Multiple sequence alignment - TraesCS4A01G330100

Loading Multiple Alignment...

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 TraesCS4A01G330100 chr4A 100.000 3182 0 0 1 3182 615108512 615105331 0.000000e+00 5877.0
1 TraesCS4A01G330100 chr5B 93.443 3035 153 18 171 3182 697348118 697345107 0.000000e+00 4460.0
2 TraesCS4A01G330100 chr5D 95.465 2271 95 3 915 3182 553469606 553471871 0.000000e+00 3616.0
3 TraesCS4A01G330100 chr5D 91.066 2317 189 7 875 3182 553461534 553459227 0.000000e+00 3116.0
4 TraesCS4A01G330100 chr5D 90.997 311 15 10 374 673 553465139 553465447 1.060000e-109 407.0
5 TraesCS4A01G330100 chr5D 94.475 181 10 0 2897 3077 553063594 553063774 2.420000e-71 279.0
6 TraesCS4A01G330100 chr5D 90.323 155 15 0 681 835 553469451 553469605 1.500000e-48 204.0
7 TraesCS4A01G330100 chr5D 88.034 117 8 2 512 624 553469334 553469448 1.990000e-27 134.0
8 TraesCS4A01G330100 chr5D 96.552 58 2 0 3125 3182 553063784 553063841 2.610000e-16 97.1
9 TraesCS4A01G330100 chr7D 80.583 103 20 0 1212 1314 459790002 459789900 2.630000e-11 80.5


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 TraesCS4A01G330100 chr4A 615105331 615108512 3181 True 5877.00 5877 100.00000 1 3182 1 chr4A.!!$R1 3181
1 TraesCS4A01G330100 chr5B 697345107 697348118 3011 True 4460.00 4460 93.44300 171 3182 1 chr5B.!!$R1 3011
2 TraesCS4A01G330100 chr5D 553459227 553461534 2307 True 3116.00 3116 91.06600 875 3182 1 chr5D.!!$R1 2307
3 TraesCS4A01G330100 chr5D 553465139 553471871 6732 False 1090.25 3616 91.20475 374 3182 4 chr5D.!!$F2 2808

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
90 91 0.037139 TGGCCACGTGCGTAAGTTAT 60.037 50.0 10.91 0.0 42.61 1.89 F
778 4810 0.179129 CACATGGAAGAAATGGCCGC 60.179 55.0 0.00 0.0 0.00 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 5318 0.252284 GAGAGGAGGGTGAGGTTGGA 60.252 60.0 0.00 0.00 0.0 3.53 R
2647 6686 0.318762 CTAGCGTCCTAGGAATGGGC 59.681 60.0 14.65 14.46 37.9 5.36 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 2.964740 GAAAGGGAAAAAGGCATCTGC 58.035 47.619 0.00 0.00 41.14 4.26
21 22 2.014010 AAGGGAAAAAGGCATCTGCA 57.986 45.000 4.33 0.00 44.36 4.41
22 23 2.242882 AGGGAAAAAGGCATCTGCAT 57.757 45.000 4.33 0.00 44.36 3.96
23 24 3.386932 AGGGAAAAAGGCATCTGCATA 57.613 42.857 4.33 0.00 44.36 3.14
24 25 3.919834 AGGGAAAAAGGCATCTGCATAT 58.080 40.909 4.33 0.00 44.36 1.78
25 26 3.640029 AGGGAAAAAGGCATCTGCATATG 59.360 43.478 7.68 7.68 44.36 1.78
26 27 3.638160 GGGAAAAAGGCATCTGCATATGA 59.362 43.478 15.70 0.00 44.36 2.15
27 28 4.099881 GGGAAAAAGGCATCTGCATATGAA 59.900 41.667 15.70 0.00 44.36 2.57
28 29 5.045872 GGAAAAAGGCATCTGCATATGAAC 58.954 41.667 15.70 7.52 44.36 3.18
29 30 3.976793 AAAGGCATCTGCATATGAACG 57.023 42.857 15.70 0.00 44.36 3.95
30 31 1.233019 AGGCATCTGCATATGAACGC 58.767 50.000 15.70 3.86 44.36 4.84
31 32 0.946528 GGCATCTGCATATGAACGCA 59.053 50.000 15.70 0.00 44.36 5.24
32 33 1.538512 GGCATCTGCATATGAACGCAT 59.461 47.619 15.70 0.00 44.36 4.73
33 34 2.581637 GCATCTGCATATGAACGCATG 58.418 47.619 15.70 2.00 41.59 4.06
34 35 2.581637 CATCTGCATATGAACGCATGC 58.418 47.619 7.91 7.91 46.21 4.06
38 39 2.410785 GCATATGAACGCATGCATGT 57.589 45.000 26.79 8.33 45.51 3.21
39 40 2.313234 GCATATGAACGCATGCATGTC 58.687 47.619 26.79 17.17 45.51 3.06
40 41 2.287129 GCATATGAACGCATGCATGTCA 60.287 45.455 26.79 21.88 45.51 3.58
41 42 3.792794 GCATATGAACGCATGCATGTCAA 60.793 43.478 26.79 13.50 45.51 3.18
42 43 2.554806 ATGAACGCATGCATGTCAAG 57.445 45.000 26.79 17.58 32.31 3.02
43 44 1.237533 TGAACGCATGCATGTCAAGT 58.762 45.000 26.79 18.16 0.00 3.16
44 45 1.608109 TGAACGCATGCATGTCAAGTT 59.392 42.857 26.79 24.04 0.00 2.66
45 46 1.980844 GAACGCATGCATGTCAAGTTG 59.019 47.619 26.79 11.09 0.00 3.16
46 47 0.241749 ACGCATGCATGTCAAGTTGG 59.758 50.000 26.79 9.38 0.00 3.77
47 48 0.457166 CGCATGCATGTCAAGTTGGG 60.457 55.000 26.79 5.46 0.00 4.12
