Multiple sequence alignment - TraesCS4A01G088900

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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 TraesCS4A01G088900 chr4A 100.000 3889 0 0 1 3889 94822307 94826195 0.000000e+00 7182.0
1 TraesCS4A01G088900 chr4A 83.938 193 29 2 1043 1234 658230893 658230702 2.390000e-42 183.0
2 TraesCS4A01G088900 chr4A 83.333 192 30 2 1044 1234 657882303 657882493 3.990000e-40 176.0
3 TraesCS4A01G088900 chr4B 95.234 2623 108 8 879 3495 455012833 455010222 0.000000e+00 4135.0
4 TraesCS4A01G088900 chr4B 90.000 460 30 8 433 883 76050595 76050143 7.240000e-162 580.0
5 TraesCS4A01G088900 chr4B 90.411 438 30 6 433 866 385954573 385954144 2.030000e-157 566.0
6 TraesCS4A01G088900 chr4B 96.012 326 9 1 3568 3889 455010221 455009896 9.570000e-146 527.0
7 TraesCS4A01G088900 chr4B 85.000 220 24 8 1 217 592994993 592994780 8.460000e-52 215.0
8 TraesCS4A01G088900 chr4B 77.431 288 55 8 2394 2676 139106968 139107250 3.110000e-36 163.0
9 TraesCS4A01G088900 chr4B 75.706 177 35 6 1806 1978 432257692 432257520 8.960000e-12 82.4
10 TraesCS4A01G088900 chr4D 96.308 2519 88 3 992 3509 369862745 369860231 0.000000e+00 4132.0
11 TraesCS4A01G088900 chr4D 95.956 2522 97 3 989 3509 369873832 369876349 0.000000e+00 4087.0
12 TraesCS4A01G088900 chr4D 95.128 390 15 1 3504 3889 369859159 369858770 2.570000e-171 612.0
13 TraesCS4A01G088900 chr4D 95.128 390 15 1 3504 3889 369877421 369877810 2.570000e-171 612.0
14 TraesCS4A01G088900 chr4D 90.370 270 22 3 9 275 369892347 369892079 6.180000e-93 351.0
15 TraesCS4A01G088900 chr4D 78.832 274 48 8 2395 2663 97383997 97384265 3.990000e-40 176.0
16 TraesCS4A01G088900 chr4D 78.409 264 48 9 2403 2663 97379113 97379370 3.110000e-36 163.0
17 TraesCS4A01G088900 chr4D 91.026 78 5 2 879 954 369890590 369890513 1.910000e-18 104.0
18 TraesCS4A01G088900 chr4D 82.278 79 13 1 1893 1970 349410897 349410819 2.510000e-07 67.6
19 TraesCS4A01G088900 chr7D 91.344 439 24 8 433 864 219836551 219836982 4.330000e-164 588.0
20 TraesCS4A01G088900 chr7D 91.304 437 25 9 432 865 379317900 379317474 5.600000e-163 584.0
21 TraesCS4A01G088900 chr7D 78.191 376 65 12 1031 1405 45551932 45552291 1.410000e-54 224.0
22 TraesCS4A01G088900 chr3A 90.703 441 29 6 431 866 209407678 209408111 9.370000e-161 577.0
23 TraesCS4A01G088900 chr3A 89.933 447 31 6 427 866 725837657 725838096 7.290000e-157 564.0
24 TraesCS4A01G088900 chr3A 79.535 215 38 4 1044 1255 713963861 713963650 8.710000e-32 148.0
25 TraesCS4A01G088900 chr7B 90.639 438 28 6 433 866 516134930 516135358 1.570000e-158 569.0
26 TraesCS4A01G088900 chr7B 87.838 222 23 3 1 218 677415128 677415349 1.390000e-64 257.0
27 TraesCS4A01G088900 chr2B 90.455 440 31 5 431 866 679154991 679155423 1.570000e-158 569.0
28 TraesCS4A01G088900 chr2B 89.978 449 30 9 425 866 622642189 622641749 2.030000e-157 566.0
29 TraesCS4A01G088900 chr7A 77.807 383 66 13 1025 1405 47690747 47691112 6.540000e-53 219.0
30 TraesCS4A01G088900 chr7A 84.971 173 23 3 1043 1214 47832613 47832443 5.170000e-39 172.0
31 TraesCS4A01G088900 chr5D 83.556 225 26 9 1 218 446257252 446257472 2.370000e-47 200.0
32 TraesCS4A01G088900 chr6D 90.123 81 4 3 56 134 16586878 16586956 6.870000e-18 102.0
33 TraesCS4A01G088900 chr1A 95.652 46 0 2 75 118 558941069 558941114 5.390000e-09 73.1


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 TraesCS4A01G088900 chr4A 94822307 94826195 3888 False 7182.0 7182 100.000 1 3889 1 chr4A.!!$F1 3888
1 TraesCS4A01G088900 chr4B 455009896 455012833 2937 True 2331.0 4135 95.623 879 3889 2 chr4B.!!$R5 3010
2 TraesCS4A01G088900 chr4D 369858770 369862745 3975 True 2372.0 4132 95.718 992 3889 2 chr4D.!!$R2 2897
3 TraesCS4A01G088900 chr4D 369873832 369877810 3978 False 2349.5 4087 95.542 989 3889 2 chr4D.!!$F3 2900
4 TraesCS4A01G088900 chr4D 369890513 369892347 1834 True 227.5 351 90.698 9 954 2 chr4D.!!$R3 945

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
409 412 0.034059 CGGCCCGCTTTAGATCAGAT 59.966 55.000 0.0 0.0 0.00 2.90 F
710 713 0.249031 GCTGAAAATATGCGGCCCAC 60.249 55.000 0.0 0.0 0.00 4.61 F
1356 1360 0.318762 GGCCTCCTTATCTACGGCAG 59.681 60.000 0.0 0.0 42.43 4.85 F
1569 1573 1.151450 CACCAACACCCTTCTGCCT 59.849 57.895 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 3001 0.032678 ACATAGAATGCTCCTCGCCG 59.967 55.0 0.00 0.00 38.05 6.46 R
2694 3781 1.289160 TCTCCAGATCCCAACCCAAG 58.711 55.0 0.00 0.00 0.00 3.61 R
2737 3824 1.150567 CTTCTGGCTCCTTGCGATCG 61.151 60.0 11.69 11.69 44.05 3.69 R
3436 4523 0.407528 TATGACTGCCCCTTTTGCCA 59.592 50.0 0.00 0.00 0.00 4.92 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
88 90 6.019156 TGTTCGTGGAATTTGCTTTTGAAATC 60.019 34.615 0.00 0.00 0.00 2.17
149 151 6.527722 ACATGTTTTCTGCAATAAATAGCACG 59.472 34.615 0.00 0.00 36.62 5.34
154 156 3.871006 TCTGCAATAAATAGCACGTCTGG 59.129 43.478 0.00 0.00 36.62 3.86
172 174 5.220970 CGTCTGGTGTTGTTCTTAAATGGTT 60.221 40.000 0.00 0.00 0.00 3.67
204 206 5.421212 AATAGTCAGTAGCACGTAGTAGC 57.579 43.478 0.00 0.00 41.61 3.58
206 208 2.937799 AGTCAGTAGCACGTAGTAGCTC 59.062 50.000 0.84 0.00 41.61 4.09
228 231 4.373348 GAGTGGTTAGCTACTCGTGAAT 57.627 45.455 7.31 0.00 42.01 2.57
237 240 7.065443 GGTTAGCTACTCGTGAATAACCATTTT 59.935 37.037 0.00 0.00 41.07 1.82
242 245 4.142902 ACTCGTGAATAACCATTTTCTGCG 60.143 41.667 0.00 0.00 0.00 5.18
253 256 3.980775 CCATTTTCTGCGGTGTTTTGTAG 59.019 43.478 0.00 0.00 0.00 2.74
261 264 1.567537 GTGTTTTGTAGCGCTGCGA 59.432 52.632 28.07 17.13 0.00 5.10
