Multiple sequence alignment - TraesCS4A01G031500

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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 TraesCS4A01G031500 chr4A 100.000 3452 0 0 1 3452 24558613 24555162 0.000000e+00 6375.0
1 TraesCS4A01G031500 chr4A 88.057 1189 138 4 1267 2453 600366328 600367514 0.000000e+00 1406.0
2 TraesCS4A01G031500 chr4A 94.677 263 14 0 157 419 207362690 207362952 3.210000e-110 409.0
3 TraesCS4A01G031500 chr4A 89.873 158 15 1 3296 3452 321329088 321329245 5.840000e-48 202.0
4 TraesCS4A01G031500 chr4D 96.796 1810 57 1 783 2591 443206281 443208090 0.000000e+00 3020.0
5 TraesCS4A01G031500 chr4D 85.868 1394 192 5 1061 2453 4067578 4066189 0.000000e+00 1478.0
6 TraesCS4A01G031500 chr4D 91.808 647 23 14 2570 3212 443208113 443208733 0.000000e+00 874.0
7 TraesCS4A01G031500 chr4D 92.258 310 22 2 492 801 443205960 443206267 4.090000e-119 438.0
8 TraesCS4A01G031500 chr4D 93.359 256 17 0 3197 3452 443208749 443209004 2.510000e-101 379.0
9 TraesCS4A01G031500 chr4B 95.447 1823 71 1 783 2605 552744230 552746040 0.000000e+00 2896.0
10 TraesCS4A01G031500 chr4B 86.328 1397 186 5 1058 2453 4688524 4689916 0.000000e+00 1517.0
11 TraesCS4A01G031500 chr4B 93.264 193 10 2 611 801 552744024 552744215 7.290000e-72 281.0
12 TraesCS4A01G031500 chr4B 89.744 156 16 0 3297 3452 86649501 86649656 2.100000e-47 200.0
13 TraesCS4A01G031500 chr4B 73.357 563 94 28 2731 3273 552746388 552746914 1.280000e-34 158.0
14 TraesCS4A01G031500 chr4B 95.000 40 2 0 3 42 28697547 28697586 2.880000e-06 63.9
15 TraesCS4A01G031500 chr5B 86.256 1397 187 5 1058 2453 641314352 641315744 0.000000e+00 1511.0
16 TraesCS4A01G031500 chr5B 81.765 170 14 6 1 157 491882500 491882665 3.620000e-25 126.0
17 TraesCS4A01G031500 chr7D 83.385 1294 199 13 1170 2451 617378018 617376729 0.000000e+00 1184.0
18 TraesCS4A01G031500 chr7D 95.000 60 2 1 417 475 112758384 112758443 3.670000e-15 93.5
19 TraesCS4A01G031500 chr7B 83.756 1262 188 14 1200 2448 711475713 711476970 0.000000e+00 1179.0
20 TraesCS4A01G031500 chr7B 83.023 1290 205 11 1170 2451 711489347 711488064 0.000000e+00 1157.0
21 TraesCS4A01G031500 chr7B 92.254 142 9 2 3287 3428 482815823 482815684 2.100000e-47 200.0
22 TraesCS4A01G031500 chr6A 96.198 263 10 0 158 420 162832956 162832694 6.840000e-117 431.0
23 TraesCS4A01G031500 chr6A 94.253 261 14 1 158 418 376473787 376474046 6.940000e-107 398.0
24 TraesCS4A01G031500 chr6A 93.561 264 17 0 157 420 410575773 410576036 8.980000e-106 394.0
25 TraesCS4A01G031500 chr6A 78.226 124 14 13 3 117 11876923 11877042 2.220000e-07 67.6
26 TraesCS4A01G031500 chr2A 93.939 264 16 0 157 420 606519324 606519061 1.930000e-107 399.0
27 TraesCS4A01G031500 chr2A 88.608 158 17 1 3296 3452 193703280 193703123 1.260000e-44 191.0
28 TraesCS4A01G031500 chr7A 93.893 262 16 0 158 419 329488540 329488279 2.500000e-106 396.0
29 TraesCS4A01G031500 chr7A 95.000 60 2 1 417 475 118104218 118104277 3.670000e-15 93.5
30 TraesCS4A01G031500 chr5A 93.893 262 16 0 158 419 512225723 512225984 2.500000e-106 396.0
31 TraesCS4A01G031500 chr1A 93.585 265 16 1 155 418 572865062 572865326 8.980000e-106 394.0
32 TraesCS4A01G031500 chr2D 92.336 274 19 2 158 430 455942485 455942213 4.180000e-104 388.0
33 TraesCS4A01G031500 chr2D 93.023 43 3 0 3 45 154845704 154845662 2.880000e-06 63.9
34 TraesCS4A01G031500 chr3D 92.053 151 12 0 3300 3450 698725 698575 2.700000e-51 213.0
35 TraesCS4A01G031500 chr3D 90.728 151 12 2 3298 3447 481710207 481710356 2.100000e-47 200.0
36 TraesCS4A01G031500 chr6B 88.235 170 15 4 3287 3452 50480525 50480693 7.560000e-47 198.0
37 TraesCS4A01G031500 chr6B 86.905 168 19 3 3284 3449 458010766 458010600 5.880000e-43 185.0
38 TraesCS4A01G031500 chr6B 80.702 171 15 13 1 160 276227163 276227000 2.180000e-22 117.0
39 TraesCS4A01G031500 chr2B 83.908 174 14 10 1 160 798313879 798314052 1.660000e-33 154.0
40 TraesCS4A01G031500 chr2B 83.908 174 13 7 2 160 73624067 73624240 5.970000e-33 152.0
41 TraesCS4A01G031500 chr2B 83.429 175 13 9 1 160 300557421 300557248 7.720000e-32 148.0
42 TraesCS4A01G031500 chr1B 84.000 175 12 13 1 160 669657452 669657625 1.660000e-33 154.0


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 TraesCS4A01G031500 chr4A 24555162 24558613 3451 True 6375.000000 6375 100.00000 1 3452 1 chr4A.!!$R1 3451
1 TraesCS4A01G031500 chr4A 600366328 600367514 1186 False 1406.000000 1406 88.05700 1267 2453 1 chr4A.!!$F3 1186
2 TraesCS4A01G031500 chr4D 4066189 4067578 1389 True 1478.000000 1478 85.86800 1061 2453 1 chr4D.!!$R1 1392
3 TraesCS4A01G031500 chr4D 443205960 443209004 3044 False 1177.750000 3020 93.55525 492 3452 4 chr4D.!!$F1 2960
4 TraesCS4A01G031500 chr4B 4688524 4689916 1392 False 1517.000000 1517 86.32800 1058 2453 1 chr4B.!!$F1 1395
5 TraesCS4A01G031500 chr4B 552744024 552746914 2890 False 1111.666667 2896 87.35600 611 3273 3 chr4B.!!$F4 2662
6 TraesCS4A01G031500 chr5B 641314352 641315744 1392 False 1511.000000 1511 86.25600 1058 2453 1 chr5B.!!$F2 1395
7 TraesCS4A01G031500 chr7D 617376729 617378018 1289 True 1184.000000 1184 83.38500 1170 2451 1 chr7D.!!$R1 1281
8 TraesCS4A01G031500 chr7B 711475713 711476970 1257 False 1179.000000 1179 83.75600 1200 2448 1 chr7B.!!$F1 1248
9 TraesCS4A01G031500 chr7B 711488064 711489347 1283 True 1157.000000 1157 83.02300 1170 2451 1 chr7B.!!$R2 1281

