Multiple sequence alignment - TraesCS6D01G367300

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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 TraesCS6D01G367300 chr6D 100.000 3534 0 0 1 3534 455133120 455136653 0.000000e+00 6527
1 TraesCS6D01G367300 chr6D 85.590 1950 184 50 552 2460 455250611 455252504 0.000000e+00 1954
2 TraesCS6D01G367300 chr6D 86.078 1099 93 24 1556 2607 455099217 455100302 0.000000e+00 1127
3 TraesCS6D01G367300 chr6D 81.414 877 97 30 655 1499 455098274 455099116 0.000000e+00 656
4 TraesCS6D01G367300 chr6D 83.550 231 38 0 2241 2471 455295234 455295464 2.140000e-52 217
5 TraesCS6D01G367300 chr6B 91.298 2195 130 27 405 2561 692258528 692260699 0.000000e+00 2939
6 TraesCS6D01G367300 chr6B 85.273 1942 190 51 552 2460 692427811 692429689 0.000000e+00 1914
7 TraesCS6D01G367300 chr6B 90.614 1449 90 21 1136 2566 692338660 692340080 0.000000e+00 1881
8 TraesCS6D01G367300 chr6B 91.354 879 50 10 2661 3534 692340073 692340930 0.000000e+00 1179
9 TraesCS6D01G367300 chr6B 85.873 1083 90 33 1556 2607 692234389 692235439 0.000000e+00 1094
10 TraesCS6D01G367300 chr6B 80.301 599 69 27 655 1220 692233324 692233906 1.180000e-109 407
11 TraesCS6D01G367300 chr6B 94.167 240 11 2 1 237 692258287 692258526 2.590000e-96 363
12 TraesCS6D01G367300 chr6B 82.176 432 49 13 702 1131 692337863 692338268 2.610000e-91 346
13 TraesCS6D01G367300 chr6B 86.498 237 24 2 1263 1499 692234060 692234288 1.630000e-63 254
14 TraesCS6D01G367300 chr6A 91.658 1822 109 21 896 2707 601872357 601874145 0.000000e+00 2483
15 TraesCS6D01G367300 chr6A 85.290 1951 185 54 552 2471 601949659 601951538 0.000000e+00 1919
16 TraesCS6D01G367300 chr6A 83.216 1984 181 79 702 2607 601472003 601473912 0.000000e+00 1679
17 TraesCS6D01G367300 chr6A 86.581 775 81 10 2766 3534 601874188 601874945 0.000000e+00 833
18 TraesCS6D01G367300 chr6A 89.189 370 37 1 552 918 601871962 601872331 3.210000e-125 459
19 TraesCS6D01G367300 chr3D 85.885 503 59 9 12 506 54718588 54719086 3.130000e-145 525
20 TraesCS6D01G367300 chr4A 83.529 255 40 2 254 507 703940239 703939986 1.640000e-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 TraesCS6D01G367300 chr6D 455133120 455136653 3533 False 6527.000000 6527 100.000000 1 3534 1 chr6D.!!$F1 3533
1 TraesCS6D01G367300 chr6D 455250611 455252504 1893 False 1954.000000 1954 85.590000 552 2460 1 chr6D.!!$F2 1908
2 TraesCS6D01G367300 chr6D 455098274 455100302 2028 False 891.500000 1127 83.746000 655 2607 2 chr6D.!!$F4 1952
3 TraesCS6D01G367300 chr6B 692427811 692429689 1878 False 1914.000000 1914 85.273000 552 2460 1 chr6B.!!$F1 1908
4 TraesCS6D01G367300 chr6B 692258287 692260699 2412 False 1651.000000 2939 92.732500 1 2561 2 chr6B.!!$F3 2560
5 TraesCS6D01G367300 chr6B 692337863 692340930 3067 False 1135.333333 1881 88.048000 702 3534 3 chr6B.!!$F4 2832
6 TraesCS6D01G367300 chr6B 692233324 692235439 2115 False 585.000000 1094 84.224000 655 2607 3 chr6B.!!$F2 1952
7 TraesCS6D01G367300 chr6A 601949659 601951538 1879 False 1919.000000 1919 85.290000 552 2471 1 chr6A.!!$F2 1919
8 TraesCS6D01G367300 chr6A 601472003 601473912 1909 False 1679.000000 1679 83.216000 702 2607 1 chr6A.!!$F1 1905
9 TraesCS6D01G367300 chr6A 601871962 601874945 2983 False 1258.333333 2483 89.142667 552 3534 3 chr6A.!!$F3 2982

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
390 394 0.036306 TTTTGTTCTCCGGCCTCTCC 59.964 55.0 0.0 0.0 0.00 3.71 F
476 480 0.037326 GTCGCTGGTGGACATCTTCA 60.037 55.0 0.0 0.0 34.56 3.02 F
756 777 0.108472 TGTGATCGGAGAGCTTGCAG 60.108 55.0 0.0 0.0 46.78 4.41 F
1813 2538 0.248134 GATCGTCGTCCTCCTCAACG 60.248 60.0 0.0 0.0 40.17 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 2717 0.685097 ACATGTACAAGAGGGCACGT 59.315 50.000 4.87 0.00 0.0 4.49 R
2366 3136 1.227089 CCTCCGCCGACATCTTCAG 60.227 63.158 0.00 0.00 0.0 3.02 R
2415 3185 2.781300 CGCCAGAGCTCTTTTCGC 59.219 61.111 15.27 12.23 36.6 4.70 R
2943 3755 0.031994 ACACCAAAGCCGAAATGTGC 59.968 50.000 0.00 0.00 0.0 4.57 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
24 25 2.341846 AACAGAGCGGTTCCTTTTCA 57.658 45.000 0.00 0.00 0.00 2.69
