Multiple sequence alignment - TraesCS7A01G241200

Loading Multiple Alignment...

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 TraesCS7A01G241200 chr7A 100.000 5368 0 0 1 5368 216725758 216731125 0.000000e+00 9913.0
1 TraesCS7A01G241200 chr7A 95.614 228 10 0 638 865 176635846 176636073 3.050000e-97 366.0
2 TraesCS7A01G241200 chr7A 85.965 114 2 10 4474 4581 216730198 216730303 5.680000e-20 110.0
3 TraesCS7A01G241200 chr7A 85.965 114 2 10 4441 4546 216730231 216730338 5.680000e-20 110.0
4 TraesCS7A01G241200 chr7D 95.180 1722 74 6 2827 4546 204727722 204729436 0.000000e+00 2712.0
5 TraesCS7A01G241200 chr7D 87.836 1340 81 35 863 2136 204725671 204726994 0.000000e+00 1496.0
6 TraesCS7A01G241200 chr7D 89.385 537 40 9 2313 2832 204727157 204727693 0.000000e+00 660.0
7 TraesCS7A01G241200 chr7D 90.323 403 17 11 4775 5171 204729923 204730309 4.800000e-140 508.0
8 TraesCS7A01G241200 chr7D 89.385 358 8 11 4474 4822 429494474 429494138 1.790000e-114 424.0
9 TraesCS7A01G241200 chr7D 90.580 276 13 10 4474 4747 204729335 204729599 2.380000e-93 353.0
10 TraesCS7A01G241200 chr7D 95.928 221 4 3 4329 4549 429494585 429494370 2.380000e-93 353.0
11 TraesCS7A01G241200 chr7D 90.377 239 15 2 4815 5048 429493992 429493757 1.880000e-79 307.0
12 TraesCS7A01G241200 chr7D 81.538 260 40 6 1881 2136 9459660 9459915 1.960000e-49 207.0
13 TraesCS7A01G241200 chr7D 96.842 95 3 0 4775 4869 429494087 429493993 5.560000e-35 159.0
14 TraesCS7A01G241200 chr7B 94.893 1684 67 11 2827 4507 168753611 168755278 0.000000e+00 2615.0
15 TraesCS7A01G241200 chr7B 89.805 1177 56 19 863 2003 168751531 168752679 0.000000e+00 1450.0
16 TraesCS7A01G241200 chr7B 91.017 846 28 14 2002 2832 168752770 168753582 0.000000e+00 1098.0
17 TraesCS7A01G241200 chr7B 87.020 886 92 5 1 864 675028496 675027612 0.000000e+00 977.0
18 TraesCS7A01G241200 chr7B 85.714 84 3 6 4525 4607 168755230 168755305 4.460000e-11 80.5
19 TraesCS7A01G241200 chr5A 96.647 865 28 1 1 864 476817267 476818131 0.000000e+00 1435.0
20 TraesCS7A01G241200 chr5A 74.483 870 210 10 5 867 384959836 384960700 3.050000e-97 366.0
21 TraesCS7A01G241200 chr5A 98.477 197 3 0 5172 5368 426300058 426300254 1.110000e-91 348.0
22 TraesCS7A01G241200 chr5A 78.328 323 45 14 1833 2136 167981352 167981036 9.180000e-43 185.0
23 TraesCS7A01G241200 chr5A 78.275 313 50 12 1833 2136 692594494 692594191 9.180000e-43 185.0
24 TraesCS7A01G241200 chr5A 77.709 323 47 14 1833 2136 677952081 677952397 1.990000e-39 174.0
25 TraesCS7A01G241200 chr3A 96.176 863 32 1 1 862 530918259 530919121 0.000000e+00 1410.0
26 TraesCS7A01G241200 chr3A 97.143 35 0 1 1017 1050 142562430 142562464 2.090000e-04 58.4
27 TraesCS7A01G241200 chr2B 88.194 864 100 2 1 863 165553151 165554013 0.000000e+00 1029.0
28 TraesCS7A01G241200 chr2B 98.477 197 3 0 5172 5368 365983973 365983777 1.110000e-91 348.0
29 TraesCS7A01G241200 chr2B 76.852 324 55 12 1829 2135 685501301 685501621 1.200000e-36 165.0
30 TraesCS7A01G241200 chr3D 83.793 870 127 7 4 862 593460995 593460129 0.000000e+00 813.0
31 TraesCS7A01G241200 chr6D 77.252 866 182 13 5 863 382730238 382729381 1.340000e-135 494.0
32 TraesCS7A01G241200 chr5D 76.709 863 188 11 5 861 429867937 429868792 8.140000e-128 468.0
33 TraesCS7A01G241200 chr5D 95.431 197 9 0 5172 5368 376661581 376661385 1.120000e-81 315.0
34 TraesCS7A01G241200 chr2A 100.000 197 0 0 5172 5368 724376162 724376358 1.100000e-96 364.0
35 TraesCS7A01G241200 chr5B 98.985 197 2 0 5172 5368 153897780 153897584 2.380000e-93 353.0
36 TraesCS7A01G241200 chr4B 98.985 197 2 0 5172 5368 563222945 563222749 2.380000e-93 353.0
37 TraesCS7A01G241200 chr4B 77.950 322 48 14 1833 2136 419180492 419180808 4.270000e-41 180.0
38 TraesCS7A01G241200 chr4A 98.985 197 2 0 5172 5368 208829786 208829982 2.380000e-93 353.0
39 TraesCS7A01G241200 chr4A 98.477 197 3 0 5172 5368 115288446 115288250 1.110000e-91 348.0
40 TraesCS7A01G241200 chr4A 78.704 324 45 16 1832 2136 368509296 368509614 1.530000e-45 195.0
41 TraesCS7A01G241200 chr1A 98.969 194 2 0 5175 5368 581435595 581435402 1.110000e-91 348.0
42 TraesCS7A01G241200 chr1D 81.818 253 43 3 611 862 280693225 280692975 5.450000e-50 209.0
43 TraesCS7A01G241200 chrUn 74.061 293 74 2 7 298 302408130 302408421 9.440000e-23 119.0
44 TraesCS7A01G241200 chr3B 74.308 253 42 13 2148 2381 294378488 294378240 9.580000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G241200 chr7A 216725758 216731125 5367 False 3377.666667 9913 90.643333 1 5368 3 chr7A.!!$F2 5367
1 TraesCS7A01G241200 chr7D 204725671 204730309 4638 False 1145.800000 2712 90.660800 863 5171 5 chr7D.!!$F2 4308
2 TraesCS7A01G241200 chr7D 429493757 429494585 828 True 310.750000 424 93.133000 4329 5048 4 chr7D.!!$R1 719
3 TraesCS7A01G241200 chr7B 168751531 168755305 3774 False 1310.875000 2615 90.357250 863 4607 4 chr7B.!!$F1 3744
4 TraesCS7A01G241200 chr7B 675027612 675028496 884 True 977.000000 977 87.020000 1 864 1 chr7B.!!$R1 863
5 TraesCS7A01G241200 chr5A 476817267 476818131 864 False 1435.000000 1435 96.647000 1 864 1 chr5A.!!$F3 863
6 TraesCS7A01G241200 chr5A 384959836 384960700 864 False 366.000000 366 74.483000 5 867 1 chr5A.!!$F1 862