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
732 735 0.249120 CCTTCGCATGGACCTGTGTA 59.751 55.000 0.00 0.00 0.0 2.90 F
1041 1078 1.131504 GAGCTGGCTATACGATCGAGG 59.868 57.143 24.34 9.32 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 1933 1.289109 CTTGGAACACGCACCGGTAG 61.289 60.000 6.87 7.33 39.29 3.18 R
2862 3174 1.003718 CTCGCGGGGTCTCCTTTTT 60.004 57.895 6.13 0.00 0.00 1.94 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
45 46 9.599866 GAAATTAAATGGAAGTATTTTGAGGGG 57.400 33.333 0.00 0.00 32.79 4.79
46 47 7.675161 ATTAAATGGAAGTATTTTGAGGGGG 57.325 36.000 0.00 0.00 32.79 5.40
66 67 5.723295 GGGGGTTATTTTAGCATATGCATG 58.277 41.667 28.62 0.00 45.16 4.06
78 79 4.469625 CATATGCATGCAGACAGTCTTC 57.530 45.455 26.69 0.00 0.00 2.87
79 80 2.783609 ATGCATGCAGACAGTCTTCT 57.216 45.000 26.69 1.43 0.00 2.85
80 81 2.090400 TGCATGCAGACAGTCTTCTC 57.910 50.000 18.46 0.00 0.00 2.87
81 82 1.622312 TGCATGCAGACAGTCTTCTCT 59.378 47.619 18.46 0.00 0.00 3.10
82 83 2.270047 GCATGCAGACAGTCTTCTCTC 58.730 52.381 14.21 0.00 0.00 3.20
83 84 2.353505 GCATGCAGACAGTCTTCTCTCA 60.354 50.000 14.21 0.00 0.00 3.27
84 85 3.863780 GCATGCAGACAGTCTTCTCTCAA 60.864 47.826 14.21 0.00 0.00 3.02
85 86 4.505808 CATGCAGACAGTCTTCTCTCAAT 58.494 43.478 0.00 0.00 0.00 2.57
86 87 4.185467 TGCAGACAGTCTTCTCTCAATC 57.815 45.455 0.00 0.00 0.00 2.67
87 88 3.056250 TGCAGACAGTCTTCTCTCAATCC 60.056 47.826 0.00 0.00 0.00 3.01
88 89 3.195396 GCAGACAGTCTTCTCTCAATCCT 59.805 47.826 0.00 0.00 0.00 3.24
89 90 4.322650 GCAGACAGTCTTCTCTCAATCCTT 60.323 45.833 0.00 0.00 0.00 3.36
90 91 5.792741 CAGACAGTCTTCTCTCAATCCTTT 58.207 41.667 0.00 0.00 0.00 3.11
91 92 5.868801 CAGACAGTCTTCTCTCAATCCTTTC 59.131 44.000 0.00 0.00 0.00 2.62
92 93 5.779771 AGACAGTCTTCTCTCAATCCTTTCT 59.220 40.000 0.00 0.00 0.00 2.52
93 94 6.036577 ACAGTCTTCTCTCAATCCTTTCTC 57.963 41.667 0.00 0.00 0.00 2.87
94 95 5.779771 ACAGTCTTCTCTCAATCCTTTCTCT 59.220 40.000 0.00 0.00 0.00 3.10
95 96 6.071391 ACAGTCTTCTCTCAATCCTTTCTCTC 60.071 42.308 0.00 0.00 0.00 3.20
96 97 6.153340 CAGTCTTCTCTCAATCCTTTCTCTCT 59.847 42.308 0.00 0.00 0.00 3.10
97 98 6.378280 AGTCTTCTCTCAATCCTTTCTCTCTC 59.622 42.308 0.00 0.00 0.00 3.20
98 99 6.152661 GTCTTCTCTCAATCCTTTCTCTCTCA 59.847 42.308 0.00 0.00 0.00 3.27
99 100 6.896860 TCTTCTCTCAATCCTTTCTCTCTCAT 59.103 38.462 0.00 0.00 0.00 2.90
100 101 6.468333 TCTCTCAATCCTTTCTCTCTCATG 57.532 41.667 0.00 0.00 0.00 3.07
101 102 6.193504 TCTCTCAATCCTTTCTCTCTCATGA 58.806 40.000 0.00 0.00 0.00 3.07
102 103 6.840181 TCTCTCAATCCTTTCTCTCTCATGAT 59.160 38.462 0.00 0.00 0.00 2.45
103 104 8.003629 TCTCTCAATCCTTTCTCTCTCATGATA 58.996 37.037 0.00 0.00 0.00 2.15
104 105 8.724113 TCTCAATCCTTTCTCTCTCATGATAT 57.276 34.615 0.00 0.00 0.00 1.63
105 106 9.819754 TCTCAATCCTTTCTCTCTCATGATATA 57.180 33.333 0.00 0.00 0.00 0.86
109 110 9.723601 AATCCTTTCTCTCTCATGATATAAAGC 57.276 33.333 0.00 0.00 0.00 3.51
110 111 7.675062 TCCTTTCTCTCTCATGATATAAAGCC 58.325 38.462 0.00 0.00 0.00 4.35
111 112 6.589523 CCTTTCTCTCTCATGATATAAAGCCG 59.410 42.308 0.00 0.00 0.00 5.52
112 113 6.901081 TTCTCTCTCATGATATAAAGCCGA 57.099 37.500 0.00 0.00 0.00 5.54
113 114 6.260870 TCTCTCTCATGATATAAAGCCGAC 57.739 41.667 0.00 0.00 0.00 4.79
114 115 5.770162 TCTCTCTCATGATATAAAGCCGACA 59.230 40.000 0.00 0.00 0.00 4.35
115 116 6.265422 TCTCTCTCATGATATAAAGCCGACAA 59.735 38.462 0.00 0.00 0.00 3.18
116 117 6.450545 TCTCTCATGATATAAAGCCGACAAG 58.549 40.000 0.00 0.00 0.00 3.16
117 118 5.541845 TCTCATGATATAAAGCCGACAAGG 58.458 41.667 0.00 0.00 44.97 3.61
118 119 5.304357 TCTCATGATATAAAGCCGACAAGGA 59.696 40.000 0.00 0.00 45.00 3.36
119 120 5.541845 TCATGATATAAAGCCGACAAGGAG 58.458 41.667 0.00 0.00 45.00 3.69
120 121 5.304357 TCATGATATAAAGCCGACAAGGAGA 59.696 40.000 0.00 0.00 45.00 3.71
121 122 5.607939 TGATATAAAGCCGACAAGGAGAA 57.392 39.130 0.00 0.00 45.00 2.87
122 123 5.601662 TGATATAAAGCCGACAAGGAGAAG 58.398 41.667 0.00 0.00 45.00 2.85
123 124 2.762535 TAAAGCCGACAAGGAGAAGG 57.237 50.000 0.00 0.00 45.00 3.46
125 126 2.436824 GCCGACAAGGAGAAGGCC 60.437 66.667 0.00 0.00 45.00 5.19
126 127 2.269241 CCGACAAGGAGAAGGCCC 59.731 66.667 0.00 0.00 45.00 5.80
127 128 2.592993 CCGACAAGGAGAAGGCCCA 61.593 63.158 0.00 0.00 45.00 5.36
128 129 1.376037 CGACAAGGAGAAGGCCCAC 60.376 63.158 0.00 0.00 0.00 4.61
129 130 1.761174 GACAAGGAGAAGGCCCACA 59.239 57.895 0.00 0.00 0.00 4.17
130 131 0.329596 GACAAGGAGAAGGCCCACAT 59.670 55.000 0.00 0.00 0.00 3.21
131 132 0.779997 ACAAGGAGAAGGCCCACATT 59.220 50.000 0.00 0.00 0.00 2.71
132 133 1.147817 ACAAGGAGAAGGCCCACATTT 59.852 47.619 0.00 0.00 0.00 2.32
133 134 2.378547 ACAAGGAGAAGGCCCACATTTA 59.621 45.455 0.00 0.00 0.00 1.40
134 135 3.011708 ACAAGGAGAAGGCCCACATTTAT 59.988 43.478 0.00 0.00 0.00 1.40
135 136 3.303351 AGGAGAAGGCCCACATTTATG 57.697 47.619 0.00 0.00 0.00 1.90
136 137 2.582636 AGGAGAAGGCCCACATTTATGT 59.417 45.455 0.00 0.00 42.84 2.29
137 138 3.785887 AGGAGAAGGCCCACATTTATGTA 59.214 43.478 0.00 0.00 39.39 2.29
138 139 4.416848 AGGAGAAGGCCCACATTTATGTAT 59.583 41.667 0.00 0.00 39.39 2.29
139 140 5.103515 AGGAGAAGGCCCACATTTATGTATT 60.104 40.000 0.00 0.00 39.39 1.89
140 141 5.598417 GGAGAAGGCCCACATTTATGTATTT 59.402 40.000 0.00 0.00 39.39 1.40
141 142 6.239036 GGAGAAGGCCCACATTTATGTATTTC 60.239 42.308 0.00 0.00 39.39 2.17
