Multiple sequence alignment - TraesCS4D01G168500

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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 TraesCS4D01G168500 chr4D 100.000 2777 0 0 1 2777 293379579 293382355 0.000000e+00 5129
1 TraesCS4D01G168500 chr4B 90.131 1915 79 53 878 2741 278411395 278413250 0.000000e+00 2388
2 TraesCS4D01G168500 chr4B 81.524 525 41 20 77 591 278406516 278406994 5.610000e-102 381
3 TraesCS4D01G168500 chr4B 93.671 158 6 2 607 761 278410830 278410986 1.660000e-57 233
4 TraesCS4D01G168500 chr4A 91.575 997 22 16 887 1870 231019397 231020344 0.000000e+00 1319
5 TraesCS4D01G168500 chr4A 88.308 650 38 13 2035 2670 231020683 231021308 0.000000e+00 745
6 TraesCS4D01G168500 chr4A 83.851 161 12 7 683 843 231018305 231018451 1.040000e-29 141
7 TraesCS4D01G168500 chr4A 90.741 108 2 1 1900 2007 231020433 231020532 1.340000e-28 137
8 TraesCS4D01G168500 chr2B 81.944 144 25 1 1221 1363 99266252 99266395 1.350000e-23 121
9 TraesCS4D01G168500 chr2A 82.270 141 24 1 1224 1363 65182726 65182866 1.350000e-23 121


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 TraesCS4D01G168500 chr4D 293379579 293382355 2776 False 5129.000000 5129 100.00000 1 2777 1 chr4D.!!$F1 2776
1 TraesCS4D01G168500 chr4B 278406516 278413250 6734 False 1000.666667 2388 88.44200 77 2741 3 chr4B.!!$F1 2664
2 TraesCS4D01G168500 chr4A 231018305 231021308 3003 False 585.500000 1319 88.61875 683 2670 4 chr4A.!!$F1 1987

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
778 4609 0.10212 TGCAGGCCAGAAAACAAACG 59.898 50.0 5.01 0.0 0.0 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 7593 0.179936 CTGCACAATCCTCCTCCTCC 59.82 60.0 0.0 0.0 0.0 4.3 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 4.803426 GCAGGAGCGACGTGAGGG 62.803 72.222 0.00 0.00 36.62 4.30
24 25 4.803426 CAGGAGCGACGTGAGGGC 62.803 72.222 0.00 0.00 36.62 5.19
26 27 4.373116 GGAGCGACGTGAGGGCAA 62.373 66.667 0.00 0.00 37.16 4.52
27 28 3.112709 GAGCGACGTGAGGGCAAC 61.113 66.667 0.00 0.00 37.16 4.17
28 29 3.858868 GAGCGACGTGAGGGCAACA 62.859 63.158 0.00 0.00 37.16 3.33
29 30 2.742372 GCGACGTGAGGGCAACAT 60.742 61.111 0.00 0.00 39.74 2.71
30 31 3.027170 GCGACGTGAGGGCAACATG 62.027 63.158 0.00 0.00 39.74 3.21
31 32 1.667830 CGACGTGAGGGCAACATGT 60.668 57.895 0.00 7.52 39.70 3.21
32 33 1.868997 GACGTGAGGGCAACATGTG 59.131 57.895 0.00 0.00 37.57 3.21
33 34 1.577328 GACGTGAGGGCAACATGTGG 61.577 60.000 0.00 0.00 37.57 4.17
34 35 1.600636 CGTGAGGGCAACATGTGGT 60.601 57.895 0.00 0.00 39.74 4.16
35 36 1.577328 CGTGAGGGCAACATGTGGTC 61.577 60.000 0.00 0.00 39.74 4.02
36 37 0.250901 GTGAGGGCAACATGTGGTCT 60.251 55.000 4.50 1.36 39.74 3.85
37 38 0.478072 TGAGGGCAACATGTGGTCTT 59.522 50.000 4.50 0.00 39.74 3.01
38 39 1.168714 GAGGGCAACATGTGGTCTTC 58.831 55.000 4.50 2.52 39.74 2.87
39 40 0.251341 AGGGCAACATGTGGTCTTCC 60.251 55.000 4.50 0.82 39.74 3.46
40 41 1.250840 GGGCAACATGTGGTCTTCCC 61.251 60.000 4.50 1.14 39.74 3.97
41 42 0.251341 GGCAACATGTGGTCTTCCCT 60.251 55.000 0.00 0.00 0.00 4.20
42 43 1.168714 GCAACATGTGGTCTTCCCTC 58.831 55.000 0.00 0.00 0.00 4.30
43 44 1.826385 CAACATGTGGTCTTCCCTCC 58.174 55.000 0.00 0.00 0.00 4.30
44 45 0.324943 AACATGTGGTCTTCCCTCCG 59.675 55.000 0.00 0.00 0.00 4.63
45 46 1.221840 CATGTGGTCTTCCCTCCGG 59.778 63.158 0.00 0.00 0.00 5.14
46 47 2.670148 ATGTGGTCTTCCCTCCGGC 61.670 63.158 0.00 0.00 0.00 6.13
47 48 4.452733 GTGGTCTTCCCTCCGGCG 62.453 72.222 0.00 0.00 0.00 6.46
50 51 3.387947 GTCTTCCCTCCGGCGGAA 61.388 66.667 30.59 16.66 37.04 4.30
51 52 2.605295 TCTTCCCTCCGGCGGAAA 60.605 61.111 30.59 19.95 38.90 3.13
52 53 2.218454 TCTTCCCTCCGGCGGAAAA 61.218 57.895 30.59 21.36 38.90 2.29
53 54 1.302993 CTTCCCTCCGGCGGAAAAA 60.303 57.895 30.59 21.02 38.90 1.94
76 77 7.734538 AAAAATTCTATGTTACATTTCCGCG 57.265 32.000 2.23 0.00 0.00 6.46
77 78 3.936902 TTCTATGTTACATTTCCGCGC 57.063 42.857 2.23 0.00 0.00 6.86
78 79 1.855978 TCTATGTTACATTTCCGCGCG 59.144 47.619 25.67 25.67 0.00 6.86
79 80 1.591158 CTATGTTACATTTCCGCGCGT 59.409 47.619 29.95 11.67 0.00 6.01
80 81 0.372334 ATGTTACATTTCCGCGCGTC 59.628 50.000 29.95 7.52 0.00 5.19
81 82 1.295645 GTTACATTTCCGCGCGTCG 60.296 57.895 29.95 14.87 38.08 5.12
111 112 4.756502 GAGTTGACTCTTGGGGTACATAC 58.243 47.826 3.93 0.00 39.81 2.39
112 113 3.194968 AGTTGACTCTTGGGGTACATACG 59.805 47.826 0.00 0.00 0.00 3.06
124 125 9.252962 CTTGGGGTACATACGTTTTTACTATAG 57.747 37.037 0.00 0.00 0.00 1.31
134 135 7.578169 ACGTTTTTACTATAGTGAACTGAGC 57.422 36.000 15.90 0.70 0.00 4.26
153 154 1.202582 GCTACACTCAGGTCGTGTGAT 59.797 52.381 6.10 0.00 44.63 3.06
154 155 2.732597 GCTACACTCAGGTCGTGTGATC 60.733 54.545 6.10 0.00 44.63 2.92
