Multiple sequence alignment - TraesCS2A01G318200

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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 TraesCS2A01G318200 chr2A 100.000 3143 0 0 1 3143 543307151 543310293 0.000000e+00 5805.0
1 TraesCS2A01G318200 chr2A 96.250 80 3 0 347 426 718112514 718112435 7.070000e-27 132.0
2 TraesCS2A01G318200 chr2A 95.455 66 3 0 2 67 706758196 706758261 4.290000e-19 106.0
3 TraesCS2A01G318200 chr2A 91.139 79 6 1 407 485 718112175 718112098 4.290000e-19 106.0
4 TraesCS2A01G318200 chr2A 92.424 66 3 1 1 66 84610937 84610874 3.340000e-15 93.5
5 TraesCS2A01G318200 chr2A 91.176 68 4 2 2 68 12905012 12904946 1.200000e-14 91.6
6 TraesCS2A01G318200 chr2B 89.049 2712 145 66 492 3138 480411604 480414228 0.000000e+00 3223.0
7 TraesCS2A01G318200 chr2B 85.612 278 26 7 70 345 480411343 480411608 2.390000e-71 279.0
8 TraesCS2A01G318200 chr2D 92.536 1956 78 28 492 2431 405275115 405277018 0.000000e+00 2741.0
9 TraesCS2A01G318200 chr2D 90.429 700 32 15 2429 3121 405277233 405277904 0.000000e+00 889.0
10 TraesCS2A01G318200 chr2D 89.928 278 18 6 70 345 405274850 405275119 1.790000e-92 350.0
11 TraesCS2A01G318200 chr3D 82.042 568 68 22 1005 1555 19880562 19881112 1.330000e-123 453.0
12 TraesCS2A01G318200 chr3D 78.715 249 27 14 1625 1863 19881134 19881366 3.270000e-30 143.0
13 TraesCS2A01G318200 chr3A 87.817 394 39 8 1165 1555 27543690 27544077 1.330000e-123 453.0
14 TraesCS2A01G318200 chr3A 75.253 396 65 26 1658 2047 27544141 27544509 1.170000e-34 158.0
15 TraesCS2A01G318200 chr3A 96.923 65 2 0 421 485 733929094 733929158 3.310000e-20 110.0
16 TraesCS2A01G318200 chr3B 84.906 371 37 8 1185 1555 31799301 31799652 1.070000e-94 357.0
17 TraesCS2A01G318200 chr7D 84.472 161 24 1 1400 1559 629248233 629248393 1.170000e-34 158.0
18 TraesCS2A01G318200 chr7D 76.655 287 48 17 1289 1559 628987361 628987078 1.180000e-29 141.0
19 TraesCS2A01G318200 chr7D 91.011 89 7 1 343 431 382736329 382736416 5.510000e-23 119.0
20 TraesCS2A01G318200 chr7D 93.671 79 5 0 346 424 577701748 577701826 5.510000e-23 119.0
21 TraesCS2A01G318200 chr7B 74.799 373 74 18 1196 1552 731243384 731243752 1.950000e-32 150.0
22 TraesCS2A01G318200 chr7B 92.537 67 5 0 2 68 636970728 636970794 2.580000e-16 97.1
23 TraesCS2A01G318200 chr7B 91.429 70 5 1 416 484 586048541 586048472 9.280000e-16 95.3
24 TraesCS2A01G318200 chr6A 97.500 80 2 0 347 426 27578340 27578419 1.520000e-28 137.0
25 TraesCS2A01G318200 chr6A 96.250 80 3 0 347 426 573146398 573146477 7.070000e-27 132.0
26 TraesCS2A01G318200 chr6A 95.455 66 3 0 2 67 97078237 97078302 4.290000e-19 106.0
27 TraesCS2A01G318200 chr5A 96.053 76 3 0 350 425 332250685 332250760 1.180000e-24 124.0
28 TraesCS2A01G318200 chr5A 91.139 79 7 0 407 485 565747932 565747854 1.190000e-19 108.0
29 TraesCS2A01G318200 chr5A 93.243 74 3 2 421 492 565748966 565748893 1.190000e-19 108.0
30 TraesCS2A01G318200 chr5A 95.312 64 3 0 2 65 138171182 138171119 5.550000e-18 102.0
31 TraesCS2A01G318200 chrUn 93.902 82 4 1 346 426 2372100 2372181 4.260000e-24 122.0
32 TraesCS2A01G318200 chr5B 93.023 86 3 2 347 431 710320122 710320039 4.260000e-24 122.0
33 TraesCS2A01G318200 chr5B 93.750 64 4 0 422 485 306404150 306404213 2.580000e-16 97.1
34 TraesCS2A01G318200 chr4A 93.902 82 4 1 346 426 375975578 375975497 4.260000e-24 122.0
35 TraesCS2A01G318200 chr1D 93.846 65 4 0 421 485 39962758 39962822 7.170000e-17 99.0
36 TraesCS2A01G318200 chr6D 93.750 64 4 0 422 485 44931153 44931216 2.580000e-16 97.1
37 TraesCS2A01G318200 chr6D 93.750 64 4 0 422 485 94596919 94596982 2.580000e-16 97.1
38 TraesCS2A01G318200 chr7A 92.308 65 3 1 2 66 637981441 637981503 1.200000e-14 91.6


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 TraesCS2A01G318200 chr2A 543307151 543310293 3142 False 5805.000000 5805 100.000000 1 3143 1 chr2A.!!$F1 3142
1 TraesCS2A01G318200 chr2B 480411343 480414228 2885 False 1751.000000 3223 87.330500 70 3138 2 chr2B.!!$F1 3068
2 TraesCS2A01G318200 chr2D 405274850 405277904 3054 False 1326.666667 2741 90.964333 70 3121 3 chr2D.!!$F1 3051
3 TraesCS2A01G318200 chr3D 19880562 19881366 804 False 298.000000 453 80.378500 1005 1863 2 chr3D.!!$F1 858
4 TraesCS2A01G318200 chr3A 27543690 27544509 819 False 305.500000 453 81.535000 1165 2047 2 chr3A.!!$F2 882

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
389 396 0.033781 TTGTGGTGCTACCGGTGTAC 59.966 55.0 19.93 16.13 42.58 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 2363 0.534877 TCACAGGAGCACACGCAAAT 60.535 50.0 0.0 0.0 42.27 2.32 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
33 34 3.354131 GCTAAGAAGCCTCCGTGAG 57.646 57.895 0.00 0.00 43.40 3.51
34 35 0.533032 GCTAAGAAGCCTCCGTGAGT 59.467 55.000 1.12 0.00 43.40 3.41
35 36 1.749634 GCTAAGAAGCCTCCGTGAGTA 59.250 52.381 1.12 0.00 43.40 2.59
