAACGAAAGCC 57.123 32.000 0.00 0.00 0.00 4.35
819 4760 3.047877 CGCGTCCGGCTCCTTTTT 61.048 61.111 0.00 0.00 40.44 1.94
848 4789 2.029221 GGCGTCCGGCTCCTATTC 59.971 66.667 5.95 0.00 42.94 1.75
851 4792 0.179081 GCGTCCGGCTCCTATTCTTT 60.179 55.000 0.00 0.00 39.11 2.52
852 4793 1.742750 GCGTCCGGCTCCTATTCTTTT 60.743 52.381 0.00 0.00 39.11 2.27
889 4830 4.828296 GGGGACGTCCGGCTCCTA 62.828 72.222 27.68 0.00 41.75 2.94
891 4832 2.132352 GGGACGTCCGGCTCCTATT 61.132 63.158 27.68 0.00 36.71 1.73
893 4834 0.177373 GGACGTCCGGCTCCTATTTT 59.823 55.000 20.85 0.00 0.00 1.82
894 4835 1.406477 GGACGTCCGGCTCCTATTTTT 60.406 52.381 20.85 0.00 0.00 1.94
947 6951 6.211584 GGCTCCTATTCAATGTCAGGTAGATA 59.788 42.308 0.00 0.00 0.00 1.98
993 6997 1.520787 CGGGTCAGGTACGCAATCC 60.521 63.158 0.00 0.00 40.99 3.01
1180 7211 2.135664 AAAGGTCACGACGTTCTGAG 57.864 50.000 0.00 0.00 38.31 3.35
1543 8991 3.392616 ACTCCTTTGAGGTGATGTCTTGT 59.607 43.478 3.28 0.00 43.29 3.16
1547 8995 2.865119 TGAGGTGATGTCTTGTGCAT 57.135 45.000 0.00 0.00 0.00 3.96
1548 8996 2.703416 TGAGGTGATGTCTTGTGCATC 58.297 47.619 0.00 0.00 42.10 3.91
1702 9172 1.076332 AGTACAATCTCAAACGCCGC 58.924 50.000 0.00 0.00 0.00 6.53
1879 9349 2.820037 GCAAGTAGCGTGGAGGGC 60.820 66.667 0.00 0.00 0.00 5.19
1880 9350 2.125106 CAAGTAGCGTGGAGGGCC 60.125 66.667 0.00 0.00 0.00 5.80
1881 9351 2.284699 AAGTAGCGTGGAGGGCCT 60.285 61.111 5.25 5.25 34.31 5.19
1882 9352 2.359967 AAGTAGCGTGGAGGGCCTC 61.360 63.158 25.80 25.80 34.31 4.70
1895 9365 3.878667 GCCTCCGCCTTGGCCTAT 61.879 66.667 3.32 0.00 43.11 2.57
1896 9366 2.427753 CCTCCGCCTTGGCCTATC 59.572 66.667 3.32 0.00 37.80 2.08
1897 9367 2.029666 CTCCGCCTTGGCCTATCG 59.970 66.667 3.32 3.02 37.80 2.92
1898 9368 2.443203 TCCGCCTTGGCCTATCGA 60.443 61.111 3.32 0.00 37.80 3.59
1899 9369 1.821061 CTCCGCCTTGGCCTATCGAT 61.821 60.000 3.32 2.16 37.80 3.59
1900 9370 1.374758 CCGCCTTGGCCTATCGATC 60.375 63.158 0.00 0.00 0.00 3.69
1901 9371 1.668294 CGCCTTGGCCTATCGATCT 59.332 57.895 0.00 0.00 0.00 2.75
1902 9372 0.389166 CGCCTTGGCCTATCGATCTC 60.389 60.000 0.00 0.00 0.00 2.75
1903 9373 0.681733 GCCTTGGCCTATCGATCTCA 59.318 55.000 0.00 0.00 0.00 3.27
1904 9374 1.070758 GCCTTGGCCTATCGATCTCAA 59.929 52.381 0.00 2.04 0.00 3.02
