Multiple sequence alignment - TraesCS2A01G393200

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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 TraesCS2A01G393200 chr2A 100.000 1732 0 0 1516 3247 642961430 642959699 0.000000e+00 3199
1 TraesCS2A01G393200 chr2A 100.000 1293 0 0 1 1293 642962945 642961653 0.000000e+00 2388
2 TraesCS2A01G393200 chr7D 97.751 1245 25 3 2005 3247 66987985 66986742 0.000000e+00 2141
3 TraesCS2A01G393200 chr7D 90.636 833 28 11 499 1293 66989680 66988860 0.000000e+00 1061
4 TraesCS2A01G393200 chr7D 94.062 421 11 4 1586 2004 66988437 66988029 7.650000e-176 627
5 TraesCS2A01G393200 chr6A 96.546 1245 40 3 2005 3247 233813790 233815033 0.000000e+00 2058
6 TraesCS2A01G393200 chr6A 89.007 846 39 18 502 1293 233812389 233813234 0.000000e+00 998
7 TraesCS2A01G393200 chr6A 97.526 485 12 0 1 485 87708256 87707772 0.000000e+00 830
8 TraesCS2A01G393200 chr6A 96.495 485 17 0 1 485 87738126 87737642 0.000000e+00 802
9 TraesCS2A01G393200 chr6A 96.495 485 15 1 1 485 87744479 87743997 0.000000e+00 800
10 TraesCS2A01G393200 chr6A 92.025 489 21 3 1516 2004 233813276 233813746 0.000000e+00 671
11 TraesCS2A01G393200 chr6A 84.384 333 35 13 503 821 134201331 134201002 8.750000e-81 311
12 TraesCS2A01G393200 chr4A 96.386 1245 40 5 2005 3247 11706857 11708098 0.000000e+00 2045
13 TraesCS2A01G393200 chr4A 96.701 485 16 0 1 485 134429074 134428590 0.000000e+00 808
14 TraesCS2A01G393200 chr4A 95.876 485 19 1 1 485 134421100 134420617 0.000000e+00 784
15 TraesCS2A01G393200 chr4A 95.464 463 21 0 831 1293 11705840 11706302 0.000000e+00 739
16 TraesCS2A01G393200 chr4A 93.047 489 17 3 1516 2004 11706342 11706813 0.000000e+00 699
17 TraesCS2A01G393200 chr4A 91.866 418 28 2 2005 2417 319831333 319830917 2.170000e-161 579
18 TraesCS2A01G393200 chr4A 93.369 377 25 0 831 1207 28272778 28273154 2.830000e-155 558
19 TraesCS2A01G393200 chr4A 90.881 329 24 5 502 825 11705421 11705748 1.380000e-118 436
20 TraesCS2A01G393200 chr4A 88.251 366 33 2 1641 2004 319831736 319831379 2.310000e-116 429
21 TraesCS2A01G393200 chr4A 89.103 156 15 2 671 825 28272559 28272713 3.310000e-45 193
22 TraesCS2A01G393200 chr2B 94.378 1245 46 13 2005 3247 621183424 621184646 0.000000e+00 1890
23 TraesCS2A01G393200 chr2B 87.131 746 44 20 597 1293 621182126 621182868 0.000000e+00 798
24 TraesCS2A01G393200 chr2B 92.449 490 16 3 1516 2004 621182911 621183380 0.000000e+00 680
25 TraesCS2A01G393200 chr2B 87.730 489 42 8 1516 2004 254137259 254137729 3.660000e-154 555
26 TraesCS2A01G393200 chr4B 89.976 1237 110 10 2005 3232 550674308 550675539 0.000000e+00 1585
27 TraesCS2A01G393200 chr4B 91.373 1136 87 7 2005 3134 16552248 16553378 0.000000e+00 1544
28 TraesCS2A01G393200 chr4B 88.525 366 31 3 1641 2004 16551846 16552202 1.790000e-117 433
29 TraesCS2A01G393200 chr4B 88.251 366 32 3 1641 2004 550673906 550674262 8.330000e-116 427
30 TraesCS2A01G393200 chr4B 90.950 221 12 6 503 716 104746182 104745963 1.140000e-74 291
31 TraesCS2A01G393200 chr7A 89.831 1239 105 15 2005 3230 228676759 228675529 0.000000e+00 1570
32 TraesCS2A01G393200 chr3B 91.285 1136 88 7 2005 3134 511030956 511029826 0.000000e+00 1539
33 TraesCS2A01G393200 chr3B 93.634 377 24 0 831 1207 395846522 395846146 6.080000e-157 564
34 TraesCS2A01G393200 chr3B 88.525 366 31 3 1641 2004 511031358 511031002 1.790000e-117 433
35 TraesCS2A01G393200 chr3B 90.278 288 17 9 547 825 395846866 395846581 1.840000e-97 366
36 TraesCS2A01G393200 chr7B 93.700 873 49 6 2377 3247 725790700 725791568 0.000000e+00 1303
37 TraesCS2A01G393200 chr7B 93.103 377 26 0 831 1207 553229385 553229761 1.320000e-153 553
38 TraesCS2A01G393200 chr1A 97.207 716 17 2 2005 2720 121880474 121879762 0.000000e+00 1208
39 TraesCS2A01G393200 chr1A 93.561 761 42 7 538 1293 121882113 121881355 0.000000e+00 1127
40 TraesCS2A01G393200 chr1A 95.775 497 12 2 1516 2004 121881013 121880518 0.000000e+00 793
41 TraesCS2A01G393200 chr5A 96.907 485 15 0 1 485 509175501 509175017 0.000000e+00 813
42 TraesCS2A01G393200 chr5A 84.646 254 25 8 501 742 44952510 44952761 1.160000e-59 241
43 TraesCS2A01G393200 chr5A 78.095 420 50 31 501 881 529915928 529916344 9.060000e-56 228
44 TraesCS2A01G393200 chr5D 87.924 472 54 3 16 485 15626226 15625756 1.320000e-153 553
45 TraesCS2A01G393200 chr5D 87.712 472 54 4 16 485 15647335 15646866 6.120000e-152 547
46 TraesCS2A01G393200 chr5D 87.553 474 51 7 16 485 252229312 252229781 2.850000e-150 542
47 TraesCS2A01G393200 chrUn 92.573 377 28 0 831 1207 391724709 391725085 2.850000e-150 542
48 TraesCS2A01G393200 chrUn 89.103 156 15 2 671 825 391724490 391724644 3.310000e-45 193
49 TraesCS2A01G393200 chr3D 84.436 257 22 11 501 742 350128713 350128966 1.510000e-58 237


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 TraesCS2A01G393200 chr2A 642959699 642962945 3246 True 2793.500000 3199 100.000000 1 3247 2 chr2A.!!$R1 3246
1 TraesCS2A01G393200 chr7D 66986742 66989680 2938 True 1276.333333 2141 94.149667 499 3247 3 chr7D.!!$R1 2748
2 TraesCS2A01G393200 chr6A 233812389 233815033 2644 False 1242.333333 2058 92.526000 502 3247 3 chr6A.!!$F1 2745
3 TraesCS2A01G393200 chr4A 11705421 11708098 2677 False 979.750000 2045 93.944500 502 3247 4 chr4A.!!$F1 2745
4 TraesCS2A01G393200 chr4A 319830917 319831736 819 True 504.000000 579 90.058500 1641 2417 2 chr4A.!!$R3 776
