Multiple sequence alignment - TraesCS4B01G313500

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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 TraesCS4B01G313500 chr4B 100.000 2570 0 0 1 2570 603165225 603167794 0.000000e+00 4747.0
1 TraesCS4B01G313500 chr4B 91.275 149 12 1 2209 2357 603186754 603186901 4.340000e-48 202.0
2 TraesCS4B01G313500 chr4B 83.099 142 20 4 2218 2357 603165443 603165582 2.680000e-25 126.0
3 TraesCS4B01G313500 chr4B 83.099 142 20 4 219 358 603167442 603167581 2.680000e-25 126.0
4 TraesCS4B01G313500 chr4A 87.250 1702 125 38 216 1859 684502348 684504015 0.000000e+00 1857.0
5 TraesCS4B01G313500 chr4A 90.202 347 33 1 1857 2202 684504159 684504505 3.900000e-123 451.0
6 TraesCS4B01G313500 chr4A 85.470 234 32 2 2192 2424 684505166 684505398 2.550000e-60 243.0
7 TraesCS4B01G313500 chr4A 90.647 139 13 0 2219 2357 684515607 684515745 4.370000e-43 185.0
8 TraesCS4B01G313500 chr4A 81.690 142 24 2 220 360 684515607 684515747 1.620000e-22 117.0
9 TraesCS4B01G313500 chr4A 82.906 117 18 2 243 358 684505216 684505331 1.260000e-18 104.0
10 TraesCS4B01G313500 chr4D 90.260 1232 60 36 638 1858 477577145 477578327 0.000000e+00 1555.0
11 TraesCS4B01G313500 chr4D 91.200 625 42 8 1952 2570 477580372 477580989 0.000000e+00 837.0
12 TraesCS4B01G313500 chr4D 95.726 117 5 0 100 216 29093478 29093362 3.380000e-44 189.0
13 TraesCS4B01G313500 chr4D 95.726 117 5 0 100 216 333227488 333227604 3.380000e-44 189.0
14 TraesCS4B01G313500 chr4D 92.366 131 10 0 2227 2357 477627238 477627368 1.210000e-43 187.0
15 TraesCS4B01G313500 chr4D 96.970 99 3 0 1857 1955 477578474 477578572 1.580000e-37 167.0
16 TraesCS4B01G313500 chr4D 88.095 84 10 0 246 329 477536156 477536239 1.630000e-17 100.0
17 TraesCS4B01G313500 chr1D 84.608 1033 121 18 656 1660 247293732 247294754 0.000000e+00 992.0
18 TraesCS4B01G313500 chr6B 84.869 1031 96 28 773 1769 15890769 15889765 0.000000e+00 985.0
19 TraesCS4B01G313500 chr6B 83.859 1047 109 28 773 1784 15919652 15918631 0.000000e+00 942.0
20 TraesCS4B01G313500 chr6B 83.763 1047 110 28 773 1784 15899794 15898773 0.000000e+00 937.0
21 TraesCS4B01G313500 chr6B 87.775 818 78 14 773 1571 15904535 15903721 0.000000e+00 937.0
22 TraesCS4B01G313500 chr6B 83.714 1050 108 34 773 1784 15924389 15923365 0.000000e+00 933.0
23 TraesCS4B01G313500 chr6B 87.653 818 79 14 773 1571 15895509 15894695 0.000000e+00 931.0
24 TraesCS4B01G313500 chr7D 95.726 117 5 0 100 216 183409774 183409658 3.380000e-44 189.0
25 TraesCS4B01G313500 chr7D 95.726 117 5 0 100 216 498734672 498734556 3.380000e-44 189.0
26 TraesCS4B01G313500 chr6D 95.726 117 5 0 100 216 128989376 128989260 3.380000e-44 189.0
27 TraesCS4B01G313500 chr5D 95.726 117 5 0 100 216 399581792 399581676 3.380000e-44 189.0
28 TraesCS4B01G313500 chr5D 95.726 117 5 0 100 216 519979413 519979529 3.380000e-44 189.0
29 TraesCS4B01G313500 chr5D 87.719 114 14 0 2242 2355 449851707 449851820 1.600000e-27 134.0
30 TraesCS4B01G313500 chr5D 82.667 150 24 2 209 356 449851671 449851820 5.770000e-27 132.0
31 TraesCS4B01G313500 chr1A 95.726 117 5 0 100 216 451750751 451750635 3.380000e-44 189.0
32 TraesCS4B01G313500 chr2B 94.958 119 6 0 103 221 43851197 43851079 1.210000e-43 187.0
33 TraesCS4B01G313500 chr2B 80.556 108 19 2 381 487 13242114 13242220 5.890000e-12 82.4
34 TraesCS4B01G313500 chr1B 80.392 255 43 5 637 890 330553896 330553648 1.210000e-43 187.0
35 TraesCS4B01G313500 chr1B 80.385 260 33 13 381 626 330554972 330554717 5.650000e-42 182.0
36 TraesCS4B01G313500 chr5B 84.138 145 21 1 235 377 549674137 549674281 3.450000e-29 139.0
37 TraesCS4B01G313500 chr5B 85.938 128 16 1 2237 2362 549674140 549674267 4.460000e-28 135.0
38 TraesCS4B01G313500 chr5A 86.290 124 17 0 2239 2362 569074942 569075065 4.460000e-28 135.0
39 TraesCS4B01G313500 chr5A 85.271 129 17 2 241 368 569074943 569075070 5.770000e-27 132.0
40 TraesCS4B01G313500 chr2A 89.796 49 5 0 436 484 2979342 2979390 2.130000e-06 63.9


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 TraesCS4B01G313500 chr4B 603165225 603167794 2569 False 1666.333333 4747 88.732667 1 2570 3 chr4B.!!$F2 2569
1 TraesCS4B01G313500 chr4A 684502348 684505398 3050 False 663.750000 1857 86.457000 216 2424 4 chr4A.!!$F1 2208
2 TraesCS4B01G313500 chr4D 477577145 477580989 3844 False 853.000000 1555 92.810000 638 2570 3 chr4D.!!$F4 1932
3 TraesCS4B01G313500 chr1D 247293732 247294754 1022 False 992.000000 992 84.608000 656 1660 1 chr1D.!!$F1 1004