1905 9375 2.289945 GCCTTGGCCTATCGATCTCAAT 60.290 50.000 0.00 0.00 0.00 2.57
1906 9376 3.594134 CCTTGGCCTATCGATCTCAATC 58.406 50.000 0.00 0.00 0.00 2.67
1907 9377 3.007290 CCTTGGCCTATCGATCTCAATCA 59.993 47.826 0.00 0.00 31.76 2.57
1908 9378 3.949842 TGGCCTATCGATCTCAATCAG 57.050 47.619 0.00 0.00 31.76 2.90
1909 9379 2.564504 TGGCCTATCGATCTCAATCAGG 59.435 50.000 0.00 1.98 31.76 3.86
1910 9380 2.615869 GCCTATCGATCTCAATCAGGC 58.384 52.381 15.37 15.37 39.83 4.85
1911 9381 2.233431 GCCTATCGATCTCAATCAGGCT 59.767 50.000 20.82 0.00 41.83 4.58
1912 9382 3.847542 CCTATCGATCTCAATCAGGCTG 58.152 50.000 8.58 8.58 31.76 4.85
1913 9383 3.509184 CCTATCGATCTCAATCAGGCTGA 59.491 47.826 21.19 21.19 31.76 4.26
1914 9384 3.663995 ATCGATCTCAATCAGGCTGAG 57.336 47.619 23.24 10.36 41.47 3.35
1918 9388 1.942776 TCTCAATCAGGCTGAGACCA 58.057 50.000 23.24 5.76 43.41 4.02
1919 9389 1.829849 TCTCAATCAGGCTGAGACCAG 59.170 52.381 23.24 14.76 43.41 4.00
1920 9390 0.907486 TCAATCAGGCTGAGACCAGG 59.093 55.000 23.24 8.20 40.72 4.45
1921 9391 0.107312 CAATCAGGCTGAGACCAGGG 60.107 60.000 23.24 3.23 40.72 4.45
1922 9392 1.919600 AATCAGGCTGAGACCAGGGC 61.920 60.000 23.24 0.00 40.72 5.19
1923 9393 4.106925 CAGGCTGAGACCAGGGCC 62.107 72.222 9.42 0.00 44.38 5.80
2344 9818 6.327177 TCTTACGCTTTTCGACATGATTAC 57.673 37.500 0.00 0.00 41.67 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 120 3.936566 ACGAGTGGGGAAGGGGGA 61.937 66.667 0.00 0.00 0.00 4.81
117 121 3.717294 CACGAGTGGGGAAGGGGG 61.717 72.222 0.00 0.00 0.00 5.40
118 122 2.606519 TCACGAGTGGGGAAGGGG 60.607 66.667 3.19 0.00 0.00 4.79
119 123 1.889530 GAGTCACGAGTGGGGAAGGG 61.890 65.000 3.19 0.00 0.00 3.95
159 316 0.531532 CTTCCTGGTAGCTGCGATGG 60.532 60.000 0.00 0.00 0.00 3.51
160 317 0.531532 CCTTCCTGGTAGCTGCGATG 60.532 60.000 0.00 0.00 0.00 3.84
161 318 0.687757 TCCTTCCTGGTAGCTGCGAT 60.688 55.000 0.00 0.00 37.07 4.58
162 319 1.304962 TCCTTCCTGGTAGCTGCGA 60.305 57.895 0.00 0.00 37.07 5.10
163 320 1.142748 CTCCTTCCTGGTAGCTGCG 59.857 63.158 0.00 0.00 37.07 5.18
164 321 1.524482 CCTCCTTCCTGGTAGCTGC 59.476 63.158 0.00 0.00 37.07 5.25
165 322 1.267574 TGCCTCCTTCCTGGTAGCTG 61.268 60.000 0.00 0.00 36.41 4.24
