Multiple sequence alignment - TraesCS2A01G172700

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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 TraesCS2A01G172700 chr2A 100.000 4785 0 0 1 4785 129867431 129872215 0.000000e+00 8837
1 TraesCS2A01G172700 chr2A 79.699 399 35 21 1 399 131483614 131483262 3.700000e-61 246
2 TraesCS2A01G172700 chr2D 96.204 4320 122 21 476 4777 124064973 124060678 0.000000e+00 7031
3 TraesCS2A01G172700 chr2D 85.036 421 30 15 1 421 70329025 70329412 9.650000e-107 398
4 TraesCS2A01G172700 chr2B 95.256 4363 120 43 476 4783 176709098 176704768 0.000000e+00 6830
5 TraesCS2A01G172700 chr2B 90.722 291 21 4 126 416 157816677 157816961 2.700000e-102 383
6 TraesCS2A01G172700 chr1D 85.714 413 24 3 1 413 351953209 351952832 2.070000e-108 403
7 TraesCS2A01G172700 chr7A 91.096 292 20 4 126 417 26811077 26811362 1.610000e-104 390
8 TraesCS2A01G172700 chr7A 90.972 288 20 4 126 413 6241518 6241799 2.700000e-102 383
9 TraesCS2A01G172700 chr3B 91.003 289 20 4 126 414 710392484 710392766 7.510000e-103 385
10 TraesCS2A01G172700 chr7D 90.657 289 20 5 126 414 621083825 621083544 1.260000e-100 377
11 TraesCS2A01G172700 chr4A 90.657 289 20 5 126 414 139995232 139995513 1.260000e-100 377
12 TraesCS2A01G172700 chr4A 89.865 296 22 6 126 420 46623033 46623321 1.630000e-99 374
13 TraesCS2A01G172700 chrUn 82.324 413 38 20 1 413 212969484 212969861 4.620000e-85 326
14 TraesCS2A01G172700 chrUn 80.872 413 44 19 1 413 71648583 71648960 4.680000e-75 292
15 TraesCS2A01G172700 chr1A 82.310 407 37 20 1 407 496552194 496552565 2.150000e-83 320
16 TraesCS2A01G172700 chr1A 81.159 414 43 20 1 414 120379539 120379161 2.800000e-77 300
17 TraesCS2A01G172700 chr1A 98.198 111 2 0 1 111 207423169 207423279 1.360000e-45 195
18 TraesCS2A01G172700 chr1A 96.396 111 4 0 1 111 84055052 84054942 2.940000e-42 183
19 TraesCS2A01G172700 chr5A 97.297 111 3 0 1 111 189217225 189217115 6.320000e-44 189


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 TraesCS2A01G172700 chr2A 129867431 129872215 4784 False 8837 8837 100.000 1 4785 1 chr2A.!!$F1 4784
1 TraesCS2A01G172700 chr2D 124060678 124064973 4295 True 7031 7031 96.204 476 4777 1 chr2D.!!$R1 4301
2 TraesCS2A01G172700 chr2B 176704768 176709098 4330 True 6830 6830 95.256 476 4783 1 chr2B.!!$R1 4307

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
407 408 0.025001 CGAATAAACCGAGCGCACAG 59.975 55.000 11.47 0.0 0.00 3.66 F
431 432 0.040425 AGTCCAAATCAAACGCGTGC 60.040 50.000 14.98 0.0 0.00 5.34 F
605 606 0.108329 ACGCCCATAGACTTCAACCG 60.108 55.000 0.00 0.0 0.00 4.44 F
1874 1875 0.738975 ACGTGGATGATGACGACGAT 59.261 50.000 0.00 0.0 40.69 3.73 F
2321 2322 1.269726 GCATGTTCAGTTTGTGGGTGG 60.270 52.381 0.00 0.0 0.00 4.61 F
3574 3608 2.600769 AGACCAGCCGTCGTCCTT 60.601 61.111 0.00 0.0 46.92 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 1530 0.745486 TCTCGTCGGCGTCCATCTTA 60.745 55.000 10.18 0.0 39.49 2.10 R
2021 2022 1.362584 TCATCCTCAACCTCCTCCTCA 59.637 52.381 0.00 0.0 0.00 3.86 R
2078 2079 1.378514 CACCGCCATAGCAACCCTT 60.379 57.895 0.00 0.0 39.83 3.95 R
3574 3608 0.107703 CTTCCGCTTGATACCCTGCA 60.108 55.000 0.00 0.0 0.00 4.41 R
3617 3651 2.426406 ATCCTCATCGTCGCTGCCA 61.426 57.895 0.00 0.0 0.00 4.92 R
4738 4807 0.334676 AAATCCCCATCGGCCAGAAA 59.665 50.000 2.24 0.0 0.00 2.52 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
80 81 3.643199 TGCTAAGCATGTCCATAACCA 57.357 42.857 0.00 0.00 31.71 3.67
81 82 4.169059 TGCTAAGCATGTCCATAACCAT 57.831 40.909 0.00 0.00 31.71 3.55
82 83 4.136796 TGCTAAGCATGTCCATAACCATC 58.863 43.478 0.00 0.00 31.71 3.51
83 84 4.136796 GCTAAGCATGTCCATAACCATCA 58.863 43.478 0.00 0.00 0.00 3.07
84 85 4.580167 GCTAAGCATGTCCATAACCATCAA 59.420 41.667 0.00 0.00 0.00 2.57
85 86 4.989279 AAGCATGTCCATAACCATCAAC 57.011 40.909 0.00 0.00 0.00 3.18
86 87 3.966979 AGCATGTCCATAACCATCAACA 58.033 40.909 0.00 0.00 0.00 3.33
87 88 3.949754 AGCATGTCCATAACCATCAACAG 59.050 43.478 0.00 0.00 0.00 3.16
88 89 3.947196 GCATGTCCATAACCATCAACAGA 59.053 43.478 0.00 0.00 0.00 3.41