26 27 2.863809 ACAGAGCGGTTCCTTTTCATT 58.136 42.857 0.00 0.00 0.00 2.57
35 36 2.832129 GTTCCTTTTCATTCCCCTTCCC 59.168 50.000 0.00 0.00 0.00 3.97
37 38 2.452823 TCCTTTTCATTCCCCTTCCCAA 59.547 45.455 0.00 0.00 0.00 4.12
53 54 0.606401 CCAAGCGAAGAGGAAAGGCA 60.606 55.000 0.00 0.00 0.00 4.75
67 68 2.825836 GGCAACCAGATCCCAGCG 60.826 66.667 0.00 0.00 0.00 5.18
118 119 2.046864 CCTCCTTCAGTCGCTCCGA 61.047 63.158 0.00 0.00 0.00 4.55
119 120 1.388065 CCTCCTTCAGTCGCTCCGAT 61.388 60.000 0.00 0.00 38.42 4.18
149 151 2.450243 GACCCCAGTCCTCTCCCA 59.550 66.667 0.00 0.00 37.00 4.37
237 241 6.259608 AGCGTCAGATAAATCTTCCTCAATTG 59.740 38.462 0.00 0.00 34.22 2.32
238 242 6.512415 GCGTCAGATAAATCTTCCTCAATTGG 60.512 42.308 5.42 0.00 34.22 3.16
239 243 6.540189 CGTCAGATAAATCTTCCTCAATTGGT 59.460 38.462 5.42 0.00 34.22 3.67
240 244 7.066284 CGTCAGATAAATCTTCCTCAATTGGTT 59.934 37.037 5.42 0.00 34.22 3.67
241 245 8.401709 GTCAGATAAATCTTCCTCAATTGGTTC 58.598 37.037 5.42 0.00 34.22 3.62
242 246 7.557719 TCAGATAAATCTTCCTCAATTGGTTCC 59.442 37.037 5.42 0.00 34.22 3.62
243 247 7.559170 CAGATAAATCTTCCTCAATTGGTTCCT 59.441 37.037 5.42 0.00 34.22 3.36
244 248 7.777440 AGATAAATCTTCCTCAATTGGTTCCTC 59.223 37.037 5.42 0.00 31.97 3.71
245 249 3.721087 TCTTCCTCAATTGGTTCCTCC 57.279 47.619 5.42 0.00 0.00 4.30
246 250 2.986019 TCTTCCTCAATTGGTTCCTCCA 59.014 45.455 5.42 0.00 45.60 3.86
253 257 3.986054 TGGTTCCTCCACAGCAGT 58.014 55.556 0.00 0.00 41.93 4.40
254 258 1.451504 TGGTTCCTCCACAGCAGTG 59.548 57.895 1.56 1.56 41.93 3.66
255 259 1.968540 GGTTCCTCCACAGCAGTGC 60.969 63.158 7.13 7.13 44.53 4.40
256 260 1.072159 GTTCCTCCACAGCAGTGCT 59.928 57.895 13.14 13.14 44.53 4.40
257 261 0.536006 GTTCCTCCACAGCAGTGCTT 60.536 55.000 16.89 4.33 44.53 3.91
258 262 0.250467 TTCCTCCACAGCAGTGCTTC 60.250 55.000 16.89 0.00 44.53 3.86
259 263 1.123861 TCCTCCACAGCAGTGCTTCT 61.124 55.000 16.89 0.00 44.53 2.85
260 264 0.954449 CCTCCACAGCAGTGCTTCTG 60.954 60.000 16.89 13.46 44.53 3.02
261 265 0.954449 CTCCACAGCAGTGCTTCTGG 60.954 60.000 24.48 24.48 44.53 3.86
262 266 2.623915 CCACAGCAGTGCTTCTGGC 61.624 63.158 16.89 0.00 44.53 4.85
263 267 2.667536 ACAGCAGTGCTTCTGGCG 60.668 61.111 16.89 5.54 45.43 5.69
264 268 3.429141 CAGCAGTGCTTCTGGCGG 61.429 66.667 16.89 0.00 45.43 6.13
265 269 3.946201 AGCAGTGCTTCTGGCGGT 61.946 61.111 13.14 0.00 45.43 5.68
266 270 3.730761 GCAGTGCTTCTGGCGGTG 61.731 66.667 8.18 0.00 45.43 4.94
267 271 3.730761 CAGTGCTTCTGGCGGTGC 61.731 66.667 7.02 7.02 45.43 5.01
268 272 3.946201 AGTGCTTCTGGCGGTGCT 61.946 61.111 13.21 0.00 45.43 4.40
269 273 2.047274 GTGCTTCTGGCGGTGCTA 60.047 61.111 13.21 0.96 45.43 3.49
270 274 1.450312 GTGCTTCTGGCGGTGCTAT 60.450 57.895 13.21 0.00 45.43 2.97
271 275 1.450134 TGCTTCTGGCGGTGCTATG 60.450 57.895 13.21 0.00 45.43 2.23
272 276 2.182842 GCTTCTGGCGGTGCTATGG 61.183 63.158 6.78 0.00 0.00 2.74
273 277 1.522092 CTTCTGGCGGTGCTATGGA 59.478 57.895 0.00 0.00 0.00 3.41
274 278 0.531532 CTTCTGGCGGTGCTATGGAG 60.532 60.000 0.00 0.00 0.00 3.86
275 279 1.264749 TTCTGGCGGTGCTATGGAGT 61.265 55.000 0.00 0.00 0.00 3.85
276 280 1.221840 CTGGCGGTGCTATGGAGTT 59.778 57.895 0.00 0.00 0.00 3.01
277 281 1.078497 TGGCGGTGCTATGGAGTTG 60.078 57.895 0.00 0.00 0.00 3.16
278 282 1.819632 GGCGGTGCTATGGAGTTGG 60.820 63.158 0.00 0.00 0.00 3.77
279 283 1.819632 GCGGTGCTATGGAGTTGGG 60.820 63.158 0.00 0.00 0.00 4.12
280 284 1.153168 CGGTGCTATGGAGTTGGGG 60.153 63.158 0.00 0.00 0.00 4.96
281 285 1.227383 GGTGCTATGGAGTTGGGGG 59.773 63.158 0.00 0.00 0.00 5.40
282 286 1.279025 GGTGCTATGGAGTTGGGGGA 61.279 60.000 0.00 0.00 0.00 4.81
283 287 0.107165 GTGCTATGGAGTTGGGGGAC 60.107 60.000 0.00 0.00 0.00 4.46
284 288 1.146263 GCTATGGAGTTGGGGGACG 59.854 63.158 0.00 0.00 0.00 4.79
285 289 1.623542 GCTATGGAGTTGGGGGACGT 61.624 60.000 0.00 0.00 0.00 4.34
286 290 0.178068 CTATGGAGTTGGGGGACGTG 59.822 60.000 0.00 0.00 0.00 4.49
287 291 0.545787 TATGGAGTTGGGGGACGTGT 60.546 55.000 0.00 0.00 0.00 4.49
288 292 1.838073 ATGGAGTTGGGGGACGTGTC 61.838 60.000 0.00 0.00 0.00 3.67
289 293 2.214920 GGAGTTGGGGGACGTGTCT 61.215 63.158 0.00 0.00 0.00 3.41
