Multiple sequence alignment - TraesCS1D01G102500

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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 TraesCS1D01G102500 chr1D 100.000 6631 0 0 1 6631 90651029 90644399 0.000000e+00 12246.0
1 TraesCS1D01G102500 chr1D 92.308 169 12 1 373 541 178466479 178466312 8.590000e-59 239.0
2 TraesCS1D01G102500 chr1D 94.286 70 4 0 2121 2190 90648843 90648774 2.530000e-19 108.0
3 TraesCS1D01G102500 chr1D 94.286 70 4 0 2187 2256 90648909 90648840 2.530000e-19 108.0
4 TraesCS1D01G102500 chr1A 96.559 5929 151 21 569 6483 86649495 86643606 0.000000e+00 9769.0
5 TraesCS1D01G102500 chr1A 91.713 181 15 0 1 181 86649669 86649489 1.100000e-62 252.0
6 TraesCS1D01G102500 chr1A 94.286 70 4 0 2187 2256 86647942 86647873 2.530000e-19 108.0
7 TraesCS1D01G102500 chr1B 97.472 5498 102 18 543 6008 145458213 145452721 0.000000e+00 9348.0
8 TraesCS1D01G102500 chr1B 94.991 539 16 5 5939 6471 145452754 145452221 0.000000e+00 835.0
9 TraesCS1D01G102500 chr1B 92.448 384 29 0 1 384 145458604 145458221 3.500000e-152 549.0
10 TraesCS1D01G102500 chr1B 89.691 97 9 1 6511 6607 575148137 575148042 9.030000e-24 122.0
11 TraesCS1D01G102500 chr1B 88.660 97 9 2 6511 6607 61671050 61671144 4.200000e-22 117.0
12 TraesCS1D01G102500 chr1B 95.714 70 3 0 2121 2190 145456569 145456500 5.430000e-21 113.0
13 TraesCS1D01G102500 chr1B 94.286 70 4 0 2187 2256 145456635 145456566 2.530000e-19 108.0
14 TraesCS1D01G102500 chr4A 94.340 159 9 0 383 541 18115555 18115397 1.850000e-60 244.0
15 TraesCS1D01G102500 chr4A 91.765 170 12 2 383 552 13266911 13267078 1.110000e-57 235.0
16 TraesCS1D01G102500 chr3B 93.789 161 10 0 381 541 571752523 571752683 6.640000e-60 243.0
17 TraesCS1D01G102500 chr3B 92.216 167 13 0 375 541 120616905 120617071 3.090000e-58 237.0
18 TraesCS1D01G102500 chr6B 92.814 167 11 1 376 541 568047058 568047224 2.390000e-59 241.0
19 TraesCS1D01G102500 chr6B 92.216 167 13 0 375 541 240046886 240047052 3.090000e-58 237.0
20 TraesCS1D01G102500 chr5A 92.308 169 13 0 373 541 290391687 290391855 2.390000e-59 241.0
21 TraesCS1D01G102500 chr5A 89.583 96 8 2 6512 6607 595103874 595103781 3.250000e-23 121.0
22 TraesCS1D01G102500 chr4D 93.252 163 11 0 379 541 238640333 238640171 2.390000e-59 241.0
23 TraesCS1D01G102500 chr2D 83.117 154 21 2 175 328 14695273 14695125 1.160000e-27 135.0
24 TraesCS1D01G102500 chr2D 92.222 90 7 0 6511 6600 648365455 648365366 1.940000e-25 128.0
25 TraesCS1D01G102500 chr7D 93.827 81 5 0 6514 6594 253162819 253162899 9.030000e-24 122.0
26 TraesCS1D01G102500 chr7D 81.410 156 22 5 175 329 17862605 17862754 3.250000e-23 121.0
27 TraesCS1D01G102500 chr7A 89.691 97 8 2 6511 6607 509758879 509758785 9.030000e-24 122.0
28 TraesCS1D01G102500 chr7A 87.879 99 10 2 6512 6609 688939624 688939527 1.510000e-21 115.0
29 TraesCS1D01G102500 chr3D 92.045 88 6 1 6509 6595 560947336 560947249 9.030000e-24 122.0
30 TraesCS1D01G102500 chr5B 88.660 97 9 2 6511 6607 7835850 7835944 4.200000e-22 117.0
31 TraesCS1D01G102500 chr2A 93.333 45 2 1 6005 6048 5188613 5188657 1.540000e-06 65.8
32 TraesCS1D01G102500 chr5D 92.857 42 3 0 293 334 383227190 383227149 2.000000e-05 62.1


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 TraesCS1D01G102500 chr1D 90644399 90651029 6630 True 4154.000000 12246 96.190667 1 6631 3 chr1D.!!$R2 6630
1 TraesCS1D01G102500 chr1A 86643606 86649669 6063 True 3376.333333 9769 94.186000 1 6483 3 chr1A.!!$R1 6482
2 TraesCS1D01G102500 chr1B 145452221 145458604 6383 True 2190.600000 9348 94.982200 1 6471 5 chr1B.!!$R2 6470

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
445 446 0.608130 AAGTGACTGCATACGGAGCA 59.392 50.000 0.00 0.00 40.19 4.26 F
1447 1453 0.029163 TTCCCTGCCATCCCCTGATA 60.029 55.000 0.00 0.00 0.00 2.15 F
1523 1529 1.125093 TTGGAGGCGAAGGAAGTGGA 61.125 55.000 0.00 0.00 0.00 4.02 F
2917 2956 2.107204 AGGAGAATGAAGGTGCACAAGT 59.893 45.455 20.43 2.02 0.00 3.16 F
4130 4169 2.032681 GAAGGCCTCAACGGTGCT 59.967 61.111 5.23 0.00 34.25 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2000 0.175302 CTGGAGTTGCATCGCTCTCT 59.825 55.000 11.50 0.0 33.63 3.10 R
2419 2426 0.320374 CACTTACCTCGGGACTTGCA 59.680 55.000 0.00 0.0 0.00 4.08 R
3515 3554 0.110373 GGCGCAGAAACTTTACACGG 60.110 55.000 10.83 0.0 0.00 4.94 R
4190 4229 1.842007 CATATCCCCTGCAGCCTGT 59.158 57.895 8.66 0.0 0.00 4.00 R
