Multiple sequence alignment - TraesCS1D01G117400

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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 TraesCS1D01G117400 chr1D 100.000 6962 0 0 1 6962 113877686 113870725 0.000000e+00 12857.0
1 TraesCS1D01G117400 chr1D 100.000 65 0 0 7314 7378 113870373 113870309 3.620000e-23 121.0
2 TraesCS1D01G117400 chr1B 96.541 5349 112 23 1648 6942 173977189 173971860 0.000000e+00 8785.0
3 TraesCS1D01G117400 chr1B 92.450 1245 50 15 366 1581 173978415 173977186 0.000000e+00 1738.0
4 TraesCS1D01G117400 chr1B 92.199 282 19 3 1 280 174087578 174087298 5.360000e-106 396.0
5 TraesCS1D01G117400 chr1B 98.113 53 1 0 6910 6962 173971862 173971810 7.880000e-15 93.5
6 TraesCS1D01G117400 chr1A 95.733 5226 144 27 1417 6591 121745447 121740250 0.000000e+00 8342.0
7 TraesCS1D01G117400 chr1A 91.870 738 31 15 369 1092 121746511 121745789 0.000000e+00 1003.0
8 TraesCS1D01G117400 chr1A 96.467 368 8 4 6593 6956 121740160 121739794 2.940000e-168 603.0
9 TraesCS1D01G117400 chr1A 93.631 314 16 2 1126 1435 121745790 121745477 4.030000e-127 466.0
10 TraesCS1D01G117400 chr1A 88.393 112 7 5 191 302 121746618 121746513 6.010000e-26 130.0
11 TraesCS1D01G117400 chr6B 93.370 4148 194 37 1477 5578 84124817 84128929 0.000000e+00 6061.0
12 TraesCS1D01G117400 chr6B 85.617 1175 83 41 5771 6880 84129027 84130180 0.000000e+00 1155.0
13 TraesCS1D01G117400 chr6B 82.188 640 57 31 784 1393 84124213 84124825 1.430000e-136 497.0
14 TraesCS1D01G117400 chr6B 85.629 167 7 5 559 708 84120029 84120195 7.660000e-35 159.0
15 TraesCS1D01G117400 chr6B 86.466 133 11 3 450 576 84119864 84119995 9.980000e-29 139.0
16 TraesCS1D01G117400 chr6A 92.974 4156 204 34 1482 5578 47898178 47902304 0.000000e+00 5976.0
17 TraesCS1D01G117400 chr6A 88.530 837 62 16 5674 6495 47902322 47903139 0.000000e+00 983.0
18 TraesCS1D01G117400 chr6A 81.818 583 47 25 843 1393 47897624 47898179 1.140000e-117 435.0
19 TraesCS1D01G117400 chr6A 83.333 252 30 8 6654 6895 47903386 47903635 9.630000e-54 222.0
20 TraesCS1D01G117400 chr6A 84.500 200 14 9 6505 6692 47903189 47903383 1.640000e-41 182.0
21 TraesCS1D01G117400 chr6A 84.091 176 8 6 559 714 47893471 47893646 1.280000e-32 152.0
22 TraesCS1D01G117400 chr6A 84.000 150 12 6 438 576 47893298 47893446 4.640000e-27 134.0
23 TraesCS1D01G117400 chrUn 94.054 3330 159 13 1487 4800 143898862 143902168 0.000000e+00 5016.0
24 TraesCS1D01G117400 chrUn 93.532 773 40 7 4816 5584 143902244 143903010 0.000000e+00 1142.0
25 TraesCS1D01G117400 chrUn 90.848 743 46 12 5771 6494 143903082 143903821 0.000000e+00 976.0
26 TraesCS1D01G117400 chrUn 82.175 662 55 31 784 1396 143898214 143898861 1.840000e-140 510.0
27 TraesCS1D01G117400 chrUn 78.709 728 98 37 1687 2364 75223049 75223769 4.090000e-117 433.0
28 TraesCS1D01G117400 chrUn 86.189 391 41 4 1487 1872 104961816 104962198 1.920000e-110 411.0
29 TraesCS1D01G117400 chrUn 79.936 314 18 11 446 715 143894336 143894648 9.770000e-44 189.0
30 TraesCS1D01G117400 chr3D 94.583 1403 63 7 1576 2975 7924966 7923574 0.000000e+00 2158.0
31 TraesCS1D01G117400 chr7D 86.869 396 38 5 1485 1875 27866464 27866078 1.470000e-116 431.0
32 TraesCS1D01G117400 chr5B 86.689 293 34 4 1585 1872 380782937 380783229 3.320000e-83 320.0
33 TraesCS1D01G117400 chr3B 78.065 310 66 2 3395 3703 525608744 525609052 2.100000e-45 195.0
34 TraesCS1D01G117400 chr6D 79.921 254 30 13 1687 1928 468945629 468945873 4.580000e-37 167.0
35 TraesCS1D01G117400 chr6D 81.935 155 15 7 2104 2248 468585696 468585545 1.300000e-22 119.0
36 TraesCS1D01G117400 chr6D 81.818 143 20 3 922 1064 468914781 468914917 1.680000e-21 115.0
37 TraesCS1D01G117400 chr6D 88.372 86 7 2 2194 2276 468916504 468916589 4.710000e-17 100.0
38 TraesCS1D01G117400 chr5A 81.250 96 16 1 209 304 36022238 36022331 7.940000e-10 76.8
39 TraesCS1D01G117400 chr5D 86.441 59 8 0 209 267 45249435 45249493 1.720000e-06 65.8
40 TraesCS1D01G117400 chr5D 94.444 36 2 0 234 269 473485294 473485259 1.000000e-03 56.5


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 TraesCS1D01G117400 chr1D 113870309 113877686 7377 True 6489.000000 12857 100.000000 1 7378 2 chr1D.!!$R1 7377
1 TraesCS1D01G117400 chr1B 173971810 173978415 6605 True 3538.833333 8785 95.701333 366 6962 3 chr1B.!!$R2 6596
2 TraesCS1D01G117400 chr1A 121739794 121746618 6824 True 2108.800000 8342 93.218800 191 6956 5 chr1A.!!$R1 6765
3 TraesCS1D01G117400 chr6B 84124213 84130180 5967 False 2571.000000 6061 87.058333 784 6880 3 chr6B.!!$F2 6096
4 TraesCS1D01G117400 chr6A 47893298 47903635 10337 False 1154.857143 5976 85.606571 438 6895 7 chr6A.!!$F1 6457
