Multiple sequence alignment - TraesCS3A01G064300

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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 TraesCS3A01G064300 chr3A 100.000 3782 0 0 1 3782 38254916 38251135 0.000000e+00 6985.0
1 TraesCS3A01G064300 chr3A 89.596 1509 97 24 1610 3076 38021525 38020035 0.000000e+00 1862.0
2 TraesCS3A01G064300 chr3A 89.447 1393 120 19 2398 3782 38236382 38235009 0.000000e+00 1733.0
3 TraesCS3A01G064300 chr3A 89.658 1286 106 17 1614 2887 38035726 38034456 0.000000e+00 1613.0
4 TraesCS3A01G064300 chr3A 82.860 1832 275 24 886 2697 10531988 10530176 0.000000e+00 1607.0
5 TraesCS3A01G064300 chr3A 73.286 700 158 25 891 1578 38036555 38035873 2.940000e-56 230.0
6 TraesCS3A01G064300 chr3A 89.256 121 12 1 522 642 38261237 38261118 2.350000e-32 150.0
7 TraesCS3A01G064300 chr3A 84.286 70 6 3 173 242 38261916 38261852 3.150000e-06 63.9
8 TraesCS3A01G064300 chr3B 93.607 2925 142 27 520 3413 47455111 47452201 0.000000e+00 4324.0
9 TraesCS3A01G064300 chr3B 86.380 1997 183 43 1610 3539 46282218 46284192 0.000000e+00 2098.0
10 TraesCS3A01G064300 chr3B 88.675 830 63 13 1 819 50349642 50350451 0.000000e+00 983.0
11 TraesCS3A01G064300 chr3B 94.485 272 12 3 845 1115 50355817 50356086 2.100000e-112 416.0
12 TraesCS3A01G064300 chr3B 82.461 382 31 7 3408 3782 47451918 47451566 6.140000e-78 302.0
13 TraesCS3A01G064300 chr3B 92.683 82 6 0 446 527 126580068 126580149 6.640000e-23 119.0
14 TraesCS3A01G064300 chr3B 90.476 84 8 0 444 527 680423381 680423298 1.110000e-20 111.0
15 TraesCS3A01G064300 chr3D 92.902 2860 151 26 589 3413 28495957 28493115 0.000000e+00 4109.0
16 TraesCS3A01G064300 chr3D 81.615 2948 381 89 706 3552 27655823 27658710 0.000000e+00 2292.0
17 TraesCS3A01G064300 chr3D 90.342 1315 111 5 1004 2314 27760363 27761665 0.000000e+00 1711.0
18 TraesCS3A01G064300 chr3D 89.195 1379 109 21 1610 2973 28129977 28128624 0.000000e+00 1685.0
19 TraesCS3A01G064300 chr3D 91.361 1227 83 12 1610 2827 28134804 28133592 0.000000e+00 1657.0
20 TraesCS3A01G064300 chr3D 85.800 1000 84 27 2308 3276 27870005 27870977 0.000000e+00 1007.0
21 TraesCS3A01G064300 chr3D 78.409 704 93 30 2947 3601 28133570 28132877 1.640000e-108 403.0
22 TraesCS3A01G064300 chr3D 85.333 375 23 14 3408 3782 28492830 28492488 3.590000e-95 359.0
23 TraesCS3A01G064300 chr3D 84.839 310 28 11 202 509 28496405 28496113 1.030000e-75 294.0
24 TraesCS3A01G064300 chr3D 79.692 325 36 15 706 1013 27759592 27759903 1.380000e-49 207.0
25 TraesCS3A01G064300 chr3D 90.741 54 3 2 506 558 28495999 28495947 1.880000e-08 71.3
26 TraesCS3A01G064300 chr1B 91.860 86 7 0 445 530 120657925 120657840 1.850000e-23 121.0
27 TraesCS3A01G064300 chr2A 90.476 84 8 0 444 527 4969535 4969452 1.110000e-20 111.0
28 TraesCS3A01G064300 chr2A 90.588 85 7 1 444 527 509547586 509547670 1.110000e-20 111.0
29 TraesCS3A01G064300 chr2A 90.588 85 7 1 444 527 593655910 593655994 1.110000e-20 111.0
30 TraesCS3A01G064300 chr7D 89.535 86 8 1 444 529 548774774 548774690 1.440000e-19 108.0


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 TraesCS3A01G064300 chr3A 38251135 38254916 3781 True 6985.000000 6985 100.000000 1 3782 1 chr3A.!!$R4 3781
1 TraesCS3A01G064300 chr3A 38020035 38021525 1490 True 1862.000000 1862 89.596000 1610 3076 1 chr3A.!!$R2 1466
2 TraesCS3A01G064300 chr3A 38235009 38236382 1373 True 1733.000000 1733 89.447000 2398 3782 1 chr3A.!!$R3 1384
3 TraesCS3A01G064300 chr3A 10530176 10531988 1812 True 1607.000000 1607 82.860000 886 2697 1 chr3A.!!$R1 1811
4 TraesCS3A01G064300 chr3A 38034456 38036555 2099 True 921.500000 1613 81.472000 891 2887 2 chr3A.!!$R5 1996
5 TraesCS3A01G064300 chr3B 47451566 47455111 3545 True 2313.000000 4324 88.034000 520 3782 2 chr3B.!!$R2 3262
6 TraesCS3A01G064300 chr3B 46282218 46284192 1974 False 2098.000000 2098 86.380000 1610 3539 1 chr3B.!!$F1 1929
7 TraesCS3A01G064300 chr3B 50349642 50350451 809 False 983.000000 983 88.675000 1 819 1 chr3B.!!$F2 818
8 TraesCS3A01G064300 chr3D 27655823 27658710 2887 False 2292.000000 2292 81.615000 706 3552 1 chr3D.!!$F1 2846
9 TraesCS3A01G064300 chr3D 28128624 28134804 6180 True 1248.333333 1685 86.321667 1610 3601 3 chr3D.!!$R1 1991
10 TraesCS3A01G064300 chr3D 28492488 28496405 3917 True 1208.325000 4109 88.453750 202 3782 4 chr3D.!!$R2 3580
11 TraesCS3A01G064300 chr3D 27870005 27870977 972 False 1007.000000 1007 85.800000 2308 3276 1 chr3D.!!$F2 968
12 TraesCS3A01G064300 chr3D 27759592 27761665 2073 False 959.000000 1711 85.017000 706 2314 2 chr3D.!!$F3 1608

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
132 133 0.036164 ACGGGTGCAAGCAAGTATCA 59.964 50.0 0.00 0.00 34.77 2.15 F
