Multiple sequence alignment - TraesCS1A01G028700

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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 TraesCS1A01G028700 chr1A 100.000 3987 0 0 1 3987 13452280 13456266 0.000000e+00 7363.0
1 TraesCS1A01G028700 chr1A 89.759 1826 170 12 2162 3978 22614668 22612851 0.000000e+00 2320.0
2 TraesCS1A01G028700 chr1A 88.093 1814 191 16 2163 3966 13665234 13667032 0.000000e+00 2130.0
3 TraesCS1A01G028700 chr1A 87.206 1829 220 9 2167 3985 12589371 12587547 0.000000e+00 2069.0
4 TraesCS1A01G028700 chr1A 88.849 1659 167 13 2333 3978 12569622 12567969 0.000000e+00 2023.0
5 TraesCS1A01G028700 chr1A 85.274 1331 156 22 843 2150 13313958 13315271 0.000000e+00 1336.0
6 TraesCS1A01G028700 chr1A 85.441 1202 137 20 833 2012 12591019 12589834 0.000000e+00 1216.0
7 TraesCS1A01G028700 chr1A 85.066 904 122 8 995 1896 13414043 13414935 0.000000e+00 909.0
8 TraesCS1A01G028700 chr1A 88.184 347 30 8 243 586 13662503 13662841 1.730000e-108 403.0
9 TraesCS1A01G028700 chr1A 83.467 375 43 11 818 1191 12572586 12572230 8.260000e-87 331.0
10 TraesCS1A01G028700 chr1A 83.792 327 24 8 292 613 12591568 12591266 2.350000e-72 283.0
11 TraesCS1A01G028700 chr1A 88.525 183 16 4 243 424 13313362 13313540 2.410000e-52 217.0
12 TraesCS1A01G028700 chr1A 86.826 167 12 2 8 164 12592576 12592410 1.140000e-40 178.0
13 TraesCS1A01G028700 chr1A 86.228 167 15 4 1 164 13567990 13568151 1.470000e-39 174.0
14 TraesCS1A01G028700 chr1A 90.756 119 8 3 290 407 13662266 13662382 5.330000e-34 156.0
15 TraesCS1A01G028700 chr1A 89.000 100 7 1 604 703 13662960 13663055 1.950000e-23 121.0
16 TraesCS1A01G028700 chr1A 87.356 87 7 1 604 690 12591233 12591151 3.280000e-16 97.1
17 TraesCS1A01G028700 chr1A 90.541 74 5 1 632 703 13313725 13313798 3.280000e-16 97.1
18 TraesCS1A01G028700 chr1A 94.000 50 3 0 758 807 22616333 22616284 4.270000e-10 76.8
19 TraesCS1A01G028700 chr1A 92.857 42 3 0 759 800 12592004 12591963 1.200000e-05 62.1
20 TraesCS1A01G028700 chr1D 92.969 3186 195 19 816 3985 11176861 11180033 0.000000e+00 4615.0
21 TraesCS1A01G028700 chr1D 90.915 1640 136 11 2336 3965 11319543 11321179 0.000000e+00 2191.0
22 TraesCS1A01G028700 chr1D 87.629 1641 181 18 2338 3966 11455550 11457180 0.000000e+00 1886.0
23 TraesCS1A01G028700 chr1D 90.521 960 79 3 904 1863 11494190 11495137 0.000000e+00 1258.0
24 TraesCS1A01G028700 chr1D 85.319 361 47 5 256 614 11176282 11176638 6.290000e-98 368.0
25 TraesCS1A01G028700 chr1D 91.473 129 8 1 458 586 11451992 11452117 1.470000e-39 174.0
26 TraesCS1A01G028700 chr1D 91.525 118 8 2 290 407 11453235 11453350 1.150000e-35 161.0
27 TraesCS1A01G028700 chr1D 82.243 107 12 3 601 703 11452211 11452314 7.100000e-13 86.1
28 TraesCS1A01G028700 chr1D 82.474 97 12 1 604 695 11176658 11176754 3.300000e-11 80.5
29 TraesCS1A01G028700 chr1D 94.000 50 3 0 758 807 11452837 11452886 4.270000e-10 76.8
30 TraesCS1A01G028700 chr1B 88.925 1851 188 10 2151 3987 16857779 16859626 0.000000e+00 2266.0
31 TraesCS1A01G028700 chr1B 89.420 1654 159 9 2342 3987 17017316 17015671 0.000000e+00 2071.0
32 TraesCS1A01G028700 chr1B 89.015 1229 115 8 933 2150 16529962 16531181 0.000000e+00 1504.0
33 TraesCS1A01G028700 chr1B 90.639 1143 90 9 958 2089 16839511 16840647 0.000000e+00 1502.0
34 TraesCS1A01G028700 chr1B 87.468 1165 119 13 998 2150 16856397 16857546 0.000000e+00 1317.0
35 TraesCS1A01G028700 chr1B 93.837 860 53 0 995 1854 17339057 17339916 0.000000e+00 1295.0
36 TraesCS1A01G028700 chr1B 91.328 911 79 0 933 1843 16518179 16519089 0.000000e+00 1245.0
37 TraesCS1A01G028700 chr1B 86.135 1154 110 14 1010 2150 16925821 16926937 0.000000e+00 1199.0
38 TraesCS1A01G028700 chr1B 93.578 436 25 1 1715 2150 16545670 16546102 0.000000e+00 647.0
39 TraesCS1A01G028700 chr1B 87.701 374 44 2 2151 2523 16531478 16531850 6.120000e-118 435.0
40 TraesCS1A01G028700 chr1B 87.733 375 42 4 2151 2523 16546399 16546771 6.120000e-118 435.0
41 TraesCS1A01G028700 chr1B 97.510 241 6 0 1910 2150 16519086 16519326 2.870000e-111 412.0
42 TraesCS1A01G028700 chr1B 91.509 212 16 2 292 502 17338622 17338832 1.400000e-74 291.0
43 TraesCS1A01G028700 chr1B 91.220 205 15 2 371 572 16517709 16517913 3.920000e-70 276.0
44 TraesCS1A01G028700 chrUn 93.743 863 54 0 995 1857 317005241 317004379 0.000000e+00 1295.0
45 TraesCS1A01G028700 chrUn 93.743 863 54 0 995 1857 317985041 317984179 0.000000e+00 1295.0
46 TraesCS1A01G028700 chrUn 93.837 860 53 0 995 1854 346217258 346218117 0.000000e+00 1295.0
47 TraesCS1A01G028700 chrUn 91.509 212 16 2 292 502 317005676 317005466 1.400000e-74 291.0
48 TraesCS1A01G028700 chrUn 91.509 212 16 2 292 502 317985476 317985266 1.400000e-74 291.0
49 TraesCS1A01G028700 chrUn 91.509 212 16 2 292 502 346216823 346217033 1.400000e-74 291.0
50 TraesCS1A01G028700 chrUn 84.354 147 20 2 2012 2156 317004373 317004228 1.490000e-29 141.0


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 TraesCS1A01G028700 chr1A 13452280 13456266 3986 False 7363.000000 7363 100.000000 1 3987 1 chr1A.!!$F2 3986
1 TraesCS1A01G028700 chr1A 22612851 22616333 3482 True 1198.400000 2320 91.879500 758 3978 2 chr1A.!!$R3 3220
