Multiple sequence alignment - TraesCS3D01G519700

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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 TraesCS3D01G519700 chr3D 100.000 5630 0 0 1 5630 602330607 602324978 0.000000e+00 10397.0
1 TraesCS3D01G519700 chr3D 93.023 43 0 2 4069 4111 309913867 309913828 6.090000e-05 60.2
2 TraesCS3D01G519700 chr3A 95.405 3482 79 21 665 4070 732062267 732058791 0.000000e+00 5469.0
3 TraesCS3D01G519700 chr3A 92.671 846 48 8 4157 5000 732058667 732057834 0.000000e+00 1206.0
4 TraesCS3D01G519700 chr3A 93.471 582 33 3 5052 5630 732057835 732057256 0.000000e+00 859.0
5 TraesCS3D01G519700 chr3A 98.479 263 4 0 127 389 631289946 631289684 1.100000e-126 464.0
6 TraesCS3D01G519700 chr3A 90.435 345 7 8 436 780 732062711 732062393 1.120000e-116 431.0
7 TraesCS3D01G519700 chr3A 93.701 127 8 0 1 127 732062840 732062714 2.070000e-44 191.0
8 TraesCS3D01G519700 chr3A 96.053 76 3 0 433 508 732062308 732062383 2.130000e-24 124.0
9 TraesCS3D01G519700 chr3A 83.544 79 3 4 4071 4139 732058747 732058669 1.310000e-06 65.8
10 TraesCS3D01G519700 chr3A 97.368 38 1 0 594 631 732062312 732062275 1.310000e-06 65.8
11 TraesCS3D01G519700 chr3B 97.202 1644 39 5 2063 3704 809605273 809603635 0.000000e+00 2774.0
12 TraesCS3D01G519700 chr3B 94.273 1624 39 13 436 2029 809606975 809605376 0.000000e+00 2435.0
13 TraesCS3D01G519700 chr3B 93.734 1564 81 9 4070 5630 809603267 809601718 0.000000e+00 2329.0
14 TraesCS3D01G519700 chr3B 96.142 337 13 0 3737 4073 809603636 809603300 8.240000e-153 551.0
15 TraesCS3D01G519700 chr3B 97.338 263 7 0 127 389 511388729 511388991 1.110000e-121 448.0
16 TraesCS3D01G519700 chr3B 89.583 48 1 3 4071 4118 606573409 606573366 2.190000e-04 58.4
17 TraesCS3D01G519700 chr4A 91.213 1855 139 18 2082 3926 617233178 617231338 0.000000e+00 2501.0
18 TraesCS3D01G519700 chr4A 86.898 1412 137 28 534 1920 617234691 617233303 0.000000e+00 1539.0
19 TraesCS3D01G519700 chr4A 86.931 857 74 22 4469 5320 617230946 617230123 0.000000e+00 928.0
20 TraesCS3D01G519700 chr4A 82.532 395 39 19 4014 4393 617231329 617230950 2.530000e-83 320.0
21 TraesCS3D01G519700 chr4A 93.023 43 2 1 4071 4113 610498629 610498588 1.690000e-05 62.1
22 TraesCS3D01G519700 chr5D 90.538 1839 134 23 2082 3915 550439514 550441317 0.000000e+00 2396.0
23 TraesCS3D01G519700 chr5D 87.792 1327 119 23 530 1833 550438182 550439488 0.000000e+00 1513.0
24 TraesCS3D01G519700 chr5D 87.052 865 72 24 4463 5320 550441706 550442537 0.000000e+00 941.0
25 TraesCS3D01G519700 chr5D 84.039 307 31 15 4098 4391 550441405 550441706 4.300000e-71 279.0
26 TraesCS3D01G519700 chr5B 91.074 1658 131 11 2082 3733 702889951 702891597 0.000000e+00 2226.0
27 TraesCS3D01G519700 chr5B 86.578 1423 138 26 535 1920 702888396 702889802 0.000000e+00 1520.0
28 TraesCS3D01G519700 chr5B 85.215 859 76 24 4469 5320 702892289 702893103 0.000000e+00 835.0
29 TraesCS3D01G519700 chr5B 96.392 194 7 0 3731 3924 702891658 702891851 2.530000e-83 320.0
30 TraesCS3D01G519700 chr5B 85.433 254 31 5 4142 4393 702892036 702892285 5.600000e-65 259.0
31 TraesCS3D01G519700 chr5B 93.023 43 2 1 4071 4113 704866480 704866521 1.690000e-05 62.1
32 TraesCS3D01G519700 chr7D 98.099 263 5 0 127 389 429475773 429475511 5.140000e-125 459.0
33 TraesCS3D01G519700 chr7D 82.353 272 27 11 2228 2490 382077123 382076864 3.420000e-52 217.0
34 TraesCS3D01G519700 chr7D 82.288 271 29 10 2228 2490 382080273 382080014 3.420000e-52 217.0
35 TraesCS3D01G519700 chr7D 87.037 54 3 3 4071 4124 41038450 41038499 2.190000e-04 58.4
36 TraesCS3D01G519700 chr7D 90.909 44 1 3 4071 4114 135026292 135026332 7.880000e-04 56.5
37 TraesCS3D01G519700 chr6B 98.106 264 3 2 127 389 173801248 173801510 5.140000e-125 459.0
38 TraesCS3D01G519700 chr4D 98.099 263 5 0 127 389 16809400 16809138 5.140000e-125 459.0
39 TraesCS3D01G519700 chr4D 93.182 44 1 2 4071 4112 494042438 494042481 4.710000e-06 63.9
40 TraesCS3D01G519700 chr2D 97.407 270 6 1 127 395 370058283 370058014 5.140000e-125 459.0
41 TraesCS3D01G519700 chr1D 98.099 263 5 0 127 389 333498248 333497986 5.140000e-125 459.0
42 TraesCS3D01G519700 chr7A 97.026 269 8 0 121 389 607557078 607556810 2.390000e-123 453.0
43 TraesCS3D01G519700 chr7A 81.985 272 28 11 2228 2490 638516904 638517163 1.590000e-50 211.0
44 TraesCS3D01G519700 chr6A 97.037 270 7 1 127 395 208511596 208511865 2.390000e-123 453.0
45 TraesCS3D01G519700 chr6A 89.362 47 3 2 4071 4117 380939740 380939696 2.190000e-04 58.4
46 TraesCS3D01G519700 chr6A 82.051 78 5 4 5507 5582 581291033 581291103 2.190000e-04 58.4
47 TraesCS3D01G519700 chr6A 82.051 78 5 4 5507 5582 581333648 581333718 2.190000e-04 58.4
48 TraesCS3D01G519700 chr1A 82.353 272 27 11 2228 2490 271752558 271752817 3.420000e-52 217.0


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 TraesCS3D01G519700 chr3D 602324978 602330607 5629 True 10397.000000 10397 100.000000 1 5630 1 chr3D.!!$R2 5629
1 TraesCS3D01G519700 chr3A 732057256 732062840 5584 True 1183.942857 5469 92.370714 1 5630 7 chr3A.!!$R2 5629
2 TraesCS3D01G519700 chr3B 809601718 809606975 5257 True 2022.250000 2774 95.337750 436 5630 4 chr3B.!!$R2 5194
3 TraesCS3D01G519700 chr4A 617230123 617234691 4568 True 1322.000000 2501 86.893500 534 5320 4 chr4A.!!$R2 4786
4 TraesCS3D01G519700 chr5D 550438182 550442537 4355 False 1282.250000 2396 87.355250 530 5320 4 chr5D.!!$F1 4790