36 37 2.165845 GCTAAGAAGCCTCCGTGAGTAA 59.834 50.000 1.12 0.00 43.40 2.24
37 38 3.181474 GCTAAGAAGCCTCCGTGAGTAAT 60.181 47.826 1.12 0.00 43.40 1.89
38 39 2.969628 AGAAGCCTCCGTGAGTAATG 57.030 50.000 1.12 0.00 0.00 1.90
39 40 2.457598 AGAAGCCTCCGTGAGTAATGA 58.542 47.619 1.12 0.00 0.00 2.57
40 41 2.428890 AGAAGCCTCCGTGAGTAATGAG 59.571 50.000 1.12 0.00 0.00 2.90
41 42 2.145397 AGCCTCCGTGAGTAATGAGA 57.855 50.000 0.00 0.00 0.00 3.27
42 43 2.457598 AGCCTCCGTGAGTAATGAGAA 58.542 47.619 0.00 0.00 0.00 2.87
43 44 3.034635 AGCCTCCGTGAGTAATGAGAAT 58.965 45.455 0.00 0.00 0.00 2.40
44 45 3.068873 AGCCTCCGTGAGTAATGAGAATC 59.931 47.826 0.00 0.00 0.00 2.52
45 46 3.068873 GCCTCCGTGAGTAATGAGAATCT 59.931 47.826 0.00 0.00 34.92 2.40
46 47 4.794655 GCCTCCGTGAGTAATGAGAATCTC 60.795 50.000 2.75 2.75 34.92 2.75
47 48 4.261825 CCTCCGTGAGTAATGAGAATCTCC 60.262 50.000 7.91 0.00 34.92 3.71
48 49 4.537751 TCCGTGAGTAATGAGAATCTCCT 58.462 43.478 7.91 0.00 34.92 3.69
49 50 4.956700 TCCGTGAGTAATGAGAATCTCCTT 59.043 41.667 7.91 6.90 34.92 3.36
50 51 5.422331 TCCGTGAGTAATGAGAATCTCCTTT 59.578 40.000 7.91 4.49 34.92 3.11
51 52 6.070767 TCCGTGAGTAATGAGAATCTCCTTTT 60.071 38.462 7.91 2.07 34.92 2.27
52 53 6.256757 CCGTGAGTAATGAGAATCTCCTTTTC 59.743 42.308 7.91 6.66 34.92 2.29
53 54 6.813649 CGTGAGTAATGAGAATCTCCTTTTCA 59.186 38.462 7.91 8.85 32.98 2.69
54 55 7.201478 CGTGAGTAATGAGAATCTCCTTTTCAC 60.201 40.741 21.33 21.33 33.67 3.18
55 56 7.065204 GTGAGTAATGAGAATCTCCTTTTCACC 59.935 40.741 21.00 11.85 32.53 4.02
56 57 6.418946 AGTAATGAGAATCTCCTTTTCACCC 58.581 40.000 7.91 0.00 31.39 4.61
57 58 3.334583 TGAGAATCTCCTTTTCACCCG 57.665 47.619 7.91 0.00 34.92 5.28
58 59 2.010497 GAGAATCTCCTTTTCACCCGC 58.990 52.381 0.00 0.00 0.00 6.13
59 60 1.351017 AGAATCTCCTTTTCACCCGCA 59.649 47.619 0.00 0.00 0.00 5.69
60 61 2.159382 GAATCTCCTTTTCACCCGCAA 58.841 47.619 0.00 0.00 0.00 4.85
61 62 2.286365 ATCTCCTTTTCACCCGCAAA 57.714 45.000 0.00 0.00 0.00 3.68
62 63 2.060050 TCTCCTTTTCACCCGCAAAA 57.940 45.000 0.00 0.00 0.00 2.44
63 64 2.379972 TCTCCTTTTCACCCGCAAAAA 58.620 42.857 0.00 0.00 0.00 1.94
145 146 4.819630 ACGAAGTTCAGCAAGGAATAAACA 59.180 37.500 3.32 0.00 37.78 2.83
150 151 2.760092 TCAGCAAGGAATAAACATGCCC 59.240 45.455 0.00 0.00 37.73 5.36
154 155 3.364549 CAAGGAATAAACATGCCCCAGA 58.635 45.455 0.00 0.00 0.00 3.86
156 157 5.139727 CAAGGAATAAACATGCCCCAGATA 58.860 41.667 0.00 0.00 0.00 1.98
169 170 1.768870 CCCAGATACCAACTACCCAGG 59.231 57.143 0.00 0.00 0.00 4.45
170 171 2.478292 CCAGATACCAACTACCCAGGT 58.522 52.381 0.00 0.00 39.41 4.00
171 172 3.631605 CCCAGATACCAACTACCCAGGTA 60.632 52.174 0.00 0.00 41.72 3.08
172 173 3.387050 CCAGATACCAACTACCCAGGTAC 59.613 52.174 0.00 0.00 40.43 3.34
173 174 4.287552 CAGATACCAACTACCCAGGTACT 58.712 47.826 0.00 0.00 40.43 2.73
269 276 1.736645 CGGTACAACTGCTCCACCG 60.737 63.158 0.00 0.00 45.25 4.94
272 279 3.248446 TACAACTGCTCCACCGGGC 62.248 63.158 6.32 0.00 0.00 6.13
273 280 4.641645 CAACTGCTCCACCGGGCA 62.642 66.667 6.32 4.38 36.94 5.36
293 300 1.709147 GGCGACATGACATCACCTGC 61.709 60.000 0.00 0.00 0.00 4.85
306 313 1.073964 CACCTGCTCGATCACACTTG 58.926 55.000 0.00 0.00 0.00 3.16
321 328 2.880890 ACACTTGAGCATGTTGTTCTCC 59.119 45.455 0.00 0.00 0.00 3.71
339 346 1.600636 CATGCTCCACACCGTTGGT 60.601 57.895 0.00 0.00 37.93 3.67
340 347 1.302511 ATGCTCCACACCGTTGGTC 60.303 57.895 0.00 0.00 37.93 4.02
341 348 2.668550 GCTCCACACCGTTGGTCC 60.669 66.667 0.00 0.00 37.93 4.46
342 349 2.825982 CTCCACACCGTTGGTCCA 59.174 61.111 0.00 0.00 37.93 4.02
343 350 1.301716 CTCCACACCGTTGGTCCAG 60.302 63.158 0.00 0.00 37.93 3.86
344 351 2.281484 CCACACCGTTGGTCCAGG 60.281 66.667 0.00 0.00 31.02 4.45
345 352 2.813726 CCACACCGTTGGTCCAGGA 61.814 63.158 4.17 0.00 31.02 3.86
346 353 1.301716 CACACCGTTGGTCCAGGAG 60.302 63.158 4.17 0.00 31.02 3.69
347 354 2.347490 CACCGTTGGTCCAGGAGG 59.653 66.667 4.17 6.06 31.02 4.30
348 355 2.928396 ACCGTTGGTCCAGGAGGG 60.928 66.667 4.17 2.71 34.83 4.30
349 356 2.606519 CCGTTGGTCCAGGAGGGA 60.607 66.667 0.00 0.00 45.89 4.20
359 366 3.438131 TCCAGGAGGGAAATATCTGGT 57.562 47.619 0.00 0.00 44.80 4.00
360 367 3.048600 TCCAGGAGGGAAATATCTGGTG 58.951 50.000 0.00 0.00 44.80 4.17
361 368 2.487986 CCAGGAGGGAAATATCTGGTGC 60.488 54.545 0.00 0.00 39.90 5.01
362 369 2.173356 CAGGAGGGAAATATCTGGTGCA 59.827 50.000 0.00 0.00 0.00 4.57
363 370 2.173569 AGGAGGGAAATATCTGGTGCAC 59.826 50.000 8.80 8.80 0.00 4.57
364 371 2.576615 GAGGGAAATATCTGGTGCACC 58.423 52.381 29.67 29.67 0.00 5.01
365 372 1.134098 AGGGAAATATCTGGTGCACCG 60.134 52.381 30.07 23.48 39.43 4.94
366 373 1.308998 GGAAATATCTGGTGCACCGG 58.691 55.000 35.06 35.06 43.86 5.28
371 378 3.241530 TCTGGTGCACCGGAGCTT 61.242 61.111 38.27 0.00 46.04 3.74
372 379 3.052082 CTGGTGCACCGGAGCTTG 61.052 66.667 37.13 13.64 45.36 4.01
373 380 3.832237 CTGGTGCACCGGAGCTTGT 62.832 63.158 37.13 0.00 45.36 3.16
