Multiple sequence alignment - TraesCS5B01G141200

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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 TraesCS5B01G141200 chr5B 100.000 3099 0 0 1 3099 266500407 266503505 0.000000e+00 5723.0
1 TraesCS5B01G141200 chr5B 89.691 97 10 0 1380 1476 402751166 402751070 1.170000e-24 124.0
2 TraesCS5B01G141200 chr5B 86.747 83 11 0 1377 1459 704916515 704916597 3.290000e-15 93.5
3 TraesCS5B01G141200 chr5D 95.149 2577 68 17 483 3042 238558312 238555776 0.000000e+00 4013.0
4 TraesCS5B01G141200 chr5D 90.722 97 9 0 1380 1476 342712637 342712541 2.510000e-26 130.0
5 TraesCS5B01G141200 chr5D 90.588 85 5 3 2865 2948 518794530 518794612 3.270000e-20 110.0
6 TraesCS5B01G141200 chr5A 93.457 2323 63 34 433 2705 316084454 316086737 0.000000e+00 3365.0
7 TraesCS5B01G141200 chr5A 88.589 333 25 3 2768 3099 316087002 316087322 2.900000e-105 392.0
8 TraesCS5B01G141200 chr4B 84.813 507 56 14 1001 1502 168984879 168985369 9.990000e-135 490.0
9 TraesCS5B01G141200 chr4D 84.556 518 53 18 1001 1505 107710734 107710231 3.590000e-134 488.0
10 TraesCS5B01G141200 chr4D 81.159 276 44 6 1001 1270 506607107 506606834 6.730000e-52 215.0
11 TraesCS5B01G141200 chr4A 83.491 527 62 20 1001 1514 468603250 468603764 4.680000e-128 468.0
12 TraesCS5B01G141200 chr4A 82.051 273 40 7 1001 1267 724782636 724782905 1.120000e-54 224.0
13 TraesCS5B01G141200 chr7A 81.685 273 41 7 1001 1267 12429646 12429377 5.200000e-53 219.0
14 TraesCS5B01G141200 chr7D 81.295 278 40 10 1001 1270 13029511 13029238 6.730000e-52 215.0
15 TraesCS5B01G141200 chr2B 94.253 87 4 1 2863 2948 781580586 781580500 6.970000e-27 132.0
16 TraesCS5B01G141200 chr3D 90.323 93 8 1 2865 2956 541196945 541196853 1.510000e-23 121.0
17 TraesCS5B01G141200 chr3D 88.764 89 7 3 2869 2955 123305962 123305875 4.230000e-19 106.0
18 TraesCS5B01G141200 chr6D 88.172 93 9 2 2856 2946 305736590 305736682 3.270000e-20 110.0
19 TraesCS5B01G141200 chr2D 89.655 87 8 1 2863 2948 564093465 564093379 3.270000e-20 110.0
20 TraesCS5B01G141200 chr2D 89.412 85 8 1 2865 2948 646251252 646251168 4.230000e-19 106.0
21 TraesCS5B01G141200 chr2D 90.000 80 4 4 1377 1454 108313429 108313506 1.970000e-17 100.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G141200 chr5B 266500407 266503505 3098 False 5723.0 5723 100.000 1 3099 1 chr5B.!!$F1 3098
1 TraesCS5B01G141200 chr5D 238555776 238558312 2536 True 4013.0 4013 95.149 483 3042 1 chr5D.!!$R1 2559
2 TraesCS5B01G141200 chr5A 316084454 316087322 2868 False 1878.5 3365 91.023 433 3099 2 chr5A.!!$F1 2666
3 TraesCS5B01G141200 chr4D 107710231 107710734 503 True 488.0 488 84.556 1001 1505 1 chr4D.!!$R1 504
4 TraesCS5B01G141200 chr4A 468603250 468603764 514 False 468.0 468 83.491 1001 1514 1 chr4A.!!$F1 513

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
386 387 0.035176 ACGTACGGCCCTTTTTGCTA 59.965 50.000 21.06 0.0 0.00 3.49 F
387 388 0.725117 CGTACGGCCCTTTTTGCTAG 59.275 55.000 7.57 0.0 0.00 3.42 F
569 586 0.969149 TGGTGAGCTTGACGAGTCAT 59.031 50.000 6.77 0.0 39.64 3.06 F
1462 1557 1.202698 ACGCACCTCAAGAAGAAGCTT 60.203 47.619 0.00 0.0 0.00 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 1557 0.394762 CCATGGCCTGCTGCTTCTTA 60.395 55.0 3.32 0.0 40.92 2.10 R
1667 1765 0.778223 CGCATGGTGATCGTCGTATG 59.222 55.0 0.00 0.0 0.00 2.39 R
1668 1766 0.939577 GCGCATGGTGATCGTCGTAT 60.940 55.0 0.30 0.0 0.00 3.06 R
2933 3267 0.339162 TGTATTACCCCCTCCGTCCA 59.661 55.0 0.00 0.0 0.00 4.02 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
20 21 4.935495 CACCTGGTGGCGCACTGT 62.935 66.667 19.23 2.60 36.63 3.55
21 22 4.935495 ACCTGGTGGCGCACTGTG 62.935 66.667 10.83 2.76 36.63 3.66
23 24 4.935495 CTGGTGGCGCACTGTGGT 62.935 66.667 10.83 0.00 34.40 4.16
24 25 4.497984 TGGTGGCGCACTGTGGTT 62.498 61.111 10.83 0.00 34.40 3.67
25 26 2.281208 GGTGGCGCACTGTGGTTA 60.281 61.111 10.83 0.00 34.40 2.85
26 27 2.325082 GGTGGCGCACTGTGGTTAG 61.325 63.158 10.83 0.00 34.40 2.34
27 28 2.031919 TGGCGCACTGTGGTTAGG 59.968 61.111 10.83 0.00 0.00 2.69
28 29 3.431725 GGCGCACTGTGGTTAGGC 61.432 66.667 10.83 0.00 0.00 3.93
29 30 3.431725 GCGCACTGTGGTTAGGCC 61.432 66.667 10.21 0.00 37.90 5.19