5 TraesCS3D01G519700 chr5B 702888396 702893103 4707 False 1032.000000 2226 88.938400 535 5320 5 chr5B.!!$F2 4785
6 TraesCS3D01G519700 chr7D 382076864 382080273 3409 True 217.000000 217 82.320500 2228 2490 2 chr7D.!!$R2 262

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
203 204 0.036294 GGGAAGTCCTCGTGAAAGGG 60.036 60.000 0.00 0.0 37.02 3.95 F
333 334 0.036294 GGGAAGTCCTCGTGAAAGGG 60.036 60.000 0.00 0.0 37.02 3.95 F
1494 1771 0.179127 TCATCAAGAGGCTTCGCTCG 60.179 55.000 0.00 0.0 0.00 5.03 F
1621 1899 0.602638 TAGTTTGGTGAGCTGTGCCG 60.603 55.000 0.00 0.0 0.00 5.69 F
1628 1906 1.202580 GGTGAGCTGTGCCGAGATAAT 60.203 52.381 0.00 0.0 0.00 1.28 F
3356 6896 1.268743 GCTTTCCGATGCCAGCATTAC 60.269 52.381 6.57 0.0 36.70 1.89 F
4034 7667 0.394565 GTGACTGCCTGAAGGAGTGT 59.605 55.000 0.00 0.0 37.39 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 2257 3.084070 GACTGAAAGGCCTTGTTGTTG 57.916 47.619 21.33 9.0 33.95 3.33 R
2204 2582 4.455877 ACCGAAGAAGAATGGACATTGAAC 59.544 41.667 1.69 0.0 0.00 3.18 R
2972 6510 3.641434 AGACAGCCAATCACATTAGCT 57.359 42.857 0.00 0.0 37.72 3.32 R
3356 6896 5.227908 AGTGATTTGTTGACTGTACGGTAG 58.772 41.667 7.48 0.0 0.00 3.18 R
3702 7268 0.035630 GAGAGCCACACAAGGAGCAT 60.036 55.000 0.00 0.0 0.00 3.79 R
4421 8228 1.133606 GTGAAAAGAACCCCCAGTGGA 60.134 52.381 11.95 0.0 35.39 4.02 R
5399 9220 1.379527 CACCTAAGGAATGGCCGAAC 58.620 55.000 0.00 0.0 43.43 3.95 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
28 29 4.329256 GCCGTGTTCTTGTTAGGATAAGAC 59.671 45.833 0.00 0.00 33.42 3.01
45 46 9.664332 AGGATAAGACGATAAGTACGTATATGT 57.336 33.333 0.00 2.56 43.97 2.29
128 129 8.315391 GGTTTACGAGAACCAAGTTTTATAGT 57.685 34.615 16.21 0.00 46.66 2.12
129 130 8.438513 GGTTTACGAGAACCAAGTTTTATAGTC 58.561 37.037 16.21 0.00 46.66 2.59
130 131 8.438513 GTTTACGAGAACCAAGTTTTATAGTCC 58.561 37.037 0.00 0.00 0.00 3.85
131 132 5.485620 ACGAGAACCAAGTTTTATAGTCCC 58.514 41.667 0.00 0.00 0.00 4.46
132 133 5.012354 ACGAGAACCAAGTTTTATAGTCCCA 59.988 40.000 0.00 0.00 0.00 4.37
133 134 6.113411 CGAGAACCAAGTTTTATAGTCCCAT 58.887 40.000 0.00 0.00 0.00 4.00
134 135 7.093201 ACGAGAACCAAGTTTTATAGTCCCATA 60.093 37.037 0.00 0.00 0.00 2.74
135 136 7.438459 CGAGAACCAAGTTTTATAGTCCCATAG 59.562 40.741 0.00 0.00 0.00 2.23
136 137 7.574607 AGAACCAAGTTTTATAGTCCCATAGG 58.425 38.462 0.00 0.00 0.00 2.57
137 138 7.404980 AGAACCAAGTTTTATAGTCCCATAGGA 59.595 37.037 0.00 0.00 41.08 2.94
138 139 7.519347 ACCAAGTTTTATAGTCCCATAGGAA 57.481 36.000 0.00 0.00 46.38 3.36
139 140 8.114301 ACCAAGTTTTATAGTCCCATAGGAAT 57.886 34.615 0.00 0.00 46.38 3.01
140 141 7.998964 ACCAAGTTTTATAGTCCCATAGGAATG 59.001 37.037 0.00 0.00 46.38 2.67
141 142 8.217799 CCAAGTTTTATAGTCCCATAGGAATGA 58.782 37.037 0.00 0.00 46.38 2.57
142 143 9.627123 CAAGTTTTATAGTCCCATAGGAATGAA 57.373 33.333 0.00 0.00 46.38 2.57
144 145 9.628500 AGTTTTATAGTCCCATAGGAATGAAAC 57.372 33.333 4.91 4.91 46.38 2.78
145 146 8.847196 GTTTTATAGTCCCATAGGAATGAAACC 58.153 37.037 0.00 0.00 46.38 3.27
146 147 3.953542 AGTCCCATAGGAATGAAACCC 57.046 47.619 0.00 0.00 46.38 4.11
147 148 2.172717 AGTCCCATAGGAATGAAACCCG 59.827 50.000 0.00 0.00 46.38 5.28
148 149 2.092592 GTCCCATAGGAATGAAACCCGT 60.093 50.000 0.00 0.00 46.38 5.28
149 150 2.578940 TCCCATAGGAATGAAACCCGTT 59.421 45.455 0.00 0.00 40.08 4.44
150 151 3.010808 TCCCATAGGAATGAAACCCGTTT 59.989 43.478 0.00 0.00 40.08 3.60
151 152 3.130340 CCCATAGGAATGAAACCCGTTTG 59.870 47.826 0.00 0.00 34.84 2.93
152 153 4.013728 CCATAGGAATGAAACCCGTTTGA 58.986 43.478 0.00 0.00 34.84 2.69
153 154 4.096382 CCATAGGAATGAAACCCGTTTGAG 59.904 45.833 0.00 0.00 34.84 3.02
154 155 1.886542 AGGAATGAAACCCGTTTGAGC 59.113 47.619 0.00 0.00 32.11 4.26
155 156 1.401018 GGAATGAAACCCGTTTGAGCG 60.401 52.381 0.00 0.00 32.11 5.03
156 157 1.533731 GAATGAAACCCGTTTGAGCGA 59.466 47.619 0.00 0.00 32.11 4.93
157 158 1.156736 ATGAAACCCGTTTGAGCGAG 58.843 50.000 0.00 0.00 32.11 5.03
158 159 0.105224 TGAAACCCGTTTGAGCGAGA 59.895 50.000 0.00 0.00 32.11 4.04
159 160 0.790814 GAAACCCGTTTGAGCGAGAG 59.209 55.000 0.00 0.00 32.11 3.20
160 161 0.106149 AAACCCGTTTGAGCGAGAGT 59.894 50.000 0.00 0.00 0.00 3.24
161 162 0.963962 AACCCGTTTGAGCGAGAGTA 59.036 50.000 0.00 0.00 0.00 2.59
162 163 0.526662 ACCCGTTTGAGCGAGAGTAG 59.473 55.000 0.00 0.00 0.00 2.57
163 164 0.526662 CCCGTTTGAGCGAGAGTAGT 59.473 55.000 0.00 0.00 0.00 2.73
164 165 1.741706 CCCGTTTGAGCGAGAGTAGTA 59.258 52.381 0.00 0.00 0.00 1.82
165 166 2.477525 CCCGTTTGAGCGAGAGTAGTAC 60.478 54.545 0.00 0.00 0.00 2.73
166 167 2.419324 CCGTTTGAGCGAGAGTAGTACT 59.581 50.000 1.37 1.37 0.00 2.73
167 168 3.620374 CCGTTTGAGCGAGAGTAGTACTA 59.380 47.826 1.88 0.00 0.00 1.82
168 169 4.260294 CCGTTTGAGCGAGAGTAGTACTAG 60.260 50.000 1.87 0.00 0.00 2.57
169 170 4.260294 CGTTTGAGCGAGAGTAGTACTAGG 60.260 50.000 1.87 0.00 0.00 3.02
170 171 4.750021 TTGAGCGAGAGTAGTACTAGGA 57.250 45.455 1.87 0.00 0.00 2.94
171 172 4.959560 TGAGCGAGAGTAGTACTAGGAT 57.040 45.455 1.87 0.00 0.00 3.24
172 173 4.633175 TGAGCGAGAGTAGTACTAGGATG 58.367 47.826 1.87 0.00 0.00 3.51
173 174 3.998341 GAGCGAGAGTAGTACTAGGATGG 59.002 52.174 1.87 0.00 0.00 3.51
174 175 3.075884 GCGAGAGTAGTACTAGGATGGG 58.924 54.545 1.87 0.00 0.00 4.00
175 176 3.496515 GCGAGAGTAGTACTAGGATGGGT 60.497 52.174 1.87 0.00 0.00 4.51
176 177 4.066490 CGAGAGTAGTACTAGGATGGGTG 58.934 52.174 1.87 0.00 0.00 4.61
