Multiple sequence alignment - TraesCS2A01G498400

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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 TraesCS2A01G498400 chr2A 100.000 2965 0 0 1 2965 728729164 728726200 0.000000e+00 5476
1 TraesCS2A01G498400 chr2A 96.461 1667 38 8 644 2292 728648658 728650321 0.000000e+00 2732
2 TraesCS2A01G498400 chr2A 93.801 1484 57 16 644 2112 728617252 728618715 0.000000e+00 2198
3 TraesCS2A01G498400 chr2A 87.119 1149 85 33 1016 2143 728753334 728752228 0.000000e+00 1243
4 TraesCS2A01G498400 chr2A 96.318 679 22 3 2288 2965 728650703 728651379 0.000000e+00 1112
5 TraesCS2A01G498400 chr2D 94.373 2328 112 11 645 2965 593857250 593859565 0.000000e+00 3555
6 TraesCS2A01G498400 chr2D 91.208 1854 86 32 645 2439 593919706 593917871 0.000000e+00 2449
7 TraesCS2A01G498400 chr2D 91.302 1828 83 31 671 2439 593899121 593897311 0.000000e+00 2425
8 TraesCS2A01G498400 chr2D 92.833 1479 74 20 644 2112 593851112 593852568 0.000000e+00 2115
9 TraesCS2A01G498400 chr2D 87.727 1157 93 26 998 2143 594068626 594067508 0.000000e+00 1304
10 TraesCS2A01G498400 chr2D 93.260 816 51 4 2152 2965 593895037 593894224 0.000000e+00 1199
11 TraesCS2A01G498400 chr2B 94.402 1572 72 9 1363 2924 720817756 720819321 0.000000e+00 2401
12 TraesCS2A01G498400 chr2B 94.278 1573 73 9 1363 2924 720913972 720912406 0.000000e+00 2390
13 TraesCS2A01G498400 chr2B 89.220 1475 95 39 711 2148 720923910 720922463 0.000000e+00 1784
14 TraesCS2A01G498400 chr2B 89.612 645 65 2 1 644 634159449 634160092 0.000000e+00 819
15 TraesCS2A01G498400 chr2B 90.849 601 35 5 645 1242 720817054 720817637 0.000000e+00 787
16 TraesCS2A01G498400 chr2B 90.849 601 35 5 645 1242 720914674 720914091 0.000000e+00 787
17 TraesCS2A01G498400 chr2B 88.372 645 72 3 1 643 800954027 800954670 0.000000e+00 773
18 TraesCS2A01G498400 chr2B 86.842 646 82 3 1 644 485316889 485316245 0.000000e+00 719
19 TraesCS2A01G498400 chr2B 85.604 646 89 4 1 643 800688103 800687459 0.000000e+00 675
20 TraesCS2A01G498400 chr2B 83.945 654 89 15 1 643 50732699 50732051 1.950000e-171 612
21 TraesCS2A01G498400 chr5A 94.852 641 33 0 3 643 705385312 705384672 0.000000e+00 1002
22 TraesCS2A01G498400 chr5B 87.752 645 75 4 1 643 478671739 478672381 0.000000e+00 750
23 TraesCS2A01G498400 chr7D 84.356 652 88 13 1 643 2604788 2605434 6.980000e-176 627
24 TraesCS2A01G498400 chr1B 84.751 623 80 14 3 616 31716639 31717255 7.030000e-171 610
25 TraesCS2A01G498400 chrUn 94.221 398 20 2 2164 2559 478471680 478472076 3.270000e-169 604


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 TraesCS2A01G498400 chr2A 728726200 728729164 2964 True 5476.0 5476 100.0000 1 2965 1 chr2A.!!$R1 2964
1 TraesCS2A01G498400 chr2A 728617252 728618715 1463 False 2198.0 2198 93.8010 644 2112 1 chr2A.!!$F1 1468
2 TraesCS2A01G498400 chr2A 728648658 728651379 2721 False 1922.0 2732 96.3895 644 2965 2 chr2A.!!$F2 2321
3 TraesCS2A01G498400 chr2A 728752228 728753334 1106 True 1243.0 1243 87.1190 1016 2143 1 chr2A.!!$R2 1127
4 TraesCS2A01G498400 chr2D 593857250 593859565 2315 False 3555.0 3555 94.3730 645 2965 1 chr2D.!!$F2 2320
5 TraesCS2A01G498400 chr2D 593917871 593919706 1835 True 2449.0 2449 91.2080 645 2439 1 chr2D.!!$R1 1794
6 TraesCS2A01G498400 chr2D 593851112 593852568 1456 False 2115.0 2115 92.8330 644 2112 1 chr2D.!!$F1 1468
7 TraesCS2A01G498400 chr2D 593894224 593899121 4897 True 1812.0 2425 92.2810 671 2965 2 chr2D.!!$R3 2294
8 TraesCS2A01G498400 chr2D 594067508 594068626 1118 True 1304.0 1304 87.7270 998 2143 1 chr2D.!!$R2 1145
9 TraesCS2A01G498400 chr2B 720922463 720923910 1447 True 1784.0 1784 89.2200 711 2148 1 chr2B.!!$R3 1437
10 TraesCS2A01G498400 chr2B 720817054 720819321 2267 False 1594.0 2401 92.6255 645 2924 2 chr2B.!!$F3 2279
11 TraesCS2A01G498400 chr2B 720912406 720914674 2268 True 1588.5 2390 92.5635 645 2924 2 chr2B.!!$R5 2279
12 TraesCS2A01G498400 chr2B 634159449 634160092 643 False 819.0 819 89.6120 1 644 1 chr2B.!!$F1 643
13 TraesCS2A01G498400 chr2B 800954027 800954670 643 False 773.0 773 88.3720 1 643 1 chr2B.!!$F2 642
14 TraesCS2A01G498400 chr2B 485316245 485316889 644 True 719.0 719 86.8420 1 644 1 chr2B.!!$R2 643
15 TraesCS2A01G498400 chr2B 800687459 800688103 644 True 675.0 675 85.6040 1 643 1 chr2B.!!$R4 642
16 TraesCS2A01G498400 chr2B 50732051 50732699 648 True 612.0 612 83.9450 1 643 1 chr2B.!!$R1 642
17 TraesCS2A01G498400 chr5A 705384672 705385312 640 True 1002.0 1002 94.8520 3 643 1 chr5A.!!$R1 640
18 TraesCS2A01G498400 chr5B 478671739 478672381 642 False 750.0 750 87.7520 1 643 1 chr5B.!!$F1 642
19 TraesCS2A01G498400 chr7D 2604788 2605434 646 False 627.0 627 84.3560 1 643 1 chr7D.!!$F1 642
20 TraesCS2A01G498400 chr1B 31716639 31717255 616 False 610.0 610 84.7510 3 616 1 chr1B.!!$F1 613

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