374 381 3.357079 GGTGCACCGGAGCTTGTG 61.357 66.667 22.49 4.12 34.99 3.33
375 382 3.357079 GTGCACCGGAGCTTGTGG 61.357 66.667 24.52 6.27 34.99 4.17
376 383 3.872603 TGCACCGGAGCTTGTGGT 61.873 61.111 24.52 6.83 36.10 4.16
378 385 3.357079 CACCGGAGCTTGTGGTGC 61.357 66.667 9.46 0.00 45.85 5.01
379 386 3.560251 ACCGGAGCTTGTGGTGCT 61.560 61.111 9.46 0.00 44.24 4.40
380 387 2.214216 ACCGGAGCTTGTGGTGCTA 61.214 57.895 9.46 0.00 41.30 3.49
381 388 1.741770 CCGGAGCTTGTGGTGCTAC 60.742 63.158 0.00 0.00 41.30 3.58
382 389 1.741770 CGGAGCTTGTGGTGCTACC 60.742 63.158 0.00 0.00 41.30 3.18
383 390 1.741770 GGAGCTTGTGGTGCTACCG 60.742 63.158 0.00 0.00 42.58 4.02
384 391 1.741770 GAGCTTGTGGTGCTACCGG 60.742 63.158 0.00 0.00 42.58 5.28
385 392 2.032071 GCTTGTGGTGCTACCGGT 59.968 61.111 13.98 13.98 42.58 5.28
386 393 2.325082 GCTTGTGGTGCTACCGGTG 61.325 63.158 19.93 8.61 42.58 4.94
387 394 1.070786 CTTGTGGTGCTACCGGTGT 59.929 57.895 19.93 0.00 42.58 4.16
388 395 0.319083 CTTGTGGTGCTACCGGTGTA 59.681 55.000 19.93 3.82 42.58 2.90
389 396 0.033781 TTGTGGTGCTACCGGTGTAC 59.966 55.000 19.93 16.13 42.58 2.90
390 397 1.079612 GTGGTGCTACCGGTGTACC 60.080 63.158 26.02 26.02 42.58 3.34
403 410 3.814005 GGTGTACCGGACTCATATTGT 57.186 47.619 9.46 0.00 0.00 2.71
404 411 3.454375 GGTGTACCGGACTCATATTGTG 58.546 50.000 9.46 0.00 0.00 3.33
405 412 2.864343 GTGTACCGGACTCATATTGTGC 59.136 50.000 9.46 0.00 0.00 4.57
406 413 2.764010 TGTACCGGACTCATATTGTGCT 59.236 45.455 9.46 0.00 0.00 4.40
407 414 3.196901 TGTACCGGACTCATATTGTGCTT 59.803 43.478 9.46 0.00 0.00 3.91
408 415 3.350219 ACCGGACTCATATTGTGCTTT 57.650 42.857 9.46 0.00 0.00 3.51
409 416 3.686016 ACCGGACTCATATTGTGCTTTT 58.314 40.909 9.46 0.00 0.00 2.27
410 417 4.839121 ACCGGACTCATATTGTGCTTTTA 58.161 39.130 9.46 0.00 0.00 1.52
411 418 5.250200 ACCGGACTCATATTGTGCTTTTAA 58.750 37.500 9.46 0.00 0.00 1.52
412 419 5.708230 ACCGGACTCATATTGTGCTTTTAAA 59.292 36.000 9.46 0.00 0.00 1.52
413 420 6.207810 ACCGGACTCATATTGTGCTTTTAAAA 59.792 34.615 9.46 0.00 0.00 1.52
414 421 7.093945 ACCGGACTCATATTGTGCTTTTAAAAT 60.094 33.333 9.46 0.00 0.00 1.82
415 422 8.402472 CCGGACTCATATTGTGCTTTTAAAATA 58.598 33.333 0.00 0.00 0.00 1.40
416 423 9.950680 CGGACTCATATTGTGCTTTTAAAATAT 57.049 29.630 0.09 0.00 0.00 1.28
445 452 8.523915 AAAAATATTCTATGACATCCTGTGCA 57.476 30.769 0.00 0.00 0.00 4.57
446 453 7.502120 AAATATTCTATGACATCCTGTGCAC 57.498 36.000 10.75 10.75 0.00 4.57
447 454 2.988010 TCTATGACATCCTGTGCACC 57.012 50.000 15.69 0.00 0.00 5.01
448 455 1.136891 TCTATGACATCCTGTGCACCG 59.863 52.381 15.69 8.02 0.00 4.94
449 456 0.177836 TATGACATCCTGTGCACCGG 59.822 55.000 20.42 20.42 0.00 5.28
450 457 1.841302 ATGACATCCTGTGCACCGGT 61.841 55.000 24.51 0.00 0.00 5.28
451 458 1.188871 TGACATCCTGTGCACCGGTA 61.189 55.000 24.51 13.21 0.00 4.02
452 459 0.460284 GACATCCTGTGCACCGGTAG 60.460 60.000 24.51 19.67 0.00 3.18
453 460 1.815421 CATCCTGTGCACCGGTAGC 60.815 63.158 24.51 14.59 0.00 3.58
454 461 2.290287 ATCCTGTGCACCGGTAGCA 61.290 57.895 24.51 22.47 40.19 3.49
455 462 1.626356 ATCCTGTGCACCGGTAGCAT 61.626 55.000 26.82 9.88 44.79 3.79
456 463 1.815421 CCTGTGCACCGGTAGCATC 60.815 63.158 26.82 21.08 44.79 3.91
457 464 1.079197 CTGTGCACCGGTAGCATCA 60.079 57.895 26.82 23.34 44.79 3.07
458 465 1.361668 CTGTGCACCGGTAGCATCAC 61.362 60.000 26.82 19.68 44.79 3.06
459 466 1.375396 GTGCACCGGTAGCATCACA 60.375 57.895 26.82 8.03 44.79 3.58
460 467 0.953471 GTGCACCGGTAGCATCACAA 60.953 55.000 26.82 7.44 44.79 3.33
461 468 0.673333 TGCACCGGTAGCATCACAAG 60.673 55.000 22.47 2.59 37.02 3.16
462 469 0.673644 GCACCGGTAGCATCACAAGT 60.674 55.000 19.85 0.00 0.00 3.16
463 470 1.078709 CACCGGTAGCATCACAAGTG 58.921 55.000 6.87 0.00 0.00 3.16
464 471 0.673644 ACCGGTAGCATCACAAGTGC 60.674 55.000 4.49 0.00 42.81 4.40
465 472 1.695893 CCGGTAGCATCACAAGTGCG 61.696 60.000 0.00 0.00 46.86 5.34
466 473 1.695893 CGGTAGCATCACAAGTGCGG 61.696 60.000 0.00 0.00 46.86 5.69
467 474 1.369091 GGTAGCATCACAAGTGCGGG 61.369 60.000 0.00 0.00 46.86 6.13
468 475 0.673644 GTAGCATCACAAGTGCGGGT 60.674 55.000 0.00 0.00 46.86 5.28
469 476 0.673333 TAGCATCACAAGTGCGGGTG 60.673 55.000 0.00 0.00 46.86 4.61
470 477 2.562912 CATCACAAGTGCGGGTGC 59.437 61.111 0.00 0.00 43.20 5.01
480 487 2.267642 GCGGGTGCACCAGATACA 59.732 61.111 36.08 0.00 42.15 2.29
481 488 1.153168 GCGGGTGCACCAGATACAT 60.153 57.895 36.08 0.00 42.15 2.29
482 489 0.748005 GCGGGTGCACCAGATACATT 60.748 55.000 36.08 0.00 42.15 2.71
483 490 1.299541 CGGGTGCACCAGATACATTC 58.700 55.000 35.78 14.93 40.22 2.67
484 491 1.680338 GGGTGCACCAGATACATTCC 58.320 55.000 35.78 11.80 39.85 3.01
485 492 1.212935 GGGTGCACCAGATACATTCCT 59.787 52.381 35.78 0.00 39.85 3.36
486 493 2.357154 GGGTGCACCAGATACATTCCTT 60.357 50.000 35.78 0.00 39.85 3.36
487 494 3.356290 GGTGCACCAGATACATTCCTTT 58.644 45.455 31.23 0.00 35.64 3.11
