Multiple sequence alignment - TraesCS5D01G555900

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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 TraesCS5D01G555900 chr5D 100.000 1658 0 0 816 2473 559442045 559440388 0.000000e+00 3062.0
1 TraesCS5D01G555900 chr5D 97.467 1658 22 2 816 2473 296179994 296178357 0.000000e+00 2811.0
2 TraesCS5D01G555900 chr5D 97.899 1618 12 3 816 2432 80200864 80202460 0.000000e+00 2780.0
3 TraesCS5D01G555900 chr5D 98.963 1543 12 2 931 2473 378329124 378330662 0.000000e+00 2758.0
4 TraesCS5D01G555900 chr5D 100.000 568 0 0 1 568 559442860 559442293 0.000000e+00 1050.0
5 TraesCS5D01G555900 chr5D 97.927 193 4 0 376 568 80200630 80200822 3.940000e-88 335.0
6 TraesCS5D01G555900 chr5D 97.409 193 5 0 376 568 80204268 80204076 1.830000e-86 329.0
7 TraesCS5D01G555900 chr5D 89.130 138 10 3 816 948 378329047 378329184 1.520000e-37 167.0
8 TraesCS5D01G555900 chr5D 100.000 72 0 0 827 898 360972606 360972535 1.540000e-27 134.0
9 TraesCS5D01G555900 chr5D 100.000 67 0 0 816 882 80204029 80203963 9.290000e-25 124.0
10 TraesCS5D01G555900 chr5D 100.000 43 0 0 2431 2473 80202652 80202694 2.040000e-11 80.5
11 TraesCS5D01G555900 chr1B 87.653 1223 93 26 954 2140 583684599 583685799 0.000000e+00 1369.0
12 TraesCS5D01G555900 chr1B 96.407 167 6 0 2307 2473 583686387 583686553 2.420000e-70 276.0
13 TraesCS5D01G555900 chr1B 94.857 175 9 0 2124 2298 583685838 583686012 8.710000e-70 274.0
14 TraesCS5D01G555900 chr1D 87.961 814 52 23 954 1752 432201723 432202505 0.000000e+00 918.0
15 TraesCS5D01G555900 chr1D 98.429 191 3 0 377 567 27849341 27849531 1.100000e-88 337.0
16 TraesCS5D01G555900 chr1D 97.006 167 5 0 2307 2473 432203456 432203622 5.210000e-72 281.0
17 TraesCS5D01G555900 chr1D 91.228 114 6 4 1737 1848 432202840 432202951 4.260000e-33 152.0
18 TraesCS5D01G555900 chr1D 98.795 83 1 0 816 898 46336 46254 5.510000e-32 148.0
19 TraesCS5D01G555900 chr1D 84.127 126 12 3 2176 2301 432202972 432203089 5.590000e-22 115.0
20 TraesCS5D01G555900 chr1A 89.065 759 37 14 954 1675 530726258 530727007 0.000000e+00 900.0
21 TraesCS5D01G555900 chr1A 90.271 627 46 10 1686 2302 530728192 530728813 0.000000e+00 806.0
22 TraesCS5D01G555900 chr1A 95.808 167 7 0 2307 2473 530729168 530729334 1.130000e-68 270.0
23 TraesCS5D01G555900 chr6B 93.883 376 22 1 1 376 20238517 20238891 1.280000e-157 566.0
24 TraesCS5D01G555900 chr7D 97.927 193 4 0 376 568 255421992 255422184 3.940000e-88 335.0
25 TraesCS5D01G555900 chr7D 96.447 197 6 1 372 568 634158134 634158329 8.530000e-85 324.0
26 TraesCS5D01G555900 chr7D 78.082 146 31 1 2015 2159 607618382 607618237 9.420000e-15 91.6
27 TraesCS5D01G555900 chr7D 77.551 147 31 2 2015 2159 610212221 610212367 1.220000e-13 87.9
28 TraesCS5D01G555900 chr6D 97.917 192 4 0 377 568 216837552 216837361 1.420000e-87 333.0
29 TraesCS5D01G555900 chr4D 97.906 191 4 0 377 567 417468384 417468194 5.100000e-87 331.0
30 TraesCS5D01G555900 chr4D 96.447 197 6 1 372 568 14673933 14673738 8.530000e-85 324.0
31 TraesCS5D01G555900 chr2D 97.906 191 4 0 377 567 166313264 166313454 5.100000e-87 331.0
32 TraesCS5D01G555900 chr2D 76.165 751 98 45 992 1707 579963476 579962772 1.100000e-83 320.0
33 TraesCS5D01G555900 chr2D 98.795 83 1 0 816 898 487362584 487362502 5.510000e-32 148.0
34 TraesCS5D01G555900 chr2D 100.000 78 0 0 821 898 503448477 503448554 7.130000e-31 145.0
35 TraesCS5D01G555900 chr5A 100.000 72 0 0 827 898 461850578 461850507 1.540000e-27 134.0


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 TraesCS5D01G555900 chr5D 559440388 559442860 2472 True 2056.000000 3062 100.000000 1 2473 2 chr5D.!!$R4 2472
1 TraesCS5D01G555900 chr5D 296178357 296179994 1637 True 2811.000000 2811 97.467000 816 2473 1 chr5D.!!$R1 1657
2 TraesCS5D01G555900 chr5D 378329047 378330662 1615 False 1462.500000 2758 94.046500 816 2473 2 chr5D.!!$F2 1657
3 TraesCS5D01G555900 chr5D 80200630 80202694 2064 False 1065.166667 2780 98.608667 376 2473 3 chr5D.!!$F1 2097
4 TraesCS5D01G555900 chr1B 583684599 583686553 1954 False 639.666667 1369 92.972333 954 2473 3 chr1B.!!$F1 1519
5 TraesCS5D01G555900 chr1D 432201723 432203622 1899 False 366.500000 918 90.080500 954 2473 4 chr1D.!!$F2 1519
6 TraesCS5D01G555900 chr1A 530726258 530729334 3076 False 658.666667 900 91.714667 954 2473 3 chr1A.!!$F1 1519
7 TraesCS5D01G555900 chr2D 579962772 579963476 704 True 320.000000 320 76.165000 992 1707 1 chr2D.!!$R2 715

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
233 234 0.026285 GGTGTACGATGAATGTGCGC 59.974 55.0 0.0 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1603 2.299013 ACACGAAGACTGATGGCTACAA 59.701 45.455 0.0 0.0 0.0 2.41 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
21 22 3.813596 GCTCCGTGCGGATTCAAT 58.186 55.556 14.04 0.00 44.24 2.57
22 23 2.098293 GCTCCGTGCGGATTCAATT 58.902 52.632 14.04 0.00 44.24 2.32
23 24 0.248215 GCTCCGTGCGGATTCAATTG 60.248 55.000 14.04 0.00 44.24 2.32
24 25 0.378257 CTCCGTGCGGATTCAATTGG 59.622 55.000 14.04 0.00 44.24 3.16