5 TraesCS1D01G117400 chrUn 143894336 143903821 9485 False 1566.600000 5016 88.109000 446 6494 5 chrUn.!!$F3 6048
6 TraesCS1D01G117400 chrUn 75223049 75223769 720 False 433.000000 433 78.709000 1687 2364 1 chrUn.!!$F1 677
7 TraesCS1D01G117400 chr3D 7923574 7924966 1392 True 2158.000000 2158 94.583000 1576 2975 1 chr3D.!!$R1 1399

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
79 80 1.000607 CTCCCGTGAGAAGTTTCGTGA 60.001 52.381 0.00 0.00 41.42 4.35 F
428 429 1.399440 TCGCCGGCGATATACTATCAC 59.601 52.381 45.37 0.97 44.01 3.06 F
1466 5756 1.187974 TCCTTTCAATGCCATGCCAG 58.812 50.000 0.00 0.00 0.00 4.85 F
2484 6873 1.051812 CCCCTGATCGCCACTCTATT 58.948 55.000 0.00 0.00 0.00 1.73 F
3002 7397 1.167851 CAGGGTTGATGATGCACGTT 58.832 50.000 0.00 0.00 0.00 3.99 F
3109 7504 3.614616 GCTTCTTCTTCCAGTATCGTGTG 59.385 47.826 0.00 0.00 0.00 3.82 F
4483 8894 3.928992 GTCTGTGTTCATCATGACGACAT 59.071 43.478 0.00 0.00 37.19 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1325 5559 0.035820 GCCACCATTAACGGACAGGA 60.036 55.000 0.00 0.0 0.00 3.86 R
1793 6121 0.387239 GGCAACAAAGACATCACCGC 60.387 55.000 0.00 0.0 0.00 5.68 R
3109 7504 1.284657 CATCACGCACTGGATGAGTC 58.715 55.000 0.00 0.0 42.73 3.36 R
3522 7922 3.367025 GCGACTCAAACGTTAACATAGCT 59.633 43.478 0.00 0.0 0.00 3.32 R
4917 9393 4.455606 GACCTTTCATCCTCATAACCTGG 58.544 47.826 0.00 0.0 0.00 4.45 R
5174 9651 7.645058 AAAGAAAATCTCACTTCCAGTTTCA 57.355 32.000 0.00 0.0 0.00 2.69 R
6503 11051 1.080093 CGCTGCAGGTTTCGTAGGA 60.080 57.895 17.12 0.0 0.00 2.94 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
40 41 7.552050 AAAAATATGGAACTTGGGATGTCAA 57.448 32.000 0.00 0.00 0.00 3.18
41 42 7.552050 AAAATATGGAACTTGGGATGTCAAA 57.448 32.000 0.00 0.00 0.00 2.69
42 43 6.530019 AATATGGAACTTGGGATGTCAAAC 57.470 37.500 0.00 0.00 0.00 2.93
43 44 3.593442 TGGAACTTGGGATGTCAAACT 57.407 42.857 0.00 0.00 0.00 2.66
44 45 3.909732 TGGAACTTGGGATGTCAAACTT 58.090 40.909 0.00 0.00 0.00 2.66
45 46 3.636300 TGGAACTTGGGATGTCAAACTTG 59.364 43.478 0.00 0.00 0.00 3.16
46 47 3.005791 GGAACTTGGGATGTCAAACTTGG 59.994 47.826 0.00 0.00 0.00 3.61
47 48 2.597455 ACTTGGGATGTCAAACTTGGG 58.403 47.619 0.00 0.00 0.00 4.12
48 49 2.091333 ACTTGGGATGTCAAACTTGGGT 60.091 45.455 0.00 0.00 0.00 4.51
49 50 3.139397 ACTTGGGATGTCAAACTTGGGTA 59.861 43.478 0.00 0.00 0.00 3.69
50 51 3.149005 TGGGATGTCAAACTTGGGTAC 57.851 47.619 0.00 0.00 0.00 3.34
67 68 3.825328 GGTACCTAATCTACTCCCGTGA 58.175 50.000 4.06 0.00 0.00 4.35
68 69 3.819902 GGTACCTAATCTACTCCCGTGAG 59.180 52.174 4.06 0.00 44.62 3.51
69 70 3.947612 ACCTAATCTACTCCCGTGAGA 57.052 47.619 0.58 0.00 41.42 3.27
70 71 4.246712 ACCTAATCTACTCCCGTGAGAA 57.753 45.455 0.58 0.00 41.42 2.87
71 72 4.208746 ACCTAATCTACTCCCGTGAGAAG 58.791 47.826 0.58 0.00 41.42 2.85
72 73 4.208746 CCTAATCTACTCCCGTGAGAAGT 58.791 47.826 0.58 0.00 41.42 3.01
73 74 4.645588 CCTAATCTACTCCCGTGAGAAGTT 59.354 45.833 0.58 0.00 41.42 2.66
74 75 5.127356 CCTAATCTACTCCCGTGAGAAGTTT 59.873 44.000 0.58 0.00 41.42 2.66
75 76 4.722361 ATCTACTCCCGTGAGAAGTTTC 57.278 45.455 0.58 0.00 41.42 2.78
76 77 2.486982 TCTACTCCCGTGAGAAGTTTCG 59.513 50.000 0.58 0.00 41.42 3.46
77 78 1.038280 ACTCCCGTGAGAAGTTTCGT 58.962 50.000 0.58 0.00 41.42 3.85
78 79 1.269621 ACTCCCGTGAGAAGTTTCGTG 60.270 52.381 0.58 0.00 41.42 4.35
79 80 1.000607 CTCCCGTGAGAAGTTTCGTGA 60.001 52.381 0.00 0.00 41.42 4.35
80 81 1.409790 TCCCGTGAGAAGTTTCGTGAA 59.590 47.619 0.00 0.00 0.00 3.18
81 82 1.792949 CCCGTGAGAAGTTTCGTGAAG 59.207 52.381 0.00 0.00 0.00 3.02
82 83 2.545113 CCCGTGAGAAGTTTCGTGAAGA 60.545 50.000 0.00 0.00 0.00 2.87
83 84 3.120792 CCGTGAGAAGTTTCGTGAAGAA 58.879 45.455 0.00 0.00 37.01 2.52
84 85 3.741344 CCGTGAGAAGTTTCGTGAAGAAT 59.259 43.478 0.00 0.00 38.86 2.40
85 86 4.921515 CCGTGAGAAGTTTCGTGAAGAATA 59.078 41.667 0.00 0.00 38.86 1.75
86 87 5.577164 CCGTGAGAAGTTTCGTGAAGAATAT 59.423 40.000 0.00 0.00 38.86 1.28
87 88 6.237595 CCGTGAGAAGTTTCGTGAAGAATATC 60.238 42.308 0.00 0.00 38.86 1.63
88 89 6.237595 CGTGAGAAGTTTCGTGAAGAATATCC 60.238 42.308 0.00 0.00 38.86 2.59
89 90 6.590292 GTGAGAAGTTTCGTGAAGAATATCCA 59.410 38.462 0.00 0.00 38.86 3.41
90 91 7.278868 GTGAGAAGTTTCGTGAAGAATATCCAT 59.721 37.037 0.00 0.00 38.86 3.41
91 92 7.278646 TGAGAAGTTTCGTGAAGAATATCCATG 59.721 37.037 0.00 0.00 38.86 3.66
92 93 7.331026 AGAAGTTTCGTGAAGAATATCCATGA 58.669 34.615 0.00 0.00 38.86 3.07
93 94 7.989741 AGAAGTTTCGTGAAGAATATCCATGAT 59.010 33.333 0.00 0.00 38.86 2.45
94 95 9.261180 GAAGTTTCGTGAAGAATATCCATGATA 57.739 33.333 0.00 0.00 38.86 2.15