488 495 4.523083 GGTGCACCAGATACATTCCTTTA 58.477 43.478 31.23 0.00 35.64 1.85
489 496 4.576463 GGTGCACCAGATACATTCCTTTAG 59.424 45.833 31.23 0.00 35.64 1.85
490 497 5.186198 GTGCACCAGATACATTCCTTTAGT 58.814 41.667 5.22 0.00 0.00 2.24
525 536 0.527565 ACCGGCAAGACATGATTTGC 59.472 50.000 22.15 22.15 46.76 3.68
558 570 2.563471 AAACCAGTCGCGATCTAGAC 57.437 50.000 14.06 0.00 37.63 2.59
567 579 1.749153 GCGATCTAGACGAGCTTGTC 58.251 55.000 24.38 24.38 39.21 3.18
579 591 4.749976 ACGAGCTTGTCTAAGGATTTCTC 58.250 43.478 0.00 0.00 34.40 2.87
622 634 2.817839 GCTACCACACCCACCATTTTCT 60.818 50.000 0.00 0.00 0.00 2.52
689 701 5.728351 AATTGTATGACATTTACGGTCGG 57.272 39.130 0.00 0.00 38.10 4.79
723 735 2.223537 ATCGCATCGCATTCAGTGTA 57.776 45.000 0.00 0.00 0.00 2.90
724 736 1.559831 TCGCATCGCATTCAGTGTAG 58.440 50.000 0.00 0.00 0.00 2.74
725 737 1.135112 TCGCATCGCATTCAGTGTAGT 60.135 47.619 0.00 0.00 0.00 2.73
726 738 1.005662 CGCATCGCATTCAGTGTAGTG 60.006 52.381 0.00 0.00 0.00 2.74
727 739 2.002586 GCATCGCATTCAGTGTAGTGT 58.997 47.619 0.00 0.00 0.00 3.55
782 794 5.258841 TCTAGATGTAGAAACGTGAAGGGA 58.741 41.667 0.00 0.00 31.94 4.20
785 797 1.621814 TGTAGAAACGTGAAGGGAGGG 59.378 52.381 0.00 0.00 0.00 4.30
787 799 1.674651 GAAACGTGAAGGGAGGGCC 60.675 63.158 0.00 0.00 0.00 5.80
788 800 2.125766 GAAACGTGAAGGGAGGGCCT 62.126 60.000 5.25 5.25 0.00 5.19
789 801 2.411765 AAACGTGAAGGGAGGGCCTG 62.412 60.000 12.95 0.00 0.00 4.85
790 802 3.322466 CGTGAAGGGAGGGCCTGT 61.322 66.667 12.95 0.00 0.00 4.00
791 803 2.352805 GTGAAGGGAGGGCCTGTG 59.647 66.667 12.95 0.00 0.00 3.66
792 804 2.935481 TGAAGGGAGGGCCTGTGG 60.935 66.667 12.95 0.00 0.00 4.17
952 968 2.500646 GCCTCCAGCTGAGCTCTC 59.499 66.667 17.39 6.86 39.98 3.20
953 969 2.059786 GCCTCCAGCTGAGCTCTCT 61.060 63.158 17.39 9.20 39.98 3.10
954 970 2.019897 GCCTCCAGCTGAGCTCTCTC 62.020 65.000 17.39 3.85 39.98 3.20
955 971 0.396139 CCTCCAGCTGAGCTCTCTCT 60.396 60.000 17.39 6.22 39.98 3.10
988 1004 3.655810 GAGCAGACCACCGCCTCAG 62.656 68.421 0.00 0.00 0.00 3.35
992 1008 3.695606 GACCACCGCCTCAGCTGA 61.696 66.667 17.19 17.19 36.60 4.26
1389 1423 2.671070 CACAAGATCGGCAGGGGT 59.329 61.111 0.00 0.00 0.00 4.95
1653 1687 4.825252 GCCGTGGCGATACCGGTT 62.825 66.667 15.04 0.00 43.56 4.44
1683 1723 1.527380 GGAGGAGAGCGACGAGGAT 60.527 63.158 0.00 0.00 0.00 3.24
2203 2283 5.839262 TGACTGTAGAAAAATGCGTGTAG 57.161 39.130 0.00 0.00 0.00 2.74
2208 2288 5.753744 TGTAGAAAAATGCGTGTAGTTTGG 58.246 37.500 0.00 0.00 0.00 3.28
2209 2289 5.527951 TGTAGAAAAATGCGTGTAGTTTGGA 59.472 36.000 0.00 0.00 0.00 3.53
2213 2299 6.420604 AGAAAAATGCGTGTAGTTTGGATTTG 59.579 34.615 0.00 0.00 34.50 2.32
2217 2303 5.752892 TGCGTGTAGTTTGGATTTGTTTA 57.247 34.783 0.00 0.00 0.00 2.01
2218 2304 5.753744 TGCGTGTAGTTTGGATTTGTTTAG 58.246 37.500 0.00 0.00 0.00 1.85
2267 2358 6.630203 TTCACCTTTTTAGTAGCCATAGGA 57.370 37.500 0.00 0.00 0.00 2.94
2268 2359 6.630203 TCACCTTTTTAGTAGCCATAGGAA 57.370 37.500 0.00 0.00 0.00 3.36
2272 2363 9.403583 CACCTTTTTAGTAGCCATAGGAAAATA 57.596 33.333 0.00 0.00 0.00 1.40
2286 2377 3.119495 AGGAAAATATTTGCGTGTGCTCC 60.119 43.478 0.39 2.54 43.34 4.70
2299 2390 1.614525 TGCTCCTGTGAGGCCTGAT 60.615 57.895 12.00 0.00 39.14 2.90
2300 2391 1.153208 GCTCCTGTGAGGCCTGATG 60.153 63.158 12.00 0.00 39.14 3.07
2420 2512 2.159448 TGTTCACTTTTGGACTTGTGCG 60.159 45.455 0.00 0.00 31.54 5.34
2438 2748 2.782615 CCCGCCTTTTCGCTTACG 59.217 61.111 0.00 0.00 42.01 3.18
2462 2772 0.915364 AGATGACAGCCTCCCCTTTC 59.085 55.000 0.00 0.00 0.00 2.62
2688 3003 1.722011 TCGTTCTTTGCGAGATTCCC 58.278 50.000 0.00 0.00 33.49 3.97
2696 3011 1.136774 GCGAGATTCCCGTTTTGGC 59.863 57.895 0.00 0.00 35.87 4.52
2718 3033 2.412112 CGTCGGTCGATCTTCCCC 59.588 66.667 0.00 0.00 42.86 4.81
2730 3045 5.473846 GTCGATCTTCCCCTTTTCTTTTCTT 59.526 40.000 0.00 0.00 0.00 2.52
2731 3046 5.705905 TCGATCTTCCCCTTTTCTTTTCTTC 59.294 40.000 0.00 0.00 0.00 2.87
2732 3047 5.707764 CGATCTTCCCCTTTTCTTTTCTTCT 59.292 40.000 0.00 0.00 0.00 2.85
2733 3048 6.128145 CGATCTTCCCCTTTTCTTTTCTTCTC 60.128 42.308 0.00 0.00 0.00 2.87
2734 3049 5.386060 TCTTCCCCTTTTCTTTTCTTCTCC 58.614 41.667 0.00 0.00 0.00 3.71
2735 3050 4.806952 TCCCCTTTTCTTTTCTTCTCCA 57.193 40.909 0.00 0.00 0.00 3.86
2759 3074 0.605589 CACTCCACTGTCTCCCTCAC 59.394 60.000 0.00 0.00 0.00 3.51
2773 3088 4.159135 TCTCCCTCACGGTCAATTTAGTAC 59.841 45.833 0.00 0.00 0.00 2.73
2774 3089 3.119388 TCCCTCACGGTCAATTTAGTACG 60.119 47.826 0.00 0.00 0.00 3.67
2790 3111 4.755266 AGTACGCCTATGAATTGGAAGT 57.245 40.909 0.00 0.00 0.00 3.01
2791 3112 4.442706 AGTACGCCTATGAATTGGAAGTG 58.557 43.478 0.00 0.00 0.00 3.16
2792 3113 3.627395 ACGCCTATGAATTGGAAGTGA 57.373 42.857 0.00 0.00 0.00 3.41
2808 3129 5.413523 TGGAAGTGAGATTCATTCATGTGTG 59.586 40.000 0.00 0.00 0.00 3.82
2907 3232 1.127951 GATAAGAACGTGGCGTGGTTG 59.872 52.381 0.00 0.00 39.99 3.77
