Multiple sequence alignment - TraesCS2B01G518700

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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 TraesCS2B01G518700 chr2B 100.000 3113 0 0 1 3113 713696154 713693042 0.000000e+00 5749.0
1 TraesCS2B01G518700 chr2B 97.633 169 4 0 190 358 664125032 664125200 1.090000e-74 291.0
2 TraesCS2B01G518700 chr2A 94.201 1966 81 15 626 2574 723828933 723826984 0.000000e+00 2968.0
3 TraesCS2B01G518700 chr2A 95.522 536 20 4 2578 3113 723826946 723826415 0.000000e+00 854.0
4 TraesCS2B01G518700 chr2A 94.495 109 2 2 357 464 723829037 723828932 6.910000e-37 165.0
5 TraesCS2B01G518700 chr4A 90.078 1925 160 14 656 2572 684976733 684978634 0.000000e+00 2468.0
6 TraesCS2B01G518700 chr4A 84.912 908 121 8 862 1764 602259897 602260793 0.000000e+00 904.0
7 TraesCS2B01G518700 chr4A 82.834 1002 158 9 1143 2131 602863252 602864252 0.000000e+00 885.0
8 TraesCS2B01G518700 chr4A 94.347 513 21 3 2603 3113 684978980 684979486 0.000000e+00 780.0
9 TraesCS2B01G518700 chr4A 82.857 350 58 2 1785 2133 602260841 602261189 2.330000e-81 313.0
10 TraesCS2B01G518700 chr4A 82.609 299 28 12 805 1097 602862955 602863235 3.100000e-60 243.0
11 TraesCS2B01G518700 chr4A 89.610 154 10 4 1 148 684976416 684976569 1.140000e-44 191.0
12 TraesCS2B01G518700 chr4A 98.276 58 1 0 407 464 684976604 684976661 5.490000e-18 102.0
13 TraesCS2B01G518700 chr2D 89.403 1925 164 19 656 2572 589503972 589502080 0.000000e+00 2388.0
14 TraesCS2B01G518700 chr2D 79.533 899 135 32 1243 2119 13770424 13771295 2.070000e-166 595.0
15 TraesCS2B01G518700 chr2D 85.714 539 26 13 2603 3113 589501732 589501217 3.560000e-144 521.0
16 TraesCS2B01G518700 chr2D 76.796 1030 168 46 1033 2037 13724213 13723230 2.140000e-141 512.0
17 TraesCS2B01G518700 chr2D 95.429 175 8 0 196 370 304655119 304655293 2.360000e-71 279.0
18 TraesCS2B01G518700 chr2D 92.899 169 12 0 464 632 475088339 475088507 2.400000e-61 246.0
19 TraesCS2B01G518700 chr2D 88.889 207 13 6 1 197 589504369 589504163 2.400000e-61 246.0
20 TraesCS2B01G518700 chr2D 94.444 108 6 0 357 464 589504164 589504057 1.920000e-37 167.0
21 TraesCS2B01G518700 chr4B 83.557 1344 194 16 805 2133 3784666 3785997 0.000000e+00 1232.0
22 TraesCS2B01G518700 chr4B 83.031 772 112 14 784 1553 3856368 3855614 0.000000e+00 682.0
23 TraesCS2B01G518700 chr4B 85.085 295 44 0 1838 2132 411851319 411851613 5.050000e-78 302.0
24 TraesCS2B01G518700 chr4B 96.491 171 4 2 191 359 431792147 431792317 6.570000e-72 281.0
25 TraesCS2B01G518700 chr4B 90.404 198 13 6 196 392 671709895 671709703 3.980000e-64 255.0
26 TraesCS2B01G518700 chr4D 82.743 1298 175 29 871 2131 3260934 3259649 0.000000e+00 1110.0
27 TraesCS2B01G518700 chr4D 83.161 1158 169 17 983 2132 2070963 2072102 0.000000e+00 1035.0
28 TraesCS2B01G518700 chr4D 93.976 166 10 0 463 628 22589303 22589468 5.150000e-63 252.0
29 TraesCS2B01G518700 chr4D 92.486 173 13 0 463 635 477898959 477898787 6.670000e-62 248.0
30 TraesCS2B01G518700 chr4D 91.111 180 13 1 463 642 75782053 75782229 1.120000e-59 241.0
31 TraesCS2B01G518700 chrUn 81.807 786 124 11 805 1579 47781076 47780299 2.620000e-180 641.0
32 TraesCS2B01G518700 chrUn 76.219 677 128 25 1302 1957 28781716 28782380 8.320000e-86 327.0
33 TraesCS2B01G518700 chrUn 85.393 89 13 0 1031 1119 28781525 28781613 3.310000e-15 93.5
34 TraesCS2B01G518700 chr5D 84.301 637 94 4 1298 1929 438553842 438553207 4.410000e-173 617.0
35 TraesCS2B01G518700 chr5D 77.530 988 136 41 996 1959 560224876 560225801 1.660000e-142 516.0
36 TraesCS2B01G518700 chr5D 91.713 181 14 1 463 642 92111549 92111729 1.850000e-62 250.0
37 TraesCS2B01G518700 chr5D 92.486 173 11 2 463 634 28487669 28487840 2.400000e-61 246.0
38 TraesCS2B01G518700 chr5D 82.524 206 24 12 196 393 553671495 553671696 1.480000e-38 171.0
39 TraesCS2B01G518700 chr7D 76.783 715 139 18 1261 1957 552325260 552325965 2.930000e-100 375.0
40 TraesCS2B01G518700 chr7B 98.204 167 3 0 196 362 497576786 497576620 3.040000e-75 292.0
41 TraesCS2B01G518700 chr7B 95.954 173 5 2 196 368 249675052 249674882 2.360000e-71 279.0
42 TraesCS2B01G518700 chr5B 97.590 166 4 0 193 358 701551646 701551811 5.080000e-73 285.0
43 TraesCS2B01G518700 chr5B 91.803 183 13 2 448 630 540367701 540367881 1.430000e-63 254.0
44 TraesCS2B01G518700 chr6D 97.576 165 4 0 196 360 90890282 90890446 1.830000e-72 283.0
45 TraesCS2B01G518700 chr6D 100.000 30 0 0 1268 1297 14523226 14523197 4.340000e-04 56.5
46 TraesCS2B01G518700 chr1B 96.000 175 6 1 192 365 561836564 561836390 1.830000e-72 283.0
47 TraesCS2B01G518700 chr3B 96.450 169 6 0 191 359 812681181 812681013 2.360000e-71 279.0
48 TraesCS2B01G518700 chr3B 91.011 178 16 0 463 640 571752689 571752512 1.120000e-59 241.0
49 TraesCS2B01G518700 chr5A 91.620 179 14 1 462 639 382566637 382566815 2.400000e-61 246.0
