Multiple sequence alignment - TraesCS4A01G457200

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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 TraesCS4A01G457200 chr4A 100.000 1608 0 0 1325 2932 722415182 722416789 0.000000e+00 2970.0
1 TraesCS4A01G457200 chr4A 100.000 1016 0 0 1 1016 722413858 722414873 0.000000e+00 1877.0
2 TraesCS4A01G457200 chr7D 95.686 1020 36 6 1 1016 14547474 14546459 0.000000e+00 1633.0
3 TraesCS4A01G457200 chr7D 95.219 1004 35 5 1 1003 14167369 14166378 0.000000e+00 1576.0
4 TraesCS4A01G457200 chr7D 93.906 361 22 0 1327 1687 14546365 14546005 1.990000e-151 545.0
5 TraesCS4A01G457200 chr7D 82.504 623 84 13 1325 1923 14177132 14176511 9.310000e-145 523.0
6 TraesCS4A01G457200 chr7D 96.694 242 7 1 1333 1573 14166073 14165832 4.550000e-108 401.0
7 TraesCS4A01G457200 chr7D 90.612 245 23 0 1679 1923 14544683 14544439 2.820000e-85 326.0
8 TraesCS4A01G457200 chr7D 91.703 229 19 0 1599 1827 14165838 14165610 4.720000e-83 318.0
9 TraesCS4A01G457200 chr7D 86.239 109 12 3 822 930 14177411 14177306 6.640000e-22 115.0
10 TraesCS4A01G457200 chr7D 93.846 65 4 0 1847 1911 14165618 14165554 6.690000e-17 99.0
11 TraesCS4A01G457200 chr7D 87.037 54 4 3 966 1016 14546471 14546418 1.130000e-04 58.4
12 TraesCS4A01G457200 chr7A 89.292 1074 84 16 1550 2617 13774383 13773335 0.000000e+00 1317.0
13 TraesCS4A01G457200 chr7A 86.475 732 68 16 1328 2029 13796459 13795729 0.000000e+00 774.0
14 TraesCS4A01G457200 chr7A 83.863 787 67 32 1331 2061 13790924 13790142 0.000000e+00 695.0
15 TraesCS4A01G457200 chr7A 86.719 512 66 2 1331 1841 13750671 13750161 4.240000e-158 568.0
16 TraesCS4A01G457200 chr7A 81.433 684 83 17 194 856 13791762 13791102 1.200000e-143 520.0
17 TraesCS4A01G457200 chr7A 88.451 355 34 3 578 932 13796960 13796613 3.490000e-114 422.0
18 TraesCS4A01G457200 chr7A 89.677 155 13 1 1927 2081 13750126 13749975 8.290000e-46 195.0
19 TraesCS4A01G457200 chr7A 84.713 157 17 4 755 909 13772464 13772313 1.820000e-32 150.0
20 TraesCS4A01G457200 chr7A 86.014 143 13 3 876 1011 13775726 13775584 2.350000e-31 147.0
21 TraesCS4A01G457200 chr7A 97.059 34 1 0 694 727 13745260 13745227 1.130000e-04 58.4
22 TraesCS4A01G457200 chr1A 83.015 524 74 6 1331 1850 29009340 29008828 7.400000e-126 460.0
23 TraesCS4A01G457200 chr1A 83.831 402 38 10 534 933 29009850 29009474 9.990000e-95 357.0
24 TraesCS4A01G457200 chr1A 88.043 92 4 2 1927 2018 29006554 29006470 5.170000e-18 102.0
25 TraesCS4A01G457200 chr1A 84.337 83 12 1 1842 1923 29006661 29006579 2.420000e-11 80.5
26 TraesCS4A01G457200 chr1B 83.582 402 40 12 534 933 44951314 44950937 1.290000e-93 353.0
27 TraesCS4A01G457200 chr1B 84.167 240 31 6 1332 1567 44950805 44950569 2.940000e-55 226.0
28 TraesCS4A01G457200 chr1B 80.882 272 24 17 1419 1663 44851682 44851412 3.860000e-44 189.0
29 TraesCS4A01G457200 chr1B 78.134 343 37 15 1697 2018 44948335 44948010 1.790000e-42 183.0
30 TraesCS4A01G457200 chr1B 87.838 74 7 2 694 765 45197922 45197849 5.210000e-13 86.1
31 TraesCS4A01G457200 chr1B 97.222 36 1 0 6 41 45197786 45197751 8.770000e-06 62.1
32 TraesCS4A01G457200 chr5D 94.444 54 3 0 2879 2932 506241114 506241167 1.870000e-12 84.2
33 TraesCS4A01G457200 chr5A 92.593 54 4 0 2879 2932 636577517 636577464 8.710000e-11 78.7
34 TraesCS4A01G457200 chr2D 92.727 55 2 2 2879 2932 490664223 490664170 8.710000e-11 78.7
35 TraesCS4A01G457200 chr2D 100.000 29 0 0 173 201 519340803 519340831 1.000000e-03 54.7
36 TraesCS4A01G457200 chr6D 90.909 55 3 2 2879 2932 417749023 417749076 4.050000e-09 73.1
37 TraesCS4A01G457200 chr6D 88.889 54 6 0 2879 2932 320164945 320164892 1.890000e-07 67.6
38 TraesCS4A01G457200 chr3D 90.741 54 5 0 2879 2932 41043526 41043473 4.050000e-09 73.1
39 TraesCS4A01G457200 chr2B 90.741 54 5 0 2879 2932 67546584 67546637 4.050000e-09 73.1
40 TraesCS4A01G457200 chr2B 100.000 29 0 0 173 201 611313143 611313171 1.000000e-03 54.7
41 TraesCS4A01G457200 chr5B 88.889 54 6 0 2879 2932 34780321 34780268 1.890000e-07 67.6
42 TraesCS4A01G457200 chr5B 100.000 29 0 0 148 176 511619643 511619671 1.000000e-03 54.7
43 TraesCS4A01G457200 chr3B 88.889 54 6 0 2879 2932 31489252 31489199 1.890000e-07 67.6


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 TraesCS4A01G457200 chr4A 722413858 722416789 2931 False 2423.500 2970 100.00000 1 2932 2 chr4A.!!$F1 2931
1 TraesCS4A01G457200 chr7D 14544439 14547474 3035 True 640.600 1633 91.81025 1 1923 4 chr7D.!!$R3 1922
2 TraesCS4A01G457200 chr7D 14165554 14167369 1815 True 598.500 1576 94.36550 1 1911 4 chr7D.!!$R1 1910
3 TraesCS4A01G457200 chr7D 14176511 14177411 900 True 319.000 523 84.37150 822 1923 2 chr7D.!!$R2 1101
4 TraesCS4A01G457200 chr7A 13790142 13796960 6818 True 602.750 774 85.05550 194 2061 4 chr7A.!!$R4 1867
5 TraesCS4A01G457200 chr7A 13772313 13775726 3413 True 538.000 1317 86.67300 755 2617 3 chr7A.!!$R3 1862
6 TraesCS4A01G457200 chr7A 13749975 13750671 696 True 381.500 568 88.19800 1331 2081 2 chr7A.!!$R2 750
