Multiple sequence alignment - TraesCS3D01G407200

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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 TraesCS3D01G407200 chr3D 100.000 2966 0 0 1 2966 520704511 520701546 0.000000e+00 5478.0
1 TraesCS3D01G407200 chr3D 88.393 1680 161 17 695 2360 520684427 520682768 0.000000e+00 1991.0
2 TraesCS3D01G407200 chr3D 88.594 1508 130 14 593 2083 520678598 520677116 0.000000e+00 1794.0
3 TraesCS3D01G407200 chr3D 85.214 514 61 12 1849 2360 520656289 520655789 5.670000e-142 514.0
4 TraesCS3D01G407200 chr3D 84.795 342 30 11 616 941 520642203 520641868 1.030000e-84 324.0
5 TraesCS3D01G407200 chr3D 85.312 320 33 7 272 583 520642583 520642270 4.770000e-83 318.0
6 TraesCS3D01G407200 chr3B 91.806 1550 108 10 984 2515 686021973 686020425 0.000000e+00 2141.0
7 TraesCS3D01G407200 chr3B 89.771 1574 128 17 597 2152 685980465 685978907 0.000000e+00 1984.0
8 TraesCS3D01G407200 chr3B 86.947 1762 181 25 593 2329 685942013 685940276 0.000000e+00 1934.0
9 TraesCS3D01G407200 chr3B 87.997 1508 138 16 593 2083 685910514 685909033 0.000000e+00 1742.0
10 TraesCS3D01G407200 chr3B 92.506 1201 89 1 984 2184 686044601 686043402 0.000000e+00 1718.0
11 TraesCS3D01G407200 chr3B 86.327 1492 145 26 616 2083 685875546 685874090 0.000000e+00 1570.0
12 TraesCS3D01G407200 chr3B 85.843 1448 190 13 915 2360 685882793 685881359 0.000000e+00 1524.0
13 TraesCS3D01G407200 chr3B 89.224 464 19 15 2507 2966 686020247 686019811 4.320000e-153 551.0
14 TraesCS3D01G407200 chr3B 87.689 463 20 17 2507 2966 685945579 685945151 3.410000e-139 505.0
15 TraesCS3D01G407200 chr3B 91.176 374 27 4 2145 2515 685978073 685977703 1.230000e-138 503.0
16 TraesCS3D01G407200 chr3B 83.784 333 38 8 268 591 685764153 685763828 4.800000e-78 302.0
17 TraesCS3D01G407200 chr3B 83.591 323 41 9 272 591 685875913 685875600 2.890000e-75 292.0
18 TraesCS3D01G407200 chr3B 87.879 231 26 1 328 556 686025824 686025594 1.350000e-68 270.0
19 TraesCS3D01G407200 chr3B 86.147 231 30 1 328 556 686045881 686045651 6.350000e-62 248.0
20 TraesCS3D01G407200 chr3A 87.574 1513 140 15 593 2083 655995329 655993843 0.000000e+00 1709.0
21 TraesCS3D01G407200 chr3A 83.841 328 36 8 272 591 655937353 655937035 2.240000e-76 296.0
22 TraesCS3D01G407200 chr3A 83.082 331 39 8 269 591 658186123 658186444 4.840000e-73 285.0
23 TraesCS3D01G407200 chr3A 92.105 38 2 1 2740 2777 487441484 487441448 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 TraesCS3D01G407200 chr3D 520701546 520704511 2965 True 5478.000000 5478 100.000000 1 2966 1 chr3D.!!$R4 2965
1 TraesCS3D01G407200 chr3D 520682768 520684427 1659 True 1991.000000 1991 88.393000 695 2360 1 chr3D.!!$R3 1665
2 TraesCS3D01G407200 chr3D 520677116 520678598 1482 True 1794.000000 1794 88.594000 593 2083 1 chr3D.!!$R2 1490
3 TraesCS3D01G407200 chr3D 520655789 520656289 500 True 514.000000 514 85.214000 1849 2360 1 chr3D.!!$R1 511
4 TraesCS3D01G407200 chr3D 520641868 520642583 715 True 321.000000 324 85.053500 272 941 2 chr3D.!!$R5 669
5 TraesCS3D01G407200 chr3B 685909033 685910514 1481 True 1742.000000 1742 87.997000 593 2083 1 chr3B.!!$R3 1490
6 TraesCS3D01G407200 chr3B 685881359 685882793 1434 True 1524.000000 1524 85.843000 915 2360 1 chr3B.!!$R2 1445
7 TraesCS3D01G407200 chr3B 685977703 685980465 2762 True 1243.500000 1984 90.473500 597 2515 2 chr3B.!!$R6 1918
8 TraesCS3D01G407200 chr3B 685940276 685945579 5303 True 1219.500000 1934 87.318000 593 2966 2 chr3B.!!$R5 2373
9 TraesCS3D01G407200 chr3B 686019811 686025824 6013 True 987.333333 2141 89.636333 328 2966 3 chr3B.!!$R7 2638
10 TraesCS3D01G407200 chr3B 686043402 686045881 2479 True 983.000000 1718 89.326500 328 2184 2 chr3B.!!$R8 1856
11 TraesCS3D01G407200 chr3B 685874090 685875913 1823 True 931.000000 1570 84.959000 272 2083 2 chr3B.!!$R4 1811
12 TraesCS3D01G407200 chr3A 655993843 655995329 1486 True 1709.000000 1709 87.574000 593 2083 1 chr3A.!!$R3 1490

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
253 254 0.039472 TGGCATGGCTGTGTTATGGT 59.961 50.0 21.08 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 7725 0.32121 ATGGGTTCGCGACAATCACA 60.321 50.0 9.15 7.79 0.0 3.58 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
26 27 6.408869 TGATGTGACAGACATGTATGACATT 58.591 36.000 26.38 16.76 45.90 2.71
27 28 6.536224 TGATGTGACAGACATGTATGACATTC 59.464 38.462 26.38 22.81 45.90 2.67
28 29 5.792741 TGTGACAGACATGTATGACATTCA 58.207 37.500 26.38 17.31 40.68 2.57
29 30 6.408869 TGTGACAGACATGTATGACATTCAT 58.591 36.000 26.38 2.20 40.68 2.57
31 32 6.536224 GTGACAGACATGTATGACATTCATGA 59.464 38.462 30.53 12.60 40.68 3.07
34 35 5.758784 CAGACATGTATGACATTCATGAGCT 59.241 40.000 30.53 24.26 39.52 4.09
35 36 5.758784 AGACATGTATGACATTCATGAGCTG 59.241 40.000 30.53 13.89 39.52 4.24
36 37 4.820173 ACATGTATGACATTCATGAGCTGG 59.180 41.667 30.53 12.04 39.52 4.85
38 39 4.193865 TGTATGACATTCATGAGCTGGTG 58.806 43.478 10.91 0.00 37.70 4.17
