Multiple sequence alignment - TraesCS2D01G388600

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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 TraesCS2D01G388600 chr2D 100.000 4065 0 0 1 4065 494657763 494653699 0.000000e+00 7507
1 TraesCS2D01G388600 chr2D 94.561 239 12 1 1 238 507052420 507052182 6.420000e-98 368
2 TraesCS2D01G388600 chr2A 93.985 3907 124 52 235 4065 639055075 639058946 0.000000e+00 5810
3 TraesCS2D01G388600 chr2B 94.784 2876 87 25 235 3085 582314828 582311991 0.000000e+00 4421
4 TraesCS2D01G388600 chr2B 94.269 1012 27 15 3080 4065 582311084 582310078 0.000000e+00 1519
5 TraesCS2D01G388600 chr2B 91.447 152 12 1 2008 2158 785621750 785621901 1.480000e-49 207
6 TraesCS2D01G388600 chr1D 96.639 238 8 0 1 238 469540519 469540756 2.940000e-106 396
7 TraesCS2D01G388600 chr1D 95.614 228 9 1 1 228 371587841 371587615 8.300000e-97 364
8 TraesCS2D01G388600 chr6D 94.515 237 13 0 1 237 427750598 427750834 2.310000e-97 366
9 TraesCS2D01G388600 chr4D 94.760 229 12 0 1 229 333989525 333989753 1.390000e-94 357
10 TraesCS2D01G388600 chr4D 93.333 240 16 0 1 240 435040946 435041185 5.000000e-94 355
11 TraesCS2D01G388600 chr4D 92.857 238 17 0 1 238 351690650 351690887 3.010000e-91 346
12 TraesCS2D01G388600 chr3D 92.000 225 16 2 3 226 456520950 456521173 8.480000e-82 315
13 TraesCS2D01G388600 chr3D 91.534 189 10 3 2 185 67023569 67023756 5.210000e-64 255
14 TraesCS2D01G388600 chr7A 92.763 152 10 1 2008 2158 138911405 138911556 6.840000e-53 219
15 TraesCS2D01G388600 chr5A 94.815 135 7 0 1848 1982 685018089 685017955 1.140000e-50 211
16 TraesCS2D01G388600 chr6B 91.447 152 12 1 2008 2158 708382045 708382196 1.480000e-49 207
17 TraesCS2D01G388600 chr3B 95.238 84 4 0 157 240 661839922 661840005 2.550000e-27 134


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 TraesCS2D01G388600 chr2D 494653699 494657763 4064 True 7507 7507 100.0000 1 4065 1 chr2D.!!$R1 4064
1 TraesCS2D01G388600 chr2A 639055075 639058946 3871 False 5810 5810 93.9850 235 4065 1 chr2A.!!$F1 3830
2 TraesCS2D01G388600 chr2B 582310078 582314828 4750 True 2970 4421 94.5265 235 4065 2 chr2B.!!$R1 3830

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
33 34 0.042188 CACACTACACTGTGCAACGC 60.042 55.0 7.9 0.0 42.39 4.84 F
45 46 0.108186 TGCAACGCCTCACAGATAGG 60.108 55.0 0.0 0.0 37.17 2.57 F
307 310 0.303796 TCTCGAATCGACCGATGACG 59.696 55.0 18.5 18.5 36.95 4.35 F
735 753 0.451383 CGCAGGAGAGACAGACAGAG 59.549 60.0 0.0 0.0 0.00 3.35 F
1422 1449 0.677731 AACCACCATGTGATCCGCAG 60.678 55.0 0.0 0.0 35.23 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 1852 1.129811 GCTTGTAAAAGGCGTATGCGT 59.870 47.619 4.81 0.0 44.10 5.24 R
2229 2276 1.301401 CTTGTCCCTGAACGCCGAA 60.301 57.895 0.00 0.0 0.00 4.30 R
2409 2456 0.618107 TGGTGGCGTTCATAGGGGTA 60.618 55.000 0.00 0.0 0.00 3.69 R
2708 2755 0.174617 CTTGAGAGGGAGAAGCCGAC 59.825 60.000 0.00 0.0 37.63 4.79 R
3604 4582 0.467290 GCACTTGGGTCCAACTTCCA 60.467 55.000 0.00 0.0 0.00 3.53 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
18 19 3.712881 GACACGAAGGCGCCACAC 61.713 66.667 31.54 17.81 42.48 3.82
19 20 4.235762 ACACGAAGGCGCCACACT 62.236 61.111 31.54 9.96 42.48 3.55
20 21 2.048597 CACGAAGGCGCCACACTA 60.049 61.111 31.54 0.00 42.48 2.74
21 22 2.048503 ACGAAGGCGCCACACTAC 60.049 61.111 31.54 11.50 42.48 2.73
22 23 2.048597 CGAAGGCGCCACACTACA 60.049 61.111 31.54 0.00 0.00 2.74
23 24 2.380410 CGAAGGCGCCACACTACAC 61.380 63.158 31.54 8.98 0.00 2.90
24 25 1.004918 GAAGGCGCCACACTACACT 60.005 57.895 31.54 0.00 0.00 3.55
25 26 1.291877 GAAGGCGCCACACTACACTG 61.292 60.000 31.54 0.00 0.00 3.66
26 27 2.030562 GGCGCCACACTACACTGT 59.969 61.111 24.80 0.00 0.00 3.55
27 28 2.317609 GGCGCCACACTACACTGTG 61.318 63.158 24.80 6.19 41.19 3.66
28 29 2.954753 GCGCCACACTACACTGTGC 61.955 63.158 7.90 0.00 40.33 4.57
29 30 1.594021 CGCCACACTACACTGTGCA 60.594 57.895 7.90 0.00 40.33 4.57
30 31 1.157257 CGCCACACTACACTGTGCAA 61.157 55.000 7.90 0.00 40.33 4.08
