Multiple sequence alignment - TraesCS2A01G276500

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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 TraesCS2A01G276500 chr2A 100.000 2198 0 0 1 2198 457221109 457218912 0.000000e+00 4060.0
1 TraesCS2A01G276500 chr2A 90.558 233 21 1 2 233 606519085 606519317 7.620000e-80 307.0
2 TraesCS2A01G276500 chr2A 90.558 233 21 1 2 233 699241092 699240860 7.620000e-80 307.0
3 TraesCS2A01G276500 chr2A 89.157 83 7 2 2118 2198 603543276 603543194 3.860000e-18 102.0
4 TraesCS2A01G276500 chr2A 89.024 82 7 2 2118 2197 164926128 164926209 1.390000e-17 100.0
5 TraesCS2A01G276500 chr2B 90.222 1309 67 29 283 1535 410942291 410940988 0.000000e+00 1652.0
6 TraesCS2A01G276500 chr2B 93.598 328 13 6 1734 2058 410940712 410940390 1.180000e-132 483.0
7 TraesCS2A01G276500 chr2B 93.229 192 13 0 1548 1739 410940940 410940749 1.280000e-72 283.0
8 TraesCS2A01G276500 chr2B 79.279 111 20 3 1735 1844 154841299 154841191 8.420000e-10 75.0
9 TraesCS2A01G276500 chr2D 89.498 1314 56 30 283 1545 345247581 345246299 0.000000e+00 1587.0
10 TraesCS2A01G276500 chr2D 94.243 469 18 7 1734 2198 345225890 345225427 0.000000e+00 708.0
11 TraesCS2A01G276500 chr2D 91.667 228 18 1 2 228 455942247 455942474 4.560000e-82 315.0
12 TraesCS2A01G276500 chr2D 88.213 263 25 5 2 261 380694312 380694571 2.120000e-80 309.0
13 TraesCS2A01G276500 chr2D 91.150 113 6 2 1546 1658 345246265 345246157 1.360000e-32 150.0
14 TraesCS2A01G276500 chr2D 93.939 66 3 1 2133 2197 285901607 285901542 4.990000e-17 99.0
15 TraesCS2A01G276500 chr7A 92.208 231 16 2 2 230 60605000 60605230 2.100000e-85 326.0
16 TraesCS2A01G276500 chr7A 90.558 233 21 1 2 233 669666379 669666611 7.620000e-80 307.0
17 TraesCS2A01G276500 chr3D 92.070 227 16 2 8 233 305497383 305497158 3.520000e-83 318.0
18 TraesCS2A01G276500 chr4B 90.948 232 20 1 3 233 22857380 22857611 5.890000e-81 311.0
19 TraesCS2A01G276500 chr4B 79.279 111 20 3 1735 1843 78503023 78503132 8.420000e-10 75.0
20 TraesCS2A01G276500 chr5A 91.228 228 19 1 2 228 336841673 336841446 2.120000e-80 309.0
21 TraesCS2A01G276500 chr6B 91.566 83 4 3 2118 2198 648802241 648802160 6.410000e-21 111.0
22 TraesCS2A01G276500 chr1B 88.636 88 6 1 487 574 655858109 655858026 1.070000e-18 104.0
23 TraesCS2A01G276500 chr4D 91.667 72 6 0 2123 2194 97693380 97693451 1.390000e-17 100.0
24 TraesCS2A01G276500 chr4D 94.737 38 2 0 1735 1772 48713668 48713705 2.360000e-05 60.2
25 TraesCS2A01G276500 chr3B 93.939 66 4 0 2133 2198 17582252 17582317 1.390000e-17 100.0
26 TraesCS2A01G276500 chr3B 88.608 79 8 1 2121 2198 253503469 253503547 6.460000e-16 95.3
27 TraesCS2A01G276500 chr6D 87.654 81 8 2 2117 2197 410203117 410203039 2.320000e-15 93.5
28 TraesCS2A01G276500 chr4A 82.955 88 12 3 1739 1824 635657500 635657586 2.340000e-10 76.8
29 TraesCS2A01G276500 chr4A 96.774 31 1 0 1739 1769 635848439 635848469 4.000000e-03 52.8
30 TraesCS2A01G276500 chr5D 77.692 130 23 5 1742 1869 536004470 536004345 8.420000e-10 75.0


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 TraesCS2A01G276500 chr2A 457218912 457221109 2197 True 4060.0 4060 100.000000 1 2198 1 chr2A.!!$R1 2197
1 TraesCS2A01G276500 chr2B 410940390 410942291 1901 True 806.0 1652 92.349667 283 2058 3 chr2B.!!$R2 1775
2 TraesCS2A01G276500 chr2D 345246157 345247581 1424 True 868.5 1587 90.324000 283 1658 2 chr2D.!!$R3 1375

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