89 90 4.581824 GCATGTCCATAACCATCAACAGAT 59.418 41.667 0.00 0.00 0.00 2.90
90 91 5.506815 GCATGTCCATAACCATCAACAGATG 60.507 44.000 0.00 0.00 39.07 2.90
91 92 5.434182 TGTCCATAACCATCAACAGATGA 57.566 39.130 7.02 0.00 41.31 2.92
92 93 5.814481 TGTCCATAACCATCAACAGATGAA 58.186 37.500 7.02 0.00 42.54 2.57
93 94 6.425735 TGTCCATAACCATCAACAGATGAAT 58.574 36.000 7.02 0.00 42.54 2.57
94 95 6.543465 TGTCCATAACCATCAACAGATGAATC 59.457 38.462 7.02 0.00 42.54 2.52
95 96 6.543465 GTCCATAACCATCAACAGATGAATCA 59.457 38.462 7.02 0.00 42.54 2.57
96 97 7.067372 GTCCATAACCATCAACAGATGAATCAA 59.933 37.037 7.02 0.00 42.54 2.57
97 98 7.781219 TCCATAACCATCAACAGATGAATCAAT 59.219 33.333 7.02 0.00 42.54 2.57
98 99 7.865889 CCATAACCATCAACAGATGAATCAATG 59.134 37.037 7.02 0.00 42.54 2.82
99 100 5.258456 ACCATCAACAGATGAATCAATGC 57.742 39.130 7.02 0.00 42.54 3.56
100 101 4.707934 ACCATCAACAGATGAATCAATGCA 59.292 37.500 7.02 0.00 42.54 3.96
101 102 5.362717 ACCATCAACAGATGAATCAATGCAT 59.637 36.000 7.02 0.00 42.54 3.96
102 103 5.691754 CCATCAACAGATGAATCAATGCATG 59.308 40.000 0.00 0.00 42.54 4.06
103 104 4.678622 TCAACAGATGAATCAATGCATGC 58.321 39.130 11.82 11.82 34.30 4.06
104 105 4.158764 TCAACAGATGAATCAATGCATGCA 59.841 37.500 25.04 25.04 34.30 3.96
105 106 4.937201 ACAGATGAATCAATGCATGCAT 57.063 36.364 27.46 27.46 38.46 3.96
106 107 6.039941 TCAACAGATGAATCAATGCATGCATA 59.960 34.615 32.36 19.13 33.20 3.14
107 108 6.590234 ACAGATGAATCAATGCATGCATAT 57.410 33.333 32.36 20.78 35.31 1.78
108 109 7.696992 ACAGATGAATCAATGCATGCATATA 57.303 32.000 32.36 22.88 35.31 0.86
109 110 8.293699 ACAGATGAATCAATGCATGCATATAT 57.706 30.769 32.36 23.98 35.31 0.86
110 111 9.403583 ACAGATGAATCAATGCATGCATATATA 57.596 29.630 32.36 18.08 35.31 0.86
139 140 7.764141 TTTTACATGGATGCATGCATATACT 57.236 32.000 32.27 12.25 36.67 2.12
140 141 7.764141 TTTACATGGATGCATGCATATACTT 57.236 32.000 32.27 19.33 36.67 2.24
141 142 8.860780 TTTACATGGATGCATGCATATACTTA 57.139 30.769 32.27 17.66 36.67 2.24
142 143 9.465199 TTTACATGGATGCATGCATATACTTAT 57.535 29.630 32.27 16.68 36.67 1.73
207 208 9.410556 AGTATGTGTTTTGAGTCATAAATTTGC 57.589 29.630 0.00 0.00 0.00 3.68
208 209 9.190858 GTATGTGTTTTGAGTCATAAATTTGCA 57.809 29.630 0.00 0.00 0.00 4.08
209 210 8.659925 ATGTGTTTTGAGTCATAAATTTGCAA 57.340 26.923 0.00 0.00 0.00 4.08
210 211 8.484641 TGTGTTTTGAGTCATAAATTTGCAAA 57.515 26.923 15.44 15.44 0.00 3.68
211 212 9.107177 TGTGTTTTGAGTCATAAATTTGCAAAT 57.893 25.926 18.99 18.99 0.00 2.32
212 213 9.934190 GTGTTTTGAGTCATAAATTTGCAAATT 57.066 25.926 27.73 27.73 40.15 1.82
242 243 9.689976 ATTACATCATTTTCAAATTCGTGTCAA 57.310 25.926 0.00 0.00 0.00 3.18
243 244 7.393551 ACATCATTTTCAAATTCGTGTCAAC 57.606 32.000 0.00 0.00 0.00 3.18
244 245 7.202526 ACATCATTTTCAAATTCGTGTCAACT 58.797 30.769 0.00 0.00 0.00 3.16
245 246 7.706179 ACATCATTTTCAAATTCGTGTCAACTT 59.294 29.630 0.00 0.00 0.00 2.66
246 247 8.542132 CATCATTTTCAAATTCGTGTCAACTTT 58.458 29.630 0.00 0.00 0.00 2.66
247 248 7.893824 TCATTTTCAAATTCGTGTCAACTTTG 58.106 30.769 0.00 0.00 0.00 2.77
248 249 6.639671 TTTTCAAATTCGTGTCAACTTTGG 57.360 33.333 0.00 0.00 0.00 3.28
249 250 4.974368 TCAAATTCGTGTCAACTTTGGT 57.026 36.364 0.00 0.00 0.00 3.67
250 251 5.317733 TCAAATTCGTGTCAACTTTGGTT 57.682 34.783 0.00 0.00 35.86 3.67
251 252 6.438259 TCAAATTCGTGTCAACTTTGGTTA 57.562 33.333 0.00 0.00 33.88 2.85
252 253 7.033530 TCAAATTCGTGTCAACTTTGGTTAT 57.966 32.000 0.00 0.00 33.88 1.89
253 254 7.484975 TCAAATTCGTGTCAACTTTGGTTATT 58.515 30.769 0.00 0.00 33.88 1.40
254 255 8.622157 TCAAATTCGTGTCAACTTTGGTTATTA 58.378 29.630 0.00 0.00 33.88 0.98
255 256 9.405587 CAAATTCGTGTCAACTTTGGTTATTAT 57.594 29.630 0.00 0.00 33.88 1.28
256 257 8.964420 AATTCGTGTCAACTTTGGTTATTATG 57.036 30.769 0.00 0.00 33.88 1.90
257 258 7.731882 TTCGTGTCAACTTTGGTTATTATGA 57.268 32.000 0.00 0.00 33.88 2.15
258 259 7.915293 TCGTGTCAACTTTGGTTATTATGAT 57.085 32.000 0.00 0.00 33.88 2.45
259 260 9.438228 TTCGTGTCAACTTTGGTTATTATGATA 57.562 29.630 0.00 0.00 33.88 2.15
260 261 9.607988 TCGTGTCAACTTTGGTTATTATGATAT 57.392 29.630 0.00 0.00 33.88 1.63