95 96 9.784531 AAGTTTCGTGAAGAATATCCATGATAT 57.215 29.630 0.00 0.00 38.86 1.63
96 97 9.784531 AGTTTCGTGAAGAATATCCATGATATT 57.215 29.630 8.65 8.65 44.72 1.28
150 151 9.747898 ATGTATAGTAAAAACTGTTTGGATGGA 57.252 29.630 6.53 0.00 0.00 3.41
151 152 9.005777 TGTATAGTAAAAACTGTTTGGATGGAC 57.994 33.333 6.53 1.81 0.00 4.02
152 153 5.784578 AGTAAAAACTGTTTGGATGGACC 57.215 39.130 6.53 0.00 39.54 4.46
153 154 3.726291 AAAAACTGTTTGGATGGACCG 57.274 42.857 6.53 0.00 42.61 4.79
154 155 2.358322 AAACTGTTTGGATGGACCGT 57.642 45.000 4.73 0.00 42.61 4.83
155 156 3.495434 AAACTGTTTGGATGGACCGTA 57.505 42.857 4.73 0.00 42.61 4.02
156 157 2.762535 ACTGTTTGGATGGACCGTAG 57.237 50.000 0.00 0.00 42.61 3.51
157 158 2.253610 ACTGTTTGGATGGACCGTAGA 58.746 47.619 0.00 0.00 42.61 2.59
158 159 2.838202 ACTGTTTGGATGGACCGTAGAT 59.162 45.455 0.00 0.00 42.61 1.98
159 160 3.263425 ACTGTTTGGATGGACCGTAGATT 59.737 43.478 0.00 0.00 42.61 2.40
160 161 3.605634 TGTTTGGATGGACCGTAGATTG 58.394 45.455 0.00 0.00 42.61 2.67
161 162 2.943033 GTTTGGATGGACCGTAGATTGG 59.057 50.000 0.00 0.00 42.61 3.16
162 163 2.168458 TGGATGGACCGTAGATTGGA 57.832 50.000 0.00 0.00 42.61 3.53
163 164 2.473070 TGGATGGACCGTAGATTGGAA 58.527 47.619 0.00 0.00 42.61 3.53
164 165 3.045634 TGGATGGACCGTAGATTGGAAT 58.954 45.455 0.00 0.00 42.61 3.01
165 166 3.181455 TGGATGGACCGTAGATTGGAATG 60.181 47.826 0.00 0.00 42.61 2.67
166 167 2.325583 TGGACCGTAGATTGGAATGC 57.674 50.000 0.00 0.00 0.00 3.56
167 168 1.557371 TGGACCGTAGATTGGAATGCA 59.443 47.619 0.00 0.00 0.00 3.96
168 169 2.172505 TGGACCGTAGATTGGAATGCAT 59.827 45.455 0.00 0.00 0.00 3.96
169 170 3.214328 GGACCGTAGATTGGAATGCATT 58.786 45.455 12.83 12.83 0.00 3.56
170 171 3.632145 GGACCGTAGATTGGAATGCATTT 59.368 43.478 14.33 0.00 0.00 2.32
171 172 4.097892 GGACCGTAGATTGGAATGCATTTT 59.902 41.667 14.33 0.00 0.00 1.82
172 173 5.248870 ACCGTAGATTGGAATGCATTTTC 57.751 39.130 14.33 9.81 0.00 2.29
173 174 4.949856 ACCGTAGATTGGAATGCATTTTCT 59.050 37.500 14.33 14.83 0.00 2.52
174 175 5.418840 ACCGTAGATTGGAATGCATTTTCTT 59.581 36.000 14.33 0.00 0.00 2.52
175 176 6.071391 ACCGTAGATTGGAATGCATTTTCTTT 60.071 34.615 14.33 1.35 0.00 2.52
176 177 7.122055 ACCGTAGATTGGAATGCATTTTCTTTA 59.878 33.333 14.33 0.42 0.00 1.85
177 178 8.137437 CCGTAGATTGGAATGCATTTTCTTTAT 58.863 33.333 14.33 2.17 0.00 1.40
178 179 9.173939 CGTAGATTGGAATGCATTTTCTTTATC 57.826 33.333 14.33 10.58 0.00 1.75
180 181 8.937634 AGATTGGAATGCATTTTCTTTATCAC 57.062 30.769 14.33 0.00 0.00 3.06
181 182 7.703621 AGATTGGAATGCATTTTCTTTATCACG 59.296 33.333 14.33 0.00 0.00 4.35
182 183 5.649557 TGGAATGCATTTTCTTTATCACGG 58.350 37.500 14.33 0.00 0.00 4.94
183 184 5.417266 TGGAATGCATTTTCTTTATCACGGA 59.583 36.000 14.33 0.00 0.00 4.69
184 185 6.096705 TGGAATGCATTTTCTTTATCACGGAT 59.903 34.615 14.33 0.00 0.00 4.18
185 186 6.418819 GGAATGCATTTTCTTTATCACGGATG 59.581 38.462 14.33 0.00 0.00 3.51
186 187 4.671377 TGCATTTTCTTTATCACGGATGC 58.329 39.130 0.00 0.00 39.15 3.91
187 188 4.044426 GCATTTTCTTTATCACGGATGCC 58.956 43.478 0.00 0.00 34.21 4.40
188 189 4.439974 GCATTTTCTTTATCACGGATGCCA 60.440 41.667 0.00 0.00 34.21 4.92
189 190 4.695217 TTTTCTTTATCACGGATGCCAC 57.305 40.909 0.00 0.00 0.00 5.01
196 197 1.647346 TCACGGATGCCACGTATTTC 58.353 50.000 0.00 0.00 43.58 2.17
207 208 4.517075 TGCCACGTATTTCATTTCTTCACA 59.483 37.500 0.00 0.00 0.00 3.58
251 252 3.138283 TGGACACCCAGATTTGATATCCC 59.862 47.826 0.00 0.00 37.58 3.85
255 256 5.588845 ACACCCAGATTTGATATCCCAAAA 58.411 37.500 0.00 0.00 39.20 2.44
259 260 7.712205 CACCCAGATTTGATATCCCAAAATTTC 59.288 37.037 0.00 0.00 39.20 2.17
260 261 7.402650 ACCCAGATTTGATATCCCAAAATTTCA 59.597 33.333 0.00 0.00 39.20 2.69
261 262 7.929785 CCCAGATTTGATATCCCAAAATTTCAG 59.070 37.037 0.00 0.00 39.20 3.02
329 330 9.628500 AAGTACTTCCTCTGTTTTGAAATAAGT 57.372 29.630 1.12 0.00 0.00 2.24
330 331 9.057089 AGTACTTCCTCTGTTTTGAAATAAGTG 57.943 33.333 0.00 0.00 0.00 3.16
331 332 7.881775 ACTTCCTCTGTTTTGAAATAAGTGT 57.118 32.000 0.00 0.00 0.00 3.55
332 333 7.931275 ACTTCCTCTGTTTTGAAATAAGTGTC 58.069 34.615 0.00 0.00 0.00 3.67
333 334 7.775561 ACTTCCTCTGTTTTGAAATAAGTGTCT 59.224 33.333 0.00 0.00 0.00 3.41
334 335 8.519799 TTCCTCTGTTTTGAAATAAGTGTCTT 57.480 30.769 0.00 0.00 0.00 3.01
335 336 8.519799 TCCTCTGTTTTGAAATAAGTGTCTTT 57.480 30.769 0.00 0.00 0.00 2.52
336 337 9.621629 TCCTCTGTTTTGAAATAAGTGTCTTTA 57.378 29.630 0.00 0.00 0.00 1.85
428 429 1.399440 TCGCCGGCGATATACTATCAC 59.601 52.381 45.37 0.97 44.01 3.06
644 706 1.843368 AGAACGGATTACCAGACGGA 58.157 50.000 0.00 0.00 35.59 4.69
1105 5297 2.556144 GGTACGTTTGTCTTTCCCCT 57.444 50.000 0.00 0.00 0.00 4.79