558 559 0.096628 AGAGACGTGCGCTAGTTACG 59.903 55.0 14.69 14.69 42.98 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2710 0.538746 TGCAGCTGGATATGCATGGG 60.539 55.0 17.12 0.0 46.97 4.0 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
59 60 2.599281 TCTCCACGCCCGACTTGA 60.599 61.111 0.00 0.00 0.00 3.02
204 205 4.736896 GGCGTCGGAGGTCACCAC 62.737 72.222 0.00 0.00 0.00 4.16
205 206 3.986006 GCGTCGGAGGTCACCACA 61.986 66.667 0.00 0.00 0.00 4.17
206 207 2.049433 CGTCGGAGGTCACCACAC 60.049 66.667 0.00 0.00 0.00 3.82
207 208 2.342648 GTCGGAGGTCACCACACC 59.657 66.667 0.00 0.00 36.58 4.16
208 209 3.299977 TCGGAGGTCACCACACCG 61.300 66.667 17.39 17.39 41.90 4.94
209 210 3.299977 CGGAGGTCACCACACCGA 61.300 66.667 18.30 0.00 42.71 4.69
210 211 2.657237 GGAGGTCACCACACCGAG 59.343 66.667 0.00 0.00 41.90 4.63
211 212 2.048127 GAGGTCACCACACCGAGC 60.048 66.667 0.00 0.00 41.90 5.03
212 213 3.916392 GAGGTCACCACACCGAGCG 62.916 68.421 0.00 0.00 41.90 5.03
230 231 4.961511 GTGCGACGGTGAGGTGCA 62.962 66.667 0.00 0.00 0.00 4.57
231 232 4.662961 TGCGACGGTGAGGTGCAG 62.663 66.667 0.00 0.00 0.00 4.41
262 263 4.247380 GGAGGGGCGCTCTGGATG 62.247 72.222 27.72 0.00 0.00 3.51
263 264 4.247380 GAGGGGCGCTCTGGATGG 62.247 72.222 22.89 0.00 0.00 3.51
267 268 4.247380 GGCGCTCTGGATGGGGAG 62.247 72.222 7.64 0.00 0.00 4.30
268 269 3.474570 GCGCTCTGGATGGGGAGT 61.475 66.667 0.00 0.00 32.67 3.85
269 270 2.503061 CGCTCTGGATGGGGAGTG 59.497 66.667 0.00 0.00 34.49 3.51
270 271 2.914289 GCTCTGGATGGGGAGTGG 59.086 66.667 0.00 0.00 32.67 4.00
271 272 1.690633 GCTCTGGATGGGGAGTGGA 60.691 63.158 0.00 0.00 32.67 4.02
272 273 1.694133 GCTCTGGATGGGGAGTGGAG 61.694 65.000 0.00 0.00 32.67 3.86
273 274 1.690633 TCTGGATGGGGAGTGGAGC 60.691 63.158 0.00 0.00 0.00 4.70
274 275 3.083349 TGGATGGGGAGTGGAGCG 61.083 66.667 0.00 0.00 0.00 5.03
275 276 2.764128 GGATGGGGAGTGGAGCGA 60.764 66.667 0.00 0.00 0.00 4.93
276 277 2.367202 GGATGGGGAGTGGAGCGAA 61.367 63.158 0.00 0.00 0.00 4.70
277 278 1.602237 GATGGGGAGTGGAGCGAAA 59.398 57.895 0.00 0.00 0.00 3.46
278 279 0.462759 GATGGGGAGTGGAGCGAAAG 60.463 60.000 0.00 0.00 0.00 2.62
326 327 4.066139 GGGGTGGGCTGCCAGAAT 62.066 66.667 22.05 0.00 0.00 2.40
327 328 2.757099 GGGTGGGCTGCCAGAATG 60.757 66.667 22.05 0.00 0.00 2.67
358 359 3.127533 GTCTGCTCGCCGGCATTT 61.128 61.111 28.98 0.00 41.63 2.32
359 360 3.126879 TCTGCTCGCCGGCATTTG 61.127 61.111 28.98 10.38 41.63 2.32
360 361 3.126879 CTGCTCGCCGGCATTTGA 61.127 61.111 28.98 14.64 41.63 2.69
361 362 2.671276 TGCTCGCCGGCATTTGAA 60.671 55.556 28.98 4.20 37.29 2.69
362 363 2.202479 GCTCGCCGGCATTTGAAC 60.202 61.111 28.98 7.00 0.00 3.18
363 364 2.485122 CTCGCCGGCATTTGAACC 59.515 61.111 28.98 0.00 0.00 3.62
364 365 3.051392 CTCGCCGGCATTTGAACCC 62.051 63.158 28.98 0.00 0.00 4.11
365 366 3.061848 CGCCGGCATTTGAACCCT 61.062 61.111 28.98 0.00 0.00 4.34
366 367 2.885113 GCCGGCATTTGAACCCTC 59.115 61.111 24.80 0.00 0.00 4.30
367 368 3.051392 GCCGGCATTTGAACCCTCG 62.051 63.158 24.80 0.00 0.00 4.63
368 369 1.674322 CCGGCATTTGAACCCTCGT 60.674 57.895 0.00 0.00 0.00 4.18
369 370 1.644786 CCGGCATTTGAACCCTCGTC 61.645 60.000 0.00 0.00 0.00 4.20
370 371 0.953471 CGGCATTTGAACCCTCGTCA 60.953 55.000 0.00 0.00 0.00 4.35
371 372 0.804989 GGCATTTGAACCCTCGTCAG 59.195 55.000 0.00 0.00 0.00 3.51
372 373 1.610624 GGCATTTGAACCCTCGTCAGA 60.611 52.381 0.00 0.00 0.00 3.27
373 374 1.734465 GCATTTGAACCCTCGTCAGAG 59.266 52.381 0.00 0.00 43.98 3.35
381 382 3.621225 CTCGTCAGAGGCATGGGA 58.379 61.111 0.00 0.00 40.75 4.37
382 383 1.900351 CTCGTCAGAGGCATGGGAA 59.100 57.895 0.00 0.00 40.75 3.97
383 384 0.460987 CTCGTCAGAGGCATGGGAAC 60.461 60.000 0.00 0.00 40.75 3.62
384 385 3.768799 CTCGTCAGAGGCATGGGAACC 62.769 61.905 0.00 0.00 45.21 3.62
395 396 2.275418 GGGAACCGGCCATGTGAT 59.725 61.111 0.00 0.00 40.86 3.06
396 397 1.529796 GGGAACCGGCCATGTGATA 59.470 57.895 0.00 0.00 40.86 2.15
397 398 0.818040 GGGAACCGGCCATGTGATAC 60.818 60.000 0.00 0.00 40.86 2.24
398 399 0.107410 GGAACCGGCCATGTGATACA 60.107 55.000 0.00 0.00 0.00 2.29
399 400 1.299541 GAACCGGCCATGTGATACAG 58.700 55.000 0.00 0.00 0.00 2.74
400 401 0.107214 AACCGGCCATGTGATACAGG 60.107 55.000 0.00 0.00 0.00 4.00
401 402 0.980754 ACCGGCCATGTGATACAGGA 60.981 55.000 0.00 0.00 30.30 3.86
402 403 0.180171 CCGGCCATGTGATACAGGAA 59.820 55.000 2.24 0.00 30.30 3.36
403 404 1.586422 CGGCCATGTGATACAGGAAG 58.414 55.000 2.24 0.00 30.30 3.46
404 405 1.811558 CGGCCATGTGATACAGGAAGG 60.812 57.143 2.24 0.00 30.30 3.46
405 406 1.490490 GGCCATGTGATACAGGAAGGA 59.510 52.381 0.00 0.00 30.30 3.36
406 407 2.092429 GGCCATGTGATACAGGAAGGAA 60.092 50.000 0.00 0.00 30.30 3.36
407 408 3.620488 GCCATGTGATACAGGAAGGAAA 58.380 45.455 0.00 0.00 30.30 3.13
408 409 3.629398 GCCATGTGATACAGGAAGGAAAG 59.371 47.826 0.00 0.00 30.30 2.62
409 410 4.202441 CCATGTGATACAGGAAGGAAAGG 58.798 47.826 0.00 0.00 30.30 3.11
410 411 4.324563 CCATGTGATACAGGAAGGAAAGGT 60.325 45.833 0.00 0.00 30.30 3.50
411 412 4.553330 TGTGATACAGGAAGGAAAGGTC 57.447 45.455 0.00 0.00 0.00 3.85