288 289 8.940768 ATCAAAACCATACCGAAATAATTTGG 57.059 30.769 0.00 0.00 44.62 3.28
337 338 9.956720 TTTTAATTTCAAACCGTATTTACCGAA 57.043 25.926 0.00 0.00 0.00 4.30
338 339 9.956720 TTTAATTTCAAACCGTATTTACCGAAA 57.043 25.926 0.00 0.00 0.00 3.46
366 367 6.667007 AATACTATACAAACCGGAAAACCG 57.333 37.500 9.46 0.00 0.00 4.44
367 368 4.006780 ACTATACAAACCGGAAAACCGT 57.993 40.909 9.46 0.00 0.00 4.83
368 369 5.146010 ACTATACAAACCGGAAAACCGTA 57.854 39.130 9.46 0.65 0.00 4.02
369 370 5.733676 ACTATACAAACCGGAAAACCGTAT 58.266 37.500 9.46 8.52 0.00 3.06
370 371 6.872920 ACTATACAAACCGGAAAACCGTATA 58.127 36.000 9.46 9.19 0.00 1.47
371 372 7.327214 ACTATACAAACCGGAAAACCGTATAA 58.673 34.615 9.46 0.00 0.00 0.98
372 373 7.821846 ACTATACAAACCGGAAAACCGTATAAA 59.178 33.333 9.46 0.00 0.00 1.40
373 374 5.107109 ACAAACCGGAAAACCGTATAAAC 57.893 39.130 9.46 0.00 0.00 2.01
374 375 4.023279 ACAAACCGGAAAACCGTATAAACC 60.023 41.667 9.46 0.00 0.00 3.27
375 376 2.345876 ACCGGAAAACCGTATAAACCG 58.654 47.619 9.46 0.00 38.83 4.44
376 377 2.028567 ACCGGAAAACCGTATAAACCGA 60.029 45.455 9.46 0.00 41.09 4.69
377 378 2.999355 CCGGAAAACCGTATAAACCGAA 59.001 45.455 0.00 0.00 41.09 4.30
378 379 3.181521 CCGGAAAACCGTATAAACCGAAC 60.182 47.826 0.00 0.00 41.09 3.95
379 380 3.181521 CGGAAAACCGTATAAACCGAACC 60.182 47.826 0.00 0.00 41.09 3.62
380 381 3.750652 GGAAAACCGTATAAACCGAACCA 59.249 43.478 0.00 0.00 0.00 3.67
381 382 4.395854 GGAAAACCGTATAAACCGAACCAT 59.604 41.667 0.00 0.00 0.00 3.55
382 383 4.950434 AAACCGTATAAACCGAACCATG 57.050 40.909 0.00 0.00 0.00 3.66
383 384 3.615224 ACCGTATAAACCGAACCATGT 57.385 42.857 0.00 0.00 0.00 3.21
384 385 4.734398 ACCGTATAAACCGAACCATGTA 57.266 40.909 0.00 0.00 0.00 2.29
385 386 5.083533 ACCGTATAAACCGAACCATGTAA 57.916 39.130 0.00 0.00 0.00 2.41
386 387 5.486526 ACCGTATAAACCGAACCATGTAAA 58.513 37.500 0.00 0.00 0.00 2.01
387 388 5.351189 ACCGTATAAACCGAACCATGTAAAC 59.649 40.000 0.00 0.00 0.00 2.01
388 389 5.220643 CCGTATAAACCGAACCATGTAAACC 60.221 44.000 0.00 0.00 0.00 3.27
389 390 4.950434 ATAAACCGAACCATGTAAACCG 57.050 40.909 0.00 0.00 0.00 4.44
390 391 2.547299 AACCGAACCATGTAAACCGA 57.453 45.000 0.00 0.00 0.00 4.69
391 392 2.547299 ACCGAACCATGTAAACCGAA 57.453 45.000 0.00 0.00 0.00 4.30
392 393 3.062122 ACCGAACCATGTAAACCGAAT 57.938 42.857 0.00 0.00 0.00 3.34
393 394 4.205065 ACCGAACCATGTAAACCGAATA 57.795 40.909 0.00 0.00 0.00 1.75
394 395 4.577875 ACCGAACCATGTAAACCGAATAA 58.422 39.130 0.00 0.00 0.00 1.40
395 396 5.002516 ACCGAACCATGTAAACCGAATAAA 58.997 37.500 0.00 0.00 0.00 1.40
396 397 5.106594 ACCGAACCATGTAAACCGAATAAAC 60.107 40.000 0.00 0.00 0.00 2.01
397 398 5.326292 CGAACCATGTAAACCGAATAAACC 58.674 41.667 0.00 0.00 0.00 3.27
398 399 4.950434 ACCATGTAAACCGAATAAACCG 57.050 40.909 0.00 0.00 0.00 4.44
399 400 4.577875 ACCATGTAAACCGAATAAACCGA 58.422 39.130 0.00 0.00 0.00 4.69
400 401 4.632688 ACCATGTAAACCGAATAAACCGAG 59.367 41.667 0.00 0.00 0.00 4.63
401 402 4.495184 CCATGTAAACCGAATAAACCGAGC 60.495 45.833 0.00 0.00 0.00 5.03
402 403 2.667481 TGTAAACCGAATAAACCGAGCG 59.333 45.455 0.00 0.00 0.00 5.03
403 404 0.445043 AAACCGAATAAACCGAGCGC 59.555 50.000 0.00 0.00 0.00 5.92
404 405 0.671163 AACCGAATAAACCGAGCGCA 60.671 50.000 11.47 0.00 0.00 6.09
405 406 1.347221 CCGAATAAACCGAGCGCAC 59.653 57.895 11.47 0.96 0.00 5.34
406 407 1.355796 CCGAATAAACCGAGCGCACA 61.356 55.000 11.47 0.00 0.00 4.57
407 408 0.025001 CGAATAAACCGAGCGCACAG 59.975 55.000 11.47 0.00 0.00 3.66
408 409 1.355971 GAATAAACCGAGCGCACAGA 58.644 50.000 11.47 0.00 0.00 3.41
409 410 1.324736 GAATAAACCGAGCGCACAGAG 59.675 52.381 11.47 0.00 0.00 3.35
410 411 0.246635 ATAAACCGAGCGCACAGAGT 59.753 50.000 11.47 0.00 0.00 3.24
411 412 0.666274 TAAACCGAGCGCACAGAGTG 60.666 55.000 11.47 0.00 36.51 3.51
412 413 2.363711 AAACCGAGCGCACAGAGTGA 62.364 55.000 11.47 0.00 35.23 3.41
413 414 2.505777 CCGAGCGCACAGAGTGAG 60.506 66.667 11.47 0.00 35.23 3.51
414 415 2.256764 CGAGCGCACAGAGTGAGT 59.743 61.111 11.47 0.00 35.84 3.41
415 416 1.799519 CGAGCGCACAGAGTGAGTC 60.800 63.158 11.47 0.00 35.84 3.36