7 TraesCS7A01G241200 chr3A 530918259 530919121 862 False 1410.000000 1410 96.176000 1 862 1 chr3A.!!$F2 861
8 TraesCS7A01G241200 chr2B 165553151 165554013 862 False 1029.000000 1029 88.194000 1 863 1 chr2B.!!$F1 862
9 TraesCS7A01G241200 chr3D 593460129 593460995 866 True 813.000000 813 83.793000 4 862 1 chr3D.!!$R1 858
10 TraesCS7A01G241200 chr6D 382729381 382730238 857 True 494.000000 494 77.252000 5 863 1 chr6D.!!$R1 858
11 TraesCS7A01G241200 chr5D 429867937 429868792 855 False 468.000000 468 76.709000 5 861 1 chr5D.!!$F1 856

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
253 254 0.039165 GAAGCTTTCGGTGCAAAGGG 60.039 55.0 0.00 0.0 34.42 3.95 F
1535 1578 0.454600 ATGCCTCTTCAGCAATTGCG 59.545 50.0 24.02 18.3 44.83 4.85 F
2282 2491 0.387239 CATCGCGTCAGATATCGGCA 60.387 55.0 5.77 0.0 0.00 5.69 F
3635 3934 0.877071 AGGCAGCAACAAAGATCACG 59.123 50.0 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1662 0.179145 CCCGGCTACTACGTGTTCTG 60.179 60.000 0.00 0.00 0.00 3.02 R
2342 2589 1.065418 AGTTTTGGGGCTCTACCGATG 60.065 52.381 0.00 0.00 40.62 3.84 R
4261 4560 0.247460 CAGGATCTCTGCAACGGTCA 59.753 55.000 0.00 0.00 36.60 4.02 R
5218 5888 0.036671 TCCACTCTGCGACTCGTAGA 60.037 55.000 16.99 16.99 45.21 2.59 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
253 254 0.039165 GAAGCTTTCGGTGCAAAGGG 60.039 55.000 0.00 0.00 34.42 3.95
365 376 7.386059 TGCTGACTATGTTAAGATCAACTTCA 58.614 34.615 0.00 0.00 39.72 3.02
378 389 1.962547 CAACTTCAACGCGTCATTTCG 59.037 47.619 14.44 1.65 0.00 3.46
437 448 2.948315 CGAGACTCTGATGGTGAGATGA 59.052 50.000 0.03 0.00 35.66 2.92
444 455 7.125507 AGACTCTGATGGTGAGATGATTTTAGT 59.874 37.037 0.00 0.00 35.66 2.24
522 533 2.084546 GCTTAAGGCAATCGAGGTTGT 58.915 47.619 4.29 0.00 41.35 3.32
548 559 1.000359 GTTGGAATGGGGAGGGTGG 60.000 63.158 0.00 0.00 0.00 4.61
840 873 3.677596 CCACCGTAATTTTGGAATGCAAC 59.322 43.478 0.00 0.00 31.39 4.17
918 951 0.918799 AGGGCCCACATGTCATACCA 60.919 55.000 27.56 0.00 0.00 3.25
1358 1401 1.843851 AGGATTCTTGCCGGTAATGGA 59.156 47.619 5.11 0.00 0.00 3.41
1397 1440 3.635373 CCATCAATTGCAGCCTACTCAAT 59.365 43.478 0.00 0.00 32.36 2.57
1472 1515 2.599281 TGCTCGTCGTTCTCCCCA 60.599 61.111 0.00 0.00 0.00 4.96
1493 1536 1.620822 ACCTCTTTGTGGTGATTGGC 58.379 50.000 0.00 0.00 36.30 4.52
1520 1563 1.824230 TGCACCAATTTGAGGTATGCC 59.176 47.619 0.00 0.00 37.23 4.40
1535 1578 0.454600 ATGCCTCTTCAGCAATTGCG 59.545 50.000 24.02 18.30 44.83 4.85
1634 1679 1.467734 AGTCAGAACACGTAGTAGCCG 59.532 52.381 0.00 0.00 41.61 5.52
1694 1747 4.405358 ACTGAGAGAATCAAGATGGACTCC 59.595 45.833 0.00 0.00 37.52 3.85
1696 1749 2.697751 AGAGAATCAAGATGGACTCCGG 59.302 50.000 0.00 0.00 37.82 5.14
1697 1750 1.139853 AGAATCAAGATGGACTCCGGC 59.860 52.381 0.00 0.00 0.00 6.13
1743 1816 0.697079 ACCAGAGTCTCTCGTGGGTA 59.303 55.000 7.64 0.00 34.44 3.69
1745 1818 2.291670 ACCAGAGTCTCTCGTGGGTATT 60.292 50.000 7.64 0.00 34.44 1.89
1764 1837 6.263168 GGGTATTGAGTTTGTTGGGATATCAG 59.737 42.308 4.83 0.00 0.00 2.90
1812 1911 1.029681 GGTTTTGGCTGAACCTCGTT 58.970 50.000 13.15 0.00 42.58 3.85
1819 1918 3.482436 TGGCTGAACCTCGTTAACAAAT 58.518 40.909 6.39 0.00 40.22 2.32
1820 1919 4.643463 TGGCTGAACCTCGTTAACAAATA 58.357 39.130 6.39 0.00 40.22 1.40
1821 1920 4.693566 TGGCTGAACCTCGTTAACAAATAG 59.306 41.667 6.39 0.00 40.22 1.73
1823 1922 4.153475 GCTGAACCTCGTTAACAAATAGCA 59.847 41.667 6.39 0.00 0.00 3.49
1870 1971 7.737972 TCATATATTGGGTTTGTATCGGTTG 57.262 36.000 0.00 0.00 0.00 3.77
1884 1985 2.639065 TCGGTTGGGCTTGAACATATC 58.361 47.619 0.00 0.00 0.00 1.63
1891 1992 2.808543 GGGCTTGAACATATCGGATGTC 59.191 50.000 0.00 0.00 0.00 3.06
2133 2342 6.546972 TGTTTCTACAAACATTACGCATGA 57.453 33.333 0.00 0.00 45.73 3.07
2134 2343 6.367421 TGTTTCTACAAACATTACGCATGAC 58.633 36.000 0.00 0.00 45.73 3.06
2135 2344 6.203915 TGTTTCTACAAACATTACGCATGACT 59.796 34.615 0.00 0.00 45.73 3.41
2136 2345 7.385478 TGTTTCTACAAACATTACGCATGACTA 59.615 33.333 0.00 0.00 45.73 2.59
2137 2346 7.892778 TTCTACAAACATTACGCATGACTAA 57.107 32.000 0.00 0.00 36.24 2.24
2138 2347 7.285783 TCTACAAACATTACGCATGACTAAC 57.714 36.000 0.00 0.00 36.24 2.34
2139 2348 5.291293 ACAAACATTACGCATGACTAACC 57.709 39.130 0.00 0.00 36.24 2.85
2140 2349 5.001232 ACAAACATTACGCATGACTAACCT 58.999 37.500 0.00 0.00 36.24 3.50
2141 2350 5.472137 ACAAACATTACGCATGACTAACCTT 59.528 36.000 0.00 0.00 36.24 3.50
2142 2351 6.651643 ACAAACATTACGCATGACTAACCTTA 59.348 34.615 0.00 0.00 36.24 2.69
2143 2352 7.173562 ACAAACATTACGCATGACTAACCTTAA 59.826 33.333 0.00 0.00 36.24 1.85
2144 2353 7.675962 AACATTACGCATGACTAACCTTAAA 57.324 32.000 0.00 0.00 36.24 1.52
2145 2354 7.675962 ACATTACGCATGACTAACCTTAAAA 57.324 32.000 0.00 0.00 36.24 1.52
2146 2355 8.101654 ACATTACGCATGACTAACCTTAAAAA 57.898 30.769 0.00 0.00 36.24 1.94
2167 2376 5.574815 AAAAACATTACGCATGACTTTGC 57.425 34.783 0.00 0.00 36.24 3.68
2170 2379 4.864916 ACATTACGCATGACTTTGCTAG 57.135 40.909 0.00 0.00 40.54 3.42
2263 2472 2.038557 ACCGGTCTATATCAATGGGCAC 59.961 50.000 0.00 0.00 0.00 5.01
2268 2477 3.372206 GTCTATATCAATGGGCACATCGC 59.628 47.826 0.00 0.00 35.94 4.58
