Multiple sequence alignment - TraesCS3D01G090100

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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 TraesCS3D01G090100 chr3D 100.000 2315 0 0 1 2315 45766776 45764462 0.000000e+00 4276.0
1 TraesCS3D01G090100 chr3D 78.399 1074 177 22 391 1442 333012494 333011454 0.000000e+00 647.0
2 TraesCS3D01G090100 chr3B 88.777 1488 110 25 389 1831 71430332 71428857 0.000000e+00 1770.0
3 TraesCS3D01G090100 chr3B 88.629 299 17 9 91 383 71430732 71430445 4.730000e-92 348.0
4 TraesCS3D01G090100 chr3B 78.451 594 85 15 870 1442 432261900 432261329 4.730000e-92 348.0
5 TraesCS3D01G090100 chr3B 89.147 129 14 0 1823 1951 71407319 71407191 6.620000e-36 161.0
6 TraesCS3D01G090100 chr3B 91.071 112 6 2 2205 2315 71406186 71406078 5.150000e-32 148.0
7 TraesCS3D01G090100 chr3A 87.397 1087 73 23 1091 2127 57288022 57286950 0.000000e+00 1190.0
8 TraesCS3D01G090100 chr3A 78.326 1075 176 20 391 1442 450712772 450711732 1.940000e-180 641.0
9 TraesCS3D01G090100 chr3A 94.301 193 11 0 389 581 57288210 57288018 1.740000e-76 296.0
10 TraesCS3D01G090100 chr3A 81.768 181 9 7 91 247 57288605 57288425 1.870000e-26 130.0
11 TraesCS3D01G090100 chr6D 79.026 1068 171 23 391 1442 94764749 94765779 0.000000e+00 682.0
12 TraesCS3D01G090100 chr2D 95.960 99 4 0 1 99 626640539 626640637 6.620000e-36 161.0
13 TraesCS3D01G090100 chr2D 98.851 87 1 0 1 87 34666922 34667008 3.080000e-34 156.0
14 TraesCS3D01G090100 chr2B 96.739 92 3 0 1 92 144249617 144249708 1.110000e-33 154.0
15 TraesCS3D01G090100 chr2B 84.043 94 14 1 1 94 50644176 50644084 3.170000e-14 89.8
16 TraesCS3D01G090100 chr2B 84.043 94 14 1 1 94 50664980 50664888 3.170000e-14 89.8
17 TraesCS3D01G090100 chr1D 97.727 88 2 0 1 88 137634101 137634188 3.980000e-33 152.0
18 TraesCS3D01G090100 chr5B 91.579 95 7 1 1 94 456276780 456276874 1.870000e-26 130.0
19 TraesCS3D01G090100 chr6B 91.860 86 7 0 1357 1442 178018523 178018438 1.120000e-23 121.0


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 TraesCS3D01G090100 chr3D 45764462 45766776 2314 True 4276.000000 4276 100.000 1 2315 1 chr3D.!!$R1 2314
1 TraesCS3D01G090100 chr3D 333011454 333012494 1040 True 647.000000 647 78.399 391 1442 1 chr3D.!!$R2 1051
2 TraesCS3D01G090100 chr3B 71428857 71430732 1875 True 1059.000000 1770 88.703 91 1831 2 chr3B.!!$R3 1740
3 TraesCS3D01G090100 chr3B 432261329 432261900 571 True 348.000000 348 78.451 870 1442 1 chr3B.!!$R1 572
4 TraesCS3D01G090100 chr3A 450711732 450712772 1040 True 641.000000 641 78.326 391 1442 1 chr3A.!!$R1 1051
5 TraesCS3D01G090100 chr3A 57286950 57288605 1655 True 538.666667 1190 87.822 91 2127 3 chr3A.!!$R2 2036
6 TraesCS3D01G090100 chr6D 94764749 94765779 1030 False 682.000000 682 79.026 391 1442 1 chr6D.!!$F1 1051

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
64 65 0.250038 TCTGCGCCAGCCATAGAATC 60.25 55.0 4.18 0.0 44.33 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 1620 0.257328 TGTGCCAAAGTGAGTTCCCA 59.743 50.0 0.0 0.0 0.0 4.37 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
23 24 2.395690 GCCGCACGATCAAACTCG 59.604 61.111 0.00 0.00 44.14 4.18
24 25 2.092291 GCCGCACGATCAAACTCGA 61.092 57.895 0.00 0.00 41.12 4.04
25 26 1.421410 GCCGCACGATCAAACTCGAT 61.421 55.000 0.00 0.00 41.12 3.59
26 27 0.572590 CCGCACGATCAAACTCGATC 59.427 55.000 0.00 0.00 41.12 3.69
32 33 1.478137 GATCAAACTCGATCGGACGG 58.522 55.000 16.41 6.06 32.97 4.79
33 34 0.527817 ATCAAACTCGATCGGACGGC 60.528 55.000 16.41 0.00 0.00 5.68
34 35 1.153823 CAAACTCGATCGGACGGCT 60.154 57.895 16.41 0.00 0.00 5.52
35 36 1.139095 AAACTCGATCGGACGGCTC 59.861 57.895 16.41 0.00 0.00 4.70
36 37 2.280823 AAACTCGATCGGACGGCTCC 62.281 60.000 16.41 0.00 0.00 4.70
37 38 3.967335 CTCGATCGGACGGCTCCC 61.967 72.222 16.41 0.00 31.93 4.30
50 51 3.522731 CTCCCGAGGAGGTCTGCG 61.523 72.222 11.05 0.00 45.43 5.18
54 55 4.504916 CGAGGAGGTCTGCGCCAG 62.505 72.222 4.18 2.24 0.00 4.85
55 56 4.828925 GAGGAGGTCTGCGCCAGC 62.829 72.222 4.18 0.22 45.41 4.85
58 59 4.479993 GAGGTCTGCGCCAGCCAT 62.480 66.667 4.18 0.00 44.33 4.40
59 60 3.083349 AGGTCTGCGCCAGCCATA 61.083 61.111 4.18 0.00 44.33 2.74
60 61 2.590007 GGTCTGCGCCAGCCATAG 60.590 66.667 4.18 0.00 44.33 2.23
61 62 2.501128 GTCTGCGCCAGCCATAGA 59.499 61.111 4.18 0.00 44.33 1.98
62 63 1.153369 GTCTGCGCCAGCCATAGAA 60.153 57.895 4.18 0.00 44.33 2.10
63 64 0.533755 GTCTGCGCCAGCCATAGAAT 60.534 55.000 4.18 0.00 44.33 2.40
64 65 0.250038 TCTGCGCCAGCCATAGAATC 60.250 55.000 4.18 0.00 44.33 2.52
65 66 0.533531 CTGCGCCAGCCATAGAATCA 60.534 55.000 4.18 0.00 44.33 2.57
66 67 0.533531 TGCGCCAGCCATAGAATCAG 60.534 55.000 4.18 0.00 44.33 2.90