166 323 0.980231 CTGCCTCCTTCCTGGTAGCT 60.980 60.000 0.00 0.00 36.41 3.32
167 324 1.524482 CTGCCTCCTTCCTGGTAGC 59.476 63.158 0.00 0.00 37.07 3.58
168 325 1.267574 TGCTGCCTCCTTCCTGGTAG 61.268 60.000 0.00 0.00 38.76 3.18
169 326 1.229496 TGCTGCCTCCTTCCTGGTA 60.229 57.895 0.00 0.00 37.07 3.25
170 327 2.530151 TGCTGCCTCCTTCCTGGT 60.530 61.111 0.00 0.00 37.07 4.00
171 328 2.045536 GTGCTGCCTCCTTCCTGG 60.046 66.667 0.00 0.00 37.10 4.45
172 329 2.045536 GGTGCTGCCTCCTTCCTG 60.046 66.667 0.00 0.00 0.00 3.86
173 330 3.334054 GGGTGCTGCCTCCTTCCT 61.334 66.667 10.01 0.00 37.43 3.36
174 331 2.900671 GATGGGTGCTGCCTCCTTCC 62.901 65.000 10.01 0.00 37.43 3.46
175 332 1.452833 GATGGGTGCTGCCTCCTTC 60.453 63.158 10.01 8.91 37.43 3.46
176 333 2.679716 GATGGGTGCTGCCTCCTT 59.320 61.111 10.01 4.24 37.43 3.36
177 334 3.790437 CGATGGGTGCTGCCTCCT 61.790 66.667 10.01 0.00 37.43 3.69
178 335 4.101448 ACGATGGGTGCTGCCTCC 62.101 66.667 0.00 0.00 37.43 4.30
179 336 2.512515 GACGATGGGTGCTGCCTC 60.513 66.667 0.00 0.00 37.43 4.70
180 337 4.457496 CGACGATGGGTGCTGCCT 62.457 66.667 0.00 0.00 37.43 4.75
189 346 1.141881 CTTCTCCACCCGACGATGG 59.858 63.158 10.86 10.86 37.32 3.51
190 347 1.519455 GCTTCTCCACCCGACGATG 60.519 63.158 0.00 0.00 0.00 3.84
191 348 2.722201 GGCTTCTCCACCCGACGAT 61.722 63.158 0.00 0.00 34.01 3.73
192 349 3.379445 GGCTTCTCCACCCGACGA 61.379 66.667 0.00 0.00 34.01 4.20
193 350 4.796231 CGGCTTCTCCACCCGACG 62.796 72.222 0.00 0.00 44.55 5.12
194 351 4.452733 CCGGCTTCTCCACCCGAC 62.453 72.222 0.00 0.00 44.55 4.79
195 352 4.689549 TCCGGCTTCTCCACCCGA 62.690 66.667 0.00 0.00 44.55 5.14
196 353 4.148825 CTCCGGCTTCTCCACCCG 62.149 72.222 0.00 0.00 41.60 5.28
197 354 3.787001 CCTCCGGCTTCTCCACCC 61.787 72.222 0.00 0.00 34.01 4.61
198 355 3.003763 ACCTCCGGCTTCTCCACC 61.004 66.667 0.00 0.00 34.01 4.61
199 356 2.266055 CACCTCCGGCTTCTCCAC 59.734 66.667 0.00 0.00 34.01 4.02
200 357 3.003173 CCACCTCCGGCTTCTCCA 61.003 66.667 0.00 0.00 34.01 3.86
201 358 2.683933 TCCACCTCCGGCTTCTCC 60.684 66.667 0.00 0.00 0.00 3.71
202 359 1.258445 TTCTCCACCTCCGGCTTCTC 61.258 60.000 0.00 0.00 0.00 2.87
203 360 1.229209 TTCTCCACCTCCGGCTTCT 60.229 57.895 0.00 0.00 0.00 2.85
204 361 1.219393 CTTCTCCACCTCCGGCTTC 59.781 63.158 0.00 0.00 0.00 3.86