48 49 0.604578 GCATGCATGTCAAGTTGGGT 59.395 50.000 26.79 0.00 0.00 4.51
49 50 1.001181 GCATGCATGTCAAGTTGGGTT 59.999 47.619 26.79 0.00 0.00 4.11
50 51 2.927871 GCATGCATGTCAAGTTGGGTTC 60.928 50.000 26.79 2.60 0.00 3.62
51 52 2.064434 TGCATGTCAAGTTGGGTTCA 57.936 45.000 2.34 0.00 0.00 3.18
52 53 1.955778 TGCATGTCAAGTTGGGTTCAG 59.044 47.619 2.34 0.00 0.00 3.02
53 54 1.270550 GCATGTCAAGTTGGGTTCAGG 59.729 52.381 2.34 1.57 0.00 3.86
54 55 2.862541 CATGTCAAGTTGGGTTCAGGA 58.137 47.619 2.34 0.00 0.00 3.86
55 56 3.221771 CATGTCAAGTTGGGTTCAGGAA 58.778 45.455 2.34 0.00 0.00 3.36
56 57 3.593442 TGTCAAGTTGGGTTCAGGAAT 57.407 42.857 2.34 0.00 0.00 3.01
57 58 4.715534 TGTCAAGTTGGGTTCAGGAATA 57.284 40.909 2.34 0.00 0.00 1.75
58 59 5.055265 TGTCAAGTTGGGTTCAGGAATAA 57.945 39.130 2.34 0.00 0.00 1.40
59 60 5.450453 TGTCAAGTTGGGTTCAGGAATAAA 58.550 37.500 2.34 0.00 0.00 1.40
60 61 5.894393 TGTCAAGTTGGGTTCAGGAATAAAA 59.106 36.000 2.34 0.00 0.00 1.52
61 62 6.183360 TGTCAAGTTGGGTTCAGGAATAAAAC 60.183 38.462 2.34 0.00 0.00 2.43
62 63 6.040504 GTCAAGTTGGGTTCAGGAATAAAACT 59.959 38.462 2.34 0.00 0.00 2.66
63 64 6.609616 TCAAGTTGGGTTCAGGAATAAAACTT 59.390 34.615 2.34 10.52 37.15 2.66
64 65 6.405278 AGTTGGGTTCAGGAATAAAACTTG 57.595 37.500 0.00 0.00 0.00 3.16
65 66 4.864704 TGGGTTCAGGAATAAAACTTGC 57.135 40.909 0.00 0.00 0.00 4.01
66 67 3.576550 TGGGTTCAGGAATAAAACTTGCC 59.423 43.478 0.00 0.00 0.00 4.52
67 68 3.056107 GGGTTCAGGAATAAAACTTGCCC 60.056 47.826 0.00 0.00 0.00 5.36
68 69 3.576550 GGTTCAGGAATAAAACTTGCCCA 59.423 43.478 0.00 0.00 0.00 5.36
69 70 4.039852 GGTTCAGGAATAAAACTTGCCCAA 59.960 41.667 0.00 0.00 0.00 4.12
70 71 5.230182 GTTCAGGAATAAAACTTGCCCAAG 58.770 41.667 6.48 6.48 43.79 3.61
84 85 2.663520 CAAGTGGCCACGTGCGTA 60.664 61.111 33.79 0.00 42.61 4.42
85 86 2.109387 AAGTGGCCACGTGCGTAA 59.891 55.556 29.68 0.00 42.61 3.18
86 87 1.959226 AAGTGGCCACGTGCGTAAG 60.959 57.895 29.68 0.00 42.61 2.34
87 88 2.653953 AAGTGGCCACGTGCGTAAGT 62.654 55.000 29.68 6.44 42.61 2.24
88 89 2.109387 TGGCCACGTGCGTAAGTT 59.891 55.556 10.91 0.00 42.61 2.66
89 90 0.945265 GTGGCCACGTGCGTAAGTTA 60.945 55.000 22.49 0.00 42.61 2.24
90 91 0.037139 TGGCCACGTGCGTAAGTTAT 60.037 50.000 10.91 0.00 42.61 1.89
91 92 0.648958 GGCCACGTGCGTAAGTTATC 59.351 55.000 10.91 0.00 42.61 1.75
92 93 1.636988 GCCACGTGCGTAAGTTATCT 58.363 50.000 10.91 0.00 41.68 1.98
93 94 1.323534 GCCACGTGCGTAAGTTATCTG 59.676 52.381 10.91 0.00 41.68 2.90
94 95 2.602878 CCACGTGCGTAAGTTATCTGT 58.397 47.619 10.91 0.00 41.68 3.41
95 96 3.761657 CCACGTGCGTAAGTTATCTGTA 58.238 45.455 10.91 0.00 41.68 2.74
96 97 3.545078 CCACGTGCGTAAGTTATCTGTAC 59.455 47.826 10.91 0.00 41.68 2.90
97 98 4.160594 CACGTGCGTAAGTTATCTGTACA 58.839 43.478 0.82 0.00 41.68 2.90
98 99 4.796830 CACGTGCGTAAGTTATCTGTACAT 59.203 41.667 0.82 0.00 41.68 2.29
99 100 4.796830 ACGTGCGTAAGTTATCTGTACATG 59.203 41.667 0.00 0.00 41.68 3.21
100 101 4.796830 CGTGCGTAAGTTATCTGTACATGT 59.203 41.667 2.69 2.69 41.68 3.21
101 102 5.287752 CGTGCGTAAGTTATCTGTACATGTT 59.712 40.000 2.30 0.00 41.68 2.71
102 103 6.466812 GTGCGTAAGTTATCTGTACATGTTG 58.533 40.000 2.30 0.00 41.68 3.33
103 104 5.579119 TGCGTAAGTTATCTGTACATGTTGG 59.421 40.000 2.30 0.00 41.68 3.77
104 105 5.808540 GCGTAAGTTATCTGTACATGTTGGA 59.191 40.000 2.30 0.29 41.68 3.53
105 106 6.311935 GCGTAAGTTATCTGTACATGTTGGAA 59.688 38.462 2.30 0.00 41.68 3.53
106 107 7.011109 GCGTAAGTTATCTGTACATGTTGGAAT 59.989 37.037 2.30 0.00 41.68 3.01
107 108 8.540492 CGTAAGTTATCTGTACATGTTGGAATC 58.460 37.037 2.30 0.00 0.00 2.52
108 109 9.378551 GTAAGTTATCTGTACATGTTGGAATCA 57.621 33.333 2.30 0.00 0.00 2.57
109 110 8.862325 AAGTTATCTGTACATGTTGGAATCAA 57.138 30.769 2.30 0.00 0.00 2.57
110 111 8.498054 AGTTATCTGTACATGTTGGAATCAAG 57.502 34.615 2.30 0.00 32.92 3.02