290 294 1.752833 GAGTTGGGGGACGTGTCTT 59.247 57.895 0.00 0.00 0.00 3.01
291 295 0.320508 GAGTTGGGGGACGTGTCTTC 60.321 60.000 0.00 0.00 0.00 2.87
292 296 1.302271 GTTGGGGGACGTGTCTTCC 60.302 63.158 0.00 3.11 0.00 3.46
293 297 1.460689 TTGGGGGACGTGTCTTCCT 60.461 57.895 0.00 0.00 33.17 3.36
294 298 1.764571 TTGGGGGACGTGTCTTCCTG 61.765 60.000 0.00 0.00 33.17 3.86
295 299 2.663196 GGGGACGTGTCTTCCTGG 59.337 66.667 0.00 0.00 33.17 4.45
296 300 2.047179 GGGACGTGTCTTCCTGGC 60.047 66.667 0.00 0.00 33.17 4.85
297 301 2.432628 GGACGTGTCTTCCTGGCG 60.433 66.667 0.00 0.00 0.00 5.69
298 302 2.338984 GACGTGTCTTCCTGGCGT 59.661 61.111 0.00 0.00 38.55 5.68
299 303 1.733399 GACGTGTCTTCCTGGCGTC 60.733 63.158 0.00 6.54 43.53 5.19
300 304 2.143594 GACGTGTCTTCCTGGCGTCT 62.144 60.000 12.89 0.00 45.52 4.18
301 305 1.444553 CGTGTCTTCCTGGCGTCTC 60.445 63.158 0.00 0.00 0.00 3.36
302 306 1.079750 GTGTCTTCCTGGCGTCTCC 60.080 63.158 0.00 0.00 0.00 3.71
303 307 1.228894 TGTCTTCCTGGCGTCTCCT 60.229 57.895 0.00 0.00 35.26 3.69
304 308 0.832135 TGTCTTCCTGGCGTCTCCTT 60.832 55.000 0.00 0.00 35.26 3.36
305 309 0.390472 GTCTTCCTGGCGTCTCCTTG 60.390 60.000 0.00 0.00 35.26 3.61
306 310 1.078848 CTTCCTGGCGTCTCCTTGG 60.079 63.158 0.00 0.00 35.26 3.61
307 311 1.535444 TTCCTGGCGTCTCCTTGGA 60.535 57.895 0.00 0.00 36.75 3.53
308 312 1.544825 TTCCTGGCGTCTCCTTGGAG 61.545 60.000 10.28 10.28 38.61 3.86
309 313 2.125350 CTGGCGTCTCCTTGGAGC 60.125 66.667 11.61 6.45 35.26 4.70
310 314 3.997064 CTGGCGTCTCCTTGGAGCG 62.997 68.421 20.68 20.68 35.26 5.03
311 315 3.760035 GGCGTCTCCTTGGAGCGA 61.760 66.667 25.63 6.21 0.00 4.93
312 316 2.507324 GCGTCTCCTTGGAGCGAC 60.507 66.667 25.63 14.72 0.00 5.19
313 317 2.202492 CGTCTCCTTGGAGCGACG 60.202 66.667 20.50 17.44 42.39 5.12
314 318 2.182030 GTCTCCTTGGAGCGACGG 59.818 66.667 11.61 0.00 0.00 4.79
315 319 3.068691 TCTCCTTGGAGCGACGGG 61.069 66.667 11.61 0.00 0.00 5.28
316 320 4.148825 CTCCTTGGAGCGACGGGG 62.149 72.222 3.51 0.00 0.00 5.73
318 322 4.452733 CCTTGGAGCGACGGGGTC 62.453 72.222 0.00 0.00 42.48 4.46
331 335 4.636435 GGGTCGGGTGTGGGTGTG 62.636 72.222 0.00 0.00 0.00 3.82
336 340 3.936203 GGGTGTGGGTGTGCGAGA 61.936 66.667 0.00 0.00 0.00 4.04
337 341 2.347490 GGTGTGGGTGTGCGAGAT 59.653 61.111 0.00 0.00 0.00 2.75
338 342 1.302511 GGTGTGGGTGTGCGAGATT 60.303 57.895 0.00 0.00 0.00 2.40
339 343 1.577328 GGTGTGGGTGTGCGAGATTG 61.577 60.000 0.00 0.00 0.00 2.67
340 344 1.302431 TGTGGGTGTGCGAGATTGG 60.302 57.895 0.00 0.00 0.00 3.16
341 345 2.359850 TGGGTGTGCGAGATTGGC 60.360 61.111 0.00 0.00 0.00 4.52
342 346 3.499737 GGGTGTGCGAGATTGGCG 61.500 66.667 0.00 0.00 0.00 5.69
343 347 3.499737 GGTGTGCGAGATTGGCGG 61.500 66.667 0.00 0.00 0.00 6.13
344 348 3.499737 GTGTGCGAGATTGGCGGG 61.500 66.667 0.00 0.00 0.00 6.13
345 349 3.700970 TGTGCGAGATTGGCGGGA 61.701 61.111 0.00 0.00 0.00 5.14
346 350 3.195698 GTGCGAGATTGGCGGGAC 61.196 66.667 0.00 0.00 0.00 4.46
359 363 2.818274 GGGACGGTGGCGTCAATC 60.818 66.667 0.00 0.00 40.34 2.67
360 364 2.264794 GGACGGTGGCGTCAATCT 59.735 61.111 0.00 0.00 40.34 2.40
361 365 1.810030 GGACGGTGGCGTCAATCTC 60.810 63.158 0.00 0.00 40.34 2.75
362 366 2.126071 ACGGTGGCGTCAATCTCG 60.126 61.111 0.00 0.00 0.00 4.04
363 367 2.126071 CGGTGGCGTCAATCTCGT 60.126 61.111 0.00 0.00 0.00 4.18
364 368 2.158959 CGGTGGCGTCAATCTCGTC 61.159 63.158 0.00 0.00 0.00 4.20
365 369 2.158959 GGTGGCGTCAATCTCGTCG 61.159 63.158 0.00 0.00 35.59 5.12
366 370 1.443872 GTGGCGTCAATCTCGTCGT 60.444 57.895 0.00 0.00 35.59 4.34
367 371 1.007336 GTGGCGTCAATCTCGTCGTT 61.007 55.000 0.00 0.00 35.59 3.85
368 372 0.731514 TGGCGTCAATCTCGTCGTTC 60.732 55.000 0.00 0.00 35.59 3.95
369 373 1.411493 GGCGTCAATCTCGTCGTTCC 61.411 60.000 0.00 0.00 0.00 3.62
370 374 0.456312 GCGTCAATCTCGTCGTTCCT 60.456 55.000 0.00 0.00 0.00 3.36
371 375 1.978542 CGTCAATCTCGTCGTTCCTT 58.021 50.000 0.00 0.00 0.00 3.36
372 376 2.325761 CGTCAATCTCGTCGTTCCTTT 58.674 47.619 0.00 0.00 0.00 3.11
373 377 2.729882 CGTCAATCTCGTCGTTCCTTTT 59.270 45.455 0.00 0.00 0.00 2.27
374 378 3.183775 CGTCAATCTCGTCGTTCCTTTTT 59.816 43.478 0.00 0.00 0.00 1.94