39 40 3.639672 ATGACATTCATGAGCTGGTGA 57.360 42.857 10.91 0.00 35.43 4.02
40 41 3.421919 TGACATTCATGAGCTGGTGAA 57.578 42.857 11.53 11.53 38.57 3.18
41 42 3.340928 TGACATTCATGAGCTGGTGAAG 58.659 45.455 13.81 9.50 37.72 3.02
42 43 3.244665 TGACATTCATGAGCTGGTGAAGT 60.245 43.478 13.81 11.73 37.72 3.01
43 44 4.020307 TGACATTCATGAGCTGGTGAAGTA 60.020 41.667 13.81 1.41 37.72 2.24
46 47 2.820178 TCATGAGCTGGTGAAGTAGGA 58.180 47.619 0.00 0.00 0.00 2.94
48 49 2.604912 TGAGCTGGTGAAGTAGGAGA 57.395 50.000 0.00 0.00 0.00 3.71
49 50 2.889512 TGAGCTGGTGAAGTAGGAGAA 58.110 47.619 0.00 0.00 0.00 2.87
52 53 2.093235 AGCTGGTGAAGTAGGAGAATGC 60.093 50.000 0.00 0.00 0.00 3.56
54 55 3.683847 GCTGGTGAAGTAGGAGAATGCAT 60.684 47.826 0.00 0.00 0.00 3.96
55 56 3.875727 CTGGTGAAGTAGGAGAATGCATG 59.124 47.826 0.00 0.00 0.00 4.06
58 59 4.095483 GGTGAAGTAGGAGAATGCATGTTG 59.905 45.833 0.00 0.00 0.00 3.33
59 60 4.697352 GTGAAGTAGGAGAATGCATGTTGT 59.303 41.667 0.00 0.00 0.00 3.32
60 61 5.874810 GTGAAGTAGGAGAATGCATGTTGTA 59.125 40.000 0.00 0.00 0.00 2.41
61 62 6.371548 GTGAAGTAGGAGAATGCATGTTGTAA 59.628 38.462 0.00 0.00 0.00 2.41
64 65 6.711277 AGTAGGAGAATGCATGTTGTAAGAA 58.289 36.000 0.00 0.00 0.00 2.52
65 66 7.341805 AGTAGGAGAATGCATGTTGTAAGAAT 58.658 34.615 0.00 0.00 0.00 2.40
67 68 9.109393 GTAGGAGAATGCATGTTGTAAGAATTA 57.891 33.333 0.00 0.00 0.00 1.40
69 70 8.049117 AGGAGAATGCATGTTGTAAGAATTAGA 58.951 33.333 0.00 0.00 0.00 2.10
70 71 8.677300 GGAGAATGCATGTTGTAAGAATTAGAA 58.323 33.333 0.00 0.00 30.75 2.10
72 73 9.236006 AGAATGCATGTTGTAAGAATTAGAAGT 57.764 29.630 0.00 0.00 34.26 3.01
75 76 9.672673 ATGCATGTTGTAAGAATTAGAAGTAGT 57.327 29.630 0.00 0.00 34.26 2.73
76 77 8.935844 TGCATGTTGTAAGAATTAGAAGTAGTG 58.064 33.333 0.00 0.00 34.26 2.74
87 88 3.769739 AGAAGTAGTGAATGTGGTGCA 57.230 42.857 0.00 0.00 0.00 4.57
88 89 4.292186 AGAAGTAGTGAATGTGGTGCAT 57.708 40.909 0.00 0.00 40.03 3.96
89 90 4.005650 AGAAGTAGTGAATGTGGTGCATG 58.994 43.478 0.00 0.00 37.96 4.06
90 91 3.423539 AGTAGTGAATGTGGTGCATGT 57.576 42.857 0.00 0.00 37.96 3.21
91 92 3.338249 AGTAGTGAATGTGGTGCATGTC 58.662 45.455 0.00 0.00 37.96 3.06
92 93 2.574006 AGTGAATGTGGTGCATGTCT 57.426 45.000 0.00 0.00 37.96 3.41
93 94 2.430465 AGTGAATGTGGTGCATGTCTC 58.570 47.619 0.00 0.00 37.96 3.36
96 97 3.004629 GTGAATGTGGTGCATGTCTCAAA 59.995 43.478 0.00 0.00 37.96 2.69
97 98 3.635836 TGAATGTGGTGCATGTCTCAAAA 59.364 39.130 0.00 0.00 37.96 2.44
98 99 4.099113 TGAATGTGGTGCATGTCTCAAAAA 59.901 37.500 0.00 0.00 37.96 1.94
100 101 5.981088 ATGTGGTGCATGTCTCAAAAATA 57.019 34.783 0.00 0.00 36.26 1.40
102 103 6.343716 TGTGGTGCATGTCTCAAAAATAAT 57.656 33.333 0.00 0.00 0.00 1.28
103 104 6.157904 TGTGGTGCATGTCTCAAAAATAATG 58.842 36.000 0.00 0.00 0.00 1.90
104 105 5.062558 GTGGTGCATGTCTCAAAAATAATGC 59.937 40.000 0.00 0.00 40.57 3.56
105 106 5.047164 TGGTGCATGTCTCAAAAATAATGCT 60.047 36.000 6.95 0.00 40.74 3.79
107 108 7.147863 TGGTGCATGTCTCAAAAATAATGCTAT 60.148 33.333 6.95 0.00 40.74 2.97
110 111 7.707464 TGCATGTCTCAAAAATAATGCTATTGG 59.293 33.333 6.95 0.00 40.74 3.16
112 113 9.976511 CATGTCTCAAAAATAATGCTATTGGAT 57.023 29.630 0.00 0.00 0.00 3.41
113 114 9.976511 ATGTCTCAAAAATAATGCTATTGGATG 57.023 29.630 0.00 0.00 0.00 3.51
114 115 7.922278 TGTCTCAAAAATAATGCTATTGGATGC 59.078 33.333 0.00 0.00 0.00 3.91
115 116 8.139989 GTCTCAAAAATAATGCTATTGGATGCT 58.860 33.333 0.00 0.00 0.00 3.79
116 117 8.139350 TCTCAAAAATAATGCTATTGGATGCTG 58.861 33.333 0.00 0.00 0.00 4.41
117 118 7.211573 TCAAAAATAATGCTATTGGATGCTGG 58.788 34.615 0.00 0.00 0.00 4.85
118 119 4.796038 AATAATGCTATTGGATGCTGGC 57.204 40.909 0.00 0.00 0.00 4.85
120 121 2.304221 ATGCTATTGGATGCTGGCAT 57.696 45.000 7.86 7.86 39.69 4.40
121 122 1.324383 TGCTATTGGATGCTGGCATG 58.676 50.000 13.04 0.00 36.70 4.06
122 123 0.601558 GCTATTGGATGCTGGCATGG 59.398 55.000 13.04 0.00 36.70 3.66
123 124 0.601558 CTATTGGATGCTGGCATGGC 59.398 55.000 13.29 13.29 36.70 4.40
124 125 0.106116 TATTGGATGCTGGCATGGCA 60.106 50.000 21.97 21.97 44.05 4.92
131 132 1.038681 TGCTGGCATGGCATACTTGG 61.039 55.000 23.59 10.93 34.56 3.61
133 134 0.742505 CTGGCATGGCATACTTGGTG 59.257 55.000 23.59 4.36 0.00 4.17
134 135 0.330941 TGGCATGGCATACTTGGTGA 59.669 50.000 19.43 0.00 0.00 4.02
135 136 1.027357 GGCATGGCATACTTGGTGAG 58.973 55.000 15.47 0.00 0.00 3.51
136 137 1.027357 GCATGGCATACTTGGTGAGG 58.973 55.000 0.00 0.00 0.00 3.86
139 140 1.357137 TGGCATACTTGGTGAGGTGA 58.643 50.000 0.00 0.00 0.00 4.02
140 141 1.702401 TGGCATACTTGGTGAGGTGAA 59.298 47.619 0.00 0.00 0.00 3.18
142 143 2.749621 GGCATACTTGGTGAGGTGAAAG 59.250 50.000 0.00 0.00 0.00 2.62
144 145 2.561478 TACTTGGTGAGGTGAAAGGC 57.439 50.000 0.00 0.00 0.00 4.35
145 146 0.846693 ACTTGGTGAGGTGAAAGGCT 59.153 50.000 0.00 0.00 0.00 4.58
146 147 1.242076 CTTGGTGAGGTGAAAGGCTG 58.758 55.000 0.00 0.00 0.00 4.85
147 148 0.823356 TTGGTGAGGTGAAAGGCTGC 60.823 55.000 0.00 0.00 0.00 5.25
148 149 1.228245 GGTGAGGTGAAAGGCTGCA 60.228 57.895 0.50 0.00 0.00 4.41
149 150 0.610232 GGTGAGGTGAAAGGCTGCAT 60.610 55.000 0.50 0.00 0.00 3.96