7 TraesCS4A01G457200 chr1A 29006470 29009850 3380 True 249.875 460 84.80650 534 2018 4 chr1A.!!$R1 1484
8 TraesCS4A01G457200 chr1B 44948010 44951314 3304 True 254.000 353 81.96100 534 2018 3 chr1B.!!$R2 1484

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
666 669 1.200020 GCTGAAACTCCCGTGGATTTG 59.800 52.381 0.0 0.0 0.00 2.32 F
1482 1547 0.179032 TCATGTGCAAGACCCACGTT 60.179 50.000 0.0 0.0 36.01 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 8709 0.104304 GTCGGGATAATCTGCACGGT 59.896 55.0 0.00 0.00 0.00 4.83 R
2909 15795 0.517316 GGACGGCAATATTCATCCGC 59.483 55.0 16.04 10.79 45.23 5.54 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
106 107 9.061435 ACCTACTATAATTTGTAGACCTCGTAC 57.939 37.037 7.13 0.00 38.62 3.67
107 108 8.226448 CCTACTATAATTTGTAGACCTCGTACG 58.774 40.741 9.53 9.53 38.62 3.67
113 114 1.276138 TGTAGACCTCGTACGGAGACA 59.724 52.381 16.52 8.58 46.23 3.41
114 115 2.289631 TGTAGACCTCGTACGGAGACAA 60.290 50.000 16.52 0.00 46.23 3.18
290 291 2.522185 ACTCTTGCGTTCCACCTAGTA 58.478 47.619 0.00 0.00 0.00 1.82
377 378 9.850198 TTTTCCAATTTCTCATTTGAATTTCCT 57.150 25.926 0.00 0.00 0.00 3.36
522 525 5.782893 TTGTGCTTACCTTGCAAGTAAAT 57.217 34.783 24.35 9.88 42.41 1.40
587 590 7.684670 TGTAGAATATTTAGCAAAACTGAGCG 58.315 34.615 0.00 0.00 35.48 5.03
665 668 1.534729 GCTGAAACTCCCGTGGATTT 58.465 50.000 0.00 0.00 0.00 2.17
666 669 1.200020 GCTGAAACTCCCGTGGATTTG 59.800 52.381 0.00 0.00 0.00 2.32
672 675 1.303236 TCCCGTGGATTTGGCACAG 60.303 57.895 0.00 0.00 42.39 3.66
791 797 6.539173 TGGGAGCAGTGAAAAATAACTCTAA 58.461 36.000 0.00 0.00 0.00 2.10
866 873 3.634910 GGTTGGTTGGTTCTCTTGCTTTA 59.365 43.478 0.00 0.00 0.00 1.85
909 917 5.887754 TGGTAAAGTTGAGGAGGCTTAAAT 58.112 37.500 0.00 0.00 0.00 1.40
1461 1526 2.930562 AGGCCCTTCTTCACCGCT 60.931 61.111 0.00 0.00 0.00 5.52
1482 1547 0.179032 TCATGTGCAAGACCCACGTT 60.179 50.000 0.00 0.00 36.01 3.99
1570 8689 2.242965 TCAATTGGTCATGCCCTGATCT 59.757 45.455 5.42 0.00 35.86 2.75
1571 8690 3.028850 CAATTGGTCATGCCCTGATCTT 58.971 45.455 0.00 0.00 35.86 2.40
1572 8691 2.425143 TTGGTCATGCCCTGATCTTC 57.575 50.000 0.00 0.00 35.86 2.87
1573 8692 1.588239 TGGTCATGCCCTGATCTTCT 58.412 50.000 0.00 0.00 35.86 2.85
1574 8693 1.487976 TGGTCATGCCCTGATCTTCTC 59.512 52.381 0.00 0.00 35.86 2.87
1575 8694 1.767681 GGTCATGCCCTGATCTTCTCT 59.232 52.381 0.00 0.00 35.97 3.10
1576 8695 2.485124 GGTCATGCCCTGATCTTCTCTG 60.485 54.545 0.00 0.00 35.97 3.35
1577 8696 1.140452 TCATGCCCTGATCTTCTCTGC 59.860 52.381 0.00 0.00 0.00 4.26
1578 8697 1.141254 CATGCCCTGATCTTCTCTGCT 59.859 52.381 0.00 0.00 0.00 4.24
1579 8698 1.283347 TGCCCTGATCTTCTCTGCTT 58.717 50.000 0.00 0.00 0.00 3.91
1580 8699 1.209019 TGCCCTGATCTTCTCTGCTTC 59.791 52.381 0.00 0.00 0.00 3.86
1581 8700 1.485895 GCCCTGATCTTCTCTGCTTCT 59.514 52.381 0.00 0.00 0.00 2.85
1582 8701 2.093021 GCCCTGATCTTCTCTGCTTCTT 60.093 50.000 0.00 0.00 0.00 2.52
1583 8702 3.533547 CCCTGATCTTCTCTGCTTCTTG 58.466 50.000 0.00 0.00 0.00 3.02
1584 8703 2.937799 CCTGATCTTCTCTGCTTCTTGC 59.062 50.000 0.00 0.00 43.25 4.01
1585 8704 2.604011 CTGATCTTCTCTGCTTCTTGCG 59.396 50.000 0.00 0.00 46.63 4.85
1586 8705 1.327156 GATCTTCTCTGCTTCTTGCGC 59.673 52.381 0.00 0.00 46.63 6.09
1587 8706 0.671781 TCTTCTCTGCTTCTTGCGCC 60.672 55.000 4.18 0.00 46.63 6.53
1588 8707 1.964290 CTTCTCTGCTTCTTGCGCCG 61.964 60.000 4.18 0.00 46.63 6.46
1589 8708 3.494336 CTCTGCTTCTTGCGCCGG 61.494 66.667 4.18 0.00 46.63 6.13
1590 8709 3.939837 CTCTGCTTCTTGCGCCGGA 62.940 63.158 5.05 0.00 46.63 5.14
1591 8710 3.793144 CTGCTTCTTGCGCCGGAC 61.793 66.667 5.05 0.00 46.63 4.79
1817 11849 2.464459 CGAAGATGTCGGCAAGGGC 61.464 63.158 0.00 0.00 46.45 5.19
1967 14207 2.483877 TGGTGCAAGTCGATTCAATGTC 59.516 45.455 0.00 0.00 0.00 3.06
2067 14310 5.036737 CGGTCATGAAATAATCAGTTTGCC 58.963 41.667 0.00 0.00 42.53 4.52
2070 14313 6.407299 GGTCATGAAATAATCAGTTTGCCCAT 60.407 38.462 0.00 0.00 42.53 4.00
2085 14328 1.338973 GCCCATGACCAAGTATGCATG 59.661 52.381 10.16 0.00 38.22 4.06
2086 14329 2.934887 CCCATGACCAAGTATGCATGA 58.065 47.619 10.16 0.00 40.29 3.07
2129 14372 8.682936 TTATCTTCCTCATTTCTTCTTATGGC 57.317 34.615 0.00 0.00 0.00 4.40
2135 14378 3.565482 TCATTTCTTCTTATGGCCGCATC 59.435 43.478 0.00 0.00 0.00 3.91
2148 14391 2.789917 GCATCTGCGCACCTCAAG 59.210 61.111 5.66 0.00 0.00 3.02
2192 14435 5.638657 TGCAAAAATATCTGGCACAATTGAC 59.361 36.000 13.59 3.47 38.70 3.18
2195 14438 6.594788 AAAATATCTGGCACAATTGACTGT 57.405 33.333 13.59 0.00 38.70 3.55
2201 14444 5.419542 TCTGGCACAATTGACTGTAGATAC 58.580 41.667 13.59 0.00 38.70 2.24
2203 14446 5.419542 TGGCACAATTGACTGTAGATACTC 58.580 41.667 13.59 0.00 31.92 2.59
2204 14447 4.811557 GGCACAATTGACTGTAGATACTCC 59.188 45.833 13.59 0.00 0.00 3.85
2205 14448 4.811557 GCACAATTGACTGTAGATACTCCC 59.188 45.833 13.59 0.00 0.00 4.30
2207 14450 6.276847 CACAATTGACTGTAGATACTCCCTC 58.723 44.000 13.59 0.00 0.00 4.30
2208 14451 5.364157 ACAATTGACTGTAGATACTCCCTCC 59.636 44.000 13.59 0.00 0.00 4.30
2210 14453 2.508716 TGACTGTAGATACTCCCTCCGT 59.491 50.000 0.00 0.00 0.00 4.69