5 TraesCS2A01G393200 chr4A 28272559 28273154 595 False 375.500000 558 91.236000 671 1207 2 chr4A.!!$F2 536
6 TraesCS2A01G393200 chr2B 621182126 621184646 2520 False 1122.666667 1890 91.319333 597 3247 3 chr2B.!!$F2 2650
7 TraesCS2A01G393200 chr4B 550673906 550675539 1633 False 1006.000000 1585 89.113500 1641 3232 2 chr4B.!!$F2 1591
8 TraesCS2A01G393200 chr4B 16551846 16553378 1532 False 988.500000 1544 89.949000 1641 3134 2 chr4B.!!$F1 1493
9 TraesCS2A01G393200 chr7A 228675529 228676759 1230 True 1570.000000 1570 89.831000 2005 3230 1 chr7A.!!$R1 1225
10 TraesCS2A01G393200 chr3B 511029826 511031358 1532 True 986.000000 1539 89.905000 1641 3134 2 chr3B.!!$R2 1493
11 TraesCS2A01G393200 chr3B 395846146 395846866 720 True 465.000000 564 91.956000 547 1207 2 chr3B.!!$R1 660
12 TraesCS2A01G393200 chr7B 725790700 725791568 868 False 1303.000000 1303 93.700000 2377 3247 1 chr7B.!!$F2 870
13 TraesCS2A01G393200 chr1A 121879762 121882113 2351 True 1042.666667 1208 95.514333 538 2720 3 chr1A.!!$R1 2182
14 TraesCS2A01G393200 chrUn 391724490 391725085 595 False 367.500000 542 90.838000 671 1207 2 chrUn.!!$F1 536

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
488 489 0.104120 TTATCCGGGCGTCACATCAG 59.896 55.0 0.0 0.0 0.0 2.90 F
496 497 0.671781 GCGTCACATCAGCTGAACCT 60.672 55.0 22.5 0.4 0.0 3.50 F
1015 1195 1.279025 GGACATGGGCAAGGGAGGTA 61.279 60.0 0.0 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 2004 1.532505 GCACAATAAGCCTGTGATGCG 60.533 52.381 7.13 0.0 45.80 4.73 R
2043 2420 3.662759 TTGTTCTCCCAGTGGAAAACT 57.337 42.857 11.95 0.0 41.42 2.66 R
2947 3336 2.767505 ACTTCATCTGTTGACGAACCC 58.232 47.619 0.00 0.0 32.84 4.11 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
27 28 4.766632 GGCTTGGCCCAGGGGAAG 62.767 72.222 7.91 4.99 44.06 3.46
28 29 3.661648 GCTTGGCCCAGGGGAAGA 61.662 66.667 7.91 0.00 37.50 2.87
29 30 2.679716 CTTGGCCCAGGGGAAGAG 59.320 66.667 7.91 0.00 37.50 2.85
30 31 2.121506 TTGGCCCAGGGGAAGAGT 60.122 61.111 7.91 0.00 37.50 3.24
31 32 1.778383 TTGGCCCAGGGGAAGAGTT 60.778 57.895 7.91 0.00 37.50 3.01
32 33 1.368268 TTGGCCCAGGGGAAGAGTTT 61.368 55.000 7.91 0.00 37.50 2.66
33 34 1.368268 TGGCCCAGGGGAAGAGTTTT 61.368 55.000 7.91 0.00 37.50 2.43
34 35 0.178932 GGCCCAGGGGAAGAGTTTTT 60.179 55.000 7.91 0.00 37.50 1.94
35 36 1.257743 GCCCAGGGGAAGAGTTTTTC 58.742 55.000 7.91 0.00 37.50 2.29
36 37 1.203063 GCCCAGGGGAAGAGTTTTTCT 60.203 52.381 7.91 0.00 37.50 2.52
38 39 3.576861 CCCAGGGGAAGAGTTTTTCTTT 58.423 45.455 0.00 0.00 46.12 2.52
39 40 3.967326 CCCAGGGGAAGAGTTTTTCTTTT 59.033 43.478 0.00 0.00 46.12 2.27
40 41 5.144832 CCCAGGGGAAGAGTTTTTCTTTTA 58.855 41.667 0.00 0.00 46.12 1.52
41 42 5.780282 CCCAGGGGAAGAGTTTTTCTTTTAT 59.220 40.000 0.00 0.00 46.12 1.40
42 43 6.270000 CCCAGGGGAAGAGTTTTTCTTTTATT 59.730 38.462 0.00 0.00 46.12 1.40
43 44 7.202093 CCCAGGGGAAGAGTTTTTCTTTTATTT 60.202 37.037 0.00 0.00 46.12 1.40
44 45 8.210946 CCAGGGGAAGAGTTTTTCTTTTATTTT 58.789 33.333 0.00 0.00 46.12 1.82
125 126 9.665264 GCAATTAGCACTATAAAATACAGGAAC 57.335 33.333 0.00 0.00 44.79 3.62
129 130 9.727859 TTAGCACTATAAAATACAGGAACAACA 57.272 29.630 0.00 0.00 0.00 3.33
130 131 8.040716 AGCACTATAAAATACAGGAACAACAC 57.959 34.615 0.00 0.00 0.00 3.32
131 132 7.120726 AGCACTATAAAATACAGGAACAACACC 59.879 37.037 0.00 0.00 0.00 4.16
132 133 7.120726 GCACTATAAAATACAGGAACAACACCT 59.879 37.037 0.00 0.00 38.40 4.00
133 134 9.661563 CACTATAAAATACAGGAACAACACCTA 57.338 33.333 0.00 0.00 35.84 3.08
139 140 4.584327 ACAGGAACAACACCTAATTTGC 57.416 40.909 0.00 0.00 35.84 3.68
140 141 4.215109 ACAGGAACAACACCTAATTTGCT 58.785 39.130 0.00 0.00 35.84 3.91
141 142 4.649218 ACAGGAACAACACCTAATTTGCTT 59.351 37.500 0.00 0.00 35.84 3.91
142 143 5.128663 ACAGGAACAACACCTAATTTGCTTT 59.871 36.000 0.00 0.00 35.84 3.51
143 144 6.048509 CAGGAACAACACCTAATTTGCTTTT 58.951 36.000 0.00 0.00 35.84 2.27
144 145 7.147811 ACAGGAACAACACCTAATTTGCTTTTA 60.148 33.333 0.00 0.00 35.84 1.52
145 146 7.169140 CAGGAACAACACCTAATTTGCTTTTAC 59.831 37.037 0.00 0.00 35.84 2.01
146 147 7.069455 AGGAACAACACCTAATTTGCTTTTACT 59.931 33.333 0.00 0.00 35.84 2.24
147 148 8.354426 GGAACAACACCTAATTTGCTTTTACTA 58.646 33.333 0.00 0.00 0.00 1.82
148 149 9.738832 GAACAACACCTAATTTGCTTTTACTAA 57.261 29.630 0.00 0.00 0.00 2.24
161 162 7.562454 TGCTTTTACTAATTATACCACTGCC 57.438 36.000 0.00 0.00 0.00 4.85
162 163 7.113437 TGCTTTTACTAATTATACCACTGCCA 58.887 34.615 0.00 0.00 0.00 4.92
163 164 7.066525 TGCTTTTACTAATTATACCACTGCCAC 59.933 37.037 0.00 0.00 0.00 5.01
164 165 7.066525 GCTTTTACTAATTATACCACTGCCACA 59.933 37.037 0.00 0.00 0.00 4.17
165 166 9.120538 CTTTTACTAATTATACCACTGCCACAT 57.879 33.333 0.00 0.00 0.00 3.21
166 167 9.469097 TTTTACTAATTATACCACTGCCACATT 57.531 29.630 0.00 0.00 0.00 2.71
167 168 9.469097 TTTACTAATTATACCACTGCCACATTT 57.531 29.630 0.00 0.00 0.00 2.32
169 170 8.677148 ACTAATTATACCACTGCCACATTTAG 57.323 34.615 0.00 0.00 0.00 1.85
170 171 8.272173 ACTAATTATACCACTGCCACATTTAGT 58.728 33.333 0.00 0.00 0.00 2.24
171 172 7.954666 AATTATACCACTGCCACATTTAGTT 57.045 32.000 0.00 0.00 0.00 2.24
172 173 7.954666 ATTATACCACTGCCACATTTAGTTT 57.045 32.000 0.00 0.00 0.00 2.66
173 174 5.643379 ATACCACTGCCACATTTAGTTTG 57.357 39.130 0.00 0.00 0.00 2.93
174 175 3.561143 ACCACTGCCACATTTAGTTTGA 58.439 40.909 0.00 0.00 0.00 2.69