2282 2491 0.387239 CATCGCGTCAGATATCGGCA 60.387 55.000 5.77 0.00 0.00 5.69
2292 2523 5.237815 GTCAGATATCGGCAATATTGGTCA 58.762 41.667 17.02 0.00 30.37 4.02
2519 2781 4.127171 TGAGAAATTGGATTAGGCGCTAC 58.873 43.478 7.64 0.00 0.00 3.58
2586 2849 2.019866 TGGGATGGGCATTGGGGAT 61.020 57.895 0.00 0.00 0.00 3.85
2610 2873 9.502091 GATATTTGATTTGTACCTGGCATAGTA 57.498 33.333 0.00 0.00 0.00 1.82
2684 2947 3.334583 TTGTGGGAAGTCTGAGCATAC 57.665 47.619 0.00 0.00 0.00 2.39
2760 3023 5.009110 TGAACATTTTGTGATCTGCCGTAAA 59.991 36.000 0.00 0.00 31.41 2.01
2843 3140 4.731720 TGAACACGATATTGCATGTTTGG 58.268 39.130 2.85 0.00 35.47 3.28
3174 3473 3.117738 ACTCTTTCCCATAAGCCCATCTG 60.118 47.826 0.00 0.00 0.00 2.90
3175 3474 1.959282 CTTTCCCATAAGCCCATCTGC 59.041 52.381 0.00 0.00 0.00 4.26
3257 3556 5.705441 GGATGAACTTGTTACCTTCATCACA 59.295 40.000 19.73 0.00 46.55 3.58
3635 3934 0.877071 AGGCAGCAACAAAGATCACG 59.123 50.000 0.00 0.00 0.00 4.35
3656 3955 3.181471 CGGAAGTGAGATTGCTATCCTGT 60.181 47.826 4.43 0.00 0.00 4.00
3689 3988 3.307674 CAGCGAGACAGCAATATCTCTC 58.692 50.000 0.00 0.00 40.15 3.20
3767 4066 0.979709 CTGGCCTGTCCTCCATCTCA 60.980 60.000 3.32 0.00 35.26 3.27
3785 4084 4.776349 TCTCACAGCTTTCCAAGTTAACA 58.224 39.130 8.61 0.00 0.00 2.41
3812 4111 1.817099 CCTTGCCGGAGCTGACATC 60.817 63.158 5.05 0.00 40.80 3.06
3866 4165 2.883386 GAGCTGCCCAATATCTTCCTTG 59.117 50.000 0.00 0.00 0.00 3.61
3931 4230 2.034687 GCTGTGTGGGAGTGGCAT 59.965 61.111 0.00 0.00 0.00 4.40
3983 4282 2.363038 TGGGAACGTACCAAGGATATCG 59.637 50.000 9.26 0.00 34.44 2.92
4193 4492 2.511600 GATCCGCTGGTTGACCCG 60.512 66.667 0.00 0.00 35.15 5.28
4250 4549 3.891586 GAACGTGCTGGAGCGTCGA 62.892 63.158 18.19 0.00 45.83 4.20
4352 4651 0.257039 GGAACCAGTGCCATCCTGAT 59.743 55.000 0.00 0.00 31.38 2.90
4506 4806 6.375736 TGACTTTGGTTTTCTCACATGTTGTA 59.624 34.615 0.00 0.00 0.00 2.41
4507 4807 6.560711 ACTTTGGTTTTCTCACATGTTGTAC 58.439 36.000 0.00 0.00 0.00 2.90
4508 4808 6.377146 ACTTTGGTTTTCTCACATGTTGTACT 59.623 34.615 0.00 0.00 0.00 2.73
4509 4809 5.749596 TGGTTTTCTCACATGTTGTACTG 57.250 39.130 0.00 0.00 0.00 2.74
4510 4810 4.578516 TGGTTTTCTCACATGTTGTACTGG 59.421 41.667 0.00 0.00 0.00 4.00
4511 4811 4.578928 GGTTTTCTCACATGTTGTACTGGT 59.421 41.667 0.00 0.00 0.00 4.00
4512 4812 5.761234 GGTTTTCTCACATGTTGTACTGGTA 59.239 40.000 0.00 0.00 0.00 3.25
4513 4813 6.430000 GGTTTTCTCACATGTTGTACTGGTAT 59.570 38.462 0.00 0.00 0.00 2.73
4514 4814 7.360946 GGTTTTCTCACATGTTGTACTGGTATC 60.361 40.741 0.00 0.00 0.00 2.24
4515 4815 6.605471 TTCTCACATGTTGTACTGGTATCT 57.395 37.500 0.00 0.00 0.00 1.98
4516 4816 6.605471 TCTCACATGTTGTACTGGTATCTT 57.395 37.500 0.00 0.00 0.00 2.40
4517 4817 7.712204 TCTCACATGTTGTACTGGTATCTTA 57.288 36.000 0.00 0.00 0.00 2.10
4518 4818 8.306313 TCTCACATGTTGTACTGGTATCTTAT 57.694 34.615 0.00 0.00 0.00 1.73
4519 4819 9.416284 TCTCACATGTTGTACTGGTATCTTATA 57.584 33.333 0.00 0.00 0.00 0.98
4521 4821 9.981114 TCACATGTTGTACTGGTATCTTATATG 57.019 33.333 0.00 0.00 0.00 1.78
4522 4822 9.981114 CACATGTTGTACTGGTATCTTATATGA 57.019 33.333 0.00 0.00 0.00 2.15
4523 4823 9.982651 ACATGTTGTACTGGTATCTTATATGAC 57.017 33.333 0.00 0.00 0.00 3.06
4529 4829 9.209048 TGTACTGGTATCTTATATGACTTTGGT 57.791 33.333 0.00 0.00 0.00 3.67
4532 4832 9.975218 ACTGGTATCTTATATGACTTTGGTTTT 57.025 29.630 0.00 0.00 0.00 2.43
4538 4838 9.739276 ATCTTATATGACTTTGGTTTTCTCACA 57.261 29.630 0.00 0.00 0.00 3.58
4539 4839 9.739276 TCTTATATGACTTTGGTTTTCTCACAT 57.261 29.630 0.00 0.00 0.00 3.21
4540 4840 9.778993 CTTATATGACTTTGGTTTTCTCACATG 57.221 33.333 0.00 0.00 0.00 3.21
4541 4841 7.765695 ATATGACTTTGGTTTTCTCACATGT 57.234 32.000 0.00 0.00 0.00 3.21
4542 4842 5.913137 TGACTTTGGTTTTCTCACATGTT 57.087 34.783 0.00 0.00 0.00 2.71
4543 4843 5.649557 TGACTTTGGTTTTCTCACATGTTG 58.350 37.500 0.00 0.00 0.00 3.33
4544 4844 5.184864 TGACTTTGGTTTTCTCACATGTTGT 59.815 36.000 0.00 0.00 0.00 3.32
4620 4920 9.661954 ATGGATCTGTCTAGGAGTTTAGATAAA 57.338 33.333 0.00 0.00 32.63 1.40
4667 4967 0.179004 TTTTGGGCGAGGAAAGCTGA 60.179 50.000 0.00 0.00 34.52 4.26
4804 5413 1.956477 GTAGGGATGGCATTTGCGAAT 59.044 47.619 0.00 0.00 43.26 3.34
4824 5433 7.116090 TGCGAATGATTTTGTTTTGATGGTAAG 59.884 33.333 0.00 0.00 0.00 2.34
4873 5537 1.514678 AAGCGAGGCATTTGCGAACA 61.515 50.000 0.00 0.00 41.40 3.18
4918 5582 0.744874 GAGCATGGTCCGCTACAGTA 59.255 55.000 14.08 0.00 40.63 2.74
4932 5596 5.175491 CCGCTACAGTACTGTTTTTCGTAAA 59.825 40.000 32.15 11.13 41.83 2.01
4933 5597 6.292274 CCGCTACAGTACTGTTTTTCGTAAAA 60.292 38.462 32.15 10.41 41.83 1.52
4934 5598 7.118724 CGCTACAGTACTGTTTTTCGTAAAAA 58.881 34.615 32.15 9.90 41.83 1.94
5003 5667 2.025981 TCTCAATTGTCATCCCACCCTG 60.026 50.000 5.13 0.00 0.00 4.45
5051 5720 3.626924 GACCAGTGCCACGACCCT 61.627 66.667 0.00 0.00 0.00 4.34
5053 5722 2.358737 CCAGTGCCACGACCCTTC 60.359 66.667 0.00 0.00 0.00 3.46
5054 5723 2.743718 CAGTGCCACGACCCTTCT 59.256 61.111 0.00 0.00 0.00 2.85
5055 5724 1.374758 CAGTGCCACGACCCTTCTC 60.375 63.158 0.00 0.00 0.00 2.87
5056 5725 1.534235 AGTGCCACGACCCTTCTCT 60.534 57.895 0.00 0.00 0.00 3.10