275 278 3.563088 GCGATGCGCGTTGATGGA 61.563 61.111 21.27 0.00 44.55 3.41
277 280 2.709475 GATGCGCGTTGATGGACC 59.291 61.111 8.43 0.00 0.00 4.46
278 281 3.155470 GATGCGCGTTGATGGACCG 62.155 63.158 8.43 0.00 0.00 4.79
280 283 3.849953 GCGCGTTGATGGACCGAC 61.850 66.667 8.43 0.00 0.00 4.79
281 284 3.186047 CGCGTTGATGGACCGACC 61.186 66.667 0.00 0.00 39.54 4.79
282 285 2.818274 GCGTTGATGGACCGACCC 60.818 66.667 0.00 0.00 38.00 4.46
283 286 2.660206 CGTTGATGGACCGACCCA 59.340 61.111 0.00 0.00 41.05 4.51
284 287 1.447838 CGTTGATGGACCGACCCAG 60.448 63.158 2.40 0.00 39.97 4.45
285 288 1.884075 CGTTGATGGACCGACCCAGA 61.884 60.000 2.40 0.00 39.97 3.86
286 289 0.323629 GTTGATGGACCGACCCAGAA 59.676 55.000 2.40 0.00 39.97 3.02
287 290 0.613260 TTGATGGACCGACCCAGAAG 59.387 55.000 2.40 0.00 39.97 2.85
288 291 0.252057 TGATGGACCGACCCAGAAGA 60.252 55.000 2.40 0.00 39.97 2.87
289 292 0.175989 GATGGACCGACCCAGAAGAC 59.824 60.000 2.40 0.00 39.97 3.01
290 293 0.544357 ATGGACCGACCCAGAAGACA 60.544 55.000 2.40 0.00 39.97 3.41
291 294 1.292541 GGACCGACCCAGAAGACAC 59.707 63.158 0.00 0.00 0.00 3.67
292 295 1.186267 GGACCGACCCAGAAGACACT 61.186 60.000 0.00 0.00 0.00 3.55
293 296 0.038159 GACCGACCCAGAAGACACTG 60.038 60.000 0.00 0.00 37.61 3.66
294 297 1.374758 CCGACCCAGAAGACACTGC 60.375 63.158 0.00 0.00 36.67 4.40
295 298 1.374758 CGACCCAGAAGACACTGCC 60.375 63.158 0.00 0.00 36.67 4.85
296 299 1.374758 GACCCAGAAGACACTGCCG 60.375 63.158 0.00 0.00 36.67 5.69
297 300 2.743928 CCCAGAAGACACTGCCGC 60.744 66.667 0.00 0.00 36.67 6.53
298 301 3.114616 CCAGAAGACACTGCCGCG 61.115 66.667 0.00 0.00 36.67 6.46
299 302 2.049156 CAGAAGACACTGCCGCGA 60.049 61.111 8.23 0.00 0.00 5.87
300 303 2.091112 CAGAAGACACTGCCGCGAG 61.091 63.158 8.23 0.00 0.00 5.03
301 304 3.482783 GAAGACACTGCCGCGAGC 61.483 66.667 8.23 10.56 44.14 5.03
322 325 4.659874 CGTTGCGTTCCGTGGCAC 62.660 66.667 7.79 7.79 39.20 5.01
323 326 3.578272 GTTGCGTTCCGTGGCACA 61.578 61.111 19.09 0.00 39.20 4.57
324 327 3.276091 TTGCGTTCCGTGGCACAG 61.276 61.111 19.09 6.46 41.80 3.66
325 328 3.741830 TTGCGTTCCGTGGCACAGA 62.742 57.895 19.09 9.25 41.80 3.41
326 329 2.970324 GCGTTCCGTGGCACAGAA 60.970 61.111 19.09 15.48 41.80 3.02
327 330 2.954753 GCGTTCCGTGGCACAGAAG 61.955 63.158 16.21 11.37 41.80 2.85
328 331 2.317609 CGTTCCGTGGCACAGAAGG 61.318 63.158 16.21 17.46 41.80 3.46
329 332 2.281484 TTCCGTGGCACAGAAGGC 60.281 61.111 19.09 0.00 41.80 4.35
330 333 4.680237 TCCGTGGCACAGAAGGCG 62.680 66.667 19.09 1.02 41.80 5.52
336 339 3.127533 GCACAGAAGGCGCGGATT 61.128 61.111 8.83 0.00 0.00 3.01
337 340 1.813753 GCACAGAAGGCGCGGATTA 60.814 57.895 8.83 0.00 0.00 1.75
338 341 1.766143 GCACAGAAGGCGCGGATTAG 61.766 60.000 8.83 0.00 0.00 1.73
339 342 1.144057 ACAGAAGGCGCGGATTAGG 59.856 57.895 8.83 0.00 0.00 2.69
340 343 1.327690 ACAGAAGGCGCGGATTAGGA 61.328 55.000 8.83 0.00 0.00 2.94
341 344 0.598680 CAGAAGGCGCGGATTAGGAG 60.599 60.000 8.83 0.00 0.00 3.69
342 345 1.956678 GAAGGCGCGGATTAGGAGC 60.957 63.158 8.83 0.00 0.00 4.70
343 346 2.370647 GAAGGCGCGGATTAGGAGCT 62.371 60.000 8.83 0.00 0.00 4.09
344 347 1.113517 AAGGCGCGGATTAGGAGCTA 61.114 55.000 8.83 0.00 0.00 3.32
345 348 0.900647 AGGCGCGGATTAGGAGCTAT 60.901 55.000 8.83 0.00 0.00 2.97
346 349 0.037232 GGCGCGGATTAGGAGCTATT 60.037 55.000 8.83 0.00 0.00 1.73
347 350 1.608283 GGCGCGGATTAGGAGCTATTT 60.608 52.381 8.83 0.00 0.00 1.40
348 351 2.143925 GCGCGGATTAGGAGCTATTTT 58.856 47.619 8.83 0.00 0.00 1.82
349 352 2.548480 GCGCGGATTAGGAGCTATTTTT 59.452 45.455 8.83 0.00 0.00 1.94
370 373 6.636454 TTTTAGGGAAGATTAAGGAGCTGA 57.364 37.500 0.00 0.00 0.00 4.26
371 374 6.831664 TTTAGGGAAGATTAAGGAGCTGAT 57.168 37.500 0.00 0.00 0.00 2.90
372 375 6.831664 TTAGGGAAGATTAAGGAGCTGATT 57.168 37.500 0.00 0.00 0.00 2.57
373 376 5.723860 AGGGAAGATTAAGGAGCTGATTT 57.276 39.130 0.00 0.00 0.00 2.17
374 377 6.084749 AGGGAAGATTAAGGAGCTGATTTT 57.915 37.500 0.00 0.00 0.00 1.82
375 378 5.890419 AGGGAAGATTAAGGAGCTGATTTTG 59.110 40.000 0.00 0.00 0.00 2.44
376 379 5.888161 GGGAAGATTAAGGAGCTGATTTTGA 59.112 40.000 0.00 0.00 0.00 2.69
377 380 6.548993 GGGAAGATTAAGGAGCTGATTTTGAT 59.451 38.462 0.00 0.00 0.00 2.57
378 381 7.255416 GGGAAGATTAAGGAGCTGATTTTGATC 60.255 40.741 0.00 0.00 0.00 2.92
379 382 7.284034 GGAAGATTAAGGAGCTGATTTTGATCA 59.716 37.037 0.00 0.00 0.00 2.92
380 383 7.565323 AGATTAAGGAGCTGATTTTGATCAC 57.435 36.000 0.00 0.00 0.00 3.06
381 384 5.801350 TTAAGGAGCTGATTTTGATCACG 57.199 39.130 0.00 0.00 0.00 4.35
382 385 2.636830 AGGAGCTGATTTTGATCACGG 58.363 47.619 0.00 0.00 0.00 4.94
383 386 2.026822 AGGAGCTGATTTTGATCACGGT 60.027 45.455 0.00 0.00 0.00 4.83
384 387 2.352960 GGAGCTGATTTTGATCACGGTC 59.647 50.000 0.00 0.00 0.00 4.79
385 388 3.265791 GAGCTGATTTTGATCACGGTCT 58.734 45.455 0.00 0.00 0.00 3.85
386 389 3.679389 AGCTGATTTTGATCACGGTCTT 58.321 40.909 0.00 0.00 0.00 3.01
387 390 3.686726 AGCTGATTTTGATCACGGTCTTC 59.313 43.478 0.00 0.00 0.00 2.87
388 391 3.181506 GCTGATTTTGATCACGGTCTTCC 60.182 47.826 0.00 0.00 0.00 3.46
389 392 3.343617 TGATTTTGATCACGGTCTTCCC 58.656 45.455 0.00 0.00 0.00 3.97
390 393 2.194201 TTTTGATCACGGTCTTCCCC 57.806 50.000 0.00 0.00 0.00 4.81
401 404 4.104183 CTTCCCCGGCCCGCTTTA 62.104 66.667 0.00 0.00 0.00 1.85
402 405 4.104183 TTCCCCGGCCCGCTTTAG 62.104 66.667 0.00 0.00 0.00 1.85
404 407 3.873812 CCCCGGCCCGCTTTAGAT 61.874 66.667 0.00 0.00 0.00 1.98
405 408 2.280865 CCCGGCCCGCTTTAGATC 60.281 66.667 0.00 0.00 0.00 2.75
