Multiple sequence alignment - TraesCS1D01G399000

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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 TraesCS1D01G399000 chr1D 100.000 5011 0 0 1 5011 465885075 465890085 0.000000e+00 9254
1 TraesCS1D01G399000 chr1D 95.192 104 4 1 4893 4996 362603832 362603730 4.010000e-36 163
2 TraesCS1D01G399000 chr1D 95.192 104 3 2 4895 4996 465942180 465942283 4.010000e-36 163
3 TraesCS1D01G399000 chr1B 94.518 2426 84 15 2186 4591 642676856 642679252 0.000000e+00 3698
4 TraesCS1D01G399000 chr1B 93.487 2088 87 33 20 2073 642674782 642676854 0.000000e+00 3057
5 TraesCS1D01G399000 chr1B 89.778 225 19 4 4778 5001 642679446 642679667 8.210000e-73 285
6 TraesCS1D01G399000 chr1B 89.231 130 14 0 2059 2188 325270355 325270484 4.010000e-36 163
7 TraesCS1D01G399000 chr1B 94.495 109 1 3 4895 5002 642734858 642734962 4.010000e-36 163
8 TraesCS1D01G399000 chr1A 91.166 2049 117 32 62 2071 558184385 558186408 0.000000e+00 2723
9 TraesCS1D01G399000 chr1A 90.732 1025 63 12 2629 3638 558187225 558188232 0.000000e+00 1338
10 TraesCS1D01G399000 chr1A 89.301 944 62 19 3655 4591 558188349 558189260 0.000000e+00 1147
11 TraesCS1D01G399000 chr1A 91.563 403 24 4 2185 2587 558186406 558186798 9.480000e-152 547
12 TraesCS1D01G399000 chr1A 79.493 434 59 20 4590 5001 558189305 558189730 1.060000e-71 281
13 TraesCS1D01G399000 chr1A 90.909 121 11 0 2068 2188 292769551 292769431 4.010000e-36 163
14 TraesCS1D01G399000 chr1A 92.793 111 4 2 4895 5002 558194442 558194551 1.870000e-34 158
15 TraesCS1D01G399000 chr5B 96.262 107 4 0 4889 4995 685441441 685441335 5.160000e-40 176
16 TraesCS1D01G399000 chr5B 96.117 103 4 0 4896 4998 685425688 685425790 8.630000e-38 169
17 TraesCS1D01G399000 chr5B 89.394 132 12 2 2059 2189 520571057 520571187 1.120000e-36 165
18 TraesCS1D01G399000 chr2D 92.500 120 9 0 2069 2188 607675741 607675860 6.670000e-39 172
19 TraesCS1D01G399000 chr4A 90.323 124 12 0 2070 2193 467246602 467246479 4.010000e-36 163
20 TraesCS1D01G399000 chr4A 93.636 110 4 2 4893 4999 625489824 625489933 1.440000e-35 161
21 TraesCS1D01G399000 chr2A 90.833 120 11 0 2069 2188 715964213 715964332 1.440000e-35 161
22 TraesCS1D01G399000 chr6D 90.323 124 9 2 2070 2193 87598596 87598716 5.190000e-35 159
23 TraesCS1D01G399000 chr6D 89.683 126 12 1 2064 2189 410395590 410395466 5.190000e-35 159
24 TraesCS1D01G399000 chr6D 87.970 133 14 2 2067 2197 125239780 125239648 6.720000e-34 156


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 TraesCS1D01G399000 chr1D 465885075 465890085 5010 False 9254.000000 9254 100.000000 1 5011 1 chr1D.!!$F1 5010
1 TraesCS1D01G399000 chr1B 642674782 642679667 4885 False 2346.666667 3698 92.594333 20 5001 3 chr1B.!!$F3 4981
2 TraesCS1D01G399000 chr1A 558184385 558189730 5345 False 1207.200000 2723 88.451000 62 5001 5 chr1A.!!$F2 4939

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
68 70 0.031178 CACACACAAAGCAAGAGGGC 59.969 55.0 0.00 0.0 0.00 5.19 F
516 547 0.036875 CCCCCTGTTCTGTTCTGGTC 59.963 60.0 0.00 0.0 0.00 4.02 F
2094 2152 0.108615 CTCCGTCTCGAATTGCCTGT 60.109 55.0 0.00 0.0 0.00 4.00 F
2183 2241 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.0 13.64 0.0 46.06 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1158 1213 1.219124 GTCCAGAGATGCCAGCGAA 59.781 57.895 0.00 0.00 0.00 4.70 R
2164 2222 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24 R
3968 4528 0.535102 GGTGGTTCCACAGTGACCAG 60.535 60.000 21.25 0.00 43.62 4.00 R
4129 4697 2.104331 GTTAGCAGCGCCGCTAGA 59.896 61.111 23.33 13.02 44.93 2.43 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
68 70 0.031178 CACACACAAAGCAAGAGGGC 59.969 55.000 0.00 0.00 0.00 5.19
70 72 1.531602 ACACAAAGCAAGAGGGCCC 60.532 57.895 16.46 16.46 0.00 5.80
86 88 2.168496 GGCCCCTTTAAAGAACTGGAC 58.832 52.381 16.98 9.51 0.00 4.02
118 122 1.108727 TGGTGGCAGGAGCAAAACAG 61.109 55.000 0.00 0.00 44.61 3.16
380 407 3.549150 CGAGCAAAGCGCGGAGAG 61.549 66.667 8.83 0.00 46.98 3.20