142 143 6.194235 AGAAGGCCCACATTTATGTATTTCA 58.806 36.000 0.00 0.00 39.39 2.69
143 144 6.667414 AGAAGGCCCACATTTATGTATTTCAA 59.333 34.615 0.00 0.00 39.39 2.69
144 145 7.345392 AGAAGGCCCACATTTATGTATTTCAAT 59.655 33.333 0.00 0.00 39.39 2.57
145 146 7.436320 AGGCCCACATTTATGTATTTCAATT 57.564 32.000 0.00 0.00 39.39 2.32
146 147 7.500141 AGGCCCACATTTATGTATTTCAATTC 58.500 34.615 0.00 0.00 39.39 2.17
147 148 7.125507 AGGCCCACATTTATGTATTTCAATTCA 59.874 33.333 0.00 0.00 39.39 2.57
148 149 7.933033 GGCCCACATTTATGTATTTCAATTCAT 59.067 33.333 0.00 0.00 39.39 2.57
149 150 8.981647 GCCCACATTTATGTATTTCAATTCATC 58.018 33.333 0.00 0.00 39.39 2.92
164 165 8.789767 TTCAATTCATCTCTCTTATACTCCCT 57.210 34.615 0.00 0.00 0.00 4.20
165 166 8.415950 TCAATTCATCTCTCTTATACTCCCTC 57.584 38.462 0.00 0.00 0.00 4.30
166 167 8.007153 TCAATTCATCTCTCTTATACTCCCTCA 58.993 37.037 0.00 0.00 0.00 3.86
167 168 8.306038 CAATTCATCTCTCTTATACTCCCTCAG 58.694 40.741 0.00 0.00 0.00 3.35
168 169 6.523035 TCATCTCTCTTATACTCCCTCAGT 57.477 41.667 0.00 0.00 39.41 3.41
169 170 6.916909 TCATCTCTCTTATACTCCCTCAGTT 58.083 40.000 0.00 0.00 36.43 3.16
170 171 7.358263 TCATCTCTCTTATACTCCCTCAGTTT 58.642 38.462 0.00 0.00 36.43 2.66
171 172 7.841729 TCATCTCTCTTATACTCCCTCAGTTTT 59.158 37.037 0.00 0.00 36.43 2.43
172 173 8.482128 CATCTCTCTTATACTCCCTCAGTTTTT 58.518 37.037 0.00 0.00 36.43 1.94
173 174 9.716556 ATCTCTCTTATACTCCCTCAGTTTTTA 57.283 33.333 0.00 0.00 36.43 1.52
174 175 9.716556 TCTCTCTTATACTCCCTCAGTTTTTAT 57.283 33.333 0.00 0.00 36.43 1.40
182 183 6.171213 ACTCCCTCAGTTTTTATTTACTCCG 58.829 40.000 0.00 0.00 26.56 4.63
183 184 4.939439 TCCCTCAGTTTTTATTTACTCCGC 59.061 41.667 0.00 0.00 0.00 5.54
184 185 4.698304 CCCTCAGTTTTTATTTACTCCGCA 59.302 41.667 0.00 0.00 0.00 5.69
185 186 5.357032 CCCTCAGTTTTTATTTACTCCGCAT 59.643 40.000 0.00 0.00 0.00 4.73
186 187 6.540914 CCCTCAGTTTTTATTTACTCCGCATA 59.459 38.462 0.00 0.00 0.00 3.14
187 188 7.228706 CCCTCAGTTTTTATTTACTCCGCATAT 59.771 37.037 0.00 0.00 0.00 1.78
188 189 8.621286 CCTCAGTTTTTATTTACTCCGCATATT 58.379 33.333 0.00 0.00 0.00 1.28
191 192 9.878599 CAGTTTTTATTTACTCCGCATATTAGG 57.121 33.333 0.00 0.00 0.00 2.69
192 193 9.623000 AGTTTTTATTTACTCCGCATATTAGGT 57.377 29.630 0.00 0.00 0.00 3.08
196 197 9.616156 TTTATTTACTCCGCATATTAGGTTTGA 57.384 29.630 0.00 0.00 0.00 2.69
197 198 6.913873 TTTACTCCGCATATTAGGTTTGAC 57.086 37.500 0.00 0.00 0.00 3.18
198 199 4.755266 ACTCCGCATATTAGGTTTGACT 57.245 40.909 0.00 0.00 0.00 3.41
199 200 5.864418 ACTCCGCATATTAGGTTTGACTA 57.136 39.130 0.00 0.00 0.00 2.59
200 201 6.229936 ACTCCGCATATTAGGTTTGACTAA 57.770 37.500 0.00 0.00 37.35 2.24
201 202 6.646267 ACTCCGCATATTAGGTTTGACTAAA 58.354 36.000 0.00 0.00 36.60 1.85
202 203 6.761714 ACTCCGCATATTAGGTTTGACTAAAG 59.238 38.462 0.00 0.00 36.60 1.85
203 204 6.646267 TCCGCATATTAGGTTTGACTAAAGT 58.354 36.000 0.00 0.00 36.60 2.66
204 205 6.759827 TCCGCATATTAGGTTTGACTAAAGTC 59.240 38.462 3.08 3.08 44.97 3.01
279 280 9.797642 ACCATAGCAAATCTATATGATGTGAAA 57.202 29.630 8.62 0.00 41.79 2.69
284 285 9.836864 AGCAAATCTATATGATGTGAAAGTACA 57.163 29.630 0.00 0.00 41.79 2.90
372 373 7.575332 TTTGTCAAAGTTTACAAAGCTTGAC 57.425 32.000 0.00 15.49 39.88 3.18
373 374 6.509418 TGTCAAAGTTTACAAAGCTTGACT 57.491 33.333 19.48 0.00 39.29 3.41
374 375 6.919721 TGTCAAAGTTTACAAAGCTTGACTT 58.080 32.000 19.48 3.36 39.29 3.01
383 384 3.420839 AAAGCTTGACTTTGACCAACG 57.579 42.857 0.00 0.00 47.00 4.10
384 385 0.663153 AGCTTGACTTTGACCAACGC 59.337 50.000 0.00 0.00 0.00 4.84
385 386 0.663153 GCTTGACTTTGACCAACGCT 59.337 50.000 0.00 0.00 0.00 5.07
386 387 1.871039 GCTTGACTTTGACCAACGCTA 59.129 47.619 0.00 0.00 0.00 4.26
387 388 2.289547 GCTTGACTTTGACCAACGCTAA 59.710 45.455 0.00 0.00 0.00 3.09
388 389 3.058224 GCTTGACTTTGACCAACGCTAAT 60.058 43.478 0.00 0.00 0.00 1.73
389 390 4.153475 GCTTGACTTTGACCAACGCTAATA 59.847 41.667 0.00 0.00 0.00 0.98
390 391 5.163754 GCTTGACTTTGACCAACGCTAATAT 60.164 40.000 0.00 0.00 0.00 1.28
391 392 5.794687 TGACTTTGACCAACGCTAATATG 57.205 39.130 0.00 0.00 0.00 1.78
392 393 4.094294 TGACTTTGACCAACGCTAATATGC 59.906 41.667 0.00 0.00 0.00 3.14
408 409 8.418267 GCTAATATGCGGACTAAATAAAAACG 57.582 34.615 0.00 0.00 0.00 3.60
409 410 7.532884 GCTAATATGCGGACTAAATAAAAACGG 59.467 37.037 0.00 0.00 0.00 4.44
410 411 7.556733 AATATGCGGACTAAATAAAAACGGA 57.443 32.000 0.00 0.00 0.00 4.69
411 412 4.932268 TGCGGACTAAATAAAAACGGAG 57.068 40.909 0.00 0.00 0.00 4.63
412 413 3.685756 TGCGGACTAAATAAAAACGGAGG 59.314 43.478 0.00 0.00 0.00 4.30
413 414 3.064408 GCGGACTAAATAAAAACGGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
414 415 4.506758 CGGACTAAATAAAAACGGAGGGA 58.493 43.478 0.00 0.00 0.00 4.20
415 416 4.569564 CGGACTAAATAAAAACGGAGGGAG 59.430 45.833 0.00 0.00 0.00 4.30
416 417 5.494724 GGACTAAATAAAAACGGAGGGAGT 58.505 41.667 0.00 0.00 0.00 3.85
417 418 6.627953 CGGACTAAATAAAAACGGAGGGAGTA 60.628 42.308 0.00 0.00 0.00 2.59
418 419 6.536582 GGACTAAATAAAAACGGAGGGAGTAC 59.463 42.308 0.00 0.00 0.00 2.73
419 420 7.008021 ACTAAATAAAAACGGAGGGAGTACA 57.992 36.000 0.00 0.00 0.00 2.90
420 421 6.875726 ACTAAATAAAAACGGAGGGAGTACAC 59.124 38.462 0.00 0.00 0.00 2.90
421 422 4.895668 ATAAAAACGGAGGGAGTACACA 57.104 40.909 0.00 0.00 0.00 3.72
422 423 3.564053 AAAAACGGAGGGAGTACACAA 57.436 42.857 0.00 0.00 0.00 3.33