406 409 2.504032 CCGGCCCGCTTTAGATCA 59.496 61.111 0.00 0.00 0.00 2.92
407 410 1.595382 CCGGCCCGCTTTAGATCAG 60.595 63.158 0.00 0.00 0.00 2.90
408 411 1.441729 CGGCCCGCTTTAGATCAGA 59.558 57.895 0.00 0.00 0.00 3.27
409 412 0.034059 CGGCCCGCTTTAGATCAGAT 59.966 55.000 0.00 0.00 0.00 2.90
410 413 1.802069 GGCCCGCTTTAGATCAGATC 58.198 55.000 1.64 1.64 0.00 2.75
411 414 1.070758 GGCCCGCTTTAGATCAGATCA 59.929 52.381 13.14 0.00 0.00 2.92
412 415 2.485479 GGCCCGCTTTAGATCAGATCAA 60.485 50.000 13.14 2.64 0.00 2.57
413 416 2.545946 GCCCGCTTTAGATCAGATCAAC 59.454 50.000 13.14 0.00 0.00 3.18
414 417 3.742640 GCCCGCTTTAGATCAGATCAACT 60.743 47.826 13.14 0.00 0.00 3.16
415 418 3.806521 CCCGCTTTAGATCAGATCAACTG 59.193 47.826 13.14 1.82 46.97 3.16
416 419 3.806521 CCGCTTTAGATCAGATCAACTGG 59.193 47.826 13.14 3.11 45.76 4.00
417 420 3.247173 CGCTTTAGATCAGATCAACTGGC 59.753 47.826 13.14 8.73 45.76 4.85
418 421 4.194640 GCTTTAGATCAGATCAACTGGCA 58.805 43.478 13.14 0.00 45.76 4.92
419 422 4.637534 GCTTTAGATCAGATCAACTGGCAA 59.362 41.667 13.14 0.00 45.76 4.52
420 423 5.448360 GCTTTAGATCAGATCAACTGGCAAC 60.448 44.000 13.14 0.00 45.76 4.17
421 424 2.996631 AGATCAGATCAACTGGCAACC 58.003 47.619 13.14 0.00 45.76 3.77
422 425 2.575279 AGATCAGATCAACTGGCAACCT 59.425 45.455 13.14 0.00 45.76 3.50
423 426 2.189594 TCAGATCAACTGGCAACCTG 57.810 50.000 0.00 0.00 45.76 4.00
424 427 1.171308 CAGATCAACTGGCAACCTGG 58.829 55.000 0.00 0.00 42.39 4.45
425 428 0.610232 AGATCAACTGGCAACCTGGC 60.610 55.000 0.00 0.00 44.03 4.85
437 440 3.339141 GCAACCTGGCCTAGATTATAGC 58.661 50.000 3.32 0.00 0.00 2.97
438 441 3.008485 GCAACCTGGCCTAGATTATAGCT 59.992 47.826 3.32 0.00 0.00 3.32
439 442 4.573900 CAACCTGGCCTAGATTATAGCTG 58.426 47.826 3.32 0.00 0.00 4.24
440 443 3.177228 ACCTGGCCTAGATTATAGCTGG 58.823 50.000 3.32 0.00 0.00 4.85
441 444 2.093235 CCTGGCCTAGATTATAGCTGGC 60.093 54.545 3.32 0.00 39.61 4.85
444 447 3.703001 GCCTAGATTATAGCTGGCCAA 57.297 47.619 7.01 0.00 34.81 4.52
445 448 4.021102 GCCTAGATTATAGCTGGCCAAA 57.979 45.455 7.01 0.00 34.81 3.28
446 449 4.593956 GCCTAGATTATAGCTGGCCAAAT 58.406 43.478 7.01 2.43 34.81 2.32
447 450 4.397417 GCCTAGATTATAGCTGGCCAAATG 59.603 45.833 7.01 0.00 34.81 2.32
448 451 4.946157 CCTAGATTATAGCTGGCCAAATGG 59.054 45.833 7.01 0.00 38.53 3.16
449 452 3.771216 AGATTATAGCTGGCCAAATGGG 58.229 45.455 7.01 0.00 40.85 4.00
481 484 4.790962 CTGGCCCGTGAGCATGCT 62.791 66.667 22.92 22.92 0.00 3.79
486 489 3.807538 CCGTGAGCATGCTGGCAC 61.808 66.667 28.27 25.10 35.83 5.01
487 490 4.156622 CGTGAGCATGCTGGCACG 62.157 66.667 33.60 33.60 46.25 5.34
488 491 4.471726 GTGAGCATGCTGGCACGC 62.472 66.667 28.27 13.60 35.15 5.34
510 513 3.365265 CCTTGGGCCAAGCACGAC 61.365 66.667 35.76 0.00 39.85 4.34
511 514 2.594303 CTTGGGCCAAGCACGACA 60.594 61.111 31.72 1.17 34.63 4.35
512 515 2.904866 TTGGGCCAAGCACGACAC 60.905 61.111 16.66 0.00 32.76 3.67
513 516 3.705934 TTGGGCCAAGCACGACACA 62.706 57.895 16.66 0.00 32.76 3.72
514 517 3.357079 GGGCCAAGCACGACACAG 61.357 66.667 4.39 0.00 0.00 3.66
515 518 3.357079 GGCCAAGCACGACACAGG 61.357 66.667 0.00 0.00 0.00 4.00
516 519 4.030452 GCCAAGCACGACACAGGC 62.030 66.667 0.00 0.00 34.71 4.85
517 520 2.281070 CCAAGCACGACACAGGCT 60.281 61.111 0.00 0.00 40.14 4.58
518 521 1.005037 CCAAGCACGACACAGGCTA 60.005 57.895 0.00 0.00 36.76 3.93
519 522 0.602638 CCAAGCACGACACAGGCTAA 60.603 55.000 0.00 0.00 36.76 3.09
520 523 1.225855 CAAGCACGACACAGGCTAAA 58.774 50.000 0.00 0.00 36.76 1.85
521 524 1.069906 CAAGCACGACACAGGCTAAAC 60.070 52.381 0.00 0.00 36.76 2.01
522 525 0.944311 AGCACGACACAGGCTAAACG 60.944 55.000 0.00 0.00 35.82 3.60
523 526 1.897398 GCACGACACAGGCTAAACGG 61.897 60.000 0.00 0.00 0.00 4.44
524 527 1.005394 ACGACACAGGCTAAACGGG 60.005 57.895 0.00 0.00 0.00 5.28
525 528 2.388232 CGACACAGGCTAAACGGGC 61.388 63.158 0.00 0.00 0.00 6.13
614 617 4.519540 GCATATGGCCCGATTACATTTT 57.480 40.909 0.00 0.00 36.11 1.82
615 618 4.881920 GCATATGGCCCGATTACATTTTT 58.118 39.130 0.00 0.00 36.11 1.94
651 654 6.392911 ACATCTATATATGGCCCAACATGT 57.607 37.500 0.00 0.00 32.39 3.21
652 655 7.509236 ACATCTATATATGGCCCAACATGTA 57.491 36.000 0.00 0.00 32.39 2.29
653 656 7.927788 ACATCTATATATGGCCCAACATGTAA 58.072 34.615 0.00 0.00 30.02 2.41
654 657 8.390143 ACATCTATATATGGCCCAACATGTAAA 58.610 33.333 0.00 0.00 30.02 2.01
655 658 9.241919 CATCTATATATGGCCCAACATGTAAAA 57.758 33.333 0.00 0.00 30.02 1.52
656 659 9.821240 ATCTATATATGGCCCAACATGTAAAAA 57.179 29.630 0.00 0.00 30.02 1.94
657 660 9.821240 TCTATATATGGCCCAACATGTAAAAAT 57.179 29.630 0.00 0.00 30.02 1.82
660 663 5.612725 ATGGCCCAACATGTAAAAATAGG 57.387 39.130 0.00 0.00 0.00 2.57
661 664 3.196685 TGGCCCAACATGTAAAAATAGGC 59.803 43.478 0.00 4.05 37.14 3.93
662 665 3.450817 GGCCCAACATGTAAAAATAGGCT 59.549 43.478 0.00 0.00 37.98 4.58
663 666 4.647399 GGCCCAACATGTAAAAATAGGCTA 59.353 41.667 0.00 0.00 37.98 3.93
664 667 5.128008 GGCCCAACATGTAAAAATAGGCTAA 59.872 40.000 0.00 0.00 37.98 3.09
665 668 6.351456 GGCCCAACATGTAAAAATAGGCTAAA 60.351 38.462 0.00 0.00 37.98 1.85
666 669 7.100409 GCCCAACATGTAAAAATAGGCTAAAA 58.900 34.615 0.00 0.00 35.00 1.52
667 670 7.604545 GCCCAACATGTAAAAATAGGCTAAAAA 59.395 33.333 0.00 0.00 35.00 1.94
690 693 3.109230 GCTCAGTGCGTCAAATAACAG 57.891 47.619 0.00 0.00 0.00 3.16
691 694 2.159653 GCTCAGTGCGTCAAATAACAGG 60.160 50.000 0.00 0.00 0.00 4.00
692 695 1.804151 TCAGTGCGTCAAATAACAGGC 59.196 47.619 0.00 0.00 0.00 4.85
693 696 1.806542 CAGTGCGTCAAATAACAGGCT 59.193 47.619 0.00 0.00 0.00 4.58