2959 3284 2.097038 GGCTGCGTCTGTGCTAGTG 61.097 63.158 0.00 0.00 35.36 2.74
3006 3358 2.667318 CGTGTGTCATGGTCGTGGC 61.667 63.158 0.00 0.00 0.00 5.01
3036 3388 3.681129 TGGAAGACCCAAGGCCAA 58.319 55.556 5.01 0.00 43.29 4.52
3037 3389 1.460255 TGGAAGACCCAAGGCCAAG 59.540 57.895 5.01 0.00 43.29 3.61
3038 3390 1.304464 GGAAGACCCAAGGCCAAGG 60.304 63.158 5.01 5.91 34.14 3.61
3039 3391 1.979155 GAAGACCCAAGGCCAAGGC 60.979 63.158 5.01 1.52 41.06 4.35
3076 3428 1.771073 CGCACCACACGAGAAGCAAA 61.771 55.000 0.00 0.00 0.00 3.68
3077 3429 0.317020 GCACCACACGAGAAGCAAAC 60.317 55.000 0.00 0.00 0.00 2.93
3078 3430 1.299541 CACCACACGAGAAGCAAACT 58.700 50.000 0.00 0.00 0.00 2.66
3079 3431 2.479837 CACCACACGAGAAGCAAACTA 58.520 47.619 0.00 0.00 0.00 2.24
3080 3432 2.476619 CACCACACGAGAAGCAAACTAG 59.523 50.000 0.00 0.00 0.00 2.57
3081 3433 2.364324 ACCACACGAGAAGCAAACTAGA 59.636 45.455 0.00 0.00 0.00 2.43
3127 3483 3.432782 GGTGTATGTGTACGTCTGCTAC 58.567 50.000 0.00 0.00 33.36 3.58
3129 3485 4.341099 GTGTATGTGTACGTCTGCTACTC 58.659 47.826 0.00 0.00 33.36 2.59
3138 3494 1.473965 CGTCTGCTACTCCATGCCAAT 60.474 52.381 0.00 0.00 0.00 3.16
3139 3495 2.224042 CGTCTGCTACTCCATGCCAATA 60.224 50.000 0.00 0.00 0.00 1.90
3140 3496 3.741075 CGTCTGCTACTCCATGCCAATAA 60.741 47.826 0.00 0.00 0.00 1.40
3141 3497 3.561725 GTCTGCTACTCCATGCCAATAAC 59.438 47.826 0.00 0.00 0.00 1.89
3142 3498 2.880890 CTGCTACTCCATGCCAATAACC 59.119 50.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.394553 GCTTCTTAGCCAATGCCAAGTTTAT 60.395 40.000 0.00 0.00 41.74 1.40
1 2 4.082245 GCTTCTTAGCCAATGCCAAGTTTA 60.082 41.667 0.00 0.00 41.74 2.01
2 3 3.306294 GCTTCTTAGCCAATGCCAAGTTT 60.306 43.478 0.00 0.00 41.74 2.66
3 4 2.232208 GCTTCTTAGCCAATGCCAAGTT 59.768 45.455 0.00 0.00 41.74 2.66
4 5 1.821136 GCTTCTTAGCCAATGCCAAGT 59.179 47.619 0.00 0.00 41.74 3.16
5 6 2.573941 GCTTCTTAGCCAATGCCAAG 57.426 50.000 0.00 0.00 41.74 3.61
16 17 4.098044 TCATTACTCACGGAGGCTTCTTAG 59.902 45.833 0.00 0.00 33.35 2.18
17 18 4.021229 TCATTACTCACGGAGGCTTCTTA 58.979 43.478 0.00 0.00 33.35 2.10
18 19 2.832129 TCATTACTCACGGAGGCTTCTT 59.168 45.455 0.00 0.00 33.35 2.52
19 20 2.428890 CTCATTACTCACGGAGGCTTCT 59.571 50.000 0.00 0.00 33.35 2.85
20 21 2.427453 TCTCATTACTCACGGAGGCTTC 59.573 50.000 5.98 0.00 33.35 3.86
21 22 2.457598 TCTCATTACTCACGGAGGCTT 58.542 47.619 5.98 0.00 33.35 4.35
22 23 2.145397 TCTCATTACTCACGGAGGCT 57.855 50.000 5.98 0.00 33.35 4.58
23 24 2.961526 TTCTCATTACTCACGGAGGC 57.038 50.000 5.98 0.00 33.35 4.70
24 25 4.261825 GGAGATTCTCATTACTCACGGAGG 60.262 50.000 15.36 0.00 30.70 4.30
25 26 4.582656 AGGAGATTCTCATTACTCACGGAG 59.417 45.833 15.36 0.03 31.93 4.63
26 27 4.537751 AGGAGATTCTCATTACTCACGGA 58.462 43.478 15.36 0.00 31.08 4.69
27 28 4.927978 AGGAGATTCTCATTACTCACGG 57.072 45.455 15.36 0.00 31.08 4.94
28 29 6.813649 TGAAAAGGAGATTCTCATTACTCACG 59.186 38.462 13.48 0.00 33.23 4.35
29 30 7.065204 GGTGAAAAGGAGATTCTCATTACTCAC 59.935 40.741 27.68 27.68 41.31 3.51
30 31 7.106239 GGTGAAAAGGAGATTCTCATTACTCA 58.894 38.462 13.48 15.00 33.23 3.41
31 32 6.540551 GGGTGAAAAGGAGATTCTCATTACTC 59.459 42.308 13.48 12.98 33.23 2.59
32 33 6.418946 GGGTGAAAAGGAGATTCTCATTACT 58.581 40.000 13.48 4.91 33.23 2.24
33 34 5.294552 CGGGTGAAAAGGAGATTCTCATTAC 59.705 44.000 13.48 8.55 33.23 1.89
34 35 5.428253 CGGGTGAAAAGGAGATTCTCATTA 58.572 41.667 13.48 0.00 33.23 1.90
35 36 4.265073 CGGGTGAAAAGGAGATTCTCATT 58.735 43.478 15.36 11.64 35.99 2.57
36 37 3.878778 CGGGTGAAAAGGAGATTCTCAT 58.121 45.455 15.36 5.46 31.08 2.90
37 38 2.615493 GCGGGTGAAAAGGAGATTCTCA 60.615 50.000 15.36 0.00 31.08 3.27
38 39 2.010497 GCGGGTGAAAAGGAGATTCTC 58.990 52.381 5.03 5.03 0.00 2.87
39 40 1.351017 TGCGGGTGAAAAGGAGATTCT 59.649 47.619 0.00 0.00 0.00 2.40
40 41 1.821216 TGCGGGTGAAAAGGAGATTC 58.179 50.000 0.00 0.00 0.00 2.52
41 42 2.286365 TTGCGGGTGAAAAGGAGATT 57.714 45.000 0.00 0.00 0.00 2.40
42 43 2.286365 TTTGCGGGTGAAAAGGAGAT 57.714 45.000 0.00 0.00 0.00 2.75
43 44 2.060050 TTTTGCGGGTGAAAAGGAGA 57.940 45.000 0.00 0.00 0.00 3.71
44 45 2.880963 TTTTTGCGGGTGAAAAGGAG 57.119 45.000 0.00 0.00 0.00 3.69
63 64 1.295792 TGTTCGACGCAGCTCTTTTT 58.704 45.000 0.00 0.00 0.00 1.94
64 65 1.512926 ATGTTCGACGCAGCTCTTTT 58.487 45.000 0.00 0.00 0.00 2.27
65 66 1.512926 AATGTTCGACGCAGCTCTTT 58.487 45.000 0.00 0.00 0.00 2.52
66 67 1.512926 AAATGTTCGACGCAGCTCTT 58.487 45.000 0.00 0.00 0.00 2.85
67 68 1.461127 GAAAATGTTCGACGCAGCTCT 59.539 47.619 0.00 0.00 0.00 4.09
68 69 1.461127 AGAAAATGTTCGACGCAGCTC 59.539 47.619 0.00 0.00 38.90 4.09
76 77 2.469886 CACGTCACGAGAAAATGTTCGA 59.530 45.455 2.91 0.00 39.93 3.71
110 111 2.605818 TGAACTTCGTCACACCTTTTCG 59.394 45.455 0.00 0.00 0.00 3.46
112 113 2.354821 GCTGAACTTCGTCACACCTTTT 59.645 45.455 0.00 0.00 0.00 2.27
140 141 3.268334 AGTTGGTATCTGGGGCATGTTTA 59.732 43.478 0.00 0.00 0.00 2.01
