Multiple sequence alignment - TraesCS1A01G401300

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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 TraesCS1A01G401300 chr1A 100.000 4343 0 0 1 4343 564752400 564748058 0.000000e+00 8021.0
1 TraesCS1A01G401300 chr1A 85.166 991 110 23 917 1905 564663824 564664779 0.000000e+00 981.0
2 TraesCS1A01G401300 chr1A 86.985 753 87 8 1916 2664 564664832 564665577 0.000000e+00 837.0
3 TraesCS1A01G401300 chr1A 88.772 570 45 10 3110 3669 564665939 564666499 0.000000e+00 680.0
4 TraesCS1A01G401300 chr1D 95.667 3577 100 17 171 3736 470886571 470883039 0.000000e+00 5696.0
5 TraesCS1A01G401300 chr1B 86.572 2532 286 35 929 3430 654504127 654506634 0.000000e+00 2743.0
6 TraesCS1A01G401300 chr1B 90.865 624 40 7 3735 4343 660813376 660812755 0.000000e+00 821.0
7 TraesCS1A01G401300 chr4D 92.652 626 30 6 3733 4343 481200075 481199451 0.000000e+00 887.0
8 TraesCS1A01G401300 chr6D 92.616 623 28 6 3735 4343 327630259 327629641 0.000000e+00 880.0
9 TraesCS1A01G401300 chr6D 91.693 626 35 7 3734 4343 11152242 11152866 0.000000e+00 852.0
10 TraesCS1A01G401300 chr7D 92.332 626 32 6 3733 4343 593174648 593174024 0.000000e+00 876.0
11 TraesCS1A01G401300 chr7D 92.456 623 30 7 3736 4343 553481258 553480638 0.000000e+00 874.0
12 TraesCS1A01G401300 chr7D 91.506 624 37 6 3735 4343 536138054 536137432 0.000000e+00 845.0
13 TraesCS1A01G401300 chr7D 91.346 624 37 7 3734 4343 8832040 8831420 0.000000e+00 837.0
14 TraesCS1A01G401300 chr3A 91.974 623 34 6 3735 4343 702537429 702536809 0.000000e+00 859.0
15 TraesCS1A01G401300 chr3A 100.000 29 0 0 1779 1807 12411025 12411053 2.000000e-03 54.7
16 TraesCS1A01G401300 chr6B 90.545 624 42 7 3734 4343 12903486 12904106 0.000000e+00 809.0
17 TraesCS1A01G401300 chr5D 90.446 471 27 8 3734 4188 385924153 385923685 4.800000e-169 604.0
18 TraesCS1A01G401300 chr3B 88.995 418 28 7 3736 4137 236719564 236719149 6.480000e-138 501.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G401300 chr1A 564748058 564752400 4342 True 8021.000000 8021 100.000000 1 4343 1 chr1A.!!$R1 4342
1 TraesCS1A01G401300 chr1A 564663824 564666499 2675 False 832.666667 981 86.974333 917 3669 3 chr1A.!!$F1 2752
2 TraesCS1A01G401300 chr1D 470883039 470886571 3532 True 5696.000000 5696 95.667000 171 3736 1 chr1D.!!$R1 3565
3 TraesCS1A01G401300 chr1B 654504127 654506634 2507 False 2743.000000 2743 86.572000 929 3430 1 chr1B.!!$F1 2501
4 TraesCS1A01G401300 chr1B 660812755 660813376 621 True 821.000000 821 90.865000 3735 4343 1 chr1B.!!$R1 608
5 TraesCS1A01G401300 chr4D 481199451 481200075 624 True 887.000000 887 92.652000 3733 4343 1 chr4D.!!$R1 610
6 TraesCS1A01G401300 chr6D 327629641 327630259 618 True 880.000000 880 92.616000 3735 4343 1 chr6D.!!$R1 608
7 TraesCS1A01G401300 chr6D 11152242 11152866 624 False 852.000000 852 91.693000 3734 4343 1 chr6D.!!$F1 609
8 TraesCS1A01G401300 chr7D 593174024 593174648 624 True 876.000000 876 92.332000 3733 4343 1 chr7D.!!$R4 610
9 TraesCS1A01G401300 chr7D 553480638 553481258 620 True 874.000000 874 92.456000 3736 4343 1 chr7D.!!$R3 607
10 TraesCS1A01G401300 chr7D 536137432 536138054 622 True 845.000000 845 91.506000 3735 4343 1 chr7D.!!$R2 608
11 TraesCS1A01G401300 chr7D 8831420 8832040 620 True 837.000000 837 91.346000 3734 4343 1 chr7D.!!$R1 609
12 TraesCS1A01G401300 chr3A 702536809 702537429 620 True 859.000000 859 91.974000 3735 4343 1 chr3A.!!$R1 608
13 TraesCS1A01G401300 chr6B 12903486 12904106 620 False 809.000000 809 90.545000 3734 4343 1 chr6B.!!$F1 609

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
135 136 0.108585 TGACTTCAGGTTCAGGTGGC 59.891 55.0 0.00 0.0 0.0 5.01 F
137 138 0.109342 ACTTCAGGTTCAGGTGGCAG 59.891 55.0 0.00 0.0 0.0 4.85 F
1707 1719 0.037882 TCTTGCTGGCGTTGAGAGAG 60.038 55.0 0.00 0.0 0.0 3.20 F
2570 2633 0.385473 CGCGCAAATTTCACCGAAGT 60.385 50.0 8.75 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1380 1389 0.329261 TGAGAATCCTGGGTGCCTTG 59.671 55.0 0.0 0.0 0.00 3.61 R
1794 1806 0.767375 AGAGTGCAAAGGAGAGGCAA 59.233 50.0 0.0 0.0 39.57 4.52 R
2922 2988 0.036732 TCTTGAGCCGTCCAAGCATT 59.963 50.0 0.0 0.0 40.45 3.56 R
3969 4085 0.035915 TCAACCGATTTGGATGGCGA 60.036 50.0 0.0 0.0 40.78 5.54 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
25 26 5.359194 TGAGATTATTTCACTCCTGGTCC 57.641 43.478 0.00 0.00 0.00 4.46
26 27 5.032846 TGAGATTATTTCACTCCTGGTCCT 58.967 41.667 0.00 0.00 0.00 3.85
27 28 6.202331 TGAGATTATTTCACTCCTGGTCCTA 58.798 40.000 0.00 0.00 0.00 2.94
