Multiple sequence alignment - TraesCS5B01G346900

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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 TraesCS5B01G346900 chr5B 100.000 2429 0 0 1 2429 528574323 528576751 0.000000e+00 4486.0
1 TraesCS5B01G346900 chr5B 88.367 851 90 8 1576 2421 528582642 528583488 0.000000e+00 1014.0
2 TraesCS5B01G346900 chr5B 89.683 252 25 1 10 260 591646769 591647020 1.080000e-83 320.0
3 TraesCS5B01G346900 chr5B 77.113 568 107 16 835 1384 528539125 528539687 8.440000e-80 307.0
4 TraesCS5B01G346900 chr5D 90.318 2169 153 27 304 2429 435263141 435265295 0.000000e+00 2789.0
5 TraesCS5B01G346900 chr5D 88.571 735 66 13 1700 2429 435270641 435271362 0.000000e+00 876.0
6 TraesCS5B01G346900 chr5D 100.000 32 0 0 329 360 435263103 435263134 2.610000e-05 60.2
7 TraesCS5B01G346900 chr5A 90.302 1392 98 13 408 1773 9386058 9384678 0.000000e+00 1788.0
8 TraesCS5B01G346900 chr5A 88.628 1363 118 20 1087 2426 549201202 549202550 0.000000e+00 1624.0
9 TraesCS5B01G346900 chr5A 92.453 795 35 7 308 1101 549200415 549201185 0.000000e+00 1112.0
10 TraesCS5B01G346900 chr5A 88.163 735 69 13 1700 2429 549211639 549212360 0.000000e+00 859.0
11 TraesCS5B01G346900 chr5A 90.323 620 50 9 1758 2371 9383406 9382791 0.000000e+00 804.0
12 TraesCS5B01G346900 chr5A 84.165 461 43 12 1342 1784 549208580 549209028 1.040000e-113 420.0
13 TraesCS5B01G346900 chr5A 76.391 593 117 16 802 1378 549155231 549155816 5.080000e-77 298.0
14 TraesCS5B01G346900 chr5A 97.980 99 2 0 309 407 9386457 9386359 3.210000e-39 172.0
15 TraesCS5B01G346900 chr2B 92.391 276 19 2 7 281 181755997 181755723 2.260000e-105 392.0
16 TraesCS5B01G346900 chr1B 91.135 282 20 4 7 285 658361096 658360817 6.340000e-101 377.0
17 TraesCS5B01G346900 chr2A 90.459 283 25 2 1 282 729288816 729289097 2.950000e-99 372.0
18 TraesCS5B01G346900 chr3B 89.568 278 25 4 10 285 117922650 117922375 1.380000e-92 350.0
19 TraesCS5B01G346900 chr3B 91.411 163 13 1 98 260 783212874 783212713 3.140000e-54 222.0
20 TraesCS5B01G346900 chr3B 83.099 142 21 3 98 239 263271002 263271140 2.540000e-25 126.0
21 TraesCS5B01G346900 chr6B 90.602 266 18 6 1 264 228695438 228695698 1.790000e-91 346.0
22 TraesCS5B01G346900 chr1A 88.172 279 30 3 6 282 77277138 77276861 1.800000e-86 329.0
23 TraesCS5B01G346900 chr7D 89.883 257 20 4 7 260 6009807 6010060 2.330000e-85 326.0
24 TraesCS5B01G346900 chr3D 86.806 288 34 4 1 286 163116425 163116710 3.900000e-83 318.0


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 TraesCS5B01G346900 chr5B 528574323 528576751 2428 False 4486.000000 4486 100.000000 1 2429 1 chr5B.!!$F2 2428
1 TraesCS5B01G346900 chr5B 528582642 528583488 846 False 1014.000000 1014 88.367000 1576 2421 1 chr5B.!!$F3 845
2 TraesCS5B01G346900 chr5B 528539125 528539687 562 False 307.000000 307 77.113000 835 1384 1 chr5B.!!$F1 549
3 TraesCS5B01G346900 chr5D 435263103 435265295 2192 False 1424.600000 2789 95.159000 304 2429 2 chr5D.!!$F2 2125
4 TraesCS5B01G346900 chr5D 435270641 435271362 721 False 876.000000 876 88.571000 1700 2429 1 chr5D.!!$F1 729
5 TraesCS5B01G346900 chr5A 549200415 549202550 2135 False 1368.000000 1624 90.540500 308 2426 2 chr5A.!!$F2 2118
6 TraesCS5B01G346900 chr5A 9382791 9386457 3666 True 921.333333 1788 92.868333 309 2371 3 chr5A.!!$R1 2062
7 TraesCS5B01G346900 chr5A 549208580 549212360 3780 False 639.500000 859 86.164000 1342 2429 2 chr5A.!!$F3 1087
8 TraesCS5B01G346900 chr5A 549155231 549155816 585 False 298.000000 298 76.391000 802 1378 1 chr5A.!!$F1 576

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
483 796 0.041535 TGGCCCTCCAAATGATTGCT 59.958 50.0 0.0 0.0 39.99 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 6378 0.392193 ATGAACTTGGCAGCTCTCCG 60.392 55.0 0.0 0.0 0.0 4.63 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.952188 CTATGAACCACATACGGATGTATATAG 57.048 37.037 14.23 12.28 44.82 1.31
27 28 8.589701 ATGAACCACATACGGATGTATATAGA 57.410 34.615 14.23 0.00 44.82 1.98
29 30 8.466798 TGAACCACATACGGATGTATATAGATG 58.533 37.037 14.23 0.00 44.82 2.90
30 31 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
31 32 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
32 33 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
33 34 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
34 35 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
35 36 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
62 63 4.270178 GAGATTCACTCATTTTGCTCCG 57.730 45.455 0.00 0.00 44.36 4.63
63 64 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
64 65 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
