Multiple sequence alignment - TraesCS2A01G047000

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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 TraesCS2A01G047000 chr2A 100.000 1588 0 0 816 2403 18341154 18342741 0.000000e+00 2933
1 TraesCS2A01G047000 chr2A 100.000 593 0 0 1 593 18340339 18340931 0.000000e+00 1096
2 TraesCS2A01G047000 chr2A 100.000 101 0 0 2575 2675 18342913 18343013 1.260000e-43 187
3 TraesCS2A01G047000 chr2D 92.235 1378 59 22 875 2226 16359660 16361015 0.000000e+00 1908
4 TraesCS2A01G047000 chr2D 87.678 211 21 2 32 237 16359138 16359348 9.570000e-60 241
5 TraesCS2A01G047000 chr2B 92.440 754 47 7 971 1719 28659374 28660122 0.000000e+00 1068
6 TraesCS2A01G047000 chr2B 92.384 302 15 6 1943 2242 28660206 28660501 8.850000e-115 424
7 TraesCS2A01G047000 chr2B 89.109 101 1 5 2575 2675 28660788 28660878 1.680000e-22 117
8 TraesCS2A01G047000 chr2B 94.521 73 2 1 2332 2402 28660683 28660755 7.830000e-21 111
9 TraesCS2A01G047000 chr7D 91.111 90 8 0 2153 2242 176452171 176452260 3.620000e-24 122


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 TraesCS2A01G047000 chr2A 18340339 18343013 2674 False 1405.333333 2933 100.0000 1 2675 3 chr2A.!!$F1 2674
1 TraesCS2A01G047000 chr2D 16359138 16361015 1877 False 1074.500000 1908 89.9565 32 2226 2 chr2D.!!$F1 2194
2 TraesCS2A01G047000 chr2B 28659374 28660878 1504 False 430.000000 1068 92.1135 971 2675 4 chr2B.!!$F1 1704

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
589 609 0.031721 GACAAGAGACGACCCGTGTT 59.968 55.0 0.0 0.0 41.37 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2408 0.386113 GCCTCTACTCTTCGGCGAAT 59.614 55.0 23.96 11.23 32.22 3.34 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
17 18 3.680156 TTGAACCGCAATCAGGGC 58.320 55.556 0.00 0.00 0.00 5.19
18 19 1.228398 TTGAACCGCAATCAGGGCA 60.228 52.632 0.00 0.00 0.00 5.36
19 20 1.523154 TTGAACCGCAATCAGGGCAC 61.523 55.000 0.00 0.00 0.00 5.01
20 21 1.971167 GAACCGCAATCAGGGCACA 60.971 57.895 0.00 0.00 0.00 4.57
21 22 2.200170 GAACCGCAATCAGGGCACAC 62.200 60.000 0.00 0.00 0.00 3.82
22 23 3.443045 CCGCAATCAGGGCACACC 61.443 66.667 0.00 0.00 40.67 4.16
23 24 2.672651 CGCAATCAGGGCACACCA 60.673 61.111 0.00 0.00 43.89 4.17
24 25 2.964978 GCAATCAGGGCACACCAC 59.035 61.111 0.00 0.00 43.89 4.16
25 26 2.981560 GCAATCAGGGCACACCACG 61.982 63.158 0.00 0.00 43.89 4.94
26 27 2.034066 AATCAGGGCACACCACGG 59.966 61.111 0.00 0.00 43.89 4.94
27 28 2.525124 AATCAGGGCACACCACGGA 61.525 57.895 0.00 0.00 43.89 4.69
28 29 1.852157 AATCAGGGCACACCACGGAT 61.852 55.000 0.00 0.00 43.89 4.18
29 30 0.980754 ATCAGGGCACACCACGGATA 60.981 55.000 0.00 0.00 43.89 2.59
30 31 1.195442 TCAGGGCACACCACGGATAA 61.195 55.000 0.00 0.00 43.89 1.75
38 39 3.021695 CACACCACGGATAAGGAGAGTA 58.978 50.000 0.00 0.00 0.00 2.59
104 105 2.048690 GGGCGAGATCCGATCTGC 60.049 66.667 15.85 16.95 40.38 4.26
106 107 1.372748 GGCGAGATCCGATCTGCAG 60.373 63.158 15.85 7.63 40.38 4.41
154 155 3.134127 GGGCCGAAAGCTTGCGAT 61.134 61.111 28.67 0.00 43.05 4.58
159 160 1.078709 CCGAAAGCTTGCGATGAAGA 58.921 50.000 28.67 0.00 0.00 2.87
163 164 3.974401 CGAAAGCTTGCGATGAAGAAAAA 59.026 39.130 22.93 0.00 0.00 1.94
179 180 0.314935 AAAAATGAGTGGCGCTGGTG 59.685 50.000 4.71 0.00 0.00 4.17
196 202 2.358737 GGAGGCACCACGGTTGAG 60.359 66.667 0.00 0.00 38.79 3.02
201 207 4.619227 CACCACGGTTGAGGGCGT 62.619 66.667 0.00 0.00 0.00 5.68
232 238 4.394712 GGCCGACAGTGGAGGTGG 62.395 72.222 7.78 0.00 0.00 4.61
258 278 3.753434 AGTGCCTCGGCGAGTCTG 61.753 66.667 32.41 19.86 45.51 3.51
259 279 4.057428 GTGCCTCGGCGAGTCTGT 62.057 66.667 32.41 0.00 45.51 3.41
260 280 4.056125 TGCCTCGGCGAGTCTGTG 62.056 66.667 32.41 19.15 45.51 3.66
261 281 4.057428 GCCTCGGCGAGTCTGTGT 62.057 66.667 32.41 0.00 0.00 3.72
262 282 2.697761 GCCTCGGCGAGTCTGTGTA 61.698 63.158 32.41 0.00 0.00 2.90
263 283 1.429825 CCTCGGCGAGTCTGTGTAG 59.570 63.158 32.41 13.05 0.00 2.74
264 284 1.025113 CCTCGGCGAGTCTGTGTAGA 61.025 60.000 32.41 0.00 0.00 2.59
265 285 0.375454 CTCGGCGAGTCTGTGTAGAG 59.625 60.000 27.92 0.00 32.48 2.43
266 286 0.036671 TCGGCGAGTCTGTGTAGAGA 60.037 55.000 4.99 0.00 32.48 3.10
267 287 0.375454 CGGCGAGTCTGTGTAGAGAG 59.625 60.000 0.00 0.00 32.48 3.20