67 68 0.533755 GCGCCAGCCATAGAATCAGT 60.534 55.000 0.00 0.00 37.42 3.41
68 69 1.506493 CGCCAGCCATAGAATCAGTC 58.494 55.000 0.00 0.00 0.00 3.51
69 70 1.506493 GCCAGCCATAGAATCAGTCG 58.494 55.000 0.00 0.00 0.00 4.18
70 71 1.875576 GCCAGCCATAGAATCAGTCGG 60.876 57.143 0.00 0.00 0.00 4.79
71 72 1.414181 CCAGCCATAGAATCAGTCGGT 59.586 52.381 0.00 0.00 0.00 4.69
72 73 2.158900 CCAGCCATAGAATCAGTCGGTT 60.159 50.000 0.00 0.00 0.00 4.44
73 74 2.868583 CAGCCATAGAATCAGTCGGTTG 59.131 50.000 0.00 0.00 0.00 3.77
74 75 2.766263 AGCCATAGAATCAGTCGGTTGA 59.234 45.455 0.00 0.00 0.00 3.18
75 76 3.197766 AGCCATAGAATCAGTCGGTTGAA 59.802 43.478 0.00 0.00 0.00 2.69
76 77 3.938963 GCCATAGAATCAGTCGGTTGAAA 59.061 43.478 0.00 0.00 0.00 2.69
77 78 4.201822 GCCATAGAATCAGTCGGTTGAAAC 60.202 45.833 0.00 0.00 0.00 2.78
78 79 4.935205 CCATAGAATCAGTCGGTTGAAACA 59.065 41.667 0.00 0.00 0.00 2.83
79 80 5.411361 CCATAGAATCAGTCGGTTGAAACAA 59.589 40.000 0.00 0.00 0.00 2.83
80 81 6.072728 CCATAGAATCAGTCGGTTGAAACAAA 60.073 38.462 0.00 0.00 0.00 2.83
81 82 5.424121 AGAATCAGTCGGTTGAAACAAAG 57.576 39.130 0.00 0.00 0.00 2.77
82 83 4.275936 AGAATCAGTCGGTTGAAACAAAGG 59.724 41.667 0.00 0.00 0.00 3.11
83 84 2.294074 TCAGTCGGTTGAAACAAAGGG 58.706 47.619 0.00 0.00 0.00 3.95
84 85 2.021457 CAGTCGGTTGAAACAAAGGGT 58.979 47.619 0.00 0.00 0.00 4.34
85 86 2.425668 CAGTCGGTTGAAACAAAGGGTT 59.574 45.455 0.00 0.00 42.98 4.11
126 127 4.152607 ACTCGTTTTAGTCTGTACGGTC 57.847 45.455 0.64 0.00 34.93 4.79
150 151 3.274288 GCCTATATAAGCATGAGCACCC 58.726 50.000 0.00 0.00 45.49 4.61
179 183 0.319083 AGACCGGATTGTAACGTGCA 59.681 50.000 9.46 0.00 0.00 4.57
180 184 0.719465 GACCGGATTGTAACGTGCAG 59.281 55.000 9.46 0.00 0.00 4.41
278 302 0.662619 CAACACCGCACACAGATTGT 59.337 50.000 0.00 0.00 39.97 2.71
319 343 5.246656 TCCTATCTTTTGTCTCCGGTTTGTA 59.753 40.000 0.00 0.00 0.00 2.41
320 344 5.581085 CCTATCTTTTGTCTCCGGTTTGTAG 59.419 44.000 0.00 0.00 0.00 2.74
321 345 4.411256 TCTTTTGTCTCCGGTTTGTAGT 57.589 40.909 0.00 0.00 0.00 2.73
322 346 5.534207 TCTTTTGTCTCCGGTTTGTAGTA 57.466 39.130 0.00 0.00 0.00 1.82
323 347 5.535333 TCTTTTGTCTCCGGTTTGTAGTAG 58.465 41.667 0.00 0.00 0.00 2.57
324 348 3.947910 TTGTCTCCGGTTTGTAGTAGG 57.052 47.619 0.00 0.00 0.00 3.18
350 374 4.124351 TAAGCGACGACGGCAGGG 62.124 66.667 9.67 0.00 40.15 4.45
383 407 4.692475 GGCGGCCAACTACCACGT 62.692 66.667 15.62 0.00 0.00 4.49
384 408 3.419759 GCGGCCAACTACCACGTG 61.420 66.667 9.08 9.08 0.00 4.49
386 410 2.032071 GGCCAACTACCACGTGCT 59.968 61.111 10.91 0.00 0.00 4.40
387 411 2.325082 GGCCAACTACCACGTGCTG 61.325 63.158 10.91 4.56 0.00 4.41
555 686 1.508088 CGCTTTCCAATGCCCTCAC 59.492 57.895 0.00 0.00 0.00 3.51
568 699 1.202818 GCCCTCACCTTCTTTGTCACT 60.203 52.381 0.00 0.00 0.00 3.41
613 744 1.478137 CCTACTACTTCATGTCGCGC 58.522 55.000 0.00 0.00 0.00 6.86
636 767 1.084370 CCCGCCTTCGAAGTCATGAC 61.084 60.000 23.03 18.47 38.10 3.06
640 771 1.630148 CCTTCGAAGTCATGACGACC 58.370 55.000 23.03 11.75 46.69 4.79
665 796 2.892425 CCGCCAAGGACGAGATGC 60.892 66.667 0.00 0.00 45.00 3.91
667 798 1.522355 CGCCAAGGACGAGATGCAT 60.522 57.895 0.00 0.00 0.00 3.96
668 799 1.091771 CGCCAAGGACGAGATGCATT 61.092 55.000 0.00 0.00 0.00 3.56
738 872 2.231964 TCACCAAGCATCAAAGGATTGC 59.768 45.455 0.00 0.00 36.45 3.56
781 915 0.441145 GACGCACCGTATTTGTGTCC 59.559 55.000 4.98 0.00 45.02 4.02
823 957 1.648467 GCACCGGCACATTCTCCTTC 61.648 60.000 0.00 0.00 40.72 3.46
898 1032 1.215647 CCAAGGCTACTTCGACGCT 59.784 57.895 0.00 0.00 33.81 5.07
907 1041 0.448593 ACTTCGACGCTGAGCTAGAC 59.551 55.000 1.78 0.00 0.00 2.59
916 1050 0.529337 CTGAGCTAGACGCATGGGTG 60.529 60.000 21.40 7.25 42.61 4.61
966 1106 2.291043 GCCAAGTTCCCTCCCTCGA 61.291 63.158 0.00 0.00 0.00 4.04
969 1109 0.905357 CAAGTTCCCTCCCTCGACAT 59.095 55.000 0.00 0.00 0.00 3.06
1001 1141 3.081804 GGTAGCAAGTTAGCAACACCAT 58.918 45.455 0.00 0.00 34.90 3.55
1242 1382 2.690778 GGGCAAGCTGCGAATCGTT 61.691 57.895 4.07 0.00 46.21 3.85
1267 1407 0.107410 AAACACCACCTCTTGTCGCA 60.107 50.000 0.00 0.00 0.00 5.10
1269 1409 0.320771 ACACCACCTCTTGTCGCATC 60.321 55.000 0.00 0.00 0.00 3.91
1296 1436 2.760374 CAACTCTCGTCTTTTGCTCCT 58.240 47.619 0.00 0.00 0.00 3.69
1320 1460 1.202417 GCGTTCTGGATGTAGCTAGCA 60.202 52.381 18.83 0.00 0.00 3.49
1323 1463 3.462021 GTTCTGGATGTAGCTAGCAAGG 58.538 50.000 18.83 0.00 0.00 3.61
1326 1466 3.774766 TCTGGATGTAGCTAGCAAGGAAA 59.225 43.478 18.83 0.00 0.00 3.13
1387 1555 8.808529 GTTCGTCGTACTATCTGTAAGTTACTA 58.191 37.037 14.00 3.22 33.39 1.82
1456 1626 4.664150 TTGACCACTGAATTTTGGGAAC 57.336 40.909 6.63 0.42 37.18 3.62
1719 1903 7.390440 AGAATGTTGAGACGTGAAATTTATCCA 59.610 33.333 0.00 0.00 0.00 3.41
