Multiple sequence alignment - TraesCS1D01G272200

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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 TraesCS1D01G272200 chr1D 100.000 2690 0 0 1 2690 366225578 366228267 0.000000e+00 4968.0
1 TraesCS1D01G272200 chr1A 86.399 1022 62 37 1207 2160 465521529 465520517 0.000000e+00 1046.0
2 TraesCS1D01G272200 chr1A 84.777 716 35 21 586 1256 465522060 465521374 0.000000e+00 651.0
3 TraesCS1D01G272200 chr1A 88.219 365 40 3 2297 2660 465519547 465519185 1.480000e-117 433.0
4 TraesCS1D01G272200 chr1A 85.813 289 22 7 150 421 465522543 465522257 3.390000e-74 289.0
5 TraesCS1D01G272200 chr1A 94.643 112 3 1 1159 1267 465521526 465521415 1.280000e-38 171.0
6 TraesCS1D01G272200 chr1A 100.000 31 0 0 1258 1288 465521409 465521379 1.040000e-04 58.4
7 TraesCS1D01G272200 chr1B 89.902 713 28 17 586 1267 491263118 491262419 0.000000e+00 878.0
8 TraesCS1D01G272200 chr1B 88.263 639 52 16 1159 1784 491262572 491261944 0.000000e+00 743.0
9 TraesCS1D01G272200 chr1B 82.162 555 46 24 1 511 491263765 491263220 6.880000e-116 427.0
10 TraesCS1D01G272200 chr1B 92.958 213 11 3 1832 2044 491261944 491261736 9.350000e-80 307.0
11 TraesCS1D01G272200 chr1B 86.331 139 8 8 1124 1256 491262514 491262381 1.000000e-29 141.0
12 TraesCS1D01G272200 chr1B 80.208 192 21 11 2047 2225 491258866 491258679 7.820000e-26 128.0
13 TraesCS1D01G272200 chr4D 94.286 35 1 1 2226 2260 119739157 119739190 5.000000e-03 52.8
14 TraesCS1D01G272200 chr2D 96.774 31 1 0 2226 2256 146534727 146534757 5.000000e-03 52.8
15 TraesCS1D01G272200 chr2D 96.774 31 1 0 2226 2256 147222740 147222770 5.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G272200 chr1D 366225578 366228267 2689 False 4968.000000 4968 100.000000 1 2690 1 chr1D.!!$F1 2689
1 TraesCS1D01G272200 chr1A 465519185 465522543 3358 True 441.400000 1046 89.975167 150 2660 6 chr1A.!!$R1 2510
2 TraesCS1D01G272200 chr1B 491258679 491263765 5086 True 437.333333 878 86.637333 1 2225 6 chr1B.!!$R1 2224

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
545 644 0.179045 GGGCACCGTCAGAGCAATAT 60.179 55.0 0.0 0.0 40.86 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 2212 0.034337 GTGTCTTCTGGCCGTAACCA 59.966 55.0 0.0 0.0 38.29 3.67 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
47 48 9.591792 GGAAATTATACGTTCTGTAAAGTACCT 57.408 33.333 0.00 0.00 36.44 3.08
60 61 8.071368 TCTGTAAAGTACCTATTTTGTTTTGCG 58.929 33.333 0.00 0.00 0.00 4.85
74 75 2.411628 TTTGCGCCTGGCTAGAATAA 57.588 45.000 17.92 0.00 44.05 1.40
75 76 1.663695 TTGCGCCTGGCTAGAATAAC 58.336 50.000 17.92 0.00 44.05 1.89
81 82 4.051922 CGCCTGGCTAGAATAACTTGTAG 58.948 47.826 17.92 0.00 32.69 2.74
82 83 4.202121 CGCCTGGCTAGAATAACTTGTAGA 60.202 45.833 17.92 0.00 31.47 2.59
89 90 6.405953 GGCTAGAATAACTTGTAGACTGCTGA 60.406 42.308 0.00 0.00 34.22 4.26
90 91 7.206687 GCTAGAATAACTTGTAGACTGCTGAT 58.793 38.462 0.00 0.00 31.47 2.90
91 92 7.168972 GCTAGAATAACTTGTAGACTGCTGATG 59.831 40.741 0.00 0.00 31.47 3.07
93 94 3.340814 AACTTGTAGACTGCTGATGGG 57.659 47.619 0.00 0.00 0.00 4.00
94 95 1.556911 ACTTGTAGACTGCTGATGGGG 59.443 52.381 0.00 0.00 0.00 4.96
95 96 1.556911 CTTGTAGACTGCTGATGGGGT 59.443 52.381 0.00 0.00 0.00 4.95
96 97 1.656587 TGTAGACTGCTGATGGGGTT 58.343 50.000 0.00 0.00 0.00 4.11
97 98 1.278985 TGTAGACTGCTGATGGGGTTG 59.721 52.381 0.00 0.00 0.00 3.77
98 99 1.555075 GTAGACTGCTGATGGGGTTGA 59.445 52.381 0.00 0.00 0.00 3.18
101 102 1.136329 ACTGCTGATGGGGTTGAGGT 61.136 55.000 0.00 0.00 0.00 3.85
102 103 0.679002 CTGCTGATGGGGTTGAGGTG 60.679 60.000 0.00 0.00 0.00 4.00
103 104 2.048603 GCTGATGGGGTTGAGGTGC 61.049 63.158 0.00 0.00 0.00 5.01
104 105 1.379044 CTGATGGGGTTGAGGTGCC 60.379 63.158 0.00 0.00 0.00 5.01
105 106 2.141011 CTGATGGGGTTGAGGTGCCA 62.141 60.000 0.00 0.00 0.00 4.92
106 107 1.307647 GATGGGGTTGAGGTGCCAT 59.692 57.895 0.00 0.00 0.00 4.40
107 108 1.000739 ATGGGGTTGAGGTGCCATG 59.999 57.895 0.00 0.00 0.00 3.66
108 109 2.362889 GGGGTTGAGGTGCCATGG 60.363 66.667 7.63 7.63 0.00 3.66
109 110 2.440599 GGGTTGAGGTGCCATGGT 59.559 61.111 14.67 0.00 0.00 3.55
110 111 1.978617 GGGTTGAGGTGCCATGGTG 60.979 63.158 14.67 0.00 0.00 4.17
111 112 1.228552 GGTTGAGGTGCCATGGTGT 60.229 57.895 14.67 0.00 0.00 4.16
119 120 1.476488 GGTGCCATGGTGTGAATAACC 59.524 52.381 14.67 5.12 38.26 2.85
