Multiple sequence alignment - TraesCS1A01G197100

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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 TraesCS1A01G197100 chr1A 100.000 4353 0 0 1 4353 355325460 355329812 0.000000e+00 8039
1 TraesCS1A01G197100 chr1B 92.003 2401 117 31 458 2822 385163650 385166011 0.000000e+00 3301
2 TraesCS1A01G197100 chr1B 92.586 1079 43 18 2821 3870 385166149 385167219 0.000000e+00 1515
3 TraesCS1A01G197100 chr1B 91.176 136 8 3 4221 4353 385169801 385169935 9.620000e-42 182
4 TraesCS1A01G197100 chr1B 78.165 316 13 14 3866 4163 385169509 385169786 2.710000e-32 150
5 TraesCS1A01G197100 chr1B 76.078 255 38 10 1 241 385163132 385163377 1.280000e-20 111
6 TraesCS1A01G197100 chr1D 91.471 1958 91 27 458 2372 283565410 283567334 0.000000e+00 2621
7 TraesCS1A01G197100 chr1D 93.248 1244 62 13 2384 3609 283567386 283568625 0.000000e+00 1812
8 TraesCS1A01G197100 chr1D 81.761 159 21 5 85 241 283564986 283565138 4.570000e-25 126


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 TraesCS1A01G197100 chr1A 355325460 355329812 4352 False 8039.000000 8039 100.000000 1 4353 1 chr1A.!!$F1 4352
1 TraesCS1A01G197100 chr1B 385163132 385169935 6803 False 1051.800000 3301 86.001600 1 4353 5 chr1B.!!$F1 4352
2 TraesCS1A01G197100 chr1D 283564986 283568625 3639 False 1519.666667 2621 88.826667 85 3609 3 chr1D.!!$F1 3524

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
23 24 0.107214 CGGGCCTGAATAAAGGAGCA 60.107 55.0 5.28 0.0 40.02 4.26 F
350 441 0.179081 GTTCACCGGTAGATGAGCCC 60.179 60.0 6.87 0.0 0.00 5.19 F
775 964 0.179171 CCGCATCTCGTCAACGTACT 60.179 55.0 2.09 0.0 40.80 2.73 F
1116 1334 0.657840 GCTCACGTCTTGCTGTTGTT 59.342 50.0 0.00 0.0 0.00 2.83 F
1998 2225 1.039068 TGGTGTGGAATTGCTGTTGG 58.961 50.0 0.00 0.0 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2225 0.687354 TCCTCTTCCTTGCCTGACAC 59.313 55.000 0.00 0.00 0.00 3.67 R
2047 2274 1.803289 GGCCATTTTCTCGCCTCAC 59.197 57.895 0.00 0.00 39.70 3.51 R
2548 2824 1.135094 ACTATGGTGGCCATCCTCAG 58.865 55.000 15.03 16.12 40.74 3.35 R
3105 3536 2.893424 ACATTGCCCATTTCTCAAGGT 58.107 42.857 0.00 0.00 31.07 3.50 R
3922 6676 0.530650 ACTTGCAGTGTCTCACGGTG 60.531 55.000 0.56 0.56 39.64 4.94 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
23 24 0.107214 CGGGCCTGAATAAAGGAGCA 60.107 55.000 5.28 0.00 40.02 4.26
24 25 1.393603 GGGCCTGAATAAAGGAGCAC 58.606 55.000 0.84 0.00 40.02 4.40
27 28 1.679032 GCCTGAATAAAGGAGCACGGT 60.679 52.381 0.00 0.00 40.02 4.83
33 34 5.116180 TGAATAAAGGAGCACGGTCAATAG 58.884 41.667 0.00 0.00 0.00 1.73
38 39 1.009829 GAGCACGGTCAATAGGCAAG 58.990 55.000 0.00 0.00 0.00 4.01
40 41 1.210478 AGCACGGTCAATAGGCAAGAT 59.790 47.619 0.00 0.00 0.00 2.40
54 55 3.831911 AGGCAAGATTTCGGGAATTTCAA 59.168 39.130 0.00 0.00 0.00 2.69
56 57 4.994217 GGCAAGATTTCGGGAATTTCAAAA 59.006 37.500 0.00 0.00 0.00 2.44
60 61 7.095271 GCAAGATTTCGGGAATTTCAAAAATCA 60.095 33.333 18.25 0.00 36.21 2.57
67 68 7.441017 TCGGGAATTTCAAAAATCATTTCAGT 58.559 30.769 0.00 0.00 0.00 3.41
93 104 8.879342 TTTTTCAGAATCCGCTTAATTTTGAA 57.121 26.923 5.16 5.16 36.20 2.69
125 136 9.762062 ATGTTTTTGTTTGGAATTCGTTTTTAC 57.238 25.926 0.00 0.00 0.00 2.01
132 143 3.892588 TGGAATTCGTTTTTACCTGGCTT 59.107 39.130 0.00 0.00 0.00 4.35
137 148 4.985538 TCGTTTTTACCTGGCTTGAAAA 57.014 36.364 0.00 0.00 0.00 2.29
139 150 5.908341 TCGTTTTTACCTGGCTTGAAAATT 58.092 33.333 0.00 0.00 0.00 1.82
155 166 9.062524 GCTTGAAAATTTGGGGTTTAAAGTATT 57.937 29.630 0.00 0.00 0.00 1.89
163 174 7.764141 TTGGGGTTTAAAGTATTTCAGTACC 57.236 36.000 0.00 0.00 40.09 3.34
164 175 6.247676 TGGGGTTTAAAGTATTTCAGTACCC 58.752 40.000 0.00 0.00 40.54 3.69
166 177 6.151648 GGGGTTTAAAGTATTTCAGTACCCAC 59.848 42.308 0.00 0.00 41.82 4.61
167 178 6.151648 GGGTTTAAAGTATTTCAGTACCCACC 59.848 42.308 0.00 0.00 40.75 4.61
168 179 6.128200 GGTTTAAAGTATTTCAGTACCCACCG 60.128 42.308 0.00 0.00 40.09 4.94
169 180 4.628963 AAAGTATTTCAGTACCCACCGT 57.371 40.909 0.00 0.00 27.08 4.83
170 181 5.743636 AAAGTATTTCAGTACCCACCGTA 57.256 39.130 0.00 0.00 27.08 4.02
178 189 6.488769 TTCAGTACCCACCGTAATAATCAT 57.511 37.500 0.00 0.00 0.00 2.45
179 190 6.488769 TCAGTACCCACCGTAATAATCATT 57.511 37.500 0.00 0.00 0.00 2.57
180 191 6.891388 TCAGTACCCACCGTAATAATCATTT 58.109 36.000 0.00 0.00 0.00 2.32
181 192 7.340256 TCAGTACCCACCGTAATAATCATTTT 58.660 34.615 0.00 0.00 0.00 1.82
182 193 7.830201 TCAGTACCCACCGTAATAATCATTTTT 59.170 33.333 0.00 0.00 0.00 1.94
233 244 7.066766 AGCTCATTAATCAGATGAACCTTGAAC 59.933 37.037 0.00 0.00 33.45 3.18
241 252 5.005740 CAGATGAACCTTGAACCTGATCAA 58.994 41.667 0.00 0.00 37.70 2.57
242 253 5.651139 CAGATGAACCTTGAACCTGATCAAT 59.349 40.000 0.00 0.00 38.55 2.57
246 337 9.512588 GATGAACCTTGAACCTGATCAATATAT 57.487 33.333 0.00 0.00 38.55 0.86
267 358 7.906199 ATATAAAAGACAGCAGTAGTCTCCT 57.094 36.000 0.00 0.00 45.11 3.69
268 359 4.529109 AAAAGACAGCAGTAGTCTCCTC 57.471 45.455 0.00 0.00 45.11 3.71
269 360 3.449746 AAGACAGCAGTAGTCTCCTCT 57.550 47.619 0.00 0.00 45.11 3.69
270 361 4.577988 AAGACAGCAGTAGTCTCCTCTA 57.422 45.455 0.00 0.00 45.11 2.43