205 362 1.229209 TCTTCTCCACCTCCGGCTT 60.229 57.895 0.00 0.00 0.00 4.35
206 363 1.684049 CTCTTCTCCACCTCCGGCT 60.684 63.158 0.00 0.00 0.00 5.52
207 364 1.671901 CTCTCTTCTCCACCTCCGGC 61.672 65.000 0.00 0.00 0.00 6.13
208 365 1.040339 CCTCTCTTCTCCACCTCCGG 61.040 65.000 0.00 0.00 0.00 5.14
209 366 0.323908 ACCTCTCTTCTCCACCTCCG 60.324 60.000 0.00 0.00 0.00 4.63
210 367 1.480789 GACCTCTCTTCTCCACCTCC 58.519 60.000 0.00 0.00 0.00 4.30
211 368 1.099689 CGACCTCTCTTCTCCACCTC 58.900 60.000 0.00 0.00 0.00 3.85
212 369 0.968393 GCGACCTCTCTTCTCCACCT 60.968 60.000 0.00 0.00 0.00 4.00
213 370 1.513622 GCGACCTCTCTTCTCCACC 59.486 63.158 0.00 0.00 0.00 4.61
214 371 1.137825 CGCGACCTCTCTTCTCCAC 59.862 63.158 0.00 0.00 0.00 4.02
215 372 2.046864 CCGCGACCTCTCTTCTCCA 61.047 63.158 8.23 0.00 0.00 3.86
216 373 1.995646 GACCGCGACCTCTCTTCTCC 61.996 65.000 8.23 0.00 0.00 3.71
217 374 1.430228 GACCGCGACCTCTCTTCTC 59.570 63.158 8.23 0.00 0.00 2.87
218 375 2.400158 CGACCGCGACCTCTCTTCT 61.400 63.158 8.23 0.00 40.82 2.85
219 376 2.100603 CGACCGCGACCTCTCTTC 59.899 66.667 8.23 0.00 40.82 2.87
220 377 2.672307 ACGACCGCGACCTCTCTT 60.672 61.111 8.23 0.00 41.64 2.85
221 378 3.432588 CACGACCGCGACCTCTCT 61.433 66.667 8.23 0.00 41.64 3.10
232 389 3.414700 CAACAGAGGCGCACGACC 61.415 66.667 10.83 0.00 0.00 4.79
233 390 4.077188 GCAACAGAGGCGCACGAC 62.077 66.667 10.83 0.00 0.00 4.34
241 398 4.335647 ACCAGCCGGCAACAGAGG 62.336 66.667 31.54 20.98 34.57 3.69
242 399 2.743928 GACCAGCCGGCAACAGAG 60.744 66.667 31.54 12.39 34.57 3.35
243 400 4.329545 GGACCAGCCGGCAACAGA 62.330 66.667 31.54 0.00 34.57 3.41
257 414 2.300967 TGGAGATGGTGCAGGGGAC 61.301 63.158 0.00 0.00 0.00 4.46
258 415 2.124768 TGGAGATGGTGCAGGGGA 59.875 61.111 0.00 0.00 0.00 4.81
259 416 2.273449 GTGGAGATGGTGCAGGGG 59.727 66.667 0.00 0.00 0.00 4.79
260 417 2.273449 GGTGGAGATGGTGCAGGG 59.727 66.667 0.00 0.00 0.00 4.45
261 418 1.377725 GTGGTGGAGATGGTGCAGG 60.378 63.158 0.00 0.00 0.00 4.85
262 419 1.742880 CGTGGTGGAGATGGTGCAG 60.743 63.158 0.00 0.00 0.00 4.41
263 420 2.347114 CGTGGTGGAGATGGTGCA 59.653 61.111 0.00 0.00 0.00 4.57
264 421 3.127533 GCGTGGTGGAGATGGTGC 61.128 66.667 0.00 0.00 0.00 5.01
265 422 2.815211 CGCGTGGTGGAGATGGTG 60.815 66.667 0.00 0.00 0.00 4.17
