Multiple sequence alignment - TraesCS4A01G088500

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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 TraesCS4A01G088500 chr4A 100.000 3686 0 0 1 3686 93979174 93982859 0.000000e+00 6807
1 TraesCS4A01G088500 chr4D 95.179 3319 114 27 380 3667 370304478 370301175 0.000000e+00 5201
2 TraesCS4A01G088500 chr4D 94.208 259 15 0 26 284 414150015 414149757 2.670000e-106 396
3 TraesCS4A01G088500 chr4B 95.553 3036 101 18 646 3649 455365813 455362780 0.000000e+00 4828
4 TraesCS4A01G088500 chr4B 87.179 156 14 6 483 637 455365942 455365792 4.890000e-39 172
5 TraesCS4A01G088500 chr3A 94.677 263 12 2 25 285 161457161 161457423 1.230000e-109 407
6 TraesCS4A01G088500 chrUn 94.615 260 13 1 26 284 68758338 68758079 5.730000e-108 401
7 TraesCS4A01G088500 chrUn 93.893 262 14 2 25 284 108799498 108799237 9.590000e-106 394
8 TraesCS4A01G088500 chr2D 94.275 262 13 2 26 285 204112684 204112945 2.060000e-107 399
9 TraesCS4A01G088500 chr7D 94.275 262 12 3 26 285 439780776 439780516 7.420000e-107 398
10 TraesCS4A01G088500 chr7D 92.989 271 16 3 23 290 101583003 101582733 3.450000e-105 392
11 TraesCS4A01G088500 chr7B 94.253 261 13 2 26 284 598954777 598955037 7.420000e-107 398
12 TraesCS4A01G088500 chr7A 93.916 263 14 2 24 284 5906676 5906414 2.670000e-106 396
13 TraesCS4A01G088500 chr6D 93.750 96 6 0 2728 2823 69940705 69940800 1.070000e-30 145
14 TraesCS4A01G088500 chr6B 92.708 96 7 0 2728 2823 144959318 144959413 4.960000e-29 139
15 TraesCS4A01G088500 chr3B 78.212 179 28 11 3454 3628 31061251 31061422 1.810000e-18 104


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 TraesCS4A01G088500 chr4A 93979174 93982859 3685 False 6807 6807 100.000 1 3686 1 chr4A.!!$F1 3685
1 TraesCS4A01G088500 chr4D 370301175 370304478 3303 True 5201 5201 95.179 380 3667 1 chr4D.!!$R1 3287
2 TraesCS4A01G088500 chr4B 455362780 455365942 3162 True 2500 4828 91.366 483 3649 2 chr4B.!!$R1 3166

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
569 581 0.176680 CCAGATTCCCGGTGAGTGAG 59.823 60.000 0.00 0.00 0.00 3.51 F
1278 1324 1.226323 CTACTCCAACGCGTCCGAG 60.226 63.158 25.57 25.57 38.29 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 1667 0.463295 AGCATCTGGAATGCCGTCAG 60.463 55.0 6.40 0.0 45.59 3.51 R
2804 2850 2.178912 ATTTGACACACGAACGGGAT 57.821 45.0 2.83 0.0 0.00 3.85 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
23 24 6.566197 CATCTTCTTCTGGCACTAAAACTT 57.434 37.500 0.00 0.00 0.00 2.66
24 25 6.376978 CATCTTCTTCTGGCACTAAAACTTG 58.623 40.000 0.00 0.00 0.00 3.16
25 26 5.437060 TCTTCTTCTGGCACTAAAACTTGT 58.563 37.500 0.00 0.00 0.00 3.16
26 27 6.588204 TCTTCTTCTGGCACTAAAACTTGTA 58.412 36.000 0.00 0.00 0.00 2.41
27 28 6.482308 TCTTCTTCTGGCACTAAAACTTGTAC 59.518 38.462 0.00 0.00 0.00 2.90
28 29 5.925509 TCTTCTGGCACTAAAACTTGTACT 58.074 37.500 0.00 0.00 0.00 2.73
29 30 5.989777 TCTTCTGGCACTAAAACTTGTACTC 59.010 40.000 0.00 0.00 0.00 2.59
30 31 4.638304 TCTGGCACTAAAACTTGTACTCC 58.362 43.478 0.00 0.00 0.00 3.85
31 32 3.746940 TGGCACTAAAACTTGTACTCCC 58.253 45.455 0.00 0.00 0.00 4.30
32 33 3.393278 TGGCACTAAAACTTGTACTCCCT 59.607 43.478 0.00 0.00 0.00 4.20
33 34 4.001652 GGCACTAAAACTTGTACTCCCTC 58.998 47.826 0.00 0.00 0.00 4.30
34 35 4.001652 GCACTAAAACTTGTACTCCCTCC 58.998 47.826 0.00 0.00 0.00 4.30
35 36 4.576879 CACTAAAACTTGTACTCCCTCCC 58.423 47.826 0.00 0.00 0.00 4.30
36 37 4.286291 CACTAAAACTTGTACTCCCTCCCT 59.714 45.833 0.00 0.00 0.00 4.20
37 38 4.912133 ACTAAAACTTGTACTCCCTCCCTT 59.088 41.667 0.00 0.00 0.00 3.95
38 39 4.808767 AAAACTTGTACTCCCTCCCTTT 57.191 40.909 0.00 0.00 0.00 3.11
39 40 4.808767 AAACTTGTACTCCCTCCCTTTT 57.191 40.909 0.00 0.00 0.00 2.27
40 41 4.808767 AACTTGTACTCCCTCCCTTTTT 57.191 40.909 0.00 0.00 0.00 1.94
64 65 9.575783 TTTTTACTCCGCATATAAAATTTGGTC 57.424 29.630 0.00 0.00 30.18 4.02
65 66 7.867305 TTACTCCGCATATAAAATTTGGTCA 57.133 32.000 0.00 0.00 0.00 4.02
66 67 6.767524 ACTCCGCATATAAAATTTGGTCAA 57.232 33.333 0.00 0.00 0.00 3.18
67 68 7.164230 ACTCCGCATATAAAATTTGGTCAAA 57.836 32.000 0.00 0.00 34.46 2.69
68 69 7.257722 ACTCCGCATATAAAATTTGGTCAAAG 58.742 34.615 0.00 0.00 33.32 2.77
69 70 7.093945 ACTCCGCATATAAAATTTGGTCAAAGT 60.094 33.333 0.00 0.00 33.32 2.66
70 71 7.254852 TCCGCATATAAAATTTGGTCAAAGTC 58.745 34.615 0.00 0.00 33.32 3.01
71 72 7.032580 CCGCATATAAAATTTGGTCAAAGTCA 58.967 34.615 0.00 0.00 33.32 3.41
72 73 7.543868 CCGCATATAAAATTTGGTCAAAGTCAA 59.456 33.333 0.00 0.00 33.32 3.18
73 74 8.920665 CGCATATAAAATTTGGTCAAAGTCAAA 58.079 29.630 0.00 0.00 37.29 2.69
