Multiple sequence alignment - TraesCS5D01G392400

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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 TraesCS5D01G392400 chr5D 100.000 9558 0 0 1 9558 460755984 460746427 0.000000e+00 17651.0
1 TraesCS5D01G392400 chr5D 77.381 336 47 16 3447 3777 450859208 450858897 1.280000e-38 172.0
2 TraesCS5D01G392400 chr5D 93.162 117 8 0 2124 2240 460753744 460753628 1.280000e-38 172.0
3 TraesCS5D01G392400 chr5D 93.162 117 8 0 2241 2357 460753861 460753745 1.280000e-38 172.0
4 TraesCS5D01G392400 chr5D 95.455 44 2 0 3040 3083 555654097 555654140 4.790000e-08 71.3
5 TraesCS5D01G392400 chr5B 94.141 5513 216 58 2241 7709 566682212 566676763 0.000000e+00 8292.0
6 TraesCS5D01G392400 chr5B 92.789 1470 83 11 7704 9162 566676730 566675273 0.000000e+00 2106.0
7 TraesCS5D01G392400 chr5B 93.016 1303 48 16 946 2240 566683367 566682100 0.000000e+00 1862.0
8 TraesCS5D01G392400 chr5B 94.209 708 20 7 1 702 566684543 566683851 0.000000e+00 1061.0
9 TraesCS5D01G392400 chr5B 94.350 177 9 1 696 871 566683891 566683715 4.400000e-68 270.0
10 TraesCS5D01G392400 chr5B 93.750 144 9 0 9237 9380 566675262 566675119 5.810000e-52 217.0
11 TraesCS5D01G392400 chr5B 93.284 134 6 1 9381 9514 566674875 566674745 2.720000e-45 195.0
12 TraesCS5D01G392400 chr5B 97.059 34 1 0 2187 2220 639736793 639736760 3.730000e-04 58.4
13 TraesCS5D01G392400 chr5A 98.463 2928 42 3 3141 6067 580941437 580938512 0.000000e+00 5155.0
14 TraesCS5D01G392400 chr5A 92.992 2754 103 31 6646 9362 580937737 580935037 0.000000e+00 3934.0
15 TraesCS5D01G392400 chr5A 91.958 1828 79 36 546 2357 580944245 580942470 0.000000e+00 2499.0
16 TraesCS5D01G392400 chr5A 89.713 1079 57 24 2124 3148 580942586 580941508 0.000000e+00 1328.0
17 TraesCS5D01G392400 chr5A 97.655 597 11 1 6057 6650 580938434 580937838 0.000000e+00 1022.0
18 TraesCS5D01G392400 chr5A 97.505 521 8 5 1 519 580944748 580944231 0.000000e+00 885.0
19 TraesCS5D01G392400 chr5A 94.017 117 7 0 2124 2240 580942469 580942353 2.740000e-40 178.0
20 TraesCS5D01G392400 chr5A 89.423 104 11 0 2629 2732 580941996 580941893 2.170000e-26 132.0
21 TraesCS5D01G392400 chr5A 85.227 88 7 2 9386 9473 580934984 580934903 1.710000e-12 86.1
22 TraesCS5D01G392400 chr5A 85.938 64 6 1 3684 3744 570006662 570006599 2.230000e-06 65.8
23 TraesCS5D01G392400 chr4D 87.500 280 33 2 1207 1486 35061921 35062198 1.200000e-83 322.0
24 TraesCS5D01G392400 chr4D 80.952 357 42 19 1374 1710 30018569 30018219 9.520000e-65 259.0
25 TraesCS5D01G392400 chr4D 79.891 368 45 18 1361 1710 38280560 38280916 9.590000e-60 243.0
26 TraesCS5D01G392400 chr4B 81.267 363 42 17 1368 1710 42762272 42762628 4.400000e-68 270.0
27 TraesCS5D01G392400 chr4B 80.054 371 46 19 1361 1710 42010568 42010931 5.730000e-62 250.0
28 TraesCS5D01G392400 chr4B 79.834 362 48 16 1368 1710 42719364 42719719 3.450000e-59 241.0
29 TraesCS5D01G392400 chr4B 77.933 358 50 22 1361 1710 42745453 42745789 7.570000e-46 196.0
30 TraesCS5D01G392400 chr4A 80.488 369 47 17 1361 1710 564945464 564945826 9.520000e-65 259.0
31 TraesCS5D01G392400 chr4A 84.034 238 33 5 6054 6288 733634348 733634583 3.470000e-54 224.0
32 TraesCS5D01G392400 chr3B 84.454 238 32 4 6055 6288 670692520 670692284 7.470000e-56 230.0
33 TraesCS5D01G392400 chr1D 83.333 240 34 5 6054 6288 7770790 7770552 5.810000e-52 217.0
34 TraesCS5D01G392400 chr1D 82.573 241 33 7 6053 6288 446708553 446708317 4.530000e-48 204.0
35 TraesCS5D01G392400 chr3D 82.845 239 36 4 6053 6288 493038555 493038319 9.730000e-50 209.0
36 TraesCS5D01G392400 chr3D 82.008 239 38 4 6053 6288 469807012 469806776 2.110000e-46 198.0
37 TraesCS5D01G392400 chr2B 82.573 241 32 7 6054 6288 734497223 734496987 4.530000e-48 204.0
38 TraesCS5D01G392400 chr6B 93.220 59 3 1 2358 2415 447886092 447886034 1.710000e-12 86.1
39 TraesCS5D01G392400 chr7B 94.118 51 3 0 3044 3094 614963427 614963477 2.860000e-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 TraesCS5D01G392400 chr5D 460746427 460755984 9557 True 5998.333333 17651 95.441333 1 9558 3 chr5D.!!$R2 9557
1 TraesCS5D01G392400 chr5B 566674745 566684543 9798 True 2000.428571 8292 93.648429 1 9514 7 chr5B.!!$R2 9513
2 TraesCS5D01G392400 chr5A 580934903 580944748 9845 True 1691.011111 5155 92.994778 1 9473 9 chr5A.!!$R2 9472

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
532 539 0.106619 GGAAGCGGAGTAGAGGAGGA 60.107 60.000 0.00 0.00 0.00 3.71 F
539 546 0.179012 GAGTAGAGGAGGACGGGGAG 60.179 65.000 0.00 0.00 0.00 4.30 F
1402 1695 0.451299 CATACTCGTCGAGATCGCCG 60.451 60.000 28.33 0.00 42.38 6.46 F
2204 2624 0.032952 GCATATCGGTCGGGTGCTAA 59.967 55.000 7.75 0.00 33.25 3.09 F
3007 3630 0.114168 ACCCCAAGCAGTTAATGGCA 59.886 50.000 0.00 0.00 32.71 4.92 F
3058 3682 2.098607 CCGAGTAGCGATTAACTGACCA 59.901 50.000 0.00 0.00 44.57 4.02 F
4946 5671 1.535462 GATGGATTTTATGACGCGGGG 59.465 52.381 12.47 0.00 0.00 5.73 F
5560 6289 1.003652 GCATTGCAGTTTGGTGTTTGC 60.004 47.619 3.15 0.00 37.09 3.68 F
6284 7105 2.042162 ACTAGTAAACCAGGACGGAGGA 59.958 50.000 0.00 0.00 38.63 3.71 F
7371 8308 2.481952 ACATTGCTCGAGAAGTTGCTTC 59.518 45.455 18.75 0.96 40.45 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2605 0.032952 TTAGCACCCGACCGATATGC 59.967 55.000 0.00 0.0 36.52 3.14 R
2192 2612 0.685458 TCCCTACTTAGCACCCGACC 60.685 60.000 0.00 0.0 0.00 4.79 R