2211 14454 3.713248 TGACTGTAGATACTCCCTCCGTA 59.287 47.826 0.00 0.00 0.00 4.02
2213 14456 3.181446 ACTGTAGATACTCCCTCCGTACC 60.181 52.174 0.00 0.00 0.00 3.34
2214 14457 3.051581 TGTAGATACTCCCTCCGTACCT 58.948 50.000 0.00 0.00 0.00 3.08
2215 14458 3.461085 TGTAGATACTCCCTCCGTACCTT 59.539 47.826 0.00 0.00 0.00 3.50
2216 14459 4.660303 TGTAGATACTCCCTCCGTACCTTA 59.340 45.833 0.00 0.00 0.00 2.69
2218 14461 5.336491 AGATACTCCCTCCGTACCTTAAT 57.664 43.478 0.00 0.00 0.00 1.40
2220 14463 3.111741 ACTCCCTCCGTACCTTAATGT 57.888 47.619 0.00 0.00 0.00 2.71
2221 14464 4.255510 ACTCCCTCCGTACCTTAATGTA 57.744 45.455 0.00 0.00 0.00 2.29
2224 14467 4.870636 TCCCTCCGTACCTTAATGTAAGA 58.129 43.478 5.63 0.41 38.02 2.10
2225 14468 4.646492 TCCCTCCGTACCTTAATGTAAGAC 59.354 45.833 5.63 0.00 38.02 3.01
2228 14471 5.393461 CCTCCGTACCTTAATGTAAGACGTT 60.393 44.000 5.63 0.00 38.02 3.99
2229 14472 6.024552 TCCGTACCTTAATGTAAGACGTTT 57.975 37.500 5.63 0.00 38.02 3.60
2231 14474 6.928492 TCCGTACCTTAATGTAAGACGTTTTT 59.072 34.615 0.00 0.00 38.02 1.94
2232 14475 7.116233 TCCGTACCTTAATGTAAGACGTTTTTC 59.884 37.037 0.00 0.00 38.02 2.29
2233 14476 6.944400 CGTACCTTAATGTAAGACGTTTTTCG 59.056 38.462 0.00 0.00 38.02 3.46
2234 14477 6.232139 ACCTTAATGTAAGACGTTTTTCGG 57.768 37.500 0.00 0.00 38.02 4.30
2235 14478 5.990996 ACCTTAATGTAAGACGTTTTTCGGA 59.009 36.000 0.00 0.00 38.02 4.55
2236 14479 6.146673 ACCTTAATGTAAGACGTTTTTCGGAG 59.853 38.462 0.00 0.00 38.02 4.63
2237 14480 6.401796 CCTTAATGTAAGACGTTTTTCGGAGG 60.402 42.308 0.00 0.00 38.02 4.30
2238 14481 2.758009 TGTAAGACGTTTTTCGGAGGG 58.242 47.619 0.00 0.00 44.69 4.30
2239 14482 2.102925 TGTAAGACGTTTTTCGGAGGGT 59.897 45.455 0.00 0.00 44.69 4.34
2240 14483 3.320541 TGTAAGACGTTTTTCGGAGGGTA 59.679 43.478 0.00 0.00 44.69 3.69
2241 14484 2.445565 AGACGTTTTTCGGAGGGTAC 57.554 50.000 0.00 0.00 44.69 3.34
2242 14485 1.966354 AGACGTTTTTCGGAGGGTACT 59.034 47.619 0.00 0.00 44.69 2.73
2243 14486 3.157087 AGACGTTTTTCGGAGGGTACTA 58.843 45.455 0.00 0.00 44.69 1.82
2244 14487 3.766051 AGACGTTTTTCGGAGGGTACTAT 59.234 43.478 0.00 0.00 44.69 2.12
2267 14510 6.455360 TTGCAGAAGGAGCAATTTATTAGG 57.545 37.500 0.00 0.00 46.13 2.69
2272 14515 4.475919 AGGAGCAATTTATTAGGCCCAT 57.524 40.909 0.00 0.00 0.00 4.00
2273 14516 4.154942 AGGAGCAATTTATTAGGCCCATG 58.845 43.478 0.00 0.00 0.00 3.66
2286 14529 1.672898 CCCATGGGCCAGTGTTTTG 59.327 57.895 20.41 3.65 0.00 2.44
2290 14535 1.270550 CATGGGCCAGTGTTTTGTCTC 59.729 52.381 13.78 0.00 0.00 3.36
2299 14544 3.369147 CAGTGTTTTGTCTCTATGCTCCG 59.631 47.826 0.00 0.00 0.00 4.63
2334 14582 5.557866 ACCACCTTCTTTCTACCATACAAC 58.442 41.667 0.00 0.00 0.00 3.32
2339 14587 8.237267 CACCTTCTTTCTACCATACAACAATTC 58.763 37.037 0.00 0.00 0.00 2.17
2342 14590 8.561738 TTCTTTCTACCATACAACAATTCTCC 57.438 34.615 0.00 0.00 0.00 3.71
2351 14599 3.399330 ACAACAATTCTCCGTCGAACAT 58.601 40.909 0.00 0.00 0.00 2.71
2357 14605 5.120208 ACAATTCTCCGTCGAACATGTAAAG 59.880 40.000 0.00 0.00 29.64 1.85
2366 14614 6.086241 CCGTCGAACATGTAAAGAAACAATTG 59.914 38.462 3.24 3.24 32.02 2.32
2369 14617 7.112984 GTCGAACATGTAAAGAAACAATTGTCC 59.887 37.037 12.39 7.17 32.02 4.02
2375 14623 4.886247 AAAGAAACAATTGTCCGTCGAA 57.114 36.364 12.39 0.00 0.00 3.71
2389 14637 3.252215 TCCGTCGAAACAATGCAAGAAAT 59.748 39.130 0.00 0.00 0.00 2.17
2391 14639 4.788100 CCGTCGAAACAATGCAAGAAATAG 59.212 41.667 0.00 0.00 0.00 1.73
2392 14640 4.260656 CGTCGAAACAATGCAAGAAATAGC 59.739 41.667 0.00 0.00 0.00 2.97
2393 14641 5.153513 GTCGAAACAATGCAAGAAATAGCA 58.846 37.500 0.00 0.00 45.92 3.49
2394 14642 5.629020 GTCGAAACAATGCAAGAAATAGCAA 59.371 36.000 0.00 0.00 44.88 3.91
2395 14643 6.143758 GTCGAAACAATGCAAGAAATAGCAAA 59.856 34.615 0.00 0.00 44.88 3.68
2396 14644 6.867816 TCGAAACAATGCAAGAAATAGCAAAT 59.132 30.769 0.00 0.00 44.88 2.32
2397 14645 7.384660 TCGAAACAATGCAAGAAATAGCAAATT 59.615 29.630 0.00 0.00 44.88 1.82
2398 14646 8.011106 CGAAACAATGCAAGAAATAGCAAATTT 58.989 29.630 0.00 0.00 44.88 1.82
2399 14647 9.667989 GAAACAATGCAAGAAATAGCAAATTTT 57.332 25.926 0.00 0.00 44.88 1.82
2430 14678 4.907269 TGGCAAATGAGGTATCTCTCCATA 59.093 41.667 4.28 0.00 40.58 2.74
2445 14693 3.055819 TCTCCATACTTCAAGCTCACACC 60.056 47.826 0.00 0.00 0.00 4.16
2448 14696 3.438087 CCATACTTCAAGCTCACACCTTG 59.562 47.826 0.00 0.00 40.72 3.61
2479 14727 2.354259 CCAACTGTTGGCAAAAGCAAA 58.646 42.857 25.21 0.00 45.17 3.68
2481 14729 3.181508 CCAACTGTTGGCAAAAGCAAAAG 60.182 43.478 25.21 3.20 45.17 2.27
2483 14731 2.235898 ACTGTTGGCAAAAGCAAAAGGA 59.764 40.909 17.35 0.00 0.00 3.36
2487 14735 4.704057 TGTTGGCAAAAGCAAAAGGAAAAT 59.296 33.333 0.00 0.00 0.00 1.82
2488 14736 5.882557 TGTTGGCAAAAGCAAAAGGAAAATA 59.117 32.000 0.00 0.00 0.00 1.40
2499 14747 8.662781 AGCAAAAGGAAAATAAAAAGGAGAAC 57.337 30.769 0.00 0.00 0.00 3.01
2521 14769 1.850998 GGGGTTAGCTTGGGAATAGGT 59.149 52.381 0.00 0.00 0.00 3.08
2558 14806 1.478105 AGTCTCATATGCGCAGTGTGA 59.522 47.619 18.32 19.31 0.00 3.58
2559 14807 2.102084 AGTCTCATATGCGCAGTGTGAT 59.898 45.455 23.91 14.76 0.00 3.06
