Multiple sequence alignment - TraesCS2B01G568700

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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 TraesCS2B01G568700 chr2B 100.000 4409 0 0 1 4409 759451537 759447129 0.000000e+00 8142.0
1 TraesCS2B01G568700 chr2B 79.355 1705 193 100 673 2274 706724162 706725810 0.000000e+00 1051.0
2 TraesCS2B01G568700 chr2B 80.000 495 50 26 2932 3416 706726532 706726987 1.980000e-83 320.0
3 TraesCS2B01G568700 chr2B 75.487 616 78 45 3587 4153 706727128 706727719 2.650000e-57 233.0
4 TraesCS2B01G568700 chr2B 84.940 166 17 5 2445 2607 706725991 706726151 1.270000e-35 161.0
5 TraesCS2B01G568700 chr2B 92.308 104 7 1 2770 2872 706726406 706726509 3.550000e-31 147.0
6 TraesCS2B01G568700 chr2A 91.045 4333 213 68 3 4280 751384630 751380418 0.000000e+00 5690.0
7 TraesCS2B01G568700 chr2A 78.988 1680 188 85 673 2274 719720773 719722365 0.000000e+00 994.0
8 TraesCS2B01G568700 chr2A 79.845 516 51 27 2909 3415 719723032 719723503 1.180000e-85 327.0
9 TraesCS2B01G568700 chr2A 79.288 309 35 17 3587 3883 719723641 719723932 5.820000e-44 189.0
10 TraesCS2B01G568700 chr2A 85.276 163 14 7 2444 2603 719722518 719722673 4.560000e-35 159.0
11 TraesCS2B01G568700 chr2A 91.398 93 8 0 4272 4364 712971475 712971383 1.290000e-25 128.0
12 TraesCS2B01G568700 chr2A 96.078 51 1 1 4359 4409 751380422 751380373 1.020000e-11 82.4
13 TraesCS2B01G568700 chr2D 93.403 3911 139 52 429 4279 619712170 619708319 0.000000e+00 5683.0
14 TraesCS2B01G568700 chr2D 82.702 607 65 20 1478 2054 585680253 585680849 1.830000e-138 503.0
15 TraesCS2B01G568700 chr2D 80.893 717 61 36 689 1351 585679407 585680101 3.060000e-136 496.0
16 TraesCS2B01G568700 chr2D 80.271 517 54 23 2909 3416 585681853 585682330 3.260000e-91 346.0
17 TraesCS2B01G568700 chr2D 77.273 550 64 37 3587 4100 585682471 585682995 2.610000e-67 267.0
18 TraesCS2B01G568700 chr2D 93.939 99 5 1 2775 2872 585681751 585681849 9.880000e-32 148.0
19 TraesCS2B01G568700 chr2D 83.636 165 15 8 2444 2603 585681342 585681499 1.280000e-30 145.0
20 TraesCS2B01G568700 chr2D 93.617 94 6 0 4272 4365 201441659 201441566 1.650000e-29 141.0
21 TraesCS2B01G568700 chr2D 91.111 90 8 0 4278 4367 325754016 325754105 5.990000e-24 122.0
22 TraesCS2B01G568700 chr2D 100.000 38 0 0 4359 4396 619708322 619708285 2.200000e-08 71.3
23 TraesCS2B01G568700 chrUn 91.837 98 8 0 4269 4366 104668799 104668896 2.140000e-28 137.0
24 TraesCS2B01G568700 chr1D 94.318 88 5 0 4276 4363 260870054 260869967 7.690000e-28 135.0
25 TraesCS2B01G568700 chr1D 92.308 91 6 1 4273 4362 321678017 321677927 1.290000e-25 128.0
26 TraesCS2B01G568700 chr7D 90.000 100 10 0 4273 4372 573905758 573905659 3.580000e-26 130.0
27 TraesCS2B01G568700 chr3A 92.391 92 6 1 4274 4365 711130465 711130375 3.580000e-26 130.0
28 TraesCS2B01G568700 chr7A 91.111 90 8 0 4277 4366 126927401 126927312 5.990000e-24 122.0
29 TraesCS2B01G568700 chr6B 100.000 28 0 0 231 258 422359726 422359699 8.000000e-03 52.8


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 TraesCS2B01G568700 chr2B 759447129 759451537 4408 True 8142.00 8142 100.00000 1 4409 1 chr2B.!!$R1 4408
1 TraesCS2B01G568700 chr2B 706724162 706727719 3557 False 382.40 1051 82.41800 673 4153 5 chr2B.!!$F1 3480
2 TraesCS2B01G568700 chr2A 751380373 751384630 4257 True 2886.20 5690 93.56150 3 4409 2 chr2A.!!$R2 4406
3 TraesCS2B01G568700 chr2A 719720773 719723932 3159 False 417.25 994 80.84925 673 3883 4 chr2A.!!$F1 3210
4 TraesCS2B01G568700 chr2D 619708285 619712170 3885 True 2877.15 5683 96.70150 429 4396 2 chr2D.!!$R2 3967
5 TraesCS2B01G568700 chr2D 585679407 585682995 3588 False 317.50 503 83.11900 689 4100 6 chr2D.!!$F2 3411

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
977 1023 0.250295 TCCACCAAGAAACGGAGCTG 60.250 55.0 0.0 0.0 0.0 4.24 F
2708 3221 0.108138 AGCGTTCATCCTTTCCTCCG 60.108 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2960 3506 0.533755 CTGGAGGATGATTCGTGGGC 60.534 60.0 0.0 0.0 0.0 5.36 R