381 408 3.971453 CGAGCAAAGCGCGGAGAGA 62.971 63.158 8.83 0.00 46.98 3.10
383 410 2.125912 GCAAAGCGCGGAGAGAGA 60.126 61.111 8.83 0.00 0.00 3.10
384 411 2.164026 GCAAAGCGCGGAGAGAGAG 61.164 63.158 8.83 0.00 0.00 3.20
387 414 1.939769 AAAGCGCGGAGAGAGAGGAC 61.940 60.000 8.83 0.00 0.00 3.85
388 415 3.134792 GCGCGGAGAGAGAGGACA 61.135 66.667 8.83 0.00 0.00 4.02
389 416 3.106552 CGCGGAGAGAGAGGACAG 58.893 66.667 0.00 0.00 0.00 3.51
390 417 2.804856 GCGGAGAGAGAGGACAGC 59.195 66.667 0.00 0.00 0.00 4.40
391 418 1.752694 GCGGAGAGAGAGGACAGCT 60.753 63.158 0.00 0.00 0.00 4.24
392 419 1.724582 GCGGAGAGAGAGGACAGCTC 61.725 65.000 0.00 0.00 0.00 4.09
516 547 0.036875 CCCCCTGTTCTGTTCTGGTC 59.963 60.000 0.00 0.00 0.00 4.02
624 659 1.269723 AGTTCATGCTCGTCGTTCTGA 59.730 47.619 0.00 0.00 0.00 3.27
638 673 0.250901 TTCTGAACTTCTGCTGCCCC 60.251 55.000 0.00 0.00 0.00 5.80
657 698 2.224113 CCCTGATTTTTGCTGTTGCTGT 60.224 45.455 0.00 0.00 40.48 4.40
688 729 1.381599 GGGCTGGCCATTTGGATCA 60.382 57.895 16.34 0.00 37.98 2.92
696 737 2.951642 GGCCATTTGGATCAGAAATCGA 59.048 45.455 0.00 0.00 37.39 3.59
697 738 3.381272 GGCCATTTGGATCAGAAATCGAA 59.619 43.478 0.00 0.00 37.39 3.71
700 741 5.009410 GCCATTTGGATCAGAAATCGAATCT 59.991 40.000 0.00 0.00 37.39 2.40
703 744 7.434307 CCATTTGGATCAGAAATCGAATCTTTG 59.566 37.037 1.62 0.00 37.39 2.77
726 768 2.749621 GTGCCGATCCTGTTTCTTGAAT 59.250 45.455 0.00 0.00 0.00 2.57
733 776 3.157087 TCCTGTTTCTTGAATTCTGGGC 58.843 45.455 7.05 0.00 0.00 5.36
737 780 5.335976 CCTGTTTCTTGAATTCTGGGCTTAC 60.336 44.000 7.05 0.00 0.00 2.34
740 783 7.001674 TGTTTCTTGAATTCTGGGCTTACTTA 58.998 34.615 7.05 0.00 0.00 2.24
741 784 7.040686 TGTTTCTTGAATTCTGGGCTTACTTAC 60.041 37.037 7.05 0.00 0.00 2.34
745 788 2.781681 TTCTGGGCTTACTTACTGGC 57.218 50.000 0.00 0.00 0.00 4.85
747 790 1.555075 TCTGGGCTTACTTACTGGCTG 59.445 52.381 0.00 0.00 0.00 4.85
748 791 0.618458 TGGGCTTACTTACTGGCTGG 59.382 55.000 0.00 0.00 0.00 4.85
749 792 0.618981 GGGCTTACTTACTGGCTGGT 59.381 55.000 0.00 0.00 0.00 4.00
751 794 2.084546 GGCTTACTTACTGGCTGGTTG 58.915 52.381 0.00 0.00 0.00 3.77
752 795 2.552373 GGCTTACTTACTGGCTGGTTGT 60.552 50.000 0.00 0.00 0.00 3.32
753 796 3.146847 GCTTACTTACTGGCTGGTTGTT 58.853 45.455 0.00 0.00 0.00 2.83
757 811 2.297701 CTTACTGGCTGGTTGTTGTGT 58.702 47.619 0.00 0.00 0.00 3.72
766 820 2.039746 CTGGTTGTTGTGTGGGGAGATA 59.960 50.000 0.00 0.00 0.00 1.98
854 908 8.100791 AGAAGTGGTTATAATTGCTGTACTGAA 58.899 33.333 3.61 0.00 0.00 3.02
855 909 8.807948 AAGTGGTTATAATTGCTGTACTGAAT 57.192 30.769 3.61 0.00 0.00 2.57
871 925 2.352960 CTGAATTCTACTTTCAGCCGGC 59.647 50.000 21.89 21.89 42.44 6.13
872 926 1.671328 GAATTCTACTTTCAGCCGGCC 59.329 52.381 26.15 5.07 0.00 6.13
881 935 3.838271 CAGCCGGCCGAGCTAAGA 61.838 66.667 31.66 0.00 38.95 2.10
952 1006 2.270047 GCATGAGCAGAAGAGACAGTC 58.730 52.381 0.00 0.00 41.58 3.51
1245 1300 1.262640 GGTCGAAGTCTAAGGGGCCA 61.263 60.000 4.39 0.00 0.00 5.36
1272 1327 0.667792 AGAGAGTTGCGTTTCGGCTC 60.668 55.000 0.00 0.00 0.00 4.70
1422 1477 3.512033 ATCGTAGTGCAGAAAGAGGTC 57.488 47.619 0.00 0.00 0.00 3.85
1453 1508 2.925170 AGCCCGAGGTTGAGCAGT 60.925 61.111 0.00 0.00 0.00 4.40
1497 1552 4.272489 TGTTGGATGATGAGGTGGATTTC 58.728 43.478 0.00 0.00 0.00 2.17
1749 1804 6.899393 ATTGTCTGCAGGAAAAATCTTACA 57.101 33.333 15.13 3.54 0.00 2.41
1800 1855 9.622004 CAAAGGAACAATGCAATCTATCATATC 57.378 33.333 0.00 0.00 0.00 1.63
1839 1894 4.220693 TGGTATAGTGCACTTTGCTGAT 57.779 40.909 27.06 13.66 45.31 2.90
2079 2137 7.396418 AGACTTACTATTCTATACTCCCTCCG 58.604 42.308 0.00 0.00 0.00 4.63
2080 2138 7.017452 AGACTTACTATTCTATACTCCCTCCGT 59.983 40.741 0.00 0.00 0.00 4.69
2081 2139 7.167535 ACTTACTATTCTATACTCCCTCCGTC 58.832 42.308 0.00 0.00 0.00 4.79
2082 2140 5.846528 ACTATTCTATACTCCCTCCGTCT 57.153 43.478 0.00 0.00 0.00 4.18
2083 2141 5.807909 ACTATTCTATACTCCCTCCGTCTC 58.192 45.833 0.00 0.00 0.00 3.36
2084 2142 2.835580 TCTATACTCCCTCCGTCTCG 57.164 55.000 0.00 0.00 0.00 4.04