25 26 0.322098 TCCGTGCGGATTCAATTGGT 60.322 50.000 9.48 0.00 39.76 3.67
26 27 0.179166 CCGTGCGGATTCAATTGGTG 60.179 55.000 4.35 0.00 37.50 4.17
27 28 0.521291 CGTGCGGATTCAATTGGTGT 59.479 50.000 5.42 0.00 0.00 4.16
28 29 1.465689 CGTGCGGATTCAATTGGTGTC 60.466 52.381 5.42 1.66 0.00 3.67
29 30 0.801872 TGCGGATTCAATTGGTGTCG 59.198 50.000 5.42 6.69 0.00 4.35
30 31 0.802494 GCGGATTCAATTGGTGTCGT 59.198 50.000 5.42 0.00 0.00 4.34
31 32 1.199097 GCGGATTCAATTGGTGTCGTT 59.801 47.619 5.42 0.00 0.00 3.85
32 33 2.417239 GCGGATTCAATTGGTGTCGTTA 59.583 45.455 5.42 0.00 0.00 3.18
33 34 3.485216 GCGGATTCAATTGGTGTCGTTAG 60.485 47.826 5.42 0.00 0.00 2.34
34 35 3.063452 CGGATTCAATTGGTGTCGTTAGG 59.937 47.826 5.42 0.00 0.00 2.69
35 36 3.181500 GGATTCAATTGGTGTCGTTAGGC 60.181 47.826 5.42 0.00 0.00 3.93
36 37 1.434555 TCAATTGGTGTCGTTAGGCG 58.565 50.000 5.42 0.00 43.01 5.52
37 38 0.179200 CAATTGGTGTCGTTAGGCGC 60.179 55.000 0.00 0.00 41.07 6.53
38 39 0.604243 AATTGGTGTCGTTAGGCGCA 60.604 50.000 10.83 0.00 41.07 6.09
39 40 0.392461 ATTGGTGTCGTTAGGCGCAT 60.392 50.000 10.83 3.98 41.07 4.73
40 41 0.604243 TTGGTGTCGTTAGGCGCATT 60.604 50.000 10.83 0.00 41.07 3.56
41 42 0.246910 TGGTGTCGTTAGGCGCATTA 59.753 50.000 10.83 0.00 41.07 1.90
42 43 0.928229 GGTGTCGTTAGGCGCATTAG 59.072 55.000 10.83 0.00 41.07 1.73
43 44 0.928229 GTGTCGTTAGGCGCATTAGG 59.072 55.000 10.83 1.06 41.07 2.69
44 45 0.808453 TGTCGTTAGGCGCATTAGGC 60.808 55.000 10.83 0.00 41.07 3.93
53 54 2.639286 GCATTAGGCCGGCGATTG 59.361 61.111 22.54 17.45 36.11 2.67
54 55 2.186826 GCATTAGGCCGGCGATTGT 61.187 57.895 22.54 4.65 36.11 2.71
55 56 1.941812 CATTAGGCCGGCGATTGTC 59.058 57.895 22.54 4.96 0.00 3.18
56 57 1.594293 ATTAGGCCGGCGATTGTCG 60.594 57.895 22.54 0.00 44.51 4.35
74 75 3.984508 TCGGATCGACTTGGATTAGAC 57.015 47.619 0.00 0.00 0.00 2.59
75 76 2.289820 TCGGATCGACTTGGATTAGACG 59.710 50.000 0.00 0.00 35.23 4.18
76 77 2.289820 CGGATCGACTTGGATTAGACGA 59.710 50.000 0.00 0.00 43.92 4.20
77 78 3.607310 CGGATCGACTTGGATTAGACGAG 60.607 52.174 0.00 0.00 43.28 4.18
78 79 3.315749 GGATCGACTTGGATTAGACGAGT 59.684 47.826 0.00 0.00 43.28 4.18
79 80 4.529446 GATCGACTTGGATTAGACGAGTC 58.471 47.826 0.00 0.00 43.28 3.36
80 81 2.681848 TCGACTTGGATTAGACGAGTCC 59.318 50.000 7.12 0.00 43.41 3.85
81 82 2.422479 CGACTTGGATTAGACGAGTCCA 59.578 50.000 7.12 0.00 43.41 4.02
82 83 3.119602 CGACTTGGATTAGACGAGTCCAA 60.120 47.826 11.20 11.20 46.67 3.53
84 85 3.887621 TTGGATTAGACGAGTCCAAGG 57.112 47.619 8.21 0.00 44.67 3.61
85 86 2.816411 TGGATTAGACGAGTCCAAGGT 58.184 47.619 0.00 0.00 38.99 3.50
86 87 2.496070 TGGATTAGACGAGTCCAAGGTG 59.504 50.000 0.00 0.00 38.99 4.00
87 88 2.758979 GGATTAGACGAGTCCAAGGTGA 59.241 50.000 0.00 0.00 32.23 4.02
88 89 3.385111 GGATTAGACGAGTCCAAGGTGAT 59.615 47.826 0.00 0.00 32.23 3.06
89 90 3.868757 TTAGACGAGTCCAAGGTGATG 57.131 47.619 0.00 0.00 0.00 3.07
90 91 0.247736 AGACGAGTCCAAGGTGATGC 59.752 55.000 0.00 0.00 0.00 3.91
91 92 0.037326 GACGAGTCCAAGGTGATGCA 60.037 55.000 0.00 0.00 0.00 3.96
92 93 0.320771 ACGAGTCCAAGGTGATGCAC 60.321 55.000 0.00 0.00 0.00 4.57
93 94 0.036952 CGAGTCCAAGGTGATGCACT 60.037 55.000 0.00 0.00 34.40 4.40
94 95 1.446907 GAGTCCAAGGTGATGCACTG 58.553 55.000 0.00 0.00 34.40 3.66
95 96 0.767375 AGTCCAAGGTGATGCACTGT 59.233 50.000 0.00 0.00 34.40 3.55
96 97 1.977854 AGTCCAAGGTGATGCACTGTA 59.022 47.619 0.00 0.00 34.40 2.74
97 98 2.076863 GTCCAAGGTGATGCACTGTAC 58.923 52.381 0.00 0.00 34.40 2.90
98 99 1.977854 TCCAAGGTGATGCACTGTACT 59.022 47.619 0.00 0.00 34.40 2.73
99 100 2.079158 CCAAGGTGATGCACTGTACTG 58.921 52.381 0.00 0.00 34.40 2.74
100 101 2.289631 CCAAGGTGATGCACTGTACTGA 60.290 50.000 6.77 0.00 34.40 3.41
101 102 2.738846 CAAGGTGATGCACTGTACTGAC 59.261 50.000 6.77 0.00 34.40 3.51
102 103 1.276421 AGGTGATGCACTGTACTGACC 59.724 52.381 6.77 2.65 34.40 4.02
103 104 1.276421 GGTGATGCACTGTACTGACCT 59.724 52.381 6.77 0.00 34.40 3.85
104 105 2.341257 GTGATGCACTGTACTGACCTG 58.659 52.381 6.77 0.00 0.00 4.00
105 106 1.276138 TGATGCACTGTACTGACCTGG 59.724 52.381 6.77 0.00 0.00 4.45
106 107 1.550524 GATGCACTGTACTGACCTGGA 59.449 52.381 6.77 0.00 0.00 3.86
107 108 1.419381 TGCACTGTACTGACCTGGAA 58.581 50.000 6.77 0.00 0.00 3.53
108 109 1.344438 TGCACTGTACTGACCTGGAAG 59.656 52.381 6.77 0.00 0.00 3.46
109 110 1.941668 GCACTGTACTGACCTGGAAGC 60.942 57.143 6.77 0.00 0.00 3.86
110 111 0.977395 ACTGTACTGACCTGGAAGCC 59.023 55.000 6.77 0.00 0.00 4.35
111 112 0.976641 CTGTACTGACCTGGAAGCCA 59.023 55.000 0.00 0.00 0.00 4.75
112 113 1.347707 CTGTACTGACCTGGAAGCCAA 59.652 52.381 0.00 0.00 30.80 4.52
113 114 1.985159 TGTACTGACCTGGAAGCCAAT 59.015 47.619 0.00 0.00 30.80 3.16
114 115 3.178046 TGTACTGACCTGGAAGCCAATA 58.822 45.455 0.00 0.00 30.80 1.90
115 116 3.197766 TGTACTGACCTGGAAGCCAATAG 59.802 47.826 0.00 0.00 30.80 1.73
116 117 1.561542 ACTGACCTGGAAGCCAATAGG 59.438 52.381 0.00 0.00 36.39 2.57
131 132 4.866921 CCAATAGGCATTGTGATGACATG 58.133 43.478 0.00 0.00 44.22 3.21
132 133 4.261867 CCAATAGGCATTGTGATGACATGG 60.262 45.833 0.00 0.00 44.22 3.66