375 379 4.455124 GTCAATCTCGTCGTTCCTTTTTG 58.545 43.478 0.00 0.00 0.00 2.44
376 380 4.025145 GTCAATCTCGTCGTTCCTTTTTGT 60.025 41.667 0.00 0.00 0.00 2.83
377 381 4.573201 TCAATCTCGTCGTTCCTTTTTGTT 59.427 37.500 0.00 0.00 0.00 2.83
378 382 4.727235 ATCTCGTCGTTCCTTTTTGTTC 57.273 40.909 0.00 0.00 0.00 3.18
379 383 3.788937 TCTCGTCGTTCCTTTTTGTTCT 58.211 40.909 0.00 0.00 0.00 3.01
380 384 3.800506 TCTCGTCGTTCCTTTTTGTTCTC 59.199 43.478 0.00 0.00 0.00 2.87
381 385 2.867975 TCGTCGTTCCTTTTTGTTCTCC 59.132 45.455 0.00 0.00 0.00 3.71
382 386 2.348218 CGTCGTTCCTTTTTGTTCTCCG 60.348 50.000 0.00 0.00 0.00 4.63
383 387 2.032290 GTCGTTCCTTTTTGTTCTCCGG 60.032 50.000 0.00 0.00 0.00 5.14
384 388 1.334689 CGTTCCTTTTTGTTCTCCGGC 60.335 52.381 0.00 0.00 0.00 6.13
385 389 1.000607 GTTCCTTTTTGTTCTCCGGCC 60.001 52.381 0.00 0.00 0.00 6.13
386 390 0.476771 TCCTTTTTGTTCTCCGGCCT 59.523 50.000 0.00 0.00 0.00 5.19
387 391 0.881796 CCTTTTTGTTCTCCGGCCTC 59.118 55.000 0.00 0.00 0.00 4.70
388 392 1.545651 CCTTTTTGTTCTCCGGCCTCT 60.546 52.381 0.00 0.00 0.00 3.69
389 393 1.807142 CTTTTTGTTCTCCGGCCTCTC 59.193 52.381 0.00 0.00 0.00 3.20
390 394 0.036306 TTTTGTTCTCCGGCCTCTCC 59.964 55.000 0.00 0.00 0.00 3.71
391 395 1.125093 TTTGTTCTCCGGCCTCTCCA 61.125 55.000 0.00 0.00 34.01 3.86
392 396 0.909610 TTGTTCTCCGGCCTCTCCAT 60.910 55.000 0.00 0.00 34.01 3.41
393 397 1.330655 TGTTCTCCGGCCTCTCCATC 61.331 60.000 0.00 0.00 34.01 3.51
394 398 1.001631 TTCTCCGGCCTCTCCATCA 59.998 57.895 0.00 0.00 34.01 3.07
395 399 1.045350 TTCTCCGGCCTCTCCATCAG 61.045 60.000 0.00 0.00 34.01 2.90
396 400 3.157252 TCCGGCCTCTCCATCAGC 61.157 66.667 0.00 0.00 34.01 4.26
397 401 3.160047 CCGGCCTCTCCATCAGCT 61.160 66.667 0.00 0.00 34.01 4.24
398 402 2.739996 CCGGCCTCTCCATCAGCTT 61.740 63.158 0.00 0.00 34.01 3.74
399 403 1.523258 CGGCCTCTCCATCAGCTTG 60.523 63.158 0.00 0.00 34.01 4.01
400 404 1.153005 GGCCTCTCCATCAGCTTGG 60.153 63.158 0.00 0.00 38.18 3.61
401 405 1.606531 GCCTCTCCATCAGCTTGGT 59.393 57.895 4.36 0.00 38.01 3.67
402 406 0.747283 GCCTCTCCATCAGCTTGGTG 60.747 60.000 4.36 2.50 38.01 4.17
423 427 3.393970 CCTCCTCCAGCGCCTTCA 61.394 66.667 2.29 0.00 0.00 3.02
462 466 2.129555 ATTGGAGCTTGGTGGTCGCT 62.130 55.000 0.00 0.00 43.60 4.93
470 474 3.936203 GGTGGTCGCTGGTGGACA 61.936 66.667 0.00 0.00 36.12 4.02
476 480 0.037326 GTCGCTGGTGGACATCTTCA 60.037 55.000 0.00 0.00 34.56 3.02
477 481 0.247460 TCGCTGGTGGACATCTTCAG 59.753 55.000 0.00 0.00 0.00 3.02
489 493 2.208431 CATCTTCAGGGCGATCTCAAC 58.792 52.381 0.00 0.00 0.00 3.18
529 533 5.696270 GGCCTCATTTGTTTTTAAGGAACAG 59.304 40.000 0.00 0.00 38.17 3.16
532 536 5.285651 TCATTTGTTTTTAAGGAACAGGCG 58.714 37.500 6.59 0.00 38.17 5.52
538 542 4.834357 TTTTAAGGAACAGGCGGTAAAC 57.166 40.909 0.00 0.00 0.00 2.01
543 547 2.074576 GGAACAGGCGGTAAACTTCTC 58.925 52.381 0.00 0.00 0.00 2.87
544 548 2.074576 GAACAGGCGGTAAACTTCTCC 58.925 52.381 0.00 0.00 0.00 3.71
545 549 1.053424 ACAGGCGGTAAACTTCTCCA 58.947 50.000 0.00 0.00 0.00 3.86
546 550 1.418637 ACAGGCGGTAAACTTCTCCAA 59.581 47.619 0.00 0.00 0.00 3.53
624 629 1.298339 GTGTGCACCAAAGCGACAC 60.298 57.895 15.69 0.00 38.41 3.67
633 639 4.616953 CACCAAAGCGACACCTTTTAAAT 58.383 39.130 0.00 0.00 32.97 1.40
756 777 0.108472 TGTGATCGGAGAGCTTGCAG 60.108 55.000 0.00 0.00 46.78 4.41
764 785 2.484417 CGGAGAGCTTGCAGATACCAAT 60.484 50.000 0.00 0.00 0.00 3.16
775 797 5.167621 TGCAGATACCAATGCAGTAATGCA 61.168 41.667 21.35 21.35 46.97 3.96
831 855 2.939103 CCTTACAATTCAGGCGAAGAGG 59.061 50.000 0.00 0.00 33.74 3.69
838 862 0.319555 TCAGGCGAAGAGGTTCAACG 60.320 55.000 0.00 0.00 32.36 4.10
930 1026 5.619220 AGAGAGTGAGACAAGAGCAAAAAT 58.381 37.500 0.00 0.00 0.00 1.82
958 1077 1.745827 CGCCCCACTGTTATACCAAGG 60.746 57.143 0.00 0.00 0.00 3.61
1104 1225 6.509523 AGATTATTTCCTCGAATTACCCCA 57.490 37.500 0.00 0.00 0.00 4.96
1237 1748 3.045142 CTTGCCACTTGCCACTGG 58.955 61.111 0.00 0.00 40.16 4.00
1504 2157 3.385577 AGCGACAGTCTCTGTTTTCTTC 58.614 45.455 3.91 0.00 45.44 2.87
1674 2399 2.675317 GCTGTGGATCTTCTACGCACTT 60.675 50.000 0.00 0.00 31.75 3.16
1813 2538 0.248134 GATCGTCGTCCTCCTCAACG 60.248 60.000 0.00 0.00 40.17 4.10
