Multiple sequence alignment - TraesCS3B01G349400

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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 TraesCS3B01G349400 chr3B 100.000 2645 0 0 1 2645 559876343 559878987 0.000000e+00 4885.0
1 TraesCS3B01G349400 chr3A 93.951 2149 81 24 526 2645 557423090 557420962 0.000000e+00 3203.0
2 TraesCS3B01G349400 chr3A 92.000 100 8 0 2 101 557423195 557423096 9.870000e-30 141.0
3 TraesCS3B01G349400 chr3D 94.266 2058 68 17 624 2645 428240571 428242614 0.000000e+00 3101.0
4 TraesCS3B01G349400 chr3D 93.461 627 28 8 1631 2247 428242783 428243406 0.000000e+00 918.0
5 TraesCS3B01G349400 chr3D 92.523 107 7 1 2 108 428240365 428240470 4.560000e-33 152.0
6 TraesCS3B01G349400 chr7A 90.404 396 24 6 110 498 264925972 264926360 2.350000e-140 508.0
7 TraesCS3B01G349400 chr7A 85.000 60 8 1 528 586 96559197 96559138 2.840000e-05 60.2
8 TraesCS3B01G349400 chr2D 88.971 408 26 12 110 507 7656713 7656315 1.100000e-133 486.0
9 TraesCS3B01G349400 chr2D 87.500 400 35 10 112 498 196003096 196003493 5.190000e-122 448.0
10 TraesCS3B01G349400 chr5D 88.529 401 32 10 109 498 118271028 118271425 8.570000e-130 473.0
11 TraesCS3B01G349400 chr5D 88.471 399 33 8 109 498 133247835 133248229 1.110000e-128 470.0
12 TraesCS3B01G349400 chr5D 88.060 402 28 13 110 498 399625008 399624614 2.400000e-125 459.0
13 TraesCS3B01G349400 chr6D 88.471 399 32 11 109 498 262290890 262290497 1.110000e-128 470.0
14 TraesCS3B01G349400 chr7D 87.940 398 37 8 110 498 616459960 616459565 2.400000e-125 459.0
15 TraesCS3B01G349400 chr7D 89.796 49 4 1 528 575 89725555 89725507 7.910000e-06 62.1
16 TraesCS3B01G349400 chr2B 87.688 398 37 10 111 498 720628731 720629126 1.120000e-123 453.0


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 TraesCS3B01G349400 chr3B 559876343 559878987 2644 False 4885.000000 4885 100.000000 1 2645 1 chr3B.!!$F1 2644
1 TraesCS3B01G349400 chr3A 557420962 557423195 2233 True 1672.000000 3203 92.975500 2 2645 2 chr3A.!!$R1 2643
2 TraesCS3B01G349400 chr3D 428240365 428243406 3041 False 1390.333333 3101 93.416667 2 2645 3 chr3D.!!$F1 2643

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
487 488 0.108186 TAAGGGTGCATGTGAGCTCG 60.108 55.0 9.64 0.0 34.99 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1874 1.522092 CAGTGGAAGCGAGGCCATA 59.478 57.895 5.01 0.0 36.41 2.74 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
21 22 2.943033 CAATTTACTAGGGAGTTGCGGG 59.057 50.000 0.00 0.00 37.10 6.13
109 110 9.372369 AGATGATTTACTAGTAACTGTTGAAGC 57.628 33.333 14.96 2.50 0.00 3.86
110 111 7.576750 TGATTTACTAGTAACTGTTGAAGCG 57.423 36.000 14.96 0.00 0.00 4.68
113 114 8.597662 ATTTACTAGTAACTGTTGAAGCGAAA 57.402 30.769 14.96 0.00 0.00 3.46
115 116 5.598769 ACTAGTAACTGTTGAAGCGAAAGT 58.401 37.500 2.69 0.00 0.00 2.66
116 117 4.795970 AGTAACTGTTGAAGCGAAAGTG 57.204 40.909 2.69 0.00 0.00 3.16
117 118 2.475200 AACTGTTGAAGCGAAAGTGC 57.525 45.000 0.00 0.00 0.00 4.40
121 122 2.288666 TGTTGAAGCGAAAGTGCTCTT 58.711 42.857 0.00 0.00 46.60 2.85
122 123 2.032054 TGTTGAAGCGAAAGTGCTCTTG 59.968 45.455 1.02 0.00 46.60 3.02
123 124 1.953559 TGAAGCGAAAGTGCTCTTGT 58.046 45.000 1.02 0.00 46.60 3.16
124 125 1.599071 TGAAGCGAAAGTGCTCTTGTG 59.401 47.619 1.02 0.00 46.60 3.33
125 126 1.867233 GAAGCGAAAGTGCTCTTGTGA 59.133 47.619 1.02 0.00 46.60 3.58
143 144 3.088044 GCTCGAGCTCACATGCAC 58.912 61.111 29.88 0.00 38.21 4.57
144 145 2.459442 GCTCGAGCTCACATGCACC 61.459 63.158 29.88 0.00 38.21 5.01
145 146 1.812922 CTCGAGCTCACATGCACCC 60.813 63.158 15.40 0.00 34.99 4.61
146 147 2.236223 CTCGAGCTCACATGCACCCT 62.236 60.000 15.40 0.00 34.99 4.34
147 148 1.376424 CGAGCTCACATGCACCCTT 60.376 57.895 15.40 0.00 34.99 3.95
148 149 0.957395 CGAGCTCACATGCACCCTTT 60.957 55.000 15.40 0.00 34.99 3.11
149 150 0.524862 GAGCTCACATGCACCCTTTG 59.475 55.000 9.40 0.00 34.99 2.77
163 164 5.551760 CACCCTTTGCTACAGTAGAATTG 57.448 43.478 12.15 0.00 0.00 2.32
164 165 5.245531 CACCCTTTGCTACAGTAGAATTGA 58.754 41.667 12.15 0.00 0.00 2.57
165 166 5.705441 CACCCTTTGCTACAGTAGAATTGAA 59.295 40.000 12.15 0.00 0.00 2.69
166 167 6.206634 CACCCTTTGCTACAGTAGAATTGAAA 59.793 38.462 12.15 1.48 0.00 2.69
167 168 6.775629 ACCCTTTGCTACAGTAGAATTGAAAA 59.224 34.615 12.15 1.50 0.00 2.29
168 169 7.286775 ACCCTTTGCTACAGTAGAATTGAAAAA 59.713 33.333 12.15 0.00 0.00 1.94
226 227 9.645059 TTACAACAAACATTGATGTCTTTTTCA 57.355 25.926 8.92 0.00 42.04 2.69
227 228 7.962917 ACAACAAACATTGATGTCTTTTTCAC 58.037 30.769 0.00 0.00 42.04 3.18
228 229 7.601886 ACAACAAACATTGATGTCTTTTTCACA 59.398 29.630 0.00 0.00 42.04 3.58
229 230 8.605746 CAACAAACATTGATGTCTTTTTCACAT 58.394 29.630 0.00 0.00 40.80 3.21