4 TraesCS4B01G313500 chr6B 15889765 15904535 14770 True 947.500000 985 86.015000 773 1784 4 chr6B.!!$R1 1011
5 TraesCS4B01G313500 chr6B 15918631 15924389 5758 True 937.500000 942 83.786500 773 1784 2 chr6B.!!$R2 1011

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
118 119 0.033796 ACATACTCCCTCCGTTCGGA 60.034 55.0 13.34 13.34 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 17912 0.393537 GCCTCCAATGTGGACAGGAG 60.394 60.0 6.73 7.73 42.67 3.69 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
27 28 2.907910 GCACGAGCTCAATTTCATGT 57.092 45.000 15.40 0.00 37.91 3.21
29 30 4.542662 GCACGAGCTCAATTTCATGTAT 57.457 40.909 15.40 0.00 37.91 2.29
30 31 5.657470 GCACGAGCTCAATTTCATGTATA 57.343 39.130 15.40 0.00 37.91 1.47
31 32 5.674008 GCACGAGCTCAATTTCATGTATAG 58.326 41.667 15.40 0.00 37.91 1.31
32 33 5.463392 GCACGAGCTCAATTTCATGTATAGA 59.537 40.000 15.40 0.00 37.91 1.98
33 34 6.018751 GCACGAGCTCAATTTCATGTATAGAA 60.019 38.462 15.40 0.00 37.91 2.10
34 35 7.562412 CACGAGCTCAATTTCATGTATAGAAG 58.438 38.462 15.40 0.00 0.00 2.85
35 36 6.201806 ACGAGCTCAATTTCATGTATAGAAGC 59.798 38.462 15.40 0.00 0.00 3.86
36 37 6.201615 CGAGCTCAATTTCATGTATAGAAGCA 59.798 38.462 15.40 0.00 0.00 3.91
37 38 7.493743 AGCTCAATTTCATGTATAGAAGCAG 57.506 36.000 10.69 0.00 0.00 4.24
38 39 7.278135 AGCTCAATTTCATGTATAGAAGCAGA 58.722 34.615 10.69 0.00 0.00 4.26
39 40 7.937942 AGCTCAATTTCATGTATAGAAGCAGAT 59.062 33.333 10.69 0.00 0.00 2.90
40 41 8.566260 GCTCAATTTCATGTATAGAAGCAGATT 58.434 33.333 0.00 0.00 0.00 2.40
96 97 2.375014 GGAACTCCCCCACAAAAGAA 57.625 50.000 0.00 0.00 0.00 2.52
97 98 2.673258 GGAACTCCCCCACAAAAGAAA 58.327 47.619 0.00 0.00 0.00 2.52
98 99 3.035363 GGAACTCCCCCACAAAAGAAAA 58.965 45.455 0.00 0.00 0.00 2.29
99 100 3.452990 GGAACTCCCCCACAAAAGAAAAA 59.547 43.478 0.00 0.00 0.00 1.94
100 101 4.439057 GAACTCCCCCACAAAAGAAAAAC 58.561 43.478 0.00 0.00 0.00 2.43
101 102 3.445987 ACTCCCCCACAAAAGAAAAACA 58.554 40.909 0.00 0.00 0.00 2.83
102 103 4.037222 ACTCCCCCACAAAAGAAAAACAT 58.963 39.130 0.00 0.00 0.00 2.71
103 104 5.212745 ACTCCCCCACAAAAGAAAAACATA 58.787 37.500 0.00 0.00 0.00 2.29
104 105 5.069914 ACTCCCCCACAAAAGAAAAACATAC 59.930 40.000 0.00 0.00 0.00 2.39
105 106 5.212745 TCCCCCACAAAAGAAAAACATACT 58.787 37.500 0.00 0.00 0.00 2.12
106 107 5.303333 TCCCCCACAAAAGAAAAACATACTC 59.697 40.000 0.00 0.00 0.00 2.59
107 108 5.510690 CCCCCACAAAAGAAAAACATACTCC 60.511 44.000 0.00 0.00 0.00 3.85
108 109 5.510690 CCCCACAAAAGAAAAACATACTCCC 60.511 44.000 0.00 0.00 0.00 4.30
109 110 5.304357 CCCACAAAAGAAAAACATACTCCCT 59.696 40.000 0.00 0.00 0.00 4.20
110 111 6.447162 CCACAAAAGAAAAACATACTCCCTC 58.553 40.000 0.00 0.00 0.00 4.30
111 112 6.447162 CACAAAAGAAAAACATACTCCCTCC 58.553 40.000 0.00 0.00 0.00 4.30
112 113 5.240844 ACAAAAGAAAAACATACTCCCTCCG 59.759 40.000 0.00 0.00 0.00 4.63
113 114 4.635699 AAGAAAAACATACTCCCTCCGT 57.364 40.909 0.00 0.00 0.00 4.69
114 115 4.635699 AGAAAAACATACTCCCTCCGTT 57.364 40.909 0.00 0.00 0.00 4.44
115 116 4.576879 AGAAAAACATACTCCCTCCGTTC 58.423 43.478 0.00 0.00 0.00 3.95
116 117 2.667473 AAACATACTCCCTCCGTTCG 57.333 50.000 0.00 0.00 0.00 3.95
117 118 0.822164 AACATACTCCCTCCGTTCGG 59.178 55.000 4.74 4.74 0.00 4.30
118 119 0.033796 ACATACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
119 120 1.108776 CATACTCCCTCCGTTCGGAA 58.891 55.000 14.79 0.00 33.41 4.30
120 121 1.687123 CATACTCCCTCCGTTCGGAAT 59.313 52.381 14.79 2.14 33.41 3.01
121 122 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
122 123 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
123 124 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
124 125 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
125 126 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
126 127 1.535437 CCCTCCGTTCGGAATTACTCG 60.535 57.143 14.79 1.97 33.41 4.18
127 128 1.133790 CCTCCGTTCGGAATTACTCGT 59.866 52.381 14.79 0.00 33.41 4.18
128 129 2.448219 CTCCGTTCGGAATTACTCGTC 58.552 52.381 14.79 0.00 33.41 4.20
129 130 1.186030 CCGTTCGGAATTACTCGTCG 58.814 55.000 5.19 0.00 0.00 5.12
130 131 1.202065 CCGTTCGGAATTACTCGTCGA 60.202 52.381 5.19 0.00 0.00 4.20
131 132 2.508867 CGTTCGGAATTACTCGTCGAA 58.491 47.619 0.00 0.00 37.48 3.71
132 133 2.525096 CGTTCGGAATTACTCGTCGAAG 59.475 50.000 0.00 0.00 39.89 3.79
133 134 3.725895 CGTTCGGAATTACTCGTCGAAGA 60.726 47.826 0.03 0.03 39.89 2.87
134 135 4.161333 GTTCGGAATTACTCGTCGAAGAA 58.839 43.478 1.95 0.00 39.69 2.52
135 136 4.424061 TCGGAATTACTCGTCGAAGAAA 57.576 40.909 1.95 0.00 39.69 2.52
136 137 4.990257 TCGGAATTACTCGTCGAAGAAAT 58.010 39.130 1.95 0.00 39.69 2.17