28 29 6.325028 TGAGATTATTTCACTCCTGGTCCTAG 59.675 42.308 0.00 0.00 0.00 3.02
29 30 6.206042 AGATTATTTCACTCCTGGTCCTAGT 58.794 40.000 0.00 0.00 0.00 2.57
30 31 5.677319 TTATTTCACTCCTGGTCCTAGTG 57.323 43.478 6.87 6.87 41.58 2.74
31 32 1.267121 TTCACTCCTGGTCCTAGTGC 58.733 55.000 8.07 0.00 40.34 4.40
32 33 0.114364 TCACTCCTGGTCCTAGTGCA 59.886 55.000 8.07 0.00 40.34 4.57
33 34 0.534412 CACTCCTGGTCCTAGTGCAG 59.466 60.000 0.90 0.00 34.73 4.41
34 35 1.261238 ACTCCTGGTCCTAGTGCAGC 61.261 60.000 0.00 0.00 0.00 5.25
35 36 1.229177 TCCTGGTCCTAGTGCAGCA 60.229 57.895 0.00 0.00 0.00 4.41
36 37 1.078848 CCTGGTCCTAGTGCAGCAC 60.079 63.158 18.55 18.55 34.10 4.40
37 38 1.673477 CTGGTCCTAGTGCAGCACA 59.327 57.895 27.35 12.26 36.74 4.57
47 48 3.644774 TGCAGCACACAACATGTTG 57.355 47.368 32.03 32.03 40.64 3.33
48 49 1.101331 TGCAGCACACAACATGTTGA 58.899 45.000 38.30 15.66 40.64 3.18
49 50 1.475682 TGCAGCACACAACATGTTGAA 59.524 42.857 38.30 6.80 40.64 2.69
50 51 2.101082 TGCAGCACACAACATGTTGAAT 59.899 40.909 38.30 24.60 40.64 2.57
51 52 3.317430 TGCAGCACACAACATGTTGAATA 59.683 39.130 38.30 16.02 40.64 1.75
52 53 3.670055 GCAGCACACAACATGTTGAATAC 59.330 43.478 38.30 25.01 40.64 1.89
53 54 4.792380 GCAGCACACAACATGTTGAATACA 60.792 41.667 38.30 0.00 40.64 2.29
54 55 4.913345 CAGCACACAACATGTTGAATACAG 59.087 41.667 38.30 22.85 40.64 2.74
55 56 4.580167 AGCACACAACATGTTGAATACAGT 59.420 37.500 38.30 23.35 40.64 3.55
56 57 5.762711 AGCACACAACATGTTGAATACAGTA 59.237 36.000 38.30 0.00 40.64 2.74
57 58 6.430925 AGCACACAACATGTTGAATACAGTAT 59.569 34.615 38.30 14.97 40.64 2.12
58 59 7.040478 AGCACACAACATGTTGAATACAGTATT 60.040 33.333 38.30 14.28 40.64 1.89
59 60 7.060979 GCACACAACATGTTGAATACAGTATTG 59.939 37.037 38.30 24.95 40.64 1.90
60 61 8.075574 CACACAACATGTTGAATACAGTATTGT 58.924 33.333 38.30 25.51 40.64 2.71
61 62 8.629158 ACACAACATGTTGAATACAGTATTGTT 58.371 29.630 38.30 13.19 38.98 2.83
62 63 9.462174 CACAACATGTTGAATACAGTATTGTTT 57.538 29.630 38.30 12.58 42.93 2.83
84 85 9.997482 TGTTTTTCAGTTTTCACTAGTTCATAC 57.003 29.630 0.00 0.00 0.00 2.39
85 86 9.997482 GTTTTTCAGTTTTCACTAGTTCATACA 57.003 29.630 0.00 0.00 0.00 2.29
87 88 7.421530 TTCAGTTTTCACTAGTTCATACAGC 57.578 36.000 0.00 0.00 0.00 4.40
88 89 6.759272 TCAGTTTTCACTAGTTCATACAGCT 58.241 36.000 0.00 0.00 0.00 4.24
89 90 7.892609 TCAGTTTTCACTAGTTCATACAGCTA 58.107 34.615 0.00 0.00 0.00 3.32
90 91 8.029522 TCAGTTTTCACTAGTTCATACAGCTAG 58.970 37.037 0.00 0.00 38.43 3.42
91 92 7.815068 CAGTTTTCACTAGTTCATACAGCTAGT 59.185 37.037 0.00 0.00 44.16 2.57
92 93 9.021807 AGTTTTCACTAGTTCATACAGCTAGTA 57.978 33.333 0.00 0.00 42.22 1.82
93 94 9.291664 GTTTTCACTAGTTCATACAGCTAGTAG 57.708 37.037 0.00 0.00 42.22 2.57
94 95 7.569639 TTCACTAGTTCATACAGCTAGTAGG 57.430 40.000 0.00 0.00 42.22 3.18
95 96 6.896883 TCACTAGTTCATACAGCTAGTAGGA 58.103 40.000 0.00 6.59 42.22 2.94
96 97 7.519057 TCACTAGTTCATACAGCTAGTAGGAT 58.481 38.462 10.13 2.28 42.46 3.24
97 98 7.445707 TCACTAGTTCATACAGCTAGTAGGATG 59.554 40.741 10.13 3.20 42.46 3.51
98 99 7.229707 CACTAGTTCATACAGCTAGTAGGATGT 59.770 40.741 10.13 0.00 42.46 3.06
99 100 7.780745 ACTAGTTCATACAGCTAGTAGGATGTT 59.219 37.037 10.13 4.36 42.46 2.71
100 101 7.425224 AGTTCATACAGCTAGTAGGATGTTT 57.575 36.000 10.13 0.00 42.46 2.83
101 102 8.534954 AGTTCATACAGCTAGTAGGATGTTTA 57.465 34.615 10.13 0.00 42.46 2.01
102 103 8.978472 AGTTCATACAGCTAGTAGGATGTTTAA 58.022 33.333 10.13 0.00 42.46 1.52
103 104 9.765795 GTTCATACAGCTAGTAGGATGTTTAAT 57.234 33.333 10.13 0.00 42.46 1.40
108 109 8.959705 ACAGCTAGTAGGATGTTTAATTTACC 57.040 34.615 0.00 0.00 31.39 2.85
109 110 8.769359 ACAGCTAGTAGGATGTTTAATTTACCT 58.231 33.333 0.00 0.00 31.39 3.08
110 111 9.046296 CAGCTAGTAGGATGTTTAATTTACCTG 57.954 37.037 0.00 0.00 0.00 4.00
111 112 8.211629 AGCTAGTAGGATGTTTAATTTACCTGG 58.788 37.037 0.00 0.00 0.00 4.45
112 113 7.991460 GCTAGTAGGATGTTTAATTTACCTGGT 59.009 37.037 4.05 4.05 0.00 4.00
113 114 9.901172 CTAGTAGGATGTTTAATTTACCTGGTT 57.099 33.333 3.84 0.00 0.00 3.67
114 115 8.803397 AGTAGGATGTTTAATTTACCTGGTTC 57.197 34.615 3.84 0.00 0.00 3.62
115 116 7.832685 AGTAGGATGTTTAATTTACCTGGTTCC 59.167 37.037 3.84 1.31 0.00 3.62
116 117 6.800890 AGGATGTTTAATTTACCTGGTTCCT 58.199 36.000 3.84 3.96 0.00 3.36
117 118 6.663523 AGGATGTTTAATTTACCTGGTTCCTG 59.336 38.462 3.84 0.00 0.00 3.86
118 119 6.661805 GGATGTTTAATTTACCTGGTTCCTGA 59.338 38.462 3.84 0.00 0.00 3.86
119 120 6.887626 TGTTTAATTTACCTGGTTCCTGAC 57.112 37.500 3.84 0.00 0.00 3.51
120 121 6.607019 TGTTTAATTTACCTGGTTCCTGACT 58.393 36.000 3.84 0.00 0.00 3.41