230 231 8.133754 ACAAACATTGATGTCTTTTTCACATG 57.866 30.769 0.00 0.00 40.80 3.21
231 232 6.774354 AACATTGATGTCTTTTTCACATGC 57.226 33.333 0.00 0.00 40.80 4.06
232 233 4.919168 ACATTGATGTCTTTTTCACATGCG 59.081 37.500 0.00 0.00 35.87 4.73
233 234 4.566545 TTGATGTCTTTTTCACATGCGT 57.433 36.364 0.00 0.00 34.49 5.24
234 235 3.887741 TGATGTCTTTTTCACATGCGTG 58.112 40.909 3.82 3.82 45.08 5.34
235 236 2.118228 TGTCTTTTTCACATGCGTGC 57.882 45.000 5.64 0.00 43.28 5.34
236 237 1.403323 TGTCTTTTTCACATGCGTGCA 59.597 42.857 5.64 0.00 43.28 4.57
237 238 2.159324 TGTCTTTTTCACATGCGTGCAA 60.159 40.909 5.64 0.00 43.28 4.08
238 239 2.857152 GTCTTTTTCACATGCGTGCAAA 59.143 40.909 5.64 2.61 43.28 3.68
239 240 3.305629 GTCTTTTTCACATGCGTGCAAAA 59.694 39.130 5.64 8.88 43.10 2.44
240 241 3.928992 TCTTTTTCACATGCGTGCAAAAA 59.071 34.783 20.09 20.09 44.11 1.94
241 242 4.569966 TCTTTTTCACATGCGTGCAAAAAT 59.430 33.333 20.97 0.00 44.11 1.82
242 243 4.871993 TTTTCACATGCGTGCAAAAATT 57.128 31.818 5.64 0.00 43.28 1.82
243 244 4.449870 TTTCACATGCGTGCAAAAATTC 57.550 36.364 5.64 0.00 43.28 2.17
244 245 3.089573 TCACATGCGTGCAAAAATTCA 57.910 38.095 5.64 0.00 43.28 2.57
245 246 3.651206 TCACATGCGTGCAAAAATTCAT 58.349 36.364 5.64 0.00 43.28 2.57
246 247 3.429207 TCACATGCGTGCAAAAATTCATG 59.571 39.130 5.64 0.00 43.28 3.07
247 248 3.429207 CACATGCGTGCAAAAATTCATGA 59.571 39.130 5.64 0.00 36.06 3.07
248 249 3.429543 ACATGCGTGCAAAAATTCATGAC 59.570 39.130 5.64 0.00 36.23 3.06
249 250 3.089573 TGCGTGCAAAAATTCATGACA 57.910 38.095 0.00 0.00 0.00 3.58
250 251 3.451526 TGCGTGCAAAAATTCATGACAA 58.548 36.364 0.00 0.00 0.00 3.18
251 252 3.867493 TGCGTGCAAAAATTCATGACAAA 59.133 34.783 0.00 0.00 0.00 2.83
252 253 4.330894 TGCGTGCAAAAATTCATGACAAAA 59.669 33.333 0.00 0.00 0.00 2.44
253 254 5.007430 TGCGTGCAAAAATTCATGACAAAAT 59.993 32.000 0.00 0.00 0.00 1.82
254 255 5.337512 GCGTGCAAAAATTCATGACAAAATG 59.662 36.000 0.00 0.00 0.00 2.32
255 256 6.647569 CGTGCAAAAATTCATGACAAAATGA 58.352 32.000 0.00 0.00 34.75 2.57
256 257 6.570789 CGTGCAAAAATTCATGACAAAATGAC 59.429 34.615 0.00 0.00 36.31 3.06
257 258 7.408123 GTGCAAAAATTCATGACAAAATGACA 58.592 30.769 0.00 0.00 36.31 3.58
258 259 8.071368 GTGCAAAAATTCATGACAAAATGACAT 58.929 29.630 0.00 0.00 36.31 3.06
259 260 8.622157 TGCAAAAATTCATGACAAAATGACATT 58.378 25.926 0.00 0.00 36.31 2.71
260 261 9.109533 GCAAAAATTCATGACAAAATGACATTC 57.890 29.630 0.05 0.00 36.31 2.67
264 265 6.954616 TTCATGACAAAATGACATTCATGC 57.045 33.333 17.52 10.10 42.15 4.06
265 266 6.026947 TCATGACAAAATGACATTCATGCA 57.973 33.333 17.52 13.69 42.15 3.96
266 267 6.096695 TCATGACAAAATGACATTCATGCAG 58.903 36.000 17.52 2.00 42.15 4.41
267 268 4.811908 TGACAAAATGACATTCATGCAGG 58.188 39.130 0.05 0.00 37.15 4.85
268 269 4.281435 TGACAAAATGACATTCATGCAGGT 59.719 37.500 0.05 0.00 37.15 4.00
269 270 4.813027 ACAAAATGACATTCATGCAGGTC 58.187 39.130 3.09 3.09 37.15 3.85
270 271 4.525487 ACAAAATGACATTCATGCAGGTCT 59.475 37.500 11.26 0.00 37.15 3.85
271 272 4.978083 AAATGACATTCATGCAGGTCTC 57.022 40.909 11.26 0.00 37.15 3.36
272 273 2.014335 TGACATTCATGCAGGTCTCG 57.986 50.000 11.26 0.00 0.00 4.04
273 274 1.293924 GACATTCATGCAGGTCTCGG 58.706 55.000 2.82 0.00 0.00 4.63
274 275 0.615331 ACATTCATGCAGGTCTCGGT 59.385 50.000 0.00 0.00 0.00 4.69
275 276 1.831106 ACATTCATGCAGGTCTCGGTA 59.169 47.619 0.00 0.00 0.00 4.02
276 277 2.236146 ACATTCATGCAGGTCTCGGTAA 59.764 45.455 0.00 0.00 0.00 2.85
277 278 3.270027 CATTCATGCAGGTCTCGGTAAA 58.730 45.455 0.00 0.00 0.00 2.01
278 279 3.410631 TTCATGCAGGTCTCGGTAAAA 57.589 42.857 0.00 0.00 0.00 1.52
279 280 3.410631 TCATGCAGGTCTCGGTAAAAA 57.589 42.857 0.00 0.00 0.00 1.94
302 303 8.770850 AAAAACAAAATCGATGCTTCAAAATG 57.229 26.923 0.00 0.00 0.00 2.32
303 304 5.520022 ACAAAATCGATGCTTCAAAATGC 57.480 34.783 0.00 0.00 0.00 3.56
304 305 5.232463 ACAAAATCGATGCTTCAAAATGCT 58.768 33.333 0.00 0.00 0.00 3.79
305 306 5.697633 ACAAAATCGATGCTTCAAAATGCTT 59.302 32.000 0.00 0.00 0.00 3.91
306 307 6.128742 ACAAAATCGATGCTTCAAAATGCTTC 60.129 34.615 0.00 0.00 0.00 3.86
307 308 3.492421 TCGATGCTTCAAAATGCTTCC 57.508 42.857 0.08 0.00 32.10 3.46
308 309 2.819019 TCGATGCTTCAAAATGCTTCCA 59.181 40.909 0.08 0.00 32.10 3.53
309 310 3.255395 TCGATGCTTCAAAATGCTTCCAA 59.745 39.130 0.08 0.00 32.10 3.53
310 311 3.989167 CGATGCTTCAAAATGCTTCCAAA 59.011 39.130 0.08 0.00 32.10 3.28
311 312 4.448395 CGATGCTTCAAAATGCTTCCAAAA 59.552 37.500 0.08 0.00 32.10 2.44
312 313 5.050227 CGATGCTTCAAAATGCTTCCAAAAA 60.050 36.000 0.08 0.00 32.10 1.94
313 314 6.347888 CGATGCTTCAAAATGCTTCCAAAAAT 60.348 34.615 0.08 0.00 32.10 1.82
314 315 7.148606 CGATGCTTCAAAATGCTTCCAAAAATA 60.149 33.333 0.08 0.00 32.10 1.40
315 316 7.424227 TGCTTCAAAATGCTTCCAAAAATAG 57.576 32.000 0.00 0.00 0.00 1.73
