Multiple sequence alignment - TraesCS2D01G553900

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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 TraesCS2D01G553900 chr2D 100.000 1992 0 0 841 2832 628411715 628413706 0.000000e+00 3679.0
1 TraesCS2D01G553900 chr2D 100.000 404 0 0 1 404 628410875 628411278 0.000000e+00 747.0
2 TraesCS2D01G553900 chr3A 93.608 1893 91 15 954 2832 483816888 483818764 0.000000e+00 2798.0
3 TraesCS2D01G553900 chr3A 93.137 1020 62 4 883 1898 134613005 134614020 0.000000e+00 1489.0
4 TraesCS2D01G553900 chr3A 92.019 1040 72 7 864 1898 134617831 134618864 0.000000e+00 1450.0
5 TraesCS2D01G553900 chr3A 88.824 859 69 16 1985 2832 342765191 342766033 0.000000e+00 1029.0
6 TraesCS2D01G553900 chr3A 87.332 521 49 10 2092 2608 39704709 39704202 5.260000e-162 580.0
7 TraesCS2D01G553900 chr6A 91.127 2006 111 25 841 2832 462401351 462403303 0.000000e+00 2656.0
8 TraesCS2D01G553900 chr6A 92.125 1054 51 12 852 1898 204306447 204305419 0.000000e+00 1458.0
9 TraesCS2D01G553900 chr6A 94.111 951 49 3 951 1898 473515703 473516649 0.000000e+00 1439.0
10 TraesCS2D01G553900 chr6A 91.643 1053 57 9 852 1898 136163835 136162808 0.000000e+00 1428.0
11 TraesCS2D01G553900 chr6A 91.143 1050 63 15 853 1898 328876416 328877439 0.000000e+00 1397.0
12 TraesCS2D01G553900 chr6A 90.503 1053 69 12 852 1898 518075153 518074126 0.000000e+00 1362.0
13 TraesCS2D01G553900 chr6A 85.994 664 51 18 1984 2640 318018219 318017591 0.000000e+00 673.0
14 TraesCS2D01G553900 chr6A 92.167 383 29 1 3 384 612155590 612155972 8.930000e-150 540.0
15 TraesCS2D01G553900 chr6A 91.136 361 16 6 1984 2343 478541307 478541652 2.550000e-130 475.0
16 TraesCS2D01G553900 chr5A 92.300 1052 51 7 852 1898 268344792 268345818 0.000000e+00 1467.0
17 TraesCS2D01G553900 chr5A 94.609 946 44 3 956 1898 109668179 109669120 0.000000e+00 1458.0
18 TraesCS2D01G553900 chr5A 91.690 361 17 6 1984 2343 202894483 202894135 3.280000e-134 488.0
19 TraesCS2D01G553900 chr5A 78.125 160 23 12 2352 2505 211427496 211427343 1.080000e-14 91.6
20 TraesCS2D01G553900 chr1A 93.975 946 49 5 957 1898 465251966 465252907 0.000000e+00 1424.0
21 TraesCS2D01G553900 chr1A 89.251 521 45 8 2092 2608 283223618 283224131 2.380000e-180 641.0
22 TraesCS2D01G553900 chr2A 91.049 1039 55 15 864 1898 154894240 154893236 0.000000e+00 1369.0
23 TraesCS2D01G553900 chr2A 89.279 569 31 17 2274 2832 365954629 365955177 0.000000e+00 686.0
24 TraesCS2D01G553900 chr2A 92.521 361 14 6 1984 2343 38021957 38022305 3.260000e-139 505.0
25 TraesCS2D01G553900 chr5D 91.451 386 29 3 6 387 2847333 2846948 6.950000e-146 527.0
26 TraesCS2D01G553900 chr5D 90.698 387 33 3 1 384 367216432 367216818 1.950000e-141 512.0
27 TraesCS2D01G553900 chr5D 90.281 391 35 3 1 388 403864765 403865155 2.520000e-140 508.0
28 TraesCS2D01G553900 chr7D 91.003 389 32 3 1 387 635753784 635753397 3.230000e-144 521.0
29 TraesCS2D01G553900 chr7D 90.306 392 33 4 1 388 134692072 134691682 2.520000e-140 508.0
30 TraesCS2D01G553900 chrUn 90.979 388 30 5 1 384 95932326 95932712 4.180000e-143 518.0
31 TraesCS2D01G553900 chr1D 90.698 387 33 3 1 384 490193644 490194030 1.950000e-141 512.0
32 TraesCS2D01G553900 chr1D 90.306 392 35 3 1 389 49786747 49786356 7.000000e-141 510.0
33 TraesCS2D01G553900 chr4A 90.909 363 16 10 1984 2343 25139684 25139336 3.300000e-129 472.0
34 TraesCS2D01G553900 chr6D 78.322 143 21 10 2352 2489 91386094 91385957 1.810000e-12 84.2


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 TraesCS2D01G553900 chr2D 628410875 628413706 2831 False 2213.0 3679 100.000 1 2832 2 chr2D.!!$F1 2831
1 TraesCS2D01G553900 chr3A 483816888 483818764 1876 False 2798.0 2798 93.608 954 2832 1 chr3A.!!$F2 1878
2 TraesCS2D01G553900 chr3A 134613005 134618864 5859 False 1469.5 1489 92.578 864 1898 2 chr3A.!!$F3 1034
3 TraesCS2D01G553900 chr3A 342765191 342766033 842 False 1029.0 1029 88.824 1985 2832 1 chr3A.!!$F1 847
4 TraesCS2D01G553900 chr3A 39704202 39704709 507 True 580.0 580 87.332 2092 2608 1 chr3A.!!$R1 516
5 TraesCS2D01G553900 chr6A 462401351 462403303 1952 False 2656.0 2656 91.127 841 2832 1 chr6A.!!$F2 1991
6 TraesCS2D01G553900 chr6A 204305419 204306447 1028 True 1458.0 1458 92.125 852 1898 1 chr6A.!!$R2 1046
7 TraesCS2D01G553900 chr6A 473515703 473516649 946 False 1439.0 1439 94.111 951 1898 1 chr6A.!!$F3 947
8 TraesCS2D01G553900 chr6A 136162808 136163835 1027 True 1428.0 1428 91.643 852 1898 1 chr6A.!!$R1 1046
9 TraesCS2D01G553900 chr6A 328876416 328877439 1023 False 1397.0 1397 91.143 853 1898 1 chr6A.!!$F1 1045
10 TraesCS2D01G553900 chr6A 518074126 518075153 1027 True 1362.0 1362 90.503 852 1898 1 chr6A.!!$R4 1046
11 TraesCS2D01G553900 chr6A 318017591 318018219 628 True 673.0 673 85.994 1984 2640 1 chr6A.!!$R3 656
12 TraesCS2D01G553900 chr5A 268344792 268345818 1026 False 1467.0 1467 92.300 852 1898 1 chr5A.!!$F2 1046
13 TraesCS2D01G553900 chr5A 109668179 109669120 941 False 1458.0 1458 94.609 956 1898 1 chr5A.!!$F1 942
14 TraesCS2D01G553900 chr1A 465251966 465252907 941 False 1424.0 1424 93.975 957 1898 1 chr1A.!!$F2 941
15 TraesCS2D01G553900 chr1A 283223618 283224131 513 False 641.0 641 89.251 2092 2608 1 chr1A.!!$F1 516
16 TraesCS2D01G553900 chr2A 154893236 154894240 1004 True 1369.0 1369 91.049 864 1898 1 chr2A.!!$R1 1034