5735 5775 0.539986 ATACGAACAATCTGCGGGGT 59.460 50.000 0.00 0.0 0.00 4.95 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
56 57 8.484008 CCTGTTTTTGTTATAAATTGGTCAACG 58.516 33.333 0.00 0.00 0.00 4.10
76 77 1.689273 GGATGCTCCTTCCACGACTAT 59.311 52.381 0.00 0.00 32.53 2.12
81 82 5.449107 TGCTCCTTCCACGACTATTATAC 57.551 43.478 0.00 0.00 0.00 1.47
99 100 7.925703 ATTATACCTCGTTGTTATCGTTGAG 57.074 36.000 0.00 0.00 0.00 3.02
141 142 4.741342 AGCGTTGTATAGTGTAGGTGTTC 58.259 43.478 0.00 0.00 0.00 3.18
195 196 5.105063 GCAATTTTAACATGCTCCCTCTTC 58.895 41.667 0.00 0.00 37.12 2.87
229 230 6.936900 CCCTCTTCACATGAGAAGTAAGAAAA 59.063 38.462 25.81 9.50 44.18 2.29
249 250 9.981460 AAGAAAATAAGAGTTAATCAGACCCAT 57.019 29.630 0.00 0.00 0.00 4.00
288 289 9.261180 TCAATGACTCGAATCCATTTTATACTC 57.739 33.333 0.00 0.00 0.00 2.59
310 311 6.431543 ACTCTTATCTCTCGTGTGAAAAGAGA 59.568 38.462 19.22 12.24 46.93 3.10
384 385 4.455124 GCAGACGCCGAATAATCAAATAC 58.545 43.478 0.00 0.00 0.00 1.89
385 386 4.211374 GCAGACGCCGAATAATCAAATACT 59.789 41.667 0.00 0.00 0.00 2.12
386 387 5.612709 GCAGACGCCGAATAATCAAATACTC 60.613 44.000 0.00 0.00 0.00 2.59
387 388 4.989168 AGACGCCGAATAATCAAATACTCC 59.011 41.667 0.00 0.00 0.00 3.85
389 390 5.305585 ACGCCGAATAATCAAATACTCCAT 58.694 37.500 0.00 0.00 0.00 3.41
390 391 5.408604 ACGCCGAATAATCAAATACTCCATC 59.591 40.000 0.00 0.00 0.00 3.51
391 392 5.163854 CGCCGAATAATCAAATACTCCATCC 60.164 44.000 0.00 0.00 0.00 3.51
392 393 5.163854 GCCGAATAATCAAATACTCCATCCG 60.164 44.000 0.00 0.00 0.00 4.18
393 394 5.932303 CCGAATAATCAAATACTCCATCCGT 59.068 40.000 0.00 0.00 0.00 4.69
394 395 6.426937 CCGAATAATCAAATACTCCATCCGTT 59.573 38.462 0.00 0.00 0.00 4.44
395 396 7.360101 CCGAATAATCAAATACTCCATCCGTTC 60.360 40.741 0.00 0.00 0.00 3.95
396 397 7.360101 CGAATAATCAAATACTCCATCCGTTCC 60.360 40.741 0.00 0.00 0.00 3.62
397 398 5.373812 AATCAAATACTCCATCCGTTCCT 57.626 39.130 0.00 0.00 0.00 3.36
398 399 6.494666 AATCAAATACTCCATCCGTTCCTA 57.505 37.500 0.00 0.00 0.00 2.94
399 400 5.943349 TCAAATACTCCATCCGTTCCTAA 57.057 39.130 0.00 0.00 0.00 2.69
400 401 6.302535 TCAAATACTCCATCCGTTCCTAAA 57.697 37.500 0.00 0.00 0.00 1.85
401 402 6.895782 TCAAATACTCCATCCGTTCCTAAAT 58.104 36.000 0.00 0.00 0.00 1.40
402 403 8.025270 TCAAATACTCCATCCGTTCCTAAATA 57.975 34.615 0.00 0.00 0.00 1.40
403 404 8.656806 TCAAATACTCCATCCGTTCCTAAATAT 58.343 33.333 0.00 0.00 0.00 1.28
404 405 9.284968 CAAATACTCCATCCGTTCCTAAATATT 57.715 33.333 0.00 0.00 0.00 1.28
405 406 9.862149 AAATACTCCATCCGTTCCTAAATATTT 57.138 29.630 5.89 5.89 0.00 1.40
406 407 8.848474 ATACTCCATCCGTTCCTAAATATTTG 57.152 34.615 11.05 1.40 0.00 2.32
407 408 6.659824 ACTCCATCCGTTCCTAAATATTTGT 58.340 36.000 11.05 0.00 0.00 2.83
408 409 6.766467 ACTCCATCCGTTCCTAAATATTTGTC 59.234 38.462 11.05 0.00 0.00 3.18
409 410 6.895782 TCCATCCGTTCCTAAATATTTGTCT 58.104 36.000 11.05 0.00 0.00 3.41
410 411 7.343357 TCCATCCGTTCCTAAATATTTGTCTT 58.657 34.615 11.05 0.00 0.00 3.01
411 412 7.832187 TCCATCCGTTCCTAAATATTTGTCTTT 59.168 33.333 11.05 0.00 0.00 2.52
412 413 8.129211 CCATCCGTTCCTAAATATTTGTCTTTC 58.871 37.037 11.05 0.00 0.00 2.62
413 414 8.893727 CATCCGTTCCTAAATATTTGTCTTTCT 58.106 33.333 11.05 0.00 0.00 2.52
415 416 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
416 417 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
431 432 9.996554 TGTCTTTCTAGATATTTCAACAAGTGA 57.003 29.630 0.00 0.00 31.86 3.41
435 436 7.834068 TCTAGATATTTCAACAAGTGACTGC 57.166 36.000 0.00 0.00 35.39 4.40
436 437 7.386059 TCTAGATATTTCAACAAGTGACTGCA 58.614 34.615 0.00 0.00 35.39 4.41
437 438 8.043113 TCTAGATATTTCAACAAGTGACTGCAT 58.957 33.333 0.00 0.00 35.39 3.96
438 439 9.317936 CTAGATATTTCAACAAGTGACTGCATA 57.682 33.333 0.00 0.00 35.39 3.14
439 440 7.978982 AGATATTTCAACAAGTGACTGCATAC 58.021 34.615 0.00 0.00 35.39 2.39
440 441 4.466567 TTTCAACAAGTGACTGCATACG 57.533 40.909 0.00 0.00 35.39 3.06
441 442 2.412870 TCAACAAGTGACTGCATACGG 58.587 47.619 0.00 0.00 0.00 4.02
442 443 2.036604 TCAACAAGTGACTGCATACGGA 59.963 45.455 0.00 0.00 0.00 4.69
443 444 2.370281 ACAAGTGACTGCATACGGAG 57.630 50.000 0.00 0.00 36.48 4.63
444 445 1.002366 CAAGTGACTGCATACGGAGC 58.998 55.000 0.00 0.00 32.91 4.70
445 446 0.608130 AAGTGACTGCATACGGAGCA 59.392 50.000 0.00 0.00 40.19 4.26
446 447 0.608130 AGTGACTGCATACGGAGCAA 59.392 50.000 0.00 0.00 42.17 3.91