423 424 3.564053 AAAACGGAGGGAGTACACAAA 57.436 42.857 0.00 0.00 0.00 2.83
424 425 3.564053 AAACGGAGGGAGTACACAAAA 57.436 42.857 0.00 0.00 0.00 2.44
425 426 2.538512 ACGGAGGGAGTACACAAAAC 57.461 50.000 0.00 0.00 0.00 2.43
426 427 1.764134 ACGGAGGGAGTACACAAAACA 59.236 47.619 0.00 0.00 0.00 2.83
427 428 2.171027 ACGGAGGGAGTACACAAAACAA 59.829 45.455 0.00 0.00 0.00 2.83
428 429 2.806244 CGGAGGGAGTACACAAAACAAG 59.194 50.000 0.00 0.00 0.00 3.16
429 430 3.146847 GGAGGGAGTACACAAAACAAGG 58.853 50.000 0.00 0.00 0.00 3.61
430 431 3.146847 GAGGGAGTACACAAAACAAGGG 58.853 50.000 0.00 0.00 0.00 3.95
431 432 1.611977 GGGAGTACACAAAACAAGGGC 59.388 52.381 0.00 0.00 0.00 5.19
432 433 1.611977 GGAGTACACAAAACAAGGGCC 59.388 52.381 0.00 0.00 0.00 5.80
433 434 1.611977 GAGTACACAAAACAAGGGCCC 59.388 52.381 16.46 16.46 0.00 5.80
434 435 1.063567 AGTACACAAAACAAGGGCCCA 60.064 47.619 27.56 0.00 0.00 5.36
435 436 1.757699 GTACACAAAACAAGGGCCCAA 59.242 47.619 27.56 0.00 0.00 4.12
436 437 1.280457 ACACAAAACAAGGGCCCAAA 58.720 45.000 27.56 0.00 0.00 3.28
437 438 1.843206 ACACAAAACAAGGGCCCAAAT 59.157 42.857 27.56 6.76 0.00 2.32
438 439 2.240921 ACACAAAACAAGGGCCCAAATT 59.759 40.909 27.56 11.92 0.00 1.82
439 440 2.877786 CACAAAACAAGGGCCCAAATTC 59.122 45.455 27.56 0.00 0.00 2.17
440 441 2.158682 ACAAAACAAGGGCCCAAATTCC 60.159 45.455 27.56 0.00 0.00 3.01
441 442 2.106338 CAAAACAAGGGCCCAAATTCCT 59.894 45.455 27.56 0.00 0.00 3.36
442 443 3.268034 AAACAAGGGCCCAAATTCCTA 57.732 42.857 27.56 0.00 0.00 2.94
443 444 3.268034 AACAAGGGCCCAAATTCCTAA 57.732 42.857 27.56 0.00 0.00 2.69
444 445 3.268034 ACAAGGGCCCAAATTCCTAAA 57.732 42.857 27.56 0.00 0.00 1.85
445 446 3.592865 ACAAGGGCCCAAATTCCTAAAA 58.407 40.909 27.56 0.00 0.00 1.52
446 447 3.582647 ACAAGGGCCCAAATTCCTAAAAG 59.417 43.478 27.56 0.00 0.00 2.27
447 448 2.187958 AGGGCCCAAATTCCTAAAAGC 58.812 47.619 27.56 0.00 0.00 3.51
448 449 1.905894 GGGCCCAAATTCCTAAAAGCA 59.094 47.619 19.95 0.00 0.00 3.91
449 450 2.354704 GGGCCCAAATTCCTAAAAGCAC 60.355 50.000 19.95 0.00 0.00 4.40
450 451 2.567169 GGCCCAAATTCCTAAAAGCACT 59.433 45.455 0.00 0.00 0.00 4.40
451 452 3.368427 GGCCCAAATTCCTAAAAGCACTC 60.368 47.826 0.00 0.00 0.00 3.51
452 453 3.368427 GCCCAAATTCCTAAAAGCACTCC 60.368 47.826 0.00 0.00 0.00 3.85
453 454 3.831911 CCCAAATTCCTAAAAGCACTCCA 59.168 43.478 0.00 0.00 0.00 3.86
454 455 4.283212 CCCAAATTCCTAAAAGCACTCCAA 59.717 41.667 0.00 0.00 0.00 3.53
455 456 5.230182 CCAAATTCCTAAAAGCACTCCAAC 58.770 41.667 0.00 0.00 0.00 3.77
456 457 4.766404 AATTCCTAAAAGCACTCCAACG 57.234 40.909 0.00 0.00 0.00 4.10
457 458 2.178912 TCCTAAAAGCACTCCAACGG 57.821 50.000 0.00 0.00 0.00 4.44
458 459 1.418637 TCCTAAAAGCACTCCAACGGT 59.581 47.619 0.00 0.00 0.00 4.83
459 460 1.535462 CCTAAAAGCACTCCAACGGTG 59.465 52.381 0.00 0.00 37.70 4.94
475 476 3.305314 TGGATGCTCCACCGGTAC 58.695 61.111 6.87 0.00 42.67 3.34
476 477 1.610967 TGGATGCTCCACCGGTACA 60.611 57.895 6.87 3.68 42.67 2.90
477 478 0.980754 TGGATGCTCCACCGGTACAT 60.981 55.000 6.87 9.16 42.67 2.29
478 479 1.045407 GGATGCTCCACCGGTACATA 58.955 55.000 6.87 0.00 36.28 2.29
479 480 1.414919 GGATGCTCCACCGGTACATAA 59.585 52.381 6.87 0.00 36.28 1.90
480 481 2.158871 GGATGCTCCACCGGTACATAAA 60.159 50.000 6.87 0.00 36.28 1.40
481 482 3.537580 GATGCTCCACCGGTACATAAAA 58.462 45.455 6.87 0.00 0.00 1.52
482 483 3.420300 TGCTCCACCGGTACATAAAAA 57.580 42.857 6.87 0.00 0.00 1.94
511 512 1.076533 CGACTGCGTACCACCATGAC 61.077 60.000 0.00 0.00 0.00 3.06
528 529 3.782042 CGGCTACGTCTTTGCCTC 58.218 61.111 16.06 0.00 44.09 4.70
529 530 1.215647 CGGCTACGTCTTTGCCTCT 59.784 57.895 16.06 0.00 44.09 3.69
560 561 2.235155 TGGCGTCTTATGCTCTTACCAA 59.765 45.455 0.00 0.00 0.00 3.67
581 582 8.409358 ACCAAGTTTTTGCTCTTATCTAATGT 57.591 30.769 0.00 0.00 32.79 2.71
603 604 7.381766 TGTGGTGTTCTAATCATTTGATCAG 57.618 36.000 0.00 0.00 32.75 2.90
609 610 8.778358 GTGTTCTAATCATTTGATCAGTATCCC 58.222 37.037 0.00 0.00 32.75 3.85
720 723 1.017177 GGTTACATGTCGCCTTCGCA 61.017 55.000 0.00 0.00 35.26 5.10
721 724 1.006832 GTTACATGTCGCCTTCGCAT 58.993 50.000 0.00 0.00 34.50 4.73
732 735 0.249120 CCTTCGCATGGACCTGTGTA 59.751 55.000 0.00 0.00 0.00 2.90
735 738 3.431626 CCTTCGCATGGACCTGTGTATTA 60.432 47.826 0.00 0.00 0.00 0.98
749 752 6.183360 ACCTGTGTATTAAAAGGGTTTGTGTG 60.183 38.462 0.00 0.00 33.87 3.82
751 754 5.892119 TGTGTATTAAAAGGGTTTGTGTGGA 59.108 36.000 0.00 0.00 0.00 4.02
754 757 2.543037 AAAAGGGTTTGTGTGGACCT 57.457 45.000 0.00 0.00 36.18 3.85
755 758 2.543037 AAAGGGTTTGTGTGGACCTT 57.457 45.000 0.00 0.00 43.01 3.50
832 868 1.797537 GCCGCGCATCAACAACTTC 60.798 57.895 8.75 0.00 0.00 3.01
864 901 2.230508 AGCAACACTGAGCCAATTGATG 59.769 45.455 7.12 0.00 0.00 3.07
870 907 2.025037 ACTGAGCCAATTGATGCCCTTA 60.025 45.455 7.12 0.00 0.00 2.69
1006 1043 3.798337 CGCACCAAAAATATCCATGCTTC 59.202 43.478 0.00 0.00 0.00 3.86
1012 1049 5.808540 CCAAAAATATCCATGCTTCACACTG 59.191 40.000 0.00 0.00 0.00 3.66
1041 1078 1.131504 GAGCTGGCTATACGATCGAGG 59.868 57.143 24.34 9.32 0.00 4.63
1911 1951 1.301087 CTACCGGTGCGTGTTCCAA 60.301 57.895 19.93 0.00 0.00 3.53
2050 2090 1.004560 CAGCTCAAGTTCGCCCTCA 60.005 57.895 0.00 0.00 0.00 3.86
2232 2275 3.579626 GACGCTGCACAAGTTCGGC 62.580 63.158 0.00 0.00 0.00 5.54
2430 2476 1.120530 ACAGATACCCGGTGGACATC 58.879 55.000 0.00 0.00 34.81 3.06