293 294 0.176680 GAGCGGATCAGCAAGGAAGA 59.823 55.0 20.15 0.00 40.15 2.87 F
1415 2047 0.251474 TACTGCTGTACCGGGACTGT 60.251 55.0 23.23 15.74 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 2153 0.965363 CCTTGTATTTGGTGCCGGCT 60.965 55.000 29.7 8.67 0.00 5.52 R
2118 2873 2.125552 CGCGTGCTCCAATCCAGA 60.126 61.111 0.0 0.00 0.00 3.86 R
3077 3890 0.400213 AGTTTGTCCCTCGGATTGCA 59.600 50.000 0.0 0.00 32.73 4.08 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
33 34 2.750948 GACACACTGTATGTTCACCGT 58.249 47.619 0.00 0.00 40.64 4.83
45 46 2.992124 TTCACCGTTGAACTCTTCCA 57.008 45.000 0.00 0.00 36.79 3.53
46 47 2.234300 TCACCGTTGAACTCTTCCAC 57.766 50.000 0.00 0.00 0.00 4.02
47 48 1.483004 TCACCGTTGAACTCTTCCACA 59.517 47.619 0.00 0.00 0.00 4.17
48 49 1.597663 CACCGTTGAACTCTTCCACAC 59.402 52.381 0.00 0.00 0.00 3.82
49 50 1.485066 ACCGTTGAACTCTTCCACACT 59.515 47.619 0.00 0.00 0.00 3.55
50 51 2.135933 CCGTTGAACTCTTCCACACTC 58.864 52.381 0.00 0.00 0.00 3.51
51 52 2.224066 CCGTTGAACTCTTCCACACTCT 60.224 50.000 0.00 0.00 0.00 3.24
52 53 2.797156 CGTTGAACTCTTCCACACTCTG 59.203 50.000 0.00 0.00 0.00 3.35
53 54 3.738281 CGTTGAACTCTTCCACACTCTGT 60.738 47.826 0.00 0.00 0.00 3.41
54 55 4.192317 GTTGAACTCTTCCACACTCTGTT 58.808 43.478 0.00 0.00 0.00 3.16
55 56 5.357257 GTTGAACTCTTCCACACTCTGTTA 58.643 41.667 0.00 0.00 0.00 2.41
56 57 5.201713 TGAACTCTTCCACACTCTGTTAG 57.798 43.478 0.00 0.00 0.00 2.34
57 58 3.669251 ACTCTTCCACACTCTGTTAGC 57.331 47.619 0.00 0.00 0.00 3.09
58 59 3.235200 ACTCTTCCACACTCTGTTAGCT 58.765 45.455 0.00 0.00 0.00 3.32
59 60 3.006323 ACTCTTCCACACTCTGTTAGCTG 59.994 47.826 0.00 0.00 0.00 4.24
60 61 2.965831 TCTTCCACACTCTGTTAGCTGT 59.034 45.455 0.00 0.00 0.00 4.40
61 62 3.005897 TCTTCCACACTCTGTTAGCTGTC 59.994 47.826 0.00 0.00 0.00 3.51
62 63 2.316108 TCCACACTCTGTTAGCTGTCA 58.684 47.619 0.00 0.00 0.00 3.58
63 64 2.035961 TCCACACTCTGTTAGCTGTCAC 59.964 50.000 0.00 0.00 0.00 3.67
64 65 2.224042 CCACACTCTGTTAGCTGTCACA 60.224 50.000 0.00 0.00 0.00 3.58
65 66 3.055591 CACACTCTGTTAGCTGTCACAG 58.944 50.000 13.68 13.68 41.65 3.66
66 67 2.036475 ACACTCTGTTAGCTGTCACAGG 59.964 50.000 17.69 12.63 40.81 4.00
67 68 2.297315 CACTCTGTTAGCTGTCACAGGA 59.703 50.000 17.69 0.00 40.81 3.86
68 69 2.560542 ACTCTGTTAGCTGTCACAGGAG 59.439 50.000 17.69 5.97 40.81 3.69
69 70 1.273606 TCTGTTAGCTGTCACAGGAGC 59.726 52.381 17.69 0.00 40.81 4.70
70 71 0.321671 TGTTAGCTGTCACAGGAGCC 59.678 55.000 7.00 0.00 35.69 4.70
71 72 0.391793 GTTAGCTGTCACAGGAGCCC 60.392 60.000 7.00 0.00 35.69 5.19
72 73 0.545309 TTAGCTGTCACAGGAGCCCT 60.545 55.000 7.00 0.00 35.69 5.19
73 74 0.335019 TAGCTGTCACAGGAGCCCTA 59.665 55.000 7.00 0.00 35.69 3.53
74 75 1.219393 GCTGTCACAGGAGCCCTAC 59.781 63.158 7.00 0.00 29.64 3.18
75 76 1.261238 GCTGTCACAGGAGCCCTACT 61.261 60.000 7.00 0.00 29.64 2.57
76 77 0.534412 CTGTCACAGGAGCCCTACTG 59.466 60.000 5.98 5.98 46.90 2.74
77 78 1.219393 GTCACAGGAGCCCTACTGC 59.781 63.158 7.43 0.00 45.43 4.40
78 79 1.229177 TCACAGGAGCCCTACTGCA 60.229 57.895 7.43 0.00 45.43 4.41
79 80 0.835971 TCACAGGAGCCCTACTGCAA 60.836 55.000 7.43 0.00 45.43 4.08
80 81 0.674895 CACAGGAGCCCTACTGCAAC 60.675 60.000 7.43 0.00 45.43 4.17
81 82 0.838122 ACAGGAGCCCTACTGCAACT 60.838 55.000 7.43 0.00 45.43 3.16
82 83 0.326264 CAGGAGCCCTACTGCAACTT 59.674 55.000 0.00 0.00 39.69 2.66
83 84 1.068121 AGGAGCCCTACTGCAACTTT 58.932 50.000 0.00 0.00 39.69 2.66
84 85 1.168714 GGAGCCCTACTGCAACTTTG 58.831 55.000 0.00 0.00 36.57 2.77
98 99 3.945179 CAACTTTGCAACTCAGAGTGAC 58.055 45.455 3.05 0.00 38.99 3.67
99 100 3.550437 ACTTTGCAACTCAGAGTGACT 57.450 42.857 3.05 0.00 38.54 3.41
100 101 3.462021 ACTTTGCAACTCAGAGTGACTC 58.538 45.455 3.05 3.98 38.54 3.36
101 102 3.133721 ACTTTGCAACTCAGAGTGACTCT 59.866 43.478 9.77 9.77 42.11 3.24
114 115 6.031751 AGAGTGACTCTGATTCAGGTTAAC 57.968 41.667 15.39 11.68 39.62 2.01
115 116 4.810790 AGTGACTCTGATTCAGGTTAACG 58.189 43.478 13.59 0.00 31.51 3.18
116 117 3.927142 GTGACTCTGATTCAGGTTAACGG 59.073 47.826 13.59 0.00 31.51 4.44
117 118 3.056107 TGACTCTGATTCAGGTTAACGGG 60.056 47.826 13.59 0.00 31.51 5.28
118 119 2.904434 ACTCTGATTCAGGTTAACGGGT 59.096 45.455 13.59 0.00 31.51 5.28
119 120 3.262420 CTCTGATTCAGGTTAACGGGTG 58.738 50.000 13.59 0.00 31.51 4.61
120 121 1.737793 CTGATTCAGGTTAACGGGTGC 59.262 52.381 5.73 0.00 0.00 5.01
121 122 1.072489 TGATTCAGGTTAACGGGTGCA 59.928 47.619 0.00 0.00 0.00 4.57
122 123 2.156098 GATTCAGGTTAACGGGTGCAA 58.844 47.619 0.00 0.00 0.00 4.08
123 124 1.600023 TTCAGGTTAACGGGTGCAAG 58.400 50.000 0.00 0.00 0.00 4.01
124 125 0.887387 TCAGGTTAACGGGTGCAAGC 60.887 55.000 0.00 0.00 0.00 4.01
125 126 1.149627 AGGTTAACGGGTGCAAGCA 59.850 52.632 0.00 0.00 34.77 3.91