4347 5003 0.178995 CCTACTACTCCCTCCGTCCC 60.179 65.0 0.0 0.0 0.0 4.46 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
19 20 1.486439 CCGAATGTTTGTGTGTTGGC 58.514 50.000 0.00 0.00 0.00 4.52
33 34 0.967380 GTTGGCTGGGCATGTAGCTT 60.967 55.000 15.09 0.00 44.79 3.74
35 36 1.379044 GGCTGGGCATGTAGCTTGT 60.379 57.895 15.09 0.00 44.79 3.16
44 45 3.848846 CATGTAGCTTGTCATGCGTAG 57.151 47.619 11.32 0.00 35.72 3.51
47 48 3.447742 TGTAGCTTGTCATGCGTAGATG 58.552 45.455 0.00 0.00 35.28 2.90
48 49 2.680312 AGCTTGTCATGCGTAGATGT 57.320 45.000 5.16 0.00 35.28 3.06
49 50 2.977914 AGCTTGTCATGCGTAGATGTT 58.022 42.857 5.16 0.00 35.28 2.71
50 51 2.674852 AGCTTGTCATGCGTAGATGTTG 59.325 45.455 5.16 0.00 35.28 3.33
59 60 1.726791 GCGTAGATGTTGGTGTGTGAG 59.273 52.381 0.00 0.00 0.00 3.51
61 62 2.766313 GTAGATGTTGGTGTGTGAGCA 58.234 47.619 0.00 0.00 0.00 4.26
85 86 4.003648 GTGGTGTATTTGGAAGTGAGAGG 58.996 47.826 0.00 0.00 0.00 3.69
95 96 1.551908 AAGTGAGAGGAGCAGCCCAG 61.552 60.000 3.08 0.00 37.37 4.45
101 102 1.357079 AGAGGAGCAGCCCAGAAAAAT 59.643 47.619 3.08 0.00 37.37 1.82
110 111 4.322198 GCAGCCCAGAAAAATGATTTCTCA 60.322 41.667 0.65 0.00 36.69 3.27
124 125 4.887655 TGATTTCTCACGGCAGATCTAGTA 59.112 41.667 0.00 0.00 0.00 1.82
132 133 3.942748 ACGGCAGATCTAGTATAGCTAGC 59.057 47.826 6.62 6.62 45.22 3.42
133 134 3.942115 CGGCAGATCTAGTATAGCTAGCA 59.058 47.826 18.83 3.19 45.22 3.49
198 199 4.639078 TGATCCAAAGGAAGTGTCATGA 57.361 40.909 0.00 0.00 34.34 3.07
209 210 8.463930 AAGGAAGTGTCATGATTTTAGTTCAA 57.536 30.769 0.00 0.00 0.00 2.69
217 218 9.474920 TGTCATGATTTTAGTTCAATTTTGACC 57.525 29.630 0.00 0.00 36.83 4.02
218 219 9.696917 GTCATGATTTTAGTTCAATTTTGACCT 57.303 29.630 0.00 0.00 36.83 3.85
249 250 9.865321 AAAATCATGACACTTATTTTGGATCTG 57.135 29.630 0.00 0.00 31.99 2.90
259 260 6.674419 ACTTATTTTGGATCTGAGGGAGTAGT 59.326 38.462 0.00 0.00 0.00 2.73
260 261 5.622346 ATTTTGGATCTGAGGGAGTAGTC 57.378 43.478 0.00 0.00 0.00 2.59
261 262 3.757947 TTGGATCTGAGGGAGTAGTCA 57.242 47.619 0.00 0.00 0.00 3.41
262 263 3.304911 TGGATCTGAGGGAGTAGTCAG 57.695 52.381 0.00 0.00 41.44 3.51
263 264 1.960689 GGATCTGAGGGAGTAGTCAGC 59.039 57.143 0.00 0.00 40.13 4.26
264 265 2.660572 GATCTGAGGGAGTAGTCAGCA 58.339 52.381 0.00 0.00 40.13 4.41
265 266 2.836636 TCTGAGGGAGTAGTCAGCAT 57.163 50.000 0.00 0.00 40.13 3.79
266 267 2.382882 TCTGAGGGAGTAGTCAGCATG 58.617 52.381 0.00 0.00 40.13 4.06
279 280 1.678970 AGCATGAGGTTTTCGGCCC 60.679 57.895 0.00 0.00 31.24 5.80
290 291 2.624364 GTTTTCGGCCCACTTTTCCTTA 59.376 45.455 0.00 0.00 0.00 2.69
294 295 3.881220 TCGGCCCACTTTTCCTTATAAG 58.119 45.455 5.43 5.43 0.00 1.73
306 307 5.759506 TTCCTTATAAGCAGAGTCTCTCG 57.240 43.478 6.99 0.00 35.36 4.04
308 309 3.568007 CCTTATAAGCAGAGTCTCTCGCT 59.432 47.826 16.47 16.47 40.12 4.93
314 315 2.094752 AGCAGAGTCTCTCGCTCTTTTC 60.095 50.000 16.47 0.00 40.97 2.29
329 330 5.507985 CGCTCTTTTCTCCATTCAAGGTTTT 60.508 40.000 0.00 0.00 0.00 2.43
330 331 6.283694 GCTCTTTTCTCCATTCAAGGTTTTT 58.716 36.000 0.00 0.00 0.00 1.94
331 332 6.201615 GCTCTTTTCTCCATTCAAGGTTTTTG 59.798 38.462 0.00 0.00 0.00 2.44
332 333 6.581712 TCTTTTCTCCATTCAAGGTTTTTGG 58.418 36.000 0.00 0.00 0.00 3.28
333 334 4.953940 TTCTCCATTCAAGGTTTTTGGG 57.046 40.909 0.00 0.00 0.00 4.12
334 335 4.191804 TCTCCATTCAAGGTTTTTGGGA 57.808 40.909 0.00 0.00 0.00 4.37
335 336 4.551671 TCTCCATTCAAGGTTTTTGGGAA 58.448 39.130 0.00 0.00 0.00 3.97
339 340 6.118852 TCCATTCAAGGTTTTTGGGAAAAAG 58.881 36.000 0.00 0.00 40.71 2.27
343 344 8.685427 CATTCAAGGTTTTTGGGAAAAAGAAAT 58.315 29.630 0.00 0.00 40.71 2.17
353 354 6.200878 TGGGAAAAAGAAATACTCACTCCT 57.799 37.500 0.00 0.00 0.00 3.69
355 356 6.715264 TGGGAAAAAGAAATACTCACTCCTTC 59.285 38.462 0.00 0.00 0.00 3.46
370 371 5.186992 TCACTCCTTCCGAAATTAGATGACA 59.813 40.000 0.00 0.00 0.00 3.58
372 373 4.766375 TCCTTCCGAAATTAGATGACACC 58.234 43.478 0.00 0.00 0.00 4.16
391 392 3.502123 CCCAAACGGGTGTATCCATAT 57.498 47.619 0.00 0.00 39.13 1.78
392 393 3.146066 CCCAAACGGGTGTATCCATATG 58.854 50.000 0.00 0.00 39.13 1.78