121 122 7.064229 TGTTTAATTTACCTGGTTCCTGACTT 58.936 34.615 3.84 0.00 0.00 3.01
122 123 7.229907 TGTTTAATTTACCTGGTTCCTGACTTC 59.770 37.037 3.84 0.00 0.00 3.01
123 124 4.993705 ATTTACCTGGTTCCTGACTTCA 57.006 40.909 3.84 0.00 0.00 3.02
124 125 4.351874 TTTACCTGGTTCCTGACTTCAG 57.648 45.455 3.84 0.00 43.40 3.02
134 135 2.175878 CTGACTTCAGGTTCAGGTGG 57.824 55.000 0.00 0.00 40.20 4.61
135 136 0.108585 TGACTTCAGGTTCAGGTGGC 59.891 55.000 0.00 0.00 0.00 5.01
136 137 0.108585 GACTTCAGGTTCAGGTGGCA 59.891 55.000 0.00 0.00 0.00 4.92
137 138 0.109342 ACTTCAGGTTCAGGTGGCAG 59.891 55.000 0.00 0.00 0.00 4.85
138 139 0.607489 CTTCAGGTTCAGGTGGCAGG 60.607 60.000 0.00 0.00 0.00 4.85
139 140 2.034687 CAGGTTCAGGTGGCAGGG 59.965 66.667 0.00 0.00 0.00 4.45
140 141 2.121963 AGGTTCAGGTGGCAGGGA 60.122 61.111 0.00 0.00 0.00 4.20
141 142 1.774217 AGGTTCAGGTGGCAGGGAA 60.774 57.895 0.00 0.00 0.00 3.97
142 143 1.152830 GGTTCAGGTGGCAGGGAAA 59.847 57.895 0.00 0.00 0.00 3.13
143 144 0.251787 GGTTCAGGTGGCAGGGAAAT 60.252 55.000 0.00 0.00 0.00 2.17
144 145 1.177401 GTTCAGGTGGCAGGGAAATC 58.823 55.000 0.00 0.00 0.00 2.17
145 146 0.776810 TTCAGGTGGCAGGGAAATCA 59.223 50.000 0.00 0.00 0.00 2.57
146 147 0.776810 TCAGGTGGCAGGGAAATCAA 59.223 50.000 0.00 0.00 0.00 2.57
147 148 1.358787 TCAGGTGGCAGGGAAATCAAT 59.641 47.619 0.00 0.00 0.00 2.57
148 149 2.181975 CAGGTGGCAGGGAAATCAATT 58.818 47.619 0.00 0.00 0.00 2.32
149 150 2.568509 CAGGTGGCAGGGAAATCAATTT 59.431 45.455 0.00 0.00 0.00 1.82
150 151 2.833943 AGGTGGCAGGGAAATCAATTTC 59.166 45.455 6.88 6.88 44.08 2.17
151 152 2.833943 GGTGGCAGGGAAATCAATTTCT 59.166 45.455 13.56 0.00 44.21 2.52
152 153 3.261643 GGTGGCAGGGAAATCAATTTCTT 59.738 43.478 13.56 2.52 44.21 2.52
153 154 4.263025 GGTGGCAGGGAAATCAATTTCTTT 60.263 41.667 13.56 2.23 44.21 2.52
154 155 4.931601 GTGGCAGGGAAATCAATTTCTTTC 59.068 41.667 13.56 5.94 44.21 2.62
155 156 4.176271 GGCAGGGAAATCAATTTCTTTCG 58.824 43.478 13.56 3.94 44.21 3.46
156 157 4.176271 GCAGGGAAATCAATTTCTTTCGG 58.824 43.478 13.56 7.28 44.21 4.30
157 158 4.082245 GCAGGGAAATCAATTTCTTTCGGA 60.082 41.667 13.56 0.00 44.21 4.55
158 159 5.402398 CAGGGAAATCAATTTCTTTCGGAC 58.598 41.667 13.56 0.00 44.21 4.79
159 160 4.156008 AGGGAAATCAATTTCTTTCGGACG 59.844 41.667 13.56 0.00 44.21 4.79
160 161 4.082949 GGGAAATCAATTTCTTTCGGACGT 60.083 41.667 13.56 0.00 44.21 4.34
161 162 5.086727 GGAAATCAATTTCTTTCGGACGTC 58.913 41.667 7.13 7.13 44.21 4.34
162 163 3.991605 ATCAATTTCTTTCGGACGTCG 57.008 42.857 9.92 5.26 40.90 5.12
163 164 2.063266 TCAATTTCTTTCGGACGTCGG 58.937 47.619 16.37 16.37 39.77 4.79
164 165 1.796459 CAATTTCTTTCGGACGTCGGT 59.204 47.619 20.84 0.00 39.77 4.69
165 166 1.706443 ATTTCTTTCGGACGTCGGTC 58.294 50.000 20.84 1.69 42.66 4.79
166 167 0.661187 TTTCTTTCGGACGTCGGTCG 60.661 55.000 20.84 13.77 44.39 4.79
167 168 1.506309 TTCTTTCGGACGTCGGTCGA 61.506 55.000 20.84 15.78 44.39 4.20
168 169 1.511464 CTTTCGGACGTCGGTCGAG 60.511 63.158 20.84 13.55 44.39 4.04
169 170 2.180131 CTTTCGGACGTCGGTCGAGT 62.180 60.000 20.84 0.00 44.39 4.18
224 225 4.440112 GGCTTCCTTGTATATGTTTGTGCC 60.440 45.833 0.00 0.00 0.00 5.01
225 226 4.730613 GCTTCCTTGTATATGTTTGTGCCG 60.731 45.833 0.00 0.00 0.00 5.69
226 227 3.945346 TCCTTGTATATGTTTGTGCCGT 58.055 40.909 0.00 0.00 0.00 5.68
227 228 3.936453 TCCTTGTATATGTTTGTGCCGTC 59.064 43.478 0.00 0.00 0.00 4.79
228 229 3.687212 CCTTGTATATGTTTGTGCCGTCA 59.313 43.478 0.00 0.00 0.00 4.35
229 230 4.155099 CCTTGTATATGTTTGTGCCGTCAA 59.845 41.667 0.00 0.00 0.00 3.18
230 231 4.937696 TGTATATGTTTGTGCCGTCAAG 57.062 40.909 0.00 0.00 0.00 3.02
231 232 4.570930 TGTATATGTTTGTGCCGTCAAGA 58.429 39.130 0.00 0.00 0.00 3.02
232 233 4.998033 TGTATATGTTTGTGCCGTCAAGAA 59.002 37.500 0.00 0.00 0.00 2.52
233 234 5.645929 TGTATATGTTTGTGCCGTCAAGAAT 59.354 36.000 0.00 0.00 0.00 2.40
234 235 5.643379 ATATGTTTGTGCCGTCAAGAATT 57.357 34.783 0.00 0.00 0.00 2.17
247 248 5.909610 CCGTCAAGAATTTGTCAAGTTTCTC 59.090 40.000 11.25 2.49 35.73 2.87
248 249 6.238484 CCGTCAAGAATTTGTCAAGTTTCTCT 60.238 38.462 11.25 0.00 35.73 3.10
259 260 9.507329 TTTGTCAAGTTTCTCTGAATTATAGCT 57.493 29.630 0.00 0.00 0.00 3.32
307 308 5.393787 CCAATGTTTCTCAACTGCTGCATAT 60.394 40.000 1.31 0.00 33.58 1.78
308 309 6.183360 CCAATGTTTCTCAACTGCTGCATATA 60.183 38.462 1.31 0.00 33.58 0.86
309 310 7.423199 CAATGTTTCTCAACTGCTGCATATAT 58.577 34.615 1.31 0.00 33.58 0.86
310 311 8.562052 CAATGTTTCTCAACTGCTGCATATATA 58.438 33.333 1.31 0.00 33.58 0.86
311 312 7.482654 TGTTTCTCAACTGCTGCATATATAC 57.517 36.000 1.31 0.00 33.58 1.47
313 314 5.806654 TCTCAACTGCTGCATATATACCA 57.193 39.130 1.31 0.00 0.00 3.25