137 138 4.796830 TCGGAATTACTCGTCGAAGAAATG 59.203 41.667 1.95 0.00 39.69 2.32
138 139 4.796830 CGGAATTACTCGTCGAAGAAATGA 59.203 41.667 1.95 0.00 39.69 2.57
139 140 5.287752 CGGAATTACTCGTCGAAGAAATGAA 59.712 40.000 1.95 0.00 39.69 2.57
140 141 6.019801 CGGAATTACTCGTCGAAGAAATGAAT 60.020 38.462 1.95 0.00 39.69 2.57
141 142 7.119997 GGAATTACTCGTCGAAGAAATGAATG 58.880 38.462 1.95 0.00 39.69 2.67
142 143 7.201530 GGAATTACTCGTCGAAGAAATGAATGT 60.202 37.037 1.95 0.00 39.69 2.71
143 144 8.697846 AATTACTCGTCGAAGAAATGAATGTA 57.302 30.769 1.95 0.00 39.69 2.29
144 145 8.873215 ATTACTCGTCGAAGAAATGAATGTAT 57.127 30.769 1.95 0.00 39.69 2.29
145 146 6.575083 ACTCGTCGAAGAAATGAATGTATG 57.425 37.500 1.95 0.00 39.69 2.39
146 147 6.100004 ACTCGTCGAAGAAATGAATGTATGT 58.900 36.000 1.95 0.00 39.69 2.29
147 148 7.255569 ACTCGTCGAAGAAATGAATGTATGTA 58.744 34.615 1.95 0.00 39.69 2.29
148 149 7.432545 ACTCGTCGAAGAAATGAATGTATGTAG 59.567 37.037 1.95 0.00 39.69 2.74
149 150 7.477494 TCGTCGAAGAAATGAATGTATGTAGA 58.523 34.615 0.00 0.00 39.69 2.59
150 151 8.135529 TCGTCGAAGAAATGAATGTATGTAGAT 58.864 33.333 0.00 0.00 39.69 1.98
151 152 8.210525 CGTCGAAGAAATGAATGTATGTAGATG 58.789 37.037 0.00 0.00 39.69 2.90
152 153 9.035607 GTCGAAGAAATGAATGTATGTAGATGT 57.964 33.333 0.00 0.00 39.69 3.06
183 184 8.771920 AGTTGTAGATACATCGATTTTTGTGA 57.228 30.769 0.00 0.00 35.89 3.58
184 185 8.656849 AGTTGTAGATACATCGATTTTTGTGAC 58.343 33.333 0.00 0.00 35.89 3.67
185 186 8.440059 GTTGTAGATACATCGATTTTTGTGACA 58.560 33.333 0.00 0.00 35.89 3.58
186 187 8.541133 TGTAGATACATCGATTTTTGTGACAA 57.459 30.769 0.00 0.00 0.00 3.18
187 188 8.655970 TGTAGATACATCGATTTTTGTGACAAG 58.344 33.333 0.00 0.00 0.00 3.16
188 189 7.672983 AGATACATCGATTTTTGTGACAAGT 57.327 32.000 0.00 0.00 0.00 3.16
189 190 8.771920 AGATACATCGATTTTTGTGACAAGTA 57.228 30.769 0.00 0.00 0.00 2.24
190 191 9.214957 AGATACATCGATTTTTGTGACAAGTAA 57.785 29.630 0.00 0.00 0.00 2.24
191 192 9.988350 GATACATCGATTTTTGTGACAAGTAAT 57.012 29.630 0.00 2.98 0.00 1.89
193 194 8.728088 ACATCGATTTTTGTGACAAGTAATTC 57.272 30.769 0.00 0.00 0.00 2.17
194 195 7.807907 ACATCGATTTTTGTGACAAGTAATTCC 59.192 33.333 0.00 0.00 0.00 3.01
195 196 6.367421 TCGATTTTTGTGACAAGTAATTCCG 58.633 36.000 0.00 4.57 0.00 4.30
196 197 6.203145 TCGATTTTTGTGACAAGTAATTCCGA 59.797 34.615 0.00 6.54 0.00 4.55
197 198 6.853872 CGATTTTTGTGACAAGTAATTCCGAA 59.146 34.615 0.00 0.00 0.00 4.30
198 199 7.149192 CGATTTTTGTGACAAGTAATTCCGAAC 60.149 37.037 0.00 0.00 0.00 3.95
199 200 4.718858 TTGTGACAAGTAATTCCGAACG 57.281 40.909 0.00 0.00 0.00 3.95
200 201 3.061322 TGTGACAAGTAATTCCGAACGG 58.939 45.455 6.94 6.94 0.00 4.44
201 202 3.243805 TGTGACAAGTAATTCCGAACGGA 60.244 43.478 12.04 12.04 43.52 4.69
202 203 3.367025 GTGACAAGTAATTCCGAACGGAG 59.633 47.826 15.34 5.60 46.06 4.63
203 204 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
204 205 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
205 206 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
206 207 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
207 208 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
208 209 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
209 210 1.400737 ATTCCGAACGGAGGGAGTAG 58.599 55.000 15.34 0.00 46.06 2.57
210 211 0.038744 TTCCGAACGGAGGGAGTAGT 59.961 55.000 15.34 0.00 46.06 2.73
211 212 0.911769 TCCGAACGGAGGGAGTAGTA 59.088 55.000 12.04 0.00 39.76 1.82
212 213 1.492176 TCCGAACGGAGGGAGTAGTAT 59.508 52.381 12.04 0.00 39.76 2.12
213 214 2.705658 TCCGAACGGAGGGAGTAGTATA 59.294 50.000 12.04 0.00 39.76 1.47
214 215 3.328931 TCCGAACGGAGGGAGTAGTATAT 59.671 47.826 12.04 0.00 39.76 0.86
217 218 4.874966 CGAACGGAGGGAGTAGTATATAGG 59.125 50.000 0.00 0.00 0.00 2.57
288 289 2.365370 CAGCCCTCTCAGCCTCCT 60.365 66.667 0.00 0.00 0.00 3.69
295 296 1.265236 CTCTCAGCCTCCTCAACAGT 58.735 55.000 0.00 0.00 0.00 3.55
329 330 0.321653 ACCCAAATCCACGACTCTGC 60.322 55.000 0.00 0.00 0.00 4.26
330 331 0.036010 CCCAAATCCACGACTCTGCT 60.036 55.000 0.00 0.00 0.00 4.24
331 332 1.611673 CCCAAATCCACGACTCTGCTT 60.612 52.381 0.00 0.00 0.00 3.91
343 344 2.545946 GACTCTGCTTTGTGTTCCTGTC 59.454 50.000 0.00 0.00 0.00 3.51
349 350 2.450160 CTTTGTGTTCCTGTCGCAAAC 58.550 47.619 0.00 0.00 39.34 2.93
360 361 1.815840 TCGCAAACGACCTGCACAA 60.816 52.632 0.00 0.00 45.12 3.33
377 378 4.447054 TGCACAAACACAAAGTTGAAACTG 59.553 37.500 0.00 0.00 41.19 3.16
380 381 5.118510 CACAAACACAAAGTTGAAACTGACC 59.881 40.000 0.00 0.00 41.19 4.02
400 401 6.194967 TGACCTCATCACCAACTCTAAGATA 58.805 40.000 0.00 0.00 29.99 1.98
