Multiple sequence alignment - TraesCS2B01G538800

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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 TraesCS2B01G538800 chr2B 100.000 2167 0 0 257 2423 734051655 734049489 0.000000e+00 4002
1 TraesCS2B01G538800 chr2B 93.857 407 25 0 995 1401 733973255 733972849 4.430000e-172 614
2 TraesCS2B01G538800 chr2B 92.111 431 28 5 977 1401 733862885 733862455 9.580000e-169 603
3 TraesCS2B01G538800 chr2B 91.395 430 37 0 972 1401 733892262 733891833 7.460000e-165 590
4 TraesCS2B01G538800 chr2B 100.000 63 0 0 1 63 734051911 734051849 1.520000e-22 117
5 TraesCS2B01G538800 chr2A 91.441 1332 74 21 679 1989 735703744 735702432 0.000000e+00 1792
6 TraesCS2B01G538800 chr2A 87.719 570 43 18 834 1401 735761303 735761847 7.300000e-180 640
7 TraesCS2B01G538800 chr2A 90.466 451 37 6 953 1401 735602916 735602470 7.460000e-165 590
8 TraesCS2B01G538800 chr2A 87.379 412 26 17 2003 2408 735702366 735701975 1.320000e-122 449
9 TraesCS2B01G538800 chr2A 90.517 116 9 2 486 600 735703862 735703748 4.170000e-33 152
10 TraesCS2B01G538800 chr2A 81.818 143 12 7 2114 2255 735762559 735762688 9.160000e-20 108
11 TraesCS2B01G538800 chr2D 88.049 1481 106 35 486 1934 603503330 603501889 0.000000e+00 1688
12 TraesCS2B01G538800 chr2D 93.126 451 24 6 952 1401 603381087 603380643 0.000000e+00 654
13 TraesCS2B01G538800 chr2D 92.824 432 29 2 972 1401 603541092 603541523 2.050000e-175 625
14 TraesCS2B01G538800 chr2D 92.908 141 9 1 2272 2412 603501673 603501534 1.140000e-48 204
15 TraesCS2B01G538800 chr2D 86.310 168 13 8 2103 2269 603501891 603501733 8.900000e-40 174
16 TraesCS2B01G538800 chr2D 83.766 154 12 11 2114 2266 603379943 603379802 1.510000e-27 134
17 TraesCS2B01G538800 chr2D 82.759 145 13 10 2114 2255 603542177 603542312 4.230000e-23 119


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 TraesCS2B01G538800 chr2B 734049489 734051911 2422 True 2059.500000 4002 100.0000 1 2423 2 chr2B.!!$R4 2422
1 TraesCS2B01G538800 chr2A 735701975 735703862 1887 True 797.666667 1792 89.7790 486 2408 3 chr2A.!!$R2 1922
2 TraesCS2B01G538800 chr2A 735761303 735762688 1385 False 374.000000 640 84.7685 834 2255 2 chr2A.!!$F1 1421
3 TraesCS2B01G538800 chr2D 603501534 603503330 1796 True 688.666667 1688 89.0890 486 2412 3 chr2D.!!$R2 1926
4 TraesCS2B01G538800 chr2D 603379802 603381087 1285 True 394.000000 654 88.4460 952 2266 2 chr2D.!!$R1 1314
5 TraesCS2B01G538800 chr2D 603541092 603542312 1220 False 372.000000 625 87.7915 972 2255 2 chr2D.!!$F1 1283

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
325 326 0.034896 AGAACCGCGTTGGATGTCTT 59.965 50.0 4.92 0.0 42.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 1772 0.25589 GCACCCCACACCTCATGTAT 59.744 55.0 0.0 0.0 40.64 2.29 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
21 22 4.572985 AACATGAAAGGATGTGTGTGTG 57.427 40.909 0.00 0.00 36.66 3.82
22 23 2.886523 ACATGAAAGGATGTGTGTGTGG 59.113 45.455 0.00 0.00 35.17 4.17
23 24 2.727123 TGAAAGGATGTGTGTGTGGT 57.273 45.000 0.00 0.00 0.00 4.16
24 25 3.011566 TGAAAGGATGTGTGTGTGGTT 57.988 42.857 0.00 0.00 0.00 3.67
25 26 3.360867 TGAAAGGATGTGTGTGTGGTTT 58.639 40.909 0.00 0.00 0.00 3.27
26 27 3.130164 TGAAAGGATGTGTGTGTGGTTTG 59.870 43.478 0.00 0.00 0.00 2.93
27 28 1.691196 AGGATGTGTGTGTGGTTTGG 58.309 50.000 0.00 0.00 0.00 3.28
28 29 0.673437 GGATGTGTGTGTGGTTTGGG 59.327 55.000 0.00 0.00 0.00 4.12
29 30 1.398692 GATGTGTGTGTGGTTTGGGT 58.601 50.000 0.00 0.00 0.00 4.51
30 31 1.066908 GATGTGTGTGTGGTTTGGGTG 59.933 52.381 0.00 0.00 0.00 4.61
31 32 0.967887 TGTGTGTGTGGTTTGGGTGG 60.968 55.000 0.00 0.00 0.00 4.61
32 33 1.380515 TGTGTGTGGTTTGGGTGGG 60.381 57.895 0.00 0.00 0.00 4.61
33 34 2.443016 TGTGTGGTTTGGGTGGGC 60.443 61.111 0.00 0.00 0.00 5.36
34 35 3.230990 GTGTGGTTTGGGTGGGCC 61.231 66.667 0.00 0.00 0.00 5.80
35 36 3.755626 TGTGGTTTGGGTGGGCCA 61.756 61.111 0.00 0.00 36.17 5.36
36 37 2.917227 GTGGTTTGGGTGGGCCAG 60.917 66.667 6.40 0.00 36.17 4.85
37 38 4.232061 TGGTTTGGGTGGGCCAGG 62.232 66.667 6.40 0.00 36.17 4.45
43 44 4.442454 GGGTGGGCCAGGGCTAAC 62.442 72.222 6.40 9.87 41.60 2.34
44 45 3.657350 GGTGGGCCAGGGCTAACA 61.657 66.667 6.40 6.13 41.60 2.41
45 46 2.438795 GTGGGCCAGGGCTAACAA 59.561 61.111 6.40 0.00 41.60 2.83
46 47 1.977009 GTGGGCCAGGGCTAACAAC 60.977 63.158 6.40 0.60 41.60 3.32
47 48 2.438795 GGGCCAGGGCTAACAACA 59.561 61.111 13.81 0.00 41.60 3.33
48 49 1.678970 GGGCCAGGGCTAACAACAG 60.679 63.158 13.81 0.00 41.60 3.16
49 50 1.678970 GGCCAGGGCTAACAACAGG 60.679 63.158 10.60 0.00 41.60 4.00
50 51 1.074951 GCCAGGGCTAACAACAGGT 59.925 57.895 2.30 0.00 38.26 4.00
51 52 1.244019 GCCAGGGCTAACAACAGGTG 61.244 60.000 2.30 0.00 38.26 4.00
52 53 0.609131 CCAGGGCTAACAACAGGTGG 60.609 60.000 0.00 0.00 0.00 4.61
53 54 0.609131 CAGGGCTAACAACAGGTGGG 60.609 60.000 0.00 0.00 0.00 4.61
54 55 1.977009 GGGCTAACAACAGGTGGGC 60.977 63.158 0.00 0.00 0.00 5.36
55 56 2.332654 GGCTAACAACAGGTGGGCG 61.333 63.158 0.00 0.00 0.00 6.13
56 57 1.599797 GCTAACAACAGGTGGGCGT 60.600 57.895 0.00 0.00 0.00 5.68
57 58 1.852067 GCTAACAACAGGTGGGCGTG 61.852 60.000 0.00 0.00 36.63 5.34
58 59 0.250124 CTAACAACAGGTGGGCGTGA 60.250 55.000 0.00 0.00 34.82 4.35
59 60 0.533308 TAACAACAGGTGGGCGTGAC 60.533 55.000 0.00 0.00 34.82 3.67