65 66 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
66 67 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
67 68 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
68 69 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
69 70 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
70 71 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
71 72 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
72 73 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
73 74 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
74 75 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
75 76 3.452755 TTGCTCCGTATGTAGTCCATG 57.547 47.619 0.00 0.00 34.86 3.66
76 77 2.661718 TGCTCCGTATGTAGTCCATGA 58.338 47.619 0.00 0.00 34.86 3.07
77 78 3.230976 TGCTCCGTATGTAGTCCATGAT 58.769 45.455 0.00 0.00 34.86 2.45
78 79 3.005791 TGCTCCGTATGTAGTCCATGATG 59.994 47.826 0.00 0.00 34.86 3.07
79 80 3.255888 GCTCCGTATGTAGTCCATGATGA 59.744 47.826 0.00 0.00 34.86 2.92
80 81 4.262036 GCTCCGTATGTAGTCCATGATGAA 60.262 45.833 0.00 0.00 34.86 2.57
81 82 5.739070 GCTCCGTATGTAGTCCATGATGAAA 60.739 44.000 0.00 0.00 34.86 2.69
82 83 6.419484 TCCGTATGTAGTCCATGATGAAAT 57.581 37.500 0.00 0.00 34.86 2.17
83 84 6.455647 TCCGTATGTAGTCCATGATGAAATC 58.544 40.000 0.00 0.00 45.83 2.17
84 85 6.267699 TCCGTATGTAGTCCATGATGAAATCT 59.732 38.462 0.00 0.00 45.81 2.40
85 86 6.587990 CCGTATGTAGTCCATGATGAAATCTC 59.412 42.308 0.00 0.00 45.81 2.75
86 87 7.374272 CGTATGTAGTCCATGATGAAATCTCT 58.626 38.462 0.00 0.00 45.81 3.10
87 88 8.515414 CGTATGTAGTCCATGATGAAATCTCTA 58.485 37.037 0.00 0.00 45.81 2.43
88 89 9.632807 GTATGTAGTCCATGATGAAATCTCTAC 57.367 37.037 0.00 0.00 45.81 2.59
89 90 7.660030 TGTAGTCCATGATGAAATCTCTACA 57.340 36.000 0.00 0.00 45.81 2.74
90 91 8.078060 TGTAGTCCATGATGAAATCTCTACAA 57.922 34.615 0.00 0.00 45.81 2.41
91 92 8.539544 TGTAGTCCATGATGAAATCTCTACAAA 58.460 33.333 0.00 0.00 45.81 2.83
92 93 9.039870 GTAGTCCATGATGAAATCTCTACAAAG 57.960 37.037 0.00 0.00 45.81 2.77
93 94 7.855375 AGTCCATGATGAAATCTCTACAAAGA 58.145 34.615 0.00 0.00 45.81 2.52
94 95 7.768120 AGTCCATGATGAAATCTCTACAAAGAC 59.232 37.037 0.00 0.00 45.81 3.01
95 96 7.768120 GTCCATGATGAAATCTCTACAAAGACT 59.232 37.037 0.00 0.00 45.81 3.24
96 97 8.324306 TCCATGATGAAATCTCTACAAAGACTT 58.676 33.333 0.00 0.00 45.81 3.01
97 98 9.605275 CCATGATGAAATCTCTACAAAGACTTA 57.395 33.333 0.00 0.00 45.81 2.24
104 105 9.752961 GAAATCTCTACAAAGACTTATACTCCC 57.247 37.037 0.00 0.00 0.00 4.30
105 106 9.495382 AAATCTCTACAAAGACTTATACTCCCT 57.505 33.333 0.00 0.00 0.00 4.20
106 107 8.700439 ATCTCTACAAAGACTTATACTCCCTC 57.300 38.462 0.00 0.00 0.00 4.30
107 108 7.061688 TCTCTACAAAGACTTATACTCCCTCC 58.938 42.308 0.00 0.00 0.00 4.30
108 109 6.738635 TCTACAAAGACTTATACTCCCTCCA 58.261 40.000 0.00 0.00 0.00 3.86
109 110 7.363031 TCTACAAAGACTTATACTCCCTCCAT 58.637 38.462 0.00 0.00 0.00 3.41
110 111 6.893020 ACAAAGACTTATACTCCCTCCATT 57.107 37.500 0.00 0.00 0.00 3.16
111 112 6.890293 ACAAAGACTTATACTCCCTCCATTC 58.110 40.000 0.00 0.00 0.00 2.67
112 113 6.126739 ACAAAGACTTATACTCCCTCCATTCC 60.127 42.308 0.00 0.00 0.00 3.01
113 114 5.426325 AGACTTATACTCCCTCCATTCCT 57.574 43.478 0.00 0.00 0.00 3.36
114 115 6.547396 AGACTTATACTCCCTCCATTCCTA 57.453 41.667 0.00 0.00 0.00 2.94
115 116 6.935036 AGACTTATACTCCCTCCATTCCTAA 58.065 40.000 0.00 0.00 0.00 2.69
116 117 7.371043 AGACTTATACTCCCTCCATTCCTAAA 58.629 38.462 0.00 0.00 0.00 1.85
117 118 8.019652 AGACTTATACTCCCTCCATTCCTAAAT 58.980 37.037 0.00 0.00 0.00 1.40
118 119 9.322769 GACTTATACTCCCTCCATTCCTAAATA 57.677 37.037 0.00 0.00 0.00 1.40
119 120 9.327731 ACTTATACTCCCTCCATTCCTAAATAG 57.672 37.037 0.00 0.00 0.00 1.73
120 121 9.327731 CTTATACTCCCTCCATTCCTAAATAGT 57.672 37.037 0.00 0.00 0.00 2.12
121 122 9.684702 TTATACTCCCTCCATTCCTAAATAGTT 57.315 33.333 0.00 0.00 0.00 2.24
122 123 6.253946 ACTCCCTCCATTCCTAAATAGTTG 57.746 41.667 0.00 0.00 0.00 3.16
123 124 5.731678 ACTCCCTCCATTCCTAAATAGTTGT 59.268 40.000 0.00 0.00 0.00 3.32
124 125 6.126739 ACTCCCTCCATTCCTAAATAGTTGTC 60.127 42.308 0.00 0.00 0.00 3.18
125 126 5.970640 TCCCTCCATTCCTAAATAGTTGTCT 59.029 40.000 0.00 0.00 0.00 3.41
126 127 6.447084 TCCCTCCATTCCTAAATAGTTGTCTT 59.553 38.462 0.00 0.00 0.00 3.01
127 128 7.036863 TCCCTCCATTCCTAAATAGTTGTCTTT 60.037 37.037 0.00 0.00 0.00 2.52
128 129 7.283354 CCCTCCATTCCTAAATAGTTGTCTTTC 59.717 40.741 0.00 0.00 0.00 2.62
129 130 8.049721 CCTCCATTCCTAAATAGTTGTCTTTCT 58.950 37.037 0.00 0.00 0.00 2.52
153 154 9.475620 TCTAGAGATTTCAAATAGACTACCACA 57.524 33.333 0.00 0.00 0.00 4.17
157 158 8.873215 AGATTTCAAATAGACTACCACATACG 57.127 34.615 0.00 0.00 0.00 3.06
