Multiple sequence alignment - TraesCS6D01G140700

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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 TraesCS6D01G140700 chr6D 100.000 2502 0 0 1 2502 110324626 110322125 0.000000e+00 4621.0
1 TraesCS6D01G140700 chr6D 95.898 1804 55 7 301 2098 80068480 80070270 0.000000e+00 2904.0
2 TraesCS6D01G140700 chr6D 97.602 417 9 1 2087 2502 80081919 80082335 0.000000e+00 713.0
3 TraesCS6D01G140700 chr6D 85.745 470 55 11 373 837 454991289 454990827 1.040000e-133 486.0
4 TraesCS6D01G140700 chr3D 97.229 2201 50 6 305 2502 46539806 46541998 0.000000e+00 3716.0
5 TraesCS6D01G140700 chr3D 92.149 1643 80 16 366 1974 585903803 585902176 0.000000e+00 2274.0
6 TraesCS6D01G140700 chr3D 96.458 367 11 1 2136 2502 585902013 585901649 2.750000e-169 604.0
7 TraesCS6D01G140700 chr1D 94.747 2151 99 12 357 2500 467457299 467455156 0.000000e+00 3334.0
8 TraesCS6D01G140700 chr1D 92.654 1021 44 10 961 1974 122263780 122262784 0.000000e+00 1441.0
9 TraesCS6D01G140700 chr1D 95.652 529 23 0 1974 2502 122262753 122262225 0.000000e+00 850.0
10 TraesCS6D01G140700 chr5D 96.276 1799 41 18 308 2104 495476152 495477926 0.000000e+00 2928.0
11 TraesCS6D01G140700 chr5A 95.601 1523 58 8 455 1974 426307127 426305611 0.000000e+00 2433.0
12 TraesCS6D01G140700 chr5A 96.786 529 17 0 1974 2502 426305580 426305052 0.000000e+00 883.0
13 TraesCS6D01G140700 chr5A 92.000 50 4 0 1058 1107 426306289 426306240 1.240000e-08 71.3
14 TraesCS6D01G140700 chr7D 93.465 1622 80 14 360 1974 602775777 602777379 0.000000e+00 2385.0
15 TraesCS6D01G140700 chr7D 95.606 1138 37 7 839 1974 590072348 590071222 0.000000e+00 1812.0
16 TraesCS6D01G140700 chr7D 96.030 529 21 0 1974 2502 590071191 590070663 0.000000e+00 861.0
17 TraesCS6D01G140700 chr7D 96.730 367 12 0 2136 2502 602777542 602777908 1.650000e-171 612.0
18 TraesCS6D01G140700 chr2D 95.534 627 27 1 306 931 590221070 590221696 0.000000e+00 1002.0
19 TraesCS6D01G140700 chr3B 87.713 529 41 2 1974 2502 241927852 241927348 1.660000e-166 595.0
20 TraesCS6D01G140700 chr1B 88.451 355 25 4 1974 2323 571153813 571154156 4.980000e-112 414.0
21 TraesCS6D01G140700 chr6B 84.959 246 9 8 42 286 198965433 198965215 9.010000e-55 224.0
22 TraesCS6D01G140700 chr6A 94.444 90 5 0 90 179 134926365 134926276 3.360000e-29 139.0
23 TraesCS6D01G140700 chr6A 83.505 97 3 6 225 309 134926257 134926162 7.420000e-11 78.7
24 TraesCS6D01G140700 chr2B 85.714 112 9 4 912 1016 649589698 649589809 7.320000e-21 111.0
25 TraesCS6D01G140700 chr2B 96.774 62 2 0 1003 1064 67279128 67279189 1.220000e-18 104.0


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 TraesCS6D01G140700 chr6D 110322125 110324626 2501 True 4621.0 4621 100.000000 1 2502 1 chr6D.!!$R1 2501
1 TraesCS6D01G140700 chr6D 80068480 80070270 1790 False 2904.0 2904 95.898000 301 2098 1 chr6D.!!$F1 1797
2 TraesCS6D01G140700 chr3D 46539806 46541998 2192 False 3716.0 3716 97.229000 305 2502 1 chr3D.!!$F1 2197
3 TraesCS6D01G140700 chr3D 585901649 585903803 2154 True 1439.0 2274 94.303500 366 2502 2 chr3D.!!$R1 2136
4 TraesCS6D01G140700 chr1D 467455156 467457299 2143 True 3334.0 3334 94.747000 357 2500 1 chr1D.!!$R1 2143
5 TraesCS6D01G140700 chr1D 122262225 122263780 1555 True 1145.5 1441 94.153000 961 2502 2 chr1D.!!$R2 1541
6 TraesCS6D01G140700 chr5D 495476152 495477926 1774 False 2928.0 2928 96.276000 308 2104 1 chr5D.!!$F1 1796
7 TraesCS6D01G140700 chr5A 426305052 426307127 2075 True 1129.1 2433 94.795667 455 2502 3 chr5A.!!$R1 2047
8 TraesCS6D01G140700 chr7D 602775777 602777908 2131 False 1498.5 2385 95.097500 360 2502 2 chr7D.!!$F1 2142
9 TraesCS6D01G140700 chr7D 590070663 590072348 1685 True 1336.5 1812 95.818000 839 2502 2 chr7D.!!$R1 1663
10 TraesCS6D01G140700 chr2D 590221070 590221696 626 False 1002.0 1002 95.534000 306 931 1 chr2D.!!$F1 625
11 TraesCS6D01G140700 chr3B 241927348 241927852 504 True 595.0 595 87.713000 1974 2502 1 chr3B.!!$R1 528

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
184 185 0.035439 TAAGCTCAAGGCCGGAAAGG 60.035 55.0 5.05 0.0 43.05 3.11 F
245 246 0.108138 AGGACCCGATCAAAAGAGCG 60.108 55.0 0.00 0.0 0.00 5.03 F
254 255 0.108804 TCAAAAGAGCGCTAGACCGG 60.109 55.0 11.50 0.0 0.00 5.28 F
281 282 0.179197 CGACGAGACACGCACTGTAT 60.179 55.0 0.00 0.0 46.94 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1073 1133 1.014044 GCACAGATCGAGCGACCAAA 61.014 55.000 0.0 0.0 0.00 3.28 R
1076 1136 2.583593 GGCACAGATCGAGCGACC 60.584 66.667 0.0 0.0 30.93 4.79 R
1369 1433 4.536765 AGCACAAAGAAGGAGAGGAAAAA 58.463 39.130 0.0 0.0 0.00 1.94 R
2189 2372 4.698780 GTGCCTAAGGTAAAATCGAAAGGT 59.301 41.667 0.0 0.0 0.00 3.50 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
41 42 9.776158 AATATTAGAGCGTTTAGATAGTGATCG 57.224 33.333 0.00 0.00 37.15 3.69
42 43 6.856135 TTAGAGCGTTTAGATAGTGATCGA 57.144 37.500 0.00 0.00 37.15 3.59
43 44 5.351233 AGAGCGTTTAGATAGTGATCGAG 57.649 43.478 0.00 0.00 37.15 4.04
44 45 5.057819 AGAGCGTTTAGATAGTGATCGAGA 58.942 41.667 0.00 0.00 37.15 4.04
45 46 5.703592 AGAGCGTTTAGATAGTGATCGAGAT 59.296 40.000 0.00 0.00 37.15 2.75