60 61 2.203139 CAACAGGTGGGCGTGACA 60.203 61.111 0.00 0.00 34.82 3.58
61 62 2.111043 AACAGGTGGGCGTGACAG 59.889 61.111 0.00 0.00 34.82 3.51
62 63 4.626081 ACAGGTGGGCGTGACAGC 62.626 66.667 0.00 0.00 36.64 4.40
273 274 2.191641 GCCCCTGCATCTGTCTCC 59.808 66.667 0.00 0.00 37.47 3.71
274 275 2.503061 CCCCTGCATCTGTCTCCG 59.497 66.667 0.00 0.00 0.00 4.63
275 276 2.503061 CCCTGCATCTGTCTCCGG 59.497 66.667 0.00 0.00 0.00 5.14
276 277 2.362369 CCCTGCATCTGTCTCCGGT 61.362 63.158 0.00 0.00 0.00 5.28
277 278 1.599047 CCTGCATCTGTCTCCGGTT 59.401 57.895 0.00 0.00 0.00 4.44
278 279 0.036010 CCTGCATCTGTCTCCGGTTT 60.036 55.000 0.00 0.00 0.00 3.27
279 280 1.081892 CTGCATCTGTCTCCGGTTTG 58.918 55.000 0.00 0.00 0.00 2.93
280 281 0.955428 TGCATCTGTCTCCGGTTTGC 60.955 55.000 0.00 2.37 0.00 3.68
281 282 1.970917 GCATCTGTCTCCGGTTTGCG 61.971 60.000 0.00 0.00 0.00 4.85
282 283 0.389817 CATCTGTCTCCGGTTTGCGA 60.390 55.000 0.00 0.00 0.00 5.10
283 284 0.108615 ATCTGTCTCCGGTTTGCGAG 60.109 55.000 0.00 0.00 0.00 5.03
284 285 1.176619 TCTGTCTCCGGTTTGCGAGA 61.177 55.000 0.00 0.00 32.72 4.04
285 286 0.734253 CTGTCTCCGGTTTGCGAGAG 60.734 60.000 0.00 0.00 35.84 3.20
286 287 1.446272 GTCTCCGGTTTGCGAGAGG 60.446 63.158 0.00 0.00 35.84 3.69
287 288 1.605451 TCTCCGGTTTGCGAGAGGA 60.605 57.895 0.00 0.00 31.53 3.71
288 289 1.183030 TCTCCGGTTTGCGAGAGGAA 61.183 55.000 0.00 0.00 40.67 3.36
296 297 4.135493 GCGAGAGGAAACGCGTGC 62.135 66.667 14.98 8.39 44.91 5.34
297 298 2.733218 CGAGAGGAAACGCGTGCA 60.733 61.111 14.98 0.00 34.13 4.57
298 299 2.720758 CGAGAGGAAACGCGTGCAG 61.721 63.158 14.98 0.00 34.13 4.41
299 300 1.372997 GAGAGGAAACGCGTGCAGA 60.373 57.895 14.98 0.00 34.13 4.26
300 301 1.618640 GAGAGGAAACGCGTGCAGAC 61.619 60.000 14.98 5.12 34.13 3.51
301 302 2.665185 AGGAAACGCGTGCAGACC 60.665 61.111 14.98 12.21 0.00 3.85
302 303 2.970324 GGAAACGCGTGCAGACCA 60.970 61.111 14.98 0.00 0.00 4.02
303 304 2.325082 GGAAACGCGTGCAGACCAT 61.325 57.895 14.98 0.00 0.00 3.55
304 305 1.017177 GGAAACGCGTGCAGACCATA 61.017 55.000 14.98 0.00 0.00 2.74
305 306 0.094730 GAAACGCGTGCAGACCATAC 59.905 55.000 14.98 0.00 0.00 2.39
306 307 0.601576 AAACGCGTGCAGACCATACA 60.602 50.000 14.98 0.00 0.00 2.29
307 308 1.014044 AACGCGTGCAGACCATACAG 61.014 55.000 14.98 0.00 0.00 2.74
308 309 1.153842 CGCGTGCAGACCATACAGA 60.154 57.895 0.00 0.00 0.00 3.41
309 310 0.735978 CGCGTGCAGACCATACAGAA 60.736 55.000 0.00 0.00 0.00 3.02
310 311 0.721718 GCGTGCAGACCATACAGAAC 59.278 55.000 0.00 0.00 0.00 3.01
311 312 1.359848 CGTGCAGACCATACAGAACC 58.640 55.000 0.00 0.00 0.00 3.62
312 313 1.359848 GTGCAGACCATACAGAACCG 58.640 55.000 0.00 0.00 0.00 4.44
313 314 0.391130 TGCAGACCATACAGAACCGC 60.391 55.000 0.00 0.00 0.00 5.68
314 315 1.421410 GCAGACCATACAGAACCGCG 61.421 60.000 0.00 0.00 0.00 6.46
315 316 0.108804 CAGACCATACAGAACCGCGT 60.109 55.000 4.92 0.00 0.00 6.01
316 317 0.606604 AGACCATACAGAACCGCGTT 59.393 50.000 4.92 0.00 0.00 4.84
317 318 0.719465 GACCATACAGAACCGCGTTG 59.281 55.000 4.92 0.09 0.00 4.10
318 319 0.672401 ACCATACAGAACCGCGTTGG 60.672 55.000 4.92 1.44 46.41 3.77
319 320 0.390603 CCATACAGAACCGCGTTGGA 60.391 55.000 4.92 0.00 42.00 3.53
320 321 1.651987 CATACAGAACCGCGTTGGAT 58.348 50.000 4.92 0.00 42.00 3.41
321 322 1.327460 CATACAGAACCGCGTTGGATG 59.673 52.381 4.92 6.66 42.00 3.51
322 323 0.319083 TACAGAACCGCGTTGGATGT 59.681 50.000 4.92 5.91 42.00 3.06
323 324 0.949105 ACAGAACCGCGTTGGATGTC 60.949 55.000 4.92 0.00 42.00 3.06
324 325 0.670546 CAGAACCGCGTTGGATGTCT 60.671 55.000 4.92 0.00 42.00 3.41
325 326 0.034896 AGAACCGCGTTGGATGTCTT 59.965 50.000 4.92 0.00 42.00 3.01
326 327 0.442699 GAACCGCGTTGGATGTCTTC 59.557 55.000 4.92 0.00 42.00 2.87
327 328 0.250124 AACCGCGTTGGATGTCTTCA 60.250 50.000 4.92 0.00 42.00 3.02
328 329 0.670546 ACCGCGTTGGATGTCTTCAG 60.671 55.000 4.92 0.00 42.00 3.02
329 330 1.421485 CGCGTTGGATGTCTTCAGC 59.579 57.895 0.00 0.00 0.00 4.26
330 331 1.421485 GCGTTGGATGTCTTCAGCG 59.579 57.895 0.00 0.00 39.85 5.18
331 332 1.970917 GCGTTGGATGTCTTCAGCGG 61.971 60.000 0.00 0.00 37.90 5.52
332 333 0.670546 CGTTGGATGTCTTCAGCGGT 60.671 55.000 0.00 0.00 34.74 5.68
333 334 1.079503 GTTGGATGTCTTCAGCGGTC 58.920 55.000 0.00 0.00 0.00 4.79
334 335 0.036388 TTGGATGTCTTCAGCGGTCC 60.036 55.000 0.00 0.00 0.00 4.46
335 336 1.519455 GGATGTCTTCAGCGGTCCG 60.519 63.158 6.99 6.99 0.00 4.79
336 337 1.511305 GATGTCTTCAGCGGTCCGA 59.489 57.895 17.49 0.00 0.00 4.55
337 338 0.108804 GATGTCTTCAGCGGTCCGAA 60.109 55.000 17.49 0.00 0.00 4.30
338 339 0.389948 ATGTCTTCAGCGGTCCGAAC 60.390 55.000 17.49 0.00 0.00 3.95
339 340 1.006571 GTCTTCAGCGGTCCGAACA 60.007 57.895 17.49 0.00 0.00 3.18
340 341 0.599204 GTCTTCAGCGGTCCGAACAA 60.599 55.000 17.49 2.14 0.00 2.83
341 342 0.599204 TCTTCAGCGGTCCGAACAAC 60.599 55.000 17.49 0.00 0.00 3.32
342 343 1.886861 CTTCAGCGGTCCGAACAACG 61.887 60.000 17.49 0.00 42.18 4.10
343 344 2.632136 TTCAGCGGTCCGAACAACGT 62.632 55.000 17.49 0.00 40.78 3.99
344 345 2.660552 AGCGGTCCGAACAACGTG 60.661 61.111 17.49 0.00 40.78 4.49
345 346 3.708734 GCGGTCCGAACAACGTGG 61.709 66.667 17.49 0.00 40.78 4.94
346 347 2.279650 CGGTCCGAACAACGTGGT 60.280 61.111 4.91 0.00 40.78 4.16
347 348 2.305127 CGGTCCGAACAACGTGGTC 61.305 63.158 4.91 0.00 40.78 4.02
348 349 1.957695 GGTCCGAACAACGTGGTCC 60.958 63.158 0.00 0.00 40.78 4.46