991 1029 0.723981 GCGATCTTTCCTGCTGTGTC 59.276 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2253 1.064946 CTCCCTGCTCTAGCGAACG 59.935 63.158 0.0 0.0 45.83 3.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.603158 TCCACGTATTAGCTTTGCTCA 57.397 42.857 0.00 0.00 40.44 4.26
22 23 3.932822 TCCACGTATTAGCTTTGCTCAA 58.067 40.909 0.00 0.00 40.44 3.02
23 24 3.932710 TCCACGTATTAGCTTTGCTCAAG 59.067 43.478 0.00 0.00 40.44 3.02
24 25 3.063997 CCACGTATTAGCTTTGCTCAAGG 59.936 47.826 0.00 0.00 40.44 3.61
25 26 3.684788 CACGTATTAGCTTTGCTCAAGGT 59.315 43.478 0.00 6.24 45.51 3.50
26 27 3.933332 ACGTATTAGCTTTGCTCAAGGTC 59.067 43.478 0.00 0.00 42.50 3.85
27 28 3.932710 CGTATTAGCTTTGCTCAAGGTCA 59.067 43.478 0.00 0.00 42.50 4.02
28 29 4.391830 CGTATTAGCTTTGCTCAAGGTCAA 59.608 41.667 0.00 0.70 42.50 3.18
29 30 5.106712 CGTATTAGCTTTGCTCAAGGTCAAA 60.107 40.000 0.00 0.00 42.50 2.69
30 31 4.568152 TTAGCTTTGCTCAAGGTCAAAC 57.432 40.909 0.00 0.00 42.50 2.93
31 32 2.659428 AGCTTTGCTCAAGGTCAAACT 58.341 42.857 0.00 0.00 39.06 2.66
32 33 3.026694 AGCTTTGCTCAAGGTCAAACTT 58.973 40.909 0.00 0.00 39.06 2.66
33 34 3.448660 AGCTTTGCTCAAGGTCAAACTTT 59.551 39.130 0.00 0.00 39.06 2.66
34 35 3.553105 GCTTTGCTCAAGGTCAAACTTTG 59.447 43.478 0.00 0.00 36.63 2.77
35 36 4.747810 CTTTGCTCAAGGTCAAACTTTGT 58.252 39.130 1.44 0.00 36.66 2.83
36 37 5.678616 GCTTTGCTCAAGGTCAAACTTTGTA 60.679 40.000 1.44 0.00 36.66 2.41
37 38 5.906113 TTGCTCAAGGTCAAACTTTGTAA 57.094 34.783 1.44 0.00 36.66 2.41
38 39 5.906113 TGCTCAAGGTCAAACTTTGTAAA 57.094 34.783 1.44 0.00 36.66 2.01
39 40 5.646606 TGCTCAAGGTCAAACTTTGTAAAC 58.353 37.500 1.44 0.00 36.66 2.01
40 41 5.417580 TGCTCAAGGTCAAACTTTGTAAACT 59.582 36.000 1.44 0.00 36.66 2.66
41 42 6.071616 TGCTCAAGGTCAAACTTTGTAAACTT 60.072 34.615 1.44 0.00 36.66 2.66
42 43 6.811665 GCTCAAGGTCAAACTTTGTAAACTTT 59.188 34.615 1.44 0.00 36.66 2.66
43 44 7.201435 GCTCAAGGTCAAACTTTGTAAACTTTG 60.201 37.037 8.97 8.97 36.66 2.77
44 45 6.588373 TCAAGGTCAAACTTTGTAAACTTTGC 59.412 34.615 9.85 0.00 36.66 3.68
45 46 6.031751 AGGTCAAACTTTGTAAACTTTGCA 57.968 33.333 1.44 0.00 0.00 4.08
46 47 6.459923 AGGTCAAACTTTGTAAACTTTGCAA 58.540 32.000 0.00 0.00 33.37 4.08
47 48 6.931840 AGGTCAAACTTTGTAAACTTTGCAAA 59.068 30.769 12.14 12.14 41.79 3.68
125 126 8.541133 TCATTATTGAATGTACTTTCACGTCA 57.459 30.769 20.40 9.22 42.71 4.35
126 127 9.161629 TCATTATTGAATGTACTTTCACGTCAT 57.838 29.630 20.40 14.54 42.71 3.06
130 131 6.902224 TGAATGTACTTTCACGTCATATGG 57.098 37.500 17.62 0.00 30.82 2.74
131 132 6.635755 TGAATGTACTTTCACGTCATATGGA 58.364 36.000 17.62 0.00 30.82 3.41
132 133 7.272244 TGAATGTACTTTCACGTCATATGGAT 58.728 34.615 17.62 0.00 30.82 3.41
133 134 7.768582 TGAATGTACTTTCACGTCATATGGATT 59.231 33.333 17.62 0.00 30.82 3.01
134 135 8.506168 AATGTACTTTCACGTCATATGGATTT 57.494 30.769 2.13 0.00 0.00 2.17
135 136 7.302350 TGTACTTTCACGTCATATGGATTTG 57.698 36.000 2.13 0.00 0.00 2.32
136 137 6.876789 TGTACTTTCACGTCATATGGATTTGT 59.123 34.615 2.13 0.00 0.00 2.83
137 138 6.817765 ACTTTCACGTCATATGGATTTGTT 57.182 33.333 2.13 0.00 0.00 2.83
138 139 7.915293 ACTTTCACGTCATATGGATTTGTTA 57.085 32.000 2.13 0.00 0.00 2.41
139 140 7.974675 ACTTTCACGTCATATGGATTTGTTAG 58.025 34.615 2.13 0.00 0.00 2.34
140 141 6.918892 TTCACGTCATATGGATTTGTTAGG 57.081 37.500 2.13 0.00 0.00 2.69
141 142 5.364778 TCACGTCATATGGATTTGTTAGGG 58.635 41.667 2.13 0.00 0.00 3.53
142 143 5.104693 TCACGTCATATGGATTTGTTAGGGT 60.105 40.000 2.13 0.00 0.00 4.34
143 144 6.098552 TCACGTCATATGGATTTGTTAGGGTA 59.901 38.462 2.13 0.00 0.00 3.69
144 145 6.764085 CACGTCATATGGATTTGTTAGGGTAA 59.236 38.462 2.13 0.00 0.00 2.85
145 146 7.281324 CACGTCATATGGATTTGTTAGGGTAAA 59.719 37.037 2.13 0.00 0.00 2.01