141 142 2.042979 AGTTGGTATCTGGGGCATGTTT 59.957 45.455 0.00 0.00 0.00 2.83
145 146 1.774856 GGTAGTTGGTATCTGGGGCAT 59.225 52.381 0.00 0.00 0.00 4.40
150 151 2.478292 ACCTGGGTAGTTGGTATCTGG 58.522 52.381 0.00 0.00 31.50 3.86
154 155 4.070681 ACAGTACCTGGGTAGTTGGTAT 57.929 45.455 4.52 0.00 38.42 2.73
156 157 2.410790 ACAGTACCTGGGTAGTTGGT 57.589 50.000 4.52 0.00 35.51 3.67
169 170 3.498927 TCAGCTTTAGCCGTACAGTAC 57.501 47.619 0.00 0.00 43.38 2.73
170 171 3.508793 ACTTCAGCTTTAGCCGTACAGTA 59.491 43.478 0.00 0.00 43.38 2.74
171 172 2.299297 ACTTCAGCTTTAGCCGTACAGT 59.701 45.455 0.00 0.00 43.38 3.55
172 173 2.960819 ACTTCAGCTTTAGCCGTACAG 58.039 47.619 0.00 0.00 43.38 2.74
173 174 3.064207 CAACTTCAGCTTTAGCCGTACA 58.936 45.455 0.00 0.00 43.38 2.90
269 276 2.124570 ATGTCATGTCGCCTGCCC 60.125 61.111 0.00 0.00 0.00 5.36
272 279 2.387309 GGTGATGTCATGTCGCCTG 58.613 57.895 7.05 0.00 41.83 4.85
273 280 4.941609 GGTGATGTCATGTCGCCT 57.058 55.556 7.05 0.00 41.83 5.52
274 281 1.709147 GCAGGTGATGTCATGTCGCC 61.709 60.000 6.33 6.33 44.67 5.54
275 282 0.742281 AGCAGGTGATGTCATGTCGC 60.742 55.000 0.00 0.00 0.00 5.19
276 283 1.284657 GAGCAGGTGATGTCATGTCG 58.715 55.000 0.00 0.00 0.00 4.35
278 285 0.897621 TCGAGCAGGTGATGTCATGT 59.102 50.000 0.00 0.00 0.00 3.21
279 286 2.133553 GATCGAGCAGGTGATGTCATG 58.866 52.381 0.00 0.00 0.00 3.07
280 287 1.758862 TGATCGAGCAGGTGATGTCAT 59.241 47.619 0.00 0.00 0.00 3.06
281 288 1.134995 GTGATCGAGCAGGTGATGTCA 60.135 52.381 2.20 0.00 0.00 3.58
293 300 2.614779 ACATGCTCAAGTGTGATCGAG 58.385 47.619 0.00 0.00 31.85 4.04
321 328 1.577328 GACCAACGGTGTGGAGCATG 61.577 60.000 13.78 0.00 41.65 4.06
339 346 3.048600 CACCAGATATTTCCCTCCTGGA 58.951 50.000 13.00 0.00 45.35 3.86
341 348 2.173356 TGCACCAGATATTTCCCTCCTG 59.827 50.000 0.00 0.00 0.00 3.86
342 349 2.173569 GTGCACCAGATATTTCCCTCCT 59.826 50.000 5.22 0.00 0.00 3.69
343 350 2.576615 GTGCACCAGATATTTCCCTCC 58.423 52.381 5.22 0.00 0.00 4.30
344 351 2.576615 GGTGCACCAGATATTTCCCTC 58.423 52.381 31.23 0.00 35.64 4.30
345 352 1.134098 CGGTGCACCAGATATTTCCCT 60.134 52.381 34.16 0.00 35.14 4.20
346 353 1.308998 CGGTGCACCAGATATTTCCC 58.691 55.000 34.16 3.99 35.14 3.97
347 354 1.134220 TCCGGTGCACCAGATATTTCC 60.134 52.381 34.16 4.55 35.14 3.13
348 355 2.213499 CTCCGGTGCACCAGATATTTC 58.787 52.381 34.16 5.28 35.14 2.17
349 356 1.747206 GCTCCGGTGCACCAGATATTT 60.747 52.381 34.16 0.00 35.14 1.40
350 357 0.179045 GCTCCGGTGCACCAGATATT 60.179 55.000 34.16 0.00 35.14 1.28
351 358 1.050988 AGCTCCGGTGCACCAGATAT 61.051 55.000 34.16 17.14 35.14 1.63
352 359 1.264749 AAGCTCCGGTGCACCAGATA 61.265 55.000 34.16 15.43 35.14 1.98
353 360 2.596851 AAGCTCCGGTGCACCAGAT 61.597 57.895 34.16 21.47 35.14 2.90
354 361 3.241530 AAGCTCCGGTGCACCAGA 61.242 61.111 34.16 27.41 35.14 3.86
355 362 3.052082 CAAGCTCCGGTGCACCAG 61.052 66.667 34.16 25.24 35.14 4.00
356 363 3.872603 ACAAGCTCCGGTGCACCA 61.873 61.111 34.16 16.11 35.14 4.17
357 364 3.357079 CACAAGCTCCGGTGCACC 61.357 66.667 28.68 26.78 34.99 5.01
358 365 3.357079 CCACAAGCTCCGGTGCAC 61.357 66.667 28.68 8.80 33.72 4.57
359 366 3.872603 ACCACAAGCTCCGGTGCA 61.873 61.111 28.68 0.00 33.72 4.57
360 367 3.357079 CACCACAAGCTCCGGTGC 61.357 66.667 20.71 20.71 43.43 5.01
362 369 2.214216 TAGCACCACAAGCTCCGGT 61.214 57.895 0.00 0.00 42.32 5.28
363 370 1.741770 GTAGCACCACAAGCTCCGG 60.742 63.158 0.00 0.00 42.32 5.14
364 371 1.741770 GGTAGCACCACAAGCTCCG 60.742 63.158 0.00 0.00 42.32 4.63
365 372 1.741770 CGGTAGCACCACAAGCTCC 60.742 63.158 6.21 0.00 42.32 4.70
366 373 1.741770 CCGGTAGCACCACAAGCTC 60.742 63.158 0.00 0.00 42.32 4.09
367 374 2.347490 CCGGTAGCACCACAAGCT 59.653 61.111 0.00 0.00 45.77 3.74
368 375 2.032071 ACCGGTAGCACCACAAGC 59.968 61.111 4.49 0.00 38.47 4.01
369 376 0.319083 TACACCGGTAGCACCACAAG 59.681 55.000 6.87 0.00 38.47 3.16
370 377 0.033781 GTACACCGGTAGCACCACAA 59.966 55.000 6.87 0.00 38.47 3.33
371 378 1.667151 GTACACCGGTAGCACCACA 59.333 57.895 6.87 0.00 38.47 4.17
372 379 1.079612 GGTACACCGGTAGCACCAC 60.080 63.158 20.88 8.21 45.18 4.16
373 380 3.379880 GGTACACCGGTAGCACCA 58.620 61.111 20.88 0.00 45.18 4.17
383 390 3.454375 CACAATATGAGTCCGGTACACC 58.546 50.000 0.00 0.00 0.00 4.16
384 391 2.864343 GCACAATATGAGTCCGGTACAC 59.136 50.000 0.00 0.00 0.00 2.90
385 392 2.764010 AGCACAATATGAGTCCGGTACA 59.236 45.455 0.00 0.40 0.00 2.90
386 393 3.454371 AGCACAATATGAGTCCGGTAC 57.546 47.619 0.00 0.00 0.00 3.34
387 394 4.481368 AAAGCACAATATGAGTCCGGTA 57.519 40.909 0.00 0.00 0.00 4.02
388 395 3.350219 AAAGCACAATATGAGTCCGGT 57.650 42.857 0.00 0.00 0.00 5.28
389 396 5.811399 TTAAAAGCACAATATGAGTCCGG 57.189 39.130 0.00 0.00 0.00 5.14
390 397 9.950680 ATATTTTAAAAGCACAATATGAGTCCG 57.049 29.630 6.79 0.00 0.00 4.79
435 442 1.815421 GCTACCGGTGCACAGGATG 60.815 63.158 37.84 28.18 46.00 3.51
436 443 1.626356 ATGCTACCGGTGCACAGGAT 61.626 55.000 37.84 24.57 43.59 3.24