1723 1907 8.020819 TGTTGAGACGTGAAATTTATCCAAATC 58.979 33.333 0.00 0.00 33.09 2.17
1788 1972 1.304381 GCATCAAAGCTCCACCCCA 60.304 57.895 0.00 0.00 0.00 4.96
1866 2050 1.340017 TGGTGGCAGCTCAAGTTATCC 60.340 52.381 18.53 0.00 0.00 2.59
1881 2065 3.118261 AGTTATCCGCCTCAACATCACAT 60.118 43.478 0.00 0.00 0.00 3.21
1903 2087 1.069823 AGATATGCTGGAGTTCTGCCG 59.930 52.381 0.00 0.00 39.24 5.69
1927 2111 3.613494 GGAGAAACTTGGACCTCCTAC 57.387 52.381 0.00 0.00 41.40 3.18
1965 2149 3.877508 GGAAATGATCCTGTTAGTTCGGG 59.122 47.826 0.00 0.00 45.56 5.14
1969 2153 1.829222 GATCCTGTTAGTTCGGGTCCA 59.171 52.381 0.00 0.00 35.51 4.02
1971 2155 1.621814 TCCTGTTAGTTCGGGTCCAAG 59.378 52.381 0.00 0.00 35.51 3.61
1977 2161 1.420430 AGTTCGGGTCCAAGAACAGA 58.580 50.000 23.18 0.00 46.54 3.41
2003 2187 4.939052 AAACTACCTCATCACCTATCCG 57.061 45.455 0.00 0.00 0.00 4.18
2059 2251 2.237392 AGCTACTTGGGATGACCTTGAC 59.763 50.000 0.00 0.00 41.11 3.18
2065 2257 4.289672 ACTTGGGATGACCTTGACATAAGT 59.710 41.667 0.00 0.00 41.11 2.24
2066 2258 4.927267 TGGGATGACCTTGACATAAGTT 57.073 40.909 0.00 0.00 41.11 2.66
2067 2259 5.255397 TGGGATGACCTTGACATAAGTTT 57.745 39.130 0.00 0.00 41.11 2.66
2068 2260 5.640147 TGGGATGACCTTGACATAAGTTTT 58.360 37.500 0.00 0.00 41.11 2.43
2099 2291 8.362639 TCTTTCTTTCTTTTCTGATCCATTTGG 58.637 33.333 0.00 0.00 0.00 3.28
2113 2305 5.621197 TCCATTTGGACATAGTTGTTTCG 57.379 39.130 0.00 0.00 39.78 3.46
2117 2309 6.072397 CCATTTGGACATAGTTGTTTCGGTTA 60.072 38.462 0.00 0.00 35.79 2.85
2118 2310 7.362574 CCATTTGGACATAGTTGTTTCGGTTAT 60.363 37.037 0.00 0.00 35.79 1.89
2127 2319 4.041938 AGTTGTTTCGGTTATCCCCTGTTA 59.958 41.667 0.00 0.00 0.00 2.41
2128 2320 3.941573 TGTTTCGGTTATCCCCTGTTAC 58.058 45.455 0.00 0.00 0.00 2.50
2129 2321 3.583966 TGTTTCGGTTATCCCCTGTTACT 59.416 43.478 0.00 0.00 0.00 2.24
2130 2322 4.041938 TGTTTCGGTTATCCCCTGTTACTT 59.958 41.667 0.00 0.00 0.00 2.24
2131 2323 5.248020 TGTTTCGGTTATCCCCTGTTACTTA 59.752 40.000 0.00 0.00 0.00 2.24
2132 2324 5.343307 TTCGGTTATCCCCTGTTACTTAC 57.657 43.478 0.00 0.00 0.00 2.34
2133 2325 4.613437 TCGGTTATCCCCTGTTACTTACT 58.387 43.478 0.00 0.00 0.00 2.24
2134 2326 5.765510 TCGGTTATCCCCTGTTACTTACTA 58.234 41.667 0.00 0.00 0.00 1.82
2135 2327 5.594317 TCGGTTATCCCCTGTTACTTACTAC 59.406 44.000 0.00 0.00 0.00 2.73
2136 2328 5.221322 CGGTTATCCCCTGTTACTTACTACC 60.221 48.000 0.00 0.00 0.00 3.18
2137 2329 5.662657 GGTTATCCCCTGTTACTTACTACCA 59.337 44.000 0.00 0.00 0.00 3.25
2138 2330 6.328410 GGTTATCCCCTGTTACTTACTACCAT 59.672 42.308 0.00 0.00 0.00 3.55
2139 2331 7.440198 GTTATCCCCTGTTACTTACTACCATC 58.560 42.308 0.00 0.00 0.00 3.51
2140 2332 4.950361 TCCCCTGTTACTTACTACCATCA 58.050 43.478 0.00 0.00 0.00 3.07
2141 2333 4.713321 TCCCCTGTTACTTACTACCATCAC 59.287 45.833 0.00 0.00 0.00 3.06
2142 2334 4.141779 CCCCTGTTACTTACTACCATCACC 60.142 50.000 0.00 0.00 0.00 4.02
2143 2335 4.468510 CCCTGTTACTTACTACCATCACCA 59.531 45.833 0.00 0.00 0.00 4.17
2144 2336 5.395324 CCCTGTTACTTACTACCATCACCAG 60.395 48.000 0.00 0.00 0.00 4.00
2145 2337 5.080969 TGTTACTTACTACCATCACCAGC 57.919 43.478 0.00 0.00 0.00 4.85
2146 2338 4.528987 TGTTACTTACTACCATCACCAGCA 59.471 41.667 0.00 0.00 0.00 4.41
2147 2339 5.012251 TGTTACTTACTACCATCACCAGCAA 59.988 40.000 0.00 0.00 0.00 3.91
2148 2340 4.844349 ACTTACTACCATCACCAGCAAT 57.156 40.909 0.00 0.00 0.00 3.56
2149 2341 4.770795 ACTTACTACCATCACCAGCAATC 58.229 43.478 0.00 0.00 0.00 2.67
2150 2342 4.471386 ACTTACTACCATCACCAGCAATCT 59.529 41.667 0.00 0.00 0.00 2.40
2151 2343 3.272574 ACTACCATCACCAGCAATCTG 57.727 47.619 0.00 0.00 40.02 2.90
2152 2344 1.945394 CTACCATCACCAGCAATCTGC 59.055 52.381 0.00 0.00 45.46 4.26
2164 2356 3.582444 GCAATCTGCTCAGTACGATTG 57.418 47.619 12.08 12.08 43.31 2.67
2165 2357 2.932614 GCAATCTGCTCAGTACGATTGT 59.067 45.455 15.69 0.00 42.74 2.71
2166 2358 3.242220 GCAATCTGCTCAGTACGATTGTG 60.242 47.826 15.69 1.14 42.74 3.33
2167 2359 4.176271 CAATCTGCTCAGTACGATTGTGA 58.824 43.478 9.48 0.00 38.45 3.58
2168 2360 3.217599 TCTGCTCAGTACGATTGTGAC 57.782 47.619 0.00 0.00 0.00 3.67
2169 2361 2.094700 TCTGCTCAGTACGATTGTGACC 60.095 50.000 0.00 0.00 0.00 4.02
2170 2362 1.616374 TGCTCAGTACGATTGTGACCA 59.384 47.619 0.00 0.00 0.00 4.02
2171 2363 2.263077 GCTCAGTACGATTGTGACCAG 58.737 52.381 0.00 0.00 0.00 4.00
2172 2364 2.263077 CTCAGTACGATTGTGACCAGC 58.737 52.381 0.00 0.00 0.00 4.85
2173 2365 1.893137 TCAGTACGATTGTGACCAGCT 59.107 47.619 0.00 0.00 0.00 4.24
2174 2366 2.299013 TCAGTACGATTGTGACCAGCTT 59.701 45.455 0.00 0.00 0.00 3.74
2175 2367 2.413112 CAGTACGATTGTGACCAGCTTG 59.587 50.000 0.00 0.00 0.00 4.01
2176 2368 1.732259 GTACGATTGTGACCAGCTTGG 59.268 52.381 0.00 1.16 45.02 3.61