416 417 1.445238 GAGCGCACAGAGTGAGTCC 60.445 63.158 11.47 0.00 35.84 3.85
417 418 2.147315 GAGCGCACAGAGTGAGTCCA 62.147 60.000 11.47 0.00 35.84 4.02
418 419 1.300931 GCGCACAGAGTGAGTCCAA 60.301 57.895 0.30 0.00 35.84 3.53
419 420 0.880278 GCGCACAGAGTGAGTCCAAA 60.880 55.000 0.30 0.00 35.84 3.28
420 421 1.800805 CGCACAGAGTGAGTCCAAAT 58.199 50.000 0.58 0.00 35.23 2.32
421 422 1.728971 CGCACAGAGTGAGTCCAAATC 59.271 52.381 0.58 0.00 35.23 2.17
422 423 2.771089 GCACAGAGTGAGTCCAAATCA 58.229 47.619 0.58 0.00 35.23 2.57
423 424 3.141398 GCACAGAGTGAGTCCAAATCAA 58.859 45.455 0.58 0.00 35.23 2.57
424 425 3.565482 GCACAGAGTGAGTCCAAATCAAA 59.435 43.478 0.58 0.00 35.23 2.69
425 426 4.555511 GCACAGAGTGAGTCCAAATCAAAC 60.556 45.833 0.58 0.00 35.23 2.93
426 427 3.809832 ACAGAGTGAGTCCAAATCAAACG 59.190 43.478 0.00 0.00 0.00 3.60
427 428 2.808543 AGAGTGAGTCCAAATCAAACGC 59.191 45.455 0.00 0.00 0.00 4.84
428 429 1.531149 AGTGAGTCCAAATCAAACGCG 59.469 47.619 3.53 3.53 0.00 6.01
429 430 1.263217 GTGAGTCCAAATCAAACGCGT 59.737 47.619 5.58 5.58 0.00 6.01
430 431 1.262950 TGAGTCCAAATCAAACGCGTG 59.737 47.619 14.98 0.00 0.00 5.34
431 432 0.040425 AGTCCAAATCAAACGCGTGC 60.040 50.000 14.98 0.00 0.00 5.34
432 433 1.001745 GTCCAAATCAAACGCGTGCC 61.002 55.000 14.98 0.00 0.00 5.01
433 434 1.007964 CCAAATCAAACGCGTGCCA 60.008 52.632 14.98 0.00 0.00 4.92
434 435 0.596083 CCAAATCAAACGCGTGCCAA 60.596 50.000 14.98 0.00 0.00 4.52
435 436 0.502275 CAAATCAAACGCGTGCCAAC 59.498 50.000 14.98 0.00 0.00 3.77
436 437 0.596341 AAATCAAACGCGTGCCAACC 60.596 50.000 14.98 0.00 0.00 3.77
437 438 2.414840 AATCAAACGCGTGCCAACCC 62.415 55.000 14.98 0.00 0.00 4.11
438 439 4.973360 CAAACGCGTGCCAACCCG 62.973 66.667 14.98 0.00 33.76 5.28
468 469 2.608988 CCCCACTGGCAGTCCTCT 60.609 66.667 19.13 0.00 0.00 3.69
469 470 1.306141 CCCCACTGGCAGTCCTCTA 60.306 63.158 19.13 0.00 0.00 2.43
470 471 1.617947 CCCCACTGGCAGTCCTCTAC 61.618 65.000 19.13 0.00 0.00 2.59
471 472 0.904865 CCCACTGGCAGTCCTCTACA 60.905 60.000 19.13 0.00 0.00 2.74
472 473 0.976641 CCACTGGCAGTCCTCTACAA 59.023 55.000 19.13 0.00 0.00 2.41
473 474 1.556911 CCACTGGCAGTCCTCTACAAT 59.443 52.381 19.13 0.00 0.00 2.71
474 475 2.419297 CCACTGGCAGTCCTCTACAATC 60.419 54.545 19.13 0.00 0.00 2.67
506 507 0.453782 GCACCACGAAACCAATACGC 60.454 55.000 0.00 0.00 0.00 4.42
516 517 0.390735 ACCAATACGCGAACTCCCAC 60.391 55.000 15.93 0.00 0.00 4.61
580 581 1.028330 GTACCCGCTAACCCAAAGCC 61.028 60.000 0.00 0.00 36.60 4.35
605 606 0.108329 ACGCCCATAGACTTCAACCG 60.108 55.000 0.00 0.00 0.00 4.44
734 735 6.465439 AGAGAAAACGATTTTGGAAAACCT 57.535 33.333 0.00 0.00 31.94 3.50
1054 1055 2.501943 ATTTCGGGAAGGGGAGGGGA 62.502 60.000 0.00 0.00 0.00 4.81
1175 1176 2.817834 GGCGCCGTCAAGTGCATA 60.818 61.111 12.58 0.00 45.18 3.14
1241 1242 2.352915 GAGCACCTCTCGATCGCG 60.353 66.667 11.09 3.99 39.35 5.87
1529 1530 2.290464 CGGACTCTCAAGTACCTCGAT 58.710 52.381 0.00 0.00 35.28 3.59
1862 1863 3.033909 TGAGGATGATGAAGACGTGGAT 58.966 45.455 0.00 0.00 0.00 3.41
1874 1875 0.738975 ACGTGGATGATGACGACGAT 59.261 50.000 0.00 0.00 40.69 3.73
2019 2020 4.271291 GCATCGATGAGGATGATGATGATG 59.729 45.833 29.20 0.00 45.27 3.07
2020 2021 5.661458 CATCGATGAGGATGATGATGATGA 58.339 41.667 21.02 0.00 45.27 2.92
2021 2022 5.934402 TCGATGAGGATGATGATGATGAT 57.066 39.130 0.00 0.00 0.00 2.45
2078 2079 1.957591 GCTGAGCCAGAGAGTAGTGGA 60.958 57.143 6.40 0.00 35.67 4.02
2117 2118 1.636003 GGGGGTGTTGGAGAAGAGATT 59.364 52.381 0.00 0.00 0.00 2.40
2180 2181 2.091610 TGGTGAGATCGGAGAGGAAGAT 60.092 50.000 0.00 0.00 43.63 2.40
2321 2322 1.269726 GCATGTTCAGTTTGTGGGTGG 60.270 52.381 0.00 0.00 0.00 4.61
2365 2369 4.227300 AGCAAGATAACTATTGACCACCCA 59.773 41.667 0.00 0.00 0.00 4.51
2386 2390 8.514594 CACCCAACTATATTGCAGGTATATTTG 58.485 37.037 16.22 16.22 30.58 2.32
2410 2414 6.770785 TGAACTGTGGCTAGTTTTTCAGTTAT 59.229 34.615 15.15 2.50 43.15 1.89
2442 2447 6.789262 AGCTTTCATGCATTAGTTATGTGTC 58.211 36.000 0.00 0.00 36.57 3.67
2580 2586 8.876790 GGTGAACACCTTGTGTATAAAGTATAC 58.123 37.037 15.69 0.00 46.79 1.47
2653 2659 5.308976 TCATGCTCCCAAGATATTGCTTA 57.691 39.130 0.00 0.00 0.00 3.09