5057 5726 1.374758 GTGCCACGACCCTTCTCTG 60.375 63.158 0.00 0.00 0.00 3.35
5058 5727 2.435059 GCCACGACCCTTCTCTGC 60.435 66.667 0.00 0.00 0.00 4.26
5059 5728 2.125912 CCACGACCCTTCTCTGCG 60.126 66.667 0.00 0.00 0.00 5.18
5060 5729 2.651361 CACGACCCTTCTCTGCGT 59.349 61.111 0.00 0.00 35.33 5.24
5061 5730 1.734477 CACGACCCTTCTCTGCGTG 60.734 63.158 0.00 0.00 44.78 5.34
5062 5731 1.901948 ACGACCCTTCTCTGCGTGA 60.902 57.895 0.00 0.00 33.52 4.35
5063 5732 1.251527 ACGACCCTTCTCTGCGTGAT 61.252 55.000 0.00 0.00 33.52 3.06
5064 5733 0.803768 CGACCCTTCTCTGCGTGATG 60.804 60.000 0.00 0.00 0.00 3.07
5065 5734 0.532573 GACCCTTCTCTGCGTGATGA 59.467 55.000 0.00 0.00 0.00 2.92
5080 5749 2.485426 GTGATGATGACACACCCAGTTG 59.515 50.000 0.00 0.00 38.05 3.16
5083 5752 2.781923 TGATGACACACCCAGTTGATG 58.218 47.619 0.00 0.00 0.00 3.07
5171 5841 2.232941 TCCGTATGTCTCCAACCAAGAC 59.767 50.000 0.00 0.00 42.83 3.01
5175 5845 2.620251 TGTCTCCAACCAAGACAGTG 57.380 50.000 1.98 0.00 46.15 3.66
5176 5846 2.115427 TGTCTCCAACCAAGACAGTGA 58.885 47.619 0.00 0.00 46.15 3.41
5177 5847 2.705658 TGTCTCCAACCAAGACAGTGAT 59.294 45.455 0.00 0.00 46.15 3.06
5178 5848 3.136443 TGTCTCCAACCAAGACAGTGATT 59.864 43.478 0.00 0.00 46.15 2.57
5179 5849 4.346709 TGTCTCCAACCAAGACAGTGATTA 59.653 41.667 0.00 0.00 46.15 1.75
5180 5850 4.691216 GTCTCCAACCAAGACAGTGATTAC 59.309 45.833 0.00 0.00 42.23 1.89
5181 5851 3.659786 TCCAACCAAGACAGTGATTACG 58.340 45.455 0.00 0.00 0.00 3.18
5182 5852 3.322541 TCCAACCAAGACAGTGATTACGA 59.677 43.478 0.00 0.00 0.00 3.43
5183 5853 3.679980 CCAACCAAGACAGTGATTACGAG 59.320 47.826 0.00 0.00 0.00 4.18
5184 5854 4.307432 CAACCAAGACAGTGATTACGAGT 58.693 43.478 0.00 0.00 0.00 4.18
5185 5855 4.175787 ACCAAGACAGTGATTACGAGTC 57.824 45.455 0.00 7.78 37.15 3.36
5186 5856 3.172050 CCAAGACAGTGATTACGAGTCG 58.828 50.000 11.85 11.85 39.83 4.18
5187 5857 3.119955 CCAAGACAGTGATTACGAGTCGA 60.120 47.826 21.50 0.00 39.83 4.20
5188 5858 4.473199 CAAGACAGTGATTACGAGTCGAA 58.527 43.478 21.50 9.61 39.83 3.71
5189 5859 4.080969 AGACAGTGATTACGAGTCGAAC 57.919 45.455 21.50 8.97 39.83 3.95
5190 5860 2.839026 GACAGTGATTACGAGTCGAACG 59.161 50.000 21.50 10.87 30.91 3.95
5191 5861 2.481568 ACAGTGATTACGAGTCGAACGA 59.518 45.455 21.50 1.91 34.70 3.85
5192 5862 2.839026 CAGTGATTACGAGTCGAACGAC 59.161 50.000 21.50 17.79 44.86 4.34
5214 5884 2.813061 AGTCTAGACTAGTCGCTCGAC 58.187 52.381 24.04 18.77 40.43 4.20
5224 5894 1.554392 GTCGCTCGACTAGTCTACGA 58.446 55.000 20.34 20.58 41.57 3.43
5232 5902 2.538437 GACTAGTCTACGAGTCGCAGA 58.462 52.381 15.91 12.45 38.48 4.26
5233 5903 2.536803 GACTAGTCTACGAGTCGCAGAG 59.463 54.545 15.74 9.29 38.48 3.35
5234 5904 2.094078 ACTAGTCTACGAGTCGCAGAGT 60.094 50.000 23.13 23.13 46.63 3.24
5235 5905 1.080298 AGTCTACGAGTCGCAGAGTG 58.920 55.000 19.96 2.23 42.24 3.51
5236 5906 0.097325 GTCTACGAGTCGCAGAGTGG 59.903 60.000 15.74 0.00 42.24 4.00
5237 5907 0.036671 TCTACGAGTCGCAGAGTGGA 60.037 55.000 13.59 0.00 42.24 4.02
5238 5908 1.018148 CTACGAGTCGCAGAGTGGAT 58.982 55.000 13.59 0.00 42.24 3.41
5239 5909 0.733150 TACGAGTCGCAGAGTGGATG 59.267 55.000 13.59 0.00 42.24 3.51
5240 5910 1.244697 ACGAGTCGCAGAGTGGATGT 61.245 55.000 13.59 0.00 42.24 3.06
5241 5911 0.524392 CGAGTCGCAGAGTGGATGTC 60.524 60.000 0.00 0.00 42.24 3.06
5242 5912 0.524392 GAGTCGCAGAGTGGATGTCG 60.524 60.000 0.00 0.00 42.24 4.35
5243 5913 0.960861 AGTCGCAGAGTGGATGTCGA 60.961 55.000 0.00 0.00 39.65 4.20
5244 5914 0.798771 GTCGCAGAGTGGATGTCGAC 60.799 60.000 9.11 9.11 38.76 4.20
5245 5915 0.960861 TCGCAGAGTGGATGTCGACT 60.961 55.000 17.92 1.84 37.63 4.18
5252 5922 4.849111 GAGTGGATGTCGACTCATTTTC 57.151 45.455 17.92 4.67 46.61 2.29
5253 5923 4.499183 GAGTGGATGTCGACTCATTTTCT 58.501 43.478 17.92 6.55 46.61 2.52
5254 5924 4.499183 AGTGGATGTCGACTCATTTTCTC 58.501 43.478 17.92 1.07 28.40 2.87
5255 5925 3.304559 GTGGATGTCGACTCATTTTCTCG 59.695 47.826 17.92 0.00 0.00 4.04
5256 5926 3.056821 TGGATGTCGACTCATTTTCTCGT 60.057 43.478 17.92 0.00 0.00 4.18
5257 5927 3.304559 GGATGTCGACTCATTTTCTCGTG 59.695 47.826 17.92 0.00 0.00 4.35
5258 5928 3.364889 TGTCGACTCATTTTCTCGTGT 57.635 42.857 17.92 0.00 0.00 4.49
5259 5929 4.492791 TGTCGACTCATTTTCTCGTGTA 57.507 40.909 17.92 0.00 0.00 2.90
5260 5930 4.473199 TGTCGACTCATTTTCTCGTGTAG 58.527 43.478 17.92 0.00 0.00 2.74
5261 5931 4.214758 TGTCGACTCATTTTCTCGTGTAGA 59.785 41.667 17.92 0.00 0.00 2.59
5262 5932 4.554200 GTCGACTCATTTTCTCGTGTAGAC 59.446 45.833 8.70 0.00 32.51 2.59
5263 5933 4.454847 TCGACTCATTTTCTCGTGTAGACT 59.545 41.667 0.00 0.00 32.51 3.24
5264 5934 5.640783 TCGACTCATTTTCTCGTGTAGACTA 59.359 40.000 0.00 0.00 32.51 2.59
5265 5935 5.733572 CGACTCATTTTCTCGTGTAGACTAC 59.266 44.000 5.62 5.62 32.51 2.73
5266 5936 6.570672 ACTCATTTTCTCGTGTAGACTACA 57.429 37.500 11.37 11.37 32.51 2.74
5267 5937 6.978338 ACTCATTTTCTCGTGTAGACTACAA 58.022 36.000 16.84 1.98 40.93 2.41
5268 5938 7.431249 ACTCATTTTCTCGTGTAGACTACAAA 58.569 34.615 16.84 7.19 40.93 2.83
5269 5939 8.088981 ACTCATTTTCTCGTGTAGACTACAAAT 58.911 33.333 16.84 9.10 40.93 2.32
5270 5940 9.569167 CTCATTTTCTCGTGTAGACTACAAATA 57.431 33.333 16.84 4.04 40.93 1.40