2177 2369 0.606401 ACGATTGTGACCAGCTTGGG 60.606 55.000 7.06 0.00 43.37 4.12
2178 2370 0.606401 CGATTGTGACCAGCTTGGGT 60.606 55.000 0.00 0.00 43.37 4.51
2179 2371 1.338674 CGATTGTGACCAGCTTGGGTA 60.339 52.381 0.00 0.00 43.37 3.69
2180 2372 2.790433 GATTGTGACCAGCTTGGGTAA 58.210 47.619 0.00 0.00 43.37 2.85
2181 2373 2.270352 TTGTGACCAGCTTGGGTAAG 57.730 50.000 0.00 0.00 43.37 2.34
2182 2374 1.429930 TGTGACCAGCTTGGGTAAGA 58.570 50.000 0.00 0.00 43.37 2.10
2183 2375 1.771854 TGTGACCAGCTTGGGTAAGAA 59.228 47.619 0.00 0.00 43.37 2.52
2184 2376 2.375174 TGTGACCAGCTTGGGTAAGAAT 59.625 45.455 0.00 0.00 43.37 2.40
2185 2377 2.749621 GTGACCAGCTTGGGTAAGAATG 59.250 50.000 0.00 0.00 43.37 2.67
2186 2378 1.745653 GACCAGCTTGGGTAAGAATGC 59.254 52.381 0.00 0.00 43.37 3.56
2187 2379 1.355720 ACCAGCTTGGGTAAGAATGCT 59.644 47.619 0.00 0.00 43.37 3.79
2188 2380 2.225117 ACCAGCTTGGGTAAGAATGCTT 60.225 45.455 0.00 0.00 43.37 3.91
2189 2381 2.424956 CCAGCTTGGGTAAGAATGCTTC 59.575 50.000 0.00 0.00 35.92 3.86
2190 2382 3.084039 CAGCTTGGGTAAGAATGCTTCA 58.916 45.455 0.00 0.00 35.92 3.02
2191 2383 3.128242 CAGCTTGGGTAAGAATGCTTCAG 59.872 47.826 0.00 0.00 35.92 3.02
2192 2384 3.009473 AGCTTGGGTAAGAATGCTTCAGA 59.991 43.478 0.00 0.00 35.92 3.27
2193 2385 3.758554 GCTTGGGTAAGAATGCTTCAGAA 59.241 43.478 0.00 0.00 35.92 3.02
2194 2386 4.218417 GCTTGGGTAAGAATGCTTCAGAAA 59.782 41.667 0.00 0.00 35.92 2.52
2195 2387 5.278957 GCTTGGGTAAGAATGCTTCAGAAAA 60.279 40.000 0.00 0.00 35.92 2.29
2196 2388 6.723298 TTGGGTAAGAATGCTTCAGAAAAA 57.277 33.333 0.00 0.00 35.56 1.94
2220 2412 9.547279 AAAAAGGATGGAGGTAATATGAGTTTT 57.453 29.630 0.00 0.00 0.00 2.43
2221 2413 8.753497 AAAGGATGGAGGTAATATGAGTTTTC 57.247 34.615 0.00 0.00 0.00 2.29
2222 2414 7.698163 AGGATGGAGGTAATATGAGTTTTCT 57.302 36.000 0.00 0.00 0.00 2.52
2223 2415 7.512992 AGGATGGAGGTAATATGAGTTTTCTG 58.487 38.462 0.00 0.00 0.00 3.02
2224 2416 6.205658 GGATGGAGGTAATATGAGTTTTCTGC 59.794 42.308 0.00 0.00 0.00 4.26
2225 2417 5.437060 TGGAGGTAATATGAGTTTTCTGCC 58.563 41.667 0.00 0.00 0.00 4.85
2226 2418 5.191722 TGGAGGTAATATGAGTTTTCTGCCT 59.808 40.000 0.00 0.00 0.00 4.75
2227 2419 5.760743 GGAGGTAATATGAGTTTTCTGCCTC 59.239 44.000 0.00 0.00 38.34 4.70
2228 2420 5.360591 AGGTAATATGAGTTTTCTGCCTCG 58.639 41.667 0.00 0.00 0.00 4.63
2229 2421 4.511826 GGTAATATGAGTTTTCTGCCTCGG 59.488 45.833 0.00 0.00 0.00 4.63
2230 2422 2.024176 TATGAGTTTTCTGCCTCGGC 57.976 50.000 0.00 0.00 42.35 5.54
2231 2423 0.678048 ATGAGTTTTCTGCCTCGGCC 60.678 55.000 5.33 0.00 41.09 6.13
2232 2424 1.302511 GAGTTTTCTGCCTCGGCCA 60.303 57.895 2.24 0.00 41.09 5.36
2233 2425 1.578206 GAGTTTTCTGCCTCGGCCAC 61.578 60.000 2.24 0.00 41.09 5.01
2234 2426 2.668212 TTTTCTGCCTCGGCCACG 60.668 61.111 2.24 0.00 41.09 4.94
2245 2437 2.004583 TCGGCCACGATAAGAAGTTG 57.995 50.000 2.24 0.00 45.59 3.16
2246 2438 1.274167 TCGGCCACGATAAGAAGTTGT 59.726 47.619 2.24 0.00 45.59 3.32
2247 2439 1.659098 CGGCCACGATAAGAAGTTGTC 59.341 52.381 2.24 0.00 44.60 3.18
2248 2440 2.695359 GGCCACGATAAGAAGTTGTCA 58.305 47.619 0.00 0.00 0.00 3.58
2249 2441 2.415512 GGCCACGATAAGAAGTTGTCAC 59.584 50.000 0.00 0.00 0.00 3.67
2250 2442 3.064207 GCCACGATAAGAAGTTGTCACA 58.936 45.455 0.00 0.00 0.00 3.58
2251 2443 3.684788 GCCACGATAAGAAGTTGTCACAT 59.315 43.478 0.00 0.00 0.00 3.21
2252 2444 4.436050 GCCACGATAAGAAGTTGTCACATG 60.436 45.833 0.00 0.00 0.00 3.21
2253 2445 4.690748 CCACGATAAGAAGTTGTCACATGT 59.309 41.667 0.00 0.00 0.00 3.21
2254 2446 5.179368 CCACGATAAGAAGTTGTCACATGTT 59.821 40.000 0.00 0.00 0.00 2.71
2255 2447 6.073369 CACGATAAGAAGTTGTCACATGTTG 58.927 40.000 0.00 0.00 0.00 3.33
2256 2448 5.179368 ACGATAAGAAGTTGTCACATGTTGG 59.821 40.000 0.00 0.00 0.00 3.77
2257 2449 3.715628 AAGAAGTTGTCACATGTTGGC 57.284 42.857 0.00 0.00 0.00 4.52
2258 2450 1.956477 AGAAGTTGTCACATGTTGGCC 59.044 47.619 0.00 0.00 0.00 5.36
2259 2451 1.000274 GAAGTTGTCACATGTTGGCCC 60.000 52.381 0.00 0.00 0.00 5.80
2260 2452 0.827507 AGTTGTCACATGTTGGCCCC 60.828 55.000 0.00 0.00 0.00 5.80
2261 2453 1.112315 GTTGTCACATGTTGGCCCCA 61.112 55.000 0.00 0.00 0.00 4.96
2262 2454 0.397675 TTGTCACATGTTGGCCCCAA 60.398 50.000 0.00 0.00 0.00 4.12
2263 2455 0.178938 TGTCACATGTTGGCCCCAAT 60.179 50.000 0.00 0.00 38.28 3.16
2264 2456 0.247185 GTCACATGTTGGCCCCAATG 59.753 55.000 0.00 3.47 38.28 2.82
2265 2457 0.113972 TCACATGTTGGCCCCAATGA 59.886 50.000 13.81 9.65 38.28 2.57
2266 2458 1.196911 CACATGTTGGCCCCAATGAT 58.803 50.000 13.81 0.00 38.28 2.45
2267 2459 1.555992 CACATGTTGGCCCCAATGATT 59.444 47.619 13.81 0.00 38.28 2.57
2268 2460 1.555992 ACATGTTGGCCCCAATGATTG 59.444 47.619 13.81 0.00 38.28 2.67