111 112 8.103305 AGTTATCTGTACATGTTGGAATCAAGT 58.897 33.333 2.30 0.00 32.92 3.16
112 113 6.748333 ATCTGTACATGTTGGAATCAAGTG 57.252 37.500 2.30 0.00 32.92 3.16
113 114 5.863965 TCTGTACATGTTGGAATCAAGTGA 58.136 37.500 2.30 0.00 32.92 3.41
114 115 6.475504 TCTGTACATGTTGGAATCAAGTGAT 58.524 36.000 2.30 0.00 36.07 3.06
115 116 6.372381 TCTGTACATGTTGGAATCAAGTGATG 59.628 38.462 2.30 0.00 34.49 3.07
116 117 6.237154 TGTACATGTTGGAATCAAGTGATGA 58.763 36.000 2.30 0.00 43.67 2.92
132 133 9.006839 TCAAGTGATGATTGGAGATTAATATGC 57.993 33.333 0.00 0.00 31.50 3.14
133 134 9.011095 CAAGTGATGATTGGAGATTAATATGCT 57.989 33.333 3.20 0.00 0.00 3.79
134 135 9.584008 AAGTGATGATTGGAGATTAATATGCTT 57.416 29.630 3.20 0.00 0.00 3.91
137 138 9.453572 TGATGATTGGAGATTAATATGCTTACC 57.546 33.333 3.20 0.00 0.00 2.85
138 139 9.678260 GATGATTGGAGATTAATATGCTTACCT 57.322 33.333 3.20 0.00 0.00 3.08
139 140 9.678260 ATGATTGGAGATTAATATGCTTACCTC 57.322 33.333 3.20 0.00 0.00 3.85
140 141 8.659527 TGATTGGAGATTAATATGCTTACCTCA 58.340 33.333 3.20 0.00 0.00 3.86
141 142 9.160496 GATTGGAGATTAATATGCTTACCTCAG 57.840 37.037 3.20 0.00 0.00 3.35
142 143 6.467677 TGGAGATTAATATGCTTACCTCAGC 58.532 40.000 3.20 0.00 40.55 4.26
143 144 6.270927 TGGAGATTAATATGCTTACCTCAGCT 59.729 38.462 3.20 0.00 40.79 4.24
144 145 7.164803 GGAGATTAATATGCTTACCTCAGCTT 58.835 38.462 0.00 0.00 40.79 3.74
145 146 7.333174 GGAGATTAATATGCTTACCTCAGCTTC 59.667 40.741 0.00 0.00 40.79 3.86
146 147 7.739825 AGATTAATATGCTTACCTCAGCTTCA 58.260 34.615 0.00 0.00 40.79 3.02
147 148 7.877097 AGATTAATATGCTTACCTCAGCTTCAG 59.123 37.037 0.00 0.00 40.79 3.02
148 149 5.365021 AATATGCTTACCTCAGCTTCAGT 57.635 39.130 0.00 0.00 40.79 3.41
149 150 3.710209 ATGCTTACCTCAGCTTCAGTT 57.290 42.857 0.00 0.00 40.79 3.16
150 151 2.771089 TGCTTACCTCAGCTTCAGTTG 58.229 47.619 0.00 0.00 40.79 3.16
151 152 1.466558 GCTTACCTCAGCTTCAGTTGC 59.533 52.381 0.00 0.00 36.79 4.17
152 153 2.079925 CTTACCTCAGCTTCAGTTGCC 58.920 52.381 0.00 0.00 0.00 4.52
153 154 1.055849 TACCTCAGCTTCAGTTGCCA 58.944 50.000 0.00 0.00 0.00 4.92
154 155 0.403271 ACCTCAGCTTCAGTTGCCAT 59.597 50.000 0.00 0.00 0.00 4.40
155 156 1.093159 CCTCAGCTTCAGTTGCCATC 58.907 55.000 0.00 0.00 0.00 3.51
156 157 1.612462 CCTCAGCTTCAGTTGCCATCA 60.612 52.381 0.00 0.00 0.00 3.07
157 158 2.366533 CTCAGCTTCAGTTGCCATCAT 58.633 47.619 0.00 0.00 0.00 2.45
158 159 2.089201 TCAGCTTCAGTTGCCATCATG 58.911 47.619 0.00 0.00 0.00 3.07
159 160 2.089201 CAGCTTCAGTTGCCATCATGA 58.911 47.619 0.00 0.00 0.00 3.07
160 161 2.688446 CAGCTTCAGTTGCCATCATGAT 59.312 45.455 1.18 1.18 0.00 2.45
161 162 3.130516 CAGCTTCAGTTGCCATCATGATT 59.869 43.478 5.16 0.00 0.00 2.57
162 163 3.130516 AGCTTCAGTTGCCATCATGATTG 59.869 43.478 5.16 3.61 0.00 2.67
163 164 3.737047 GCTTCAGTTGCCATCATGATTGG 60.737 47.826 5.16 12.03 0.00 3.16
164 165 2.380941 TCAGTTGCCATCATGATTGGG 58.619 47.619 19.47 14.34 0.00 4.12
165 166 1.411246 CAGTTGCCATCATGATTGGGG 59.589 52.381 19.47 13.76 0.00 4.96
166 167 1.288633 AGTTGCCATCATGATTGGGGA 59.711 47.619 19.47 12.43 0.00 4.81
167 168 2.090943 AGTTGCCATCATGATTGGGGAT 60.091 45.455 19.47 1.57 0.00 3.85
168 169 2.701951 GTTGCCATCATGATTGGGGATT 59.298 45.455 19.47 0.00 0.00 3.01
169 170 2.600790 TGCCATCATGATTGGGGATTC 58.399 47.619 19.47 8.20 0.00 2.52
170 171 2.091222 TGCCATCATGATTGGGGATTCA 60.091 45.455 19.47 9.99 0.00 2.57
171 172 2.967201 GCCATCATGATTGGGGATTCAA 59.033 45.455 19.47 0.00 0.00 2.69
172 173 3.581332 GCCATCATGATTGGGGATTCAAT 59.419 43.478 19.47 0.00 39.76 2.57
173 174 4.041198 GCCATCATGATTGGGGATTCAATT 59.959 41.667 19.47 0.00 37.47 2.32
174 175 5.547465 CCATCATGATTGGGGATTCAATTG 58.453 41.667 5.16 0.00 37.47 2.32
175 176 4.675976 TCATGATTGGGGATTCAATTGC 57.324 40.909 0.00 0.00 37.47 3.56
176 177 4.031611 TCATGATTGGGGATTCAATTGCA 58.968 39.130 0.00 0.00 37.47 4.08
177 178 4.656575 TCATGATTGGGGATTCAATTGCAT 59.343 37.500 0.00 0.00 37.47 3.96