3050 3066 2.768253 TGTGGGCTTAGACAGATGTG 57.232 50.000 0.00 0.00 0.00 3.21
3233 3267 9.476202 GCTAATTTGTTTCTTTTACCACTCAAT 57.524 29.630 0.00 0.00 0.00 2.57
3574 3608 2.600769 AGACCAGCCGTCGTCCTT 60.601 61.111 0.00 0.00 46.92 3.36
3617 3651 2.700783 TGATGACCCATCAGGCAGT 58.299 52.632 5.61 0.00 44.60 4.40
3993 4036 5.058490 CCTTTGAAATTCCTGTTGCATTGT 58.942 37.500 0.00 0.00 0.00 2.71
4260 4318 2.290577 CCCTCCTATAGCAAATGGGCTC 60.291 54.545 0.00 0.00 44.54 4.70
4327 4385 0.946221 CTGTGTCTCTGGTTCACGGC 60.946 60.000 0.00 0.00 35.20 5.68
4388 4447 4.087892 CTCTGCCAGGTGGGTCCG 62.088 72.222 0.00 0.00 41.99 4.79
4472 4534 2.656069 CGGTGGGTAGGTGGGTGAG 61.656 68.421 0.00 0.00 0.00 3.51
4473 4535 2.298661 GGTGGGTAGGTGGGTGAGG 61.299 68.421 0.00 0.00 0.00 3.86
4474 4536 1.229400 GTGGGTAGGTGGGTGAGGA 60.229 63.158 0.00 0.00 0.00 3.71
4475 4537 0.620700 GTGGGTAGGTGGGTGAGGAT 60.621 60.000 0.00 0.00 0.00 3.24
4476 4538 0.620410 TGGGTAGGTGGGTGAGGATG 60.620 60.000 0.00 0.00 0.00 3.51
4738 4807 2.034221 GGCGACCCTGCTCCTTTT 59.966 61.111 0.00 0.00 34.52 2.27
4756 4826 0.334676 TTTTCTGGCCGATGGGGATT 59.665 50.000 0.00 0.00 38.47 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 3.643199 TGGTTATGGACATGCTTAGCA 57.357 42.857 10.09 10.09 44.86 3.49
61 62 4.136796 TGATGGTTATGGACATGCTTAGC 58.863 43.478 0.00 0.00 0.00 3.09
62 63 5.589855 TGTTGATGGTTATGGACATGCTTAG 59.410 40.000 0.00 0.00 0.00 2.18
63 64 5.504853 TGTTGATGGTTATGGACATGCTTA 58.495 37.500 0.00 0.00 0.00 3.09
64 65 4.343231 TGTTGATGGTTATGGACATGCTT 58.657 39.130 0.00 0.00 0.00 3.91
65 66 3.949754 CTGTTGATGGTTATGGACATGCT 59.050 43.478 0.00 0.00 0.00 3.79
66 67 3.947196 TCTGTTGATGGTTATGGACATGC 59.053 43.478 0.00 0.00 0.00 4.06
67 68 6.068473 CATCTGTTGATGGTTATGGACATG 57.932 41.667 0.00 0.00 44.63 3.21
79 80 8.425429 ATGCATGCATTGATTCATCTGTTGATG 61.425 37.037 27.46 0.03 41.31 3.07
80 81 5.163457 TGCATGCATTGATTCATCTGTTGAT 60.163 36.000 18.46 0.00 33.34 2.57
81 82 4.158764 TGCATGCATTGATTCATCTGTTGA 59.841 37.500 18.46 0.00 0.00 3.18
82 83 4.429108 TGCATGCATTGATTCATCTGTTG 58.571 39.130 18.46 0.00 0.00 3.33
83 84 4.729227 TGCATGCATTGATTCATCTGTT 57.271 36.364 18.46 0.00 0.00 3.16
84 85 4.937201 ATGCATGCATTGATTCATCTGT 57.063 36.364 27.46 1.07 31.82 3.41
181 182 9.410556 GCAAATTTATGACTCAAAACACATACT 57.589 29.630 0.00 0.00 0.00 2.12
182 183 9.190858 TGCAAATTTATGACTCAAAACACATAC 57.809 29.630 0.00 0.00 0.00 2.39
183 184 9.755804 TTGCAAATTTATGACTCAAAACACATA 57.244 25.926 0.00 0.00 0.00 2.29
184 185 8.659925 TTGCAAATTTATGACTCAAAACACAT 57.340 26.923 0.00 0.00 0.00 3.21
185 186 8.484641 TTTGCAAATTTATGACTCAAAACACA 57.515 26.923 8.05 0.00 0.00 3.72
186 187 9.934190 AATTTGCAAATTTATGACTCAAAACAC 57.066 25.926 27.73 0.00 35.16 3.32
216 217 9.689976 TTGACACGAATTTGAAAATGATGTAAT 57.310 25.926 0.00 0.00 0.00 1.89
217 218 8.963130 GTTGACACGAATTTGAAAATGATGTAA 58.037 29.630 0.00 0.00 0.00 2.41
218 219 8.349245 AGTTGACACGAATTTGAAAATGATGTA 58.651 29.630 0.00 0.00 0.00 2.29
219 220 7.202526 AGTTGACACGAATTTGAAAATGATGT 58.797 30.769 0.00 0.00 0.00 3.06
220 221 7.627585 AGTTGACACGAATTTGAAAATGATG 57.372 32.000 0.00 0.00 0.00 3.07
221 222 8.542132 CAAAGTTGACACGAATTTGAAAATGAT 58.458 29.630 0.00 0.00 33.69 2.45
222 223 7.009999 CCAAAGTTGACACGAATTTGAAAATGA 59.990 33.333 11.70 0.00 33.69 2.57
223 224 7.118724 CCAAAGTTGACACGAATTTGAAAATG 58.881 34.615 11.70 0.00 33.69 2.32
224 225 6.816140 ACCAAAGTTGACACGAATTTGAAAAT 59.184 30.769 11.70 0.00 33.69 1.82
225 226 6.159988 ACCAAAGTTGACACGAATTTGAAAA 58.840 32.000 11.70 0.00 33.69 2.29
226 227 5.715070 ACCAAAGTTGACACGAATTTGAAA 58.285 33.333 11.70 0.00 33.69 2.69
227 228 5.317733 ACCAAAGTTGACACGAATTTGAA 57.682 34.783 11.70 0.00 33.69 2.69
228 229 4.974368 ACCAAAGTTGACACGAATTTGA 57.026 36.364 11.70 0.00 33.69 2.69
229 230 7.692908 AATAACCAAAGTTGACACGAATTTG 57.307 32.000 0.00 0.00 36.68 2.32
230 231 9.405587 CATAATAACCAAAGTTGACACGAATTT 57.594 29.630 0.00 0.00 36.68 1.82
231 232 8.788806 TCATAATAACCAAAGTTGACACGAATT 58.211 29.630 0.00 0.00 36.68 2.17