447 448 1.001974 AGTGACTGCATACGGAGCAAA 59.998 47.619 0.00 0.00 42.17 3.68
448 449 1.804151 GTGACTGCATACGGAGCAAAA 59.196 47.619 0.00 0.00 42.17 2.44
449 450 2.420022 GTGACTGCATACGGAGCAAAAT 59.580 45.455 0.00 0.00 42.17 1.82
450 451 2.419673 TGACTGCATACGGAGCAAAATG 59.580 45.455 0.00 0.00 42.17 2.32
451 452 2.677836 GACTGCATACGGAGCAAAATGA 59.322 45.455 0.00 0.00 42.17 2.57
452 453 2.679837 ACTGCATACGGAGCAAAATGAG 59.320 45.455 0.00 0.00 42.17 2.90
453 454 2.679837 CTGCATACGGAGCAAAATGAGT 59.320 45.455 0.00 0.00 42.17 3.41
454 455 2.419673 TGCATACGGAGCAAAATGAGTG 59.580 45.455 0.00 0.00 39.39 3.51
455 456 2.677836 GCATACGGAGCAAAATGAGTGA 59.322 45.455 0.00 0.00 0.00 3.41
456 457 3.126858 GCATACGGAGCAAAATGAGTGAA 59.873 43.478 0.00 0.00 0.00 3.18
457 458 4.201950 GCATACGGAGCAAAATGAGTGAAT 60.202 41.667 0.00 0.00 0.00 2.57
458 459 5.505286 CATACGGAGCAAAATGAGTGAATC 58.495 41.667 0.00 0.00 0.00 2.52
459 460 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
460 461 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
461 462 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
462 463 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
463 464 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
550 551 4.955811 TTAGGAACAGAGAAAGTCAGCA 57.044 40.909 0.00 0.00 0.00 4.41
599 600 1.774639 TACAGGTCGTTTTGCGTCTC 58.225 50.000 0.00 0.00 42.13 3.36
718 723 7.888250 AGAAAAGGAATAAGGAGGCAATAAG 57.112 36.000 0.00 0.00 0.00 1.73
1262 1268 3.967467 AGGAGATGGGAAAGATGCAAT 57.033 42.857 0.00 0.00 0.00 3.56
1267 1273 3.383825 AGATGGGAAAGATGCAATTGAGC 59.616 43.478 10.34 0.00 0.00 4.26
1271 1277 1.745087 GAAAGATGCAATTGAGCGGGA 59.255 47.619 10.34 0.00 37.31 5.14
1274 1280 0.464373 GATGCAATTGAGCGGGAGGA 60.464 55.000 10.34 0.00 37.31 3.71
1287 1293 2.180276 CGGGAGGAAGAAGAGAAGGAA 58.820 52.381 0.00 0.00 0.00 3.36
1447 1453 0.029163 TTCCCTGCCATCCCCTGATA 60.029 55.000 0.00 0.00 0.00 2.15
1451 1457 2.032681 GCCATCCCCTGATACGCC 59.967 66.667 0.00 0.00 0.00 5.68
1523 1529 1.125093 TTGGAGGCGAAGGAAGTGGA 61.125 55.000 0.00 0.00 0.00 4.02
1878 1884 4.819088 GGGCCTCTTCAATCAGATACTTTC 59.181 45.833 0.84 0.00 0.00 2.62
2275 2282 4.332819 GTGGTAAGTGGACATGCTCAATAC 59.667 45.833 0.00 0.00 0.00 1.89
2419 2426 2.187946 CCCGAGCCAGAAAGCGAT 59.812 61.111 0.00 0.00 38.01 4.58
2584 2593 3.677424 GCTCCTTCAAGCGTAGATGTTCT 60.677 47.826 0.00 0.00 31.56 3.01
2591 2600 3.868757 AGCGTAGATGTTCTGCTTACA 57.131 42.857 0.00 0.00 30.27 2.41
2812 2821 2.441750 TGGTTAGCCACAAAGAAGAGGT 59.558 45.455 0.00 0.00 40.46 3.85
2917 2956 2.107204 AGGAGAATGAAGGTGCACAAGT 59.893 45.455 20.43 2.02 0.00 3.16
3065 3104 5.980698 CACGAGTTGCAATCATAGAGAAT 57.019 39.130 0.59 0.00 0.00 2.40
3338 3377 3.904800 TCGCAAGATGGTTCCAGAATA 57.095 42.857 0.00 0.00 45.01 1.75
3515 3554 3.503363 TGCATGACAAGGTTGAGTTGATC 59.497 43.478 0.00 0.00 0.00 2.92
3874 3913 3.248602 GGTGTCAAGATACGGATCATTGC 59.751 47.826 10.99 8.31 34.17 3.56
3992 4031 3.949754 TCGTTCTATATGTGGACCGTCTT 59.050 43.478 0.00 0.00 0.00 3.01
4130 4169 2.032681 GAAGGCCTCAACGGTGCT 59.967 61.111 5.23 0.00 34.25 4.40
4190 4229 5.067954 CACATTATCCAGCAATCCATCAGA 58.932 41.667 0.00 0.00 0.00 3.27
4472 4511 1.000955 TCAAGAGCTCACCCGAAACTC 59.999 52.381 17.77 0.00 0.00 3.01
4781 4820 0.946700 TCGCAGGCGAAAACGATCAA 60.947 50.000 14.68 0.00 46.01 2.57
5141 5180 2.291741 GCGGCAGCTTGCTTATATTCTT 59.708 45.455 0.00 0.00 44.28 2.52
5376 5415 5.053978 AGATTATCCAATTGGTCAGTCCC 57.946 43.478 23.76 8.72 36.34 4.46
5447 5486 0.255890 GGGCTAATCTGCAGTCCCAA 59.744 55.000 14.67 0.00 31.16 4.12
5883 5923 7.370383 TGCTGTCCATCTTTTTAATGTTCTTC 58.630 34.615 0.00 0.00 0.00 2.87
5893 5933 4.678509 TTAATGTTCTTCACCGCATGAC 57.321 40.909 0.00 0.00 36.92 3.06
6035 6112 6.128795 CCTCTCTTCACAAATGTAAGACGTTC 60.129 42.308 0.00 0.00 0.00 3.95
6088 6167 6.121776 ACAGGTTGTATCATACTGGTTTCA 57.878 37.500 0.00 0.00 33.63 2.69
6118 6197 8.644216 TCAATCTCAGGTAGTGTTACTTGTTAA 58.356 33.333 0.00 0.00 37.90 2.01
6145 6224 6.401903 GCGACAATCATGCTTAATATCTCCAG 60.402 42.308 0.00 0.00 0.00 3.86
6172 6251 3.303132 CCGACTGTGCAGTTTTTGAGTAC 60.303 47.826 6.28 0.00 42.66 2.73
6254 6333 2.707849 CGAACGGGTGGATCCTCGT 61.708 63.158 14.23 16.51 41.99 4.18
6255 6334 1.141234 GAACGGGTGGATCCTCGTC 59.859 63.158 21.77 14.39 40.35 4.20
6279 6358 6.716628 TCTCTGACCAATAAAAGATGCAAACT 59.283 34.615 0.00 0.00 0.00 2.66