5271 5941 9.350357 TCATTTTCTCGTGTAGACTACAAATAC 57.650 33.333 16.84 4.10 40.93 1.89
5272 5942 7.786305 TTTTCTCGTGTAGACTACAAATACG 57.214 36.000 16.84 15.25 40.93 3.06
5273 5943 6.726258 TTCTCGTGTAGACTACAAATACGA 57.274 37.500 16.84 18.21 40.93 3.43
5274 5944 6.341880 TCTCGTGTAGACTACAAATACGAG 57.658 41.667 29.49 29.49 45.25 4.18
5275 5945 5.871524 TCTCGTGTAGACTACAAATACGAGT 59.128 40.000 31.45 0.00 44.71 4.18
5276 5946 6.035435 TCTCGTGTAGACTACAAATACGAGTC 59.965 42.308 31.45 14.46 44.71 3.36
5277 5947 4.954405 CGTGTAGACTACAAATACGAGTCG 59.046 45.833 16.84 11.85 43.57 4.18
5278 5948 5.220284 CGTGTAGACTACAAATACGAGTCGA 60.220 44.000 21.50 3.11 43.57 4.20
5279 5949 6.184015 GTGTAGACTACAAATACGAGTCGAG 58.816 44.000 21.50 6.57 43.57 4.04
5280 5950 4.275838 AGACTACAAATACGAGTCGAGC 57.724 45.455 21.50 1.05 43.57 5.03
5281 5951 3.065095 AGACTACAAATACGAGTCGAGCC 59.935 47.826 21.50 0.00 43.57 4.70
5282 5952 2.223203 ACTACAAATACGAGTCGAGCCG 60.223 50.000 21.50 5.90 0.00 5.52
5283 5953 0.524862 ACAAATACGAGTCGAGCCGT 59.475 50.000 21.50 14.99 42.15 5.68
5284 5954 0.914551 CAAATACGAGTCGAGCCGTG 59.085 55.000 21.50 6.57 39.54 4.94
5285 5955 0.524862 AAATACGAGTCGAGCCGTGT 59.475 50.000 21.50 11.43 39.54 4.49
5286 5956 0.098376 AATACGAGTCGAGCCGTGTC 59.902 55.000 21.50 0.00 39.54 3.67
5287 5957 0.743701 ATACGAGTCGAGCCGTGTCT 60.744 55.000 21.50 0.00 39.54 3.41
5288 5958 1.632948 TACGAGTCGAGCCGTGTCTG 61.633 60.000 21.50 0.00 39.54 3.51
5289 5959 2.179517 GAGTCGAGCCGTGTCTGG 59.820 66.667 0.00 0.00 0.00 3.86
5290 5960 2.282251 AGTCGAGCCGTGTCTGGA 60.282 61.111 0.00 0.00 0.00 3.86
5291 5961 2.126424 GTCGAGCCGTGTCTGGAC 60.126 66.667 0.00 0.00 35.31 4.02
5292 5962 2.282251 TCGAGCCGTGTCTGGACT 60.282 61.111 2.38 0.00 0.00 3.85
5293 5963 1.002990 TCGAGCCGTGTCTGGACTA 60.003 57.895 2.38 0.00 0.00 2.59
5294 5964 1.025113 TCGAGCCGTGTCTGGACTAG 61.025 60.000 2.38 0.00 0.00 2.57
5295 5965 1.306642 CGAGCCGTGTCTGGACTAGT 61.307 60.000 0.00 0.00 0.00 2.57
5296 5966 0.452585 GAGCCGTGTCTGGACTAGTC 59.547 60.000 14.87 14.87 0.00 2.59
5297 5967 1.136984 GCCGTGTCTGGACTAGTCG 59.863 63.158 16.56 4.17 0.00 4.18
5298 5968 1.303799 GCCGTGTCTGGACTAGTCGA 61.304 60.000 16.56 12.04 0.00 4.20
5299 5969 0.447011 CCGTGTCTGGACTAGTCGAC 59.553 60.000 16.56 17.82 0.00 4.20
5300 5970 0.094901 CGTGTCTGGACTAGTCGACG 59.905 60.000 16.56 14.11 0.00 5.12
5301 5971 1.436600 GTGTCTGGACTAGTCGACGA 58.563 55.000 16.56 3.61 0.00 4.20
5302 5972 1.128321 GTGTCTGGACTAGTCGACGAC 59.872 57.143 20.25 20.25 0.00 4.34
5303 5973 1.001746 TGTCTGGACTAGTCGACGACT 59.998 52.381 31.23 31.23 45.54 4.18
5304 5974 2.232208 TGTCTGGACTAGTCGACGACTA 59.768 50.000 30.23 30.23 41.51 2.59
5314 5984 2.495270 AGTCGACGACTAGTCTGGACTA 59.505 50.000 28.28 9.68 43.74 2.59
5328 5998 6.770542 AGTCTGGACTAGTCGACATATATGA 58.229 40.000 24.17 9.27 40.43 2.15
5329 5999 6.876789 AGTCTGGACTAGTCGACATATATGAG 59.123 42.308 24.17 12.19 40.43 2.90
5330 6000 6.651643 GTCTGGACTAGTCGACATATATGAGT 59.348 42.308 19.63 10.54 0.00 3.41
5331 6001 6.874664 TCTGGACTAGTCGACATATATGAGTC 59.125 42.308 19.63 17.59 33.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
253 254 1.378531 TTCAGCCACATTATGACGCC 58.621 50.000 0.00 0.00 0.00 5.68
337 346 7.038659 AGTTGATCTTAACATAGTCAGCAGAC 58.961 38.462 0.05 0.05 37.74 3.51
338 347 7.175347 AGTTGATCTTAACATAGTCAGCAGA 57.825 36.000 0.00 0.00 33.02 4.26
365 376 0.876777 TCCACACGAAATGACGCGTT 60.877 50.000 15.53 0.00 38.92 4.84
378 389 0.460284 CGCTGACCCTGTATCCACAC 60.460 60.000 0.00 0.00 0.00 3.82
437 448 1.271926 ACCTCCTGCCGCAACTAAAAT 60.272 47.619 0.00 0.00 0.00 1.82
444 455 0.179015 TTGTAAACCTCCTGCCGCAA 60.179 50.000 0.00 0.00 0.00 4.85
522 533 3.563261 CCTCCCCATTCCAACATGTACAA 60.563 47.826 0.00 0.00 0.00 2.41
548 559 1.534729 AGGCAATCGGTCTGGAAAAC 58.465 50.000 0.00 0.00 0.00 2.43
670 681 5.680619 TCTCTTGGCTGAAAAACTACAGAA 58.319 37.500 0.00 0.00 36.38 3.02
874 907 4.696402 TGCCGTCGTTCTATTTGGTTTTAT 59.304 37.500 0.00 0.00 0.00 1.40
959 1002 2.583593 GTCAGATGCGCGGAGACC 60.584 66.667 8.83 0.00 0.00 3.85
1061 1104 3.151022 CGACCAGGCCTCCTCCTC 61.151 72.222 0.00 0.00 33.25 3.71
1062 1105 3.673597 TCGACCAGGCCTCCTCCT 61.674 66.667 0.00 0.00 36.78 3.69
1125 1168 2.835431 GAGCAGGCGGCCTCTAGA 60.835 66.667 20.97 0.00 46.50 2.43
1377 1420 4.337555 GTCATTGAGTAGGCTGCAATTGAT 59.662 41.667 10.34 0.00 30.37 2.57
1472 1515 3.356290 GCCAATCACCACAAAGAGGTAT 58.644 45.455 0.00 0.00 37.23 2.73
1493 1536 1.466167 CTCAAATTGGTGCACCTCTCG 59.534 52.381 34.75 19.54 36.82 4.04
1520 1563 2.693797 AACACGCAATTGCTGAAGAG 57.306 45.000 26.86 13.31 39.32 2.85
1535 1578 2.081462 ACCCGTAGCATAAGCAAACAC 58.919 47.619 0.00 0.00 45.49 3.32
1608 1653 5.634020 GCTACTACGTGTTCTGACTCAAAAT 59.366 40.000 0.00 0.00 0.00 1.82
1613 1658 2.475852 CGGCTACTACGTGTTCTGACTC 60.476 54.545 0.00 0.00 0.00 3.36
1614 1659 1.467734 CGGCTACTACGTGTTCTGACT 59.532 52.381 0.00 0.00 0.00 3.41
1615 1660 1.467035 CCGGCTACTACGTGTTCTGAC 60.467 57.143 0.00 0.00 0.00 3.51
1616 1661 0.806868 CCGGCTACTACGTGTTCTGA 59.193 55.000 0.00 0.00 0.00 3.27
1617 1662 0.179145 CCCGGCTACTACGTGTTCTG 60.179 60.000 0.00 0.00 0.00 3.02