349 350 2.027897 TCCGAACAACGTGGTCCG 59.972 61.111 0.00 0.00 44.03 4.79
350 351 3.039588 CCGAACAACGTGGTCCGG 61.040 66.667 6.28 6.28 42.24 5.14
351 352 2.027897 CGAACAACGTGGTCCGGA 59.972 61.111 0.00 0.00 42.24 5.14
352 353 2.305127 CGAACAACGTGGTCCGGAC 61.305 63.158 27.04 27.04 42.24 4.79
353 354 2.279650 AACAACGTGGTCCGGACG 60.280 61.111 27.68 19.79 42.24 4.79
354 355 3.795499 AACAACGTGGTCCGGACGG 62.795 63.158 27.68 20.67 41.21 4.79
355 356 3.980989 CAACGTGGTCCGGACGGA 61.981 66.667 27.68 14.50 41.21 4.69
363 364 3.147595 TCCGGACGGATGCAGGAG 61.148 66.667 9.76 0.00 39.76 3.69
364 365 4.227134 CCGGACGGATGCAGGAGG 62.227 72.222 4.40 0.00 37.50 4.30
365 366 3.461773 CGGACGGATGCAGGAGGT 61.462 66.667 0.00 0.00 0.00 3.85
366 367 2.990479 GGACGGATGCAGGAGGTT 59.010 61.111 0.00 0.00 0.00 3.50
367 368 1.299976 GGACGGATGCAGGAGGTTT 59.700 57.895 0.00 0.00 0.00 3.27
368 369 0.539986 GGACGGATGCAGGAGGTTTA 59.460 55.000 0.00 0.00 0.00 2.01
369 370 1.473434 GGACGGATGCAGGAGGTTTAG 60.473 57.143 0.00 0.00 0.00 1.85
370 371 0.541863 ACGGATGCAGGAGGTTTAGG 59.458 55.000 0.00 0.00 0.00 2.69
371 372 0.179045 CGGATGCAGGAGGTTTAGGG 60.179 60.000 0.00 0.00 0.00 3.53
372 373 1.213296 GGATGCAGGAGGTTTAGGGA 58.787 55.000 0.00 0.00 0.00 4.20
373 374 1.777272 GGATGCAGGAGGTTTAGGGAT 59.223 52.381 0.00 0.00 0.00 3.85
374 375 2.224646 GGATGCAGGAGGTTTAGGGATC 60.225 54.545 0.00 0.00 0.00 3.36
375 376 0.830648 TGCAGGAGGTTTAGGGATCG 59.169 55.000 0.00 0.00 0.00 3.69
376 377 1.120530 GCAGGAGGTTTAGGGATCGA 58.879 55.000 0.00 0.00 0.00 3.59
377 378 1.202545 GCAGGAGGTTTAGGGATCGAC 60.203 57.143 0.00 0.00 0.00 4.20
378 379 1.413077 CAGGAGGTTTAGGGATCGACC 59.587 57.143 0.00 0.00 38.08 4.79
379 380 1.291335 AGGAGGTTTAGGGATCGACCT 59.709 52.381 0.00 0.00 44.85 3.85
380 381 2.117051 GGAGGTTTAGGGATCGACCTT 58.883 52.381 0.00 0.00 42.35 3.50
381 382 3.052338 AGGAGGTTTAGGGATCGACCTTA 60.052 47.826 0.00 0.00 42.35 2.69
382 383 3.321396 GGAGGTTTAGGGATCGACCTTAG 59.679 52.174 0.00 0.00 42.35 2.18
383 384 4.213513 GAGGTTTAGGGATCGACCTTAGA 58.786 47.826 0.00 0.00 42.35 2.10
384 385 4.216708 AGGTTTAGGGATCGACCTTAGAG 58.783 47.826 0.00 0.00 39.41 2.43
385 386 4.079327 AGGTTTAGGGATCGACCTTAGAGA 60.079 45.833 0.00 0.00 39.41 3.10
386 387 4.833938 GGTTTAGGGATCGACCTTAGAGAT 59.166 45.833 0.00 0.00 42.09 2.75
387 388 5.279056 GGTTTAGGGATCGACCTTAGAGATG 60.279 48.000 0.00 0.00 42.09 2.90
388 389 2.243810 AGGGATCGACCTTAGAGATGC 58.756 52.381 0.00 0.00 37.69 3.91
389 390 1.273886 GGGATCGACCTTAGAGATGCC 59.726 57.143 6.96 6.96 43.63 4.40
390 391 1.273886 GGATCGACCTTAGAGATGCCC 59.726 57.143 0.00 0.00 35.41 5.36
391 392 2.243810 GATCGACCTTAGAGATGCCCT 58.756 52.381 0.00 0.00 0.00 5.19
392 393 2.160721 TCGACCTTAGAGATGCCCTT 57.839 50.000 0.00 0.00 0.00 3.95
393 394 3.308035 TCGACCTTAGAGATGCCCTTA 57.692 47.619 0.00 0.00 0.00 2.69
394 395 3.638860 TCGACCTTAGAGATGCCCTTAA 58.361 45.455 0.00 0.00 0.00 1.85
395 396 3.383825 TCGACCTTAGAGATGCCCTTAAC 59.616 47.826 0.00 0.00 0.00 2.01
396 397 3.132289 CGACCTTAGAGATGCCCTTAACA 59.868 47.826 0.00 0.00 0.00 2.41
397 398 4.382685 CGACCTTAGAGATGCCCTTAACAA 60.383 45.833 0.00 0.00 0.00 2.83
398 399 4.844884 ACCTTAGAGATGCCCTTAACAAC 58.155 43.478 0.00 0.00 0.00 3.32
399 400 3.871594 CCTTAGAGATGCCCTTAACAACG 59.128 47.826 0.00 0.00 0.00 4.10
400 401 4.504858 CTTAGAGATGCCCTTAACAACGT 58.495 43.478 0.00 0.00 0.00 3.99
401 402 2.973945 AGAGATGCCCTTAACAACGTC 58.026 47.619 0.00 0.00 0.00 4.34
402 403 1.659098 GAGATGCCCTTAACAACGTCG 59.341 52.381 0.00 0.00 0.00 5.12
403 404 0.725117 GATGCCCTTAACAACGTCGG 59.275 55.000 0.00 0.00 0.00 4.79
404 405 0.675522 ATGCCCTTAACAACGTCGGG 60.676 55.000 0.00 0.00 37.97 5.14
405 406 1.004679 GCCCTTAACAACGTCGGGA 60.005 57.895 0.00 0.00 37.05 5.14
406 407 1.017701 GCCCTTAACAACGTCGGGAG 61.018 60.000 0.00 0.00 37.05 4.30
407 408 0.319405 CCCTTAACAACGTCGGGAGT 59.681 55.000 0.00 0.00 37.05 3.85
408 409 1.670967 CCCTTAACAACGTCGGGAGTC 60.671 57.143 0.00 0.00 37.05 3.36
409 410 1.271656 CCTTAACAACGTCGGGAGTCT 59.728 52.381 0.00 0.00 0.00 3.24
410 411 2.288640 CCTTAACAACGTCGGGAGTCTT 60.289 50.000 0.00 0.00 0.00 3.01
411 412 2.427232 TAACAACGTCGGGAGTCTTG 57.573 50.000 0.00 0.00 0.00 3.02
412 413 0.878961 AACAACGTCGGGAGTCTTGC 60.879 55.000 0.00 0.00 0.00 4.01
413 414 1.006102 CAACGTCGGGAGTCTTGCT 60.006 57.895 0.00 0.00 0.00 3.91
414 415 1.009389 CAACGTCGGGAGTCTTGCTC 61.009 60.000 0.00 0.00 43.39 4.26
415 416 2.202492 CGTCGGGAGTCTTGCTCG 60.202 66.667 0.00 0.00 45.03 5.03
416 417 2.963371 GTCGGGAGTCTTGCTCGT 59.037 61.111 0.00 0.00 45.03 4.18
417 418 1.289380 GTCGGGAGTCTTGCTCGTT 59.711 57.895 0.00 0.00 45.03 3.85
418 419 0.319641 GTCGGGAGTCTTGCTCGTTT 60.320 55.000 0.00 0.00 45.03 3.60
419 420 0.391597 TCGGGAGTCTTGCTCGTTTT 59.608 50.000 0.00 0.00 45.03 2.43
420 421 0.512952 CGGGAGTCTTGCTCGTTTTG 59.487 55.000 0.00 0.00 45.03 2.44
421 422 0.238553 GGGAGTCTTGCTCGTTTTGC 59.761 55.000 0.00 0.00 45.03 3.68
422 423 0.944386 GGAGTCTTGCTCGTTTTGCA 59.056 50.000 0.00 0.00 45.03 4.08
423 424 1.537202 GGAGTCTTGCTCGTTTTGCAT 59.463 47.619 0.00 0.00 45.03 3.96
424 425 2.030805 GGAGTCTTGCTCGTTTTGCATT 60.031 45.455 0.00 0.00 45.03 3.56
425 426 3.550842 GGAGTCTTGCTCGTTTTGCATTT 60.551 43.478 0.00 0.00 45.03 2.32
426 427 4.044426 GAGTCTTGCTCGTTTTGCATTTT 58.956 39.130 0.00 0.00 40.34 1.82
