Multiple sequence alignment - TraesCS5D01G450500

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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 TraesCS5D01G450500 chr5D 100.000 3476 0 0 1 3476 498780017 498776542 0.000000e+00 6420
1 TraesCS5D01G450500 chr5B 93.984 1712 60 17 950 2631 618477018 618475320 0.000000e+00 2551
2 TraesCS5D01G450500 chr5B 89.322 590 38 9 2641 3219 618475279 618474704 0.000000e+00 717
3 TraesCS5D01G450500 chr5B 83.507 479 55 12 268 744 618484857 618484401 3.210000e-115 425
4 TraesCS5D01G450500 chr5B 90.667 150 9 2 3330 3475 618474519 618474371 9.840000e-46 195
5 TraesCS5D01G450500 chr5A 94.579 1605 43 16 1033 2607 623216056 623214466 0.000000e+00 2442
6 TraesCS5D01G450500 chr5A 84.437 861 79 28 2644 3475 623214243 623213409 0.000000e+00 797
7 TraesCS5D01G450500 chr5A 83.604 738 93 17 194 907 623220297 623219564 0.000000e+00 667
8 TraesCS5D01G450500 chr5A 87.037 270 30 1 593 857 306491493 306491762 2.030000e-77 300
9 TraesCS5D01G450500 chr4A 87.452 263 27 2 593 850 742457766 742458027 7.290000e-77 298
10 TraesCS5D01G450500 chr6D 86.842 266 28 3 593 853 389923181 389922918 1.220000e-74 291
11 TraesCS5D01G450500 chr7D 89.091 220 14 5 635 846 403783137 403783354 7.400000e-67 265
12 TraesCS5D01G450500 chr7A 86.166 253 23 5 603 846 462341384 462341633 2.660000e-66 263
13 TraesCS5D01G450500 chr3D 85.385 260 31 4 598 852 570507552 570507295 2.660000e-66 263
14 TraesCS5D01G450500 chr3A 85.271 258 30 3 604 856 162215805 162215551 3.440000e-65 259
15 TraesCS5D01G450500 chr1D 82.657 271 38 7 590 856 371580033 371580298 7.500000e-57 231
16 TraesCS5D01G450500 chr2D 81.419 296 40 12 1394 1678 364169572 364169281 9.710000e-56 228
17 TraesCS5D01G450500 chr2B 81.419 296 40 12 1394 1678 432559136 432558845 9.710000e-56 228
18 TraesCS5D01G450500 chr2A 83.607 244 34 4 1441 1678 490665290 490665047 1.260000e-54 224


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 TraesCS5D01G450500 chr5D 498776542 498780017 3475 True 6420.000000 6420 100.000000 1 3476 1 chr5D.!!$R1 3475
1 TraesCS5D01G450500 chr5B 618474371 618477018 2647 True 1154.333333 2551 91.324333 950 3475 3 chr5B.!!$R2 2525
2 TraesCS5D01G450500 chr5A 623213409 623220297 6888 True 1302.000000 2442 87.540000 194 3475 3 chr5A.!!$R1 3281

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
937 957 0.034337 TGAGTAACACAACGAGGGCC 59.966 55.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2934 6602 0.439985 CGCTGTCTGGTGTTTGATCG 59.56 55.0 0.0 0.0 0.0 3.69 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
23 24 6.908870 CTCAAAGGACATTATGTTCGATGA 57.091 37.500 11.79 11.79 29.06 2.92
24 25 7.488187 CTCAAAGGACATTATGTTCGATGAT 57.512 36.000 12.44 0.00 29.42 2.45
25 26 8.593492 CTCAAAGGACATTATGTTCGATGATA 57.407 34.615 12.44 0.00 29.42 2.15
26 27 8.956533 TCAAAGGACATTATGTTCGATGATAA 57.043 30.769 9.32 0.00 29.06 1.75
27 28 8.826710 TCAAAGGACATTATGTTCGATGATAAC 58.173 33.333 9.32 0.00 29.06 1.89
28 29 8.611757 CAAAGGACATTATGTTCGATGATAACA 58.388 33.333 0.00 0.00 40.85 2.41
29 30 7.715265 AGGACATTATGTTCGATGATAACAC 57.285 36.000 0.00 0.00 39.51 3.32
30 31 7.272244 AGGACATTATGTTCGATGATAACACA 58.728 34.615 0.00 0.00 39.51 3.72
31 32 7.933577 AGGACATTATGTTCGATGATAACACAT 59.066 33.333 0.00 2.54 39.51 3.21
32 33 8.011673 GGACATTATGTTCGATGATAACACATG 58.988 37.037 0.00 6.73 39.51 3.21
33 34 7.355017 ACATTATGTTCGATGATAACACATGC 58.645 34.615 6.85 0.00 39.51 4.06
34 35 6.917217 TTATGTTCGATGATAACACATGCA 57.083 33.333 6.85 0.00 39.51 3.96
35 36 5.816449 ATGTTCGATGATAACACATGCAA 57.184 34.783 0.00 0.00 39.51 4.08
36 37 4.968626 TGTTCGATGATAACACATGCAAC 58.031 39.130 0.00 0.00 32.07 4.17
37 38 4.694982 TGTTCGATGATAACACATGCAACT 59.305 37.500 0.00 0.00 32.07 3.16
38 39 5.872070 TGTTCGATGATAACACATGCAACTA 59.128 36.000 0.00 0.00 32.07 2.24
39 40 6.538381 TGTTCGATGATAACACATGCAACTAT 59.462 34.615 0.00 0.00 32.07 2.12
40 41 6.769608 TCGATGATAACACATGCAACTATC 57.230 37.500 0.00 0.00 0.00 2.08
41 42 6.279882 TCGATGATAACACATGCAACTATCA 58.720 36.000 0.00 8.83 34.44 2.15
42 43 6.760770 TCGATGATAACACATGCAACTATCAA 59.239 34.615 9.92 0.00 33.83 2.57
43 44 7.442062 TCGATGATAACACATGCAACTATCAAT 59.558 33.333 9.92 2.69 33.83 2.57
44 45 8.071967 CGATGATAACACATGCAACTATCAATT 58.928 33.333 9.92 0.00 33.83 2.32