268 288 1.740297 GGCGAGTCTGTGTAGAGAGA 58.260 55.000 0.00 0.00 32.48 3.10
269 289 1.668751 GGCGAGTCTGTGTAGAGAGAG 59.331 57.143 0.00 0.00 32.48 3.20
270 290 2.623535 GCGAGTCTGTGTAGAGAGAGA 58.376 52.381 0.00 0.00 32.48 3.10
271 291 3.202906 GCGAGTCTGTGTAGAGAGAGAT 58.797 50.000 0.00 0.00 32.48 2.75
275 295 5.584649 CGAGTCTGTGTAGAGAGAGATTCTT 59.415 44.000 0.00 0.00 35.87 2.52
278 298 8.189119 AGTCTGTGTAGAGAGAGATTCTTTTT 57.811 34.615 0.00 0.00 35.87 1.94
302 322 7.455641 TTTTTCTAGGAGACTGTGTAGAGAG 57.544 40.000 0.00 0.00 43.88 3.20
303 323 6.375830 TTTCTAGGAGACTGTGTAGAGAGA 57.624 41.667 0.00 0.00 43.88 3.10
304 324 6.375830 TTCTAGGAGACTGTGTAGAGAGAA 57.624 41.667 0.00 0.00 43.88 2.87
305 325 6.569127 TCTAGGAGACTGTGTAGAGAGAAT 57.431 41.667 0.00 0.00 43.88 2.40
306 326 6.964464 TCTAGGAGACTGTGTAGAGAGAATT 58.036 40.000 0.00 0.00 43.88 2.17
307 327 7.406916 TCTAGGAGACTGTGTAGAGAGAATTT 58.593 38.462 0.00 0.00 43.88 1.82
308 328 6.279513 AGGAGACTGTGTAGAGAGAATTTG 57.720 41.667 0.00 0.00 41.13 2.32
309 329 5.777732 AGGAGACTGTGTAGAGAGAATTTGT 59.222 40.000 0.00 0.00 41.13 2.83
310 330 6.268847 AGGAGACTGTGTAGAGAGAATTTGTT 59.731 38.462 0.00 0.00 41.13 2.83
311 331 6.931840 GGAGACTGTGTAGAGAGAATTTGTTT 59.068 38.462 0.00 0.00 0.00 2.83
312 332 7.442666 GGAGACTGTGTAGAGAGAATTTGTTTT 59.557 37.037 0.00 0.00 0.00 2.43
313 333 8.738645 AGACTGTGTAGAGAGAATTTGTTTTT 57.261 30.769 0.00 0.00 0.00 1.94
336 356 7.761038 TTTTGAGACACTGTGTATAGAGAGA 57.239 36.000 14.31 0.00 0.00 3.10
337 357 7.946381 TTTGAGACACTGTGTATAGAGAGAT 57.054 36.000 14.31 0.00 0.00 2.75
338 358 7.946381 TTGAGACACTGTGTATAGAGAGATT 57.054 36.000 14.31 0.00 0.00 2.40
339 359 7.946381 TGAGACACTGTGTATAGAGAGATTT 57.054 36.000 14.31 0.00 0.00 2.17
340 360 8.354711 TGAGACACTGTGTATAGAGAGATTTT 57.645 34.615 14.31 0.00 0.00 1.82
341 361 8.807118 TGAGACACTGTGTATAGAGAGATTTTT 58.193 33.333 14.31 0.00 0.00 1.94
364 384 6.716934 TTTTAGGGCTCTGTGTATAGAGAG 57.283 41.667 9.05 9.05 45.61 3.20
365 385 5.648330 TTAGGGCTCTGTGTATAGAGAGA 57.352 43.478 16.55 2.68 44.80 3.10
366 386 4.740154 AGGGCTCTGTGTATAGAGAGAT 57.260 45.455 16.55 0.23 44.80 2.75
367 387 5.851808 AGGGCTCTGTGTATAGAGAGATA 57.148 43.478 16.55 0.00 44.80 1.98
368 388 6.401537 AGGGCTCTGTGTATAGAGAGATAT 57.598 41.667 16.55 0.00 44.80 1.63
369 389 6.186957 AGGGCTCTGTGTATAGAGAGATATG 58.813 44.000 16.55 0.00 44.80 1.78
370 390 5.163561 GGGCTCTGTGTATAGAGAGATATGC 60.164 48.000 16.55 2.58 44.80 3.14
371 391 5.448496 GGCTCTGTGTATAGAGAGATATGCG 60.448 48.000 16.55 0.00 44.80 4.73
372 392 5.123186 GCTCTGTGTATAGAGAGATATGCGT 59.877 44.000 16.55 0.00 44.80 5.24
373 393 6.487689 TCTGTGTATAGAGAGATATGCGTG 57.512 41.667 0.00 0.00 0.00 5.34
374 394 5.048153 TGTGTATAGAGAGATATGCGTGC 57.952 43.478 0.00 0.00 0.00 5.34
375 395 4.092120 GTGTATAGAGAGATATGCGTGCG 58.908 47.826 0.00 0.00 0.00 5.34
376 396 3.751698 TGTATAGAGAGATATGCGTGCGT 59.248 43.478 0.00 0.00 0.00 5.24
377 397 2.688364 TAGAGAGATATGCGTGCGTG 57.312 50.000 0.00 0.00 0.00 5.34
378 398 0.741326 AGAGAGATATGCGTGCGTGT 59.259 50.000 0.00 0.00 0.00 4.49
379 399 0.848942 GAGAGATATGCGTGCGTGTG 59.151 55.000 0.00 0.00 0.00 3.82
380 400 0.528466 AGAGATATGCGTGCGTGTGG 60.528 55.000 0.00 0.00 0.00 4.17
381 401 1.490693 GAGATATGCGTGCGTGTGGG 61.491 60.000 0.00 0.00 0.00 4.61
382 402 2.513666 ATATGCGTGCGTGTGGGG 60.514 61.111 0.00 0.00 0.00 4.96
391 411 4.263572 CGTGTGGGGCTGTGGGAA 62.264 66.667 0.00 0.00 0.00 3.97
392 412 2.197324 GTGTGGGGCTGTGGGAAA 59.803 61.111 0.00 0.00 0.00 3.13
393 413 2.197324 TGTGGGGCTGTGGGAAAC 59.803 61.111 0.00 0.00 0.00 2.78
394 414 2.197324 GTGGGGCTGTGGGAAACA 59.803 61.111 0.00 0.00 37.22 2.83
448 468 2.975536 GACCGACCAATGGACCGA 59.024 61.111 6.16 0.00 0.00 4.69
451 471 1.591594 CCGACCAATGGACCGATCG 60.592 63.158 6.16 8.51 0.00 3.69
452 472 1.141019 CGACCAATGGACCGATCGT 59.859 57.895 15.09 1.83 0.00 3.73
453 473 0.459585 CGACCAATGGACCGATCGTT 60.460 55.000 15.09 0.00 0.00 3.85
454 474 1.287425 GACCAATGGACCGATCGTTC 58.713 55.000 15.09 9.55 0.00 3.95
477 497 3.302129 GGGAATTTGCAGCCCCTG 58.698 61.111 7.33 0.00 35.76 4.45
494 514 2.101917 CCCTGCTGATAATGGGCTTTTG 59.898 50.000 0.00 0.00 32.49 2.44
