Multiple sequence alignment - TraesCS1B01G386300

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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 TraesCS1B01G386300 chr1B 100.000 2607 0 0 1 2607 620454994 620452388 0.000000e+00 4815.0
1 TraesCS1B01G386300 chr1B 80.349 229 28 11 878 1097 620495928 620495708 9.660000e-35 158.0
2 TraesCS1B01G386300 chr1D 92.690 1067 42 17 617 1668 451383833 451384878 0.000000e+00 1506.0
3 TraesCS1B01G386300 chr1D 93.689 206 7 1 1 200 451383626 451383831 1.170000e-78 303.0
4 TraesCS1B01G386300 chr6B 93.458 963 36 6 1670 2607 15266242 15267202 0.000000e+00 1404.0
5 TraesCS1B01G386300 chr2B 91.864 971 44 11 1671 2607 258457597 258458566 0.000000e+00 1323.0
6 TraesCS1B01G386300 chr2B 95.642 413 13 3 201 612 36803724 36804132 0.000000e+00 658.0
7 TraesCS1B01G386300 chr2B 94.762 420 20 2 201 620 710142756 710142339 0.000000e+00 652.0
8 TraesCS1B01G386300 chr2B 94.326 423 19 4 201 623 547039546 547039129 0.000000e+00 643.0
9 TraesCS1B01G386300 chr3D 88.720 922 55 5 1733 2607 43578362 43579281 0.000000e+00 1081.0
10 TraesCS1B01G386300 chr7A 91.034 803 47 3 1827 2607 655413146 655413945 0.000000e+00 1061.0
11 TraesCS1B01G386300 chr4A 91.034 803 47 3 1827 2607 312727755 312728554 0.000000e+00 1061.0
12 TraesCS1B01G386300 chr4A 94.444 90 4 1 1736 1824 73936270 73936181 1.260000e-28 137.0
13 TraesCS1B01G386300 chr4A 92.308 65 4 1 1671 1734 73936382 73936318 9.940000e-15 91.6
14 TraesCS1B01G386300 chr1A 90.617 810 49 5 1822 2607 525138794 525139600 0.000000e+00 1050.0
15 TraesCS1B01G386300 chr1A 89.461 854 58 21 830 1668 546178072 546178908 0.000000e+00 1050.0
16 TraesCS1B01G386300 chr1A 88.165 921 52 9 1736 2607 504405915 504405003 0.000000e+00 1044.0
17 TraesCS1B01G386300 chr1A 90.399 802 52 4 1828 2607 522979310 522978512 0.000000e+00 1031.0
18 TraesCS1B01G386300 chr1A 87.459 917 58 32 795 1671 546193716 546194615 0.000000e+00 1003.0
19 TraesCS1B01G386300 chr1A 98.693 153 2 0 617 769 546177536 546177688 3.310000e-69 272.0
20 TraesCS1B01G386300 chr1A 89.320 206 10 4 1 200 546177335 546177534 5.570000e-62 248.0
21 TraesCS1B01G386300 chr1A 95.312 64 3 0 1671 1734 504406025 504405962 4.590000e-18 102.0
22 TraesCS1B01G386300 chr1A 100.000 50 0 0 151 200 546193551 546193600 2.760000e-15 93.5
23 TraesCS1B01G386300 chr5A 87.849 930 54 17 1733 2607 678671942 678672867 0.000000e+00 1037.0
24 TraesCS1B01G386300 chr5A 93.750 64 4 0 1671 1734 678671835 678671898 2.140000e-16 97.1
25 TraesCS1B01G386300 chr3B 96.126 413 13 3 201 612 735592155 735591745 0.000000e+00 671.0
26 TraesCS1B01G386300 chr3B 95.422 415 17 2 200 613 794837458 794837045 0.000000e+00 660.0
27 TraesCS1B01G386300 chr3B 95.631 412 15 3 201 612 633369951 633370359 0.000000e+00 658.0
28 TraesCS1B01G386300 chr3B 94.431 413 17 5 201 612 595242117 595241710 4.730000e-177 630.0
29 TraesCS1B01G386300 chr4B 95.146 412 18 2 201 612 123459602 123460011 0.000000e+00 649.0
30 TraesCS1B01G386300 chr7B 93.556 419 24 3 198 614 546015535 546015952 2.850000e-174 621.0
31 TraesCS1B01G386300 chr7B 83.604 555 42 5 1736 2243 71131018 71130466 2.350000e-130 475.0
32 TraesCS1B01G386300 chr6D 94.444 90 4 1 1733 1821 423817335 423817424 1.260000e-28 137.0
33 TraesCS1B01G386300 chr6D 95.312 64 3 0 1671 1734 423817228 423817291 4.590000e-18 102.0
34 TraesCS1B01G386300 chr2D 91.753 97 7 1 1733 1828 327743107 327743203 1.630000e-27 134.0
35 TraesCS1B01G386300 chr6A 88.158 76 5 3 1660 1734 146739536 146739608 1.290000e-13 87.9
36 TraesCS1B01G386300 chr2A 87.097 62 8 0 1671 1732 667016140 667016201 1.290000e-08 71.3


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 TraesCS1B01G386300 chr1B 620452388 620454994 2606 True 4815.000000 4815 100.000000 1 2607 1 chr1B.!!$R1 2606
1 TraesCS1B01G386300 chr1D 451383626 451384878 1252 False 904.500000 1506 93.189500 1 1668 2 chr1D.!!$F1 1667
2 TraesCS1B01G386300 chr6B 15266242 15267202 960 False 1404.000000 1404 93.458000 1670 2607 1 chr6B.!!$F1 937
3 TraesCS1B01G386300 chr2B 258457597 258458566 969 False 1323.000000 1323 91.864000 1671 2607 1 chr2B.!!$F2 936
4 TraesCS1B01G386300 chr3D 43578362 43579281 919 False 1081.000000 1081 88.720000 1733 2607 1 chr3D.!!$F1 874
5 TraesCS1B01G386300 chr7A 655413146 655413945 799 False 1061.000000 1061 91.034000 1827 2607 1 chr7A.!!$F1 780
6 TraesCS1B01G386300 chr4A 312727755 312728554 799 False 1061.000000 1061 91.034000 1827 2607 1 chr4A.!!$F1 780
7 TraesCS1B01G386300 chr1A 525138794 525139600 806 False 1050.000000 1050 90.617000 1822 2607 1 chr1A.!!$F1 785
8 TraesCS1B01G386300 chr1A 522978512 522979310 798 True 1031.000000 1031 90.399000 1828 2607 1 chr1A.!!$R1 779
9 TraesCS1B01G386300 chr1A 504405003 504406025 1022 True 573.000000 1044 91.738500 1671 2607 2 chr1A.!!$R2 936
10 TraesCS1B01G386300 chr1A 546193551 546194615 1064 False 548.250000 1003 93.729500 151 1671 2 chr1A.!!$F3 1520
11 TraesCS1B01G386300 chr1A 546177335 546178908 1573 False 523.333333 1050 92.491333 1 1668 3 chr1A.!!$F2 1667
12 TraesCS1B01G386300 chr5A 678671835 678672867 1032 False 567.050000 1037 90.799500 1671 2607 2 chr5A.!!$F1 936
13 TraesCS1B01G386300 chr7B 71130466 71131018 552 True 475.000000 475 83.604000 1736 2243 1 chr7B.!!$R1 507

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
488 495 0.033366 AGTTGAATTTTGGGGCGCAC 59.967 50.0 10.83 4.83 0.00 5.34 F