31 32 0.307760 GCCACACTACACTGTGCAAC 59.692 55.000 7.90 0.00 40.33 4.17
32 33 0.581529 CCACACTACACTGTGCAACG 59.418 55.000 7.90 0.00 42.39 4.10
33 34 0.042188 CACACTACACTGTGCAACGC 60.042 55.000 7.90 0.00 42.39 4.84
34 35 1.157870 ACACTACACTGTGCAACGCC 61.158 55.000 7.90 0.00 42.39 5.68
35 36 0.880278 CACTACACTGTGCAACGCCT 60.880 55.000 7.90 0.00 42.39 5.52
36 37 0.600255 ACTACACTGTGCAACGCCTC 60.600 55.000 7.90 0.00 42.39 4.70
37 38 0.599991 CTACACTGTGCAACGCCTCA 60.600 55.000 7.90 0.00 42.39 3.86
38 39 0.878523 TACACTGTGCAACGCCTCAC 60.879 55.000 7.90 0.00 42.39 3.51
39 40 2.179547 CACTGTGCAACGCCTCACA 61.180 57.895 0.00 4.54 42.39 3.58
41 42 2.503546 TGTGCAACGCCTCACAGA 59.496 55.556 0.00 0.00 42.39 3.41
42 43 1.071299 TGTGCAACGCCTCACAGAT 59.929 52.632 0.00 0.00 42.39 2.90
43 44 0.320050 TGTGCAACGCCTCACAGATA 59.680 50.000 0.00 0.00 42.39 1.98
44 45 1.002366 GTGCAACGCCTCACAGATAG 58.998 55.000 0.00 0.00 33.63 2.08
45 46 0.108186 TGCAACGCCTCACAGATAGG 60.108 55.000 0.00 0.00 37.17 2.57
51 52 3.875838 CCTCACAGATAGGCGCTAC 57.124 57.895 7.64 0.00 0.00 3.58
52 53 1.032794 CCTCACAGATAGGCGCTACA 58.967 55.000 7.64 0.00 0.00 2.74
53 54 1.269309 CCTCACAGATAGGCGCTACAC 60.269 57.143 7.64 0.00 0.00 2.90
55 56 0.595053 CACAGATAGGCGCTACACGG 60.595 60.000 7.64 0.58 43.93 4.94
79 80 4.429212 TCGCACCCGTGTGATCCG 62.429 66.667 0.90 0.00 45.76 4.18
80 81 4.429212 CGCACCCGTGTGATCCGA 62.429 66.667 0.90 0.00 45.76 4.55
81 82 2.047655 GCACCCGTGTGATCCGAA 60.048 61.111 0.90 0.00 45.76 4.30
82 83 1.669760 GCACCCGTGTGATCCGAAA 60.670 57.895 0.90 0.00 45.76 3.46
83 84 1.231958 GCACCCGTGTGATCCGAAAA 61.232 55.000 0.90 0.00 45.76 2.29
84 85 1.448985 CACCCGTGTGATCCGAAAAT 58.551 50.000 0.00 0.00 45.76 1.82
85 86 1.810151 CACCCGTGTGATCCGAAAATT 59.190 47.619 0.00 0.00 45.76 1.82
86 87 3.004171 CACCCGTGTGATCCGAAAATTA 58.996 45.455 0.00 0.00 45.76 1.40
87 88 3.004862 ACCCGTGTGATCCGAAAATTAC 58.995 45.455 0.00 0.00 0.00 1.89
88 89 3.267483 CCCGTGTGATCCGAAAATTACT 58.733 45.455 0.00 0.00 0.00 2.24
89 90 4.081531 ACCCGTGTGATCCGAAAATTACTA 60.082 41.667 0.00 0.00 0.00 1.82
90 91 4.871557 CCCGTGTGATCCGAAAATTACTAA 59.128 41.667 0.00 0.00 0.00 2.24
91 92 5.006358 CCCGTGTGATCCGAAAATTACTAAG 59.994 44.000 0.00 0.00 0.00 2.18
92 93 5.579511 CCGTGTGATCCGAAAATTACTAAGT 59.420 40.000 0.00 0.00 0.00 2.24
93 94 6.237755 CCGTGTGATCCGAAAATTACTAAGTC 60.238 42.308 0.00 0.00 0.00 3.01
94 95 6.309494 CGTGTGATCCGAAAATTACTAAGTCA 59.691 38.462 0.00 0.00 0.00 3.41
95 96 7.462856 CGTGTGATCCGAAAATTACTAAGTCAG 60.463 40.741 0.00 0.00 0.00 3.51
96 97 7.331193 GTGTGATCCGAAAATTACTAAGTCAGT 59.669 37.037 0.00 0.00 41.62 3.41
97 98 7.330946 TGTGATCCGAAAATTACTAAGTCAGTG 59.669 37.037 0.00 0.00 38.24 3.66
98 99 7.331193 GTGATCCGAAAATTACTAAGTCAGTGT 59.669 37.037 0.00 0.00 38.24 3.55
99 100 7.330946 TGATCCGAAAATTACTAAGTCAGTGTG 59.669 37.037 0.00 0.00 38.24 3.82
100 101 5.407387 TCCGAAAATTACTAAGTCAGTGTGC 59.593 40.000 0.00 0.00 38.24 4.57
101 102 5.178623 CCGAAAATTACTAAGTCAGTGTGCA 59.821 40.000 0.00 0.00 38.24 4.57
102 103 6.299604 CGAAAATTACTAAGTCAGTGTGCAG 58.700 40.000 0.00 0.00 38.24 4.41
103 104 5.613358 AAATTACTAAGTCAGTGTGCAGC 57.387 39.130 0.00 0.00 38.24 5.25
104 105 2.347697 TACTAAGTCAGTGTGCAGCG 57.652 50.000 0.00 0.00 38.24 5.18
105 106 0.946221 ACTAAGTCAGTGTGCAGCGC 60.946 55.000 0.00 0.00 35.62 5.92
106 107 1.630244 CTAAGTCAGTGTGCAGCGCC 61.630 60.000 2.29 0.00 0.00 6.53
107 108 2.099652 TAAGTCAGTGTGCAGCGCCT 62.100 55.000 2.29 0.00 0.00 5.52
108 109 2.048222 GTCAGTGTGCAGCGCCTA 60.048 61.111 2.29 0.00 0.00 3.93
109 110 2.097038 GTCAGTGTGCAGCGCCTAG 61.097 63.158 2.29 0.00 0.00 3.02
123 124 1.068250 CCTAGCTCCTAGGCGTTGC 59.932 63.158 2.96 5.87 45.64 4.17
124 125 1.676678 CCTAGCTCCTAGGCGTTGCA 61.677 60.000 2.96 0.00 45.64 4.08
125 126 0.528684 CTAGCTCCTAGGCGTTGCAC 60.529 60.000 2.96 0.00 37.29 4.57
126 127 0.970937 TAGCTCCTAGGCGTTGCACT 60.971 55.000 2.96 0.00 37.29 4.40