412 413 3.056107 TGTGATACAGGAAGGAAAGGTCG 60.056 47.826 0.00 0.00 0.00 4.79
413 414 2.093658 TGATACAGGAAGGAAAGGTCGC 60.094 50.000 0.00 0.00 0.00 5.19
414 415 1.640917 TACAGGAAGGAAAGGTCGCT 58.359 50.000 0.00 0.00 0.00 4.93
415 416 0.321996 ACAGGAAGGAAAGGTCGCTC 59.678 55.000 0.00 0.00 0.00 5.03
416 417 0.610687 CAGGAAGGAAAGGTCGCTCT 59.389 55.000 0.00 0.00 0.00 4.09
417 418 0.610687 AGGAAGGAAAGGTCGCTCTG 59.389 55.000 0.00 0.00 0.00 3.35
418 419 0.608640 GGAAGGAAAGGTCGCTCTGA 59.391 55.000 0.00 0.00 0.00 3.27
419 420 1.208293 GGAAGGAAAGGTCGCTCTGAT 59.792 52.381 0.00 0.00 0.00 2.90
420 421 2.431057 GGAAGGAAAGGTCGCTCTGATA 59.569 50.000 0.00 0.00 0.00 2.15
421 422 3.449632 GAAGGAAAGGTCGCTCTGATAC 58.550 50.000 0.00 0.00 0.00 2.24
422 423 1.757699 AGGAAAGGTCGCTCTGATACC 59.242 52.381 0.00 0.00 0.00 2.73
423 424 1.480954 GGAAAGGTCGCTCTGATACCA 59.519 52.381 6.72 0.00 35.64 3.25
424 425 2.093658 GGAAAGGTCGCTCTGATACCAA 60.094 50.000 6.72 0.00 35.64 3.67
425 426 2.969628 AAGGTCGCTCTGATACCAAG 57.030 50.000 6.72 0.00 35.64 3.61
426 427 2.145397 AGGTCGCTCTGATACCAAGA 57.855 50.000 6.72 0.00 35.64 3.02
427 428 2.457598 AGGTCGCTCTGATACCAAGAA 58.542 47.619 6.72 0.00 35.64 2.52
428 429 2.428890 AGGTCGCTCTGATACCAAGAAG 59.571 50.000 6.72 0.00 35.64 2.85
429 430 2.427453 GGTCGCTCTGATACCAAGAAGA 59.573 50.000 0.00 0.00 33.28 2.87
430 431 3.119101 GGTCGCTCTGATACCAAGAAGAA 60.119 47.826 0.00 0.00 33.28 2.52
431 432 4.109050 GTCGCTCTGATACCAAGAAGAAG 58.891 47.826 0.00 0.00 0.00 2.85
432 433 4.017126 TCGCTCTGATACCAAGAAGAAGA 58.983 43.478 0.00 0.00 0.00 2.87
433 434 4.462834 TCGCTCTGATACCAAGAAGAAGAA 59.537 41.667 0.00 0.00 0.00 2.52
434 435 5.127845 TCGCTCTGATACCAAGAAGAAGAAT 59.872 40.000 0.00 0.00 0.00 2.40
435 436 5.233902 CGCTCTGATACCAAGAAGAAGAATG 59.766 44.000 0.00 0.00 0.00 2.67
436 437 6.344500 GCTCTGATACCAAGAAGAAGAATGA 58.656 40.000 0.00 0.00 0.00 2.57
437 438 6.479660 GCTCTGATACCAAGAAGAAGAATGAG 59.520 42.308 0.00 0.00 0.00 2.90
438 439 7.632462 GCTCTGATACCAAGAAGAAGAATGAGA 60.632 40.741 0.00 0.00 0.00 3.27
439 440 8.138928 TCTGATACCAAGAAGAAGAATGAGAA 57.861 34.615 0.00 0.00 0.00 2.87
440 441 8.766476 TCTGATACCAAGAAGAAGAATGAGAAT 58.234 33.333 0.00 0.00 0.00 2.40
441 442 8.954950 TGATACCAAGAAGAAGAATGAGAATC 57.045 34.615 0.00 0.00 0.00 2.52
442 443 8.766476 TGATACCAAGAAGAAGAATGAGAATCT 58.234 33.333 0.00 0.00 34.92 2.40
443 444 8.961294 ATACCAAGAAGAAGAATGAGAATCTG 57.039 34.615 0.00 0.00 34.92 2.90
444 445 6.179040 ACCAAGAAGAAGAATGAGAATCTGG 58.821 40.000 0.00 0.00 34.92 3.86
445 446 5.589452 CCAAGAAGAAGAATGAGAATCTGGG 59.411 44.000 0.00 0.00 34.92 4.45
446 447 6.179040 CAAGAAGAAGAATGAGAATCTGGGT 58.821 40.000 0.00 0.00 34.92 4.51
447 448 5.743117 AGAAGAAGAATGAGAATCTGGGTG 58.257 41.667 0.00 0.00 34.92 4.61
448 449 5.250313 AGAAGAAGAATGAGAATCTGGGTGT 59.750 40.000 0.00 0.00 34.92 4.16
449 450 5.511386 AGAAGAATGAGAATCTGGGTGTT 57.489 39.130 0.00 0.00 34.92 3.32
450 451 5.251764 AGAAGAATGAGAATCTGGGTGTTG 58.748 41.667 0.00 0.00 34.92 3.33
451 452 4.647564 AGAATGAGAATCTGGGTGTTGT 57.352 40.909 0.00 0.00 34.92 3.32
452 453 5.762179 AGAATGAGAATCTGGGTGTTGTA 57.238 39.130 0.00 0.00 34.92 2.41
453 454 6.319048 AGAATGAGAATCTGGGTGTTGTAT 57.681 37.500 0.00 0.00 34.92 2.29
454 455 6.725364 AGAATGAGAATCTGGGTGTTGTATT 58.275 36.000 0.00 0.00 34.92 1.89
455 456 7.861629 AGAATGAGAATCTGGGTGTTGTATTA 58.138 34.615 0.00 0.00 34.92 0.98
456 457 7.770897 AGAATGAGAATCTGGGTGTTGTATTAC 59.229 37.037 0.00 0.00 34.92 1.89
457 458 6.367374 TGAGAATCTGGGTGTTGTATTACA 57.633 37.500 0.00 0.00 34.92 2.41
458 459 6.774673 TGAGAATCTGGGTGTTGTATTACAA 58.225 36.000 5.14 5.14 33.37 2.41
459 460 7.227873 TGAGAATCTGGGTGTTGTATTACAAA 58.772 34.615 10.73 0.10 36.36 2.83
460 461 7.390440 TGAGAATCTGGGTGTTGTATTACAAAG 59.610 37.037 10.73 5.09 36.36 2.77
461 462 6.659242 AGAATCTGGGTGTTGTATTACAAAGG 59.341 38.462 10.73 0.00 40.15 3.11
462 463 5.570205 TCTGGGTGTTGTATTACAAAGGA 57.430 39.130 10.73 1.89 40.15 3.36
463 464 5.942961 TCTGGGTGTTGTATTACAAAGGAA 58.057 37.500 10.73 0.00 40.15 3.36
464 465 6.001460 TCTGGGTGTTGTATTACAAAGGAAG 58.999 40.000 10.73 6.14 40.15 3.46
465 466 5.074115 TGGGTGTTGTATTACAAAGGAAGG 58.926 41.667 10.73 0.00 40.15 3.46
466 467 4.082408 GGGTGTTGTATTACAAAGGAAGGC 60.082 45.833 10.73 0.00 40.15 4.35
467 468 4.521256 GGTGTTGTATTACAAAGGAAGGCA 59.479 41.667 10.73 0.97 40.15 4.75
468 469 5.185056 GGTGTTGTATTACAAAGGAAGGCAT 59.815 40.000 10.73 0.00 40.15 4.40
469 470 6.376018 GGTGTTGTATTACAAAGGAAGGCATA 59.624 38.462 10.73 0.00 40.15 3.14
470 471 7.415206 GGTGTTGTATTACAAAGGAAGGCATAG 60.415 40.741 10.73 0.00 40.15 2.23
471 472 6.094881 TGTTGTATTACAAAGGAAGGCATAGC 59.905 38.462 10.73 0.00 40.15 2.97
472 473 5.592688 TTGTATTACAAAGGAAGGCATAGCC 59.407 40.000 6.79 0.00 41.42 3.93
486 487 5.677319 GGCATAGCCTTATATACACAGGA 57.323 43.478 0.00 0.00 46.69 3.86
487 488 5.665459 GGCATAGCCTTATATACACAGGAG 58.335 45.833 0.00 0.00 46.69 3.69
488 489 5.422331 GGCATAGCCTTATATACACAGGAGA 59.578 44.000 0.00 0.00 46.69 3.71