1618 1663 1.318158 CCCCGGCTACTACGTGTTCT 61.318 60.000 0.00 0.00 0.00 3.01
1634 1679 2.422945 CCCTTGTACTTATTGAGGCCCC 60.423 54.545 0.00 0.00 0.00 5.80
1697 1750 4.796231 CTCCCTCCGTGAACCGCG 62.796 72.222 0.00 0.00 37.10 6.46
1701 1754 1.186267 AGACCACTCCCTCCGTGAAC 61.186 60.000 0.00 0.00 34.35 3.18
1703 1756 1.304217 GAGACCACTCCCTCCGTGA 60.304 63.158 0.00 0.00 37.19 4.35
1743 1816 8.497745 ACTATCTGATATCCCAACAAACTCAAT 58.502 33.333 0.00 0.00 0.00 2.57
1745 1818 7.437713 ACTATCTGATATCCCAACAAACTCA 57.562 36.000 0.00 0.00 0.00 3.41
1764 1837 3.713764 CCATGGGATCCCCTGATACTATC 59.286 52.174 31.57 3.64 45.70 2.08
1784 1883 1.707989 TCAGCCAAAACCTACATCCCA 59.292 47.619 0.00 0.00 0.00 4.37
1812 1911 6.714810 ACCTTGATTGACACTGCTATTTGTTA 59.285 34.615 0.00 0.00 0.00 2.41
1819 1918 4.350368 TGAACCTTGATTGACACTGCTA 57.650 40.909 0.00 0.00 0.00 3.49
1820 1919 3.213206 TGAACCTTGATTGACACTGCT 57.787 42.857 0.00 0.00 0.00 4.24
1821 1920 3.066621 TGTTGAACCTTGATTGACACTGC 59.933 43.478 0.00 0.00 0.00 4.40
1823 1922 6.942005 TGATATGTTGAACCTTGATTGACACT 59.058 34.615 0.00 0.00 0.00 3.55
1870 1971 2.808543 GACATCCGATATGTTCAAGCCC 59.191 50.000 5.07 0.00 31.52 5.19
1884 1985 1.728425 TCGTCCGATATACGACATCCG 59.272 52.381 0.00 0.00 43.90 4.18
1964 2080 7.707035 ACCATACATTTTGTTTTCGCTGTAAAA 59.293 29.630 0.00 0.00 0.00 1.52
1968 2084 4.981674 CACCATACATTTTGTTTTCGCTGT 59.018 37.500 0.00 0.00 0.00 4.40
1969 2085 4.981674 ACACCATACATTTTGTTTTCGCTG 59.018 37.500 0.00 0.00 0.00 5.18
1972 2088 9.186323 TCATTAACACCATACATTTTGTTTTCG 57.814 29.630 0.00 0.00 34.15 3.46
2145 2354 5.574815 GCAAAGTCATGCGTAATGTTTTT 57.425 34.783 0.00 1.55 37.56 1.94
2239 2448 3.118738 GCCCATTGATATAGACCGGTAGG 60.119 52.174 7.34 0.00 45.13 3.18
2240 2449 3.513912 TGCCCATTGATATAGACCGGTAG 59.486 47.826 7.34 0.00 0.00 3.18
2263 2472 0.387239 TGCCGATATCTGACGCGATG 60.387 55.000 15.93 1.69 0.00 3.84
2268 2477 4.245660 ACCAATATTGCCGATATCTGACG 58.754 43.478 10.11 0.00 30.50 4.35
2292 2523 3.830744 TCCGATGTGGACCGAAATATT 57.169 42.857 0.00 0.00 43.74 1.28
2342 2589 1.065418 AGTTTTGGGGCTCTACCGATG 60.065 52.381 0.00 0.00 40.62 3.84
2519 2781 5.293324 TGCAATAATACTAGGCAACAGTTCG 59.707 40.000 0.00 0.00 41.41 3.95
2586 2849 9.860650 ATTACTATGCCAGGTACAAATCAAATA 57.139 29.630 0.00 0.00 0.00 1.40
2760 3023 4.400251 CCTTTGAACATGTGTGCTATGGAT 59.600 41.667 0.00 0.00 29.28 3.41
3635 3934 4.125703 CACAGGATAGCAATCTCACTTCC 58.874 47.826 0.00 0.00 32.29 3.46
3644 3943 5.396884 GGTTAAGAGACCACAGGATAGCAAT 60.397 44.000 0.00 0.00 39.57 3.56
3650 3949 2.237392 GCTGGTTAAGAGACCACAGGAT 59.763 50.000 0.00 0.00 44.53 3.24
3689 3988 1.171308 CCAAGTTGGTGCAGGATGAG 58.829 55.000 14.21 0.00 32.01 2.90
3785 4084 0.541863 CTCCGGCAAGGTCCAATAGT 59.458 55.000 0.00 0.00 41.99 2.12
3812 4111 0.738762 CTGACAGACCTGCATCGGTG 60.739 60.000 1.69 0.00 37.42 4.94
3866 4165 1.534595 CTTCTGCAACTCCTCAAGCAC 59.465 52.381 0.00 0.00 32.87 4.40
3931 4230 2.034053 GCGACCAAGGTTTTGTTGATGA 59.966 45.455 0.00 0.00 32.21 2.92
3983 4282 0.535335 TCAATGTGACGGCTCTACCC 59.465 55.000 0.00 0.00 33.26 3.69
4250 4549 4.640690 ACGGTCAGACTGCCCCCT 62.641 66.667 9.52 0.00 0.00 4.79
4261 4560 0.247460 CAGGATCTCTGCAACGGTCA 59.753 55.000 0.00 0.00 36.60 4.02
4352 4651 2.285083 GCATATTACAGGGTGCGAACA 58.715 47.619 0.00 0.00 0.00 3.18
4389 4688 3.011566 ACACCAACAGGAATGTCACAA 57.988 42.857 0.00 0.00 0.00 3.33
4390 4689 2.687425 CAACACCAACAGGAATGTCACA 59.313 45.455 0.00 0.00 0.00 3.58
4506 4806 9.975218 AAAACCAAAGTCATATAAGATACCAGT 57.025 29.630 0.00 0.00 0.00 4.00
4512 4812 9.739276 TGTGAGAAAACCAAAGTCATATAAGAT 57.261 29.630 0.00 0.00 0.00 2.40
4513 4813 9.739276 ATGTGAGAAAACCAAAGTCATATAAGA 57.261 29.630 0.00 0.00 0.00 2.10
4514 4814 9.778993 CATGTGAGAAAACCAAAGTCATATAAG 57.221 33.333 0.00 0.00 0.00 1.73
4515 4815 9.295825 ACATGTGAGAAAACCAAAGTCATATAA 57.704 29.630 0.00 0.00 0.00 0.98
4516 4816 8.862325 ACATGTGAGAAAACCAAAGTCATATA 57.138 30.769 0.00 0.00 0.00 0.86
4517 4817 7.765695 ACATGTGAGAAAACCAAAGTCATAT 57.234 32.000 0.00 0.00 0.00 1.78
4518 4818 7.068103 ACAACATGTGAGAAAACCAAAGTCATA 59.932 33.333 0.00 0.00 0.00 2.15
4519 4819 6.127366 ACAACATGTGAGAAAACCAAAGTCAT 60.127 34.615 0.00 0.00 0.00 3.06
4520 4820 5.184864 ACAACATGTGAGAAAACCAAAGTCA 59.815 36.000 0.00 0.00 0.00 3.41
4521 4821 5.650543 ACAACATGTGAGAAAACCAAAGTC 58.349 37.500 0.00 0.00 0.00 3.01
4522 4822 5.659440 ACAACATGTGAGAAAACCAAAGT 57.341 34.783 0.00 0.00 0.00 2.66
4523 4823 6.692681 CAGTACAACATGTGAGAAAACCAAAG 59.307 38.462 0.00 0.00 0.00 2.77
4524 4824 6.405286 CCAGTACAACATGTGAGAAAACCAAA 60.405 38.462 0.00 0.00 0.00 3.28
4525 4825 5.067153 CCAGTACAACATGTGAGAAAACCAA 59.933 40.000 0.00 0.00 0.00 3.67
4526 4826 4.578516 CCAGTACAACATGTGAGAAAACCA 59.421 41.667 0.00 0.00 0.00 3.67
4527 4827 4.578928 ACCAGTACAACATGTGAGAAAACC 59.421 41.667 0.00 0.00 0.00 3.27
4528 4828 5.751243 ACCAGTACAACATGTGAGAAAAC 57.249 39.130 0.00 0.00 0.00 2.43
4529 4829 7.450074 AGATACCAGTACAACATGTGAGAAAA 58.550 34.615 0.00 0.00 0.00 2.29
4530 4830 7.004555 AGATACCAGTACAACATGTGAGAAA 57.995 36.000 0.00 0.00 0.00 2.52
4531 4831 6.605471 AGATACCAGTACAACATGTGAGAA 57.395 37.500 0.00 0.00 0.00 2.87
