Multiple sequence alignment - TraesCS2A01G385300

Loading Multiple Alignment...

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 TraesCS2A01G385300 chr2A 100.000 4398 0 0 1 4398 631638011 631642408 0.000000e+00 8122.0
1 TraesCS2A01G385300 chr2A 86.755 151 19 1 319 468 637364674 637364524 2.720000e-37 167.0
2 TraesCS2A01G385300 chr2D 94.155 2960 105 30 679 3608 485999054 486001975 0.000000e+00 4446.0
3 TraesCS2A01G385300 chr2D 91.262 515 16 3 3892 4377 486002260 486002774 0.000000e+00 675.0
4 TraesCS2A01G385300 chr2D 93.548 248 9 2 3620 3860 486001951 486002198 3.230000e-96 363.0
5 TraesCS2A01G385300 chr2D 83.495 206 29 5 2 205 485998758 485998960 2.090000e-43 187.0
6 TraesCS2A01G385300 chr2B 94.665 2718 83 13 923 3608 571042578 571045265 0.000000e+00 4159.0
7 TraesCS2A01G385300 chr2B 91.566 498 9 7 3620 4085 571045241 571045737 0.000000e+00 656.0
8 TraesCS2A01G385300 chr2B 91.549 284 18 5 4115 4398 571045959 571046236 1.920000e-103 387.0
9 TraesCS2A01G385300 chr2B 86.232 276 25 8 615 884 571041961 571042229 2.000000e-73 287.0
10 TraesCS2A01G385300 chr2B 86.452 155 18 2 322 474 469577369 469577522 2.720000e-37 167.0
11 TraesCS2A01G385300 chr2B 94.915 59 3 0 317 375 79676185 79676127 4.680000e-15 93.5
12 TraesCS2A01G385300 chr6B 87.417 151 18 1 319 468 474319983 474320133 5.850000e-39 172.0
13 TraesCS2A01G385300 chr6B 86.395 147 17 2 323 468 41255593 41255737 1.640000e-34 158.0
14 TraesCS2A01G385300 chr1B 87.333 150 19 0 319 468 401309784 401309933 5.850000e-39 172.0
15 TraesCS2A01G385300 chr1B 86.755 151 19 1 319 468 560743583 560743433 2.720000e-37 167.0
16 TraesCS2A01G385300 chr1B 96.429 84 3 0 386 469 501941653 501941736 5.930000e-29 139.0
17 TraesCS2A01G385300 chr5A 97.647 85 2 0 386 470 521007385 521007469 3.540000e-31 147.0
18 TraesCS2A01G385300 chr5A 85.417 96 11 3 154 249 541944588 541944680 3.620000e-16 97.1
19 TraesCS2A01G385300 chr4B 97.590 83 2 0 386 468 52869886 52869804 4.590000e-30 143.0
20 TraesCS2A01G385300 chr4B 80.412 97 13 5 168 262 396447872 396447780 7.890000e-08 69.4
21 TraesCS2A01G385300 chr4B 89.130 46 5 0 168 213 657082050 657082095 1.710000e-04 58.4
22 TraesCS2A01G385300 chr7B 95.455 88 4 0 386 473 84643439 84643352 1.650000e-29 141.0
23 TraesCS2A01G385300 chr7B 82.979 94 14 2 169 262 665690698 665690789 2.820000e-12 84.2
24 TraesCS2A01G385300 chr6A 90.588 85 6 1 170 254 568499440 568499522 1.290000e-20 111.0
25 TraesCS2A01G385300 chr3B 81.333 150 9 3 320 469 197789972 197789842 2.160000e-18 104.0
26 TraesCS2A01G385300 chr5D 86.458 96 9 3 169 263 332584388 332584296 7.780000e-18 102.0
27 TraesCS2A01G385300 chr5D 86.170 94 11 1 169 262 360916309 360916218 2.800000e-17 100.0
28 TraesCS2A01G385300 chr1D 84.906 106 11 4 168 272 53223903 53224004 7.780000e-18 102.0
29 TraesCS2A01G385300 chr4D 85.263 95 10 2 169 263 64709168 64709078 1.300000e-15 95.3
30 TraesCS2A01G385300 chr6D 86.747 83 8 2 169 250 407181440 407181360 6.060000e-14 89.8
31 TraesCS2A01G385300 chr6D 80.000 95 10 6 168 256 321987989 321988080 1.320000e-05 62.1
32 TraesCS2A01G385300 chr4A 83.505 97 14 2 168 264 666934405 666934499 6.060000e-14 89.8
33 TraesCS2A01G385300 chr5B 85.542 83 9 3 168 249 698467192 698467272 2.820000e-12 84.2
34 TraesCS2A01G385300 chr3D 91.228 57 5 0 482 538 579506355 579506411 1.310000e-10 78.7


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 TraesCS2A01G385300 chr2A 631638011 631642408 4397 False 8122.00 8122 100.000 1 4398 1 chr2A.!!$F1 4397
1 TraesCS2A01G385300 chr2D 485998758 486002774 4016 False 1417.75 4446 90.615 2 4377 4 chr2D.!!$F1 4375
2 TraesCS2A01G385300 chr2B 571041961 571046236 4275 False 1372.25 4159 91.003 615 4398 4 chr2B.!!$F2 3783

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
471 472 0.042131 TGGGACGGAGGGAGTATGTT 59.958 55.0 0.0 0.0 0.0 2.71 F
519 520 0.098025 ACGTTCGTGCAAGTTTGGTG 59.902 50.0 0.0 0.0 0.0 4.17 F
1746 2088 0.109532 TGCGTGGAACCTTCATTGGA 59.890 50.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 2088 0.179084 CGGAGACACGTAATGGCCAT 60.179 55.0 14.09 14.09 36.75 4.40 R
1914 2256 0.533755 CAGGCGAGGAATGGATGGTC 60.534 60.0 0.00 0.00 0.00 4.02 R
3608 3967 0.457035 ACACAGGCACACAGCTTTTG 59.543 50.0 0.00 0.00 44.79 2.44 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
61 62 3.827898 GCGAGCCTACCAGCGACT 61.828 66.667 0.00 0.00 38.01 4.18
64 65 1.096386 CGAGCCTACCAGCGACTAGT 61.096 60.000 0.00 0.00 38.01 2.57
75 76 3.696782 CGACTAGTCGTGGGTTCAG 57.303 57.895 32.24 5.74 46.99 3.02
87 88 1.774300 GGTTCAGAACCCCACCCAT 59.226 57.895 20.57 0.00 46.12 4.00
91 92 3.672503 AGAACCCCACCCATGCCC 61.673 66.667 0.00 0.00 0.00 5.36
108 109 5.812127 CCATGCCCTAGCTTTTTCATTTTAC 59.188 40.000 0.00 0.00 40.80 2.01
117 118 6.464222 AGCTTTTTCATTTTACTTTAGGGGC 58.536 36.000 0.00 0.00 0.00 5.80
126 127 8.058847 TCATTTTACTTTAGGGGCTCAATACAT 58.941 33.333 0.00 0.00 0.00 2.29
127 128 9.349713 CATTTTACTTTAGGGGCTCAATACATA 57.650 33.333 0.00 0.00 0.00 2.29
176 177 9.937876 TTCTATAAATATATGGATCCTCCGTCT 57.062 33.333 14.23 0.00 40.17 4.18
177 178 9.937876 TCTATAAATATATGGATCCTCCGTCTT 57.062 33.333 14.23 2.87 40.17 3.01
195 196 6.647895 TCCGTCTTAAAATAAGTGTCTCAACC 59.352 38.462 0.00 0.00 0.00 3.77
198 199 9.199982 CGTCTTAAAATAAGTGTCTCAACCTTA 57.800 33.333 0.00 0.00 0.00 2.69