1984 2717 5.181009 CAAACCTCATACTTCAGCTCATGA 58.819 41.667 0.00 0.00 35.62 3.07
1987 2724 3.181482 CCTCATACTTCAGCTCATGACGT 60.181 47.826 0.00 0.00 42.58 4.34
1989 2726 1.996292 TACTTCAGCTCATGACGTGC 58.004 50.000 0.00 0.00 40.38 5.34
2011 2748 3.748048 CCCTCTTGTACATGTGTCAACTG 59.252 47.826 9.11 7.19 0.00 3.16
2366 3136 1.927569 GAAGGAGGGGAAAGAGGGGC 61.928 65.000 0.00 0.00 0.00 5.80
2375 3145 1.283321 GGAAAGAGGGGCTGAAGATGT 59.717 52.381 0.00 0.00 0.00 3.06
2415 3185 1.197721 GGTGATCAACGTTGGCAAGAG 59.802 52.381 27.02 0.00 0.00 2.85
2592 3389 4.496895 GTGCAAGCTTTAATATTCGTGCAG 59.503 41.667 13.21 5.63 42.57 4.41
2652 3449 7.445096 TGATGCTTCTTTTCTGTTAGATCAACA 59.555 33.333 9.41 9.41 44.97 3.33
2674 3471 7.268199 ACATGTTGATTGTATGAGGCATAAG 57.732 36.000 0.00 0.00 0.00 1.73
2710 3510 2.435372 AACTCTGCTTTCACCAACCA 57.565 45.000 0.00 0.00 0.00 3.67
2712 3512 3.788227 ACTCTGCTTTCACCAACCATA 57.212 42.857 0.00 0.00 0.00 2.74
2745 3545 2.327002 CTTTCACCGCGCCCATGATG 62.327 60.000 0.00 0.00 0.00 3.07
2747 3547 2.592574 CACCGCGCCCATGATGAT 60.593 61.111 0.00 0.00 0.00 2.45
2748 3548 2.188829 CACCGCGCCCATGATGATT 61.189 57.895 0.00 0.00 0.00 2.57
2749 3549 0.884259 CACCGCGCCCATGATGATTA 60.884 55.000 0.00 0.00 0.00 1.75
2750 3550 0.603707 ACCGCGCCCATGATGATTAG 60.604 55.000 0.00 0.00 0.00 1.73
2752 3552 1.073964 CGCGCCCATGATGATTAGAG 58.926 55.000 0.00 0.00 0.00 2.43
2754 3554 1.271054 GCGCCCATGATGATTAGAGGT 60.271 52.381 0.00 0.00 0.00 3.85
2755 3555 2.811873 GCGCCCATGATGATTAGAGGTT 60.812 50.000 0.00 0.00 0.00 3.50
2759 3559 5.122869 CGCCCATGATGATTAGAGGTTATTG 59.877 44.000 0.00 0.00 0.00 1.90
2760 3560 5.105997 GCCCATGATGATTAGAGGTTATTGC 60.106 44.000 0.00 0.00 0.00 3.56
2762 3562 5.934043 CCATGATGATTAGAGGTTATTGCGA 59.066 40.000 0.00 0.00 0.00 5.10
2763 3563 6.596888 CCATGATGATTAGAGGTTATTGCGAT 59.403 38.462 0.00 0.00 0.00 4.58
2764 3564 7.413767 CCATGATGATTAGAGGTTATTGCGATG 60.414 40.741 0.00 0.00 0.00 3.84
2784 3596 6.096036 CGATGATTAGAGGTTATTGCGATCT 58.904 40.000 0.00 0.00 0.00 2.75
2799 3611 2.719046 GCGATCTGTTGTTTCGTTTTGG 59.281 45.455 0.00 0.00 35.40 3.28
2891 3703 6.649141 TGTGCTAATAGAGACGACATTTGTTT 59.351 34.615 0.00 0.00 0.00 2.83
2925 3737 0.392060 AGTTATTCGGTGCGGGGTTC 60.392 55.000 0.00 0.00 0.00 3.62
2943 3755 4.081586 GGGTTCTAGTGTCCTTAGTCCTTG 60.082 50.000 0.00 0.00 0.00 3.61
3082 3894 2.124109 TCGCTCATCTCGGCTCCT 60.124 61.111 0.00 0.00 0.00 3.69
3092 3908 2.125350 CGGCTCCTTGCTCCACTC 60.125 66.667 0.00 0.00 42.39 3.51
3450 4271 8.795786 TTAAATGTTCACAGTTGTCAATAAGC 57.204 30.769 2.94 0.00 35.62 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.034089 CTTCGCTTGGGAAGGGGAAT 60.034 55.000 16.50 0.00 39.76 3.01
26 27 1.537889 TCTTCGCTTGGGAAGGGGA 60.538 57.895 21.60 5.89 42.88 4.81
35 36 1.068954 GTTGCCTTTCCTCTTCGCTTG 60.069 52.381 0.00 0.00 0.00 4.01
37 38 0.606673 GGTTGCCTTTCCTCTTCGCT 60.607 55.000 0.00 0.00 0.00 4.93
53 54 1.982395 TCGACGCTGGGATCTGGTT 60.982 57.895 0.00 0.00 0.00 3.67
139 141 4.957327 ACTATCTACAAACTGGGAGAGGAC 59.043 45.833 0.00 0.00 0.00 3.85
149 151 7.677319 ACCTAACCCTACAACTATCTACAAACT 59.323 37.037 0.00 0.00 0.00 2.66
207 211 3.104843 AGATTTATCTGACGCTGCTCC 57.895 47.619 0.00 0.00 35.42 4.70
237 241 1.968540 GCACTGCTGTGGAGGAACC 60.969 63.158 23.15 3.07 43.97 3.62
238 242 0.536006 AAGCACTGCTGTGGAGGAAC 60.536 55.000 23.15 7.18 43.97 3.62
239 243 0.250467 GAAGCACTGCTGTGGAGGAA 60.250 55.000 23.15 0.00 43.97 3.36
240 244 1.123861 AGAAGCACTGCTGTGGAGGA 61.124 55.000 23.15 0.00 43.97 3.71
241 245 0.954449 CAGAAGCACTGCTGTGGAGG 60.954 60.000 23.15 0.36 43.97 4.30
242 246 0.954449 CCAGAAGCACTGCTGTGGAG 60.954 60.000 23.15 0.72 42.72 3.86
243 247 1.071987 CCAGAAGCACTGCTGTGGA 59.928 57.895 23.15 0.00 42.72 4.02
244 248 2.623915 GCCAGAAGCACTGCTGTGG 61.624 63.158 23.15 21.37 44.52 4.17
245 249 2.952245 GCCAGAAGCACTGCTGTG 59.048 61.111 18.54 18.54 44.52 3.66
246 250 2.667536 CGCCAGAAGCACTGCTGT 60.668 61.111 3.73 0.00 44.52 4.40
247 251 3.429141 CCGCCAGAAGCACTGCTG 61.429 66.667 3.73 0.00 44.52 4.41