6409 6488 9.391006 GAATTTGGATTACTGATACCTGTAACA 57.609 33.333 0.00 0.00 38.78 2.41
6432 6511 4.878397 ACTATATGTTTCTGCAGTTCTGCC 59.122 41.667 19.91 6.68 0.00 4.85
6483 6565 3.385433 TCCTAAAATCCCATGCATTGCAG 59.615 43.478 17.52 8.97 43.65 4.41
6484 6566 3.385433 CCTAAAATCCCATGCATTGCAGA 59.615 43.478 17.52 9.36 43.65 4.26
6485 6567 4.039973 CCTAAAATCCCATGCATTGCAGAT 59.960 41.667 17.52 11.25 43.65 2.90
6486 6568 5.244402 CCTAAAATCCCATGCATTGCAGATA 59.756 40.000 17.52 3.07 43.65 1.98
6487 6569 4.595762 AAATCCCATGCATTGCAGATAC 57.404 40.909 17.52 0.00 43.65 2.24
6488 6570 2.732844 TCCCATGCATTGCAGATACA 57.267 45.000 17.52 0.00 43.65 2.29
6489 6571 3.015675 TCCCATGCATTGCAGATACAA 57.984 42.857 17.52 0.00 43.65 2.41
6490 6572 3.568443 TCCCATGCATTGCAGATACAAT 58.432 40.909 17.52 0.00 43.65 2.71
6491 6573 4.727677 TCCCATGCATTGCAGATACAATA 58.272 39.130 17.52 0.00 43.65 1.90
6492 6574 5.326900 TCCCATGCATTGCAGATACAATAT 58.673 37.500 17.52 0.00 43.65 1.28
6493 6575 5.776208 TCCCATGCATTGCAGATACAATATT 59.224 36.000 17.52 0.00 43.65 1.28
6494 6576 6.268158 TCCCATGCATTGCAGATACAATATTT 59.732 34.615 17.52 0.00 43.65 1.40
6495 6577 6.932400 CCCATGCATTGCAGATACAATATTTT 59.068 34.615 17.52 0.00 43.65 1.82
6496 6578 7.442969 CCCATGCATTGCAGATACAATATTTTT 59.557 33.333 17.52 0.00 43.65 1.94
6521 6603 8.561738 TTTTCTTTCTGTTCTTGTAGAAGTGT 57.438 30.769 0.00 0.00 34.42 3.55
6522 6604 9.661563 TTTTCTTTCTGTTCTTGTAGAAGTGTA 57.338 29.630 0.00 0.00 34.42 2.90
6523 6605 9.832445 TTTCTTTCTGTTCTTGTAGAAGTGTAT 57.168 29.630 0.00 0.00 34.42 2.29
6524 6606 8.818141 TCTTTCTGTTCTTGTAGAAGTGTATG 57.182 34.615 0.00 0.00 34.42 2.39
6525 6607 7.385205 TCTTTCTGTTCTTGTAGAAGTGTATGC 59.615 37.037 0.00 0.00 34.42 3.14
6526 6608 6.346477 TCTGTTCTTGTAGAAGTGTATGCT 57.654 37.500 0.00 0.00 34.42 3.79
6527 6609 6.390721 TCTGTTCTTGTAGAAGTGTATGCTC 58.609 40.000 0.00 0.00 34.42 4.26
6528 6610 6.209589 TCTGTTCTTGTAGAAGTGTATGCTCT 59.790 38.462 0.00 0.00 34.42 4.09
6529 6611 7.393515 TCTGTTCTTGTAGAAGTGTATGCTCTA 59.606 37.037 0.00 0.00 34.42 2.43
6530 6612 7.539436 TGTTCTTGTAGAAGTGTATGCTCTAG 58.461 38.462 0.00 0.00 34.42 2.43
6531 6613 6.137794 TCTTGTAGAAGTGTATGCTCTAGC 57.862 41.667 0.00 0.00 42.50 3.42
6532 6614 4.920640 TGTAGAAGTGTATGCTCTAGCC 57.079 45.455 0.00 0.00 41.18 3.93
6533 6615 4.278310 TGTAGAAGTGTATGCTCTAGCCA 58.722 43.478 0.00 0.00 41.18 4.75
6534 6616 4.709886 TGTAGAAGTGTATGCTCTAGCCAA 59.290 41.667 0.00 0.00 41.18 4.52
6535 6617 5.363868 TGTAGAAGTGTATGCTCTAGCCAAT 59.636 40.000 0.00 0.00 41.18 3.16
6536 6618 4.701765 AGAAGTGTATGCTCTAGCCAATG 58.298 43.478 0.00 0.00 41.18 2.82
6537 6619 2.843701 AGTGTATGCTCTAGCCAATGC 58.156 47.619 0.00 0.00 41.18 3.56
6538 6620 2.171237 AGTGTATGCTCTAGCCAATGCA 59.829 45.455 0.00 0.00 41.13 3.96
6539 6621 2.945008 GTGTATGCTCTAGCCAATGCAA 59.055 45.455 0.00 0.00 41.13 4.08
6540 6622 2.945008 TGTATGCTCTAGCCAATGCAAC 59.055 45.455 0.00 0.00 41.13 4.17
6541 6623 1.396653 ATGCTCTAGCCAATGCAACC 58.603 50.000 0.00 0.00 41.13 3.77
6542 6624 0.038021 TGCTCTAGCCAATGCAACCA 59.962 50.000 0.00 0.00 41.13 3.67
6543 6625 1.176527 GCTCTAGCCAATGCAACCAA 58.823 50.000 0.00 0.00 41.13 3.67
6544 6626 1.545582 GCTCTAGCCAATGCAACCAAA 59.454 47.619 0.00 0.00 41.13 3.28
6545 6627 2.029110 GCTCTAGCCAATGCAACCAAAA 60.029 45.455 0.00 0.00 41.13 2.44
6546 6628 3.554752 GCTCTAGCCAATGCAACCAAAAA 60.555 43.478 0.00 0.00 41.13 1.94
6572 6654 8.783660 ACCAATCTAATGGAATAGACTAGTCA 57.216 34.615 24.44 11.06 43.54 3.41
6573 6655 9.213777 ACCAATCTAATGGAATAGACTAGTCAA 57.786 33.333 24.44 0.70 43.54 3.18
6593 6675 8.997621 AGTCAATACATTTATACGTCAACACT 57.002 30.769 0.00 0.00 0.00 3.55
6594 6676 9.084164 AGTCAATACATTTATACGTCAACACTC 57.916 33.333 0.00 0.00 0.00 3.51
6595 6677 8.325997 GTCAATACATTTATACGTCAACACTCC 58.674 37.037 0.00 0.00 0.00 3.85
6596 6678 7.221259 TCAATACATTTATACGTCAACACTCCG 59.779 37.037 0.00 0.00 0.00 4.63
6597 6679 3.615496 ACATTTATACGTCAACACTCCGC 59.385 43.478 0.00 0.00 0.00 5.54
6598 6680 2.282701 TTATACGTCAACACTCCGCC 57.717 50.000 0.00 0.00 0.00 6.13
6599 6681 1.466856 TATACGTCAACACTCCGCCT 58.533 50.000 0.00 0.00 0.00 5.52
6600 6682 1.466856 ATACGTCAACACTCCGCCTA 58.533 50.000 0.00 0.00 0.00 3.93
6601 6683 1.246649 TACGTCAACACTCCGCCTAA 58.753 50.000 0.00 0.00 0.00 2.69
6602 6684 0.390124 ACGTCAACACTCCGCCTAAA 59.610 50.000 0.00 0.00 0.00 1.85