427 428 4.432712 AGTCTTGCTCGTTTTGCATTTTT 58.567 34.783 0.00 0.00 40.34 1.94
469 470 4.455917 TTTTTCGCGATTGTACTCGTTT 57.544 36.364 10.88 0.00 40.73 3.60
470 471 4.455917 TTTTCGCGATTGTACTCGTTTT 57.544 36.364 10.88 0.00 40.73 2.43
471 472 4.455917 TTTCGCGATTGTACTCGTTTTT 57.544 36.364 10.88 0.00 40.73 1.94
472 473 3.693300 TCGCGATTGTACTCGTTTTTC 57.307 42.857 3.71 0.00 40.73 2.29
473 474 3.311106 TCGCGATTGTACTCGTTTTTCT 58.689 40.909 3.71 0.00 40.73 2.52
474 475 3.120616 TCGCGATTGTACTCGTTTTTCTG 59.879 43.478 3.71 0.00 40.73 3.02
475 476 3.121126 CGCGATTGTACTCGTTTTTCTGT 60.121 43.478 0.00 0.00 40.73 3.41
476 477 4.088923 CGCGATTGTACTCGTTTTTCTGTA 59.911 41.667 0.00 0.00 40.73 2.74
477 478 5.539207 GCGATTGTACTCGTTTTTCTGTAG 58.461 41.667 6.41 0.00 40.73 2.74
478 479 5.444218 GCGATTGTACTCGTTTTTCTGTAGG 60.444 44.000 6.41 0.00 40.73 3.18
479 480 5.860182 CGATTGTACTCGTTTTTCTGTAGGA 59.140 40.000 0.00 0.00 34.00 2.94
480 481 6.033619 CGATTGTACTCGTTTTTCTGTAGGAG 59.966 42.308 0.00 0.00 34.00 3.69
481 482 5.779529 TGTACTCGTTTTTCTGTAGGAGT 57.220 39.130 0.00 0.00 41.06 3.85
482 483 6.882610 TGTACTCGTTTTTCTGTAGGAGTA 57.117 37.500 0.00 0.00 39.44 2.59
483 484 6.906659 TGTACTCGTTTTTCTGTAGGAGTAG 58.093 40.000 0.00 0.00 40.41 2.57
484 485 6.488006 TGTACTCGTTTTTCTGTAGGAGTAGT 59.512 38.462 0.00 0.00 40.41 2.73
491 492 2.089980 TCTGTAGGAGTAGTCCAACGC 58.910 52.381 19.00 6.15 46.80 4.84
569 570 5.540911 GGAAATTCAGCTGTCAAATCCAAA 58.459 37.500 14.67 0.00 0.00 3.28
573 577 8.454570 AAATTCAGCTGTCAAATCCAAATTTT 57.545 26.923 14.67 0.00 32.69 1.82
630 634 3.208383 CGCCACACACCAGCAACA 61.208 61.111 0.00 0.00 0.00 3.33
646 650 0.820074 AACAAATCCGACGGCAACCA 60.820 50.000 9.66 0.00 0.00 3.67
647 651 1.209127 CAAATCCGACGGCAACCAC 59.791 57.895 9.66 0.00 0.00 4.16
648 652 1.072505 AAATCCGACGGCAACCACT 59.927 52.632 9.66 0.00 0.00 4.00
651 655 2.107041 ATCCGACGGCAACCACTCAA 62.107 55.000 9.66 0.00 0.00 3.02
661 665 2.440247 CCACTCAAATCCCGCCCC 60.440 66.667 0.00 0.00 0.00 5.80
665 669 4.794648 TCAAATCCCGCCCCGCAG 62.795 66.667 0.00 0.00 0.00 5.18
706 710 2.559231 GAGAAGAATCCGGCCCTACTAG 59.441 54.545 0.00 0.00 0.00 2.57
749 753 2.178984 ACCTGTGATTCCCTTCCCAAAA 59.821 45.455 0.00 0.00 0.00 2.44
763 768 2.983030 AAAACCCGCAGCATCGCA 60.983 55.556 0.00 0.00 0.00 5.10
832 838 2.493099 TAAATACCCCGCCTTCCCTA 57.507 50.000 0.00 0.00 0.00 3.53
887 893 4.618227 GCAACAACCAACAAAGAACAGAGT 60.618 41.667 0.00 0.00 0.00 3.24
894 900 6.597562 ACCAACAAAGAACAGAGTACCATAA 58.402 36.000 0.00 0.00 0.00 1.90
925 935 0.814457 AGCCACACAGAGAGATCGAC 59.186 55.000 0.00 0.00 0.00 4.20
926 936 0.524392 GCCACACAGAGAGATCGACG 60.524 60.000 0.00 0.00 0.00 5.12
960 974 0.104855 TTAGCCATCGCCTAGCACAG 59.895 55.000 0.00 0.00 34.57 3.66
970 984 2.029288 CTAGCACAGCACACCACCG 61.029 63.158 0.00 0.00 0.00 4.94
1029 1056 4.545706 GCCATCGCCATCCACGGA 62.546 66.667 0.00 0.00 0.00 4.69
1417 1448 3.810941 GGTAATCCATCAATTAACGCCGA 59.189 43.478 0.00 0.00 0.00 5.54
1418 1449 4.454504 GGTAATCCATCAATTAACGCCGAT 59.545 41.667 0.00 0.00 0.00 4.18
1449 1482 5.190132 TCTTTTGATACGGGATTAACCTCCA 59.810 40.000 0.00 0.00 37.01 3.86
1514 1554 3.408634 AGTAACGTAAAACATGCTGCCT 58.591 40.909 0.00 0.00 0.00 4.75
1515 1555 2.989422 AACGTAAAACATGCTGCCTC 57.011 45.000 0.00 0.00 0.00 4.70
1516 1556 1.165270 ACGTAAAACATGCTGCCTCC 58.835 50.000 0.00 0.00 0.00 4.30
1517 1557 0.451783 CGTAAAACATGCTGCCTCCC 59.548 55.000 0.00 0.00 0.00 4.30
1535 1575 4.785376 CCTCCCTATGGCCATCTAGTTAAT 59.215 45.833 24.80 0.00 0.00 1.40
1584 1635 6.517914 TTTAATTGAAAACAATCACGTGCC 57.482 33.333 11.67 0.00 0.00 5.01
1589 1640 1.805428 AAACAATCACGTGCCCCTGC 61.805 55.000 11.67 0.00 38.26 4.85
1654 1705 2.851534 CCGAAATTTCTCGTGGAAAGC 58.148 47.619 15.92 0.00 45.61 3.51
1687 1772 2.429571 GGTGCGCTCGACACGTTA 60.430 61.111 9.73 0.00 38.98 3.18
1690 1775 0.564767 GTGCGCTCGACACGTTATAC 59.435 55.000 9.73 0.00 0.00 1.47
1695 1780 2.714480 CGCTCGACACGTTATACATGAG 59.286 50.000 0.00 0.00 0.00 2.90
1746 1841 4.202461 TGTCCAGCTGAACCTTTTCTGTAT 60.202 41.667 17.39 0.00 34.11 2.29
1858 1995 6.238593 CCTGCAAGATATTTTGGAGTAGCTTC 60.239 42.308 21.06 0.00 42.78 3.86
1922 2061 6.357579 TCATTTTGGGTAAGCATGTCATTT 57.642 33.333 0.00 0.00 0.00 2.32
1989 2139 5.746990 AGACAGAGTTAGGTTAGCACAAT 57.253 39.130 0.00 0.00 0.00 2.71
1991 2141 6.868622 AGACAGAGTTAGGTTAGCACAATAG 58.131 40.000 0.00 0.00 0.00 1.73
1992 2142 5.420409 ACAGAGTTAGGTTAGCACAATAGC 58.580 41.667 0.00 0.00 0.00 2.97
2001 2151 4.333926 GGTTAGCACAATAGCTCAAGAAGG 59.666 45.833 0.00 0.00 45.26 3.46
2093 2315 1.752788 GCACCTACCAAAACACACCCT 60.753 52.381 0.00 0.00 0.00 4.34
2095 2317 2.360801 CACCTACCAAAACACACCCTTG 59.639 50.000 0.00 0.00 0.00 3.61
2144 2466 1.686355 AGATCGTGCAGCTAGCTAGT 58.314 50.000 18.86 6.34 45.94 2.57
2145 2467 2.852449 AGATCGTGCAGCTAGCTAGTA 58.148 47.619 18.86 8.82 45.94 1.82
2146 2468 2.550606 AGATCGTGCAGCTAGCTAGTAC 59.449 50.000 18.86 18.61 45.94 2.73
2170 2492 1.076192 AGCAGCTGCACCAAAGGAT 59.924 52.632 38.24 13.55 45.16 3.24
2259 2586 7.122055 TGGTCGGCACTATTTCTCATTAAATTT 59.878 33.333 0.00 0.00 31.63 1.82
2285 2668 5.879223 ACAAAGATCACTTGTCAGATCCATC 59.121 40.000 7.24 0.00 41.16 3.51
2309 2705 4.680407 ACCTAGGATGGTTACTGTACACA 58.320 43.478 17.98 0.00 36.89 3.72
2310 2706 4.710375 ACCTAGGATGGTTACTGTACACAG 59.290 45.833 17.98 7.82 42.71 3.66