30 31 2.746277 CGCACTGTGGTTAGGCCC 60.746 66.667 10.21 0.00 36.04 5.80
31 32 2.746277 GCACTGTGGTTAGGCCCG 60.746 66.667 10.21 0.00 36.04 6.13
32 33 2.046314 CACTGTGGTTAGGCCCGG 60.046 66.667 0.00 0.00 36.04 5.73
33 34 3.327404 ACTGTGGTTAGGCCCGGG 61.327 66.667 19.09 19.09 36.04 5.73
34 35 4.109675 CTGTGGTTAGGCCCGGGG 62.110 72.222 25.28 9.31 36.04 5.73
35 36 4.660611 TGTGGTTAGGCCCGGGGA 62.661 66.667 25.28 0.00 36.04 4.81
36 37 3.793888 GTGGTTAGGCCCGGGGAG 61.794 72.222 25.28 0.00 36.04 4.30
39 40 4.176752 GTTAGGCCCGGGGAGCTG 62.177 72.222 25.28 0.00 0.00 4.24
45 46 4.676951 CCCGGGGAGCTGGCAAAA 62.677 66.667 14.71 0.00 0.00 2.44
46 47 2.600173 CCGGGGAGCTGGCAAAAA 60.600 61.111 0.00 0.00 0.00 1.94
98 99 5.551760 AAAAATCGATTGTCAGCGAGAAT 57.448 34.783 12.25 1.66 40.14 2.40
99 100 5.551760 AAAATCGATTGTCAGCGAGAATT 57.448 34.783 12.25 0.00 40.14 2.17
100 101 4.785669 AATCGATTGTCAGCGAGAATTC 57.214 40.909 10.50 0.00 40.14 2.17
113 114 3.810373 CGAGAATTCGTTTTCCCTGTTG 58.190 45.455 0.00 0.00 41.84 3.33
114 115 3.565516 GAGAATTCGTTTTCCCTGTTGC 58.434 45.455 0.00 0.00 0.00 4.17
115 116 2.955660 AGAATTCGTTTTCCCTGTTGCA 59.044 40.909 0.00 0.00 0.00 4.08
116 117 3.383185 AGAATTCGTTTTCCCTGTTGCAA 59.617 39.130 0.00 0.00 0.00 4.08
117 118 4.039124 AGAATTCGTTTTCCCTGTTGCAAT 59.961 37.500 0.59 0.00 0.00 3.56
118 119 2.791383 TCGTTTTCCCTGTTGCAATG 57.209 45.000 0.59 0.00 0.00 2.82
119 120 1.139163 CGTTTTCCCTGTTGCAATGC 58.861 50.000 0.59 0.00 0.00 3.56
120 121 1.537776 CGTTTTCCCTGTTGCAATGCA 60.538 47.619 2.72 2.72 36.47 3.96
121 122 1.866601 GTTTTCCCTGTTGCAATGCAC 59.133 47.619 7.72 4.04 38.71 4.57
122 123 1.117994 TTTCCCTGTTGCAATGCACA 58.882 45.000 7.72 8.81 38.71 4.57
123 124 0.675083 TTCCCTGTTGCAATGCACAG 59.325 50.000 22.07 22.07 38.71 3.66
124 125 1.373748 CCCTGTTGCAATGCACAGC 60.374 57.895 22.99 12.38 38.71 4.40
125 126 1.364536 CCTGTTGCAATGCACAGCA 59.635 52.632 22.99 10.56 44.86 4.41
132 133 3.881780 TGCAATGCACAGCAAATTTTC 57.118 38.095 2.72 0.00 43.62 2.29
133 134 2.221286 TGCAATGCACAGCAAATTTTCG 59.779 40.909 2.72 0.00 43.62 3.46
134 135 2.475864 GCAATGCACAGCAAATTTTCGA 59.524 40.909 0.00 0.00 43.62 3.71
135 136 3.422603 GCAATGCACAGCAAATTTTCGAG 60.423 43.478 0.00 0.00 43.62 4.04
136 137 3.921119 ATGCACAGCAAATTTTCGAGA 57.079 38.095 0.00 0.00 43.62 4.04
137 138 3.921119 TGCACAGCAAATTTTCGAGAT 57.079 38.095 0.00 0.00 34.76 2.75
138 139 5.565592 ATGCACAGCAAATTTTCGAGATA 57.434 34.783 0.00 0.00 43.62 1.98
139 140 5.369685 TGCACAGCAAATTTTCGAGATAA 57.630 34.783 0.00 0.00 34.76 1.75
140 141 5.767269 TGCACAGCAAATTTTCGAGATAAA 58.233 33.333 0.00 0.00 34.76 1.40
141 142 6.389091 TGCACAGCAAATTTTCGAGATAAAT 58.611 32.000 0.00 0.00 34.76 1.40
142 143 6.308524 TGCACAGCAAATTTTCGAGATAAATG 59.691 34.615 0.00 0.00 34.76 2.32
143 144 6.308766 GCACAGCAAATTTTCGAGATAAATGT 59.691 34.615 0.00 0.00 0.00 2.71
144 145 7.660059 CACAGCAAATTTTCGAGATAAATGTG 58.340 34.615 6.80 6.80 34.66 3.21
145 146 7.326789 CACAGCAAATTTTCGAGATAAATGTGT 59.673 33.333 11.18 4.15 34.25 3.72
146 147 7.538678 ACAGCAAATTTTCGAGATAAATGTGTC 59.461 33.333 11.18 5.75 34.25 3.67
147 148 7.538334 CAGCAAATTTTCGAGATAAATGTGTCA 59.462 33.333 11.18 0.00 34.25 3.58
148 149 7.538678 AGCAAATTTTCGAGATAAATGTGTCAC 59.461 33.333 11.18 0.00 34.25 3.67
149 150 7.201350 GCAAATTTTCGAGATAAATGTGTCACC 60.201 37.037 11.18 0.00 34.25 4.02
150 151 7.687941 AATTTTCGAGATAAATGTGTCACCT 57.312 32.000 0.00 0.00 0.00 4.00
151 152 6.480524 TTTTCGAGATAAATGTGTCACCTG 57.519 37.500 0.00 0.00 0.00 4.00
152 153 5.400066 TTCGAGATAAATGTGTCACCTGA 57.600 39.130 0.00 0.00 0.00 3.86
153 154 4.744570 TCGAGATAAATGTGTCACCTGAC 58.255 43.478 0.00 0.00 44.97 3.51
154 155 4.462834 TCGAGATAAATGTGTCACCTGACT 59.537 41.667 6.97 0.00 44.99 3.41
155 156 5.650703 TCGAGATAAATGTGTCACCTGACTA 59.349 40.000 6.97 0.00 44.99 2.59
156 157 5.974158 CGAGATAAATGTGTCACCTGACTAG 59.026 44.000 6.97 0.00 44.99 2.57
157 158 6.183360 CGAGATAAATGTGTCACCTGACTAGA 60.183 42.308 6.97 0.00 44.99 2.43
158 159 7.482169 AGATAAATGTGTCACCTGACTAGAA 57.518 36.000 6.97 0.00 44.99 2.10
159 160 8.083828 AGATAAATGTGTCACCTGACTAGAAT 57.916 34.615 6.97 0.00 44.99 2.40
160 161 8.543774 AGATAAATGTGTCACCTGACTAGAATT 58.456 33.333 6.97 0.06 44.99 2.17
