Multiple sequence alignment - TraesCS5A01G445800

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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 TraesCS5A01G445800 chr5A 100.000 2273 0 0 1 2273 625907587 625909859 0.000000e+00 4198.0
1 TraesCS5A01G445800 chr5A 85.294 102 8 7 1755 1853 616050366 616050463 5.170000e-17 99.0
2 TraesCS5A01G445800 chr3B 93.424 1612 76 5 459 2046 631966003 631964398 0.000000e+00 2362.0
3 TraesCS5A01G445800 chr3B 83.409 1097 128 21 498 1570 56750621 56751687 0.000000e+00 968.0
4 TraesCS5A01G445800 chr3B 94.898 98 4 1 2060 2157 631964414 631964318 3.910000e-33 152.0
5 TraesCS5A01G445800 chr4D 93.238 1612 80 5 459 2046 442616693 442615087 0.000000e+00 2346.0
6 TraesCS5A01G445800 chr4D 96.729 214 6 1 2060 2273 442615103 442614891 2.780000e-94 355.0
7 TraesCS5A01G445800 chr4D 85.526 76 3 7 1959 2031 322908013 322908083 3.130000e-09 73.1
8 TraesCS5A01G445800 chr4D 97.143 35 1 0 2164 2198 442615029 442614995 2.440000e-05 60.2
9 TraesCS5A01G445800 chr2B 93.035 1608 73 9 460 2043 105806257 105807849 0.000000e+00 2313.0
10 TraesCS5A01G445800 chr2B 95.536 112 5 0 2060 2171 105807836 105807947 1.790000e-41 180.0
11 TraesCS5A01G445800 chr2B 89.130 46 5 0 3 48 184514254 184514299 8.770000e-05 58.4
12 TraesCS5A01G445800 chr6D 91.620 1611 84 14 461 2046 337843270 337844854 0.000000e+00 2180.0
13 TraesCS5A01G445800 chr6D 98.214 112 2 0 2060 2171 337844838 337844949 1.780000e-46 196.0
14 TraesCS5A01G445800 chr6D 95.455 110 5 0 2164 2273 337844913 337845022 2.320000e-40 176.0
15 TraesCS5A01G445800 chr7D 91.643 1065 59 8 668 1712 45657961 45659015 0.000000e+00 1447.0
16 TraesCS5A01G445800 chr7D 96.346 301 6 2 1746 2046 45659016 45659311 7.300000e-135 490.0
17 TraesCS5A01G445800 chr7D 96.729 214 6 1 2060 2273 45659295 45659507 2.780000e-94 355.0
18 TraesCS5A01G445800 chr7D 94.495 218 12 0 459 676 45657532 45657749 1.010000e-88 337.0
19 TraesCS5A01G445800 chr7A 89.448 815 49 9 698 1485 579816755 579815951 0.000000e+00 994.0
20 TraesCS5A01G445800 chr7A 94.415 573 20 7 1480 2046 579811722 579811156 0.000000e+00 870.0
21 TraesCS5A01G445800 chr7A 94.355 248 14 0 455 702 579839582 579839335 4.580000e-102 381.0
22 TraesCS5A01G445800 chr7A 97.842 139 2 1 2060 2198 579811172 579811035 2.920000e-59 239.0
23 TraesCS5A01G445800 chr7A 92.908 141 8 1 2135 2273 579811069 579810929 1.060000e-48 204.0
24 TraesCS5A01G445800 chr7A 97.297 37 1 0 2164 2200 579811098 579811062 1.880000e-06 63.9
25 TraesCS5A01G445800 chr3D 84.811 981 110 15 612 1570 34689829 34688866 0.000000e+00 950.0
26 TraesCS5A01G445800 chr3D 90.574 488 34 4 1567 2046 34610264 34609781 8.860000e-179 636.0
27 TraesCS5A01G445800 chr1D 91.360 706 35 4 1347 2046 9331192 9331877 0.000000e+00 942.0
28 TraesCS5A01G445800 chr1D 95.794 214 7 2 2060 2273 9331861 9332072 6.010000e-91 344.0
29 TraesCS5A01G445800 chr7B 92.308 455 31 4 502 955 590100475 590100926 0.000000e+00 643.0
30 TraesCS5A01G445800 chr2A 91.667 48 4 0 6 53 398417675 398417628 1.460000e-07 67.6
31 TraesCS5A01G445800 chr6A 90.196 51 4 1 3 52 585414237 585414287 5.240000e-07 65.8


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 TraesCS5A01G445800 chr5A 625907587 625909859 2272 False 4198.000000 4198 100.000000 1 2273 1 chr5A.!!$F2 2272
1 TraesCS5A01G445800 chr3B 631964318 631966003 1685 True 1257.000000 2362 94.161000 459 2157 2 chr3B.!!$R1 1698
2 TraesCS5A01G445800 chr3B 56750621 56751687 1066 False 968.000000 968 83.409000 498 1570 1 chr3B.!!$F1 1072
3 TraesCS5A01G445800 chr4D 442614891 442616693 1802 True 920.400000 2346 95.703333 459 2273 3 chr4D.!!$R1 1814
4 TraesCS5A01G445800 chr2B 105806257 105807947 1690 False 1246.500000 2313 94.285500 460 2171 2 chr2B.!!$F2 1711
5 TraesCS5A01G445800 chr6D 337843270 337845022 1752 False 850.666667 2180 95.096333 461 2273 3 chr6D.!!$F1 1812
6 TraesCS5A01G445800 chr7D 45657532 45659507 1975 False 657.250000 1447 94.803250 459 2273 4 chr7D.!!$F1 1814
7 TraesCS5A01G445800 chr7A 579815951 579816755 804 True 994.000000 994 89.448000 698 1485 1 chr7A.!!$R1 787
8 TraesCS5A01G445800 chr7A 579810929 579811722 793 True 344.225000 870 95.615500 1480 2273 4 chr7A.!!$R3 793
9 TraesCS5A01G445800 chr3D 34688866 34689829 963 True 950.000000 950 84.811000 612 1570 1 chr3D.!!$R2 958
10 TraesCS5A01G445800 chr1D 9331192 9332072 880 False 643.000000 942 93.577000 1347 2273 2 chr1D.!!$F1 926

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
442 443 0.036294 GCGAGTAGTTTCTTGGGCCT 60.036 55.0 4.53 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 1714 0.868406 CGAAGGAAACTGCTGGACAC 59.132 55.0 0.0 0.0 42.68 3.67 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
94 95 4.790765 TGATATCGAGCTATTGAGTGGG 57.209 45.455 0.00 0.00 0.00 4.61
95 96 4.152647 TGATATCGAGCTATTGAGTGGGT 58.847 43.478 0.00 0.00 0.00 4.51
96 97 4.218635 TGATATCGAGCTATTGAGTGGGTC 59.781 45.833 0.00 0.00 33.02 4.46