127 128 0.970937 AGCTCCTAGGCGTTGCACTA 60.971 55.000 2.96 0.00 37.29 2.74
128 129 0.528684 GCTCCTAGGCGTTGCACTAG 60.529 60.000 2.96 2.78 37.12 2.57
129 130 0.818296 CTCCTAGGCGTTGCACTAGT 59.182 55.000 2.96 0.00 35.93 2.57
130 131 0.530744 TCCTAGGCGTTGCACTAGTG 59.469 55.000 18.93 18.93 35.93 2.74
141 142 3.027312 CACTAGTGCAGCGACTGAG 57.973 57.895 10.54 2.45 32.44 3.35
142 143 0.523519 CACTAGTGCAGCGACTGAGA 59.476 55.000 10.54 0.00 32.44 3.27
143 144 0.808125 ACTAGTGCAGCGACTGAGAG 59.192 55.000 10.46 4.43 32.44 3.20
144 145 0.808125 CTAGTGCAGCGACTGAGAGT 59.192 55.000 10.46 2.71 32.44 3.24
145 146 1.201181 CTAGTGCAGCGACTGAGAGTT 59.799 52.381 10.46 0.00 32.44 3.01
146 147 1.248486 AGTGCAGCGACTGAGAGTTA 58.752 50.000 10.46 0.00 32.44 2.24
147 148 1.201181 AGTGCAGCGACTGAGAGTTAG 59.799 52.381 10.46 0.00 32.44 2.34
148 149 0.528017 TGCAGCGACTGAGAGTTAGG 59.472 55.000 10.46 0.00 32.44 2.69
149 150 0.804156 GCAGCGACTGAGAGTTAGGC 60.804 60.000 10.46 0.00 32.44 3.93
151 152 4.386245 CGACTGAGAGTTAGGCGC 57.614 61.111 0.00 0.00 40.14 6.53
152 153 1.226717 CGACTGAGAGTTAGGCGCC 60.227 63.158 21.89 21.89 40.14 6.53
153 154 1.890894 GACTGAGAGTTAGGCGCCA 59.109 57.895 31.54 12.31 0.00 5.69
154 155 0.458716 GACTGAGAGTTAGGCGCCAC 60.459 60.000 31.54 19.69 0.00 5.01
155 156 1.517257 CTGAGAGTTAGGCGCCACG 60.517 63.158 31.54 1.54 0.00 4.94
156 157 2.202756 GAGAGTTAGGCGCCACGG 60.203 66.667 31.54 0.00 0.00 4.94
157 158 3.718210 GAGAGTTAGGCGCCACGGG 62.718 68.421 31.54 0.00 0.00 5.28
158 159 4.078516 GAGTTAGGCGCCACGGGT 62.079 66.667 31.54 10.27 0.00 5.28
159 160 4.078516 AGTTAGGCGCCACGGGTC 62.079 66.667 31.54 12.28 0.00 4.46
160 161 4.382320 GTTAGGCGCCACGGGTCA 62.382 66.667 31.54 0.02 0.00 4.02
161 162 4.077184 TTAGGCGCCACGGGTCAG 62.077 66.667 31.54 0.00 0.00 3.51
172 173 2.746277 GGGTCAGCCGCGTGAAAT 60.746 61.111 4.92 0.00 34.97 2.17
173 174 1.448893 GGGTCAGCCGCGTGAAATA 60.449 57.895 4.92 0.00 34.97 1.40
174 175 1.429148 GGGTCAGCCGCGTGAAATAG 61.429 60.000 4.92 0.00 34.97 1.73
175 176 0.739813 GGTCAGCCGCGTGAAATAGT 60.740 55.000 4.92 0.00 0.00 2.12
176 177 1.076332 GTCAGCCGCGTGAAATAGTT 58.924 50.000 4.92 0.00 0.00 2.24
177 178 1.463444 GTCAGCCGCGTGAAATAGTTT 59.537 47.619 4.92 0.00 0.00 2.66
178 179 1.730064 TCAGCCGCGTGAAATAGTTTC 59.270 47.619 4.92 0.00 40.08 2.78
179 180 1.463056 CAGCCGCGTGAAATAGTTTCA 59.537 47.619 4.92 1.24 46.68 2.69
189 190 5.917541 TGAAATAGTTTCACGGACAGTTC 57.082 39.130 1.24 0.00 44.21 3.01
190 191 5.361427 TGAAATAGTTTCACGGACAGTTCA 58.639 37.500 1.24 0.00 44.21 3.18
191 192 5.995282 TGAAATAGTTTCACGGACAGTTCAT 59.005 36.000 1.24 0.00 44.21 2.57
192 193 6.485313 TGAAATAGTTTCACGGACAGTTCATT 59.515 34.615 1.24 0.00 44.21 2.57
193 194 6.877611 AATAGTTTCACGGACAGTTCATTT 57.122 33.333 0.00 0.00 0.00 2.32
194 195 6.877611 ATAGTTTCACGGACAGTTCATTTT 57.122 33.333 0.00 0.00 0.00 1.82
195 196 7.972832 ATAGTTTCACGGACAGTTCATTTTA 57.027 32.000 0.00 0.00 0.00 1.52
196 197 6.877611 AGTTTCACGGACAGTTCATTTTAT 57.122 33.333 0.00 0.00 0.00 1.40
197 198 6.668323 AGTTTCACGGACAGTTCATTTTATG 58.332 36.000 0.00 0.00 0.00 1.90
198 199 6.485313 AGTTTCACGGACAGTTCATTTTATGA 59.515 34.615 0.00 0.00 37.55 2.15
199 200 7.174946 AGTTTCACGGACAGTTCATTTTATGAT 59.825 33.333 0.00 0.00 39.39 2.45
200 201 7.447374 TTCACGGACAGTTCATTTTATGATT 57.553 32.000 0.00 0.00 39.39 2.57
201 202 7.447374 TCACGGACAGTTCATTTTATGATTT 57.553 32.000 0.00 0.00 39.39 2.17
202 203 7.304735 TCACGGACAGTTCATTTTATGATTTG 58.695 34.615 0.00 0.00 39.39 2.32
203 204 7.174080 TCACGGACAGTTCATTTTATGATTTGA 59.826 33.333 0.00 0.00 39.39 2.69
204 205 7.970061 CACGGACAGTTCATTTTATGATTTGAT 59.030 33.333 0.00 0.00 39.39 2.57
205 206 8.522830 ACGGACAGTTCATTTTATGATTTGATT 58.477 29.630 0.00 0.00 39.39 2.57
206 207 9.357652 CGGACAGTTCATTTTATGATTTGATTT 57.642 29.630 0.00 0.00 39.39 2.17
209 210 9.912634 ACAGTTCATTTTATGATTTGATTTCGT 57.087 25.926 0.00 0.00 39.39 3.85
227 228 9.834628 TGATTTCGTCAATAGGTTAAATTTGTC 57.165 29.630 0.00 0.00 32.78 3.18