256 257 9.753674 ATTAAGACACTTATTTTGGAATGGAGA 57.246 29.630 0.00 0.00 0.00 3.71
257 258 9.581289 TTAAGACACTTATTTTGGAATGGAGAA 57.419 29.630 0.00 0.00 0.00 2.87
258 259 8.477419 AAGACACTTATTTTGGAATGGAGAAA 57.523 30.769 0.00 0.00 0.00 2.52
259 260 8.115490 AGACACTTATTTTGGAATGGAGAAAG 57.885 34.615 0.00 0.00 0.00 2.62
260 261 7.725844 AGACACTTATTTTGGAATGGAGAAAGT 59.274 33.333 0.00 0.00 0.00 2.66
261 262 8.934023 ACACTTATTTTGGAATGGAGAAAGTA 57.066 30.769 0.00 0.00 0.00 2.24
262 263 9.533831 ACACTTATTTTGGAATGGAGAAAGTAT 57.466 29.630 0.00 0.00 0.00 2.12
264 265 9.753674 ACTTATTTTGGAATGGAGAAAGTATCA 57.246 29.630 0.00 0.00 0.00 2.15
267 268 6.455360 TTTGGAATGGAGAAAGTATCATGC 57.545 37.500 0.00 0.00 0.00 4.06
268 269 5.114764 TGGAATGGAGAAAGTATCATGCA 57.885 39.130 0.00 0.00 0.00 3.96
269 270 5.508567 TGGAATGGAGAAAGTATCATGCAA 58.491 37.500 0.00 0.00 0.00 4.08
270 271 5.357878 TGGAATGGAGAAAGTATCATGCAAC 59.642 40.000 0.00 0.00 0.00 4.17
271 272 5.357878 GGAATGGAGAAAGTATCATGCAACA 59.642 40.000 0.00 0.00 0.00 3.33
272 273 6.040166 GGAATGGAGAAAGTATCATGCAACAT 59.960 38.462 0.00 0.00 0.00 2.71
273 274 6.630444 ATGGAGAAAGTATCATGCAACATC 57.370 37.500 0.00 0.00 0.00 3.06
274 275 5.499313 TGGAGAAAGTATCATGCAACATCA 58.501 37.500 0.00 0.00 0.00 3.07
275 276 5.587443 TGGAGAAAGTATCATGCAACATCAG 59.413 40.000 0.00 0.00 0.00 2.90
276 277 5.587844 GGAGAAAGTATCATGCAACATCAGT 59.412 40.000 0.00 0.00 0.00 3.41
277 278 6.094603 GGAGAAAGTATCATGCAACATCAGTT 59.905 38.462 0.00 0.00 38.88 3.16
291 292 3.953775 AGTTGACGGTGGGCCCTG 61.954 66.667 25.70 15.55 0.00 4.45
322 323 1.335810 CATGCTATGCAGGCGACAAAT 59.664 47.619 9.38 0.00 43.65 2.32
323 324 2.323968 TGCTATGCAGGCGACAAATA 57.676 45.000 9.38 0.00 33.32 1.40
324 325 1.939934 TGCTATGCAGGCGACAAATAC 59.060 47.619 9.38 0.00 33.32 1.89
325 326 2.213499 GCTATGCAGGCGACAAATACT 58.787 47.619 0.00 0.00 0.00 2.12
326 327 2.221981 GCTATGCAGGCGACAAATACTC 59.778 50.000 0.00 0.00 0.00 2.59
327 328 1.668419 ATGCAGGCGACAAATACTCC 58.332 50.000 0.00 0.00 0.00 3.85
328 329 0.392461 TGCAGGCGACAAATACTCCC 60.392 55.000 0.00 0.00 0.00 4.30
329 330 0.107654 GCAGGCGACAAATACTCCCT 60.108 55.000 0.00 0.00 0.00 4.20
330 331 1.941325 CAGGCGACAAATACTCCCTC 58.059 55.000 0.00 0.00 0.00 4.30
331 332 0.831307 AGGCGACAAATACTCCCTCC 59.169 55.000 0.00 0.00 0.00 4.30
332 333 0.529992 GGCGACAAATACTCCCTCCG 60.530 60.000 0.00 0.00 0.00 4.63
333 334 0.175073 GCGACAAATACTCCCTCCGT 59.825 55.000 0.00 0.00 0.00 4.69
334 335 1.801765 GCGACAAATACTCCCTCCGTC 60.802 57.143 0.00 0.00 0.00 4.79
335 336 1.202382 CGACAAATACTCCCTCCGTCC 60.202 57.143 0.00 0.00 0.00 4.79
336 337 1.138464 GACAAATACTCCCTCCGTCCC 59.862 57.143 0.00 0.00 0.00 4.46
337 338 1.200519 CAAATACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
338 339 1.557832 CAAATACTCCCTCCGTCCCAA 59.442 52.381 0.00 0.00 0.00 4.12
339 340 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
340 341 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
341 342 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
342 343 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
343 344 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
344 345 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
345 346 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
346 347 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
347 348 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
348 349 3.560453 CCCTCCGTCCCAAAATTCTTGTA 60.560 47.826 0.00 0.00 0.00 2.41
349 350 4.270008 CCTCCGTCCCAAAATTCTTGTAT 58.730 43.478 0.00 0.00 0.00 2.29
350 351 4.705023 CCTCCGTCCCAAAATTCTTGTATT 59.295 41.667 0.00 0.00 0.00 1.89
351 352 5.883673 CCTCCGTCCCAAAATTCTTGTATTA 59.116 40.000 0.00 0.00 0.00 0.98
352 353 6.038271 CCTCCGTCCCAAAATTCTTGTATTAG 59.962 42.308 0.00 0.00 0.00 1.73
353 354 6.713276 TCCGTCCCAAAATTCTTGTATTAGA 58.287 36.000 0.00 0.00 0.00 2.10
354 355 7.343357 TCCGTCCCAAAATTCTTGTATTAGAT 58.657 34.615 0.00 0.00 0.00 1.98
355 356 7.832187 TCCGTCCCAAAATTCTTGTATTAGATT 59.168 33.333 0.00 0.00 0.00 2.40
356 357 8.466798 CCGTCCCAAAATTCTTGTATTAGATTT 58.533 33.333 0.00 0.00 0.00 2.17
403 404 7.908827 TTTTTGCGGATGTATCTAACACTAA 57.091 32.000 0.00 0.00 42.09 2.24
404 405 7.908827 TTTTGCGGATGTATCTAACACTAAA 57.091 32.000 0.00 0.00 42.09 1.85
405 406 7.908827 TTTGCGGATGTATCTAACACTAAAA 57.091 32.000 0.00 0.00 42.09 1.52
406 407 8.500753 TTTGCGGATGTATCTAACACTAAAAT 57.499 30.769 0.00 0.00 42.09 1.82
407 408 9.602568 TTTGCGGATGTATCTAACACTAAAATA 57.397 29.630 0.00 0.00 42.09 1.40
408 409 9.772973 TTGCGGATGTATCTAACACTAAAATAT 57.227 29.630 0.00 0.00 42.09 1.28
409 410 9.203421 TGCGGATGTATCTAACACTAAAATATG 57.797 33.333 0.00 0.00 42.09 1.78
410 411 9.419297 GCGGATGTATCTAACACTAAAATATGA 57.581 33.333 0.00 0.00 42.09 2.15
455 456 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
456 457 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
457 458 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
458 459 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
459 460 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
460 461 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
461 462 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
462 463 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