50 TraesCS2B01G518700 chr1D 89.024 82 9 0 1038 1119 72497946 72498027 5.490000e-18 102.0


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 TraesCS2B01G518700 chr2B 713693042 713696154 3112 True 5749.00 5749 100.000000 1 3113 1 chr2B.!!$R1 3112
1 TraesCS2B01G518700 chr2A 723826415 723829037 2622 True 1329.00 2968 94.739333 357 3113 3 chr2A.!!$R1 2756
2 TraesCS2B01G518700 chr4A 684976416 684979486 3070 False 885.25 2468 93.077750 1 3113 4 chr4A.!!$F3 3112
3 TraesCS2B01G518700 chr4A 602259897 602261189 1292 False 608.50 904 83.884500 862 2133 2 chr4A.!!$F1 1271
4 TraesCS2B01G518700 chr4A 602862955 602864252 1297 False 564.00 885 82.721500 805 2131 2 chr4A.!!$F2 1326
5 TraesCS2B01G518700 chr2D 589501217 589504369 3152 True 830.50 2388 89.612500 1 3113 4 chr2D.!!$R2 3112
6 TraesCS2B01G518700 chr2D 13770424 13771295 871 False 595.00 595 79.533000 1243 2119 1 chr2D.!!$F1 876
7 TraesCS2B01G518700 chr2D 13723230 13724213 983 True 512.00 512 76.796000 1033 2037 1 chr2D.!!$R1 1004
8 TraesCS2B01G518700 chr4B 3784666 3785997 1331 False 1232.00 1232 83.557000 805 2133 1 chr4B.!!$F1 1328
9 TraesCS2B01G518700 chr4B 3855614 3856368 754 True 682.00 682 83.031000 784 1553 1 chr4B.!!$R1 769
10 TraesCS2B01G518700 chr4D 3259649 3260934 1285 True 1110.00 1110 82.743000 871 2131 1 chr4D.!!$R1 1260
11 TraesCS2B01G518700 chr4D 2070963 2072102 1139 False 1035.00 1035 83.161000 983 2132 1 chr4D.!!$F1 1149
12 TraesCS2B01G518700 chrUn 47780299 47781076 777 True 641.00 641 81.807000 805 1579 1 chrUn.!!$R1 774
13 TraesCS2B01G518700 chrUn 28781525 28782380 855 False 210.25 327 80.806000 1031 1957 2 chrUn.!!$F1 926
14 TraesCS2B01G518700 chr5D 438553207 438553842 635 True 617.00 617 84.301000 1298 1929 1 chr5D.!!$R1 631
15 TraesCS2B01G518700 chr5D 560224876 560225801 925 False 516.00 516 77.530000 996 1959 1 chr5D.!!$F4 963
16 TraesCS2B01G518700 chr7D 552325260 552325965 705 False 375.00 375 76.783000 1261 1957 1 chr7D.!!$F1 696

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
476 487 0.033306 ACTCCTACTCCCTCCGTTCC 60.033 60.0 0.0 0.0 0.0 3.62 F
477 488 0.259356 CTCCTACTCCCTCCGTTCCT 59.741 60.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 2023 1.000521 CTGGCATGTCCACCCACAT 60.001 57.895 4.93 0.0 40.72 3.21 R
2382 2615 1.531883 GCTTAAATGAAAGCGGCGAGG 60.532 52.381 12.98 0.0 42.21 4.63 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
49 52 8.718102 TTTAGCGAATAGAAGAACAGCTTATT 57.282 30.769 0.00 0.00 36.83 1.40
103 107 9.797556 GAACCCCTATACAAATAAAACATTCAC 57.202 33.333 0.00 0.00 0.00 3.18
114 122 0.944386 AACATTCACACGTGGACAGC 59.056 50.000 21.57 0.00 0.00 4.40
128 136 4.319177 GTGGACAGCTACTCATCTTTTGT 58.681 43.478 0.00 0.00 0.00 2.83
190 201 8.416329 GCACACTTTTATGATTTCCATCCTTAT 58.584 33.333 0.00 0.00 36.71 1.73
192 203 9.479549 ACACTTTTATGATTTCCATCCTTATGT 57.520 29.630 0.00 0.00 36.71 2.29
200 211 8.519799 TGATTTCCATCCTTATGTTTTACTCC 57.480 34.615 0.00 0.00 0.00 3.85
201 212 7.559897 TGATTTCCATCCTTATGTTTTACTCCC 59.440 37.037 0.00 0.00 0.00 4.30
202 213 6.652205 TTCCATCCTTATGTTTTACTCCCT 57.348 37.500 0.00 0.00 0.00 4.20
203 214 6.248569 TCCATCCTTATGTTTTACTCCCTC 57.751 41.667 0.00 0.00 0.00 4.30
204 215 5.132144 TCCATCCTTATGTTTTACTCCCTCC 59.868 44.000 0.00 0.00 0.00 4.30
205 216 4.748277 TCCTTATGTTTTACTCCCTCCG 57.252 45.455 0.00 0.00 0.00 4.63
206 217 4.098894 TCCTTATGTTTTACTCCCTCCGT 58.901 43.478 0.00 0.00 0.00 4.69
207 218 4.533311 TCCTTATGTTTTACTCCCTCCGTT 59.467 41.667 0.00 0.00 0.00 4.44
208 219 4.874396 CCTTATGTTTTACTCCCTCCGTTC 59.126 45.833 0.00 0.00 0.00 3.95
209 220 2.845363 TGTTTTACTCCCTCCGTTCC 57.155 50.000 0.00 0.00 0.00 3.62
210 221 2.332117 TGTTTTACTCCCTCCGTTCCT 58.668 47.619 0.00 0.00 0.00 3.36
211 222 3.509442 TGTTTTACTCCCTCCGTTCCTA 58.491 45.455 0.00 0.00 0.00 2.94
212 223 3.903090 TGTTTTACTCCCTCCGTTCCTAA 59.097 43.478 0.00 0.00 0.00 2.69
213 224 4.347583 TGTTTTACTCCCTCCGTTCCTAAA 59.652 41.667 0.00 0.00 0.00 1.85
214 225 5.013391 TGTTTTACTCCCTCCGTTCCTAAAT 59.987 40.000 0.00 0.00 0.00 1.40
215 226 6.213195 TGTTTTACTCCCTCCGTTCCTAAATA 59.787 38.462 0.00 0.00 0.00 1.40
216 227 7.092757 TGTTTTACTCCCTCCGTTCCTAAATAT 60.093 37.037 0.00 0.00 0.00 1.28
217 228 8.424133 GTTTTACTCCCTCCGTTCCTAAATATA 58.576 37.037 0.00 0.00 0.00 0.86
218 229 8.551682 TTTACTCCCTCCGTTCCTAAATATAA 57.448 34.615 0.00 0.00 0.00 0.98
219 230 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
220 231 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
221 232 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
222 233 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
223 234 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
224 235 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
225 236 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
