Multiple sequence alignment - TraesCS4D01G342400

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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 TraesCS4D01G342400 chr4D 100.000 3001 0 0 1 3001 498901729 498898729 0.000000e+00 5542.0
1 TraesCS4D01G342400 chr5A 94.203 759 23 9 1404 2158 679667359 679666618 0.000000e+00 1138.0
2 TraesCS4D01G342400 chr5A 89.704 845 43 14 2182 3001 679666686 679665861 0.000000e+00 1038.0
3 TraesCS4D01G342400 chr5A 92.086 417 25 3 864 1277 679668076 679667665 5.580000e-162 580.0
4 TraesCS4D01G342400 chr5A 90.428 397 38 0 81 477 679671609 679671213 9.530000e-145 523.0
5 TraesCS4D01G342400 chr5A 86.889 389 30 9 475 849 679668522 679668141 1.660000e-112 416.0
6 TraesCS4D01G342400 chr4B 89.567 786 31 17 1412 2158 641270684 641269911 0.000000e+00 950.0
7 TraesCS4D01G342400 chr4B 94.251 574 26 3 2429 3001 641269847 641269280 0.000000e+00 870.0
8 TraesCS4D01G342400 chr4B 93.814 388 16 5 843 1222 641271515 641271128 7.210000e-161 577.0
9 TraesCS4D01G342400 chr3B 82.143 112 20 0 1669 1780 761195837 761195948 2.460000e-16 97.1
10 TraesCS4D01G342400 chr3B 80.000 100 18 2 1891 1989 761062196 761062294 4.150000e-09 73.1


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 TraesCS4D01G342400 chr4D 498898729 498901729 3000 True 5542 5542 100.000 1 3001 1 chr4D.!!$R1 3000
1 TraesCS4D01G342400 chr5A 679665861 679671609 5748 True 739 1138 90.662 81 3001 5 chr5A.!!$R1 2920
2 TraesCS4D01G342400 chr4B 641269280 641271515 2235 True 799 950 92.544 843 3001 3 chr4B.!!$R1 2158

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
75 76 0.395724 GATTGGAATGGCCCGACCTT 60.396 55.0 0.0 0.0 40.22 3.50 F
222 223 0.407139 ATTTCACTCCTGCCAAGCCT 59.593 50.0 0.0 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 4063 0.038251 CAGAGGTGCTGCACGAACTA 60.038 55.0 24.86 0.0 37.9 2.24 R
2015 5110 0.183971 TGGCCGGACTTGGAGAAAAA 59.816 50.0 9.82 0.0 0.0 1.94 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.647771 GGGAGGCAGGGTCGGTTT 61.648 66.667 0.00 0.00 0.00 3.27
41 42 2.046217 GGAGGCAGGGTCGGTTTC 60.046 66.667 0.00 0.00 0.00 2.78
42 43 2.747686 GAGGCAGGGTCGGTTTCA 59.252 61.111 0.00 0.00 0.00 2.69
43 44 1.671379 GAGGCAGGGTCGGTTTCAC 60.671 63.158 0.00 0.00 0.00 3.18
44 45 2.671963 GGCAGGGTCGGTTTCACC 60.672 66.667 0.00 0.00 34.05 4.02
64 65 2.516930 CTGGCGCCCGATTGGAAT 60.517 61.111 26.77 0.00 37.49 3.01
65 66 2.828095 TGGCGCCCGATTGGAATG 60.828 61.111 26.77 0.00 37.49 2.67
66 67 3.595758 GGCGCCCGATTGGAATGG 61.596 66.667 18.11 0.00 37.49 3.16
67 68 4.270376 GCGCCCGATTGGAATGGC 62.270 66.667 0.00 0.00 40.54 4.40
68 69 3.595758 CGCCCGATTGGAATGGCC 61.596 66.667 0.00 0.00 40.87 5.36
69 70 3.226537 GCCCGATTGGAATGGCCC 61.227 66.667 0.00 0.00 37.94 5.80
70 71 2.906897 CCCGATTGGAATGGCCCG 60.907 66.667 0.00 0.00 37.49 6.13
71 72 2.191908 CCGATTGGAATGGCCCGA 59.808 61.111 0.00 0.00 37.49 5.14
72 73 2.186826 CCGATTGGAATGGCCCGAC 61.187 63.158 0.00 0.00 37.49 4.79
73 74 2.186826 CGATTGGAATGGCCCGACC 61.187 63.158 0.00 0.57 39.84 4.79
74 75 1.227383 GATTGGAATGGCCCGACCT 59.773 57.895 0.00 0.00 40.22 3.85
75 76 0.395724 GATTGGAATGGCCCGACCTT 60.396 55.000 0.00 0.00 40.22 3.50
76 77 0.684153 ATTGGAATGGCCCGACCTTG 60.684 55.000 0.00 0.00 40.22 3.61
77 78 2.440247 GGAATGGCCCGACCTTGG 60.440 66.667 0.00 0.00 40.22 3.61
93 94 4.191015 GGGAAGGACGATGGGGGC 62.191 72.222 0.00 0.00 0.00 5.80
94 95 3.090532 GGAAGGACGATGGGGGCT 61.091 66.667 0.00 0.00 0.00 5.19
100 101 4.115199 ACGATGGGGGCTTCCTGC 62.115 66.667 0.00 0.00 41.94 4.85
114 115 1.890979 CCTGCGGCTCCATGATGAC 60.891 63.158 0.00 0.00 0.00 3.06
168 169 2.209064 GACAGCAAGGTAGCGGACGA 62.209 60.000 0.00 0.00 40.15 4.20
194 195 4.082523 CAAGAGCGGGAAGGGCGA 62.083 66.667 0.00 0.00 35.00 5.54
204 205 1.376812 GAAGGGCGACGGGTGAAAT 60.377 57.895 0.00 0.00 0.00 2.17
222 223 0.407139 ATTTCACTCCTGCCAAGCCT 59.593 50.000 0.00 0.00 0.00 4.58