608 615 0.764890 CCGGGCTCCAGGATGAATTA 59.235 55.0 0.00 0.00 39.69 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1935 0.367887 CGCGCGATACATCCATCATG 59.632 55.0 28.94 0.0 38.64 3.07 R
2484 2996 0.388520 GCCAATCGGACAACAAAGGC 60.389 55.0 0.00 0.0 0.00 4.35 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
27 28 8.608844 TTTATGCATTTGTTTTATTCGGGTTT 57.391 26.923 3.54 0.00 0.00 3.27
132 139 4.890581 AGGAGTGAGAACGATAGCTTACAT 59.109 41.667 0.00 0.00 42.67 2.29
200 207 7.865707 ACTCCAACGTAGGTAGTAATTATACG 58.134 38.462 11.96 11.96 43.53 3.06
201 208 7.041098 ACTCCAACGTAGGTAGTAATTATACGG 60.041 40.741 16.00 4.77 42.53 4.02
202 209 6.995686 TCCAACGTAGGTAGTAATTATACGGA 59.004 38.462 16.00 5.33 42.53 4.69
203 210 7.041372 TCCAACGTAGGTAGTAATTATACGGAC 60.041 40.741 16.00 8.18 42.53 4.79
204 211 6.467723 ACGTAGGTAGTAATTATACGGACG 57.532 41.667 16.00 16.65 42.53 4.79
205 212 5.107065 ACGTAGGTAGTAATTATACGGACGC 60.107 44.000 16.00 0.00 42.53 5.19
206 213 4.410492 AGGTAGTAATTATACGGACGCG 57.590 45.455 3.53 3.53 37.11 6.01
207 214 3.189287 AGGTAGTAATTATACGGACGCGG 59.811 47.826 12.47 0.00 37.11 6.46
208 215 3.188460 GGTAGTAATTATACGGACGCGGA 59.812 47.826 12.47 0.00 37.11 5.54
209 216 3.549299 AGTAATTATACGGACGCGGAG 57.451 47.619 12.47 3.25 37.11 4.63
210 217 2.880890 AGTAATTATACGGACGCGGAGT 59.119 45.455 12.47 9.94 37.11 3.85
211 218 2.877043 AATTATACGGACGCGGAGTT 57.123 45.000 12.47 0.00 0.00 3.01
212 219 2.877043 ATTATACGGACGCGGAGTTT 57.123 45.000 12.47 5.10 0.00 2.66
213 220 2.652941 TTATACGGACGCGGAGTTTT 57.347 45.000 12.47 1.58 0.00 2.43
214 221 1.912001 TATACGGACGCGGAGTTTTG 58.088 50.000 12.47 0.00 0.00 2.44
215 222 0.738412 ATACGGACGCGGAGTTTTGG 60.738 55.000 12.47 0.00 0.00 3.28
216 223 4.084888 CGGACGCGGAGTTTTGGC 62.085 66.667 12.47 0.00 0.00 4.52
217 224 2.668550 GGACGCGGAGTTTTGGCT 60.669 61.111 12.47 0.00 0.00 4.75
218 225 2.677979 GGACGCGGAGTTTTGGCTC 61.678 63.158 12.47 0.00 34.89 4.70
224 231 3.062466 GAGTTTTGGCTCCCGGGC 61.062 66.667 18.49 4.47 41.27 6.13
225 232 3.569200 GAGTTTTGGCTCCCGGGCT 62.569 63.158 18.49 3.64 41.48 5.19
226 233 3.062466 GTTTTGGCTCCCGGGCTC 61.062 66.667 18.49 9.71 41.48 4.70
227 234 3.575247 TTTTGGCTCCCGGGCTCA 61.575 61.111 18.49 11.07 41.48 4.26
228 235 2.917897 TTTTGGCTCCCGGGCTCAT 61.918 57.895 18.49 0.00 41.48 2.90
229 236 2.837031 TTTTGGCTCCCGGGCTCATC 62.837 60.000 18.49 3.79 41.48 2.92
230 237 4.804420 TGGCTCCCGGGCTCATCT 62.804 66.667 18.49 0.00 41.48 2.90
231 238 4.247380 GGCTCCCGGGCTCATCTG 62.247 72.222 18.49 0.33 37.53 2.90
232 239 4.925861 GCTCCCGGGCTCATCTGC 62.926 72.222 18.49 7.22 0.00 4.26
233 240 3.473647 CTCCCGGGCTCATCTGCA 61.474 66.667 18.49 0.00 34.04 4.41
234 241 3.746949 CTCCCGGGCTCATCTGCAC 62.747 68.421 18.49 0.00 34.04 4.57
235 242 4.864334 CCCGGGCTCATCTGCACC 62.864 72.222 8.08 0.00 31.60 5.01
236 243 4.864334 CCGGGCTCATCTGCACCC 62.864 72.222 0.00 0.00 39.12 4.61
237 244 4.100084 CGGGCTCATCTGCACCCA 62.100 66.667 8.42 0.00 42.97 4.51
238 245 2.439156 GGGCTCATCTGCACCCAC 60.439 66.667 2.99 0.00 42.33 4.61
239 246 2.821366 GGCTCATCTGCACCCACG 60.821 66.667 0.00 0.00 34.04 4.94
240 247 3.503363 GCTCATCTGCACCCACGC 61.503 66.667 0.00 0.00 0.00 5.34
241 248 2.267006 CTCATCTGCACCCACGCT 59.733 61.111 0.00 0.00 0.00 5.07
242 249 1.812922 CTCATCTGCACCCACGCTC 60.813 63.158 0.00 0.00 0.00 5.03
243 250 2.046988 CATCTGCACCCACGCTCA 60.047 61.111 0.00 0.00 0.00 4.26
244 251 2.104859 CATCTGCACCCACGCTCAG 61.105 63.158 0.00 0.00 0.00 3.35
245 252 3.965539 ATCTGCACCCACGCTCAGC 62.966 63.158 0.00 0.00 0.00 4.26
246 253 4.994471 CTGCACCCACGCTCAGCA 62.994 66.667 0.00 0.00 0.00 4.41
247 254 4.560743 TGCACCCACGCTCAGCAA 62.561 61.111 0.00 0.00 31.42 3.91
248 255 3.286751 GCACCCACGCTCAGCAAA 61.287 61.111 0.00 0.00 0.00 3.68
249 256 2.844451 GCACCCACGCTCAGCAAAA 61.844 57.895 0.00 0.00 0.00 2.44
250 257 1.732917 CACCCACGCTCAGCAAAAA 59.267 52.632 0.00 0.00 0.00 1.94
317 324 6.854496 TTATGGTGGTAGATAATTTGACGC 57.146 37.500 0.00 0.00 0.00 5.19
318 325 3.191669 TGGTGGTAGATAATTTGACGCG 58.808 45.455 3.53 3.53 0.00 6.01
319 326 3.192466 GGTGGTAGATAATTTGACGCGT 58.808 45.455 13.85 13.85 0.00 6.01
320 327 3.000925 GGTGGTAGATAATTTGACGCGTG 59.999 47.826 20.70 0.00 0.00 5.34
321 328 3.861113 GTGGTAGATAATTTGACGCGTGA 59.139 43.478 20.70 4.74 0.00 4.35
322 329 4.026804 GTGGTAGATAATTTGACGCGTGAG 60.027 45.833 20.70 0.00 0.00 3.51
323 330 3.489785 GGTAGATAATTTGACGCGTGAGG 59.510 47.826 20.70 0.00 0.00 3.86
324 331 3.247006 AGATAATTTGACGCGTGAGGT 57.753 42.857 20.70 0.00 0.00 3.85
325 332 4.380841 AGATAATTTGACGCGTGAGGTA 57.619 40.909 20.70 1.46 0.00 3.08
326 333 4.110482 AGATAATTTGACGCGTGAGGTAC 58.890 43.478 20.70 0.06 0.00 3.34
334 341 2.344500 CGTGAGGTACGCCCCAAA 59.656 61.111 0.00 0.00 46.92 3.28
335 342 1.301874 CGTGAGGTACGCCCCAAAA 60.302 57.895 0.00 0.00 46.92 2.44
336 343 0.675522 CGTGAGGTACGCCCCAAAAT 60.676 55.000 0.00 0.00 46.92 1.82
337 344 1.541379 GTGAGGTACGCCCCAAAATT 58.459 50.000 0.00 0.00 34.57 1.82
338 345 1.471287 GTGAGGTACGCCCCAAAATTC 59.529 52.381 0.00 0.00 34.57 2.17
339 346 1.074084 TGAGGTACGCCCCAAAATTCA 59.926 47.619 0.00 0.00 34.57 2.57
340 347 2.164338 GAGGTACGCCCCAAAATTCAA 58.836 47.619 0.00 0.00 34.57 2.69
341 348 1.890489 AGGTACGCCCCAAAATTCAAC 59.110 47.619 0.00 0.00 34.57 3.18
342 349 1.890489 GGTACGCCCCAAAATTCAACT 59.110 47.619 0.00 0.00 0.00 3.16
343 350 2.094906 GGTACGCCCCAAAATTCAACTC 60.095 50.000 0.00 0.00 0.00 3.01