495 515 2.482490 CCTGCTGATAATGGGCTTTTGC 60.482 50.000 0.00 0.00 46.64 3.68
508 528 1.228533 CTTTTGCATGTGTTTGGGCC 58.771 50.000 0.00 0.00 0.00 5.80
510 530 1.340399 TTTGCATGTGTTTGGGCCCA 61.340 50.000 24.45 24.45 0.00 5.36
511 531 1.756408 TTGCATGTGTTTGGGCCCAG 61.756 55.000 26.87 12.94 0.00 4.45
517 537 0.109723 GTGTTTGGGCCCAGTACTGA 59.890 55.000 29.02 13.17 0.00 3.41
537 557 1.143684 AGTAGTAATACGGGCCGGAGA 59.856 52.381 31.78 15.62 0.00 3.71
555 575 2.295349 GAGACACGAAAGAGGTGGTGTA 59.705 50.000 0.00 0.00 43.14 2.90
556 576 2.696707 AGACACGAAAGAGGTGGTGTAA 59.303 45.455 0.00 0.00 43.14 2.41
557 577 3.323979 AGACACGAAAGAGGTGGTGTAAT 59.676 43.478 0.00 0.00 43.14 1.89
558 578 3.660865 ACACGAAAGAGGTGGTGTAATC 58.339 45.455 0.00 0.00 41.46 1.75
559 579 3.000727 CACGAAAGAGGTGGTGTAATCC 58.999 50.000 0.00 0.00 0.00 3.01
560 580 2.268298 CGAAAGAGGTGGTGTAATCCG 58.732 52.381 0.00 0.00 0.00 4.18
561 581 2.094390 CGAAAGAGGTGGTGTAATCCGA 60.094 50.000 0.00 0.00 0.00 4.55
562 582 3.430374 CGAAAGAGGTGGTGTAATCCGAT 60.430 47.826 0.00 0.00 0.00 4.18
565 585 0.750850 AGGTGGTGTAATCCGATCGG 59.249 55.000 28.62 28.62 0.00 4.18
583 603 0.100861 GGATCGGACAAGAGACGACC 59.899 60.000 0.00 0.00 39.64 4.79
584 604 0.100861 GATCGGACAAGAGACGACCC 59.899 60.000 0.00 0.00 39.64 4.46
585 605 1.654954 ATCGGACAAGAGACGACCCG 61.655 60.000 0.00 0.00 39.64 5.28
586 606 2.623915 CGGACAAGAGACGACCCGT 61.624 63.158 0.00 0.00 45.10 5.28
587 607 1.080705 GGACAAGAGACGACCCGTG 60.081 63.158 0.00 0.00 41.37 4.94
588 608 1.658673 GACAAGAGACGACCCGTGT 59.341 57.895 0.00 0.00 41.37 4.49
589 609 0.031721 GACAAGAGACGACCCGTGTT 59.968 55.000 0.00 0.00 41.37 3.32
590 610 0.462789 ACAAGAGACGACCCGTGTTT 59.537 50.000 0.00 0.00 41.37 2.83
591 611 0.859232 CAAGAGACGACCCGTGTTTG 59.141 55.000 0.00 0.00 41.37 2.93
592 612 0.462789 AAGAGACGACCCGTGTTTGT 59.537 50.000 0.00 0.00 41.37 2.83
836 856 2.291365 GACCCGTGTTTGGTAACTTGT 58.709 47.619 0.00 0.00 35.85 3.16
881 922 2.809601 GGAGGCGCACACGTACAG 60.810 66.667 10.83 0.00 42.83 2.74
904 945 8.001875 ACAGAGGTCCTTCGATGCTATATATAT 58.998 37.037 0.00 0.00 0.00 0.86
905 946 9.508642 CAGAGGTCCTTCGATGCTATATATATA 57.491 37.037 2.49 2.49 0.00 0.86
939 980 0.379669 ACGTCGTGACTCGTGACTTT 59.620 50.000 0.00 0.00 38.85 2.66
964 1005 8.651391 TTTTGAGAAGATCGTTAGTTTGTACA 57.349 30.769 0.00 0.00 0.00 2.90
965 1006 7.869016 TTGAGAAGATCGTTAGTTTGTACAG 57.131 36.000 0.00 0.00 0.00 2.74
966 1007 6.978338 TGAGAAGATCGTTAGTTTGTACAGT 58.022 36.000 0.00 0.00 0.00 3.55
967 1008 8.102800 TGAGAAGATCGTTAGTTTGTACAGTA 57.897 34.615 0.00 0.00 0.00 2.74
968 1009 8.019669 TGAGAAGATCGTTAGTTTGTACAGTAC 58.980 37.037 3.49 3.49 0.00 2.73
969 1010 7.020010 AGAAGATCGTTAGTTTGTACAGTACG 58.980 38.462 6.23 3.63 0.00 3.67
979 1020 5.239306 AGTTTGTACAGTACGTGCTACTACA 59.761 40.000 5.64 11.86 33.53 2.74
983 1024 2.353889 ACAGTACGTGCTACTACATCCG 59.646 50.000 5.64 0.00 33.53 4.18
986 1027 0.179145 ACGTGCTACTACATCCGCAC 60.179 55.000 0.00 0.00 46.74 5.34
988 1029 3.733236 TGCTACTACATCCGCACAC 57.267 52.632 0.00 0.00 0.00 3.82
1006 1048 5.447573 GCACACAGAAGAAGAAGATGTTTC 58.552 41.667 0.00 0.00 0.00 2.78
1171 1213 3.876320 GGAGATGAAGAAGAATCTGGCAC 59.124 47.826 0.00 0.00 35.59 5.01
1175 1220 2.003301 GAAGAAGAATCTGGCACCGAC 58.997 52.381 0.00 0.00 35.59 4.79
1207 1252 1.332552 CCGACGAGAAAAACAACACCG 60.333 52.381 0.00 0.00 0.00 4.94
1224 1269 1.084370 CCGGCAAGGAGATCGTTGTC 61.084 60.000 14.64 12.06 45.00 3.18
1584 1629 1.958205 CATGAAGCTCCGGATCGCC 60.958 63.158 3.57 0.00 0.00 5.54
1730 1775 0.321671 ACTCTTGTGTGGCGTGCTAT 59.678 50.000 0.00 0.00 0.00 2.97
1739 1784 3.608506 GTGTGGCGTGCTATATATTCTCG 59.391 47.826 0.00 0.00 0.00 4.04
1740 1785 2.599082 GTGGCGTGCTATATATTCTCGC 59.401 50.000 17.94 17.94 40.56 5.03
1759 1808 3.691118 TCGCGTGGTACTATGTAGAAGTT 59.309 43.478 5.77 0.00 0.00 2.66
1764 1813 6.624423 GCGTGGTACTATGTAGAAGTTTCTCA 60.624 42.308 0.00 0.00 38.70 3.27
1765 1814 6.746364 CGTGGTACTATGTAGAAGTTTCTCAC 59.254 42.308 0.00 0.00 38.70 3.51
1780 1829 9.346725 GAAGTTTCTCACCATGATGAAAAATAC 57.653 33.333 0.00 0.00 30.95 1.89
1910 1965 0.459585 CGCACCTGCACGTTACCTAT 60.460 55.000 0.00 0.00 42.21 2.57
2057 2126 6.816640 ACATATGTAGACGCTTACAACAACAT 59.183 34.615 6.56 0.00 37.13 2.71