97 98 1.847328 TCGAGCTATTGAGTGGGTCA 58.153 50.000 0.00 0.00 35.76 4.02
126 127 4.861102 CTGAAGATCAGGTTGGCTTTTT 57.139 40.909 0.00 0.00 40.71 1.94
160 161 9.821240 AGCTATATATATGGCTCATACTTAGCT 57.179 33.333 23.69 13.17 45.75 3.32
168 169 9.853177 ATATGGCTCATACTTAGCTAACTTTTT 57.147 29.630 0.86 0.00 39.97 1.94
200 201 9.970395 TCAGTCTTAAGTTGAACTAAAATACGA 57.030 29.630 0.00 0.52 0.00 3.43
217 218 8.816640 AAAATACGAATCAATTTCAAACAGCT 57.183 26.923 0.00 0.00 33.66 4.24
218 219 8.452989 AAATACGAATCAATTTCAAACAGCTC 57.547 30.769 0.00 0.00 33.66 4.09
219 220 5.437289 ACGAATCAATTTCAAACAGCTCA 57.563 34.783 0.00 0.00 33.66 4.26
220 221 5.215160 ACGAATCAATTTCAAACAGCTCAC 58.785 37.500 0.00 0.00 33.66 3.51
221 222 4.319115 CGAATCAATTTCAAACAGCTCACG 59.681 41.667 0.00 0.00 33.66 4.35
222 223 5.437289 AATCAATTTCAAACAGCTCACGA 57.563 34.783 0.00 0.00 0.00 4.35
223 224 4.472691 TCAATTTCAAACAGCTCACGAG 57.527 40.909 0.00 0.00 0.00 4.18
224 225 7.801482 GAATCAATTTCAAACAGCTCACGAGC 61.801 42.308 11.14 11.14 43.09 5.03
237 238 3.448686 CTCACGAGCCTCGATATTTTGT 58.551 45.455 22.80 0.00 43.74 2.83
238 239 3.186909 TCACGAGCCTCGATATTTTGTG 58.813 45.455 22.80 5.92 43.74 3.33
239 240 2.285220 CACGAGCCTCGATATTTTGTGG 59.715 50.000 22.80 0.00 43.74 4.17
240 241 1.261619 CGAGCCTCGATATTTTGTGGC 59.738 52.381 8.82 8.07 43.74 5.01
241 242 2.288666 GAGCCTCGATATTTTGTGGCA 58.711 47.619 15.99 0.00 44.92 4.92
242 243 2.017049 AGCCTCGATATTTTGTGGCAC 58.983 47.619 11.55 11.55 44.92 5.01
243 244 1.065551 GCCTCGATATTTTGTGGCACC 59.934 52.381 16.26 0.00 42.92 5.01
244 245 1.676006 CCTCGATATTTTGTGGCACCC 59.324 52.381 16.26 0.00 0.00 4.61
245 246 2.643551 CTCGATATTTTGTGGCACCCT 58.356 47.619 16.26 0.00 0.00 4.34
246 247 3.433031 CCTCGATATTTTGTGGCACCCTA 60.433 47.826 16.26 0.00 0.00 3.53
247 248 4.389374 CTCGATATTTTGTGGCACCCTAT 58.611 43.478 16.26 7.84 0.00 2.57
248 249 4.385825 TCGATATTTTGTGGCACCCTATC 58.614 43.478 16.26 13.65 0.00 2.08
249 250 4.102524 TCGATATTTTGTGGCACCCTATCT 59.897 41.667 16.26 0.00 0.00 1.98
250 251 5.305902 TCGATATTTTGTGGCACCCTATCTA 59.694 40.000 16.26 5.75 0.00 1.98
251 252 5.408604 CGATATTTTGTGGCACCCTATCTAC 59.591 44.000 16.26 0.09 0.00 2.59
252 253 2.684001 TTTGTGGCACCCTATCTACG 57.316 50.000 16.26 0.00 0.00 3.51
253 254 1.563924 TTGTGGCACCCTATCTACGT 58.436 50.000 16.26 0.00 0.00 3.57
254 255 0.821517 TGTGGCACCCTATCTACGTG 59.178 55.000 16.26 0.00 0.00 4.49
255 256 1.108776 GTGGCACCCTATCTACGTGA 58.891 55.000 6.29 0.00 0.00 4.35
256 257 1.108776 TGGCACCCTATCTACGTGAC 58.891 55.000 0.00 0.00 36.00 3.67
257 258 1.108776 GGCACCCTATCTACGTGACA 58.891 55.000 0.00 0.00 35.50 3.58
258 259 1.479323 GGCACCCTATCTACGTGACAA 59.521 52.381 0.00 0.00 35.50 3.18
259 260 2.102588 GGCACCCTATCTACGTGACAAT 59.897 50.000 0.00 0.00 35.50 2.71
260 261 3.319972 GGCACCCTATCTACGTGACAATA 59.680 47.826 0.00 0.00 35.50 1.90
261 262 4.021368 GGCACCCTATCTACGTGACAATAT 60.021 45.833 0.00 0.00 35.50 1.28
262 263 5.510861 GGCACCCTATCTACGTGACAATATT 60.511 44.000 0.00 0.00 35.50 1.28
263 264 6.294899 GGCACCCTATCTACGTGACAATATTA 60.295 42.308 0.00 0.00 35.50 0.98
264 265 7.321153 GCACCCTATCTACGTGACAATATTAT 58.679 38.462 0.00 0.00 0.00 1.28
265 266 7.275779 GCACCCTATCTACGTGACAATATTATG 59.724 40.741 0.00 0.00 0.00 1.90
266 267 7.759886 CACCCTATCTACGTGACAATATTATGG 59.240 40.741 0.00 0.00 0.00 2.74
267 268 6.757010 CCCTATCTACGTGACAATATTATGGC 59.243 42.308 0.00 0.00 0.00 4.40
268 269 7.320399 CCTATCTACGTGACAATATTATGGCA 58.680 38.462 0.00 0.00 35.49 4.92
281 282 3.159615 TGGCACACATCTCCAGCA 58.840 55.556 0.00 0.00 0.00 4.41
282 283 1.302752 TGGCACACATCTCCAGCAC 60.303 57.895 0.00 0.00 0.00 4.40
283 284 1.302752 GGCACACATCTCCAGCACA 60.303 57.895 0.00 0.00 0.00 4.57
284 285 0.679002 GGCACACATCTCCAGCACAT 60.679 55.000 0.00 0.00 0.00 3.21
285 286 1.407299 GGCACACATCTCCAGCACATA 60.407 52.381 0.00 0.00 0.00 2.29
286 287 2.358957 GCACACATCTCCAGCACATAA 58.641 47.619 0.00 0.00 0.00 1.90
287 288 2.096496 GCACACATCTCCAGCACATAAC 59.904 50.000 0.00 0.00 0.00 1.89
288 289 3.603532 CACACATCTCCAGCACATAACT 58.396 45.455 0.00 0.00 0.00 2.24
289 290 3.373130 CACACATCTCCAGCACATAACTG 59.627 47.826 0.00 0.00 34.82 3.16
296 297 2.768253 CAGCACATAACTGGAGGTGA 57.232 50.000 0.00 0.00 34.13 4.02
297 298 2.625737 CAGCACATAACTGGAGGTGAG 58.374 52.381 0.00 0.00 34.13 3.51
298 299 2.234661 CAGCACATAACTGGAGGTGAGA 59.765 50.000 0.00 0.00 34.13 3.27
299 300 2.499289 AGCACATAACTGGAGGTGAGAG 59.501 50.000 0.00 0.00 33.16 3.20
300 301 2.234908 GCACATAACTGGAGGTGAGAGT 59.765 50.000 0.00 0.00 33.16 3.24
301 302 3.677424 GCACATAACTGGAGGTGAGAGTC 60.677 52.174 0.00 0.00 33.16 3.36
302 303 3.100671 ACATAACTGGAGGTGAGAGTCC 58.899 50.000 0.00 0.00 0.00 3.85
303 304 1.835494 TAACTGGAGGTGAGAGTCCG 58.165 55.000 0.00 0.00 35.37 4.79
304 305 0.900647 AACTGGAGGTGAGAGTCCGG 60.901 60.000 0.00 0.00 43.93 5.14
305 306 1.000771 CTGGAGGTGAGAGTCCGGA 60.001 63.158 0.00 0.00 41.23 5.14
306 307 1.304217 TGGAGGTGAGAGTCCGGAC 60.304 63.158 27.67 27.67 35.37 4.79