437 444 2.238847 GATGCTACCGGTGCACAGGA 62.239 60.000 37.84 19.65 43.59 3.86
438 445 1.815421 GATGCTACCGGTGCACAGG 60.815 63.158 31.20 31.20 43.59 4.00
439 446 1.079197 TGATGCTACCGGTGCACAG 60.079 57.895 26.70 15.33 43.59 3.66
440 447 1.375396 GTGATGCTACCGGTGCACA 60.375 57.895 26.70 22.58 43.59 4.57
441 448 0.953471 TTGTGATGCTACCGGTGCAC 60.953 55.000 26.70 20.55 43.59 4.57
442 449 0.673333 CTTGTGATGCTACCGGTGCA 60.673 55.000 26.46 26.46 44.95 4.57
443 450 0.673644 ACTTGTGATGCTACCGGTGC 60.674 55.000 19.93 19.04 0.00 5.01
444 451 1.078709 CACTTGTGATGCTACCGGTG 58.921 55.000 19.93 8.61 0.00 4.94
445 452 0.673644 GCACTTGTGATGCTACCGGT 60.674 55.000 13.98 13.98 40.08 5.28
446 453 1.695893 CGCACTTGTGATGCTACCGG 61.696 60.000 0.00 0.00 41.10 5.28
447 454 1.695893 CCGCACTTGTGATGCTACCG 61.696 60.000 4.79 0.00 41.10 4.02
448 455 1.369091 CCCGCACTTGTGATGCTACC 61.369 60.000 4.79 0.00 41.10 3.18
449 456 0.673644 ACCCGCACTTGTGATGCTAC 60.674 55.000 4.79 0.00 41.10 3.58
450 457 0.673333 CACCCGCACTTGTGATGCTA 60.673 55.000 4.79 0.00 41.10 3.49
451 458 1.968017 CACCCGCACTTGTGATGCT 60.968 57.895 4.79 0.00 41.10 3.79
452 459 2.562912 CACCCGCACTTGTGATGC 59.437 61.111 4.79 0.00 39.81 3.91
453 460 2.260154 TGCACCCGCACTTGTGATG 61.260 57.895 4.79 0.00 45.36 3.07
454 461 2.112928 TGCACCCGCACTTGTGAT 59.887 55.556 4.79 0.00 45.36 3.06
463 470 0.748005 AATGTATCTGGTGCACCCGC 60.748 55.000 32.62 17.42 35.15 6.13
464 471 1.299541 GAATGTATCTGGTGCACCCG 58.700 55.000 32.62 26.50 35.15 5.28
465 472 1.212935 AGGAATGTATCTGGTGCACCC 59.787 52.381 32.62 17.27 34.29 4.61
466 473 2.717639 AGGAATGTATCTGGTGCACC 57.282 50.000 29.67 29.67 0.00 5.01
467 474 5.186198 ACTAAAGGAATGTATCTGGTGCAC 58.814 41.667 8.80 8.80 0.00 4.57
468 475 5.428253 GACTAAAGGAATGTATCTGGTGCA 58.572 41.667 0.00 0.00 0.00 4.57
469 476 4.816925 GGACTAAAGGAATGTATCTGGTGC 59.183 45.833 0.00 0.00 0.00 5.01
470 477 5.989477 TGGACTAAAGGAATGTATCTGGTG 58.011 41.667 0.00 0.00 0.00 4.17
471 478 5.131142 CCTGGACTAAAGGAATGTATCTGGT 59.869 44.000 0.00 0.00 36.91 4.00
472 479 5.131142 ACCTGGACTAAAGGAATGTATCTGG 59.869 44.000 0.00 0.00 38.27 3.86
473 480 6.051717 CACCTGGACTAAAGGAATGTATCTG 58.948 44.000 0.00 0.00 38.27 2.90
474 481 5.726793 ACACCTGGACTAAAGGAATGTATCT 59.273 40.000 0.00 0.00 38.27 1.98
475 482 5.990668 ACACCTGGACTAAAGGAATGTATC 58.009 41.667 0.00 0.00 38.27 2.24
476 483 6.408206 GCTACACCTGGACTAAAGGAATGTAT 60.408 42.308 0.00 0.00 38.27 2.29
477 484 5.105064 GCTACACCTGGACTAAAGGAATGTA 60.105 44.000 0.00 0.00 38.27 2.29
478 485 4.323562 GCTACACCTGGACTAAAGGAATGT 60.324 45.833 0.00 0.00 38.27 2.71
479 486 4.192317 GCTACACCTGGACTAAAGGAATG 58.808 47.826 0.00 0.00 38.27 2.67
480 487 3.844211 TGCTACACCTGGACTAAAGGAAT 59.156 43.478 0.00 0.00 38.27 3.01
481 488 3.244582 TGCTACACCTGGACTAAAGGAA 58.755 45.455 0.00 0.00 38.27 3.36
482 489 2.897350 TGCTACACCTGGACTAAAGGA 58.103 47.619 0.00 0.00 38.27 3.36
483 490 3.535561 CATGCTACACCTGGACTAAAGG 58.464 50.000 0.00 0.00 40.93 3.11
484 491 2.939103 GCATGCTACACCTGGACTAAAG 59.061 50.000 11.37 0.00 0.00 1.85
485 492 2.304470 TGCATGCTACACCTGGACTAAA 59.696 45.455 20.33 0.00 0.00 1.85
486 493 1.905894 TGCATGCTACACCTGGACTAA 59.094 47.619 20.33 0.00 0.00 2.24
487 494 1.207089 GTGCATGCTACACCTGGACTA 59.793 52.381 20.33 0.00 31.67 2.59
488 495 0.036010 GTGCATGCTACACCTGGACT 60.036 55.000 20.33 0.00 31.67 3.85
489 496 2.471255 GTGCATGCTACACCTGGAC 58.529 57.895 20.33 0.83 31.67 4.02
525 536 4.035558 CGACTGGTTTTCATATGACATGGG 59.964 45.833 4.48 0.00 0.00 4.00
558 570 3.794028 CGAGAAATCCTTAGACAAGCTCG 59.206 47.826 0.00 0.00 34.97 5.03
567 579 2.579207 TGACGCCGAGAAATCCTTAG 57.421 50.000 0.00 0.00 0.00 2.18
579 591 2.408835 GATTGCCCAATGACGCCG 59.591 61.111 0.00 0.00 0.00 6.46
723 735 4.655963 ACTACTGATTTTGCCATCACACT 58.344 39.130 0.00 0.00 0.00 3.55
724 736 4.455533 TGACTACTGATTTTGCCATCACAC 59.544 41.667 0.00 0.00 0.00 3.82
725 737 4.650734 TGACTACTGATTTTGCCATCACA 58.349 39.130 0.00 0.00 0.00 3.58
726 738 5.627499 TTGACTACTGATTTTGCCATCAC 57.373 39.130 0.00 0.00 0.00 3.06
727 739 5.335897 GCTTTGACTACTGATTTTGCCATCA 60.336 40.000 0.00 0.00 0.00 3.07
782 794 3.889692 CACCACACCACAGGCCCT 61.890 66.667 0.00 0.00 0.00 5.19
785 797 1.303236 TATGCACCACACCACAGGC 60.303 57.895 0.00 0.00 0.00 4.85
787 799 1.536766 CTTGTATGCACCACACCACAG 59.463 52.381 2.53 0.00 30.51 3.66
788 800 1.141858 TCTTGTATGCACCACACCACA 59.858 47.619 2.53 0.00 0.00 4.17
789 801 1.806542 CTCTTGTATGCACCACACCAC 59.193 52.381 2.53 0.00 0.00 4.16
790 802 1.881925 GCTCTTGTATGCACCACACCA 60.882 52.381 2.53 0.00 0.00 4.17
791 803 0.804989 GCTCTTGTATGCACCACACC 59.195 55.000 2.53 0.00 0.00 4.16
792 804 1.522668 TGCTCTTGTATGCACCACAC 58.477 50.000 2.53 0.00 33.94 3.82
821 833 3.741344 AGAAATTTTCTGACGAGTGGACG 59.259 43.478 10.82 0.00 38.91 4.79