4532 4832 6.605471 AAGATACCAGTACAACATGTGAGA 57.395 37.500 0.00 0.00 0.00 3.27
4533 4833 8.197439 TCATAAGATACCAGTACAACATGTGAG 58.803 37.037 0.00 0.00 0.00 3.51
4534 4834 7.979537 GTCATAAGATACCAGTACAACATGTGA 59.020 37.037 0.00 0.00 0.00 3.58
4535 4835 7.981789 AGTCATAAGATACCAGTACAACATGTG 59.018 37.037 0.00 0.00 0.00 3.21
4536 4836 8.079211 AGTCATAAGATACCAGTACAACATGT 57.921 34.615 0.00 0.00 0.00 3.21
4537 4837 8.948631 AAGTCATAAGATACCAGTACAACATG 57.051 34.615 0.00 0.00 0.00 3.21
4538 4838 9.383519 CAAAGTCATAAGATACCAGTACAACAT 57.616 33.333 0.00 0.00 0.00 2.71
4539 4839 7.822334 CCAAAGTCATAAGATACCAGTACAACA 59.178 37.037 0.00 0.00 0.00 3.33
4540 4840 7.822822 ACCAAAGTCATAAGATACCAGTACAAC 59.177 37.037 0.00 0.00 0.00 3.32
4541 4841 7.913789 ACCAAAGTCATAAGATACCAGTACAA 58.086 34.615 0.00 0.00 0.00 2.41
4542 4842 7.490657 ACCAAAGTCATAAGATACCAGTACA 57.509 36.000 0.00 0.00 0.00 2.90
4543 4843 8.788325 AAACCAAAGTCATAAGATACCAGTAC 57.212 34.615 0.00 0.00 0.00 2.73
4544 4844 9.444600 GAAAACCAAAGTCATAAGATACCAGTA 57.555 33.333 0.00 0.00 0.00 2.74
4667 4967 2.396590 AATCCGTTGCTGACCGTATT 57.603 45.000 0.00 0.00 0.00 1.89
4804 5413 8.037758 ACACAACTTACCATCAAAACAAAATCA 58.962 29.630 0.00 0.00 0.00 2.57
4824 5433 0.600782 CCATGCTTGCCCAACACAAC 60.601 55.000 0.00 0.00 0.00 3.32
4873 5537 6.127675 GGCCAATGCAAATTACCATCAAAATT 60.128 34.615 0.00 0.00 40.13 1.82
4945 5609 5.853282 GCAAATTATATTGTCGTGAGGATGC 59.147 40.000 0.00 0.00 32.80 3.91
5030 5699 2.598099 TCGTGGCACTGGTCGGTA 60.598 61.111 16.72 0.00 0.00 4.02
5051 5720 2.029110 TGTGTCATCATCACGCAGAGAA 60.029 45.455 0.00 0.00 38.48 2.87
5053 5722 1.657594 GTGTGTCATCATCACGCAGAG 59.342 52.381 5.02 0.00 43.19 3.35
5054 5723 1.672737 GGTGTGTCATCATCACGCAGA 60.673 52.381 10.82 0.00 44.77 4.26
5055 5724 0.723414 GGTGTGTCATCATCACGCAG 59.277 55.000 10.82 0.00 44.77 5.18
5056 5725 0.673333 GGGTGTGTCATCATCACGCA 60.673 55.000 10.82 0.00 44.77 5.24
5057 5726 0.673333 TGGGTGTGTCATCATCACGC 60.673 55.000 0.00 0.00 43.03 5.34
5058 5727 1.338105 ACTGGGTGTGTCATCATCACG 60.338 52.381 0.00 0.00 38.48 4.35
5059 5728 2.479566 ACTGGGTGTGTCATCATCAC 57.520 50.000 0.00 0.00 36.48 3.06
5060 5729 2.371510 TCAACTGGGTGTGTCATCATCA 59.628 45.455 0.00 0.00 0.00 3.07
5061 5730 3.057969 TCAACTGGGTGTGTCATCATC 57.942 47.619 0.00 0.00 0.00 2.92
5062 5731 3.009363 TCATCAACTGGGTGTGTCATCAT 59.991 43.478 0.00 0.00 0.00 2.45
5063 5732 2.371510 TCATCAACTGGGTGTGTCATCA 59.628 45.455 0.00 0.00 0.00 3.07
5064 5733 3.057969 TCATCAACTGGGTGTGTCATC 57.942 47.619 0.00 0.00 0.00 2.92
5065 5734 3.726557 ATCATCAACTGGGTGTGTCAT 57.273 42.857 0.00 0.00 0.00 3.06
5080 5749 2.826428 TGCTCTCGTGGCTTAATCATC 58.174 47.619 0.00 0.00 0.00 2.92
5083 5752 3.437049 AGTTTTGCTCTCGTGGCTTAATC 59.563 43.478 0.00 0.00 0.00 1.75
5171 5841 2.839026 GTCGTTCGACTCGTAATCACTG 59.161 50.000 16.50 0.00 32.82 3.66
5172 5842 2.740981 AGTCGTTCGACTCGTAATCACT 59.259 45.455 19.92 2.97 41.08 3.41
5173 5843 3.114693 AGTCGTTCGACTCGTAATCAC 57.885 47.619 19.92 1.04 41.08 3.06
5174 5844 3.928992 ACTAGTCGTTCGACTCGTAATCA 59.071 43.478 27.01 10.46 43.52 2.57
5175 5845 4.267452 AGACTAGTCGTTCGACTCGTAATC 59.733 45.833 27.01 18.19 43.52 1.75
5176 5846 4.180057 AGACTAGTCGTTCGACTCGTAAT 58.820 43.478 27.01 17.08 43.52 1.89
5177 5847 3.579709 AGACTAGTCGTTCGACTCGTAA 58.420 45.455 27.01 12.04 43.52 3.18
5178 5848 3.223423 AGACTAGTCGTTCGACTCGTA 57.777 47.619 27.01 12.36 43.52 3.43
5179 5849 2.077413 AGACTAGTCGTTCGACTCGT 57.923 50.000 27.01 25.73 43.52 4.18
5180 5850 3.240401 GTCTAGACTAGTCGTTCGACTCG 59.760 52.174 27.01 23.14 43.52 4.18
5181 5851 4.423732 AGTCTAGACTAGTCGTTCGACTC 58.576 47.826 27.01 15.60 43.52 3.36
5182 5852 4.454728 AGTCTAGACTAGTCGTTCGACT 57.545 45.455 24.04 26.54 45.99 4.18
5193 5863 3.963665 GTCGAGCGACTAGTCTAGACTA 58.036 50.000 27.03 27.03 39.77 2.59
5194 5864 2.813061 GTCGAGCGACTAGTCTAGACT 58.187 52.381 27.72 27.72 41.57 3.24
5205 5875 1.518102 CTCGTAGACTAGTCGAGCGAC 59.482 57.143 24.53 14.65 42.94 5.19
5206 5876 1.837648 CTCGTAGACTAGTCGAGCGA 58.162 55.000 25.67 25.67 42.94 4.93
5212 5882 2.536803 CTCTGCGACTCGTAGACTAGTC 59.463 54.545 15.41 15.41 42.90 2.59
5213 5883 2.094078 ACTCTGCGACTCGTAGACTAGT 60.094 50.000 14.44 9.11 42.90 2.57
5214 5884 2.283086 CACTCTGCGACTCGTAGACTAG 59.717 54.545 14.44 8.54 42.90 2.57
5215 5885 2.269172 CACTCTGCGACTCGTAGACTA 58.731 52.381 14.44 0.00 42.90 2.59
5216 5886 1.080298 CACTCTGCGACTCGTAGACT 58.920 55.000 14.44 4.31 42.90 3.24
5217 5887 0.097325 CCACTCTGCGACTCGTAGAC 59.903 60.000 14.44 0.00 42.90 2.59
5218 5888 0.036671 TCCACTCTGCGACTCGTAGA 60.037 55.000 16.99 16.99 45.21 2.59
5219 5889 1.018148 ATCCACTCTGCGACTCGTAG 58.982 55.000 10.04 10.04 40.69 3.51
5220 5890 0.733150 CATCCACTCTGCGACTCGTA 59.267 55.000 0.00 0.00 0.00 3.43
5221 5891 1.244697 ACATCCACTCTGCGACTCGT 61.245 55.000 0.00 0.00 0.00 4.18
5222 5892 0.524392 GACATCCACTCTGCGACTCG 60.524 60.000 0.00 0.00 0.00 4.18
5223 5893 0.524392 CGACATCCACTCTGCGACTC 60.524 60.000 0.00 0.00 0.00 3.36
5224 5894 0.960861 TCGACATCCACTCTGCGACT 60.961 55.000 0.00 0.00 0.00 4.18
5225 5895 0.798771 GTCGACATCCACTCTGCGAC 60.799 60.000 11.55 0.00 40.75 5.19