52 53 9.926158 ACACATGCAACTATCAATTAAAAATCA 57.074 25.926 0.00 0.00 0.00 2.57
112 113 8.535690 AAAACAAAAGAACGAACATAAAACCA 57.464 26.923 0.00 0.00 0.00 3.67
113 114 8.535690 AAACAAAAGAACGAACATAAAACCAA 57.464 26.923 0.00 0.00 0.00 3.67
114 115 8.535690 AACAAAAGAACGAACATAAAACCAAA 57.464 26.923 0.00 0.00 0.00 3.28
115 116 8.535690 ACAAAAGAACGAACATAAAACCAAAA 57.464 26.923 0.00 0.00 0.00 2.44
116 117 8.989980 ACAAAAGAACGAACATAAAACCAAAAA 58.010 25.926 0.00 0.00 0.00 1.94
146 147 9.898152 ATAACAAATTCAAGAAAGGGAAAAACA 57.102 25.926 0.00 0.00 0.00 2.83
147 148 8.628630 AACAAATTCAAGAAAGGGAAAAACAA 57.371 26.923 0.00 0.00 0.00 2.83
148 149 8.628630 ACAAATTCAAGAAAGGGAAAAACAAA 57.371 26.923 0.00 0.00 0.00 2.83
149 150 9.072375 ACAAATTCAAGAAAGGGAAAAACAAAA 57.928 25.926 0.00 0.00 0.00 2.44
150 151 9.905171 CAAATTCAAGAAAGGGAAAAACAAAAA 57.095 25.926 0.00 0.00 0.00 1.94
154 155 9.905171 TTCAAGAAAGGGAAAAACAAAAATTTG 57.095 25.926 4.40 4.40 43.62 2.32
155 156 8.518702 TCAAGAAAGGGAAAAACAAAAATTTGG 58.481 29.630 10.38 0.00 42.34 3.28
156 157 8.303156 CAAGAAAGGGAAAAACAAAAATTTGGT 58.697 29.630 10.38 0.54 42.34 3.67
157 158 8.050778 AGAAAGGGAAAAACAAAAATTTGGTC 57.949 30.769 10.38 2.79 42.34 4.02
158 159 7.667635 AGAAAGGGAAAAACAAAAATTTGGTCA 59.332 29.630 10.38 0.00 42.34 4.02
159 160 7.389803 AAGGGAAAAACAAAAATTTGGTCAG 57.610 32.000 10.38 0.00 42.34 3.51
160 161 6.716284 AGGGAAAAACAAAAATTTGGTCAGA 58.284 32.000 10.38 0.00 42.34 3.27
161 162 7.171653 AGGGAAAAACAAAAATTTGGTCAGAA 58.828 30.769 10.38 0.00 42.34 3.02
162 163 7.336679 AGGGAAAAACAAAAATTTGGTCAGAAG 59.663 33.333 10.38 0.00 42.34 2.85
163 164 6.966632 GGAAAAACAAAAATTTGGTCAGAAGC 59.033 34.615 10.38 0.00 42.34 3.86
164 165 7.148255 GGAAAAACAAAAATTTGGTCAGAAGCT 60.148 33.333 10.38 0.00 42.34 3.74
165 166 7.686438 AAAACAAAAATTTGGTCAGAAGCTT 57.314 28.000 0.00 0.00 42.34 3.74
166 167 6.908870 AACAAAAATTTGGTCAGAAGCTTC 57.091 33.333 19.11 19.11 42.34 3.86
167 168 6.225981 ACAAAAATTTGGTCAGAAGCTTCT 57.774 33.333 23.49 23.49 42.34 2.85
168 169 7.346751 ACAAAAATTTGGTCAGAAGCTTCTA 57.653 32.000 28.02 12.57 42.34 2.10
169 170 7.203218 ACAAAAATTTGGTCAGAAGCTTCTAC 58.797 34.615 28.02 22.82 42.34 2.59
170 171 6.959639 AAAATTTGGTCAGAAGCTTCTACA 57.040 33.333 28.02 22.38 35.34 2.74
171 172 6.959639 AAATTTGGTCAGAAGCTTCTACAA 57.040 33.333 28.02 26.01 35.34 2.41
172 173 6.566197 AATTTGGTCAGAAGCTTCTACAAG 57.434 37.500 28.02 16.01 35.34 3.16
187 188 6.811253 TTCTACAAGCAATACAAAATCGGT 57.189 33.333 0.00 0.00 0.00 4.69
188 189 6.417191 TCTACAAGCAATACAAAATCGGTC 57.583 37.500 0.00 0.00 0.00 4.79
189 190 5.935206 TCTACAAGCAATACAAAATCGGTCA 59.065 36.000 0.00 0.00 0.00 4.02
190 191 5.446143 ACAAGCAATACAAAATCGGTCAA 57.554 34.783 0.00 0.00 0.00 3.18
191 192 5.460646 ACAAGCAATACAAAATCGGTCAAG 58.539 37.500 0.00 0.00 0.00 3.02
192 193 4.096732 AGCAATACAAAATCGGTCAAGC 57.903 40.909 0.00 0.00 0.00 4.01
193 194 3.505680 AGCAATACAAAATCGGTCAAGCA 59.494 39.130 0.00 0.00 0.00 3.91
194 195 4.022416 AGCAATACAAAATCGGTCAAGCAA 60.022 37.500 0.00 0.00 0.00 3.91
195 196 4.864247 GCAATACAAAATCGGTCAAGCAAT 59.136 37.500 0.00 0.00 0.00 3.56
196 197 6.033341 GCAATACAAAATCGGTCAAGCAATA 58.967 36.000 0.00 0.00 0.00 1.90
197 198 6.697019 GCAATACAAAATCGGTCAAGCAATAT 59.303 34.615 0.00 0.00 0.00 1.28
198 199 7.306167 GCAATACAAAATCGGTCAAGCAATATG 60.306 37.037 0.00 0.00 0.00 1.78
199 200 5.895636 ACAAAATCGGTCAAGCAATATGA 57.104 34.783 0.00 0.00 0.00 2.15
200 201 6.266168 ACAAAATCGGTCAAGCAATATGAA 57.734 33.333 0.00 0.00 0.00 2.57
201 202 6.324819 ACAAAATCGGTCAAGCAATATGAAG 58.675 36.000 0.00 0.00 0.00 3.02
202 203 5.505173 AAATCGGTCAAGCAATATGAAGG 57.495 39.130 0.00 0.00 0.00 3.46
203 204 3.904800 TCGGTCAAGCAATATGAAGGA 57.095 42.857 0.00 0.00 0.00 3.36
204 205 3.797039 TCGGTCAAGCAATATGAAGGAG 58.203 45.455 0.00 0.00 0.00 3.69
205 206 2.289002 CGGTCAAGCAATATGAAGGAGC 59.711 50.000 0.00 0.00 0.00 4.70
206 207 3.549794 GGTCAAGCAATATGAAGGAGCT 58.450 45.455 0.00 0.00 37.08 4.09
207 208 4.708177 GGTCAAGCAATATGAAGGAGCTA 58.292 43.478 0.00 0.00 34.66 3.32
208 209 5.312079 GGTCAAGCAATATGAAGGAGCTAT 58.688 41.667 0.00 0.00 34.66 2.97
209 210 5.767168 GGTCAAGCAATATGAAGGAGCTATT 59.233 40.000 0.00 0.00 34.66 1.73
210 211 6.264067 GGTCAAGCAATATGAAGGAGCTATTT 59.736 38.462 0.00 0.00 34.66 1.40
