Multiple sequence alignment - TraesCS2A01G591600

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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 TraesCS2A01G591600 chr2A 100.000 3089 0 0 1 3089 779218290 779215202 0.000000e+00 5705.0
1 TraesCS2A01G591600 chr2D 92.675 2034 103 16 534 2538 634295399 634297415 0.000000e+00 2889.0
2 TraesCS2A01G591600 chr2D 90.054 553 26 9 2536 3088 634297495 634298018 0.000000e+00 689.0
3 TraesCS2A01G591600 chr2D 88.148 135 4 7 357 489 634295283 634295407 1.920000e-32 150.0
4 TraesCS2A01G591600 chr2B 91.400 2035 117 21 534 2535 777329438 777331447 0.000000e+00 2736.0
5 TraesCS2A01G591600 chr2B 88.689 557 26 15 2536 3088 777331531 777332054 0.000000e+00 645.0
6 TraesCS2A01G591600 chr2B 92.424 132 10 0 358 489 777329315 777329446 4.070000e-44 189.0
7 TraesCS2A01G591600 chr6A 87.423 326 41 0 1154 1479 302779985 302780310 2.910000e-100 375.0
8 TraesCS2A01G591600 chr6A 94.872 78 4 0 1820 1897 302781380 302781457 4.180000e-24 122.0
9 TraesCS2A01G591600 chr6D 94.872 78 4 0 1820 1897 220936009 220935932 4.180000e-24 122.0
10 TraesCS2A01G591600 chr6B 94.872 78 4 0 1820 1897 396435026 396434949 4.180000e-24 122.0
11 TraesCS2A01G591600 chr3B 97.059 34 0 1 95 127 191193740 191193773 4.300000e-04 56.5


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 TraesCS2A01G591600 chr2A 779215202 779218290 3088 True 5705.000000 5705 100.000000 1 3089 1 chr2A.!!$R1 3088
1 TraesCS2A01G591600 chr2D 634295283 634298018 2735 False 1242.666667 2889 90.292333 357 3088 3 chr2D.!!$F1 2731
2 TraesCS2A01G591600 chr2B 777329315 777332054 2739 False 1190.000000 2736 90.837667 358 3088 3 chr2B.!!$F1 2730
3 TraesCS2A01G591600 chr6A 302779985 302781457 1472 False 248.500000 375 91.147500 1154 1897 2 chr6A.!!$F1 743

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
208 209 0.103390 ACAAAAAGCCGAAAACCCCG 59.897 50.0 0.00 0.00 0.00 5.73 F
312 313 0.251341 AGTGATTGTTGGGTGGCTCC 60.251 55.0 0.00 0.00 0.00 4.70 F
339 340 0.393132 GCCCTCCTCAACTAGTTGCC 60.393 60.0 27.49 8.22 40.24 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2495 0.819259 TGTTGCAGCTGGGAGTCAAC 60.819 55.0 20.67 20.67 37.94 3.18 R
1878 2637 1.342074 TCTTGCCGGAGATATCAGGG 58.658 55.0 5.05 4.05 0.00 4.45 R
2326 3125 0.035458 AAGAGAGGGGAACAGCAACG 59.965 55.0 0.00 0.00 0.00 4.10 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
22 23 5.508200 CTTTGCTACTACTCACCTAGGAG 57.492 47.826 17.98 8.08 42.62 3.69
23 24 4.857130 TTGCTACTACTCACCTAGGAGA 57.143 45.455 17.98 12.87 38.65 3.71
24 25 4.153673 TGCTACTACTCACCTAGGAGAC 57.846 50.000 17.98 0.00 38.65 3.36
25 26 3.117963 TGCTACTACTCACCTAGGAGACC 60.118 52.174 17.98 0.00 38.65 3.85
26 27 3.136992 GCTACTACTCACCTAGGAGACCT 59.863 52.174 17.98 1.26 38.65 3.85
27 28 4.347583 GCTACTACTCACCTAGGAGACCTA 59.652 50.000 17.98 2.44 38.65 3.08
39 40 4.081695 AGGAGACCTAGGTTTGAATCCT 57.918 45.455 17.53 18.99 38.91 3.24
40 41 5.222278 AGGAGACCTAGGTTTGAATCCTA 57.778 43.478 17.53 2.31 34.21 2.94
56 57 2.682594 TCCTAGGTGGATCCTCATGTG 58.317 52.381 14.23 4.99 44.42 3.21
57 58 1.071385 CCTAGGTGGATCCTCATGTGC 59.929 57.143 14.23 0.00 44.42 4.57
58 59 0.752658 TAGGTGGATCCTCATGTGCG 59.247 55.000 14.23 0.00 44.42 5.34
59 60 2.182842 GGTGGATCCTCATGTGCGC 61.183 63.158 14.23 0.00 0.00 6.09
60 61 1.153289 GTGGATCCTCATGTGCGCT 60.153 57.895 14.23 0.00 0.00 5.92
61 62 0.745845 GTGGATCCTCATGTGCGCTT 60.746 55.000 14.23 0.00 0.00 4.68
62 63 0.462581 TGGATCCTCATGTGCGCTTC 60.463 55.000 14.23 2.14 0.00 3.86
63 64 0.462581 GGATCCTCATGTGCGCTTCA 60.463 55.000 9.73 8.76 0.00 3.02
64 65 1.372582 GATCCTCATGTGCGCTTCAA 58.627 50.000 9.73 0.00 0.00 2.69
65 66 1.739466 GATCCTCATGTGCGCTTCAAA 59.261 47.619 9.73 0.67 0.00 2.69
66 67 1.603456 TCCTCATGTGCGCTTCAAAA 58.397 45.000 9.73 0.33 0.00 2.44
67 68 1.536766 TCCTCATGTGCGCTTCAAAAG 59.463 47.619 9.73 9.49 0.00 2.27
68 69 1.401931 CCTCATGTGCGCTTCAAAAGG 60.402 52.381 9.73 14.12 0.00 3.11
69 70 1.536766 CTCATGTGCGCTTCAAAAGGA 59.463 47.619 9.73 4.85 0.00 3.36
70 71 1.536766 TCATGTGCGCTTCAAAAGGAG 59.463 47.619 9.73 0.00 0.00 3.69
71 72 0.242017 ATGTGCGCTTCAAAAGGAGC 59.758 50.000 9.73 0.00 0.00 4.70
72 73 1.100463 TGTGCGCTTCAAAAGGAGCA 61.100 50.000 9.73 0.00 36.05 4.26
73 74 1.654220 TGCGCTTCAAAAGGAGCAC 59.346 52.632 9.73 0.00 33.74 4.40
74 75 1.441016 GCGCTTCAAAAGGAGCACG 60.441 57.895 0.00 0.00 0.00 5.34
75 76 1.941812 CGCTTCAAAAGGAGCACGT 59.058 52.632 0.00 0.00 0.00 4.49
76 77 0.307760 CGCTTCAAAAGGAGCACGTT 59.692 50.000 0.00 0.00 0.00 3.99
77 78 1.268539 CGCTTCAAAAGGAGCACGTTT 60.269 47.619 0.00 0.00 35.96 3.60
78 79 2.794631 CGCTTCAAAAGGAGCACGTTTT 60.795 45.455 8.46 8.46 42.30 2.43
79 80 3.186909 GCTTCAAAAGGAGCACGTTTTT 58.813 40.909 11.12 1.39 40.51 1.94
96 97 2.793278 TTTTCCCTTTTCGAGCTTGC 57.207 45.000 0.00 0.00 0.00 4.01
97 98 1.981256 TTTCCCTTTTCGAGCTTGCT 58.019 45.000 0.00 0.00 0.00 3.91