161 162 6.808008 AAATGTGTCACCTGACTAGAATTG 57.192 37.500 6.97 0.00 44.99 2.32
162 163 5.745312 ATGTGTCACCTGACTAGAATTGA 57.255 39.130 6.97 0.00 44.99 2.57
163 164 5.745312 TGTGTCACCTGACTAGAATTGAT 57.255 39.130 6.97 0.00 44.99 2.57
164 165 6.850752 TGTGTCACCTGACTAGAATTGATA 57.149 37.500 6.97 0.00 44.99 2.15
165 166 7.239763 TGTGTCACCTGACTAGAATTGATAA 57.760 36.000 6.97 0.00 44.99 1.75
166 167 7.676004 TGTGTCACCTGACTAGAATTGATAAA 58.324 34.615 6.97 0.00 44.99 1.40
167 168 8.321353 TGTGTCACCTGACTAGAATTGATAAAT 58.679 33.333 6.97 0.00 44.99 1.40
168 169 9.167311 GTGTCACCTGACTAGAATTGATAAATT 57.833 33.333 6.97 0.00 44.99 1.82
169 170 9.166173 TGTCACCTGACTAGAATTGATAAATTG 57.834 33.333 6.97 0.00 44.99 2.32
170 171 8.125448 GTCACCTGACTAGAATTGATAAATTGC 58.875 37.037 0.00 0.00 41.65 3.56
171 172 7.828717 TCACCTGACTAGAATTGATAAATTGCA 59.171 33.333 0.00 0.00 0.00 4.08
172 173 8.461222 CACCTGACTAGAATTGATAAATTGCAA 58.539 33.333 0.00 0.00 0.00 4.08
173 174 8.680903 ACCTGACTAGAATTGATAAATTGCAAG 58.319 33.333 4.94 0.00 0.00 4.01
174 175 8.896744 CCTGACTAGAATTGATAAATTGCAAGA 58.103 33.333 4.94 0.00 0.00 3.02
194 195 9.254133 TGCAAGATATTTATTTCTTCTCTCTCG 57.746 33.333 0.00 0.00 29.85 4.04
195 196 9.255304 GCAAGATATTTATTTCTTCTCTCTCGT 57.745 33.333 0.00 0.00 29.85 4.18
198 199 9.255304 AGATATTTATTTCTTCTCTCTCGTTGC 57.745 33.333 0.00 0.00 0.00 4.17
199 200 8.948631 ATATTTATTTCTTCTCTCTCGTTGCA 57.051 30.769 0.00 0.00 0.00 4.08
200 201 7.672983 ATTTATTTCTTCTCTCTCGTTGCAA 57.327 32.000 0.00 0.00 0.00 4.08
201 202 4.999751 ATTTCTTCTCTCTCGTTGCAAC 57.000 40.909 19.89 19.89 0.00 4.17
210 211 3.945436 CGTTGCAACGCCTAGACA 58.055 55.556 35.89 0.00 46.06 3.41
211 212 2.456000 CGTTGCAACGCCTAGACAT 58.544 52.632 35.89 0.00 46.06 3.06
212 213 0.095245 CGTTGCAACGCCTAGACATG 59.905 55.000 35.89 9.09 46.06 3.21
213 214 1.156736 GTTGCAACGCCTAGACATGT 58.843 50.000 14.90 0.00 0.00 3.21
214 215 1.535462 GTTGCAACGCCTAGACATGTT 59.465 47.619 14.90 0.00 0.00 2.71
215 216 1.890876 TGCAACGCCTAGACATGTTT 58.109 45.000 0.00 0.00 0.00 2.83
216 217 1.535028 TGCAACGCCTAGACATGTTTG 59.465 47.619 0.00 0.00 0.00 2.93
217 218 1.729149 GCAACGCCTAGACATGTTTGC 60.729 52.381 12.03 12.03 0.00 3.68
218 219 1.806542 CAACGCCTAGACATGTTTGCT 59.193 47.619 0.00 0.00 0.00 3.91
219 220 3.000041 CAACGCCTAGACATGTTTGCTA 59.000 45.455 0.00 0.00 0.00 3.49
220 221 3.543680 ACGCCTAGACATGTTTGCTAT 57.456 42.857 0.00 0.00 0.00 2.97
221 222 4.665833 ACGCCTAGACATGTTTGCTATA 57.334 40.909 0.00 0.00 0.00 1.31
222 223 5.215252 ACGCCTAGACATGTTTGCTATAT 57.785 39.130 0.00 0.00 0.00 0.86
223 224 5.611374 ACGCCTAGACATGTTTGCTATATT 58.389 37.500 0.00 0.00 0.00 1.28
224 225 6.755206 ACGCCTAGACATGTTTGCTATATTA 58.245 36.000 0.00 0.00 0.00 0.98
225 226 6.645415 ACGCCTAGACATGTTTGCTATATTAC 59.355 38.462 0.00 0.00 0.00 1.89
226 227 6.645003 CGCCTAGACATGTTTGCTATATTACA 59.355 38.462 0.00 0.00 0.00 2.41
227 228 7.170828 CGCCTAGACATGTTTGCTATATTACAA 59.829 37.037 0.00 0.00 0.00 2.41
228 229 8.836413 GCCTAGACATGTTTGCTATATTACAAA 58.164 33.333 0.00 0.13 33.55 2.83
341 342 9.579932 TCAATTTACAGAGCTAGAGATATGAGA 57.420 33.333 0.00 0.00 0.00 3.27
344 345 7.936496 TTACAGAGCTAGAGATATGAGATGG 57.064 40.000 0.00 0.00 0.00 3.51
345 346 5.891198 ACAGAGCTAGAGATATGAGATGGT 58.109 41.667 0.00 0.00 0.00 3.55
346 347 6.314120 ACAGAGCTAGAGATATGAGATGGTT 58.686 40.000 0.00 0.00 0.00 3.67
347 348 7.465960 ACAGAGCTAGAGATATGAGATGGTTA 58.534 38.462 0.00 0.00 0.00 2.85
348 349 8.115384 ACAGAGCTAGAGATATGAGATGGTTAT 58.885 37.037 0.00 0.00 0.00 1.89
349 350 8.970020 CAGAGCTAGAGATATGAGATGGTTATT 58.030 37.037 0.00 0.00 0.00 1.40
350 351 9.545928 AGAGCTAGAGATATGAGATGGTTATTT 57.454 33.333 0.00 0.00 0.00 1.40
373 374 3.579147 TTTCTCTTGTTGCAACGTACG 57.421 42.857 23.79 15.01 0.00 3.67
374 375 1.493772 TCTCTTGTTGCAACGTACGG 58.506 50.000 23.79 12.77 0.00 4.02
375 376 0.110823 CTCTTGTTGCAACGTACGGC 60.111 55.000 23.79 14.66 0.00 5.68
376 377 1.082366 CTTGTTGCAACGTACGGCC 60.082 57.895 23.79 7.64 0.00 6.13
377 378 2.452366 CTTGTTGCAACGTACGGCCC 62.452 60.000 23.79 7.27 0.00 5.80
378 379 2.667199 GTTGCAACGTACGGCCCT 60.667 61.111 21.06 0.00 0.00 5.19
379 380 2.111460 TTGCAACGTACGGCCCTT 59.889 55.556 21.06 1.11 0.00 3.95