316 317 6.991531 TGCTTCAAAATGCTTCCAAAAATAGT 59.008 30.769 0.00 0.00 0.00 2.12
317 318 7.498570 TGCTTCAAAATGCTTCCAAAAATAGTT 59.501 29.630 0.00 0.00 0.00 2.24
318 319 8.344831 GCTTCAAAATGCTTCCAAAAATAGTTT 58.655 29.630 0.00 0.00 0.00 2.66
357 358 2.151502 TTTTTGTCAAGGCCTCCACA 57.848 45.000 5.23 9.48 0.00 4.17
358 359 2.151502 TTTTGTCAAGGCCTCCACAA 57.848 45.000 20.56 20.56 0.00 3.33
359 360 2.151502 TTTGTCAAGGCCTCCACAAA 57.848 45.000 27.09 27.09 36.60 2.83
360 361 2.380064 TTGTCAAGGCCTCCACAAAT 57.620 45.000 21.67 0.00 0.00 2.32
361 362 1.619654 TGTCAAGGCCTCCACAAATG 58.380 50.000 5.23 0.00 0.00 2.32
362 363 1.133513 TGTCAAGGCCTCCACAAATGT 60.134 47.619 5.23 0.00 0.00 2.71
363 364 1.541588 GTCAAGGCCTCCACAAATGTC 59.458 52.381 5.23 0.00 0.00 3.06
364 365 1.144708 TCAAGGCCTCCACAAATGTCA 59.855 47.619 5.23 0.00 0.00 3.58
365 366 2.173519 CAAGGCCTCCACAAATGTCAT 58.826 47.619 5.23 0.00 0.00 3.06
366 367 2.564062 CAAGGCCTCCACAAATGTCATT 59.436 45.455 5.23 0.00 0.00 2.57
367 368 2.893424 AGGCCTCCACAAATGTCATTT 58.107 42.857 0.00 4.91 0.00 2.32
368 369 2.827921 AGGCCTCCACAAATGTCATTTC 59.172 45.455 7.87 0.00 0.00 2.17
369 370 2.562298 GGCCTCCACAAATGTCATTTCA 59.438 45.455 7.87 0.00 0.00 2.69
370 371 3.196254 GGCCTCCACAAATGTCATTTCAT 59.804 43.478 7.87 0.00 0.00 2.57
371 372 4.427312 GCCTCCACAAATGTCATTTCATC 58.573 43.478 7.87 0.00 0.00 2.92
372 373 4.082081 GCCTCCACAAATGTCATTTCATCA 60.082 41.667 7.87 0.00 0.00 3.07
373 374 5.394883 GCCTCCACAAATGTCATTTCATCAT 60.395 40.000 7.87 0.00 0.00 2.45
374 375 6.040247 CCTCCACAAATGTCATTTCATCATG 58.960 40.000 7.87 0.00 0.00 3.07
375 376 6.127563 CCTCCACAAATGTCATTTCATCATGA 60.128 38.462 7.87 0.00 0.00 3.07
376 377 7.229581 TCCACAAATGTCATTTCATCATGAA 57.770 32.000 7.87 0.00 34.89 2.57
387 388 2.878580 TCATCATGAAAATTGGCACGC 58.121 42.857 0.00 0.00 0.00 5.34
388 389 2.230750 TCATCATGAAAATTGGCACGCA 59.769 40.909 0.00 0.00 0.00 5.24
389 390 3.119065 TCATCATGAAAATTGGCACGCAT 60.119 39.130 0.00 0.00 0.00 4.73
390 391 2.608268 TCATGAAAATTGGCACGCATG 58.392 42.857 0.00 0.00 35.63 4.06
391 392 2.029200 TCATGAAAATTGGCACGCATGT 60.029 40.909 0.00 0.00 35.75 3.21
404 405 2.984562 ACGCATGTGAACCATACATCA 58.015 42.857 14.43 0.00 36.67 3.07
405 406 3.342719 ACGCATGTGAACCATACATCAA 58.657 40.909 14.43 0.00 36.67 2.57
406 407 3.947196 ACGCATGTGAACCATACATCAAT 59.053 39.130 14.43 0.00 36.67 2.57
407 408 4.201940 ACGCATGTGAACCATACATCAATG 60.202 41.667 14.43 0.00 36.67 2.82
408 409 4.035441 CGCATGTGAACCATACATCAATGA 59.965 41.667 0.00 0.00 36.67 2.57
409 410 5.278120 CGCATGTGAACCATACATCAATGAT 60.278 40.000 0.00 0.00 36.67 2.45
410 411 6.509656 GCATGTGAACCATACATCAATGATT 58.490 36.000 0.00 0.00 36.67 2.57
411 412 6.419710 GCATGTGAACCATACATCAATGATTG 59.580 38.462 0.00 0.00 36.67 2.67
412 413 7.485810 CATGTGAACCATACATCAATGATTGT 58.514 34.615 4.93 0.00 36.67 2.71
413 414 7.465353 TGTGAACCATACATCAATGATTGTT 57.535 32.000 4.93 0.00 0.00 2.83
414 415 7.314393 TGTGAACCATACATCAATGATTGTTG 58.686 34.615 13.17 13.17 36.63 3.33
415 416 7.176340 TGTGAACCATACATCAATGATTGTTGA 59.824 33.333 19.76 6.93 41.88 3.18
416 417 7.485913 GTGAACCATACATCAATGATTGTTGAC 59.514 37.037 19.76 4.57 40.60 3.18
417 418 7.176340 TGAACCATACATCAATGATTGTTGACA 59.824 33.333 19.76 9.49 40.60 3.58
418 419 7.465353 ACCATACATCAATGATTGTTGACAA 57.535 32.000 19.76 0.00 40.60 3.18
419 420 7.894708 ACCATACATCAATGATTGTTGACAAA 58.105 30.769 19.76 5.81 40.60 2.83
420 421 8.366401 ACCATACATCAATGATTGTTGACAAAA 58.634 29.630 19.76 3.88 40.60 2.44
421 422 9.205719 CCATACATCAATGATTGTTGACAAAAA 57.794 29.630 19.76 0.00 40.60 1.94
476 477 7.876896 TTTTTCGATTTTATTGTAAGGGTGC 57.123 32.000 0.00 0.00 0.00 5.01
477 478 6.576662 TTTCGATTTTATTGTAAGGGTGCA 57.423 33.333 0.00 0.00 0.00 4.57
478 479 6.767524 TTCGATTTTATTGTAAGGGTGCAT 57.232 33.333 0.00 0.00 0.00 3.96
479 480 6.130298 TCGATTTTATTGTAAGGGTGCATG 57.870 37.500 0.00 0.00 0.00 4.06
480 481 5.650266 TCGATTTTATTGTAAGGGTGCATGT 59.350 36.000 0.00 0.00 0.00 3.21
481 482 5.743398 CGATTTTATTGTAAGGGTGCATGTG 59.257 40.000 0.00 0.00 0.00 3.21
482 483 6.404184 CGATTTTATTGTAAGGGTGCATGTGA 60.404 38.462 0.00 0.00 0.00 3.58
483 484 5.895636 TTTATTGTAAGGGTGCATGTGAG 57.104 39.130 0.00 0.00 0.00 3.51
484 485 1.533625 TTGTAAGGGTGCATGTGAGC 58.466 50.000 0.00 0.00 0.00 4.26
485 486 0.692476 TGTAAGGGTGCATGTGAGCT 59.308 50.000 0.00 0.00 34.99 4.09
486 487 1.339055 TGTAAGGGTGCATGTGAGCTC 60.339 52.381 6.82 6.82 34.99 4.09
487 488 0.108186 TAAGGGTGCATGTGAGCTCG 60.108 55.000 9.64 0.00 34.99 5.03
488 489 1.830587 AAGGGTGCATGTGAGCTCGA 61.831 55.000 9.64 0.00 34.99 4.04
489 490 1.812922 GGGTGCATGTGAGCTCGAG 60.813 63.158 8.45 8.45 34.99 4.04
490 491 2.459442 GGTGCATGTGAGCTCGAGC 61.459 63.158 30.01 30.01 42.49 5.03