266 423 4.082523 CCGCGTGGTGGAGATGGT 62.083 66.667 6.91 0.00 34.74 3.55
268 425 4.457496 AGCCGCGTGGTGGAGATG 62.457 66.667 17.91 0.00 34.74 2.90
269 426 4.457496 CAGCCGCGTGGTGGAGAT 62.457 66.667 17.91 0.00 38.83 2.75
284 441 4.717629 TCGTCGTCCGCCTTGCAG 62.718 66.667 0.00 0.00 36.19 4.41
285 442 4.717629 CTCGTCGTCCGCCTTGCA 62.718 66.667 0.00 0.00 36.19 4.08
287 444 4.421479 AGCTCGTCGTCCGCCTTG 62.421 66.667 0.00 0.00 36.19 3.61
288 445 4.117661 GAGCTCGTCGTCCGCCTT 62.118 66.667 0.00 0.00 36.19 4.35
299 456 1.086067 ATCCATGTGCAACGAGCTCG 61.086 55.000 33.45 33.45 45.94 5.03
300 457 0.376152 CATCCATGTGCAACGAGCTC 59.624 55.000 2.73 2.73 45.94 4.09
301 458 0.321919 ACATCCATGTGCAACGAGCT 60.322 50.000 0.00 0.00 45.94 4.09
302 459 2.174334 ACATCCATGTGCAACGAGC 58.826 52.632 0.00 0.00 42.39 5.03
501 658 6.903883 AGTTGACCGTTGACATATTATGAC 57.096 37.500 10.62 5.04 0.00 3.06
502 659 8.875803 GTTTAGTTGACCGTTGACATATTATGA 58.124 33.333 10.62 0.00 0.00 2.15
503 660 8.661257 TGTTTAGTTGACCGTTGACATATTATG 58.339 33.333 2.03 2.03 0.00 1.90
504 661 8.780846 TGTTTAGTTGACCGTTGACATATTAT 57.219 30.769 0.00 0.00 0.00 1.28
505 662 7.874016 ACTGTTTAGTTGACCGTTGACATATTA 59.126 33.333 0.00 0.00 31.66 0.98
506 663 6.708949 ACTGTTTAGTTGACCGTTGACATATT 59.291 34.615 0.00 0.00 31.66 1.28
507 664 6.228258 ACTGTTTAGTTGACCGTTGACATAT 58.772 36.000 0.00 0.00 31.66 1.78
508 665 5.603596 ACTGTTTAGTTGACCGTTGACATA 58.396 37.500 0.00 0.00 31.66 2.29
509 666 4.448210 ACTGTTTAGTTGACCGTTGACAT 58.552 39.130 0.00 0.00 31.66 3.06
510 667 3.864243 ACTGTTTAGTTGACCGTTGACA 58.136 40.909 0.00 0.00 31.66 3.58
511 668 3.866910 TGACTGTTTAGTTGACCGTTGAC 59.133 43.478 0.00 0.00 37.25 3.18
512 669 4.126208 TGACTGTTTAGTTGACCGTTGA 57.874 40.909 0.00 0.00 37.25 3.18
513 670 4.868450 TTGACTGTTTAGTTGACCGTTG 57.132 40.909 0.00 0.00 37.25 4.10
514 671 5.820947 AGATTTGACTGTTTAGTTGACCGTT 59.179 36.000 0.00 0.00 37.25 4.44
515 672 5.365619 AGATTTGACTGTTTAGTTGACCGT 58.634 37.500 0.00 0.00 37.25 4.83
516 673 5.924475 AGATTTGACTGTTTAGTTGACCG 57.076 39.130 0.00 0.00 37.25 4.79
517 674 9.665264 CTTTTAGATTTGACTGTTTAGTTGACC 57.335 33.333 0.00 0.00 37.25 4.02