228 229 9.834628 GATTTCGTCAATAGGTTAAATTTGTCA 57.165 29.630 0.00 0.00 0.00 3.58
284 287 3.395858 TCTTAAGCTCTACGTACACGC 57.604 47.619 0.85 0.00 44.43 5.34
305 308 2.014857 ACTTCTCGAATCGACCGATGA 58.985 47.619 0.00 8.81 35.35 2.92
306 309 2.223294 ACTTCTCGAATCGACCGATGAC 60.223 50.000 0.00 3.30 35.35 3.06
307 310 0.303796 TCTCGAATCGACCGATGACG 59.696 55.000 18.50 18.50 36.95 4.35
325 328 5.934935 TGACGACCCAATCTTTTAGAAAC 57.065 39.130 0.00 0.00 0.00 2.78
454 467 6.404293 GGCAACATAGATTAGCCTTTTCGAAA 60.404 38.462 6.47 6.47 42.01 3.46
471 484 2.806745 CGAAAGCCATCCATCGTACCAT 60.807 50.000 0.00 0.00 0.00 3.55
472 485 3.554129 CGAAAGCCATCCATCGTACCATA 60.554 47.826 0.00 0.00 0.00 2.74
477 493 3.864921 GCCATCCATCGTACCATAGGTTC 60.865 52.174 0.00 0.00 37.09 3.62
516 532 4.787871 GCTTGAGCTCCACACAGT 57.212 55.556 12.15 0.00 38.21 3.55
517 533 3.012560 GCTTGAGCTCCACACAGTT 57.987 52.632 12.15 0.00 38.21 3.16
518 534 0.871057 GCTTGAGCTCCACACAGTTC 59.129 55.000 12.15 0.00 38.21 3.01
519 535 1.811558 GCTTGAGCTCCACACAGTTCA 60.812 52.381 12.15 0.00 38.21 3.18
561 577 6.460953 GCTTATTTATTCGGGGCATTTTCTCA 60.461 38.462 0.00 0.00 0.00 3.27
568 584 2.415893 CGGGGCATTTTCTCATGTTGTC 60.416 50.000 0.00 0.00 0.00 3.18
695 711 3.268986 CGAGAGCAGTCAGTCGGT 58.731 61.111 0.00 0.00 0.00 4.69
730 748 1.621992 AAAGACGCAGGAGAGACAGA 58.378 50.000 0.00 0.00 0.00 3.41
731 749 0.885196 AAGACGCAGGAGAGACAGAC 59.115 55.000 0.00 0.00 0.00 3.51
735 753 0.451383 CGCAGGAGAGACAGACAGAG 59.549 60.000 0.00 0.00 0.00 3.35
742 760 1.427368 AGAGACAGACAGAGACCAGGT 59.573 52.381 0.00 0.00 0.00 4.00
968 991 0.987294 CCAAGAGCAAAGGAGGAGGA 59.013 55.000 0.00 0.00 0.00 3.71
969 992 1.065564 CCAAGAGCAAAGGAGGAGGAG 60.066 57.143 0.00 0.00 0.00 3.69
1422 1449 0.677731 AACCACCATGTGATCCGCAG 60.678 55.000 0.00 0.00 35.23 5.18
1436 1463 4.637977 TGATCCGCAGCATAATTAACAACA 59.362 37.500 0.00 0.00 0.00 3.33
1438 1465 4.257731 TCCGCAGCATAATTAACAACAGA 58.742 39.130 0.00 0.00 0.00 3.41
1443 1470 5.335127 CAGCATAATTAACAACAGACTGCC 58.665 41.667 1.25 0.00 0.00 4.85
1444 1471 4.094887 AGCATAATTAACAACAGACTGCCG 59.905 41.667 1.25 0.00 0.00 5.69
1475 1502 4.686972 GGCCAAGAGCATTCTAAATTTCC 58.313 43.478 0.00 0.00 46.50 3.13
1484 1511 6.535274 GCATTCTAAATTTCCAATGCCATC 57.465 37.500 24.07 7.91 43.52 3.51
1511 1538 4.616181 AAATACACCGTAAATCTGCAGC 57.384 40.909 9.47 0.00 0.00 5.25
1786 1813 1.743321 CTCATCCTCCTCCTCACCGC 61.743 65.000 0.00 0.00 0.00 5.68
1825 1852 6.384224 GGTATATACCGACACATTTCATCGA 58.616 40.000 16.11 0.00 38.10 3.59
2229 2276 3.832492 GAGAGCGCGCCCTTCTCT 61.832 66.667 30.53 25.28 39.66 3.10
2409 2456 3.246880 GTCCACCCTTCCACCGGT 61.247 66.667 0.00 0.00 0.00 5.28
2466 2513 5.172205 TCATCACAATGTTGCCAATTCATG 58.828 37.500 0.00 0.00 34.32 3.07
2524 2571 3.055530 GCTCTGTCCATACATATCCAGGG 60.056 52.174 0.00 0.00 34.37 4.45
2809 2856 1.133253 CGCAATCTTCCACTGCACG 59.867 57.895 0.00 0.00 35.78 5.34
2863 2910 1.519455 GACGGTTCCTCTGATGCCG 60.519 63.158 0.00 0.00 41.92 5.69
2918 2965 2.619931 TCCTCATGACAACCCTGAAGA 58.380 47.619 0.00 0.00 0.00 2.87
3070 3117 5.221441 TGCAGACATATTATCTTAGCGGTGT 60.221 40.000 0.00 0.00 0.00 4.16
3085 3132 8.301720 TCTTAGCGGTGTCATCGTAATAATAAT 58.698 33.333 7.44 0.00 0.00 1.28
3088 4049 8.997621 AGCGGTGTCATCGTAATAATAATAAT 57.002 30.769 7.44 0.00 0.00 1.28
3130 4091 3.138283 ACCTGTCTCCTTGGAAATGTTCA 59.862 43.478 0.00 0.00 0.00 3.18
3239 4201 2.693074 CCAAAACTGTTGGCCTGTAACT 59.307 45.455 3.32 0.00 32.18 2.24
3568 4546 4.342092 CCAAACAAACAGAGGAAATCCACT 59.658 41.667 1.67 0.00 37.43 4.00
3570 4548 6.294176 CCAAACAAACAGAGGAAATCCACTAG 60.294 42.308 1.67 0.00 35.12 2.57
3571 4549 5.825593 ACAAACAGAGGAAATCCACTAGA 57.174 39.130 0.00 0.00 35.12 2.43
3604 4582 8.648693 ACACTACAATCTAGAACCAACTAAACT 58.351 33.333 0.00 0.00 0.00 2.66
3649 4627 2.621998 CTGGCTGGGAAAATAGATGCAG 59.378 50.000 0.00 0.00 0.00 4.41
3679 4657 4.664688 ATCCTCATTTCTTCAAGGGTGT 57.335 40.909 0.00 0.00 0.00 4.16
