Multiple sequence alignment - TraesCS3B01G553800

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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 TraesCS3B01G553800 chr3B 100.000 2465 0 0 1 2465 788059587 788057123 0.000000e+00 4553.0
1 TraesCS3B01G553800 chr3B 85.312 994 87 33 799 1747 787990008 787990987 0.000000e+00 972.0
2 TraesCS3B01G553800 chr3B 85.321 981 89 31 802 1741 787472342 787473308 0.000000e+00 963.0
3 TraesCS3B01G553800 chr3B 83.590 780 97 22 989 1746 788073572 788072802 0.000000e+00 702.0
4 TraesCS3B01G553800 chr3B 89.662 503 47 5 1965 2462 787992087 787992589 9.620000e-179 636.0
5 TraesCS3B01G553800 chr3B 82.992 635 74 17 989 1600 787995500 787996123 6.000000e-151 544.0
6 TraesCS3B01G553800 chr3B 91.071 392 29 4 4 389 787988527 787988136 2.170000e-145 525.0
7 TraesCS3B01G553800 chr3B 90.909 396 28 4 1 389 788078908 788079302 2.170000e-145 525.0
8 TraesCS3B01G553800 chr3B 86.560 439 43 7 1316 1743 787991337 787991770 1.030000e-128 470.0
9 TraesCS3B01G553800 chr3B 99.571 233 1 0 161 393 788060639 788060871 2.270000e-115 425.0
10 TraesCS3B01G553800 chr3B 88.450 329 20 6 442 770 787989393 787989703 4.970000e-102 381.0
11 TraesCS3B01G553800 chr3B 80.627 351 43 20 1418 1746 788067727 788067380 5.260000e-62 248.0
12 TraesCS3B01G553800 chr3B 92.857 168 12 0 448 615 788078028 788077861 6.810000e-61 244.0
13 TraesCS3B01G553800 chr3B 87.387 111 10 4 1751 1860 145697120 145697013 9.260000e-25 124.0
14 TraesCS3B01G553800 chr3A 88.245 1157 93 16 802 1936 719354280 719353145 0.000000e+00 1343.0
15 TraesCS3B01G553800 chr3A 91.107 506 40 2 1965 2465 719353058 719352553 0.000000e+00 680.0
16 TraesCS3B01G553800 chr3A 82.943 768 89 27 989 1746 719337323 719336588 0.000000e+00 654.0
17 TraesCS3B01G553800 chr3A 89.463 503 49 4 1965 2465 719359985 719359485 1.240000e-177 632.0
18 TraesCS3B01G553800 chr3A 85.842 558 67 6 989 1544 719350076 719349529 1.270000e-162 582.0
19 TraesCS3B01G553800 chr3A 90.365 301 25 2 448 748 719354866 719354570 2.300000e-105 392.0
20 TraesCS3B01G553800 chr3D 86.192 956 92 22 991 1936 589572851 589571926 0.000000e+00 998.0
21 TraesCS3B01G553800 chr3D 84.458 978 93 32 804 1748 589433006 589432055 0.000000e+00 909.0
22 TraesCS3B01G553800 chr3D 88.467 737 57 13 875 1591 589506111 589505383 0.000000e+00 865.0
23 TraesCS3B01G553800 chr3D 83.590 780 83 32 989 1736 589417750 589416984 0.000000e+00 689.0
24 TraesCS3B01G553800 chr3D 88.556 367 23 8 1965 2331 589571834 589571487 6.300000e-116 427.0
25 TraesCS3B01G553800 chr3D 89.557 316 28 3 432 747 589437535 589437225 1.780000e-106 396.0
26 TraesCS3B01G553800 chr3D 89.474 285 29 1 448 732 589563888 589563605 2.330000e-95 359.0
27 TraesCS3B01G553800 chr3D 90.295 237 17 1 448 678 589493969 589493733 3.080000e-79 305.0
28 TraesCS3B01G553800 chr3D 94.245 139 7 1 2327 2465 589569606 589569469 6.910000e-51 211.0
29 TraesCS3B01G553800 chr3D 84.390 205 13 8 802 988 589417982 589417779 1.510000e-42 183.0
30 TraesCS3B01G553800 chr3D 79.570 186 20 8 802 971 589573094 589572911 1.550000e-22 117.0
31 TraesCS3B01G553800 chr3D 97.727 44 1 0 702 745 589493734 589493691 2.630000e-10 76.8
32 TraesCS3B01G553800 chr2D 89.286 112 11 1 1751 1862 24923758 24923648 3.310000e-29 139.0
33 TraesCS3B01G553800 chr1D 86.992 123 15 1 1740 1862 221874265 221874144 1.190000e-28 137.0
34 TraesCS3B01G553800 chr2A 89.720 107 10 1 1751 1857 155753160 155753055 4.280000e-28 135.0
35 TraesCS3B01G553800 chr7D 87.500 112 12 2 1751 1862 256228098 256227989 7.160000e-26 128.0
36 TraesCS3B01G553800 chr6B 85.484 124 16 2 1740 1862 711762372 711762250 7.160000e-26 128.0
37 TraesCS3B01G553800 chr6D 85.124 121 17 1 1742 1862 17203489 17203370 3.330000e-24 122.0


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 TraesCS3B01G553800 chr3B 788057123 788059587 2464 True 4553.00 4553 100.00000 1 2465 1 chr3B.!!$R3 2464
1 TraesCS3B01G553800 chr3B 787472342 787473308 966 False 963.00 963 85.32100 802 1741 1 chr3B.!!$F1 939
2 TraesCS3B01G553800 chr3B 788072802 788073572 770 True 702.00 702 83.59000 989 1746 1 chr3B.!!$R5 757
3 TraesCS3B01G553800 chr3B 787989393 787996123 6730 False 600.60 972 86.59520 442 2462 5 chr3B.!!$F4 2020
4 TraesCS3B01G553800 chr3A 719349529 719354866 5337 True 749.25 1343 88.88975 448 2465 4 chr3A.!!$R3 2017
5 TraesCS3B01G553800 chr3A 719336588 719337323 735 True 654.00 654 82.94300 989 1746 1 chr3A.!!$R1 757
6 TraesCS3B01G553800 chr3A 719359485 719359985 500 True 632.00 632 89.46300 1965 2465 1 chr3A.!!$R2 500
7 TraesCS3B01G553800 chr3D 589432055 589433006 951 True 909.00 909 84.45800 804 1748 1 chr3D.!!$R1 944
8 TraesCS3B01G553800 chr3D 589505383 589506111 728 True 865.00 865 88.46700 875 1591 1 chr3D.!!$R3 716
9 TraesCS3B01G553800 chr3D 589569469 589573094 3625 True 438.25 998 87.14075 802 2465 4 chr3D.!!$R7 1663
10 TraesCS3B01G553800 chr3D 589416984 589417982 998 True 436.00 689 83.99000 802 1736 2 chr3D.!!$R5 934

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
415 416 0.03601 ATCTGTGGCTAGGTGTGCAC 60.036 55.0 10.75 10.75 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 2967 0.18135 GGTTTGGAGCCGAGGATGAT 59.819 55.0 0.0 0.0 0.0 2.45 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