2568 14816 0.930310 CGCAGTGTGATATGGTTCCG 59.070 55.000 0.00 0.00 0.00 4.30
2582 14830 1.202545 GGTTCCGGGCAGATAGACTTC 60.203 57.143 0.00 0.00 0.00 3.01
2592 14840 3.614150 GCAGATAGACTTCGTTGTCCACA 60.614 47.826 6.87 0.00 37.66 4.17
2612 14860 3.146066 CAACCGGTTCCTCATCAAAGAA 58.854 45.455 19.24 0.00 0.00 2.52
2613 14861 3.721087 ACCGGTTCCTCATCAAAGAAT 57.279 42.857 0.00 0.00 0.00 2.40
2614 14862 3.347216 ACCGGTTCCTCATCAAAGAATG 58.653 45.455 0.00 0.00 0.00 2.67
2615 14863 3.244911 ACCGGTTCCTCATCAAAGAATGT 60.245 43.478 0.00 0.00 0.00 2.71
2616 14864 3.127548 CCGGTTCCTCATCAAAGAATGTG 59.872 47.826 0.00 0.00 0.00 3.21
2617 14865 3.753272 CGGTTCCTCATCAAAGAATGTGT 59.247 43.478 0.00 0.00 0.00 3.72
2618 14866 4.142816 CGGTTCCTCATCAAAGAATGTGTC 60.143 45.833 0.00 0.00 0.00 3.67
2619 14867 5.006386 GGTTCCTCATCAAAGAATGTGTCT 58.994 41.667 0.00 0.00 38.69 3.41
2620 14868 6.173339 GGTTCCTCATCAAAGAATGTGTCTA 58.827 40.000 0.00 0.00 34.56 2.59
2621 14869 6.314896 GGTTCCTCATCAAAGAATGTGTCTAG 59.685 42.308 0.00 0.00 34.56 2.43
2622 14870 5.982356 TCCTCATCAAAGAATGTGTCTAGG 58.018 41.667 0.00 0.00 34.56 3.02
2623 14871 4.574013 CCTCATCAAAGAATGTGTCTAGGC 59.426 45.833 0.00 0.00 34.56 3.93
2624 14872 4.183865 TCATCAAAGAATGTGTCTAGGCG 58.816 43.478 0.00 0.00 34.56 5.52
2625 14873 2.972625 TCAAAGAATGTGTCTAGGCGG 58.027 47.619 0.00 0.00 34.56 6.13
2626 14874 1.398390 CAAAGAATGTGTCTAGGCGGC 59.602 52.381 0.00 0.00 34.56 6.53
2627 14875 0.905357 AAGAATGTGTCTAGGCGGCT 59.095 50.000 18.33 18.33 34.56 5.52
2628 14876 0.176680 AGAATGTGTCTAGGCGGCTG 59.823 55.000 23.55 11.80 33.56 4.85
2629 14877 0.175760 GAATGTGTCTAGGCGGCTGA 59.824 55.000 23.55 14.06 0.00 4.26
2630 14878 0.108138 AATGTGTCTAGGCGGCTGAC 60.108 55.000 23.55 24.15 0.00 3.51
2642 14890 2.658593 GCTGACGTGTGCGACTGT 60.659 61.111 0.00 0.00 42.00 3.55
2645 14893 4.046998 GACGTGTGCGACTGTGCG 62.047 66.667 0.00 0.00 42.00 5.34
2668 14916 3.545481 GCGATGACCTGTGCGACG 61.545 66.667 0.00 0.00 0.00 5.12
2685 14933 3.869272 GGCGCGGTGCTGAATCAG 61.869 66.667 13.85 5.78 45.43 2.90
2686 14934 3.121030 GCGCGGTGCTGAATCAGT 61.121 61.111 12.29 0.00 41.73 3.41
2687 14935 2.680913 GCGCGGTGCTGAATCAGTT 61.681 57.895 12.29 0.00 41.73 3.16
2688 14936 1.358725 GCGCGGTGCTGAATCAGTTA 61.359 55.000 12.29 0.00 41.73 2.24
2689 14937 1.075542 CGCGGTGCTGAATCAGTTAA 58.924 50.000 12.29 0.00 33.43 2.01
2690 14938 1.201921 CGCGGTGCTGAATCAGTTAAC 60.202 52.381 12.29 8.01 33.43 2.01
2691 14939 2.076863 GCGGTGCTGAATCAGTTAACT 58.923 47.619 12.29 1.12 33.43 2.24
2692 14940 2.159653 GCGGTGCTGAATCAGTTAACTG 60.160 50.000 26.60 26.60 45.08 3.16
2693 14941 2.159653 CGGTGCTGAATCAGTTAACTGC 60.160 50.000 27.49 16.70 43.46 4.40
2694 14942 2.813754 GGTGCTGAATCAGTTAACTGCA 59.186 45.455 27.49 18.92 43.46 4.41
2695 14943 3.253188 GGTGCTGAATCAGTTAACTGCAA 59.747 43.478 27.49 14.23 43.46 4.08
2696 14944 4.082571 GGTGCTGAATCAGTTAACTGCAAT 60.083 41.667 27.49 15.78 43.46 3.56
2697 14945 5.123820 GGTGCTGAATCAGTTAACTGCAATA 59.876 40.000 27.49 13.18 43.46 1.90
2698 14946 6.349280 GGTGCTGAATCAGTTAACTGCAATAA 60.349 38.462 27.49 12.83 43.46 1.40
2700 14948 6.430925 TGCTGAATCAGTTAACTGCAATAACT 59.569 34.615 27.49 15.39 42.73 2.24
2710 14958 9.587772 AGTTAACTGCAATAACTGTATACTCAG 57.412 33.333 18.75 0.00 40.97 3.35
2711 14959 9.582431 GTTAACTGCAATAACTGTATACTCAGA 57.418 33.333 12.53 0.00 38.63 3.27
2712 14960 9.582431 TTAACTGCAATAACTGTATACTCAGAC 57.418 33.333 4.17 0.00 38.63 3.51
2713 14961 7.411486 ACTGCAATAACTGTATACTCAGACT 57.589 36.000 4.17 0.00 38.63 3.24
2714 14962 7.261325 ACTGCAATAACTGTATACTCAGACTG 58.739 38.462 4.17 0.00 38.63 3.51
2715 14963 7.093727 ACTGCAATAACTGTATACTCAGACTGT 60.094 37.037 4.17 0.00 38.63 3.55
2716 14964 8.288689 TGCAATAACTGTATACTCAGACTGTA 57.711 34.615 4.17 0.00 38.63 2.74
2717 14965 8.914011 TGCAATAACTGTATACTCAGACTGTAT 58.086 33.333 4.17 0.00 38.63 2.29
2718 14966 9.751542 GCAATAACTGTATACTCAGACTGTATT 57.248 33.333 4.17 0.00 38.63 1.89
2722 14970 7.956328 ACTGTATACTCAGACTGTATTTCCA 57.044 36.000 4.17 0.00 38.63 3.53
2725 14973 9.823647 CTGTATACTCAGACTGTATTTCCAATT 57.176 33.333 4.17 0.00 37.61 2.32
2730 14978 8.918202 ACTCAGACTGTATTTCCAATTACAAA 57.082 30.769 1.59 0.00 0.00 2.83
2731 14979 9.003658 ACTCAGACTGTATTTCCAATTACAAAG 57.996 33.333 1.59 0.00 0.00 2.77
2735 14983 9.349713 AGACTGTATTTCCAATTACAAAGACAA 57.650 29.630 9.02 0.00 34.29 3.18
2767 15015 8.589701 TTGTCATTAGAGTAGTATTCCAGTGA 57.410 34.615 0.00 0.00 0.00 3.41
2768 15016 8.768501 TGTCATTAGAGTAGTATTCCAGTGAT 57.231 34.615 0.00 0.00 0.00 3.06
2769 15017 8.851145 TGTCATTAGAGTAGTATTCCAGTGATC 58.149 37.037 0.00 0.00 0.00 2.92
2771 15019 9.647918 TCATTAGAGTAGTATTCCAGTGATCTT 57.352 33.333 0.00 0.00 0.00 2.40
2772 15020 9.906660 CATTAGAGTAGTATTCCAGTGATCTTC 57.093 37.037 0.00 0.00 0.00 2.87
2773 15021 9.875708 ATTAGAGTAGTATTCCAGTGATCTTCT 57.124 33.333 0.00 0.00 0.00 2.85
2774 15022 9.702253 TTAGAGTAGTATTCCAGTGATCTTCTT 57.298 33.333 0.00 0.00 0.00 2.52
2775 15023 8.602472 AGAGTAGTATTCCAGTGATCTTCTTT 57.398 34.615 0.00 0.00 0.00 2.52