409 410 9.606631 ATCACCAACTCTAAGATAATCTTGTTC 57.393 33.333 0.00 0.00 37.29 3.18
424 425 0.682532 TGTTCAGCACTTGTGGGCAA 60.683 50.000 2.81 0.00 0.00 4.52
427 428 0.961019 TCAGCACTTGTGGGCAATTC 59.039 50.000 2.81 0.00 33.65 2.17
433 434 2.801113 CTTGTGGGCAATTCACGGCG 62.801 60.000 4.80 4.80 37.91 6.46
453 454 4.423732 GCGGTTGATTCATGCACTTTTAT 58.576 39.130 0.00 0.00 0.00 1.40
456 457 6.267817 CGGTTGATTCATGCACTTTTATCAT 58.732 36.000 0.00 0.00 0.00 2.45
458 459 7.037438 GGTTGATTCATGCACTTTTATCATGT 58.963 34.615 0.00 0.00 38.82 3.21
554 578 9.244799 CAAGTATACGCAACATATCAAGTTCTA 57.755 33.333 0.00 0.00 0.00 2.10
579 603 3.740044 AATGTGTTGTGCATACGTAGC 57.260 42.857 0.08 5.78 0.00 3.58
581 605 3.579335 TGTGTTGTGCATACGTAGCTA 57.421 42.857 15.00 0.00 0.00 3.32
584 608 4.150980 TGTGTTGTGCATACGTAGCTAAAC 59.849 41.667 15.00 16.52 0.00 2.01
585 609 4.387862 GTGTTGTGCATACGTAGCTAAACT 59.612 41.667 20.98 0.00 32.76 2.66
594 618 4.332428 ACGTAGCTAAACTGGAGTTTGT 57.668 40.909 13.87 0.95 46.56 2.83
609 638 5.538053 TGGAGTTTGTATGCAAAAAGATGGA 59.462 36.000 10.72 0.00 45.01 3.41
612 641 6.458210 AGTTTGTATGCAAAAAGATGGAAGG 58.542 36.000 10.72 0.00 45.01 3.46
640 669 6.882610 AAGAAAAGATGTGCACAATAGTCA 57.117 33.333 25.72 0.00 0.00 3.41
646 675 3.311486 TGTGCACAATAGTCACGATCA 57.689 42.857 19.28 0.00 32.21 2.92
652 681 3.241553 CACAATAGTCACGATCAGAAGCG 59.758 47.826 0.00 0.00 40.92 4.68
692 727 7.201145 GCAGAATGTTGCTATCAATTCATTCT 58.799 34.615 14.61 14.61 46.12 2.40
713 748 6.109156 TCTGTTACTTGAACCTATTCTGCA 57.891 37.500 0.00 0.00 37.22 4.41
714 749 6.711277 TCTGTTACTTGAACCTATTCTGCAT 58.289 36.000 0.00 0.00 37.22 3.96
715 750 7.168219 TCTGTTACTTGAACCTATTCTGCATT 58.832 34.615 0.00 0.00 37.22 3.56
720 755 9.595823 TTACTTGAACCTATTCTGCATTAGTAC 57.404 33.333 0.00 0.00 35.69 2.73
732 767 7.050970 TCTGCATTAGTACTTTATCATCCGT 57.949 36.000 0.00 0.00 0.00 4.69
733 768 7.497595 TCTGCATTAGTACTTTATCATCCGTT 58.502 34.615 0.00 0.00 0.00 4.44
740 775 7.772332 AGTACTTTATCATCCGTTCAATCAC 57.228 36.000 0.00 0.00 0.00 3.06
742 777 4.034048 ACTTTATCATCCGTTCAATCACGC 59.966 41.667 0.00 0.00 38.93 5.34
743 778 0.930310 ATCATCCGTTCAATCACGCG 59.070 50.000 3.53 3.53 38.93 6.01
765 800 1.300465 CCGATGGATCACGCTGAGG 60.300 63.158 0.00 0.00 0.00 3.86
865 5649 2.668457 CGTGGAGAACATGCAACTAGTC 59.332 50.000 0.00 0.00 0.00 2.59
866 5650 3.003480 GTGGAGAACATGCAACTAGTCC 58.997 50.000 0.00 0.00 0.00 3.85
880 5664 2.429610 ACTAGTCCGTGTTCACAACTGT 59.570 45.455 14.19 9.50 0.00 3.55
881 5665 1.935933 AGTCCGTGTTCACAACTGTC 58.064 50.000 3.87 0.00 0.00 3.51
882 5666 1.206132 AGTCCGTGTTCACAACTGTCA 59.794 47.619 3.87 0.00 0.00 3.58
883 5667 2.004017 GTCCGTGTTCACAACTGTCAA 58.996 47.619 3.87 0.00 0.00 3.18
884 5668 2.004017 TCCGTGTTCACAACTGTCAAC 58.996 47.619 3.87 0.00 0.00 3.18
885 5669 2.006888 CCGTGTTCACAACTGTCAACT 58.993 47.619 0.00 0.00 0.00 3.16
887 5671 2.670905 CGTGTTCACAACTGTCAACTGA 59.329 45.455 0.00 0.00 0.00 3.41
947 5757 2.492484 ACCACGCAAAAACAAACCAGTA 59.508 40.909 0.00 0.00 0.00 2.74
956 5767 4.464069 AAACAAACCAGTAAGCAGCAAA 57.536 36.364 0.00 0.00 0.00 3.68
957 5768 4.670896 AACAAACCAGTAAGCAGCAAAT 57.329 36.364 0.00 0.00 0.00 2.32
1045 5856 0.179065 CATGGCGATCTTCCTGCTGA 60.179 55.000 0.00 0.00 0.00 4.26
1066 5877 3.775654 CGCTCTCCACCTCCCACC 61.776 72.222 0.00 0.00 0.00 4.61
1191 6002 0.546122 ATGGCAAGAGATACCCGCAA 59.454 50.000 0.00 0.00 0.00 4.85
1294 6105 0.321671 CCCATCGGAGTGTGACAACT 59.678 55.000 0.00 0.00 0.00 3.16
1392 15228 3.657398 ATCAAGATCAGTGCCAATGGA 57.343 42.857 2.05 0.00 0.00 3.41
1485 15321 0.752054 CACCCTGTGCCAACAACATT 59.248 50.000 0.00 0.00 35.37 2.71
1577 15413 1.131638 TCTGACCAGTGAGCACCTTT 58.868 50.000 0.00 0.00 0.00 3.11
1579 15415 0.179020 TGACCAGTGAGCACCTTTGG 60.179 55.000 6.00 6.00 35.07 3.28
1591 15427 4.678622 AGCACCTTTGGTTTTTCTAAACG 58.321 39.130 0.00 0.00 43.68 3.60
1656 15495 6.417044 GTCGGTCACAGTGTCATGTATATAAC 59.583 42.308 0.00 0.00 0.00 1.89
1690 15545 4.422592 AGTTACACAGATCCTATAGGGGGA 59.577 45.833 18.97 0.00 37.26 4.81
1764 15624 5.300752 CCTATTGTTTAGCACCGATGAGAT 58.699 41.667 0.00 0.00 0.00 2.75
1788 15648 5.758296 TGTTCTTGTGTGTGATCTTCTAACC 59.242 40.000 0.00 0.00 0.00 2.85
1792 15660 5.029807 TGTGTGTGATCTTCTAACCACAA 57.970 39.130 0.00 0.00 40.63 3.33
1806 15674 2.020720 ACCACAATCGCACAAACTGAA 58.979 42.857 0.00 0.00 0.00 3.02
1883 15902 2.772287 CTCACCTTGGAGTCTTCAACC 58.228 52.381 0.00 0.00 0.00 3.77
1958 17780 2.823959 AGGTTCCCGACATACACCTTA 58.176 47.619 0.00 0.00 33.89 2.69