307 308 1.000646 GGAGGTGAGAGTCCGGACT 60.001 63.158 36.89 36.89 45.84 3.85
308 309 0.255318 GGAGGTGAGAGTCCGGACTA 59.745 60.000 36.38 19.40 42.66 2.59
309 310 1.670791 GAGGTGAGAGTCCGGACTAG 58.329 60.000 36.38 0.00 42.66 2.57
310 311 0.993470 AGGTGAGAGTCCGGACTAGT 59.007 55.000 36.38 26.12 42.66 2.57
311 312 1.355043 AGGTGAGAGTCCGGACTAGTT 59.645 52.381 36.38 24.05 42.66 2.24
312 313 2.169330 GGTGAGAGTCCGGACTAGTTT 58.831 52.381 36.38 21.55 42.66 2.66
313 314 2.561858 GGTGAGAGTCCGGACTAGTTTT 59.438 50.000 36.38 19.09 42.66 2.43
314 315 3.760684 GGTGAGAGTCCGGACTAGTTTTA 59.239 47.826 36.38 16.71 42.66 1.52
315 316 4.401837 GGTGAGAGTCCGGACTAGTTTTAT 59.598 45.833 36.38 13.11 42.66 1.40
316 317 5.105432 GGTGAGAGTCCGGACTAGTTTTATT 60.105 44.000 36.38 12.29 42.66 1.40
317 318 6.096001 GGTGAGAGTCCGGACTAGTTTTATTA 59.904 42.308 36.38 12.63 42.66 0.98
318 319 7.201893 GGTGAGAGTCCGGACTAGTTTTATTAT 60.202 40.741 36.38 10.88 42.66 1.28
319 320 8.196103 GTGAGAGTCCGGACTAGTTTTATTATT 58.804 37.037 36.38 10.66 42.66 1.40
320 321 9.412460 TGAGAGTCCGGACTAGTTTTATTATTA 57.588 33.333 36.38 3.34 42.66 0.98
349 350 2.162716 GACAAGTGGTCATCGTGCC 58.837 57.895 0.00 0.00 46.19 5.01
350 351 1.298859 GACAAGTGGTCATCGTGCCC 61.299 60.000 0.00 0.00 46.19 5.36
351 352 1.302431 CAAGTGGTCATCGTGCCCA 60.302 57.895 0.00 0.00 0.00 5.36
352 353 0.677731 CAAGTGGTCATCGTGCCCAT 60.678 55.000 0.00 0.00 0.00 4.00
353 354 0.677731 AAGTGGTCATCGTGCCCATG 60.678 55.000 0.00 0.00 0.00 3.66
354 355 1.078497 GTGGTCATCGTGCCCATGA 60.078 57.895 0.00 0.00 0.00 3.07
355 356 1.078497 TGGTCATCGTGCCCATGAC 60.078 57.895 10.04 10.04 46.50 3.06
356 357 4.615901 GTCATCGTGCCCATGACA 57.384 55.556 12.57 0.00 46.48 3.58
357 358 2.387309 GTCATCGTGCCCATGACAG 58.613 57.895 12.57 0.00 46.48 3.51
358 359 0.108186 GTCATCGTGCCCATGACAGA 60.108 55.000 12.57 0.00 46.48 3.41
359 360 0.108186 TCATCGTGCCCATGACAGAC 60.108 55.000 0.00 0.00 0.00 3.51
360 361 1.091771 CATCGTGCCCATGACAGACC 61.092 60.000 0.00 0.00 0.00 3.85
361 362 2.257409 ATCGTGCCCATGACAGACCC 62.257 60.000 0.00 0.00 0.00 4.46
362 363 2.044946 GTGCCCATGACAGACCCC 60.045 66.667 0.00 0.00 0.00 4.95
363 364 3.716195 TGCCCATGACAGACCCCG 61.716 66.667 0.00 0.00 0.00 5.73
364 365 3.399181 GCCCATGACAGACCCCGA 61.399 66.667 0.00 0.00 0.00 5.14
365 366 2.903357 CCCATGACAGACCCCGAG 59.097 66.667 0.00 0.00 0.00 4.63
366 367 1.685765 CCCATGACAGACCCCGAGA 60.686 63.158 0.00 0.00 0.00 4.04
367 368 1.680522 CCCATGACAGACCCCGAGAG 61.681 65.000 0.00 0.00 0.00 3.20
385 386 6.249035 CGAGAGGATTCTTATAGTCCAGAC 57.751 45.833 0.00 0.00 34.42 3.51
386 387 6.001460 CGAGAGGATTCTTATAGTCCAGACT 58.999 44.000 5.50 5.50 38.44 3.24
387 388 7.162761 CGAGAGGATTCTTATAGTCCAGACTA 58.837 42.308 9.84 9.84 39.86 2.59
388 389 7.333423 CGAGAGGATTCTTATAGTCCAGACTAG 59.667 44.444 12.72 2.26 39.36 2.57
389 390 8.052621 AGAGGATTCTTATAGTCCAGACTAGT 57.947 38.462 12.72 0.00 45.94 2.57
390 391 7.942341 AGAGGATTCTTATAGTCCAGACTAGTG 59.058 40.741 12.72 6.08 45.94 2.74
391 392 7.007723 AGGATTCTTATAGTCCAGACTAGTGG 58.992 42.308 12.72 0.00 45.94 4.00
392 393 6.778559 GGATTCTTATAGTCCAGACTAGTGGT 59.221 42.308 12.72 0.00 45.94 4.16
393 394 7.040271 GGATTCTTATAGTCCAGACTAGTGGTC 60.040 44.444 12.72 0.00 45.94 4.02
394 395 6.323210 TCTTATAGTCCAGACTAGTGGTCA 57.677 41.667 12.72 0.00 45.94 4.02
395 396 6.120905 TCTTATAGTCCAGACTAGTGGTCAC 58.879 44.000 12.72 0.00 45.94 3.67
396 397 1.926108 AGTCCAGACTAGTGGTCACC 58.074 55.000 9.52 0.00 46.72 4.02
397 398 1.429687 AGTCCAGACTAGTGGTCACCT 59.570 52.381 9.52 0.00 46.72 4.00
398 399 1.819903 GTCCAGACTAGTGGTCACCTC 59.180 57.143 9.52 0.00 46.72 3.85
399 400 1.187087 CCAGACTAGTGGTCACCTCC 58.813 60.000 9.52 0.00 46.72 4.30
400 401 1.187087 CAGACTAGTGGTCACCTCCC 58.813 60.000 9.52 0.00 46.72 4.30
401 402 0.784495 AGACTAGTGGTCACCTCCCA 59.216 55.000 9.52 0.00 46.72 4.37
402 403 1.149288 AGACTAGTGGTCACCTCCCAA 59.851 52.381 9.52 0.00 46.72 4.12
403 404 1.550976 GACTAGTGGTCACCTCCCAAG 59.449 57.143 0.00 0.00 43.94 3.61
404 405 1.132817 ACTAGTGGTCACCTCCCAAGT 60.133 52.381 0.00 0.00 32.72 3.16
405 406 1.550976 CTAGTGGTCACCTCCCAAGTC 59.449 57.143 0.00 0.00 32.72 3.01
406 407 1.128188 AGTGGTCACCTCCCAAGTCC 61.128 60.000 0.00 0.00 32.72 3.85
407 408 1.846124 TGGTCACCTCCCAAGTCCC 60.846 63.158 0.00 0.00 0.00 4.46
408 409 1.846124 GGTCACCTCCCAAGTCCCA 60.846 63.158 0.00 0.00 0.00 4.37
409 410 1.423794 GGTCACCTCCCAAGTCCCAA 61.424 60.000 0.00 0.00 0.00 4.12
410 411 0.698818 GTCACCTCCCAAGTCCCAAT 59.301 55.000 0.00 0.00 0.00 3.16
411 412 1.075536 GTCACCTCCCAAGTCCCAATT 59.924 52.381 0.00 0.00 0.00 2.32
412 413 1.354368 TCACCTCCCAAGTCCCAATTC 59.646 52.381 0.00 0.00 0.00 2.17
413 414 0.328258 ACCTCCCAAGTCCCAATTCG 59.672 55.000 0.00 0.00 0.00 3.34
414 415 0.328258 CCTCCCAAGTCCCAATTCGT 59.672 55.000 0.00 0.00 0.00 3.85
415 416 1.271926 CCTCCCAAGTCCCAATTCGTT 60.272 52.381 0.00 0.00 0.00 3.85
416 417 2.084546 CTCCCAAGTCCCAATTCGTTC 58.915 52.381 0.00 0.00 0.00 3.95