133 134 3.118629 TGAATAACCTGTAGCCTGCTCTG 60.119 47.826 0.00 0.00 0.00 3.35
134 135 1.938585 TAACCTGTAGCCTGCTCTGT 58.061 50.000 0.00 0.00 0.00 3.41
145 146 1.392589 CTGCTCTGTTGTGGTTTGGT 58.607 50.000 0.00 0.00 0.00 3.67
195 200 2.829720 TCTGTGTGCCGGTTTCTACTAT 59.170 45.455 1.90 0.00 0.00 2.12
199 204 3.864003 GTGTGCCGGTTTCTACTATCTTC 59.136 47.826 1.90 0.00 0.00 2.87
247 258 3.822735 TGCTTCTTGGAAGTTCTCATTGG 59.177 43.478 2.25 0.00 0.00 3.16
271 292 5.642919 GTGTTAACCACGTATTGTTGGGATA 59.357 40.000 2.48 0.00 33.61 2.59
274 295 7.230108 TGTTAACCACGTATTGTTGGGATAAAA 59.770 33.333 2.48 0.00 0.00 1.52
311 334 2.340210 TCACCACAGCTAAAGTGCAA 57.660 45.000 0.00 0.00 35.69 4.08
342 365 2.481952 GACTGCTTGGTCACATGAGTTC 59.518 50.000 0.00 0.00 36.35 3.01
343 366 2.105477 ACTGCTTGGTCACATGAGTTCT 59.895 45.455 0.00 0.00 0.00 3.01
344 367 2.483106 CTGCTTGGTCACATGAGTTCTG 59.517 50.000 0.00 0.00 0.00 3.02
355 379 3.319972 ACATGAGTTCTGCATTTGCTGTT 59.680 39.130 0.00 0.00 42.66 3.16
363 387 5.772825 TCTGCATTTGCTGTTTTTCTAGT 57.227 34.783 3.94 0.00 42.66 2.57
386 410 0.776451 GTCGTGTGTACTCTGCAACG 59.224 55.000 0.00 0.00 0.00 4.10
392 421 1.037493 TGTACTCTGCAACGTGACCT 58.963 50.000 0.00 0.00 0.00 3.85
421 450 3.242518 CTCGCAAGTCGTCACTGAATTA 58.757 45.455 0.00 0.00 39.67 1.40
424 453 3.367932 CGCAAGTCGTCACTGAATTATGT 59.632 43.478 0.00 0.00 31.06 2.29
425 454 4.561213 CGCAAGTCGTCACTGAATTATGTA 59.439 41.667 0.00 0.00 31.06 2.29
426 455 5.498700 CGCAAGTCGTCACTGAATTATGTAC 60.499 44.000 0.00 0.00 31.06 2.90
428 457 4.103357 AGTCGTCACTGAATTATGTACGC 58.897 43.478 0.00 0.00 0.00 4.42
430 459 3.129813 TCGTCACTGAATTATGTACGCCT 59.870 43.478 0.00 0.00 0.00 5.52
431 460 3.242944 CGTCACTGAATTATGTACGCCTG 59.757 47.826 0.00 0.00 0.00 4.85
434 484 3.309682 CACTGAATTATGTACGCCTGGTG 59.690 47.826 5.54 5.54 0.00 4.17
451 501 0.614134 GTGGTCCTCCCGTCCTAACT 60.614 60.000 0.00 0.00 35.15 2.24
460 510 4.874396 CCTCCCGTCCTAACTTAAAATCAC 59.126 45.833 0.00 0.00 0.00 3.06
463 513 4.874396 CCCGTCCTAACTTAAAATCACTCC 59.126 45.833 0.00 0.00 0.00 3.85
492 552 8.777865 TCCTTCACATTCTCAAAGTATACAAG 57.222 34.615 5.50 0.00 0.00 3.16
517 577 4.012374 TCCATTTCAAGTGGAAGATGAGC 58.988 43.478 0.00 0.00 42.56 4.26
518 578 3.181503 CCATTTCAAGTGGAAGATGAGCG 60.182 47.826 0.00 0.00 39.12 5.03
528 627 1.028330 AAGATGAGCGCACACATGGG 61.028 55.000 10.42 0.00 41.65 4.00
544 643 1.220749 GGGCACCGTCAGAGCAATA 59.779 57.895 0.00 0.00 40.86 1.90
545 644 0.179045 GGGCACCGTCAGAGCAATAT 60.179 55.000 0.00 0.00 40.86 1.28
546 645 1.221414 GGCACCGTCAGAGCAATATC 58.779 55.000 0.00 0.00 0.00 1.63
547 646 1.202580 GGCACCGTCAGAGCAATATCT 60.203 52.381 0.00 0.00 0.00 1.98
548 647 2.131183 GCACCGTCAGAGCAATATCTC 58.869 52.381 0.00 0.00 0.00 2.75
549 648 2.748605 CACCGTCAGAGCAATATCTCC 58.251 52.381 0.00 0.00 33.66 3.71
550 649 1.338337 ACCGTCAGAGCAATATCTCCG 59.662 52.381 0.00 0.00 33.66 4.63
551 650 1.413382 CGTCAGAGCAATATCTCCGC 58.587 55.000 0.00 0.00 33.66 5.54
552 651 1.413382 GTCAGAGCAATATCTCCGCG 58.587 55.000 0.00 0.00 33.66 6.46
553 652 0.319040 TCAGAGCAATATCTCCGCGC 60.319 55.000 0.00 0.00 33.66 6.86
554 653 0.598419 CAGAGCAATATCTCCGCGCA 60.598 55.000 8.75 0.00 33.66 6.09
555 654 0.598680 AGAGCAATATCTCCGCGCAC 60.599 55.000 8.75 0.00 33.66 5.34
556 655 1.880601 GAGCAATATCTCCGCGCACG 61.881 60.000 8.75 0.00 39.67 5.34
557 656 2.546321 CAATATCTCCGCGCACGC 59.454 61.111 8.75 4.64 38.22 5.34
577 676 2.720067 GCGTGCGATAGTAGAAACTAGC 59.280 50.000 0.00 0.00 41.46 3.42
583 682 4.498345 GCGATAGTAGAAACTAGCAGCAGT 60.498 45.833 0.00 0.00 43.39 4.40
729 852 0.936600 AAAGCCGTTTTGCATTGCAC 59.063 45.000 11.66 0.00 38.71 4.57
760 883 3.370672 GGCCAAAACAAACAACAAGAGTG 59.629 43.478 0.00 0.00 0.00 3.51
915 1045 1.266446 GTCGTCGCTCCCCTATACTTC 59.734 57.143 0.00 0.00 0.00 3.01
996 1126 0.988832 TGCCCTGTATTTCTTCGGGT 59.011 50.000 0.00 0.00 37.24 5.28
997 1127 2.093341 GTGCCCTGTATTTCTTCGGGTA 60.093 50.000 0.00 0.00 37.24 3.69
998 1128 2.775384 TGCCCTGTATTTCTTCGGGTAT 59.225 45.455 0.00 0.00 37.24 2.73
999 1129 3.181458 TGCCCTGTATTTCTTCGGGTATC 60.181 47.826 0.00 0.00 37.24 2.24
1001 1131 4.505039 GCCCTGTATTTCTTCGGGTATCAT 60.505 45.833 0.00 0.00 37.24 2.45
1003 1133 4.997395 CCTGTATTTCTTCGGGTATCATGG 59.003 45.833 0.00 0.00 0.00 3.66