271 362 4.150897 AGACAGCAGTAGTCTCCTCTAG 57.849 50.000 0.00 0.00 42.40 2.43
272 363 2.616842 GACAGCAGTAGTCTCCTCTAGC 59.383 54.545 0.00 0.00 33.29 3.42
273 364 2.025793 ACAGCAGTAGTCTCCTCTAGCA 60.026 50.000 0.00 0.00 0.00 3.49
274 365 3.221771 CAGCAGTAGTCTCCTCTAGCAT 58.778 50.000 0.00 0.00 0.00 3.79
275 366 3.004629 CAGCAGTAGTCTCCTCTAGCATG 59.995 52.174 0.00 0.00 0.00 4.06
276 367 3.117701 AGCAGTAGTCTCCTCTAGCATGA 60.118 47.826 0.00 0.00 0.00 3.07
277 368 3.253188 GCAGTAGTCTCCTCTAGCATGAG 59.747 52.174 0.00 0.00 0.00 2.90
278 369 4.713553 CAGTAGTCTCCTCTAGCATGAGA 58.286 47.826 0.00 2.67 36.23 3.27
279 370 5.129634 CAGTAGTCTCCTCTAGCATGAGAA 58.870 45.833 0.00 0.00 36.93 2.87
280 371 5.592282 CAGTAGTCTCCTCTAGCATGAGAAA 59.408 44.000 0.00 0.00 36.93 2.52
281 372 6.096141 CAGTAGTCTCCTCTAGCATGAGAAAA 59.904 42.308 0.00 0.00 36.93 2.29
282 373 5.596836 AGTCTCCTCTAGCATGAGAAAAG 57.403 43.478 0.00 0.00 36.93 2.27
283 374 5.022787 AGTCTCCTCTAGCATGAGAAAAGT 58.977 41.667 0.00 0.00 36.93 2.66
284 375 5.483583 AGTCTCCTCTAGCATGAGAAAAGTT 59.516 40.000 0.00 0.00 36.93 2.66
285 376 6.013812 AGTCTCCTCTAGCATGAGAAAAGTTT 60.014 38.462 0.00 0.00 36.93 2.66
286 377 6.312672 GTCTCCTCTAGCATGAGAAAAGTTTC 59.687 42.308 0.00 0.00 36.93 2.78
287 378 6.014242 TCTCCTCTAGCATGAGAAAAGTTTCA 60.014 38.462 0.00 0.00 39.61 2.69
288 379 6.169094 TCCTCTAGCATGAGAAAAGTTTCAG 58.831 40.000 0.00 0.00 39.61 3.02
289 380 5.353678 CCTCTAGCATGAGAAAAGTTTCAGG 59.646 44.000 0.00 0.00 39.61 3.86
290 381 5.869579 TCTAGCATGAGAAAAGTTTCAGGT 58.130 37.500 0.00 2.26 39.61 4.00
291 382 6.299141 TCTAGCATGAGAAAAGTTTCAGGTT 58.701 36.000 0.00 0.00 39.61 3.50
292 383 5.859205 AGCATGAGAAAAGTTTCAGGTTT 57.141 34.783 0.00 0.00 39.61 3.27
293 384 6.225981 AGCATGAGAAAAGTTTCAGGTTTT 57.774 33.333 0.00 0.00 39.61 2.43
294 385 6.643388 AGCATGAGAAAAGTTTCAGGTTTTT 58.357 32.000 0.00 0.00 39.61 1.94
338 429 9.632969 CTATTTATTTCGATTTACTGTTCACCG 57.367 33.333 0.00 0.00 0.00 4.94
339 430 4.939509 ATTTCGATTTACTGTTCACCGG 57.060 40.909 0.00 0.00 0.00 5.28
340 431 3.389925 TTCGATTTACTGTTCACCGGT 57.610 42.857 0.00 0.00 36.38 5.28
341 432 4.517952 TTCGATTTACTGTTCACCGGTA 57.482 40.909 6.87 0.00 33.63 4.02
342 433 4.100707 TCGATTTACTGTTCACCGGTAG 57.899 45.455 6.87 2.99 36.30 3.18
343 434 3.758023 TCGATTTACTGTTCACCGGTAGA 59.242 43.478 6.87 4.45 36.30 2.59
344 435 4.400251 TCGATTTACTGTTCACCGGTAGAT 59.600 41.667 6.87 0.00 36.30 1.98
345 436 4.503007 CGATTTACTGTTCACCGGTAGATG 59.497 45.833 6.87 0.00 36.30 2.90
346 437 5.657474 GATTTACTGTTCACCGGTAGATGA 58.343 41.667 6.87 0.00 36.30 2.92
347 438 4.713824 TTACTGTTCACCGGTAGATGAG 57.286 45.455 6.87 8.68 36.30 2.90
348 439 1.204941 ACTGTTCACCGGTAGATGAGC 59.795 52.381 6.87 2.80 0.00 4.26
349 440 0.535335 TGTTCACCGGTAGATGAGCC 59.465 55.000 6.87 0.00 0.00 4.70
350 441 0.179081 GTTCACCGGTAGATGAGCCC 60.179 60.000 6.87 0.00 0.00 5.19
351 442 1.335132 TTCACCGGTAGATGAGCCCC 61.335 60.000 6.87 0.00 0.00 5.80
352 443 2.838225 ACCGGTAGATGAGCCCCG 60.838 66.667 4.49 0.00 40.12 5.73
354 445 3.616721 CGGTAGATGAGCCCCGGG 61.617 72.222 15.80 15.80 36.84 5.73
365 456 3.646715 CCCCGGGCTCCAGTTGAA 61.647 66.667 17.73 0.00 0.00 2.69
366 457 2.677228 CCCGGGCTCCAGTTGAAT 59.323 61.111 8.08 0.00 0.00 2.57
367 458 1.000896 CCCGGGCTCCAGTTGAATT 60.001 57.895 8.08 0.00 0.00 2.17
368 459 0.254747 CCCGGGCTCCAGTTGAATTA 59.745 55.000 8.08 0.00 0.00 1.40
369 460 1.133792 CCCGGGCTCCAGTTGAATTAT 60.134 52.381 8.08 0.00 0.00 1.28
370 461 2.222027 CCGGGCTCCAGTTGAATTATC 58.778 52.381 0.00 0.00 0.00 1.75
371 462 1.867233 CGGGCTCCAGTTGAATTATCG 59.133 52.381 0.00 0.00 0.00 2.92
397 488 4.046462 CCGTGTCTACTTTTCTTCGTCAA 58.954 43.478 0.00 0.00 0.00 3.18
398 489 4.684703 CCGTGTCTACTTTTCTTCGTCAAT 59.315 41.667 0.00 0.00 0.00 2.57
399 490 5.164080 CCGTGTCTACTTTTCTTCGTCAATC 60.164 44.000 0.00 0.00 0.00 2.67
400 491 5.441614 CGTGTCTACTTTTCTTCGTCAATCG 60.442 44.000 0.00 0.00 41.41 3.34
401 492 5.401674 GTGTCTACTTTTCTTCGTCAATCGT 59.598 40.000 0.00 0.00 40.80 3.73
402 493 5.628193 TGTCTACTTTTCTTCGTCAATCGTC 59.372 40.000 0.00 0.00 40.80 4.20
403 494 5.628193 GTCTACTTTTCTTCGTCAATCGTCA 59.372 40.000 0.00 0.00 40.80 4.35
404 495 6.143438 GTCTACTTTTCTTCGTCAATCGTCAA 59.857 38.462 0.00 0.00 40.80 3.18
405 496 5.330271 ACTTTTCTTCGTCAATCGTCAAG 57.670 39.130 0.00 0.00 40.80 3.02
407 498 2.724977 TCTTCGTCAATCGTCAAGCT 57.275 45.000 0.00 0.00 40.80 3.74
409 500 1.656095 CTTCGTCAATCGTCAAGCTCC 59.344 52.381 0.00 0.00 40.80 4.70
411 502 1.204704 TCGTCAATCGTCAAGCTCCAT 59.795 47.619 0.00 0.00 40.80 3.41
415 506 4.184629 GTCAATCGTCAAGCTCCATTAGT 58.815 43.478 0.00 0.00 0.00 2.24
416 507 5.348986 GTCAATCGTCAAGCTCCATTAGTA 58.651 41.667 0.00 0.00 0.00 1.82
417 508 5.232414 GTCAATCGTCAAGCTCCATTAGTAC 59.768 44.000 0.00 0.00 0.00 2.73
423 586 5.622460 CGTCAAGCTCCATTAGTACTTCACT 60.622 44.000 0.00 0.00 41.62 3.41
466 629 4.084287 AGGTAGGTTAGTCACACGAATGA 58.916 43.478 0.00 0.00 0.00 2.57
467 630 4.710375 AGGTAGGTTAGTCACACGAATGAT 59.290 41.667 0.00 0.00 0.00 2.45