380 381 1.526455 TTGCAACGTACGGCCCTTT 60.526 52.632 21.06 0.69 0.00 3.11
381 382 1.102222 TTGCAACGTACGGCCCTTTT 61.102 50.000 21.06 0.00 0.00 2.27
382 383 1.102222 TGCAACGTACGGCCCTTTTT 61.102 50.000 21.06 0.00 0.00 1.94
383 384 0.662077 GCAACGTACGGCCCTTTTTG 60.662 55.000 21.06 13.49 0.00 2.44
384 385 0.662077 CAACGTACGGCCCTTTTTGC 60.662 55.000 21.06 0.00 0.00 3.68
385 386 0.820482 AACGTACGGCCCTTTTTGCT 60.820 50.000 21.06 0.00 0.00 3.91
386 387 0.035176 ACGTACGGCCCTTTTTGCTA 59.965 50.000 21.06 0.00 0.00 3.49
387 388 0.725117 CGTACGGCCCTTTTTGCTAG 59.275 55.000 7.57 0.00 0.00 3.42
388 389 1.817357 GTACGGCCCTTTTTGCTAGT 58.183 50.000 0.00 0.00 0.00 2.57
389 390 2.156917 GTACGGCCCTTTTTGCTAGTT 58.843 47.619 0.00 0.00 0.00 2.24
390 391 2.572209 ACGGCCCTTTTTGCTAGTTA 57.428 45.000 0.00 0.00 0.00 2.24
391 392 2.433436 ACGGCCCTTTTTGCTAGTTAG 58.567 47.619 0.00 0.00 0.00 2.34
392 393 2.039348 ACGGCCCTTTTTGCTAGTTAGA 59.961 45.455 0.00 0.00 0.00 2.10
393 394 3.078837 CGGCCCTTTTTGCTAGTTAGAA 58.921 45.455 0.00 0.00 0.00 2.10
394 395 3.127030 CGGCCCTTTTTGCTAGTTAGAAG 59.873 47.826 0.00 0.00 0.00 2.85
395 396 3.444034 GGCCCTTTTTGCTAGTTAGAAGG 59.556 47.826 0.00 7.94 34.76 3.46
396 397 3.119459 GCCCTTTTTGCTAGTTAGAAGGC 60.119 47.826 8.93 0.00 33.89 4.35
397 398 4.336280 CCCTTTTTGCTAGTTAGAAGGCT 58.664 43.478 8.93 0.00 33.89 4.58
398 399 5.497474 CCCTTTTTGCTAGTTAGAAGGCTA 58.503 41.667 8.93 0.00 33.89 3.93
399 400 5.944007 CCCTTTTTGCTAGTTAGAAGGCTAA 59.056 40.000 8.93 0.00 33.89 3.09
400 401 6.603599 CCCTTTTTGCTAGTTAGAAGGCTAAT 59.396 38.462 8.93 0.00 38.74 1.73
401 402 7.773690 CCCTTTTTGCTAGTTAGAAGGCTAATA 59.226 37.037 8.93 0.00 38.74 0.98
402 403 9.174166 CCTTTTTGCTAGTTAGAAGGCTAATAA 57.826 33.333 0.00 0.00 38.74 1.40
468 469 3.683937 ATGGTTGTTGCAGCGGGC 61.684 61.111 0.00 0.00 45.13 6.13
474 475 2.046314 GTTGCAGCGGGCTCCTTA 60.046 61.111 5.05 0.00 45.15 2.69
481 482 1.625818 CAGCGGGCTCCTTAAGGATAT 59.374 52.381 24.48 4.78 44.46 1.63
485 486 3.616802 GCGGGCTCCTTAAGGATATGTAC 60.617 52.174 24.48 9.35 44.46 2.90
486 487 3.576982 CGGGCTCCTTAAGGATATGTACA 59.423 47.826 24.48 0.00 44.46 2.90
554 571 5.647658 TGAAATGCCTTGACTAGTTATGGTG 59.352 40.000 17.60 0.00 0.00 4.17
569 586 0.969149 TGGTGAGCTTGACGAGTCAT 59.031 50.000 6.77 0.00 39.64 3.06
949 977 2.552743 ACACGAGTGAGAAAGACGATCA 59.447 45.455 10.50 0.00 0.00 2.92
955 983 3.006323 AGTGAGAAAGACGATCAAGCTGT 59.994 43.478 0.00 0.00 0.00 4.40
964 1004 3.070018 ACGATCAAGCTGTCAAAAGGAG 58.930 45.455 0.00 0.00 0.00 3.69
965 1005 3.244215 ACGATCAAGCTGTCAAAAGGAGA 60.244 43.478 0.00 0.00 0.00 3.71
966 1006 3.748048 CGATCAAGCTGTCAAAAGGAGAA 59.252 43.478 0.00 0.00 0.00 2.87
967 1007 4.142945 CGATCAAGCTGTCAAAAGGAGAAG 60.143 45.833 0.00 0.00 0.00 2.85
968 1008 4.422073 TCAAGCTGTCAAAAGGAGAAGA 57.578 40.909 0.00 0.00 0.00 2.87
969 1009 4.384056 TCAAGCTGTCAAAAGGAGAAGAG 58.616 43.478 0.00 0.00 0.00 2.85
970 1010 3.415457 AGCTGTCAAAAGGAGAAGAGG 57.585 47.619 0.00 0.00 0.00 3.69
971 1011 2.708325 AGCTGTCAAAAGGAGAAGAGGT 59.292 45.455 0.00 0.00 0.00 3.85
972 1012 3.070748 GCTGTCAAAAGGAGAAGAGGTC 58.929 50.000 0.00 0.00 0.00 3.85
973 1013 3.321497 CTGTCAAAAGGAGAAGAGGTCG 58.679 50.000 0.00 0.00 0.00 4.79
974 1014 2.963101 TGTCAAAAGGAGAAGAGGTCGA 59.037 45.455 0.00 0.00 0.00 4.20
975 1015 3.005897 TGTCAAAAGGAGAAGAGGTCGAG 59.994 47.826 0.00 0.00 0.00 4.04
976 1016 3.256136 GTCAAAAGGAGAAGAGGTCGAGA 59.744 47.826 0.00 0.00 0.00 4.04
977 1017 3.508012 TCAAAAGGAGAAGAGGTCGAGAG 59.492 47.826 0.00 0.00 0.00 3.20
978 1018 2.137810 AAGGAGAAGAGGTCGAGAGG 57.862 55.000 0.00 0.00 0.00 3.69
979 1019 1.291109 AGGAGAAGAGGTCGAGAGGA 58.709 55.000 0.00 0.00 0.00 3.71
980 1020 1.211949 AGGAGAAGAGGTCGAGAGGAG 59.788 57.143 0.00 0.00 0.00 3.69
981 1021 1.675552 GAGAAGAGGTCGAGAGGAGG 58.324 60.000 0.00 0.00 0.00 4.30
1279 1319 3.136009 ACAGGTAACCAACTAAGCCAC 57.864 47.619 0.00 0.00 37.17 5.01
1304 1395 2.012902 GATCGATCGTCCGGGTTGGT 62.013 60.000 15.94 0.00 39.52 3.67
1363 1454 8.109634 ACATGATCTAATAACAACTCTTTGGGT 58.890 33.333 0.00 0.00 37.00 4.51
1462 1557 1.202698 ACGCACCTCAAGAAGAAGCTT 60.203 47.619 0.00 0.00 0.00 3.74
1494 1589 3.957535 CATGGGCGCCATCTTCGC 61.958 66.667 30.85 9.47 43.15 4.70
1535 1633 3.518998 GCTCCGCCGAGACAGCTA 61.519 66.667 6.23 0.00 38.52 3.32