17 TraesCS2D01G553900 chr2A 365954629 365955177 548 False 686.0 686 89.279 2274 2832 1 chr2A.!!$F2 558

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
191 192 0.034089 AATGGTTGTGGGCTAGGAGC 60.034 55.0 0.0 0.0 41.46 4.70 F
256 257 0.035439 CCAGACAAACCGGCACCTAT 60.035 55.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1107 1114 1.138859 CATGAGGCCGAAGTACATGGA 59.861 52.381 0.0 0.0 35.96 3.41 R
2155 7011 1.626321 TCGGTGAAATGACCTAGGCAA 59.374 47.619 9.3 0.0 33.35 4.52 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
20 21 3.914984 GTGAGCTAGAGCACCACAA 57.085 52.632 16.95 0.00 45.16 3.33
21 22 2.169832 GTGAGCTAGAGCACCACAAA 57.830 50.000 16.95 0.00 45.16 2.83
22 23 2.072298 GTGAGCTAGAGCACCACAAAG 58.928 52.381 16.95 0.00 45.16 2.77
23 24 1.082690 GAGCTAGAGCACCACAAAGC 58.917 55.000 4.01 0.00 45.16 3.51
24 25 0.689623 AGCTAGAGCACCACAAAGCT 59.310 50.000 4.01 0.00 45.16 3.74
29 30 3.621953 AGCACCACAAAGCTCTCTC 57.378 52.632 0.00 0.00 36.00 3.20
30 31 0.761187 AGCACCACAAAGCTCTCTCA 59.239 50.000 0.00 0.00 36.00 3.27
31 32 1.350351 AGCACCACAAAGCTCTCTCAT 59.650 47.619 0.00 0.00 36.00 2.90
32 33 1.467734 GCACCACAAAGCTCTCTCATG 59.532 52.381 0.00 0.00 0.00 3.07
33 34 2.082231 CACCACAAAGCTCTCTCATGG 58.918 52.381 0.00 0.00 0.00 3.66
34 35 1.701847 ACCACAAAGCTCTCTCATGGT 59.298 47.619 0.00 0.00 34.13 3.55
35 36 2.107204 ACCACAAAGCTCTCTCATGGTT 59.893 45.455 0.00 0.00 35.43 3.67
36 37 2.486982 CCACAAAGCTCTCTCATGGTTG 59.513 50.000 0.00 0.00 0.00 3.77
37 38 2.486982 CACAAAGCTCTCTCATGGTTGG 59.513 50.000 0.00 0.00 0.00 3.77
38 39 1.471684 CAAAGCTCTCTCATGGTTGGC 59.528 52.381 0.00 0.00 0.00 4.52
39 40 0.034670 AAGCTCTCTCATGGTTGGCC 60.035 55.000 0.00 0.00 0.00 5.36
67 68 3.873449 GCACTCACTGCTCTGCTC 58.127 61.111 0.00 0.00 43.33 4.26
68 69 2.093473 GCACTCACTGCTCTGCTCG 61.093 63.158 0.00 0.00 43.33 5.03
69 70 2.093473 CACTCACTGCTCTGCTCGC 61.093 63.158 0.00 0.00 0.00 5.03
70 71 2.879933 CTCACTGCTCTGCTCGCG 60.880 66.667 0.00 0.00 0.00 5.87
71 72 4.426112 TCACTGCTCTGCTCGCGG 62.426 66.667 6.13 0.00 39.62 6.46
84 85 3.552384 CGCGGGCAAGGGGGTATA 61.552 66.667 0.00 0.00 0.00 1.47
85 86 2.890766 CGCGGGCAAGGGGGTATAT 61.891 63.158 0.00 0.00 0.00 0.86
86 87 1.546589 CGCGGGCAAGGGGGTATATA 61.547 60.000 0.00 0.00 0.00 0.86
87 88 0.916809 GCGGGCAAGGGGGTATATAT 59.083 55.000 0.00 0.00 0.00 0.86
88 89 2.121129 GCGGGCAAGGGGGTATATATA 58.879 52.381 0.00 0.00 0.00 0.86
89 90 2.104281 GCGGGCAAGGGGGTATATATAG 59.896 54.545 0.00 0.00 0.00 1.31
90 91 2.704065 CGGGCAAGGGGGTATATATAGG 59.296 54.545 0.00 0.00 0.00 2.57
91 92 2.442126 GGGCAAGGGGGTATATATAGGC 59.558 54.545 0.00 0.00 0.00 3.93
92 93 3.120108 GGCAAGGGGGTATATATAGGCA 58.880 50.000 0.00 0.00 0.00 4.75
93 94 3.722101 GGCAAGGGGGTATATATAGGCAT 59.278 47.826 0.00 0.00 0.00 4.40
94 95 4.202472 GGCAAGGGGGTATATATAGGCATC 60.202 50.000 0.00 0.00 0.00 3.91
95 96 4.660771 GCAAGGGGGTATATATAGGCATCT 59.339 45.833 0.00 0.00 0.00 2.90
96 97 5.221742 GCAAGGGGGTATATATAGGCATCTC 60.222 48.000 0.00 0.00 0.00 2.75
97 98 5.768454 AGGGGGTATATATAGGCATCTCA 57.232 43.478 0.00 0.00 0.00 3.27
98 99 6.314697 AGGGGGTATATATAGGCATCTCAT 57.685 41.667 0.00 0.00 0.00 2.90
99 100 6.707868 AGGGGGTATATATAGGCATCTCATT 58.292 40.000 0.00 0.00 0.00 2.57
100 101 6.560304 AGGGGGTATATATAGGCATCTCATTG 59.440 42.308 0.00 0.00 0.00 2.82
101 102 6.240002 GGGGGTATATATAGGCATCTCATTGG 60.240 46.154 0.00 0.00 0.00 3.16
102 103 6.330250 GGGGTATATATAGGCATCTCATTGGT 59.670 42.308 0.00 0.00 0.00 3.67
103 104 7.445945 GGGTATATATAGGCATCTCATTGGTC 58.554 42.308 0.00 0.00 0.00 4.02
104 105 7.445945 GGTATATATAGGCATCTCATTGGTCC 58.554 42.308 0.00 0.00 0.00 4.46
105 106 4.851639 ATATAGGCATCTCATTGGTCCC 57.148 45.455 0.00 0.00 0.00 4.46
106 107 0.758734 TAGGCATCTCATTGGTCCCG 59.241 55.000 0.00 0.00 0.00 5.14
107 108 1.526917 GGCATCTCATTGGTCCCGG 60.527 63.158 0.00 0.00 0.00 5.73
108 109 1.224592 GCATCTCATTGGTCCCGGT 59.775 57.895 0.00 0.00 0.00 5.28
109 110 0.394352 GCATCTCATTGGTCCCGGTT 60.394 55.000 0.00 0.00 0.00 4.44
110 111 1.668419 CATCTCATTGGTCCCGGTTC 58.332 55.000 0.00 0.00 0.00 3.62
111 112 0.178068 ATCTCATTGGTCCCGGTTCG 59.822 55.000 0.00 0.00 0.00 3.95
112 113 1.189524 TCTCATTGGTCCCGGTTCGT 61.190 55.000 0.00 0.00 0.00 3.85
113 114 1.004320 TCATTGGTCCCGGTTCGTG 60.004 57.895 0.00 0.00 0.00 4.35
114 115 2.038269 CATTGGTCCCGGTTCGTGG 61.038 63.158 0.00 0.00 0.00 4.94
115 116 3.912745 ATTGGTCCCGGTTCGTGGC 62.913 63.158 0.00 0.00 0.00 5.01
120 121 4.323477 CCCGGTTCGTGGCTGGAA 62.323 66.667 0.00 0.00 34.35 3.53
121 122 3.047877 CCGGTTCGTGGCTGGAAC 61.048 66.667 11.23 11.23 42.32 3.62
124 125 3.047877 GTTCGTGGCTGGAACCGG 61.048 66.667 0.00 0.00 38.23 5.28
125 126 4.323477 TTCGTGGCTGGAACCGGG 62.323 66.667 6.32 0.00 0.00 5.73
128 129 3.637273 GTGGCTGGAACCGGGACT 61.637 66.667 6.32 0.00 0.00 3.85
129 130 2.120940 TGGCTGGAACCGGGACTA 59.879 61.111 6.32 0.00 0.00 2.59
130 131 1.536907 TGGCTGGAACCGGGACTAA 60.537 57.895 6.32 0.00 0.00 2.24
131 132 1.128809 TGGCTGGAACCGGGACTAAA 61.129 55.000 6.32 0.00 0.00 1.85
132 133 0.392595 GGCTGGAACCGGGACTAAAG 60.393 60.000 6.32 0.00 0.00 1.85
133 134 0.392595 GCTGGAACCGGGACTAAAGG 60.393 60.000 6.32 0.00 0.00 3.11
134 135 1.272807 CTGGAACCGGGACTAAAGGA 58.727 55.000 6.32 0.00 0.00 3.36