46 47 6.205853 AGAGCGTTTAGATAGTGATCGAGATT 59.794 38.462 0.00 0.00 37.15 2.40
47 48 6.740110 AGCGTTTAGATAGTGATCGAGATTT 58.260 36.000 0.00 0.00 37.15 2.17
48 49 7.203910 AGCGTTTAGATAGTGATCGAGATTTT 58.796 34.615 0.00 0.00 37.15 1.82
49 50 7.168302 AGCGTTTAGATAGTGATCGAGATTTTG 59.832 37.037 0.00 0.00 37.15 2.44
50 51 7.043325 GCGTTTAGATAGTGATCGAGATTTTGT 60.043 37.037 0.00 0.00 37.15 2.83
51 52 8.262588 CGTTTAGATAGTGATCGAGATTTTGTG 58.737 37.037 0.00 0.00 37.15 3.33
52 53 9.302345 GTTTAGATAGTGATCGAGATTTTGTGA 57.698 33.333 0.00 0.00 37.15 3.58
53 54 8.858003 TTAGATAGTGATCGAGATTTTGTGAC 57.142 34.615 0.00 0.00 37.15 3.67
54 55 6.867550 AGATAGTGATCGAGATTTTGTGACA 58.132 36.000 0.00 0.00 37.15 3.58
55 56 7.495901 AGATAGTGATCGAGATTTTGTGACAT 58.504 34.615 0.00 0.00 37.15 3.06
56 57 7.651304 AGATAGTGATCGAGATTTTGTGACATC 59.349 37.037 0.00 0.00 37.15 3.06
57 58 4.564372 AGTGATCGAGATTTTGTGACATCG 59.436 41.667 0.00 0.00 0.00 3.84
58 59 4.562789 GTGATCGAGATTTTGTGACATCGA 59.437 41.667 10.15 10.15 42.58 3.59
59 60 4.800471 TGATCGAGATTTTGTGACATCGAG 59.200 41.667 12.76 0.00 41.80 4.04
60 61 4.174411 TCGAGATTTTGTGACATCGAGT 57.826 40.909 4.33 0.00 34.57 4.18
61 62 3.920412 TCGAGATTTTGTGACATCGAGTG 59.080 43.478 4.33 0.00 34.57 3.51
62 63 3.061295 CGAGATTTTGTGACATCGAGTGG 59.939 47.826 0.00 0.00 32.13 4.00
63 64 3.338249 AGATTTTGTGACATCGAGTGGG 58.662 45.455 0.00 0.00 0.00 4.61
64 65 2.631160 TTTTGTGACATCGAGTGGGT 57.369 45.000 0.00 0.00 0.00 4.51
65 66 1.877637 TTTGTGACATCGAGTGGGTG 58.122 50.000 0.00 0.00 0.00 4.61
66 67 1.044611 TTGTGACATCGAGTGGGTGA 58.955 50.000 0.00 0.00 0.00 4.02
67 68 1.044611 TGTGACATCGAGTGGGTGAA 58.955 50.000 0.00 0.00 0.00 3.18
68 69 1.270094 TGTGACATCGAGTGGGTGAAC 60.270 52.381 0.00 0.00 0.00 3.18
69 70 1.000955 GTGACATCGAGTGGGTGAACT 59.999 52.381 0.00 0.00 0.00 3.01
70 71 1.272490 TGACATCGAGTGGGTGAACTC 59.728 52.381 0.00 0.00 42.68 3.01
76 77 2.825861 GAGTGGGTGAACTCGGTAAA 57.174 50.000 0.00 0.00 37.44 2.01
77 78 3.329929 GAGTGGGTGAACTCGGTAAAT 57.670 47.619 0.00 0.00 37.44 1.40
78 79 3.671716 GAGTGGGTGAACTCGGTAAATT 58.328 45.455 0.00 0.00 37.44 1.82
79 80 4.824289 GAGTGGGTGAACTCGGTAAATTA 58.176 43.478 0.00 0.00 37.44 1.40
80 81 4.828829 AGTGGGTGAACTCGGTAAATTAG 58.171 43.478 0.00 0.00 0.00 1.73
81 82 4.529377 AGTGGGTGAACTCGGTAAATTAGA 59.471 41.667 0.00 0.00 0.00 2.10
82 83 5.189145 AGTGGGTGAACTCGGTAAATTAGAT 59.811 40.000 0.00 0.00 0.00 1.98
83 84 5.293569 GTGGGTGAACTCGGTAAATTAGATG 59.706 44.000 0.00 0.00 0.00 2.90
84 85 4.272748 GGGTGAACTCGGTAAATTAGATGC 59.727 45.833 0.00 0.00 0.00 3.91
85 86 4.025979 GGTGAACTCGGTAAATTAGATGCG 60.026 45.833 0.00 0.00 0.00 4.73
86 87 4.802039 GTGAACTCGGTAAATTAGATGCGA 59.198 41.667 0.00 0.00 0.00 5.10
87 88 4.802039 TGAACTCGGTAAATTAGATGCGAC 59.198 41.667 0.00 0.00 0.00 5.19
88 89 4.650754 ACTCGGTAAATTAGATGCGACT 57.349 40.909 0.00 0.00 0.00 4.18
89 90 5.762825 ACTCGGTAAATTAGATGCGACTA 57.237 39.130 0.00 0.00 0.00 2.59
90 91 6.328641 ACTCGGTAAATTAGATGCGACTAT 57.671 37.500 0.00 0.00 0.00 2.12
91 92 6.150318 ACTCGGTAAATTAGATGCGACTATG 58.850 40.000 0.00 0.00 0.00 2.23
92 93 4.921515 TCGGTAAATTAGATGCGACTATGC 59.078 41.667 0.00 0.00 0.00 3.14
93 94 4.201494 CGGTAAATTAGATGCGACTATGCG 60.201 45.833 0.00 0.00 37.81 4.73
94 95 4.921515 GGTAAATTAGATGCGACTATGCGA 59.078 41.667 0.00 0.00 37.81 5.10
95 96 5.061064 GGTAAATTAGATGCGACTATGCGAG 59.939 44.000 0.00 0.00 37.81 5.03
96 97 2.706555 TTAGATGCGACTATGCGAGG 57.293 50.000 0.00 0.00 37.81 4.63
97 98 0.881796 TAGATGCGACTATGCGAGGG 59.118 55.000 0.00 0.00 37.81 4.30
98 99 0.823769 AGATGCGACTATGCGAGGGA 60.824 55.000 0.00 0.00 37.81 4.20
99 100 0.664767 GATGCGACTATGCGAGGGAC 60.665 60.000 0.00 0.00 37.81 4.46
100 101 2.027751 GCGACTATGCGAGGGACC 59.972 66.667 0.00 0.00 0.00 4.46
101 102 2.782222 GCGACTATGCGAGGGACCA 61.782 63.158 0.00 0.00 0.00 4.02
102 103 2.041976 CGACTATGCGAGGGACCAT 58.958 57.895 0.00 0.00 0.00 3.55
103 104 0.319040 CGACTATGCGAGGGACCATG 60.319 60.000 0.00 0.00 0.00 3.66
104 105 0.601311 GACTATGCGAGGGACCATGC 60.601 60.000 0.00 0.00 0.00 4.06
105 106 1.337384 ACTATGCGAGGGACCATGCA 61.337 55.000 9.45 9.45 42.22 3.96
106 107 2.921435 ATGCGAGGGACCATGCAT 59.079 55.556 12.67 12.67 42.84 3.96
107 108 0.250424 TATGCGAGGGACCATGCATG 60.250 55.000 20.19 20.19 46.68 4.06
108 109 1.986632 ATGCGAGGGACCATGCATGA 61.987 55.000 28.31 4.75 45.64 3.07
109 110 2.182842 GCGAGGGACCATGCATGAC 61.183 63.158 28.31 19.48 0.00 3.06
110 111 1.524621 CGAGGGACCATGCATGACC 60.525 63.158 28.31 26.12 0.00 4.02
111 112 1.152881 GAGGGACCATGCATGACCC 60.153 63.158 34.37 34.37 41.23 4.46
112 113 1.925285 GAGGGACCATGCATGACCCA 61.925 60.000 38.18 2.74 42.38 4.51
113 114 1.754234 GGGACCATGCATGACCCAC 60.754 63.158 35.34 21.18 40.89 4.61
114 115 1.754234 GGACCATGCATGACCCACC 60.754 63.158 28.31 17.38 0.00 4.61
115 116 2.045045 ACCATGCATGACCCACCG 60.045 61.111 28.31 11.52 0.00 4.94
116 117 3.520862 CCATGCATGACCCACCGC 61.521 66.667 28.31 0.00 0.00 5.68
117 118 3.520862 CATGCATGACCCACCGCC 61.521 66.667 22.59 0.00 0.00 6.13