251 252 4.926140 GCTTTAGCAAATCTGGCCTATT 57.074 40.909 3.32 0.49 41.59 1.73
252 253 4.614946 GCTTTAGCAAATCTGGCCTATTG 58.385 43.478 3.32 5.17 41.59 1.90
253 254 4.500375 GCTTTAGCAAATCTGGCCTATTGG 60.500 45.833 3.32 2.68 41.59 3.16
256 257 1.411501 GCAAATCTGGCCTATTGGGGA 60.412 52.381 3.32 0.00 35.12 4.81
259 260 3.319031 AATCTGGCCTATTGGGGAAAG 57.681 47.619 3.32 0.00 35.12 2.62
262 263 0.553862 TGGCCTATTGGGGAAAGGGA 60.554 55.000 3.32 0.00 35.12 4.20
268 269 3.136626 CCTATTGGGGAAAGGGAGTACTG 59.863 52.174 0.00 0.00 0.00 2.74
281 282 3.319689 GGGAGTACTGGAGATGCTCTTAC 59.680 52.174 0.00 0.00 0.00 2.34
290 291 4.530553 TGGAGATGCTCTTACACAAACCTA 59.469 41.667 0.00 0.00 0.00 3.08
297 298 3.244582 TCTTACACAAACCTAGCCAGGA 58.755 45.455 4.75 0.00 45.91 3.86
298 299 3.844211 TCTTACACAAACCTAGCCAGGAT 59.156 43.478 4.75 0.00 45.91 3.24
303 304 0.107654 AAACCTAGCCAGGATCGTGC 60.108 55.000 4.75 5.90 45.91 5.34
327 328 2.438254 GACCGGCATGTGCATGGA 60.438 61.111 18.56 0.00 44.36 3.41
332 333 1.405797 CCGGCATGTGCATGGAATTTT 60.406 47.619 13.28 0.00 44.36 1.82
335 336 1.399089 GCATGTGCATGGAATTTTGGC 59.601 47.619 13.28 0.00 41.59 4.52
338 339 0.740516 GTGCATGGAATTTTGGCCCG 60.741 55.000 0.00 0.00 0.00 6.13
373 374 3.889196 TGGCACGTGATTAAAAGTGTC 57.111 42.857 22.23 0.00 39.41 3.67
374 375 2.222213 TGGCACGTGATTAAAAGTGTCG 59.778 45.455 22.23 0.00 41.59 4.35
376 377 2.222445 GCACGTGATTAAAAGTGTCGGT 59.778 45.455 22.23 0.00 36.99 4.69
379 380 3.061322 CGTGATTAAAAGTGTCGGTCCA 58.939 45.455 0.00 0.00 0.00 4.02
386 387 2.432628 GTGTCGGTCCAGCCTTCG 60.433 66.667 0.00 0.00 34.25 3.79
390 391 3.382832 CGGTCCAGCCTTCGACCT 61.383 66.667 6.25 0.00 45.41 3.85
391 392 2.266055 GGTCCAGCCTTCGACCTG 59.734 66.667 1.20 0.00 44.40 4.00
394 395 4.020617 CCAGCCTTCGACCTGCCA 62.021 66.667 0.00 0.00 0.00 4.92
395 396 2.270205 CAGCCTTCGACCTGCCAT 59.730 61.111 0.00 0.00 0.00 4.40
398 399 2.989639 CCTTCGACCTGCCATGGA 59.010 61.111 18.40 0.00 0.00 3.41
415 416 2.706890 TGGAACAAGGCCGATCTAAAC 58.293 47.619 0.00 0.00 31.92 2.01
429 430 1.903860 TCTAAACGCCAGGCCTTAAGA 59.096 47.619 0.00 1.27 0.00 2.10
430 431 2.007608 CTAAACGCCAGGCCTTAAGAC 58.992 52.381 0.00 0.00 0.00 3.01
431 432 0.109723 AAACGCCAGGCCTTAAGACA 59.890 50.000 0.00 0.00 0.00 3.41
432 433 0.109723 AACGCCAGGCCTTAAGACAA 59.890 50.000 0.00 0.00 0.00 3.18
433 434 0.605589 ACGCCAGGCCTTAAGACAAC 60.606 55.000 0.00 0.00 0.00 3.32
442 454 5.480422 CAGGCCTTAAGACAACCCTTTTATT 59.520 40.000 0.00 0.00 0.00 1.40
450 462 2.370519 ACAACCCTTTTATTTGTGGGCC 59.629 45.455 0.00 0.00 43.25 5.80
451 463 1.262417 ACCCTTTTATTTGTGGGCCG 58.738 50.000 0.00 0.00 43.25 6.13
457 469 0.323816 TTATTTGTGGGCCGGCATGA 60.324 50.000 30.85 8.16 0.00 3.07
493 506 0.179119 CCCGTCCGGCTTGTAACTAG 60.179 60.000 0.00 0.00 0.00 2.57
505 518 9.106070 CCGGCTTGTAACTAGTTATTTTTCTAT 57.894 33.333 18.03 0.00 0.00 1.98
601 614 9.352191 TCTTCTGTAGTTTTTACTACTGTCTCT 57.648 33.333 14.46 0.00 42.16 3.10
658 671 9.628983 CTTAAGTAAAACGTAGTGAAGTTTGAC 57.371 33.333 0.00 1.42 45.00 3.18
900 920 9.476202 ACATAAACCTGAAAAGCTAAAAATGAC 57.524 29.630 0.00 0.00 0.00 3.06
903 923 6.385649 ACCTGAAAAGCTAAAAATGACGAA 57.614 33.333 0.00 0.00 0.00 3.85
907 927 3.850122 AAGCTAAAAATGACGAAGGCC 57.150 42.857 0.00 0.00 0.00 5.19
909 929 3.356290 AGCTAAAAATGACGAAGGCCAT 58.644 40.909 5.01 0.00 0.00 4.40
911 931 4.220602 AGCTAAAAATGACGAAGGCCATTT 59.779 37.500 5.01 0.00 43.04 2.32
935 955 4.886247 TTTTTGAGTAACACAACGAGGG 57.114 40.909 0.00 0.00 0.00 4.30
936 956 1.873698 TTGAGTAACACAACGAGGGC 58.126 50.000 0.00 0.00 0.00 5.19
937 957 0.034337 TGAGTAACACAACGAGGGCC 59.966 55.000 0.00 0.00 0.00 5.80
938 958 0.034337 GAGTAACACAACGAGGGCCA 59.966 55.000 6.18 0.00 0.00 5.36
939 959 0.034896 AGTAACACAACGAGGGCCAG 59.965 55.000 6.18 0.96 0.00 4.85
940 960 1.302192 TAACACAACGAGGGCCAGC 60.302 57.895 6.18 0.00 0.00 4.85
977 997 1.021968 CCGGGCTTTATAACTGGTGC 58.978 55.000 0.00 0.00 0.00 5.01
981 1001 1.379527 GCTTTATAACTGGTGCGCCT 58.620 50.000 18.96 0.00 35.27 5.52
1029 4461 1.303091 GCCGCACGACCCTTTTACAT 61.303 55.000 0.00 0.00 0.00 2.29
1031 4463 1.434555 CGCACGACCCTTTTACATGA 58.565 50.000 0.00 0.00 0.00 3.07
1043 4475 1.375853 TTACATGAGCCGTGCCATGC 61.376 55.000 18.11 0.59 39.22 4.06
