Multiple sequence alignment - TraesCS2B01G478100

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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 TraesCS2B01G478100 chr2B 100.000 6092 0 0 1 6092 675357444 675351353 0.000000e+00 11250
1 TraesCS2B01G478100 chr2B 88.536 881 56 16 633 1507 675324210 675325051 0.000000e+00 1026
2 TraesCS2B01G478100 chr2B 93.827 81 3 2 3191 3269 354879131 354879211 2.980000e-23 121
3 TraesCS2B01G478100 chr2A 95.027 3961 100 30 2169 6092 704775896 704771996 0.000000e+00 6133
4 TraesCS2B01G478100 chr2A 91.048 1698 50 31 480 2137 704777534 704775899 0.000000e+00 2200
5 TraesCS2B01G478100 chr2A 88.023 885 62 20 633 1509 704734920 704735768 0.000000e+00 1007
6 TraesCS2B01G478100 chr2A 99.329 149 1 0 233 381 101995725 101995873 2.800000e-68 270
7 TraesCS2B01G478100 chr2A 95.302 149 7 0 233 381 51667538 51667390 2.840000e-58 237
8 TraesCS2B01G478100 chr2A 92.667 150 9 2 233 381 51667387 51667239 1.330000e-51 215
9 TraesCS2B01G478100 chr2A 92.157 153 11 1 234 385 738115969 738115817 1.330000e-51 215
10 TraesCS2B01G478100 chr2A 92.771 83 4 2 3191 3271 632952987 632952905 1.070000e-22 119
11 TraesCS2B01G478100 chr2A 89.247 93 5 5 3191 3279 617178884 617178793 1.790000e-20 111
12 TraesCS2B01G478100 chr2D 93.482 2869 93 45 380 3192 564096392 564093562 0.000000e+00 4176
13 TraesCS2B01G478100 chr2D 92.429 1453 69 14 4664 6092 564092109 564090674 0.000000e+00 2036
14 TraesCS2B01G478100 chr2D 91.196 761 53 6 3360 4107 564093380 564092621 0.000000e+00 1022
15 TraesCS2B01G478100 chr2D 92.148 433 19 4 4163 4580 564092620 564092188 1.130000e-166 597
16 TraesCS2B01G478100 chr2D 88.750 240 12 8 1 231 564096623 564096390 4.650000e-71 279
17 TraesCS2B01G478100 chr6D 86.395 588 69 10 1175 1756 344207791 344208373 3.100000e-177 632
18 TraesCS2B01G478100 chr6D 86.940 268 31 4 4189 4453 344210870 344211136 1.280000e-76 298
19 TraesCS2B01G478100 chr6D 90.446 157 15 0 225 381 53575745 53575901 2.230000e-49 207
20 TraesCS2B01G478100 chr6A 86.395 588 69 10 1175 1756 484608363 484608945 3.100000e-177 632
21 TraesCS2B01G478100 chr6A 86.567 268 32 4 4189 4453 484611611 484611877 5.970000e-75 292
22 TraesCS2B01G478100 chr6B 85.690 587 73 10 1176 1756 519720320 519720901 5.220000e-170 608
23 TraesCS2B01G478100 chr6B 86.940 268 31 4 4189 4453 519723964 519724230 1.280000e-76 298
24 TraesCS2B01G478100 chr5D 83.264 478 66 12 1286 1756 489905883 489906353 1.570000e-115 427
25 TraesCS2B01G478100 chr5D 89.744 156 16 0 233 388 383783083 383782928 3.720000e-47 200
26 TraesCS2B01G478100 chr5D 93.902 82 3 2 3191 3270 310705272 310705353 8.290000e-24 122
27 TraesCS2B01G478100 chr5A 82.947 475 73 8 1286 1756 611564618 611565088 7.300000e-114 422
28 TraesCS2B01G478100 chr5A 92.771 83 4 2 3191 3271 472310947 472311029 1.070000e-22 119
29 TraesCS2B01G478100 chr3A 95.973 149 6 0 233 381 685441226 685441078 6.100000e-60 243
30 TraesCS2B01G478100 chr3A 91.613 155 12 1 237 390 651584011 651584165 4.780000e-51 213
31 TraesCS2B01G478100 chr3B 94.937 79 1 3 3191 3267 55740982 55741059 2.980000e-23 121
32 TraesCS2B01G478100 chr3B 89.474 95 3 6 3191 3280 795334405 795334313 4.990000e-21 113
33 TraesCS2B01G478100 chr4B 81.633 147 23 4 233 377 586244952 586244808 1.070000e-22 119
34 TraesCS2B01G478100 chr4B 90.909 88 5 3 3191 3275 670388310 670388397 1.390000e-21 115
35 TraesCS2B01G478100 chr3D 86.111 108 11 4 3171 3276 402465345 402465450 4.990000e-21 113


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 TraesCS2B01G478100 chr2B 675351353 675357444 6091 True 11250.0 11250 100.0000 1 6092 1 chr2B.!!$R1 6091
1 TraesCS2B01G478100 chr2B 675324210 675325051 841 False 1026.0 1026 88.5360 633 1507 1 chr2B.!!$F2 874
2 TraesCS2B01G478100 chr2A 704771996 704777534 5538 True 4166.5 6133 93.0375 480 6092 2 chr2A.!!$R5 5612
3 TraesCS2B01G478100 chr2A 704734920 704735768 848 False 1007.0 1007 88.0230 633 1509 1 chr2A.!!$F2 876
4 TraesCS2B01G478100 chr2D 564090674 564096623 5949 True 1622.0 4176 91.6010 1 6092 5 chr2D.!!$R1 6091