2 TraesCS1A01G028700 chr1A 12567969 12572586 4617 True 1177.000000 2023 86.158000 818 3978 2 chr1A.!!$R1 3160
3 TraesCS1A01G028700 chr1A 13414043 13414935 892 False 909.000000 909 85.066000 995 1896 1 chr1A.!!$F1 901
4 TraesCS1A01G028700 chr1A 13662266 13667032 4766 False 702.500000 2130 89.008250 243 3966 4 chr1A.!!$F5 3723
5 TraesCS1A01G028700 chr1A 12587547 12592576 5029 True 650.866667 2069 87.246333 8 3985 6 chr1A.!!$R2 3977
6 TraesCS1A01G028700 chr1A 13313362 13315271 1909 False 550.033333 1336 88.113333 243 2150 3 chr1A.!!$F4 1907
7 TraesCS1A01G028700 chr1D 11319543 11321179 1636 False 2191.000000 2191 90.915000 2336 3965 1 chr1D.!!$F1 1629
8 TraesCS1A01G028700 chr1D 11176282 11180033 3751 False 1687.833333 4615 86.920667 256 3985 3 chr1D.!!$F3 3729
9 TraesCS1A01G028700 chr1D 11494190 11495137 947 False 1258.000000 1258 90.521000 904 1863 1 chr1D.!!$F2 959
10 TraesCS1A01G028700 chr1D 11451992 11457180 5188 False 476.780000 1886 89.374000 290 3966 5 chr1D.!!$F4 3676
11 TraesCS1A01G028700 chr1B 17015671 17017316 1645 True 2071.000000 2071 89.420000 2342 3987 1 chr1B.!!$R1 1645
12 TraesCS1A01G028700 chr1B 16856397 16859626 3229 False 1791.500000 2266 88.196500 998 3987 2 chr1B.!!$F6 2989
13 TraesCS1A01G028700 chr1B 16839511 16840647 1136 False 1502.000000 1502 90.639000 958 2089 1 chr1B.!!$F1 1131
14 TraesCS1A01G028700 chr1B 16925821 16926937 1116 False 1199.000000 1199 86.135000 1010 2150 1 chr1B.!!$F2 1140
15 TraesCS1A01G028700 chr1B 16529962 16531850 1888 False 969.500000 1504 88.358000 933 2523 2 chr1B.!!$F4 1590
16 TraesCS1A01G028700 chr1B 17338622 17339916 1294 False 793.000000 1295 92.673000 292 1854 2 chr1B.!!$F7 1562
17 TraesCS1A01G028700 chr1B 16517709 16519326 1617 False 644.333333 1245 93.352667 371 2150 3 chr1B.!!$F3 1779
18 TraesCS1A01G028700 chr1B 16545670 16546771 1101 False 541.000000 647 90.655500 1715 2523 2 chr1B.!!$F5 808
19 TraesCS1A01G028700 chrUn 317984179 317985476 1297 True 793.000000 1295 92.626000 292 1857 2 chrUn.!!$R2 1565
20 TraesCS1A01G028700 chrUn 346216823 346218117 1294 False 793.000000 1295 92.673000 292 1854 2 chrUn.!!$F1 1562
21 TraesCS1A01G028700 chrUn 317004228 317005676 1448 True 575.666667 1295 89.868667 292 2156 3 chrUn.!!$R1 1864

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
203 214 0.041684 TCTGCTCCTCATCTCCACCA 59.958 55.0 0.00 0.00 0.00 4.17 F
574 1424 0.097150 TCAGATCGAGTGAAGCGACG 59.903 55.0 0.00 0.00 40.94 5.12 F
1241 5122 0.175760 AACATGGAGGATGTCGTCGG 59.824 55.0 0.00 0.00 45.12 4.79 F
2468 7424 0.094216 CGAGTTTGAGACGCATGCTG 59.906 55.0 17.13 11.87 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 5435 0.107312 CACCCTCCATGGAGAGCAAG 60.107 60.000 38.37 22.65 44.53 4.01 R
1706 5596 2.887151 AACCTTCTTCATGTCAGGGG 57.113 50.000 0.00 0.33 0.00 4.79 R
2773 7736 4.302067 TCTTATGGAAGAGCCTTCTGGAT 58.698 43.478 12.71 7.11 36.75 3.41 R
3814 8791 1.152030 ACAGAGACCAAGAGCCCCA 60.152 57.895 0.00 0.00 0.00 4.96 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
30 31 3.008923 TGAATGACCCACTGCACTGAATA 59.991 43.478 0.00 0.00 0.00 1.75
36 37 4.917385 ACCCACTGCACTGAATAATTACA 58.083 39.130 0.00 0.00 0.00 2.41
39 40 5.357878 CCCACTGCACTGAATAATTACATGT 59.642 40.000 2.69 2.69 0.00 3.21
68 69 3.005261 AGCAGTACTATTCAGAGGCATCG 59.995 47.826 0.00 0.00 0.00 3.84
91 96 1.414550 GGGGCTCTGTATCTCTTGACC 59.585 57.143 0.00 0.00 0.00 4.02
100 105 3.324846 TGTATCTCTTGACCTGCTGTTGT 59.675 43.478 0.00 0.00 0.00 3.32
131 142 1.755959 CTCAGTCCTCATCTCCACCAG 59.244 57.143 0.00 0.00 0.00 4.00
132 143 0.177604 CAGTCCTCATCTCCACCAGC 59.822 60.000 0.00 0.00 0.00 4.85
133 144 1.142748 GTCCTCATCTCCACCAGCG 59.857 63.158 0.00 0.00 0.00 5.18
134 145 1.000359 TCCTCATCTCCACCAGCGA 60.000 57.895 0.00 0.00 0.00 4.93
135 146 1.142748 CCTCATCTCCACCAGCGAC 59.857 63.158 0.00 0.00 0.00 5.19
136 147 1.607801 CCTCATCTCCACCAGCGACA 61.608 60.000 0.00 0.00 0.00 4.35
137 148 0.179116 CTCATCTCCACCAGCGACAG 60.179 60.000 0.00 0.00 0.00 3.51
138 149 0.611896 TCATCTCCACCAGCGACAGA 60.612 55.000 0.00 0.00 0.00 3.41
139 150 0.179116 CATCTCCACCAGCGACAGAG 60.179 60.000 0.00 0.00 0.00 3.35
140 151 0.323816 ATCTCCACCAGCGACAGAGA 60.324 55.000 0.00 0.00 37.94 3.10
141 152 0.962855 TCTCCACCAGCGACAGAGAG 60.963 60.000 0.00 0.00 0.00 3.20
142 153 2.125753 CCACCAGCGACAGAGAGC 60.126 66.667 0.00 0.00 0.00 4.09
143 154 2.644212 CCACCAGCGACAGAGAGCT 61.644 63.158 0.00 0.00 45.74 4.09
144 155 1.153862 CACCAGCGACAGAGAGCTC 60.154 63.158 5.27 5.27 42.52 4.09
145 156 2.347322 ACCAGCGACAGAGAGCTCC 61.347 63.158 10.93 1.70 42.52 4.70
146 157 2.493973 CAGCGACAGAGAGCTCCC 59.506 66.667 10.93 0.00 42.52 4.30
147 158 2.051518 CAGCGACAGAGAGCTCCCT 61.052 63.158 10.93 0.00 42.52 4.20
148 159 1.752694 AGCGACAGAGAGCTCCCTC 60.753 63.158 10.93 1.96 39.98 4.30
149 160 2.781158 GCGACAGAGAGCTCCCTCC 61.781 68.421 10.93 0.00 38.96 4.30
150 161 2.124693 CGACAGAGAGCTCCCTCCC 61.125 68.421 10.93 0.00 38.96 4.30
151 162 1.309688 GACAGAGAGCTCCCTCCCT 59.690 63.158 10.93 0.00 38.96 4.20