232 233 8.330466 TCATAATAACCAAAGTTGACACGAAT 57.670 30.769 0.00 0.00 36.68 3.34
233 234 7.731882 TCATAATAACCAAAGTTGACACGAA 57.268 32.000 0.00 0.00 36.68 3.85
234 235 7.915293 ATCATAATAACCAAAGTTGACACGA 57.085 32.000 0.00 0.00 36.68 4.35
263 264 8.536175 ACCAAATTATTTCGGTATGGTTTTGAT 58.464 29.630 9.07 0.00 36.32 2.57
264 265 7.897864 ACCAAATTATTTCGGTATGGTTTTGA 58.102 30.769 9.07 0.00 36.32 2.69
265 266 9.810545 ATACCAAATTATTTCGGTATGGTTTTG 57.189 29.630 20.38 0.00 41.95 2.44
274 275 9.558396 TTTCGGTATATACCAAATTATTTCGGT 57.442 29.630 27.58 13.35 46.80 4.69
275 276 9.815936 GTTTCGGTATATACCAAATTATTTCGG 57.184 33.333 27.58 9.93 46.80 4.30
276 277 9.815936 GGTTTCGGTATATACCAAATTATTTCG 57.184 33.333 27.58 12.15 46.80 3.46
277 278 9.815936 CGGTTTCGGTATATACCAAATTATTTC 57.184 33.333 27.58 14.34 46.80 2.17
278 279 9.558396 TCGGTTTCGGTATATACCAAATTATTT 57.442 29.630 27.58 0.00 46.80 1.40
279 280 9.558396 TTCGGTTTCGGTATATACCAAATTATT 57.442 29.630 27.58 0.00 46.80 1.40
280 281 9.729281 ATTCGGTTTCGGTATATACCAAATTAT 57.271 29.630 27.58 15.42 46.80 1.28
281 282 9.558396 AATTCGGTTTCGGTATATACCAAATTA 57.442 29.630 27.58 14.29 46.80 1.40
282 283 8.454570 AATTCGGTTTCGGTATATACCAAATT 57.545 30.769 27.58 17.17 46.80 1.82
283 284 9.729281 ATAATTCGGTTTCGGTATATACCAAAT 57.271 29.630 27.58 10.95 46.80 2.32
311 312 9.956720 TTCGGTAAATACGGTTTGAAATTAAAA 57.043 25.926 0.00 0.00 0.00 1.52
312 313 9.956720 TTTCGGTAAATACGGTTTGAAATTAAA 57.043 25.926 0.00 0.00 0.00 1.52
358 359 3.750652 TGGTTCGGTTTATACGGTTTTCC 59.249 43.478 0.00 0.00 0.00 3.13
359 360 5.106594 ACATGGTTCGGTTTATACGGTTTTC 60.107 40.000 0.00 0.00 0.00 2.29
360 361 4.761227 ACATGGTTCGGTTTATACGGTTTT 59.239 37.500 0.00 0.00 0.00 2.43
361 362 4.325972 ACATGGTTCGGTTTATACGGTTT 58.674 39.130 0.00 0.00 0.00 3.27
362 363 3.941573 ACATGGTTCGGTTTATACGGTT 58.058 40.909 0.00 0.00 0.00 4.44
363 364 3.615224 ACATGGTTCGGTTTATACGGT 57.385 42.857 0.00 0.00 0.00 4.83
364 365 5.220643 GGTTTACATGGTTCGGTTTATACGG 60.221 44.000 0.00 0.00 0.00 4.02
365 366 5.500610 CGGTTTACATGGTTCGGTTTATACG 60.501 44.000 0.00 0.00 0.00 3.06
366 367 5.580297 TCGGTTTACATGGTTCGGTTTATAC 59.420 40.000 0.00 0.00 0.00 1.47
367 368 5.728471 TCGGTTTACATGGTTCGGTTTATA 58.272 37.500 0.00 0.00 0.00 0.98
368 369 4.577875 TCGGTTTACATGGTTCGGTTTAT 58.422 39.130 0.00 0.00 0.00 1.40
369 370 4.000331 TCGGTTTACATGGTTCGGTTTA 58.000 40.909 0.00 0.00 0.00 2.01
370 371 2.848691 TCGGTTTACATGGTTCGGTTT 58.151 42.857 0.00 0.00 0.00 3.27
371 372 2.547299 TCGGTTTACATGGTTCGGTT 57.453 45.000 0.00 0.00 0.00 4.44
372 373 2.547299 TTCGGTTTACATGGTTCGGT 57.453 45.000 0.00 0.00 0.00 4.69
373 374 5.326292 GTTTATTCGGTTTACATGGTTCGG 58.674 41.667 0.00 0.00 0.00 4.30
374 375 5.326292 GGTTTATTCGGTTTACATGGTTCG 58.674 41.667 0.00 0.00 0.00 3.95
375 376 5.122082 TCGGTTTATTCGGTTTACATGGTTC 59.878 40.000 0.00 0.00 0.00 3.62
376 377 5.002516 TCGGTTTATTCGGTTTACATGGTT 58.997 37.500 0.00 0.00 0.00 3.67
377 378 4.577875 TCGGTTTATTCGGTTTACATGGT 58.422 39.130 0.00 0.00 0.00 3.55
378 379 4.495184 GCTCGGTTTATTCGGTTTACATGG 60.495 45.833 0.00 0.00 0.00 3.66
379 380 4.584394 GCTCGGTTTATTCGGTTTACATG 58.416 43.478 0.00 0.00 0.00 3.21
380 381 3.307782 CGCTCGGTTTATTCGGTTTACAT 59.692 43.478 0.00 0.00 0.00 2.29
381 382 2.667481 CGCTCGGTTTATTCGGTTTACA 59.333 45.455 0.00 0.00 0.00 2.41
382 383 2.535534 GCGCTCGGTTTATTCGGTTTAC 60.536 50.000 0.00 0.00 0.00 2.01
383 384 1.660104 GCGCTCGGTTTATTCGGTTTA 59.340 47.619 0.00 0.00 0.00 2.01
384 385 0.445043 GCGCTCGGTTTATTCGGTTT 59.555 50.000 0.00 0.00 0.00 3.27
385 386 0.671163 TGCGCTCGGTTTATTCGGTT 60.671 50.000 9.73 0.00 0.00 4.44
386 387 1.079681 TGCGCTCGGTTTATTCGGT 60.080 52.632 9.73 0.00 0.00 4.69
387 388 1.347221 GTGCGCTCGGTTTATTCGG 59.653 57.895 9.73 0.00 0.00 4.30
388 389 0.025001 CTGTGCGCTCGGTTTATTCG 59.975 55.000 9.73 0.00 0.00 3.34
389 390 1.324736 CTCTGTGCGCTCGGTTTATTC 59.675 52.381 17.19 0.00 0.00 1.75
390 391 1.337823 ACTCTGTGCGCTCGGTTTATT 60.338 47.619 17.19 0.00 0.00 1.40
391 392 0.246635 ACTCTGTGCGCTCGGTTTAT 59.753 50.000 17.19 0.25 0.00 1.40