503 504 3.850657 GCTCGAGCTCACATAAATGTC 57.149 47.619 29.88 0.00 37.17 3.06
504 505 2.541762 GCTCGAGCTCACATAAATGTCC 59.458 50.000 29.88 0.00 37.17 4.02
505 506 3.126831 CTCGAGCTCACATAAATGTCCC 58.873 50.000 15.40 0.00 39.39 4.46
506 507 2.766263 TCGAGCTCACATAAATGTCCCT 59.234 45.455 15.40 0.00 39.39 4.20
507 508 2.868583 CGAGCTCACATAAATGTCCCTG 59.131 50.000 15.40 0.00 39.39 4.45
508 509 3.679917 CGAGCTCACATAAATGTCCCTGT 60.680 47.826 15.40 0.00 39.39 4.00
509 510 4.265073 GAGCTCACATAAATGTCCCTGTT 58.735 43.478 9.40 0.00 39.39 3.16
510 511 4.012374 AGCTCACATAAATGTCCCTGTTG 58.988 43.478 0.00 0.00 39.39 3.33
511 512 4.009675 GCTCACATAAATGTCCCTGTTGA 58.990 43.478 0.00 0.00 39.39 3.18
512 513 4.458989 GCTCACATAAATGTCCCTGTTGAA 59.541 41.667 0.00 0.00 39.39 2.69
513 514 5.392380 GCTCACATAAATGTCCCTGTTGAAG 60.392 44.000 0.00 0.00 39.39 3.02
514 515 5.875224 TCACATAAATGTCCCTGTTGAAGA 58.125 37.500 0.00 0.00 39.39 2.87
515 516 6.484288 TCACATAAATGTCCCTGTTGAAGAT 58.516 36.000 0.00 0.00 39.39 2.40
516 517 6.375174 TCACATAAATGTCCCTGTTGAAGATG 59.625 38.462 0.00 0.00 39.39 2.90
517 518 6.375174 CACATAAATGTCCCTGTTGAAGATGA 59.625 38.462 0.00 0.00 39.39 2.92
518 519 7.067859 CACATAAATGTCCCTGTTGAAGATGAT 59.932 37.037 0.00 0.00 39.39 2.45
519 520 8.274322 ACATAAATGTCCCTGTTGAAGATGATA 58.726 33.333 0.00 0.00 35.87 2.15
520 521 8.781196 CATAAATGTCCCTGTTGAAGATGATAG 58.219 37.037 0.00 0.00 0.00 2.08
521 522 4.142609 TGTCCCTGTTGAAGATGATAGC 57.857 45.455 0.00 0.00 0.00 2.97
522 523 3.776969 TGTCCCTGTTGAAGATGATAGCT 59.223 43.478 0.00 0.00 0.00 3.32
523 524 4.225942 TGTCCCTGTTGAAGATGATAGCTT 59.774 41.667 0.00 0.00 0.00 3.74
524 525 4.813697 GTCCCTGTTGAAGATGATAGCTTC 59.186 45.833 0.00 0.20 41.57 3.86
525 526 4.133078 CCCTGTTGAAGATGATAGCTTCC 58.867 47.826 0.00 0.00 40.73 3.46
526 527 4.141528 CCCTGTTGAAGATGATAGCTTCCT 60.142 45.833 0.00 0.00 40.73 3.36
533 535 6.240894 TGAAGATGATAGCTTCCTTGTGTTT 58.759 36.000 0.00 0.00 40.73 2.83
534 536 7.394016 TGAAGATGATAGCTTCCTTGTGTTTA 58.606 34.615 0.00 0.00 40.73 2.01
536 538 8.814038 AAGATGATAGCTTCCTTGTGTTTATT 57.186 30.769 0.00 0.00 0.00 1.40
552 554 8.902540 TGTGTTTATTACTCATTTCTGTCTGT 57.097 30.769 0.00 0.00 0.00 3.41
564 566 7.694886 TCATTTCTGTCTGTATGTAGTCTACG 58.305 38.462 5.55 0.00 0.00 3.51
598 600 8.560355 TCGAAAACATCTTCCATTCATCTTTA 57.440 30.769 0.00 0.00 0.00 1.85
602 604 8.655935 AAACATCTTCCATTCATCTTTACCTT 57.344 30.769 0.00 0.00 0.00 3.50
613 615 6.485830 TCATCTTTACCTTACAGGAGATGG 57.514 41.667 15.16 0.00 41.22 3.51
622 624 6.262207 ACCTTACAGGAGATGGTTTACTAGT 58.738 40.000 0.00 0.00 37.67 2.57
643 645 7.927629 ACTAGTAACCGTTGAAGATTGTAAACA 59.072 33.333 0.00 0.00 0.00 2.83
723 726 1.764571 TTGGTTGGCCGACTAGCAGT 61.765 55.000 22.72 0.00 37.67 4.40
750 756 2.947127 AGCTTCAGAAGAAAGGCAGT 57.053 45.000 14.86 0.00 32.35 4.40
796 805 3.741029 TGCGATCTTGCAGACTACC 57.259 52.632 0.00 0.00 40.62 3.18
836 845 4.377431 GCATCAAAGACTCCACACTTTACG 60.377 45.833 0.00 0.00 35.07 3.18
858 867 2.029649 CGAAACCCCTCGTAGTTCTTCA 60.030 50.000 0.00 0.00 34.08 3.02
895 914 4.677151 ACCCCGCTTCCTTCCCCT 62.677 66.667 0.00 0.00 0.00 4.79
899 918 1.687493 CCGCTTCCTTCCCCTCTCT 60.687 63.158 0.00 0.00 0.00 3.10
900 919 1.519719 CGCTTCCTTCCCCTCTCTG 59.480 63.158 0.00 0.00 0.00 3.35
901 920 1.261238 CGCTTCCTTCCCCTCTCTGT 61.261 60.000 0.00 0.00 0.00 3.41
1404 1427 2.668280 GGACGCCGTCAAGCTCAAC 61.668 63.158 20.08 0.00 33.68 3.18
1660 1683 2.743664 CTGTGAACAATGATCGGCTTGA 59.256 45.455 8.86 0.00 0.00 3.02
1671 1694 2.099141 TCGGCTTGATTCAGAGTTGG 57.901 50.000 0.00 0.00 0.00 3.77
1678 1701 4.759183 GCTTGATTCAGAGTTGGTTCTTCT 59.241 41.667 0.00 0.00 0.00 2.85
1794 1817 1.972588 AAGTTGCCCCCTACAGATCT 58.027 50.000 0.00 0.00 0.00 2.75
1807 1830 7.202093 CCCCCTACAGATCTATTGTTTCATACA 60.202 40.741 0.00 0.00 34.12 2.29
1851 1874 4.812091 TGTATTCAGCGTACAGTGTGTTTT 59.188 37.500 5.88 0.00 0.00 2.43
1910 1933 2.687935 TGGTTTTGTTCTGAGCTGTTCC 59.312 45.455 0.00 0.00 0.00 3.62
2010 2033 8.721478 GTTCTATTCTTTGTCAATAACAGAGCA 58.279 33.333 0.00 0.00 39.40 4.26
2028 2051 9.783081 AACAGAGCAAATTTTATGAAAAATCCT 57.217 25.926 0.00 0.00 43.04 3.24
2098 2127 7.774625 TGATGTCCATCAATTGTAGAATGCTTA 59.225 33.333 7.49 0.00 44.14 3.09
2133 2162 9.618890 CTTTCTATTGGATATGTTTCTTCTCCA 57.381 33.333 0.00 0.00 34.27 3.86
2157 2186 7.972277 CCATCAATAATATGGAGCAATAAGTGC 59.028 37.037 0.00 0.00 45.77 4.40
2348 2377 3.935203 GTCATGATGTGTCTACACTTGGG 59.065 47.826 13.95 1.61 46.55 4.12
2406 2436 9.656323 TTAGTATGGATAGTGTATTCCAACTCT 57.344 33.333 0.00 0.00 35.71 3.24
2407 2437 7.957002 AGTATGGATAGTGTATTCCAACTCTG 58.043 38.462 0.00 0.00 35.71 3.35
2408 2438 6.814954 ATGGATAGTGTATTCCAACTCTGT 57.185 37.500 0.00 0.00 35.71 3.41