2085 2143 2.323599 TCTATACTCCCTCCGTCTCGA 58.676 52.381 0.00 0.00 0.00 4.04
2086 2144 2.702478 TCTATACTCCCTCCGTCTCGAA 59.298 50.000 0.00 0.00 0.00 3.71
2087 2145 2.660670 ATACTCCCTCCGTCTCGAAT 57.339 50.000 0.00 0.00 0.00 3.34
2088 2146 2.431954 TACTCCCTCCGTCTCGAATT 57.568 50.000 0.00 0.00 0.00 2.17
2089 2147 0.818296 ACTCCCTCCGTCTCGAATTG 59.182 55.000 0.00 0.00 0.00 2.32
2090 2148 0.528684 CTCCCTCCGTCTCGAATTGC 60.529 60.000 0.00 0.00 0.00 3.56
2091 2149 1.521681 CCCTCCGTCTCGAATTGCC 60.522 63.158 0.00 0.00 0.00 4.52
2092 2150 1.517832 CCTCCGTCTCGAATTGCCT 59.482 57.895 0.00 0.00 0.00 4.75
2093 2151 0.807667 CCTCCGTCTCGAATTGCCTG 60.808 60.000 0.00 0.00 0.00 4.85
2094 2152 0.108615 CTCCGTCTCGAATTGCCTGT 60.109 55.000 0.00 0.00 0.00 4.00
2095 2153 0.108804 TCCGTCTCGAATTGCCTGTC 60.109 55.000 0.00 0.00 0.00 3.51
2096 2154 1.413767 CCGTCTCGAATTGCCTGTCG 61.414 60.000 0.00 0.00 38.62 4.35
2097 2155 1.710339 GTCTCGAATTGCCTGTCGC 59.290 57.895 0.00 0.00 37.19 5.19
2106 2164 3.871701 TGCCTGTCGCATAAATGGA 57.128 47.368 0.00 0.00 44.64 3.41
2107 2165 2.346766 TGCCTGTCGCATAAATGGAT 57.653 45.000 0.00 0.00 44.64 3.41
2108 2166 3.483808 TGCCTGTCGCATAAATGGATA 57.516 42.857 0.00 0.00 44.64 2.59
2109 2167 3.402110 TGCCTGTCGCATAAATGGATAG 58.598 45.455 0.00 0.00 44.64 2.08
2110 2168 3.070878 TGCCTGTCGCATAAATGGATAGA 59.929 43.478 6.71 0.00 44.64 1.98
2111 2169 4.065088 GCCTGTCGCATAAATGGATAGAA 58.935 43.478 6.71 0.00 37.47 2.10
2112 2170 4.515191 GCCTGTCGCATAAATGGATAGAAA 59.485 41.667 6.71 0.00 37.47 2.52
2113 2171 5.182001 GCCTGTCGCATAAATGGATAGAAAT 59.818 40.000 6.71 0.00 37.47 2.17
2114 2172 6.605849 CCTGTCGCATAAATGGATAGAAATG 58.394 40.000 6.71 0.00 0.00 2.32
2115 2173 6.348786 CCTGTCGCATAAATGGATAGAAATGG 60.349 42.308 6.71 0.00 0.00 3.16
2116 2174 6.295249 TGTCGCATAAATGGATAGAAATGGA 58.705 36.000 0.00 0.00 0.00 3.41
2117 2175 6.942005 TGTCGCATAAATGGATAGAAATGGAT 59.058 34.615 0.00 0.00 0.00 3.41
2118 2176 7.094677 TGTCGCATAAATGGATAGAAATGGATG 60.095 37.037 0.00 0.00 0.00 3.51
2119 2177 6.942005 TCGCATAAATGGATAGAAATGGATGT 59.058 34.615 0.00 0.00 0.00 3.06
2120 2178 8.100164 TCGCATAAATGGATAGAAATGGATGTA 58.900 33.333 0.00 0.00 0.00 2.29
2121 2179 8.896744 CGCATAAATGGATAGAAATGGATGTAT 58.103 33.333 0.00 0.00 0.00 2.29
2129 2187 9.607333 TGGATAGAAATGGATGTATCTAGAACT 57.393 33.333 0.00 0.00 0.00 3.01
2160 2218 6.604012 ACGTCTAGATACATCTATTTCTGCG 58.396 40.000 0.00 0.00 38.60 5.18
2161 2219 6.427242 ACGTCTAGATACATCTATTTCTGCGA 59.573 38.462 0.00 0.00 38.60 5.10
2162 2220 6.739100 CGTCTAGATACATCTATTTCTGCGAC 59.261 42.308 0.00 2.21 38.60 5.19
2163 2221 7.571428 CGTCTAGATACATCTATTTCTGCGACA 60.571 40.741 0.00 0.00 38.60 4.35
2164 2222 8.076781 GTCTAGATACATCTATTTCTGCGACAA 58.923 37.037 0.00 0.00 38.60 3.18
2165 2223 8.293157 TCTAGATACATCTATTTCTGCGACAAG 58.707 37.037 0.00 0.00 38.60 3.16
2166 2224 6.810911 AGATACATCTATTTCTGCGACAAGT 58.189 36.000 0.00 0.00 34.85 3.16
2167 2225 7.941919 AGATACATCTATTTCTGCGACAAGTA 58.058 34.615 0.00 0.00 34.85 2.24
2168 2226 8.414003 AGATACATCTATTTCTGCGACAAGTAA 58.586 33.333 0.00 0.00 34.85 2.24
2169 2227 9.197694 GATACATCTATTTCTGCGACAAGTAAT 57.802 33.333 0.00 0.00 0.00 1.89
2170 2228 7.849804 ACATCTATTTCTGCGACAAGTAATT 57.150 32.000 0.00 0.00 0.00 1.40
2171 2229 7.910304 ACATCTATTTCTGCGACAAGTAATTC 58.090 34.615 0.00 0.00 0.00 2.17
2172 2230 6.903883 TCTATTTCTGCGACAAGTAATTCC 57.096 37.500 0.00 0.00 0.00 3.01
2173 2231 4.600012 ATTTCTGCGACAAGTAATTCCG 57.400 40.909 0.00 0.00 0.00 4.30
2174 2232 2.004583 TCTGCGACAAGTAATTCCGG 57.995 50.000 0.00 0.00 0.00 5.14
2175 2233 1.546923 TCTGCGACAAGTAATTCCGGA 59.453 47.619 0.00 0.00 0.00 5.14
2176 2234 1.659098 CTGCGACAAGTAATTCCGGAC 59.341 52.381 1.83 0.00 0.00 4.79
2177 2235 0.643820 GCGACAAGTAATTCCGGACG 59.356 55.000 1.83 1.53 0.00 4.79
2178 2236 1.274596 CGACAAGTAATTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