226 237 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
241 252 6.783708 AGTCTTTGTAGAGATTCCACTAGG 57.216 41.667 0.00 0.00 0.00 3.02
242 253 6.257586 AGTCTTTGTAGAGATTCCACTAGGT 58.742 40.000 0.00 0.00 35.89 3.08
243 254 6.153680 AGTCTTTGTAGAGATTCCACTAGGTG 59.846 42.308 0.00 0.00 35.89 4.00
255 266 3.984508 CACTAGGTGGACTACATACGG 57.015 52.381 0.00 0.00 0.00 4.02
256 267 3.548770 CACTAGGTGGACTACATACGGA 58.451 50.000 0.00 0.00 0.00 4.69
257 268 3.564644 CACTAGGTGGACTACATACGGAG 59.435 52.174 0.00 0.00 0.00 4.63
258 269 1.400737 AGGTGGACTACATACGGAGC 58.599 55.000 0.00 0.00 0.00 4.70
259 270 1.108776 GGTGGACTACATACGGAGCA 58.891 55.000 0.00 0.00 0.00 4.26
260 271 1.479323 GGTGGACTACATACGGAGCAA 59.521 52.381 0.00 0.00 0.00 3.91
261 272 2.093869 GGTGGACTACATACGGAGCAAA 60.094 50.000 0.00 0.00 0.00 3.68
262 273 3.592059 GTGGACTACATACGGAGCAAAA 58.408 45.455 0.00 0.00 0.00 2.44
263 274 4.189231 GTGGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
264 275 4.034048 GTGGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
265 276 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
266 277 4.873827 GGACTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.00 0.00 2.57
267 278 5.527582 GGACTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
268 279 6.363577 ACTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
269 280 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
270 281 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
271 282 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
272 283 6.498304 ACATACGGAGCAAAATGAATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
273 284 6.319658 ACATACGGAGCAAAATGAATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
274 285 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
275 286 6.757897 ACGGAGCAAAATGAATGAATCTAA 57.242 33.333 0.00 0.00 0.00 2.10
276 287 7.156876 ACGGAGCAAAATGAATGAATCTAAA 57.843 32.000 0.00 0.00 0.00 1.85
277 288 7.029563 ACGGAGCAAAATGAATGAATCTAAAC 58.970 34.615 0.00 0.00 0.00 2.01
278 289 7.094205 ACGGAGCAAAATGAATGAATCTAAACT 60.094 33.333 0.00 0.00 0.00 2.66
279 290 7.756722 CGGAGCAAAATGAATGAATCTAAACTT 59.243 33.333 0.00 0.00 0.00 2.66
302 313 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
304 315 9.719355 TTAAAATGCATCTATATACATCCGTGT 57.281 29.630 0.00 0.00 42.39 4.49
305 316 7.601073 AAATGCATCTATATACATCCGTGTG 57.399 36.000 0.00 0.00 39.39 3.82
306 317 4.494484 TGCATCTATATACATCCGTGTGC 58.506 43.478 0.00 0.00 39.39 4.57
307 318 3.547868 GCATCTATATACATCCGTGTGCG 59.452 47.826 0.00 0.00 39.39 5.34
321 332 4.545823 CGTGTGCGGTTTATAATGGAAT 57.454 40.909 0.00 0.00 0.00 3.01
322 333 4.523813 CGTGTGCGGTTTATAATGGAATC 58.476 43.478 0.00 0.00 0.00 2.52
323 334 4.272504 CGTGTGCGGTTTATAATGGAATCT 59.727 41.667 0.00 0.00 0.00 2.40
324 335 5.558273 CGTGTGCGGTTTATAATGGAATCTC 60.558 44.000 0.00 0.00 0.00 2.75
325 336 5.527582 GTGTGCGGTTTATAATGGAATCTCT 59.472 40.000 0.00 0.00 0.00 3.10
326 337 6.704493 GTGTGCGGTTTATAATGGAATCTCTA 59.296 38.462 0.00 0.00 0.00 2.43
327 338 6.704493 TGTGCGGTTTATAATGGAATCTCTAC 59.296 38.462 0.00 0.00 0.00 2.59
328 339 6.704493 GTGCGGTTTATAATGGAATCTCTACA 59.296 38.462 0.00 0.00 0.00 2.74
329 340 7.225931 GTGCGGTTTATAATGGAATCTCTACAA 59.774 37.037 0.00 0.00 0.00 2.41
330 341 7.771361 TGCGGTTTATAATGGAATCTCTACAAA 59.229 33.333 0.00 0.00 0.00 2.83
331 342 8.283291 GCGGTTTATAATGGAATCTCTACAAAG 58.717 37.037 0.00 0.00 0.00 2.77
332 343 9.542462 CGGTTTATAATGGAATCTCTACAAAGA 57.458 33.333 0.00 0.00 0.00 2.52
340 351 9.965902 AATGGAATCTCTACAAAGACTTACATT 57.034 29.630 0.00 0.00 30.67 2.71
341 352 9.965902 ATGGAATCTCTACAAAGACTTACATTT 57.034 29.630 0.00 0.00 0.00 2.32
347 358 9.924650 TCTCTACAAAGACTTACATTTAGGAAC 57.075 33.333 0.00 0.00 0.00 3.62
348 359 8.752766 TCTACAAAGACTTACATTTAGGAACG 57.247 34.615 0.00 0.00 0.00 3.95
349 360 6.796705 ACAAAGACTTACATTTAGGAACGG 57.203 37.500 0.00 0.00 0.00 4.44
350 361 6.527423 ACAAAGACTTACATTTAGGAACGGA 58.473 36.000 0.00 0.00 0.00 4.69
351 362 6.649557 ACAAAGACTTACATTTAGGAACGGAG 59.350 38.462 0.00 0.00 0.00 4.63
352 363 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
353 364 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
354 365 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
355 366 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
443 454 6.252967 TGTGCTGGTAATATCAAACTGTTG 57.747 37.500 0.00 0.00 35.95 3.33
464 475 6.096987 TGTTGATCATTGTCCTAGACTCCTAC 59.903 42.308 0.00 0.00 33.15 3.18
465 476 6.019656 TGATCATTGTCCTAGACTCCTACT 57.980 41.667 0.00 0.00 33.15 2.57
466 477 6.065374 TGATCATTGTCCTAGACTCCTACTC 58.935 44.000 0.00 0.00 33.15 2.59
467 478 4.794334 TCATTGTCCTAGACTCCTACTCC 58.206 47.826 0.00 0.00 33.15 3.85
468 479 3.666345 TTGTCCTAGACTCCTACTCCC 57.334 52.381 0.00 0.00 33.15 4.30