463 464 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
464 465 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
465 466 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
471 472 0.042131 TGGGACGGAGGGAGTATGTT 59.958 55.000 0.00 0.00 0.00 2.71
480 481 2.365941 GAGGGAGTATGTTCAGGTAGGC 59.634 54.545 0.00 0.00 0.00 3.93
489 490 3.826524 TGTTCAGGTAGGCAAAATGTGA 58.173 40.909 0.00 0.00 0.00 3.58
490 491 3.568007 TGTTCAGGTAGGCAAAATGTGAC 59.432 43.478 0.00 0.00 34.17 3.67
492 493 1.468520 CAGGTAGGCAAAATGTGACCG 59.531 52.381 0.00 0.00 34.75 4.79
493 494 1.073284 AGGTAGGCAAAATGTGACCGT 59.927 47.619 0.00 0.00 34.75 4.83
499 500 6.038936 GGTAGGCAAAATGTGACCGTATTTAT 59.961 38.462 0.00 0.00 34.75 1.40
517 518 2.961522 ATACGTTCGTGCAAGTTTGG 57.038 45.000 8.14 0.00 0.00 3.28
518 519 1.654317 TACGTTCGTGCAAGTTTGGT 58.346 45.000 8.14 0.00 0.00 3.67
519 520 0.098025 ACGTTCGTGCAAGTTTGGTG 59.902 50.000 0.00 0.00 0.00 4.17
520 521 0.591236 CGTTCGTGCAAGTTTGGTGG 60.591 55.000 0.00 0.00 0.00 4.61
521 522 0.869880 GTTCGTGCAAGTTTGGTGGC 60.870 55.000 0.00 0.00 0.00 5.01
522 523 2.010582 TTCGTGCAAGTTTGGTGGCC 62.011 55.000 0.00 0.00 0.00 5.36
523 524 2.780094 CGTGCAAGTTTGGTGGCCA 61.780 57.895 0.00 0.00 0.00 5.36
524 525 1.519719 GTGCAAGTTTGGTGGCCAA 59.480 52.632 7.24 0.00 42.29 4.52
535 536 4.696479 TTGGTGGCCAAAAACACATATT 57.304 36.364 7.24 0.00 40.92 1.28
536 537 4.696479 TGGTGGCCAAAAACACATATTT 57.304 36.364 7.24 0.00 39.31 1.40
537 538 5.041191 TGGTGGCCAAAAACACATATTTT 57.959 34.783 7.24 0.00 39.31 1.82
538 539 6.174720 TGGTGGCCAAAAACACATATTTTA 57.825 33.333 7.24 0.00 39.31 1.52
539 540 6.773638 TGGTGGCCAAAAACACATATTTTAT 58.226 32.000 7.24 0.00 39.31 1.40
540 541 7.907389 TGGTGGCCAAAAACACATATTTTATA 58.093 30.769 7.24 0.00 39.31 0.98
541 542 8.375506 TGGTGGCCAAAAACACATATTTTATAA 58.624 29.630 7.24 0.00 39.31 0.98
542 543 9.220767 GGTGGCCAAAAACACATATTTTATAAA 57.779 29.630 7.24 0.00 39.31 1.40
567 568 9.444600 AATTTATACATCAAACTAACGGTCACT 57.555 29.630 0.00 0.00 0.00 3.41
568 569 8.836268 TTTATACATCAAACTAACGGTCACTT 57.164 30.769 0.00 0.00 0.00 3.16
569 570 6.721571 ATACATCAAACTAACGGTCACTTG 57.278 37.500 0.00 0.00 0.00 3.16
570 571 4.448210 ACATCAAACTAACGGTCACTTGT 58.552 39.130 0.00 0.00 0.00 3.16
571 572 4.510340 ACATCAAACTAACGGTCACTTGTC 59.490 41.667 0.00 0.00 0.00 3.18
572 573 4.126208 TCAAACTAACGGTCACTTGTCA 57.874 40.909 0.00 0.00 0.00 3.58
573 574 3.866910 TCAAACTAACGGTCACTTGTCAC 59.133 43.478 0.00 0.00 0.00 3.67
574 575 2.129823 ACTAACGGTCACTTGTCACG 57.870 50.000 0.00 0.00 0.00 4.35
575 576 1.406539 ACTAACGGTCACTTGTCACGT 59.593 47.619 0.00 0.00 39.74 4.49
576 577 2.618241 ACTAACGGTCACTTGTCACGTA 59.382 45.455 0.00 0.00 36.69 3.57
577 578 1.843992 AACGGTCACTTGTCACGTAC 58.156 50.000 0.00 0.00 36.69 3.67
578 579 1.027357 ACGGTCACTTGTCACGTACT 58.973 50.000 0.00 0.00 35.85 2.73
579 580 2.221169 ACGGTCACTTGTCACGTACTA 58.779 47.619 0.00 0.00 35.85 1.82
580 581 2.031682 ACGGTCACTTGTCACGTACTAC 60.032 50.000 0.00 0.00 35.85 2.73
581 582 2.031769 CGGTCACTTGTCACGTACTACA 60.032 50.000 0.00 0.00 0.00 2.74
582 583 3.548616 CGGTCACTTGTCACGTACTACAA 60.549 47.826 9.21 9.21 34.57 2.41
589 590 6.823678 CTTGTCACGTACTACAAGTTTTCT 57.176 37.500 20.92 0.00 44.83 2.52
590 591 6.578020 TTGTCACGTACTACAAGTTTTCTG 57.422 37.500 6.28 0.00 32.11 3.02
591 592 5.893687 TGTCACGTACTACAAGTTTTCTGA 58.106 37.500 0.00 0.00 0.00 3.27
592 593 5.745294 TGTCACGTACTACAAGTTTTCTGAC 59.255 40.000 0.00 0.00 0.00 3.51
593 594 5.975939 GTCACGTACTACAAGTTTTCTGACT 59.024 40.000 0.00 0.00 0.00 3.41
594 595 6.142002 GTCACGTACTACAAGTTTTCTGACTC 59.858 42.308 0.00 0.00 0.00 3.36
595 596 5.401674 CACGTACTACAAGTTTTCTGACTCC 59.598 44.000 0.00 0.00 0.00 3.85
596 597 5.301298 ACGTACTACAAGTTTTCTGACTCCT 59.699 40.000 0.00 0.00 0.00 3.69
597 598 5.857517 CGTACTACAAGTTTTCTGACTCCTC 59.142 44.000 0.00 0.00 0.00 3.71
598 599 4.872664 ACTACAAGTTTTCTGACTCCTCG 58.127 43.478 0.00 0.00 0.00 4.63
599 600 3.113260 ACAAGTTTTCTGACTCCTCGG 57.887 47.619 0.00 0.00 0.00 4.63
600 601 2.434702 ACAAGTTTTCTGACTCCTCGGT 59.565 45.455 0.00 0.00 0.00 4.69
601 602 2.802816 CAAGTTTTCTGACTCCTCGGTG 59.197 50.000 0.00 0.00 0.00 4.94
602 603 2.040178 AGTTTTCTGACTCCTCGGTGT 58.960 47.619 0.00 0.00 0.00 4.16
603 604 3.228453 AGTTTTCTGACTCCTCGGTGTA 58.772 45.455 0.00 0.00 0.00 2.90
604 605 3.833070 AGTTTTCTGACTCCTCGGTGTAT 59.167 43.478 0.00 0.00 0.00 2.29
605 606 4.283722 AGTTTTCTGACTCCTCGGTGTATT 59.716 41.667 0.00 0.00 0.00 1.89
606 607 4.884668 TTTCTGACTCCTCGGTGTATTT 57.115 40.909 0.00 0.00 0.00 1.40
607 608 5.988310 TTTCTGACTCCTCGGTGTATTTA 57.012 39.130 0.00 0.00 0.00 1.40
608 609 4.978083 TCTGACTCCTCGGTGTATTTAC 57.022 45.455 0.00 0.00 0.00 2.01
609 610 3.698040 TCTGACTCCTCGGTGTATTTACC 59.302 47.826 0.00 0.00 37.37 2.85
610 611 3.700038 CTGACTCCTCGGTGTATTTACCT 59.300 47.826 0.00 0.00 38.62 3.08
611 612 3.698040 TGACTCCTCGGTGTATTTACCTC 59.302 47.826 0.00 0.00 38.62 3.85
612 613 3.698040 GACTCCTCGGTGTATTTACCTCA 59.302 47.826 0.00 0.00 38.62 3.86
613 614 4.287552 ACTCCTCGGTGTATTTACCTCAT 58.712 43.478 0.00 0.00 38.62 2.90
643 644 5.681639 TCTGCATGACTTGATTGAGATCAT 58.318 37.500 0.00 0.00 41.71 2.45
644 645 5.758784 TCTGCATGACTTGATTGAGATCATC 59.241 40.000 0.00 0.00 41.71 2.92
645 646 5.433526 TGCATGACTTGATTGAGATCATCA 58.566 37.500 0.00 0.00 41.71 3.07