133 134 1.108776 AGGCATTGTGATGACATGGC 58.891 50.000 11.15 11.15 44.22 4.40
134 135 0.103572 GGCATTGTGATGACATGGCC 59.896 55.000 10.98 10.98 41.23 5.36
135 136 0.818938 GCATTGTGATGACATGGCCA 59.181 50.000 8.56 8.56 35.16 5.36
136 137 1.411246 GCATTGTGATGACATGGCCAT 59.589 47.619 14.09 14.09 35.16 4.40
137 138 2.801699 GCATTGTGATGACATGGCCATG 60.802 50.000 38.53 38.53 37.97 3.66
147 148 2.048444 CATGGCCATGTTCTAGTGCT 57.952 50.000 33.68 0.00 34.23 4.40
148 149 1.945394 CATGGCCATGTTCTAGTGCTC 59.055 52.381 33.68 0.00 34.23 4.26
149 150 0.253044 TGGCCATGTTCTAGTGCTCC 59.747 55.000 0.00 0.00 0.00 4.70
150 151 0.253044 GGCCATGTTCTAGTGCTCCA 59.747 55.000 0.00 0.00 0.00 3.86
151 152 1.373570 GCCATGTTCTAGTGCTCCAC 58.626 55.000 0.00 0.00 34.10 4.02
152 153 1.339055 GCCATGTTCTAGTGCTCCACA 60.339 52.381 0.00 0.00 36.74 4.17
153 154 2.625737 CCATGTTCTAGTGCTCCACAG 58.374 52.381 0.00 0.00 36.74 3.66
154 155 2.027745 CCATGTTCTAGTGCTCCACAGT 60.028 50.000 0.00 0.00 36.74 3.55
155 156 3.557898 CCATGTTCTAGTGCTCCACAGTT 60.558 47.826 0.00 0.00 36.74 3.16
156 157 4.322725 CCATGTTCTAGTGCTCCACAGTTA 60.323 45.833 0.00 0.00 36.74 2.24
157 158 4.252971 TGTTCTAGTGCTCCACAGTTAC 57.747 45.455 0.00 0.00 36.74 2.50
158 159 3.895656 TGTTCTAGTGCTCCACAGTTACT 59.104 43.478 0.00 0.00 36.74 2.24
159 160 4.022242 TGTTCTAGTGCTCCACAGTTACTC 60.022 45.833 0.00 0.00 36.74 2.59
160 161 3.763057 TCTAGTGCTCCACAGTTACTCA 58.237 45.455 0.00 0.00 36.74 3.41
161 162 2.821991 AGTGCTCCACAGTTACTCAC 57.178 50.000 0.00 0.00 36.74 3.51
162 163 2.039418 AGTGCTCCACAGTTACTCACA 58.961 47.619 3.19 0.00 36.74 3.58
163 164 2.036475 AGTGCTCCACAGTTACTCACAG 59.964 50.000 3.19 0.00 36.74 3.66
164 165 1.270305 TGCTCCACAGTTACTCACAGC 60.270 52.381 0.00 0.00 0.00 4.40
165 166 1.270305 GCTCCACAGTTACTCACAGCA 60.270 52.381 0.00 0.00 0.00 4.41
166 167 2.806745 GCTCCACAGTTACTCACAGCAA 60.807 50.000 0.00 0.00 0.00 3.91
167 168 2.802816 CTCCACAGTTACTCACAGCAAC 59.197 50.000 0.00 0.00 0.00 4.17
168 169 1.526887 CCACAGTTACTCACAGCAACG 59.473 52.381 0.00 0.00 0.00 4.10
169 170 1.070577 CACAGTTACTCACAGCAACGC 60.071 52.381 0.00 0.00 0.00 4.84
170 171 0.161658 CAGTTACTCACAGCAACGCG 59.838 55.000 3.53 3.53 0.00 6.01
171 172 0.031585 AGTTACTCACAGCAACGCGA 59.968 50.000 15.93 0.00 0.00 5.87
172 173 0.161024 GTTACTCACAGCAACGCGAC 59.839 55.000 15.93 0.83 0.00 5.19
173 174 1.272784 TTACTCACAGCAACGCGACG 61.273 55.000 15.93 3.67 0.00 5.12
174 175 2.120355 TACTCACAGCAACGCGACGA 62.120 55.000 15.93 0.00 0.00 4.20
175 176 2.710971 CTCACAGCAACGCGACGAG 61.711 63.158 15.93 0.00 0.00 4.18
176 177 3.030308 CACAGCAACGCGACGAGT 61.030 61.111 15.93 0.00 0.00 4.18
177 178 1.728074 CACAGCAACGCGACGAGTA 60.728 57.895 15.93 0.00 0.00 2.59
178 179 1.008194 ACAGCAACGCGACGAGTAA 60.008 52.632 15.93 0.00 0.00 2.24
179 180 1.002250 ACAGCAACGCGACGAGTAAG 61.002 55.000 15.93 2.20 0.00 2.34
180 181 0.728129 CAGCAACGCGACGAGTAAGA 60.728 55.000 15.93 0.00 0.00 2.10
181 182 0.454620 AGCAACGCGACGAGTAAGAG 60.455 55.000 15.93 0.00 0.00 2.85
182 183 1.403972 GCAACGCGACGAGTAAGAGG 61.404 60.000 15.93 0.00 0.00 3.69
183 184 0.167470 CAACGCGACGAGTAAGAGGA 59.833 55.000 15.93 0.00 0.00 3.71
184 185 0.877071 AACGCGACGAGTAAGAGGAA 59.123 50.000 15.93 0.00 0.00 3.36
185 186 0.447011 ACGCGACGAGTAAGAGGAAG 59.553 55.000 15.93 0.00 0.00 3.46
186 187 0.447011 CGCGACGAGTAAGAGGAAGT 59.553 55.000 0.00 0.00 0.00 3.01
187 188 1.135746 CGCGACGAGTAAGAGGAAGTT 60.136 52.381 0.00 0.00 0.00 2.66
188 189 2.251893 GCGACGAGTAAGAGGAAGTTG 58.748 52.381 0.00 0.00 0.00 3.16
189 190 2.864968 CGACGAGTAAGAGGAAGTTGG 58.135 52.381 0.00 0.00 0.00 3.77
190 191 2.608268 GACGAGTAAGAGGAAGTTGGC 58.392 52.381 0.00 0.00 0.00 4.52
191 192 1.968493 ACGAGTAAGAGGAAGTTGGCA 59.032 47.619 0.00 0.00 0.00 4.92
192 193 2.367567 ACGAGTAAGAGGAAGTTGGCAA 59.632 45.455 0.00 0.00 0.00 4.52
193 194 2.996621 CGAGTAAGAGGAAGTTGGCAAG 59.003 50.000 0.00 0.00 0.00 4.01
194 195 2.744741 GAGTAAGAGGAAGTTGGCAAGC 59.255 50.000 0.00 0.00 0.00 4.01
195 196 1.464997 GTAAGAGGAAGTTGGCAAGCG 59.535 52.381 0.00 0.00 0.00 4.68
196 197 1.518903 AAGAGGAAGTTGGCAAGCGC 61.519 55.000 0.00 0.00 37.44 5.92
197 198 2.203337 AGGAAGTTGGCAAGCGCA 60.203 55.556 11.47 0.00 41.24 6.09
198 199 2.050077 GGAAGTTGGCAAGCGCAC 60.050 61.111 11.47 0.00 41.24 5.34
199 200 2.721231 GAAGTTGGCAAGCGCACA 59.279 55.556 11.47 0.00 41.24 4.57
200 201 1.065600 GAAGTTGGCAAGCGCACAA 59.934 52.632 11.47 6.45 41.24 3.33
201 202 1.208642 GAAGTTGGCAAGCGCACAAC 61.209 55.000 21.59 21.59 43.70 3.32
202 203 2.935122 AAGTTGGCAAGCGCACAACG 62.935 55.000 22.31 4.86 45.86 4.10
203 204 4.263209 TTGGCAAGCGCACAACGG 62.263 61.111 11.47 0.00 43.93 4.44
206 207 4.629115 GCAAGCGCACAACGGCTT 62.629 61.111 11.47 0.00 43.93 4.35
207 208 2.427410 CAAGCGCACAACGGCTTC 60.427 61.111 11.47 0.00 43.93 3.86
208 209 2.591715 AAGCGCACAACGGCTTCT 60.592 55.556 11.47 0.00 43.93 2.85
209 210 2.186826 AAGCGCACAACGGCTTCTT 61.187 52.632 11.47 0.00 43.93 2.52
210 211 2.392613 AAGCGCACAACGGCTTCTTG 62.393 55.000 11.47 0.00 43.93 3.02