158 159 7.926555 AGATTTCAAATAGACTACCACATACGG 59.073 37.037 0.00 0.00 0.00 4.02
159 160 6.778834 TTCAAATAGACTACCACATACGGA 57.221 37.500 0.00 0.00 0.00 4.69
160 161 6.971726 TCAAATAGACTACCACATACGGAT 57.028 37.500 0.00 0.00 0.00 4.18
161 162 6.745116 TCAAATAGACTACCACATACGGATG 58.255 40.000 5.94 5.94 39.16 3.51
163 164 7.503230 TCAAATAGACTACCACATACGGATGTA 59.497 37.037 14.23 0.00 44.82 2.29
164 165 6.814506 ATAGACTACCACATACGGATGTAC 57.185 41.667 14.23 1.48 44.82 2.90
165 166 4.529897 AGACTACCACATACGGATGTACA 58.470 43.478 14.23 0.00 44.82 2.90
166 167 5.138276 AGACTACCACATACGGATGTACAT 58.862 41.667 14.23 8.43 44.82 2.29
167 168 6.301486 AGACTACCACATACGGATGTACATA 58.699 40.000 14.23 5.36 44.82 2.29
168 169 6.430308 AGACTACCACATACGGATGTACATAG 59.570 42.308 14.23 16.35 44.82 2.23
169 170 6.301486 ACTACCACATACGGATGTACATAGA 58.699 40.000 22.62 5.04 44.82 1.98
170 171 5.449107 ACCACATACGGATGTACATAGAC 57.551 43.478 14.23 1.53 44.82 2.59
171 172 4.891168 ACCACATACGGATGTACATAGACA 59.109 41.667 14.23 1.12 44.82 3.41
172 173 5.538813 ACCACATACGGATGTACATAGACAT 59.461 40.000 14.23 3.26 44.82 3.06
173 174 6.717997 ACCACATACGGATGTACATAGACATA 59.282 38.462 14.23 0.00 44.82 2.29
174 175 7.396339 ACCACATACGGATGTACATAGACATAT 59.604 37.037 14.23 0.00 44.82 1.78
175 176 8.251026 CCACATACGGATGTACATAGACATATT 58.749 37.037 14.23 0.00 44.82 1.28
176 177 9.639601 CACATACGGATGTACATAGACATATTT 57.360 33.333 14.23 0.00 44.82 1.40
203 204 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
204 205 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
205 206 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
206 207 6.094603 GTGTAGATTCACTCATTTTGCTCCAT 59.905 38.462 0.00 0.00 35.68 3.41
207 208 7.280876 GTGTAGATTCACTCATTTTGCTCCATA 59.719 37.037 0.00 0.00 35.68 2.74
208 209 7.994911 TGTAGATTCACTCATTTTGCTCCATAT 59.005 33.333 0.00 0.00 0.00 1.78
209 210 7.273320 AGATTCACTCATTTTGCTCCATATG 57.727 36.000 0.00 0.00 0.00 1.78
210 211 6.832384 AGATTCACTCATTTTGCTCCATATGT 59.168 34.615 1.24 0.00 0.00 2.29
211 212 7.994911 AGATTCACTCATTTTGCTCCATATGTA 59.005 33.333 1.24 0.00 0.00 2.29
212 213 7.558161 TTCACTCATTTTGCTCCATATGTAG 57.442 36.000 1.24 0.00 0.00 2.74
213 214 6.653020 TCACTCATTTTGCTCCATATGTAGT 58.347 36.000 1.24 0.00 0.00 2.73
214 215 6.763135 TCACTCATTTTGCTCCATATGTAGTC 59.237 38.462 1.24 0.00 0.00 2.59
215 216 6.539826 CACTCATTTTGCTCCATATGTAGTCA 59.460 38.462 1.24 0.00 0.00 3.41
216 217 6.540189 ACTCATTTTGCTCCATATGTAGTCAC 59.460 38.462 1.24 0.00 0.00 3.67
217 218 6.653020 TCATTTTGCTCCATATGTAGTCACT 58.347 36.000 1.24 0.00 0.00 3.41
218 219 7.112122 TCATTTTGCTCCATATGTAGTCACTT 58.888 34.615 1.24 0.00 0.00 3.16
219 220 7.611467 TCATTTTGCTCCATATGTAGTCACTTT 59.389 33.333 1.24 0.00 0.00 2.66
220 221 7.759489 TTTTGCTCCATATGTAGTCACTTTT 57.241 32.000 1.24 0.00 0.00 2.27
221 222 7.759489 TTTGCTCCATATGTAGTCACTTTTT 57.241 32.000 1.24 0.00 0.00 1.94
222 223 6.741992 TGCTCCATATGTAGTCACTTTTTG 57.258 37.500 1.24 0.00 0.00 2.44
223 224 6.472016 TGCTCCATATGTAGTCACTTTTTGA 58.528 36.000 1.24 0.00 0.00 2.69
224 225 6.939730 TGCTCCATATGTAGTCACTTTTTGAA 59.060 34.615 1.24 0.00 35.39 2.69
225 226 7.446931 TGCTCCATATGTAGTCACTTTTTGAAA 59.553 33.333 1.24 0.00 35.39 2.69
226 227 8.462016 GCTCCATATGTAGTCACTTTTTGAAAT 58.538 33.333 1.24 0.00 35.39 2.17
227 228 9.994432 CTCCATATGTAGTCACTTTTTGAAATC 57.006 33.333 1.24 0.00 35.39 2.17
228 229 9.739276 TCCATATGTAGTCACTTTTTGAAATCT 57.261 29.630 1.24 0.00 35.39 2.40
229 230 9.994432 CCATATGTAGTCACTTTTTGAAATCTC 57.006 33.333 1.24 0.00 35.39 2.75
237 238 9.838339 AGTCACTTTTTGAAATCTCTAGAAAGA 57.162 29.630 0.00 0.00 35.39 2.52
238 239 9.871299 GTCACTTTTTGAAATCTCTAGAAAGAC 57.129 33.333 0.00 0.00 35.39 3.01
239 240 9.613428 TCACTTTTTGAAATCTCTAGAAAGACA 57.387 29.630 0.00 0.00 0.00 3.41
253 254 9.291664 CTCTAGAAAGACAAGTATTTAGGAACG 57.708 37.037 0.00 0.00 0.00 3.95
254 255 8.248945 TCTAGAAAGACAAGTATTTAGGAACGG 58.751 37.037 0.00 0.00 0.00 4.44
255 256 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
256 257 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
257 258 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
258 259 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
259 260 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
260 261 4.081254 ACAAGTATTTAGGAACGGAGGGAC 60.081 45.833 0.00 0.00 0.00 4.46
262 263 5.134725 AGTATTTAGGAACGGAGGGACTA 57.865 43.478 0.00 0.00 41.55 2.59
263 264 5.713807 AGTATTTAGGAACGGAGGGACTAT 58.286 41.667 0.00 0.00 41.55 2.12
264 265 6.141790 AGTATTTAGGAACGGAGGGACTATT 58.858 40.000 0.00 0.00 41.55 1.73