126 127 0.466555 AGGTTAACGGGTGCAAGCAA 60.467 50.000 0.00 0.00 34.77 3.91
127 128 0.039527 GGTTAACGGGTGCAAGCAAG 60.040 55.000 0.00 0.00 34.77 4.01
128 129 0.666374 GTTAACGGGTGCAAGCAAGT 59.334 50.000 0.00 0.00 34.77 3.16
129 130 1.874872 GTTAACGGGTGCAAGCAAGTA 59.125 47.619 0.00 0.00 34.77 2.24
130 131 2.483014 TAACGGGTGCAAGCAAGTAT 57.517 45.000 0.00 0.00 34.77 2.12
131 132 1.165270 AACGGGTGCAAGCAAGTATC 58.835 50.000 0.00 0.00 34.77 2.24
132 133 0.036164 ACGGGTGCAAGCAAGTATCA 59.964 50.000 0.00 0.00 34.77 2.15
133 134 1.340017 ACGGGTGCAAGCAAGTATCAT 60.340 47.619 0.00 0.00 34.77 2.45
134 135 2.093181 ACGGGTGCAAGCAAGTATCATA 60.093 45.455 0.00 0.00 34.77 2.15
135 136 2.942376 CGGGTGCAAGCAAGTATCATAA 59.058 45.455 0.00 0.00 34.77 1.90
136 137 3.242739 CGGGTGCAAGCAAGTATCATAAC 60.243 47.826 0.00 0.00 34.77 1.89
137 138 3.242739 GGGTGCAAGCAAGTATCATAACG 60.243 47.826 0.00 0.00 34.77 3.18
138 139 3.354397 GTGCAAGCAAGTATCATAACGC 58.646 45.455 0.00 0.00 0.00 4.84
139 140 3.006247 TGCAAGCAAGTATCATAACGCA 58.994 40.909 0.00 0.00 0.00 5.24
140 141 3.181511 TGCAAGCAAGTATCATAACGCAC 60.182 43.478 0.00 0.00 0.00 5.34
141 142 3.597324 CAAGCAAGTATCATAACGCACG 58.403 45.455 0.00 0.00 0.00 5.34
142 143 1.593006 AGCAAGTATCATAACGCACGC 59.407 47.619 0.00 0.00 0.00 5.34
143 144 1.326245 GCAAGTATCATAACGCACGCA 59.674 47.619 0.00 0.00 0.00 5.24
144 145 2.845764 GCAAGTATCATAACGCACGCAC 60.846 50.000 0.00 0.00 0.00 5.34
145 146 2.287393 AGTATCATAACGCACGCACA 57.713 45.000 0.00 0.00 0.00 4.57
146 147 2.821546 AGTATCATAACGCACGCACAT 58.178 42.857 0.00 0.00 0.00 3.21
147 148 2.539688 AGTATCATAACGCACGCACATG 59.460 45.455 0.00 0.00 0.00 3.21
148 149 0.657312 ATCATAACGCACGCACATGG 59.343 50.000 0.00 0.00 0.00 3.66
149 150 1.583451 CATAACGCACGCACATGGC 60.583 57.895 0.00 0.00 39.90 4.40
150 151 2.037702 ATAACGCACGCACATGGCA 61.038 52.632 0.00 0.00 45.17 4.92
151 152 1.980951 ATAACGCACGCACATGGCAG 61.981 55.000 0.00 0.00 45.17 4.85
153 154 4.746951 CGCACGCACATGGCAGTG 62.747 66.667 17.71 17.71 45.17 3.66
154 155 3.356267 GCACGCACATGGCAGTGA 61.356 61.111 22.13 0.00 44.32 3.41
155 156 2.693762 GCACGCACATGGCAGTGAT 61.694 57.895 22.13 5.32 44.32 3.06
156 157 1.135939 CACGCACATGGCAGTGATG 59.864 57.895 17.47 11.80 44.32 3.07
157 158 2.042259 ACGCACATGGCAGTGATGG 61.042 57.895 17.47 9.86 45.17 3.51
158 159 2.493030 GCACATGGCAGTGATGGC 59.507 61.111 17.47 8.40 42.05 4.40
164 165 2.512515 GGCAGTGATGGCCGTCTC 60.513 66.667 25.20 21.30 42.39 3.36
165 166 2.581354 GCAGTGATGGCCGTCTCT 59.419 61.111 25.20 23.19 0.00 3.10
166 167 1.078848 GCAGTGATGGCCGTCTCTT 60.079 57.895 23.83 8.45 0.00 2.85
167 168 1.086634 GCAGTGATGGCCGTCTCTTC 61.087 60.000 23.83 17.05 0.00 2.87
168 169 0.247460 CAGTGATGGCCGTCTCTTCA 59.753 55.000 23.83 2.97 0.00 3.02
169 170 0.534412 AGTGATGGCCGTCTCTTCAG 59.466 55.000 25.20 0.00 0.00 3.02
170 171 1.086634 GTGATGGCCGTCTCTTCAGC 61.087 60.000 25.20 0.00 0.00 4.26
171 172 1.260538 TGATGGCCGTCTCTTCAGCT 61.261 55.000 25.20 0.00 0.00 4.24
172 173 0.529555 GATGGCCGTCTCTTCAGCTC 60.530 60.000 18.25 0.00 0.00 4.09
173 174 1.260538 ATGGCCGTCTCTTCAGCTCA 61.261 55.000 0.00 0.00 0.00 4.26
174 175 1.446966 GGCCGTCTCTTCAGCTCAC 60.447 63.158 0.00 0.00 0.00 3.51
175 176 1.446966 GCCGTCTCTTCAGCTCACC 60.447 63.158 0.00 0.00 0.00 4.02
176 177 1.153939 CCGTCTCTTCAGCTCACCG 60.154 63.158 0.00 0.00 0.00 4.94
177 178 1.803519 CGTCTCTTCAGCTCACCGC 60.804 63.158 0.00 0.00 39.57 5.68
186 187 2.358003 GCTCACCGCTGTCAGCTT 60.358 61.111 22.13 6.63 39.60 3.74
187 188 2.386660 GCTCACCGCTGTCAGCTTC 61.387 63.158 22.13 1.87 39.60 3.86
188 189 1.005748 CTCACCGCTGTCAGCTTCA 60.006 57.895 22.13 3.22 39.60 3.02
189 190 1.005748 TCACCGCTGTCAGCTTCAG 60.006 57.895 22.13 10.67 39.60 3.02
200 201 4.500265 GCTTCAGCTTGACCCCAA 57.500 55.556 0.00 0.00 38.21 4.12
213 214 2.203625 CCCAACCCAACCACCAGG 60.204 66.667 0.00 0.00 42.21 4.45
254 255 5.601662 TCTTCACTCTTGACCTTTACTGTG 58.398 41.667 0.00 0.00 0.00 3.66
255 256 4.336889 TCACTCTTGACCTTTACTGTGG 57.663 45.455 0.00 0.00 0.00 4.17
288 289 4.121691 CTGGAGCGGATCAGCAAG 57.878 61.111 20.15 10.20 40.15 4.01
289 290 1.523258 CTGGAGCGGATCAGCAAGG 60.523 63.158 20.15 3.53 40.15 3.61
290 291 1.964608 CTGGAGCGGATCAGCAAGGA 61.965 60.000 20.15 0.13 40.15 3.36
291 292 1.221840 GGAGCGGATCAGCAAGGAA 59.778 57.895 20.15 0.00 40.15 3.36
292 293 0.813210 GGAGCGGATCAGCAAGGAAG 60.813 60.000 20.15 0.00 40.15 3.46
293 294 0.176680 GAGCGGATCAGCAAGGAAGA 59.823 55.000 20.15 0.00 40.15 2.87
294 295 0.615331 AGCGGATCAGCAAGGAAGAA 59.385 50.000 20.15 0.00 40.15 2.52
295 296 1.003580 AGCGGATCAGCAAGGAAGAAA 59.996 47.619 20.15 0.00 40.15 2.52
296 297 1.399791 GCGGATCAGCAAGGAAGAAAG 59.600 52.381 13.30 0.00 37.05 2.62