60 61 7.733402 AAAAACTCATGCATGCTAAACAAAT 57.267 28.000 22.25 0.00 0.00 2.32
61 62 8.830201 AAAAACTCATGCATGCTAAACAAATA 57.170 26.923 22.25 0.00 0.00 1.40
62 63 8.830201 AAAACTCATGCATGCTAAACAAATAA 57.170 26.923 22.25 0.00 0.00 1.40
63 64 9.439500 AAAACTCATGCATGCTAAACAAATAAT 57.561 25.926 22.25 0.00 0.00 1.28
66 67 9.687210 ACTCATGCATGCTAAACAAATAATATG 57.313 29.630 22.25 9.18 0.00 1.78
67 68 9.902196 CTCATGCATGCTAAACAAATAATATGA 57.098 29.630 22.25 12.88 0.00 2.15
106 107 9.685276 ATACCAACAATAGAGAATTCATGTTCA 57.315 29.630 8.44 0.52 29.87 3.18
107 108 8.408043 ACCAACAATAGAGAATTCATGTTCAA 57.592 30.769 8.44 0.00 29.87 2.69
108 109 8.859090 ACCAACAATAGAGAATTCATGTTCAAA 58.141 29.630 8.44 0.00 29.87 2.69
109 110 9.350357 CCAACAATAGAGAATTCATGTTCAAAG 57.650 33.333 8.44 0.46 29.87 2.77
112 113 9.288576 ACAATAGAGAATTCATGTTCAAAGACA 57.711 29.630 8.44 0.00 0.00 3.41
115 116 9.730705 ATAGAGAATTCATGTTCAAAGACAAGA 57.269 29.630 8.44 0.00 32.47 3.02
116 117 8.455903 AGAGAATTCATGTTCAAAGACAAGAA 57.544 30.769 8.44 0.00 40.27 2.52
117 118 8.906867 AGAGAATTCATGTTCAAAGACAAGAAA 58.093 29.630 8.44 0.00 39.67 2.52
118 119 9.178427 GAGAATTCATGTTCAAAGACAAGAAAG 57.822 33.333 8.44 0.00 39.67 2.62
119 120 8.139989 AGAATTCATGTTCAAAGACAAGAAAGG 58.860 33.333 8.44 0.00 39.67 3.11
120 121 7.587037 ATTCATGTTCAAAGACAAGAAAGGA 57.413 32.000 0.00 0.00 39.67 3.36
121 122 7.403312 TTCATGTTCAAAGACAAGAAAGGAA 57.597 32.000 0.00 0.00 35.18 3.36
122 123 7.403312 TCATGTTCAAAGACAAGAAAGGAAA 57.597 32.000 0.00 0.00 32.47 3.13
123 124 7.835822 TCATGTTCAAAGACAAGAAAGGAAAA 58.164 30.769 0.00 0.00 32.47 2.29
124 125 8.477256 TCATGTTCAAAGACAAGAAAGGAAAAT 58.523 29.630 0.00 0.00 32.47 1.82
125 126 9.101655 CATGTTCAAAGACAAGAAAGGAAAATT 57.898 29.630 0.00 0.00 32.47 1.82
126 127 9.671279 ATGTTCAAAGACAAGAAAGGAAAATTT 57.329 25.926 0.00 0.00 32.47 1.82
127 128 9.500785 TGTTCAAAGACAAGAAAGGAAAATTTT 57.499 25.926 2.28 2.28 0.00 1.82
128 129 9.759259 GTTCAAAGACAAGAAAGGAAAATTTTG 57.241 29.630 8.47 0.00 0.00 2.44
129 130 8.491331 TCAAAGACAAGAAAGGAAAATTTTGG 57.509 30.769 8.47 0.00 0.00 3.28
130 131 8.100164 TCAAAGACAAGAAAGGAAAATTTTGGT 58.900 29.630 8.47 0.00 0.00 3.67
131 132 9.377312 CAAAGACAAGAAAGGAAAATTTTGGTA 57.623 29.630 8.47 0.00 0.00 3.25
132 133 9.599866 AAAGACAAGAAAGGAAAATTTTGGTAG 57.400 29.630 8.47 0.00 0.00 3.18
133 134 7.726216 AGACAAGAAAGGAAAATTTTGGTAGG 58.274 34.615 8.47 0.00 0.00 3.18
134 135 7.563556 AGACAAGAAAGGAAAATTTTGGTAGGA 59.436 33.333 8.47 0.00 0.00 2.94
135 136 8.084985 ACAAGAAAGGAAAATTTTGGTAGGAA 57.915 30.769 8.47 0.00 0.00 3.36
136 137 7.985184 ACAAGAAAGGAAAATTTTGGTAGGAAC 59.015 33.333 8.47 0.00 0.00 3.62
137 138 7.669089 AGAAAGGAAAATTTTGGTAGGAACA 57.331 32.000 8.47 0.00 0.00 3.18
138 139 8.262601 AGAAAGGAAAATTTTGGTAGGAACAT 57.737 30.769 8.47 0.00 0.00 2.71
139 140 9.374711 AGAAAGGAAAATTTTGGTAGGAACATA 57.625 29.630 8.47 0.00 0.00 2.29
140 141 9.419297 GAAAGGAAAATTTTGGTAGGAACATAC 57.581 33.333 8.47 0.00 0.00 2.39
141 142 7.476540 AGGAAAATTTTGGTAGGAACATACC 57.523 36.000 8.47 8.46 44.73 2.73
151 152 4.866486 GGTAGGAACATACCACTGTTAACG 59.134 45.833 10.21 0.00 44.04 3.18
152 153 4.877378 AGGAACATACCACTGTTAACGA 57.123 40.909 0.26 0.00 39.40 3.85
153 154 4.817517 AGGAACATACCACTGTTAACGAG 58.182 43.478 0.26 2.63 39.40 4.18
154 155 4.282703 AGGAACATACCACTGTTAACGAGT 59.717 41.667 0.26 3.25 39.40 4.18
155 156 4.624452 GGAACATACCACTGTTAACGAGTC 59.376 45.833 0.26 0.00 39.40 3.36
156 157 4.859304 ACATACCACTGTTAACGAGTCA 57.141 40.909 0.26 0.00 0.00 3.41
157 158 4.806330 ACATACCACTGTTAACGAGTCAG 58.194 43.478 0.26 0.00 35.60 3.51
158 159 4.521639 ACATACCACTGTTAACGAGTCAGA 59.478 41.667 0.26 0.00 33.93 3.27
159 160 3.644884 ACCACTGTTAACGAGTCAGAG 57.355 47.619 0.26 0.00 33.93 3.35
160 161 2.288273 ACCACTGTTAACGAGTCAGAGC 60.288 50.000 0.26 0.00 33.93 4.09
161 162 2.029828 CCACTGTTAACGAGTCAGAGCT 60.030 50.000 0.26 0.00 33.93 4.09
162 163 2.983136 CACTGTTAACGAGTCAGAGCTG 59.017 50.000 0.00 0.00 33.93 4.24
163 164 2.885266 ACTGTTAACGAGTCAGAGCTGA 59.115 45.455 0.00 0.00 37.24 4.26
164 165 3.057876 ACTGTTAACGAGTCAGAGCTGAG 60.058 47.826 0.00 0.00 40.75 3.35
165 166 2.229062 TGTTAACGAGTCAGAGCTGAGG 59.771 50.000 0.00 0.00 40.75 3.86
166 167 2.488545 GTTAACGAGTCAGAGCTGAGGA 59.511 50.000 0.00 0.00 40.75 3.71
167 168 1.621992 AACGAGTCAGAGCTGAGGAA 58.378 50.000 0.00 0.00 40.75 3.36
168 169 1.173043 ACGAGTCAGAGCTGAGGAAG 58.827 55.000 0.00 0.00 40.75 3.46
169 170 0.455410 CGAGTCAGAGCTGAGGAAGG 59.545 60.000 0.00 0.00 40.75 3.46
170 171 1.555967 GAGTCAGAGCTGAGGAAGGT 58.444 55.000 0.00 0.00 40.75 3.50
171 172 1.899142 GAGTCAGAGCTGAGGAAGGTT 59.101 52.381 0.00 0.00 40.75 3.50
172 173 2.301583 GAGTCAGAGCTGAGGAAGGTTT 59.698 50.000 0.00 0.00 40.75 3.27
173 174 2.301583 AGTCAGAGCTGAGGAAGGTTTC 59.698 50.000 0.00 0.00 40.75 2.78
174 175 1.273606 TCAGAGCTGAGGAAGGTTTCG 59.726 52.381 0.00 0.00 36.52 3.46
175 176 1.273606 CAGAGCTGAGGAAGGTTTCGA 59.726 52.381 0.00 0.00 36.52 3.71
176 177 1.273886 AGAGCTGAGGAAGGTTTCGAC 59.726 52.381 0.00 0.00 36.52 4.20