5 TraesCS2B01G478100 chr6D 344207791 344211136 3345 False 465.0 632 86.6675 1175 4453 2 chr6D.!!$F2 3278
6 TraesCS2B01G478100 chr6A 484608363 484611877 3514 False 462.0 632 86.4810 1175 4453 2 chr6A.!!$F1 3278
7 TraesCS2B01G478100 chr6B 519720320 519724230 3910 False 453.0 608 86.3150 1176 4453 2 chr6B.!!$F1 3277

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
594 625 0.099259 CAGCGTACGTCCGTCCAATA 59.901 55.000 17.90 0.0 0.0 1.90 F
595 626 0.099436 AGCGTACGTCCGTCCAATAC 59.901 55.000 17.90 0.0 0.0 1.89 F
679 731 1.153349 GCTAGCTTTCCCCAGACCG 60.153 63.158 7.70 0.0 0.0 4.79 F
710 772 1.303615 GGGTGGAGACGAGAGGAGA 59.696 63.158 0.00 0.0 0.0 3.71 F
1920 2031 1.535462 CCCGCGATTGGATTTGGATAC 59.465 52.381 8.23 0.0 0.0 2.24 F
3073 3859 1.582502 GTTGAACGATCTTCTACGCGG 59.417 52.381 12.47 0.0 0.0 6.46 F
4276 5752 1.151668 AGAGTTCATCGCTGCAACAC 58.848 50.000 0.00 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2538 2859 0.601046 TTCCTTGCTGTGTCTCTGCG 60.601 55.000 0.26 0.0 42.62 5.18 R
3030 3816 4.247267 ACTGGCAAAGAATGAATGTGTG 57.753 40.909 0.00 0.0 0.00 3.82 R
3097 3883 5.036117 TCATAGATAGCCCAAACAGAACC 57.964 43.478 0.00 0.0 0.00 3.62 R
3189 3975 9.654663 AAACGCTCTTATATTTCTTTACAGAGT 57.345 29.630 0.00 0.0 30.86 3.24 R
3815 4848 2.179427 GCCCTAAAGAAAGCCACCAAT 58.821 47.619 0.00 0.0 0.00 3.16 R
5028 6544 1.438651 TTCTCATTGTTCTTCGCCCG 58.561 50.000 0.00 0.0 0.00 6.13 R
5889 7413 0.407139 ACTTGCCTTCTTGGATGCCT 59.593 50.000 0.00 0.0 38.35 4.75 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
84 85 4.351054 CACCTGACCACCCCCAGC 62.351 72.222 0.00 0.00 0.00 4.85
85 86 4.599500 ACCTGACCACCCCCAGCT 62.599 66.667 0.00 0.00 0.00 4.24
86 87 4.039092 CCTGACCACCCCCAGCTG 62.039 72.222 6.78 6.78 0.00 4.24
95 96 4.147449 CCCCAGCTGCGACGATGA 62.147 66.667 8.66 0.00 0.00 2.92
96 97 2.584418 CCCAGCTGCGACGATGAG 60.584 66.667 8.66 0.00 0.00 2.90
99 100 1.445066 CAGCTGCGACGATGAGTGT 60.445 57.895 0.00 0.00 0.00 3.55
118 123 2.555325 TGTAGTTCAGTGTACCTGTCCG 59.445 50.000 10.08 0.00 42.19 4.79
164 169 3.398353 GACCTCCTCCTTCGCGTCG 62.398 68.421 5.77 0.00 0.00 5.12
231 242 3.074412 GCAAGCACACTGTACCAACTAT 58.926 45.455 0.00 0.00 0.00 2.12
232 243 3.120199 GCAAGCACACTGTACCAACTATG 60.120 47.826 0.00 0.00 0.00 2.23
243 254 1.185315 CCAACTATGGCCCTGTTTGG 58.815 55.000 0.00 4.46 40.58 3.28
251 262 3.993535 CCCTGTTTGGCAGCTCTC 58.006 61.111 0.00 0.00 43.71 3.20
252 263 1.676967 CCCTGTTTGGCAGCTCTCC 60.677 63.158 0.00 0.00 43.71 3.71
253 264 2.037136 CCTGTTTGGCAGCTCTCCG 61.037 63.158 0.00 0.00 43.71 4.63
254 265 2.669569 TGTTTGGCAGCTCTCCGC 60.670 61.111 0.00 0.00 39.57 5.54
269 280 4.749310 CGCTCCACGGCTCAGCTT 62.749 66.667 0.00 0.00 38.44 3.74
270 281 2.817396 GCTCCACGGCTCAGCTTC 60.817 66.667 0.00 0.00 0.00 3.86
271 282 2.977178 CTCCACGGCTCAGCTTCT 59.023 61.111 0.00 0.00 0.00 2.85
272 283 1.447489 CTCCACGGCTCAGCTTCTG 60.447 63.158 0.00 0.00 0.00 3.02
273 284 2.435586 CCACGGCTCAGCTTCTGG 60.436 66.667 0.00 0.00 31.51 3.86
274 285 2.659016 CACGGCTCAGCTTCTGGA 59.341 61.111 0.00 0.00 31.51 3.86
275 286 1.447489 CACGGCTCAGCTTCTGGAG 60.447 63.158 0.00 0.00 31.51 3.86
310 321 3.819919 GCGCCGTAGCCTATTTTTC 57.180 52.632 0.00 0.00 34.57 2.29
311 322 1.296727 GCGCCGTAGCCTATTTTTCT 58.703 50.000 0.00 0.00 34.57 2.52
312 323 1.003866 GCGCCGTAGCCTATTTTTCTG 60.004 52.381 0.00 0.00 34.57 3.02
313 324 1.597663 CGCCGTAGCCTATTTTTCTGG 59.402 52.381 0.00 0.00 34.57 3.86
314 325 2.740580 CGCCGTAGCCTATTTTTCTGGA 60.741 50.000 0.00 0.00 34.57 3.86
315 326 2.872858 GCCGTAGCCTATTTTTCTGGAG 59.127 50.000 0.00 0.00 0.00 3.86
316 327 3.681874 GCCGTAGCCTATTTTTCTGGAGT 60.682 47.826 0.00 0.00 0.00 3.85
317 328 4.120589 CCGTAGCCTATTTTTCTGGAGTC 58.879 47.826 0.00 0.00 0.00 3.36
318 329 4.382685 CCGTAGCCTATTTTTCTGGAGTCA 60.383 45.833 0.00 0.00 0.00 3.41
319 330 5.360591 CGTAGCCTATTTTTCTGGAGTCAT 58.639 41.667 0.00 0.00 0.00 3.06
320 331 5.463724 CGTAGCCTATTTTTCTGGAGTCATC 59.536 44.000 0.00 0.00 0.00 2.92
321 332 5.441718 AGCCTATTTTTCTGGAGTCATCA 57.558 39.130 0.00 0.00 0.00 3.07