297 298 2.936993 GCGGATCAGCAAGGAAGAAAGA 60.937 50.000 13.30 0.00 37.05 2.52
306 307 2.325583 AGGAAGAAAGACGTGCAACA 57.674 45.000 0.00 0.00 35.74 3.33
309 310 2.286418 GGAAGAAAGACGTGCAACACAG 60.286 50.000 0.00 0.00 35.74 3.66
310 311 2.309528 AGAAAGACGTGCAACACAGA 57.690 45.000 0.00 0.00 35.74 3.41
353 355 2.095263 ACATGCCGCAGTGTGTTTTATC 60.095 45.455 2.46 0.00 0.00 1.75
372 374 9.701355 GTTTTATCCATGTGAAAACACAAAAAG 57.299 29.630 16.30 0.00 40.91 2.27
373 375 9.658799 TTTTATCCATGTGAAAACACAAAAAGA 57.341 25.926 7.12 3.20 38.69 2.52
377 379 8.558973 TCCATGTGAAAACACAAAAAGAAAAT 57.441 26.923 7.12 0.00 38.69 1.82
386 388 9.586435 AAAACACAAAAAGAAAATCCTACTCTG 57.414 29.630 0.00 0.00 0.00 3.35
390 392 7.857885 CACAAAAAGAAAATCCTACTCTGTGAC 59.142 37.037 0.00 0.00 0.00 3.67
396 398 2.281539 TCCTACTCTGTGACGGTGAA 57.718 50.000 0.00 0.00 0.00 3.18
427 429 6.977502 CCAAACTGTGTGTTTTATTCATGTGA 59.022 34.615 0.00 0.00 45.69 3.58
448 450 3.391506 AAACACCTACGTAACACTCCC 57.608 47.619 0.00 0.00 0.00 4.30
449 451 2.299326 ACACCTACGTAACACTCCCT 57.701 50.000 0.00 0.00 0.00 4.20
450 452 2.165998 ACACCTACGTAACACTCCCTC 58.834 52.381 0.00 0.00 0.00 4.30
451 453 2.224967 ACACCTACGTAACACTCCCTCT 60.225 50.000 0.00 0.00 0.00 3.69
457 459 4.715527 ACGTAACACTCCCTCTGTAATC 57.284 45.455 0.00 0.00 0.00 1.75
486 489 7.829378 ATAAGACGTTTTTAGAGTCCATGAC 57.171 36.000 0.00 0.00 35.65 3.06
487 490 4.235360 AGACGTTTTTAGAGTCCATGACG 58.765 43.478 0.00 0.00 37.67 4.35
554 673 1.274798 GATTTGGCACCGTGTTTGCG 61.275 55.000 0.00 0.00 41.18 4.85
555 674 2.010582 ATTTGGCACCGTGTTTGCGT 62.011 50.000 0.00 0.00 41.18 5.24
575 694 3.119531 CGTATTCCTTGCAGCCAAAATCA 60.120 43.478 0.00 0.00 0.00 2.57
584 703 2.409378 GCAGCCAAAATCATCAAACACG 59.591 45.455 0.00 0.00 0.00 4.49
603 722 8.621487 CAAACACGTTAGTTATACGGATATACG 58.379 37.037 5.59 5.59 42.99 3.06
611 730 7.108841 AGTTATACGGATATACGGATGCAAT 57.891 36.000 15.77 0.00 38.05 3.56
613 732 8.038944 AGTTATACGGATATACGGATGCAATTT 58.961 33.333 15.77 0.00 38.05 1.82
622 741 2.637382 ACGGATGCAATTTCCCCTTTTT 59.363 40.909 0.00 0.00 0.00 1.94
666 792 7.551035 AATAATTTGCAAGCAAACAAGTTCA 57.449 28.000 21.04 0.00 46.80 3.18
779 907 4.074970 CTGCTTATCCCACACAACTCTTT 58.925 43.478 0.00 0.00 0.00 2.52
780 910 4.469657 TGCTTATCCCACACAACTCTTTT 58.530 39.130 0.00 0.00 0.00 2.27
898 1060 2.520741 CCGCTCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
899 1061 2.600731 CGCTCCTCCTCCTCCTCT 59.399 66.667 0.00 0.00 0.00 3.69
900 1062 1.528309 CGCTCCTCCTCCTCCTCTC 60.528 68.421 0.00 0.00 0.00 3.20
912 1074 2.197324 CCTCTCCCTCCTCCTCCG 59.803 72.222 0.00 0.00 0.00 4.63
1046 1678 2.738521 CCTCAACACGGGCGACAG 60.739 66.667 0.00 0.00 0.00 3.51
1226 1858 4.367450 CAGGATTTCTTCGACATCTCCTC 58.633 47.826 0.00 0.00 29.31 3.71
1255 1887 0.888736 CTTCAACGTGCCCATGGACA 60.889 55.000 15.22 4.40 0.00 4.02
1256 1888 0.466372 TTCAACGTGCCCATGGACAA 60.466 50.000 15.22 0.00 0.00 3.18
1413 2045 2.576298 GTACTGCTGTACCGGGACT 58.424 57.895 19.95 0.00 42.25 3.85
1415 2047 0.251474 TACTGCTGTACCGGGACTGT 60.251 55.000 23.23 15.74 0.00 3.55
1521 2153 1.108727 CCAGCACTTTCAGTTGCCCA 61.109 55.000 0.00 0.00 0.00 5.36
1643 2386 4.337836 GCCAACAACCATGAAACCAAAATT 59.662 37.500 0.00 0.00 0.00 1.82
1959 2711 4.039124 GGTCAGGGCAAAAGAGAATTTTCA 59.961 41.667 0.00 0.00 0.00 2.69
2023 2775 4.761739 TGGTGAGATTGATTGGTTTCTGTC 59.238 41.667 0.00 0.00 0.00 3.51
2028 2780 5.634118 AGATTGATTGGTTTCTGTCCAGAA 58.366 37.500 5.64 5.64 44.94 3.02
2117 2872 2.485814 GACATGACAAGGTTGCTTCTCC 59.514 50.000 0.00 0.00 0.00 3.71
2118 2873 2.107204 ACATGACAAGGTTGCTTCTCCT 59.893 45.455 0.00 0.00 35.34 3.69
2119 2874 2.550830 TGACAAGGTTGCTTCTCCTC 57.449 50.000 0.00 0.00 33.09 3.71
2373 3128 3.057969 TGGTTGACATCACAGATCACC 57.942 47.619 0.00 0.00 0.00 4.02
2609 3372 2.229543 TGTGGTGCTTGCAGATTGATTC 59.770 45.455 0.00 0.00 0.00 2.52
2780 3543 1.223077 AGATGTATCAGGCCCCAGGTA 59.777 52.381 0.00 0.00 0.00 3.08
2827 3592 4.137116 AGCCAATTAGATTGTGCGTAGA 57.863 40.909 0.58 0.00 39.67 2.59
2831 3596 5.502544 GCCAATTAGATTGTGCGTAGAAGAC 60.503 44.000 0.58 0.00 38.59 3.01
2833 3598 6.313905 CCAATTAGATTGTGCGTAGAAGACTT 59.686 38.462 0.00 0.00 38.59 3.01
2834 3599 7.491372 CCAATTAGATTGTGCGTAGAAGACTTA 59.509 37.037 0.00 0.00 38.59 2.24
2835 3600 9.035607 CAATTAGATTGTGCGTAGAAGACTTAT 57.964 33.333 0.00 0.00 35.57 1.73
2841 3606 6.583912 TGTGCGTAGAAGACTTATTTATGC 57.416 37.500 9.48 9.48 0.00 3.14
2845 3611 6.257849 TGCGTAGAAGACTTATTTATGCAAGG 59.742 38.462 13.92 0.00 34.39 3.61
2943 3713 4.041567 TCTCAGTATTGCAAACCTTCCTCA 59.958 41.667 1.71 0.00 0.00 3.86
2946 3716 4.520492 CAGTATTGCAAACCTTCCTCAGTT 59.480 41.667 1.71 0.00 0.00 3.16
2974 3744 8.562892 ACAACAGATGAACTCATTTTTACTCTG 58.437 33.333 0.00 0.00 36.57 3.35
