Multiple sequence alignment - TraesCS7B01G163600

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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 TraesCS7B01G163600 chr7B 100.000 4543 0 0 1 4543 225513378 225508836 0.000000e+00 8390.0
1 TraesCS7B01G163600 chr7B 98.745 2390 13 5 378 2755 225404738 225402354 0.000000e+00 4231.0
2 TraesCS7B01G163600 chr7B 97.999 1799 15 3 2748 4543 225393595 225391815 0.000000e+00 3103.0
3 TraesCS7B01G163600 chr7B 99.383 162 0 1 4069 4230 225392131 225391971 4.450000e-75 292.0
4 TraesCS7B01G163600 chr7B 99.375 160 0 1 4071 4230 225509150 225508992 5.750000e-74 289.0
5 TraesCS7B01G163600 chr7B 99.375 160 0 1 4229 4387 225509308 225509149 5.750000e-74 289.0
6 TraesCS7B01G163600 chr7B 98.125 160 2 1 4229 4387 225392287 225392128 1.240000e-70 278.0
7 TraesCS7B01G163600 chr7B 95.238 147 7 0 4 150 225404880 225404734 2.730000e-57 233.0
8 TraesCS7B01G163600 chr7B 89.744 78 5 3 74 150 134634231 134634156 3.740000e-16 97.1
9 TraesCS7B01G163600 chr7B 97.826 46 1 0 4330 4375 225391971 225391926 3.770000e-11 80.5
10 TraesCS7B01G163600 chr7B 97.826 46 1 0 4173 4218 225391971 225391926 3.770000e-11 80.5
11 TraesCS7B01G163600 chr7B 95.652 46 2 0 4387 4432 225392028 225391983 1.750000e-09 75.0
12 TraesCS7B01G163600 chr7B 95.652 46 2 0 4387 4432 225392185 225392140 1.750000e-09 75.0
13 TraesCS7B01G163600 chr7B 95.652 46 2 0 4330 4375 225508992 225508947 1.750000e-09 75.0
14 TraesCS7B01G163600 chr7B 95.652 46 2 0 4173 4218 225508992 225508947 1.750000e-09 75.0
15 TraesCS7B01G163600 chr7B 95.652 46 2 0 4387 4432 225509049 225509004 1.750000e-09 75.0
16 TraesCS7B01G163600 chr7B 95.652 46 2 0 4387 4432 225509206 225509161 1.750000e-09 75.0
17 TraesCS7B01G163600 chr7B 94.872 39 0 2 144 181 393406658 393406621 4.910000e-05 60.2
18 TraesCS7B01G163600 chr7A 94.219 3754 122 26 534 4230 265932015 265928300 0.000000e+00 5642.0
19 TraesCS7B01G163600 chr7A 94.340 265 7 2 4229 4490 265503712 265503453 2.550000e-107 399.0
20 TraesCS7B01G163600 chr7A 97.073 205 6 0 179 383 43166100 43165896 3.360000e-91 346.0
21 TraesCS7B01G163600 chr7A 88.168 262 12 7 3983 4230 265503812 265503556 1.240000e-75 294.0
22 TraesCS7B01G163600 chr7A 91.038 212 10 4 3715 3919 265504026 265503817 1.240000e-70 278.0
23 TraesCS7B01G163600 chr7A 96.319 163 4 2 4229 4390 265928458 265928297 2.690000e-67 267.0
24 TraesCS7B01G163600 chr7A 92.486 173 13 0 3373 3545 265504636 265504464 9.760000e-62 248.0
25 TraesCS7B01G163600 chr7A 95.652 46 2 0 4498 4543 265928118 265928073 1.750000e-09 75.0
26 TraesCS7B01G163600 chr7D 96.642 1638 30 8 1927 3563 248471724 248470111 0.000000e+00 2697.0
27 TraesCS7B01G163600 chr7D 95.147 1360 49 6 587 1930 248476692 248475334 0.000000e+00 2130.0
28 TraesCS7B01G163600 chr7D 84.923 849 54 21 3298 4097 247890609 247889786 0.000000e+00 791.0
29 TraesCS7B01G163600 chr7D 92.260 323 19 4 3594 3911 248469812 248469491 1.930000e-123 453.0
30 TraesCS7B01G163600 chr7D 92.188 192 9 4 4291 4476 247886125 247885934 2.690000e-67 267.0
31 TraesCS7B01G163600 chr7D 94.262 122 3 2 4273 4390 248468198 248468077 2.790000e-42 183.0
32 TraesCS7B01G163600 chr7D 94.958 119 3 2 4115 4230 248468198 248468080 2.790000e-42 183.0
33 TraesCS7B01G163600 chr7D 93.204 103 2 4 4133 4230 247886125 247886023 3.660000e-31 147.0
34 TraesCS7B01G163600 chr7D 93.443 61 4 0 90 150 237270805 237270745 1.740000e-14 91.6
35 TraesCS7B01G163600 chr7D 93.220 59 3 1 4485 4543 247885839 247885782 8.100000e-13 86.1
36 TraesCS7B01G163600 chr7D 97.826 46 1 0 4330 4375 247886023 247885978 3.770000e-11 80.5
37 TraesCS7B01G163600 chr7D 97.826 46 1 0 4173 4218 247886023 247885978 3.770000e-11 80.5
38 TraesCS7B01G163600 chr3D 97.537 203 5 0 179 381 17667044 17667246 9.350000e-92 348.0
39 TraesCS7B01G163600 chr2B 97.073 205 6 0 179 383 762498888 762498684 3.360000e-91 346.0
40 TraesCS7B01G163600 chr2B 96.602 206 7 0 179 384 496074104 496074309 4.350000e-90 342.0
41 TraesCS7B01G163600 chr2B 95.735 211 7 2 176 386 652824049 652824257 5.630000e-89 339.0
42 TraesCS7B01G163600 chr2B 89.655 58 4 2 378 435 198447681 198447626 6.300000e-09 73.1
43 TraesCS7B01G163600 chr2B 90.698 43 3 1 133 175 245141345 245141386 6.350000e-04 56.5
44 TraesCS7B01G163600 chr4B 97.059 204 6 0 179 382 217744020 217743817 1.210000e-90 344.0
45 TraesCS7B01G163600 chr1A 97.059 204 6 0 179 382 396451606 396451403 1.210000e-90 344.0
46 TraesCS7B01G163600 chr5B 94.545 220 9 2 168 387 517204652 517204436 2.020000e-88 337.0
47 TraesCS7B01G163600 chr5B 89.706 68 7 0 83 150 444768668 444768601 2.250000e-13 87.9
48 TraesCS7B01G163600 chr5B 94.231 52 2 1 367 418 216649377 216649427 1.360000e-10 78.7