2776 15024 8.474025 AGAGTAGTATTCCAGTGATCTTCTTTG 58.526 37.037 0.00 0.00 0.00 2.77
2777 15025 8.140112 AGTAGTATTCCAGTGATCTTCTTTGT 57.860 34.615 0.00 0.00 0.00 2.83
2778 15026 8.598041 AGTAGTATTCCAGTGATCTTCTTTGTT 58.402 33.333 0.00 0.00 0.00 2.83
2781 15029 4.336889 TCCAGTGATCTTCTTTGTTCGT 57.663 40.909 0.00 0.00 0.00 3.85
2783 15031 5.849510 TCCAGTGATCTTCTTTGTTCGTTA 58.150 37.500 0.00 0.00 0.00 3.18
2784 15032 6.464222 TCCAGTGATCTTCTTTGTTCGTTAT 58.536 36.000 0.00 0.00 0.00 1.89
2785 15033 7.608153 TCCAGTGATCTTCTTTGTTCGTTATA 58.392 34.615 0.00 0.00 0.00 0.98
2786 15034 7.759886 TCCAGTGATCTTCTTTGTTCGTTATAG 59.240 37.037 0.00 0.00 0.00 1.31
2787 15035 7.394872 CAGTGATCTTCTTTGTTCGTTATAGC 58.605 38.462 0.00 0.00 0.00 2.97
2789 15037 7.276658 AGTGATCTTCTTTGTTCGTTATAGCTG 59.723 37.037 0.00 0.00 0.00 4.24
2791 15039 7.817478 TGATCTTCTTTGTTCGTTATAGCTGAA 59.183 33.333 0.00 0.00 0.00 3.02
2792 15040 7.956420 TCTTCTTTGTTCGTTATAGCTGAAA 57.044 32.000 0.00 0.00 0.00 2.69
2794 15042 8.999431 TCTTCTTTGTTCGTTATAGCTGAAAAT 58.001 29.630 0.00 0.00 0.00 1.82
2856 15742 8.777865 TGATTTATATAGCTGATACTGTTGGC 57.222 34.615 0.00 0.00 0.00 4.52
2857 15743 8.374743 TGATTTATATAGCTGATACTGTTGGCA 58.625 33.333 0.00 0.00 0.00 4.92
2866 15752 4.141144 CTGTTGGCAGTGACGGTT 57.859 55.556 0.00 0.00 37.92 4.44
2867 15753 3.299050 CTGTTGGCAGTGACGGTTA 57.701 52.632 0.00 0.00 37.92 2.85
2868 15754 1.588674 CTGTTGGCAGTGACGGTTAA 58.411 50.000 0.00 0.00 37.92 2.01
2870 15756 2.552315 CTGTTGGCAGTGACGGTTAAAT 59.448 45.455 0.00 0.00 37.92 1.40
2873 15759 3.907894 TGGCAGTGACGGTTAAATTTC 57.092 42.857 0.00 0.00 0.00 2.17
2874 15760 3.215151 TGGCAGTGACGGTTAAATTTCA 58.785 40.909 0.00 0.00 0.00 2.69
2876 15762 3.223157 GCAGTGACGGTTAAATTTCACG 58.777 45.455 0.00 0.59 42.66 4.35
2877 15763 3.303526 GCAGTGACGGTTAAATTTCACGT 60.304 43.478 12.57 12.57 42.66 4.49
2878 15764 4.084433 GCAGTGACGGTTAAATTTCACGTA 60.084 41.667 12.66 2.79 42.66 3.57
2879 15765 5.368374 CAGTGACGGTTAAATTTCACGTAC 58.632 41.667 12.66 11.26 42.66 3.67
2880 15766 4.448732 AGTGACGGTTAAATTTCACGTACC 59.551 41.667 12.66 7.94 42.66 3.34
2881 15767 4.210955 GTGACGGTTAAATTTCACGTACCA 59.789 41.667 12.66 6.96 37.96 3.25
2885 15771 3.119743 GGTTAAATTTCACGTACCAGGGC 60.120 47.826 0.00 0.00 0.00 5.19
2887 15773 0.675522 AATTTCACGTACCAGGGCGG 60.676 55.000 9.97 0.79 42.50 6.13
2897 15783 3.917760 CAGGGCGGTCTCGGGATC 61.918 72.222 0.00 0.00 36.79 3.36
2898 15784 4.458829 AGGGCGGTCTCGGGATCA 62.459 66.667 0.00 0.00 36.79 2.92
2899 15785 3.234730 GGGCGGTCTCGGGATCAT 61.235 66.667 0.00 0.00 36.79 2.45
2901 15787 1.146263 GGCGGTCTCGGGATCATTT 59.854 57.895 0.00 0.00 36.79 2.32
2902 15788 0.880718 GGCGGTCTCGGGATCATTTC 60.881 60.000 0.00 0.00 36.79 2.17
2903 15789 0.179084 GCGGTCTCGGGATCATTTCA 60.179 55.000 0.00 0.00 36.79 2.69
2905 15791 2.408050 CGGTCTCGGGATCATTTCATC 58.592 52.381 0.00 0.00 0.00 2.92
2906 15792 2.772287 GGTCTCGGGATCATTTCATCC 58.228 52.381 0.00 0.00 41.74 3.51
2907 15793 2.104792 GGTCTCGGGATCATTTCATCCA 59.895 50.000 0.00 0.00 44.00 3.41
2908 15794 3.433598 GGTCTCGGGATCATTTCATCCAA 60.434 47.826 0.00 0.00 44.00 3.53
2909 15795 3.812053 GTCTCGGGATCATTTCATCCAAG 59.188 47.826 0.00 0.00 44.00 3.61
2911 15797 1.265095 CGGGATCATTTCATCCAAGCG 59.735 52.381 0.00 0.00 44.00 4.68
2912 15798 1.610522 GGGATCATTTCATCCAAGCGG 59.389 52.381 0.00 0.00 44.00 5.52
2924 15810 2.229792 TCCAAGCGGATGAATATTGCC 58.770 47.619 0.00 0.00 35.91 4.52
2925 15811 1.069022 CCAAGCGGATGAATATTGCCG 60.069 52.381 13.72 13.72 46.14 5.69
2926 15812 1.603802 CAAGCGGATGAATATTGCCGT 59.396 47.619 17.30 6.58 45.22 5.68
2927 15813 1.512926 AGCGGATGAATATTGCCGTC 58.487 50.000 17.30 11.88 45.22 4.79
2929 15815 1.878102 GCGGATGAATATTGCCGTCCT 60.878 52.381 17.30 0.00 45.22 3.85
2930 15816 2.069273 CGGATGAATATTGCCGTCCTC 58.931 52.381 11.63 0.00 38.99 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 250 7.442656 AGAGTAACTGCTACAAGTGTACAAAT 58.557 34.615 0.00 0.00 32.37 2.32
290 291 8.125978 TCATGTAAAAGAAAAGGATGCAGAAT 57.874 30.769 0.00 0.00 0.00 2.40
522 525 6.169800 GCTCCAGGTAATTGCCAAATAAAAA 58.830 36.000 15.49 0.00 0.00 1.94
581 584 1.202582 AGCTACACTAACACCGCTCAG 59.797 52.381 0.00 0.00 0.00 3.35
587 590 4.645588 ACTCATAGGAGCTACACTAACACC 59.354 45.833 3.87 0.00 45.42 4.16
665 668 5.013704 TCCTAGAGTTATTTTTCCTGTGCCA 59.986 40.000 0.00 0.00 0.00 4.92
666 669 5.497474 TCCTAGAGTTATTTTTCCTGTGCC 58.503 41.667 0.00 0.00 0.00 5.01
672 675 6.768381 CCCATGACTCCTAGAGTTATTTTTCC 59.232 42.308 0.00 0.00 43.53 3.13
909 917 2.203195 AGCGACTGTGCAGCCAAA 60.203 55.556 0.00 0.00 37.31 3.28
970 1010 2.083002 GCAGGCAAGGAAGAAGAAGAG 58.917 52.381 0.00 0.00 0.00 2.85
1461 1526 0.884259 CGTGGGTCTTGCACATGACA 60.884 55.000 15.86 0.00 39.87 3.58
1482 1547 0.543277 CCAGCACATAGGGCTTCTGA 59.457 55.000 0.00 0.00 40.23 3.27
1570 8689 2.029288 CGGCGCAAGAAGCAGAGAA 61.029 57.895 10.83 0.00 46.13 2.87
1571 8690 2.433145 CGGCGCAAGAAGCAGAGA 60.433 61.111 10.83 0.00 46.13 3.10
1572 8691 3.494336 CCGGCGCAAGAAGCAGAG 61.494 66.667 10.83 0.00 46.13 3.35