1148 1308 2.435059 GGCTGACGAGAAGGTGCC 60.435 66.667 0.00 0.00 0.00 5.01
1275 1435 4.819761 GCGGAGAGCGTCATGGCA 62.820 66.667 0.00 0.00 35.41 4.92
1276 1436 2.584418 CGGAGAGCGTCATGGCAG 60.584 66.667 0.00 0.00 34.64 4.85
1277 1437 2.894387 GGAGAGCGTCATGGCAGC 60.894 66.667 0.00 1.72 34.64 5.25
1278 1438 2.894387 GAGAGCGTCATGGCAGCC 60.894 66.667 3.66 3.66 34.64 4.85
1279 1439 4.827087 AGAGCGTCATGGCAGCCG 62.827 66.667 7.03 0.00 34.64 5.52
1287 1447 4.845580 ATGGCAGCCGGCGAGAAG 62.846 66.667 23.20 11.07 46.16 2.85
1298 1458 4.052229 CGAGAAGGTGCCGGACGT 62.052 66.667 5.05 0.00 0.00 4.34
1299 1459 2.432628 GAGAAGGTGCCGGACGTG 60.433 66.667 5.05 0.00 0.00 4.49
1300 1460 3.934391 GAGAAGGTGCCGGACGTGG 62.934 68.421 5.05 0.00 0.00 4.94
1301 1461 3.998672 GAAGGTGCCGGACGTGGA 61.999 66.667 5.05 0.00 0.00 4.02
1302 1462 3.934391 GAAGGTGCCGGACGTGGAG 62.934 68.421 5.05 0.00 0.00 3.86
1589 1758 3.562393 GGGAAGGGGGAGAAAAAGAAGAG 60.562 52.174 0.00 0.00 0.00 2.85
1605 1774 3.406595 GAGAAGGGCGATGGGTGGG 62.407 68.421 0.00 0.00 0.00 4.61
1662 1837 2.032528 CCGTGCAAGGCCAAGAGA 59.967 61.111 5.51 0.00 0.00 3.10
1663 1838 1.377725 CCGTGCAAGGCCAAGAGAT 60.378 57.895 5.51 0.00 0.00 2.75
1664 1839 1.372087 CCGTGCAAGGCCAAGAGATC 61.372 60.000 5.51 0.00 0.00 2.75
1691 1866 2.636830 ACGCCGAAGAACTAGCTAGTA 58.363 47.619 26.29 0.00 34.99 1.82
1809 1994 3.843619 TGGGTGGAAGAGATTGTGATGTA 59.156 43.478 0.00 0.00 0.00 2.29
1811 1996 4.878397 GGGTGGAAGAGATTGTGATGTAAG 59.122 45.833 0.00 0.00 0.00 2.34
1812 1997 5.338381 GGGTGGAAGAGATTGTGATGTAAGA 60.338 44.000 0.00 0.00 0.00 2.10
1813 1998 6.352516 GGTGGAAGAGATTGTGATGTAAGAT 58.647 40.000 0.00 0.00 0.00 2.40
1814 1999 6.259608 GGTGGAAGAGATTGTGATGTAAGATG 59.740 42.308 0.00 0.00 0.00 2.90
1821 2006 8.147058 AGAGATTGTGATGTAAGATGGATGTAC 58.853 37.037 0.00 0.00 0.00 2.90
1827 2012 3.956233 TGTAAGATGGATGTACGTACGC 58.044 45.455 20.18 14.33 0.00 4.42
1831 2016 0.744874 ATGGATGTACGTACGCAGCT 59.255 50.000 20.18 0.00 0.00 4.24
1843 2028 0.031314 ACGCAGCTATCGATCTGGTG 59.969 55.000 19.62 19.62 0.00 4.17
1903 2092 5.868801 CACATTGCGTCTGGGAATTTTATTT 59.131 36.000 0.00 0.00 34.03 1.40
1909 2100 5.798434 GCGTCTGGGAATTTTATTTGTGTAC 59.202 40.000 0.00 0.00 0.00 2.90
1911 2102 7.021196 CGTCTGGGAATTTTATTTGTGTACAG 58.979 38.462 0.00 0.00 0.00 2.74
1912 2103 7.308348 CGTCTGGGAATTTTATTTGTGTACAGT 60.308 37.037 0.00 0.00 0.00 3.55
1913 2104 7.807907 GTCTGGGAATTTTATTTGTGTACAGTG 59.192 37.037 0.00 0.00 0.00 3.66
1915 2106 8.693120 TGGGAATTTTATTTGTGTACAGTGTA 57.307 30.769 0.00 0.00 0.00 2.90
1916 2107 8.569641 TGGGAATTTTATTTGTGTACAGTGTAC 58.430 33.333 23.85 23.85 0.00 2.90
1917 2108 8.789762 GGGAATTTTATTTGTGTACAGTGTACT 58.210 33.333 28.78 14.37 0.00 2.73
1918 2109 9.821662 GGAATTTTATTTGTGTACAGTGTACTC 57.178 33.333 28.78 25.65 0.00 2.59
1978 2169 2.035530 TGCACATATTGGCATGTCGA 57.964 45.000 0.00 0.00 37.02 4.20
2021 2212 1.000283 GGATCCTGCATCGATCGTTCT 60.000 52.381 15.94 0.00 37.58 3.01
2049 2253 3.219281 GGCCAGAAGACACCAAAGTAAA 58.781 45.455 0.00 0.00 0.00 2.01
2078 5137 4.604156 TGAGAGGAGAAGACAGCAAGATA 58.396 43.478 0.00 0.00 0.00 1.98
2080 5139 5.105554 TGAGAGGAGAAGACAGCAAGATAAC 60.106 44.000 0.00 0.00 0.00 1.89
2089 5149 0.328258 AGCAAGATAACGGGCCAAGT 59.672 50.000 4.39 0.00 0.00 3.16
2109 5169 1.067364 TCGACCGTCAGTAGCAAAACA 59.933 47.619 0.00 0.00 0.00 2.83
2111 5171 2.159841 CGACCGTCAGTAGCAAAACATG 60.160 50.000 0.00 0.00 0.00 3.21
2156 5228 3.455910 TGCTCACAGCCCATCTAGTTATT 59.544 43.478 0.00 0.00 41.51 1.40
2157 5229 4.080356 TGCTCACAGCCCATCTAGTTATTT 60.080 41.667 0.00 0.00 41.51 1.40
2158 5230 4.884164 GCTCACAGCCCATCTAGTTATTTT 59.116 41.667 0.00 0.00 34.48 1.82
2159 5231 5.358160 GCTCACAGCCCATCTAGTTATTTTT 59.642 40.000 0.00 0.00 34.48 1.94
2160 5232 6.458888 GCTCACAGCCCATCTAGTTATTTTTC 60.459 42.308 0.00 0.00 34.48 2.29
2164 5236 7.970614 CACAGCCCATCTAGTTATTTTTCTTTC 59.029 37.037 0.00 0.00 0.00 2.62
2227 5299 4.576053 TGATGCACACAGCCTTATATTCAC 59.424 41.667 0.00 0.00 44.83 3.18
2228 5300 2.935849 TGCACACAGCCTTATATTCACG 59.064 45.455 0.00 0.00 44.83 4.35
2229 5301 2.287915 GCACACAGCCTTATATTCACGG 59.712 50.000 0.00 0.00 37.23 4.94
2230 5302 2.872245 CACACAGCCTTATATTCACGGG 59.128 50.000 0.00 0.00 0.00 5.28
2231 5303 1.873591 CACAGCCTTATATTCACGGGC 59.126 52.381 0.00 0.00 42.74 6.13