489 490 6.406400 GGCATAGCCTTATATACACAGGAGAG 60.406 46.154 0.00 0.00 46.69 3.20
490 491 6.568869 CATAGCCTTATATACACAGGAGAGC 58.431 44.000 3.51 0.00 0.00 4.09
491 492 4.483950 AGCCTTATATACACAGGAGAGCA 58.516 43.478 3.51 0.00 0.00 4.26
492 493 4.282195 AGCCTTATATACACAGGAGAGCAC 59.718 45.833 3.51 0.00 0.00 4.40
493 494 4.799678 CCTTATATACACAGGAGAGCACG 58.200 47.826 0.00 0.00 0.00 5.34
494 495 2.802787 ATATACACAGGAGAGCACGC 57.197 50.000 0.00 0.00 0.00 5.34
495 496 0.380733 TATACACAGGAGAGCACGCG 59.619 55.000 3.53 3.53 0.00 6.01
496 497 2.890847 ATACACAGGAGAGCACGCGC 62.891 60.000 5.73 0.00 38.99 6.86
498 499 4.731612 ACAGGAGAGCACGCGCAG 62.732 66.667 5.73 0.00 42.27 5.18
511 512 4.954970 CGCAGGTGCTGGGTTGGT 62.955 66.667 0.00 0.00 39.17 3.67
512 513 2.521708 GCAGGTGCTGGGTTGGTT 60.522 61.111 0.00 0.00 38.21 3.67
513 514 1.228429 GCAGGTGCTGGGTTGGTTA 60.228 57.895 0.00 0.00 38.21 2.85
514 515 1.524008 GCAGGTGCTGGGTTGGTTAC 61.524 60.000 0.00 0.00 38.21 2.50
515 516 0.179004 CAGGTGCTGGGTTGGTTACA 60.179 55.000 0.00 0.00 0.00 2.41
516 517 0.553819 AGGTGCTGGGTTGGTTACAA 59.446 50.000 0.00 0.00 0.00 2.41
528 529 3.857157 TGGTTACAACAGAAAGGAGCT 57.143 42.857 0.00 0.00 0.00 4.09
529 530 4.967084 TGGTTACAACAGAAAGGAGCTA 57.033 40.909 0.00 0.00 0.00 3.32
530 531 4.894784 TGGTTACAACAGAAAGGAGCTAG 58.105 43.478 0.00 0.00 0.00 3.42
531 532 4.347000 TGGTTACAACAGAAAGGAGCTAGT 59.653 41.667 0.00 0.00 0.00 2.57
532 533 4.930405 GGTTACAACAGAAAGGAGCTAGTC 59.070 45.833 0.00 0.00 0.00 2.59
533 534 5.279556 GGTTACAACAGAAAGGAGCTAGTCT 60.280 44.000 0.00 0.00 0.00 3.24
534 535 4.529109 ACAACAGAAAGGAGCTAGTCTC 57.471 45.455 5.83 5.83 41.15 3.36
542 543 3.015516 GAGCTAGTCTCCCGGAGAG 57.984 63.158 18.00 8.47 39.53 3.20
549 550 4.180946 CTCCCGGAGAGACGTGCG 62.181 72.222 9.01 0.00 46.50 5.34
552 553 3.506096 CCGGAGAGACGTGCGCTA 61.506 66.667 9.73 0.00 0.00 4.26
553 554 2.023461 CGGAGAGACGTGCGCTAG 59.977 66.667 9.73 4.86 0.00 3.42
554 555 2.751913 CGGAGAGACGTGCGCTAGT 61.752 63.158 9.73 8.72 0.00 2.57
555 556 1.507174 GGAGAGACGTGCGCTAGTT 59.493 57.895 9.73 0.00 0.00 2.24
556 557 0.731417 GGAGAGACGTGCGCTAGTTA 59.269 55.000 9.73 0.00 0.00 2.24
557 558 1.531470 GGAGAGACGTGCGCTAGTTAC 60.531 57.143 9.73 6.97 0.00 2.50
558 559 0.096628 AGAGACGTGCGCTAGTTACG 59.903 55.000 14.69 14.69 42.98 3.18
584 585 2.764128 GGGGAGAGGCCACGATCA 60.764 66.667 5.01 0.00 38.95 2.92
585 586 2.501610 GGGAGAGGCCACGATCAC 59.498 66.667 5.01 0.00 38.95 3.06
586 587 2.501610 GGAGAGGCCACGATCACC 59.498 66.667 5.01 0.00 36.34 4.02
587 588 2.105128 GAGAGGCCACGATCACCG 59.895 66.667 5.01 0.00 45.44 4.94
588 589 4.148825 AGAGGCCACGATCACCGC 62.149 66.667 5.01 0.00 43.32 5.68
589 590 4.451150 GAGGCCACGATCACCGCA 62.451 66.667 5.01 0.00 43.32 5.69
590 591 3.740128 GAGGCCACGATCACCGCAT 62.740 63.158 5.01 0.00 43.32 4.73
591 592 3.576356 GGCCACGATCACCGCATG 61.576 66.667 0.00 0.00 43.32 4.06
592 593 3.576356 GCCACGATCACCGCATGG 61.576 66.667 0.00 0.00 43.32 3.66
593 594 2.186644 CCACGATCACCGCATGGA 59.813 61.111 0.00 0.00 43.32 3.41
594 595 1.884464 CCACGATCACCGCATGGAG 60.884 63.158 0.00 0.00 43.32 3.86
595 596 1.141665 CACGATCACCGCATGGAGA 59.858 57.895 0.00 0.00 43.32 3.71
596 597 0.873312 CACGATCACCGCATGGAGAG 60.873 60.000 0.00 0.00 43.32 3.20
597 598 1.953138 CGATCACCGCATGGAGAGC 60.953 63.158 0.00 0.00 38.31 4.09
639 640 2.619362 CGGTGTTAGCCGTTTTCCA 58.381 52.632 0.00 0.00 46.11 3.53
640 641 0.945813 CGGTGTTAGCCGTTTTCCAA 59.054 50.000 0.00 0.00 46.11 3.53
641 642 1.334329 CGGTGTTAGCCGTTTTCCAAC 60.334 52.381 0.00 0.00 46.11 3.77
642 643 1.677052 GGTGTTAGCCGTTTTCCAACA 59.323 47.619 0.00 0.00 32.54 3.33
679 680 0.531090 GGTACACCGTTGTGCTGACA 60.531 55.000 0.68 0.00 46.86 3.58
681 682 1.871039 GTACACCGTTGTGCTGACAAT 59.129 47.619 0.00 0.00 46.86 2.71
709 710 2.028203 TGTCGTCAAATCCAGATGCTGA 60.028 45.455 0.00 0.00 32.44 4.26
717 718 4.620589 AATCCAGATGCTGACAGATAGG 57.379 45.455 6.65 0.23 32.44 2.57
721 722 3.367190 CCAGATGCTGACAGATAGGATCG 60.367 52.174 6.65 0.00 44.64 3.69
726 730 5.635417 TGCTGACAGATAGGATCGATTAG 57.365 43.478 6.65 0.00 0.00 1.73
868 875 8.196771 AGACACTTTTGCATTTGACTGAAAATA 58.803 29.630 0.00 0.00 0.00 1.40
1968 2709 1.433471 CTGCCGCAGTACTGATCGA 59.567 57.895 27.08 6.03 0.00 3.59
1969 2710 0.867753 CTGCCGCAGTACTGATCGAC 60.868 60.000 27.08 13.92 0.00 4.20
1970 2711 1.589196 GCCGCAGTACTGATCGACC 60.589 63.158 27.08 11.30 0.00 4.79
1971 2712 1.065928 CCGCAGTACTGATCGACCC 59.934 63.158 27.08 5.72 0.00 4.46
1972 2713 1.663379 CCGCAGTACTGATCGACCCA 61.663 60.000 27.08 0.00 0.00 4.51
1973 2714 0.385751 CGCAGTACTGATCGACCCAT 59.614 55.000 27.08 0.00 0.00 4.00
1974 2715 1.858091 GCAGTACTGATCGACCCATG 58.142 55.000 27.08 0.00 0.00 3.66
1975 2716 1.858091 CAGTACTGATCGACCCATGC 58.142 55.000 18.45 0.00 0.00 4.06
1976 2717 1.136891 CAGTACTGATCGACCCATGCA 59.863 52.381 18.45 0.00 0.00 3.96
1977 2718 2.042464 AGTACTGATCGACCCATGCAT 58.958 47.619 0.00 0.00 0.00 3.96