2572 2618 1.197492 TGCTCATCATGTTCACGTTGC 59.803 47.619 0.00 0.00 0.00 4.17
2574 2620 0.165727 TCATCATGTTCACGTTGCGC 59.834 50.000 0.00 0.00 0.00 6.09
2593 2639 7.359681 CGTTGCGCCAAATAATATACTGTATGA 60.360 37.037 4.18 0.00 0.00 2.15
2679 2788 8.944212 AGTACGCAACTTGTTTGTATAATTTC 57.056 30.769 0.00 0.00 37.54 2.17
2729 3034 2.500229 TGAAAACAATCCCACTCGACC 58.500 47.619 0.00 0.00 0.00 4.79
2739 3044 2.693591 TCCCACTCGACCAATATCTCAC 59.306 50.000 0.00 0.00 0.00 3.51
2802 3114 5.245531 ACACATGACATCAAACCGATAGTT 58.754 37.500 0.00 0.00 41.81 2.24
2850 3162 2.550978 GTTGGGTCGACATGGTATGAG 58.449 52.381 18.91 0.00 0.00 2.90
2851 3163 2.153034 TGGGTCGACATGGTATGAGA 57.847 50.000 18.91 0.00 0.00 3.27
2852 3164 2.462723 TGGGTCGACATGGTATGAGAA 58.537 47.619 18.91 0.00 0.00 2.87
2853 3165 2.167693 TGGGTCGACATGGTATGAGAAC 59.832 50.000 18.91 0.00 0.00 3.01
2854 3166 2.483188 GGGTCGACATGGTATGAGAACC 60.483 54.545 18.91 0.08 39.53 3.62
2855 3167 2.483188 GGTCGACATGGTATGAGAACCC 60.483 54.545 18.91 0.00 38.90 4.11
2856 3168 1.407618 TCGACATGGTATGAGAACCCG 59.592 52.381 0.00 0.00 38.90 5.28
2857 3169 1.583054 GACATGGTATGAGAACCCGC 58.417 55.000 0.00 0.00 38.90 6.13
2858 3170 0.908910 ACATGGTATGAGAACCCGCA 59.091 50.000 0.00 0.00 38.90 5.69
2859 3171 1.280710 ACATGGTATGAGAACCCGCAA 59.719 47.619 0.00 0.00 38.90 4.85
2860 3172 2.290641 ACATGGTATGAGAACCCGCAAA 60.291 45.455 0.00 0.00 38.90 3.68
2861 3173 2.570415 TGGTATGAGAACCCGCAAAA 57.430 45.000 0.00 0.00 38.90 2.44
2862 3174 2.865079 TGGTATGAGAACCCGCAAAAA 58.135 42.857 0.00 0.00 38.90 1.94
2882 3194 1.889530 AAAAGGAGACCCCGCGAGAG 61.890 60.000 8.23 0.00 40.87 3.20
2890 3202 2.560119 CCCCGCGAGAGAGATCCAG 61.560 68.421 8.23 0.00 0.00 3.86
2985 3298 9.839185 ATGTACTTGGGATGTATTAGTACCTAT 57.161 33.333 0.00 0.00 40.09 2.57
3023 3342 6.998074 TGCCACTCCTTTACTGGATAATTATG 59.002 38.462 1.78 0.00 35.30 1.90
3081 3401 7.878547 TGCAAGACATGACCAATCAATATAA 57.121 32.000 0.00 0.00 38.69 0.98
3104 3424 4.974438 TCCCCCTCCACAGCCGTT 62.974 66.667 0.00 0.00 0.00 4.44
3142 3462 4.378774 TCTCTCGAGTAGTCCGGATTTAG 58.621 47.826 7.81 0.00 0.00 1.85
3212 3533 0.692476 CCCAAGTCACATGGTGGAGA 59.308 55.000 0.00 0.00 36.14 3.71
3213 3534 1.073763 CCCAAGTCACATGGTGGAGAA 59.926 52.381 0.00 0.00 36.14 2.87
3214 3535 2.488891 CCCAAGTCACATGGTGGAGAAA 60.489 50.000 0.00 0.00 36.14 2.52
3215 3536 3.424703 CCAAGTCACATGGTGGAGAAAT 58.575 45.455 0.00 0.00 33.87 2.17
3216 3537 4.567537 CCCAAGTCACATGGTGGAGAAATA 60.568 45.833 0.00 0.00 36.14 1.40
3273 3627 1.880027 GCAGTTTGAGTTCGACCCATT 59.120 47.619 0.00 0.00 0.00 3.16
3291 3645 3.259374 CCATTCCACGAGGCATATACTCT 59.741 47.826 0.00 0.00 32.83 3.24
3294 3648 3.833732 TCCACGAGGCATATACTCTCTT 58.166 45.455 0.00 0.00 32.83 2.85
3295 3649 4.215908 TCCACGAGGCATATACTCTCTTT 58.784 43.478 0.00 0.00 32.83 2.52
3296 3650 4.038042 TCCACGAGGCATATACTCTCTTTG 59.962 45.833 0.00 0.00 32.83 2.77
3411 3765 8.084073 CCACCAAACATATATCATTGGATTCAC 58.916 37.037 23.60 0.00 44.01 3.18
3432 3786 8.744568 TTCACCATTGCATATACTTTGACATA 57.255 30.769 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.599866 CCCCTCAAAATACTTCCATTTAATTTC 57.400 33.333 0.00 0.00 0.00 2.17
20 21 8.548025 CCCCCTCAAAATACTTCCATTTAATTT 58.452 33.333 0.00 0.00 0.00 1.82
21 22 8.089625 CCCCCTCAAAATACTTCCATTTAATT 57.910 34.615 0.00 0.00 0.00 1.40
22 23 7.675161 CCCCCTCAAAATACTTCCATTTAAT 57.325 36.000 0.00 0.00 0.00 1.40
43 44 5.723295 CATGCATATGCTAAAATAACCCCC 58.277 41.667 27.13 0.00 42.66 5.40
57 58 4.127907 AGAAGACTGTCTGCATGCATATG 58.872 43.478 22.97 10.20 37.36 1.78
58 59 4.101274 AGAGAAGACTGTCTGCATGCATAT 59.899 41.667 22.97 0.00 0.00 1.78
59 60 3.450096 AGAGAAGACTGTCTGCATGCATA 59.550 43.478 22.97 11.96 0.00 3.14
60 61 2.236644 AGAGAAGACTGTCTGCATGCAT 59.763 45.455 22.97 5.46 0.00 3.96
61 62 1.622312 AGAGAAGACTGTCTGCATGCA 59.378 47.619 21.29 21.29 0.00 3.96
62 63 2.270047 GAGAGAAGACTGTCTGCATGC 58.730 52.381 17.86 11.82 34.23 4.06
63 64 3.589495 TGAGAGAAGACTGTCTGCATG 57.411 47.619 17.86 0.00 37.33 4.06
64 65 4.382901 GGATTGAGAGAAGACTGTCTGCAT 60.383 45.833 17.86 5.93 37.33 3.96
65 66 3.056250 GGATTGAGAGAAGACTGTCTGCA 60.056 47.826 17.86 6.12 37.33 4.41
66 67 3.195396 AGGATTGAGAGAAGACTGTCTGC 59.805 47.826 11.71 9.69 37.33 4.26
67 68 5.404466 AAGGATTGAGAGAAGACTGTCTG 57.596 43.478 11.71 0.00 37.33 3.51
68 69 5.779771 AGAAAGGATTGAGAGAAGACTGTCT 59.220 40.000 4.06 4.06 37.33 3.41
69 70 6.036577 AGAAAGGATTGAGAGAAGACTGTC 57.963 41.667 0.00 0.00 37.02 3.51
70 71 5.779771 AGAGAAAGGATTGAGAGAAGACTGT 59.220 40.000 0.00 0.00 0.00 3.55
71 72 6.153340 AGAGAGAAAGGATTGAGAGAAGACTG 59.847 42.308 0.00 0.00 0.00 3.51
72 73 6.256053 AGAGAGAAAGGATTGAGAGAAGACT 58.744 40.000 0.00 0.00 0.00 3.24
73 74 6.152661 TGAGAGAGAAAGGATTGAGAGAAGAC 59.847 42.308 0.00 0.00 0.00 3.01
74 75 6.252233 TGAGAGAGAAAGGATTGAGAGAAGA 58.748 40.000 0.00 0.00 0.00 2.87
75 76 6.528537 TGAGAGAGAAAGGATTGAGAGAAG 57.471 41.667 0.00 0.00 0.00 2.85
76 77 6.666980 TCATGAGAGAGAAAGGATTGAGAGAA 59.333 38.462 0.00 0.00 0.00 2.87
77 78 6.193504 TCATGAGAGAGAAAGGATTGAGAGA 58.806 40.000 0.00 0.00 0.00 3.10
78 79 6.468333 TCATGAGAGAGAAAGGATTGAGAG 57.532 41.667 0.00 0.00 0.00 3.20
79 80 8.724113 ATATCATGAGAGAGAAAGGATTGAGA 57.276 34.615 0.09 0.00 0.00 3.27
83 84 9.723601 GCTTTATATCATGAGAGAGAAAGGATT 57.276 33.333 17.19 0.00 41.90 3.01