469 480 2.861261 TGTCCTAGACTCCTACTCCCT 58.139 52.381 0.00 0.00 33.15 4.20
470 481 2.778850 TGTCCTAGACTCCTACTCCCTC 59.221 54.545 0.00 0.00 33.15 4.30
471 482 2.107031 GTCCTAGACTCCTACTCCCTCC 59.893 59.091 0.00 0.00 0.00 4.30
472 483 1.072648 CCTAGACTCCTACTCCCTCCG 59.927 61.905 0.00 0.00 0.00 4.63
473 484 1.770061 CTAGACTCCTACTCCCTCCGT 59.230 57.143 0.00 0.00 0.00 4.69
474 485 1.001282 AGACTCCTACTCCCTCCGTT 58.999 55.000 0.00 0.00 0.00 4.44
475 486 1.064537 AGACTCCTACTCCCTCCGTTC 60.065 57.143 0.00 0.00 0.00 3.95
476 487 0.033306 ACTCCTACTCCCTCCGTTCC 60.033 60.000 0.00 0.00 0.00 3.62
477 488 0.259356 CTCCTACTCCCTCCGTTCCT 59.741 60.000 0.00 0.00 0.00 3.36
478 489 1.493871 CTCCTACTCCCTCCGTTCCTA 59.506 57.143 0.00 0.00 0.00 2.94
479 490 1.925255 TCCTACTCCCTCCGTTCCTAA 59.075 52.381 0.00 0.00 0.00 2.69
480 491 2.312741 TCCTACTCCCTCCGTTCCTAAA 59.687 50.000 0.00 0.00 0.00 1.85
481 492 3.052338 TCCTACTCCCTCCGTTCCTAAAT 60.052 47.826 0.00 0.00 0.00 1.40
482 493 4.168675 TCCTACTCCCTCCGTTCCTAAATA 59.831 45.833 0.00 0.00 0.00 1.40
483 494 5.085219 CCTACTCCCTCCGTTCCTAAATAT 58.915 45.833 0.00 0.00 0.00 1.28
484 495 6.045931 TCCTACTCCCTCCGTTCCTAAATATA 59.954 42.308 0.00 0.00 0.00 0.86
485 496 6.723052 CCTACTCCCTCCGTTCCTAAATATAA 59.277 42.308 0.00 0.00 0.00 0.98
486 497 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
487 498 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
488 499 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
489 500 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
490 501 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
491 502 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
492 503 7.656542 CCCTCCGTTCCTAAATATAAGTCTTTC 59.343 40.741 0.00 0.00 0.00 2.62
493 504 8.422566 CCTCCGTTCCTAAATATAAGTCTTTCT 58.577 37.037 0.00 0.00 0.00 2.52
521 532 9.901724 GAGTTATCAAATTGACTAACACATACG 57.098 33.333 19.92 0.00 30.23 3.06
522 533 8.879759 AGTTATCAAATTGACTAACACATACGG 58.120 33.333 19.92 0.00 30.23 4.02
523 534 8.875803 GTTATCAAATTGACTAACACATACGGA 58.124 33.333 16.20 0.00 0.00 4.69
524 535 9.607988 TTATCAAATTGACTAACACATACGGAT 57.392 29.630 0.00 0.00 0.00 4.18
525 536 7.302350 TCAAATTGACTAACACATACGGATG 57.698 36.000 5.94 5.94 39.16 3.51
527 538 8.035984 TCAAATTGACTAACACATACGGATGTA 58.964 33.333 14.23 0.00 44.82 2.29
528 539 8.826710 CAAATTGACTAACACATACGGATGTAT 58.173 33.333 14.23 8.21 44.82 2.29
533 544 9.729281 TGACTAACACATACGGATGTATATAGA 57.271 33.333 23.23 8.05 44.82 1.98
534 545 9.985318 GACTAACACATACGGATGTATATAGAC 57.015 37.037 23.23 17.02 44.82 2.59
535 546 9.511272 ACTAACACATACGGATGTATATAGACA 57.489 33.333 23.23 2.07 44.82 3.41
558 569 9.593134 GACATCATTTAGAGTGTAGATTCACTT 57.407 33.333 0.98 0.00 46.81 3.16
559 570 9.376075 ACATCATTTAGAGTGTAGATTCACTTG 57.624 33.333 0.98 0.00 46.81 3.16
560 571 9.376075 CATCATTTAGAGTGTAGATTCACTTGT 57.624 33.333 0.98 0.00 46.81 3.16
561 572 9.950496 ATCATTTAGAGTGTAGATTCACTTGTT 57.050 29.630 0.98 0.00 46.81 2.83
562 573 9.778741 TCATTTAGAGTGTAGATTCACTTGTTT 57.221 29.630 0.98 0.00 46.81 2.83
565 576 6.305693 AGAGTGTAGATTCACTTGTTTTGC 57.694 37.500 0.98 0.00 46.81 3.68
566 577 6.058183 AGAGTGTAGATTCACTTGTTTTGCT 58.942 36.000 0.98 0.00 46.81 3.91
567 578 6.203723 AGAGTGTAGATTCACTTGTTTTGCTC 59.796 38.462 0.98 0.00 46.81 4.26
568 579 5.239525 AGTGTAGATTCACTTGTTTTGCTCC 59.760 40.000 0.00 0.00 44.92 4.70
569 580 3.904136 AGATTCACTTGTTTTGCTCCG 57.096 42.857 0.00 0.00 0.00 4.63
570 581 3.214328 AGATTCACTTGTTTTGCTCCGT 58.786 40.909 0.00 0.00 0.00 4.69
571 582 4.385825 AGATTCACTTGTTTTGCTCCGTA 58.614 39.130 0.00 0.00 0.00 4.02
572 583 5.003804 AGATTCACTTGTTTTGCTCCGTAT 58.996 37.500 0.00 0.00 0.00 3.06
573 584 4.481930 TTCACTTGTTTTGCTCCGTATG 57.518 40.909 0.00 0.00 0.00 2.39
574 585 3.472652 TCACTTGTTTTGCTCCGTATGT 58.527 40.909 0.00 0.00 0.00 2.29
575 586 4.633175 TCACTTGTTTTGCTCCGTATGTA 58.367 39.130 0.00 0.00 0.00 2.29
576 587 4.688879 TCACTTGTTTTGCTCCGTATGTAG 59.311 41.667 0.00 0.00 0.00 2.74
577 588 4.451096 CACTTGTTTTGCTCCGTATGTAGT 59.549 41.667 0.00 0.00 0.00 2.73
578 589 4.689345 ACTTGTTTTGCTCCGTATGTAGTC 59.311 41.667 0.00 0.00 0.00 2.59
579 590 4.260139 TGTTTTGCTCCGTATGTAGTCA 57.740 40.909 0.00 0.00 0.00 3.41
580 591 3.991773 TGTTTTGCTCCGTATGTAGTCAC 59.008 43.478 0.00 0.00 0.00 3.67
581 592 4.243270 GTTTTGCTCCGTATGTAGTCACT 58.757 43.478 0.00 0.00 0.00 3.41
582 593 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
583 594 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
584 595 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
585 596 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
586 597 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
587 598 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
588 599 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
