Multiple sequence alignment - TraesCS1D01G148400

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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 TraesCS1D01G148400 chr1D 100.000 5687 0 0 1 5687 204299315 204293629 0.000000e+00 10503.0
1 TraesCS1D01G148400 chr1D 82.171 129 21 2 15 142 462645836 462645963 6.020000e-20 110.0
2 TraesCS1D01G148400 chr1A 97.045 2335 49 12 2518 4839 259996383 259994056 0.000000e+00 3912.0
3 TraesCS1D01G148400 chr1A 91.504 1742 71 31 768 2481 259998076 259996384 0.000000e+00 2326.0
4 TraesCS1D01G148400 chr1A 90.372 779 63 6 1 777 260023846 260023078 0.000000e+00 1013.0
5 TraesCS1D01G148400 chr1A 84.195 348 19 19 5111 5436 259993358 259993025 7.160000e-79 305.0
6 TraesCS1D01G148400 chr1A 91.781 219 14 2 4831 5046 259993597 259993380 9.260000e-78 302.0
7 TraesCS1D01G148400 chr1B 96.359 1950 40 10 2927 4869 299975888 299973963 0.000000e+00 3179.0
8 TraesCS1D01G148400 chr1B 91.156 2205 80 35 704 2863 299978455 299976321 0.000000e+00 2885.0
9 TraesCS1D01G148400 chr1B 96.749 646 19 2 4826 5470 299973961 299973317 0.000000e+00 1075.0
10 TraesCS1D01G148400 chr1B 85.321 218 28 2 1 218 299982495 299982282 7.420000e-54 222.0
11 TraesCS1D01G148400 chr5D 99.107 224 0 1 5466 5687 179923931 179924154 8.880000e-108 401.0
12 TraesCS1D01G148400 chr5D 100.000 217 0 0 5471 5687 293149128 293149344 8.880000e-108 401.0
13 TraesCS1D01G148400 chr5D 100.000 215 0 0 5473 5687 214177740 214177526 1.150000e-106 398.0
14 TraesCS1D01G148400 chr5D 100.000 214 0 0 5474 5687 342160291 342160504 4.130000e-106 396.0
15 TraesCS1D01G148400 chr5D 82.237 152 18 8 1 148 13904823 13904677 7.740000e-24 122.0
16 TraesCS1D01G148400 chr3D 100.000 217 0 0 5471 5687 129451608 129451392 8.880000e-108 401.0
17 TraesCS1D01G148400 chr3D 76.923 182 33 6 333 509 4606207 4606384 1.690000e-15 95.3
18 TraesCS1D01G148400 chr3D 81.034 116 20 2 1 115 400184665 400184779 2.180000e-14 91.6
19 TraesCS1D01G148400 chr6D 100.000 216 0 0 5472 5687 101060 100845 3.190000e-107 399.0
20 TraesCS1D01G148400 chr6D 100.000 215 0 0 5473 5687 68362820 68363034 1.150000e-106 398.0
21 TraesCS1D01G148400 chr6D 100.000 215 0 0 5473 5687 433658409 433658195 1.150000e-106 398.0
22 TraesCS1D01G148400 chr6D 80.769 130 21 4 531 658 206587713 206587586 1.300000e-16 99.0
23 TraesCS1D01G148400 chr6D 80.000 130 22 4 531 658 341080574 341080701 6.070000e-15 93.5
24 TraesCS1D01G148400 chr6D 79.137 139 25 4 522 658 421886090 421886226 6.070000e-15 93.5
25 TraesCS1D01G148400 chr6D 82.407 108 15 4 552 657 21047398 21047503 2.180000e-14 91.6
26 TraesCS1D01G148400 chr6D 78.862 123 26 0 531 653 257598294 257598416 3.650000e-12 84.2
27 TraesCS1D01G148400 chrUn 100.000 214 0 0 5474 5687 90088877 90088664 4.130000e-106 396.0
28 TraesCS1D01G148400 chr7B 87.970 133 16 0 10 142 467454734 467454866 2.120000e-34 158.0
29 TraesCS1D01G148400 chr5B 81.119 143 25 2 1 142 13288388 13288247 4.660000e-21 113.0
30 TraesCS1D01G148400 chr5B 88.000 50 5 1 432 481 623164550 623164502 2.210000e-04 58.4
31 TraesCS1D01G148400 chr5B 88.000 50 5 1 432 481 626835530 626835482 2.210000e-04 58.4
32 TraesCS1D01G148400 chr4B 81.022 137 24 2 6 141 40166818 40166683 2.170000e-19 108.0
33 TraesCS1D01G148400 chr3B 92.105 76 6 0 6 81 597109473 597109398 2.170000e-19 108.0
34 TraesCS1D01G148400 chr7D 81.651 109 16 4 552 658 430111964 430111858 2.820000e-13 87.9
35 TraesCS1D01G148400 chr7A 81.651 109 16 4 552 658 16122465 16122571 2.820000e-13 87.9
36 TraesCS1D01G148400 chr6B 78.740 127 19 7 531 653 198989695 198989817 1.700000e-10 78.7


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 TraesCS1D01G148400 chr1D 204293629 204299315 5686 True 10503.00 10503 100.00000 1 5687 1 chr1D.!!$R1 5686
1 TraesCS1D01G148400 chr1A 259993025 259998076 5051 True 1711.25 3912 91.13125 768 5436 4 chr1A.!!$R2 4668
2 TraesCS1D01G148400 chr1A 260023078 260023846 768 True 1013.00 1013 90.37200 1 777 1 chr1A.!!$R1 776
3 TraesCS1D01G148400 chr1B 299973317 299982495 9178 True 1840.25 3179 92.39625 1 5470 4 chr1B.!!$R1 5469

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
524 3840 0.034089 ACCCCTTCAACAGCCATAGC 60.034 55.0 0.00 0.00 40.32 2.97 F
1039 4451 0.107459 CCTCTACAAGCCAAGCCTCC 60.107 60.0 0.00 0.00 0.00 4.30 F
2237 5656 0.040204 CATGGCCTCTCCCCTGTTTT 59.960 55.0 3.32 0.00 0.00 2.43 F
2497 5927 0.178909 ATGGCCCCAAATTGTCACCA 60.179 50.0 0.00 1.51 0.00 4.17 F
2854 6293 0.394352 GGGACAATGGGTGCAGGTAG 60.394 60.0 0.00 0.00 40.06 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 5017 0.454452 GCCGAAGCGTGAAATGGAAC 60.454 55.000 0.0 0.0 0.00 3.62 R
2854 6293 0.478507 CCCCCTCTCTCTCTCTCTCC 59.521 65.000 0.0 0.0 0.00 3.71 R