2235 2305 6.069673 ACAATTGTACTGGATGATTGTAGGGA 60.070 38.462 9.97 0.00 38.69 4.20
2279 2378 9.178758 GAAGGACCTACAACTTTTTATGATGAT 57.821 33.333 0.00 0.00 0.00 2.45
2284 2383 9.520515 ACCTACAACTTTTTATGATGATGTCTT 57.479 29.630 0.00 0.00 0.00 3.01
2285 2384 9.994432 CCTACAACTTTTTATGATGATGTCTTC 57.006 33.333 0.00 0.00 0.00 2.87
2286 2385 9.694520 CTACAACTTTTTATGATGATGTCTTCG 57.305 33.333 0.00 0.00 0.00 3.79
2287 2386 8.099364 ACAACTTTTTATGATGATGTCTTCGT 57.901 30.769 0.00 0.00 0.00 3.85
2290 2389 8.771920 ACTTTTTATGATGATGTCTTCGTACA 57.228 30.769 0.00 0.00 0.00 2.90
2291 2390 9.214957 ACTTTTTATGATGATGTCTTCGTACAA 57.785 29.630 0.00 0.00 32.02 2.41
2292 2391 9.478019 CTTTTTATGATGATGTCTTCGTACAAC 57.522 33.333 0.00 0.00 32.02 3.32
2293 2392 8.771920 TTTTATGATGATGTCTTCGTACAACT 57.228 30.769 0.00 0.00 32.02 3.16
2294 2393 7.987268 TTATGATGATGTCTTCGTACAACTC 57.013 36.000 0.00 0.00 32.02 3.01
2295 2394 5.385509 TGATGATGTCTTCGTACAACTCA 57.614 39.130 0.00 0.00 32.02 3.41
2296 2395 5.965922 TGATGATGTCTTCGTACAACTCAT 58.034 37.500 0.00 0.00 33.75 2.90
2297 2396 6.036470 TGATGATGTCTTCGTACAACTCATC 58.964 40.000 16.31 16.31 41.75 2.92
2298 2397 5.644977 TGATGTCTTCGTACAACTCATCT 57.355 39.130 12.64 0.00 33.67 2.90
2299 2398 6.025749 TGATGTCTTCGTACAACTCATCTT 57.974 37.500 12.64 0.00 33.67 2.40
2300 2399 6.093404 TGATGTCTTCGTACAACTCATCTTC 58.907 40.000 12.64 0.00 33.67 2.87
2301 2400 4.473199 TGTCTTCGTACAACTCATCTTCG 58.527 43.478 0.00 0.00 0.00 3.79
2303 2402 5.179929 TGTCTTCGTACAACTCATCTTCGTA 59.820 40.000 0.00 0.00 0.00 3.43
2304 2403 5.507527 GTCTTCGTACAACTCATCTTCGTAC 59.492 44.000 0.00 0.00 0.00 3.67
2305 2404 5.179929 TCTTCGTACAACTCATCTTCGTACA 59.820 40.000 0.00 0.00 33.61 2.90
2306 2405 4.966249 TCGTACAACTCATCTTCGTACAG 58.034 43.478 0.00 0.00 33.61 2.74
2307 2406 4.692155 TCGTACAACTCATCTTCGTACAGA 59.308 41.667 0.00 0.00 33.61 3.41
2308 2407 4.787083 CGTACAACTCATCTTCGTACAGAC 59.213 45.833 0.00 0.00 33.61 3.51
2309 2408 4.848562 ACAACTCATCTTCGTACAGACA 57.151 40.909 0.00 0.00 0.00 3.41
2310 2409 5.392767 ACAACTCATCTTCGTACAGACAT 57.607 39.130 0.00 0.00 0.00 3.06
2312 2411 5.864474 ACAACTCATCTTCGTACAGACATTC 59.136 40.000 0.00 0.00 0.00 2.67
2313 2412 4.663166 ACTCATCTTCGTACAGACATTCG 58.337 43.478 0.00 0.00 0.00 3.34
2315 2414 2.273370 TCTTCGTACAGACATTCGCC 57.727 50.000 0.00 0.00 0.00 5.54
2316 2415 0.914551 CTTCGTACAGACATTCGCCG 59.085 55.000 0.00 0.00 0.00 6.46
2317 2416 0.522626 TTCGTACAGACATTCGCCGA 59.477 50.000 0.00 0.00 0.00 5.54
2318 2417 0.522626 TCGTACAGACATTCGCCGAA 59.477 50.000 0.33 0.33 0.00 4.30
2319 2418 0.914551 CGTACAGACATTCGCCGAAG 59.085 55.000 5.52 0.25 0.00 3.79
2320 2419 1.466866 CGTACAGACATTCGCCGAAGA 60.467 52.381 5.52 0.00 0.00 2.87
2321 2420 2.186076 GTACAGACATTCGCCGAAGAG 58.814 52.381 5.52 3.04 0.00 2.85
2322 2421 0.603569 ACAGACATTCGCCGAAGAGT 59.396 50.000 5.52 6.55 0.00 3.24
2323 2422 1.816835 ACAGACATTCGCCGAAGAGTA 59.183 47.619 5.52 0.00 0.00 2.59
2325 2424 2.097629 CAGACATTCGCCGAAGAGTAGA 59.902 50.000 5.52 0.00 0.00 2.59
2326 2425 2.356382 AGACATTCGCCGAAGAGTAGAG 59.644 50.000 5.52 0.00 0.00 2.43
2327 2426 1.405821 ACATTCGCCGAAGAGTAGAGG 59.594 52.381 5.52 0.00 0.00 3.69
2328 2427 0.386113 ATTCGCCGAAGAGTAGAGGC 59.614 55.000 5.52 0.00 45.67 4.70
2329 2428 1.664321 TTCGCCGAAGAGTAGAGGCC 61.664 60.000 0.00 0.00 46.36 5.19
2349 2511 7.725844 AGAGGCCGAATGAAAATATCCTTTATT 59.274 33.333 0.00 0.00 0.00 1.40
2390 2554 5.643348 TCATCTTCGTACAGACATGCAATTT 59.357 36.000 0.00 0.00 0.00 1.82
2402 2566 2.126914 TGCAATTTTGAACCGAACCG 57.873 45.000 0.00 0.00 0.00 4.44
2598 2762 6.853720 CATGATATTCTTCTGATTGGCCATC 58.146 40.000 6.09 7.28 0.00 3.51
2614 2778 1.466167 CCATCTTTGGTCGAGTGCTTG 59.534 52.381 0.00 0.00 38.30 4.01
2616 2780 2.839486 TCTTTGGTCGAGTGCTTGAT 57.161 45.000 0.00 0.00 0.00 2.57
2617 2781 2.416747 TCTTTGGTCGAGTGCTTGATG 58.583 47.619 0.00 0.00 0.00 3.07
2618 2782 1.466167 CTTTGGTCGAGTGCTTGATGG 59.534 52.381 0.00 0.00 0.00 3.51
2619 2783 0.955428 TTGGTCGAGTGCTTGATGGC 60.955 55.000 0.00 0.00 0.00 4.40
2620 2784 1.375908 GGTCGAGTGCTTGATGGCA 60.376 57.895 0.00 0.00 40.15 4.92
2621 2785 1.364626 GGTCGAGTGCTTGATGGCAG 61.365 60.000 0.00 0.00 43.25 4.85