399 400 6.428083 ACGGGTGTATCCATATGTATTTCA 57.572 37.500 1.24 0.00 38.11 2.69
417 418 8.138074 TGTATTTCAGTGCTAGATACATCTGTC 58.862 37.037 1.88 0.00 37.76 3.51
418 419 6.782082 TTTCAGTGCTAGATACATCTGTCT 57.218 37.500 1.88 0.00 37.76 3.41
420 421 5.440610 TCAGTGCTAGATACATCTGTCTGA 58.559 41.667 1.88 7.40 37.76 3.27
424 425 4.640647 TGCTAGATACATCTGTCTGAACGT 59.359 41.667 1.88 0.00 37.76 3.99
425 426 5.209240 GCTAGATACATCTGTCTGAACGTC 58.791 45.833 1.88 0.00 37.76 4.34
426 427 5.220873 GCTAGATACATCTGTCTGAACGTCA 60.221 44.000 1.88 0.00 37.76 4.35
427 428 5.644977 AGATACATCTGTCTGAACGTCAA 57.355 39.130 0.00 0.00 35.42 3.18
440 441 4.370049 TGAACGTCAACTAATTTCGGACA 58.630 39.130 0.00 0.00 0.00 4.02
441 442 4.992319 TGAACGTCAACTAATTTCGGACAT 59.008 37.500 0.00 0.00 0.00 3.06
509 510 8.788325 AACCTTAACAACACTATGATAAGTCC 57.212 34.615 0.00 0.00 35.22 3.85
510 511 7.336396 ACCTTAACAACACTATGATAAGTCCC 58.664 38.462 0.00 0.00 35.22 4.46
532 533 4.152402 CCTTTCGTTGTTGGTAGTCATCTG 59.848 45.833 0.00 0.00 0.00 2.90
533 534 3.313012 TCGTTGTTGGTAGTCATCTGG 57.687 47.619 0.00 0.00 0.00 3.86
584 586 8.828688 AGACAATAAGAGGTTACTGTTACAAC 57.171 34.615 0.00 0.00 35.56 3.32
585 587 8.648693 AGACAATAAGAGGTTACTGTTACAACT 58.351 33.333 0.00 0.00 35.56 3.16
613 618 7.409465 ACAAGACAAGATCGAGAGTTAAAAC 57.591 36.000 0.00 0.00 0.00 2.43
618 623 5.927115 ACAAGATCGAGAGTTAAAACAGACC 59.073 40.000 0.00 0.00 0.00 3.85
629 634 1.125633 AAACAGACCACTACCGGTGT 58.874 50.000 19.93 10.78 43.94 4.16
630 635 4.988065 CAGACCACTACCGGTGTG 57.012 61.111 19.93 21.67 43.14 3.82
654 659 3.555917 ACGAGAGTGTTGTGTAGTAGC 57.444 47.619 0.00 0.00 46.97 3.58
677 685 3.316868 GCTCTACTCTAGTGATGTGGGTC 59.683 52.174 0.00 0.00 0.00 4.46
702 711 2.315925 ACGACCGCTTGATCATGATT 57.684 45.000 10.14 0.00 0.00 2.57
976 1022 0.693049 ATCCACCAAGAAACGGAGCT 59.307 50.000 0.00 0.00 0.00 4.09
977 1023 0.250295 TCCACCAAGAAACGGAGCTG 60.250 55.000 0.00 0.00 0.00 4.24
978 1024 0.535102 CCACCAAGAAACGGAGCTGT 60.535 55.000 0.00 0.00 0.00 4.40
1032 1082 2.515290 CTGATGCATGCCGCTCCA 60.515 61.111 16.68 4.92 43.06 3.86
1041 1091 2.060567 ATGCCGCTCCAGCCATGTAT 62.061 55.000 0.00 0.00 37.91 2.29
1323 1388 3.119096 GGCTTCGCCGACTGGAAC 61.119 66.667 0.00 0.00 39.62 3.62
1400 1465 1.366494 CGATTGATTCGCCGTTCGC 60.366 57.895 0.00 0.00 41.69 4.70
1423 1495 6.500041 GCCCGTGATCTCTTACTATCATATC 58.500 44.000 0.00 0.00 34.77 1.63
1872 2017 4.729918 GGCCAGACAGGTGCCAGG 62.730 72.222 0.00 0.00 44.70 4.45
1873 2018 4.729918 GCCAGACAGGTGCCAGGG 62.730 72.222 0.00 0.00 40.61 4.45
2142 2416 6.120220 AGTAGGTGGCTGATTGTAATTTACC 58.880 40.000 4.17 0.00 0.00 2.85
2345 2679 7.931015 AATCATAGATGGTTAGGTTAGGTCA 57.069 36.000 0.00 0.00 27.27 4.02
2346 2680 6.726490 TCATAGATGGTTAGGTTAGGTCAC 57.274 41.667 0.00 0.00 0.00 3.67
2427 2787 3.492102 AATACATAGACGCAAGCCCAT 57.508 42.857 0.00 0.00 45.62 4.00
2428 2788 2.526304 TACATAGACGCAAGCCCATC 57.474 50.000 0.00 0.00 45.62 3.51
2429 2789 0.179045 ACATAGACGCAAGCCCATCC 60.179 55.000 0.00 0.00 45.62 3.51
2432 2792 1.419381 TAGACGCAAGCCCATCCATA 58.581 50.000 0.00 0.00 45.62 2.74
2434 2794 1.160137 GACGCAAGCCCATCCATATC 58.840 55.000 0.00 0.00 45.62 1.63
2435 2795 0.603707 ACGCAAGCCCATCCATATCG 60.604 55.000 0.00 0.00 45.62 2.92
2436 2796 0.320683 CGCAAGCCCATCCATATCGA 60.321 55.000 0.00 0.00 0.00 3.59
2437 2797 1.676916 CGCAAGCCCATCCATATCGAT 60.677 52.381 2.16 2.16 0.00 3.59
2438 2798 1.741706 GCAAGCCCATCCATATCGATG 59.258 52.381 8.54 3.51 39.54 3.84
2439 2799 1.741706 CAAGCCCATCCATATCGATGC 59.258 52.381 8.54 0.00 38.68 3.91
2440 2800 0.986527 AGCCCATCCATATCGATGCA 59.013 50.000 8.54 0.00 38.68 3.96
2441 2801 1.562942 AGCCCATCCATATCGATGCAT 59.437 47.619 8.54 0.00 38.68 3.96
2654 3025 6.401394 TGCTAGATATATTGCACATGACCTC 58.599 40.000 0.00 0.00 0.00 3.85
2670 3046 3.243873 TGACCTCGAGTATCATCCAATGC 60.244 47.826 12.31 0.00 33.17 3.56
2708 3221 0.108138 AGCGTTCATCCTTTCCTCCG 60.108 55.000 0.00 0.00 0.00 4.63
3005 3551 0.179089 CCATTGGAGACCGAGCTCAG 60.179 60.000 15.40 4.66 36.62 3.35