177 178 0.038159 AGCTGAGGAAGGTTTCGACG 60.038 55.000 0.00 0.00 30.45 5.12
178 179 0.038526 GCTGAGGAAGGTTTCGACGA 60.039 55.000 0.00 0.00 0.00 4.20
179 180 1.699343 CTGAGGAAGGTTTCGACGAC 58.301 55.000 0.00 0.00 0.00 4.34
180 181 1.000607 CTGAGGAAGGTTTCGACGACA 60.001 52.381 0.00 0.00 0.00 4.35
181 182 1.409790 TGAGGAAGGTTTCGACGACAA 59.590 47.619 0.00 0.00 0.00 3.18
182 183 2.036733 TGAGGAAGGTTTCGACGACAAT 59.963 45.455 0.00 0.00 0.00 2.71
183 184 2.666994 GAGGAAGGTTTCGACGACAATC 59.333 50.000 0.00 0.00 0.00 2.67
184 185 2.299297 AGGAAGGTTTCGACGACAATCT 59.701 45.455 0.00 0.00 0.00 2.40
185 186 3.508793 AGGAAGGTTTCGACGACAATCTA 59.491 43.478 0.00 0.00 0.00 1.98
186 187 4.021719 AGGAAGGTTTCGACGACAATCTAA 60.022 41.667 0.00 0.00 0.00 2.10
187 188 4.868734 GGAAGGTTTCGACGACAATCTAAT 59.131 41.667 0.00 0.00 0.00 1.73
188 189 5.350640 GGAAGGTTTCGACGACAATCTAATT 59.649 40.000 0.00 0.00 0.00 1.40
189 190 5.779806 AGGTTTCGACGACAATCTAATTG 57.220 39.130 0.00 0.00 45.59 2.32
205 206 9.979270 CAATCTAATTGTTCTCACTTGATACAC 57.021 33.333 0.00 0.00 35.57 2.90
206 207 9.725019 AATCTAATTGTTCTCACTTGATACACA 57.275 29.630 0.00 0.00 0.00 3.72
207 208 9.896645 ATCTAATTGTTCTCACTTGATACACAT 57.103 29.630 0.00 0.00 0.00 3.21
211 212 9.725019 AATTGTTCTCACTTGATACACATAAGA 57.275 29.630 0.00 0.00 0.00 2.10
212 213 9.725019 ATTGTTCTCACTTGATACACATAAGAA 57.275 29.630 0.00 0.00 0.00 2.52
213 214 8.534333 TGTTCTCACTTGATACACATAAGAAC 57.466 34.615 0.00 0.00 40.12 3.01
214 215 8.367911 TGTTCTCACTTGATACACATAAGAACT 58.632 33.333 11.36 0.00 40.27 3.01
215 216 9.856488 GTTCTCACTTGATACACATAAGAACTA 57.144 33.333 0.00 0.00 37.92 2.24
218 219 8.648557 TCACTTGATACACATAAGAACTATGC 57.351 34.615 0.00 0.00 41.13 3.14
219 220 8.478066 TCACTTGATACACATAAGAACTATGCT 58.522 33.333 0.00 0.00 41.13 3.79
220 221 9.102757 CACTTGATACACATAAGAACTATGCTT 57.897 33.333 0.00 0.00 41.13 3.91
221 222 9.672673 ACTTGATACACATAAGAACTATGCTTT 57.327 29.630 0.00 0.00 41.13 3.51
224 225 9.665719 TGATACACATAAGAACTATGCTTTTCA 57.334 29.630 0.00 0.00 41.13 2.69
264 265 8.700973 AGATAGTCTGATTTTCTAGAAACCTCC 58.299 37.037 17.51 7.67 0.00 4.30
265 266 6.688073 AGTCTGATTTTCTAGAAACCTCCA 57.312 37.500 17.51 11.33 0.00 3.86
266 267 7.079451 AGTCTGATTTTCTAGAAACCTCCAA 57.921 36.000 17.51 2.48 0.00 3.53
267 268 7.518188 AGTCTGATTTTCTAGAAACCTCCAAA 58.482 34.615 17.51 1.74 0.00 3.28
268 269 8.166726 AGTCTGATTTTCTAGAAACCTCCAAAT 58.833 33.333 17.51 6.70 0.00 2.32
269 270 8.797438 GTCTGATTTTCTAGAAACCTCCAAATT 58.203 33.333 17.51 0.00 0.00 1.82
297 298 9.944663 TTGTTAGATTCATACACTTTGAAACAC 57.055 29.630 0.00 0.00 36.72 3.32
298 299 9.337396 TGTTAGATTCATACACTTTGAAACACT 57.663 29.630 0.00 0.00 36.72 3.55
299 300 9.813080 GTTAGATTCATACACTTTGAAACACTC 57.187 33.333 0.00 0.00 36.72 3.51
300 301 7.440523 AGATTCATACACTTTGAAACACTCC 57.559 36.000 0.00 0.00 36.72 3.85
301 302 7.227156 AGATTCATACACTTTGAAACACTCCT 58.773 34.615 0.00 0.00 36.72 3.69
302 303 7.721399 AGATTCATACACTTTGAAACACTCCTT 59.279 33.333 0.00 0.00 36.72 3.36
303 304 8.918202 ATTCATACACTTTGAAACACTCCTTA 57.082 30.769 0.00 0.00 36.72 2.69
304 305 7.724305 TCATACACTTTGAAACACTCCTTAC 57.276 36.000 0.00 0.00 0.00 2.34
305 306 6.708949 TCATACACTTTGAAACACTCCTTACC 59.291 38.462 0.00 0.00 0.00 2.85
306 307 4.850680 ACACTTTGAAACACTCCTTACCA 58.149 39.130 0.00 0.00 0.00 3.25
307 308 4.881850 ACACTTTGAAACACTCCTTACCAG 59.118 41.667 0.00 0.00 0.00 4.00
308 309 4.275936 CACTTTGAAACACTCCTTACCAGG 59.724 45.833 0.00 0.00 42.50 4.45
309 310 4.079958 ACTTTGAAACACTCCTTACCAGGT 60.080 41.667 0.00 0.00 41.69 4.00
310 311 4.513406 TTGAAACACTCCTTACCAGGTT 57.487 40.909 0.00 0.00 41.69 3.50
311 312 4.513406 TGAAACACTCCTTACCAGGTTT 57.487 40.909 0.00 0.00 41.69 3.27
312 313 4.457466 TGAAACACTCCTTACCAGGTTTC 58.543 43.478 0.00 0.00 42.52 2.78
313 314 2.833631 ACACTCCTTACCAGGTTTCG 57.166 50.000 0.00 0.00 41.69 3.46
314 315 2.322658 ACACTCCTTACCAGGTTTCGA 58.677 47.619 0.00 0.00 41.69 3.71
315 316 2.299297 ACACTCCTTACCAGGTTTCGAG 59.701 50.000 0.00 2.60 41.69 4.04
316 317 2.561419 CACTCCTTACCAGGTTTCGAGA 59.439 50.000 13.75 0.00 41.69 4.04
317 318 3.195825 CACTCCTTACCAGGTTTCGAGAT 59.804 47.826 13.75 0.28 41.69 2.75
318 319 4.401519 CACTCCTTACCAGGTTTCGAGATA 59.598 45.833 13.75 0.00 41.69 1.98
319 320 5.069251 CACTCCTTACCAGGTTTCGAGATAT 59.931 44.000 13.75 0.00 41.69 1.63
320 321 5.661759 ACTCCTTACCAGGTTTCGAGATATT 59.338 40.000 13.75 0.00 41.69 1.28
321 322 6.156429 ACTCCTTACCAGGTTTCGAGATATTT 59.844 38.462 13.75 0.00 41.69 1.40
322 323 7.343833 ACTCCTTACCAGGTTTCGAGATATTTA 59.656 37.037 13.75 0.00 41.69 1.40
323 324 8.081517 TCCTTACCAGGTTTCGAGATATTTAA 57.918 34.615 0.00 0.00 41.69 1.52
324 325 8.202137 TCCTTACCAGGTTTCGAGATATTTAAG 58.798 37.037 0.00 0.00 41.69 1.85
325 326 7.441458 CCTTACCAGGTTTCGAGATATTTAAGG 59.559 40.741 0.00 0.00 35.06 2.69
326 327 6.555463 ACCAGGTTTCGAGATATTTAAGGA 57.445 37.500 0.00 0.00 0.00 3.36
327 328 7.138054 ACCAGGTTTCGAGATATTTAAGGAT 57.862 36.000 0.00 0.00 0.00 3.24
328 329 8.258850 ACCAGGTTTCGAGATATTTAAGGATA 57.741 34.615 0.00 0.00 0.00 2.59
329 330 8.148999 ACCAGGTTTCGAGATATTTAAGGATAC 58.851 37.037 0.00 0.00 0.00 2.24