118 119 4.045781 ATGCATGACCCACCGCCA 62.046 61.111 0.00 0.00 0.00 5.69
119 120 3.363410 ATGCATGACCCACCGCCAT 62.363 57.895 0.00 0.00 0.00 4.40
120 121 1.993701 ATGCATGACCCACCGCCATA 61.994 55.000 0.00 0.00 0.00 2.74
121 122 1.453015 GCATGACCCACCGCCATAA 60.453 57.895 0.00 0.00 0.00 1.90
122 123 1.447317 GCATGACCCACCGCCATAAG 61.447 60.000 0.00 0.00 0.00 1.73
123 124 0.107214 CATGACCCACCGCCATAAGT 60.107 55.000 0.00 0.00 0.00 2.24
124 125 0.107214 ATGACCCACCGCCATAAGTG 60.107 55.000 0.00 0.00 0.00 3.16
125 126 1.298667 GACCCACCGCCATAAGTGT 59.701 57.895 0.00 0.00 31.88 3.55
126 127 1.002624 ACCCACCGCCATAAGTGTG 60.003 57.895 0.00 0.00 31.88 3.82
127 128 2.406616 CCCACCGCCATAAGTGTGC 61.407 63.158 0.00 0.00 31.88 4.57
128 129 2.406616 CCACCGCCATAAGTGTGCC 61.407 63.158 0.00 0.00 31.88 5.01
129 130 2.435938 ACCGCCATAAGTGTGCCG 60.436 61.111 0.00 0.00 0.00 5.69
130 131 3.202001 CCGCCATAAGTGTGCCGG 61.202 66.667 0.00 0.00 0.00 6.13
131 132 3.876198 CGCCATAAGTGTGCCGGC 61.876 66.667 22.73 22.73 39.45 6.13
132 133 3.518068 GCCATAAGTGTGCCGGCC 61.518 66.667 26.77 16.24 36.73 6.13
133 134 2.045438 CCATAAGTGTGCCGGCCA 60.045 61.111 26.77 18.95 0.00 5.36
134 135 2.406616 CCATAAGTGTGCCGGCCAC 61.407 63.158 29.70 29.70 44.90 5.01
141 142 2.360600 GTGCCGGCCACATTACCA 60.361 61.111 26.77 0.00 44.06 3.25
142 143 2.360600 TGCCGGCCACATTACCAC 60.361 61.111 26.77 0.00 0.00 4.16
143 144 2.045340 GCCGGCCACATTACCACT 60.045 61.111 18.11 0.00 0.00 4.00
144 145 2.406616 GCCGGCCACATTACCACTG 61.407 63.158 18.11 0.00 0.00 3.66
145 146 1.002624 CCGGCCACATTACCACTGT 60.003 57.895 2.24 0.00 0.00 3.55
146 147 0.608035 CCGGCCACATTACCACTGTT 60.608 55.000 2.24 0.00 0.00 3.16
147 148 1.243902 CGGCCACATTACCACTGTTT 58.756 50.000 2.24 0.00 0.00 2.83
148 149 1.068610 CGGCCACATTACCACTGTTTG 60.069 52.381 2.24 0.00 0.00 2.93
149 150 1.336795 GGCCACATTACCACTGTTTGC 60.337 52.381 0.00 0.00 0.00 3.68
150 151 1.339610 GCCACATTACCACTGTTTGCA 59.660 47.619 0.00 0.00 0.00 4.08
151 152 2.862140 GCCACATTACCACTGTTTGCAC 60.862 50.000 0.00 0.00 0.00 4.57
152 153 2.604373 CCACATTACCACTGTTTGCACG 60.604 50.000 0.00 0.00 0.00 5.34
153 154 1.001815 ACATTACCACTGTTTGCACGC 60.002 47.619 0.00 0.00 0.00 5.34
154 155 1.266718 CATTACCACTGTTTGCACGCT 59.733 47.619 0.00 0.00 0.00 5.07
155 156 0.941542 TTACCACTGTTTGCACGCTC 59.058 50.000 0.00 0.00 0.00 5.03
156 157 0.179070 TACCACTGTTTGCACGCTCA 60.179 50.000 0.00 0.00 0.00 4.26
157 158 1.280746 CCACTGTTTGCACGCTCAG 59.719 57.895 0.00 0.00 0.00 3.35
158 159 1.369689 CACTGTTTGCACGCTCAGC 60.370 57.895 0.00 0.00 0.00 4.26
169 170 3.341835 GCTCAGCGCCGGATAAGC 61.342 66.667 5.05 4.30 0.00 3.09
170 171 2.419198 CTCAGCGCCGGATAAGCT 59.581 61.111 5.05 7.03 42.64 3.74
171 172 1.663074 CTCAGCGCCGGATAAGCTC 60.663 63.158 5.05 0.00 39.48 4.09
172 173 2.106938 CAGCGCCGGATAAGCTCA 59.893 61.111 5.05 0.00 39.48 4.26
173 174 1.521457 CAGCGCCGGATAAGCTCAA 60.521 57.895 5.05 0.00 39.48 3.02
174 175 1.227380 AGCGCCGGATAAGCTCAAG 60.227 57.895 5.05 0.00 36.33 3.02
175 176 2.247437 GCGCCGGATAAGCTCAAGG 61.247 63.158 5.05 0.00 0.00 3.61
176 177 2.247437 CGCCGGATAAGCTCAAGGC 61.247 63.158 5.05 8.12 42.45 4.35
177 178 1.894282 GCCGGATAAGCTCAAGGCC 60.894 63.158 5.05 0.00 40.99 5.19
178 179 1.595382 CCGGATAAGCTCAAGGCCG 60.595 63.158 0.00 0.00 43.05 6.13
179 180 1.595382 CGGATAAGCTCAAGGCCGG 60.595 63.158 0.00 0.00 43.05 6.13
180 181 1.830145 GGATAAGCTCAAGGCCGGA 59.170 57.895 5.05 0.00 43.05 5.14
181 182 0.180406 GGATAAGCTCAAGGCCGGAA 59.820 55.000 5.05 0.00 43.05 4.30
182 183 1.408266 GGATAAGCTCAAGGCCGGAAA 60.408 52.381 5.05 0.00 43.05 3.13
183 184 1.943340 GATAAGCTCAAGGCCGGAAAG 59.057 52.381 5.05 0.00 43.05 2.62
184 185 0.035439 TAAGCTCAAGGCCGGAAAGG 60.035 55.000 5.05 0.00 43.05 3.11
201 202 4.865761 GCGTACGCCGAGATGCCA 62.866 66.667 29.51 0.00 39.56 4.92
202 203 2.202690 CGTACGCCGAGATGCCAA 60.203 61.111 0.52 0.00 39.56 4.52
203 204 1.807981 CGTACGCCGAGATGCCAAA 60.808 57.895 0.52 0.00 39.56 3.28
204 205 1.752501 CGTACGCCGAGATGCCAAAG 61.753 60.000 0.52 0.00 39.56 2.77
205 206 0.459585 GTACGCCGAGATGCCAAAGA 60.460 55.000 0.00 0.00 0.00 2.52
206 207 0.248012 TACGCCGAGATGCCAAAGAA 59.752 50.000 0.00 0.00 0.00 2.52
207 208 1.021390 ACGCCGAGATGCCAAAGAAG 61.021 55.000 0.00 0.00 0.00 2.85
208 209 0.740868 CGCCGAGATGCCAAAGAAGA 60.741 55.000 0.00 0.00 0.00 2.87
209 210 1.012841 GCCGAGATGCCAAAGAAGAG 58.987 55.000 0.00 0.00 0.00 2.85
210 211 1.677217 GCCGAGATGCCAAAGAAGAGT 60.677 52.381 0.00 0.00 0.00 3.24
211 212 2.418746 GCCGAGATGCCAAAGAAGAGTA 60.419 50.000 0.00 0.00 0.00 2.59
212 213 3.452474 CCGAGATGCCAAAGAAGAGTAG 58.548 50.000 0.00 0.00 0.00 2.57
213 214 3.131223 CCGAGATGCCAAAGAAGAGTAGA 59.869 47.826 0.00 0.00 0.00 2.59
214 215 4.358851 CGAGATGCCAAAGAAGAGTAGAG 58.641 47.826 0.00 0.00 0.00 2.43
215 216 4.097135 CGAGATGCCAAAGAAGAGTAGAGA 59.903 45.833 0.00 0.00 0.00 3.10
216 217 5.337578 AGATGCCAAAGAAGAGTAGAGAC 57.662 43.478 0.00 0.00 0.00 3.36
217 218 4.774726 AGATGCCAAAGAAGAGTAGAGACA 59.225 41.667 0.00 0.00 0.00 3.41
218 219 4.258702 TGCCAAAGAAGAGTAGAGACAC 57.741 45.455 0.00 0.00 0.00 3.67