694 697 1.806542 AGTGCGTCAAATAACAGGCTG 59.193 47.619 14.16 14.16 0.00 4.85
695 698 1.804151 GTGCGTCAAATAACAGGCTGA 59.196 47.619 23.66 0.00 0.00 4.26
696 699 2.225491 GTGCGTCAAATAACAGGCTGAA 59.775 45.455 23.66 9.24 0.00 3.02
697 700 2.881513 TGCGTCAAATAACAGGCTGAAA 59.118 40.909 23.66 8.84 0.00 2.69
698 701 3.316588 TGCGTCAAATAACAGGCTGAAAA 59.683 39.130 23.66 6.07 0.00 2.29
699 702 4.022416 TGCGTCAAATAACAGGCTGAAAAT 60.022 37.500 23.66 8.29 0.00 1.82
700 703 5.182190 TGCGTCAAATAACAGGCTGAAAATA 59.818 36.000 23.66 8.85 0.00 1.40
701 704 6.127758 TGCGTCAAATAACAGGCTGAAAATAT 60.128 34.615 23.66 10.72 0.00 1.28
702 705 6.197096 GCGTCAAATAACAGGCTGAAAATATG 59.803 38.462 23.66 12.30 0.00 1.78
703 706 6.197096 CGTCAAATAACAGGCTGAAAATATGC 59.803 38.462 23.66 4.75 0.00 3.14
704 707 6.197096 GTCAAATAACAGGCTGAAAATATGCG 59.803 38.462 23.66 8.60 0.00 4.73
705 708 4.836125 ATAACAGGCTGAAAATATGCGG 57.164 40.909 23.66 0.00 0.00 5.69
706 709 0.740737 ACAGGCTGAAAATATGCGGC 59.259 50.000 23.66 0.00 35.68 6.53
709 712 2.114638 GCTGAAAATATGCGGCCCA 58.885 52.632 0.00 0.00 0.00 5.36
710 713 0.249031 GCTGAAAATATGCGGCCCAC 60.249 55.000 0.00 0.00 0.00 4.61
711 714 0.385390 CTGAAAATATGCGGCCCACC 59.615 55.000 0.00 0.00 0.00 4.61
729 732 2.559330 GTGCTAAACGGGCCAACG 59.441 61.111 4.39 1.48 40.31 4.10
742 745 3.591835 CAACGTGCCGGCCTGTTT 61.592 61.111 26.77 9.04 0.00 2.83
743 746 2.111460 AACGTGCCGGCCTGTTTA 59.889 55.556 26.77 0.00 0.00 2.01
744 747 2.255881 AACGTGCCGGCCTGTTTAC 61.256 57.895 26.77 13.53 0.00 2.01
745 748 2.358247 CGTGCCGGCCTGTTTACT 60.358 61.111 26.77 0.00 0.00 2.24
746 749 1.079681 CGTGCCGGCCTGTTTACTA 60.080 57.895 26.77 0.00 0.00 1.82
747 750 0.671163 CGTGCCGGCCTGTTTACTAA 60.671 55.000 26.77 0.00 0.00 2.24
748 751 0.800631 GTGCCGGCCTGTTTACTAAC 59.199 55.000 26.77 7.29 34.75 2.34
749 752 0.688487 TGCCGGCCTGTTTACTAACT 59.312 50.000 26.77 0.00 35.24 2.24
750 753 1.084289 GCCGGCCTGTTTACTAACTG 58.916 55.000 18.11 0.00 35.24 3.16
755 758 1.734163 CCTGTTTACTAACTGGGCCG 58.266 55.000 0.00 0.00 44.96 6.13
756 759 1.002773 CCTGTTTACTAACTGGGCCGT 59.997 52.381 0.00 0.00 44.96 5.68
757 760 2.073816 CTGTTTACTAACTGGGCCGTG 58.926 52.381 0.00 0.00 35.24 4.94
758 761 1.270947 TGTTTACTAACTGGGCCGTGG 60.271 52.381 0.00 0.00 35.24 4.94
759 762 0.325602 TTTACTAACTGGGCCGTGGG 59.674 55.000 0.00 0.00 0.00 4.61
760 763 1.555477 TTACTAACTGGGCCGTGGGG 61.555 60.000 0.00 0.00 0.00 4.96
761 764 2.752036 TACTAACTGGGCCGTGGGGT 62.752 60.000 0.00 0.00 34.97 4.95
762 765 3.324108 TAACTGGGCCGTGGGGTC 61.324 66.667 0.00 0.00 37.12 4.46
763 766 3.857521 TAACTGGGCCGTGGGGTCT 62.858 63.158 0.00 0.00 38.30 3.85
806 809 3.447040 GGCACGGCCCGTATAGTA 58.553 61.111 9.25 0.00 44.06 1.82
807 810 1.741525 GGCACGGCCCGTATAGTAA 59.258 57.895 9.25 0.00 44.06 2.24
808 811 0.319405 GGCACGGCCCGTATAGTAAT 59.681 55.000 9.25 0.00 44.06 1.89
809 812 1.670967 GGCACGGCCCGTATAGTAATC 60.671 57.143 9.25 0.00 44.06 1.75
810 813 1.973138 CACGGCCCGTATAGTAATCG 58.027 55.000 9.25 0.00 38.32 3.34
811 814 1.267806 CACGGCCCGTATAGTAATCGT 59.732 52.381 9.25 0.00 38.32 3.73
812 815 1.267806 ACGGCCCGTATAGTAATCGTG 59.732 52.381 7.20 0.00 38.73 4.35
813 816 1.706443 GGCCCGTATAGTAATCGTGC 58.294 55.000 0.00 0.00 0.00 5.34
814 817 1.670967 GGCCCGTATAGTAATCGTGCC 60.671 57.143 7.70 7.70 40.23 5.01
815 818 1.670967 GCCCGTATAGTAATCGTGCCC 60.671 57.143 0.00 0.00 0.00 5.36
816 819 1.891150 CCCGTATAGTAATCGTGCCCT 59.109 52.381 0.00 0.00 0.00 5.19
817 820 2.352421 CCCGTATAGTAATCGTGCCCTG 60.352 54.545 0.00 0.00 0.00 4.45
818 821 2.352421 CCGTATAGTAATCGTGCCCTGG 60.352 54.545 0.00 0.00 0.00 4.45
819 822 2.295349 CGTATAGTAATCGTGCCCTGGT 59.705 50.000 0.00 0.00 0.00 4.00
820 823 2.910688 ATAGTAATCGTGCCCTGGTG 57.089 50.000 0.00 0.00 0.00 4.17
821 824 1.855295 TAGTAATCGTGCCCTGGTGA 58.145 50.000 0.00 0.00 0.00 4.02
822 825 0.537188 AGTAATCGTGCCCTGGTGAG 59.463 55.000 0.00 0.00 0.00 3.51
823 826 1.090052 GTAATCGTGCCCTGGTGAGC 61.090 60.000 0.00 0.00 0.00 4.26
824 827 2.252072 TAATCGTGCCCTGGTGAGCC 62.252 60.000 0.00 0.00 0.00 4.70
852 855 2.895372 GGGCCAGGCACGATTACG 60.895 66.667 15.19 0.00 45.75 3.18
853 856 2.185867 GGCCAGGCACGATTACGA 59.814 61.111 15.19 0.00 42.66 3.43
854 857 1.227556 GGCCAGGCACGATTACGAT 60.228 57.895 15.19 0.00 42.66 3.73
855 858 1.498865 GGCCAGGCACGATTACGATG 61.499 60.000 15.19 0.00 42.66 3.84
856 859 1.498865 GCCAGGCACGATTACGATGG 61.499 60.000 6.55 0.00 42.66 3.51
857 860 0.880278 CCAGGCACGATTACGATGGG 60.880 60.000 0.00 0.00 42.66 4.00
858 861 1.227556 AGGCACGATTACGATGGGC 60.228 57.895 0.00 0.00 42.66 5.36
859 862 2.251642 GGCACGATTACGATGGGCC 61.252 63.158 0.00 0.00 42.66 5.80
860 863 2.594962 GCACGATTACGATGGGCCG 61.595 63.158 0.00 0.00 42.66 6.13
861 864 1.954146 CACGATTACGATGGGCCGG 60.954 63.158 0.00 0.00 42.66 6.13
862 865 3.041940 CGATTACGATGGGCCGGC 61.042 66.667 21.18 21.18 42.66 6.13
863 866 2.668550 GATTACGATGGGCCGGCC 60.669 66.667 38.57 38.57 0.00 6.13
912 915 1.482593 CACCTGTAGATCTCCACCCAC 59.517 57.143 0.00 0.00 0.00 4.61
922 926 0.539669 CTCCACCCACCAGTTTTCCC 60.540 60.000 0.00 0.00 0.00 3.97
954 958 6.243216 AGAACAAAACCCAACACTAGTAGA 57.757 37.500 3.59 0.00 0.00 2.59
955 959 6.289064 AGAACAAAACCCAACACTAGTAGAG 58.711 40.000 3.59 0.00 0.00 2.43
956 960 5.625568 ACAAAACCCAACACTAGTAGAGT 57.374 39.130 3.59 0.00 39.82 3.24
957 961 6.736110 ACAAAACCCAACACTAGTAGAGTA 57.264 37.500 3.59 0.00 35.64 2.59
958 962 6.756221 ACAAAACCCAACACTAGTAGAGTAG 58.244 40.000 3.59 0.00 35.64 2.57