152 163 0.755327 GACAGAGAGCTCCCTCCCTC 60.755 65.000 10.93 0.00 38.96 4.30
153 164 1.221213 ACAGAGAGCTCCCTCCCTCT 61.221 60.000 10.93 2.23 40.93 3.69
154 165 4.599036 GAGAGCTCCCTCCCTCTC 57.401 66.667 10.93 2.34 44.95 3.20
155 166 3.863685 AGAGCTCCCTCCCTCTCA 58.136 61.111 10.93 0.00 38.96 3.27
156 167 2.341952 AGAGCTCCCTCCCTCTCAT 58.658 57.895 10.93 0.00 38.96 2.90
157 168 0.188342 AGAGCTCCCTCCCTCTCATC 59.812 60.000 10.93 0.00 38.96 2.92
158 169 0.188342 GAGCTCCCTCCCTCTCATCT 59.812 60.000 0.87 0.00 31.68 2.90
159 170 0.188342 AGCTCCCTCCCTCTCATCTC 59.812 60.000 0.00 0.00 0.00 2.75
160 171 0.105760 GCTCCCTCCCTCTCATCTCA 60.106 60.000 0.00 0.00 0.00 3.27
161 172 1.999648 CTCCCTCCCTCTCATCTCAG 58.000 60.000 0.00 0.00 0.00 3.35
162 173 1.217689 CTCCCTCCCTCTCATCTCAGT 59.782 57.143 0.00 0.00 0.00 3.41
163 174 1.216678 TCCCTCCCTCTCATCTCAGTC 59.783 57.143 0.00 0.00 0.00 3.51
164 175 1.217689 CCCTCCCTCTCATCTCAGTCT 59.782 57.143 0.00 0.00 0.00 3.24
165 176 2.309613 CCTCCCTCTCATCTCAGTCTG 58.690 57.143 0.00 0.00 0.00 3.51
166 177 2.358090 CCTCCCTCTCATCTCAGTCTGT 60.358 54.545 0.00 0.00 0.00 3.41
167 178 3.364549 CTCCCTCTCATCTCAGTCTGTT 58.635 50.000 0.00 0.00 0.00 3.16
168 179 3.095332 TCCCTCTCATCTCAGTCTGTTG 58.905 50.000 0.00 0.00 0.00 3.33
169 180 2.830923 CCCTCTCATCTCAGTCTGTTGT 59.169 50.000 0.00 0.00 0.00 3.32
170 181 3.260380 CCCTCTCATCTCAGTCTGTTGTT 59.740 47.826 0.00 0.00 0.00 2.83
171 182 4.244066 CCTCTCATCTCAGTCTGTTGTTG 58.756 47.826 0.00 1.02 0.00 3.33
172 183 4.244066 CTCTCATCTCAGTCTGTTGTTGG 58.756 47.826 0.00 0.00 0.00 3.77
173 184 3.643320 TCTCATCTCAGTCTGTTGTTGGT 59.357 43.478 0.00 0.00 0.00 3.67
174 185 3.732212 TCATCTCAGTCTGTTGTTGGTG 58.268 45.455 0.00 0.00 0.00 4.17
175 186 3.387699 TCATCTCAGTCTGTTGTTGGTGA 59.612 43.478 0.00 0.00 0.00 4.02
176 187 3.459232 TCTCAGTCTGTTGTTGGTGAG 57.541 47.619 0.00 0.00 34.06 3.51
177 188 2.103094 TCTCAGTCTGTTGTTGGTGAGG 59.897 50.000 0.00 0.00 33.66 3.86
178 189 1.837439 TCAGTCTGTTGTTGGTGAGGT 59.163 47.619 0.00 0.00 0.00 3.85
179 190 2.158957 TCAGTCTGTTGTTGGTGAGGTC 60.159 50.000 0.00 0.00 0.00 3.85
180 191 2.119495 AGTCTGTTGTTGGTGAGGTCT 58.881 47.619 0.00 0.00 0.00 3.85
181 192 2.505819 AGTCTGTTGTTGGTGAGGTCTT 59.494 45.455 0.00 0.00 0.00 3.01
182 193 2.872858 GTCTGTTGTTGGTGAGGTCTTC 59.127 50.000 0.00 0.00 0.00 2.87
183 194 2.158813 TCTGTTGTTGGTGAGGTCTTCC 60.159 50.000 0.00 0.00 0.00 3.46
193 204 3.298320 AGGTCTTCCTCTGCTCCTC 57.702 57.895 0.00 0.00 40.58 3.71
194 205 0.411452 AGGTCTTCCTCTGCTCCTCA 59.589 55.000 0.00 0.00 40.58 3.86
195 206 1.008206 AGGTCTTCCTCTGCTCCTCAT 59.992 52.381 0.00 0.00 40.58 2.90
196 207 1.412343 GGTCTTCCTCTGCTCCTCATC 59.588 57.143 0.00 0.00 0.00 2.92
197 208 2.387757 GTCTTCCTCTGCTCCTCATCT 58.612 52.381 0.00 0.00 0.00 2.90
198 209 2.362077 GTCTTCCTCTGCTCCTCATCTC 59.638 54.545 0.00 0.00 0.00 2.75
199 210 1.688197 CTTCCTCTGCTCCTCATCTCC 59.312 57.143 0.00 0.00 0.00 3.71
200 211 0.633378 TCCTCTGCTCCTCATCTCCA 59.367 55.000 0.00 0.00 0.00 3.86
201 212 0.752054 CCTCTGCTCCTCATCTCCAC 59.248 60.000 0.00 0.00 0.00 4.02
202 213 0.752054 CTCTGCTCCTCATCTCCACC 59.248 60.000 0.00 0.00 0.00 4.61
203 214 0.041684 TCTGCTCCTCATCTCCACCA 59.958 55.000 0.00 0.00 0.00 4.17
211 222 0.541998 TCATCTCCACCACCGACAGT 60.542 55.000 0.00 0.00 0.00 3.55
235 246 1.688197 CTCCCTTCCTCTCATCTCAGC 59.312 57.143 0.00 0.00 0.00 4.26
240 251 0.932955 TCCTCTCATCTCAGCCCTCT 59.067 55.000 0.00 0.00 0.00 3.69
241 252 1.133513 TCCTCTCATCTCAGCCCTCTC 60.134 57.143 0.00 0.00 0.00 3.20
242 253 1.411359 CCTCTCATCTCAGCCCTCTCA 60.411 57.143 0.00 0.00 0.00 3.27
244 255 2.559668 CTCTCATCTCAGCCCTCTCATC 59.440 54.545 0.00 0.00 0.00 2.92
246 257 1.062658 TCATCTCAGCCCTCTCATCCA 60.063 52.381 0.00 0.00 0.00 3.41
247 258 1.979308 CATCTCAGCCCTCTCATCCAT 59.021 52.381 0.00 0.00 0.00 3.41
249 260 0.686224 CTCAGCCCTCTCATCCATCC 59.314 60.000 0.00 0.00 0.00 3.51
250 261 1.117749 TCAGCCCTCTCATCCATCCG 61.118 60.000 0.00 0.00 0.00 4.18
251 262 2.031768 GCCCTCTCATCCATCCGC 59.968 66.667 0.00 0.00 0.00 5.54
263 864 1.973281 CATCCGCCCTTGTTGCTGT 60.973 57.895 0.00 0.00 0.00 4.40
273 874 2.486982 CCTTGTTGCTGTTCTCATCCAG 59.513 50.000 0.00 0.00 0.00 3.86
278 879 0.809241 GCTGTTCTCATCCAGCCTCG 60.809 60.000 0.24 0.00 46.55 4.63
279 880 0.809241 CTGTTCTCATCCAGCCTCGC 60.809 60.000 0.00 0.00 0.00 5.03
280 881 1.522580 GTTCTCATCCAGCCTCGCC 60.523 63.158 0.00 0.00 0.00 5.54
281 882 2.735772 TTCTCATCCAGCCTCGCCC 61.736 63.158 0.00 0.00 0.00 6.13
282 883 4.247380 CTCATCCAGCCTCGCCCC 62.247 72.222 0.00 0.00 0.00 5.80
283 884 4.804420 TCATCCAGCCTCGCCCCT 62.804 66.667 0.00 0.00 0.00 4.79
284 885 4.559063 CATCCAGCCTCGCCCCTG 62.559 72.222 0.00 0.00 0.00 4.45
297 1110 1.641552 GCCCCTGCCAGTTGGGTATA 61.642 60.000 7.74 0.00 41.82 1.47
302 1115 3.222603 CCTGCCAGTTGGGTATATTTCC 58.777 50.000 0.00 0.00 39.65 3.13
320 1134 3.485463 TCCTGTCGATTTGTTTCCAGT 57.515 42.857 0.00 0.00 0.00 4.00
433 1247 5.426689 TTCCAGTCATTATTCAGAGCACT 57.573 39.130 0.00 0.00 0.00 4.40
484 1298 3.441101 GCCTGGTAAAAATTTCCCTCCT 58.559 45.455 0.00 0.00 0.00 3.69
495 1309 8.956446 AAAAATTTCCCTCCTATCTTTCTTGA 57.044 30.769 0.00 0.00 0.00 3.02