135 136 1.207329 CTGGAACCGGGACTAAAGGAG 59.793 57.143 6.32 0.00 0.00 3.69
136 137 0.107800 GGAACCGGGACTAAAGGAGC 60.108 60.000 6.32 0.00 0.00 4.70
137 138 0.107800 GAACCGGGACTAAAGGAGCC 60.108 60.000 6.32 0.00 0.00 4.70
138 139 1.559965 AACCGGGACTAAAGGAGCCC 61.560 60.000 6.32 0.00 37.86 5.19
139 140 2.743179 CCGGGACTAAAGGAGCCCC 61.743 68.421 0.00 0.00 37.93 5.80
149 150 4.426313 GGAGCCCCTTTGGTCCCG 62.426 72.222 0.00 0.00 45.21 5.14
150 151 4.426313 GAGCCCCTTTGGTCCCGG 62.426 72.222 0.00 0.00 36.04 5.73
152 153 4.295199 GCCCCTTTGGTCCCGGTT 62.295 66.667 0.00 0.00 36.04 4.44
153 154 2.282887 CCCCTTTGGTCCCGGTTG 60.283 66.667 0.00 0.00 0.00 3.77
154 155 2.989253 CCCTTTGGTCCCGGTTGC 60.989 66.667 0.00 0.00 0.00 4.17
155 156 2.203422 CCTTTGGTCCCGGTTGCA 60.203 61.111 0.00 0.00 0.00 4.08
156 157 1.830408 CCTTTGGTCCCGGTTGCAA 60.830 57.895 0.00 0.00 0.00 4.08
157 158 1.362355 CTTTGGTCCCGGTTGCAAC 59.638 57.895 21.59 21.59 0.00 4.17
158 159 2.082629 CTTTGGTCCCGGTTGCAACC 62.083 60.000 34.48 34.48 45.76 3.77
167 168 4.411136 GTTGCAACCACAAACCGG 57.589 55.556 19.15 0.00 0.00 5.28
168 169 1.227118 GTTGCAACCACAAACCGGG 60.227 57.895 19.15 0.00 0.00 5.73
169 170 1.379977 TTGCAACCACAAACCGGGA 60.380 52.632 6.32 0.00 0.00 5.14
170 171 1.668101 TTGCAACCACAAACCGGGAC 61.668 55.000 6.32 0.00 0.00 4.46
171 172 2.852180 GCAACCACAAACCGGGACC 61.852 63.158 6.32 0.00 0.00 4.46
172 173 1.454111 CAACCACAAACCGGGACCA 60.454 57.895 6.32 0.00 0.00 4.02
173 174 1.038130 CAACCACAAACCGGGACCAA 61.038 55.000 6.32 0.00 0.00 3.67
174 175 0.105913 AACCACAAACCGGGACCAAT 60.106 50.000 6.32 0.00 0.00 3.16
175 176 0.825840 ACCACAAACCGGGACCAATG 60.826 55.000 6.32 0.00 0.00 2.82
176 177 1.531739 CCACAAACCGGGACCAATGG 61.532 60.000 6.32 0.00 0.00 3.16
177 178 0.825840 CACAAACCGGGACCAATGGT 60.826 55.000 3.74 3.74 39.44 3.55
179 180 0.316841 CAAACCGGGACCAATGGTTG 59.683 55.000 6.30 0.00 44.93 3.77
180 181 0.105913 AAACCGGGACCAATGGTTGT 60.106 50.000 6.30 0.00 44.93 3.32
181 182 0.825840 AACCGGGACCAATGGTTGTG 60.826 55.000 6.30 0.00 44.05 3.33
182 183 1.976474 CCGGGACCAATGGTTGTGG 60.976 63.158 6.30 4.83 42.28 4.17
183 184 1.976474 CGGGACCAATGGTTGTGGG 60.976 63.158 6.30 0.00 40.75 4.61
184 185 2.282783 GGGACCAATGGTTGTGGGC 61.283 63.158 6.30 0.00 44.26 5.36
185 186 1.228862 GGACCAATGGTTGTGGGCT 60.229 57.895 6.30 0.00 44.42 5.19
186 187 0.039035 GGACCAATGGTTGTGGGCTA 59.961 55.000 6.30 0.00 44.42 3.93
187 188 1.463674 GACCAATGGTTGTGGGCTAG 58.536 55.000 6.30 0.00 41.44 3.42
188 189 0.039618 ACCAATGGTTGTGGGCTAGG 59.960 55.000 0.00 0.00 40.75 3.02
189 190 0.331278 CCAATGGTTGTGGGCTAGGA 59.669 55.000 0.00 0.00 32.03 2.94
190 191 1.683011 CCAATGGTTGTGGGCTAGGAG 60.683 57.143 0.00 0.00 32.03 3.69
191 192 0.034089 AATGGTTGTGGGCTAGGAGC 60.034 55.000 0.00 0.00 41.46 4.70
192 193 2.125106 GGTTGTGGGCTAGGAGCG 60.125 66.667 0.00 0.00 43.62 5.03
193 194 2.656069 GGTTGTGGGCTAGGAGCGA 61.656 63.158 0.00 0.00 43.62 4.93
194 195 1.153549 GTTGTGGGCTAGGAGCGAG 60.154 63.158 0.00 0.00 43.62 5.03
195 196 2.359169 TTGTGGGCTAGGAGCGAGG 61.359 63.158 0.00 0.00 43.62 4.63
196 197 4.228567 GTGGGCTAGGAGCGAGGC 62.229 72.222 0.00 0.00 43.62 4.70
200 201 3.237741 GCTAGGAGCGAGGCCCAT 61.238 66.667 0.00 0.00 0.00 4.00
201 202 2.812619 GCTAGGAGCGAGGCCCATT 61.813 63.158 0.00 0.00 0.00 3.16
202 203 1.070445 CTAGGAGCGAGGCCCATTG 59.930 63.158 0.00 0.00 0.00 2.82
203 204 2.388890 CTAGGAGCGAGGCCCATTGG 62.389 65.000 0.00 0.00 0.00 3.16
204 205 4.115199 GGAGCGAGGCCCATTGGT 62.115 66.667 0.00 0.00 0.00 3.67
205 206 2.514824 GAGCGAGGCCCATTGGTC 60.515 66.667 0.00 0.00 36.05 4.02
206 207 4.115199 AGCGAGGCCCATTGGTCC 62.115 66.667 0.00 0.00 36.69 4.46
208 209 4.856801 CGAGGCCCATTGGTCCCG 62.857 72.222 0.00 0.00 36.69 5.14
209 210 4.506255 GAGGCCCATTGGTCCCGG 62.506 72.222 0.00 0.00 36.69 5.73
212 213 4.376170 GCCCATTGGTCCCGGGTT 62.376 66.667 22.86 0.00 42.44 4.11
213 214 2.362375 CCCATTGGTCCCGGGTTG 60.362 66.667 22.86 11.32 35.03 3.77
214 215 2.438795 CCATTGGTCCCGGGTTGT 59.561 61.111 22.86 0.09 0.00 3.32
215 216 1.976474 CCATTGGTCCCGGGTTGTG 60.976 63.158 22.86 13.08 0.00 3.33
216 217 1.228429 CATTGGTCCCGGGTTGTGT 60.228 57.895 22.86 2.13 0.00 3.72
217 218 0.825840 CATTGGTCCCGGGTTGTGTT 60.826 55.000 22.86 0.00 0.00 3.32
218 219 0.105913 ATTGGTCCCGGGTTGTGTTT 60.106 50.000 22.86 0.00 0.00 2.83
219 220 1.038130 TTGGTCCCGGGTTGTGTTTG 61.038 55.000 22.86 0.00 0.00 2.93
220 221 2.197605 GGTCCCGGGTTGTGTTTGG 61.198 63.158 22.86 0.00 0.00 3.28
221 222 1.152922 GTCCCGGGTTGTGTTTGGA 60.153 57.895 22.86 0.00 0.00 3.53
222 223 0.752376 GTCCCGGGTTGTGTTTGGAA 60.752 55.000 22.86 0.00 0.00 3.53
223 224 0.752376 TCCCGGGTTGTGTTTGGAAC 60.752 55.000 22.86 0.00 0.00 3.62
224 225 0.753848 CCCGGGTTGTGTTTGGAACT 60.754 55.000 14.18 0.00 0.00 3.01
225 226 0.383949 CCGGGTTGTGTTTGGAACTG 59.616 55.000 0.00 0.00 0.00 3.16
226 227 0.383949 CGGGTTGTGTTTGGAACTGG 59.616 55.000 0.00 0.00 0.00 4.00
227 228 0.750249 GGGTTGTGTTTGGAACTGGG 59.250 55.000 0.00 0.00 0.00 4.45
228 229 1.686741 GGGTTGTGTTTGGAACTGGGA 60.687 52.381 0.00 0.00 0.00 4.37
229 230 1.407618 GGTTGTGTTTGGAACTGGGAC 59.592 52.381 0.00 0.00 0.00 4.46
230 231 1.407618 GTTGTGTTTGGAACTGGGACC 59.592 52.381 0.00 0.00 0.00 4.46
231 232 0.626382 TGTGTTTGGAACTGGGACCA 59.374 50.000 0.00 0.00 0.00 4.02