330 331 7.603024 CCAGGTTTCGAGATATTTAAGGATACC 59.397 40.741 0.00 0.00 37.17 2.73
331 332 8.148351 CAGGTTTCGAGATATTTAAGGATACCA 58.852 37.037 0.00 0.00 30.87 3.25
332 333 8.881262 AGGTTTCGAGATATTTAAGGATACCAT 58.119 33.333 0.00 0.00 30.87 3.55
333 334 8.936864 GGTTTCGAGATATTTAAGGATACCATG 58.063 37.037 0.00 0.00 37.17 3.66
334 335 9.706691 GTTTCGAGATATTTAAGGATACCATGA 57.293 33.333 0.00 0.00 37.17 3.07
336 337 9.706691 TTCGAGATATTTAAGGATACCATGAAC 57.293 33.333 0.00 0.00 37.17 3.18
337 338 8.866093 TCGAGATATTTAAGGATACCATGAACA 58.134 33.333 0.00 0.00 37.17 3.18
338 339 9.658799 CGAGATATTTAAGGATACCATGAACAT 57.341 33.333 0.00 0.00 37.17 2.71
346 347 7.959658 AAGGATACCATGAACATTGAATTGA 57.040 32.000 0.00 0.00 37.17 2.57
347 348 8.543293 AAGGATACCATGAACATTGAATTGAT 57.457 30.769 0.00 0.00 37.17 2.57
348 349 9.645128 AAGGATACCATGAACATTGAATTGATA 57.355 29.630 0.00 0.00 37.17 2.15
349 350 9.818270 AGGATACCATGAACATTGAATTGATAT 57.182 29.630 0.00 0.00 37.17 1.63
375 376 8.045720 AGATTCACTCTAATAAATAAGGGGCA 57.954 34.615 0.00 0.00 30.26 5.36
376 377 8.673251 AGATTCACTCTAATAAATAAGGGGCAT 58.327 33.333 0.00 0.00 30.26 4.40
377 378 9.959721 GATTCACTCTAATAAATAAGGGGCATA 57.040 33.333 0.00 0.00 0.00 3.14
378 379 9.740710 ATTCACTCTAATAAATAAGGGGCATAC 57.259 33.333 0.00 0.00 0.00 2.39
379 380 8.270137 TCACTCTAATAAATAAGGGGCATACA 57.730 34.615 0.00 0.00 0.00 2.29
380 381 8.890472 TCACTCTAATAAATAAGGGGCATACAT 58.110 33.333 0.00 0.00 0.00 2.29
381 382 9.520515 CACTCTAATAAATAAGGGGCATACATT 57.479 33.333 0.00 0.00 0.00 2.71
390 391 8.608185 AATAAGGGGCATACATTAATATTGGG 57.392 34.615 0.00 0.00 0.00 4.12
391 392 4.946646 AGGGGCATACATTAATATTGGGG 58.053 43.478 0.00 0.00 0.00 4.96
392 393 4.030216 GGGGCATACATTAATATTGGGGG 58.970 47.826 0.00 0.00 0.00 5.40
393 394 3.450817 GGGCATACATTAATATTGGGGGC 59.549 47.826 0.00 0.00 0.00 5.80
394 395 3.450817 GGCATACATTAATATTGGGGGCC 59.549 47.826 0.00 0.00 0.00 5.80
395 396 3.450817 GCATACATTAATATTGGGGGCCC 59.549 47.826 15.76 15.76 0.00 5.80
396 397 4.682563 CATACATTAATATTGGGGGCCCA 58.317 43.478 26.86 4.56 45.63 5.36
397 398 3.941258 ACATTAATATTGGGGGCCCAT 57.059 42.857 26.86 13.18 46.64 4.00
398 399 3.790126 ACATTAATATTGGGGGCCCATC 58.210 45.455 26.86 16.10 46.64 3.51
399 400 3.405805 ACATTAATATTGGGGGCCCATCT 59.594 43.478 26.86 10.20 46.64 2.90
400 401 3.541242 TTAATATTGGGGGCCCATCTG 57.459 47.619 26.86 0.00 46.64 2.90
401 402 1.244366 AATATTGGGGGCCCATCTGT 58.756 50.000 26.86 7.68 46.64 3.41
402 403 0.484212 ATATTGGGGGCCCATCTGTG 59.516 55.000 26.86 0.00 46.64 3.66
403 404 1.654137 TATTGGGGGCCCATCTGTGG 61.654 60.000 26.86 0.00 46.64 4.17
409 410 3.324713 GCCCATCTGTGGCTAGGT 58.675 61.111 0.00 0.00 45.70 3.08
410 411 1.153086 GCCCATCTGTGGCTAGGTG 60.153 63.158 0.00 0.00 45.70 4.00
411 412 1.915078 GCCCATCTGTGGCTAGGTGT 61.915 60.000 0.00 0.00 45.70 4.16
412 413 0.107508 CCCATCTGTGGCTAGGTGTG 60.108 60.000 0.00 0.00 44.62 3.82
413 414 0.745845 CCATCTGTGGCTAGGTGTGC 60.746 60.000 0.00 0.00 39.01 4.57
414 415 0.036105 CATCTGTGGCTAGGTGTGCA 60.036 55.000 0.00 0.00 0.00 4.57
415 416 0.036010 ATCTGTGGCTAGGTGTGCAC 60.036 55.000 10.75 10.75 0.00 4.57
416 417 1.071299 CTGTGGCTAGGTGTGCACA 59.929 57.895 17.42 17.42 0.00 4.57
417 418 0.321919 CTGTGGCTAGGTGTGCACAT 60.322 55.000 24.69 10.81 0.00 3.21
418 419 0.606130 TGTGGCTAGGTGTGCACATG 60.606 55.000 24.69 14.31 0.00 3.21
419 420 1.002257 TGGCTAGGTGTGCACATGG 60.002 57.895 24.69 11.25 0.00 3.66
420 421 1.002134 GGCTAGGTGTGCACATGGT 60.002 57.895 24.69 12.97 0.00 3.55
421 422 1.308069 GGCTAGGTGTGCACATGGTG 61.308 60.000 24.69 14.66 36.51 4.17
422 423 1.308069 GCTAGGTGTGCACATGGTGG 61.308 60.000 24.69 13.27 33.64 4.61
423 424 0.677731 CTAGGTGTGCACATGGTGGG 60.678 60.000 24.69 7.85 33.64 4.61
424 425 1.422977 TAGGTGTGCACATGGTGGGT 61.423 55.000 24.69 5.38 33.64 4.51
425 426 2.563798 GGTGTGCACATGGTGGGTG 61.564 63.158 24.69 0.00 39.25 4.61
426 427 1.528076 GTGTGCACATGGTGGGTGA 60.528 57.895 24.69 0.00 38.54 4.02
427 428 1.528076 TGTGCACATGGTGGGTGAC 60.528 57.895 17.42 0.00 38.54 3.67
439 440 4.724022 GGTGACCATAGCGTACCG 57.276 61.111 0.00 0.00 0.00 4.02
440 441 2.109431 GGTGACCATAGCGTACCGA 58.891 57.895 0.00 0.00 0.00 4.69
445 446 1.612463 GACCATAGCGTACCGAGGATT 59.388 52.381 0.00 0.00 0.00 3.01
446 447 2.035576 GACCATAGCGTACCGAGGATTT 59.964 50.000 0.00 0.00 0.00 2.17
452 453 0.107848 CGTACCGAGGATTTTGGCCT 60.108 55.000 3.32 0.00 38.81 5.19
511 512 0.393537 GCTTGTCAGGGGAGATGTGG 60.394 60.000 0.00 0.00 0.00 4.17
514 515 2.284625 TCAGGGGAGATGTGGCGT 60.285 61.111 0.00 0.00 0.00 5.68
556 557 1.869132 GGAGCGTTAAGTTGACCGTTT 59.131 47.619 0.00 0.00 0.00 3.60
640 641 8.453238 TTTGACAATTTAACTAGCACCTTGTA 57.547 30.769 0.00 0.00 0.00 2.41
767 784 9.594478 CCAAATAAATGGTTGGAAAATACTACC 57.406 33.333 0.00 0.00 46.11 3.18
850 1182 3.157252 GGCATCTCTCCTCCCGCA 61.157 66.667 0.00 0.00 0.00 5.69
851 1183 2.735772 GGCATCTCTCCTCCCGCAA 61.736 63.158 0.00 0.00 0.00 4.85
866 1198 2.947621 CAATGCATGCTGTCGCGC 60.948 61.111 20.33 0.00 39.65 6.86
868 1200 2.980378 AATGCATGCTGTCGCGCAA 61.980 52.632 20.33 0.00 44.06 4.85
869 1201 2.274232 AATGCATGCTGTCGCGCAAT 62.274 50.000 20.33 0.00 44.06 3.56