2311 2707 6.850893 ACCTAGGATGGTTACTGTACACAGC 61.851 48.000 17.98 0.00 41.60 4.40
2337 2733 1.880027 CACCCCTGTTTCTACTTGCAC 59.120 52.381 0.00 0.00 0.00 4.57
2408 2804 3.896133 ACCACTCGCGTCGTGTGT 61.896 61.111 22.55 18.13 45.69 3.72
2410 2806 3.394874 CACTCGCGTCGTGTGTGG 61.395 66.667 25.59 12.28 43.34 4.17
2417 2813 2.669569 GTCGTGTGTGGCAGCCAT 60.670 61.111 19.75 0.00 35.28 4.40
2418 2814 2.669229 TCGTGTGTGGCAGCCATG 60.669 61.111 19.75 5.84 35.28 3.66
2419 2815 3.740397 CGTGTGTGGCAGCCATGG 61.740 66.667 19.75 7.63 35.28 3.66
2420 2816 3.376078 GTGTGTGGCAGCCATGGG 61.376 66.667 19.75 0.00 35.28 4.00
2421 2817 3.578286 TGTGTGGCAGCCATGGGA 61.578 61.111 19.75 0.00 35.28 4.37
2422 2818 3.064324 GTGTGGCAGCCATGGGAC 61.064 66.667 19.75 8.69 35.28 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.318839 CCACACACACATCCTTTCATGTT 59.681 43.478 0.00 0.00 34.60 2.71
1 2 2.886523 CCACACACACATCCTTTCATGT 59.113 45.455 0.00 0.00 37.49 3.21
2 3 2.886523 ACCACACACACATCCTTTCATG 59.113 45.455 0.00 0.00 0.00 3.07
4 5 2.727123 ACCACACACACATCCTTTCA 57.273 45.000 0.00 0.00 0.00 2.69
5 6 3.490761 CCAAACCACACACACATCCTTTC 60.491 47.826 0.00 0.00 0.00 2.62
7 8 2.031120 CCAAACCACACACACATCCTT 58.969 47.619 0.00 0.00 0.00 3.36
8 9 1.691196 CCAAACCACACACACATCCT 58.309 50.000 0.00 0.00 0.00 3.24
9 10 0.673437 CCCAAACCACACACACATCC 59.327 55.000 0.00 0.00 0.00 3.51
10 11 1.066908 CACCCAAACCACACACACATC 59.933 52.381 0.00 0.00 0.00 3.06
11 12 1.110442 CACCCAAACCACACACACAT 58.890 50.000 0.00 0.00 0.00 3.21
12 13 0.967887 CCACCCAAACCACACACACA 60.968 55.000 0.00 0.00 0.00 3.72
13 14 1.671901 CCCACCCAAACCACACACAC 61.672 60.000 0.00 0.00 0.00 3.82
14 15 1.380515 CCCACCCAAACCACACACA 60.381 57.895 0.00 0.00 0.00 3.72
15 16 2.791868 GCCCACCCAAACCACACAC 61.792 63.158 0.00 0.00 0.00 3.82
16 17 2.443016 GCCCACCCAAACCACACA 60.443 61.111 0.00 0.00 0.00 3.72
17 18 3.230990 GGCCCACCCAAACCACAC 61.231 66.667 0.00 0.00 0.00 3.82
18 19 3.747521 CTGGCCCACCCAAACCACA 62.748 63.158 0.00 0.00 44.81 4.17
19 20 2.917227 CTGGCCCACCCAAACCAC 60.917 66.667 0.00 0.00 44.81 4.16
20 21 4.232061 CCTGGCCCACCCAAACCA 62.232 66.667 0.00 0.00 44.81 3.67
26 27 4.442454 GTTAGCCCTGGCCCACCC 62.442 72.222 4.13 0.00 43.17 4.61
27 28 3.218386 TTGTTAGCCCTGGCCCACC 62.218 63.158 4.13 0.00 43.17 4.61
28 29 1.977009 GTTGTTAGCCCTGGCCCAC 60.977 63.158 4.13 2.45 43.17 4.61
29 30 2.424842 CTGTTGTTAGCCCTGGCCCA 62.425 60.000 4.13 0.00 43.17 5.36
30 31 1.678970 CTGTTGTTAGCCCTGGCCC 60.679 63.158 4.13 0.00 43.17 5.80
31 32 1.678970 CCTGTTGTTAGCCCTGGCC 60.679 63.158 4.13 0.00 43.17 5.36
32 33 1.074951 ACCTGTTGTTAGCCCTGGC 59.925 57.895 0.00 0.00 42.33 4.85
33 34 0.609131 CCACCTGTTGTTAGCCCTGG 60.609 60.000 0.00 0.00 0.00 4.45
34 35 0.609131 CCCACCTGTTGTTAGCCCTG 60.609 60.000 0.00 0.00 0.00 4.45
35 36 1.767692 CCCACCTGTTGTTAGCCCT 59.232 57.895 0.00 0.00 0.00 5.19
36 37 1.977009 GCCCACCTGTTGTTAGCCC 60.977 63.158 0.00 0.00 0.00 5.19
37 38 2.332654 CGCCCACCTGTTGTTAGCC 61.333 63.158 0.00 0.00 0.00 3.93
38 39 1.599797 ACGCCCACCTGTTGTTAGC 60.600 57.895 0.00 0.00 0.00 3.09
39 40 0.250124 TCACGCCCACCTGTTGTTAG 60.250 55.000 0.00 0.00 0.00 2.34
40 41 0.533308 GTCACGCCCACCTGTTGTTA 60.533 55.000 0.00 0.00 0.00 2.41
41 42 1.822186 GTCACGCCCACCTGTTGTT 60.822 57.895 0.00 0.00 0.00 2.83
42 43 2.203153 GTCACGCCCACCTGTTGT 60.203 61.111 0.00 0.00 0.00 3.32
43 44 2.203139 TGTCACGCCCACCTGTTG 60.203 61.111 0.00 0.00 0.00 3.33
44 45 2.111043 CTGTCACGCCCACCTGTT 59.889 61.111 0.00 0.00 0.00 3.16
45 46 4.626081 GCTGTCACGCCCACCTGT 62.626 66.667 0.00 0.00 0.00 4.00
256 257 2.191641 GGAGACAGATGCAGGGGC 59.808 66.667 0.00 0.00 41.68 5.80
257 258 2.503061 CGGAGACAGATGCAGGGG 59.497 66.667 0.00 0.00 0.00 4.79
258 259 1.903877 AACCGGAGACAGATGCAGGG 61.904 60.000 9.46 0.00 0.00 4.45
259 260 0.036010 AAACCGGAGACAGATGCAGG 60.036 55.000 9.46 0.00 0.00 4.85
260 261 1.081892 CAAACCGGAGACAGATGCAG 58.918 55.000 9.46 0.00 0.00 4.41
261 262 0.955428 GCAAACCGGAGACAGATGCA 60.955 55.000 9.46 0.00 32.80 3.96
262 263 1.796796 GCAAACCGGAGACAGATGC 59.203 57.895 9.46 3.71 0.00 3.91
263 264 0.389817 TCGCAAACCGGAGACAGATG 60.390 55.000 9.46 0.00 37.59 2.90
264 265 0.108615 CTCGCAAACCGGAGACAGAT 60.109 55.000 9.46 0.00 37.59 2.90
265 266 1.176619 TCTCGCAAACCGGAGACAGA 61.177 55.000 9.46 0.45 37.59 3.41
266 267 0.734253 CTCTCGCAAACCGGAGACAG 60.734 60.000 9.46 0.00 36.79 3.51
267 268 1.289066 CTCTCGCAAACCGGAGACA 59.711 57.895 9.46 0.00 36.79 3.41
268 269 1.446272 CCTCTCGCAAACCGGAGAC 60.446 63.158 9.46 0.00 36.79 3.36
269 270 1.183030 TTCCTCTCGCAAACCGGAGA 61.183 55.000 9.46 0.00 36.79 3.71
270 271 0.320421 TTTCCTCTCGCAAACCGGAG 60.320 55.000 9.46 0.00 37.59 4.63
271 272 0.601841 GTTTCCTCTCGCAAACCGGA 60.602 55.000 9.46 0.00 37.59 5.14
272 273 1.866925 GTTTCCTCTCGCAAACCGG 59.133 57.895 0.00 0.00 37.59 5.28
273 274 1.491563 CGTTTCCTCTCGCAAACCG 59.508 57.895 0.00 0.00 38.61 4.44
280 281 2.720758 CTGCACGCGTTTCCTCTCG 61.721 63.158 10.22 0.00 0.00 4.04
281 282 1.372997 TCTGCACGCGTTTCCTCTC 60.373 57.895 10.22 0.00 0.00 3.20
282 283 1.664965 GTCTGCACGCGTTTCCTCT 60.665 57.895 10.22 0.00 0.00 3.69
283 284 2.668280 GGTCTGCACGCGTTTCCTC 61.668 63.158 10.22 0.00 0.00 3.71
284 285 2.665185 GGTCTGCACGCGTTTCCT 60.665 61.111 10.22 0.00 0.00 3.36