2283 2475 7.587037 CCAATGATTGGGTACAATAATCAGT 57.413 36.000 16.42 14.45 46.89 3.41
2284 2476 7.428020 CCAATGATTGGGTACAATAATCAGTG 58.572 38.462 24.14 24.14 46.89 3.66
2287 2479 9.425248 AATGATTGGGTACAATAATCAGTGATT 57.575 29.630 21.57 21.57 46.89 2.57
2289 2481 9.913310 TGATTGGGTACAATAATCAGTGATTAA 57.087 29.630 25.41 11.02 46.89 1.40
2292 2484 9.913310 TTGGGTACAATAATCAGTGATTAATGA 57.087 29.630 33.04 20.29 37.51 2.57
2293 2485 9.337396 TGGGTACAATAATCAGTGATTAATGAC 57.663 33.333 33.04 26.30 37.51 3.06
2294 2486 8.784043 GGGTACAATAATCAGTGATTAATGACC 58.216 37.037 33.04 30.50 37.51 4.02
2295 2487 9.337396 GGTACAATAATCAGTGATTAATGACCA 57.663 33.333 33.04 20.53 37.51 4.02
2299 2491 9.188588 CAATAATCAGTGATTAATGACCAATGC 57.811 33.333 26.69 0.00 37.51 3.56
2300 2492 4.880886 TCAGTGATTAATGACCAATGCG 57.119 40.909 1.04 0.00 0.00 4.73
2301 2493 4.512484 TCAGTGATTAATGACCAATGCGA 58.488 39.130 1.04 0.00 0.00 5.10
2302 2494 4.571984 TCAGTGATTAATGACCAATGCGAG 59.428 41.667 1.04 0.00 0.00 5.03
2303 2495 3.313526 AGTGATTAATGACCAATGCGAGC 59.686 43.478 1.04 0.00 0.00 5.03
2304 2496 3.313526 GTGATTAATGACCAATGCGAGCT 59.686 43.478 0.00 0.00 0.00 4.09
2305 2497 4.511454 GTGATTAATGACCAATGCGAGCTA 59.489 41.667 0.00 0.00 0.00 3.32
2306 2498 4.751600 TGATTAATGACCAATGCGAGCTAG 59.248 41.667 0.00 0.00 0.00 3.42
2307 2499 1.959042 AATGACCAATGCGAGCTAGG 58.041 50.000 0.00 0.00 0.00 3.02
2308 2500 0.533755 ATGACCAATGCGAGCTAGGC 60.534 55.000 2.37 2.37 0.00 3.93
2309 2501 1.153369 GACCAATGCGAGCTAGGCA 60.153 57.895 13.65 13.65 45.71 4.75
2314 2506 2.104928 TGCGAGCTAGGCATCACG 59.895 61.111 7.79 0.00 35.04 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.787676 TTTGATCGTGCGGCGCTG 61.788 61.111 33.26 24.29 41.07 5.18
3 4 3.788766 GTTTGATCGTGCGGCGCT 61.789 61.111 33.26 13.02 41.07 5.92
4 5 3.702334 GAGTTTGATCGTGCGGCGC 62.702 63.158 27.44 27.44 41.07 6.53
5 6 2.395690 GAGTTTGATCGTGCGGCG 59.604 61.111 0.51 0.51 43.01 6.46
6 7 1.421410 ATCGAGTTTGATCGTGCGGC 61.421 55.000 0.00 0.00 43.20 6.53
7 8 0.572590 GATCGAGTTTGATCGTGCGG 59.427 55.000 0.00 0.00 43.20 5.69
13 14 1.478137 CCGTCCGATCGAGTTTGATC 58.522 55.000 18.66 0.07 41.10 2.92
14 15 0.527817 GCCGTCCGATCGAGTTTGAT 60.528 55.000 18.66 0.00 0.00 2.57
15 16 1.153901 GCCGTCCGATCGAGTTTGA 60.154 57.895 18.66 1.16 0.00 2.69
16 17 1.140407 GAGCCGTCCGATCGAGTTTG 61.140 60.000 18.66 0.00 0.00 2.93
17 18 1.139095 GAGCCGTCCGATCGAGTTT 59.861 57.895 18.66 0.00 0.00 2.66
18 19 2.772691 GGAGCCGTCCGATCGAGTT 61.773 63.158 18.66 0.00 31.37 3.01
19 20 3.210528 GGAGCCGTCCGATCGAGT 61.211 66.667 18.66 0.00 31.37 4.18
20 21 3.967335 GGGAGCCGTCCGATCGAG 61.967 72.222 18.66 6.99 45.05 4.04
37 38 4.504916 CTGGCGCAGACCTCCTCG 62.505 72.222 10.83 0.00 32.44 4.63
38 39 4.828925 GCTGGCGCAGACCTCCTC 62.829 72.222 10.83 0.00 32.44 3.71
41 42 2.985512 CTATGGCTGGCGCAGACCTC 62.986 65.000 10.83 0.00 39.07 3.85
42 43 3.083349 TATGGCTGGCGCAGACCT 61.083 61.111 10.83 2.59 39.07 3.85
43 44 2.590007 CTATGGCTGGCGCAGACC 60.590 66.667 10.83 7.38 39.07 3.85
44 45 0.533755 ATTCTATGGCTGGCGCAGAC 60.534 55.000 10.83 7.84 40.49 3.51
45 46 0.250038 GATTCTATGGCTGGCGCAGA 60.250 55.000 10.83 0.00 38.10 4.26
46 47 0.533531 TGATTCTATGGCTGGCGCAG 60.534 55.000 10.83 6.07 38.10 5.18
47 48 0.533531 CTGATTCTATGGCTGGCGCA 60.534 55.000 10.83 0.00 38.10 6.09
48 49 0.533755 ACTGATTCTATGGCTGGCGC 60.534 55.000 0.00 0.00 0.00 6.53
49 50 1.506493 GACTGATTCTATGGCTGGCG 58.494 55.000 0.00 0.00 0.00 5.69
50 51 1.506493 CGACTGATTCTATGGCTGGC 58.494 55.000 0.00 0.00 0.00 4.85
51 52 1.414181 ACCGACTGATTCTATGGCTGG 59.586 52.381 0.00 0.00 0.00 4.85
52 53 2.868583 CAACCGACTGATTCTATGGCTG 59.131 50.000 0.00 0.00 0.00 4.85
53 54 2.766263 TCAACCGACTGATTCTATGGCT 59.234 45.455 0.00 0.00 0.00 4.75
54 55 3.179443 TCAACCGACTGATTCTATGGC 57.821 47.619 0.00 0.00 0.00 4.40
55 56 4.935205 TGTTTCAACCGACTGATTCTATGG 59.065 41.667 0.00 0.00 0.00 2.74
56 57 6.480524 TTGTTTCAACCGACTGATTCTATG 57.519 37.500 0.00 0.00 0.00 2.23
57 58 6.149474 CCTTTGTTTCAACCGACTGATTCTAT 59.851 38.462 0.00 0.00 0.00 1.98
58 59 5.468746 CCTTTGTTTCAACCGACTGATTCTA 59.531 40.000 0.00 0.00 0.00 2.10
59 60 4.275936 CCTTTGTTTCAACCGACTGATTCT 59.724 41.667 0.00 0.00 0.00 2.40
60 61 4.537015 CCTTTGTTTCAACCGACTGATTC 58.463 43.478 0.00 0.00 0.00 2.52
61 62 3.317993 CCCTTTGTTTCAACCGACTGATT 59.682 43.478 0.00 0.00 0.00 2.57
62 63 2.884639 CCCTTTGTTTCAACCGACTGAT 59.115 45.455 0.00 0.00 0.00 2.90
63 64 2.294074 CCCTTTGTTTCAACCGACTGA 58.706 47.619 0.00 0.00 0.00 3.41
64 65 2.021457 ACCCTTTGTTTCAACCGACTG 58.979 47.619 0.00 0.00 0.00 3.51
65 66 2.430248 ACCCTTTGTTTCAACCGACT 57.570 45.000 0.00 0.00 0.00 4.18