574 1424 0.097150 TCAGATCGAGTGAAGCGACG 59.903 55.000 0.00 0.00 40.94 5.12
613 1530 1.004080 TGTTCTGCTCTGCTCTGCC 60.004 57.895 0.00 0.00 0.00 4.85
615 1532 0.604780 GTTCTGCTCTGCTCTGCCAA 60.605 55.000 0.00 0.00 0.00 4.52
620 1560 0.321475 GCTCTGCTCTGCCAAGAAGT 60.321 55.000 0.00 0.00 30.03 3.01
641 1645 1.077716 CAAAGGTGGGTCCGGATCC 60.078 63.158 28.04 28.04 41.99 3.36
642 1646 1.229853 AAAGGTGGGTCCGGATCCT 60.230 57.895 33.44 21.72 41.99 3.24
703 1810 6.140737 CGTTGAAATTAAAGCTTCACACAGTC 59.859 38.462 0.00 0.00 31.41 3.51
704 1811 6.691754 TGAAATTAAAGCTTCACACAGTCA 57.308 33.333 0.00 0.00 0.00 3.41
705 1812 7.275888 TGAAATTAAAGCTTCACACAGTCAT 57.724 32.000 0.00 0.00 0.00 3.06
706 1813 7.715657 TGAAATTAAAGCTTCACACAGTCATT 58.284 30.769 0.00 0.00 0.00 2.57
707 1814 8.845227 TGAAATTAAAGCTTCACACAGTCATTA 58.155 29.630 0.00 0.00 0.00 1.90
708 1815 9.846248 GAAATTAAAGCTTCACACAGTCATTAT 57.154 29.630 0.00 0.00 0.00 1.28
709 1816 9.630098 AAATTAAAGCTTCACACAGTCATTATG 57.370 29.630 0.00 0.00 0.00 1.90
710 1817 4.691860 AAGCTTCACACAGTCATTATGC 57.308 40.909 0.00 0.00 0.00 3.14
711 1818 3.678289 AGCTTCACACAGTCATTATGCA 58.322 40.909 0.00 0.00 0.00 3.96
712 1819 3.688185 AGCTTCACACAGTCATTATGCAG 59.312 43.478 0.00 0.00 0.00 4.41
713 1820 3.730061 GCTTCACACAGTCATTATGCAGC 60.730 47.826 0.00 0.00 0.00 5.25
714 1821 3.339253 TCACACAGTCATTATGCAGCT 57.661 42.857 0.00 0.00 0.00 4.24
715 1822 3.264947 TCACACAGTCATTATGCAGCTC 58.735 45.455 0.00 0.00 0.00 4.09
716 1823 3.004862 CACACAGTCATTATGCAGCTCA 58.995 45.455 0.00 0.00 0.00 4.26
717 1824 3.063588 CACACAGTCATTATGCAGCTCAG 59.936 47.826 0.00 0.00 0.00 3.35
718 1825 3.268330 CACAGTCATTATGCAGCTCAGT 58.732 45.455 0.00 0.00 0.00 3.41
719 1826 3.688185 CACAGTCATTATGCAGCTCAGTT 59.312 43.478 0.00 0.00 0.00 3.16
720 1827 3.937706 ACAGTCATTATGCAGCTCAGTTC 59.062 43.478 0.00 0.00 0.00 3.01
721 1828 4.190001 CAGTCATTATGCAGCTCAGTTCT 58.810 43.478 0.00 0.00 0.00 3.01
722 1829 5.105187 ACAGTCATTATGCAGCTCAGTTCTA 60.105 40.000 0.00 0.00 0.00 2.10
723 1830 5.462729 CAGTCATTATGCAGCTCAGTTCTAG 59.537 44.000 0.00 0.00 0.00 2.43
724 1831 5.128499 AGTCATTATGCAGCTCAGTTCTAGT 59.872 40.000 0.00 0.00 0.00 2.57
725 1832 5.233902 GTCATTATGCAGCTCAGTTCTAGTG 59.766 44.000 0.00 0.00 0.00 2.74
726 1833 5.127682 TCATTATGCAGCTCAGTTCTAGTGA 59.872 40.000 0.00 0.00 0.00 3.41
727 1834 3.969287 ATGCAGCTCAGTTCTAGTGAA 57.031 42.857 0.00 0.00 0.00 3.18
728 1835 3.309961 TGCAGCTCAGTTCTAGTGAAG 57.690 47.619 0.00 0.00 32.15 3.02
729 1836 1.999024 GCAGCTCAGTTCTAGTGAAGC 59.001 52.381 0.00 0.00 32.15 3.86
730 1837 2.257894 CAGCTCAGTTCTAGTGAAGCG 58.742 52.381 0.00 0.00 31.53 4.68
731 1838 1.889829 AGCTCAGTTCTAGTGAAGCGT 59.110 47.619 0.00 0.00 31.53 5.07
732 1839 2.297597 AGCTCAGTTCTAGTGAAGCGTT 59.702 45.455 0.00 0.00 31.53 4.84
733 1840 3.060602 GCTCAGTTCTAGTGAAGCGTTT 58.939 45.455 0.00 0.00 32.15 3.60
734 1841 4.022242 AGCTCAGTTCTAGTGAAGCGTTTA 60.022 41.667 0.00 0.00 31.53 2.01
735 1842 4.684703 GCTCAGTTCTAGTGAAGCGTTTAA 59.315 41.667 0.00 0.00 32.15 1.52
736 1843 5.348997 GCTCAGTTCTAGTGAAGCGTTTAAT 59.651 40.000 0.00 0.00 32.15 1.40
737 1844 6.454450 GCTCAGTTCTAGTGAAGCGTTTAATC 60.454 42.308 0.00 0.00 32.15 1.75
738 1845 5.571741 TCAGTTCTAGTGAAGCGTTTAATCG 59.428 40.000 1.50 1.50 32.15 3.34
739 1846 5.571741 CAGTTCTAGTGAAGCGTTTAATCGA 59.428 40.000 10.05 0.00 32.15 3.59
740 1847 5.800941 AGTTCTAGTGAAGCGTTTAATCGAG 59.199 40.000 10.05 0.00 32.15 4.04
741 1848 5.306532 TCTAGTGAAGCGTTTAATCGAGT 57.693 39.130 10.05 0.00 0.00 4.18
742 1849 5.093457 TCTAGTGAAGCGTTTAATCGAGTG 58.907 41.667 10.05 0.00 0.00 3.51
743 1850 3.909430 AGTGAAGCGTTTAATCGAGTGA 58.091 40.909 10.05 0.00 0.00 3.41
744 1851 4.304110 AGTGAAGCGTTTAATCGAGTGAA 58.696 39.130 10.05 0.00 0.00 3.18
745 1852 4.386049 AGTGAAGCGTTTAATCGAGTGAAG 59.614 41.667 10.05 0.00 0.00 3.02
746 1853 3.122948 TGAAGCGTTTAATCGAGTGAAGC 59.877 43.478 10.05 0.00 0.00 3.86
747 1854 2.000447 AGCGTTTAATCGAGTGAAGCC 59.000 47.619 10.05 0.00 0.00 4.35
748 1855 1.730064 GCGTTTAATCGAGTGAAGCCA 59.270 47.619 10.05 0.00 0.00 4.75
749 1856 2.474032 GCGTTTAATCGAGTGAAGCCAC 60.474 50.000 10.05 0.00 43.50 5.01
750 1857 2.093783 CGTTTAATCGAGTGAAGCCACC 59.906 50.000 0.00 0.00 44.22 4.61
751 1858 3.335579 GTTTAATCGAGTGAAGCCACCT 58.664 45.455 0.00 0.00 44.22 4.00
752 1859 2.961526 TAATCGAGTGAAGCCACCTC 57.038 50.000 0.00 0.00 44.22 3.85
753 1860 0.250513 AATCGAGTGAAGCCACCTCC 59.749 55.000 0.00 0.00 44.22 4.30
754 1861 0.904865 ATCGAGTGAAGCCACCTCCA 60.905 55.000 0.00 0.00 44.22 3.86
755 1862 1.374758 CGAGTGAAGCCACCTCCAC 60.375 63.158 0.00 0.00 44.22 4.02
756 1863 1.374758 GAGTGAAGCCACCTCCACG 60.375 63.158 0.00 0.00 44.22 4.94
757 1864 3.050275 GTGAAGCCACCTCCACGC 61.050 66.667 0.00 0.00 37.33 5.34
758 1865 3.241530 TGAAGCCACCTCCACGCT 61.242 61.111 0.00 0.00 0.00 5.07
759 1866 2.435059 GAAGCCACCTCCACGCTC 60.435 66.667 0.00 0.00 30.92 5.03
760 1867 3.240134 GAAGCCACCTCCACGCTCA 62.240 63.158 0.00 0.00 30.92 4.26
761 1868 3.537206 AAGCCACCTCCACGCTCAC 62.537 63.158 0.00 0.00 30.92 3.51
763 1870 3.680786 CCACCTCCACGCTCACGA 61.681 66.667 0.00 0.00 43.93 4.35