2054 2827 1.244816 CCGATCTATCTACCACGGCA 58.755 55.000 0.00 0.00 34.36 5.69
2055 2828 1.819288 CCGATCTATCTACCACGGCAT 59.181 52.381 0.00 0.00 34.36 4.40
2056 2829 3.014623 CCGATCTATCTACCACGGCATA 58.985 50.000 0.00 0.00 34.36 3.14
2057 2830 3.632604 CCGATCTATCTACCACGGCATAT 59.367 47.826 0.00 0.00 34.36 1.78
2068 2841 2.230508 CCACGGCATATATACACGACCT 59.769 50.000 8.87 0.00 0.00 3.85
2148 2939 7.719483 TCAAGATTTTTCATTCTTGTTGCTCT 58.281 30.769 11.24 0.00 45.77 4.09
2162 2953 4.385825 TGTTGCTCTACGGATGTTTTCTT 58.614 39.130 0.00 0.00 0.00 2.52
2262 3062 1.270199 GGTTGCATGCATGAACCAACA 60.270 47.619 33.19 20.54 37.96 3.33
2331 3517 6.561614 ACACACCACGACTACAATAATCTAG 58.438 40.000 0.00 0.00 0.00 2.43
2423 6203 5.392380 CGATCAAAAGAAAGCTTACCATGCT 60.392 40.000 0.00 0.00 43.32 3.79
2430 6210 3.515330 AAGCTTACCATGCTCAATTGC 57.485 42.857 0.00 0.00 40.22 3.56
2477 6257 3.895041 AGGGTTACCACCAAAAACATCAG 59.105 43.478 2.98 0.00 46.43 2.90
2631 6414 5.061920 ACTCGACACTCATTTAAGACCTC 57.938 43.478 0.00 0.00 0.00 3.85
2641 6424 9.553064 CACTCATTTAAGACCTCAATAATAGCT 57.447 33.333 0.00 0.00 0.00 3.32
2869 6656 9.605275 CTCTCCTTTTCCTTTTTCTTTCATTTT 57.395 29.630 0.00 0.00 0.00 1.82
2916 6703 4.462834 CCCATGTTTACTTTCCCTTCTTCC 59.537 45.833 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 2.106166 GCATCATGTCCTTCATCCTCCT 59.894 50.000 0.00 0.00 34.09 3.69
187 188 4.736896 GTGGTGACCTCCGACGCC 62.737 72.222 2.11 0.00 37.22 5.68
188 189 3.986006 TGTGGTGACCTCCGACGC 61.986 66.667 2.11 0.00 0.00 5.19
189 190 2.049433 GTGTGGTGACCTCCGACG 60.049 66.667 2.11 0.00 0.00 5.12
190 191 2.342648 GGTGTGGTGACCTCCGAC 59.657 66.667 2.11 0.00 32.69 4.79
191 192 3.299977 CGGTGTGGTGACCTCCGA 61.300 66.667 21.56 0.00 38.85 4.55
192 193 3.282745 CTCGGTGTGGTGACCTCCG 62.283 68.421 20.62 20.62 38.31 4.63
193 194 2.657237 CTCGGTGTGGTGACCTCC 59.343 66.667 2.11 2.09 33.35 4.30
194 195 2.048127 GCTCGGTGTGGTGACCTC 60.048 66.667 2.11 0.00 33.35 3.85
195 196 3.991051 CGCTCGGTGTGGTGACCT 61.991 66.667 2.11 0.00 33.35 3.85
213 214 4.961511 TGCACCTCACCGTCGCAC 62.962 66.667 0.00 0.00 0.00 5.34
214 215 4.662961 CTGCACCTCACCGTCGCA 62.663 66.667 0.00 0.00 0.00 5.10
221 222 4.385405 AGCTCCGCTGCACCTCAC 62.385 66.667 0.00 0.00 37.57 3.51
245 246 4.247380 CATCCAGAGCGCCCCTCC 62.247 72.222 2.29 0.00 41.74 4.30
246 247 4.247380 CCATCCAGAGCGCCCCTC 62.247 72.222 2.29 0.00 41.07 4.30
250 251 4.247380 CTCCCCATCCAGAGCGCC 62.247 72.222 2.29 0.00 0.00 6.53
251 252 3.474570 ACTCCCCATCCAGAGCGC 61.475 66.667 0.00 0.00 33.18 5.92
252 253 2.503061 CACTCCCCATCCAGAGCG 59.497 66.667 0.00 0.00 33.18 5.03
253 254 1.690633 TCCACTCCCCATCCAGAGC 60.691 63.158 0.00 0.00 33.18 4.09
254 255 1.694133 GCTCCACTCCCCATCCAGAG 61.694 65.000 0.00 0.00 36.16 3.35
255 256 1.690633 GCTCCACTCCCCATCCAGA 60.691 63.158 0.00 0.00 0.00 3.86
256 257 2.914289 GCTCCACTCCCCATCCAG 59.086 66.667 0.00 0.00 0.00 3.86
257 258 3.083349 CGCTCCACTCCCCATCCA 61.083 66.667 0.00 0.00 0.00 3.41
258 259 1.910580 TTTCGCTCCACTCCCCATCC 61.911 60.000 0.00 0.00 0.00 3.51
259 260 0.462759 CTTTCGCTCCACTCCCCATC 60.463 60.000 0.00 0.00 0.00 3.51
260 261 1.604378 CTTTCGCTCCACTCCCCAT 59.396 57.895 0.00 0.00 0.00 4.00
261 262 3.068881 CTTTCGCTCCACTCCCCA 58.931 61.111 0.00 0.00 0.00 4.96
262 263 2.436824 GCTTTCGCTCCACTCCCC 60.437 66.667 0.00 0.00 0.00 4.81
263 264 1.743252 CTGCTTTCGCTCCACTCCC 60.743 63.158 0.00 0.00 36.97 4.30
264 265 1.004440 ACTGCTTTCGCTCCACTCC 60.004 57.895 0.00 0.00 36.97 3.85
265 266 1.294659 CCACTGCTTTCGCTCCACTC 61.295 60.000 0.00 0.00 36.97 3.51
266 267 1.302033 CCACTGCTTTCGCTCCACT 60.302 57.895 0.00 0.00 36.97 4.00
267 268 2.328099 CCCACTGCTTTCGCTCCAC 61.328 63.158 0.00 0.00 36.97 4.02
268 269 2.032528 CCCACTGCTTTCGCTCCA 59.967 61.111 0.00 0.00 36.97 3.86
269 270 3.435186 GCCCACTGCTTTCGCTCC 61.435 66.667 0.00 0.00 36.87 4.70
270 271 2.669569 TGCCCACTGCTTTCGCTC 60.670 61.111 0.00 0.00 42.00 5.03
271 272 2.670934 CTGCCCACTGCTTTCGCT 60.671 61.111 0.00 0.00 42.00 4.93
272 273 4.410743 GCTGCCCACTGCTTTCGC 62.411 66.667 0.00 0.00 42.00 4.70
273 274 4.093952 CGCTGCCCACTGCTTTCG 62.094 66.667 0.00 0.00 42.00 3.46
274 275 3.741476 CCGCTGCCCACTGCTTTC 61.741 66.667 0.00 0.00 42.00 2.62
275 276 4.269523 TCCGCTGCCCACTGCTTT 62.270 61.111 0.00 0.00 42.00 3.51
276 277 4.711949 CTCCGCTGCCCACTGCTT 62.712 66.667 0.00 0.00 42.00 3.91
309 310 4.066139 ATTCTGGCAGCCCACCCC 62.066 66.667 9.64 0.00 35.79 4.95
310 311 2.757099 CATTCTGGCAGCCCACCC 60.757 66.667 9.64 0.00 35.79 4.61
311 312 2.757099 CCATTCTGGCAGCCCACC 60.757 66.667 9.64 0.00 35.79 4.61
312 313 2.048603 GTCCATTCTGGCAGCCCAC 61.049 63.158 9.64 0.00 37.47 4.61
313 314 2.356278 GTCCATTCTGGCAGCCCA 59.644 61.111 9.64 0.00 37.47 5.36
314 315 2.825836 CGTCCATTCTGGCAGCCC 60.826 66.667 9.64 0.00 37.47 5.19
315 316 3.512516 GCGTCCATTCTGGCAGCC 61.513 66.667 10.34 3.66 37.47 4.85
316 317 3.512516 GGCGTCCATTCTGGCAGC 61.513 66.667 10.34 0.00 37.47 5.25