2988 3611 0.114168 TGCCATTAACTGCTTGGGGT 59.886 50.000 0.38 0.0 0.00 4.95 R
3914 4638 2.050144 ACTTCTCTCTCTGGCAAACCA 58.950 47.619 0.00 0.0 46.51 3.67 R
4946 5671 0.164647 GCATGAACGGCATATCTCGC 59.835 55.000 0.00 0.0 34.82 5.03 R
5029 5754 2.315925 ACGGATAGGAATGTGCACTG 57.684 50.000 19.41 0.0 0.00 3.66 R
6722 7650 1.137086 CGACTGAGGGGAACATACCTG 59.863 57.143 0.00 0.0 37.18 4.00 R
7371 8308 1.610038 TGTGCATCTCCAACAAAGCAG 59.390 47.619 0.00 0.0 32.03 4.24 R
7492 8429 2.358957 TGCAAAGGAATGGATCTGTCG 58.641 47.619 0.00 0.0 0.00 4.35 R
8656 9637 0.034767 CAGAAGCTGGCCAGATCCAA 60.035 55.000 37.21 0.0 35.36 3.53 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
421 425 2.124236 CGTACGCCTCCTCCTCCT 60.124 66.667 0.52 0.00 0.00 3.69
530 537 1.448922 CGGGAAGCGGAGTAGAGGAG 61.449 65.000 0.00 0.00 0.00 3.69
531 538 1.110518 GGGAAGCGGAGTAGAGGAGG 61.111 65.000 0.00 0.00 0.00 4.30
532 539 0.106619 GGAAGCGGAGTAGAGGAGGA 60.107 60.000 0.00 0.00 0.00 3.71
533 540 1.026584 GAAGCGGAGTAGAGGAGGAC 58.973 60.000 0.00 0.00 0.00 3.85
534 541 0.748729 AAGCGGAGTAGAGGAGGACG 60.749 60.000 0.00 0.00 0.00 4.79
535 542 2.188161 GCGGAGTAGAGGAGGACGG 61.188 68.421 0.00 0.00 0.00 4.79
536 543 1.526455 CGGAGTAGAGGAGGACGGG 60.526 68.421 0.00 0.00 0.00 5.28
537 544 1.152715 GGAGTAGAGGAGGACGGGG 60.153 68.421 0.00 0.00 0.00 5.73
538 545 1.643475 GGAGTAGAGGAGGACGGGGA 61.643 65.000 0.00 0.00 0.00 4.81
539 546 0.179012 GAGTAGAGGAGGACGGGGAG 60.179 65.000 0.00 0.00 0.00 4.30
540 547 1.152715 GTAGAGGAGGACGGGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
541 548 2.392816 TAGAGGAGGACGGGGAGGG 61.393 68.421 0.00 0.00 0.00 4.30
542 549 4.862823 GAGGAGGACGGGGAGGGG 62.863 77.778 0.00 0.00 0.00 4.79
703 718 3.775654 GAGCCTGACCCCGACCTG 61.776 72.222 0.00 0.00 0.00 4.00
706 721 3.391382 CCTGACCCCGACCTGGAC 61.391 72.222 0.00 0.00 42.00 4.02
707 722 3.391382 CTGACCCCGACCTGGACC 61.391 72.222 0.00 0.00 42.00 4.46
854 870 3.600388 CGGTCCAAATCTCAGCTTTAGT 58.400 45.455 0.00 0.00 0.00 2.24
872 888 9.623350 AGCTTTAGTATAGCTTAACTTATACGC 57.377 33.333 9.10 0.34 46.42 4.42
878 894 2.367894 AGCTTAACTTATACGCTCCCCC 59.632 50.000 0.00 0.00 0.00 5.40
897 913 0.933700 CCCCTCCTCCTCTCTCTCTT 59.066 60.000 0.00 0.00 0.00 2.85
900 916 3.031013 CCCTCCTCCTCTCTCTCTTTTC 58.969 54.545 0.00 0.00 0.00 2.29
904 920 2.292851 CCTCCTCTCTCTCTTTTCCCCT 60.293 54.545 0.00 0.00 0.00 4.79
905 921 3.031013 CTCCTCTCTCTCTTTTCCCCTC 58.969 54.545 0.00 0.00 0.00 4.30
1402 1695 0.451299 CATACTCGTCGAGATCGCCG 60.451 60.000 28.33 0.00 42.38 6.46
1460 1753 0.911053 TCCATCAGGTATGCTGCACA 59.089 50.000 3.57 0.00 33.92 4.57
1490 1785 1.093159 CTCAATTGACAGCTCTGCCC 58.907 55.000 3.38 0.00 0.00 5.36
1522 1821 2.177173 GCTAATTTTGCTACAGTGCGC 58.823 47.619 0.00 0.00 35.36 6.09
1560 1859 8.308931 TGGTTAATTTACTGTTCTCGTGTCTAT 58.691 33.333 0.00 0.00 0.00 1.98
1696 1998 6.826741 TGGATGTGTATAAGAAACCTTTAGCC 59.173 38.462 0.00 0.00 0.00 3.93
1708 2010 3.379452 ACCTTTAGCCAGACTAGCATCT 58.621 45.455 0.00 0.00 30.79 2.90
1709 2011 4.547671 ACCTTTAGCCAGACTAGCATCTA 58.452 43.478 0.00 0.00 30.79 1.98
1710 2012 4.342665 ACCTTTAGCCAGACTAGCATCTAC 59.657 45.833 0.00 0.00 30.79 2.59
1711 2013 4.586841 CCTTTAGCCAGACTAGCATCTACT 59.413 45.833 0.00 0.00 30.79 2.57
1712 2014 5.508825 CCTTTAGCCAGACTAGCATCTACTG 60.509 48.000 0.00 0.00 30.79 2.74
1837 2140 5.809562 TGAATTGTTTGTTGTGGCTACTTTG 59.190 36.000 0.64 0.00 0.00 2.77
1976 2279 9.646427 CTTACTTTAACTAGCTGTTCTGAATCT 57.354 33.333 0.00 0.00 39.89 2.40
1977 2280 7.897575 ACTTTAACTAGCTGTTCTGAATCTG 57.102 36.000 0.00 0.00 39.89 2.90
1978 2281 7.445945 ACTTTAACTAGCTGTTCTGAATCTGT 58.554 34.615 0.00 0.00 39.89 3.41
1979 2282 7.934120 ACTTTAACTAGCTGTTCTGAATCTGTT 59.066 33.333 0.00 3.12 39.89 3.16
2126 2546 9.033481 CAGATGTTTAAAAGTTCAAATGCTTGA 57.967 29.630 0.00 0.00 39.87 3.02
2167 2587 9.908152 ATTTTGTGGTCTAAATTTAGTTGTAGC 57.092 29.630 21.69 13.77 32.61 3.58
2168 2588 8.453238 TTTGTGGTCTAAATTTAGTTGTAGCA 57.547 30.769 21.69 15.80 32.61 3.49
2169 2589 8.453238 TTGTGGTCTAAATTTAGTTGTAGCAA 57.547 30.769 21.69 16.58 32.61 3.91
2170 2590 8.453238 TGTGGTCTAAATTTAGTTGTAGCAAA 57.547 30.769 21.69 12.17 32.61 3.68
2171 2591 8.904834 TGTGGTCTAAATTTAGTTGTAGCAAAA 58.095 29.630 21.69 9.53 32.61 2.44
2172 2592 9.177304 GTGGTCTAAATTTAGTTGTAGCAAAAC 57.823 33.333 21.69 10.34 32.61 2.43
2173 2593 9.127277 TGGTCTAAATTTAGTTGTAGCAAAACT 57.873 29.630 21.69 4.43 40.82 2.66
2174 2594 9.608617 GGTCTAAATTTAGTTGTAGCAAAACTC 57.391 33.333 21.69 3.38 38.73 3.01
2179 2599 9.516314 AAATTTAGTTGTAGCAAAACTCTCAAC 57.484 29.630 2.40 0.00 40.54 3.18
2180 2600 7.859325 TTTAGTTGTAGCAAAACTCTCAACT 57.141 32.000 11.88 11.88 46.20 3.16
2181 2601 5.741388 AGTTGTAGCAAAACTCTCAACTG 57.259 39.130 7.41 0.00 44.55 3.16
2182 2602 4.576463 AGTTGTAGCAAAACTCTCAACTGG 59.424 41.667 7.41 0.00 44.55 4.00
2183 2603 4.150897 TGTAGCAAAACTCTCAACTGGT 57.849 40.909 0.00 0.00 0.00 4.00
2184 2604 3.876914 TGTAGCAAAACTCTCAACTGGTG 59.123 43.478 0.00 0.00 0.00 4.17
2185 2605 2.301346 AGCAAAACTCTCAACTGGTGG 58.699 47.619 0.00 0.00 0.00 4.61
2186 2606 1.269257 GCAAAACTCTCAACTGGTGGC 60.269 52.381 0.00 0.00 0.00 5.01
2187 2607 2.023673 CAAAACTCTCAACTGGTGGCA 58.976 47.619 0.00 0.00 0.00 4.92
2188 2608 2.624838 CAAAACTCTCAACTGGTGGCAT 59.375 45.455 0.00 0.00 0.00 4.40
2189 2609 3.788227 AAACTCTCAACTGGTGGCATA 57.212 42.857 0.00 0.00 0.00 3.14