392 393 0.666274 CACTCTGTGCGCTCGGTTTA 60.666 55.000 17.19 0.00 0.00 2.01
393 394 1.956170 CACTCTGTGCGCTCGGTTT 60.956 57.895 17.19 3.71 0.00 3.27
394 395 2.356313 CACTCTGTGCGCTCGGTT 60.356 61.111 17.19 4.05 0.00 4.44
395 396 3.274455 CTCACTCTGTGCGCTCGGT 62.274 63.158 17.19 7.34 32.98 4.69
396 397 2.505777 CTCACTCTGTGCGCTCGG 60.506 66.667 9.73 11.04 32.98 4.63
397 398 1.799519 GACTCACTCTGTGCGCTCG 60.800 63.158 9.73 1.74 32.98 5.03
398 399 1.445238 GGACTCACTCTGTGCGCTC 60.445 63.158 9.73 5.51 32.98 5.03
399 400 1.748329 TTGGACTCACTCTGTGCGCT 61.748 55.000 9.73 0.00 32.98 5.92
400 401 0.880278 TTTGGACTCACTCTGTGCGC 60.880 55.000 0.00 0.00 32.98 6.09
401 402 1.728971 GATTTGGACTCACTCTGTGCG 59.271 52.381 0.00 0.00 32.98 5.34
402 403 2.771089 TGATTTGGACTCACTCTGTGC 58.229 47.619 0.00 0.00 32.98 4.57
403 404 4.319046 CGTTTGATTTGGACTCACTCTGTG 60.319 45.833 0.00 0.00 34.45 3.66
404 405 3.809832 CGTTTGATTTGGACTCACTCTGT 59.190 43.478 0.00 0.00 0.00 3.41
405 406 3.364366 GCGTTTGATTTGGACTCACTCTG 60.364 47.826 0.00 0.00 0.00 3.35
406 407 2.808543 GCGTTTGATTTGGACTCACTCT 59.191 45.455 0.00 0.00 0.00 3.24
407 408 2.411547 CGCGTTTGATTTGGACTCACTC 60.412 50.000 0.00 0.00 0.00 3.51
408 409 1.531149 CGCGTTTGATTTGGACTCACT 59.469 47.619 0.00 0.00 0.00 3.41
409 410 1.263217 ACGCGTTTGATTTGGACTCAC 59.737 47.619 5.58 0.00 0.00 3.51
410 411 1.262950 CACGCGTTTGATTTGGACTCA 59.737 47.619 10.22 0.00 0.00 3.41
411 412 1.950472 CACGCGTTTGATTTGGACTC 58.050 50.000 10.22 0.00 0.00 3.36
412 413 0.040425 GCACGCGTTTGATTTGGACT 60.040 50.000 10.22 0.00 0.00 3.85
413 414 1.001745 GGCACGCGTTTGATTTGGAC 61.002 55.000 10.22 0.00 0.00 4.02
414 415 1.284408 GGCACGCGTTTGATTTGGA 59.716 52.632 10.22 0.00 0.00 3.53
415 416 0.596083 TTGGCACGCGTTTGATTTGG 60.596 50.000 10.22 0.00 0.00 3.28
416 417 0.502275 GTTGGCACGCGTTTGATTTG 59.498 50.000 10.22 0.00 0.00 2.32
417 418 0.596341 GGTTGGCACGCGTTTGATTT 60.596 50.000 10.22 0.00 0.00 2.17
418 419 1.007849 GGTTGGCACGCGTTTGATT 60.008 52.632 10.22 0.00 0.00 2.57
419 420 2.642700 GGTTGGCACGCGTTTGAT 59.357 55.556 10.22 0.00 0.00 2.57
420 421 3.587933 GGGTTGGCACGCGTTTGA 61.588 61.111 10.22 0.00 0.00 2.69
451 452 1.306141 TAGAGGACTGCCAGTGGGG 60.306 63.158 12.15 0.00 40.85 4.96
452 453 0.904865 TGTAGAGGACTGCCAGTGGG 60.905 60.000 12.15 0.00 36.29 4.61
453 454 0.976641 TTGTAGAGGACTGCCAGTGG 59.023 55.000 0.00 4.20 36.29 4.00
454 455 2.736719 CGATTGTAGAGGACTGCCAGTG 60.737 54.545 0.00 0.00 36.29 3.66
455 456 1.478510 CGATTGTAGAGGACTGCCAGT 59.521 52.381 0.00 0.00 36.29 4.00
456 457 1.202463 CCGATTGTAGAGGACTGCCAG 60.202 57.143 0.00 0.00 36.29 4.85
457 458 0.824109 CCGATTGTAGAGGACTGCCA 59.176 55.000 0.00 0.00 36.29 4.92
458 459 0.105039 CCCGATTGTAGAGGACTGCC 59.895 60.000 0.00 0.00 0.00 4.85
459 460 0.530870 GCCCGATTGTAGAGGACTGC 60.531 60.000 0.00 0.00 0.00 4.40
460 461 0.824109 TGCCCGATTGTAGAGGACTG 59.176 55.000 0.00 0.00 0.00 3.51
461 462 1.482593 CTTGCCCGATTGTAGAGGACT 59.517 52.381 0.00 0.00 0.00 3.85
462 463 1.473434 CCTTGCCCGATTGTAGAGGAC 60.473 57.143 0.00 0.00 0.00 3.85
463 464 0.830648 CCTTGCCCGATTGTAGAGGA 59.169 55.000 0.00 0.00 0.00 3.71
464 465 0.179045 CCCTTGCCCGATTGTAGAGG 60.179 60.000 0.00 0.00 0.00 3.69
465 466 0.541863 ACCCTTGCCCGATTGTAGAG 59.458 55.000 0.00 0.00 0.00 2.43
466 467 1.760613 CTACCCTTGCCCGATTGTAGA 59.239 52.381 0.00 0.00 0.00 2.59
467 468 1.202651 CCTACCCTTGCCCGATTGTAG 60.203 57.143 0.00 0.00 0.00 2.74
468 469 0.834612 CCTACCCTTGCCCGATTGTA 59.165 55.000 0.00 0.00 0.00 2.41
469 470 1.607612 CCTACCCTTGCCCGATTGT 59.392 57.895 0.00 0.00 0.00 2.71
470 471 1.823899 GCCTACCCTTGCCCGATTG 60.824 63.158 0.00 0.00 0.00 2.67
471 472 2.305607 TGCCTACCCTTGCCCGATT 61.306 57.895 0.00 0.00 0.00 3.34
472 473 2.690881 TGCCTACCCTTGCCCGAT 60.691 61.111 0.00 0.00 0.00 4.18
473 474 3.712907 GTGCCTACCCTTGCCCGA 61.713 66.667 0.00 0.00 0.00 5.14
474 475 4.796495 GGTGCCTACCCTTGCCCG 62.796 72.222 0.00 0.00 41.36 6.13
506 507 2.499685 GGATCGGGTGGGAGTTCG 59.500 66.667 0.00 0.00 0.00 3.95
580 581 1.659098 GAAGTCTATGGGCGTTGTTCG 59.341 52.381 0.00 0.00 43.12 3.95