66 67 3.513680 AAACCCTTTGTTTCAACCGAC 57.486 42.857 0.00 0.00 43.74 4.79
67 68 4.021368 TGAAAAACCCTTTGTTTCAACCGA 60.021 37.500 0.00 0.00 46.39 4.69
68 69 4.246458 TGAAAAACCCTTTGTTTCAACCG 58.754 39.130 0.00 0.00 46.39 4.44
69 70 7.551262 ACTTATGAAAAACCCTTTGTTTCAACC 59.449 33.333 2.52 0.00 46.39 3.77
70 71 8.487313 ACTTATGAAAAACCCTTTGTTTCAAC 57.513 30.769 2.52 0.00 46.39 3.18
108 109 2.653584 CACGACCGTACAGACTAAAACG 59.346 50.000 0.00 0.00 35.20 3.60
126 127 3.369147 GTGCTCATGCTTATATAGGCACG 59.631 47.826 20.50 13.64 41.19 5.34
150 151 2.159282 ACAATCCGGTCTACAACGCTAG 60.159 50.000 0.00 0.00 0.00 3.42
179 183 6.944862 AGTATTGTGCCTTTTTCAATCTCTCT 59.055 34.615 0.00 0.00 34.35 3.10
180 184 7.025963 CAGTATTGTGCCTTTTTCAATCTCTC 58.974 38.462 0.00 0.00 34.35 3.20
350 374 3.151022 CCTGACCCTCCTCCTCGC 61.151 72.222 0.00 0.00 0.00 5.03
387 411 2.886124 GTGACGCTAGCCGGAAGC 60.886 66.667 16.94 16.94 42.52 3.86
542 673 1.075601 AAGAAGGTGAGGGCATTGGA 58.924 50.000 0.00 0.00 0.00 3.53
543 674 1.547372 CAAAGAAGGTGAGGGCATTGG 59.453 52.381 0.00 0.00 0.00 3.16
555 686 1.466167 CATCGGCAGTGACAAAGAAGG 59.534 52.381 0.00 0.00 0.00 3.46
568 699 0.795698 CGAACAACATGTCATCGGCA 59.204 50.000 15.94 0.00 29.72 5.69
613 744 3.372554 GACTTCGAAGGCGGGAGGG 62.373 68.421 27.86 1.90 38.28 4.30
738 872 1.146263 GGGTGAAGGGCGTAGGATG 59.854 63.158 0.00 0.00 0.00 3.51
808 942 0.389817 TGTCGAAGGAGAATGTGCCG 60.390 55.000 0.00 0.00 0.00 5.69
814 948 1.403679 CTCTCGCTGTCGAAGGAGAAT 59.596 52.381 0.00 0.00 44.98 2.40
907 1041 4.108299 TGTAGCCCCACCCATGCG 62.108 66.667 0.00 0.00 0.00 4.73
966 1106 1.153489 CTACCGCTGCTGCTGATGT 60.153 57.895 13.70 8.37 36.97 3.06
969 1109 3.238755 TTGCTACCGCTGCTGCTGA 62.239 57.895 13.70 0.00 36.97 4.26
980 1120 2.500229 TGGTGTTGCTAACTTGCTACC 58.500 47.619 0.00 0.00 37.76 3.18
981 1121 3.670627 GCATGGTGTTGCTAACTTGCTAC 60.671 47.826 0.00 0.00 39.57 3.58
982 1122 2.487762 GCATGGTGTTGCTAACTTGCTA 59.512 45.455 0.00 0.00 39.57 3.49
986 1126 1.270550 GCTGCATGGTGTTGCTAACTT 59.729 47.619 0.00 0.00 43.18 2.66
987 1127 0.883833 GCTGCATGGTGTTGCTAACT 59.116 50.000 0.00 0.00 43.18 2.24
988 1128 0.597568 TGCTGCATGGTGTTGCTAAC 59.402 50.000 0.00 0.00 43.18 2.34
989 1129 0.883153 CTGCTGCATGGTGTTGCTAA 59.117 50.000 1.31 0.00 43.18 3.09
1015 1155 0.465705 TCCTTGGCTATCTTCCAGCG 59.534 55.000 0.00 0.00 40.05 5.18
1242 1382 2.238646 ACAAGAGGTGGTGTTTCTGTCA 59.761 45.455 0.00 0.00 0.00 3.58
1296 1436 2.100197 AGCTACATCCAGAACGCTACA 58.900 47.619 0.00 0.00 0.00 2.74
1331 1471 7.682741 GCCTCTATACTTCACATACGGTTACAA 60.683 40.741 0.00 0.00 0.00 2.41
1333 1499 6.016443 AGCCTCTATACTTCACATACGGTTAC 60.016 42.308 0.00 0.00 0.00 2.50
1338 1504 7.147143 ACATAGCCTCTATACTTCACATACG 57.853 40.000 0.00 0.00 0.00 3.06
1345 1511 5.049543 ACGACGAACATAGCCTCTATACTTC 60.050 44.000 0.00 0.00 0.00 3.01
1353 1519 4.451774 AGATAGTACGACGAACATAGCCTC 59.548 45.833 0.00 0.00 0.00 4.70
1387 1555 7.004691 GGCCTTGTATATAGAAAAATGGAGGT 58.995 38.462 0.00 0.00 0.00 3.85
1442 1612 5.291971 CCAAAGTGAGTTCCCAAAATTCAG 58.708 41.667 0.00 0.00 0.00 3.02
1446 1616 3.037549 TGCCAAAGTGAGTTCCCAAAAT 58.962 40.909 0.00 0.00 0.00 1.82
1450 1620 0.257328 TGTGCCAAAGTGAGTTCCCA 59.743 50.000 0.00 0.00 0.00 4.37
1456 1626 0.524862 GCTCCATGTGCCAAAGTGAG 59.475 55.000 0.00 0.00 0.00 3.51
1686 1862 2.866156 ACGTCTCAACATTCTGTGTGTG 59.134 45.455 0.00 0.00 41.14 3.82
1692 1868 7.693951 GGATAAATTTCACGTCTCAACATTCTG 59.306 37.037 0.00 0.00 0.00 3.02
1705 1881 7.807433 TGTCACAAGATTTGGATAAATTTCACG 59.193 33.333 0.00 0.00 36.66 4.35
1758 1942 3.062042 GCTTTGATGCTCCTGGTTTTTG 58.938 45.455 0.00 0.00 0.00 2.44
1780 1964 3.230134 CTCAAAATCAAAGTGGGGTGGA 58.770 45.455 0.00 0.00 0.00 4.02
1788 1972 5.083533 TGGTTTGTGCTCAAAATCAAAGT 57.916 34.783 15.02 0.00 43.78 2.66
1866 2050 2.014335 TCTGATGTGATGTTGAGGCG 57.986 50.000 0.00 0.00 0.00 5.52
1881 2065 2.103771 GGCAGAACTCCAGCATATCTGA 59.896 50.000 5.34 0.00 45.72 3.27
1903 2087 2.155279 GAGGTCCAAGTTTCTCCTTGC 58.845 52.381 0.00 0.00 40.40 4.01
1916 2100 2.838202 GGAATGACAAGTAGGAGGTCCA 59.162 50.000 0.00 0.00 38.89 4.02
1919 2103 3.772025 CTGAGGAATGACAAGTAGGAGGT 59.228 47.826 0.00 0.00 0.00 3.85
1962 2146 4.695560 GGTCTGTTCTTGGACCCG 57.304 61.111 0.00 0.00 44.35 5.28
1965 2149 4.983671 AGTTTTTGGTCTGTTCTTGGAC 57.016 40.909 0.00 0.00 0.00 4.02
1969 2153 5.751586 TGAGGTAGTTTTTGGTCTGTTCTT 58.248 37.500 0.00 0.00 0.00 2.52
1971 2155 5.763204 TGATGAGGTAGTTTTTGGTCTGTTC 59.237 40.000 0.00 0.00 0.00 3.18
1977 2161 4.724279 AGGTGATGAGGTAGTTTTTGGT 57.276 40.909 0.00 0.00 0.00 3.67
2029 2215 1.902508 TCCCAAGTAGCTGTTCAGGAG 59.097 52.381 0.00 0.00 0.00 3.69