227 228 4.399395 TCCTGCCAAGCCTGAGCG 62.399 66.667 0.00 0.00 46.67 5.03
235 236 2.515901 AGCCTGAGCGGGTTTTGT 59.484 55.556 0.00 0.00 41.88 2.83
236 237 1.898574 AGCCTGAGCGGGTTTTGTG 60.899 57.895 0.00 0.00 41.88 3.33
251 252 1.032794 TTGTGTATGCGCAAACCCAA 58.967 45.000 17.11 12.91 41.52 4.12
253 254 0.732538 GTGTATGCGCAAACCCAAGC 60.733 55.000 17.11 0.00 0.00 4.01
254 255 0.893270 TGTATGCGCAAACCCAAGCT 60.893 50.000 17.11 0.00 0.00 3.74
255 256 1.091537 GTATGCGCAAACCCAAGCTA 58.908 50.000 17.11 0.00 0.00 3.32
278 279 4.344102 ACCAATACTCTACATATGCGGTGT 59.656 41.667 1.58 5.67 0.00 4.16
281 282 2.108168 ACTCTACATATGCGGTGTGGT 58.892 47.619 1.58 0.00 31.00 4.16
304 305 5.738619 AGGCCCATTTTTAAGTTTACTGG 57.261 39.130 0.00 0.00 0.00 4.00
306 307 4.323180 GGCCCATTTTTAAGTTTACTGGGG 60.323 45.833 6.83 0.00 41.77 4.96
307 308 4.323180 GCCCATTTTTAAGTTTACTGGGGG 60.323 45.833 6.83 0.00 41.77 5.40
316 317 4.741928 AGTTTACTGGGGGAAAATGAGT 57.258 40.909 0.00 0.00 0.00 3.41
332 333 7.148787 GGAAAATGAGTACACTCGAGTTTACAG 60.149 40.741 32.45 18.39 45.72 2.74
489 3183 0.601558 GGCGAGTCCAAGTAGTGACA 59.398 55.000 0.00 0.00 33.89 3.58
496 3190 2.738846 GTCCAAGTAGTGACATGCAGTG 59.261 50.000 0.00 0.00 0.00 3.66
516 3210 8.094548 TGCAGTGTAGCTTATTTTTCTTCTCTA 58.905 33.333 0.00 0.00 34.99 2.43
771 3479 6.545504 AAAAGTGATAGTGTGTACTGCAAG 57.454 37.500 0.00 0.00 37.78 4.01
833 3541 1.065126 AGCATTTACCACTCAGCTCCC 60.065 52.381 0.00 0.00 0.00 4.30
966 3731 1.908340 ATCCTCACTCCAGCAGCACC 61.908 60.000 0.00 0.00 0.00 5.01
993 3759 3.673484 GCACCAACACCGCAGCAT 61.673 61.111 0.00 0.00 0.00 3.79
994 3760 3.041701 CACCAACACCGCAGCATT 58.958 55.556 0.00 0.00 0.00 3.56
1195 3964 3.458189 GAGGATGAAGACGGTAACCATG 58.542 50.000 0.00 0.00 0.00 3.66
1223 3993 3.831911 CTCCCTTTTGCATTTCCACCTTA 59.168 43.478 0.00 0.00 0.00 2.69
1224 3994 3.576550 TCCCTTTTGCATTTCCACCTTAC 59.423 43.478 0.00 0.00 0.00 2.34
1225 3995 3.306710 CCCTTTTGCATTTCCACCTTACC 60.307 47.826 0.00 0.00 0.00 2.85
1226 3996 3.578282 CCTTTTGCATTTCCACCTTACCT 59.422 43.478 0.00 0.00 0.00 3.08
1227 3997 4.040339 CCTTTTGCATTTCCACCTTACCTT 59.960 41.667 0.00 0.00 0.00 3.50
1228 3998 4.599047 TTTGCATTTCCACCTTACCTTG 57.401 40.909 0.00 0.00 0.00 3.61
1230 4000 2.890311 TGCATTTCCACCTTACCTTGTG 59.110 45.455 0.00 0.00 0.00 3.33
1231 4001 3.153919 GCATTTCCACCTTACCTTGTGA 58.846 45.455 0.00 0.00 34.37 3.58
1251 4021 9.429359 CTTGTGATATCTTCTTTCAGTTACACT 57.571 33.333 3.98 0.00 0.00 3.55
1259 4029 4.439057 TCTTTCAGTTACACTGTGTGACC 58.561 43.478 26.15 13.29 46.03 4.02
1264 4034 2.689471 AGTTACACTGTGTGACCGTGTA 59.311 45.455 26.15 6.95 43.18 2.90
1279 4049 4.939509 CCGTGTAGGTTCCATTGTTTAG 57.060 45.455 0.00 0.00 34.51 1.85
1285 4055 6.657541 GTGTAGGTTCCATTGTTTAGGAATGA 59.342 38.462 0.00 0.00 44.98 2.57
1288 4058 6.256053 AGGTTCCATTGTTTAGGAATGATGT 58.744 36.000 0.00 0.00 44.98 3.06
1293 4063 9.699410 TTCCATTGTTTAGGAATGATGTTAGAT 57.301 29.630 0.00 0.00 38.91 1.98
1304 4074 6.074088 GGAATGATGTTAGATAGTTCGTGCAG 60.074 42.308 0.00 0.00 0.00 4.41
1306 4076 3.586100 TGTTAGATAGTTCGTGCAGCA 57.414 42.857 0.00 0.00 0.00 4.41
1307 4077 3.250744 TGTTAGATAGTTCGTGCAGCAC 58.749 45.455 16.21 16.21 0.00 4.40
1308 4078 2.579207 TAGATAGTTCGTGCAGCACC 57.421 50.000 20.16 6.06 0.00 5.01
1309 4079 0.898320 AGATAGTTCGTGCAGCACCT 59.102 50.000 20.16 13.35 0.00 4.00
1346 4146 7.813148 GCACTGTAATTCTATAGCTATCGGAAA 59.187 37.037 10.16 1.26 0.00 3.13
1365 4165 4.142902 GGAAATGAGTGGTCATGTAACGTG 60.143 45.833 0.00 0.00 43.04 4.49
1367 4167 1.689813 TGAGTGGTCATGTAACGTGGT 59.310 47.619 0.00 0.00 0.00 4.16
1381 4207 0.460284 CGTGGTGTGGTAGATGAGCC 60.460 60.000 0.00 0.00 0.00 4.70
1394 4220 1.065701 GATGAGCCAGATTTGCAGCTG 59.934 52.381 10.11 10.11 35.23 4.24
1402 4228 1.211457 AGATTTGCAGCTGGGGAGTAG 59.789 52.381 17.12 0.00 0.00 2.57
1616 4686 8.892723 TCTATGTATGTAAAATTGTTCAGGCTG 58.107 33.333 8.58 8.58 0.00 4.85