285 286 1.017177 TATGGTCTGCACGCGTTTCC 61.017 55.000 10.22 8.48 0.00 3.13
286 287 0.094730 GTATGGTCTGCACGCGTTTC 59.905 55.000 10.22 4.94 0.00 2.78
287 288 0.601576 TGTATGGTCTGCACGCGTTT 60.602 50.000 10.22 0.00 0.00 3.60
288 289 1.005512 TGTATGGTCTGCACGCGTT 60.006 52.632 10.22 0.00 0.00 4.84
289 290 1.446099 CTGTATGGTCTGCACGCGT 60.446 57.895 5.58 5.58 0.00 6.01
290 291 0.735978 TTCTGTATGGTCTGCACGCG 60.736 55.000 3.53 3.53 0.00 6.01
291 292 0.721718 GTTCTGTATGGTCTGCACGC 59.278 55.000 0.00 0.00 0.00 5.34
292 293 1.359848 GGTTCTGTATGGTCTGCACG 58.640 55.000 0.00 0.00 0.00 5.34
293 294 1.359848 CGGTTCTGTATGGTCTGCAC 58.640 55.000 0.00 0.00 0.00 4.57
294 295 0.391130 GCGGTTCTGTATGGTCTGCA 60.391 55.000 0.00 0.00 0.00 4.41
295 296 1.421410 CGCGGTTCTGTATGGTCTGC 61.421 60.000 0.00 0.00 0.00 4.26
296 297 0.108804 ACGCGGTTCTGTATGGTCTG 60.109 55.000 12.47 0.00 0.00 3.51
297 298 0.606604 AACGCGGTTCTGTATGGTCT 59.393 50.000 12.47 0.00 0.00 3.85
298 299 0.719465 CAACGCGGTTCTGTATGGTC 59.281 55.000 12.47 0.00 0.00 4.02
299 300 0.672401 CCAACGCGGTTCTGTATGGT 60.672 55.000 12.47 0.00 0.00 3.55
300 301 0.390603 TCCAACGCGGTTCTGTATGG 60.391 55.000 12.47 0.00 35.57 2.74
301 302 1.327460 CATCCAACGCGGTTCTGTATG 59.673 52.381 12.47 1.02 35.57 2.39
302 303 1.066430 ACATCCAACGCGGTTCTGTAT 60.066 47.619 12.47 0.00 35.57 2.29
303 304 0.319083 ACATCCAACGCGGTTCTGTA 59.681 50.000 12.47 0.00 35.57 2.74
304 305 0.949105 GACATCCAACGCGGTTCTGT 60.949 55.000 12.47 6.91 35.57 3.41
305 306 0.670546 AGACATCCAACGCGGTTCTG 60.671 55.000 12.47 3.10 35.57 3.02
306 307 0.034896 AAGACATCCAACGCGGTTCT 59.965 50.000 12.47 0.00 35.57 3.01
307 308 0.442699 GAAGACATCCAACGCGGTTC 59.557 55.000 12.47 0.00 35.57 3.62
308 309 0.250124 TGAAGACATCCAACGCGGTT 60.250 50.000 12.47 0.00 35.57 4.44
309 310 0.670546 CTGAAGACATCCAACGCGGT 60.671 55.000 12.47 0.00 35.57 5.68
310 311 1.970917 GCTGAAGACATCCAACGCGG 61.971 60.000 12.47 0.00 0.00 6.46
311 312 1.421485 GCTGAAGACATCCAACGCG 59.579 57.895 3.53 3.53 0.00 6.01
312 313 1.421485 CGCTGAAGACATCCAACGC 59.579 57.895 0.00 0.00 0.00 4.84
313 314 0.670546 ACCGCTGAAGACATCCAACG 60.671 55.000 0.00 0.00 0.00 4.10
314 315 1.079503 GACCGCTGAAGACATCCAAC 58.920 55.000 0.00 0.00 0.00 3.77
315 316 0.036388 GGACCGCTGAAGACATCCAA 60.036 55.000 0.00 0.00 0.00 3.53
316 317 1.596934 GGACCGCTGAAGACATCCA 59.403 57.895 0.00 0.00 0.00 3.41
317 318 1.519455 CGGACCGCTGAAGACATCC 60.519 63.158 0.00 0.00 0.00 3.51
318 319 0.108804 TTCGGACCGCTGAAGACATC 60.109 55.000 9.66 0.00 34.53 3.06
319 320 0.389948 GTTCGGACCGCTGAAGACAT 60.390 55.000 9.66 0.00 39.96 3.06
320 321 1.006571 GTTCGGACCGCTGAAGACA 60.007 57.895 9.66 0.00 39.96 3.41
321 322 0.599204 TTGTTCGGACCGCTGAAGAC 60.599 55.000 9.66 1.57 39.96 3.01
322 323 0.599204 GTTGTTCGGACCGCTGAAGA 60.599 55.000 9.66 0.00 39.96 2.87
323 324 1.860078 GTTGTTCGGACCGCTGAAG 59.140 57.895 9.66 0.00 39.96 3.02
324 325 1.952133 CGTTGTTCGGACCGCTGAA 60.952 57.895 9.66 0.00 37.07 3.02
325 326 2.355363 CGTTGTTCGGACCGCTGA 60.355 61.111 9.66 0.00 35.71 4.26
326 327 2.660552 ACGTTGTTCGGACCGCTG 60.661 61.111 9.66 0.00 44.69 5.18
327 328 2.660552 CACGTTGTTCGGACCGCT 60.661 61.111 9.66 0.00 44.69 5.52
328 329 3.708734 CCACGTTGTTCGGACCGC 61.709 66.667 9.66 0.00 44.69 5.68
329 330 2.279650 ACCACGTTGTTCGGACCG 60.280 61.111 7.84 7.84 44.69 4.79
330 331 1.957695 GGACCACGTTGTTCGGACC 60.958 63.158 0.00 0.00 44.69 4.46
331 332 2.305127 CGGACCACGTTGTTCGGAC 61.305 63.158 12.46 0.00 44.69 4.79
332 333 2.027897 CGGACCACGTTGTTCGGA 59.972 61.111 12.46 0.00 44.69 4.55
334 335 2.027897 TCCGGACCACGTTGTTCG 59.972 61.111 13.29 13.29 46.00 3.95
335 336 2.305127 CGTCCGGACCACGTTGTTC 61.305 63.158 28.52 0.00 42.24 3.18
336 337 2.279650 CGTCCGGACCACGTTGTT 60.280 61.111 28.52 0.00 42.24 2.83
337 338 4.289245 CCGTCCGGACCACGTTGT 62.289 66.667 28.52 0.00 42.24 3.32
338 339 3.980989 TCCGTCCGGACCACGTTG 61.981 66.667 28.52 13.18 39.76 4.10
347 348 4.227134 CCTCCTGCATCCGTCCGG 62.227 72.222 0.00 0.00 0.00 5.14
348 349 2.521958 AAACCTCCTGCATCCGTCCG 62.522 60.000 0.00 0.00 0.00 4.79
349 350 0.539986 TAAACCTCCTGCATCCGTCC 59.460 55.000 0.00 0.00 0.00 4.79
350 351 1.473434 CCTAAACCTCCTGCATCCGTC 60.473 57.143 0.00 0.00 0.00 4.79
351 352 0.541863 CCTAAACCTCCTGCATCCGT 59.458 55.000 0.00 0.00 0.00 4.69
352 353 0.179045 CCCTAAACCTCCTGCATCCG 60.179 60.000 0.00 0.00 0.00 4.18
353 354 1.213296 TCCCTAAACCTCCTGCATCC 58.787 55.000 0.00 0.00 0.00 3.51
354 355 2.548920 CGATCCCTAAACCTCCTGCATC 60.549 54.545 0.00 0.00 0.00 3.91
355 356 1.417890 CGATCCCTAAACCTCCTGCAT 59.582 52.381 0.00 0.00 0.00 3.96
356 357 0.830648 CGATCCCTAAACCTCCTGCA 59.169 55.000 0.00 0.00 0.00 4.41
357 358 1.120530 TCGATCCCTAAACCTCCTGC 58.879 55.000 0.00 0.00 0.00 4.85
358 359 1.413077 GGTCGATCCCTAAACCTCCTG 59.587 57.143 0.00 0.00 0.00 3.86
359 360 1.291335 AGGTCGATCCCTAAACCTCCT 59.709 52.381 0.00 0.00 37.59 3.69
360 361 1.790818 AGGTCGATCCCTAAACCTCC 58.209 55.000 0.00 0.00 37.59 4.30
361 362 4.213513 TCTAAGGTCGATCCCTAAACCTC 58.786 47.826 0.00 0.00 41.25 3.85
362 363 4.079327 TCTCTAAGGTCGATCCCTAAACCT 60.079 45.833 0.00 0.00 43.96 3.50
363 364 4.213513 TCTCTAAGGTCGATCCCTAAACC 58.786 47.826 0.00 0.00 36.75 3.27
364 365 5.774630 CATCTCTAAGGTCGATCCCTAAAC 58.225 45.833 0.00 0.00 36.75 2.01