150 151 0.524862 GTGAGGTGAAAGGCTGCATG 59.475 55.000 0.50 0.00 0.00 4.06
151 152 0.111061 TGAGGTGAAAGGCTGCATGT 59.889 50.000 0.50 0.00 0.00 3.21
152 153 1.251251 GAGGTGAAAGGCTGCATGTT 58.749 50.000 0.50 0.00 0.00 2.71
153 154 2.224744 TGAGGTGAAAGGCTGCATGTTA 60.225 45.455 0.50 0.00 0.00 2.41
154 155 3.019564 GAGGTGAAAGGCTGCATGTTAT 58.980 45.455 0.50 0.00 0.00 1.89
156 157 3.834231 AGGTGAAAGGCTGCATGTTATTT 59.166 39.130 0.50 0.00 0.00 1.40
158 159 5.480073 AGGTGAAAGGCTGCATGTTATTTTA 59.520 36.000 0.50 0.00 0.00 1.52
159 160 6.155049 AGGTGAAAGGCTGCATGTTATTTTAT 59.845 34.615 0.50 0.00 0.00 1.40
160 161 6.818142 GGTGAAAGGCTGCATGTTATTTTATT 59.182 34.615 0.50 0.00 0.00 1.40
161 162 7.334171 GGTGAAAGGCTGCATGTTATTTTATTT 59.666 33.333 0.50 0.00 0.00 1.40
162 163 8.720562 GTGAAAGGCTGCATGTTATTTTATTTT 58.279 29.630 0.50 0.00 0.00 1.82
163 164 9.282569 TGAAAGGCTGCATGTTATTTTATTTTT 57.717 25.926 0.50 0.00 0.00 1.94
190 191 9.717942 TTTGCTTGTAATAGGCATAATTTTTGT 57.282 25.926 0.00 0.00 41.39 2.83
218 219 9.666191 AGAATATAGGATATAGGATGCACATCA 57.334 33.333 12.43 0.00 39.54 3.07
221 222 5.171339 AGGATATAGGATGCACATCAACC 57.829 43.478 12.43 6.09 39.54 3.77
222 223 4.598807 AGGATATAGGATGCACATCAACCA 59.401 41.667 12.43 0.00 39.86 3.67
223 224 4.940046 GGATATAGGATGCACATCAACCAG 59.060 45.833 12.43 0.00 39.86 4.00
224 225 5.280164 GGATATAGGATGCACATCAACCAGA 60.280 44.000 12.43 0.00 39.86 3.86
225 226 4.719026 ATAGGATGCACATCAACCAGAT 57.281 40.909 12.43 0.00 39.86 2.90
227 228 2.240414 AGGATGCACATCAACCAGATCA 59.760 45.455 12.43 0.00 39.86 2.92
228 229 2.617308 GGATGCACATCAACCAGATCAG 59.383 50.000 12.43 0.00 39.54 2.90
229 230 2.118313 TGCACATCAACCAGATCAGG 57.882 50.000 1.93 1.93 33.72 3.86
230 231 0.737219 GCACATCAACCAGATCAGGC 59.263 55.000 3.64 0.00 33.72 4.85
231 232 1.681166 GCACATCAACCAGATCAGGCT 60.681 52.381 3.64 0.00 33.72 4.58
232 233 2.286872 CACATCAACCAGATCAGGCTC 58.713 52.381 3.64 0.00 33.72 4.70
233 234 1.134580 ACATCAACCAGATCAGGCTCG 60.135 52.381 3.64 0.00 33.72 5.03
235 236 0.247460 TCAACCAGATCAGGCTCGTG 59.753 55.000 3.64 0.00 0.00 4.35
237 238 2.202987 CCAGATCAGGCTCGTGGC 60.203 66.667 2.35 2.35 40.90 5.01
244 245 4.790962 AGGCTCGTGGCATGGCTG 62.791 66.667 21.08 12.87 44.01 4.85
246 247 3.807538 GCTCGTGGCATGGCTGTG 61.808 66.667 21.08 13.94 41.35 3.66
248 249 1.968017 CTCGTGGCATGGCTGTGTT 60.968 57.895 21.08 0.00 0.00 3.32
251 252 0.099259 CGTGGCATGGCTGTGTTATG 59.901 55.000 21.08 0.13 0.00 1.90
252 253 0.457035 GTGGCATGGCTGTGTTATGG 59.543 55.000 21.08 0.00 0.00 2.74
253 254 0.039472 TGGCATGGCTGTGTTATGGT 59.961 50.000 21.08 0.00 0.00 3.55
255 256 1.176527 GCATGGCTGTGTTATGGTGT 58.823 50.000 0.00 0.00 0.00 4.16
256 257 1.545582 GCATGGCTGTGTTATGGTGTT 59.454 47.619 0.00 0.00 0.00 3.32
257 258 2.752354 GCATGGCTGTGTTATGGTGTTA 59.248 45.455 0.00 0.00 0.00 2.41
258 259 3.181497 GCATGGCTGTGTTATGGTGTTAG 60.181 47.826 0.00 0.00 0.00 2.34
259 260 4.260985 CATGGCTGTGTTATGGTGTTAGA 58.739 43.478 0.00 0.00 0.00 2.10
261 262 4.720046 TGGCTGTGTTATGGTGTTAGAAA 58.280 39.130 0.00 0.00 0.00 2.52
262 263 5.133941 TGGCTGTGTTATGGTGTTAGAAAA 58.866 37.500 0.00 0.00 0.00 2.29
263 264 5.009210 TGGCTGTGTTATGGTGTTAGAAAAC 59.991 40.000 0.00 0.00 36.07 2.43
264 265 5.009210 GGCTGTGTTATGGTGTTAGAAAACA 59.991 40.000 0.00 0.00 43.32 2.83
265 266 6.460399 GGCTGTGTTATGGTGTTAGAAAACAA 60.460 38.462 0.00 0.00 46.84 2.83
296 297 3.389925 AGTCACAAAATTGGCACATGG 57.610 42.857 0.00 0.00 39.30 3.66
299 300 3.876320 GTCACAAAATTGGCACATGGTTT 59.124 39.130 0.00 0.00 39.30 3.27
301 302 4.946157 TCACAAAATTGGCACATGGTTTTT 59.054 33.333 0.00 0.00 39.30 1.94
373 374 8.388853 GCTAGTAGTATTCTAAACCAAAAGTGC 58.611 37.037 0.00 0.00 0.00 4.40
420 424 9.840427 TGTATAAAATAGAAGCAAAAAGTCTGC 57.160 29.630 0.00 0.00 40.24 4.26
422 426 4.425577 AATAGAAGCAAAAAGTCTGCCG 57.574 40.909 0.00 0.00 40.86 5.69
427 431 1.199624 GCAAAAAGTCTGCCGTTGTG 58.800 50.000 0.00 0.00 33.51 3.33
571 581 7.428183 ACATATCGCATGTTGAATAACGAAAAC 59.572 33.333 0.00 0.00 39.71 2.43
573 583 5.143660 TCGCATGTTGAATAACGAAAACTG 58.856 37.500 0.00 0.00 39.71 3.16
628 3615 8.826710 CATATACAACACAATATTTCGTGAGGT 58.173 33.333 11.70 10.69 36.91 3.85
660 3649 4.793201 TCTTAGAGGATCATCAGGACGAA 58.207 43.478 10.44 0.00 37.82 3.85
690 3681 5.298083 CAACTTTCGCGCTAATCATATACG 58.702 41.667 5.56 0.00 0.00 3.06
691 3682 4.790878 ACTTTCGCGCTAATCATATACGA 58.209 39.130 5.56 0.00 0.00 3.43
692 3683 5.217393 ACTTTCGCGCTAATCATATACGAA 58.783 37.500 5.56 0.00 36.40 3.85
693 3684 5.862323 ACTTTCGCGCTAATCATATACGAAT 59.138 36.000 5.56 0.00 37.81 3.34
723 3717 3.271014 CAGCCTCGTGCAGCAAAT 58.729 55.556 0.00 0.00 44.83 2.32
735 3735 1.080298 AGCAAATGAAAGCTGCGGC 60.080 52.632 10.33 10.33 40.13 6.53
739 3739 1.181098 AAATGAAAGCTGCGGCAGGT 61.181 50.000 27.50 27.50 44.48 4.00
809 3818 3.380004 TCAAACACGCTTCCACAAAATCT 59.620 39.130 0.00 0.00 0.00 2.40
810 3819 4.111916 CAAACACGCTTCCACAAAATCTT 58.888 39.130 0.00 0.00 0.00 2.40