49 TraesCS7B01G163600 chr3A 94.419 215 9 2 168 382 739283619 739283830 1.220000e-85 327.0
50 TraesCS7B01G163600 chr3A 94.737 38 1 1 138 175 169857242 169857206 1.770000e-04 58.4
51 TraesCS7B01G163600 chr3A 89.362 47 2 3 147 191 623301329 623301284 6.350000e-04 56.5
52 TraesCS7B01G163600 chr5A 94.118 204 12 0 179 382 665445643 665445846 1.230000e-80 311.0
53 TraesCS7B01G163600 chr6B 95.238 63 3 0 88 150 49828779 49828841 2.890000e-17 100.0
54 TraesCS7B01G163600 chr2A 84.536 97 12 3 287 382 163450125 163450031 4.840000e-15 93.5
55 TraesCS7B01G163600 chr2A 95.833 48 2 0 378 425 92494465 92494418 1.360000e-10 78.7
56 TraesCS7B01G163600 chr2A 93.750 48 2 1 366 412 700986219 700986266 2.270000e-08 71.3
57 TraesCS7B01G163600 chr2A 100.000 33 0 0 143 175 634886389 634886421 1.360000e-05 62.1
58 TraesCS7B01G163600 chr6A 90.909 66 5 1 85 150 599809029 599808965 2.250000e-13 87.9
59 TraesCS7B01G163600 chr6A 93.023 43 0 3 145 185 4774558 4774599 4.910000e-05 60.2
60 TraesCS7B01G163600 chr6A 97.059 34 1 0 142 175 558902802 558902835 1.770000e-04 58.4
61 TraesCS7B01G163600 chr6A 100.000 28 0 0 3889 3916 12895022 12895049 8.000000e-03 52.8
62 TraesCS7B01G163600 chr6D 88.732 71 7 1 81 150 374820198 374820268 8.100000e-13 86.1
63 TraesCS7B01G163600 chr6D 89.831 59 2 3 378 432 466538171 466538113 6.300000e-09 73.1
64 TraesCS7B01G163600 chr3B 88.732 71 6 2 81 150 373620206 373620275 8.100000e-13 86.1
65 TraesCS7B01G163600 chr3B 88.571 70 8 0 81 150 719044119 719044050 8.100000e-13 86.1
66 TraesCS7B01G163600 chr5D 97.826 46 1 0 373 418 546568744 546568789 3.770000e-11 80.5
67 TraesCS7B01G163600 chr4A 89.286 56 5 1 378 432 133061451 133061506 8.160000e-08 69.4
68 TraesCS7B01G163600 chr4A 97.143 35 1 0 141 175 234138318 234138352 4.910000e-05 60.2
69 TraesCS7B01G163600 chr4A 97.059 34 1 0 142 175 501937757 501937790 1.770000e-04 58.4
70 TraesCS7B01G163600 chr4A 89.362 47 2 3 147 191 241020269 241020314 6.350000e-04 56.5
71 TraesCS7B01G163600 chr4D 86.154 65 4 5 378 441 175794958 175794898 1.050000e-06 65.8
72 TraesCS7B01G163600 chrUn 97.143 35 1 0 141 175 3944708 3944742 4.910000e-05 60.2
73 TraesCS7B01G163600 chrUn 97.143 35 1 0 141 175 284394741 284394775 4.910000e-05 60.2
74 TraesCS7B01G163600 chr1D 100.000 28 0 0 3887 3914 462088011 462087984 8.000000e-03 52.8


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 TraesCS7B01G163600 chr7B 225508836 225513378 4542 True 8390.000000 8390 100.000000 1 4543 1 chr7B.!!$R2 4542
1 TraesCS7B01G163600 chr7B 225402354 225404880 2526 True 2232.000000 4231 96.991500 4 2755 2 chr7B.!!$R5 2751
2 TraesCS7B01G163600 chr7B 225391815 225393595 1780 True 569.142857 3103 97.494714 2748 4543 7 chr7B.!!$R4 1795
3 TraesCS7B01G163600 chr7A 265928073 265932015 3942 True 1994.666667 5642 95.396667 534 4543 3 chr7A.!!$R3 4009
4 TraesCS7B01G163600 chr7A 265503453 265504636 1183 True 304.750000 399 91.508000 3373 4490 4 chr7A.!!$R2 1117
5 TraesCS7B01G163600 chr7D 248468077 248476692 8615 True 1129.200000 2697 94.653800 587 4390 5 chr7D.!!$R3 3803
6 TraesCS7B01G163600 chr7D 247885782 247890609 4827 True 242.016667 791 93.197833 3298 4543 6 chr7D.!!$R2 1245

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
164 165 0.412640 AGTACTCCCTCCGGTCCTTT 59.587 55.000 0.0 0.00 0.00 3.11 F
656 661 1.067985 CACTCTTCTCAGCGAGCAAGA 60.068 52.381 0.0 13.69 30.99 3.02 F
858 864 1.661509 GCTTGTTCTTGCAACCGGC 60.662 57.895 0.0 0.00 45.13 6.13 F
1370 1376 3.561143 TCAGTATTGTGGTGGCTGTTTT 58.439 40.909 0.0 0.00 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1273 1279 3.704800 TCCACAATTCCCGTACATCAA 57.295 42.857 0.00 0.0 0.00 2.57 R
1465 1471 3.876341 AGGAAACAAAACTGTCGGTACA 58.124 40.909 0.00 0.0 0.00 2.90 R
2250 5881 4.118168 AGTTGGAGGATTCACCAATGTT 57.882 40.909 6.15 0.0 43.56 2.71 R
3862 8031 7.232941 ACAGAGGTAGAACAAGTTACAGTACAT 59.767 37.037 0.00 0.0 0.00 2.29 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
57 58 2.915463 AGTAAAATCGAAGTCGCTCACG 59.085 45.455 0.00 0.00 39.60 4.35
101 102 1.755393 AACACACACTCCCTCCGTCC 61.755 60.000 0.00 0.00 0.00 4.79
119 120 4.277423 CCGTCCCAAAATAAGTGTCTTGTT 59.723 41.667 0.00 0.00 0.00 2.83
120 121 5.221165 CCGTCCCAAAATAAGTGTCTTGTTT 60.221 40.000 0.00 0.00 0.00 2.83
153 154 6.723131 CTTTGCACTAAAGTTAGTACTCCC 57.277 41.667 0.00 0.00 41.82 4.30
154 155 6.429521 TTTGCACTAAAGTTAGTACTCCCT 57.570 37.500 0.00 0.00 41.82 4.20
155 156 5.656213 TGCACTAAAGTTAGTACTCCCTC 57.344 43.478 0.00 0.00 41.82 4.30
156 157 4.465305 TGCACTAAAGTTAGTACTCCCTCC 59.535 45.833 0.00 0.00 41.82 4.30
157 158 4.439837 GCACTAAAGTTAGTACTCCCTCCG 60.440 50.000 0.00 0.00 41.82 4.63