219 220 3.246619 GCCAAAGAAGAGTAGAGACACG 58.753 50.000 0.00 0.00 0.00 4.49
220 221 3.839293 CCAAAGAAGAGTAGAGACACGG 58.161 50.000 0.00 0.00 0.00 4.94
221 222 3.367498 CCAAAGAAGAGTAGAGACACGGG 60.367 52.174 0.00 0.00 0.00 5.28
222 223 2.131776 AGAAGAGTAGAGACACGGGG 57.868 55.000 0.00 0.00 0.00 5.73
223 224 1.634459 AGAAGAGTAGAGACACGGGGA 59.366 52.381 0.00 0.00 0.00 4.81
224 225 2.041350 AGAAGAGTAGAGACACGGGGAA 59.959 50.000 0.00 0.00 0.00 3.97
225 226 2.131776 AGAGTAGAGACACGGGGAAG 57.868 55.000 0.00 0.00 0.00 3.46
226 227 1.634459 AGAGTAGAGACACGGGGAAGA 59.366 52.381 0.00 0.00 0.00 2.87
227 228 2.018515 GAGTAGAGACACGGGGAAGAG 58.981 57.143 0.00 0.00 0.00 2.85
228 229 1.104630 GTAGAGACACGGGGAAGAGG 58.895 60.000 0.00 0.00 0.00 3.69
229 230 0.997363 TAGAGACACGGGGAAGAGGA 59.003 55.000 0.00 0.00 0.00 3.71
230 231 0.612453 AGAGACACGGGGAAGAGGAC 60.612 60.000 0.00 0.00 0.00 3.85
231 232 1.605971 GAGACACGGGGAAGAGGACC 61.606 65.000 0.00 0.00 0.00 4.46
232 233 2.606826 ACACGGGGAAGAGGACCC 60.607 66.667 0.00 0.00 46.05 4.46
237 238 4.375406 GGGAAGAGGACCCGATCA 57.625 61.111 0.00 0.00 37.85 2.92
238 239 2.604118 GGGAAGAGGACCCGATCAA 58.396 57.895 0.00 0.00 37.85 2.57
239 240 0.909623 GGGAAGAGGACCCGATCAAA 59.090 55.000 0.00 0.00 37.85 2.69
240 241 1.280998 GGGAAGAGGACCCGATCAAAA 59.719 52.381 0.00 0.00 37.85 2.44
241 242 2.633488 GGAAGAGGACCCGATCAAAAG 58.367 52.381 0.00 0.00 0.00 2.27
242 243 2.236395 GGAAGAGGACCCGATCAAAAGA 59.764 50.000 0.00 0.00 0.00 2.52
243 244 3.526534 GAAGAGGACCCGATCAAAAGAG 58.473 50.000 0.00 0.00 0.00 2.85
244 245 1.208293 AGAGGACCCGATCAAAAGAGC 59.792 52.381 0.00 0.00 0.00 4.09
245 246 0.108138 AGGACCCGATCAAAAGAGCG 60.108 55.000 0.00 0.00 0.00 5.03
246 247 1.706287 GGACCCGATCAAAAGAGCGC 61.706 60.000 0.00 0.00 32.08 5.92
247 248 0.741221 GACCCGATCAAAAGAGCGCT 60.741 55.000 11.27 11.27 32.08 5.92
248 249 0.535335 ACCCGATCAAAAGAGCGCTA 59.465 50.000 11.50 0.00 32.08 4.26
249 250 1.212616 CCCGATCAAAAGAGCGCTAG 58.787 55.000 11.50 0.00 32.08 3.42
250 251 1.202417 CCCGATCAAAAGAGCGCTAGA 60.202 52.381 11.50 3.98 32.08 2.43
251 252 1.855360 CCGATCAAAAGAGCGCTAGAC 59.145 52.381 11.50 0.00 32.08 2.59
252 253 1.855360 CGATCAAAAGAGCGCTAGACC 59.145 52.381 11.50 0.00 0.00 3.85
253 254 1.855360 GATCAAAAGAGCGCTAGACCG 59.145 52.381 11.50 0.00 0.00 4.79
254 255 0.108804 TCAAAAGAGCGCTAGACCGG 60.109 55.000 11.50 0.00 0.00 5.28
255 256 0.389948 CAAAAGAGCGCTAGACCGGT 60.390 55.000 11.50 6.92 42.17 5.28
256 257 0.389948 AAAAGAGCGCTAGACCGGTG 60.390 55.000 14.63 0.00 39.26 4.94
257 258 2.837371 AAAGAGCGCTAGACCGGTGC 62.837 60.000 14.63 9.25 39.26 5.01
259 260 3.382832 AGCGCTAGACCGGTGCTT 61.383 61.111 14.63 0.00 46.53 3.91
260 261 3.188786 GCGCTAGACCGGTGCTTG 61.189 66.667 14.63 11.31 37.25 4.01
261 262 3.188786 CGCTAGACCGGTGCTTGC 61.189 66.667 14.63 19.40 0.00 4.01
262 263 2.820037 GCTAGACCGGTGCTTGCC 60.820 66.667 14.63 0.00 0.00 4.52
270 271 3.112709 GGTGCTTGCCGACGAGAC 61.113 66.667 0.00 0.00 0.00 3.36
271 272 2.355837 GTGCTTGCCGACGAGACA 60.356 61.111 0.00 0.00 0.00 3.41
272 273 2.355837 TGCTTGCCGACGAGACAC 60.356 61.111 0.00 0.00 0.00 3.67
274 275 3.470567 CTTGCCGACGAGACACGC 61.471 66.667 0.00 0.00 46.94 5.34
275 276 4.273257 TTGCCGACGAGACACGCA 62.273 61.111 0.00 0.00 46.94 5.24
276 277 4.994201 TGCCGACGAGACACGCAC 62.994 66.667 0.00 0.00 46.94 5.34
277 278 4.702081 GCCGACGAGACACGCACT 62.702 66.667 0.00 0.00 46.94 4.40
278 279 2.801162 CCGACGAGACACGCACTG 60.801 66.667 0.00 0.00 46.94 3.66
279 280 2.051256 CGACGAGACACGCACTGT 60.051 61.111 0.00 0.00 46.94 3.55
280 281 1.205820 CGACGAGACACGCACTGTA 59.794 57.895 0.00 0.00 46.94 2.74
281 282 0.179197 CGACGAGACACGCACTGTAT 60.179 55.000 0.00 0.00 46.94 2.29
282 283 1.536149 GACGAGACACGCACTGTATC 58.464 55.000 0.00 0.00 46.94 2.24
284 285 3.990546 GAGACACGCACTGTATCGA 57.009 52.632 8.31 0.00 31.56 3.59
285 286 2.257974 GAGACACGCACTGTATCGAA 57.742 50.000 8.31 0.00 31.56 3.71
286 287 1.912110 GAGACACGCACTGTATCGAAC 59.088 52.381 8.31 0.00 31.56 3.95
287 288 0.633733 GACACGCACTGTATCGAACG 59.366 55.000 8.31 0.00 31.03 3.95
288 289 0.239082 ACACGCACTGTATCGAACGA 59.761 50.000 8.31 0.00 0.00 3.85
289 290 1.333115 CACGCACTGTATCGAACGAA 58.667 50.000 0.12 0.00 0.00 3.85
290 291 1.057285 CACGCACTGTATCGAACGAAC 59.943 52.381 0.12 2.47 0.00 3.95
291 292 0.290840 CGCACTGTATCGAACGAACG 59.709 55.000 0.12 0.00 0.00 3.95
292 293 0.638746 GCACTGTATCGAACGAACGG 59.361 55.000 0.12 8.42 0.00 4.44
293 294 1.730121 GCACTGTATCGAACGAACGGA 60.730 52.381 17.65 0.00 0.00 4.69
294 295 2.174764 CACTGTATCGAACGAACGGAG 58.825 52.381 17.65 10.66 0.00 4.63
295 296 1.131883 ACTGTATCGAACGAACGGAGG 59.868 52.381 17.65 5.27 0.00 4.30
296 297 1.399440 CTGTATCGAACGAACGGAGGA 59.601 52.381 0.12 0.00 0.00 3.71
297 298 1.131126 TGTATCGAACGAACGGAGGAC 59.869 52.381 0.12 0.00 0.00 3.85
323 324 6.724351 AGGCATGCATCCAGATATATGTTAA 58.276 36.000 21.36 0.00 0.00 2.01
327 328 8.680001 GCATGCATCCAGATATATGTTAATTGA 58.320 33.333 14.21 0.00 0.00 2.57
340 341 4.922206 TGTTAATTGAGAGAACATGGGCT 58.078 39.130 0.00 0.00 0.00 5.19