211 212 2.252260 CGCACAACGGCTTCTTGG 59.748 61.111 0.00 0.00 38.44 3.61
212 213 2.050077 GCACAACGGCTTCTTGGC 60.050 61.111 0.00 0.00 37.94 4.52
213 214 2.844451 GCACAACGGCTTCTTGGCA 61.844 57.895 0.00 0.00 41.89 4.92
214 215 1.283793 CACAACGGCTTCTTGGCAG 59.716 57.895 0.00 0.00 41.89 4.85
215 216 1.898574 ACAACGGCTTCTTGGCAGG 60.899 57.895 0.00 0.00 41.89 4.85
216 217 1.898574 CAACGGCTTCTTGGCAGGT 60.899 57.895 0.00 0.00 41.89 4.00
217 218 1.898574 AACGGCTTCTTGGCAGGTG 60.899 57.895 0.00 0.00 41.89 4.00
218 219 2.281761 CGGCTTCTTGGCAGGTGT 60.282 61.111 0.00 0.00 41.89 4.16
219 220 1.003839 CGGCTTCTTGGCAGGTGTA 60.004 57.895 0.00 0.00 41.89 2.90
220 221 1.298859 CGGCTTCTTGGCAGGTGTAC 61.299 60.000 0.00 0.00 41.89 2.90
221 222 1.298859 GGCTTCTTGGCAGGTGTACG 61.299 60.000 0.00 0.00 41.37 3.67
222 223 0.320421 GCTTCTTGGCAGGTGTACGA 60.320 55.000 0.00 0.00 0.00 3.43
223 224 1.676014 GCTTCTTGGCAGGTGTACGAT 60.676 52.381 0.00 0.00 0.00 3.73
224 225 2.002586 CTTCTTGGCAGGTGTACGATG 58.997 52.381 0.00 0.00 0.00 3.84
225 226 1.262417 TCTTGGCAGGTGTACGATGA 58.738 50.000 0.00 0.00 0.00 2.92
226 227 1.621317 TCTTGGCAGGTGTACGATGAA 59.379 47.619 0.00 0.00 0.00 2.57
227 228 2.236146 TCTTGGCAGGTGTACGATGAAT 59.764 45.455 0.00 0.00 0.00 2.57
228 229 2.022764 TGGCAGGTGTACGATGAATG 57.977 50.000 0.00 0.00 0.00 2.67
229 230 1.277842 TGGCAGGTGTACGATGAATGT 59.722 47.619 0.00 0.00 0.00 2.71
230 231 1.665679 GGCAGGTGTACGATGAATGTG 59.334 52.381 0.00 0.00 0.00 3.21
231 232 1.062587 GCAGGTGTACGATGAATGTGC 59.937 52.381 0.00 0.00 0.00 4.57
232 233 1.324435 CAGGTGTACGATGAATGTGCG 59.676 52.381 0.00 0.00 0.00 5.34
233 234 0.026285 GGTGTACGATGAATGTGCGC 59.974 55.000 0.00 0.00 0.00 6.09
234 235 0.314259 GTGTACGATGAATGTGCGCG 60.314 55.000 0.00 0.00 0.00 6.86
235 236 1.366494 GTACGATGAATGTGCGCGC 60.366 57.895 27.26 27.26 0.00 6.86
236 237 2.521771 TACGATGAATGTGCGCGCC 61.522 57.895 30.77 20.33 0.00 6.53
237 238 4.596180 CGATGAATGTGCGCGCCC 62.596 66.667 30.77 19.65 0.00 6.13
238 239 3.204827 GATGAATGTGCGCGCCCT 61.205 61.111 30.77 10.30 0.00 5.19
239 240 3.173390 GATGAATGTGCGCGCCCTC 62.173 63.158 30.77 19.02 0.00 4.30
240 241 3.687321 ATGAATGTGCGCGCCCTCT 62.687 57.895 30.77 10.95 0.00 3.69
241 242 3.869272 GAATGTGCGCGCCCTCTG 61.869 66.667 30.77 0.00 0.00 3.35
242 243 4.704833 AATGTGCGCGCCCTCTGT 62.705 61.111 30.77 5.90 0.00 3.41
248 249 4.504916 CGCGCCCTCTGTCTCCTG 62.505 72.222 0.00 0.00 0.00 3.86
249 250 4.154347 GCGCCCTCTGTCTCCTGG 62.154 72.222 0.00 0.00 0.00 4.45
250 251 4.154347 CGCCCTCTGTCTCCTGGC 62.154 72.222 0.00 0.00 38.74 4.85
251 252 2.686835 GCCCTCTGTCTCCTGGCT 60.687 66.667 0.00 0.00 39.05 4.75
252 253 2.297129 GCCCTCTGTCTCCTGGCTT 61.297 63.158 0.00 0.00 39.05 4.35
253 254 1.904032 CCCTCTGTCTCCTGGCTTC 59.096 63.158 0.00 0.00 0.00 3.86
254 255 0.617249 CCCTCTGTCTCCTGGCTTCT 60.617 60.000 0.00 0.00 0.00 2.85
255 256 0.823460 CCTCTGTCTCCTGGCTTCTC 59.177 60.000 0.00 0.00 0.00 2.87
256 257 1.554836 CTCTGTCTCCTGGCTTCTCA 58.445 55.000 0.00 0.00 0.00 3.27
257 258 2.109774 CTCTGTCTCCTGGCTTCTCAT 58.890 52.381 0.00 0.00 0.00 2.90
258 259 1.829849 TCTGTCTCCTGGCTTCTCATG 59.170 52.381 0.00 0.00 0.00 3.07
259 260 0.907486 TGTCTCCTGGCTTCTCATGG 59.093 55.000 0.00 0.00 0.00 3.66
260 261 1.198713 GTCTCCTGGCTTCTCATGGA 58.801 55.000 0.00 0.00 0.00 3.41
261 262 1.138661 GTCTCCTGGCTTCTCATGGAG 59.861 57.143 0.00 0.00 44.00 3.86
262 263 0.179051 CTCCTGGCTTCTCATGGAGC 60.179 60.000 7.76 7.76 37.98 4.70
263 264 0.619832 TCCTGGCTTCTCATGGAGCT 60.620 55.000 13.66 0.00 0.00 4.09
264 265 1.126488 CCTGGCTTCTCATGGAGCTA 58.874 55.000 13.66 8.75 0.00 3.32
265 266 1.202627 CCTGGCTTCTCATGGAGCTAC 60.203 57.143 13.66 0.00 0.00 3.58
266 267 0.461548 TGGCTTCTCATGGAGCTACG 59.538 55.000 13.66 0.00 0.00 3.51
267 268 0.878086 GGCTTCTCATGGAGCTACGC 60.878 60.000 13.66 0.00 0.00 4.42
268 269 0.179100 GCTTCTCATGGAGCTACGCA 60.179 55.000 8.71 0.00 0.00 5.24
269 270 1.565305 CTTCTCATGGAGCTACGCAC 58.435 55.000 0.00 0.00 0.00 5.34
270 271 0.175760 TTCTCATGGAGCTACGCACC 59.824 55.000 0.00 0.00 39.68 5.01
271 272 1.227380 CTCATGGAGCTACGCACCC 60.227 63.158 0.00 0.00 38.50 4.61
272 273 2.203070 CATGGAGCTACGCACCCC 60.203 66.667 0.00 0.00 38.50 4.95
273 274 2.687200 ATGGAGCTACGCACCCCA 60.687 61.111 0.00 0.00 38.50 4.96
274 275 2.072487 ATGGAGCTACGCACCCCAT 61.072 57.895 0.00 0.00 38.50 4.00
275 276 0.762842 ATGGAGCTACGCACCCCATA 60.763 55.000 0.00 0.00 38.50 2.74
276 277 1.367840 GGAGCTACGCACCCCATAG 59.632 63.158 0.00 0.00 33.27 2.23
277 278 1.301009 GAGCTACGCACCCCATAGC 60.301 63.158 0.00 0.00 41.39 2.97
278 279 2.028125 GAGCTACGCACCCCATAGCA 62.028 60.000 5.38 0.00 43.13 3.49
279 280 1.595382 GCTACGCACCCCATAGCAG 60.595 63.158 0.00 0.00 40.87 4.24
280 281 1.069765 CTACGCACCCCATAGCAGG 59.930 63.158 0.00 0.00 0.00 4.85
281 282 2.996168 CTACGCACCCCATAGCAGGC 62.996 65.000 0.00 0.00 0.00 4.85
326 327 4.363990 CCGACGGCAGCTCACACT 62.364 66.667 0.00 0.00 0.00 3.55
327 328 2.807045 CGACGGCAGCTCACACTC 60.807 66.667 0.00 0.00 0.00 3.51