158 159 4.097589 CACTAAAGTTAGTACTCCCTCCGG 59.902 50.000 0.00 0.00 41.82 5.14
159 160 2.915657 AAGTTAGTACTCCCTCCGGT 57.084 50.000 0.00 0.00 31.99 5.28
160 161 2.433662 AGTTAGTACTCCCTCCGGTC 57.566 55.000 0.00 0.00 0.00 4.79
161 162 1.064091 AGTTAGTACTCCCTCCGGTCC 60.064 57.143 0.00 0.00 0.00 4.46
162 163 1.064091 GTTAGTACTCCCTCCGGTCCT 60.064 57.143 0.00 0.00 0.00 3.85
163 164 1.302907 TAGTACTCCCTCCGGTCCTT 58.697 55.000 0.00 0.00 0.00 3.36
164 165 0.412640 AGTACTCCCTCCGGTCCTTT 59.587 55.000 0.00 0.00 0.00 3.11
165 166 1.203275 AGTACTCCCTCCGGTCCTTTT 60.203 52.381 0.00 0.00 0.00 2.27
166 167 1.627329 GTACTCCCTCCGGTCCTTTTT 59.373 52.381 0.00 0.00 0.00 1.94
167 168 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
168 169 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
169 170 1.907255 CTCCCTCCGGTCCTTTTTACT 59.093 52.381 0.00 0.00 0.00 2.24
170 171 2.305052 CTCCCTCCGGTCCTTTTTACTT 59.695 50.000 0.00 0.00 0.00 2.24
171 172 2.712627 TCCCTCCGGTCCTTTTTACTTT 59.287 45.455 0.00 0.00 0.00 2.66
172 173 2.817844 CCCTCCGGTCCTTTTTACTTTG 59.182 50.000 0.00 0.00 0.00 2.77
173 174 2.228103 CCTCCGGTCCTTTTTACTTTGC 59.772 50.000 0.00 0.00 0.00 3.68
174 175 2.882137 CTCCGGTCCTTTTTACTTTGCA 59.118 45.455 0.00 0.00 0.00 4.08
175 176 2.619646 TCCGGTCCTTTTTACTTTGCAC 59.380 45.455 0.00 0.00 0.00 4.57
176 177 2.621526 CCGGTCCTTTTTACTTTGCACT 59.378 45.455 0.00 0.00 0.00 4.40
177 178 3.816523 CCGGTCCTTTTTACTTTGCACTA 59.183 43.478 0.00 0.00 0.00 2.74
178 179 4.276431 CCGGTCCTTTTTACTTTGCACTAA 59.724 41.667 0.00 0.00 0.00 2.24
179 180 5.221087 CCGGTCCTTTTTACTTTGCACTAAA 60.221 40.000 0.00 0.00 0.00 1.85
192 193 7.538303 CTTTGCACTAAAGTTTGACCAAATT 57.462 32.000 0.00 0.00 40.71 1.82
193 194 7.913674 TTTGCACTAAAGTTTGACCAAATTT 57.086 28.000 0.00 0.00 32.66 1.82
194 195 9.092876 CTTTGCACTAAAGTTTGACCAAATTTA 57.907 29.630 0.00 6.73 40.71 1.40
195 196 9.606631 TTTGCACTAAAGTTTGACCAAATTTAT 57.393 25.926 0.00 0.00 31.37 1.40
273 274 7.559486 TCCCGAGATGAATCTAATGATATTGG 58.441 38.462 0.00 0.00 37.25 3.16
274 275 7.180946 TCCCGAGATGAATCTAATGATATTGGT 59.819 37.037 0.00 0.00 37.25 3.67
275 276 7.279536 CCCGAGATGAATCTAATGATATTGGTG 59.720 40.741 0.00 0.00 37.25 4.17
276 277 7.821359 CCGAGATGAATCTAATGATATTGGTGT 59.179 37.037 0.00 0.00 37.25 4.16
277 278 9.212641 CGAGATGAATCTAATGATATTGGTGTT 57.787 33.333 0.00 0.00 37.25 3.32
279 280 9.857656 AGATGAATCTAATGATATTGGTGTTGT 57.142 29.630 0.00 0.00 34.85 3.32
332 333 5.972107 CTTGGTCAAAGTTGGATGAGATT 57.028 39.130 0.00 0.00 0.00 2.40
333 334 5.706916 CTTGGTCAAAGTTGGATGAGATTG 58.293 41.667 0.00 0.00 0.00 2.67
334 335 4.984295 TGGTCAAAGTTGGATGAGATTGA 58.016 39.130 0.00 0.00 0.00 2.57
335 336 4.761739 TGGTCAAAGTTGGATGAGATTGAC 59.238 41.667 7.68 7.68 43.51 3.18
336 337 5.006386 GGTCAAAGTTGGATGAGATTGACT 58.994 41.667 13.97 0.00 43.66 3.41
337 338 5.474876 GGTCAAAGTTGGATGAGATTGACTT 59.525 40.000 13.97 0.00 43.66 3.01
338 339 6.015940 GGTCAAAGTTGGATGAGATTGACTTT 60.016 38.462 13.97 0.00 43.66 2.66
339 340 7.174946 GGTCAAAGTTGGATGAGATTGACTTTA 59.825 37.037 13.97 0.00 43.66 1.85
340 341 8.233190 GTCAAAGTTGGATGAGATTGACTTTAG 58.767 37.037 8.70 0.00 41.92 1.85
341 342 8.156820 TCAAAGTTGGATGAGATTGACTTTAGA 58.843 33.333 0.00 0.00 36.06 2.10
342 343 7.913674 AAGTTGGATGAGATTGACTTTAGAC 57.086 36.000 0.00 0.00 0.00 2.59
343 344 7.009179 AGTTGGATGAGATTGACTTTAGACA 57.991 36.000 0.00 0.00 0.00 3.41
344 345 7.453393 AGTTGGATGAGATTGACTTTAGACAA 58.547 34.615 0.00 0.00 34.59 3.18
345 346 7.939039 AGTTGGATGAGATTGACTTTAGACAAA 59.061 33.333 0.00 0.00 33.89 2.83
346 347 7.672983 TGGATGAGATTGACTTTAGACAAAC 57.327 36.000 0.00 0.00 33.89 2.93
347 348 6.655003 TGGATGAGATTGACTTTAGACAAACC 59.345 38.462 0.00 0.00 33.89 3.27
348 349 6.881602 GGATGAGATTGACTTTAGACAAACCT 59.118 38.462 0.00 0.89 33.89 3.50
349 350 8.041323 GGATGAGATTGACTTTAGACAAACCTA 58.959 37.037 0.00 0.00 33.89 3.08
350 351 9.436957 GATGAGATTGACTTTAGACAAACCTAA 57.563 33.333 0.00 0.00 33.89 2.69
351 352 9.965902 ATGAGATTGACTTTAGACAAACCTAAT 57.034 29.630 0.00 0.00 33.89 1.73
352 353 9.219603 TGAGATTGACTTTAGACAAACCTAATG 57.780 33.333 0.00 0.00 33.89 1.90
353 354 9.220767 GAGATTGACTTTAGACAAACCTAATGT 57.779 33.333 0.00 0.00 38.73 2.71
354 355 9.003658 AGATTGACTTTAGACAAACCTAATGTG 57.996 33.333 0.00 0.00 37.23 3.21
355 356 6.554334 TGACTTTAGACAAACCTAATGTGC 57.446 37.500 0.00 0.00 37.23 4.57
356 357 6.058833 TGACTTTAGACAAACCTAATGTGCA 58.941 36.000 0.00 0.00 37.23 4.57
357 358 6.204688 TGACTTTAGACAAACCTAATGTGCAG 59.795 38.462 0.00 0.00 37.23 4.41
358 359 6.296026 ACTTTAGACAAACCTAATGTGCAGA 58.704 36.000 0.00 0.00 36.37 4.26
359 360 6.428159 ACTTTAGACAAACCTAATGTGCAGAG 59.572 38.462 0.00 0.00 36.37 3.35