2980 3772 8.682936 ATGAACTCATTTTTACTCTGTTGAGT 57.317 30.769 4.11 4.11 43.89 3.41
3033 3832 7.443575 AGCTATCATGGCTGAAATTACTAACAG 59.556 37.037 0.00 0.00 38.73 3.16
3042 3841 9.923143 GGCTGAAATTACTAACAGGTTTTAAAT 57.077 29.630 0.00 0.00 0.00 1.40
3058 3858 6.072728 GGTTTTAAATTTCCCATTGCTCCAAC 60.073 38.462 0.00 0.00 0.00 3.77
3077 3890 7.346751 TCCAACAAAGCAGAGAAGTAAATTT 57.653 32.000 0.00 0.00 0.00 1.82
3093 3906 2.214376 ATTTGCAATCCGAGGGACAA 57.786 45.000 0.00 0.00 32.98 3.18
3121 3936 2.024176 ACACCGATCAGTTGGTATGC 57.976 50.000 0.00 0.00 40.32 3.14
3167 3982 0.403655 TGCAGCATTTCCACTGGGTA 59.596 50.000 0.00 0.00 34.38 3.69
3182 4004 6.003950 CCACTGGGTATTTATGACATTAGGG 58.996 44.000 0.00 0.00 0.00 3.53
3191 4013 2.113860 TGACATTAGGGACAGCTTGC 57.886 50.000 0.00 0.00 0.00 4.01
3202 4025 2.560105 GGACAGCTTGCTTTCCTCAAAT 59.440 45.455 17.66 0.00 0.00 2.32
3221 4044 2.276732 TGGAGAAAAGGTGGCTCAAG 57.723 50.000 0.00 0.00 0.00 3.02
3236 4059 3.074412 GCTCAAGCCTTGTTGTAAGCTA 58.926 45.455 4.04 0.00 34.49 3.32
3237 4060 3.691609 GCTCAAGCCTTGTTGTAAGCTAT 59.308 43.478 4.04 0.00 34.49 2.97
3252 4075 7.057149 TGTAAGCTATTTACGAGAAAACTGC 57.943 36.000 0.00 0.00 43.78 4.40
3319 4192 5.862924 TTGATGAGATGTTTCTTCGTTCC 57.137 39.130 0.00 0.00 30.30 3.62
3334 4207 2.154462 CGTTCCTGCTTCCATTGACTT 58.846 47.619 0.00 0.00 0.00 3.01
3339 4214 4.096681 TCCTGCTTCCATTGACTTAGAGA 58.903 43.478 0.00 0.00 0.00 3.10
3345 4220 8.181904 TGCTTCCATTGACTTAGAGAATTTTT 57.818 30.769 0.00 0.00 0.00 1.94
3442 4610 8.538409 AAATGTAGCTTGCAAATTTAAGGAAG 57.462 30.769 0.00 5.68 36.43 3.46
3471 4640 8.383175 ACAGTAAATTTCCTAGATTTGTCCAGA 58.617 33.333 0.00 0.00 0.00 3.86
3510 4684 6.480524 TCATTTTCATCAGTTAAGGTCACG 57.519 37.500 0.00 0.00 0.00 4.35
3571 4754 5.382664 GGTTTCCCCTCATATGGTTCTTA 57.617 43.478 2.13 0.00 0.00 2.10
3572 4755 5.131067 GGTTTCCCCTCATATGGTTCTTAC 58.869 45.833 2.13 0.00 0.00 2.34
3673 4856 5.472148 ACTTGTAATCGTATTCAACACCGA 58.528 37.500 0.00 0.00 0.00 4.69
3674 4857 6.103997 ACTTGTAATCGTATTCAACACCGAT 58.896 36.000 0.00 0.00 41.41 4.18
3675 4858 5.959652 TGTAATCGTATTCAACACCGATG 57.040 39.130 0.00 0.00 39.73 3.84
3676 4859 4.806775 TGTAATCGTATTCAACACCGATGG 59.193 41.667 0.00 0.00 39.73 3.51
3677 4860 2.303163 TCGTATTCAACACCGATGGG 57.697 50.000 0.00 0.00 40.11 4.00
3678 4861 0.655733 CGTATTCAACACCGATGGGC 59.344 55.000 0.00 0.00 36.48 5.36
3679 4862 0.655733 GTATTCAACACCGATGGGCG 59.344 55.000 0.00 0.00 36.48 6.13
3680 4863 0.537653 TATTCAACACCGATGGGCGA 59.462 50.000 0.00 0.00 44.57 5.54
3738 4922 6.620877 TTGGAACAGTATCCTACAAGTCAT 57.379 37.500 0.00 0.00 42.39 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.487714 AACAGAGTGTGGAAGAGTTCAA 57.512 40.909 0.00 0.00 0.00 2.69
40 41 3.243873 TGACAGCTAACAGAGTGTGGAAG 60.244 47.826 0.00 0.00 0.00 3.46
41 42 2.698274 TGACAGCTAACAGAGTGTGGAA 59.302 45.455 0.00 0.00 0.00 3.53
42 43 2.035961 GTGACAGCTAACAGAGTGTGGA 59.964 50.000 0.00 0.00 0.00 4.02
43 44 2.224042 TGTGACAGCTAACAGAGTGTGG 60.224 50.000 0.00 0.00 0.00 4.17
44 45 3.055591 CTGTGACAGCTAACAGAGTGTG 58.944 50.000 15.03 0.00 45.43 3.82
45 46 2.036475 CCTGTGACAGCTAACAGAGTGT 59.964 50.000 19.68 0.00 45.43 3.55
46 47 2.297315 TCCTGTGACAGCTAACAGAGTG 59.703 50.000 19.68 10.03 45.43 3.51
47 48 2.560542 CTCCTGTGACAGCTAACAGAGT 59.439 50.000 19.68 0.00 45.43 3.24
48 49 2.673610 GCTCCTGTGACAGCTAACAGAG 60.674 54.545 19.68 14.30 45.43 3.35
49 50 1.273606 GCTCCTGTGACAGCTAACAGA 59.726 52.381 19.68 6.89 45.43 3.41
50 51 1.674221 GGCTCCTGTGACAGCTAACAG 60.674 57.143 7.16 13.75 42.83 3.16
51 52 0.321671 GGCTCCTGTGACAGCTAACA 59.678 55.000 7.16 0.00 35.82 2.41
52 53 0.391793 GGGCTCCTGTGACAGCTAAC 60.392 60.000 7.16 0.00 35.82 2.34
53 54 0.545309 AGGGCTCCTGTGACAGCTAA 60.545 55.000 7.16 0.00 35.82 3.09
54 55 0.335019 TAGGGCTCCTGTGACAGCTA 59.665 55.000 7.16 0.00 35.82 3.32
55 56 1.079256 TAGGGCTCCTGTGACAGCT 59.921 57.895 7.16 0.85 35.82 4.24
56 57 1.219393 GTAGGGCTCCTGTGACAGC 59.781 63.158 7.16 0.00 34.61 4.40
57 58 0.534412 CAGTAGGGCTCCTGTGACAG 59.466 60.000 5.42 5.42 34.61 3.51
58 59 1.544825 GCAGTAGGGCTCCTGTGACA 61.545 60.000 4.16 0.00 34.61 3.58
59 60 1.219393 GCAGTAGGGCTCCTGTGAC 59.781 63.158 4.16 0.00 34.61 3.67
60 61 0.835971 TTGCAGTAGGGCTCCTGTGA 60.836 55.000 4.16 0.00 34.61 3.58
61 62 0.674895 GTTGCAGTAGGGCTCCTGTG 60.675 60.000 4.16 3.36 34.61 3.66
62 63 0.838122 AGTTGCAGTAGGGCTCCTGT 60.838 55.000 4.16 0.00 34.61 4.00
63 64 0.326264 AAGTTGCAGTAGGGCTCCTG 59.674 55.000 4.16 0.00 34.61 3.86
64 65 1.068121 AAAGTTGCAGTAGGGCTCCT 58.932 50.000 0.00 0.00 37.71 3.69
65 66 1.168714 CAAAGTTGCAGTAGGGCTCC 58.831 55.000 0.00 0.00 34.04 4.70
