Multiple sequence alignment - TraesCS6D01G370100

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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 TraesCS6D01G370100 chr6D 100.000 3285 0 0 1 3285 456431042 456434326 0.000000e+00 6067
1 TraesCS6D01G370100 chr6D 94.444 828 41 4 2459 3285 456449290 456450113 0.000000e+00 1269
2 TraesCS6D01G370100 chr6A 90.130 1074 52 25 602 1633 603137823 603138884 0.000000e+00 1347
3 TraesCS6D01G370100 chr6A 94.678 451 23 1 2009 2458 603138880 603139330 0.000000e+00 699
4 TraesCS6D01G370100 chr6A 93.333 375 25 0 1636 2010 613600363 613599989 3.700000e-154 555
5 TraesCS6D01G370100 chr6A 84.532 278 27 8 219 486 603137271 603137542 9.040000e-66 261
6 TraesCS6D01G370100 chr6B 87.089 1185 82 25 483 1612 693946972 693948140 0.000000e+00 1275
7 TraesCS6D01G370100 chr6B 90.419 501 38 6 1140 1636 694104415 694104909 0.000000e+00 651
8 TraesCS6D01G370100 chr6B 87.778 450 45 8 2010 2454 694104903 694105347 4.860000e-143 518
9 TraesCS6D01G370100 chr6B 85.906 447 59 3 2010 2454 693948147 693948591 1.070000e-129 473
10 TraesCS6D01G370100 chr6B 86.683 398 30 8 507 899 694101236 694101615 1.410000e-113 420
11 TraesCS6D01G370100 chr6B 80.961 541 47 20 617 1136 694103692 694104197 8.600000e-101 377
12 TraesCS6D01G370100 chr2D 94.641 821 38 4 2459 3276 593680962 593680145 0.000000e+00 1267
13 TraesCS6D01G370100 chr2D 93.494 830 46 6 2459 3285 593673758 593672934 0.000000e+00 1227
14 TraesCS6D01G370100 chr7D 93.878 833 40 9 2458 3285 242401318 242400492 0.000000e+00 1245
15 TraesCS6D01G370100 chr7D 93.614 830 46 5 2459 3285 72304663 72303838 0.000000e+00 1232
16 TraesCS6D01G370100 chr7D 93.373 830 46 7 2459 3282 242385829 242385003 0.000000e+00 1219
17 TraesCS6D01G370100 chr5D 93.591 827 49 3 2459 3285 30361778 30362600 0.000000e+00 1230
18 TraesCS6D01G370100 chr5D 93.333 375 25 0 1636 2010 3587766 3587392 3.700000e-154 555
19 TraesCS6D01G370100 chr3D 93.198 838 47 6 2453 3285 365826086 365825254 0.000000e+00 1223
20 TraesCS6D01G370100 chr3D 93.470 827 47 5 2459 3282 103529450 103530272 0.000000e+00 1221
21 TraesCS6D01G370100 chr3D 94.415 376 20 1 1636 2010 573446799 573446424 7.900000e-161 577
22 TraesCS6D01G370100 chr5B 93.600 375 24 0 1636 2010 522853771 522854145 7.960000e-156 560
23 TraesCS6D01G370100 chr2B 93.600 375 24 0 1636 2010 625162227 625162601 7.960000e-156 560
24 TraesCS6D01G370100 chr2B 93.351 376 25 0 1635 2010 625160177 625160552 1.030000e-154 556
25 TraesCS6D01G370100 chr1B 93.369 377 23 2 1636 2011 41415009 41414634 1.030000e-154 556
26 TraesCS6D01G370100 chr4D 93.103 377 25 1 1635 2010 306402580 306402204 4.790000e-153 551
27 TraesCS6D01G370100 chr3B 93.103 377 25 1 1635 2010 409530555 409530179 4.790000e-153 551


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 TraesCS6D01G370100 chr6D 456431042 456434326 3284 False 6067.0 6067 100.00000 1 3285 1 chr6D.!!$F1 3284
1 TraesCS6D01G370100 chr6D 456449290 456450113 823 False 1269.0 1269 94.44400 2459 3285 1 chr6D.!!$F2 826
2 TraesCS6D01G370100 chr6A 603137271 603139330 2059 False 769.0 1347 89.78000 219 2458 3 chr6A.!!$F1 2239
3 TraesCS6D01G370100 chr6B 693946972 693948591 1619 False 874.0 1275 86.49750 483 2454 2 chr6B.!!$F1 1971
4 TraesCS6D01G370100 chr6B 694101236 694105347 4111 False 491.5 651 86.46025 507 2454 4 chr6B.!!$F2 1947
5 TraesCS6D01G370100 chr2D 593680145 593680962 817 True 1267.0 1267 94.64100 2459 3276 1 chr2D.!!$R2 817
6 TraesCS6D01G370100 chr2D 593672934 593673758 824 True 1227.0 1227 93.49400 2459 3285 1 chr2D.!!$R1 826
7 TraesCS6D01G370100 chr7D 242400492 242401318 826 True 1245.0 1245 93.87800 2458 3285 1 chr7D.!!$R3 827
8 TraesCS6D01G370100 chr7D 72303838 72304663 825 True 1232.0 1232 93.61400 2459 3285 1 chr7D.!!$R1 826
9 TraesCS6D01G370100 chr7D 242385003 242385829 826 True 1219.0 1219 93.37300 2459 3282 1 chr7D.!!$R2 823
10 TraesCS6D01G370100 chr5D 30361778 30362600 822 False 1230.0 1230 93.59100 2459 3285 1 chr5D.!!$F1 826
11 TraesCS6D01G370100 chr3D 365825254 365826086 832 True 1223.0 1223 93.19800 2453 3285 1 chr3D.!!$R1 832
12 TraesCS6D01G370100 chr3D 103529450 103530272 822 False 1221.0 1221 93.47000 2459 3282 1 chr3D.!!$F1 823
13 TraesCS6D01G370100 chr2B 625160177 625162601 2424 False 558.0 560 93.47550 1635 2010 2 chr2B.!!$F1 375

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
173 174 0.106318 GCTCTTGGAAGGGATGGCAT 60.106 55.0 0.0 0.0 0.00 4.40 F
763 1001 0.174389 GCATCGCCACTCTTCTGAGA 59.826 55.0 0.0 0.0 42.73 3.27 F
1675 4508 0.381089 ACCGTCGATCATCCGAGAAC 59.619 55.0 0.0 0.0 39.43 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 4490 0.317938 GGTTCTCGGATGATCGACGG 60.318 60.0 0.0 0.0 35.18 4.79 R