545 733 3.509967 GGTTAAGTGAGTGGGAAATTGGG 59.490 47.826 0.00 0.00 0.00 4.12
561 749 1.133809 TGGGTGGGTTCCTCTTCCTG 61.134 60.000 0.00 0.00 0.00 3.86
624 812 3.066064 TCAATGGGAAAACACACAACTCG 59.934 43.478 0.00 0.00 0.00 4.18
681 869 0.761187 GGTCATATCTGCCTGCCTGA 59.239 55.000 0.00 0.00 0.00 3.86
686 874 0.618680 TATCTGCCTGCCTGACCTGT 60.619 55.000 0.00 0.00 0.00 4.00
687 875 2.194388 ATCTGCCTGCCTGACCTGTG 62.194 60.000 0.00 0.00 0.00 3.66
688 876 2.848679 TGCCTGCCTGACCTGTGA 60.849 61.111 0.00 0.00 0.00 3.58
722 911 0.599991 TCATGACGACACACAGCACC 60.600 55.000 0.00 0.00 0.00 5.01
732 921 4.972733 ACAGCACCCGCCATGCAA 62.973 61.111 0.00 0.00 45.92 4.08
733 922 3.682885 CAGCACCCGCCATGCAAA 61.683 61.111 0.00 0.00 45.92 3.68
734 923 2.681064 AGCACCCGCCATGCAAAT 60.681 55.556 0.00 0.00 45.92 2.32
735 924 2.509786 GCACCCGCCATGCAAATG 60.510 61.111 0.00 0.00 42.88 2.32
736 925 2.184836 CACCCGCCATGCAAATGG 59.815 61.111 1.68 1.68 44.44 3.16
737 926 2.037049 ACCCGCCATGCAAATGGA 59.963 55.556 10.63 0.00 44.39 3.41
738 927 1.608918 ACCCGCCATGCAAATGGAA 60.609 52.632 10.63 0.00 44.39 3.53
739 928 0.977108 ACCCGCCATGCAAATGGAAT 60.977 50.000 10.63 0.00 44.39 3.01
740 929 0.531090 CCCGCCATGCAAATGGAATG 60.531 55.000 10.63 0.00 44.39 2.67
741 930 0.531090 CCGCCATGCAAATGGAATGG 60.531 55.000 10.63 3.09 44.39 3.16
746 935 3.432467 GCCATGCAAATGGAATGGAATGA 60.432 43.478 10.63 0.00 44.39 2.57
752 941 5.875910 TGCAAATGGAATGGAATGAAATGAC 59.124 36.000 0.00 0.00 0.00 3.06
757 946 4.650588 TGGAATGGAATGAAATGACATCCC 59.349 41.667 0.00 0.00 0.00 3.85
775 964 0.179171 CCGCATCTCGTCAACGTACT 60.179 55.000 2.09 0.00 40.80 2.73
783 972 3.605056 TCTCGTCAACGTACTTATTTGCG 59.395 43.478 2.09 0.00 40.80 4.85
791 980 4.300803 ACGTACTTATTTGCGTGAACAGA 58.699 39.130 0.00 0.00 36.16 3.41
892 1095 4.080638 GGAATCCATCAGATCAGGTATCCC 60.081 50.000 0.00 0.00 34.90 3.85
964 1173 0.715551 CATATATCGCGCGTGCATGT 59.284 50.000 30.98 16.56 42.97 3.21
965 1174 0.992072 ATATATCGCGCGTGCATGTC 59.008 50.000 30.98 0.00 42.97 3.06
1029 1241 1.124462 CATTAGTCACTAGCTCGCGC 58.876 55.000 0.00 0.00 0.00 6.86
1115 1333 1.490693 CGCTCACGTCTTGCTGTTGT 61.491 55.000 0.00 0.00 33.53 3.32
1116 1334 0.657840 GCTCACGTCTTGCTGTTGTT 59.342 50.000 0.00 0.00 0.00 2.83
1117 1335 1.864711 GCTCACGTCTTGCTGTTGTTA 59.135 47.619 0.00 0.00 0.00 2.41
1118 1336 2.348591 GCTCACGTCTTGCTGTTGTTAC 60.349 50.000 0.00 0.00 0.00 2.50
1122 1340 1.589803 GTCTTGCTGTTGTTACCGGT 58.410 50.000 13.98 13.98 0.00 5.28
1123 1341 2.758009 GTCTTGCTGTTGTTACCGGTA 58.242 47.619 11.16 11.16 0.00 4.02
1124 1342 2.735134 GTCTTGCTGTTGTTACCGGTAG 59.265 50.000 15.20 4.80 0.00 3.18
1125 1343 2.366266 TCTTGCTGTTGTTACCGGTAGT 59.634 45.455 15.20 0.00 0.00 2.73
1183 1401 2.250939 CGCTTCACAACTCCGGCAA 61.251 57.895 0.00 0.00 0.00 4.52
1303 1521 1.404315 GGCTTCTACCACTTCGTCCAG 60.404 57.143 0.00 0.00 0.00 3.86
1586 1804 2.278857 CCTTCGACCGCCTGATCG 60.279 66.667 0.00 0.00 39.72 3.69
1659 1877 2.081212 CGCTCGACGTCACCTTCAC 61.081 63.158 17.16 0.00 36.87 3.18
1788 2006 1.242076 CTGCCTGGAACAAGGTTCTG 58.758 55.000 0.00 3.27 38.70 3.02
1936 2162 6.902948 TCGCGCAAGTATACATGTTTTTAATC 59.097 34.615 8.75 0.00 41.68 1.75
1994 2221 3.508793 AGATTCTTGGTGTGGAATTGCTG 59.491 43.478 0.00 0.00 33.05 4.41
1998 2225 1.039068 TGGTGTGGAATTGCTGTTGG 58.961 50.000 0.00 0.00 0.00 3.77
2027 2254 3.434739 GCAAGGAAGAGGATCATGGATGT 60.435 47.826 0.00 0.00 37.82 3.06
2045 2272 6.662755 TGGATGTACTGAGGCAAGAAATATT 58.337 36.000 0.00 0.00 0.00 1.28
2047 2274 6.073548 GGATGTACTGAGGCAAGAAATATTCG 60.074 42.308 0.00 0.00 34.02 3.34
2389 2665 2.158490 TGAGCTGCATATTTGGCCCATA 60.158 45.455 0.00 0.00 0.00 2.74
2547 2823 4.631813 GCATACAAGACGGTCAAAGAATCT 59.368 41.667 11.27 0.00 0.00 2.40
2548 2824 5.220491 GCATACAAGACGGTCAAAGAATCTC 60.220 44.000 11.27 0.00 0.00 2.75
2603 2879 2.743928 GGCACTCAAGGACTGCCG 60.744 66.667 1.97 0.00 41.15 5.69
2645 2923 6.326323 ACCTCTCTGATTTATTCTTCCTCCTC 59.674 42.308 0.00 0.00 0.00 3.71
2799 3082 5.293569 CCTTCCAGGTTCAACGTATGTATTC 59.706 44.000 0.00 0.00 0.00 1.75
3037 3467 9.033481 CAAGTTTCTTTATTTGATGCAAACAGA 57.967 29.630 0.00 0.00 36.13 3.41
3051 3481 3.559242 GCAAACAGATATGAGCTGGAGAC 59.441 47.826 0.00 0.00 37.69 3.36
3057 3487 7.372260 ACAGATATGAGCTGGAGACTAAAAT 57.628 36.000 0.00 0.00 37.69 1.82
3136 3567 1.657751 GGGCAATGTTTCCGAGGCTC 61.658 60.000 3.87 3.87 0.00 4.70
3397 3828 0.820891 AGTGCTGCTGGTCTTTGTGG 60.821 55.000 0.00 0.00 0.00 4.17
3486 3923 7.756395 TTTCTTTCAGAGCTGAGATGAAAAT 57.244 32.000 15.39 0.00 41.11 1.82
3609 4051 5.310857 AGCATAGTTTCCCTCCCCTATTTAG 59.689 44.000 0.00 0.00 0.00 1.85
3728 4171 3.745975 TGTGACTTGCTTATGAAACTCCG 59.254 43.478 0.00 0.00 0.00 4.63
3734 4177 6.170506 ACTTGCTTATGAAACTCCGTATTCA 58.829 36.000 0.00 0.00 39.66 2.57
3736 4179 7.985184 ACTTGCTTATGAAACTCCGTATTCATA 59.015 33.333 4.56 4.56 42.77 2.15
3738 4181 8.902540 TGCTTATGAAACTCCGTATTCATATT 57.097 30.769 8.53 0.00 43.97 1.28
3775 4235 7.290813 AGAGTGAATATTCCAAATAAGTCCCC 58.709 38.462 12.90 0.00 0.00 4.81
3797 4257 5.241728 CCCAGTCTGAACTCATATGACGATA 59.758 44.000 0.00 0.00 31.71 2.92