360 361 4.357918 AGACAAACCTAATGTGCAGAGT 57.642 40.909 0.00 0.00 0.00 3.24
361 362 5.483685 AGACAAACCTAATGTGCAGAGTA 57.516 39.130 0.00 0.00 0.00 2.59
362 363 5.865085 AGACAAACCTAATGTGCAGAGTAA 58.135 37.500 0.00 0.00 0.00 2.24
363 364 6.296026 AGACAAACCTAATGTGCAGAGTAAA 58.704 36.000 0.00 0.00 0.00 2.01
364 365 6.770785 AGACAAACCTAATGTGCAGAGTAAAA 59.229 34.615 0.00 0.00 0.00 1.52
365 366 7.284489 AGACAAACCTAATGTGCAGAGTAAAAA 59.716 33.333 0.00 0.00 0.00 1.94
366 367 7.425606 ACAAACCTAATGTGCAGAGTAAAAAG 58.574 34.615 0.00 0.00 0.00 2.27
367 368 6.575162 AACCTAATGTGCAGAGTAAAAAGG 57.425 37.500 0.00 0.00 0.00 3.11
368 369 5.876357 ACCTAATGTGCAGAGTAAAAAGGA 58.124 37.500 5.00 0.00 0.00 3.36
369 370 5.705905 ACCTAATGTGCAGAGTAAAAAGGAC 59.294 40.000 5.00 0.00 0.00 3.85
370 371 5.123979 CCTAATGTGCAGAGTAAAAAGGACC 59.876 44.000 0.00 0.00 0.00 4.46
371 372 2.489971 TGTGCAGAGTAAAAAGGACCG 58.510 47.619 0.00 0.00 0.00 4.79
372 373 1.804748 GTGCAGAGTAAAAAGGACCGG 59.195 52.381 0.00 0.00 0.00 5.28
373 374 1.695242 TGCAGAGTAAAAAGGACCGGA 59.305 47.619 9.46 0.00 0.00 5.14
374 375 2.289444 TGCAGAGTAAAAAGGACCGGAG 60.289 50.000 9.46 0.00 0.00 4.63
422 423 2.169330 GGGACGGAGGAGGTATCATAC 58.831 57.143 0.00 0.00 0.00 2.39
423 424 2.490351 GGGACGGAGGAGGTATCATACA 60.490 54.545 0.00 0.00 0.00 2.29
424 425 3.432378 GGACGGAGGAGGTATCATACAT 58.568 50.000 0.00 0.00 0.00 2.29
656 661 1.067985 CACTCTTCTCAGCGAGCAAGA 60.068 52.381 0.00 13.69 30.99 3.02
698 704 4.002506 TGACATCACCACGCGCCT 62.003 61.111 5.73 0.00 0.00 5.52
858 864 1.661509 GCTTGTTCTTGCAACCGGC 60.662 57.895 0.00 0.00 45.13 6.13
1370 1376 3.561143 TCAGTATTGTGGTGGCTGTTTT 58.439 40.909 0.00 0.00 0.00 2.43
2250 5881 1.555075 CTCATCCTCCGGAACCAGAAA 59.445 52.381 5.23 0.00 34.34 2.52
3862 8031 7.437267 GCCACAGTTATCGCTATTTACTTAAGA 59.563 37.037 10.09 0.00 0.00 2.10
3902 8114 5.827797 TCTACCTCTGTTGAACTGCAAAAAT 59.172 36.000 0.00 0.00 38.44 1.82
3948 8739 6.123045 AGTAACAATTAACCTGCCTAGTGT 57.877 37.500 0.00 0.00 0.00 3.55
4006 8829 7.439056 ACAAAATGTCATTTCAGGTTGTTCATC 59.561 33.333 11.19 0.00 29.84 2.92
4035 8858 0.541764 GAAATGCTTCACCCCACCCA 60.542 55.000 0.00 0.00 0.00 4.51
4036 8859 0.831711 AAATGCTTCACCCCACCCAC 60.832 55.000 0.00 0.00 0.00 4.61
4037 8860 2.730129 AATGCTTCACCCCACCCACC 62.730 60.000 0.00 0.00 0.00 4.61
4038 8861 4.678743 GCTTCACCCCACCCACCC 62.679 72.222 0.00 0.00 0.00 4.61
4039 8862 3.979497 CTTCACCCCACCCACCCC 61.979 72.222 0.00 0.00 0.00 4.95
4040 8863 4.865228 TTCACCCCACCCACCCCA 62.865 66.667 0.00 0.00 0.00 4.96
4206 13076 1.352622 TGTCCACAAGGCAGGGTCTT 61.353 55.000 0.00 0.00 33.74 3.01
4207 13077 0.690762 GTCCACAAGGCAGGGTCTTA 59.309 55.000 0.00 0.00 33.74 2.10
4208 13078 1.282157 GTCCACAAGGCAGGGTCTTAT 59.718 52.381 0.00 0.00 33.74 1.73
4209 13079 1.992557 TCCACAAGGCAGGGTCTTATT 59.007 47.619 0.00 0.00 33.74 1.40
4210 13080 2.026262 TCCACAAGGCAGGGTCTTATTC 60.026 50.000 0.00 0.00 33.74 1.75
4211 13081 2.369394 CACAAGGCAGGGTCTTATTCC 58.631 52.381 0.00 0.00 0.00 3.01
4212 13082 1.992557 ACAAGGCAGGGTCTTATTCCA 59.007 47.619 0.00 0.00 0.00 3.53
4213 13083 2.378547 ACAAGGCAGGGTCTTATTCCAA 59.621 45.455 0.00 0.00 0.00 3.53
4214 13084 3.181423 ACAAGGCAGGGTCTTATTCCAAA 60.181 43.478 0.00 0.00 0.00 3.28
4215 13085 3.825908 AGGCAGGGTCTTATTCCAAAA 57.174 42.857 0.00 0.00 0.00 2.44
4216 13086 4.126520 AGGCAGGGTCTTATTCCAAAAA 57.873 40.909 0.00 0.00 0.00 1.94
4217 13087 4.687976 AGGCAGGGTCTTATTCCAAAAAT 58.312 39.130 0.00 0.00 0.00 1.82
4218 13088 4.467438 AGGCAGGGTCTTATTCCAAAAATG 59.533 41.667 0.00 0.00 0.00 2.32
4219 13089 4.222810 GGCAGGGTCTTATTCCAAAAATGT 59.777 41.667 0.00 0.00 0.00 2.71
4220 13090 5.420739 GGCAGGGTCTTATTCCAAAAATGTA 59.579 40.000 0.00 0.00 0.00 2.29
4221 13091 6.071051 GGCAGGGTCTTATTCCAAAAATGTAA 60.071 38.462 0.00 0.00 0.00 2.41
4222 13092 6.811665 GCAGGGTCTTATTCCAAAAATGTAAC 59.188 38.462 0.00 0.00 0.00 2.50
4223 13093 7.320399 CAGGGTCTTATTCCAAAAATGTAACC 58.680 38.462 0.00 0.00 0.00 2.85
4224 13094 7.013834 AGGGTCTTATTCCAAAAATGTAACCA 58.986 34.615 0.00 0.00 0.00 3.67
4225 13095 7.511028 AGGGTCTTATTCCAAAAATGTAACCAA 59.489 33.333 0.00 0.00 0.00 3.67
4226 13096 8.318412 GGGTCTTATTCCAAAAATGTAACCAAT 58.682 33.333 0.00 0.00 0.00 3.16
4227 13097 9.719355 GGTCTTATTCCAAAAATGTAACCAATT 57.281 29.630 0.00 0.00 0.00 2.32
4233 13103 7.954788 TCCAAAAATGTAACCAATTTAGCAC 57.045 32.000 0.00 0.00 0.00 4.40
4234 13104 7.731054 TCCAAAAATGTAACCAATTTAGCACT 58.269 30.769 0.00 0.00 0.00 4.40
4235 13105 7.870445 TCCAAAAATGTAACCAATTTAGCACTC 59.130 33.333 0.00 0.00 0.00 3.51
4236 13106 7.872483 CCAAAAATGTAACCAATTTAGCACTCT 59.128 33.333 0.00 0.00 0.00 3.24
4237 13107 9.260002 CAAAAATGTAACCAATTTAGCACTCTT 57.740 29.630 0.00 0.00 0.00 2.85