3784 7607 1.743772 CGATGGGAATTCGAGTGGCTT 60.744 52.381 0.0 0.0 38.88 4.35 R
4241 8070 1.600485 ACGGAAACAAAGCTAACACGG 59.400 47.619 0.0 0.0 0.00 4.94 R
4828 8666 1.467342 GGATCGCCCACTAAAACACAC 59.533 52.381 0.0 0.0 34.14 3.82 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
86 87 5.538813 TGGCGTAAGGTACAATATGAGAGAT 59.461 40.000 0.00 0.00 38.28 2.75
127 128 4.202727 TGCTCTCCTCCCTGCTTATATAGT 60.203 45.833 0.00 0.00 0.00 2.12
133 134 5.080337 CCTCCCTGCTTATATAGTGTGAGA 58.920 45.833 0.00 0.00 0.00 3.27
162 163 9.905713 GGAGGGTATTAAATGCTATTGATGATA 57.094 33.333 0.00 0.00 0.00 2.15
262 3497 2.287547 CCGCGCTATTAATTGCATTGGT 60.288 45.455 19.50 0.00 0.00 3.67
266 3501 3.552684 CGCTATTAATTGCATTGGTGGGG 60.553 47.826 19.50 0.00 0.00 4.96
267 3502 3.244181 GCTATTAATTGCATTGGTGGGGG 60.244 47.826 15.67 0.00 0.00 5.40
268 3503 2.630889 TTAATTGCATTGGTGGGGGA 57.369 45.000 0.00 0.00 0.00 4.81
269 3504 2.157640 TAATTGCATTGGTGGGGGAG 57.842 50.000 0.00 0.00 0.00 4.30
270 3505 0.618393 AATTGCATTGGTGGGGGAGG 60.618 55.000 0.00 0.00 0.00 4.30
271 3506 2.534594 ATTGCATTGGTGGGGGAGGG 62.535 60.000 0.00 0.00 0.00 4.30
294 3529 2.100916 TGAAATCCTAGAGTGTAGCCGC 59.899 50.000 0.00 0.00 0.00 6.53
301 3536 2.995574 AGTGTAGCCGCCCGACTT 60.996 61.111 0.00 0.00 0.00 3.01
314 3549 2.872038 GCCCGACTTTTGAGTCATGTCT 60.872 50.000 14.96 0.00 38.65 3.41
332 3567 2.673368 GTCTGTTAGAGGTGGCAATTCG 59.327 50.000 0.00 0.00 0.00 3.34
349 3585 5.337554 CAATTCGATCGTAGACACTTGGTA 58.662 41.667 15.94 0.00 42.51 3.25
351 3587 2.679837 TCGATCGTAGACACTTGGTACC 59.320 50.000 15.94 4.43 42.51 3.34
393 3629 5.116882 GGTATCTCATGTCTTGGGTTGTAC 58.883 45.833 0.00 0.00 0.00 2.90
481 3720 1.680249 GCCTTAGGCTGGGCTATATGC 60.680 57.143 17.16 4.95 46.69 3.14
482 3721 1.406069 CCTTAGGCTGGGCTATATGCG 60.406 57.143 0.00 0.00 44.05 4.73
497 3736 5.347907 GCTATATGCGTGTGTAGGTTTATCC 59.652 44.000 0.00 0.00 0.00 2.59
499 3738 1.624312 TGCGTGTGTAGGTTTATCCCA 59.376 47.619 0.00 0.00 36.75 4.37
524 3840 0.034089 ACCCCTTCAACAGCCATAGC 60.034 55.000 0.00 0.00 40.32 2.97
547 3863 5.278315 GCACACTCTCCGGTTTCTTTTATTT 60.278 40.000 0.00 0.00 0.00 1.40
595 3911 9.961266 GTCAAACTTTGTAAATTTTAACCACAC 57.039 29.630 0.00 0.00 0.00 3.82
597 3913 9.965748 CAAACTTTGTAAATTTTAACCACACTG 57.034 29.630 0.00 0.00 0.00 3.66
692 4039 7.759433 TGTCTTGTGAAAGTTGAATTTCTTTCC 59.241 33.333 19.28 14.32 44.88 3.13
694 4041 7.975616 TCTTGTGAAAGTTGAATTTCTTTCCAG 59.024 33.333 19.28 14.97 44.88 3.86
695 4042 7.169158 TGTGAAAGTTGAATTTCTTTCCAGT 57.831 32.000 19.28 0.00 44.88 4.00
699 4046 8.405531 TGAAAGTTGAATTTCTTTCCAGTACTG 58.594 33.333 16.34 16.34 44.88 2.74
731 4108 3.544698 AAAGGGACAGGAGTGAGAGTA 57.455 47.619 0.00 0.00 0.00 2.59
760 4137 1.477685 AACACCCGTCACTACCCCAG 61.478 60.000 0.00 0.00 0.00 4.45
765 4142 1.375523 CGTCACTACCCCAGCAACC 60.376 63.158 0.00 0.00 0.00 3.77
791 4168 0.748450 ACAAGCAAATGCACACAGCT 59.252 45.000 8.28 0.00 45.94 4.24
844 4226 4.201802 GCGCCCCACATAAAAATGAAAATG 60.202 41.667 0.00 0.00 0.00 2.32
1034 4446 2.626840 GCTCTTCCTCTACAAGCCAAG 58.373 52.381 0.00 0.00 0.00 3.61
1035 4447 2.626840 CTCTTCCTCTACAAGCCAAGC 58.373 52.381 0.00 0.00 0.00 4.01
1036 4448 1.279271 TCTTCCTCTACAAGCCAAGCC 59.721 52.381 0.00 0.00 0.00 4.35
1037 4449 1.280421 CTTCCTCTACAAGCCAAGCCT 59.720 52.381 0.00 0.00 0.00 4.58
1038 4450 0.905357 TCCTCTACAAGCCAAGCCTC 59.095 55.000 0.00 0.00 0.00 4.70
1039 4451 0.107459 CCTCTACAAGCCAAGCCTCC 60.107 60.000 0.00 0.00 0.00 4.30
1040 4452 0.107459 CTCTACAAGCCAAGCCTCCC 60.107 60.000 0.00 0.00 0.00 4.30
1041 4453 1.077429 CTACAAGCCAAGCCTCCCC 60.077 63.158 0.00 0.00 0.00 4.81
1042 4454 1.541368 TACAAGCCAAGCCTCCCCT 60.541 57.895 0.00 0.00 0.00 4.79
1110 4522 1.441732 CGCCTACCAATTTACCCGCC 61.442 60.000 0.00 0.00 0.00 6.13
1488 4900 4.181010 CCATGGGGAGGTGAGCCG 62.181 72.222 2.85 0.00 40.50 5.52
1489 4901 4.864334 CATGGGGAGGTGAGCCGC 62.864 72.222 0.00 0.00 40.50 6.53
1608 5021 3.391506 AAGCTTTGGATTGCTTGTTCC 57.608 42.857 0.00 0.00 46.25 3.62
1614 5027 4.952071 TTGGATTGCTTGTTCCATTTCA 57.048 36.364 0.00 0.00 41.52 2.69
1631 5044 2.022129 CACGCTTCGGCTCGTTTCT 61.022 57.895 0.00 0.00 36.73 2.52
1659 5072 3.489738 CCTTGTCAGTTTGGCTTGTTCTG 60.490 47.826 0.00 0.00 0.00 3.02
1721 5134 9.261035 TGCTATTTTCCCCAATATCTTTGTTAA 57.739 29.630 0.00 0.00 0.00 2.01
1722 5135 9.750125 GCTATTTTCCCCAATATCTTTGTTAAG 57.250 33.333 0.00 0.00 0.00 1.85
1723 5136 9.750125 CTATTTTCCCCAATATCTTTGTTAAGC 57.250 33.333 0.00 0.00 0.00 3.09
1726 5139 6.773976 TCCCCAATATCTTTGTTAAGCTTG 57.226 37.500 9.86 0.00 0.00 4.01
1727 5140 5.656416 TCCCCAATATCTTTGTTAAGCTTGG 59.344 40.000 9.86 0.00 36.25 3.61