341 342 4.943705 TGTTAATTGAGAGAACATGGGCTC 59.056 41.667 8.55 8.55 0.00 4.70
351 352 2.836636 ACATGGGCTCTCTCAGAGTA 57.163 50.000 0.36 0.00 44.12 2.59
371 372 0.525455 CAGCGATTCATGACCGTCGA 60.525 55.000 21.68 0.00 36.25 4.20
495 498 3.192922 GCCACCGCGCGTAATTCT 61.193 61.111 29.95 0.00 0.00 2.40
540 544 2.817844 GTCATTTCACCAACAGGGGTAC 59.182 50.000 0.00 0.00 39.79 3.34
555 559 0.891904 GGTACAAAAAGGAGGCGGCA 60.892 55.000 13.08 0.00 0.00 5.69
646 650 1.811266 CCCGCACCATGTCTTCTCG 60.811 63.158 0.00 0.00 0.00 4.04
1073 1133 1.079127 CCCTCGTTCTTGCCGTCAT 60.079 57.895 0.00 0.00 0.00 3.06
1076 1136 1.135972 CCTCGTTCTTGCCGTCATTTG 60.136 52.381 0.00 0.00 0.00 2.32
1670 1758 8.499967 GGTGCTTTTGTTCTTTTCTTTGTTTTA 58.500 29.630 0.00 0.00 0.00 1.52
1754 1842 4.382040 CGTCCTCTGTTGTGATATTGAGGT 60.382 45.833 0.00 0.00 41.14 3.85
1995 2148 4.222145 CCACAAACCTAGGCTTAGTCAGTA 59.778 45.833 9.30 0.00 0.00 2.74
2043 2196 2.806745 GCCCAGCAGCGTATTTATCTGA 60.807 50.000 0.00 0.00 0.00 3.27
2189 2372 2.356665 TGCAAGGTGGCAGTAAAAGA 57.643 45.000 0.00 0.00 39.25 2.52
2317 2500 5.942236 TGATTGCAGTTAAAAGAGAGCTGAT 59.058 36.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.776158 CGATCACTATCTAAACGCTCTAATATT 57.224 33.333 0.00 0.00 0.00 1.28
16 17 9.163899 TCGATCACTATCTAAACGCTCTAATAT 57.836 33.333 0.00 0.00 0.00 1.28
17 18 8.543862 TCGATCACTATCTAAACGCTCTAATA 57.456 34.615 0.00 0.00 0.00 0.98
18 19 7.388224 TCTCGATCACTATCTAAACGCTCTAAT 59.612 37.037 0.00 0.00 0.00 1.73
19 20 6.704937 TCTCGATCACTATCTAAACGCTCTAA 59.295 38.462 0.00 0.00 0.00 2.10
20 21 6.221659 TCTCGATCACTATCTAAACGCTCTA 58.778 40.000 0.00 0.00 0.00 2.43
21 22 5.057819 TCTCGATCACTATCTAAACGCTCT 58.942 41.667 0.00 0.00 0.00 4.09
22 23 5.345609 TCTCGATCACTATCTAAACGCTC 57.654 43.478 0.00 0.00 0.00 5.03
23 24 5.950758 ATCTCGATCACTATCTAAACGCT 57.049 39.130 0.00 0.00 0.00 5.07
24 25 6.994868 AAATCTCGATCACTATCTAAACGC 57.005 37.500 0.00 0.00 0.00 4.84
25 26 8.262588 CACAAAATCTCGATCACTATCTAAACG 58.737 37.037 0.00 0.00 0.00 3.60
26 27 9.302345 TCACAAAATCTCGATCACTATCTAAAC 57.698 33.333 0.00 0.00 0.00 2.01
27 28 9.302345 GTCACAAAATCTCGATCACTATCTAAA 57.698 33.333 0.00 0.00 0.00 1.85
28 29 8.466798 TGTCACAAAATCTCGATCACTATCTAA 58.533 33.333 0.00 0.00 0.00 2.10
29 30 7.996385 TGTCACAAAATCTCGATCACTATCTA 58.004 34.615 0.00 0.00 0.00 1.98
30 31 6.867550 TGTCACAAAATCTCGATCACTATCT 58.132 36.000 0.00 0.00 0.00 1.98
31 32 7.357941 CGATGTCACAAAATCTCGATCACTATC 60.358 40.741 0.00 0.00 0.00 2.08
32 33 6.419116 CGATGTCACAAAATCTCGATCACTAT 59.581 38.462 0.00 0.00 0.00 2.12
33 34 5.743872 CGATGTCACAAAATCTCGATCACTA 59.256 40.000 0.00 0.00 0.00 2.74
34 35 4.564372 CGATGTCACAAAATCTCGATCACT 59.436 41.667 0.00 0.00 0.00 3.41
35 36 4.562789 TCGATGTCACAAAATCTCGATCAC 59.437 41.667 0.00 0.00 30.94 3.06
36 37 4.743493 TCGATGTCACAAAATCTCGATCA 58.257 39.130 0.00 0.00 30.94 2.92
37 38 4.800993 ACTCGATGTCACAAAATCTCGATC 59.199 41.667 1.07 0.00 34.97 3.69
38 39 4.564372 CACTCGATGTCACAAAATCTCGAT 59.436 41.667 1.07 0.00 34.97 3.59
39 40 3.920412 CACTCGATGTCACAAAATCTCGA 59.080 43.478 0.78 0.78 34.39 4.04
40 41 3.061295 CCACTCGATGTCACAAAATCTCG 59.939 47.826 0.00 0.00 0.00 4.04
41 42 3.372206 CCCACTCGATGTCACAAAATCTC 59.628 47.826 0.00 0.00 0.00 2.75
42 43 3.244561 ACCCACTCGATGTCACAAAATCT 60.245 43.478 0.00 0.00 0.00 2.40
43 44 3.074412 ACCCACTCGATGTCACAAAATC 58.926 45.455 0.00 0.00 0.00 2.17
44 45 2.813754 CACCCACTCGATGTCACAAAAT 59.186 45.455 0.00 0.00 0.00 1.82
45 46 2.158885 TCACCCACTCGATGTCACAAAA 60.159 45.455 0.00 0.00 0.00 2.44
46 47 1.414550 TCACCCACTCGATGTCACAAA 59.585 47.619 0.00 0.00 0.00 2.83
47 48 1.044611 TCACCCACTCGATGTCACAA 58.955 50.000 0.00 0.00 0.00 3.33
48 49 1.044611 TTCACCCACTCGATGTCACA 58.955 50.000 0.00 0.00 0.00 3.58
49 50 1.000955 AGTTCACCCACTCGATGTCAC 59.999 52.381 0.00 0.00 0.00 3.67
50 51 1.272490 GAGTTCACCCACTCGATGTCA 59.728 52.381 0.00 0.00 34.12 3.58
51 52 1.997669 GAGTTCACCCACTCGATGTC 58.002 55.000 0.00 0.00 34.12 3.06
57 58 2.825861 TTTACCGAGTTCACCCACTC 57.174 50.000 0.00 0.00 40.02 3.51
58 59 3.782656 AATTTACCGAGTTCACCCACT 57.217 42.857 0.00 0.00 0.00 4.00
59 60 4.824289 TCTAATTTACCGAGTTCACCCAC 58.176 43.478 0.00 0.00 0.00 4.61
60 61 5.424757 CATCTAATTTACCGAGTTCACCCA 58.575 41.667 0.00 0.00 0.00 4.51
61 62 4.272748 GCATCTAATTTACCGAGTTCACCC 59.727 45.833 0.00 0.00 0.00 4.61
62 63 4.025979 CGCATCTAATTTACCGAGTTCACC 60.026 45.833 0.00 0.00 0.00 4.02
63 64 4.802039 TCGCATCTAATTTACCGAGTTCAC 59.198 41.667 0.00 0.00 0.00 3.18
64 65 4.802039 GTCGCATCTAATTTACCGAGTTCA 59.198 41.667 0.00 0.00 0.00 3.18
65 66 5.041940 AGTCGCATCTAATTTACCGAGTTC 58.958 41.667 0.00 0.00 0.00 3.01
66 67 5.007385 AGTCGCATCTAATTTACCGAGTT 57.993 39.130 0.00 0.00 0.00 3.01
67 68 4.650754 AGTCGCATCTAATTTACCGAGT 57.349 40.909 0.00 0.00 0.00 4.18
68 69 5.061064 GCATAGTCGCATCTAATTTACCGAG 59.939 44.000 0.00 0.00 0.00 4.63
69 70 4.921515 GCATAGTCGCATCTAATTTACCGA 59.078 41.667 0.00 0.00 0.00 4.69
70 71 4.201494 CGCATAGTCGCATCTAATTTACCG 60.201 45.833 0.00 0.00 0.00 4.02
71 72 4.921515 TCGCATAGTCGCATCTAATTTACC 59.078 41.667 0.00 0.00 0.00 2.85