248 252 3.946201 ACCGCCAGAAGCACTGCT 61.946 61.111 0.00 0.00 44.52 4.24
249 253 3.730761 CACCGCCAGAAGCACTGC 61.731 66.667 5.57 0.00 44.52 4.40
250 254 2.786539 TAGCACCGCCAGAAGCACTG 62.787 60.000 4.31 4.31 44.04 3.66
251 255 1.903877 ATAGCACCGCCAGAAGCACT 61.904 55.000 0.00 0.00 44.04 4.40
252 256 1.450312 ATAGCACCGCCAGAAGCAC 60.450 57.895 0.00 0.00 44.04 4.40
253 257 1.450134 CATAGCACCGCCAGAAGCA 60.450 57.895 0.00 0.00 44.04 3.91
254 258 2.182842 CCATAGCACCGCCAGAAGC 61.183 63.158 0.00 0.00 38.52 3.86
255 259 0.531532 CTCCATAGCACCGCCAGAAG 60.532 60.000 0.00 0.00 0.00 2.85
256 260 1.264749 ACTCCATAGCACCGCCAGAA 61.265 55.000 0.00 0.00 0.00 3.02
257 261 1.264749 AACTCCATAGCACCGCCAGA 61.265 55.000 0.00 0.00 0.00 3.86
258 262 1.091771 CAACTCCATAGCACCGCCAG 61.092 60.000 0.00 0.00 0.00 4.85
259 263 1.078497 CAACTCCATAGCACCGCCA 60.078 57.895 0.00 0.00 0.00 5.69
260 264 1.819632 CCAACTCCATAGCACCGCC 60.820 63.158 0.00 0.00 0.00 6.13
261 265 1.819632 CCCAACTCCATAGCACCGC 60.820 63.158 0.00 0.00 0.00 5.68
262 266 1.153168 CCCCAACTCCATAGCACCG 60.153 63.158 0.00 0.00 0.00 4.94
263 267 1.227383 CCCCCAACTCCATAGCACC 59.773 63.158 0.00 0.00 0.00 5.01
264 268 0.107165 GTCCCCCAACTCCATAGCAC 60.107 60.000 0.00 0.00 0.00 4.40
265 269 1.622607 CGTCCCCCAACTCCATAGCA 61.623 60.000 0.00 0.00 0.00 3.49
266 270 1.146263 CGTCCCCCAACTCCATAGC 59.854 63.158 0.00 0.00 0.00 2.97
267 271 0.178068 CACGTCCCCCAACTCCATAG 59.822 60.000 0.00 0.00 0.00 2.23
268 272 0.545787 ACACGTCCCCCAACTCCATA 60.546 55.000 0.00 0.00 0.00 2.74
269 273 1.838073 GACACGTCCCCCAACTCCAT 61.838 60.000 0.00 0.00 0.00 3.41
270 274 2.446994 ACACGTCCCCCAACTCCA 60.447 61.111 0.00 0.00 0.00 3.86
271 275 1.765597 AAGACACGTCCCCCAACTCC 61.766 60.000 0.00 0.00 0.00 3.85
272 276 0.320508 GAAGACACGTCCCCCAACTC 60.321 60.000 0.00 0.00 0.00 3.01
273 277 1.752833 GAAGACACGTCCCCCAACT 59.247 57.895 0.00 0.00 0.00 3.16
274 278 1.302271 GGAAGACACGTCCCCCAAC 60.302 63.158 0.00 0.00 0.00 3.77
275 279 1.460689 AGGAAGACACGTCCCCCAA 60.461 57.895 7.82 0.00 35.59 4.12
276 280 2.203182 AGGAAGACACGTCCCCCA 59.797 61.111 7.82 0.00 35.59 4.96
277 281 2.663196 CAGGAAGACACGTCCCCC 59.337 66.667 0.00 0.00 35.59 5.40
278 282 2.663196 CCAGGAAGACACGTCCCC 59.337 66.667 0.00 0.00 35.59 4.81
279 283 2.047179 GCCAGGAAGACACGTCCC 60.047 66.667 0.00 0.00 35.59 4.46
280 284 2.432628 CGCCAGGAAGACACGTCC 60.433 66.667 0.00 0.00 35.17 4.79
281 285 1.733399 GACGCCAGGAAGACACGTC 60.733 63.158 0.00 0.00 45.10 4.34
282 286 2.143594 GAGACGCCAGGAAGACACGT 62.144 60.000 0.00 0.00 40.11 4.49
283 287 1.444553 GAGACGCCAGGAAGACACG 60.445 63.158 0.00 0.00 0.00 4.49
284 288 1.079750 GGAGACGCCAGGAAGACAC 60.080 63.158 0.00 0.00 36.34 3.67
285 289 0.832135 AAGGAGACGCCAGGAAGACA 60.832 55.000 0.00 0.00 40.02 3.41
286 290 0.390472 CAAGGAGACGCCAGGAAGAC 60.390 60.000 0.00 0.00 40.02 3.01
287 291 1.544825 CCAAGGAGACGCCAGGAAGA 61.545 60.000 0.00 0.00 40.02 2.87
288 292 1.078848 CCAAGGAGACGCCAGGAAG 60.079 63.158 0.00 0.00 40.02 3.46
289 293 1.535444 TCCAAGGAGACGCCAGGAA 60.535 57.895 6.91 0.00 39.35 3.36
290 294 1.984570 CTCCAAGGAGACGCCAGGA 60.985 63.158 10.66 8.70 44.53 3.86
291 295 2.581354 CTCCAAGGAGACGCCAGG 59.419 66.667 10.66 0.00 44.53 4.45
292 296 2.125350 GCTCCAAGGAGACGCCAG 60.125 66.667 19.99 0.00 44.53 4.85
293 297 4.069232 CGCTCCAAGGAGACGCCA 62.069 66.667 19.99 0.00 44.53 5.69
294 298 3.760035 TCGCTCCAAGGAGACGCC 61.760 66.667 19.99 1.09 44.53 5.68
295 299 2.507324 GTCGCTCCAAGGAGACGC 60.507 66.667 19.99 13.35 44.53 5.19
297 301 2.182030 CCGTCGCTCCAAGGAGAC 59.818 66.667 19.99 9.08 44.53 3.36
298 302 3.068691 CCCGTCGCTCCAAGGAGA 61.069 66.667 19.99 0.00 44.53 3.71
299 303 4.148825 CCCCGTCGCTCCAAGGAG 62.149 72.222 11.80 11.80 44.56 3.69
301 305 4.452733 GACCCCGTCGCTCCAAGG 62.453 72.222 0.00 0.00 0.00 3.61
314 318 4.636435 CACACCCACACCCGACCC 62.636 72.222 0.00 0.00 0.00 4.46
319 323 2.748058 AATCTCGCACACCCACACCC 62.748 60.000 0.00 0.00 0.00 4.61
320 324 1.302511 AATCTCGCACACCCACACC 60.303 57.895 0.00 0.00 0.00 4.16
321 325 1.577328 CCAATCTCGCACACCCACAC 61.577 60.000 0.00 0.00 0.00 3.82
322 326 1.302431 CCAATCTCGCACACCCACA 60.302 57.895 0.00 0.00 0.00 4.17