2005 5100 2.512515 GCTCACCGCCTAGCCTTG 60.513 66.667 0.00 0.00 32.40 3.61
2015 5110 0.250513 CCTAGCCTTGTTCGCTTCCT 59.749 55.000 0.00 0.00 37.79 3.36
2034 5129 0.183971 TTTTTCTCCAAGTCCGGCCA 59.816 50.000 2.24 0.00 0.00 5.36
2094 5191 2.545731 GTGTGTTTTGCCGTGGATTTT 58.454 42.857 0.00 0.00 0.00 1.82
2095 5192 2.538037 GTGTGTTTTGCCGTGGATTTTC 59.462 45.455 0.00 0.00 0.00 2.29
2113 5210 6.094742 GGATTTTCATCCCTTTGTTCTCTCTC 59.905 42.308 0.00 0.00 43.29 3.20
2114 5211 5.567037 TTTCATCCCTTTGTTCTCTCTCA 57.433 39.130 0.00 0.00 0.00 3.27
2115 5212 5.567037 TTCATCCCTTTGTTCTCTCTCAA 57.433 39.130 0.00 0.00 0.00 3.02
2116 5213 5.768980 TCATCCCTTTGTTCTCTCTCAAT 57.231 39.130 0.00 0.00 0.00 2.57
2117 5214 5.738909 TCATCCCTTTGTTCTCTCTCAATC 58.261 41.667 0.00 0.00 0.00 2.67
2119 5216 5.768980 TCCCTTTGTTCTCTCTCAATCAT 57.231 39.130 0.00 0.00 0.00 2.45
2120 5217 6.874278 TCCCTTTGTTCTCTCTCAATCATA 57.126 37.500 0.00 0.00 0.00 2.15
2121 5218 7.443302 TCCCTTTGTTCTCTCTCAATCATAT 57.557 36.000 0.00 0.00 0.00 1.78
2122 5219 7.278135 TCCCTTTGTTCTCTCTCAATCATATG 58.722 38.462 0.00 0.00 0.00 1.78
2123 5220 7.052873 CCCTTTGTTCTCTCTCAATCATATGT 58.947 38.462 1.90 0.00 0.00 2.29
2124 5221 7.012138 CCCTTTGTTCTCTCTCAATCATATGTG 59.988 40.741 1.90 0.00 0.00 3.21
2125 5222 7.767659 CCTTTGTTCTCTCTCAATCATATGTGA 59.232 37.037 1.90 0.00 39.04 3.58
2126 5223 9.159364 CTTTGTTCTCTCTCAATCATATGTGAA 57.841 33.333 1.90 0.00 38.01 3.18
2127 5224 8.484641 TTGTTCTCTCTCAATCATATGTGAAC 57.515 34.615 1.90 0.00 38.01 3.18
2128 5225 6.753744 TGTTCTCTCTCAATCATATGTGAACG 59.246 38.462 1.90 0.00 38.01 3.95
2129 5226 6.456795 TCTCTCTCAATCATATGTGAACGT 57.543 37.500 1.90 0.00 38.01 3.99
2130 5227 6.867550 TCTCTCTCAATCATATGTGAACGTT 58.132 36.000 0.00 0.00 38.01 3.99
2131 5228 6.753744 TCTCTCTCAATCATATGTGAACGTTG 59.246 38.462 5.00 0.00 38.01 4.10
2132 5229 5.291858 TCTCTCAATCATATGTGAACGTTGC 59.708 40.000 5.00 0.00 38.01 4.17
2133 5230 4.934602 TCTCAATCATATGTGAACGTTGCA 59.065 37.500 5.00 4.91 38.01 4.08
2134 5231 4.968626 TCAATCATATGTGAACGTTGCAC 58.031 39.130 5.00 14.10 38.01 4.57
2135 5232 4.097714 CAATCATATGTGAACGTTGCACC 58.902 43.478 20.58 3.67 38.01 5.01
2136 5233 2.772287 TCATATGTGAACGTTGCACCA 58.228 42.857 20.58 12.90 35.43 4.17
2137 5234 3.342719 TCATATGTGAACGTTGCACCAT 58.657 40.909 20.58 16.85 35.43 3.55
2138 5235 3.126686 TCATATGTGAACGTTGCACCATG 59.873 43.478 20.58 20.78 35.43 3.66
2139 5236 1.317613 ATGTGAACGTTGCACCATGT 58.682 45.000 20.58 8.04 35.43 3.21
2140 5237 1.098869 TGTGAACGTTGCACCATGTT 58.901 45.000 20.58 0.00 35.43 2.71
2141 5238 1.202234 TGTGAACGTTGCACCATGTTG 60.202 47.619 20.58 0.00 35.43 3.33
2142 5239 1.098869 TGAACGTTGCACCATGTTGT 58.901 45.000 5.00 0.00 0.00 3.32
2143 5240 1.064803 TGAACGTTGCACCATGTTGTC 59.935 47.619 5.00 0.00 0.00 3.18
2144 5241 1.064803 GAACGTTGCACCATGTTGTCA 59.935 47.619 5.00 0.00 0.00 3.58
2145 5242 0.662619 ACGTTGCACCATGTTGTCAG 59.337 50.000 0.00 0.00 0.00 3.51
2146 5243 0.662619 CGTTGCACCATGTTGTCAGT 59.337 50.000 0.00 0.00 0.00 3.41
2147 5244 1.065401 CGTTGCACCATGTTGTCAGTT 59.935 47.619 0.00 0.00 0.00 3.16
2148 5245 2.479389 CGTTGCACCATGTTGTCAGTTT 60.479 45.455 0.00 0.00 0.00 2.66
2149 5246 3.115554 GTTGCACCATGTTGTCAGTTTC 58.884 45.455 0.00 0.00 0.00 2.78
2150 5247 1.333308 TGCACCATGTTGTCAGTTTCG 59.667 47.619 0.00 0.00 0.00 3.46
2151 5248 1.601903 GCACCATGTTGTCAGTTTCGA 59.398 47.619 0.00 0.00 0.00 3.71
2152 5249 2.349817 GCACCATGTTGTCAGTTTCGAG 60.350 50.000 0.00 0.00 0.00 4.04
2153 5250 3.130633 CACCATGTTGTCAGTTTCGAGA 58.869 45.455 0.00 0.00 0.00 4.04
2154 5251 3.748048 CACCATGTTGTCAGTTTCGAGAT 59.252 43.478 0.00 0.00 0.00 2.75
2155 5252 4.929211 CACCATGTTGTCAGTTTCGAGATA 59.071 41.667 0.00 0.00 0.00 1.98
2156 5253 5.582269 CACCATGTTGTCAGTTTCGAGATAT 59.418 40.000 0.00 0.00 0.00 1.63
2157 5254 5.582269 ACCATGTTGTCAGTTTCGAGATATG 59.418 40.000 0.00 0.00 0.00 1.78