3439 4027 0.739813 GGCTTGATGAACGTACGGCT 60.740 55.000 21.06 5.97 0.00 5.52
3463 4051 2.209838 TCCGATCGATCAGAAGCAAC 57.790 50.000 24.40 0.00 0.00 4.17
3464 4052 1.202417 TCCGATCGATCAGAAGCAACC 60.202 52.381 24.40 0.00 0.00 3.77
3535 4133 5.950758 ATCTCGTAGTAACAGCCTATGAG 57.049 43.478 9.39 9.39 44.51 2.90
3583 4181 4.528206 CCACCAAGGAAGGAAGCTTAATTT 59.472 41.667 0.00 0.00 41.22 1.82
3669 4267 8.972662 TCAGGTTCATCAGGGAATAATCTATA 57.027 34.615 0.00 0.00 0.00 1.31
3670 4268 9.566331 TCAGGTTCATCAGGGAATAATCTATAT 57.434 33.333 0.00 0.00 0.00 0.86
3701 4304 1.888512 GGATCTGCTAGCTGAGAGGAG 59.111 57.143 25.68 9.68 33.92 3.69
3702 4305 2.586425 GATCTGCTAGCTGAGAGGAGT 58.414 52.381 25.68 10.95 34.26 3.85
3704 4307 2.925724 TCTGCTAGCTGAGAGGAGTAC 58.074 52.381 19.26 0.00 34.26 2.73
3749 4352 2.393362 GATCGTCGTCGTCGTCGT 59.607 61.111 18.44 8.49 45.27 4.34
3750 4353 1.643785 GATCGTCGTCGTCGTCGTC 60.644 63.158 18.44 12.59 45.27 4.20
3753 4356 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
3754 4357 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
3763 4374 3.266964 TCGTCGTCGATCGGGTTT 58.733 55.556 16.41 0.00 41.35 3.27
3918 4550 8.957466 AGGATTTGTACTACCAAATAAAGAAGC 58.043 33.333 0.00 0.00 43.28 3.86
3951 4583 0.237761 GATTGATCTCAGCATGCGGC 59.762 55.000 13.45 0.00 45.30 6.53
3967 4599 1.379527 CGGCTTACACCTTTGGATCC 58.620 55.000 4.20 4.20 0.00 3.36
4141 4793 7.672983 ATGTGTTTCTTATTGTGTGGTCTAG 57.327 36.000 0.00 0.00 0.00 2.43
4157 4809 4.223032 TGGTCTAGGTTTCATTCCTCTCAC 59.777 45.833 0.00 0.00 36.60 3.51
4158 4810 4.468153 GGTCTAGGTTTCATTCCTCTCACT 59.532 45.833 0.00 0.00 36.60 3.41
4188 4840 1.332997 CGAGACAGGTCCCGTGTATAC 59.667 57.143 0.00 0.00 0.00 1.47
4289 4945 7.834068 TTGCATAACAAGTATTCTCTCTGTC 57.166 36.000 0.00 0.00 33.24 3.51
4290 4946 6.341316 TGCATAACAAGTATTCTCTCTGTCC 58.659 40.000 0.00 0.00 0.00 4.02
4291 4947 5.755861 GCATAACAAGTATTCTCTCTGTCCC 59.244 44.000 0.00 0.00 0.00 4.46
4292 4948 6.630413 GCATAACAAGTATTCTCTCTGTCCCA 60.630 42.308 0.00 0.00 0.00 4.37
4293 4949 7.504403 CATAACAAGTATTCTCTCTGTCCCAT 58.496 38.462 0.00 0.00 0.00 4.00
4294 4950 8.642432 CATAACAAGTATTCTCTCTGTCCCATA 58.358 37.037 0.00 0.00 0.00 2.74
4295 4951 7.496346 AACAAGTATTCTCTCTGTCCCATAA 57.504 36.000 0.00 0.00 0.00 1.90
4296 4952 7.682787 ACAAGTATTCTCTCTGTCCCATAAT 57.317 36.000 0.00 0.00 0.00 1.28
4297 4953 8.783660 ACAAGTATTCTCTCTGTCCCATAATA 57.216 34.615 0.00 0.00 0.00 0.98
4298 4954 9.386122 ACAAGTATTCTCTCTGTCCCATAATAT 57.614 33.333 0.00 0.00 0.00 1.28
4305 4961 8.112016 TCTCTCTGTCCCATAATATAAGAACG 57.888 38.462 0.00 0.00 0.00 3.95
4306 4962 7.724506 TCTCTCTGTCCCATAATATAAGAACGT 59.275 37.037 0.00 0.00 0.00 3.99
4307 4963 8.246430 TCTCTGTCCCATAATATAAGAACGTT 57.754 34.615 0.00 0.00 0.00 3.99
4308 4964 8.701895 TCTCTGTCCCATAATATAAGAACGTTT 58.298 33.333 0.46 0.00 0.00 3.60
4309 4965 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
4310 4966 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
4311 4967 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
4312 4968 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
4313 4969 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
4314 4970 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
4315 4971 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
4320 4976 3.580794 AGAACGTTTTTGACACTACGC 57.419 42.857 0.46 0.00 37.51 4.42
4321 4977 3.192466 AGAACGTTTTTGACACTACGCT 58.808 40.909 0.46 0.00 37.51 5.07
4322 4978 4.362279 AGAACGTTTTTGACACTACGCTA 58.638 39.130 0.46 0.00 37.51 4.26
4323 4979 4.443394 AGAACGTTTTTGACACTACGCTAG 59.557 41.667 0.46 0.00 37.51 3.42
4324 4980 3.709987 ACGTTTTTGACACTACGCTAGT 58.290 40.909 0.00 0.00 40.28 2.57
4336 4992 4.741342 ACTACGCTAGTGTAAAAATCGCT 58.259 39.130 16.56 0.00 37.69 4.93
4337 4993 5.166398 ACTACGCTAGTGTAAAAATCGCTT 58.834 37.500 16.56 0.00 37.69 4.68
4338 4994 5.636543 ACTACGCTAGTGTAAAAATCGCTTT 59.363 36.000 16.56 0.00 37.69 3.51
4339 4995 5.352643 ACGCTAGTGTAAAAATCGCTTTT 57.647 34.783 7.28 0.00 40.42 2.27