98 99 1.981256 TTCCCTTTTCGAGCTTGCTT 58.019 45.000 0.00 0.00 0.00 3.91
99 100 1.523758 TCCCTTTTCGAGCTTGCTTC 58.476 50.000 0.00 0.00 0.00 3.86
100 101 1.072331 TCCCTTTTCGAGCTTGCTTCT 59.928 47.619 0.00 0.00 0.00 2.85
101 102 1.466558 CCCTTTTCGAGCTTGCTTCTC 59.533 52.381 0.00 0.00 0.00 2.87
105 106 3.549150 CGAGCTTGCTTCTCGCGG 61.549 66.667 6.13 0.00 45.32 6.46
106 107 2.125912 GAGCTTGCTTCTCGCGGA 60.126 61.111 6.13 0.00 43.27 5.54
107 108 1.738099 GAGCTTGCTTCTCGCGGAA 60.738 57.895 6.13 8.10 43.27 4.30
121 122 2.496942 CGGAAGCAAATCCATGGCT 58.503 52.632 6.96 0.00 39.61 4.75
122 123 0.383231 CGGAAGCAAATCCATGGCTC 59.617 55.000 6.96 0.00 39.61 4.70
123 124 0.749049 GGAAGCAAATCCATGGCTCC 59.251 55.000 6.96 0.36 39.42 4.70
124 125 0.749049 GAAGCAAATCCATGGCTCCC 59.251 55.000 6.96 0.00 36.76 4.30
125 126 1.039233 AAGCAAATCCATGGCTCCCG 61.039 55.000 6.96 0.00 36.76 5.14
126 127 1.453745 GCAAATCCATGGCTCCCGA 60.454 57.895 6.96 0.00 0.00 5.14
127 128 1.037030 GCAAATCCATGGCTCCCGAA 61.037 55.000 6.96 0.00 0.00 4.30
128 129 1.027357 CAAATCCATGGCTCCCGAAG 58.973 55.000 6.96 0.00 0.00 3.79
180 181 5.924475 TTTCAAGAAGCTAAGAAAGACCG 57.076 39.130 0.00 0.00 0.00 4.79
181 182 3.926616 TCAAGAAGCTAAGAAAGACCGG 58.073 45.455 0.00 0.00 0.00 5.28
182 183 3.323979 TCAAGAAGCTAAGAAAGACCGGT 59.676 43.478 6.92 6.92 0.00 5.28
183 184 3.320673 AGAAGCTAAGAAAGACCGGTG 57.679 47.619 14.63 0.00 0.00 4.94
184 185 2.897969 AGAAGCTAAGAAAGACCGGTGA 59.102 45.455 14.63 0.00 0.00 4.02
185 186 3.323979 AGAAGCTAAGAAAGACCGGTGAA 59.676 43.478 14.63 0.00 0.00 3.18
186 187 3.764237 AGCTAAGAAAGACCGGTGAAA 57.236 42.857 14.63 0.00 0.00 2.69
187 188 4.081322 AGCTAAGAAAGACCGGTGAAAA 57.919 40.909 14.63 0.00 0.00 2.29
188 189 4.457466 AGCTAAGAAAGACCGGTGAAAAA 58.543 39.130 14.63 0.00 0.00 1.94
206 207 4.688511 AAAAACAAAAAGCCGAAAACCC 57.311 36.364 0.00 0.00 0.00 4.11
207 208 2.319136 AACAAAAAGCCGAAAACCCC 57.681 45.000 0.00 0.00 0.00 4.95
208 209 0.103390 ACAAAAAGCCGAAAACCCCG 59.897 50.000 0.00 0.00 0.00 5.73
209 210 0.386113 CAAAAAGCCGAAAACCCCGA 59.614 50.000 0.00 0.00 0.00 5.14
210 211 1.112950 AAAAAGCCGAAAACCCCGAA 58.887 45.000 0.00 0.00 0.00 4.30
211 212 1.112950 AAAAGCCGAAAACCCCGAAA 58.887 45.000 0.00 0.00 0.00 3.46
212 213 1.112950 AAAGCCGAAAACCCCGAAAA 58.887 45.000 0.00 0.00 0.00 2.29
213 214 1.112950 AAGCCGAAAACCCCGAAAAA 58.887 45.000 0.00 0.00 0.00 1.94
214 215 0.386476 AGCCGAAAACCCCGAAAAAC 59.614 50.000 0.00 0.00 0.00 2.43
215 216 0.598158 GCCGAAAACCCCGAAAAACC 60.598 55.000 0.00 0.00 0.00 3.27
216 217 0.745468 CCGAAAACCCCGAAAAACCA 59.255 50.000 0.00 0.00 0.00 3.67
217 218 1.341852 CCGAAAACCCCGAAAAACCAT 59.658 47.619 0.00 0.00 0.00 3.55
218 219 2.608506 CCGAAAACCCCGAAAAACCATC 60.609 50.000 0.00 0.00 0.00 3.51
219 220 2.295070 CGAAAACCCCGAAAAACCATCT 59.705 45.455 0.00 0.00 0.00 2.90
220 221 3.502979 CGAAAACCCCGAAAAACCATCTA 59.497 43.478 0.00 0.00 0.00 1.98
221 222 4.023021 CGAAAACCCCGAAAAACCATCTAA 60.023 41.667 0.00 0.00 0.00 2.10
222 223 5.507650 CGAAAACCCCGAAAAACCATCTAAA 60.508 40.000 0.00 0.00 0.00 1.85
223 224 5.873146 AAACCCCGAAAAACCATCTAAAA 57.127 34.783 0.00 0.00 0.00 1.52
224 225 5.873146 AACCCCGAAAAACCATCTAAAAA 57.127 34.783 0.00 0.00 0.00 1.94
225 226 5.462530 ACCCCGAAAAACCATCTAAAAAG 57.537 39.130 0.00 0.00 0.00 2.27
226 227 4.242475 CCCCGAAAAACCATCTAAAAAGC 58.758 43.478 0.00 0.00 0.00 3.51
227 228 4.242475 CCCGAAAAACCATCTAAAAAGCC 58.758 43.478 0.00 0.00 0.00 4.35
228 229 4.262249 CCCGAAAAACCATCTAAAAAGCCA 60.262 41.667 0.00 0.00 0.00 4.75
229 230 5.293560 CCGAAAAACCATCTAAAAAGCCAA 58.706 37.500 0.00 0.00 0.00 4.52
230 231 5.755861 CCGAAAAACCATCTAAAAAGCCAAA 59.244 36.000 0.00 0.00 0.00 3.28
231 232 6.258947 CCGAAAAACCATCTAAAAAGCCAAAA 59.741 34.615 0.00 0.00 0.00 2.44
232 233 7.123190 CGAAAAACCATCTAAAAAGCCAAAAC 58.877 34.615 0.00 0.00 0.00 2.43
233 234 6.935741 AAAACCATCTAAAAAGCCAAAACC 57.064 33.333 0.00 0.00 0.00 3.27
234 235 4.251543 ACCATCTAAAAAGCCAAAACCG 57.748 40.909 0.00 0.00 0.00 4.44
235 236 2.993220 CCATCTAAAAAGCCAAAACCGC 59.007 45.455 0.00 0.00 0.00 5.68
236 237 2.409152 TCTAAAAAGCCAAAACCGCG 57.591 45.000 0.00 0.00 0.00 6.46
237 238 1.677052 TCTAAAAAGCCAAAACCGCGT 59.323 42.857 4.92 0.00 0.00 6.01
238 239 1.784283 CTAAAAAGCCAAAACCGCGTG 59.216 47.619 4.92 0.00 0.00 5.34
239 240 1.425267 AAAAAGCCAAAACCGCGTGC 61.425 50.000 4.92 0.00 0.00 5.34
240 241 4.622456 AAGCCAAAACCGCGTGCG 62.622 61.111 4.92 7.38 39.44 5.34
251 252 3.369701 CGCGTGCGGAAAAATGTAA 57.630 47.368 6.30 0.00 35.56 2.41
252 253 1.676057 CGCGTGCGGAAAAATGTAAA 58.324 45.000 6.30 0.00 35.56 2.01
253 254 2.246789 CGCGTGCGGAAAAATGTAAAT 58.753 42.857 6.30 0.00 35.56 1.40
254 255 3.418094 CGCGTGCGGAAAAATGTAAATA 58.582 40.909 6.30 0.00 35.56 1.40
255 256 3.846896 CGCGTGCGGAAAAATGTAAATAA 59.153 39.130 6.30 0.00 35.56 1.40
256 257 4.321217 CGCGTGCGGAAAAATGTAAATAAA 59.679 37.500 6.30 0.00 35.56 1.40