146 147 7.996644 ACGTCATATGGATTTGTTAGGGTAAAT 59.003 33.333 2.13 0.00 0.00 1.40
147 148 8.289618 CGTCATATGGATTTGTTAGGGTAAATG 58.710 37.037 2.13 0.00 0.00 2.32
148 149 9.131791 GTCATATGGATTTGTTAGGGTAAATGT 57.868 33.333 2.13 0.00 0.00 2.71
149 150 9.707957 TCATATGGATTTGTTAGGGTAAATGTT 57.292 29.630 2.13 0.00 0.00 2.71
152 153 7.604657 TGGATTTGTTAGGGTAAATGTTTGT 57.395 32.000 0.00 0.00 0.00 2.83
153 154 8.707796 TGGATTTGTTAGGGTAAATGTTTGTA 57.292 30.769 0.00 0.00 0.00 2.41
154 155 9.315363 TGGATTTGTTAGGGTAAATGTTTGTAT 57.685 29.630 0.00 0.00 0.00 2.29
214 215 6.985188 GACTTCAGTCAAACCTAATATGCA 57.015 37.500 1.86 0.00 44.18 3.96
215 216 6.992063 ACTTCAGTCAAACCTAATATGCAG 57.008 37.500 0.00 0.00 0.00 4.41
216 217 6.711277 ACTTCAGTCAAACCTAATATGCAGA 58.289 36.000 0.00 0.00 0.00 4.26
217 218 6.820656 ACTTCAGTCAAACCTAATATGCAGAG 59.179 38.462 0.00 0.00 0.00 3.35
218 219 6.299805 TCAGTCAAACCTAATATGCAGAGT 57.700 37.500 0.00 0.00 0.00 3.24
219 220 7.418337 TCAGTCAAACCTAATATGCAGAGTA 57.582 36.000 0.00 0.00 0.00 2.59
220 221 7.847096 TCAGTCAAACCTAATATGCAGAGTAA 58.153 34.615 0.00 0.00 0.00 2.24
221 222 8.318412 TCAGTCAAACCTAATATGCAGAGTAAA 58.682 33.333 0.00 0.00 0.00 2.01
222 223 9.113838 CAGTCAAACCTAATATGCAGAGTAAAT 57.886 33.333 0.00 0.00 0.00 1.40
236 237 8.896320 TGCAGAGTAAATAAAAACAGAGTACA 57.104 30.769 0.00 0.00 0.00 2.90
237 238 9.502091 TGCAGAGTAAATAAAAACAGAGTACAT 57.498 29.630 0.00 0.00 0.00 2.29
238 239 9.974750 GCAGAGTAAATAAAAACAGAGTACATC 57.025 33.333 0.00 0.00 0.00 3.06
246 247 9.793259 AATAAAAACAGAGTACATCCTTTCTGA 57.207 29.630 12.91 0.00 39.46 3.27
247 248 7.497925 AAAAACAGAGTACATCCTTTCTGAC 57.502 36.000 12.91 0.00 39.46 3.51
248 249 6.426646 AAACAGAGTACATCCTTTCTGACT 57.573 37.500 12.91 0.00 39.46 3.41
249 250 5.652994 ACAGAGTACATCCTTTCTGACTC 57.347 43.478 12.91 0.00 39.46 3.36
250 251 4.156922 ACAGAGTACATCCTTTCTGACTCG 59.843 45.833 12.91 0.00 39.46 4.18
251 252 4.396478 CAGAGTACATCCTTTCTGACTCGA 59.604 45.833 2.22 0.00 39.46 4.04
252 253 5.010933 AGAGTACATCCTTTCTGACTCGAA 58.989 41.667 0.00 0.00 38.64 3.71
253 254 5.061920 AGTACATCCTTTCTGACTCGAAC 57.938 43.478 0.00 0.00 0.00 3.95
254 255 4.767928 AGTACATCCTTTCTGACTCGAACT 59.232 41.667 0.00 0.00 0.00 3.01
255 256 4.181309 ACATCCTTTCTGACTCGAACTC 57.819 45.455 0.00 0.00 0.00 3.01
256 257 3.829601 ACATCCTTTCTGACTCGAACTCT 59.170 43.478 0.00 0.00 0.00 3.24
257 258 5.010933 ACATCCTTTCTGACTCGAACTCTA 58.989 41.667 0.00 0.00 0.00 2.43
258 259 5.654650 ACATCCTTTCTGACTCGAACTCTAT 59.345 40.000 0.00 0.00 0.00 1.98
259 260 6.829298 ACATCCTTTCTGACTCGAACTCTATA 59.171 38.462 0.00 0.00 0.00 1.31
260 261 7.339721 ACATCCTTTCTGACTCGAACTCTATAA 59.660 37.037 0.00 0.00 0.00 0.98
261 262 7.323049 TCCTTTCTGACTCGAACTCTATAAG 57.677 40.000 0.00 0.00 0.00 1.73
262 263 7.110810 TCCTTTCTGACTCGAACTCTATAAGA 58.889 38.462 0.00 0.00 0.00 2.10
263 264 7.066043 TCCTTTCTGACTCGAACTCTATAAGAC 59.934 40.741 0.00 0.00 0.00 3.01
264 265 7.148222 CCTTTCTGACTCGAACTCTATAAGACA 60.148 40.741 0.00 0.00 0.00 3.41
265 266 7.867305 TTCTGACTCGAACTCTATAAGACAT 57.133 36.000 0.00 0.00 0.00 3.06
266 267 7.867305 TCTGACTCGAACTCTATAAGACATT 57.133 36.000 0.00 0.00 0.00 2.71
267 268 8.959705 TCTGACTCGAACTCTATAAGACATTA 57.040 34.615 0.00 0.00 0.00 1.90
268 269 9.392259 TCTGACTCGAACTCTATAAGACATTAA 57.608 33.333 0.00 0.00 0.00 1.40
269 270 9.658475 CTGACTCGAACTCTATAAGACATTAAG 57.342 37.037 0.00 0.00 0.00 1.85
270 271 9.392259 TGACTCGAACTCTATAAGACATTAAGA 57.608 33.333 0.00 0.00 0.00 2.10
291 292 5.984725 AGATACACGATACATTTGGTCCAA 58.015 37.500 0.00 0.00 0.00 3.53