1573 8692 4.002506 TCCGGCGCAAGAAGCAGA 62.003 61.111 10.83 0.00 46.13 4.26
1574 8693 3.793144 GTCCGGCGCAAGAAGCAG 61.793 66.667 10.83 0.00 46.13 4.24
1584 8703 2.971428 ATAATCTGCACGGTCCGGCG 62.971 60.000 17.28 7.44 0.00 6.46
1585 8704 1.222115 GATAATCTGCACGGTCCGGC 61.222 60.000 17.28 16.17 0.00 6.13
1586 8705 0.600255 GGATAATCTGCACGGTCCGG 60.600 60.000 17.28 5.79 0.00 5.14
1587 8706 0.600255 GGGATAATCTGCACGGTCCG 60.600 60.000 10.48 10.48 0.00 4.79
1588 8707 0.600255 CGGGATAATCTGCACGGTCC 60.600 60.000 0.00 0.00 0.00 4.46
1589 8708 0.387929 TCGGGATAATCTGCACGGTC 59.612 55.000 0.00 0.00 0.00 4.79
1590 8709 0.104304 GTCGGGATAATCTGCACGGT 59.896 55.000 0.00 0.00 0.00 4.83
1591 8710 0.389391 AGTCGGGATAATCTGCACGG 59.611 55.000 0.00 0.00 0.00 4.94
1592 8711 1.067060 TGAGTCGGGATAATCTGCACG 59.933 52.381 0.00 0.00 0.00 5.34
1593 8712 2.101582 AGTGAGTCGGGATAATCTGCAC 59.898 50.000 0.00 0.00 0.00 4.57
1594 8713 2.388735 AGTGAGTCGGGATAATCTGCA 58.611 47.619 0.00 0.00 0.00 4.41
1595 8714 3.385577 GAAGTGAGTCGGGATAATCTGC 58.614 50.000 0.00 0.00 0.00 4.26
1596 8715 3.384789 TGGAAGTGAGTCGGGATAATCTG 59.615 47.826 0.00 0.00 0.00 2.90
1597 8716 3.639094 CTGGAAGTGAGTCGGGATAATCT 59.361 47.826 0.00 0.00 0.00 2.40
1598 8717 3.800604 GCTGGAAGTGAGTCGGGATAATC 60.801 52.174 0.00 0.00 35.30 1.75
1599 8718 2.103263 GCTGGAAGTGAGTCGGGATAAT 59.897 50.000 0.00 0.00 35.30 1.28
1600 8719 1.480954 GCTGGAAGTGAGTCGGGATAA 59.519 52.381 0.00 0.00 35.30 1.75
1601 8720 1.112113 GCTGGAAGTGAGTCGGGATA 58.888 55.000 0.00 0.00 35.30 2.59
1885 14094 1.924320 CTCGTCGGTGGTGTCTCCTC 61.924 65.000 0.00 0.00 37.07 3.71
2067 14310 3.949754 AGTTCATGCATACTTGGTCATGG 59.050 43.478 0.00 0.00 37.49 3.66
2070 14313 4.558226 AGAGTTCATGCATACTTGGTCA 57.442 40.909 0.00 0.00 0.00 4.02
2085 14328 7.778470 AGATAATGGAATTGACGAAGAGTTC 57.222 36.000 0.00 0.00 36.99 3.01
2086 14329 7.281100 GGAAGATAATGGAATTGACGAAGAGTT 59.719 37.037 0.00 0.00 36.99 3.01
2135 14378 2.938451 TCATAAATCTTGAGGTGCGCAG 59.062 45.455 12.22 0.00 0.00 5.18
2148 14391 7.903995 TTGCATGGAAAAACCTTCATAAATC 57.096 32.000 0.00 0.00 39.86 2.17
2192 14435 3.072768 AGGTACGGAGGGAGTATCTACAG 59.927 52.174 0.00 0.00 34.10 2.74
2195 14438 5.912149 TTAAGGTACGGAGGGAGTATCTA 57.088 43.478 0.00 0.00 34.71 1.98
2201 14444 4.891756 TCTTACATTAAGGTACGGAGGGAG 59.108 45.833 0.00 0.00 36.45 4.30
2203 14446 4.498682 CGTCTTACATTAAGGTACGGAGGG 60.499 50.000 0.00 0.00 34.39 4.30
2204 14447 4.096984 ACGTCTTACATTAAGGTACGGAGG 59.903 45.833 15.80 15.21 39.12 4.30
2205 14448 5.240713 ACGTCTTACATTAAGGTACGGAG 57.759 43.478 15.80 5.37 39.12 4.63
2207 14450 6.710692 AAAACGTCTTACATTAAGGTACGG 57.289 37.500 15.80 6.18 39.12 4.02
2208 14451 6.944400 CGAAAAACGTCTTACATTAAGGTACG 59.056 38.462 11.31 11.31 40.04 3.67
2210 14453 7.151308 TCCGAAAAACGTCTTACATTAAGGTA 58.849 34.615 0.00 0.00 40.78 3.08
2211 14454 5.990996 TCCGAAAAACGTCTTACATTAAGGT 59.009 36.000 0.00 0.00 40.78 3.50
2213 14456 6.401796 CCCTCCGAAAAACGTCTTACATTAAG 60.402 42.308 0.00 0.00 40.78 1.85
2214 14457 5.409214 CCCTCCGAAAAACGTCTTACATTAA 59.591 40.000 0.00 0.00 40.78 1.40
2215 14458 4.931002 CCCTCCGAAAAACGTCTTACATTA 59.069 41.667 0.00 0.00 40.78 1.90
2216 14459 3.749609 CCCTCCGAAAAACGTCTTACATT 59.250 43.478 0.00 0.00 40.78 2.71
2218 14461 2.102925 ACCCTCCGAAAAACGTCTTACA 59.897 45.455 0.00 0.00 40.78 2.41
2220 14463 3.573967 AGTACCCTCCGAAAAACGTCTTA 59.426 43.478 0.00 0.00 40.78 2.10
2221 14464 2.366590 AGTACCCTCCGAAAAACGTCTT 59.633 45.455 0.00 0.00 40.78 3.01
2224 14467 4.248058 CAATAGTACCCTCCGAAAAACGT 58.752 43.478 0.00 0.00 40.78 3.99
2225 14468 3.063045 GCAATAGTACCCTCCGAAAAACG 59.937 47.826 0.00 0.00 42.18 3.60
2228 14471 3.516300 TCTGCAATAGTACCCTCCGAAAA 59.484 43.478 0.00 0.00 0.00 2.29
2229 14472 3.101437 TCTGCAATAGTACCCTCCGAAA 58.899 45.455 0.00 0.00 0.00 3.46
2231 14474 2.447408 TCTGCAATAGTACCCTCCGA 57.553 50.000 0.00 0.00 0.00 4.55
2232 14475 2.224066 CCTTCTGCAATAGTACCCTCCG 60.224 54.545 0.00 0.00 0.00 4.63
2233 14476 3.039011 TCCTTCTGCAATAGTACCCTCC 58.961 50.000 0.00 0.00 0.00 4.30
2234 14477 3.493524 GCTCCTTCTGCAATAGTACCCTC 60.494 52.174 0.00 0.00 0.00 4.30
2235 14478 2.436173 GCTCCTTCTGCAATAGTACCCT 59.564 50.000 0.00 0.00 0.00 4.34
2236 14479 2.170607 TGCTCCTTCTGCAATAGTACCC 59.829 50.000 0.00 0.00 37.51 3.69
2237 14480 3.543680 TGCTCCTTCTGCAATAGTACC 57.456 47.619 0.00 0.00 37.51 3.34
2272 14515 0.550914 AGAGACAAAACACTGGCCCA 59.449 50.000 0.00 0.00 0.00 5.36
2273 14516 2.561478 TAGAGACAAAACACTGGCCC 57.439 50.000 0.00 0.00 0.00 5.80
2286 14529 0.824759 AACCCACGGAGCATAGAGAC 59.175 55.000 0.00 0.00 0.00 3.36
2290 14535 5.668558 GTTAAATAACCCACGGAGCATAG 57.331 43.478 0.00 0.00 0.00 2.23
2320 14565 6.469410 ACGGAGAATTGTTGTATGGTAGAAA 58.531 36.000 0.00 0.00 0.00 2.52
2323 14571 4.503007 CGACGGAGAATTGTTGTATGGTAG 59.497 45.833 0.00 0.00 0.00 3.18
2334 14582 5.347635 TCTTTACATGTTCGACGGAGAATTG 59.652 40.000 2.30 3.33 32.25 2.32
2339 14587 4.446385 TGTTTCTTTACATGTTCGACGGAG 59.554 41.667 2.30 0.00 0.00 4.63