1059 4491 0.324645 ATGCCAGGCCCTTTTACAGG 60.325 55.000 9.64 0.00 43.49 4.00
1092 4524 1.202722 CGTGACCCTTTTACACCACCT 60.203 52.381 0.00 0.00 0.00 4.00
1174 4615 1.075698 TCCGCCCACAATCCCTAAAAA 59.924 47.619 0.00 0.00 0.00 1.94
1175 4616 1.476488 CCGCCCACAATCCCTAAAAAG 59.524 52.381 0.00 0.00 0.00 2.27
1684 5128 2.362120 GAAGGTCGAGGTCGGGGA 60.362 66.667 0.00 0.00 40.29 4.81
1758 5205 2.281345 GCGCATGGAGGAGGATGG 60.281 66.667 0.30 0.00 0.00 3.51
1762 5209 0.108207 GCATGGAGGAGGATGGTGAG 59.892 60.000 0.00 0.00 0.00 3.51
1763 5210 0.763652 CATGGAGGAGGATGGTGAGG 59.236 60.000 0.00 0.00 0.00 3.86
1764 5211 0.644380 ATGGAGGAGGATGGTGAGGA 59.356 55.000 0.00 0.00 0.00 3.71
1786 5233 2.123640 GAGACGGGGGAGGAGGAG 60.124 72.222 0.00 0.00 0.00 3.69
1957 5413 1.010797 CATCGCCTTGCCGATTTCG 60.011 57.895 0.00 0.00 44.85 3.46
2012 5468 1.489881 GCAAGGCACAACAAAAGGCG 61.490 55.000 0.00 0.00 0.00 5.52
2085 5541 2.202676 GAGCGGGCAGAAGAGACG 60.203 66.667 0.00 0.00 0.00 4.18
2165 5621 1.520342 CTAGAGCGGAACAGCCAGC 60.520 63.158 0.00 0.00 38.01 4.85
2168 5624 4.749310 AGCGGAACAGCCAGCTCG 62.749 66.667 0.00 0.00 40.76 5.03
2372 5829 9.256228 GTACAGATTGGTATAGGAGGATGATTA 57.744 37.037 0.00 0.00 0.00 1.75
2427 5884 3.435327 TGATGAACTTGTTCCGGAATTCG 59.565 43.478 22.04 13.49 38.88 3.34
2553 6012 5.423015 AGATCTTGATTGTGTATTGCGTCT 58.577 37.500 0.00 0.00 0.00 4.18
2590 6056 9.109393 TGGAAATATGTATCTTTTGCTGAGTAC 57.891 33.333 0.00 0.00 0.00 2.73
2631 6175 0.034574 TTGCCCTGTCACAAGTGTGT 60.035 50.000 11.06 0.00 45.76 3.72
2666 6321 5.760484 ACCCAAAATGTTTCCTATGCAAT 57.240 34.783 0.00 0.00 0.00 3.56
2792 6455 9.832445 CTCCAAAGTAAATTAATGCTAGAGGTA 57.168 33.333 0.00 0.00 0.00 3.08
2803 6466 4.277515 TGCTAGAGGTATGATGGAATGC 57.722 45.455 0.00 0.00 0.00 3.56
2878 6544 2.009774 GGACATGGTGGAATGAACTCG 58.990 52.381 0.00 0.00 0.00 4.18
2895 6561 3.931578 ACTCGACAAAATCCAGAGAAGG 58.068 45.455 0.00 0.00 33.53 3.46
2898 6564 2.027192 CGACAAAATCCAGAGAAGGGGA 60.027 50.000 0.00 0.00 37.64 4.81
2902 6568 4.588951 ACAAAATCCAGAGAAGGGGAAAAC 59.411 41.667 0.00 0.00 36.62 2.43
2910 6578 3.641436 AGAGAAGGGGAAAACGCAAAAAT 59.359 39.130 0.00 0.00 33.80 1.82
2925 6593 4.853743 CGCAAAAATTTCTGGAGAAGTAGC 59.146 41.667 0.00 0.00 35.21 3.58
2934 6602 1.476891 TGGAGAAGTAGCGTGGATGAC 59.523 52.381 0.00 0.00 0.00 3.06
2997 6665 2.949106 CTGCGGGTGAAGCACTTG 59.051 61.111 0.00 0.00 40.01 3.16
3071 6740 2.026262 GGAGTTGAAGCAGGGTATGGAA 60.026 50.000 0.00 0.00 0.00 3.53
3077 6746 0.835941 AGCAGGGTATGGAAGCTGAG 59.164 55.000 0.00 0.00 33.67 3.35
3094 6763 0.028374 GAGAGCTCTAGTTCGTCGCC 59.972 60.000 18.25 0.00 0.00 5.54
3095 6764 1.064458 GAGCTCTAGTTCGTCGCCC 59.936 63.158 6.43 0.00 0.00 6.13
3096 6765 2.104530 GCTCTAGTTCGTCGCCCC 59.895 66.667 0.00 0.00 0.00 5.80
3097 6766 2.416432 GCTCTAGTTCGTCGCCCCT 61.416 63.158 0.00 0.00 0.00 4.79
3098 6767 1.433879 CTCTAGTTCGTCGCCCCTG 59.566 63.158 0.00 0.00 0.00 4.45
3099 6768 1.303888 TCTAGTTCGTCGCCCCTGT 60.304 57.895 0.00 0.00 0.00 4.00
3100 6769 1.153823 CTAGTTCGTCGCCCCTGTG 60.154 63.158 0.00 0.00 0.00 3.66
3101 6770 1.874345 CTAGTTCGTCGCCCCTGTGT 61.874 60.000 0.00 0.00 0.00 3.72
3102 6771 2.149803 TAGTTCGTCGCCCCTGTGTG 62.150 60.000 0.00 0.00 0.00 3.82
3103 6772 4.980805 TTCGTCGCCCCTGTGTGC 62.981 66.667 0.00 0.00 0.00 4.57
3116 6785 3.300009 CCTGTGTGCGATTTTTCAAGAC 58.700 45.455 0.00 0.00 0.00 3.01
3123 6792 3.226347 GCGATTTTTCAAGACGTGAAGG 58.774 45.455 0.00 0.00 46.85 3.46
3133 6802 2.143925 AGACGTGAAGGCTTTTGCTAC 58.856 47.619 0.00 0.00 46.54 3.58
3140 6809 4.022849 GTGAAGGCTTTTGCTACACTTCAT 60.023 41.667 0.00 0.00 44.98 2.57
3153 6822 7.939782 TGCTACACTTCATTTTCTGAATTTCA 58.060 30.769 0.00 0.00 42.87 2.69
3168 6837 7.417612 TCTGAATTTCAAAAGTCTTGTACTGC 58.582 34.615 0.01 0.00 38.88 4.40
3169 6838 6.503524 TGAATTTCAAAAGTCTTGTACTGCC 58.496 36.000 0.00 0.00 38.88 4.85
3231 6928 2.696707 CAGCAATGGTTTCCATATGCCT 59.303 45.455 20.64 12.25 44.40 4.75
3243 6940 2.550855 CCATATGCCTGATGTAACGGCT 60.551 50.000 0.00 0.00 44.09 5.52
3270 6967 6.883756 TGTGCCTGATGTAATGTCTTTATTGA 59.116 34.615 0.00 0.00 0.00 2.57
3298 6995 8.517062 AGCAATTTAGCTCTTTGATGTAATCT 57.483 30.769 0.00 0.00 42.41 2.40
3306 7003 8.674263 AGCTCTTTGATGTAATCTCTTATTGG 57.326 34.615 0.00 0.00 45.81 3.16