2190 2610 4.307032 AAACTCTCAACTGGTGGCATAT 57.693 40.909 0.00 0.00 0.00 1.78
2191 2611 3.550437 ACTCTCAACTGGTGGCATATC 57.450 47.619 0.00 0.00 0.00 1.63
2192 2612 2.159043 ACTCTCAACTGGTGGCATATCG 60.159 50.000 0.00 0.00 0.00 2.92
2193 2613 1.138859 TCTCAACTGGTGGCATATCGG 59.861 52.381 0.00 0.00 0.00 4.18
2194 2614 0.908910 TCAACTGGTGGCATATCGGT 59.091 50.000 0.00 0.00 0.00 4.69
2195 2615 1.134521 TCAACTGGTGGCATATCGGTC 60.135 52.381 0.00 0.00 0.00 4.79
2196 2616 0.179084 AACTGGTGGCATATCGGTCG 60.179 55.000 0.00 0.00 0.00 4.79
2197 2617 1.300931 CTGGTGGCATATCGGTCGG 60.301 63.158 0.00 0.00 0.00 4.79
2198 2618 2.030562 GGTGGCATATCGGTCGGG 59.969 66.667 0.00 0.00 0.00 5.14
2199 2619 2.803817 GGTGGCATATCGGTCGGGT 61.804 63.158 0.00 0.00 0.00 5.28
2200 2620 1.594293 GTGGCATATCGGTCGGGTG 60.594 63.158 0.00 0.00 0.00 4.61
2201 2621 2.665185 GGCATATCGGTCGGGTGC 60.665 66.667 0.00 6.88 35.17 5.01
2202 2622 2.421739 GCATATCGGTCGGGTGCT 59.578 61.111 7.75 0.00 33.25 4.40
2203 2623 1.663739 GCATATCGGTCGGGTGCTA 59.336 57.895 7.75 0.00 33.25 3.49
2204 2624 0.032952 GCATATCGGTCGGGTGCTAA 59.967 55.000 7.75 0.00 33.25 3.09
2205 2625 1.935300 GCATATCGGTCGGGTGCTAAG 60.935 57.143 7.75 0.00 33.25 2.18
2206 2626 1.340248 CATATCGGTCGGGTGCTAAGT 59.660 52.381 0.00 0.00 0.00 2.24
2207 2627 2.346766 TATCGGTCGGGTGCTAAGTA 57.653 50.000 0.00 0.00 0.00 2.24
2208 2628 1.030457 ATCGGTCGGGTGCTAAGTAG 58.970 55.000 0.00 0.00 0.00 2.57
2209 2629 1.033746 TCGGTCGGGTGCTAAGTAGG 61.034 60.000 0.00 0.00 0.00 3.18
2210 2630 1.821258 GGTCGGGTGCTAAGTAGGG 59.179 63.158 0.00 0.00 0.00 3.53
2211 2631 0.685458 GGTCGGGTGCTAAGTAGGGA 60.685 60.000 0.00 0.00 0.00 4.20
2212 2632 1.411041 GTCGGGTGCTAAGTAGGGAT 58.589 55.000 0.00 0.00 0.00 3.85
2213 2633 2.590821 GTCGGGTGCTAAGTAGGGATA 58.409 52.381 0.00 0.00 0.00 2.59
2214 2634 2.961062 GTCGGGTGCTAAGTAGGGATAA 59.039 50.000 0.00 0.00 0.00 1.75
2215 2635 3.385755 GTCGGGTGCTAAGTAGGGATAAA 59.614 47.826 0.00 0.00 0.00 1.40
2216 2636 4.040095 GTCGGGTGCTAAGTAGGGATAAAT 59.960 45.833 0.00 0.00 0.00 1.40
2217 2637 4.657039 TCGGGTGCTAAGTAGGGATAAATT 59.343 41.667 0.00 0.00 0.00 1.82
2218 2638 4.755123 CGGGTGCTAAGTAGGGATAAATTG 59.245 45.833 0.00 0.00 0.00 2.32
2219 2639 5.070685 GGGTGCTAAGTAGGGATAAATTGG 58.929 45.833 0.00 0.00 0.00 3.16
2220 2640 4.519350 GGTGCTAAGTAGGGATAAATTGGC 59.481 45.833 0.00 0.00 0.00 4.52
2221 2641 4.213482 GTGCTAAGTAGGGATAAATTGGCG 59.787 45.833 0.00 0.00 30.85 5.69
2222 2642 3.751698 GCTAAGTAGGGATAAATTGGCGG 59.248 47.826 0.00 0.00 0.00 6.13
2223 2643 4.504340 GCTAAGTAGGGATAAATTGGCGGA 60.504 45.833 0.00 0.00 0.00 5.54
2224 2644 4.724279 AAGTAGGGATAAATTGGCGGAT 57.276 40.909 0.00 0.00 0.00 4.18
2225 2645 4.287766 AGTAGGGATAAATTGGCGGATC 57.712 45.455 0.00 0.00 0.00 3.36
2226 2646 2.185004 AGGGATAAATTGGCGGATCG 57.815 50.000 0.00 0.00 0.00 3.69
2240 2660 3.594603 CGGATCGCCCTATTAACTGAT 57.405 47.619 0.00 0.00 0.00 2.90
2241 2661 3.926616 CGGATCGCCCTATTAACTGATT 58.073 45.455 0.00 0.00 0.00 2.57
2242 2662 3.679980 CGGATCGCCCTATTAACTGATTG 59.320 47.826 0.00 0.00 0.00 2.67
2243 2663 4.560716 CGGATCGCCCTATTAACTGATTGA 60.561 45.833 0.00 0.00 0.00 2.57
2244 2664 5.305585 GGATCGCCCTATTAACTGATTGAA 58.694 41.667 0.00 0.00 0.00 2.69
2245 2665 5.940470 GGATCGCCCTATTAACTGATTGAAT 59.060 40.000 0.00 0.00 0.00 2.57
2246 2666 6.128172 GGATCGCCCTATTAACTGATTGAATG 60.128 42.308 0.00 0.00 0.00 2.67
2247 2667 5.924356 TCGCCCTATTAACTGATTGAATGA 58.076 37.500 0.00 0.00 0.00 2.57
2248 2668 6.533730 TCGCCCTATTAACTGATTGAATGAT 58.466 36.000 0.00 0.00 0.00 2.45
2249 2669 6.427853 TCGCCCTATTAACTGATTGAATGATG 59.572 38.462 0.00 0.00 0.00 3.07
2250 2670 6.427853 CGCCCTATTAACTGATTGAATGATGA 59.572 38.462 0.00 0.00 0.00 2.92
2251 2671 7.120285 CGCCCTATTAACTGATTGAATGATGAT 59.880 37.037 0.00 0.00 0.00 2.45
2252 2672 8.800332 GCCCTATTAACTGATTGAATGATGATT 58.200 33.333 0.00 0.00 0.00 2.57
2266 2686 8.686397 TGAATGATGATTAAACGATTTTGTGG 57.314 30.769 0.00 0.00 0.00 4.17
2267 2687 8.303156 TGAATGATGATTAAACGATTTTGTGGT 58.697 29.630 0.00 0.00 0.00 4.16
2268 2688 8.687824 AATGATGATTAAACGATTTTGTGGTC 57.312 30.769 0.00 0.00 0.00 4.02
2269 2689 7.447374 TGATGATTAAACGATTTTGTGGTCT 57.553 32.000 0.00 0.00 0.00 3.85
2270 2690 8.554835 TGATGATTAAACGATTTTGTGGTCTA 57.445 30.769 0.00 0.00 0.00 2.59
2271 2691 9.004717 TGATGATTAAACGATTTTGTGGTCTAA 57.995 29.630 0.00 0.00 0.00 2.10
2272 2692 9.834628 GATGATTAAACGATTTTGTGGTCTAAA 57.165 29.630 0.00 0.00 0.00 1.85
2331 2868 0.962489 CGGGTGCTGAGTAGGGATAG 59.038 60.000 0.00 0.00 0.00 2.08
2332 2869 1.754555 CGGGTGCTGAGTAGGGATAGT 60.755 57.143 0.00 0.00 0.00 2.12
2513 3052 2.445845 AGGGTAGCAGGGCGCATA 60.446 61.111 10.83 0.00 46.13 3.14
2706 3329 4.754667 GGGGACGGAGCCGACAAC 62.755 72.222 16.83 6.37 42.83 3.32
2707 3330 4.754667 GGGACGGAGCCGACAACC 62.755 72.222 16.83 12.10 42.83 3.77
2708 3331 3.692406 GGACGGAGCCGACAACCT 61.692 66.667 16.83 0.00 42.83 3.50
2709 3332 2.432628 GACGGAGCCGACAACCTG 60.433 66.667 16.83 0.00 42.83 4.00
2710 3333 3.222354 GACGGAGCCGACAACCTGT 62.222 63.158 16.83 0.00 42.83 4.00
2711 3334 2.432628 CGGAGCCGACAACCTGTC 60.433 66.667 2.00 0.00 43.65 3.51
2719 3342 2.559785 GACAACCTGTCATGGGCTG 58.440 57.895 1.92 0.00 46.22 4.85
2720 3343 1.589716 GACAACCTGTCATGGGCTGC 61.590 60.000 1.92 0.00 46.22 5.25
2721 3344 1.303888 CAACCTGTCATGGGCTGCT 60.304 57.895 0.00 0.00 0.00 4.24