84 85 8.320617 GGCTTTATATCATGAGAGAGAAAGGAT 58.679 37.037 17.19 0.00 41.90 3.24
85 86 7.524532 CGGCTTTATATCATGAGAGAGAAAGGA 60.525 40.741 17.19 0.00 41.90 3.36
86 87 6.589523 CGGCTTTATATCATGAGAGAGAAAGG 59.410 42.308 17.19 4.37 41.90 3.11
87 88 7.328249 GTCGGCTTTATATCATGAGAGAGAAAG 59.672 40.741 13.70 13.70 43.51 2.62
88 89 7.148641 GTCGGCTTTATATCATGAGAGAGAAA 58.851 38.462 0.09 0.00 0.00 2.52
89 90 6.265422 TGTCGGCTTTATATCATGAGAGAGAA 59.735 38.462 0.09 0.00 0.00 2.87
90 91 5.770162 TGTCGGCTTTATATCATGAGAGAGA 59.230 40.000 0.09 0.00 0.00 3.10
91 92 6.018589 TGTCGGCTTTATATCATGAGAGAG 57.981 41.667 0.09 0.00 0.00 3.20
92 93 6.405278 TTGTCGGCTTTATATCATGAGAGA 57.595 37.500 0.09 0.00 0.00 3.10
93 94 5.636965 CCTTGTCGGCTTTATATCATGAGAG 59.363 44.000 0.09 0.00 0.00 3.20
94 95 5.304357 TCCTTGTCGGCTTTATATCATGAGA 59.696 40.000 0.09 0.00 0.00 3.27
95 96 5.541845 TCCTTGTCGGCTTTATATCATGAG 58.458 41.667 0.09 0.00 0.00 2.90
96 97 5.304357 TCTCCTTGTCGGCTTTATATCATGA 59.696 40.000 0.00 0.00 0.00 3.07
97 98 5.541845 TCTCCTTGTCGGCTTTATATCATG 58.458 41.667 0.00 0.00 0.00 3.07
98 99 5.808366 TCTCCTTGTCGGCTTTATATCAT 57.192 39.130 0.00 0.00 0.00 2.45
99 100 5.453339 CCTTCTCCTTGTCGGCTTTATATCA 60.453 44.000 0.00 0.00 0.00 2.15
100 101 4.991687 CCTTCTCCTTGTCGGCTTTATATC 59.008 45.833 0.00 0.00 0.00 1.63
101 102 4.743955 GCCTTCTCCTTGTCGGCTTTATAT 60.744 45.833 0.00 0.00 37.76 0.86
102 103 3.431766 GCCTTCTCCTTGTCGGCTTTATA 60.432 47.826 0.00 0.00 37.76 0.98
103 104 2.681097 GCCTTCTCCTTGTCGGCTTTAT 60.681 50.000 0.00 0.00 37.76 1.40
104 105 1.338769 GCCTTCTCCTTGTCGGCTTTA 60.339 52.381 0.00 0.00 37.76 1.85
105 106 0.606673 GCCTTCTCCTTGTCGGCTTT 60.607 55.000 0.00 0.00 37.76 3.51
106 107 1.003233 GCCTTCTCCTTGTCGGCTT 60.003 57.895 0.00 0.00 37.76 4.35
107 108 2.665603 GCCTTCTCCTTGTCGGCT 59.334 61.111 0.00 0.00 37.76 5.52
108 109 2.436824 GGCCTTCTCCTTGTCGGC 60.437 66.667 0.00 0.00 39.98 5.54
109 110 2.269241 GGGCCTTCTCCTTGTCGG 59.731 66.667 0.84 0.00 0.00 4.79
110 111 1.376037 GTGGGCCTTCTCCTTGTCG 60.376 63.158 4.53 0.00 0.00 4.35
111 112 0.329596 ATGTGGGCCTTCTCCTTGTC 59.670 55.000 4.53 0.00 0.00 3.18
112 113 0.779997 AATGTGGGCCTTCTCCTTGT 59.220 50.000 4.53 0.00 0.00 3.16
113 114 1.928868 AAATGTGGGCCTTCTCCTTG 58.071 50.000 4.53 0.00 0.00 3.61
114 115 3.011708 ACATAAATGTGGGCCTTCTCCTT 59.988 43.478 4.53 0.00 40.03 3.36
115 116 2.582636 ACATAAATGTGGGCCTTCTCCT 59.417 45.455 4.53 0.00 40.03 3.69
116 117 3.018423 ACATAAATGTGGGCCTTCTCC 57.982 47.619 4.53 0.00 40.03 3.71
117 118 6.321181 TGAAATACATAAATGTGGGCCTTCTC 59.679 38.462 4.53 0.00 41.89 2.87
118 119 6.194235 TGAAATACATAAATGTGGGCCTTCT 58.806 36.000 4.53 0.00 41.89 2.85
119 120 6.463995 TGAAATACATAAATGTGGGCCTTC 57.536 37.500 4.53 0.00 41.89 3.46
120 121 6.865834 TTGAAATACATAAATGTGGGCCTT 57.134 33.333 4.53 0.00 41.89 4.35
121 122 7.125507 TGAATTGAAATACATAAATGTGGGCCT 59.874 33.333 4.53 0.00 41.89 5.19
122 123 7.271511 TGAATTGAAATACATAAATGTGGGCC 58.728 34.615 5.85 0.00 41.89 5.80
123 124 8.891671 ATGAATTGAAATACATAAATGTGGGC 57.108 30.769 5.85 0.00 41.89 5.36
138 139 9.218525 AGGGAGTATAAGAGAGATGAATTGAAA 57.781 33.333 0.00 0.00 0.00 2.69
139 140 8.789767 AGGGAGTATAAGAGAGATGAATTGAA 57.210 34.615 0.00 0.00 0.00 2.69
140 141 8.007153 TGAGGGAGTATAAGAGAGATGAATTGA 58.993 37.037 0.00 0.00 0.00 2.57
141 142 8.187913 TGAGGGAGTATAAGAGAGATGAATTG 57.812 38.462 0.00 0.00 0.00 2.32
142 143 8.010105 ACTGAGGGAGTATAAGAGAGATGAATT 58.990 37.037 0.00 0.00 30.86 2.17
143 144 7.534852 ACTGAGGGAGTATAAGAGAGATGAAT 58.465 38.462 0.00 0.00 30.86 2.57
144 145 6.916909 ACTGAGGGAGTATAAGAGAGATGAA 58.083 40.000 0.00 0.00 30.86 2.57
145 146 6.523035 ACTGAGGGAGTATAAGAGAGATGA 57.477 41.667 0.00 0.00 30.86 2.92
146 147 7.595819 AAACTGAGGGAGTATAAGAGAGATG 57.404 40.000 0.00 0.00 33.09 2.90
147 148 8.616799 AAAAACTGAGGGAGTATAAGAGAGAT 57.383 34.615 0.00 0.00 33.09 2.75
148 149 9.716556 ATAAAAACTGAGGGAGTATAAGAGAGA 57.283 33.333 0.00 0.00 33.09 3.10
156 157 7.985752 CGGAGTAAATAAAAACTGAGGGAGTAT 59.014 37.037 0.00 0.00 33.09 2.12
157 158 7.325694 CGGAGTAAATAAAAACTGAGGGAGTA 58.674 38.462 0.00 0.00 33.09 2.59
158 159 6.171213 CGGAGTAAATAAAAACTGAGGGAGT 58.829 40.000 0.00 0.00 35.94 3.85
159 160 5.064834 GCGGAGTAAATAAAAACTGAGGGAG 59.935 44.000 0.00 0.00 0.00 4.30
160 161 4.939439 GCGGAGTAAATAAAAACTGAGGGA 59.061 41.667 0.00 0.00 0.00 4.20
161 162 4.698304 TGCGGAGTAAATAAAAACTGAGGG 59.302 41.667 0.00 0.00 0.00 4.30
162 163 5.873179 TGCGGAGTAAATAAAAACTGAGG 57.127 39.130 0.00 0.00 0.00 3.86
165 166 9.878599 CCTAATATGCGGAGTAAATAAAAACTG 57.121 33.333 0.00 0.00 0.00 3.16
166 167 9.623000 ACCTAATATGCGGAGTAAATAAAAACT 57.377 29.630 0.00 0.00 0.00 2.66
170 171 9.616156 TCAAACCTAATATGCGGAGTAAATAAA 57.384 29.630 0.00 0.00 0.00 1.40
171 172 9.048446 GTCAAACCTAATATGCGGAGTAAATAA 57.952 33.333 0.00 0.00 0.00 1.40
172 173 8.426489 AGTCAAACCTAATATGCGGAGTAAATA 58.574 33.333 0.00 0.00 0.00 1.40
173 174 7.280356 AGTCAAACCTAATATGCGGAGTAAAT 58.720 34.615 0.00 0.00 0.00 1.40
174 175 6.646267 AGTCAAACCTAATATGCGGAGTAAA 58.354 36.000 0.00 0.00 0.00 2.01
175 176 6.229936 AGTCAAACCTAATATGCGGAGTAA 57.770 37.500 0.00 0.00 0.00 2.24
176 177 5.864418 AGTCAAACCTAATATGCGGAGTA 57.136 39.130 0.00 0.00 0.00 2.59
177 178 4.755266 AGTCAAACCTAATATGCGGAGT 57.245 40.909 0.00 0.00 0.00 3.85