328 329 2.653702 GACGGCAGCTCACACTCT 59.346 61.111 0.00 0.00 0.00 3.24
329 330 1.005630 GACGGCAGCTCACACTCTT 60.006 57.895 0.00 0.00 0.00 2.85
330 331 1.287730 GACGGCAGCTCACACTCTTG 61.288 60.000 0.00 0.00 0.00 3.02
331 332 1.301244 CGGCAGCTCACACTCTTGT 60.301 57.895 0.00 0.00 35.84 3.16
351 352 3.443925 GCCAAGGGCCGCTCTTTC 61.444 66.667 1.60 0.00 44.06 2.62
352 353 2.751837 CCAAGGGCCGCTCTTTCC 60.752 66.667 1.60 0.00 0.00 3.13
353 354 2.352805 CAAGGGCCGCTCTTTCCT 59.647 61.111 1.60 0.00 0.00 3.36
354 355 1.746991 CAAGGGCCGCTCTTTCCTC 60.747 63.158 1.60 0.00 0.00 3.71
355 356 2.224159 AAGGGCCGCTCTTTCCTCA 61.224 57.895 0.00 0.00 0.00 3.86
356 357 2.124942 GGGCCGCTCTTTCCTCAG 60.125 66.667 0.00 0.00 0.00 3.35
357 358 2.665603 GGCCGCTCTTTCCTCAGT 59.334 61.111 0.00 0.00 0.00 3.41
358 359 1.743252 GGCCGCTCTTTCCTCAGTG 60.743 63.158 0.00 0.00 0.00 3.66
359 360 1.293498 GCCGCTCTTTCCTCAGTGA 59.707 57.895 0.00 0.00 0.00 3.41
360 361 0.739112 GCCGCTCTTTCCTCAGTGAG 60.739 60.000 13.56 13.56 0.00 3.51
361 362 0.891373 CCGCTCTTTCCTCAGTGAGA 59.109 55.000 22.09 5.00 0.00 3.27
362 363 1.403514 CCGCTCTTTCCTCAGTGAGAC 60.404 57.143 22.09 1.28 0.00 3.36
363 364 1.730772 CGCTCTTTCCTCAGTGAGACG 60.731 57.143 22.09 5.89 0.00 4.18
364 365 1.271102 GCTCTTTCCTCAGTGAGACGT 59.729 52.381 22.09 0.00 0.00 4.34
365 366 2.288518 GCTCTTTCCTCAGTGAGACGTT 60.289 50.000 22.09 0.00 0.00 3.99
366 367 3.057456 GCTCTTTCCTCAGTGAGACGTTA 60.057 47.826 22.09 3.29 0.00 3.18
367 368 4.477780 CTCTTTCCTCAGTGAGACGTTAC 58.522 47.826 22.09 0.00 0.00 2.50
368 369 4.142790 TCTTTCCTCAGTGAGACGTTACT 58.857 43.478 22.09 0.00 0.00 2.24
369 370 4.583489 TCTTTCCTCAGTGAGACGTTACTT 59.417 41.667 22.09 0.00 0.00 2.24
370 371 4.500603 TTCCTCAGTGAGACGTTACTTC 57.499 45.455 22.09 0.00 0.00 3.01
371 372 3.752665 TCCTCAGTGAGACGTTACTTCT 58.247 45.455 22.09 0.00 0.00 2.85
372 373 3.752222 TCCTCAGTGAGACGTTACTTCTC 59.248 47.826 22.09 11.30 40.10 2.87
373 374 3.502595 CCTCAGTGAGACGTTACTTCTCA 59.497 47.826 22.09 16.01 45.84 3.27
396 397 5.063944 CAGCGAGTAAATTGCACAGAAGTAT 59.936 40.000 0.00 0.00 41.26 2.12
399 400 6.238211 GCGAGTAAATTGCACAGAAGTATCAT 60.238 38.462 0.00 0.00 38.31 2.45
1040 1041 2.788191 AAGTCCTTCTTCCGGCAGCG 62.788 60.000 0.00 0.00 0.00 5.18
1545 1603 2.106511 TGGTTCTGCCTACTGCTTCTTT 59.893 45.455 0.00 0.00 42.00 2.52
1602 1684 3.562505 GTCTGTACGTTTGTGTCGATCT 58.437 45.455 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.179166 CACCAATTGAATCCGCACGG 60.179 55.000 7.12 1.73 0.00 4.94
8 9 0.521291 ACACCAATTGAATCCGCACG 59.479 50.000 7.12 0.00 0.00 5.34
9 10 1.465689 CGACACCAATTGAATCCGCAC 60.466 52.381 7.12 0.00 0.00 5.34
10 11 0.801872 CGACACCAATTGAATCCGCA 59.198 50.000 7.12 0.00 0.00 5.69
11 12 0.802494 ACGACACCAATTGAATCCGC 59.198 50.000 7.12 0.00 0.00 5.54
12 13 3.063452 CCTAACGACACCAATTGAATCCG 59.937 47.826 7.12 7.75 0.00 4.18
13 14 3.181500 GCCTAACGACACCAATTGAATCC 60.181 47.826 7.12 0.00 0.00 3.01
14 15 4.016113 GCCTAACGACACCAATTGAATC 57.984 45.455 7.12 0.32 0.00 2.52
28 29 2.594962 CGGCCTAATGCGCCTAACG 61.595 63.158 4.18 0.00 44.73 3.18
29 30 2.251642 CCGGCCTAATGCGCCTAAC 61.252 63.158 4.18 0.00 44.73 2.34
30 31 2.110213 CCGGCCTAATGCGCCTAA 59.890 61.111 4.18 0.00 44.73 2.69
31 32 4.619227 GCCGGCCTAATGCGCCTA 62.619 66.667 18.11 0.00 44.73 3.93
36 37 2.117941 GACAATCGCCGGCCTAATGC 62.118 60.000 23.46 2.66 40.16 3.56
37 38 1.831389 CGACAATCGCCGGCCTAATG 61.831 60.000 23.46 17.11 31.14 1.90
38 39 1.594293 CGACAATCGCCGGCCTAAT 60.594 57.895 23.46 9.51 31.14 1.73
39 40 2.202824 CGACAATCGCCGGCCTAA 60.203 61.111 23.46 7.13 31.14 2.69
40 41 4.215742 CCGACAATCGCCGGCCTA 62.216 66.667 23.46 10.21 38.82 3.93
42 43 4.910585 ATCCGACAATCGCCGGCC 62.911 66.667 23.46 4.12 44.96 6.13
43 44 3.338676 GATCCGACAATCGCCGGC 61.339 66.667 19.07 19.07 44.96 6.13
44 45 3.030308 CGATCCGACAATCGCCGG 61.030 66.667 0.00 0.00 46.57 6.13
45 46 2.025584 TCGATCCGACAATCGCCG 59.974 61.111 9.14 0.00 46.28 6.46
54 55 2.289820 CGTCTAATCCAAGTCGATCCGA 59.710 50.000 0.00 0.00 31.00 4.55
55 56 2.289820 TCGTCTAATCCAAGTCGATCCG 59.710 50.000 0.00 0.00 33.25 4.18
56 57 3.315749 ACTCGTCTAATCCAAGTCGATCC 59.684 47.826 0.00 0.00 36.66 3.36
57 58 4.529446 GACTCGTCTAATCCAAGTCGATC 58.471 47.826 0.00 0.00 36.66 3.69
58 59 3.315749 GGACTCGTCTAATCCAAGTCGAT 59.684 47.826 0.00 0.00 36.66 3.59
59 60 2.681848 GGACTCGTCTAATCCAAGTCGA 59.318 50.000 0.00 0.00 37.76 4.20
60 61 2.422479 TGGACTCGTCTAATCCAAGTCG 59.578 50.000 0.00 0.00 39.60 4.18
61 62 4.451629 TTGGACTCGTCTAATCCAAGTC 57.548 45.455 0.80 0.00 45.46 3.01
65 66 2.496070 CACCTTGGACTCGTCTAATCCA 59.504 50.000 0.00 0.00 40.83 3.41
66 67 2.758979 TCACCTTGGACTCGTCTAATCC 59.241 50.000 0.00 0.00 29.71 3.01
67 68 4.363999 CATCACCTTGGACTCGTCTAATC 58.636 47.826 0.00 0.00 29.71 1.75
68 69 3.430929 GCATCACCTTGGACTCGTCTAAT 60.431 47.826 0.00 0.00 29.71 1.73
69 70 2.094182 GCATCACCTTGGACTCGTCTAA 60.094 50.000 0.00 0.00 0.00 2.10
70 71 1.476891 GCATCACCTTGGACTCGTCTA 59.523 52.381 0.00 0.00 0.00 2.59
71 72 0.247736 GCATCACCTTGGACTCGTCT 59.752 55.000 0.00 0.00 0.00 4.18