3802 4262 8.251026 AGTCTGAACTCATATGACGATACAAAA 58.749 33.333 0.00 0.00 33.40 2.44
3888 6642 2.387757 ACCAATTGTATGGGCACATCC 58.612 47.619 3.67 0.00 45.18 3.51
3913 6667 2.734755 TGCTAGGGAACATGGGATTG 57.265 50.000 0.00 0.00 0.00 2.67
3914 6668 1.922447 TGCTAGGGAACATGGGATTGT 59.078 47.619 0.00 0.00 0.00 2.71
3915 6669 3.119319 TGCTAGGGAACATGGGATTGTA 58.881 45.455 0.00 0.00 0.00 2.41
3916 6670 3.118038 TGCTAGGGAACATGGGATTGTAC 60.118 47.826 0.00 0.00 0.00 2.90
3917 6671 3.747708 GCTAGGGAACATGGGATTGTACC 60.748 52.174 0.00 0.00 0.00 3.34
3918 6672 1.211949 AGGGAACATGGGATTGTACCG 59.788 52.381 0.00 0.00 34.00 4.02
3919 6673 1.210967 GGGAACATGGGATTGTACCGA 59.789 52.381 0.00 0.00 0.00 4.69
3920 6674 2.285977 GGAACATGGGATTGTACCGAC 58.714 52.381 0.00 0.00 0.00 4.79
3921 6675 2.285977 GAACATGGGATTGTACCGACC 58.714 52.381 0.00 0.00 0.00 4.79
3922 6676 0.544697 ACATGGGATTGTACCGACCC 59.455 55.000 10.25 10.25 42.37 4.46
3924 6678 1.984817 TGGGATTGTACCGACCCAC 59.015 57.895 14.33 0.00 46.04 4.61
3925 6679 1.222661 GGGATTGTACCGACCCACC 59.777 63.158 11.74 0.00 41.72 4.61
3928 6682 0.738412 GATTGTACCGACCCACCGTG 60.738 60.000 0.00 0.00 0.00 4.94
3934 6688 2.049433 CGACCCACCGTGAGACAC 60.049 66.667 0.00 0.00 0.00 3.67
3983 6741 9.565090 TGTTACTCATAGGTCGTATACAATACT 57.435 33.333 3.32 0.00 0.00 2.12
4040 6798 6.817184 ACTGTATTCGAGTTGTATAATGGCT 58.183 36.000 0.00 0.00 0.00 4.75
4041 6799 7.272978 ACTGTATTCGAGTTGTATAATGGCTT 58.727 34.615 0.00 0.00 0.00 4.35
4042 6800 7.224753 ACTGTATTCGAGTTGTATAATGGCTTG 59.775 37.037 0.00 0.00 0.00 4.01
4043 6801 4.875544 TTCGAGTTGTATAATGGCTTGC 57.124 40.909 0.00 0.00 0.00 4.01
4044 6802 4.137116 TCGAGTTGTATAATGGCTTGCT 57.863 40.909 0.00 0.00 0.00 3.91
4045 6803 4.513442 TCGAGTTGTATAATGGCTTGCTT 58.487 39.130 0.00 0.00 0.00 3.91
4046 6804 5.666462 TCGAGTTGTATAATGGCTTGCTTA 58.334 37.500 0.00 0.00 0.00 3.09
4047 6805 5.753438 TCGAGTTGTATAATGGCTTGCTTAG 59.247 40.000 0.00 0.00 0.00 2.18
4048 6806 5.050091 CGAGTTGTATAATGGCTTGCTTAGG 60.050 44.000 0.00 0.00 0.00 2.69
4049 6807 5.133221 AGTTGTATAATGGCTTGCTTAGGG 58.867 41.667 0.00 0.00 0.00 3.53
4050 6808 5.104109 AGTTGTATAATGGCTTGCTTAGGGA 60.104 40.000 0.00 0.00 0.00 4.20
4051 6809 5.582950 TGTATAATGGCTTGCTTAGGGAT 57.417 39.130 0.00 0.00 0.00 3.85
4052 6810 5.952387 TGTATAATGGCTTGCTTAGGGATT 58.048 37.500 0.00 0.00 0.00 3.01
4053 6811 5.769662 TGTATAATGGCTTGCTTAGGGATTG 59.230 40.000 0.00 0.00 0.00 2.67
4054 6812 1.406903 ATGGCTTGCTTAGGGATTGC 58.593 50.000 0.00 0.00 0.00 3.56
4055 6813 0.684153 TGGCTTGCTTAGGGATTGCC 60.684 55.000 4.48 4.48 39.33 4.52
4056 6814 0.684153 GGCTTGCTTAGGGATTGCCA 60.684 55.000 0.00 0.00 38.79 4.92
4057 6815 1.185315 GCTTGCTTAGGGATTGCCAA 58.815 50.000 0.00 0.00 35.15 4.52
4058 6816 1.550072 GCTTGCTTAGGGATTGCCAAA 59.450 47.619 0.00 0.00 35.15 3.28
4059 6817 2.169144 GCTTGCTTAGGGATTGCCAAAT 59.831 45.455 0.00 0.00 35.15 2.32
4060 6818 3.788937 CTTGCTTAGGGATTGCCAAATG 58.211 45.455 0.00 0.00 35.15 2.32
4119 6891 6.731467 AGTTAAGGATAATCAAGAAAGGCCA 58.269 36.000 5.01 0.00 0.00 5.36
4134 6906 4.316025 AAGGCCAAGCTTATTTCTACCA 57.684 40.909 5.01 0.00 0.00 3.25
4163 6935 3.194542 AGAAGGTCGAACTGATTCCTGAG 59.805 47.826 2.28 0.00 0.00 3.35
4166 6938 2.996621 GGTCGAACTGATTCCTGAGTTG 59.003 50.000 0.00 0.00 32.47 3.16
4167 6939 2.996621 GTCGAACTGATTCCTGAGTTGG 59.003 50.000 0.00 0.00 32.47 3.77
4170 6942 3.927142 CGAACTGATTCCTGAGTTGGTAC 59.073 47.826 0.00 0.00 32.47 3.34
4172 6944 5.491982 GAACTGATTCCTGAGTTGGTACAT 58.508 41.667 0.00 0.00 39.30 2.29
4173 6945 6.620877 AACTGATTCCTGAGTTGGTACATA 57.379 37.500 0.00 0.00 39.30 2.29
4174 6946 6.620877 ACTGATTCCTGAGTTGGTACATAA 57.379 37.500 0.00 0.00 39.30 1.90
4175 6947 7.200434 ACTGATTCCTGAGTTGGTACATAAT 57.800 36.000 0.00 0.00 39.30 1.28
4176 6948 7.633789 ACTGATTCCTGAGTTGGTACATAATT 58.366 34.615 0.00 0.00 39.30 1.40
4177 6949 8.109634 ACTGATTCCTGAGTTGGTACATAATTT 58.890 33.333 0.00 0.00 39.30 1.82
4178 6950 8.279970 TGATTCCTGAGTTGGTACATAATTTG 57.720 34.615 0.00 0.00 39.30 2.32
4179 6951 6.509418 TTCCTGAGTTGGTACATAATTTGC 57.491 37.500 0.00 0.00 39.30 3.68
4180 6952 4.947388 TCCTGAGTTGGTACATAATTTGCC 59.053 41.667 0.00 0.00 39.30 4.52
4181 6953 4.097892 CCTGAGTTGGTACATAATTTGCCC 59.902 45.833 0.00 0.00 39.30 5.36
4182 6954 4.667573 TGAGTTGGTACATAATTTGCCCA 58.332 39.130 0.00 0.00 39.30 5.36
4183 6955 5.080337 TGAGTTGGTACATAATTTGCCCAA 58.920 37.500 0.00 0.00 39.30 4.12
4184 6956 5.719085 TGAGTTGGTACATAATTTGCCCAAT 59.281 36.000 0.00 5.74 40.07 3.16
4185 6957 6.212388 TGAGTTGGTACATAATTTGCCCAATT 59.788 34.615 0.00 9.36 40.07 2.32
4186 6958 7.014988 AGTTGGTACATAATTTGCCCAATTT 57.985 32.000 0.00 0.00 40.07 1.82
4187 6959 7.457561 AGTTGGTACATAATTTGCCCAATTTT 58.542 30.769 0.00 0.00 40.07 1.82
4188 6960 7.606073 AGTTGGTACATAATTTGCCCAATTTTC 59.394 33.333 0.00 4.50 40.07 2.29
4189 6961 6.102663 TGGTACATAATTTGCCCAATTTTCG 58.897 36.000 0.00 0.00 36.43 3.46
4190 6962 6.071334 TGGTACATAATTTGCCCAATTTTCGA 60.071 34.615 0.00 0.00 36.43 3.71