296 299 2.365582 GATACATTTGGTCCAACGGCT 58.634 47.619 2.98 0.00 0.00 5.52
312 315 3.858247 ACGGCTACAGTATTTCTTGACC 58.142 45.455 0.00 0.00 0.00 4.02
323 326 5.934625 AGTATTTCTTGACCAAGTAGCAGTG 59.065 40.000 9.31 0.00 39.38 3.66
368 378 3.507233 AGATTGTTCATGTTGGCGACATT 59.493 39.130 17.77 2.33 46.80 2.71
575 586 1.739562 CTGCGACACTTCCTCTGCC 60.740 63.158 0.00 0.00 0.00 4.85
622 644 8.012241 CGTAGTATTATACGGTTCTACTTGTCC 58.988 40.741 0.00 0.00 43.70 4.02
654 676 2.035442 GGTTCAAGAGCCGGAGTGC 61.035 63.158 5.05 0.00 0.00 4.40
768 790 2.038837 GTTTACCGAGGGCACTGGC 61.039 63.158 0.00 0.00 40.13 4.85
769 791 2.221299 TTTACCGAGGGCACTGGCT 61.221 57.895 0.00 0.00 40.87 4.75
770 792 2.463589 TTTACCGAGGGCACTGGCTG 62.464 60.000 0.00 0.00 40.87 4.85
845 876 1.740025 CGAGCTTCCTCCAATCCAAAC 59.260 52.381 0.00 0.00 34.49 2.93
855 886 3.686016 TCCAATCCAAACTAACCTCAGC 58.314 45.455 0.00 0.00 0.00 4.26
880 911 2.359981 AGCCAGACATTGCTGCATAT 57.640 45.000 1.84 0.00 36.23 1.78
900 931 6.308766 GCATATAAGCACAAAACCAGAACTTG 59.691 38.462 0.00 0.00 0.00 3.16
916 947 4.509600 AGAACTTGAAGCTCGAAAACAGAG 59.490 41.667 0.00 0.00 38.68 3.35
919 950 3.735237 TGAAGCTCGAAAACAGAGAGT 57.265 42.857 0.00 0.00 37.93 3.24
920 951 4.848562 TGAAGCTCGAAAACAGAGAGTA 57.151 40.909 0.00 0.00 37.93 2.59
922 953 4.278669 TGAAGCTCGAAAACAGAGAGTACT 59.721 41.667 0.00 0.00 37.93 2.73
924 955 3.191791 AGCTCGAAAACAGAGAGTACTCC 59.808 47.826 19.38 10.83 43.53 3.85
925 956 3.057456 GCTCGAAAACAGAGAGTACTCCA 60.057 47.826 19.38 0.00 43.53 3.86
927 958 3.255149 TCGAAAACAGAGAGTACTCCACC 59.745 47.826 19.38 9.08 43.53 4.61
928 959 3.614390 CGAAAACAGAGAGTACTCCACCC 60.614 52.174 19.38 6.66 43.53 4.61
929 960 3.261818 AAACAGAGAGTACTCCACCCT 57.738 47.619 19.38 8.78 43.53 4.34
930 961 2.223803 ACAGAGAGTACTCCACCCTG 57.776 55.000 19.38 20.36 43.53 4.45
931 962 1.429687 ACAGAGAGTACTCCACCCTGT 59.570 52.381 19.38 20.91 43.53 4.00
944 975 1.417890 CACCCTGTTCCTGTGTCTCTT 59.582 52.381 0.00 0.00 0.00 2.85
958 989 3.810386 GTGTCTCTTTTGGGTTCAGTCTC 59.190 47.826 0.00 0.00 0.00 3.36
989 1027 1.372087 GGGCGATCTTTCCTGCTGTG 61.372 60.000 0.00 0.00 0.00 3.66
991 1029 0.723981 GCGATCTTTCCTGCTGTGTC 59.276 55.000 0.00 0.00 0.00 3.67
992 1030 1.941209 GCGATCTTTCCTGCTGTGTCA 60.941 52.381 0.00 0.00 0.00 3.58
1022 1066 2.358247 GGCGACGGTGAACATGGT 60.358 61.111 0.00 0.00 0.00 3.55
1023 1067 2.677003 GGCGACGGTGAACATGGTG 61.677 63.158 0.00 0.00 0.00 4.17
1299 1343 5.300752 ACCTTGAAGATGAACAGTACAGTG 58.699 41.667 0.00 0.00 0.00 3.66
1308 1352 1.254026 ACAGTACAGTGCCGCTCTTA 58.746 50.000 0.00 0.00 0.00 2.10
1320 1364 3.067833 GCCGCTCTTACTTTGTTTCTCT 58.932 45.455 0.00 0.00 0.00 3.10
1331 1375 4.142381 ACTTTGTTTCTCTGGTGTTTCTGC 60.142 41.667 0.00 0.00 0.00 4.26
1363 1407 1.468914 GGTGCAGGATCTTCGTTTTCC 59.531 52.381 0.00 0.00 0.00 3.13
1421 1475 1.140852 TCCAGTTCCTGACTTGTGGTG 59.859 52.381 0.00 0.00 36.10 4.17
1451 1505 2.358898 CCTTAAATGTGAATCCCCTGCG 59.641 50.000 0.00 0.00 0.00 5.18
1452 1506 2.799126 TAAATGTGAATCCCCTGCGT 57.201 45.000 0.00 0.00 0.00 5.24
1453 1507 1.176527 AAATGTGAATCCCCTGCGTG 58.823 50.000 0.00 0.00 0.00 5.34
1454 1508 0.327924 AATGTGAATCCCCTGCGTGA 59.672 50.000 0.00 0.00 0.00 4.35
1455 1509 0.327924 ATGTGAATCCCCTGCGTGAA 59.672 50.000 0.00 0.00 0.00 3.18
1457 1511 1.271871 TGTGAATCCCCTGCGTGAATT 60.272 47.619 0.00 0.00 0.00 2.17
1458 1512 2.026729 TGTGAATCCCCTGCGTGAATTA 60.027 45.455 0.00 0.00 0.00 1.40
1461 1515 2.622064 ATCCCCTGCGTGAATTAGAC 57.378 50.000 0.00 0.00 0.00 2.59
1464 1518 2.039216 TCCCCTGCGTGAATTAGACAAA 59.961 45.455 0.00 0.00 0.00 2.83