870 1202 2.930012 ATGCATGCTGTCGCGCAATG 62.930 55.000 20.33 6.07 44.06 2.82
871 1203 2.786584 CATGCTGTCGCGCAATGA 59.213 55.556 8.75 0.00 44.06 2.57
872 1204 1.297378 CATGCTGTCGCGCAATGAG 60.297 57.895 8.75 0.00 44.06 2.90
1254 1654 2.772691 GGACGCGGACGAGGAGAAT 61.773 63.158 12.47 0.00 43.93 2.40
1293 1693 3.382832 CTGAGGGAGGCGTTCGGT 61.383 66.667 0.00 0.00 0.00 4.69
1296 1696 1.363080 GAGGGAGGCGTTCGGTATC 59.637 63.158 0.00 0.00 0.00 2.24
1303 1703 0.040603 GGCGTTCGGTATCTACGAGG 60.041 60.000 0.00 0.00 41.81 4.63
1399 1799 4.471908 AGTGCCGCGCCATGATCA 62.472 61.111 0.00 0.00 0.00 2.92
1504 1922 5.186021 ACTCAACCATATATCATCTCGGTCC 59.814 44.000 0.00 0.00 0.00 4.46
1511 1929 4.727507 ATATCATCTCGGTCCTGCATAC 57.272 45.455 0.00 0.00 0.00 2.39
1515 1949 1.227380 CTCGGTCCTGCATACAGCC 60.227 63.158 0.00 0.00 43.02 4.85
1603 2053 7.330262 TGATGCACAGACAGTAATTGATCTAA 58.670 34.615 0.00 0.00 0.00 2.10
1621 2860 8.964476 TGATCTAAGTGATATTTTTGGTCTCC 57.036 34.615 0.00 0.00 35.14 3.71
1667 2912 2.171003 GGATTGTGGGTTTCTCAAGGG 58.829 52.381 0.00 0.00 33.15 3.95
1718 2967 2.642311 TGAATGTGAAGGGGCTGACTTA 59.358 45.455 0.00 0.00 0.00 2.24
1749 2998 2.582052 CTCCAAACCCTTTACAGCACA 58.418 47.619 0.00 0.00 0.00 4.57
1776 3025 5.602145 TGGCAATATTTGGAAAGGGGAATAG 59.398 40.000 0.00 0.00 0.00 1.73
1812 3061 7.118496 AGGGAGTTGTATTGAGATTAGACAG 57.882 40.000 0.00 0.00 0.00 3.51
1815 3064 7.363880 GGGAGTTGTATTGAGATTAGACAGTGA 60.364 40.741 0.00 0.00 0.00 3.41
1832 3081 7.155328 AGACAGTGAGATGAGTCGTTTTATTT 58.845 34.615 0.00 0.00 36.18 1.40
1841 3090 7.611855 AGATGAGTCGTTTTATTTCCAATCCTT 59.388 33.333 0.00 0.00 0.00 3.36
1847 3096 8.484799 GTCGTTTTATTTCCAATCCTTTGTTTC 58.515 33.333 0.00 0.00 0.00 2.78
1872 3121 1.065418 ACGATTGGAAGTCCCATGACC 60.065 52.381 0.00 0.00 46.10 4.02
1917 3166 4.641989 CCCTCCAACCAAACAATAGATCTG 59.358 45.833 5.18 0.00 0.00 2.90
1925 3174 7.009179 ACCAAACAATAGATCTGAAGTCTCA 57.991 36.000 5.18 0.00 0.00 3.27
1930 3179 7.904558 ACAATAGATCTGAAGTCTCATACCA 57.095 36.000 5.18 0.00 0.00 3.25
1961 3222 3.688235 TCTAATTACCCCCAACCAAACG 58.312 45.455 0.00 0.00 0.00 3.60
1962 3223 2.679429 AATTACCCCCAACCAAACGA 57.321 45.000 0.00 0.00 0.00 3.85
1963 3224 1.913778 ATTACCCCCAACCAAACGAC 58.086 50.000 0.00 0.00 0.00 4.34
2026 3370 6.371278 TCCGTGTAGGGATTAAATCTCTAGT 58.629 40.000 0.00 0.00 42.75 2.57
2076 3420 0.037160 TTCGGTTAAACCCCTCCTGC 59.963 55.000 0.00 0.00 33.75 4.85
2138 3482 1.967535 CCGAGAGTTCACCTGCAGA 59.032 57.895 17.39 0.00 0.00 4.26
2442 5680 7.496591 TCGGGTTATATGGTTTACATTTGAGAC 59.503 37.037 0.00 0.00 41.03 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 7.733402 ATTTGTTTAGCATGCATGAGTTTTT 57.267 28.000 30.64 9.69 0.00 1.94
37 38 8.830201 TTATTTGTTTAGCATGCATGAGTTTT 57.170 26.923 30.64 11.37 0.00 2.43
40 41 9.687210 CATATTATTTGTTTAGCATGCATGAGT 57.313 29.630 30.64 17.96 0.00 3.41
41 42 9.902196 TCATATTATTTGTTTAGCATGCATGAG 57.098 29.630 30.64 5.13 0.00 2.90
80 81 9.685276 TGAACATGAATTCTCTATTGTTGGTAT 57.315 29.630 7.05 0.00 0.00 2.73
81 82 9.513906 TTGAACATGAATTCTCTATTGTTGGTA 57.486 29.630 7.05 0.00 0.00 3.25
82 83 8.408043 TTGAACATGAATTCTCTATTGTTGGT 57.592 30.769 7.05 0.00 0.00 3.67
83 84 9.350357 CTTTGAACATGAATTCTCTATTGTTGG 57.650 33.333 7.05 0.00 0.00 3.77
86 87 9.288576 TGTCTTTGAACATGAATTCTCTATTGT 57.711 29.630 7.05 0.60 0.00 2.71
89 90 9.730705 TCTTGTCTTTGAACATGAATTCTCTAT 57.269 29.630 7.05 0.00 32.31 1.98
90 91 9.559732 TTCTTGTCTTTGAACATGAATTCTCTA 57.440 29.630 7.05 0.00 37.99 2.43
91 92 8.455903 TTCTTGTCTTTGAACATGAATTCTCT 57.544 30.769 7.05 0.00 37.99 3.10
92 93 9.178427 CTTTCTTGTCTTTGAACATGAATTCTC 57.822 33.333 7.05 0.00 40.70 2.87
93 94 8.139989 CCTTTCTTGTCTTTGAACATGAATTCT 58.860 33.333 7.05 0.00 40.70 2.40
94 95 8.137437 TCCTTTCTTGTCTTTGAACATGAATTC 58.863 33.333 0.00 0.00 40.70 2.17
95 96 8.010733 TCCTTTCTTGTCTTTGAACATGAATT 57.989 30.769 0.00 0.00 40.70 2.17
96 97 7.587037 TCCTTTCTTGTCTTTGAACATGAAT 57.413 32.000 0.00 0.00 40.70 2.57
97 98 7.403312 TTCCTTTCTTGTCTTTGAACATGAA 57.597 32.000 0.00 2.37 39.89 2.57
98 99 7.403312 TTTCCTTTCTTGTCTTTGAACATGA 57.597 32.000 0.00 0.00 33.10 3.07
99 100 8.652810 ATTTTCCTTTCTTGTCTTTGAACATG 57.347 30.769 0.00 0.00 0.00 3.21
100 101 9.671279 AAATTTTCCTTTCTTGTCTTTGAACAT 57.329 25.926 0.00 0.00 0.00 2.71
101 102 9.500785 AAAATTTTCCTTTCTTGTCTTTGAACA 57.499 25.926 0.00 0.00 0.00 3.18
102 103 9.759259 CAAAATTTTCCTTTCTTGTCTTTGAAC 57.241 29.630 0.00 0.00 0.00 3.18
103 104 8.945057 CCAAAATTTTCCTTTCTTGTCTTTGAA 58.055 29.630 0.00 0.00 0.00 2.69
104 105 8.100164 ACCAAAATTTTCCTTTCTTGTCTTTGA 58.900 29.630 0.00 0.00 0.00 2.69
105 106 8.267620 ACCAAAATTTTCCTTTCTTGTCTTTG 57.732 30.769 0.00 0.00 0.00 2.77
106 107 9.599866 CTACCAAAATTTTCCTTTCTTGTCTTT 57.400 29.630 0.00 0.00 0.00 2.52
107 108 8.204160 CCTACCAAAATTTTCCTTTCTTGTCTT 58.796 33.333 0.00 0.00 0.00 3.01
108 109 7.563556 TCCTACCAAAATTTTCCTTTCTTGTCT 59.436 33.333 0.00 0.00 0.00 3.41
109 110 7.722363 TCCTACCAAAATTTTCCTTTCTTGTC 58.278 34.615 0.00 0.00 0.00 3.18
110 111 7.669089 TCCTACCAAAATTTTCCTTTCTTGT 57.331 32.000 0.00 0.00 0.00 3.16
111 112 7.984617 TGTTCCTACCAAAATTTTCCTTTCTTG 59.015 33.333 0.00 0.00 0.00 3.02