3311 7008 8.668510 TTTGATGTAATCTCTTATTGGAGAGC 57.331 34.615 0.00 0.00 45.81 4.09
3312 7009 7.365497 TGATGTAATCTCTTATTGGAGAGCA 57.635 36.000 0.00 0.00 45.81 4.26
3315 7012 9.282569 GATGTAATCTCTTATTGGAGAGCAATT 57.717 33.333 0.00 0.00 44.24 2.32
3319 7016 7.742556 ATCTCTTATTGGAGAGCAATTTAGC 57.257 36.000 0.00 0.00 44.24 3.09
3400 7151 1.474077 CATTTGGAGCTACAAGGCCAC 59.526 52.381 12.08 0.00 0.00 5.01
3413 7164 3.573967 ACAAGGCCACAGAAATTACTTGG 59.426 43.478 5.01 0.00 38.43 3.61
3455 7206 7.445121 TCCATCAATCAATATCAGTACTCCAC 58.555 38.462 0.00 0.00 0.00 4.02
3475 7226 6.008331 TCCACACGCTACTCCATATATAACT 58.992 40.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.826710 GTTATCATCGAACATAATGTCCTTTGA 58.173 33.333 0.00 0.00 0.00 2.69
2 3 8.611757 TGTTATCATCGAACATAATGTCCTTTG 58.388 33.333 0.00 0.00 31.92 2.77
4 5 7.768582 TGTGTTATCATCGAACATAATGTCCTT 59.231 33.333 0.00 0.00 38.94 3.36
5 6 7.272244 TGTGTTATCATCGAACATAATGTCCT 58.728 34.615 0.00 0.00 38.94 3.85
6 7 7.477144 TGTGTTATCATCGAACATAATGTCC 57.523 36.000 0.00 0.00 38.94 4.02
7 8 7.531871 GCATGTGTTATCATCGAACATAATGTC 59.468 37.037 0.00 0.00 38.94 3.06
9 10 7.354257 TGCATGTGTTATCATCGAACATAATG 58.646 34.615 0.00 0.00 38.94 1.90
10 11 7.495135 TGCATGTGTTATCATCGAACATAAT 57.505 32.000 0.00 0.00 38.94 1.28
11 12 6.917217 TGCATGTGTTATCATCGAACATAA 57.083 33.333 0.00 0.00 38.94 1.90
12 13 6.538381 AGTTGCATGTGTTATCATCGAACATA 59.462 34.615 0.00 0.00 38.94 2.29
13 14 5.355071 AGTTGCATGTGTTATCATCGAACAT 59.645 36.000 0.00 0.00 38.94 2.71
15 16 5.221891 AGTTGCATGTGTTATCATCGAAC 57.778 39.130 0.00 0.00 0.00 3.95
18 19 6.529463 TGATAGTTGCATGTGTTATCATCG 57.471 37.500 0.00 0.00 0.00 3.84
26 27 9.926158 TGATTTTTAATTGATAGTTGCATGTGT 57.074 25.926 0.00 0.00 0.00 3.72
86 87 8.989980 TGGTTTTATGTTCGTTCTTTTGTTTTT 58.010 25.926 0.00 0.00 0.00 1.94
87 88 8.535690 TGGTTTTATGTTCGTTCTTTTGTTTT 57.464 26.923 0.00 0.00 0.00 2.43
88 89 8.535690 TTGGTTTTATGTTCGTTCTTTTGTTT 57.464 26.923 0.00 0.00 0.00 2.83
89 90 8.535690 TTTGGTTTTATGTTCGTTCTTTTGTT 57.464 26.923 0.00 0.00 0.00 2.83
90 91 8.535690 TTTTGGTTTTATGTTCGTTCTTTTGT 57.464 26.923 0.00 0.00 0.00 2.83
120 121 9.898152 TGTTTTTCCCTTTCTTGAATTTGTTAT 57.102 25.926 0.00 0.00 0.00 1.89
121 122 9.726438 TTGTTTTTCCCTTTCTTGAATTTGTTA 57.274 25.926 0.00 0.00 0.00 2.41
122 123 8.628630 TTGTTTTTCCCTTTCTTGAATTTGTT 57.371 26.923 0.00 0.00 0.00 2.83
123 124 8.628630 TTTGTTTTTCCCTTTCTTGAATTTGT 57.371 26.923 0.00 0.00 0.00 2.83
124 125 9.905171 TTTTTGTTTTTCCCTTTCTTGAATTTG 57.095 25.926 0.00 0.00 0.00 2.32
128 129 9.905171 CAAATTTTTGTTTTTCCCTTTCTTGAA 57.095 25.926 0.00 0.00 33.59 2.69
129 130 8.518702 CCAAATTTTTGTTTTTCCCTTTCTTGA 58.481 29.630 2.63 0.00 36.45 3.02
130 131 8.303156 ACCAAATTTTTGTTTTTCCCTTTCTTG 58.697 29.630 2.63 0.00 36.45 3.02
131 132 8.415950 ACCAAATTTTTGTTTTTCCCTTTCTT 57.584 26.923 2.63 0.00 36.45 2.52
132 133 7.667635 TGACCAAATTTTTGTTTTTCCCTTTCT 59.332 29.630 2.63 0.00 36.45 2.52
133 134 7.821652 TGACCAAATTTTTGTTTTTCCCTTTC 58.178 30.769 2.63 0.00 36.45 2.62
134 135 7.667635 TCTGACCAAATTTTTGTTTTTCCCTTT 59.332 29.630 2.63 0.00 36.45 3.11
135 136 7.171653 TCTGACCAAATTTTTGTTTTTCCCTT 58.828 30.769 2.63 0.00 36.45 3.95
136 137 6.716284 TCTGACCAAATTTTTGTTTTTCCCT 58.284 32.000 2.63 0.00 36.45 4.20
137 138 6.993786 TCTGACCAAATTTTTGTTTTTCCC 57.006 33.333 2.63 0.00 36.45 3.97
138 139 6.966632 GCTTCTGACCAAATTTTTGTTTTTCC 59.033 34.615 2.63 0.00 36.45 3.13
139 140 7.751732 AGCTTCTGACCAAATTTTTGTTTTTC 58.248 30.769 2.63 0.00 36.45 2.29
140 141 7.686438 AGCTTCTGACCAAATTTTTGTTTTT 57.314 28.000 2.63 0.00 36.45 1.94
141 142 7.607607 AGAAGCTTCTGACCAAATTTTTGTTTT 59.392 29.630 27.96 0.00 35.89 2.43
142 143 7.105588 AGAAGCTTCTGACCAAATTTTTGTTT 58.894 30.769 27.96 0.00 35.89 2.83
143 144 6.643388 AGAAGCTTCTGACCAAATTTTTGTT 58.357 32.000 27.96 0.00 35.89 2.83
144 145 6.225981 AGAAGCTTCTGACCAAATTTTTGT 57.774 33.333 27.96 0.00 35.89 2.83
145 146 7.202526 TGTAGAAGCTTCTGACCAAATTTTTG 58.797 34.615 34.26 0.00 38.19 2.44
146 147 7.346751 TGTAGAAGCTTCTGACCAAATTTTT 57.653 32.000 34.26 9.88 38.19 1.94
147 148 6.959639 TGTAGAAGCTTCTGACCAAATTTT 57.040 33.333 34.26 10.08 38.19 1.82
148 149 6.959639 TTGTAGAAGCTTCTGACCAAATTT 57.040 33.333 34.26 10.58 38.19 1.82
149 150 6.566197 CTTGTAGAAGCTTCTGACCAAATT 57.434 37.500 34.26 11.29 38.19 1.82