4191 6963 6.983890 GGTACATAATTTGCCCAATTTTCGAT 59.016 34.615 0.00 0.00 36.43 3.59
4192 6964 6.907206 ACATAATTTGCCCAATTTTCGATG 57.093 33.333 0.00 0.00 36.43 3.84
4193 6965 6.638610 ACATAATTTGCCCAATTTTCGATGA 58.361 32.000 0.00 0.00 36.43 2.92
4194 6966 7.274447 ACATAATTTGCCCAATTTTCGATGAT 58.726 30.769 0.00 0.00 36.43 2.45
4195 6967 7.769970 ACATAATTTGCCCAATTTTCGATGATT 59.230 29.630 0.00 0.00 36.43 2.57
4196 6968 9.258826 CATAATTTGCCCAATTTTCGATGATTA 57.741 29.630 0.00 0.00 36.43 1.75
4197 6969 7.538303 AATTTGCCCAATTTTCGATGATTAC 57.462 32.000 0.00 0.00 30.09 1.89
4198 6970 5.651387 TTGCCCAATTTTCGATGATTACA 57.349 34.783 0.00 0.00 0.00 2.41
4199 6971 5.850557 TGCCCAATTTTCGATGATTACAT 57.149 34.783 0.00 0.00 39.67 2.29
4200 6972 5.590145 TGCCCAATTTTCGATGATTACATG 58.410 37.500 0.00 0.00 36.82 3.21
4201 6973 5.359292 TGCCCAATTTTCGATGATTACATGA 59.641 36.000 0.00 0.00 36.82 3.07
4202 6974 5.916883 GCCCAATTTTCGATGATTACATGAG 59.083 40.000 0.00 0.00 36.82 2.90
4203 6975 6.460123 GCCCAATTTTCGATGATTACATGAGT 60.460 38.462 0.00 0.00 36.82 3.41
4204 6976 7.483307 CCCAATTTTCGATGATTACATGAGTT 58.517 34.615 0.00 0.00 36.82 3.01
4205 6977 7.433131 CCCAATTTTCGATGATTACATGAGTTG 59.567 37.037 0.00 0.00 36.82 3.16
4206 6978 7.433131 CCAATTTTCGATGATTACATGAGTTGG 59.567 37.037 0.00 0.00 36.82 3.77
4207 6979 7.630242 ATTTTCGATGATTACATGAGTTGGT 57.370 32.000 0.00 0.00 36.82 3.67
4208 6980 8.731275 ATTTTCGATGATTACATGAGTTGGTA 57.269 30.769 0.00 0.00 36.82 3.25
4209 6981 7.534085 TTTCGATGATTACATGAGTTGGTAC 57.466 36.000 0.00 0.00 36.82 3.34
4210 6982 6.215495 TCGATGATTACATGAGTTGGTACA 57.785 37.500 0.00 0.00 36.82 2.90
4211 6983 6.816136 TCGATGATTACATGAGTTGGTACAT 58.184 36.000 0.00 0.00 35.69 2.29
4212 6984 7.947282 TCGATGATTACATGAGTTGGTACATA 58.053 34.615 0.00 0.00 35.69 2.29
4213 6985 8.417884 TCGATGATTACATGAGTTGGTACATAA 58.582 33.333 0.00 0.00 35.69 1.90
4214 6986 9.208022 CGATGATTACATGAGTTGGTACATAAT 57.792 33.333 0.00 0.00 35.69 1.28
4290 7063 5.887598 TCAAATTTCATCTCACTACATGGGG 59.112 40.000 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.972625 TGACCGTGCTCCTTTATTCAG 58.027 47.619 0.00 0.00 0.00 3.02
10 11 3.410631 TTGACCGTGCTCCTTTATTCA 57.589 42.857 0.00 0.00 0.00 2.57
14 15 2.419574 GCCTATTGACCGTGCTCCTTTA 60.420 50.000 0.00 0.00 0.00 1.85
15 16 1.679032 GCCTATTGACCGTGCTCCTTT 60.679 52.381 0.00 0.00 0.00 3.11
16 17 0.107654 GCCTATTGACCGTGCTCCTT 60.108 55.000 0.00 0.00 0.00 3.36
23 24 2.936498 CGAAATCTTGCCTATTGACCGT 59.064 45.455 0.00 0.00 0.00 4.83
24 25 2.287915 CCGAAATCTTGCCTATTGACCG 59.712 50.000 0.00 0.00 0.00 4.79
27 28 3.924114 TCCCGAAATCTTGCCTATTGA 57.076 42.857 0.00 0.00 0.00 2.57
33 34 3.866883 TGAAATTCCCGAAATCTTGCC 57.133 42.857 0.00 0.00 0.00 4.52
38 39 9.759259 GAAATGATTTTTGAAATTCCCGAAATC 57.241 29.630 13.80 13.80 35.28 2.17
40 41 8.668510 TGAAATGATTTTTGAAATTCCCGAAA 57.331 26.923 0.00 0.00 0.00 3.46
101 112 8.444715 AGGTAAAAACGAATTCCAAACAAAAAC 58.555 29.630 0.00 0.00 0.00 2.43
102 113 8.443937 CAGGTAAAAACGAATTCCAAACAAAAA 58.556 29.630 0.00 0.00 0.00 1.94
111 122 4.022676 TCAAGCCAGGTAAAAACGAATTCC 60.023 41.667 0.00 0.00 0.00 3.01
125 136 1.699083 ACCCCAAATTTTCAAGCCAGG 59.301 47.619 0.00 0.00 0.00 4.45
137 148 8.809066 GGTACTGAAATACTTTAAACCCCAAAT 58.191 33.333 0.00 0.00 0.00 2.32
139 150 6.720748 GGGTACTGAAATACTTTAAACCCCAA 59.279 38.462 0.00 0.00 38.47 4.12
155 166 5.936187 TGATTATTACGGTGGGTACTGAA 57.064 39.130 0.00 0.00 36.65 3.02
182 193 9.820229 CTATCACGCAGAGTAATTTTACAAAAA 57.180 29.630 3.50 0.00 36.12 1.94
184 195 7.333423 AGCTATCACGCAGAGTAATTTTACAAA 59.667 33.333 3.50 0.00 36.12 2.83
186 197 6.338146 AGCTATCACGCAGAGTAATTTTACA 58.662 36.000 3.50 0.00 36.12 2.41
187 198 6.475727 TGAGCTATCACGCAGAGTAATTTTAC 59.524 38.462 0.00 0.00 0.00 2.01
189 200 5.419542 TGAGCTATCACGCAGAGTAATTTT 58.580 37.500 0.00 0.00 0.00 1.82
202 213 7.877097 AGGTTCATCTGATTAATGAGCTATCAC 59.123 37.037 0.00 0.00 38.57 3.06
233 244 9.499479 ACTGCTGTCTTTTATATATTGATCAGG 57.501 33.333 0.00 0.00 0.00 3.86
241 252 9.594936 AGGAGACTACTGCTGTCTTTTATATAT 57.405 33.333 0.00 0.00 43.88 0.86
242 253 8.998277 AGGAGACTACTGCTGTCTTTTATATA 57.002 34.615 0.00 0.00 43.88 0.86
246 337 5.326069 AGAGGAGACTACTGCTGTCTTTTA 58.674 41.667 0.00 0.00 44.53 1.52
253 344 2.649190 TGCTAGAGGAGACTACTGCTG 58.351 52.381 0.00 0.00 44.53 4.41
265 356 5.353678 CCTGAAACTTTTCTCATGCTAGAGG 59.646 44.000 0.00 0.00 38.02 3.69
266 357 5.936956 ACCTGAAACTTTTCTCATGCTAGAG 59.063 40.000 0.00 0.22 38.02 2.43
267 358 5.869579 ACCTGAAACTTTTCTCATGCTAGA 58.130 37.500 0.00 0.00 38.02 2.43
268 359 6.566197 AACCTGAAACTTTTCTCATGCTAG 57.434 37.500 3.48 0.00 38.02 3.42
269 360 6.959639 AAACCTGAAACTTTTCTCATGCTA 57.040 33.333 3.48 0.00 38.02 3.49
270 361 5.859205 AAACCTGAAACTTTTCTCATGCT 57.141 34.783 3.48 0.00 38.02 3.79
271 362 6.908870 AAAAACCTGAAACTTTTCTCATGC 57.091 33.333 3.48 0.00 38.02 4.06
312 403 9.632969 CGGTGAACAGTAAATCGAAATAAATAG 57.367 33.333 0.00 0.00 0.00 1.73
313 404 8.605746 CCGGTGAACAGTAAATCGAAATAAATA 58.394 33.333 0.00 0.00 0.00 1.40
314 405 7.120138 ACCGGTGAACAGTAAATCGAAATAAAT 59.880 33.333 6.12 0.00 0.00 1.40