811 3820 5.066634 TCAAACACGCTTCCACAAAATCTTA 59.933 36.000 0.00 0.00 0.00 2.10
812 3821 4.483476 ACACGCTTCCACAAAATCTTAC 57.517 40.909 0.00 0.00 0.00 2.34
813 3822 3.252458 ACACGCTTCCACAAAATCTTACC 59.748 43.478 0.00 0.00 0.00 2.85
814 3823 3.252215 CACGCTTCCACAAAATCTTACCA 59.748 43.478 0.00 0.00 0.00 3.25
815 3824 3.886505 ACGCTTCCACAAAATCTTACCAA 59.113 39.130 0.00 0.00 0.00 3.67
816 3825 4.226761 CGCTTCCACAAAATCTTACCAAC 58.773 43.478 0.00 0.00 0.00 3.77
817 3826 4.261405 CGCTTCCACAAAATCTTACCAACA 60.261 41.667 0.00 0.00 0.00 3.33
818 3827 5.596845 GCTTCCACAAAATCTTACCAACAA 58.403 37.500 0.00 0.00 0.00 2.83
819 3828 5.691754 GCTTCCACAAAATCTTACCAACAAG 59.308 40.000 0.00 0.00 0.00 3.16
820 3829 6.682861 GCTTCCACAAAATCTTACCAACAAGT 60.683 38.462 0.00 0.00 0.00 3.16
821 3830 6.783708 TCCACAAAATCTTACCAACAAGTT 57.216 33.333 0.00 0.00 0.00 2.66
822 3831 6.801575 TCCACAAAATCTTACCAACAAGTTC 58.198 36.000 0.00 0.00 0.00 3.01
823 3832 6.378564 TCCACAAAATCTTACCAACAAGTTCA 59.621 34.615 0.00 0.00 0.00 3.18
824 3833 7.038659 CCACAAAATCTTACCAACAAGTTCAA 58.961 34.615 0.00 0.00 0.00 2.69
825 3834 7.010091 CCACAAAATCTTACCAACAAGTTCAAC 59.990 37.037 0.00 0.00 0.00 3.18
826 3835 7.543868 CACAAAATCTTACCAACAAGTTCAACA 59.456 33.333 0.00 0.00 0.00 3.33
827 3836 7.544217 ACAAAATCTTACCAACAAGTTCAACAC 59.456 33.333 0.00 0.00 0.00 3.32
828 3837 5.767816 ATCTTACCAACAAGTTCAACACC 57.232 39.130 0.00 0.00 0.00 4.16
834 3866 1.102978 ACAAGTTCAACACCCTGCAC 58.897 50.000 0.00 0.00 0.00 4.57
841 3873 2.209315 AACACCCTGCACAATGGCC 61.209 57.895 0.00 0.00 0.00 5.36
869 3902 8.235359 ACTATATATAGCTTCCATACCGTTCC 57.765 38.462 18.00 0.00 33.68 3.62
894 3928 0.108207 CCCTCACATCCATCTCTGCC 59.892 60.000 0.00 0.00 0.00 4.85
909 6511 6.267014 CCATCTCTGCCATATTCCTTCATTTT 59.733 38.462 0.00 0.00 0.00 1.82
942 6547 0.313043 GCTTGCCAATCCATCCATCG 59.687 55.000 0.00 0.00 0.00 3.84
953 6558 1.067516 CCATCCATCGGTGGCAAATTC 59.932 52.381 10.80 0.00 45.63 2.17
1020 6631 2.991540 GCCGCTTCCCCTTGCTTT 60.992 61.111 0.00 0.00 0.00 3.51
1021 6632 2.574018 GCCGCTTCCCCTTGCTTTT 61.574 57.895 0.00 0.00 0.00 2.27
1179 6796 2.047655 GTCCGGCGTGTCATCCAA 60.048 61.111 6.01 0.00 0.00 3.53
1327 6944 3.607370 GAGGTCCCTGCCAACGACC 62.607 68.421 2.32 2.32 45.40 4.79
1422 7039 2.125512 GCCGACATCCTCGCACTT 60.126 61.111 0.00 0.00 41.46 3.16
1593 7210 2.711922 GGCCCTCGACGACACTGAT 61.712 63.158 0.00 0.00 0.00 2.90
1608 7225 0.179089 CTGATCTTGTCGCCCTCCAG 60.179 60.000 0.00 0.00 0.00 3.86
1796 7413 1.084289 GTAATGTTGTCCGACCCTGC 58.916 55.000 0.00 0.00 0.00 4.85
1833 7450 1.289109 CGCCGATCGTTCACAGGTTT 61.289 55.000 15.09 0.00 0.00 3.27
1979 7596 7.814264 AACCCTATTGATGAATGAGATTGAC 57.186 36.000 0.00 0.00 0.00 3.18
1980 7597 6.903516 ACCCTATTGATGAATGAGATTGACA 58.096 36.000 0.00 0.00 0.00 3.58
2052 7672 7.166167 TCATTCTAACTGTAAAGGGTTCCTTC 58.834 38.462 0.00 0.00 43.92 3.46
2129 7754 2.161410 TCGCGAACCCATTCTTTTCATG 59.839 45.455 6.20 0.00 32.12 3.07
2134 7759 1.551883 ACCCATTCTTTTCATGCCAGC 59.448 47.619 0.00 0.00 0.00 4.85
2218 8686 6.813649 GTGTAAGATCACTGCTACAGAATGAA 59.186 38.462 0.78 0.00 36.00 2.57
2289 8764 4.675114 CCTTTGTCAAAACGTGCATAGTTC 59.325 41.667 10.31 0.76 0.00 3.01
2294 8769 6.367421 TGTCAAAACGTGCATAGTTCAATAC 58.633 36.000 10.31 7.83 0.00 1.89
2302 8777 7.045416 ACGTGCATAGTTCAATACCTATTTGA 58.955 34.615 0.00 0.00 0.00 2.69
2360 8835 9.174799 GCAAGTATTTGTGCCTCTGATTTCAGA 62.175 40.741 9.77 9.77 42.04 3.27
2419 8908 2.761208 AGACCTGGTTAGAGTGATTCGG 59.239 50.000 0.00 0.00 0.00 4.30
2424 8913 1.757699 GGTTAGAGTGATTCGGAGCCT 59.242 52.381 0.00 0.00 0.00 4.58
2427 8916 1.144936 GAGTGATTCGGAGCCTGGG 59.855 63.158 0.00 0.00 0.00 4.45
2449 8938 4.802051 GCCGCTCCTGCCCATGAA 62.802 66.667 0.00 0.00 35.36 2.57
2457 8946 3.195396 GCTCCTGCCCATGAACATTAAAA 59.805 43.478 0.00 0.00 0.00 1.52
2567 9242 5.710513 TTCATGGTGTTTGGAGATTTGAG 57.289 39.130 0.00 0.00 0.00 3.02
2667 9343 1.454111 CGACCTCCTCGGATGTCCT 60.454 63.158 13.48 0.00 38.87 3.85
2676 9352 1.548719 CTCGGATGTCCTAACACCACA 59.451 52.381 0.00 0.00 38.48 4.17
2679 9355 3.142951 CGGATGTCCTAACACCACAAAA 58.857 45.455 0.00 0.00 38.48 2.44
2680 9356 3.566322 CGGATGTCCTAACACCACAAAAA 59.434 43.478 0.00 0.00 38.48 1.94
2687 9363 6.814146 TGTCCTAACACCACAAAAATTTTCAC 59.186 34.615 3.41 0.00 0.00 3.18
2817 9500 8.923838 AGACCCAATTATACTATCATGATCCT 57.076 34.615 12.53 0.67 0.00 3.24
2818 9501 8.766476 AGACCCAATTATACTATCATGATCCTG 58.234 37.037 12.53 6.60 0.00 3.86
2819 9502 7.865820 ACCCAATTATACTATCATGATCCTGG 58.134 38.462 12.53 8.09 0.00 4.45
2820 9503 7.092264 ACCCAATTATACTATCATGATCCTGGG 60.092 40.741 12.53 17.29 42.45 4.45
2821 9504 6.769822 CCAATTATACTATCATGATCCTGGGC 59.230 42.308 12.53 0.00 0.00 5.36
2822 9505 7.366281 CCAATTATACTATCATGATCCTGGGCT 60.366 40.741 12.53 0.00 0.00 5.19
2823 9506 6.798427 TTATACTATCATGATCCTGGGCTC 57.202 41.667 12.53 0.00 0.00 4.70
2824 9507 2.981921 ACTATCATGATCCTGGGCTCA 58.018 47.619 12.53 0.00 0.00 4.26