4269 13139 6.642707 TTTTTGATGTAACAGTAGTTGGGG 57.357 37.500 0.00 0.00 38.69 4.96
4270 13140 5.570205 TTTGATGTAACAGTAGTTGGGGA 57.430 39.130 0.00 0.00 38.69 4.81
4271 13141 5.772393 TTGATGTAACAGTAGTTGGGGAT 57.228 39.130 0.00 0.00 38.69 3.85
4272 13142 6.877668 TTGATGTAACAGTAGTTGGGGATA 57.122 37.500 0.00 0.00 38.69 2.59
4273 13143 7.446106 TTGATGTAACAGTAGTTGGGGATAT 57.554 36.000 0.00 0.00 38.69 1.63
4274 13144 7.062749 TGATGTAACAGTAGTTGGGGATATC 57.937 40.000 0.00 0.00 38.69 1.63
4275 13145 6.844388 TGATGTAACAGTAGTTGGGGATATCT 59.156 38.462 2.05 0.00 38.69 1.98
4276 13146 7.347222 TGATGTAACAGTAGTTGGGGATATCTT 59.653 37.037 2.05 0.00 38.69 2.40
4277 13147 8.792830 ATGTAACAGTAGTTGGGGATATCTTA 57.207 34.615 2.05 0.00 38.69 2.10
4278 13148 8.792830 TGTAACAGTAGTTGGGGATATCTTAT 57.207 34.615 2.05 0.00 38.69 1.73
4279 13149 9.220906 TGTAACAGTAGTTGGGGATATCTTATT 57.779 33.333 2.05 0.00 38.69 1.40
4283 13153 9.670442 ACAGTAGTTGGGGATATCTTATTAAGA 57.330 33.333 8.53 8.53 42.69 2.10
4284 13154 9.930693 CAGTAGTTGGGGATATCTTATTAAGAC 57.069 37.037 8.27 0.00 41.01 3.01
4285 13155 9.670442 AGTAGTTGGGGATATCTTATTAAGACA 57.330 33.333 8.27 0.00 41.01 3.41
4288 13158 9.170890 AGTTGGGGATATCTTATTAAGACATCA 57.829 33.333 20.72 4.45 42.00 3.07
4289 13159 9.220767 GTTGGGGATATCTTATTAAGACATCAC 57.779 37.037 20.72 18.31 42.74 3.06
4290 13160 8.504811 TGGGGATATCTTATTAAGACATCACA 57.495 34.615 22.30 17.42 44.74 3.58
4291 13161 8.375506 TGGGGATATCTTATTAAGACATCACAC 58.624 37.037 22.30 14.63 44.74 3.82
4292 13162 8.375506 GGGGATATCTTATTAAGACATCACACA 58.624 37.037 22.30 0.00 44.74 3.72
4293 13163 9.778741 GGGATATCTTATTAAGACATCACACAA 57.221 33.333 20.72 0.00 42.93 3.33
4296 13166 9.836864 ATATCTTATTAAGACATCACACAAGCA 57.163 29.630 8.27 0.00 41.01 3.91
4297 13167 8.743085 ATCTTATTAAGACATCACACAAGCAT 57.257 30.769 8.27 0.00 41.01 3.79
4298 13168 9.836864 ATCTTATTAAGACATCACACAAGCATA 57.163 29.630 8.27 0.00 41.01 3.14
4299 13169 9.836864 TCTTATTAAGACATCACACAAGCATAT 57.163 29.630 1.90 0.00 31.20 1.78
4328 13198 9.793259 AATTAACAAGTCTTCCTCTGATACAAA 57.207 29.630 0.00 0.00 0.00 2.83
4329 13199 9.793259 ATTAACAAGTCTTCCTCTGATACAAAA 57.207 29.630 0.00 0.00 0.00 2.44
4330 13200 9.621629 TTAACAAGTCTTCCTCTGATACAAAAA 57.378 29.630 0.00 0.00 0.00 1.94
4331 13201 8.697507 AACAAGTCTTCCTCTGATACAAAAAT 57.302 30.769 0.00 0.00 0.00 1.82
4332 13202 8.329203 ACAAGTCTTCCTCTGATACAAAAATC 57.671 34.615 0.00 0.00 0.00 2.17
4333 13203 7.391833 ACAAGTCTTCCTCTGATACAAAAATCC 59.608 37.037 0.00 0.00 0.00 3.01
4334 13204 7.020827 AGTCTTCCTCTGATACAAAAATCCA 57.979 36.000 0.00 0.00 0.00 3.41
4335 13205 7.461749 AGTCTTCCTCTGATACAAAAATCCAA 58.538 34.615 0.00 0.00 0.00 3.53
4336 13206 7.391833 AGTCTTCCTCTGATACAAAAATCCAAC 59.608 37.037 0.00 0.00 0.00 3.77
4337 13207 6.659242 TCTTCCTCTGATACAAAAATCCAACC 59.341 38.462 0.00 0.00 0.00 3.77
4338 13208 4.941263 TCCTCTGATACAAAAATCCAACCG 59.059 41.667 0.00 0.00 0.00 4.44
4339 13209 4.700213 CCTCTGATACAAAAATCCAACCGT 59.300 41.667 0.00 0.00 0.00 4.83
4340 13210 5.391950 CCTCTGATACAAAAATCCAACCGTG 60.392 44.000 0.00 0.00 0.00 4.94
4341 13211 5.067273 TCTGATACAAAAATCCAACCGTGT 58.933 37.500 0.00 0.00 0.00 4.49
4342 13212 5.533154 TCTGATACAAAAATCCAACCGTGTT 59.467 36.000 0.00 0.00 0.00 3.32
4343 13213 5.524284 TGATACAAAAATCCAACCGTGTTG 58.476 37.500 9.11 9.11 0.00 3.33
4344 13214 3.878160 ACAAAAATCCAACCGTGTTGT 57.122 38.095 13.41 0.00 0.00 3.32
4345 13215 3.516615 ACAAAAATCCAACCGTGTTGTG 58.483 40.909 13.41 7.99 0.00 3.33
4346 13216 3.056465 ACAAAAATCCAACCGTGTTGTGT 60.056 39.130 13.41 8.46 0.00 3.72
4347 13217 3.430333 AAAATCCAACCGTGTTGTGTC 57.570 42.857 13.41 0.00 0.00 3.67
4348 13218 1.314730 AATCCAACCGTGTTGTGTCC 58.685 50.000 13.41 0.00 0.00 4.02
4349 13219 0.181587 ATCCAACCGTGTTGTGTCCA 59.818 50.000 13.41 0.00 0.00 4.02
4350 13220 0.745128 TCCAACCGTGTTGTGTCCAC 60.745 55.000 13.41 0.00 0.00 4.02
4351 13221 1.027255 CCAACCGTGTTGTGTCCACA 61.027 55.000 13.41 0.00 39.98 4.17
4358 13228 4.577152 TTGTGTCCACAAGGCAGG 57.423 55.556 8.71 0.00 45.42 4.85
4359 13229 1.152777 TTGTGTCCACAAGGCAGGG 60.153 57.895 8.71 0.00 45.42 4.45
4360 13230 1.932156 TTGTGTCCACAAGGCAGGGT 61.932 55.000 8.71 0.00 45.42 4.34
4361 13231 1.600916 GTGTCCACAAGGCAGGGTC 60.601 63.158 0.00 0.00 33.74 4.46
4362 13232 1.770110 TGTCCACAAGGCAGGGTCT 60.770 57.895 0.00 0.00 33.74 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 6.884836 GGAGGGAGTGTGTGTTTATAGAAAAT 59.115 38.462 0.00 0.00 0.00 1.82
88 89 0.328258 ATTTTGGGACGGAGGGAGTG 59.672 55.000 0.00 0.00 0.00 3.51
153 154 2.882137 TGCAAAGTAAAAAGGACCGGAG 59.118 45.455 9.46 0.00 0.00 4.63
154 155 2.619646 GTGCAAAGTAAAAAGGACCGGA 59.380 45.455 9.46 0.00 0.00 5.14