175 176 3.569701 ACCACTGCCACATTTAGTTTGAG 59.430 43.478 0.00 0.00 0.00 3.02
176 177 3.057315 CCACTGCCACATTTAGTTTGAGG 60.057 47.826 0.00 0.00 0.00 3.86
177 178 3.569701 CACTGCCACATTTAGTTTGAGGT 59.430 43.478 0.00 0.00 0.00 3.85
178 179 4.037923 CACTGCCACATTTAGTTTGAGGTT 59.962 41.667 0.00 0.00 0.00 3.50
179 180 4.278419 ACTGCCACATTTAGTTTGAGGTTC 59.722 41.667 0.00 0.00 0.00 3.62
180 181 4.211125 TGCCACATTTAGTTTGAGGTTCA 58.789 39.130 0.00 0.00 0.00 3.18
181 182 4.646945 TGCCACATTTAGTTTGAGGTTCAA 59.353 37.500 0.00 0.00 34.03 2.69
182 183 5.127845 TGCCACATTTAGTTTGAGGTTCAAA 59.872 36.000 0.36 0.36 43.37 2.69
183 184 6.183360 TGCCACATTTAGTTTGAGGTTCAAAT 60.183 34.615 7.42 1.24 46.55 2.32
184 185 7.014711 TGCCACATTTAGTTTGAGGTTCAAATA 59.985 33.333 7.42 0.47 46.55 1.40
185 186 7.870445 GCCACATTTAGTTTGAGGTTCAAATAA 59.130 33.333 7.42 5.41 46.55 1.40
186 187 9.757227 CCACATTTAGTTTGAGGTTCAAATAAA 57.243 29.630 7.42 11.79 46.55 1.40
238 239 7.905126 AGCATTTAATAATTGTTTTTAGCCGC 58.095 30.769 0.00 0.00 0.00 6.53
239 240 7.763985 AGCATTTAATAATTGTTTTTAGCCGCT 59.236 29.630 0.00 0.00 0.00 5.52
240 241 7.845622 GCATTTAATAATTGTTTTTAGCCGCTG 59.154 33.333 2.16 0.00 0.00 5.18
241 242 8.868916 CATTTAATAATTGTTTTTAGCCGCTGT 58.131 29.630 2.16 0.00 0.00 4.40
242 243 8.819643 TTTAATAATTGTTTTTAGCCGCTGTT 57.180 26.923 2.16 0.00 0.00 3.16
243 244 9.909644 TTTAATAATTGTTTTTAGCCGCTGTTA 57.090 25.926 2.16 0.00 0.00 2.41
248 249 8.628882 AATTGTTTTTAGCCGCTGTTATATTC 57.371 30.769 2.16 0.00 0.00 1.75
249 250 5.802064 TGTTTTTAGCCGCTGTTATATTCG 58.198 37.500 2.16 0.00 0.00 3.34
250 251 5.352016 TGTTTTTAGCCGCTGTTATATTCGT 59.648 36.000 2.16 0.00 0.00 3.85
251 252 6.534436 TGTTTTTAGCCGCTGTTATATTCGTA 59.466 34.615 2.16 0.00 0.00 3.43
252 253 7.064371 TGTTTTTAGCCGCTGTTATATTCGTAA 59.936 33.333 2.16 0.00 0.00 3.18
253 254 7.536895 TTTTAGCCGCTGTTATATTCGTAAA 57.463 32.000 2.16 0.00 0.00 2.01
254 255 7.536895 TTTAGCCGCTGTTATATTCGTAAAA 57.463 32.000 2.16 0.00 0.00 1.52
255 256 5.652744 AGCCGCTGTTATATTCGTAAAAG 57.347 39.130 0.00 0.00 0.00 2.27
256 257 5.353938 AGCCGCTGTTATATTCGTAAAAGA 58.646 37.500 0.00 0.00 0.00 2.52
257 258 5.462398 AGCCGCTGTTATATTCGTAAAAGAG 59.538 40.000 0.00 0.00 0.00 2.85
258 259 5.667175 CCGCTGTTATATTCGTAAAAGAGC 58.333 41.667 0.00 0.00 0.00 4.09
259 260 5.233476 CCGCTGTTATATTCGTAAAAGAGCA 59.767 40.000 4.32 0.00 0.00 4.26
260 261 6.073765 CCGCTGTTATATTCGTAAAAGAGCAT 60.074 38.462 4.32 0.00 0.00 3.79
261 262 7.345192 CGCTGTTATATTCGTAAAAGAGCATT 58.655 34.615 4.32 0.00 0.00 3.56
262 263 7.850982 CGCTGTTATATTCGTAAAAGAGCATTT 59.149 33.333 4.32 0.00 0.00 2.32
289 290 9.892130 AAATACTTTTACAAAAATGTTGGGTCA 57.108 25.926 0.00 0.00 35.35 4.02
290 291 9.541143 AATACTTTTACAAAAATGTTGGGTCAG 57.459 29.630 0.00 0.00 35.35 3.51
291 292 5.815222 ACTTTTACAAAAATGTTGGGTCAGC 59.185 36.000 0.00 0.00 30.97 4.26
292 293 5.344743 TTTACAAAAATGTTGGGTCAGCA 57.655 34.783 0.00 0.00 0.00 4.41
293 294 3.177997 ACAAAAATGTTGGGTCAGCAC 57.822 42.857 0.00 0.00 0.00 4.40
294 295 2.158971 ACAAAAATGTTGGGTCAGCACC 60.159 45.455 0.00 0.00 42.90 5.01
295 296 1.786937 AAAATGTTGGGTCAGCACCA 58.213 45.000 0.00 0.00 45.94 4.17
296 297 2.014010 AAATGTTGGGTCAGCACCAT 57.986 45.000 0.00 0.00 45.94 3.55
297 298 2.897271 AATGTTGGGTCAGCACCATA 57.103 45.000 0.00 0.00 45.94 2.74
298 299 2.897271 ATGTTGGGTCAGCACCATAA 57.103 45.000 0.00 0.00 45.94 1.90
299 300 2.897271 TGTTGGGTCAGCACCATAAT 57.103 45.000 0.00 0.00 45.94 1.28
300 301 3.168035 TGTTGGGTCAGCACCATAATT 57.832 42.857 0.00 0.00 45.94 1.40
301 302 3.505386 TGTTGGGTCAGCACCATAATTT 58.495 40.909 0.00 0.00 45.94 1.82
302 303 3.257873 TGTTGGGTCAGCACCATAATTTG 59.742 43.478 0.00 0.00 45.94 2.32
303 304 3.168035 TGGGTCAGCACCATAATTTGT 57.832 42.857 0.00 0.00 45.94 2.83
304 305 3.505386 TGGGTCAGCACCATAATTTGTT 58.495 40.909 0.00 0.00 45.94 2.83
305 306 4.667573 TGGGTCAGCACCATAATTTGTTA 58.332 39.130 0.00 0.00 45.94 2.41
306 307 5.268387 TGGGTCAGCACCATAATTTGTTAT 58.732 37.500 0.00 0.00 45.94 1.89
307 308 5.126869 TGGGTCAGCACCATAATTTGTTATG 59.873 40.000 0.00 2.05 45.94 1.90
326 327 9.636879 TTGTTATGGAATATTTGACACACATTG 57.363 29.630 0.00 0.00 0.00 2.82
327 328 9.018582 TGTTATGGAATATTTGACACACATTGA 57.981 29.630 0.00 0.00 0.00 2.57
328 329 9.853555 GTTATGGAATATTTGACACACATTGAA 57.146 29.630 0.00 0.00 0.00 2.69
341 342 9.518906 TGACACACATTGAATATTTCATTATGC 57.481 29.630 0.00 0.00 39.84 3.14
342 343 9.518906 GACACACATTGAATATTTCATTATGCA 57.481 29.630 0.00 0.00 39.84 3.96
358 359 9.708092 TTCATTATGCATGTTTGAGAAATTTGA 57.292 25.926 10.16 0.00 34.06 2.69
359 360 9.708092 TCATTATGCATGTTTGAGAAATTTGAA 57.292 25.926 10.16 0.00 34.06 2.69
364 365 9.672086 ATGCATGTTTGAGAAATTTGAATTTTG 57.328 25.926 0.00 0.00 38.64 2.44
365 366 8.129840 TGCATGTTTGAGAAATTTGAATTTTGG 58.870 29.630 0.00 0.00 38.64 3.28
366 367 8.344098 GCATGTTTGAGAAATTTGAATTTTGGA 58.656 29.630 0.00 0.00 38.64 3.53
367 368 9.654417 CATGTTTGAGAAATTTGAATTTTGGAC 57.346 29.630 0.00 1.29 38.64 4.02
368 369 9.617523 ATGTTTGAGAAATTTGAATTTTGGACT 57.382 25.926 0.00 0.00 38.64 3.85
369 370 9.447157 TGTTTGAGAAATTTGAATTTTGGACTT 57.553 25.926 0.00 0.00 38.64 3.01
401 402 9.722184 TGAATTGAATTTGAATTATGCTTTGGA 57.278 25.926 0.00 0.00 0.00 3.53
404 405 9.893634 ATTGAATTTGAATTATGCTTTGGATCA 57.106 25.926 0.00 0.00 0.00 2.92
405 406 9.722184 TTGAATTTGAATTATGCTTTGGATCAA 57.278 25.926 0.00 0.00 0.00 2.57