1728 5141 5.351458 CCCAATATCTTTGTTAAGCTTGGC 58.649 41.667 9.86 1.97 35.75 4.52
1729 5142 5.127682 CCCAATATCTTTGTTAAGCTTGGCT 59.872 40.000 9.86 0.00 42.56 4.75
1730 5143 6.038356 CCAATATCTTTGTTAAGCTTGGCTG 58.962 40.000 9.86 0.00 39.62 4.85
1779 5197 6.311690 GCTAACTCTTCTTTCGCTATTTGAGT 59.688 38.462 0.00 0.00 35.40 3.41
1857 5275 7.500992 TCTTTTCTCTAGTGTGAGTGTTGAAT 58.499 34.615 0.00 0.00 35.68 2.57
1944 5362 9.554395 TCCAAAAATTTATTCCAAGAAACTTCC 57.446 29.630 0.00 0.00 0.00 3.46
2035 5453 8.909423 ATTTATCTCAAGAAACCCCCAATTTA 57.091 30.769 0.00 0.00 0.00 1.40
2048 5466 8.679344 AACCCCCAATTTATTTCTATGTTTCT 57.321 30.769 0.00 0.00 0.00 2.52
2078 5496 0.755327 AGTGAAGTTGTTGCACCCCC 60.755 55.000 0.00 0.00 33.14 5.40
2079 5497 1.040339 GTGAAGTTGTTGCACCCCCA 61.040 55.000 0.00 0.00 0.00 4.96
2080 5498 0.324738 TGAAGTTGTTGCACCCCCAA 60.325 50.000 0.00 0.00 0.00 4.12
2081 5499 0.827368 GAAGTTGTTGCACCCCCAAA 59.173 50.000 0.00 0.00 0.00 3.28
2082 5500 1.208293 GAAGTTGTTGCACCCCCAAAA 59.792 47.619 0.00 0.00 0.00 2.44
2083 5501 0.539518 AGTTGTTGCACCCCCAAAAC 59.460 50.000 0.00 0.00 0.00 2.43
2084 5502 0.539518 GTTGTTGCACCCCCAAAACT 59.460 50.000 0.00 0.00 0.00 2.66
2085 5503 0.827368 TTGTTGCACCCCCAAAACTC 59.173 50.000 0.00 0.00 0.00 3.01
2234 5653 2.693864 CCATGGCCTCTCCCCTGT 60.694 66.667 3.32 0.00 0.00 4.00
2235 5654 2.311854 CCATGGCCTCTCCCCTGTT 61.312 63.158 3.32 0.00 0.00 3.16
2236 5655 1.693640 CATGGCCTCTCCCCTGTTT 59.306 57.895 3.32 0.00 0.00 2.83
2237 5656 0.040204 CATGGCCTCTCCCCTGTTTT 59.960 55.000 3.32 0.00 0.00 2.43
2238 5657 0.786435 ATGGCCTCTCCCCTGTTTTT 59.214 50.000 3.32 0.00 0.00 1.94
2255 5674 3.312736 TTTTTCTTTGCTCTCCCCTGT 57.687 42.857 0.00 0.00 0.00 4.00
2321 5748 7.011669 CCAATATTTTAGCAATCAAAAGCCCTG 59.988 37.037 0.00 0.00 0.00 4.45
2497 5927 0.178909 ATGGCCCCAAATTGTCACCA 60.179 50.000 0.00 1.51 0.00 4.17
2508 5938 5.122082 CCAAATTGTCACCACCATTAAATGC 59.878 40.000 0.00 0.00 0.00 3.56
2854 6293 0.394352 GGGACAATGGGTGCAGGTAG 60.394 60.000 0.00 0.00 40.06 3.18
2855 6294 0.394352 GGACAATGGGTGCAGGTAGG 60.394 60.000 0.00 0.00 37.84 3.18
2856 6295 0.618458 GACAATGGGTGCAGGTAGGA 59.382 55.000 0.00 0.00 0.00 2.94
2857 6296 0.620556 ACAATGGGTGCAGGTAGGAG 59.379 55.000 0.00 0.00 0.00 3.69
3477 7298 4.142038 ACTAACCTTAGGCAAGTTTGGTG 58.858 43.478 0.00 0.00 28.80 4.17
3646 7469 6.154363 CAGGTGATTTTTCCCCTTTTGCTATA 59.846 38.462 0.00 0.00 0.00 1.31
3784 7607 1.073763 CCTGGATCCACAACAAGACCA 59.926 52.381 11.44 0.00 0.00 4.02
3996 7825 3.405831 CAGTGAAGAATGCCAACTCAGA 58.594 45.455 0.00 0.00 0.00 3.27
4304 8133 3.034635 CCTGTAGTAGCCTCAATGGTCT 58.965 50.000 0.00 0.00 38.35 3.85
4348 8177 4.431378 TGAGTTACACCCTAATCCCTCAA 58.569 43.478 0.00 0.00 0.00 3.02
4658 8490 1.093159 GCATCTTGCTCAGTCAAGGG 58.907 55.000 8.44 4.11 42.68 3.95
4754 8589 0.108424 GCTACTGCTACTGCTGCTGT 60.108 55.000 16.37 16.37 43.23 4.40
4785 8622 3.054802 AGCCTGGATTCTACTTGGAGTTG 60.055 47.826 0.00 0.00 0.00 3.16
4787 8624 4.256920 CCTGGATTCTACTTGGAGTTGTG 58.743 47.826 0.00 0.00 0.00 3.33
4828 8666 4.154556 TGTGCATTGTGATGTGTGATACAG 59.845 41.667 0.00 0.00 43.80 2.74
4913 9218 2.029518 GGGCTTGTTGCACTTGCC 59.970 61.111 9.82 9.82 43.01 4.52
4959 9267 4.632153 ACTCTGCTGTTAAACTGGTAGTG 58.368 43.478 0.00 0.00 0.00 2.74
5008 9316 1.702957 CCCCTTTTGGTGTCTGGTCTA 59.297 52.381 0.00 0.00 38.10 2.59
5014 9322 1.304713 GGTGTCTGGTCTACGGGGA 60.305 63.158 0.00 0.00 0.00 4.81
5015 9323 1.321074 GGTGTCTGGTCTACGGGGAG 61.321 65.000 0.00 0.00 0.00 4.30
5252 9561 6.875076 TCTGTATCTGTAAGGTTTAGGCTTC 58.125 40.000 0.00 0.00 0.00 3.86
5470 9801 6.884836 GGTACCACCTCTGTTCTGAATTATTT 59.115 38.462 7.15 0.00 34.73 1.40
5471 9802 7.393515 GGTACCACCTCTGTTCTGAATTATTTT 59.606 37.037 7.15 0.00 34.73 1.82
5472 9803 7.839680 ACCACCTCTGTTCTGAATTATTTTT 57.160 32.000 0.00 0.00 0.00 1.94
5500 9831 9.973450 TTTTTCGATAAAGGACATTTCATTGAA 57.027 25.926 0.00 0.00 32.01 2.69
5504 9835 9.830975 TCGATAAAGGACATTTCATTGAATAGA 57.169 29.630 0.00 0.00 32.01 1.98
5540 9871 7.315142 TGATACAATCATGTCAAAAGAAAGCC 58.685 34.615 0.00 0.00 41.05 4.35
5541 9872 4.886579 ACAATCATGTCAAAAGAAAGCCC 58.113 39.130 0.00 0.00 33.41 5.19
5542 9873 3.855689 ATCATGTCAAAAGAAAGCCCG 57.144 42.857 0.00 0.00 0.00 6.13
5543 9874 1.885887 TCATGTCAAAAGAAAGCCCGG 59.114 47.619 0.00 0.00 0.00 5.73
5544 9875 0.603065 ATGTCAAAAGAAAGCCCGGC 59.397 50.000 0.00 0.00 0.00 6.13
5545 9876 1.289066 GTCAAAAGAAAGCCCGGCC 59.711 57.895 5.55 0.00 0.00 6.13
5546 9877 1.152830 TCAAAAGAAAGCCCGGCCT 59.847 52.632 5.55 0.00 0.00 5.19
5547 9878 0.893727 TCAAAAGAAAGCCCGGCCTC 60.894 55.000 5.55 3.17 0.00 4.70
5548 9879 0.895559 CAAAAGAAAGCCCGGCCTCT 60.896 55.000 5.55 5.76 0.00 3.69