79 80 8.474006 AAAATTTGGTCAAAGTCAAACTACAC 57.526 30.769 0.00 0.00 35.97 2.90
80 81 6.767524 ATTTGGTCAAAGTCAAACTACACA 57.232 33.333 2.55 0.00 35.97 3.72
81 82 6.576662 TTTGGTCAAAGTCAAACTACACAA 57.423 33.333 0.00 0.00 0.00 3.33
82 83 6.576662 TTGGTCAAAGTCAAACTACACAAA 57.423 33.333 0.00 0.00 0.00 2.83
83 84 6.189677 TGGTCAAAGTCAAACTACACAAAG 57.810 37.500 0.00 0.00 0.00 2.77
84 85 5.708230 TGGTCAAAGTCAAACTACACAAAGT 59.292 36.000 0.00 0.00 0.00 2.66
85 86 6.207810 TGGTCAAAGTCAAACTACACAAAGTT 59.792 34.615 0.00 0.00 41.46 2.66
96 97 8.840833 AAACTACACAAAGTTTGACCAAATTT 57.159 26.923 22.23 11.30 45.60 1.82
97 98 9.930693 AAACTACACAAAGTTTGACCAAATTTA 57.069 25.926 22.23 0.00 45.60 1.40
166 167 7.372634 GAAAATACGTTTCATGATGCATCAG 57.627 36.000 31.36 22.78 44.42 2.90
167 168 6.682423 AAATACGTTTCATGATGCATCAGA 57.318 33.333 31.36 24.38 40.64 3.27
168 169 6.872628 AATACGTTTCATGATGCATCAGAT 57.127 33.333 31.36 15.67 40.64 2.90
169 170 7.967890 AATACGTTTCATGATGCATCAGATA 57.032 32.000 31.36 20.21 40.64 1.98
170 171 7.967890 ATACGTTTCATGATGCATCAGATAA 57.032 32.000 31.36 21.85 40.64 1.75
171 172 6.872628 ACGTTTCATGATGCATCAGATAAT 57.127 33.333 31.36 14.19 40.64 1.28
172 173 7.967890 ACGTTTCATGATGCATCAGATAATA 57.032 32.000 31.36 13.66 40.64 0.98
173 174 8.557592 ACGTTTCATGATGCATCAGATAATAT 57.442 30.769 31.36 12.75 40.64 1.28
174 175 9.006839 ACGTTTCATGATGCATCAGATAATATT 57.993 29.630 31.36 12.02 40.64 1.28
241 242 6.732896 TCAAACTCTAGAAAGGTTGACTCT 57.267 37.500 8.08 0.00 45.63 3.24
242 243 6.516718 TCAAACTCTAGAAAGGTTGACTCTG 58.483 40.000 8.08 0.00 45.63 3.35
243 244 6.323996 TCAAACTCTAGAAAGGTTGACTCTGA 59.676 38.462 8.08 1.08 45.63 3.27
244 245 5.715434 ACTCTAGAAAGGTTGACTCTGAC 57.285 43.478 0.00 0.00 0.00 3.51
245 246 4.525100 ACTCTAGAAAGGTTGACTCTGACC 59.475 45.833 0.00 0.00 36.15 4.02
246 247 4.480115 TCTAGAAAGGTTGACTCTGACCA 58.520 43.478 0.00 0.00 38.42 4.02
247 248 4.899457 TCTAGAAAGGTTGACTCTGACCAA 59.101 41.667 0.00 0.00 38.42 3.67
248 249 4.503714 AGAAAGGTTGACTCTGACCAAA 57.496 40.909 0.00 0.00 38.42 3.28
249 250 4.200092 AGAAAGGTTGACTCTGACCAAAC 58.800 43.478 0.00 0.00 38.42 2.93
250 251 2.640316 AGGTTGACTCTGACCAAACC 57.360 50.000 0.00 0.00 38.42 3.27
251 252 2.127708 AGGTTGACTCTGACCAAACCT 58.872 47.619 0.00 0.00 38.42 3.50
252 253 2.509964 AGGTTGACTCTGACCAAACCTT 59.490 45.455 0.00 0.00 38.42 3.50
253 254 3.714798 AGGTTGACTCTGACCAAACCTTA 59.285 43.478 0.00 0.00 38.42 2.69
254 255 4.351111 AGGTTGACTCTGACCAAACCTTAT 59.649 41.667 0.00 0.00 38.42 1.73
255 256 5.546499 AGGTTGACTCTGACCAAACCTTATA 59.454 40.000 0.00 0.00 38.42 0.98
256 257 6.215636 AGGTTGACTCTGACCAAACCTTATAT 59.784 38.462 0.00 0.00 38.42 0.86
257 258 7.402071 AGGTTGACTCTGACCAAACCTTATATA 59.598 37.037 0.00 0.00 38.42 0.86
258 259 8.211629 GGTTGACTCTGACCAAACCTTATATAT 58.788 37.037 0.00 0.00 35.95 0.86
259 260 9.046296 GTTGACTCTGACCAAACCTTATATATG 57.954 37.037 0.00 0.00 0.00 1.78
260 261 8.547481 TGACTCTGACCAAACCTTATATATGA 57.453 34.615 0.00 0.00 0.00 2.15
261 262 8.988060 TGACTCTGACCAAACCTTATATATGAA 58.012 33.333 0.00 0.00 0.00 2.57
262 263 9.262358 GACTCTGACCAAACCTTATATATGAAC 57.738 37.037 0.00 0.00 0.00 3.18
263 264 8.993424 ACTCTGACCAAACCTTATATATGAACT 58.007 33.333 0.00 0.00 0.00 3.01
279 280 5.959618 ATGAACTAAAAAGAAACGGAGGG 57.040 39.130 0.00 0.00 0.00 4.30
280 281 5.038651 TGAACTAAAAAGAAACGGAGGGA 57.961 39.130 0.00 0.00 0.00 4.20
281 282 5.061179 TGAACTAAAAAGAAACGGAGGGAG 58.939 41.667 0.00 0.00 0.00 4.30
282 283 4.701651 ACTAAAAAGAAACGGAGGGAGT 57.298 40.909 0.00 0.00 0.00 3.85
283 284 5.813513 ACTAAAAAGAAACGGAGGGAGTA 57.186 39.130 0.00 0.00 0.00 2.59
284 285 6.370186 ACTAAAAAGAAACGGAGGGAGTAT 57.630 37.500 0.00 0.00 0.00 2.12
285 286 6.171213 ACTAAAAAGAAACGGAGGGAGTATG 58.829 40.000 0.00 0.00 0.00 2.39
286 287 4.903045 AAAAGAAACGGAGGGAGTATGA 57.097 40.909 0.00 0.00 0.00 2.15
287 288 4.473477 AAAGAAACGGAGGGAGTATGAG 57.527 45.455 0.00 0.00 0.00 2.90
288 289 3.383698 AGAAACGGAGGGAGTATGAGA 57.616 47.619 0.00 0.00 0.00 3.27
289 290 3.917300 AGAAACGGAGGGAGTATGAGAT 58.083 45.455 0.00 0.00 0.00 2.75
290 291 4.290942 AGAAACGGAGGGAGTATGAGATT 58.709 43.478 0.00 0.00 0.00 2.40
291 292 4.100189 AGAAACGGAGGGAGTATGAGATTG 59.900 45.833 0.00 0.00 0.00 2.67
292 293 1.689273 ACGGAGGGAGTATGAGATTGC 59.311 52.381 0.00 0.00 0.00 3.56
293 294 1.001406 CGGAGGGAGTATGAGATTGCC 59.999 57.143 0.00 0.00 0.00 4.52
294 295 2.050144 GGAGGGAGTATGAGATTGCCA 58.950 52.381 0.00 0.00 0.00 4.92
295 296 2.224402 GGAGGGAGTATGAGATTGCCAC 60.224 54.545 0.00 0.00 0.00 5.01