1325 5559 2.627945 TCGTAGATTTGCCGCATTTCT 58.372 42.857 9.72 9.72 0.00 2.52
1466 5756 1.187974 TCCTTTCAATGCCATGCCAG 58.812 50.000 0.00 0.00 0.00 4.85
1656 5967 1.680338 GTACATGGGGGATTGCTGTC 58.320 55.000 0.00 0.00 0.00 3.51
1793 6121 1.101049 ACTGTTGGTGTTTCGGCCAG 61.101 55.000 2.24 0.00 36.00 4.85
1809 6137 1.238439 CCAGCGGTGATGTCTTTGTT 58.762 50.000 17.83 0.00 0.00 2.83
2484 6873 1.051812 CCCCTGATCGCCACTCTATT 58.948 55.000 0.00 0.00 0.00 1.73
3002 7397 1.167851 CAGGGTTGATGATGCACGTT 58.832 50.000 0.00 0.00 0.00 3.99
3109 7504 3.614616 GCTTCTTCTTCCAGTATCGTGTG 59.385 47.826 0.00 0.00 0.00 3.82
3281 7678 7.388437 AGTTACGACAAATGGGTCTACATTTA 58.612 34.615 4.10 0.00 46.27 1.40
3522 7922 5.499313 TGCTATGTTTCTGATGATGGTTCA 58.501 37.500 0.00 0.00 36.00 3.18
3531 7931 6.484364 TCTGATGATGGTTCAGCTATGTTA 57.516 37.500 0.00 0.00 40.35 2.41
3710 8110 4.122776 CGAGCAATGAAGGTAAGCTACAT 58.877 43.478 0.00 0.00 35.36 2.29
3789 8189 6.311690 GGTATGCTTTGTTTCAGAGAGAGTAC 59.688 42.308 0.00 0.00 0.00 2.73
4483 8894 3.928992 GTCTGTGTTCATCATGACGACAT 59.071 43.478 0.00 0.00 37.19 3.06
4917 9393 8.655092 CAACTAATCACTCTTTCTGAATCTCAC 58.345 37.037 0.00 0.00 0.00 3.51
5304 9781 0.659427 CAATCTACTGCATGCCACCG 59.341 55.000 16.68 3.50 0.00 4.94
5382 9859 2.370445 CCGATGGGCTCTTGGGTCT 61.370 63.158 0.00 0.00 0.00 3.85
5517 9994 4.523083 TCCCACTTATTGCCTATTGTGTC 58.477 43.478 0.00 0.00 0.00 3.67
5535 10012 2.762887 TGTCCTTCCTGCTATCTGTCTG 59.237 50.000 0.00 0.00 0.00 3.51
5661 10138 8.755977 AGAGAAAAATGTTTTGGCTGATCATAT 58.244 29.630 0.00 0.00 0.00 1.78
5707 10184 8.306313 TGTCCTTCTAGTTAAATCTCTGCATA 57.694 34.615 0.00 0.00 0.00 3.14
6167 10645 0.104409 AGTCCTGGGGTCCACTCTTT 60.104 55.000 0.00 0.00 0.00 2.52
6420 10915 1.068127 CCCCTCGTGTAAATACCGGAG 59.932 57.143 9.46 0.00 0.00 4.63
6503 11051 4.263639 GCCCCTTTGTTAGTAGTACCCTTT 60.264 45.833 0.00 0.00 0.00 3.11
6537 11088 4.225984 TGCAGCGTACATTGTGATTTTTC 58.774 39.130 0.00 0.00 0.00 2.29
6540 11091 4.853196 CAGCGTACATTGTGATTTTTCCTG 59.147 41.667 0.00 0.00 0.00 3.86
6546 11102 5.776744 ACATTGTGATTTTTCCTGCTCTTC 58.223 37.500 0.00 0.00 0.00 2.87
6558 11117 3.072915 TCCTGCTCTTCTTCCATTTGTGA 59.927 43.478 0.00 0.00 0.00 3.58
6619 11269 6.809689 TGTCAGAACGTATTTACACACTATGG 59.190 38.462 0.00 0.00 0.00 2.74
6622 11272 6.257849 CAGAACGTATTTACACACTATGGCAT 59.742 38.462 4.88 4.88 0.00 4.40
6759 11476 2.965572 AATTTGGCATGAACCGATGG 57.034 45.000 0.00 0.00 0.00 3.51
7334 12084 3.110139 CGCAAGGTGTGTGCAACT 58.890 55.556 0.00 0.00 46.21 3.16
7341 12091 2.446435 AGGTGTGTGCAACTTTTCAGT 58.554 42.857 0.00 0.00 40.28 3.41
7342 12092 2.164219 AGGTGTGTGCAACTTTTCAGTG 59.836 45.455 0.00 0.00 40.28 3.66
7343 12093 2.094752 GGTGTGTGCAACTTTTCAGTGT 60.095 45.455 0.00 0.00 38.04 3.55
7344 12094 3.574614 GTGTGTGCAACTTTTCAGTGTT 58.425 40.909 0.00 0.00 38.04 3.32
7345 12095 4.380023 GGTGTGTGCAACTTTTCAGTGTTA 60.380 41.667 0.00 0.00 38.04 2.41
7346 12096 4.793216 GTGTGTGCAACTTTTCAGTGTTAG 59.207 41.667 0.00 0.00 38.04 2.34
7347 12097 4.142491 TGTGTGCAACTTTTCAGTGTTAGG 60.142 41.667 0.00 0.00 38.04 2.69
7348 12098 4.095782 GTGTGCAACTTTTCAGTGTTAGGA 59.904 41.667 0.00 0.00 38.04 2.94
7349 12099 4.095782 TGTGCAACTTTTCAGTGTTAGGAC 59.904 41.667 0.00 0.00 38.04 3.85
7350 12100 4.095782 GTGCAACTTTTCAGTGTTAGGACA 59.904 41.667 0.00 0.00 31.60 4.02
7351 12101 4.887071 TGCAACTTTTCAGTGTTAGGACAT 59.113 37.500 0.00 0.00 38.23 3.06
7352 12102 5.359576 TGCAACTTTTCAGTGTTAGGACATT 59.640 36.000 0.00 0.00 38.23 2.71
7353 12103 6.127479 TGCAACTTTTCAGTGTTAGGACATTT 60.127 34.615 0.00 0.00 38.23 2.32
7354 12104 6.198966 GCAACTTTTCAGTGTTAGGACATTTG 59.801 38.462 0.00 0.00 38.23 2.32
7355 12105 7.479980 CAACTTTTCAGTGTTAGGACATTTGA 58.520 34.615 0.00 0.00 38.23 2.69
7356 12106 7.264373 ACTTTTCAGTGTTAGGACATTTGAG 57.736 36.000 0.00 0.00 38.23 3.02
7357 12107 6.263168 ACTTTTCAGTGTTAGGACATTTGAGG 59.737 38.462 0.00 0.00 38.23 3.86
7358 12108 5.560722 TTCAGTGTTAGGACATTTGAGGA 57.439 39.130 0.00 0.00 38.23 3.71
7359 12109 5.152623 TCAGTGTTAGGACATTTGAGGAG 57.847 43.478 0.00 0.00 38.23 3.69
7360 12110 3.686726 CAGTGTTAGGACATTTGAGGAGC 59.313 47.826 0.00 0.00 38.23 4.70
7361 12111 3.327757 AGTGTTAGGACATTTGAGGAGCA 59.672 43.478 0.00 0.00 38.23 4.26
7362 12112 3.437049 GTGTTAGGACATTTGAGGAGCAC 59.563 47.826 0.00 0.00 38.23 4.40
7363 12113 2.672961 TAGGACATTTGAGGAGCACG 57.327 50.000 0.00 0.00 0.00 5.34
7364 12114 0.687354 AGGACATTTGAGGAGCACGT 59.313 50.000 0.00 0.00 0.00 4.49
7365 12115 0.798776 GGACATTTGAGGAGCACGTG 59.201 55.000 12.28 12.28 0.00 4.49
7366 12116 1.608025 GGACATTTGAGGAGCACGTGA 60.608 52.381 22.23 0.00 0.00 4.35