589 600 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
590 601 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
591 602 7.604549 TCCGTATGTAGTCACTTGTTGAAATA 58.395 34.615 0.00 0.00 35.39 1.40
592 603 8.255206 TCCGTATGTAGTCACTTGTTGAAATAT 58.745 33.333 0.00 0.00 35.39 1.28
593 604 8.540492 CCGTATGTAGTCACTTGTTGAAATATC 58.460 37.037 0.00 0.00 35.39 1.63
594 605 9.302345 CGTATGTAGTCACTTGTTGAAATATCT 57.698 33.333 0.00 0.00 35.39 1.98
603 614 9.996554 TCACTTGTTGAAATATCTAGAAAGACA 57.003 29.630 0.00 0.00 33.57 3.41
618 629 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
619 630 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
620 631 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
621 632 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
622 633 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
623 634 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
628 639 3.744940 TTTAGGAACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
637 648 6.374053 GGAACGGAGGGAGTAGAATATAGTAC 59.626 46.154 0.00 0.00 0.00 2.73
666 677 1.000145 GCGGCAGTACTACTCAAAGC 59.000 55.000 0.00 0.00 0.00 3.51
697 762 5.631119 TCTTAAGGCCTTGGCTATTATTCC 58.369 41.667 28.77 0.00 37.50 3.01
711 776 7.883311 TGGCTATTATTCCTCTTATTTGGCTAC 59.117 37.037 0.00 0.00 0.00 3.58
718 783 4.468510 TCCTCTTATTTGGCTACCTCGAAA 59.531 41.667 0.00 0.00 0.00 3.46
732 797 6.759827 GCTACCTCGAAATAGTGAAATTACCA 59.240 38.462 4.91 0.00 0.00 3.25
733 798 7.441458 GCTACCTCGAAATAGTGAAATTACCAT 59.559 37.037 4.91 0.00 0.00 3.55
734 799 9.326413 CTACCTCGAAATAGTGAAATTACCATT 57.674 33.333 0.00 0.00 0.00 3.16
735 800 8.209917 ACCTCGAAATAGTGAAATTACCATTC 57.790 34.615 0.00 0.00 0.00 2.67
736 801 7.011109 ACCTCGAAATAGTGAAATTACCATTCG 59.989 37.037 0.00 0.00 0.00 3.34
737 802 7.223971 CCTCGAAATAGTGAAATTACCATTCGA 59.776 37.037 0.00 0.00 0.00 3.71
738 803 8.657074 TCGAAATAGTGAAATTACCATTCGAT 57.343 30.769 0.00 0.00 0.00 3.59
739 804 8.547894 TCGAAATAGTGAAATTACCATTCGATG 58.452 33.333 0.00 0.00 0.00 3.84
1234 1354 1.611474 ATCCAAGCGAGCTGAGCTGA 61.611 55.000 13.71 1.18 45.31 4.26
1255 1375 2.046700 CTTCGGTAAAGGCGGCCA 60.047 61.111 23.09 0.00 0.00 5.36
1593 1770 3.006756 GCTGCTGTCGGAGGCACTA 62.007 63.158 0.00 0.00 36.97 2.74
1628 1805 1.081833 ACCTGGAGGAGGATGCTGT 59.918 57.895 0.00 0.00 46.33 4.40
1694 1877 2.672996 GCACCTGACGTTGGGCAT 60.673 61.111 12.19 0.00 0.00 4.40
1767 1950 4.021925 GGCCTCCAGGTGCTCGTT 62.022 66.667 0.00 0.00 37.57 3.85
1796 2012 4.583489 ACTACAGGAAGACGACAAGAAGAA 59.417 41.667 0.00 0.00 0.00 2.52
1807 2023 4.245660 CGACAAGAAGAAGTTGGATGCTA 58.754 43.478 0.00 0.00 0.00 3.49
1819 2035 0.546122 GGATGCTATGTGGGTGGACA 59.454 55.000 0.00 0.00 0.00 4.02
1961 2180 4.722700 GGCCTGCTTCTTCCGGCA 62.723 66.667 0.00 0.00 44.23 5.69
2138 2363 4.034510 CCATCCGATCAAAACTACAAGCTC 59.965 45.833 0.00 0.00 0.00 4.09
2180 2405 6.185511 CCAATCATATCCATCCTAGCAATGT 58.814 40.000 0.00 0.00 0.00 2.71
2243 2469 5.717078 ATATGTATCCAAGCAATGCAAGG 57.283 39.130 8.35 8.90 0.00 3.61
2381 2614 3.326297 CAGGAAAAGTCAGGGAACTCTCT 59.674 47.826 0.00 0.00 40.21 3.10
2382 2615 3.580895 AGGAAAAGTCAGGGAACTCTCTC 59.419 47.826 0.00 0.00 40.21 3.20
2383 2616 3.307129 GGAAAAGTCAGGGAACTCTCTCC 60.307 52.174 0.00 0.00 40.21 3.71
2384 2617 3.268034 AAAGTCAGGGAACTCTCTCCT 57.732 47.619 0.00 0.00 40.21 3.69
2385 2618 2.525105 AGTCAGGGAACTCTCTCCTC 57.475 55.000 0.00 0.00 40.21 3.71
2417 2650 6.480763 TCATTTAAGCAGGTTCATTACAGGA 58.519 36.000 0.00 0.00 0.00 3.86
2580 2849 5.008019 CAGAAACTGCATATATTGTTCGGCT 59.992 40.000 0.00 0.00 0.00 5.52
2669 3219 7.408756 ACAATGCCATGACATACTAAAACAT 57.591 32.000 0.00 0.00 0.00 2.71
2695 3245 5.659440 ATACCCACAAATCAACATCCAAC 57.341 39.130 0.00 0.00 0.00 3.77
2710 3286 4.925054 ACATCCAACAATTCAAATCAAGCG 59.075 37.500 0.00 0.00 0.00 4.68
2801 3377 6.253727 GCGAGGCATTACAGATATACATACAC 59.746 42.308 0.00 0.00 0.00 2.90
2832 3408 3.805066 TGAGGAATCACACCCAATTGA 57.195 42.857 7.12 0.00 0.00 2.57
3041 3619 9.903682 ATAATTCAGTATTGCATGAATAACAGC 57.096 29.630 12.43 0.00 43.56 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.489160 TCAATAAGCTGTTCTTCTATTCGCTA 58.511 34.615 0.00 0.00 36.25 4.26
27 28 6.341316 TCAATAAGCTGTTCTTCTATTCGCT 58.659 36.000 0.00 0.00 36.25 4.93
28 29 6.589830 TCAATAAGCTGTTCTTCTATTCGC 57.410 37.500 0.00 0.00 36.25 4.70
29 30 8.357796 TCATCAATAAGCTGTTCTTCTATTCG 57.642 34.615 0.00 0.00 36.25 3.34
103 107 1.474478 AGATGAGTAGCTGTCCACGTG 59.526 52.381 9.08 9.08 0.00 4.49
190 201 2.332117 AGGAACGGAGGGAGTAAAACA 58.668 47.619 0.00 0.00 0.00 2.83
192 203 5.767277 ATTTAGGAACGGAGGGAGTAAAA 57.233 39.130 0.00 0.00 0.00 1.52
195 206 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
196 207 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
197 208 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