265 266 5.970501 ATTTAGGAACGGAGGGACTATTT 57.029 39.130 0.00 0.00 41.55 1.40
266 267 7.786464 AGTATTTAGGAACGGAGGGACTATTTA 59.214 37.037 0.00 0.00 41.55 1.40
267 268 6.475596 TTTAGGAACGGAGGGACTATTTAG 57.524 41.667 0.00 0.00 41.55 1.85
268 269 3.306613 AGGAACGGAGGGACTATTTAGG 58.693 50.000 0.00 0.00 41.55 2.69
269 270 3.052338 AGGAACGGAGGGACTATTTAGGA 60.052 47.826 0.00 0.00 41.55 2.94
270 271 3.708121 GGAACGGAGGGACTATTTAGGAA 59.292 47.826 0.00 0.00 41.55 3.36
271 272 4.442612 GGAACGGAGGGACTATTTAGGAAC 60.443 50.000 0.00 0.00 41.55 3.62
272 273 2.692041 ACGGAGGGACTATTTAGGAACG 59.308 50.000 0.00 0.00 41.55 3.95
273 274 2.035576 CGGAGGGACTATTTAGGAACGG 59.964 54.545 0.00 0.00 41.55 4.44
274 275 3.303049 GGAGGGACTATTTAGGAACGGA 58.697 50.000 0.00 0.00 41.55 4.69
275 276 3.321396 GGAGGGACTATTTAGGAACGGAG 59.679 52.174 0.00 0.00 41.55 4.63
276 277 3.306613 AGGGACTATTTAGGAACGGAGG 58.693 50.000 0.00 0.00 36.02 4.30
277 278 2.367894 GGGACTATTTAGGAACGGAGGG 59.632 54.545 0.00 0.00 0.00 4.30
278 279 3.303049 GGACTATTTAGGAACGGAGGGA 58.697 50.000 0.00 0.00 0.00 4.20
279 280 3.321396 GGACTATTTAGGAACGGAGGGAG 59.679 52.174 0.00 0.00 0.00 4.30
280 281 3.959449 GACTATTTAGGAACGGAGGGAGT 59.041 47.826 0.00 0.00 0.00 3.85
281 282 5.134725 ACTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
282 283 5.713807 ACTATTTAGGAACGGAGGGAGTAT 58.286 41.667 0.00 0.00 0.00 2.12
283 284 6.856757 ACTATTTAGGAACGGAGGGAGTATA 58.143 40.000 0.00 0.00 0.00 1.47
284 285 7.477008 ACTATTTAGGAACGGAGGGAGTATAT 58.523 38.462 0.00 0.00 0.00 0.86
285 286 8.618385 ACTATTTAGGAACGGAGGGAGTATATA 58.382 37.037 0.00 0.00 0.00 0.86
286 287 9.471702 CTATTTAGGAACGGAGGGAGTATATAA 57.528 37.037 0.00 0.00 0.00 0.98
287 288 8.912614 ATTTAGGAACGGAGGGAGTATATAAT 57.087 34.615 0.00 0.00 0.00 1.28
289 290 9.827198 TTTAGGAACGGAGGGAGTATATAATAA 57.173 33.333 0.00 0.00 0.00 1.40
290 291 7.715266 AGGAACGGAGGGAGTATATAATAAC 57.285 40.000 0.00 0.00 0.00 1.89
291 292 7.243824 AGGAACGGAGGGAGTATATAATAACA 58.756 38.462 0.00 0.00 0.00 2.41
292 293 7.899709 AGGAACGGAGGGAGTATATAATAACAT 59.100 37.037 0.00 0.00 0.00 2.71
293 294 9.193806 GGAACGGAGGGAGTATATAATAACATA 57.806 37.037 0.00 0.00 0.00 2.29
475 785 0.251297 CATGACACTGGCCCTCCAAA 60.251 55.000 0.00 0.00 42.91 3.28
483 796 0.041535 TGGCCCTCCAAATGATTGCT 59.958 50.000 0.00 0.00 39.99 3.91
484 797 0.462789 GGCCCTCCAAATGATTGCTG 59.537 55.000 0.00 0.00 35.10 4.41
485 798 0.179092 GCCCTCCAAATGATTGCTGC 60.179 55.000 0.00 0.00 35.10 5.25
489 802 3.370103 CCCTCCAAATGATTGCTGCAATT 60.370 43.478 26.87 11.23 33.90 2.32
558 871 7.532571 TCATTGTGAAATCATTACTCTTGCAG 58.467 34.615 0.00 0.00 0.00 4.41
595 908 0.608640 ATCCTTGACGGTGTCACTCC 59.391 55.000 2.35 0.00 42.60 3.85
742 1056 2.029380 CGTGTCACTTATCCACCAGACA 60.029 50.000 0.65 0.00 34.02 3.41
745 1059 2.939103 GTCACTTATCCACCAGACATGC 59.061 50.000 0.00 0.00 0.00 4.06
954 1305 4.151157 GCTTCATCCACAAACAAAGCATTC 59.849 41.667 0.00 0.00 39.07 2.67
963 1314 2.693797 ACAAAGCATTCGCAACTCAG 57.306 45.000 0.00 0.00 42.27 3.35
970 1321 4.177190 GCATTCGCAACTCAGCTAGAGC 62.177 54.545 11.60 0.00 42.60 4.09
1071 1424 4.882396 GCTCTCGGGAGGAAGCGC 62.882 72.222 15.59 0.00 39.80 5.92
1072 1425 3.144193 CTCTCGGGAGGAAGCGCT 61.144 66.667 2.64 2.64 36.03 5.92
1123 1507 2.641559 GCTCAACAGCAGTGGCAC 59.358 61.111 10.29 10.29 46.06 5.01
1306 1693 2.602890 ATGGAGTACGCCATGTCCA 58.397 52.632 27.89 15.20 46.62 4.02
1538 1942 4.373672 CGATCGAAAAACGGTTACAAACAC 59.626 41.667 10.26 0.00 42.82 3.32
1553 1957 2.030562 CACCGTTCCTCCAGCGTT 59.969 61.111 0.00 0.00 0.00 4.84
1603 2007 4.150804 GTCGCTTTTAGGACTTGAACAGAG 59.849 45.833 0.00 0.00 0.00 3.35
1607 2011 5.751243 TTTTAGGACTTGAACAGAGCAAC 57.249 39.130 0.00 0.00 0.00 4.17
1638 2042 1.218875 TTCTGCACAGTTACGTGGCG 61.219 55.000 0.00 0.00 37.37 5.69
1675 2079 2.718563 ACAAAGAAACGTTCAGGTGGT 58.281 42.857 0.00 0.00 0.00 4.16
1690 2095 3.499918 CAGGTGGTCAGAGAAATGTTCAC 59.500 47.826 0.00 0.00 0.00 3.18
1747 4847 4.215109 CCCCAATTTGATAAATCCGTCCT 58.785 43.478 0.00 0.00 0.00 3.85
1785 6174 3.287867 AATGCCCTGATCCAGTACAAG 57.712 47.619 0.00 0.00 0.00 3.16
1881 6271 1.731160 GCAAGTTGCTAGACTCTGCAG 59.269 52.381 20.71 7.63 40.96 4.41
1961 6352 0.172352 CTCAGTTGAGACTCGAGGCC 59.828 60.000 16.58 7.28 44.74 5.19
1962 6353 1.153939 CAGTTGAGACTCGAGGCCG 60.154 63.158 16.58 0.00 32.54 6.13
1972 6363 3.501396 CGAGGCCGTCGTACCTAA 58.499 61.111 14.22 0.00 44.20 2.69
1980 6371 2.606272 GCCGTCGTACCTAATTTTCCAG 59.394 50.000 0.00 0.00 0.00 3.86
1981 6372 2.606272 CCGTCGTACCTAATTTTCCAGC 59.394 50.000 0.00 0.00 0.00 4.85
1987 6378 4.213482 CGTACCTAATTTTCCAGCATAGCC 59.787 45.833 0.00 0.00 0.00 3.93