7367 12117 2.143122 GACATTTGAGGAGCACGTGAA 58.857 47.619 22.23 2.43 0.00 3.18
7368 12118 2.548057 GACATTTGAGGAGCACGTGAAA 59.452 45.455 22.23 10.08 0.00 2.69
7369 12119 2.948979 ACATTTGAGGAGCACGTGAAAA 59.051 40.909 22.23 9.26 0.00 2.29
7370 12120 3.380004 ACATTTGAGGAGCACGTGAAAAA 59.620 39.130 22.23 9.61 0.00 1.94
7371 12121 3.691049 TTTGAGGAGCACGTGAAAAAG 57.309 42.857 22.23 0.00 0.00 2.27
7372 12122 2.613026 TGAGGAGCACGTGAAAAAGA 57.387 45.000 22.23 0.00 0.00 2.52
7373 12123 2.912771 TGAGGAGCACGTGAAAAAGAA 58.087 42.857 22.23 0.00 0.00 2.52
7374 12124 3.275143 TGAGGAGCACGTGAAAAAGAAA 58.725 40.909 22.23 0.00 0.00 2.52
7375 12125 3.692101 TGAGGAGCACGTGAAAAAGAAAA 59.308 39.130 22.23 0.00 0.00 2.29
7376 12126 4.338118 TGAGGAGCACGTGAAAAAGAAAAT 59.662 37.500 22.23 0.00 0.00 1.82
7377 12127 5.163561 TGAGGAGCACGTGAAAAAGAAAATT 60.164 36.000 22.23 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.552050 TTGACATCCCAAGTTCCATATTTTT 57.448 32.000 0.00 0.00 0.00 1.94
17 18 7.235399 AGTTTGACATCCCAAGTTCCATATTTT 59.765 33.333 0.00 0.00 0.00 1.82
18 19 6.725834 AGTTTGACATCCCAAGTTCCATATTT 59.274 34.615 0.00 0.00 0.00 1.40
19 20 6.256053 AGTTTGACATCCCAAGTTCCATATT 58.744 36.000 0.00 0.00 0.00 1.28
20 21 5.831103 AGTTTGACATCCCAAGTTCCATAT 58.169 37.500 0.00 0.00 0.00 1.78
21 22 5.255397 AGTTTGACATCCCAAGTTCCATA 57.745 39.130 0.00 0.00 0.00 2.74
22 23 4.118168 AGTTTGACATCCCAAGTTCCAT 57.882 40.909 0.00 0.00 0.00 3.41
23 24 3.593442 AGTTTGACATCCCAAGTTCCA 57.407 42.857 0.00 0.00 0.00 3.53
24 25 3.005791 CCAAGTTTGACATCCCAAGTTCC 59.994 47.826 0.00 0.00 0.00 3.62
25 26 3.005791 CCCAAGTTTGACATCCCAAGTTC 59.994 47.826 0.00 0.00 0.00 3.01
26 27 2.965147 CCCAAGTTTGACATCCCAAGTT 59.035 45.455 0.00 0.00 0.00 2.66
27 28 2.091333 ACCCAAGTTTGACATCCCAAGT 60.091 45.455 0.00 0.00 0.00 3.16
28 29 2.597455 ACCCAAGTTTGACATCCCAAG 58.403 47.619 0.00 0.00 0.00 3.61
29 30 2.765689 ACCCAAGTTTGACATCCCAA 57.234 45.000 0.00 0.00 0.00 4.12
30 31 2.224917 GGTACCCAAGTTTGACATCCCA 60.225 50.000 0.00 0.00 0.00 4.37
31 32 2.041216 AGGTACCCAAGTTTGACATCCC 59.959 50.000 8.74 0.00 0.00 3.85
32 33 3.434940 AGGTACCCAAGTTTGACATCC 57.565 47.619 8.74 0.00 0.00 3.51
33 34 6.415573 AGATTAGGTACCCAAGTTTGACATC 58.584 40.000 8.74 0.00 0.00 3.06
34 35 6.388619 AGATTAGGTACCCAAGTTTGACAT 57.611 37.500 8.74 0.00 0.00 3.06
35 36 5.836024 AGATTAGGTACCCAAGTTTGACA 57.164 39.130 8.74 0.00 0.00 3.58
36 37 6.944096 AGTAGATTAGGTACCCAAGTTTGAC 58.056 40.000 8.74 0.00 0.00 3.18
37 38 6.155737 GGAGTAGATTAGGTACCCAAGTTTGA 59.844 42.308 8.74 0.00 0.00 2.69
38 39 6.346896 GGAGTAGATTAGGTACCCAAGTTTG 58.653 44.000 8.74 0.00 0.00 2.93
39 40 5.427806 GGGAGTAGATTAGGTACCCAAGTTT 59.572 44.000 8.74 0.00 36.27 2.66
40 41 4.967442 GGGAGTAGATTAGGTACCCAAGTT 59.033 45.833 8.74 0.00 36.27 2.66
41 42 4.554683 GGGAGTAGATTAGGTACCCAAGT 58.445 47.826 8.74 0.00 36.27 3.16
42 43 3.573110 CGGGAGTAGATTAGGTACCCAAG 59.427 52.174 8.74 0.00 36.04 3.61
43 44 3.052642 ACGGGAGTAGATTAGGTACCCAA 60.053 47.826 8.74 0.43 44.60 4.12
44 45 2.515429 ACGGGAGTAGATTAGGTACCCA 59.485 50.000 8.74 0.00 44.60 4.51
45 46 2.889678 CACGGGAGTAGATTAGGTACCC 59.110 54.545 8.74 0.00 44.67 3.69
46 47 3.819902 CTCACGGGAGTAGATTAGGTACC 59.180 52.174 6.49 2.73 44.67 3.34
47 48 4.712476 TCTCACGGGAGTAGATTAGGTAC 58.288 47.826 15.72 0.00 44.67 3.34
48 49 5.104193 ACTTCTCACGGGAGTAGATTAGGTA 60.104 44.000 25.96 0.00 44.67 3.08
49 50 3.947612 TCTCACGGGAGTAGATTAGGT 57.052 47.619 15.72 0.00 44.67 3.08
50 51 4.208746 ACTTCTCACGGGAGTAGATTAGG 58.791 47.826 25.96 3.91 44.67 2.69
51 52 5.838531 AACTTCTCACGGGAGTAGATTAG 57.161 43.478 25.96 11.80 44.67 1.73
52 53 5.163683 CGAAACTTCTCACGGGAGTAGATTA 60.164 44.000 25.96 0.00 44.67 1.75
53 54 4.380655 CGAAACTTCTCACGGGAGTAGATT 60.381 45.833 25.96 20.43 44.67 2.40
54 55 3.128938 CGAAACTTCTCACGGGAGTAGAT 59.871 47.826 25.96 13.03 44.67 1.98
55 56 2.486982 CGAAACTTCTCACGGGAGTAGA 59.513 50.000 25.96 8.00 44.67 2.59
56 57 2.228343 ACGAAACTTCTCACGGGAGTAG 59.772 50.000 18.70 18.70 44.67 2.57
57 58 2.030540 CACGAAACTTCTCACGGGAGTA 60.031 50.000 15.72 3.75 44.67 2.59
59 60 1.000607 TCACGAAACTTCTCACGGGAG 60.001 52.381 8.88 8.88 42.80 4.30
60 61 1.034356 TCACGAAACTTCTCACGGGA 58.966 50.000 0.00 0.00 35.84 5.14
61 62 1.792949 CTTCACGAAACTTCTCACGGG 59.207 52.381 0.00 0.00 0.00 5.28
62 63 2.739292 TCTTCACGAAACTTCTCACGG 58.261 47.619 0.00 0.00 0.00 4.94
63 64 4.974103 ATTCTTCACGAAACTTCTCACG 57.026 40.909 0.00 0.00 34.79 4.35
64 65 6.590292 TGGATATTCTTCACGAAACTTCTCAC 59.410 38.462 0.00 0.00 34.79 3.51
65 66 6.697395 TGGATATTCTTCACGAAACTTCTCA 58.303 36.000 0.00 0.00 34.79 3.27