2212 7098 0.394352 GGTGGTCCGATGAAGCCATT 60.394 55.0 0.0 0.0 33.20 3.16 R
3044 7945 0.682852 CACGTTACTTGGGGAGGTGA 59.317 55.0 0.0 0.0 0.00 4.02 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
24 25 7.624360 TTTGTCTTGTTCAAGAGTGTTACAT 57.376 32.000 14.42 0.00 0.00 2.29
25 26 6.603237 TGTCTTGTTCAAGAGTGTTACATG 57.397 37.500 14.42 0.00 0.00 3.21
26 27 6.345298 TGTCTTGTTCAAGAGTGTTACATGA 58.655 36.000 14.42 0.00 0.00 3.07
27 28 6.992123 TGTCTTGTTCAAGAGTGTTACATGAT 59.008 34.615 14.42 0.00 32.70 2.45
28 29 7.041848 TGTCTTGTTCAAGAGTGTTACATGATG 60.042 37.037 14.42 0.00 32.70 3.07
29 30 6.992123 TCTTGTTCAAGAGTGTTACATGATGT 59.008 34.615 10.67 2.65 0.00 3.06
30 31 7.498900 TCTTGTTCAAGAGTGTTACATGATGTT 59.501 33.333 2.29 0.00 0.00 2.71
31 32 7.566760 TGTTCAAGAGTGTTACATGATGTTT 57.433 32.000 2.29 0.00 0.00 2.83
32 33 7.639039 TGTTCAAGAGTGTTACATGATGTTTC 58.361 34.615 2.29 0.00 0.00 2.78
33 34 7.281999 TGTTCAAGAGTGTTACATGATGTTTCA 59.718 33.333 2.29 0.73 36.00 2.69
34 35 7.984422 TCAAGAGTGTTACATGATGTTTCAT 57.016 32.000 2.29 0.00 43.51 2.57
35 36 8.032952 TCAAGAGTGTTACATGATGTTTCATC 57.967 34.615 2.29 3.16 40.70 2.92
36 37 6.653273 AGAGTGTTACATGATGTTTCATCG 57.347 37.500 2.29 0.00 40.70 3.84
37 38 6.398095 AGAGTGTTACATGATGTTTCATCGA 58.602 36.000 2.29 0.00 40.70 3.59
38 39 7.044181 AGAGTGTTACATGATGTTTCATCGAT 58.956 34.615 2.29 0.00 40.70 3.59
39 40 7.008440 AGTGTTACATGATGTTTCATCGATG 57.992 36.000 19.61 19.61 40.70 3.84
40 41 6.595326 AGTGTTACATGATGTTTCATCGATGT 59.405 34.615 24.09 19.96 40.70 3.06
41 42 7.119699 AGTGTTACATGATGTTTCATCGATGTT 59.880 33.333 24.09 6.32 40.70 2.71
42 43 7.750458 GTGTTACATGATGTTTCATCGATGTTT 59.250 33.333 24.09 6.65 40.70 2.83
43 44 8.296000 TGTTACATGATGTTTCATCGATGTTTT 58.704 29.630 24.09 6.99 40.70 2.43
44 45 9.128107 GTTACATGATGTTTCATCGATGTTTTT 57.872 29.630 24.09 7.67 40.70 1.94
66 67 7.424227 TTTTAAATGTATCGTGGAGTTTCGT 57.576 32.000 0.00 0.00 0.00 3.85
67 68 6.636666 TTAAATGTATCGTGGAGTTTCGTC 57.363 37.500 0.00 0.00 0.00 4.20
68 69 2.251869 TGTATCGTGGAGTTTCGTCG 57.748 50.000 0.00 0.00 0.00 5.12
69 70 1.536766 TGTATCGTGGAGTTTCGTCGT 59.463 47.619 0.00 0.00 0.00 4.34
70 71 1.909532 GTATCGTGGAGTTTCGTCGTG 59.090 52.381 0.00 0.00 0.00 4.35
71 72 0.313043 ATCGTGGAGTTTCGTCGTGT 59.687 50.000 0.00 0.00 0.00 4.49
72 73 0.943673 TCGTGGAGTTTCGTCGTGTA 59.056 50.000 0.00 0.00 0.00 2.90
73 74 1.536766 TCGTGGAGTTTCGTCGTGTAT 59.463 47.619 0.00 0.00 0.00 2.29
74 75 1.909532 CGTGGAGTTTCGTCGTGTATC 59.090 52.381 0.00 0.00 0.00 2.24
75 76 2.666344 CGTGGAGTTTCGTCGTGTATCA 60.666 50.000 0.00 0.00 0.00 2.15
76 77 3.311106 GTGGAGTTTCGTCGTGTATCAA 58.689 45.455 0.00 0.00 0.00 2.57
77 78 3.924686 GTGGAGTTTCGTCGTGTATCAAT 59.075 43.478 0.00 0.00 0.00 2.57
78 79 5.097529 GTGGAGTTTCGTCGTGTATCAATA 58.902 41.667 0.00 0.00 0.00 1.90
79 80 5.574055 GTGGAGTTTCGTCGTGTATCAATAA 59.426 40.000 0.00 0.00 0.00 1.40
80 81 6.089820 GTGGAGTTTCGTCGTGTATCAATAAA 59.910 38.462 0.00 0.00 0.00 1.40
81 82 6.814644 TGGAGTTTCGTCGTGTATCAATAAAT 59.185 34.615 0.00 0.00 0.00 1.40
82 83 7.975058 TGGAGTTTCGTCGTGTATCAATAAATA 59.025 33.333 0.00 0.00 0.00 1.40
83 84 8.810427 GGAGTTTCGTCGTGTATCAATAAATAA 58.190 33.333 0.00 0.00 0.00 1.40
84 85 9.831054 GAGTTTCGTCGTGTATCAATAAATAAG 57.169 33.333 0.00 0.00 0.00 1.73
85 86 8.814235 AGTTTCGTCGTGTATCAATAAATAAGG 58.186 33.333 0.00 0.00 0.00 2.69
86 87 7.703298 TTCGTCGTGTATCAATAAATAAGGG 57.297 36.000 0.00 0.00 0.00 3.95
87 88 7.041635 TCGTCGTGTATCAATAAATAAGGGA 57.958 36.000 0.00 0.00 0.00 4.20
88 89 7.143340 TCGTCGTGTATCAATAAATAAGGGAG 58.857 38.462 0.00 0.00 0.00 4.30
89 90 6.921857 CGTCGTGTATCAATAAATAAGGGAGT 59.078 38.462 0.00 0.00 0.00 3.85
90 91 8.077991 CGTCGTGTATCAATAAATAAGGGAGTA 58.922 37.037 0.00 0.00 0.00 2.59
91 92 9.189723 GTCGTGTATCAATAAATAAGGGAGTAC 57.810 37.037 0.00 0.00 0.00 2.73
92 93 9.139734 TCGTGTATCAATAAATAAGGGAGTACT 57.860 33.333 0.00 0.00 0.00 2.73
132 133 5.968528 AAGAGAGTACTCGTCAGATTTGT 57.031 39.130 17.07 0.00 46.64 2.83
133 134 8.734218 ATAAGAGAGTACTCGTCAGATTTGTA 57.266 34.615 17.07 0.78 46.64 2.41
134 135 7.633193 AAGAGAGTACTCGTCAGATTTGTAT 57.367 36.000 17.07 0.00 46.64 2.29
135 136 7.022055 AGAGAGTACTCGTCAGATTTGTATG 57.978 40.000 17.07 0.00 46.64 2.39
136 137 6.600032 AGAGAGTACTCGTCAGATTTGTATGT 59.400 38.462 17.07 0.00 46.64 2.29
137 138 7.769507 AGAGAGTACTCGTCAGATTTGTATGTA 59.230 37.037 17.07 0.00 46.64 2.29
138 139 8.277490 AGAGTACTCGTCAGATTTGTATGTAA 57.723 34.615 17.07 0.00 34.09 2.41
139 140 8.904834 AGAGTACTCGTCAGATTTGTATGTAAT 58.095 33.333 17.07 0.00 34.09 1.89