155 156 2.621526 AGTGCAAAGTAAAAAGGACCGG 59.378 45.455 0.00 0.00 0.00 5.28
156 157 3.982576 AGTGCAAAGTAAAAAGGACCG 57.017 42.857 0.00 0.00 0.00 4.79
169 170 7.913674 AAATTTGGTCAAACTTTAGTGCAAA 57.086 28.000 0.00 0.00 32.51 3.68
247 248 8.209584 CCAATATCATTAGATTCATCTCGGGAT 58.790 37.037 0.00 0.00 38.32 3.85
248 249 7.180946 ACCAATATCATTAGATTCATCTCGGGA 59.819 37.037 0.00 0.00 38.32 5.14
249 250 7.279536 CACCAATATCATTAGATTCATCTCGGG 59.720 40.741 0.00 0.00 38.32 5.14
250 251 7.821359 ACACCAATATCATTAGATTCATCTCGG 59.179 37.037 0.00 0.00 38.32 4.63
251 252 8.768957 ACACCAATATCATTAGATTCATCTCG 57.231 34.615 0.00 0.00 38.32 4.04
253 254 9.857656 ACAACACCAATATCATTAGATTCATCT 57.142 29.630 0.00 0.00 40.86 2.90
310 311 5.474532 TCAATCTCATCCAACTTTGACCAAG 59.525 40.000 0.00 0.00 38.64 3.61
311 312 5.241506 GTCAATCTCATCCAACTTTGACCAA 59.758 40.000 0.00 0.00 37.86 3.67
312 313 4.761739 GTCAATCTCATCCAACTTTGACCA 59.238 41.667 0.00 0.00 37.86 4.02
313 314 5.006386 AGTCAATCTCATCCAACTTTGACC 58.994 41.667 9.31 0.00 42.29 4.02
314 315 6.566197 AAGTCAATCTCATCCAACTTTGAC 57.434 37.500 5.67 5.67 41.88 3.18
315 316 8.156820 TCTAAAGTCAATCTCATCCAACTTTGA 58.843 33.333 8.19 2.69 37.48 2.69
316 317 8.233190 GTCTAAAGTCAATCTCATCCAACTTTG 58.767 37.037 8.19 0.82 37.48 2.77
317 318 7.939039 TGTCTAAAGTCAATCTCATCCAACTTT 59.061 33.333 0.00 0.00 39.51 2.66
318 319 7.453393 TGTCTAAAGTCAATCTCATCCAACTT 58.547 34.615 0.00 0.00 0.00 2.66
319 320 7.009179 TGTCTAAAGTCAATCTCATCCAACT 57.991 36.000 0.00 0.00 0.00 3.16
320 321 7.672983 TTGTCTAAAGTCAATCTCATCCAAC 57.327 36.000 0.00 0.00 0.00 3.77
321 322 7.174946 GGTTTGTCTAAAGTCAATCTCATCCAA 59.825 37.037 0.00 0.00 0.00 3.53
322 323 6.655003 GGTTTGTCTAAAGTCAATCTCATCCA 59.345 38.462 0.00 0.00 0.00 3.41
323 324 6.881602 AGGTTTGTCTAAAGTCAATCTCATCC 59.118 38.462 0.00 0.00 0.00 3.51
324 325 7.913674 AGGTTTGTCTAAAGTCAATCTCATC 57.086 36.000 0.00 0.00 0.00 2.92
325 326 9.965902 ATTAGGTTTGTCTAAAGTCAATCTCAT 57.034 29.630 0.00 0.00 33.54 2.90
326 327 9.219603 CATTAGGTTTGTCTAAAGTCAATCTCA 57.780 33.333 0.00 0.00 33.54 3.27
327 328 9.220767 ACATTAGGTTTGTCTAAAGTCAATCTC 57.779 33.333 0.00 0.00 33.54 2.75
328 329 9.003658 CACATTAGGTTTGTCTAAAGTCAATCT 57.996 33.333 0.00 0.00 31.38 2.40
329 330 7.750903 GCACATTAGGTTTGTCTAAAGTCAATC 59.249 37.037 0.00 0.00 31.38 2.67
330 331 7.230510 TGCACATTAGGTTTGTCTAAAGTCAAT 59.769 33.333 0.00 0.00 31.38 2.57
331 332 6.544197 TGCACATTAGGTTTGTCTAAAGTCAA 59.456 34.615 0.00 0.00 31.38 3.18
332 333 6.058833 TGCACATTAGGTTTGTCTAAAGTCA 58.941 36.000 0.00 0.00 31.38 3.41
333 334 6.426937 TCTGCACATTAGGTTTGTCTAAAGTC 59.573 38.462 0.00 0.00 31.38 3.01
334 335 6.296026 TCTGCACATTAGGTTTGTCTAAAGT 58.704 36.000 0.00 0.00 33.21 2.66
335 336 6.428159 ACTCTGCACATTAGGTTTGTCTAAAG 59.572 38.462 0.00 0.00 33.54 1.85
336 337 6.296026 ACTCTGCACATTAGGTTTGTCTAAA 58.704 36.000 0.00 0.00 33.54 1.85
337 338 5.865085 ACTCTGCACATTAGGTTTGTCTAA 58.135 37.500 0.00 0.00 34.23 2.10
338 339 5.483685 ACTCTGCACATTAGGTTTGTCTA 57.516 39.130 0.00 0.00 0.00 2.59
339 340 4.357918 ACTCTGCACATTAGGTTTGTCT 57.642 40.909 0.00 0.00 0.00 3.41
340 341 6.554334 TTTACTCTGCACATTAGGTTTGTC 57.446 37.500 0.00 0.00 0.00 3.18
341 342 6.952773 TTTTACTCTGCACATTAGGTTTGT 57.047 33.333 0.00 0.00 0.00 2.83
342 343 6.863126 CCTTTTTACTCTGCACATTAGGTTTG 59.137 38.462 0.00 0.00 0.00 2.93
343 344 6.775629 TCCTTTTTACTCTGCACATTAGGTTT 59.224 34.615 0.00 0.00 0.00 3.27
344 345 6.206829 GTCCTTTTTACTCTGCACATTAGGTT 59.793 38.462 0.00 0.00 0.00 3.50
345 346 5.705905 GTCCTTTTTACTCTGCACATTAGGT 59.294 40.000 0.00 0.00 0.00 3.08
346 347 5.123979 GGTCCTTTTTACTCTGCACATTAGG 59.876 44.000 0.00 0.00 0.00 2.69
347 348 5.163854 CGGTCCTTTTTACTCTGCACATTAG 60.164 44.000 0.00 0.00 0.00 1.73
348 349 4.693566 CGGTCCTTTTTACTCTGCACATTA 59.306 41.667 0.00 0.00 0.00 1.90
349 350 3.502211 CGGTCCTTTTTACTCTGCACATT 59.498 43.478 0.00 0.00 0.00 2.71
350 351 3.074412 CGGTCCTTTTTACTCTGCACAT 58.926 45.455 0.00 0.00 0.00 3.21
351 352 2.489971 CGGTCCTTTTTACTCTGCACA 58.510 47.619 0.00 0.00 0.00 4.57
352 353 1.804748 CCGGTCCTTTTTACTCTGCAC 59.195 52.381 0.00 0.00 0.00 4.57
353 354 1.695242 TCCGGTCCTTTTTACTCTGCA 59.305 47.619 0.00 0.00 0.00 4.41
354 355 2.347731 CTCCGGTCCTTTTTACTCTGC 58.652 52.381 0.00 0.00 0.00 4.26
355 356 2.565834 TCCTCCGGTCCTTTTTACTCTG 59.434 50.000 0.00 0.00 0.00 3.35
356 357 2.898662 TCCTCCGGTCCTTTTTACTCT 58.101 47.619 0.00 0.00 0.00 3.24
357 358 3.007723 ACTTCCTCCGGTCCTTTTTACTC 59.992 47.826 0.00 0.00 0.00 2.59
358 359 2.977580 ACTTCCTCCGGTCCTTTTTACT 59.022 45.455 0.00 0.00 0.00 2.24
359 360 3.413846 ACTTCCTCCGGTCCTTTTTAC 57.586 47.619 0.00 0.00 0.00 2.01