365 366 4.281182 GCATCTCTAAGGTCGATCCCTAAA 59.719 45.833 0.00 0.00 36.75 1.85
366 367 3.827302 GCATCTCTAAGGTCGATCCCTAA 59.173 47.826 0.00 0.00 36.75 2.69
367 368 3.422796 GCATCTCTAAGGTCGATCCCTA 58.577 50.000 0.00 0.00 36.75 3.53
368 369 2.243810 GCATCTCTAAGGTCGATCCCT 58.756 52.381 0.00 0.00 36.75 4.20
369 370 1.273886 GGCATCTCTAAGGTCGATCCC 59.726 57.143 0.00 0.00 36.75 3.85
370 371 1.273886 GGGCATCTCTAAGGTCGATCC 59.726 57.143 0.00 0.00 0.00 3.36
371 372 2.243810 AGGGCATCTCTAAGGTCGATC 58.756 52.381 0.00 0.00 0.00 3.69
372 373 2.390225 AGGGCATCTCTAAGGTCGAT 57.610 50.000 0.00 0.00 0.00 3.59
373 374 2.160721 AAGGGCATCTCTAAGGTCGA 57.839 50.000 0.00 0.00 0.00 4.20
374 375 3.132289 TGTTAAGGGCATCTCTAAGGTCG 59.868 47.826 0.00 0.00 0.00 4.79
375 376 4.755266 TGTTAAGGGCATCTCTAAGGTC 57.245 45.455 0.00 0.00 0.00 3.85
376 377 4.623171 CGTTGTTAAGGGCATCTCTAAGGT 60.623 45.833 0.00 0.00 0.00 3.50
377 378 3.871594 CGTTGTTAAGGGCATCTCTAAGG 59.128 47.826 0.00 0.00 0.00 2.69
378 379 4.504858 ACGTTGTTAAGGGCATCTCTAAG 58.495 43.478 0.00 0.00 0.00 2.18
379 380 4.501071 GACGTTGTTAAGGGCATCTCTAA 58.499 43.478 0.00 0.00 0.00 2.10
380 381 3.428452 CGACGTTGTTAAGGGCATCTCTA 60.428 47.826 0.00 0.00 0.00 2.43
381 382 2.674177 CGACGTTGTTAAGGGCATCTCT 60.674 50.000 0.00 0.00 0.00 3.10
382 383 1.659098 CGACGTTGTTAAGGGCATCTC 59.341 52.381 0.00 0.00 0.00 2.75
383 384 1.674817 CCGACGTTGTTAAGGGCATCT 60.675 52.381 1.30 0.00 0.00 2.90
384 385 0.725117 CCGACGTTGTTAAGGGCATC 59.275 55.000 1.30 0.00 0.00 3.91
385 386 0.675522 CCCGACGTTGTTAAGGGCAT 60.676 55.000 1.30 0.00 35.09 4.40
386 387 1.301874 CCCGACGTTGTTAAGGGCA 60.302 57.895 1.30 0.00 35.09 5.36
387 388 1.004679 TCCCGACGTTGTTAAGGGC 60.005 57.895 1.30 0.00 41.76 5.19
388 389 0.319405 ACTCCCGACGTTGTTAAGGG 59.681 55.000 1.30 3.23 43.32 3.95
389 390 1.271656 AGACTCCCGACGTTGTTAAGG 59.728 52.381 1.30 0.00 0.00 2.69
390 391 2.719426 AGACTCCCGACGTTGTTAAG 57.281 50.000 1.30 0.00 0.00 1.85
391 392 2.746269 CAAGACTCCCGACGTTGTTAA 58.254 47.619 1.30 0.00 0.00 2.01
392 393 1.603678 GCAAGACTCCCGACGTTGTTA 60.604 52.381 1.30 0.00 0.00 2.41
393 394 0.878961 GCAAGACTCCCGACGTTGTT 60.879 55.000 1.30 0.00 0.00 2.83
394 395 1.300697 GCAAGACTCCCGACGTTGT 60.301 57.895 1.30 0.00 0.00 3.32
395 396 1.006102 AGCAAGACTCCCGACGTTG 60.006 57.895 0.00 0.00 0.00 4.10
396 397 1.289380 GAGCAAGACTCCCGACGTT 59.711 57.895 0.00 0.00 39.75 3.99
397 398 2.963371 GAGCAAGACTCCCGACGT 59.037 61.111 0.00 0.00 39.75 4.34
398 399 2.202492 CGAGCAAGACTCCCGACG 60.202 66.667 0.00 0.00 43.01 5.12
399 400 0.319641 AAACGAGCAAGACTCCCGAC 60.320 55.000 0.00 0.00 43.01 4.79
400 401 0.391597 AAAACGAGCAAGACTCCCGA 59.608 50.000 0.00 0.00 43.01 5.14
401 402 0.512952 CAAAACGAGCAAGACTCCCG 59.487 55.000 0.00 0.00 43.01 5.14
402 403 0.238553 GCAAAACGAGCAAGACTCCC 59.761 55.000 0.00 0.00 43.01 4.30
403 404 0.944386 TGCAAAACGAGCAAGACTCC 59.056 50.000 0.00 0.00 43.01 3.85
404 405 2.977405 ATGCAAAACGAGCAAGACTC 57.023 45.000 0.00 0.00 46.27 3.36
405 406 3.715628 AAATGCAAAACGAGCAAGACT 57.284 38.095 0.00 0.00 46.27 3.24
406 407 4.777140 AAAAATGCAAAACGAGCAAGAC 57.223 36.364 0.00 0.00 46.27 3.01
448 449 4.455917 AAACGAGTACAATCGCGAAAAA 57.544 36.364 15.24 0.00 46.60 1.94
449 450 4.455917 AAAACGAGTACAATCGCGAAAA 57.544 36.364 15.24 0.00 46.60 2.29
450 451 4.209703 AGAAAAACGAGTACAATCGCGAAA 59.790 37.500 15.24 0.00 46.60 3.46
451 452 3.737266 AGAAAAACGAGTACAATCGCGAA 59.263 39.130 15.24 0.00 46.60 4.70
452 453 3.120616 CAGAAAAACGAGTACAATCGCGA 59.879 43.478 13.09 13.09 46.60 5.87
453 454 3.121126 ACAGAAAAACGAGTACAATCGCG 60.121 43.478 0.00 0.00 46.60 5.87
454 455 4.385244 ACAGAAAAACGAGTACAATCGC 57.615 40.909 4.57 0.00 46.60 4.58
456 457 6.867293 ACTCCTACAGAAAAACGAGTACAATC 59.133 38.462 0.00 0.00 0.00 2.67
457 458 6.756221 ACTCCTACAGAAAAACGAGTACAAT 58.244 36.000 0.00 0.00 0.00 2.71
458 459 6.152932 ACTCCTACAGAAAAACGAGTACAA 57.847 37.500 0.00 0.00 0.00 2.41
459 460 5.779529 ACTCCTACAGAAAAACGAGTACA 57.220 39.130 0.00 0.00 0.00 2.90
460 461 6.907741 ACTACTCCTACAGAAAAACGAGTAC 58.092 40.000 0.00 0.00 32.98 2.73
461 462 6.150140 GGACTACTCCTACAGAAAAACGAGTA 59.850 42.308 0.00 0.00 32.98 2.59
462 463 5.048154 GGACTACTCCTACAGAAAAACGAGT 60.048 44.000 0.00 0.00 34.99 4.18
463 464 5.048224 TGGACTACTCCTACAGAAAAACGAG 60.048 44.000 0.00 0.00 37.48 4.18
464 465 4.828939 TGGACTACTCCTACAGAAAAACGA 59.171 41.667 0.00 0.00 37.48 3.85
465 466 5.130292 TGGACTACTCCTACAGAAAAACG 57.870 43.478 0.00 0.00 37.48 3.60
466 467 5.404667 CGTTGGACTACTCCTACAGAAAAAC 59.595 44.000 4.47 0.00 41.12 2.43
467 468 5.535333 CGTTGGACTACTCCTACAGAAAAA 58.465 41.667 4.47 0.00 41.12 1.94
468 469 4.560108 GCGTTGGACTACTCCTACAGAAAA 60.560 45.833 4.47 0.00 41.12 2.29
469 470 3.057033 GCGTTGGACTACTCCTACAGAAA 60.057 47.826 4.47 0.00 41.12 2.52
470 471 2.490903 GCGTTGGACTACTCCTACAGAA 59.509 50.000 4.47 0.00 41.12 3.02
471 472 2.089980 GCGTTGGACTACTCCTACAGA 58.910 52.381 4.47 0.00 41.12 3.41
472 473 1.816835 TGCGTTGGACTACTCCTACAG 59.183 52.381 4.47 0.00 41.12 2.74
473 474 1.913778 TGCGTTGGACTACTCCTACA 58.086 50.000 4.47 0.00 41.12 2.74
474 475 3.187700 CATTGCGTTGGACTACTCCTAC 58.812 50.000 0.00 0.00 38.54 3.18
475 476 2.418197 GCATTGCGTTGGACTACTCCTA 60.418 50.000 0.00 0.00 37.48 2.94
476 477 1.676014 GCATTGCGTTGGACTACTCCT 60.676 52.381 0.00 0.00 37.48 3.69