344 351 1.698506 ACGCCCCAAAATTCAACTCA 58.301 45.000 0.00 0.00 0.00 3.41
345 352 2.247358 ACGCCCCAAAATTCAACTCAT 58.753 42.857 0.00 0.00 0.00 2.90
346 353 2.632512 ACGCCCCAAAATTCAACTCATT 59.367 40.909 0.00 0.00 0.00 2.57
347 354 3.070878 ACGCCCCAAAATTCAACTCATTT 59.929 39.130 0.00 0.00 0.00 2.32
348 355 3.432933 CGCCCCAAAATTCAACTCATTTG 59.567 43.478 0.00 0.00 36.42 2.32
349 356 4.640364 GCCCCAAAATTCAACTCATTTGA 58.360 39.130 0.00 0.00 42.83 2.69
350 357 4.692155 GCCCCAAAATTCAACTCATTTGAG 59.308 41.667 6.03 6.03 45.22 3.02
351 358 4.692155 CCCCAAAATTCAACTCATTTGAGC 59.308 41.667 7.48 0.00 45.22 4.26
352 359 5.299148 CCCAAAATTCAACTCATTTGAGCA 58.701 37.500 7.48 0.00 45.22 4.26
353 360 5.178067 CCCAAAATTCAACTCATTTGAGCAC 59.822 40.000 7.48 0.00 45.22 4.40
354 361 5.178067 CCAAAATTCAACTCATTTGAGCACC 59.822 40.000 7.48 0.00 45.22 5.01
355 362 5.796424 AAATTCAACTCATTTGAGCACCT 57.204 34.783 7.48 0.00 45.22 4.00
356 363 4.778534 ATTCAACTCATTTGAGCACCTG 57.221 40.909 7.48 1.37 45.22 4.00
357 364 3.490439 TCAACTCATTTGAGCACCTGA 57.510 42.857 7.48 3.49 45.79 3.86
358 365 3.405831 TCAACTCATTTGAGCACCTGAG 58.594 45.455 7.48 6.84 45.79 3.35
359 366 1.818642 ACTCATTTGAGCACCTGAGC 58.181 50.000 7.48 0.00 45.79 4.26
360 367 1.072806 ACTCATTTGAGCACCTGAGCA 59.927 47.619 7.48 0.00 45.79 4.26
361 368 1.738350 CTCATTTGAGCACCTGAGCAG 59.262 52.381 0.00 0.00 35.13 4.24
362 369 0.170561 CATTTGAGCACCTGAGCAGC 59.829 55.000 0.00 0.00 36.85 5.25
363 370 0.037877 ATTTGAGCACCTGAGCAGCT 59.962 50.000 0.00 0.00 42.17 4.24
366 373 2.980475 AGCACCTGAGCAGCTCTC 59.020 61.111 23.15 7.39 42.23 3.20
367 374 2.508887 GCACCTGAGCAGCTCTCG 60.509 66.667 23.15 14.69 44.86 4.04
368 375 2.183811 CACCTGAGCAGCTCTCGG 59.816 66.667 23.15 22.77 44.86 4.63
369 376 3.768922 ACCTGAGCAGCTCTCGGC 61.769 66.667 23.15 0.00 45.00 5.54
370 377 3.767806 CCTGAGCAGCTCTCGGCA 61.768 66.667 23.15 2.15 45.00 5.69
371 378 2.263852 CTGAGCAGCTCTCGGCAA 59.736 61.111 23.15 0.68 44.86 4.52
372 379 1.375140 CTGAGCAGCTCTCGGCAAA 60.375 57.895 23.15 0.00 44.86 3.68
373 380 0.952497 CTGAGCAGCTCTCGGCAAAA 60.952 55.000 23.15 0.00 44.86 2.44
374 381 0.534877 TGAGCAGCTCTCGGCAAAAA 60.535 50.000 23.15 0.00 44.86 1.94
392 399 4.341366 AAAAAGACAAAATCAGGGCCTG 57.659 40.909 28.01 28.01 0.00 4.85
393 400 2.683211 AAGACAAAATCAGGGCCTGT 57.317 45.000 31.60 17.12 32.61 4.00
394 401 3.806949 AAGACAAAATCAGGGCCTGTA 57.193 42.857 31.60 19.20 32.61 2.74
395 402 3.806949 AGACAAAATCAGGGCCTGTAA 57.193 42.857 31.60 15.52 32.61 2.41
396 403 4.112634 AGACAAAATCAGGGCCTGTAAA 57.887 40.909 31.60 14.73 32.61 2.01
397 404 4.479158 AGACAAAATCAGGGCCTGTAAAA 58.521 39.130 31.60 14.34 32.61 1.52
398 405 4.898861 AGACAAAATCAGGGCCTGTAAAAA 59.101 37.500 31.60 13.93 32.61 1.94
399 406 5.543790 AGACAAAATCAGGGCCTGTAAAAAT 59.456 36.000 31.60 15.68 32.61 1.82
400 407 5.550290 ACAAAATCAGGGCCTGTAAAAATG 58.450 37.500 31.60 23.53 32.61 2.32
401 408 5.071653 ACAAAATCAGGGCCTGTAAAAATGT 59.928 36.000 31.60 24.09 32.61 2.71
402 409 6.268847 ACAAAATCAGGGCCTGTAAAAATGTA 59.731 34.615 31.60 10.82 32.61 2.29
403 410 7.038373 ACAAAATCAGGGCCTGTAAAAATGTAT 60.038 33.333 31.60 12.72 32.61 2.29
404 411 8.474025 CAAAATCAGGGCCTGTAAAAATGTATA 58.526 33.333 31.60 9.50 32.61 1.47
405 412 7.582667 AATCAGGGCCTGTAAAAATGTATAC 57.417 36.000 31.60 0.00 32.61 1.47
406 413 6.321821 TCAGGGCCTGTAAAAATGTATACT 57.678 37.500 31.60 0.00 32.61 2.12
407 414 6.119536 TCAGGGCCTGTAAAAATGTATACTG 58.880 40.000 31.60 2.13 32.61 2.74
408 415 5.885912 CAGGGCCTGTAAAAATGTATACTGT 59.114 40.000 25.74 0.00 0.00 3.55
409 416 6.377146 CAGGGCCTGTAAAAATGTATACTGTT 59.623 38.462 25.74 0.00 0.00 3.16
410 417 6.602009 AGGGCCTGTAAAAATGTATACTGTTC 59.398 38.462 4.50 0.00 0.00 3.18
411 418 6.376018 GGGCCTGTAAAAATGTATACTGTTCA 59.624 38.462 0.84 0.00 0.00 3.18
412 419 7.248437 GGCCTGTAAAAATGTATACTGTTCAC 58.752 38.462 4.17 1.91 0.00 3.18
413 420 6.959311 GCCTGTAAAAATGTATACTGTTCACG 59.041 38.462 4.17 0.00 0.00 4.35
414 421 6.959311 CCTGTAAAAATGTATACTGTTCACGC 59.041 38.462 4.17 0.00 0.00 5.34
415 422 7.360522 CCTGTAAAAATGTATACTGTTCACGCA 60.361 37.037 4.17 0.00 0.00 5.24
416 423 7.292292 TGTAAAAATGTATACTGTTCACGCAC 58.708 34.615 4.17 0.00 0.00 5.34
417 424 6.554334 AAAAATGTATACTGTTCACGCACT 57.446 33.333 4.17 0.00 0.00 4.40
418 425 5.530519 AAATGTATACTGTTCACGCACTG 57.469 39.130 4.17 0.00 0.00 3.66
419 426 3.653539 TGTATACTGTTCACGCACTGT 57.346 42.857 4.17 0.00 33.75 3.55
420 427 3.985008 TGTATACTGTTCACGCACTGTT 58.015 40.909 4.17 0.00 31.81 3.16
421 428 4.373527 TGTATACTGTTCACGCACTGTTT 58.626 39.130 4.17 0.00 31.81 2.83
422 429 4.812091 TGTATACTGTTCACGCACTGTTTT 59.188 37.500 4.17 0.00 31.81 2.43
423 430 2.542766 ACTGTTCACGCACTGTTTTG 57.457 45.000 0.00 0.00 0.00 2.44
424 431 2.080693 ACTGTTCACGCACTGTTTTGA 58.919 42.857 0.00 0.00 0.00 2.69
425 432 2.159572 ACTGTTCACGCACTGTTTTGAC 60.160 45.455 0.00 0.00 0.00 3.18
426 433 1.131504 TGTTCACGCACTGTTTTGACC 59.868 47.619 0.00 0.00 0.00 4.02
427 434 1.400494 GTTCACGCACTGTTTTGACCT 59.600 47.619 0.00 0.00 0.00 3.85
428 435 1.013596 TCACGCACTGTTTTGACCTG 58.986 50.000 0.00 0.00 0.00 4.00
429 436 1.013596 CACGCACTGTTTTGACCTGA 58.986 50.000 0.00 0.00 0.00 3.86
430 437 1.603802 CACGCACTGTTTTGACCTGAT 59.396 47.619 0.00 0.00 0.00 2.90
431 438 2.033299 CACGCACTGTTTTGACCTGATT 59.967 45.455 0.00 0.00 0.00 2.57
432 439 2.687935 ACGCACTGTTTTGACCTGATTT 59.312 40.909 0.00 0.00 0.00 2.17