406 407 9.722184 TGAATTTGAATTATGCTTTGGATCAAA 57.278 25.926 0.00 0.00 38.98 2.69
409 410 9.893634 ATTTGAATTATGCTTTGGATCAAATGA 57.106 25.926 9.32 0.00 41.71 2.57
410 411 8.936070 TTGAATTATGCTTTGGATCAAATGAG 57.064 30.769 0.00 0.00 32.70 2.90
411 412 7.494211 TGAATTATGCTTTGGATCAAATGAGG 58.506 34.615 0.00 0.00 32.70 3.86
412 413 7.342541 TGAATTATGCTTTGGATCAAATGAGGA 59.657 33.333 0.00 0.00 32.70 3.71
413 414 7.850935 ATTATGCTTTGGATCAAATGAGGAT 57.149 32.000 0.00 0.00 32.70 3.24
414 415 7.664552 TTATGCTTTGGATCAAATGAGGATT 57.335 32.000 0.00 0.00 32.70 3.01
415 416 8.765488 TTATGCTTTGGATCAAATGAGGATTA 57.235 30.769 0.00 0.00 32.70 1.75
416 417 6.704289 TGCTTTGGATCAAATGAGGATTAG 57.296 37.500 0.00 0.00 32.70 1.73
417 418 5.068198 TGCTTTGGATCAAATGAGGATTAGC 59.932 40.000 0.00 0.00 32.70 3.09
418 419 5.068198 GCTTTGGATCAAATGAGGATTAGCA 59.932 40.000 0.00 0.00 32.70 3.49
419 420 6.406177 GCTTTGGATCAAATGAGGATTAGCAA 60.406 38.462 0.00 0.00 32.70 3.91
420 421 6.455360 TTGGATCAAATGAGGATTAGCAAC 57.545 37.500 0.00 0.00 0.00 4.17
421 422 5.508567 TGGATCAAATGAGGATTAGCAACA 58.491 37.500 0.00 0.00 0.00 3.33
422 423 5.951148 TGGATCAAATGAGGATTAGCAACAA 59.049 36.000 0.00 0.00 0.00 2.83
423 424 6.608405 TGGATCAAATGAGGATTAGCAACAAT 59.392 34.615 0.00 0.00 0.00 2.71
424 425 7.779326 TGGATCAAATGAGGATTAGCAACAATA 59.221 33.333 0.00 0.00 0.00 1.90
425 426 8.295288 GGATCAAATGAGGATTAGCAACAATAG 58.705 37.037 0.00 0.00 0.00 1.73
426 427 8.757982 ATCAAATGAGGATTAGCAACAATAGT 57.242 30.769 0.00 0.00 0.00 2.12
427 428 7.988737 TCAAATGAGGATTAGCAACAATAGTG 58.011 34.615 0.00 0.00 0.00 2.74
428 429 7.611467 TCAAATGAGGATTAGCAACAATAGTGT 59.389 33.333 0.00 0.00 40.75 3.55
429 430 6.932356 ATGAGGATTAGCAACAATAGTGTG 57.068 37.500 0.00 0.00 38.27 3.82
430 431 6.048732 TGAGGATTAGCAACAATAGTGTGA 57.951 37.500 0.00 0.00 38.27 3.58
431 432 6.653020 TGAGGATTAGCAACAATAGTGTGAT 58.347 36.000 0.00 0.00 38.27 3.06
432 433 6.539826 TGAGGATTAGCAACAATAGTGTGATG 59.460 38.462 0.00 0.00 38.27 3.07
433 434 6.653020 AGGATTAGCAACAATAGTGTGATGA 58.347 36.000 0.00 0.00 38.27 2.92
434 435 6.540189 AGGATTAGCAACAATAGTGTGATGAC 59.460 38.462 0.00 0.00 38.27 3.06
435 436 6.316140 GGATTAGCAACAATAGTGTGATGACA 59.684 38.462 0.00 0.00 38.27 3.58
436 437 7.012704 GGATTAGCAACAATAGTGTGATGACAT 59.987 37.037 0.00 0.00 38.27 3.06
437 438 5.556355 AGCAACAATAGTGTGATGACATG 57.444 39.130 0.00 0.00 38.27 3.21
438 439 4.397103 AGCAACAATAGTGTGATGACATGG 59.603 41.667 0.00 0.00 38.27 3.66
439 440 4.665212 CAACAATAGTGTGATGACATGGC 58.335 43.478 0.00 0.00 38.27 4.40
440 441 3.954200 ACAATAGTGTGATGACATGGCA 58.046 40.909 2.18 2.18 36.31 4.92
441 442 3.691118 ACAATAGTGTGATGACATGGCAC 59.309 43.478 1.45 3.24 36.31 5.01
442 443 2.401583 TAGTGTGATGACATGGCACC 57.598 50.000 1.45 0.00 33.63 5.01
443 444 0.401356 AGTGTGATGACATGGCACCA 59.599 50.000 1.45 0.00 33.63 4.17
444 445 1.005097 AGTGTGATGACATGGCACCAT 59.995 47.619 1.45 0.00 37.08 3.55
445 446 1.402968 GTGTGATGACATGGCACCATC 59.597 52.381 1.45 15.32 37.71 3.51
446 447 1.004511 TGTGATGACATGGCACCATCA 59.995 47.619 18.91 18.91 42.84 3.07
447 448 2.093890 GTGATGACATGGCACCATCAA 58.906 47.619 22.32 10.38 45.41 2.57
448 449 2.093890 TGATGACATGGCACCATCAAC 58.906 47.619 19.92 10.61 42.33 3.18
449 450 2.093890 GATGACATGGCACCATCAACA 58.906 47.619 1.45 1.24 37.30 3.33
450 451 1.536940 TGACATGGCACCATCAACAG 58.463 50.000 0.00 0.00 33.90 3.16
451 452 0.813184 GACATGGCACCATCAACAGG 59.187 55.000 0.00 0.00 33.90 4.00
452 453 0.612732 ACATGGCACCATCAACAGGG 60.613 55.000 0.00 0.00 33.90 4.45
453 454 1.000739 ATGGCACCATCAACAGGGG 59.999 57.895 0.00 0.00 29.42 4.79
454 455 1.508667 ATGGCACCATCAACAGGGGA 61.509 55.000 0.00 0.00 29.42 4.81
455 456 1.307647 GGCACCATCAACAGGGGAT 59.692 57.895 0.00 0.00 0.00 3.85
456 457 0.324645 GGCACCATCAACAGGGGATT 60.325 55.000 0.00 0.00 0.00 3.01
457 458 1.064017 GGCACCATCAACAGGGGATTA 60.064 52.381 0.00 0.00 0.00 1.75
458 459 2.024414 GCACCATCAACAGGGGATTAC 58.976 52.381 0.00 0.00 0.00 1.89
459 460 2.357154 GCACCATCAACAGGGGATTACT 60.357 50.000 0.00 0.00 0.00 2.24
460 461 3.282021 CACCATCAACAGGGGATTACTG 58.718 50.000 0.00 0.00 41.64 2.74
470 471 6.576778 ACAGGGGATTACTGTAGCTTAATT 57.423 37.500 0.00 0.00 46.62 1.40
471 472 7.685849 ACAGGGGATTACTGTAGCTTAATTA 57.314 36.000 0.00 0.00 46.62 1.40
472 473 8.276453 ACAGGGGATTACTGTAGCTTAATTAT 57.724 34.615 0.00 0.00 46.62 1.28
473 474 8.376270 ACAGGGGATTACTGTAGCTTAATTATC 58.624 37.037 0.00 0.00 46.62 1.75
474 475 7.824779 CAGGGGATTACTGTAGCTTAATTATCC 59.175 40.741 0.00 0.00 0.00 2.59
475 476 6.817140 GGGGATTACTGTAGCTTAATTATCCG 59.183 42.308 0.00 0.00 31.87 4.18
476 477 6.817140 GGGATTACTGTAGCTTAATTATCCGG 59.183 42.308 0.00 0.00 31.87 5.14
477 478 6.817140 GGATTACTGTAGCTTAATTATCCGGG 59.183 42.308 0.00 0.00 0.00 5.73
478 479 4.004196 ACTGTAGCTTAATTATCCGGGC 57.996 45.455 0.00 0.00 0.00 6.13
479 480 2.993899 CTGTAGCTTAATTATCCGGGCG 59.006 50.000 0.00 0.00 0.00 6.13
480 481 2.366266 TGTAGCTTAATTATCCGGGCGT 59.634 45.455 0.00 0.00 0.00 5.68
481 482 2.165319 AGCTTAATTATCCGGGCGTC 57.835 50.000 0.00 0.00 0.00 5.19
482 483 1.414919 AGCTTAATTATCCGGGCGTCA 59.585 47.619 0.00 0.00 0.00 4.35
483 484 1.529865 GCTTAATTATCCGGGCGTCAC 59.470 52.381 0.00 0.00 0.00 3.67
484 485 2.828877 CTTAATTATCCGGGCGTCACA 58.171 47.619 0.00 0.00 0.00 3.58