3783 4761 7.809806 GCTATAATGCTCCATCCAAACATTTAC 59.190 37.037 0.00 0.00 33.31 2.01
3790 4788 6.751888 GCTCCATCCAAACATTTACATACAAC 59.248 38.462 0.00 0.00 0.00 3.32
3942 4940 9.706691 TCAAGTTTTACTCCAGTAGAATAACAG 57.293 33.333 0.00 0.00 29.25 3.16
3946 4944 9.485206 GTTTTACTCCAGTAGAATAACAGTTCA 57.515 33.333 0.00 0.00 29.25 3.18
4032 5031 5.047164 CACATTTTCCACATCAATCAAGGGA 60.047 40.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.758770 TAGTGTGGCGCCTTCGTGTC 62.759 60.000 29.70 10.72 38.14 3.67
2 3 2.863346 TAGTGTGGCGCCTTCGTGT 61.863 57.895 29.70 9.85 38.14 4.49
3 4 2.048597 TAGTGTGGCGCCTTCGTG 60.049 61.111 29.70 0.00 38.14 4.35
4 5 2.048503 GTAGTGTGGCGCCTTCGT 60.049 61.111 29.70 12.53 38.14 3.85
5 6 2.048597 TGTAGTGTGGCGCCTTCG 60.049 61.111 29.70 0.00 39.07 3.79
6 7 1.004918 AGTGTAGTGTGGCGCCTTC 60.005 57.895 29.70 20.58 0.00 3.46
7 8 1.301716 CAGTGTAGTGTGGCGCCTT 60.302 57.895 29.70 13.03 0.00 4.35
8 9 2.343758 CAGTGTAGTGTGGCGCCT 59.656 61.111 29.70 9.99 0.00 5.52
9 10 2.030562 ACAGTGTAGTGTGGCGCC 59.969 61.111 22.73 22.73 0.00 6.53
10 11 2.954753 GCACAGTGTAGTGTGGCGC 61.955 63.158 18.52 0.00 46.73 6.53
11 12 1.157257 TTGCACAGTGTAGTGTGGCG 61.157 55.000 18.52 0.00 46.73 5.69
12 13 0.307760 GTTGCACAGTGTAGTGTGGC 59.692 55.000 18.52 12.34 46.73 5.01
13 14 0.581529 CGTTGCACAGTGTAGTGTGG 59.418 55.000 18.52 1.81 46.73 4.17
15 16 1.157870 GGCGTTGCACAGTGTAGTGT 61.158 55.000 1.61 0.00 41.52 3.55
16 17 0.880278 AGGCGTTGCACAGTGTAGTG 60.880 55.000 1.61 0.00 42.37 2.74
17 18 0.600255 GAGGCGTTGCACAGTGTAGT 60.600 55.000 1.61 0.00 0.00 2.73
18 19 0.599991 TGAGGCGTTGCACAGTGTAG 60.600 55.000 1.61 0.00 0.00 2.74
19 20 0.878523 GTGAGGCGTTGCACAGTGTA 60.879 55.000 1.61 0.00 35.19 2.90
20 21 2.180204 GTGAGGCGTTGCACAGTGT 61.180 57.895 1.61 0.00 35.19 3.55
21 22 2.179547 TGTGAGGCGTTGCACAGTG 61.180 57.895 0.00 0.00 39.86 3.66
22 23 2.189257 TGTGAGGCGTTGCACAGT 59.811 55.556 0.00 0.00 39.86 3.55
24 25 0.320050 TATCTGTGAGGCGTTGCACA 59.680 50.000 0.00 0.00 42.25 4.57
25 26 1.002366 CTATCTGTGAGGCGTTGCAC 58.998 55.000 0.00 0.00 35.63 4.57
26 27 0.108186 CCTATCTGTGAGGCGTTGCA 60.108 55.000 0.00 0.00 0.00 4.08
27 28 2.682893 CCTATCTGTGAGGCGTTGC 58.317 57.895 0.00 0.00 0.00 4.17
33 34 1.032794 TGTAGCGCCTATCTGTGAGG 58.967 55.000 2.29 0.00 37.12 3.86
34 35 1.598183 CGTGTAGCGCCTATCTGTGAG 60.598 57.143 2.29 0.00 0.00 3.51
35 36 0.380733 CGTGTAGCGCCTATCTGTGA 59.619 55.000 2.29 0.00 0.00 3.58
36 37 0.595053 CCGTGTAGCGCCTATCTGTG 60.595 60.000 2.29 0.00 39.71 3.66
37 38 1.734137 CCGTGTAGCGCCTATCTGT 59.266 57.895 2.29 0.00 39.71 3.41
38 39 1.661821 GCCGTGTAGCGCCTATCTG 60.662 63.158 2.29 0.00 39.71 2.90
39 40 2.728817 GCCGTGTAGCGCCTATCT 59.271 61.111 2.29 0.00 39.71 1.98
40 41 2.355956 GGCCGTGTAGCGCCTATC 60.356 66.667 2.29 0.00 39.71 2.08
41 42 3.151710 TGGCCGTGTAGCGCCTAT 61.152 61.111 2.29 0.00 39.71 2.57
42 43 3.833645 CTGGCCGTGTAGCGCCTA 61.834 66.667 2.29 0.00 39.71 3.93
60 61 3.179265 GATCACACGGGTGCGACG 61.179 66.667 14.50 0.00 44.87 5.12
61 62 2.813908 GGATCACACGGGTGCGAC 60.814 66.667 14.50 6.54 44.87 5.19
62 63 4.429212 CGGATCACACGGGTGCGA 62.429 66.667 14.50 0.00 44.87 5.10
63 64 3.925362 TTCGGATCACACGGGTGCG 62.925 63.158 14.50 11.68 44.87 5.34
64 65 1.231958 TTTTCGGATCACACGGGTGC 61.232 55.000 14.50 0.00 44.87 5.01
65 66 1.448985 ATTTTCGGATCACACGGGTG 58.551 50.000 12.84 12.84 46.66 4.61
66 67 2.194201 AATTTTCGGATCACACGGGT 57.806 45.000 0.00 0.00 0.00 5.28
67 68 3.267483 AGTAATTTTCGGATCACACGGG 58.733 45.455 0.00 0.00 0.00 5.28
68 69 5.579511 ACTTAGTAATTTTCGGATCACACGG 59.420 40.000 0.00 0.00 0.00 4.94
69 70 6.309494 TGACTTAGTAATTTTCGGATCACACG 59.691 38.462 0.00 0.00 0.00 4.49
70 71 7.331193 ACTGACTTAGTAATTTTCGGATCACAC 59.669 37.037 0.00 0.00 38.04 3.82
71 72 7.330946 CACTGACTTAGTAATTTTCGGATCACA 59.669 37.037 0.00 0.00 37.60 3.58
72 73 7.331193 ACACTGACTTAGTAATTTTCGGATCAC 59.669 37.037 0.00 0.00 37.60 3.06
73 74 7.330946 CACACTGACTTAGTAATTTTCGGATCA 59.669 37.037 0.00 0.00 37.60 2.92