2158 5255 5.496387 CATGTTGTCAGTTTCGAGATATGC 58.504 41.667 0.00 0.00 0.00 3.14
2159 5256 4.565022 TGTTGTCAGTTTCGAGATATGCA 58.435 39.130 0.00 0.00 0.00 3.96
2160 5257 5.178061 TGTTGTCAGTTTCGAGATATGCAT 58.822 37.500 3.79 3.79 0.00 3.96
2161 5258 5.063817 TGTTGTCAGTTTCGAGATATGCATG 59.936 40.000 10.16 0.00 0.00 4.06
2162 5259 3.557185 TGTCAGTTTCGAGATATGCATGC 59.443 43.478 11.82 11.82 0.00 4.06
2163 5260 2.796593 TCAGTTTCGAGATATGCATGCG 59.203 45.455 14.09 8.02 0.00 4.73
2164 5261 2.096565 CAGTTTCGAGATATGCATGCGG 60.097 50.000 14.09 0.00 0.00 5.69
2165 5262 1.867233 GTTTCGAGATATGCATGCGGT 59.133 47.619 14.09 6.93 0.00 5.68
2166 5263 1.501169 TTCGAGATATGCATGCGGTG 58.499 50.000 14.09 0.00 0.00 4.94
2167 5264 0.389025 TCGAGATATGCATGCGGTGT 59.611 50.000 14.09 2.23 0.00 4.16
2168 5265 0.509929 CGAGATATGCATGCGGTGTG 59.490 55.000 14.09 0.00 0.00 3.82
2169 5266 1.586422 GAGATATGCATGCGGTGTGT 58.414 50.000 14.09 0.87 0.00 3.72
2170 5267 1.942657 GAGATATGCATGCGGTGTGTT 59.057 47.619 14.09 0.00 0.00 3.32
2171 5268 2.355756 GAGATATGCATGCGGTGTGTTT 59.644 45.455 14.09 0.00 0.00 2.83
2172 5269 2.754552 AGATATGCATGCGGTGTGTTTT 59.245 40.909 14.09 0.00 0.00 2.43
2173 5270 2.344504 TATGCATGCGGTGTGTTTTG 57.655 45.000 14.09 0.00 0.00 2.44
2174 5271 0.945265 ATGCATGCGGTGTGTTTTGC 60.945 50.000 14.09 0.00 0.00 3.68
2175 5272 2.309501 GCATGCGGTGTGTTTTGCC 61.310 57.895 0.00 0.00 0.00 4.52
2177 5274 2.485795 ATGCGGTGTGTTTTGCCGT 61.486 52.632 4.16 0.00 46.41 5.68
2178 5275 1.167155 ATGCGGTGTGTTTTGCCGTA 61.167 50.000 4.16 0.00 46.41 4.02
2179 5276 1.082366 GCGGTGTGTTTTGCCGTAG 60.082 57.895 4.16 0.00 46.41 3.51
2180 5277 1.500512 GCGGTGTGTTTTGCCGTAGA 61.501 55.000 4.16 0.00 46.41 2.59
2202 5299 8.994170 GTAGATTTGCATCCCTTTTATCTCTAC 58.006 37.037 0.00 0.00 0.00 2.59
2203 5300 7.001073 AGATTTGCATCCCTTTTATCTCTACC 58.999 38.462 0.00 0.00 0.00 3.18
2204 5301 5.708736 TTGCATCCCTTTTATCTCTACCA 57.291 39.130 0.00 0.00 0.00 3.25
2205 5302 5.912149 TGCATCCCTTTTATCTCTACCAT 57.088 39.130 0.00 0.00 0.00 3.55
2206 5303 7.387265 TTGCATCCCTTTTATCTCTACCATA 57.613 36.000 0.00 0.00 0.00 2.74
2267 5364 5.769484 TCGAGATATGTTAGTGTTCCTCC 57.231 43.478 0.00 0.00 0.00 4.30
2281 5378 3.888930 TGTTCCTCCTTCAATTGGTCAAC 59.111 43.478 5.42 0.92 0.00 3.18
2312 5409 8.582657 TCTAGTTTCAGTATCTCTATATGGCC 57.417 38.462 0.00 0.00 0.00 5.36
2313 5410 6.274157 AGTTTCAGTATCTCTATATGGCCG 57.726 41.667 0.00 0.00 0.00 6.13
2314 5411 6.010850 AGTTTCAGTATCTCTATATGGCCGA 58.989 40.000 0.00 0.00 0.00 5.54
2334 5431 0.984230 TTGCCTCGGAATGGAGTTCT 59.016 50.000 0.00 0.00 37.01 3.01
2344 5459 4.811557 CGGAATGGAGTTCTTATGGTCTTC 59.188 45.833 0.00 0.00 37.01 2.87
2380 5495 1.061131 CGACCAGCAATCGTTTAGCAG 59.939 52.381 0.00 0.00 34.84 4.24
2393 5508 9.340695 CAATCGTTTAGCAGTATGAAAATGAAA 57.659 29.630 0.00 0.00 39.92 2.69
2396 5511 6.022251 CGTTTAGCAGTATGAAAATGAAAGCG 60.022 38.462 0.00 0.00 39.69 4.68
2410 5525 2.290367 TGAAAGCGCCGAATAATCCATG 59.710 45.455 2.29 0.00 0.00 3.66
2584 5701 1.868713 TTTATCCCGCCTCACCAGTA 58.131 50.000 0.00 0.00 0.00 2.74
2585 5702 1.868713 TTATCCCGCCTCACCAGTAA 58.131 50.000 0.00 0.00 0.00 2.24
2586 5703 1.410004 TATCCCGCCTCACCAGTAAG 58.590 55.000 0.00 0.00 0.00 2.34
2587 5704 0.617820 ATCCCGCCTCACCAGTAAGT 60.618 55.000 0.00 0.00 0.00 2.24
2653 5770 6.321690 GGTAAAAGTATCCTCTGCTCTCACTA 59.678 42.308 0.00 0.00 0.00 2.74
2745 5863 3.005261 TGCTGTGTAAAAATGCCGAATGT 59.995 39.130 0.00 0.00 0.00 2.71
2746 5864 3.608073 GCTGTGTAAAAATGCCGAATGTC 59.392 43.478 0.00 0.00 0.00 3.06
2755 5873 2.542020 TGCCGAATGTCTCTCAACAA 57.458 45.000 0.00 0.00 31.81 2.83
2769 5887 3.498018 TCTCAACAACACCACAATGATCG 59.502 43.478 0.00 0.00 0.00 3.69
2798 5919 8.709386 ACAACACTAATAGCTATCACTTCTTG 57.291 34.615 6.72 7.41 0.00 3.02
2903 6024 3.366629 GGCTCTCCGACACACTCA 58.633 61.111 0.00 0.00 0.00 3.41
2915 6036 0.536724 CACACTCATCGGTCCATCCA 59.463 55.000 0.00 0.00 35.57 3.41