2622 2786 0.390340 GTCGAGTGCTTGATGGCAGA 60.390 55.000 0.00 0.00 43.25 4.26
2623 2787 0.390340 TCGAGTGCTTGATGGCAGAC 60.390 55.000 0.00 0.00 43.25 3.51
2624 2788 0.671472 CGAGTGCTTGATGGCAGACA 60.671 55.000 0.00 0.00 43.25 3.41
2625 2789 1.085091 GAGTGCTTGATGGCAGACAG 58.915 55.000 0.00 0.00 43.25 3.51
2626 2790 0.959372 AGTGCTTGATGGCAGACAGC 60.959 55.000 7.45 7.45 43.25 4.40
2627 2791 0.959372 GTGCTTGATGGCAGACAGCT 60.959 55.000 13.73 0.00 43.25 4.24
2628 2792 0.251033 TGCTTGATGGCAGACAGCTT 60.251 50.000 13.73 0.00 44.79 3.74
2629 2793 0.450983 GCTTGATGGCAGACAGCTTC 59.549 55.000 0.00 0.00 44.79 3.86
2630 2794 1.817357 CTTGATGGCAGACAGCTTCA 58.183 50.000 0.00 0.00 44.79 3.02
2631 2795 1.467734 CTTGATGGCAGACAGCTTCAC 59.532 52.381 0.00 0.00 44.79 3.18
2632 2796 0.397564 TGATGGCAGACAGCTTCACA 59.602 50.000 0.00 0.00 44.79 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.228398 TGCCCTGATTGCGGTTCAA 60.228 52.632 0.00 0.00 39.32 2.69
1 2 1.971167 GTGCCCTGATTGCGGTTCA 60.971 57.895 0.00 0.00 0.00 3.18
2 3 1.971167 TGTGCCCTGATTGCGGTTC 60.971 57.895 0.00 0.00 0.00 3.62
3 4 2.115052 TGTGCCCTGATTGCGGTT 59.885 55.556 0.00 0.00 0.00 4.44
4 5 2.672996 GTGTGCCCTGATTGCGGT 60.673 61.111 0.00 0.00 0.00 5.68
5 6 3.443045 GGTGTGCCCTGATTGCGG 61.443 66.667 0.00 0.00 0.00 5.69
6 7 2.672651 TGGTGTGCCCTGATTGCG 60.673 61.111 0.00 0.00 0.00 4.85
7 8 2.964978 GTGGTGTGCCCTGATTGC 59.035 61.111 0.00 0.00 0.00 3.56
8 9 2.334946 CCGTGGTGTGCCCTGATTG 61.335 63.158 0.00 0.00 0.00 2.67
9 10 1.852157 ATCCGTGGTGTGCCCTGATT 61.852 55.000 0.00 0.00 0.00 2.57
10 11 0.980754 TATCCGTGGTGTGCCCTGAT 60.981 55.000 0.00 0.00 0.00 2.90
11 12 1.195442 TTATCCGTGGTGTGCCCTGA 61.195 55.000 0.00 0.00 0.00 3.86
12 13 0.744414 CTTATCCGTGGTGTGCCCTG 60.744 60.000 0.00 0.00 0.00 4.45
13 14 1.602237 CTTATCCGTGGTGTGCCCT 59.398 57.895 0.00 0.00 0.00 5.19
14 15 1.451387 CCTTATCCGTGGTGTGCCC 60.451 63.158 0.00 0.00 0.00 5.36
15 16 0.462047 CTCCTTATCCGTGGTGTGCC 60.462 60.000 0.00 0.00 0.00 5.01
16 17 0.535335 TCTCCTTATCCGTGGTGTGC 59.465 55.000 0.00 0.00 0.00 4.57
17 18 1.825474 ACTCTCCTTATCCGTGGTGTG 59.175 52.381 0.00 0.00 0.00 3.82
18 19 2.233305 ACTCTCCTTATCCGTGGTGT 57.767 50.000 0.00 0.00 0.00 4.16
19 20 2.623889 CCTACTCTCCTTATCCGTGGTG 59.376 54.545 0.00 0.00 0.00 4.17
20 21 2.512896 TCCTACTCTCCTTATCCGTGGT 59.487 50.000 0.00 0.00 0.00 4.16
21 22 3.150767 CTCCTACTCTCCTTATCCGTGG 58.849 54.545 0.00 0.00 0.00 4.94
22 23 2.554893 GCTCCTACTCTCCTTATCCGTG 59.445 54.545 0.00 0.00 0.00 4.94
23 24 2.444010 AGCTCCTACTCTCCTTATCCGT 59.556 50.000 0.00 0.00 0.00 4.69
24 25 2.817258 CAGCTCCTACTCTCCTTATCCG 59.183 54.545 0.00 0.00 0.00 4.18
25 26 4.079253 CTCAGCTCCTACTCTCCTTATCC 58.921 52.174 0.00 0.00 0.00 2.59
26 27 3.506067 GCTCAGCTCCTACTCTCCTTATC 59.494 52.174 0.00 0.00 0.00 1.75
27 28 3.117322 TGCTCAGCTCCTACTCTCCTTAT 60.117 47.826 0.00 0.00 0.00 1.73
28 29 2.242452 TGCTCAGCTCCTACTCTCCTTA 59.758 50.000 0.00 0.00 0.00 2.69
29 30 1.006519 TGCTCAGCTCCTACTCTCCTT 59.993 52.381 0.00 0.00 0.00 3.36
30 31 0.628522 TGCTCAGCTCCTACTCTCCT 59.371 55.000 0.00 0.00 0.00 3.69
104 105 2.432628 GCGACGGGGTTGAGACTG 60.433 66.667 0.00 0.00 0.00 3.51
163 164 2.360350 CCACCAGCGCCACTCATT 60.360 61.111 2.29 0.00 0.00 2.57
164 165 3.320879 CTCCACCAGCGCCACTCAT 62.321 63.158 2.29 0.00 0.00 2.90
179 180 2.358737 CTCAACCGTGGTGCCTCC 60.359 66.667 0.00 0.00 0.00 4.30
249 269 1.668751 CTCTCTCTACACAGACTCGCC 59.331 57.143 0.00 0.00 0.00 5.54
278 298 7.232188 TCTCTCTACACAGTCTCCTAGAAAAA 58.768 38.462 0.00 0.00 0.00 1.94
283 303 7.122055 ACAAATTCTCTCTACACAGTCTCCTAG 59.878 40.741 0.00 0.00 0.00 3.02
287 307 7.954788 AAACAAATTCTCTCTACACAGTCTC 57.045 36.000 0.00 0.00 0.00 3.36
311 331 8.178313 TCTCTCTATACACAGTGTCTCAAAAA 57.822 34.615 10.23 0.00 0.00 1.94
312 332 7.761038 TCTCTCTATACACAGTGTCTCAAAA 57.239 36.000 10.23 0.00 0.00 2.44
313 333 7.946381 ATCTCTCTATACACAGTGTCTCAAA 57.054 36.000 10.23 0.00 0.00 2.69
314 334 7.946381 AATCTCTCTATACACAGTGTCTCAA 57.054 36.000 10.23 0.00 0.00 3.02
315 335 7.946381 AAATCTCTCTATACACAGTGTCTCA 57.054 36.000 10.23 0.00 0.00 3.27
340 360 6.895756 TCTCTCTATACACAGAGCCCTAAAAA 59.104 38.462 0.00 0.00 41.61 1.94