5226 5896 0.960861 AGTCGACATCCACTCTGCGA 60.961 55.000 19.50 0.00 0.00 5.10
5227 5897 0.524392 GAGTCGACATCCACTCTGCG 60.524 60.000 19.50 0.00 36.80 5.18
5228 5898 0.528017 TGAGTCGACATCCACTCTGC 59.472 55.000 19.50 0.00 39.92 4.26
5229 5899 3.516981 AATGAGTCGACATCCACTCTG 57.483 47.619 19.50 0.00 39.92 3.35
5230 5900 4.221703 AGAAAATGAGTCGACATCCACTCT 59.778 41.667 19.50 9.58 39.92 3.24
5231 5901 4.499183 AGAAAATGAGTCGACATCCACTC 58.501 43.478 19.50 5.79 39.70 3.51
5232 5902 4.499183 GAGAAAATGAGTCGACATCCACT 58.501 43.478 19.50 7.77 0.00 4.00
5233 5903 3.304559 CGAGAAAATGAGTCGACATCCAC 59.695 47.826 19.50 4.23 35.70 4.02
5234 5904 3.056821 ACGAGAAAATGAGTCGACATCCA 60.057 43.478 19.50 12.67 37.16 3.41
5235 5905 3.304559 CACGAGAAAATGAGTCGACATCC 59.695 47.826 19.50 6.99 37.16 3.51
5236 5906 3.921021 ACACGAGAAAATGAGTCGACATC 59.079 43.478 19.50 12.61 37.16 3.06
5237 5907 3.914312 ACACGAGAAAATGAGTCGACAT 58.086 40.909 19.50 0.00 37.16 3.06
5238 5908 3.364889 ACACGAGAAAATGAGTCGACA 57.635 42.857 19.50 0.00 37.16 4.35
5239 5909 4.554200 GTCTACACGAGAAAATGAGTCGAC 59.446 45.833 7.70 7.70 35.37 4.20
5240 5910 4.454847 AGTCTACACGAGAAAATGAGTCGA 59.545 41.667 0.00 0.00 35.37 4.20
5241 5911 4.724303 AGTCTACACGAGAAAATGAGTCG 58.276 43.478 0.00 0.00 35.37 4.18
5242 5912 6.609533 TGTAGTCTACACGAGAAAATGAGTC 58.390 40.000 8.70 0.00 35.37 3.36
5243 5913 6.570672 TGTAGTCTACACGAGAAAATGAGT 57.429 37.500 8.70 0.00 35.37 3.41
5244 5914 7.869016 TTTGTAGTCTACACGAGAAAATGAG 57.131 36.000 12.37 0.00 38.63 2.90
5245 5915 9.350357 GTATTTGTAGTCTACACGAGAAAATGA 57.650 33.333 12.37 0.00 38.63 2.57
5246 5916 8.311822 CGTATTTGTAGTCTACACGAGAAAATG 58.688 37.037 12.37 0.00 38.63 2.32
5247 5917 8.239314 TCGTATTTGTAGTCTACACGAGAAAAT 58.761 33.333 12.37 10.51 38.63 1.82
5248 5918 7.584108 TCGTATTTGTAGTCTACACGAGAAAA 58.416 34.615 12.37 3.84 38.63 2.29
5249 5919 7.095060 ACTCGTATTTGTAGTCTACACGAGAAA 60.095 37.037 34.40 20.15 46.02 2.52
5250 5920 6.369890 ACTCGTATTTGTAGTCTACACGAGAA 59.630 38.462 34.40 20.42 46.02 2.87
5251 5921 5.871524 ACTCGTATTTGTAGTCTACACGAGA 59.128 40.000 34.40 20.50 46.02 4.04
5253 5923 5.220284 CGACTCGTATTTGTAGTCTACACGA 60.220 44.000 12.37 15.51 38.63 4.35
5254 5924 4.954405 CGACTCGTATTTGTAGTCTACACG 59.046 45.833 12.37 12.31 38.63 4.49
5255 5925 6.099579 TCGACTCGTATTTGTAGTCTACAC 57.900 41.667 12.37 0.60 38.63 2.90
5256 5926 5.220548 GCTCGACTCGTATTTGTAGTCTACA 60.221 44.000 8.70 8.70 37.97 2.74
5257 5927 5.196825 GCTCGACTCGTATTTGTAGTCTAC 58.803 45.833 2.81 2.81 37.97 2.59
5258 5928 4.272018 GGCTCGACTCGTATTTGTAGTCTA 59.728 45.833 0.00 0.00 37.97 2.59
5259 5929 3.065095 GGCTCGACTCGTATTTGTAGTCT 59.935 47.826 0.00 0.00 37.97 3.24
5260 5930 3.361414 GGCTCGACTCGTATTTGTAGTC 58.639 50.000 0.00 0.00 36.99 2.59
5261 5931 2.223203 CGGCTCGACTCGTATTTGTAGT 60.223 50.000 0.00 0.00 0.00 2.73
5262 5932 2.223203 ACGGCTCGACTCGTATTTGTAG 60.223 50.000 6.52 0.00 37.88 2.74
5263 5933 1.739466 ACGGCTCGACTCGTATTTGTA 59.261 47.619 6.52 0.00 37.88 2.41
5264 5934 0.524862 ACGGCTCGACTCGTATTTGT 59.475 50.000 6.52 0.00 37.88 2.83
5265 5935 0.914551 CACGGCTCGACTCGTATTTG 59.085 55.000 7.79 0.00 37.88 2.32
5266 5936 0.524862 ACACGGCTCGACTCGTATTT 59.475 50.000 7.79 0.00 37.88 1.40
5267 5937 0.098376 GACACGGCTCGACTCGTATT 59.902 55.000 7.79 0.00 37.88 1.89
5268 5938 0.743701 AGACACGGCTCGACTCGTAT 60.744 55.000 7.79 0.00 37.88 3.06
5269 5939 1.375140 AGACACGGCTCGACTCGTA 60.375 57.895 7.79 0.00 37.88 3.43
5270 5940 2.668889 AGACACGGCTCGACTCGT 60.669 61.111 0.00 2.87 40.49 4.18
5271 5941 2.202362 CAGACACGGCTCGACTCG 60.202 66.667 1.50 0.00 0.00 4.18
5272 5942 2.179517 CCAGACACGGCTCGACTC 59.820 66.667 1.50 0.00 0.00 3.36
5273 5943 2.282251 TCCAGACACGGCTCGACT 60.282 61.111 1.50 0.00 0.00 4.18
5274 5944 1.303799 TAGTCCAGACACGGCTCGAC 61.304 60.000 0.00 0.00 0.00 4.20
5275 5945 1.002990 TAGTCCAGACACGGCTCGA 60.003 57.895 0.00 0.00 0.00 4.04
5276 5946 1.306642 ACTAGTCCAGACACGGCTCG 61.307 60.000 0.00 0.00 0.00 5.03
5277 5947 0.452585 GACTAGTCCAGACACGGCTC 59.547 60.000 12.13 0.00 0.00 4.70
5278 5948 1.306642 CGACTAGTCCAGACACGGCT 61.307 60.000 17.23 0.00 0.00 5.52
5279 5949 1.136984 CGACTAGTCCAGACACGGC 59.863 63.158 17.23 0.00 0.00 5.68
5280 5950 0.447011 GTCGACTAGTCCAGACACGG 59.553 60.000 19.95 5.26 34.09 4.94
5281 5951 0.094901 CGTCGACTAGTCCAGACACG 59.905 60.000 22.73 16.49 33.56 4.49
5282 5952 1.128321 GTCGTCGACTAGTCCAGACAC 59.872 57.143 23.71 17.98 33.56 3.67
5283 5953 1.001746 AGTCGTCGACTAGTCCAGACA 59.998 52.381 25.94 15.20 41.51 3.41
5284 5954 1.724429 AGTCGTCGACTAGTCCAGAC 58.276 55.000 25.94 22.29 41.51 3.51
5303 5973 7.904205 TCATATATGTCGACTAGTCCAGACTA 58.096 38.462 23.17 16.06 42.54 2.59
5304 5974 6.770542 TCATATATGTCGACTAGTCCAGACT 58.229 40.000 23.17 14.95 45.02 3.24
5305 5975 6.651643 ACTCATATATGTCGACTAGTCCAGAC 59.348 42.308 17.92 18.10 0.00 3.51
5306 5976 6.770542 ACTCATATATGTCGACTAGTCCAGA 58.229 40.000 17.92 8.00 0.00 3.86
5307 5977 7.067532 GACTCATATATGTCGACTAGTCCAG 57.932 44.000 17.92 4.40 0.00 3.86


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

AutoCloner maintained by Alex Coulton.