322 333 5.819991 AGCCTATTTTTCTGGAGTCATCAA 58.180 37.500 0.00 0.00 0.00 2.57
323 334 6.248433 AGCCTATTTTTCTGGAGTCATCAAA 58.752 36.000 0.00 0.00 0.00 2.69
324 335 6.376581 AGCCTATTTTTCTGGAGTCATCAAAG 59.623 38.462 0.00 0.00 0.00 2.77
325 336 6.151817 GCCTATTTTTCTGGAGTCATCAAAGT 59.848 38.462 0.00 0.00 0.00 2.66
326 337 7.533426 CCTATTTTTCTGGAGTCATCAAAGTG 58.467 38.462 0.00 0.00 0.00 3.16
327 338 5.772825 TTTTTCTGGAGTCATCAAAGTGG 57.227 39.130 0.00 0.00 0.00 4.00
328 339 2.479566 TCTGGAGTCATCAAAGTGGC 57.520 50.000 0.00 0.00 0.00 5.01
329 340 1.081892 CTGGAGTCATCAAAGTGGCG 58.918 55.000 0.00 0.00 0.00 5.69
330 341 0.955428 TGGAGTCATCAAAGTGGCGC 60.955 55.000 0.00 0.00 0.00 6.53
331 342 0.674895 GGAGTCATCAAAGTGGCGCT 60.675 55.000 7.64 0.00 0.00 5.92
332 343 0.723981 GAGTCATCAAAGTGGCGCTC 59.276 55.000 7.64 0.45 0.00 5.03
333 344 0.674895 AGTCATCAAAGTGGCGCTCC 60.675 55.000 7.64 0.00 0.00 4.70
334 345 1.741401 TCATCAAAGTGGCGCTCCG 60.741 57.895 7.64 0.00 34.14 4.63
347 358 3.314331 CTCCGCCGGCTCCCATAT 61.314 66.667 26.68 0.00 0.00 1.78
348 359 2.847234 TCCGCCGGCTCCCATATT 60.847 61.111 26.68 0.00 0.00 1.28
349 360 2.113139 CCGCCGGCTCCCATATTT 59.887 61.111 26.68 0.00 0.00 1.40
350 361 1.528309 CCGCCGGCTCCCATATTTT 60.528 57.895 26.68 0.00 0.00 1.82
351 362 1.654220 CGCCGGCTCCCATATTTTG 59.346 57.895 26.68 0.00 0.00 2.44
352 363 1.795170 CGCCGGCTCCCATATTTTGG 61.795 60.000 26.68 0.00 46.00 3.28
361 372 2.754012 CCATATTTTGGGGAGCTGGA 57.246 50.000 0.00 0.00 42.33 3.86
362 373 3.249481 CCATATTTTGGGGAGCTGGAT 57.751 47.619 0.00 0.00 42.33 3.41
363 374 2.895404 CCATATTTTGGGGAGCTGGATG 59.105 50.000 0.00 0.00 42.33 3.51
364 375 3.436906 CCATATTTTGGGGAGCTGGATGA 60.437 47.826 0.00 0.00 42.33 2.92
365 376 2.149973 ATTTTGGGGAGCTGGATGAC 57.850 50.000 0.00 0.00 0.00 3.06
366 377 1.075601 TTTTGGGGAGCTGGATGACT 58.924 50.000 0.00 0.00 0.00 3.41
367 378 0.329261 TTTGGGGAGCTGGATGACTG 59.671 55.000 0.00 0.00 0.00 3.51
368 379 2.191641 GGGGAGCTGGATGACTGC 59.808 66.667 0.00 0.00 43.63 4.40
369 380 2.191641 GGGAGCTGGATGACTGCC 59.808 66.667 0.00 0.00 44.29 4.85
370 381 2.202987 GGAGCTGGATGACTGCCG 60.203 66.667 0.00 0.00 44.29 5.69
371 382 2.725312 GGAGCTGGATGACTGCCGA 61.725 63.158 0.00 0.00 44.29 5.54
372 383 1.219124 GAGCTGGATGACTGCCGAA 59.781 57.895 0.00 0.00 44.29 4.30
373 384 1.078848 AGCTGGATGACTGCCGAAC 60.079 57.895 0.00 0.00 44.29 3.95
374 385 1.375908 GCTGGATGACTGCCGAACA 60.376 57.895 0.00 0.00 38.01 3.18
400 411 5.732810 GCTCTATATAAACCGGCGTATCCTC 60.733 48.000 6.01 0.00 0.00 3.71
404 419 2.188062 AAACCGGCGTATCCTCAAAA 57.812 45.000 6.01 0.00 0.00 2.44
412 427 4.210537 CGGCGTATCCTCAAAACGAATAAT 59.789 41.667 0.00 0.00 38.89 1.28
418 433 9.976255 CGTATCCTCAAAACGAATAATTAAACA 57.024 29.630 0.00 0.00 38.89 2.83
421 436 9.716507 ATCCTCAAAACGAATAATTAAACATCG 57.283 29.630 10.08 10.08 39.30 3.84
423 438 8.785101 CCTCAAAACGAATAATTAAACATCGTG 58.215 33.333 15.17 7.42 45.03 4.35
430 445 7.483691 ACGAATAATTAAACATCGTGCCTTTTC 59.516 33.333 14.24 0.00 44.20 2.29
432 447 3.926821 TTAAACATCGTGCCTTTTCCC 57.073 42.857 0.00 0.00 0.00 3.97
456 471 7.306925 CCCAAAAACAGCTAAAAATAAACGTCC 60.307 37.037 0.00 0.00 0.00 4.79
463 478 6.736853 CAGCTAAAAATAAACGTCCTTCTTCG 59.263 38.462 0.00 0.00 0.00 3.79
466 481 7.799914 GCTAAAAATAAACGTCCTTCTTCGAAA 59.200 33.333 0.00 0.00 0.00 3.46
467 482 9.821662 CTAAAAATAAACGTCCTTCTTCGAAAT 57.178 29.630 0.00 0.00 0.00 2.17
469 484 9.524106 AAAAATAAACGTCCTTCTTCGAAATTT 57.476 25.926 0.00 0.00 0.00 1.82
470 485 9.524106 AAAATAAACGTCCTTCTTCGAAATTTT 57.476 25.926 0.00 1.48 0.00 1.82
471 486 9.524106 AAATAAACGTCCTTCTTCGAAATTTTT 57.476 25.926 0.00 0.00 0.00 1.94
520 535 1.739067 GGGACGGTGATCTTCCTTTG 58.261 55.000 0.00 0.00 0.00 2.77
529 548 2.042842 TGATCTTCCTTTGCATTCCCCA 59.957 45.455 0.00 0.00 0.00 4.96
593 624 1.153901 CAGCGTACGTCCGTCCAAT 60.154 57.895 17.90 0.00 0.00 3.16
594 625 0.099259 CAGCGTACGTCCGTCCAATA 59.901 55.000 17.90 0.00 0.00 1.90
595 626 0.099436 AGCGTACGTCCGTCCAATAC 59.901 55.000 17.90 0.00 0.00 1.89