76 77 7.696813 GAGTCACTCTGAGTTGCAAAGTTGC 62.697 48.000 7.77 9.11 41.35 4.17
77 78 3.624861 AGTCACTCTGAGTTGCAAAGTTG 59.375 43.478 7.77 0.00 0.00 3.16
78 79 3.873952 GAGTCACTCTGAGTTGCAAAGTT 59.126 43.478 7.77 0.00 28.50 2.66
79 80 3.133721 AGAGTCACTCTGAGTTGCAAAGT 59.866 43.478 6.50 0.00 39.62 2.66
80 81 3.726607 AGAGTCACTCTGAGTTGCAAAG 58.273 45.455 6.50 0.00 39.62 2.77
81 82 3.827008 AGAGTCACTCTGAGTTGCAAA 57.173 42.857 6.50 0.00 39.62 3.68
91 92 5.336055 CGTTAACCTGAATCAGAGTCACTCT 60.336 44.000 12.53 0.00 42.11 3.24
92 93 4.859798 CGTTAACCTGAATCAGAGTCACTC 59.140 45.833 12.53 0.00 32.44 3.51
93 94 4.322049 CCGTTAACCTGAATCAGAGTCACT 60.322 45.833 12.53 0.00 32.44 3.41
94 95 3.927142 CCGTTAACCTGAATCAGAGTCAC 59.073 47.826 12.53 7.66 32.44 3.67
95 96 3.056107 CCCGTTAACCTGAATCAGAGTCA 60.056 47.826 12.53 0.00 32.44 3.41
96 97 3.056035 ACCCGTTAACCTGAATCAGAGTC 60.056 47.826 12.53 0.00 32.44 3.36
97 98 2.904434 ACCCGTTAACCTGAATCAGAGT 59.096 45.455 12.53 5.22 32.44 3.24
98 99 3.262420 CACCCGTTAACCTGAATCAGAG 58.738 50.000 12.53 4.56 32.44 3.35
99 100 2.614481 GCACCCGTTAACCTGAATCAGA 60.614 50.000 12.53 0.00 32.44 3.27
100 101 1.737793 GCACCCGTTAACCTGAATCAG 59.262 52.381 2.68 2.68 0.00 2.90
101 102 1.072489 TGCACCCGTTAACCTGAATCA 59.928 47.619 0.00 0.00 0.00 2.57
102 103 1.816074 TGCACCCGTTAACCTGAATC 58.184 50.000 0.00 0.00 0.00 2.52
103 104 2.159382 CTTGCACCCGTTAACCTGAAT 58.841 47.619 0.00 0.00 0.00 2.57
104 105 1.600023 CTTGCACCCGTTAACCTGAA 58.400 50.000 0.00 0.00 0.00 3.02
105 106 0.887387 GCTTGCACCCGTTAACCTGA 60.887 55.000 0.00 0.00 0.00 3.86
106 107 1.169661 TGCTTGCACCCGTTAACCTG 61.170 55.000 0.00 0.00 0.00 4.00
107 108 0.466555 TTGCTTGCACCCGTTAACCT 60.467 50.000 0.00 0.00 0.00 3.50
108 109 0.039527 CTTGCTTGCACCCGTTAACC 60.040 55.000 0.00 0.00 0.00 2.85
109 110 0.666374 ACTTGCTTGCACCCGTTAAC 59.334 50.000 0.00 0.00 0.00 2.01
110 111 2.257691 TACTTGCTTGCACCCGTTAA 57.742 45.000 0.00 0.00 0.00 2.01
111 112 2.289756 TGATACTTGCTTGCACCCGTTA 60.290 45.455 0.00 0.00 0.00 3.18
112 113 1.165270 GATACTTGCTTGCACCCGTT 58.835 50.000 0.00 0.00 0.00 4.44
113 114 0.036164 TGATACTTGCTTGCACCCGT 59.964 50.000 0.00 0.00 0.00 5.28
114 115 1.382522 ATGATACTTGCTTGCACCCG 58.617 50.000 0.00 0.00 0.00 5.28
115 116 3.242739 CGTTATGATACTTGCTTGCACCC 60.243 47.826 0.00 0.00 0.00 4.61
116 117 3.788797 GCGTTATGATACTTGCTTGCACC 60.789 47.826 0.00 0.00 0.00 5.01
117 118 3.181511 TGCGTTATGATACTTGCTTGCAC 60.182 43.478 0.00 0.00 0.00 4.57
118 119 3.006247 TGCGTTATGATACTTGCTTGCA 58.994 40.909 0.00 0.00 0.00 4.08
119 120 3.354397 GTGCGTTATGATACTTGCTTGC 58.646 45.455 0.00 0.00 0.00 4.01
120 121 3.597324 CGTGCGTTATGATACTTGCTTG 58.403 45.455 0.00 0.00 0.00 4.01
121 122 2.030457 GCGTGCGTTATGATACTTGCTT 59.970 45.455 0.00 0.00 0.00 3.91
122 123 1.593006 GCGTGCGTTATGATACTTGCT 59.407 47.619 0.00 0.00 0.00 3.91
123 124 1.326245 TGCGTGCGTTATGATACTTGC 59.674 47.619 0.00 0.00 0.00 4.01
124 125 2.347150 TGTGCGTGCGTTATGATACTTG 59.653 45.455 0.00 0.00 0.00 3.16
125 126 2.612604 TGTGCGTGCGTTATGATACTT 58.387 42.857 0.00 0.00 0.00 2.24
126 127 2.287393 TGTGCGTGCGTTATGATACT 57.713 45.000 0.00 0.00 0.00 2.12
127 128 2.348498 CCATGTGCGTGCGTTATGATAC 60.348 50.000 0.00 0.00 0.00 2.24
128 129 1.864082 CCATGTGCGTGCGTTATGATA 59.136 47.619 0.00 0.00 0.00 2.15
129 130 0.657312 CCATGTGCGTGCGTTATGAT 59.343 50.000 0.00 0.00 0.00 2.45
130 131 1.976478 GCCATGTGCGTGCGTTATGA 61.976 55.000 0.00 0.00 0.00 2.15
131 132 1.583451 GCCATGTGCGTGCGTTATG 60.583 57.895 0.00 0.00 0.00 1.90
132 133 1.980951 CTGCCATGTGCGTGCGTTAT 61.981 55.000 0.00 0.00 45.60 1.89
133 134 2.666526 TGCCATGTGCGTGCGTTA 60.667 55.556 0.00 0.00 45.60 3.18
134 135 4.029186 CTGCCATGTGCGTGCGTT 62.029 61.111 0.00 0.00 45.60 4.84
136 137 4.746951 CACTGCCATGTGCGTGCG 62.747 66.667 13.44 0.00 45.60 5.34
137 138 2.693762 ATCACTGCCATGTGCGTGC 61.694 57.895 17.45 5.50 45.60 5.34
138 139 1.135939 CATCACTGCCATGTGCGTG 59.864 57.895 16.77 16.77 45.60 5.34
139 140 2.042259 CCATCACTGCCATGTGCGT 61.042 57.895 0.00 0.00 45.60 5.24
140 141 2.795973 CCATCACTGCCATGTGCG 59.204 61.111 0.00 0.00 45.60 5.34
141 142 2.493030 GCCATCACTGCCATGTGC 59.507 61.111 0.00 0.00 37.81 4.57
147 148 2.512515 GAGACGGCCATCACTGCC 60.513 66.667 0.00 0.00 45.70 4.85
148 149 1.078848 AAGAGACGGCCATCACTGC 60.079 57.895 0.00 0.00 0.00 4.40
149 150 0.247460 TGAAGAGACGGCCATCACTG 59.753 55.000 0.00 0.00 0.00 3.66
150 151 0.534412 CTGAAGAGACGGCCATCACT 59.466 55.000 0.00 0.00 0.00 3.41
151 152 1.086634 GCTGAAGAGACGGCCATCAC 61.087 60.000 0.00 0.00 36.30 3.06
152 153 1.219124 GCTGAAGAGACGGCCATCA 59.781 57.895 0.00 0.00 36.30 3.07
153 154 0.529555 GAGCTGAAGAGACGGCCATC 60.530 60.000 2.24 0.00 42.44 3.51