198 209 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
199 210 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
200 211 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
201 212 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
215 226 8.919145 CCTAGTGGAATCTCTACAAAGACTTAT 58.081 37.037 0.00 0.00 34.57 1.73
216 227 7.894364 ACCTAGTGGAATCTCTACAAAGACTTA 59.106 37.037 0.00 0.00 37.04 2.24
217 228 6.726764 ACCTAGTGGAATCTCTACAAAGACTT 59.273 38.462 0.00 0.00 37.04 3.01
218 229 6.153680 CACCTAGTGGAATCTCTACAAAGACT 59.846 42.308 0.00 0.00 37.04 3.24
219 230 6.334202 CACCTAGTGGAATCTCTACAAAGAC 58.666 44.000 0.00 0.00 37.04 3.01
220 231 6.531503 CACCTAGTGGAATCTCTACAAAGA 57.468 41.667 0.00 0.00 37.04 2.52
235 246 3.548770 TCCGTATGTAGTCCACCTAGTG 58.451 50.000 0.00 0.00 0.00 2.74
236 247 3.818180 CTCCGTATGTAGTCCACCTAGT 58.182 50.000 0.00 0.00 0.00 2.57
237 248 2.553172 GCTCCGTATGTAGTCCACCTAG 59.447 54.545 0.00 0.00 0.00 3.02
238 249 2.092267 TGCTCCGTATGTAGTCCACCTA 60.092 50.000 0.00 0.00 0.00 3.08
239 250 1.341679 TGCTCCGTATGTAGTCCACCT 60.342 52.381 0.00 0.00 0.00 4.00
240 251 1.108776 TGCTCCGTATGTAGTCCACC 58.891 55.000 0.00 0.00 0.00 4.61
241 252 2.953466 TTGCTCCGTATGTAGTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
242 253 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
243 254 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
244 255 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
245 256 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
246 257 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
247 258 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
248 259 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
249 260 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
250 261 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
251 262 7.857734 TTAGATTCATTCATTTTGCTCCGTA 57.142 32.000 0.00 0.00 0.00 4.02
252 263 6.757897 TTAGATTCATTCATTTTGCTCCGT 57.242 33.333 0.00 0.00 0.00 4.69
253 264 7.253422 AGTTTAGATTCATTCATTTTGCTCCG 58.747 34.615 0.00 0.00 0.00 4.63
254 265 8.992835 AAGTTTAGATTCATTCATTTTGCTCC 57.007 30.769 0.00 0.00 0.00 4.70
276 287 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
278 289 9.719355 ACACGGATGTATATAGATGCATTTTAA 57.281 29.630 11.19 0.00 38.38 1.52
279 290 9.150348 CACACGGATGTATATAGATGCATTTTA 57.850 33.333 11.19 0.00 38.38 1.52
280 291 7.361201 GCACACGGATGTATATAGATGCATTTT 60.361 37.037 11.19 0.00 38.38 1.82
281 292 6.092670 GCACACGGATGTATATAGATGCATTT 59.907 38.462 11.19 0.00 38.38 2.32
282 293 5.582269 GCACACGGATGTATATAGATGCATT 59.418 40.000 11.19 0.00 38.38 3.56
283 294 5.111989 GCACACGGATGTATATAGATGCAT 58.888 41.667 11.19 0.00 40.68 3.96
284 295 4.494484 GCACACGGATGTATATAGATGCA 58.506 43.478 11.19 0.00 36.72 3.96
285 296 3.547868 CGCACACGGATGTATATAGATGC 59.452 47.826 0.00 0.00 36.72 3.91
300 311 4.272504 AGATTCCATTATAAACCGCACACG 59.727 41.667 0.00 0.00 39.67 4.49
301 312 5.527582 AGAGATTCCATTATAAACCGCACAC 59.472 40.000 0.00 0.00 0.00 3.82
302 313 5.680619 AGAGATTCCATTATAAACCGCACA 58.319 37.500 0.00 0.00 0.00 4.57
303 314 6.704493 TGTAGAGATTCCATTATAAACCGCAC 59.296 38.462 0.00 0.00 0.00 5.34
304 315 6.822442 TGTAGAGATTCCATTATAAACCGCA 58.178 36.000 0.00 0.00 0.00 5.69
305 316 7.724305 TTGTAGAGATTCCATTATAAACCGC 57.276 36.000 0.00 0.00 0.00 5.68
306 317 9.542462 TCTTTGTAGAGATTCCATTATAAACCG 57.458 33.333 0.00 0.00 0.00 4.44
314 325 9.965902 AATGTAAGTCTTTGTAGAGATTCCATT 57.034 29.630 0.00 0.00 0.00 3.16
315 326 9.965902 AAATGTAAGTCTTTGTAGAGATTCCAT 57.034 29.630 0.00 0.00 0.00 3.41
321 332 9.924650 GTTCCTAAATGTAAGTCTTTGTAGAGA 57.075 33.333 0.00 0.00 0.00 3.10
322 333 8.861101 CGTTCCTAAATGTAAGTCTTTGTAGAG 58.139 37.037 0.00 0.00 0.00 2.43
323 334 7.816031 CCGTTCCTAAATGTAAGTCTTTGTAGA 59.184 37.037 0.00 0.00 0.00 2.59
324 335 7.816031 TCCGTTCCTAAATGTAAGTCTTTGTAG 59.184 37.037 0.00 0.00 0.00 2.74
325 336 7.669427 TCCGTTCCTAAATGTAAGTCTTTGTA 58.331 34.615 0.00 0.00 0.00 2.41
326 337 6.527423 TCCGTTCCTAAATGTAAGTCTTTGT 58.473 36.000 0.00 0.00 0.00 2.83
327 338 6.092259 CCTCCGTTCCTAAATGTAAGTCTTTG 59.908 42.308 0.00 0.00 0.00 2.77
328 339 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
329 340 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
330 341 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
331 342 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
332 343 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
333 344 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
334 345 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
335 346 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
336 347 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
337 348 4.957684 ATACTCCCTCCGTTCCTAAATG 57.042 45.455 0.00 0.00 0.00 2.32