155 156 1.621992 ACACTCAGGTCGTGTGATCT 58.378 50.000 0.00 0.00 43.44 2.75
156 157 1.964223 ACACTCAGGTCGTGTGATCTT 59.036 47.619 0.00 0.00 43.44 2.40
157 158 3.154710 ACACTCAGGTCGTGTGATCTTA 58.845 45.455 0.00 0.00 43.44 2.10
158 159 3.764434 ACACTCAGGTCGTGTGATCTTAT 59.236 43.478 0.00 0.00 43.44 1.73
159 160 4.108336 CACTCAGGTCGTGTGATCTTATG 58.892 47.826 1.86 0.00 40.79 1.90
160 161 3.119291 CTCAGGTCGTGTGATCTTATGC 58.881 50.000 0.00 0.00 31.49 3.14
161 162 2.495669 TCAGGTCGTGTGATCTTATGCA 59.504 45.455 0.00 0.00 31.49 3.96
162 163 3.056179 TCAGGTCGTGTGATCTTATGCAA 60.056 43.478 0.00 0.00 31.49 4.08
163 164 3.308053 CAGGTCGTGTGATCTTATGCAAG 59.692 47.826 0.00 0.00 31.49 4.01
164 165 3.195610 AGGTCGTGTGATCTTATGCAAGA 59.804 43.478 0.00 0.00 44.77 3.02
181 182 6.856135 TGCAAGATCTTATGCACTATGAAG 57.144 37.500 16.40 0.00 46.87 3.02
184 185 6.481313 GCAAGATCTTATGCACTATGAAGACA 59.519 38.462 13.41 0.00 42.12 3.41
185 186 7.011763 GCAAGATCTTATGCACTATGAAGACAA 59.988 37.037 13.41 0.00 42.12 3.18
186 187 8.333908 CAAGATCTTATGCACTATGAAGACAAC 58.666 37.037 7.86 0.00 31.05 3.32
190 191 7.330262 TCTTATGCACTATGAAGACAACATCA 58.670 34.615 0.00 0.00 0.00 3.07
197 198 1.197492 TGAAGACAACATCATGCACGC 59.803 47.619 0.00 0.00 0.00 5.34
198 199 1.197492 GAAGACAACATCATGCACGCA 59.803 47.619 0.00 0.00 0.00 5.24
203 204 3.697982 ACAACATCATGCACGCATAATG 58.302 40.909 12.65 12.65 37.90 1.90
215 222 6.456447 GCACGCATAATGCAAATTTATGAT 57.544 33.333 18.43 6.40 45.36 2.45
216 223 7.565450 GCACGCATAATGCAAATTTATGATA 57.435 32.000 18.43 0.00 45.36 2.15
217 224 7.660059 GCACGCATAATGCAAATTTATGATAG 58.340 34.615 18.43 12.17 45.36 2.08
219 226 9.396938 CACGCATAATGCAAATTTATGATAGAA 57.603 29.630 18.43 0.00 45.36 2.10
220 227 9.398170 ACGCATAATGCAAATTTATGATAGAAC 57.602 29.630 18.43 3.37 45.36 3.01
221 228 8.569683 CGCATAATGCAAATTTATGATAGAACG 58.430 33.333 18.43 9.73 45.36 3.95
223 230 6.974677 AATGCAAATTTATGATAGAACGCG 57.025 33.333 3.53 3.53 0.00 6.01
229 236 3.786516 TTATGATAGAACGCGGTGTGA 57.213 42.857 12.47 0.00 0.00 3.58
234 241 2.736144 TAGAACGCGGTGTGAGAAAT 57.264 45.000 12.47 0.00 0.00 2.17
243 250 4.259970 CGCGGTGTGAGAAATCTAAATCTG 60.260 45.833 0.00 0.00 0.00 2.90
278 285 2.357952 GACAGTTTCCACCACAAGGAAC 59.642 50.000 0.00 0.00 44.41 3.62
279 286 2.025321 ACAGTTTCCACCACAAGGAACT 60.025 45.455 0.00 0.00 44.41 3.01
281 288 3.815401 CAGTTTCCACCACAAGGAACTAG 59.185 47.826 0.00 0.00 44.41 2.57
283 290 3.764237 TTCCACCACAAGGAACTAGAC 57.236 47.619 0.00 0.00 40.11 2.59
284 291 1.975680 TCCACCACAAGGAACTAGACC 59.024 52.381 0.00 0.00 38.49 3.85
285 292 1.337823 CCACCACAAGGAACTAGACCG 60.338 57.143 0.00 0.00 38.49 4.79
289 296 2.036733 CCACAAGGAACTAGACCGAACA 59.963 50.000 0.00 0.00 38.49 3.18
296 303 2.181954 ACTAGACCGAACAGAGTCGT 57.818 50.000 0.00 0.00 39.43 4.34
303 310 1.618861 CGAACAGAGTCGTGTGATCC 58.381 55.000 0.00 0.00 36.26 3.36
304 311 1.200252 CGAACAGAGTCGTGTGATCCT 59.800 52.381 0.00 0.00 36.26 3.24
305 312 2.418976 CGAACAGAGTCGTGTGATCCTA 59.581 50.000 0.00 0.00 36.26 2.94
306 313 3.728268 CGAACAGAGTCGTGTGATCCTAC 60.728 52.174 0.00 0.00 36.26 3.18
307 314 1.738350 ACAGAGTCGTGTGATCCTACG 59.262 52.381 11.35 11.35 41.38 3.51
308 315 0.733729 AGAGTCGTGTGATCCTACGC 59.266 55.000 12.42 8.70 39.94 4.42
309 316 0.450583 GAGTCGTGTGATCCTACGCA 59.549 55.000 12.42 0.00 39.94 5.24
310 317 0.170561 AGTCGTGTGATCCTACGCAC 59.829 55.000 12.42 11.29 44.55 5.34
311 318 0.801067 GTCGTGTGATCCTACGCACC 60.801 60.000 12.42 2.19 44.99 5.01
312 319 1.214325 CGTGTGATCCTACGCACCA 59.786 57.895 6.00 0.00 44.99 4.17
313 320 0.179111 CGTGTGATCCTACGCACCAT 60.179 55.000 6.00 0.00 44.99 3.55
314 321 1.290203 GTGTGATCCTACGCACCATG 58.710 55.000 0.00 0.00 42.95 3.66
315 322 1.134818 GTGTGATCCTACGCACCATGA 60.135 52.381 0.00 0.00 42.95 3.07
316 323 1.552792 TGTGATCCTACGCACCATGAA 59.447 47.619 0.00 0.00 34.19 2.57
317 324 2.027653 TGTGATCCTACGCACCATGAAA 60.028 45.455 0.00 0.00 34.19 2.69
318 325 3.006940 GTGATCCTACGCACCATGAAAA 58.993 45.455 0.00 0.00 0.00 2.29
319 326 3.627577 GTGATCCTACGCACCATGAAAAT 59.372 43.478 0.00 0.00 0.00 1.82
320 327 3.627123 TGATCCTACGCACCATGAAAATG 59.373 43.478 0.00 0.00 0.00 2.32
321 328 2.364632 TCCTACGCACCATGAAAATGG 58.635 47.619 3.16 3.16 46.92 3.16
335 342 5.478233 TGAAAATGGTATCATACACGCAC 57.522 39.130 0.00 0.00 32.44 5.34
348 355 8.607441 ATCATACACGCACAATACAAATCTAT 57.393 30.769 0.00 0.00 0.00 1.98
349 356 7.850501 TCATACACGCACAATACAAATCTATG 58.149 34.615 0.00 0.00 0.00 2.23
351 358 6.925610 ACACGCACAATACAAATCTATGAT 57.074 33.333 0.00 0.00 0.00 2.45
352 359 9.705290 ATACACGCACAATACAAATCTATGATA 57.295 29.630 0.00 0.00 0.00 2.15