360 361 3.903090 TGTACTTCCTCCGGTCCTTTTTA 59.097 43.478 0.00 0.00 0.00 1.52
361 362 2.707257 TGTACTTCCTCCGGTCCTTTTT 59.293 45.455 0.00 0.00 0.00 1.94
362 363 2.332117 TGTACTTCCTCCGGTCCTTTT 58.668 47.619 0.00 0.00 0.00 2.27
363 364 2.019807 TGTACTTCCTCCGGTCCTTT 57.980 50.000 0.00 0.00 0.00 3.11
364 365 2.019807 TTGTACTTCCTCCGGTCCTT 57.980 50.000 0.00 0.00 0.00 3.36
365 366 1.900486 CTTTGTACTTCCTCCGGTCCT 59.100 52.381 0.00 0.00 0.00 3.85
366 367 1.622312 ACTTTGTACTTCCTCCGGTCC 59.378 52.381 0.00 0.00 0.00 4.46
367 368 3.064931 CAACTTTGTACTTCCTCCGGTC 58.935 50.000 0.00 0.00 0.00 4.79
368 369 2.701951 TCAACTTTGTACTTCCTCCGGT 59.298 45.455 0.00 0.00 0.00 5.28
369 370 3.006537 TCTCAACTTTGTACTTCCTCCGG 59.993 47.826 0.00 0.00 0.00 5.14
370 371 3.988517 GTCTCAACTTTGTACTTCCTCCG 59.011 47.826 0.00 0.00 0.00 4.63
371 372 4.750598 GTGTCTCAACTTTGTACTTCCTCC 59.249 45.833 0.00 0.00 0.00 4.30
372 373 5.602628 AGTGTCTCAACTTTGTACTTCCTC 58.397 41.667 0.00 0.00 0.00 3.71
373 374 5.615925 AGTGTCTCAACTTTGTACTTCCT 57.384 39.130 0.00 0.00 0.00 3.36
374 375 7.964604 ATAAGTGTCTCAACTTTGTACTTCC 57.035 36.000 0.00 0.00 40.77 3.46
377 378 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
378 379 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
379 380 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
380 381 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
381 382 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
441 442 5.655532 AGATAATGTGCCAGCAAAATCTCTT 59.344 36.000 0.00 0.00 0.00 2.85
491 492 1.978580 AGGAGATGTTTCCGTTGACCT 59.021 47.619 0.00 0.00 42.29 3.85
492 493 2.028020 AGAGGAGATGTTTCCGTTGACC 60.028 50.000 0.00 0.00 42.29 4.02
656 661 0.253327 GGATCCCAAGAAGGCGAGTT 59.747 55.000 0.00 0.00 35.39 3.01
858 864 3.722555 TCAAGCGAAATGAAAGCTACG 57.277 42.857 0.00 0.00 40.78 3.51
1273 1279 3.704800 TCCACAATTCCCGTACATCAA 57.295 42.857 0.00 0.00 0.00 2.57
1370 1376 7.362056 GGCTCATGAAATGTACAGCTAAGAAAA 60.362 37.037 0.33 0.00 46.80 2.29
1465 1471 3.876341 AGGAAACAAAACTGTCGGTACA 58.124 40.909 0.00 0.00 0.00 2.90
2250 5881 4.118168 AGTTGGAGGATTCACCAATGTT 57.882 40.909 6.15 0.00 43.56 2.71
3862 8031 7.232941 ACAGAGGTAGAACAAGTTACAGTACAT 59.767 37.037 0.00 0.00 0.00 2.29
3876 8045 3.728845 TGCAGTTCAACAGAGGTAGAAC 58.271 45.455 0.00 0.00 40.37 3.01
3878 8047 4.415881 TTTGCAGTTCAACAGAGGTAGA 57.584 40.909 0.00 0.00 33.73 2.59
3902 8114 8.246430 ACTTCCTCCGTTCATAATATAAGACA 57.754 34.615 0.00 0.00 0.00 3.41
3948 8739 8.019094 CAGCGAGCATTCAATATTTGATGAATA 58.981 33.333 10.54 0.00 42.72 1.75
4006 8829 5.010012 GGGGTGAAGCATTTCCTAACATATG 59.990 44.000 0.00 0.00 32.09 1.78
4036 8859 3.851184 TTGGGGTTGGGGTTGGGG 61.851 66.667 0.00 0.00 0.00 4.96
4037 8860 2.525629 GTTGGGGTTGGGGTTGGG 60.526 66.667 0.00 0.00 0.00 4.12
4038 8861 1.383248 TTGTTGGGGTTGGGGTTGG 60.383 57.895 0.00 0.00 0.00 3.77
4039 8862 1.691195 GGTTGTTGGGGTTGGGGTTG 61.691 60.000 0.00 0.00 0.00 3.77
4040 8863 1.383386 GGTTGTTGGGGTTGGGGTT 60.383 57.895 0.00 0.00 0.00 4.11
4207 13077 8.998377 GTGCTAAATTGGTTACATTTTTGGAAT 58.002 29.630 0.00 0.00 33.59 3.01
4208 13078 8.207545 AGTGCTAAATTGGTTACATTTTTGGAA 58.792 29.630 0.00 0.00 33.59 3.53
4209 13079 7.731054 AGTGCTAAATTGGTTACATTTTTGGA 58.269 30.769 0.00 0.00 33.59 3.53
4210 13080 7.872483 AGAGTGCTAAATTGGTTACATTTTTGG 59.128 33.333 0.00 0.00 33.59 3.28
4211 13081 8.816640 AGAGTGCTAAATTGGTTACATTTTTG 57.183 30.769 0.00 0.00 33.59 2.44
4246 13116 6.366340 TCCCCAACTACTGTTACATCAAAAA 58.634 36.000 0.00 0.00 34.60 1.94
4247 13117 5.942961 TCCCCAACTACTGTTACATCAAAA 58.057 37.500 0.00 0.00 34.60 2.44
4248 13118 5.570205 TCCCCAACTACTGTTACATCAAA 57.430 39.130 0.00 0.00 34.60 2.69
4249 13119 5.772393 ATCCCCAACTACTGTTACATCAA 57.228 39.130 0.00 0.00 34.60 2.57
4250 13120 6.844388 AGATATCCCCAACTACTGTTACATCA 59.156 38.462 0.00 0.00 34.60 3.07
4251 13121 7.304497 AGATATCCCCAACTACTGTTACATC 57.696 40.000 0.00 0.00 34.60 3.06
4252 13122 7.691993 AAGATATCCCCAACTACTGTTACAT 57.308 36.000 0.00 0.00 34.60 2.29
4253 13123 8.792830 ATAAGATATCCCCAACTACTGTTACA 57.207 34.615 0.00 0.00 34.60 2.41
4257 13127 9.670442 TCTTAATAAGATATCCCCAACTACTGT 57.330 33.333 0.00 0.00 31.20 3.55
4258 13128 9.930693 GTCTTAATAAGATATCCCCAACTACTG 57.069 37.037 5.96 0.00 40.18 2.74
4259 13129 9.670442 TGTCTTAATAAGATATCCCCAACTACT 57.330 33.333 5.96 0.00 40.18 2.57
4270 13140 9.836864 TGCTTGTGTGATGTCTTAATAAGATAT 57.163 29.630 11.28 11.28 41.35 1.63
4271 13141 9.836864 ATGCTTGTGTGATGTCTTAATAAGATA 57.163 29.630 5.96 3.91 40.18 1.98
4272 13142 8.743085 ATGCTTGTGTGATGTCTTAATAAGAT 57.257 30.769 5.96 0.00 40.18 2.40
4273 13143 9.836864 ATATGCTTGTGTGATGTCTTAATAAGA 57.163 29.630 0.00 0.00 34.51 2.10