163 164 6.842163 ACCGATTTTGTATTGCTTGTAGAAG 58.158 36.000 0.00 0.00 0.00 2.85
164 165 6.428465 TGACCGATTTTGTATTGCTTGTAGAA 59.572 34.615 0.00 0.00 0.00 2.10
165 166 5.935206 TGACCGATTTTGTATTGCTTGTAGA 59.065 36.000 0.00 0.00 0.00 2.59
166 167 6.176975 TGACCGATTTTGTATTGCTTGTAG 57.823 37.500 0.00 0.00 0.00 2.74
167 168 6.561737 TTGACCGATTTTGTATTGCTTGTA 57.438 33.333 0.00 0.00 0.00 2.41
168 169 5.446143 TTGACCGATTTTGTATTGCTTGT 57.554 34.783 0.00 0.00 0.00 3.16
169 170 4.324402 GCTTGACCGATTTTGTATTGCTTG 59.676 41.667 0.00 0.00 0.00 4.01
170 171 4.022416 TGCTTGACCGATTTTGTATTGCTT 60.022 37.500 0.00 0.00 0.00 3.91
171 172 3.505680 TGCTTGACCGATTTTGTATTGCT 59.494 39.130 0.00 0.00 0.00 3.91
172 173 3.832276 TGCTTGACCGATTTTGTATTGC 58.168 40.909 0.00 0.00 0.00 3.56
173 174 7.914871 TCATATTGCTTGACCGATTTTGTATTG 59.085 33.333 0.00 0.00 0.00 1.90
174 175 7.995289 TCATATTGCTTGACCGATTTTGTATT 58.005 30.769 0.00 0.00 0.00 1.89
175 176 7.566760 TCATATTGCTTGACCGATTTTGTAT 57.433 32.000 0.00 0.00 0.00 2.29
176 177 6.993786 TCATATTGCTTGACCGATTTTGTA 57.006 33.333 0.00 0.00 0.00 2.41
177 178 5.895636 TCATATTGCTTGACCGATTTTGT 57.104 34.783 0.00 0.00 0.00 2.83
178 179 5.745294 CCTTCATATTGCTTGACCGATTTTG 59.255 40.000 0.00 0.00 0.00 2.44
179 180 5.652014 TCCTTCATATTGCTTGACCGATTTT 59.348 36.000 0.00 0.00 0.00 1.82
180 181 5.192927 TCCTTCATATTGCTTGACCGATTT 58.807 37.500 0.00 0.00 0.00 2.17
181 182 4.780815 TCCTTCATATTGCTTGACCGATT 58.219 39.130 0.00 0.00 0.00 3.34
182 183 4.384056 CTCCTTCATATTGCTTGACCGAT 58.616 43.478 0.00 0.00 0.00 4.18
183 184 3.797039 CTCCTTCATATTGCTTGACCGA 58.203 45.455 0.00 0.00 0.00 4.69
184 185 2.289002 GCTCCTTCATATTGCTTGACCG 59.711 50.000 0.00 0.00 0.00 4.79
185 186 3.549794 AGCTCCTTCATATTGCTTGACC 58.450 45.455 0.00 0.00 0.00 4.02
186 187 6.874288 AATAGCTCCTTCATATTGCTTGAC 57.126 37.500 0.00 0.00 35.47 3.18
187 188 7.886629 AAAATAGCTCCTTCATATTGCTTGA 57.113 32.000 0.00 0.00 35.47 3.02
188 189 8.411683 AGAAAAATAGCTCCTTCATATTGCTTG 58.588 33.333 0.00 0.00 35.47 4.01
189 190 8.530804 AGAAAAATAGCTCCTTCATATTGCTT 57.469 30.769 0.00 0.00 35.47 3.91
190 191 8.530804 AAGAAAAATAGCTCCTTCATATTGCT 57.469 30.769 0.00 0.00 37.72 3.91
191 192 8.628280 AGAAGAAAAATAGCTCCTTCATATTGC 58.372 33.333 0.00 0.00 36.59 3.56
194 195 9.911788 TCAAGAAGAAAAATAGCTCCTTCATAT 57.088 29.630 0.00 0.00 36.59 1.78
195 196 9.911788 ATCAAGAAGAAAAATAGCTCCTTCATA 57.088 29.630 0.00 0.00 36.59 2.15
196 197 8.820153 ATCAAGAAGAAAAATAGCTCCTTCAT 57.180 30.769 0.00 0.00 36.59 2.57
197 198 8.105829 AGATCAAGAAGAAAAATAGCTCCTTCA 58.894 33.333 0.00 0.00 36.59 3.02
198 199 8.504812 AGATCAAGAAGAAAAATAGCTCCTTC 57.495 34.615 0.00 0.00 34.92 3.46
199 200 9.612066 CTAGATCAAGAAGAAAAATAGCTCCTT 57.388 33.333 0.00 0.00 0.00 3.36
200 201 8.767436 ACTAGATCAAGAAGAAAAATAGCTCCT 58.233 33.333 0.00 0.00 0.00 3.69
201 202 8.956533 ACTAGATCAAGAAGAAAAATAGCTCC 57.043 34.615 0.00 0.00 0.00 4.70
203 204 9.732130 ACAACTAGATCAAGAAGAAAAATAGCT 57.268 29.630 0.00 0.00 0.00 3.32
204 205 9.766277 CACAACTAGATCAAGAAGAAAAATAGC 57.234 33.333 0.00 0.00 0.00 2.97
205 206 9.766277 GCACAACTAGATCAAGAAGAAAAATAG 57.234 33.333 0.00 0.00 0.00 1.73
206 207 9.507329 AGCACAACTAGATCAAGAAGAAAAATA 57.493 29.630 0.00 0.00 0.00 1.40
207 208 8.401490 AGCACAACTAGATCAAGAAGAAAAAT 57.599 30.769 0.00 0.00 0.00 1.82
208 209 7.807977 AGCACAACTAGATCAAGAAGAAAAA 57.192 32.000 0.00 0.00 0.00 1.94
209 210 7.807977 AAGCACAACTAGATCAAGAAGAAAA 57.192 32.000 0.00 0.00 0.00 2.29
210 211 7.807977 AAAGCACAACTAGATCAAGAAGAAA 57.192 32.000 0.00 0.00 0.00 2.52
243 244 0.553862 TCCCTTTCCCCAATAGGCCA 60.554 55.000 5.01 0.00 0.00 5.36
245 246 0.927029 ACTCCCTTTCCCCAATAGGC 59.073 55.000 0.00 0.00 0.00 3.93
251 252 0.494551 TCCAGTACTCCCTTTCCCCA 59.505 55.000 0.00 0.00 0.00 4.96
252 253 1.205055 CTCCAGTACTCCCTTTCCCC 58.795 60.000 0.00 0.00 0.00 4.81
253 254 2.249309 TCTCCAGTACTCCCTTTCCC 57.751 55.000 0.00 0.00 0.00 3.97
256 257 2.769095 GAGCATCTCCAGTACTCCCTTT 59.231 50.000 0.00 0.00 0.00 3.11
281 282 1.066143 ACGATCCTGGCTAGGTTTGTG 60.066 52.381 16.69 5.63 44.88 3.33
318 319 0.324285 GGGCCAAAATTCCATGCACA 59.676 50.000 4.39 0.00 0.00 4.57
319 320 0.740516 CGGGCCAAAATTCCATGCAC 60.741 55.000 4.39 0.00 0.00 4.57
327 328 1.296068 CATGTGCCGGGCCAAAATT 59.704 52.632 17.97 0.00 0.00 1.82