6603 6685 0.788391 CGTCAACACTCCGCCTAAAC 59.212 55.000 0.00 0.00 0.00 2.01
6604 6686 0.788391 GTCAACACTCCGCCTAAACG 59.212 55.000 0.00 0.00 0.00 3.60
6605 6687 0.390124 TCAACACTCCGCCTAAACGT 59.610 50.000 0.00 0.00 0.00 3.99
6606 6688 0.511221 CAACACTCCGCCTAAACGTG 59.489 55.000 0.00 0.00 0.00 4.49
6607 6689 0.601841 AACACTCCGCCTAAACGTGG 60.602 55.000 0.00 0.00 34.52 4.94
6608 6690 1.290955 CACTCCGCCTAAACGTGGA 59.709 57.895 0.00 0.00 40.14 4.02
6609 6691 1.012486 CACTCCGCCTAAACGTGGAC 61.012 60.000 0.00 0.00 37.51 4.02
6610 6692 1.447314 CTCCGCCTAAACGTGGACC 60.447 63.158 0.00 0.00 37.51 4.46
6611 6693 2.812178 CCGCCTAAACGTGGACCG 60.812 66.667 0.00 0.00 44.03 4.79
6612 6694 2.259204 CGCCTAAACGTGGACCGA 59.741 61.111 0.00 0.00 40.70 4.69
6613 6695 1.373246 CGCCTAAACGTGGACCGAA 60.373 57.895 0.00 0.00 40.70 4.30
6614 6696 0.945265 CGCCTAAACGTGGACCGAAA 60.945 55.000 0.00 0.00 40.70 3.46
6615 6697 0.794473 GCCTAAACGTGGACCGAAAG 59.206 55.000 0.00 0.00 40.70 2.62
6616 6698 1.875157 GCCTAAACGTGGACCGAAAGT 60.875 52.381 0.00 0.00 40.70 2.66
6617 6699 1.796459 CCTAAACGTGGACCGAAAGTG 59.204 52.381 0.00 0.00 40.70 3.16
6618 6700 2.546373 CCTAAACGTGGACCGAAAGTGA 60.546 50.000 0.00 0.00 40.70 3.41
6619 6701 1.578583 AAACGTGGACCGAAAGTGAG 58.421 50.000 0.00 0.00 40.70 3.51
6620 6702 0.462789 AACGTGGACCGAAAGTGAGT 59.537 50.000 0.00 0.00 40.70 3.41
6621 6703 0.462789 ACGTGGACCGAAAGTGAGTT 59.537 50.000 0.00 0.00 40.70 3.01
6622 6704 0.859232 CGTGGACCGAAAGTGAGTTG 59.141 55.000 0.00 0.00 39.56 3.16
6623 6705 0.586802 GTGGACCGAAAGTGAGTTGC 59.413 55.000 0.00 0.00 0.00 4.17
6624 6706 0.179234 TGGACCGAAAGTGAGTTGCA 59.821 50.000 0.00 0.00 0.00 4.08
6625 6707 1.305201 GGACCGAAAGTGAGTTGCAA 58.695 50.000 0.00 0.00 0.00 4.08
6626 6708 1.880027 GGACCGAAAGTGAGTTGCAAT 59.120 47.619 0.59 0.00 0.00 3.56
6627 6709 2.293399 GGACCGAAAGTGAGTTGCAATT 59.707 45.455 0.59 0.00 36.14 2.32
6628 6710 3.243401 GGACCGAAAGTGAGTTGCAATTT 60.243 43.478 0.59 0.00 46.36 1.82
6629 6711 4.023536 GGACCGAAAGTGAGTTGCAATTTA 60.024 41.667 0.59 0.00 44.02 1.40
6630 6712 5.506649 GGACCGAAAGTGAGTTGCAATTTAA 60.507 40.000 0.59 0.00 44.02 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.823745 AACAGGACTGAAAATCATACAAACT 57.176 32.000 6.29 0.00 0.00 2.66
76 77 6.748658 CACTCAACGATAACAACGAGGTATAA 59.251 38.462 0.00 0.00 27.68 0.98
81 82 2.666508 CCACTCAACGATAACAACGAGG 59.333 50.000 0.00 0.00 34.70 4.63
99 100 1.448985 TTGAAGACCGCAATAGCCAC 58.551 50.000 0.00 0.00 37.52 5.01
277 278 9.952188 TCACACGAGAGATAAGAGTATAAAATG 57.048 33.333 0.00 0.00 0.00 2.32
288 289 6.529829 CCTTCTCTTTTCACACGAGAGATAAG 59.470 42.308 3.43 0.00 43.77 1.73
292 293 3.637229 ACCTTCTCTTTTCACACGAGAGA 59.363 43.478 0.00 0.00 42.95 3.10
310 311 4.640771 TTGACATGCTTCCTCTTACCTT 57.359 40.909 0.00 0.00 0.00 3.50
336 337 7.368059 CGAAGCTTGAAAAATTACTAGGGTTT 58.632 34.615 2.10 0.00 0.00 3.27
337 338 6.072119 CCGAAGCTTGAAAAATTACTAGGGTT 60.072 38.462 2.10 0.00 0.00 4.11
338 339 5.414765 CCGAAGCTTGAAAAATTACTAGGGT 59.585 40.000 2.10 0.00 0.00 4.34
384 385 6.992715 AGACAAATATTTAGGAACGGATGGAG 59.007 38.462 0.00 0.00 0.00 3.86
385 386 6.895782 AGACAAATATTTAGGAACGGATGGA 58.104 36.000 0.00 0.00 0.00 3.41
386 387 7.568199 AAGACAAATATTTAGGAACGGATGG 57.432 36.000 0.00 0.00 0.00 3.51
387 388 8.893727 AGAAAGACAAATATTTAGGAACGGATG 58.106 33.333 0.00 0.00 0.00 3.51
389 390 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
390 391 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
405 406 9.996554 TCACTTGTTGAAATATCTAGAAAGACA 57.003 29.630 0.00 0.00 33.57 3.41
409 410 8.721478 GCAGTCACTTGTTGAAATATCTAGAAA 58.279 33.333 0.00 0.00 35.39 2.52
410 411 7.877612 TGCAGTCACTTGTTGAAATATCTAGAA 59.122 33.333 0.00 0.00 35.39 2.10
411 412 7.386059 TGCAGTCACTTGTTGAAATATCTAGA 58.614 34.615 0.00 0.00 35.39 2.43
412 413 7.601073 TGCAGTCACTTGTTGAAATATCTAG 57.399 36.000 0.00 0.00 35.39 2.43
413 414 9.098355 GTATGCAGTCACTTGTTGAAATATCTA 57.902 33.333 0.00 0.00 35.39 1.98
414 415 7.201556 CGTATGCAGTCACTTGTTGAAATATCT 60.202 37.037 0.00 0.00 35.39 1.98
415 416 6.901887 CGTATGCAGTCACTTGTTGAAATATC 59.098 38.462 0.00 0.00 35.39 1.63
416 417 6.183360 CCGTATGCAGTCACTTGTTGAAATAT 60.183 38.462 0.00 0.00 35.39 1.28
417 418 5.121611 CCGTATGCAGTCACTTGTTGAAATA 59.878 40.000 0.00 0.00 35.39 1.40
418 419 4.083324 CCGTATGCAGTCACTTGTTGAAAT 60.083 41.667 0.00 0.00 35.39 2.17