646 647 5.296035 TGCATGACTTGATTGAGATCATCAC 59.704 40.000 0.00 0.00 41.71 3.06
647 648 5.277876 GCATGACTTGATTGAGATCATCACC 60.278 44.000 0.00 0.00 41.71 4.02
648 649 5.425196 TGACTTGATTGAGATCATCACCA 57.575 39.130 0.00 0.00 41.71 4.17
649 650 5.425630 TGACTTGATTGAGATCATCACCAG 58.574 41.667 0.00 0.00 41.71 4.00
650 651 5.046087 TGACTTGATTGAGATCATCACCAGT 60.046 40.000 0.00 0.00 41.71 4.00
651 652 5.183969 ACTTGATTGAGATCATCACCAGTG 58.816 41.667 0.00 0.00 41.71 3.66
652 653 4.146745 TGATTGAGATCATCACCAGTGG 57.853 45.455 7.91 7.91 37.37 4.00
658 659 3.176411 AGATCATCACCAGTGGAACAGA 58.824 45.455 18.40 8.82 41.80 3.41
671 672 1.478510 GGAACAGAGCTGGAGATCGAA 59.521 52.381 0.00 0.00 35.26 3.71
712 713 4.505808 TCCGAATAAAATACTGGCACGAA 58.494 39.130 0.00 0.00 0.00 3.85
717 718 6.454054 CGAATAAAATACTGGCACGAAACGTA 60.454 38.462 0.00 0.00 38.32 3.57
728 729 1.620413 CGAAACGTAAGGTCCCACGC 61.620 60.000 12.36 0.00 41.80 5.34
770 771 1.371022 CGCCTCGATCGGTCATCAG 60.371 63.158 16.41 3.64 0.00 2.90
773 774 1.025041 CCTCGATCGGTCATCAGTCA 58.975 55.000 16.41 0.00 0.00 3.41
774 775 1.611006 CCTCGATCGGTCATCAGTCAT 59.389 52.381 16.41 0.00 0.00 3.06
777 778 2.033424 TCGATCGGTCATCAGTCATCAC 59.967 50.000 16.41 0.00 0.00 3.06
780 781 2.446435 TCGGTCATCAGTCATCACTCA 58.554 47.619 0.00 0.00 0.00 3.41
843 853 2.983592 CTCCACCCCAACAACGGC 60.984 66.667 0.00 0.00 0.00 5.68
854 864 0.673644 AACAACGGCCAGATTCCTCG 60.674 55.000 2.24 0.00 0.00 4.63
961 1286 4.258702 ACTCCATCTAAATCGAATCCCG 57.741 45.455 0.00 0.00 40.25 5.14
967 1292 0.534203 TAAATCGAATCCCGCAGCCC 60.534 55.000 0.00 0.00 38.37 5.19
968 1293 2.550699 AAATCGAATCCCGCAGCCCA 62.551 55.000 0.00 0.00 38.37 5.36
969 1294 3.757248 ATCGAATCCCGCAGCCCAC 62.757 63.158 0.00 0.00 38.37 4.61
1137 1465 2.265904 GGTTTTGGAGCACCCCGTC 61.266 63.158 0.00 0.00 34.81 4.79
1138 1466 2.114411 TTTTGGAGCACCCCGTCC 59.886 61.111 0.00 0.00 34.81 4.79
1139 1467 2.457323 TTTTGGAGCACCCCGTCCT 61.457 57.895 0.00 0.00 33.57 3.85
1140 1468 2.690653 TTTTGGAGCACCCCGTCCTG 62.691 60.000 0.00 0.00 33.57 3.86
1178 1506 3.295228 CTTGGTTGCGGCGAGTTCG 62.295 63.158 12.98 0.00 43.27 3.95
1190 1518 1.140407 CGAGTTCGTTCCTGATCGGC 61.140 60.000 0.00 0.00 34.11 5.54
1192 1520 0.608640 AGTTCGTTCCTGATCGGCTT 59.391 50.000 0.00 0.00 0.00 4.35
1332 1660 4.077184 CGCTGGCCGTGGAGGTTA 62.077 66.667 0.00 0.00 43.70 2.85
1372 1700 4.840005 GAGCCCCGGAAAGGAGCG 62.840 72.222 0.73 0.00 45.00 5.03
1410 1738 0.593773 ACATTGCGTCGTTGTTTGCC 60.594 50.000 0.00 0.00 0.00 4.52
1438 1766 2.584418 CCTGTGCTCGGATGCTCG 60.584 66.667 0.00 0.00 0.00 5.03
1449 1777 2.124903 CGGATGCTCGTGTTATGTACC 58.875 52.381 0.00 0.00 0.00 3.34
1467 1809 2.023771 CTGTGTGAGTGTGCGCGAT 61.024 57.895 12.10 0.00 0.00 4.58
1704 2046 3.626924 GGAGGTGGTCACTGCCGT 61.627 66.667 0.93 0.00 0.00 5.68
1733 2075 2.125753 GAGAGCTGAGGTGCGTGG 60.126 66.667 0.00 0.00 38.13 4.94
1746 2088 0.109532 TGCGTGGAACCTTCATTGGA 59.890 50.000 0.00 0.00 0.00 3.53
1754 2096 2.555732 ACCTTCATTGGATGGCCATT 57.444 45.000 21.84 0.00 45.46 3.16
1755 2097 3.686227 ACCTTCATTGGATGGCCATTA 57.314 42.857 21.84 9.75 45.46 1.90
1763 2105 1.134521 TGGATGGCCATTACGTGTCTC 60.135 52.381 21.84 3.90 39.92 3.36
1764 2106 1.583054 GATGGCCATTACGTGTCTCC 58.417 55.000 21.84 0.00 0.00 3.71
1828 2170 1.174712 TTCTTGGCAGGCAGTTGAGC 61.175 55.000 0.00 0.00 0.00 4.26
1902 2244 2.364448 ACTCCCCGGAAGAGAGCC 60.364 66.667 23.50 0.00 35.51 4.70
1914 2256 1.373497 GAGAGCCGAGGTGTGTGTG 60.373 63.158 0.00 0.00 0.00 3.82
1926 2268 1.812571 GTGTGTGTGACCATCCATTCC 59.187 52.381 0.00 0.00 0.00 3.01
1966 2308 2.097466 CCTGTGCATGTTTACGGATTCC 59.903 50.000 0.00 0.00 0.00 3.01
1969 2311 4.580868 TGTGCATGTTTACGGATTCCTTA 58.419 39.130 0.30 0.00 0.00 2.69
2073 2415 0.959372 CCTTGCTGCAGGAGAAGGTG 60.959 60.000 17.12 0.13 35.71 4.00
2169 2511 8.641498 AACTCAGGTAGATGAATGAAATGTTT 57.359 30.769 0.00 0.00 0.00 2.83
2221 2563 9.170734 CAGATTATGTGCCTGTTAATATATGCT 57.829 33.333 0.00 0.00 0.00 3.79
2291 2633 4.540824 GTGGCAAGAAGAAAGTGACATTC 58.459 43.478 0.00 0.00 31.67 2.67
2408 2750 3.813443 ACACATGCAGAAGACTGTTCTT 58.187 40.909 0.00 0.00 45.35 2.52
2489 2831 5.127194 TGAGTATGGTGAGGATGACAACTAC 59.873 44.000 0.00 0.00 0.00 2.73
2660 3002 4.982701 AGCAGCCCTGTGCCCAAC 62.983 66.667 0.00 0.00 45.20 3.77
2732 3074 3.296854 TCACCGTGATAGAAGCCAGTAT 58.703 45.455 0.00 0.00 0.00 2.12
2888 3230 4.074970 AGGTTGCAAATCAGACGAAGATT 58.925 39.130 0.00 0.00 37.30 2.40
3560 3919 1.765904 TGCCGGATATAGAAGTGCCAA 59.234 47.619 5.05 0.00 0.00 4.52
3608 3967 2.864946 TGTGTGCATTGCAAATTGTGAC 59.135 40.909 13.94 0.00 41.47 3.67
3609 3968 2.864946 GTGTGCATTGCAAATTGTGACA 59.135 40.909 13.94 1.38 41.47 3.58
3612 3971 4.393990 TGTGCATTGCAAATTGTGACAAAA 59.606 33.333 13.94 0.00 41.47 2.44
3613 3972 4.965158 GTGCATTGCAAATTGTGACAAAAG 59.035 37.500 13.94 0.00 41.47 2.27
3614 3973 3.969981 GCATTGCAAATTGTGACAAAAGC 59.030 39.130 1.71 7.53 30.51 3.51
3615 3974 4.260866 GCATTGCAAATTGTGACAAAAGCT 60.261 37.500 1.71 0.00 32.39 3.74
3616 3975 4.861389 TTGCAAATTGTGACAAAAGCTG 57.139 36.364 16.76 7.79 0.00 4.24
3617 3976 3.859443 TGCAAATTGTGACAAAAGCTGT 58.141 36.364 16.76 0.00 42.61 4.40
3618 3977 3.617706 TGCAAATTGTGACAAAAGCTGTG 59.382 39.130 16.76 2.87 38.84 3.66