323 327 2.690778 GCCAATCTCGCACACCCAC 61.691 63.158 0.00 0.00 0.00 4.61
324 328 2.359850 GCCAATCTCGCACACCCA 60.360 61.111 0.00 0.00 0.00 4.51
325 329 3.499737 CGCCAATCTCGCACACCC 61.500 66.667 0.00 0.00 0.00 4.61
326 330 3.499737 CCGCCAATCTCGCACACC 61.500 66.667 0.00 0.00 0.00 4.16
327 331 3.499737 CCCGCCAATCTCGCACAC 61.500 66.667 0.00 0.00 0.00 3.82
328 332 3.700970 TCCCGCCAATCTCGCACA 61.701 61.111 0.00 0.00 0.00 4.57
329 333 3.195698 GTCCCGCCAATCTCGCAC 61.196 66.667 0.00 0.00 0.00 5.34
330 334 4.812476 CGTCCCGCCAATCTCGCA 62.812 66.667 0.00 0.00 0.00 5.10
332 336 4.143333 ACCGTCCCGCCAATCTCG 62.143 66.667 0.00 0.00 0.00 4.04
333 337 2.511600 CACCGTCCCGCCAATCTC 60.512 66.667 0.00 0.00 0.00 2.75
334 338 4.096003 CCACCGTCCCGCCAATCT 62.096 66.667 0.00 0.00 0.00 2.40
346 350 2.126071 ACGAGATTGACGCCACCG 60.126 61.111 0.00 0.00 41.14 4.94
347 351 2.158959 CGACGAGATTGACGCCACC 61.159 63.158 0.00 0.00 0.00 4.61
348 352 1.007336 AACGACGAGATTGACGCCAC 61.007 55.000 0.00 0.00 0.00 5.01
349 353 0.731514 GAACGACGAGATTGACGCCA 60.732 55.000 0.00 0.00 0.00 5.69
350 354 1.411493 GGAACGACGAGATTGACGCC 61.411 60.000 0.00 0.00 0.00 5.68
351 355 0.456312 AGGAACGACGAGATTGACGC 60.456 55.000 0.00 0.00 0.00 5.19
352 356 1.978542 AAGGAACGACGAGATTGACG 58.021 50.000 0.00 0.00 0.00 4.35
353 357 4.025145 ACAAAAAGGAACGACGAGATTGAC 60.025 41.667 0.00 0.00 0.00 3.18
354 358 4.124238 ACAAAAAGGAACGACGAGATTGA 58.876 39.130 0.00 0.00 0.00 2.57
355 359 4.468095 ACAAAAAGGAACGACGAGATTG 57.532 40.909 0.00 0.00 0.00 2.67
356 360 4.814771 AGAACAAAAAGGAACGACGAGATT 59.185 37.500 0.00 0.00 0.00 2.40
357 361 4.377897 AGAACAAAAAGGAACGACGAGAT 58.622 39.130 0.00 0.00 0.00 2.75
358 362 3.788937 AGAACAAAAAGGAACGACGAGA 58.211 40.909 0.00 0.00 0.00 4.04
359 363 3.059800 GGAGAACAAAAAGGAACGACGAG 60.060 47.826 0.00 0.00 0.00 4.18
360 364 2.867975 GGAGAACAAAAAGGAACGACGA 59.132 45.455 0.00 0.00 0.00 4.20
361 365 2.348218 CGGAGAACAAAAAGGAACGACG 60.348 50.000 0.00 0.00 0.00 5.12
362 366 2.032290 CCGGAGAACAAAAAGGAACGAC 60.032 50.000 0.00 0.00 0.00 4.34
363 367 2.215196 CCGGAGAACAAAAAGGAACGA 58.785 47.619 0.00 0.00 0.00 3.85
364 368 1.334689 GCCGGAGAACAAAAAGGAACG 60.335 52.381 5.05 0.00 0.00 3.95
365 369 1.000607 GGCCGGAGAACAAAAAGGAAC 60.001 52.381 5.05 0.00 0.00 3.62
366 370 1.133606 AGGCCGGAGAACAAAAAGGAA 60.134 47.619 5.05 0.00 0.00 3.36
367 371 0.476771 AGGCCGGAGAACAAAAAGGA 59.523 50.000 5.05 0.00 0.00 3.36
368 372 0.881796 GAGGCCGGAGAACAAAAAGG 59.118 55.000 5.05 0.00 0.00 3.11
369 373 1.807142 GAGAGGCCGGAGAACAAAAAG 59.193 52.381 5.05 0.00 0.00 2.27
370 374 1.544759 GGAGAGGCCGGAGAACAAAAA 60.545 52.381 5.05 0.00 0.00 1.94
371 375 0.036306 GGAGAGGCCGGAGAACAAAA 59.964 55.000 5.05 0.00 0.00 2.44
372 376 1.125093 TGGAGAGGCCGGAGAACAAA 61.125 55.000 5.05 0.00 40.66 2.83
373 377 0.909610 ATGGAGAGGCCGGAGAACAA 60.910 55.000 5.05 0.00 40.66 2.83
374 378 1.306141 ATGGAGAGGCCGGAGAACA 60.306 57.895 5.05 0.00 40.66 3.18
375 379 1.330655 TGATGGAGAGGCCGGAGAAC 61.331 60.000 5.05 0.00 40.66 3.01
376 380 1.001631 TGATGGAGAGGCCGGAGAA 59.998 57.895 5.05 0.00 40.66 2.87
377 381 1.456518 CTGATGGAGAGGCCGGAGA 60.457 63.158 5.05 0.00 40.66 3.71
378 382 3.136750 CTGATGGAGAGGCCGGAG 58.863 66.667 5.05 0.00 40.66 4.63
379 383 3.157252 GCTGATGGAGAGGCCGGA 61.157 66.667 5.05 0.00 40.66 5.14
380 384 2.739996 AAGCTGATGGAGAGGCCGG 61.740 63.158 0.00 0.00 40.66 6.13
381 385 1.523258 CAAGCTGATGGAGAGGCCG 60.523 63.158 0.00 0.00 40.66 6.13
382 386 1.153005 CCAAGCTGATGGAGAGGCC 60.153 63.158 0.00 0.00 43.54 5.19
383 387 0.747283 CACCAAGCTGATGGAGAGGC 60.747 60.000 11.52 0.00 43.54 4.70
384 388 0.107312 CCACCAAGCTGATGGAGAGG 60.107 60.000 11.52 6.26 43.54 3.69
385 389 0.747283 GCCACCAAGCTGATGGAGAG 60.747 60.000 11.52 0.89 43.54 3.20
386 390 1.300963 GCCACCAAGCTGATGGAGA 59.699 57.895 11.52 0.00 43.54 3.71
387 391 2.110967 CGCCACCAAGCTGATGGAG 61.111 63.158 11.52 6.02 43.54 3.86
388 392 2.046023 CGCCACCAAGCTGATGGA 60.046 61.111 11.52 0.00 43.54 3.41
389 393 3.818787 GCGCCACCAAGCTGATGG 61.819 66.667 2.71 2.71 46.38 3.51