296 297 2.703007 GAGGGAGTATGAGATTGCCACT 59.297 50.000 0.00 0.00 0.00 4.00
297 298 3.898123 GAGGGAGTATGAGATTGCCACTA 59.102 47.826 0.00 0.00 0.00 2.74
298 299 4.497516 AGGGAGTATGAGATTGCCACTAT 58.502 43.478 0.00 0.00 0.00 2.12
299 300 4.285517 AGGGAGTATGAGATTGCCACTATG 59.714 45.833 0.00 0.00 0.00 2.23
300 301 4.040952 GGGAGTATGAGATTGCCACTATGT 59.959 45.833 0.00 0.00 0.00 2.29
301 302 5.246203 GGGAGTATGAGATTGCCACTATGTA 59.754 44.000 0.00 0.00 0.00 2.29
302 303 6.070538 GGGAGTATGAGATTGCCACTATGTAT 60.071 42.308 0.00 0.00 0.00 2.29
303 304 7.390027 GGAGTATGAGATTGCCACTATGTATT 58.610 38.462 0.00 0.00 0.00 1.89
304 305 7.880195 GGAGTATGAGATTGCCACTATGTATTT 59.120 37.037 0.00 0.00 0.00 1.40
305 306 9.277783 GAGTATGAGATTGCCACTATGTATTTT 57.722 33.333 0.00 0.00 0.00 1.82
306 307 9.060347 AGTATGAGATTGCCACTATGTATTTTG 57.940 33.333 0.00 0.00 0.00 2.44
307 308 7.886629 ATGAGATTGCCACTATGTATTTTGT 57.113 32.000 0.00 0.00 0.00 2.83
308 309 8.978874 ATGAGATTGCCACTATGTATTTTGTA 57.021 30.769 0.00 0.00 0.00 2.41
309 310 8.208718 TGAGATTGCCACTATGTATTTTGTAC 57.791 34.615 0.00 0.00 0.00 2.90
310 311 8.046708 TGAGATTGCCACTATGTATTTTGTACT 58.953 33.333 0.00 0.00 0.00 2.73
311 312 8.213518 AGATTGCCACTATGTATTTTGTACTG 57.786 34.615 0.00 0.00 0.00 2.74
312 313 7.829211 AGATTGCCACTATGTATTTTGTACTGT 59.171 33.333 0.00 0.00 0.00 3.55
313 314 7.753309 TTGCCACTATGTATTTTGTACTGTT 57.247 32.000 0.00 0.00 0.00 3.16
314 315 7.753309 TGCCACTATGTATTTTGTACTGTTT 57.247 32.000 0.00 0.00 0.00 2.83
315 316 7.589395 TGCCACTATGTATTTTGTACTGTTTG 58.411 34.615 0.00 0.00 0.00 2.93
316 317 6.526674 GCCACTATGTATTTTGTACTGTTTGC 59.473 38.462 0.00 0.00 0.00 3.68
317 318 7.574967 GCCACTATGTATTTTGTACTGTTTGCT 60.575 37.037 0.00 0.00 0.00 3.91
318 319 7.750458 CCACTATGTATTTTGTACTGTTTGCTG 59.250 37.037 0.00 0.00 0.00 4.41
319 320 7.271223 CACTATGTATTTTGTACTGTTTGCTGC 59.729 37.037 0.00 0.00 0.00 5.25
320 321 5.506686 TGTATTTTGTACTGTTTGCTGCA 57.493 34.783 0.00 0.00 0.00 4.41
321 322 5.895928 TGTATTTTGTACTGTTTGCTGCAA 58.104 33.333 11.69 11.69 0.00 4.08
322 323 5.976534 TGTATTTTGTACTGTTTGCTGCAAG 59.023 36.000 15.39 6.72 0.00 4.01
336 337 3.037431 CTGCAAGCTGAGACTAGTTGT 57.963 47.619 0.00 0.00 0.00 3.32
337 338 3.397482 CTGCAAGCTGAGACTAGTTGTT 58.603 45.455 0.00 0.00 0.00 2.83
338 339 3.133691 TGCAAGCTGAGACTAGTTGTTG 58.866 45.455 0.00 0.00 0.00 3.33
339 340 3.181466 TGCAAGCTGAGACTAGTTGTTGA 60.181 43.478 0.00 0.00 0.00 3.18
340 341 3.431572 GCAAGCTGAGACTAGTTGTTGAG 59.568 47.826 0.00 0.00 0.00 3.02
341 342 4.797604 GCAAGCTGAGACTAGTTGTTGAGA 60.798 45.833 0.00 0.00 0.00 3.27
342 343 5.292765 CAAGCTGAGACTAGTTGTTGAGAA 58.707 41.667 0.00 0.00 0.00 2.87
343 344 4.877282 AGCTGAGACTAGTTGTTGAGAAC 58.123 43.478 0.00 0.00 0.00 3.01
344 345 4.342378 AGCTGAGACTAGTTGTTGAGAACA 59.658 41.667 0.00 0.00 40.21 3.18
356 357 6.524101 TTGTTGAGAACAAGCCTAAACTTT 57.476 33.333 0.00 0.00 45.79 2.66
357 358 5.890334 TGTTGAGAACAAGCCTAAACTTTG 58.110 37.500 0.00 0.00 38.72 2.77
358 359 5.417580 TGTTGAGAACAAGCCTAAACTTTGT 59.582 36.000 0.00 0.00 38.72 2.83
359 360 6.071616 TGTTGAGAACAAGCCTAAACTTTGTT 60.072 34.615 1.86 1.86 38.72 2.83
360 361 6.524101 TGAGAACAAGCCTAAACTTTGTTT 57.476 33.333 3.68 1.33 0.00 2.83
361 362 6.930731 TGAGAACAAGCCTAAACTTTGTTTT 58.069 32.000 0.94 0.00 0.00 2.43
362 363 7.382898 TGAGAACAAGCCTAAACTTTGTTTTT 58.617 30.769 0.94 0.00 0.00 1.94
363 364 8.524487 TGAGAACAAGCCTAAACTTTGTTTTTA 58.476 29.630 0.94 0.00 0.00 1.52
364 365 8.926715 AGAACAAGCCTAAACTTTGTTTTTAG 57.073 30.769 0.94 0.00 36.62 1.85
365 366 8.745590 AGAACAAGCCTAAACTTTGTTTTTAGA 58.254 29.630 0.94 0.00 38.36 2.10
366 367 8.926715 AACAAGCCTAAACTTTGTTTTTAGAG 57.073 30.769 0.94 0.00 38.36 2.43
367 368 8.288689 ACAAGCCTAAACTTTGTTTTTAGAGA 57.711 30.769 0.94 0.00 38.36 3.10
368 369 8.745590 ACAAGCCTAAACTTTGTTTTTAGAGAA 58.254 29.630 0.94 0.00 38.36 2.87
369 370 9.020813 CAAGCCTAAACTTTGTTTTTAGAGAAC 57.979 33.333 0.94 0.00 38.36 3.01
370 371 8.521170 AGCCTAAACTTTGTTTTTAGAGAACT 57.479 30.769 0.94 0.00 38.36 3.01
371 372 8.622157 AGCCTAAACTTTGTTTTTAGAGAACTC 58.378 33.333 0.94 0.00 38.36 3.01
372 373 8.622157 GCCTAAACTTTGTTTTTAGAGAACTCT 58.378 33.333 9.33 9.33 38.36 3.24
373 374 9.937175 CCTAAACTTTGTTTTTAGAGAACTCTG 57.063 33.333 13.73 0.00 40.71 3.35
378 379 9.444600 ACTTTGTTTTTAGAGAACTCTGTTACA 57.555 29.630 13.73 9.59 40.71 2.41
412 413 4.646040 TGATGATTTATCAAACCCCAGCAG 59.354 41.667 0.00 0.00 42.69 4.24
436 437 1.122632 TGGCCTTTGTAGACGGGTCA 61.123 55.000 3.32 0.00 0.00 4.02
446 447 2.729028 AGACGGGTCAAATATTGGGG 57.271 50.000 1.17 0.00 0.00 4.96