2179 2237 1.135315 CGACAAGTAATTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2180 2238 2.537401 GACAAGTAATTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2181 2239 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2182 2240 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2183 2241 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
2184 2242 0.826062 GTAATTCCGGACGGAGGGAA 59.174 55.000 13.64 5.91 46.06 3.97
2230 2288 5.580691 TGTTACATCTTCCTTGCTTATGACG 59.419 40.000 0.00 0.00 0.00 4.35
2402 2460 2.064014 GCAGCCAATGAAGCAAGTTTC 58.936 47.619 0.00 0.00 0.00 2.78
2541 2599 2.366916 ACTGTGACAGGAACCTTCTCTG 59.633 50.000 17.92 0.00 35.51 3.35
2592 2650 6.827762 TCCCTTTTCTTTTTGCAACAAATCAT 59.172 30.769 0.00 0.00 0.00 2.45
2661 3104 6.205853 TGAGTACCAGCGTCACAAAAATATTT 59.794 34.615 0.00 0.00 0.00 1.40
2758 3201 8.839310 TTTGTTCATGGTAAACAAATATTGGG 57.161 30.769 15.97 0.00 46.28 4.12
3322 3765 2.230266 CCGTCGATTCCCAATTGGTTTT 59.770 45.455 22.91 6.85 34.77 2.43
3572 4017 4.215399 GCAAACTGCACAGTACCTATCAAA 59.785 41.667 3.26 0.00 44.26 2.69
3663 4205 0.598065 ATCAAGACAAAACCAGCCGC 59.402 50.000 0.00 0.00 0.00 6.53
3688 4246 6.043411 GGGATATCTTAAGCAACTATAGCCG 58.957 44.000 2.05 0.00 30.95 5.52
3712 4270 5.520288 GCTAGTATGTCTCGAAGAAAATGCA 59.480 40.000 0.00 0.00 34.09 3.96
3797 4355 9.521841 TTTACATGGGTAACAGAATTCATGTAA 57.478 29.630 17.34 17.34 46.80 2.41
3802 4360 9.693739 ATGGGTAACAGAATTCATGTAACATAA 57.306 29.630 8.44 0.00 39.74 1.90
3914 4474 0.179234 TTCCAGACAACTGCAACCGA 59.821 50.000 0.00 0.00 42.25 4.69
3917 4477 1.299541 CAGACAACTGCAACCGAGTT 58.700 50.000 0.00 0.00 37.33 3.01
3968 4528 4.832608 CTCAACTACCCCGCCGGC 62.833 72.222 19.07 19.07 33.26 6.13
4242 4814 2.507484 CAATCAGAACTGCCTGACCAA 58.493 47.619 0.00 0.00 44.93 3.67
4286 4859 2.671070 CGCTGTATTCTTTTTGTGCCCC 60.671 50.000 0.00 0.00 0.00 5.80
4292 4865 1.028905 TCTTTTTGTGCCCCTTCGTG 58.971 50.000 0.00 0.00 0.00 4.35
4333 4906 3.506067 GTGCATACTGCCCTGTAGTTTTT 59.494 43.478 0.00 0.00 44.23 1.94
4439 5014 6.582295 GCAATACCACAGATTTGTAACTGTTG 59.418 38.462 2.69 0.00 43.52 3.33
4446 5021 7.628286 CACAGATTTGTAACTGTTGACCCAGT 61.628 42.308 2.69 0.00 43.52 4.00
4453 5028 5.761234 TGTAACTGTTGACCCAGTAATGAAC 59.239 40.000 2.69 0.00 44.74 3.18
4487 5067 4.819630 TGTAAGCTGTGTCGAATTCCTTTT 59.180 37.500 0.00 0.00 0.00 2.27
4490 5070 2.293399 GCTGTGTCGAATTCCTTTTGGT 59.707 45.455 0.00 0.00 41.38 3.67
4506 5086 6.425721 TCCTTTTGGTGTCTTAACTGTAATCG 59.574 38.462 0.00 0.00 41.38 3.34
4562 5142 7.214467 TGTAAAGAATTTCTTTCGATTGCCT 57.786 32.000 23.94 4.02 42.60 4.75
4565 5145 2.947448 ATTTCTTTCGATTGCCTGGC 57.053 45.000 12.87 12.87 0.00 4.85
4602 5229 4.717280 TCCCAACCTTTAACCAAACATGTT 59.283 37.500 4.92 4.92 0.00 2.71
4603 5230 5.897824 TCCCAACCTTTAACCAAACATGTTA 59.102 36.000 12.39 0.00 0.00 2.41
4625 5252 4.242475 AGTGCAAATGATGAGCAAACATG 58.758 39.130 0.00 0.00 40.35 3.21
4651 5278 5.079689 TGTGATTCGAACATTACTGGCTA 57.920 39.130 0.00 0.00 0.00 3.93
4652 5279 4.868171 TGTGATTCGAACATTACTGGCTAC 59.132 41.667 0.00 0.00 0.00 3.58
4666 5293 1.341852 TGGCTACGCACAAGTAGTTGA 59.658 47.619 17.23 0.00 44.33 3.18
4667 5294 2.028476 TGGCTACGCACAAGTAGTTGAT 60.028 45.455 17.23 0.00 44.33 2.57
4683 5310 6.939163 AGTAGTTGATCTCTTTGTTGCAGAAT 59.061 34.615 0.00 0.00 0.00 2.40
4697 5324 5.163426 TGTTGCAGAATTTTGTGATCAACCT 60.163 36.000 0.00 0.00 33.65 3.50
4712 5348 2.431260 CCTGTTTGGTGCATGCGC 60.431 61.111 23.05 23.05 39.24 6.09
4725 5361 1.939934 GCATGCGCTCCTGTAAACATA 59.060 47.619 9.73 0.00 34.30 2.29
4727 5363 2.309528 TGCGCTCCTGTAAACATAGG 57.690 50.000 9.73 0.00 35.34 2.57
4728 5364 1.828595 TGCGCTCCTGTAAACATAGGA 59.171 47.619 9.73 0.00 40.68 2.94
4740 5376 2.509166 ACATAGGAGTCCTGTGACGA 57.491 50.000 35.02 11.05 43.99 4.20
4741 5377 2.093106 ACATAGGAGTCCTGTGACGAC 58.907 52.381 35.02 0.00 43.99 4.34
4742 5378 1.064208 CATAGGAGTCCTGTGACGACG 59.936 57.143 27.32 2.36 43.99 5.12
4743 5379 0.035881 TAGGAGTCCTGTGACGACGT 59.964 55.000 22.69 0.00 46.51 4.34