72 73 5.061064 CCTCGCATAGTCGCATCTAATTTAC 59.939 44.000 0.00 0.00 0.00 2.01
73 74 5.161358 CCTCGCATAGTCGCATCTAATTTA 58.839 41.667 0.00 0.00 0.00 1.40
74 75 3.990469 CCTCGCATAGTCGCATCTAATTT 59.010 43.478 0.00 0.00 0.00 1.82
75 76 3.579709 CCTCGCATAGTCGCATCTAATT 58.420 45.455 0.00 0.00 0.00 1.40
76 77 2.094494 CCCTCGCATAGTCGCATCTAAT 60.094 50.000 0.00 0.00 0.00 1.73
77 78 1.269723 CCCTCGCATAGTCGCATCTAA 59.730 52.381 0.00 0.00 0.00 2.10
78 79 0.881796 CCCTCGCATAGTCGCATCTA 59.118 55.000 0.00 0.00 0.00 1.98
79 80 0.823769 TCCCTCGCATAGTCGCATCT 60.824 55.000 0.00 0.00 0.00 2.90
80 81 0.664767 GTCCCTCGCATAGTCGCATC 60.665 60.000 0.00 0.00 0.00 3.91
81 82 1.364171 GTCCCTCGCATAGTCGCAT 59.636 57.895 0.00 0.00 0.00 4.73
82 83 2.782222 GGTCCCTCGCATAGTCGCA 61.782 63.158 0.00 0.00 0.00 5.10
83 84 2.027751 GGTCCCTCGCATAGTCGC 59.972 66.667 0.00 0.00 0.00 5.19
84 85 0.319040 CATGGTCCCTCGCATAGTCG 60.319 60.000 0.00 0.00 0.00 4.18
85 86 0.601311 GCATGGTCCCTCGCATAGTC 60.601 60.000 0.00 0.00 0.00 2.59
86 87 1.337384 TGCATGGTCCCTCGCATAGT 61.337 55.000 0.00 0.00 0.00 2.12
87 88 0.035881 ATGCATGGTCCCTCGCATAG 59.964 55.000 0.00 0.00 43.04 2.23
88 89 0.250424 CATGCATGGTCCCTCGCATA 60.250 55.000 19.40 0.00 42.99 3.14
89 90 1.527611 CATGCATGGTCCCTCGCAT 60.528 57.895 19.40 7.07 45.65 4.73
90 91 2.124612 CATGCATGGTCCCTCGCA 60.125 61.111 19.40 3.30 39.01 5.10
91 92 2.182842 GTCATGCATGGTCCCTCGC 61.183 63.158 25.97 3.79 0.00 5.03
92 93 1.524621 GGTCATGCATGGTCCCTCG 60.525 63.158 25.97 0.00 0.00 4.63
93 94 1.152881 GGGTCATGCATGGTCCCTC 60.153 63.158 33.48 19.63 38.41 4.30
94 95 1.930133 TGGGTCATGCATGGTCCCT 60.930 57.895 36.52 5.34 40.40 4.20
95 96 1.754234 GTGGGTCATGCATGGTCCC 60.754 63.158 33.82 33.82 40.27 4.46
96 97 1.754234 GGTGGGTCATGCATGGTCC 60.754 63.158 25.97 24.76 0.00 4.46
97 98 2.114670 CGGTGGGTCATGCATGGTC 61.115 63.158 25.97 18.17 0.00 4.02
98 99 2.045045 CGGTGGGTCATGCATGGT 60.045 61.111 25.97 0.00 0.00 3.55
99 100 3.520862 GCGGTGGGTCATGCATGG 61.521 66.667 25.97 9.48 0.00 3.66
100 101 3.520862 GGCGGTGGGTCATGCATG 61.521 66.667 21.07 21.07 0.00 4.06
101 102 1.993701 TATGGCGGTGGGTCATGCAT 61.994 55.000 0.00 0.00 42.10 3.96
102 103 2.203549 TTATGGCGGTGGGTCATGCA 62.204 55.000 0.00 0.00 42.10 3.96
103 104 1.447317 CTTATGGCGGTGGGTCATGC 61.447 60.000 0.00 0.00 42.10 4.06
104 105 0.107214 ACTTATGGCGGTGGGTCATG 60.107 55.000 0.00 0.00 42.10 3.07
105 106 0.107214 CACTTATGGCGGTGGGTCAT 60.107 55.000 0.00 0.00 44.80 3.06
106 107 1.298340 CACTTATGGCGGTGGGTCA 59.702 57.895 0.00 0.00 32.67 4.02
107 108 1.024579 CACACTTATGGCGGTGGGTC 61.025 60.000 0.00 0.00 37.72 4.46
108 109 1.002624 CACACTTATGGCGGTGGGT 60.003 57.895 0.00 0.00 37.72 4.51
109 110 2.406616 GCACACTTATGGCGGTGGG 61.407 63.158 0.00 0.00 39.58 4.61
110 111 2.406616 GGCACACTTATGGCGGTGG 61.407 63.158 0.00 0.00 37.72 4.61
111 112 3.187058 GGCACACTTATGGCGGTG 58.813 61.111 0.00 0.00 39.13 4.94
115 116 3.518068 GGCCGGCACACTTATGGC 61.518 66.667 30.85 1.84 44.98 4.40
116 117 2.045438 TGGCCGGCACACTTATGG 60.045 61.111 30.85 0.00 0.00 2.74
117 118 1.031571 ATGTGGCCGGCACACTTATG 61.032 55.000 33.43 0.00 39.52 1.90
118 119 0.323360 AATGTGGCCGGCACACTTAT 60.323 50.000 33.43 23.16 39.52 1.73
119 120 0.325272 TAATGTGGCCGGCACACTTA 59.675 50.000 33.43 26.81 39.52 2.24
120 121 1.074072 TAATGTGGCCGGCACACTT 59.926 52.632 33.43 27.99 39.52 3.16
121 122 1.674322 GTAATGTGGCCGGCACACT 60.674 57.895 33.43 25.18 39.52 3.55
122 123 2.696759 GGTAATGTGGCCGGCACAC 61.697 63.158 29.98 29.98 39.26 3.82
123 124 2.360600 GGTAATGTGGCCGGCACA 60.361 61.111 30.85 27.86 36.95 4.57
124 125 2.360600 TGGTAATGTGGCCGGCAC 60.361 61.111 30.85 23.59 0.00 5.01
125 126 2.360600 GTGGTAATGTGGCCGGCA 60.361 61.111 30.85 12.04 0.00 5.69
126 127 2.045340 AGTGGTAATGTGGCCGGC 60.045 61.111 21.18 21.18 0.00 6.13
127 128 0.608035 AACAGTGGTAATGTGGCCGG 60.608 55.000 0.00 0.00 0.00 6.13
128 129 1.068610 CAAACAGTGGTAATGTGGCCG 60.069 52.381 0.00 0.00 0.00 6.13
129 130 1.336795 GCAAACAGTGGTAATGTGGCC 60.337 52.381 0.00 0.00 0.00 5.36
130 131 1.339610 TGCAAACAGTGGTAATGTGGC 59.660 47.619 0.00 0.00 34.27 5.01
131 132 2.604373 CGTGCAAACAGTGGTAATGTGG 60.604 50.000 0.00 0.00 0.00 4.17
132 133 2.649516 CGTGCAAACAGTGGTAATGTG 58.350 47.619 0.00 0.00 0.00 3.21
133 134 1.001815 GCGTGCAAACAGTGGTAATGT 60.002 47.619 0.00 0.00 0.00 2.71
134 135 1.266718 AGCGTGCAAACAGTGGTAATG 59.733 47.619 0.00 0.00 0.00 1.90
135 136 1.535462 GAGCGTGCAAACAGTGGTAAT 59.465 47.619 0.00 0.00 0.00 1.89
136 137 0.941542 GAGCGTGCAAACAGTGGTAA 59.058 50.000 0.00 0.00 0.00 2.85
137 138 0.179070 TGAGCGTGCAAACAGTGGTA 60.179 50.000 0.00 0.00 0.00 3.25
138 139 1.439353 CTGAGCGTGCAAACAGTGGT 61.439 55.000 0.00 0.00 0.00 4.16
139 140 1.280746 CTGAGCGTGCAAACAGTGG 59.719 57.895 0.00 0.00 0.00 4.00
140 141 1.369689 GCTGAGCGTGCAAACAGTG 60.370 57.895 12.47 0.00 33.57 3.66
141 142 3.025619 GCTGAGCGTGCAAACAGT 58.974 55.556 12.47 0.00 33.57 3.55
153 154 1.663074 GAGCTTATCCGGCGCTGAG 60.663 63.158 20.25 8.17 33.47 3.35
154 155 1.955495 TTGAGCTTATCCGGCGCTGA 61.955 55.000 20.25 10.50 33.47 4.26