2022 6413 4.826556 AGTTCATTACTCAGAGCAGGAAC 58.173 43.478 15.43 15.43 35.00 3.62
2094 6485 3.704800 TCATATCGTGGTTGGTTCCAA 57.295 42.857 0.00 0.00 39.34 3.53
2104 6496 4.099419 GTGGTTGGTTCCAATTCAAGTTCT 59.901 41.667 7.56 0.00 39.34 3.01
2105 6497 4.099266 TGGTTGGTTCCAATTCAAGTTCTG 59.901 41.667 7.56 0.00 34.24 3.02
2106 6498 4.051237 GTTGGTTCCAATTCAAGTTCTGC 58.949 43.478 7.56 0.00 0.00 4.26
2192 6586 6.350110 GCTTGAGAATTTGGCAAACATAGGTA 60.350 38.462 16.00 0.00 0.00 3.08
2218 6613 5.123979 AGCTTCAAATTCCCGTTGACTATTC 59.876 40.000 0.00 0.00 34.78 1.75
2247 6642 4.634000 GTTTTGCAAACGTCTTCCAAAAC 58.366 39.130 12.39 20.54 44.13 2.43
2255 6650 6.208644 CAAACGTCTTCCAAAACTCATCAAT 58.791 36.000 0.00 0.00 0.00 2.57
2261 6656 7.202526 GTCTTCCAAAACTCATCAATGAAACA 58.797 34.615 0.00 0.00 36.18 2.83
2262 6657 7.869429 GTCTTCCAAAACTCATCAATGAAACAT 59.131 33.333 0.00 0.00 36.18 2.71
2331 6726 9.453572 TGCTGAATCTTATCAAGAACATTTAGT 57.546 29.630 0.00 0.00 41.63 2.24
2399 6796 6.323482 TGACATTTTCAGAAAATTCCCACTGA 59.677 34.615 17.12 0.00 38.97 3.41
2428 6825 9.334947 TGCTAAGATGAGAAAATAGGATCTTTG 57.665 33.333 0.00 0.00 35.50 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.952188 CTATATACATCCGTATGTGGTTCATAG 57.048 37.037 3.56 0.80 45.99 2.23
2 3 8.589701 TCTATATACATCCGTATGTGGTTCAT 57.410 34.615 3.56 0.00 45.99 2.57
3 4 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
4 5 7.435488 GCATCTATATACATCCGTATGTGGTTC 59.565 40.741 3.56 0.00 45.99 3.62
5 6 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
7 8 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
8 9 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
14 15 9.809096 ACTCTAAAATGCATCTATATACATCCG 57.191 33.333 0.00 0.00 0.00 4.18
23 24 9.270640 GTGAATCTCACTCTAAAATGCATCTAT 57.729 33.333 0.00 0.00 43.73 1.98
24 25 8.654230 GTGAATCTCACTCTAAAATGCATCTA 57.346 34.615 0.00 0.00 43.73 1.98
42 43 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
43 44 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
44 45 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
45 46 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
46 47 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
47 48 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
48 49 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
49 50 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
50 51 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
51 52 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
52 53 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
53 54 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
54 55 3.449377 TCATGGACTACATACGGAGCAAA 59.551 43.478 0.00 0.00 37.84 3.68
55 56 3.028130 TCATGGACTACATACGGAGCAA 58.972 45.455 0.00 0.00 37.84 3.91
56 57 2.661718 TCATGGACTACATACGGAGCA 58.338 47.619 0.00 0.00 37.84 4.26
57 58 3.255888 TCATCATGGACTACATACGGAGC 59.744 47.826 0.00 0.00 37.84 4.70
58 59 5.453567 TTCATCATGGACTACATACGGAG 57.546 43.478 0.00 0.00 37.84 4.63
59 60 5.862678 TTTCATCATGGACTACATACGGA 57.137 39.130 0.00 0.00 37.84 4.69
60 61 6.459066 AGATTTCATCATGGACTACATACGG 58.541 40.000 0.00 0.00 37.84 4.02
61 62 7.374272 AGAGATTTCATCATGGACTACATACG 58.626 38.462 0.00 0.00 37.84 3.06
62 63 9.632807 GTAGAGATTTCATCATGGACTACATAC 57.367 37.037 0.00 0.00 37.84 2.39
63 64 9.367160 TGTAGAGATTTCATCATGGACTACATA 57.633 33.333 0.00 0.00 37.84 2.29
64 65 8.255111 TGTAGAGATTTCATCATGGACTACAT 57.745 34.615 0.00 0.00 41.57 2.29
65 66 7.660030 TGTAGAGATTTCATCATGGACTACA 57.340 36.000 0.00 0.00 36.46 2.74
66 67 8.948631 TTTGTAGAGATTTCATCATGGACTAC 57.051 34.615 0.00 0.00 0.00 2.73
67 68 8.981659 TCTTTGTAGAGATTTCATCATGGACTA 58.018 33.333 0.00 0.00 0.00 2.59
68 69 7.768120 GTCTTTGTAGAGATTTCATCATGGACT 59.232 37.037 0.00 0.00 0.00 3.85
69 70 7.768120 AGTCTTTGTAGAGATTTCATCATGGAC 59.232 37.037 0.00 0.00 0.00 4.02
70 71 7.855375 AGTCTTTGTAGAGATTTCATCATGGA 58.145 34.615 0.00 0.00 0.00 3.41
71 72 8.503458 AAGTCTTTGTAGAGATTTCATCATGG 57.497 34.615 0.00 0.00 0.00 3.66
78 79 9.752961 GGGAGTATAAGTCTTTGTAGAGATTTC 57.247 37.037 0.00 0.00 29.76 2.17
79 80 9.495382 AGGGAGTATAAGTCTTTGTAGAGATTT 57.505 33.333 0.00 0.00 31.59 2.17
80 81 9.138596 GAGGGAGTATAAGTCTTTGTAGAGATT 57.861 37.037 0.00 0.00 0.00 2.40
81 82 7.726738 GGAGGGAGTATAAGTCTTTGTAGAGAT 59.273 40.741 0.00 0.00 0.00 2.75
82 83 7.061688 GGAGGGAGTATAAGTCTTTGTAGAGA 58.938 42.308 0.00 0.00 0.00 3.10
83 84 6.834451 TGGAGGGAGTATAAGTCTTTGTAGAG 59.166 42.308 0.00 0.00 0.00 2.43
84 85 6.738635 TGGAGGGAGTATAAGTCTTTGTAGA 58.261 40.000 0.00 0.00 0.00 2.59
85 86 7.604657 ATGGAGGGAGTATAAGTCTTTGTAG 57.395 40.000 0.00 0.00 0.00 2.74