140 141 9.517609 GAGTACTCGTCAGATTTGTATGTAATT 57.482 33.333 7.22 0.00 0.00 1.40
141 142 9.871238 AGTACTCGTCAGATTTGTATGTAATTT 57.129 29.630 0.00 0.00 0.00 1.82
143 144 8.771920 ACTCGTCAGATTTGTATGTAATTTCA 57.228 30.769 0.00 0.00 0.00 2.69
144 145 8.873830 ACTCGTCAGATTTGTATGTAATTTCAG 58.126 33.333 0.00 0.00 0.00 3.02
145 146 8.996024 TCGTCAGATTTGTATGTAATTTCAGA 57.004 30.769 0.00 0.00 0.00 3.27
146 147 9.087424 TCGTCAGATTTGTATGTAATTTCAGAG 57.913 33.333 0.00 0.00 0.00 3.35
147 148 8.331022 CGTCAGATTTGTATGTAATTTCAGAGG 58.669 37.037 0.00 0.00 0.00 3.69
148 149 8.616076 GTCAGATTTGTATGTAATTTCAGAGGG 58.384 37.037 0.00 0.00 0.00 4.30
149 150 8.328758 TCAGATTTGTATGTAATTTCAGAGGGT 58.671 33.333 0.00 0.00 0.00 4.34
150 151 9.613428 CAGATTTGTATGTAATTTCAGAGGGTA 57.387 33.333 0.00 0.00 0.00 3.69
155 156 8.220755 TGTATGTAATTTCAGAGGGTATTTGC 57.779 34.615 0.00 0.00 0.00 3.68
156 157 8.052748 TGTATGTAATTTCAGAGGGTATTTGCT 58.947 33.333 0.00 0.00 0.00 3.91
157 158 7.573968 ATGTAATTTCAGAGGGTATTTGCTC 57.426 36.000 0.00 0.00 0.00 4.26
158 159 6.721318 TGTAATTTCAGAGGGTATTTGCTCT 58.279 36.000 0.00 0.00 0.00 4.09
159 160 7.175104 TGTAATTTCAGAGGGTATTTGCTCTT 58.825 34.615 0.00 0.00 0.00 2.85
160 161 6.521151 AATTTCAGAGGGTATTTGCTCTTG 57.479 37.500 0.00 0.00 0.00 3.02
161 162 3.634397 TCAGAGGGTATTTGCTCTTGG 57.366 47.619 0.00 0.00 0.00 3.61
162 163 3.181329 TCAGAGGGTATTTGCTCTTGGA 58.819 45.455 0.00 0.00 0.00 3.53
163 164 3.587061 TCAGAGGGTATTTGCTCTTGGAA 59.413 43.478 0.00 0.00 0.00 3.53
164 165 3.944015 CAGAGGGTATTTGCTCTTGGAAG 59.056 47.826 0.00 0.00 0.00 3.46
165 166 3.054065 AGAGGGTATTTGCTCTTGGAAGG 60.054 47.826 0.00 0.00 0.00 3.46
166 167 2.024941 AGGGTATTTGCTCTTGGAAGGG 60.025 50.000 0.00 0.00 0.00 3.95
167 168 2.025321 GGGTATTTGCTCTTGGAAGGGA 60.025 50.000 0.00 0.00 0.00 4.20
168 169 3.373110 GGGTATTTGCTCTTGGAAGGGAT 60.373 47.826 0.00 0.00 0.00 3.85
169 170 3.633986 GGTATTTGCTCTTGGAAGGGATG 59.366 47.826 0.00 0.00 0.00 3.51
170 171 2.220653 TTTGCTCTTGGAAGGGATGG 57.779 50.000 0.00 0.00 0.00 3.51
171 172 0.323725 TTGCTCTTGGAAGGGATGGC 60.324 55.000 0.00 0.00 0.00 4.40
172 173 1.304282 GCTCTTGGAAGGGATGGCA 59.696 57.895 0.00 0.00 0.00 4.92
173 174 0.106318 GCTCTTGGAAGGGATGGCAT 60.106 55.000 0.00 0.00 0.00 4.40
174 175 1.978454 CTCTTGGAAGGGATGGCATC 58.022 55.000 19.23 19.23 0.00 3.91
175 176 1.493871 CTCTTGGAAGGGATGGCATCT 59.506 52.381 25.48 7.44 0.00 2.90
176 177 1.492176 TCTTGGAAGGGATGGCATCTC 59.508 52.381 25.48 22.87 0.00 2.75
177 178 1.213678 CTTGGAAGGGATGGCATCTCA 59.786 52.381 28.10 14.71 30.04 3.27
178 179 1.526315 TGGAAGGGATGGCATCTCAT 58.474 50.000 28.10 17.77 30.04 2.90
179 180 1.422781 TGGAAGGGATGGCATCTCATC 59.577 52.381 28.10 24.60 41.93 2.92
180 181 1.422781 GGAAGGGATGGCATCTCATCA 59.577 52.381 28.02 0.00 43.82 3.07
181 182 2.158564 GGAAGGGATGGCATCTCATCAA 60.159 50.000 28.02 0.00 43.82 2.57
182 183 2.953284 AGGGATGGCATCTCATCAAG 57.047 50.000 28.10 0.00 43.82 3.02
183 184 2.415624 AGGGATGGCATCTCATCAAGA 58.584 47.619 28.10 0.00 43.82 3.02
184 185 2.372504 AGGGATGGCATCTCATCAAGAG 59.627 50.000 28.10 0.00 43.82 2.85
185 186 2.106166 GGGATGGCATCTCATCAAGAGT 59.894 50.000 25.48 0.00 43.82 3.24
186 187 3.434739 GGGATGGCATCTCATCAAGAGTT 60.435 47.826 25.48 0.00 43.82 3.01
187 188 3.814283 GGATGGCATCTCATCAAGAGTTC 59.186 47.826 25.48 1.88 43.82 3.01
188 189 2.897436 TGGCATCTCATCAAGAGTTCG 58.103 47.619 0.00 0.00 44.98 3.95
189 190 1.596727 GGCATCTCATCAAGAGTTCGC 59.403 52.381 0.00 0.00 44.98 4.70
190 191 2.548875 GCATCTCATCAAGAGTTCGCT 58.451 47.619 0.00 0.00 44.98 4.93
191 192 3.491619 GGCATCTCATCAAGAGTTCGCTA 60.492 47.826 0.00 0.00 44.98 4.26
192 193 3.489047 GCATCTCATCAAGAGTTCGCTAC 59.511 47.826 0.00 0.00 44.98 3.58
193 194 4.676546 CATCTCATCAAGAGTTCGCTACA 58.323 43.478 0.00 0.00 44.98 2.74
194 195 4.991153 TCTCATCAAGAGTTCGCTACAT 57.009 40.909 0.00 0.00 44.98 2.29
195 196 6.442112 CATCTCATCAAGAGTTCGCTACATA 58.558 40.000 0.00 0.00 44.98 2.29
196 197 6.451064 TCTCATCAAGAGTTCGCTACATAA 57.549 37.500 0.00 0.00 44.98 1.90
197 198 6.863275 TCTCATCAAGAGTTCGCTACATAAA 58.137 36.000 0.00 0.00 44.98 1.40
198 199 6.975197 TCTCATCAAGAGTTCGCTACATAAAG 59.025 38.462 0.00 0.00 44.98 1.85
199 200 6.631016 TCATCAAGAGTTCGCTACATAAAGT 58.369 36.000 0.00 0.00 0.00 2.66
200 201 7.097192 TCATCAAGAGTTCGCTACATAAAGTT 58.903 34.615 0.00 0.00 0.00 2.66
201 202 7.602644 TCATCAAGAGTTCGCTACATAAAGTTT 59.397 33.333 0.00 0.00 0.00 2.66
202 203 7.724305 TCAAGAGTTCGCTACATAAAGTTTT 57.276 32.000 0.00 0.00 0.00 2.43
203 204 8.821147 TCAAGAGTTCGCTACATAAAGTTTTA 57.179 30.769 0.00 0.00 0.00 1.52