155 156 1.493950 CTTGAGCTTATCCGGCGCTG 61.494 60.000 9.96 9.96 33.47 5.18
156 157 1.227380 CTTGAGCTTATCCGGCGCT 60.227 57.895 7.64 1.14 36.57 5.92
157 158 2.247437 CCTTGAGCTTATCCGGCGC 61.247 63.158 0.00 0.00 34.52 6.53
158 159 2.247437 GCCTTGAGCTTATCCGGCG 61.247 63.158 0.00 0.00 38.99 6.46
159 160 1.894282 GGCCTTGAGCTTATCCGGC 60.894 63.158 0.00 5.68 43.05 6.13
160 161 1.595382 CGGCCTTGAGCTTATCCGG 60.595 63.158 0.00 0.00 43.05 5.14
161 162 1.595382 CCGGCCTTGAGCTTATCCG 60.595 63.158 0.00 7.18 43.05 4.18
162 163 0.180406 TTCCGGCCTTGAGCTTATCC 59.820 55.000 0.00 0.00 43.05 2.59
163 164 1.943340 CTTTCCGGCCTTGAGCTTATC 59.057 52.381 0.00 0.00 43.05 1.75
164 165 1.408822 CCTTTCCGGCCTTGAGCTTAT 60.409 52.381 0.00 0.00 43.05 1.73
165 166 0.035439 CCTTTCCGGCCTTGAGCTTA 60.035 55.000 0.00 0.00 43.05 3.09
166 167 1.303643 CCTTTCCGGCCTTGAGCTT 60.304 57.895 0.00 0.00 43.05 3.74
167 168 2.352805 CCTTTCCGGCCTTGAGCT 59.647 61.111 0.00 0.00 43.05 4.09
184 185 4.865761 TGGCATCTCGGCGTACGC 62.866 66.667 31.54 31.54 45.16 4.42
185 186 1.752501 CTTTGGCATCTCGGCGTACG 61.753 60.000 11.84 11.84 45.16 3.67
186 187 0.459585 TCTTTGGCATCTCGGCGTAC 60.460 55.000 6.85 0.00 45.16 3.67
187 188 0.248012 TTCTTTGGCATCTCGGCGTA 59.752 50.000 6.85 0.00 45.16 4.42
188 189 1.003839 TTCTTTGGCATCTCGGCGT 60.004 52.632 6.85 0.00 45.16 5.68
189 190 0.740868 TCTTCTTTGGCATCTCGGCG 60.741 55.000 0.00 0.00 45.16 6.46
190 191 1.012841 CTCTTCTTTGGCATCTCGGC 58.987 55.000 0.00 0.00 41.67 5.54
191 192 2.393271 ACTCTTCTTTGGCATCTCGG 57.607 50.000 0.00 0.00 0.00 4.63
192 193 4.097135 TCTCTACTCTTCTTTGGCATCTCG 59.903 45.833 0.00 0.00 0.00 4.04
193 194 5.105554 TGTCTCTACTCTTCTTTGGCATCTC 60.106 44.000 0.00 0.00 0.00 2.75
194 195 4.774726 TGTCTCTACTCTTCTTTGGCATCT 59.225 41.667 0.00 0.00 0.00 2.90
195 196 4.867608 GTGTCTCTACTCTTCTTTGGCATC 59.132 45.833 0.00 0.00 0.00 3.91
196 197 4.619394 CGTGTCTCTACTCTTCTTTGGCAT 60.619 45.833 0.00 0.00 0.00 4.40
197 198 3.305403 CGTGTCTCTACTCTTCTTTGGCA 60.305 47.826 0.00 0.00 0.00 4.92
198 199 3.246619 CGTGTCTCTACTCTTCTTTGGC 58.753 50.000 0.00 0.00 0.00 4.52
199 200 3.367498 CCCGTGTCTCTACTCTTCTTTGG 60.367 52.174 0.00 0.00 0.00 3.28
200 201 3.367498 CCCCGTGTCTCTACTCTTCTTTG 60.367 52.174 0.00 0.00 0.00 2.77
201 202 2.826725 CCCCGTGTCTCTACTCTTCTTT 59.173 50.000 0.00 0.00 0.00 2.52
202 203 2.041350 TCCCCGTGTCTCTACTCTTCTT 59.959 50.000 0.00 0.00 0.00 2.52
203 204 1.634459 TCCCCGTGTCTCTACTCTTCT 59.366 52.381 0.00 0.00 0.00 2.85
204 205 2.125773 TCCCCGTGTCTCTACTCTTC 57.874 55.000 0.00 0.00 0.00 2.87
205 206 2.041350 TCTTCCCCGTGTCTCTACTCTT 59.959 50.000 0.00 0.00 0.00 2.85
206 207 1.634459 TCTTCCCCGTGTCTCTACTCT 59.366 52.381 0.00 0.00 0.00 3.24
207 208 2.018515 CTCTTCCCCGTGTCTCTACTC 58.981 57.143 0.00 0.00 0.00 2.59
208 209 1.341187 CCTCTTCCCCGTGTCTCTACT 60.341 57.143 0.00 0.00 0.00 2.57
209 210 1.104630 CCTCTTCCCCGTGTCTCTAC 58.895 60.000 0.00 0.00 0.00 2.59
210 211 0.997363 TCCTCTTCCCCGTGTCTCTA 59.003 55.000 0.00 0.00 0.00 2.43
211 212 0.612453 GTCCTCTTCCCCGTGTCTCT 60.612 60.000 0.00 0.00 0.00 3.10
212 213 1.605971 GGTCCTCTTCCCCGTGTCTC 61.606 65.000 0.00 0.00 0.00 3.36
213 214 1.609794 GGTCCTCTTCCCCGTGTCT 60.610 63.158 0.00 0.00 0.00 3.41
214 215 2.657066 GGGTCCTCTTCCCCGTGTC 61.657 68.421 0.00 0.00 39.08 3.67
215 216 2.606826 GGGTCCTCTTCCCCGTGT 60.607 66.667 0.00 0.00 39.08 4.49
219 220 0.981277 TTGATCGGGTCCTCTTCCCC 60.981 60.000 0.00 0.00 41.78 4.81
220 221 0.909623 TTTGATCGGGTCCTCTTCCC 59.090 55.000 0.00 0.00 41.41 3.97
221 222 2.236395 TCTTTTGATCGGGTCCTCTTCC 59.764 50.000 0.00 0.00 0.00 3.46
222 223 3.526534 CTCTTTTGATCGGGTCCTCTTC 58.473 50.000 0.00 0.00 0.00 2.87
223 224 2.355209 GCTCTTTTGATCGGGTCCTCTT 60.355 50.000 0.00 0.00 0.00 2.85
224 225 1.208293 GCTCTTTTGATCGGGTCCTCT 59.792 52.381 0.00 0.00 0.00 3.69
225 226 1.657822 GCTCTTTTGATCGGGTCCTC 58.342 55.000 0.00 0.00 0.00 3.71
226 227 0.108138 CGCTCTTTTGATCGGGTCCT 60.108 55.000 0.00 0.00 34.79 3.85
227 228 1.706287 GCGCTCTTTTGATCGGGTCC 61.706 60.000 0.00 0.00 38.37 4.46
228 229 0.741221 AGCGCTCTTTTGATCGGGTC 60.741 55.000 2.64 0.00 38.37 4.46
229 230 0.535335 TAGCGCTCTTTTGATCGGGT 59.465 50.000 16.34 0.00 38.37 5.28
230 231 1.202417 TCTAGCGCTCTTTTGATCGGG 60.202 52.381 16.34 0.00 38.37 5.14
231 232 1.855360 GTCTAGCGCTCTTTTGATCGG 59.145 52.381 16.34 0.00 38.37 4.18
232 233 1.855360 GGTCTAGCGCTCTTTTGATCG 59.145 52.381 16.34 0.00 40.58 3.69
233 234 1.855360 CGGTCTAGCGCTCTTTTGATC 59.145 52.381 16.34 5.34 0.00 2.92
234 235 1.471676 CCGGTCTAGCGCTCTTTTGAT 60.472 52.381 16.34 0.00 0.00 2.57
235 236 0.108804 CCGGTCTAGCGCTCTTTTGA 60.109 55.000 16.34 2.76 0.00 2.69
236 237 0.389948 ACCGGTCTAGCGCTCTTTTG 60.390 55.000 16.34 1.95 0.00 2.44
237 238 0.389948 CACCGGTCTAGCGCTCTTTT 60.390 55.000 16.34 0.00 0.00 2.27
238 239 1.215647 CACCGGTCTAGCGCTCTTT 59.784 57.895 16.34 0.00 0.00 2.52
239 240 2.885861 CACCGGTCTAGCGCTCTT 59.114 61.111 16.34 0.00 0.00 2.85
240 241 3.827898 GCACCGGTCTAGCGCTCT 61.828 66.667 16.34 0.00 0.00 4.09
241 242 3.358076 AAGCACCGGTCTAGCGCTC 62.358 63.158 16.34 0.00 31.17 5.03