1964 17786 2.167693 CCCGACATACACCTTAGCTTCA 59.832 50.000 0.00 0.00 0.00 3.02
1976 17798 1.106285 TAGCTTCATCGAGCAGCTCA 58.894 50.000 22.49 9.85 43.03 4.26
1983 17805 2.997621 ATCGAGCAGCTCATCGTCGC 62.998 60.000 22.49 0.00 39.86 5.19
2000 17822 3.546617 GTCGCACTCAGACATATACTCG 58.453 50.000 0.00 0.00 38.42 4.18
2021 17843 1.067142 TCATCCACTTCGTGCTGGTAC 60.067 52.381 0.00 0.00 31.34 3.34
2044 17866 1.450211 CTTGTCGTTGAGGGGTGGT 59.550 57.895 0.00 0.00 0.00 4.16
2045 17867 0.682852 CTTGTCGTTGAGGGGTGGTA 59.317 55.000 0.00 0.00 0.00 3.25
2057 17879 1.273438 GGGGTGGTACCTCTAGGAACA 60.273 57.143 14.36 0.00 35.29 3.18
2069 17891 4.389576 GGAACAGCCTTGCGCACG 62.390 66.667 11.12 8.76 41.38 5.34
2074 17896 2.124983 AGCCTTGCGCACGATCAT 60.125 55.556 16.43 0.00 41.38 2.45
2105 17927 0.401738 ACACCTCCTGTCCACATTGG 59.598 55.000 0.00 0.00 39.43 3.16
2169 17992 7.228108 ACCACAAGCTACATCTCATATGAATTG 59.772 37.037 6.90 9.53 0.00 2.32
2185 18008 3.253921 TGAATTGACCATGACAACTGCAG 59.746 43.478 13.48 13.48 0.00 4.41
2233 18727 5.473039 ACAAATAAACAAGCCTCATCAAGC 58.527 37.500 0.00 0.00 0.00 4.01
2240 18734 1.174783 AGCCTCATCAAGCTGCAAAG 58.825 50.000 1.02 0.00 38.11 2.77
2292 18786 1.515020 CCTCTCAGCCTCCTGAACG 59.485 63.158 0.00 0.00 46.84 3.95
2363 18857 1.129811 GTAAACGACCTGCAAATCCCG 59.870 52.381 0.00 0.00 0.00 5.14
2374 18868 3.792401 TGCAAATCCCGACAGTACATAG 58.208 45.455 0.00 0.00 0.00 2.23
2425 18924 7.624764 GCCAAAAAGAAAACATGCATATCCTTG 60.625 37.037 0.00 0.00 0.00 3.61
2443 18942 1.753930 TGTGCCGAATGCTGATGAAT 58.246 45.000 0.00 0.00 42.00 2.57
2444 18943 1.402613 TGTGCCGAATGCTGATGAATG 59.597 47.619 0.00 0.00 42.00 2.67
2445 18944 1.672363 GTGCCGAATGCTGATGAATGA 59.328 47.619 0.00 0.00 42.00 2.57
2446 18945 2.097954 GTGCCGAATGCTGATGAATGAA 59.902 45.455 0.00 0.00 42.00 2.57
2450 18949 4.443394 GCCGAATGCTGATGAATGAAATTC 59.557 41.667 0.00 0.00 44.91 2.17
2470 18969 9.516546 GAAATTCTCCCTAAAGAAAAAGGAGTA 57.483 33.333 4.41 0.00 43.80 2.59
2481 18980 3.457610 AAAAGGAGTACCGACGAAACA 57.542 42.857 0.00 0.00 41.83 2.83
2519 19018 6.090763 TGCAGTACTGATAAAAACAGATCACG 59.909 38.462 27.08 0.00 38.55 4.35
2522 19021 9.135843 CAGTACTGATAAAAACAGATCACGTAA 57.864 33.333 18.45 0.00 38.55 3.18
2535 19034 7.464358 ACAGATCACGTAACAATTTAATGAGC 58.536 34.615 0.00 0.00 0.00 4.26
2556 19055 3.711086 CAGTGATCAATCCGAGTGGTAG 58.289 50.000 0.00 0.00 36.30 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.907910 ACATGAAATTGAGCTCGTGC 57.092 45.000 9.64 0.07 40.05 5.34
9 10 7.468922 TTCTATACATGAAATTGAGCTCGTG 57.531 36.000 9.64 0.00 35.18 4.35
10 11 6.201806 GCTTCTATACATGAAATTGAGCTCGT 59.798 38.462 9.64 0.38 0.00 4.18
11 12 6.201615 TGCTTCTATACATGAAATTGAGCTCG 59.798 38.462 9.64 0.00 0.00 5.03
12 13 7.440556 TCTGCTTCTATACATGAAATTGAGCTC 59.559 37.037 6.82 6.82 0.00 4.09
13 14 7.278135 TCTGCTTCTATACATGAAATTGAGCT 58.722 34.615 0.00 0.00 0.00 4.09
14 15 7.488187 TCTGCTTCTATACATGAAATTGAGC 57.512 36.000 0.00 2.88 0.00 4.26
77 78 2.375014 TTCTTTTGTGGGGGAGTTCC 57.625 50.000 0.00 0.00 0.00 3.62
78 79 4.081365 TGTTTTTCTTTTGTGGGGGAGTTC 60.081 41.667 0.00 0.00 0.00 3.01
79 80 3.841255 TGTTTTTCTTTTGTGGGGGAGTT 59.159 39.130 0.00 0.00 0.00 3.01
80 81 3.445987 TGTTTTTCTTTTGTGGGGGAGT 58.554 40.909 0.00 0.00 0.00 3.85
81 82 4.687901 ATGTTTTTCTTTTGTGGGGGAG 57.312 40.909 0.00 0.00 0.00 4.30
82 83 5.212745 AGTATGTTTTTCTTTTGTGGGGGA 58.787 37.500 0.00 0.00 0.00 4.81
83 84 5.510690 GGAGTATGTTTTTCTTTTGTGGGGG 60.511 44.000 0.00 0.00 0.00 5.40
84 85 5.510690 GGGAGTATGTTTTTCTTTTGTGGGG 60.511 44.000 0.00 0.00 0.00 4.96
85 86 5.304357 AGGGAGTATGTTTTTCTTTTGTGGG 59.696 40.000 0.00 0.00 0.00 4.61
86 87 6.405278 AGGGAGTATGTTTTTCTTTTGTGG 57.595 37.500 0.00 0.00 0.00 4.17
87 88 6.447162 GGAGGGAGTATGTTTTTCTTTTGTG 58.553 40.000 0.00 0.00 0.00 3.33
88 89 5.240844 CGGAGGGAGTATGTTTTTCTTTTGT 59.759 40.000 0.00 0.00 0.00 2.83
89 90 5.240844 ACGGAGGGAGTATGTTTTTCTTTTG 59.759 40.000 0.00 0.00 0.00 2.44
90 91 5.382616 ACGGAGGGAGTATGTTTTTCTTTT 58.617 37.500 0.00 0.00 0.00 2.27
91 92 4.981812 ACGGAGGGAGTATGTTTTTCTTT 58.018 39.130 0.00 0.00 0.00 2.52
92 93 4.635699 ACGGAGGGAGTATGTTTTTCTT 57.364 40.909 0.00 0.00 0.00 2.52
93 94 4.576879 GAACGGAGGGAGTATGTTTTTCT 58.423 43.478 0.00 0.00 0.00 2.52
94 95 3.370061 CGAACGGAGGGAGTATGTTTTTC 59.630 47.826 0.00 0.00 0.00 2.29
95 96 3.332034 CGAACGGAGGGAGTATGTTTTT 58.668 45.455 0.00 0.00 0.00 1.94
96 97 2.354403 CCGAACGGAGGGAGTATGTTTT 60.354 50.000 7.53 0.00 37.50 2.43
97 98 1.206371 CCGAACGGAGGGAGTATGTTT 59.794 52.381 7.53 0.00 37.50 2.83