2428 2458 8.304596 ACTCTGTTACTTCTCGATGTCAATAAA 58.695 33.333 0.00 0.00 0.00 1.40
2430 2460 8.520351 TCTGTTACTTCTCGATGTCAATAAAGA 58.480 33.333 0.00 0.00 0.00 2.52
2472 2502 9.621629 TTCTGAATTGTTCCTTTCTTTGTACTA 57.378 29.630 0.00 0.00 0.00 1.82
2525 2555 9.630098 GCCATCAATATGTGTAATTTGGATTAG 57.370 33.333 0.00 0.00 0.00 1.73
2567 2597 8.618702 ATGATAAAAATGCATTTTTGTGTGGA 57.381 26.923 40.73 28.32 46.17 4.02
2570 2600 9.384682 GATAAAAATGCATTTTTGTGTGGAAAG 57.615 29.630 40.73 0.00 46.17 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.943033 CCCGCAACTCCCTAGTAAATTG 59.057 50.000 0.00 0.00 33.75 2.32
20 21 4.373156 AGAAATATGTATGGGGTGCTCC 57.627 45.455 0.00 0.00 0.00 4.70
21 22 6.360370 TCTAGAAATATGTATGGGGTGCTC 57.640 41.667 0.00 0.00 0.00 4.26
127 128 1.812922 GGGTGCATGTGAGCTCGAG 60.813 63.158 8.45 8.45 34.99 4.04
128 129 1.830587 AAGGGTGCATGTGAGCTCGA 61.831 55.000 9.64 0.00 34.99 4.04
129 130 0.957395 AAAGGGTGCATGTGAGCTCG 60.957 55.000 9.64 0.00 34.99 5.03
130 131 0.524862 CAAAGGGTGCATGTGAGCTC 59.475 55.000 6.82 6.82 34.99 4.09
141 142 5.245531 TCAATTCTACTGTAGCAAAGGGTG 58.754 41.667 9.98 2.14 0.00 4.61
142 143 5.499004 TCAATTCTACTGTAGCAAAGGGT 57.501 39.130 9.98 0.00 0.00 4.34
143 144 6.817765 TTTCAATTCTACTGTAGCAAAGGG 57.182 37.500 9.98 0.00 0.00 3.95
200 201 9.645059 TGAAAAAGACATCAATGTTTGTTGTAA 57.355 25.926 0.00 0.00 42.05 2.41
201 202 9.081997 GTGAAAAAGACATCAATGTTTGTTGTA 57.918 29.630 0.00 0.00 42.05 2.41
202 203 7.601886 TGTGAAAAAGACATCAATGTTTGTTGT 59.398 29.630 4.15 4.15 44.00 3.32
203 204 7.961855 TGTGAAAAAGACATCAATGTTTGTTG 58.038 30.769 0.00 0.00 41.95 3.33
204 205 8.605746 CATGTGAAAAAGACATCAATGTTTGTT 58.394 29.630 0.00 0.00 41.95 2.83
205 206 7.254522 GCATGTGAAAAAGACATCAATGTTTGT 60.255 33.333 0.00 0.00 41.95 2.83
206 207 7.067116 GCATGTGAAAAAGACATCAATGTTTG 58.933 34.615 0.00 0.00 41.95 2.93
207 208 6.074195 CGCATGTGAAAAAGACATCAATGTTT 60.074 34.615 0.00 0.00 41.95 2.83
208 209 5.403166 CGCATGTGAAAAAGACATCAATGTT 59.597 36.000 0.00 0.00 41.95 2.71
209 210 4.919168 CGCATGTGAAAAAGACATCAATGT 59.081 37.500 0.00 0.00 45.16 2.71
210 211 4.919168 ACGCATGTGAAAAAGACATCAATG 59.081 37.500 14.43 0.00 0.00 2.82
211 212 5.125100 ACGCATGTGAAAAAGACATCAAT 57.875 34.783 14.43 0.00 0.00 2.57
212 213 4.566545 ACGCATGTGAAAAAGACATCAA 57.433 36.364 14.43 0.00 0.00 2.57
226 227 3.429543 GTCATGAATTTTTGCACGCATGT 59.570 39.130 0.00 0.00 35.75 3.21
227 228 3.429207 TGTCATGAATTTTTGCACGCATG 59.571 39.130 0.00 0.00 35.63 4.06
228 229 3.651206 TGTCATGAATTTTTGCACGCAT 58.349 36.364 0.00 0.00 0.00 4.73
229 230 3.089573 TGTCATGAATTTTTGCACGCA 57.910 38.095 0.00 0.00 0.00 5.24
230 231 4.449870 TTTGTCATGAATTTTTGCACGC 57.550 36.364 0.00 0.00 0.00 5.34
231 232 6.570789 GTCATTTTGTCATGAATTTTTGCACG 59.429 34.615 0.00 0.00 34.89 5.34
232 233 7.408123 TGTCATTTTGTCATGAATTTTTGCAC 58.592 30.769 0.00 0.00 34.89 4.57
233 234 7.549615 TGTCATTTTGTCATGAATTTTTGCA 57.450 28.000 0.00 0.00 34.89 4.08
234 235 9.109533 GAATGTCATTTTGTCATGAATTTTTGC 57.890 29.630 0.00 0.00 34.89 3.68
238 239 8.447833 GCATGAATGTCATTTTGTCATGAATTT 58.552 29.630 21.57 0.00 45.44 1.82
239 240 7.604545 TGCATGAATGTCATTTTGTCATGAATT 59.395 29.630 21.57 0.00 45.44 2.17
240 241 7.100409 TGCATGAATGTCATTTTGTCATGAAT 58.900 30.769 21.57 0.00 45.44 2.57
241 242 6.456501 TGCATGAATGTCATTTTGTCATGAA 58.543 32.000 21.57 13.06 45.44 2.57
242 243 6.026947 TGCATGAATGTCATTTTGTCATGA 57.973 33.333 21.57 9.62 45.44 3.07
243 244 5.290885 CCTGCATGAATGTCATTTTGTCATG 59.709 40.000 16.16 16.16 45.40 3.07
244 245 5.046878 ACCTGCATGAATGTCATTTTGTCAT 60.047 36.000 0.00 0.00 34.28 3.06
245 246 4.281435 ACCTGCATGAATGTCATTTTGTCA 59.719 37.500 0.00 0.00 34.28 3.58
246 247 4.813027 ACCTGCATGAATGTCATTTTGTC 58.187 39.130 0.00 0.01 34.28 3.18
247 248 4.525487 AGACCTGCATGAATGTCATTTTGT 59.475 37.500 11.29 0.00 34.28 2.83
248 249 5.068234 AGACCTGCATGAATGTCATTTTG 57.932 39.130 11.29 2.73 34.28 2.44
249 250 4.142534 CGAGACCTGCATGAATGTCATTTT 60.143 41.667 11.29 0.00 34.28 1.82
250 251 3.376234 CGAGACCTGCATGAATGTCATTT 59.624 43.478 11.29 0.00 34.28 2.32
251 252 2.941064 CGAGACCTGCATGAATGTCATT 59.059 45.455 11.29 0.00 34.28 2.57
252 253 2.558378 CGAGACCTGCATGAATGTCAT 58.442 47.619 11.29 0.00 37.65 3.06
253 254 1.405933 CCGAGACCTGCATGAATGTCA 60.406 52.381 11.29 0.00 0.00 3.58
254 255 1.293924 CCGAGACCTGCATGAATGTC 58.706 55.000 0.00 0.00 0.00 3.06
255 256 0.615331 ACCGAGACCTGCATGAATGT 59.385 50.000 0.00 0.00 0.00 2.71
256 257 2.602257 TACCGAGACCTGCATGAATG 57.398 50.000 0.00 0.00 0.00 2.67
257 258 3.627395 TTTACCGAGACCTGCATGAAT 57.373 42.857 0.00 0.00 0.00 2.57
258 259 3.410631 TTTTACCGAGACCTGCATGAA 57.589 42.857 0.00 0.00 0.00 2.57