2342 14590 6.631238 ACAATTGTTTCTTTACATGTTCGACG 59.369 34.615 2.30 0.00 0.00 5.12
2351 14599 4.809958 TCGACGGACAATTGTTTCTTTACA 59.190 37.500 13.36 0.00 0.00 2.41
2357 14605 3.942739 TGTTTCGACGGACAATTGTTTC 58.057 40.909 13.36 8.86 0.00 2.78
2366 14614 1.529438 TCTTGCATTGTTTCGACGGAC 59.471 47.619 0.00 0.00 0.00 4.79
2369 14617 4.260656 GCTATTTCTTGCATTGTTTCGACG 59.739 41.667 0.00 0.00 0.00 5.12
2389 14637 6.745159 TTGCCAGTCGTATAAAATTTGCTA 57.255 33.333 0.00 0.00 0.00 3.49
2391 14639 6.529829 TCATTTGCCAGTCGTATAAAATTTGC 59.470 34.615 0.00 0.00 0.00 3.68
2392 14640 7.220683 CCTCATTTGCCAGTCGTATAAAATTTG 59.779 37.037 0.00 0.00 0.00 2.32
2393 14641 7.093945 ACCTCATTTGCCAGTCGTATAAAATTT 60.094 33.333 0.00 0.00 0.00 1.82
2394 14642 6.377146 ACCTCATTTGCCAGTCGTATAAAATT 59.623 34.615 0.00 0.00 0.00 1.82
2395 14643 5.885912 ACCTCATTTGCCAGTCGTATAAAAT 59.114 36.000 0.00 0.00 0.00 1.82
2396 14644 5.250200 ACCTCATTTGCCAGTCGTATAAAA 58.750 37.500 0.00 0.00 0.00 1.52
2397 14645 4.839121 ACCTCATTTGCCAGTCGTATAAA 58.161 39.130 0.00 0.00 0.00 1.40
2398 14646 4.481368 ACCTCATTTGCCAGTCGTATAA 57.519 40.909 0.00 0.00 0.00 0.98
2399 14647 5.538813 AGATACCTCATTTGCCAGTCGTATA 59.461 40.000 0.00 0.00 0.00 1.47
2400 14648 4.345257 AGATACCTCATTTGCCAGTCGTAT 59.655 41.667 0.00 0.00 0.00 3.06
2445 14693 2.086869 CAGTTGGTATGTGGGAGCAAG 58.913 52.381 0.00 0.00 35.13 4.01
2448 14696 1.812571 CAACAGTTGGTATGTGGGAGC 59.187 52.381 5.25 0.00 0.00 4.70
2479 14727 5.245301 CCCCGTTCTCCTTTTTATTTTCCTT 59.755 40.000 0.00 0.00 0.00 3.36
2481 14729 4.081862 CCCCCGTTCTCCTTTTTATTTTCC 60.082 45.833 0.00 0.00 0.00 3.13
2483 14731 4.485875 ACCCCCGTTCTCCTTTTTATTTT 58.514 39.130 0.00 0.00 0.00 1.82
2487 14735 3.559811 GCTAACCCCCGTTCTCCTTTTTA 60.560 47.826 0.00 0.00 33.17 1.52
2488 14736 2.816712 GCTAACCCCCGTTCTCCTTTTT 60.817 50.000 0.00 0.00 33.17 1.94
2499 14747 0.841289 TATTCCCAAGCTAACCCCCG 59.159 55.000 0.00 0.00 0.00 5.73
2521 14769 4.253685 GAGACTTTCCATTTCGGATGTCA 58.746 43.478 13.54 0.00 45.80 3.58
2540 14788 2.896745 ATCACACTGCGCATATGAGA 57.103 45.000 24.10 21.51 0.00 3.27
2545 14793 2.908688 ACCATATCACACTGCGCATA 57.091 45.000 12.24 0.00 0.00 3.14
2558 14806 2.567615 GTCTATCTGCCCGGAACCATAT 59.432 50.000 0.73 0.00 0.00 1.78
2559 14807 1.968493 GTCTATCTGCCCGGAACCATA 59.032 52.381 0.73 0.00 0.00 2.74
2568 14816 2.541556 GACAACGAAGTCTATCTGCCC 58.458 52.381 0.00 0.00 45.00 5.36
2592 14840 3.502123 TTCTTTGATGAGGAACCGGTT 57.498 42.857 22.50 22.50 0.00 4.44
2612 14860 1.517832 GTCAGCCGCCTAGACACAT 59.482 57.895 0.00 0.00 32.68 3.21
2613 14861 2.970639 GTCAGCCGCCTAGACACA 59.029 61.111 0.00 0.00 32.68 3.72
2614 14862 2.202623 CGTCAGCCGCCTAGACAC 60.203 66.667 8.41 0.00 32.68 3.67
2615 14863 2.675423 ACGTCAGCCGCCTAGACA 60.675 61.111 8.41 0.00 41.42 3.41
2616 14864 2.202623 CACGTCAGCCGCCTAGAC 60.203 66.667 0.00 0.00 41.42 2.59
2617 14865 2.675423 ACACGTCAGCCGCCTAGA 60.675 61.111 0.00 0.00 41.42 2.43
2618 14866 2.507102 CACACGTCAGCCGCCTAG 60.507 66.667 0.00 0.00 41.42 3.02
2619 14867 4.735132 GCACACGTCAGCCGCCTA 62.735 66.667 0.00 0.00 41.42 3.93
2624 14872 3.406361 CAGTCGCACACGTCAGCC 61.406 66.667 3.40 0.00 41.18 4.85
2625 14873 2.658593 ACAGTCGCACACGTCAGC 60.659 61.111 0.00 0.00 41.18 4.26
2626 14874 2.932083 GCACAGTCGCACACGTCAG 61.932 63.158 0.00 0.00 41.18 3.51
2627 14875 2.959599 GCACAGTCGCACACGTCA 60.960 61.111 0.00 0.00 41.18 4.35
2628 14876 4.046998 CGCACAGTCGCACACGTC 62.047 66.667 0.00 0.00 41.18 4.34
2631 14879 4.000557 CACCGCACAGTCGCACAC 62.001 66.667 0.00 0.00 0.00 3.82
2645 14893 2.046892 ACAGGTCATCGCTGCACC 60.047 61.111 0.00 0.00 0.00 5.01
2650 14898 2.125912 GTCGCACAGGTCATCGCT 60.126 61.111 0.00 0.00 0.00 4.93
2651 14899 3.545481 CGTCGCACAGGTCATCGC 61.545 66.667 0.00 0.00 0.00 4.58
2652 14900 2.880879 CCGTCGCACAGGTCATCG 60.881 66.667 0.00 0.00 0.00 3.84
2668 14916 3.869272 CTGATTCAGCACCGCGCC 61.869 66.667 0.00 0.00 44.04 6.53
2671 14919 2.076863 AGTTAACTGATTCAGCACCGC 58.923 47.619 13.64 1.37 34.37 5.68
2684 14932 9.587772 CTGAGTATACAGTTATTGCAGTTAACT 57.412 33.333 14.90 14.90 39.80 2.24
2685 14933 9.582431 TCTGAGTATACAGTTATTGCAGTTAAC 57.418 33.333 5.50 11.65 38.79 2.01
2686 14934 9.582431 GTCTGAGTATACAGTTATTGCAGTTAA 57.418 33.333 5.50 0.00 38.79 2.01
2687 14935 8.967918 AGTCTGAGTATACAGTTATTGCAGTTA 58.032 33.333 5.50 0.00 38.79 2.24
2688 14936 7.761704 CAGTCTGAGTATACAGTTATTGCAGTT 59.238 37.037 5.50 0.00 38.79 3.16
2689 14937 7.093727 ACAGTCTGAGTATACAGTTATTGCAGT 60.094 37.037 6.91 0.00 38.79 4.40
2690 14938 7.261325 ACAGTCTGAGTATACAGTTATTGCAG 58.739 38.462 6.91 0.00 38.79 4.41
2691 14939 7.170393 ACAGTCTGAGTATACAGTTATTGCA 57.830 36.000 6.91 0.00 38.79 4.08
2692 14940 9.751542 AATACAGTCTGAGTATACAGTTATTGC 57.248 33.333 6.91 0.00 38.79 3.56
2696 14944 9.470399 TGGAAATACAGTCTGAGTATACAGTTA 57.530 33.333 6.91 0.00 38.79 2.24
2697 14945 8.362464 TGGAAATACAGTCTGAGTATACAGTT 57.638 34.615 6.91 0.00 38.79 3.16
2698 14946 7.956328 TGGAAATACAGTCTGAGTATACAGT 57.044 36.000 6.91 0.00 38.79 3.55