2232 5304 1.148310 CAGCCTTATATTCACGGGCG 58.852 55.000 0.00 0.00 46.44 6.13
2235 5307 1.939838 GCCTTATATTCACGGGCGGAG 60.940 57.143 0.00 0.00 33.30 4.63
2282 5589 2.588877 CCCTTGGCCTACGCATCG 60.589 66.667 3.32 0.00 36.38 3.84
2284 5591 1.592669 CCTTGGCCTACGCATCGAG 60.593 63.158 3.32 0.00 36.38 4.04
2285 5592 1.141881 CTTGGCCTACGCATCGAGT 59.858 57.895 3.32 0.00 36.38 4.18
2286 5593 1.148157 CTTGGCCTACGCATCGAGTG 61.148 60.000 3.32 0.00 36.38 3.51
2287 5594 1.884075 TTGGCCTACGCATCGAGTGT 61.884 55.000 3.32 0.00 44.62 3.55
2288 5595 1.033202 TGGCCTACGCATCGAGTGTA 61.033 55.000 3.32 0.00 42.05 2.90
2322 6233 1.999648 TCAACAAGGGCATGAAGCTT 58.000 45.000 0.00 0.00 44.79 3.74
2328 6239 1.026718 AGGGCATGAAGCTTGTACGC 61.027 55.000 2.10 0.40 44.79 4.42
2332 6243 2.106683 ATGAAGCTTGTACGCCGGC 61.107 57.895 19.07 19.07 0.00 6.13
2349 6260 0.179009 GGCATTGCCTGATCTAGCCA 60.179 55.000 20.66 0.00 46.69 4.75
2350 6261 0.950116 GCATTGCCTGATCTAGCCAC 59.050 55.000 0.00 0.00 0.00 5.01
2351 6262 1.748244 GCATTGCCTGATCTAGCCACA 60.748 52.381 0.00 0.00 0.00 4.17
2352 6263 2.646930 CATTGCCTGATCTAGCCACAA 58.353 47.619 5.28 0.00 0.00 3.33
2353 6264 2.113860 TTGCCTGATCTAGCCACAAC 57.886 50.000 5.28 0.00 0.00 3.32
2354 6265 0.253044 TGCCTGATCTAGCCACAACC 59.747 55.000 5.28 0.00 0.00 3.77
2355 6266 0.464554 GCCTGATCTAGCCACAACCC 60.465 60.000 0.00 0.00 0.00 4.11
2356 6267 0.179073 CCTGATCTAGCCACAACCCG 60.179 60.000 0.00 0.00 0.00 5.28
2358 6269 1.146263 GATCTAGCCACAACCCGGG 59.854 63.158 22.25 22.25 0.00 5.73
2359 6270 1.615424 ATCTAGCCACAACCCGGGT 60.615 57.895 24.16 24.16 38.05 5.28
2361 6272 1.074248 CTAGCCACAACCCGGGTTT 59.926 57.895 36.59 23.52 36.00 3.27
2362 6273 0.538746 CTAGCCACAACCCGGGTTTT 60.539 55.000 36.59 28.12 36.00 2.43
2363 6274 0.537828 TAGCCACAACCCGGGTTTTC 60.538 55.000 36.59 22.95 36.00 2.29
2364 6275 2.128507 GCCACAACCCGGGTTTTCA 61.129 57.895 36.59 0.00 36.00 2.69
2372 6283 1.478916 ACCCGGGTTTTCACAAACTTG 59.521 47.619 24.16 0.00 41.92 3.16
2383 6294 8.450180 GGTTTTCACAAACTTGTCATCAAATTT 58.550 29.630 0.00 0.00 41.92 1.82
2395 6306 5.638657 TGTCATCAAATTTAGCATTGCCAAC 59.361 36.000 4.70 0.00 0.00 3.77
2412 6323 1.252904 AACAACCTCGCTACCGGCTA 61.253 55.000 0.00 0.00 39.13 3.93
2452 6363 4.444022 CGGATCCTGATTGTTGGAGAAGAT 60.444 45.833 10.75 0.00 35.63 2.40
2485 6396 3.984200 GAGCACCGCCGTCCTACAC 62.984 68.421 0.00 0.00 0.00 2.90
2492 6403 2.882876 CCGTCCTACACCTCACCG 59.117 66.667 0.00 0.00 0.00 4.94
2507 6418 3.177600 CCGTGCTTCCGGTCATTG 58.822 61.111 0.00 0.00 43.07 2.82
2508 6419 1.375396 CCGTGCTTCCGGTCATTGA 60.375 57.895 0.00 0.00 43.07 2.57
2509 6420 0.744414 CCGTGCTTCCGGTCATTGAT 60.744 55.000 0.00 0.00 43.07 2.57
2515 6426 0.037447 TTCCGGTCATTGATGCACCA 59.963 50.000 0.00 0.00 32.12 4.17
2534 6445 3.452264 ACCACCTTTGATCTCATCGATGA 59.548 43.478 25.80 25.80 35.16 2.92
2553 6464 6.015856 TCGATGAGAGAGAGGGAAATATGAAC 60.016 42.308 0.00 0.00 0.00 3.18
2559 6470 3.545703 AGAGGGAAATATGAACGCAAGG 58.454 45.455 0.00 0.00 46.39 3.61
2566 6477 1.200519 TATGAACGCAAGGTAGCCCT 58.799 50.000 0.00 0.00 45.63 5.19
2572 6484 1.838077 ACGCAAGGTAGCCCTATTTCT 59.162 47.619 0.00 0.00 41.56 2.52
2583 6495 2.917933 CCCTATTTCTCCGTCATTGCA 58.082 47.619 0.00 0.00 0.00 4.08
2584 6496 2.874701 CCCTATTTCTCCGTCATTGCAG 59.125 50.000 0.00 0.00 0.00 4.41
2603 6515 2.044806 GCCACCTCATAGACCGCCAT 62.045 60.000 0.00 0.00 0.00 4.40
2605 6517 0.319040 CACCTCATAGACCGCCATCG 60.319 60.000 0.00 0.00 0.00 3.84
2618 6530 1.671054 CCATCGTTGCGGTCACCTT 60.671 57.895 0.00 0.00 0.00 3.50
2628 6540 1.153349 GGTCACCTTGCGGATCCTC 60.153 63.158 10.75 1.54 0.00 3.71
2630 6542 1.306141 TCACCTTGCGGATCCTCCT 60.306 57.895 10.75 0.00 33.30 3.69
2634 6546 1.402896 CCTTGCGGATCCTCCTAGCA 61.403 60.000 10.75 8.73 32.32 3.49
2661 6573 4.066614 GGCCACTACCCTGATCCA 57.933 61.111 0.00 0.00 0.00 3.41
2662 6574 1.527370 GGCCACTACCCTGATCCAC 59.473 63.158 0.00 0.00 0.00 4.02
2663 6575 1.271840 GGCCACTACCCTGATCCACA 61.272 60.000 0.00 0.00 0.00 4.17
2664 6576 0.839946 GCCACTACCCTGATCCACAT 59.160 55.000 0.00 0.00 0.00 3.21
2665 6577 2.047061 GCCACTACCCTGATCCACATA 58.953 52.381 0.00 0.00 0.00 2.29
2666 6578 2.037772 GCCACTACCCTGATCCACATAG 59.962 54.545 0.00 0.00 0.00 2.23
2667 6579 2.037772 CCACTACCCTGATCCACATAGC 59.962 54.545 0.00 0.00 0.00 2.97