178 179 4.675976 TGATTGGGGATTCAATTGCATC 57.324 40.909 9.32 9.32 37.47 3.91
188 189 3.632643 TCAATTGCATCAGAGCTGGTA 57.367 42.857 0.00 0.00 34.99 3.25
203 207 2.668457 GCTGGTAATTGACTGACGACTG 59.332 50.000 0.00 0.00 0.00 3.51
210 214 0.598419 TGACTGACGACTGCTTGCAG 60.598 55.000 19.62 19.62 0.00 4.41
235 239 6.717540 GGAGTATCATGTGGAGTACAGAGTAT 59.282 42.308 0.00 0.00 43.80 2.12
247 251 5.710984 AGTACAGAGTATTTTGTCCAGTCG 58.289 41.667 0.00 0.00 0.00 4.18
265 269 4.679654 CAGTCGGTTTTCTAATTTGTTGGC 59.320 41.667 0.00 0.00 0.00 4.52
272 276 7.254590 CGGTTTTCTAATTTGTTGGCAATTTCA 60.255 33.333 1.92 0.00 34.18 2.69
275 279 8.954950 TTTCTAATTTGTTGGCAATTTCAGAA 57.045 26.923 1.92 5.64 34.18 3.02
371 375 1.945387 ACCATGTAGATTGCAGAGCG 58.055 50.000 0.00 0.00 0.00 5.03
372 376 1.224075 CCATGTAGATTGCAGAGCGG 58.776 55.000 0.00 0.00 0.00 5.52
493 507 4.688413 GCCACCTCGAAGATCTTATCAATC 59.312 45.833 8.25 0.00 33.89 2.67
623 655 4.343231 TCTTTTTGGCCTTCATGCATCTA 58.657 39.130 3.32 0.00 0.00 1.98
645 677 7.680730 TCTAAGAGAGGTAGCAAAATCAACTT 58.319 34.615 0.00 0.00 0.00 2.66
646 678 6.566197 AAGAGAGGTAGCAAAATCAACTTG 57.434 37.500 0.00 0.00 0.00 3.16
647 679 5.006386 AGAGAGGTAGCAAAATCAACTTGG 58.994 41.667 0.00 0.00 0.00 3.61
648 680 4.082125 AGAGGTAGCAAAATCAACTTGGG 58.918 43.478 0.00 0.00 0.00 4.12
736 4768 5.127491 AGTCTGAAACTAGGACGGAGATAG 58.873 45.833 0.00 0.00 36.07 2.08
756 4788 6.822676 AGATAGCTGGAAGAAGACTTGAATTG 59.177 38.462 0.00 0.00 36.39 2.32
766 4798 4.025040 AGACTTGAATTGCTCACATGGA 57.975 40.909 0.00 0.00 32.21 3.41
776 4808 1.135721 GCTCACATGGAAGAAATGGCC 59.864 52.381 0.00 0.00 0.00 5.36
777 4809 1.402968 CTCACATGGAAGAAATGGCCG 59.597 52.381 0.00 0.00 0.00 6.13
778 4810 0.179129 CACATGGAAGAAATGGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
794 4826 1.338389 GCCGCAAAGTAGGTTAGGTGA 60.338 52.381 0.00 0.00 0.00 4.02
799 4831 5.048294 CCGCAAAGTAGGTTAGGTGAAAATT 60.048 40.000 0.00 0.00 0.00 1.82
816 4848 9.764363 GGTGAAAATTTGGAAGAAGAATTTAGT 57.236 29.630 0.00 0.00 33.26 2.24
822 4854 7.421530 TTTGGAAGAAGAATTTAGTGTCTCG 57.578 36.000 0.00 0.00 0.00 4.04
853 4885 2.033141 GCAAGCAGAGCACCCAGA 59.967 61.111 0.00 0.00 0.00 3.86
928 4963 3.797546 GCGCTTGCAGCTCACCTC 61.798 66.667 0.00 0.00 39.60 3.85
937 4972 1.675415 GCAGCTCACCTCTTCTCCTTG 60.675 57.143 0.00 0.00 0.00 3.61
953 4988 5.865085 TCTCCTTGTTTGTATAAGTGCAGT 58.135 37.500 0.00 0.00 0.00 4.40
1077 5113 4.157958 GCTGCCGCTGCTTCTTCG 62.158 66.667 14.47 0.00 38.71 3.79
1177 5216 0.478072 ATGGGTGCAGAACAACTCCA 59.522 50.000 0.00 0.00 35.72 3.86
1197 5236 2.035312 CCTTTCTGCAGCTGGCCT 59.965 61.111 17.12 0.00 43.89 5.19
1206 5245 3.958860 AGCTGGCCTGGTGTCACC 61.959 66.667 15.64 15.64 39.22 4.02
1215 5254 4.012895 GGTGTCACCTGCAACGCG 62.013 66.667 15.22 3.53 34.73 6.01
1249 5288 1.251527 GCTGGACCTCGAGAACTCCA 61.252 60.000 15.71 18.15 0.00 3.86
1270 5309 2.520020 TCGATGGCCGGATACCGT 60.520 61.111 5.05 0.00 46.80 4.83
1279 5318 1.464376 CCGGATACCGTCCTGCATCT 61.464 60.000 0.00 0.00 46.80 2.90
1317 5356 0.328258 CAAGAATCCACTTCCCGGGT 59.672 55.000 22.86 0.00 34.11 5.28
1347 5386 2.104859 CAGTCACATCCCAGCGCAG 61.105 63.158 11.47 0.00 0.00 5.18
1512 5551 1.435515 GACGCTCCGCAATCTCTCT 59.564 57.895 0.00 0.00 0.00 3.10
1692 5731 4.124970 ACTTGGTAAGAAACAACCTCGAC 58.875 43.478 0.00 0.00 36.67 4.20
1716 5755 5.351948 GAGAGATACCTCCTGCTCTTTTT 57.648 43.478 0.00 0.00 40.30 1.94
1852 5891 2.749839 TTGCAGGCACCATACCGC 60.750 61.111 0.00 0.00 0.00 5.68
2048 6087 3.660865 ACCTTAGTTTAGCCGTCAACAG 58.339 45.455 0.00 0.00 0.00 3.16
2053 6092 6.203338 CCTTAGTTTAGCCGTCAACAGTTTTA 59.797 38.462 0.00 0.00 0.00 1.52
2224 6263 4.329638 TGGCATTATCCCTTCTTTTGGA 57.670 40.909 0.00 0.00 34.54 3.53
2558 6597 3.953712 TGACATACGTGGACTTGTCAT 57.046 42.857 0.00 0.00 42.46 3.06