177 178 4.202336 CGAGAGTAGTACTAGGATGGGTGA 60.202 50.000 1.87 0.00 0.00 4.02
178 179 5.051409 AGAGTAGTACTAGGATGGGTGAC 57.949 47.826 1.87 0.00 0.00 3.67
190 191 4.234673 GGTGACCTCCTGGGAAGT 57.765 61.111 0.00 0.00 38.76 3.01
191 192 1.984020 GGTGACCTCCTGGGAAGTC 59.016 63.158 10.52 10.52 36.44 3.01
192 193 1.554583 GGTGACCTCCTGGGAAGTCC 61.555 65.000 13.79 6.97 35.38 3.85
193 194 0.545548 GTGACCTCCTGGGAAGTCCT 60.546 60.000 13.79 0.00 35.38 3.85
194 195 0.252284 TGACCTCCTGGGAAGTCCTC 60.252 60.000 13.79 0.00 35.38 3.71
195 196 1.305381 ACCTCCTGGGAAGTCCTCG 60.305 63.158 0.00 0.00 38.76 4.63
196 197 1.305381 CCTCCTGGGAAGTCCTCGT 60.305 63.158 0.00 0.00 37.23 4.18
197 198 1.608717 CCTCCTGGGAAGTCCTCGTG 61.609 65.000 0.00 0.00 37.23 4.35
198 199 0.612174 CTCCTGGGAAGTCCTCGTGA 60.612 60.000 0.00 0.00 36.20 4.35
199 200 0.178944 TCCTGGGAAGTCCTCGTGAA 60.179 55.000 0.00 0.00 36.20 3.18
200 201 0.685097 CCTGGGAAGTCCTCGTGAAA 59.315 55.000 0.00 0.00 36.20 2.69
201 202 1.338200 CCTGGGAAGTCCTCGTGAAAG 60.338 57.143 0.00 0.00 36.20 2.62
202 203 0.685097 TGGGAAGTCCTCGTGAAAGG 59.315 55.000 0.00 0.00 37.81 3.11
203 204 0.036294 GGGAAGTCCTCGTGAAAGGG 60.036 60.000 0.00 0.00 37.02 3.95
204 205 0.685660 GGAAGTCCTCGTGAAAGGGT 59.314 55.000 0.00 0.00 37.02 4.34
205 206 1.071857 GGAAGTCCTCGTGAAAGGGTT 59.928 52.381 0.00 0.00 37.02 4.11
206 207 2.486727 GGAAGTCCTCGTGAAAGGGTTT 60.487 50.000 0.00 0.00 37.02 3.27
207 208 2.545537 AGTCCTCGTGAAAGGGTTTC 57.454 50.000 0.00 0.00 40.08 2.78
208 209 1.766496 AGTCCTCGTGAAAGGGTTTCA 59.234 47.619 0.00 0.00 46.68 2.69
221 222 8.752005 TGAAAGGGTTTCATATCTAAGGATTG 57.248 34.615 0.00 0.00 44.21 2.67
222 223 8.336235 TGAAAGGGTTTCATATCTAAGGATTGT 58.664 33.333 0.00 0.00 44.21 2.71
223 224 8.525290 AAAGGGTTTCATATCTAAGGATTGTG 57.475 34.615 0.00 0.00 33.71 3.33
224 225 7.451731 AGGGTTTCATATCTAAGGATTGTGA 57.548 36.000 0.00 0.00 33.71 3.58
225 226 8.050316 AGGGTTTCATATCTAAGGATTGTGAT 57.950 34.615 0.00 0.00 33.71 3.06
226 227 9.170890 AGGGTTTCATATCTAAGGATTGTGATA 57.829 33.333 0.00 0.00 32.46 2.15
227 228 9.442047 GGGTTTCATATCTAAGGATTGTGATAG 57.558 37.037 0.00 0.00 31.83 2.08
228 229 9.442047 GGTTTCATATCTAAGGATTGTGATAGG 57.558 37.037 0.00 0.00 31.83 2.57
229 230 8.940952 GTTTCATATCTAAGGATTGTGATAGGC 58.059 37.037 0.00 0.00 31.64 3.93
230 231 8.441311 TTCATATCTAAGGATTGTGATAGGCT 57.559 34.615 0.00 0.00 31.64 4.58
231 232 8.441311 TCATATCTAAGGATTGTGATAGGCTT 57.559 34.615 0.00 0.00 31.64 4.35
232 233 8.316946 TCATATCTAAGGATTGTGATAGGCTTG 58.683 37.037 0.00 0.00 31.64 4.01
233 234 5.296151 TCTAAGGATTGTGATAGGCTTGG 57.704 43.478 0.00 0.00 0.00 3.61
234 235 2.355010 AGGATTGTGATAGGCTTGGC 57.645 50.000 0.00 0.00 0.00 4.52
235 236 0.947244 GGATTGTGATAGGCTTGGCG 59.053 55.000 0.00 0.00 0.00 5.69
236 237 1.475034 GGATTGTGATAGGCTTGGCGA 60.475 52.381 0.00 0.00 0.00 5.54
237 238 1.869767 GATTGTGATAGGCTTGGCGAG 59.130 52.381 0.00 0.00 0.00 5.03
248 249 4.458666 TGGCGAGCCAACGTAAAA 57.541 50.000 15.24 0.00 44.12 1.52
249 250 2.704108 TGGCGAGCCAACGTAAAAA 58.296 47.368 15.24 0.00 44.12 1.94
250 251 0.308376 TGGCGAGCCAACGTAAAAAC 59.692 50.000 15.24 0.00 44.12 2.43
251 252 0.589708 GGCGAGCCAACGTAAAAACT 59.410 50.000 9.58 0.00 35.81 2.66
252 253 1.799994 GGCGAGCCAACGTAAAAACTA 59.200 47.619 9.58 0.00 35.81 2.24
253 254 2.159747 GGCGAGCCAACGTAAAAACTAG 60.160 50.000 9.58 0.00 35.81 2.57
254 255 2.723923 GCGAGCCAACGTAAAAACTAGC 60.724 50.000 0.00 0.00 35.59 3.42
255 256 2.159747 CGAGCCAACGTAAAAACTAGCC 60.160 50.000 0.00 0.00 0.00 3.93
256 257 2.809696 GAGCCAACGTAAAAACTAGCCA 59.190 45.455 0.00 0.00 0.00 4.75
257 258 2.812011 AGCCAACGTAAAAACTAGCCAG 59.188 45.455 0.00 0.00 0.00 4.85
258 259 2.551032 GCCAACGTAAAAACTAGCCAGT 59.449 45.455 0.00 0.00 36.19 4.00
259 260 3.364664 GCCAACGTAAAAACTAGCCAGTC 60.365 47.826 0.00 0.00 32.29 3.51
260 261 4.062991 CCAACGTAAAAACTAGCCAGTCT 58.937 43.478 0.00 0.00 32.29 3.24
261 262 4.514066 CCAACGTAAAAACTAGCCAGTCTT 59.486 41.667 0.00 0.00 32.29 3.01
262 263 5.008316 CCAACGTAAAAACTAGCCAGTCTTT 59.992 40.000 0.00 0.00 32.29 2.52
263 264 6.459161 CCAACGTAAAAACTAGCCAGTCTTTT 60.459 38.462 0.00 0.85 32.29 2.27
264 265 6.056428 ACGTAAAAACTAGCCAGTCTTTTG 57.944 37.500 12.02 0.82 32.29 2.44
265 266 5.008316 ACGTAAAAACTAGCCAGTCTTTTGG 59.992 40.000 12.02 8.37 41.35 3.28
266 267 4.937201 AAAAACTAGCCAGTCTTTTGGG 57.063 40.909 0.00 0.00 38.72 4.12
268 269 4.717279 AAACTAGCCAGTCTTTTGGGTA 57.283 40.909 4.17 4.17 46.57 3.69
269 270 4.929146 AACTAGCCAGTCTTTTGGGTAT 57.071 40.909 4.61 0.00 46.74 2.73
270 271 4.222124 ACTAGCCAGTCTTTTGGGTATG 57.778 45.455 4.61 2.96 46.74 2.39
271 272 3.844211 ACTAGCCAGTCTTTTGGGTATGA 59.156 43.478 4.61 0.00 46.74 2.15
272 273 3.806949 AGCCAGTCTTTTGGGTATGAA 57.193 42.857 0.00 0.00 46.57 2.57
273 274 4.112634 AGCCAGTCTTTTGGGTATGAAA 57.887 40.909 0.00 0.00 46.57 2.69
274 275 3.826729 AGCCAGTCTTTTGGGTATGAAAC 59.173 43.478 0.00 0.00 46.57 2.78
275 276 5.294122 AGCCAGTCTTTTGGGTATGAAACC 61.294 45.833 0.00 0.00 46.57 3.27
295 296 2.822764 CCATTTGGGCGAGAGTAGTAC 58.177 52.381 0.00 0.00 0.00 2.73
296 297 2.431057 CCATTTGGGCGAGAGTAGTACT 59.569 50.000 1.37 1.37 0.00 2.73
297 298 3.635373 CCATTTGGGCGAGAGTAGTACTA 59.365 47.826 1.88 0.00 0.00 1.82
298 299 4.261656 CCATTTGGGCGAGAGTAGTACTAG 60.262 50.000 1.87 0.00 0.00 2.57
299 300 2.634815 TGGGCGAGAGTAGTACTAGG 57.365 55.000 1.87 0.00 0.00 3.02