4340 4996 6.470557 ACGCTAGTGTAAAAATCGCTTTTA 57.529 33.333 7.28 0.00 38.26 1.52
4341 4997 7.068692 ACGCTAGTGTAAAAATCGCTTTTAT 57.931 32.000 7.28 0.00 40.68 1.40
4342 4998 8.188531 ACGCTAGTGTAAAAATCGCTTTTATA 57.811 30.769 7.28 0.00 40.68 0.98
4343 4999 8.823818 ACGCTAGTGTAAAAATCGCTTTTATAT 58.176 29.630 7.28 0.00 40.68 0.86
4344 5000 9.646336 CGCTAGTGTAAAAATCGCTTTTATATT 57.354 29.630 0.00 0.02 40.68 1.28
4353 5009 6.737254 AATCGCTTTTATATTATGGGACGG 57.263 37.500 0.00 0.00 0.00 4.79
4354 5010 5.471556 TCGCTTTTATATTATGGGACGGA 57.528 39.130 0.00 0.00 0.00 4.69
4355 5011 5.475719 TCGCTTTTATATTATGGGACGGAG 58.524 41.667 0.00 0.00 0.00 4.63
4356 5012 4.630069 CGCTTTTATATTATGGGACGGAGG 59.370 45.833 0.00 0.00 0.00 4.30
4357 5013 4.941873 GCTTTTATATTATGGGACGGAGGG 59.058 45.833 0.00 0.00 0.00 4.30
4358 5014 5.280317 GCTTTTATATTATGGGACGGAGGGA 60.280 44.000 0.00 0.00 0.00 4.20
4401 5057 4.692625 CGATGAAACTCACCTGAAAGTGAT 59.307 41.667 0.00 0.00 45.39 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.066908 AGCCAACACACAAACATTCGG 59.933 47.619 0.00 0.00 0.00 4.30
1 2 2.118683 CAGCCAACACACAAACATTCG 58.881 47.619 0.00 0.00 0.00 3.34
9 10 2.198150 ATGCCCAGCCAACACACA 59.802 55.556 0.00 0.00 0.00 3.72
19 20 1.674441 CATGACAAGCTACATGCCCAG 59.326 52.381 12.95 0.00 44.23 4.45
33 34 2.289382 ACACCAACATCTACGCATGACA 60.289 45.455 0.00 0.00 0.00 3.58
35 36 2.289382 ACACACCAACATCTACGCATGA 60.289 45.455 0.00 0.00 0.00 3.07
41 42 2.766313 TGCTCACACACCAACATCTAC 58.234 47.619 0.00 0.00 0.00 2.59
42 43 3.181455 ACTTGCTCACACACCAACATCTA 60.181 43.478 0.00 0.00 0.00 1.98
43 44 2.224606 CTTGCTCACACACCAACATCT 58.775 47.619 0.00 0.00 0.00 2.90
44 45 1.949525 ACTTGCTCACACACCAACATC 59.050 47.619 0.00 0.00 0.00 3.06
47 48 0.381801 CCACTTGCTCACACACCAAC 59.618 55.000 0.00 0.00 0.00 3.77
48 49 0.034574 ACCACTTGCTCACACACCAA 60.035 50.000 0.00 0.00 0.00 3.67
49 50 0.747644 CACCACTTGCTCACACACCA 60.748 55.000 0.00 0.00 0.00 4.17
50 51 0.748005 ACACCACTTGCTCACACACC 60.748 55.000 0.00 0.00 0.00 4.16
59 60 3.568007 TCACTTCCAAATACACCACTTGC 59.432 43.478 0.00 0.00 0.00 4.01
61 62 5.304686 TCTCACTTCCAAATACACCACTT 57.695 39.130 0.00 0.00 0.00 3.16
85 86 3.881937 AATCATTTTTCTGGGCTGCTC 57.118 42.857 0.00 0.00 0.00 4.26
95 96 5.046910 TCTGCCGTGAGAAATCATTTTTC 57.953 39.130 0.00 0.00 0.00 2.29
101 102 3.701542 ACTAGATCTGCCGTGAGAAATCA 59.298 43.478 5.18 0.00 0.00 2.57
124 125 3.922171 AAGCTCAAACCTGCTAGCTAT 57.078 42.857 17.23 0.00 44.30 2.97
132 133 4.037923 ACCAACACAATAAGCTCAAACCTG 59.962 41.667 0.00 0.00 0.00 4.00
133 134 4.215109 ACCAACACAATAAGCTCAAACCT 58.785 39.130 0.00 0.00 0.00 3.50
176 177 4.984295 TCATGACACTTCCTTTGGATCAA 58.016 39.130 0.00 0.00 0.00 2.57
177 178 4.639078 TCATGACACTTCCTTTGGATCA 57.361 40.909 0.00 0.00 0.00 2.92
185 186 8.641498 ATTGAACTAAAATCATGACACTTCCT 57.359 30.769 0.00 0.00 0.00 3.36
186 187 9.696917 AAATTGAACTAAAATCATGACACTTCC 57.303 29.630 0.00 0.00 0.00 3.46
233 234 5.749462 ACTCCCTCAGATCCAAAATAAGTG 58.251 41.667 0.00 0.00 0.00 3.16
236 237 6.672218 TGACTACTCCCTCAGATCCAAAATAA 59.328 38.462 0.00 0.00 0.00 1.40
243 244 1.960689 GCTGACTACTCCCTCAGATCC 59.039 57.143 0.00 0.00 36.75 3.36
246 247 2.024941 TCATGCTGACTACTCCCTCAGA 60.025 50.000 0.00 0.00 36.75 3.27
248 249 2.382882 CTCATGCTGACTACTCCCTCA 58.617 52.381 0.00 0.00 0.00 3.86
249 250 1.686052 CCTCATGCTGACTACTCCCTC 59.314 57.143 0.00 0.00 0.00 4.30
259 260 0.960364 GGCCGAAAACCTCATGCTGA 60.960 55.000 0.00 0.00 0.00 4.26
260 261 1.508088 GGCCGAAAACCTCATGCTG 59.492 57.895 0.00 0.00 0.00 4.41
261 262 1.678970 GGGCCGAAAACCTCATGCT 60.679 57.895 0.00 0.00 0.00 3.79
262 263 1.976474 TGGGCCGAAAACCTCATGC 60.976 57.895 0.00 0.00 0.00 4.06
263 264 0.609131 AGTGGGCCGAAAACCTCATG 60.609 55.000 0.00 0.00 0.00 3.07
264 265 0.112412 AAGTGGGCCGAAAACCTCAT 59.888 50.000 0.00 0.00 0.00 2.90
265 266 0.106419 AAAGTGGGCCGAAAACCTCA 60.106 50.000 0.00 0.00 0.00 3.86
266 267 1.000607 GAAAAGTGGGCCGAAAACCTC 60.001 52.381 0.00 0.00 0.00 3.85
267 268 1.037493 GAAAAGTGGGCCGAAAACCT 58.963 50.000 0.00 0.00 0.00 3.50