3619 3978 3.618150 GCAAATTGTGACAAAAGCTGTGT 59.382 39.130 0.62 3.02 38.84 3.72
3620 3979 4.492895 GCAAATTGTGACAAAAGCTGTGTG 60.493 41.667 0.62 0.00 38.84 3.82
3621 3980 2.276472 TTGTGACAAAAGCTGTGTGC 57.724 45.000 7.99 2.47 38.84 4.57
3622 3981 0.455410 TGTGACAAAAGCTGTGTGCC 59.545 50.000 7.99 0.00 44.23 5.01
3623 3982 0.740737 GTGACAAAAGCTGTGTGCCT 59.259 50.000 7.99 0.00 44.23 4.75
3624 3983 0.740149 TGACAAAAGCTGTGTGCCTG 59.260 50.000 7.99 0.00 44.23 4.85
3625 3984 0.740737 GACAAAAGCTGTGTGCCTGT 59.259 50.000 7.99 0.00 44.23 4.00
3626 3985 0.457035 ACAAAAGCTGTGTGCCTGTG 59.543 50.000 2.59 0.00 44.23 3.66
3627 3986 0.457035 CAAAAGCTGTGTGCCTGTGT 59.543 50.000 0.00 0.00 44.23 3.72
3628 3987 0.457035 AAAAGCTGTGTGCCTGTGTG 59.543 50.000 0.00 0.00 44.23 3.82
3629 3988 2.008268 AAAGCTGTGTGCCTGTGTGC 62.008 55.000 0.00 0.00 44.23 4.57
3630 3989 3.211245 GCTGTGTGCCTGTGTGCA 61.211 61.111 0.00 0.00 39.37 4.57
3631 3990 2.558286 GCTGTGTGCCTGTGTGCAT 61.558 57.895 0.00 0.00 44.30 3.96
3632 3991 2.035421 CTGTGTGCCTGTGTGCATT 58.965 52.632 0.00 0.00 44.30 3.56
3633 3992 0.318360 CTGTGTGCCTGTGTGCATTG 60.318 55.000 0.00 0.00 44.30 2.82
3634 3993 1.662446 GTGTGCCTGTGTGCATTGC 60.662 57.895 0.46 0.46 44.30 3.56
3635 3994 2.125961 TGTGCCTGTGTGCATTGCA 61.126 52.632 7.38 7.38 44.30 4.08
3636 3995 1.067749 GTGCCTGTGTGCATTGCAA 59.932 52.632 13.94 0.00 44.30 4.08
3637 3996 0.530211 GTGCCTGTGTGCATTGCAAA 60.530 50.000 13.94 4.85 44.30 3.68
3638 3997 0.393448 TGCCTGTGTGCATTGCAAAT 59.607 45.000 13.94 0.00 41.47 2.32
3639 3998 1.202663 TGCCTGTGTGCATTGCAAATT 60.203 42.857 13.94 0.00 41.47 1.82
3640 3999 1.195900 GCCTGTGTGCATTGCAAATTG 59.804 47.619 13.94 0.00 41.47 2.32
3641 4000 2.485903 CCTGTGTGCATTGCAAATTGT 58.514 42.857 13.94 0.00 41.47 2.71
3725 4084 7.169645 GCTTGCTTTCATTTTTCTATGACAACA 59.830 33.333 0.00 0.00 34.41 3.33
3773 4132 3.319122 GTGGAGACAAAAGCTGGAAATGT 59.681 43.478 0.00 0.00 46.06 2.71
4008 4442 2.615747 GCTTAGTCAACCTCTTGGGACC 60.616 54.545 0.00 0.00 38.76 4.46
4030 4464 3.693085 CACTCATGGCTGCTAATTCAGTT 59.307 43.478 0.00 0.00 36.49 3.16
4081 4518 4.221041 TGCAAATGATGGTTCACATGATGT 59.779 37.500 0.00 0.00 40.72 3.06
4089 4526 7.337938 TGATGGTTCACATGATGTAATACTGT 58.662 34.615 0.00 0.00 40.72 3.55
4093 4530 7.828717 TGGTTCACATGATGTAATACTGTGATT 59.171 33.333 12.06 0.00 43.22 2.57
4113 4742 2.971901 ATTCTTCTCGGGGGTTTTGT 57.028 45.000 0.00 0.00 0.00 2.83
4121 4750 2.203437 GGGGTTTTGTGGCGACCT 60.203 61.111 0.00 0.00 33.90 3.85
4143 4772 5.535783 CCTATGGGATTTGTTGCATACATGA 59.464 40.000 0.00 0.00 33.44 3.07
4189 4822 4.952460 TGAAGTAGTGTGACCCTTTGTAC 58.048 43.478 0.00 0.00 0.00 2.90
4308 4941 1.595382 ATAGCAATGCGGTCTCGGC 60.595 57.895 0.00 0.00 36.79 5.54
4355 4988 2.180204 GCGTGTCGGCAGCCAATAT 61.180 57.895 13.30 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.181475 GCCGGTGATGTTTCTATCTCAGA 60.181 47.826 1.90 0.00 0.00 3.27
7 8 3.126831 GCCGGTGATGTTTCTATCTCAG 58.873 50.000 1.90 0.00 0.00 3.35
8 9 2.158957 GGCCGGTGATGTTTCTATCTCA 60.159 50.000 1.90 0.00 0.00 3.27
9 10 2.103263 AGGCCGGTGATGTTTCTATCTC 59.897 50.000 1.90 0.00 0.00 2.75
12 13 1.134098 CCAGGCCGGTGATGTTTCTAT 60.134 52.381 1.90 0.00 0.00 1.98
59 60 1.617357 GGTTCTGAACCCACGACTAGT 59.383 52.381 25.74 0.00 46.12 2.57
74 75 2.798760 TAGGGCATGGGTGGGGTTCT 62.799 60.000 0.00 0.00 0.00 3.01
75 76 2.284515 CTAGGGCATGGGTGGGGTTC 62.285 65.000 0.00 0.00 0.00 3.62
80 81 0.324645 AAAAGCTAGGGCATGGGTGG 60.325 55.000 0.00 0.00 41.70 4.61
87 88 6.664428 AAGTAAAATGAAAAAGCTAGGGCA 57.336 33.333 0.00 0.00 41.70 5.36
91 92 7.759886 GCCCCTAAAGTAAAATGAAAAAGCTAG 59.240 37.037 0.00 0.00 0.00 3.42
165 166 7.266400 AGACACTTATTTTAAGACGGAGGATC 58.734 38.462 1.47 0.00 0.00 3.36
166 167 7.093465 TGAGACACTTATTTTAAGACGGAGGAT 60.093 37.037 1.47 0.00 0.00 3.24
169 170 7.148623 GGTTGAGACACTTATTTTAAGACGGAG 60.149 40.741 1.47 0.00 0.00 4.63
171 172 6.649557 AGGTTGAGACACTTATTTTAAGACGG 59.350 38.462 1.47 0.00 0.00 4.79
172 173 7.653767 AGGTTGAGACACTTATTTTAAGACG 57.346 36.000 1.47 0.00 0.00 4.18
230 231 9.753674 TCTCCATTCCAAAATAAGTGTCTTAAT 57.246 29.630 0.00 0.00 0.00 1.40
231 232 9.581289 TTCTCCATTCCAAAATAAGTGTCTTAA 57.419 29.630 0.00 0.00 0.00 1.85
232 233 9.581289 TTTCTCCATTCCAAAATAAGTGTCTTA 57.419 29.630 0.00 0.00 0.00 2.10
233 234 8.477419 TTTCTCCATTCCAAAATAAGTGTCTT 57.523 30.769 0.00 0.00 0.00 3.01
234 235 7.725844 ACTTTCTCCATTCCAAAATAAGTGTCT 59.274 33.333 0.00 0.00 0.00 3.41
235 236 7.886338 ACTTTCTCCATTCCAAAATAAGTGTC 58.114 34.615 0.00 0.00 0.00 3.67
236 237 7.839680 ACTTTCTCCATTCCAAAATAAGTGT 57.160 32.000 0.00 0.00 0.00 3.55
238 239 9.753674 TGATACTTTCTCCATTCCAAAATAAGT 57.246 29.630 0.00 0.00 0.00 2.24
241 242 8.632679 GCATGATACTTTCTCCATTCCAAAATA 58.367 33.333 0.00 0.00 0.00 1.40
242 243 7.124599 TGCATGATACTTTCTCCATTCCAAAAT 59.875 33.333 0.00 0.00 0.00 1.82
243 244 6.436847 TGCATGATACTTTCTCCATTCCAAAA 59.563 34.615 0.00 0.00 0.00 2.44
244 245 5.951148 TGCATGATACTTTCTCCATTCCAAA 59.049 36.000 0.00 0.00 0.00 3.28
245 246 5.508567 TGCATGATACTTTCTCCATTCCAA 58.491 37.500 0.00 0.00 0.00 3.53
246 247 5.114764 TGCATGATACTTTCTCCATTCCA 57.885 39.130 0.00 0.00 0.00 3.53
247 248 5.357878 TGTTGCATGATACTTTCTCCATTCC 59.642 40.000 0.00 0.00 0.00 3.01
248 249 6.441093 TGTTGCATGATACTTTCTCCATTC 57.559 37.500 0.00 0.00 0.00 2.67