1465 1519 2.161609 CCCCTGCGTGAATTAGACAAAC 59.838 50.000 0.00 0.00 0.00 2.93
1469 1523 5.354234 CCCTGCGTGAATTAGACAAACTATT 59.646 40.000 0.00 0.00 0.00 1.73
1471 1525 6.092122 CCTGCGTGAATTAGACAAACTATTCA 59.908 38.462 0.00 0.00 32.21 2.57
1473 1527 6.871492 TGCGTGAATTAGACAAACTATTCAGA 59.129 34.615 0.00 0.00 33.67 3.27
1508 1577 2.474526 CGCTCCATCGTAGCAGTTTTTG 60.475 50.000 0.00 0.00 40.08 2.44
1541 1610 2.835027 GGTTTCCTACCTCCAATAGCG 58.165 52.381 0.00 0.00 44.10 4.26
1565 1675 7.575343 GCGGTAAATCTTAACGAGGAGATATCT 60.575 40.741 4.47 4.47 32.52 1.98
1569 1679 5.063017 TCTTAACGAGGAGATATCTGGGT 57.937 43.478 10.74 0.00 0.00 4.51
1693 1803 2.817258 CGTTTGAAGGGGTTTGCATCTA 59.183 45.455 0.00 0.00 0.00 1.98
1698 1808 6.524101 TTGAAGGGGTTTGCATCTATAAAC 57.476 37.500 0.00 0.00 36.35 2.01
1703 1813 5.479027 AGGGGTTTGCATCTATAAACGTTTT 59.521 36.000 20.19 9.61 37.59 2.43
1707 1817 8.641155 GGGTTTGCATCTATAAACGTTTTAAAC 58.359 33.333 20.19 15.10 37.59 2.01
1814 1969 4.398319 AGATGTTCGTTTGACATTCCCTT 58.602 39.130 0.00 0.00 37.83 3.95
1815 1970 4.827284 AGATGTTCGTTTGACATTCCCTTT 59.173 37.500 0.00 0.00 37.83 3.11
1821 1976 3.610114 CGTTTGACATTCCCTTTCAGCTG 60.610 47.826 7.63 7.63 0.00 4.24
1831 1986 2.215478 CTTTCAGCTGACGTTCGCCG 62.215 60.000 18.03 0.00 44.03 6.46
1848 2003 3.579586 TCGCCGGTTATCATTACCCTAAT 59.420 43.478 1.90 0.00 31.75 1.73
1849 2004 4.040706 TCGCCGGTTATCATTACCCTAATT 59.959 41.667 1.90 0.00 31.75 1.40
1850 2005 4.153475 CGCCGGTTATCATTACCCTAATTG 59.847 45.833 1.90 0.00 31.75 2.32
1897 2052 2.228138 GGTCACCGAGTGTGTGTTAA 57.772 50.000 4.33 0.00 45.61 2.01
1912 2067 8.863086 AGTGTGTGTTAACTACCAACTTCTATA 58.137 33.333 7.22 0.00 0.00 1.31
1984 2139 8.415950 TGTTTGAACCTAATATGGTGTTGAAT 57.584 30.769 0.00 0.00 40.73 2.57
2014 2169 6.903883 AACATGATAGGAAATGTACGACAC 57.096 37.500 0.00 0.00 35.99 3.67
2022 2177 8.836268 ATAGGAAATGTACGACACAAAAGTAA 57.164 30.769 0.00 0.00 41.55 2.24
2026 2181 8.006027 GGAAATGTACGACACAAAAGTAACTAC 58.994 37.037 0.00 0.00 41.55 2.73
2059 2214 4.095410 TGCAGTTATAGTGCACAAATGC 57.905 40.909 25.10 25.10 46.61 3.56
2067 2222 4.584688 GCACAAATGCCAAGCCTC 57.415 55.556 0.00 0.00 46.97 4.70
2068 2223 1.079612 GCACAAATGCCAAGCCTCC 60.080 57.895 0.00 0.00 46.97 4.30
2069 2224 1.538687 GCACAAATGCCAAGCCTCCT 61.539 55.000 0.00 0.00 46.97 3.69
2070 2225 0.529378 CACAAATGCCAAGCCTCCTC 59.471 55.000 0.00 0.00 0.00 3.71
2071 2226 0.962356 ACAAATGCCAAGCCTCCTCG 60.962 55.000 0.00 0.00 0.00 4.63
2072 2227 2.048603 AAATGCCAAGCCTCCTCGC 61.049 57.895 0.00 0.00 0.00 5.03
2073 2228 4.496336 ATGCCAAGCCTCCTCGCC 62.496 66.667 0.00 0.00 0.00 5.54
2111 2266 4.492160 CGGGCGTTCGCTAGAGCA 62.492 66.667 16.40 0.00 42.21 4.26
2112 2267 2.583593 GGGCGTTCGCTAGAGCAG 60.584 66.667 16.40 0.00 42.21 4.24
2113 2268 2.583593 GGCGTTCGCTAGAGCAGG 60.584 66.667 16.40 0.00 42.21 4.85
2114 2269 2.583593 GCGTTCGCTAGAGCAGGG 60.584 66.667 9.99 0.00 42.21 4.45
2115 2270 3.064987 GCGTTCGCTAGAGCAGGGA 62.065 63.158 9.99 0.00 43.97 4.20
2116 2271 1.064946 CGTTCGCTAGAGCAGGGAG 59.935 63.158 1.89 0.00 45.96 4.30
2117 2272 1.227118 GTTCGCTAGAGCAGGGAGC 60.227 63.158 1.89 0.00 45.96 4.70
2118 2273 2.427245 TTCGCTAGAGCAGGGAGCC 61.427 63.158 1.89 0.00 45.96 4.70
2134 2289 4.704833 CCACCTGCTCCCACACCG 62.705 72.222 0.00 0.00 0.00 4.94
2135 2290 4.704833 CACCTGCTCCCACACCGG 62.705 72.222 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.137116 TGAGCAAAGCTAATACGTGGAT 57.863 40.909 0.00 0.00 39.88 3.41
2 3 3.063997 CCTTGAGCAAAGCTAATACGTGG 59.936 47.826 0.00 0.00 39.88 4.94