417 418 0.802494 CCCAAGTCCCAATTCGTTCG 59.198 55.000 0.00 0.00 0.00 3.95
418 419 1.609580 CCCAAGTCCCAATTCGTTCGA 60.610 52.381 0.00 0.00 0.00 3.71
419 420 2.356135 CCAAGTCCCAATTCGTTCGAT 58.644 47.619 0.00 0.00 0.00 3.59
420 421 2.747446 CCAAGTCCCAATTCGTTCGATT 59.253 45.455 0.00 0.00 0.00 3.34
421 422 3.426159 CCAAGTCCCAATTCGTTCGATTG 60.426 47.826 0.00 3.73 0.00 2.67
422 423 3.053831 AGTCCCAATTCGTTCGATTGT 57.946 42.857 0.00 0.00 0.00 2.71
423 424 2.742053 AGTCCCAATTCGTTCGATTGTG 59.258 45.455 0.00 0.00 0.00 3.33
424 425 1.466950 TCCCAATTCGTTCGATTGTGC 59.533 47.619 0.00 0.00 0.00 4.57
425 426 1.523501 CCAATTCGTTCGATTGTGCG 58.476 50.000 0.00 0.00 0.00 5.34
426 427 1.127766 CCAATTCGTTCGATTGTGCGA 59.872 47.619 0.00 0.00 38.72 5.10
427 428 2.421523 CAATTCGTTCGATTGTGCGAG 58.578 47.619 0.00 0.00 41.79 5.03
428 429 1.710013 ATTCGTTCGATTGTGCGAGT 58.290 45.000 0.00 0.00 41.79 4.18
429 430 2.334971 TTCGTTCGATTGTGCGAGTA 57.665 45.000 0.00 0.00 41.79 2.59
430 431 1.891178 TCGTTCGATTGTGCGAGTAG 58.109 50.000 0.00 0.00 41.79 2.57
431 432 1.198408 TCGTTCGATTGTGCGAGTAGT 59.802 47.619 0.00 0.00 41.79 2.73
432 433 1.983605 CGTTCGATTGTGCGAGTAGTT 59.016 47.619 0.00 0.00 41.79 2.24
433 434 2.407361 CGTTCGATTGTGCGAGTAGTTT 59.593 45.455 0.00 0.00 41.79 2.66
434 435 3.479866 CGTTCGATTGTGCGAGTAGTTTC 60.480 47.826 0.00 0.00 41.79 2.78
435 436 3.570926 TCGATTGTGCGAGTAGTTTCT 57.429 42.857 0.00 0.00 35.01 2.52
436 437 3.909430 TCGATTGTGCGAGTAGTTTCTT 58.091 40.909 0.00 0.00 35.01 2.52
437 438 3.673338 TCGATTGTGCGAGTAGTTTCTTG 59.327 43.478 0.00 0.00 35.01 3.02
438 439 3.181530 CGATTGTGCGAGTAGTTTCTTGG 60.182 47.826 0.00 0.00 0.00 3.61
439 440 2.163818 TGTGCGAGTAGTTTCTTGGG 57.836 50.000 0.00 0.00 0.00 4.12
440 441 0.796927 GTGCGAGTAGTTTCTTGGGC 59.203 55.000 0.00 0.00 0.00 5.36
441 442 0.321298 TGCGAGTAGTTTCTTGGGCC 60.321 55.000 0.00 0.00 0.00 5.80
442 443 0.036294 GCGAGTAGTTTCTTGGGCCT 60.036 55.000 4.53 0.00 0.00 5.19
443 444 1.206371 GCGAGTAGTTTCTTGGGCCTA 59.794 52.381 4.53 0.00 0.00 3.93
444 445 2.354403 GCGAGTAGTTTCTTGGGCCTAA 60.354 50.000 4.53 0.38 0.00 2.69
445 446 3.681874 GCGAGTAGTTTCTTGGGCCTAAT 60.682 47.826 0.33 0.00 0.00 1.73
446 447 4.442472 GCGAGTAGTTTCTTGGGCCTAATA 60.442 45.833 0.33 0.00 0.00 0.98
447 448 5.290386 CGAGTAGTTTCTTGGGCCTAATAG 58.710 45.833 0.33 0.00 0.00 1.73
448 449 5.612351 GAGTAGTTTCTTGGGCCTAATAGG 58.388 45.833 0.33 0.99 38.80 2.57
449 450 5.037598 AGTAGTTTCTTGGGCCTAATAGGT 58.962 41.667 0.33 0.00 37.80 3.08
450 451 4.948062 AGTTTCTTGGGCCTAATAGGTT 57.052 40.909 0.33 0.00 37.80 3.50
451 452 5.270979 AGTTTCTTGGGCCTAATAGGTTT 57.729 39.130 0.33 0.00 37.80 3.27
452 453 5.651303 AGTTTCTTGGGCCTAATAGGTTTT 58.349 37.500 0.33 0.00 37.80 2.43
453 454 6.082031 AGTTTCTTGGGCCTAATAGGTTTTT 58.918 36.000 0.33 0.00 37.80 1.94
483 484 4.475051 AATACTAACGCCCACATGTGTA 57.525 40.909 23.79 8.79 0.00 2.90
492 493 1.606668 CCCACATGTGTAAGCGTTTGT 59.393 47.619 23.79 0.00 0.00 2.83
498 499 5.120053 CACATGTGTAAGCGTTTGTATCTCA 59.880 40.000 18.03 0.00 0.00 3.27
651 653 1.954362 CTTCCCACTCCTCGCCTCAG 61.954 65.000 0.00 0.00 0.00 3.35
678 900 2.762554 CCCCACTCACCCACACCAA 61.763 63.158 0.00 0.00 0.00 3.67
682 904 1.073125 CCACTCACCCACACCAATACA 59.927 52.381 0.00 0.00 0.00 2.29
748 977 4.570663 GTGGATCCCGGCGACTCG 62.571 72.222 9.30 0.00 0.00 4.18
793 1022 0.988678 GTTGGAGGGCCCTAGATGGT 60.989 60.000 28.78 0.00 35.38 3.55
1009 1241 2.762234 GCGACGGAGATGACGAGGT 61.762 63.158 0.00 0.00 34.93 3.85
1060 1292 1.878088 ACAACGAGACGCTACTCAAGA 59.122 47.619 0.00 0.00 36.80 3.02
1197 1429 1.537397 AGGTGAGGAGAGCAAGGCA 60.537 57.895 0.00 0.00 0.00 4.75
1210 1442 1.302511 AAGGCAATGAACGAGGCGT 60.303 52.632 0.00 0.00 43.97 5.68
1411 1663 3.749064 AGCGGAGATGTGCGTCGT 61.749 61.111 5.52 0.00 40.19 4.34
1478 1730 1.598130 GCGTGTCCAGCAGTTTCCT 60.598 57.895 0.00 0.00 34.19 3.36
1526 1778 3.164479 CAGGATCCCCATGGCGAT 58.836 61.111 11.83 11.83 33.88 4.58
1591 1843 0.541392 ACCAGATGCGCATGGAGTTA 59.459 50.000 31.47 0.00 39.02 2.24
1612 1864 3.595758 GGCCCCGGCAATGATTCG 61.596 66.667 8.23 0.00 44.11 3.34
1906 2165 5.356190 TGCAGATTTGTTTTTCATGGCAAAA 59.644 32.000 0.00 0.00 34.99 2.44
1936 2195 6.215121 TCAACTGACATGGCAATTTTTACAG 58.785 36.000 1.11 0.00 0.00 2.74
1948 2207 5.163693 GCAATTTTTACAGCGGTGTATAGGT 60.164 40.000 26.48 12.09 38.98 3.08
1949 2208 6.624204 GCAATTTTTACAGCGGTGTATAGGTT 60.624 38.462 26.48 16.44 38.98 3.50
1950 2209 6.673154 ATTTTTACAGCGGTGTATAGGTTC 57.327 37.500 26.48 0.00 38.98 3.62
1951 2210 3.806625 TTACAGCGGTGTATAGGTTCC 57.193 47.619 26.48 0.00 38.98 3.62
2039 2298 6.998968 TTTTTGCCATGTCAAACTGAATTT 57.001 29.167 0.50 0.00 35.86 1.82
2040 2299 6.998968 TTTTGCCATGTCAAACTGAATTTT 57.001 29.167 0.50 0.00 35.86 1.82
2041 2300 5.987777 TTGCCATGTCAAACTGAATTTTG 57.012 34.783 0.00 0.00 37.75 2.44
2042 2301 5.021033 TGCCATGTCAAACTGAATTTTGT 57.979 34.783 0.00 0.00 37.66 2.83