605 606 2.126189 GTAGACGTGTGGGTCCGC 60.126 66.667 0.00 0.00 37.66 5.54
859 860 1.136961 TATATGGGCGGCCAATGGGA 61.137 55.000 36.08 17.66 35.59 4.37
1054 1055 4.020218 CCTCGTCCATCTCTCTATCTCTCT 60.020 50.000 0.00 0.00 0.00 3.10
1529 1530 0.745486 TCTCGTCGGCGTCCATCTTA 60.745 55.000 10.18 0.00 39.49 2.10
1780 1781 3.832237 CTGTGGTGGTGCTCGGCTT 62.832 63.158 0.00 0.00 0.00 4.35
1862 1863 1.405105 TCTGCATCATCGTCGTCATCA 59.595 47.619 0.00 0.00 0.00 3.07
1874 1875 3.067320 CCTCATACTCTTCGTCTGCATCA 59.933 47.826 0.00 0.00 0.00 3.07
2019 2020 2.166907 TCCTCAACCTCCTCCTCATC 57.833 55.000 0.00 0.00 0.00 2.92
2020 2021 2.022625 TCATCCTCAACCTCCTCCTCAT 60.023 50.000 0.00 0.00 0.00 2.90
2021 2022 1.362584 TCATCCTCAACCTCCTCCTCA 59.637 52.381 0.00 0.00 0.00 3.86
2078 2079 1.378514 CACCGCCATAGCAACCCTT 60.379 57.895 0.00 0.00 39.83 3.95
2102 2103 4.286808 TGTCCATCAATCTCTTCTCCAACA 59.713 41.667 0.00 0.00 0.00 3.33
2117 2118 1.629861 TCACCTTGCTCATGTCCATCA 59.370 47.619 0.00 0.00 0.00 3.07
2180 2181 5.841237 CCTACTATCCTCCAATCTTTCCTCA 59.159 44.000 0.00 0.00 0.00 3.86
2321 2322 9.760660 CTTGCTAAACAATATGACTAGAACAAC 57.239 33.333 0.00 0.00 37.72 3.32
2386 2390 5.500645 AACTGAAAAACTAGCCACAGTTC 57.499 39.130 0.00 1.08 42.30 3.01
2419 2423 5.973565 GGACACATAACTAATGCATGAAAGC 59.026 40.000 0.00 0.00 39.39 3.51
2421 2425 7.176515 ACAAGGACACATAACTAATGCATGAAA 59.823 33.333 0.00 0.00 39.39 2.69
2442 2447 6.808212 CCACATAATCAGCAAACTTAACAAGG 59.192 38.462 0.00 0.00 0.00 3.61
2580 2586 7.569677 TTTCGTTAAAACAACTTTTCCACAG 57.430 32.000 0.00 0.00 31.74 3.66
2593 2599 8.682128 TCCATATGAGCAAATTTCGTTAAAAC 57.318 30.769 3.65 0.00 0.00 2.43
2681 2687 4.431416 TTTGAGGGTACAGAGCTTTCAA 57.569 40.909 0.00 0.00 0.00 2.69
2747 2755 6.725834 AGAAATCAGAATCCCCAAGCTTTTAA 59.274 34.615 0.00 0.00 0.00 1.52
2748 2756 6.256053 AGAAATCAGAATCCCCAAGCTTTTA 58.744 36.000 0.00 0.00 0.00 1.52
2749 2757 5.089434 AGAAATCAGAATCCCCAAGCTTTT 58.911 37.500 0.00 0.00 0.00 2.27
2750 2758 4.681484 AGAAATCAGAATCCCCAAGCTTT 58.319 39.130 0.00 0.00 0.00 3.51
2898 2906 8.579850 TGCTTAACTGATGTATCCAAATCTTT 57.420 30.769 0.00 0.00 0.00 2.52
3050 3066 5.874810 TCTTACTAAACATGCATCAGGTGAC 59.125 40.000 0.00 0.00 0.00 3.67
3128 3145 4.214310 CACCAAGATAATGGCCATTACCA 58.786 43.478 35.00 19.82 44.75 3.25
3226 3260 8.618677 AGATAACAGCATAACATGAATTGAGTG 58.381 33.333 0.00 0.00 0.00 3.51
3233 3267 8.969260 ATCTGAAGATAACAGCATAACATGAA 57.031 30.769 0.00 0.00 35.61 2.57
3478 3512 3.525199 AGGGTCAGCAATATCAAAGTCCT 59.475 43.478 0.00 0.00 0.00 3.85
3574 3608 0.107703 CTTCCGCTTGATACCCTGCA 60.108 55.000 0.00 0.00 0.00 4.41
3617 3651 2.426406 ATCCTCATCGTCGCTGCCA 61.426 57.895 0.00 0.00 0.00 4.92
3750 3793 3.660501 GGAAACCCACCATTTCTGTTC 57.339 47.619 0.00 0.00 36.49 3.18
3776 3819 4.928601 ACAAGAAAAACGGCTAAGGAAAC 58.071 39.130 0.00 0.00 0.00 2.78
3958 4001 5.306937 GGAATTTCAAAGGAAGGAGGGAAAA 59.693 40.000 0.00 0.00 33.82 2.29
4260 4318 7.099120 AGCCAAAAATTGCTAAATAACTCCAG 58.901 34.615 0.00 0.00 35.69 3.86
4388 4447 0.741221 CCAAAGCTAGTCACGGGAGC 60.741 60.000 0.00 0.00 36.42 4.70
4391 4450 1.745489 GGCCAAAGCTAGTCACGGG 60.745 63.158 0.00 0.00 39.73 5.28
4397 4456 2.670148 CCCCGAGGCCAAAGCTAGT 61.670 63.158 5.01 0.00 39.73 2.57
4462 4524 0.990282 CATCCCATCCTCACCCACCT 60.990 60.000 0.00 0.00 0.00 4.00
4472 4534 1.376424 ATCGCATCGCATCCCATCC 60.376 57.895 0.00 0.00 0.00 3.51
4473 4535 1.792301 CATCGCATCGCATCCCATC 59.208 57.895 0.00 0.00 0.00 3.51
4474 4536 2.330372 GCATCGCATCGCATCCCAT 61.330 57.895 0.00 0.00 0.00 4.00
4475 4537 2.974148 GCATCGCATCGCATCCCA 60.974 61.111 0.00 0.00 0.00 4.37
4476 4538 4.081030 CGCATCGCATCGCATCCC 62.081 66.667 0.00 0.00 0.00 3.85
4654 4721 2.423660 GGGATCTTCTCTCCTCCTCGAA 60.424 54.545 0.00 0.00 33.05 3.71
4738 4807 0.334676 AAATCCCCATCGGCCAGAAA 59.665 50.000 2.24 0.00 0.00 2.52
4741 4810 1.318576 GTAAAATCCCCATCGGCCAG 58.681 55.000 2.24 0.00 0.00 4.85
4756 4826 4.041762 CAGGGGCAGGGGCGTAAA 62.042 66.667 0.00 0.00 42.47 2.01


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

AutoCloner maintained by Alex Coulton.