74 75 7.674240 GCACACTGACTTAGTAATTTTCGGATC 60.674 40.741 0.00 0.00 37.60 3.36
75 76 6.092259 GCACACTGACTTAGTAATTTTCGGAT 59.908 38.462 0.00 0.00 37.60 4.18
76 77 5.407387 GCACACTGACTTAGTAATTTTCGGA 59.593 40.000 0.00 0.00 37.60 4.55
77 78 5.178623 TGCACACTGACTTAGTAATTTTCGG 59.821 40.000 0.00 0.00 37.60 4.30
78 79 6.223138 TGCACACTGACTTAGTAATTTTCG 57.777 37.500 0.00 0.00 37.60 3.46
79 80 6.080406 GCTGCACACTGACTTAGTAATTTTC 58.920 40.000 0.00 0.00 37.60 2.29
80 81 5.334105 CGCTGCACACTGACTTAGTAATTTT 60.334 40.000 0.00 0.00 37.60 1.82
81 82 4.152402 CGCTGCACACTGACTTAGTAATTT 59.848 41.667 0.00 0.00 37.60 1.82
82 83 3.679980 CGCTGCACACTGACTTAGTAATT 59.320 43.478 0.00 0.00 37.60 1.40
83 84 3.254060 CGCTGCACACTGACTTAGTAAT 58.746 45.455 0.00 0.00 37.60 1.89
84 85 2.672714 CGCTGCACACTGACTTAGTAA 58.327 47.619 0.00 0.00 37.60 2.24
85 86 1.668919 GCGCTGCACACTGACTTAGTA 60.669 52.381 0.00 0.00 37.60 1.82
86 87 0.946221 GCGCTGCACACTGACTTAGT 60.946 55.000 0.00 0.00 41.36 2.24
87 88 1.630244 GGCGCTGCACACTGACTTAG 61.630 60.000 7.64 0.00 0.00 2.18
88 89 1.667830 GGCGCTGCACACTGACTTA 60.668 57.895 7.64 0.00 0.00 2.24
89 90 2.099652 TAGGCGCTGCACACTGACTT 62.100 55.000 7.64 0.00 0.00 3.01
90 91 2.498291 CTAGGCGCTGCACACTGACT 62.498 60.000 7.64 0.00 0.00 3.41
91 92 2.048222 TAGGCGCTGCACACTGAC 60.048 61.111 7.64 0.00 0.00 3.51
92 93 2.262603 CTAGGCGCTGCACACTGA 59.737 61.111 7.64 0.00 0.00 3.41
93 94 3.494336 GCTAGGCGCTGCACACTG 61.494 66.667 7.64 0.00 35.14 3.66
106 107 0.528684 GTGCAACGCCTAGGAGCTAG 60.529 60.000 14.75 3.92 34.16 3.42
107 108 0.970937 AGTGCAACGCCTAGGAGCTA 60.971 55.000 14.75 0.00 45.86 3.32
108 109 0.970937 TAGTGCAACGCCTAGGAGCT 60.971 55.000 14.75 3.79 45.86 4.09
109 110 0.528684 CTAGTGCAACGCCTAGGAGC 60.529 60.000 14.75 10.85 45.86 4.70
110 111 0.818296 ACTAGTGCAACGCCTAGGAG 59.182 55.000 14.75 12.99 45.86 3.69
111 112 0.530744 CACTAGTGCAACGCCTAGGA 59.469 55.000 14.75 0.00 45.86 2.94
112 113 3.050703 CACTAGTGCAACGCCTAGG 57.949 57.895 10.54 3.67 45.86 3.02
123 124 0.523519 TCTCAGTCGCTGCACTAGTG 59.476 55.000 18.93 18.93 38.28 2.74
124 125 0.808125 CTCTCAGTCGCTGCACTAGT 59.192 55.000 0.00 0.00 0.00 2.57
125 126 0.808125 ACTCTCAGTCGCTGCACTAG 59.192 55.000 0.00 0.00 0.00 2.57
126 127 1.248486 AACTCTCAGTCGCTGCACTA 58.752 50.000 0.00 0.00 0.00 2.74
127 128 1.201181 CTAACTCTCAGTCGCTGCACT 59.799 52.381 0.00 0.00 0.00 4.40
128 129 1.623359 CTAACTCTCAGTCGCTGCAC 58.377 55.000 0.00 0.00 0.00 4.57
129 130 0.528017 CCTAACTCTCAGTCGCTGCA 59.472 55.000 0.00 0.00 0.00 4.41
130 131 0.804156 GCCTAACTCTCAGTCGCTGC 60.804 60.000 2.45 0.00 0.00 5.25
131 132 0.524392 CGCCTAACTCTCAGTCGCTG 60.524 60.000 1.02 1.02 0.00 5.18
132 133 1.803943 CGCCTAACTCTCAGTCGCT 59.196 57.895 0.00 0.00 0.00 4.93
133 134 1.874466 GCGCCTAACTCTCAGTCGC 60.874 63.158 0.00 0.00 32.20 5.19
134 135 1.226717 GGCGCCTAACTCTCAGTCG 60.227 63.158 22.15 0.00 0.00 4.18
135 136 0.458716 GTGGCGCCTAACTCTCAGTC 60.459 60.000 29.70 0.00 0.00 3.51
136 137 1.592223 GTGGCGCCTAACTCTCAGT 59.408 57.895 29.70 0.00 0.00 3.41
137 138 1.517257 CGTGGCGCCTAACTCTCAG 60.517 63.158 29.70 0.96 0.00 3.35
138 139 2.571757 CGTGGCGCCTAACTCTCA 59.428 61.111 29.70 0.07 0.00 3.27
139 140 2.202756 CCGTGGCGCCTAACTCTC 60.203 66.667 29.70 8.06 0.00 3.20
140 141 3.771160 CCCGTGGCGCCTAACTCT 61.771 66.667 29.70 0.00 0.00 3.24
141 142 4.078516 ACCCGTGGCGCCTAACTC 62.079 66.667 29.70 11.56 0.00 3.01
142 143 4.078516 GACCCGTGGCGCCTAACT 62.079 66.667 29.70 5.90 0.00 2.24
143 144 4.382320 TGACCCGTGGCGCCTAAC 62.382 66.667 29.70 17.80 0.00 2.34
144 145 4.077184 CTGACCCGTGGCGCCTAA 62.077 66.667 29.70 4.80 0.00 2.69
155 156 1.429148 CTATTTCACGCGGCTGACCC 61.429 60.000 12.47 0.00 0.00 4.46
156 157 0.739813 ACTATTTCACGCGGCTGACC 60.740 55.000 12.47 0.00 0.00 4.02
157 158 1.076332 AACTATTTCACGCGGCTGAC 58.924 50.000 12.47 0.00 0.00 3.51
158 159 1.730064 GAAACTATTTCACGCGGCTGA 59.270 47.619 12.47 2.44 39.45 4.26
159 160 1.463056 TGAAACTATTTCACGCGGCTG 59.537 47.619 12.47 0.00 44.21 4.85