2043 2302 4.809958 TGCCATGTCAAACTGAATTTTGTG 59.190 37.500 0.00 0.00 37.66 3.33
2044 2303 4.810491 GCCATGTCAAACTGAATTTTGTGT 59.190 37.500 0.00 0.00 37.66 3.72
2045 2304 5.982516 GCCATGTCAAACTGAATTTTGTGTA 59.017 36.000 0.00 0.00 37.66 2.90
2046 2305 6.074356 GCCATGTCAAACTGAATTTTGTGTAC 60.074 38.462 0.00 0.00 37.66 2.90
2047 2306 6.420604 CCATGTCAAACTGAATTTTGTGTACC 59.579 38.462 0.00 0.00 37.66 3.34
2048 2307 5.897050 TGTCAAACTGAATTTTGTGTACCC 58.103 37.500 0.00 0.00 37.66 3.69
2049 2308 5.163499 TGTCAAACTGAATTTTGTGTACCCC 60.163 40.000 0.00 0.00 37.66 4.95
2050 2309 4.036971 TCAAACTGAATTTTGTGTACCCCG 59.963 41.667 0.00 0.00 37.66 5.73
2051 2310 1.883926 ACTGAATTTTGTGTACCCCGC 59.116 47.619 0.00 0.00 0.00 6.13
2052 2311 1.883275 CTGAATTTTGTGTACCCCGCA 59.117 47.619 0.00 0.00 0.00 5.69
2053 2312 2.294791 CTGAATTTTGTGTACCCCGCAA 59.705 45.455 0.00 0.00 41.66 4.85
2157 2416 5.384063 TTTTCGTGGTATTTCACATGCAT 57.616 34.783 0.00 0.00 37.50 3.96
2205 2493 3.247173 GCACGGCAATTTTTCATTCACAA 59.753 39.130 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 8.633561 CCCACTCAATAGCTCGATATCATATAA 58.366 37.037 3.12 0.00 0.00 0.98
69 70 7.780271 ACCCACTCAATAGCTCGATATCATATA 59.220 37.037 3.12 0.00 0.00 0.86
70 71 6.609212 ACCCACTCAATAGCTCGATATCATAT 59.391 38.462 3.12 0.00 0.00 1.78
71 72 5.952347 ACCCACTCAATAGCTCGATATCATA 59.048 40.000 3.12 0.00 0.00 2.15
72 73 4.774726 ACCCACTCAATAGCTCGATATCAT 59.225 41.667 3.12 0.00 0.00 2.45
73 74 4.152647 ACCCACTCAATAGCTCGATATCA 58.847 43.478 3.12 0.00 0.00 2.15
74 75 4.218635 TGACCCACTCAATAGCTCGATATC 59.781 45.833 0.00 0.00 0.00 1.63
75 76 4.152647 TGACCCACTCAATAGCTCGATAT 58.847 43.478 0.00 0.00 0.00 1.63
76 77 3.562182 TGACCCACTCAATAGCTCGATA 58.438 45.455 0.00 0.00 0.00 2.92
77 78 2.388735 TGACCCACTCAATAGCTCGAT 58.611 47.619 0.00 0.00 0.00 3.59
78 79 1.847328 TGACCCACTCAATAGCTCGA 58.153 50.000 0.00 0.00 0.00 4.04
79 80 2.672961 TTGACCCACTCAATAGCTCG 57.327 50.000 0.00 0.00 33.65 5.03
80 81 3.878778 ACATTGACCCACTCAATAGCTC 58.121 45.455 0.00 0.00 46.27 4.09
81 82 4.012374 CAACATTGACCCACTCAATAGCT 58.988 43.478 0.00 0.00 46.27 3.32
82 83 4.009675 TCAACATTGACCCACTCAATAGC 58.990 43.478 0.00 0.00 46.27 2.97
83 84 5.551760 GTCAACATTGACCCACTCAATAG 57.448 43.478 12.83 0.00 46.27 1.73
95 96 5.233083 ACCTGATCTTCAGTCAACATTGA 57.767 39.130 4.00 0.00 42.80 2.57
96 97 5.335426 CCAACCTGATCTTCAGTCAACATTG 60.335 44.000 4.00 0.00 42.80 2.82
97 98 4.763793 CCAACCTGATCTTCAGTCAACATT 59.236 41.667 4.00 0.00 42.80 2.71
98 99 4.330250 CCAACCTGATCTTCAGTCAACAT 58.670 43.478 4.00 0.00 42.80 2.71
99 100 3.743521 CCAACCTGATCTTCAGTCAACA 58.256 45.455 4.00 0.00 42.80 3.33
100 101 2.485814 GCCAACCTGATCTTCAGTCAAC 59.514 50.000 4.00 0.00 42.80 3.18
101 102 2.373169 AGCCAACCTGATCTTCAGTCAA 59.627 45.455 4.00 0.00 42.80 3.18
102 103 1.980765 AGCCAACCTGATCTTCAGTCA 59.019 47.619 4.00 0.00 42.80 3.41
103 104 2.777832 AGCCAACCTGATCTTCAGTC 57.222 50.000 4.00 0.00 42.80 3.51
104 105 3.515602 AAAGCCAACCTGATCTTCAGT 57.484 42.857 4.00 0.00 42.80 3.41
105 106 4.861102 AAAAAGCCAACCTGATCTTCAG 57.139 40.909 0.00 0.00 43.91 3.02
134 135 9.821240 AGCTAAGTATGAGCCATATATATAGCT 57.179 33.333 14.51 14.51 46.92 3.32
142 143 9.853177 AAAAAGTTAGCTAAGTATGAGCCATAT 57.147 29.630 14.18 0.00 46.92 1.78
174 175 9.970395 TCGTATTTTAGTTCAACTTAAGACTGA 57.030 29.630 10.09 8.57 0.00 3.41
191 192 9.906660 AGCTGTTTGAAATTGATTCGTATTTTA 57.093 25.926 0.00 0.00 41.18 1.52
192 193 8.816640 AGCTGTTTGAAATTGATTCGTATTTT 57.183 26.923 0.00 0.00 41.18 1.82
193 194 8.081633 TGAGCTGTTTGAAATTGATTCGTATTT 58.918 29.630 0.00 0.00 41.18 1.40
194 195 7.538678 GTGAGCTGTTTGAAATTGATTCGTATT 59.461 33.333 0.00 0.00 41.18 1.89
195 196 7.023575 GTGAGCTGTTTGAAATTGATTCGTAT 58.976 34.615 0.00 0.00 41.18 3.06
196 197 6.370593 GTGAGCTGTTTGAAATTGATTCGTA 58.629 36.000 0.00 0.00 41.18 3.43
197 198 5.215160 GTGAGCTGTTTGAAATTGATTCGT 58.785 37.500 0.00 0.00 41.18 3.85
198 199 4.319115 CGTGAGCTGTTTGAAATTGATTCG 59.681 41.667 0.00 0.00 41.18 3.34
199 200 5.451908 TCGTGAGCTGTTTGAAATTGATTC 58.548 37.500 0.00 0.00 38.60 2.52
200 201 5.437289 TCGTGAGCTGTTTGAAATTGATT 57.563 34.783 0.00 0.00 0.00 2.57
201 202 5.039480 CTCGTGAGCTGTTTGAAATTGAT 57.961 39.130 0.00 0.00 0.00 2.57
202 203 4.472691 CTCGTGAGCTGTTTGAAATTGA 57.527 40.909 0.00 0.00 0.00 2.57
216 217 3.243877 CACAAAATATCGAGGCTCGTGAG 59.756 47.826 33.31 18.81 41.35 3.51
217 218 3.186909 CACAAAATATCGAGGCTCGTGA 58.813 45.455 33.31 23.17 41.35 4.35
218 219 2.285220 CCACAAAATATCGAGGCTCGTG 59.715 50.000 33.31 25.01 41.35 4.35
219 220 2.550978 CCACAAAATATCGAGGCTCGT 58.449 47.619 33.31 23.11 41.35 4.18
220 221 1.261619 GCCACAAAATATCGAGGCTCG 59.738 52.381 30.10 30.10 42.10 5.03
221 222 2.032178 GTGCCACAAAATATCGAGGCTC 59.968 50.000 3.87 3.87 42.46 4.70
222 223 2.017049 GTGCCACAAAATATCGAGGCT 58.983 47.619 9.17 0.00 42.46 4.58
223 224 1.065551 GGTGCCACAAAATATCGAGGC 59.934 52.381 0.00 1.35 42.32 4.70
224 225 1.676006 GGGTGCCACAAAATATCGAGG 59.324 52.381 0.00 0.00 0.00 4.63