232 233 1.006043 TGTGTTTGGAACTGGGACCAA 59.994 47.619 0.00 0.00 43.22 3.67
235 236 2.080654 TTTGGAACTGGGACCAAAGG 57.919 50.000 0.00 0.00 46.69 3.11
236 237 0.187361 TTGGAACTGGGACCAAAGGG 59.813 55.000 0.00 0.00 42.18 3.95
237 238 1.606601 GGAACTGGGACCAAAGGGC 60.607 63.158 0.00 0.00 37.90 5.19
244 245 4.920828 GACCAAAGGGCCAGACAA 57.079 55.556 6.18 0.00 37.90 3.18
245 246 3.125520 GACCAAAGGGCCAGACAAA 57.874 52.632 6.18 0.00 37.90 2.83
246 247 0.673985 GACCAAAGGGCCAGACAAAC 59.326 55.000 6.18 0.00 37.90 2.93
247 248 0.759060 ACCAAAGGGCCAGACAAACC 60.759 55.000 6.18 0.00 37.90 3.27
248 249 1.659794 CAAAGGGCCAGACAAACCG 59.340 57.895 6.18 0.00 0.00 4.44
249 250 1.530655 AAAGGGCCAGACAAACCGG 60.531 57.895 6.18 0.00 0.00 5.28
250 251 4.660938 AGGGCCAGACAAACCGGC 62.661 66.667 6.18 0.00 45.47 6.13
253 254 3.670377 GCCAGACAAACCGGCACC 61.670 66.667 0.00 0.00 45.52 5.01
254 255 2.113139 CCAGACAAACCGGCACCT 59.887 61.111 0.00 0.00 0.00 4.00
255 256 1.373435 CCAGACAAACCGGCACCTA 59.627 57.895 0.00 0.00 0.00 3.08
256 257 0.035439 CCAGACAAACCGGCACCTAT 60.035 55.000 0.00 0.00 0.00 2.57
257 258 1.086696 CAGACAAACCGGCACCTATG 58.913 55.000 0.00 0.00 0.00 2.23
258 259 0.035439 AGACAAACCGGCACCTATGG 60.035 55.000 0.00 0.00 0.00 2.74
265 266 3.792736 GGCACCTATGGCCCACGA 61.793 66.667 0.00 0.00 45.87 4.35
266 267 2.203070 GCACCTATGGCCCACGAG 60.203 66.667 0.00 0.00 0.00 4.18
267 268 2.505982 CACCTATGGCCCACGAGG 59.494 66.667 11.26 11.26 39.47 4.63
294 295 4.410400 CCCCCTGGCCTCACGAAC 62.410 72.222 3.32 0.00 0.00 3.95
295 296 4.410400 CCCCTGGCCTCACGAACC 62.410 72.222 3.32 0.00 0.00 3.62
296 297 4.760047 CCCTGGCCTCACGAACCG 62.760 72.222 3.32 0.00 0.00 4.44
297 298 4.760047 CCTGGCCTCACGAACCGG 62.760 72.222 3.32 0.00 0.00 5.28
298 299 4.760047 CTGGCCTCACGAACCGGG 62.760 72.222 6.32 0.00 0.00 5.73
300 301 4.754667 GGCCTCACGAACCGGGAC 62.755 72.222 6.32 0.00 32.99 4.46
301 302 4.754667 GCCTCACGAACCGGGACC 62.755 72.222 6.32 0.00 32.99 4.46
302 303 4.430765 CCTCACGAACCGGGACCG 62.431 72.222 6.32 8.74 32.99 4.79
303 304 3.367743 CTCACGAACCGGGACCGA 61.368 66.667 13.13 1.61 42.83 4.69
304 305 2.677524 TCACGAACCGGGACCGAT 60.678 61.111 13.13 0.03 42.83 4.18
305 306 2.508439 CACGAACCGGGACCGATG 60.508 66.667 13.13 0.00 42.83 3.84
306 307 4.446413 ACGAACCGGGACCGATGC 62.446 66.667 13.13 0.00 42.83 3.91
308 309 4.851179 GAACCGGGACCGATGCCC 62.851 72.222 13.13 0.00 42.83 5.36
313 314 4.586235 GGGACCGATGCCCCCATG 62.586 72.222 0.00 0.00 39.81 3.66
314 315 4.586235 GGACCGATGCCCCCATGG 62.586 72.222 4.14 4.14 37.09 3.66
324 325 4.123545 CCCCATGGGTCCCGGTTC 62.124 72.222 29.33 0.00 38.25 3.62
325 326 4.483243 CCCATGGGTCCCGGTTCG 62.483 72.222 23.93 0.00 0.00 3.95
326 327 3.712907 CCATGGGTCCCGGTTCGT 61.713 66.667 2.85 0.00 0.00 3.85
327 328 2.360767 CCATGGGTCCCGGTTCGTA 61.361 63.158 2.85 0.00 0.00 3.43
328 329 1.597989 CATGGGTCCCGGTTCGTAA 59.402 57.895 2.65 0.00 0.00 3.18
329 330 0.461339 CATGGGTCCCGGTTCGTAAG 60.461 60.000 2.65 0.00 0.00 2.34
330 331 0.906282 ATGGGTCCCGGTTCGTAAGT 60.906 55.000 2.65 0.00 39.48 2.24
331 332 1.079612 GGGTCCCGGTTCGTAAGTG 60.080 63.158 0.00 0.00 39.48 3.16
332 333 1.535204 GGGTCCCGGTTCGTAAGTGA 61.535 60.000 0.00 0.00 39.48 3.41
333 334 0.318120 GGTCCCGGTTCGTAAGTGAA 59.682 55.000 0.00 0.00 39.48 3.18
334 335 1.422388 GTCCCGGTTCGTAAGTGAAC 58.578 55.000 0.00 0.00 45.91 3.18
339 340 3.892200 GTTCGTAAGTGAACCGGGA 57.108 52.632 6.32 0.00 41.88 5.14
340 341 2.375173 GTTCGTAAGTGAACCGGGAT 57.625 50.000 6.32 0.00 41.88 3.85
341 342 2.691927 GTTCGTAAGTGAACCGGGATT 58.308 47.619 6.32 0.00 41.88 3.01
342 343 3.848726 GTTCGTAAGTGAACCGGGATTA 58.151 45.455 6.32 0.00 41.88 1.75
343 344 4.244862 GTTCGTAAGTGAACCGGGATTAA 58.755 43.478 6.32 0.00 41.88 1.40
344 345 4.741321 TCGTAAGTGAACCGGGATTAAT 57.259 40.909 6.32 0.00 39.48 1.40
345 346 4.435425 TCGTAAGTGAACCGGGATTAATG 58.565 43.478 6.32 0.00 39.48 1.90
346 347 3.558418 CGTAAGTGAACCGGGATTAATGG 59.442 47.826 6.32 0.00 0.00 3.16
347 348 2.729028 AGTGAACCGGGATTAATGGG 57.271 50.000 6.32 0.00 0.00 4.00
348 349 1.029681 GTGAACCGGGATTAATGGGC 58.970 55.000 6.32 0.00 0.00 5.36
349 350 0.923358 TGAACCGGGATTAATGGGCT 59.077 50.000 6.32 0.00 0.00 5.19
350 351 1.286553 TGAACCGGGATTAATGGGCTT 59.713 47.619 6.32 0.00 0.00 4.35
351 352 2.510382 TGAACCGGGATTAATGGGCTTA 59.490 45.455 6.32 0.00 0.00 3.09
352 353 2.651382 ACCGGGATTAATGGGCTTAC 57.349 50.000 6.32 0.00 0.00 2.34
353 354 1.144298 ACCGGGATTAATGGGCTTACC 59.856 52.381 6.32 0.00 40.81 2.85
363 364 4.484872 GGCTTACCCGGCCTGGAC 62.485 72.222 21.63 6.01 45.57 4.02
364 365 4.484872 GCTTACCCGGCCTGGACC 62.485 72.222 21.63 0.96 42.00 4.46
365 366 3.006728 CTTACCCGGCCTGGACCA 61.007 66.667 21.63 1.34 42.00 4.02
366 367 2.529643 TTACCCGGCCTGGACCAA 60.530 61.111 21.63 7.80 42.00 3.67
367 368 2.132089 CTTACCCGGCCTGGACCAAA 62.132 60.000 21.63 7.43 42.00 3.28
368 369 2.132089 TTACCCGGCCTGGACCAAAG 62.132 60.000 21.63 2.26 42.00 2.77
371 372 4.351054 CGGCCTGGACCAAAGCCT 62.351 66.667 25.43 0.00 43.48 4.58
372 373 2.118294 GGCCTGGACCAAAGCCTT 59.882 61.111 22.59 0.00 42.34 4.35
373 374 2.278330 GGCCTGGACCAAAGCCTTG 61.278 63.158 22.59 0.00 42.34 3.61
374 375 1.531602 GCCTGGACCAAAGCCTTGT 60.532 57.895 0.00 0.00 0.00 3.16
375 376 1.115326 GCCTGGACCAAAGCCTTGTT 61.115 55.000 0.00 0.00 0.00 2.83