86 87 7.070821 GGAATGGAGGGAGTATAAGTCTTTGTA 59.929 40.741 0.00 0.00 0.00 2.41
87 88 6.126739 GGAATGGAGGGAGTATAAGTCTTTGT 60.127 42.308 0.00 0.00 0.00 2.83
88 89 6.100424 AGGAATGGAGGGAGTATAAGTCTTTG 59.900 42.308 0.00 0.00 0.00 2.77
89 90 6.213525 AGGAATGGAGGGAGTATAAGTCTTT 58.786 40.000 0.00 0.00 0.00 2.52
90 91 5.793967 AGGAATGGAGGGAGTATAAGTCTT 58.206 41.667 0.00 0.00 0.00 3.01
91 92 5.426325 AGGAATGGAGGGAGTATAAGTCT 57.574 43.478 0.00 0.00 0.00 3.24
92 93 7.613551 TTTAGGAATGGAGGGAGTATAAGTC 57.386 40.000 0.00 0.00 0.00 3.01
93 94 9.327731 CTATTTAGGAATGGAGGGAGTATAAGT 57.672 37.037 0.00 0.00 0.00 2.24
94 95 9.327731 ACTATTTAGGAATGGAGGGAGTATAAG 57.672 37.037 0.00 0.00 0.00 1.73
95 96 9.684702 AACTATTTAGGAATGGAGGGAGTATAA 57.315 33.333 0.00 0.00 0.00 0.98
96 97 9.101325 CAACTATTTAGGAATGGAGGGAGTATA 57.899 37.037 0.00 0.00 0.00 1.47
97 98 7.572861 ACAACTATTTAGGAATGGAGGGAGTAT 59.427 37.037 0.00 0.00 0.00 2.12
98 99 6.906901 ACAACTATTTAGGAATGGAGGGAGTA 59.093 38.462 0.00 0.00 0.00 2.59
99 100 5.731678 ACAACTATTTAGGAATGGAGGGAGT 59.268 40.000 0.00 0.00 0.00 3.85
100 101 6.100424 AGACAACTATTTAGGAATGGAGGGAG 59.900 42.308 0.00 0.00 0.00 4.30
101 102 5.970640 AGACAACTATTTAGGAATGGAGGGA 59.029 40.000 0.00 0.00 0.00 4.20
102 103 6.253946 AGACAACTATTTAGGAATGGAGGG 57.746 41.667 0.00 0.00 0.00 4.30
103 104 8.049721 AGAAAGACAACTATTTAGGAATGGAGG 58.950 37.037 0.00 0.00 0.00 4.30
127 128 9.475620 TGTGGTAGTCTATTTGAAATCTCTAGA 57.524 33.333 0.00 0.00 0.00 2.43
131 132 8.969267 CGTATGTGGTAGTCTATTTGAAATCTC 58.031 37.037 0.00 0.00 0.00 2.75
132 133 7.926555 CCGTATGTGGTAGTCTATTTGAAATCT 59.073 37.037 0.00 0.00 0.00 2.40
133 134 7.924412 TCCGTATGTGGTAGTCTATTTGAAATC 59.076 37.037 0.00 0.00 0.00 2.17
134 135 7.788026 TCCGTATGTGGTAGTCTATTTGAAAT 58.212 34.615 0.00 0.00 0.00 2.17
135 136 7.172868 TCCGTATGTGGTAGTCTATTTGAAA 57.827 36.000 0.00 0.00 0.00 2.69
136 137 6.778834 TCCGTATGTGGTAGTCTATTTGAA 57.221 37.500 0.00 0.00 0.00 2.69
137 138 6.322969 ACATCCGTATGTGGTAGTCTATTTGA 59.677 38.462 0.00 0.00 44.79 2.69
138 139 6.513180 ACATCCGTATGTGGTAGTCTATTTG 58.487 40.000 0.00 0.00 44.79 2.32
139 140 6.726490 ACATCCGTATGTGGTAGTCTATTT 57.274 37.500 0.00 0.00 44.79 1.40
140 141 6.774170 TGTACATCCGTATGTGGTAGTCTATT 59.226 38.462 3.56 0.00 45.99 1.73
141 142 6.301486 TGTACATCCGTATGTGGTAGTCTAT 58.699 40.000 3.56 0.00 45.99 1.98
142 143 5.683681 TGTACATCCGTATGTGGTAGTCTA 58.316 41.667 3.56 0.00 45.99 2.59
143 144 4.529897 TGTACATCCGTATGTGGTAGTCT 58.470 43.478 3.56 0.00 45.99 3.24
144 145 4.906065 TGTACATCCGTATGTGGTAGTC 57.094 45.455 3.56 0.00 45.99 2.59
145 146 6.206243 GTCTATGTACATCCGTATGTGGTAGT 59.794 42.308 12.68 0.00 45.99 2.73
146 147 6.206048 TGTCTATGTACATCCGTATGTGGTAG 59.794 42.308 12.68 0.00 45.99 3.18
147 148 6.063404 TGTCTATGTACATCCGTATGTGGTA 58.937 40.000 12.68 0.00 45.99 3.25
148 149 4.891168 TGTCTATGTACATCCGTATGTGGT 59.109 41.667 12.68 0.00 45.99 4.16
149 150 5.447624 TGTCTATGTACATCCGTATGTGG 57.552 43.478 12.68 0.00 45.99 4.17
150 151 9.639601 AAATATGTCTATGTACATCCGTATGTG 57.360 33.333 12.68 0.00 45.99 3.21
181 182 5.412594 TGGAGCAAAATGAGTGAATCTACAC 59.587 40.000 0.00 0.00 40.60 2.90
182 183 5.559770 TGGAGCAAAATGAGTGAATCTACA 58.440 37.500 0.00 0.00 0.00 2.74
183 184 6.690194 ATGGAGCAAAATGAGTGAATCTAC 57.310 37.500 0.00 0.00 0.00 2.59
184 185 7.994911 ACATATGGAGCAAAATGAGTGAATCTA 59.005 33.333 7.80 0.00 0.00 1.98
185 186 6.832384 ACATATGGAGCAAAATGAGTGAATCT 59.168 34.615 7.80 0.00 0.00 2.40
186 187 7.035840 ACATATGGAGCAAAATGAGTGAATC 57.964 36.000 7.80 0.00 0.00 2.52
187 188 7.776969 ACTACATATGGAGCAAAATGAGTGAAT 59.223 33.333 15.30 0.00 0.00 2.57
188 189 7.112122 ACTACATATGGAGCAAAATGAGTGAA 58.888 34.615 15.30 0.00 0.00 3.18
189 190 6.653020 ACTACATATGGAGCAAAATGAGTGA 58.347 36.000 15.30 0.00 0.00 3.41
190 191 6.539826 TGACTACATATGGAGCAAAATGAGTG 59.460 38.462 15.30 0.00 0.00 3.51
191 192 6.540189 GTGACTACATATGGAGCAAAATGAGT 59.460 38.462 15.30 0.00 0.00 3.41
192 193 6.765036 AGTGACTACATATGGAGCAAAATGAG 59.235 38.462 15.30 0.00 0.00 2.90
193 194 6.653020 AGTGACTACATATGGAGCAAAATGA 58.347 36.000 15.30 0.00 0.00 2.57
194 195 6.932356 AGTGACTACATATGGAGCAAAATG 57.068 37.500 15.30 0.00 0.00 2.32
195 196 7.944729 AAAGTGACTACATATGGAGCAAAAT 57.055 32.000 15.30 0.00 0.00 1.82
196 197 7.759489 AAAAGTGACTACATATGGAGCAAAA 57.241 32.000 15.30 0.00 0.00 2.44
197 198 7.446931 TCAAAAAGTGACTACATATGGAGCAAA 59.553 33.333 15.30 0.00 0.00 3.68
198 199 6.939730 TCAAAAAGTGACTACATATGGAGCAA 59.060 34.615 15.30 0.16 0.00 3.91
199 200 6.472016 TCAAAAAGTGACTACATATGGAGCA 58.528 36.000 15.30 10.95 0.00 4.26