315 406 6.427547 ACCGGTGAACAGTAAATCGAAATAAA 59.572 34.615 6.12 0.00 0.00 1.40
316 407 5.933463 ACCGGTGAACAGTAAATCGAAATAA 59.067 36.000 6.12 0.00 0.00 1.40
317 408 5.481105 ACCGGTGAACAGTAAATCGAAATA 58.519 37.500 6.12 0.00 0.00 1.40
318 409 4.320870 ACCGGTGAACAGTAAATCGAAAT 58.679 39.130 6.12 0.00 0.00 2.17
319 410 3.731089 ACCGGTGAACAGTAAATCGAAA 58.269 40.909 6.12 0.00 0.00 3.46
320 411 3.389925 ACCGGTGAACAGTAAATCGAA 57.610 42.857 6.12 0.00 0.00 3.71
321 412 3.758023 TCTACCGGTGAACAGTAAATCGA 59.242 43.478 19.93 0.00 0.00 3.59
322 413 4.100707 TCTACCGGTGAACAGTAAATCG 57.899 45.455 19.93 0.00 0.00 3.34
323 414 5.657474 TCATCTACCGGTGAACAGTAAATC 58.343 41.667 19.93 0.00 0.00 2.17
324 415 5.661458 CTCATCTACCGGTGAACAGTAAAT 58.339 41.667 19.93 0.00 0.00 1.40
325 416 4.619863 GCTCATCTACCGGTGAACAGTAAA 60.620 45.833 19.93 0.00 0.00 2.01
326 417 3.119245 GCTCATCTACCGGTGAACAGTAA 60.119 47.826 19.93 0.00 0.00 2.24
327 418 2.426024 GCTCATCTACCGGTGAACAGTA 59.574 50.000 19.93 0.00 0.00 2.74
328 419 1.204941 GCTCATCTACCGGTGAACAGT 59.795 52.381 19.93 0.00 0.00 3.55
329 420 1.471676 GGCTCATCTACCGGTGAACAG 60.472 57.143 19.93 6.55 0.00 3.16
330 421 0.535335 GGCTCATCTACCGGTGAACA 59.465 55.000 19.93 0.00 0.00 3.18
331 422 0.179081 GGGCTCATCTACCGGTGAAC 60.179 60.000 19.93 0.35 0.00 3.18
332 423 1.335132 GGGGCTCATCTACCGGTGAA 61.335 60.000 19.93 5.07 0.00 3.18
333 424 1.760875 GGGGCTCATCTACCGGTGA 60.761 63.158 19.93 13.35 0.00 4.02
334 425 2.822399 GGGGCTCATCTACCGGTG 59.178 66.667 19.93 7.59 0.00 4.94
335 426 2.838225 CGGGGCTCATCTACCGGT 60.838 66.667 13.98 13.98 42.48 5.28
337 428 3.616721 CCCGGGGCTCATCTACCG 61.617 72.222 14.71 0.00 45.57 4.02
338 429 3.942439 GCCCGGGGCTCATCTACC 61.942 72.222 30.86 0.00 46.69 3.18
348 439 2.499303 AATTCAACTGGAGCCCGGGG 62.499 60.000 25.28 9.31 33.40 5.73
349 440 0.254747 TAATTCAACTGGAGCCCGGG 59.745 55.000 19.09 19.09 33.40 5.73
350 441 2.222027 GATAATTCAACTGGAGCCCGG 58.778 52.381 0.00 0.00 35.68 5.73
351 442 1.867233 CGATAATTCAACTGGAGCCCG 59.133 52.381 0.00 0.00 0.00 6.13
352 443 1.604278 GCGATAATTCAACTGGAGCCC 59.396 52.381 0.00 0.00 0.00 5.19
353 444 1.604278 GGCGATAATTCAACTGGAGCC 59.396 52.381 0.00 0.00 35.00 4.70
354 445 2.545946 GAGGCGATAATTCAACTGGAGC 59.454 50.000 0.00 0.00 0.00 4.70
355 446 3.134458 GGAGGCGATAATTCAACTGGAG 58.866 50.000 0.00 0.00 0.00 3.86
356 447 2.483013 CGGAGGCGATAATTCAACTGGA 60.483 50.000 0.00 0.00 0.00 3.86
357 448 1.867233 CGGAGGCGATAATTCAACTGG 59.133 52.381 0.00 0.00 0.00 4.00
358 449 2.285220 CACGGAGGCGATAATTCAACTG 59.715 50.000 0.00 0.00 0.00 3.16
359 450 2.093658 ACACGGAGGCGATAATTCAACT 60.094 45.455 0.00 0.00 0.00 3.16
360 451 2.277084 ACACGGAGGCGATAATTCAAC 58.723 47.619 0.00 0.00 0.00 3.18
361 452 2.167693 AGACACGGAGGCGATAATTCAA 59.832 45.455 0.00 0.00 0.00 2.69
362 453 1.754803 AGACACGGAGGCGATAATTCA 59.245 47.619 0.00 0.00 0.00 2.57
363 454 2.510768 AGACACGGAGGCGATAATTC 57.489 50.000 0.00 0.00 0.00 2.17
364 455 2.957006 AGTAGACACGGAGGCGATAATT 59.043 45.455 0.00 0.00 0.00 1.40
365 456 2.584236 AGTAGACACGGAGGCGATAAT 58.416 47.619 0.00 0.00 0.00 1.28
366 457 2.048444 AGTAGACACGGAGGCGATAA 57.952 50.000 0.00 0.00 0.00 1.75
367 458 2.048444 AAGTAGACACGGAGGCGATA 57.952 50.000 0.00 0.00 0.00 2.92
368 459 1.183549 AAAGTAGACACGGAGGCGAT 58.816 50.000 0.00 0.00 0.00 4.58
369 460 0.963962 AAAAGTAGACACGGAGGCGA 59.036 50.000 0.00 0.00 0.00 5.54
370 461 1.067776 AGAAAAGTAGACACGGAGGCG 60.068 52.381 0.00 0.00 0.00 5.52
371 462 2.745515 AGAAAAGTAGACACGGAGGC 57.254 50.000 0.00 0.00 0.00 4.70
397 488 5.127194 TGAAGTACTAATGGAGCTTGACGAT 59.873 40.000 0.00 0.00 0.00 3.73
398 489 4.461431 TGAAGTACTAATGGAGCTTGACGA 59.539 41.667 0.00 0.00 0.00 4.20
399 490 4.563184 GTGAAGTACTAATGGAGCTTGACG 59.437 45.833 0.00 0.00 0.00 4.35
400 491 5.725362 AGTGAAGTACTAATGGAGCTTGAC 58.275 41.667 0.00 0.00 38.04 3.18
401 492 6.663953 ACTAGTGAAGTACTAATGGAGCTTGA 59.336 38.462 0.00 0.00 41.20 3.02
402 493 6.868622 ACTAGTGAAGTACTAATGGAGCTTG 58.131 40.000 0.00 0.00 41.20 4.01
403 494 7.201839 GCTACTAGTGAAGTACTAATGGAGCTT 60.202 40.741 5.39 0.00 39.33 3.74
404 495 6.263617 GCTACTAGTGAAGTACTAATGGAGCT 59.736 42.308 5.39 0.00 39.33 4.09
405 496 6.263617 AGCTACTAGTGAAGTACTAATGGAGC 59.736 42.308 5.39 0.84 41.21 4.70
407 498 8.492782 AGTAGCTACTAGTGAAGTACTAATGGA 58.507 37.037 24.97 0.00 41.20 3.41
409 500 9.550406 AGAGTAGCTACTAGTGAAGTACTAATG 57.450 37.037 26.11 0.00 41.20 1.90
439 602 4.012374 CGTGTGACTAACCTACCTTCCTA 58.988 47.826 0.00 0.00 0.00 2.94
440 603 2.824341 CGTGTGACTAACCTACCTTCCT 59.176 50.000 0.00 0.00 0.00 3.36
441 604 2.821969 TCGTGTGACTAACCTACCTTCC 59.178 50.000 0.00 0.00 0.00 3.46
442 605 4.510038 TTCGTGTGACTAACCTACCTTC 57.490 45.455 0.00 0.00 0.00 3.46
454 617 7.462462 CGATCATCATCATATCATTCGTGTGAC 60.462 40.741 0.00 0.00 0.00 3.67
466 629 4.831674 TGGCCTTCGATCATCATCATAT 57.168 40.909 3.32 0.00 0.00 1.78
467 630 4.831674 ATGGCCTTCGATCATCATCATA 57.168 40.909 3.32 0.00 0.00 2.15
545 733 0.615850 CTCCAGGAAGAGGAACCCAC 59.384 60.000 0.00 0.00 34.08 4.61