485 486 3.399330 CTTAATTATCCGGGCGTCACAT 58.601 45.455 0.00 0.00 0.00 3.21
486 487 1.878953 AATTATCCGGGCGTCACATC 58.121 50.000 0.00 0.00 0.00 3.06
487 488 0.756294 ATTATCCGGGCGTCACATCA 59.244 50.000 0.00 0.00 0.00 3.07
488 489 0.104120 TTATCCGGGCGTCACATCAG 59.896 55.000 0.00 0.00 0.00 2.90
489 490 2.363711 TATCCGGGCGTCACATCAGC 62.364 60.000 0.00 0.00 0.00 4.26
490 491 4.457496 CCGGGCGTCACATCAGCT 62.457 66.667 0.00 0.00 0.00 4.24
491 492 3.190849 CGGGCGTCACATCAGCTG 61.191 66.667 7.63 7.63 0.00 4.24
492 493 2.265739 GGGCGTCACATCAGCTGA 59.734 61.111 20.79 20.79 0.00 4.26
493 494 1.375908 GGGCGTCACATCAGCTGAA 60.376 57.895 22.50 0.00 0.00 3.02
494 495 1.639298 GGGCGTCACATCAGCTGAAC 61.639 60.000 22.50 13.33 0.00 3.18
495 496 1.639298 GGCGTCACATCAGCTGAACC 61.639 60.000 22.50 9.75 0.00 3.62
496 497 0.671781 GCGTCACATCAGCTGAACCT 60.672 55.000 22.50 0.40 0.00 3.50
497 498 1.354040 CGTCACATCAGCTGAACCTC 58.646 55.000 22.50 9.53 0.00 3.85
498 499 1.337167 CGTCACATCAGCTGAACCTCA 60.337 52.381 22.50 0.78 0.00 3.86
499 500 2.676176 CGTCACATCAGCTGAACCTCAT 60.676 50.000 22.50 0.00 0.00 2.90
500 501 2.935201 GTCACATCAGCTGAACCTCATC 59.065 50.000 22.50 4.85 0.00 2.92
580 582 4.785346 AACCTGCAATCTGATGGTCTAT 57.215 40.909 0.00 0.00 0.00 1.98
593 595 4.631377 TGATGGTCTATGTCGCTTCAAAAG 59.369 41.667 0.00 0.00 0.00 2.27
720 733 2.203938 TCCCTGCCCGACCTCTTT 60.204 61.111 0.00 0.00 0.00 2.52
793 830 3.314331 CCACGCCCACTCTCCAGT 61.314 66.667 0.00 0.00 0.00 4.00
1006 1186 3.780173 TCGATGCGGACATGGGCA 61.780 61.111 10.18 10.18 44.29 5.36
1015 1195 1.279025 GGACATGGGCAAGGGAGGTA 61.279 60.000 0.00 0.00 0.00 3.08
1196 1376 5.816682 TCCTCTCTCACATACACAGTTCTA 58.183 41.667 0.00 0.00 0.00 2.10
1578 1890 5.426509 TCTGTATGTGACTGATGAAAGGGAT 59.573 40.000 0.00 0.00 31.57 3.85
1672 2004 9.464714 CACATGTTGTAGGAATATAGACAGTAC 57.535 37.037 0.00 0.00 0.00 2.73
1718 2050 7.228507 CCGATGTTCTCAATGGTATCCAAAATA 59.771 37.037 0.00 0.00 36.95 1.40
1940 2272 7.930325 TCAATGAAATGCAAACCTGTTCATTTA 59.070 29.630 14.10 8.12 43.09 1.40
2043 2420 7.118245 CGATGTCCTATATTTCTATGCTTGCAA 59.882 37.037 0.00 0.00 0.00 4.08
2053 2430 4.144297 TCTATGCTTGCAAGTTTTCCACT 58.856 39.130 26.55 8.99 37.30 4.00
2125 2507 9.932207 TCTTGCAATGTCATTCTTTCATTATTT 57.068 25.926 0.00 0.00 31.76 1.40
2309 2691 4.463050 AGTTTGATAGGTTTCCCCAACA 57.537 40.909 0.00 0.00 37.07 3.33
2395 2779 5.003160 TGTCACAGTTTGATCGATCCATTT 58.997 37.500 22.31 3.54 36.32 2.32
2451 2835 7.103641 GGATACAAGGTTCATTGTAGTCTTGA 58.896 38.462 13.75 0.00 45.96 3.02
2481 2865 6.491745 TGGAATACCAAGAAAAAGCATGTGTA 59.508 34.615 0.00 0.00 43.91 2.90
2808 3197 5.649395 TGTTCCATATTCCTCTTTTCTGCTG 59.351 40.000 0.00 0.00 0.00 4.41
2822 3211 9.741647 CTCTTTTCTGCTGATTTTTAGAGTTTT 57.258 29.630 0.00 0.00 0.00 2.43
2980 3369 5.794894 ACAGATGAAGTAATCAACCGTTCT 58.205 37.500 0.00 0.00 42.54 3.01
3008 3397 7.713518 TGAGGGATTAGGAGTACATCATCTAT 58.286 38.462 0.00 0.00 0.00 1.98
3125 3515 2.290008 TGGCGATAAACACATGACCAGT 60.290 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.651980 CTCTTCCCCTGGGCCAAGC 62.652 68.421 8.04 0.00 34.68 4.01
12 13 1.793820 AACTCTTCCCCTGGGCCAAG 61.794 60.000 8.04 11.51 34.68 3.61
13 14 1.368268 AAACTCTTCCCCTGGGCCAA 61.368 55.000 8.04 0.85 34.68 4.52
14 15 1.368268 AAAACTCTTCCCCTGGGCCA 61.368 55.000 7.39 5.85 34.68 5.36
15 16 0.178932 AAAAACTCTTCCCCTGGGCC 60.179 55.000 7.39 0.00 34.68 5.80
16 17 1.203063 AGAAAAACTCTTCCCCTGGGC 60.203 52.381 7.39 0.00 34.68 5.36
17 18 2.980246 AGAAAAACTCTTCCCCTGGG 57.020 50.000 5.50 5.50 0.00 4.45
18 19 6.918067 ATAAAAGAAAAACTCTTCCCCTGG 57.082 37.500 0.00 0.00 44.00 4.45
98 99 9.627123 TTCCTGTATTTTATAGTGCTAATTGCT 57.373 29.630 0.00 0.00 43.37 3.91
99 100 9.665264 GTTCCTGTATTTTATAGTGCTAATTGC 57.335 33.333 0.00 0.00 43.25 3.56
103 104 9.727859 TGTTGTTCCTGTATTTTATAGTGCTAA 57.272 29.630 0.00 0.00 0.00 3.09
104 105 9.158233 GTGTTGTTCCTGTATTTTATAGTGCTA 57.842 33.333 0.00 0.00 0.00 3.49
105 106 7.120726 GGTGTTGTTCCTGTATTTTATAGTGCT 59.879 37.037 0.00 0.00 0.00 4.40
106 107 7.120726 AGGTGTTGTTCCTGTATTTTATAGTGC 59.879 37.037 0.00 0.00 33.62 4.40
107 108 8.561738 AGGTGTTGTTCCTGTATTTTATAGTG 57.438 34.615 0.00 0.00 33.62 2.74
113 114 7.655732 GCAAATTAGGTGTTGTTCCTGTATTTT 59.344 33.333 0.00 0.00 36.60 1.82
114 115 7.015195 AGCAAATTAGGTGTTGTTCCTGTATTT 59.985 33.333 0.00 0.00 36.60 1.40
115 116 6.493458 AGCAAATTAGGTGTTGTTCCTGTATT 59.507 34.615 0.00 0.00 36.60 1.89
116 117 6.010219 AGCAAATTAGGTGTTGTTCCTGTAT 58.990 36.000 0.00 0.00 36.60 2.29
117 118 5.381757 AGCAAATTAGGTGTTGTTCCTGTA 58.618 37.500 0.00 0.00 36.60 2.74
118 119 4.215109 AGCAAATTAGGTGTTGTTCCTGT 58.785 39.130 0.00 0.00 36.60 4.00
119 120 4.853924 AGCAAATTAGGTGTTGTTCCTG 57.146 40.909 0.00 0.00 36.60 3.86
120 121 5.869649 AAAGCAAATTAGGTGTTGTTCCT 57.130 34.783 0.00 0.00 38.91 3.36
121 122 7.207383 AGTAAAAGCAAATTAGGTGTTGTTCC 58.793 34.615 0.00 0.00 0.00 3.62
122 123 9.738832 TTAGTAAAAGCAAATTAGGTGTTGTTC 57.261 29.630 0.00 0.00 0.00 3.18
135 136 8.463607 GGCAGTGGTATAATTAGTAAAAGCAAA 58.536 33.333 0.00 0.00 0.00 3.68
136 137 7.612244 TGGCAGTGGTATAATTAGTAAAAGCAA 59.388 33.333 0.00 0.00 0.00 3.91
137 138 7.066525 GTGGCAGTGGTATAATTAGTAAAAGCA 59.933 37.037 0.00 0.00 0.00 3.91
138 139 7.066525 TGTGGCAGTGGTATAATTAGTAAAAGC 59.933 37.037 0.00 0.00 0.00 3.51