806 1913 2.861006 GCTTCGGCTTCGTTGTCC 59.139 61.111 0.00 0.00 38.08 4.02
807 1914 2.677979 GCTTCGGCTTCGTTGTCCC 61.678 63.158 0.00 0.00 38.08 4.46
808 1915 2.031465 TTCGGCTTCGTTGTCCCC 59.969 61.111 0.00 0.00 35.06 4.81
809 1916 2.725203 CTTCGGCTTCGTTGTCCCCA 62.725 60.000 0.00 0.00 35.06 4.96
810 1917 2.999739 TTCGGCTTCGTTGTCCCCAC 63.000 60.000 0.00 0.00 35.06 4.61
811 1918 2.112297 GGCTTCGTTGTCCCCACA 59.888 61.111 0.00 0.00 0.00 4.17
812 1919 1.966451 GGCTTCGTTGTCCCCACAG 60.966 63.158 0.00 0.00 32.71 3.66
813 1920 2.617274 GCTTCGTTGTCCCCACAGC 61.617 63.158 0.00 0.00 32.71 4.40
817 1924 4.980805 GTTGTCCCCACAGCGCGA 62.981 66.667 12.10 0.00 32.71 5.87
818 1925 4.980805 TTGTCCCCACAGCGCGAC 62.981 66.667 12.10 2.40 32.71 5.19
831 1938 2.488355 GCGACCATCCGACGAAGA 59.512 61.111 0.00 0.00 0.00 2.87
853 1961 3.173240 GCCGTCGTGTTCGCTCTC 61.173 66.667 0.00 0.00 36.96 3.20
854 1962 2.561885 CCGTCGTGTTCGCTCTCT 59.438 61.111 0.00 0.00 36.96 3.10
855 1963 1.081376 CCGTCGTGTTCGCTCTCTT 60.081 57.895 0.00 0.00 36.96 2.85
881 1989 2.201210 CCAAAGGTGGGCTTGGGT 59.799 61.111 0.00 0.00 41.77 4.51
883 1991 1.908299 CAAAGGTGGGCTTGGGTCC 60.908 63.158 0.00 0.00 37.81 4.46
889 1997 1.691219 TGGGCTTGGGTCCAGAATC 59.309 57.895 0.00 0.00 43.05 2.52
890 1998 1.076705 GGGCTTGGGTCCAGAATCC 60.077 63.158 0.00 0.00 37.14 3.01
891 1999 1.575447 GGGCTTGGGTCCAGAATCCT 61.575 60.000 0.00 0.00 37.14 3.24
892 2000 1.213296 GGCTTGGGTCCAGAATCCTA 58.787 55.000 0.00 0.00 0.00 2.94
893 2001 1.134068 GGCTTGGGTCCAGAATCCTAC 60.134 57.143 0.00 0.00 0.00 3.18
895 2003 2.173569 GCTTGGGTCCAGAATCCTACAT 59.826 50.000 0.00 0.00 0.00 2.29
896 2004 3.372025 GCTTGGGTCCAGAATCCTACATT 60.372 47.826 0.00 0.00 0.00 2.71
897 2005 4.455606 CTTGGGTCCAGAATCCTACATTC 58.544 47.826 0.00 0.00 0.00 2.67
898 2006 3.459828 TGGGTCCAGAATCCTACATTCA 58.540 45.455 0.00 0.00 0.00 2.57
899 2007 3.199946 TGGGTCCAGAATCCTACATTCAC 59.800 47.826 0.00 0.00 0.00 3.18
900 2008 3.458189 GGTCCAGAATCCTACATTCACG 58.542 50.000 0.00 0.00 0.00 4.35
901 2009 2.866762 GTCCAGAATCCTACATTCACGC 59.133 50.000 0.00 0.00 0.00 5.34
902 2010 2.499693 TCCAGAATCCTACATTCACGCA 59.500 45.455 0.00 0.00 0.00 5.24
927 2035 2.551071 GGCTTGGCAACTCAGTTCTAGT 60.551 50.000 0.00 0.00 37.61 2.57
931 2039 2.289072 TGGCAACTCAGTTCTAGTGCTC 60.289 50.000 0.00 0.00 37.61 4.26
938 2046 2.826128 TCAGTTCTAGTGCTCGGATTGT 59.174 45.455 0.00 0.00 0.00 2.71
939 2047 3.258372 TCAGTTCTAGTGCTCGGATTGTT 59.742 43.478 0.00 0.00 0.00 2.83
990 3668 4.934356 AGGTTTCCAGCTGATTAATCCAA 58.066 39.130 17.39 0.00 0.00 3.53
1206 5087 2.202797 CTCTGGGCCGACGATGTG 60.203 66.667 0.00 0.00 0.00 3.21
1241 5122 0.175760 AACATGGAGGATGTCGTCGG 59.824 55.000 0.00 0.00 45.12 4.79
1471 5358 5.526111 CCTACGGAACCAATTGTTATCGATT 59.474 40.000 1.71 0.00 37.29 3.34
1476 5363 5.743872 GGAACCAATTGTTATCGATTCTTGC 59.256 40.000 1.71 0.00 37.29 4.01
1706 5596 0.249573 TTTGTTCCCGTCGGTCAGAC 60.250 55.000 11.06 3.78 46.16 3.51
1804 5723 8.530311 TGGATGCAAATCAGCTTATTAAAAAGA 58.470 29.630 0.00 0.00 34.99 2.52
1859 5781 7.647318 TGCATCAGTTACAACAAAAATGTACAG 59.353 33.333 0.33 0.00 33.22 2.74
2468 7424 0.094216 CGAGTTTGAGACGCATGCTG 59.906 55.000 17.13 11.87 0.00 4.41
2501 7458 8.403236 AGTTCGTTTTTGAATATATGCCCTTAC 58.597 33.333 0.00 0.00 0.00 2.34
2773 7736 8.463930 AAATGAAACCTCTTTGTACTGATGAA 57.536 30.769 0.00 0.00 0.00 2.57
3038 8003 9.881649 CTATCTTTCAGCTATTATAATCTGCCA 57.118 33.333 15.47 4.92 0.00 4.92
3071 8036 6.872020 TGAAAACTTGTCTACTGTACCTATGC 59.128 38.462 0.00 0.00 0.00 3.14
3167 8132 2.518407 TGGAGATCAAGGGACTAGCCTA 59.482 50.000 0.00 0.00 38.49 3.93
3201 8166 6.487103 GGATTAAATTACTTCAACCAGCTCG 58.513 40.000 0.00 0.00 0.00 5.03
3242 8207 5.452496 CCAGCCAATATATGATCGACTAGGG 60.452 48.000 0.00 0.00 0.00 3.53
3269 8234 1.086696 ATGCTTGCCGTGTACATGAC 58.913 50.000 16.87 5.46 0.00 3.06
3660 8634 2.559440 CTGAGATAGGAAACCTGCAGC 58.441 52.381 8.66 0.00 34.61 5.25
3717 8694 3.969642 GAATTGCCGCCCGCTGTTG 62.970 63.158 0.00 0.00 38.78 3.33
3814 8791 5.563592 TCTGACATCCATTGAAGTGTTGAT 58.436 37.500 0.00 0.00 0.00 2.57
3819 8796 1.205417 CCATTGAAGTGTTGATGGGGC 59.795 52.381 0.00 0.00 36.29 5.80
3921 8898 7.893302 AGGATGGTAGTTTGGATTTGTATGAAA 59.107 33.333 0.00 0.00 0.00 2.69
3979 8959 9.507280 CATTGAAAGCCTATATATTAATTGCGG 57.493 33.333 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.002430 GCAGTGGGTCATTCAGAGACA 59.998 52.381 0.00 0.00 37.74 3.41
5 6 1.002888 AGTGCAGTGGGTCATTCAGAG 59.997 52.381 0.00 0.00 0.00 3.35
6 7 1.059098 AGTGCAGTGGGTCATTCAGA 58.941 50.000 0.00 0.00 0.00 3.27
10 11 2.592102 ATTCAGTGCAGTGGGTCATT 57.408 45.000 21.21 0.00 0.00 2.57
68 69 1.139853 CAAGAGATACAGAGCCCCCAC 59.860 57.143 0.00 0.00 0.00 4.61
76 77 3.435275 ACAGCAGGTCAAGAGATACAGA 58.565 45.455 0.00 0.00 0.00 3.41
77 78 3.883830 ACAGCAGGTCAAGAGATACAG 57.116 47.619 0.00 0.00 0.00 2.74
91 96 3.144506 AGATGAAGACCAACAACAGCAG 58.855 45.455 0.00 0.00 0.00 4.24
100 105 3.510459 TGAGGACTGAGATGAAGACCAA 58.490 45.455 0.00 0.00 32.67 3.67
131 142 2.781158 GGAGGGAGCTCTCTGTCGC 61.781 68.421 24.07 6.10 34.39 5.19