2668 6580 2.700371 CACTACCCTGATCCACATAGCA 59.300 50.000 0.00 0.00 0.00 3.49
2669 6581 2.700897 ACTACCCTGATCCACATAGCAC 59.299 50.000 0.00 0.00 0.00 4.40
2670 6582 0.839946 ACCCTGATCCACATAGCACC 59.160 55.000 0.00 0.00 0.00 5.01
2671 6583 0.109342 CCCTGATCCACATAGCACCC 59.891 60.000 0.00 0.00 0.00 4.61
2672 6584 0.839277 CCTGATCCACATAGCACCCA 59.161 55.000 0.00 0.00 0.00 4.51
2673 6585 1.422781 CCTGATCCACATAGCACCCAT 59.577 52.381 0.00 0.00 0.00 4.00
2674 6586 2.551721 CCTGATCCACATAGCACCCATC 60.552 54.545 0.00 0.00 0.00 3.51
2675 6587 1.070601 TGATCCACATAGCACCCATCG 59.929 52.381 0.00 0.00 0.00 3.84
2676 6588 0.397941 ATCCACATAGCACCCATCGG 59.602 55.000 0.00 0.00 0.00 4.18
2677 6589 1.893808 CCACATAGCACCCATCGGC 60.894 63.158 0.00 0.00 0.00 5.54
2678 6590 2.108976 ACATAGCACCCATCGGCG 59.891 61.111 0.00 0.00 34.54 6.46
2679 6591 2.666190 CATAGCACCCATCGGCGG 60.666 66.667 7.21 0.00 34.54 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.057174 CCAGGCGCAAAACAAAATAGGTA 60.057 43.478 10.83 0.00 0.00 3.08
44 45 2.288763 CCAGGCGCAAAACAAAATAGGT 60.289 45.455 10.83 0.00 0.00 3.08
45 46 2.336667 CCAGGCGCAAAACAAAATAGG 58.663 47.619 10.83 0.00 0.00 2.57
47 48 1.342819 AGCCAGGCGCAAAACAAAATA 59.657 42.857 10.83 0.00 41.38 1.40
48 49 0.106521 AGCCAGGCGCAAAACAAAAT 59.893 45.000 10.83 0.00 41.38 1.82
49 50 0.747255 TAGCCAGGCGCAAAACAAAA 59.253 45.000 10.83 0.00 41.38 2.44
60 61 5.051153 GTCTACAAGTTATTCTAGCCAGGC 58.949 45.833 1.84 1.84 0.00 4.85
74 75 1.556911 CCCCATCAGCAGTCTACAAGT 59.443 52.381 0.00 0.00 0.00 3.16
75 76 1.556911 ACCCCATCAGCAGTCTACAAG 59.443 52.381 0.00 0.00 0.00 3.16
81 82 0.393537 CCTCAACCCCATCAGCAGTC 60.394 60.000 0.00 0.00 0.00 3.51
82 83 1.136329 ACCTCAACCCCATCAGCAGT 61.136 55.000 0.00 0.00 0.00 4.40
89 90 1.000739 CATGGCACCTCAACCCCAT 59.999 57.895 0.00 0.00 38.56 4.00
90 91 2.440147 CATGGCACCTCAACCCCA 59.560 61.111 0.00 0.00 0.00 4.96
91 92 2.362889 CCATGGCACCTCAACCCC 60.363 66.667 0.00 0.00 0.00 4.95
93 94 1.228552 ACACCATGGCACCTCAACC 60.229 57.895 13.04 0.00 0.00 3.77
94 95 0.537143 TCACACCATGGCACCTCAAC 60.537 55.000 13.04 0.00 0.00 3.18
95 96 0.184692 TTCACACCATGGCACCTCAA 59.815 50.000 13.04 0.00 0.00 3.02
96 97 0.405198 ATTCACACCATGGCACCTCA 59.595 50.000 13.04 0.00 0.00 3.86
97 98 2.418368 TATTCACACCATGGCACCTC 57.582 50.000 13.04 0.00 0.00 3.85
98 99 2.446435 GTTATTCACACCATGGCACCT 58.554 47.619 13.04 0.00 0.00 4.00
101 102 2.224992 ACAGGTTATTCACACCATGGCA 60.225 45.455 13.04 0.00 36.67 4.92
102 103 2.446435 ACAGGTTATTCACACCATGGC 58.554 47.619 13.04 0.00 36.67 4.40
103 104 3.627577 GCTACAGGTTATTCACACCATGG 59.372 47.826 11.19 11.19 36.67 3.66
104 105 3.627577 GGCTACAGGTTATTCACACCATG 59.372 47.826 0.00 0.00 36.67 3.66
105 106 3.523564 AGGCTACAGGTTATTCACACCAT 59.476 43.478 0.00 0.00 36.67 3.55
106 107 2.910319 AGGCTACAGGTTATTCACACCA 59.090 45.455 0.00 0.00 36.67 4.17
107 108 3.270877 CAGGCTACAGGTTATTCACACC 58.729 50.000 0.00 0.00 34.06 4.16
108 109 2.678336 GCAGGCTACAGGTTATTCACAC 59.322 50.000 0.00 0.00 0.00 3.82
109 110 2.571653 AGCAGGCTACAGGTTATTCACA 59.428 45.455 0.00 0.00 0.00 3.58
110 111 3.118592 AGAGCAGGCTACAGGTTATTCAC 60.119 47.826 0.00 0.00 0.00 3.18
111 112 3.107601 AGAGCAGGCTACAGGTTATTCA 58.892 45.455 0.00 0.00 0.00 2.57
119 120 1.436600 CACAACAGAGCAGGCTACAG 58.563 55.000 0.00 0.00 0.00 2.74
133 134 1.810532 TGGCGAACCAAACCACAAC 59.189 52.632 0.00 0.00 45.37 3.32
134 135 4.338815 TGGCGAACCAAACCACAA 57.661 50.000 0.00 0.00 45.37 3.33
145 146 1.093972 CATGCTAACACCATGGCGAA 58.906 50.000 13.04 0.00 37.12 4.70
155 156 5.647658 CACAGATAAAGGGAACATGCTAACA 59.352 40.000 0.00 0.00 0.00 2.41
169 174 3.074412 AGAAACCGGCACACAGATAAAG 58.926 45.455 0.00 0.00 0.00 1.85
195 200 4.044308 TCAGGCAATAATACCAGGGAAGA 58.956 43.478 0.00 0.00 0.00 2.87
199 204 2.174639 TGGTCAGGCAATAATACCAGGG 59.825 50.000 0.00 0.00 35.34 4.45
247 258 3.814283 TCCCAACAATACGTGGTTAACAC 59.186 43.478 8.10 3.28 46.78 3.32
311 334 0.036010 CCAAGCAGTCAATCTCCGGT 60.036 55.000 0.00 0.00 0.00 5.28
342 365 5.766222 AGACTAGAAAAACAGCAAATGCAG 58.234 37.500 8.28 1.87 45.16 4.41
343 366 5.560760 CGAGACTAGAAAAACAGCAAATGCA 60.561 40.000 8.28 0.00 45.16 3.96
344 367 4.848299 CGAGACTAGAAAAACAGCAAATGC 59.152 41.667 0.00 0.00 42.49 3.56
355 379 3.976793 ACACACGACGAGACTAGAAAA 57.023 42.857 0.00 0.00 0.00 2.29