338 349 6.785963 TGAATATACTCCCTCCGTTCCTAAAT 59.214 38.462 0.00 0.00 0.00 1.40
339 350 6.138263 TGAATATACTCCCTCCGTTCCTAAA 58.862 40.000 0.00 0.00 0.00 1.85
340 351 5.708544 TGAATATACTCCCTCCGTTCCTAA 58.291 41.667 0.00 0.00 0.00 2.69
341 352 5.329191 TGAATATACTCCCTCCGTTCCTA 57.671 43.478 0.00 0.00 0.00 2.94
342 353 4.194678 TGAATATACTCCCTCCGTTCCT 57.805 45.455 0.00 0.00 0.00 3.36
343 354 4.587684 TCTTGAATATACTCCCTCCGTTCC 59.412 45.833 0.00 0.00 0.00 3.62
344 355 5.786264 TCTTGAATATACTCCCTCCGTTC 57.214 43.478 0.00 0.00 0.00 3.95
345 356 6.749036 ATTCTTGAATATACTCCCTCCGTT 57.251 37.500 0.00 0.00 0.00 4.44
346 357 6.525629 CAATTCTTGAATATACTCCCTCCGT 58.474 40.000 0.00 0.00 0.00 4.69
347 358 5.409826 GCAATTCTTGAATATACTCCCTCCG 59.590 44.000 0.00 0.00 0.00 4.63
348 359 6.299141 TGCAATTCTTGAATATACTCCCTCC 58.701 40.000 0.00 0.00 0.00 4.30
349 360 7.992754 ATGCAATTCTTGAATATACTCCCTC 57.007 36.000 0.00 0.00 0.00 4.30
352 363 9.565213 GCATAATGCAATTCTTGAATATACTCC 57.435 33.333 0.00 0.00 44.26 3.85
443 454 5.475564 GGAGTAGGAGTCTAGGACAATGATC 59.524 48.000 0.52 0.00 34.60 2.92
464 475 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
465 476 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
466 477 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
467 478 8.422566 AGAAAGACTTATATTTAGGAACGGAGG 58.577 37.037 0.00 0.00 0.00 4.30
495 506 9.901724 CGTATGTGTTAGTCAATTTGATAACTC 57.098 33.333 20.19 18.30 29.75 3.01
496 507 8.879759 CCGTATGTGTTAGTCAATTTGATAACT 58.120 33.333 20.19 11.22 29.75 2.24
497 508 8.875803 TCCGTATGTGTTAGTCAATTTGATAAC 58.124 33.333 16.50 16.50 0.00 1.89
498 509 9.607988 ATCCGTATGTGTTAGTCAATTTGATAA 57.392 29.630 1.78 0.78 0.00 1.75
499 510 9.040939 CATCCGTATGTGTTAGTCAATTTGATA 57.959 33.333 1.78 0.00 0.00 2.15
500 511 7.552687 ACATCCGTATGTGTTAGTCAATTTGAT 59.447 33.333 1.78 0.00 44.79 2.57
501 512 6.876789 ACATCCGTATGTGTTAGTCAATTTGA 59.123 34.615 0.00 0.00 44.79 2.69
502 513 7.072177 ACATCCGTATGTGTTAGTCAATTTG 57.928 36.000 0.00 0.00 44.79 2.32
503 514 8.958119 ATACATCCGTATGTGTTAGTCAATTT 57.042 30.769 3.56 0.00 45.99 1.82
507 518 9.729281 TCTATATACATCCGTATGTGTTAGTCA 57.271 33.333 3.56 0.00 45.99 3.41
508 519 9.985318 GTCTATATACATCCGTATGTGTTAGTC 57.015 37.037 3.56 0.00 45.99 2.59
509 520 9.511272 TGTCTATATACATCCGTATGTGTTAGT 57.489 33.333 3.56 0.00 45.99 2.24
531 542 8.976353 AGTGAATCTACACTCTAAATGATGTCT 58.024 33.333 0.00 0.00 46.36 3.41
545 556 5.452777 GGAGCAAAACAAGTGAATCTACAC 58.547 41.667 0.00 0.00 40.60 2.90
546 557 4.213270 CGGAGCAAAACAAGTGAATCTACA 59.787 41.667 0.00 0.00 0.00 2.74
547 558 4.213482 ACGGAGCAAAACAAGTGAATCTAC 59.787 41.667 0.00 0.00 0.00 2.59
548 559 4.385825 ACGGAGCAAAACAAGTGAATCTA 58.614 39.130 0.00 0.00 0.00 1.98
549 560 3.214328 ACGGAGCAAAACAAGTGAATCT 58.786 40.909 0.00 0.00 0.00 2.40
550 561 3.626028 ACGGAGCAAAACAAGTGAATC 57.374 42.857 0.00 0.00 0.00 2.52
551 562 4.518970 ACATACGGAGCAAAACAAGTGAAT 59.481 37.500 0.00 0.00 0.00 2.57
552 563 3.880490 ACATACGGAGCAAAACAAGTGAA 59.120 39.130 0.00 0.00 0.00 3.18
553 564 3.472652 ACATACGGAGCAAAACAAGTGA 58.527 40.909 0.00 0.00 0.00 3.41
554 565 3.896648 ACATACGGAGCAAAACAAGTG 57.103 42.857 0.00 0.00 0.00 3.16
555 566 4.638304 ACTACATACGGAGCAAAACAAGT 58.362 39.130 0.00 0.00 0.00 3.16
556 567 4.688879 TGACTACATACGGAGCAAAACAAG 59.311 41.667 0.00 0.00 0.00 3.16
557 568 4.449743 GTGACTACATACGGAGCAAAACAA 59.550 41.667 0.00 0.00 0.00 2.83
558 569 3.991773 GTGACTACATACGGAGCAAAACA 59.008 43.478 0.00 0.00 0.00 2.83
559 570 4.243270 AGTGACTACATACGGAGCAAAAC 58.757 43.478 0.00 0.00 0.00 2.43
560 571 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
561 572 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
562 573 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
563 574 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
564 575 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
565 576 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
566 577 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
567 578 6.721571 ATTTCAACAAGTGACTACATACGG 57.278 37.500 0.00 0.00 35.39 4.02
568 579 9.302345 AGATATTTCAACAAGTGACTACATACG 57.698 33.333 0.00 0.00 35.39 3.06
577 588 9.996554 TGTCTTTCTAGATATTTCAACAAGTGA 57.003 29.630 0.00 0.00 31.86 3.41
592 603 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
593 604 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
594 605 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
595 606 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
596 607 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
597 608 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
598 609 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
599 610 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
600 611 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