419 420 3.249799 CCGTATGCAGTCACTTGTTGAAA 59.750 43.478 0.00 0.00 35.39 2.69
420 421 2.805671 CCGTATGCAGTCACTTGTTGAA 59.194 45.455 0.00 0.00 35.39 2.69
421 422 2.036604 TCCGTATGCAGTCACTTGTTGA 59.963 45.455 0.00 0.00 0.00 3.18
422 423 2.412870 TCCGTATGCAGTCACTTGTTG 58.587 47.619 0.00 0.00 0.00 3.33
423 424 2.688507 CTCCGTATGCAGTCACTTGTT 58.311 47.619 0.00 0.00 0.00 2.83
424 425 1.673033 GCTCCGTATGCAGTCACTTGT 60.673 52.381 0.00 0.00 0.00 3.16
425 426 1.002366 GCTCCGTATGCAGTCACTTG 58.998 55.000 0.00 0.00 0.00 3.16
426 427 0.608130 TGCTCCGTATGCAGTCACTT 59.392 50.000 0.00 0.00 35.31 3.16
427 428 0.608130 TTGCTCCGTATGCAGTCACT 59.392 50.000 0.00 0.00 41.71 3.41
428 429 1.438651 TTTGCTCCGTATGCAGTCAC 58.561 50.000 0.00 0.00 41.71 3.67
429 430 2.177394 TTTTGCTCCGTATGCAGTCA 57.823 45.000 0.00 0.00 41.71 3.41
430 431 2.677836 TCATTTTGCTCCGTATGCAGTC 59.322 45.455 0.00 0.00 41.71 3.51
431 432 2.679837 CTCATTTTGCTCCGTATGCAGT 59.320 45.455 0.00 0.00 41.71 4.40
432 433 2.679837 ACTCATTTTGCTCCGTATGCAG 59.320 45.455 0.00 0.00 41.71 4.41
433 434 2.419673 CACTCATTTTGCTCCGTATGCA 59.580 45.455 0.00 0.00 38.80 3.96
434 435 2.677836 TCACTCATTTTGCTCCGTATGC 59.322 45.455 0.00 0.00 0.00 3.14
435 436 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
436 437 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
437 438 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
438 439 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
439 440 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
440 441 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
441 442 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
442 443 7.516198 AAAGTGTAGATTCACTCATTTTGCT 57.484 32.000 0.00 0.00 46.25 3.91
443 444 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
521 522 9.793259 TGACTTTCTCTGTTCCTAAATATTTGT 57.207 29.630 11.05 0.00 0.00 2.83
523 524 8.951243 GCTGACTTTCTCTGTTCCTAAATATTT 58.049 33.333 5.89 5.89 0.00 1.40
524 525 8.103305 TGCTGACTTTCTCTGTTCCTAAATATT 58.897 33.333 0.00 0.00 0.00 1.28
525 526 7.550906 GTGCTGACTTTCTCTGTTCCTAAATAT 59.449 37.037 0.00 0.00 0.00 1.28
526 527 6.874134 GTGCTGACTTTCTCTGTTCCTAAATA 59.126 38.462 0.00 0.00 0.00 1.40
527 528 5.703130 GTGCTGACTTTCTCTGTTCCTAAAT 59.297 40.000 0.00 0.00 0.00 1.40
528 529 5.057149 GTGCTGACTTTCTCTGTTCCTAAA 58.943 41.667 0.00 0.00 0.00 1.85
529 530 4.632153 GTGCTGACTTTCTCTGTTCCTAA 58.368 43.478 0.00 0.00 0.00 2.69
530 531 3.305403 CGTGCTGACTTTCTCTGTTCCTA 60.305 47.826 0.00 0.00 0.00 2.94
531 532 2.546795 CGTGCTGACTTTCTCTGTTCCT 60.547 50.000 0.00 0.00 0.00 3.36
532 533 1.795286 CGTGCTGACTTTCTCTGTTCC 59.205 52.381 0.00 0.00 0.00 3.62
533 534 2.219674 CACGTGCTGACTTTCTCTGTTC 59.780 50.000 0.82 0.00 0.00 3.18
534 535 2.205074 CACGTGCTGACTTTCTCTGTT 58.795 47.619 0.82 0.00 0.00 3.16
535 536 1.137086 ACACGTGCTGACTTTCTCTGT 59.863 47.619 17.22 0.00 0.00 3.41
536 537 1.858091 ACACGTGCTGACTTTCTCTG 58.142 50.000 17.22 0.00 0.00 3.35
537 538 2.623889 ACTACACGTGCTGACTTTCTCT 59.376 45.455 17.22 0.00 0.00 3.10
538 539 3.014604 ACTACACGTGCTGACTTTCTC 57.985 47.619 17.22 0.00 0.00 2.87
539 540 3.454371 AACTACACGTGCTGACTTTCT 57.546 42.857 17.22 0.00 0.00 2.52
540 541 3.308866 ACAAACTACACGTGCTGACTTTC 59.691 43.478 17.22 0.00 0.00 2.62
541 542 3.063452 CACAAACTACACGTGCTGACTTT 59.937 43.478 17.22 3.57 0.00 2.66
548 549 8.889849 AAAATTATATCACAAACTACACGTGC 57.110 30.769 17.22 0.00 0.00 5.34
599 600 7.106663 ACGATAGAAAAGAAGAAGAACAACG 57.893 36.000 0.00 0.00 41.38 4.10
685 687 9.686683 CCTCCTTATTCCTTTTCTATTTTCTGA 57.313 33.333 0.00 0.00 0.00 3.27
718 723 1.202188 GCTGGTGATAAGGCGCTTTTC 60.202 52.381 11.00 8.61 0.00 2.29
1119 1125 3.120191 CCCTCCCCTACTCCACCT 58.880 66.667 0.00 0.00 0.00 4.00
1262 1268 0.898320 CTCTTCTTCCTCCCGCTCAA 59.102 55.000 0.00 0.00 0.00 3.02
1267 1273 1.853963 TCCTTCTCTTCTTCCTCCCG 58.146 55.000 0.00 0.00 0.00 5.14
1271 1277 4.352893 CTCCTCTTCCTTCTCTTCTTCCT 58.647 47.826 0.00 0.00 0.00 3.36
1274 1280 4.352893 CTCCTCCTCTTCCTTCTCTTCTT 58.647 47.826 0.00 0.00 0.00 2.52
1447 1453 1.407979 CTTCTTATCACCTACCGGCGT 59.592 52.381 6.01 0.00 0.00 5.68
1451 1457 2.693591 TCAGGCTTCTTATCACCTACCG 59.306 50.000 0.00 0.00 0.00 4.02
1523 1529 2.657296 CGTCGAGTGCCACGTTGT 60.657 61.111 0.00 0.00 0.00 3.32
1593 1599 1.019673 CACCATCATCTTTGCCTCCG 58.980 55.000 0.00 0.00 0.00 4.63