72 73 0.037326 TGCATCACCTTGGACTCGTC 60.037 55.000 0.00 0.00 0.00 4.20
73 74 0.320771 GTGCATCACCTTGGACTCGT 60.321 55.000 0.00 0.00 35.32 4.18
74 75 0.036952 AGTGCATCACCTTGGACTCG 60.037 55.000 0.00 0.00 43.83 4.18
75 76 1.271054 ACAGTGCATCACCTTGGACTC 60.271 52.381 0.00 0.00 43.83 3.36
77 78 2.076863 GTACAGTGCATCACCTTGGAC 58.923 52.381 0.00 0.00 38.14 4.02
78 79 1.977854 AGTACAGTGCATCACCTTGGA 59.022 47.619 0.00 0.00 34.49 3.53
79 80 2.079158 CAGTACAGTGCATCACCTTGG 58.921 52.381 0.00 0.00 34.49 3.61
80 81 2.738846 GTCAGTACAGTGCATCACCTTG 59.261 50.000 0.00 0.00 34.49 3.61
81 82 2.289694 GGTCAGTACAGTGCATCACCTT 60.290 50.000 0.00 0.00 34.49 3.50
82 83 1.276421 GGTCAGTACAGTGCATCACCT 59.724 52.381 0.00 0.00 34.49 4.00
83 84 1.276421 AGGTCAGTACAGTGCATCACC 59.724 52.381 0.00 0.00 34.49 4.02
84 85 2.341257 CAGGTCAGTACAGTGCATCAC 58.659 52.381 0.00 0.00 34.10 3.06
85 86 1.276138 CCAGGTCAGTACAGTGCATCA 59.724 52.381 0.00 0.00 0.00 3.07
86 87 1.550524 TCCAGGTCAGTACAGTGCATC 59.449 52.381 0.00 0.00 0.00 3.91
87 88 1.644509 TCCAGGTCAGTACAGTGCAT 58.355 50.000 0.00 0.00 0.00 3.96
88 89 1.344438 CTTCCAGGTCAGTACAGTGCA 59.656 52.381 0.00 0.00 0.00 4.57
89 90 1.941668 GCTTCCAGGTCAGTACAGTGC 60.942 57.143 0.00 0.00 0.00 4.40
90 91 1.338200 GGCTTCCAGGTCAGTACAGTG 60.338 57.143 0.00 0.00 0.00 3.66
91 92 0.977395 GGCTTCCAGGTCAGTACAGT 59.023 55.000 0.00 0.00 0.00 3.55
92 93 0.976641 TGGCTTCCAGGTCAGTACAG 59.023 55.000 0.00 0.00 0.00 2.74
93 94 1.429930 TTGGCTTCCAGGTCAGTACA 58.570 50.000 0.00 0.00 33.81 2.90
94 95 2.789409 ATTGGCTTCCAGGTCAGTAC 57.211 50.000 0.00 0.00 33.81 2.73
95 96 2.771943 CCTATTGGCTTCCAGGTCAGTA 59.228 50.000 0.00 0.00 33.81 2.74
96 97 1.561542 CCTATTGGCTTCCAGGTCAGT 59.438 52.381 0.00 0.00 33.81 3.41
97 98 2.338577 CCTATTGGCTTCCAGGTCAG 57.661 55.000 0.00 0.00 33.81 3.51
109 110 4.261867 CCATGTCATCACAATGCCTATTGG 60.262 45.833 5.17 0.00 46.33 3.16
110 111 7.738227 GGCCATGTCATCACAATGCCTATTG 62.738 48.000 5.75 0.00 44.37 1.90
111 112 3.319972 GCCATGTCATCACAATGCCTATT 59.680 43.478 0.00 0.00 35.64 1.73
112 113 2.889045 GCCATGTCATCACAATGCCTAT 59.111 45.455 0.00 0.00 35.64 2.57
113 114 2.300433 GCCATGTCATCACAATGCCTA 58.700 47.619 0.00 0.00 35.64 3.93
114 115 1.108776 GCCATGTCATCACAATGCCT 58.891 50.000 0.00 0.00 35.64 4.75
115 116 0.103572 GGCCATGTCATCACAATGCC 59.896 55.000 0.00 0.00 42.66 4.40
116 117 0.818938 TGGCCATGTCATCACAATGC 59.181 50.000 0.00 0.00 35.64 3.56
117 118 3.092334 CATGGCCATGTCATCACAATG 57.908 47.619 33.68 8.86 35.64 2.82
128 129 1.945394 GAGCACTAGAACATGGCCATG 59.055 52.381 38.53 38.53 44.15 3.66
129 130 1.133976 GGAGCACTAGAACATGGCCAT 60.134 52.381 14.09 14.09 0.00 4.40
130 131 0.253044 GGAGCACTAGAACATGGCCA 59.747 55.000 8.56 8.56 0.00 5.36
131 132 0.253044 TGGAGCACTAGAACATGGCC 59.747 55.000 0.00 0.00 0.00 5.36
132 133 1.339055 TGTGGAGCACTAGAACATGGC 60.339 52.381 0.00 0.00 35.11 4.40
133 134 2.027745 ACTGTGGAGCACTAGAACATGG 60.028 50.000 0.00 0.00 35.11 3.66
134 135 3.325293 ACTGTGGAGCACTAGAACATG 57.675 47.619 0.00 0.00 35.11 3.21
135 136 4.528596 AGTAACTGTGGAGCACTAGAACAT 59.471 41.667 0.00 0.00 35.11 2.71
136 137 3.895656 AGTAACTGTGGAGCACTAGAACA 59.104 43.478 0.00 0.00 35.11 3.18
137 138 4.022242 TGAGTAACTGTGGAGCACTAGAAC 60.022 45.833 0.00 0.00 35.11 3.01
138 139 4.022242 GTGAGTAACTGTGGAGCACTAGAA 60.022 45.833 0.00 0.00 35.11 2.10
139 140 3.506455 GTGAGTAACTGTGGAGCACTAGA 59.494 47.826 0.00 0.00 35.11 2.43
140 141 3.255888 TGTGAGTAACTGTGGAGCACTAG 59.744 47.826 0.00 0.00 35.11 2.57
141 142 3.227614 TGTGAGTAACTGTGGAGCACTA 58.772 45.455 0.00 0.00 35.11 2.74
142 143 2.036475 CTGTGAGTAACTGTGGAGCACT 59.964 50.000 0.00 0.00 35.11 4.40
143 144 2.408050 CTGTGAGTAACTGTGGAGCAC 58.592 52.381 0.00 0.00 34.56 4.40
144 145 1.270305 GCTGTGAGTAACTGTGGAGCA 60.270 52.381 0.00 0.00 0.00 4.26
145 146 1.270305 TGCTGTGAGTAACTGTGGAGC 60.270 52.381 0.00 0.00 0.00 4.70
146 147 2.802816 GTTGCTGTGAGTAACTGTGGAG 59.197 50.000 0.00 0.00 37.74 3.86
147 148 2.801699 CGTTGCTGTGAGTAACTGTGGA 60.802 50.000 0.00 0.00 38.44 4.02
148 149 1.526887 CGTTGCTGTGAGTAACTGTGG 59.473 52.381 0.00 0.00 38.44 4.17
149 150 1.070577 GCGTTGCTGTGAGTAACTGTG 60.071 52.381 0.00 0.00 38.44 3.66
150 151 1.217882 GCGTTGCTGTGAGTAACTGT 58.782 50.000 0.00 0.00 38.44 3.55
151 152 0.161658 CGCGTTGCTGTGAGTAACTG 59.838 55.000 0.00 0.00 38.44 3.16
152 153 0.031585 TCGCGTTGCTGTGAGTAACT 59.968 50.000 5.77 0.00 38.44 2.24
153 154 0.161024 GTCGCGTTGCTGTGAGTAAC 59.839 55.000 5.77 0.00 37.44 2.50
154 155 1.272784 CGTCGCGTTGCTGTGAGTAA 61.273 55.000 5.77 0.00 0.00 2.24
155 156 1.728074 CGTCGCGTTGCTGTGAGTA 60.728 57.895 5.77 0.00 0.00 2.59
156 157 3.030308 CGTCGCGTTGCTGTGAGT 61.030 61.111 5.77 0.00 0.00 3.41
157 158 2.710971 CTCGTCGCGTTGCTGTGAG 61.711 63.158 5.77 0.46 0.00 3.51
158 159 2.120355 TACTCGTCGCGTTGCTGTGA 62.120 55.000 5.77 0.00 0.00 3.58
159 160 1.272784 TTACTCGTCGCGTTGCTGTG 61.273 55.000 5.77 0.00 0.00 3.66
160 161 1.002250 CTTACTCGTCGCGTTGCTGT 61.002 55.000 5.77 2.92 0.00 4.40