449 450 3.093814 GACGGGTCAAATATTGGGGTTT 58.906 45.455 0.00 0.00 0.00 3.27
452 453 3.368948 CGGGTCAAATATTGGGGTTTTGG 60.369 47.826 0.00 0.00 32.52 3.28
500 505 9.541143 GGAGTTTGTTTTTCTTTAATCATTGGA 57.459 29.630 0.00 0.00 0.00 3.53
518 523 7.709947 TCATTGGACATTATCATCTTCTTTGC 58.290 34.615 0.00 0.00 0.00 3.68
524 529 8.814235 GGACATTATCATCTTCTTTGCAAAATG 58.186 33.333 13.84 13.45 0.00 2.32
567 579 0.324943 AACCAGATTCCCGGTGAGTG 59.675 55.000 0.00 0.00 35.08 3.51
569 581 0.176680 CCAGATTCCCGGTGAGTGAG 59.823 60.000 0.00 0.00 0.00 3.51
571 583 1.276421 CAGATTCCCGGTGAGTGAGTT 59.724 52.381 0.00 0.00 0.00 3.01
572 584 2.496070 CAGATTCCCGGTGAGTGAGTTA 59.504 50.000 0.00 0.00 0.00 2.24
573 585 3.133003 CAGATTCCCGGTGAGTGAGTTAT 59.867 47.826 0.00 0.00 0.00 1.89
574 586 3.775316 AGATTCCCGGTGAGTGAGTTATT 59.225 43.478 0.00 0.00 0.00 1.40
575 587 4.960469 AGATTCCCGGTGAGTGAGTTATTA 59.040 41.667 0.00 0.00 0.00 0.98
579 591 5.240121 TCCCGGTGAGTGAGTTATTAAAAC 58.760 41.667 0.00 0.00 0.00 2.43
626 639 9.829507 TTCCTTTGCAAAAATAGAAAATTCTCA 57.170 25.926 13.84 0.00 38.70 3.27
627 640 9.480053 TCCTTTGCAAAAATAGAAAATTCTCAG 57.520 29.630 13.84 0.00 38.70 3.35
628 641 9.264719 CCTTTGCAAAAATAGAAAATTCTCAGT 57.735 29.630 13.84 0.00 38.70 3.41
631 644 9.683069 TTGCAAAAATAGAAAATTCTCAGTCTC 57.317 29.630 0.00 0.00 38.70 3.36
632 645 9.071276 TGCAAAAATAGAAAATTCTCAGTCTCT 57.929 29.630 0.00 0.00 38.70 3.10
633 646 9.553418 GCAAAAATAGAAAATTCTCAGTCTCTC 57.447 33.333 0.00 0.00 38.70 3.20
638 651 6.194796 AGAAAATTCTCAGTCTCTCTCTCG 57.805 41.667 0.00 0.00 29.94 4.04
639 652 5.710099 AGAAAATTCTCAGTCTCTCTCTCGT 59.290 40.000 0.00 0.00 29.94 4.18
640 653 5.975693 AAATTCTCAGTCTCTCTCTCGTT 57.024 39.130 0.00 0.00 0.00 3.85
641 654 5.975693 AATTCTCAGTCTCTCTCTCGTTT 57.024 39.130 0.00 0.00 0.00 3.60
642 655 5.975693 ATTCTCAGTCTCTCTCTCGTTTT 57.024 39.130 0.00 0.00 0.00 2.43
643 656 5.776173 TTCTCAGTCTCTCTCTCGTTTTT 57.224 39.130 0.00 0.00 0.00 1.94
748 794 7.860373 TCCATGTGATTTAACGAGAAAAACAAG 59.140 33.333 0.00 0.00 0.00 3.16
804 850 1.599047 GAGGCTAGAACCTGCTGCA 59.401 57.895 0.88 0.88 41.32 4.41
894 940 1.513622 GAGCTCCCGTGTCCTTCTC 59.486 63.158 0.87 0.00 0.00 2.87
975 1021 1.367471 TCCAACGTGGAGACAGCAG 59.633 57.895 0.00 0.00 42.67 4.24
1254 1300 1.964373 AACCATGTTCACGGACGGC 60.964 57.895 0.00 0.00 0.00 5.68
1278 1324 1.226323 CTACTCCAACGCGTCCGAG 60.226 63.158 25.57 25.57 38.29 4.63
1767 1813 3.731728 GAGGGCATCCAGTGGGCA 61.732 66.667 9.92 0.00 34.83 5.36
1770 1816 2.520260 GGCATCCAGTGGGCATCC 60.520 66.667 9.92 2.15 0.00 3.51
1788 1834 1.826921 CCTGATGCAGGCCATGACC 60.827 63.158 5.01 0.00 45.13 4.02
1914 1960 2.835895 TTCGCGGGATCCATCGGA 60.836 61.111 15.23 7.97 35.55 4.55
2658 2704 2.350197 CGACTACGTTGACTCGTTCCTT 60.350 50.000 3.44 0.00 43.80 3.36
2823 2869 2.073816 GATCCCGTTCGTGTGTCAAAT 58.926 47.619 0.00 0.00 0.00 2.32
3075 3121 1.133976 ACTTGCTTTGGCTGACAGAGT 60.134 47.619 6.65 0.00 39.59 3.24
3191 3238 5.246981 TCTCAAGGTCACCAGAAATTGAT 57.753 39.130 0.00 0.00 32.94 2.57
3194 3241 6.016024 TCTCAAGGTCACCAGAAATTGATTTG 60.016 38.462 0.00 0.00 32.94 2.32
3196 3243 3.259123 AGGTCACCAGAAATTGATTTGGC 59.741 43.478 0.00 0.00 0.00 4.52
3205 3252 3.683365 AATTGATTTGGCCCTGACAAC 57.317 42.857 0.00 0.00 26.20 3.32
3359 3409 7.255312 CCCACTAATGCATTTTAAATACCGCTA 60.255 37.037 18.75 0.00 0.00 4.26
3403 3453 6.435277 TCAAGATTTGAGAAAATCCCCTTCTG 59.565 38.462 7.41 0.00 39.39 3.02
3422 3485 1.604378 CCCCCGAGCTCATTTGAGT 59.396 57.895 15.40 0.00 43.85 3.41
3425 3488 2.162681 CCCCGAGCTCATTTGAGTTTT 58.837 47.619 15.40 0.00 43.85 2.43
3440 3503 8.755018 CATTTGAGTTTTGGATGAACAGTAAAC 58.245 33.333 0.00 0.00 0.00 2.01
3444 3507 5.238650 AGTTTTGGATGAACAGTAAACTCCG 59.761 40.000 0.00 0.00 32.14 4.63
3450 3513 6.488683 TGGATGAACAGTAAACTCCGAAAAAT 59.511 34.615 0.00 0.00 0.00 1.82
3451 3514 6.801862 GGATGAACAGTAAACTCCGAAAAATG 59.198 38.462 0.00 0.00 0.00 2.32
3452 3515 6.928979 TGAACAGTAAACTCCGAAAAATGA 57.071 33.333 0.00 0.00 0.00 2.57
3515 3590 3.631144 TCTCAGTGCTTGCAAATTTTCG 58.369 40.909 0.00 0.00 0.00 3.46
3539 3614 2.033801 CCGAAATCACATTCATGGAGGC 59.966 50.000 0.00 0.00 0.00 4.70
3544 3619 0.458669 CACATTCATGGAGGCCTTGC 59.541 55.000 6.77 0.00 0.00 4.01
3578 3654 8.878769 ACAAAATCGACACTTAAAATGCTTTTT 58.121 25.926 14.02 14.02 38.56 1.94
3596 3672 8.321650 TGCTTTTTAAATAGCATTTTTGGGAG 57.678 30.769 23.97 0.00 42.12 4.30
3597 3673 7.094848 TGCTTTTTAAATAGCATTTTTGGGAGC 60.095 33.333 23.97 1.25 42.12 4.70
3599 3675 8.860780 TTTTTAAATAGCATTTTTGGGAGCAT 57.139 26.923 0.00 0.00 0.00 3.79