249 250 6.604396 TGATGTTGCATGATACTTTCTCCATT 59.396 34.615 0.00 0.00 0.00 3.16
250 251 6.124340 TGATGTTGCATGATACTTTCTCCAT 58.876 36.000 0.00 0.00 0.00 3.41
251 252 5.499313 TGATGTTGCATGATACTTTCTCCA 58.501 37.500 0.00 0.00 0.00 3.86
252 253 5.587844 ACTGATGTTGCATGATACTTTCTCC 59.412 40.000 0.00 0.00 0.00 3.71
253 254 6.674694 ACTGATGTTGCATGATACTTTCTC 57.325 37.500 0.00 0.00 0.00 2.87
254 255 6.849502 CAACTGATGTTGCATGATACTTTCT 58.150 36.000 0.00 0.00 45.57 2.52
268 269 0.889186 GCCCACCGTCAACTGATGTT 60.889 55.000 0.00 0.00 36.75 2.71
269 270 1.302511 GCCCACCGTCAACTGATGT 60.303 57.895 0.00 0.00 0.00 3.06
270 271 2.040544 GGCCCACCGTCAACTGATG 61.041 63.158 0.00 0.00 0.00 3.07
271 272 2.351276 GGCCCACCGTCAACTGAT 59.649 61.111 0.00 0.00 0.00 2.90
272 273 3.948719 GGGCCCACCGTCAACTGA 61.949 66.667 19.95 0.00 36.48 3.41
273 274 3.953775 AGGGCCCACCGTCAACTG 61.954 66.667 27.56 0.00 46.96 3.16
274 275 3.953775 CAGGGCCCACCGTCAACT 61.954 66.667 27.56 0.00 46.96 3.16
314 315 0.175073 ACGGAGGGAGTATTTGTCGC 59.825 55.000 0.00 0.00 0.00 5.19
316 317 1.138464 GGGACGGAGGGAGTATTTGTC 59.862 57.143 0.00 0.00 0.00 3.18
318 319 1.200519 TGGGACGGAGGGAGTATTTG 58.799 55.000 0.00 0.00 0.00 2.32
322 323 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
323 324 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
324 325 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
325 326 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
326 327 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
327 328 2.514803 ACAAGAATTTTGGGACGGAGG 58.485 47.619 0.00 0.00 0.00 4.30
328 329 5.897377 AATACAAGAATTTTGGGACGGAG 57.103 39.130 0.00 0.00 0.00 4.63
329 330 6.713276 TCTAATACAAGAATTTTGGGACGGA 58.287 36.000 0.00 0.00 0.00 4.69
330 331 6.995511 TCTAATACAAGAATTTTGGGACGG 57.004 37.500 0.00 0.00 0.00 4.79
379 380 7.908827 TTAGTGTTAGATACATCCGCAAAAA 57.091 32.000 0.00 0.00 39.39 1.94
380 381 7.908827 TTTAGTGTTAGATACATCCGCAAAA 57.091 32.000 0.00 0.00 39.39 2.44
381 382 7.908827 TTTTAGTGTTAGATACATCCGCAAA 57.091 32.000 0.00 0.00 39.39 3.68
382 383 9.772973 ATATTTTAGTGTTAGATACATCCGCAA 57.227 29.630 0.00 0.00 39.39 4.85
383 384 9.203421 CATATTTTAGTGTTAGATACATCCGCA 57.797 33.333 0.00 0.00 39.39 5.69
384 385 9.419297 TCATATTTTAGTGTTAGATACATCCGC 57.581 33.333 0.00 0.00 39.39 5.54
429 430 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
430 431 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
431 432 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
432 433 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
433 434 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
434 435 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
435 436 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
436 437 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
437 438 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
438 439 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
439 440 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
440 441 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
441 442 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
442 443 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
443 444 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
444 445 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
445 446 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
446 447 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
447 448 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
448 449 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
449 450 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
450 451 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
451 452 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
452 453 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
453 454 0.751452 GAACATACTCCCTCCGTCCC 59.249 60.000 0.00 0.00 0.00 4.46
454 455 1.409427 CTGAACATACTCCCTCCGTCC 59.591 57.143 0.00 0.00 0.00 4.79
455 456 1.409427 CCTGAACATACTCCCTCCGTC 59.591 57.143 0.00 0.00 0.00 4.79
456 457 1.273098 ACCTGAACATACTCCCTCCGT 60.273 52.381 0.00 0.00 0.00 4.69
457 458 1.486211 ACCTGAACATACTCCCTCCG 58.514 55.000 0.00 0.00 0.00 4.63
458 459 2.966516 CCTACCTGAACATACTCCCTCC 59.033 54.545 0.00 0.00 0.00 4.30
459 460 2.365941 GCCTACCTGAACATACTCCCTC 59.634 54.545 0.00 0.00 0.00 4.30
460 461 2.292918 TGCCTACCTGAACATACTCCCT 60.293 50.000 0.00 0.00 0.00 4.20
461 462 2.116238 TGCCTACCTGAACATACTCCC 58.884 52.381 0.00 0.00 0.00 4.30
462 463 3.906720 TTGCCTACCTGAACATACTCC 57.093 47.619 0.00 0.00 0.00 3.85
463 464 5.648092 ACATTTTGCCTACCTGAACATACTC 59.352 40.000 0.00 0.00 0.00 2.59
464 465 5.415701 CACATTTTGCCTACCTGAACATACT 59.584 40.000 0.00 0.00 0.00 2.12
465 466 5.414454 TCACATTTTGCCTACCTGAACATAC 59.586 40.000 0.00 0.00 0.00 2.39
471 472 2.790433 GGTCACATTTTGCCTACCTGA 58.210 47.619 0.00 0.00 0.00 3.86
492 493 6.463576 CCAAACTTGCACGAACGTATAAATAC 59.536 38.462 0.00 0.00 0.00 1.89
493 494 6.147492 ACCAAACTTGCACGAACGTATAAATA 59.853 34.615 0.00 0.00 0.00 1.40
499 500 1.328069 CACCAAACTTGCACGAACGTA 59.672 47.619 0.00 0.00 0.00 3.57
502 503 0.869880 GCCACCAAACTTGCACGAAC 60.870 55.000 0.00 0.00 0.00 3.95
503 504 1.435515 GCCACCAAACTTGCACGAA 59.564 52.632 0.00 0.00 0.00 3.85