363 387 0.516001 GCAGAGTACACACGACGAGA 59.484 55.000 0.00 0.00 0.00 4.04
386 410 4.683832 ACTTGCGAGTCAATATAGGTCAC 58.316 43.478 0.00 0.00 33.57 3.67
421 450 1.612442 AGGACCACCAGGCGTACAT 60.612 57.895 0.00 0.00 39.06 2.29
424 453 2.682494 GGAGGACCACCAGGCGTA 60.682 66.667 2.58 0.00 39.06 4.42
428 457 3.391382 GACGGGAGGACCACCAGG 61.391 72.222 12.40 5.08 40.22 4.45
430 459 2.096707 TTAGGACGGGAGGACCACCA 62.097 60.000 10.41 0.00 40.22 4.17
431 460 1.305549 TTAGGACGGGAGGACCACC 60.306 63.158 0.00 0.00 40.22 4.61
434 484 2.149973 TAAGTTAGGACGGGAGGACC 57.850 55.000 0.00 0.00 0.00 4.46
451 501 6.837312 TGTGAAGGAGAAGGAGTGATTTTAA 58.163 36.000 0.00 0.00 0.00 1.52
460 510 4.815533 TGAGAATGTGAAGGAGAAGGAG 57.184 45.455 0.00 0.00 0.00 3.69
463 513 9.092876 GTATACTTTGAGAATGTGAAGGAGAAG 57.907 37.037 0.00 0.00 0.00 2.85
492 552 4.400251 TCATCTTCCACTTGAAATGGATGC 59.600 41.667 0.00 0.00 45.71 3.91
511 571 3.104766 CCCATGTGTGCGCTCATC 58.895 61.111 16.02 9.82 0.00 2.92
512 572 3.136123 GCCCATGTGTGCGCTCAT 61.136 61.111 16.02 8.95 0.00 2.90
514 574 4.107051 GTGCCCATGTGTGCGCTC 62.107 66.667 9.73 5.51 35.20 5.03
518 578 3.737172 GACGGTGCCCATGTGTGC 61.737 66.667 0.00 0.00 0.00 4.57
528 627 2.131183 GAGATATTGCTCTGACGGTGC 58.869 52.381 1.25 1.25 35.27 5.01
531 630 1.932604 GCGGAGATATTGCTCTGACGG 60.933 57.143 0.00 0.00 42.63 4.79
553 652 1.252015 GTTTCTACTATCGCACGCGTG 59.748 52.381 34.01 34.01 40.74 5.34
554 653 1.131883 AGTTTCTACTATCGCACGCGT 59.868 47.619 5.58 5.58 35.21 6.01
555 654 1.823828 AGTTTCTACTATCGCACGCG 58.176 50.000 3.53 3.53 35.07 6.01
556 655 2.720067 GCTAGTTTCTACTATCGCACGC 59.280 50.000 0.00 0.00 36.32 5.34
557 656 3.948851 TGCTAGTTTCTACTATCGCACG 58.051 45.455 0.00 0.00 34.78 5.34
558 657 3.731717 GCTGCTAGTTTCTACTATCGCAC 59.268 47.826 0.00 0.00 34.78 5.34
559 658 3.380320 TGCTGCTAGTTTCTACTATCGCA 59.620 43.478 0.00 0.00 36.35 5.10
560 659 3.966154 TGCTGCTAGTTTCTACTATCGC 58.034 45.455 0.00 0.00 36.32 4.58
561 660 5.176407 ACTGCTGCTAGTTTCTACTATCG 57.824 43.478 0.00 0.00 36.32 2.92
562 661 7.266922 ACTACTGCTGCTAGTTTCTACTATC 57.733 40.000 0.00 0.00 36.32 2.08
563 662 7.484975 CAACTACTGCTGCTAGTTTCTACTAT 58.515 38.462 10.54 0.00 36.32 2.12
564 663 6.853720 CAACTACTGCTGCTAGTTTCTACTA 58.146 40.000 10.54 0.00 33.05 1.82
565 664 5.715070 CAACTACTGCTGCTAGTTTCTACT 58.285 41.667 10.54 0.00 33.05 2.57
729 852 4.508662 TGTTTGTTTTGGCCAAGTTTAGG 58.491 39.130 19.48 0.00 0.00 2.69
760 883 0.529555 TCGGTTTTGCCTTTGCTTGC 60.530 50.000 0.00 0.00 38.71 4.01
915 1045 4.143326 CGCGCGGGATAAATATATATGCTG 60.143 45.833 24.84 0.00 34.23 4.41
996 1126 3.249189 GGCGCCTCCCCCATGATA 61.249 66.667 22.15 0.00 0.00 2.15
1023 1180 1.139734 CATCTCCACCGTGGTCGAG 59.860 63.158 17.32 7.28 39.03 4.04
1134 1294 4.373116 GCCGGCACCTTCTCGTCA 62.373 66.667 24.80 0.00 0.00 4.35
1157 1317 4.742201 TGTCCGCGCTCTTGCTCC 62.742 66.667 5.56 0.00 36.97 4.70
1176 1336 3.997064 CTTCTCGCCAGCCCTGACG 62.997 68.421 0.00 0.00 37.80 4.35
1177 1337 2.125350 CTTCTCGCCAGCCCTGAC 60.125 66.667 0.00 0.00 0.00 3.51
1178 1338 3.393970 CCTTCTCGCCAGCCCTGA 61.394 66.667 0.00 0.00 0.00 3.86
1179 1339 4.479993 CCCTTCTCGCCAGCCCTG 62.480 72.222 0.00 0.00 0.00 4.45
1208 1368 3.639541 CTGTCCGCGCTCTTGCTCT 62.640 63.158 5.56 0.00 36.97 4.09
1270 1430 4.845580 CTTCTCGCCGGCTGCCAT 62.846 66.667 26.68 0.00 36.24 4.40
1281 1441 4.052229 ACGTCCGGCACCTTCTCG 62.052 66.667 0.00 0.00 0.00 4.04
1282 1442 2.432628 CACGTCCGGCACCTTCTC 60.433 66.667 0.00 0.00 0.00 2.87
1283 1443 4.003788 CCACGTCCGGCACCTTCT 62.004 66.667 0.00 0.00 0.00 2.85
1284 1444 3.934391 CTCCACGTCCGGCACCTTC 62.934 68.421 0.00 0.00 0.00 3.46
1285 1445 4.003788 CTCCACGTCCGGCACCTT 62.004 66.667 0.00 0.00 0.00 3.50
1286 1446 4.988716 TCTCCACGTCCGGCACCT 62.989 66.667 0.00 0.00 0.00 4.00
1287 1447 4.436998 CTCTCCACGTCCGGCACC 62.437 72.222 0.00 0.00 0.00 5.01
1290 1450 4.373116 TTGCTCTCCACGTCCGGC 62.373 66.667 0.00 0.00 0.00 6.13
1291 1451 2.125912 CTTGCTCTCCACGTCCGG 60.126 66.667 0.00 0.00 0.00 5.14
1292 1452 1.153939 CTCTTGCTCTCCACGTCCG 60.154 63.158 0.00 0.00 0.00 4.79
1293 1453 1.446966 GCTCTTGCTCTCCACGTCC 60.447 63.158 0.00 0.00 36.03 4.79
1294 1454 1.803519 CGCTCTTGCTCTCCACGTC 60.804 63.158 0.00 0.00 36.97 4.34
1295 1455 2.259818 CGCTCTTGCTCTCCACGT 59.740 61.111 0.00 0.00 36.97 4.49