1536 1634 2.851071 GCTCCGCCGAGACAGCTAT 61.851 63.158 6.23 0.00 38.52 2.97
1600 1698 2.583319 CACCATGACGCGATCGCT 60.583 61.111 34.69 22.77 39.84 4.93
1667 1765 4.767255 CGGAGGTCACCCAGCAGC 62.767 72.222 0.00 0.00 0.00 5.25
1668 1766 3.640407 GGAGGTCACCCAGCAGCA 61.640 66.667 0.00 0.00 0.00 4.41
1833 1931 0.744414 CCCAACATAGCCGTGGTCAG 60.744 60.000 0.00 0.00 0.00 3.51
2145 2252 1.408969 AAGGCAAACCAACGAACCAT 58.591 45.000 0.00 0.00 39.06 3.55
2307 2415 6.153680 ACACCATCAAGTTAACTAGAGAGAGG 59.846 42.308 8.92 14.27 0.00 3.69
2308 2416 5.128008 ACCATCAAGTTAACTAGAGAGAGGC 59.872 44.000 8.92 0.00 0.00 4.70
2383 2514 2.092212 GGGATGATGAGAAGAAGGCCAA 60.092 50.000 5.01 0.00 0.00 4.52
2426 2557 5.123344 ACAGTAACAGGAATTCAATAACGGC 59.877 40.000 7.93 0.00 0.00 5.68
2545 2677 3.712016 TTCTGGGTTATAGTGCAAGCA 57.288 42.857 0.00 0.00 0.00 3.91
2613 2745 9.962783 ACGGAGTATGAATATAAGTTAGTGAAC 57.037 33.333 0.00 0.00 41.94 3.18
2743 2875 6.432403 AAAAAGCTAGAGAGAGGGGATATG 57.568 41.667 0.00 0.00 0.00 1.78
2796 3130 7.040494 TGATCACATTCACTGCAAAAGAAAAA 58.960 30.769 0.00 0.00 0.00 1.94
2973 3308 2.231716 AGCCTTTTTAGCCCGGATTT 57.768 45.000 0.73 0.00 0.00 2.17
3044 3379 6.974965 ACTATCTGCTTCCAAAAGAAAACTG 58.025 36.000 0.00 0.00 34.14 3.16
3045 3380 6.772716 ACTATCTGCTTCCAAAAGAAAACTGA 59.227 34.615 0.00 0.00 34.14 3.41
3049 3384 4.156922 TGCTTCCAAAAGAAAACTGAACGA 59.843 37.500 0.00 0.00 34.14 3.85
3071 3406 6.592607 ACGAATTTAAAAGCTATTCACCGAGA 59.407 34.615 6.90 0.00 0.00 4.04
3077 3412 6.723131 AAAAGCTATTCACCGAGAAAGTAC 57.277 37.500 0.00 0.00 40.22 2.73
3094 3429 7.974504 AGAAAGTACCTTTCAGGAAAGATACA 58.025 34.615 22.17 5.28 45.55 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.935495 ACCACAGTGCGCCACCAG 62.935 66.667 4.18 1.92 34.49 4.00
7 8 3.108288 TAACCACAGTGCGCCACCA 62.108 57.895 4.18 0.00 34.49 4.17
8 9 2.281208 TAACCACAGTGCGCCACC 60.281 61.111 4.18 0.00 34.49 4.61
9 10 2.325082 CCTAACCACAGTGCGCCAC 61.325 63.158 4.18 3.02 34.10 5.01
10 11 2.031919 CCTAACCACAGTGCGCCA 59.968 61.111 4.18 0.00 0.00 5.69
11 12 3.431725 GCCTAACCACAGTGCGCC 61.432 66.667 4.18 0.00 0.00 6.53
12 13 3.431725 GGCCTAACCACAGTGCGC 61.432 66.667 0.00 0.00 38.86 6.09
13 14 2.746277 GGGCCTAACCACAGTGCG 60.746 66.667 0.84 0.00 42.05 5.34
14 15 2.746277 CGGGCCTAACCACAGTGC 60.746 66.667 0.84 0.00 42.05 4.40
15 16 2.046314 CCGGGCCTAACCACAGTG 60.046 66.667 0.84 0.00 42.05 3.66
16 17 3.327404 CCCGGGCCTAACCACAGT 61.327 66.667 8.08 0.00 42.05 3.55
17 18 4.109675 CCCCGGGCCTAACCACAG 62.110 72.222 17.73 0.00 42.05 3.66
18 19 4.660611 TCCCCGGGCCTAACCACA 62.661 66.667 17.73 0.00 42.05 4.17
19 20 3.793888 CTCCCCGGGCCTAACCAC 61.794 72.222 17.73 0.00 42.05 4.16
22 23 4.176752 CAGCTCCCCGGGCCTAAC 62.177 72.222 17.73 1.49 0.00 2.34
28 29 4.676951 TTTTGCCAGCTCCCCGGG 62.677 66.667 15.80 15.80 0.00 5.73
29 30 2.600173 TTTTTGCCAGCTCCCCGG 60.600 61.111 0.00 0.00 0.00 5.73
76 77 5.551760 ATTCTCGCTGACAATCGATTTTT 57.448 34.783 8.21 0.00 33.98 1.94
77 78 5.551760 AATTCTCGCTGACAATCGATTTT 57.448 34.783 8.21 1.20 33.98 1.82
78 79 4.259970 CGAATTCTCGCTGACAATCGATTT 60.260 41.667 8.21 0.00 38.45 2.17
79 80 3.243877 CGAATTCTCGCTGACAATCGATT 59.756 43.478 4.39 4.39 38.45 3.34
80 81 2.791560 CGAATTCTCGCTGACAATCGAT 59.208 45.455 3.52 0.00 38.45 3.59
81 82 2.185262 CGAATTCTCGCTGACAATCGA 58.815 47.619 3.52 0.00 38.45 3.59
82 83 2.617836 CGAATTCTCGCTGACAATCG 57.382 50.000 3.52 0.00 38.45 3.34
93 94 3.004315 TGCAACAGGGAAAACGAATTCTC 59.996 43.478 3.52 0.00 0.00 2.87
94 95 2.955660 TGCAACAGGGAAAACGAATTCT 59.044 40.909 3.52 0.00 0.00 2.40
95 96 3.363341 TGCAACAGGGAAAACGAATTC 57.637 42.857 0.00 0.00 0.00 2.17
96 97 3.810310 TTGCAACAGGGAAAACGAATT 57.190 38.095 0.00 0.00 0.00 2.17
97 98 3.652274 CATTGCAACAGGGAAAACGAAT 58.348 40.909 0.00 0.00 0.00 3.34
98 99 2.801342 GCATTGCAACAGGGAAAACGAA 60.801 45.455 0.00 0.00 0.00 3.85
99 100 1.269517 GCATTGCAACAGGGAAAACGA 60.270 47.619 0.00 0.00 0.00 3.85
100 101 1.139163 GCATTGCAACAGGGAAAACG 58.861 50.000 0.00 0.00 0.00 3.60
101 102 1.866601 GTGCATTGCAACAGGGAAAAC 59.133 47.619 13.94 0.00 41.47 2.43
102 103 1.483827 TGTGCATTGCAACAGGGAAAA 59.516 42.857 13.94 0.00 41.47 2.29