965 969 4.923516 ACACTAGTAGAGTAGGTCACCA 57.076 45.455 3.59 0.00 35.64 4.17
969 973 1.641714 AGTAGAGTAGGTCACCAGCCT 59.358 52.381 0.00 0.00 40.00 4.58
1027 1031 4.243008 TCCGCGGTGAAGGTTGCA 62.243 61.111 27.15 0.00 0.00 4.08
1303 1307 1.839424 GCTTCTTGCCTGGGTACAAT 58.161 50.000 0.00 0.00 35.15 2.71
1356 1360 0.318762 GGCCTCCTTATCTACGGCAG 59.681 60.000 0.00 0.00 42.43 4.85
1374 1378 1.374758 GTGAGTGGAGGGCGTTCTG 60.375 63.158 0.00 0.00 0.00 3.02
1393 1397 2.194597 GTGGTCAACCCTGCCACA 59.805 61.111 7.93 0.00 43.53 4.17
1569 1573 1.151450 CACCAACACCCTTCTGCCT 59.849 57.895 0.00 0.00 0.00 4.75
1688 1692 6.349363 GGAACAAACCATTGAAGAGGACATAC 60.349 42.308 0.00 0.00 38.94 2.39
1699 1703 2.574929 GACATACCCGCACCGTCA 59.425 61.111 0.00 0.00 0.00 4.35
1703 1707 2.585341 ATACCCGCACCGTCACCAA 61.585 57.895 0.00 0.00 0.00 3.67
1721 1725 3.084786 CCAATTGAGGTTCCAGAAGACC 58.915 50.000 7.12 0.00 36.15 3.85
1750 1754 4.061131 TGAGGATCCAGAAGACTTGGTA 57.939 45.455 15.82 0.00 0.00 3.25
1890 2972 7.147915 GCTGGATAGATTGGAACCAACATTTTA 60.148 37.037 8.50 0.00 38.88 1.52
1891 2973 8.837099 TGGATAGATTGGAACCAACATTTTAT 57.163 30.769 8.50 0.00 38.88 1.40
1919 3001 2.103736 GGCGCTACGGTGTCTACC 59.896 66.667 7.64 0.00 43.89 3.18
2563 3650 8.619546 GCTTATCATCTGAATAGCTCAAAAGTT 58.380 33.333 0.00 0.00 34.07 2.66
2694 3781 4.637534 TGCTTGAGATTATTCCTTCACTGC 59.362 41.667 0.00 0.00 0.00 4.40
2785 3872 2.029110 AGATTGATGTTGCGGGGTTTTG 60.029 45.455 0.00 0.00 0.00 2.44
2820 3907 4.099266 AGCTCGAAGCATAGAAGTGAGAAT 59.901 41.667 9.09 0.00 45.56 2.40
2852 3939 6.726490 AGTCGCTAGAAAATAGGATAACCA 57.274 37.500 0.00 0.00 38.94 3.67
2872 3959 4.755123 ACCAAATTGGACAGAACTTACTCG 59.245 41.667 20.25 0.00 40.96 4.18
3033 4120 7.334921 CGGTTTAAATACCAGGACATGTTCTTA 59.665 37.037 3.05 0.00 38.12 2.10
3034 4121 9.185680 GGTTTAAATACCAGGACATGTTCTTAT 57.814 33.333 3.05 0.00 38.12 1.73
3232 4319 1.892391 GGCTAACCGCTGCATACCC 60.892 63.158 0.00 0.00 39.13 3.69
3293 4380 3.179443 AGTGTGTTCAGTTCATGTCGT 57.821 42.857 0.00 0.00 0.00 4.34
3307 4394 5.134202 TCATGTCGTGTATGTCAGTTTCT 57.866 39.130 0.00 0.00 0.00 2.52
3389 4476 7.667043 TGTCTATGTACCTTGAATTGTCAAC 57.333 36.000 0.00 0.00 38.88 3.18
3436 4523 7.288810 TCTTCAATGGCTCTACACAAATTTT 57.711 32.000 0.00 0.00 0.00 1.82
3446 4533 5.363939 TCTACACAAATTTTGGCAAAAGGG 58.636 37.500 27.21 18.50 33.22 3.95
3484 4571 3.970721 TGCCGTGCATTGAGACAG 58.029 55.556 0.00 0.00 31.71 3.51
3509 4596 8.765219 AGTTGCTTCGTACACATGAATAATATC 58.235 33.333 0.00 0.00 0.00 1.63
3571 5735 5.082059 GCGGTATGCGATTCATTTCTATTG 58.918 41.667 0.00 0.00 36.63 1.90
3619 5783 5.113502 AGTTAGCTCAACATTTTCACTGC 57.886 39.130 0.00 0.00 39.81 4.40
3673 5837 2.270205 CGGCCTGAACATGGAGCT 59.730 61.111 0.00 0.00 0.00 4.09
3701 5865 2.030540 GCAAACCGGGTAAAGTTCTTCC 60.031 50.000 6.32 0.00 0.00 3.46
3797 5965 4.832248 TCTTCGGTTGACATTTAGCATCT 58.168 39.130 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 73 8.134905 AGTTCACAGATTTCAAAAGCAAATTC 57.865 30.769 0.00 0.00 0.00 2.17
88 90 8.870160 TGAACCAAAAATTTGATAGTTCACAG 57.130 30.769 17.53 0.20 39.56 3.66
133 135 3.623060 ACCAGACGTGCTATTTATTGCAG 59.377 43.478 0.00 0.00 39.07 4.41
149 151 5.767816 ACCATTTAAGAACAACACCAGAC 57.232 39.130 0.00 0.00 0.00 3.51
154 156 3.662186 CGCGAACCATTTAAGAACAACAC 59.338 43.478 0.00 0.00 0.00 3.32
172 174 4.035909 TGCTACTGACTATTTACATCGCGA 59.964 41.667 13.09 13.09 0.00 5.87
228 231 4.142138 ACAAAACACCGCAGAAAATGGTTA 60.142 37.500 0.00 0.00 32.48 2.85
237 240 1.837538 GCGCTACAAAACACCGCAGA 61.838 55.000 0.00 0.00 43.67 4.26
242 245 1.440353 CGCAGCGCTACAAAACACC 60.440 57.895 10.99 0.00 0.00 4.16
261 264 3.195002 CGGTCCATCAACGCGCAT 61.195 61.111 5.73 0.00 0.00 4.73
266 269 1.447838 CTGGGTCGGTCCATCAACG 60.448 63.158 0.00 0.00 36.05 4.10
275 278 2.050269 CAGTGTCTTCTGGGTCGGT 58.950 57.895 0.00 0.00 0.00 4.69
277 280 1.374758 GGCAGTGTCTTCTGGGTCG 60.375 63.158 0.00 0.00 36.12 4.79
278 281 1.374758 CGGCAGTGTCTTCTGGGTC 60.375 63.158 0.00 0.00 36.12 4.46
280 283 2.743928 GCGGCAGTGTCTTCTGGG 60.744 66.667 0.00 0.00 36.12 4.45
281 284 3.114616 CGCGGCAGTGTCTTCTGG 61.115 66.667 0.00 0.00 36.12 3.86
282 285 2.049156 TCGCGGCAGTGTCTTCTG 60.049 61.111 6.13 0.00 38.35 3.02
283 286 2.259818 CTCGCGGCAGTGTCTTCT 59.740 61.111 6.13 0.00 0.00 2.85
284 287 3.482783 GCTCGCGGCAGTGTCTTC 61.483 66.667 6.13 0.00 41.35 2.87
311 314 2.617274 GCCTTCTGTGCCACGGAAC 61.617 63.158 15.00 3.27 38.47 3.62
312 315 2.281484 GCCTTCTGTGCCACGGAA 60.281 61.111 17.71 17.71 40.89 4.30
313 316 4.680237 CGCCTTCTGTGCCACGGA 62.680 66.667 1.22 1.22 0.00 4.69
320 323 1.154205 CCTAATCCGCGCCTTCTGTG 61.154 60.000 0.00 0.00 0.00 3.66
321 324 1.144057 CCTAATCCGCGCCTTCTGT 59.856 57.895 0.00 0.00 0.00 3.41
322 325 0.598680 CTCCTAATCCGCGCCTTCTG 60.599 60.000 0.00 0.00 0.00 3.02
323 326 1.742768 CTCCTAATCCGCGCCTTCT 59.257 57.895 0.00 0.00 0.00 2.85
324 327 1.956678 GCTCCTAATCCGCGCCTTC 60.957 63.158 0.00 0.00 0.00 3.46
325 328 1.113517 TAGCTCCTAATCCGCGCCTT 61.114 55.000 0.00 0.00 0.00 4.35
326 329 0.900647 ATAGCTCCTAATCCGCGCCT 60.901 55.000 0.00 0.00 0.00 5.52
327 330 0.037232 AATAGCTCCTAATCCGCGCC 60.037 55.000 0.00 0.00 0.00 6.53
328 331 1.797025 AAATAGCTCCTAATCCGCGC 58.203 50.000 0.00 0.00 0.00 6.86
346 349 7.027874 TCAGCTCCTTAATCTTCCCTAAAAA 57.972 36.000 0.00 0.00 0.00 1.94
347 350 6.636454 TCAGCTCCTTAATCTTCCCTAAAA 57.364 37.500 0.00 0.00 0.00 1.52
348 351 6.831664 ATCAGCTCCTTAATCTTCCCTAAA 57.168 37.500 0.00 0.00 0.00 1.85