523 680 9.665264 GGTTGACTTTTAGATTTGACTGTTTAG 57.335 33.333 0.00 0.00 0.00 1.85
524 681 9.403583 AGGTTGACTTTTAGATTTGACTGTTTA 57.596 29.630 0.00 0.00 0.00 2.01
525 682 8.190784 CAGGTTGACTTTTAGATTTGACTGTTT 58.809 33.333 0.00 0.00 0.00 2.83
526 683 7.556275 TCAGGTTGACTTTTAGATTTGACTGTT 59.444 33.333 0.00 0.00 0.00 3.16
527 684 7.012421 GTCAGGTTGACTTTTAGATTTGACTGT 59.988 37.037 2.08 0.00 43.73 3.55
528 685 7.355778 GTCAGGTTGACTTTTAGATTTGACTG 58.644 38.462 2.08 0.00 43.73 3.51
529 686 6.202954 CGTCAGGTTGACTTTTAGATTTGACT 59.797 38.462 7.52 0.00 44.85 3.41
530 687 6.018180 ACGTCAGGTTGACTTTTAGATTTGAC 60.018 38.462 7.52 0.00 44.85 3.18
531 688 6.053005 ACGTCAGGTTGACTTTTAGATTTGA 58.947 36.000 7.52 0.00 44.85 2.69
532 689 6.018262 TGACGTCAGGTTGACTTTTAGATTTG 60.018 38.462 15.76 0.00 44.85 2.32
533 690 6.053005 TGACGTCAGGTTGACTTTTAGATTT 58.947 36.000 15.76 0.00 44.85 2.17
534 691 5.607477 TGACGTCAGGTTGACTTTTAGATT 58.393 37.500 15.76 0.00 44.85 2.40
535 692 5.209818 TGACGTCAGGTTGACTTTTAGAT 57.790 39.130 15.76 0.00 44.85 1.98
536 693 4.659111 TGACGTCAGGTTGACTTTTAGA 57.341 40.909 15.76 0.00 44.85 2.10
537 694 6.422701 TGTTATGACGTCAGGTTGACTTTTAG 59.577 38.462 24.41 0.00 44.85 1.85
538 695 6.282167 TGTTATGACGTCAGGTTGACTTTTA 58.718 36.000 24.41 4.26 44.85 1.52
539 696 5.120399 TGTTATGACGTCAGGTTGACTTTT 58.880 37.500 24.41 5.30 44.85 2.27
540 697 4.699637 TGTTATGACGTCAGGTTGACTTT 58.300 39.130 24.41 6.07 44.85 2.66
541 698 4.330944 TGTTATGACGTCAGGTTGACTT 57.669 40.909 24.41 6.83 44.85 3.01
542 699 4.245660 CATGTTATGACGTCAGGTTGACT 58.754 43.478 24.41 7.61 44.85 3.41
543 700 3.994392 ACATGTTATGACGTCAGGTTGAC 59.006 43.478 24.41 14.13 43.65 3.18
544 701 4.242475 GACATGTTATGACGTCAGGTTGA 58.758 43.478 24.41 6.94 0.00 3.18
545 702 3.993736 TGACATGTTATGACGTCAGGTTG 59.006 43.478 24.41 17.24 33.61 3.77
546 703 4.265904 TGACATGTTATGACGTCAGGTT 57.734 40.909 24.41 9.95 33.61 3.50
547 704 3.953712 TGACATGTTATGACGTCAGGT 57.046 42.857 24.41 10.73 33.61 4.00
548 705 3.060761 CGTTGACATGTTATGACGTCAGG 59.939 47.826 24.41 10.79 39.39 3.86
549 706 3.060761 CCGTTGACATGTTATGACGTCAG 59.939 47.826 24.41 11.37 39.39 3.51
550 707 2.990514 CCGTTGACATGTTATGACGTCA 59.009 45.455 22.48 22.48 36.63 4.35