578 766 1.961277 CGGCCGCATATTCTGGTCC 60.961 63.158 14.67 0.00 0.00 4.46
624 812 7.173390 ACCAAAGTTCAGTCAGCTTTATTAGTC 59.827 37.037 0.00 0.00 32.01 2.59
681 869 1.625818 CTTAGCTTCCAGGTCACAGGT 59.374 52.381 0.00 0.00 0.00 4.00
686 874 4.033009 TCATGATCTTAGCTTCCAGGTCA 58.967 43.478 5.85 5.85 34.61 4.02
687 875 4.376146 GTCATGATCTTAGCTTCCAGGTC 58.624 47.826 0.00 0.00 0.00 3.85
688 876 3.181471 CGTCATGATCTTAGCTTCCAGGT 60.181 47.826 0.00 0.00 0.00 4.00
732 921 6.183361 GGGATGTCATTTCATTCCATTCCATT 60.183 38.462 0.00 0.00 41.73 3.16
733 922 5.306160 GGGATGTCATTTCATTCCATTCCAT 59.694 40.000 0.00 0.00 41.73 3.41
734 923 4.650588 GGGATGTCATTTCATTCCATTCCA 59.349 41.667 0.00 0.00 41.73 3.53
735 924 4.261741 CGGGATGTCATTTCATTCCATTCC 60.262 45.833 5.09 0.00 42.11 3.01
736 925 4.794003 GCGGGATGTCATTTCATTCCATTC 60.794 45.833 5.09 0.00 42.11 2.67
737 926 3.068590 GCGGGATGTCATTTCATTCCATT 59.931 43.478 5.09 0.00 42.11 3.16
738 927 2.624838 GCGGGATGTCATTTCATTCCAT 59.375 45.455 5.09 0.00 42.11 3.41
739 928 2.023673 GCGGGATGTCATTTCATTCCA 58.976 47.619 5.09 0.00 42.11 3.53
740 929 2.023673 TGCGGGATGTCATTTCATTCC 58.976 47.619 0.00 0.00 39.45 3.01
741 930 3.567164 AGATGCGGGATGTCATTTCATTC 59.433 43.478 0.00 0.00 0.00 2.67
746 935 1.134401 ACGAGATGCGGGATGTCATTT 60.134 47.619 7.38 0.00 46.49 2.32
752 941 1.482621 CGTTGACGAGATGCGGGATG 61.483 60.000 0.00 0.00 46.49 3.51
775 964 3.673338 CGTCTCTCTGTTCACGCAAATAA 59.327 43.478 0.00 0.00 0.00 1.40
783 972 5.065346 TGAGTATCATCGTCTCTCTGTTCAC 59.935 44.000 0.00 0.00 42.56 3.18
892 1095 0.321387 CATGGCGATGGATCCTGGAG 60.321 60.000 14.23 3.09 0.00 3.86
936 1139 1.130749 GCGCGATATATGACCGAGTCT 59.869 52.381 12.10 0.00 33.15 3.24
964 1173 1.067060 ACGCACGCATATCTAAGCAGA 59.933 47.619 0.00 0.00 34.56 4.26
965 1174 1.190984 CACGCACGCATATCTAAGCAG 59.809 52.381 0.00 0.00 0.00 4.24
993 1202 0.036164 ATGTGGTTTCACTGGCGCTA 59.964 50.000 7.64 0.00 43.94 4.26
1099 1317 2.206750 GGTAACAACAGCAAGACGTGA 58.793 47.619 0.00 0.00 0.00 4.35
1106 1324 2.758009 GACTACCGGTAACAACAGCAA 58.242 47.619 16.65 0.00 0.00 3.91
1115 1333 2.749865 CGCCGACGACTACCGGTAA 61.750 63.158 16.65 0.00 46.84 2.85
1116 1334 3.195002 CGCCGACGACTACCGGTA 61.195 66.667 14.95 14.95 46.84 4.02
1122 1340 4.246206 CGATGCCGCCGACGACTA 62.246 66.667 0.00 0.00 43.93 2.59
1165 1383 2.175184 CTTGCCGGAGTTGTGAAGCG 62.175 60.000 5.05 0.00 0.00 4.68
1788 2006 1.823976 GGTACCTGTAGGCCTCTGC 59.176 63.158 9.68 0.86 39.32 4.26
1839 2057 7.654116 TGGCGGAAAAAGTAAAAAGAAATAAGG 59.346 33.333 0.00 0.00 0.00 2.69
1860 2078 1.375396 TGATGGTTTCGAGTGGCGG 60.375 57.895 0.00 0.00 41.33 6.13
1936 2162 6.633500 TTCCCTTCTTGTGAATTTGTAGTG 57.367 37.500 0.00 0.00 0.00 2.74
1994 2221 0.954452 CTTCCTTGCCTGACACCAAC 59.046 55.000 0.00 0.00 0.00 3.77
1998 2225 0.687354 TCCTCTTCCTTGCCTGACAC 59.313 55.000 0.00 0.00 0.00 3.67
2027 2254 5.972935 TCACGAATATTTCTTGCCTCAGTA 58.027 37.500 0.00 0.00 0.00 2.74
2047 2274 1.803289 GGCCATTTTCTCGCCTCAC 59.197 57.895 0.00 0.00 39.70 3.51
2240 2467 8.715439 ACAAGGGTTTGTTTGTAGCTAACAACT 61.715 37.037 11.85 5.02 45.01 3.16
2242 2469 5.419471 ACAAGGGTTTGTTTGTAGCTAACAA 59.581 36.000 8.82 8.82 45.01 2.83
2244 2471 5.509716 ACAAGGGTTTGTTTGTAGCTAAC 57.490 39.130 0.00 0.00 45.01 2.34
2260 2487 2.948979 TGCACTCAGTTACAAACAAGGG 59.051 45.455 0.00 0.00 0.00 3.95
2414 2690 9.570468 ACATATACAGAGAGAATTGCAATCAAT 57.430 29.630 13.38 1.27 44.32 2.57
2547 2823 1.344393 ACTATGGTGGCCATCCTCAGA 60.344 52.381 15.03 4.62 40.74 3.27
2548 2824 1.135094 ACTATGGTGGCCATCCTCAG 58.865 55.000 15.03 16.12 40.74 3.35
2603 2879 3.150458 AGGTTTAGTTACCTGCAACCC 57.850 47.619 0.00 0.00 46.71 4.11
2625 2901 4.651503 AGCGAGGAGGAAGAATAAATCAGA 59.348 41.667 0.00 0.00 0.00 3.27
2658 2936 6.929049 CCTGTTGTTACTTGTCTCTGTCAATA 59.071 38.462 0.00 0.00 0.00 1.90
2662 2945 4.945246 TCCTGTTGTTACTTGTCTCTGTC 58.055 43.478 0.00 0.00 0.00 3.51
2789 3072 6.978659 TCTTCAGGCTTACAAGAATACATACG 59.021 38.462 0.00 0.00 0.00 3.06
3105 3536 2.893424 ACATTGCCCATTTCTCAAGGT 58.107 42.857 0.00 0.00 31.07 3.50
3136 3567 1.551430 TGAATTGGGCAGCCATTCTTG 59.449 47.619 20.12 0.00 0.00 3.02
3361 3792 3.823304 AGCACTTCATTGTCCCTTTCTTC 59.177 43.478 0.00 0.00 0.00 2.87
3447 3879 6.040842 TCTGAAAGAAATTTCTGAGGGTTTGG 59.959 38.462 21.15 8.35 42.31 3.28
3486 3923 4.934001 GCTGAGACTTTGATGATCTGTTGA 59.066 41.667 0.00 0.00 0.00 3.18
3609 4051 4.455877 ACACATTCTTCATCGACCCTTTTC 59.544 41.667 0.00 0.00 0.00 2.29
3676 4119 5.127031 GCCCATGGTTGTTCAAGTACATTAT 59.873 40.000 11.73 0.00 0.00 1.28
3693 4136 2.425143 AGTCACATACTTGCCCATGG 57.575 50.000 4.14 4.14 33.35 3.66
3753 4213 6.833933 ACTGGGGACTTATTTGGAATATTCAC 59.166 38.462 17.07 7.28 0.00 3.18
3775 4235 6.729187 TGTATCGTCATATGAGTTCAGACTG 58.271 40.000 5.42 0.00 35.88 3.51
3913 6667 1.973281 TCTCACGGTGGGTCGGTAC 60.973 63.158 8.06 0.00 0.00 3.34
3914 6668 1.973281 GTCTCACGGTGGGTCGGTA 60.973 63.158 8.06 0.00 0.00 4.02
3915 6669 3.300765 GTCTCACGGTGGGTCGGT 61.301 66.667 8.06 0.00 0.00 4.69
3916 6670 3.299977 TGTCTCACGGTGGGTCGG 61.300 66.667 8.06 0.00 0.00 4.79