357 366 7.798516 CGCACAATACAAATCTATGATACAACC 59.201 37.037 0.00 0.00 0.00 3.77
360 369 9.866655 ACAATACAAATCTATGATACAACCCAT 57.133 29.630 0.00 0.00 0.00 4.00
381 390 5.415077 CCATATGGAGAGATCAAAATCTGGC 59.585 44.000 17.49 0.00 38.85 4.85
388 397 8.219868 TGGAGAGATCAAAATCTGGCAAATATA 58.780 33.333 0.00 0.00 42.46 0.86
398 407 6.764308 ATCTGGCAAATATATAAGCGCATT 57.236 33.333 11.47 3.50 0.00 3.56
404 413 5.739161 GCAAATATATAAGCGCATTGTAGGC 59.261 40.000 11.47 0.00 0.00 3.93
440 449 2.433662 TGCATGCACCCTGCTTAATA 57.566 45.000 18.46 0.00 45.31 0.98
490 499 4.452733 GGACAAGAGGCGACCCCG 62.453 72.222 0.00 0.00 39.21 5.73
497 506 3.711059 GAGGCGACCCCGGAGTCTA 62.711 68.421 14.73 0.00 39.21 2.59
561 570 4.662961 CGTGGCGTGCAGACTGGA 62.663 66.667 4.26 0.00 0.00 3.86
575 584 3.535629 CTGGAGGCTGCACCAACGA 62.536 63.158 3.93 0.00 43.14 3.85
591 600 6.808212 GCACCAACGAAATACTACTACTGTAA 59.192 38.462 0.00 0.00 0.00 2.41
593 602 9.017669 CACCAACGAAATACTACTACTGTAATC 57.982 37.037 0.00 0.00 0.00 1.75
607 4332 8.503458 ACTACTGTAATCACTAATCAGTACGT 57.497 34.615 0.00 0.00 39.54 3.57
608 4333 9.605275 ACTACTGTAATCACTAATCAGTACGTA 57.395 33.333 0.00 0.00 39.54 3.57
609 4334 9.861138 CTACTGTAATCACTAATCAGTACGTAC 57.139 37.037 18.10 18.10 39.54 3.67
636 4464 2.762535 GCAGTAAGCACTAGTTGGGA 57.237 50.000 0.00 0.00 44.79 4.37
637 4465 3.268023 GCAGTAAGCACTAGTTGGGAT 57.732 47.619 0.00 0.00 44.79 3.85
638 4466 3.610911 GCAGTAAGCACTAGTTGGGATT 58.389 45.455 0.00 0.00 44.79 3.01
681 4512 2.628657 GCTATAGATATACAGGCCGGGG 59.371 54.545 8.08 0.00 0.00 5.73
711 4542 4.789012 AATGTGTGCCAACTTGATAAGG 57.211 40.909 0.00 0.00 0.00 2.69
764 4595 1.364626 GCTGACGACCTCAATGCAGG 61.365 60.000 0.00 0.00 39.80 4.85
765 4596 1.364626 CTGACGACCTCAATGCAGGC 61.365 60.000 0.00 0.00 36.98 4.85
766 4597 2.045926 ACGACCTCAATGCAGGCC 60.046 61.111 0.00 0.00 36.98 5.19
767 4598 2.046023 CGACCTCAATGCAGGCCA 60.046 61.111 5.01 0.00 36.98 5.36
768 4599 2.110967 CGACCTCAATGCAGGCCAG 61.111 63.158 5.01 0.00 36.98 4.85
769 4600 1.300963 GACCTCAATGCAGGCCAGA 59.699 57.895 5.01 0.00 36.98 3.86
770 4601 0.322816 GACCTCAATGCAGGCCAGAA 60.323 55.000 5.01 0.00 36.98 3.02
771 4602 0.112995 ACCTCAATGCAGGCCAGAAA 59.887 50.000 5.01 0.00 36.98 2.52
772 4603 1.259609 CCTCAATGCAGGCCAGAAAA 58.740 50.000 5.01 0.00 0.00 2.29
773 4604 1.067354 CCTCAATGCAGGCCAGAAAAC 60.067 52.381 5.01 0.00 0.00 2.43
774 4605 1.614903 CTCAATGCAGGCCAGAAAACA 59.385 47.619 5.01 0.00 0.00 2.83
775 4606 2.036217 CTCAATGCAGGCCAGAAAACAA 59.964 45.455 5.01 0.00 0.00 2.83
776 4607 2.433604 TCAATGCAGGCCAGAAAACAAA 59.566 40.909 5.01 0.00 0.00 2.83
777 4608 2.531522 ATGCAGGCCAGAAAACAAAC 57.468 45.000 5.01 0.00 0.00 2.93
778 4609 0.102120 TGCAGGCCAGAAAACAAACG 59.898 50.000 5.01 0.00 0.00 3.60
781 4612 1.111277 AGGCCAGAAAACAAACGCTT 58.889 45.000 5.01 0.00 0.00 4.68
790 4621 6.355638 CAGAAAACAAACGCTTCTACTACTG 58.644 40.000 0.00 0.00 0.00 2.74
799 4630 4.069304 CGCTTCTACTACTGCCTATCTCT 58.931 47.826 0.00 0.00 0.00 3.10
803 4634 7.110155 GCTTCTACTACTGCCTATCTCTATCT 58.890 42.308 0.00 0.00 0.00 1.98
847 4678 9.781425 ATATAATCTCTCTCTCTCTCTCTCTCT 57.219 37.037 0.00 0.00 0.00 3.10
848 4679 6.418057 AATCTCTCTCTCTCTCTCTCTCTC 57.582 45.833 0.00 0.00 0.00 3.20
849 4680 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
850 4681 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
851 4682 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
853 4684 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
854 4685 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
857 4688 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
859 4690 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
861 4692 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
862 4693 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
863 4694 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
864 4695 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
865 4696 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
866 4697 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
867 4698 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
868 4699 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
869 4700 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
870 4701 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
871 4702 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
891 5974 1.930503 TCTTGTGTAGTTGCGTGTGTG 59.069 47.619 0.00 0.00 0.00 3.82
893 5976 1.003108 TGTGTAGTTGCGTGTGTGTG 58.997 50.000 0.00 0.00 0.00 3.82
894 5977 1.003851 GTGTAGTTGCGTGTGTGTGT 58.996 50.000 0.00 0.00 0.00 3.72