349 352 6.831664 AATCAGCTCCTTAATCTTCCCTAA 57.168 37.500 0.00 0.00 0.00 2.69
350 353 6.831664 AAATCAGCTCCTTAATCTTCCCTA 57.168 37.500 0.00 0.00 0.00 3.53
351 354 5.723860 AAATCAGCTCCTTAATCTTCCCT 57.276 39.130 0.00 0.00 0.00 4.20
352 355 5.888161 TCAAAATCAGCTCCTTAATCTTCCC 59.112 40.000 0.00 0.00 0.00 3.97
353 356 7.284034 TGATCAAAATCAGCTCCTTAATCTTCC 59.716 37.037 0.00 0.00 36.98 3.46
354 357 8.127954 GTGATCAAAATCAGCTCCTTAATCTTC 58.872 37.037 0.00 0.00 42.53 2.87
355 358 7.201679 CGTGATCAAAATCAGCTCCTTAATCTT 60.202 37.037 0.00 0.00 42.53 2.40
356 359 6.259608 CGTGATCAAAATCAGCTCCTTAATCT 59.740 38.462 0.00 0.00 42.53 2.40
357 360 6.425504 CGTGATCAAAATCAGCTCCTTAATC 58.574 40.000 0.00 0.00 42.53 1.75
358 361 5.297776 CCGTGATCAAAATCAGCTCCTTAAT 59.702 40.000 0.00 0.00 42.53 1.40
359 362 4.635765 CCGTGATCAAAATCAGCTCCTTAA 59.364 41.667 0.00 0.00 42.53 1.85
360 363 4.191544 CCGTGATCAAAATCAGCTCCTTA 58.808 43.478 0.00 0.00 42.53 2.69
361 364 3.012518 CCGTGATCAAAATCAGCTCCTT 58.987 45.455 0.00 0.00 42.53 3.36
362 365 2.026822 ACCGTGATCAAAATCAGCTCCT 60.027 45.455 0.00 0.00 42.53 3.69
363 366 2.352960 GACCGTGATCAAAATCAGCTCC 59.647 50.000 0.00 0.00 42.53 4.70
364 367 3.265791 AGACCGTGATCAAAATCAGCTC 58.734 45.455 0.00 0.00 42.53 4.09
365 368 3.340814 AGACCGTGATCAAAATCAGCT 57.659 42.857 0.00 0.00 42.53 4.24
366 369 3.181506 GGAAGACCGTGATCAAAATCAGC 60.182 47.826 0.00 0.00 42.53 4.26
367 370 3.375299 GGGAAGACCGTGATCAAAATCAG 59.625 47.826 0.00 0.00 42.53 2.90
368 371 3.343617 GGGAAGACCGTGATCAAAATCA 58.656 45.455 0.00 0.00 36.98 2.57
369 372 2.683362 GGGGAAGACCGTGATCAAAATC 59.317 50.000 0.00 0.00 41.60 2.17
370 373 2.723273 GGGGAAGACCGTGATCAAAAT 58.277 47.619 0.00 0.00 41.60 1.82
371 374 2.194201 GGGGAAGACCGTGATCAAAA 57.806 50.000 0.00 0.00 41.60 2.44
372 375 3.948735 GGGGAAGACCGTGATCAAA 57.051 52.632 0.00 0.00 41.60 2.69
384 387 4.104183 TAAAGCGGGCCGGGGAAG 62.104 66.667 29.48 0.00 0.00 3.46
385 388 4.104183 CTAAAGCGGGCCGGGGAA 62.104 66.667 29.48 0.00 0.00 3.97
387 390 3.826926 GATCTAAAGCGGGCCGGGG 62.827 68.421 29.48 0.00 0.00 5.73
388 391 2.280865 GATCTAAAGCGGGCCGGG 60.281 66.667 29.48 0.00 0.00 5.73
389 392 1.595382 CTGATCTAAAGCGGGCCGG 60.595 63.158 29.48 10.74 0.00 6.13
390 393 0.034059 ATCTGATCTAAAGCGGGCCG 59.966 55.000 24.35 24.35 0.00 6.13
391 394 1.070758 TGATCTGATCTAAAGCGGGCC 59.929 52.381 17.82 0.00 0.00 5.80
392 395 2.533266 TGATCTGATCTAAAGCGGGC 57.467 50.000 17.82 0.00 0.00 6.13
393 396 3.806521 CAGTTGATCTGATCTAAAGCGGG 59.193 47.826 17.82 0.00 46.27 6.13
394 397 3.806521 CCAGTTGATCTGATCTAAAGCGG 59.193 47.826 17.82 7.80 46.27 5.52
395 398 3.247173 GCCAGTTGATCTGATCTAAAGCG 59.753 47.826 17.82 3.70 46.27 4.68
396 399 4.194640 TGCCAGTTGATCTGATCTAAAGC 58.805 43.478 17.82 13.39 46.27 3.51
397 400 5.065731 GGTTGCCAGTTGATCTGATCTAAAG 59.934 44.000 17.82 7.03 46.27 1.85
398 401 4.943705 GGTTGCCAGTTGATCTGATCTAAA 59.056 41.667 17.82 3.06 46.27 1.85
399 402 4.225942 AGGTTGCCAGTTGATCTGATCTAA 59.774 41.667 17.82 8.42 46.27 2.10
400 403 3.776969 AGGTTGCCAGTTGATCTGATCTA 59.223 43.478 17.82 8.37 46.27 1.98
401 404 2.575279 AGGTTGCCAGTTGATCTGATCT 59.425 45.455 17.82 0.00 46.27 2.75
402 405 2.681848 CAGGTTGCCAGTTGATCTGATC 59.318 50.000 10.72 10.72 46.27 2.92
403 406 2.619849 CCAGGTTGCCAGTTGATCTGAT 60.620 50.000 0.00 0.00 46.27 2.90
404 407 1.271543 CCAGGTTGCCAGTTGATCTGA 60.272 52.381 0.00 0.00 46.27 3.27
405 408 1.171308 CCAGGTTGCCAGTTGATCTG 58.829 55.000 0.00 0.00 43.27 2.90
406 409 0.610232 GCCAGGTTGCCAGTTGATCT 60.610 55.000 0.00 0.00 0.00 2.75
407 410 1.885871 GCCAGGTTGCCAGTTGATC 59.114 57.895 0.00 0.00 0.00 2.92
408 411 4.102113 GCCAGGTTGCCAGTTGAT 57.898 55.556 0.00 0.00 0.00 2.57
416 419 3.008485 AGCTATAATCTAGGCCAGGTTGC 59.992 47.826 5.01 3.43 0.00 4.17
417 420 4.564406 CCAGCTATAATCTAGGCCAGGTTG 60.564 50.000 5.01 0.00 0.00 3.77
418 421 3.584848 CCAGCTATAATCTAGGCCAGGTT 59.415 47.826 5.01 5.69 0.00 3.50
419 422 3.177228 CCAGCTATAATCTAGGCCAGGT 58.823 50.000 5.01 0.00 0.00 4.00
420 423 2.093235 GCCAGCTATAATCTAGGCCAGG 60.093 54.545 5.01 0.00 36.17 4.45
421 424 3.258971 GCCAGCTATAATCTAGGCCAG 57.741 52.381 5.01 0.00 36.17 4.85
424 427 3.703001 TTGGCCAGCTATAATCTAGGC 57.297 47.619 5.11 0.00 41.29 3.93
425 428 4.946157 CCATTTGGCCAGCTATAATCTAGG 59.054 45.833 5.11 0.00 0.00 3.02
426 429 4.946157 CCCATTTGGCCAGCTATAATCTAG 59.054 45.833 5.11 0.00 0.00 2.43
427 430 4.922206 CCCATTTGGCCAGCTATAATCTA 58.078 43.478 5.11 0.00 0.00 1.98
428 431 3.771216 CCCATTTGGCCAGCTATAATCT 58.229 45.455 5.11 0.00 0.00 2.40
464 467 4.790962 AGCATGCTCACGGGCCAG 62.791 66.667 16.30 1.85 0.00 4.85
469 472 3.807538 GTGCCAGCATGCTCACGG 61.808 66.667 19.68 17.72 30.79 4.94
493 496 3.365265 GTCGTGCTTGGCCCAAGG 61.365 66.667 24.41 8.64 41.31 3.61
494 497 2.594303 TGTCGTGCTTGGCCCAAG 60.594 61.111 19.47 19.47 43.57 3.61
495 498 2.904866 GTGTCGTGCTTGGCCCAA 60.905 61.111 0.00 0.00 0.00 4.12
496 499 4.182433 TGTGTCGTGCTTGGCCCA 62.182 61.111 0.00 0.00 0.00 5.36
497 500 3.357079 CTGTGTCGTGCTTGGCCC 61.357 66.667 0.00 0.00 0.00 5.80
498 501 3.357079 CCTGTGTCGTGCTTGGCC 61.357 66.667 0.00 0.00 0.00 5.36
499 502 4.030452 GCCTGTGTCGTGCTTGGC 62.030 66.667 0.00 0.00 0.00 4.52
500 503 0.602638 TTAGCCTGTGTCGTGCTTGG 60.603 55.000 0.00 0.00 36.57 3.61
501 504 1.069906 GTTTAGCCTGTGTCGTGCTTG 60.070 52.381 0.00 0.00 36.57 4.01
502 505 1.226746 GTTTAGCCTGTGTCGTGCTT 58.773 50.000 0.00 0.00 36.57 3.91