433 440 3.044986 CGCACTGTTTTGACCTGATTTG 58.955 45.455 0.00 0.00 0.00 2.32
434 441 3.489059 CGCACTGTTTTGACCTGATTTGT 60.489 43.478 0.00 0.00 0.00 2.83
435 442 4.044426 GCACTGTTTTGACCTGATTTGTC 58.956 43.478 0.00 0.00 0.00 3.18
436 443 4.202050 GCACTGTTTTGACCTGATTTGTCT 60.202 41.667 0.00 0.00 33.83 3.41
437 444 5.679638 GCACTGTTTTGACCTGATTTGTCTT 60.680 40.000 0.00 0.00 33.83 3.01
438 445 6.332630 CACTGTTTTGACCTGATTTGTCTTT 58.667 36.000 0.00 0.00 33.83 2.52
439 446 6.813152 CACTGTTTTGACCTGATTTGTCTTTT 59.187 34.615 0.00 0.00 33.83 2.27
440 447 7.331687 CACTGTTTTGACCTGATTTGTCTTTTT 59.668 33.333 0.00 0.00 33.83 1.94
456 463 2.831685 TTTTTGCCGAGAGCTACTCA 57.168 45.000 11.93 0.00 45.14 3.41
457 464 2.370281 TTTTGCCGAGAGCTACTCAG 57.630 50.000 11.93 3.88 45.14 3.35
458 465 1.545841 TTTGCCGAGAGCTACTCAGA 58.454 50.000 11.93 0.00 45.14 3.27
459 466 1.769026 TTGCCGAGAGCTACTCAGAT 58.231 50.000 11.93 0.00 45.14 2.90
460 467 1.028130 TGCCGAGAGCTACTCAGATG 58.972 55.000 11.93 1.60 45.14 2.90
461 468 1.028905 GCCGAGAGCTACTCAGATGT 58.971 55.000 11.93 0.00 45.14 3.06
462 469 1.001815 GCCGAGAGCTACTCAGATGTC 60.002 57.143 11.93 0.00 45.14 3.06
463 470 1.606668 CCGAGAGCTACTCAGATGTCC 59.393 57.143 11.93 0.00 45.14 4.02
464 471 2.293170 CGAGAGCTACTCAGATGTCCA 58.707 52.381 11.93 0.00 45.14 4.02
465 472 2.685388 CGAGAGCTACTCAGATGTCCAA 59.315 50.000 11.93 0.00 45.14 3.53
466 473 3.129462 CGAGAGCTACTCAGATGTCCAAA 59.871 47.826 11.93 0.00 45.14 3.28
467 474 4.202101 CGAGAGCTACTCAGATGTCCAAAT 60.202 45.833 11.93 0.00 45.14 2.32
468 475 5.009110 CGAGAGCTACTCAGATGTCCAAATA 59.991 44.000 11.93 0.00 45.14 1.40
469 476 6.460261 CGAGAGCTACTCAGATGTCCAAATAA 60.460 42.308 11.93 0.00 45.14 1.40
470 477 6.815089 AGAGCTACTCAGATGTCCAAATAAG 58.185 40.000 0.00 0.00 32.06 1.73
471 478 6.382570 AGAGCTACTCAGATGTCCAAATAAGT 59.617 38.462 0.00 0.00 32.06 2.24
472 479 6.951971 AGCTACTCAGATGTCCAAATAAGTT 58.048 36.000 0.00 0.00 0.00 2.66
473 480 6.820656 AGCTACTCAGATGTCCAAATAAGTTG 59.179 38.462 0.00 0.00 36.94 3.16
474 481 6.818644 GCTACTCAGATGTCCAAATAAGTTGA 59.181 38.462 0.00 0.00 39.87 3.18
475 482 7.334421 GCTACTCAGATGTCCAAATAAGTTGAA 59.666 37.037 0.00 0.00 39.87 2.69
476 483 9.388506 CTACTCAGATGTCCAAATAAGTTGAAT 57.611 33.333 0.00 0.00 39.87 2.57
477 484 8.641498 ACTCAGATGTCCAAATAAGTTGAATT 57.359 30.769 0.00 0.00 39.87 2.17
478 485 9.082313 ACTCAGATGTCCAAATAAGTTGAATTT 57.918 29.630 0.00 0.00 39.87 1.82
479 486 9.918630 CTCAGATGTCCAAATAAGTTGAATTTT 57.081 29.630 0.00 0.00 39.87 1.82
480 487 9.695526 TCAGATGTCCAAATAAGTTGAATTTTG 57.304 29.630 0.00 0.00 39.87 2.44
481 488 8.928733 CAGATGTCCAAATAAGTTGAATTTTGG 58.071 33.333 6.89 6.89 46.09 3.28
482 489 8.096414 AGATGTCCAAATAAGTTGAATTTTGGG 58.904 33.333 12.01 3.08 45.23 4.12
483 490 6.529220 TGTCCAAATAAGTTGAATTTTGGGG 58.471 36.000 12.01 2.57 45.23 4.96
484 491 5.411361 GTCCAAATAAGTTGAATTTTGGGGC 59.589 40.000 12.01 4.11 45.23 5.80
485 492 4.391523 CCAAATAAGTTGAATTTTGGGGCG 59.608 41.667 5.56 0.00 42.74 6.13
486 493 2.734276 TAAGTTGAATTTTGGGGCGC 57.266 45.000 0.00 0.00 0.00 6.53
487 494 0.755686 AAGTTGAATTTTGGGGCGCA 59.244 45.000 10.83 0.00 0.00 6.09
488 495 0.033366 AGTTGAATTTTGGGGCGCAC 59.967 50.000 10.83 4.83 0.00 5.34
489 496 0.948623 GTTGAATTTTGGGGCGCACC 60.949 55.000 25.59 25.59 39.11 5.01
490 497 1.118356 TTGAATTTTGGGGCGCACCT 61.118 50.000 32.18 9.19 40.03 4.00
491 498 1.215382 GAATTTTGGGGCGCACCTC 59.785 57.895 32.18 15.41 40.03 3.85
502 509 3.253955 GCACCTCACGCGTCAAAT 58.746 55.556 9.86 0.00 0.00 2.32
503 510 1.574428 GCACCTCACGCGTCAAATT 59.426 52.632 9.86 0.00 0.00 1.82
504 511 0.793861 GCACCTCACGCGTCAAATTA 59.206 50.000 9.86 0.00 0.00 1.40
505 512 1.396996 GCACCTCACGCGTCAAATTAT 59.603 47.619 9.86 0.00 0.00 1.28
506 513 2.536928 GCACCTCACGCGTCAAATTATC 60.537 50.000 9.86 0.00 0.00 1.75
507 514 2.930040 CACCTCACGCGTCAAATTATCT 59.070 45.455 9.86 0.00 0.00 1.98
508 515 4.109766 CACCTCACGCGTCAAATTATCTA 58.890 43.478 9.86 0.00 0.00 1.98
509 516 4.026804 CACCTCACGCGTCAAATTATCTAC 60.027 45.833 9.86 0.00 0.00 2.59
510 517 3.489785 CCTCACGCGTCAAATTATCTACC 59.510 47.826 9.86 0.00 0.00 3.18
511 518 4.109766 CTCACGCGTCAAATTATCTACCA 58.890 43.478 9.86 0.00 0.00 3.25
512 519 3.861113 TCACGCGTCAAATTATCTACCAC 59.139 43.478 9.86 0.00 0.00 4.16
513 520 3.000925 CACGCGTCAAATTATCTACCACC 59.999 47.826 9.86 0.00 0.00 4.61
514 521 3.191669 CGCGTCAAATTATCTACCACCA 58.808 45.455 0.00 0.00 0.00 4.17
515 522 3.000925 CGCGTCAAATTATCTACCACCAC 59.999 47.826 0.00 0.00 0.00 4.16
516 523 3.936453 GCGTCAAATTATCTACCACCACA 59.064 43.478 0.00 0.00 0.00 4.17
517 524 4.393680 GCGTCAAATTATCTACCACCACAA 59.606 41.667 0.00 0.00 0.00 3.33
518 525 5.106475 GCGTCAAATTATCTACCACCACAAA 60.106 40.000 0.00 0.00 0.00 2.83
519 526 6.568844 GCGTCAAATTATCTACCACCACAAAA 60.569 38.462 0.00 0.00 0.00 2.44
520 527 7.364200 CGTCAAATTATCTACCACCACAAAAA 58.636 34.615 0.00 0.00 0.00 1.94
592 599 4.247380 GGGAGCAGATGAGCCCGG 62.247 72.222 0.00 0.00 34.23 5.73
593 600 4.247380 GGAGCAGATGAGCCCGGG 62.247 72.222 19.09 19.09 34.23 5.73
594 601 4.925861 GAGCAGATGAGCCCGGGC 62.926 72.222 39.29 39.29 42.33 6.13
605 612 3.089874 CCCGGGCTCCAGGATGAA 61.090 66.667 8.08 0.00 39.69 2.57
606 613 2.455565 CCCGGGCTCCAGGATGAAT 61.456 63.158 8.08 0.00 39.69 2.57
607 614 1.533711 CCGGGCTCCAGGATGAATT 59.466 57.895 0.00 0.00 39.69 2.17
608 615 0.764890 CCGGGCTCCAGGATGAATTA 59.235 55.000 0.00 0.00 39.69 1.40