242 243 3.382832 AAGCACCGGTCTAGCGCT 61.383 61.111 17.26 17.26 33.45 5.92
243 244 3.188786 CAAGCACCGGTCTAGCGC 61.189 66.667 2.59 4.54 0.00 5.92
244 245 3.188786 GCAAGCACCGGTCTAGCG 61.189 66.667 2.59 0.00 0.00 4.26
245 246 2.820037 GGCAAGCACCGGTCTAGC 60.820 66.667 2.59 5.49 0.00 3.42
253 254 3.112709 GTCTCGTCGGCAAGCACC 61.113 66.667 0.00 0.00 0.00 5.01
254 255 2.355837 TGTCTCGTCGGCAAGCAC 60.356 61.111 0.00 0.00 0.00 4.40
255 256 2.355837 GTGTCTCGTCGGCAAGCA 60.356 61.111 0.00 0.00 0.00 3.91
256 257 3.470567 CGTGTCTCGTCGGCAAGC 61.471 66.667 0.00 0.00 34.52 4.01
257 258 3.470567 GCGTGTCTCGTCGGCAAG 61.471 66.667 0.00 0.00 42.13 4.01
258 259 4.273257 TGCGTGTCTCGTCGGCAA 62.273 61.111 0.00 0.00 42.13 4.52
259 260 4.994201 GTGCGTGTCTCGTCGGCA 62.994 66.667 0.00 0.00 42.13 5.69
260 261 4.702081 AGTGCGTGTCTCGTCGGC 62.702 66.667 0.00 0.00 42.13 5.54
261 262 2.178892 TACAGTGCGTGTCTCGTCGG 62.179 60.000 0.00 0.00 40.94 4.79
262 263 0.179197 ATACAGTGCGTGTCTCGTCG 60.179 55.000 0.00 0.00 40.94 5.12
263 264 1.536149 GATACAGTGCGTGTCTCGTC 58.464 55.000 0.00 0.00 40.94 4.20
264 265 0.179197 CGATACAGTGCGTGTCTCGT 60.179 55.000 14.82 0.00 45.81 4.18
265 266 2.555770 CGATACAGTGCGTGTCTCG 58.444 57.895 10.89 10.89 45.73 4.04
266 267 1.912110 GTTCGATACAGTGCGTGTCTC 59.088 52.381 0.00 0.00 40.94 3.36
267 268 1.728179 CGTTCGATACAGTGCGTGTCT 60.728 52.381 0.00 0.00 40.94 3.41
268 269 0.633733 CGTTCGATACAGTGCGTGTC 59.366 55.000 0.00 0.00 40.94 3.67
269 270 0.239082 TCGTTCGATACAGTGCGTGT 59.761 50.000 0.00 0.00 43.86 4.49
270 271 1.057285 GTTCGTTCGATACAGTGCGTG 59.943 52.381 0.00 0.00 0.00 5.34
271 272 1.334054 GTTCGTTCGATACAGTGCGT 58.666 50.000 0.00 0.00 0.00 5.24
272 273 0.290840 CGTTCGTTCGATACAGTGCG 59.709 55.000 0.00 0.00 0.00 5.34
273 274 0.638746 CCGTTCGTTCGATACAGTGC 59.361 55.000 0.00 0.00 0.00 4.40
274 275 2.174764 CTCCGTTCGTTCGATACAGTG 58.825 52.381 0.00 0.00 0.00 3.66
275 276 1.131883 CCTCCGTTCGTTCGATACAGT 59.868 52.381 0.00 0.00 0.00 3.55
276 277 1.399440 TCCTCCGTTCGTTCGATACAG 59.601 52.381 0.00 0.00 0.00 2.74
277 278 1.131126 GTCCTCCGTTCGTTCGATACA 59.869 52.381 0.00 0.00 0.00 2.29
278 279 1.820092 GTCCTCCGTTCGTTCGATAC 58.180 55.000 0.00 0.00 0.00 2.24
279 280 0.374758 CGTCCTCCGTTCGTTCGATA 59.625 55.000 0.00 0.00 0.00 2.92
280 281 1.136147 CGTCCTCCGTTCGTTCGAT 59.864 57.895 0.00 0.00 0.00 3.59
281 282 1.904852 CTCGTCCTCCGTTCGTTCGA 61.905 60.000 3.93 0.00 37.94 3.71
282 283 1.511464 CTCGTCCTCCGTTCGTTCG 60.511 63.158 0.00 0.00 37.94 3.95
283 284 1.154073 CCTCGTCCTCCGTTCGTTC 60.154 63.158 0.00 0.00 37.94 3.95
284 285 2.960170 CCTCGTCCTCCGTTCGTT 59.040 61.111 0.00 0.00 37.94 3.85
285 286 3.745803 GCCTCGTCCTCCGTTCGT 61.746 66.667 0.00 0.00 37.94 3.85
286 287 3.064987 ATGCCTCGTCCTCCGTTCG 62.065 63.158 0.00 0.00 37.94 3.95
287 288 1.519455 CATGCCTCGTCCTCCGTTC 60.519 63.158 0.00 0.00 37.94 3.95
288 289 2.579201 CATGCCTCGTCCTCCGTT 59.421 61.111 0.00 0.00 37.94 4.44
289 290 4.148825 GCATGCCTCGTCCTCCGT 62.149 66.667 6.36 0.00 37.94 4.69
290 291 3.451556 ATGCATGCCTCGTCCTCCG 62.452 63.158 16.68 0.00 38.13 4.63
291 292 1.596477 GATGCATGCCTCGTCCTCC 60.596 63.158 16.68 0.00 0.00 4.30
292 293 1.596477 GGATGCATGCCTCGTCCTC 60.596 63.158 16.68 0.00 36.83 3.71
293 294 2.321263 CTGGATGCATGCCTCGTCCT 62.321 60.000 16.68 0.00 39.71 3.85
294 295 1.890979 CTGGATGCATGCCTCGTCC 60.891 63.158 16.68 16.84 39.50 4.79
295 296 0.250209 ATCTGGATGCATGCCTCGTC 60.250 55.000 16.68 8.01 0.00 4.20
296 297 1.051008 TATCTGGATGCATGCCTCGT 58.949 50.000 16.68 4.84 0.00 4.18
297 298 2.398252 ATATCTGGATGCATGCCTCG 57.602 50.000 16.68 3.38 0.00 4.63
298 299 4.778579 ACATATATCTGGATGCATGCCTC 58.221 43.478 16.68 15.19 0.00 4.70
299 300 4.857130 ACATATATCTGGATGCATGCCT 57.143 40.909 16.68 4.84 0.00 4.75
340 341 3.610911 TGAATCGCTGTACTCTGAGAGA 58.389 45.455 17.71 0.00 33.32 3.10
341 342 4.036144 TCATGAATCGCTGTACTCTGAGAG 59.964 45.833 12.44 8.15 35.52 3.20
351 352 0.802222 CGACGGTCATGAATCGCTGT 60.802 55.000 16.52 7.31 0.00 4.40
371 372 4.414852 CAGAACGCATCAAAAATCCGATT 58.585 39.130 0.00 0.00 0.00 3.34
540 544 2.650778 GGTGCCGCCTCCTTTTTG 59.349 61.111 0.00 0.00 0.00 2.44
555 559 2.063774 CTAGGGTTTCACCACGGGT 58.936 57.895 0.00 0.00 41.02 5.28
637 641 4.742201 GGCGCCTGCGAGAAGACA 62.742 66.667 22.15 0.00 44.10 3.41
1073 1133 1.014044 GCACAGATCGAGCGACCAAA 61.014 55.000 0.00 0.00 0.00 3.28
1076 1136 2.583593 GGCACAGATCGAGCGACC 60.584 66.667 0.00 0.00 30.93 4.79
1369 1433 4.536765 AGCACAAAGAAGGAGAGGAAAAA 58.463 39.130 0.00 0.00 0.00 1.94
1754 1842 7.335924 GGACAACAGTAAATTGAAGCCTACATA 59.664 37.037 0.00 0.00 0.00 2.29
1886 1977 5.945784 AGCATTGACTGAATAGGTAGCAAAA 59.054 36.000 0.00 0.00 0.00 2.44
2067 2220 6.214412 AGGTGAACTGACCTTTCTCTAATCAT 59.786 38.462 0.00 0.00 44.53 2.45
2189 2372 4.698780 GTGCCTAAGGTAAAATCGAAAGGT 59.301 41.667 0.00 0.00 0.00 3.50
2275 2458 8.915871 TGCAATCAAAGATAAGATTTGTTAGC 57.084 30.769 0.00 0.00 38.50 3.09
2317 2500 1.602237 CTTTCCCAGGCGAGCCTAA 59.398 57.895 17.13 4.98 46.28 2.69


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

AutoCloner maintained by Alex Coulton.