2722 3345 1.001641 AACCTGTCATGGGCTGCTC 60.002 57.895 0.00 0.00 0.00 4.26
2723 3346 1.782201 AACCTGTCATGGGCTGCTCA 61.782 55.000 3.90 3.90 0.00 4.26
2724 3347 1.451567 CCTGTCATGGGCTGCTCAG 60.452 63.158 8.73 0.25 0.00 3.35
2725 3348 1.451567 CTGTCATGGGCTGCTCAGG 60.452 63.158 8.06 8.06 0.00 3.86
2726 3349 2.124403 GTCATGGGCTGCTCAGGG 60.124 66.667 14.81 5.97 0.00 4.45
2727 3350 2.285592 TCATGGGCTGCTCAGGGA 60.286 61.111 14.81 8.43 0.00 4.20
2728 3351 2.192443 CATGGGCTGCTCAGGGAG 59.808 66.667 8.73 0.00 0.00 4.30
2729 3352 3.095163 ATGGGCTGCTCAGGGAGG 61.095 66.667 8.73 0.00 0.00 4.30
3007 3630 0.114168 ACCCCAAGCAGTTAATGGCA 59.886 50.000 0.00 0.00 32.71 4.92
3058 3682 2.098607 CCGAGTAGCGATTAACTGACCA 59.901 50.000 0.00 0.00 44.57 4.02
3213 3936 5.819991 ACTTGTATGGTGTTCCTGATGATT 58.180 37.500 0.00 0.00 34.23 2.57
3575 4299 9.482627 CAGTATCTTAATCTTCAGGTATGTTCC 57.517 37.037 0.00 0.00 0.00 3.62
4382 5107 3.730761 CAACAGCAGGCTCGCCAC 61.731 66.667 11.02 1.72 38.92 5.01
4618 5343 3.824133 TGATGCTTCAGGACCAATATGG 58.176 45.455 0.00 0.00 45.02 2.74
4946 5671 1.535462 GATGGATTTTATGACGCGGGG 59.465 52.381 12.47 0.00 0.00 5.73
5029 5754 6.565999 CGTGAAGTTATTCTTTTGGACAGGTC 60.566 42.308 0.00 0.00 36.40 3.85
5101 5829 7.212976 TGTATGCTCTTTCTGATTGGTCTATC 58.787 38.462 0.00 0.00 0.00 2.08
5449 6178 2.558359 AGCATCAAAACAAGCCAGTACC 59.442 45.455 0.00 0.00 0.00 3.34
5455 6184 1.498176 AACAAGCCAGTACCCCTCCC 61.498 60.000 0.00 0.00 0.00 4.30
5560 6289 1.003652 GCATTGCAGTTTGGTGTTTGC 60.004 47.619 3.15 0.00 37.09 3.68
5755 6484 3.010027 TCATGCTTGGAATGTTGTCCCTA 59.990 43.478 0.00 0.00 36.80 3.53
6284 7105 2.042162 ACTAGTAAACCAGGACGGAGGA 59.958 50.000 0.00 0.00 38.63 3.71
6500 7323 6.331572 TCACCCTGTATTGGTATGATATGGTT 59.668 38.462 0.00 0.00 33.84 3.67
6722 7650 5.291293 ACTAATTATGTGCACGTGGTTTC 57.709 39.130 21.92 0.18 0.00 2.78
6948 7880 5.933790 TGTTTCATGTATTTACTTGGCGTC 58.066 37.500 0.00 0.00 33.60 5.19
7210 8142 8.859090 ACTGAAGGTAAATTCATTTGTTCATCA 58.141 29.630 0.00 0.00 38.47 3.07
7230 8162 8.985315 TCATCATTATGAGCCTTCTTGTATTT 57.015 30.769 0.29 0.00 37.20 1.40
7371 8308 2.481952 ACATTGCTCGAGAAGTTGCTTC 59.518 45.455 18.75 0.96 40.45 3.86
7442 8379 4.853924 AGCGAGAATGTTTTGGTTGATT 57.146 36.364 0.00 0.00 0.00 2.57
7492 8429 6.367422 CACCAGTAGTCAAACTCTCTGATTTC 59.633 42.308 11.29 0.00 34.52 2.17
7664 8601 4.177165 AGCATTCATTTGAACATTGCGA 57.823 36.364 10.19 0.00 40.52 5.10
7882 8860 5.163216 TGCCATGTATCCTGTGTGATGATTA 60.163 40.000 0.00 0.00 0.00 1.75
7972 8950 8.854614 AGCCACTTGGATTTCAGTATATTATC 57.145 34.615 0.00 0.00 37.39 1.75
8024 9004 2.959465 ATCAGCAAATAGGCCCCTAC 57.041 50.000 0.00 0.00 0.00 3.18
8100 9080 4.893424 AAATAAAGCGGTATTGATGCGT 57.107 36.364 0.00 0.00 0.00 5.24
8145 9126 5.338708 GGAAGTGGATATCTGGTCATATGGG 60.339 48.000 2.13 0.00 0.00 4.00
8175 9156 1.909376 TCGAGATGCTTACACTTCGC 58.091 50.000 0.00 0.00 35.85 4.70
8558 9539 2.158986 ACATGCTATGACCTGAGCTGAC 60.159 50.000 0.00 0.00 39.54 3.51
8561 9542 0.755686 CTATGACCTGAGCTGACCCC 59.244 60.000 0.00 0.00 0.00 4.95
8568 9549 1.903877 CTGAGCTGACCCCGTGGATT 61.904 60.000 0.00 0.00 34.81 3.01
8590 9571 4.914983 TCTGAATGAGAAAGCTGATGGTT 58.085 39.130 0.00 0.00 35.14 3.67
8611 9592 4.416533 CAGTCTCGCTGCCAGATC 57.583 61.111 0.00 0.00 38.52 2.75
8636 9617 1.000060 TCGGTCAGGACAGGTTAAACG 60.000 52.381 1.41 0.00 0.00 3.60
8639 9620 1.345415 GTCAGGACAGGTTAAACGGGA 59.655 52.381 0.00 0.00 0.00 5.14
8641 9622 1.071071 CAGGACAGGTTAAACGGGACA 59.929 52.381 0.00 0.00 0.00 4.02
8643 9624 1.154197 GACAGGTTAAACGGGACAGC 58.846 55.000 0.00 0.00 0.00 4.40
8655 9636 1.414158 GGGACAGCTATAGCAGGTCA 58.586 55.000 32.58 0.00 44.21 4.02
8656 9637 1.974236 GGGACAGCTATAGCAGGTCAT 59.026 52.381 32.58 12.76 44.21 3.06
8674 9655 0.924823 ATTGGATCTGGCCAGCTTCT 59.075 50.000 28.91 12.12 39.52 2.85
8761 9742 3.243737 GGAAAAAGTCAAACCAAGGCGAT 60.244 43.478 0.00 0.00 0.00 4.58
8765 9746 1.976474 TCAAACCAAGGCGATGGGC 60.976 57.895 15.36 0.00 45.18 5.36
8880 9861 9.308318 GTGTGTGTATGTGTATGTCATGTAATA 57.692 33.333 0.00 0.00 0.00 0.98
8990 9979 5.562917 TGTATCTGTGTACGTACGATTGTC 58.437 41.667 24.41 8.56 0.00 3.18
9004 9993 2.507110 ATTGTCGGTCCAGCGGTGAG 62.507 60.000 17.83 6.46 0.00 3.51
9014 10003 4.617875 GCGGTGAGCCATGTAACT 57.382 55.556 0.00 0.00 40.81 2.24
9095 10086 2.760092 GTTATGATTTCCCTGCCAGCAA 59.240 45.455 0.00 0.00 0.00 3.91
9103 10094 2.378038 TCCCTGCCAGCAATTGTATTC 58.622 47.619 7.40 0.00 0.00 1.75
9104 10095 2.101783 CCCTGCCAGCAATTGTATTCA 58.898 47.619 7.40 0.43 0.00 2.57
9114 10105 5.678483 CAGCAATTGTATTCATAGTTGTCGC 59.322 40.000 7.40 0.00 0.00 5.19
9119 10110 0.814010 ATTCATAGTTGTCGCCGGCC 60.814 55.000 23.46 8.57 0.00 6.13
9157 10148 1.002033 GTGGCTGTGCAAAGTCAAGAG 60.002 52.381 14.05 0.00 32.56 2.85
9162 10153 4.202010 GGCTGTGCAAAGTCAAGAGTTTTA 60.202 41.667 2.82 0.00 32.02 1.52
9163 10154 5.507985 GGCTGTGCAAAGTCAAGAGTTTTAT 60.508 40.000 2.82 0.00 32.02 1.40
9168 10159 6.142958 GTGCAAAGTCAAGAGTTTTATTCAGC 59.857 38.462 0.27 1.77 32.02 4.26
9190 10181 7.124901 TCAGCATATCATTAGTATTCCCTCCTC 59.875 40.741 0.00 0.00 0.00 3.71
9191 10182 6.385467 AGCATATCATTAGTATTCCCTCCTCC 59.615 42.308 0.00 0.00 0.00 4.30
9193 10184 7.634649 GCATATCATTAGTATTCCCTCCTCCAG 60.635 44.444 0.00 0.00 0.00 3.86
9197 10188 6.104243 TCATTAGTATTCCCTCCTCCAGAGTA 59.896 42.308 0.00 0.00 41.47 2.59