2705 14953 8.918202 TTTGTAATTGGAAATACAGTCTGAGT 57.082 30.769 6.91 0.00 33.85 3.41
2708 14956 8.783093 TGTCTTTGTAATTGGAAATACAGTCTG 58.217 33.333 0.00 0.00 33.85 3.51
2709 14957 8.918202 TGTCTTTGTAATTGGAAATACAGTCT 57.082 30.769 0.00 0.00 33.85 3.24
2741 14989 9.201989 TCACTGGAATACTACTCTAATGACAAT 57.798 33.333 0.00 0.00 0.00 2.71
2743 14991 8.768501 ATCACTGGAATACTACTCTAATGACA 57.231 34.615 0.00 0.00 0.00 3.58
2745 14993 9.647918 AAGATCACTGGAATACTACTCTAATGA 57.352 33.333 0.00 0.00 0.00 2.57
2746 14994 9.906660 GAAGATCACTGGAATACTACTCTAATG 57.093 37.037 0.00 0.00 0.00 1.90
2747 14995 9.875708 AGAAGATCACTGGAATACTACTCTAAT 57.124 33.333 0.00 0.00 0.00 1.73
2748 14996 9.702253 AAGAAGATCACTGGAATACTACTCTAA 57.298 33.333 0.00 0.00 0.00 2.10
2751 14999 8.254508 ACAAAGAAGATCACTGGAATACTACTC 58.745 37.037 0.00 0.00 0.00 2.59
2752 15000 8.140112 ACAAAGAAGATCACTGGAATACTACT 57.860 34.615 0.00 0.00 0.00 2.57
2754 15002 7.759886 CGAACAAAGAAGATCACTGGAATACTA 59.240 37.037 0.00 0.00 0.00 1.82
2755 15003 6.591834 CGAACAAAGAAGATCACTGGAATACT 59.408 38.462 0.00 0.00 0.00 2.12
2756 15004 6.369065 ACGAACAAAGAAGATCACTGGAATAC 59.631 38.462 0.00 0.00 0.00 1.89
2758 15006 5.308825 ACGAACAAAGAAGATCACTGGAAT 58.691 37.500 0.00 0.00 0.00 3.01
2760 15008 4.336889 ACGAACAAAGAAGATCACTGGA 57.663 40.909 0.00 0.00 0.00 3.86
2761 15009 6.727824 ATAACGAACAAAGAAGATCACTGG 57.272 37.500 0.00 0.00 0.00 4.00
2764 15012 7.275779 TCAGCTATAACGAACAAAGAAGATCAC 59.724 37.037 0.00 0.00 0.00 3.06
2765 15013 7.320399 TCAGCTATAACGAACAAAGAAGATCA 58.680 34.615 0.00 0.00 0.00 2.92
2767 15015 8.547967 TTTCAGCTATAACGAACAAAGAAGAT 57.452 30.769 0.00 0.00 0.00 2.40
2768 15016 7.956420 TTTCAGCTATAACGAACAAAGAAGA 57.044 32.000 0.00 0.00 0.00 2.87
2795 15043 9.911788 AGTGATGATCCATTTAAGTTCAACTAT 57.088 29.630 0.00 0.00 0.00 2.12
2796 15044 9.166173 CAGTGATGATCCATTTAAGTTCAACTA 57.834 33.333 0.00 0.00 0.00 2.24
2797 15045 7.884877 TCAGTGATGATCCATTTAAGTTCAACT 59.115 33.333 0.00 0.00 0.00 3.16
2798 15046 8.044060 TCAGTGATGATCCATTTAAGTTCAAC 57.956 34.615 0.00 0.00 0.00 3.18
2799 15047 8.634335 TTCAGTGATGATCCATTTAAGTTCAA 57.366 30.769 0.00 0.00 0.00 2.69
2800 15048 8.634335 TTTCAGTGATGATCCATTTAAGTTCA 57.366 30.769 0.00 0.00 0.00 3.18
2833 15719 8.783833 CTGCCAACAGTATCAGCTATATAAAT 57.216 34.615 0.00 0.00 39.22 1.40
2850 15736 2.039818 TTTAACCGTCACTGCCAACA 57.960 45.000 0.00 0.00 0.00 3.33
2851 15737 3.636282 AATTTAACCGTCACTGCCAAC 57.364 42.857 0.00 0.00 0.00 3.77
2852 15738 3.632604 TGAAATTTAACCGTCACTGCCAA 59.367 39.130 0.00 0.00 0.00 4.52
2853 15739 3.003897 GTGAAATTTAACCGTCACTGCCA 59.996 43.478 0.00 0.00 37.88 4.92
2854 15740 3.561503 GTGAAATTTAACCGTCACTGCC 58.438 45.455 0.00 0.00 37.88 4.85
2855 15741 3.223157 CGTGAAATTTAACCGTCACTGC 58.777 45.455 0.00 0.00 38.57 4.40
2856 15742 4.461992 ACGTGAAATTTAACCGTCACTG 57.538 40.909 0.00 0.00 38.57 3.66
2857 15743 4.448732 GGTACGTGAAATTTAACCGTCACT 59.551 41.667 11.17 0.10 38.57 3.41
2858 15744 4.210955 TGGTACGTGAAATTTAACCGTCAC 59.789 41.667 11.17 4.53 37.59 3.67
2859 15745 4.375272 TGGTACGTGAAATTTAACCGTCA 58.625 39.130 11.17 4.22 33.32 4.35
2860 15746 4.143052 CCTGGTACGTGAAATTTAACCGTC 60.143 45.833 11.17 5.60 33.32 4.79
2861 15747 3.747529 CCTGGTACGTGAAATTTAACCGT 59.252 43.478 0.00 12.14 35.68 4.83
2862 15748 3.125658 CCCTGGTACGTGAAATTTAACCG 59.874 47.826 0.00 1.62 0.00 4.44
2863 15749 3.119743 GCCCTGGTACGTGAAATTTAACC 60.120 47.826 0.00 0.00 0.00 2.85
2864 15750 3.425227 CGCCCTGGTACGTGAAATTTAAC 60.425 47.826 0.00 0.00 0.00 2.01
2866 15752 2.348660 CGCCCTGGTACGTGAAATTTA 58.651 47.619 0.00 0.00 0.00 1.40
2867 15753 1.161843 CGCCCTGGTACGTGAAATTT 58.838 50.000 0.00 0.00 0.00 1.82
2868 15754 0.675522 CCGCCCTGGTACGTGAAATT 60.676 55.000 0.00 0.00 0.00 1.82
2870 15756 2.344500 CCGCCCTGGTACGTGAAA 59.656 61.111 0.00 0.00 0.00 2.69
2880 15766 3.917760 GATCCCGAGACCGCCCTG 61.918 72.222 0.00 0.00 0.00 4.45
2881 15767 3.758133 ATGATCCCGAGACCGCCCT 62.758 63.158 0.00 0.00 0.00 5.19
2885 15771 2.408050 GATGAAATGATCCCGAGACCG 58.592 52.381 0.00 0.00 0.00 4.79
2887 15773 3.475566 TGGATGAAATGATCCCGAGAC 57.524 47.619 0.00 0.00 41.31 3.36
2888 15774 3.745480 GCTTGGATGAAATGATCCCGAGA 60.745 47.826 0.00 0.00 41.31 4.04
2889 15775 2.551459 GCTTGGATGAAATGATCCCGAG 59.449 50.000 0.00 0.00 41.31 4.63
2891 15777 1.265095 CGCTTGGATGAAATGATCCCG 59.735 52.381 0.00 0.00 41.31 5.14
2892 15778 1.610522 CCGCTTGGATGAAATGATCCC 59.389 52.381 0.00 0.00 41.31 3.85
2893 15779 2.575532 TCCGCTTGGATGAAATGATCC 58.424 47.619 0.00 0.00 42.23 3.36
2905 15791 1.069022 CGGCAATATTCATCCGCTTGG 60.069 52.381 7.21 0.00 35.20 3.61
2906 15792 1.603802 ACGGCAATATTCATCCGCTTG 59.396 47.619 16.04 4.11 45.23 4.01
2907 15793 1.873591 GACGGCAATATTCATCCGCTT 59.126 47.619 16.04 3.00 45.23 4.68
2908 15794 1.512926 GACGGCAATATTCATCCGCT 58.487 50.000 16.04 7.32 45.23 5.52
2909 15795 0.517316 GGACGGCAATATTCATCCGC 59.483 55.000 16.04 10.79 45.23 5.54
2911 15797 3.409026 AGAGGACGGCAATATTCATCC 57.591 47.619 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.