204 205 8.922676 TCAAGAGTTCGCTACATAAAGTTTTAG 58.077 33.333 0.00 0.00 0.00 1.85
205 206 8.922676 CAAGAGTTCGCTACATAAAGTTTTAGA 58.077 33.333 0.00 0.00 0.00 2.10
206 207 9.485206 AAGAGTTCGCTACATAAAGTTTTAGAA 57.515 29.630 0.00 0.00 0.00 2.10
207 208 9.485206 AGAGTTCGCTACATAAAGTTTTAGAAA 57.515 29.630 0.00 0.00 0.00 2.52
258 259 0.460987 GCAAGTGCGCCTAGACTCAT 60.461 55.000 4.18 0.00 0.00 2.90
259 260 1.565305 CAAGTGCGCCTAGACTCATC 58.435 55.000 4.18 0.00 0.00 2.92
262 263 0.867753 GTGCGCCTAGACTCATCACG 60.868 60.000 4.18 0.00 0.00 4.35
263 264 1.313091 TGCGCCTAGACTCATCACGT 61.313 55.000 4.18 0.00 0.00 4.49
264 265 0.179134 GCGCCTAGACTCATCACGTT 60.179 55.000 0.00 0.00 0.00 3.99
265 266 1.828832 CGCCTAGACTCATCACGTTC 58.171 55.000 0.00 0.00 0.00 3.95
266 267 1.534175 CGCCTAGACTCATCACGTTCC 60.534 57.143 0.00 0.00 0.00 3.62
267 268 1.476891 GCCTAGACTCATCACGTTCCA 59.523 52.381 0.00 0.00 0.00 3.53
269 270 3.616560 GCCTAGACTCATCACGTTCCAAA 60.617 47.826 0.00 0.00 0.00 3.28
270 271 4.759782 CCTAGACTCATCACGTTCCAAAT 58.240 43.478 0.00 0.00 0.00 2.32
271 272 5.681437 GCCTAGACTCATCACGTTCCAAATA 60.681 44.000 0.00 0.00 0.00 1.40
272 273 6.516718 CCTAGACTCATCACGTTCCAAATAT 58.483 40.000 0.00 0.00 0.00 1.28
273 274 6.986817 CCTAGACTCATCACGTTCCAAATATT 59.013 38.462 0.00 0.00 0.00 1.28
314 315 9.035607 GCACTCTTTCTGATATCGAAATTTAGA 57.964 33.333 17.21 3.34 30.75 2.10
329 330 8.511321 TCGAAATTTAGAAAAGAGCAAAGCATA 58.489 29.630 0.00 0.00 0.00 3.14
336 337 6.088824 AGAAAAGAGCAAAGCATATGTTTCG 58.911 36.000 5.19 0.00 0.00 3.46
339 340 4.002982 AGAGCAAAGCATATGTTTCGTCA 58.997 39.130 5.19 0.00 0.00 4.35
347 348 7.435068 AAGCATATGTTTCGTCACTAAACTT 57.565 32.000 4.29 3.10 37.64 2.66
350 351 8.604035 AGCATATGTTTCGTCACTAAACTTATG 58.396 33.333 23.35 23.35 45.81 1.90
355 356 3.857052 TCGTCACTAAACTTATGGGCTG 58.143 45.455 0.00 0.00 0.00 4.85
379 390 3.059166 GCCATCAATTTCACAACCACAC 58.941 45.455 0.00 0.00 0.00 3.82
398 409 3.149196 CACAGGCTGTACCATGAACTTT 58.851 45.455 21.59 0.00 43.14 2.66
416 427 2.409152 TTCAAAAACCGGACGCATTC 57.591 45.000 9.46 0.00 0.00 2.67
417 428 1.309950 TCAAAAACCGGACGCATTCA 58.690 45.000 9.46 0.00 0.00 2.57
441 452 1.267365 CCCATTTTGCATACAACGCG 58.733 50.000 3.53 3.53 34.87 6.01
442 453 1.135546 CCCATTTTGCATACAACGCGA 60.136 47.619 15.93 0.00 34.87 5.87
443 454 1.910819 CCATTTTGCATACAACGCGAC 59.089 47.619 15.93 0.00 34.87 5.19
444 455 1.910819 CATTTTGCATACAACGCGACC 59.089 47.619 15.93 0.00 34.87 4.79
456 467 2.946762 GCGACCTGCACCAGAAAC 59.053 61.111 0.00 0.00 45.45 2.78
458 469 1.966451 CGACCTGCACCAGAAACCC 60.966 63.158 0.00 0.00 32.44 4.11
468 479 3.023832 CACCAGAAACCCTTGAACAACT 58.976 45.455 0.00 0.00 0.00 3.16
469 480 3.023832 ACCAGAAACCCTTGAACAACTG 58.976 45.455 0.00 0.00 0.00 3.16
486 712 4.953579 ACAACTGTAGGTCAAAACATGGTT 59.046 37.500 0.00 0.00 0.00 3.67
496 722 6.431234 AGGTCAAAACATGGTTAATCTCACTC 59.569 38.462 0.00 0.00 0.00 3.51
525 755 3.636300 CTGGTTTTCACAGTGGATGGAAA 59.364 43.478 0.00 0.00 0.00 3.13
550 784 1.768603 CACGCACGCAAAAAGATGC 59.231 52.632 0.00 0.00 42.94 3.91
613 848 4.439700 GGGTGACTCGATCGTAATCTTTGA 60.440 45.833 15.94 0.00 0.00 2.69
698 935 4.430765 CTCCCCAACCGACGACCG 62.431 72.222 0.00 0.00 38.18 4.79
702 939 2.646719 CCAACCGACGACCGAGAA 59.353 61.111 0.00 0.00 41.76 2.87
725 962 8.830741 AGAAGGATTTTATATACTCCTCCCATG 58.169 37.037 3.15 0.00 37.13 3.66
738 975 2.184830 CCCATGCTGAGCACATCCG 61.185 63.158 10.33 0.00 43.04 4.18
763 1001 0.174389 GCATCGCCACTCTTCTGAGA 59.826 55.000 0.00 0.00 42.73 3.27
775 1015 6.037726 CACTCTTCTGAGATCTGAGATGTTG 58.962 44.000 19.73 16.42 42.73 3.33
776 1016 5.008619 TCTTCTGAGATCTGAGATGTTGC 57.991 43.478 19.73 0.00 0.00 4.17
777 1017 4.710865 TCTTCTGAGATCTGAGATGTTGCT 59.289 41.667 19.73 0.00 0.00 3.91
932 2986 3.406361 CACACGACACCTGCTCGC 61.406 66.667 0.00 0.00 34.34 5.03
938 2992 2.280389 ACACCTGCTCGCACACAG 60.280 61.111 0.00 0.00 0.00 3.66
973 3027 2.350498 CGGCGGAACCAAAAGTATAGTG 59.650 50.000 0.00 0.00 39.03 2.74
1091 3183 1.103803 TCGCTTCTACTAGCACCTGG 58.896 55.000 0.00 0.00 41.28 4.45
1093 3185 1.202313 CGCTTCTACTAGCACCTGGAC 60.202 57.143 0.00 0.00 41.28 4.02
1101 3193 1.827344 CTAGCACCTGGACATCACAGA 59.173 52.381 0.00 0.00 38.20 3.41
1122 3733 6.836007 ACAGAGTTTTTCCTTTTCCTTCTGAT 59.164 34.615 4.84 0.00 34.96 2.90
1255 4080 0.689080 GAGGTGGGAGCTCAGATGGA 60.689 60.000 17.19 0.00 42.03 3.41
1404 4232 7.246311 ACGCTTGATTCATTACTGAAAGAATG 58.754 34.615 0.00 0.00 44.29 2.67
1494 4322 3.650942 AGATGGTCAGGTTTCACTGGTAA 59.349 43.478 0.00 0.00 38.98 2.85
1572 4404 7.794349 GTGTTTTCTTAGATCGAACAGTTCTTG 59.206 37.037 11.60 0.00 31.58 3.02