257 258 5.164177 CGCGTGCGGAAAAATGTAAATAAAA 60.164 36.000 6.30 0.00 35.56 1.52
258 259 6.453134 CGCGTGCGGAAAAATGTAAATAAAAT 60.453 34.615 6.30 0.00 35.56 1.82
259 260 7.253354 CGCGTGCGGAAAAATGTAAATAAAATA 60.253 33.333 6.30 0.00 35.56 1.40
260 261 8.373992 GCGTGCGGAAAAATGTAAATAAAATAA 58.626 29.630 0.00 0.00 0.00 1.40
309 310 0.318120 CCAAGTGATTGTTGGGTGGC 59.682 55.000 0.00 0.00 40.83 5.01
310 311 1.331214 CAAGTGATTGTTGGGTGGCT 58.669 50.000 0.00 0.00 0.00 4.75
311 312 1.270550 CAAGTGATTGTTGGGTGGCTC 59.729 52.381 0.00 0.00 0.00 4.70
312 313 0.251341 AGTGATTGTTGGGTGGCTCC 60.251 55.000 0.00 0.00 0.00 4.70
335 336 3.308626 GGAGCCCTCCTCAACTAGT 57.691 57.895 7.08 0.00 46.16 2.57
336 337 1.574263 GGAGCCCTCCTCAACTAGTT 58.426 55.000 1.12 1.12 46.16 2.24
337 338 1.208293 GGAGCCCTCCTCAACTAGTTG 59.792 57.143 26.60 26.60 46.16 3.16
338 339 0.615850 AGCCCTCCTCAACTAGTTGC 59.384 55.000 27.49 15.67 40.24 4.17
339 340 0.393132 GCCCTCCTCAACTAGTTGCC 60.393 60.000 27.49 8.22 40.24 4.52
340 341 1.280457 CCCTCCTCAACTAGTTGCCT 58.720 55.000 27.49 0.00 40.24 4.75
341 342 2.467880 CCCTCCTCAACTAGTTGCCTA 58.532 52.381 27.49 14.85 40.24 3.93
342 343 2.432510 CCCTCCTCAACTAGTTGCCTAG 59.567 54.545 27.49 21.52 45.27 3.02
343 344 2.432510 CCTCCTCAACTAGTTGCCTAGG 59.567 54.545 27.49 26.40 44.25 3.02
344 345 3.366396 CTCCTCAACTAGTTGCCTAGGA 58.634 50.000 29.13 29.13 44.25 2.94
345 346 3.769844 CTCCTCAACTAGTTGCCTAGGAA 59.230 47.826 29.97 20.03 44.25 3.36
346 347 4.164981 TCCTCAACTAGTTGCCTAGGAAA 58.835 43.478 29.12 16.02 44.25 3.13
347 348 4.020485 TCCTCAACTAGTTGCCTAGGAAAC 60.020 45.833 29.12 23.61 44.25 2.78
348 349 4.262894 CCTCAACTAGTTGCCTAGGAAACA 60.263 45.833 30.74 17.23 44.25 2.83
349 350 5.491982 CTCAACTAGTTGCCTAGGAAACAT 58.508 41.667 30.74 19.08 44.25 2.71
350 351 5.876357 TCAACTAGTTGCCTAGGAAACATT 58.124 37.500 30.74 19.66 44.25 2.71
351 352 6.303839 TCAACTAGTTGCCTAGGAAACATTT 58.696 36.000 30.74 18.39 44.25 2.32
352 353 6.430000 TCAACTAGTTGCCTAGGAAACATTTC 59.570 38.462 30.74 7.15 44.25 2.17
353 354 6.128138 ACTAGTTGCCTAGGAAACATTTCT 57.872 37.500 30.74 14.72 44.25 2.52
354 355 6.174049 ACTAGTTGCCTAGGAAACATTTCTC 58.826 40.000 30.74 5.70 44.25 2.87
355 356 5.248380 AGTTGCCTAGGAAACATTTCTCT 57.752 39.130 30.74 8.77 36.14 3.10
360 361 5.164233 GCCTAGGAAACATTTCTCTTTTGC 58.836 41.667 14.75 0.00 37.35 3.68
371 372 1.087501 CTCTTTTGCTTAGGGCCGTC 58.912 55.000 0.00 0.00 40.92 4.79
375 376 1.243902 TTTGCTTAGGGCCGTCTTTG 58.756 50.000 0.00 0.00 40.92 2.77
386 387 1.099689 CCGTCTTTGTGTTTGTGGGT 58.900 50.000 0.00 0.00 0.00 4.51
392 393 5.278604 GTCTTTGTGTTTGTGGGTTGTATC 58.721 41.667 0.00 0.00 0.00 2.24
489 492 1.522258 CGCACTTGGACAAAAACATGC 59.478 47.619 0.00 0.00 0.00 4.06
490 493 1.866601 GCACTTGGACAAAAACATGCC 59.133 47.619 0.00 0.00 0.00 4.40
491 494 2.482864 CACTTGGACAAAAACATGCCC 58.517 47.619 0.00 0.00 0.00 5.36
492 495 2.114616 ACTTGGACAAAAACATGCCCA 58.885 42.857 0.00 0.00 30.28 5.36
493 496 2.503356 ACTTGGACAAAAACATGCCCAA 59.497 40.909 0.00 0.00 40.04 4.12
494 497 2.906691 TGGACAAAAACATGCCCAAG 57.093 45.000 0.00 0.00 29.12 3.61
495 498 2.114616 TGGACAAAAACATGCCCAAGT 58.885 42.857 0.00 0.00 29.12 3.16
496 499 2.158986 TGGACAAAAACATGCCCAAGTG 60.159 45.455 0.00 0.00 29.12 3.16
497 500 2.158971 GGACAAAAACATGCCCAAGTGT 60.159 45.455 0.00 0.00 0.00 3.55
498 501 3.530535 GACAAAAACATGCCCAAGTGTT 58.469 40.909 0.00 0.00 40.06 3.32
502 505 2.618442 AACATGCCCAAGTGTTTTGG 57.382 45.000 0.00 0.00 35.13 3.28
503 506 1.786937 ACATGCCCAAGTGTTTTGGA 58.213 45.000 7.48 0.00 42.06 3.53
504 507 1.412343 ACATGCCCAAGTGTTTTGGAC 59.588 47.619 7.48 0.00 42.06 4.02
505 508 1.411977 CATGCCCAAGTGTTTTGGACA 59.588 47.619 7.48 2.52 42.06 4.02
506 509 1.561643 TGCCCAAGTGTTTTGGACAA 58.438 45.000 7.48 0.00 42.06 3.18
507 510 1.902508 TGCCCAAGTGTTTTGGACAAA 59.097 42.857 7.48 0.00 42.06 2.83
508 511 2.303022 TGCCCAAGTGTTTTGGACAAAA 59.697 40.909 7.48 6.14 42.06 2.44
509 512 3.244561 TGCCCAAGTGTTTTGGACAAAAA 60.245 39.130 11.39 0.00 41.37 1.94
519 522 4.974368 TTTGGACAAAAACATGAGTCGT 57.026 36.364 0.00 0.00 31.93 4.34
520 523 4.974368 TTGGACAAAAACATGAGTCGTT 57.026 36.364 0.00 0.00 31.93 3.85
521 524 4.974368 TGGACAAAAACATGAGTCGTTT 57.026 36.364 0.00 0.00 38.19 3.60
522 525 4.915704 TGGACAAAAACATGAGTCGTTTC 58.084 39.130 0.00 0.00 35.57 2.78
523 526 4.201970 TGGACAAAAACATGAGTCGTTTCC 60.202 41.667 0.00 0.00 35.57 3.13
524 527 4.287720 GACAAAAACATGAGTCGTTTCCC 58.712 43.478 0.00 0.00 35.57 3.97
525 528 3.951680 ACAAAAACATGAGTCGTTTCCCT 59.048 39.130 0.00 0.00 35.57 4.20
526 529 4.036380 ACAAAAACATGAGTCGTTTCCCTC 59.964 41.667 0.00 0.00 35.57 4.30
527 530 3.485463 AAACATGAGTCGTTTCCCTCA 57.515 42.857 0.00 0.00 41.61 3.86
528 531 3.485463 AACATGAGTCGTTTCCCTCAA 57.515 42.857 0.00 0.00 40.81 3.02
529 532 3.485463 ACATGAGTCGTTTCCCTCAAA 57.515 42.857 0.00 0.00 40.81 2.69
530 533 3.815809 ACATGAGTCGTTTCCCTCAAAA 58.184 40.909 0.00 0.00 40.81 2.44