341 361 6.432581 TCTCTCTATACACAGAGCCCTAAAA 58.567 40.000 0.00 0.00 41.61 1.52
342 362 6.014771 TCTCTCTATACACAGAGCCCTAAA 57.985 41.667 0.00 0.00 41.61 1.85
343 363 5.648330 TCTCTCTATACACAGAGCCCTAA 57.352 43.478 0.00 0.00 41.61 2.69
344 364 5.851808 ATCTCTCTATACACAGAGCCCTA 57.148 43.478 0.00 0.00 41.61 3.53
345 365 4.740154 ATCTCTCTATACACAGAGCCCT 57.260 45.455 0.00 0.00 41.61 5.19
346 366 5.163561 GCATATCTCTCTATACACAGAGCCC 60.164 48.000 0.00 0.00 41.61 5.19
347 367 5.448496 CGCATATCTCTCTATACACAGAGCC 60.448 48.000 0.00 0.00 41.61 4.70
348 368 5.123186 ACGCATATCTCTCTATACACAGAGC 59.877 44.000 0.00 0.00 41.61 4.09
349 369 6.541969 CACGCATATCTCTCTATACACAGAG 58.458 44.000 0.00 0.00 42.96 3.35
350 370 5.106515 GCACGCATATCTCTCTATACACAGA 60.107 44.000 0.00 0.00 0.00 3.41
351 371 5.092105 GCACGCATATCTCTCTATACACAG 58.908 45.833 0.00 0.00 0.00 3.66
352 372 4.378459 CGCACGCATATCTCTCTATACACA 60.378 45.833 0.00 0.00 0.00 3.72
353 373 4.092120 CGCACGCATATCTCTCTATACAC 58.908 47.826 0.00 0.00 0.00 2.90
354 374 3.751698 ACGCACGCATATCTCTCTATACA 59.248 43.478 0.00 0.00 0.00 2.29
355 375 4.092120 CACGCACGCATATCTCTCTATAC 58.908 47.826 0.00 0.00 0.00 1.47
356 376 3.751698 ACACGCACGCATATCTCTCTATA 59.248 43.478 0.00 0.00 0.00 1.31
357 377 2.554462 ACACGCACGCATATCTCTCTAT 59.446 45.455 0.00 0.00 0.00 1.98
358 378 1.947456 ACACGCACGCATATCTCTCTA 59.053 47.619 0.00 0.00 0.00 2.43
359 379 0.741326 ACACGCACGCATATCTCTCT 59.259 50.000 0.00 0.00 0.00 3.10
360 380 0.848942 CACACGCACGCATATCTCTC 59.151 55.000 0.00 0.00 0.00 3.20
361 381 0.528466 CCACACGCACGCATATCTCT 60.528 55.000 0.00 0.00 0.00 3.10
362 382 1.490693 CCCACACGCACGCATATCTC 61.491 60.000 0.00 0.00 0.00 2.75
363 383 1.521457 CCCACACGCACGCATATCT 60.521 57.895 0.00 0.00 0.00 1.98
364 384 2.534019 CCCCACACGCACGCATATC 61.534 63.158 0.00 0.00 0.00 1.63
365 385 2.513666 CCCCACACGCACGCATAT 60.514 61.111 0.00 0.00 0.00 1.78
374 394 3.783362 TTTCCCACAGCCCCACACG 62.783 63.158 0.00 0.00 0.00 4.49
375 395 2.197324 TTTCCCACAGCCCCACAC 59.803 61.111 0.00 0.00 0.00 3.82
376 396 2.197324 GTTTCCCACAGCCCCACA 59.803 61.111 0.00 0.00 0.00 4.17
377 397 2.197324 TGTTTCCCACAGCCCCAC 59.803 61.111 0.00 0.00 0.00 4.61
378 398 2.197324 GTGTTTCCCACAGCCCCA 59.803 61.111 0.00 0.00 43.92 4.96
379 399 2.983592 CGTGTTTCCCACAGCCCC 60.984 66.667 0.00 0.00 44.78 5.80
380 400 3.670377 GCGTGTTTCCCACAGCCC 61.670 66.667 0.00 0.00 44.78 5.19
381 401 2.010582 TTTGCGTGTTTCCCACAGCC 62.011 55.000 0.00 0.00 44.78 4.85
382 402 0.869880 GTTTGCGTGTTTCCCACAGC 60.870 55.000 0.00 0.00 44.78 4.40
383 403 0.591236 CGTTTGCGTGTTTCCCACAG 60.591 55.000 0.00 0.00 44.78 3.66
384 404 1.429825 CGTTTGCGTGTTTCCCACA 59.570 52.632 0.00 0.00 44.78 4.17
385 405 1.942223 GCGTTTGCGTGTTTCCCAC 60.942 57.895 0.00 0.00 40.81 4.61
386 406 2.409651 GCGTTTGCGTGTTTCCCA 59.590 55.556 0.00 0.00 40.81 4.37
432 452 1.520666 GATCGGTCCATTGGTCGGT 59.479 57.895 16.56 12.05 0.00 4.69
433 453 1.591594 CGATCGGTCCATTGGTCGG 60.592 63.158 7.38 10.14 0.00 4.79
434 454 0.459585 AACGATCGGTCCATTGGTCG 60.460 55.000 20.98 10.19 35.42 4.79
435 455 1.287425 GAACGATCGGTCCATTGGTC 58.713 55.000 22.68 0.00 0.00 4.02
436 456 3.453559 GAACGATCGGTCCATTGGT 57.546 52.632 22.68 0.00 0.00 3.67
453 473 0.903942 GCTGCAAATTCCCCAATGGA 59.096 50.000 0.00 0.00 43.18 3.41
454 474 0.107557 GGCTGCAAATTCCCCAATGG 60.108 55.000 0.50 0.00 0.00 3.16
475 495 2.166870 TGCAAAAGCCCATTATCAGCAG 59.833 45.455 0.00 0.00 0.00 4.24
477 497 2.965572 TGCAAAAGCCCATTATCAGC 57.034 45.000 0.00 0.00 0.00 4.26
483 503 2.879646 CAAACACATGCAAAAGCCCATT 59.120 40.909 0.00 0.00 0.00 3.16
494 514 0.897863 TACTGGGCCCAAACACATGC 60.898 55.000 28.29 0.00 0.00 4.06
495 515 0.887933 GTACTGGGCCCAAACACATG 59.112 55.000 28.29 15.02 0.00 3.21
496 516 0.777446 AGTACTGGGCCCAAACACAT 59.223 50.000 29.61 13.40 0.00 3.21
498 518 0.109723 TCAGTACTGGGCCCAAACAC 59.890 55.000 29.61 24.19 0.00 3.32
508 528 4.023365 GCCCGTATTACTACTCAGTACTGG 60.023 50.000 22.48 15.10 36.98 4.00
510 530 4.140536 GGCCCGTATTACTACTCAGTACT 58.859 47.826 0.00 0.00 36.98 2.73
511 531 3.058639 CGGCCCGTATTACTACTCAGTAC 60.059 52.174 0.00 0.00 36.98 2.73
517 537 1.143684 TCTCCGGCCCGTATTACTACT 59.856 52.381 0.85 0.00 0.00 2.57