300 301 2.121948 TGGGCGAGAGTAGTACTAGGA 58.878 52.381 1.87 0.00 0.00 2.94
301 302 2.709934 TGGGCGAGAGTAGTACTAGGAT 59.290 50.000 1.87 0.00 0.00 3.24
302 303 3.075884 GGGCGAGAGTAGTACTAGGATG 58.924 54.545 1.87 0.00 0.00 3.51
303 304 3.075884 GGCGAGAGTAGTACTAGGATGG 58.924 54.545 1.87 0.00 0.00 3.51
304 305 3.075884 GCGAGAGTAGTACTAGGATGGG 58.924 54.545 1.87 0.00 0.00 4.00
305 306 3.496515 GCGAGAGTAGTACTAGGATGGGT 60.497 52.174 1.87 0.00 0.00 4.51
306 307 4.066490 CGAGAGTAGTACTAGGATGGGTG 58.934 52.174 1.87 0.00 0.00 4.61
307 308 4.202336 CGAGAGTAGTACTAGGATGGGTGA 60.202 50.000 1.87 0.00 0.00 4.02
308 309 5.051409 AGAGTAGTACTAGGATGGGTGAC 57.949 47.826 1.87 0.00 0.00 3.67
320 321 4.234673 GGTGACCTCCTGGGAAGT 57.765 61.111 0.00 0.00 38.76 3.01
321 322 1.984020 GGTGACCTCCTGGGAAGTC 59.016 63.158 10.52 10.52 36.44 3.01
322 323 1.554583 GGTGACCTCCTGGGAAGTCC 61.555 65.000 13.79 6.97 35.38 3.85
323 324 0.545548 GTGACCTCCTGGGAAGTCCT 60.546 60.000 13.79 0.00 35.38 3.85
324 325 0.252284 TGACCTCCTGGGAAGTCCTC 60.252 60.000 13.79 0.00 35.38 3.71
325 326 1.305381 ACCTCCTGGGAAGTCCTCG 60.305 63.158 0.00 0.00 38.76 4.63
326 327 1.305381 CCTCCTGGGAAGTCCTCGT 60.305 63.158 0.00 0.00 37.23 4.18
327 328 1.608717 CCTCCTGGGAAGTCCTCGTG 61.609 65.000 0.00 0.00 37.23 4.35
328 329 0.612174 CTCCTGGGAAGTCCTCGTGA 60.612 60.000 0.00 0.00 36.20 4.35
329 330 0.178944 TCCTGGGAAGTCCTCGTGAA 60.179 55.000 0.00 0.00 36.20 3.18
330 331 0.685097 CCTGGGAAGTCCTCGTGAAA 59.315 55.000 0.00 0.00 36.20 2.69
331 332 1.338200 CCTGGGAAGTCCTCGTGAAAG 60.338 57.143 0.00 0.00 36.20 2.62
332 333 0.685097 TGGGAAGTCCTCGTGAAAGG 59.315 55.000 0.00 0.00 37.81 3.11
333 334 0.036294 GGGAAGTCCTCGTGAAAGGG 60.036 60.000 0.00 0.00 37.02 3.95
334 335 0.685660 GGAAGTCCTCGTGAAAGGGT 59.314 55.000 0.00 0.00 37.02 4.34
335 336 1.071857 GGAAGTCCTCGTGAAAGGGTT 59.928 52.381 0.00 0.00 37.02 4.11
336 337 2.486727 GGAAGTCCTCGTGAAAGGGTTT 60.487 50.000 0.00 0.00 37.02 3.27
337 338 2.545537 AGTCCTCGTGAAAGGGTTTC 57.454 50.000 0.00 0.00 40.08 2.78
338 339 1.766496 AGTCCTCGTGAAAGGGTTTCA 59.234 47.619 0.00 0.00 46.68 2.69
348 349 5.975988 TGAAAGGGTTTCATATCTAGCCT 57.024 39.130 0.00 0.00 44.21 4.58
350 351 6.827727 TGAAAGGGTTTCATATCTAGCCTAC 58.172 40.000 0.00 0.00 44.21 3.18
351 352 5.827326 AAGGGTTTCATATCTAGCCTACC 57.173 43.478 0.00 0.00 38.75 3.18
352 353 4.168883 AGGGTTTCATATCTAGCCTACCC 58.831 47.826 0.00 0.00 43.42 3.69
353 354 3.263681 GGGTTTCATATCTAGCCTACCCC 59.736 52.174 0.00 0.00 38.39 4.95
354 355 3.908103 GGTTTCATATCTAGCCTACCCCA 59.092 47.826 0.00 0.00 0.00 4.96
355 356 4.349930 GGTTTCATATCTAGCCTACCCCAA 59.650 45.833 0.00 0.00 0.00 4.12
356 357 5.306394 GTTTCATATCTAGCCTACCCCAAC 58.694 45.833 0.00 0.00 0.00 3.77
357 358 4.487282 TCATATCTAGCCTACCCCAACT 57.513 45.455 0.00 0.00 0.00 3.16
358 359 4.827789 TCATATCTAGCCTACCCCAACTT 58.172 43.478 0.00 0.00 0.00 2.66
359 360 5.972698 TCATATCTAGCCTACCCCAACTTA 58.027 41.667 0.00 0.00 0.00 2.24
360 361 6.571624 TCATATCTAGCCTACCCCAACTTAT 58.428 40.000 0.00 0.00 0.00 1.73
361 362 7.023120 TCATATCTAGCCTACCCCAACTTATT 58.977 38.462 0.00 0.00 0.00 1.40
362 363 7.516209 TCATATCTAGCCTACCCCAACTTATTT 59.484 37.037 0.00 0.00 0.00 1.40
363 364 5.367945 TCTAGCCTACCCCAACTTATTTG 57.632 43.478 0.00 0.00 34.63 2.32
378 379 6.451064 ACTTATTTGGGATAAAAGGCTTCG 57.549 37.500 0.00 0.00 0.00 3.79
379 380 5.949952 ACTTATTTGGGATAAAAGGCTTCGT 59.050 36.000 0.00 0.00 0.00 3.85
380 381 7.114095 ACTTATTTGGGATAAAAGGCTTCGTA 58.886 34.615 0.00 0.00 0.00 3.43
381 382 7.612633 ACTTATTTGGGATAAAAGGCTTCGTAA 59.387 33.333 0.00 0.00 0.00 3.18
382 383 5.890424 TTTGGGATAAAAGGCTTCGTAAG 57.110 39.130 0.00 0.00 0.00 2.34
383 384 4.563140 TGGGATAAAAGGCTTCGTAAGT 57.437 40.909 0.00 0.00 39.48 2.24
384 385 5.680594 TGGGATAAAAGGCTTCGTAAGTA 57.319 39.130 0.00 0.00 39.48 2.24
385 386 6.052405 TGGGATAAAAGGCTTCGTAAGTAA 57.948 37.500 0.00 0.00 39.48 2.24
386 387 6.110707 TGGGATAAAAGGCTTCGTAAGTAAG 58.889 40.000 0.00 0.00 39.48 2.34
387 388 6.111382 GGGATAAAAGGCTTCGTAAGTAAGT 58.889 40.000 0.00 0.00 39.48 2.24
388 389 7.093377 TGGGATAAAAGGCTTCGTAAGTAAGTA 60.093 37.037 0.00 0.00 39.48 2.24
389 390 7.223582 GGGATAAAAGGCTTCGTAAGTAAGTAC 59.776 40.741 0.00 0.00 39.48 2.73
390 391 7.043788 GGATAAAAGGCTTCGTAAGTAAGTACG 60.044 40.741 0.00 0.00 46.50 3.67
402 403 7.936950 GTAAGTAAGTACGAGAACCAAGTTT 57.063 36.000 0.00 0.00 0.00 2.66
403 404 8.357796 GTAAGTAAGTACGAGAACCAAGTTTT 57.642 34.615 0.00 0.00 0.00 2.43
404 405 9.463443 GTAAGTAAGTACGAGAACCAAGTTTTA 57.537 33.333 0.00 0.00 0.00 1.52
726 736 7.760794 ACATGAATAATCGACAACGGTTACTTA 59.239 33.333 0.00 0.00 45.66 2.24
792 1049 1.009829 GCCGATTGAGCGACTGATTT 58.990 50.000 0.00 0.00 0.00 2.17
873 1130 6.741992 TGTTTGATTCTTATCATTCTGCGT 57.258 33.333 0.00 0.00 40.37 5.24
1242 1516 1.201429 ACCCTTACCCTGGTGCTGAG 61.201 60.000 0.00 0.00 32.36 3.35
1494 1771 0.179127 TCATCAAGAGGCTTCGCTCG 60.179 55.000 0.00 0.00 0.00 5.03
1621 1899 0.602638 TAGTTTGGTGAGCTGTGCCG 60.603 55.000 0.00 0.00 0.00 5.69
1628 1906 1.202580 GGTGAGCTGTGCCGAGATAAT 60.203 52.381 0.00 0.00 0.00 1.28
1637 1915 4.769688 TGTGCCGAGATAATGTGAGATTT 58.230 39.130 0.00 0.00 0.00 2.17
1638 1916 5.185454 TGTGCCGAGATAATGTGAGATTTT 58.815 37.500 0.00 0.00 0.00 1.82
1640 1918 5.525378 GTGCCGAGATAATGTGAGATTTTCT 59.475 40.000 0.00 0.00 0.00 2.52