98 99 0.822164 CCGAACGGAGGGAGTATGTT 59.178 55.000 7.53 0.00 37.50 2.71
99 100 0.033796 TCCGAACGGAGGGAGTATGT 60.034 55.000 12.04 0.00 39.76 2.29
100 101 1.108776 TTCCGAACGGAGGGAGTATG 58.891 55.000 15.34 0.00 46.06 2.39
101 102 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
102 103 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
103 104 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
104 105 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
105 106 1.753073 GAGTAATTCCGAACGGAGGGA 59.247 52.381 15.34 2.49 46.06 4.20
106 107 1.535437 CGAGTAATTCCGAACGGAGGG 60.535 57.143 15.34 0.00 46.06 4.30
107 108 1.133790 ACGAGTAATTCCGAACGGAGG 59.866 52.381 15.34 4.28 46.06 4.30
108 109 2.448219 GACGAGTAATTCCGAACGGAG 58.552 52.381 15.34 5.60 46.06 4.63
109 110 1.202065 CGACGAGTAATTCCGAACGGA 60.202 52.381 12.04 12.04 43.52 4.69
110 111 1.186030 CGACGAGTAATTCCGAACGG 58.814 55.000 6.94 6.94 0.00 4.44
111 112 2.163826 TCGACGAGTAATTCCGAACG 57.836 50.000 0.00 0.00 0.00 3.95
112 113 3.751621 TCTTCGACGAGTAATTCCGAAC 58.248 45.455 0.00 0.00 35.71 3.95
113 114 4.424061 TTCTTCGACGAGTAATTCCGAA 57.576 40.909 0.00 0.00 37.61 4.30
114 115 4.424061 TTTCTTCGACGAGTAATTCCGA 57.576 40.909 0.00 0.00 0.00 4.55
115 116 4.796830 TCATTTCTTCGACGAGTAATTCCG 59.203 41.667 0.00 0.00 0.00 4.30
116 117 6.642683 TTCATTTCTTCGACGAGTAATTCC 57.357 37.500 0.00 0.00 0.00 3.01
117 118 7.676393 ACATTCATTTCTTCGACGAGTAATTC 58.324 34.615 0.00 0.00 0.00 2.17
118 119 7.596749 ACATTCATTTCTTCGACGAGTAATT 57.403 32.000 0.00 0.00 0.00 1.40
119 120 8.755941 CATACATTCATTTCTTCGACGAGTAAT 58.244 33.333 0.00 0.00 0.00 1.89
120 121 7.758076 ACATACATTCATTTCTTCGACGAGTAA 59.242 33.333 0.00 0.00 0.00 2.24
121 122 7.255569 ACATACATTCATTTCTTCGACGAGTA 58.744 34.615 0.00 0.00 0.00 2.59
122 123 6.100004 ACATACATTCATTTCTTCGACGAGT 58.900 36.000 0.00 0.00 0.00 4.18
123 124 6.575083 ACATACATTCATTTCTTCGACGAG 57.425 37.500 0.00 0.00 0.00 4.18
124 125 7.477494 TCTACATACATTCATTTCTTCGACGA 58.523 34.615 0.00 0.00 0.00 4.20
125 126 7.679659 TCTACATACATTCATTTCTTCGACG 57.320 36.000 0.00 0.00 0.00 5.12
126 127 9.035607 ACATCTACATACATTCATTTCTTCGAC 57.964 33.333 0.00 0.00 0.00 4.20
157 158 9.863845 TCACAAAAATCGATGTATCTACAACTA 57.136 29.630 0.00 0.00 39.99 2.24
158 159 8.656849 GTCACAAAAATCGATGTATCTACAACT 58.343 33.333 0.00 0.00 39.99 3.16
159 160 8.440059 TGTCACAAAAATCGATGTATCTACAAC 58.560 33.333 0.00 0.00 39.99 3.32
160 161 8.541133 TGTCACAAAAATCGATGTATCTACAA 57.459 30.769 0.00 0.00 39.99 2.41
161 162 8.541133 TTGTCACAAAAATCGATGTATCTACA 57.459 30.769 0.00 0.00 40.98 2.74
162 163 8.656849 ACTTGTCACAAAAATCGATGTATCTAC 58.343 33.333 0.00 0.00 0.00 2.59
163 164 8.771920 ACTTGTCACAAAAATCGATGTATCTA 57.228 30.769 0.00 0.00 0.00 1.98
164 165 7.672983 ACTTGTCACAAAAATCGATGTATCT 57.327 32.000 0.00 0.00 0.00 1.98
165 166 9.988350 ATTACTTGTCACAAAAATCGATGTATC 57.012 29.630 0.00 0.00 0.00 2.24
167 168 9.820229 GAATTACTTGTCACAAAAATCGATGTA 57.180 29.630 0.00 0.00 0.00 2.29
168 169 7.807907 GGAATTACTTGTCACAAAAATCGATGT 59.192 33.333 0.00 0.00 0.00 3.06
169 170 7.007367 CGGAATTACTTGTCACAAAAATCGATG 59.993 37.037 0.00 0.00 0.00 3.84
170 171 7.021196 CGGAATTACTTGTCACAAAAATCGAT 58.979 34.615 0.00 0.00 0.00 3.59
171 172 6.203145 TCGGAATTACTTGTCACAAAAATCGA 59.797 34.615 0.00 0.00 0.00 3.59
172 173 6.367421 TCGGAATTACTTGTCACAAAAATCG 58.633 36.000 0.00 0.00 0.00 3.34
173 174 7.149192 CGTTCGGAATTACTTGTCACAAAAATC 60.149 37.037 0.00 0.00 0.00 2.17
174 175 6.635239 CGTTCGGAATTACTTGTCACAAAAAT 59.365 34.615 0.00 0.00 0.00 1.82
175 176 5.966503 CGTTCGGAATTACTTGTCACAAAAA 59.033 36.000 0.00 0.00 0.00 1.94
176 177 5.503498 CGTTCGGAATTACTTGTCACAAAA 58.497 37.500 0.00 0.00 0.00 2.44
177 178 4.024725 CCGTTCGGAATTACTTGTCACAAA 60.025 41.667 5.19 0.00 0.00 2.83
178 179 3.495377 CCGTTCGGAATTACTTGTCACAA 59.505 43.478 5.19 0.00 0.00 3.33
179 180 3.061322 CCGTTCGGAATTACTTGTCACA 58.939 45.455 5.19 0.00 0.00 3.58
180 181 3.319755 TCCGTTCGGAATTACTTGTCAC 58.680 45.455 11.66 0.00 0.00 3.67
181 182 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
182 183 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
183 184 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
184 185 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
185 186 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
186 187 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
187 188 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
188 189 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