3917 6671 2.049433 GTGTCTCACGGTGGGTCG 60.049 66.667 8.06 0.00 0.00 4.79
3918 6672 1.006102 CAGTGTCTCACGGTGGGTC 60.006 63.158 8.06 2.81 39.64 4.46
3919 6673 3.138625 CAGTGTCTCACGGTGGGT 58.861 61.111 8.06 0.00 39.64 4.51
3920 6674 2.357517 GCAGTGTCTCACGGTGGG 60.358 66.667 8.50 4.66 39.64 4.61
3921 6675 1.224069 CTTGCAGTGTCTCACGGTGG 61.224 60.000 8.50 0.00 39.64 4.61
3922 6676 0.530650 ACTTGCAGTGTCTCACGGTG 60.531 55.000 0.56 0.56 39.64 4.94
3923 6677 0.530650 CACTTGCAGTGTCTCACGGT 60.531 55.000 7.80 0.00 41.19 4.83
3924 6678 2.229039 CACTTGCAGTGTCTCACGG 58.771 57.895 7.80 0.00 41.19 4.94
4016 6774 6.817184 AGCCATTATACAACTCGAATACAGT 58.183 36.000 0.00 0.00 0.00 3.55
4017 6775 7.567571 CAAGCCATTATACAACTCGAATACAG 58.432 38.462 0.00 0.00 0.00 2.74
4024 6782 4.882671 AAGCAAGCCATTATACAACTCG 57.117 40.909 0.00 0.00 0.00 4.18
4032 6790 3.575687 GCAATCCCTAAGCAAGCCATTAT 59.424 43.478 0.00 0.00 0.00 1.28
4040 6798 3.172339 ACATTTGGCAATCCCTAAGCAA 58.828 40.909 0.00 0.00 31.86 3.91
4041 6799 2.818921 ACATTTGGCAATCCCTAAGCA 58.181 42.857 0.00 0.00 31.86 3.91
4042 6800 3.954258 AGTACATTTGGCAATCCCTAAGC 59.046 43.478 0.00 0.00 31.86 3.09
4043 6801 5.192927 TGAGTACATTTGGCAATCCCTAAG 58.807 41.667 0.00 0.00 31.86 2.18
4044 6802 5.186256 TGAGTACATTTGGCAATCCCTAA 57.814 39.130 0.00 0.00 32.88 2.69
4045 6803 4.853468 TGAGTACATTTGGCAATCCCTA 57.147 40.909 0.00 0.00 0.00 3.53
4046 6804 3.737559 TGAGTACATTTGGCAATCCCT 57.262 42.857 0.00 0.00 0.00 4.20
4047 6805 6.463995 TTATTGAGTACATTTGGCAATCCC 57.536 37.500 0.00 0.00 32.13 3.85
4048 6806 7.439056 CCAATTATTGAGTACATTTGGCAATCC 59.561 37.037 6.50 0.00 32.13 3.01
4049 6807 7.439056 CCCAATTATTGAGTACATTTGGCAATC 59.561 37.037 6.50 0.00 32.13 2.67
4050 6808 7.274447 CCCAATTATTGAGTACATTTGGCAAT 58.726 34.615 6.50 0.00 34.05 3.56
4051 6809 6.638610 CCCAATTATTGAGTACATTTGGCAA 58.361 36.000 6.50 0.00 0.00 4.52
4052 6810 5.395103 GCCCAATTATTGAGTACATTTGGCA 60.395 40.000 6.50 0.00 0.00 4.92
4053 6811 5.049828 GCCCAATTATTGAGTACATTTGGC 58.950 41.667 6.50 3.66 0.00 4.52
4054 6812 6.096705 TCTGCCCAATTATTGAGTACATTTGG 59.903 38.462 6.50 0.00 0.00 3.28
4055 6813 7.099266 TCTGCCCAATTATTGAGTACATTTG 57.901 36.000 6.50 0.00 0.00 2.32
4056 6814 7.902920 ATCTGCCCAATTATTGAGTACATTT 57.097 32.000 6.50 0.00 0.00 2.32
4057 6815 7.902920 AATCTGCCCAATTATTGAGTACATT 57.097 32.000 6.50 0.00 0.00 2.71
4058 6816 8.995027 TTAATCTGCCCAATTATTGAGTACAT 57.005 30.769 6.50 0.00 0.00 2.29
4059 6817 8.815565 TTTAATCTGCCCAATTATTGAGTACA 57.184 30.769 6.50 0.00 0.00 2.90
4106 6864 5.718607 AGAAATAAGCTTGGCCTTTCTTGAT 59.281 36.000 9.86 0.00 32.43 2.57
4111 6883 4.705023 TGGTAGAAATAAGCTTGGCCTTTC 59.295 41.667 9.86 12.22 0.00 2.62
4163 6935 7.412455 CGAAAATTGGGCAAATTATGTACCAAC 60.412 37.037 0.00 7.22 44.90 3.77
4166 6938 6.334202 TCGAAAATTGGGCAAATTATGTACC 58.666 36.000 0.00 0.00 37.51 3.34
4167 6939 7.704472 TCATCGAAAATTGGGCAAATTATGTAC 59.296 33.333 0.00 0.00 37.51 2.90
4170 6942 7.718272 ATCATCGAAAATTGGGCAAATTATG 57.282 32.000 0.00 1.22 37.51 1.90
4172 6944 8.253810 TGTAATCATCGAAAATTGGGCAAATTA 58.746 29.630 0.00 0.00 37.51 1.40
4173 6945 7.102346 TGTAATCATCGAAAATTGGGCAAATT 58.898 30.769 0.00 0.00 40.32 1.82
4174 6946 6.638610 TGTAATCATCGAAAATTGGGCAAAT 58.361 32.000 0.00 0.00 0.00 2.32
4175 6947 6.030548 TGTAATCATCGAAAATTGGGCAAA 57.969 33.333 0.00 0.00 0.00 3.68
4176 6948 5.651387 TGTAATCATCGAAAATTGGGCAA 57.349 34.783 0.00 0.00 0.00 4.52
4177 6949 5.359292 TCATGTAATCATCGAAAATTGGGCA 59.641 36.000 0.00 0.00 31.15 5.36
4178 6950 5.830912 TCATGTAATCATCGAAAATTGGGC 58.169 37.500 0.00 0.00 31.15 5.36
4179 6951 7.031226 ACTCATGTAATCATCGAAAATTGGG 57.969 36.000 0.00 0.00 31.15 4.12
4180 6952 7.433131 CCAACTCATGTAATCATCGAAAATTGG 59.567 37.037 0.00 0.00 31.15 3.16
4181 6953 7.970061 ACCAACTCATGTAATCATCGAAAATTG 59.030 33.333 0.00 0.00 31.15 2.32
4182 6954 8.055279 ACCAACTCATGTAATCATCGAAAATT 57.945 30.769 0.00 0.00 31.15 1.82
4183 6955 7.630242 ACCAACTCATGTAATCATCGAAAAT 57.370 32.000 0.00 0.00 31.15 1.82
4184 6956 7.604545 TGTACCAACTCATGTAATCATCGAAAA 59.395 33.333 0.00 0.00 31.15 2.29
4185 6957 7.100409 TGTACCAACTCATGTAATCATCGAAA 58.900 34.615 0.00 0.00 31.15 3.46
4186 6958 6.635755 TGTACCAACTCATGTAATCATCGAA 58.364 36.000 0.00 0.00 31.15 3.71
4187 6959 6.215495 TGTACCAACTCATGTAATCATCGA 57.785 37.500 0.00 0.00 31.15 3.59
4188 6960 8.587952 TTATGTACCAACTCATGTAATCATCG 57.412 34.615 0.00 0.00 31.15 3.84
4225 6997 2.599082 GAGAAACATCTCTGGCGTAACG 59.401 50.000 0.00 0.00 34.12 3.18
4229 7001 1.066573 CCTGAGAAACATCTCTGGCGT 60.067 52.381 15.79 0.00 44.76 5.68
4267 7040 5.068198 CCCCCATGTAGTGAGATGAAATTTG 59.932 44.000 0.00 0.00 0.00 2.32
4279 7052 1.631388 TGTACCAACCCCCATGTAGTG 59.369 52.381 0.00 0.00 0.00 2.74
4283 7056 1.074889 GTTCTGTACCAACCCCCATGT 59.925 52.381 0.00 0.00 0.00 3.21
4314 7087 7.072177 TCTCAAGCAAAATATTGTTAGGACG 57.928 36.000 0.00 0.00 38.85 4.79
4316 7089 9.905713 ATACTCTCAAGCAAAATATTGTTAGGA 57.094 29.630 0.00 0.00 38.85 2.94


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

AutoCloner maintained by Alex Coulton.