531 534 4.204012 ACATGAGTCGTTTCCCTCAAAAA 58.796 39.130 0.00 0.00 40.81 1.94
740 747 1.835693 GGCCTCCCTCCTCTCAATG 59.164 63.158 0.00 0.00 0.00 2.82
762 769 4.081198 TGTCACTGTTTCCTTGGCAAAAAT 60.081 37.500 0.00 0.00 0.00 1.82
771 778 5.975693 TCCTTGGCAAAAATAGAACGAAT 57.024 34.783 0.00 0.00 0.00 3.34
772 779 6.339587 TCCTTGGCAAAAATAGAACGAATT 57.660 33.333 0.00 0.00 0.00 2.17
774 781 8.062065 TCCTTGGCAAAAATAGAACGAATTAT 57.938 30.769 0.00 0.00 0.00 1.28
775 782 8.527810 TCCTTGGCAAAAATAGAACGAATTATT 58.472 29.630 0.00 0.00 0.00 1.40
961 988 4.328712 GGTCGTTTGATTGTTGTTTTTGCT 59.671 37.500 0.00 0.00 0.00 3.91
965 992 6.073548 TCGTTTGATTGTTGTTTTTGCTTGTT 60.074 30.769 0.00 0.00 0.00 2.83
969 996 3.820777 TGTTGTTTTTGCTTGTTTGCC 57.179 38.095 0.00 0.00 0.00 4.52
992 1019 1.254026 TTCAGAGTCGTTCCGTGGAT 58.746 50.000 0.00 0.00 0.00 3.41
1110 1140 3.771160 ATCCGCGCGACCCTCTTT 61.771 61.111 34.63 3.03 0.00 2.52
1164 1194 0.798776 CGGTGAAGCAGGTGATCAAC 59.201 55.000 1.26 1.26 0.00 3.18
1203 1233 5.840243 TTGAATGGGAAGAGCATTATGTG 57.160 39.130 0.00 0.00 0.00 3.21
1326 1356 2.951458 GGAAAAGGCCACCGTTCG 59.049 61.111 5.01 0.00 0.00 3.95
1353 1383 1.188219 TCACGCTGAGGAAGGAGCTT 61.188 55.000 0.00 0.00 32.70 3.74
1812 2495 2.679342 TTTGATCGGAGGCCTGGGG 61.679 63.158 12.00 0.00 0.00 4.96
1944 2703 1.934525 CTGAGTGCTGTCATGATGCTC 59.065 52.381 19.54 16.72 0.00 4.26
1986 2745 2.690778 GGCAGACCGCATCCACAAC 61.691 63.158 0.00 0.00 45.17 3.32
2091 2858 4.201950 GCAGTTTGCGGTCATATCTGATTT 60.202 41.667 0.00 0.00 31.71 2.17
2103 2874 5.366477 TCATATCTGATTTAGCACCACCTCA 59.634 40.000 0.00 0.00 0.00 3.86
2114 2885 2.608752 GCACCACCTCATGCTTTTTCTG 60.609 50.000 0.00 0.00 38.84 3.02
2151 2922 6.171921 TCCCCAAATTTTGTTTGCTATCATG 58.828 36.000 8.26 0.00 0.00 3.07
2189 2960 6.860080 AGTTAAGACCGTCGAAGAATAATCA 58.140 36.000 0.00 0.00 39.69 2.57
2197 2968 6.201044 ACCGTCGAAGAATAATCATCACATTC 59.799 38.462 0.00 0.00 39.69 2.67
2214 2985 7.403312 TCACATTCTTTGTTCTTGGAAAAGA 57.597 32.000 0.00 0.00 37.97 2.52
2224 2995 6.811954 TGTTCTTGGAAAAGATTTACCAACC 58.188 36.000 0.00 0.00 37.46 3.77
2227 2998 7.669089 TCTTGGAAAAGATTTACCAACCTTT 57.331 32.000 0.00 0.00 37.46 3.11
2326 3125 4.141914 ACTGGATTTCGATCTGTTACCTCC 60.142 45.833 0.00 0.00 0.00 4.30
2346 3145 1.275291 CGTTGCTGTTCCCCTCTCTTA 59.725 52.381 0.00 0.00 0.00 2.10
2351 3150 2.303311 GCTGTTCCCCTCTCTTAAGTGT 59.697 50.000 1.63 0.00 0.00 3.55
2352 3151 3.866449 GCTGTTCCCCTCTCTTAAGTGTG 60.866 52.174 1.63 1.07 0.00 3.82
2353 3152 3.578716 CTGTTCCCCTCTCTTAAGTGTGA 59.421 47.826 1.63 0.00 0.00 3.58
2354 3153 4.168101 TGTTCCCCTCTCTTAAGTGTGAT 58.832 43.478 1.63 0.00 0.00 3.06
2355 3154 4.597507 TGTTCCCCTCTCTTAAGTGTGATT 59.402 41.667 1.63 0.00 0.00 2.57
2367 3166 1.001181 AGTGTGATTTTGGTGCCATGC 59.999 47.619 0.00 0.00 0.00 4.06
2369 3168 0.737019 GTGATTTTGGTGCCATGCGG 60.737 55.000 0.00 0.00 0.00 5.69
2434 3235 2.957006 TCTCTAATGCCCTCCTACGTTC 59.043 50.000 0.00 0.00 0.00 3.95
2438 3239 0.032017 ATGCCCTCCTACGTTCTCCT 60.032 55.000 0.00 0.00 0.00 3.69
2469 3270 3.390311 ACCAAACCGTATCCTATCCTTCC 59.610 47.826 0.00 0.00 0.00 3.46
2620 3504 3.961480 TCATCGACAACACCTCTGATT 57.039 42.857 0.00 0.00 0.00 2.57
2643 3530 2.427905 GCAGCATGTGCGTGTGTG 60.428 61.111 0.00 0.00 43.99 3.82
2644 3531 3.185082 GCAGCATGTGCGTGTGTGT 62.185 57.895 0.00 0.00 43.99 3.72
2684 3571 5.997129 TGTGATTCTGTGAGAGCATTGTTAA 59.003 36.000 0.00 0.00 0.00 2.01
2790 3677 6.198650 TGGTCTTGAATTTATGTGATGCAG 57.801 37.500 0.00 0.00 0.00 4.41
2839 3726 1.334869 GGATATGAAGCTTGTTGGCCG 59.665 52.381 2.10 0.00 0.00 6.13
2846 3733 1.598130 GCTTGTTGGCCGTCACTCT 60.598 57.895 0.00 0.00 0.00 3.24
2910 3798 9.153479 ACAAAATAGCATGGCCCTTAAAATATA 57.847 29.630 0.00 0.00 0.00 0.86
2919 3807 9.975218 CATGGCCCTTAAAATATACTATTAGGT 57.025 33.333 0.00 0.00 0.00 3.08
2922 3810 8.737175 GGCCCTTAAAATATACTATTAGGTTGC 58.263 37.037 0.00 0.00 0.00 4.17
2923 3811 9.516546 GCCCTTAAAATATACTATTAGGTTGCT 57.483 33.333 0.00 0.00 0.00 3.91
2931 3819 9.894783 AATATACTATTAGGTTGCTATATCGCG 57.105 33.333 0.00 0.00 0.00 5.87
2974 3862 7.409661 GCGAAACATTGTACACTGAATTTCATG 60.410 37.037 19.02 8.29 0.00 3.07
2975 3863 7.060979 CGAAACATTGTACACTGAATTTCATGG 59.939 37.037 19.02 4.87 0.00 3.66
2976 3864 7.523293 AACATTGTACACTGAATTTCATGGA 57.477 32.000 19.02 0.00 0.00 3.41
2977 3865 7.523293 ACATTGTACACTGAATTTCATGGAA 57.477 32.000 19.02 0.00 0.00 3.53
2978 3866 8.125978 ACATTGTACACTGAATTTCATGGAAT 57.874 30.769 19.02 0.00 0.00 3.01
2979 3867 8.246180 ACATTGTACACTGAATTTCATGGAATC 58.754 33.333 19.02 0.00 0.00 2.52
2980 3868 6.421377 TGTACACTGAATTTCATGGAATCG 57.579 37.500 0.00 0.00 0.00 3.34
2981 3869 5.937540 TGTACACTGAATTTCATGGAATCGT 59.062 36.000 0.00 0.00 0.00 3.73
2982 3870 7.100409 TGTACACTGAATTTCATGGAATCGTA 58.900 34.615 0.00 0.00 0.00 3.43
2983 3871 7.768582 TGTACACTGAATTTCATGGAATCGTAT 59.231 33.333 0.00 0.00 0.00 3.06