679 731 1.153349 GCTAGCTTTCCCCAGACCG 60.153 63.158 7.70 0.00 0.00 4.79
710 772 1.303615 GGGTGGAGACGAGAGGAGA 59.696 63.158 0.00 0.00 0.00 3.71
1100 1175 2.256158 CCGCGACTACGACCACAA 59.744 61.111 8.23 0.00 42.66 3.33
1920 2031 1.535462 CCCGCGATTGGATTTGGATAC 59.465 52.381 8.23 0.00 0.00 2.24
1940 2069 8.050325 TGGATACTACTCCTAGATGCTTATCTC 58.950 40.741 0.00 0.00 36.20 2.75
1941 2070 8.272173 GGATACTACTCCTAGATGCTTATCTCT 58.728 40.741 0.00 0.00 32.18 3.10
1942 2071 9.109393 GATACTACTCCTAGATGCTTATCTCTG 57.891 40.741 0.00 0.00 32.36 3.35
1943 2072 6.848069 ACTACTCCTAGATGCTTATCTCTGT 58.152 40.000 0.00 0.00 32.36 3.41
2067 2196 6.861065 TTCACACCAGTCTTTCTGAAATAC 57.139 37.500 9.82 9.82 46.27 1.89
2070 2199 7.152645 TCACACCAGTCTTTCTGAAATACTAC 58.847 38.462 17.42 8.29 46.27 2.73
2225 2354 8.243426 CAGTCTATTCTAGAATCTACATGGAGC 58.757 40.741 21.17 7.36 36.40 4.70
2241 2371 2.152016 GGAGCCTTTCCGGTTATATGC 58.848 52.381 0.00 0.00 35.91 3.14
3030 3816 2.341257 TCGCTCTGTCAGAATTGCTTC 58.659 47.619 3.67 0.00 0.00 3.86
3073 3859 1.582502 GTTGAACGATCTTCTACGCGG 59.417 52.381 12.47 0.00 0.00 6.46
3097 3883 6.404734 GGAATAGTACTTTGGCTGTTCCATTG 60.405 42.308 0.00 0.00 45.97 2.82
3187 3973 8.722480 TTACTTGACTGGATTCACATTATCTG 57.278 34.615 0.00 0.00 0.00 2.90
3188 3974 6.715280 ACTTGACTGGATTCACATTATCTGT 58.285 36.000 0.00 0.00 39.20 3.41
3189 3975 7.851228 ACTTGACTGGATTCACATTATCTGTA 58.149 34.615 0.00 0.00 35.91 2.74
3228 4019 7.811117 ATAAGAGCGTTTAGATCACTACTCT 57.189 36.000 0.00 0.00 37.82 3.24
3229 4020 8.905660 ATAAGAGCGTTTAGATCACTACTCTA 57.094 34.615 0.00 0.00 37.82 2.43
3231 4022 6.350906 AGAGCGTTTAGATCACTACTCTAGT 58.649 40.000 0.00 0.00 37.82 2.57
3244 4035 4.573201 ACTACTCTAGTGATCTGAACGCTC 59.427 45.833 4.17 0.00 37.69 5.03
3246 4037 4.013728 ACTCTAGTGATCTGAACGCTCTT 58.986 43.478 4.17 0.00 0.00 2.85
3247 4038 5.186942 ACTCTAGTGATCTGAACGCTCTTA 58.813 41.667 4.17 0.00 0.00 2.10
3248 4039 5.648526 ACTCTAGTGATCTGAACGCTCTTAA 59.351 40.000 4.17 0.00 0.00 1.85
3249 4040 6.320164 ACTCTAGTGATCTGAACGCTCTTAAT 59.680 38.462 4.17 0.00 0.00 1.40
3250 4041 7.101652 TCTAGTGATCTGAACGCTCTTAATT 57.898 36.000 4.17 0.00 0.00 1.40
3251 4042 7.548097 TCTAGTGATCTGAACGCTCTTAATTT 58.452 34.615 4.17 0.00 0.00 1.82
3252 4043 6.654793 AGTGATCTGAACGCTCTTAATTTC 57.345 37.500 0.00 0.00 0.00 2.17
3253 4044 6.402222 AGTGATCTGAACGCTCTTAATTTCT 58.598 36.000 0.00 0.00 0.00 2.52
3254 4045 6.876257 AGTGATCTGAACGCTCTTAATTTCTT 59.124 34.615 0.00 0.00 0.00 2.52
3255 4046 7.389053 AGTGATCTGAACGCTCTTAATTTCTTT 59.611 33.333 0.00 0.00 0.00 2.52
3256 4047 8.656849 GTGATCTGAACGCTCTTAATTTCTTTA 58.343 33.333 0.00 0.00 0.00 1.85
3257 4048 8.656849 TGATCTGAACGCTCTTAATTTCTTTAC 58.343 33.333 0.00 0.00 0.00 2.01
3258 4049 7.045725 TCTGAACGCTCTTAATTTCTTTACG 57.954 36.000 0.00 0.00 0.00 3.18
3259 4050 6.090358 TCTGAACGCTCTTAATTTCTTTACGG 59.910 38.462 0.00 0.00 0.00 4.02
3260 4051 5.697633 TGAACGCTCTTAATTTCTTTACGGT 59.302 36.000 0.00 0.00 0.00 4.83
3815 4848 8.898761 TGTTCTTCTTACAGTTGCATCTTTTTA 58.101 29.630 0.00 0.00 0.00 1.52
4276 5752 1.151668 AGAGTTCATCGCTGCAACAC 58.848 50.000 0.00 0.00 0.00 3.32
4591 6085 2.906389 TCAGTAGTCCAGCCAAGACAAT 59.094 45.455 1.74 0.00 36.68 2.71
4623 6117 2.256117 ACCGAGGTTTCCAGTCTTTG 57.744 50.000 0.00 0.00 0.00 2.77
4689 6183 9.331282 ACTAGATACTTGCAATTAGGATCAAAC 57.669 33.333 10.97 0.00 35.74 2.93
4720 6215 2.956333 GTGTGGGAAACATATTAGGCCC 59.044 50.000 0.00 0.00 41.97 5.80
4900 6401 7.917505 ACATAGCTCATTTGCTGCTTTATTAAC 59.082 33.333 0.00 0.00 43.87 2.01
4974 6490 2.373169 TGCTCTCTTTTGTCAGGATGGT 59.627 45.455 0.00 0.00 36.16 3.55
4980 6496 2.198827 TTTGTCAGGATGGTCGCATT 57.801 45.000 0.00 0.00 36.16 3.56
5028 6544 0.469892 CCAAGGGCAATATGGGGGTC 60.470 60.000 0.00 0.00 0.00 4.46
5107 6623 2.730382 TCTAGGCTTCCACGATGTACA 58.270 47.619 0.00 0.00 0.00 2.90
5108 6624 3.296854 TCTAGGCTTCCACGATGTACAT 58.703 45.455 8.43 8.43 0.00 2.29
5109 6625 4.466827 TCTAGGCTTCCACGATGTACATA 58.533 43.478 8.71 0.00 0.00 2.29