2825 9508 2.905085 ACTATCATGATCCTGGGCTCAG 59.095 50.000 12.53 6.61 40.59 3.35
2826 9509 2.113807 ATCATGATCCTGGGCTCAGA 57.886 50.000 17.43 0.97 43.49 3.27
2827 9510 1.126488 TCATGATCCTGGGCTCAGAC 58.874 55.000 17.43 6.81 43.49 3.51
2828 9511 0.835276 CATGATCCTGGGCTCAGACA 59.165 55.000 17.43 12.64 43.49 3.41
2829 9512 1.420514 CATGATCCTGGGCTCAGACAT 59.579 52.381 17.43 14.39 43.49 3.06
2830 9513 1.588239 TGATCCTGGGCTCAGACATT 58.412 50.000 17.43 0.00 43.49 2.71
2831 9514 2.763039 TGATCCTGGGCTCAGACATTA 58.237 47.619 17.43 0.04 43.49 1.90
2832 9515 3.321039 TGATCCTGGGCTCAGACATTAT 58.679 45.455 17.43 0.00 43.49 1.28
2833 9516 4.492646 TGATCCTGGGCTCAGACATTATA 58.507 43.478 17.43 0.00 43.49 0.98
2834 9517 5.096521 TGATCCTGGGCTCAGACATTATAT 58.903 41.667 17.43 0.00 43.49 0.86
2835 9518 4.897509 TCCTGGGCTCAGACATTATATG 57.102 45.455 17.43 0.00 43.49 1.78
2836 9519 4.492646 TCCTGGGCTCAGACATTATATGA 58.507 43.478 17.43 0.00 43.49 2.15
2837 9520 5.096521 TCCTGGGCTCAGACATTATATGAT 58.903 41.667 17.43 0.00 43.49 2.45
2857 9540 6.183810 TGATCCTGAAGAACATCATGCTAT 57.816 37.500 0.00 0.00 0.00 2.97
2858 9541 6.228995 TGATCCTGAAGAACATCATGCTATC 58.771 40.000 0.00 0.00 0.00 2.08
2895 9578 5.454232 GCGGGAATAAACATTTACACATTCG 59.546 40.000 0.00 0.00 0.00 3.34
2900 9583 8.402472 GGAATAAACATTTACACATTCGATCCA 58.598 33.333 0.00 0.00 0.00 3.41
2918 9601 5.279960 CGATCCAATTATACAGACCCATCCA 60.280 44.000 0.00 0.00 0.00 3.41
2933 9616 4.347583 ACCCATCCATTTTGCTCAAAAAGA 59.652 37.500 11.23 11.20 42.71 2.52
2934 9617 5.163216 ACCCATCCATTTTGCTCAAAAAGAA 60.163 36.000 11.23 1.75 42.71 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.111247 TGTCATACATGTCTGTCACATCATA 57.889 36.000 0.00 0.00 44.60 2.15
1 2 5.981174 TGTCATACATGTCTGTCACATCAT 58.019 37.500 0.00 0.00 44.60 2.45
2 3 5.404466 TGTCATACATGTCTGTCACATCA 57.596 39.130 0.00 0.00 44.60 3.07
3 4 6.536224 TGAATGTCATACATGTCTGTCACATC 59.464 38.462 14.83 14.22 44.60 3.06
4 5 7.012044 CATGAATGTCATACATGTCTGTCACAT 59.988 37.037 12.06 11.39 39.75 3.21
6 7 6.536224 TCATGAATGTCATACATGTCTGTCAC 59.464 38.462 12.06 5.08 37.97 3.67
7 8 6.642430 TCATGAATGTCATACATGTCTGTCA 58.358 36.000 12.17 12.17 37.97 3.58
10 11 5.758784 AGCTCATGAATGTCATACATGTCTG 59.241 40.000 0.00 2.54 37.97 3.51
11 12 5.758784 CAGCTCATGAATGTCATACATGTCT 59.241 40.000 0.00 0.00 37.97 3.41
12 13 5.049612 CCAGCTCATGAATGTCATACATGTC 60.050 44.000 0.00 0.00 37.97 3.06
13 14 4.820173 CCAGCTCATGAATGTCATACATGT 59.180 41.667 2.69 2.69 37.97 3.21
14 15 4.820173 ACCAGCTCATGAATGTCATACATG 59.180 41.667 0.00 0.00 37.97 3.21
15 16 4.820173 CACCAGCTCATGAATGTCATACAT 59.180 41.667 0.00 0.00 41.31 2.29
16 17 4.080975 TCACCAGCTCATGAATGTCATACA 60.081 41.667 0.00 0.00 34.28 2.29
19 20 3.639672 TCACCAGCTCATGAATGTCAT 57.360 42.857 0.00 0.00 37.65 3.06
20 21 3.244665 ACTTCACCAGCTCATGAATGTCA 60.245 43.478 9.14 0.00 34.43 3.58
21 22 3.341823 ACTTCACCAGCTCATGAATGTC 58.658 45.455 9.14 0.00 34.43 3.06
22 23 3.430042 ACTTCACCAGCTCATGAATGT 57.570 42.857 9.14 7.37 34.43 2.71
23 24 3.875727 CCTACTTCACCAGCTCATGAATG 59.124 47.826 9.14 0.00 34.43 2.67
26 27 2.762887 CTCCTACTTCACCAGCTCATGA 59.237 50.000 0.00 0.00 0.00 3.07
27 28 2.762887 TCTCCTACTTCACCAGCTCATG 59.237 50.000 0.00 0.00 0.00 3.07
28 29 3.107402 TCTCCTACTTCACCAGCTCAT 57.893 47.619 0.00 0.00 0.00 2.90
29 30 2.604912 TCTCCTACTTCACCAGCTCA 57.395 50.000 0.00 0.00 0.00 4.26
31 32 2.093235 GCATTCTCCTACTTCACCAGCT 60.093 50.000 0.00 0.00 0.00 4.24
34 35 3.264193 ACATGCATTCTCCTACTTCACCA 59.736 43.478 0.00 0.00 0.00 4.17
35 36 3.878778 ACATGCATTCTCCTACTTCACC 58.121 45.455 0.00 0.00 0.00 4.02
36 37 4.697352 ACAACATGCATTCTCCTACTTCAC 59.303 41.667 0.00 0.00 0.00 3.18
38 39 6.818644 TCTTACAACATGCATTCTCCTACTTC 59.181 38.462 0.00 0.00 0.00 3.01
39 40 6.711277 TCTTACAACATGCATTCTCCTACTT 58.289 36.000 0.00 0.00 0.00 2.24
40 41 6.299805 TCTTACAACATGCATTCTCCTACT 57.700 37.500 0.00 0.00 0.00 2.57
41 42 6.985188 TTCTTACAACATGCATTCTCCTAC 57.015 37.500 0.00 0.00 0.00 3.18
42 43 9.330063 CTAATTCTTACAACATGCATTCTCCTA 57.670 33.333 0.00 0.00 0.00 2.94
43 44 8.049117 TCTAATTCTTACAACATGCATTCTCCT 58.951 33.333 0.00 0.00 0.00 3.69
46 47 9.236006 ACTTCTAATTCTTACAACATGCATTCT 57.764 29.630 0.00 0.00 0.00 2.40
49 50 9.672673 ACTACTTCTAATTCTTACAACATGCAT 57.327 29.630 0.00 0.00 0.00 3.96
58 59 9.654663 ACCACATTCACTACTTCTAATTCTTAC 57.345 33.333 0.00 0.00 0.00 2.34
59 60 9.653287 CACCACATTCACTACTTCTAATTCTTA 57.347 33.333 0.00 0.00 0.00 2.10
60 61 7.119846 GCACCACATTCACTACTTCTAATTCTT 59.880 37.037 0.00 0.00 0.00 2.52
61 62 6.595716 GCACCACATTCACTACTTCTAATTCT 59.404 38.462 0.00 0.00 0.00 2.40
64 65 5.804639 TGCACCACATTCACTACTTCTAAT 58.195 37.500 0.00 0.00 0.00 1.73
65 66 5.222079 TGCACCACATTCACTACTTCTAA 57.778 39.130 0.00 0.00 0.00 2.10
67 68 3.769739 TGCACCACATTCACTACTTCT 57.230 42.857 0.00 0.00 0.00 2.85
69 70 3.753272 GACATGCACCACATTCACTACTT 59.247 43.478 0.00 0.00 36.64 2.24
70 71 3.008375 AGACATGCACCACATTCACTACT 59.992 43.478 0.00 0.00 36.64 2.57