895 5978 1.003108 TGTAGTTGCGTGTGTGTGTG 58.997 50.000 0.00 0.00 0.00 3.82
896 5979 1.003851 GTAGTTGCGTGTGTGTGTGT 58.996 50.000 0.00 0.00 0.00 3.72
897 5980 1.003108 TAGTTGCGTGTGTGTGTGTG 58.997 50.000 0.00 0.00 0.00 3.82
898 5981 0.953471 AGTTGCGTGTGTGTGTGTGT 60.953 50.000 0.00 0.00 0.00 3.72
899 5982 0.792729 GTTGCGTGTGTGTGTGTGTG 60.793 55.000 0.00 0.00 0.00 3.82
900 5983 1.231296 TTGCGTGTGTGTGTGTGTGT 61.231 50.000 0.00 0.00 0.00 3.72
901 5984 0.389948 TGCGTGTGTGTGTGTGTGTA 60.390 50.000 0.00 0.00 0.00 2.90
902 5985 0.934496 GCGTGTGTGTGTGTGTGTAT 59.066 50.000 0.00 0.00 0.00 2.29
903 5986 2.128821 GCGTGTGTGTGTGTGTGTATA 58.871 47.619 0.00 0.00 0.00 1.47
904 5987 2.540516 GCGTGTGTGTGTGTGTGTATAA 59.459 45.455 0.00 0.00 0.00 0.98
905 5988 3.001431 GCGTGTGTGTGTGTGTGTATAAA 59.999 43.478 0.00 0.00 0.00 1.40
906 5989 4.319190 GCGTGTGTGTGTGTGTGTATAAAT 60.319 41.667 0.00 0.00 0.00 1.40
992 6088 2.673368 GTGGAAGAGTTAATCTGTGCGG 59.327 50.000 0.00 0.00 38.67 5.69
995 6091 0.107654 AGAGTTAATCTGTGCGGGCC 60.108 55.000 0.00 0.00 36.69 5.80
1181 6279 2.833794 CCAAGTCGTCAAAGACCAAGA 58.166 47.619 0.00 0.00 41.83 3.02
1182 6280 2.544267 CCAAGTCGTCAAAGACCAAGAC 59.456 50.000 0.00 0.00 41.83 3.01
1183 6281 2.528041 AGTCGTCAAAGACCAAGACC 57.472 50.000 0.00 0.00 41.83 3.85
1184 6282 1.760613 AGTCGTCAAAGACCAAGACCA 59.239 47.619 0.00 0.00 41.83 4.02
1185 6283 2.169769 AGTCGTCAAAGACCAAGACCAA 59.830 45.455 0.00 0.00 41.83 3.67
1186 6284 2.544267 GTCGTCAAAGACCAAGACCAAG 59.456 50.000 0.00 0.00 35.22 3.61
1187 6285 1.873591 CGTCAAAGACCAAGACCAAGG 59.126 52.381 0.00 0.00 0.00 3.61
1188 6286 2.230660 GTCAAAGACCAAGACCAAGGG 58.769 52.381 0.00 0.00 0.00 3.95
1189 6287 1.144913 TCAAAGACCAAGACCAAGGGG 59.855 52.381 0.00 0.00 41.29 4.79
1190 6288 1.144913 CAAAGACCAAGACCAAGGGGA 59.855 52.381 0.00 0.00 38.05 4.81
1191 6289 1.529744 AAGACCAAGACCAAGGGGAA 58.470 50.000 0.00 0.00 38.05 3.97
1192 6290 1.068121 AGACCAAGACCAAGGGGAAG 58.932 55.000 0.00 0.00 38.05 3.46
1193 6291 0.038310 GACCAAGACCAAGGGGAAGG 59.962 60.000 0.00 0.00 38.05 3.46
1194 6292 0.402861 ACCAAGACCAAGGGGAAGGA 60.403 55.000 0.00 0.00 38.05 3.36
1195 6293 0.329596 CCAAGACCAAGGGGAAGGAG 59.670 60.000 0.00 0.00 38.05 3.69
1402 6506 2.634940 CTCCAGGTCCTCAAGAAGTTCA 59.365 50.000 5.50 0.00 0.00 3.18
1545 6649 4.069232 TTCAGGAGCGACGGCCAG 62.069 66.667 2.24 0.00 41.24 4.85
1812 6919 1.427368 TGCAGGGACAGGGTGTAATTT 59.573 47.619 0.00 0.00 0.00 1.82
1857 6964 2.547642 GCATCTATCCTGCAGACCAGTC 60.548 54.545 17.39 0.00 40.06 3.51
1986 7153 1.898330 AAATGTTTGGCGCCCCATCC 61.898 55.000 26.77 7.89 41.78 3.51
2064 7364 2.226315 ACCCAGCAGTCATGGCAGA 61.226 57.895 0.00 0.00 36.43 4.26
2066 7366 1.310933 CCCAGCAGTCATGGCAGAAC 61.311 60.000 0.00 0.00 36.43 3.01
2067 7367 1.310933 CCAGCAGTCATGGCAGAACC 61.311 60.000 0.00 0.00 39.84 3.62
2068 7368 1.376424 AGCAGTCATGGCAGAACCG 60.376 57.895 0.00 0.00 43.94 4.44
2069 7369 1.672356 GCAGTCATGGCAGAACCGT 60.672 57.895 0.00 0.00 43.94 4.83
2177 7477 4.040461 TCAACTTCTGGAGGTTCAGTAAGG 59.960 45.833 0.00 0.00 36.25 2.69
2268 7584 9.664332 TTCATCATTTAAGAAGAAGAAGAGGAG 57.336 33.333 0.00 0.00 0.00 3.69
2271 7587 7.846066 TCATTTAAGAAGAAGAAGAGGAGGAG 58.154 38.462 0.00 0.00 0.00 3.69
2274 7590 3.981212 AGAAGAAGAAGAGGAGGAGGAG 58.019 50.000 0.00 0.00 0.00 3.69
2277 7593 2.244769 AGAAGAAGAGGAGGAGGAGGAG 59.755 54.545 0.00 0.00 0.00 3.69
2302 7621 3.451178 GGAGGAGGATTGTGCAGTTAGTA 59.549 47.826 0.00 0.00 0.00 1.82
2303 7622 4.081087 GGAGGAGGATTGTGCAGTTAGTAA 60.081 45.833 0.00 0.00 0.00 2.24
2408 7728 2.673833 GACTTCTTCACCATCGACGTT 58.326 47.619 0.00 0.00 0.00 3.99
2409 7729 3.057734 GACTTCTTCACCATCGACGTTT 58.942 45.455 0.00 0.00 0.00 3.60
2414 7734 5.823209 TCTTCACCATCGACGTTTATAGA 57.177 39.130 0.00 0.00 0.00 1.98
2415 7735 5.817988 TCTTCACCATCGACGTTTATAGAG 58.182 41.667 0.00 0.00 0.00 2.43
2421 7741 4.854291 CCATCGACGTTTATAGAGATGAGC 59.146 45.833 4.99 0.00 38.08 4.26
2469 7790 6.053005 AGAGACGACTAGACTATTCTTCAGG 58.947 44.000 0.00 0.00 32.75 3.86
2470 7791 5.747342 AGACGACTAGACTATTCTTCAGGT 58.253 41.667 0.00 0.00 32.75 4.00
2538 7859 5.002516 GGAATGATCTCATCCACTTGATCC 58.997 45.833 0.00 0.00 35.10 3.36
2539 7860 5.455755 GGAATGATCTCATCCACTTGATCCA 60.456 44.000 0.00 0.00 35.10 3.41
2540 7861 5.844773 ATGATCTCATCCACTTGATCCAT 57.155 39.130 0.00 0.00 35.69 3.41
2541 7862 4.969484 TGATCTCATCCACTTGATCCATG 58.031 43.478 0.00 0.00 35.69 3.66
2542 7863 4.411212 TGATCTCATCCACTTGATCCATGT 59.589 41.667 0.00 0.00 35.69 3.21
2543 7864 4.146745 TCTCATCCACTTGATCCATGTG 57.853 45.455 0.00 0.00 38.63 3.21
2702 8046 8.749026 TTTCCCAAAAATTTATATGCATGCAT 57.251 26.923 33.92 33.92 40.19 3.96