161 162 0.728129 TCTTACTCGTCGCGTTGCTG 60.728 55.000 5.77 0.00 0.00 4.41
162 163 0.454620 CTCTTACTCGTCGCGTTGCT 60.455 55.000 5.77 0.00 0.00 3.91
163 164 1.403972 CCTCTTACTCGTCGCGTTGC 61.404 60.000 5.77 0.00 0.00 4.17
164 165 0.167470 TCCTCTTACTCGTCGCGTTG 59.833 55.000 5.77 0.00 0.00 4.10
165 166 0.877071 TTCCTCTTACTCGTCGCGTT 59.123 50.000 5.77 0.00 0.00 4.84
166 167 0.447011 CTTCCTCTTACTCGTCGCGT 59.553 55.000 5.77 0.00 0.00 6.01
167 168 0.447011 ACTTCCTCTTACTCGTCGCG 59.553 55.000 0.00 0.00 0.00 5.87
168 169 2.251893 CAACTTCCTCTTACTCGTCGC 58.748 52.381 0.00 0.00 0.00 5.19
169 170 2.864968 CCAACTTCCTCTTACTCGTCG 58.135 52.381 0.00 0.00 0.00 5.12
170 171 2.029290 TGCCAACTTCCTCTTACTCGTC 60.029 50.000 0.00 0.00 0.00 4.20
171 172 1.968493 TGCCAACTTCCTCTTACTCGT 59.032 47.619 0.00 0.00 0.00 4.18
172 173 2.743636 TGCCAACTTCCTCTTACTCG 57.256 50.000 0.00 0.00 0.00 4.18
173 174 2.744741 GCTTGCCAACTTCCTCTTACTC 59.255 50.000 0.00 0.00 0.00 2.59
174 175 2.784347 GCTTGCCAACTTCCTCTTACT 58.216 47.619 0.00 0.00 0.00 2.24
175 176 1.464997 CGCTTGCCAACTTCCTCTTAC 59.535 52.381 0.00 0.00 0.00 2.34
176 177 1.808411 CGCTTGCCAACTTCCTCTTA 58.192 50.000 0.00 0.00 0.00 2.10
177 178 1.518903 GCGCTTGCCAACTTCCTCTT 61.519 55.000 0.00 0.00 0.00 2.85
178 179 1.968540 GCGCTTGCCAACTTCCTCT 60.969 57.895 0.00 0.00 0.00 3.69
179 180 2.260869 TGCGCTTGCCAACTTCCTC 61.261 57.895 9.73 0.00 38.03 3.71
180 181 2.203337 TGCGCTTGCCAACTTCCT 60.203 55.556 9.73 0.00 38.03 3.36
181 182 2.050077 GTGCGCTTGCCAACTTCC 60.050 61.111 9.73 0.00 38.03 3.46
182 183 1.065600 TTGTGCGCTTGCCAACTTC 59.934 52.632 9.73 0.00 38.03 3.01
183 184 1.226945 GTTGTGCGCTTGCCAACTT 60.227 52.632 9.73 0.00 42.00 2.66
184 185 2.412937 GTTGTGCGCTTGCCAACT 59.587 55.556 9.73 0.00 42.00 3.16
185 186 3.024043 CGTTGTGCGCTTGCCAAC 61.024 61.111 9.73 14.66 41.91 3.77
186 187 4.263209 CCGTTGTGCGCTTGCCAA 62.263 61.111 9.73 3.53 39.71 4.52
189 190 4.629115 AAGCCGTTGTGCGCTTGC 62.629 61.111 9.73 1.97 39.71 4.01
190 191 2.392613 AAGAAGCCGTTGTGCGCTTG 62.393 55.000 9.73 0.00 37.19 4.01
191 192 2.186826 AAGAAGCCGTTGTGCGCTT 61.187 52.632 9.73 0.00 38.76 4.68
192 193 2.591715 AAGAAGCCGTTGTGCGCT 60.592 55.556 9.73 0.00 39.71 5.92
193 194 2.427410 CAAGAAGCCGTTGTGCGC 60.427 61.111 0.00 0.00 39.71 6.09
194 195 2.252260 CCAAGAAGCCGTTGTGCG 59.748 61.111 0.00 0.00 40.95 5.34
195 196 2.050077 GCCAAGAAGCCGTTGTGC 60.050 61.111 0.00 0.00 0.00 4.57
196 197 1.283793 CTGCCAAGAAGCCGTTGTG 59.716 57.895 0.00 0.00 0.00 3.33
197 198 1.898574 CCTGCCAAGAAGCCGTTGT 60.899 57.895 0.00 0.00 0.00 3.32
198 199 1.898574 ACCTGCCAAGAAGCCGTTG 60.899 57.895 0.00 0.00 0.00 4.10
199 200 1.898574 CACCTGCCAAGAAGCCGTT 60.899 57.895 0.00 0.00 0.00 4.44
200 201 1.764571 TACACCTGCCAAGAAGCCGT 61.765 55.000 0.00 0.00 0.00 5.68
201 202 1.003839 TACACCTGCCAAGAAGCCG 60.004 57.895 0.00 0.00 0.00 5.52
202 203 1.298859 CGTACACCTGCCAAGAAGCC 61.299 60.000 0.00 0.00 0.00 4.35
203 204 0.320421 TCGTACACCTGCCAAGAAGC 60.320 55.000 0.00 0.00 0.00 3.86
204 205 2.002586 CATCGTACACCTGCCAAGAAG 58.997 52.381 0.00 0.00 0.00 2.85
205 206 1.621317 TCATCGTACACCTGCCAAGAA 59.379 47.619 0.00 0.00 0.00 2.52
206 207 1.262417 TCATCGTACACCTGCCAAGA 58.738 50.000 0.00 0.00 0.00 3.02
207 208 2.093306 TTCATCGTACACCTGCCAAG 57.907 50.000 0.00 0.00 0.00 3.61
208 209 2.290008 ACATTCATCGTACACCTGCCAA 60.290 45.455 0.00 0.00 0.00 4.52
209 210 1.277842 ACATTCATCGTACACCTGCCA 59.722 47.619 0.00 0.00 0.00 4.92
210 211 1.665679 CACATTCATCGTACACCTGCC 59.334 52.381 0.00 0.00 0.00 4.85
211 212 1.062587 GCACATTCATCGTACACCTGC 59.937 52.381 0.00 0.00 0.00 4.85
212 213 1.324435 CGCACATTCATCGTACACCTG 59.676 52.381 0.00 0.00 0.00 4.00
213 214 1.640428 CGCACATTCATCGTACACCT 58.360 50.000 0.00 0.00 0.00 4.00
214 215 0.026285 GCGCACATTCATCGTACACC 59.974 55.000 0.30 0.00 0.00 4.16
215 216 0.314259 CGCGCACATTCATCGTACAC 60.314 55.000 8.75 0.00 0.00 2.90
216 217 1.995228 CGCGCACATTCATCGTACA 59.005 52.632 8.75 0.00 0.00 2.90
217 218 1.366494 GCGCGCACATTCATCGTAC 60.366 57.895 29.10 0.00 0.00 3.67
218 219 2.521771 GGCGCGCACATTCATCGTA 61.522 57.895 34.42 0.00 0.00 3.43
219 220 3.864686 GGCGCGCACATTCATCGT 61.865 61.111 34.42 0.00 0.00 3.73
220 221 4.596180 GGGCGCGCACATTCATCG 62.596 66.667 34.42 0.00 0.00 3.84
221 222 3.173390 GAGGGCGCGCACATTCATC 62.173 63.158 37.52 20.53 0.00 2.92
222 223 3.204827 GAGGGCGCGCACATTCAT 61.205 61.111 37.52 15.34 0.00 2.57
223 224 4.393155 AGAGGGCGCGCACATTCA 62.393 61.111 37.52 0.00 0.00 2.57
224 225 3.869272 CAGAGGGCGCGCACATTC 61.869 66.667 37.52 25.40 0.00 2.67
225 226 4.704833 ACAGAGGGCGCGCACATT 62.705 61.111 37.52 20.69 0.00 2.71
231 232 4.504916 CAGGAGACAGAGGGCGCG 62.505 72.222 0.00 0.00 0.00 6.86
232 233 4.154347 CCAGGAGACAGAGGGCGC 62.154 72.222 0.00 0.00 0.00 6.53
233 234 4.154347 GCCAGGAGACAGAGGGCG 62.154 72.222 0.00 0.00 34.56 6.13
234 235 2.250741 GAAGCCAGGAGACAGAGGGC 62.251 65.000 0.00 0.00 44.92 5.19
235 236 0.617249 AGAAGCCAGGAGACAGAGGG 60.617 60.000 0.00 0.00 0.00 4.30
236 237 0.823460 GAGAAGCCAGGAGACAGAGG 59.177 60.000 0.00 0.00 0.00 3.69