1798 2079 8.115384 TCCGCCCCTAAGTATACTTTGTATATA 58.885 37.037 22.66 2.85 37.40 0.86
2192 2570 7.326454 TGTTGAACAATTCCAACATTTTGAGA 58.674 30.769 11.40 0.00 45.13 3.27
2204 2582 8.680001 TCCAACATTTTGAGATCTGATATGTTG 58.320 33.333 26.22 26.22 45.26 3.33
2463 5995 3.250280 GTGTCAGATGCTTCTATGCCATG 59.750 47.826 1.16 0.00 0.00 3.66
2972 6510 3.067106 GCATCTTCGTCTTCTTGTTCCA 58.933 45.455 0.00 0.00 0.00 3.53
3356 6896 1.268743 GCTTTCCGATGCCAGCATTAC 60.269 52.381 6.57 0.00 36.70 1.89
3677 7217 4.043561 TCACCATAAACCCTTTCTAAGCCA 59.956 41.667 0.00 0.00 0.00 4.75
3866 7498 1.780503 AAGTAATGGGGAAGCATGGC 58.219 50.000 0.00 0.00 0.00 4.40
3987 7620 2.452600 AAAGGTGTGGAAAAGAGGCA 57.547 45.000 0.00 0.00 0.00 4.75
3990 7623 1.145738 AGGTGTGGAAAAGAGGCACAT 59.854 47.619 0.00 0.00 0.00 3.21
4004 7637 5.688807 AGAGGCACATGTAGATAGCAAAAT 58.311 37.500 0.00 0.00 0.00 1.82
4005 7638 6.125029 AGAGGCACATGTAGATAGCAAAATT 58.875 36.000 0.00 0.00 0.00 1.82
4006 7639 6.604795 AGAGGCACATGTAGATAGCAAAATTT 59.395 34.615 0.00 0.00 0.00 1.82
4034 7667 0.394565 GTGACTGCCTGAAGGAGTGT 59.605 55.000 0.00 0.00 37.39 3.55
4288 8090 4.042311 TCAGGCAACCTTTGTACAGGATTA 59.958 41.667 8.09 0.00 37.39 1.75
4289 8091 4.396166 CAGGCAACCTTTGTACAGGATTAG 59.604 45.833 8.09 0.00 37.39 1.73
4324 8127 8.107399 ACATATGGAAAGCATGATCAGTTATG 57.893 34.615 7.80 0.00 0.00 1.90
4421 8228 9.095065 GTATGGTTTCACGTTCTATTTCACTAT 57.905 33.333 0.00 0.00 0.00 2.12
4453 8261 4.401202 GGTTCTTTTCACCTTTTCCTCACA 59.599 41.667 0.00 0.00 0.00 3.58
4460 8268 5.723672 TCACCTTTTCCTCACAGTACTAG 57.276 43.478 0.00 0.00 0.00 2.57
4464 8272 5.601313 ACCTTTTCCTCACAGTACTAGTTCA 59.399 40.000 0.00 0.00 0.00 3.18
4467 8275 5.707242 TTCCTCACAGTACTAGTTCACAG 57.293 43.478 0.00 0.00 0.00 3.66
4515 8323 2.613133 GCAGATTTCTGGAGCTGACATC 59.387 50.000 9.49 0.00 43.94 3.06
4574 8382 1.272369 TGCTCACATATTTGGCACCCA 60.272 47.619 0.00 0.00 0.00 4.51
4957 8771 0.106519 CAGTATGGAAGGGGCCCTTG 60.107 60.000 41.66 22.69 44.82 3.61
4961 8775 2.035783 GGAAGGGGCCCTTGACAC 59.964 66.667 41.66 26.01 44.82 3.67
4964 8778 2.081585 GAAGGGGCCCTTGACACCTT 62.082 60.000 41.66 16.59 44.82 3.50
5114 8932 7.511959 ACCAAGTAGAATTCTTGTCCTTTTC 57.488 36.000 14.36 0.00 40.15 2.29
5128 8946 6.627087 TGTCCTTTTCCATGATAGACTTCT 57.373 37.500 0.00 0.00 0.00 2.85
5133 8951 8.206867 TCCTTTTCCATGATAGACTTCTACATG 58.793 37.037 15.11 15.11 37.51 3.21
5135 8953 8.948631 TTTTCCATGATAGACTTCTACATGAC 57.051 34.615 19.64 2.29 38.61 3.06
5156 8974 2.875933 CCGTTCTTGTACTCTTTTGCCA 59.124 45.455 0.00 0.00 0.00 4.92
5323 9144 8.171164 AGTAAAATTCTTCCTGTTCTTTCCAG 57.829 34.615 0.00 0.00 0.00 3.86
5378 9199 7.817418 ATAGATTCTGTACTTGACTCCTCTC 57.183 40.000 0.00 0.00 0.00 3.20
5379 9200 5.826643 AGATTCTGTACTTGACTCCTCTCT 58.173 41.667 0.00 0.00 0.00 3.10
5399 9220 6.346896 TCTCTCCAATCATCATCTCAACTTG 58.653 40.000 0.00 0.00 0.00 3.16
5405 9226 3.002791 TCATCATCTCAACTTGTTCGGC 58.997 45.455 0.00 0.00 0.00 5.54
5534 9356 2.231235 CCCTTGTCAAATAGGTGTTGGC 59.769 50.000 0.00 0.00 0.00 4.52
5614 9436 3.364460 TCCCATTCATCACCGTCATTT 57.636 42.857 0.00 0.00 0.00 2.32
5624 9446 2.026729 TCACCGTCATTTCTTGGCCATA 60.027 45.455 6.09 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 8.922058 TTATCGTCTTATCCTAACAAGAACAC 57.078 34.615 0.00 0.00 32.79 3.32
127 128 2.092592 ACGGGTTTCATTCCTATGGGAC 60.093 50.000 0.00 0.00 42.05 4.46
128 129 2.201830 ACGGGTTTCATTCCTATGGGA 58.798 47.619 0.00 0.00 40.36 4.37
129 130 2.729028 ACGGGTTTCATTCCTATGGG 57.271 50.000 0.00 0.00 32.40 4.00
130 131 4.013728 TCAAACGGGTTTCATTCCTATGG 58.986 43.478 0.00 0.00 32.40 2.74
131 132 4.438744 GCTCAAACGGGTTTCATTCCTATG 60.439 45.833 0.00 0.00 0.00 2.23
132 133 3.694566 GCTCAAACGGGTTTCATTCCTAT 59.305 43.478 0.00 0.00 0.00 2.57
133 134 3.078837 GCTCAAACGGGTTTCATTCCTA 58.921 45.455 0.00 0.00 0.00 2.94
134 135 1.886542 GCTCAAACGGGTTTCATTCCT 59.113 47.619 0.00 0.00 0.00 3.36
135 136 1.401018 CGCTCAAACGGGTTTCATTCC 60.401 52.381 0.00 0.00 0.00 3.01
136 137 1.533731 TCGCTCAAACGGGTTTCATTC 59.466 47.619 0.00 0.00 0.00 2.67
137 138 1.535462 CTCGCTCAAACGGGTTTCATT 59.465 47.619 0.00 0.00 0.00 2.57
138 139 1.156736 CTCGCTCAAACGGGTTTCAT 58.843 50.000 0.00 0.00 0.00 2.57
139 140 0.105224 TCTCGCTCAAACGGGTTTCA 59.895 50.000 0.00 0.00 34.33 2.69
140 141 0.790814 CTCTCGCTCAAACGGGTTTC 59.209 55.000 0.00 0.00 34.33 2.78
141 142 0.106149 ACTCTCGCTCAAACGGGTTT 59.894 50.000 0.00 0.00 34.33 3.27
142 143 0.963962 TACTCTCGCTCAAACGGGTT 59.036 50.000 0.00 0.00 34.33 4.11
143 144 0.526662 CTACTCTCGCTCAAACGGGT 59.473 55.000 0.00 0.00 34.33 5.28
144 145 0.526662 ACTACTCTCGCTCAAACGGG 59.473 55.000 0.00 0.00 33.83 5.28
145 146 2.419324 AGTACTACTCTCGCTCAAACGG 59.581 50.000 0.00 0.00 0.00 4.44
146 147 3.743567 AGTACTACTCTCGCTCAAACG 57.256 47.619 0.00 0.00 0.00 3.60
147 148 4.874966 TCCTAGTACTACTCTCGCTCAAAC 59.125 45.833 0.00 0.00 0.00 2.93
148 149 5.095145 TCCTAGTACTACTCTCGCTCAAA 57.905 43.478 0.00 0.00 0.00 2.69
149 150 4.750021 TCCTAGTACTACTCTCGCTCAA 57.250 45.455 0.00 0.00 0.00 3.02
150 151 4.503469 CCATCCTAGTACTACTCTCGCTCA 60.503 50.000 0.00 0.00 0.00 4.26
151 152 3.998341 CCATCCTAGTACTACTCTCGCTC 59.002 52.174 0.00 0.00 0.00 5.03
152 153 3.244630 CCCATCCTAGTACTACTCTCGCT 60.245 52.174 0.00 0.00 0.00 4.93
153 154 3.075884 CCCATCCTAGTACTACTCTCGC 58.924 54.545 0.00 0.00 0.00 5.03
154 155 4.066490 CACCCATCCTAGTACTACTCTCG 58.934 52.174 0.00 0.00 0.00 4.04