5110 6626 3.454371 AGGCTTCCACGATGTACATAC 57.546 47.619 8.71 1.95 0.00 2.39
5111 6627 2.764010 AGGCTTCCACGATGTACATACA 59.236 45.455 8.71 0.00 40.98 2.29
5112 6628 3.123804 GGCTTCCACGATGTACATACAG 58.876 50.000 8.71 6.15 39.92 2.74
5148 6664 3.983044 TTAGCTTCTTCCTGTCTTCCC 57.017 47.619 0.00 0.00 0.00 3.97
5156 6672 1.030488 TCCTGTCTTCCCGCTCTACG 61.030 60.000 0.00 0.00 43.15 3.51
5351 6867 6.876257 CCTACTATATCTGCCTGGAATTGTTC 59.124 42.308 0.00 0.00 0.00 3.18
5401 6917 3.829948 CATGTCCAGTTTGATGAACAGC 58.170 45.455 0.00 0.00 40.84 4.40
5538 7054 4.181010 CTGTCCCTGGCATCCCCG 62.181 72.222 0.00 0.00 35.87 5.73
5570 7086 2.439135 TGCACATAGCTATCACATGGGT 59.561 45.455 2.34 0.00 45.94 4.51
5593 7109 0.321210 TTCATCGGCGCTTTCAAGGA 60.321 50.000 7.64 0.00 0.00 3.36
5594 7110 0.321210 TCATCGGCGCTTTCAAGGAA 60.321 50.000 7.64 0.00 0.00 3.36
5595 7111 0.521291 CATCGGCGCTTTCAAGGAAA 59.479 50.000 7.64 0.00 0.00 3.13
5596 7112 0.521735 ATCGGCGCTTTCAAGGAAAC 59.478 50.000 7.64 0.00 0.00 2.78
5597 7113 1.081442 CGGCGCTTTCAAGGAAACC 60.081 57.895 7.64 0.00 0.00 3.27
5612 7136 1.804748 GAAACCACTGGCGAACCTAAG 59.195 52.381 0.00 0.00 36.63 2.18
5709 7233 2.025155 GAATCTGACGGGCTACAGAGA 58.975 52.381 0.00 0.00 44.50 3.10
5726 7250 4.658901 ACAGAGAAAAAGAACTACAGGGGA 59.341 41.667 0.00 0.00 0.00 4.81
5731 7255 6.010850 AGAAAAAGAACTACAGGGGATTTCC 58.989 40.000 0.00 0.00 0.00 3.13
5732 7256 5.333566 AAAAGAACTACAGGGGATTTCCA 57.666 39.130 0.00 0.00 37.91 3.53
5745 7269 3.545703 GGATTTCCATGGTCACCAGTAG 58.454 50.000 12.58 0.00 36.75 2.57
5793 7317 0.250124 AGTGGTGAAATCGAACGGCA 60.250 50.000 0.00 0.00 0.00 5.69
5889 7413 4.096231 CGCAGGTTTTTCATGATGTGGATA 59.904 41.667 0.00 0.00 0.00 2.59
5958 7482 2.100418 CTCGCTGTGATGGATCTCAGAA 59.900 50.000 18.50 7.89 46.08 3.02
5985 7509 1.676635 CTCGGTCCTCACGTACCCA 60.677 63.158 0.00 0.00 31.68 4.51
5988 7512 1.079336 GGTCCTCACGTACCCAAGC 60.079 63.158 0.00 0.00 0.00 4.01
5994 7518 4.308458 ACGTACCCAAGCTGCGCA 62.308 61.111 10.98 10.98 0.00 6.09
6009 7533 0.307146 GCGCAATCTTCTCCATGAGC 59.693 55.000 0.30 0.00 0.00 4.26
6015 7539 4.744259 GCAATCTTCTCCATGAGCTCATCT 60.744 45.833 26.44 4.92 33.61 2.90
6084 7608 9.985730 TCTGCTTTGAAGATATGAATTTTGTTT 57.014 25.926 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 2.177977 GAACTACACTCATCGTCGCAG 58.822 52.381 0.00 0.00 0.00 5.18
85 86 1.538075 TGAACTACACTCATCGTCGCA 59.462 47.619 0.00 0.00 0.00 5.10
86 87 2.177977 CTGAACTACACTCATCGTCGC 58.822 52.381 0.00 0.00 0.00 5.19
88 89 4.162096 ACACTGAACTACACTCATCGTC 57.838 45.455 0.00 0.00 0.00 4.20
90 91 4.156190 AGGTACACTGAACTACACTCATCG 59.844 45.833 0.00 0.00 0.00 3.84
91 92 5.646577 AGGTACACTGAACTACACTCATC 57.353 43.478 0.00 0.00 0.00 2.92
140 145 3.003763 AAGGAGGAGGTCGGCACC 61.004 66.667 0.00 0.00 44.19 5.01
153 158 4.430765 GGAAGGCGACGCGAAGGA 62.431 66.667 15.93 0.00 0.00 3.36
164 169 2.696125 TGGGGAGGGATGGAAGGC 60.696 66.667 0.00 0.00 0.00 4.35
216 227 1.280998 GGGCCATAGTTGGTACAGTGT 59.719 52.381 4.39 0.00 45.57 3.55
237 248 2.669569 GCGGAGAGCTGCCAAACA 60.670 61.111 0.00 0.00 44.04 2.83
252 263 4.749310 AAGCTGAGCCGTGGAGCG 62.749 66.667 0.00 0.00 37.81 5.03
253 264 2.817396 GAAGCTGAGCCGTGGAGC 60.817 66.667 0.00 0.00 0.00 4.70
254 265 1.447489 CAGAAGCTGAGCCGTGGAG 60.447 63.158 0.00 0.00 32.44 3.86
255 266 2.659016 CAGAAGCTGAGCCGTGGA 59.341 61.111 0.00 0.00 32.44 4.02
256 267 2.435586 CCAGAAGCTGAGCCGTGG 60.436 66.667 0.00 1.36 32.44 4.94
257 268 1.447489 CTCCAGAAGCTGAGCCGTG 60.447 63.158 0.00 0.00 32.44 4.94
258 269 2.977178 CTCCAGAAGCTGAGCCGT 59.023 61.111 0.00 0.00 32.44 5.68
267 278 4.521062 CTCCGGCCGCTCCAGAAG 62.521 72.222 22.85 2.99 34.01 2.85
292 303 1.003866 CAGAAAAATAGGCTACGGCGC 60.004 52.381 6.90 0.00 39.81 6.53
293 304 1.597663 CCAGAAAAATAGGCTACGGCG 59.402 52.381 4.80 4.80 39.81 6.46
294 305 2.872858 CTCCAGAAAAATAGGCTACGGC 59.127 50.000 0.00 0.00 37.82 5.68
295 306 4.120589 GACTCCAGAAAAATAGGCTACGG 58.879 47.826 0.00 0.00 0.00 4.02
296 307 4.755411 TGACTCCAGAAAAATAGGCTACG 58.245 43.478 0.00 0.00 0.00 3.51