1600 1606 4.217118 GCTGTCAAACTCACCATCATCTTT 59.783 41.667 0.00 0.00 0.00 2.52
1994 2000 0.175302 CTGGAGTTGCATCGCTCTCT 59.825 55.000 11.50 0.00 33.63 3.10
2235 2242 2.114670 ACCGGGCTTGCATCATTCG 61.115 57.895 6.32 0.00 0.00 3.34
2275 2282 8.540492 CATTACTAGGTAGTAGCAACGAAATTG 58.460 37.037 1.58 0.00 39.69 2.32
2419 2426 0.320374 CACTTACCTCGGGACTTGCA 59.680 55.000 0.00 0.00 0.00 4.08
2476 2483 8.506921 TCTTTATATCCCCAATCCACATTAACA 58.493 33.333 0.00 0.00 0.00 2.41
2477 2484 8.934023 TCTTTATATCCCCAATCCACATTAAC 57.066 34.615 0.00 0.00 0.00 2.01
2591 2600 2.221169 TGTGCGTTCTCATTGCTTTCT 58.779 42.857 0.00 0.00 0.00 2.52
2812 2821 5.430886 CCACAACTATCTCATCATCACCAA 58.569 41.667 0.00 0.00 0.00 3.67
2879 2918 0.758734 CCTCACCACCTGTGTCTTCA 59.241 55.000 0.00 0.00 45.61 3.02
2917 2956 4.022589 CCTCTACTTCACGGTCAGTAACAA 60.023 45.833 0.00 0.00 0.00 2.83
3338 3377 4.467769 CAGCAGGTCTATCCATGGAAAAT 58.532 43.478 20.67 4.84 39.02 1.82
3515 3554 0.110373 GGCGCAGAAACTTTACACGG 60.110 55.000 10.83 0.00 0.00 4.94
3992 4031 2.937519 AGATCACGGCTCAGACTATCA 58.062 47.619 0.00 0.00 0.00 2.15
4130 4169 6.152831 CCATCAATACCTCGTATGTCATAGGA 59.847 42.308 13.24 13.24 33.16 2.94
4190 4229 1.842007 CATATCCCCTGCAGCCTGT 59.158 57.895 8.66 0.00 0.00 4.00
4781 4820 5.014544 TGAAACATTTTCTGGAGGAGGATCT 59.985 40.000 0.00 0.00 33.73 2.75
4973 5012 4.335416 CTGGGAATTTGTTAAGGAGAGCA 58.665 43.478 0.00 0.00 0.00 4.26
5376 5415 0.890996 GACAGGCCCAAGGTTGACAG 60.891 60.000 0.00 0.00 0.00 3.51
5447 5486 2.576191 TGAACCCCTTCCAATCGAGAAT 59.424 45.455 0.00 0.00 0.00 2.40
5735 5775 0.539986 ATACGAACAATCTGCGGGGT 59.460 50.000 0.00 0.00 0.00 4.95
5839 5879 5.351465 ACAGCAACAACGGTAATTGATAGAG 59.649 40.000 8.11 0.00 33.57 2.43
5883 5923 1.934589 TATTTCCTCGTCATGCGGTG 58.065 50.000 9.16 4.02 41.72 4.94
5924 5964 3.699038 CTCTGGGTTTGTTCCAAGTCAAA 59.301 43.478 0.00 0.00 33.36 2.69
5946 5986 4.283467 ACTCCCTCCCAAAATAAAACAAGC 59.717 41.667 0.00 0.00 0.00 4.01
6035 6112 3.636764 ACTCCCTTTGTTTAAACTGCCAG 59.363 43.478 18.72 9.11 0.00 4.85
6088 6167 6.249951 AGTAACACTACCTGAGATTGAGACT 58.750 40.000 0.00 0.00 0.00 3.24
6118 6197 5.555017 AGATATTAAGCATGATTGTCGCCT 58.445 37.500 6.43 0.00 0.00 5.52
6145 6224 4.449743 TCAAAAACTGCACAGTCGGTATAC 59.550 41.667 3.32 0.00 41.58 1.47
6172 6251 4.206609 GCAAGTACTACGGCTATTTTCTCG 59.793 45.833 0.00 0.00 0.00 4.04
6254 6333 6.716628 AGTTTGCATCTTTTATTGGTCAGAGA 59.283 34.615 0.00 0.00 0.00 3.10
6255 6334 6.917533 AGTTTGCATCTTTTATTGGTCAGAG 58.082 36.000 0.00 0.00 0.00 3.35
6279 6358 3.657610 ACTGTACCAGGGATCATCATGA 58.342 45.455 0.00 0.00 35.51 3.07
6384 6463 9.174166 GTGTTACAGGTATCAGTAATCCAAATT 57.826 33.333 0.00 0.00 33.30 1.82
6432 6511 9.319143 CAGGTAATAGTTAATCACCAGAAGAAG 57.681 37.037 0.00 0.00 0.00 2.85
6495 6577 9.010029 ACACTTCTACAAGAACAGAAAGAAAAA 57.990 29.630 0.00 0.00 33.34 1.94
6496 6578 8.561738 ACACTTCTACAAGAACAGAAAGAAAA 57.438 30.769 0.00 0.00 33.34 2.29
6497 6579 9.832445 ATACACTTCTACAAGAACAGAAAGAAA 57.168 29.630 0.00 0.00 33.34 2.52
6498 6580 9.261180 CATACACTTCTACAAGAACAGAAAGAA 57.739 33.333 0.00 0.00 33.34 2.52
6499 6581 7.385205 GCATACACTTCTACAAGAACAGAAAGA 59.615 37.037 0.00 0.00 33.34 2.52
6500 6582 7.386299 AGCATACACTTCTACAAGAACAGAAAG 59.614 37.037 0.00 0.00 33.34 2.62
6501 6583 7.217200 AGCATACACTTCTACAAGAACAGAAA 58.783 34.615 0.00 0.00 33.34 2.52
6502 6584 6.759272 AGCATACACTTCTACAAGAACAGAA 58.241 36.000 0.00 0.00 33.34 3.02
6503 6585 6.209589 AGAGCATACACTTCTACAAGAACAGA 59.790 38.462 0.00 0.00 33.34 3.41
6504 6586 6.393990 AGAGCATACACTTCTACAAGAACAG 58.606 40.000 0.00 0.00 33.34 3.16
6505 6587 6.346477 AGAGCATACACTTCTACAAGAACA 57.654 37.500 0.00 0.00 33.34 3.18
6506 6588 6.474102 GCTAGAGCATACACTTCTACAAGAAC 59.526 42.308 0.00 0.00 41.59 3.01
6507 6589 6.405953 GGCTAGAGCATACACTTCTACAAGAA 60.406 42.308 3.54 0.00 44.36 2.52
6508 6590 5.067936 GGCTAGAGCATACACTTCTACAAGA 59.932 44.000 3.54 0.00 44.36 3.02
6509 6591 5.163509 TGGCTAGAGCATACACTTCTACAAG 60.164 44.000 3.54 0.00 44.36 3.16
6510 6592 4.709886 TGGCTAGAGCATACACTTCTACAA 59.290 41.667 3.54 0.00 44.36 2.41
6511 6593 4.278310 TGGCTAGAGCATACACTTCTACA 58.722 43.478 3.54 0.00 44.36 2.74
6512 6594 4.920640 TGGCTAGAGCATACACTTCTAC 57.079 45.455 3.54 0.00 44.36 2.59
6513 6595 5.740224 GCATTGGCTAGAGCATACACTTCTA 60.740 44.000 3.54 0.00 44.36 2.10