2917 6038 0.536724 CACTCATCGGTCCATCCACA 59.463 55.000 0.00 0.00 35.57 4.17
2924 6045 0.810031 CGGTCCATCCACAATCGGAC 60.810 60.000 0.00 0.00 45.95 4.79
2930 6051 2.800544 CCATCCACAATCGGACGTATTC 59.199 50.000 0.00 0.00 38.07 1.75
2933 6054 2.494471 TCCACAATCGGACGTATTCACT 59.506 45.455 0.00 0.00 0.00 3.41
2942 6063 0.885879 ACGTATTCACTCTGACCGCA 59.114 50.000 0.00 0.00 0.00 5.69
2945 6066 3.043586 CGTATTCACTCTGACCGCATAC 58.956 50.000 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.700365 GTCGGGCAAAACTGCGGC 62.700 66.667 0.00 0.00 35.24 6.53
1 2 4.383602 CGTCGGGCAAAACTGCGG 62.384 66.667 0.00 0.00 35.24 5.69
23 24 3.623703 GAAACCGACCCTGCCTCCC 62.624 68.421 0.00 0.00 0.00 4.30
24 25 2.046217 GAAACCGACCCTGCCTCC 60.046 66.667 0.00 0.00 0.00 4.30
25 26 1.671379 GTGAAACCGACCCTGCCTC 60.671 63.158 0.00 0.00 0.00 4.70
26 27 2.430367 GTGAAACCGACCCTGCCT 59.570 61.111 0.00 0.00 0.00 4.75
47 48 2.516930 ATTCCAATCGGGCGCCAG 60.517 61.111 30.85 26.21 36.21 4.85
48 49 2.828095 CATTCCAATCGGGCGCCA 60.828 61.111 30.85 9.36 36.21 5.69
49 50 3.595758 CCATTCCAATCGGGCGCC 61.596 66.667 21.18 21.18 36.21 6.53
50 51 4.270376 GCCATTCCAATCGGGCGC 62.270 66.667 0.00 0.00 36.58 6.53
52 53 3.226537 GGGCCATTCCAATCGGGC 61.227 66.667 4.39 0.00 45.67 6.13
53 54 2.906897 CGGGCCATTCCAATCGGG 60.907 66.667 4.39 0.00 36.21 5.14
54 55 2.186826 GTCGGGCCATTCCAATCGG 61.187 63.158 4.39 0.00 36.21 4.18
55 56 2.186826 GGTCGGGCCATTCCAATCG 61.187 63.158 4.39 0.00 37.17 3.34
56 57 0.395724 AAGGTCGGGCCATTCCAATC 60.396 55.000 4.39 0.00 40.61 2.67
57 58 0.684153 CAAGGTCGGGCCATTCCAAT 60.684 55.000 4.39 0.00 40.61 3.16
58 59 1.304052 CAAGGTCGGGCCATTCCAA 60.304 57.895 4.39 0.00 40.61 3.53
59 60 2.354729 CAAGGTCGGGCCATTCCA 59.645 61.111 4.39 0.00 40.61 3.53
60 61 2.440247 CCAAGGTCGGGCCATTCC 60.440 66.667 4.39 2.75 40.61 3.01
61 62 2.440247 CCCAAGGTCGGGCCATTC 60.440 66.667 4.39 0.00 40.07 2.67
62 63 2.499303 CTTCCCAAGGTCGGGCCATT 62.499 60.000 4.39 0.00 46.92 3.16
63 64 2.938798 TTCCCAAGGTCGGGCCAT 60.939 61.111 4.39 0.00 46.92 4.40
64 65 3.646715 CTTCCCAAGGTCGGGCCA 61.647 66.667 4.39 0.00 46.92 5.36
65 66 4.426313 CCTTCCCAAGGTCGGGCC 62.426 72.222 0.00 0.00 46.92 5.80
73 74 1.224592 CCCCATCGTCCTTCCCAAG 59.775 63.158 0.00 0.00 0.00 3.61
74 75 2.305607 CCCCCATCGTCCTTCCCAA 61.306 63.158 0.00 0.00 0.00 4.12
75 76 2.690881 CCCCCATCGTCCTTCCCA 60.691 66.667 0.00 0.00 0.00 4.37
76 77 4.191015 GCCCCCATCGTCCTTCCC 62.191 72.222 0.00 0.00 0.00 3.97
77 78 2.610532 GAAGCCCCCATCGTCCTTCC 62.611 65.000 0.00 0.00 0.00 3.46
78 79 1.153147 GAAGCCCCCATCGTCCTTC 60.153 63.158 0.00 0.00 0.00 3.46
79 80 2.680370 GGAAGCCCCCATCGTCCTT 61.680 63.158 0.00 0.00 0.00 3.36
100 101 3.333189 CGCGTCATCATGGAGCCG 61.333 66.667 0.00 0.00 0.00 5.52
126 127 2.674380 CCTGCCTGACCAGCCAAC 60.674 66.667 0.00 0.00 0.00 3.77
131 132 4.767255 GTCGCCCTGCCTGACCAG 62.767 72.222 0.00 0.00 0.00 4.00
150 151 2.261671 CGTCCGCTACCTTGCTGT 59.738 61.111 0.00 0.00 0.00 4.40
154 155 2.202570 CCGTCGTCCGCTACCTTG 60.203 66.667 0.00 0.00 34.38 3.61
155 156 2.360350 TCCGTCGTCCGCTACCTT 60.360 61.111 0.00 0.00 34.38 3.50
177 178 4.082523 TCGCCCTTCCCGCTCTTG 62.083 66.667 0.00 0.00 0.00 3.02
204 205 0.538057 CAGGCTTGGCAGGAGTGAAA 60.538 55.000 0.00 0.00 0.00 2.69
222 223 0.878416 GCATACACAAAACCCGCTCA 59.122 50.000 0.00 0.00 0.00 4.26
227 228 1.790043 GTTTGCGCATACACAAAACCC 59.210 47.619 23.55 0.00 37.50 4.11
231 232 1.032794 TGGGTTTGCGCATACACAAA 58.967 45.000 29.80 11.02 33.55 2.83
235 236 0.893270 AGCTTGGGTTTGCGCATACA 60.893 50.000 28.09 14.93 37.40 2.29
236 237 1.091537 TAGCTTGGGTTTGCGCATAC 58.908 50.000 20.95 20.95 37.40 2.39
251 252 5.105716 CCGCATATGTAGAGTATTGGTAGCT 60.106 44.000 4.29 0.00 0.00 3.32
253 254 6.093404 CACCGCATATGTAGAGTATTGGTAG 58.907 44.000 4.29 0.00 0.00 3.18
254 255 5.537295 ACACCGCATATGTAGAGTATTGGTA 59.463 40.000 4.29 0.00 0.00 3.25
255 256 4.344102 ACACCGCATATGTAGAGTATTGGT 59.656 41.667 4.29 0.00 0.00 3.67