3600 3676 8.491331 TTTTAAATAGCATTTTTGGGAGCATC 57.509 30.769 0.00 0.00 0.00 3.91
3602 3678 4.931661 ATAGCATTTTTGGGAGCATCAG 57.068 40.909 0.00 0.00 36.25 2.90
3642 3721 5.994668 ACTTCCAGAAAAGTTTGCACAAAAA 59.005 32.000 0.00 0.00 36.02 1.94
3683 3762 8.670804 TTTGTTTTTGATTTTGCTGTTCATTG 57.329 26.923 0.00 0.00 0.00 2.82
3684 3763 6.783162 TGTTTTTGATTTTGCTGTTCATTGG 58.217 32.000 0.00 0.00 0.00 3.16
3685 3764 6.183360 TGTTTTTGATTTTGCTGTTCATTGGG 60.183 34.615 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.016777 ACAAGTTTTAGTGCCAGAAGAAGATG 60.017 38.462 0.00 0.00 0.00 2.90
1 2 6.064717 ACAAGTTTTAGTGCCAGAAGAAGAT 58.935 36.000 0.00 0.00 0.00 2.40
2 3 5.437060 ACAAGTTTTAGTGCCAGAAGAAGA 58.563 37.500 0.00 0.00 0.00 2.87
3 4 5.757850 ACAAGTTTTAGTGCCAGAAGAAG 57.242 39.130 0.00 0.00 0.00 2.85
4 5 6.354130 AGTACAAGTTTTAGTGCCAGAAGAA 58.646 36.000 0.00 0.00 0.00 2.52
5 6 5.925509 AGTACAAGTTTTAGTGCCAGAAGA 58.074 37.500 0.00 0.00 0.00 2.87
6 7 5.179555 GGAGTACAAGTTTTAGTGCCAGAAG 59.820 44.000 0.00 0.00 0.00 2.85
7 8 5.061179 GGAGTACAAGTTTTAGTGCCAGAA 58.939 41.667 0.00 0.00 0.00 3.02
8 9 4.504340 GGGAGTACAAGTTTTAGTGCCAGA 60.504 45.833 9.00 0.00 32.09 3.86
9 10 3.751698 GGGAGTACAAGTTTTAGTGCCAG 59.248 47.826 9.00 0.00 32.09 4.85
10 11 3.393278 AGGGAGTACAAGTTTTAGTGCCA 59.607 43.478 14.67 0.00 33.77 4.92
11 12 4.001652 GAGGGAGTACAAGTTTTAGTGCC 58.998 47.826 6.36 6.36 31.96 5.01
12 13 4.001652 GGAGGGAGTACAAGTTTTAGTGC 58.998 47.826 0.00 0.00 0.00 4.40
13 14 4.286291 AGGGAGGGAGTACAAGTTTTAGTG 59.714 45.833 0.00 0.00 0.00 2.74
14 15 4.500452 AGGGAGGGAGTACAAGTTTTAGT 58.500 43.478 0.00 0.00 0.00 2.24
15 16 5.500546 AAGGGAGGGAGTACAAGTTTTAG 57.499 43.478 0.00 0.00 0.00 1.85
16 17 5.917545 AAAGGGAGGGAGTACAAGTTTTA 57.082 39.130 0.00 0.00 0.00 1.52
17 18 4.808767 AAAGGGAGGGAGTACAAGTTTT 57.191 40.909 0.00 0.00 0.00 2.43
18 19 4.808767 AAAAGGGAGGGAGTACAAGTTT 57.191 40.909 0.00 0.00 0.00 2.66
19 20 4.808767 AAAAAGGGAGGGAGTACAAGTT 57.191 40.909 0.00 0.00 0.00 2.66
38 39 9.575783 GACCAAATTTTATATGCGGAGTAAAAA 57.424 29.630 11.91 5.26 32.84 1.94
39 40 8.740906 TGACCAAATTTTATATGCGGAGTAAAA 58.259 29.630 10.79 10.79 33.41 1.52
40 41 8.282455 TGACCAAATTTTATATGCGGAGTAAA 57.718 30.769 0.00 0.00 0.00 2.01
41 42 7.867305 TGACCAAATTTTATATGCGGAGTAA 57.133 32.000 0.00 0.00 0.00 2.24
42 43 7.867305 TTGACCAAATTTTATATGCGGAGTA 57.133 32.000 0.00 0.00 0.00 2.59
43 44 6.767524 TTGACCAAATTTTATATGCGGAGT 57.232 33.333 0.00 0.00 0.00 3.85
44 45 7.257722 ACTTTGACCAAATTTTATATGCGGAG 58.742 34.615 0.00 0.00 0.00 4.63
45 46 7.094162 TGACTTTGACCAAATTTTATATGCGGA 60.094 33.333 0.00 0.00 0.00 5.54
46 47 7.032580 TGACTTTGACCAAATTTTATATGCGG 58.967 34.615 0.00 0.00 0.00 5.69
47 48 8.459521 TTGACTTTGACCAAATTTTATATGCG 57.540 30.769 0.00 0.00 0.00 4.73
53 54 9.575783 GTGTAGTTTGACTTTGACCAAATTTTA 57.424 29.630 0.00 0.00 35.14 1.52
54 55 8.091449 TGTGTAGTTTGACTTTGACCAAATTTT 58.909 29.630 0.00 0.00 35.14 1.82
55 56 7.607250 TGTGTAGTTTGACTTTGACCAAATTT 58.393 30.769 0.00 0.00 35.14 1.82
56 57 7.164230 TGTGTAGTTTGACTTTGACCAAATT 57.836 32.000 0.00 0.00 35.14 1.82
57 58 6.767524 TGTGTAGTTTGACTTTGACCAAAT 57.232 33.333 0.00 0.00 35.14 2.32
58 59 6.576662 TTGTGTAGTTTGACTTTGACCAAA 57.423 33.333 0.00 0.00 0.00 3.28
59 60 6.207810 ACTTTGTGTAGTTTGACTTTGACCAA 59.792 34.615 0.00 0.00 0.00 3.67
60 61 5.708230 ACTTTGTGTAGTTTGACTTTGACCA 59.292 36.000 0.00 0.00 0.00 4.02
61 62 6.190954 ACTTTGTGTAGTTTGACTTTGACC 57.809 37.500 0.00 0.00 0.00 4.02
71 72 8.840833 AAATTTGGTCAAACTTTGTGTAGTTT 57.159 26.923 1.44 0.00 46.42 2.66
142 143 7.188834 TCTGATGCATCATGAAACGTATTTTC 58.811 34.615 28.81 0.00 37.41 2.29
143 144 7.087409 TCTGATGCATCATGAAACGTATTTT 57.913 32.000 28.81 0.00 36.02 1.82
144 145 6.682423 TCTGATGCATCATGAAACGTATTT 57.318 33.333 28.81 0.00 36.02 1.40
145 146 6.872628 ATCTGATGCATCATGAAACGTATT 57.127 33.333 28.81 9.38 36.02 1.89
146 147 7.967890 TTATCTGATGCATCATGAAACGTAT 57.032 32.000 28.81 13.90 36.02 3.06
147 148 7.967890 ATTATCTGATGCATCATGAAACGTA 57.032 32.000 28.81 13.95 36.02 3.57
148 149 6.872628 ATTATCTGATGCATCATGAAACGT 57.127 33.333 28.81 14.78 36.02 3.99
210 211 9.110502 CAACCTTTCTAGAGTTTGACTAACTTT 57.889 33.333 3.78 1.31 47.00 2.66
211 212 8.483758 TCAACCTTTCTAGAGTTTGACTAACTT 58.516 33.333 3.78 0.00 47.00 2.66
213 214 7.927092 AGTCAACCTTTCTAGAGTTTGACTAAC 59.073 37.037 24.46 10.02 33.82 2.34
214 215 8.019656 AGTCAACCTTTCTAGAGTTTGACTAA 57.980 34.615 24.46 4.52 33.82 2.24
215 216 7.506261 AGAGTCAACCTTTCTAGAGTTTGACTA 59.494 37.037 25.10 0.00 34.76 2.59