2729 8073 2.570442 TGAAACGCCCAAACTTGTTC 57.430 45.000 0.00 0.00 0.00 3.18
2741 8085 4.441913 CCAAACTTGTTCTTGCACAGGATT 60.442 41.667 0.00 0.00 0.00 3.01
2742 8086 4.574599 AACTTGTTCTTGCACAGGATTC 57.425 40.909 0.00 0.00 0.00 2.52
2743 8087 3.554934 ACTTGTTCTTGCACAGGATTCA 58.445 40.909 0.00 0.00 0.00 2.57
2744 8088 4.147321 ACTTGTTCTTGCACAGGATTCAT 58.853 39.130 0.00 0.00 0.00 2.57
2745 8089 4.586001 ACTTGTTCTTGCACAGGATTCATT 59.414 37.500 0.00 0.00 0.00 2.57
2746 8090 5.069516 ACTTGTTCTTGCACAGGATTCATTT 59.930 36.000 0.00 0.00 0.00 2.32
2747 8091 6.265196 ACTTGTTCTTGCACAGGATTCATTTA 59.735 34.615 0.00 0.00 0.00 1.40
2748 8092 6.012658 TGTTCTTGCACAGGATTCATTTAC 57.987 37.500 0.00 0.00 0.00 2.01
2749 8093 5.769662 TGTTCTTGCACAGGATTCATTTACT 59.230 36.000 0.00 0.00 0.00 2.24
2750 8094 6.072508 TGTTCTTGCACAGGATTCATTTACTC 60.073 38.462 0.00 0.00 0.00 2.59
2751 8095 4.631377 TCTTGCACAGGATTCATTTACTCG 59.369 41.667 0.00 0.00 0.00 4.18
2752 8096 4.200838 TGCACAGGATTCATTTACTCGA 57.799 40.909 0.00 0.00 0.00 4.04
2753 8097 4.574892 TGCACAGGATTCATTTACTCGAA 58.425 39.130 0.00 0.00 0.00 3.71
2754 8098 4.391830 TGCACAGGATTCATTTACTCGAAC 59.608 41.667 0.00 0.00 0.00 3.95
2755 8099 4.631813 GCACAGGATTCATTTACTCGAACT 59.368 41.667 0.00 0.00 0.00 3.01
2756 8100 5.810587 GCACAGGATTCATTTACTCGAACTA 59.189 40.000 0.00 0.00 0.00 2.24
2757 8101 6.480320 GCACAGGATTCATTTACTCGAACTAT 59.520 38.462 0.00 0.00 0.00 2.12
2758 8102 7.011482 GCACAGGATTCATTTACTCGAACTATT 59.989 37.037 0.00 0.00 0.00 1.73
2759 8103 8.883731 CACAGGATTCATTTACTCGAACTATTT 58.116 33.333 0.00 0.00 0.00 1.40
2760 8104 9.449719 ACAGGATTCATTTACTCGAACTATTTT 57.550 29.630 0.00 0.00 0.00 1.82
2761 8105 9.922305 CAGGATTCATTTACTCGAACTATTTTC 57.078 33.333 0.00 0.00 0.00 2.29
2762 8106 9.892130 AGGATTCATTTACTCGAACTATTTTCT 57.108 29.630 0.00 0.00 0.00 2.52
2763 8107 9.922305 GGATTCATTTACTCGAACTATTTTCTG 57.078 33.333 0.00 0.00 0.00 3.02
2764 8108 9.922305 GATTCATTTACTCGAACTATTTTCTGG 57.078 33.333 0.00 0.00 0.00 3.86
2765 8109 9.667107 ATTCATTTACTCGAACTATTTTCTGGA 57.333 29.630 0.00 0.00 0.00 3.86
2766 8110 9.667107 TTCATTTACTCGAACTATTTTCTGGAT 57.333 29.630 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.803426 CCCTCACGTCGCTCCTGC 62.803 72.222 0.00 0.00 0.00 4.85
7 8 4.803426 GCCCTCACGTCGCTCCTG 62.803 72.222 0.00 0.00 0.00 3.86
9 10 4.373116 TTGCCCTCACGTCGCTCC 62.373 66.667 0.00 0.00 0.00 4.70
10 11 3.112709 GTTGCCCTCACGTCGCTC 61.113 66.667 0.00 0.00 0.00 5.03
11 12 3.240134 ATGTTGCCCTCACGTCGCT 62.240 57.895 0.00 0.00 0.00 4.93
12 13 2.742372 ATGTTGCCCTCACGTCGC 60.742 61.111 0.00 0.00 0.00 5.19
13 14 1.667830 ACATGTTGCCCTCACGTCG 60.668 57.895 0.00 0.00 0.00 5.12
14 15 1.577328 CCACATGTTGCCCTCACGTC 61.577 60.000 0.00 0.00 0.00 4.34
15 16 1.600636 CCACATGTTGCCCTCACGT 60.601 57.895 0.00 0.00 0.00 4.49
16 17 1.577328 GACCACATGTTGCCCTCACG 61.577 60.000 0.00 0.00 0.00 4.35
17 18 0.250901 AGACCACATGTTGCCCTCAC 60.251 55.000 0.00 0.00 0.00 3.51
18 19 0.478072 AAGACCACATGTTGCCCTCA 59.522 50.000 0.00 0.00 0.00 3.86
19 20 1.168714 GAAGACCACATGTTGCCCTC 58.831 55.000 0.00 0.00 0.00 4.30
20 21 0.251341 GGAAGACCACATGTTGCCCT 60.251 55.000 0.00 0.00 35.97 5.19
21 22 1.250840 GGGAAGACCACATGTTGCCC 61.251 60.000 0.00 0.00 36.17 5.36
22 23 0.251341 AGGGAAGACCACATGTTGCC 60.251 55.000 0.00 0.00 41.96 4.52
23 24 1.168714 GAGGGAAGACCACATGTTGC 58.831 55.000 0.00 0.00 43.89 4.17
24 25 1.826385 GGAGGGAAGACCACATGTTG 58.174 55.000 0.00 0.00 43.89 3.33
25 26 0.324943 CGGAGGGAAGACCACATGTT 59.675 55.000 0.00 0.00 43.89 2.71
26 27 1.983224 CGGAGGGAAGACCACATGT 59.017 57.895 0.00 0.00 43.89 3.21
27 28 4.941609 CGGAGGGAAGACCACATG 57.058 61.111 0.00 0.00 43.89 3.21
52 53 6.252655 GCGCGGAAATGTAACATAGAATTTTT 59.747 34.615 8.83 0.00 0.00 1.94
53 54 5.741982 GCGCGGAAATGTAACATAGAATTTT 59.258 36.000 8.83 0.00 0.00 1.82
54 55 5.270853 GCGCGGAAATGTAACATAGAATTT 58.729 37.500 8.83 0.00 0.00 1.82
55 56 4.551990 CGCGCGGAAATGTAACATAGAATT 60.552 41.667 24.84 0.00 0.00 2.17
56 57 3.059868 CGCGCGGAAATGTAACATAGAAT 60.060 43.478 24.84 0.00 0.00 2.40
57 58 2.283086 CGCGCGGAAATGTAACATAGAA 59.717 45.455 24.84 0.00 0.00 2.10
58 59 1.855978 CGCGCGGAAATGTAACATAGA 59.144 47.619 24.84 0.00 0.00 1.98
59 60 1.591158 ACGCGCGGAAATGTAACATAG 59.409 47.619 35.22 0.00 0.00 2.23
60 61 1.589320 GACGCGCGGAAATGTAACATA 59.411 47.619 35.22 0.00 0.00 2.29
61 62 0.372334 GACGCGCGGAAATGTAACAT 59.628 50.000 35.22 7.97 0.00 2.71
62 63 1.782807 GACGCGCGGAAATGTAACA 59.217 52.632 35.22 0.00 0.00 2.41
63 64 1.295645 CGACGCGCGGAAATGTAAC 60.296 57.895 35.22 11.64 36.03 2.50