139 140 8.500753 TGTGGCAGTGGTATAATTAGTAAAAG 57.499 34.615 0.00 0.00 0.00 2.27
140 141 9.469097 AATGTGGCAGTGGTATAATTAGTAAAA 57.531 29.630 0.00 0.00 0.00 1.52
141 142 9.469097 AAATGTGGCAGTGGTATAATTAGTAAA 57.531 29.630 0.00 0.00 0.00 2.01
143 144 9.772973 CTAAATGTGGCAGTGGTATAATTAGTA 57.227 33.333 0.00 0.00 0.00 1.82
144 145 8.272173 ACTAAATGTGGCAGTGGTATAATTAGT 58.728 33.333 0.00 0.00 0.00 2.24
145 146 8.677148 ACTAAATGTGGCAGTGGTATAATTAG 57.323 34.615 0.00 0.00 0.00 1.73
146 147 9.469097 AAACTAAATGTGGCAGTGGTATAATTA 57.531 29.630 0.00 0.00 0.00 1.40
147 148 7.954666 AACTAAATGTGGCAGTGGTATAATT 57.045 32.000 0.00 0.00 0.00 1.40
148 149 7.613801 TCAAACTAAATGTGGCAGTGGTATAAT 59.386 33.333 0.00 0.00 0.00 1.28
149 150 6.943146 TCAAACTAAATGTGGCAGTGGTATAA 59.057 34.615 0.00 0.00 0.00 0.98
150 151 6.477253 TCAAACTAAATGTGGCAGTGGTATA 58.523 36.000 0.00 0.00 0.00 1.47
151 152 5.321102 TCAAACTAAATGTGGCAGTGGTAT 58.679 37.500 0.00 0.00 0.00 2.73
152 153 4.720046 TCAAACTAAATGTGGCAGTGGTA 58.280 39.130 0.00 0.00 0.00 3.25
153 154 3.561143 TCAAACTAAATGTGGCAGTGGT 58.439 40.909 0.00 0.00 0.00 4.16
154 155 3.057315 CCTCAAACTAAATGTGGCAGTGG 60.057 47.826 0.00 0.00 0.00 4.00
155 156 3.569701 ACCTCAAACTAAATGTGGCAGTG 59.430 43.478 0.00 0.00 35.37 3.66
156 157 3.832527 ACCTCAAACTAAATGTGGCAGT 58.167 40.909 0.00 0.00 35.37 4.40
157 158 4.278170 TGAACCTCAAACTAAATGTGGCAG 59.722 41.667 0.00 0.00 35.37 4.85
158 159 4.211125 TGAACCTCAAACTAAATGTGGCA 58.789 39.130 0.00 0.00 35.37 4.92
159 160 4.846779 TGAACCTCAAACTAAATGTGGC 57.153 40.909 0.00 0.00 35.37 5.01
212 213 8.387354 GCGGCTAAAAACAATTATTAAATGCTT 58.613 29.630 0.00 0.00 0.00 3.91
213 214 7.763985 AGCGGCTAAAAACAATTATTAAATGCT 59.236 29.630 0.00 0.00 0.00 3.79
214 215 7.845622 CAGCGGCTAAAAACAATTATTAAATGC 59.154 33.333 0.26 0.00 0.00 3.56
215 216 8.868916 ACAGCGGCTAAAAACAATTATTAAATG 58.131 29.630 0.26 0.00 0.00 2.32
216 217 8.996024 ACAGCGGCTAAAAACAATTATTAAAT 57.004 26.923 0.26 0.00 0.00 1.40
217 218 8.819643 AACAGCGGCTAAAAACAATTATTAAA 57.180 26.923 0.26 0.00 0.00 1.52
222 223 9.724839 GAATATAACAGCGGCTAAAAACAATTA 57.275 29.630 0.26 0.00 0.00 1.40
223 224 7.431084 CGAATATAACAGCGGCTAAAAACAATT 59.569 33.333 0.26 0.00 0.00 2.32
224 225 6.910433 CGAATATAACAGCGGCTAAAAACAAT 59.090 34.615 0.26 0.00 0.00 2.71
225 226 6.128227 ACGAATATAACAGCGGCTAAAAACAA 60.128 34.615 0.26 0.00 0.00 2.83
226 227 5.352016 ACGAATATAACAGCGGCTAAAAACA 59.648 36.000 0.26 0.00 0.00 2.83
227 228 5.803118 ACGAATATAACAGCGGCTAAAAAC 58.197 37.500 0.26 0.00 0.00 2.43
228 229 7.536895 TTACGAATATAACAGCGGCTAAAAA 57.463 32.000 0.26 0.00 0.00 1.94
229 230 7.536895 TTTACGAATATAACAGCGGCTAAAA 57.463 32.000 0.26 0.00 0.00 1.52
230 231 7.492020 TCTTTTACGAATATAACAGCGGCTAAA 59.508 33.333 0.26 0.00 0.00 1.85
231 232 6.979817 TCTTTTACGAATATAACAGCGGCTAA 59.020 34.615 0.26 0.00 0.00 3.09
232 233 6.506147 TCTTTTACGAATATAACAGCGGCTA 58.494 36.000 0.26 0.00 0.00 3.93
233 234 5.353938 TCTTTTACGAATATAACAGCGGCT 58.646 37.500 0.00 0.00 0.00 5.52
234 235 5.646467 TCTTTTACGAATATAACAGCGGC 57.354 39.130 0.00 0.00 0.00 6.53
235 236 5.233476 TGCTCTTTTACGAATATAACAGCGG 59.767 40.000 0.00 0.00 0.00 5.52
236 237 6.268797 TGCTCTTTTACGAATATAACAGCG 57.731 37.500 0.00 0.00 0.00 5.18
263 264 9.892130 TGACCCAACATTTTTGTAAAAGTATTT 57.108 25.926 0.00 0.00 42.41 1.40
264 265 9.541143 CTGACCCAACATTTTTGTAAAAGTATT 57.459 29.630 0.00 0.00 0.00 1.89
265 266 7.655732 GCTGACCCAACATTTTTGTAAAAGTAT 59.344 33.333 0.00 0.00 0.00 2.12
266 267 6.981559 GCTGACCCAACATTTTTGTAAAAGTA 59.018 34.615 0.00 0.00 0.00 2.24
267 268 5.815222 GCTGACCCAACATTTTTGTAAAAGT 59.185 36.000 0.00 0.00 0.00 2.66
268 269 5.814705 TGCTGACCCAACATTTTTGTAAAAG 59.185 36.000 0.00 0.00 0.00 2.27
269 270 5.582665 GTGCTGACCCAACATTTTTGTAAAA 59.417 36.000 0.00 0.00 0.00 1.52
270 271 5.112686 GTGCTGACCCAACATTTTTGTAAA 58.887 37.500 0.00 0.00 0.00 2.01
271 272 4.442192 GGTGCTGACCCAACATTTTTGTAA 60.442 41.667 0.00 0.00 36.03 2.41
272 273 3.068873 GGTGCTGACCCAACATTTTTGTA 59.931 43.478 0.00 0.00 36.03 2.41
273 274 2.158971 GGTGCTGACCCAACATTTTTGT 60.159 45.455 0.00 0.00 36.03 2.83
274 275 2.158986 TGGTGCTGACCCAACATTTTTG 60.159 45.455 0.00 0.00 42.34 2.44
275 276 2.114616 TGGTGCTGACCCAACATTTTT 58.885 42.857 0.00 0.00 42.34 1.94
276 277 1.786937 TGGTGCTGACCCAACATTTT 58.213 45.000 0.00 0.00 42.34 1.82
277 278 2.014010 ATGGTGCTGACCCAACATTT 57.986 45.000 0.00 0.00 40.06 2.32
278 279 2.897271 TATGGTGCTGACCCAACATT 57.103 45.000 0.00 0.00 40.06 2.71
279 280 2.897271 TTATGGTGCTGACCCAACAT 57.103 45.000 0.00 0.00 44.76 2.71
280 281 2.897271 ATTATGGTGCTGACCCAACA 57.103 45.000 0.00 0.00 42.34 3.33
281 282 3.258123 ACAAATTATGGTGCTGACCCAAC 59.742 43.478 0.00 0.00 42.34 3.77
282 283 3.505386 ACAAATTATGGTGCTGACCCAA 58.495 40.909 0.00 0.00 42.34 4.12
283 284 3.168035 ACAAATTATGGTGCTGACCCA 57.832 42.857 0.00 0.00 42.34 4.51
284 285 5.591099 CATAACAAATTATGGTGCTGACCC 58.409 41.667 0.00 0.00 42.75 4.46
300 301 9.636879 CAATGTGTGTCAAATATTCCATAACAA 57.363 29.630 0.00 0.00 0.00 2.83
301 302 9.018582 TCAATGTGTGTCAAATATTCCATAACA 57.981 29.630 0.00 0.00 0.00 2.41
302 303 9.853555 TTCAATGTGTGTCAAATATTCCATAAC 57.146 29.630 0.00 0.00 0.00 1.89
315 316 9.518906 GCATAATGAAATATTCAATGTGTGTCA 57.481 29.630 6.72 0.00 43.95 3.58
316 317 9.518906 TGCATAATGAAATATTCAATGTGTGTC 57.481 29.630 6.72 0.00 43.95 3.67