317 318 3.197790 CGGCGTCCATTCTGGCAG 61.198 66.667 8.58 8.58 37.47 4.85
318 319 4.776322 CCGGCGTCCATTCTGGCA 62.776 66.667 6.01 0.00 37.47 4.92
345 346 2.202479 GTTCAAATGCCGGCGAGC 60.202 61.111 23.90 11.15 0.00 5.03
346 347 2.485122 GGTTCAAATGCCGGCGAG 59.515 61.111 23.90 11.49 0.00 5.03
347 348 3.059386 GGGTTCAAATGCCGGCGA 61.059 61.111 23.90 10.16 0.00 5.54
348 349 3.051392 GAGGGTTCAAATGCCGGCG 62.051 63.158 23.90 7.44 0.00 6.46
349 350 2.885113 GAGGGTTCAAATGCCGGC 59.115 61.111 22.73 22.73 0.00 6.13
350 351 1.644786 GACGAGGGTTCAAATGCCGG 61.645 60.000 0.00 0.00 0.00 6.13
351 352 0.953471 TGACGAGGGTTCAAATGCCG 60.953 55.000 0.00 0.00 0.00 5.69
352 353 0.804989 CTGACGAGGGTTCAAATGCC 59.195 55.000 0.00 0.00 0.00 4.40
353 354 1.734465 CTCTGACGAGGGTTCAAATGC 59.266 52.381 0.00 0.00 33.51 3.56
364 365 0.460987 GTTCCCATGCCTCTGACGAG 60.461 60.000 0.00 0.00 37.01 4.18
365 366 1.596934 GTTCCCATGCCTCTGACGA 59.403 57.895 0.00 0.00 0.00 4.20
366 367 1.450312 GGTTCCCATGCCTCTGACG 60.450 63.158 0.00 0.00 0.00 4.35
367 368 1.450312 CGGTTCCCATGCCTCTGAC 60.450 63.158 0.00 0.00 0.00 3.51
368 369 2.669133 CCGGTTCCCATGCCTCTGA 61.669 63.158 0.00 0.00 0.00 3.27
369 370 2.124570 CCGGTTCCCATGCCTCTG 60.125 66.667 0.00 0.00 0.00 3.35
370 371 4.115199 GCCGGTTCCCATGCCTCT 62.115 66.667 1.90 0.00 0.00 3.69
373 374 4.839706 ATGGCCGGTTCCCATGCC 62.840 66.667 10.93 0.00 41.40 4.40
376 377 1.936767 ATCACATGGCCGGTTCCCAT 61.937 55.000 1.90 4.53 43.70 4.00
377 378 1.275421 TATCACATGGCCGGTTCCCA 61.275 55.000 1.90 1.63 36.66 4.37
378 379 0.818040 GTATCACATGGCCGGTTCCC 60.818 60.000 1.90 0.00 0.00 3.97
379 380 0.107410 TGTATCACATGGCCGGTTCC 60.107 55.000 1.90 0.00 0.00 3.62
380 381 1.299541 CTGTATCACATGGCCGGTTC 58.700 55.000 1.90 0.00 0.00 3.62
381 382 0.107214 CCTGTATCACATGGCCGGTT 60.107 55.000 1.90 0.00 0.00 4.44
382 383 0.980754 TCCTGTATCACATGGCCGGT 60.981 55.000 1.90 0.00 0.00 5.28
383 384 0.180171 TTCCTGTATCACATGGCCGG 59.820 55.000 0.00 0.00 0.00 6.13
384 385 1.586422 CTTCCTGTATCACATGGCCG 58.414 55.000 0.00 0.00 0.00 6.13
385 386 1.490490 TCCTTCCTGTATCACATGGCC 59.510 52.381 0.00 0.00 0.00 5.36
386 387 3.281727 TTCCTTCCTGTATCACATGGC 57.718 47.619 0.00 0.00 0.00 4.40
387 388 4.202441 CCTTTCCTTCCTGTATCACATGG 58.798 47.826 0.00 0.00 0.00 3.66
388 389 4.848357 ACCTTTCCTTCCTGTATCACATG 58.152 43.478 0.00 0.00 0.00 3.21
389 390 4.383118 CGACCTTTCCTTCCTGTATCACAT 60.383 45.833 0.00 0.00 0.00 3.21
390 391 3.056107 CGACCTTTCCTTCCTGTATCACA 60.056 47.826 0.00 0.00 0.00 3.58
391 392 3.522553 CGACCTTTCCTTCCTGTATCAC 58.477 50.000 0.00 0.00 0.00 3.06
392 393 2.093658 GCGACCTTTCCTTCCTGTATCA 60.094 50.000 0.00 0.00 0.00 2.15
393 394 2.168728 AGCGACCTTTCCTTCCTGTATC 59.831 50.000 0.00 0.00 0.00 2.24
394 395 2.168728 GAGCGACCTTTCCTTCCTGTAT 59.831 50.000 0.00 0.00 0.00 2.29
395 396 1.549170 GAGCGACCTTTCCTTCCTGTA 59.451 52.381 0.00 0.00 0.00 2.74
396 397 0.321996 GAGCGACCTTTCCTTCCTGT 59.678 55.000 0.00 0.00 0.00 4.00
397 398 0.610687 AGAGCGACCTTTCCTTCCTG 59.389 55.000 0.00 0.00 0.00 3.86
398 399 0.610687 CAGAGCGACCTTTCCTTCCT 59.389 55.000 0.00 0.00 0.00 3.36
399 400 0.608640 TCAGAGCGACCTTTCCTTCC 59.391 55.000 0.00 0.00 0.00 3.46
400 401 2.682155 ATCAGAGCGACCTTTCCTTC 57.318 50.000 0.00 0.00 0.00 3.46
401 402 2.168728 GGTATCAGAGCGACCTTTCCTT 59.831 50.000 0.00 0.00 0.00 3.36
402 403 1.757699 GGTATCAGAGCGACCTTTCCT 59.242 52.381 0.00 0.00 0.00 3.36
403 404 1.480954 TGGTATCAGAGCGACCTTTCC 59.519 52.381 0.00 0.00 34.13 3.13
404 405 2.961526 TGGTATCAGAGCGACCTTTC 57.038 50.000 0.00 0.00 34.13 2.62
405 406 2.832129 TCTTGGTATCAGAGCGACCTTT 59.168 45.455 0.00 0.00 34.13 3.11
406 407 2.457598 TCTTGGTATCAGAGCGACCTT 58.542 47.619 0.00 0.00 34.13 3.50
407 408 2.145397 TCTTGGTATCAGAGCGACCT 57.855 50.000 0.00 0.00 34.13 3.85
408 409 2.427453 TCTTCTTGGTATCAGAGCGACC 59.573 50.000 0.00 0.00 0.00 4.79
409 410 3.784701 TCTTCTTGGTATCAGAGCGAC 57.215 47.619 0.00 0.00 0.00 5.19
410 411 4.017126 TCTTCTTCTTGGTATCAGAGCGA 58.983 43.478 0.00 0.00 0.00 4.93
411 412 4.377839 TCTTCTTCTTGGTATCAGAGCG 57.622 45.455 0.00 0.00 0.00 5.03
412 413 6.344500 TCATTCTTCTTCTTGGTATCAGAGC 58.656 40.000 0.00 0.00 0.00 4.09
413 414 7.780064 TCTCATTCTTCTTCTTGGTATCAGAG 58.220 38.462 0.00 0.00 0.00 3.35
414 415 7.724490 TCTCATTCTTCTTCTTGGTATCAGA 57.276 36.000 0.00 0.00 0.00 3.27
415 416 8.961294 ATTCTCATTCTTCTTCTTGGTATCAG 57.039 34.615 0.00 0.00 0.00 2.90
416 417 8.766476 AGATTCTCATTCTTCTTCTTGGTATCA 58.234 33.333 0.00 0.00 0.00 2.15
417 418 9.044150 CAGATTCTCATTCTTCTTCTTGGTATC 57.956 37.037 0.00 0.00 0.00 2.24
418 419 7.992033 CCAGATTCTCATTCTTCTTCTTGGTAT 59.008 37.037 0.00 0.00 0.00 2.73
419 420 7.334090 CCAGATTCTCATTCTTCTTCTTGGTA 58.666 38.462 0.00 0.00 0.00 3.25
420 421 6.179040 CCAGATTCTCATTCTTCTTCTTGGT 58.821 40.000 0.00 0.00 0.00 3.67
421 422 5.589452 CCCAGATTCTCATTCTTCTTCTTGG 59.411 44.000 0.00 0.00 0.00 3.61
422 423 6.093771 CACCCAGATTCTCATTCTTCTTCTTG 59.906 42.308 0.00 0.00 0.00 3.02