200 201 6.985188 TCAAAAAGTGACTACATATGGAGC 57.015 37.500 15.30 8.47 0.00 4.70
201 202 9.994432 GATTTCAAAAAGTGACTACATATGGAG 57.006 33.333 13.77 13.77 35.39 3.86
202 203 9.739276 AGATTTCAAAAAGTGACTACATATGGA 57.261 29.630 7.80 0.00 35.39 3.41
203 204 9.994432 GAGATTTCAAAAAGTGACTACATATGG 57.006 33.333 7.80 0.00 35.39 2.74
211 212 9.838339 TCTTTCTAGAGATTTCAAAAAGTGACT 57.162 29.630 0.00 0.00 35.39 3.41
212 213 9.871299 GTCTTTCTAGAGATTTCAAAAAGTGAC 57.129 33.333 0.00 0.00 35.39 3.67
213 214 9.613428 TGTCTTTCTAGAGATTTCAAAAAGTGA 57.387 29.630 0.00 0.00 0.00 3.41
227 228 9.291664 CGTTCCTAAATACTTGTCTTTCTAGAG 57.708 37.037 0.00 0.00 0.00 2.43
228 229 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
229 230 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
230 231 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
231 232 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
232 233 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
233 234 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
234 235 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
235 236 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
236 237 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
237 238 4.081254 GTCCCTCCGTTCCTAAATACTTGT 60.081 45.833 0.00 0.00 0.00 3.16
238 239 4.161754 AGTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
239 240 4.359996 AGTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
240 241 3.991683 AGTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
241 242 6.416631 AATAGTCCCTCCGTTCCTAAATAC 57.583 41.667 0.00 0.00 0.00 1.89
242 243 7.234166 CCTAAATAGTCCCTCCGTTCCTAAATA 59.766 40.741 0.00 0.00 0.00 1.40
243 244 5.970501 AAATAGTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
244 245 5.364735 CCTAAATAGTCCCTCCGTTCCTAAA 59.635 44.000 0.00 0.00 0.00 1.85
245 246 4.897670 CCTAAATAGTCCCTCCGTTCCTAA 59.102 45.833 0.00 0.00 0.00 2.69
246 247 4.168675 TCCTAAATAGTCCCTCCGTTCCTA 59.831 45.833 0.00 0.00 0.00 2.94
247 248 3.052338 TCCTAAATAGTCCCTCCGTTCCT 60.052 47.826 0.00 0.00 0.00 3.36
248 249 3.303049 TCCTAAATAGTCCCTCCGTTCC 58.697 50.000 0.00 0.00 0.00 3.62
249 250 4.691175 GTTCCTAAATAGTCCCTCCGTTC 58.309 47.826 0.00 0.00 0.00 3.95
250 251 3.131755 CGTTCCTAAATAGTCCCTCCGTT 59.868 47.826 0.00 0.00 0.00 4.44
251 252 2.692041 CGTTCCTAAATAGTCCCTCCGT 59.308 50.000 0.00 0.00 0.00 4.69
252 253 2.035576 CCGTTCCTAAATAGTCCCTCCG 59.964 54.545 0.00 0.00 0.00 4.63
253 254 3.303049 TCCGTTCCTAAATAGTCCCTCC 58.697 50.000 0.00 0.00 0.00 4.30
254 255 3.321396 CCTCCGTTCCTAAATAGTCCCTC 59.679 52.174 0.00 0.00 0.00 4.30
255 256 3.306613 CCTCCGTTCCTAAATAGTCCCT 58.693 50.000 0.00 0.00 0.00 4.20
256 257 2.367894 CCCTCCGTTCCTAAATAGTCCC 59.632 54.545 0.00 0.00 0.00 4.46
257 258 3.303049 TCCCTCCGTTCCTAAATAGTCC 58.697 50.000 0.00 0.00 0.00 3.85
258 259 3.959449 ACTCCCTCCGTTCCTAAATAGTC 59.041 47.826 0.00 0.00 0.00 2.59
259 260 3.991683 ACTCCCTCCGTTCCTAAATAGT 58.008 45.455 0.00 0.00 0.00 2.12
260 261 7.957992 ATATACTCCCTCCGTTCCTAAATAG 57.042 40.000 0.00 0.00 0.00 1.73
262 263 8.912614 ATTATATACTCCCTCCGTTCCTAAAT 57.087 34.615 0.00 0.00 0.00 1.40
263 264 9.827198 TTATTATATACTCCCTCCGTTCCTAAA 57.173 33.333 0.00 0.00 0.00 1.85
264 265 9.247861 GTTATTATATACTCCCTCCGTTCCTAA 57.752 37.037 0.00 0.00 0.00 2.69
265 266 8.393259 TGTTATTATATACTCCCTCCGTTCCTA 58.607 37.037 0.00 0.00 0.00 2.94
266 267 7.243824 TGTTATTATATACTCCCTCCGTTCCT 58.756 38.462 0.00 0.00 0.00 3.36
267 268 7.472334 TGTTATTATATACTCCCTCCGTTCC 57.528 40.000 0.00 0.00 0.00 3.62
285 286 9.687210 TTCTACGCGATGAGTTATTATGTTATT 57.313 29.630 15.93 0.00 0.00 1.40
286 287 9.343103 CTTCTACGCGATGAGTTATTATGTTAT 57.657 33.333 15.93 0.00 0.00 1.89
287 288 8.347771 ACTTCTACGCGATGAGTTATTATGTTA 58.652 33.333 15.93 0.00 0.00 2.41
288 289 7.201145 ACTTCTACGCGATGAGTTATTATGTT 58.799 34.615 15.93 0.00 0.00 2.71
289 290 6.736123 ACTTCTACGCGATGAGTTATTATGT 58.264 36.000 15.93 0.00 0.00 2.29
290 291 6.856426 TGACTTCTACGCGATGAGTTATTATG 59.144 38.462 15.93 0.00 0.00 1.90
291 292 6.967135 TGACTTCTACGCGATGAGTTATTAT 58.033 36.000 15.93 0.00 0.00 1.28
292 293 6.367686 TGACTTCTACGCGATGAGTTATTA 57.632 37.500 15.93 0.00 0.00 0.98
293 294 5.244785 TGACTTCTACGCGATGAGTTATT 57.755 39.130 15.93 0.00 0.00 1.40
294 295 4.261238 CCTGACTTCTACGCGATGAGTTAT 60.261 45.833 15.93 0.00 0.00 1.89
295 296 3.064958 CCTGACTTCTACGCGATGAGTTA 59.935 47.826 15.93 7.02 0.00 2.24
296 297 2.159366 CCTGACTTCTACGCGATGAGTT 60.159 50.000 15.93 0.67 0.00 3.01
297 298 1.402259 CCTGACTTCTACGCGATGAGT 59.598 52.381 15.93 11.08 0.00 3.41
298 299 1.402259 ACCTGACTTCTACGCGATGAG 59.598 52.381 15.93 7.15 0.00 2.90