551 708 2.991190 ACCGTTGACATGTTATGACGTC 59.009 45.455 9.11 9.11 0.00 4.34
552 709 2.991190 GACCGTTGACATGTTATGACGT 59.009 45.455 12.19 0.00 0.00 4.34
553 710 2.990514 TGACCGTTGACATGTTATGACG 59.009 45.455 0.00 3.71 0.00 4.35
578 735 8.190784 CAGGTTGACTTTTAGATTTGACTGTTT 58.809 33.333 0.00 0.00 0.00 2.83
668 825 3.625313 CACAAAATTGGTTGGTTGTTCCC 59.375 43.478 0.00 0.00 31.98 3.97
724 882 6.420604 CACATTACAGGCTTTCGTTTCAAAAT 59.579 34.615 0.00 0.00 0.00 1.82
830 4771 3.516866 GAATAGGAGCCGGACGCCC 62.517 68.421 5.05 3.97 39.50 6.13
831 4772 2.029221 GAATAGGAGCCGGACGCC 59.971 66.667 5.05 8.26 38.78 5.68
833 4774 2.311124 AAAAGAATAGGAGCCGGACG 57.689 50.000 5.05 0.00 0.00 4.79
872 4813 4.828296 TAGGAGCCGGACGTCCCC 62.828 72.222 28.52 22.41 32.70 4.81
874 4815 0.177373 AAAATAGGAGCCGGACGTCC 59.823 55.000 25.28 25.28 0.00 4.79
875 4816 2.019948 AAAAATAGGAGCCGGACGTC 57.980 50.000 5.05 7.13 0.00 4.34
912 4853 4.828296 TAGGAGCCGGACGTCCCC 62.828 72.222 28.52 22.41 32.70 4.81
913 4854 2.085042 GAATAGGAGCCGGACGTCCC 62.085 65.000 28.52 15.65 32.70 4.46
914 4855 1.363080 GAATAGGAGCCGGACGTCC 59.637 63.158 25.28 25.28 0.00 4.79
915 4856 0.458669 TTGAATAGGAGCCGGACGTC 59.541 55.000 5.05 7.13 0.00 4.34
916 4857 1.120530 ATTGAATAGGAGCCGGACGT 58.879 50.000 5.05 2.14 0.00 4.34
947 6951 2.278596 CGGACGCGGTCGAATCAT 60.279 61.111 12.47 0.00 39.41 2.45
993 6997 1.134367 TGTAGTCGAATTCGGAGGCAG 59.866 52.381 26.47 0.00 40.29 4.85
1180 7211 1.484240 ACCAGATAGAGGTGCTTCTGC 59.516 52.381 0.00 0.00 38.13 4.26
1477 8925 0.749049 TCAGCGCATACAGCATCTCT 59.251 50.000 11.47 0.00 46.13 3.10
1543 8991 3.972133 ACAAGGATTTGGAGATGATGCA 58.028 40.909 0.00 0.00 38.66 3.96
1672 9142 3.000727 GAGATTGTACTTGTTGACCCCG 58.999 50.000 0.00 0.00 0.00 5.73
1702 9172 2.408050 CTGGTGTCGAAAGAGAAGGTG 58.592 52.381 0.00 0.00 43.49 4.00
1879 9349 2.427753 GATAGGCCAAGGCGGAGG 59.572 66.667 5.01 0.00 43.06 4.30
1880 9350 1.821061 ATCGATAGGCCAAGGCGGAG 61.821 60.000 5.01 0.00 43.06 4.63
1881 9351 1.816863 GATCGATAGGCCAAGGCGGA 61.817 60.000 5.01 0.00 43.06 5.54
1882 9352 1.374758 GATCGATAGGCCAAGGCGG 60.375 63.158 5.01 0.00 43.06 6.13
1883 9353 0.389166 GAGATCGATAGGCCAAGGCG 60.389 60.000 5.01 2.86 43.06 5.52
1884 9354 0.681733 TGAGATCGATAGGCCAAGGC 59.318 55.000 5.01 1.52 41.06 4.35