225 226 2.643551 AGGGTGCCACAAAATATCGAG 58.356 47.619 0.00 0.00 0.00 4.04
226 227 2.799126 AGGGTGCCACAAAATATCGA 57.201 45.000 0.00 0.00 0.00 3.59
227 228 4.389374 AGATAGGGTGCCACAAAATATCG 58.611 43.478 0.00 0.00 0.00 2.92
228 229 5.408604 CGTAGATAGGGTGCCACAAAATATC 59.591 44.000 0.00 0.00 0.00 1.63
229 230 5.163237 ACGTAGATAGGGTGCCACAAAATAT 60.163 40.000 0.00 0.00 0.00 1.28
230 231 4.162698 ACGTAGATAGGGTGCCACAAAATA 59.837 41.667 0.00 0.00 0.00 1.40
231 232 3.054655 ACGTAGATAGGGTGCCACAAAAT 60.055 43.478 0.00 0.00 0.00 1.82
232 233 2.303600 ACGTAGATAGGGTGCCACAAAA 59.696 45.455 0.00 0.00 0.00 2.44
233 234 1.903860 ACGTAGATAGGGTGCCACAAA 59.096 47.619 0.00 0.00 0.00 2.83
234 235 1.206132 CACGTAGATAGGGTGCCACAA 59.794 52.381 0.00 0.00 0.00 3.33
235 236 0.821517 CACGTAGATAGGGTGCCACA 59.178 55.000 0.00 0.00 0.00 4.17
236 237 1.108776 TCACGTAGATAGGGTGCCAC 58.891 55.000 0.00 0.00 0.00 5.01
237 238 1.108776 GTCACGTAGATAGGGTGCCA 58.891 55.000 0.00 0.00 0.00 4.92
238 239 1.108776 TGTCACGTAGATAGGGTGCC 58.891 55.000 0.00 0.00 0.00 5.01
239 240 2.953466 TTGTCACGTAGATAGGGTGC 57.047 50.000 0.00 0.00 0.00 5.01
240 241 7.759886 CCATAATATTGTCACGTAGATAGGGTG 59.240 40.741 0.00 0.00 0.00 4.61
241 242 7.578955 GCCATAATATTGTCACGTAGATAGGGT 60.579 40.741 0.00 0.00 0.00 4.34
242 243 6.757010 GCCATAATATTGTCACGTAGATAGGG 59.243 42.308 0.00 0.00 0.00 3.53
243 244 7.275779 GTGCCATAATATTGTCACGTAGATAGG 59.724 40.741 0.00 0.00 0.00 2.57
244 245 7.812669 TGTGCCATAATATTGTCACGTAGATAG 59.187 37.037 0.00 0.00 0.00 2.08
245 246 7.597369 GTGTGCCATAATATTGTCACGTAGATA 59.403 37.037 0.00 0.00 0.00 1.98
246 247 6.423905 GTGTGCCATAATATTGTCACGTAGAT 59.576 38.462 0.00 0.00 0.00 1.98
247 248 5.751509 GTGTGCCATAATATTGTCACGTAGA 59.248 40.000 0.00 0.00 0.00 2.59
248 249 5.522097 TGTGTGCCATAATATTGTCACGTAG 59.478 40.000 0.00 0.00 0.00 3.51
249 250 5.420409 TGTGTGCCATAATATTGTCACGTA 58.580 37.500 0.00 0.00 0.00 3.57
250 251 4.257731 TGTGTGCCATAATATTGTCACGT 58.742 39.130 0.00 0.00 0.00 4.49
251 252 4.873768 TGTGTGCCATAATATTGTCACG 57.126 40.909 0.00 0.00 0.00 4.35
252 253 6.293626 GGAGATGTGTGCCATAATATTGTCAC 60.294 42.308 0.00 0.00 32.56 3.67
253 254 5.764686 GGAGATGTGTGCCATAATATTGTCA 59.235 40.000 0.00 0.00 32.56 3.58
254 255 5.764686 TGGAGATGTGTGCCATAATATTGTC 59.235 40.000 0.00 0.00 32.56 3.18
255 256 5.693961 TGGAGATGTGTGCCATAATATTGT 58.306 37.500 0.00 0.00 32.56 2.71
256 257 5.335426 GCTGGAGATGTGTGCCATAATATTG 60.335 44.000 0.00 0.00 32.56 1.90
257 258 4.763793 GCTGGAGATGTGTGCCATAATATT 59.236 41.667 0.00 0.00 32.56 1.28
258 259 4.202493 TGCTGGAGATGTGTGCCATAATAT 60.202 41.667 0.00 0.00 32.56 1.28
259 260 3.136260 TGCTGGAGATGTGTGCCATAATA 59.864 43.478 0.00 0.00 32.56 0.98
260 261 2.092267 TGCTGGAGATGTGTGCCATAAT 60.092 45.455 0.00 0.00 32.56 1.28
261 262 1.281577 TGCTGGAGATGTGTGCCATAA 59.718 47.619 0.00 0.00 32.56 1.90
262 263 0.911053 TGCTGGAGATGTGTGCCATA 59.089 50.000 0.00 0.00 32.56 2.74
263 264 0.679002 GTGCTGGAGATGTGTGCCAT 60.679 55.000 0.00 0.00 36.13 4.40
264 265 1.302752 GTGCTGGAGATGTGTGCCA 60.303 57.895 0.00 0.00 0.00 4.92
265 266 0.679002 ATGTGCTGGAGATGTGTGCC 60.679 55.000 0.00 0.00 0.00 5.01
266 267 2.028420 TATGTGCTGGAGATGTGTGC 57.972 50.000 0.00 0.00 0.00 4.57
267 268 3.373130 CAGTTATGTGCTGGAGATGTGTG 59.627 47.826 0.00 0.00 0.00 3.82
268 269 3.603532 CAGTTATGTGCTGGAGATGTGT 58.396 45.455 0.00 0.00 0.00 3.72
277 278 2.234661 TCTCACCTCCAGTTATGTGCTG 59.765 50.000 0.00 0.00 0.00 4.41
278 279 2.499289 CTCTCACCTCCAGTTATGTGCT 59.501 50.000 0.00 0.00 0.00 4.40
279 280 2.234908 ACTCTCACCTCCAGTTATGTGC 59.765 50.000 0.00 0.00 0.00 4.57
280 281 3.118956 GGACTCTCACCTCCAGTTATGTG 60.119 52.174 0.00 0.00 0.00 3.21
281 282 3.100671 GGACTCTCACCTCCAGTTATGT 58.899 50.000 0.00 0.00 0.00 2.29
282 283 2.099921 CGGACTCTCACCTCCAGTTATG 59.900 54.545 0.00 0.00 0.00 1.90
283 284 2.379972 CGGACTCTCACCTCCAGTTAT 58.620 52.381 0.00 0.00 0.00 1.89
284 285 1.616187 CCGGACTCTCACCTCCAGTTA 60.616 57.143 0.00 0.00 0.00 2.24
285 286 0.900647 CCGGACTCTCACCTCCAGTT 60.901 60.000 0.00 0.00 0.00 3.16
286 287 1.304547 CCGGACTCTCACCTCCAGT 60.305 63.158 0.00 0.00 0.00 4.00
287 288 1.000771 TCCGGACTCTCACCTCCAG 60.001 63.158 0.00 0.00 0.00 3.86
288 289 1.304217 GTCCGGACTCTCACCTCCA 60.304 63.158 27.64 0.00 0.00 3.86
289 290 0.255318 TAGTCCGGACTCTCACCTCC 59.745 60.000 39.49 6.84 42.54 4.30
290 291 1.065272 ACTAGTCCGGACTCTCACCTC 60.065 57.143 39.49 7.68 42.54 3.85
291 292 0.993470 ACTAGTCCGGACTCTCACCT 59.007 55.000 39.49 17.69 42.54 4.00
292 293 1.836802 AACTAGTCCGGACTCTCACC 58.163 55.000 39.49 9.37 42.54 4.02
293 294 3.938289 AAAACTAGTCCGGACTCTCAC 57.062 47.619 39.49 10.88 42.54 3.51
294 295 7.893124 ATAATAAAACTAGTCCGGACTCTCA 57.107 36.000 39.49 22.15 42.54 3.27
331 332 2.162716 GGCACGATGACCACTTGTC 58.837 57.895 0.00 0.00 44.72 3.18
332 333 4.379174 GGCACGATGACCACTTGT 57.621 55.556 0.00 0.00 0.00 3.16
341 342 1.091771 GGTCTGTCATGGGCACGATG 61.092 60.000 0.00 0.00 46.09 3.84