4302 13172 9.793259 TTTGTATCAGAGGAAGACTTGTTAATT 57.207 29.630 0.00 0.00 0.00 1.40
4303 13173 9.793259 TTTTGTATCAGAGGAAGACTTGTTAAT 57.207 29.630 0.00 0.00 0.00 1.40
4304 13174 9.621629 TTTTTGTATCAGAGGAAGACTTGTTAA 57.378 29.630 0.00 0.00 0.00 2.01
4305 13175 9.793259 ATTTTTGTATCAGAGGAAGACTTGTTA 57.207 29.630 0.00 0.00 0.00 2.41
4306 13176 8.697507 ATTTTTGTATCAGAGGAAGACTTGTT 57.302 30.769 0.00 0.00 0.00 2.83
4307 13177 7.391833 GGATTTTTGTATCAGAGGAAGACTTGT 59.608 37.037 0.00 0.00 0.00 3.16
4308 13178 7.391554 TGGATTTTTGTATCAGAGGAAGACTTG 59.608 37.037 0.00 0.00 0.00 3.16
4309 13179 7.461749 TGGATTTTTGTATCAGAGGAAGACTT 58.538 34.615 0.00 0.00 0.00 3.01
4310 13180 7.020827 TGGATTTTTGTATCAGAGGAAGACT 57.979 36.000 0.00 0.00 0.00 3.24
4311 13181 7.362142 GGTTGGATTTTTGTATCAGAGGAAGAC 60.362 40.741 0.00 0.00 0.00 3.01
4312 13182 6.659242 GGTTGGATTTTTGTATCAGAGGAAGA 59.341 38.462 0.00 0.00 0.00 2.87
4313 13183 6.403636 CGGTTGGATTTTTGTATCAGAGGAAG 60.404 42.308 0.00 0.00 0.00 3.46
4314 13184 5.414454 CGGTTGGATTTTTGTATCAGAGGAA 59.586 40.000 0.00 0.00 0.00 3.36
4315 13185 4.941263 CGGTTGGATTTTTGTATCAGAGGA 59.059 41.667 0.00 0.00 0.00 3.71
4316 13186 4.700213 ACGGTTGGATTTTTGTATCAGAGG 59.300 41.667 0.00 0.00 0.00 3.69
4317 13187 5.181245 ACACGGTTGGATTTTTGTATCAGAG 59.819 40.000 0.00 0.00 0.00 3.35
4318 13188 5.067273 ACACGGTTGGATTTTTGTATCAGA 58.933 37.500 0.00 0.00 0.00 3.27
4319 13189 5.371115 ACACGGTTGGATTTTTGTATCAG 57.629 39.130 0.00 0.00 0.00 2.90
4320 13190 5.067936 ACAACACGGTTGGATTTTTGTATCA 59.932 36.000 17.36 0.00 0.00 2.15
4321 13191 5.401079 CACAACACGGTTGGATTTTTGTATC 59.599 40.000 17.36 0.00 0.00 2.24
4322 13192 5.163499 ACACAACACGGTTGGATTTTTGTAT 60.163 36.000 17.36 0.00 0.00 2.29
4323 13193 4.158025 ACACAACACGGTTGGATTTTTGTA 59.842 37.500 17.36 0.00 0.00 2.41
4324 13194 3.056465 ACACAACACGGTTGGATTTTTGT 60.056 39.130 17.36 10.38 0.00 2.83
4325 13195 3.516615 ACACAACACGGTTGGATTTTTG 58.483 40.909 17.36 9.91 0.00 2.44
4326 13196 3.429684 GGACACAACACGGTTGGATTTTT 60.430 43.478 17.36 0.00 0.00 1.94
4327 13197 2.100087 GGACACAACACGGTTGGATTTT 59.900 45.455 17.36 0.00 0.00 1.82
4328 13198 1.679153 GGACACAACACGGTTGGATTT 59.321 47.619 17.36 2.97 0.00 2.17
4329 13199 1.314730 GGACACAACACGGTTGGATT 58.685 50.000 17.36 4.89 0.00 3.01
4330 13200 0.181587 TGGACACAACACGGTTGGAT 59.818 50.000 17.36 7.78 0.00 3.41
4331 13201 0.745128 GTGGACACAACACGGTTGGA 60.745 55.000 17.36 0.00 0.00 3.53
4332 13202 1.027255 TGTGGACACAACACGGTTGG 61.027 55.000 17.36 10.68 41.64 3.77
4333 13203 0.805614 TTGTGGACACAACACGGTTG 59.194 50.000 13.42 13.18 45.42 3.77
4334 13204 1.091537 CTTGTGGACACAACACGGTT 58.908 50.000 13.42 0.00 45.42 4.44
4335 13205 0.746563 CCTTGTGGACACAACACGGT 60.747 55.000 13.42 0.00 45.42 4.83
4336 13206 2.021722 CCTTGTGGACACAACACGG 58.978 57.895 13.42 10.04 45.42 4.94
4337 13207 1.355210 GCCTTGTGGACACAACACG 59.645 57.895 13.42 5.09 45.42 4.49
4338 13208 0.381801 CTGCCTTGTGGACACAACAC 59.618 55.000 13.42 9.18 45.42 3.32
4339 13209 0.751277 CCTGCCTTGTGGACACAACA 60.751 55.000 13.42 10.25 45.42 3.33
4340 13210 1.455383 CCCTGCCTTGTGGACACAAC 61.455 60.000 13.42 6.35 45.42 3.32
4342 13212 2.337879 GACCCTGCCTTGTGGACACA 62.338 60.000 0.13 0.13 39.98 3.72
4343 13213 1.600916 GACCCTGCCTTGTGGACAC 60.601 63.158 0.00 0.00 34.57 3.67
4344 13214 1.352622 AAGACCCTGCCTTGTGGACA 61.353 55.000 0.00 0.00 34.57 4.02
4345 13215 0.690762 TAAGACCCTGCCTTGTGGAC 59.309 55.000 0.00 0.00 34.57 4.02
4346 13216 1.668826 ATAAGACCCTGCCTTGTGGA 58.331 50.000 0.00 0.00 34.57 4.02
4347 13217 2.369394 GAATAAGACCCTGCCTTGTGG 58.631 52.381 0.00 0.00 0.00 4.17
4348 13218 2.290896 TGGAATAAGACCCTGCCTTGTG 60.291 50.000 0.00 0.00 0.00 3.33
4349 13219 1.992557 TGGAATAAGACCCTGCCTTGT 59.007 47.619 0.00 0.00 0.00 3.16
4350 13220 2.806945 TGGAATAAGACCCTGCCTTG 57.193 50.000 0.00 0.00 0.00 3.61
4351 13221 3.825908 TTTGGAATAAGACCCTGCCTT 57.174 42.857 0.00 0.00 0.00 4.35
4352 13222 3.825908 TTTTGGAATAAGACCCTGCCT 57.174 42.857 0.00 0.00 0.00 4.75
4353 13223 4.222810 ACATTTTTGGAATAAGACCCTGCC 59.777 41.667 0.00 0.00 0.00 4.85
4354 13224 5.405935 ACATTTTTGGAATAAGACCCTGC 57.594 39.130 0.00 0.00 0.00 4.85
4355 13225 7.039363 TGGTTACATTTTTGGAATAAGACCCTG 60.039 37.037 0.00 0.00 0.00 4.45
4356 13226 7.013834 TGGTTACATTTTTGGAATAAGACCCT 58.986 34.615 0.00 0.00 0.00 4.34
4357 13227 7.234661 TGGTTACATTTTTGGAATAAGACCC 57.765 36.000 0.00 0.00 0.00 4.46
4358 13228 9.719355 AATTGGTTACATTTTTGGAATAAGACC 57.281 29.630 0.00 0.00 0.00 3.85
4393 13263 0.531974 GCCTTGTGGACAGAACACGA 60.532 55.000 0.00 0.00 41.64 4.35


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

AutoCloner maintained by Alex Coulton.