1640 4473 9.264719 AGTAACAAAACCACTAGTATGTGTTAC 57.735 33.333 24.48 24.48 42.88 2.50
1657 4490 5.414454 TGTGTTACAATAAATCTGAGCCCAC 59.586 40.000 0.00 0.00 0.00 4.61
1675 4508 0.381089 ACCGTCGATCATCCGAGAAC 59.619 55.000 0.00 0.00 39.43 3.01
1691 4524 2.548057 GAGAACCAAGCAATCACACGAA 59.452 45.455 0.00 0.00 0.00 3.85
1730 4563 4.158209 TGTTAACGAGGTTCACCGATATGA 59.842 41.667 0.26 0.00 42.08 2.15
1842 6724 1.833787 GCTTCCCCTGTGTTCCGGTA 61.834 60.000 0.00 0.00 0.00 4.02
1852 6734 5.395990 CCCTGTGTTCCGGTACTATTATGTT 60.396 44.000 12.78 0.00 0.00 2.71
1907 6789 7.235079 GCTATATATGAGAGGCCTAGGATACA 58.765 42.308 14.75 5.03 41.41 2.29
1933 6815 0.537188 CTACTTGGACACGGCTCCAT 59.463 55.000 4.30 0.00 40.18 3.41
1937 6819 1.414181 CTTGGACACGGCTCCATATCT 59.586 52.381 4.30 0.00 40.18 1.98
1941 6823 3.646162 TGGACACGGCTCCATATCTTATT 59.354 43.478 0.00 0.00 35.23 1.40
2002 6884 7.553334 ACCTTGTACACTATATTCGACACAAT 58.447 34.615 0.00 0.00 0.00 2.71
2010 6892 9.302345 ACACTATATTCGACACAATTCTAACAG 57.698 33.333 0.00 0.00 0.00 3.16
2011 6893 9.302345 CACTATATTCGACACAATTCTAACAGT 57.698 33.333 0.00 0.00 0.00 3.55
2131 7014 3.771160 ACCGGCGGTGTCTCCATC 61.771 66.667 33.71 0.00 32.98 3.51
2157 7040 4.515361 CAAGAGCTGATGAAGAAGATGGT 58.485 43.478 0.00 0.00 0.00 3.55
2183 7066 4.564116 GCGCCATGTGGATGCAGC 62.564 66.667 2.55 0.00 37.82 5.25
2220 7106 3.297134 TGGGACTATCCAAATGGCTTC 57.703 47.619 0.00 0.00 38.64 3.86
2226 7112 2.734755 ATCCAAATGGCTTCATCGGA 57.265 45.000 0.00 0.00 34.44 4.55
2343 7229 8.511604 AGTATTGAGAATAAATCCCTTGTGTG 57.488 34.615 0.00 0.00 0.00 3.82
2364 7250 1.065491 CACGATGTTCAGAATGGGGGA 60.065 52.381 0.00 0.00 36.16 4.81
2518 7406 5.452496 CGTGTCACCAAGATCAATCTAGGAT 60.452 44.000 0.00 0.00 35.76 3.24
2615 7511 3.504863 GTTAATGGAGTCGTACTCGCAA 58.495 45.455 8.33 0.08 45.96 4.85
2689 7585 2.602878 CGTTCAACACACGTATAGCCT 58.397 47.619 0.00 0.00 32.80 4.58
2691 7587 2.004583 TCAACACACGTATAGCCTGC 57.995 50.000 0.00 0.00 0.00 4.85
2716 7612 2.497675 CGTCTCCTCCTTCTTGATCCAA 59.502 50.000 0.00 0.00 0.00 3.53
2802 7698 2.927856 TTCTCCGGCAGGGCTTCA 60.928 61.111 2.05 0.00 38.33 3.02
2826 7722 3.342926 AGCACTATGGAAGAGGAGGAT 57.657 47.619 0.00 0.00 0.00 3.24
2838 7734 2.584965 AGAGGAGGATGAGTTGGAGAGA 59.415 50.000 0.00 0.00 0.00 3.10
2911 7808 0.492276 TATAGGGGGAAGGGGAGAGC 59.508 60.000 0.00 0.00 0.00 4.09
3227 8130 2.692041 CCGGACTCTAATACCCTTCGTT 59.308 50.000 0.00 0.00 0.00 3.85
3268 8171 1.223763 GGACCATTCCGGAACTCCC 59.776 63.158 21.56 14.42 38.63 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.844696 TCATGTAACACTCTTGAACAAGAC 57.155 37.500 12.40 4.52 42.06 3.01
4 5 6.992123 ACATCATGTAACACTCTTGAACAAGA 59.008 34.615 15.05 15.05 44.47 3.02
5 6 7.194607 ACATCATGTAACACTCTTGAACAAG 57.805 36.000 8.09 8.09 39.71 3.16
7 8 7.281999 TGAAACATCATGTAACACTCTTGAACA 59.718 33.333 0.00 0.00 0.00 3.18
8 9 7.639039 TGAAACATCATGTAACACTCTTGAAC 58.361 34.615 0.00 0.00 0.00 3.18
9 10 7.800155 TGAAACATCATGTAACACTCTTGAA 57.200 32.000 0.00 0.00 0.00 2.69
10 11 7.148590 CGATGAAACATCATGTAACACTCTTGA 60.149 37.037 11.39 0.00 0.00 3.02
11 12 6.957635 CGATGAAACATCATGTAACACTCTTG 59.042 38.462 11.39 0.00 0.00 3.02
12 13 6.873605 TCGATGAAACATCATGTAACACTCTT 59.126 34.615 11.39 0.00 0.00 2.85
13 14 6.398095 TCGATGAAACATCATGTAACACTCT 58.602 36.000 11.39 0.00 0.00 3.24
14 15 6.647212 TCGATGAAACATCATGTAACACTC 57.353 37.500 11.39 0.00 0.00 3.51
15 16 6.595326 ACATCGATGAAACATCATGTAACACT 59.405 34.615 31.33 0.00 0.00 3.55
16 17 6.775088 ACATCGATGAAACATCATGTAACAC 58.225 36.000 31.33 0.00 0.00 3.32
17 18 6.983474 ACATCGATGAAACATCATGTAACA 57.017 33.333 31.33 0.00 0.00 2.41
18 19 8.673626 AAAACATCGATGAAACATCATGTAAC 57.326 30.769 31.33 0.00 0.00 2.50
41 42 7.863666 ACGAAACTCCACGATACATTTAAAAA 58.136 30.769 0.00 0.00 0.00 1.94
42 43 7.424227 ACGAAACTCCACGATACATTTAAAA 57.576 32.000 0.00 0.00 0.00 1.52
43 44 6.183360 CGACGAAACTCCACGATACATTTAAA 60.183 38.462 0.00 0.00 0.00 1.52
44 45 5.286797 CGACGAAACTCCACGATACATTTAA 59.713 40.000 0.00 0.00 0.00 1.52
45 46 4.794762 CGACGAAACTCCACGATACATTTA 59.205 41.667 0.00 0.00 0.00 1.40
46 47 3.611113 CGACGAAACTCCACGATACATTT 59.389 43.478 0.00 0.00 0.00 2.32
47 48 3.176708 CGACGAAACTCCACGATACATT 58.823 45.455 0.00 0.00 0.00 2.71
48 49 2.163010 ACGACGAAACTCCACGATACAT 59.837 45.455 0.00 0.00 0.00 2.29
49 50 1.536766 ACGACGAAACTCCACGATACA 59.463 47.619 0.00 0.00 0.00 2.29
50 51 1.909532 CACGACGAAACTCCACGATAC 59.090 52.381 0.00 0.00 0.00 2.24
51 52 1.536766 ACACGACGAAACTCCACGATA 59.463 47.619 0.00 0.00 0.00 2.92
52 53 0.313043 ACACGACGAAACTCCACGAT 59.687 50.000 0.00 0.00 0.00 3.73