609 616 1.352352 CCGGGCTCCAGGATGAATTAT 59.648 52.381 0.00 0.00 39.69 1.28
610 617 2.616510 CCGGGCTCCAGGATGAATTATC 60.617 54.545 0.00 0.00 39.69 1.75
611 618 2.704572 GGGCTCCAGGATGAATTATCG 58.295 52.381 0.00 0.00 39.69 2.92
612 619 2.616510 GGGCTCCAGGATGAATTATCGG 60.617 54.545 0.00 0.00 39.69 4.18
613 620 2.039084 GGCTCCAGGATGAATTATCGGT 59.961 50.000 0.00 0.00 39.69 4.69
614 621 3.260884 GGCTCCAGGATGAATTATCGGTA 59.739 47.826 0.00 0.00 39.69 4.02
615 622 4.080863 GGCTCCAGGATGAATTATCGGTAT 60.081 45.833 0.00 0.00 39.69 2.73
773 821 2.614057 GTGGGCAACATGCTGATACTAC 59.386 50.000 0.00 0.00 44.28 2.73
774 822 2.505407 TGGGCAACATGCTGATACTACT 59.495 45.455 0.00 0.00 44.28 2.57
775 823 3.709141 TGGGCAACATGCTGATACTACTA 59.291 43.478 0.00 0.00 44.28 1.82
776 824 4.202253 TGGGCAACATGCTGATACTACTAG 60.202 45.833 0.00 0.00 44.28 2.57
803 881 6.591935 AGAAGACTGTTTGTATCTTTGGTCA 58.408 36.000 0.00 0.00 32.83 4.02
874 1211 4.573201 AGACTCATACGTTGACTAGAGAGC 59.427 45.833 0.00 0.00 0.00 4.09
915 1254 4.008933 GTGTGAGCACTCCGGCCT 62.009 66.667 0.00 0.00 42.13 5.19
930 1276 2.028112 CCGGCCTGCAGTACATATATGT 60.028 50.000 21.57 21.57 44.48 2.29
951 1297 1.845809 CGTTGCTCACAGCCTCAACC 61.846 60.000 0.00 0.00 41.51 3.77
966 1314 3.056035 CCTCAACCCACAGTTCTAGTACC 60.056 52.174 0.00 0.00 36.18 3.34
1014 1371 4.596643 CCTTAACCCATGGAGAGATCATCT 59.403 45.833 15.22 0.00 42.61 2.90
1143 1502 1.261885 TGTCCGTTTTGTACACATGCG 59.738 47.619 0.00 0.00 0.00 4.73
1163 1525 1.405105 GTGCATGCACGATTTATGGGT 59.595 47.619 33.20 0.00 37.19 4.51
1195 1557 6.145534 TCTGTTCACAAGAATACACGATTCAC 59.854 38.462 0.00 0.00 45.69 3.18
1196 1558 5.755861 TGTTCACAAGAATACACGATTCACA 59.244 36.000 0.00 0.00 45.69 3.58
1200 1562 6.311200 TCACAAGAATACACGATTCACAGATG 59.689 38.462 0.00 0.00 45.69 2.90
1251 1613 7.119262 CGTTTGGTACAGGACAATTTCTCTTAT 59.881 37.037 0.00 0.00 42.39 1.73
1289 1651 2.205074 CTTCAGGTGATGCATACGACC 58.795 52.381 12.23 12.23 0.00 4.79
1373 1735 4.776322 TCGCCGATGTTGCAGGGG 62.776 66.667 0.02 0.02 39.06 4.79
1500 1889 1.069765 CGACTGAACCTGCACCACT 59.930 57.895 0.00 0.00 0.00 4.00
1553 1942 2.442643 GGCACCCACCCATGATGG 60.443 66.667 3.98 3.98 37.25 3.51
1554 1943 2.682846 GCACCCACCCATGATGGA 59.317 61.111 14.26 0.00 40.96 3.41
1555 1944 1.231068 GCACCCACCCATGATGGAT 59.769 57.895 14.26 0.00 40.96 3.41
1556 1945 1.111116 GCACCCACCCATGATGGATG 61.111 60.000 14.26 5.78 40.96 3.51
1557 1946 0.259647 CACCCACCCATGATGGATGT 59.740 55.000 14.26 0.00 40.96 3.06
1558 1947 1.494296 CACCCACCCATGATGGATGTA 59.506 52.381 14.26 0.00 40.96 2.29
1559 1948 2.108776 CACCCACCCATGATGGATGTAT 59.891 50.000 14.26 0.00 40.96 2.29
1560 1949 2.376518 ACCCACCCATGATGGATGTATC 59.623 50.000 14.26 0.00 40.96 2.24
1577 1975 4.362946 CGCGCGCGTTTCTCCAAA 62.363 61.111 42.49 0.00 34.35 3.28
1685 2087 2.038033 GTGTGAACTAGTAGTTGGGGCA 59.962 50.000 20.21 8.94 38.80 5.36
1759 2206 5.475719 ACATGCAATTCTTGATGGAACTTG 58.524 37.500 0.00 0.00 0.00 3.16
1816 2265 1.214367 CCACGCCCACAACGATATAC 58.786 55.000 0.00 0.00 0.00 1.47
1817 2266 1.471851 CCACGCCCACAACGATATACA 60.472 52.381 0.00 0.00 0.00 2.29
1818 2267 2.479837 CACGCCCACAACGATATACAT 58.520 47.619 0.00 0.00 0.00 2.29
1819 2268 2.475111 CACGCCCACAACGATATACATC 59.525 50.000 0.00 0.00 0.00 3.06
1914 2388 2.972505 CCGTGCGGCTGACAAAGT 60.973 61.111 0.00 0.00 0.00 2.66
2100 2612 6.350361 CCACTTCATATTTTTGGCATGACTGA 60.350 38.462 0.00 0.00 0.00 3.41
2149 2661 0.884514 TCTGAGAGAAGCGAGTGTGG 59.115 55.000 0.00 0.00 0.00 4.17
2192 2704 0.460987 CGGATCACCTTGTGGCTCTC 60.461 60.000 0.00 0.00 36.63 3.20
2256 2768 5.542779 ACTTGCTCGTGAAGATAGAAAACT 58.457 37.500 0.00 0.00 0.00 2.66
2436 2948 1.072331 GCCCACTGAAAGGAGTCAGAA 59.928 52.381 9.10 0.00 46.76 3.02
2484 2996 5.350633 TCTTCAAATTGTGCAAAGGAACTG 58.649 37.500 0.00 0.00 40.86 3.16
2497 3009 0.310854 GGAACTGCCTTTGTTGTCCG 59.689 55.000 0.00 0.00 0.00 4.79
2556 3068 4.840271 TCAGTCTCCGTCTATCTACAACA 58.160 43.478 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.020378 CGTTGCACCGGAAACCCG 62.020 66.667 9.46 0.00 46.35 5.28
132 139 3.181484 GGCAATGATTGTAGCTTCATGCA 60.181 43.478 15.03 7.80 45.94 3.96
200 207 2.668550 AGCCAAAACTCCGCGTCC 60.669 61.111 4.92 0.00 0.00 4.79
201 208 2.677979 GGAGCCAAAACTCCGCGTC 61.678 63.158 4.92 0.00 46.52 5.19
202 209 2.668550 GGAGCCAAAACTCCGCGT 60.669 61.111 4.92 0.00 46.52 6.01
207 214 3.062466 GCCCGGGAGCCAAAACTC 61.062 66.667 29.31 0.00 35.86 3.01
208 215 3.569200 GAGCCCGGGAGCCAAAACT 62.569 63.158 29.31 9.07 0.00 2.66
209 216 3.062466 GAGCCCGGGAGCCAAAAC 61.062 66.667 29.31 2.84 0.00 2.43
210 217 2.837031 GATGAGCCCGGGAGCCAAAA 62.837 60.000 29.31 1.13 0.00 2.44
211 218 3.338250 ATGAGCCCGGGAGCCAAA 61.338 61.111 29.31 2.41 0.00 3.28
212 219 3.797353 GATGAGCCCGGGAGCCAA 61.797 66.667 29.31 4.14 0.00 4.52
213 220 4.804420 AGATGAGCCCGGGAGCCA 62.804 66.667 29.31 18.65 0.00 4.75
214 221 4.247380 CAGATGAGCCCGGGAGCC 62.247 72.222 29.31 12.80 0.00 4.70
215 222 4.925861 GCAGATGAGCCCGGGAGC 62.926 72.222 29.31 16.09 0.00 4.70
216 223 3.473647 TGCAGATGAGCCCGGGAG 61.474 66.667 29.31 0.00 0.00 4.30
217 224 3.785859 GTGCAGATGAGCCCGGGA 61.786 66.667 29.31 2.74 0.00 5.14
218 225 4.864334 GGTGCAGATGAGCCCGGG 62.864 72.222 19.09 19.09 0.00 5.73
219 226 4.864334 GGGTGCAGATGAGCCCGG 62.864 72.222 0.00 0.00 0.00 5.73
220 227 4.100084 TGGGTGCAGATGAGCCCG 62.100 66.667 3.57 0.00 43.89 6.13