9198 10189 4.187506 AGTATTCCCTCCTCCAGAGTAC 57.812 50.000 0.00 0.00 41.47 2.73
9199 10190 3.532232 AGTATTCCCTCCTCCAGAGTACA 59.468 47.826 0.00 0.00 41.47 2.90
9200 10191 2.534042 TTCCCTCCTCCAGAGTACAG 57.466 55.000 0.00 0.00 41.47 2.74
9201 10192 0.033011 TCCCTCCTCCAGAGTACAGC 60.033 60.000 0.00 0.00 41.47 4.40
9202 10193 1.388065 CCCTCCTCCAGAGTACAGCG 61.388 65.000 0.00 0.00 41.47 5.18
9203 10194 1.435515 CTCCTCCAGAGTACAGCGC 59.564 63.158 0.00 0.00 37.87 5.92
9204 10195 1.000771 TCCTCCAGAGTACAGCGCT 60.001 57.895 2.64 2.64 0.00 5.92
9206 10197 0.665835 CCTCCAGAGTACAGCGCTAG 59.334 60.000 10.99 7.53 0.00 3.42
9207 10198 1.384525 CTCCAGAGTACAGCGCTAGT 58.615 55.000 10.99 13.71 0.00 2.57
9208 10199 1.064803 CTCCAGAGTACAGCGCTAGTG 59.935 57.143 10.99 0.20 0.00 2.74
9209 10200 0.526524 CCAGAGTACAGCGCTAGTGC 60.527 60.000 20.73 20.73 0.00 4.40
9210 10201 0.171231 CAGAGTACAGCGCTAGTGCA 59.829 55.000 28.83 6.88 39.64 4.57
9211 10202 1.107114 AGAGTACAGCGCTAGTGCAT 58.893 50.000 28.83 18.78 39.64 3.96
9212 10203 2.033424 CAGAGTACAGCGCTAGTGCATA 59.967 50.000 28.83 17.79 39.64 3.14
9213 10204 2.033550 AGAGTACAGCGCTAGTGCATAC 59.966 50.000 28.83 26.28 39.64 2.39
9214 10205 2.025155 AGTACAGCGCTAGTGCATACT 58.975 47.619 28.83 27.76 40.99 2.12
9215 10206 2.033550 AGTACAGCGCTAGTGCATACTC 59.966 50.000 28.83 14.77 35.40 2.59
9216 10207 0.103208 ACAGCGCTAGTGCATACTCC 59.897 55.000 28.83 0.00 38.36 3.85
9217 10208 0.103026 CAGCGCTAGTGCATACTCCA 59.897 55.000 28.83 0.00 38.36 3.86
9262 10259 2.850647 GGATGCAAAGTCTCGTACGTAC 59.149 50.000 15.90 15.90 0.00 3.67
9325 10322 3.831715 AAATCTTGGAAAGTGCGCTAC 57.168 42.857 9.73 5.32 46.34 3.58
9377 10378 3.130340 ACATTTCAAACAACGAAGGCTGT 59.870 39.130 0.00 0.00 0.00 4.40
9516 10760 3.857217 CTCCAGCAGAGCATCAACT 57.143 52.632 0.00 0.00 37.82 3.16
9517 10761 2.110901 CTCCAGCAGAGCATCAACTT 57.889 50.000 0.00 0.00 37.82 2.66
9518 10762 2.434428 CTCCAGCAGAGCATCAACTTT 58.566 47.619 0.00 0.00 37.82 2.66
9519 10763 3.603532 CTCCAGCAGAGCATCAACTTTA 58.396 45.455 0.00 0.00 37.82 1.85
9520 10764 3.338249 TCCAGCAGAGCATCAACTTTAC 58.662 45.455 0.00 0.00 37.82 2.01
9521 10765 3.076621 CCAGCAGAGCATCAACTTTACA 58.923 45.455 0.00 0.00 37.82 2.41
9522 10766 3.120060 CCAGCAGAGCATCAACTTTACAC 60.120 47.826 0.00 0.00 37.82 2.90
9523 10767 3.750130 CAGCAGAGCATCAACTTTACACT 59.250 43.478 0.00 0.00 37.82 3.55
9524 10768 3.999663 AGCAGAGCATCAACTTTACACTC 59.000 43.478 0.00 0.00 37.82 3.51
9525 10769 3.999663 GCAGAGCATCAACTTTACACTCT 59.000 43.478 0.00 0.00 37.82 3.24
9526 10770 4.453819 GCAGAGCATCAACTTTACACTCTT 59.546 41.667 0.00 0.00 37.82 2.85
9527 10771 5.049129 GCAGAGCATCAACTTTACACTCTTT 60.049 40.000 0.00 0.00 37.82 2.52
9528 10772 6.514048 GCAGAGCATCAACTTTACACTCTTTT 60.514 38.462 0.00 0.00 37.82 2.27
9529 10773 7.420800 CAGAGCATCAACTTTACACTCTTTTT 58.579 34.615 0.00 0.00 37.82 1.94
9552 10796 7.817418 TTTTTGGAGTAGCATCAACTTTACT 57.183 32.000 0.00 0.00 0.00 2.24
9553 10797 7.817418 TTTTGGAGTAGCATCAACTTTACTT 57.183 32.000 0.00 0.00 0.00 2.24
9554 10798 6.801539 TTGGAGTAGCATCAACTTTACTTG 57.198 37.500 0.00 0.00 0.00 3.16
9555 10799 5.245531 TGGAGTAGCATCAACTTTACTTGG 58.754 41.667 0.00 0.00 0.00 3.61
9556 10800 5.221843 TGGAGTAGCATCAACTTTACTTGGT 60.222 40.000 0.00 0.00 0.00 3.67
9557 10801 5.122396 GGAGTAGCATCAACTTTACTTGGTG 59.878 44.000 0.00 0.00 35.64 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
482 489 2.097038 CGACTCCTTCTGCCGCTTG 61.097 63.158 0.00 0.00 0.00 4.01
568 575 0.107703 TGGTTGATCCACATCGCTCC 60.108 55.000 0.00 0.00 41.93 4.70
605 614 1.251251 CCACTTTGAAAGAGGCCCAG 58.749 55.000 12.53 0.00 32.51 4.45
800 816 3.838903 AGTTTCTGTCTCGAGGGGTAAAT 59.161 43.478 13.56 0.33 0.00 1.40
854 870 5.420104 GGGGGAGCGTATAAGTTAAGCTATA 59.580 44.000 9.80 0.00 38.39 1.31
878 894 0.933700 AAGAGAGAGAGGAGGAGGGG 59.066 60.000 0.00 0.00 0.00 4.79
882 898 2.292587 GGGGAAAAGAGAGAGAGGAGGA 60.293 54.545 0.00 0.00 0.00 3.71
885 901 2.292587 GGAGGGGAAAAGAGAGAGAGGA 60.293 54.545 0.00 0.00 0.00 3.71
886 902 2.115427 GGAGGGGAAAAGAGAGAGAGG 58.885 57.143 0.00 0.00 0.00 3.69
897 913 2.121872 TGAACGGGGGAGGGGAAA 60.122 61.111 0.00 0.00 0.00 3.13
900 916 4.029809 GTGTGAACGGGGGAGGGG 62.030 72.222 0.00 0.00 0.00 4.79
904 920 0.898789 GAGAGAGTGTGAACGGGGGA 60.899 60.000 0.00 0.00 0.00 4.81
905 921 1.592223 GAGAGAGTGTGAACGGGGG 59.408 63.158 0.00 0.00 0.00 5.40
1460 1753 4.389374 CTGTCAATTGAGGTAGTGGTGTT 58.611 43.478 8.80 0.00 0.00 3.32
1522 1821 9.651913 ACAGTAAATTAACCATAAGCAATTTGG 57.348 29.630 0.00 0.00 33.75 3.28
1614 1913 2.719531 TGGCACTAGAAAACACACCA 57.280 45.000 0.00 0.00 0.00 4.17
1615 1914 4.584327 AAATGGCACTAGAAAACACACC 57.416 40.909 0.00 0.00 0.00 4.16
1728 2030 2.742428 ATTGCACCAGACCAGCATAT 57.258 45.000 0.00 0.00 38.19 1.78
1729 2031 2.512692 AATTGCACCAGACCAGCATA 57.487 45.000 0.00 0.00 38.19 3.14
1730 2032 1.636148 AAATTGCACCAGACCAGCAT 58.364 45.000 0.00 0.00 38.19 3.79
1731 2033 1.412079 AAAATTGCACCAGACCAGCA 58.588 45.000 0.00 0.00 36.32 4.41
1733 2035 2.364970 TGGAAAAATTGCACCAGACCAG 59.635 45.455 0.00 0.00 0.00 4.00
1735 2037 3.328505 CATGGAAAAATTGCACCAGACC 58.671 45.455 0.00 0.00 35.84 3.85
1736 2038 2.738314 GCATGGAAAAATTGCACCAGAC 59.262 45.455 0.00 0.00 36.40 3.51
1737 2039 2.289569 GGCATGGAAAAATTGCACCAGA 60.290 45.455 0.00 0.00 38.12 3.86
1738 2040 2.078392 GGCATGGAAAAATTGCACCAG 58.922 47.619 0.00 0.00 38.12 4.00