53 54 0.943673 TACACGACGAAACTCCACGA 59.056 50.000 0.00 0.00 0.00 4.35
54 55 1.909532 GATACACGACGAAACTCCACG 59.090 52.381 0.00 0.00 0.00 4.94
55 56 2.937591 TGATACACGACGAAACTCCAC 58.062 47.619 0.00 0.00 0.00 4.02
56 57 3.646611 TTGATACACGACGAAACTCCA 57.353 42.857 0.00 0.00 0.00 3.86
57 58 6.636666 TTTATTGATACACGACGAAACTCC 57.363 37.500 0.00 0.00 0.00 3.85
58 59 9.831054 CTTATTTATTGATACACGACGAAACTC 57.169 33.333 0.00 0.00 0.00 3.01
59 60 8.814235 CCTTATTTATTGATACACGACGAAACT 58.186 33.333 0.00 0.00 0.00 2.66
60 61 8.060090 CCCTTATTTATTGATACACGACGAAAC 58.940 37.037 0.00 0.00 0.00 2.78
61 62 7.980662 TCCCTTATTTATTGATACACGACGAAA 59.019 33.333 0.00 0.00 0.00 3.46
62 63 7.490840 TCCCTTATTTATTGATACACGACGAA 58.509 34.615 0.00 0.00 0.00 3.85
63 64 7.041635 TCCCTTATTTATTGATACACGACGA 57.958 36.000 0.00 0.00 0.00 4.20
64 65 6.921857 ACTCCCTTATTTATTGATACACGACG 59.078 38.462 0.00 0.00 0.00 5.12
65 66 9.189723 GTACTCCCTTATTTATTGATACACGAC 57.810 37.037 0.00 0.00 0.00 4.34
66 67 9.139734 AGTACTCCCTTATTTATTGATACACGA 57.860 33.333 0.00 0.00 0.00 4.35
106 107 9.175312 ACAAATCTGACGAGTACTCTCTTATTA 57.825 33.333 20.34 1.12 38.45 0.98
107 108 8.057536 ACAAATCTGACGAGTACTCTCTTATT 57.942 34.615 20.34 14.90 38.45 1.40
108 109 7.633193 ACAAATCTGACGAGTACTCTCTTAT 57.367 36.000 20.34 10.96 38.45 1.73
109 110 8.613482 CATACAAATCTGACGAGTACTCTCTTA 58.387 37.037 20.34 9.47 38.45 2.10
110 111 5.968528 ACAAATCTGACGAGTACTCTCTT 57.031 39.130 20.34 4.85 38.45 2.85
111 112 6.600032 ACATACAAATCTGACGAGTACTCTCT 59.400 38.462 20.34 5.51 38.45 3.10
112 113 6.787225 ACATACAAATCTGACGAGTACTCTC 58.213 40.000 20.34 15.94 37.35 3.20
113 114 6.761099 ACATACAAATCTGACGAGTACTCT 57.239 37.500 20.34 7.83 0.00 3.24
114 115 9.517609 AATTACATACAAATCTGACGAGTACTC 57.482 33.333 13.18 13.18 0.00 2.59
115 116 9.871238 AAATTACATACAAATCTGACGAGTACT 57.129 29.630 0.00 0.00 0.00 2.73
117 118 9.863845 TGAAATTACATACAAATCTGACGAGTA 57.136 29.630 0.00 0.00 0.00 2.59
118 119 8.771920 TGAAATTACATACAAATCTGACGAGT 57.228 30.769 0.00 0.00 0.00 4.18
119 120 9.087424 TCTGAAATTACATACAAATCTGACGAG 57.913 33.333 0.00 0.00 0.00 4.18
120 121 8.996024 TCTGAAATTACATACAAATCTGACGA 57.004 30.769 0.00 0.00 0.00 4.20
121 122 8.331022 CCTCTGAAATTACATACAAATCTGACG 58.669 37.037 0.00 0.00 0.00 4.35
122 123 8.616076 CCCTCTGAAATTACATACAAATCTGAC 58.384 37.037 0.00 0.00 0.00 3.51
123 124 8.328758 ACCCTCTGAAATTACATACAAATCTGA 58.671 33.333 0.00 0.00 0.00 3.27
124 125 8.511604 ACCCTCTGAAATTACATACAAATCTG 57.488 34.615 0.00 0.00 0.00 2.90
129 130 8.682710 GCAAATACCCTCTGAAATTACATACAA 58.317 33.333 0.00 0.00 0.00 2.41
130 131 8.052748 AGCAAATACCCTCTGAAATTACATACA 58.947 33.333 0.00 0.00 0.00 2.29
131 132 8.451908 AGCAAATACCCTCTGAAATTACATAC 57.548 34.615 0.00 0.00 0.00 2.39
132 133 8.494433 AGAGCAAATACCCTCTGAAATTACATA 58.506 33.333 0.00 0.00 37.07 2.29
133 134 7.349598 AGAGCAAATACCCTCTGAAATTACAT 58.650 34.615 0.00 0.00 37.07 2.29
134 135 6.721318 AGAGCAAATACCCTCTGAAATTACA 58.279 36.000 0.00 0.00 37.07 2.41
135 136 7.415653 CCAAGAGCAAATACCCTCTGAAATTAC 60.416 40.741 0.00 0.00 38.38 1.89
136 137 6.603201 CCAAGAGCAAATACCCTCTGAAATTA 59.397 38.462 0.00 0.00 38.38 1.40
137 138 5.420104 CCAAGAGCAAATACCCTCTGAAATT 59.580 40.000 0.00 0.00 38.38 1.82
138 139 4.952335 CCAAGAGCAAATACCCTCTGAAAT 59.048 41.667 0.00 0.00 38.38 2.17
139 140 4.042809 TCCAAGAGCAAATACCCTCTGAAA 59.957 41.667 0.00 0.00 38.38 2.69
140 141 3.587061 TCCAAGAGCAAATACCCTCTGAA 59.413 43.478 0.00 0.00 38.38 3.02
141 142 3.181329 TCCAAGAGCAAATACCCTCTGA 58.819 45.455 0.00 0.00 38.38 3.27
142 143 3.634397 TCCAAGAGCAAATACCCTCTG 57.366 47.619 0.00 0.00 38.38 3.35
143 144 3.054065 CCTTCCAAGAGCAAATACCCTCT 60.054 47.826 0.00 0.00 40.00 3.69
144 145 3.282885 CCTTCCAAGAGCAAATACCCTC 58.717 50.000 0.00 0.00 0.00 4.30
145 146 2.024941 CCCTTCCAAGAGCAAATACCCT 60.025 50.000 0.00 0.00 0.00 4.34
146 147 2.025321 TCCCTTCCAAGAGCAAATACCC 60.025 50.000 0.00 0.00 0.00 3.69
147 148 3.366052 TCCCTTCCAAGAGCAAATACC 57.634 47.619 0.00 0.00 0.00 2.73
148 149 3.633986 CCATCCCTTCCAAGAGCAAATAC 59.366 47.826 0.00 0.00 0.00 1.89
149 150 3.902218 CCATCCCTTCCAAGAGCAAATA 58.098 45.455 0.00 0.00 0.00 1.40
150 151 2.743553 CCATCCCTTCCAAGAGCAAAT 58.256 47.619 0.00 0.00 0.00 2.32
151 152 1.892329 GCCATCCCTTCCAAGAGCAAA 60.892 52.381 0.00 0.00 0.00 3.68
152 153 0.323725 GCCATCCCTTCCAAGAGCAA 60.324 55.000 0.00 0.00 0.00 3.91
153 154 1.304282 GCCATCCCTTCCAAGAGCA 59.696 57.895 0.00 0.00 0.00 4.26
154 155 0.106318 ATGCCATCCCTTCCAAGAGC 60.106 55.000 0.00 0.00 0.00 4.09
155 156 1.493871 AGATGCCATCCCTTCCAAGAG 59.506 52.381 0.00 0.00 0.00 2.85