4 5 3.933332 GACCTTGAGCAAAGCTAATACGT 59.067 43.478 0.00 0.00 39.88 3.57
5 6 3.932710 TGACCTTGAGCAAAGCTAATACG 59.067 43.478 0.00 0.00 39.88 3.06
6 7 5.880054 TTGACCTTGAGCAAAGCTAATAC 57.120 39.130 0.00 0.00 39.88 1.89
7 8 6.003950 AGTTTGACCTTGAGCAAAGCTAATA 58.996 36.000 0.00 0.00 39.88 0.98
8 9 4.829492 AGTTTGACCTTGAGCAAAGCTAAT 59.171 37.500 0.00 0.00 39.88 1.73
9 10 4.207165 AGTTTGACCTTGAGCAAAGCTAA 58.793 39.130 0.00 0.00 39.88 3.09
10 11 3.820557 AGTTTGACCTTGAGCAAAGCTA 58.179 40.909 0.00 0.00 39.88 3.32
11 12 2.659428 AGTTTGACCTTGAGCAAAGCT 58.341 42.857 0.00 0.00 43.88 3.74
12 13 3.443099 AAGTTTGACCTTGAGCAAAGC 57.557 42.857 0.00 0.00 34.95 3.51
13 14 4.747810 ACAAAGTTTGACCTTGAGCAAAG 58.252 39.130 22.23 0.00 34.95 2.77
14 15 4.799564 ACAAAGTTTGACCTTGAGCAAA 57.200 36.364 22.23 0.00 0.00 3.68
15 16 5.906113 TTACAAAGTTTGACCTTGAGCAA 57.094 34.783 22.23 0.00 0.00 3.91
16 17 5.417580 AGTTTACAAAGTTTGACCTTGAGCA 59.582 36.000 22.23 0.00 0.00 4.26
17 18 5.891451 AGTTTACAAAGTTTGACCTTGAGC 58.109 37.500 22.23 0.00 0.00 4.26
100 101 8.541133 TGACGTGAAAGTACATTCAATAATGA 57.459 30.769 14.64 0.00 44.50 2.57
104 105 9.040939 CCATATGACGTGAAAGTACATTCAATA 57.959 33.333 14.64 9.55 40.76 1.90
105 106 7.768582 TCCATATGACGTGAAAGTACATTCAAT 59.231 33.333 14.64 6.81 40.76 2.57
106 107 7.100409 TCCATATGACGTGAAAGTACATTCAA 58.900 34.615 14.64 0.60 40.76 2.69
107 108 6.635755 TCCATATGACGTGAAAGTACATTCA 58.364 36.000 9.38 9.38 36.99 2.57
108 109 7.715265 ATCCATATGACGTGAAAGTACATTC 57.285 36.000 3.65 3.88 0.00 2.67
109 110 8.397906 CAAATCCATATGACGTGAAAGTACATT 58.602 33.333 3.65 0.00 0.00 2.71
110 111 7.552687 ACAAATCCATATGACGTGAAAGTACAT 59.447 33.333 3.65 0.00 0.00 2.29
111 112 6.876789 ACAAATCCATATGACGTGAAAGTACA 59.123 34.615 3.65 0.00 0.00 2.90
112 113 7.303634 ACAAATCCATATGACGTGAAAGTAC 57.696 36.000 3.65 0.00 0.00 2.73
113 114 7.915293 AACAAATCCATATGACGTGAAAGTA 57.085 32.000 3.65 0.00 0.00 2.24
114 115 6.817765 AACAAATCCATATGACGTGAAAGT 57.182 33.333 3.65 0.00 0.00 2.66
115 116 7.409697 CCTAACAAATCCATATGACGTGAAAG 58.590 38.462 3.65 1.18 0.00 2.62
116 117 6.317642 CCCTAACAAATCCATATGACGTGAAA 59.682 38.462 3.65 0.00 0.00 2.69
117 118 5.820423 CCCTAACAAATCCATATGACGTGAA 59.180 40.000 3.65 0.00 0.00 3.18
118 119 5.104693 ACCCTAACAAATCCATATGACGTGA 60.105 40.000 3.65 0.00 0.00 4.35
119 120 5.123227 ACCCTAACAAATCCATATGACGTG 58.877 41.667 3.65 0.00 0.00 4.49
120 121 5.367945 ACCCTAACAAATCCATATGACGT 57.632 39.130 3.65 0.00 0.00 4.34
121 122 7.795482 TTTACCCTAACAAATCCATATGACG 57.205 36.000 3.65 0.00 0.00 4.35
122 123 9.131791 ACATTTACCCTAACAAATCCATATGAC 57.868 33.333 3.65 0.00 0.00 3.06
123 124 9.707957 AACATTTACCCTAACAAATCCATATGA 57.292 29.630 3.65 0.00 0.00 2.15
126 127 9.315363 ACAAACATTTACCCTAACAAATCCATA 57.685 29.630 0.00 0.00 0.00 2.74
127 128 8.201242 ACAAACATTTACCCTAACAAATCCAT 57.799 30.769 0.00 0.00 0.00 3.41
128 129 7.604657 ACAAACATTTACCCTAACAAATCCA 57.395 32.000 0.00 0.00 0.00 3.41
191 192 6.818644 TCTGCATATTAGGTTTGACTGAAGTC 59.181 38.462 3.41 3.41 44.97 3.01
192 193 6.711277 TCTGCATATTAGGTTTGACTGAAGT 58.289 36.000 0.00 0.00 0.00 3.01
193 194 6.820656 ACTCTGCATATTAGGTTTGACTGAAG 59.179 38.462 0.00 0.00 0.00 3.02
194 195 6.711277 ACTCTGCATATTAGGTTTGACTGAA 58.289 36.000 0.00 0.00 0.00 3.02
195 196 6.299805 ACTCTGCATATTAGGTTTGACTGA 57.700 37.500 0.00 0.00 0.00 3.41
196 197 8.492673 TTTACTCTGCATATTAGGTTTGACTG 57.507 34.615 0.00 0.00 0.00 3.51
210 211 9.502091 TGTACTCTGTTTTTATTTACTCTGCAT 57.498 29.630 0.00 0.00 0.00 3.96
211 212 8.896320 TGTACTCTGTTTTTATTTACTCTGCA 57.104 30.769 0.00 0.00 0.00 4.41