504 505 2.485795 GGCCACCAAACTTGCACGA 61.486 57.895 0.00 0.00 0.00 4.35
505 506 2.027460 GGCCACCAAACTTGCACG 59.973 61.111 0.00 0.00 0.00 5.34
506 507 0.107945 TTTGGCCACCAAACTTGCAC 60.108 50.000 3.88 0.00 46.92 4.57
541 542 9.444600 AGTGACCGTTAGTTTGATGTATAAATT 57.555 29.630 0.00 0.00 0.00 1.82
542 543 9.444600 AAGTGACCGTTAGTTTGATGTATAAAT 57.555 29.630 0.00 0.00 0.00 1.40
543 544 8.714179 CAAGTGACCGTTAGTTTGATGTATAAA 58.286 33.333 0.00 0.00 0.00 1.40
544 545 7.874016 ACAAGTGACCGTTAGTTTGATGTATAA 59.126 33.333 0.00 0.00 0.00 0.98
545 546 7.380536 ACAAGTGACCGTTAGTTTGATGTATA 58.619 34.615 0.00 0.00 0.00 1.47
546 547 6.228258 ACAAGTGACCGTTAGTTTGATGTAT 58.772 36.000 0.00 0.00 0.00 2.29
547 548 5.603596 ACAAGTGACCGTTAGTTTGATGTA 58.396 37.500 0.00 0.00 0.00 2.29
548 549 4.448210 ACAAGTGACCGTTAGTTTGATGT 58.552 39.130 0.00 0.00 0.00 3.06
549 550 4.509970 TGACAAGTGACCGTTAGTTTGATG 59.490 41.667 0.00 0.00 0.00 3.07
550 551 4.510340 GTGACAAGTGACCGTTAGTTTGAT 59.490 41.667 0.00 0.00 0.00 2.57
551 552 3.866910 GTGACAAGTGACCGTTAGTTTGA 59.133 43.478 0.00 0.00 0.00 2.69
552 553 3.302221 CGTGACAAGTGACCGTTAGTTTG 60.302 47.826 0.00 0.00 0.00 2.93
553 554 2.861935 CGTGACAAGTGACCGTTAGTTT 59.138 45.455 0.00 0.00 0.00 2.66
554 555 2.159198 ACGTGACAAGTGACCGTTAGTT 60.159 45.455 0.00 0.00 0.00 2.24
555 556 1.406539 ACGTGACAAGTGACCGTTAGT 59.593 47.619 0.00 0.00 0.00 2.24
556 557 2.129823 ACGTGACAAGTGACCGTTAG 57.870 50.000 0.00 0.00 0.00 2.34
557 558 2.618241 AGTACGTGACAAGTGACCGTTA 59.382 45.455 4.12 0.00 33.32 3.18
558 559 1.406539 AGTACGTGACAAGTGACCGTT 59.593 47.619 4.12 0.00 33.32 4.44
559 560 1.027357 AGTACGTGACAAGTGACCGT 58.973 50.000 4.12 0.00 35.68 4.83
560 561 2.031769 TGTAGTACGTGACAAGTGACCG 60.032 50.000 4.12 0.00 0.00 4.79
561 562 3.631145 TGTAGTACGTGACAAGTGACC 57.369 47.619 4.12 0.00 0.00 4.02
567 568 6.254157 GTCAGAAAACTTGTAGTACGTGACAA 59.746 38.462 0.00 5.33 34.49 3.18
568 569 5.745294 GTCAGAAAACTTGTAGTACGTGACA 59.255 40.000 0.00 0.00 32.63 3.58
569 570 5.975939 AGTCAGAAAACTTGTAGTACGTGAC 59.024 40.000 0.00 0.00 0.00 3.67
570 571 6.140303 AGTCAGAAAACTTGTAGTACGTGA 57.860 37.500 0.00 0.00 0.00 4.35
571 572 5.401674 GGAGTCAGAAAACTTGTAGTACGTG 59.598 44.000 0.00 0.00 0.00 4.49
572 573 5.301298 AGGAGTCAGAAAACTTGTAGTACGT 59.699 40.000 0.00 0.00 0.00 3.57
573 574 5.770417 AGGAGTCAGAAAACTTGTAGTACG 58.230 41.667 0.00 0.00 0.00 3.67
574 575 5.857517 CGAGGAGTCAGAAAACTTGTAGTAC 59.142 44.000 0.00 0.00 0.00 2.73
575 576 5.048224 CCGAGGAGTCAGAAAACTTGTAGTA 60.048 44.000 0.00 0.00 0.00 1.82
576 577 4.262079 CCGAGGAGTCAGAAAACTTGTAGT 60.262 45.833 0.00 0.00 0.00 2.73
577 578 4.238514 CCGAGGAGTCAGAAAACTTGTAG 58.761 47.826 0.00 0.00 0.00 2.74
578 579 3.640029 ACCGAGGAGTCAGAAAACTTGTA 59.360 43.478 0.00 0.00 0.00 2.41
579 580 2.434702 ACCGAGGAGTCAGAAAACTTGT 59.565 45.455 0.00 0.00 0.00 3.16
580 581 2.802816 CACCGAGGAGTCAGAAAACTTG 59.197 50.000 0.00 0.00 0.00 3.16
581 582 2.434702 ACACCGAGGAGTCAGAAAACTT 59.565 45.455 0.00 0.00 0.00 2.66
582 583 2.040178 ACACCGAGGAGTCAGAAAACT 58.960 47.619 0.00 0.00 0.00 2.66
583 584 2.528041 ACACCGAGGAGTCAGAAAAC 57.472 50.000 0.00 0.00 0.00 2.43
584 585 4.884668 AATACACCGAGGAGTCAGAAAA 57.115 40.909 0.00 0.00 0.00 2.29
585 586 4.884668 AAATACACCGAGGAGTCAGAAA 57.115 40.909 0.00 0.00 0.00 2.52
586 587 4.159135 GGTAAATACACCGAGGAGTCAGAA 59.841 45.833 0.00 0.00 0.00 3.02
587 588 3.698040 GGTAAATACACCGAGGAGTCAGA 59.302 47.826 0.00 0.00 0.00 3.27
588 589 3.700038 AGGTAAATACACCGAGGAGTCAG 59.300 47.826 0.00 0.00 43.84 3.51
589 590 3.698040 GAGGTAAATACACCGAGGAGTCA 59.302 47.826 0.00 0.00 43.84 3.41
590 591 3.698040 TGAGGTAAATACACCGAGGAGTC 59.302 47.826 0.00 0.00 43.84 3.36
591 592 3.705051 TGAGGTAAATACACCGAGGAGT 58.295 45.455 0.00 0.00 43.84 3.85
592 593 4.939052 ATGAGGTAAATACACCGAGGAG 57.061 45.455 0.00 0.00 43.84 3.69
593 594 6.795144 TTTATGAGGTAAATACACCGAGGA 57.205 37.500 0.00 0.00 43.84 3.71
594 595 7.852971 TTTTTATGAGGTAAATACACCGAGG 57.147 36.000 0.00 0.00 43.84 4.63
624 625 5.820947 TGGTGATGATCTCAATCAAGTCATG 59.179 40.000 0.00 0.00 44.85 3.07
627 628 5.293814 CACTGGTGATGATCTCAATCAAGTC 59.706 44.000 0.00 0.00 44.85 3.01
629 630 4.575236 CCACTGGTGATGATCTCAATCAAG 59.425 45.833 1.93 0.00 44.85 3.02
633 634 4.019051 TGTTCCACTGGTGATGATCTCAAT 60.019 41.667 1.93 0.00 35.07 2.57
643 644 0.394192 CAGCTCTGTTCCACTGGTGA 59.606 55.000 1.93 0.00 0.00 4.02
644 645 0.604780 CCAGCTCTGTTCCACTGGTG 60.605 60.000 0.00 0.00 43.86 4.17
645 646 1.757306 CCAGCTCTGTTCCACTGGT 59.243 57.895 0.00 0.00 43.86 4.00
646 647 4.709840 CCAGCTCTGTTCCACTGG 57.290 61.111 0.00 0.00 43.45 4.00
647 648 0.972134 TCTCCAGCTCTGTTCCACTG 59.028 55.000 0.00 0.00 0.00 3.66
648 649 1.830477 GATCTCCAGCTCTGTTCCACT 59.170 52.381 0.00 0.00 0.00 4.00
649 650 1.470632 CGATCTCCAGCTCTGTTCCAC 60.471 57.143 0.00 0.00 0.00 4.02
650 651 0.820226 CGATCTCCAGCTCTGTTCCA 59.180 55.000 0.00 0.00 0.00 3.53
651 652 1.107114 TCGATCTCCAGCTCTGTTCC 58.893 55.000 0.00 0.00 0.00 3.62
652 653 2.094494 TGTTCGATCTCCAGCTCTGTTC 60.094 50.000 0.00 0.00 0.00 3.18
658 659 1.745141 GCCAATGTTCGATCTCCAGCT 60.745 52.381 0.00 0.00 0.00 4.24
671 672 1.339929 GAAGTTTGAACGGGCCAATGT 59.660 47.619 4.39 0.00 0.00 2.71
712 713 1.301165 GTGCGTGGGACCTTACGTT 60.301 57.895 18.41 0.00 41.98 3.99