376 377 1.413118 CCTGGACCAAAGCCTTGTTT 58.587 50.000 0.00 0.00 0.00 2.83
377 378 1.762370 CCTGGACCAAAGCCTTGTTTT 59.238 47.619 0.00 0.00 0.00 2.43
378 379 2.224042 CCTGGACCAAAGCCTTGTTTTC 60.224 50.000 0.00 0.00 0.00 2.29
379 380 2.695147 CTGGACCAAAGCCTTGTTTTCT 59.305 45.455 0.00 0.00 0.00 2.52
380 381 3.888930 CTGGACCAAAGCCTTGTTTTCTA 59.111 43.478 0.00 0.00 0.00 2.10
381 382 3.634910 TGGACCAAAGCCTTGTTTTCTAC 59.365 43.478 0.00 0.00 0.00 2.59
382 383 3.889538 GGACCAAAGCCTTGTTTTCTACT 59.110 43.478 0.00 0.00 0.00 2.57
383 384 5.067954 GGACCAAAGCCTTGTTTTCTACTA 58.932 41.667 0.00 0.00 0.00 1.82
384 385 5.048921 GGACCAAAGCCTTGTTTTCTACTAC 60.049 44.000 0.00 0.00 0.00 2.73
385 386 5.691896 ACCAAAGCCTTGTTTTCTACTACT 58.308 37.500 0.00 0.00 0.00 2.57
386 387 5.531287 ACCAAAGCCTTGTTTTCTACTACTG 59.469 40.000 0.00 0.00 0.00 2.74
387 388 5.452777 CAAAGCCTTGTTTTCTACTACTGC 58.547 41.667 0.00 0.00 0.00 4.40
388 389 3.676093 AGCCTTGTTTTCTACTACTGCC 58.324 45.455 0.00 0.00 0.00 4.85
389 390 2.747989 GCCTTGTTTTCTACTACTGCCC 59.252 50.000 0.00 0.00 0.00 5.36
390 391 3.000727 CCTTGTTTTCTACTACTGCCCG 58.999 50.000 0.00 0.00 0.00 6.13
391 392 3.556423 CCTTGTTTTCTACTACTGCCCGT 60.556 47.826 0.00 0.00 0.00 5.28
392 393 3.034721 TGTTTTCTACTACTGCCCGTG 57.965 47.619 0.00 0.00 0.00 4.94
393 394 2.629137 TGTTTTCTACTACTGCCCGTGA 59.371 45.455 0.00 0.00 0.00 4.35
394 395 2.991866 GTTTTCTACTACTGCCCGTGAC 59.008 50.000 0.00 0.00 0.00 3.67
395 396 1.913778 TTCTACTACTGCCCGTGACA 58.086 50.000 0.00 0.00 0.00 3.58
396 397 1.171308 TCTACTACTGCCCGTGACAC 58.829 55.000 0.00 0.00 0.00 3.67
397 398 0.172803 CTACTACTGCCCGTGACACC 59.827 60.000 0.00 0.00 0.00 4.16
398 399 1.252904 TACTACTGCCCGTGACACCC 61.253 60.000 0.00 0.00 0.00 4.61
399 400 3.310860 CTACTGCCCGTGACACCCC 62.311 68.421 0.00 0.00 0.00 4.95
944 946 4.760047 AGTGCGGCGTGCCCTTAG 62.760 66.667 9.37 0.00 45.60 2.18
1039 1043 0.035439 GTGCAGCCTGCCCTTTACTA 60.035 55.000 15.29 0.00 44.23 1.82
1358 1365 1.153329 AGCAACCCGTTCGTGAACA 60.153 52.632 12.76 0.00 41.20 3.18
1360 1367 0.385473 GCAACCCGTTCGTGAACATG 60.385 55.000 12.76 5.47 41.20 3.21
1361 1368 1.222300 CAACCCGTTCGTGAACATGA 58.778 50.000 12.76 0.00 41.20 3.07
1362 1369 1.600013 CAACCCGTTCGTGAACATGAA 59.400 47.619 12.76 5.50 41.20 2.57
1668 1678 0.824109 TTAGCATACTGAGCAGGCGT 59.176 50.000 2.20 0.00 0.00 5.68
1671 1681 1.709147 GCATACTGAGCAGGCGTTGG 61.709 60.000 2.20 0.00 0.00 3.77
1799 6653 8.962884 AGAAAACCATGCTGTTTCTTATTTTT 57.037 26.923 9.47 0.00 37.46 1.94
1972 6826 4.143333 AACCTCCCGACGCCGATG 62.143 66.667 0.00 0.00 38.22 3.84
2030 6884 4.081586 TGTTGTGCATACTACGGATTGGTA 60.082 41.667 0.00 0.00 35.67 3.25
2041 6895 5.887598 ACTACGGATTGGTATACTGTGTACA 59.112 40.000 15.20 0.00 0.00 2.90
2133 6988 9.529823 TGAAGTTCGGAGGTATAACATATAGAT 57.470 33.333 0.00 0.00 0.00 1.98
2209 7066 3.740832 TGCATAGAAAGTGTCACACGAAG 59.259 43.478 1.22 0.00 39.64 3.79
2580 7451 3.219281 TGGTACAAAGCCAGAAAAGTCC 58.781 45.455 0.00 0.00 31.92 3.85
2637 7509 5.066593 GGAAAAATGGGGTTGCATTGTTTA 58.933 37.500 0.00 0.00 0.00 2.01
2791 7669 0.107643 TGTGCCTCCAATGACGACAA 59.892 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.609061 GCTTTGTGGTGCTCTAGCTCA 60.609 52.381 3.26 0.00 42.66 4.26
4 5 1.082690 GCTTTGTGGTGCTCTAGCTC 58.917 55.000 3.26 0.00 42.66 4.09
5 6 0.689623 AGCTTTGTGGTGCTCTAGCT 59.310 50.000 3.26 0.00 42.66 3.32
6 7 3.239861 AGCTTTGTGGTGCTCTAGC 57.760 52.632 0.00 0.00 42.50 3.42
11 12 0.761187 TGAGAGAGCTTTGTGGTGCT 59.239 50.000 0.00 0.00 42.82 4.40
14 15 1.701847 ACCATGAGAGAGCTTTGTGGT 59.298 47.619 0.00 0.00 32.24 4.16
15 16 2.486472 ACCATGAGAGAGCTTTGTGG 57.514 50.000 0.00 0.00 0.00 4.17
17 18 2.787994 CCAACCATGAGAGAGCTTTGT 58.212 47.619 0.00 0.00 0.00 2.83
18 19 1.471684 GCCAACCATGAGAGAGCTTTG 59.528 52.381 0.00 0.00 0.00 2.77
19 20 1.615384 GGCCAACCATGAGAGAGCTTT 60.615 52.381 0.00 0.00 35.26 3.51
20 21 0.034670 GGCCAACCATGAGAGAGCTT 60.035 55.000 0.00 0.00 35.26 3.74
21 22 1.203441 TGGCCAACCATGAGAGAGCT 61.203 55.000 0.61 0.00 42.67 4.09
22 23 1.300963 TGGCCAACCATGAGAGAGC 59.699 57.895 0.61 0.00 42.67 4.09
51 52 2.093473 GCGAGCAGAGCAGTGAGTG 61.093 63.158 0.00 0.00 34.19 3.51
52 53 2.261052 GCGAGCAGAGCAGTGAGT 59.739 61.111 0.00 0.00 34.19 3.41
53 54 2.879933 CGCGAGCAGAGCAGTGAG 60.880 66.667 0.00 0.00 34.19 3.51
54 55 4.426112 CCGCGAGCAGAGCAGTGA 62.426 66.667 8.23 0.00 34.19 3.41
66 67 3.916632 TATATACCCCCTTGCCCGCGA 62.917 57.143 8.23 0.00 0.00 5.87
67 68 1.546589 TATATACCCCCTTGCCCGCG 61.547 60.000 0.00 0.00 0.00 6.46
68 69 0.916809 ATATATACCCCCTTGCCCGC 59.083 55.000 0.00 0.00 0.00 6.13
69 70 2.704065 CCTATATATACCCCCTTGCCCG 59.296 54.545 0.00 0.00 0.00 6.13
70 71 2.442126 GCCTATATATACCCCCTTGCCC 59.558 54.545 0.00 0.00 0.00 5.36
71 72 3.120108 TGCCTATATATACCCCCTTGCC 58.880 50.000 0.00 0.00 0.00 4.52
72 73 4.660771 AGATGCCTATATATACCCCCTTGC 59.339 45.833 0.00 0.00 0.00 4.01
73 74 5.905331 TGAGATGCCTATATATACCCCCTTG 59.095 44.000 0.00 0.00 0.00 3.61
74 75 6.118042 TGAGATGCCTATATATACCCCCTT 57.882 41.667 0.00 0.00 0.00 3.95
75 76 5.768454 TGAGATGCCTATATATACCCCCT 57.232 43.478 0.00 0.00 0.00 4.79
76 77 6.240002 CCAATGAGATGCCTATATATACCCCC 60.240 46.154 0.00 0.00 0.00 5.40
77 78 6.330250 ACCAATGAGATGCCTATATATACCCC 59.670 42.308 0.00 0.00 0.00 4.95