6514 6596 4.701765 CATTGGCTAGAGCATACACTTCT 58.298 43.478 3.54 0.00 44.36 2.85
6515 6597 3.249559 GCATTGGCTAGAGCATACACTTC 59.750 47.826 3.54 0.00 44.36 3.01
6516 6598 3.209410 GCATTGGCTAGAGCATACACTT 58.791 45.455 3.54 0.00 44.36 3.16
6517 6599 2.171237 TGCATTGGCTAGAGCATACACT 59.829 45.455 3.54 0.00 44.36 3.55
6518 6600 2.564771 TGCATTGGCTAGAGCATACAC 58.435 47.619 3.54 0.00 44.36 2.90
6519 6601 2.945008 GTTGCATTGGCTAGAGCATACA 59.055 45.455 3.54 0.00 44.36 2.29
6520 6602 2.291741 GGTTGCATTGGCTAGAGCATAC 59.708 50.000 3.54 2.41 44.36 2.39
6521 6603 2.092484 TGGTTGCATTGGCTAGAGCATA 60.092 45.455 3.54 0.00 44.36 3.14
6522 6604 1.341285 TGGTTGCATTGGCTAGAGCAT 60.341 47.619 3.54 0.00 44.36 3.79
6523 6605 0.038021 TGGTTGCATTGGCTAGAGCA 59.962 50.000 3.54 0.00 44.36 4.26
6524 6606 1.176527 TTGGTTGCATTGGCTAGAGC 58.823 50.000 0.00 0.00 41.91 4.09
6525 6607 3.940209 TTTTGGTTGCATTGGCTAGAG 57.060 42.857 0.00 0.00 41.91 2.43
6546 6628 9.213777 TGACTAGTCTATTCCATTAGATTGGTT 57.786 33.333 23.01 0.00 38.01 3.67
6547 6629 8.783660 TGACTAGTCTATTCCATTAGATTGGT 57.216 34.615 23.01 0.00 38.01 3.67
6568 6650 8.997621 AGTGTTGACGTATAAATGTATTGACT 57.002 30.769 0.00 0.00 0.00 3.41
6569 6651 8.325997 GGAGTGTTGACGTATAAATGTATTGAC 58.674 37.037 0.00 0.00 0.00 3.18
6570 6652 7.221259 CGGAGTGTTGACGTATAAATGTATTGA 59.779 37.037 0.00 0.00 0.00 2.57
6571 6653 7.334749 CGGAGTGTTGACGTATAAATGTATTG 58.665 38.462 0.00 0.00 0.00 1.90
6572 6654 6.019318 GCGGAGTGTTGACGTATAAATGTATT 60.019 38.462 0.00 0.00 0.00 1.89
6573 6655 5.461078 GCGGAGTGTTGACGTATAAATGTAT 59.539 40.000 0.00 0.00 0.00 2.29
6574 6656 4.799949 GCGGAGTGTTGACGTATAAATGTA 59.200 41.667 0.00 0.00 0.00 2.29
6575 6657 3.615496 GCGGAGTGTTGACGTATAAATGT 59.385 43.478 0.00 0.00 0.00 2.71
6576 6658 3.000925 GGCGGAGTGTTGACGTATAAATG 59.999 47.826 0.00 0.00 0.00 2.32
6577 6659 3.118884 AGGCGGAGTGTTGACGTATAAAT 60.119 43.478 0.00 0.00 0.00 1.40
6578 6660 2.231964 AGGCGGAGTGTTGACGTATAAA 59.768 45.455 0.00 0.00 0.00 1.40
6579 6661 1.820519 AGGCGGAGTGTTGACGTATAA 59.179 47.619 0.00 0.00 0.00 0.98
6580 6662 1.466856 AGGCGGAGTGTTGACGTATA 58.533 50.000 0.00 0.00 0.00 1.47
6581 6663 1.466856 TAGGCGGAGTGTTGACGTAT 58.533 50.000 0.00 0.00 0.00 3.06
6582 6664 1.246649 TTAGGCGGAGTGTTGACGTA 58.753 50.000 0.00 0.00 0.00 3.57
6583 6665 0.390124 TTTAGGCGGAGTGTTGACGT 59.610 50.000 0.00 0.00 0.00 4.34
6584 6666 0.788391 GTTTAGGCGGAGTGTTGACG 59.212 55.000 0.00 0.00 0.00 4.35
6585 6667 0.788391 CGTTTAGGCGGAGTGTTGAC 59.212 55.000 0.00 0.00 0.00 3.18
6586 6668 0.390124 ACGTTTAGGCGGAGTGTTGA 59.610 50.000 0.00 0.00 35.98 3.18
6587 6669 0.511221 CACGTTTAGGCGGAGTGTTG 59.489 55.000 0.00 0.00 35.98 3.33
6588 6670 0.601841 CCACGTTTAGGCGGAGTGTT 60.602 55.000 0.00 0.00 35.98 3.32
6589 6671 1.005394 CCACGTTTAGGCGGAGTGT 60.005 57.895 0.00 0.00 35.98 3.55
6590 6672 1.012486 GTCCACGTTTAGGCGGAGTG 61.012 60.000 0.00 0.00 35.98 3.51
6591 6673 1.291272 GTCCACGTTTAGGCGGAGT 59.709 57.895 0.00 0.00 35.98 3.85
6592 6674 1.447314 GGTCCACGTTTAGGCGGAG 60.447 63.158 0.00 0.00 35.98 4.63
6593 6675 2.658422 GGTCCACGTTTAGGCGGA 59.342 61.111 0.00 0.00 35.98 5.54
6594 6676 2.768503 TTCGGTCCACGTTTAGGCGG 62.769 60.000 0.00 0.00 44.69 6.13
6595 6677 0.945265 TTTCGGTCCACGTTTAGGCG 60.945 55.000 0.00 0.00 44.69 5.52
6596 6678 0.794473 CTTTCGGTCCACGTTTAGGC 59.206 55.000 0.00 0.00 44.69 3.93
6597 6679 1.796459 CACTTTCGGTCCACGTTTAGG 59.204 52.381 0.00 0.00 44.69 2.69
6598 6680 2.729882 CTCACTTTCGGTCCACGTTTAG 59.270 50.000 0.00 0.00 44.69 1.85
6599 6681 2.101249 ACTCACTTTCGGTCCACGTTTA 59.899 45.455 0.00 0.00 44.69 2.01
6600 6682 1.134610 ACTCACTTTCGGTCCACGTTT 60.135 47.619 0.00 0.00 44.69 3.60
6601 6683 0.462789 ACTCACTTTCGGTCCACGTT 59.537 50.000 0.00 0.00 44.69 3.99
6602 6684 0.462789 AACTCACTTTCGGTCCACGT 59.537 50.000 0.00 0.00 44.69 4.49
6603 6685 0.859232 CAACTCACTTTCGGTCCACG 59.141 55.000 0.00 0.00 46.11 4.94
6604 6686 0.586802 GCAACTCACTTTCGGTCCAC 59.413 55.000 0.00 0.00 0.00 4.02
6605 6687 0.179234 TGCAACTCACTTTCGGTCCA 59.821 50.000 0.00 0.00 0.00 4.02
6606 6688 1.305201 TTGCAACTCACTTTCGGTCC 58.695 50.000 0.00 0.00 0.00 4.46
6607 6689 3.626028 AATTGCAACTCACTTTCGGTC 57.374 42.857 0.00 0.00 0.00 4.79
6608 6690 5.508200 TTAAATTGCAACTCACTTTCGGT 57.492 34.783 0.00 0.00 31.27 4.69


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

AutoCloner maintained by Alex Coulton.