66 67 7.492669 TCATGGATATTCTTCACGAAACTTCTC 59.507 37.037 0.00 0.00 34.79 2.87
67 68 7.331026 TCATGGATATTCTTCACGAAACTTCT 58.669 34.615 0.00 0.00 34.79 2.85
68 69 7.539712 TCATGGATATTCTTCACGAAACTTC 57.460 36.000 0.00 0.00 34.79 3.01
69 70 9.784531 ATATCATGGATATTCTTCACGAAACTT 57.215 29.630 0.00 0.00 32.00 2.66
70 71 9.784531 AATATCATGGATATTCTTCACGAAACT 57.215 29.630 5.81 0.00 40.02 2.66
124 125 9.747898 TCCATCCAAACAGTTTTTACTATACAT 57.252 29.630 0.00 0.00 0.00 2.29
125 126 9.005777 GTCCATCCAAACAGTTTTTACTATACA 57.994 33.333 0.00 0.00 0.00 2.29
126 127 8.456471 GGTCCATCCAAACAGTTTTTACTATAC 58.544 37.037 0.00 0.00 35.97 1.47
127 128 7.334921 CGGTCCATCCAAACAGTTTTTACTATA 59.665 37.037 0.00 0.00 35.57 1.31
128 129 6.150474 CGGTCCATCCAAACAGTTTTTACTAT 59.850 38.462 0.00 0.00 35.57 2.12
129 130 5.470777 CGGTCCATCCAAACAGTTTTTACTA 59.529 40.000 0.00 0.00 35.57 1.82
130 131 4.277423 CGGTCCATCCAAACAGTTTTTACT 59.723 41.667 0.00 0.00 35.57 2.24
131 132 4.037089 ACGGTCCATCCAAACAGTTTTTAC 59.963 41.667 0.00 0.00 35.57 2.01
132 133 4.208746 ACGGTCCATCCAAACAGTTTTTA 58.791 39.130 0.00 0.00 35.57 1.52
133 134 3.028130 ACGGTCCATCCAAACAGTTTTT 58.972 40.909 0.00 0.00 35.57 1.94
134 135 2.661718 ACGGTCCATCCAAACAGTTTT 58.338 42.857 0.00 0.00 35.57 2.43
135 136 2.358322 ACGGTCCATCCAAACAGTTT 57.642 45.000 0.00 0.00 35.57 2.66
136 137 2.635915 TCTACGGTCCATCCAAACAGTT 59.364 45.455 0.00 0.00 35.57 3.16
137 138 2.253610 TCTACGGTCCATCCAAACAGT 58.746 47.619 0.00 0.00 35.57 3.55
138 139 3.543680 ATCTACGGTCCATCCAAACAG 57.456 47.619 0.00 0.00 35.57 3.16
139 140 3.605634 CAATCTACGGTCCATCCAAACA 58.394 45.455 0.00 0.00 35.57 2.83
140 141 2.943033 CCAATCTACGGTCCATCCAAAC 59.057 50.000 0.00 0.00 35.57 2.93
141 142 2.841266 TCCAATCTACGGTCCATCCAAA 59.159 45.455 0.00 0.00 35.57 3.28
142 143 2.473070 TCCAATCTACGGTCCATCCAA 58.527 47.619 0.00 0.00 35.57 3.53
143 144 2.168458 TCCAATCTACGGTCCATCCA 57.832 50.000 0.00 0.00 35.57 3.41
144 145 3.403038 CATTCCAATCTACGGTCCATCC 58.597 50.000 0.00 0.00 0.00 3.51
145 146 2.808543 GCATTCCAATCTACGGTCCATC 59.191 50.000 0.00 0.00 0.00 3.51
146 147 2.172505 TGCATTCCAATCTACGGTCCAT 59.827 45.455 0.00 0.00 0.00 3.41
147 148 1.557371 TGCATTCCAATCTACGGTCCA 59.443 47.619 0.00 0.00 0.00 4.02
148 149 2.325583 TGCATTCCAATCTACGGTCC 57.674 50.000 0.00 0.00 0.00 4.46
149 150 4.900635 AAATGCATTCCAATCTACGGTC 57.099 40.909 13.38 0.00 0.00 4.79
150 151 4.949856 AGAAAATGCATTCCAATCTACGGT 59.050 37.500 13.38 0.00 0.00 4.83
151 152 5.505173 AGAAAATGCATTCCAATCTACGG 57.495 39.130 13.38 0.00 0.00 4.02
152 153 9.173939 GATAAAGAAAATGCATTCCAATCTACG 57.826 33.333 13.38 0.00 0.00 3.51
155 156 7.703621 CGTGATAAAGAAAATGCATTCCAATCT 59.296 33.333 13.38 11.13 0.00 2.40
156 157 7.043192 CCGTGATAAAGAAAATGCATTCCAATC 60.043 37.037 13.38 9.08 0.00 2.67
157 158 6.757947 CCGTGATAAAGAAAATGCATTCCAAT 59.242 34.615 13.38 0.00 0.00 3.16
158 159 6.071672 TCCGTGATAAAGAAAATGCATTCCAA 60.072 34.615 13.38 0.00 0.00 3.53
159 160 5.417266 TCCGTGATAAAGAAAATGCATTCCA 59.583 36.000 13.38 0.00 0.00 3.53
160 161 5.890334 TCCGTGATAAAGAAAATGCATTCC 58.110 37.500 13.38 7.99 0.00 3.01
161 162 6.074676 GCATCCGTGATAAAGAAAATGCATTC 60.075 38.462 13.38 1.61 38.44 2.67
162 163 5.750067 GCATCCGTGATAAAGAAAATGCATT 59.250 36.000 5.99 5.99 38.44 3.56
163 164 5.284079 GCATCCGTGATAAAGAAAATGCAT 58.716 37.500 0.00 0.00 38.44 3.96
164 165 4.439974 GGCATCCGTGATAAAGAAAATGCA 60.440 41.667 0.00 0.00 39.91 3.96
165 166 4.044426 GGCATCCGTGATAAAGAAAATGC 58.956 43.478 0.00 0.00 37.98 3.56
166 167 5.036737 GTGGCATCCGTGATAAAGAAAATG 58.963 41.667 0.00 0.00 0.00 2.32
167 168 4.201910 CGTGGCATCCGTGATAAAGAAAAT 60.202 41.667 0.00 0.00 0.00 1.82
168 169 3.126171 CGTGGCATCCGTGATAAAGAAAA 59.874 43.478 0.00 0.00 0.00 2.29
169 170 2.675844 CGTGGCATCCGTGATAAAGAAA 59.324 45.455 0.00 0.00 0.00 2.52
170 171 2.276201 CGTGGCATCCGTGATAAAGAA 58.724 47.619 0.00 0.00 0.00 2.52
171 172 1.206132 ACGTGGCATCCGTGATAAAGA 59.794 47.619 2.09 0.00 37.12 2.52
172 173 1.651987 ACGTGGCATCCGTGATAAAG 58.348 50.000 2.09 0.00 37.12 1.85
173 174 2.963548 TACGTGGCATCCGTGATAAA 57.036 45.000 12.72 0.00 39.22 1.40
174 175 3.462483 AATACGTGGCATCCGTGATAA 57.538 42.857 12.72 0.00 39.22 1.75
175 176 3.181474 TGAAATACGTGGCATCCGTGATA 60.181 43.478 12.72 0.00 39.22 2.15
176 177 2.210116 GAAATACGTGGCATCCGTGAT 58.790 47.619 12.72 0.00 39.22 3.06
177 178 1.066787 TGAAATACGTGGCATCCGTGA 60.067 47.619 12.72 0.00 39.22 4.35
178 179 1.364721 TGAAATACGTGGCATCCGTG 58.635 50.000 12.72 0.00 39.22 4.94
179 180 2.325583 ATGAAATACGTGGCATCCGT 57.674 45.000 8.25 8.25 42.06 4.69