314 315 6.364568 TCTCAACTGCTGCATATATACCAT 57.635 37.500 1.31 0.00 0.00 3.55
315 316 6.772605 TCTCAACTGCTGCATATATACCATT 58.227 36.000 1.31 0.00 0.00 3.16
316 317 6.875726 TCTCAACTGCTGCATATATACCATTC 59.124 38.462 1.31 0.00 0.00 2.67
317 318 6.772605 TCAACTGCTGCATATATACCATTCT 58.227 36.000 1.31 0.00 0.00 2.40
318 319 6.875726 TCAACTGCTGCATATATACCATTCTC 59.124 38.462 1.31 0.00 0.00 2.87
320 321 7.013823 ACTGCTGCATATATACCATTCTCTT 57.986 36.000 1.31 0.00 0.00 2.85
321 322 7.456725 ACTGCTGCATATATACCATTCTCTTT 58.543 34.615 1.31 0.00 0.00 2.52
322 323 7.941238 ACTGCTGCATATATACCATTCTCTTTT 59.059 33.333 1.31 0.00 0.00 2.27
323 324 8.696043 TGCTGCATATATACCATTCTCTTTTT 57.304 30.769 0.00 0.00 0.00 1.94
423 424 3.492102 AGCTAGAAACAGAACAGCCAA 57.508 42.857 0.00 0.00 32.58 4.52
463 464 2.030007 CACAGGCAATTAACCACACAGG 60.030 50.000 0.00 0.00 45.67 4.00
529 530 4.110493 GCATAGAGCACACCGGAC 57.890 61.111 9.46 0.00 44.79 4.79
564 566 2.438800 ACGAGTAGCCACTACAGGAT 57.561 50.000 7.45 0.00 39.22 3.24
578 580 8.585881 GCCACTACAGGATATGACTAGATAAAA 58.414 37.037 0.00 0.00 0.00 1.52
592 595 7.403231 TGACTAGATAAAAGAGGAACAAGGGAT 59.597 37.037 0.00 0.00 0.00 3.85
599 602 3.960571 AGAGGAACAAGGGATGAACATG 58.039 45.455 0.00 0.00 0.00 3.21
663 666 2.568090 GCCCAAACATGCGTCCTG 59.432 61.111 0.00 0.00 0.00 3.86
669 672 2.422597 CAAACATGCGTCCTGGAGTAA 58.577 47.619 0.00 0.00 0.00 2.24
753 756 4.116926 CAAGATTGGCTTGCCCCA 57.883 55.556 9.35 0.00 46.67 4.96
766 769 3.429410 GCTTGCCCCATTTGTGAGATAAC 60.429 47.826 0.00 0.00 0.00 1.89
781 784 8.725405 TGTGAGATAACGGCATAGATTAAAAA 57.275 30.769 0.00 0.00 0.00 1.94
832 835 2.137523 GTTCAAACCAGGCTGCATTTG 58.862 47.619 25.10 25.10 34.11 2.32
876 879 1.152819 AGCCAGGCTGCATACCATG 60.153 57.895 15.24 0.00 37.57 3.66
896 899 4.530094 TGCCGTTCGTCAATTTCATATC 57.470 40.909 0.00 0.00 0.00 1.63
904 907 7.798052 CGTTCGTCAATTTCATATCATTATGCA 59.202 33.333 0.00 0.00 36.03 3.96
1146 1155 1.503542 GCATCGGTCAACAGGCAAG 59.496 57.895 0.00 0.00 0.00 4.01
1380 1389 1.372087 CTGCCAACATCCTTCGCTCC 61.372 60.000 0.00 0.00 0.00 4.70
1391 1400 3.551496 TTCGCTCCAAGGCACCCAG 62.551 63.158 0.00 0.00 0.00 4.45
1707 1719 0.037882 TCTTGCTGGCGTTGAGAGAG 60.038 55.000 0.00 0.00 0.00 3.20
1794 1806 0.543174 ACGAGGAGCTCAAGGACCTT 60.543 55.000 17.19 0.00 32.53 3.50
1821 1833 3.071602 TCTCCTTTGCACTCTACAAGCTT 59.928 43.478 0.00 0.00 0.00 3.74
2001 2055 1.881973 AGGCATGCCATAGTATTTGCG 59.118 47.619 37.18 0.00 38.92 4.85
2010 2064 4.789802 GCCATAGTATTTGCGAAAGGCTTC 60.790 45.833 0.00 0.00 44.05 3.86
2049 2103 4.492646 TGCTATCCACCATTCTGATAGGA 58.507 43.478 0.00 0.00 0.00 2.94
2279 2333 1.602237 GAAGCCCGATGACCAAGGA 59.398 57.895 0.00 0.00 0.00 3.36
2478 2532 4.145052 TCAACTGTCTCAGAGACTGCTTA 58.855 43.478 28.56 15.87 45.27 3.09
2537 2591 1.815817 GCATTTGGCAAAGTCGGGGT 61.816 55.000 18.61 0.00 43.97 4.95
2570 2633 0.385473 CGCGCAAATTTCACCGAAGT 60.385 50.000 8.75 0.00 0.00 3.01
2616 2679 2.602878 CACATTCTGCTGATTTGGCAC 58.397 47.619 0.00 0.00 35.71 5.01
2808 2874 1.274728 CTCACACTGGTTCCTCCTCTG 59.725 57.143 0.00 0.00 37.07 3.35
2922 2988 2.983192 TCCTTGTTATCAGTCCACCCAA 59.017 45.455 0.00 0.00 0.00 4.12
2973 3039 9.585099 GCATCAGAGGAGATAGAATTGTATAAG 57.415 37.037 0.00 0.00 0.00 1.73
3222 3309 1.686325 GCTCTGGCGGGGAGTTCATA 61.686 60.000 0.00 0.00 33.73 2.15
3267 3354 3.942439 GCCGGCATCCTAGGGGAC 61.942 72.222 24.80 2.74 45.43 4.46
3291 3378 1.134694 GCACGGCGACCAAGATTTC 59.865 57.895 16.62 0.00 0.00 2.17
3443 3538 0.315568 GAAGCTATCCGAGGCGACAT 59.684 55.000 0.00 0.00 0.00 3.06
3494 3589 1.067846 TGGGTGACGATCTTCGACTTG 60.068 52.381 3.62 0.00 43.74 3.16
3495 3590 0.992802 GGTGACGATCTTCGACTTGC 59.007 55.000 3.62 0.00 43.74 4.01
3496 3591 1.402984 GGTGACGATCTTCGACTTGCT 60.403 52.381 3.62 0.00 43.74 3.91
3497 3592 2.329379 GTGACGATCTTCGACTTGCTT 58.671 47.619 3.62 0.00 43.74 3.91
3498 3593 2.091277 GTGACGATCTTCGACTTGCTTG 59.909 50.000 3.62 0.00 43.74 4.01
3499 3594 2.030274 TGACGATCTTCGACTTGCTTGA 60.030 45.455 3.62 0.00 43.74 3.02
3500 3595 2.596419 GACGATCTTCGACTTGCTTGAG 59.404 50.000 3.62 0.00 43.74 3.02
3501 3596 1.923204 CGATCTTCGACTTGCTTGAGG 59.077 52.381 0.00 0.00 43.74 3.86
3572 3677 6.687105 CGTAGTTATTTGTTGCTATTTCCTGC 59.313 38.462 0.00 0.00 0.00 4.85
3577 3682 4.935352 TTGTTGCTATTTCCTGCTGTTT 57.065 36.364 0.00 0.00 0.00 2.83
3584 3689 3.923017 ATTTCCTGCTGTTTGCTGTAC 57.077 42.857 0.00 0.00 43.37 2.90
3603 3708 4.984161 TGTACGCCTAGTTTTGTTGACTAC 59.016 41.667 0.00 0.00 0.00 2.73