390 394 3.818787 GGCGCCACCAAGCTGATG 61.819 66.667 24.80 0.00 38.86 3.07
391 395 3.984193 GAGGCGCCACCAAGCTGAT 62.984 63.158 31.54 2.38 43.14 2.90
392 396 4.704833 GAGGCGCCACCAAGCTGA 62.705 66.667 31.54 0.00 43.14 4.26
396 400 4.785453 GGAGGAGGCGCCACCAAG 62.785 72.222 39.03 0.00 45.87 3.61
416 420 1.661341 CTTCCATCCTCTTGAAGGCG 58.339 55.000 0.00 0.00 45.78 5.52
423 427 5.339530 CCAATACAAGACCTTCCATCCTCTT 60.340 44.000 0.00 0.00 0.00 2.85
429 433 3.525199 AGCTCCAATACAAGACCTTCCAT 59.475 43.478 0.00 0.00 0.00 3.41
462 466 1.685224 GCCCTGAAGATGTCCACCA 59.315 57.895 0.00 0.00 0.00 4.17
470 474 1.202463 CGTTGAGATCGCCCTGAAGAT 60.202 52.381 0.00 0.00 0.00 2.40
489 493 2.809601 CCAAACCTCTCGACGGCG 60.810 66.667 2.87 2.87 39.35 6.46
529 533 3.994204 TTTTTGGAGAAGTTTACCGCC 57.006 42.857 0.00 0.00 0.00 6.13
775 797 6.241645 GGTGCTTTATATAGGCAGGAAGATT 58.758 40.000 11.17 0.00 36.62 2.40
831 855 2.473235 GAGCTCTCTGTGTTCGTTGAAC 59.527 50.000 6.43 2.80 42.26 3.18
930 1026 1.568504 AACAGTGGGGCGAGAGATTA 58.431 50.000 0.00 0.00 0.00 1.75
958 1077 4.019501 AGAGGGATATGAGATGGATGCAAC 60.020 45.833 0.00 0.00 0.00 4.17
1237 1748 7.035840 AGGCTACATCAATTCATCAATCAAC 57.964 36.000 0.00 0.00 0.00 3.18
1674 2399 2.879233 GCCCTCACCGGTCTTGACA 61.879 63.158 2.59 0.00 0.00 3.58
1734 2459 3.560481 CGAGGTACATGACGATGTAGACT 59.440 47.826 0.00 0.00 44.16 3.24
1984 2717 0.685097 ACATGTACAAGAGGGCACGT 59.315 50.000 4.87 0.00 0.00 4.49
1987 2724 1.696884 TGACACATGTACAAGAGGGCA 59.303 47.619 4.87 2.16 0.00 5.36
1989 2726 3.748048 CAGTTGACACATGTACAAGAGGG 59.252 47.826 14.95 0.00 0.00 4.30
2011 2748 2.820197 GGGGAAAGGAACACATCAAGTC 59.180 50.000 0.00 0.00 0.00 3.01
2366 3136 1.227089 CCTCCGCCGACATCTTCAG 60.227 63.158 0.00 0.00 0.00 3.02
2415 3185 2.781300 CGCCAGAGCTCTTTTCGC 59.219 61.111 15.27 12.23 36.60 4.70
2566 3363 5.320723 CACGAATATTAAAGCTTGCACGAA 58.679 37.500 0.00 0.00 0.00 3.85
2652 3449 6.323203 GCTTATGCCTCATACAATCAACAT 57.677 37.500 0.00 0.00 0.00 2.71
2674 3471 5.561725 GCAGAGTTAGCAGCTATTAAATGGC 60.562 44.000 2.02 0.00 36.97 4.40
2740 3540 7.389232 TCATCGCAATAACCTCTAATCATCAT 58.611 34.615 0.00 0.00 0.00 2.45
2745 3545 8.988064 TCTAATCATCGCAATAACCTCTAATC 57.012 34.615 0.00 0.00 0.00 1.75
2747 3547 7.015292 ACCTCTAATCATCGCAATAACCTCTAA 59.985 37.037 0.00 0.00 0.00 2.10
2748 3548 6.493802 ACCTCTAATCATCGCAATAACCTCTA 59.506 38.462 0.00 0.00 0.00 2.43
2749 3549 5.305644 ACCTCTAATCATCGCAATAACCTCT 59.694 40.000 0.00 0.00 0.00 3.69
2750 3550 5.542779 ACCTCTAATCATCGCAATAACCTC 58.457 41.667 0.00 0.00 0.00 3.85
2752 3552 7.907214 ATAACCTCTAATCATCGCAATAACC 57.093 36.000 0.00 0.00 0.00 2.85
2754 3554 7.360017 CGCAATAACCTCTAATCATCGCAATAA 60.360 37.037 0.00 0.00 0.00 1.40
2755 3555 6.090763 CGCAATAACCTCTAATCATCGCAATA 59.909 38.462 0.00 0.00 0.00 1.90
2759 3559 3.987868 TCGCAATAACCTCTAATCATCGC 59.012 43.478 0.00 0.00 0.00 4.58
2760 3560 6.034363 CAGATCGCAATAACCTCTAATCATCG 59.966 42.308 0.00 0.00 0.00 3.84
2762 3562 6.763355 ACAGATCGCAATAACCTCTAATCAT 58.237 36.000 0.00 0.00 0.00 2.45
2763 3563 6.161855 ACAGATCGCAATAACCTCTAATCA 57.838 37.500 0.00 0.00 0.00 2.57
2764 3564 6.480320 ACAACAGATCGCAATAACCTCTAATC 59.520 38.462 0.00 0.00 0.00 1.75
2784 3596 7.015877 GCAAATAAAACCAAAACGAAACAACA 58.984 30.769 0.00 0.00 0.00 3.33
2799 3611 1.613270 CCTGTCGGCGCAAATAAAAC 58.387 50.000 10.83 0.00 0.00 2.43
2873 3685 6.591834 CCTCTCAAAACAAATGTCGTCTCTAT 59.408 38.462 0.00 0.00 0.00 1.98
2891 3703 5.163405 CCGAATAACTCCAATCTCCTCTCAA 60.163 44.000 0.00 0.00 0.00 3.02
2925 3737 3.258372 TGTGCAAGGACTAAGGACACTAG 59.742 47.826 0.00 0.00 0.00 2.57
2943 3755 0.031994 ACACCAAAGCCGAAATGTGC 59.968 50.000 0.00 0.00 0.00 4.57
2984 3796 5.706369 GCATGAATATGAGCTCTCAAGGAAT 59.294 40.000 16.19 0.17 43.58 3.01
3082 3894 1.826340 TAAGCAGGCGAGTGGAGCAA 61.826 55.000 0.00 0.00 36.08 3.91
3215 4034 8.903570 TGTGTTTTTAGTGTGTGACATTTTAG 57.096 30.769 0.00 0.00 0.00 1.85
3216 4035 9.295214 CATGTGTTTTTAGTGTGTGACATTTTA 57.705 29.630 0.00 0.00 0.00 1.52
3413 4234 9.019764 ACTGTGAACATTTAAAAATTCTGAACG 57.980 29.630 13.15 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.