2030 2216 2.024176 TCCCAAGTAGCTGTTCAGGA 57.976 50.000 0.00 0.00 0.00 3.86
2099 2291 4.573607 GGGGATAACCGAAACAACTATGTC 59.426 45.833 0.00 0.00 38.54 3.06
2113 2305 5.662657 TGGTAGTAAGTAACAGGGGATAACC 59.337 44.000 0.00 0.00 39.11 2.85
2117 2309 5.365895 GTGATGGTAGTAAGTAACAGGGGAT 59.634 44.000 0.00 0.00 29.47 3.85
2118 2310 4.713321 GTGATGGTAGTAAGTAACAGGGGA 59.287 45.833 0.00 0.00 29.47 4.81
2127 2319 4.471386 AGATTGCTGGTGATGGTAGTAAGT 59.529 41.667 0.00 0.00 0.00 2.24
2128 2320 4.813161 CAGATTGCTGGTGATGGTAGTAAG 59.187 45.833 0.00 0.00 38.51 2.34
2129 2321 4.769688 CAGATTGCTGGTGATGGTAGTAA 58.230 43.478 0.00 0.00 38.51 2.24
2130 2322 3.432186 GCAGATTGCTGGTGATGGTAGTA 60.432 47.826 0.00 0.00 42.53 1.82
2131 2323 2.681976 GCAGATTGCTGGTGATGGTAGT 60.682 50.000 0.00 0.00 42.53 2.73
2132 2324 1.945394 GCAGATTGCTGGTGATGGTAG 59.055 52.381 0.00 0.00 42.53 3.18
2133 2325 2.042686 GCAGATTGCTGGTGATGGTA 57.957 50.000 0.00 0.00 42.53 3.25
2134 2326 2.877975 GCAGATTGCTGGTGATGGT 58.122 52.632 0.00 0.00 42.53 3.55
2144 2336 3.582444 CAATCGTACTGAGCAGATTGC 57.418 47.619 4.21 0.00 41.96 3.56
2146 2338 4.177026 GTCACAATCGTACTGAGCAGATT 58.823 43.478 4.21 0.00 34.06 2.40
2147 2339 3.429547 GGTCACAATCGTACTGAGCAGAT 60.430 47.826 4.21 0.00 33.51 2.90
2148 2340 2.094700 GGTCACAATCGTACTGAGCAGA 60.095 50.000 4.21 0.00 33.51 4.26
2149 2341 2.263077 GGTCACAATCGTACTGAGCAG 58.737 52.381 6.42 0.00 33.51 4.24
2150 2342 1.616374 TGGTCACAATCGTACTGAGCA 59.384 47.619 9.19 9.19 39.48 4.26
2151 2343 2.263077 CTGGTCACAATCGTACTGAGC 58.737 52.381 4.74 4.74 33.83 4.26
2152 2344 2.094494 AGCTGGTCACAATCGTACTGAG 60.094 50.000 0.00 0.00 0.00 3.35
2153 2345 1.893137 AGCTGGTCACAATCGTACTGA 59.107 47.619 0.00 0.00 0.00 3.41
2154 2346 2.370281 AGCTGGTCACAATCGTACTG 57.630 50.000 0.00 0.00 0.00 2.74
2155 2347 2.612972 CCAAGCTGGTCACAATCGTACT 60.613 50.000 0.00 0.00 31.35 2.73
2156 2348 1.732259 CCAAGCTGGTCACAATCGTAC 59.268 52.381 0.00 0.00 31.35 3.67
2157 2349 1.338674 CCCAAGCTGGTCACAATCGTA 60.339 52.381 0.00 0.00 35.17 3.43
2158 2350 0.606401 CCCAAGCTGGTCACAATCGT 60.606 55.000 0.00 0.00 35.17 3.73
2159 2351 0.606401 ACCCAAGCTGGTCACAATCG 60.606 55.000 0.00 0.00 35.17 3.34
2160 2352 2.489938 TACCCAAGCTGGTCACAATC 57.510 50.000 0.00 0.00 39.91 2.67
2161 2353 2.375174 TCTTACCCAAGCTGGTCACAAT 59.625 45.455 0.00 0.00 39.91 2.71
2162 2354 1.771854 TCTTACCCAAGCTGGTCACAA 59.228 47.619 0.00 0.00 39.91 3.33
2163 2355 1.429930 TCTTACCCAAGCTGGTCACA 58.570 50.000 0.00 0.00 39.91 3.58
2164 2356 2.561478 TTCTTACCCAAGCTGGTCAC 57.439 50.000 0.00 0.00 39.91 3.67
2165 2357 2.879756 GCATTCTTACCCAAGCTGGTCA 60.880 50.000 0.00 0.00 39.91 4.02
2166 2358 1.745653 GCATTCTTACCCAAGCTGGTC 59.254 52.381 0.00 0.00 39.91 4.02
2167 2359 1.355720 AGCATTCTTACCCAAGCTGGT 59.644 47.619 0.82 0.82 42.62 4.00
2168 2360 2.134789 AGCATTCTTACCCAAGCTGG 57.865 50.000 0.00 0.00 37.25 4.85
2169 2361 3.772060 GAAGCATTCTTACCCAAGCTG 57.228 47.619 0.00 0.00 43.23 4.24
2194 2386 9.547279 AAAACTCATATTACCTCCATCCTTTTT 57.453 29.630 0.00 0.00 0.00 1.94
2195 2387 9.190317 GAAAACTCATATTACCTCCATCCTTTT 57.810 33.333 0.00 0.00 0.00 2.27
2196 2388 8.560903 AGAAAACTCATATTACCTCCATCCTTT 58.439 33.333 0.00 0.00 0.00 3.11
2197 2389 7.995488 CAGAAAACTCATATTACCTCCATCCTT 59.005 37.037 0.00 0.00 0.00 3.36
2198 2390 7.512992 CAGAAAACTCATATTACCTCCATCCT 58.487 38.462 0.00 0.00 0.00 3.24
2199 2391 6.205658 GCAGAAAACTCATATTACCTCCATCC 59.794 42.308 0.00 0.00 0.00 3.51
2200 2392 6.205658 GGCAGAAAACTCATATTACCTCCATC 59.794 42.308 0.00 0.00 0.00 3.51
2201 2393 6.064717 GGCAGAAAACTCATATTACCTCCAT 58.935 40.000 0.00 0.00 0.00 3.41
2202 2394 5.191722 AGGCAGAAAACTCATATTACCTCCA 59.808 40.000 0.00 0.00 0.00 3.86
2203 2395 5.685728 AGGCAGAAAACTCATATTACCTCC 58.314 41.667 0.00 0.00 0.00 4.30
2204 2396 5.463724 CGAGGCAGAAAACTCATATTACCTC 59.536 44.000 0.00 0.00 37.26 3.85
2205 2397 5.360591 CGAGGCAGAAAACTCATATTACCT 58.639 41.667 0.00 0.00 33.36 3.08
2206 2398 4.511826 CCGAGGCAGAAAACTCATATTACC 59.488 45.833 0.00 0.00 33.36 2.85
2207 2399 4.024809 GCCGAGGCAGAAAACTCATATTAC 60.025 45.833 9.58 0.00 41.49 1.89
2208 2400 4.127171 GCCGAGGCAGAAAACTCATATTA 58.873 43.478 9.58 0.00 41.49 0.98
2209 2401 2.945668 GCCGAGGCAGAAAACTCATATT 59.054 45.455 9.58 0.00 41.49 1.28
2210 2402 2.565841 GCCGAGGCAGAAAACTCATAT 58.434 47.619 9.58 0.00 41.49 1.78
2211 2403 1.406887 GGCCGAGGCAGAAAACTCATA 60.407 52.381 16.65 0.00 44.11 2.15
2212 2404 0.678048 GGCCGAGGCAGAAAACTCAT 60.678 55.000 16.65 0.00 44.11 2.90
2213 2405 1.302511 GGCCGAGGCAGAAAACTCA 60.303 57.895 16.65 0.00 44.11 3.41
2214 2406 1.302511 TGGCCGAGGCAGAAAACTC 60.303 57.895 16.65 0.00 44.11 3.01