103 104 1.068895 CTGTGCATTGCAACAGGGAAA 59.931 47.619 22.70 0.00 41.47 3.13
104 105 0.675083 CTGTGCATTGCAACAGGGAA 59.325 50.000 22.70 3.65 41.47 3.97
105 106 1.808531 GCTGTGCATTGCAACAGGGA 61.809 55.000 27.26 2.02 41.47 4.20
106 107 1.373748 GCTGTGCATTGCAACAGGG 60.374 57.895 27.26 14.54 41.47 4.45
107 108 0.249531 TTGCTGTGCATTGCAACAGG 60.250 50.000 27.26 15.33 43.17 4.00
108 109 1.573026 TTTGCTGTGCATTGCAACAG 58.427 45.000 24.57 24.57 46.91 3.16
109 110 2.242047 ATTTGCTGTGCATTGCAACA 57.758 40.000 22.84 12.47 46.91 3.33
110 111 3.612472 AAATTTGCTGTGCATTGCAAC 57.388 38.095 22.84 8.44 46.91 4.17
111 112 3.303197 CGAAAATTTGCTGTGCATTGCAA 60.303 39.130 20.36 20.36 45.83 4.08
112 113 2.221286 CGAAAATTTGCTGTGCATTGCA 59.779 40.909 7.38 7.38 38.76 4.08
113 114 2.475864 TCGAAAATTTGCTGTGCATTGC 59.524 40.909 0.46 0.46 38.76 3.56
114 115 3.982701 TCTCGAAAATTTGCTGTGCATTG 59.017 39.130 0.00 0.00 38.76 2.82
115 116 4.241590 TCTCGAAAATTTGCTGTGCATT 57.758 36.364 0.00 0.00 38.76 3.56
116 117 3.921119 TCTCGAAAATTTGCTGTGCAT 57.079 38.095 0.00 0.00 38.76 3.96
117 118 3.921119 ATCTCGAAAATTTGCTGTGCA 57.079 38.095 0.00 0.00 36.47 4.57
118 119 6.308766 ACATTTATCTCGAAAATTTGCTGTGC 59.691 34.615 0.00 0.00 0.00 4.57
119 120 7.326789 ACACATTTATCTCGAAAATTTGCTGTG 59.673 33.333 8.59 8.59 30.61 3.66
120 121 7.370383 ACACATTTATCTCGAAAATTTGCTGT 58.630 30.769 6.98 0.00 30.61 4.40
121 122 7.538334 TGACACATTTATCTCGAAAATTTGCTG 59.462 33.333 6.98 0.00 30.61 4.41
122 123 7.538678 GTGACACATTTATCTCGAAAATTTGCT 59.461 33.333 0.00 0.00 30.61 3.91
123 124 7.201350 GGTGACACATTTATCTCGAAAATTTGC 60.201 37.037 8.08 0.00 30.61 3.68
124 125 8.023128 AGGTGACACATTTATCTCGAAAATTTG 58.977 33.333 8.08 5.91 32.71 2.32
125 126 8.023128 CAGGTGACACATTTATCTCGAAAATTT 58.977 33.333 8.08 0.00 0.00 1.82
126 127 7.390440 TCAGGTGACACATTTATCTCGAAAATT 59.610 33.333 8.08 0.00 0.00 1.82
127 128 6.878923 TCAGGTGACACATTTATCTCGAAAAT 59.121 34.615 8.08 0.00 0.00 1.82
128 129 6.147164 GTCAGGTGACACATTTATCTCGAAAA 59.853 38.462 8.08 0.00 44.18 2.29
129 130 5.637810 GTCAGGTGACACATTTATCTCGAAA 59.362 40.000 8.08 0.00 44.18 3.46
130 131 5.168569 GTCAGGTGACACATTTATCTCGAA 58.831 41.667 8.08 0.00 44.18 3.71
131 132 4.744570 GTCAGGTGACACATTTATCTCGA 58.255 43.478 8.08 0.00 44.18 4.04
143 144 9.166173 CAATTTATCAATTCTAGTCAGGTGACA 57.834 33.333 12.54 0.00 37.74 3.58
144 145 8.125448 GCAATTTATCAATTCTAGTCAGGTGAC 58.875 37.037 1.60 1.60 36.59 3.67
145 146 7.828717 TGCAATTTATCAATTCTAGTCAGGTGA 59.171 33.333 0.00 0.00 29.41 4.02
146 147 7.988737 TGCAATTTATCAATTCTAGTCAGGTG 58.011 34.615 0.00 0.00 29.41 4.00
147 148 8.579850 TTGCAATTTATCAATTCTAGTCAGGT 57.420 30.769 0.00 0.00 29.41 4.00
148 149 8.896744 TCTTGCAATTTATCAATTCTAGTCAGG 58.103 33.333 0.00 0.00 29.41 3.86
168 169 9.254133 CGAGAGAGAAGAAATAAATATCTTGCA 57.746 33.333 0.00 0.00 36.08 4.08
169 170 9.255304 ACGAGAGAGAAGAAATAAATATCTTGC 57.745 33.333 0.00 0.00 36.08 4.01
172 173 9.255304 GCAACGAGAGAGAAGAAATAAATATCT 57.745 33.333 0.00 0.00 0.00 1.98
173 174 9.035607 TGCAACGAGAGAGAAGAAATAAATATC 57.964 33.333 0.00 0.00 0.00 1.63
174 175 8.948631 TGCAACGAGAGAGAAGAAATAAATAT 57.051 30.769 0.00 0.00 0.00 1.28
175 176 8.656849 GTTGCAACGAGAGAGAAGAAATAAATA 58.343 33.333 14.90 0.00 0.00 1.40
176 177 7.522374 GTTGCAACGAGAGAGAAGAAATAAAT 58.478 34.615 14.90 0.00 0.00 1.40
177 178 6.888430 GTTGCAACGAGAGAGAAGAAATAAA 58.112 36.000 14.90 0.00 0.00 1.40
178 179 6.467723 GTTGCAACGAGAGAGAAGAAATAA 57.532 37.500 14.90 0.00 0.00 1.40
180 181 4.999751 GTTGCAACGAGAGAGAAGAAAT 57.000 40.909 14.90 0.00 0.00 2.17
194 195 1.156736 ACATGTCTAGGCGTTGCAAC 58.843 50.000 19.89 19.89 0.00 4.17
195 196 1.890876 AACATGTCTAGGCGTTGCAA 58.109 45.000 0.00 0.00 0.00 4.08
196 197 1.535028 CAAACATGTCTAGGCGTTGCA 59.465 47.619 0.00 0.00 0.00 4.08
197 198 1.729149 GCAAACATGTCTAGGCGTTGC 60.729 52.381 12.03 12.03 0.00 4.17
198 199 1.806542 AGCAAACATGTCTAGGCGTTG 59.193 47.619 0.00 0.00 0.00 4.10
199 200 2.185004 AGCAAACATGTCTAGGCGTT 57.815 45.000 0.00 0.00 0.00 4.84
200 201 3.543680 ATAGCAAACATGTCTAGGCGT 57.456 42.857 0.00 0.00 0.00 5.68
201 202 6.645003 TGTAATATAGCAAACATGTCTAGGCG 59.355 38.462 0.00 0.00 0.00 5.52
202 203 7.962964 TGTAATATAGCAAACATGTCTAGGC 57.037 36.000 0.00 0.55 0.00 3.93