5549 9880 0.895559 AAAAGAAAGCCCGGCCTCTG 60.896 55.000 5.55 0.00 0.00 3.35
5550 9881 3.927481 AAGAAAGCCCGGCCTCTGC 62.927 63.158 5.55 0.00 0.00 4.26
5551 9882 4.722700 GAAAGCCCGGCCTCTGCA 62.723 66.667 5.55 0.00 40.13 4.41
5552 9883 4.052518 AAAGCCCGGCCTCTGCAT 62.053 61.111 5.55 0.00 40.13 3.96
5553 9884 2.608970 GAAAGCCCGGCCTCTGCATA 62.609 60.000 5.55 0.00 40.13 3.14
5554 9885 2.615227 AAAGCCCGGCCTCTGCATAG 62.615 60.000 5.55 0.00 40.13 2.23
5556 9887 3.554342 CCCGGCCTCTGCATAGCT 61.554 66.667 0.00 0.00 40.13 3.32
5557 9888 2.210013 CCCGGCCTCTGCATAGCTA 61.210 63.158 0.00 0.00 40.13 3.32
5558 9889 1.291588 CCGGCCTCTGCATAGCTAG 59.708 63.158 0.00 0.00 40.13 3.42
5559 9890 1.181741 CCGGCCTCTGCATAGCTAGA 61.182 60.000 0.00 0.00 40.13 2.43
5560 9891 0.894141 CGGCCTCTGCATAGCTAGAT 59.106 55.000 0.00 0.00 40.13 1.98
5561 9892 1.403914 CGGCCTCTGCATAGCTAGATG 60.404 57.143 0.00 0.00 40.13 2.90
5570 9901 2.141517 CATAGCTAGATGCACACAGCC 58.858 52.381 10.69 0.00 45.94 4.85
5571 9902 1.194218 TAGCTAGATGCACACAGCCA 58.806 50.000 10.69 0.00 45.94 4.75
5572 9903 0.325933 AGCTAGATGCACACAGCCAA 59.674 50.000 10.69 0.00 45.94 4.52
5573 9904 1.167851 GCTAGATGCACACAGCCAAA 58.832 50.000 0.00 0.00 44.83 3.28
5574 9905 1.541147 GCTAGATGCACACAGCCAAAA 59.459 47.619 0.00 0.00 44.83 2.44
5575 9906 2.030007 GCTAGATGCACACAGCCAAAAA 60.030 45.455 0.00 0.00 44.83 1.94
5595 9926 6.686484 AAAAATCCAGAGCACCCTAAAAAT 57.314 33.333 0.00 0.00 0.00 1.82
5596 9927 7.790782 AAAAATCCAGAGCACCCTAAAAATA 57.209 32.000 0.00 0.00 0.00 1.40
5597 9928 7.790782 AAAATCCAGAGCACCCTAAAAATAA 57.209 32.000 0.00 0.00 0.00 1.40
5598 9929 7.790782 AAATCCAGAGCACCCTAAAAATAAA 57.209 32.000 0.00 0.00 0.00 1.40
5599 9930 7.790782 AATCCAGAGCACCCTAAAAATAAAA 57.209 32.000 0.00 0.00 0.00 1.52
5600 9931 7.978099 ATCCAGAGCACCCTAAAAATAAAAT 57.022 32.000 0.00 0.00 0.00 1.82
5601 9932 9.487442 AATCCAGAGCACCCTAAAAATAAAATA 57.513 29.630 0.00 0.00 0.00 1.40
5602 9933 8.887264 TCCAGAGCACCCTAAAAATAAAATAA 57.113 30.769 0.00 0.00 0.00 1.40
5603 9934 9.487442 TCCAGAGCACCCTAAAAATAAAATAAT 57.513 29.630 0.00 0.00 0.00 1.28
5621 9952 8.789825 AAAATAATTTGATACAATGCCAAGCA 57.210 26.923 0.00 0.00 44.86 3.91
5622 9953 8.789825 AAATAATTTGATACAATGCCAAGCAA 57.210 26.923 0.00 0.00 43.62 3.91
5623 9954 8.967664 AATAATTTGATACAATGCCAAGCAAT 57.032 26.923 0.00 0.00 43.62 3.56
5626 9957 8.789825 AATTTGATACAATGCCAAGCAATAAA 57.210 26.923 0.00 0.00 43.62 1.40
5627 9958 8.967664 ATTTGATACAATGCCAAGCAATAAAT 57.032 26.923 0.00 0.00 43.62 1.40
5628 9959 8.422973 TTTGATACAATGCCAAGCAATAAATC 57.577 30.769 0.00 0.00 43.62 2.17
5629 9960 6.207928 TGATACAATGCCAAGCAATAAATCG 58.792 36.000 0.00 0.00 43.62 3.34
5630 9961 4.454728 ACAATGCCAAGCAATAAATCGT 57.545 36.364 0.00 0.00 43.62 3.73
5631 9962 4.175516 ACAATGCCAAGCAATAAATCGTG 58.824 39.130 0.00 0.00 43.62 4.35
5632 9963 4.175516 CAATGCCAAGCAATAAATCGTGT 58.824 39.130 0.00 0.00 43.62 4.49
5633 9964 3.485947 TGCCAAGCAATAAATCGTGTC 57.514 42.857 0.00 0.00 34.76 3.67
5634 9965 2.163412 TGCCAAGCAATAAATCGTGTCC 59.837 45.455 0.00 0.00 34.76 4.02
5635 9966 2.163412 GCCAAGCAATAAATCGTGTCCA 59.837 45.455 0.00 0.00 0.00 4.02
5636 9967 3.731867 GCCAAGCAATAAATCGTGTCCAG 60.732 47.826 0.00 0.00 0.00 3.86
5637 9968 3.429085 CAAGCAATAAATCGTGTCCAGC 58.571 45.455 0.00 0.00 0.00 4.85
5638 9969 2.017049 AGCAATAAATCGTGTCCAGCC 58.983 47.619 0.00 0.00 0.00 4.85
5639 9970 2.017049 GCAATAAATCGTGTCCAGCCT 58.983 47.619 0.00 0.00 0.00 4.58
5640 9971 3.118408 AGCAATAAATCGTGTCCAGCCTA 60.118 43.478 0.00 0.00 0.00 3.93
5641 9972 3.625764 GCAATAAATCGTGTCCAGCCTAA 59.374 43.478 0.00 0.00 0.00 2.69
5642 9973 4.260784 GCAATAAATCGTGTCCAGCCTAAG 60.261 45.833 0.00 0.00 0.00 2.18
5643 9974 2.403252 AAATCGTGTCCAGCCTAAGG 57.597 50.000 0.00 0.00 0.00 2.69
5644 9975 1.568504 AATCGTGTCCAGCCTAAGGA 58.431 50.000 0.00 0.00 0.00 3.36
5645 9976 1.115467 ATCGTGTCCAGCCTAAGGAG 58.885 55.000 0.00 0.00 35.42 3.69
5646 9977 1.153549 CGTGTCCAGCCTAAGGAGC 60.154 63.158 0.00 0.00 35.42 4.70
5647 9978 1.153549 GTGTCCAGCCTAAGGAGCG 60.154 63.158 0.00 0.00 35.42 5.03
5648 9979 2.359169 TGTCCAGCCTAAGGAGCGG 61.359 63.158 0.00 0.00 35.42 5.52
5649 9980 2.038975 TCCAGCCTAAGGAGCGGT 59.961 61.111 0.00 0.00 34.64 5.68
5650 9981 1.041447 GTCCAGCCTAAGGAGCGGTA 61.041 60.000 0.00 0.00 35.42 4.02
5651 9982 0.324923 TCCAGCCTAAGGAGCGGTAA 60.325 55.000 0.00 0.00 34.64 2.85
5652 9983 0.539986 CCAGCCTAAGGAGCGGTAAA 59.460 55.000 0.00 0.00 34.64 2.01
5653 9984 1.141053 CCAGCCTAAGGAGCGGTAAAT 59.859 52.381 0.00 0.00 34.64 1.40
5654 9985 2.484889 CAGCCTAAGGAGCGGTAAATC 58.515 52.381 0.00 0.00 34.64 2.17
5655 9986 1.416772 AGCCTAAGGAGCGGTAAATCC 59.583 52.381 0.00 0.00 35.71 3.01