221 228 2.439156 GTGGGTGCAGATGAGCCC 60.439 66.667 0.81 0.81 41.42 5.19
222 229 2.821366 CGTGGGTGCAGATGAGCC 60.821 66.667 0.00 0.00 0.00 4.70
223 230 3.503363 GCGTGGGTGCAGATGAGC 61.503 66.667 0.00 0.00 34.15 4.26
224 231 1.812922 GAGCGTGGGTGCAGATGAG 60.813 63.158 0.00 0.00 37.31 2.90
225 232 2.265739 GAGCGTGGGTGCAGATGA 59.734 61.111 0.00 0.00 37.31 2.92
226 233 2.046988 TGAGCGTGGGTGCAGATG 60.047 61.111 0.00 0.00 37.31 2.90
227 234 2.267006 CTGAGCGTGGGTGCAGAT 59.733 61.111 0.00 0.00 37.31 2.90
228 235 4.687215 GCTGAGCGTGGGTGCAGA 62.687 66.667 0.00 0.00 37.31 4.26
229 236 4.994471 TGCTGAGCGTGGGTGCAG 62.994 66.667 0.00 0.00 37.31 4.41
230 237 4.560743 TTGCTGAGCGTGGGTGCA 62.561 61.111 0.00 0.00 37.31 4.57
231 238 2.348605 TTTTTGCTGAGCGTGGGTGC 62.349 55.000 0.00 0.00 0.00 5.01
232 239 1.732917 TTTTTGCTGAGCGTGGGTG 59.267 52.632 0.00 0.00 0.00 4.61
233 240 4.251246 TTTTTGCTGAGCGTGGGT 57.749 50.000 0.00 0.00 0.00 4.51
291 298 8.185505 GCGTCAAATTATCTACCACCATAAAAA 58.814 33.333 0.00 0.00 0.00 1.94
292 299 7.466185 CGCGTCAAATTATCTACCACCATAAAA 60.466 37.037 0.00 0.00 0.00 1.52
293 300 6.018588 CGCGTCAAATTATCTACCACCATAAA 60.019 38.462 0.00 0.00 0.00 1.40
294 301 5.464057 CGCGTCAAATTATCTACCACCATAA 59.536 40.000 0.00 0.00 0.00 1.90
295 302 4.986034 CGCGTCAAATTATCTACCACCATA 59.014 41.667 0.00 0.00 0.00 2.74
296 303 3.807622 CGCGTCAAATTATCTACCACCAT 59.192 43.478 0.00 0.00 0.00 3.55
297 304 3.191669 CGCGTCAAATTATCTACCACCA 58.808 45.455 0.00 0.00 0.00 4.17
298 305 3.000925 CACGCGTCAAATTATCTACCACC 59.999 47.826 9.86 0.00 0.00 4.61
299 306 3.861113 TCACGCGTCAAATTATCTACCAC 59.139 43.478 9.86 0.00 0.00 4.16
300 307 4.109766 CTCACGCGTCAAATTATCTACCA 58.890 43.478 9.86 0.00 0.00 3.25
301 308 3.489785 CCTCACGCGTCAAATTATCTACC 59.510 47.826 9.86 0.00 0.00 3.18
302 309 4.110482 ACCTCACGCGTCAAATTATCTAC 58.890 43.478 9.86 0.00 0.00 2.59
303 310 4.380841 ACCTCACGCGTCAAATTATCTA 57.619 40.909 9.86 0.00 0.00 1.98
304 311 3.247006 ACCTCACGCGTCAAATTATCT 57.753 42.857 9.86 0.00 0.00 1.98
305 312 3.061403 CGTACCTCACGCGTCAAATTATC 60.061 47.826 9.86 0.00 45.03 1.75
306 313 2.855963 CGTACCTCACGCGTCAAATTAT 59.144 45.455 9.86 0.00 45.03 1.28
307 314 2.252747 CGTACCTCACGCGTCAAATTA 58.747 47.619 9.86 0.00 45.03 1.40
308 315 1.065358 CGTACCTCACGCGTCAAATT 58.935 50.000 9.86 0.00 45.03 1.82
309 316 2.733127 CGTACCTCACGCGTCAAAT 58.267 52.632 9.86 0.00 45.03 2.32
310 317 4.231753 CGTACCTCACGCGTCAAA 57.768 55.556 9.86 0.00 45.03 2.69
320 327 1.828979 TGAATTTTGGGGCGTACCTC 58.171 50.000 0.00 0.00 40.03 3.85
321 328 1.890489 GTTGAATTTTGGGGCGTACCT 59.110 47.619 0.00 0.00 40.03 3.08
322 329 1.890489 AGTTGAATTTTGGGGCGTACC 59.110 47.619 0.00 0.00 39.11 3.34
323 330 2.554893 TGAGTTGAATTTTGGGGCGTAC 59.445 45.455 0.00 0.00 0.00 3.67
324 331 2.865079 TGAGTTGAATTTTGGGGCGTA 58.135 42.857 0.00 0.00 0.00 4.42
325 332 1.698506 TGAGTTGAATTTTGGGGCGT 58.301 45.000 0.00 0.00 0.00 5.68
326 333 3.317603 AATGAGTTGAATTTTGGGGCG 57.682 42.857 0.00 0.00 0.00 6.13
327 334 4.640364 TCAAATGAGTTGAATTTTGGGGC 58.360 39.130 0.00 0.00 43.43 5.80
328 335 4.692155 GCTCAAATGAGTTGAATTTTGGGG 59.308 41.667 11.77 0.00 45.67 4.96
329 336 5.178067 GTGCTCAAATGAGTTGAATTTTGGG 59.822 40.000 11.77 0.00 45.67 4.12
330 337 5.178067 GGTGCTCAAATGAGTTGAATTTTGG 59.822 40.000 11.77 0.00 45.67 3.28
331 338 5.987347 AGGTGCTCAAATGAGTTGAATTTTG 59.013 36.000 11.77 0.00 45.67 2.44
332 339 5.987347 CAGGTGCTCAAATGAGTTGAATTTT 59.013 36.000 11.77 0.00 45.67 1.82
333 340 5.302568 TCAGGTGCTCAAATGAGTTGAATTT 59.697 36.000 11.77 0.00 45.67 1.82
334 341 4.828939 TCAGGTGCTCAAATGAGTTGAATT 59.171 37.500 11.77 0.00 45.67 2.17
335 342 4.401022 TCAGGTGCTCAAATGAGTTGAAT 58.599 39.130 11.77 0.00 45.67 2.57
336 343 3.817084 CTCAGGTGCTCAAATGAGTTGAA 59.183 43.478 11.77 0.00 45.67 2.69
337 344 3.405831 CTCAGGTGCTCAAATGAGTTGA 58.594 45.455 11.77 0.00 44.20 3.18
338 345 2.095364 GCTCAGGTGCTCAAATGAGTTG 60.095 50.000 11.77 6.26 43.85 3.16
339 346 2.157738 GCTCAGGTGCTCAAATGAGTT 58.842 47.619 11.77 0.00 43.85 3.01
340 347 1.072806 TGCTCAGGTGCTCAAATGAGT 59.927 47.619 11.77 0.00 43.85 3.41
341 348 1.738350 CTGCTCAGGTGCTCAAATGAG 59.262 52.381 6.05 6.05 44.75 2.90
342 349 1.817357 CTGCTCAGGTGCTCAAATGA 58.183 50.000 0.00 0.00 0.00 2.57
343 350 0.170561 GCTGCTCAGGTGCTCAAATG 59.829 55.000 0.00 0.00 0.00 2.32
344 351 0.037877 AGCTGCTCAGGTGCTCAAAT 59.962 50.000 0.00 0.00 37.82 2.32
345 352 1.453235 AGCTGCTCAGGTGCTCAAA 59.547 52.632 0.00 0.00 37.82 2.69
346 353 3.154787 AGCTGCTCAGGTGCTCAA 58.845 55.556 0.00 0.00 37.82 3.02
349 356 2.980475 GAGAGCTGCTCAGGTGCT 59.020 61.111 29.49 9.44 43.38 4.40
350 357 2.508887 CGAGAGCTGCTCAGGTGC 60.509 66.667 29.49 12.92 44.15 5.01
351 358 2.183811 CCGAGAGCTGCTCAGGTG 59.816 66.667 29.49 15.88 44.15 4.00
352 359 3.768922 GCCGAGAGCTGCTCAGGT 61.769 66.667 30.79 15.51 44.15 4.00
353 360 2.793160 TTTGCCGAGAGCTGCTCAGG 62.793 60.000 29.49 28.90 44.15 3.86
354 361 0.952497 TTTTGCCGAGAGCTGCTCAG 60.952 55.000 29.49 21.79 44.15 3.35
355 362 0.534877 TTTTTGCCGAGAGCTGCTCA 60.535 50.000 29.49 8.15 44.15 4.26
356 363 2.247790 TTTTTGCCGAGAGCTGCTC 58.752 52.632 21.72 21.72 44.23 4.26
357 364 4.481195 TTTTTGCCGAGAGCTGCT 57.519 50.000 0.00 0.00 44.23 4.24
371 378 3.711190 ACAGGCCCTGATTTTGTCTTTTT 59.289 39.130 19.90 0.00 35.18 1.94
372 379 3.308401 ACAGGCCCTGATTTTGTCTTTT 58.692 40.909 19.90 0.00 35.18 2.27
373 380 2.962859 ACAGGCCCTGATTTTGTCTTT 58.037 42.857 19.90 0.00 35.18 2.52