112 113 8.084985 TGTTCCTACCAAAATTTTCCTTTCTT 57.915 30.769 0.00 0.00 0.00 2.52
113 114 7.669089 TGTTCCTACCAAAATTTTCCTTTCT 57.331 32.000 0.00 0.00 0.00 2.52
114 115 9.419297 GTATGTTCCTACCAAAATTTTCCTTTC 57.581 33.333 0.00 0.00 0.00 2.62
115 116 8.372459 GGTATGTTCCTACCAAAATTTTCCTTT 58.628 33.333 0.00 0.00 40.81 3.11
116 117 7.511028 TGGTATGTTCCTACCAAAATTTTCCTT 59.489 33.333 0.00 0.00 46.33 3.36
117 118 7.013834 TGGTATGTTCCTACCAAAATTTTCCT 58.986 34.615 0.00 0.00 46.33 3.36
118 119 7.234661 TGGTATGTTCCTACCAAAATTTTCC 57.765 36.000 0.00 0.00 46.33 3.13
127 128 5.567224 CGTTAACAGTGGTATGTTCCTACCA 60.567 44.000 6.39 0.00 46.97 3.25
128 129 4.866486 CGTTAACAGTGGTATGTTCCTACC 59.134 45.833 6.39 0.00 42.33 3.18
129 130 5.713025 TCGTTAACAGTGGTATGTTCCTAC 58.287 41.667 6.39 0.00 42.33 3.18
130 131 5.477984 ACTCGTTAACAGTGGTATGTTCCTA 59.522 40.000 6.39 0.00 42.33 2.94
131 132 4.282703 ACTCGTTAACAGTGGTATGTTCCT 59.717 41.667 6.39 0.00 42.33 3.36
132 133 4.563061 ACTCGTTAACAGTGGTATGTTCC 58.437 43.478 6.39 0.00 42.33 3.62
133 134 5.224888 TGACTCGTTAACAGTGGTATGTTC 58.775 41.667 13.23 1.17 42.33 3.18
134 135 5.010314 TCTGACTCGTTAACAGTGGTATGTT 59.990 40.000 13.23 0.00 45.19 2.71
135 136 4.521639 TCTGACTCGTTAACAGTGGTATGT 59.478 41.667 13.23 0.00 33.93 2.29
136 137 5.055642 TCTGACTCGTTAACAGTGGTATG 57.944 43.478 13.23 0.00 33.93 2.39
137 138 4.380655 GCTCTGACTCGTTAACAGTGGTAT 60.381 45.833 13.23 0.00 33.93 2.73
138 139 3.057736 GCTCTGACTCGTTAACAGTGGTA 60.058 47.826 13.23 0.00 33.93 3.25
139 140 2.288273 GCTCTGACTCGTTAACAGTGGT 60.288 50.000 13.23 0.00 33.93 4.16
140 141 2.029828 AGCTCTGACTCGTTAACAGTGG 60.030 50.000 13.23 7.80 33.93 4.00
141 142 2.983136 CAGCTCTGACTCGTTAACAGTG 59.017 50.000 13.23 6.67 33.93 3.66
142 143 2.885266 TCAGCTCTGACTCGTTAACAGT 59.115 45.455 6.39 8.24 34.14 3.55
143 144 3.497118 CTCAGCTCTGACTCGTTAACAG 58.503 50.000 6.39 5.11 35.46 3.16
144 145 2.229062 CCTCAGCTCTGACTCGTTAACA 59.771 50.000 6.39 0.00 35.46 2.41
145 146 2.488545 TCCTCAGCTCTGACTCGTTAAC 59.511 50.000 0.00 0.00 35.46 2.01
146 147 2.791655 TCCTCAGCTCTGACTCGTTAA 58.208 47.619 0.00 0.00 35.46 2.01
147 148 2.491675 TCCTCAGCTCTGACTCGTTA 57.508 50.000 0.00 0.00 35.46 3.18
148 149 1.543802 CTTCCTCAGCTCTGACTCGTT 59.456 52.381 0.00 0.00 35.46 3.85
149 150 1.173043 CTTCCTCAGCTCTGACTCGT 58.827 55.000 0.00 0.00 35.46 4.18
150 151 0.455410 CCTTCCTCAGCTCTGACTCG 59.545 60.000 0.00 0.00 35.46 4.18
151 152 1.555967 ACCTTCCTCAGCTCTGACTC 58.444 55.000 0.00 0.00 35.46 3.36
152 153 2.022718 AACCTTCCTCAGCTCTGACT 57.977 50.000 0.00 0.00 35.46 3.41
153 154 2.694213 GAAACCTTCCTCAGCTCTGAC 58.306 52.381 0.00 0.00 35.46 3.51
154 155 1.273606 CGAAACCTTCCTCAGCTCTGA 59.726 52.381 0.00 0.00 38.06 3.27
155 156 1.273606 TCGAAACCTTCCTCAGCTCTG 59.726 52.381 0.00 0.00 0.00 3.35
156 157 1.273886 GTCGAAACCTTCCTCAGCTCT 59.726 52.381 0.00 0.00 0.00 4.09
157 158 1.715993 GTCGAAACCTTCCTCAGCTC 58.284 55.000 0.00 0.00 0.00 4.09
158 159 0.038159 CGTCGAAACCTTCCTCAGCT 60.038 55.000 0.00 0.00 0.00 4.24
159 160 0.038526 TCGTCGAAACCTTCCTCAGC 60.039 55.000 0.00 0.00 0.00 4.26
160 161 1.000607 TGTCGTCGAAACCTTCCTCAG 60.001 52.381 0.00 0.00 0.00 3.35
161 162 1.034356 TGTCGTCGAAACCTTCCTCA 58.966 50.000 0.00 0.00 0.00 3.86
162 163 2.144482 TTGTCGTCGAAACCTTCCTC 57.856 50.000 0.00 0.00 0.00 3.71
163 164 2.299297 AGATTGTCGTCGAAACCTTCCT 59.701 45.455 0.00 0.00 0.00 3.36
164 165 2.685100 AGATTGTCGTCGAAACCTTCC 58.315 47.619 0.00 0.00 0.00 3.46
165 166 6.241385 CAATTAGATTGTCGTCGAAACCTTC 58.759 40.000 0.00 0.00 35.57 3.46
166 167 6.165659 CAATTAGATTGTCGTCGAAACCTT 57.834 37.500 0.00 0.00 35.57 3.50
167 168 5.779806 CAATTAGATTGTCGTCGAAACCT 57.220 39.130 0.00 0.00 35.57 3.50
179 180 9.979270 GTGTATCAAGTGAGAACAATTAGATTG 57.021 33.333 0.00 0.00 45.59 2.67
180 181 9.725019 TGTGTATCAAGTGAGAACAATTAGATT 57.275 29.630 1.94 0.00 32.98 2.40
181 182 9.896645 ATGTGTATCAAGTGAGAACAATTAGAT 57.103 29.630 1.94 0.00 32.98 1.98
185 186 9.725019 TCTTATGTGTATCAAGTGAGAACAATT 57.275 29.630 1.94 0.00 34.60 2.32
186 187 9.725019 TTCTTATGTGTATCAAGTGAGAACAAT 57.275 29.630 1.94 2.43 0.00 2.71
187 188 8.988934 GTTCTTATGTGTATCAAGTGAGAACAA 58.011 33.333 0.00 0.00 39.88 2.83
188 189 8.367911 AGTTCTTATGTGTATCAAGTGAGAACA 58.632 33.333 12.98 2.57 41.57 3.18
189 190 8.764524 AGTTCTTATGTGTATCAAGTGAGAAC 57.235 34.615 0.00 0.00 40.22 3.01
192 193 8.759641 GCATAGTTCTTATGTGTATCAAGTGAG 58.240 37.037 0.00 0.00 41.08 3.51
193 194 8.478066 AGCATAGTTCTTATGTGTATCAAGTGA 58.522 33.333 0.00 0.00 41.08 3.41
194 195 8.654230 AGCATAGTTCTTATGTGTATCAAGTG 57.346 34.615 0.00 0.00 41.08 3.16
195 196 9.672673 AAAGCATAGTTCTTATGTGTATCAAGT 57.327 29.630 0.00 0.00 41.08 3.16
198 199 9.665719 TGAAAAGCATAGTTCTTATGTGTATCA 57.334 29.630 0.00 0.00 41.08 2.15
238 239 8.700973 GGAGGTTTCTAGAAAATCAGACTATCT 58.299 37.037 19.30 0.00 31.33 1.98
239 240 8.478877 TGGAGGTTTCTAGAAAATCAGACTATC 58.521 37.037 19.30 8.97 31.33 2.08
240 241 8.380742 TGGAGGTTTCTAGAAAATCAGACTAT 57.619 34.615 19.30 0.94 31.33 2.12
241 242 7.792364 TGGAGGTTTCTAGAAAATCAGACTA 57.208 36.000 19.30 4.31 31.33 2.59
242 243 6.688073 TGGAGGTTTCTAGAAAATCAGACT 57.312 37.500 19.30 10.53 31.33 3.24