281 282 5.717654 CCCAGTAAACTTAAAAATGGGCCTA 59.282 40.000 4.53 0.00 39.50 3.93
304 305 3.056035 ACTCGAGTGTACTCATTTTCCCC 60.056 47.826 19.30 0.00 43.00 4.81
306 307 6.643770 TGTAAACTCGAGTGTACTCATTTTCC 59.356 38.462 34.66 14.73 43.00 3.13
307 308 7.381678 ACTGTAAACTCGAGTGTACTCATTTTC 59.618 37.037 34.66 16.27 43.00 2.29
316 317 7.389884 AGAACAGATACTGTAAACTCGAGTGTA 59.610 37.037 20.85 15.96 44.62 2.90
332 333 7.067494 AGGCATAAAAATGACCAGAACAGATAC 59.933 37.037 0.00 0.00 0.00 2.24
450 451 3.649073 CCCATCATTAGCGATACGTGAA 58.351 45.455 0.00 0.00 0.00 3.18
489 3183 7.609532 AGAGAAGAAAAATAAGCTACACTGCAT 59.390 33.333 0.00 0.00 34.99 3.96
762 3470 7.422399 TGGTATGAAAAACTTTCTTGCAGTAC 58.578 34.615 1.22 0.00 0.00 2.73
763 3471 7.575414 TGGTATGAAAAACTTTCTTGCAGTA 57.425 32.000 1.22 0.00 0.00 2.74
802 3510 6.763135 TGAGTGGTAAATGCTATCATCACTTC 59.237 38.462 0.00 0.00 35.48 3.01
845 3607 1.271163 TGGGCTGGTTTACTGTAGCAC 60.271 52.381 0.00 0.00 39.93 4.40
966 3731 1.227823 TGTTGGTGCAGGAACGAGG 60.228 57.895 0.00 0.00 0.00 4.63
1195 3964 1.260544 AATGCAAAAGGGAGCAGGAC 58.739 50.000 0.00 0.00 44.94 3.85
1223 3993 8.375506 TGTAACTGAAAGAAGATATCACAAGGT 58.624 33.333 5.32 0.00 37.43 3.50
1224 3994 8.660373 GTGTAACTGAAAGAAGATATCACAAGG 58.340 37.037 5.32 0.00 37.43 3.61
1259 4029 4.571919 TCCTAAACAATGGAACCTACACG 58.428 43.478 0.00 0.00 0.00 4.49
1264 4034 6.256053 ACATCATTCCTAAACAATGGAACCT 58.744 36.000 0.00 0.00 44.02 3.50
1275 4045 9.529325 CACGAACTATCTAACATCATTCCTAAA 57.471 33.333 0.00 0.00 0.00 1.85
1278 4048 5.986135 GCACGAACTATCTAACATCATTCCT 59.014 40.000 0.00 0.00 0.00 3.36
1279 4049 5.753438 TGCACGAACTATCTAACATCATTCC 59.247 40.000 0.00 0.00 0.00 3.01
1285 4055 3.865745 GTGCTGCACGAACTATCTAACAT 59.134 43.478 17.93 0.00 0.00 2.71
1288 4058 2.496070 AGGTGCTGCACGAACTATCTAA 59.504 45.455 24.86 0.00 34.83 2.10
1293 4063 0.038251 CAGAGGTGCTGCACGAACTA 60.038 55.000 24.86 0.00 37.90 2.24
1306 4076 1.027357 CAGTGCAAAAGCACAGAGGT 58.973 50.000 20.98 0.00 42.56 3.85
1307 4077 1.027357 ACAGTGCAAAAGCACAGAGG 58.973 50.000 20.98 10.58 42.56 3.69
1308 4078 3.969117 TTACAGTGCAAAAGCACAGAG 57.031 42.857 20.98 13.00 42.56 3.35
1309 4079 4.580167 AGAATTACAGTGCAAAAGCACAGA 59.420 37.500 20.98 4.51 42.56 3.41
1330 4114 6.010850 ACCACTCATTTCCGATAGCTATAGA 58.989 40.000 14.74 8.41 0.00 1.98
1331 4115 6.071896 TGACCACTCATTTCCGATAGCTATAG 60.072 42.308 6.13 6.54 0.00 1.31
1332 4116 5.773176 TGACCACTCATTTCCGATAGCTATA 59.227 40.000 6.13 0.00 0.00 1.31
1333 4117 4.588951 TGACCACTCATTTCCGATAGCTAT 59.411 41.667 5.76 5.76 0.00 2.97
1346 4146 2.301870 ACCACGTTACATGACCACTCAT 59.698 45.455 0.00 0.00 37.65 2.90
1365 4165 1.195115 TCTGGCTCATCTACCACACC 58.805 55.000 0.00 0.00 0.00 4.16
1367 4167 3.877559 CAAATCTGGCTCATCTACCACA 58.122 45.455 0.00 0.00 0.00 4.17
1381 4207 0.323178 ACTCCCCAGCTGCAAATCTG 60.323 55.000 8.66 0.00 0.00 2.90
1394 4220 1.134371 AGACGTACGTACCTACTCCCC 60.134 57.143 22.87 4.52 0.00 4.81
1402 4228 1.069022 TGCAAGTCAGACGTACGTACC 60.069 52.381 22.87 10.14 0.00 3.34
1462 4524 3.068691 TCTGCTTCGACCCCTCGG 61.069 66.667 0.00 0.00 40.58 4.63
1601 4663 4.933400 GCATGAATCAGCCTGAACAATTTT 59.067 37.500 0.00 0.00 0.00 1.82
1641 4711 2.363683 GAACAGGATCTGAAGCCCAAG 58.636 52.381 1.59 0.00 35.18 3.61
2005 5100 3.315470 ACTTGGAGAAAAAGGAAGCGAAC 59.685 43.478 0.00 0.00 0.00 3.95
2015 5110 0.183971 TGGCCGGACTTGGAGAAAAA 59.816 50.000 9.82 0.00 0.00 1.94
2034 5129 1.306997 TCCGGCAGGGAAAGATCCT 60.307 57.895 2.05 0.00 43.62 3.24
2039 5134 0.249489 CGATACTCCGGCAGGGAAAG 60.249 60.000 2.05 0.00 46.61 2.62
2043 5138 0.526662 GATACGATACTCCGGCAGGG 59.473 60.000 2.05 0.00 38.33 4.45
2094 5191 5.249163 TGATTGAGAGAGAACAAAGGGATGA 59.751 40.000 0.00 0.00 0.00 2.92
2095 5192 5.494724 TGATTGAGAGAGAACAAAGGGATG 58.505 41.667 0.00 0.00 0.00 3.51
2100 5197 8.713737 TCACATATGATTGAGAGAGAACAAAG 57.286 34.615 10.38 0.00 0.00 2.77