5657 9988 2.631545 GCCTAAGGAGCGGTAAATCCTA 59.368 50.000 0.00 0.00 45.39 2.94
5658 9989 3.261137 GCCTAAGGAGCGGTAAATCCTAT 59.739 47.826 0.00 0.00 45.39 2.57
5659 9990 4.621038 GCCTAAGGAGCGGTAAATCCTATC 60.621 50.000 0.00 0.00 45.39 2.08
5660 9991 4.081586 CCTAAGGAGCGGTAAATCCTATCC 60.082 50.000 0.00 0.00 45.39 2.59
5661 9992 1.893801 AGGAGCGGTAAATCCTATCCG 59.106 52.381 0.00 0.00 44.28 4.18
5662 9993 1.617357 GGAGCGGTAAATCCTATCCGT 59.383 52.381 0.00 0.00 44.07 4.69
5663 9994 2.821969 GGAGCGGTAAATCCTATCCGTA 59.178 50.000 0.00 0.00 44.07 4.02
5664 9995 3.256631 GGAGCGGTAAATCCTATCCGTAA 59.743 47.826 0.00 0.00 44.07 3.18
5665 9996 4.262164 GGAGCGGTAAATCCTATCCGTAAA 60.262 45.833 0.00 0.00 44.07 2.01
5666 9997 5.476614 GAGCGGTAAATCCTATCCGTAAAT 58.523 41.667 0.00 0.00 44.07 1.40
5667 9998 5.476614 AGCGGTAAATCCTATCCGTAAATC 58.523 41.667 0.00 0.00 44.07 2.17
5668 9999 5.011329 AGCGGTAAATCCTATCCGTAAATCA 59.989 40.000 0.00 0.00 44.07 2.57
5669 10000 5.119743 GCGGTAAATCCTATCCGTAAATCAC 59.880 44.000 0.00 0.00 44.07 3.06
5670 10001 6.218019 CGGTAAATCCTATCCGTAAATCACA 58.782 40.000 0.00 0.00 38.45 3.58
5671 10002 6.145048 CGGTAAATCCTATCCGTAAATCACAC 59.855 42.308 0.00 0.00 38.45 3.82
5672 10003 6.426025 GGTAAATCCTATCCGTAAATCACACC 59.574 42.308 0.00 0.00 0.00 4.16
5673 10004 3.720949 TCCTATCCGTAAATCACACCG 57.279 47.619 0.00 0.00 0.00 4.94
5674 10005 2.132762 CCTATCCGTAAATCACACCGC 58.867 52.381 0.00 0.00 0.00 5.68
5675 10006 2.132762 CTATCCGTAAATCACACCGCC 58.867 52.381 0.00 0.00 0.00 6.13
5676 10007 0.250793 ATCCGTAAATCACACCGCCA 59.749 50.000 0.00 0.00 0.00 5.69
5677 10008 0.250793 TCCGTAAATCACACCGCCAT 59.749 50.000 0.00 0.00 0.00 4.40
5678 10009 0.655733 CCGTAAATCACACCGCCATC 59.344 55.000 0.00 0.00 0.00 3.51
5679 10010 0.655733 CGTAAATCACACCGCCATCC 59.344 55.000 0.00 0.00 0.00 3.51
5680 10011 1.745232 GTAAATCACACCGCCATCCA 58.255 50.000 0.00 0.00 0.00 3.41
5681 10012 2.297701 GTAAATCACACCGCCATCCAT 58.702 47.619 0.00 0.00 0.00 3.41
5682 10013 1.105457 AAATCACACCGCCATCCATG 58.895 50.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.465403 CCTCCACCAGAGAGGGCG 61.465 72.222 0.00 0.00 46.50 6.13
86 87 1.961793 CACCGGACTGAGGTTTCAAA 58.038 50.000 9.46 0.00 40.59 2.69
127 128 6.558775 AGCATTTAATACCCTCCTATCTCACA 59.441 38.462 0.00 0.00 0.00 3.58
133 134 9.911788 CATCAATAGCATTTAATACCCTCCTAT 57.088 33.333 0.00 0.00 0.00 2.57
162 163 2.592102 AACAGTTGGTCATGCCTCAT 57.408 45.000 7.54 0.00 38.35 2.90
242 3477 2.720578 CACCAATGCAATTAATAGCGCG 59.279 45.455 0.00 0.00 32.46 6.86
251 3486 0.618393 CCTCCCCCACCAATGCAATT 60.618 55.000 0.00 0.00 36.63 2.32
262 3497 2.645604 GGATTTCATCCCTCCCCCA 58.354 57.895 0.00 0.00 43.88 4.96
271 3506 4.551388 CGGCTACACTCTAGGATTTCATC 58.449 47.826 0.00 0.00 0.00 2.92
288 3523 1.079405 CTCAAAAGTCGGGCGGCTA 60.079 57.895 9.56 0.00 0.00 3.93
290 3525 2.668550 ACTCAAAAGTCGGGCGGC 60.669 61.111 0.00 0.00 0.00 6.53
301 3536 5.511373 CCACCTCTAACAGACATGACTCAAA 60.511 44.000 0.00 0.00 0.00 2.69
314 3549 3.531538 GATCGAATTGCCACCTCTAACA 58.468 45.455 0.00 0.00 0.00 2.41
332 3567 2.421424 ACGGTACCAAGTGTCTACGATC 59.579 50.000 13.54 0.00 0.00 3.69
393 3629 0.321564 TCAACCACGCTCAATGAGGG 60.322 55.000 23.20 23.20 46.05 4.30
481 3720 3.604875 ACTGGGATAAACCTACACACG 57.395 47.619 0.00 0.00 38.98 4.49
482 3721 6.988580 GGTTATACTGGGATAAACCTACACAC 59.011 42.308 0.00 0.00 38.98 3.82
497 3736 3.279434 GCTGTTGAAGGGGTTATACTGG 58.721 50.000 0.00 0.00 0.00 4.00
499 3738 2.916934 TGGCTGTTGAAGGGGTTATACT 59.083 45.455 0.00 0.00 0.00 2.12
524 3840 5.941948 AATAAAAGAAACCGGAGAGTGTG 57.058 39.130 9.46 0.00 0.00 3.82
719 4096 5.611128 TCGTGTATAGTACTCTCACTCCT 57.389 43.478 0.00 0.00 0.00 3.69
731 4108 2.095059 GTGACGGGTGTTCGTGTATAGT 60.095 50.000 0.00 0.00 43.96 2.12
760 4137 2.010582 TTGCTTGTTCACGGGGTTGC 62.011 55.000 0.00 0.00 0.00 4.17
765 4142 0.031857 TGCATTTGCTTGTTCACGGG 59.968 50.000 3.94 0.00 42.66 5.28
791 4168 1.621317 TGTGACAGTTTAGGATGGCGA 59.379 47.619 0.00 0.00 0.00 5.54
851 4233 8.768397 AGAAAGTGGGACTTATTTTTCCTTTTT 58.232 29.630 0.00 0.00 37.47 1.94
872 4254 3.728385 ATGGTTTCCAGGGAGAGAAAG 57.272 47.619 0.00 0.00 36.75 2.62
875 4257 5.592587 TTTTTATGGTTTCCAGGGAGAGA 57.407 39.130 0.00 0.00 36.75 3.10
906 4291 2.843401 TGGATTTCCTTTTCGACGGA 57.157 45.000 0.00 0.00 36.82 4.69
948 4333 3.227614 GGAGGCTTAGGTAAGAGAGAGG 58.772 54.545 0.71 0.00 35.33 3.69
1014 4423 2.626840 CTTGGCTTGTAGAGGAAGAGC 58.373 52.381 0.00 0.00 0.00 4.09
1110 4522 0.746563 TTGGCGGATTTAAGCGAGGG 60.747 55.000 0.00 0.00 0.00 4.30
1604 5017 0.454452 GCCGAAGCGTGAAATGGAAC 60.454 55.000 0.00 0.00 0.00 3.62
1608 5021 1.059369 CGAGCCGAAGCGTGAAATG 59.941 57.895 0.00 0.00 46.67 2.32