180 181 3.312421 AGAAATGAAATACGTGGCATCCG 59.688 43.478 0.00 0.00 0.00 4.18
181 182 4.900635 AGAAATGAAATACGTGGCATCC 57.099 40.909 0.00 0.00 0.00 3.51
182 183 5.739161 GTGAAGAAATGAAATACGTGGCATC 59.261 40.000 0.00 0.00 0.00 3.91
183 184 5.182950 TGTGAAGAAATGAAATACGTGGCAT 59.817 36.000 0.00 0.00 0.00 4.40
184 185 4.517075 TGTGAAGAAATGAAATACGTGGCA 59.483 37.500 0.00 0.00 0.00 4.92
185 186 5.041951 TGTGAAGAAATGAAATACGTGGC 57.958 39.130 0.00 0.00 0.00 5.01
186 187 7.647715 AGTTTTGTGAAGAAATGAAATACGTGG 59.352 33.333 0.00 0.00 0.00 4.94
187 188 8.560576 AGTTTTGTGAAGAAATGAAATACGTG 57.439 30.769 0.00 0.00 0.00 4.49
196 197 7.908082 TCTCGTGTTTAGTTTTGTGAAGAAATG 59.092 33.333 0.00 0.00 0.00 2.32
207 208 7.384387 GTCCATTCTACTCTCGTGTTTAGTTTT 59.616 37.037 0.00 0.00 0.00 2.43
218 219 2.099921 CTGGGTGTCCATTCTACTCTCG 59.900 54.545 0.00 0.00 43.11 4.04
303 304 9.628500 ACTTATTTCAAAACAGAGGAAGTACTT 57.372 29.630 8.13 8.13 0.00 2.24
304 305 9.057089 CACTTATTTCAAAACAGAGGAAGTACT 57.943 33.333 0.00 0.00 0.00 2.73
305 306 8.837389 ACACTTATTTCAAAACAGAGGAAGTAC 58.163 33.333 0.00 0.00 0.00 2.73
306 307 8.974060 ACACTTATTTCAAAACAGAGGAAGTA 57.026 30.769 0.00 0.00 0.00 2.24
307 308 7.775561 AGACACTTATTTCAAAACAGAGGAAGT 59.224 33.333 0.00 0.00 0.00 3.01
308 309 8.159344 AGACACTTATTTCAAAACAGAGGAAG 57.841 34.615 0.00 0.00 0.00 3.46
309 310 8.519799 AAGACACTTATTTCAAAACAGAGGAA 57.480 30.769 0.00 0.00 0.00 3.36
310 311 8.519799 AAAGACACTTATTTCAAAACAGAGGA 57.480 30.769 0.00 0.00 0.00 3.71
360 361 8.765517 GCCAAGGCCCTTATATAATACTACTAA 58.234 37.037 0.00 0.00 34.56 2.24
361 362 7.902401 TGCCAAGGCCCTTATATAATACTACTA 59.098 37.037 8.89 0.00 41.09 1.82
362 363 6.733807 TGCCAAGGCCCTTATATAATACTACT 59.266 38.462 8.89 0.00 41.09 2.57
363 364 6.822170 GTGCCAAGGCCCTTATATAATACTAC 59.178 42.308 8.89 0.00 41.09 2.73
364 365 6.069847 GGTGCCAAGGCCCTTATATAATACTA 60.070 42.308 8.89 0.00 41.09 1.82
644 706 4.440112 GCTCGGGCTTTGCATTAAACTAAT 60.440 41.667 0.00 0.00 35.22 1.73
773 4440 2.435805 TCCTCCTATCTTGTCATGGCAC 59.564 50.000 0.00 0.00 0.00 5.01
924 5099 0.550914 AGAGAGAGAGGCACGGAGAT 59.449 55.000 0.00 0.00 0.00 2.75
935 5110 1.472552 CGAAGGCGAGAGAGAGAGAGA 60.473 57.143 0.00 0.00 40.82 3.10
936 5111 0.937304 CGAAGGCGAGAGAGAGAGAG 59.063 60.000 0.00 0.00 40.82 3.20
937 5112 0.250793 ACGAAGGCGAGAGAGAGAGA 59.749 55.000 0.00 0.00 41.64 3.10
1096 5285 2.180276 CGGAAGAGAGAAGGGGAAAGA 58.820 52.381 0.00 0.00 0.00 2.52
1099 5291 1.265454 GCCGGAAGAGAGAAGGGGAA 61.265 60.000 5.05 0.00 0.00 3.97
1105 5297 2.660064 GGCAGGCCGGAAGAGAGAA 61.660 63.158 5.05 0.00 0.00 2.87
1188 5382 2.573869 CAGATCCACCGACACGCT 59.426 61.111 0.00 0.00 0.00 5.07
1192 5386 2.662596 GCACCAGATCCACCGACA 59.337 61.111 0.00 0.00 0.00 4.35
1217 5418 1.227263 CGCAACCTAGATCCACCGG 60.227 63.158 0.00 0.00 0.00 5.28
1325 5559 0.035820 GCCACCATTAACGGACAGGA 60.036 55.000 0.00 0.00 0.00 3.86
1420 5662 3.828023 GGTTGTGGGTGTGGGGGT 61.828 66.667 0.00 0.00 0.00 4.95
1421 5663 3.826822 TGGTTGTGGGTGTGGGGG 61.827 66.667 0.00 0.00 0.00 5.40
1422 5664 2.520741 GTGGTTGTGGGTGTGGGG 60.521 66.667 0.00 0.00 0.00 4.96
1466 5756 3.087031 CAGATAATCCCCATGCCATGAC 58.913 50.000 6.18 0.00 0.00 3.06
1472 5762 3.228188 TGGAACAGATAATCCCCATGC 57.772 47.619 0.00 0.00 34.68 4.06
1656 5967 3.876274 TTACACAGCTTGCTAGGAGAG 57.124 47.619 0.00 0.00 0.00 3.20
1793 6121 0.387239 GGCAACAAAGACATCACCGC 60.387 55.000 0.00 0.00 0.00 5.68
2432 6821 4.464947 GATTTCCCCCGAGATCTGAAAAT 58.535 43.478 0.00 0.00 29.05 1.82
2457 6846 1.958205 GCGATCAGGGGAAGCATCG 60.958 63.158 0.00 0.00 40.89 3.84
2484 6873 2.334946 GCTTGATGTTGGGCTGCGA 61.335 57.895 0.00 0.00 0.00 5.10
2824 7213 8.200792 AGAATAGTCACTGATTACAATGGAGAC 58.799 37.037 0.00 0.00 0.00 3.36
3002 7397 2.621998 GCACTATACGGCTCAGAGGTAA 59.378 50.000 0.00 0.00 0.00 2.85
3109 7504 1.284657 CATCACGCACTGGATGAGTC 58.715 55.000 0.00 0.00 42.73 3.36
3281 7678 6.709281 TGTTATGGTGCCAAAAATCATGAAT 58.291 32.000 0.00 0.00 0.00 2.57
3522 7922 3.367025 GCGACTCAAACGTTAACATAGCT 59.633 43.478 0.00 0.00 0.00 3.32
3710 8110 4.760530 AGAGCAATCTAAGCATGTGGTA 57.239 40.909 0.00 0.00 0.00 3.25
4483 8894 5.858381 AGCATGTAAGAGACAAGAAAGTGA 58.142 37.500 0.00 0.00 42.78 3.41
4853 9325 5.072741 TCAGAATCTCAAGAACCAAAAGGG 58.927 41.667 0.00 0.00 44.81 3.95
4917 9393 4.455606 GACCTTTCATCCTCATAACCTGG 58.544 47.826 0.00 0.00 0.00 4.45
5174 9651 7.645058 AAAGAAAATCTCACTTCCAGTTTCA 57.355 32.000 0.00 0.00 0.00 2.69
5304 9781 1.744320 AACCCTTGAAACAAGGCCGC 61.744 55.000 20.90 0.00 36.10 6.53
5517 9994 1.761784 AGCAGACAGATAGCAGGAAGG 59.238 52.381 0.00 0.00 0.00 3.46