259 260 3.410631 TTTTTACCGAGACCTGCATGA 57.589 42.857 0.00 0.00 0.00 3.07
277 278 7.376601 GCATTTTGAAGCATCGATTTTGTTTTT 59.623 29.630 0.00 0.00 0.00 1.94
278 279 6.852345 GCATTTTGAAGCATCGATTTTGTTTT 59.148 30.769 0.00 0.00 0.00 2.43
279 280 6.203338 AGCATTTTGAAGCATCGATTTTGTTT 59.797 30.769 0.00 0.00 0.00 2.83
280 281 5.697633 AGCATTTTGAAGCATCGATTTTGTT 59.302 32.000 0.00 0.00 0.00 2.83
281 282 5.232463 AGCATTTTGAAGCATCGATTTTGT 58.768 33.333 0.00 0.00 0.00 2.83
282 283 5.773239 AGCATTTTGAAGCATCGATTTTG 57.227 34.783 0.00 0.00 0.00 2.44
283 284 5.349543 GGAAGCATTTTGAAGCATCGATTTT 59.650 36.000 0.00 0.00 29.82 1.82
284 285 4.866486 GGAAGCATTTTGAAGCATCGATTT 59.134 37.500 0.00 0.00 29.82 2.17
285 286 4.082081 TGGAAGCATTTTGAAGCATCGATT 60.082 37.500 0.00 0.00 29.82 3.34
286 287 3.444742 TGGAAGCATTTTGAAGCATCGAT 59.555 39.130 0.00 0.00 29.82 3.59
287 288 2.819019 TGGAAGCATTTTGAAGCATCGA 59.181 40.909 0.00 0.00 29.82 3.59
288 289 3.220507 TGGAAGCATTTTGAAGCATCG 57.779 42.857 0.00 0.00 29.82 3.84
289 290 5.927954 TTTTGGAAGCATTTTGAAGCATC 57.072 34.783 0.00 0.00 0.00 3.91
290 291 6.887626 ATTTTTGGAAGCATTTTGAAGCAT 57.112 29.167 0.00 0.00 0.00 3.79
291 292 6.991531 ACTATTTTTGGAAGCATTTTGAAGCA 59.008 30.769 0.00 0.00 0.00 3.91
292 293 7.425577 ACTATTTTTGGAAGCATTTTGAAGC 57.574 32.000 0.00 0.00 0.00 3.86
338 339 2.151502 TGTGGAGGCCTTGACAAAAA 57.848 45.000 6.77 0.00 0.00 1.94
339 340 2.151502 TTGTGGAGGCCTTGACAAAA 57.848 45.000 22.05 13.99 0.00 2.44
340 341 2.151502 TTTGTGGAGGCCTTGACAAA 57.848 45.000 27.30 27.30 36.27 2.83
341 342 1.962807 CATTTGTGGAGGCCTTGACAA 59.037 47.619 20.97 20.97 0.00 3.18
342 343 1.133513 ACATTTGTGGAGGCCTTGACA 60.134 47.619 6.77 10.49 0.00 3.58
343 344 1.541588 GACATTTGTGGAGGCCTTGAC 59.458 52.381 6.77 7.51 0.00 3.18
344 345 1.144708 TGACATTTGTGGAGGCCTTGA 59.855 47.619 6.77 0.00 0.00 3.02
345 346 1.619654 TGACATTTGTGGAGGCCTTG 58.380 50.000 6.77 0.69 0.00 3.61
346 347 2.610438 ATGACATTTGTGGAGGCCTT 57.390 45.000 6.77 0.00 0.00 4.35
347 348 2.610438 AATGACATTTGTGGAGGCCT 57.390 45.000 3.86 3.86 0.00 5.19
348 349 2.562298 TGAAATGACATTTGTGGAGGCC 59.438 45.455 18.00 0.00 31.47 5.19
349 350 3.940209 TGAAATGACATTTGTGGAGGC 57.060 42.857 18.00 2.75 31.47 4.70
350 351 5.648178 TGATGAAATGACATTTGTGGAGG 57.352 39.130 18.00 0.00 31.47 4.30
351 352 6.859017 TCATGATGAAATGACATTTGTGGAG 58.141 36.000 18.00 4.29 31.58 3.86
352 353 6.837471 TCATGATGAAATGACATTTGTGGA 57.163 33.333 18.00 4.61 31.58 4.02
353 354 7.892778 TTTCATGATGAAATGACATTTGTGG 57.107 32.000 18.00 2.52 41.02 4.17
356 357 9.767684 CCAATTTTCATGATGAAATGACATTTG 57.232 29.630 20.04 15.11 44.75 2.32
357 358 8.455682 GCCAATTTTCATGATGAAATGACATTT 58.544 29.630 20.04 13.24 44.75 2.32
358 359 7.608376 TGCCAATTTTCATGATGAAATGACATT 59.392 29.630 20.04 13.78 44.75 2.71
359 360 7.065324 GTGCCAATTTTCATGATGAAATGACAT 59.935 33.333 20.04 8.87 44.75 3.06
360 361 6.369340 GTGCCAATTTTCATGATGAAATGACA 59.631 34.615 20.04 12.62 44.75 3.58
361 362 6.454583 CGTGCCAATTTTCATGATGAAATGAC 60.455 38.462 20.04 10.37 44.75 3.06
362 363 5.577554 CGTGCCAATTTTCATGATGAAATGA 59.422 36.000 20.04 7.97 44.75 2.57
363 364 5.725590 GCGTGCCAATTTTCATGATGAAATG 60.726 40.000 20.04 15.77 44.75 2.32
364 365 4.330620 GCGTGCCAATTTTCATGATGAAAT 59.669 37.500 20.04 4.92 44.75 2.17
365 366 3.679025 GCGTGCCAATTTTCATGATGAAA 59.321 39.130 16.04 16.04 43.84 2.69
366 367 3.252400 GCGTGCCAATTTTCATGATGAA 58.748 40.909 3.29 3.29 34.03 2.57
367 368 2.230750 TGCGTGCCAATTTTCATGATGA 59.769 40.909 0.00 0.00 0.00 2.92
368 369 2.608268 TGCGTGCCAATTTTCATGATG 58.392 42.857 0.00 0.00 0.00 3.07
369 370 3.191669 CATGCGTGCCAATTTTCATGAT 58.808 40.909 0.00 0.00 34.79 2.45
370 371 2.029200 ACATGCGTGCCAATTTTCATGA 60.029 40.909 5.64 0.00 36.23 3.07
371 372 2.092995 CACATGCGTGCCAATTTTCATG 59.907 45.455 5.64 0.00 36.06 3.07
372 373 2.029200 TCACATGCGTGCCAATTTTCAT 60.029 40.909 5.64 0.00 43.28 2.57
373 374 1.339291 TCACATGCGTGCCAATTTTCA 59.661 42.857 5.64 0.00 43.28 2.69
374 375 2.063156 TCACATGCGTGCCAATTTTC 57.937 45.000 5.64 0.00 43.28 2.29
375 376 2.134346 GTTCACATGCGTGCCAATTTT 58.866 42.857 5.64 0.00 43.28 1.82
376 377 1.605202 GGTTCACATGCGTGCCAATTT 60.605 47.619 5.64 0.00 43.28 1.82
377 378 0.038343 GGTTCACATGCGTGCCAATT 60.038 50.000 5.64 0.00 43.28 2.32
378 379 1.177895 TGGTTCACATGCGTGCCAAT 61.178 50.000 5.64 0.00 43.28 3.16
379 380 1.177895 ATGGTTCACATGCGTGCCAA 61.178 50.000 5.64 0.00 43.28 4.52
380 381 0.322008 TATGGTTCACATGCGTGCCA 60.322 50.000 5.64 5.61 43.28 4.92
381 382 0.098728 GTATGGTTCACATGCGTGCC 59.901 55.000 5.64 0.00 43.28 5.01
382 383 0.801872 TGTATGGTTCACATGCGTGC 59.198 50.000 5.64 0.00 44.14 5.34
383 384 2.677337 TGATGTATGGTTCACATGCGTG 59.323 45.455 3.82 3.82 44.14 5.34