132 143 2.124693 GGGAGGGAGCTCTCTGTCG 61.125 68.421 24.07 0.00 34.39 4.35
133 144 0.755327 GAGGGAGGGAGCTCTCTGTC 60.755 65.000 24.07 12.93 33.68 3.51
134 145 1.221213 AGAGGGAGGGAGCTCTCTGT 61.221 60.000 24.07 4.93 33.68 3.41
135 146 0.468029 GAGAGGGAGGGAGCTCTCTG 60.468 65.000 24.07 0.00 39.22 3.35
136 147 0.923729 TGAGAGGGAGGGAGCTCTCT 60.924 60.000 18.34 18.34 41.88 3.10
137 148 0.188342 ATGAGAGGGAGGGAGCTCTC 59.812 60.000 14.64 10.30 41.76 3.20
138 149 0.188342 GATGAGAGGGAGGGAGCTCT 59.812 60.000 14.64 0.00 0.00 4.09
139 150 0.188342 AGATGAGAGGGAGGGAGCTC 59.812 60.000 4.71 4.71 0.00 4.09
140 151 0.188342 GAGATGAGAGGGAGGGAGCT 59.812 60.000 0.00 0.00 0.00 4.09
141 152 0.105760 TGAGATGAGAGGGAGGGAGC 60.106 60.000 0.00 0.00 0.00 4.70
142 153 1.217689 ACTGAGATGAGAGGGAGGGAG 59.782 57.143 0.00 0.00 0.00 4.30
143 154 1.216678 GACTGAGATGAGAGGGAGGGA 59.783 57.143 0.00 0.00 0.00 4.20
144 155 1.217689 AGACTGAGATGAGAGGGAGGG 59.782 57.143 0.00 0.00 0.00 4.30
145 156 2.309613 CAGACTGAGATGAGAGGGAGG 58.690 57.143 0.00 0.00 0.00 4.30
146 157 3.017048 ACAGACTGAGATGAGAGGGAG 57.983 52.381 10.08 0.00 0.00 4.30
147 158 3.095332 CAACAGACTGAGATGAGAGGGA 58.905 50.000 10.08 0.00 0.00 4.20
148 159 2.830923 ACAACAGACTGAGATGAGAGGG 59.169 50.000 10.08 0.00 0.00 4.30
149 160 4.244066 CAACAACAGACTGAGATGAGAGG 58.756 47.826 10.08 0.00 0.00 3.69
150 161 4.244066 CCAACAACAGACTGAGATGAGAG 58.756 47.826 10.08 1.92 0.00 3.20
151 162 3.643320 ACCAACAACAGACTGAGATGAGA 59.357 43.478 10.08 0.00 0.00 3.27
152 163 3.744942 CACCAACAACAGACTGAGATGAG 59.255 47.826 10.08 3.91 0.00 2.90
153 164 3.387699 TCACCAACAACAGACTGAGATGA 59.612 43.478 10.08 0.44 0.00 2.92
154 165 3.732212 TCACCAACAACAGACTGAGATG 58.268 45.455 10.08 7.69 0.00 2.90
155 166 3.244353 CCTCACCAACAACAGACTGAGAT 60.244 47.826 10.08 0.00 0.00 2.75
156 167 2.103094 CCTCACCAACAACAGACTGAGA 59.897 50.000 10.08 0.00 0.00 3.27
157 168 2.158900 ACCTCACCAACAACAGACTGAG 60.159 50.000 10.08 3.79 0.00 3.35
158 169 1.837439 ACCTCACCAACAACAGACTGA 59.163 47.619 10.08 0.00 0.00 3.41
159 170 2.158900 AGACCTCACCAACAACAGACTG 60.159 50.000 0.00 0.00 0.00 3.51
160 171 2.119495 AGACCTCACCAACAACAGACT 58.881 47.619 0.00 0.00 0.00 3.24
161 172 2.622064 AGACCTCACCAACAACAGAC 57.378 50.000 0.00 0.00 0.00 3.51
162 173 2.158813 GGAAGACCTCACCAACAACAGA 60.159 50.000 0.00 0.00 0.00 3.41
163 174 2.158755 AGGAAGACCTCACCAACAACAG 60.159 50.000 0.00 0.00 44.13 3.16
164 175 1.843851 AGGAAGACCTCACCAACAACA 59.156 47.619 0.00 0.00 44.13 3.33
165 176 2.640316 AGGAAGACCTCACCAACAAC 57.360 50.000 0.00 0.00 44.13 3.32
176 187 1.412343 GATGAGGAGCAGAGGAAGACC 59.588 57.143 0.00 0.00 0.00 3.85
177 188 2.362077 GAGATGAGGAGCAGAGGAAGAC 59.638 54.545 0.00 0.00 0.00 3.01
178 189 2.665165 GAGATGAGGAGCAGAGGAAGA 58.335 52.381 0.00 0.00 0.00 2.87
179 190 1.688197 GGAGATGAGGAGCAGAGGAAG 59.312 57.143 0.00 0.00 0.00 3.46
180 191 1.007600 TGGAGATGAGGAGCAGAGGAA 59.992 52.381 0.00 0.00 0.00 3.36
181 192 0.633378 TGGAGATGAGGAGCAGAGGA 59.367 55.000 0.00 0.00 0.00 3.71
182 193 0.752054 GTGGAGATGAGGAGCAGAGG 59.248 60.000 0.00 0.00 0.00 3.69
183 194 0.752054 GGTGGAGATGAGGAGCAGAG 59.248 60.000 0.00 0.00 0.00 3.35
184 195 0.041684 TGGTGGAGATGAGGAGCAGA 59.958 55.000 0.00 0.00 0.00 4.26
185 196 0.177604 GTGGTGGAGATGAGGAGCAG 59.822 60.000 0.00 0.00 0.00 4.24
186 197 1.267574 GGTGGTGGAGATGAGGAGCA 61.268 60.000 0.00 0.00 0.00 4.26
187 198 1.524482 GGTGGTGGAGATGAGGAGC 59.476 63.158 0.00 0.00 0.00 4.70
188 199 0.684479 TCGGTGGTGGAGATGAGGAG 60.684 60.000 0.00 0.00 0.00 3.69
189 200 0.970937 GTCGGTGGTGGAGATGAGGA 60.971 60.000 0.00 0.00 0.00 3.71
190 201 1.257750 TGTCGGTGGTGGAGATGAGG 61.258 60.000 0.00 0.00 0.00 3.86
191 202 0.174389 CTGTCGGTGGTGGAGATGAG 59.826 60.000 0.00 0.00 0.00 2.90
192 203 0.541998 ACTGTCGGTGGTGGAGATGA 60.542 55.000 0.00 0.00 0.00 2.92
193 204 0.390340 CACTGTCGGTGGTGGAGATG 60.390 60.000 3.65 0.00 41.90 2.90
194 205 1.975327 CACTGTCGGTGGTGGAGAT 59.025 57.895 3.65 0.00 41.90 2.75
195 206 3.455152 CACTGTCGGTGGTGGAGA 58.545 61.111 3.65 0.00 41.90 3.71
203 214 2.100879 GAAGGGAGCACACTGTCGGT 62.101 60.000 0.00 0.00 0.00 4.69
211 222 1.198713 GATGAGAGGAAGGGAGCACA 58.801 55.000 0.00 0.00 0.00 4.57
235 246 2.746359 GGCGGATGGATGAGAGGG 59.254 66.667 0.00 0.00 0.00 4.30
240 251 0.394216 CAACAAGGGCGGATGGATGA 60.394 55.000 0.00 0.00 0.00 2.92
241 252 2.008268 GCAACAAGGGCGGATGGATG 62.008 60.000 0.00 0.00 0.00 3.51
242 253 1.754234 GCAACAAGGGCGGATGGAT 60.754 57.895 0.00 0.00 0.00 3.41
244 255 2.361610 AGCAACAAGGGCGGATGG 60.362 61.111 0.00 0.00 36.08 3.51
246 257 1.228552 AACAGCAACAAGGGCGGAT 60.229 52.632 0.00 0.00 36.08 4.18
247 258 1.896660 GAACAGCAACAAGGGCGGA 60.897 57.895 0.00 0.00 36.08 5.54
249 260 1.165907 TGAGAACAGCAACAAGGGCG 61.166 55.000 0.00 0.00 36.08 6.13
250 261 1.200948 GATGAGAACAGCAACAAGGGC 59.799 52.381 0.00 0.00 32.22 5.19
251 262 1.815003 GGATGAGAACAGCAACAAGGG 59.185 52.381 0.00 0.00 33.73 3.95
263 864 2.735772 GGGCGAGGCTGGATGAGAA 61.736 63.158 0.00 0.00 0.00 2.87
281 882 3.117512 AGGAAATATACCCAACTGGCAGG 60.118 47.826 20.34 3.94 37.83 4.85