374 381 2.683211 ACAGGCCCTGATTTTGTCTT 57.317 45.000 19.90 0.00 35.18 3.01
375 382 3.806949 TTACAGGCCCTGATTTTGTCT 57.193 42.857 19.90 0.00 35.18 3.41
376 383 4.864704 TTTTACAGGCCCTGATTTTGTC 57.135 40.909 19.90 0.00 35.18 3.18
377 384 5.071653 ACATTTTTACAGGCCCTGATTTTGT 59.928 36.000 19.90 9.97 35.18 2.83
378 385 5.550290 ACATTTTTACAGGCCCTGATTTTG 58.450 37.500 19.90 9.35 35.18 2.44
379 386 5.823861 ACATTTTTACAGGCCCTGATTTT 57.176 34.783 19.90 0.00 35.18 1.82
380 387 7.839200 AGTATACATTTTTACAGGCCCTGATTT 59.161 33.333 19.90 0.00 35.18 2.17
381 388 7.285401 CAGTATACATTTTTACAGGCCCTGATT 59.715 37.037 19.90 0.00 35.18 2.57
382 389 6.772716 CAGTATACATTTTTACAGGCCCTGAT 59.227 38.462 19.90 4.31 35.18 2.90
383 390 6.119536 CAGTATACATTTTTACAGGCCCTGA 58.880 40.000 19.90 0.00 35.18 3.86
384 391 5.885912 ACAGTATACATTTTTACAGGCCCTG 59.114 40.000 9.83 9.83 37.52 4.45
385 392 6.074698 ACAGTATACATTTTTACAGGCCCT 57.925 37.500 5.50 0.00 0.00 5.19
386 393 6.376018 TGAACAGTATACATTTTTACAGGCCC 59.624 38.462 5.50 0.00 0.00 5.80
387 394 7.248437 GTGAACAGTATACATTTTTACAGGCC 58.752 38.462 5.50 0.00 0.00 5.19
388 395 6.959311 CGTGAACAGTATACATTTTTACAGGC 59.041 38.462 5.50 0.00 0.00 4.85
389 396 6.959311 GCGTGAACAGTATACATTTTTACAGG 59.041 38.462 5.50 3.47 0.00 4.00
390 397 7.477422 GTGCGTGAACAGTATACATTTTTACAG 59.523 37.037 5.50 1.34 0.00 2.74
391 398 7.171848 AGTGCGTGAACAGTATACATTTTTACA 59.828 33.333 5.50 0.00 0.00 2.41
392 399 7.477422 CAGTGCGTGAACAGTATACATTTTTAC 59.523 37.037 5.50 1.57 0.00 2.01
393 400 7.171848 ACAGTGCGTGAACAGTATACATTTTTA 59.828 33.333 5.50 0.00 0.00 1.52
394 401 6.017440 ACAGTGCGTGAACAGTATACATTTTT 60.017 34.615 5.50 0.00 0.00 1.94
395 402 5.468746 ACAGTGCGTGAACAGTATACATTTT 59.531 36.000 5.50 0.00 0.00 1.82
396 403 4.994852 ACAGTGCGTGAACAGTATACATTT 59.005 37.500 5.50 0.00 0.00 2.32
397 404 4.566004 ACAGTGCGTGAACAGTATACATT 58.434 39.130 5.50 0.00 0.00 2.71
398 405 4.188247 ACAGTGCGTGAACAGTATACAT 57.812 40.909 5.50 0.00 0.00 2.29
399 406 3.653539 ACAGTGCGTGAACAGTATACA 57.346 42.857 5.50 0.00 0.00 2.29
400 407 4.985044 AAACAGTGCGTGAACAGTATAC 57.015 40.909 0.00 0.00 0.00 1.47
401 408 5.050634 GTCAAAACAGTGCGTGAACAGTATA 60.051 40.000 0.00 0.00 0.00 1.47
402 409 3.874543 TCAAAACAGTGCGTGAACAGTAT 59.125 39.130 0.00 0.00 0.00 2.12
403 410 3.062909 GTCAAAACAGTGCGTGAACAGTA 59.937 43.478 0.00 0.00 0.00 2.74
404 411 2.080693 TCAAAACAGTGCGTGAACAGT 58.919 42.857 0.00 0.00 0.00 3.55
405 412 2.440501 GTCAAAACAGTGCGTGAACAG 58.559 47.619 0.00 0.00 0.00 3.16
406 413 1.131504 GGTCAAAACAGTGCGTGAACA 59.868 47.619 2.35 0.00 0.00 3.18
407 414 1.400494 AGGTCAAAACAGTGCGTGAAC 59.600 47.619 0.00 0.00 0.00 3.18
408 415 1.400142 CAGGTCAAAACAGTGCGTGAA 59.600 47.619 0.00 0.00 0.00 3.18
409 416 1.013596 CAGGTCAAAACAGTGCGTGA 58.986 50.000 0.00 0.00 0.00 4.35
410 417 1.013596 TCAGGTCAAAACAGTGCGTG 58.986 50.000 0.00 0.00 0.00 5.34
411 418 1.967319 ATCAGGTCAAAACAGTGCGT 58.033 45.000 0.00 0.00 0.00 5.24
412 419 3.044986 CAAATCAGGTCAAAACAGTGCG 58.955 45.455 0.00 0.00 0.00 5.34
413 420 4.044426 GACAAATCAGGTCAAAACAGTGC 58.956 43.478 0.00 0.00 35.36 4.40
414 421 5.505173 AGACAAATCAGGTCAAAACAGTG 57.495 39.130 0.00 0.00 37.74 3.66
415 422 6.530019 AAAGACAAATCAGGTCAAAACAGT 57.470 33.333 0.00 0.00 37.74 3.55
416 423 7.832503 AAAAAGACAAATCAGGTCAAAACAG 57.167 32.000 0.00 0.00 37.74 3.16
437 444 2.299013 TCTGAGTAGCTCTCGGCAAAAA 59.701 45.455 13.94 0.00 46.16 1.94
438 445 1.893137 TCTGAGTAGCTCTCGGCAAAA 59.107 47.619 13.94 0.00 46.16 2.44
439 446 1.545841 TCTGAGTAGCTCTCGGCAAA 58.454 50.000 13.94 0.00 46.16 3.68
440 447 1.406898 CATCTGAGTAGCTCTCGGCAA 59.593 52.381 13.94 2.94 46.16 4.52
441 448 1.028130 CATCTGAGTAGCTCTCGGCA 58.972 55.000 13.94 6.78 46.16 5.69
442 449 1.001815 GACATCTGAGTAGCTCTCGGC 60.002 57.143 13.94 0.00 46.16 5.54
444 451 2.293170 TGGACATCTGAGTAGCTCTCG 58.707 52.381 0.00 0.00 45.46 4.04
445 452 4.727507 TTTGGACATCTGAGTAGCTCTC 57.272 45.455 0.00 0.00 43.03 3.20
446 453 6.382570 ACTTATTTGGACATCTGAGTAGCTCT 59.617 38.462 0.00 0.00 0.00 4.09
447 454 6.578023 ACTTATTTGGACATCTGAGTAGCTC 58.422 40.000 0.00 0.00 0.00 4.09
448 455 6.552445 ACTTATTTGGACATCTGAGTAGCT 57.448 37.500 0.00 0.00 0.00 3.32
449 456 6.818644 TCAACTTATTTGGACATCTGAGTAGC 59.181 38.462 0.00 0.00 35.69 3.58
450 457 8.777865 TTCAACTTATTTGGACATCTGAGTAG 57.222 34.615 0.00 0.00 35.69 2.57
451 458 9.739276 AATTCAACTTATTTGGACATCTGAGTA 57.261 29.630 0.00 0.00 35.69 2.59
452 459 8.641498 AATTCAACTTATTTGGACATCTGAGT 57.359 30.769 0.00 0.00 35.69 3.41
453 460 9.918630 AAAATTCAACTTATTTGGACATCTGAG 57.081 29.630 0.00 0.00 35.69 3.35
454 461 9.695526 CAAAATTCAACTTATTTGGACATCTGA 57.304 29.630 0.00 0.00 35.69 3.27
463 470 4.142924 GCGCCCCAAAATTCAACTTATTTG 60.143 41.667 0.00 0.00 36.42 2.32
464 471 4.000325 GCGCCCCAAAATTCAACTTATTT 59.000 39.130 0.00 0.00 0.00 1.40
465 472 3.007398 TGCGCCCCAAAATTCAACTTATT 59.993 39.130 4.18 0.00 0.00 1.40
466 473 2.564947 TGCGCCCCAAAATTCAACTTAT 59.435 40.909 4.18 0.00 0.00 1.73
467 474 1.964223 TGCGCCCCAAAATTCAACTTA 59.036 42.857 4.18 0.00 0.00 2.24
468 475 0.755686 TGCGCCCCAAAATTCAACTT 59.244 45.000 4.18 0.00 0.00 2.66
469 476 0.033366 GTGCGCCCCAAAATTCAACT 59.967 50.000 4.18 0.00 0.00 3.16
470 477 0.948623 GGTGCGCCCCAAAATTCAAC 60.949 55.000 3.18 0.00 0.00 3.18
471 478 1.118356 AGGTGCGCCCCAAAATTCAA 61.118 50.000 12.68 0.00 34.57 2.69