1885 9355 3.007290 TGATTGAGATCGATAGGCCAAGG 59.993 47.826 5.01 0.00 34.91 3.61
1886 9356 4.244066 CTGATTGAGATCGATAGGCCAAG 58.756 47.826 5.01 0.00 34.91 3.61
1887 9357 3.007290 CCTGATTGAGATCGATAGGCCAA 59.993 47.826 5.01 0.84 34.91 4.52
1888 9358 2.564504 CCTGATTGAGATCGATAGGCCA 59.435 50.000 5.01 0.00 34.91 5.36
1889 9359 2.676463 GCCTGATTGAGATCGATAGGCC 60.676 54.545 18.42 0.00 34.91 5.19
1890 9360 2.233431 AGCCTGATTGAGATCGATAGGC 59.767 50.000 20.63 20.63 39.93 3.93
1891 9361 3.509184 TCAGCCTGATTGAGATCGATAGG 59.491 47.826 0.00 0.13 34.91 2.57
1892 9362 4.458642 TCTCAGCCTGATTGAGATCGATAG 59.541 45.833 0.00 0.00 44.47 2.08
1893 9363 4.401925 TCTCAGCCTGATTGAGATCGATA 58.598 43.478 0.00 0.00 44.47 2.92
1894 9364 3.229293 TCTCAGCCTGATTGAGATCGAT 58.771 45.455 0.00 0.00 44.47 3.59
1895 9365 2.659428 TCTCAGCCTGATTGAGATCGA 58.341 47.619 0.00 0.00 44.47 3.59
1899 9369 1.829849 CTGGTCTCAGCCTGATTGAGA 59.170 52.381 0.00 1.07 46.47 3.27
1900 9370 1.134461 CCTGGTCTCAGCCTGATTGAG 60.134 57.143 0.00 0.00 42.68 3.02
1901 9371 0.907486 CCTGGTCTCAGCCTGATTGA 59.093 55.000 0.00 0.00 39.61 2.57
1902 9372 0.107312 CCCTGGTCTCAGCCTGATTG 60.107 60.000 0.00 0.00 39.61 2.67
1903 9373 1.919600 GCCCTGGTCTCAGCCTGATT 61.920 60.000 0.00 0.00 39.61 2.57
1904 9374 2.373707 GCCCTGGTCTCAGCCTGAT 61.374 63.158 0.00 0.00 39.61 2.90
1905 9375 3.005539 GCCCTGGTCTCAGCCTGA 61.006 66.667 0.00 0.00 39.61 3.86
1906 9376 4.106925 GGCCCTGGTCTCAGCCTG 62.107 72.222 0.00 0.00 42.34 4.85
1908 9378 4.106925 CAGGCCCTGGTCTCAGCC 62.107 72.222 1.63 3.01 46.13 4.85
1909 9379 2.373707 ATCAGGCCCTGGTCTCAGC 61.374 63.158 11.68 0.00 39.61 4.26
1910 9380 1.525923 CATCAGGCCCTGGTCTCAG 59.474 63.158 11.68 0.00 40.59 3.35
1911 9381 1.997311 CCATCAGGCCCTGGTCTCA 60.997 63.158 11.68 0.00 31.51 3.27
1912 9382 2.914289 CCATCAGGCCCTGGTCTC 59.086 66.667 11.68 0.00 31.51 3.36
2344 9818 0.179073 AGTGATCCAAGAATCCGGCG 60.179 55.000 0.00 0.00 0.00 6.46
2569 10043 0.404812 GCTACGAGGAGGGATAGGGA 59.595 60.000 0.00 0.00 0.00 4.20
2684 10173 4.778143 GCCCGTCCAGAACCGCAT 62.778 66.667 0.00 0.00 0.00 4.73
2747 10236 3.382832 CTCTTCGGTGGAGGCGGT 61.383 66.667 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.