537 557 3.556423 GGATTACACCACCTCTTTCGTGT 60.556 47.826 0.00 0.00 41.98 4.49
560 580 1.334239 CGTCTCTTGTCCGATCCGATC 60.334 57.143 0.00 0.00 0.00 3.69
561 581 0.663688 CGTCTCTTGTCCGATCCGAT 59.336 55.000 0.00 0.00 0.00 4.18
562 582 0.392060 TCGTCTCTTGTCCGATCCGA 60.392 55.000 0.00 0.00 0.00 4.55
565 585 0.100861 GGGTCGTCTCTTGTCCGATC 59.899 60.000 0.00 0.00 32.68 3.69
815 835 1.262151 CAAGTTACCAAACACGGGTCG 59.738 52.381 0.00 0.00 39.85 4.79
820 840 6.400303 CCGACTATAACAAGTTACCAAACACG 60.400 42.308 0.00 0.00 38.12 4.49
822 842 6.757237 TCCGACTATAACAAGTTACCAAACA 58.243 36.000 0.00 0.00 38.12 2.83
832 852 4.579454 TTCCCGATCCGACTATAACAAG 57.421 45.455 0.00 0.00 0.00 3.16
864 890 2.809601 CTGTACGTGTGCGCCTCC 60.810 66.667 4.18 0.00 42.83 4.30
876 902 1.751924 AGCATCGAAGGACCTCTGTAC 59.248 52.381 0.00 0.00 0.00 2.90
904 945 1.153726 CGTGCTGGGTGTGCGTATA 60.154 57.895 0.00 0.00 0.00 1.47
905 946 2.434185 CGTGCTGGGTGTGCGTAT 60.434 61.111 0.00 0.00 0.00 3.06
906 947 3.851845 GACGTGCTGGGTGTGCGTA 62.852 63.158 0.00 0.00 35.86 4.42
939 980 8.651391 TGTACAAACTAACGATCTTCTCAAAA 57.349 30.769 0.00 0.00 0.00 2.44
943 984 7.215942 CGTACTGTACAAACTAACGATCTTCTC 59.784 40.741 17.35 0.00 31.66 2.87
948 989 5.219914 GCACGTACTGTACAAACTAACGATC 60.220 44.000 17.35 7.99 33.17 3.69
949 990 4.618489 GCACGTACTGTACAAACTAACGAT 59.382 41.667 17.35 0.00 33.17 3.73
950 991 3.974401 GCACGTACTGTACAAACTAACGA 59.026 43.478 17.35 0.00 33.17 3.85
955 996 4.843220 AGTAGCACGTACTGTACAAACT 57.157 40.909 17.35 12.25 40.76 2.66
957 998 5.687770 TGTAGTAGCACGTACTGTACAAA 57.312 39.130 17.35 0.00 42.37 2.83
959 1000 4.333649 GGATGTAGTAGCACGTACTGTACA 59.666 45.833 17.35 12.65 42.37 2.90
960 1001 4.551603 CGGATGTAGTAGCACGTACTGTAC 60.552 50.000 7.90 7.90 42.37 2.90
961 1002 3.557185 CGGATGTAGTAGCACGTACTGTA 59.443 47.826 0.00 0.00 42.37 2.74
962 1003 2.353889 CGGATGTAGTAGCACGTACTGT 59.646 50.000 0.00 0.00 42.37 3.55
963 1004 2.853662 GCGGATGTAGTAGCACGTACTG 60.854 54.545 0.00 0.00 42.37 2.74
964 1005 1.332997 GCGGATGTAGTAGCACGTACT 59.667 52.381 0.00 0.00 44.69 2.73
965 1006 1.064505 TGCGGATGTAGTAGCACGTAC 59.935 52.381 0.00 0.00 34.39 3.67
966 1007 1.381522 TGCGGATGTAGTAGCACGTA 58.618 50.000 0.00 0.00 34.39 3.57
967 1008 2.186155 TGCGGATGTAGTAGCACGT 58.814 52.632 0.00 0.00 34.39 4.49
979 1020 2.300152 TCTTCTTCTTCTGTGTGCGGAT 59.700 45.455 0.00 0.00 0.00 4.18
983 1024 5.429957 AAACATCTTCTTCTTCTGTGTGC 57.570 39.130 0.00 0.00 0.00 4.57
986 1027 6.484643 TGAAGGAAACATCTTCTTCTTCTGTG 59.515 38.462 0.00 0.00 40.73 3.66
988 1029 7.012704 TGTTGAAGGAAACATCTTCTTCTTCTG 59.987 37.037 0.00 0.00 40.73 3.02
1006 1048 0.933097 CGAGCCGATGATGTTGAAGG 59.067 55.000 0.00 0.00 0.00 3.46
1058 1100 3.716539 ATGGCCGACGACATGTCCG 62.717 63.158 20.03 17.30 45.23 4.79
1059 1101 2.173669 CATGGCCGACGACATGTCC 61.174 63.158 20.03 6.16 45.23 4.02
1194 1239 1.135333 TCCTTGCCGGTGTTGTTTTTC 59.865 47.619 1.90 0.00 0.00 2.29
1207 1252 1.696832 GCGACAACGATCTCCTTGCC 61.697 60.000 0.00 0.00 42.66 4.52
1325 1370 3.234041 CGAGCGTCGTCAGCTTCG 61.234 66.667 0.00 2.12 46.13 3.79
1383 1428 1.482593 ACGTCCATCTTGATGAGGGTC 59.517 52.381 11.76 0.00 46.03 4.46
1387 1432 2.606725 GCTTCACGTCCATCTTGATGAG 59.393 50.000 11.76 5.87 0.00 2.90
1389 1434 2.349590 TGCTTCACGTCCATCTTGATG 58.650 47.619 3.77 3.77 0.00 3.07
1584 1629 4.379243 ACCTCGTCCTGGCGCTTG 62.379 66.667 7.64 0.00 0.00 4.01
1730 1775 7.099120 TCTACATAGTACCACGCGAGAATATA 58.901 38.462 15.93 0.00 0.00 0.86
1739 1784 5.648572 AGAAACTTCTACATAGTACCACGC 58.351 41.667 0.00 0.00 35.34 5.34
1740 1785 6.746364 GTGAGAAACTTCTACATAGTACCACG 59.254 42.308 0.00 0.00 37.73 4.94
1759 1808 8.421249 AAAGGTATTTTTCATCATGGTGAGAA 57.579 30.769 9.00 8.37 0.00 2.87
1798 1852 9.498176 TTTGTCATGATCGATGATGAATAGATT 57.502 29.630 25.99 0.00 43.20 2.40
1898 1953 2.220133 CCGCAATACATAGGTAACGTGC 59.780 50.000 9.79 9.79 46.39 5.34
1910 1965 2.025155 ACCAAACACAACCGCAATACA 58.975 42.857 0.00 0.00 0.00 2.29
1987 2056 5.410355 TCTACCCACACAATAAGTACACC 57.590 43.478 0.00 0.00 0.00 4.16
2057 2126 7.837689 GTGTATCCATAGGGGTGAGTATATGTA 59.162 40.741 0.00 0.00 38.11 2.29
2089 2159 1.098050 GCCTACGAGGACGAGGTTAA 58.902 55.000 5.24 0.00 37.67 2.01
2235 2305 0.680280 TCGGCCTCTACTCTTCGCTT 60.680 55.000 0.00 0.00 0.00 4.68