4744 5380 0.822532 AGGAGTCCTGTGACGACGTT 60.823 55.000 12.07 0.00 46.51 3.99
4745 5381 0.386985 GGAGTCCTGTGACGACGTTC 60.387 60.000 0.13 0.00 46.51 3.95
4746 5382 0.386985 GAGTCCTGTGACGACGTTCC 60.387 60.000 0.13 0.00 46.51 3.62
4748 5384 0.031721 GTCCTGTGACGACGTTCCTT 59.968 55.000 0.13 0.00 0.00 3.36
4749 5385 0.313043 TCCTGTGACGACGTTCCTTC 59.687 55.000 0.13 0.00 0.00 3.46
4750 5386 0.314302 CCTGTGACGACGTTCCTTCT 59.686 55.000 0.13 0.00 0.00 2.85
4751 5387 1.269621 CCTGTGACGACGTTCCTTCTT 60.270 52.381 0.13 0.00 0.00 2.52
4752 5388 2.470821 CTGTGACGACGTTCCTTCTTT 58.529 47.619 0.13 0.00 0.00 2.52
4753 5389 2.864343 CTGTGACGACGTTCCTTCTTTT 59.136 45.455 0.13 0.00 0.00 2.27
4754 5390 3.264104 TGTGACGACGTTCCTTCTTTTT 58.736 40.909 0.13 0.00 0.00 1.94
4755 5391 4.431809 TGTGACGACGTTCCTTCTTTTTA 58.568 39.130 0.13 0.00 0.00 1.52
4759 5395 7.224362 TGTGACGACGTTCCTTCTTTTTATTTA 59.776 33.333 0.13 0.00 0.00 1.40
4760 5396 8.063630 GTGACGACGTTCCTTCTTTTTATTTAA 58.936 33.333 0.13 0.00 0.00 1.52
4761 5397 8.776470 TGACGACGTTCCTTCTTTTTATTTAAT 58.224 29.630 0.13 0.00 0.00 1.40
4762 5398 9.259015 GACGACGTTCCTTCTTTTTATTTAATC 57.741 33.333 0.13 0.00 0.00 1.75
4764 5400 9.769093 CGACGTTCCTTCTTTTTATTTAATCAT 57.231 29.630 0.00 0.00 0.00 2.45
4837 5485 8.827177 ATCCAGTATACGTGTATACATTTTGG 57.173 34.615 24.50 22.01 46.33 3.28
4839 5487 6.480651 CCAGTATACGTGTATACATTTTGGCA 59.519 38.462 24.50 0.00 46.33 4.92
4862 5510 3.065575 CCATCAGGCGTACAAGTCC 57.934 57.895 0.00 0.00 0.00 3.85
4873 5521 7.554835 TCAGGCGTACAAGTCCATATAAAATTT 59.445 33.333 0.00 0.00 0.00 1.82
4980 5628 1.855360 GAATCCTGCTGTCGACGATTC 59.145 52.381 20.09 20.09 34.02 2.52
4985 5633 2.061773 CTGCTGTCGACGATTCACTTT 58.938 47.619 11.62 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.866910 GTGTGCCAAAGGATGCAATTATG 59.133 43.478 0.00 0.00 39.57 1.90
49 50 0.031178 GCCCTCTTGCTTTGTGTGTG 59.969 55.000 0.00 0.00 0.00 3.82
68 70 3.412237 TCGTCCAGTTCTTTAAAGGGG 57.588 47.619 15.13 11.40 0.00 4.79
70 72 6.037830 TGTTCTTTCGTCCAGTTCTTTAAAGG 59.962 38.462 15.13 0.00 0.00 3.11
86 88 1.938861 CCACCACGGTGTTCTTTCG 59.061 57.895 14.93 0.00 44.02 3.46
105 109 0.169672 CGATGGCTGTTTTGCTCCTG 59.830 55.000 0.00 0.00 0.00 3.86
235 248 0.503805 TAGGGAGGGGAAGGGGAAAA 59.496 55.000 0.00 0.00 0.00 2.29
374 401 1.436195 CGAGCTGTCCTCTCTCTCCG 61.436 65.000 0.00 0.00 38.49 4.63
377 404 0.107214 CCTCGAGCTGTCCTCTCTCT 60.107 60.000 6.99 0.00 38.49 3.10
378 405 0.107410 TCCTCGAGCTGTCCTCTCTC 60.107 60.000 6.99 0.00 38.49 3.20
379 406 0.393808 GTCCTCGAGCTGTCCTCTCT 60.394 60.000 6.99 0.00 38.49 3.10
380 407 1.381165 GGTCCTCGAGCTGTCCTCTC 61.381 65.000 6.99 0.00 38.49 3.20
381 408 1.379309 GGTCCTCGAGCTGTCCTCT 60.379 63.158 6.99 0.00 38.49 3.69
382 409 2.766400 CGGTCCTCGAGCTGTCCTC 61.766 68.421 6.99 0.00 42.43 3.71
383 410 2.752238 CGGTCCTCGAGCTGTCCT 60.752 66.667 6.99 0.00 42.43 3.85
384 411 3.827898 CCGGTCCTCGAGCTGTCC 61.828 72.222 6.99 5.23 42.43 4.02
387 414 3.522731 CTCCCGGTCCTCGAGCTG 61.523 72.222 6.99 0.00 42.43 4.24
388 415 4.824515 CCTCCCGGTCCTCGAGCT 62.825 72.222 6.99 0.00 42.43 4.09
389 416 4.816984 TCCTCCCGGTCCTCGAGC 62.817 72.222 6.99 0.00 42.43 5.03
390 417 2.517402 CTCCTCCCGGTCCTCGAG 60.517 72.222 5.13 5.13 42.43 4.04
391 418 4.816984 GCTCCTCCCGGTCCTCGA 62.817 72.222 0.00 0.00 42.43 4.04
439 466 4.222847 GGATCTGGACGCCGGACC 62.223 72.222 5.05 5.62 42.23 4.46
624 659 0.407139 AATCAGGGGCAGCAGAAGTT 59.593 50.000 0.00 0.00 0.00 2.66
638 673 2.220133 GCACAGCAACAGCAAAAATCAG 59.780 45.455 0.00 0.00 0.00 2.90
671 712 0.396139 TCTGATCCAAATGGCCAGCC 60.396 55.000 13.05 0.38 36.35 4.85
688 729 2.755103 GGCACCCAAAGATTCGATTTCT 59.245 45.455 0.00 0.00 0.00 2.52
696 737 0.625849 AGGATCGGCACCCAAAGATT 59.374 50.000 0.00 0.00 0.00 2.40
697 738 0.107017 CAGGATCGGCACCCAAAGAT 60.107 55.000 0.00 0.00 0.00 2.40
700 741 0.178975 AAACAGGATCGGCACCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