78 79 7.380423 ACCAATGAGATGCCTATATATACCC 57.620 40.000 0.00 0.00 0.00 3.69
79 80 7.445945 GGACCAATGAGATGCCTATATATACC 58.554 42.308 0.00 0.00 0.00 2.73
80 81 7.445945 GGGACCAATGAGATGCCTATATATAC 58.554 42.308 0.00 0.00 0.00 1.47
81 82 6.267699 CGGGACCAATGAGATGCCTATATATA 59.732 42.308 0.00 0.00 0.00 0.86
82 83 5.070981 CGGGACCAATGAGATGCCTATATAT 59.929 44.000 0.00 0.00 0.00 0.86
83 84 4.405680 CGGGACCAATGAGATGCCTATATA 59.594 45.833 0.00 0.00 0.00 0.86
84 85 3.198635 CGGGACCAATGAGATGCCTATAT 59.801 47.826 0.00 0.00 0.00 0.86
85 86 2.567169 CGGGACCAATGAGATGCCTATA 59.433 50.000 0.00 0.00 0.00 1.31
86 87 1.349026 CGGGACCAATGAGATGCCTAT 59.651 52.381 0.00 0.00 0.00 2.57
87 88 0.758734 CGGGACCAATGAGATGCCTA 59.241 55.000 0.00 0.00 0.00 3.93
88 89 1.528824 CGGGACCAATGAGATGCCT 59.471 57.895 0.00 0.00 0.00 4.75
89 90 1.526917 CCGGGACCAATGAGATGCC 60.527 63.158 0.00 0.00 0.00 4.40
90 91 0.394352 AACCGGGACCAATGAGATGC 60.394 55.000 6.32 0.00 0.00 3.91
91 92 1.668419 GAACCGGGACCAATGAGATG 58.332 55.000 6.32 0.00 0.00 2.90
92 93 0.178068 CGAACCGGGACCAATGAGAT 59.822 55.000 6.32 0.00 0.00 2.75
93 94 1.189524 ACGAACCGGGACCAATGAGA 61.190 55.000 6.32 0.00 0.00 3.27
94 95 1.019278 CACGAACCGGGACCAATGAG 61.019 60.000 6.32 0.00 28.17 2.90
95 96 1.004320 CACGAACCGGGACCAATGA 60.004 57.895 6.32 0.00 28.17 2.57
96 97 2.038269 CCACGAACCGGGACCAATG 61.038 63.158 6.32 0.00 28.17 2.82
97 98 2.349755 CCACGAACCGGGACCAAT 59.650 61.111 6.32 0.00 28.17 3.16
98 99 4.629523 GCCACGAACCGGGACCAA 62.630 66.667 6.32 0.00 28.17 3.67
103 104 4.323477 TTCCAGCCACGAACCGGG 62.323 66.667 6.32 0.00 0.00 5.73
104 105 3.047877 GTTCCAGCCACGAACCGG 61.048 66.667 0.00 0.00 34.75 5.28
107 108 3.047877 CCGGTTCCAGCCACGAAC 61.048 66.667 0.00 0.66 39.12 3.95
108 109 4.323477 CCCGGTTCCAGCCACGAA 62.323 66.667 0.00 0.00 0.00 3.85
111 112 1.833787 TTAGTCCCGGTTCCAGCCAC 61.834 60.000 0.00 0.00 0.00 5.01
112 113 1.128809 TTTAGTCCCGGTTCCAGCCA 61.129 55.000 0.00 0.00 0.00 4.75
113 114 0.392595 CTTTAGTCCCGGTTCCAGCC 60.393 60.000 0.00 0.00 0.00 4.85
114 115 0.392595 CCTTTAGTCCCGGTTCCAGC 60.393 60.000 0.00 0.00 0.00 4.85
115 116 1.207329 CTCCTTTAGTCCCGGTTCCAG 59.793 57.143 0.00 0.00 0.00 3.86
116 117 1.272807 CTCCTTTAGTCCCGGTTCCA 58.727 55.000 0.00 0.00 0.00 3.53
117 118 0.107800 GCTCCTTTAGTCCCGGTTCC 60.108 60.000 0.00 0.00 0.00 3.62
118 119 0.107800 GGCTCCTTTAGTCCCGGTTC 60.108 60.000 0.00 0.00 0.00 3.62
119 120 1.559965 GGGCTCCTTTAGTCCCGGTT 61.560 60.000 0.00 0.00 45.06 4.44
120 121 1.993948 GGGCTCCTTTAGTCCCGGT 60.994 63.158 0.00 0.00 45.06 5.28
121 122 2.908796 GGGCTCCTTTAGTCCCGG 59.091 66.667 0.00 0.00 45.06 5.73
131 132 2.941583 GGGACCAAAGGGGCTCCT 60.942 66.667 0.00 0.00 44.19 3.69
132 133 4.426313 CGGGACCAAAGGGGCTCC 62.426 72.222 0.00 0.00 41.10 4.70
133 134 4.426313 CCGGGACCAAAGGGGCTC 62.426 72.222 0.00 0.00 44.19 4.70
135 136 4.295199 AACCGGGACCAAAGGGGC 62.295 66.667 6.32 0.00 43.93 5.80
136 137 2.282887 CAACCGGGACCAAAGGGG 60.283 66.667 6.32 0.00 44.81 4.79
137 138 2.989253 GCAACCGGGACCAAAGGG 60.989 66.667 6.32 0.00 41.29 3.95
138 139 1.830408 TTGCAACCGGGACCAAAGG 60.830 57.895 6.32 0.00 0.00 3.11
139 140 1.362355 GTTGCAACCGGGACCAAAG 59.638 57.895 19.15 0.00 0.00 2.77
140 141 2.128507 GGTTGCAACCGGGACCAAA 61.129 57.895 31.73 0.00 39.66 3.28
141 142 2.519780 GGTTGCAACCGGGACCAA 60.520 61.111 31.73 2.23 39.66 3.67
150 151 1.227118 CCCGGTTTGTGGTTGCAAC 60.227 57.895 21.59 21.59 0.00 4.17
151 152 1.379977 TCCCGGTTTGTGGTTGCAA 60.380 52.632 0.00 0.00 0.00 4.08
152 153 2.122167 GTCCCGGTTTGTGGTTGCA 61.122 57.895 0.00 0.00 0.00 4.08
153 154 2.725641 GTCCCGGTTTGTGGTTGC 59.274 61.111 0.00 0.00 0.00 4.17
154 155 1.038130 TTGGTCCCGGTTTGTGGTTG 61.038 55.000 0.00 0.00 0.00 3.77
155 156 0.105913 ATTGGTCCCGGTTTGTGGTT 60.106 50.000 0.00 0.00 0.00 3.67
156 157 0.825840 CATTGGTCCCGGTTTGTGGT 60.826 55.000 0.00 0.00 0.00 4.16
157 158 1.531739 CCATTGGTCCCGGTTTGTGG 61.532 60.000 0.00 0.00 0.00 4.17
158 159 0.825840 ACCATTGGTCCCGGTTTGTG 60.826 55.000 1.37 0.00 0.00 3.33
159 160 0.105913 AACCATTGGTCCCGGTTTGT 60.106 50.000 9.22 0.00 40.08 2.83
160 161 0.316841 CAACCATTGGTCCCGGTTTG 59.683 55.000 9.22 0.00 41.07 2.93
161 162 0.105913 ACAACCATTGGTCCCGGTTT 60.106 50.000 9.22 0.00 41.07 3.27
162 163 0.825840 CACAACCATTGGTCCCGGTT 60.826 55.000 9.22 2.36 43.82 4.44
163 164 1.228429 CACAACCATTGGTCCCGGT 60.228 57.895 9.22 2.87 33.12 5.28
164 165 1.976474 CCACAACCATTGGTCCCGG 60.976 63.158 9.22 5.92 33.12 5.73
165 166 1.976474 CCCACAACCATTGGTCCCG 60.976 63.158 9.22 3.64 33.12 5.14
166 167 2.282783 GCCCACAACCATTGGTCCC 61.283 63.158 9.22 0.00 33.12 4.46
167 168 0.039035 TAGCCCACAACCATTGGTCC 59.961 55.000 9.22 0.00 33.12 4.46
168 169 1.463674 CTAGCCCACAACCATTGGTC 58.536 55.000 9.22 0.00 33.12 4.02
169 170 0.039618 CCTAGCCCACAACCATTGGT 59.960 55.000 1.37 1.37 37.65 3.67
170 171 0.331278 TCCTAGCCCACAACCATTGG 59.669 55.000 0.00 0.00 34.12 3.16
171 172 1.755179 CTCCTAGCCCACAACCATTG 58.245 55.000 0.00 0.00 0.00 2.82
172 173 0.034089 GCTCCTAGCCCACAACCATT 60.034 55.000 0.00 0.00 34.48 3.16
173 174 1.609783 GCTCCTAGCCCACAACCAT 59.390 57.895 0.00 0.00 34.48 3.55
174 175 2.954684 CGCTCCTAGCCCACAACCA 61.955 63.158 0.00 0.00 38.18 3.67
175 176 2.125106 CGCTCCTAGCCCACAACC 60.125 66.667 0.00 0.00 38.18 3.77