1614 5027 0.878961 AAAGAAACGAGCCGAAGCGT 60.879 50.000 1.50 0.00 46.67 5.07
1645 5058 1.021968 ACGGACAGAACAAGCCAAAC 58.978 50.000 0.00 0.00 0.00 2.93
1721 5134 1.901833 CCCCAATAAAACAGCCAAGCT 59.098 47.619 0.00 0.00 40.77 3.74
1722 5135 1.899142 TCCCCAATAAAACAGCCAAGC 59.101 47.619 0.00 0.00 0.00 4.01
1723 5136 4.824479 AATCCCCAATAAAACAGCCAAG 57.176 40.909 0.00 0.00 0.00 3.61
1749 5167 2.353803 GCGAAAGAAGAGTTAGCCAGGA 60.354 50.000 0.00 0.00 0.00 3.86
1750 5168 2.003301 GCGAAAGAAGAGTTAGCCAGG 58.997 52.381 0.00 0.00 0.00 4.45
1751 5169 2.966050 AGCGAAAGAAGAGTTAGCCAG 58.034 47.619 0.00 0.00 0.00 4.85
1753 5171 5.581085 TCAAATAGCGAAAGAAGAGTTAGCC 59.419 40.000 0.00 0.00 0.00 3.93
1754 5172 6.311690 ACTCAAATAGCGAAAGAAGAGTTAGC 59.688 38.462 0.00 0.00 31.61 3.09
1779 5197 5.335113 GCAACAACAGAGAACTATTGCATCA 60.335 40.000 0.00 0.00 40.46 3.07
1873 5291 2.637872 CGGAGAGGGCCAGGAAATTATA 59.362 50.000 6.18 0.00 0.00 0.98
1874 5292 1.421646 CGGAGAGGGCCAGGAAATTAT 59.578 52.381 6.18 0.00 0.00 1.28
1939 5357 2.632763 AGGCTACTGAGAAGGGAAGT 57.367 50.000 0.00 0.00 0.00 3.01
1941 5359 5.487488 TCAAAATAGGCTACTGAGAAGGGAA 59.513 40.000 0.00 0.00 0.00 3.97
1942 5360 5.030147 TCAAAATAGGCTACTGAGAAGGGA 58.970 41.667 0.00 0.00 0.00 4.20
1943 5361 5.359194 TCAAAATAGGCTACTGAGAAGGG 57.641 43.478 0.00 0.00 0.00 3.95
1944 5362 6.644347 TCTTCAAAATAGGCTACTGAGAAGG 58.356 40.000 19.64 8.74 32.90 3.46
1976 5394 2.672996 ATTTCGCGGCTGCTTGGT 60.673 55.556 17.03 0.00 39.65 3.67
2048 5466 7.062839 GTGCAACAACTTCACTTGAACAAAATA 59.937 33.333 0.00 0.00 36.32 1.40
2080 5498 9.726438 ACTAGTGTTATAATTGAGCTTGAGTTT 57.274 29.630 0.00 0.00 0.00 2.66
2081 5499 9.155975 CACTAGTGTTATAATTGAGCTTGAGTT 57.844 33.333 15.06 0.00 0.00 3.01
2082 5500 8.314751 ACACTAGTGTTATAATTGAGCTTGAGT 58.685 33.333 22.95 0.00 41.83 3.41
2083 5501 8.598924 CACACTAGTGTTATAATTGAGCTTGAG 58.401 37.037 25.89 4.82 42.83 3.02
2084 5502 7.549134 CCACACTAGTGTTATAATTGAGCTTGA 59.451 37.037 25.89 0.00 44.39 3.02
2085 5503 7.334421 ACCACACTAGTGTTATAATTGAGCTTG 59.666 37.037 25.89 9.28 44.39 4.01
2235 5654 3.312736 ACAGGGGAGAGCAAAGAAAAA 57.687 42.857 0.00 0.00 0.00 1.94
2236 5655 3.312736 AACAGGGGAGAGCAAAGAAAA 57.687 42.857 0.00 0.00 0.00 2.29
2237 5656 3.312736 AAACAGGGGAGAGCAAAGAAA 57.687 42.857 0.00 0.00 0.00 2.52
2238 5657 3.312736 AAAACAGGGGAGAGCAAAGAA 57.687 42.857 0.00 0.00 0.00 2.52
2239 5658 3.312736 AAAAACAGGGGAGAGCAAAGA 57.687 42.857 0.00 0.00 0.00 2.52
2300 5727 4.835678 CCAGGGCTTTTGATTGCTAAAAT 58.164 39.130 0.00 0.00 0.00 1.82
2321 5748 4.635223 AGAGAAATTTCTTGCAAAAGGCC 58.365 39.130 21.33 0.00 38.76 5.19
2497 5927 5.774690 TCCTTTCACTTCAGCATTTAATGGT 59.225 36.000 3.59 3.59 42.61 3.55
2508 5938 1.338200 CGACCCCTCCTTTCACTTCAG 60.338 57.143 0.00 0.00 0.00 3.02
2540 5970 2.412870 TGCACACAAATCTCTGGTACG 58.587 47.619 0.00 0.00 0.00 3.67
2854 6293 0.478507 CCCCCTCTCTCTCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
2946 6767 1.131638 AAGACACCTCCAAGCTGTGA 58.868 50.000 8.03 0.00 34.18 3.58
3441 7262 7.470841 GCCTAAGGTTAGTTCAAACAAATTGGA 60.471 37.037 0.00 0.00 39.62 3.53
3477 7298 3.742369 CCACAATTTGCCACACATTTCTC 59.258 43.478 0.00 0.00 0.00 2.87
3563 7384 3.187842 TCGATATCATCCGTGGTCGTAAG 59.812 47.826 3.12 0.00 35.01 2.34
3567 7389 2.921634 ATCGATATCATCCGTGGTCG 57.078 50.000 0.00 0.00 0.00 4.79
3633 7456 4.410555 AGAGAGGAAGTATAGCAAAAGGGG 59.589 45.833 0.00 0.00 0.00 4.79
3646 7469 7.554959 TTAGAAACAACCATAGAGAGGAAGT 57.445 36.000 0.00 0.00 0.00 3.01
3784 7607 1.743772 CGATGGGAATTCGAGTGGCTT 60.744 52.381 0.00 0.00 38.88 4.35
3996 7825 2.479389 CGTGTCAAAACCACATTGCACT 60.479 45.455 0.00 0.00 35.05 4.40
4241 8070 1.600485 ACGGAAACAAAGCTAACACGG 59.400 47.619 0.00 0.00 0.00 4.94
4304 8133 8.094548 ACTCAGCATTACTTCTGTATGTTACAA 58.905 33.333 0.00 0.00 38.38 2.41
4348 8177 4.391155 TGCTAACGGTTACATTGGAGTTT 58.609 39.130 0.00 0.00 0.00 2.66
4754 8589 7.445121 CAAGTAGAATCCAGGCTCATGTATTA 58.555 38.462 0.00 0.00 0.00 0.98
4828 8666 1.467342 GGATCGCCCACTAAAACACAC 59.533 52.381 0.00 0.00 34.14 3.82
4959 9267 1.757682 TGGACACTGTCAAAACCACC 58.242 50.000 11.34 0.00 33.68 4.61
5014 9322 2.234143 GCAAGTGGAAAGGAGAAAGCT 58.766 47.619 0.00 0.00 0.00 3.74
5015 9323 1.270826 GGCAAGTGGAAAGGAGAAAGC 59.729 52.381 0.00 0.00 0.00 3.51
5047 9355 5.871524 GCACTGTCATTCATCTCAGTAAAGA 59.128 40.000 0.00 0.00 38.79 2.52
5052 9360 3.977134 AGCACTGTCATTCATCTCAGT 57.023 42.857 0.00 0.00 41.02 3.41
5054 9362 5.065235 TGAAAAGCACTGTCATTCATCTCA 58.935 37.500 0.00 0.00 0.00 3.27
5175 9483 9.209175 GATGAGTGTAGAAAACAACTAGACAAT 57.791 33.333 0.00 0.00 40.63 2.71
5198 9507 0.179129 GCACCGGCCAAAATCTGATG 60.179 55.000 0.00 0.00 0.00 3.07