703 744 0.322546 AAGAAACAGGATCGGCACCC 60.323 55.000 0.00 0.00 0.00 4.61
726 768 2.027192 CAGCCAGTAAGTAAGCCCAGAA 60.027 50.000 0.00 0.00 0.00 3.02
733 776 4.024048 CACAACAACCAGCCAGTAAGTAAG 60.024 45.833 0.00 0.00 0.00 2.34
737 780 2.033299 CACACAACAACCAGCCAGTAAG 59.967 50.000 0.00 0.00 0.00 2.34
740 783 1.037030 CCACACAACAACCAGCCAGT 61.037 55.000 0.00 0.00 0.00 4.00
741 784 1.735360 CCACACAACAACCAGCCAG 59.265 57.895 0.00 0.00 0.00 4.85
745 788 0.182537 TCTCCCCACACAACAACCAG 59.817 55.000 0.00 0.00 0.00 4.00
747 790 2.871096 TATCTCCCCACACAACAACC 57.129 50.000 0.00 0.00 0.00 3.77
748 791 4.192317 GAGATATCTCCCCACACAACAAC 58.808 47.826 20.33 0.00 37.02 3.32
749 792 4.487714 GAGATATCTCCCCACACAACAA 57.512 45.455 20.33 0.00 37.02 2.83
766 820 2.765689 AAGGATCACGGAGAGGAGAT 57.234 50.000 0.00 0.00 0.00 2.75
854 908 0.462047 CGGCCGGCTGAAAGTAGAAT 60.462 55.000 32.31 0.00 35.30 2.40
855 909 1.079405 CGGCCGGCTGAAAGTAGAA 60.079 57.895 32.31 0.00 35.30 2.10
868 922 0.931005 GAATTGTCTTAGCTCGGCCG 59.069 55.000 22.12 22.12 0.00 6.13
869 923 2.317530 AGAATTGTCTTAGCTCGGCC 57.682 50.000 0.00 0.00 0.00 6.13
870 924 3.262420 TGAAGAATTGTCTTAGCTCGGC 58.738 45.455 0.00 0.00 44.42 5.54
871 925 4.932200 AGTTGAAGAATTGTCTTAGCTCGG 59.068 41.667 0.00 0.00 44.42 4.63
872 926 5.220117 CGAGTTGAAGAATTGTCTTAGCTCG 60.220 44.000 15.56 15.56 44.42 5.03
881 935 6.636850 GCAAATACAACGAGTTGAAGAATTGT 59.363 34.615 21.14 1.07 42.93 2.71
952 1006 4.720649 TTAGTCCAAGATCACTTCTCCG 57.279 45.455 0.00 0.00 33.70 4.63
1158 1213 1.219124 GTCCAGAGATGCCAGCGAA 59.781 57.895 0.00 0.00 0.00 4.70
1245 1300 1.670406 CGCAACTCTCTTGCAGCCT 60.670 57.895 5.93 0.00 45.14 4.58
1266 1321 3.243367 CCATGAAACAAACAAAGAGCCGA 60.243 43.478 0.00 0.00 0.00 5.54
1272 1327 2.794350 GCCGACCATGAAACAAACAAAG 59.206 45.455 0.00 0.00 0.00 2.77
1422 1477 1.450312 GGGCTCATCAACCACCTCG 60.450 63.158 0.00 0.00 0.00 4.63
1497 1552 2.022129 AGGTTTCGCAGCTTCGACG 61.022 57.895 8.28 0.00 38.30 5.12
1749 1804 3.006967 AGACAGCAATCTTCCGTACACTT 59.993 43.478 0.00 0.00 0.00 3.16
1839 1894 4.161377 TCACCCATGTATGATCGTTCTTCA 59.839 41.667 0.00 0.00 0.00 3.02
2069 2127 2.022195 CAATTCGAGACGGAGGGAGTA 58.978 52.381 0.00 0.00 0.00 2.59
2073 2131 1.521681 GGCAATTCGAGACGGAGGG 60.522 63.158 0.00 0.00 0.00 4.30
2074 2132 0.807667 CAGGCAATTCGAGACGGAGG 60.808 60.000 0.00 0.00 0.00 4.30
2075 2133 0.108615 ACAGGCAATTCGAGACGGAG 60.109 55.000 0.00 0.00 0.00 4.63
2076 2134 0.108804 GACAGGCAATTCGAGACGGA 60.109 55.000 0.00 0.00 0.00 4.69
2077 2135 1.413767 CGACAGGCAATTCGAGACGG 61.414 60.000 0.00 0.00 37.43 4.79
2078 2136 1.991430 CGACAGGCAATTCGAGACG 59.009 57.895 0.00 0.00 37.43 4.18
2079 2137 1.710339 GCGACAGGCAATTCGAGAC 59.290 57.895 6.60 0.00 42.87 3.36
2080 2138 4.185413 GCGACAGGCAATTCGAGA 57.815 55.556 6.60 0.00 42.87 4.04
2089 2147 3.664107 TCTATCCATTTATGCGACAGGC 58.336 45.455 0.00 0.00 43.96 4.85
2090 2148 6.348786 CCATTTCTATCCATTTATGCGACAGG 60.349 42.308 0.00 0.00 0.00 4.00
2091 2149 6.427853 TCCATTTCTATCCATTTATGCGACAG 59.572 38.462 0.00 0.00 0.00 3.51
2092 2150 6.295249 TCCATTTCTATCCATTTATGCGACA 58.705 36.000 0.00 0.00 0.00 4.35
2093 2151 6.801539 TCCATTTCTATCCATTTATGCGAC 57.198 37.500 0.00 0.00 0.00 5.19
2094 2152 6.942005 ACATCCATTTCTATCCATTTATGCGA 59.058 34.615 0.00 0.00 0.00 5.10
2095 2153 7.149569 ACATCCATTTCTATCCATTTATGCG 57.850 36.000 0.00 0.00 0.00 4.73
2103 2161 9.607333 AGTTCTAGATACATCCATTTCTATCCA 57.393 33.333 0.00 0.00 0.00 3.41
2134 2192 8.391859 CGCAGAAATAGATGTATCTAGACGTAT 58.608 37.037 0.00 0.00 42.20 3.06
2135 2193 7.601508 TCGCAGAAATAGATGTATCTAGACGTA 59.398 37.037 0.00 0.00 42.20 3.57
2136 2194 6.427242 TCGCAGAAATAGATGTATCTAGACGT 59.573 38.462 0.00 0.00 42.20 4.34
2137 2195 6.739100 GTCGCAGAAATAGATGTATCTAGACG 59.261 42.308 0.00 5.27 39.84 4.18
2138 2196 7.585867 TGTCGCAGAAATAGATGTATCTAGAC 58.414 38.462 0.00 7.60 39.84 2.59
2139 2197 7.745620 TGTCGCAGAAATAGATGTATCTAGA 57.254 36.000 7.57 0.00 39.84 2.43