155 156 5.065235 GTCACCCATCCTAGTACTACTCTC 58.935 50.000 0.00 0.00 0.00 3.20
156 157 4.141205 GGTCACCCATCCTAGTACTACTCT 60.141 50.000 0.00 0.00 0.00 3.24
157 158 4.141205 AGGTCACCCATCCTAGTACTACTC 60.141 50.000 0.00 0.00 31.66 2.59
158 159 3.792684 AGGTCACCCATCCTAGTACTACT 59.207 47.826 0.00 0.00 31.66 2.57
159 160 4.143543 GAGGTCACCCATCCTAGTACTAC 58.856 52.174 0.00 0.00 33.83 2.73
160 161 3.139770 GGAGGTCACCCATCCTAGTACTA 59.860 52.174 1.89 1.89 33.83 1.82
161 162 2.091222 GGAGGTCACCCATCCTAGTACT 60.091 54.545 0.00 0.00 33.83 2.73
162 163 2.091222 AGGAGGTCACCCATCCTAGTAC 60.091 54.545 2.60 0.00 36.91 2.73
163 164 2.091278 CAGGAGGTCACCCATCCTAGTA 60.091 54.545 4.27 0.00 36.69 1.82
164 165 1.019650 AGGAGGTCACCCATCCTAGT 58.980 55.000 2.60 0.00 36.91 2.57
165 166 1.418334 CAGGAGGTCACCCATCCTAG 58.582 60.000 4.27 0.00 36.69 3.02
166 167 0.031111 CCAGGAGGTCACCCATCCTA 60.031 60.000 4.27 0.00 36.69 2.94
167 168 1.307343 CCAGGAGGTCACCCATCCT 60.307 63.158 0.00 0.00 38.30 3.24
168 169 2.378634 CCCAGGAGGTCACCCATCC 61.379 68.421 0.00 0.00 0.00 3.51
169 170 0.914417 TTCCCAGGAGGTCACCCATC 60.914 60.000 0.00 0.00 36.75 3.51
170 171 0.916358 CTTCCCAGGAGGTCACCCAT 60.916 60.000 0.00 0.00 36.75 4.00
171 172 1.538876 CTTCCCAGGAGGTCACCCA 60.539 63.158 0.00 0.00 36.75 4.51
172 173 1.539124 ACTTCCCAGGAGGTCACCC 60.539 63.158 0.00 0.00 36.75 4.61
173 174 1.984020 GACTTCCCAGGAGGTCACC 59.016 63.158 20.66 0.00 46.32 4.02
176 177 1.324005 CGAGGACTTCCCAGGAGGTC 61.324 65.000 18.15 18.15 46.33 3.85
177 178 1.305381 CGAGGACTTCCCAGGAGGT 60.305 63.158 0.31 0.31 37.15 3.85
178 179 1.305381 ACGAGGACTTCCCAGGAGG 60.305 63.158 0.00 0.00 37.41 4.30
179 180 0.612174 TCACGAGGACTTCCCAGGAG 60.612 60.000 0.00 0.00 37.41 3.69
180 181 0.178944 TTCACGAGGACTTCCCAGGA 60.179 55.000 0.00 0.00 37.41 3.86
181 182 0.685097 TTTCACGAGGACTTCCCAGG 59.315 55.000 0.00 0.00 37.41 4.45
182 183 1.338200 CCTTTCACGAGGACTTCCCAG 60.338 57.143 0.00 0.00 39.25 4.45
183 184 0.685097 CCTTTCACGAGGACTTCCCA 59.315 55.000 0.00 0.00 39.25 4.37
184 185 0.036294 CCCTTTCACGAGGACTTCCC 60.036 60.000 0.00 0.00 39.25 3.97
185 186 0.685660 ACCCTTTCACGAGGACTTCC 59.314 55.000 0.00 0.00 39.25 3.46
186 187 2.545537 AACCCTTTCACGAGGACTTC 57.454 50.000 0.00 0.00 39.25 3.01
187 188 2.171870 TGAAACCCTTTCACGAGGACTT 59.828 45.455 0.00 0.00 44.21 3.01
188 189 1.766496 TGAAACCCTTTCACGAGGACT 59.234 47.619 0.00 0.00 44.21 3.85
189 190 2.249844 TGAAACCCTTTCACGAGGAC 57.750 50.000 0.00 0.00 44.21 3.85
197 198 8.624776 CACAATCCTTAGATATGAAACCCTTTC 58.375 37.037 0.00 0.00 34.58 2.62
198 199 8.336235 TCACAATCCTTAGATATGAAACCCTTT 58.664 33.333 0.00 0.00 30.42 3.11
199 200 7.872138 TCACAATCCTTAGATATGAAACCCTT 58.128 34.615 0.00 0.00 30.42 3.95
200 201 7.451731 TCACAATCCTTAGATATGAAACCCT 57.548 36.000 0.00 0.00 30.42 4.34
201 202 9.442047 CTATCACAATCCTTAGATATGAAACCC 57.558 37.037 0.00 0.00 30.42 4.11
202 203 9.442047 CCTATCACAATCCTTAGATATGAAACC 57.558 37.037 0.00 0.00 30.42 3.27
203 204 8.940952 GCCTATCACAATCCTTAGATATGAAAC 58.059 37.037 0.00 0.00 30.42 2.78
204 205 8.884323 AGCCTATCACAATCCTTAGATATGAAA 58.116 33.333 0.00 0.00 30.42 2.69
205 206 8.441311 AGCCTATCACAATCCTTAGATATGAA 57.559 34.615 0.00 0.00 30.42 2.57
206 207 8.316946 CAAGCCTATCACAATCCTTAGATATGA 58.683 37.037 0.00 0.00 30.42 2.15
207 208 7.551974 CCAAGCCTATCACAATCCTTAGATATG 59.448 40.741 0.00 0.00 30.42 1.78
208 209 7.628234 CCAAGCCTATCACAATCCTTAGATAT 58.372 38.462 0.00 0.00 30.42 1.63
209 210 6.520742 GCCAAGCCTATCACAATCCTTAGATA 60.521 42.308 0.00 0.00 30.42 1.98
210 211 5.747248 GCCAAGCCTATCACAATCCTTAGAT 60.747 44.000 0.00 0.00 0.00 1.98
211 212 4.444876 GCCAAGCCTATCACAATCCTTAGA 60.445 45.833 0.00 0.00 0.00 2.10
212 213 3.817647 GCCAAGCCTATCACAATCCTTAG 59.182 47.826 0.00 0.00 0.00 2.18
213 214 3.744214 CGCCAAGCCTATCACAATCCTTA 60.744 47.826 0.00 0.00 0.00 2.69
214 215 2.659428 GCCAAGCCTATCACAATCCTT 58.341 47.619 0.00 0.00 0.00 3.36
215 216 1.475751 CGCCAAGCCTATCACAATCCT 60.476 52.381 0.00 0.00 0.00 3.24
216 217 0.947244 CGCCAAGCCTATCACAATCC 59.053 55.000 0.00 0.00 0.00 3.01
217 218 1.869767 CTCGCCAAGCCTATCACAATC 59.130 52.381 0.00 0.00 0.00 2.67
218 219 1.959042 CTCGCCAAGCCTATCACAAT 58.041 50.000 0.00 0.00 0.00 2.71
219 220 0.744414 GCTCGCCAAGCCTATCACAA 60.744 55.000 0.00 0.00 45.92 3.33
220 221 1.153369 GCTCGCCAAGCCTATCACA 60.153 57.895 0.00 0.00 45.92 3.58
221 222 3.724494 GCTCGCCAAGCCTATCAC 58.276 61.111 0.00 0.00 45.92 3.06
231 232 0.308376 GTTTTTACGTTGGCTCGCCA 59.692 50.000 6.52 6.52 45.63 5.69
232 233 0.589708 AGTTTTTACGTTGGCTCGCC 59.410 50.000 0.00 0.00 0.00 5.54
233 234 2.723923 GCTAGTTTTTACGTTGGCTCGC 60.724 50.000 0.00 0.00 0.00 5.03
234 235 2.159747 GGCTAGTTTTTACGTTGGCTCG 60.160 50.000 0.00 1.70 0.00 5.03
235 236 2.809696 TGGCTAGTTTTTACGTTGGCTC 59.190 45.455 0.00 0.00 0.00 4.70
236 237 2.812011 CTGGCTAGTTTTTACGTTGGCT 59.188 45.455 0.00 0.00 0.00 4.75
237 238 2.551032 ACTGGCTAGTTTTTACGTTGGC 59.449 45.455 0.00 0.00 31.66 4.52
238 239 4.062991 AGACTGGCTAGTTTTTACGTTGG 58.937 43.478 3.47 0.00 37.25 3.77
239 240 5.668558 AAGACTGGCTAGTTTTTACGTTG 57.331 39.130 3.47 0.00 37.25 4.10
240 241 6.459161 CCAAAAGACTGGCTAGTTTTTACGTT 60.459 38.462 17.28 1.45 39.50 3.99
241 242 5.008316 CCAAAAGACTGGCTAGTTTTTACGT 59.992 40.000 17.28 1.78 39.50 3.57
242 243 5.449304 CCAAAAGACTGGCTAGTTTTTACG 58.551 41.667 17.28 12.06 39.50 3.18