243 244 7.745620 TTTGGAGGTTTCTAGAAAATCAGAC 57.254 36.000 19.30 6.82 31.33 3.51
244 245 8.940397 AATTTGGAGGTTTCTAGAAAATCAGA 57.060 30.769 19.30 10.56 31.33 3.27
271 272 9.944663 GTGTTTCAAAGTGTATGAATCTAACAA 57.055 29.630 0.00 0.00 36.72 2.83
272 273 9.337396 AGTGTTTCAAAGTGTATGAATCTAACA 57.663 29.630 0.00 0.00 36.72 2.41
273 274 9.813080 GAGTGTTTCAAAGTGTATGAATCTAAC 57.187 33.333 0.00 0.00 36.72 2.34
274 275 8.999431 GGAGTGTTTCAAAGTGTATGAATCTAA 58.001 33.333 0.00 0.00 36.72 2.10
275 276 8.375506 AGGAGTGTTTCAAAGTGTATGAATCTA 58.624 33.333 0.00 0.00 36.72 1.98
276 277 7.227156 AGGAGTGTTTCAAAGTGTATGAATCT 58.773 34.615 0.00 0.00 36.72 2.40
277 278 7.440523 AGGAGTGTTTCAAAGTGTATGAATC 57.559 36.000 0.00 0.00 36.72 2.52
278 279 7.823745 AAGGAGTGTTTCAAAGTGTATGAAT 57.176 32.000 0.00 0.00 36.72 2.57
279 280 7.227910 GGTAAGGAGTGTTTCAAAGTGTATGAA 59.772 37.037 0.00 0.00 35.11 2.57
280 281 6.708949 GGTAAGGAGTGTTTCAAAGTGTATGA 59.291 38.462 0.00 0.00 0.00 2.15
281 282 6.485313 TGGTAAGGAGTGTTTCAAAGTGTATG 59.515 38.462 0.00 0.00 0.00 2.39
282 283 6.597562 TGGTAAGGAGTGTTTCAAAGTGTAT 58.402 36.000 0.00 0.00 0.00 2.29
283 284 5.991861 TGGTAAGGAGTGTTTCAAAGTGTA 58.008 37.500 0.00 0.00 0.00 2.90
284 285 4.850680 TGGTAAGGAGTGTTTCAAAGTGT 58.149 39.130 0.00 0.00 0.00 3.55
285 286 5.424121 CTGGTAAGGAGTGTTTCAAAGTG 57.576 43.478 0.00 0.00 0.00 3.16
300 301 8.202137 TCCTTAAATATCTCGAAACCTGGTAAG 58.798 37.037 0.00 0.00 0.00 2.34
301 302 8.081517 TCCTTAAATATCTCGAAACCTGGTAA 57.918 34.615 0.00 0.00 0.00 2.85
302 303 7.664552 TCCTTAAATATCTCGAAACCTGGTA 57.335 36.000 0.00 0.00 0.00 3.25
303 304 6.555463 TCCTTAAATATCTCGAAACCTGGT 57.445 37.500 0.00 0.00 0.00 4.00
304 305 7.603024 GGTATCCTTAAATATCTCGAAACCTGG 59.397 40.741 0.00 0.00 0.00 4.45
305 306 8.148351 TGGTATCCTTAAATATCTCGAAACCTG 58.852 37.037 0.00 0.00 0.00 4.00
306 307 8.258850 TGGTATCCTTAAATATCTCGAAACCT 57.741 34.615 0.00 0.00 0.00 3.50
307 308 8.936864 CATGGTATCCTTAAATATCTCGAAACC 58.063 37.037 0.00 0.00 0.00 3.27
308 309 9.706691 TCATGGTATCCTTAAATATCTCGAAAC 57.293 33.333 0.00 0.00 0.00 2.78
310 311 9.706691 GTTCATGGTATCCTTAAATATCTCGAA 57.293 33.333 0.00 0.00 0.00 3.71
311 312 8.866093 TGTTCATGGTATCCTTAAATATCTCGA 58.134 33.333 0.00 0.00 0.00 4.04
312 313 9.658799 ATGTTCATGGTATCCTTAAATATCTCG 57.341 33.333 0.00 0.00 0.00 4.04
320 321 9.473007 TCAATTCAATGTTCATGGTATCCTTAA 57.527 29.630 0.00 0.00 0.00 1.85
321 322 9.645128 ATCAATTCAATGTTCATGGTATCCTTA 57.355 29.630 0.00 0.00 0.00 2.69
322 323 7.959658 TCAATTCAATGTTCATGGTATCCTT 57.040 32.000 0.00 0.00 0.00 3.36
323 324 9.818270 ATATCAATTCAATGTTCATGGTATCCT 57.182 29.630 0.00 0.00 0.00 3.24
349 350 9.166222 TGCCCCTTATTTATTAGAGTGAATCTA 57.834 33.333 0.00 0.00 39.64 1.98
350 351 8.045720 TGCCCCTTATTTATTAGAGTGAATCT 57.954 34.615 0.00 0.00 42.47 2.40
351 352 8.870075 ATGCCCCTTATTTATTAGAGTGAATC 57.130 34.615 0.00 0.00 0.00 2.52
352 353 9.740710 GTATGCCCCTTATTTATTAGAGTGAAT 57.259 33.333 0.00 0.00 0.00 2.57
353 354 8.719596 TGTATGCCCCTTATTTATTAGAGTGAA 58.280 33.333 0.00 0.00 0.00 3.18
354 355 8.270137 TGTATGCCCCTTATTTATTAGAGTGA 57.730 34.615 0.00 0.00 0.00 3.41
355 356 9.520515 AATGTATGCCCCTTATTTATTAGAGTG 57.479 33.333 0.00 0.00 0.00 3.51
364 365 9.045745 CCCAATATTAATGTATGCCCCTTATTT 57.954 33.333 0.00 0.00 0.00 1.40
365 366 7.623278 CCCCAATATTAATGTATGCCCCTTATT 59.377 37.037 0.00 0.00 0.00 1.40
366 367 7.132128 CCCCAATATTAATGTATGCCCCTTAT 58.868 38.462 0.00 0.00 0.00 1.73
367 368 6.498538 CCCCAATATTAATGTATGCCCCTTA 58.501 40.000 0.00 0.00 0.00 2.69
368 369 5.341169 CCCCAATATTAATGTATGCCCCTT 58.659 41.667 0.00 0.00 0.00 3.95
369 370 4.264804 CCCCCAATATTAATGTATGCCCCT 60.265 45.833 0.00 0.00 0.00 4.79
370 371 4.030216 CCCCCAATATTAATGTATGCCCC 58.970 47.826 0.00 0.00 0.00 5.80
371 372 3.450817 GCCCCCAATATTAATGTATGCCC 59.549 47.826 0.00 0.00 0.00 5.36
372 373 3.450817 GGCCCCCAATATTAATGTATGCC 59.549 47.826 0.00 0.00 0.00 4.40
373 374 3.450817 GGGCCCCCAATATTAATGTATGC 59.549 47.826 12.23 0.00 35.81 3.14
374 375 4.682563 TGGGCCCCCAATATTAATGTATG 58.317 43.478 22.27 0.00 44.12 2.39
395 396 0.036105 TGCACACCTAGCCACAGATG 60.036 55.000 0.00 0.00 0.00 2.90
396 397 0.036010 GTGCACACCTAGCCACAGAT 60.036 55.000 13.17 0.00 0.00 2.90
397 398 1.371183 GTGCACACCTAGCCACAGA 59.629 57.895 13.17 0.00 0.00 3.41
398 399 0.321919 ATGTGCACACCTAGCCACAG 60.322 55.000 24.37 0.00 0.00 3.66
399 400 0.606130 CATGTGCACACCTAGCCACA 60.606 55.000 24.37 0.00 0.00 4.17
400 401 1.308069 CCATGTGCACACCTAGCCAC 61.308 60.000 24.37 0.00 0.00 5.01
401 402 1.002257 CCATGTGCACACCTAGCCA 60.002 57.895 24.37 0.00 0.00 4.75
402 403 1.002134 ACCATGTGCACACCTAGCC 60.002 57.895 24.37 0.00 0.00 3.93
403 404 1.308069 CCACCATGTGCACACCTAGC 61.308 60.000 24.37 0.00 31.34 3.42
404 405 0.677731 CCCACCATGTGCACACCTAG 60.678 60.000 24.37 13.37 31.34 3.02
405 406 1.378378 CCCACCATGTGCACACCTA 59.622 57.895 24.37 0.00 31.34 3.08
406 407 2.115910 CCCACCATGTGCACACCT 59.884 61.111 24.37 3.91 31.34 4.00
407 408 2.203480 ACCCACCATGTGCACACC 60.203 61.111 24.37 0.00 31.34 4.16
408 409 1.528076 TCACCCACCATGTGCACAC 60.528 57.895 24.37 0.00 33.71 3.82