1296 1456 3.184683 GCGCTCTTGCTCTCCACG 61.185 66.667 0.00 0.00 36.97 4.94
1297 1457 3.184683 CGCGCTCTTGCTCTCCAC 61.185 66.667 5.56 0.00 36.97 4.02
1298 1458 4.441695 CCGCGCTCTTGCTCTCCA 62.442 66.667 5.56 0.00 36.97 3.86
1346 1509 1.001269 GGCACCCCCTCTTTACCAC 60.001 63.158 0.00 0.00 0.00 4.16
1370 1533 2.849120 CTTCCCGGTGCTGCTCTCAG 62.849 65.000 0.00 0.00 43.16 3.35
1371 1534 2.922503 TTCCCGGTGCTGCTCTCA 60.923 61.111 0.00 0.00 0.00 3.27
1413 1576 4.388499 TCTTGTCCGCCGCCCTTC 62.388 66.667 0.00 0.00 0.00 3.46
1419 1582 3.685214 CTCCTCGTCTTGTCCGCCG 62.685 68.421 0.00 0.00 0.00 6.46
1491 1654 5.314718 TCCTCCTCGTGTTCCTGTATATA 57.685 43.478 0.00 0.00 0.00 0.86
1589 1758 4.506255 CCCCACCCATCGCCCTTC 62.506 72.222 0.00 0.00 0.00 3.46
1662 1837 0.974010 TTCTTCGGCGTACCCCTGAT 60.974 55.000 6.85 0.00 0.00 2.90
1663 1838 1.607178 TTCTTCGGCGTACCCCTGA 60.607 57.895 6.85 0.00 0.00 3.86
1664 1839 1.447314 GTTCTTCGGCGTACCCCTG 60.447 63.158 6.85 0.00 0.00 4.45
1691 1866 1.816835 ACGACGACTCACACCACATAT 59.183 47.619 0.00 0.00 0.00 1.78
1809 1994 2.798499 GCTGCGTACGTACATCCATCTT 60.798 50.000 24.50 0.00 0.00 2.40
1811 1996 1.129326 GCTGCGTACGTACATCCATC 58.871 55.000 24.50 10.44 0.00 3.51
1812 1997 0.744874 AGCTGCGTACGTACATCCAT 59.255 50.000 24.50 5.33 0.00 3.41
1813 1998 1.381522 TAGCTGCGTACGTACATCCA 58.618 50.000 24.50 16.17 0.00 3.41
1814 1999 2.582687 GATAGCTGCGTACGTACATCC 58.417 52.381 24.50 12.70 0.00 3.51
1821 2006 1.596703 CAGATCGATAGCTGCGTACG 58.403 55.000 11.84 11.84 0.00 3.67
1827 2012 2.879002 ACACACCAGATCGATAGCTG 57.121 50.000 0.00 2.14 0.00 4.24
1831 2016 2.169769 GGGGAAACACACCAGATCGATA 59.830 50.000 0.00 0.00 42.69 2.92
1843 2028 2.879103 TCTTCCATGAGGGGAAACAC 57.121 50.000 0.00 0.00 45.87 3.32
1911 2102 4.102649 GCCAAACAACAAAGTGAGTACAC 58.897 43.478 0.00 0.00 46.24 2.90
1912 2103 3.759086 TGCCAAACAACAAAGTGAGTACA 59.241 39.130 0.00 0.00 0.00 2.90
1913 2104 4.364415 TGCCAAACAACAAAGTGAGTAC 57.636 40.909 0.00 0.00 0.00 2.73
1915 2106 3.430651 CCATGCCAAACAACAAAGTGAGT 60.431 43.478 0.00 0.00 0.00 3.41
1916 2107 3.125316 CCATGCCAAACAACAAAGTGAG 58.875 45.455 0.00 0.00 0.00 3.51
1917 2108 2.741228 GCCATGCCAAACAACAAAGTGA 60.741 45.455 0.00 0.00 0.00 3.41
1918 2109 1.598601 GCCATGCCAAACAACAAAGTG 59.401 47.619 0.00 0.00 0.00 3.16
1919 2110 1.209019 TGCCATGCCAAACAACAAAGT 59.791 42.857 0.00 0.00 0.00 2.66
1920 2111 1.950828 TGCCATGCCAAACAACAAAG 58.049 45.000 0.00 0.00 0.00 2.77
1921 2112 2.408271 TTGCCATGCCAAACAACAAA 57.592 40.000 0.00 0.00 0.00 2.83
1925 2116 0.964700 TCGATTGCCATGCCAAACAA 59.035 45.000 0.00 0.00 0.00 2.83
1932 2123 0.657312 TGAACGATCGATTGCCATGC 59.343 50.000 24.34 0.00 0.00 4.06
1978 2169 2.991190 CACAATAACGACCGCAGTAGTT 59.009 45.455 3.99 3.99 43.27 2.24
2021 2212 0.034337 GTGTCTTCTGGCCGTAACCA 59.966 55.000 0.00 0.00 38.29 3.67
2033 2224 3.304726 GCTGCCTTTACTTTGGTGTCTTC 60.305 47.826 0.00 0.00 0.00 2.87
2049 2253 0.040942 TCTTCTCCTCTCAGCTGCCT 59.959 55.000 9.47 0.00 0.00 4.75
2078 5137 4.675029 CGGTCGACTTGGCCCGTT 62.675 66.667 16.46 0.00 35.78 4.44
2089 5149 1.067364 TGTTTTGCTACTGACGGTCGA 59.933 47.619 3.34 0.00 0.00 4.20
2118 5178 1.387084 GAGCAATGACTCGTGTCGTTC 59.613 52.381 19.35 14.56 46.12 3.95
2126 5198 1.364626 GGGCTGTGAGCAATGACTCG 61.365 60.000 0.00 0.00 44.75 4.18
2156 5228 6.806668 ACCCTCATTCCAAAAGAAAGAAAA 57.193 33.333 0.00 0.00 38.21 2.29
2157 5229 7.782644 TCTTACCCTCATTCCAAAAGAAAGAAA 59.217 33.333 0.00 0.00 38.21 2.52
2158 5230 7.230712 GTCTTACCCTCATTCCAAAAGAAAGAA 59.769 37.037 0.00 0.00 38.21 2.52
2159 5231 6.715264 GTCTTACCCTCATTCCAAAAGAAAGA 59.285 38.462 0.00 0.00 38.21 2.52
2160 5232 6.071896 GGTCTTACCCTCATTCCAAAAGAAAG 60.072 42.308 0.00 0.00 32.68 2.62
2188 5260 1.960040 ATCACTCGATGCGAAGGCCA 61.960 55.000 5.01 0.00 38.85 5.36
2236 5308 3.989787 GGCTTGGCCCAAACGTGG 61.990 66.667 0.00 0.00 44.06 4.94
2258 5330 1.677637 CGTAGGCCAAGGGTCTCTCC 61.678 65.000 5.01 0.00 36.89 3.71
2260 5332 2.359967 GCGTAGGCCAAGGGTCTCT 61.360 63.158 5.01 0.00 36.89 3.10
2261 5333 1.972660 ATGCGTAGGCCAAGGGTCTC 61.973 60.000 5.01 0.00 36.89 3.36
2262 5334 1.972660 GATGCGTAGGCCAAGGGTCT 61.973 60.000 5.01 0.00 42.13 3.85
2263 5335 1.523938 GATGCGTAGGCCAAGGGTC 60.524 63.158 5.01 0.00 38.85 4.46