275 276 3.361786 TGCTTATAAGGAAAAGTGGGCC 58.638 45.455 14.28 0.00 0.00 5.80
279 280 7.327214 AGAGACTCTGCTTATAAGGAAAAGTG 58.673 38.462 19.84 8.54 0.00 3.16
290 291 2.930950 AGAGCGAGAGACTCTGCTTAT 58.069 47.619 22.24 15.03 41.03 1.73
294 295 2.094752 AGAAAAGAGCGAGAGACTCTGC 60.095 50.000 10.44 13.44 41.47 4.26
306 307 5.459536 AAACCTTGAATGGAGAAAAGAGC 57.540 39.130 0.00 0.00 0.00 4.09
308 309 6.407979 CCCAAAAACCTTGAATGGAGAAAAGA 60.408 38.462 0.00 0.00 32.82 2.52
314 315 4.953940 TTCCCAAAAACCTTGAATGGAG 57.046 40.909 0.00 0.00 32.82 3.86
329 330 6.610830 AGGAGTGAGTATTTCTTTTTCCCAA 58.389 36.000 0.00 0.00 0.00 4.12
330 331 6.200878 AGGAGTGAGTATTTCTTTTTCCCA 57.799 37.500 0.00 0.00 0.00 4.37
331 332 6.151312 GGAAGGAGTGAGTATTTCTTTTTCCC 59.849 42.308 0.00 0.00 0.00 3.97
332 333 6.128254 CGGAAGGAGTGAGTATTTCTTTTTCC 60.128 42.308 0.00 0.00 0.00 3.13
333 334 6.649557 TCGGAAGGAGTGAGTATTTCTTTTTC 59.350 38.462 0.00 0.00 0.00 2.29
334 335 6.531021 TCGGAAGGAGTGAGTATTTCTTTTT 58.469 36.000 0.00 0.00 0.00 1.94
335 336 6.110411 TCGGAAGGAGTGAGTATTTCTTTT 57.890 37.500 0.00 0.00 0.00 2.27
339 340 6.986904 AATTTCGGAAGGAGTGAGTATTTC 57.013 37.500 0.00 0.00 0.00 2.17
343 344 6.605995 TCATCTAATTTCGGAAGGAGTGAGTA 59.394 38.462 0.00 0.00 0.00 2.59
353 354 4.561500 TGGGTGTCATCTAATTTCGGAA 57.438 40.909 0.00 0.00 0.00 4.30
355 356 4.436852 CGTTTGGGTGTCATCTAATTTCGG 60.437 45.833 0.00 0.00 0.00 4.30
386 387 9.881649 ATGTATCTAGCACTGAAATACATATGG 57.118 33.333 7.80 0.00 40.14 2.74
391 392 8.011844 ACAGATGTATCTAGCACTGAAATACA 57.988 34.615 0.00 1.90 37.26 2.29
392 393 8.356657 AGACAGATGTATCTAGCACTGAAATAC 58.643 37.037 0.00 0.00 34.85 1.89
399 400 5.220951 CGTTCAGACAGATGTATCTAGCACT 60.221 44.000 0.00 0.00 34.85 4.40
414 415 4.446385 CCGAAATTAGTTGACGTTCAGACA 59.554 41.667 0.00 0.00 0.00 3.41
415 416 4.682860 TCCGAAATTAGTTGACGTTCAGAC 59.317 41.667 0.00 0.00 0.00 3.51
417 418 4.446385 TGTCCGAAATTAGTTGACGTTCAG 59.554 41.667 0.00 0.00 0.00 3.02
418 419 4.370049 TGTCCGAAATTAGTTGACGTTCA 58.630 39.130 0.00 0.00 0.00 3.18
420 421 5.579511 CCTATGTCCGAAATTAGTTGACGTT 59.420 40.000 0.00 0.00 0.00 3.99
424 425 6.942976 ACTTCCTATGTCCGAAATTAGTTGA 58.057 36.000 0.00 0.00 0.00 3.18
425 426 8.888579 ATACTTCCTATGTCCGAAATTAGTTG 57.111 34.615 0.00 0.00 0.00 3.16
426 427 9.326413 CAATACTTCCTATGTCCGAAATTAGTT 57.674 33.333 0.00 0.00 0.00 2.24
427 428 8.701895 TCAATACTTCCTATGTCCGAAATTAGT 58.298 33.333 0.00 0.00 0.00 2.24
509 510 4.152402 CAGATGACTACCAACAACGAAAGG 59.848 45.833 0.00 0.00 0.00 3.11
510 511 4.152402 CCAGATGACTACCAACAACGAAAG 59.848 45.833 0.00 0.00 0.00 2.62
532 533 1.440938 TTGCCGTATGCCGTAATGCC 61.441 55.000 0.00 0.00 40.16 4.40
533 534 0.378962 TTTGCCGTATGCCGTAATGC 59.621 50.000 0.00 0.00 40.16 3.56
548 550 5.710567 ACCTCTTATTGTCTTAGGGTTTTGC 59.289 40.000 0.00 0.00 0.00 3.68
583 585 6.174760 ACTCTCGATCTTGTCTTGTAGTAGT 58.825 40.000 0.00 0.00 0.00 2.73
584 586 6.671614 ACTCTCGATCTTGTCTTGTAGTAG 57.328 41.667 0.00 0.00 0.00 2.57
585 587 8.557592 TTAACTCTCGATCTTGTCTTGTAGTA 57.442 34.615 0.00 0.00 0.00 1.82
629 634 0.108377 ACACAACACTCTCGTGCACA 60.108 50.000 18.64 3.15 45.10 4.57
630 635 1.787155 CTACACAACACTCTCGTGCAC 59.213 52.381 6.82 6.82 45.10 4.57
652 657 2.616376 CACATCACTAGAGTAGAGCGCT 59.384 50.000 11.27 11.27 0.00 5.92
653 658 2.287308 CCACATCACTAGAGTAGAGCGC 60.287 54.545 0.00 0.00 0.00 5.92
654 659 2.292016 CCCACATCACTAGAGTAGAGCG 59.708 54.545 0.00 0.00 0.00 5.03
677 685 0.093026 GATCAAGCGGTCGTTGAACG 59.907 55.000 12.12 12.12 46.38 3.95
702 711 3.145286 TCAAATCGATCTGGTGCAACAA 58.855 40.909 5.64 0.00 39.98 2.83
960 1006 0.588252 CACAGCTCCGTTTCTTGGTG 59.412 55.000 0.00 0.00 0.00 4.17
976 1022 1.141665 CGATCTGCCGATCACCACA 59.858 57.895 17.00 0.00 45.11 4.17
977 1023 0.872021 GTCGATCTGCCGATCACCAC 60.872 60.000 17.00 7.33 45.11 4.16
978 1024 1.437573 GTCGATCTGCCGATCACCA 59.562 57.895 17.00 0.00 45.11 4.17
1026 1076 1.139989 CGTTATACATGGCTGGAGCG 58.860 55.000 0.00 0.00 43.26 5.03