72 73 3.007831 TGAGACATGCACCACATTCACTA 59.992 43.478 0.00 0.00 36.64 2.74
74 75 2.153645 TGAGACATGCACCACATTCAC 58.846 47.619 0.00 0.00 36.64 3.18
75 76 2.565046 TGAGACATGCACCACATTCA 57.435 45.000 0.00 0.00 36.64 2.57
76 77 3.921119 TTTGAGACATGCACCACATTC 57.079 42.857 0.00 0.00 36.64 2.67
79 80 5.781210 TTATTTTTGAGACATGCACCACA 57.219 34.783 0.00 0.00 0.00 4.17
80 81 5.062558 GCATTATTTTTGAGACATGCACCAC 59.937 40.000 0.00 0.00 37.54 4.16
87 88 9.976511 CATCCAATAGCATTATTTTTGAGACAT 57.023 29.630 0.00 0.00 0.00 3.06
88 89 7.922278 GCATCCAATAGCATTATTTTTGAGACA 59.078 33.333 0.00 0.00 0.00 3.41
89 90 8.139989 AGCATCCAATAGCATTATTTTTGAGAC 58.860 33.333 0.00 0.00 0.00 3.36
90 91 8.139350 CAGCATCCAATAGCATTATTTTTGAGA 58.861 33.333 0.00 0.00 0.00 3.27
91 92 7.384115 CCAGCATCCAATAGCATTATTTTTGAG 59.616 37.037 0.00 0.00 0.00 3.02
92 93 7.211573 CCAGCATCCAATAGCATTATTTTTGA 58.788 34.615 0.00 0.00 0.00 2.69
93 94 6.073440 GCCAGCATCCAATAGCATTATTTTTG 60.073 38.462 0.00 0.00 0.00 2.44
96 97 4.589798 TGCCAGCATCCAATAGCATTATTT 59.410 37.500 0.00 0.00 0.00 1.40
97 98 4.154176 TGCCAGCATCCAATAGCATTATT 58.846 39.130 0.00 0.00 0.00 1.40
98 99 3.770046 TGCCAGCATCCAATAGCATTAT 58.230 40.909 0.00 0.00 0.00 1.28
100 101 2.076207 TGCCAGCATCCAATAGCATT 57.924 45.000 0.00 0.00 0.00 3.56
102 103 1.324383 CATGCCAGCATCCAATAGCA 58.676 50.000 1.19 0.00 33.90 3.49
103 104 0.601558 CCATGCCAGCATCCAATAGC 59.398 55.000 1.19 0.00 33.90 2.97
104 105 0.601558 GCCATGCCAGCATCCAATAG 59.398 55.000 1.19 0.00 33.90 1.73
105 106 0.106116 TGCCATGCCAGCATCCAATA 60.106 50.000 1.19 0.00 34.69 1.90
107 108 2.037527 TGCCATGCCAGCATCCAA 59.962 55.556 1.19 0.00 34.69 3.53
112 113 1.038681 CCAAGTATGCCATGCCAGCA 61.039 55.000 0.00 0.00 45.94 4.41
113 114 1.039233 ACCAAGTATGCCATGCCAGC 61.039 55.000 0.00 0.00 0.00 4.85
114 115 0.742505 CACCAAGTATGCCATGCCAG 59.257 55.000 0.00 0.00 0.00 4.85
115 116 0.330941 TCACCAAGTATGCCATGCCA 59.669 50.000 0.00 0.00 0.00 4.92
116 117 1.027357 CTCACCAAGTATGCCATGCC 58.973 55.000 0.00 0.00 0.00 4.40
117 118 1.027357 CCTCACCAAGTATGCCATGC 58.973 55.000 0.00 0.00 0.00 4.06
118 119 2.019249 CACCTCACCAAGTATGCCATG 58.981 52.381 0.00 0.00 0.00 3.66
120 121 1.357137 TCACCTCACCAAGTATGCCA 58.643 50.000 0.00 0.00 0.00 4.92
121 122 2.489938 TTCACCTCACCAAGTATGCC 57.510 50.000 0.00 0.00 0.00 4.40
122 123 2.749621 CCTTTCACCTCACCAAGTATGC 59.250 50.000 0.00 0.00 0.00 3.14
123 124 2.749621 GCCTTTCACCTCACCAAGTATG 59.250 50.000 0.00 0.00 0.00 2.39
124 125 2.644798 AGCCTTTCACCTCACCAAGTAT 59.355 45.455 0.00 0.00 0.00 2.12
125 126 2.054799 AGCCTTTCACCTCACCAAGTA 58.945 47.619 0.00 0.00 0.00 2.24
126 127 0.846693 AGCCTTTCACCTCACCAAGT 59.153 50.000 0.00 0.00 0.00 3.16
127 128 1.242076 CAGCCTTTCACCTCACCAAG 58.758 55.000 0.00 0.00 0.00 3.61
131 132 0.524862 CATGCAGCCTTTCACCTCAC 59.475 55.000 0.00 0.00 0.00 3.51
133 134 1.251251 AACATGCAGCCTTTCACCTC 58.749 50.000 0.00 0.00 0.00 3.85
134 135 2.584835 TAACATGCAGCCTTTCACCT 57.415 45.000 0.00 0.00 0.00 4.00
135 136 3.874392 AATAACATGCAGCCTTTCACC 57.126 42.857 0.00 0.00 0.00 4.02
136 137 7.832503 AATAAAATAACATGCAGCCTTTCAC 57.167 32.000 0.00 0.00 0.00 3.18
164 165 9.717942 ACAAAAATTATGCCTATTACAAGCAAA 57.282 25.926 0.00 0.00 40.46 3.68
192 193 9.666191 TGATGTGCATCCTATATCCTATATTCT 57.334 33.333 9.39 0.00 37.02 2.40
195 196 8.654997 GGTTGATGTGCATCCTATATCCTATAT 58.345 37.037 9.39 0.00 37.02 0.86
196 197 7.623278 TGGTTGATGTGCATCCTATATCCTATA 59.377 37.037 9.39 0.00 37.28 1.31
199 200 4.598807 TGGTTGATGTGCATCCTATATCCT 59.401 41.667 9.39 0.00 37.28 3.24
200 201 4.910195 TGGTTGATGTGCATCCTATATCC 58.090 43.478 9.39 1.46 37.28 2.59
201 202 5.798132 TCTGGTTGATGTGCATCCTATATC 58.202 41.667 9.39 0.00 37.28 1.63
203 204 5.307716 TGATCTGGTTGATGTGCATCCTATA 59.692 40.000 9.39 0.00 37.28 1.31
204 205 4.103627 TGATCTGGTTGATGTGCATCCTAT 59.896 41.667 9.39 0.00 37.28 2.57
205 206 3.455543 TGATCTGGTTGATGTGCATCCTA 59.544 43.478 9.39 0.00 37.28 2.94
207 208 2.617308 CTGATCTGGTTGATGTGCATCC 59.383 50.000 9.39 0.00 37.02 3.51
208 209 2.617308 CCTGATCTGGTTGATGTGCATC 59.383 50.000 10.40 5.30 35.14 3.91
209 210 2.651455 CCTGATCTGGTTGATGTGCAT 58.349 47.619 10.40 0.00 35.14 3.96
211 212 0.737219 GCCTGATCTGGTTGATGTGC 59.263 55.000 18.82 0.00 35.14 4.57
212 213 2.286872 GAGCCTGATCTGGTTGATGTG 58.713 52.381 18.82 0.00 35.14 3.21
213 214 1.134580 CGAGCCTGATCTGGTTGATGT 60.135 52.381 18.82 0.00 35.14 3.06
214 215 1.134580 ACGAGCCTGATCTGGTTGATG 60.135 52.381 18.82 8.48 35.14 3.07
215 216 1.134580 CACGAGCCTGATCTGGTTGAT 60.135 52.381 18.82 4.37 38.27 2.57
217 218 0.742281 CCACGAGCCTGATCTGGTTG 60.742 60.000 18.82 11.61 0.00 3.77
218 219 1.599047 CCACGAGCCTGATCTGGTT 59.401 57.895 18.82 13.73 0.00 3.67
219 220 3.023949 GCCACGAGCCTGATCTGGT 62.024 63.158 18.82 6.92 34.35 4.00
221 222 1.145598 ATGCCACGAGCCTGATCTG 59.854 57.895 0.00 0.00 42.71 2.90
222 223 1.145598 CATGCCACGAGCCTGATCT 59.854 57.895 0.00 0.00 39.28 2.75
223 224 1.890979 CCATGCCACGAGCCTGATC 60.891 63.158 8.51 0.00 39.28 2.92