315 316 9.579932 TCTCATATCTCTAGCTCTGTAAATTGA 57.420 33.333 0.00 0.00 0.00 2.57
318 319 8.970020 CCATCTCATATCTCTAGCTCTGTAAAT 58.030 37.037 0.00 0.00 0.00 1.40
319 320 7.947332 ACCATCTCATATCTCTAGCTCTGTAAA 59.053 37.037 0.00 0.00 0.00 2.01
320 321 7.465960 ACCATCTCATATCTCTAGCTCTGTAA 58.534 38.462 0.00 0.00 0.00 2.41
321 322 7.026697 ACCATCTCATATCTCTAGCTCTGTA 57.973 40.000 0.00 0.00 0.00 2.74
322 323 5.891198 ACCATCTCATATCTCTAGCTCTGT 58.109 41.667 0.00 0.00 0.00 3.41
323 324 6.839124 AACCATCTCATATCTCTAGCTCTG 57.161 41.667 0.00 0.00 0.00 3.35
324 325 9.545928 AAATAACCATCTCATATCTCTAGCTCT 57.454 33.333 0.00 0.00 0.00 4.09
351 352 4.336101 CGTACGTTGCAACAAGAGAAAAA 58.664 39.130 28.01 0.70 0.00 1.94
352 353 3.242478 CCGTACGTTGCAACAAGAGAAAA 60.242 43.478 28.01 2.20 0.00 2.29
353 354 2.285756 CCGTACGTTGCAACAAGAGAAA 59.714 45.455 28.01 3.23 0.00 2.52
354 355 1.862201 CCGTACGTTGCAACAAGAGAA 59.138 47.619 28.01 4.60 0.00 2.87
355 356 1.493772 CCGTACGTTGCAACAAGAGA 58.506 50.000 28.01 6.13 0.00 3.10
356 357 0.110823 GCCGTACGTTGCAACAAGAG 60.111 55.000 28.01 14.64 0.00 2.85
357 358 1.500512 GGCCGTACGTTGCAACAAGA 61.501 55.000 28.01 10.42 0.00 3.02
358 359 1.082366 GGCCGTACGTTGCAACAAG 60.082 57.895 28.01 15.70 0.00 3.16
359 360 2.544698 GGGCCGTACGTTGCAACAA 61.545 57.895 28.01 13.51 0.00 2.83
360 361 2.944409 AAGGGCCGTACGTTGCAACA 62.944 55.000 28.01 7.99 0.00 3.33
361 362 1.788067 AAAGGGCCGTACGTTGCAAC 61.788 55.000 19.89 19.89 0.00 4.17
362 363 1.102222 AAAAGGGCCGTACGTTGCAA 61.102 50.000 15.21 0.00 0.00 4.08
363 364 1.102222 AAAAAGGGCCGTACGTTGCA 61.102 50.000 15.21 0.00 0.00 4.08
364 365 0.662077 CAAAAAGGGCCGTACGTTGC 60.662 55.000 15.21 11.21 0.00 4.17
365 366 0.662077 GCAAAAAGGGCCGTACGTTG 60.662 55.000 15.21 10.95 0.00 4.10
366 367 0.820482 AGCAAAAAGGGCCGTACGTT 60.820 50.000 15.21 0.00 0.00 3.99
367 368 0.035176 TAGCAAAAAGGGCCGTACGT 59.965 50.000 15.21 0.00 0.00 3.57
368 369 0.725117 CTAGCAAAAAGGGCCGTACG 59.275 55.000 8.69 8.69 0.00 3.67
369 370 1.817357 ACTAGCAAAAAGGGCCGTAC 58.183 50.000 0.00 0.00 0.00 3.67
370 371 2.572209 AACTAGCAAAAAGGGCCGTA 57.428 45.000 0.00 0.00 0.00 4.02
371 372 2.039348 TCTAACTAGCAAAAAGGGCCGT 59.961 45.455 0.00 0.00 0.00 5.68
372 373 2.706890 TCTAACTAGCAAAAAGGGCCG 58.293 47.619 0.00 0.00 0.00 6.13
373 374 3.444034 CCTTCTAACTAGCAAAAAGGGCC 59.556 47.826 0.00 0.00 31.63 5.80
374 375 3.119459 GCCTTCTAACTAGCAAAAAGGGC 60.119 47.826 13.45 6.18 35.02 5.19
375 376 4.336280 AGCCTTCTAACTAGCAAAAAGGG 58.664 43.478 13.45 0.93 35.02 3.95
376 377 7.631717 ATTAGCCTTCTAACTAGCAAAAAGG 57.368 36.000 9.21 9.21 37.59 3.11
378 379 8.674607 GCTTATTAGCCTTCTAACTAGCAAAAA 58.325 33.333 11.85 0.00 40.54 1.94
379 380 8.209917 GCTTATTAGCCTTCTAACTAGCAAAA 57.790 34.615 11.85 0.00 40.54 2.44
380 381 7.787725 GCTTATTAGCCTTCTAACTAGCAAA 57.212 36.000 11.85 0.00 40.54 3.68
418 419 4.862371 AGGCCTATTCCCGTCAATAAAAA 58.138 39.130 1.29 0.00 0.00 1.94
419 420 4.513406 AGGCCTATTCCCGTCAATAAAA 57.487 40.909 1.29 0.00 0.00 1.52
420 421 5.633655 TTAGGCCTATTCCCGTCAATAAA 57.366 39.130 14.74 0.00 0.00 1.40
421 422 5.633655 TTTAGGCCTATTCCCGTCAATAA 57.366 39.130 14.74 0.00 0.00 1.40
422 423 5.836024 ATTTAGGCCTATTCCCGTCAATA 57.164 39.130 14.74 0.00 0.00 1.90
423 424 4.724279 ATTTAGGCCTATTCCCGTCAAT 57.276 40.909 14.74 4.74 0.00 2.57
424 425 4.513406 AATTTAGGCCTATTCCCGTCAA 57.487 40.909 14.74 2.18 0.00 3.18
425 426 4.165372 AGAAATTTAGGCCTATTCCCGTCA 59.835 41.667 14.74 0.00 0.00 4.35
426 427 4.715713 AGAAATTTAGGCCTATTCCCGTC 58.284 43.478 14.74 6.92 0.00 4.79
427 428 4.790718 AGAAATTTAGGCCTATTCCCGT 57.209 40.909 14.74 0.00 0.00 5.28
428 429 5.130350 TGAAGAAATTTAGGCCTATTCCCG 58.870 41.667 14.74 0.00 0.00 5.14
429 430 6.015095 CCATGAAGAAATTTAGGCCTATTCCC 60.015 42.308 14.74 9.84 0.00 3.97
430 431 6.551227 ACCATGAAGAAATTTAGGCCTATTCC 59.449 38.462 14.74 3.90 0.00 3.01
431 432 7.588497 ACCATGAAGAAATTTAGGCCTATTC 57.412 36.000 14.74 14.52 0.00 1.75
474 475 8.508875 CAAAACGGTAAAGTTGTACATATCCTT 58.491 33.333 0.00 0.00 34.14 3.36
481 482 6.150809 AGGAAACAAAACGGTAAAGTTGTACA 59.849 34.615 0.00 0.00 33.18 2.90
485 486 6.469915 GTGTAGGAAACAAAACGGTAAAGTTG 59.530 38.462 0.00 0.00 40.63 3.16