216 217 6.325286 AGAGTCAACCTTTCTAGAGTTTGACT 59.675 38.462 25.22 25.22 36.01 3.41
217 218 6.422400 CAGAGTCAACCTTTCTAGAGTTTGAC 59.578 42.308 19.87 19.87 0.00 3.18
218 219 6.323996 TCAGAGTCAACCTTTCTAGAGTTTGA 59.676 38.462 0.00 0.00 0.00 2.69
219 220 6.422400 GTCAGAGTCAACCTTTCTAGAGTTTG 59.578 42.308 0.00 0.00 0.00 2.93
220 221 6.463190 GGTCAGAGTCAACCTTTCTAGAGTTT 60.463 42.308 7.32 0.00 32.54 2.66
221 222 5.011227 GGTCAGAGTCAACCTTTCTAGAGTT 59.989 44.000 7.32 0.00 32.54 3.01
222 223 4.525100 GGTCAGAGTCAACCTTTCTAGAGT 59.475 45.833 7.32 0.00 32.54 3.24
223 224 4.524714 TGGTCAGAGTCAACCTTTCTAGAG 59.475 45.833 13.93 0.00 36.47 2.43
224 225 4.480115 TGGTCAGAGTCAACCTTTCTAGA 58.520 43.478 13.93 0.00 36.47 2.43
225 226 4.873746 TGGTCAGAGTCAACCTTTCTAG 57.126 45.455 13.93 0.00 36.47 2.43
226 227 5.365619 GTTTGGTCAGAGTCAACCTTTCTA 58.634 41.667 13.93 0.00 36.47 2.10
227 228 4.200092 GTTTGGTCAGAGTCAACCTTTCT 58.800 43.478 13.93 0.00 36.47 2.52
228 229 3.315470 GGTTTGGTCAGAGTCAACCTTTC 59.685 47.826 13.93 5.96 36.47 2.62
229 230 3.053619 AGGTTTGGTCAGAGTCAACCTTT 60.054 43.478 13.93 0.00 36.47 3.11
230 231 2.509964 AGGTTTGGTCAGAGTCAACCTT 59.490 45.455 13.93 0.00 36.47 3.50
231 232 2.127708 AGGTTTGGTCAGAGTCAACCT 58.872 47.619 13.93 9.62 36.47 3.50
232 233 2.640316 AGGTTTGGTCAGAGTCAACC 57.360 50.000 7.58 7.58 36.03 3.77
233 234 9.046296 CATATATAAGGTTTGGTCAGAGTCAAC 57.954 37.037 0.00 0.00 0.00 3.18
234 235 8.988060 TCATATATAAGGTTTGGTCAGAGTCAA 58.012 33.333 0.00 0.00 0.00 3.18
235 236 8.547481 TCATATATAAGGTTTGGTCAGAGTCA 57.453 34.615 0.00 0.00 0.00 3.41
236 237 9.262358 GTTCATATATAAGGTTTGGTCAGAGTC 57.738 37.037 0.00 0.00 0.00 3.36
237 238 8.993424 AGTTCATATATAAGGTTTGGTCAGAGT 58.007 33.333 0.00 0.00 0.00 3.24
253 254 9.338622 CCCTCCGTTTCTTTTTAGTTCATATAT 57.661 33.333 0.00 0.00 0.00 0.86
254 255 8.542080 TCCCTCCGTTTCTTTTTAGTTCATATA 58.458 33.333 0.00 0.00 0.00 0.86
255 256 7.399634 TCCCTCCGTTTCTTTTTAGTTCATAT 58.600 34.615 0.00 0.00 0.00 1.78
256 257 6.771573 TCCCTCCGTTTCTTTTTAGTTCATA 58.228 36.000 0.00 0.00 0.00 2.15
257 258 5.627135 TCCCTCCGTTTCTTTTTAGTTCAT 58.373 37.500 0.00 0.00 0.00 2.57
258 259 5.038651 TCCCTCCGTTTCTTTTTAGTTCA 57.961 39.130 0.00 0.00 0.00 3.18
259 260 5.061853 ACTCCCTCCGTTTCTTTTTAGTTC 58.938 41.667 0.00 0.00 0.00 3.01
260 261 5.045012 ACTCCCTCCGTTTCTTTTTAGTT 57.955 39.130 0.00 0.00 0.00 2.24
261 262 4.701651 ACTCCCTCCGTTTCTTTTTAGT 57.298 40.909 0.00 0.00 0.00 2.24
262 263 6.403878 TCATACTCCCTCCGTTTCTTTTTAG 58.596 40.000 0.00 0.00 0.00 1.85
263 264 6.211986 TCTCATACTCCCTCCGTTTCTTTTTA 59.788 38.462 0.00 0.00 0.00 1.52
264 265 5.012768 TCTCATACTCCCTCCGTTTCTTTTT 59.987 40.000 0.00 0.00 0.00 1.94
265 266 4.530946 TCTCATACTCCCTCCGTTTCTTTT 59.469 41.667 0.00 0.00 0.00 2.27
266 267 4.094476 TCTCATACTCCCTCCGTTTCTTT 58.906 43.478 0.00 0.00 0.00 2.52
267 268 3.709587 TCTCATACTCCCTCCGTTTCTT 58.290 45.455 0.00 0.00 0.00 2.52
268 269 3.383698 TCTCATACTCCCTCCGTTTCT 57.616 47.619 0.00 0.00 0.00 2.52
269 270 4.372656 CAATCTCATACTCCCTCCGTTTC 58.627 47.826 0.00 0.00 0.00 2.78
270 271 3.432326 GCAATCTCATACTCCCTCCGTTT 60.432 47.826 0.00 0.00 0.00 3.60
271 272 2.103263 GCAATCTCATACTCCCTCCGTT 59.897 50.000 0.00 0.00 0.00 4.44
272 273 1.689273 GCAATCTCATACTCCCTCCGT 59.311 52.381 0.00 0.00 0.00 4.69
273 274 1.001406 GGCAATCTCATACTCCCTCCG 59.999 57.143 0.00 0.00 0.00 4.63
274 275 2.050144 TGGCAATCTCATACTCCCTCC 58.950 52.381 0.00 0.00 0.00 4.30
275 276 2.703007 AGTGGCAATCTCATACTCCCTC 59.297 50.000 0.00 0.00 0.00 4.30
276 277 2.769209 AGTGGCAATCTCATACTCCCT 58.231 47.619 0.00 0.00 0.00 4.20
277 278 4.040952 ACATAGTGGCAATCTCATACTCCC 59.959 45.833 0.00 0.00 0.00 4.30
278 279 5.220710 ACATAGTGGCAATCTCATACTCC 57.779 43.478 0.00 0.00 0.00 3.85
279 280 8.839310 AAATACATAGTGGCAATCTCATACTC 57.161 34.615 0.00 0.00 0.00 2.59
280 281 9.060347 CAAAATACATAGTGGCAATCTCATACT 57.940 33.333 0.00 0.00 0.00 2.12
281 282 8.840321 ACAAAATACATAGTGGCAATCTCATAC 58.160 33.333 0.00 0.00 0.00 2.39
282 283 8.978874 ACAAAATACATAGTGGCAATCTCATA 57.021 30.769 0.00 0.00 0.00 2.15
283 284 7.886629 ACAAAATACATAGTGGCAATCTCAT 57.113 32.000 0.00 0.00 0.00 2.90
284 285 8.046708 AGTACAAAATACATAGTGGCAATCTCA 58.953 33.333 0.00 0.00 0.00 3.27
285 286 8.338259 CAGTACAAAATACATAGTGGCAATCTC 58.662 37.037 0.00 0.00 0.00 2.75
286 287 7.829211 ACAGTACAAAATACATAGTGGCAATCT 59.171 33.333 0.00 0.00 0.00 2.40
287 288 7.985476 ACAGTACAAAATACATAGTGGCAATC 58.015 34.615 0.00 0.00 0.00 2.67
288 289 7.938140 ACAGTACAAAATACATAGTGGCAAT 57.062 32.000 0.00 0.00 0.00 3.56