717 718 0.322322 TTTATCGTGCGTGGGACCTT 59.678 50.000 0.00 0.00 0.00 3.50
764 765 2.093816 GCTGGTGAGTGATGACTGATGA 60.094 50.000 0.00 0.00 30.16 2.92
770 771 1.357258 CTGCGCTGGTGAGTGATGAC 61.357 60.000 9.73 0.00 0.00 3.06
773 774 2.435586 GCTGCGCTGGTGAGTGAT 60.436 61.111 16.47 0.00 0.00 3.06
774 775 4.687215 GGCTGCGCTGGTGAGTGA 62.687 66.667 16.47 0.00 0.00 3.41
854 864 1.706287 GCGTCTCCCTTTGGATTCGC 61.706 60.000 12.19 12.19 46.74 4.70
900 910 1.703411 TTGAACTGAGCTTTTGGGGG 58.297 50.000 0.00 0.00 0.00 5.40
901 911 2.224042 GGTTTGAACTGAGCTTTTGGGG 60.224 50.000 0.00 0.00 0.00 4.96
1137 1465 2.515071 CCTAGCTAGGGCAGGCAGG 61.515 68.421 29.47 5.40 39.86 4.85
1138 1466 3.146182 CCTAGCTAGGGCAGGCAG 58.854 66.667 29.47 3.52 39.86 4.85
1178 1506 0.322546 ACCCAAAGCCGATCAGGAAC 60.323 55.000 7.64 0.00 45.00 3.62
1246 1574 4.988598 ACACCTGCTTCGCCACCG 62.989 66.667 0.00 0.00 0.00 4.94
1372 1700 5.810080 ATGTAGGTTATAAGCTCACCTCC 57.190 43.478 19.99 0.00 40.29 4.30
1438 1766 4.447724 CACACTCACACAGGTACATAACAC 59.552 45.833 0.00 0.00 0.00 3.32
1449 1777 0.732538 TATCGCGCACACTCACACAG 60.733 55.000 8.75 0.00 0.00 3.66
1704 2046 3.719121 GCTCTCTTCCAGGGCTCA 58.281 61.111 0.00 0.00 46.57 4.26
1733 2075 1.851304 TGGCCATCCAATGAAGGTTC 58.149 50.000 0.00 0.00 39.99 3.62
1746 2088 0.179084 CGGAGACACGTAATGGCCAT 60.179 55.000 14.09 14.09 36.75 4.40
1763 2105 1.531149 ACAGAATCTGAAAACACGCGG 59.469 47.619 18.20 1.27 35.18 6.46
1764 2106 2.220824 TGACAGAATCTGAAAACACGCG 59.779 45.455 18.20 3.53 35.18 6.01
1767 2109 7.484035 AGTTACTGACAGAATCTGAAAACAC 57.516 36.000 18.20 6.25 35.18 3.32
1828 2170 3.793144 GGCGCTTCCTTGTGCTCG 61.793 66.667 7.64 0.00 42.46 5.03
1902 2244 0.670546 GGATGGTCACACACACCTCG 60.671 60.000 0.00 0.00 34.66 4.63
1914 2256 0.533755 CAGGCGAGGAATGGATGGTC 60.534 60.000 0.00 0.00 0.00 4.02
1926 2268 1.787847 CAACGTAAAGGCAGGCGAG 59.212 57.895 0.00 0.00 0.00 5.03
1966 2308 5.971202 CCACAGCAAACACAAGTTACTTAAG 59.029 40.000 0.00 0.00 36.84 1.85
1969 2311 3.761752 ACCACAGCAAACACAAGTTACTT 59.238 39.130 0.00 0.00 36.84 2.24
2073 2415 1.004440 GGAGAGTGGTGGTGTGAGC 60.004 63.158 0.00 0.00 0.00 4.26
2194 2536 9.166173 GCATATATTAACAGGCACATAATCTGA 57.834 33.333 0.00 0.00 33.19 3.27
2221 2563 4.080919 CCTCCCTACACATCATGAAAGACA 60.081 45.833 0.00 0.00 0.00 3.41
2291 2633 6.325849 TCGTATGTTGTAACATTCATGTCG 57.674 37.500 14.69 9.71 46.95 4.35
2408 2750 4.202020 CCGTACCGATGATTCTCTGAGAAA 60.202 45.833 22.68 9.05 37.82 2.52
2489 2831 3.315418 CTCTGCATCACTATCATCACCG 58.685 50.000 0.00 0.00 0.00 4.94
2732 3074 1.670791 GGTTCAAAACAGGACGGACA 58.329 50.000 0.00 0.00 0.00 4.02
2888 3230 0.617535 TGCTAGAGTTGCTAGGGCCA 60.618 55.000 6.18 0.00 45.55 5.36
3560 3919 4.060205 GTCATGCAAACAAGCCAATTCTT 58.940 39.130 0.00 0.00 0.00 2.52
3608 3967 0.457035 ACACAGGCACACAGCTTTTG 59.543 50.000 0.00 0.00 44.79 2.44
3609 3968 0.457035 CACACAGGCACACAGCTTTT 59.543 50.000 0.00 0.00 44.79 2.27
3612 3971 2.903855 GCACACAGGCACACAGCT 60.904 61.111 0.00 0.00 44.79 4.24
3613 3972 3.211245 TGCACACAGGCACACAGC 61.211 61.111 0.00 0.00 39.25 4.40
3620 3979 1.195900 CAATTTGCAATGCACACAGGC 59.804 47.619 7.72 0.00 38.71 4.85
3621 3980 2.222213 CACAATTTGCAATGCACACAGG 59.778 45.455 7.72 0.00 38.71 4.00
3622 3981 3.124560 TCACAATTTGCAATGCACACAG 58.875 40.909 7.72 0.00 38.71 3.66
3623 3982 3.175109 TCACAATTTGCAATGCACACA 57.825 38.095 7.72 0.00 38.71 3.72
3624 3983 4.533225 TTTCACAATTTGCAATGCACAC 57.467 36.364 7.72 0.00 38.71 3.82
3625 3984 5.556355 TTTTTCACAATTTGCAATGCACA 57.444 30.435 7.72 0.46 38.71 4.57
3626 3985 6.074782 CCAATTTTTCACAATTTGCAATGCAC 60.075 34.615 7.72 0.00 38.71 4.57
3627 3986 5.977725 CCAATTTTTCACAATTTGCAATGCA 59.022 32.000 2.72 2.72 36.47 3.96
3628 3987 5.978322 ACCAATTTTTCACAATTTGCAATGC 59.022 32.000 0.00 0.00 0.00 3.56
3629 3988 7.988904 AACCAATTTTTCACAATTTGCAATG 57.011 28.000 0.00 0.00 0.00 2.82
3637 3996 9.777297 AGCAACTAATAACCAATTTTTCACAAT 57.223 25.926 0.00 0.00 0.00 2.71
3638 3997 9.255304 GAGCAACTAATAACCAATTTTTCACAA 57.745 29.630 0.00 0.00 0.00 3.33
3639 3998 8.417106 TGAGCAACTAATAACCAATTTTTCACA 58.583 29.630 0.00 0.00 0.00 3.58
3640 3999 8.810652 TGAGCAACTAATAACCAATTTTTCAC 57.189 30.769 0.00 0.00 0.00 3.18
3641 4000 9.638239 GATGAGCAACTAATAACCAATTTTTCA 57.362 29.630 0.00 0.00 0.00 2.69
3725 4084 1.360393 TTCAGAACCCACAAGGCCCT 61.360 55.000 0.00 0.00 40.58 5.19
3773 4132 1.606668 GTGAAATCGAGGTTGTGCCAA 59.393 47.619 0.00 0.00 40.61 4.52
4008 4442 3.276857 ACTGAATTAGCAGCCATGAGTG 58.723 45.455 0.00 0.00 39.51 3.51
4030 4464 1.535028 CACAATGTTTGCGCTAGTCCA 59.465 47.619 9.73 0.00 0.00 4.02
4081 4518 7.256190 CCCCCGAGAAGAATAATCACAGTATTA 60.256 40.741 0.00 0.00 0.00 0.98
4089 4526 4.855298 AAACCCCCGAGAAGAATAATCA 57.145 40.909 0.00 0.00 0.00 2.57
4093 4530 3.560453 CCACAAAACCCCCGAGAAGAATA 60.560 47.826 0.00 0.00 0.00 1.75
4113 4742 0.916086 ACAAATCCCATAGGTCGCCA 59.084 50.000 0.00 0.00 0.00 5.69
4121 4750 7.415592 TTTCATGTATGCAACAAATCCCATA 57.584 32.000 0.00 0.00 42.70 2.74
4150 4779 2.542020 TCAAAACTCTCATGTGGCGA 57.458 45.000 0.00 0.00 0.00 5.54
4308 4941 1.137872 GGTGTGGCCTGATCTAGACAG 59.862 57.143 3.32 12.68 35.43 3.51
4324 4957 1.578583 GACACGCACAAAGTAGGTGT 58.421 50.000 5.45 5.45 43.87 4.16


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

AutoCloner maintained by Alex Coulton.