342 343 1.221840 GGTCTGTCATGGGCACGAT 59.778 57.895 0.00 0.00 0.00 3.73
343 344 2.662596 GGTCTGTCATGGGCACGA 59.337 61.111 0.00 0.00 0.00 4.35
344 345 2.436646 GGGTCTGTCATGGGCACG 60.437 66.667 0.00 0.00 0.00 5.34
345 346 2.044946 GGGGTCTGTCATGGGCAC 60.045 66.667 0.00 0.00 0.00 5.01
346 347 3.716195 CGGGGTCTGTCATGGGCA 61.716 66.667 0.00 0.00 0.00 5.36
347 348 3.391665 CTCGGGGTCTGTCATGGGC 62.392 68.421 0.00 0.00 0.00 5.36
348 349 1.680522 CTCTCGGGGTCTGTCATGGG 61.681 65.000 0.00 0.00 0.00 4.00
349 350 1.680522 CCTCTCGGGGTCTGTCATGG 61.681 65.000 0.00 0.00 0.00 3.66
350 351 0.684479 TCCTCTCGGGGTCTGTCATG 60.684 60.000 0.00 0.00 35.33 3.07
351 352 0.263172 ATCCTCTCGGGGTCTGTCAT 59.737 55.000 0.00 0.00 35.33 3.06
352 353 0.041238 AATCCTCTCGGGGTCTGTCA 59.959 55.000 0.00 0.00 35.33 3.58
353 354 0.747852 GAATCCTCTCGGGGTCTGTC 59.252 60.000 0.00 0.00 35.33 3.51
354 355 0.336737 AGAATCCTCTCGGGGTCTGT 59.663 55.000 0.00 0.00 35.33 3.41
355 356 1.490574 AAGAATCCTCTCGGGGTCTG 58.509 55.000 0.00 0.00 32.63 3.51
356 357 3.621682 ATAAGAATCCTCTCGGGGTCT 57.378 47.619 0.00 0.00 33.32 3.85
357 358 4.409187 ACTATAAGAATCCTCTCGGGGTC 58.591 47.826 0.00 0.00 35.33 4.46
358 359 4.409187 GACTATAAGAATCCTCTCGGGGT 58.591 47.826 0.00 0.00 35.33 4.95
359 360 3.764972 GGACTATAAGAATCCTCTCGGGG 59.235 52.174 0.00 0.00 35.33 5.73
360 361 4.408276 TGGACTATAAGAATCCTCTCGGG 58.592 47.826 0.00 0.00 33.34 5.14
361 362 5.182380 GTCTGGACTATAAGAATCCTCTCGG 59.818 48.000 0.00 0.00 33.34 4.63
362 363 6.001460 AGTCTGGACTATAAGAATCCTCTCG 58.999 44.000 0.95 0.00 40.43 4.04
363 364 8.161425 ACTAGTCTGGACTATAAGAATCCTCTC 58.839 40.741 10.39 0.00 42.44 3.20
364 365 7.942341 CACTAGTCTGGACTATAAGAATCCTCT 59.058 40.741 10.39 0.00 42.44 3.69
365 366 7.175990 CCACTAGTCTGGACTATAAGAATCCTC 59.824 44.444 10.39 0.00 42.44 3.71
366 367 7.007723 CCACTAGTCTGGACTATAAGAATCCT 58.992 42.308 10.39 0.00 42.44 3.24
367 368 6.778559 ACCACTAGTCTGGACTATAAGAATCC 59.221 42.308 10.39 0.00 42.44 3.01
368 369 7.502895 TGACCACTAGTCTGGACTATAAGAATC 59.497 40.741 10.39 5.78 46.46 2.52
369 370 7.285858 GTGACCACTAGTCTGGACTATAAGAAT 59.714 40.741 10.39 0.00 46.46 2.40
370 371 6.602406 GTGACCACTAGTCTGGACTATAAGAA 59.398 42.308 10.39 0.00 46.46 2.52
371 372 6.120905 GTGACCACTAGTCTGGACTATAAGA 58.879 44.000 10.39 0.00 46.46 2.10
372 373 5.299782 GGTGACCACTAGTCTGGACTATAAG 59.700 48.000 10.39 4.60 46.46 1.73
373 374 5.044328 AGGTGACCACTAGTCTGGACTATAA 60.044 44.000 3.63 0.00 46.46 0.98
374 375 4.477581 AGGTGACCACTAGTCTGGACTATA 59.522 45.833 3.63 0.00 46.46 1.31
375 376 3.269906 AGGTGACCACTAGTCTGGACTAT 59.730 47.826 3.63 0.00 46.46 2.12
376 377 2.648304 AGGTGACCACTAGTCTGGACTA 59.352 50.000 3.63 9.68 46.46 2.59
377 378 1.429687 AGGTGACCACTAGTCTGGACT 59.570 52.381 3.63 8.36 46.46 3.85
378 379 1.819903 GAGGTGACCACTAGTCTGGAC 59.180 57.143 3.63 1.12 46.46 4.02
379 380 1.272536 GGAGGTGACCACTAGTCTGGA 60.273 57.143 3.63 0.00 46.46 3.86
380 381 1.187087 GGAGGTGACCACTAGTCTGG 58.813 60.000 3.63 0.00 46.46 3.86
381 382 1.187087 GGGAGGTGACCACTAGTCTG 58.813 60.000 3.63 0.00 46.46 3.51
382 383 0.784495 TGGGAGGTGACCACTAGTCT 59.216 55.000 3.63 0.00 46.46 3.24
383 384 1.550976 CTTGGGAGGTGACCACTAGTC 59.449 57.143 3.63 0.00 46.51 2.59
384 385 1.132817 ACTTGGGAGGTGACCACTAGT 60.133 52.381 3.63 3.40 37.82 2.57
385 386 1.550976 GACTTGGGAGGTGACCACTAG 59.449 57.143 3.63 2.74 37.82 2.57
386 387 1.640917 GACTTGGGAGGTGACCACTA 58.359 55.000 3.63 0.00 37.82 2.74
387 388 1.128188 GGACTTGGGAGGTGACCACT 61.128 60.000 3.63 0.00 37.82 4.00
388 389 1.375326 GGACTTGGGAGGTGACCAC 59.625 63.158 3.63 0.00 37.82 4.16
389 390 1.846124 GGGACTTGGGAGGTGACCA 60.846 63.158 3.63 0.00 35.88 4.02
390 391 1.423794 TTGGGACTTGGGAGGTGACC 61.424 60.000 0.00 0.00 0.00 4.02
391 392 0.698818 ATTGGGACTTGGGAGGTGAC 59.301 55.000 0.00 0.00 0.00 3.67
392 393 1.354368 GAATTGGGACTTGGGAGGTGA 59.646 52.381 0.00 0.00 0.00 4.02
393 394 1.839424 GAATTGGGACTTGGGAGGTG 58.161 55.000 0.00 0.00 0.00 4.00
394 395 0.328258 CGAATTGGGACTTGGGAGGT 59.672 55.000 0.00 0.00 0.00 3.85
395 396 0.328258 ACGAATTGGGACTTGGGAGG 59.672 55.000 0.00 0.00 0.00 4.30
396 397 2.084546 GAACGAATTGGGACTTGGGAG 58.915 52.381 0.00 0.00 0.00 4.30
397 398 1.609580 CGAACGAATTGGGACTTGGGA 60.610 52.381 0.00 0.00 0.00 4.37
398 399 0.802494 CGAACGAATTGGGACTTGGG 59.198 55.000 0.00 0.00 0.00 4.12
399 400 1.803334 TCGAACGAATTGGGACTTGG 58.197 50.000 0.00 0.00 0.00 3.61
400 401 3.188460 ACAATCGAACGAATTGGGACTTG 59.812 43.478 16.63 10.57 0.00 3.16
401 402 3.188460 CACAATCGAACGAATTGGGACTT 59.812 43.478 16.63 0.00 30.71 3.01
402 403 2.742053 CACAATCGAACGAATTGGGACT 59.258 45.455 16.63 2.18 30.71 3.85
403 404 2.727916 GCACAATCGAACGAATTGGGAC 60.728 50.000 18.05 10.26 30.71 4.46
404 405 1.466950 GCACAATCGAACGAATTGGGA 59.533 47.619 18.05 0.00 30.71 4.37
405 406 1.790123 CGCACAATCGAACGAATTGGG 60.790 52.381 16.63 14.92 0.00 4.12
406 407 1.127766 TCGCACAATCGAACGAATTGG 59.872 47.619 16.63 0.00 35.31 3.16