859 871 2.094700 GGGAAATTCGCACCTTCCTTTC 60.095 50.000 5.11 0.00 38.94 2.62
936 952 0.396139 AGAGAGAGCTCAGCTGGAGG 60.396 60.000 17.77 5.90 44.22 4.30
948 964 6.471233 TCTACAAGAGAGAGAGAGAGAGAG 57.529 45.833 0.00 0.00 0.00 3.20
988 1004 2.223340 CCGCAACCATAGAATTGTCAGC 60.223 50.000 0.00 0.00 0.00 4.26
992 1008 0.732571 CGCCGCAACCATAGAATTGT 59.267 50.000 0.00 0.00 0.00 2.71
1029 1045 0.257616 AGAGAAGGACGAGGAGGAGG 59.742 60.000 0.00 0.00 0.00 4.30
1030 1046 1.388547 CAGAGAAGGACGAGGAGGAG 58.611 60.000 0.00 0.00 0.00 3.69
1031 1047 0.681564 GCAGAGAAGGACGAGGAGGA 60.682 60.000 0.00 0.00 0.00 3.71
1653 1687 2.286962 TCCTCCTCCTCCTCCCGA 60.287 66.667 0.00 0.00 0.00 5.14
1683 1723 2.683933 GCCTCCTCCTTCCGGTCA 60.684 66.667 0.00 0.00 0.00 4.02
2203 2283 9.139174 CATACCATCAACTAAACAAATCCAAAC 57.861 33.333 0.00 0.00 0.00 2.93
2257 2348 5.825679 ACACGCAAATATTTTCCTATGGCTA 59.174 36.000 0.00 0.00 0.00 3.93
2258 2349 4.644685 ACACGCAAATATTTTCCTATGGCT 59.355 37.500 0.00 0.00 0.00 4.75
2259 2350 4.739716 CACACGCAAATATTTTCCTATGGC 59.260 41.667 0.00 0.00 0.00 4.40
2261 2352 5.581605 AGCACACGCAAATATTTTCCTATG 58.418 37.500 0.00 0.00 42.27 2.23
2263 2354 4.095782 GGAGCACACGCAAATATTTTCCTA 59.904 41.667 0.00 0.00 42.27 2.94
2264 2355 3.119495 GGAGCACACGCAAATATTTTCCT 60.119 43.478 0.00 0.00 42.27 3.36
2265 2356 3.119495 AGGAGCACACGCAAATATTTTCC 60.119 43.478 0.00 0.78 42.27 3.13
2267 2358 3.255642 ACAGGAGCACACGCAAATATTTT 59.744 39.130 0.00 0.00 42.27 1.82
2268 2359 2.819608 ACAGGAGCACACGCAAATATTT 59.180 40.909 0.00 0.00 42.27 1.40
2272 2363 0.534877 TCACAGGAGCACACGCAAAT 60.535 50.000 0.00 0.00 42.27 2.32
2286 2377 2.354259 GAGAAACATCAGGCCTCACAG 58.646 52.381 0.00 0.00 0.00 3.66
2299 2390 4.570772 CAGAGTCAAAGGAAACGAGAAACA 59.429 41.667 0.00 0.00 0.00 2.83
2300 2391 4.024809 CCAGAGTCAAAGGAAACGAGAAAC 60.025 45.833 0.00 0.00 0.00 2.78
2345 2437 1.202580 CGGATGGAGGAATCCACAGAC 60.203 57.143 0.61 0.00 45.64 3.51
2420 2512 2.483745 GTAAGCGAAAAGGCGGGC 59.516 61.111 0.00 0.00 38.18 6.13
2438 2748 0.396060 GGGAGGCTGTCATCTCATCC 59.604 60.000 0.00 0.00 0.00 3.51
2499 2813 8.943002 CCGTCTCTTAACCAAAGTTGTATTATT 58.057 33.333 0.00 0.00 36.68 1.40
2500 2814 8.098912 ACCGTCTCTTAACCAAAGTTGTATTAT 58.901 33.333 0.00 0.00 36.68 1.28
2501 2815 7.385752 CACCGTCTCTTAACCAAAGTTGTATTA 59.614 37.037 0.00 0.00 36.68 0.98
2502 2816 6.204108 CACCGTCTCTTAACCAAAGTTGTATT 59.796 38.462 0.00 0.00 36.68 1.89
2503 2817 5.699458 CACCGTCTCTTAACCAAAGTTGTAT 59.301 40.000 0.00 0.00 36.68 2.29
2504 2818 5.051816 CACCGTCTCTTAACCAAAGTTGTA 58.948 41.667 0.00 0.00 36.68 2.41
2688 3003 4.383602 CGACGCCCAGCCAAAACG 62.384 66.667 0.00 0.00 0.00 3.60
2696 3011 2.938539 GAAGATCGACCGACGCCCAG 62.939 65.000 0.00 0.00 42.26 4.45
2718 3033 7.720442 AGTGGAAATGGAGAAGAAAAGAAAAG 58.280 34.615 0.00 0.00 0.00 2.27
2730 3045 2.303022 GACAGTGGAGTGGAAATGGAGA 59.697 50.000 0.00 0.00 0.00 3.71
2731 3046 2.304180 AGACAGTGGAGTGGAAATGGAG 59.696 50.000 0.00 0.00 0.00 3.86
2732 3047 2.303022 GAGACAGTGGAGTGGAAATGGA 59.697 50.000 0.00 0.00 0.00 3.41
2733 3048 2.616510 GGAGACAGTGGAGTGGAAATGG 60.617 54.545 0.00 0.00 0.00 3.16
2734 3049 2.616510 GGGAGACAGTGGAGTGGAAATG 60.617 54.545 0.00 0.00 0.00 2.32
2735 3050 1.630878 GGGAGACAGTGGAGTGGAAAT 59.369 52.381 0.00 0.00 0.00 2.17
2759 3074 4.613944 TCATAGGCGTACTAAATTGACCG 58.386 43.478 0.00 0.00 34.79 4.79
2773 3088 3.797039 TCTCACTTCCAATTCATAGGCG 58.203 45.455 0.00 0.00 0.00 5.52
2774 3089 5.824624 TGAATCTCACTTCCAATTCATAGGC 59.175 40.000 0.00 0.00 34.20 3.93
2790 3111 5.315348 TGTTCCACACATGAATGAATCTCA 58.685 37.500 0.00 0.00 0.00 3.27
2791 3112 5.885230 TGTTCCACACATGAATGAATCTC 57.115 39.130 0.00 0.00 0.00 2.75
2792 3113 5.771666 AGTTGTTCCACACATGAATGAATCT 59.228 36.000 0.00 0.00 34.43 2.40
2808 3129 1.606601 GCCTCCCCCAAGTTGTTCC 60.607 63.158 1.45 0.00 0.00 3.62
2875 3196 4.745125 CACGTTCTTATCCGCTCACATATT 59.255 41.667 0.00 0.00 0.00 1.28
2880 3201 1.278238 CCACGTTCTTATCCGCTCAC 58.722 55.000 0.00 0.00 0.00 3.51
2923 3248 3.775654 GCTACGCAGGCCAGGACT 61.776 66.667 5.01 0.00 0.00 3.85
2959 3284 2.556559 CCCTCTGCTAGATCCTCCTACC 60.557 59.091 0.00 0.00 0.00 3.18
3039 3391 1.007387 GTTTCTGTTGCCGCCTTGG 60.007 57.895 0.00 0.00 42.50 3.61
3040 3392 1.370414 CGTTTCTGTTGCCGCCTTG 60.370 57.895 0.00 0.00 0.00 3.61
3076 3428 3.129109 CACGAGCAATGCATGATCTAGT 58.871 45.455 8.35 1.58 42.36 2.57
3077 3429 3.387397 TCACGAGCAATGCATGATCTAG 58.613 45.455 8.35 0.93 42.36 2.43
3078 3430 3.457610 TCACGAGCAATGCATGATCTA 57.542 42.857 8.35 0.00 42.36 1.98
3079 3431 2.320745 TCACGAGCAATGCATGATCT 57.679 45.000 8.35 0.00 42.36 2.75
3080 3432 2.610833 TCTTCACGAGCAATGCATGATC 59.389 45.455 8.35 2.02 41.11 2.92
3081 3433 2.635714 TCTTCACGAGCAATGCATGAT 58.364 42.857 8.35 0.00 0.00 2.45
3104 3458 1.738030 GCAGACGTACACATACACCCC 60.738 57.143 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.