289 290 7.753309 AACAGTACAAAATACATAGTGGCAA 57.247 32.000 0.00 0.00 0.00 4.52
290 291 7.589395 CAAACAGTACAAAATACATAGTGGCA 58.411 34.615 0.00 0.00 0.00 4.92
291 292 6.526674 GCAAACAGTACAAAATACATAGTGGC 59.473 38.462 0.00 0.00 0.00 5.01
292 293 7.750458 CAGCAAACAGTACAAAATACATAGTGG 59.250 37.037 0.00 0.00 0.00 4.00
293 294 7.271223 GCAGCAAACAGTACAAAATACATAGTG 59.729 37.037 0.00 0.00 0.00 2.74
294 295 7.040755 TGCAGCAAACAGTACAAAATACATAGT 60.041 33.333 0.00 0.00 0.00 2.12
295 296 7.304735 TGCAGCAAACAGTACAAAATACATAG 58.695 34.615 0.00 0.00 0.00 2.23
296 297 7.208225 TGCAGCAAACAGTACAAAATACATA 57.792 32.000 0.00 0.00 0.00 2.29
297 298 6.083098 TGCAGCAAACAGTACAAAATACAT 57.917 33.333 0.00 0.00 0.00 2.29
298 299 5.506686 TGCAGCAAACAGTACAAAATACA 57.493 34.783 0.00 0.00 0.00 2.29
299 300 5.107875 GCTTGCAGCAAACAGTACAAAATAC 60.108 40.000 9.65 0.00 41.89 1.89
300 301 4.981674 GCTTGCAGCAAACAGTACAAAATA 59.018 37.500 9.65 0.00 41.89 1.40
301 302 3.803778 GCTTGCAGCAAACAGTACAAAAT 59.196 39.130 9.65 0.00 41.89 1.82
302 303 3.119173 AGCTTGCAGCAAACAGTACAAAA 60.119 39.130 9.65 0.00 45.56 2.44
303 304 2.426738 AGCTTGCAGCAAACAGTACAAA 59.573 40.909 9.65 0.00 45.56 2.83
304 305 2.023673 AGCTTGCAGCAAACAGTACAA 58.976 42.857 9.65 0.00 45.56 2.41
305 306 1.334556 CAGCTTGCAGCAAACAGTACA 59.665 47.619 9.65 0.00 45.56 2.90
306 307 1.603802 TCAGCTTGCAGCAAACAGTAC 59.396 47.619 9.65 0.00 45.56 2.73
307 308 1.875514 CTCAGCTTGCAGCAAACAGTA 59.124 47.619 9.65 0.00 45.56 2.74
308 309 0.666913 CTCAGCTTGCAGCAAACAGT 59.333 50.000 9.65 0.00 45.56 3.55
309 310 0.949397 TCTCAGCTTGCAGCAAACAG 59.051 50.000 9.65 1.61 45.56 3.16
310 311 0.664761 GTCTCAGCTTGCAGCAAACA 59.335 50.000 9.65 0.00 45.56 2.83
311 312 0.950116 AGTCTCAGCTTGCAGCAAAC 59.050 50.000 9.65 4.64 45.56 2.93
312 313 2.224378 ACTAGTCTCAGCTTGCAGCAAA 60.224 45.455 9.65 0.00 45.56 3.68
313 314 1.345741 ACTAGTCTCAGCTTGCAGCAA 59.654 47.619 7.81 7.81 45.56 3.91
314 315 0.972134 ACTAGTCTCAGCTTGCAGCA 59.028 50.000 10.16 0.00 45.56 4.41
315 316 1.731160 CAACTAGTCTCAGCTTGCAGC 59.269 52.381 0.00 0.47 42.84 5.25
316 317 3.037431 ACAACTAGTCTCAGCTTGCAG 57.963 47.619 0.00 0.00 0.00 4.41
317 318 3.133691 CAACAACTAGTCTCAGCTTGCA 58.866 45.455 0.00 0.00 0.00 4.08
318 319 3.393800 TCAACAACTAGTCTCAGCTTGC 58.606 45.455 0.00 0.00 0.00 4.01
319 320 4.876125 TCTCAACAACTAGTCTCAGCTTG 58.124 43.478 0.00 0.00 0.00 4.01
320 321 5.163405 TGTTCTCAACAACTAGTCTCAGCTT 60.163 40.000 0.00 0.00 38.72 3.74
321 322 4.342378 TGTTCTCAACAACTAGTCTCAGCT 59.658 41.667 0.00 0.00 38.72 4.24
322 323 4.621991 TGTTCTCAACAACTAGTCTCAGC 58.378 43.478 0.00 0.00 38.72 4.26
323 324 5.176590 GCTTGTTCTCAACAACTAGTCTCAG 59.823 44.000 0.00 0.00 45.79 3.35
324 325 5.050490 GCTTGTTCTCAACAACTAGTCTCA 58.950 41.667 0.00 0.00 45.79 3.27
325 326 4.449405 GGCTTGTTCTCAACAACTAGTCTC 59.551 45.833 0.00 0.00 45.79 3.36
326 327 4.101741 AGGCTTGTTCTCAACAACTAGTCT 59.898 41.667 0.00 0.00 45.79 3.24
327 328 4.381411 AGGCTTGTTCTCAACAACTAGTC 58.619 43.478 0.00 0.00 45.79 2.59
328 329 4.423625 AGGCTTGTTCTCAACAACTAGT 57.576 40.909 0.00 0.00 45.79 2.57
329 330 6.483640 AGTTTAGGCTTGTTCTCAACAACTAG 59.516 38.462 0.00 0.00 45.79 2.57
330 331 6.354130 AGTTTAGGCTTGTTCTCAACAACTA 58.646 36.000 0.00 0.00 45.79 2.24
331 332 5.193679 AGTTTAGGCTTGTTCTCAACAACT 58.806 37.500 0.00 0.00 45.79 3.16
332 333 5.500645 AGTTTAGGCTTGTTCTCAACAAC 57.499 39.130 0.00 0.00 45.79 3.32
334 335 5.417580 ACAAAGTTTAGGCTTGTTCTCAACA 59.582 36.000 0.00 0.00 40.21 3.33
335 336 5.891451 ACAAAGTTTAGGCTTGTTCTCAAC 58.109 37.500 0.00 0.00 0.00 3.18
336 337 6.524101 AACAAAGTTTAGGCTTGTTCTCAA 57.476 33.333 0.00 0.00 0.00 3.02
337 338 6.524101 AAACAAAGTTTAGGCTTGTTCTCA 57.476 33.333 0.00 0.00 0.00 3.27
338 339 7.827819 AAAAACAAAGTTTAGGCTTGTTCTC 57.172 32.000 0.00 0.00 0.00 2.87
339 340 8.745590 TCTAAAAACAAAGTTTAGGCTTGTTCT 58.254 29.630 0.00 0.00 38.53 3.01
340 341 8.920509 TCTAAAAACAAAGTTTAGGCTTGTTC 57.079 30.769 0.00 0.00 38.53 3.18
341 342 8.745590 TCTCTAAAAACAAAGTTTAGGCTTGTT 58.254 29.630 0.00 0.00 38.53 2.83
342 343 8.288689 TCTCTAAAAACAAAGTTTAGGCTTGT 57.711 30.769 0.00 0.00 38.53 3.16
343 344 9.020813 GTTCTCTAAAAACAAAGTTTAGGCTTG 57.979 33.333 0.00 0.00 38.53 4.01
344 345 8.967918 AGTTCTCTAAAAACAAAGTTTAGGCTT 58.032 29.630 0.00 0.00 38.53 4.35
345 346 8.521170 AGTTCTCTAAAAACAAAGTTTAGGCT 57.479 30.769 0.00 0.00 38.53 4.58
346 347 8.622157 AGAGTTCTCTAAAAACAAAGTTTAGGC 58.378 33.333 0.01 0.00 38.53 3.93
347 348 9.937175 CAGAGTTCTCTAAAAACAAAGTTTAGG 57.063 33.333 1.83 0.00 38.53 2.69