156 157 1.492176 GAGATGCCATCCCTTCCAAGA 59.508 52.381 0.00 0.00 0.00 3.02
157 158 1.213678 TGAGATGCCATCCCTTCCAAG 59.786 52.381 0.00 0.00 0.00 3.61
158 159 1.297968 TGAGATGCCATCCCTTCCAA 58.702 50.000 0.00 0.00 0.00 3.53
159 160 1.422781 GATGAGATGCCATCCCTTCCA 59.577 52.381 0.00 0.00 37.54 3.53
160 161 1.422781 TGATGAGATGCCATCCCTTCC 59.577 52.381 0.00 0.00 41.60 3.46
161 162 2.945080 TGATGAGATGCCATCCCTTC 57.055 50.000 0.00 0.00 41.60 3.46
162 163 2.781757 TCTTGATGAGATGCCATCCCTT 59.218 45.455 0.00 0.00 41.60 3.95
163 164 2.372504 CTCTTGATGAGATGCCATCCCT 59.627 50.000 0.00 0.00 45.39 4.20
164 165 2.106166 ACTCTTGATGAGATGCCATCCC 59.894 50.000 0.00 0.00 45.39 3.85
165 166 3.488778 ACTCTTGATGAGATGCCATCC 57.511 47.619 0.00 0.00 45.39 3.51
166 167 3.493877 CGAACTCTTGATGAGATGCCATC 59.506 47.826 2.06 0.00 45.39 3.51
167 168 3.464907 CGAACTCTTGATGAGATGCCAT 58.535 45.455 2.06 0.00 45.39 4.40
168 169 2.897436 CGAACTCTTGATGAGATGCCA 58.103 47.619 2.06 0.00 45.39 4.92
169 170 1.596727 GCGAACTCTTGATGAGATGCC 59.403 52.381 2.06 0.00 45.39 4.40
170 171 2.548875 AGCGAACTCTTGATGAGATGC 58.451 47.619 2.06 3.35 45.39 3.91
171 172 4.676546 TGTAGCGAACTCTTGATGAGATG 58.323 43.478 2.06 0.00 45.39 2.90
172 173 4.991153 TGTAGCGAACTCTTGATGAGAT 57.009 40.909 2.06 0.00 45.39 2.75
173 174 4.991153 ATGTAGCGAACTCTTGATGAGA 57.009 40.909 2.06 0.00 45.39 3.27
175 176 6.631016 ACTTTATGTAGCGAACTCTTGATGA 58.369 36.000 0.00 0.00 0.00 2.92
176 177 6.893958 ACTTTATGTAGCGAACTCTTGATG 57.106 37.500 0.00 0.00 0.00 3.07
177 178 7.907214 AAACTTTATGTAGCGAACTCTTGAT 57.093 32.000 0.00 0.00 0.00 2.57
178 179 7.724305 AAAACTTTATGTAGCGAACTCTTGA 57.276 32.000 0.00 0.00 0.00 3.02
179 180 8.922676 TCTAAAACTTTATGTAGCGAACTCTTG 58.077 33.333 0.00 0.00 0.00 3.02
180 181 9.485206 TTCTAAAACTTTATGTAGCGAACTCTT 57.515 29.630 0.00 0.00 0.00 2.85
181 182 9.485206 TTTCTAAAACTTTATGTAGCGAACTCT 57.515 29.630 0.00 0.00 0.00 3.24
242 243 0.457851 GTGATGAGTCTAGGCGCACT 59.542 55.000 10.83 3.10 0.00 4.40
248 249 3.868757 TTGGAACGTGATGAGTCTAGG 57.131 47.619 0.00 0.00 0.00 3.02
255 256 5.123186 GGTGTGAATATTTGGAACGTGATGA 59.877 40.000 0.00 0.00 0.00 2.92
258 259 3.754323 GGGTGTGAATATTTGGAACGTGA 59.246 43.478 0.00 0.00 0.00 4.35
259 260 3.425625 CGGGTGTGAATATTTGGAACGTG 60.426 47.826 0.00 0.00 0.00 4.49
262 263 4.007659 ACTCGGGTGTGAATATTTGGAAC 58.992 43.478 0.00 0.00 0.00 3.62
263 264 4.295141 ACTCGGGTGTGAATATTTGGAA 57.705 40.909 0.00 0.00 0.00 3.53
264 265 3.992943 ACTCGGGTGTGAATATTTGGA 57.007 42.857 0.00 0.00 0.00 3.53
265 266 5.448632 GCTTTACTCGGGTGTGAATATTTGG 60.449 44.000 0.00 0.00 0.00 3.28
266 267 5.123186 TGCTTTACTCGGGTGTGAATATTTG 59.877 40.000 0.00 0.00 0.00 2.32
267 268 5.123344 GTGCTTTACTCGGGTGTGAATATTT 59.877 40.000 0.00 0.00 0.00 1.40
269 270 4.081087 AGTGCTTTACTCGGGTGTGAATAT 60.081 41.667 0.00 0.00 33.17 1.28
270 271 3.259876 AGTGCTTTACTCGGGTGTGAATA 59.740 43.478 0.00 0.00 33.17 1.75
271 272 2.038557 AGTGCTTTACTCGGGTGTGAAT 59.961 45.455 0.00 0.00 33.17 2.57
272 273 1.414919 AGTGCTTTACTCGGGTGTGAA 59.585 47.619 0.00 0.00 33.17 3.18
273 274 1.000506 GAGTGCTTTACTCGGGTGTGA 59.999 52.381 0.00 0.00 45.77 3.58
314 315 5.772521 ACGAAACATATGCTTTGCTCTTTT 58.227 33.333 1.58 0.00 0.00 2.27
329 330 5.123344 GCCCATAAGTTTAGTGACGAAACAT 59.877 40.000 20.43 12.81 38.91 2.71
331 332 4.694037 AGCCCATAAGTTTAGTGACGAAAC 59.306 41.667 12.47 12.47 37.11 2.78
336 337 4.035675 GCATCAGCCCATAAGTTTAGTGAC 59.964 45.833 0.00 0.00 33.58 3.67
355 356 3.928375 GTGGTTGTGAAATTGATGGCATC 59.072 43.478 20.52 20.52 0.00 3.91
363 374 2.101249 AGCCTGTGTGGTTGTGAAATTG 59.899 45.455 0.00 0.00 38.35 2.32
364 375 2.101249 CAGCCTGTGTGGTTGTGAAATT 59.899 45.455 0.00 0.00 41.43 1.82
398 409 1.265635 CTGAATGCGTCCGGTTTTTGA 59.734 47.619 0.00 0.00 0.00 2.69
416 427 2.455557 TGTATGCAAAATGGGGGACTG 58.544 47.619 0.00 0.00 0.00 3.51
417 428 2.831526 GTTGTATGCAAAATGGGGGACT 59.168 45.455 0.00 0.00 36.22 3.85
441 452 0.178990 AAGGGTTTCTGGTGCAGGTC 60.179 55.000 0.00 0.00 31.51 3.85
442 453 0.468029 CAAGGGTTTCTGGTGCAGGT 60.468 55.000 0.00 0.00 31.51 4.00
443 454 0.178992 TCAAGGGTTTCTGGTGCAGG 60.179 55.000 0.00 0.00 31.51 4.85
444 455 1.338020 GTTCAAGGGTTTCTGGTGCAG 59.662 52.381 0.00 0.00 0.00 4.41
456 467 3.485463 TGACCTACAGTTGTTCAAGGG 57.515 47.619 4.96 0.00 0.00 3.95
458 469 6.189677 TGTTTTGACCTACAGTTGTTCAAG 57.810 37.500 0.00 0.00 0.00 3.02
468 479 7.174253 GTGAGATTAACCATGTTTTGACCTACA 59.826 37.037 0.00 0.00 0.00 2.74
469 480 7.390718 AGTGAGATTAACCATGTTTTGACCTAC 59.609 37.037 0.00 0.00 0.00 3.18
486 712 1.751351 CCAGCTGTCCGAGTGAGATTA 59.249 52.381 13.81 0.00 0.00 1.75