212 213 9.974750 GATGTACTCTGTTTTTATTTACTCTGC 57.025 33.333 0.00 0.00 0.00 4.26
220 221 9.793259 TCAGAAAGGATGTACTCTGTTTTTATT 57.207 29.630 7.26 0.00 37.25 1.40
221 222 9.220767 GTCAGAAAGGATGTACTCTGTTTTTAT 57.779 33.333 7.26 0.00 37.25 1.40
222 223 8.429641 AGTCAGAAAGGATGTACTCTGTTTTTA 58.570 33.333 7.26 0.00 37.25 1.52
223 224 7.283329 AGTCAGAAAGGATGTACTCTGTTTTT 58.717 34.615 7.26 0.00 37.25 1.94
224 225 6.831976 AGTCAGAAAGGATGTACTCTGTTTT 58.168 36.000 7.26 0.00 37.25 2.43
225 226 6.426646 AGTCAGAAAGGATGTACTCTGTTT 57.573 37.500 7.26 0.00 37.25 2.83
226 227 5.336055 CGAGTCAGAAAGGATGTACTCTGTT 60.336 44.000 7.26 0.00 37.25 3.16
227 228 4.156922 CGAGTCAGAAAGGATGTACTCTGT 59.843 45.833 7.26 0.00 37.25 3.41
228 229 4.396478 TCGAGTCAGAAAGGATGTACTCTG 59.604 45.833 0.00 0.00 37.28 3.35
229 230 4.590918 TCGAGTCAGAAAGGATGTACTCT 58.409 43.478 0.00 0.00 32.96 3.24
230 231 4.966965 TCGAGTCAGAAAGGATGTACTC 57.033 45.455 0.00 0.00 0.00 2.59
231 232 4.767928 AGTTCGAGTCAGAAAGGATGTACT 59.232 41.667 0.00 0.00 0.00 2.73
232 233 5.061920 AGTTCGAGTCAGAAAGGATGTAC 57.938 43.478 0.00 0.00 0.00 2.90
233 234 5.010933 AGAGTTCGAGTCAGAAAGGATGTA 58.989 41.667 0.00 0.00 0.00 2.29
234 235 3.829601 AGAGTTCGAGTCAGAAAGGATGT 59.170 43.478 0.00 0.00 0.00 3.06
235 236 4.448537 AGAGTTCGAGTCAGAAAGGATG 57.551 45.455 0.00 0.00 0.00 3.51
236 237 7.776030 TCTTATAGAGTTCGAGTCAGAAAGGAT 59.224 37.037 0.00 0.00 0.00 3.24
237 238 7.066043 GTCTTATAGAGTTCGAGTCAGAAAGGA 59.934 40.741 0.00 0.00 0.00 3.36
238 239 7.148222 TGTCTTATAGAGTTCGAGTCAGAAAGG 60.148 40.741 0.00 0.00 0.00 3.11
239 240 7.753659 TGTCTTATAGAGTTCGAGTCAGAAAG 58.246 38.462 0.00 1.15 0.00 2.62
240 241 7.683437 TGTCTTATAGAGTTCGAGTCAGAAA 57.317 36.000 0.00 0.00 0.00 2.52
241 242 7.867305 ATGTCTTATAGAGTTCGAGTCAGAA 57.133 36.000 0.00 0.00 0.00 3.02
242 243 7.867305 AATGTCTTATAGAGTTCGAGTCAGA 57.133 36.000 0.00 0.00 0.00 3.27
243 244 9.658475 CTTAATGTCTTATAGAGTTCGAGTCAG 57.342 37.037 0.00 0.00 0.00 3.51
244 245 9.392259 TCTTAATGTCTTATAGAGTTCGAGTCA 57.608 33.333 0.00 0.00 0.00 3.41
260 261 9.261180 CCAAATGTATCGTGTATCTTAATGTCT 57.739 33.333 0.00 0.00 0.00 3.41
261 262 9.042008 ACCAAATGTATCGTGTATCTTAATGTC 57.958 33.333 0.00 0.00 0.00 3.06
262 263 8.958119 ACCAAATGTATCGTGTATCTTAATGT 57.042 30.769 0.00 0.00 0.00 2.71
263 264 8.495949 GGACCAAATGTATCGTGTATCTTAATG 58.504 37.037 0.00 0.00 0.00 1.90
264 265 8.208224 TGGACCAAATGTATCGTGTATCTTAAT 58.792 33.333 0.00 0.00 0.00 1.40
265 266 7.557724 TGGACCAAATGTATCGTGTATCTTAA 58.442 34.615 0.00 0.00 0.00 1.85
266 267 7.114866 TGGACCAAATGTATCGTGTATCTTA 57.885 36.000 0.00 0.00 0.00 2.10
267 268 5.984725 TGGACCAAATGTATCGTGTATCTT 58.015 37.500 0.00 0.00 0.00 2.40
268 269 5.607939 TGGACCAAATGTATCGTGTATCT 57.392 39.130 0.00 0.00 0.00 1.98
269 270 5.276678 CGTTGGACCAAATGTATCGTGTATC 60.277 44.000 8.94 0.00 0.00 2.24
270 271 4.569162 CGTTGGACCAAATGTATCGTGTAT 59.431 41.667 8.94 0.00 0.00 2.29
271 272 3.927758 CGTTGGACCAAATGTATCGTGTA 59.072 43.478 8.94 0.00 0.00 2.90
272 273 2.739913 CGTTGGACCAAATGTATCGTGT 59.260 45.455 8.94 0.00 0.00 4.49
273 274 2.095213 CCGTTGGACCAAATGTATCGTG 59.905 50.000 8.94 0.00 0.00 4.35
274 275 2.352388 CCGTTGGACCAAATGTATCGT 58.648 47.619 8.94 0.00 0.00 3.73
275 276 1.063469 GCCGTTGGACCAAATGTATCG 59.937 52.381 8.94 7.08 0.00 2.92
276 277 2.365582 AGCCGTTGGACCAAATGTATC 58.634 47.619 8.94 0.00 0.00 2.24
277 278 2.507407 AGCCGTTGGACCAAATGTAT 57.493 45.000 8.94 0.00 0.00 2.29
278 279 2.038689 TGTAGCCGTTGGACCAAATGTA 59.961 45.455 8.94 0.00 0.00 2.29