154 155 1.260538 TGAGCTGAAGAGACGGCCAT 61.261 55.000 2.24 0.00 42.44 4.40
155 156 1.908299 TGAGCTGAAGAGACGGCCA 60.908 57.895 2.24 0.00 42.44 5.36
156 157 1.446966 GTGAGCTGAAGAGACGGCC 60.447 63.158 0.00 0.00 42.44 6.13
157 158 1.446966 GGTGAGCTGAAGAGACGGC 60.447 63.158 0.00 0.00 41.86 5.68
158 159 1.153939 CGGTGAGCTGAAGAGACGG 60.154 63.158 0.00 0.00 0.00 4.79
159 160 1.803519 GCGGTGAGCTGAAGAGACG 60.804 63.158 0.00 0.00 44.04 4.18
160 161 4.177229 GCGGTGAGCTGAAGAGAC 57.823 61.111 0.00 0.00 44.04 3.36
183 184 1.527433 GGTTGGGGTCAAGCTGAAGC 61.527 60.000 0.00 0.00 45.10 3.86
184 185 0.895559 GGGTTGGGGTCAAGCTGAAG 60.896 60.000 7.98 0.00 46.98 3.02
185 186 1.152830 GGGTTGGGGTCAAGCTGAA 59.847 57.895 7.98 0.00 46.98 3.02
186 187 1.650242 TTGGGTTGGGGTCAAGCTGA 61.650 55.000 7.98 0.00 46.98 4.26
187 188 1.152567 TTGGGTTGGGGTCAAGCTG 60.153 57.895 7.98 0.00 46.98 4.24
188 189 1.152546 GTTGGGTTGGGGTCAAGCT 60.153 57.895 7.98 0.00 46.98 3.74
190 191 1.112916 GTGGTTGGGTTGGGGTCAAG 61.113 60.000 0.00 0.00 32.92 3.02
191 192 1.075896 GTGGTTGGGTTGGGGTCAA 60.076 57.895 0.00 0.00 0.00 3.18
192 193 2.604152 GTGGTTGGGTTGGGGTCA 59.396 61.111 0.00 0.00 0.00 4.02
193 194 2.203582 GGTGGTTGGGTTGGGGTC 60.204 66.667 0.00 0.00 0.00 4.46
194 195 3.030611 TGGTGGTTGGGTTGGGGT 61.031 61.111 0.00 0.00 0.00 4.95
195 196 2.203625 CTGGTGGTTGGGTTGGGG 60.204 66.667 0.00 0.00 0.00 4.96
196 197 2.203625 CCTGGTGGTTGGGTTGGG 60.204 66.667 0.00 0.00 0.00 4.12
197 198 1.832167 CACCTGGTGGTTGGGTTGG 60.832 63.158 19.23 0.00 46.05 3.77
198 199 2.498056 GCACCTGGTGGTTGGGTTG 61.498 63.158 27.02 0.00 46.05 3.77
199 200 2.123468 GCACCTGGTGGTTGGGTT 60.123 61.111 27.02 0.00 46.05 4.11
200 201 3.103213 AGCACCTGGTGGTTGGGT 61.103 61.111 24.92 2.71 46.05 4.51
215 216 4.225208 GTGAAGATCACTTTGCAAGAAGC 58.775 43.478 0.00 0.00 43.73 3.86
233 234 4.703897 CCACAGTAAAGGTCAAGAGTGAA 58.296 43.478 0.00 0.00 34.87 3.18
234 235 3.494398 GCCACAGTAAAGGTCAAGAGTGA 60.494 47.826 0.00 0.00 0.00 3.41
235 236 2.808543 GCCACAGTAAAGGTCAAGAGTG 59.191 50.000 0.00 0.00 0.00 3.51
243 244 2.100749 GCTTTGTTGCCACAGTAAAGGT 59.899 45.455 3.77 0.00 33.22 3.50
246 247 3.492309 CCATGCTTTGTTGCCACAGTAAA 60.492 43.478 0.00 0.00 33.22 2.01
249 250 0.390124 CCATGCTTTGTTGCCACAGT 59.610 50.000 0.00 0.00 33.22 3.55
254 255 4.584688 GCTCCATGCTTTGTTGCC 57.415 55.556 0.00 0.00 38.95 4.52
272 273 1.552799 TTCCTTGCTGATCCGCTCCA 61.553 55.000 10.62 0.00 0.00 3.86
276 277 1.399791 CTTTCTTCCTTGCTGATCCGC 59.600 52.381 1.59 1.59 0.00 5.54
277 278 2.675348 GTCTTTCTTCCTTGCTGATCCG 59.325 50.000 0.00 0.00 0.00 4.18
279 280 3.124297 CACGTCTTTCTTCCTTGCTGATC 59.876 47.826 0.00 0.00 0.00 2.92
281 282 2.483876 CACGTCTTTCTTCCTTGCTGA 58.516 47.619 0.00 0.00 0.00 4.26
282 283 1.069636 GCACGTCTTTCTTCCTTGCTG 60.070 52.381 0.00 0.00 0.00 4.41
284 285 0.944386 TGCACGTCTTTCTTCCTTGC 59.056 50.000 0.00 0.00 0.00 4.01
285 286 2.354510 TGTTGCACGTCTTTCTTCCTTG 59.645 45.455 0.00 0.00 0.00 3.61
286 287 2.354821 GTGTTGCACGTCTTTCTTCCTT 59.645 45.455 0.00 0.00 0.00 3.36
287 288 1.940613 GTGTTGCACGTCTTTCTTCCT 59.059 47.619 0.00 0.00 0.00 3.36
288 289 1.668751 TGTGTTGCACGTCTTTCTTCC 59.331 47.619 0.00 0.00 37.14 3.46
289 290 2.607635 TCTGTGTTGCACGTCTTTCTTC 59.392 45.455 0.00 0.00 37.14 2.87
290 291 2.627945 TCTGTGTTGCACGTCTTTCTT 58.372 42.857 0.00 0.00 37.14 2.52
291 292 2.309528 TCTGTGTTGCACGTCTTTCT 57.690 45.000 0.00 0.00 37.14 2.52
292 293 3.181510 ACTTTCTGTGTTGCACGTCTTTC 60.182 43.478 0.00 0.00 37.14 2.62
293 294 2.747446 ACTTTCTGTGTTGCACGTCTTT 59.253 40.909 0.00 0.00 37.14 2.52
294 295 2.356135 ACTTTCTGTGTTGCACGTCTT 58.644 42.857 0.00 0.00 37.14 3.01
295 296 2.024176 ACTTTCTGTGTTGCACGTCT 57.976 45.000 0.00 0.00 37.14 4.18
296 297 2.825086 AACTTTCTGTGTTGCACGTC 57.175 45.000 0.00 0.00 37.14 4.34
297 298 2.747446 AGAAACTTTCTGTGTTGCACGT 59.253 40.909 3.07 0.00 38.91 4.49
330 331 1.100463 AAACACACTGCGGCATGTCA 61.100 50.000 1.75 0.00 0.00 3.58
372 374 3.927142 CACCGTCACAGAGTAGGATTTTC 59.073 47.826 0.00 0.00 0.00 2.29
373 375 3.576982 TCACCGTCACAGAGTAGGATTTT 59.423 43.478 0.00 0.00 0.00 1.82
377 379 2.281539 TTCACCGTCACAGAGTAGGA 57.718 50.000 0.00 0.00 0.00 2.94
386 388 3.624410 AGTTTGGTAAGTTTCACCGTCAC 59.376 43.478 0.00 0.00 39.04 3.67
390 392 3.375922 ACACAGTTTGGTAAGTTTCACCG 59.624 43.478 0.00 0.00 39.04 4.94
427 429 3.389002 AGGGAGTGTTACGTAGGTGTTTT 59.611 43.478 0.00 0.00 0.00 2.43
437 439 4.985538 AGATTACAGAGGGAGTGTTACG 57.014 45.455 0.00 0.00 0.00 3.18
510 513 9.515226 TCTGAGCAAATACTACCTTTGTAATTT 57.485 29.630 0.00 0.00 36.26 1.82
511 514 9.686683 ATCTGAGCAAATACTACCTTTGTAATT 57.313 29.630 0.00 0.00 36.26 1.40
513 516 9.515226 AAATCTGAGCAAATACTACCTTTGTAA 57.485 29.630 0.00 0.00 36.26 2.41