2984 3872 7.019774 ACACTGAATTTCATGGAATCGTATG 57.980 36.000 0.00 0.12 0.00 2.39
2985 3873 6.823182 ACACTGAATTTCATGGAATCGTATGA 59.177 34.615 0.00 0.00 0.00 2.15
3052 3940 4.254492 GGATTTAGATCTTGGCGGTATCC 58.746 47.826 0.00 0.20 32.66 2.59
3053 3941 4.262894 GGATTTAGATCTTGGCGGTATCCA 60.263 45.833 0.00 0.00 32.66 3.41
3067 3955 4.557695 GCGGTATCCAGAGACATTCTACTG 60.558 50.000 0.00 0.00 33.83 2.74
3068 3956 4.580995 CGGTATCCAGAGACATTCTACTGT 59.419 45.833 0.00 0.00 33.83 3.55
3082 3970 3.302161 TCTACTGTTGCCCGGTACATAT 58.698 45.455 0.00 0.00 33.63 1.78
3088 3976 2.812011 GTTGCCCGGTACATATGAATCC 59.188 50.000 10.38 7.51 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.066764 GTCTCCTAGGTGAGTAGTAGCAAAG 59.933 48.000 13.84 0.00 33.93 2.77
1 2 4.948621 GTCTCCTAGGTGAGTAGTAGCAAA 59.051 45.833 13.84 0.00 33.93 3.68
2 3 4.525024 GTCTCCTAGGTGAGTAGTAGCAA 58.475 47.826 13.84 0.00 33.93 3.91
3 4 3.117963 GGTCTCCTAGGTGAGTAGTAGCA 60.118 52.174 13.84 0.00 33.93 3.49
4 5 3.136992 AGGTCTCCTAGGTGAGTAGTAGC 59.863 52.174 13.84 1.84 33.93 3.58
17 18 5.222278 AGGATTCAAACCTAGGTCTCCTA 57.778 43.478 16.64 0.32 35.84 2.94
18 19 4.081695 AGGATTCAAACCTAGGTCTCCT 57.918 45.455 16.64 17.30 35.84 3.69
41 42 2.182842 GCGCACATGAGGATCCACC 61.183 63.158 15.82 5.84 39.35 4.61
42 43 0.745845 AAGCGCACATGAGGATCCAC 60.746 55.000 15.82 8.65 0.00 4.02
43 44 0.462581 GAAGCGCACATGAGGATCCA 60.463 55.000 15.82 0.00 0.00 3.41
44 45 0.462581 TGAAGCGCACATGAGGATCC 60.463 55.000 11.47 2.48 0.00 3.36
45 46 1.372582 TTGAAGCGCACATGAGGATC 58.627 50.000 11.47 0.00 0.00 3.36
46 47 1.825090 TTTGAAGCGCACATGAGGAT 58.175 45.000 11.47 0.00 0.00 3.24
47 48 1.536766 CTTTTGAAGCGCACATGAGGA 59.463 47.619 11.47 0.00 0.00 3.71
48 49 1.401931 CCTTTTGAAGCGCACATGAGG 60.402 52.381 11.47 14.60 0.00 3.86
49 50 1.536766 TCCTTTTGAAGCGCACATGAG 59.463 47.619 11.47 9.89 0.00 2.90
50 51 1.536766 CTCCTTTTGAAGCGCACATGA 59.463 47.619 11.47 3.79 0.00 3.07
51 52 1.973138 CTCCTTTTGAAGCGCACATG 58.027 50.000 11.47 0.00 0.00 3.21
52 53 0.242017 GCTCCTTTTGAAGCGCACAT 59.758 50.000 11.47 0.00 0.00 3.21
53 54 1.100463 TGCTCCTTTTGAAGCGCACA 61.100 50.000 11.47 6.70 31.47 4.57
54 55 0.661483 GTGCTCCTTTTGAAGCGCAC 60.661 55.000 11.47 3.52 42.65 5.34
55 56 1.654220 GTGCTCCTTTTGAAGCGCA 59.346 52.632 11.47 0.00 37.67 6.09
56 57 1.441016 CGTGCTCCTTTTGAAGCGC 60.441 57.895 0.00 0.00 34.81 5.92
57 58 0.307760 AACGTGCTCCTTTTGAAGCG 59.692 50.000 0.00 0.00 0.00 4.68
58 59 2.492019 AAACGTGCTCCTTTTGAAGC 57.508 45.000 0.00 0.00 0.00 3.86
76 77 2.693074 AGCAAGCTCGAAAAGGGAAAAA 59.307 40.909 0.00 0.00 0.00 1.94
77 78 2.306847 AGCAAGCTCGAAAAGGGAAAA 58.693 42.857 0.00 0.00 0.00 2.29
78 79 1.981256 AGCAAGCTCGAAAAGGGAAA 58.019 45.000 0.00 0.00 0.00 3.13
79 80 1.880027 GAAGCAAGCTCGAAAAGGGAA 59.120 47.619 0.00 0.00 0.00 3.97
80 81 1.072331 AGAAGCAAGCTCGAAAAGGGA 59.928 47.619 0.00 0.00 0.00 4.20
81 82 1.466558 GAGAAGCAAGCTCGAAAAGGG 59.533 52.381 0.00 0.00 0.00 3.95
82 83 2.890442 GAGAAGCAAGCTCGAAAAGG 57.110 50.000 0.00 0.00 0.00 3.11
89 90 1.691215 CTTCCGCGAGAAGCAAGCTC 61.691 60.000 19.55 0.00 45.38 4.09
90 91 1.739562 CTTCCGCGAGAAGCAAGCT 60.740 57.895 19.55 0.00 45.38 3.74
91 92 2.781300 CTTCCGCGAGAAGCAAGC 59.219 61.111 19.55 0.00 45.38 4.01
97 98 0.321210 TGGATTTGCTTCCGCGAGAA 60.321 50.000 8.23 8.88 38.74 2.87
98 99 0.107703 ATGGATTTGCTTCCGCGAGA 60.108 50.000 8.23 0.00 38.74 4.04
99 100 0.028505 CATGGATTTGCTTCCGCGAG 59.971 55.000 8.23 0.00 38.74 5.03
100 101 1.375853 CCATGGATTTGCTTCCGCGA 61.376 55.000 8.23 0.00 38.74 5.87
101 102 1.064621 CCATGGATTTGCTTCCGCG 59.935 57.895 5.56 0.00 38.74 6.46
102 103 1.227060 GCCATGGATTTGCTTCCGC 60.227 57.895 18.40 0.00 38.74 5.54
103 104 0.383231 GAGCCATGGATTTGCTTCCG 59.617 55.000 18.40 0.00 38.74 4.30
104 105 0.749049 GGAGCCATGGATTTGCTTCC 59.251 55.000 18.40 0.72 34.99 3.46
105 106 0.749049 GGGAGCCATGGATTTGCTTC 59.251 55.000 18.40 2.92 34.99 3.86
106 107 1.039233 CGGGAGCCATGGATTTGCTT 61.039 55.000 18.40 0.00 34.99 3.91
107 108 1.454479 CGGGAGCCATGGATTTGCT 60.454 57.895 18.40 4.16 38.24 3.91
108 109 1.037030 TTCGGGAGCCATGGATTTGC 61.037 55.000 18.40 5.05 0.00 3.68
109 110 1.027357 CTTCGGGAGCCATGGATTTG 58.973 55.000 18.40 3.04 0.00 2.32
110 111 0.106519 CCTTCGGGAGCCATGGATTT 60.107 55.000 18.40 0.00 37.25 2.17
111 112 1.533711 CCTTCGGGAGCCATGGATT 59.466 57.895 18.40 1.53 37.25 3.01
112 113 3.244616 CCTTCGGGAGCCATGGAT 58.755 61.111 18.40 10.08 37.25 3.41
122 123 0.601057 AACGCATTTTTCCCTTCGGG 59.399 50.000 0.00 0.00 46.11 5.14
123 124 2.432206 AAACGCATTTTTCCCTTCGG 57.568 45.000 0.00 0.00 0.00 4.30
156 157 6.238648 CCGGTCTTTCTTAGCTTCTTGAAAAA 60.239 38.462 0.00 0.00 0.00 1.94
157 158 5.238650 CCGGTCTTTCTTAGCTTCTTGAAAA 59.761 40.000 0.00 0.00 0.00 2.29
158 159 4.755123 CCGGTCTTTCTTAGCTTCTTGAAA 59.245 41.667 0.00 0.00 0.00 2.69
159 160 4.202326 ACCGGTCTTTCTTAGCTTCTTGAA 60.202 41.667 0.00 0.00 0.00 2.69