64 65 3.074296 CGACGCGCGGAAATGTAA 58.926 55.556 35.22 0.00 36.03 2.41
73 74 1.056750 CTCTAAAAACCGACGCGCG 59.943 57.895 30.96 30.96 40.47 6.86
74 75 0.509929 AACTCTAAAAACCGACGCGC 59.490 50.000 5.73 0.00 0.00 6.86
75 76 1.788308 TCAACTCTAAAAACCGACGCG 59.212 47.619 3.53 3.53 0.00 6.01
76 77 2.798847 AGTCAACTCTAAAAACCGACGC 59.201 45.455 0.00 0.00 0.00 5.19
77 78 4.626321 GAGTCAACTCTAAAAACCGACG 57.374 45.455 2.86 0.00 39.81 5.12
111 112 7.813852 AGCTCAGTTCACTATAGTAAAAACG 57.186 36.000 4.74 7.47 0.00 3.60
112 113 9.635520 TGTAGCTCAGTTCACTATAGTAAAAAC 57.364 33.333 4.74 10.30 0.00 2.43
158 159 6.481313 GTCTTCATAGTGCATAAGATCTTGCA 59.519 38.462 18.47 17.35 46.03 4.08
159 160 6.481313 TGTCTTCATAGTGCATAAGATCTTGC 59.519 38.462 18.47 14.85 39.33 4.01
160 161 8.333908 GTTGTCTTCATAGTGCATAAGATCTTG 58.666 37.037 18.47 4.01 31.16 3.02
161 162 8.043113 TGTTGTCTTCATAGTGCATAAGATCTT 58.957 33.333 13.56 13.56 31.16 2.40
162 163 7.559486 TGTTGTCTTCATAGTGCATAAGATCT 58.441 34.615 0.00 0.00 31.16 2.75
163 164 7.776933 TGTTGTCTTCATAGTGCATAAGATC 57.223 36.000 0.00 0.00 31.16 2.75
164 165 7.989170 TGATGTTGTCTTCATAGTGCATAAGAT 59.011 33.333 0.00 0.00 31.16 2.40
169 170 5.220989 GCATGATGTTGTCTTCATAGTGCAT 60.221 40.000 0.00 0.00 36.91 3.96
181 182 3.403613 TTATGCGTGCATGATGTTGTC 57.596 42.857 17.21 0.00 37.82 3.18
184 185 2.734670 GCATTATGCGTGCATGATGTT 58.265 42.857 28.87 5.28 45.97 2.71
185 186 2.410785 GCATTATGCGTGCATGATGT 57.589 45.000 28.87 5.92 45.97 3.06
197 198 8.569683 CGCGTTCTATCATAAATTTGCATTATG 58.430 33.333 10.90 10.90 40.50 1.90
198 199 7.750458 CCGCGTTCTATCATAAATTTGCATTAT 59.250 33.333 4.92 0.00 0.00 1.28
203 204 4.670621 CACCGCGTTCTATCATAAATTTGC 59.329 41.667 4.92 0.00 0.00 3.68
215 222 2.230508 AGATTTCTCACACCGCGTTCTA 59.769 45.455 4.92 0.00 0.00 2.10
216 223 1.000955 AGATTTCTCACACCGCGTTCT 59.999 47.619 4.92 0.00 0.00 3.01
217 224 1.429463 AGATTTCTCACACCGCGTTC 58.571 50.000 4.92 0.00 0.00 3.95
219 226 2.736144 TTAGATTTCTCACACCGCGT 57.264 45.000 4.92 0.00 0.00 6.01
220 227 3.865745 AGATTTAGATTTCTCACACCGCG 59.134 43.478 0.00 0.00 0.00 6.46
221 228 4.034510 CCAGATTTAGATTTCTCACACCGC 59.965 45.833 0.00 0.00 0.00 5.68
223 230 8.561738 TTTACCAGATTTAGATTTCTCACACC 57.438 34.615 0.00 0.00 0.00 4.16
243 250 5.294356 GGAAACTGTCCATTTGGTTTTACC 58.706 41.667 0.00 0.00 46.97 2.85
262 269 3.181448 GGTCTAGTTCCTTGTGGTGGAAA 60.181 47.826 0.00 0.00 44.14 3.13
270 277 3.228453 TCTGTTCGGTCTAGTTCCTTGT 58.772 45.455 0.00 0.00 0.00 3.16
278 285 1.805345 ACACGACTCTGTTCGGTCTAG 59.195 52.381 0.00 0.00 43.58 2.43
279 286 1.534163 CACACGACTCTGTTCGGTCTA 59.466 52.381 0.00 0.00 43.58 2.59
281 288 0.309922 TCACACGACTCTGTTCGGTC 59.690 55.000 0.00 0.00 43.58 4.79
283 290 1.618861 GATCACACGACTCTGTTCGG 58.381 55.000 0.00 0.00 43.58 4.30
284 291 1.200252 AGGATCACACGACTCTGTTCG 59.800 52.381 0.00 0.00 44.87 3.95
285 292 3.728268 CGTAGGATCACACGACTCTGTTC 60.728 52.174 11.67 0.00 40.56 3.18
289 296 0.733729 GCGTAGGATCACACGACTCT 59.266 55.000 19.05 0.00 40.56 3.24
296 303 1.190643 TCATGGTGCGTAGGATCACA 58.809 50.000 0.00 0.00 45.63 3.58
311 318 5.909054 GTGCGTGTATGATACCATTTTCATG 59.091 40.000 0.00 0.00 34.52 3.07
312 319 5.588246 TGTGCGTGTATGATACCATTTTCAT 59.412 36.000 0.00 0.00 36.57 2.57
313 320 4.938226 TGTGCGTGTATGATACCATTTTCA 59.062 37.500 0.00 0.00 34.31 2.69
314 321 5.478233 TGTGCGTGTATGATACCATTTTC 57.522 39.130 0.00 0.00 34.31 2.29
315 322 5.888691 TTGTGCGTGTATGATACCATTTT 57.111 34.783 0.00 0.00 34.31 1.82
316 323 6.540551 TGTATTGTGCGTGTATGATACCATTT 59.459 34.615 0.00 0.00 34.31 2.32
317 324 6.052360 TGTATTGTGCGTGTATGATACCATT 58.948 36.000 0.00 0.00 34.31 3.16
318 325 5.606505 TGTATTGTGCGTGTATGATACCAT 58.393 37.500 0.00 0.00 36.81 3.55
319 326 5.012328 TGTATTGTGCGTGTATGATACCA 57.988 39.130 0.00 0.00 0.00 3.25
320 327 5.977171 TTGTATTGTGCGTGTATGATACC 57.023 39.130 0.00 0.00 0.00 2.73
321 328 7.851508 AGATTTGTATTGTGCGTGTATGATAC 58.148 34.615 0.00 0.00 0.00 2.24
348 355 6.084060 TGATCTCTCCATATGGGTTGTATCA 58.916 40.000 21.78 18.68 38.11 2.15
349 356 6.611613 TGATCTCTCCATATGGGTTGTATC 57.388 41.667 21.78 16.69 38.11 2.24
351 358 6.823286 TTTGATCTCTCCATATGGGTTGTA 57.177 37.500 21.78 0.67 38.11 2.41
352 359 5.715439 TTTGATCTCTCCATATGGGTTGT 57.285 39.130 21.78 4.73 38.11 3.32
357 366 5.415077 GCCAGATTTTGATCTCTCCATATGG 59.585 44.000 16.25 16.25 0.00 2.74
360 369 5.635278 TGCCAGATTTTGATCTCTCCATA 57.365 39.130 0.00 0.00 0.00 2.74
381 390 5.959527 CGCCTACAATGCGCTTATATATTTG 59.040 40.000 9.73 0.00 46.01 2.32
398 407 1.738346 ATGCATCTCGCTCGCCTACA 61.738 55.000 0.00 0.00 43.06 2.74
404 413 1.204312 CATGCATGCATCTCGCTCG 59.796 57.895 30.07 13.50 43.06 5.03