224 225 2.191375 CCATGCCACGAGCCTGAT 59.809 61.111 8.51 0.00 39.28 2.90
225 226 4.783621 GCCATGCCACGAGCCTGA 62.784 66.667 8.51 0.00 39.28 3.86
227 228 4.790962 CAGCCATGCCACGAGCCT 62.791 66.667 0.00 0.00 42.71 4.58
229 230 3.807538 CACAGCCATGCCACGAGC 61.808 66.667 0.00 0.00 44.14 5.03
230 231 0.673333 TAACACAGCCATGCCACGAG 60.673 55.000 0.00 0.00 0.00 4.18
231 232 0.035534 ATAACACAGCCATGCCACGA 60.036 50.000 0.00 0.00 0.00 4.35
232 233 0.099259 CATAACACAGCCATGCCACG 59.901 55.000 0.00 0.00 0.00 4.94
233 234 0.457035 CCATAACACAGCCATGCCAC 59.543 55.000 0.00 0.00 0.00 5.01
235 236 0.457035 CACCATAACACAGCCATGCC 59.543 55.000 0.00 0.00 0.00 4.40
237 238 4.260985 TCTAACACCATAACACAGCCATG 58.739 43.478 0.00 0.00 0.00 3.66
240 241 5.009210 TGTTTTCTAACACCATAACACAGCC 59.991 40.000 0.00 0.00 39.29 4.85
241 242 6.067263 TGTTTTCTAACACCATAACACAGC 57.933 37.500 0.00 0.00 39.29 4.40
242 243 6.915843 GGTTGTTTTCTAACACCATAACACAG 59.084 38.462 0.00 0.00 43.66 3.66
243 244 6.377429 TGGTTGTTTTCTAACACCATAACACA 59.623 34.615 0.00 0.00 43.66 3.72
244 245 6.797454 TGGTTGTTTTCTAACACCATAACAC 58.203 36.000 0.00 0.00 43.66 3.32
245 246 7.406031 TTGGTTGTTTTCTAACACCATAACA 57.594 32.000 10.75 0.00 43.66 2.41
246 247 8.880878 AATTGGTTGTTTTCTAACACCATAAC 57.119 30.769 10.75 0.00 43.66 1.89
264 265 8.998377 GCCAATTTTGTGACTAATTAATTGGTT 58.002 29.630 17.13 3.08 46.91 3.67
265 266 8.153550 TGCCAATTTTGTGACTAATTAATTGGT 58.846 29.630 16.19 16.19 46.91 3.67
268 269 9.723601 ATGTGCCAATTTTGTGACTAATTAATT 57.276 25.926 5.89 5.89 0.00 1.40
269 270 9.153721 CATGTGCCAATTTTGTGACTAATTAAT 57.846 29.630 0.00 0.00 0.00 1.40
270 271 7.601886 CCATGTGCCAATTTTGTGACTAATTAA 59.398 33.333 0.00 0.00 0.00 1.40
317 318 6.756542 CCACGGAAACTCTTTTCAAGATTTTT 59.243 34.615 4.03 0.13 42.72 1.94
326 327 3.611766 GCCATTCCACGGAAACTCTTTTC 60.612 47.826 1.93 0.00 40.54 2.29
333 334 2.109425 ACTAGCCATTCCACGGAAAC 57.891 50.000 1.93 0.00 37.69 2.78
340 341 7.346175 TGGTTTAGAATACTACTAGCCATTCCA 59.654 37.037 0.00 0.00 0.00 3.53
373 374 1.532868 CGGGAAGTCTTCAACAAGCAG 59.467 52.381 14.49 0.00 0.00 4.24
454 458 7.065803 CCGTGTGATCCTTACATTTGTTCTATT 59.934 37.037 0.00 0.00 0.00 1.73
526 536 1.128692 GTCGTGGCTTTGCATGTACTC 59.871 52.381 0.00 0.00 0.00 2.59
527 537 1.156736 GTCGTGGCTTTGCATGTACT 58.843 50.000 0.00 0.00 0.00 2.73
552 562 6.636850 AGTTCAGTTTTCGTTATTCAACATGC 59.363 34.615 0.00 0.00 34.05 4.06
565 575 4.263800 CGTCAGACAAAGTTCAGTTTTCG 58.736 43.478 0.41 0.00 0.00 3.46
571 581 3.364366 GGATTGCGTCAGACAAAGTTCAG 60.364 47.826 0.41 0.00 0.00 3.02
573 583 2.548057 TGGATTGCGTCAGACAAAGTTC 59.452 45.455 0.41 0.00 0.00 3.01
645 3633 3.491792 GGAAGAGTTCGTCCTGATGATCC 60.492 52.174 6.82 0.00 40.65 3.36
660 3649 0.249911 AGCGCGAAAGTTGGAAGAGT 60.250 50.000 12.10 0.00 0.00 3.24
690 3681 5.237344 ACGAGGCTGCTGACATTATTTATTC 59.763 40.000 0.00 0.00 0.00 1.75
691 3682 5.008019 CACGAGGCTGCTGACATTATTTATT 59.992 40.000 0.00 0.00 0.00 1.40
692 3683 4.512944 CACGAGGCTGCTGACATTATTTAT 59.487 41.667 0.00 0.00 0.00 1.40
693 3684 3.871006 CACGAGGCTGCTGACATTATTTA 59.129 43.478 0.00 0.00 0.00 1.40
701 3695 3.117171 CTGCACGAGGCTGCTGAC 61.117 66.667 0.00 0.00 45.15 3.51
723 3717 2.979676 CACCTGCCGCAGCTTTCA 60.980 61.111 15.36 0.00 40.80 2.69
735 3735 1.884075 TAGCACTGCCGTACCACCTG 61.884 60.000 0.00 0.00 0.00 4.00
739 3739 2.100252 GAGTATTAGCACTGCCGTACCA 59.900 50.000 0.00 0.00 0.00 3.25
809 3818 3.697045 CAGGGTGTTGAACTTGTTGGTAA 59.303 43.478 0.00 0.00 0.00 2.85
810 3819 3.283751 CAGGGTGTTGAACTTGTTGGTA 58.716 45.455 0.00 0.00 0.00 3.25
811 3820 2.099405 CAGGGTGTTGAACTTGTTGGT 58.901 47.619 0.00 0.00 0.00 3.67
812 3821 1.202405 GCAGGGTGTTGAACTTGTTGG 60.202 52.381 0.00 0.00 0.00 3.77
813 3822 1.476085 TGCAGGGTGTTGAACTTGTTG 59.524 47.619 0.00 0.00 0.00 3.33
814 3823 1.476488 GTGCAGGGTGTTGAACTTGTT 59.524 47.619 0.00 0.00 0.00 2.83
815 3824 1.102978 GTGCAGGGTGTTGAACTTGT 58.897 50.000 0.00 0.00 0.00 3.16
816 3825 1.102154 TGTGCAGGGTGTTGAACTTG 58.898 50.000 0.00 0.00 0.00 3.16
817 3826 1.846007 TTGTGCAGGGTGTTGAACTT 58.154 45.000 0.00 0.00 0.00 2.66
818 3827 1.682854 CATTGTGCAGGGTGTTGAACT 59.317 47.619 0.00 0.00 0.00 3.01
819 3828 1.269726 CCATTGTGCAGGGTGTTGAAC 60.270 52.381 0.00 0.00 0.00 3.18
820 3829 1.039068 CCATTGTGCAGGGTGTTGAA 58.961 50.000 0.00 0.00 0.00 2.69
821 3830 1.462731 GCCATTGTGCAGGGTGTTGA 61.463 55.000 0.00 0.00 0.00 3.18
822 3831 1.005867 GCCATTGTGCAGGGTGTTG 60.006 57.895 0.00 0.00 0.00 3.33
823 3832 2.209315 GGCCATTGTGCAGGGTGTT 61.209 57.895 0.00 0.00 0.00 3.32
824 3833 2.601367 GGCCATTGTGCAGGGTGT 60.601 61.111 0.00 0.00 0.00 4.16
825 3834 2.601067 TGGCCATTGTGCAGGGTG 60.601 61.111 0.00 0.00 0.00 4.61
826 3835 2.283388 CTGGCCATTGTGCAGGGT 60.283 61.111 5.51 0.00 0.00 4.34
827 3836 2.036098 TCTGGCCATTGTGCAGGG 59.964 61.111 5.51 0.00 0.00 4.45
828 3837 0.035152 TAGTCTGGCCATTGTGCAGG 60.035 55.000 5.51 0.00 0.00 4.85
834 3866 6.989169 GGAAGCTATATATAGTCTGGCCATTG 59.011 42.308 18.81 0.00 32.96 2.82