189 190 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
190 191 1.341778 ACTACTCCCTCCGTTCGGAAT 60.342 52.381 14.79 2.09 33.41 3.01
191 192 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
192 193 0.911769 TACTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
193 194 1.978454 ATACTACTCCCTCCGTTCGG 58.022 55.000 4.74 4.74 0.00 4.30
194 195 4.874966 CCTATATACTACTCCCTCCGTTCG 59.125 50.000 0.00 0.00 0.00 3.95
195 196 6.059787 TCCTATATACTACTCCCTCCGTTC 57.940 45.833 0.00 0.00 0.00 3.95
196 197 6.045341 AGTTCCTATATACTACTCCCTCCGTT 59.955 42.308 0.00 0.00 0.00 4.44
197 198 5.551189 AGTTCCTATATACTACTCCCTCCGT 59.449 44.000 0.00 0.00 0.00 4.69
198 199 6.064735 AGTTCCTATATACTACTCCCTCCG 57.935 45.833 0.00 0.00 0.00 4.63
199 200 8.267183 GTCTAGTTCCTATATACTACTCCCTCC 58.733 44.444 0.00 0.00 0.00 4.30
200 201 8.267183 GGTCTAGTTCCTATATACTACTCCCTC 58.733 44.444 0.00 0.00 0.00 4.30
201 202 7.968903 AGGTCTAGTTCCTATATACTACTCCCT 59.031 40.741 7.30 0.00 33.04 4.20
202 203 8.161640 AGGTCTAGTTCCTATATACTACTCCC 57.838 42.308 7.30 0.00 33.04 4.30
233 234 9.923786 CATCGCTATGTAAGTGTACTCTATATC 57.076 37.037 0.00 0.00 37.01 1.63
244 245 5.049828 TGATGTTCCATCGCTATGTAAGTG 58.950 41.667 0.00 0.00 37.03 3.16
267 268 3.325753 GGCTGAGAGGGCTGTGGT 61.326 66.667 0.00 0.00 0.00 4.16
269 270 2.583520 GAGGCTGAGAGGGCTGTG 59.416 66.667 0.00 0.00 42.23 3.66
288 289 4.681074 TTGTCACCATGAGTACTGTTGA 57.319 40.909 0.00 0.00 0.00 3.18
317 318 0.464036 ACACAAAGCAGAGTCGTGGA 59.536 50.000 0.00 0.00 31.83 4.02
329 330 2.450160 GTTTGCGACAGGAACACAAAG 58.550 47.619 0.00 0.00 31.39 2.77
330 331 1.202087 CGTTTGCGACAGGAACACAAA 60.202 47.619 0.00 0.00 41.33 2.83
331 332 0.375454 CGTTTGCGACAGGAACACAA 59.625 50.000 0.00 0.00 41.33 3.33
343 344 1.063327 TTTGTGCAGGTCGTTTGCG 59.937 52.632 0.00 0.00 44.40 4.85
349 350 1.132262 ACTTTGTGTTTGTGCAGGTCG 59.868 47.619 0.00 0.00 0.00 4.79
360 361 4.764823 TGAGGTCAGTTTCAACTTTGTGTT 59.235 37.500 0.00 0.00 37.08 3.32
377 378 5.606348 ATCTTAGAGTTGGTGATGAGGTC 57.394 43.478 0.00 0.00 0.00 3.85
380 381 9.258826 CAAGATTATCTTAGAGTTGGTGATGAG 57.741 37.037 7.18 0.00 33.78 2.90
400 401 2.624838 CCCACAAGTGCTGAACAAGATT 59.375 45.455 0.00 0.00 0.00 2.40
409 410 0.675083 TGAATTGCCCACAAGTGCTG 59.325 50.000 0.00 0.00 39.69 4.41
424 425 1.401552 CATGAATCAACCGCCGTGAAT 59.598 47.619 0.00 0.00 0.00 2.57
427 428 1.226379 GCATGAATCAACCGCCGTG 60.226 57.895 0.00 0.00 0.00 4.94
433 434 7.037438 ACATGATAAAAGTGCATGAATCAACC 58.963 34.615 0.00 0.00 41.35 3.77
528 548 8.131455 AGAACTTGATATGTTGCGTATACTTG 57.869 34.615 0.56 0.00 0.00 3.16
529 549 9.811995 TTAGAACTTGATATGTTGCGTATACTT 57.188 29.630 0.56 0.00 0.00 2.24
544 568 9.410556 GCACAACACATTAATTTAGAACTTGAT 57.589 29.630 0.00 0.00 0.00 2.57
554 578 6.745450 GCTACGTATGCACAACACATTAATTT 59.255 34.615 10.79 0.00 0.00 1.82
566 590 3.193903 TCCAGTTTAGCTACGTATGCACA 59.806 43.478 15.98 4.38 0.00 4.57
579 603 8.134895 TCTTTTTGCATACAAACTCCAGTTTAG 58.865 33.333 4.38 3.05 45.29 1.85
581 605 6.872920 TCTTTTTGCATACAAACTCCAGTTT 58.127 32.000 0.00 0.00 45.29 2.66
584 608 5.865552 CCATCTTTTTGCATACAAACTCCAG 59.134 40.000 0.00 0.00 45.29 3.86
585 609 5.538053 TCCATCTTTTTGCATACAAACTCCA 59.462 36.000 0.00 0.00 45.29 3.86
618 647 5.106948 CGTGACTATTGTGCACATCTTTTCT 60.107 40.000 22.39 0.00 32.96 2.52
626 655 3.056891 TCTGATCGTGACTATTGTGCACA 60.057 43.478 17.42 17.42 32.96 4.57
627 656 3.511699 TCTGATCGTGACTATTGTGCAC 58.488 45.455 10.75 10.75 0.00 4.57
628 657 3.866883 TCTGATCGTGACTATTGTGCA 57.133 42.857 0.00 0.00 0.00 4.57
629 658 3.000724 GCTTCTGATCGTGACTATTGTGC 59.999 47.826 0.00 0.00 0.00 4.57
631 660 3.119459 ACGCTTCTGATCGTGACTATTGT 60.119 43.478 4.98 0.00 37.55 2.71
632 661 3.439293 ACGCTTCTGATCGTGACTATTG 58.561 45.455 4.98 0.00 37.55 1.90
633 662 3.696898 GACGCTTCTGATCGTGACTATT 58.303 45.455 9.62 0.00 39.22 1.73
635 664 1.062148 CGACGCTTCTGATCGTGACTA 59.938 52.381 9.62 0.00 39.22 2.59
636 665 0.179187 CGACGCTTCTGATCGTGACT 60.179 55.000 9.62 0.00 39.22 3.41
640 669 1.592400 TTCCCGACGCTTCTGATCGT 61.592 55.000 5.39 5.39 42.09 3.73
646 675 1.003718 CCCTTTTCCCGACGCTTCT 60.004 57.895 0.00 0.00 0.00 2.85
652 681 1.971695 CTGCCACCCTTTTCCCGAC 60.972 63.158 0.00 0.00 0.00 4.79
692 727 8.100791 ACTAATGCAGAATAGGTTCAAGTAACA 58.899 33.333 0.00 0.00 40.08 2.41
696 731 7.852263 AGTACTAATGCAGAATAGGTTCAAGT 58.148 34.615 0.00 0.00 36.79 3.16
714 749 9.309516 GTGATTGAACGGATGATAAAGTACTAA 57.690 33.333 0.00 0.00 0.00 2.24
715 750 7.646526 CGTGATTGAACGGATGATAAAGTACTA 59.353 37.037 0.00 0.00 39.89 1.82