5252 9561 4.187694 GGATGCTGTCAGTCTTAGGAAAG 58.812 47.826 0.93 0.00 0.00 2.62
5474 9805 9.973450 TTCAATGAAATGTCCTTTATCGAAAAA 57.027 25.926 0.00 0.00 0.00 1.94
5478 9809 9.830975 TCTATTCAATGAAATGTCCTTTATCGA 57.169 29.630 0.00 0.00 0.00 3.59
5506 9837 9.933723 TTTGACATGATTGTATCATCTCGATAT 57.066 29.630 0.00 0.00 46.62 1.63
5507 9838 9.762933 TTTTGACATGATTGTATCATCTCGATA 57.237 29.630 0.00 0.00 46.62 2.92
5508 9839 8.667076 TTTTGACATGATTGTATCATCTCGAT 57.333 30.769 0.00 0.00 46.62 3.59
5509 9840 7.981225 TCTTTTGACATGATTGTATCATCTCGA 59.019 33.333 0.00 0.00 46.62 4.04
5510 9841 8.134905 TCTTTTGACATGATTGTATCATCTCG 57.865 34.615 0.00 0.00 46.62 4.04
5513 9844 9.017669 GCTTTCTTTTGACATGATTGTATCATC 57.982 33.333 0.00 0.00 46.62 2.92
5515 9846 7.315142 GGCTTTCTTTTGACATGATTGTATCA 58.685 34.615 0.00 0.00 44.55 2.15
5516 9847 6.753744 GGGCTTTCTTTTGACATGATTGTATC 59.246 38.462 0.00 0.00 35.79 2.24
5517 9848 6.625740 CGGGCTTTCTTTTGACATGATTGTAT 60.626 38.462 0.00 0.00 35.79 2.29
5518 9849 5.335583 CGGGCTTTCTTTTGACATGATTGTA 60.336 40.000 0.00 0.00 35.79 2.41
5519 9850 4.559300 CGGGCTTTCTTTTGACATGATTGT 60.559 41.667 0.00 0.00 39.32 2.71
5520 9851 3.922240 CGGGCTTTCTTTTGACATGATTG 59.078 43.478 0.00 0.00 0.00 2.67
5521 9852 3.056607 CCGGGCTTTCTTTTGACATGATT 60.057 43.478 0.00 0.00 0.00 2.57
5522 9853 2.493278 CCGGGCTTTCTTTTGACATGAT 59.507 45.455 0.00 0.00 0.00 2.45
5523 9854 1.885887 CCGGGCTTTCTTTTGACATGA 59.114 47.619 0.00 0.00 0.00 3.07
5524 9855 1.669795 GCCGGGCTTTCTTTTGACATG 60.670 52.381 12.87 0.00 0.00 3.21
5525 9856 0.603065 GCCGGGCTTTCTTTTGACAT 59.397 50.000 12.87 0.00 0.00 3.06
5526 9857 1.460273 GGCCGGGCTTTCTTTTGACA 61.460 55.000 22.87 0.00 0.00 3.58
5527 9858 1.179174 AGGCCGGGCTTTCTTTTGAC 61.179 55.000 27.45 0.00 0.00 3.18
5528 9859 0.893727 GAGGCCGGGCTTTCTTTTGA 60.894 55.000 33.28 0.00 0.00 2.69
5529 9860 0.895559 AGAGGCCGGGCTTTCTTTTG 60.896 55.000 33.28 0.00 0.00 2.44
5530 9861 0.895559 CAGAGGCCGGGCTTTCTTTT 60.896 55.000 33.28 7.87 0.00 2.27
5531 9862 1.303643 CAGAGGCCGGGCTTTCTTT 60.304 57.895 33.28 8.77 0.00 2.52
5532 9863 2.352805 CAGAGGCCGGGCTTTCTT 59.647 61.111 33.28 15.22 0.00 2.52
5533 9864 4.416738 GCAGAGGCCGGGCTTTCT 62.417 66.667 33.28 22.65 0.00 2.52
5534 9865 2.608970 TATGCAGAGGCCGGGCTTTC 62.609 60.000 33.28 20.57 40.13 2.62
5535 9866 2.615227 CTATGCAGAGGCCGGGCTTT 62.615 60.000 33.28 24.87 40.13 3.51
5536 9867 3.089874 TATGCAGAGGCCGGGCTT 61.090 61.111 33.28 18.37 40.13 4.35
5537 9868 3.554342 CTATGCAGAGGCCGGGCT 61.554 66.667 33.40 33.40 40.13 5.19
5539 9870 2.164865 CTAGCTATGCAGAGGCCGGG 62.165 65.000 10.92 0.00 40.13 5.73
5540 9871 1.181741 TCTAGCTATGCAGAGGCCGG 61.182 60.000 10.92 0.00 40.13 6.13
5541 9872 0.894141 ATCTAGCTATGCAGAGGCCG 59.106 55.000 10.92 0.48 40.13 6.13
5542 9873 2.383368 CATCTAGCTATGCAGAGGCC 57.617 55.000 10.92 0.00 40.13 5.19
5550 9881 2.141517 GGCTGTGTGCATCTAGCTATG 58.858 52.381 15.51 0.00 45.94 2.23
5551 9882 1.764723 TGGCTGTGTGCATCTAGCTAT 59.235 47.619 15.51 0.00 45.94 2.97
5552 9883 1.194218 TGGCTGTGTGCATCTAGCTA 58.806 50.000 15.51 9.22 45.94 3.32
5553 9884 0.325933 TTGGCTGTGTGCATCTAGCT 59.674 50.000 15.51 0.00 45.94 3.32
5554 9885 1.167851 TTTGGCTGTGTGCATCTAGC 58.832 50.000 9.68 9.68 45.15 3.42
5555 9886 3.921119 TTTTTGGCTGTGTGCATCTAG 57.079 42.857 0.00 0.00 45.15 2.43
5572 9903 6.686484 ATTTTTAGGGTGCTCTGGATTTTT 57.314 33.333 0.00 0.00 0.00 1.94
5573 9904 7.790782 TTATTTTTAGGGTGCTCTGGATTTT 57.209 32.000 0.00 0.00 0.00 1.82
5574 9905 7.790782 TTTATTTTTAGGGTGCTCTGGATTT 57.209 32.000 0.00 0.00 0.00 2.17
5575 9906 7.790782 TTTTATTTTTAGGGTGCTCTGGATT 57.209 32.000 0.00 0.00 0.00 3.01
5576 9907 7.978099 ATTTTATTTTTAGGGTGCTCTGGAT 57.022 32.000 0.00 0.00 0.00 3.41
5577 9908 8.887264 TTATTTTATTTTTAGGGTGCTCTGGA 57.113 30.769 0.00 0.00 0.00 3.86
5595 9926 9.881649 TGCTTGGCATTGTATCAAATTATTTTA 57.118 25.926 0.00 0.00 31.71 1.52
5596 9927 8.789825 TGCTTGGCATTGTATCAAATTATTTT 57.210 26.923 0.00 0.00 31.71 1.82
5597 9928 8.789825 TTGCTTGGCATTGTATCAAATTATTT 57.210 26.923 0.00 0.00 38.76 1.40
5598 9929 8.967664 ATTGCTTGGCATTGTATCAAATTATT 57.032 26.923 0.00 0.00 38.76 1.40
5600 9931 9.881649 TTTATTGCTTGGCATTGTATCAAATTA 57.118 25.926 0.00 0.00 38.76 1.40
5601 9932 8.789825 TTTATTGCTTGGCATTGTATCAAATT 57.210 26.923 0.00 0.00 38.76 1.82
5602 9933 8.967664 ATTTATTGCTTGGCATTGTATCAAAT 57.032 26.923 0.00 0.00 38.76 2.32
5603 9934 7.222417 CGATTTATTGCTTGGCATTGTATCAAA 59.778 33.333 0.00 0.00 38.76 2.69
5604 9935 6.696583 CGATTTATTGCTTGGCATTGTATCAA 59.303 34.615 0.00 0.00 38.76 2.57
5605 9936 6.183360 ACGATTTATTGCTTGGCATTGTATCA 60.183 34.615 0.00 0.00 38.76 2.15
5606 9937 6.142798 CACGATTTATTGCTTGGCATTGTATC 59.857 38.462 0.00 0.00 38.76 2.24