423 424 6.179040 CACCCAGATTCTCATTCTTCTTCTT 58.821 40.000 0.00 0.00 0.00 2.52
424 425 5.250313 ACACCCAGATTCTCATTCTTCTTCT 59.750 40.000 0.00 0.00 0.00 2.85
425 426 5.495640 ACACCCAGATTCTCATTCTTCTTC 58.504 41.667 0.00 0.00 0.00 2.87
426 427 5.511386 ACACCCAGATTCTCATTCTTCTT 57.489 39.130 0.00 0.00 0.00 2.52
427 428 5.222007 ACAACACCCAGATTCTCATTCTTCT 60.222 40.000 0.00 0.00 0.00 2.85
428 429 5.006386 ACAACACCCAGATTCTCATTCTTC 58.994 41.667 0.00 0.00 0.00 2.87
429 430 4.990526 ACAACACCCAGATTCTCATTCTT 58.009 39.130 0.00 0.00 0.00 2.52
430 431 4.647564 ACAACACCCAGATTCTCATTCT 57.352 40.909 0.00 0.00 0.00 2.40
431 432 7.552687 TGTAATACAACACCCAGATTCTCATTC 59.447 37.037 0.00 0.00 0.00 2.67
432 433 7.402054 TGTAATACAACACCCAGATTCTCATT 58.598 34.615 0.00 0.00 0.00 2.57
433 434 6.957631 TGTAATACAACACCCAGATTCTCAT 58.042 36.000 0.00 0.00 0.00 2.90
434 435 6.367374 TGTAATACAACACCCAGATTCTCA 57.633 37.500 0.00 0.00 0.00 3.27
435 436 7.148239 CCTTTGTAATACAACACCCAGATTCTC 60.148 40.741 5.19 0.00 37.90 2.87
436 437 6.659242 CCTTTGTAATACAACACCCAGATTCT 59.341 38.462 5.19 0.00 37.90 2.40
437 438 6.657541 TCCTTTGTAATACAACACCCAGATTC 59.342 38.462 5.19 0.00 37.90 2.52
438 439 6.548321 TCCTTTGTAATACAACACCCAGATT 58.452 36.000 5.19 0.00 37.90 2.40
439 440 6.134535 TCCTTTGTAATACAACACCCAGAT 57.865 37.500 5.19 0.00 37.90 2.90
440 441 5.570205 TCCTTTGTAATACAACACCCAGA 57.430 39.130 5.19 0.00 37.90 3.86
441 442 5.183140 CCTTCCTTTGTAATACAACACCCAG 59.817 44.000 5.19 0.39 37.90 4.45
442 443 5.074115 CCTTCCTTTGTAATACAACACCCA 58.926 41.667 5.19 0.00 37.90 4.51
443 444 4.082408 GCCTTCCTTTGTAATACAACACCC 60.082 45.833 5.19 0.00 37.90 4.61
444 445 4.521256 TGCCTTCCTTTGTAATACAACACC 59.479 41.667 5.19 0.00 37.90 4.16
445 446 5.699097 TGCCTTCCTTTGTAATACAACAC 57.301 39.130 5.19 0.00 37.90 3.32
446 447 6.094881 GCTATGCCTTCCTTTGTAATACAACA 59.905 38.462 5.19 0.00 37.90 3.33
447 448 6.459710 GGCTATGCCTTCCTTTGTAATACAAC 60.460 42.308 5.19 0.00 46.69 3.32
448 449 5.592688 GGCTATGCCTTCCTTTGTAATACAA 59.407 40.000 1.08 1.08 46.69 2.41
449 450 5.130350 GGCTATGCCTTCCTTTGTAATACA 58.870 41.667 0.73 0.00 46.69 2.29
450 451 5.690997 GGCTATGCCTTCCTTTGTAATAC 57.309 43.478 0.73 0.00 46.69 1.89
465 466 6.531503 TCTCCTGTGTATATAAGGCTATGC 57.468 41.667 0.00 0.00 0.00 3.14
466 467 6.153510 TGCTCTCCTGTGTATATAAGGCTATG 59.846 42.308 0.00 0.00 0.00 2.23
467 468 6.153680 GTGCTCTCCTGTGTATATAAGGCTAT 59.846 42.308 0.00 0.00 0.00 2.97
468 469 5.477291 GTGCTCTCCTGTGTATATAAGGCTA 59.523 44.000 0.00 0.00 0.00 3.93
469 470 4.282195 GTGCTCTCCTGTGTATATAAGGCT 59.718 45.833 0.00 0.00 0.00 4.58
470 471 4.561105 GTGCTCTCCTGTGTATATAAGGC 58.439 47.826 0.00 0.00 0.00 4.35
471 472 4.799678 CGTGCTCTCCTGTGTATATAAGG 58.200 47.826 0.00 0.00 0.00 2.69
472 473 4.230657 GCGTGCTCTCCTGTGTATATAAG 58.769 47.826 0.00 0.00 0.00 1.73
473 474 3.304458 CGCGTGCTCTCCTGTGTATATAA 60.304 47.826 0.00 0.00 0.00 0.98
474 475 2.225727 CGCGTGCTCTCCTGTGTATATA 59.774 50.000 0.00 0.00 0.00 0.86
475 476 1.001268 CGCGTGCTCTCCTGTGTATAT 60.001 52.381 0.00 0.00 0.00 0.86
476 477 0.380733 CGCGTGCTCTCCTGTGTATA 59.619 55.000 0.00 0.00 0.00 1.47
477 478 1.139734 CGCGTGCTCTCCTGTGTAT 59.860 57.895 0.00 0.00 0.00 2.29
478 479 2.566529 CGCGTGCTCTCCTGTGTA 59.433 61.111 0.00 0.00 0.00 2.90
481 482 4.731612 CTGCGCGTGCTCTCCTGT 62.732 66.667 23.16 0.00 43.34 4.00
495 496 1.228429 TAACCAACCCAGCACCTGC 60.228 57.895 0.00 0.00 42.49 4.85
496 497 0.179004 TGTAACCAACCCAGCACCTG 60.179 55.000 0.00 0.00 0.00 4.00
497 498 0.553819 TTGTAACCAACCCAGCACCT 59.446 50.000 0.00 0.00 0.00 4.00
498 499 0.671796 GTTGTAACCAACCCAGCACC 59.328 55.000 0.00 0.00 44.25 5.01
507 508 4.164843 AGCTCCTTTCTGTTGTAACCAA 57.835 40.909 0.00 0.00 0.00 3.67
508 509 3.857157 AGCTCCTTTCTGTTGTAACCA 57.143 42.857 0.00 0.00 0.00 3.67
509 510 4.895961 ACTAGCTCCTTTCTGTTGTAACC 58.104 43.478 0.00 0.00 0.00 2.85
510 511 5.785243 AGACTAGCTCCTTTCTGTTGTAAC 58.215 41.667 0.00 0.00 0.00 2.50
511 512 6.026947 GAGACTAGCTCCTTTCTGTTGTAA 57.973 41.667 0.00 0.00 37.69 2.41
512 513 5.646577 GAGACTAGCTCCTTTCTGTTGTA 57.353 43.478 0.00 0.00 37.69 2.41
513 514 4.529109 GAGACTAGCTCCTTTCTGTTGT 57.471 45.455 0.00 0.00 37.69 3.32
524 525 0.470766 TCTCTCCGGGAGACTAGCTC 59.529 60.000 22.70 5.83 45.20 4.09
525 526 2.622739 TCTCTCCGGGAGACTAGCT 58.377 57.895 22.70 0.00 45.20 3.32
532 533 4.180946 CGCACGTCTCTCCGGGAG 62.181 72.222 18.25 18.25 43.12 4.30
535 536 3.456431 CTAGCGCACGTCTCTCCGG 62.456 68.421 11.47 0.00 0.00 5.14
536 537 2.023461 CTAGCGCACGTCTCTCCG 59.977 66.667 11.47 0.00 0.00 4.63
537 538 0.731417 TAACTAGCGCACGTCTCTCC 59.269 55.000 11.47 0.00 0.00 3.71
538 539 1.812662 GTAACTAGCGCACGTCTCTC 58.187 55.000 11.47 0.00 0.00 3.20
539 540 0.096628 CGTAACTAGCGCACGTCTCT 59.903 55.000 11.47 0.00 0.00 3.10
540 541 2.552431 CGTAACTAGCGCACGTCTC 58.448 57.895 11.47 2.15 0.00 3.36
541 542 4.759564 CGTAACTAGCGCACGTCT 57.240 55.556 11.47 0.00 0.00 4.18