2259 2358 9.994432 GAAGACATCATCATAAAAAGTTGTAGG 57.006 33.333 0.00 0.00 0.00 3.18
2265 2364 8.771920 TGTACGAAGACATCATCATAAAAAGT 57.228 30.769 0.00 0.00 0.00 2.66
2274 2373 6.269315 AGATGAGTTGTACGAAGACATCATC 58.731 40.000 18.87 16.71 41.75 2.92
2279 2378 4.023450 ACGAAGATGAGTTGTACGAAGACA 60.023 41.667 0.00 0.00 0.00 3.41
2284 2383 4.692155 TCTGTACGAAGATGAGTTGTACGA 59.308 41.667 0.00 0.00 38.53 3.43
2285 2384 4.787083 GTCTGTACGAAGATGAGTTGTACG 59.213 45.833 0.00 0.00 38.53 3.67
2286 2385 5.696822 TGTCTGTACGAAGATGAGTTGTAC 58.303 41.667 0.00 0.00 36.74 2.90
2287 2386 5.952526 TGTCTGTACGAAGATGAGTTGTA 57.047 39.130 0.00 0.00 0.00 2.41
2290 2389 5.096169 CGAATGTCTGTACGAAGATGAGTT 58.904 41.667 0.00 0.00 0.00 3.01
2291 2390 4.663166 CGAATGTCTGTACGAAGATGAGT 58.337 43.478 0.00 0.00 0.00 3.41
2292 2391 3.483922 GCGAATGTCTGTACGAAGATGAG 59.516 47.826 0.00 0.00 0.00 2.90
2293 2392 3.435566 GCGAATGTCTGTACGAAGATGA 58.564 45.455 0.00 0.00 0.00 2.92
2294 2393 2.535984 GGCGAATGTCTGTACGAAGATG 59.464 50.000 0.00 0.00 0.00 2.90
2295 2394 2.794981 CGGCGAATGTCTGTACGAAGAT 60.795 50.000 0.00 0.00 0.00 2.40
2296 2395 1.466866 CGGCGAATGTCTGTACGAAGA 60.467 52.381 0.00 0.00 0.00 2.87
2297 2396 0.914551 CGGCGAATGTCTGTACGAAG 59.085 55.000 0.00 0.00 0.00 3.79
2298 2397 0.522626 TCGGCGAATGTCTGTACGAA 59.477 50.000 7.35 0.00 0.00 3.85
2299 2398 0.522626 TTCGGCGAATGTCTGTACGA 59.477 50.000 19.83 0.00 0.00 3.43
2300 2399 0.914551 CTTCGGCGAATGTCTGTACG 59.085 55.000 23.96 3.97 0.00 3.67
2301 2400 2.186076 CTCTTCGGCGAATGTCTGTAC 58.814 52.381 23.96 0.00 0.00 2.90
2303 2402 0.603569 ACTCTTCGGCGAATGTCTGT 59.396 50.000 23.96 13.76 0.00 3.41
2304 2403 2.097629 TCTACTCTTCGGCGAATGTCTG 59.902 50.000 23.96 18.26 0.00 3.51
2305 2404 2.356382 CTCTACTCTTCGGCGAATGTCT 59.644 50.000 23.96 8.47 0.00 3.41
2306 2405 2.541999 CCTCTACTCTTCGGCGAATGTC 60.542 54.545 23.96 0.00 0.00 3.06
2307 2406 1.405821 CCTCTACTCTTCGGCGAATGT 59.594 52.381 23.96 24.08 0.00 2.71
2308 2407 1.866063 GCCTCTACTCTTCGGCGAATG 60.866 57.143 23.96 19.93 32.22 2.67
2309 2408 0.386113 GCCTCTACTCTTCGGCGAAT 59.614 55.000 23.96 11.23 32.22 3.34
2310 2409 1.664321 GGCCTCTACTCTTCGGCGAA 61.664 60.000 22.33 22.33 43.38 4.70
2312 2411 2.413765 GGCCTCTACTCTTCGGCG 59.586 66.667 0.00 0.00 43.38 6.46
2313 2412 1.664321 TTCGGCCTCTACTCTTCGGC 61.664 60.000 0.00 0.00 41.75 5.54
2315 2414 1.676529 TCATTCGGCCTCTACTCTTCG 59.323 52.381 0.00 0.00 0.00 3.79
2316 2415 3.802948 TTCATTCGGCCTCTACTCTTC 57.197 47.619 0.00 0.00 0.00 2.87
2317 2416 4.553330 TTTTCATTCGGCCTCTACTCTT 57.447 40.909 0.00 0.00 0.00 2.85
2318 2417 4.762289 ATTTTCATTCGGCCTCTACTCT 57.238 40.909 0.00 0.00 0.00 3.24
2319 2418 5.639931 GGATATTTTCATTCGGCCTCTACTC 59.360 44.000 0.00 0.00 0.00 2.59
2320 2419 5.308237 AGGATATTTTCATTCGGCCTCTACT 59.692 40.000 0.00 0.00 0.00 2.57
2321 2420 5.552178 AGGATATTTTCATTCGGCCTCTAC 58.448 41.667 0.00 0.00 0.00 2.59
2322 2421 5.825593 AGGATATTTTCATTCGGCCTCTA 57.174 39.130 0.00 0.00 0.00 2.43
2323 2422 4.713792 AGGATATTTTCATTCGGCCTCT 57.286 40.909 0.00 0.00 0.00 3.69
2325 2424 7.505585 TCAATAAAGGATATTTTCATTCGGCCT 59.494 33.333 0.00 0.00 0.00 5.19
2326 2425 7.657336 TCAATAAAGGATATTTTCATTCGGCC 58.343 34.615 0.00 0.00 0.00 6.13
2327 2426 9.528018 TTTCAATAAAGGATATTTTCATTCGGC 57.472 29.630 0.00 0.00 0.00 5.54
2598 2762 1.466167 CCATCAAGCACTCGACCAAAG 59.534 52.381 0.00 0.00 0.00 2.77
2614 2778 1.527034 TTGTGAAGCTGTCTGCCATC 58.473 50.000 0.00 0.00 44.23 3.51
2616 2780 1.311859 CTTTGTGAAGCTGTCTGCCA 58.688 50.000 0.00 0.00 44.23 4.92
2626 2790 1.067354 GGCCATCCTTGCTTTGTGAAG 60.067 52.381 0.00 0.00 35.92 3.02
2627 2791 0.968405 GGCCATCCTTGCTTTGTGAA 59.032 50.000 0.00 0.00 0.00 3.18
2628 2792 0.112995 AGGCCATCCTTGCTTTGTGA 59.887 50.000 5.01 0.00 40.66 3.58
2629 2793 0.529378 GAGGCCATCCTTGCTTTGTG 59.471 55.000 5.01 0.00 44.46 3.33
2630 2794 0.112995 TGAGGCCATCCTTGCTTTGT 59.887 50.000 5.01 0.00 44.46 2.83
2631 2795 0.529378 GTGAGGCCATCCTTGCTTTG 59.471 55.000 5.01 0.00 44.46 2.77
2632 2796 0.112995 TGTGAGGCCATCCTTGCTTT 59.887 50.000 5.01 0.00 44.46 3.51


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

AutoCloner maintained by Alex Coulton.