601 612 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
602 613 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
603 614 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
604 615 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
605 616 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
606 617 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
607 618 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
608 619 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
609 620 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
610 621 3.967467 ATTCTACTCCCTCCGTTCCTA 57.033 47.619 0.00 0.00 0.00 2.94
611 622 2.850695 ATTCTACTCCCTCCGTTCCT 57.149 50.000 0.00 0.00 0.00 3.36
612 623 5.323581 ACTATATTCTACTCCCTCCGTTCC 58.676 45.833 0.00 0.00 0.00 3.62
613 624 7.167535 AGTACTATATTCTACTCCCTCCGTTC 58.832 42.308 0.00 0.00 0.00 3.95
614 625 7.089106 AGTACTATATTCTACTCCCTCCGTT 57.911 40.000 0.00 0.00 0.00 4.44
615 626 6.700845 AGTACTATATTCTACTCCCTCCGT 57.299 41.667 0.00 0.00 0.00 4.69
616 627 7.619050 TGTAGTACTATATTCTACTCCCTCCG 58.381 42.308 5.75 0.00 36.16 4.63
617 628 7.553760 GCTGTAGTACTATATTCTACTCCCTCC 59.446 44.444 5.75 0.00 36.16 4.30
618 629 8.102047 TGCTGTAGTACTATATTCTACTCCCTC 58.898 40.741 5.75 0.00 36.16 4.30
619 630 7.884354 GTGCTGTAGTACTATATTCTACTCCCT 59.116 40.741 5.75 0.00 36.16 4.20
620 631 7.664731 TGTGCTGTAGTACTATATTCTACTCCC 59.335 40.741 5.75 0.00 36.16 4.30
621 632 8.618702 TGTGCTGTAGTACTATATTCTACTCC 57.381 38.462 5.75 0.00 36.16 3.85
622 633 8.231837 GCTGTGCTGTAGTACTATATTCTACTC 58.768 40.741 5.75 0.00 36.16 2.59
623 634 7.095144 CGCTGTGCTGTAGTACTATATTCTACT 60.095 40.741 5.75 0.00 36.16 2.57
628 639 4.558898 GCCGCTGTGCTGTAGTACTATATT 60.559 45.833 5.75 0.00 0.00 1.28
637 648 1.078759 GTACTGCCGCTGTGCTGTAG 61.079 60.000 12.77 0.00 43.43 2.74
666 677 0.253327 AAGGCCTTAAGAAGAGCGGG 59.747 55.000 18.87 0.00 0.00 6.13
697 762 7.169982 CACTATTTCGAGGTAGCCAAATAAGAG 59.830 40.741 6.18 0.00 0.00 2.85
711 776 7.223971 TCGAATGGTAATTTCACTATTTCGAGG 59.776 37.037 10.68 0.00 30.64 4.63
736 801 2.611225 AAGACCAGGCTCGAATCATC 57.389 50.000 0.00 0.00 0.00 2.92
737 802 2.237143 TCAAAGACCAGGCTCGAATCAT 59.763 45.455 0.00 0.00 0.00 2.45
738 803 1.623311 TCAAAGACCAGGCTCGAATCA 59.377 47.619 0.00 0.00 0.00 2.57
739 804 2.386661 TCAAAGACCAGGCTCGAATC 57.613 50.000 0.00 0.00 0.00 2.52
1234 1354 1.520787 CCGCCTTTACCGAAGCGAT 60.521 57.895 4.61 0.00 37.19 4.58
1239 1359 2.358984 GTGGCCGCCTTTACCGAA 60.359 61.111 11.61 0.00 0.00 4.30
1240 1360 3.599285 CTGTGGCCGCCTTTACCGA 62.599 63.158 15.15 0.00 0.00 4.69
1255 1375 1.122019 AAGAAGCCCACCGTCTCTGT 61.122 55.000 0.00 0.00 30.68 3.41
1767 1950 1.162698 CGTCTTCCTGTAGTCCGTCA 58.837 55.000 0.00 0.00 0.00 4.35
1796 2012 1.064463 CCACCCACATAGCATCCAACT 60.064 52.381 0.00 0.00 0.00 3.16
1807 2023 1.000521 CTGGCATGTCCACCCACAT 60.001 57.895 4.93 0.00 40.72 3.21
1976 2195 2.354103 GGCTGTAGCACTCTCATTGACA 60.354 50.000 6.18 0.00 44.36 3.58
1982 2201 2.038952 ACAATTGGCTGTAGCACTCTCA 59.961 45.455 10.83 0.00 44.36 3.27
2180 2405 5.278907 CCACAAACACAATCCAAGCATCTTA 60.279 40.000 0.00 0.00 0.00 2.10
2223 2449 6.474263 GCACCTTGCATTGCTTGGATACAT 62.474 45.833 21.27 2.46 45.99 2.29
2224 2450 5.232180 GCACCTTGCATTGCTTGGATACA 62.232 47.826 21.27 0.00 45.32 2.29
2243 2469 6.646240 TGGAAAGCAGAAAAGATTAATTGCAC 59.354 34.615 9.55 2.30 34.17 4.57
2305 2531 4.574013 CAGTATCTTGCTCCCTGTTTCATC 59.426 45.833 0.00 0.00 0.00 2.92
2381 2614 2.006888 CTTAAATGAAAGCGGCGAGGA 58.993 47.619 12.98 0.00 0.00 3.71
2382 2615 1.531883 GCTTAAATGAAAGCGGCGAGG 60.532 52.381 12.98 0.00 42.21 4.63
2383 2616 1.815132 GCTTAAATGAAAGCGGCGAG 58.185 50.000 12.98 0.00 42.21 5.03
2384 2617 3.988459 GCTTAAATGAAAGCGGCGA 57.012 47.368 12.98 0.00 42.21 5.54
2417 2650 6.293407 GCGTGCTGGTGACATATATAATTTGT 60.293 38.462 0.00 0.00 41.51 2.83
2572 2805 4.576053 CCAATCAATTAGATGAGCCGAACA 59.424 41.667 0.00 0.00 36.96 3.18
2573 2806 4.576463 ACCAATCAATTAGATGAGCCGAAC 59.424 41.667 0.00 0.00 36.96 3.95
2575 2808 4.422073 ACCAATCAATTAGATGAGCCGA 57.578 40.909 0.00 0.00 36.96 5.54
2580 2849 7.861629 ACAGACCTTACCAATCAATTAGATGA 58.138 34.615 0.00 0.00 36.96 2.92
2669 3219 4.709397 GGATGTTGATTTGTGGGTATTGGA 59.291 41.667 0.00 0.00 0.00 3.53
2695 3245 7.565450 TCATGTTTACGCTTGATTTGAATTG 57.435 32.000 0.00 0.00 0.00 2.32
2710 3286 8.688151 ACCTAGTATCTGAGACTTCATGTTTAC 58.312 37.037 10.54 0.00 31.68 2.01
2801 3377 6.385033 GGTGTGATTCCTCAATTTCTTCTTG 58.615 40.000 0.00 0.00 31.85 3.02
2832 3408 5.804639 TCATTGTTGTATAACCTGTGAGCT 58.195 37.500 0.00 0.00 35.92 4.09
2923 3499 0.107945 ATCTTGAGTCTCGCCTTGGC 60.108 55.000 0.75 0.75 0.00 4.52
2929 3505 3.579709 TGAAGTTGATCTTGAGTCTCGC 58.420 45.455 0.00 0.00 36.40 5.03


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

AutoCloner maintained by Alex Coulton.