2104 5201 6.754209 ACGTTCACATATGATTGAGAGAGAAC 59.246 38.462 10.38 7.82 33.85 3.01
2113 5210 4.097714 GGTGCAACGTTCACATATGATTG 58.902 43.478 23.10 0.00 38.12 2.67
2114 5211 3.755905 TGGTGCAACGTTCACATATGATT 59.244 39.130 23.10 0.00 38.12 2.57
2115 5212 3.342719 TGGTGCAACGTTCACATATGAT 58.657 40.909 23.10 0.00 38.12 2.45
2116 5213 2.772287 TGGTGCAACGTTCACATATGA 58.228 42.857 23.10 0.00 38.12 2.15
2117 5214 3.119884 ACATGGTGCAACGTTCACATATG 60.120 43.478 24.64 24.64 38.12 1.78
2119 5216 2.499197 ACATGGTGCAACGTTCACATA 58.501 42.857 23.10 15.63 38.12 2.29
2120 5217 1.317613 ACATGGTGCAACGTTCACAT 58.682 45.000 23.10 12.78 38.12 3.21
2121 5218 1.098869 AACATGGTGCAACGTTCACA 58.901 45.000 23.10 12.90 38.12 3.58
2122 5219 1.202245 ACAACATGGTGCAACGTTCAC 60.202 47.619 11.63 17.28 38.12 3.18
2123 5220 1.064803 GACAACATGGTGCAACGTTCA 59.935 47.619 11.63 0.00 38.12 3.18
2124 5221 1.064803 TGACAACATGGTGCAACGTTC 59.935 47.619 11.63 0.00 38.12 3.95
2125 5222 1.065401 CTGACAACATGGTGCAACGTT 59.935 47.619 11.63 0.00 38.12 3.99
2126 5223 0.662619 CTGACAACATGGTGCAACGT 59.337 50.000 11.63 0.00 38.12 3.99
2127 5224 0.662619 ACTGACAACATGGTGCAACG 59.337 50.000 11.63 2.12 38.12 4.10
2128 5225 2.869233 AACTGACAACATGGTGCAAC 57.131 45.000 11.63 0.00 0.00 4.17
2129 5226 2.223456 CGAAACTGACAACATGGTGCAA 60.223 45.455 11.63 0.00 0.00 4.08
2130 5227 1.333308 CGAAACTGACAACATGGTGCA 59.667 47.619 11.63 9.13 0.00 4.57
2131 5228 1.601903 TCGAAACTGACAACATGGTGC 59.398 47.619 11.63 4.33 0.00 5.01
2132 5229 3.130633 TCTCGAAACTGACAACATGGTG 58.869 45.455 9.83 9.83 0.00 4.17
2133 5230 3.469008 TCTCGAAACTGACAACATGGT 57.531 42.857 0.00 0.00 0.00 3.55
2134 5231 5.503031 GCATATCTCGAAACTGACAACATGG 60.503 44.000 0.00 0.00 0.00 3.66
2135 5232 5.063817 TGCATATCTCGAAACTGACAACATG 59.936 40.000 0.00 0.00 0.00 3.21
2136 5233 5.178061 TGCATATCTCGAAACTGACAACAT 58.822 37.500 0.00 0.00 0.00 2.71
2137 5234 4.565022 TGCATATCTCGAAACTGACAACA 58.435 39.130 0.00 0.00 0.00 3.33
2138 5235 5.496387 CATGCATATCTCGAAACTGACAAC 58.504 41.667 0.00 0.00 0.00 3.32
2139 5236 4.034394 GCATGCATATCTCGAAACTGACAA 59.966 41.667 14.21 0.00 0.00 3.18
2140 5237 3.557185 GCATGCATATCTCGAAACTGACA 59.443 43.478 14.21 0.00 0.00 3.58
2141 5238 3.362401 CGCATGCATATCTCGAAACTGAC 60.362 47.826 19.57 0.00 0.00 3.51
2142 5239 2.796593 CGCATGCATATCTCGAAACTGA 59.203 45.455 19.57 0.00 0.00 3.41
2143 5240 2.096565 CCGCATGCATATCTCGAAACTG 60.097 50.000 19.57 0.00 0.00 3.16
2144 5241 2.138320 CCGCATGCATATCTCGAAACT 58.862 47.619 19.57 0.00 0.00 2.66
2145 5242 1.867233 ACCGCATGCATATCTCGAAAC 59.133 47.619 19.57 0.00 0.00 2.78
2146 5243 1.866601 CACCGCATGCATATCTCGAAA 59.133 47.619 19.57 0.00 0.00 3.46
2147 5244 1.202521 ACACCGCATGCATATCTCGAA 60.203 47.619 19.57 0.00 0.00 3.71
2148 5245 0.389025 ACACCGCATGCATATCTCGA 59.611 50.000 19.57 0.00 0.00 4.04
2149 5246 0.509929 CACACCGCATGCATATCTCG 59.490 55.000 19.57 0.74 0.00 4.04
2150 5247 1.586422 ACACACCGCATGCATATCTC 58.414 50.000 19.57 0.00 0.00 2.75
2151 5248 2.042686 AACACACCGCATGCATATCT 57.957 45.000 19.57 0.00 0.00 1.98
2152 5249 2.849880 AAACACACCGCATGCATATC 57.150 45.000 19.57 0.00 0.00 1.63
2153 5250 2.878580 CAAAACACACCGCATGCATAT 58.121 42.857 19.57 0.00 0.00 1.78
2154 5251 1.668337 GCAAAACACACCGCATGCATA 60.668 47.619 19.57 0.00 34.10 3.14
2155 5252 0.945265 GCAAAACACACCGCATGCAT 60.945 50.000 19.57 1.32 34.10 3.96
2156 5253 1.591059 GCAAAACACACCGCATGCA 60.591 52.632 19.57 0.00 34.10 3.96
2157 5254 2.309501 GGCAAAACACACCGCATGC 61.310 57.895 7.91 7.91 0.00 4.06
2158 5255 2.015627 CGGCAAAACACACCGCATG 61.016 57.895 0.00 0.00 40.55 4.06
2159 5256 2.334653 CGGCAAAACACACCGCAT 59.665 55.556 0.00 0.00 40.55 4.73
2163 5260 3.305110 CAAATCTACGGCAAAACACACC 58.695 45.455 0.00 0.00 0.00 4.16
2164 5261 2.724174 GCAAATCTACGGCAAAACACAC 59.276 45.455 0.00 0.00 0.00 3.82
2165 5262 2.359214 TGCAAATCTACGGCAAAACACA 59.641 40.909 0.00 0.00 34.05 3.72