243 244 5.301045 ACCCAAAAGACTGGCTAGTTTTTAC 59.699 40.000 17.28 0.00 39.50 2.01
244 245 5.451354 ACCCAAAAGACTGGCTAGTTTTTA 58.549 37.500 17.28 0.00 39.50 1.52
245 246 4.286707 ACCCAAAAGACTGGCTAGTTTTT 58.713 39.130 12.22 12.22 41.44 1.94
246 247 3.910989 ACCCAAAAGACTGGCTAGTTTT 58.089 40.909 3.47 1.40 37.25 2.43
247 248 3.595190 ACCCAAAAGACTGGCTAGTTT 57.405 42.857 3.47 0.00 37.25 2.66
248 249 4.288626 TCATACCCAAAAGACTGGCTAGTT 59.711 41.667 3.47 0.00 37.25 2.24
249 250 3.844211 TCATACCCAAAAGACTGGCTAGT 59.156 43.478 0.69 0.69 40.66 2.57
250 251 4.487714 TCATACCCAAAAGACTGGCTAG 57.512 45.455 0.00 0.00 34.88 3.42
251 252 4.919774 TTCATACCCAAAAGACTGGCTA 57.080 40.909 0.00 0.00 34.88 3.93
252 253 3.806949 TTCATACCCAAAAGACTGGCT 57.193 42.857 0.00 0.00 34.88 4.75
253 254 3.056821 GGTTTCATACCCAAAAGACTGGC 60.057 47.826 0.00 0.00 41.43 4.85
254 255 4.783764 GGTTTCATACCCAAAAGACTGG 57.216 45.455 0.00 0.00 41.43 4.00
275 276 2.431057 AGTACTACTCTCGCCCAAATGG 59.569 50.000 0.00 0.00 37.09 3.16
276 277 3.802948 AGTACTACTCTCGCCCAAATG 57.197 47.619 0.00 0.00 0.00 2.32
277 278 3.890147 CCTAGTACTACTCTCGCCCAAAT 59.110 47.826 0.00 0.00 0.00 2.32
278 279 3.054139 TCCTAGTACTACTCTCGCCCAAA 60.054 47.826 0.00 0.00 0.00 3.28
279 280 2.507058 TCCTAGTACTACTCTCGCCCAA 59.493 50.000 0.00 0.00 0.00 4.12
280 281 2.121948 TCCTAGTACTACTCTCGCCCA 58.878 52.381 0.00 0.00 0.00 5.36
281 282 2.926778 TCCTAGTACTACTCTCGCCC 57.073 55.000 0.00 0.00 0.00 6.13
282 283 3.075884 CCATCCTAGTACTACTCTCGCC 58.924 54.545 0.00 0.00 0.00 5.54
283 284 3.075884 CCCATCCTAGTACTACTCTCGC 58.924 54.545 0.00 0.00 0.00 5.03
284 285 4.066490 CACCCATCCTAGTACTACTCTCG 58.934 52.174 0.00 0.00 0.00 4.04
285 286 5.065235 GTCACCCATCCTAGTACTACTCTC 58.935 50.000 0.00 0.00 0.00 3.20
286 287 4.141205 GGTCACCCATCCTAGTACTACTCT 60.141 50.000 0.00 0.00 0.00 3.24
287 288 4.141205 AGGTCACCCATCCTAGTACTACTC 60.141 50.000 0.00 0.00 31.66 2.59
288 289 3.792684 AGGTCACCCATCCTAGTACTACT 59.207 47.826 0.00 0.00 31.66 2.57
289 290 4.143543 GAGGTCACCCATCCTAGTACTAC 58.856 52.174 0.00 0.00 33.83 2.73
290 291 3.139770 GGAGGTCACCCATCCTAGTACTA 59.860 52.174 1.89 1.89 33.83 1.82
291 292 2.091222 GGAGGTCACCCATCCTAGTACT 60.091 54.545 0.00 0.00 33.83 2.73
292 293 2.091222 AGGAGGTCACCCATCCTAGTAC 60.091 54.545 2.60 0.00 36.91 2.73
293 294 2.091278 CAGGAGGTCACCCATCCTAGTA 60.091 54.545 4.27 0.00 36.69 1.82
294 295 1.019650 AGGAGGTCACCCATCCTAGT 58.980 55.000 2.60 0.00 36.91 2.57
295 296 1.418334 CAGGAGGTCACCCATCCTAG 58.582 60.000 4.27 0.00 36.69 3.02
296 297 0.031111 CCAGGAGGTCACCCATCCTA 60.031 60.000 4.27 0.00 36.69 2.94
297 298 1.307343 CCAGGAGGTCACCCATCCT 60.307 63.158 0.00 0.00 38.30 3.24
298 299 2.378634 CCCAGGAGGTCACCCATCC 61.379 68.421 0.00 0.00 0.00 3.51
299 300 0.914417 TTCCCAGGAGGTCACCCATC 60.914 60.000 0.00 0.00 36.75 3.51
300 301 0.916358 CTTCCCAGGAGGTCACCCAT 60.916 60.000 0.00 0.00 36.75 4.00
301 302 1.538876 CTTCCCAGGAGGTCACCCA 60.539 63.158 0.00 0.00 36.75 4.51
302 303 1.539124 ACTTCCCAGGAGGTCACCC 60.539 63.158 0.00 0.00 36.75 4.61
303 304 1.984020 GACTTCCCAGGAGGTCACC 59.016 63.158 20.66 0.00 46.32 4.02
306 307 1.324005 CGAGGACTTCCCAGGAGGTC 61.324 65.000 18.15 18.15 46.33 3.85
307 308 1.305381 CGAGGACTTCCCAGGAGGT 60.305 63.158 0.31 0.31 37.15 3.85
308 309 1.305381 ACGAGGACTTCCCAGGAGG 60.305 63.158 0.00 0.00 37.41 4.30
309 310 0.612174 TCACGAGGACTTCCCAGGAG 60.612 60.000 0.00 0.00 37.41 3.69
310 311 0.178944 TTCACGAGGACTTCCCAGGA 60.179 55.000 0.00 0.00 37.41 3.86
311 312 0.685097 TTTCACGAGGACTTCCCAGG 59.315 55.000 0.00 0.00 37.41 4.45
312 313 1.338200 CCTTTCACGAGGACTTCCCAG 60.338 57.143 0.00 0.00 39.25 4.45
313 314 0.685097 CCTTTCACGAGGACTTCCCA 59.315 55.000 0.00 0.00 39.25 4.37
314 315 0.036294 CCCTTTCACGAGGACTTCCC 60.036 60.000 0.00 0.00 39.25 3.97
315 316 0.685660 ACCCTTTCACGAGGACTTCC 59.314 55.000 0.00 0.00 39.25 3.46
316 317 2.545537 AACCCTTTCACGAGGACTTC 57.454 50.000 0.00 0.00 39.25 3.01
317 318 2.171870 TGAAACCCTTTCACGAGGACTT 59.828 45.455 0.00 0.00 44.21 3.01
318 319 1.766496 TGAAACCCTTTCACGAGGACT 59.234 47.619 0.00 0.00 44.21 3.85
319 320 2.249844 TGAAACCCTTTCACGAGGAC 57.750 50.000 0.00 0.00 44.21 3.85
327 328 6.231951 GGTAGGCTAGATATGAAACCCTTTC 58.768 44.000 0.00 0.00 40.08 2.62
328 329 5.073280 GGGTAGGCTAGATATGAAACCCTTT 59.927 44.000 8.73 0.00 41.75 3.11
329 330 4.597940 GGGTAGGCTAGATATGAAACCCTT 59.402 45.833 8.73 0.00 41.75 3.95
330 331 4.168883 GGGTAGGCTAGATATGAAACCCT 58.831 47.826 8.73 0.00 41.75 4.34
331 332 3.263681 GGGGTAGGCTAGATATGAAACCC 59.736 52.174 7.65 7.65 43.82 4.11
332 333 3.908103 TGGGGTAGGCTAGATATGAAACC 59.092 47.826 0.00 0.00 0.00 3.27
333 334 5.071923 AGTTGGGGTAGGCTAGATATGAAAC 59.928 44.000 0.00 0.00 0.00 2.78
334 335 5.224441 AGTTGGGGTAGGCTAGATATGAAA 58.776 41.667 0.00 0.00 0.00 2.69
335 336 4.827789 AGTTGGGGTAGGCTAGATATGAA 58.172 43.478 0.00 0.00 0.00 2.57
336 337 4.487282 AGTTGGGGTAGGCTAGATATGA 57.513 45.455 0.00 0.00 0.00 2.15
337 338 6.875972 ATAAGTTGGGGTAGGCTAGATATG 57.124 41.667 0.00 0.00 0.00 1.78
338 339 7.690256 CAAATAAGTTGGGGTAGGCTAGATAT 58.310 38.462 0.00 0.00 33.18 1.63
339 340 7.074653 CAAATAAGTTGGGGTAGGCTAGATA 57.925 40.000 0.00 0.00 33.18 1.98
340 341 5.941788 CAAATAAGTTGGGGTAGGCTAGAT 58.058 41.667 0.00 0.00 33.18 1.98
341 342 5.367945 CAAATAAGTTGGGGTAGGCTAGA 57.632 43.478 0.00 0.00 33.18 2.43