3605 3710 4.304939 ACGCCTAGTTTTGTTGACTACTC 58.695 43.478 0.00 0.00 0.00 2.59
3606 3711 3.678548 CGCCTAGTTTTGTTGACTACTCC 59.321 47.826 0.00 0.00 0.00 3.85
3607 3712 4.560919 CGCCTAGTTTTGTTGACTACTCCT 60.561 45.833 0.00 0.00 0.00 3.69
3609 3714 6.461640 GCCTAGTTTTGTTGACTACTCCTTA 58.538 40.000 0.00 0.00 0.00 2.69
3610 3715 6.590677 GCCTAGTTTTGTTGACTACTCCTTAG 59.409 42.308 0.00 0.00 0.00 2.18
3611 3716 7.525029 GCCTAGTTTTGTTGACTACTCCTTAGA 60.525 40.741 0.00 0.00 0.00 2.10
3612 3717 8.532819 CCTAGTTTTGTTGACTACTCCTTAGAT 58.467 37.037 0.00 0.00 0.00 1.98
3613 3718 9.360093 CTAGTTTTGTTGACTACTCCTTAGATG 57.640 37.037 0.00 0.00 0.00 2.90
3656 3762 3.127533 GCATCTGACGGTGTGGCC 61.128 66.667 0.00 0.00 0.00 5.36
3679 3792 1.364626 GCACTGGAGATGCAGGTTCG 61.365 60.000 6.30 0.00 42.88 3.95
3729 3842 3.551635 TGGAAATGGGGGTTGTATGTT 57.448 42.857 0.00 0.00 0.00 2.71
3736 3849 4.472690 TGGGGGTTGTATGTTACCTTTT 57.527 40.909 0.00 0.00 34.75 2.27
3737 3850 4.817286 TGGGGGTTGTATGTTACCTTTTT 58.183 39.130 0.00 0.00 34.75 1.94
3738 3851 4.833938 TGGGGGTTGTATGTTACCTTTTTC 59.166 41.667 0.00 0.00 34.75 2.29
3739 3852 5.081728 GGGGGTTGTATGTTACCTTTTTCT 58.918 41.667 0.00 0.00 34.75 2.52
3749 3862 9.940166 GTATGTTACCTTTTTCTTTCGAAAAGA 57.060 29.630 12.41 8.74 46.45 2.52
3769 3882 2.066999 GGATCTTCCCGGCCTCTGT 61.067 63.158 0.00 0.00 0.00 3.41
3770 3883 1.144936 GATCTTCCCGGCCTCTGTG 59.855 63.158 0.00 0.00 0.00 3.66
3940 4056 2.419297 CGGCTGGCAAAAGAGAGATAGT 60.419 50.000 1.08 0.00 0.00 2.12
4012 4128 2.982339 ATACCGAGCTACCATCTCCT 57.018 50.000 0.00 0.00 0.00 3.69
4139 4269 9.883142 TTCTGTTAAAAACCAAATCATTTCTGT 57.117 25.926 0.00 0.00 0.00 3.41
4156 4286 8.206867 TCATTTCTGTAATTCCAGATAGTCCAG 58.793 37.037 1.11 0.00 40.96 3.86
4241 4371 3.945921 TGTCCCAAATAACGTGTTGACAA 59.054 39.130 8.11 0.00 0.00 3.18
4246 4376 7.010645 GTCCCAAATAACGTGTTGACAAAATTT 59.989 33.333 8.11 0.00 0.00 1.82
4321 4451 2.035832 CGGGCAATCAAGAAAAAGGTGT 59.964 45.455 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.515514 AGGACCAGGAGTGAAATAATCTCATAT 59.484 37.037 0.00 0.00 0.00 1.78
2 3 5.669447 AGGACCAGGAGTGAAATAATCTCAT 59.331 40.000 0.00 0.00 0.00 2.90
4 5 5.622346 AGGACCAGGAGTGAAATAATCTC 57.378 43.478 0.00 0.00 0.00 2.75
5 6 6.098982 CACTAGGACCAGGAGTGAAATAATCT 59.901 42.308 13.35 0.00 42.65 2.40
6 7 6.284459 CACTAGGACCAGGAGTGAAATAATC 58.716 44.000 13.35 0.00 42.65 1.75
7 8 5.396884 GCACTAGGACCAGGAGTGAAATAAT 60.397 44.000 19.87 0.00 42.65 1.28
8 9 4.081087 GCACTAGGACCAGGAGTGAAATAA 60.081 45.833 19.87 0.00 42.65 1.40
9 10 3.451178 GCACTAGGACCAGGAGTGAAATA 59.549 47.826 19.87 0.00 42.65 1.40
10 11 2.237392 GCACTAGGACCAGGAGTGAAAT 59.763 50.000 19.87 0.00 42.65 2.17
11 12 1.623811 GCACTAGGACCAGGAGTGAAA 59.376 52.381 19.87 0.00 42.65 2.69
12 13 1.267121 GCACTAGGACCAGGAGTGAA 58.733 55.000 19.87 0.00 42.65 3.18
13 14 0.114364 TGCACTAGGACCAGGAGTGA 59.886 55.000 19.87 7.10 42.65 3.41
14 15 0.534412 CTGCACTAGGACCAGGAGTG 59.466 60.000 14.00 14.00 42.86 3.51
15 16 1.261238 GCTGCACTAGGACCAGGAGT 61.261 60.000 0.00 0.00 0.00 3.85
16 17 1.260538 TGCTGCACTAGGACCAGGAG 61.261 60.000 0.00 0.00 0.00 3.69
17 18 1.229177 TGCTGCACTAGGACCAGGA 60.229 57.895 0.00 0.00 0.00 3.86
18 19 1.078848 GTGCTGCACTAGGACCAGG 60.079 63.158 24.68 0.00 41.47 4.45
19 20 0.671781 GTGTGCTGCACTAGGACCAG 60.672 60.000 30.43 0.00 46.21 4.00
20 21 1.371183 GTGTGCTGCACTAGGACCA 59.629 57.895 30.43 8.47 46.21 4.02
21 22 0.250295 TTGTGTGCTGCACTAGGACC 60.250 55.000 30.43 13.31 46.21 4.46
29 30 1.101331 TCAACATGTTGTGTGCTGCA 58.899 45.000 31.99 12.47 41.14 4.41
30 31 2.206815 TTCAACATGTTGTGTGCTGC 57.793 45.000 31.99 0.00 41.14 5.25
31 32 4.857799 TGTATTCAACATGTTGTGTGCTG 58.142 39.130 31.99 11.33 41.14 4.41
32 33 4.580167 ACTGTATTCAACATGTTGTGTGCT 59.420 37.500 31.99 17.87 41.14 4.40
33 34 4.858935 ACTGTATTCAACATGTTGTGTGC 58.141 39.130 31.99 24.59 41.14 4.57
34 35 8.075574 ACAATACTGTATTCAACATGTTGTGTG 58.924 33.333 31.99 20.38 35.94 3.82
35 36 8.165239 ACAATACTGTATTCAACATGTTGTGT 57.835 30.769 31.99 22.71 36.91 3.72
36 37 9.462174 AAACAATACTGTATTCAACATGTTGTG 57.538 29.630 31.99 22.16 37.54 3.33
58 59 9.997482 GTATGAACTAGTGAAAACTGAAAAACA 57.003 29.630 0.00 0.00 0.00 2.83
59 60 9.997482 TGTATGAACTAGTGAAAACTGAAAAAC 57.003 29.630 0.00 0.00 0.00 2.43
61 62 8.342634 GCTGTATGAACTAGTGAAAACTGAAAA 58.657 33.333 0.00 0.00 0.00 2.29
62 63 7.715249 AGCTGTATGAACTAGTGAAAACTGAAA 59.285 33.333 0.00 0.00 0.00 2.69
63 64 7.217200 AGCTGTATGAACTAGTGAAAACTGAA 58.783 34.615 0.00 0.00 0.00 3.02
64 65 6.759272 AGCTGTATGAACTAGTGAAAACTGA 58.241 36.000 0.00 0.00 0.00 3.41