566 567 3.917760 GATCGTGGCCTCTCCCCG 61.918 72.222 3.32 0.00 0.00 5.73
567 568 2.764128 TGATCGTGGCCTCTCCCC 60.764 66.667 3.32 0.00 0.00 4.81
568 569 2.501610 GTGATCGTGGCCTCTCCC 59.498 66.667 3.32 0.00 0.00 4.30
569 570 2.501610 GGTGATCGTGGCCTCTCC 59.498 66.667 3.32 0.00 0.00 3.71
570 571 2.105128 CGGTGATCGTGGCCTCTC 59.895 66.667 3.32 0.00 0.00 3.20
571 572 4.148825 GCGGTGATCGTGGCCTCT 62.149 66.667 3.32 0.00 41.72 3.69
572 573 3.740128 ATGCGGTGATCGTGGCCTC 62.740 63.158 3.32 0.00 41.72 4.70
573 574 3.785859 ATGCGGTGATCGTGGCCT 61.786 61.111 3.32 0.00 41.72 5.19
574 575 3.576356 CATGCGGTGATCGTGGCC 61.576 66.667 0.00 0.00 41.72 5.36
575 576 3.576356 CCATGCGGTGATCGTGGC 61.576 66.667 0.00 0.00 41.72 5.01
576 577 1.884464 CTCCATGCGGTGATCGTGG 60.884 63.158 0.00 0.00 41.72 4.94
577 578 0.873312 CTCTCCATGCGGTGATCGTG 60.873 60.000 0.00 0.00 41.72 4.35
578 579 1.439228 CTCTCCATGCGGTGATCGT 59.561 57.895 0.00 0.00 41.72 3.73
579 580 1.953138 GCTCTCCATGCGGTGATCG 60.953 63.158 0.00 0.00 42.76 3.69
580 581 4.040068 GCTCTCCATGCGGTGATC 57.960 61.111 0.00 0.00 34.35 2.92
622 623 1.677052 TGTTGGAAAACGGCTAACACC 59.323 47.619 0.00 0.00 32.80 4.16
623 624 2.723209 GTGTTGGAAAACGGCTAACAC 58.277 47.619 0.00 0.00 45.71 3.32
624 625 2.366533 TGTGTTGGAAAACGGCTAACA 58.633 42.857 0.00 0.00 34.90 2.41
625 626 3.110358 GTTGTGTTGGAAAACGGCTAAC 58.890 45.455 0.00 0.00 0.00 2.34
626 627 2.099427 GGTTGTGTTGGAAAACGGCTAA 59.901 45.455 0.00 0.00 0.00 3.09
627 628 1.677052 GGTTGTGTTGGAAAACGGCTA 59.323 47.619 0.00 0.00 0.00 3.93
628 629 0.458260 GGTTGTGTTGGAAAACGGCT 59.542 50.000 0.00 0.00 0.00 5.52
629 630 0.173708 TGGTTGTGTTGGAAAACGGC 59.826 50.000 0.00 0.00 0.00 5.68
630 631 2.535331 CTTGGTTGTGTTGGAAAACGG 58.465 47.619 0.00 0.00 0.00 4.44
631 632 1.923864 GCTTGGTTGTGTTGGAAAACG 59.076 47.619 0.00 0.00 0.00 3.60
632 633 1.923864 CGCTTGGTTGTGTTGGAAAAC 59.076 47.619 0.00 0.00 0.00 2.43
633 634 1.134965 CCGCTTGGTTGTGTTGGAAAA 60.135 47.619 0.00 0.00 0.00 2.29
634 635 0.457851 CCGCTTGGTTGTGTTGGAAA 59.542 50.000 0.00 0.00 0.00 3.13
635 636 0.394488 TCCGCTTGGTTGTGTTGGAA 60.394 50.000 0.00 0.00 0.00 3.53
636 637 0.394488 TTCCGCTTGGTTGTGTTGGA 60.394 50.000 0.00 0.00 0.00 3.53
637 638 0.030638 CTTCCGCTTGGTTGTGTTGG 59.969 55.000 0.00 0.00 0.00 3.77
638 639 0.738389 ACTTCCGCTTGGTTGTGTTG 59.262 50.000 0.00 0.00 0.00 3.33
639 640 1.944709 GTACTTCCGCTTGGTTGTGTT 59.055 47.619 0.00 0.00 0.00 3.32
640 641 1.589803 GTACTTCCGCTTGGTTGTGT 58.410 50.000 0.00 0.00 0.00 3.72
641 642 0.511221 CGTACTTCCGCTTGGTTGTG 59.489 55.000 0.00 0.00 0.00 3.33
642 643 0.601841 CCGTACTTCCGCTTGGTTGT 60.602 55.000 0.00 0.00 0.00 3.32
662 663 2.248280 ATTGTCAGCACAACGGTGTA 57.752 45.000 5.39 0.00 45.47 2.90
679 680 8.830580 CATCTGGATTTGACGACATAGTTAATT 58.169 33.333 0.00 0.00 0.00 1.40
681 682 6.257849 GCATCTGGATTTGACGACATAGTTAA 59.742 38.462 0.00 0.00 0.00 2.01
726 730 8.511321 TGTTGTCAGGTTGTTCAATTATCATAC 58.489 33.333 0.00 0.00 0.00 2.39
743 747 2.550830 ACCTAGTGCTTGTTGTCAGG 57.449 50.000 0.00 0.00 0.00 3.86
745 749 2.632996 AGCTACCTAGTGCTTGTTGTCA 59.367 45.455 0.00 0.00 35.86 3.58
868 875 2.680913 GCGTTGCGGATCTGTGCTT 61.681 57.895 2.89 0.00 0.00 3.91
1968 2709 0.538977 GCAGCTGGATATGCATGGGT 60.539 55.000 17.12 0.00 42.11 4.51
1969 2710 0.538746 TGCAGCTGGATATGCATGGG 60.539 55.000 17.12 0.00 46.97 4.00
1970 2711 3.030415 TGCAGCTGGATATGCATGG 57.970 52.632 17.12 0.00 46.97 3.66
1974 2715 1.202615 TCAGACTGCAGCTGGATATGC 60.203 52.381 26.99 0.29 42.86 3.14
1975 2716 2.904697 TCAGACTGCAGCTGGATATG 57.095 50.000 26.99 11.57 34.20 1.78
1976 2717 2.029200 CGATCAGACTGCAGCTGGATAT 60.029 50.000 26.99 18.14 34.20 1.63
1977 2718 1.339291 CGATCAGACTGCAGCTGGATA 59.661 52.381 26.99 15.25 34.20 2.59
2055 2828 9.869757 CAATGGAATCAATAGGTCGTGTATATA 57.130 33.333 0.00 0.00 0.00 0.86
2056 2829 7.824289 CCAATGGAATCAATAGGTCGTGTATAT 59.176 37.037 0.00 0.00 0.00 0.86
2057 2830 7.158697 CCAATGGAATCAATAGGTCGTGTATA 58.841 38.462 0.00 0.00 0.00 1.47
2068 2841 7.976414 AAATGAAGTCCCAATGGAATCAATA 57.024 32.000 0.00 0.00 44.07 1.90
2148 2939 4.627284 TTGGAGGAAGAAAACATCCGTA 57.373 40.909 0.00 0.00 40.49 4.02
2162 2953 5.549742 AGCATTGAACAAAATTTGGAGGA 57.450 34.783 10.71 0.00 34.12 3.71
2216 3014 5.067954 TCATGCCTTATGTGATCCATTCAG 58.932 41.667 2.58 1.09 38.01 3.02
2262 3062 0.777446 TTCTTTAGTGGGCCTGGCTT 59.223 50.000 19.68 4.80 0.00 4.35
2357 6120 1.754226 TGCGGGATTTAGGCCAAAATC 59.246 47.619 5.01 12.27 42.59 2.17
2423 6203 2.159184 TGAAAAAGCACCACGCAATTGA 60.159 40.909 10.34 0.00 46.13 2.57
2430 6210 1.336440 TGGTCATGAAAAAGCACCACG 59.664 47.619 0.00 0.00 31.99 4.94
2548 6328 7.571080 ACCTCTCTCTATAGAAAAAGGTACG 57.429 40.000 20.29 1.91 0.00 3.67
2603 6386 8.718734 GGTCTTAAATGAGTGTCGAGTTAATTT 58.281 33.333 0.00 0.00 0.00 1.82
2927 6714 4.142447 CCCTGTCGTCGAAAATAGAAGAGA 60.142 45.833 0.00 0.00 0.00 3.10
2929 6716 3.508793 ACCCTGTCGTCGAAAATAGAAGA 59.491 43.478 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.