384 385 2.984562 TGATGTATGGTTCACATGCGT 58.015 42.857 0.00 0.00 44.14 5.24
385 386 4.035441 TCATTGATGTATGGTTCACATGCG 59.965 41.667 0.00 0.00 44.14 4.73
386 387 5.503662 TCATTGATGTATGGTTCACATGC 57.496 39.130 0.00 0.00 40.82 4.06
387 388 7.485810 ACAATCATTGATGTATGGTTCACATG 58.514 34.615 3.79 0.00 40.82 3.21
388 389 7.649533 ACAATCATTGATGTATGGTTCACAT 57.350 32.000 3.79 0.00 43.68 3.21
389 390 7.176340 TCAACAATCATTGATGTATGGTTCACA 59.824 33.333 3.79 0.00 33.62 3.58
390 391 7.485913 GTCAACAATCATTGATGTATGGTTCAC 59.514 37.037 3.79 0.00 40.60 3.18
391 392 7.176340 TGTCAACAATCATTGATGTATGGTTCA 59.824 33.333 3.79 0.00 40.60 3.18
392 393 7.537715 TGTCAACAATCATTGATGTATGGTTC 58.462 34.615 3.79 0.00 40.60 3.62
393 394 7.465353 TGTCAACAATCATTGATGTATGGTT 57.535 32.000 3.79 0.00 40.60 3.67
394 395 7.465353 TTGTCAACAATCATTGATGTATGGT 57.535 32.000 3.79 0.00 40.60 3.55
395 396 8.760103 TTTTGTCAACAATCATTGATGTATGG 57.240 30.769 3.79 0.00 40.60 2.74
452 453 7.434492 TGCACCCTTACAATAAAATCGAAAAA 58.566 30.769 0.00 0.00 0.00 1.94
453 454 6.982852 TGCACCCTTACAATAAAATCGAAAA 58.017 32.000 0.00 0.00 0.00 2.29
454 455 6.576662 TGCACCCTTACAATAAAATCGAAA 57.423 33.333 0.00 0.00 0.00 3.46
455 456 6.151985 ACATGCACCCTTACAATAAAATCGAA 59.848 34.615 0.00 0.00 0.00 3.71
456 457 5.650266 ACATGCACCCTTACAATAAAATCGA 59.350 36.000 0.00 0.00 0.00 3.59
457 458 5.743398 CACATGCACCCTTACAATAAAATCG 59.257 40.000 0.00 0.00 0.00 3.34
458 459 6.862209 TCACATGCACCCTTACAATAAAATC 58.138 36.000 0.00 0.00 0.00 2.17
459 460 6.627953 GCTCACATGCACCCTTACAATAAAAT 60.628 38.462 0.00 0.00 0.00 1.82
460 461 5.336372 GCTCACATGCACCCTTACAATAAAA 60.336 40.000 0.00 0.00 0.00 1.52
461 462 4.157656 GCTCACATGCACCCTTACAATAAA 59.842 41.667 0.00 0.00 0.00 1.40
462 463 3.694072 GCTCACATGCACCCTTACAATAA 59.306 43.478 0.00 0.00 0.00 1.40
463 464 3.054434 AGCTCACATGCACCCTTACAATA 60.054 43.478 0.00 0.00 34.99 1.90
464 465 2.094675 GCTCACATGCACCCTTACAAT 58.905 47.619 0.00 0.00 0.00 2.71
465 466 1.073763 AGCTCACATGCACCCTTACAA 59.926 47.619 0.00 0.00 34.99 2.41
466 467 0.692476 AGCTCACATGCACCCTTACA 59.308 50.000 0.00 0.00 34.99 2.41
467 468 1.373570 GAGCTCACATGCACCCTTAC 58.626 55.000 9.40 0.00 34.99 2.34
468 469 0.108186 CGAGCTCACATGCACCCTTA 60.108 55.000 15.40 0.00 34.99 2.69
469 470 1.376424 CGAGCTCACATGCACCCTT 60.376 57.895 15.40 0.00 34.99 3.95
470 471 2.236223 CTCGAGCTCACATGCACCCT 62.236 60.000 15.40 0.00 34.99 4.34
471 472 1.812922 CTCGAGCTCACATGCACCC 60.813 63.158 15.40 0.00 34.99 4.61
472 473 2.459442 GCTCGAGCTCACATGCACC 61.459 63.158 29.88 0.00 38.21 5.01
473 474 3.088044 GCTCGAGCTCACATGCAC 58.912 61.111 29.88 0.00 38.21 4.57
482 483 3.533606 ACATTTATGTGAGCTCGAGCT 57.466 42.857 38.87 38.87 43.61 4.09
483 484 2.541762 GGACATTTATGTGAGCTCGAGC 59.458 50.000 30.01 30.01 41.95 5.03
484 485 3.126831 GGGACATTTATGTGAGCTCGAG 58.873 50.000 8.45 8.45 41.95 4.04
485 486 2.766263 AGGGACATTTATGTGAGCTCGA 59.234 45.455 9.64 0.00 41.95 4.04
486 487 2.868583 CAGGGACATTTATGTGAGCTCG 59.131 50.000 9.64 0.00 41.95 5.03
487 488 3.878778 ACAGGGACATTTATGTGAGCTC 58.121 45.455 6.82 6.82 41.95 4.09
488 489 4.012374 CAACAGGGACATTTATGTGAGCT 58.988 43.478 0.00 0.00 41.95 4.09
489 490 4.009675 TCAACAGGGACATTTATGTGAGC 58.990 43.478 0.00 0.00 41.95 4.26
490 491 5.939883 TCTTCAACAGGGACATTTATGTGAG 59.060 40.000 0.00 0.00 41.95 3.51
491 492 5.875224 TCTTCAACAGGGACATTTATGTGA 58.125 37.500 0.00 0.00 41.95 3.58
492 493 6.375174 TCATCTTCAACAGGGACATTTATGTG 59.625 38.462 0.00 0.00 41.95 3.21
493 494 6.484288 TCATCTTCAACAGGGACATTTATGT 58.516 36.000 0.00 0.00 45.16 2.29
494 495 7.578310 ATCATCTTCAACAGGGACATTTATG 57.422 36.000 0.00 0.00 0.00 1.90
495 496 7.446625 GCTATCATCTTCAACAGGGACATTTAT 59.553 37.037 0.00 0.00 0.00 1.40
496 497 6.767902 GCTATCATCTTCAACAGGGACATTTA 59.232 38.462 0.00 0.00 0.00 1.40
497 498 5.591877 GCTATCATCTTCAACAGGGACATTT 59.408 40.000 0.00 0.00 0.00 2.32
498 499 5.104193 AGCTATCATCTTCAACAGGGACATT 60.104 40.000 0.00 0.00 0.00 2.71
499 500 4.411540 AGCTATCATCTTCAACAGGGACAT 59.588 41.667 0.00 0.00 0.00 3.06
500 501 3.776969 AGCTATCATCTTCAACAGGGACA 59.223 43.478 0.00 0.00 0.00 4.02
501 502 4.414337 AGCTATCATCTTCAACAGGGAC 57.586 45.455 0.00 0.00 0.00 4.46
502 503 4.141620 GGAAGCTATCATCTTCAACAGGGA 60.142 45.833 5.30 0.00 41.16 4.20
503 504 4.133078 GGAAGCTATCATCTTCAACAGGG 58.867 47.826 5.30 0.00 41.16 4.45
504 505 5.033589 AGGAAGCTATCATCTTCAACAGG 57.966 43.478 5.30 0.00 41.16 4.00
505 506 5.879223 ACAAGGAAGCTATCATCTTCAACAG 59.121 40.000 5.30 0.00 41.16 3.16
506 507 5.645067 CACAAGGAAGCTATCATCTTCAACA 59.355 40.000 5.30 0.00 41.16 3.33
507 508 5.645497 ACACAAGGAAGCTATCATCTTCAAC 59.355 40.000 5.30 0.00 41.16 3.18