1837 2140 7.698130 CAGCTAATGTGCAGGTTATAAAACTTC 59.302 37.037 0.00 0.00 34.06 3.01
1976 2279 2.582052 CACTGCCAAACTAGGGAAACA 58.418 47.619 0.00 0.00 0.00 2.83
1977 2280 1.269723 GCACTGCCAAACTAGGGAAAC 59.730 52.381 0.00 0.00 0.00 2.78
1978 2281 1.133637 TGCACTGCCAAACTAGGGAAA 60.134 47.619 0.00 0.00 0.00 3.13
1979 2282 0.476338 TGCACTGCCAAACTAGGGAA 59.524 50.000 0.00 0.00 0.00 3.97
2161 2581 4.335315 CACCAGTTGAGAGTTTTGCTACAA 59.665 41.667 0.00 0.00 0.00 2.41
2162 2582 3.876914 CACCAGTTGAGAGTTTTGCTACA 59.123 43.478 0.00 0.00 0.00 2.74
2163 2583 3.251004 CCACCAGTTGAGAGTTTTGCTAC 59.749 47.826 0.00 0.00 0.00 3.58
2164 2584 3.476552 CCACCAGTTGAGAGTTTTGCTA 58.523 45.455 0.00 0.00 0.00 3.49
2165 2585 2.301346 CCACCAGTTGAGAGTTTTGCT 58.699 47.619 0.00 0.00 0.00 3.91
2166 2586 1.269257 GCCACCAGTTGAGAGTTTTGC 60.269 52.381 0.00 0.00 0.00 3.68
2167 2587 2.023673 TGCCACCAGTTGAGAGTTTTG 58.976 47.619 0.00 0.00 0.00 2.44
2168 2588 2.435372 TGCCACCAGTTGAGAGTTTT 57.565 45.000 0.00 0.00 0.00 2.43
2169 2589 2.664402 ATGCCACCAGTTGAGAGTTT 57.336 45.000 0.00 0.00 0.00 2.66
2170 2590 3.679917 CGATATGCCACCAGTTGAGAGTT 60.680 47.826 0.00 0.00 0.00 3.01
2171 2591 2.159043 CGATATGCCACCAGTTGAGAGT 60.159 50.000 0.00 0.00 0.00 3.24
2172 2592 2.477825 CGATATGCCACCAGTTGAGAG 58.522 52.381 0.00 0.00 0.00 3.20
2173 2593 1.138859 CCGATATGCCACCAGTTGAGA 59.861 52.381 0.00 0.00 0.00 3.27
2174 2594 1.134401 ACCGATATGCCACCAGTTGAG 60.134 52.381 0.00 0.00 0.00 3.02
2175 2595 0.908910 ACCGATATGCCACCAGTTGA 59.091 50.000 0.00 0.00 0.00 3.18
2176 2596 1.299541 GACCGATATGCCACCAGTTG 58.700 55.000 0.00 0.00 0.00 3.16
2177 2597 0.179084 CGACCGATATGCCACCAGTT 60.179 55.000 0.00 0.00 0.00 3.16
2178 2598 1.441729 CGACCGATATGCCACCAGT 59.558 57.895 0.00 0.00 0.00 4.00
2179 2599 1.300931 CCGACCGATATGCCACCAG 60.301 63.158 0.00 0.00 0.00 4.00
2180 2600 2.802724 CCCGACCGATATGCCACCA 61.803 63.158 0.00 0.00 0.00 4.17
2181 2601 2.030562 CCCGACCGATATGCCACC 59.969 66.667 0.00 0.00 0.00 4.61
2182 2602 1.594293 CACCCGACCGATATGCCAC 60.594 63.158 0.00 0.00 0.00 5.01
2183 2603 2.818841 CACCCGACCGATATGCCA 59.181 61.111 0.00 0.00 0.00 4.92
2184 2604 1.812686 TAGCACCCGACCGATATGCC 61.813 60.000 8.22 0.00 36.96 4.40
2185 2605 0.032952 TTAGCACCCGACCGATATGC 59.967 55.000 0.00 0.00 36.52 3.14
2186 2606 1.340248 ACTTAGCACCCGACCGATATG 59.660 52.381 0.00 0.00 0.00 1.78
2187 2607 1.700955 ACTTAGCACCCGACCGATAT 58.299 50.000 0.00 0.00 0.00 1.63
2188 2608 2.224606 CTACTTAGCACCCGACCGATA 58.775 52.381 0.00 0.00 0.00 2.92
2189 2609 1.030457 CTACTTAGCACCCGACCGAT 58.970 55.000 0.00 0.00 0.00 4.18
2190 2610 1.033746 CCTACTTAGCACCCGACCGA 61.034 60.000 0.00 0.00 0.00 4.69
2191 2611 1.436336 CCTACTTAGCACCCGACCG 59.564 63.158 0.00 0.00 0.00 4.79
2192 2612 0.685458 TCCCTACTTAGCACCCGACC 60.685 60.000 0.00 0.00 0.00 4.79
2193 2613 1.411041 ATCCCTACTTAGCACCCGAC 58.589 55.000 0.00 0.00 0.00 4.79
2194 2614 3.317455 TTATCCCTACTTAGCACCCGA 57.683 47.619 0.00 0.00 0.00 5.14
2195 2615 4.618920 ATTTATCCCTACTTAGCACCCG 57.381 45.455 0.00 0.00 0.00 5.28
2196 2616 5.070685 CCAATTTATCCCTACTTAGCACCC 58.929 45.833 0.00 0.00 0.00 4.61
2197 2617 4.519350 GCCAATTTATCCCTACTTAGCACC 59.481 45.833 0.00 0.00 0.00 5.01
2198 2618 4.213482 CGCCAATTTATCCCTACTTAGCAC 59.787 45.833 0.00 0.00 0.00 4.40
2199 2619 4.385825 CGCCAATTTATCCCTACTTAGCA 58.614 43.478 0.00 0.00 0.00 3.49
2200 2620 3.751698 CCGCCAATTTATCCCTACTTAGC 59.248 47.826 0.00 0.00 0.00 3.09
2201 2621 5.223449 TCCGCCAATTTATCCCTACTTAG 57.777 43.478 0.00 0.00 0.00 2.18
2202 2622 5.568023 CGATCCGCCAATTTATCCCTACTTA 60.568 44.000 0.00 0.00 0.00 2.24
2203 2623 4.652822 GATCCGCCAATTTATCCCTACTT 58.347 43.478 0.00 0.00 0.00 2.24
2204 2624 3.306780 CGATCCGCCAATTTATCCCTACT 60.307 47.826 0.00 0.00 0.00 2.57
2205 2625 3.000727 CGATCCGCCAATTTATCCCTAC 58.999 50.000 0.00 0.00 0.00 3.18
2206 2626 3.328382 CGATCCGCCAATTTATCCCTA 57.672 47.619 0.00 0.00 0.00 3.53
2207 2627 2.185004 CGATCCGCCAATTTATCCCT 57.815 50.000 0.00 0.00 0.00 4.20
2220 2640 3.594603 ATCAGTTAATAGGGCGATCCG 57.405 47.619 0.00 0.00 41.52 4.18
2221 2641 4.894784 TCAATCAGTTAATAGGGCGATCC 58.105 43.478 0.00 0.00 0.00 3.36
2222 2642 6.650807 TCATTCAATCAGTTAATAGGGCGATC 59.349 38.462 0.00 0.00 0.00 3.69
2223 2643 6.533730 TCATTCAATCAGTTAATAGGGCGAT 58.466 36.000 0.00 0.00 0.00 4.58
2224 2644 5.924356 TCATTCAATCAGTTAATAGGGCGA 58.076 37.500 0.00 0.00 0.00 5.54
2225 2645 6.427853 TCATCATTCAATCAGTTAATAGGGCG 59.572 38.462 0.00 0.00 0.00 6.13
2226 2646 7.750229 TCATCATTCAATCAGTTAATAGGGC 57.250 36.000 0.00 0.00 0.00 5.19
2240 2660 9.138062 CCACAAAATCGTTTAATCATCATTCAA 57.862 29.630 0.00 0.00 0.00 2.69
2241 2661 8.303156 ACCACAAAATCGTTTAATCATCATTCA 58.697 29.630 0.00 0.00 0.00 2.57
2242 2662 8.687824 ACCACAAAATCGTTTAATCATCATTC 57.312 30.769 0.00 0.00 0.00 2.67
2243 2663 8.522830 AGACCACAAAATCGTTTAATCATCATT 58.477 29.630 0.00 0.00 0.00 2.57
2244 2664 8.055279 AGACCACAAAATCGTTTAATCATCAT 57.945 30.769 0.00 0.00 0.00 2.45
2245 2665 7.447374 AGACCACAAAATCGTTTAATCATCA 57.553 32.000 0.00 0.00 0.00 3.07
2246 2666 9.834628 TTTAGACCACAAAATCGTTTAATCATC 57.165 29.630 0.00 0.00 0.00 2.92
2254 2674 9.458374 CAACTAAATTTAGACCACAAAATCGTT 57.542 29.630 27.92 8.17 34.84 3.85
2255 2675 8.626526 ACAACTAAATTTAGACCACAAAATCGT 58.373 29.630 27.92 2.64 34.84 3.73