2215 2407 1.600916 GTGGCCGAGGCAGAAAACT 60.601 57.895 16.65 0.00 44.11 2.66
2216 2408 2.954611 GTGGCCGAGGCAGAAAAC 59.045 61.111 16.65 2.36 44.11 2.43
2217 2409 2.668212 CGTGGCCGAGGCAGAAAA 60.668 61.111 16.65 0.00 44.11 2.29
2218 2410 3.621805 TCGTGGCCGAGGCAGAAA 61.622 61.111 16.65 0.00 44.11 2.52
2227 2419 1.659098 GACAACTTCTTATCGTGGCCG 59.341 52.381 0.00 0.00 0.00 6.13
2228 2420 2.415512 GTGACAACTTCTTATCGTGGCC 59.584 50.000 0.00 0.00 0.00 5.36
2229 2421 3.064207 TGTGACAACTTCTTATCGTGGC 58.936 45.455 0.00 0.00 0.00 5.01
2230 2422 4.690748 ACATGTGACAACTTCTTATCGTGG 59.309 41.667 0.00 0.00 0.00 4.94
2231 2423 5.845985 ACATGTGACAACTTCTTATCGTG 57.154 39.130 0.00 0.00 0.00 4.35
2232 2424 5.179368 CCAACATGTGACAACTTCTTATCGT 59.821 40.000 0.00 0.00 0.00 3.73
2233 2425 5.621422 CCAACATGTGACAACTTCTTATCG 58.379 41.667 0.00 0.00 0.00 2.92
2234 2426 5.393962 GCCAACATGTGACAACTTCTTATC 58.606 41.667 0.00 0.00 0.00 1.75
2235 2427 4.218417 GGCCAACATGTGACAACTTCTTAT 59.782 41.667 0.00 0.00 0.00 1.73
2236 2428 3.568007 GGCCAACATGTGACAACTTCTTA 59.432 43.478 0.00 0.00 0.00 2.10
2237 2429 2.362077 GGCCAACATGTGACAACTTCTT 59.638 45.455 0.00 0.00 0.00 2.52
2238 2430 1.956477 GGCCAACATGTGACAACTTCT 59.044 47.619 0.00 0.00 0.00 2.85
2239 2431 1.000274 GGGCCAACATGTGACAACTTC 60.000 52.381 4.39 0.00 0.00 3.01
2240 2432 1.039856 GGGCCAACATGTGACAACTT 58.960 50.000 4.39 0.00 0.00 2.66
2241 2433 0.827507 GGGGCCAACATGTGACAACT 60.828 55.000 4.39 0.00 0.00 3.16
2242 2434 1.112315 TGGGGCCAACATGTGACAAC 61.112 55.000 4.39 0.00 0.00 3.32
2243 2435 0.397675 TTGGGGCCAACATGTGACAA 60.398 50.000 4.39 0.00 0.00 3.18
2244 2436 0.178938 ATTGGGGCCAACATGTGACA 60.179 50.000 4.39 0.00 38.88 3.58
2245 2437 0.247185 CATTGGGGCCAACATGTGAC 59.753 55.000 4.39 0.00 38.88 3.67
2246 2438 0.113972 TCATTGGGGCCAACATGTGA 59.886 50.000 4.39 7.99 38.88 3.58
2247 2439 1.196911 ATCATTGGGGCCAACATGTG 58.803 50.000 4.39 5.73 38.88 3.21
2248 2440 1.555992 CAATCATTGGGGCCAACATGT 59.444 47.619 4.39 0.00 38.88 3.21
2249 2441 2.319136 CAATCATTGGGGCCAACATG 57.681 50.000 4.39 4.04 38.88 3.21
2260 2452 8.224389 TCACTGATTATTGTACCCAATCATTG 57.776 34.615 16.83 16.83 41.50 2.82
2261 2453 9.425248 AATCACTGATTATTGTACCCAATCATT 57.575 29.630 2.17 6.38 41.50 2.57
2263 2455 9.913310 TTAATCACTGATTATTGTACCCAATCA 57.087 29.630 11.51 11.27 41.50 2.57
2266 2458 9.913310 TCATTAATCACTGATTATTGTACCCAA 57.087 29.630 21.95 6.82 37.26 4.12
2267 2459 9.337396 GTCATTAATCACTGATTATTGTACCCA 57.663 33.333 21.95 9.12 37.26 4.51
2268 2460 8.784043 GGTCATTAATCACTGATTATTGTACCC 58.216 37.037 21.95 18.13 37.26 3.69
2269 2461 9.337396 TGGTCATTAATCACTGATTATTGTACC 57.663 33.333 24.42 24.42 37.26 3.34
2273 2465 9.188588 GCATTGGTCATTAATCACTGATTATTG 57.811 33.333 19.20 19.20 37.29 1.90
2274 2466 8.077991 CGCATTGGTCATTAATCACTGATTATT 58.922 33.333 11.51 6.39 34.95 1.40
2275 2467 7.445096 TCGCATTGGTCATTAATCACTGATTAT 59.555 33.333 11.51 1.53 34.95 1.28
2276 2468 6.765512 TCGCATTGGTCATTAATCACTGATTA 59.234 34.615 7.31 7.31 33.95 1.75
2277 2469 5.589855 TCGCATTGGTCATTAATCACTGATT 59.410 36.000 9.26 9.26 36.20 2.57
2278 2470 5.125356 TCGCATTGGTCATTAATCACTGAT 58.875 37.500 0.00 0.00 0.00 2.90
2279 2471 4.512484 TCGCATTGGTCATTAATCACTGA 58.488 39.130 0.00 0.00 0.00 3.41
2280 2472 4.787563 GCTCGCATTGGTCATTAATCACTG 60.788 45.833 0.00 0.00 0.00 3.66
2281 2473 3.313526 GCTCGCATTGGTCATTAATCACT 59.686 43.478 0.00 0.00 0.00 3.41
2282 2474 3.313526 AGCTCGCATTGGTCATTAATCAC 59.686 43.478 0.00 0.00 0.00 3.06
2283 2475 3.544684 AGCTCGCATTGGTCATTAATCA 58.455 40.909 0.00 0.00 0.00 2.57
2284 2476 4.153117 CCTAGCTCGCATTGGTCATTAATC 59.847 45.833 0.00 0.00 0.00 1.75
2285 2477 4.067896 CCTAGCTCGCATTGGTCATTAAT 58.932 43.478 0.00 0.00 0.00 1.40
2286 2478 3.466836 CCTAGCTCGCATTGGTCATTAA 58.533 45.455 0.00 0.00 0.00 1.40
2287 2479 2.806745 GCCTAGCTCGCATTGGTCATTA 60.807 50.000 0.00 0.00 0.00 1.90
2288 2480 1.959042 CCTAGCTCGCATTGGTCATT 58.041 50.000 0.00 0.00 0.00 2.57
2289 2481 0.533755 GCCTAGCTCGCATTGGTCAT 60.534 55.000 0.00 0.00 0.00 3.06
2290 2482 1.153369 GCCTAGCTCGCATTGGTCA 60.153 57.895 0.00 0.00 0.00 4.02
2291 2483 0.533755 ATGCCTAGCTCGCATTGGTC 60.534 55.000 13.94 0.00 44.48 4.02
2292 2484 0.533755 GATGCCTAGCTCGCATTGGT 60.534 55.000 19.16 1.65 46.76 3.67
2293 2485 0.533531 TGATGCCTAGCTCGCATTGG 60.534 55.000 19.16 2.81 46.76 3.16
2294 2486 0.585357 GTGATGCCTAGCTCGCATTG 59.415 55.000 19.16 0.00 46.76 2.82
2295 2487 0.877649 CGTGATGCCTAGCTCGCATT 60.878 55.000 19.16 6.52 46.76 3.56
2297 2489 2.104928 CGTGATGCCTAGCTCGCA 59.895 61.111 10.54 10.54 41.28 5.10


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

AutoCloner maintained by Alex Coulton.