282 883 3.885297 CAGGAAATATACCCAACTGGCAG 59.115 47.826 14.16 14.16 37.83 4.85
283 884 3.268334 ACAGGAAATATACCCAACTGGCA 59.732 43.478 0.00 0.00 37.83 4.92
284 885 3.883489 GACAGGAAATATACCCAACTGGC 59.117 47.826 0.00 0.00 37.83 4.85
285 886 4.127171 CGACAGGAAATATACCCAACTGG 58.873 47.826 0.00 0.00 41.37 4.00
286 887 5.018539 TCGACAGGAAATATACCCAACTG 57.981 43.478 0.00 0.00 0.00 3.16
287 888 5.888982 ATCGACAGGAAATATACCCAACT 57.111 39.130 0.00 0.00 0.00 3.16
288 889 6.317893 ACAAATCGACAGGAAATATACCCAAC 59.682 38.462 0.00 0.00 0.00 3.77
289 890 6.419791 ACAAATCGACAGGAAATATACCCAA 58.580 36.000 0.00 0.00 0.00 4.12
297 1110 4.827284 ACTGGAAACAAATCGACAGGAAAT 59.173 37.500 0.00 0.00 42.06 2.17
302 1115 6.725246 ACTTTAACTGGAAACAAATCGACAG 58.275 36.000 0.00 0.00 42.06 3.51
381 1195 3.243839 CCCTGGATTCAACCAACACAAAG 60.244 47.826 0.00 0.00 39.59 2.77
433 1247 2.288213 GGGTCAGTCGATTCGATGCATA 60.288 50.000 12.54 0.00 38.42 3.14
444 1258 3.138798 GCTAGCCGGGTCAGTCGA 61.139 66.667 10.79 0.00 0.00 4.20
445 1259 4.554363 CGCTAGCCGGGTCAGTCG 62.554 72.222 10.79 5.86 0.00 4.18
555 1405 0.097150 CGTCGCTTCACTCGATCTGA 59.903 55.000 0.00 0.00 38.29 3.27
588 1438 1.139654 AGCAGAGCAGAACACAACAGA 59.860 47.619 0.00 0.00 0.00 3.41
590 1507 1.139654 AGAGCAGAGCAGAACACAACA 59.860 47.619 0.00 0.00 0.00 3.33
613 1530 4.010349 GGACCCACCTTTGATACTTCTTG 58.990 47.826 0.00 0.00 35.41 3.02
615 1532 2.236395 CGGACCCACCTTTGATACTTCT 59.764 50.000 0.00 0.00 36.31 2.85
620 1560 1.766496 GATCCGGACCCACCTTTGATA 59.234 52.381 6.12 0.00 36.31 2.15
641 1645 3.806591 CTGCCAATCCAAACTGCAG 57.193 52.632 13.48 13.48 42.85 4.41
642 1646 0.828762 AGCTGCCAATCCAAACTGCA 60.829 50.000 0.00 0.00 0.00 4.41
703 1810 5.354767 TCACTAGAACTGAGCTGCATAATG 58.645 41.667 1.02 0.00 0.00 1.90
704 1811 5.604758 TCACTAGAACTGAGCTGCATAAT 57.395 39.130 1.02 0.00 0.00 1.28
705 1812 5.405935 TTCACTAGAACTGAGCTGCATAA 57.594 39.130 1.02 0.00 0.00 1.90
706 1813 4.679106 GCTTCACTAGAACTGAGCTGCATA 60.679 45.833 1.02 0.00 0.00 3.14
707 1814 3.859443 CTTCACTAGAACTGAGCTGCAT 58.141 45.455 1.02 0.00 0.00 3.96
708 1815 2.611473 GCTTCACTAGAACTGAGCTGCA 60.611 50.000 1.02 0.00 0.00 4.41
709 1816 1.999024 GCTTCACTAGAACTGAGCTGC 59.001 52.381 0.00 0.00 0.00 5.25
710 1817 2.257894 CGCTTCACTAGAACTGAGCTG 58.742 52.381 0.00 0.00 0.00 4.24
711 1818 1.889829 ACGCTTCACTAGAACTGAGCT 59.110 47.619 0.00 0.00 0.00 4.09
712 1819 2.355717 ACGCTTCACTAGAACTGAGC 57.644 50.000 0.00 0.00 0.00 4.26
713 1820 6.237332 CGATTAAACGCTTCACTAGAACTGAG 60.237 42.308 0.00 0.00 0.00 3.35
714 1821 5.571741 CGATTAAACGCTTCACTAGAACTGA 59.428 40.000 0.00 0.00 0.00 3.41
715 1822 5.571741 TCGATTAAACGCTTCACTAGAACTG 59.428 40.000 0.00 0.00 0.00 3.16
716 1823 5.706916 TCGATTAAACGCTTCACTAGAACT 58.293 37.500 0.00 0.00 0.00 3.01
717 1824 5.572126 ACTCGATTAAACGCTTCACTAGAAC 59.428 40.000 0.00 0.00 0.00 3.01
718 1825 5.571741 CACTCGATTAAACGCTTCACTAGAA 59.428 40.000 0.00 0.00 0.00 2.10
719 1826 5.093457 CACTCGATTAAACGCTTCACTAGA 58.907 41.667 0.00 0.00 0.00 2.43
720 1827 5.093457 TCACTCGATTAAACGCTTCACTAG 58.907 41.667 0.00 0.00 0.00 2.57
721 1828 5.050644 TCACTCGATTAAACGCTTCACTA 57.949 39.130 0.00 0.00 0.00 2.74
722 1829 3.909430 TCACTCGATTAAACGCTTCACT 58.091 40.909 0.00 0.00 0.00 3.41
723 1830 4.629065 CTTCACTCGATTAAACGCTTCAC 58.371 43.478 0.00 0.00 0.00 3.18
724 1831 3.122948 GCTTCACTCGATTAAACGCTTCA 59.877 43.478 0.00 0.00 0.00 3.02
725 1832 3.483738 GGCTTCACTCGATTAAACGCTTC 60.484 47.826 0.00 0.00 0.00 3.86
726 1833 2.415512 GGCTTCACTCGATTAAACGCTT 59.584 45.455 0.00 0.00 0.00 4.68
727 1834 2.000447 GGCTTCACTCGATTAAACGCT 59.000 47.619 0.00 0.00 0.00 5.07
728 1835 1.730064 TGGCTTCACTCGATTAAACGC 59.270 47.619 0.00 0.00 0.00 4.84
729 1836 2.093783 GGTGGCTTCACTCGATTAAACG 59.906 50.000 0.00 0.00 41.00 3.60
730 1837 3.335579 AGGTGGCTTCACTCGATTAAAC 58.664 45.455 0.00 0.00 41.00 2.01
731 1838 3.596214 GAGGTGGCTTCACTCGATTAAA 58.404 45.455 0.00 0.00 41.00 1.52
732 1839 2.093658 GGAGGTGGCTTCACTCGATTAA 60.094 50.000 0.00 0.00 41.00 1.40
733 1840 1.480954 GGAGGTGGCTTCACTCGATTA 59.519 52.381 0.00 0.00 41.00 1.75
734 1841 0.250513 GGAGGTGGCTTCACTCGATT 59.749 55.000 0.00 0.00 41.00 3.34
735 1842 0.904865 TGGAGGTGGCTTCACTCGAT 60.905 55.000 0.00 0.00 41.00 3.59
736 1843 1.533033 TGGAGGTGGCTTCACTCGA 60.533 57.895 0.00 0.00 41.00 4.04
737 1844 1.374758 GTGGAGGTGGCTTCACTCG 60.375 63.158 0.00 0.00 41.00 4.18
738 1845 1.374758 CGTGGAGGTGGCTTCACTC 60.375 63.158 0.00 0.00 41.00 3.51
739 1846 2.743718 CGTGGAGGTGGCTTCACT 59.256 61.111 0.00 0.00 41.00 3.41
740 1847 3.050275 GCGTGGAGGTGGCTTCAC 61.050 66.667 0.00 0.00 40.52 3.18
741 1848 3.240134 GAGCGTGGAGGTGGCTTCA 62.240 63.158 0.00 0.00 37.10 3.02
742 1849 2.435059 GAGCGTGGAGGTGGCTTC 60.435 66.667 0.00 0.00 37.10 3.86
743 1850 3.241530 TGAGCGTGGAGGTGGCTT 61.242 61.111 0.00 0.00 37.10 4.35
744 1851 4.008933 GTGAGCGTGGAGGTGGCT 62.009 66.667 0.00 0.00 40.29 4.75
746 1853 2.507110 ATTCGTGAGCGTGGAGGTGG 62.507 60.000 0.00 0.00 39.49 4.61
747 1854 1.078759 GATTCGTGAGCGTGGAGGTG 61.079 60.000 0.00 0.00 39.49 4.00
748 1855 1.215647 GATTCGTGAGCGTGGAGGT 59.784 57.895 0.00 0.00 39.49 3.85