1323 1388 4.319477 CGAACAACTCACATGTAAGGGTTG 60.319 45.833 21.41 21.41 39.58 3.77
1400 1465 7.631717 TGATATGATAGTAAGAGATCACGGG 57.368 40.000 0.00 0.00 34.98 5.28
1441 1527 4.340097 TCACGGGAGTATGTACTTATGTGG 59.660 45.833 14.18 0.00 44.67 4.17
1448 1552 2.100916 GCATGTCACGGGAGTATGTACT 59.899 50.000 12.06 0.00 44.67 2.73
1830 1975 3.386078 CCATCTGCTGGTACTGATACTGT 59.614 47.826 0.00 0.00 40.49 3.55
2058 2204 9.345517 CTGCTAGTAGAGTATCGTAGTAGTAAG 57.654 40.741 0.81 0.00 42.67 2.34
2234 2514 1.153823 CGACGGCGTCTCCATTCTT 60.154 57.895 33.90 0.00 34.01 2.52
2327 2661 5.836024 TTTGTGACCTAACCTAACCATCT 57.164 39.130 0.00 0.00 0.00 2.90
2344 2678 3.446161 AGATCCAAGTGGCATGATTTGTG 59.554 43.478 0.00 0.00 34.44 3.33
2345 2679 3.698040 GAGATCCAAGTGGCATGATTTGT 59.302 43.478 0.00 0.00 34.44 2.83
2346 2680 3.952323 AGAGATCCAAGTGGCATGATTTG 59.048 43.478 0.00 0.00 34.44 2.32
2401 2761 6.434965 TGGGCTTGCGTCTATGTATTATACTA 59.565 38.462 3.92 0.00 0.00 1.82
2402 2762 5.245301 TGGGCTTGCGTCTATGTATTATACT 59.755 40.000 3.92 0.00 0.00 2.12
2422 2782 2.048444 ATGCATCGATATGGATGGGC 57.952 50.000 23.98 14.14 42.04 5.36
2438 2798 4.023792 TCAATCGGTAAAGATGCATCATGC 60.024 41.667 27.81 18.37 45.29 4.06
2439 2799 5.678132 TCAATCGGTAAAGATGCATCATG 57.322 39.130 27.81 10.74 0.00 3.07
2440 2800 6.889301 AATCAATCGGTAAAGATGCATCAT 57.111 33.333 27.81 14.43 0.00 2.45
2441 2801 7.800155 TTAATCAATCGGTAAAGATGCATCA 57.200 32.000 27.81 5.22 0.00 3.07
2588 2959 1.752498 TGCATGCATGAAAAGCCTAGG 59.248 47.619 30.64 3.67 0.00 3.02
2643 3014 2.871182 TGATACTCGAGGTCATGTGC 57.129 50.000 18.41 0.00 0.00 4.57
2654 3025 1.501169 TGCGCATTGGATGATACTCG 58.499 50.000 5.66 0.00 0.00 4.18
2670 3046 2.475852 GCTTTTGCAGAGAAGAGATGCG 60.476 50.000 9.82 0.00 46.58 4.73
2708 3221 3.058155 TGATAGTAGATCTCGAAAGGCGC 60.058 47.826 0.00 0.00 40.61 6.53
2960 3506 0.533755 CTGGAGGATGATTCGTGGGC 60.534 60.000 0.00 0.00 0.00 5.36
3005 3551 2.669364 CAAGGTTGCAGAGACAAATGC 58.331 47.619 0.00 0.00 42.86 3.56
3463 4051 1.592669 GATCGATCTGTGCGTGGGG 60.593 63.158 18.29 0.00 0.00 4.96
3464 4052 1.592669 GGATCGATCTGTGCGTGGG 60.593 63.158 23.96 0.00 0.00 4.61
3485 4073 2.295070 TCAAGATCGAGGAACGTTGTCA 59.705 45.455 5.00 0.00 43.13 3.58
3517 4109 3.710326 TGCTCATAGGCTGTTACTACG 57.290 47.619 0.00 0.00 0.00 3.51
3535 4133 7.855904 GGTGCTACTACATGTTACAAATTATGC 59.144 37.037 2.30 0.00 0.00 3.14
3583 4181 9.494055 AGGTTCATCTAGCTTAGCCATATAATA 57.506 33.333 0.00 0.00 0.00 0.98
3669 4267 6.022315 AGCTAGCAGATCCCTTAGTCAATAT 58.978 40.000 18.83 0.00 0.00 1.28
3670 4268 5.244851 CAGCTAGCAGATCCCTTAGTCAATA 59.755 44.000 18.83 0.00 0.00 1.90
3701 4304 4.146616 CAGCGCGACATAATTCAGTAGTAC 59.853 45.833 12.10 0.00 0.00 2.73
3702 4305 4.035909 TCAGCGCGACATAATTCAGTAGTA 59.964 41.667 12.10 0.00 0.00 1.82
3704 4307 3.372060 TCAGCGCGACATAATTCAGTAG 58.628 45.455 12.10 0.00 0.00 2.57
3749 4352 1.744522 TCATACAAACCCGATCGACGA 59.255 47.619 18.66 0.00 45.77 4.20
3750 4353 2.197792 TCATACAAACCCGATCGACG 57.802 50.000 18.66 8.71 42.18 5.12
3753 4356 3.202906 ACCAATCATACAAACCCGATCG 58.797 45.455 8.51 8.51 0.00 3.69
3754 4357 4.398044 ACAACCAATCATACAAACCCGATC 59.602 41.667 0.00 0.00 0.00 3.69
3755 4358 4.340617 ACAACCAATCATACAAACCCGAT 58.659 39.130 0.00 0.00 0.00 4.18
3757 4360 4.513198 AACAACCAATCATACAAACCCG 57.487 40.909 0.00 0.00 0.00 5.28
3763 4374 5.536538 TGCAAACCTAACAACCAATCATACA 59.463 36.000 0.00 0.00 0.00 2.29
3918 4550 0.181114 TCAATCAAGGGGAGATGCCG 59.819 55.000 0.00 0.00 37.63 5.69
3951 4583 1.379527 GCCGGATCCAAAGGTGTAAG 58.620 55.000 13.41 0.00 0.00 2.34
3967 4599 0.314935 AAAACAAGAGCATGTGGCCG 59.685 50.000 0.00 0.00 46.50 6.13
4117 4769 6.655003 CCTAGACCACACAATAAGAAACACAT 59.345 38.462 0.00 0.00 0.00 3.21
4141 4793 3.425162 ACCAGTGAGAGGAATGAAACC 57.575 47.619 0.00 0.00 0.00 3.27
4157 4809 0.246635 CCTGTCTCGGTTGGTACCAG 59.753 60.000 15.65 3.79 45.31 4.00
4158 4810 0.470456 ACCTGTCTCGGTTGGTACCA 60.470 55.000 11.60 11.60 45.31 3.25
4172 4824 2.519771 TGAGTATACACGGGACCTGT 57.480 50.000 0.00 0.00 0.00 4.00