426 435 5.337578 TTGGAAATTATTAAGCAGGGTGC 57.662 39.130 0.00 0.00 45.46 5.01
455 464 5.549742 TGTCCCTTTGAATTGAATTGCTT 57.450 34.783 0.00 0.00 0.00 3.91
463 472 2.095059 CGCCTCTTGTCCCTTTGAATTG 60.095 50.000 0.00 0.00 0.00 2.32
468 477 0.955919 GGTCGCCTCTTGTCCCTTTG 60.956 60.000 0.00 0.00 0.00 2.77
472 481 4.097361 GGGGTCGCCTCTTGTCCC 62.097 72.222 0.00 0.00 37.59 4.46
490 499 1.810532 CCGACCAGCACTAGACTCC 59.189 63.158 0.00 0.00 0.00 3.85
497 506 2.980233 GCTTTGCCGACCAGCACT 60.980 61.111 0.00 0.00 43.97 4.40
555 564 1.968540 GTTGGTGCAGCCTCCAGTC 60.969 63.158 14.36 0.00 36.12 3.51
561 570 1.165270 GTATTTCGTTGGTGCAGCCT 58.835 50.000 14.36 0.00 38.35 4.58
591 600 5.967469 CGTACGTACGTACTGATTAGTGAT 58.033 41.667 40.05 12.57 46.22 3.06
605 4330 2.357793 GCTTACTGCTACGTACGTACG 58.642 52.381 38.49 38.49 45.87 3.67
606 4331 3.094294 GTGCTTACTGCTACGTACGTAC 58.906 50.000 23.60 19.21 43.37 3.67
607 4332 3.002791 AGTGCTTACTGCTACGTACGTA 58.997 45.455 25.41 25.41 43.37 3.57
608 4333 1.808945 AGTGCTTACTGCTACGTACGT 59.191 47.619 25.98 25.98 43.37 3.57
609 4334 2.539346 AGTGCTTACTGCTACGTACG 57.461 50.000 15.01 15.01 43.37 3.67
656 4487 4.830046 CCGGCCTGTATATCTATAGCTGAT 59.170 45.833 0.00 0.00 0.00 2.90
681 4512 4.504858 AGTTGGCACACATTACTAGCTAC 58.495 43.478 0.00 0.00 39.29 3.58
711 4542 7.376866 CACTTACCGCATTTGATTTATGTCATC 59.623 37.037 0.00 0.00 0.00 2.92
764 4595 2.492019 AGAAGCGTTTGTTTTCTGGC 57.508 45.000 0.00 0.00 30.41 4.85
765 4596 4.813296 AGTAGAAGCGTTTGTTTTCTGG 57.187 40.909 0.00 0.00 33.51 3.86
766 4597 6.355638 CAGTAGTAGAAGCGTTTGTTTTCTG 58.644 40.000 0.00 0.00 33.51 3.02
767 4598 5.050295 GCAGTAGTAGAAGCGTTTGTTTTCT 60.050 40.000 0.00 0.00 35.49 2.52
768 4599 5.138095 GCAGTAGTAGAAGCGTTTGTTTTC 58.862 41.667 0.00 0.00 0.00 2.29
769 4600 4.024302 GGCAGTAGTAGAAGCGTTTGTTTT 60.024 41.667 0.00 0.00 0.00 2.43
770 4601 3.497262 GGCAGTAGTAGAAGCGTTTGTTT 59.503 43.478 0.00 0.00 0.00 2.83
771 4602 3.064931 GGCAGTAGTAGAAGCGTTTGTT 58.935 45.455 0.00 0.00 0.00 2.83
772 4603 2.299297 AGGCAGTAGTAGAAGCGTTTGT 59.701 45.455 0.00 0.00 0.00 2.83
773 4604 2.960819 AGGCAGTAGTAGAAGCGTTTG 58.039 47.619 0.00 0.00 0.00 2.93
774 4605 4.645588 AGATAGGCAGTAGTAGAAGCGTTT 59.354 41.667 0.00 0.00 0.00 3.60
775 4606 4.208746 AGATAGGCAGTAGTAGAAGCGTT 58.791 43.478 0.00 0.00 0.00 4.84
776 4607 3.816523 GAGATAGGCAGTAGTAGAAGCGT 59.183 47.826 0.00 0.00 0.00 5.07
777 4608 4.069304 AGAGATAGGCAGTAGTAGAAGCG 58.931 47.826 0.00 0.00 0.00 4.68
778 4609 7.110155 AGATAGAGATAGGCAGTAGTAGAAGC 58.890 42.308 0.00 0.00 0.00 3.86
781 4612 6.157297 GGGAGATAGAGATAGGCAGTAGTAGA 59.843 46.154 0.00 0.00 0.00 2.59
790 4621 2.490115 CGTGTGGGAGATAGAGATAGGC 59.510 54.545 0.00 0.00 0.00 3.93
799 4630 5.664294 TTAGCTTAAACGTGTGGGAGATA 57.336 39.130 0.00 0.00 0.00 1.98
803 4634 8.426489 AGATTATATTAGCTTAAACGTGTGGGA 58.574 33.333 0.00 0.00 0.00 4.37
843 4674 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
844 4675 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
845 4676 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
846 4677 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
847 4678 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
848 4679 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
849 4680 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
850 4681 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
851 4682 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
853 4684 5.026121 ACAAGAGAGAGAGAGAGAGAGAGA 58.974 45.833 0.00 0.00 0.00 3.10
854 4685 5.114780 CACAAGAGAGAGAGAGAGAGAGAG 58.885 50.000 0.00 0.00 0.00 3.20
857 4688 4.908601 ACACAAGAGAGAGAGAGAGAGA 57.091 45.455 0.00 0.00 0.00 3.10
859 4690 5.755409 ACTACACAAGAGAGAGAGAGAGA 57.245 43.478 0.00 0.00 0.00 3.10
861 4692 4.457603 GCAACTACACAAGAGAGAGAGAGA 59.542 45.833 0.00 0.00 0.00 3.10
862 4693 4.671508 CGCAACTACACAAGAGAGAGAGAG 60.672 50.000 0.00 0.00 0.00 3.20
863 4694 3.189495 CGCAACTACACAAGAGAGAGAGA 59.811 47.826 0.00 0.00 0.00 3.10
864 4695 3.057876 ACGCAACTACACAAGAGAGAGAG 60.058 47.826 0.00 0.00 0.00 3.20
865 4696 2.885266 ACGCAACTACACAAGAGAGAGA 59.115 45.455 0.00 0.00 0.00 3.10
866 4697 2.983136 CACGCAACTACACAAGAGAGAG 59.017 50.000 0.00 0.00 0.00 3.20
867 4698 2.361119 ACACGCAACTACACAAGAGAGA 59.639 45.455 0.00 0.00 0.00 3.10
868 4699 2.472861 CACACGCAACTACACAAGAGAG 59.527 50.000 0.00 0.00 0.00 3.20
869 4700 2.159156 ACACACGCAACTACACAAGAGA 60.159 45.455 0.00 0.00 0.00 3.10
870 4701 2.033747 CACACACGCAACTACACAAGAG 60.034 50.000 0.00 0.00 0.00 2.85
871 4702 1.930503 CACACACGCAACTACACAAGA 59.069 47.619 0.00 0.00 0.00 3.02