407 408 2.159841 ACTCGCACAATCGAACGAATTG 60.160 45.455 0.12 8.82 38.08 2.32
408 409 2.066262 ACTCGCACAATCGAACGAATT 58.934 42.857 0.12 0.00 38.08 2.17
409 410 1.710013 ACTCGCACAATCGAACGAAT 58.290 45.000 0.12 0.00 38.08 3.34
410 411 2.247637 CTACTCGCACAATCGAACGAA 58.752 47.619 0.12 0.00 38.08 3.85
411 412 1.198408 ACTACTCGCACAATCGAACGA 59.802 47.619 0.00 0.00 38.08 3.85
412 413 1.614385 ACTACTCGCACAATCGAACG 58.386 50.000 0.00 0.00 38.08 3.95
413 414 3.673809 AGAAACTACTCGCACAATCGAAC 59.326 43.478 0.00 0.00 38.08 3.95
414 415 3.909430 AGAAACTACTCGCACAATCGAA 58.091 40.909 0.00 0.00 38.08 3.71
415 416 3.570926 AGAAACTACTCGCACAATCGA 57.429 42.857 0.00 0.00 36.94 3.59
416 417 3.181530 CCAAGAAACTACTCGCACAATCG 60.182 47.826 0.00 0.00 0.00 3.34
417 418 3.125316 CCCAAGAAACTACTCGCACAATC 59.875 47.826 0.00 0.00 0.00 2.67
418 419 3.074412 CCCAAGAAACTACTCGCACAAT 58.926 45.455 0.00 0.00 0.00 2.71
419 420 2.489971 CCCAAGAAACTACTCGCACAA 58.510 47.619 0.00 0.00 0.00 3.33
420 421 1.876416 GCCCAAGAAACTACTCGCACA 60.876 52.381 0.00 0.00 0.00 4.57
421 422 0.796927 GCCCAAGAAACTACTCGCAC 59.203 55.000 0.00 0.00 0.00 5.34
422 423 0.321298 GGCCCAAGAAACTACTCGCA 60.321 55.000 0.00 0.00 0.00 5.10
423 424 0.036294 AGGCCCAAGAAACTACTCGC 60.036 55.000 0.00 0.00 0.00 5.03
424 425 3.604875 TTAGGCCCAAGAAACTACTCG 57.395 47.619 0.00 0.00 0.00 4.18
425 426 5.130643 ACCTATTAGGCCCAAGAAACTACTC 59.869 44.000 9.77 0.00 39.63 2.59
426 427 5.037598 ACCTATTAGGCCCAAGAAACTACT 58.962 41.667 9.77 0.00 39.63 2.57
427 428 5.369409 ACCTATTAGGCCCAAGAAACTAC 57.631 43.478 9.77 0.00 39.63 2.73
428 429 6.397217 AAACCTATTAGGCCCAAGAAACTA 57.603 37.500 9.77 0.00 39.63 2.24
429 430 4.948062 AACCTATTAGGCCCAAGAAACT 57.052 40.909 9.77 0.00 39.63 2.66
430 431 5.995565 AAAACCTATTAGGCCCAAGAAAC 57.004 39.130 9.77 0.00 39.63 2.78
453 454 5.008415 TGTGGGCGTTAGTATTTTCGAAAAA 59.992 36.000 25.77 13.11 0.00 1.94
454 455 4.514441 TGTGGGCGTTAGTATTTTCGAAAA 59.486 37.500 24.43 24.43 0.00 2.29
455 456 4.063689 TGTGGGCGTTAGTATTTTCGAAA 58.936 39.130 6.47 6.47 0.00 3.46
456 457 3.661944 TGTGGGCGTTAGTATTTTCGAA 58.338 40.909 0.00 0.00 0.00 3.71
457 458 3.316071 TGTGGGCGTTAGTATTTTCGA 57.684 42.857 0.00 0.00 0.00 3.71
483 484 2.224426 TGTGGGTGAGATACAAACGCTT 60.224 45.455 0.00 0.00 0.00 4.68
492 493 0.530744 GAGTGCGTGTGGGTGAGATA 59.469 55.000 0.00 0.00 0.00 1.98
498 499 2.048222 CATCGAGTGCGTGTGGGT 60.048 61.111 0.00 0.00 38.98 4.51
517 518 1.514678 TTTGTGCAGCGTGATGGACC 61.515 55.000 7.29 0.00 40.49 4.46
614 615 2.785357 AGATAAGGTGAGGGAGAGGG 57.215 55.000 0.00 0.00 0.00 4.30
651 653 1.248486 GGTGAGTGGGGAAGAAAAGC 58.752 55.000 0.00 0.00 0.00 3.51
678 900 5.385198 GAGGAGAGAAGAGGAGTGATGTAT 58.615 45.833 0.00 0.00 0.00 2.29
682 904 2.091333 GGGAGGAGAGAAGAGGAGTGAT 60.091 54.545 0.00 0.00 0.00 3.06
786 1015 2.090775 TCCAGCCATCTACCACCATCTA 60.091 50.000 0.00 0.00 0.00 1.98
793 1022 1.490490 GTTGGATCCAGCCATCTACCA 59.510 52.381 17.35 0.00 37.86 3.25
1009 1241 3.071206 GCACCTCCTCGAGCTCCA 61.071 66.667 6.99 0.00 0.00 3.86
1031 1263 0.663568 CGTCTCGTTGTCTTCGGCTT 60.664 55.000 0.00 0.00 0.00 4.35
1040 1272 1.878088 TCTTGAGTAGCGTCTCGTTGT 59.122 47.619 6.68 0.00 37.28 3.32
1177 1409 1.835927 GCCTTGCTCTCCTCACCTGT 61.836 60.000 0.00 0.00 0.00 4.00
1197 1429 3.118454 CGCCACGCCTCGTTCATT 61.118 61.111 0.00 0.00 38.32 2.57
1270 1503 4.323477 CCAAAGTCGCCCCCGTCA 62.323 66.667 0.00 0.00 35.54 4.35
1281 1533 1.898574 CAGCCGCACCTTCCAAAGT 60.899 57.895 0.00 0.00 0.00 2.66
1411 1663 2.046023 CAGGCATTCCAGCGGTCA 60.046 61.111 0.00 0.00 34.64 4.02
1462 1714 0.868406 CGAAGGAAACTGCTGGACAC 59.132 55.000 0.00 0.00 42.68 3.67
1591 1843 2.803593 AATCATTGCCGGGGCCAAGT 62.804 55.000 4.39 0.00 41.09 3.16
1612 1864 1.210155 GAACAGCAACGCACCATCC 59.790 57.895 0.00 0.00 0.00 3.51
1936 2195 1.483415 TGGAAGGAACCTATACACCGC 59.517 52.381 0.00 0.00 0.00 5.68
1948 2207 6.831353 TCACTAACAACAAAAGATGGAAGGAA 59.169 34.615 0.00 0.00 0.00 3.36
1949 2208 6.361433 TCACTAACAACAAAAGATGGAAGGA 58.639 36.000 0.00 0.00 0.00 3.36
1950 2209 6.633500 TCACTAACAACAAAAGATGGAAGG 57.367 37.500 0.00 0.00 0.00 3.46
1951 2210 9.831737 CTATTCACTAACAACAAAAGATGGAAG 57.168 33.333 0.00 0.00 0.00 3.46
2032 2291 1.883275 TGCGGGGTACACAAAATTCAG 59.117 47.619 0.00 0.00 0.00 3.02
2033 2292 1.982660 TGCGGGGTACACAAAATTCA 58.017 45.000 0.00 0.00 0.00 2.57
2034 2293 3.372660 TTTGCGGGGTACACAAAATTC 57.627 42.857 0.00 0.00 30.75 2.17
2035 2294 3.821421 TTTTGCGGGGTACACAAAATT 57.179 38.095 0.00 0.00 38.11 1.82
2036 2295 3.821421 TTTTTGCGGGGTACACAAAAT 57.179 38.095 12.88 0.00 41.44 1.82
2083 2342 7.254863 GGCTTTTCAGAAATTGATGCTTCAAAA 60.255 33.333 17.82 5.19 44.70 2.44
2157 2416 6.528321 TGTGAAATACCATGAAAAATTGCCA 58.472 32.000 0.00 0.00 0.00 4.92
2231 2521 6.549952 TGTTCAAAAATTTGCCATGTTGTTC 58.450 32.000 0.98 0.00 38.05 3.18


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

AutoCloner maintained by Alex Coulton.