4177 4829 1.607148 CAGCGATGAGTATACACGGGA 59.393 52.381 5.50 0.00 0.00 5.14
4287 4943 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
4288 4944 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
4289 4945 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
4294 4950 7.953710 GCGTAGTGTCAAAAACGTTCTTATATT 59.046 33.333 0.00 0.00 37.64 1.28
4295 4951 7.330208 AGCGTAGTGTCAAAAACGTTCTTATAT 59.670 33.333 0.00 0.00 37.64 0.86
4296 4952 6.642131 AGCGTAGTGTCAAAAACGTTCTTATA 59.358 34.615 0.00 0.00 37.64 0.98
4297 4953 5.464389 AGCGTAGTGTCAAAAACGTTCTTAT 59.536 36.000 0.00 0.00 37.64 1.73
4298 4954 4.805192 AGCGTAGTGTCAAAAACGTTCTTA 59.195 37.500 0.00 0.00 37.64 2.10
4299 4955 3.619929 AGCGTAGTGTCAAAAACGTTCTT 59.380 39.130 0.00 0.00 37.64 2.52
4300 4956 3.192466 AGCGTAGTGTCAAAAACGTTCT 58.808 40.909 0.00 0.00 37.64 3.01
4301 4957 3.580794 AGCGTAGTGTCAAAAACGTTC 57.419 42.857 0.00 0.00 37.64 3.95
4302 4958 4.114794 ACTAGCGTAGTGTCAAAAACGTT 58.885 39.130 0.00 0.00 37.69 3.99
4303 4959 3.709987 ACTAGCGTAGTGTCAAAAACGT 58.290 40.909 0.00 0.00 37.69 3.99
4313 4969 7.830018 AAAAGCGATTTTTACACTAGCGTAGTG 60.830 37.037 5.38 17.89 44.53 2.74
4314 4970 4.741342 AGCGATTTTTACACTAGCGTAGT 58.259 39.130 0.00 0.00 40.28 2.73
4315 4971 5.697848 AAGCGATTTTTACACTAGCGTAG 57.302 39.130 0.00 0.00 0.00 3.51
4316 4972 6.470557 AAAAGCGATTTTTACACTAGCGTA 57.529 33.333 5.38 0.00 37.22 4.42
4317 4973 5.352643 AAAAGCGATTTTTACACTAGCGT 57.647 34.783 5.38 0.00 37.22 5.07
4318 4974 9.646336 AATATAAAAGCGATTTTTACACTAGCG 57.354 29.630 17.42 0.00 42.39 4.26
4327 4983 8.079809 CCGTCCCATAATATAAAAGCGATTTTT 58.920 33.333 17.42 9.71 41.68 1.94
4328 4984 7.446013 TCCGTCCCATAATATAAAAGCGATTTT 59.554 33.333 16.41 16.41 32.27 1.82
4329 4985 6.938030 TCCGTCCCATAATATAAAAGCGATTT 59.062 34.615 0.00 0.00 34.92 2.17
4330 4986 6.469410 TCCGTCCCATAATATAAAAGCGATT 58.531 36.000 0.00 0.00 0.00 3.34
4331 4987 6.045072 TCCGTCCCATAATATAAAAGCGAT 57.955 37.500 0.00 0.00 0.00 4.58
4332 4988 5.471556 TCCGTCCCATAATATAAAAGCGA 57.528 39.130 0.00 0.00 0.00 4.93
4333 4989 4.630069 CCTCCGTCCCATAATATAAAAGCG 59.370 45.833 0.00 0.00 0.00 4.68
4334 4990 4.941873 CCCTCCGTCCCATAATATAAAAGC 59.058 45.833 0.00 0.00 0.00 3.51
4335 4991 6.013639 ACTCCCTCCGTCCCATAATATAAAAG 60.014 42.308 0.00 0.00 0.00 2.27
4336 4992 5.847817 ACTCCCTCCGTCCCATAATATAAAA 59.152 40.000 0.00 0.00 0.00 1.52
4337 4993 5.408824 ACTCCCTCCGTCCCATAATATAAA 58.591 41.667 0.00 0.00 0.00 1.40
4338 4994 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4339 4995 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4340 4996 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4341 4997 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
4342 4998 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
4343 4999 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
4344 5000 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
4345 5001 1.145325 CTACTACTCCCTCCGTCCCAT 59.855 57.143 0.00 0.00 0.00 4.00
4346 5002 0.549950 CTACTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
4347 5003 0.178995 CCTACTACTCCCTCCGTCCC 60.179 65.000 0.00 0.00 0.00 4.46
4348 5004 0.178995 CCCTACTACTCCCTCCGTCC 60.179 65.000 0.00 0.00 0.00 4.79
4349 5005 0.178995 CCCCTACTACTCCCTCCGTC 60.179 65.000 0.00 0.00 0.00 4.79
4350 5006 0.923233 ACCCCTACTACTCCCTCCGT 60.923 60.000 0.00 0.00 0.00 4.69
4351 5007 1.073603 CTACCCCTACTACTCCCTCCG 59.926 61.905 0.00 0.00 0.00 4.63
4352 5008 2.142756 ACTACCCCTACTACTCCCTCC 58.857 57.143 0.00 0.00 0.00 4.30
4353 5009 5.394562 TTTACTACCCCTACTACTCCCTC 57.605 47.826 0.00 0.00 0.00 4.30
4354 5010 5.775268 CTTTTACTACCCCTACTACTCCCT 58.225 45.833 0.00 0.00 0.00 4.20
4355 5011 4.343526 GCTTTTACTACCCCTACTACTCCC 59.656 50.000 0.00 0.00 0.00 4.30
4356 5012 4.037327 CGCTTTTACTACCCCTACTACTCC 59.963 50.000 0.00 0.00 0.00 3.85
4357 5013 4.884164 TCGCTTTTACTACCCCTACTACTC 59.116 45.833 0.00 0.00 0.00 2.59
4358 5014 4.860022 TCGCTTTTACTACCCCTACTACT 58.140 43.478 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.