720 755 4.518217 GCGTGATTGAACGGATGATAAAG 58.482 43.478 0.00 0.00 43.75 1.85
730 765 2.981969 GGAAACGCGTGATTGAACG 58.018 52.632 14.98 0.00 46.30 3.95
743 778 0.652592 CAGCGTGATCCATCGGAAAC 59.347 55.000 0.00 0.00 34.34 2.78
765 800 0.249489 AGGACGGACATATTCTGCGC 60.249 55.000 0.00 0.00 33.21 6.09
767 802 7.097192 TGATAAATAGGACGGACATATTCTGC 58.903 38.462 0.00 0.00 34.94 4.26
865 5649 2.006888 AGTTGACAGTTGTGAACACGG 58.993 47.619 15.18 0.00 43.13 4.94
866 5650 2.670905 TCAGTTGACAGTTGTGAACACG 59.329 45.455 15.18 7.32 43.13 4.49
887 5671 8.732531 GGCTCGACTTTATATAGTGATCTACTT 58.267 37.037 0.09 0.00 40.89 2.24
911 5708 0.742635 GTGGTTAGAGAGCTGCAGGC 60.743 60.000 17.12 7.98 42.19 4.85
947 5757 5.305386 ACCCTCTTTTTCTTATTTGCTGCTT 59.695 36.000 0.00 0.00 0.00 3.91
956 5767 8.990163 TTGAACTGTAACCCTCTTTTTCTTAT 57.010 30.769 0.00 0.00 0.00 1.73
957 5768 8.050930 ACTTGAACTGTAACCCTCTTTTTCTTA 58.949 33.333 0.00 0.00 0.00 2.10
1032 5843 1.505477 GCGCCATCAGCAGGAAGATC 61.505 60.000 0.00 0.00 44.04 2.75
1045 5856 3.474570 GGAGGTGGAGAGCGCCAT 61.475 66.667 2.29 0.00 40.68 4.40
1191 6002 3.480133 GGGGGCGAGCAGTGGTAT 61.480 66.667 0.00 0.00 0.00 2.73
1294 6105 0.471191 TCCTCGTCGCTATGGTAGGA 59.529 55.000 0.00 0.00 0.00 2.94
1392 15228 0.601841 CCTTGGCGTACACGGAGTTT 60.602 55.000 3.67 0.00 41.61 2.66
1577 15413 4.035909 GCTCACCTTCGTTTAGAAAAACCA 59.964 41.667 0.00 0.00 41.68 3.67
1579 15415 4.209112 CGCTCACCTTCGTTTAGAAAAAC 58.791 43.478 0.00 0.00 41.36 2.43
1591 15427 2.970974 GCAACCTGCGCTCACCTTC 61.971 63.158 9.73 0.00 31.71 3.46
1690 15545 9.716531 CACACAATCATATACATAATCTGACCT 57.283 33.333 0.00 0.00 0.00 3.85
1739 15599 3.118408 TCATCGGTGCTAAACAATAGGCT 60.118 43.478 0.00 0.00 0.00 4.58
1746 15606 3.610040 ACATCTCATCGGTGCTAAACA 57.390 42.857 0.00 0.00 0.00 2.83
1764 15624 5.758296 GGTTAGAAGATCACACACAAGAACA 59.242 40.000 0.00 0.00 0.00 3.18
1788 15648 3.607422 TCTTCAGTTTGTGCGATTGTG 57.393 42.857 0.00 0.00 0.00 3.33
1792 15660 4.630894 TTTGTTCTTCAGTTTGTGCGAT 57.369 36.364 0.00 0.00 0.00 4.58
1883 15902 2.293677 ACTCTTCGAGTATGCCGGTATG 59.706 50.000 16.11 0.00 41.51 2.39
1964 17786 1.009108 CGACGATGAGCTGCTCGAT 60.009 57.895 23.35 17.31 38.24 3.59
1976 17798 3.815962 AGTATATGTCTGAGTGCGACGAT 59.184 43.478 0.00 0.00 34.17 3.73
1983 17805 5.239525 TGGATGACGAGTATATGTCTGAGTG 59.760 44.000 0.00 0.00 36.10 3.51
2025 17847 1.302511 CCACCCCTCAACGACAAGG 60.303 63.158 0.00 0.00 0.00 3.61
2036 17858 1.008084 GTTCCTAGAGGTACCACCCCT 59.992 57.143 15.94 7.92 39.75 4.79
2044 17866 1.831736 GCAAGGCTGTTCCTAGAGGTA 59.168 52.381 0.00 0.00 46.94 3.08
2045 17867 0.615850 GCAAGGCTGTTCCTAGAGGT 59.384 55.000 0.00 0.00 46.94 3.85
2055 17877 3.121030 GATCGTGCGCAAGGCTGT 61.121 61.111 23.00 7.26 44.05 4.40
2057 17879 1.143838 TATGATCGTGCGCAAGGCT 59.856 52.632 23.00 11.00 44.05 4.58
2090 17912 0.393537 GCCTCCAATGTGGACAGGAG 60.394 60.000 6.73 7.73 42.67 3.69
2105 17927 2.756760 TCATGCTTTTCTGATTGGCCTC 59.243 45.455 3.32 0.00 0.00 4.70
2169 17992 1.896220 TTCCTGCAGTTGTCATGGTC 58.104 50.000 13.81 0.00 0.00 4.02
2233 18727 5.359756 TGGCTATGTGAGTATACTTTGCAG 58.640 41.667 6.88 2.96 31.55 4.41
2240 18734 6.835819 TCTACCATGGCTATGTGAGTATAC 57.164 41.667 13.04 0.00 32.21 1.47
2425 18924 7.918341 GAATTTCATTCATCAGCATTCGGCAC 61.918 42.308 0.00 0.00 41.22 5.01
2443 18942 8.004801 ACTCCTTTTTCTTTAGGGAGAATTTCA 58.995 33.333 13.30 0.00 44.37 2.69
2444 18943 8.410673 ACTCCTTTTTCTTTAGGGAGAATTTC 57.589 34.615 13.30 0.00 44.37 2.17
2445 18944 9.298250 GTACTCCTTTTTCTTTAGGGAGAATTT 57.702 33.333 13.30 0.00 44.37 1.82
2446 18945 7.889073 GGTACTCCTTTTTCTTTAGGGAGAATT 59.111 37.037 13.30 0.00 44.37 2.17
2450 18949 5.046807 TCGGTACTCCTTTTTCTTTAGGGAG 60.047 44.000 0.00 0.00 46.27 4.30
2453 18952 4.624452 CGTCGGTACTCCTTTTTCTTTAGG 59.376 45.833 0.00 0.00 0.00 2.69
2455 18954 5.452078 TCGTCGGTACTCCTTTTTCTTTA 57.548 39.130 0.00 0.00 0.00 1.85
2458 18957 4.053983 GTTTCGTCGGTACTCCTTTTTCT 58.946 43.478 0.00 0.00 0.00 2.52
2459 18958 3.803778 TGTTTCGTCGGTACTCCTTTTTC 59.196 43.478 0.00 0.00 0.00 2.29
2470 18969 1.060986 GTGTCGTTTTGTTTCGTCGGT 59.939 47.619 0.00 0.00 0.00 4.69
2481 18980 4.049186 CAGTACTGCACTAGTGTCGTTTT 58.951 43.478 23.44 9.76 40.65 2.43
2519 19018 9.793252 ATTGATCACTGCTCATTAAATTGTTAC 57.207 29.630 0.00 0.00 0.00 2.50
2522 19021 7.486647 GGATTGATCACTGCTCATTAAATTGT 58.513 34.615 0.00 0.00 0.00 2.71
2535 19034 2.680312 ACCACTCGGATTGATCACTG 57.320 50.000 0.00 0.00 35.59 3.66


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

AutoCloner maintained by Alex Coulton.