332 333 9.708092 TCAAATTTCTCAAACATGCATAATGAA 57.292 25.926 0.00 0.00 38.72 2.57
333 334 9.708092 TTCAAATTTCTCAAACATGCATAATGA 57.292 25.926 0.00 3.47 38.72 2.57
338 339 9.672086 CAAAATTCAAATTTCTCAAACATGCAT 57.328 25.926 0.00 0.00 37.62 3.96
339 340 8.129840 CCAAAATTCAAATTTCTCAAACATGCA 58.870 29.630 1.43 0.00 37.62 3.96
340 341 8.344098 TCCAAAATTCAAATTTCTCAAACATGC 58.656 29.630 1.43 0.00 37.62 4.06
341 342 9.654417 GTCCAAAATTCAAATTTCTCAAACATG 57.346 29.630 1.43 0.00 37.62 3.21
342 343 9.617523 AGTCCAAAATTCAAATTTCTCAAACAT 57.382 25.926 1.43 0.00 37.62 2.71
343 344 9.447157 AAGTCCAAAATTCAAATTTCTCAAACA 57.553 25.926 1.43 0.00 37.62 2.83
375 376 9.722184 TCCAAAGCATAATTCAAATTCAATTCA 57.278 25.926 0.00 0.00 0.00 2.57
378 379 9.893634 TGATCCAAAGCATAATTCAAATTCAAT 57.106 25.926 0.00 0.00 0.00 2.57
379 380 9.722184 TTGATCCAAAGCATAATTCAAATTCAA 57.278 25.926 0.00 0.00 0.00 2.69
380 381 9.722184 TTTGATCCAAAGCATAATTCAAATTCA 57.278 25.926 0.00 0.00 29.45 2.57
383 384 9.893634 TCATTTGATCCAAAGCATAATTCAAAT 57.106 25.926 0.00 0.00 40.84 2.32
384 385 9.373603 CTCATTTGATCCAAAGCATAATTCAAA 57.626 29.630 0.00 0.00 36.76 2.69
385 386 7.982919 CCTCATTTGATCCAAAGCATAATTCAA 59.017 33.333 0.00 0.00 36.76 2.69
386 387 7.342541 TCCTCATTTGATCCAAAGCATAATTCA 59.657 33.333 0.00 0.00 36.76 2.57
387 388 7.719483 TCCTCATTTGATCCAAAGCATAATTC 58.281 34.615 0.00 0.00 36.76 2.17
388 389 7.664552 TCCTCATTTGATCCAAAGCATAATT 57.335 32.000 0.00 0.00 36.76 1.40
389 390 7.850935 ATCCTCATTTGATCCAAAGCATAAT 57.149 32.000 0.00 0.00 36.76 1.28
390 391 7.664552 AATCCTCATTTGATCCAAAGCATAA 57.335 32.000 0.00 0.00 36.76 1.90
391 392 7.040201 GCTAATCCTCATTTGATCCAAAGCATA 60.040 37.037 0.00 0.00 36.76 3.14
392 393 6.239232 GCTAATCCTCATTTGATCCAAAGCAT 60.239 38.462 0.00 0.00 36.76 3.79
393 394 5.068198 GCTAATCCTCATTTGATCCAAAGCA 59.932 40.000 0.00 0.00 36.76 3.91
394 395 5.068198 TGCTAATCCTCATTTGATCCAAAGC 59.932 40.000 0.00 0.00 36.76 3.51
395 396 6.704289 TGCTAATCCTCATTTGATCCAAAG 57.296 37.500 0.00 0.00 36.76 2.77
396 397 6.436847 TGTTGCTAATCCTCATTTGATCCAAA 59.563 34.615 0.00 0.00 37.75 3.28
397 398 5.951148 TGTTGCTAATCCTCATTTGATCCAA 59.049 36.000 0.00 0.00 0.00 3.53
398 399 5.508567 TGTTGCTAATCCTCATTTGATCCA 58.491 37.500 0.00 0.00 0.00 3.41
399 400 6.455360 TTGTTGCTAATCCTCATTTGATCC 57.545 37.500 0.00 0.00 0.00 3.36
400 401 8.844244 ACTATTGTTGCTAATCCTCATTTGATC 58.156 33.333 0.00 0.00 0.00 2.92
401 402 8.627403 CACTATTGTTGCTAATCCTCATTTGAT 58.373 33.333 0.00 0.00 0.00 2.57
402 403 7.611467 ACACTATTGTTGCTAATCCTCATTTGA 59.389 33.333 0.00 0.00 28.43 2.69
403 404 7.699391 CACACTATTGTTGCTAATCCTCATTTG 59.301 37.037 0.00 0.00 31.66 2.32
404 405 7.611467 TCACACTATTGTTGCTAATCCTCATTT 59.389 33.333 0.00 0.00 31.66 2.32
405 406 7.112122 TCACACTATTGTTGCTAATCCTCATT 58.888 34.615 0.00 0.00 31.66 2.57
406 407 6.653020 TCACACTATTGTTGCTAATCCTCAT 58.347 36.000 0.00 0.00 31.66 2.90
407 408 6.048732 TCACACTATTGTTGCTAATCCTCA 57.951 37.500 0.00 0.00 31.66 3.86
408 409 6.763135 TCATCACACTATTGTTGCTAATCCTC 59.237 38.462 0.00 0.00 31.66 3.71
409 410 6.540189 GTCATCACACTATTGTTGCTAATCCT 59.460 38.462 0.00 0.00 31.66 3.24
410 411 6.316140 TGTCATCACACTATTGTTGCTAATCC 59.684 38.462 0.00 0.00 31.66 3.01
411 412 7.307493 TGTCATCACACTATTGTTGCTAATC 57.693 36.000 0.00 0.00 31.66 1.75
412 413 7.201758 CCATGTCATCACACTATTGTTGCTAAT 60.202 37.037 0.00 0.00 34.48 1.73
413 414 6.093909 CCATGTCATCACACTATTGTTGCTAA 59.906 38.462 0.00 0.00 34.48 3.09
414 415 5.585844 CCATGTCATCACACTATTGTTGCTA 59.414 40.000 0.00 0.00 34.48 3.49
415 416 4.397103 CCATGTCATCACACTATTGTTGCT 59.603 41.667 0.00 0.00 34.48 3.91
416 417 4.665212 CCATGTCATCACACTATTGTTGC 58.335 43.478 0.00 0.00 34.48 4.17
417 418 4.156373 TGCCATGTCATCACACTATTGTTG 59.844 41.667 0.00 0.00 34.48 3.33
418 419 4.156556 GTGCCATGTCATCACACTATTGTT 59.843 41.667 7.27 0.00 34.48 2.83
419 420 3.691118 GTGCCATGTCATCACACTATTGT 59.309 43.478 7.27 0.00 34.48 2.71
420 421 3.065786 GGTGCCATGTCATCACACTATTG 59.934 47.826 12.32 0.00 34.48 1.90
421 422 3.282021 GGTGCCATGTCATCACACTATT 58.718 45.455 12.32 0.00 34.48 1.73
422 423 2.239402 TGGTGCCATGTCATCACACTAT 59.761 45.455 12.32 0.00 34.48 2.12
423 424 1.627834 TGGTGCCATGTCATCACACTA 59.372 47.619 12.32 5.92 34.48 2.74
424 425 0.401356 TGGTGCCATGTCATCACACT 59.599 50.000 12.32 0.00 34.48 3.55
425 426 1.402968 GATGGTGCCATGTCATCACAC 59.597 52.381 8.64 6.59 37.72 3.82
426 427 1.004511 TGATGGTGCCATGTCATCACA 59.995 47.619 8.64 0.00 41.31 3.58
427 428 1.753930 TGATGGTGCCATGTCATCAC 58.246 50.000 8.64 0.00 41.31 3.06
428 429 2.093890 GTTGATGGTGCCATGTCATCA 58.906 47.619 8.64 0.00 43.53 3.07
429 430 2.093890 TGTTGATGGTGCCATGTCATC 58.906 47.619 8.64 2.74 36.70 2.92
430 431 2.097036 CTGTTGATGGTGCCATGTCAT 58.903 47.619 8.64 0.00 36.70 3.06
431 432 1.536940 CTGTTGATGGTGCCATGTCA 58.463 50.000 8.64 0.00 36.70 3.58
432 433 0.813184 CCTGTTGATGGTGCCATGTC 59.187 55.000 8.64 0.00 36.70 3.06
433 434 0.612732 CCCTGTTGATGGTGCCATGT 60.613 55.000 8.64 0.00 36.70 3.21
434 435 1.324740 CCCCTGTTGATGGTGCCATG 61.325 60.000 8.64 0.00 36.70 3.66
435 436 1.000739 CCCCTGTTGATGGTGCCAT 59.999 57.895 2.95 2.95 39.69 4.40
436 437 1.508667 ATCCCCTGTTGATGGTGCCA 61.509 55.000 0.00 0.00 0.00 4.92
437 438 0.324645 AATCCCCTGTTGATGGTGCC 60.325 55.000 0.00 0.00 0.00 5.01
438 439 2.024414 GTAATCCCCTGTTGATGGTGC 58.976 52.381 0.00 0.00 0.00 5.01