2641 6680 9.836864 AACCTCTTCTTGCAAGAAAATAATTTT 57.163 25.926 34.71 20.83 43.84 1.82
2647 6686 9.487790 TTCTTGCAAGAAAATAATTTTAGTGGG 57.512 29.630 34.01 1.16 41.75 4.61
2790 6829 1.859302 TTGTCCCACAACCAGCTTTT 58.141 45.000 0.00 0.00 32.34 2.27
2863 6902 5.592104 ATTTTTCCAACAACCGTCTTTCT 57.408 34.783 0.00 0.00 0.00 2.52
2899 6938 2.496070 TGCTCTAGGTGCTTGTATTCGT 59.504 45.455 9.39 0.00 0.00 3.85
3014 7053 2.599848 CGAAACAACTTGAGCGGTGAAG 60.600 50.000 12.38 12.38 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.299867 TGCAGATGCCTTTTTCCCTTTC 59.700 45.455 1.72 0.00 41.18 2.62
2 3 2.014010 TGCAGATGCCTTTTTCCCTT 57.986 45.000 1.72 0.00 41.18 3.95
3 4 2.242882 ATGCAGATGCCTTTTTCCCT 57.757 45.000 1.72 0.00 41.18 4.20
5 6 4.924305 TCATATGCAGATGCCTTTTTCC 57.076 40.909 16.53 0.00 41.18 3.13
6 7 4.736793 CGTTCATATGCAGATGCCTTTTTC 59.263 41.667 16.53 1.43 41.18 2.29
7 8 4.675510 CGTTCATATGCAGATGCCTTTTT 58.324 39.130 16.53 0.00 41.18 1.94
8 9 3.489738 GCGTTCATATGCAGATGCCTTTT 60.490 43.478 16.53 0.00 41.18 2.27
9 10 2.033801 GCGTTCATATGCAGATGCCTTT 59.966 45.455 16.53 0.00 41.18 3.11
11 12 1.233019 GCGTTCATATGCAGATGCCT 58.767 50.000 16.53 0.00 41.18 4.75
12 13 0.946528 TGCGTTCATATGCAGATGCC 59.053 50.000 16.53 8.37 41.26 4.40
20 21 3.612472 TGACATGCATGCGTTCATATG 57.388 42.857 26.53 10.69 0.00 1.78
21 22 3.628942 ACTTGACATGCATGCGTTCATAT 59.371 39.130 26.53 10.69 0.00 1.78
22 23 3.009026 ACTTGACATGCATGCGTTCATA 58.991 40.909 26.53 11.86 0.00 2.15
23 24 1.814394 ACTTGACATGCATGCGTTCAT 59.186 42.857 26.53 5.71 0.00 2.57
24 25 1.237533 ACTTGACATGCATGCGTTCA 58.762 45.000 26.53 19.08 0.00 3.18
25 26 1.980844 CAACTTGACATGCATGCGTTC 59.019 47.619 26.53 16.69 0.00 3.95
26 27 1.336148 CCAACTTGACATGCATGCGTT 60.336 47.619 26.53 19.43 0.00 4.84
27 28 0.241749 CCAACTTGACATGCATGCGT 59.758 50.000 26.53 10.53 0.00 5.24
28 29 0.457166 CCCAACTTGACATGCATGCG 60.457 55.000 26.53 14.33 0.00 4.73
29 30 0.604578 ACCCAACTTGACATGCATGC 59.395 50.000 26.53 18.59 0.00 4.06
30 31 2.296752 TGAACCCAACTTGACATGCATG 59.703 45.455 25.09 25.09 0.00 4.06
31 32 2.559668 CTGAACCCAACTTGACATGCAT 59.440 45.455 0.00 0.00 0.00 3.96
32 33 1.955778 CTGAACCCAACTTGACATGCA 59.044 47.619 0.00 0.00 0.00 3.96
33 34 1.270550 CCTGAACCCAACTTGACATGC 59.729 52.381 0.00 0.00 0.00 4.06
34 35 2.862541 TCCTGAACCCAACTTGACATG 58.137 47.619 0.00 0.00 0.00 3.21
35 36 3.593442 TTCCTGAACCCAACTTGACAT 57.407 42.857 0.00 0.00 0.00 3.06
36 37 3.593442 ATTCCTGAACCCAACTTGACA 57.407 42.857 0.00 0.00 0.00 3.58
37 38 6.040504 AGTTTTATTCCTGAACCCAACTTGAC 59.959 38.462 0.00 0.00 0.00 3.18
38 39 6.133356 AGTTTTATTCCTGAACCCAACTTGA 58.867 36.000 0.00 0.00 0.00 3.02
39 40 6.405278 AGTTTTATTCCTGAACCCAACTTG 57.595 37.500 0.00 0.00 0.00 3.16
40 41 6.685368 GCAAGTTTTATTCCTGAACCCAACTT 60.685 38.462 6.43 6.43 34.35 2.66
41 42 5.221441 GCAAGTTTTATTCCTGAACCCAACT 60.221 40.000 0.00 0.00 0.00 3.16
42 43 4.988540 GCAAGTTTTATTCCTGAACCCAAC 59.011 41.667 0.00 0.00 0.00 3.77
43 44 4.039852 GGCAAGTTTTATTCCTGAACCCAA 59.960 41.667 0.00 0.00 0.00 4.12
44 45 3.576550 GGCAAGTTTTATTCCTGAACCCA 59.423 43.478 0.00 0.00 0.00 4.51
45 46 3.056107 GGGCAAGTTTTATTCCTGAACCC 60.056 47.826 0.00 0.00 0.00 4.11
46 47 3.576550 TGGGCAAGTTTTATTCCTGAACC 59.423 43.478 0.00 0.00 0.00 3.62
47 48 4.864704 TGGGCAAGTTTTATTCCTGAAC 57.135 40.909 0.00 0.00 0.00 3.18
48 49 5.467035 CTTGGGCAAGTTTTATTCCTGAA 57.533 39.130 0.00 0.00 33.87 3.02
67 68 2.170260 CTTACGCACGTGGCCACTTG 62.170 60.000 32.27 32.27 40.31 3.16
68 69 1.959226 CTTACGCACGTGGCCACTT 60.959 57.895 32.28 22.25 40.31 3.16
69 70 2.357034 CTTACGCACGTGGCCACT 60.357 61.111 32.28 16.67 40.31 4.00
70 71 0.945265 TAACTTACGCACGTGGCCAC 60.945 55.000 26.78 26.78 40.31 5.01
71 72 0.037139 ATAACTTACGCACGTGGCCA 60.037 50.000 18.88 0.00 40.31 5.36
72 73 0.648958 GATAACTTACGCACGTGGCC 59.351 55.000 18.88 0.00 40.31 5.36