160 161 1.803334 TGAAACTATTTCACGCGGCT 58.197 45.000 12.47 0.00 44.21 5.52
167 168 5.361427 TGAACTGTCCGTGAAACTATTTCA 58.639 37.500 0.00 0.00 46.68 2.69
168 169 5.917541 TGAACTGTCCGTGAAACTATTTC 57.082 39.130 0.00 0.00 40.08 2.17
169 170 6.877611 AATGAACTGTCCGTGAAACTATTT 57.122 33.333 0.00 0.00 31.75 1.40
170 171 6.877611 AAATGAACTGTCCGTGAAACTATT 57.122 33.333 0.00 0.00 31.75 1.73
171 172 6.877611 AAAATGAACTGTCCGTGAAACTAT 57.122 33.333 0.00 0.00 31.75 2.12
172 173 7.658167 TCATAAAATGAACTGTCCGTGAAACTA 59.342 33.333 0.00 0.00 36.11 2.24
173 174 6.485313 TCATAAAATGAACTGTCCGTGAAACT 59.515 34.615 0.00 0.00 36.11 2.66
174 175 6.664515 TCATAAAATGAACTGTCCGTGAAAC 58.335 36.000 0.00 0.00 36.11 2.78
175 176 6.869315 TCATAAAATGAACTGTCCGTGAAA 57.131 33.333 0.00 0.00 36.11 2.69
176 177 7.447374 AATCATAAAATGAACTGTCCGTGAA 57.553 32.000 0.00 0.00 43.50 3.18
177 178 7.174080 TCAAATCATAAAATGAACTGTCCGTGA 59.826 33.333 0.00 0.00 43.50 4.35
178 179 7.304735 TCAAATCATAAAATGAACTGTCCGTG 58.695 34.615 0.00 0.00 43.50 4.94
179 180 7.447374 TCAAATCATAAAATGAACTGTCCGT 57.553 32.000 0.00 0.00 43.50 4.69
180 181 8.915871 AATCAAATCATAAAATGAACTGTCCG 57.084 30.769 0.00 0.00 43.50 4.79
183 184 9.912634 ACGAAATCAAATCATAAAATGAACTGT 57.087 25.926 0.00 0.00 43.50 3.55
201 202 9.834628 GACAAATTTAACCTATTGACGAAATCA 57.165 29.630 0.00 0.00 34.65 2.57
202 203 9.834628 TGACAAATTTAACCTATTGACGAAATC 57.165 29.630 0.00 0.00 0.00 2.17
210 211 9.824534 GGCAAATTTGACAAATTTAACCTATTG 57.175 29.630 29.34 19.77 46.34 1.90
211 212 8.716909 CGGCAAATTTGACAAATTTAACCTATT 58.283 29.630 30.99 15.15 46.34 1.73
212 213 7.148490 GCGGCAAATTTGACAAATTTAACCTAT 60.148 33.333 30.99 15.65 46.34 2.57
213 214 6.146347 GCGGCAAATTTGACAAATTTAACCTA 59.854 34.615 30.99 5.02 46.34 3.08
214 215 5.049749 GCGGCAAATTTGACAAATTTAACCT 60.050 36.000 30.99 16.64 46.34 3.50
215 216 5.143660 GCGGCAAATTTGACAAATTTAACC 58.856 37.500 29.34 28.65 46.34 2.85
216 217 5.742446 TGCGGCAAATTTGACAAATTTAAC 58.258 33.333 29.34 24.33 46.34 2.01
217 218 5.525378 ACTGCGGCAAATTTGACAAATTTAA 59.475 32.000 29.34 16.21 46.34 1.52
218 219 5.053145 ACTGCGGCAAATTTGACAAATTTA 58.947 33.333 29.34 17.47 46.34 1.40
220 221 3.465871 ACTGCGGCAAATTTGACAAATT 58.534 36.364 23.49 18.41 42.62 1.82
221 222 3.110447 ACTGCGGCAAATTTGACAAAT 57.890 38.095 23.49 7.62 35.35 2.32
222 223 2.593346 ACTGCGGCAAATTTGACAAA 57.407 40.000 23.49 9.87 35.35 2.83
223 224 2.200067 CAACTGCGGCAAATTTGACAA 58.800 42.857 23.49 10.23 35.35 3.18
224 225 1.135915 ACAACTGCGGCAAATTTGACA 59.864 42.857 23.49 14.93 35.35 3.58
225 226 1.786579 GACAACTGCGGCAAATTTGAC 59.213 47.619 22.31 18.50 0.00 3.18
226 227 1.406898 TGACAACTGCGGCAAATTTGA 59.593 42.857 22.31 0.00 0.00 2.69
227 228 1.788308 CTGACAACTGCGGCAAATTTG 59.212 47.619 14.03 14.03 0.00 2.32
228 229 1.869342 GCTGACAACTGCGGCAAATTT 60.869 47.619 3.44 0.00 37.58 1.82
229 230 0.318955 GCTGACAACTGCGGCAAATT 60.319 50.000 3.44 0.00 37.58 1.82
230 231 1.286880 GCTGACAACTGCGGCAAAT 59.713 52.632 3.44 0.00 37.58 2.32
231 232 2.117779 TGCTGACAACTGCGGCAAA 61.118 52.632 3.44 0.00 44.07 3.68
232 233 2.515757 TGCTGACAACTGCGGCAA 60.516 55.556 3.44 0.00 44.07 4.52
233 234 3.279116 GTGCTGACAACTGCGGCA 61.279 61.111 1.29 1.29 44.77 5.69
234 235 3.245948 CTGTGCTGACAACTGCGGC 62.246 63.158 0.00 0.00 42.50 6.53
235 236 2.941333 CTGTGCTGACAACTGCGG 59.059 61.111 0.00 0.00 42.50 5.69
236 237 2.249535 AGCTGTGCTGACAACTGCG 61.250 57.895 0.00 0.00 42.50 5.18
237 238 3.741860 AGCTGTGCTGACAACTGC 58.258 55.556 0.00 1.94 37.57 4.40
284 287 2.112522 CATCGGTCGATTCGAGAAGTG 58.887 52.381 9.42 3.33 40.09 3.16
305 308 5.127491 TGTGTTTCTAAAAGATTGGGTCGT 58.873 37.500 0.00 0.00 0.00 4.34
306 309 5.238650 ACTGTGTTTCTAAAAGATTGGGTCG 59.761 40.000 0.00 0.00 0.00 4.79
307 310 6.635030 ACTGTGTTTCTAAAAGATTGGGTC 57.365 37.500 0.00 0.00 0.00 4.46
454 467 1.902508 CCTATGGTACGATGGATGGCT 59.097 52.381 2.71 0.00 0.00 4.75
471 484 3.764434 GCCTGATCTCGGATATGAACCTA 59.236 47.826 5.89 0.00 0.00 3.08