496 722 0.588252 CTGTGAAAACCAGCTGTCCG 59.412 55.000 13.81 0.00 0.00 4.79
525 755 2.604644 TTTTGCGTGCGTGCATGTGT 62.605 50.000 14.92 0.00 45.78 3.72
550 784 2.812011 CGTCCCTACCAAAAGGTCAAAG 59.188 50.000 0.00 0.00 34.56 2.77
603 838 7.311408 ACACGTAGTAGTCCTTCAAAGATTAC 58.689 38.462 0.00 0.00 41.61 1.89
698 935 8.437274 TGGGAGGAGTATATAAAATCCTTCTC 57.563 38.462 13.93 7.31 42.27 2.87
702 939 6.737608 AGCATGGGAGGAGTATATAAAATCCT 59.262 38.462 10.69 10.69 44.90 3.24
738 975 1.651240 AAGAGTGGCGATGCATGCAC 61.651 55.000 25.37 15.77 0.00 4.57
763 1001 9.110502 CATGCATATATTAGCAACATCTCAGAT 57.889 33.333 0.00 0.00 44.88 2.90
775 1015 2.348362 TCGCGTGCATGCATATATTAGC 59.652 45.455 29.23 17.81 34.15 3.09
776 1016 3.614176 AGTCGCGTGCATGCATATATTAG 59.386 43.478 29.23 11.34 34.15 1.73
777 1017 3.584834 AGTCGCGTGCATGCATATATTA 58.415 40.909 29.23 4.99 34.15 0.98
932 2986 2.225491 CGGTGGTGGTAATTTCTGTGTG 59.775 50.000 0.00 0.00 0.00 3.82
938 2992 1.798087 CGCCGGTGGTGGTAATTTC 59.202 57.895 7.26 0.00 0.00 2.17
973 3027 0.108472 GTTGGTGCCGGAGTACTACC 60.108 60.000 5.05 1.94 0.00 3.18
1043 3116 1.592110 CGTGTTTCTTGTGTGCTCACG 60.592 52.381 13.76 0.00 46.49 4.35
1073 3160 1.103803 TCCAGGTGCTAGTAGAAGCG 58.896 55.000 0.00 0.00 45.85 4.68
1074 3161 1.825474 TGTCCAGGTGCTAGTAGAAGC 59.175 52.381 0.00 0.00 43.08 3.86
1075 3162 3.701542 TGATGTCCAGGTGCTAGTAGAAG 59.298 47.826 0.00 0.00 0.00 2.85
1091 3183 6.039829 AGGAAAAGGAAAAACTCTGTGATGTC 59.960 38.462 0.00 0.00 0.00 3.06
1093 3185 6.396829 AGGAAAAGGAAAAACTCTGTGATG 57.603 37.500 0.00 0.00 0.00 3.07
1122 3733 5.132502 CCTGCTCCATCCACACATTAATTA 58.867 41.667 0.00 0.00 0.00 1.40
1130 3741 2.439156 GCCCTGCTCCATCCACAC 60.439 66.667 0.00 0.00 0.00 3.82
1282 4107 4.933064 GGGATCTCGCAGCCGTCG 62.933 72.222 0.00 0.00 35.54 5.12
1439 4267 5.761234 GTCCTAAACTTAACATGTGTGGTCA 59.239 40.000 0.00 0.00 0.00 4.02
1442 4270 6.485313 TCAAGTCCTAAACTTAACATGTGTGG 59.515 38.462 0.00 0.00 46.69 4.17
1572 4404 5.107133 TGCTACTATTTCTAAGTCAACGCC 58.893 41.667 0.00 0.00 0.00 5.68
1640 4473 2.614057 GACGGTGGGCTCAGATTTATTG 59.386 50.000 0.00 0.00 0.00 1.90
1649 4482 2.016393 GATGATCGACGGTGGGCTCA 62.016 60.000 0.00 0.00 0.00 4.26
1653 4486 2.027605 CGGATGATCGACGGTGGG 59.972 66.667 0.00 0.00 0.00 4.61
1657 4490 0.317938 GGTTCTCGGATGATCGACGG 60.318 60.000 0.00 0.00 35.18 4.79
1675 4508 1.660052 CGTGTTCGTGTGATTGCTTGG 60.660 52.381 0.00 0.00 0.00 3.61
1691 4524 2.234300 AACAAATCTCGGTGTCGTGT 57.766 45.000 0.00 0.00 37.69 4.49
1730 4563 4.103928 AGGCCCCGGGGATGTAGT 62.104 66.667 44.86 16.75 37.50 2.73
1768 6650 1.274596 CGGTATTGTAGCGGTGTCAC 58.725 55.000 0.00 0.00 45.08 3.67
1820 6702 3.056328 GAACACAGGGGAAGCCGC 61.056 66.667 0.00 0.00 36.67 6.53
1833 6715 4.081031 TGCCAACATAATAGTACCGGAACA 60.081 41.667 9.46 0.00 0.00 3.18
1842 6724 7.602644 CGATGTAACCTATGCCAACATAATAGT 59.397 37.037 0.00 0.00 38.29 2.12
1852 6734 2.235155 ACACACGATGTAACCTATGCCA 59.765 45.455 0.00 0.00 40.88 4.92
1941 6823 8.734218 TGGACTTGTAGTTGTATTGTGTTTAA 57.266 30.769 0.00 0.00 0.00 1.52
2002 6884 9.244799 CGAAGCATGTATAACATACTGTTAGAA 57.755 33.333 5.99 0.00 44.89 2.10
2010 6892 7.906160 AGAACAACGAAGCATGTATAACATAC 58.094 34.615 0.00 0.00 36.53 2.39
2011 6893 8.487313 AAGAACAACGAAGCATGTATAACATA 57.513 30.769 0.00 0.00 36.53 2.29
2012 6894 6.985188 AGAACAACGAAGCATGTATAACAT 57.015 33.333 0.00 0.00 39.91 2.71
2013 6895 6.795098 AAGAACAACGAAGCATGTATAACA 57.205 33.333 0.00 0.00 30.59 2.41
2131 7014 2.398252 TCTTCATCAGCTCTTGGCAG 57.602 50.000 0.00 0.00 44.79 4.85
2183 7066 1.039233 CCAATGTAGGGCTGGGCAAG 61.039 60.000 0.00 0.00 0.00 4.01
2212 7098 0.394352 GGTGGTCCGATGAAGCCATT 60.394 55.000 0.00 0.00 33.20 3.16
2226 7112 1.192428 GAACTCTGGATACGGGTGGT 58.808 55.000 0.00 0.00 45.79 4.16
2338 7224 1.946745 TTCTGAACATCGTGCACACA 58.053 45.000 18.64 2.29 0.00 3.72
2343 7229 0.734889 CCCCATTCTGAACATCGTGC 59.265 55.000 0.00 0.00 0.00 5.34
2364 7250 5.414765 GGGACACTTGATATCGGAAAACTTT 59.585 40.000 0.00 0.00 0.00 2.66
2518 7406 2.881513 CCTCTCTCTCGTTGCTAGCATA 59.118 50.000 20.13 6.88 0.00 3.14
2619 7515 3.757745 GGATCTTCCGCGATTTGAAAA 57.242 42.857 8.23 0.00 0.00 2.29
2716 7612 1.981495 CAACTTCTCCTCTCCCCTTGT 59.019 52.381 0.00 0.00 0.00 3.16
2802 7698 2.503356 CTCCTCTTCCATAGTGCTTGGT 59.497 50.000 0.00 0.00 35.64 3.67
2813 7709 2.191400 CCAACTCATCCTCCTCTTCCA 58.809 52.381 0.00 0.00 0.00 3.53
2826 7722 1.944177 CCCTTCCTCTCTCCAACTCA 58.056 55.000 0.00 0.00 0.00 3.41
3044 7945 0.682852 CACGTTACTTGGGGAGGTGA 59.317 55.000 0.00 0.00 0.00 4.02
3227 8130 4.217767 CGGAGGTGAAGATCGGTATATTGA 59.782 45.833 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.