2258 2678 9.908152 GCTACAACTAAATTTAGACCACAAAAT 57.092 29.630 27.92 3.18 34.84 1.82
2259 2679 8.904834 TGCTACAACTAAATTTAGACCACAAAA 58.095 29.630 27.92 7.64 34.84 2.44
2260 2680 8.453238 TGCTACAACTAAATTTAGACCACAAA 57.547 30.769 27.92 8.85 34.84 2.83
2261 2681 8.453238 TTGCTACAACTAAATTTAGACCACAA 57.547 30.769 27.92 19.44 34.84 3.33
2262 2682 8.453238 TTTGCTACAACTAAATTTAGACCACA 57.547 30.769 27.92 15.74 34.84 4.17
2263 2683 9.908152 ATTTTGCTACAACTAAATTTAGACCAC 57.092 29.630 27.92 13.80 34.84 4.16
2272 2692 9.683069 CAGTTGAGAATTTTGCTACAACTAAAT 57.317 29.630 0.00 0.00 43.48 1.40
2273 2693 8.134895 CCAGTTGAGAATTTTGCTACAACTAAA 58.865 33.333 0.00 0.00 43.48 1.85
2274 2694 7.284489 ACCAGTTGAGAATTTTGCTACAACTAA 59.716 33.333 0.00 0.00 43.48 2.24
2275 2695 6.770785 ACCAGTTGAGAATTTTGCTACAACTA 59.229 34.615 0.00 0.00 43.48 2.24
2276 2696 5.594317 ACCAGTTGAGAATTTTGCTACAACT 59.406 36.000 0.00 0.00 45.25 3.16
2277 2697 5.831997 ACCAGTTGAGAATTTTGCTACAAC 58.168 37.500 0.00 0.00 38.15 3.32
2513 3052 3.499918 GTGTTGTACTTCTGCTGCTGATT 59.500 43.478 10.09 3.63 0.00 2.57
2580 3119 2.302260 CTTCATCGTCTGCTCCTCCTA 58.698 52.381 0.00 0.00 0.00 2.94
2705 3328 2.194388 CTGAGCAGCCCATGACAGGT 62.194 60.000 0.00 0.00 33.88 4.00
2706 3329 1.451567 CTGAGCAGCCCATGACAGG 60.452 63.158 0.00 0.00 33.88 4.00
2707 3330 1.451567 CCTGAGCAGCCCATGACAG 60.452 63.158 0.00 0.00 35.81 3.51
2708 3331 2.672908 CCTGAGCAGCCCATGACA 59.327 61.111 0.00 0.00 0.00 3.58
2709 3332 2.124403 CCCTGAGCAGCCCATGAC 60.124 66.667 0.00 0.00 0.00 3.06
2710 3333 2.285592 TCCCTGAGCAGCCCATGA 60.286 61.111 0.00 0.00 0.00 3.07
2711 3334 2.192443 CTCCCTGAGCAGCCCATG 59.808 66.667 0.00 0.00 0.00 3.66
2712 3335 3.095163 CCTCCCTGAGCAGCCCAT 61.095 66.667 0.00 0.00 0.00 4.00
2740 3363 3.300013 AGCCCCTAACGAGCTGTC 58.700 61.111 0.00 0.00 34.99 3.51
2743 3366 2.685380 AGCAGCCCCTAACGAGCT 60.685 61.111 0.00 0.00 37.32 4.09
2750 3373 2.041508 CTCCCTGAGCAGCCCCTA 60.042 66.667 0.00 0.00 0.00 3.53
2988 3611 0.114168 TGCCATTAACTGCTTGGGGT 59.886 50.000 0.38 0.00 0.00 4.95
3007 3630 4.263068 CCAGATATGAAAGGCCCTATTCGT 60.263 45.833 0.00 6.30 0.00 3.85
3271 3995 9.855021 AGATATTTAAAAAGGAATGTGAAACCG 57.145 29.630 0.00 0.00 34.36 4.44
3575 4299 4.301628 GTGGAAAGCAAAACTTCTGATGG 58.698 43.478 0.00 0.00 37.75 3.51
3914 4638 2.050144 ACTTCTCTCTCTGGCAAACCA 58.950 47.619 0.00 0.00 46.51 3.67
3915 4639 2.810852 CAACTTCTCTCTCTGGCAAACC 59.189 50.000 0.00 0.00 0.00 3.27
4382 5107 2.383527 GCTGGACTCCAAACGCTCG 61.384 63.158 0.00 0.00 30.80 5.03
4618 5343 8.134895 TCATATTTATTCCAGTTTTTCCATCGC 58.865 33.333 0.00 0.00 0.00 4.58
4946 5671 0.164647 GCATGAACGGCATATCTCGC 59.835 55.000 0.00 0.00 34.82 5.03
5029 5754 2.315925 ACGGATAGGAATGTGCACTG 57.684 50.000 19.41 0.00 0.00 3.66
5101 5829 5.303165 TGCAAACATATCCTATGCTCTCAG 58.697 41.667 0.00 0.00 37.86 3.35
5455 6184 2.556622 ACCAGTAAAATTGAAGTGCCCG 59.443 45.455 0.00 0.00 0.00 6.13
5503 6232 7.619302 ACAATGCCTGAATTATTCCTTTCCTTA 59.381 33.333 2.22 0.00 0.00 2.69
5560 6289 1.888436 TTAGGACAGCTCGGTGCCTG 61.888 60.000 16.71 0.01 44.23 4.85
5755 6484 8.440771 CCTTACCAAGATATTCCCTTGTCTAAT 58.559 37.037 0.00 0.00 39.36 1.73
6722 7650 1.137086 CGACTGAGGGGAACATACCTG 59.863 57.143 0.00 0.00 37.18 4.00
6948 7880 2.418628 ACCGTATCTGCATTTGAAACCG 59.581 45.455 0.00 0.00 0.00 4.44
7210 8142 8.579850 TCAACAAATACAAGAAGGCTCATAAT 57.420 30.769 0.00 0.00 0.00 1.28
7280 8216 7.386059 AGTTTTGTCAAATAGCCCTAATTTGG 58.614 34.615 0.00 0.00 36.32 3.28
7371 8308 1.610038 TGTGCATCTCCAACAAAGCAG 59.390 47.619 0.00 0.00 32.03 4.24
7442 8379 3.118629 CCATGACTCCTCTTCGAATCCAA 60.119 47.826 0.00 0.00 0.00 3.53
7492 8429 2.358957 TGCAAAGGAATGGATCTGTCG 58.641 47.619 0.00 0.00 0.00 4.35
7677 8617 8.242729 TCAGAGCTATTCAATATGAGTTGAGA 57.757 34.615 0.00 0.00 39.13 3.27
7717 8695 2.836981 AGAAACATGGCTGAGCTACTCT 59.163 45.455 3.72 0.00 0.00 3.24
7882 8860 6.326064 ACAGGATAGTCAGCAATCAGAGTAAT 59.674 38.462 0.00 0.00 0.00 1.89
8024 9004 7.397476 TCTGATTAGCATAATCTGGTAGGTAGG 59.603 40.741 13.24 0.00 38.94 3.18
8100 9080 6.788598 TCCTGCATCAAAGCCATATTTAAA 57.211 33.333 0.00 0.00 0.00 1.52
8145 9126 8.818057 AGTGTAAGCATCTCGAATATAAAACAC 58.182 33.333 7.64 7.64 33.09 3.32
8308 9289 8.544687 TCTTCCTCTGATGAGATAGAATTCAA 57.455 34.615 8.44 0.00 42.73 2.69
8319 9300 4.155644 GCCTTTGTTTCTTCCTCTGATGAG 59.844 45.833 0.00 0.00 39.92 2.90
8395 9376 1.075601 TGATCCCCAACTTCAGCCTT 58.924 50.000 0.00 0.00 0.00 4.35
8482 9463 3.405093 CTTGGGGCGCCTAGATGCA 62.405 63.158 28.56 2.56 0.00 3.96
8558 9539 1.486310 TCTCATTCAGAATCCACGGGG 59.514 52.381 0.00 0.00 0.00 5.73
8561 9542 3.937706 AGCTTTCTCATTCAGAATCCACG 59.062 43.478 0.00 0.00 41.02 4.94
8568 9549 4.564782 ACCATCAGCTTTCTCATTCAGA 57.435 40.909 0.00 0.00 0.00 3.27
8611 9592 4.135153 CTGTCCTGACCGAGGCCG 62.135 72.222 0.00 0.00 42.47 6.13
8617 9598 1.425412 CGTTTAACCTGTCCTGACCG 58.575 55.000 0.00 0.00 0.00 4.79
8636 9617 1.414158 TGACCTGCTATAGCTGTCCC 58.586 55.000 29.10 18.97 40.35 4.46
8639 9620 3.041211 TCCAATGACCTGCTATAGCTGT 58.959 45.455 24.61 20.44 42.66 4.40
8641 9622 4.020396 CAGATCCAATGACCTGCTATAGCT 60.020 45.833 24.61 5.44 42.66 3.32
8643 9624 4.829968 CCAGATCCAATGACCTGCTATAG 58.170 47.826 0.00 0.00 0.00 1.31
8655 9636 0.924823 AGAAGCTGGCCAGATCCAAT 59.075 50.000 37.21 15.72 35.36 3.16
8656 9637 0.034767 CAGAAGCTGGCCAGATCCAA 60.035 55.000 37.21 0.00 35.36 3.53