160 161 3.323979 ACCGGTCTTTCTTAGCTTCTTGA 59.676 43.478 0.00 0.00 0.00 3.02
161 162 3.433615 CACCGGTCTTTCTTAGCTTCTTG 59.566 47.826 2.59 0.00 0.00 3.02
162 163 3.323979 TCACCGGTCTTTCTTAGCTTCTT 59.676 43.478 2.59 0.00 0.00 2.52
163 164 2.897969 TCACCGGTCTTTCTTAGCTTCT 59.102 45.455 2.59 0.00 0.00 2.85
164 165 3.314541 TCACCGGTCTTTCTTAGCTTC 57.685 47.619 2.59 0.00 0.00 3.86
165 166 3.764237 TTCACCGGTCTTTCTTAGCTT 57.236 42.857 2.59 0.00 0.00 3.74
166 167 3.764237 TTTCACCGGTCTTTCTTAGCT 57.236 42.857 2.59 0.00 0.00 3.32
167 168 4.823790 TTTTTCACCGGTCTTTCTTAGC 57.176 40.909 2.59 0.00 0.00 3.09
185 186 3.440872 GGGGTTTTCGGCTTTTTGTTTTT 59.559 39.130 0.00 0.00 0.00 1.94
186 187 3.011119 GGGGTTTTCGGCTTTTTGTTTT 58.989 40.909 0.00 0.00 0.00 2.43
187 188 2.634600 GGGGTTTTCGGCTTTTTGTTT 58.365 42.857 0.00 0.00 0.00 2.83
188 189 1.471851 CGGGGTTTTCGGCTTTTTGTT 60.472 47.619 0.00 0.00 0.00 2.83
189 190 0.103390 CGGGGTTTTCGGCTTTTTGT 59.897 50.000 0.00 0.00 0.00 2.83
190 191 0.386113 TCGGGGTTTTCGGCTTTTTG 59.614 50.000 0.00 0.00 0.00 2.44
191 192 1.112950 TTCGGGGTTTTCGGCTTTTT 58.887 45.000 0.00 0.00 0.00 1.94
192 193 1.112950 TTTCGGGGTTTTCGGCTTTT 58.887 45.000 0.00 0.00 0.00 2.27
193 194 1.112950 TTTTCGGGGTTTTCGGCTTT 58.887 45.000 0.00 0.00 0.00 3.51
194 195 1.112950 TTTTTCGGGGTTTTCGGCTT 58.887 45.000 0.00 0.00 0.00 4.35
195 196 0.386476 GTTTTTCGGGGTTTTCGGCT 59.614 50.000 0.00 0.00 0.00 5.52
196 197 0.598158 GGTTTTTCGGGGTTTTCGGC 60.598 55.000 0.00 0.00 0.00 5.54
197 198 0.745468 TGGTTTTTCGGGGTTTTCGG 59.255 50.000 0.00 0.00 0.00 4.30
198 199 2.295070 AGATGGTTTTTCGGGGTTTTCG 59.705 45.455 0.00 0.00 0.00 3.46
199 200 5.456548 TTAGATGGTTTTTCGGGGTTTTC 57.543 39.130 0.00 0.00 0.00 2.29
200 201 5.873146 TTTAGATGGTTTTTCGGGGTTTT 57.127 34.783 0.00 0.00 0.00 2.43
201 202 5.873146 TTTTAGATGGTTTTTCGGGGTTT 57.127 34.783 0.00 0.00 0.00 3.27
202 203 5.740803 GCTTTTTAGATGGTTTTTCGGGGTT 60.741 40.000 0.00 0.00 0.00 4.11
203 204 4.262292 GCTTTTTAGATGGTTTTTCGGGGT 60.262 41.667 0.00 0.00 0.00 4.95
204 205 4.242475 GCTTTTTAGATGGTTTTTCGGGG 58.758 43.478 0.00 0.00 0.00 5.73
205 206 4.242475 GGCTTTTTAGATGGTTTTTCGGG 58.758 43.478 0.00 0.00 0.00 5.14
206 207 4.877282 TGGCTTTTTAGATGGTTTTTCGG 58.123 39.130 0.00 0.00 0.00 4.30
207 208 6.836577 TTTGGCTTTTTAGATGGTTTTTCG 57.163 33.333 0.00 0.00 0.00 3.46
208 209 7.414436 GGTTTTGGCTTTTTAGATGGTTTTTC 58.586 34.615 0.00 0.00 0.00 2.29
209 210 6.037720 CGGTTTTGGCTTTTTAGATGGTTTTT 59.962 34.615 0.00 0.00 0.00 1.94
210 211 5.525745 CGGTTTTGGCTTTTTAGATGGTTTT 59.474 36.000 0.00 0.00 0.00 2.43
211 212 5.053811 CGGTTTTGGCTTTTTAGATGGTTT 58.946 37.500 0.00 0.00 0.00 3.27
212 213 4.627058 CGGTTTTGGCTTTTTAGATGGTT 58.373 39.130 0.00 0.00 0.00 3.67
213 214 3.554129 GCGGTTTTGGCTTTTTAGATGGT 60.554 43.478 0.00 0.00 0.00 3.55
214 215 2.993220 GCGGTTTTGGCTTTTTAGATGG 59.007 45.455 0.00 0.00 0.00 3.51
215 216 2.661195 CGCGGTTTTGGCTTTTTAGATG 59.339 45.455 0.00 0.00 0.00 2.90
216 217 2.295070 ACGCGGTTTTGGCTTTTTAGAT 59.705 40.909 12.47 0.00 0.00 1.98
217 218 1.677052 ACGCGGTTTTGGCTTTTTAGA 59.323 42.857 12.47 0.00 0.00 2.10
218 219 1.784283 CACGCGGTTTTGGCTTTTTAG 59.216 47.619 12.47 0.00 0.00 1.85
219 220 1.841450 CACGCGGTTTTGGCTTTTTA 58.159 45.000 12.47 0.00 0.00 1.52
220 221 1.425267 GCACGCGGTTTTGGCTTTTT 61.425 50.000 12.47 0.00 0.00 1.94
221 222 1.880796 GCACGCGGTTTTGGCTTTT 60.881 52.632 12.47 0.00 0.00 2.27
222 223 2.279186 GCACGCGGTTTTGGCTTT 60.279 55.556 12.47 0.00 0.00 3.51
223 224 4.622456 CGCACGCGGTTTTGGCTT 62.622 61.111 12.47 0.00 35.56 4.35
233 234 1.676057 TTTACATTTTTCCGCACGCG 58.324 45.000 3.53 3.53 39.44 6.01
234 235 5.748872 TTTATTTACATTTTTCCGCACGC 57.251 34.783 0.00 0.00 0.00 5.34
246 247 9.649316 TCCCTCCGGATTTTATTTTATTTACAT 57.351 29.630 3.57 0.00 31.13 2.29
247 248 9.127277 CTCCCTCCGGATTTTATTTTATTTACA 57.873 33.333 3.57 0.00 37.60 2.41
248 249 8.080417 GCTCCCTCCGGATTTTATTTTATTTAC 58.920 37.037 3.57 0.00 37.60 2.01
249 250 7.040961 CGCTCCCTCCGGATTTTATTTTATTTA 60.041 37.037 3.57 0.00 37.60 1.40
250 251 6.238925 CGCTCCCTCCGGATTTTATTTTATTT 60.239 38.462 3.57 0.00 37.60 1.40
251 252 5.240844 CGCTCCCTCCGGATTTTATTTTATT 59.759 40.000 3.57 0.00 37.60 1.40
252 253 4.760204 CGCTCCCTCCGGATTTTATTTTAT 59.240 41.667 3.57 0.00 37.60 1.40
253 254 4.131596 CGCTCCCTCCGGATTTTATTTTA 58.868 43.478 3.57 0.00 37.60 1.52
254 255 2.949644 CGCTCCCTCCGGATTTTATTTT 59.050 45.455 3.57 0.00 37.60 1.82
255 256 2.572290 CGCTCCCTCCGGATTTTATTT 58.428 47.619 3.57 0.00 37.60 1.40
256 257 1.814248 GCGCTCCCTCCGGATTTTATT 60.814 52.381 3.57 0.00 37.60 1.40
257 258 0.250338 GCGCTCCCTCCGGATTTTAT 60.250 55.000 3.57 0.00 37.60 1.40
258 259 1.145377 GCGCTCCCTCCGGATTTTA 59.855 57.895 3.57 0.00 37.60 1.52
259 260 2.124695 GCGCTCCCTCCGGATTTT 60.125 61.111 3.57 0.00 37.60 1.82
260 261 4.176752 GGCGCTCCCTCCGGATTT 62.177 66.667 3.57 0.00 37.60 2.17
290 291 0.318120 GCCACCCAACAATCACTTGG 59.682 55.000 0.00 0.00 38.37 3.61