176 177 1.153549 CTCGCTCCTAGCCCACAAC 60.154 63.158 0.00 0.00 38.18 3.32
177 178 2.359169 CCTCGCTCCTAGCCCACAA 61.359 63.158 0.00 0.00 38.18 3.33
178 179 2.759973 CCTCGCTCCTAGCCCACA 60.760 66.667 0.00 0.00 38.18 4.17
179 180 4.228567 GCCTCGCTCCTAGCCCAC 62.229 72.222 0.00 0.00 38.18 4.61
183 184 2.812619 AATGGGCCTCGCTCCTAGC 61.813 63.158 4.53 0.00 38.02 3.42
184 185 1.070445 CAATGGGCCTCGCTCCTAG 59.930 63.158 4.53 0.00 0.00 3.02
185 186 2.443394 CCAATGGGCCTCGCTCCTA 61.443 63.158 4.53 0.00 0.00 2.94
186 187 3.801997 CCAATGGGCCTCGCTCCT 61.802 66.667 4.53 0.00 0.00 3.69
187 188 4.115199 ACCAATGGGCCTCGCTCC 62.115 66.667 4.53 0.00 37.90 4.70
188 189 2.514824 GACCAATGGGCCTCGCTC 60.515 66.667 4.53 0.00 37.90 5.03
197 198 1.976474 CACAACCCGGGACCAATGG 60.976 63.158 32.02 3.60 0.00 3.16
198 199 0.825840 AACACAACCCGGGACCAATG 60.826 55.000 32.02 19.29 0.00 2.82
199 200 0.105913 AAACACAACCCGGGACCAAT 60.106 50.000 32.02 6.48 0.00 3.16
200 201 1.038130 CAAACACAACCCGGGACCAA 61.038 55.000 32.02 0.00 0.00 3.67
201 202 1.454111 CAAACACAACCCGGGACCA 60.454 57.895 32.02 0.00 0.00 4.02
202 203 2.197605 CCAAACACAACCCGGGACC 61.198 63.158 32.02 0.00 0.00 4.46
203 204 0.752376 TTCCAAACACAACCCGGGAC 60.752 55.000 32.02 0.00 0.00 4.46
204 205 0.752376 GTTCCAAACACAACCCGGGA 60.752 55.000 32.02 0.00 0.00 5.14
205 206 0.753848 AGTTCCAAACACAACCCGGG 60.754 55.000 22.25 22.25 0.00 5.73
206 207 0.383949 CAGTTCCAAACACAACCCGG 59.616 55.000 0.00 0.00 0.00 5.73
207 208 0.383949 CCAGTTCCAAACACAACCCG 59.616 55.000 0.00 0.00 0.00 5.28
208 209 0.750249 CCCAGTTCCAAACACAACCC 59.250 55.000 0.00 0.00 0.00 4.11
209 210 1.407618 GTCCCAGTTCCAAACACAACC 59.592 52.381 0.00 0.00 0.00 3.77
210 211 1.407618 GGTCCCAGTTCCAAACACAAC 59.592 52.381 0.00 0.00 0.00 3.32
211 212 1.006043 TGGTCCCAGTTCCAAACACAA 59.994 47.619 0.00 0.00 0.00 3.33
212 213 0.626382 TGGTCCCAGTTCCAAACACA 59.374 50.000 0.00 0.00 0.00 3.72
213 214 1.770294 TTGGTCCCAGTTCCAAACAC 58.230 50.000 0.00 0.00 40.21 3.32
214 215 2.383855 CTTTGGTCCCAGTTCCAAACA 58.616 47.619 5.43 0.00 45.13 2.83
215 216 1.686587 CCTTTGGTCCCAGTTCCAAAC 59.313 52.381 5.43 0.00 45.13 2.93
216 217 1.412361 CCCTTTGGTCCCAGTTCCAAA 60.412 52.381 8.68 8.68 46.93 3.28
217 218 0.187361 CCCTTTGGTCCCAGTTCCAA 59.813 55.000 0.00 0.00 41.22 3.53
218 219 1.850549 CCCTTTGGTCCCAGTTCCA 59.149 57.895 0.00 0.00 0.00 3.53
219 220 1.606601 GCCCTTTGGTCCCAGTTCC 60.607 63.158 0.00 0.00 0.00 3.62
220 221 1.606601 GGCCCTTTGGTCCCAGTTC 60.607 63.158 0.00 0.00 0.00 3.01
221 222 2.371897 CTGGCCCTTTGGTCCCAGTT 62.372 60.000 0.00 0.00 36.32 3.16
222 223 2.780924 TGGCCCTTTGGTCCCAGT 60.781 61.111 0.00 0.00 34.32 4.00
223 224 2.036256 CTGGCCCTTTGGTCCCAG 59.964 66.667 0.00 6.28 34.32 4.45
224 225 2.451493 TCTGGCCCTTTGGTCCCA 60.451 61.111 0.00 0.00 34.32 4.37
225 226 2.035783 GTCTGGCCCTTTGGTCCC 59.964 66.667 0.00 0.00 34.32 4.46
226 227 0.469144 TTTGTCTGGCCCTTTGGTCC 60.469 55.000 0.00 0.00 34.32 4.46
227 228 0.673985 GTTTGTCTGGCCCTTTGGTC 59.326 55.000 0.00 0.00 36.51 4.02
228 229 0.759060 GGTTTGTCTGGCCCTTTGGT 60.759 55.000 0.00 0.00 0.00 3.67
229 230 1.805428 CGGTTTGTCTGGCCCTTTGG 61.805 60.000 0.00 0.00 0.00 3.28
230 231 1.659794 CGGTTTGTCTGGCCCTTTG 59.340 57.895 0.00 0.00 0.00 2.77
231 232 1.530655 CCGGTTTGTCTGGCCCTTT 60.531 57.895 0.00 0.00 35.61 3.11
232 233 2.115266 CCGGTTTGTCTGGCCCTT 59.885 61.111 0.00 0.00 35.61 3.95
237 238 0.035439 ATAGGTGCCGGTTTGTCTGG 60.035 55.000 1.90 0.00 45.06 3.86
238 239 1.086696 CATAGGTGCCGGTTTGTCTG 58.913 55.000 1.90 0.00 0.00 3.51
239 240 0.035439 CCATAGGTGCCGGTTTGTCT 60.035 55.000 1.90 0.00 0.00 3.41
240 241 1.654023 GCCATAGGTGCCGGTTTGTC 61.654 60.000 1.90 0.00 0.00 3.18
241 242 1.677633 GCCATAGGTGCCGGTTTGT 60.678 57.895 1.90 0.00 0.00 2.83
242 243 2.414785 GGCCATAGGTGCCGGTTTG 61.415 63.158 1.90 0.00 39.48 2.93
243 244 2.044352 GGCCATAGGTGCCGGTTT 60.044 61.111 1.90 0.00 39.48 3.27
249 250 2.203070 CTCGTGGGCCATAGGTGC 60.203 66.667 10.70 0.00 0.00 5.01
250 251 2.505982 CCTCGTGGGCCATAGGTG 59.494 66.667 23.25 11.77 0.00 4.00
277 278 4.410400 GTTCGTGAGGCCAGGGGG 62.410 72.222 5.01 0.00 37.18 5.40
278 279 4.410400 GGTTCGTGAGGCCAGGGG 62.410 72.222 5.01 0.00 0.00 4.79
279 280 4.760047 CGGTTCGTGAGGCCAGGG 62.760 72.222 5.01 0.00 0.00 4.45
280 281 4.760047 CCGGTTCGTGAGGCCAGG 62.760 72.222 5.01 0.00 0.00 4.45
281 282 4.760047 CCCGGTTCGTGAGGCCAG 62.760 72.222 5.01 0.00 0.00 4.85
283 284 4.754667 GTCCCGGTTCGTGAGGCC 62.755 72.222 0.00 0.00 0.00 5.19
284 285 4.754667 GGTCCCGGTTCGTGAGGC 62.755 72.222 0.00 0.00 0.00 4.70
285 286 4.430765 CGGTCCCGGTTCGTGAGG 62.431 72.222 0.00 0.00 35.56 3.86
286 287 2.707849 ATCGGTCCCGGTTCGTGAG 61.708 63.158 5.80 0.00 40.25 3.51
287 288 2.677524 ATCGGTCCCGGTTCGTGA 60.678 61.111 5.80 0.00 40.25 4.35
288 289 2.508439 CATCGGTCCCGGTTCGTG 60.508 66.667 5.80 0.00 40.25 4.35
289 290 4.446413 GCATCGGTCCCGGTTCGT 62.446 66.667 5.80 0.00 40.25 3.85
291 292 4.851179 GGGCATCGGTCCCGGTTC 62.851 72.222 5.80 0.00 40.25 3.62
297 298 4.586235 CCATGGGGGCATCGGTCC 62.586 72.222 2.85 0.00 38.40 4.46
308 309 4.483243 CGAACCGGGACCCATGGG 62.483 72.222 30.23 30.23 42.03 4.00
309 310 1.901654 TTACGAACCGGGACCCATGG 61.902 60.000 12.15 4.14 0.00 3.66
310 311 0.461339 CTTACGAACCGGGACCCATG 60.461 60.000 12.15 3.12 0.00 3.66