352 353 9.444600 TGTAACAGAGTTCTCTAAAAACAAAGT 57.555 29.630 1.83 0.00 0.00 2.66
363 364 9.574516 AAAAACCATATTGTAACAGAGTTCTCT 57.425 29.630 0.00 0.00 0.00 3.10
364 365 9.612620 CAAAAACCATATTGTAACAGAGTTCTC 57.387 33.333 0.00 0.00 0.00 2.87
365 366 9.349713 TCAAAAACCATATTGTAACAGAGTTCT 57.650 29.630 0.00 0.00 0.00 3.01
367 368 9.912634 CATCAAAAACCATATTGTAACAGAGTT 57.087 29.630 0.00 0.00 0.00 3.01
368 369 9.295825 TCATCAAAAACCATATTGTAACAGAGT 57.704 29.630 0.00 0.00 0.00 3.24
396 397 1.992557 ACCTCTGCTGGGGTTTGATAA 59.007 47.619 9.79 0.00 30.80 1.75
436 437 7.232330 CCAATGTTTTCCAAAACCCCAATATTT 59.768 33.333 11.50 0.00 45.82 1.40
446 447 5.024785 TGGTACCCAATGTTTTCCAAAAC 57.975 39.130 10.07 7.81 46.40 2.43
449 450 3.580458 CCATGGTACCCAATGTTTTCCAA 59.420 43.478 10.07 0.00 36.95 3.53
452 453 2.093711 GCCCATGGTACCCAATGTTTTC 60.094 50.000 11.73 0.00 36.95 2.29
471 473 5.980715 TGATTAAAGAAAAACAAACTCCGCC 59.019 36.000 0.00 0.00 0.00 6.13
500 505 9.715121 AACATTTTGCAAAGAAGATGATAATGT 57.285 25.926 22.31 16.77 0.00 2.71
651 664 7.856894 GCATTAAGCAAGAAGAGAATGAGAATC 59.143 37.037 0.00 0.00 44.79 2.52
652 665 7.705214 GCATTAAGCAAGAAGAGAATGAGAAT 58.295 34.615 0.00 0.00 44.79 2.40
653 666 7.081526 GCATTAAGCAAGAAGAGAATGAGAA 57.918 36.000 0.00 0.00 44.79 2.87
654 667 6.674694 GCATTAAGCAAGAAGAGAATGAGA 57.325 37.500 0.00 0.00 44.79 3.27
804 850 1.901464 AAAACCGGCATTGGCTCGT 60.901 52.632 0.00 1.54 40.87 4.18
856 902 7.550906 GGAGCTCGCTTATTTATAGAAATGGAT 59.449 37.037 7.83 0.00 35.96 3.41
862 908 4.280174 ACGGGAGCTCGCTTATTTATAGAA 59.720 41.667 26.13 0.00 0.00 2.10
863 909 3.825014 ACGGGAGCTCGCTTATTTATAGA 59.175 43.478 26.13 0.00 0.00 1.98
894 940 3.621715 GGGAGCACGGATTTTACAAGTAG 59.378 47.826 0.00 0.00 0.00 2.57
975 1021 1.007336 CCTCGTTGTCACGCTGTACC 61.007 60.000 0.00 0.00 46.70 3.34
1107 1153 2.203126 GGGGAGAGCGCATTCCAG 60.203 66.667 25.45 0.00 35.09 3.86
1254 1300 2.125106 GCGTTGGAGTAGCAGGGG 60.125 66.667 0.00 0.00 0.00 4.79
1596 1642 4.562425 CCGGTGCTGTGGTGGTGT 62.562 66.667 0.00 0.00 0.00 4.16
1621 1667 0.463295 AGCATCTGGAATGCCGTCAG 60.463 55.000 6.40 0.00 45.59 3.51
1863 1909 4.785453 CCGGCCTCTTGGACTGCC 62.785 72.222 0.00 0.00 39.94 4.85
1914 1960 1.906824 TCCGAACGAGAAGGGCTGT 60.907 57.895 0.00 0.00 0.00 4.40
2722 2768 4.929146 AAAGCTGACTACCCCAACTATT 57.071 40.909 0.00 0.00 0.00 1.73
2804 2850 2.178912 ATTTGACACACGAACGGGAT 57.821 45.000 2.83 0.00 0.00 3.85
2823 2869 4.123506 TCAACGTCTTGCAATTGACAGTA 58.876 39.130 10.34 0.00 33.18 2.74
2990 3036 4.078336 TCTCCCCTGGATAAGATTCAGTCT 60.078 45.833 0.00 0.00 39.43 3.24
3191 3238 5.825679 GTGTATATATGTTGTCAGGGCCAAA 59.174 40.000 6.18 0.00 0.00 3.28
3194 3241 4.968259 TGTGTATATATGTTGTCAGGGCC 58.032 43.478 0.00 0.00 0.00 5.80
3196 3243 6.054941 TGCTTGTGTATATATGTTGTCAGGG 58.945 40.000 0.00 0.00 0.00 4.45
3282 3332 0.392336 TTGGCCACCAGACAAAATGC 59.608 50.000 3.88 0.00 33.81 3.56
3381 3431 4.708909 GCAGAAGGGGATTTTCTCAAATCT 59.291 41.667 7.45 0.00 45.45 2.40
3384 3434 3.165071 GGCAGAAGGGGATTTTCTCAAA 58.835 45.455 0.00 0.00 32.75 2.69
3403 3453 1.821332 CTCAAATGAGCTCGGGGGC 60.821 63.158 9.64 0.00 35.13 5.80
3422 3485 5.369833 TCGGAGTTTACTGTTCATCCAAAA 58.630 37.500 0.00 0.00 0.00 2.44
3425 3488 4.610605 TTCGGAGTTTACTGTTCATCCA 57.389 40.909 0.00 0.00 0.00 3.41
3462 3525 9.033481 TGTTGAAGTTTGCATTAAAAGAATCAG 57.967 29.630 0.00 0.00 0.00 2.90
3463 3526 8.939201 TGTTGAAGTTTGCATTAAAAGAATCA 57.061 26.923 0.00 0.00 0.00 2.57
3466 3529 9.985318 CATTTGTTGAAGTTTGCATTAAAAGAA 57.015 25.926 0.00 0.00 0.00 2.52
3467 3530 9.160496 ACATTTGTTGAAGTTTGCATTAAAAGA 57.840 25.926 0.00 0.00 0.00 2.52
3468 3531 9.771915 AACATTTGTTGAAGTTTGCATTAAAAG 57.228 25.926 0.00 0.00 36.80 2.27
3469 3532 9.766277 GAACATTTGTTGAAGTTTGCATTAAAA 57.234 25.926 0.00 0.00 38.56 1.52
3470 3533 9.160496 AGAACATTTGTTGAAGTTTGCATTAAA 57.840 25.926 0.00 0.00 38.56 1.52
3471 3534 8.715191 AGAACATTTGTTGAAGTTTGCATTAA 57.285 26.923 0.00 0.00 38.56 1.40
3472 3535 7.978414 TGAGAACATTTGTTGAAGTTTGCATTA 59.022 29.630 0.00 0.00 38.56 1.90
3473 3536 6.817641 TGAGAACATTTGTTGAAGTTTGCATT 59.182 30.769 0.00 0.00 38.56 3.56
3474 3537 6.339730 TGAGAACATTTGTTGAAGTTTGCAT 58.660 32.000 0.00 0.00 38.56 3.96
3515 3590 3.278574 TCCATGAATGTGATTTCGGGAC 58.721 45.455 0.00 0.00 30.94 4.46
3578 3654 6.380846 ACTGATGCTCCCAAAAATGCTATTTA 59.619 34.615 0.00 0.00 0.00 1.40
3657 3736 9.291664 CAATGAACAGCAAAATCAAAAACAAAT 57.708 25.926 0.00 0.00 0.00 2.32
3662 3741 6.374565 CCCAATGAACAGCAAAATCAAAAA 57.625 33.333 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.