297 308 6.349300 TGATGACTCCAGAAAAATAGGCTAC 58.651 40.000 0.00 0.00 0.00 3.58
298 309 6.560003 TGATGACTCCAGAAAAATAGGCTA 57.440 37.500 0.00 0.00 0.00 3.93
299 310 5.441718 TGATGACTCCAGAAAAATAGGCT 57.558 39.130 0.00 0.00 0.00 4.58
300 311 6.151817 ACTTTGATGACTCCAGAAAAATAGGC 59.848 38.462 0.00 0.00 0.00 3.93
301 312 7.362401 CCACTTTGATGACTCCAGAAAAATAGG 60.362 40.741 0.00 0.00 0.00 2.57
302 313 7.533426 CCACTTTGATGACTCCAGAAAAATAG 58.467 38.462 0.00 0.00 0.00 1.73
303 314 6.071952 GCCACTTTGATGACTCCAGAAAAATA 60.072 38.462 0.00 0.00 0.00 1.40
304 315 5.279156 GCCACTTTGATGACTCCAGAAAAAT 60.279 40.000 0.00 0.00 0.00 1.82
305 316 4.037923 GCCACTTTGATGACTCCAGAAAAA 59.962 41.667 0.00 0.00 0.00 1.94
306 317 3.569701 GCCACTTTGATGACTCCAGAAAA 59.430 43.478 0.00 0.00 0.00 2.29
307 318 3.149196 GCCACTTTGATGACTCCAGAAA 58.851 45.455 0.00 0.00 0.00 2.52
308 319 2.783135 GCCACTTTGATGACTCCAGAA 58.217 47.619 0.00 0.00 0.00 3.02
309 320 1.338105 CGCCACTTTGATGACTCCAGA 60.338 52.381 0.00 0.00 0.00 3.86
310 321 1.081892 CGCCACTTTGATGACTCCAG 58.918 55.000 0.00 0.00 0.00 3.86
311 322 0.955428 GCGCCACTTTGATGACTCCA 60.955 55.000 0.00 0.00 0.00 3.86
312 323 0.674895 AGCGCCACTTTGATGACTCC 60.675 55.000 2.29 0.00 0.00 3.85
313 324 0.723981 GAGCGCCACTTTGATGACTC 59.276 55.000 2.29 0.00 0.00 3.36
314 325 0.674895 GGAGCGCCACTTTGATGACT 60.675 55.000 2.29 0.00 0.00 3.41
315 326 1.796796 GGAGCGCCACTTTGATGAC 59.203 57.895 2.29 0.00 0.00 3.06
316 327 1.741401 CGGAGCGCCACTTTGATGA 60.741 57.895 7.44 0.00 0.00 2.92
317 328 2.787249 CGGAGCGCCACTTTGATG 59.213 61.111 7.44 0.00 0.00 3.07
330 341 2.397413 AAATATGGGAGCCGGCGGAG 62.397 60.000 33.44 3.96 0.00 4.63
331 342 1.990160 AAAATATGGGAGCCGGCGGA 61.990 55.000 33.44 8.81 0.00 5.54
332 343 1.528309 AAAATATGGGAGCCGGCGG 60.528 57.895 24.35 24.35 0.00 6.13
333 344 1.654220 CAAAATATGGGAGCCGGCG 59.346 57.895 23.20 0.00 0.00 6.46
334 345 2.041153 CCAAAATATGGGAGCCGGC 58.959 57.895 21.89 21.89 46.27 6.13
343 354 3.571401 GTCATCCAGCTCCCCAAAATATG 59.429 47.826 0.00 0.00 0.00 1.78
344 355 3.464833 AGTCATCCAGCTCCCCAAAATAT 59.535 43.478 0.00 0.00 0.00 1.28
345 356 2.852449 AGTCATCCAGCTCCCCAAAATA 59.148 45.455 0.00 0.00 0.00 1.40
346 357 1.642762 AGTCATCCAGCTCCCCAAAAT 59.357 47.619 0.00 0.00 0.00 1.82
347 358 1.075601 AGTCATCCAGCTCCCCAAAA 58.924 50.000 0.00 0.00 0.00 2.44
348 359 0.329261 CAGTCATCCAGCTCCCCAAA 59.671 55.000 0.00 0.00 0.00 3.28
349 360 1.993653 CAGTCATCCAGCTCCCCAA 59.006 57.895 0.00 0.00 0.00 4.12
350 361 2.673200 GCAGTCATCCAGCTCCCCA 61.673 63.158 0.00 0.00 0.00 4.96
351 362 2.191641 GCAGTCATCCAGCTCCCC 59.808 66.667 0.00 0.00 0.00 4.81
352 363 2.191641 GGCAGTCATCCAGCTCCC 59.808 66.667 0.00 0.00 0.00 4.30
353 364 2.202987 CGGCAGTCATCCAGCTCC 60.203 66.667 0.00 0.00 0.00 4.70
354 365 1.086634 GTTCGGCAGTCATCCAGCTC 61.087 60.000 0.00 0.00 0.00 4.09
355 366 1.078848 GTTCGGCAGTCATCCAGCT 60.079 57.895 0.00 0.00 0.00 4.24
356 367 1.364626 CTGTTCGGCAGTCATCCAGC 61.365 60.000 0.00 0.00 40.27 4.85
357 368 0.742281 CCTGTTCGGCAGTCATCCAG 60.742 60.000 7.05 0.00 43.55 3.86
358 369 1.296392 CCTGTTCGGCAGTCATCCA 59.704 57.895 7.05 0.00 43.55 3.41
359 370 4.208632 CCTGTTCGGCAGTCATCC 57.791 61.111 7.05 0.00 43.55 3.51
368 379 4.235360 CGGTTTATATAGAGCCTGTTCGG 58.765 47.826 0.00 0.00 0.00 4.30
369 380 4.235360 CCGGTTTATATAGAGCCTGTTCG 58.765 47.826 0.00 0.00 0.00 3.95
370 381 3.995048 GCCGGTTTATATAGAGCCTGTTC 59.005 47.826 1.90 0.00 0.00 3.18
371 382 3.554337 CGCCGGTTTATATAGAGCCTGTT 60.554 47.826 1.90 0.00 0.00 3.16
372 383 2.029290 CGCCGGTTTATATAGAGCCTGT 60.029 50.000 1.90 0.00 0.00 4.00
373 384 2.029290 ACGCCGGTTTATATAGAGCCTG 60.029 50.000 1.90 0.00 0.00 4.85
374 385 2.245582 ACGCCGGTTTATATAGAGCCT 58.754 47.619 1.90 0.00 0.00 4.58
375 386 2.738013 ACGCCGGTTTATATAGAGCC 57.262 50.000 1.90 0.00 0.00 4.70
376 387 4.097589 AGGATACGCCGGTTTATATAGAGC 59.902 45.833 1.90 0.00 43.43 4.09
377 388 5.356190 TGAGGATACGCCGGTTTATATAGAG 59.644 44.000 1.90 0.00 43.43 2.43
378 389 5.255687 TGAGGATACGCCGGTTTATATAGA 58.744 41.667 1.90 0.00 43.43 1.98