472 485 2.564947 GCCTGATCTCGGATATGAACCT 59.435 50.000 5.89 0.00 0.00 3.50
477 493 4.569966 GCTAATTGCCTGATCTCGGATATG 59.430 45.833 5.89 0.00 35.15 1.78
513 529 6.817641 AGCTAGAGAGTTTCATGAATGAACTG 59.182 38.462 14.50 3.26 45.63 3.16
516 532 9.896645 AATAAGCTAGAGAGTTTCATGAATGAA 57.103 29.630 9.40 1.55 44.42 2.57
517 533 9.896645 AAATAAGCTAGAGAGTTTCATGAATGA 57.103 29.630 9.40 0.00 34.44 2.57
536 552 5.842907 AGAAAATGCCCCGAATAAATAAGC 58.157 37.500 0.00 0.00 0.00 3.09
537 553 7.038154 TGAGAAAATGCCCCGAATAAATAAG 57.962 36.000 0.00 0.00 0.00 1.73
544 560 2.738743 ACATGAGAAAATGCCCCGAAT 58.261 42.857 0.00 0.00 0.00 3.34
561 577 3.120338 CCTTATTTGCACGACGACAACAT 60.120 43.478 0.00 5.38 0.00 2.71
568 584 2.734606 TGAACTCCTTATTTGCACGACG 59.265 45.455 0.00 0.00 0.00 5.12
651 667 2.359107 TGGGTCGAGAGCGTACGT 60.359 61.111 17.90 3.43 38.98 3.57
730 748 2.683768 AGTTCAAGACCTGGTCTCTGT 58.316 47.619 28.46 11.66 42.59 3.41
731 749 4.082845 TCTAGTTCAAGACCTGGTCTCTG 58.917 47.826 28.46 24.75 42.59 3.35
735 753 3.259625 AGCTTCTAGTTCAAGACCTGGTC 59.740 47.826 19.20 19.20 0.00 4.02
742 760 3.071602 AGGTTGCAGCTTCTAGTTCAAGA 59.928 43.478 0.00 0.00 0.00 3.02
841 859 2.426023 GACGGTGGGCAGTGAAGT 59.574 61.111 0.00 0.00 0.00 3.01
1422 1449 4.094294 TCGGCAGTCTGTTGTTAATTATGC 59.906 41.667 0.93 0.00 0.00 3.14
1444 1471 3.431725 CTCTTGGCCGGCCGTTTC 61.432 66.667 39.00 17.07 39.42 2.78
1475 1502 4.104776 GTGTATTTTGGACGATGGCATTG 58.895 43.478 13.27 13.27 0.00 2.82
1484 1511 5.556470 CAGATTTACGGTGTATTTTGGACG 58.444 41.667 0.00 0.00 0.00 4.79
1511 1538 5.321516 GGACAACCAAAACGATAAATCGAG 58.678 41.667 18.54 5.82 43.36 4.04
1546 1573 7.753309 AGTAGTATACAAACATTTGCAACCA 57.247 32.000 0.00 0.00 46.26 3.67
1786 1813 4.815533 ATATACCTGTAGCAGAGGCATG 57.184 45.455 0.00 0.00 44.61 4.06
1825 1852 1.129811 GCTTGTAAAAGGCGTATGCGT 59.870 47.619 4.81 0.00 44.10 5.24
2229 2276 1.301401 CTTGTCCCTGAACGCCGAA 60.301 57.895 0.00 0.00 0.00 4.30
2379 2426 3.267233 TGGACCTTGGCCAGCCAT 61.267 61.111 13.10 0.00 46.64 4.40
2409 2456 0.618107 TGGTGGCGTTCATAGGGGTA 60.618 55.000 0.00 0.00 0.00 3.69
2466 2513 5.148651 ACATACACAAGTTAGTGGGAGTC 57.851 43.478 9.32 0.00 43.72 3.36
2524 2571 1.354506 GATTGATGCCGTGCAGAGC 59.645 57.895 4.90 0.84 43.65 4.09
2708 2755 0.174617 CTTGAGAGGGAGAAGCCGAC 59.825 60.000 0.00 0.00 37.63 4.79
2833 2880 3.310860 AACCGTCCACTCCGATGGC 62.311 63.158 0.00 0.00 41.92 4.40
2836 2883 3.295800 GGAACCGTCCACTCCGAT 58.704 61.111 0.00 0.00 44.26 4.18
2881 2928 5.034852 TGAGGAACACATTCAGAAAGACA 57.965 39.130 0.00 0.00 36.46 3.41
2887 2934 4.622260 TGTCATGAGGAACACATTCAGA 57.378 40.909 0.00 0.00 37.60 3.27
3085 3132 6.702723 GGTAAGCGTATGTCCATGTTGTATTA 59.297 38.462 0.00 0.00 0.00 0.98
3088 4049 4.160814 AGGTAAGCGTATGTCCATGTTGTA 59.839 41.667 0.00 0.00 0.00 2.41
3089 4050 3.055385 AGGTAAGCGTATGTCCATGTTGT 60.055 43.478 0.00 0.00 0.00 3.32
3500 4478 5.426504 CACTGTTATGCCTCAGAAGAAGAT 58.573 41.667 0.00 0.00 35.84 2.40
3570 4548 8.999431 TGGTTCTAGATTGTAGTGTGATTTTTC 58.001 33.333 0.00 0.00 0.00 2.29
3571 4549 8.918202 TGGTTCTAGATTGTAGTGTGATTTTT 57.082 30.769 0.00 0.00 0.00 1.94
3604 4582 0.467290 GCACTTGGGTCCAACTTCCA 60.467 55.000 0.00 0.00 0.00 3.53
3617 4595 1.970114 CCAGCCAGGTGAGCACTTG 60.970 63.158 5.83 5.83 38.04 3.16
3618 4596 2.433446 CCAGCCAGGTGAGCACTT 59.567 61.111 0.00 0.00 0.00 3.16
3619 4597 3.644606 CCCAGCCAGGTGAGCACT 61.645 66.667 0.00 0.00 34.66 4.40
3620 4598 2.697147 TTTCCCAGCCAGGTGAGCAC 62.697 60.000 0.00 0.00 34.66 4.40
3621 4599 2.005606 TTTTCCCAGCCAGGTGAGCA 62.006 55.000 0.00 0.00 34.66 4.26
3649 4627 7.811713 CCTTGAAGAAATGAGGATTTGAACTTC 59.188 37.037 0.00 0.00 34.00 3.01
3942 4940 6.856426 GCAAGGTAACATTTGTCTAAGTGAAC 59.144 38.462 0.00 0.00 41.41 3.18
3946 4944 5.381757 TGGCAAGGTAACATTTGTCTAAGT 58.618 37.500 0.00 0.00 41.41 2.24
4032 5031 5.841957 ACTCTTTTGCAGTGAACATTTCT 57.158 34.783 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.