2266 5338 1.592669 CTCGATGCGTAGGCCAAGG 60.593 63.158 5.01 0.00 38.85 3.61
2267 5339 1.141881 ACTCGATGCGTAGGCCAAG 59.858 57.895 5.01 0.00 38.85 3.61
2268 5340 1.153647 CACTCGATGCGTAGGCCAA 60.154 57.895 5.01 0.00 38.85 4.52
2269 5341 1.033202 TACACTCGATGCGTAGGCCA 61.033 55.000 5.01 0.00 38.85 5.36
2274 5581 5.678132 TTTATAGCTACACTCGATGCGTA 57.322 39.130 0.00 0.00 0.00 4.42
2282 5589 9.151471 TGTTGAAGATGTTTTATAGCTACACTC 57.849 33.333 0.00 0.00 0.00 3.51
2284 5591 9.760660 CTTGTTGAAGATGTTTTATAGCTACAC 57.239 33.333 0.00 0.00 0.00 2.90
2285 5592 8.946085 CCTTGTTGAAGATGTTTTATAGCTACA 58.054 33.333 0.00 0.00 0.00 2.74
2286 5593 8.398665 CCCTTGTTGAAGATGTTTTATAGCTAC 58.601 37.037 0.00 0.00 0.00 3.58
2287 5594 7.067008 GCCCTTGTTGAAGATGTTTTATAGCTA 59.933 37.037 0.00 0.00 0.00 3.32
2288 5595 6.127619 GCCCTTGTTGAAGATGTTTTATAGCT 60.128 38.462 0.00 0.00 0.00 3.32
2289 5596 6.036470 GCCCTTGTTGAAGATGTTTTATAGC 58.964 40.000 0.00 0.00 0.00 2.97
2290 5597 7.156876 TGCCCTTGTTGAAGATGTTTTATAG 57.843 36.000 0.00 0.00 0.00 1.31
2291 5598 7.395772 TCATGCCCTTGTTGAAGATGTTTTATA 59.604 33.333 0.00 0.00 0.00 0.98
2292 5599 6.211184 TCATGCCCTTGTTGAAGATGTTTTAT 59.789 34.615 0.00 0.00 0.00 1.40
2294 5601 4.344679 TCATGCCCTTGTTGAAGATGTTTT 59.655 37.500 0.00 0.00 0.00 2.43
2295 5602 3.896888 TCATGCCCTTGTTGAAGATGTTT 59.103 39.130 0.00 0.00 0.00 2.83
2339 6250 1.622607 CCCGGGTTGTGGCTAGATCA 61.623 60.000 14.18 0.00 0.00 2.92
2349 6260 1.205179 GTTTGTGAAAACCCGGGTTGT 59.795 47.619 38.87 34.55 38.47 3.32
2350 6261 1.478916 AGTTTGTGAAAACCCGGGTTG 59.521 47.619 38.87 7.23 38.47 3.77
2351 6262 1.855295 AGTTTGTGAAAACCCGGGTT 58.145 45.000 33.74 33.74 40.45 4.11
2352 6263 1.478916 CAAGTTTGTGAAAACCCGGGT 59.521 47.619 24.16 24.16 33.28 5.28
2353 6264 1.478916 ACAAGTTTGTGAAAACCCGGG 59.521 47.619 22.25 22.25 40.49 5.73
2354 6265 2.164624 TGACAAGTTTGTGAAAACCCGG 59.835 45.455 1.62 0.00 42.43 5.73
2355 6266 3.495670 TGACAAGTTTGTGAAAACCCG 57.504 42.857 1.62 0.00 42.43 5.28
2356 6267 5.004922 TGATGACAAGTTTGTGAAAACCC 57.995 39.130 1.62 0.00 42.43 4.11
2361 6272 7.978414 TGCTAAATTTGATGACAAGTTTGTGAA 59.022 29.630 1.62 0.00 42.70 3.18
2362 6273 7.487484 TGCTAAATTTGATGACAAGTTTGTGA 58.513 30.769 1.62 0.00 42.70 3.58
2363 6274 7.697352 TGCTAAATTTGATGACAAGTTTGTG 57.303 32.000 1.62 7.21 42.70 3.33
2364 6275 8.767085 CAATGCTAAATTTGATGACAAGTTTGT 58.233 29.630 0.00 0.00 42.70 2.83
2372 6283 5.638657 TGTTGGCAATGCTAAATTTGATGAC 59.361 36.000 5.40 0.00 29.49 3.06
2383 6294 1.164411 CGAGGTTGTTGGCAATGCTA 58.836 50.000 1.92 0.00 36.92 3.49
2385 6296 1.734117 GCGAGGTTGTTGGCAATGC 60.734 57.895 1.92 0.00 36.92 3.56
2412 6323 1.614903 TCCGGTTAGTGATGTGTCGTT 59.385 47.619 0.00 0.00 0.00 3.85
2475 6386 1.975407 ACGGTGAGGTGTAGGACGG 60.975 63.158 0.00 0.00 0.00 4.79
2492 6403 0.099436 GCATCAATGACCGGAAGCAC 59.901 55.000 9.46 0.00 0.00 4.40
2505 6416 3.084039 GAGATCAAAGGTGGTGCATCAA 58.916 45.455 0.00 0.00 0.00 2.57
2507 6418 2.715046 TGAGATCAAAGGTGGTGCATC 58.285 47.619 0.00 0.00 0.00 3.91
2508 6419 2.885135 TGAGATCAAAGGTGGTGCAT 57.115 45.000 0.00 0.00 0.00 3.96
2509 6420 2.715046 GATGAGATCAAAGGTGGTGCA 58.285 47.619 0.00 0.00 0.00 4.57
2534 6445 3.706594 TGCGTTCATATTTCCCTCTCTCT 59.293 43.478 0.00 0.00 0.00 3.10
2541 6452 3.003378 GCTACCTTGCGTTCATATTTCCC 59.997 47.826 0.00 0.00 0.00 3.97
2559 6470 4.058817 CAATGACGGAGAAATAGGGCTAC 58.941 47.826 0.00 0.00 0.00 3.58
2566 6477 2.288666 GGCTGCAATGACGGAGAAATA 58.711 47.619 0.50 0.00 0.00 1.40
2572 6484 2.359850 GGTGGCTGCAATGACGGA 60.360 61.111 0.50 0.00 0.00 4.69
2583 6495 2.435693 GGCGGTCTATGAGGTGGCT 61.436 63.158 0.00 0.00 0.00 4.75
2584 6496 2.044806 ATGGCGGTCTATGAGGTGGC 62.045 60.000 0.00 0.00 0.00 5.01
2603 6515 2.970324 GCAAGGTGACCGCAACGA 60.970 61.111 0.00 0.00 36.63 3.85
2628 6540 3.470888 CCCTGGGGACGTGCTAGG 61.471 72.222 18.87 18.87 37.50 3.02
2650 6562 2.047061 GGTGCTATGTGGATCAGGGTA 58.953 52.381 0.00 0.00 0.00 3.69
2660 6572 2.246739 CGCCGATGGGTGCTATGTG 61.247 63.158 0.00 0.00 36.93 3.21
2661 6573 2.108976 CGCCGATGGGTGCTATGT 59.891 61.111 0.00 0.00 36.93 2.29
2662 6574 2.666190 CCGCCGATGGGTGCTATG 60.666 66.667 1.02 0.00 42.73 2.23
2663 6575 3.941188 CCCGCCGATGGGTGCTAT 61.941 66.667 1.02 0.00 44.76 2.97


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

AutoCloner maintained by Alex Coulton.