178 179 6.761714 ACTTTAGTCAAACCTAATATGCGGAG 59.238 38.462 0.00 0.00 0.00 4.63
179 180 6.646267 ACTTTAGTCAAACCTAATATGCGGA 58.354 36.000 0.00 0.00 0.00 5.54
180 181 6.920569 ACTTTAGTCAAACCTAATATGCGG 57.079 37.500 0.00 0.00 0.00 5.69
253 254 9.797642 TTTCACATCATATAGATTTGCTATGGT 57.202 29.630 0.00 0.00 40.05 3.55
258 259 9.836864 TGTACTTTCACATCATATAGATTTGCT 57.163 29.630 0.00 0.00 34.99 3.91
348 349 7.375053 AGTCAAGCTTTGTAAACTTTGACAAA 58.625 30.769 20.02 0.00 41.90 2.83
349 350 6.919721 AGTCAAGCTTTGTAAACTTTGACAA 58.080 32.000 20.02 0.88 33.81 3.18
350 351 6.509418 AGTCAAGCTTTGTAAACTTTGACA 57.491 33.333 20.02 0.00 30.59 3.58
351 352 7.812309 AAAGTCAAGCTTTGTAAACTTTGAC 57.188 32.000 14.76 14.88 45.00 3.18
364 365 1.065551 GCGTTGGTCAAAGTCAAGCTT 59.934 47.619 0.00 0.00 39.52 3.74
365 366 0.663153 GCGTTGGTCAAAGTCAAGCT 59.337 50.000 0.00 0.00 0.00 3.74
366 367 0.663153 AGCGTTGGTCAAAGTCAAGC 59.337 50.000 0.00 0.00 0.00 4.01
367 368 4.749245 ATTAGCGTTGGTCAAAGTCAAG 57.251 40.909 0.00 0.00 0.00 3.02
368 369 5.391523 GCATATTAGCGTTGGTCAAAGTCAA 60.392 40.000 0.00 0.00 0.00 3.18
369 370 4.094294 GCATATTAGCGTTGGTCAAAGTCA 59.906 41.667 0.00 0.00 0.00 3.41
370 371 4.588278 GCATATTAGCGTTGGTCAAAGTC 58.412 43.478 0.00 0.00 0.00 3.01
371 372 4.616181 GCATATTAGCGTTGGTCAAAGT 57.384 40.909 0.00 0.00 0.00 2.66
383 384 7.532884 CCGTTTTTATTTAGTCCGCATATTAGC 59.467 37.037 0.00 0.00 0.00 3.09
384 385 8.767085 TCCGTTTTTATTTAGTCCGCATATTAG 58.233 33.333 0.00 0.00 0.00 1.73
385 386 8.659925 TCCGTTTTTATTTAGTCCGCATATTA 57.340 30.769 0.00 0.00 0.00 0.98
386 387 7.255001 CCTCCGTTTTTATTTAGTCCGCATATT 60.255 37.037 0.00 0.00 0.00 1.28
387 388 6.204108 CCTCCGTTTTTATTTAGTCCGCATAT 59.796 38.462 0.00 0.00 0.00 1.78
388 389 5.524646 CCTCCGTTTTTATTTAGTCCGCATA 59.475 40.000 0.00 0.00 0.00 3.14
389 390 4.334481 CCTCCGTTTTTATTTAGTCCGCAT 59.666 41.667 0.00 0.00 0.00 4.73
390 391 3.685756 CCTCCGTTTTTATTTAGTCCGCA 59.314 43.478 0.00 0.00 0.00 5.69
391 392 3.064408 CCCTCCGTTTTTATTTAGTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
392 393 4.506758 TCCCTCCGTTTTTATTTAGTCCG 58.493 43.478 0.00 0.00 0.00 4.79
393 394 5.494724 ACTCCCTCCGTTTTTATTTAGTCC 58.505 41.667 0.00 0.00 0.00 3.85
394 395 7.063898 GTGTACTCCCTCCGTTTTTATTTAGTC 59.936 40.741 0.00 0.00 0.00 2.59
395 396 6.875726 GTGTACTCCCTCCGTTTTTATTTAGT 59.124 38.462 0.00 0.00 0.00 2.24
396 397 6.875195 TGTGTACTCCCTCCGTTTTTATTTAG 59.125 38.462 0.00 0.00 0.00 1.85
397 398 6.767456 TGTGTACTCCCTCCGTTTTTATTTA 58.233 36.000 0.00 0.00 0.00 1.40
398 399 5.623169 TGTGTACTCCCTCCGTTTTTATTT 58.377 37.500 0.00 0.00 0.00 1.40
399 400 5.231702 TGTGTACTCCCTCCGTTTTTATT 57.768 39.130 0.00 0.00 0.00 1.40
400 401 4.895668 TGTGTACTCCCTCCGTTTTTAT 57.104 40.909 0.00 0.00 0.00 1.40
401 402 4.686191 TTGTGTACTCCCTCCGTTTTTA 57.314 40.909 0.00 0.00 0.00 1.52
402 403 3.564053 TTGTGTACTCCCTCCGTTTTT 57.436 42.857 0.00 0.00 0.00 1.94
403 404 3.564053 TTTGTGTACTCCCTCCGTTTT 57.436 42.857 0.00 0.00 0.00 2.43
404 405 3.208594 GTTTTGTGTACTCCCTCCGTTT 58.791 45.455 0.00 0.00 0.00 3.60
405 406 2.171027 TGTTTTGTGTACTCCCTCCGTT 59.829 45.455 0.00 0.00 0.00 4.44
406 407 1.764134 TGTTTTGTGTACTCCCTCCGT 59.236 47.619 0.00 0.00 0.00 4.69
407 408 2.536761 TGTTTTGTGTACTCCCTCCG 57.463 50.000 0.00 0.00 0.00 4.63
408 409 3.146847 CCTTGTTTTGTGTACTCCCTCC 58.853 50.000 0.00 0.00 0.00 4.30
409 410 3.146847 CCCTTGTTTTGTGTACTCCCTC 58.853 50.000 0.00 0.00 0.00 4.30
410 411 2.751816 GCCCTTGTTTTGTGTACTCCCT 60.752 50.000 0.00 0.00 0.00 4.20
411 412 1.611977 GCCCTTGTTTTGTGTACTCCC 59.388 52.381 0.00 0.00 0.00 4.30
412 413 1.611977 GGCCCTTGTTTTGTGTACTCC 59.388 52.381 0.00 0.00 0.00 3.85
413 414 1.611977 GGGCCCTTGTTTTGTGTACTC 59.388 52.381 17.04 0.00 0.00 2.59
414 415 1.063567 TGGGCCCTTGTTTTGTGTACT 60.064 47.619 25.70 0.00 0.00 2.73
415 416 1.404843 TGGGCCCTTGTTTTGTGTAC 58.595 50.000 25.70 0.00 0.00 2.90
416 417 2.160721 TTGGGCCCTTGTTTTGTGTA 57.839 45.000 25.70 0.00 0.00 2.90
417 418 1.280457 TTTGGGCCCTTGTTTTGTGT 58.720 45.000 25.70 0.00 0.00 3.72
418 419 2.636647 ATTTGGGCCCTTGTTTTGTG 57.363 45.000 25.70 0.00 0.00 3.33
419 420 2.158682 GGAATTTGGGCCCTTGTTTTGT 60.159 45.455 25.70 0.00 0.00 2.83
420 421 2.106338 AGGAATTTGGGCCCTTGTTTTG 59.894 45.455 25.70 0.00 0.00 2.44
421 422 2.417652 AGGAATTTGGGCCCTTGTTTT 58.582 42.857 25.70 9.52 0.00 2.43
422 423 2.116869 AGGAATTTGGGCCCTTGTTT 57.883 45.000 25.70 11.45 0.00 2.83
423 424 3.268034 TTAGGAATTTGGGCCCTTGTT 57.732 42.857 25.70 14.55 0.00 2.83
424 425 3.268034 TTTAGGAATTTGGGCCCTTGT 57.732 42.857 25.70 5.30 0.00 3.16
425 426 3.619733 GCTTTTAGGAATTTGGGCCCTTG 60.620 47.826 25.70 0.00 0.00 3.61
426 427 2.571653 GCTTTTAGGAATTTGGGCCCTT 59.428 45.455 25.70 9.32 0.00 3.95
427 428 2.187958 GCTTTTAGGAATTTGGGCCCT 58.812 47.619 25.70 0.66 0.00 5.19
428 429 1.905894 TGCTTTTAGGAATTTGGGCCC 59.094 47.619 17.59 17.59 0.00 5.80
429 430 2.567169 AGTGCTTTTAGGAATTTGGGCC 59.433 45.455 0.00 0.00 0.00 5.80
430 431 3.368427 GGAGTGCTTTTAGGAATTTGGGC 60.368 47.826 0.00 0.00 0.00 5.36
431 432 3.831911 TGGAGTGCTTTTAGGAATTTGGG 59.168 43.478 0.00 0.00 0.00 4.12
432 433 5.230182 GTTGGAGTGCTTTTAGGAATTTGG 58.770 41.667 0.00 0.00 0.00 3.28
433 434 4.917415 CGTTGGAGTGCTTTTAGGAATTTG 59.083 41.667 0.00 0.00 0.00 2.32
434 435 4.022329 CCGTTGGAGTGCTTTTAGGAATTT 60.022 41.667 0.00 0.00 0.00 1.82