900 5983 9.902196 CCGAGTGTGTGTGTGTATATATTTATA 57.098 33.333 0.00 0.00 0.00 0.98
901 5984 8.635328 TCCGAGTGTGTGTGTGTATATATTTAT 58.365 33.333 0.00 0.00 0.00 1.40
902 5985 7.916977 GTCCGAGTGTGTGTGTGTATATATTTA 59.083 37.037 0.00 0.00 0.00 1.40
903 5986 6.755141 GTCCGAGTGTGTGTGTGTATATATTT 59.245 38.462 0.00 0.00 0.00 1.40
904 5987 6.270815 GTCCGAGTGTGTGTGTGTATATATT 58.729 40.000 0.00 0.00 0.00 1.28
905 5988 5.221185 GGTCCGAGTGTGTGTGTGTATATAT 60.221 44.000 0.00 0.00 0.00 0.86
906 5989 4.096833 GGTCCGAGTGTGTGTGTGTATATA 59.903 45.833 0.00 0.00 0.00 0.86
992 6088 4.864334 CGCCTCCCATGAGTGGCC 62.864 72.222 13.88 0.00 44.62 5.36
995 6091 2.046023 TTGCGCCTCCCATGAGTG 60.046 61.111 4.18 0.00 36.86 3.51
1095 6193 2.707849 GGCCGGCGTGTCTTCTAGA 61.708 63.158 22.54 0.00 0.00 2.43
1181 6279 2.204306 CCCCTCCTTCCCCTTGGT 60.204 66.667 0.00 0.00 0.00 3.67
1182 6280 1.543896 TTCCCCTCCTTCCCCTTGG 60.544 63.158 0.00 0.00 0.00 3.61
1183 6281 1.575447 CCTTCCCCTCCTTCCCCTTG 61.575 65.000 0.00 0.00 0.00 3.61
1184 6282 1.230314 CCTTCCCCTCCTTCCCCTT 60.230 63.158 0.00 0.00 0.00 3.95
1185 6283 2.461637 CCTTCCCCTCCTTCCCCT 59.538 66.667 0.00 0.00 0.00 4.79
1186 6284 2.696504 CCCTTCCCCTCCTTCCCC 60.697 72.222 0.00 0.00 0.00 4.81
1187 6285 2.696504 CCCCTTCCCCTCCTTCCC 60.697 72.222 0.00 0.00 0.00 3.97
1188 6286 1.230182 TTCCCCTTCCCCTCCTTCC 60.230 63.158 0.00 0.00 0.00 3.46
1189 6287 0.253207 TCTTCCCCTTCCCCTCCTTC 60.253 60.000 0.00 0.00 0.00 3.46
1190 6288 0.253394 CTCTTCCCCTTCCCCTCCTT 60.253 60.000 0.00 0.00 0.00 3.36
1191 6289 1.398234 CTCTTCCCCTTCCCCTCCT 59.602 63.158 0.00 0.00 0.00 3.69
1192 6290 2.379459 GCTCTTCCCCTTCCCCTCC 61.379 68.421 0.00 0.00 0.00 4.30
1193 6291 1.616628 TGCTCTTCCCCTTCCCCTC 60.617 63.158 0.00 0.00 0.00 4.30
1194 6292 1.925972 GTGCTCTTCCCCTTCCCCT 60.926 63.158 0.00 0.00 0.00 4.79
1195 6293 2.203549 CTGTGCTCTTCCCCTTCCCC 62.204 65.000 0.00 0.00 0.00 4.81
1402 6506 2.181773 TGTACCCCTCCCACCTCCT 61.182 63.158 0.00 0.00 0.00 3.69
1812 6919 4.835678 TCTGAGCATGCATCTAACAAGAA 58.164 39.130 21.98 0.00 0.00 2.52
1841 6948 3.107402 AGAAGACTGGTCTGCAGGATA 57.893 47.619 15.13 0.00 40.36 2.59
1842 6949 1.949799 AGAAGACTGGTCTGCAGGAT 58.050 50.000 15.13 0.00 40.36 3.24
1852 6959 7.800155 AGAAAGAAAGAAAGAAGAAGACTGG 57.200 36.000 0.00 0.00 0.00 4.00
1857 6964 9.860898 TTTCCAAAGAAAGAAAGAAAGAAGAAG 57.139 29.630 0.00 0.00 37.07 2.85
2064 7364 3.181490 GGCAAGAAGAAGAAAACACGGTT 60.181 43.478 0.00 0.00 0.00 4.44
2066 7366 2.618709 AGGCAAGAAGAAGAAAACACGG 59.381 45.455 0.00 0.00 0.00 4.94
2067 7367 3.971032 AGGCAAGAAGAAGAAAACACG 57.029 42.857 0.00 0.00 0.00 4.49
2068 7368 6.378710 AACTAGGCAAGAAGAAGAAAACAC 57.621 37.500 0.00 0.00 0.00 3.32
2069 7369 7.773690 AGTTAACTAGGCAAGAAGAAGAAAACA 59.226 33.333 6.26 0.00 0.00 2.83
2070 7370 8.070769 CAGTTAACTAGGCAAGAAGAAGAAAAC 58.929 37.037 8.04 0.00 0.00 2.43
2071 7371 7.990886 TCAGTTAACTAGGCAAGAAGAAGAAAA 59.009 33.333 8.04 0.00 0.00 2.29
2075 7375 7.148340 CCATTCAGTTAACTAGGCAAGAAGAAG 60.148 40.741 8.04 2.01 0.00 2.85
2265 7581 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
2266 7582 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
2267 7583 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
2268 7584 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
2271 7587 0.565674 AATCCTCCTCCTCCTCCTCC 59.434 60.000 0.00 0.00 0.00 4.30
2274 7590 1.127343 CACAATCCTCCTCCTCCTCC 58.873 60.000 0.00 0.00 0.00 4.30
2277 7593 0.179936 CTGCACAATCCTCCTCCTCC 59.820 60.000 0.00 0.00 0.00 4.30
2302 7621 4.799564 TTGTGCCTGTTTCTTTTCACTT 57.200 36.364 0.00 0.00 0.00 3.16
2303 7622 4.799564 TTTGTGCCTGTTTCTTTTCACT 57.200 36.364 0.00 0.00 0.00 3.41
2408 7728 9.760926 ATGGTCTTACATAGCTCATCTCTATAA 57.239 33.333 0.00 0.00 0.00 0.98
2409 7729 9.760926 AATGGTCTTACATAGCTCATCTCTATA 57.239 33.333 0.00 0.00 0.00 1.31
2414 7734 9.499479 CAAATAATGGTCTTACATAGCTCATCT 57.501 33.333 0.00 0.00 0.00 2.90
2415 7735 9.277783 ACAAATAATGGTCTTACATAGCTCATC 57.722 33.333 0.00 0.00 0.00 2.92
2469 7790 5.748630 TCTGCACGTCTCATATTATTGTGAC 59.251 40.000 0.00 0.00 36.98 3.67
2470 7791 5.901552 TCTGCACGTCTCATATTATTGTGA 58.098 37.500 0.00 0.00 0.00 3.58
2538 7859 1.131126 GGACTTGCCGACATTCACATG 59.869 52.381 0.00 0.00 36.34 3.21
2539 7860 1.453155 GGACTTGCCGACATTCACAT 58.547 50.000 0.00 0.00 0.00 3.21
2540 7861 2.927004 GGACTTGCCGACATTCACA 58.073 52.632 0.00 0.00 0.00 3.58
2675 8019 9.017509 TGCATGCATATAAATTTTTGGGAAAAA 57.982 25.926 18.46 0.00 43.76 1.94
2702 8046 3.754323 AGTTTGGGCGTTTCATCGAAATA 59.246 39.130 0.00 0.00 33.97 1.40
2729 8073 4.631377 TCGAGTAAATGAATCCTGTGCAAG 59.369 41.667 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.