409 410 1.528076 GTCACCCACCATGTGCACA 60.528 57.895 24.08 24.08 33.71 4.57
410 411 2.268076 GGTCACCCACCATGTGCAC 61.268 63.158 10.75 10.75 45.98 4.57
411 412 2.115052 GGTCACCCACCATGTGCA 59.885 61.111 0.00 0.00 45.98 4.57
418 419 0.179092 GTACGCTATGGTCACCCACC 60.179 60.000 0.00 0.00 45.65 4.61
419 420 0.179092 GGTACGCTATGGTCACCCAC 60.179 60.000 0.00 0.00 45.65 4.61
434 435 1.339727 ACAGGCCAAAATCCTCGGTAC 60.340 52.381 5.01 0.00 0.00 3.34
435 436 0.988832 ACAGGCCAAAATCCTCGGTA 59.011 50.000 5.01 0.00 0.00 4.02
436 437 0.112412 AACAGGCCAAAATCCTCGGT 59.888 50.000 5.01 0.00 0.00 4.69
437 438 1.256812 AAACAGGCCAAAATCCTCGG 58.743 50.000 5.01 0.00 0.00 4.63
438 439 3.127030 GTCTAAACAGGCCAAAATCCTCG 59.873 47.826 5.01 0.00 0.00 4.63
439 440 3.127030 CGTCTAAACAGGCCAAAATCCTC 59.873 47.826 5.01 0.00 0.00 3.71
440 441 3.081804 CGTCTAAACAGGCCAAAATCCT 58.918 45.455 5.01 0.00 0.00 3.24
445 446 6.440436 GTTTAAATCGTCTAAACAGGCCAAA 58.560 36.000 5.01 0.00 38.54 3.28
446 447 5.334260 CGTTTAAATCGTCTAAACAGGCCAA 60.334 40.000 5.01 0.00 38.58 4.52
452 453 8.281194 TGTAAATGCGTTTAAATCGTCTAAACA 58.719 29.630 12.62 2.34 38.58 2.83
506 507 1.873591 GAGTTGACTTTCACGCCACAT 59.126 47.619 0.00 0.00 0.00 3.21
511 512 3.423123 CGTAATGGAGTTGACTTTCACGC 60.423 47.826 0.00 0.00 0.00 5.34
539 540 3.031126 GTCAAAACGGTCAACTTAACGC 58.969 45.455 0.00 0.00 0.00 4.84
556 557 2.525629 TGAGCCCCCACGAGTCAA 60.526 61.111 0.00 0.00 0.00 3.18
761 762 2.410060 CATCGTGCCGCGGTAGTA 59.590 61.111 28.70 13.73 41.72 1.82
850 1182 3.433453 TGCGCGACAGCATGCATT 61.433 55.556 21.98 5.47 45.49 3.56
864 1196 1.888215 ATACTCATGGGCTCATTGCG 58.112 50.000 0.00 0.00 44.05 4.85
866 1198 6.037940 GTGCATATATACTCATGGGCTCATTG 59.962 42.308 0.00 0.00 0.00 2.82
868 1200 5.190330 TGTGCATATATACTCATGGGCTCAT 59.810 40.000 0.00 0.00 0.00 2.90
869 1201 4.531732 TGTGCATATATACTCATGGGCTCA 59.468 41.667 0.00 0.00 0.00 4.26
870 1202 4.872691 GTGTGCATATATACTCATGGGCTC 59.127 45.833 0.00 0.00 0.00 4.70
871 1203 4.621510 CGTGTGCATATATACTCATGGGCT 60.622 45.833 0.00 0.00 0.00 5.19
872 1204 3.618594 CGTGTGCATATATACTCATGGGC 59.381 47.826 0.00 0.00 0.00 5.36
998 1393 1.801771 CCGTCTTTGTCGCAACCATTA 59.198 47.619 0.00 0.00 0.00 1.90
1138 1533 4.988598 CGACGCCACCAGTGCCTT 62.989 66.667 0.00 0.00 0.00 4.35
1163 1558 3.545124 AACAGCCCATCGCCGTCAA 62.545 57.895 0.00 0.00 38.78 3.18
1236 1636 2.772691 ATTCTCCTCGTCCGCGTCC 61.773 63.158 4.92 0.00 39.49 4.79
1237 1637 1.586564 CATTCTCCTCGTCCGCGTC 60.587 63.158 4.92 0.00 39.49 5.19
1238 1638 2.044555 TCATTCTCCTCGTCCGCGT 61.045 57.895 4.92 0.00 39.49 6.01
1239 1639 1.586564 GTCATTCTCCTCGTCCGCG 60.587 63.158 0.00 0.00 39.92 6.46
1240 1640 1.586564 CGTCATTCTCCTCGTCCGC 60.587 63.158 0.00 0.00 0.00 5.54
1254 1654 2.121538 CCGGATCCTCAGCTCGTCA 61.122 63.158 10.75 0.00 0.00 4.35
1293 1693 1.063492 TGCCCTTCCACCTCGTAGATA 60.063 52.381 0.00 0.00 33.89 1.98
1296 1696 1.517832 CTGCCCTTCCACCTCGTAG 59.482 63.158 0.00 0.00 0.00 3.51
1399 1799 1.556911 ACCATCAAGATCGAACTGGCT 59.443 47.619 0.00 0.00 0.00 4.75
1403 1803 2.417379 CCGTCACCATCAAGATCGAACT 60.417 50.000 0.00 0.00 0.00 3.01
1482 1888 5.185828 CAGGACCGAGATGATATATGGTTGA 59.814 44.000 0.00 0.00 0.00 3.18
1504 1922 2.182842 GCGAAGGGGCTGTATGCAG 61.183 63.158 6.42 6.42 45.15 4.41
1511 1929 2.815647 GAACGAGCGAAGGGGCTG 60.816 66.667 0.00 0.00 44.93 4.85
1515 1949 1.656652 ATGAATGAACGAGCGAAGGG 58.343 50.000 0.00 0.00 0.00 3.95
1603 2053 5.989477 TCGATGGAGACCAAAAATATCACT 58.011 37.500 0.00 0.00 36.95 3.41
1610 2843 3.435327 CGACAATCGATGGAGACCAAAAA 59.565 43.478 6.84 0.00 43.74 1.94
1621 2860 1.325640 CAAGAGCACCGACAATCGATG 59.674 52.381 0.00 0.00 43.74 3.84
1667 2912 5.350633 TCATTCATTTCGGGCATTTGAATC 58.649 37.500 0.00 0.00 35.44 2.52
1718 2967 0.181350 GGTTTGGAGCCGAGGATGAT 59.819 55.000 0.00 0.00 0.00 2.45
1749 2998 4.787534 TCCCCTTTCCAAATATTGCCAAAT 59.212 37.500 0.00 0.00 0.00 2.32
1776 3025 8.483758 TCAATACAACTCCCTACTCTAAATTCC 58.516 37.037 0.00 0.00 0.00 3.01
1812 3061 6.721571 TGGAAATAAAACGACTCATCTCAC 57.278 37.500 0.00 0.00 0.00 3.51
1815 3064 7.112779 AGGATTGGAAATAAAACGACTCATCT 58.887 34.615 0.00 0.00 0.00 2.90
1832 3081 0.239879 GCGCGAAACAAAGGATTGGA 59.760 50.000 12.10 0.00 41.01 3.53
1847 3096 2.395690 GACTTCCAATCGTGCGCG 59.604 61.111 14.79 14.79 39.92 6.86
1917 3166 5.542779 AGTTGTGAAGTGGTATGAGACTTC 58.457 41.667 0.00 0.00 45.60 3.01
1925 3174 7.336396 GGGTAATTAGAGTTGTGAAGTGGTAT 58.664 38.462 0.00 0.00 0.00 2.73
1930 3179 4.600111 TGGGGGTAATTAGAGTTGTGAAGT 59.400 41.667 0.00 0.00 0.00 3.01
1938 3187 4.669700 GTTTGGTTGGGGGTAATTAGAGT 58.330 43.478 0.00 0.00 0.00 3.24
1982 3326 1.423794 TTGGTTGAGGGAGTGGGGAC 61.424 60.000 0.00 0.00 0.00 4.46
2026 3370 1.306997 AGCGAGGGATTGAGGGGAA 60.307 57.895 0.00 0.00 0.00 3.97
2094 3438 0.597568 CGAAGCCCAATGCAAACTCA 59.402 50.000 0.00 0.00 44.83 3.41
2138 3482 1.520600 GGAAACAAACCACGCGGGAT 61.521 55.000 11.66 0.00 41.15 3.85
2265 3613 3.000819 CCGCTGGGGTGTACCTCA 61.001 66.667 3.18 3.18 46.15 3.86
2344 5577 1.446907 CAGCCCTCTAAGTGCTTGTG 58.553 55.000 0.00 0.00 31.77 3.33
2442 5680 4.801330 TCGGTATATTGGGTGCTATGAG 57.199 45.455 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.