8765 9746 2.863153 CTTCAGCGGCCAAAGTCG 59.137 61.111 2.24 0.00 46.28 4.18
8823 9804 2.037251 GGAGACTGCTACAACAGGTGAA 59.963 50.000 0.00 0.00 42.21 3.18
8916 9900 9.880064 CGATAACTTAGAAGACTCGATTGAATA 57.120 33.333 0.00 0.00 31.56 1.75
8917 9901 8.622157 TCGATAACTTAGAAGACTCGATTGAAT 58.378 33.333 0.00 0.00 32.99 2.57
8919 9903 7.549615 TCGATAACTTAGAAGACTCGATTGA 57.450 36.000 0.00 0.00 32.99 2.57
8920 9904 8.789881 AATCGATAACTTAGAAGACTCGATTG 57.210 34.615 23.63 7.09 43.52 2.67
8923 9907 8.557864 CCTAAATCGATAACTTAGAAGACTCGA 58.442 37.037 14.28 13.57 37.74 4.04
8924 9908 8.344098 ACCTAAATCGATAACTTAGAAGACTCG 58.656 37.037 14.28 2.21 0.00 4.18
8925 9909 9.667989 GACCTAAATCGATAACTTAGAAGACTC 57.332 37.037 14.28 1.61 0.00 3.36
8926 9910 9.186837 TGACCTAAATCGATAACTTAGAAGACT 57.813 33.333 14.28 0.00 0.00 3.24
8929 9913 9.250624 CCTTGACCTAAATCGATAACTTAGAAG 57.749 37.037 14.28 10.52 0.00 2.85
8930 9914 7.709613 GCCTTGACCTAAATCGATAACTTAGAA 59.290 37.037 14.28 3.60 0.00 2.10
9004 9993 5.355350 ACTCAGCATTCTAAAGTTACATGGC 59.645 40.000 0.00 0.00 0.00 4.40
9014 10003 7.561021 TTGTTACACAACTCAGCATTCTAAA 57.439 32.000 0.00 0.00 32.34 1.85
9060 10049 3.769739 TCATAACACACAGCCTCTGTT 57.230 42.857 0.00 0.00 42.59 3.16
9061 10050 3.988976 ATCATAACACACAGCCTCTGT 57.011 42.857 0.00 0.00 46.51 3.41
9062 10051 4.095483 GGAAATCATAACACACAGCCTCTG 59.905 45.833 0.00 0.00 37.52 3.35
9095 10086 3.807622 CCGGCGACAACTATGAATACAAT 59.192 43.478 9.30 0.00 0.00 2.71
9103 10094 1.302383 TTTGGCCGGCGACAACTATG 61.302 55.000 22.54 0.00 0.00 2.23
9104 10095 0.606944 TTTTGGCCGGCGACAACTAT 60.607 50.000 22.54 0.00 0.00 2.12
9114 10105 1.577421 CCTGTAACGTTTTGGCCGG 59.423 57.895 5.91 0.00 0.00 6.13
9119 10110 0.306533 ACAGCGCCTGTAACGTTTTG 59.693 50.000 5.91 0.00 43.46 2.44
9162 10153 8.270744 GGAGGGAATACTAATGATATGCTGAAT 58.729 37.037 0.00 0.00 0.00 2.57
9163 10154 7.459125 AGGAGGGAATACTAATGATATGCTGAA 59.541 37.037 0.00 0.00 0.00 3.02
9168 10159 7.621285 TCTGGAGGAGGGAATACTAATGATATG 59.379 40.741 0.00 0.00 0.00 1.78
9173 10164 5.151454 ACTCTGGAGGAGGGAATACTAATG 58.849 45.833 2.58 0.00 45.83 1.90
9181 10172 1.619977 GCTGTACTCTGGAGGAGGGAA 60.620 57.143 2.58 0.00 45.83 3.97
9183 10174 1.388065 CGCTGTACTCTGGAGGAGGG 61.388 65.000 2.58 0.75 45.83 4.30
9184 10175 2.010582 GCGCTGTACTCTGGAGGAGG 62.011 65.000 0.00 0.00 45.83 4.30
9185 10176 1.034838 AGCGCTGTACTCTGGAGGAG 61.035 60.000 10.39 0.00 46.87 3.69
9186 10177 0.255033 TAGCGCTGTACTCTGGAGGA 59.745 55.000 22.90 0.00 0.00 3.71
9190 10181 0.526524 GCACTAGCGCTGTACTCTGG 60.527 60.000 22.90 4.48 0.00 3.86
9191 10182 0.171231 TGCACTAGCGCTGTACTCTG 59.829 55.000 22.90 6.80 46.23 3.35
9193 10184 2.033550 AGTATGCACTAGCGCTGTACTC 59.966 50.000 22.90 5.86 46.23 2.59
9197 10188 0.103208 GGAGTATGCACTAGCGCTGT 59.897 55.000 22.90 13.53 46.23 4.40
9198 10189 0.103026 TGGAGTATGCACTAGCGCTG 59.897 55.000 22.90 12.81 46.23 5.18
9199 10190 0.387202 CTGGAGTATGCACTAGCGCT 59.613 55.000 17.26 17.26 46.23 5.92
9200 10191 0.103208 ACTGGAGTATGCACTAGCGC 59.897 55.000 0.00 0.00 46.23 5.92
9201 10192 3.924918 ATACTGGAGTATGCACTAGCG 57.075 47.619 0.00 0.00 39.57 4.26
9210 10201 3.519510 ACACCAAGTGCATACTGGAGTAT 59.480 43.478 16.13 0.00 38.07 2.12
9211 10202 2.903784 ACACCAAGTGCATACTGGAGTA 59.096 45.455 16.13 0.00 37.19 2.59
9212 10203 1.699634 ACACCAAGTGCATACTGGAGT 59.300 47.619 16.13 12.10 37.19 3.85
9213 10204 2.479566 ACACCAAGTGCATACTGGAG 57.520 50.000 16.13 11.57 37.19 3.86
9214 10205 4.359434 TTTACACCAAGTGCATACTGGA 57.641 40.909 16.13 0.00 37.19 3.86
9215 10206 4.759693 TCTTTTACACCAAGTGCATACTGG 59.240 41.667 9.46 9.46 37.19 4.00
9216 10207 5.940192 TCTTTTACACCAAGTGCATACTG 57.060 39.130 0.00 0.00 37.19 2.74
9217 10208 6.071952 CCAATCTTTTACACCAAGTGCATACT 60.072 38.462 0.00 0.00 36.98 2.12
9230 10221 6.348458 CGAGACTTTGCATCCAATCTTTTACA 60.348 38.462 0.00 0.00 0.00 2.41
9262 10259 7.444629 TGAAGAGAGAAAGTTTCATTCCATG 57.555 36.000 17.65 0.00 0.00 3.66
9271 10268 6.941436 AGATCTGCATTGAAGAGAGAAAGTTT 59.059 34.615 0.00 0.00 0.00 2.66
9272 10269 6.474630 AGATCTGCATTGAAGAGAGAAAGTT 58.525 36.000 0.00 0.00 0.00 2.66
9285 10282 0.814410 AGCCTGCGAGATCTGCATTG 60.814 55.000 16.70 12.99 42.32 2.82
9344 10345 5.499139 TGTTTGAAATGTCTGGTTGACTC 57.501 39.130 0.00 0.00 45.54 3.36
9377 10378 2.841215 CACTTGTCCACCCGAAACTAA 58.159 47.619 0.00 0.00 0.00 2.24
9441 10685 7.441760 CAGGCGAGAATTCTACTCTTACTAGTA 59.558 40.741 8.25 0.00 32.87 1.82
9443 10687 6.664515 CAGGCGAGAATTCTACTCTTACTAG 58.335 44.000 8.25 0.00 32.87 2.57
9450 10694 2.586258 TGCAGGCGAGAATTCTACTC 57.414 50.000 8.25 0.75 0.00 2.59
9483 10727 1.929836 CTGGAGTACATTTCAGCTCGC 59.070 52.381 0.00 0.00 0.00 5.03
9484 10728 1.929836 GCTGGAGTACATTTCAGCTCG 59.070 52.381 16.84 0.00 46.29 5.03
9528 10772 7.817418 AGTAAAGTTGATGCTACTCCAAAAA 57.183 32.000 0.00 0.00 0.00 1.94
9529 10773 7.255451 CCAAGTAAAGTTGATGCTACTCCAAAA 60.255 37.037 0.00 0.00 0.00 2.44
9530 10774 6.206634 CCAAGTAAAGTTGATGCTACTCCAAA 59.793 38.462 0.00 0.00 0.00 3.28
9531 10775 5.705441 CCAAGTAAAGTTGATGCTACTCCAA 59.295 40.000 0.00 0.00 0.00 3.53
9532 10776 5.221843 ACCAAGTAAAGTTGATGCTACTCCA 60.222 40.000 0.00 0.00 0.00 3.86
9533 10777 5.122396 CACCAAGTAAAGTTGATGCTACTCC 59.878 44.000 0.00 0.00 0.00 3.85
9534 10778 6.170675 CACCAAGTAAAGTTGATGCTACTC 57.829 41.667 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.