472 479 1.531739 GAGGTGCGCCCCAAAATTCA 61.532 55.000 12.68 0.00 34.57 2.57
473 480 1.215382 GAGGTGCGCCCCAAAATTC 59.785 57.895 12.68 0.00 34.57 2.17
474 481 1.532794 TGAGGTGCGCCCCAAAATT 60.533 52.632 12.68 0.00 34.57 1.82
475 482 2.117206 TGAGGTGCGCCCCAAAAT 59.883 55.556 12.68 0.00 34.57 1.82
476 483 2.909965 GTGAGGTGCGCCCCAAAA 60.910 61.111 12.68 0.00 34.57 2.44
485 492 0.793861 TAATTTGACGCGTGAGGTGC 59.206 50.000 20.70 0.06 0.00 5.01
486 493 2.930040 AGATAATTTGACGCGTGAGGTG 59.070 45.455 20.70 0.00 0.00 4.00
487 494 3.247006 AGATAATTTGACGCGTGAGGT 57.753 42.857 20.70 0.00 0.00 3.85
488 495 3.489785 GGTAGATAATTTGACGCGTGAGG 59.510 47.826 20.70 0.00 0.00 3.86
489 496 4.026804 GTGGTAGATAATTTGACGCGTGAG 60.027 45.833 20.70 0.00 0.00 3.51
490 497 3.861113 GTGGTAGATAATTTGACGCGTGA 59.139 43.478 20.70 4.74 0.00 4.35
491 498 3.000925 GGTGGTAGATAATTTGACGCGTG 59.999 47.826 20.70 0.00 0.00 5.34
492 499 3.192466 GGTGGTAGATAATTTGACGCGT 58.808 45.455 13.85 13.85 0.00 6.01
493 500 3.000925 GTGGTGGTAGATAATTTGACGCG 59.999 47.826 3.53 3.53 0.00 6.01
494 501 3.936453 TGTGGTGGTAGATAATTTGACGC 59.064 43.478 0.00 0.00 0.00 5.19
495 502 6.489127 TTTGTGGTGGTAGATAATTTGACG 57.511 37.500 0.00 0.00 0.00 4.35
563 570 1.518056 CTGCTCCCGCTCAGCAAAAA 61.518 55.000 0.00 0.00 46.22 1.94
564 571 1.968017 CTGCTCCCGCTCAGCAAAA 60.968 57.895 0.00 0.00 46.22 2.44
565 572 2.189191 ATCTGCTCCCGCTCAGCAAA 62.189 55.000 0.00 0.00 46.22 3.68
566 573 2.663075 ATCTGCTCCCGCTCAGCAA 61.663 57.895 0.00 0.00 46.22 3.91
567 574 3.079478 ATCTGCTCCCGCTCAGCA 61.079 61.111 0.00 1.68 44.80 4.41
568 575 2.588314 CATCTGCTCCCGCTCAGC 60.588 66.667 0.00 0.00 36.97 4.26
569 576 1.067749 CTCATCTGCTCCCGCTCAG 59.932 63.158 0.00 0.00 36.97 3.35
570 577 3.086391 GCTCATCTGCTCCCGCTCA 62.086 63.158 0.00 0.00 36.97 4.26
571 578 2.280052 GCTCATCTGCTCCCGCTC 60.280 66.667 0.00 0.00 36.97 5.03
572 579 3.859414 GGCTCATCTGCTCCCGCT 61.859 66.667 0.00 0.00 36.97 5.52
573 580 4.925861 GGGCTCATCTGCTCCCGC 62.926 72.222 0.00 0.00 0.00 6.13
575 582 4.247380 CCGGGCTCATCTGCTCCC 62.247 72.222 0.00 0.00 35.42 4.30
576 583 4.247380 CCCGGGCTCATCTGCTCC 62.247 72.222 8.08 0.00 0.00 4.70
577 584 4.925861 GCCCGGGCTCATCTGCTC 62.926 72.222 38.76 4.71 38.26 4.26
589 596 0.764890 TAATTCATCCTGGAGCCCGG 59.235 55.000 1.52 0.00 0.00 5.73
590 597 2.704572 GATAATTCATCCTGGAGCCCG 58.295 52.381 1.52 0.00 0.00 6.13
591 598 2.616510 CCGATAATTCATCCTGGAGCCC 60.617 54.545 1.52 0.00 0.00 5.19
592 599 2.039084 ACCGATAATTCATCCTGGAGCC 59.961 50.000 1.52 0.00 0.00 4.70
593 600 3.409026 ACCGATAATTCATCCTGGAGC 57.591 47.619 1.52 0.00 0.00 4.70
594 601 7.170393 TGTATACCGATAATTCATCCTGGAG 57.830 40.000 1.52 0.00 0.00 3.86
595 602 7.733773 ATGTATACCGATAATTCATCCTGGA 57.266 36.000 0.00 0.00 0.00 3.86
607 614 9.665719 TGTAACCGTAGAATATGTATACCGATA 57.334 33.333 0.00 0.00 0.00 2.92
608 615 8.454106 GTGTAACCGTAGAATATGTATACCGAT 58.546 37.037 0.00 0.00 0.00 4.18
609 616 7.443879 TGTGTAACCGTAGAATATGTATACCGA 59.556 37.037 0.00 0.00 34.36 4.69
610 617 7.535258 GTGTGTAACCGTAGAATATGTATACCG 59.465 40.741 0.00 0.00 34.36 4.02
611 618 7.809806 GGTGTGTAACCGTAGAATATGTATACC 59.190 40.741 0.00 0.00 39.81 2.73
612 619 8.733857 GGTGTGTAACCGTAGAATATGTATAC 57.266 38.462 0.00 0.00 39.81 1.47
773 821 9.081997 CAAAGATACAAACAGTCTTCTAGCTAG 57.918 37.037 15.01 15.01 31.37 3.42
774 822 8.035394 CCAAAGATACAAACAGTCTTCTAGCTA 58.965 37.037 0.00 0.00 31.37 3.32
775 823 6.876257 CCAAAGATACAAACAGTCTTCTAGCT 59.124 38.462 0.00 0.00 31.37 3.32
776 824 6.651225 ACCAAAGATACAAACAGTCTTCTAGC 59.349 38.462 0.00 0.00 31.37 3.42
803 881 4.767409 GTGTCAAAGGGGCTTCTCTTTTAT 59.233 41.667 0.00 0.00 31.60 1.40
908 1247 2.003937 TATATGTACTGCAGGCCGGA 57.996 50.000 19.93 0.02 0.00 5.14
915 1254 5.356426 AGCAACGAACATATATGTACTGCA 58.644 37.500 26.48 0.00 40.80 4.41
930 1276 0.179059 TTGAGGCTGTGAGCAACGAA 60.179 50.000 0.00 0.00 44.75 3.85
951 1297 3.021695 TGGATCGGTACTAGAACTGTGG 58.978 50.000 0.00 0.00 0.00 4.17
966 1314 2.028130 AGAGTAGCTTCCTGTGGATCG 58.972 52.381 0.00 0.00 0.00 3.69
1143 1502 1.405105 ACCCATAAATCGTGCATGCAC 59.595 47.619 35.76 35.76 43.01 4.57
1159 1521 6.428083 TCTTGTGAACAGAAACTATACCCA 57.572 37.500 0.00 0.00 0.00 4.51
1163 1525 9.135843 CGTGTATTCTTGTGAACAGAAACTATA 57.864 33.333 0.00 0.00 34.71 1.31
1195 1557 9.480053 AATCAACAAACCAAGAAAATACATCTG 57.520 29.630 0.00 0.00 0.00 2.90
1200 1562 8.272866 CGGAAAATCAACAAACCAAGAAAATAC 58.727 33.333 0.00 0.00 0.00 1.89
1251 1613 5.132043 TGAAGTGGGGAAAAGGTAAGAAA 57.868 39.130 0.00 0.00 0.00 2.52
1289 1651 1.891060 GACGCGAGCAGGTTCTTGTG 61.891 60.000 15.93 0.00 34.84 3.33
1373 1735 1.535437 CGTATACTTGGGACGCCTGTC 60.535 57.143 0.56 0.00 44.72 3.51
1546 1935 0.367887 CGCGCGATACATCCATCATG 59.632 55.000 28.94 0.00 38.64 3.07
1577 1975 2.890945 TCGTCACATATCCCATGATCGT 59.109 45.455 0.00 0.00 32.18 3.73
1759 2206 6.591935 TCCTCAGGTGATGTTCCAATATAAC 58.408 40.000 0.00 0.00 0.00 1.89
2149 2661 5.062308 GGAAGTCAGTGTATGTTTGATCGAC 59.938 44.000 0.00 0.00 0.00 4.20
2256 2768 3.315191 CAGAAAAGAAGAACCGGAAGCAA 59.685 43.478 9.46 0.00 0.00 3.91
2343 2855 6.330250 CCTCTATTTTCTCCTATTCCTCCCAA 59.670 42.308 0.00 0.00 0.00 4.12
2484 2996 0.388520 GCCAATCGGACAACAAAGGC 60.389 55.000 0.00 0.00 0.00 4.35
2497 3009 5.053145 ACTTTGATGTCTATCGAGCCAATC 58.947 41.667 0.00 0.00 36.04 2.67


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

AutoCloner maintained by Alex Coulton.