503 506 0.944311 CGTTTAGCCTGTGTCGTGCT 60.944 55.000 0.00 0.00 39.10 4.40
504 507 1.491563 CGTTTAGCCTGTGTCGTGC 59.508 57.895 0.00 0.00 0.00 5.34
505 508 1.289109 CCCGTTTAGCCTGTGTCGTG 61.289 60.000 0.00 0.00 0.00 4.35
506 509 1.005394 CCCGTTTAGCCTGTGTCGT 60.005 57.895 0.00 0.00 0.00 4.34
507 510 2.388232 GCCCGTTTAGCCTGTGTCG 61.388 63.158 0.00 0.00 0.00 4.35
508 511 3.574780 GCCCGTTTAGCCTGTGTC 58.425 61.111 0.00 0.00 0.00 3.67
516 519 4.825252 CGGACCCGGCCCGTTTAG 62.825 72.222 21.04 0.00 41.91 1.85
593 596 4.519540 AAAATGTAATCGGGCCATATGC 57.480 40.909 4.39 0.00 40.16 3.14
625 628 9.224486 ACATGTTGGGCCATATATAGATGTATA 57.776 33.333 14.29 0.00 0.00 1.47
626 629 8.106017 ACATGTTGGGCCATATATAGATGTAT 57.894 34.615 14.29 0.00 0.00 2.29
627 630 7.509236 ACATGTTGGGCCATATATAGATGTA 57.491 36.000 14.29 0.00 0.00 2.29
628 631 6.392911 ACATGTTGGGCCATATATAGATGT 57.607 37.500 7.26 9.71 0.00 3.06
629 632 8.806429 TTTACATGTTGGGCCATATATAGATG 57.194 34.615 7.26 8.99 0.00 2.90
630 633 9.821240 TTTTTACATGTTGGGCCATATATAGAT 57.179 29.630 7.26 0.00 0.00 1.98
631 634 9.821240 ATTTTTACATGTTGGGCCATATATAGA 57.179 29.630 7.26 0.00 0.00 1.98
634 637 9.034800 CCTATTTTTACATGTTGGGCCATATAT 57.965 33.333 7.26 0.00 0.00 0.86
635 638 7.039363 GCCTATTTTTACATGTTGGGCCATATA 60.039 37.037 7.26 0.00 0.00 0.86
636 639 6.239572 GCCTATTTTTACATGTTGGGCCATAT 60.240 38.462 7.26 1.89 0.00 1.78
637 640 5.069781 GCCTATTTTTACATGTTGGGCCATA 59.930 40.000 7.26 0.00 0.00 2.74
638 641 4.141733 GCCTATTTTTACATGTTGGGCCAT 60.142 41.667 7.26 0.00 0.00 4.40
639 642 3.196685 GCCTATTTTTACATGTTGGGCCA 59.803 43.478 0.00 0.00 0.00 5.36
640 643 3.450817 AGCCTATTTTTACATGTTGGGCC 59.549 43.478 15.83 0.00 37.98 5.80
641 644 4.736126 AGCCTATTTTTACATGTTGGGC 57.264 40.909 12.57 12.57 37.57 5.36
670 673 2.159653 CCTGTTATTTGACGCACTGAGC 60.160 50.000 0.00 0.00 40.87 4.26
671 674 2.159653 GCCTGTTATTTGACGCACTGAG 60.160 50.000 0.00 0.00 0.00 3.35
672 675 1.804151 GCCTGTTATTTGACGCACTGA 59.196 47.619 0.00 0.00 0.00 3.41
673 676 1.806542 AGCCTGTTATTTGACGCACTG 59.193 47.619 0.00 0.00 0.00 3.66
674 677 1.806542 CAGCCTGTTATTTGACGCACT 59.193 47.619 0.00 0.00 0.00 4.40
675 678 1.804151 TCAGCCTGTTATTTGACGCAC 59.196 47.619 0.00 0.00 0.00 5.34
676 679 2.177394 TCAGCCTGTTATTTGACGCA 57.823 45.000 0.00 0.00 0.00 5.24
677 680 3.552604 TTTCAGCCTGTTATTTGACGC 57.447 42.857 0.00 0.00 0.00 5.19
678 681 6.197096 GCATATTTTCAGCCTGTTATTTGACG 59.803 38.462 0.00 0.00 0.00 4.35
679 682 6.197096 CGCATATTTTCAGCCTGTTATTTGAC 59.803 38.462 0.00 0.00 0.00 3.18
680 683 6.264832 CGCATATTTTCAGCCTGTTATTTGA 58.735 36.000 0.00 0.00 0.00 2.69
681 684 5.459762 CCGCATATTTTCAGCCTGTTATTTG 59.540 40.000 0.00 0.00 0.00 2.32
682 685 5.591099 CCGCATATTTTCAGCCTGTTATTT 58.409 37.500 0.00 0.00 0.00 1.40
683 686 4.499696 GCCGCATATTTTCAGCCTGTTATT 60.500 41.667 0.00 0.00 0.00 1.40
684 687 3.004734 GCCGCATATTTTCAGCCTGTTAT 59.995 43.478 0.00 0.00 0.00 1.89
685 688 2.357637 GCCGCATATTTTCAGCCTGTTA 59.642 45.455 0.00 0.00 0.00 2.41
686 689 1.134946 GCCGCATATTTTCAGCCTGTT 59.865 47.619 0.00 0.00 0.00 3.16
687 690 0.740737 GCCGCATATTTTCAGCCTGT 59.259 50.000 0.00 0.00 0.00 4.00
688 691 0.031178 GGCCGCATATTTTCAGCCTG 59.969 55.000 0.00 0.00 37.42 4.85
689 692 1.109323 GGGCCGCATATTTTCAGCCT 61.109 55.000 0.00 0.00 40.32 4.58
690 693 1.363807 GGGCCGCATATTTTCAGCC 59.636 57.895 0.00 0.00 39.73 4.85
691 694 0.249031 GTGGGCCGCATATTTTCAGC 60.249 55.000 13.30 0.00 0.00 4.26
692 695 0.385390 GGTGGGCCGCATATTTTCAG 59.615 55.000 20.39 0.00 0.00 3.02
693 696 2.499214 GGTGGGCCGCATATTTTCA 58.501 52.632 20.39 0.00 0.00 2.69
704 707 3.428282 CGTTTAGCACGGTGGGCC 61.428 66.667 10.60 0.00 45.89 5.80
712 715 2.255881 ACGTTGGCCCGTTTAGCAC 61.256 57.895 0.00 0.00 37.96 4.40
713 716 2.111460 ACGTTGGCCCGTTTAGCA 59.889 55.556 0.00 0.00 37.96 3.49
714 717 2.559330 CACGTTGGCCCGTTTAGC 59.441 61.111 4.13 0.00 39.45 3.09
715 718 2.559330 GCACGTTGGCCCGTTTAG 59.441 61.111 4.13 0.00 39.45 1.85
728 731 2.854945 GTTAGTAAACAGGCCGGCACG 61.855 57.143 30.85 20.95 43.34 5.34
729 732 0.800631 GTTAGTAAACAGGCCGGCAC 59.199 55.000 30.85 16.91 35.56 5.01
730 733 0.688487 AGTTAGTAAACAGGCCGGCA 59.312 50.000 30.85 2.40 38.12 5.69
731 734 1.084289 CAGTTAGTAAACAGGCCGGC 58.916 55.000 21.18 21.18 38.12 6.13
732 735 1.677820 CCCAGTTAGTAAACAGGCCGG 60.678 57.143 0.00 0.00 40.13 6.13
733 736 1.734163 CCCAGTTAGTAAACAGGCCG 58.266 55.000 0.00 0.00 40.13 6.13
734 737 1.460504 GCCCAGTTAGTAAACAGGCC 58.539 55.000 0.00 0.00 45.06 5.19
736 739 1.002773 ACGGCCCAGTTAGTAAACAGG 59.997 52.381 0.00 0.00 40.91 4.00
737 740 2.073816 CACGGCCCAGTTAGTAAACAG 58.926 52.381 0.00 0.00 38.12 3.16
738 741 1.270947 CCACGGCCCAGTTAGTAAACA 60.271 52.381 0.00 0.00 38.12 2.83
739 742 1.445871 CCACGGCCCAGTTAGTAAAC 58.554 55.000 0.00 0.00 35.72 2.01
740 743 0.325602 CCCACGGCCCAGTTAGTAAA 59.674 55.000 0.00 0.00 0.00 2.01
741 744 1.555477 CCCCACGGCCCAGTTAGTAA 61.555 60.000 0.00 0.00 0.00 2.24
742 745 1.991167 CCCCACGGCCCAGTTAGTA 60.991 63.158 0.00 0.00 0.00 1.82
743 746 3.327404 CCCCACGGCCCAGTTAGT 61.327 66.667 0.00 0.00 0.00 2.24
744 747 3.325201 GACCCCACGGCCCAGTTAG 62.325 68.421 0.00 0.00 0.00 2.34
745 748 3.324108 GACCCCACGGCCCAGTTA 61.324 66.667 0.00 0.00 0.00 2.24
790 793 1.706443 GATTACTATACGGGCCGTGC 58.294 55.000 39.80 15.03 41.39 5.34
791 794 1.267806 ACGATTACTATACGGGCCGTG 59.732 52.381 39.80 26.05 41.39 4.94
792 795 1.267806 CACGATTACTATACGGGCCGT 59.732 52.381 35.91 35.91 44.35 5.68
793 796 1.973138 CACGATTACTATACGGGCCG 58.027 55.000 27.06 27.06 0.00 6.13