508 509 5.809001 ACACAAGGAAGCTATCATCTTCAA 58.191 37.500 5.30 0.00 41.16 2.69
509 510 5.426689 ACACAAGGAAGCTATCATCTTCA 57.573 39.130 5.30 0.00 41.16 3.02
510 511 6.749923 AAACACAAGGAAGCTATCATCTTC 57.250 37.500 0.00 0.00 39.26 2.87
511 512 8.814038 AATAAACACAAGGAAGCTATCATCTT 57.186 30.769 0.00 0.00 0.00 2.40
512 513 9.331282 GTAATAAACACAAGGAAGCTATCATCT 57.669 33.333 0.00 0.00 0.00 2.90
513 514 9.331282 AGTAATAAACACAAGGAAGCTATCATC 57.669 33.333 0.00 0.00 0.00 2.92
514 515 9.331282 GAGTAATAAACACAAGGAAGCTATCAT 57.669 33.333 0.00 0.00 0.00 2.45
515 516 8.318412 TGAGTAATAAACACAAGGAAGCTATCA 58.682 33.333 0.00 0.00 0.00 2.15
516 517 8.718102 TGAGTAATAAACACAAGGAAGCTATC 57.282 34.615 0.00 0.00 0.00 2.08
517 518 9.686683 AATGAGTAATAAACACAAGGAAGCTAT 57.313 29.630 0.00 0.00 32.16 2.97
518 519 9.515226 AAATGAGTAATAAACACAAGGAAGCTA 57.485 29.630 0.00 0.00 32.16 3.32
519 520 8.409358 AAATGAGTAATAAACACAAGGAAGCT 57.591 30.769 0.00 0.00 32.16 3.74
520 521 8.515414 AGAAATGAGTAATAAACACAAGGAAGC 58.485 33.333 0.00 0.00 32.16 3.86
521 522 9.831737 CAGAAATGAGTAATAAACACAAGGAAG 57.168 33.333 0.00 0.00 32.16 3.46
522 523 9.349713 ACAGAAATGAGTAATAAACACAAGGAA 57.650 29.630 0.00 0.00 32.16 3.36
523 524 8.918202 ACAGAAATGAGTAATAAACACAAGGA 57.082 30.769 0.00 0.00 32.16 3.36
524 525 9.003658 AGACAGAAATGAGTAATAAACACAAGG 57.996 33.333 0.00 0.00 32.16 3.61
525 526 9.817365 CAGACAGAAATGAGTAATAAACACAAG 57.183 33.333 0.00 0.00 32.16 3.16
526 527 9.337396 ACAGACAGAAATGAGTAATAAACACAA 57.663 29.630 0.00 0.00 32.16 3.33
536 538 8.809468 AGACTACATACAGACAGAAATGAGTA 57.191 34.615 0.00 0.00 0.00 2.59
575 577 8.743714 AGGTAAAGATGAATGGAAGATGTTTTC 58.256 33.333 0.00 0.00 0.00 2.29
602 604 6.319658 CGGTTACTAGTAAACCATCTCCTGTA 59.680 42.308 22.13 0.00 29.15 2.74
613 615 8.302965 ACAATCTTCAACGGTTACTAGTAAAC 57.697 34.615 19.02 19.02 0.00 2.01
622 624 7.419204 CCTTTGTTTACAATCTTCAACGGTTA 58.581 34.615 0.00 0.00 35.55 2.85
643 645 2.489073 CCTGTGGTTTACTGCTCCCTTT 60.489 50.000 0.00 0.00 0.00 3.11
723 726 5.221126 GCCTTTCTTCTGAAGCTTTCTTTCA 60.221 40.000 12.54 0.00 33.28 2.69
750 756 1.705154 CGCTGTGCACGCGTTTATA 59.295 52.632 32.72 8.20 45.13 0.98
836 845 0.245813 AGAACTACGAGGGGTTTCGC 59.754 55.000 0.00 0.00 44.15 4.70
858 867 1.230281 TGGGGAAGCTTGGGAGGAT 60.230 57.895 2.10 0.00 0.00 3.24
895 914 1.809869 CGCGAGATTGGGACAGAGA 59.190 57.895 0.00 0.00 42.39 3.10
899 918 3.754530 TCGCGCGAGATTGGGACA 61.755 61.111 31.40 1.45 0.00 4.02
900 919 3.255379 GTCGCGCGAGATTGGGAC 61.255 66.667 35.75 16.01 40.19 4.46
901 920 4.847516 CGTCGCGCGAGATTGGGA 62.848 66.667 35.75 5.99 44.77 4.37
1660 1683 6.830838 ACAGAAAAGAAGAACCAACTCTGAAT 59.169 34.615 2.95 0.00 34.51 2.57
1671 1694 6.753744 AGCATGACAAAACAGAAAAGAAGAAC 59.246 34.615 0.00 0.00 0.00 3.01
1678 1701 5.964758 ACAAGAGCATGACAAAACAGAAAA 58.035 33.333 0.00 0.00 0.00 2.29
1807 1830 6.786843 ACAATCAAGGGTCCCTATAATCAT 57.213 37.500 12.06 0.00 31.13 2.45
1851 1874 1.522092 CAGTGGAAGCGAGGCCATA 59.478 57.895 5.01 0.00 36.41 2.74
1910 1933 9.741168 CAACATCGTAACAAAGTAGAAACATAG 57.259 33.333 0.00 0.00 0.00 2.23
1952 1975 7.360861 CCAAATTACACATATATAGCACCCACG 60.361 40.741 0.00 0.00 0.00 4.94
2086 2115 5.499004 AGGACAAAGGTAAGCATTCTACA 57.501 39.130 0.00 0.00 0.00 2.74
2098 2127 7.643123 ACATATCCAATAGAAAGGACAAAGGT 58.357 34.615 0.00 0.00 36.60 3.50
2157 2186 6.039717 CACCAGGACAGTGGAATATAAATTGG 59.960 42.308 0.00 0.00 40.44 3.16
2169 2198 5.551305 TCATAATATCACCAGGACAGTGG 57.449 43.478 0.00 0.00 44.01 4.00
2348 2377 9.332301 CAAATCAATGATGCAATTTGGTTAAAC 57.668 29.630 10.21 0.00 0.00 2.01
2382 2411 7.565398 ACAGAGTTGGAATACACTATCCATACT 59.435 37.037 0.00 3.07 44.83 2.12
2400 2430 5.461526 TGACATCGAGAAGTAACAGAGTTG 58.538 41.667 0.00 0.00 0.00 3.16
2402 2432 5.707242 TTGACATCGAGAAGTAACAGAGT 57.293 39.130 0.00 0.00 0.00 3.24
2403 2433 8.689251 TTTATTGACATCGAGAAGTAACAGAG 57.311 34.615 0.00 0.00 0.00 3.35
2404 2434 8.520351 TCTTTATTGACATCGAGAAGTAACAGA 58.480 33.333 0.00 0.00 0.00 3.41
2405 2435 8.689251 TCTTTATTGACATCGAGAAGTAACAG 57.311 34.615 0.00 0.00 0.00 3.16
2406 2436 9.653287 AATCTTTATTGACATCGAGAAGTAACA 57.347 29.630 0.00 0.00 0.00 2.41
2428 2458 6.959639 TCAGAAGCAAACCTTACAAAATCT 57.040 33.333 0.00 0.00 32.78 2.40
2430 2460 7.986889 ACAATTCAGAAGCAAACCTTACAAAAT 59.013 29.630 0.00 0.00 32.78 1.82
2472 2502 2.832129 AGTAGTGATCCAACGACCACAT 59.168 45.455 0.00 0.00 32.35 3.21
2525 2555 9.950680 TTTTTATCATTGACAAACAAGAGAGTC 57.049 29.630 0.00 0.00 42.02 3.36
2561 2591 3.372206 CAGAATCCATCGACTTTCCACAC 59.628 47.826 0.00 0.00 0.00 3.82
2567 2597 3.411446 TGCAACAGAATCCATCGACTTT 58.589 40.909 0.00 0.00 0.00 2.66
2570 2600 5.446709 CAATATGCAACAGAATCCATCGAC 58.553 41.667 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.