379 390 5.571784 TGAGGATACGCCGGTTTATATAG 57.428 43.478 1.90 0.00 43.43 1.31
380 391 5.981088 TTGAGGATACGCCGGTTTATATA 57.019 39.130 1.90 0.00 43.43 0.86
381 392 4.877378 TTGAGGATACGCCGGTTTATAT 57.123 40.909 1.90 0.00 43.43 0.86
382 393 4.669206 TTTGAGGATACGCCGGTTTATA 57.331 40.909 1.90 0.00 43.43 0.98
400 411 7.272515 AGGCACGATGTTTAATTATTCGTTTTG 59.727 33.333 9.28 3.33 0.00 2.44
404 419 6.431198 AAGGCACGATGTTTAATTATTCGT 57.569 33.333 0.00 7.19 0.00 3.85
412 427 3.223435 TGGGAAAAGGCACGATGTTTAA 58.777 40.909 0.00 0.00 0.00 1.52
418 433 2.432510 TGTTTTTGGGAAAAGGCACGAT 59.567 40.909 0.00 0.00 35.53 3.73
419 434 1.825474 TGTTTTTGGGAAAAGGCACGA 59.175 42.857 0.00 0.00 35.53 4.35
421 436 1.939934 GCTGTTTTTGGGAAAAGGCAC 59.060 47.619 0.00 0.00 35.53 5.01
422 437 1.836802 AGCTGTTTTTGGGAAAAGGCA 59.163 42.857 0.00 0.00 37.24 4.75
423 438 2.620251 AGCTGTTTTTGGGAAAAGGC 57.380 45.000 0.00 0.00 35.53 4.35
430 445 7.306925 GGACGTTTATTTTTAGCTGTTTTTGGG 60.307 37.037 0.00 0.00 0.00 4.12
432 447 8.347729 AGGACGTTTATTTTTAGCTGTTTTTG 57.652 30.769 0.00 0.00 0.00 2.44
499 514 0.613853 AAGGAAGATCACCGTCCCGA 60.614 55.000 0.00 0.00 43.39 5.14
502 517 1.087501 GCAAAGGAAGATCACCGTCC 58.912 55.000 0.00 0.00 42.79 4.79
520 535 2.513666 TGCGATCGTGGGGAATGC 60.514 61.111 17.81 0.00 0.00 3.56
593 624 2.502130 TGTGGATTGATTGGCCTACGTA 59.498 45.455 3.32 0.00 0.00 3.57
594 625 1.280710 TGTGGATTGATTGGCCTACGT 59.719 47.619 3.32 0.00 0.00 3.57
595 626 1.670811 GTGTGGATTGATTGGCCTACG 59.329 52.381 3.32 0.00 0.00 3.51
596 627 1.670811 CGTGTGGATTGATTGGCCTAC 59.329 52.381 3.32 0.00 0.00 3.18
599 630 1.139520 GCGTGTGGATTGATTGGCC 59.860 57.895 0.00 0.00 0.00 5.36
710 772 1.222936 CATGGCGGCTTCTTCTCCT 59.777 57.895 11.43 0.00 0.00 3.69
748 810 3.435186 GAGGTGGGAAAGCAGCGC 61.435 66.667 0.00 0.00 0.00 5.92
749 811 2.747855 GGAGGTGGGAAAGCAGCG 60.748 66.667 0.00 0.00 0.00 5.18
750 812 1.377856 GAGGAGGTGGGAAAGCAGC 60.378 63.158 0.00 0.00 0.00 5.25
751 813 1.078848 CGAGGAGGTGGGAAAGCAG 60.079 63.158 0.00 0.00 0.00 4.24
752 814 0.909610 ATCGAGGAGGTGGGAAAGCA 60.910 55.000 0.00 0.00 0.00 3.91
753 815 1.120530 TATCGAGGAGGTGGGAAAGC 58.879 55.000 0.00 0.00 0.00 3.51
754 816 3.906720 TTTATCGAGGAGGTGGGAAAG 57.093 47.619 0.00 0.00 0.00 2.62
813 878 0.105709 GAAGGGGAGAGGAGAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
1920 2031 8.856153 TTACAGAGATAAGCATCTAGGAGTAG 57.144 38.462 0.00 0.00 41.78 2.57
1941 2070 9.599866 CCTTCATAGTTTAGTGACATGATTACA 57.400 33.333 0.00 0.00 0.00 2.41
1942 2071 9.817809 TCCTTCATAGTTTAGTGACATGATTAC 57.182 33.333 0.00 0.00 0.00 1.89
1990 2119 6.525121 TCACGTAAAAGTTCTCATGACTTG 57.475 37.500 0.00 0.00 0.00 3.16
2067 2196 4.703897 TGAGTTTCCCAGTGAACTTGTAG 58.296 43.478 0.00 0.00 31.05 2.74
2070 2199 3.503748 GGATGAGTTTCCCAGTGAACTTG 59.496 47.826 0.00 0.00 31.05 3.16
2241 2371 6.959361 AGTGCATCACAAAGTTTACAGTAAG 58.041 36.000 0.00 0.00 36.74 2.34
2538 2859 0.601046 TTCCTTGCTGTGTCTCTGCG 60.601 55.000 0.26 0.00 42.62 5.18
3030 3816 4.247267 ACTGGCAAAGAATGAATGTGTG 57.753 40.909 0.00 0.00 0.00 3.82
3097 3883 5.036117 TCATAGATAGCCCAAACAGAACC 57.964 43.478 0.00 0.00 0.00 3.62
3187 3973 9.733219 ACGCTCTTATATTTCTTTACAGAGTAC 57.267 33.333 0.00 0.00 30.86 2.73
3189 3975 9.654663 AAACGCTCTTATATTTCTTTACAGAGT 57.345 29.630 0.00 0.00 30.86 3.24
3225 4016 4.630894 AAGAGCGTTCAGATCACTAGAG 57.369 45.455 1.01 0.00 37.82 2.43
3226 4017 6.701145 ATTAAGAGCGTTCAGATCACTAGA 57.299 37.500 1.01 0.00 37.82 2.43
3227 4018 7.704472 AGAAATTAAGAGCGTTCAGATCACTAG 59.296 37.037 1.01 0.00 37.82 2.57
3228 4019 7.548097 AGAAATTAAGAGCGTTCAGATCACTA 58.452 34.615 1.01 0.00 37.82 2.74
3229 4020 6.402222 AGAAATTAAGAGCGTTCAGATCACT 58.598 36.000 1.01 0.00 37.82 3.41
3231 4022 7.672983 AAAGAAATTAAGAGCGTTCAGATCA 57.327 32.000 1.01 0.00 37.82 2.92
3232 4023 7.841758 CGTAAAGAAATTAAGAGCGTTCAGATC 59.158 37.037 1.01 0.00 35.01 2.75
3233 4024 7.201530 CCGTAAAGAAATTAAGAGCGTTCAGAT 60.202 37.037 1.01 0.00 0.00 2.90