73 74 1.323534 CAGATAACTTACGCACGTGGC 59.676 52.381 18.88 8.78 39.90 5.01
74 75 2.602878 ACAGATAACTTACGCACGTGG 58.397 47.619 18.88 10.05 0.00 4.94
75 76 4.160594 TGTACAGATAACTTACGCACGTG 58.839 43.478 12.28 12.28 0.00 4.49
76 77 4.424061 TGTACAGATAACTTACGCACGT 57.576 40.909 0.00 0.00 0.00 4.49
77 78 4.796830 ACATGTACAGATAACTTACGCACG 59.203 41.667 0.00 0.00 0.00 5.34
78 79 6.455113 CCAACATGTACAGATAACTTACGCAC 60.455 42.308 0.00 0.00 0.00 5.34
79 80 5.579119 CCAACATGTACAGATAACTTACGCA 59.421 40.000 0.00 0.00 0.00 5.24
80 81 5.808540 TCCAACATGTACAGATAACTTACGC 59.191 40.000 0.00 0.00 0.00 4.42
81 82 7.821595 TTCCAACATGTACAGATAACTTACG 57.178 36.000 0.00 0.00 0.00 3.18
82 83 9.378551 TGATTCCAACATGTACAGATAACTTAC 57.621 33.333 0.00 0.00 0.00 2.34
83 84 9.952030 TTGATTCCAACATGTACAGATAACTTA 57.048 29.630 0.00 0.00 0.00 2.24
84 85 8.862325 TTGATTCCAACATGTACAGATAACTT 57.138 30.769 0.00 0.00 0.00 2.66
85 86 8.103305 ACTTGATTCCAACATGTACAGATAACT 58.897 33.333 0.00 0.00 0.00 2.24
86 87 8.177663 CACTTGATTCCAACATGTACAGATAAC 58.822 37.037 0.00 0.00 0.00 1.89
87 88 8.100164 TCACTTGATTCCAACATGTACAGATAA 58.900 33.333 0.00 0.00 0.00 1.75
88 89 7.619965 TCACTTGATTCCAACATGTACAGATA 58.380 34.615 0.00 0.00 0.00 1.98
89 90 6.475504 TCACTTGATTCCAACATGTACAGAT 58.524 36.000 0.00 0.00 0.00 2.90
90 91 5.863965 TCACTTGATTCCAACATGTACAGA 58.136 37.500 0.00 0.00 0.00 3.41
91 92 6.372381 TCATCACTTGATTCCAACATGTACAG 59.628 38.462 0.00 0.00 31.21 2.74
92 93 6.237154 TCATCACTTGATTCCAACATGTACA 58.763 36.000 0.00 0.00 31.21 2.90
93 94 6.741992 TCATCACTTGATTCCAACATGTAC 57.258 37.500 0.00 0.00 31.21 2.90
106 107 9.006839 GCATATTAATCTCCAATCATCACTTGA 57.993 33.333 0.00 0.00 39.12 3.02
107 108 9.011095 AGCATATTAATCTCCAATCATCACTTG 57.989 33.333 0.00 0.00 0.00 3.16
108 109 9.584008 AAGCATATTAATCTCCAATCATCACTT 57.416 29.630 0.00 0.00 0.00 3.16
111 112 9.453572 GGTAAGCATATTAATCTCCAATCATCA 57.546 33.333 0.00 0.00 0.00 3.07
112 113 9.678260 AGGTAAGCATATTAATCTCCAATCATC 57.322 33.333 0.00 0.00 0.00 2.92
113 114 9.678260 GAGGTAAGCATATTAATCTCCAATCAT 57.322 33.333 0.00 0.00 0.00 2.45
114 115 8.659527 TGAGGTAAGCATATTAATCTCCAATCA 58.340 33.333 0.00 0.00 0.00 2.57
115 116 9.160496 CTGAGGTAAGCATATTAATCTCCAATC 57.840 37.037 0.00 0.00 0.00 2.67
116 117 7.609532 GCTGAGGTAAGCATATTAATCTCCAAT 59.390 37.037 0.00 0.00 43.01 3.16
117 118 6.936900 GCTGAGGTAAGCATATTAATCTCCAA 59.063 38.462 0.00 0.00 43.01 3.53
118 119 6.270927 AGCTGAGGTAAGCATATTAATCTCCA 59.729 38.462 0.00 0.00 46.08 3.86
119 120 6.706295 AGCTGAGGTAAGCATATTAATCTCC 58.294 40.000 0.00 0.00 46.08 3.71
120 121 7.875041 TGAAGCTGAGGTAAGCATATTAATCTC 59.125 37.037 0.00 0.00 46.08 2.75
121 122 7.739825 TGAAGCTGAGGTAAGCATATTAATCT 58.260 34.615 0.00 0.00 46.08 2.40
122 123 7.659390 ACTGAAGCTGAGGTAAGCATATTAATC 59.341 37.037 0.00 0.00 46.08 1.75
123 124 7.512992 ACTGAAGCTGAGGTAAGCATATTAAT 58.487 34.615 0.00 0.00 46.08 1.40
124 125 6.889198 ACTGAAGCTGAGGTAAGCATATTAA 58.111 36.000 0.00 0.00 46.08 1.40
125 126 6.485830 ACTGAAGCTGAGGTAAGCATATTA 57.514 37.500 0.00 0.00 46.08 0.98
126 127 5.365021 ACTGAAGCTGAGGTAAGCATATT 57.635 39.130 0.00 0.00 46.08 1.28
127 128 5.121811 CAACTGAAGCTGAGGTAAGCATAT 58.878 41.667 0.00 0.00 46.08 1.78
128 129 4.507710 CAACTGAAGCTGAGGTAAGCATA 58.492 43.478 0.00 0.00 46.08 3.14
129 130 3.341823 CAACTGAAGCTGAGGTAAGCAT 58.658 45.455 0.00 0.00 46.08 3.79
130 131 2.771089 CAACTGAAGCTGAGGTAAGCA 58.229 47.619 0.00 0.00 46.08 3.91
131 132 1.466558 GCAACTGAAGCTGAGGTAAGC 59.533 52.381 0.00 0.00 43.88 3.09
132 133 2.079925 GGCAACTGAAGCTGAGGTAAG 58.920 52.381 0.00 0.00 0.00 2.34
133 134 1.419762 TGGCAACTGAAGCTGAGGTAA 59.580 47.619 0.00 0.00 37.61 2.85
134 135 1.055849 TGGCAACTGAAGCTGAGGTA 58.944 50.000 0.00 0.00 37.61 3.08
135 136 0.403271 ATGGCAACTGAAGCTGAGGT 59.597 50.000 0.00 0.00 37.61 3.85