2140 2198 8.079203 ACTTGTCGCAGAAATAGATGTATCTAG 58.921 37.037 7.57 0.00 39.84 2.43
2141 2199 7.941919 ACTTGTCGCAGAAATAGATGTATCTA 58.058 34.615 4.22 4.22 40.45 1.98
2142 2200 6.810911 ACTTGTCGCAGAAATAGATGTATCT 58.189 36.000 0.00 0.00 39.69 1.98
2143 2201 8.575565 TTACTTGTCGCAGAAATAGATGTATC 57.424 34.615 0.00 0.00 39.69 2.24
2144 2202 9.547753 AATTACTTGTCGCAGAAATAGATGTAT 57.452 29.630 0.00 0.00 39.69 2.29
2145 2203 8.942338 AATTACTTGTCGCAGAAATAGATGTA 57.058 30.769 0.00 0.00 39.69 2.29
2146 2204 7.011482 GGAATTACTTGTCGCAGAAATAGATGT 59.989 37.037 0.00 0.00 39.69 3.06
2147 2205 7.348201 GGAATTACTTGTCGCAGAAATAGATG 58.652 38.462 0.00 0.00 39.69 2.90
2148 2206 6.201044 CGGAATTACTTGTCGCAGAAATAGAT 59.799 38.462 0.00 0.00 39.69 1.98
2149 2207 5.518847 CGGAATTACTTGTCGCAGAAATAGA 59.481 40.000 0.00 0.00 39.69 1.98
2150 2208 5.276868 CCGGAATTACTTGTCGCAGAAATAG 60.277 44.000 0.00 0.00 39.69 1.73
2151 2209 4.569162 CCGGAATTACTTGTCGCAGAAATA 59.431 41.667 0.00 0.00 39.69 1.40
2152 2210 3.374058 CCGGAATTACTTGTCGCAGAAAT 59.626 43.478 0.00 0.00 39.69 2.17
2153 2211 2.739913 CCGGAATTACTTGTCGCAGAAA 59.260 45.455 0.00 0.00 39.69 2.52
2154 2212 2.028839 TCCGGAATTACTTGTCGCAGAA 60.029 45.455 0.00 0.00 39.69 3.02
2155 2213 1.546923 TCCGGAATTACTTGTCGCAGA 59.453 47.619 0.00 0.00 0.00 4.26
2156 2214 1.659098 GTCCGGAATTACTTGTCGCAG 59.341 52.381 5.23 0.00 0.00 5.18
2157 2215 1.717194 GTCCGGAATTACTTGTCGCA 58.283 50.000 5.23 0.00 0.00 5.10
2158 2216 0.643820 CGTCCGGAATTACTTGTCGC 59.356 55.000 5.23 0.00 0.00 5.19
2159 2217 1.135315 TCCGTCCGGAATTACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2160 2218 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2161 2219 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2162 2220 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2163 2221 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
2164 2222 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
2165 2223 0.826062 TTCCCTCCGTCCGGAATTAC 59.174 55.000 5.23 0.00 44.66 1.89
2166 2224 1.797320 ATTCCCTCCGTCCGGAATTA 58.203 50.000 5.23 0.00 44.75 1.40
2167 2225 1.797320 TATTCCCTCCGTCCGGAATT 58.203 50.000 5.23 0.00 44.75 2.17
2168 2226 4.394102 ATTCCCTCCGTCCGGAAT 57.606 55.556 5.23 0.00 44.66 3.01
2169 2227 1.797320 AATATTCCCTCCGTCCGGAA 58.203 50.000 5.23 0.00 44.66 4.30
2170 2228 2.681319 TAATATTCCCTCCGTCCGGA 57.319 50.000 0.00 0.00 42.90 5.14
2171 2229 5.357257 CAATATAATATTCCCTCCGTCCGG 58.643 45.833 0.00 0.00 0.00 5.14
2172 2230 4.809426 GCAATATAATATTCCCTCCGTCCG 59.191 45.833 0.00 0.00 0.00 4.79
2173 2231 5.741011 TGCAATATAATATTCCCTCCGTCC 58.259 41.667 0.00 0.00 0.00 4.79
2174 2232 7.047891 TCATGCAATATAATATTCCCTCCGTC 58.952 38.462 0.00 0.00 0.00 4.79
2175 2233 6.957631 TCATGCAATATAATATTCCCTCCGT 58.042 36.000 0.00 0.00 0.00 4.69
2176 2234 7.864108 TTCATGCAATATAATATTCCCTCCG 57.136 36.000 0.00 0.00 0.00 4.63
2177 2235 9.412460 TCATTCATGCAATATAATATTCCCTCC 57.588 33.333 0.00 0.00 0.00 4.30
2179 2237 9.986157 ACTCATTCATGCAATATAATATTCCCT 57.014 29.630 0.00 0.00 0.00 4.20
2230 2288 5.230942 ACACTCAACATAGTACTGACTTGC 58.769 41.667 5.39 0.00 37.10 4.01
2244 2302 4.455533 GCAAGGATCATGTAACACTCAACA 59.544 41.667 0.00 0.00 0.00 3.33
2402 2460 6.939622 TCCTAGCCATGTGTATGAGATTATG 58.060 40.000 0.00 0.00 36.36 1.90
2541 2599 9.476202 AAATTTACAAGTGGATTTTTCTAGTGC 57.524 29.630 0.00 0.00 0.00 4.40
2608 2666 7.552687 CAGTATAAGCTAGGTCCAACAATTGAA 59.447 37.037 13.59 0.00 0.00 2.69
2661 3104 4.901250 TCATTCAGCATCATGTAGGTAGGA 59.099 41.667 0.00 0.00 0.00 2.94
2751 3194 4.509843 GCTGGAATCTGGAATCCCCAATAT 60.510 45.833 0.00 0.00 46.07 1.28
2758 3201 1.978454 CTGGCTGGAATCTGGAATCC 58.022 55.000 0.00 0.00 36.21 3.01
3062 3505 8.960591 CAAAGTCCATGATATTGTTTTACCTCT 58.039 33.333 0.00 0.00 0.00 3.69
3068 3511 6.650390 GGCAACAAAGTCCATGATATTGTTTT 59.350 34.615 12.87 0.00 40.98 2.43
3170 3613 3.124921 ACCAACGCGCCTGCATAC 61.125 61.111 5.73 0.00 42.97 2.39
3322 3765 3.096092 ACTGTTGAAAGCAAACCCAGAA 58.904 40.909 0.00 0.00 35.42 3.02