353 354 6.751888 CGAAGCCTTTTATCCCAAATAAGTTG 59.248 38.462 0.00 0.00 36.94 3.16
354 355 6.436218 ACGAAGCCTTTTATCCCAAATAAGTT 59.564 34.615 0.00 0.00 0.00 2.66
355 356 5.949952 ACGAAGCCTTTTATCCCAAATAAGT 59.050 36.000 0.00 0.00 0.00 2.24
356 357 6.451064 ACGAAGCCTTTTATCCCAAATAAG 57.549 37.500 0.00 0.00 0.00 1.73
357 358 7.612633 ACTTACGAAGCCTTTTATCCCAAATAA 59.387 33.333 0.00 0.00 0.00 1.40
358 359 7.114095 ACTTACGAAGCCTTTTATCCCAAATA 58.886 34.615 0.00 0.00 0.00 1.40
359 360 5.949952 ACTTACGAAGCCTTTTATCCCAAAT 59.050 36.000 0.00 0.00 0.00 2.32
360 361 5.318630 ACTTACGAAGCCTTTTATCCCAAA 58.681 37.500 0.00 0.00 0.00 3.28
361 362 4.913784 ACTTACGAAGCCTTTTATCCCAA 58.086 39.130 0.00 0.00 0.00 4.12
362 363 4.563140 ACTTACGAAGCCTTTTATCCCA 57.437 40.909 0.00 0.00 0.00 4.37
363 364 6.111382 ACTTACTTACGAAGCCTTTTATCCC 58.889 40.000 0.00 0.00 0.00 3.85
364 365 7.043788 CGTACTTACTTACGAAGCCTTTTATCC 60.044 40.741 0.00 0.00 46.37 2.59
365 366 7.825654 CGTACTTACTTACGAAGCCTTTTATC 58.174 38.462 0.00 0.00 46.37 1.75
366 367 7.746526 CGTACTTACTTACGAAGCCTTTTAT 57.253 36.000 0.00 0.00 46.37 1.40
377 378 5.693814 ACTTGGTTCTCGTACTTACTTACG 58.306 41.667 0.00 0.00 45.10 3.18
378 379 7.936950 AAACTTGGTTCTCGTACTTACTTAC 57.063 36.000 0.00 0.00 0.00 2.34
428 429 5.805728 TCTAACAAACTCCTGGAGATTTCC 58.194 41.667 29.71 0.00 44.31 3.13
429 430 7.929941 ATTCTAACAAACTCCTGGAGATTTC 57.070 36.000 29.71 0.00 33.32 2.17
430 431 7.309438 GCAATTCTAACAAACTCCTGGAGATTT 60.309 37.037 29.71 20.74 33.32 2.17
431 432 6.151817 GCAATTCTAACAAACTCCTGGAGATT 59.848 38.462 29.71 21.19 33.32 2.40
432 433 5.649831 GCAATTCTAACAAACTCCTGGAGAT 59.350 40.000 29.71 16.04 33.32 2.75
433 434 5.003804 GCAATTCTAACAAACTCCTGGAGA 58.996 41.667 29.71 5.54 33.32 3.71
434 435 4.156739 GGCAATTCTAACAAACTCCTGGAG 59.843 45.833 22.00 22.00 35.52 3.86
726 736 7.013083 CAGCAAGCTTATCCATAAGAACTCAAT 59.987 37.037 10.05 0.00 41.72 2.57
792 1049 0.843309 ATGTGGCCATGATTCCGGTA 59.157 50.000 9.72 0.00 0.00 4.02
873 1130 8.251026 GGTATAGACATTCATCCGACATGATAA 58.749 37.037 0.00 0.00 0.00 1.75
1628 1906 9.256228 ACCTACTCACTAATAGAAAATCTCACA 57.744 33.333 0.00 0.00 0.00 3.58
1950 2257 3.084070 GACTGAAAGGCCTTGTTGTTG 57.916 47.619 21.33 9.00 33.95 3.33
2192 2570 8.529424 AATGGACATTGAACAACATATCAGAT 57.471 30.769 0.00 0.00 0.00 2.90
2204 2582 4.455877 ACCGAAGAAGAATGGACATTGAAC 59.544 41.667 1.69 0.00 0.00 3.18
2972 6510 3.641434 AGACAGCCAATCACATTAGCT 57.359 42.857 0.00 0.00 37.72 3.32
3356 6896 5.227908 AGTGATTTGTTGACTGTACGGTAG 58.772 41.667 7.48 0.00 0.00 3.18
3702 7268 0.035630 GAGAGCCACACAAGGAGCAT 60.036 55.000 0.00 0.00 0.00 3.79
3776 7408 6.003326 TCTGATCAGTGGTAATCAGCAAAAA 58.997 36.000 21.92 0.00 45.53 1.94
3830 7462 6.378280 CCATTACTTTTGAAAGGCCACTAGAT 59.622 38.462 5.01 0.00 40.31 1.98
3866 7498 8.576442 ACCTTTCTAATATTGTCCAAGTTTGTG 58.424 33.333 0.00 0.00 0.00 3.33
3946 7579 6.530019 TTACTAGATGCTGAACTCACATCA 57.470 37.500 17.12 0.00 42.12 3.07
4034 7667 3.041211 CCCATATGAACTGGAGTGAGGA 58.959 50.000 3.65 0.00 35.70 3.71
4188 7989 8.778059 TCTGTAGTCATGGATAAAATTACCCTT 58.222 33.333 0.00 0.00 0.00 3.95
4211 8012 7.064609 ACACCATTACGTTCTACATTTCATCTG 59.935 37.037 0.00 0.00 0.00 2.90
4288 8090 2.330440 TCCATATGTTCATGCGTGCT 57.670 45.000 0.00 0.00 0.00 4.40
4289 8091 3.365832 CTTTCCATATGTTCATGCGTGC 58.634 45.455 0.00 0.00 0.00 5.34
4396 8203 9.309516 GATAGTGAAATAGAACGTGAAACCATA 57.690 33.333 0.00 0.00 0.00 2.74
4421 8228 1.133606 GTGAAAAGAACCCCCAGTGGA 60.134 52.381 11.95 0.00 35.39 4.02
4453 8261 5.221441 TGCATGTCAACTGTGAACTAGTACT 60.221 40.000 0.00 0.00 34.87 2.73
4460 8268 4.227512 TGATTGCATGTCAACTGTGAAC 57.772 40.909 4.96 0.00 37.53 3.18
4464 8272 5.654603 ATCAATGATTGCATGTCAACTGT 57.345 34.783 0.00 0.00 37.53 3.55
4467 8275 9.740239 AGTTATAATCAATGATTGCATGTCAAC 57.260 29.630 17.93 10.38 37.53 3.18
4574 8382 2.898738 CCGACTGCCTCTGCTCAT 59.101 61.111 0.00 0.00 38.71 2.90
4946 8760 1.664956 AAAGGTGTCAAGGGCCCCTT 61.665 55.000 21.43 9.97 45.88 3.95
4964 8778 2.926838 GTTCTGTTTGAAGCGGCAAAAA 59.073 40.909 1.45 3.43 39.26 1.94
4972 8786 2.056577 GCTGCATGTTCTGTTTGAAGC 58.943 47.619 0.00 0.00 35.01 3.86
5073 8888 5.321102 ACTTGGTAATGGTGCAACAGATTA 58.679 37.500 11.62 1.54 39.98 1.75
5114 8932 5.010112 ACGGTCATGTAGAAGTCTATCATGG 59.990 44.000 19.50 12.32 37.87 3.66
5128 8946 5.717078 AAGAGTACAAGAACGGTCATGTA 57.283 39.130 14.18 14.18 37.00 2.29
5133 8951 3.059120 GGCAAAAGAGTACAAGAACGGTC 60.059 47.826 0.00 0.00 0.00 4.79
5135 8953 2.875933 TGGCAAAAGAGTACAAGAACGG 59.124 45.455 0.00 0.00 0.00 4.44
5156 8974 8.083828 ACTGAAGACTATCAATCATGGTAAGT 57.916 34.615 0.00 0.00 0.00 2.24
5358 9179 4.953579 GGAGAGAGGAGTCAAGTACAGAAT 59.046 45.833 0.00 0.00 0.00 2.40
5378 9199 6.456584 CGAACAAGTTGAGATGATGATTGGAG 60.457 42.308 10.54 0.00 0.00 3.86
5379 9200 5.352293 CGAACAAGTTGAGATGATGATTGGA 59.648 40.000 10.54 0.00 0.00 3.53
5399 9220 1.379527 CACCTAAGGAATGGCCGAAC 58.620 55.000 0.00 0.00 43.43 3.95
5405 9226 6.192970 AGAACATATCCACCTAAGGAATGG 57.807 41.667 0.00 0.00 41.92 3.16
5437 9258 7.029563 CCTAGTTGATGCCAAAGAAACATAAC 58.970 38.462 0.00 0.00 33.49 1.89
5450 9272 2.973694 TTACCGACCTAGTTGATGCC 57.026 50.000 0.00 0.00 0.00 4.40
5498 9320 5.841810 TGACAAGGGCAAGAATTTTACTTG 58.158 37.500 0.00 0.00 44.92 3.16
5534 9356 7.338800 ACATAATTTTCAGGCCATTACTCAG 57.661 36.000 5.01 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.