136 137 1.093159 GATGGCAACTGAAGCTGAGG 58.907 55.000 0.00 0.00 37.61 3.86
137 138 1.817357 TGATGGCAACTGAAGCTGAG 58.183 50.000 0.00 0.00 37.61 3.35
138 139 2.089201 CATGATGGCAACTGAAGCTGA 58.911 47.619 0.00 0.00 37.61 4.26
139 140 2.089201 TCATGATGGCAACTGAAGCTG 58.911 47.619 0.00 0.00 37.61 4.24
140 141 2.502142 TCATGATGGCAACTGAAGCT 57.498 45.000 0.00 0.00 37.61 3.74
141 142 3.444916 CAATCATGATGGCAACTGAAGC 58.555 45.455 9.46 0.00 37.61 3.86
142 143 3.181479 CCCAATCATGATGGCAACTGAAG 60.181 47.826 9.46 0.00 36.58 3.02
143 144 2.761767 CCCAATCATGATGGCAACTGAA 59.238 45.455 9.46 0.00 36.58 3.02
144 145 2.380941 CCCAATCATGATGGCAACTGA 58.619 47.619 9.46 0.00 36.58 3.41
145 146 1.411246 CCCCAATCATGATGGCAACTG 59.589 52.381 9.46 2.30 36.58 3.16
146 147 1.288633 TCCCCAATCATGATGGCAACT 59.711 47.619 9.46 0.00 36.58 3.16
147 148 1.779221 TCCCCAATCATGATGGCAAC 58.221 50.000 9.46 0.00 36.58 4.17
148 149 2.779429 ATCCCCAATCATGATGGCAA 57.221 45.000 9.46 4.50 36.58 4.52
149 150 2.091222 TGAATCCCCAATCATGATGGCA 60.091 45.455 9.46 0.00 36.58 4.92
150 151 2.600790 TGAATCCCCAATCATGATGGC 58.399 47.619 9.46 1.33 36.58 4.40
151 152 5.547465 CAATTGAATCCCCAATCATGATGG 58.453 41.667 9.46 12.36 35.86 3.51
152 153 4.994852 GCAATTGAATCCCCAATCATGATG 59.005 41.667 9.46 3.68 35.86 3.07
153 154 4.656575 TGCAATTGAATCCCCAATCATGAT 59.343 37.500 10.34 1.18 35.86 2.45
154 155 4.031611 TGCAATTGAATCCCCAATCATGA 58.968 39.130 10.34 0.00 35.86 3.07
155 156 4.409718 TGCAATTGAATCCCCAATCATG 57.590 40.909 10.34 0.00 35.86 3.07
156 157 4.656575 TGATGCAATTGAATCCCCAATCAT 59.343 37.500 21.54 5.86 35.86 2.45
157 158 4.031611 TGATGCAATTGAATCCCCAATCA 58.968 39.130 21.54 1.96 35.86 2.57
158 159 4.342951 TCTGATGCAATTGAATCCCCAATC 59.657 41.667 21.54 0.00 35.86 2.67
159 160 4.291792 TCTGATGCAATTGAATCCCCAAT 58.708 39.130 21.54 0.00 38.30 3.16
160 161 3.702548 CTCTGATGCAATTGAATCCCCAA 59.297 43.478 21.54 4.25 0.00 4.12
161 162 3.293337 CTCTGATGCAATTGAATCCCCA 58.707 45.455 21.54 5.20 0.00 4.96
162 163 2.035576 GCTCTGATGCAATTGAATCCCC 59.964 50.000 21.54 5.66 0.00 4.81
163 164 2.957006 AGCTCTGATGCAATTGAATCCC 59.043 45.455 21.54 9.03 34.99 3.85
164 165 3.243434 CCAGCTCTGATGCAATTGAATCC 60.243 47.826 21.54 7.91 34.99 3.01
165 166 3.380637 ACCAGCTCTGATGCAATTGAATC 59.619 43.478 18.31 18.31 34.99 2.52
166 167 3.362706 ACCAGCTCTGATGCAATTGAAT 58.637 40.909 10.34 3.41 34.99 2.57
167 168 2.799017 ACCAGCTCTGATGCAATTGAA 58.201 42.857 10.34 0.00 34.99 2.69
168 169 2.502142 ACCAGCTCTGATGCAATTGA 57.498 45.000 10.34 0.00 34.99 2.57
169 170 4.913335 ATTACCAGCTCTGATGCAATTG 57.087 40.909 0.00 0.00 34.99 2.32
170 171 4.951715 TCAATTACCAGCTCTGATGCAATT 59.048 37.500 0.00 0.00 34.99 2.32
171 172 4.337555 GTCAATTACCAGCTCTGATGCAAT 59.662 41.667 0.00 0.00 34.99 3.56
172 173 3.691118 GTCAATTACCAGCTCTGATGCAA 59.309 43.478 0.00 0.00 34.99 4.08
173 174 3.054875 AGTCAATTACCAGCTCTGATGCA 60.055 43.478 0.00 0.00 34.99 3.96
174 175 3.311871 CAGTCAATTACCAGCTCTGATGC 59.688 47.826 0.00 0.00 0.00 3.91
175 176 4.569966 GTCAGTCAATTACCAGCTCTGATG 59.430 45.833 0.00 0.00 33.98 3.07
176 177 4.679106 CGTCAGTCAATTACCAGCTCTGAT 60.679 45.833 0.00 0.00 33.98 2.90
177 178 3.367395 CGTCAGTCAATTACCAGCTCTGA 60.367 47.826 0.00 0.00 0.00 3.27
178 179 2.926200 CGTCAGTCAATTACCAGCTCTG 59.074 50.000 0.00 0.00 0.00 3.35
188 189 1.532868 GCAAGCAGTCGTCAGTCAATT 59.467 47.619 0.00 0.00 0.00 2.32
203 207 1.945394 CCACATGATACTCCTGCAAGC 59.055 52.381 0.00 0.00 0.00 4.01
210 214 4.890581 ACTCTGTACTCCACATGATACTCC 59.109 45.833 0.00 0.00 36.29 3.85
222 226 6.038997 ACTGGACAAAATACTCTGTACTCC 57.961 41.667 0.00 0.00 0.00 3.85
224 228 5.336531 CCGACTGGACAAAATACTCTGTACT 60.337 44.000 0.00 0.00 37.49 2.73
228 232 3.926616 ACCGACTGGACAAAATACTCTG 58.073 45.455 0.00 0.00 39.21 3.35
235 239 6.702716 AATTAGAAAACCGACTGGACAAAA 57.297 33.333 0.00 0.00 39.21 2.44