3235 4026 6.128634 ACCGTAAAGAAATTAAGAGCGTTCAG 60.129 38.462 1.01 0.00 0.00 3.02
3236 4027 5.697633 ACCGTAAAGAAATTAAGAGCGTTCA 59.302 36.000 1.01 0.00 0.00 3.18
3237 4028 6.013689 CACCGTAAAGAAATTAAGAGCGTTC 58.986 40.000 0.00 0.00 0.00 3.95
3239 4030 4.390909 CCACCGTAAAGAAATTAAGAGCGT 59.609 41.667 0.00 0.00 0.00 5.07
3240 4031 4.628333 TCCACCGTAAAGAAATTAAGAGCG 59.372 41.667 0.00 0.00 0.00 5.03
3241 4032 5.642491 ACTCCACCGTAAAGAAATTAAGAGC 59.358 40.000 0.00 0.00 0.00 4.09
3244 4035 9.643693 TTAGTACTCCACCGTAAAGAAATTAAG 57.356 33.333 0.00 0.00 0.00 1.85
3248 4039 9.760077 CATATTAGTACTCCACCGTAAAGAAAT 57.240 33.333 0.00 0.00 0.00 2.17
3249 4040 8.970020 TCATATTAGTACTCCACCGTAAAGAAA 58.030 33.333 0.00 0.00 0.00 2.52
3250 4041 8.523915 TCATATTAGTACTCCACCGTAAAGAA 57.476 34.615 0.00 0.00 0.00 2.52
3251 4042 7.255381 GCTCATATTAGTACTCCACCGTAAAGA 60.255 40.741 0.00 0.00 0.00 2.52
3252 4043 6.862090 GCTCATATTAGTACTCCACCGTAAAG 59.138 42.308 0.00 0.00 0.00 1.85
3253 4044 6.321945 TGCTCATATTAGTACTCCACCGTAAA 59.678 38.462 0.00 0.00 0.00 2.01
3254 4045 5.829391 TGCTCATATTAGTACTCCACCGTAA 59.171 40.000 0.00 0.00 0.00 3.18
3255 4046 5.379187 TGCTCATATTAGTACTCCACCGTA 58.621 41.667 0.00 0.00 0.00 4.02
3256 4047 4.212716 TGCTCATATTAGTACTCCACCGT 58.787 43.478 0.00 0.00 0.00 4.83
3257 4048 4.848562 TGCTCATATTAGTACTCCACCG 57.151 45.455 0.00 0.00 0.00 4.94
3258 4049 7.278868 GCATATTGCTCATATTAGTACTCCACC 59.721 40.741 0.00 0.00 40.96 4.61
3259 4050 8.190888 GCATATTGCTCATATTAGTACTCCAC 57.809 38.462 0.00 0.00 40.96 4.02
3296 4087 7.669304 TCATGTCATACAAAGGAAGAATGGAAA 59.331 33.333 0.00 0.00 0.00 3.13
3815 4848 2.179427 GCCCTAAAGAAAGCCACCAAT 58.821 47.619 0.00 0.00 0.00 3.16
4276 5752 3.002042 CGCTCCAGTTTATTCAGATGCAG 59.998 47.826 0.00 0.00 0.00 4.41
4623 6117 2.834549 TGAGAGACCATGTTCCTCTTCC 59.165 50.000 9.26 1.31 37.40 3.46
4689 6183 2.234908 TGTTTCCCACACCCAAAAAGTG 59.765 45.455 0.00 0.00 41.15 3.16
4789 6290 7.148086 GCACAAATCTATGTCCACTGGAATTTA 60.148 37.037 0.00 0.00 31.38 1.40
4900 6401 9.378551 TGTTACTAACAGAACCATAAGCATTAG 57.621 33.333 0.00 0.00 36.25 1.73
4974 6490 5.185454 ACAAATTCTCCATAGTCAATGCGA 58.815 37.500 0.00 0.00 33.92 5.10
5028 6544 1.438651 TTCTCATTGTTCTTCGCCCG 58.561 50.000 0.00 0.00 0.00 6.13
5092 6608 4.041740 TCTGTATGTACATCGTGGAAGC 57.958 45.455 12.68 0.00 35.36 3.86
5148 6664 1.795889 GCAGGAAGTCTTCGTAGAGCG 60.796 57.143 7.45 0.00 38.43 5.03
5156 6672 2.993899 TCGAAAATCGCAGGAAGTCTTC 59.006 45.455 3.80 3.80 40.21 2.87
5351 6867 3.826157 TGGGACAAGCCATTTTAAGAGTG 59.174 43.478 0.00 0.00 38.95 3.51
5401 6917 3.200825 AGGAAGTAACATCACATCCAGGG 59.799 47.826 0.94 0.00 38.49 4.45
5593 7109 1.892209 CTTAGGTTCGCCAGTGGTTT 58.108 50.000 11.74 0.00 40.60 3.27
5594 7110 0.605589 GCTTAGGTTCGCCAGTGGTT 60.606 55.000 11.74 0.00 40.60 3.67
5595 7111 1.003718 GCTTAGGTTCGCCAGTGGT 60.004 57.895 11.74 0.00 40.60 4.16
5596 7112 1.745489 GGCTTAGGTTCGCCAGTGG 60.745 63.158 4.20 4.20 45.59 4.00
5597 7113 3.890674 GGCTTAGGTTCGCCAGTG 58.109 61.111 0.00 0.00 45.59 3.66
5612 7136 3.055819 TCTGTCCACTATTTGTCTGAGGC 60.056 47.826 0.00 0.00 0.00 4.70
5658 7182 5.046520 ACCACAGAGGAGTAAAATGTCTACC 60.047 44.000 0.00 0.00 41.22 3.18
5709 7233 5.711698 TGGAAATCCCCTGTAGTTCTTTTT 58.288 37.500 0.00 0.00 34.29 1.94
5726 7250 3.054361 GGACTACTGGTGACCATGGAAAT 60.054 47.826 21.47 0.00 30.82 2.17
5731 7255 0.541863 GGGGACTACTGGTGACCATG 59.458 60.000 4.03 1.83 30.82 3.66
5732 7256 0.976073 CGGGGACTACTGGTGACCAT 60.976 60.000 4.03 0.00 30.82 3.55
5793 7317 2.496070 TCGGGAGTTTGTGATTCGAGAT 59.504 45.455 0.00 0.00 0.00 2.75
5889 7413 0.407139 ACTTGCCTTCTTGGATGCCT 59.593 50.000 0.00 0.00 38.35 4.75
5900 7424 2.905415 TGGGATCATGAACTTGCCTT 57.095 45.000 0.00 0.00 0.00 4.35
5988 7512 1.598132 CTCATGGAGAAGATTGCGCAG 59.402 52.381 11.31 0.00 0.00 5.18
5994 7518 6.349243 CTAGATGAGCTCATGGAGAAGATT 57.651 41.667 33.33 6.37 36.57 2.40
6049 7573 3.123804 TCTTCAAAGCAGAAGACGTGAC 58.876 45.455 10.92 0.00 46.62 3.67


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

AutoCloner maintained by Alex Coulton.