5607 9938 5.978919 CACGATTTATTGCTTGGCATTGTAT 59.021 36.000 0.00 0.00 38.76 2.29
5608 9939 5.105957 ACACGATTTATTGCTTGGCATTGTA 60.106 36.000 0.00 0.00 38.76 2.41
5609 9940 4.175516 CACGATTTATTGCTTGGCATTGT 58.824 39.130 0.00 0.00 38.76 2.71
5610 9941 4.175516 ACACGATTTATTGCTTGGCATTG 58.824 39.130 0.00 0.00 38.76 2.82
5611 9942 4.423732 GACACGATTTATTGCTTGGCATT 58.576 39.130 0.00 0.00 38.76 3.56
5612 9943 3.181487 GGACACGATTTATTGCTTGGCAT 60.181 43.478 0.00 0.00 38.76 4.40
5613 9944 2.163412 GGACACGATTTATTGCTTGGCA 59.837 45.455 0.00 0.00 36.47 4.92
5614 9945 2.163412 TGGACACGATTTATTGCTTGGC 59.837 45.455 0.00 0.00 0.00 4.52
5615 9946 3.731867 GCTGGACACGATTTATTGCTTGG 60.732 47.826 0.00 0.00 0.00 3.61
5616 9947 3.429085 GCTGGACACGATTTATTGCTTG 58.571 45.455 0.00 0.00 0.00 4.01
5617 9948 2.423538 GGCTGGACACGATTTATTGCTT 59.576 45.455 0.00 0.00 0.00 3.91
5618 9949 2.017049 GGCTGGACACGATTTATTGCT 58.983 47.619 0.00 0.00 0.00 3.91
5619 9950 2.017049 AGGCTGGACACGATTTATTGC 58.983 47.619 0.00 0.00 0.00 3.56
5620 9951 4.273480 CCTTAGGCTGGACACGATTTATTG 59.727 45.833 0.00 0.00 0.00 1.90
5621 9952 4.163458 TCCTTAGGCTGGACACGATTTATT 59.837 41.667 0.00 0.00 0.00 1.40
5622 9953 3.709653 TCCTTAGGCTGGACACGATTTAT 59.290 43.478 0.00 0.00 0.00 1.40
5623 9954 3.101437 TCCTTAGGCTGGACACGATTTA 58.899 45.455 0.00 0.00 0.00 1.40
5624 9955 1.906574 TCCTTAGGCTGGACACGATTT 59.093 47.619 0.00 0.00 0.00 2.17
5625 9956 1.482593 CTCCTTAGGCTGGACACGATT 59.517 52.381 0.00 0.00 0.00 3.34
5626 9957 1.115467 CTCCTTAGGCTGGACACGAT 58.885 55.000 0.00 0.00 0.00 3.73
5627 9958 1.605058 GCTCCTTAGGCTGGACACGA 61.605 60.000 0.00 0.00 0.00 4.35
5628 9959 1.153549 GCTCCTTAGGCTGGACACG 60.154 63.158 0.00 0.00 0.00 4.49
5629 9960 1.153549 CGCTCCTTAGGCTGGACAC 60.154 63.158 0.00 0.00 0.00 3.67
5630 9961 2.359169 CCGCTCCTTAGGCTGGACA 61.359 63.158 0.00 0.00 0.00 4.02
5631 9962 1.041447 TACCGCTCCTTAGGCTGGAC 61.041 60.000 9.61 0.00 0.00 4.02
5632 9963 0.324923 TTACCGCTCCTTAGGCTGGA 60.325 55.000 9.61 0.00 0.00 3.86
5633 9964 0.539986 TTTACCGCTCCTTAGGCTGG 59.460 55.000 0.00 0.00 0.00 4.85
5634 9965 2.484889 GATTTACCGCTCCTTAGGCTG 58.515 52.381 0.00 0.00 0.00 4.85
5635 9966 1.416772 GGATTTACCGCTCCTTAGGCT 59.583 52.381 0.00 0.00 0.00 4.58
5636 9967 1.416772 AGGATTTACCGCTCCTTAGGC 59.583 52.381 0.00 0.00 38.81 3.93
5637 9968 4.081586 GGATAGGATTTACCGCTCCTTAGG 60.082 50.000 0.00 0.00 42.03 2.69
5638 9969 4.380655 CGGATAGGATTTACCGCTCCTTAG 60.381 50.000 0.00 0.00 42.03 2.18
5639 9970 3.508793 CGGATAGGATTTACCGCTCCTTA 59.491 47.826 0.00 0.00 42.03 2.69
5640 9971 2.299297 CGGATAGGATTTACCGCTCCTT 59.701 50.000 0.00 0.00 42.03 3.36
5641 9972 1.893801 CGGATAGGATTTACCGCTCCT 59.106 52.381 0.00 0.00 44.18 3.69
5642 9973 2.365408 CGGATAGGATTTACCGCTCC 57.635 55.000 0.00 0.00 44.74 4.70
5647 9978 6.426025 GGTGTGATTTACGGATAGGATTTACC 59.574 42.308 0.00 0.00 39.35 2.85
5648 9979 6.145048 CGGTGTGATTTACGGATAGGATTTAC 59.855 42.308 0.00 0.00 0.00 2.01
5649 9980 6.218019 CGGTGTGATTTACGGATAGGATTTA 58.782 40.000 0.00 0.00 0.00 1.40
5650 9981 5.054477 CGGTGTGATTTACGGATAGGATTT 58.946 41.667 0.00 0.00 0.00 2.17
5651 9982 4.628074 CGGTGTGATTTACGGATAGGATT 58.372 43.478 0.00 0.00 0.00 3.01
5652 9983 3.554337 GCGGTGTGATTTACGGATAGGAT 60.554 47.826 0.00 0.00 0.00 3.24
5653 9984 2.223876 GCGGTGTGATTTACGGATAGGA 60.224 50.000 0.00 0.00 0.00 2.94
5654 9985 2.132762 GCGGTGTGATTTACGGATAGG 58.867 52.381 0.00 0.00 0.00 2.57
5655 9986 2.132762 GGCGGTGTGATTTACGGATAG 58.867 52.381 0.00 0.00 0.00 2.08
5656 9987 1.481363 TGGCGGTGTGATTTACGGATA 59.519 47.619 0.00 0.00 0.00 2.59
5657 9988 0.250793 TGGCGGTGTGATTTACGGAT 59.749 50.000 0.00 0.00 0.00 4.18
5658 9989 0.250793 ATGGCGGTGTGATTTACGGA 59.749 50.000 0.00 0.00 0.00 4.69
5659 9990 0.655733 GATGGCGGTGTGATTTACGG 59.344 55.000 0.00 0.00 0.00 4.02
5660 9991 0.655733 GGATGGCGGTGTGATTTACG 59.344 55.000 0.00 0.00 0.00 3.18
5661 9992 1.745232 TGGATGGCGGTGTGATTTAC 58.255 50.000 0.00 0.00 0.00 2.01
5662 9993 2.296792 CATGGATGGCGGTGTGATTTA 58.703 47.619 0.00 0.00 0.00 1.40
5663 9994 1.105457 CATGGATGGCGGTGTGATTT 58.895 50.000 0.00 0.00 0.00 2.17
5664 9995 0.752743 CCATGGATGGCGGTGTGATT 60.753 55.000 5.56 0.00 41.75 2.57
5665 9996 1.152902 CCATGGATGGCGGTGTGAT 60.153 57.895 5.56 0.00 41.75 3.06
5666 9997 2.271821 CCATGGATGGCGGTGTGA 59.728 61.111 5.56 0.00 41.75 3.58
5667 9998 2.829914 CCCATGGATGGCGGTGTG 60.830 66.667 15.22 0.00 46.70 3.82
5668 9999 4.127744 CCCCATGGATGGCGGTGT 62.128 66.667 15.22 0.00 46.70 4.16
5669 10000 4.900704 CCCCCATGGATGGCGGTG 62.901 72.222 15.22 0.00 46.70 4.94


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

AutoCloner maintained by Alex Coulton.