515 518 7.094205 CCAAATCTGAGCAAATACTACCTTTGT 60.094 37.037 0.00 0.00 36.26 2.83
554 673 4.454728 TGATTTTGGCTGCAAGGAATAC 57.545 40.909 0.50 0.00 0.00 1.89
555 674 4.710865 TGATGATTTTGGCTGCAAGGAATA 59.289 37.500 0.50 0.00 0.00 1.75
584 703 7.475015 TGCATCCGTATATCCGTATAACTAAC 58.525 38.462 0.00 0.00 0.00 2.34
593 712 4.000988 GGAAATTGCATCCGTATATCCGT 58.999 43.478 0.00 0.00 0.00 4.69
622 741 8.995027 ATTATTTATATCTGTGTGGCTTCCAA 57.005 30.769 0.00 0.00 34.18 3.53
629 748 8.971321 GCTTGCAAATTATTTATATCTGTGTGG 58.029 33.333 0.00 0.00 0.00 4.17
666 792 1.729586 TAGGACCAGGCTTGACTGTT 58.270 50.000 0.00 0.00 36.75 3.16
762 890 3.998341 GCGTAAAAGAGTTGTGTGGGATA 59.002 43.478 0.00 0.00 0.00 2.59
898 1060 3.151022 GCACGGAGGAGGAGGGAG 61.151 72.222 0.00 0.00 0.00 4.30
899 1061 3.673597 AGCACGGAGGAGGAGGGA 61.674 66.667 0.00 0.00 0.00 4.20
900 1062 3.465403 CAGCACGGAGGAGGAGGG 61.465 72.222 0.00 0.00 0.00 4.30
1070 1702 4.379243 CGAAGGAGCAGCCCGTGT 62.379 66.667 0.00 0.00 37.37 4.49
1226 1858 1.006102 ACGTTGAAGCCCTCGACAG 60.006 57.895 5.00 1.32 38.25 3.51
1305 1937 1.302383 CCGTTATGTTGGCTCCGCAA 61.302 55.000 0.00 0.00 0.00 4.85
1412 2044 1.007734 CTGCAGTTGCTTGCCACAG 60.008 57.895 5.25 0.00 43.43 3.66
1413 2045 3.121934 CTGCAGTTGCTTGCCACA 58.878 55.556 5.25 0.00 43.43 4.17
1415 2047 2.834043 TGCTGCAGTTGCTTGCCA 60.834 55.556 16.64 0.00 43.43 4.92
1521 2153 0.965363 CCTTGTATTTGGTGCCGGCT 60.965 55.000 29.70 8.67 0.00 5.52
1533 2165 4.850386 AGGGGACAAAAGACTACCTTGTAT 59.150 41.667 0.00 0.00 33.53 2.29
1959 2711 2.787994 CCAATTGTCTGAACCTCTGCT 58.212 47.619 4.43 0.00 0.00 4.24
2023 2775 4.176120 AGAGCCTATGGGATTTTTCTGG 57.824 45.455 0.00 0.00 33.58 3.86
2028 2780 5.669798 ATACCAAGAGCCTATGGGATTTT 57.330 39.130 0.00 0.00 36.88 1.82
2117 2872 2.169789 CGCGTGCTCCAATCCAGAG 61.170 63.158 0.00 0.00 0.00 3.35
2118 2873 2.125552 CGCGTGCTCCAATCCAGA 60.126 61.111 0.00 0.00 0.00 3.86
2119 2874 3.197790 CCGCGTGCTCCAATCCAG 61.198 66.667 4.92 0.00 0.00 3.86
2145 2900 4.660771 AGGCCCTTAGCTATGTGAGTTATT 59.339 41.667 0.00 0.00 43.05 1.40
2373 3128 4.626042 AGCTGTAGATATCTGCCTTTTCG 58.374 43.478 15.79 0.37 0.00 3.46
2780 3543 6.322201 ACCTTTGTCATGATTGTCTCTGTTTT 59.678 34.615 0.00 0.00 0.00 2.43
2827 3592 6.591448 GCTTTTGCCTTGCATAAATAAGTCTT 59.409 34.615 0.00 0.00 38.76 3.01
2845 3611 1.069049 ACAACAGACCATGGCTTTTGC 59.931 47.619 23.50 6.23 46.64 3.68
2946 3716 8.450578 AGTAAAAATGAGTTCATCTGTTGTGA 57.549 30.769 0.00 0.00 35.10 3.58
2974 3744 1.429463 CGCTACAGGTGGAACTCAAC 58.571 55.000 0.00 0.00 36.74 3.18
2980 3772 1.003118 AGATTTGCGCTACAGGTGGAA 59.997 47.619 9.73 0.00 34.09 3.53
3033 3832 5.555966 TGGAGCAATGGGAAATTTAAAACC 58.444 37.500 0.00 0.00 0.00 3.27
3042 3841 2.224257 GCTTTGTTGGAGCAATGGGAAA 60.224 45.455 0.00 0.00 39.89 3.13
3058 3858 7.148689 GGATTGCAAATTTACTTCTCTGCTTTG 60.149 37.037 1.71 0.00 0.00 2.77
3077 3890 0.400213 AGTTTGTCCCTCGGATTGCA 59.600 50.000 0.00 0.00 32.73 4.08
3093 3906 6.235664 ACCAACTGATCGGTGTTTATTAGTT 58.764 36.000 8.25 0.00 33.60 2.24
3167 3982 5.300286 GCAAGCTGTCCCTAATGTCATAAAT 59.700 40.000 0.00 0.00 0.00 1.40
3182 4004 3.572584 CATTTGAGGAAAGCAAGCTGTC 58.427 45.455 3.59 3.59 0.00 3.51
3202 4025 1.819305 GCTTGAGCCACCTTTTCTCCA 60.819 52.381 0.00 0.00 34.31 3.86
3221 4044 5.579511 TCTCGTAAATAGCTTACAACAAGGC 59.420 40.000 0.00 0.00 40.07 4.35
3225 4048 8.492748 CAGTTTTCTCGTAAATAGCTTACAACA 58.507 33.333 0.00 0.00 40.07 3.33
3236 4059 9.394477 GTAGAATTTTGCAGTTTTCTCGTAAAT 57.606 29.630 9.52 0.00 31.29 1.40
3237 4060 8.399425 TGTAGAATTTTGCAGTTTTCTCGTAAA 58.601 29.630 9.52 0.00 31.29 2.01
3319 4192 6.998968 AATTCTCTAAGTCAATGGAAGCAG 57.001 37.500 0.00 0.00 0.00 4.24
3421 4589 8.079809 TGTTACTTCCTTAAATTTGCAAGCTAC 58.920 33.333 0.00 1.31 0.00 3.58
3455 4623 5.763204 GTGTTGTTTCTGGACAAATCTAGGA 59.237 40.000 0.00 0.00 40.86 2.94
3499 4673 1.017177 TGCGGCATCGTGACCTTAAC 61.017 55.000 0.00 0.00 38.89 2.01
3510 4684 1.890979 CCAGGATCTGTGCGGCATC 60.891 63.158 5.72 0.00 0.00 3.91
3571 4754 4.596212 AGGCTAGGTTAGTGTTAGGTTTGT 59.404 41.667 0.00 0.00 0.00 2.83
3572 4755 5.161943 AGGCTAGGTTAGTGTTAGGTTTG 57.838 43.478 0.00 0.00 0.00 2.93
3673 4856 4.115199 GTGCCTCCCTTCGCCCAT 62.115 66.667 0.00 0.00 0.00 4.00
3675 4858 2.265467 TTATGTGCCTCCCTTCGCCC 62.265 60.000 0.00 0.00 0.00 6.13
3676 4859 0.393808 TTTATGTGCCTCCCTTCGCC 60.394 55.000 0.00 0.00 0.00 5.54
3677 4860 1.017387 CTTTATGTGCCTCCCTTCGC 58.983 55.000 0.00 0.00 0.00 4.70
3678 4861 1.209504 TCCTTTATGTGCCTCCCTTCG 59.790 52.381 0.00 0.00 0.00 3.79
3679 4862 2.644676 GTCCTTTATGTGCCTCCCTTC 58.355 52.381 0.00 0.00 0.00 3.46
3680 4863 1.285078 GGTCCTTTATGTGCCTCCCTT 59.715 52.381 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.