247 251 7.924940 TGAAATTGCCAACAAATTAGAAAACC 58.075 30.769 0.00 0.00 39.77 3.27
371 375 5.181433 GTGAAATCCAAGAACACTAACCTCC 59.819 44.000 0.00 0.00 0.00 4.30
372 376 5.763204 TGTGAAATCCAAGAACACTAACCTC 59.237 40.000 0.00 0.00 33.41 3.85
467 481 0.108615 AAGATCTTCGAGGTGGCACG 60.109 55.000 12.17 0.00 0.00 5.34
552 566 4.960469 TGTTATAGGAACCCAACTCGATCT 59.040 41.667 0.00 0.00 0.00 2.75
623 655 5.474876 CCAAGTTGATTTTGCTACCTCTCTT 59.525 40.000 3.87 0.00 0.00 2.85
645 677 6.836527 TGAAAGATTTTCTTTTGGACTACCCA 59.163 34.615 4.16 0.00 45.85 4.51
646 678 7.284919 TGAAAGATTTTCTTTTGGACTACCC 57.715 36.000 4.16 0.00 45.85 3.69
647 679 9.411801 GATTGAAAGATTTTCTTTTGGACTACC 57.588 33.333 4.16 0.00 45.85 3.18
648 680 9.965824 TGATTGAAAGATTTTCTTTTGGACTAC 57.034 29.630 4.16 0.00 45.85 2.73
688 4720 2.561209 TCCCACCAGCTATCTTGGTA 57.439 50.000 0.00 0.00 34.10 3.25
736 4768 3.505293 AGCAATTCAAGTCTTCTTCCAGC 59.495 43.478 0.00 0.00 0.00 4.85
756 4788 1.135721 GGCCATTTCTTCCATGTGAGC 59.864 52.381 0.00 0.00 0.00 4.26
766 4798 1.818674 CCTACTTTGCGGCCATTTCTT 59.181 47.619 2.24 0.00 0.00 2.52
776 4808 5.622770 ATTTTCACCTAACCTACTTTGCG 57.377 39.130 0.00 0.00 0.00 4.85
777 4809 6.645003 CCAAATTTTCACCTAACCTACTTTGC 59.355 38.462 0.00 0.00 0.00 3.68
778 4810 7.947282 TCCAAATTTTCACCTAACCTACTTTG 58.053 34.615 0.00 0.00 0.00 2.77
799 4831 5.408604 GCGAGACACTAAATTCTTCTTCCAA 59.591 40.000 0.00 0.00 0.00 3.53
816 4848 2.349590 CCATTTCTGTCATGCGAGACA 58.650 47.619 10.18 10.18 45.64 3.41
818 4850 1.338960 TGCCATTTCTGTCATGCGAGA 60.339 47.619 0.00 0.00 0.00 4.04
822 4854 1.067425 TGCTTGCCATTTCTGTCATGC 60.067 47.619 0.00 0.00 0.00 4.06
928 4963 6.428159 ACTGCACTTATACAAACAAGGAGAAG 59.572 38.462 0.00 0.00 0.00 2.85
1077 5113 2.047655 TCGGTGGCGTTGGATGAC 60.048 61.111 0.00 0.00 0.00 3.06
1148 5187 3.455469 GCACCCATGAGCCAAGGC 61.455 66.667 2.02 2.02 42.33 4.35
1177 5216 1.379576 GCCAGCTGCAGAAAGGGAT 60.380 57.895 20.43 0.00 40.77 3.85
1197 5236 2.899838 GCGTTGCAGGTGACACCA 60.900 61.111 26.30 2.96 41.95 4.17
1215 5254 2.729862 AGCGCAACGACACGAGAC 60.730 61.111 11.47 0.00 0.00 3.36
1270 5309 0.615331 GTGAGGTTGGAGATGCAGGA 59.385 55.000 0.00 0.00 0.00 3.86
1279 5318 0.252284 GAGAGGAGGGTGAGGTTGGA 60.252 60.000 0.00 0.00 0.00 3.53
1332 5371 3.709633 AGCTGCGCTGGGATGTGA 61.710 61.111 16.47 0.00 37.57 3.58
1350 5389 2.282040 AACCTGCTCAGCTGCCAC 60.282 61.111 9.47 0.76 0.00 5.01
1351 5390 2.281970 CAACCTGCTCAGCTGCCA 60.282 61.111 9.47 7.78 0.00 4.92
1461 5500 4.140924 TCTGGGATATCTCCACTGAGCTTA 60.141 45.833 0.00 0.00 44.08 3.09
1512 5551 1.160946 TGCGAGCAAGGCGTAAAACA 61.161 50.000 0.00 0.00 0.00 2.83
1584 5623 2.037121 TGCGAGGATGACAGAAACAAGA 59.963 45.455 0.00 0.00 0.00 3.02
1852 5891 4.395231 GGAAGAAAAATTACCCAGAGTCGG 59.605 45.833 0.00 0.00 0.00 4.79
1996 6035 5.192927 TGAAGACATGTTGAATATGGGGAC 58.807 41.667 0.00 0.00 0.00 4.46
2048 6087 6.649141 GTCAAATGGAAGTTCCCCAATAAAAC 59.351 38.462 19.42 4.12 37.22 2.43
2053 6092 3.855668 TGTCAAATGGAAGTTCCCCAAT 58.144 40.909 19.42 3.39 37.22 3.16
2124 6163 2.179427 CAGGGATTTTTCCTCCAACCC 58.821 52.381 0.00 0.00 34.24 4.11
2224 6263 9.654919 ATTAGCTCTTCTAGGTTAGAAAGAGAT 57.345 33.333 16.73 13.83 43.63 2.75
2558 6597 1.070134 CTGTCCGGAAAGTCTGTTCCA 59.930 52.381 14.07 0.00 46.45 3.53
2641 6680 0.645496 TCCTAGGAATGGGCCCACTA 59.355 55.000 31.51 22.82 0.00 2.74
2647 6686 0.318762 CTAGCGTCCTAGGAATGGGC 59.681 60.000 14.65 14.46 37.90 5.36
2863 6902 1.565759 AGAGCAGTTGGAATATGCCCA 59.434 47.619 0.00 0.00 40.89 5.36
2899 6938 1.005569 TCTAAGCGAAGGGACTCCAGA 59.994 52.381 0.00 0.00 38.49 3.86
3014 7053 3.296854 AGGACTGGAAAAAGTTTGGGAC 58.703 45.455 0.00 0.00 0.00 4.46
3051 7090 4.058817 GTCGTTGAAGGACAAGTTGAGAT 58.941 43.478 10.54 0.00 39.30 2.75
3103 7142 7.012421 ACAGACACCTCACTAGAATTTTGAAAC 59.988 37.037 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.