349 350 4.083324 ACACTTTTAATCACGTGCCATGAG 60.083 41.667 11.67 6.87 0.00 2.90
355 356 2.222445 ACCGACACTTTTAATCACGTGC 59.778 45.455 11.67 0.00 0.00 5.34
360 361 3.071479 GCTGGACCGACACTTTTAATCA 58.929 45.455 0.00 0.00 0.00 2.57
376 377 3.706373 GGCAGGTCGAAGGCTGGA 61.706 66.667 0.00 0.00 0.00 3.86
379 380 2.270205 CATGGCAGGTCGAAGGCT 59.730 61.111 8.43 0.00 0.00 4.58
386 387 2.571548 CCTTGTTCCATGGCAGGTC 58.428 57.895 6.96 0.00 0.00 3.85
394 395 3.279434 GTTTAGATCGGCCTTGTTCCAT 58.721 45.455 0.00 0.00 0.00 3.41
395 396 2.706890 GTTTAGATCGGCCTTGTTCCA 58.293 47.619 0.00 0.00 0.00 3.53
398 399 1.084289 GCGTTTAGATCGGCCTTGTT 58.916 50.000 0.00 0.00 0.00 2.83
412 413 0.109723 TGTCTTAAGGCCTGGCGTTT 59.890 50.000 28.96 19.56 37.76 3.60
415 416 1.305930 GGTTGTCTTAAGGCCTGGCG 61.306 60.000 5.69 0.00 0.00 5.69
429 430 2.370519 GGCCCACAAATAAAAGGGTTGT 59.629 45.455 0.00 0.00 43.42 3.32
430 431 2.611722 CGGCCCACAAATAAAAGGGTTG 60.612 50.000 0.00 0.00 43.42 3.77
431 432 1.621317 CGGCCCACAAATAAAAGGGTT 59.379 47.619 0.00 0.00 43.42 4.11
432 433 1.262417 CGGCCCACAAATAAAAGGGT 58.738 50.000 0.00 0.00 43.42 4.34
433 434 0.534873 CCGGCCCACAAATAAAAGGG 59.465 55.000 0.00 0.00 44.37 3.95
450 462 2.896854 CCATGTCGGGTCATGCCG 60.897 66.667 5.49 5.49 42.44 5.69
451 463 3.211963 GCCATGTCGGGTCATGCC 61.212 66.667 9.46 0.00 42.44 4.40
477 490 6.732531 AAAATAACTAGTTACAAGCCGGAC 57.267 37.500 17.45 0.00 0.00 4.79
479 492 7.373778 AGAAAAATAACTAGTTACAAGCCGG 57.626 36.000 17.45 0.00 0.00 6.13
517 530 9.612066 AATCTCCAAAAGTTAAGAAATGCAAAA 57.388 25.926 0.00 0.00 0.00 2.44
576 589 9.400638 CAGAGACAGTAGTAAAAACTACAGAAG 57.599 37.037 15.84 7.02 43.62 2.85
637 650 9.023967 TCTTAGTCAAACTTCACTACGTTTTAC 57.976 33.333 0.00 0.00 31.46 2.01
639 652 8.658499 ATCTTAGTCAAACTTCACTACGTTTT 57.342 30.769 0.00 0.00 31.46 2.43
865 885 7.821846 AGCTTTTCAGGTTTATGTTTGAACAAA 59.178 29.630 0.10 0.00 43.03 2.83
869 889 9.877178 TTTTAGCTTTTCAGGTTTATGTTTGAA 57.123 25.926 0.00 0.00 31.45 2.69
870 890 9.877178 TTTTTAGCTTTTCAGGTTTATGTTTGA 57.123 25.926 0.00 0.00 31.45 2.69
875 895 8.638565 CGTCATTTTTAGCTTTTCAGGTTTATG 58.361 33.333 0.00 0.00 31.45 1.90
877 897 7.932335 TCGTCATTTTTAGCTTTTCAGGTTTA 58.068 30.769 0.00 0.00 31.45 2.01
883 903 5.219633 GCCTTCGTCATTTTTAGCTTTTCA 58.780 37.500 0.00 0.00 0.00 2.69
885 905 4.038642 TGGCCTTCGTCATTTTTAGCTTTT 59.961 37.500 3.32 0.00 0.00 2.27
888 908 2.790433 TGGCCTTCGTCATTTTTAGCT 58.210 42.857 3.32 0.00 0.00 3.32
914 934 3.065648 GCCCTCGTTGTGTTACTCAAAAA 59.934 43.478 1.26 0.00 0.00 1.94
915 935 2.614983 GCCCTCGTTGTGTTACTCAAAA 59.385 45.455 1.26 0.00 0.00 2.44
916 936 2.215196 GCCCTCGTTGTGTTACTCAAA 58.785 47.619 1.26 0.00 0.00 2.69
917 937 1.541670 GGCCCTCGTTGTGTTACTCAA 60.542 52.381 0.00 0.00 0.00 3.02
918 938 0.034337 GGCCCTCGTTGTGTTACTCA 59.966 55.000 0.00 0.00 0.00 3.41
919 939 0.034337 TGGCCCTCGTTGTGTTACTC 59.966 55.000 0.00 0.00 0.00 2.59
920 940 0.034896 CTGGCCCTCGTTGTGTTACT 59.965 55.000 0.00 0.00 0.00 2.24
921 941 1.574702 GCTGGCCCTCGTTGTGTTAC 61.575 60.000 0.00 0.00 0.00 2.50
922 942 1.302192 GCTGGCCCTCGTTGTGTTA 60.302 57.895 0.00 0.00 0.00 2.41
923 943 2.594592 GCTGGCCCTCGTTGTGTT 60.595 61.111 0.00 0.00 0.00 3.32
924 944 3.560251 AGCTGGCCCTCGTTGTGT 61.560 61.111 0.00 0.00 0.00 3.72
925 945 3.052082 CAGCTGGCCCTCGTTGTG 61.052 66.667 5.57 0.00 0.00 3.33
926 946 3.560251 ACAGCTGGCCCTCGTTGT 61.560 61.111 19.93 0.00 0.00 3.32
927 947 3.052082 CACAGCTGGCCCTCGTTG 61.052 66.667 19.93 0.00 0.00 4.10
1017 1039 1.737793 CACGGCTCATGTAAAAGGGTC 59.262 52.381 0.00 0.00 0.00 4.46
1092 4524 4.566545 TTCTTTTTGAGCGAATGAAGCA 57.433 36.364 0.00 0.00 37.01 3.91
1174 4615 0.827507 ATTTGGTGGGCGCAAGTTCT 60.828 50.000 10.83 0.00 41.68 3.01
1175 4616 0.388520 GATTTGGTGGGCGCAAGTTC 60.389 55.000 10.83 0.00 41.68 3.01
1713 5157 1.344953 TACTTCCTCCATGGCGGCAT 61.345 55.000 20.18 20.18 35.26 4.40
1721 5165 0.421904 ACCACCCCTACTTCCTCCAT 59.578 55.000 0.00 0.00 0.00 3.41
1758 5205 1.755008 CCCGTCTCCTCCTCCTCAC 60.755 68.421 0.00 0.00 0.00 3.51
1762 5209 3.742248 CTCCCCCGTCTCCTCCTCC 62.742 73.684 0.00 0.00 0.00 4.30
1763 5210 2.123640 CTCCCCCGTCTCCTCCTC 60.124 72.222 0.00 0.00 0.00 3.71
1764 5211 3.756783 CCTCCCCCGTCTCCTCCT 61.757 72.222 0.00 0.00 0.00 3.69