291 292 1.270550 GAGCCACCCAACAATCACTTG 59.729 52.381 0.00 0.00 38.39 3.16
292 293 1.620822 GAGCCACCCAACAATCACTT 58.379 50.000 0.00 0.00 0.00 3.16
293 294 0.251341 GGAGCCACCCAACAATCACT 60.251 55.000 0.00 0.00 0.00 3.41
294 295 2.267045 GGAGCCACCCAACAATCAC 58.733 57.895 0.00 0.00 0.00 3.06
295 296 4.841441 GGAGCCACCCAACAATCA 57.159 55.556 0.00 0.00 0.00 2.57
317 318 4.634731 GCAACTAGTTGAGGAGGGCTCC 62.635 59.091 34.43 12.28 43.91 4.70
318 319 1.406205 GCAACTAGTTGAGGAGGGCTC 60.406 57.143 34.43 12.95 42.93 4.70
319 320 0.615850 GCAACTAGTTGAGGAGGGCT 59.384 55.000 34.43 0.00 42.93 5.19
320 321 0.393132 GGCAACTAGTTGAGGAGGGC 60.393 60.000 34.43 19.11 42.93 5.19
321 322 3.863407 GGCAACTAGTTGAGGAGGG 57.137 57.895 34.43 10.73 42.93 4.30
332 333 6.374417 AGAGAAATGTTTCCTAGGCAACTA 57.626 37.500 22.44 11.22 42.55 2.24
333 334 5.248380 AGAGAAATGTTTCCTAGGCAACT 57.752 39.130 22.44 5.17 44.12 3.16
334 335 5.966742 AAGAGAAATGTTTCCTAGGCAAC 57.033 39.130 16.47 16.47 37.92 4.17
335 336 6.738453 GCAAAAGAGAAATGTTTCCTAGGCAA 60.738 38.462 2.96 0.00 37.92 4.52
336 337 5.278957 GCAAAAGAGAAATGTTTCCTAGGCA 60.279 40.000 2.96 0.00 37.92 4.75
337 338 5.047731 AGCAAAAGAGAAATGTTTCCTAGGC 60.048 40.000 2.96 0.00 37.92 3.93
338 339 6.581171 AGCAAAAGAGAAATGTTTCCTAGG 57.419 37.500 0.82 0.82 37.92 3.02
339 340 8.239998 CCTAAGCAAAAGAGAAATGTTTCCTAG 58.760 37.037 2.04 0.00 37.92 3.02
340 341 7.176690 CCCTAAGCAAAAGAGAAATGTTTCCTA 59.823 37.037 2.04 0.00 37.92 2.94
341 342 6.015095 CCCTAAGCAAAAGAGAAATGTTTCCT 60.015 38.462 2.04 0.00 37.92 3.36
342 343 6.159293 CCCTAAGCAAAAGAGAAATGTTTCC 58.841 40.000 2.04 0.00 37.92 3.13
343 344 5.635280 GCCCTAAGCAAAAGAGAAATGTTTC 59.365 40.000 0.00 0.00 42.97 2.78
344 345 5.511373 GGCCCTAAGCAAAAGAGAAATGTTT 60.511 40.000 0.00 0.00 46.50 2.83
345 346 4.021104 GGCCCTAAGCAAAAGAGAAATGTT 60.021 41.667 0.00 0.00 46.50 2.71
346 347 3.511540 GGCCCTAAGCAAAAGAGAAATGT 59.488 43.478 0.00 0.00 46.50 2.71
347 348 3.428045 CGGCCCTAAGCAAAAGAGAAATG 60.428 47.826 0.00 0.00 46.50 2.32
348 349 2.755103 CGGCCCTAAGCAAAAGAGAAAT 59.245 45.455 0.00 0.00 46.50 2.17
349 350 2.159382 CGGCCCTAAGCAAAAGAGAAA 58.841 47.619 0.00 0.00 46.50 2.52
350 351 1.073284 ACGGCCCTAAGCAAAAGAGAA 59.927 47.619 0.00 0.00 46.50 2.87
351 352 0.690762 ACGGCCCTAAGCAAAAGAGA 59.309 50.000 0.00 0.00 46.50 3.10
352 353 1.087501 GACGGCCCTAAGCAAAAGAG 58.912 55.000 0.00 0.00 46.50 2.85
353 354 0.690762 AGACGGCCCTAAGCAAAAGA 59.309 50.000 0.00 0.00 46.50 2.52
354 355 1.534729 AAGACGGCCCTAAGCAAAAG 58.465 50.000 0.00 0.00 46.50 2.27
355 356 1.611491 CAAAGACGGCCCTAAGCAAAA 59.389 47.619 0.00 0.00 46.50 2.44
360 361 1.892209 AACACAAAGACGGCCCTAAG 58.108 50.000 0.00 0.00 0.00 2.18
371 372 5.299279 AGAGATACAACCCACAAACACAAAG 59.701 40.000 0.00 0.00 0.00 2.77
375 376 4.819630 TCAAGAGATACAACCCACAAACAC 59.180 41.667 0.00 0.00 0.00 3.32
386 387 5.013704 TGGGCTTTTAGGTCAAGAGATACAA 59.986 40.000 0.00 0.00 0.00 2.41
392 393 3.425162 ACTGGGCTTTTAGGTCAAGAG 57.575 47.619 0.00 0.00 0.00 2.85
497 500 5.317733 ACGACTCATGTTTTTGTCCAAAA 57.682 34.783 1.18 1.18 38.40 2.44
498 501 4.974368 ACGACTCATGTTTTTGTCCAAA 57.026 36.364 0.00 0.00 0.00 3.28
499 502 4.974368 AACGACTCATGTTTTTGTCCAA 57.026 36.364 0.00 0.00 0.00 3.53
500 503 4.201970 GGAAACGACTCATGTTTTTGTCCA 60.202 41.667 0.00 0.00 39.51 4.02
501 504 4.287720 GGAAACGACTCATGTTTTTGTCC 58.712 43.478 0.00 0.00 39.51 4.02
502 505 4.036380 AGGGAAACGACTCATGTTTTTGTC 59.964 41.667 0.00 0.00 39.51 3.18
503 506 3.951680 AGGGAAACGACTCATGTTTTTGT 59.048 39.130 0.00 0.00 39.51 2.83
504 507 4.036262 TGAGGGAAACGACTCATGTTTTTG 59.964 41.667 0.00 0.00 39.51 2.44
505 508 4.204012 TGAGGGAAACGACTCATGTTTTT 58.796 39.130 0.00 0.00 39.51 1.94
506 509 3.815809 TGAGGGAAACGACTCATGTTTT 58.184 40.909 0.00 0.00 39.51 2.43
507 510 3.485463 TGAGGGAAACGACTCATGTTT 57.515 42.857 0.00 0.00 41.94 2.83
508 511 3.485463 TTGAGGGAAACGACTCATGTT 57.515 42.857 0.00 0.00 42.73 2.71
509 512 3.485463 TTTGAGGGAAACGACTCATGT 57.515 42.857 0.00 0.00 42.73 3.21
510 513 4.829064 TTTTTGAGGGAAACGACTCATG 57.171 40.909 0.00 0.00 42.73 3.07
533 536 9.442047 AGATAAATCTTCTCGACTCATGTTTTT 57.558 29.630 0.00 0.00 31.97 1.94
534 537 8.877779 CAGATAAATCTTCTCGACTCATGTTTT 58.122 33.333 0.00 0.00 34.22 2.43
535 538 8.037758 ACAGATAAATCTTCTCGACTCATGTTT 58.962 33.333 0.00 0.00 34.22 2.83
536 539 7.551585 ACAGATAAATCTTCTCGACTCATGTT 58.448 34.615 0.00 0.00 34.22 2.71
537 540 7.106439 ACAGATAAATCTTCTCGACTCATGT 57.894 36.000 0.00 0.00 34.22 3.21
538 541 7.490725 ACAACAGATAAATCTTCTCGACTCATG 59.509 37.037 0.00 0.00 34.22 3.07
539 542 7.551585 ACAACAGATAAATCTTCTCGACTCAT 58.448 34.615 0.00 0.00 34.22 2.90
540 543 6.925211 ACAACAGATAAATCTTCTCGACTCA 58.075 36.000 0.00 0.00 34.22 3.41
541 544 7.166804 GCTACAACAGATAAATCTTCTCGACTC 59.833 40.741 0.00 0.00 34.22 3.36
740 747 3.518634 TTTTGCCAAGGAAACAGTGAC 57.481 42.857 0.00 0.00 0.00 3.67