486 487 6.150809 TGTGTAGGAAACAAAACGGTAAAGTT 59.849 34.615 0.00 0.00 40.63 2.66
554 571 1.728971 CACCAATGACTCGTCAAGCTC 59.271 52.381 3.60 0.00 43.58 4.09
569 586 1.457267 ATGCAAGCCACCACACCAA 60.457 52.632 0.00 0.00 0.00 3.67
949 977 3.137360 ACCTCTTCTCCTTTTGACAGCTT 59.863 43.478 0.00 0.00 0.00 3.74
955 983 3.497332 TCTCGACCTCTTCTCCTTTTGA 58.503 45.455 0.00 0.00 0.00 2.69
964 1004 0.256464 TCCCTCCTCTCGACCTCTTC 59.744 60.000 0.00 0.00 0.00 2.87
965 1005 0.705253 TTCCCTCCTCTCGACCTCTT 59.295 55.000 0.00 0.00 0.00 2.85
966 1006 0.257616 CTTCCCTCCTCTCGACCTCT 59.742 60.000 0.00 0.00 0.00 3.69
967 1007 0.753848 CCTTCCCTCCTCTCGACCTC 60.754 65.000 0.00 0.00 0.00 3.85
968 1008 1.308326 CCTTCCCTCCTCTCGACCT 59.692 63.158 0.00 0.00 0.00 3.85
969 1009 1.000612 ACCTTCCCTCCTCTCGACC 59.999 63.158 0.00 0.00 0.00 4.79
970 1010 0.323542 TCACCTTCCCTCCTCTCGAC 60.324 60.000 0.00 0.00 0.00 4.20
971 1011 0.631753 ATCACCTTCCCTCCTCTCGA 59.368 55.000 0.00 0.00 0.00 4.04
972 1012 1.036707 GATCACCTTCCCTCCTCTCG 58.963 60.000 0.00 0.00 0.00 4.04
973 1013 1.036707 CGATCACCTTCCCTCCTCTC 58.963 60.000 0.00 0.00 0.00 3.20
974 1014 0.397816 CCGATCACCTTCCCTCCTCT 60.398 60.000 0.00 0.00 0.00 3.69
975 1015 0.688087 ACCGATCACCTTCCCTCCTC 60.688 60.000 0.00 0.00 0.00 3.71
976 1016 0.688087 GACCGATCACCTTCCCTCCT 60.688 60.000 0.00 0.00 0.00 3.69
977 1017 1.823976 GACCGATCACCTTCCCTCC 59.176 63.158 0.00 0.00 0.00 4.30
978 1018 1.035932 TCGACCGATCACCTTCCCTC 61.036 60.000 0.00 0.00 0.00 4.30
979 1019 0.397254 ATCGACCGATCACCTTCCCT 60.397 55.000 0.00 0.00 0.00 4.20
980 1020 2.125178 ATCGACCGATCACCTTCCC 58.875 57.895 0.00 0.00 0.00 3.97
1021 1061 0.817634 TTCTTCACGCCCACCTTGTG 60.818 55.000 0.00 0.00 34.96 3.33
1359 1450 1.761711 TCTACATTCCCCCAAACCCA 58.238 50.000 0.00 0.00 0.00 4.51
1360 1451 2.666317 CATCTACATTCCCCCAAACCC 58.334 52.381 0.00 0.00 0.00 4.11
1361 1452 2.666317 CCATCTACATTCCCCCAAACC 58.334 52.381 0.00 0.00 0.00 3.27
1363 1454 1.063266 GCCCATCTACATTCCCCCAAA 60.063 52.381 0.00 0.00 0.00 3.28
1462 1557 0.394762 CCATGGCCTGCTGCTTCTTA 60.395 55.000 3.32 0.00 40.92 2.10
1667 1765 0.778223 CGCATGGTGATCGTCGTATG 59.222 55.000 0.00 0.00 0.00 2.39
1668 1766 0.939577 GCGCATGGTGATCGTCGTAT 60.940 55.000 0.30 0.00 0.00 3.06
1833 1931 1.087501 GAAGGACATGAAAGGGTCGC 58.912 55.000 0.00 0.00 34.87 5.19
1874 1972 2.048127 GACGAAAGCCAGCTCGGT 60.048 61.111 6.30 0.00 39.38 4.69
2105 2212 4.537135 TTTCCAGCTAGTACCACAGAAG 57.463 45.455 0.00 0.00 0.00 2.85
2106 2213 4.262894 CCTTTTCCAGCTAGTACCACAGAA 60.263 45.833 0.00 0.00 0.00 3.02
2107 2214 3.260884 CCTTTTCCAGCTAGTACCACAGA 59.739 47.826 0.00 0.00 0.00 3.41
2307 2415 8.880750 ACGTCTCTATAATTAACTTCCTTTTGC 58.119 33.333 0.00 0.00 0.00 3.68
2383 2514 1.140312 TCTTGTTCCTTCTGGCCACT 58.860 50.000 0.00 0.00 0.00 4.00
2426 2557 1.053048 GATCATACATCACGTCGCGG 58.947 55.000 6.13 0.00 0.00 6.46
2517 2648 5.531659 TGCACTATAACCCAGAAACGAAAAA 59.468 36.000 0.00 0.00 0.00 1.94
2522 2653 3.181510 GCTTGCACTATAACCCAGAAACG 60.182 47.826 0.00 0.00 0.00 3.60
2613 2745 6.396829 AGAATCAAGACAAAAACAGAAGGG 57.603 37.500 0.00 0.00 0.00 3.95
2796 3130 6.335471 TGCAGTGAATGTGATCATCTTTTT 57.665 33.333 0.00 0.00 32.56 1.94
2797 3131 5.970317 TGCAGTGAATGTGATCATCTTTT 57.030 34.783 0.00 0.00 32.56 2.27
2798 3132 5.970317 TTGCAGTGAATGTGATCATCTTT 57.030 34.783 0.00 0.00 32.56 2.52
2799 3133 5.970317 TTTGCAGTGAATGTGATCATCTT 57.030 34.783 0.00 0.00 32.56 2.40
2826 3160 4.574599 ATCTGCGAGTTGCTTTCTTTTT 57.425 36.364 3.50 0.00 46.63 1.94
2827 3161 4.574599 AATCTGCGAGTTGCTTTCTTTT 57.425 36.364 3.50 0.00 46.63 2.27
2828 3162 5.886960 ATAATCTGCGAGTTGCTTTCTTT 57.113 34.783 3.50 0.00 46.63 2.52
2921 3255 4.161754 CCCCTCCGTCCATAATATAAGACC 59.838 50.000 0.00 0.00 0.00 3.85
2933 3267 0.339162 TGTATTACCCCCTCCGTCCA 59.661 55.000 0.00 0.00 0.00 4.02
2973 3308 5.903198 AATGGTTCATCTTTTCCCCAAAA 57.097 34.783 0.00 0.00 0.00 2.44
3044 3379 7.238571 TCGGTGAATAGCTTTTAAATTCGTTC 58.761 34.615 0.00 0.00 33.28 3.95
3045 3380 7.118680 TCTCGGTGAATAGCTTTTAAATTCGTT 59.881 33.333 0.00 0.00 33.28 3.85
3049 3384 8.793592 ACTTTCTCGGTGAATAGCTTTTAAATT 58.206 29.630 0.00 0.00 34.24 1.82


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

AutoCloner maintained by Alex Coulton.