477 478 0.727398 GCATTGCGTTGGACTACTCC 59.273 55.000 0.00 0.00 37.04 3.85
478 479 1.661112 GAGCATTGCGTTGGACTACTC 59.339 52.381 2.38 0.00 0.00 2.59
479 480 1.276421 AGAGCATTGCGTTGGACTACT 59.724 47.619 2.38 0.00 0.00 2.57
480 481 1.394917 CAGAGCATTGCGTTGGACTAC 59.605 52.381 2.38 0.00 0.00 2.73
481 482 1.725641 CAGAGCATTGCGTTGGACTA 58.274 50.000 2.38 0.00 0.00 2.59
482 483 1.580845 GCAGAGCATTGCGTTGGACT 61.581 55.000 14.42 2.92 33.90 3.85
483 484 1.154150 GCAGAGCATTGCGTTGGAC 60.154 57.895 14.42 1.06 33.90 4.02
484 485 2.334946 GGCAGAGCATTGCGTTGGA 61.335 57.895 14.42 0.00 45.00 3.53
491 492 1.077644 AGGCAGAGGCAGAGCATTG 60.078 57.895 0.00 0.00 43.71 2.82
608 612 2.663520 CTGGTGTGTGGCGCGTAA 60.664 61.111 8.43 0.00 0.00 3.18
613 617 2.276863 TTTGTTGCTGGTGTGTGGCG 62.277 55.000 0.00 0.00 0.00 5.69
614 618 0.104671 ATTTGTTGCTGGTGTGTGGC 59.895 50.000 0.00 0.00 0.00 5.01
630 634 0.953960 GAGTGGTTGCCGTCGGATTT 60.954 55.000 17.49 0.00 0.00 2.17
646 650 4.796495 GCGGGGCGGGATTTGAGT 62.796 66.667 0.00 0.00 0.00 3.41
647 651 4.794648 TGCGGGGCGGGATTTGAG 62.795 66.667 0.00 0.00 0.00 3.02
648 652 4.794648 CTGCGGGGCGGGATTTGA 62.795 66.667 0.00 0.00 0.00 2.69
706 710 2.741211 GAGGAAACCGTCACGCCC 60.741 66.667 0.00 0.00 0.00 6.13
749 753 3.737172 GTTTGCGATGCTGCGGGT 61.737 61.111 0.00 0.00 37.81 5.28
781 786 3.787001 GGGTGGCTCTTCTCCGGG 61.787 72.222 0.00 0.00 0.00 5.73
832 838 2.238646 TGTGTGTGTTGGAGAAGAAGGT 59.761 45.455 0.00 0.00 0.00 3.50
887 893 3.068590 GGCTACGGCTAGTTGTTATGGTA 59.931 47.826 0.00 0.00 38.73 3.25
894 900 0.037605 GTGTGGCTACGGCTAGTTGT 60.038 55.000 0.00 0.00 38.73 3.32
970 984 3.190738 TAGGTGCTGGTGGTGGTGC 62.191 63.158 0.00 0.00 0.00 5.01
1167 1194 3.462678 GGGTCCGTCTCCAGCTCC 61.463 72.222 0.00 0.00 0.00 4.70
1290 1317 2.022934 GGGTTTTTAACGGTGGACACA 58.977 47.619 4.69 0.00 0.00 3.72
1514 1554 4.466370 CGATTAACTAGATGGCCATAGGGA 59.534 45.833 20.84 2.84 35.59 4.20
1515 1555 4.466370 TCGATTAACTAGATGGCCATAGGG 59.534 45.833 20.84 13.57 37.18 3.53
1516 1556 5.661056 TCGATTAACTAGATGGCCATAGG 57.339 43.478 20.84 13.94 0.00 2.57
1517 1557 8.553459 AATTTCGATTAACTAGATGGCCATAG 57.447 34.615 20.84 16.35 0.00 2.23
1584 1635 4.559063 CTCTCCGCCATGGCAGGG 62.559 72.222 34.93 27.81 42.06 4.45
1589 1640 1.153489 CTGTCACTCTCCGCCATGG 60.153 63.158 7.63 7.63 40.09 3.66
1600 1651 0.822532 ACTCCGTCCGTTCTGTCACT 60.823 55.000 0.00 0.00 0.00 3.41
1654 1705 2.988493 CGCACCACAATTTTCAAGGATG 59.012 45.455 0.00 0.00 0.00 3.51
1687 1772 0.255890 GCACCCCACACCTCATGTAT 59.744 55.000 0.00 0.00 40.64 2.29
1690 1775 2.747460 CGCACCCCACACCTCATG 60.747 66.667 0.00 0.00 0.00 3.07
1746 1841 2.168728 TGTTGGTGCTGTGTACACTACA 59.831 45.455 25.60 19.80 38.14 2.74
1858 1995 1.153353 ACAAATTACACACGGAGCCG 58.847 50.000 7.48 7.48 46.03 5.52
1956 2095 2.922740 ACTCTGTCTTTTACCCGCAA 57.077 45.000 0.00 0.00 0.00 4.85
1989 2139 2.501723 GGGACATGACCTTCTTGAGCTA 59.498 50.000 13.95 0.00 0.00 3.32
1991 2141 1.280421 AGGGACATGACCTTCTTGAGC 59.720 52.381 13.95 0.00 33.64 4.26
1992 2142 2.355513 CCAGGGACATGACCTTCTTGAG 60.356 54.545 13.95 1.57 35.78 3.02
2001 2151 3.244770 TGTTAGGAAACCAGGGACATGAC 60.245 47.826 0.00 0.00 34.49 3.06
2093 2315 1.211703 TCTTGAGGCTGTTGTCACCAA 59.788 47.619 0.00 0.00 0.00 3.67
2095 2317 1.202698 ACTCTTGAGGCTGTTGTCACC 60.203 52.381 0.00 0.00 0.00 4.02
2098 2320 3.627577 TGAAAACTCTTGAGGCTGTTGTC 59.372 43.478 0.00 0.00 0.00 3.18
2099 2321 3.620488 TGAAAACTCTTGAGGCTGTTGT 58.380 40.909 0.00 0.00 0.00 3.32
2100 2322 3.629398 ACTGAAAACTCTTGAGGCTGTTG 59.371 43.478 0.00 0.00 0.00 3.33
2101 2323 3.879892 GACTGAAAACTCTTGAGGCTGTT 59.120 43.478 0.00 0.00 0.00 3.16
2102 2324 3.118261 TGACTGAAAACTCTTGAGGCTGT 60.118 43.478 0.00 0.06 0.00 4.40
2105 2327 4.130118 TCTTGACTGAAAACTCTTGAGGC 58.870 43.478 2.55 0.00 0.00 4.70
2106 2328 5.119898 CGATCTTGACTGAAAACTCTTGAGG 59.880 44.000 2.55 0.00 0.00 3.86
2110 2332 4.212214 GCACGATCTTGACTGAAAACTCTT 59.788 41.667 2.89 0.00 0.00 2.85
2170 2492 0.447406 CGCATGCGACAAAGATGGAA 59.553 50.000 35.82 0.00 42.83 3.53
2259 2586 6.768483 TGGATCTGACAAGTGATCTTTGTTA 58.232 36.000 14.53 10.92 39.09 2.41
2285 2668 6.849028 CTGTGTACAGTAACCATCCTAGGTTG 60.849 46.154 9.08 10.91 43.10 3.77
2307 2703 2.203538 CAGGGGTGCTTTGGCTGT 60.204 61.111 0.00 0.00 39.59 4.40
2308 2704 1.402107 AAACAGGGGTGCTTTGGCTG 61.402 55.000 0.00 0.00 39.59 4.85
2309 2705 1.075301 AAACAGGGGTGCTTTGGCT 60.075 52.632 0.00 0.00 39.59 4.75
2310 2706 1.115326 AGAAACAGGGGTGCTTTGGC 61.115 55.000 0.00 0.00 39.26 4.52
2311 2707 1.886542 GTAGAAACAGGGGTGCTTTGG 59.113 52.381 0.00 0.00 0.00 3.28
2312 2708 2.863809 AGTAGAAACAGGGGTGCTTTG 58.136 47.619 0.00 0.00 0.00 2.77
2313 2709 3.222603 CAAGTAGAAACAGGGGTGCTTT 58.777 45.455 0.00 0.00 0.00 3.51
2314 2710 2.863809 CAAGTAGAAACAGGGGTGCTT 58.136 47.619 0.00 0.00 0.00 3.91
2315 2711 1.545651 GCAAGTAGAAACAGGGGTGCT 60.546 52.381 0.00 0.00 0.00 4.40
2316 2712 0.881796 GCAAGTAGAAACAGGGGTGC 59.118 55.000 0.00 0.00 0.00 5.01
2317 2713 1.880027 GTGCAAGTAGAAACAGGGGTG 59.120 52.381 0.00 0.00 0.00 4.61
2318 2714 1.542547 CGTGCAAGTAGAAACAGGGGT 60.543 52.381 0.00 0.00 0.00 4.95
2319 2715 1.156736 CGTGCAAGTAGAAACAGGGG 58.843 55.000 0.00 0.00 0.00 4.79
2337 2733 2.650778 GCCAAAAACAGGGGAGCG 59.349 61.111 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.