311 312 0.906282 ACTTACGAACCGGGACCCAT 60.906 55.000 12.15 0.00 0.00 4.00
312 313 1.533753 ACTTACGAACCGGGACCCA 60.534 57.895 12.15 0.00 0.00 4.51
313 314 1.079612 CACTTACGAACCGGGACCC 60.080 63.158 6.32 0.00 0.00 4.46
314 315 0.318120 TTCACTTACGAACCGGGACC 59.682 55.000 6.32 0.00 0.00 4.46
315 316 1.422388 GTTCACTTACGAACCGGGAC 58.578 55.000 6.32 0.00 39.52 4.46
316 317 3.892200 GTTCACTTACGAACCGGGA 57.108 52.632 6.32 0.00 39.52 5.14
321 322 2.375173 ATCCCGGTTCACTTACGAAC 57.625 50.000 0.00 0.00 43.75 3.95
322 323 4.533919 TTAATCCCGGTTCACTTACGAA 57.466 40.909 0.00 0.00 0.00 3.85
323 324 4.435425 CATTAATCCCGGTTCACTTACGA 58.565 43.478 0.00 0.00 0.00 3.43
324 325 3.558418 CCATTAATCCCGGTTCACTTACG 59.442 47.826 0.00 0.00 0.00 3.18
325 326 3.881089 CCCATTAATCCCGGTTCACTTAC 59.119 47.826 0.00 0.00 0.00 2.34
326 327 3.686120 GCCCATTAATCCCGGTTCACTTA 60.686 47.826 0.00 0.00 0.00 2.24
327 328 2.948600 GCCCATTAATCCCGGTTCACTT 60.949 50.000 0.00 0.00 0.00 3.16
328 329 1.409661 GCCCATTAATCCCGGTTCACT 60.410 52.381 0.00 0.00 0.00 3.41
329 330 1.029681 GCCCATTAATCCCGGTTCAC 58.970 55.000 0.00 0.00 0.00 3.18
330 331 0.923358 AGCCCATTAATCCCGGTTCA 59.077 50.000 0.00 0.00 0.00 3.18
331 332 2.067365 AAGCCCATTAATCCCGGTTC 57.933 50.000 0.00 0.00 0.00 3.62
332 333 2.423803 GGTAAGCCCATTAATCCCGGTT 60.424 50.000 0.00 0.00 0.00 4.44
333 334 1.144298 GGTAAGCCCATTAATCCCGGT 59.856 52.381 0.00 0.00 0.00 5.28
334 335 1.905637 GGTAAGCCCATTAATCCCGG 58.094 55.000 0.00 0.00 0.00 5.73
347 348 4.484872 GGTCCAGGCCGGGTAAGC 62.485 72.222 22.25 9.46 34.36 3.09
348 349 2.132089 TTTGGTCCAGGCCGGGTAAG 62.132 60.000 22.25 0.00 34.36 2.34
349 350 2.132089 CTTTGGTCCAGGCCGGGTAA 62.132 60.000 22.25 12.58 34.36 2.85
350 351 2.529643 TTTGGTCCAGGCCGGGTA 60.530 61.111 22.25 5.89 34.36 3.69
351 352 3.966543 CTTTGGTCCAGGCCGGGT 61.967 66.667 22.25 0.00 34.36 5.28
355 356 2.118294 AAGGCTTTGGTCCAGGCC 59.882 61.111 22.87 22.87 44.38 5.19
356 357 1.115326 AACAAGGCTTTGGTCCAGGC 61.115 55.000 13.65 9.58 38.66 4.85
357 358 1.413118 AAACAAGGCTTTGGTCCAGG 58.587 50.000 13.65 0.00 38.66 4.45
358 359 2.695147 AGAAAACAAGGCTTTGGTCCAG 59.305 45.455 13.65 0.00 38.66 3.86
359 360 2.745968 AGAAAACAAGGCTTTGGTCCA 58.254 42.857 13.65 0.00 38.66 4.02
360 361 3.889538 AGTAGAAAACAAGGCTTTGGTCC 59.110 43.478 13.65 2.36 38.66 4.46
361 362 5.763698 AGTAGTAGAAAACAAGGCTTTGGTC 59.236 40.000 13.65 7.21 38.66 4.02
362 363 5.531287 CAGTAGTAGAAAACAAGGCTTTGGT 59.469 40.000 13.65 2.75 38.66 3.67
363 364 5.562890 GCAGTAGTAGAAAACAAGGCTTTGG 60.563 44.000 13.65 0.00 38.66 3.28
364 365 5.452777 GCAGTAGTAGAAAACAAGGCTTTG 58.547 41.667 7.07 7.07 40.24 2.77
365 366 4.519350 GGCAGTAGTAGAAAACAAGGCTTT 59.481 41.667 0.00 0.00 0.00 3.51
366 367 4.072839 GGCAGTAGTAGAAAACAAGGCTT 58.927 43.478 0.00 0.00 0.00 4.35
367 368 3.559384 GGGCAGTAGTAGAAAACAAGGCT 60.559 47.826 0.00 0.00 0.00 4.58
368 369 2.747989 GGGCAGTAGTAGAAAACAAGGC 59.252 50.000 0.00 0.00 0.00 4.35
369 370 3.000727 CGGGCAGTAGTAGAAAACAAGG 58.999 50.000 0.00 0.00 0.00 3.61
370 371 3.432252 CACGGGCAGTAGTAGAAAACAAG 59.568 47.826 0.00 0.00 0.00 3.16
371 372 3.069872 TCACGGGCAGTAGTAGAAAACAA 59.930 43.478 0.00 0.00 0.00 2.83
372 373 2.629137 TCACGGGCAGTAGTAGAAAACA 59.371 45.455 0.00 0.00 0.00 2.83
373 374 2.991866 GTCACGGGCAGTAGTAGAAAAC 59.008 50.000 0.00 0.00 0.00 2.43
374 375 2.629137 TGTCACGGGCAGTAGTAGAAAA 59.371 45.455 0.00 0.00 0.00 2.29
375 376 2.029649 GTGTCACGGGCAGTAGTAGAAA 60.030 50.000 0.00 0.00 0.00 2.52
376 377 1.542915 GTGTCACGGGCAGTAGTAGAA 59.457 52.381 0.00 0.00 0.00 2.10
377 378 1.171308 GTGTCACGGGCAGTAGTAGA 58.829 55.000 0.00 0.00 0.00 2.59
378 379 0.172803 GGTGTCACGGGCAGTAGTAG 59.827 60.000 0.00 0.00 0.00 2.57
379 380 1.252904 GGGTGTCACGGGCAGTAGTA 61.253 60.000 0.00 0.00 0.00 1.82
380 381 2.580601 GGGTGTCACGGGCAGTAGT 61.581 63.158 0.00 0.00 0.00 2.73
381 382 2.264794 GGGTGTCACGGGCAGTAG 59.735 66.667 0.00 0.00 0.00 2.57
382 383 3.315949 GGGGTGTCACGGGCAGTA 61.316 66.667 0.00 0.00 0.00 2.74
894 895 4.430765 GGACGGTGACATCGCGGT 62.431 66.667 8.31 0.00 41.56 5.68
972 976 3.984200 GAGGGAAGTTCGCGTCGGG 62.984 68.421 13.65 2.31 34.19 5.14
976 980 0.179108 GCATAGAGGGAAGTTCGCGT 60.179 55.000 13.65 8.36 34.19 6.01
1107 1114 1.138859 CATGAGGCCGAAGTACATGGA 59.861 52.381 0.00 0.00 35.96 3.41
1358 1365 2.912956 TGCCCTTGTACTCCTTCTTCAT 59.087 45.455 0.00 0.00 0.00 2.57
1360 1367 3.198853 AGATGCCCTTGTACTCCTTCTTC 59.801 47.826 0.00 0.00 0.00 2.87
1361 1368 3.185455 AGATGCCCTTGTACTCCTTCTT 58.815 45.455 0.00 0.00 0.00 2.52
1362 1369 2.839228 AGATGCCCTTGTACTCCTTCT 58.161 47.619 0.00 0.00 0.00 2.85
1668 1678 4.224274 CGGTATACGCCGCCCCAA 62.224 66.667 0.00 0.00 45.47 4.12
1893 6747 5.616270 TCACAAATTCTACTGCTGGTGTTA 58.384 37.500 0.00 0.00 0.00 2.41
2030 6884 8.094548 ACACACAAGAATACATGTACACAGTAT 58.905 33.333 7.96 14.07 0.00 2.12
2155 7011 1.626321 TCGGTGAAATGACCTAGGCAA 59.374 47.619 9.30 0.00 33.35 4.52
2540 7411 8.006298 TGTACCAAACATTGAATTTCTCTGTT 57.994 30.769 9.79 9.79 31.43 3.16
2666 7542 8.958175 TTGTAATAAACATCTAACCGCTTTTG 57.042 30.769 0.00 0.00 38.10 2.44
2781 7659 3.364460 TCCCATCCATTTGTCGTCATT 57.636 42.857 0.00 0.00 0.00 2.57
2791 7669 2.057140 TGTCCATCGATCCCATCCATT 58.943 47.619 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.