841 3873 8.453238 ACGGTATGGAAGCTATATATAGTCTG 57.547 38.462 18.81 6.86 32.96 3.51
894 3928 8.074972 GCTGCTAGAAGAAAATGAAGGAATATG 58.925 37.037 0.27 0.00 0.00 1.78
942 6547 0.319405 AAGCTGCTGAATTTGCCACC 59.681 50.000 1.35 0.00 0.00 4.61
953 6558 4.450053 AGAAGGCTAGAATTAAGCTGCTG 58.550 43.478 1.35 0.00 39.97 4.41
1012 6623 0.940991 GCAGCCAACGAAAAGCAAGG 60.941 55.000 0.00 0.00 0.00 3.61
1146 6763 1.011968 GGACAATGTCGCGTGCACTA 61.012 55.000 16.19 0.00 32.65 2.74
1170 6787 2.622011 GCGGGCGTTTTGGATGACA 61.622 57.895 0.00 0.00 0.00 3.58
1297 6914 1.324005 GGGACCTCCTTCTCGGTCTG 61.324 65.000 8.20 0.00 46.94 3.51
1298 6915 1.000612 GGGACCTCCTTCTCGGTCT 59.999 63.158 8.20 0.00 46.94 3.85
1337 6954 0.601841 GTCGACCACATCAAACCCGT 60.602 55.000 3.51 0.00 0.00 5.28
1422 7039 0.820226 CAACTGAGATCTCGGAGGCA 59.180 55.000 33.50 8.82 39.24 4.75
1577 7194 0.811915 AAGATCAGTGTCGTCGAGGG 59.188 55.000 5.12 0.00 0.00 4.30
1608 7225 3.365265 CCAAAGGTGTGCGCTCCC 61.365 66.667 14.55 8.90 0.00 4.30
1680 7297 0.828022 TGTCGAGGTTCACCAGTGTT 59.172 50.000 0.00 0.00 38.89 3.32
2100 7725 0.321210 ATGGGTTCGCGACAATCACA 60.321 50.000 9.15 7.79 0.00 3.58
2129 7754 2.869233 TTGAAAACAAGTCAGCTGGC 57.131 45.000 11.28 11.28 0.00 4.85
2218 8686 4.240881 AGGTATGCAGTTCCATGACATT 57.759 40.909 0.00 0.00 0.00 2.71
2251 8725 0.667184 AAAGGCAATGGCGCGAAAAG 60.667 50.000 12.10 0.00 42.47 2.27
2360 8835 6.658816 TGAATGTGTACATGCTTATTCCTGTT 59.341 34.615 0.00 0.00 36.56 3.16
2364 8839 7.141363 GGATTGAATGTGTACATGCTTATTCC 58.859 38.462 0.00 0.00 36.56 3.01
2586 9261 9.877178 TTTTTAAAGTTTCTTTGAGCACCATTA 57.123 25.926 5.19 0.00 0.00 1.90
2667 9343 5.168569 TGCGTGAAAATTTTTGTGGTGTTA 58.831 33.333 4.63 0.00 0.00 2.41
2676 9352 3.066380 GCCAGGATGCGTGAAAATTTTT 58.934 40.909 4.63 0.00 31.97 1.94
2679 9355 1.255882 TGCCAGGATGCGTGAAAATT 58.744 45.000 0.00 0.00 31.97 1.82
2680 9356 1.406539 GATGCCAGGATGCGTGAAAAT 59.593 47.619 0.00 0.00 31.97 1.82
2687 9363 0.035036 ATCAGAGATGCCAGGATGCG 59.965 55.000 0.00 0.00 31.97 4.73
2750 9427 4.936411 GGATCATATGCTCCTGATGAACAG 59.064 45.833 16.77 0.00 45.36 3.16
2806 9489 2.902486 GTCTGAGCCCAGGATCATGATA 59.098 50.000 9.37 0.00 39.91 2.15
2807 9490 1.698532 GTCTGAGCCCAGGATCATGAT 59.301 52.381 8.25 8.25 39.91 2.45
2808 9491 1.126488 GTCTGAGCCCAGGATCATGA 58.874 55.000 9.37 0.00 39.91 3.07
2809 9492 0.835276 TGTCTGAGCCCAGGATCATG 59.165 55.000 4.88 0.00 39.91 3.07
2810 9493 1.817087 ATGTCTGAGCCCAGGATCAT 58.183 50.000 4.88 0.00 39.91 2.45
2811 9494 1.588239 AATGTCTGAGCCCAGGATCA 58.412 50.000 4.31 4.31 40.76 2.92
2812 9495 5.188555 TCATATAATGTCTGAGCCCAGGATC 59.811 44.000 0.00 0.00 40.76 3.36
2813 9496 5.096521 TCATATAATGTCTGAGCCCAGGAT 58.903 41.667 0.00 0.00 40.76 3.24
2814 9497 4.492646 TCATATAATGTCTGAGCCCAGGA 58.507 43.478 0.00 0.00 40.76 3.86
2815 9498 4.897509 TCATATAATGTCTGAGCCCAGG 57.102 45.455 0.00 0.00 40.76 4.45
2816 9499 5.189342 AGGATCATATAATGTCTGAGCCCAG 59.811 44.000 4.35 0.00 44.59 4.45
2817 9500 5.046087 CAGGATCATATAATGTCTGAGCCCA 60.046 44.000 4.35 0.00 44.59 5.36
2818 9501 5.188555 TCAGGATCATATAATGTCTGAGCCC 59.811 44.000 4.35 0.00 44.59 5.19
2819 9502 6.291648 TCAGGATCATATAATGTCTGAGCC 57.708 41.667 0.20 0.20 44.01 4.70
2820 9503 7.609960 TCTTCAGGATCATATAATGTCTGAGC 58.390 38.462 0.00 0.00 35.86 4.26
2821 9504 9.421806 GTTCTTCAGGATCATATAATGTCTGAG 57.578 37.037 0.00 0.00 35.86 3.35
2822 9505 8.927411 TGTTCTTCAGGATCATATAATGTCTGA 58.073 33.333 0.00 0.00 34.23 3.27
2823 9506 9.722184 ATGTTCTTCAGGATCATATAATGTCTG 57.278 33.333 0.00 0.00 33.91 3.51
2824 9507 9.941325 GATGTTCTTCAGGATCATATAATGTCT 57.059 33.333 0.00 0.00 35.30 3.41
2825 9508 9.716531 TGATGTTCTTCAGGATCATATAATGTC 57.283 33.333 0.00 0.00 35.30 3.06
2828 9511 9.175312 GCATGATGTTCTTCAGGATCATATAAT 57.825 33.333 0.00 0.00 35.30 1.28
2829 9512 8.380867 AGCATGATGTTCTTCAGGATCATATAA 58.619 33.333 0.00 0.00 35.30 0.98
2830 9513 7.914859 AGCATGATGTTCTTCAGGATCATATA 58.085 34.615 0.00 0.00 35.30 0.86
2831 9514 6.780901 AGCATGATGTTCTTCAGGATCATAT 58.219 36.000 0.00 0.00 35.30 1.78
2832 9515 6.183810 AGCATGATGTTCTTCAGGATCATA 57.816 37.500 0.00 0.00 35.30 2.15
2833 9516 5.050126 AGCATGATGTTCTTCAGGATCAT 57.950 39.130 0.00 0.00 37.15 2.45
2834 9517 4.498894 AGCATGATGTTCTTCAGGATCA 57.501 40.909 0.00 0.00 29.04 2.92
2835 9518 6.228995 TGATAGCATGATGTTCTTCAGGATC 58.771 40.000 0.00 0.00 28.15 3.36
2836 9519 6.183810 TGATAGCATGATGTTCTTCAGGAT 57.816 37.500 0.00 1.57 30.45 3.24
2837 9520 5.619132 TGATAGCATGATGTTCTTCAGGA 57.381 39.130 0.00 0.00 29.04 3.86
2857 9540 0.556258 TCCCGCCCTTCTAGAGATGA 59.444 55.000 0.00 0.00 0.00 2.92
2858 9541 1.414158 TTCCCGCCCTTCTAGAGATG 58.586 55.000 0.00 0.00 0.00 2.90
2895 9578 6.126863 TGGATGGGTCTGTATAATTGGATC 57.873 41.667 0.00 0.00 0.00 3.36
2900 9583 6.840705 AGCAAAATGGATGGGTCTGTATAATT 59.159 34.615 0.00 0.00 0.00 1.40
2907 9590 2.449464 TGAGCAAAATGGATGGGTCTG 58.551 47.619 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.