796 799 1.891150 AGGGCACGATTACTATACGGG 59.109 52.381 0.00 0.00 0.00 5.28
797 800 2.352421 CCAGGGCACGATTACTATACGG 60.352 54.545 0.00 0.00 0.00 4.02
798 801 2.295349 ACCAGGGCACGATTACTATACG 59.705 50.000 0.00 0.00 0.00 3.06
799 802 3.319972 TCACCAGGGCACGATTACTATAC 59.680 47.826 0.00 0.00 0.00 1.47
800 803 3.568443 TCACCAGGGCACGATTACTATA 58.432 45.455 0.00 0.00 0.00 1.31
801 804 2.365617 CTCACCAGGGCACGATTACTAT 59.634 50.000 0.00 0.00 0.00 2.12
802 805 1.754803 CTCACCAGGGCACGATTACTA 59.245 52.381 0.00 0.00 0.00 1.82
803 806 0.537188 CTCACCAGGGCACGATTACT 59.463 55.000 0.00 0.00 0.00 2.24
804 807 1.090052 GCTCACCAGGGCACGATTAC 61.090 60.000 0.00 0.00 0.00 1.89
805 808 1.220749 GCTCACCAGGGCACGATTA 59.779 57.895 0.00 0.00 0.00 1.75
806 809 2.045926 GCTCACCAGGGCACGATT 60.046 61.111 0.00 0.00 0.00 3.34
807 810 4.101448 GGCTCACCAGGGCACGAT 62.101 66.667 0.00 0.00 35.26 3.73
833 836 4.169696 TAATCGTGCCTGGCCCGG 62.170 66.667 22.84 9.24 0.00 5.73
834 837 2.895372 GTAATCGTGCCTGGCCCG 60.895 66.667 17.67 17.67 0.00 6.13
835 838 2.660258 ATCGTAATCGTGCCTGGCCC 62.660 60.000 17.53 2.94 38.33 5.80
836 839 1.227556 ATCGTAATCGTGCCTGGCC 60.228 57.895 17.53 6.66 38.33 5.36
837 840 1.498865 CCATCGTAATCGTGCCTGGC 61.499 60.000 12.87 12.87 38.33 4.85
838 841 0.880278 CCCATCGTAATCGTGCCTGG 60.880 60.000 0.00 0.00 38.33 4.45
839 842 1.498865 GCCCATCGTAATCGTGCCTG 61.499 60.000 0.00 0.00 38.33 4.85
840 843 1.227556 GCCCATCGTAATCGTGCCT 60.228 57.895 0.00 0.00 38.33 4.75
841 844 2.251642 GGCCCATCGTAATCGTGCC 61.252 63.158 0.00 0.00 38.33 5.01
842 845 2.594962 CGGCCCATCGTAATCGTGC 61.595 63.158 0.00 0.00 38.33 5.34
843 846 1.954146 CCGGCCCATCGTAATCGTG 60.954 63.158 0.00 0.00 38.33 4.35
844 847 2.420043 CCGGCCCATCGTAATCGT 59.580 61.111 0.00 0.00 38.33 3.73
845 848 3.041940 GCCGGCCCATCGTAATCG 61.042 66.667 18.11 0.00 38.55 3.34
846 849 2.668550 GGCCGGCCCATCGTAATC 60.669 66.667 36.64 5.01 0.00 1.75
862 865 4.609018 CATACCTGGCCGAGCGGG 62.609 72.222 11.30 0.00 39.58 6.13
863 866 4.609018 CCATACCTGGCCGAGCGG 62.609 72.222 4.20 4.20 35.23 5.52
931 935 6.126854 ACTCTACTAGTGTTGGGTTTTGTTCT 60.127 38.462 5.39 0.00 36.93 3.01
954 958 1.549170 CGTTTAGGCTGGTGACCTACT 59.451 52.381 2.11 0.67 39.52 2.57
955 959 2.005560 GCGTTTAGGCTGGTGACCTAC 61.006 57.143 2.11 0.00 39.52 3.18
956 960 0.248289 GCGTTTAGGCTGGTGACCTA 59.752 55.000 2.11 0.00 38.81 3.08
957 961 1.003718 GCGTTTAGGCTGGTGACCT 60.004 57.895 2.11 0.00 41.57 3.85
958 962 1.003718 AGCGTTTAGGCTGGTGACC 60.004 57.895 0.00 0.00 42.86 4.02
981 985 1.800286 GCAGATCGAAAGCAAATGGCC 60.800 52.381 0.00 0.00 46.50 5.36
985 989 0.099436 GGCGCAGATCGAAAGCAAAT 59.901 50.000 10.83 0.00 41.67 2.32
990 994 1.150567 CTGGAGGCGCAGATCGAAAG 61.151 60.000 10.83 0.00 41.67 2.62
1016 1020 1.068055 CATGGCTTCTGCAACCTTCAC 60.068 52.381 0.00 0.00 41.91 3.18
1027 1031 0.179073 CCGTCGAATCCATGGCTTCT 60.179 55.000 22.52 1.01 0.00 2.85
1199 1203 4.343811 AGTCGATGTAGTTGACGAAGAG 57.656 45.455 0.00 0.00 44.59 2.85
1303 1307 2.230992 CACAATTGGCTCGAAATCCCAA 59.769 45.455 10.83 8.39 42.30 4.12
1356 1360 1.374758 CAGAACGCCCTCCACTCAC 60.375 63.158 0.00 0.00 0.00 3.51
1374 1378 4.947147 TGGCAGGGTTGACCACGC 62.947 66.667 2.12 3.70 43.89 5.34
1569 1573 5.410132 TCAAACAACGAGAAAAACTCAGTGA 59.590 36.000 0.00 0.00 45.14 3.41
1688 1692 2.671619 AATTGGTGACGGTGCGGG 60.672 61.111 0.00 0.00 0.00 6.13
1699 1703 3.498661 GGTCTTCTGGAACCTCAATTGGT 60.499 47.826 5.42 0.00 43.11 3.67
1721 1725 5.130145 AGTCTTCTGGATCCTCAATTAGTGG 59.870 44.000 14.23 0.00 0.00 4.00
1750 1754 3.907221 CCATGAGGATGGTGGAAATTCT 58.093 45.455 0.00 0.00 43.98 2.40
1919 3001 0.032678 ACATAGAATGCTCCTCGCCG 59.967 55.000 0.00 0.00 38.05 6.46
1931 3013 2.741517 CACCACGACAATGCACATAGAA 59.258 45.455 0.00 0.00 0.00 2.10
2172 3256 4.356436 CCCTTTTTCTGATTTCCCCAGAT 58.644 43.478 0.00 0.00 40.02 2.90
2694 3781 1.289160 TCTCCAGATCCCAACCCAAG 58.711 55.000 0.00 0.00 0.00 3.61
2737 3824 1.150567 CTTCTGGCTCCTTGCGATCG 61.151 60.000 11.69 11.69 44.05 3.69
2785 3872 3.243068 TGCTTCGAGCTCTTTCCAAAAAC 60.243 43.478 12.85 0.00 42.97 2.43
2820 3907 7.876068 TCCTATTTTCTAGCGACTTCTTTGAAA 59.124 33.333 0.00 0.00 0.00 2.69
2852 3939 5.223449 TCCGAGTAAGTTCTGTCCAATTT 57.777 39.130 0.00 0.00 0.00 1.82
2872 3959 6.920817 AGGAAGTTTACGAAATGGAAATTCC 58.079 36.000 4.79 4.79 36.96 3.01
3033 4120 5.334879 GCGTGACCAAAAGTAGACATGAAAT 60.335 40.000 0.00 0.00 0.00 2.17
3034 4121 4.024387 GCGTGACCAAAAGTAGACATGAAA 60.024 41.667 0.00 0.00 0.00 2.69
3045 4132 3.181501 TGAACAAAGAGCGTGACCAAAAG 60.182 43.478 0.00 0.00 0.00 2.27
3079 4166 2.930040 GCACGCACATATCTACTTGTGT 59.070 45.455 5.11 0.00 44.01 3.72
3232 4319 6.035217 TCATGATTCATTAACATTGTTGCCG 58.965 36.000 12.30 0.58 0.00 5.69
3389 4476 8.856490 AGAAAAATTGCGTATTTAAGCCTATG 57.144 30.769 0.00 0.00 35.39 2.23
3436 4523 0.407528 TATGACTGCCCCTTTTGCCA 59.592 50.000 0.00 0.00 0.00 4.92
3446 4533 4.035675 GCATAGGTTTCTGTTATGACTGCC 59.964 45.833 0.00 0.00 0.00 4.85
3484 4571 8.547894 TGATATTATTCATGTGTACGAAGCAAC 58.452 33.333 0.00 0.00 0.00 4.17
3509 4596 0.671163 AAGCAAACATGGGCGCAATG 60.671 50.000 17.84 17.84 34.54 2.82
3619 5783 0.516877 TTGCAGAGCAAAACGATCGG 59.483 50.000 20.98 2.04 45.96 4.18
3673 5837 2.054232 TTACCCGGTTTGCTGTTGAA 57.946 45.000 0.00 0.00 0.00 2.69
3797 5965 2.203922 TACCTCAGGCTGGCCACA 60.204 61.111 15.73 0.00 38.92 4.17


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

AutoCloner maintained by Alex Coulton.