2166 5263 3.006659 TGCAAATCTACGGCAAAACAC 57.993 42.857 0.00 0.00 34.05 3.32
2167 5264 3.366883 GGATGCAAATCTACGGCAAAACA 60.367 43.478 0.00 0.00 41.43 2.83
2168 5265 3.179048 GGATGCAAATCTACGGCAAAAC 58.821 45.455 0.00 0.00 41.43 2.43
2169 5266 2.165437 GGGATGCAAATCTACGGCAAAA 59.835 45.455 0.00 0.00 41.43 2.44
2170 5267 1.748493 GGGATGCAAATCTACGGCAAA 59.252 47.619 0.00 0.00 41.43 3.68
2171 5268 1.064758 AGGGATGCAAATCTACGGCAA 60.065 47.619 0.00 0.00 41.43 4.52
2172 5269 0.546122 AGGGATGCAAATCTACGGCA 59.454 50.000 0.00 0.00 42.43 5.69
2173 5270 1.680338 AAGGGATGCAAATCTACGGC 58.320 50.000 0.00 0.00 0.00 5.68
2174 5271 5.765182 AGATAAAAGGGATGCAAATCTACGG 59.235 40.000 0.00 0.00 0.00 4.02
2175 5272 6.708054 AGAGATAAAAGGGATGCAAATCTACG 59.292 38.462 0.00 0.00 0.00 3.51
2176 5273 8.994170 GTAGAGATAAAAGGGATGCAAATCTAC 58.006 37.037 0.00 0.00 0.00 2.59
2177 5274 8.157476 GGTAGAGATAAAAGGGATGCAAATCTA 58.843 37.037 0.00 0.00 0.00 1.98
2178 5275 7.001073 GGTAGAGATAAAAGGGATGCAAATCT 58.999 38.462 0.00 0.00 0.00 2.40
2179 5276 6.772716 TGGTAGAGATAAAAGGGATGCAAATC 59.227 38.462 0.00 0.00 0.00 2.17
2180 5277 6.672593 TGGTAGAGATAAAAGGGATGCAAAT 58.327 36.000 0.00 0.00 0.00 2.32
2202 5299 2.466846 GTCCACGTACGATTGGTATGG 58.533 52.381 24.41 16.89 41.55 2.74
2203 5300 2.114056 CGTCCACGTACGATTGGTATG 58.886 52.381 24.41 7.57 45.68 2.39
2204 5301 2.480224 CGTCCACGTACGATTGGTAT 57.520 50.000 24.41 0.00 45.68 2.73
2205 5302 3.994729 CGTCCACGTACGATTGGTA 57.005 52.632 24.41 7.51 45.68 3.25
2206 5303 4.874534 CGTCCACGTACGATTGGT 57.125 55.556 24.41 0.00 45.68 3.67
2267 5364 8.103948 ACTAGATTTCAGTTGACCAATTGAAG 57.896 34.615 16.40 9.97 44.17 3.02
2313 5410 1.943340 GAACTCCATTCCGAGGCAATC 59.057 52.381 0.00 0.00 33.93 2.67
2314 5411 1.561542 AGAACTCCATTCCGAGGCAAT 59.438 47.619 0.00 0.00 38.16 3.56
2344 5459 5.163764 TGCTGGTCGCAGTAGAAATTAATTG 60.164 40.000 0.39 0.00 45.47 2.32
2374 5489 5.331902 GCGCTTTCATTTTCATACTGCTAA 58.668 37.500 0.00 0.00 0.00 3.09
2380 5495 3.398954 TCGGCGCTTTCATTTTCATAC 57.601 42.857 7.64 0.00 0.00 2.39
2393 5508 1.237285 GCCATGGATTATTCGGCGCT 61.237 55.000 18.40 0.00 32.14 5.92
2396 5511 0.238289 CACGCCATGGATTATTCGGC 59.762 55.000 18.40 0.00 39.45 5.54
2410 5525 1.259840 TACCCTTACCCTGTCACGCC 61.260 60.000 0.00 0.00 0.00 5.68
2413 5528 4.263594 TGGAATTTACCCTTACCCTGTCAC 60.264 45.833 0.00 0.00 0.00 3.67
2487 5604 9.160412 AGCCCTCTTATTCTATTGTACTGTATT 57.840 33.333 0.00 0.00 0.00 1.89
2511 5628 6.661377 TCTGATATAGGATAGACAAGTGGAGC 59.339 42.308 0.00 0.00 0.00 4.70
2587 5704 9.208022 CGCTGGATGTCATTAGAGATTTATTTA 57.792 33.333 3.06 0.00 0.00 1.40
2653 5770 3.326946 AGATAGACAGGCAGAGGTGAT 57.673 47.619 0.00 0.00 0.00 3.06
2745 5863 4.149511 TCATTGTGGTGTTGTTGAGAGA 57.850 40.909 0.00 0.00 0.00 3.10
2746 5864 4.377738 CGATCATTGTGGTGTTGTTGAGAG 60.378 45.833 0.00 0.00 0.00 3.20
2755 5873 0.881118 GTTGGCGATCATTGTGGTGT 59.119 50.000 0.00 0.00 0.00 4.16
2769 5887 5.817816 AGTGATAGCTATTAGTGTTGTTGGC 59.182 40.000 7.87 0.00 0.00 4.52
2813 5934 2.094417 GCTTCTGAATCGAAGTTTCCCG 59.906 50.000 13.32 0.00 41.84 5.14
2897 6018 0.537188 GTGGATGGACCGATGAGTGT 59.463 55.000 0.00 0.00 42.61 3.55
2903 6024 0.106708 CCGATTGTGGATGGACCGAT 59.893 55.000 0.00 0.00 42.61 4.18
2915 6036 3.442625 TCAGAGTGAATACGTCCGATTGT 59.557 43.478 0.00 0.00 0.00 2.71
2917 6038 3.181489 GGTCAGAGTGAATACGTCCGATT 60.181 47.826 0.00 0.00 0.00 3.34
2924 6045 2.209838 ATGCGGTCAGAGTGAATACG 57.790 50.000 0.00 0.00 0.00 3.06
2930 6051 2.078849 TTGTGTATGCGGTCAGAGTG 57.921 50.000 0.00 0.00 0.00 3.51
2933 6054 3.610040 AGATTTGTGTATGCGGTCAGA 57.390 42.857 0.00 0.00 0.00 3.27
2942 6063 7.395190 TGCTCATGCTAAAAGATTTGTGTAT 57.605 32.000 0.00 0.00 40.48 2.29
2945 6066 5.100259 CCTGCTCATGCTAAAAGATTTGTG 58.900 41.667 0.00 0.00 40.48 3.33


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

AutoCloner maintained by Alex Coulton.