65 66 7.815068 ACTAGCTGTATGAACTAGTGAAAACTG 59.185 37.037 0.00 0.00 43.74 3.16
66 67 7.897864 ACTAGCTGTATGAACTAGTGAAAACT 58.102 34.615 0.00 0.00 43.74 2.66
67 68 9.291664 CTACTAGCTGTATGAACTAGTGAAAAC 57.708 37.037 11.21 0.00 44.74 2.43
68 69 8.467598 CCTACTAGCTGTATGAACTAGTGAAAA 58.532 37.037 11.21 0.00 44.74 2.29
69 70 7.832685 TCCTACTAGCTGTATGAACTAGTGAAA 59.167 37.037 11.21 0.00 44.74 2.69
70 71 7.344134 TCCTACTAGCTGTATGAACTAGTGAA 58.656 38.462 11.21 0.00 44.74 3.18
71 72 6.896883 TCCTACTAGCTGTATGAACTAGTGA 58.103 40.000 11.21 0.18 44.74 3.41
72 73 7.229707 ACATCCTACTAGCTGTATGAACTAGTG 59.770 40.741 11.21 3.20 44.74 2.74
73 74 7.291566 ACATCCTACTAGCTGTATGAACTAGT 58.708 38.462 0.00 7.07 46.30 2.57
74 75 7.753309 ACATCCTACTAGCTGTATGAACTAG 57.247 40.000 0.00 0.00 39.44 2.57
75 76 8.534954 AAACATCCTACTAGCTGTATGAACTA 57.465 34.615 0.00 0.00 31.39 2.24
76 77 7.425224 AAACATCCTACTAGCTGTATGAACT 57.575 36.000 0.00 0.00 31.39 3.01
77 78 9.765795 ATTAAACATCCTACTAGCTGTATGAAC 57.234 33.333 0.00 0.00 31.39 3.18
83 84 8.769359 AGGTAAATTAAACATCCTACTAGCTGT 58.231 33.333 0.00 0.00 0.00 4.40
84 85 9.046296 CAGGTAAATTAAACATCCTACTAGCTG 57.954 37.037 0.00 0.00 0.00 4.24
85 86 8.211629 CCAGGTAAATTAAACATCCTACTAGCT 58.788 37.037 0.00 0.00 0.00 3.32
86 87 7.991460 ACCAGGTAAATTAAACATCCTACTAGC 59.009 37.037 0.00 0.00 0.00 3.42
87 88 9.901172 AACCAGGTAAATTAAACATCCTACTAG 57.099 33.333 0.00 0.00 0.00 2.57
88 89 9.895138 GAACCAGGTAAATTAAACATCCTACTA 57.105 33.333 0.00 0.00 0.00 1.82
89 90 7.832685 GGAACCAGGTAAATTAAACATCCTACT 59.167 37.037 0.00 0.00 0.00 2.57
90 91 7.832685 AGGAACCAGGTAAATTAAACATCCTAC 59.167 37.037 0.00 0.00 30.97 3.18
91 92 7.832187 CAGGAACCAGGTAAATTAAACATCCTA 59.168 37.037 0.00 0.00 31.52 2.94
92 93 6.663523 CAGGAACCAGGTAAATTAAACATCCT 59.336 38.462 0.00 0.00 32.85 3.24
93 94 6.661805 TCAGGAACCAGGTAAATTAAACATCC 59.338 38.462 0.00 0.00 0.00 3.51
94 95 7.393515 AGTCAGGAACCAGGTAAATTAAACATC 59.606 37.037 0.00 0.00 0.00 3.06
95 96 7.238710 AGTCAGGAACCAGGTAAATTAAACAT 58.761 34.615 0.00 0.00 0.00 2.71
96 97 6.607019 AGTCAGGAACCAGGTAAATTAAACA 58.393 36.000 0.00 0.00 0.00 2.83
97 98 7.229907 TGAAGTCAGGAACCAGGTAAATTAAAC 59.770 37.037 0.00 0.00 0.00 2.01
98 99 7.291566 TGAAGTCAGGAACCAGGTAAATTAAA 58.708 34.615 0.00 0.00 0.00 1.52
99 100 6.843752 TGAAGTCAGGAACCAGGTAAATTAA 58.156 36.000 0.00 0.00 0.00 1.40
100 101 6.442541 TGAAGTCAGGAACCAGGTAAATTA 57.557 37.500 0.00 0.00 0.00 1.40
101 102 5.316987 CTGAAGTCAGGAACCAGGTAAATT 58.683 41.667 0.00 0.00 40.20 1.82
102 103 4.911390 CTGAAGTCAGGAACCAGGTAAAT 58.089 43.478 0.00 0.00 40.20 1.40
103 104 4.351874 CTGAAGTCAGGAACCAGGTAAA 57.648 45.455 0.00 0.00 40.20 2.01
115 116 1.879796 GCCACCTGAACCTGAAGTCAG 60.880 57.143 1.05 1.05 43.40 3.51
116 117 0.108585 GCCACCTGAACCTGAAGTCA 59.891 55.000 0.00 0.00 0.00 3.41
117 118 0.108585 TGCCACCTGAACCTGAAGTC 59.891 55.000 0.00 0.00 0.00 3.01
118 119 0.109342 CTGCCACCTGAACCTGAAGT 59.891 55.000 0.00 0.00 0.00 3.01
119 120 0.607489 CCTGCCACCTGAACCTGAAG 60.607 60.000 0.00 0.00 0.00 3.02
120 121 1.455849 CCTGCCACCTGAACCTGAA 59.544 57.895 0.00 0.00 0.00 3.02
121 122 2.528818 CCCTGCCACCTGAACCTGA 61.529 63.158 0.00 0.00 0.00 3.86
122 123 2.034687 CCCTGCCACCTGAACCTG 59.965 66.667 0.00 0.00 0.00 4.00
123 124 1.360393 TTTCCCTGCCACCTGAACCT 61.360 55.000 0.00 0.00 0.00 3.50
124 125 0.251787 ATTTCCCTGCCACCTGAACC 60.252 55.000 0.00 0.00 0.00 3.62
125 126 1.177401 GATTTCCCTGCCACCTGAAC 58.823 55.000 0.00 0.00 0.00 3.18
126 127 0.776810 TGATTTCCCTGCCACCTGAA 59.223 50.000 0.00 0.00 0.00 3.02
127 128 0.776810 TTGATTTCCCTGCCACCTGA 59.223 50.000 0.00 0.00 0.00 3.86
128 129 1.856629 ATTGATTTCCCTGCCACCTG 58.143 50.000 0.00 0.00 0.00 4.00
129 130 2.629017 AATTGATTTCCCTGCCACCT 57.371 45.000 0.00 0.00 0.00 4.00
130 131 2.833943 AGAAATTGATTTCCCTGCCACC 59.166 45.455 11.72 0.00 45.52 4.61
131 132 4.541973 AAGAAATTGATTTCCCTGCCAC 57.458 40.909 11.72 0.00 45.52 5.01
132 133 4.321899 CGAAAGAAATTGATTTCCCTGCCA 60.322 41.667 11.72 0.00 45.52 4.92
133 134 4.176271 CGAAAGAAATTGATTTCCCTGCC 58.824 43.478 11.72 0.00 45.52 4.85
134 135 4.082245 TCCGAAAGAAATTGATTTCCCTGC 60.082 41.667 11.72 0.16 45.52 4.85
135 136 5.402398 GTCCGAAAGAAATTGATTTCCCTG 58.598 41.667 11.72 2.19 45.52 4.45
136 137 4.156008 CGTCCGAAAGAAATTGATTTCCCT 59.844 41.667 11.72 1.36 45.52 4.20
137 138 4.082949 ACGTCCGAAAGAAATTGATTTCCC 60.083 41.667 11.72 3.12 45.52 3.97
138 139 5.043189 ACGTCCGAAAGAAATTGATTTCC 57.957 39.130 11.72 0.00 45.52 3.13
139 140 4.781528 CGACGTCCGAAAGAAATTGATTTC 59.218 41.667 10.58 8.11 42.48 2.17