435 436 3.506067 CCGTTGGAGTGCTTTTAGGAATT 59.494 43.478 0.00 0.00 0.00 2.17
436 437 3.081804 CCGTTGGAGTGCTTTTAGGAAT 58.918 45.455 0.00 0.00 0.00 3.01
437 438 2.158726 ACCGTTGGAGTGCTTTTAGGAA 60.159 45.455 0.00 0.00 0.00 3.36
438 439 1.418637 ACCGTTGGAGTGCTTTTAGGA 59.581 47.619 0.00 0.00 0.00 2.94
439 440 1.535462 CACCGTTGGAGTGCTTTTAGG 59.465 52.381 0.00 0.00 0.00 2.69
440 441 2.969443 CACCGTTGGAGTGCTTTTAG 57.031 50.000 0.00 0.00 0.00 1.85
460 461 2.902705 TTATGTACCGGTGGAGCATC 57.097 50.000 19.93 0.00 0.00 3.91
461 462 3.637911 TTTTATGTACCGGTGGAGCAT 57.362 42.857 19.93 17.43 0.00 3.79
462 463 3.420300 TTTTTATGTACCGGTGGAGCA 57.580 42.857 19.93 11.30 0.00 4.26
481 482 4.142643 TGGTACGCAGTCGAAAAAGTTTTT 60.143 37.500 13.35 13.35 43.93 1.94
482 483 3.374678 TGGTACGCAGTCGAAAAAGTTTT 59.625 39.130 0.00 0.00 43.93 2.43
483 484 2.937799 TGGTACGCAGTCGAAAAAGTTT 59.062 40.909 0.00 0.00 43.93 2.66
484 485 2.286025 GTGGTACGCAGTCGAAAAAGTT 59.714 45.455 0.00 0.00 43.93 2.66
485 486 1.862827 GTGGTACGCAGTCGAAAAAGT 59.137 47.619 0.00 0.00 43.93 2.66
486 487 1.193874 GGTGGTACGCAGTCGAAAAAG 59.806 52.381 0.00 0.00 43.93 2.27
487 488 1.219646 GGTGGTACGCAGTCGAAAAA 58.780 50.000 0.00 0.00 43.93 1.94
488 489 0.104487 TGGTGGTACGCAGTCGAAAA 59.896 50.000 0.00 0.00 43.93 2.29
489 490 0.319083 ATGGTGGTACGCAGTCGAAA 59.681 50.000 0.00 0.00 43.93 3.46
490 491 0.389296 CATGGTGGTACGCAGTCGAA 60.389 55.000 0.00 0.00 43.93 3.71
493 494 1.076533 CGTCATGGTGGTACGCAGTC 61.077 60.000 0.00 0.00 43.93 3.51
496 497 2.263227 CCGTCATGGTGGTACGCA 59.737 61.111 0.00 0.00 43.02 5.24
499 500 0.526954 CGTAGCCGTCATGGTGGTAC 60.527 60.000 6.10 7.40 41.21 3.34
539 540 1.828595 TGGTAAGAGCATAAGACGCCA 59.171 47.619 0.00 0.00 0.00 5.69
542 543 6.481954 AAAACTTGGTAAGAGCATAAGACG 57.518 37.500 0.00 0.00 0.00 4.18
560 561 7.448469 ACACCACATTAGATAAGAGCAAAAACT 59.552 33.333 0.00 0.00 0.00 2.66
581 582 9.330063 GATACTGATCAAATGATTAGAACACCA 57.670 33.333 18.67 0.90 39.64 4.17
597 598 7.282585 CCTTAACAGAAATGGGATACTGATCA 58.717 38.462 0.00 0.00 33.27 2.92
603 604 7.773690 TCTTAAGCCTTAACAGAAATGGGATAC 59.226 37.037 0.00 0.00 0.00 2.24
609 610 7.875971 ACTTGTCTTAAGCCTTAACAGAAATG 58.124 34.615 0.00 0.00 0.00 2.32
670 671 9.537852 TGACTAGGTTGTTAAGAGTTAGGATAA 57.462 33.333 0.00 0.00 0.00 1.75
720 723 5.530176 ACCCTTTTAATACACAGGTCCAT 57.470 39.130 0.00 0.00 0.00 3.41
721 724 5.327737 AACCCTTTTAATACACAGGTCCA 57.672 39.130 0.00 0.00 0.00 4.02
732 735 4.552674 AGGTCCACACAAACCCTTTTAAT 58.447 39.130 0.00 0.00 36.11 1.40
735 738 2.543037 AGGTCCACACAAACCCTTTT 57.457 45.000 0.00 0.00 36.11 2.27
749 752 7.764901 CCGATATATTTTCCTAGCTAAAGGTCC 59.235 40.741 2.42 0.00 37.91 4.46
751 754 7.104290 GCCGATATATTTTCCTAGCTAAAGGT 58.896 38.462 2.42 0.00 37.91 3.50
754 757 6.927416 TCGCCGATATATTTTCCTAGCTAAA 58.073 36.000 0.00 0.00 0.00 1.85
755 758 6.519679 TCGCCGATATATTTTCCTAGCTAA 57.480 37.500 0.00 0.00 0.00 3.09
832 868 2.822561 TCAGTGTTGCTCCTAGACAGAG 59.177 50.000 0.00 0.00 0.00 3.35
1006 1043 3.108289 CTCGGCGAGTGCAGTGTG 61.108 66.667 27.92 0.16 45.35 3.82
1041 1078 1.596477 GATGGACGGGCTCATGCTC 60.596 63.158 0.00 0.00 39.59 4.26
1236 1273 4.124351 CGGAAGCCGGCGTAGTCA 62.124 66.667 23.20 0.00 44.15 3.41
1893 1933 1.289109 CTTGGAACACGCACCGGTAG 61.289 60.000 6.87 7.33 39.29 3.18
1911 1951 3.756783 CCCTCCCCGTCCTCCTCT 61.757 72.222 0.00 0.00 0.00 3.69
2050 2090 2.509336 CTTCCGCGCGATGAAGGT 60.509 61.111 34.63 0.00 35.44 3.50
2232 2275 3.150895 GAGCTGCTCGACGTGTTG 58.849 61.111 14.68 0.00 0.00 3.33
2430 2476 2.521958 AATGGCTGAGAACGTCGGGG 62.522 60.000 0.00 0.00 31.26 5.73
2470 2516 4.363999 CATGACGAACTGTAATCCTCTCC 58.636 47.826 0.00 0.00 0.00 3.71
2554 2600 1.787989 GCGCAACGTGAACATGATGAG 60.788 52.381 0.30 6.18 0.00 2.90
2696 2805 9.209175 TGGGATTGTTTTCAAAATAATTAACCG 57.791 29.630 6.33 0.00 43.39 4.44
2751 3060 8.982685 CATCAACCAATAACTATGCTAGTGTAG 58.017 37.037 0.00 0.00 39.39 2.74
2802 3114 5.928976 AGTGTCCTAGCATGCATTTGTATA 58.071 37.500 21.98 0.00 0.00 1.47
2862 3174 1.003718 CTCGCGGGGTCTCCTTTTT 60.004 57.895 6.13 0.00 0.00 1.94
2863 3175 1.889530 CTCTCGCGGGGTCTCCTTTT 61.890 60.000 5.94 0.00 0.00 2.27
2864 3176 2.283676 TCTCGCGGGGTCTCCTTT 60.284 61.111 5.94 0.00 0.00 3.11
2865 3177 2.756283 CTCTCGCGGGGTCTCCTT 60.756 66.667 5.94 0.00 0.00 3.36
2866 3178 3.707640 CTCTCTCGCGGGGTCTCCT 62.708 68.421 5.94 0.00 0.00 3.69
2867 3179 2.969300 ATCTCTCTCGCGGGGTCTCC 62.969 65.000 5.94 0.00 0.00 3.71
2868 3180 1.512156 GATCTCTCTCGCGGGGTCTC 61.512 65.000 5.94 0.00 0.00 3.36
2869 3181 1.527380 GATCTCTCTCGCGGGGTCT 60.527 63.158 5.94 0.00 0.00 3.85
2882 3194 2.042464 TGGCATGTAGGACTGGATCTC 58.958 52.381 0.00 0.00 0.00 2.75
2890 3202 1.696063 ATGGCAATGGCATGTAGGAC 58.304 50.000 21.71 0.00 46.89 3.85
2986 3299 9.646522 AGTAAAGGAGTGGCATTTCATAATATT 57.353 29.630 0.00 0.00 32.08 1.28
2989 3305 6.322201 CCAGTAAAGGAGTGGCATTTCATAAT 59.678 38.462 0.00 0.00 41.89 1.28
3069 3389 6.614657 AGGGGGAAGTCTTTATATTGATTGG 58.385 40.000 0.00 0.00 0.00 3.16
3081 3401 1.492993 GCTGTGGAGGGGGAAGTCTT 61.493 60.000 0.00 0.00 0.00 3.01
3104 3424 6.015856 ACTCGAGAGATCAAAACTTCTCTTGA 60.016 38.462 21.68 15.57 43.55 3.02
3273 3627 3.510531 AGAGAGTATATGCCTCGTGGA 57.489 47.619 7.92 0.00 34.08 4.02


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

AutoCloner maintained by Alex Coulton.