749 1856 0.803768 CAGATTCGTGAGCGTGGAGG 60.804 60.000 0.00 0.00 39.49 4.30
750 1857 0.803768 CCAGATTCGTGAGCGTGGAG 60.804 60.000 0.00 0.00 39.49 3.86
751 1858 1.215382 CCAGATTCGTGAGCGTGGA 59.785 57.895 0.00 0.00 39.49 4.02
752 1859 2.456119 GCCAGATTCGTGAGCGTGG 61.456 63.158 0.00 0.00 39.49 4.94
753 1860 2.456119 GGCCAGATTCGTGAGCGTG 61.456 63.158 0.00 0.00 39.49 5.34
754 1861 2.125512 GGCCAGATTCGTGAGCGT 60.126 61.111 0.00 0.00 39.49 5.07
755 1862 1.880340 GAGGCCAGATTCGTGAGCG 60.880 63.158 5.01 0.00 39.92 5.03
756 1863 0.809241 CAGAGGCCAGATTCGTGAGC 60.809 60.000 5.01 0.00 0.00 4.26
757 1864 0.179089 CCAGAGGCCAGATTCGTGAG 60.179 60.000 5.01 0.00 0.00 3.51
758 1865 0.904865 ACCAGAGGCCAGATTCGTGA 60.905 55.000 5.01 0.00 0.00 4.35
759 1866 0.742281 CACCAGAGGCCAGATTCGTG 60.742 60.000 5.01 0.00 0.00 4.35
760 1867 1.599047 CACCAGAGGCCAGATTCGT 59.401 57.895 5.01 0.00 0.00 3.85
761 1868 1.817099 GCACCAGAGGCCAGATTCG 60.817 63.158 5.01 0.00 0.00 3.34
762 1869 4.232310 GCACCAGAGGCCAGATTC 57.768 61.111 5.01 0.00 0.00 2.52
793 1900 3.047877 GTGGGGACAACGAAGCCG 61.048 66.667 0.00 0.00 46.06 5.52
794 1901 1.966451 CTGTGGGGACAACGAAGCC 60.966 63.158 0.00 0.00 46.06 4.35
808 1915 4.794439 TCGGATGGTCGCGCTGTG 62.794 66.667 5.56 0.00 0.00 3.66
809 1916 4.796231 GTCGGATGGTCGCGCTGT 62.796 66.667 5.56 0.00 0.00 4.40
813 1920 2.949678 CTTCGTCGGATGGTCGCG 60.950 66.667 0.00 0.00 0.00 5.87
814 1921 1.872679 GTCTTCGTCGGATGGTCGC 60.873 63.158 0.00 0.00 0.00 5.19
815 1922 1.582937 CGTCTTCGTCGGATGGTCG 60.583 63.158 0.00 0.00 0.00 4.79
816 1923 4.379221 CGTCTTCGTCGGATGGTC 57.621 61.111 0.00 0.00 0.00 4.02
840 1947 0.666374 TCACAAGAGAGCGAACACGA 59.334 50.000 0.00 0.00 0.00 4.35
841 1948 1.453524 CTTCACAAGAGAGCGAACACG 59.546 52.381 0.00 0.00 0.00 4.49
853 1961 0.318107 CACCTTTGGCGCTTCACAAG 60.318 55.000 7.64 2.57 0.00 3.16
854 1962 1.732917 CACCTTTGGCGCTTCACAA 59.267 52.632 7.64 0.00 0.00 3.33
855 1963 2.192861 CCACCTTTGGCGCTTCACA 61.193 57.895 7.64 0.00 35.56 3.58
873 1981 1.134068 GTAGGATTCTGGACCCAAGCC 60.134 57.143 0.13 0.13 0.00 4.35
880 1988 2.866762 GCGTGAATGTAGGATTCTGGAC 59.133 50.000 0.00 0.00 0.00 4.02
881 1989 2.499693 TGCGTGAATGTAGGATTCTGGA 59.500 45.455 0.00 0.00 0.00 3.86
883 1991 5.268544 CAAATGCGTGAATGTAGGATTCTG 58.731 41.667 0.00 0.00 0.00 3.02
885 1993 4.601019 CCAAATGCGTGAATGTAGGATTC 58.399 43.478 0.00 0.00 0.00 2.52
886 1994 3.181487 GCCAAATGCGTGAATGTAGGATT 60.181 43.478 0.00 0.00 0.00 3.01
887 1995 2.358898 GCCAAATGCGTGAATGTAGGAT 59.641 45.455 0.00 0.00 0.00 3.24
889 1997 2.193306 GCCAAATGCGTGAATGTAGG 57.807 50.000 0.00 0.00 0.00 3.18
900 2008 0.033781 TGAGTTGCCAAGCCAAATGC 59.966 50.000 0.00 0.00 41.71 3.56
901 2009 1.342174 ACTGAGTTGCCAAGCCAAATG 59.658 47.619 0.00 0.00 0.00 2.32
902 2010 1.708341 ACTGAGTTGCCAAGCCAAAT 58.292 45.000 0.00 0.00 0.00 2.32
927 2035 3.938963 GGATCTGTAAAACAATCCGAGCA 59.061 43.478 0.00 0.00 31.36 4.26
931 2039 5.424757 TGTAGGGATCTGTAAAACAATCCG 58.575 41.667 0.00 0.00 37.01 4.18
938 2046 7.119709 TCGATGAATGTAGGGATCTGTAAAA 57.880 36.000 0.00 0.00 0.00 1.52
939 2047 6.724893 TCGATGAATGTAGGGATCTGTAAA 57.275 37.500 0.00 0.00 0.00 2.01
984 3662 7.778853 ACAATATTCATGAGAGCTCTTTGGATT 59.221 33.333 19.36 14.57 0.00 3.01
990 3668 5.752472 CGTGACAATATTCATGAGAGCTCTT 59.248 40.000 19.36 2.77 34.86 2.85
1028 3718 2.599597 CCAGCTTGGGGATCAGGG 59.400 66.667 0.00 0.00 32.67 4.45
1284 5165 3.414700 CTGCCGGAGTTGTCGTGC 61.415 66.667 5.05 0.00 0.00 5.34
1476 5363 2.143122 TCTGCGTACAAAGCTTGAAGG 58.857 47.619 0.00 0.00 35.28 3.46
1548 5435 0.107312 CACCCTCCATGGAGAGCAAG 60.107 60.000 38.37 22.65 44.53 4.01
1650 5540 7.062605 TCGAAATCACCTTTAATCTTGTCGTAC 59.937 37.037 0.00 0.00 0.00 3.67
1706 5596 2.887151 AACCTTCTTCATGTCAGGGG 57.113 50.000 0.00 0.33 0.00 4.79
1804 5723 7.992033 CCTCTTGTTCTCTAGGAATTCATGAAT 59.008 37.037 15.36 15.36 36.24 2.57
2501 7458 5.677319 ATATGGGTGGAACTATACATCGG 57.323 43.478 0.00 0.00 36.74 4.18
2773 7736 4.302067 TCTTATGGAAGAGCCTTCTGGAT 58.698 43.478 12.71 7.11 36.75 3.41
3035 8000 4.699257 AGACAAGTTTTCAGATGAGATGGC 59.301 41.667 0.00 0.00 0.00 4.40
3038 8003 7.675062 ACAGTAGACAAGTTTTCAGATGAGAT 58.325 34.615 0.00 0.00 0.00 2.75
3071 8036 8.262933 TCAATGGTGCTATCTTCTGGATATATG 58.737 37.037 0.00 0.00 36.45 1.78
3167 8132 9.921637 TTGAAGTAATTTAATCCGAGCAAAAAT 57.078 25.926 0.00 0.00 0.00 1.82
3201 8166 8.854614 ATTGGCTGGATCATACTTCTATTAAC 57.145 34.615 0.00 0.00 0.00 2.01
3242 8207 0.588252 CACGGCAAGCATATACCTGC 59.412 55.000 0.00 0.00 42.62 4.85
3660 8634 6.648879 TTTAAGATCCAACACCTCCAAAAG 57.351 37.500 0.00 0.00 0.00 2.27
3717 8694 7.797062 AGGTAGATTAATCTTCTCAACTTCCC 58.203 38.462 22.60 2.97 38.32 3.97
3814 8791 1.152030 ACAGAGACCAAGAGCCCCA 60.152 57.895 0.00 0.00 0.00 4.96
3819 8796 6.402983 GCAATAATGTTCACAGAGACCAAGAG 60.403 42.308 0.00 0.00 0.00 2.85
3876 8853 4.321718 TCCTTGAAGTGAATCAGAAGCAG 58.678 43.478 0.00 0.00 0.00 4.24
3877 8854 4.356405 TCCTTGAAGTGAATCAGAAGCA 57.644 40.909 0.00 0.00 0.00 3.91
3921 8898 1.270358 GCCCAGAGACTTCACGAAACT 60.270 52.381 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.