237 238 1.554836 TGAGAAGCCAGGAGACAGAG 58.445 55.000 0.00 0.00 0.00 3.35
238 239 1.829849 CATGAGAAGCCAGGAGACAGA 59.170 52.381 0.00 0.00 0.00 3.41
239 240 1.134461 CCATGAGAAGCCAGGAGACAG 60.134 57.143 0.00 0.00 0.00 3.51
240 241 0.907486 CCATGAGAAGCCAGGAGACA 59.093 55.000 0.00 0.00 0.00 3.41
241 242 1.138661 CTCCATGAGAAGCCAGGAGAC 59.861 57.143 0.00 0.00 46.89 3.36
242 243 1.493861 CTCCATGAGAAGCCAGGAGA 58.506 55.000 0.00 0.00 46.89 3.71
243 244 0.179051 GCTCCATGAGAAGCCAGGAG 60.179 60.000 0.00 0.00 46.71 3.69
244 245 0.619832 AGCTCCATGAGAAGCCAGGA 60.620 55.000 10.04 0.00 0.00 3.86
245 246 1.126488 TAGCTCCATGAGAAGCCAGG 58.874 55.000 10.04 0.00 0.00 4.45
246 247 1.537776 CGTAGCTCCATGAGAAGCCAG 60.538 57.143 10.04 1.24 0.00 4.85
247 248 0.461548 CGTAGCTCCATGAGAAGCCA 59.538 55.000 10.04 0.00 0.00 4.75
248 249 3.280920 CGTAGCTCCATGAGAAGCC 57.719 57.895 10.04 0.00 0.00 4.35
262 263 1.069765 CCTGCTATGGGGTGCGTAG 59.930 63.158 0.00 0.00 0.00 3.51
263 264 3.101796 GCCTGCTATGGGGTGCGTA 62.102 63.158 0.00 0.00 0.00 4.42
264 265 4.489771 GCCTGCTATGGGGTGCGT 62.490 66.667 0.00 0.00 0.00 5.24
309 310 4.363990 AGTGTGAGCTGCCGTCGG 62.364 66.667 6.99 6.99 0.00 4.79
310 311 2.755542 AAGAGTGTGAGCTGCCGTCG 62.756 60.000 0.00 0.00 0.00 5.12
311 312 1.005630 AAGAGTGTGAGCTGCCGTC 60.006 57.895 0.00 0.00 0.00 4.79
312 313 1.301244 CAAGAGTGTGAGCTGCCGT 60.301 57.895 0.00 0.00 0.00 5.68
313 314 1.301244 ACAAGAGTGTGAGCTGCCG 60.301 57.895 0.00 0.00 36.31 5.69
314 315 4.787871 ACAAGAGTGTGAGCTGCC 57.212 55.556 0.00 0.00 36.31 4.85
335 336 2.751837 GGAAAGAGCGGCCCTTGG 60.752 66.667 0.00 0.00 0.00 3.61
336 337 1.746991 GAGGAAAGAGCGGCCCTTG 60.747 63.158 0.00 0.00 0.00 3.61
337 338 2.190488 CTGAGGAAAGAGCGGCCCTT 62.190 60.000 0.00 0.00 0.00 3.95
338 339 2.607750 TGAGGAAAGAGCGGCCCT 60.608 61.111 0.00 0.00 0.00 5.19
339 340 2.124942 CTGAGGAAAGAGCGGCCC 60.125 66.667 0.00 0.00 0.00 5.80
340 341 1.743252 CACTGAGGAAAGAGCGGCC 60.743 63.158 0.00 0.00 0.00 6.13
341 342 0.739112 CTCACTGAGGAAAGAGCGGC 60.739 60.000 0.00 0.00 0.00 6.53
342 343 0.891373 TCTCACTGAGGAAAGAGCGG 59.109 55.000 6.20 0.00 0.00 5.52
343 344 1.730772 CGTCTCACTGAGGAAAGAGCG 60.731 57.143 6.20 0.00 32.72 5.03
344 345 1.271102 ACGTCTCACTGAGGAAAGAGC 59.729 52.381 6.20 0.00 34.87 4.09
345 346 3.651803 AACGTCTCACTGAGGAAAGAG 57.348 47.619 6.20 0.00 34.87 2.85
346 347 4.142790 AGTAACGTCTCACTGAGGAAAGA 58.857 43.478 6.20 0.00 34.87 2.52
347 348 4.506886 AGTAACGTCTCACTGAGGAAAG 57.493 45.455 6.20 0.00 34.87 2.62
348 349 4.583489 AGAAGTAACGTCTCACTGAGGAAA 59.417 41.667 6.20 0.00 34.87 3.13
349 350 4.142790 AGAAGTAACGTCTCACTGAGGAA 58.857 43.478 6.20 0.00 34.87 3.36
350 351 3.752222 GAGAAGTAACGTCTCACTGAGGA 59.248 47.826 6.20 0.00 41.08 3.71
351 352 3.502595 TGAGAAGTAACGTCTCACTGAGG 59.497 47.826 10.54 0.00 45.11 3.86
352 353 4.717991 CTGAGAAGTAACGTCTCACTGAG 58.282 47.826 10.54 0.00 45.11 3.35
353 354 3.058155 GCTGAGAAGTAACGTCTCACTGA 60.058 47.826 10.54 0.00 45.11 3.41
354 355 3.238441 GCTGAGAAGTAACGTCTCACTG 58.762 50.000 10.54 4.82 45.11 3.66
355 356 2.095668 CGCTGAGAAGTAACGTCTCACT 60.096 50.000 10.54 0.00 45.11 3.41
356 357 2.095869 TCGCTGAGAAGTAACGTCTCAC 60.096 50.000 10.54 7.71 45.11 3.51
358 359 2.160022 ACTCGCTGAGAAGTAACGTCTC 59.840 50.000 11.64 5.78 41.66 3.36
359 360 2.152830 ACTCGCTGAGAAGTAACGTCT 58.847 47.619 11.64 0.00 33.32 4.18
360 361 2.615489 ACTCGCTGAGAAGTAACGTC 57.385 50.000 11.64 0.00 33.32 4.34
361 362 4.494350 TTTACTCGCTGAGAAGTAACGT 57.506 40.909 11.64 0.00 33.32 3.99
362 363 5.721510 GCAATTTACTCGCTGAGAAGTAACG 60.722 44.000 11.64 0.00 33.32 3.18
363 364 5.120208 TGCAATTTACTCGCTGAGAAGTAAC 59.880 40.000 11.64 0.00 33.32 2.50
364 365 5.120208 GTGCAATTTACTCGCTGAGAAGTAA 59.880 40.000 11.64 4.42 33.32 2.24
365 366 4.625742 GTGCAATTTACTCGCTGAGAAGTA 59.374 41.667 11.64 0.00 33.32 2.24
366 367 3.433615 GTGCAATTTACTCGCTGAGAAGT 59.566 43.478 11.64 0.00 33.32 3.01
367 368 3.433274 TGTGCAATTTACTCGCTGAGAAG 59.567 43.478 11.64 0.00 33.32 2.85
368 369 3.398406 TGTGCAATTTACTCGCTGAGAA 58.602 40.909 11.64 0.00 33.32 2.87
369 370 2.995939 CTGTGCAATTTACTCGCTGAGA 59.004 45.455 11.64 0.00 33.32 3.27
370 371 2.995939 TCTGTGCAATTTACTCGCTGAG 59.004 45.455 0.00 4.36 35.52 3.35
371 372 3.038788 TCTGTGCAATTTACTCGCTGA 57.961 42.857 0.00 0.00 0.00 4.26
372 373 3.187227 ACTTCTGTGCAATTTACTCGCTG 59.813 43.478 0.00 0.00 0.00 5.18
373 374 3.403038 ACTTCTGTGCAATTTACTCGCT 58.597 40.909 0.00 0.00 0.00 4.93
374 375 3.813529 ACTTCTGTGCAATTTACTCGC 57.186 42.857 0.00 0.00 0.00 5.03
396 397 4.802307 TGCTTCCAATGCCCTAATTATGA 58.198 39.130 0.00 0.00 0.00 2.15
399 400 4.518278 TCTGCTTCCAATGCCCTAATTA 57.482 40.909 0.00 0.00 0.00 1.40
404 405 1.481871 CAATCTGCTTCCAATGCCCT 58.518 50.000 0.00 0.00 0.00 5.19
456 457 0.251653 ACGTCTAGCCCCAGACTTGA 60.252 55.000 8.56 0.00 42.36 3.02
989 990 1.817350 CGCTCCTCATGGCTCTCTCTA 60.817 57.143 0.00 0.00 0.00 2.43
1545 1603 2.299013 ACACGAAGACTGATGGCTACAA 59.701 45.455 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.