775 782 1.628447 CGATCGGAACCGCGGAAAAA 61.628 55.000 35.90 13.41 39.59 1.94
777 784 2.507547 CGATCGGAACCGCGGAAA 60.508 61.111 35.90 12.21 39.59 3.13
848 855 5.479716 TCATGCATGCATCGATAATCATC 57.520 39.130 30.07 0.00 33.90 2.92
849 856 5.821204 CATCATGCATGCATCGATAATCAT 58.179 37.500 30.07 11.77 33.90 2.45
850 857 5.229921 CATCATGCATGCATCGATAATCA 57.770 39.130 30.07 9.25 33.90 2.57
961 988 2.354510 CGACTCTGAAACAGGCAAACAA 59.645 45.455 0.00 0.00 31.51 2.83
965 992 2.210116 GAACGACTCTGAAACAGGCAA 58.790 47.619 0.00 0.00 31.51 4.52
1059 1089 3.839432 GAGAAGGAGGACGCCCCG 61.839 72.222 0.00 0.00 40.87 5.73
1101 1131 2.732619 ATCGCCGGGAAAGAGGGTC 61.733 63.158 2.18 0.00 0.00 4.46
1164 1194 3.556543 AATTGGCACGCCTGCAACG 62.557 57.895 9.92 7.21 46.28 4.10
1203 1233 2.124695 GGATCAACCTCCGTGCCC 60.125 66.667 0.00 0.00 35.41 5.36
1653 1967 2.925706 TCAGGGTACTTGGCGGCA 60.926 61.111 7.97 7.97 0.00 5.69
1812 2495 0.819259 TGTTGCAGCTGGGAGTCAAC 60.819 55.000 20.67 20.67 37.94 3.18
1878 2637 1.342074 TCTTGCCGGAGATATCAGGG 58.658 55.000 5.05 4.05 0.00 4.45
1962 2721 3.315142 GATGCGGTCTGCCTGGTCA 62.315 63.158 0.00 0.00 45.60 4.02
1986 2745 4.552365 ATGGTGCGGAGGATGGCG 62.552 66.667 0.00 0.00 0.00 5.69
2151 2922 5.741425 GGTCTTAACTAAACCGTGTCAAAC 58.259 41.667 0.00 0.00 0.00 2.93
2189 2960 8.010733 TCTTTTCCAAGAACAAAGAATGTGAT 57.989 30.769 0.00 0.00 42.99 3.06
2197 2968 8.817100 GTTGGTAAATCTTTTCCAAGAACAAAG 58.183 33.333 12.36 0.00 44.63 2.77
2224 2995 8.712285 TTATTATGGACGACCTTGACTAAAAG 57.288 34.615 5.33 0.00 37.04 2.27
2227 2998 8.014070 TGATTATTATGGACGACCTTGACTAA 57.986 34.615 5.33 0.49 37.04 2.24
2326 3125 0.035458 AAGAGAGGGGAACAGCAACG 59.965 55.000 0.00 0.00 0.00 4.10
2346 3145 2.548493 GCATGGCACCAAAATCACACTT 60.548 45.455 0.00 0.00 0.00 3.16
2351 3150 1.184322 ACCGCATGGCACCAAAATCA 61.184 50.000 0.00 0.00 39.70 2.57
2352 3151 0.037419 AACCGCATGGCACCAAAATC 60.037 50.000 0.00 0.00 39.70 2.17
2353 3152 0.320596 CAACCGCATGGCACCAAAAT 60.321 50.000 0.00 0.00 39.70 1.82
2354 3153 1.068753 CAACCGCATGGCACCAAAA 59.931 52.632 0.00 0.00 39.70 2.44
2355 3154 1.680522 AACAACCGCATGGCACCAAA 61.681 50.000 0.00 0.00 39.70 3.28
2367 3166 1.931551 CCAGACACGACAACAACCG 59.068 57.895 0.00 0.00 0.00 4.44
2369 3168 0.304705 CTGCCAGACACGACAACAAC 59.695 55.000 0.00 0.00 0.00 3.32
2434 3235 3.262420 CGGTTTGGTGATTCACTAGGAG 58.738 50.000 16.02 0.76 34.40 3.69
2438 3239 4.468510 AGGATACGGTTTGGTGATTCACTA 59.531 41.667 16.02 7.78 46.39 2.74
2469 3270 2.376808 AAGTGGATGCAAGACGAGAG 57.623 50.000 0.00 0.00 0.00 3.20
2641 3528 0.034896 AGACGGAATCCACACCACAC 59.965 55.000 0.00 0.00 0.00 3.82
2642 3529 0.034756 CAGACGGAATCCACACCACA 59.965 55.000 0.00 0.00 0.00 4.17
2643 3530 0.034896 ACAGACGGAATCCACACCAC 59.965 55.000 0.00 0.00 0.00 4.16
2644 3531 0.034756 CACAGACGGAATCCACACCA 59.965 55.000 0.00 0.00 0.00 4.17
2645 3532 0.320374 TCACAGACGGAATCCACACC 59.680 55.000 0.00 0.00 0.00 4.16
2790 3677 4.640201 TGGAGCAATAAATTGTACTCCTGC 59.360 41.667 20.63 9.69 42.56 4.85
2839 3726 7.548097 TCATTGTCAATTAGTCCTAGAGTGAC 58.452 38.462 0.00 0.00 35.57 3.67
2880 3768 4.183223 AGGGCCATGCTATTTTGTCATA 57.817 40.909 6.18 0.00 0.00 2.15
2881 3769 3.036452 AGGGCCATGCTATTTTGTCAT 57.964 42.857 6.18 0.00 0.00 3.06
2910 3798 4.158025 AGCGCGATATAGCAACCTAATAGT 59.842 41.667 12.10 0.00 36.85 2.12
2931 3819 2.953806 CGCTAATTACGCGCTATAGC 57.046 50.000 15.09 15.09 44.33 2.97
2940 3828 6.676995 CAGTGTACAATGTTTCGCTAATTACG 59.323 38.462 15.00 2.32 0.00 3.18
2942 3830 7.892778 TCAGTGTACAATGTTTCGCTAATTA 57.107 32.000 21.56 0.00 0.00 1.40
2952 3840 7.523293 TCCATGAAATTCAGTGTACAATGTT 57.477 32.000 21.56 9.95 0.00 2.71
2974 3862 3.321497 GCACTCATCCTCATACGATTCC 58.679 50.000 0.00 0.00 0.00 3.01
2975 3863 2.983136 CGCACTCATCCTCATACGATTC 59.017 50.000 0.00 0.00 0.00 2.52
2976 3864 2.288457 CCGCACTCATCCTCATACGATT 60.288 50.000 0.00 0.00 0.00 3.34
2977 3865 1.270826 CCGCACTCATCCTCATACGAT 59.729 52.381 0.00 0.00 0.00 3.73
2978 3866 0.668535 CCGCACTCATCCTCATACGA 59.331 55.000 0.00 0.00 0.00 3.43
2979 3867 0.385751 ACCGCACTCATCCTCATACG 59.614 55.000 0.00 0.00 0.00 3.06
2980 3868 1.539065 CCACCGCACTCATCCTCATAC 60.539 57.143 0.00 0.00 0.00 2.39
2981 3869 0.752658 CCACCGCACTCATCCTCATA 59.247 55.000 0.00 0.00 0.00 2.15
2982 3870 0.977627 TCCACCGCACTCATCCTCAT 60.978 55.000 0.00 0.00 0.00 2.90
2983 3871 1.191489 TTCCACCGCACTCATCCTCA 61.191 55.000 0.00 0.00 0.00 3.86
2984 3872 0.036388 TTTCCACCGCACTCATCCTC 60.036 55.000 0.00 0.00 0.00 3.71
2985 3873 0.400213 TTTTCCACCGCACTCATCCT 59.600 50.000 0.00 0.00 0.00 3.24
3052 3940 3.265791 GGGCAACAGTAGAATGTCTCTG 58.734 50.000 0.00 0.00 34.79 3.35
3053 3941 2.093973 CGGGCAACAGTAGAATGTCTCT 60.094 50.000 0.00 0.00 36.75 3.10
3067 3955 2.812011 GGATTCATATGTACCGGGCAAC 59.188 50.000 6.32 0.99 0.00 4.17
3068 3956 3.134574 GGATTCATATGTACCGGGCAA 57.865 47.619 6.32 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.