5535 10012 5.812127 GGGAATGATAAATTTGTTGGTGAGC 59.188 40.000 0.00 0.00 0.00 4.26
5661 10138 5.991328 CAGAGCTCTGCCGAAATATAAAA 57.009 39.130 29.79 0.00 37.15 1.52
5707 10184 5.013183 ACACCTGATGGTAAGAGTTTTAGCT 59.987 40.000 4.49 0.00 46.60 3.32
5716 10193 3.056821 CACGAAGACACCTGATGGTAAGA 60.057 47.826 0.00 0.00 46.60 2.10
6167 10645 5.243981 CAGATTGAGAAGAAGAGCTTTCCA 58.756 41.667 0.00 0.00 36.83 3.53
6459 10960 8.065007 AGGGGCAATAATTTAGATAAAACTCCA 58.935 33.333 0.00 0.00 0.00 3.86
6503 11051 1.080093 CGCTGCAGGTTTCGTAGGA 60.080 57.895 17.12 0.00 0.00 2.94
6537 11088 3.415212 TCACAAATGGAAGAAGAGCAGG 58.585 45.455 0.00 0.00 0.00 4.85
6540 11091 6.258947 GGTAGTATCACAAATGGAAGAAGAGC 59.741 42.308 0.00 0.00 0.00 4.09
6546 11102 6.655003 ACAACAGGTAGTATCACAAATGGAAG 59.345 38.462 0.00 0.00 0.00 3.46
6558 11117 7.996098 ATAAGCAACAAACAACAGGTAGTAT 57.004 32.000 0.00 0.00 0.00 2.12
6619 11269 6.016777 ACAGCTGCCTTATAAATAGTTGATGC 60.017 38.462 15.27 0.00 0.00 3.91
6622 11272 7.109501 TGAACAGCTGCCTTATAAATAGTTGA 58.890 34.615 15.27 0.00 0.00 3.18
6759 11476 7.871853 ACATTATTAACTGAAATATCGCCACC 58.128 34.615 0.00 0.00 0.00 4.61
7313 12063 3.585990 GCACACACCTTGCGCACT 61.586 61.111 11.12 0.00 33.12 4.40
7314 12064 3.408501 TTGCACACACCTTGCGCAC 62.409 57.895 11.12 0.00 43.03 5.34
7315 12065 3.136791 TTGCACACACCTTGCGCA 61.137 55.556 5.66 5.66 41.61 6.09
7316 12066 2.612219 AAGTTGCACACACCTTGCGC 62.612 55.000 0.00 0.00 43.34 6.09
7317 12067 0.179140 AAAGTTGCACACACCTTGCG 60.179 50.000 0.00 0.00 43.34 4.85
7318 12068 1.926510 GAAAAGTTGCACACACCTTGC 59.073 47.619 0.00 0.00 40.63 4.01
7319 12069 3.181397 CTGAAAAGTTGCACACACCTTG 58.819 45.455 0.00 0.00 27.64 3.61
7320 12070 2.825532 ACTGAAAAGTTGCACACACCTT 59.174 40.909 0.00 0.00 28.22 3.50
7321 12071 2.164219 CACTGAAAAGTTGCACACACCT 59.836 45.455 0.00 0.00 0.00 4.00
7322 12072 2.094752 ACACTGAAAAGTTGCACACACC 60.095 45.455 0.00 0.00 0.00 4.16
7323 12073 3.216147 ACACTGAAAAGTTGCACACAC 57.784 42.857 0.00 0.00 0.00 3.82
7324 12074 3.932545 AACACTGAAAAGTTGCACACA 57.067 38.095 0.00 0.00 0.00 3.72
7325 12075 4.095782 TCCTAACACTGAAAAGTTGCACAC 59.904 41.667 0.00 0.00 0.00 3.82
7326 12076 4.095782 GTCCTAACACTGAAAAGTTGCACA 59.904 41.667 0.00 0.00 0.00 4.57
7327 12077 4.095782 TGTCCTAACACTGAAAAGTTGCAC 59.904 41.667 0.00 0.00 0.00 4.57
7328 12078 4.265893 TGTCCTAACACTGAAAAGTTGCA 58.734 39.130 0.00 0.00 0.00 4.08
7329 12079 4.893424 TGTCCTAACACTGAAAAGTTGC 57.107 40.909 0.00 0.00 0.00 4.17
7330 12080 7.479980 TCAAATGTCCTAACACTGAAAAGTTG 58.520 34.615 0.00 0.00 38.48 3.16
7331 12081 7.201821 CCTCAAATGTCCTAACACTGAAAAGTT 60.202 37.037 0.00 0.00 38.48 2.66
7332 12082 6.263168 CCTCAAATGTCCTAACACTGAAAAGT 59.737 38.462 0.00 0.00 38.48 2.66
7333 12083 6.486657 TCCTCAAATGTCCTAACACTGAAAAG 59.513 38.462 0.00 0.00 38.48 2.27
7334 12084 6.361433 TCCTCAAATGTCCTAACACTGAAAA 58.639 36.000 0.00 0.00 38.48 2.29
7335 12085 5.935945 TCCTCAAATGTCCTAACACTGAAA 58.064 37.500 0.00 0.00 38.48 2.69
7336 12086 5.551233 CTCCTCAAATGTCCTAACACTGAA 58.449 41.667 0.00 0.00 38.48 3.02
7337 12087 4.563580 GCTCCTCAAATGTCCTAACACTGA 60.564 45.833 0.00 0.00 38.48 3.41
7338 12088 3.686726 GCTCCTCAAATGTCCTAACACTG 59.313 47.826 0.00 0.00 38.48 3.66
7339 12089 3.327757 TGCTCCTCAAATGTCCTAACACT 59.672 43.478 0.00 0.00 38.48 3.55
7340 12090 3.437049 GTGCTCCTCAAATGTCCTAACAC 59.563 47.826 0.00 0.00 38.48 3.32
7341 12091 3.674997 GTGCTCCTCAAATGTCCTAACA 58.325 45.455 0.00 0.00 40.38 2.41
7342 12092 2.673368 CGTGCTCCTCAAATGTCCTAAC 59.327 50.000 0.00 0.00 0.00 2.34
7343 12093 2.301870 ACGTGCTCCTCAAATGTCCTAA 59.698 45.455 0.00 0.00 0.00 2.69
7344 12094 1.899814 ACGTGCTCCTCAAATGTCCTA 59.100 47.619 0.00 0.00 0.00 2.94
7345 12095 0.687354 ACGTGCTCCTCAAATGTCCT 59.313 50.000 0.00 0.00 0.00 3.85
7346 12096 0.798776 CACGTGCTCCTCAAATGTCC 59.201 55.000 0.82 0.00 0.00 4.02
7347 12097 1.795768 TCACGTGCTCCTCAAATGTC 58.204 50.000 11.67 0.00 0.00 3.06
7348 12098 2.254546 TTCACGTGCTCCTCAAATGT 57.745 45.000 11.67 0.00 0.00 2.71
7349 12099 3.624326 TTTTCACGTGCTCCTCAAATG 57.376 42.857 11.67 0.00 0.00 2.32
7350 12100 3.882888 TCTTTTTCACGTGCTCCTCAAAT 59.117 39.130 11.67 0.00 0.00 2.32
7351 12101 3.275143 TCTTTTTCACGTGCTCCTCAAA 58.725 40.909 11.67 1.89 0.00 2.69
7352 12102 2.912771 TCTTTTTCACGTGCTCCTCAA 58.087 42.857 11.67 0.00 0.00 3.02
7353 12103 2.613026 TCTTTTTCACGTGCTCCTCA 57.387 45.000 11.67 0.00 0.00 3.86
7354 12104 3.963383 TTTCTTTTTCACGTGCTCCTC 57.037 42.857 11.67 0.00 0.00 3.71
7355 12105 4.918810 ATTTTCTTTTTCACGTGCTCCT 57.081 36.364 11.67 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.