140 141 4.378046 CCGACGTCCGAAAGAAATTGATTT 60.378 41.667 10.58 0.00 41.76 2.17
141 142 3.124636 CCGACGTCCGAAAGAAATTGATT 59.875 43.478 10.58 0.00 41.76 2.57
142 143 2.671396 CCGACGTCCGAAAGAAATTGAT 59.329 45.455 10.58 0.00 41.76 2.57
143 144 2.063266 CCGACGTCCGAAAGAAATTGA 58.937 47.619 10.58 0.00 41.76 2.57
144 145 1.796459 ACCGACGTCCGAAAGAAATTG 59.204 47.619 10.58 0.00 41.76 2.32
145 146 2.064014 GACCGACGTCCGAAAGAAATT 58.936 47.619 10.58 0.00 41.76 1.82
146 147 1.706443 GACCGACGTCCGAAAGAAAT 58.294 50.000 10.58 0.00 41.76 2.17
147 148 0.661187 CGACCGACGTCCGAAAGAAA 60.661 55.000 10.58 0.00 41.76 2.52
148 149 1.081906 CGACCGACGTCCGAAAGAA 60.082 57.895 10.58 0.00 41.76 2.52
149 150 1.904852 CTCGACCGACGTCCGAAAGA 61.905 60.000 10.58 2.79 43.13 2.52
150 151 1.511464 CTCGACCGACGTCCGAAAG 60.511 63.158 10.58 0.00 43.13 2.62
151 152 2.253758 ACTCGACCGACGTCCGAAA 61.254 57.895 10.58 0.00 43.13 3.46
152 153 2.666190 ACTCGACCGACGTCCGAA 60.666 61.111 10.58 0.00 43.13 4.30
153 154 3.417224 CACTCGACCGACGTCCGA 61.417 66.667 10.58 12.30 43.13 4.55
154 155 4.456253 CCACTCGACCGACGTCCG 62.456 72.222 10.58 8.21 43.13 4.79
155 156 1.930908 AATCCACTCGACCGACGTCC 61.931 60.000 10.58 0.00 43.13 4.79
156 157 0.522915 GAATCCACTCGACCGACGTC 60.523 60.000 5.18 5.18 43.13 4.34
157 158 0.959372 AGAATCCACTCGACCGACGT 60.959 55.000 0.00 0.00 43.13 4.34
158 159 0.523546 CAGAATCCACTCGACCGACG 60.524 60.000 0.00 0.00 44.09 5.12
159 160 0.526662 ACAGAATCCACTCGACCGAC 59.473 55.000 0.00 0.00 0.00 4.79
160 161 1.741706 GTACAGAATCCACTCGACCGA 59.258 52.381 0.00 0.00 0.00 4.69
161 162 1.531264 CGTACAGAATCCACTCGACCG 60.531 57.143 0.00 0.00 0.00 4.79
162 163 1.471684 ACGTACAGAATCCACTCGACC 59.528 52.381 0.00 0.00 0.00 4.79
163 164 2.915738 ACGTACAGAATCCACTCGAC 57.084 50.000 0.00 0.00 0.00 4.20
164 165 3.603532 AGTACGTACAGAATCCACTCGA 58.396 45.455 26.55 0.00 0.00 4.04
165 166 4.142752 TGAAGTACGTACAGAATCCACTCG 60.143 45.833 26.55 0.00 0.00 4.18
166 167 5.306532 TGAAGTACGTACAGAATCCACTC 57.693 43.478 26.55 9.33 0.00 3.51
167 168 4.158025 CCTGAAGTACGTACAGAATCCACT 59.842 45.833 26.55 2.04 34.07 4.00
168 169 4.082354 ACCTGAAGTACGTACAGAATCCAC 60.082 45.833 26.55 9.27 34.07 4.02
169 170 4.084287 ACCTGAAGTACGTACAGAATCCA 58.916 43.478 26.55 13.08 34.07 3.41
224 225 6.630443 CAGAGAAACTTGACAAATTCTTGACG 59.370 38.462 14.01 0.00 36.33 4.35
225 226 7.697691 TCAGAGAAACTTGACAAATTCTTGAC 58.302 34.615 14.01 5.47 36.33 3.18
226 227 7.864108 TCAGAGAAACTTGACAAATTCTTGA 57.136 32.000 14.01 14.66 36.33 3.02
227 228 9.525409 AATTCAGAGAAACTTGACAAATTCTTG 57.475 29.630 14.01 13.34 38.61 3.02
233 234 9.507329 AGCTATAATTCAGAGAAACTTGACAAA 57.493 29.630 0.00 0.00 0.00 2.83
234 235 9.507329 AAGCTATAATTCAGAGAAACTTGACAA 57.493 29.630 0.00 0.00 0.00 3.18
259 260 1.500108 CAGCTTGCCAAAAATGCGAA 58.500 45.000 0.00 0.00 0.00 4.70
321 322 3.057174 AGGTGTGCTCGTTGTTTCAAAAA 60.057 39.130 0.00 0.00 0.00 1.94
322 323 2.490115 AGGTGTGCTCGTTGTTTCAAAA 59.510 40.909 0.00 0.00 0.00 2.44
323 324 2.088423 AGGTGTGCTCGTTGTTTCAAA 58.912 42.857 0.00 0.00 0.00 2.69
324 325 1.668751 GAGGTGTGCTCGTTGTTTCAA 59.331 47.619 0.00 0.00 0.00 2.69
325 326 1.295792 GAGGTGTGCTCGTTGTTTCA 58.704 50.000 0.00 0.00 0.00 2.69
326 327 0.232303 CGAGGTGTGCTCGTTGTTTC 59.768 55.000 0.00 0.00 39.25 2.78
327 328 2.307363 CGAGGTGTGCTCGTTGTTT 58.693 52.632 0.00 0.00 39.25 2.83
328 329 4.027755 CGAGGTGTGCTCGTTGTT 57.972 55.556 0.00 0.00 39.25 2.83
334 335 0.992802 GAAATCGACGAGGTGTGCTC 59.007 55.000 3.01 0.00 0.00 4.26
335 336 0.389948 GGAAATCGACGAGGTGTGCT 60.390 55.000 3.01 0.00 0.00 4.40
336 337 0.669318 TGGAAATCGACGAGGTGTGC 60.669 55.000 3.01 0.00 0.00 4.57
337 338 2.010145 ATGGAAATCGACGAGGTGTG 57.990 50.000 3.01 0.00 0.00 3.82
338 339 2.762535 AATGGAAATCGACGAGGTGT 57.237 45.000 3.01 0.00 0.00 4.16
339 340 4.430007 TCTAAATGGAAATCGACGAGGTG 58.570 43.478 3.01 0.00 0.00 4.00
423 424 5.451798 CCTGTGCCATGTTAGAACACTTTTT 60.452 40.000 0.00 0.00 42.51 1.94
427 428 2.783135 CCTGTGCCATGTTAGAACACT 58.217 47.619 0.00 0.00 42.51 3.55
436 437 1.550072 GGTTAATTGCCTGTGCCATGT 59.450 47.619 0.00 0.00 36.33 3.21
445 446 1.923356 CCCTGTGTGGTTAATTGCCT 58.077 50.000 0.00 0.00 0.00 4.75
564 566 8.705594 CCCTTGTTCCTCTTTTATCTAGTCATA 58.294 37.037 0.00 0.00 0.00 2.15
578 580 3.331889 ACATGTTCATCCCTTGTTCCTCT 59.668 43.478 0.00 0.00 0.00 3.69
581 583 3.420893 TCACATGTTCATCCCTTGTTCC 58.579 45.455 0.00 0.00 0.00 3.62
620 623 1.294041 TGTACCCAGGATTGCCATGA 58.706 50.000 0.00 0.00 36.29 3.07