1786 5233 1.074850 CCCCTTCCCTCTCTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
1957 5413 2.216898 CTTGATGCCTCCGAATTCTCC 58.783 52.381 3.52 0.00 0.00 3.71
2012 5468 1.755783 CTTGATGCCCTCCTTGCCC 60.756 63.158 0.00 0.00 0.00 5.36
2372 5829 2.579860 AGGAATCAAATGCCAGGAGAGT 59.420 45.455 0.00 0.00 0.00 3.24
2547 6006 0.592637 CCATTTCAGCACAAGACGCA 59.407 50.000 0.00 0.00 0.00 5.24
2553 6012 8.523915 AGATACATATTTCCATTTCAGCACAA 57.476 30.769 0.00 0.00 0.00 3.33
2590 6056 9.597999 GGCAAATAAGCTTAGAAACAATTTTTG 57.402 29.630 12.54 13.82 34.17 2.44
2596 6062 5.538433 ACAGGGCAAATAAGCTTAGAAACAA 59.462 36.000 12.54 0.00 34.17 2.83
2631 6175 5.527385 ACATTTTGGGTTGATGATATCCCA 58.473 37.500 0.00 0.00 46.77 4.37
2632 6176 6.484364 AACATTTTGGGTTGATGATATCCC 57.516 37.500 0.00 0.00 40.26 3.85
2634 6178 7.785033 AGGAAACATTTTGGGTTGATGATATC 58.215 34.615 0.00 0.00 0.00 1.63
2638 6182 6.574073 GCATAGGAAACATTTTGGGTTGATGA 60.574 38.462 0.00 0.00 0.00 2.92
2639 6183 5.581874 GCATAGGAAACATTTTGGGTTGATG 59.418 40.000 0.00 0.00 0.00 3.07
2702 6357 4.339247 ACACTTGCTTCACTAATTTGCACT 59.661 37.500 0.00 0.00 33.13 4.40
2762 6417 9.899661 TCTAGCATTAATTTACTTTGGAGCTAA 57.100 29.630 0.00 0.00 31.41 3.09
2792 6455 3.321111 GCAGATTCCTTGCATTCCATCAT 59.679 43.478 0.00 0.00 0.00 2.45
2803 6466 2.099263 CCTTCATGCTGCAGATTCCTTG 59.901 50.000 20.43 8.18 0.00 3.61
2878 6544 3.721087 TCCCCTTCTCTGGATTTTGTC 57.279 47.619 0.00 0.00 0.00 3.18
2895 6561 4.123506 TCCAGAAATTTTTGCGTTTTCCC 58.876 39.130 3.20 0.00 31.25 3.97
2898 6564 6.106003 ACTTCTCCAGAAATTTTTGCGTTTT 58.894 32.000 3.20 0.00 33.07 2.43
2902 6568 4.853743 GCTACTTCTCCAGAAATTTTTGCG 59.146 41.667 3.20 0.00 33.07 4.85
2910 6578 2.244695 TCCACGCTACTTCTCCAGAAA 58.755 47.619 0.00 0.00 33.07 2.52
2934 6602 0.439985 CGCTGTCTGGTGTTTGATCG 59.560 55.000 0.00 0.00 0.00 3.69
3010 6678 2.231380 ACCTTGCCCATTCCCGACT 61.231 57.895 0.00 0.00 0.00 4.18
3013 6681 3.451894 GCACCTTGCCCATTCCCG 61.452 66.667 0.00 0.00 37.42 5.14
3043 6712 3.209410 CCCTGCTTCAACTCCATATCAC 58.791 50.000 0.00 0.00 0.00 3.06
3077 6746 1.064458 GGGCGACGAACTAGAGCTC 59.936 63.158 5.27 5.27 0.00 4.09
3085 6754 3.041940 CACACAGGGGCGACGAAC 61.042 66.667 0.00 0.00 0.00 3.95
3094 6763 2.293122 TCTTGAAAAATCGCACACAGGG 59.707 45.455 0.00 0.00 0.00 4.45
3095 6764 3.300009 GTCTTGAAAAATCGCACACAGG 58.700 45.455 0.00 0.00 0.00 4.00
3096 6765 2.966708 CGTCTTGAAAAATCGCACACAG 59.033 45.455 0.00 0.00 0.00 3.66
3097 6766 2.353269 ACGTCTTGAAAAATCGCACACA 59.647 40.909 0.00 0.00 0.00 3.72
3098 6767 2.713976 CACGTCTTGAAAAATCGCACAC 59.286 45.455 0.00 0.00 0.00 3.82
3099 6768 2.609916 TCACGTCTTGAAAAATCGCACA 59.390 40.909 0.00 0.00 0.00 4.57
3100 6769 3.247563 TCACGTCTTGAAAAATCGCAC 57.752 42.857 0.00 0.00 0.00 5.34
3101 6770 3.303725 CCTTCACGTCTTGAAAAATCGCA 60.304 43.478 0.00 0.00 43.90 5.10
3102 6771 3.226347 CCTTCACGTCTTGAAAAATCGC 58.774 45.455 0.00 0.00 43.90 4.58
3103 6772 3.058914 AGCCTTCACGTCTTGAAAAATCG 60.059 43.478 0.00 0.00 43.90 3.34
3116 6785 1.873591 AGTGTAGCAAAAGCCTTCACG 59.126 47.619 0.00 0.00 36.23 4.35
3123 6792 6.208644 TCAGAAAATGAAGTGTAGCAAAAGC 58.791 36.000 0.00 0.00 34.02 3.51
3153 6822 4.164843 TCTTGGGCAGTACAAGACTTTT 57.835 40.909 3.94 0.00 46.70 2.27
3160 6829 3.222173 ACATGTTCTTGGGCAGTACAA 57.778 42.857 0.00 0.00 36.47 2.41
3168 6837 7.013559 TGAGCAATATCATTACATGTTCTTGGG 59.986 37.037 2.30 0.00 0.00 4.12
3169 6838 7.933396 TGAGCAATATCATTACATGTTCTTGG 58.067 34.615 2.30 0.00 0.00 3.61
3231 6928 3.137484 GCACAGAGCCGTTACATCA 57.863 52.632 0.00 0.00 37.23 3.07
3243 6940 4.558226 AAGACATTACATCAGGCACAGA 57.442 40.909 0.00 0.00 0.00 3.41
3287 6984 7.795047 TGCTCTCCAATAAGAGATTACATCAA 58.205 34.615 5.13 0.00 44.67 2.57
3295 6992 7.516452 AGCTAAATTGCTCTCCAATAAGAGAT 58.484 34.615 5.13 0.00 44.67 2.75
3317 7014 8.669243 GCATGTAAACAACTAATAGAAAGAGCT 58.331 33.333 0.00 0.00 0.00 4.09
3318 7015 8.669243 AGCATGTAAACAACTAATAGAAAGAGC 58.331 33.333 0.00 0.00 0.00 4.09
3325 7022 8.208718 TGCCTAAGCATGTAAACAACTAATAG 57.791 34.615 0.00 0.00 46.52 1.73
3400 7151 6.638468 GTCTTGCAAGTTCCAAGTAATTTCTG 59.362 38.462 25.19 0.00 40.35 3.02
3413 7164 4.937620 TGATGGATACTGTCTTGCAAGTTC 59.062 41.667 25.19 18.85 37.61 3.01


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

AutoCloner maintained by Alex Coulton.