439 440 3.282021 CAGTAATCCCCTGTTGATGGTG 58.718 50.000 0.00 0.00 0.00 4.17
440 441 2.919602 ACAGTAATCCCCTGTTGATGGT 59.080 45.455 0.00 0.00 40.14 3.55
441 442 3.652057 ACAGTAATCCCCTGTTGATGG 57.348 47.619 0.00 0.00 40.14 3.51
442 443 4.130118 GCTACAGTAATCCCCTGTTGATG 58.870 47.826 6.25 0.00 42.83 3.07
443 444 4.040755 AGCTACAGTAATCCCCTGTTGAT 58.959 43.478 6.25 0.00 42.83 2.57
444 445 3.450904 AGCTACAGTAATCCCCTGTTGA 58.549 45.455 6.25 0.00 42.83 3.18
445 446 3.914426 AGCTACAGTAATCCCCTGTTG 57.086 47.619 0.00 0.00 42.83 3.33
446 447 6.576778 ATTAAGCTACAGTAATCCCCTGTT 57.423 37.500 0.00 0.00 42.83 3.16
447 448 6.576778 AATTAAGCTACAGTAATCCCCTGT 57.423 37.500 0.00 0.00 44.90 4.00
448 449 7.824779 GGATAATTAAGCTACAGTAATCCCCTG 59.175 40.741 0.00 0.00 36.01 4.45
449 450 7.310485 CGGATAATTAAGCTACAGTAATCCCCT 60.310 40.741 0.00 0.00 0.00 4.79
450 451 6.817140 CGGATAATTAAGCTACAGTAATCCCC 59.183 42.308 0.00 0.00 0.00 4.81
451 452 6.817140 CCGGATAATTAAGCTACAGTAATCCC 59.183 42.308 0.00 0.00 0.00 3.85
452 453 6.817140 CCCGGATAATTAAGCTACAGTAATCC 59.183 42.308 0.73 0.00 0.00 3.01
453 454 6.313164 GCCCGGATAATTAAGCTACAGTAATC 59.687 42.308 0.73 0.00 0.00 1.75
454 455 6.171213 GCCCGGATAATTAAGCTACAGTAAT 58.829 40.000 0.73 0.00 0.00 1.89
455 456 5.544650 GCCCGGATAATTAAGCTACAGTAA 58.455 41.667 0.73 0.00 0.00 2.24
456 457 4.321452 CGCCCGGATAATTAAGCTACAGTA 60.321 45.833 0.73 0.00 0.00 2.74
457 458 3.554337 CGCCCGGATAATTAAGCTACAGT 60.554 47.826 0.73 0.00 0.00 3.55
458 459 2.993899 CGCCCGGATAATTAAGCTACAG 59.006 50.000 0.73 0.00 0.00 2.74
459 460 2.366266 ACGCCCGGATAATTAAGCTACA 59.634 45.455 0.73 0.00 0.00 2.74
460 461 2.991866 GACGCCCGGATAATTAAGCTAC 59.008 50.000 0.73 0.00 0.00 3.58
461 462 2.629137 TGACGCCCGGATAATTAAGCTA 59.371 45.455 0.73 0.00 0.00 3.32
462 463 1.414919 TGACGCCCGGATAATTAAGCT 59.585 47.619 0.73 0.00 0.00 3.74
463 464 1.529865 GTGACGCCCGGATAATTAAGC 59.470 52.381 0.73 0.00 0.00 3.09
464 465 2.828877 TGTGACGCCCGGATAATTAAG 58.171 47.619 0.73 0.00 0.00 1.85
465 466 2.983907 TGTGACGCCCGGATAATTAA 57.016 45.000 0.73 0.00 0.00 1.40
466 467 2.365941 TGATGTGACGCCCGGATAATTA 59.634 45.455 0.73 0.00 0.00 1.40
467 468 1.140052 TGATGTGACGCCCGGATAATT 59.860 47.619 0.73 0.00 0.00 1.40
468 469 0.756294 TGATGTGACGCCCGGATAAT 59.244 50.000 0.73 0.00 0.00 1.28
469 470 0.104120 CTGATGTGACGCCCGGATAA 59.896 55.000 0.73 0.00 0.00 1.75
470 471 1.739667 CTGATGTGACGCCCGGATA 59.260 57.895 0.73 0.00 0.00 2.59
471 472 2.501128 CTGATGTGACGCCCGGAT 59.499 61.111 0.73 0.00 0.00 4.18
472 473 4.451150 GCTGATGTGACGCCCGGA 62.451 66.667 0.73 0.00 0.00 5.14
473 474 4.457496 AGCTGATGTGACGCCCGG 62.457 66.667 0.00 0.00 0.00 5.73
474 475 3.190849 CAGCTGATGTGACGCCCG 61.191 66.667 8.42 0.00 0.00 6.13
475 476 1.375908 TTCAGCTGATGTGACGCCC 60.376 57.895 19.04 0.00 0.00 6.13
476 477 1.639298 GGTTCAGCTGATGTGACGCC 61.639 60.000 19.04 7.67 0.00 5.68
477 478 0.671781 AGGTTCAGCTGATGTGACGC 60.672 55.000 19.04 6.91 0.00 5.19
478 479 1.337167 TGAGGTTCAGCTGATGTGACG 60.337 52.381 19.04 0.00 0.00 4.35
479 480 2.462456 TGAGGTTCAGCTGATGTGAC 57.538 50.000 19.04 12.55 0.00 3.67
480 481 2.836372 AGATGAGGTTCAGCTGATGTGA 59.164 45.455 19.04 0.00 42.17 3.58
481 482 3.263489 AGATGAGGTTCAGCTGATGTG 57.737 47.619 19.04 0.00 42.17 3.21
482 483 4.900652 AGATAGATGAGGTTCAGCTGATGT 59.099 41.667 19.04 4.85 43.72 3.06
483 484 5.471556 AGATAGATGAGGTTCAGCTGATG 57.528 43.478 19.04 0.00 43.72 3.07
484 485 6.314120 AGTAGATAGATGAGGTTCAGCTGAT 58.686 40.000 19.04 1.77 43.72 2.90
485 486 5.700183 AGTAGATAGATGAGGTTCAGCTGA 58.300 41.667 13.74 13.74 43.72 4.26
486 487 7.148086 GGATAGTAGATAGATGAGGTTCAGCTG 60.148 44.444 7.63 7.63 43.72 4.24
487 488 6.889722 GGATAGTAGATAGATGAGGTTCAGCT 59.110 42.308 2.22 2.22 45.99 4.24
488 489 6.889722 AGGATAGTAGATAGATGAGGTTCAGC 59.110 42.308 0.00 0.00 31.96 4.26
521 523 0.836400 TGGTTCTCCGCCCTCTCTTT 60.836 55.000 0.00 0.00 36.30 2.52
580 582 2.750166 TGTTTGGTCTTTTGAAGCGACA 59.250 40.909 0.00 0.00 0.00 4.35
703 716 2.203938 AAAGAGGTCGGGCAGGGA 60.204 61.111 0.00 0.00 0.00 4.20
720 733 2.041301 CGGGGAGTATGTGGGGGA 60.041 66.667 0.00 0.00 0.00 4.81
1052 1232 0.961358 CCTTCGGAGAGGAGACACGT 60.961 60.000 0.00 0.00 38.43 4.49
1196 1376 1.700186 GAGTTGGACAAGAGAAGGGGT 59.300 52.381 0.00 0.00 0.00 4.95
1607 1931 4.017126 ACTGTGTCATGATAGAAGGACGA 58.983 43.478 0.00 0.00 33.04 4.20
1652 1976 6.947644 TGCGTACTGTCTATATTCCTACAA 57.052 37.500 0.00 0.00 0.00 2.41
1672 2004 1.532505 GCACAATAAGCCTGTGATGCG 60.533 52.381 7.13 0.00 45.80 4.73
1693 2025 6.435430 TTTTGGATACCATTGAGAACATCG 57.565 37.500 0.00 0.00 31.53 3.84
2043 2420 3.662759 TTGTTCTCCCAGTGGAAAACT 57.337 42.857 11.95 0.00 41.42 2.66
2053 2430 5.441718 AGCATCTAGAAATTGTTCTCCCA 57.558 39.130 0.00 0.00 43.30 4.37
2125 2507 6.428083 TTTCCTTGTGAGACACATACCTTA 57.572 37.500 5.43 0.00 44.16 2.69
2467 2851 5.376854 ACCACTCATACACATGCTTTTTC 57.623 39.130 0.00 0.00 31.73 2.29
2477 2861 6.732154 TCTAAACGCTATACCACTCATACAC 58.268 40.000 0.00 0.00 0.00 2.90
2481 2865 6.040504 TGACATCTAAACGCTATACCACTCAT 59.959 38.462 0.00 0.00 0.00 2.90
2947 3336 2.767505 ACTTCATCTGTTGACGAACCC 58.232 47.619 0.00 0.00 32.84 4.11
2980 3369 8.180165 AGATGATGTACTCCTAATCCCTCATTA 58.820 37.037 0.00 0.00 0.00 1.90
3079 3468 5.640357 CACAATGCCTGCAAATAAGAACAAT 59.360 36.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.