624 627 2.863809 CCTAATGTACCCAGGATTGCC 58.136 52.381 0.00 0.00 0.00 4.52
669 672 1.211457 AGAAGGCGATGCAGGAGATTT 59.789 47.619 0.00 0.00 0.00 2.17
744 747 1.188863 ATCTCACAAATGGGGCAAGC 58.811 50.000 0.00 0.00 0.00 4.01
753 756 8.902540 TTAATCTATGCCGTTATCTCACAAAT 57.097 30.769 0.00 0.00 0.00 2.32
766 769 5.215160 GGCTGTCATTTTTAATCTATGCCG 58.785 41.667 0.00 0.00 0.00 5.69
781 784 0.182061 AATGATCCTGCGGCTGTCAT 59.818 50.000 0.00 4.45 0.00 3.06
876 879 4.530094 TGATATGAAATTGACGAACGGC 57.470 40.909 0.00 0.00 0.00 5.68
1146 1155 2.996249 TCAGAGTCATTCTCATGGCC 57.004 50.000 0.00 0.00 44.98 5.36
1380 1389 0.329261 TGAGAATCCTGGGTGCCTTG 59.671 55.000 0.00 0.00 0.00 3.61
1391 1400 4.010349 CCAACCAGTTACCTTGAGAATCC 58.990 47.826 0.00 0.00 0.00 3.01
1707 1719 1.134551 GTCAGGATCTCCTTGTGCTCC 60.135 57.143 0.00 0.00 46.09 4.70
1794 1806 0.767375 AGAGTGCAAAGGAGAGGCAA 59.233 50.000 0.00 0.00 39.57 4.52
2001 2055 1.678101 CGGATGAATGGGAAGCCTTTC 59.322 52.381 0.00 0.00 0.00 2.62
2010 2064 1.228063 CAGGAGCCGGATGAATGGG 60.228 63.158 5.05 0.00 0.00 4.00
2049 2103 2.605299 GCCATGCCTCCAATCCCT 59.395 61.111 0.00 0.00 0.00 4.20
2269 2323 1.679944 CCGCACAAGATCCTTGGTCAT 60.680 52.381 10.91 0.00 0.00 3.06
2279 2333 0.322975 ACAGAGCTTCCGCACAAGAT 59.677 50.000 0.00 0.00 39.10 2.40
2404 2458 4.562082 TGTACAAAGTACCTGGAACATCG 58.438 43.478 0.00 0.00 38.20 3.84
2534 2588 1.900585 GCGAAAACCGTCGGTTACCC 61.901 60.000 29.05 18.71 46.20 3.69
2537 2591 2.656807 GCGCGAAAACCGTCGGTTA 61.657 57.895 29.05 0.00 46.20 2.85
2541 2595 0.994737 AATTTGCGCGAAAACCGTCG 60.995 50.000 15.98 0.00 43.98 5.12
2570 2633 2.799126 ATCCTTCACGCCATTTACCA 57.201 45.000 0.00 0.00 0.00 3.25
2608 2671 2.498481 AGCATGTAGCAATGTGCCAAAT 59.502 40.909 0.00 0.00 46.52 2.32
2922 2988 0.036732 TCTTGAGCCGTCCAAGCATT 59.963 50.000 0.00 0.00 40.45 3.56
3079 3145 3.583383 GCTGAACGCTTCTGCCAT 58.417 55.556 14.25 0.00 45.46 4.40
3222 3309 1.237285 GCAACGCCCAGAGATGTGTT 61.237 55.000 0.00 0.00 35.71 3.32
3291 3378 2.526077 TCTTGCGTTAGTGCTGTATCG 58.474 47.619 0.00 0.00 35.36 2.92
3390 3477 3.278574 TGAAGCATATTTCGAACCCCAG 58.721 45.455 0.00 0.00 0.00 4.45
3494 3589 1.101331 CCAGCTTTGATCCCTCAAGC 58.899 55.000 7.58 7.58 42.19 4.01
3495 3590 2.641305 CTCCAGCTTTGATCCCTCAAG 58.359 52.381 0.00 0.00 42.19 3.02
3496 3591 1.283029 CCTCCAGCTTTGATCCCTCAA 59.717 52.381 0.00 0.00 39.62 3.02
3497 3592 0.914644 CCTCCAGCTTTGATCCCTCA 59.085 55.000 0.00 0.00 0.00 3.86
3498 3593 0.915364 ACCTCCAGCTTTGATCCCTC 59.085 55.000 0.00 0.00 0.00 4.30
3499 3594 1.005215 CAACCTCCAGCTTTGATCCCT 59.995 52.381 0.00 0.00 0.00 4.20
3500 3595 1.467920 CAACCTCCAGCTTTGATCCC 58.532 55.000 0.00 0.00 0.00 3.85
3501 3596 0.813821 GCAACCTCCAGCTTTGATCC 59.186 55.000 0.00 0.00 0.00 3.36
3584 3689 3.678548 GGAGTAGTCAACAAAACTAGGCG 59.321 47.826 0.00 0.00 30.11 5.52
3603 3708 5.971763 AGACAGCAAACTACATCTAAGGAG 58.028 41.667 0.00 0.00 0.00 3.69
3605 3710 5.352569 CCAAGACAGCAAACTACATCTAAGG 59.647 44.000 0.00 0.00 0.00 2.69
3606 3711 5.352569 CCCAAGACAGCAAACTACATCTAAG 59.647 44.000 0.00 0.00 0.00 2.18
3607 3712 5.221843 ACCCAAGACAGCAAACTACATCTAA 60.222 40.000 0.00 0.00 0.00 2.10
3609 3714 3.073062 ACCCAAGACAGCAAACTACATCT 59.927 43.478 0.00 0.00 0.00 2.90
3610 3715 3.412386 ACCCAAGACAGCAAACTACATC 58.588 45.455 0.00 0.00 0.00 3.06
3611 3716 3.508845 ACCCAAGACAGCAAACTACAT 57.491 42.857 0.00 0.00 0.00 2.29
3612 3717 3.290948 AACCCAAGACAGCAAACTACA 57.709 42.857 0.00 0.00 0.00 2.74
3613 3718 5.761165 TTTAACCCAAGACAGCAAACTAC 57.239 39.130 0.00 0.00 0.00 2.73
3656 3762 1.025113 CCTGCATCTCCAGTGCACAG 61.025 60.000 21.04 11.53 46.76 3.66
3674 3780 1.871676 GTTTGGGACTCTTCACGAACC 59.128 52.381 0.00 0.00 42.02 3.62
3737 3850 4.833390 GGAAGATCCCTCTTTTCGAAAGA 58.167 43.478 10.98 9.74 41.87 2.52
3769 3882 1.921243 CCGTATGCATCGTTCTGACA 58.079 50.000 0.19 0.00 0.00 3.58
3770 3883 0.577269 GCCGTATGCATCGTTCTGAC 59.423 55.000 0.19 0.00 40.77 3.51
3969 4085 0.035915 TCAACCGATTTGGATGGCGA 60.036 50.000 0.00 0.00 40.78 5.54
4032 4148 0.918799 TGGAGGCCAGGGAGCATTTA 60.919 55.000 5.01 0.00 0.00 1.40
4063 4193 3.501396 CGAGCCACGGCATTGATT 58.499 55.556 11.35 0.00 44.88 2.57
4139 4269 6.156949 ACTTTGCTCTGGACTATCTGGAATTA 59.843 38.462 0.00 0.00 0.00 1.40
4156 4286 2.813754 TGTTGGAGTATGCACTTTGCTC 59.186 45.455 0.00 0.00 45.31 4.26
4191 4321 4.591321 AATGGGATTGAGCCTGACTTAA 57.409 40.909 0.00 0.00 0.00 1.85
4270 4400 2.046314 CTTTGGCGGACGGTCCAT 60.046 61.111 25.80 0.00 35.91 3.41


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

AutoCloner maintained by Alex Coulton.