3663 4205 6.043411 GGCTATAGTTGCTTAAGATATCCCG 58.957 44.000 6.67 0.00 0.00 5.14
3688 4246 5.520288 TGCATTTTCTTCGAGACATACTAGC 59.480 40.000 0.00 0.00 0.00 3.42
3712 4270 5.658190 AGGTCACAAAAATAGCCATAATGCT 59.342 36.000 0.00 0.00 45.38 3.79
3802 4360 9.520515 AGTCAGGTCAGTAAAATAATTTGATGT 57.479 29.630 0.00 0.00 0.00 3.06
3808 4366 9.959721 ACACATAGTCAGGTCAGTAAAATAATT 57.040 29.630 0.00 0.00 0.00 1.40
3914 4474 2.354805 GGCGAAGTTCCAGACCATAACT 60.355 50.000 0.00 0.00 35.01 2.24
3917 4477 0.539986 GGGCGAAGTTCCAGACCATA 59.460 55.000 0.00 0.00 32.05 2.74
3968 4528 0.535102 GGTGGTTCCACAGTGACCAG 60.535 60.000 21.25 0.00 43.62 4.00
4129 4697 2.104331 GTTAGCAGCGCCGCTAGA 59.896 61.111 23.33 13.02 44.93 2.43
4249 4821 2.076100 CAGCGAGCACACAAAATAGGA 58.924 47.619 0.00 0.00 0.00 2.94
4250 4822 1.806542 ACAGCGAGCACACAAAATAGG 59.193 47.619 0.00 0.00 0.00 2.57
4286 4859 0.822164 AATACGGAGGGGACACGAAG 59.178 55.000 0.00 0.00 36.87 3.79
4292 4865 2.420466 GGCGAATACGGAGGGGAC 59.580 66.667 0.00 0.00 40.15 4.46
4333 4906 0.825840 CAGAAAGGCCGTGGGGAAAA 60.826 55.000 0.00 0.00 34.06 2.29
4439 5014 3.870633 AGACGAGTTCATTACTGGGTC 57.129 47.619 0.00 0.00 37.17 4.46
4446 5021 5.450137 GCTTACAGCCTAGACGAGTTCATTA 60.450 44.000 0.00 0.00 34.48 1.90
4453 5028 1.746220 ACAGCTTACAGCCTAGACGAG 59.254 52.381 0.00 0.00 43.77 4.18
4477 5057 7.039313 ACAGTTAAGACACCAAAAGGAATTC 57.961 36.000 0.00 0.00 0.00 2.17
4487 5067 6.330004 TGTACGATTACAGTTAAGACACCA 57.670 37.500 0.00 0.00 32.98 4.17
4506 5086 4.404507 ACAATTTCACAGCGTCATGTAC 57.595 40.909 0.00 0.00 0.00 2.90
4562 5142 2.758327 ACGGCTATGACCTCGCCA 60.758 61.111 0.00 0.00 43.95 5.69
4565 5145 1.672854 TTGGGACGGCTATGACCTCG 61.673 60.000 0.00 0.00 0.00 4.63
4602 5229 5.404096 CATGTTTGCTCATCATTTGCACTA 58.596 37.500 0.00 0.00 36.37 2.74
4603 5230 4.242475 CATGTTTGCTCATCATTTGCACT 58.758 39.130 0.00 0.00 36.37 4.40
4625 5252 4.496341 CCAGTAATGTTCGAATCACATGCC 60.496 45.833 0.00 0.00 34.97 4.40
4651 5278 3.944055 AGAGATCAACTACTTGTGCGT 57.056 42.857 0.00 0.00 0.00 5.24
4652 5279 4.449068 ACAAAGAGATCAACTACTTGTGCG 59.551 41.667 0.00 0.00 34.39 5.34
4666 5293 6.808829 TCACAAAATTCTGCAACAAAGAGAT 58.191 32.000 0.00 0.00 0.00 2.75
4667 5294 6.206395 TCACAAAATTCTGCAACAAAGAGA 57.794 33.333 0.00 0.00 0.00 3.10
4697 5324 2.644418 GAGCGCATGCACCAAACA 59.356 55.556 19.57 0.00 46.23 2.83
4725 5361 0.822532 AACGTCGTCACAGGACTCCT 60.823 55.000 0.00 0.00 42.05 3.69
4727 5363 0.386985 GGAACGTCGTCACAGGACTC 60.387 60.000 0.00 0.00 42.05 3.36
4728 5364 0.822532 AGGAACGTCGTCACAGGACT 60.823 55.000 0.00 0.00 42.05 3.85
4731 5367 0.314302 AGAAGGAACGTCGTCACAGG 59.686 55.000 0.00 0.00 42.91 4.00
4733 5369 2.589798 AAAGAAGGAACGTCGTCACA 57.410 45.000 0.00 0.00 42.91 3.58
4734 5370 3.938778 AAAAAGAAGGAACGTCGTCAC 57.061 42.857 0.00 0.00 42.91 3.67
4761 5397 8.816144 GCCGCAAAATTCTTTATTTATGAATGA 58.184 29.630 0.00 0.00 35.39 2.57
4762 5398 8.602328 TGCCGCAAAATTCTTTATTTATGAATG 58.398 29.630 0.00 0.00 35.39 2.67
4764 5400 7.816995 AGTGCCGCAAAATTCTTTATTTATGAA 59.183 29.630 0.00 0.00 35.39 2.57
4765 5401 7.319646 AGTGCCGCAAAATTCTTTATTTATGA 58.680 30.769 0.00 0.00 35.39 2.15
4766 5402 7.524294 AGTGCCGCAAAATTCTTTATTTATG 57.476 32.000 0.00 0.00 35.39 1.90
4769 5405 6.687604 ACTAGTGCCGCAAAATTCTTTATTT 58.312 32.000 0.00 0.00 38.08 1.40
4770 5406 6.267496 ACTAGTGCCGCAAAATTCTTTATT 57.733 33.333 0.00 0.00 0.00 1.40
4771 5407 5.897377 ACTAGTGCCGCAAAATTCTTTAT 57.103 34.783 0.00 0.00 0.00 1.40
4773 5409 4.584327 AACTAGTGCCGCAAAATTCTTT 57.416 36.364 0.00 0.00 0.00 2.52
4774 5410 4.298332 CAAACTAGTGCCGCAAAATTCTT 58.702 39.130 0.00 0.00 0.00 2.52
4776 5412 2.986479 CCAAACTAGTGCCGCAAAATTC 59.014 45.455 0.00 0.00 0.00 2.17
4873 5521 6.019075 CGACTTTGATGTCAACACTCACTTAA 60.019 38.462 0.00 0.00 36.82 1.85
4892 5540 2.758979 ACCACTCGGACATATCGACTTT 59.241 45.455 0.00 0.00 35.59 2.66


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

AutoCloner maintained by Alex Coulton.