299 300 1.460504 ACCTGACTTCTACGCGATGA 58.539 50.000 15.93 7.51 0.00 2.92
300 301 2.287069 CCTACCTGACTTCTACGCGATG 60.287 54.545 15.93 4.70 0.00 3.84
301 302 1.948145 CCTACCTGACTTCTACGCGAT 59.052 52.381 15.93 0.00 0.00 4.58
302 303 1.376543 CCTACCTGACTTCTACGCGA 58.623 55.000 15.93 0.00 0.00 5.87
303 304 0.248539 GCCTACCTGACTTCTACGCG 60.249 60.000 3.53 3.53 0.00 6.01
304 305 0.102663 GGCCTACCTGACTTCTACGC 59.897 60.000 0.00 0.00 0.00 4.42
305 306 1.471119 TGGCCTACCTGACTTCTACG 58.529 55.000 3.32 0.00 36.63 3.51
306 307 5.609533 TTAATGGCCTACCTGACTTCTAC 57.390 43.478 3.32 0.00 36.63 2.59
483 796 3.639716 TTCATCAACGCTGAAATTGCA 57.360 38.095 0.00 0.00 34.49 4.08
484 797 4.877942 CAATTCATCAACGCTGAAATTGC 58.122 39.130 11.13 0.00 34.98 3.56
485 798 4.386350 TGCAATTCATCAACGCTGAAATTG 59.614 37.500 16.36 16.36 40.08 2.32
489 802 2.813172 TCTGCAATTCATCAACGCTGAA 59.187 40.909 0.00 0.00 37.06 3.02
558 871 5.146010 AGGATGAGCTACTTATGCTTAGC 57.854 43.478 0.00 0.00 41.30 3.09
575 888 1.673033 GGAGTGACACCGTCAAGGATG 60.673 57.143 0.84 0.00 44.49 3.51
595 908 9.740239 CATCTTATTTGGAATCTTGTGTTATGG 57.260 33.333 0.00 0.00 0.00 2.74
635 948 0.394899 CATCTTGGGTCCAGCCTTCC 60.395 60.000 0.00 0.00 37.43 3.46
745 1059 1.072331 GATGGGTACTGCCATAGTGGG 59.928 57.143 3.86 0.00 40.65 4.61
794 1109 3.317149 TGCAAGCAGATCAAGGATTATGC 59.683 43.478 0.00 8.47 36.19 3.14
963 1314 0.905357 TGGGAGTTGGAAGCTCTAGC 59.095 55.000 0.00 0.00 42.49 3.42
1071 1424 2.292016 TGTTGTTGCCGTCATGGTAAAG 59.708 45.455 0.00 0.00 44.51 1.85
1072 1425 2.292016 CTGTTGTTGCCGTCATGGTAAA 59.708 45.455 0.00 0.00 44.51 2.01
1123 1507 1.892819 ATGACACAGTGGCCCTCTCG 61.893 60.000 3.17 0.00 0.00 4.04
1306 1693 1.907936 AGAGGCACTTCTTCTGAGCAT 59.092 47.619 0.00 0.00 41.55 3.79
1394 1782 5.124457 CAGACAATAACATGCTGGCTAACTT 59.876 40.000 0.00 0.00 0.00 2.66
1461 1852 4.162320 TCTTTCCTGCTTCCTACATCGAAT 59.838 41.667 0.00 0.00 0.00 3.34
1475 1866 3.563390 GCATAGAACATCCTCTTTCCTGC 59.437 47.826 0.00 0.00 0.00 4.85
1516 1907 4.671964 GGTGTTTGTAACCGTTTTTCGATC 59.328 41.667 0.00 0.00 42.86 3.69
1538 1942 2.589798 TATAAACGCTGGAGGAACGG 57.410 50.000 0.00 0.00 0.00 4.44
1603 2007 5.091431 GTGCAGAAGAATATGTTGAGTTGC 58.909 41.667 0.00 0.00 0.00 4.17
1607 2011 6.492007 AACTGTGCAGAAGAATATGTTGAG 57.508 37.500 6.17 0.00 0.00 3.02
1638 2042 6.877611 TCTTTGTAAATTTCTGGGTCTGAC 57.122 37.500 0.00 0.00 0.00 3.51
1675 2079 4.389992 GCTCATTCGTGAACATTTCTCTGA 59.610 41.667 0.00 0.00 0.00 3.27
1772 6161 4.558226 AGCACAATCTTGTACTGGATCA 57.442 40.909 0.00 0.00 39.91 2.92
1785 6174 6.705863 AGGATCCTAATGAAAAGCACAATC 57.294 37.500 14.27 0.00 0.00 2.67
1877 6267 3.218470 AGCGCTTTGGTTGCTGCA 61.218 55.556 2.64 0.00 37.62 4.41
1956 6347 2.591571 AAATTAGGTACGACGGCCTC 57.408 50.000 15.03 0.00 36.38 4.70
1961 6352 3.255725 TGCTGGAAAATTAGGTACGACG 58.744 45.455 0.00 0.00 0.00 5.12
1962 6353 5.050295 GCTATGCTGGAAAATTAGGTACGAC 60.050 44.000 0.00 0.00 0.00 4.34
1968 6359 3.904136 CGGCTATGCTGGAAAATTAGG 57.096 47.619 0.00 0.00 0.00 2.69
1980 6371 2.664518 GCAGCTCTCCGGCTATGC 60.665 66.667 0.00 0.00 41.00 3.14
1981 6372 2.030262 GGCAGCTCTCCGGCTATG 59.970 66.667 0.00 0.00 41.00 2.23
1987 6378 0.392193 ATGAACTTGGCAGCTCTCCG 60.392 55.000 0.00 0.00 0.00 4.63
2022 6413 6.420903 TGTCTTTCGTCTGATCTTGTTGTAAG 59.579 38.462 0.00 0.00 0.00 2.34
2113 6505 1.686587 CCTCGATGGCATGGTAGTGTA 59.313 52.381 3.81 0.00 0.00 2.90
2120 6512 1.334869 GCTTAAACCTCGATGGCATGG 59.665 52.381 3.81 3.19 40.22 3.66
2121 6513 1.334869 GGCTTAAACCTCGATGGCATG 59.665 52.381 3.81 0.00 40.22 4.06
2125 6517 1.954927 GAGGGCTTAAACCTCGATGG 58.045 55.000 9.42 0.00 44.50 3.51
2162 6556 2.309613 TGCCAAATTCTCAAGCACTGT 58.690 42.857 0.00 0.00 0.00 3.55
2192 6586 4.589908 AGTCAACGGGAATTTGAAGCTAT 58.410 39.130 0.00 0.00 34.78 2.97
2218 6613 5.220209 GGAAGACGTTTGCAAAACTTGAAAG 60.220 40.000 22.84 4.82 27.89 2.62
2255 6650 6.538742 GCCTGCTAGTCAGTAAATATGTTTCA 59.461 38.462 11.57 0.00 41.25 2.69
2261 6656 5.600484 AGTCAGCCTGCTAGTCAGTAAATAT 59.400 40.000 11.57 0.00 41.25 1.28
2262 6657 4.956700 AGTCAGCCTGCTAGTCAGTAAATA 59.043 41.667 11.57 0.00 41.25 1.40
2266 6661 2.516227 AGTCAGCCTGCTAGTCAGTA 57.484 50.000 11.57 0.00 41.25 2.74
2297 6692 5.475273 TGATAAGATTCAGCAAGCTTTCG 57.525 39.130 0.00 0.00 39.08 3.46
2331 6726 2.095768 GCATCTTTTGCGTTGCTACTCA 60.096 45.455 0.00 0.00 42.54 3.41
2393 6790 4.933505 TCTCATCTTAGCAGATCAGTGG 57.066 45.455 0.00 0.00 37.71 4.00
2399 6796 9.103582 AGATCCTATTTTCTCATCTTAGCAGAT 57.896 33.333 0.00 0.00 40.79 2.90


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

AutoCloner maintained by Alex Coulton.