279 280 1.202830 TGTAGCCGTTGGACCAAATGT 60.203 47.619 8.94 0.00 0.00 2.71
280 281 1.468520 CTGTAGCCGTTGGACCAAATG 59.531 52.381 8.94 4.57 0.00 2.32
281 282 1.073284 ACTGTAGCCGTTGGACCAAAT 59.927 47.619 8.94 0.00 0.00 2.32
291 292 3.259876 TGGTCAAGAAATACTGTAGCCGT 59.740 43.478 0.00 0.00 0.00 5.68
296 299 6.999950 TGCTACTTGGTCAAGAAATACTGTA 58.000 36.000 16.55 0.00 40.79 2.74
312 315 3.189910 TGTCGTACTACCACTGCTACTTG 59.810 47.826 0.00 0.00 0.00 3.16
323 326 2.224079 TCGTGTTCACTGTCGTACTACC 59.776 50.000 1.53 0.00 0.00 3.18
368 378 1.271379 AGACACGCATCGTCCTTGTTA 59.729 47.619 0.00 0.00 38.32 2.41
564 575 2.726351 GGCTAGCGGCAGAGGAAGT 61.726 63.158 9.00 0.00 44.01 3.01
594 605 8.338259 ACAAGTAGAACCGTATAATACTACGTG 58.662 37.037 0.76 0.76 42.21 4.49
622 644 1.021202 TGAACCGTTCCAGCTTGTTG 58.979 50.000 8.80 0.00 0.00 3.33
650 672 2.458610 CGCACGATCATGCTGCACT 61.459 57.895 12.50 0.00 43.80 4.40
768 790 4.529219 TGGCGTGCGGCTATCCAG 62.529 66.667 18.31 0.00 42.94 3.86
769 791 4.830765 GTGGCGTGCGGCTATCCA 62.831 66.667 18.31 2.52 42.94 3.41
845 876 0.463620 GGCTGAGGAGCTGAGGTTAG 59.536 60.000 0.00 0.00 45.44 2.34
855 886 0.252479 AGCAATGTCTGGCTGAGGAG 59.748 55.000 0.00 0.00 39.30 3.69
880 911 5.678616 GCTTCAAGTTCTGGTTTTGTGCTTA 60.679 40.000 0.00 0.00 0.00 3.09
891 922 3.312421 TGTTTTCGAGCTTCAAGTTCTGG 59.688 43.478 0.00 0.00 0.00 3.86
900 931 4.800784 AGTACTCTCTGTTTTCGAGCTTC 58.199 43.478 0.00 0.00 0.00 3.86
916 947 1.550976 CAGGAACAGGGTGGAGTACTC 59.449 57.143 14.87 14.87 0.00 2.59
919 950 1.348064 CACAGGAACAGGGTGGAGTA 58.652 55.000 0.00 0.00 0.00 2.59
920 951 0.694444 ACACAGGAACAGGGTGGAGT 60.694 55.000 0.00 0.00 36.87 3.85
922 953 0.399949 AGACACAGGAACAGGGTGGA 60.400 55.000 0.00 0.00 36.87 4.02
924 955 1.051812 AGAGACACAGGAACAGGGTG 58.948 55.000 0.00 0.00 38.47 4.61
925 956 1.807814 AAGAGACACAGGAACAGGGT 58.192 50.000 0.00 0.00 0.00 4.34
927 958 2.880890 CCAAAAGAGACACAGGAACAGG 59.119 50.000 0.00 0.00 0.00 4.00
928 959 2.880890 CCCAAAAGAGACACAGGAACAG 59.119 50.000 0.00 0.00 0.00 3.16
929 960 2.241176 ACCCAAAAGAGACACAGGAACA 59.759 45.455 0.00 0.00 0.00 3.18
930 961 2.932261 ACCCAAAAGAGACACAGGAAC 58.068 47.619 0.00 0.00 0.00 3.62
931 962 3.053991 TGAACCCAAAAGAGACACAGGAA 60.054 43.478 0.00 0.00 0.00 3.36
944 975 3.967326 TCAAGAGAGAGACTGAACCCAAA 59.033 43.478 0.00 0.00 0.00 3.28
958 989 2.045280 ATCGCCCCGATCAAGAGAG 58.955 57.895 0.00 0.00 43.45 3.20
989 1027 2.740714 GCCGCCATTGTCGTCTGAC 61.741 63.158 0.00 0.00 45.71 3.51
991 1029 3.853330 CGCCGCCATTGTCGTCTG 61.853 66.667 0.00 0.00 0.00 3.51
992 1030 4.063967 TCGCCGCCATTGTCGTCT 62.064 61.111 0.00 0.00 0.00 4.18
1013 1057 0.888736 CACCGCCTTCACCATGTTCA 60.889 55.000 0.00 0.00 0.00 3.18
1022 1066 3.286751 GCAGCAACACCGCCTTCA 61.287 61.111 0.00 0.00 0.00 3.02
1023 1067 2.970974 GAGCAGCAACACCGCCTTC 61.971 63.158 0.00 0.00 0.00 3.46
1109 1153 0.392595 GATCCCGTTCTCCAACCACC 60.393 60.000 0.00 0.00 0.00 4.61
1117 1161 1.367840 CCATCCCGATCCCGTTCTC 59.632 63.158 0.00 0.00 0.00 2.87
1299 1343 3.067833 AGAGAAACAAAGTAAGAGCGGC 58.932 45.455 0.00 0.00 0.00 6.53
1308 1352 4.142381 GCAGAAACACCAGAGAAACAAAGT 60.142 41.667 0.00 0.00 0.00 2.66
1320 1364 0.876777 CCACGTACGCAGAAACACCA 60.877 55.000 16.72 0.00 0.00 4.17
1331 1375 4.302509 TGCACCCCACCACGTACG 62.303 66.667 15.01 15.01 0.00 3.67
1363 1407 3.551659 GCTTTGGTCTCAGAAAAAGGCAG 60.552 47.826 11.37 0.00 31.67 4.85
1421 1475 7.210174 GGGATTCACATTTAAGGCTTAATTCC 58.790 38.462 19.65 9.06 0.00 3.01
1464 1518 7.817962 AGCGCCGTAATATATTTTCTGAATAGT 59.182 33.333 2.29 0.00 0.00 2.12
1465 1519 8.186178 AGCGCCGTAATATATTTTCTGAATAG 57.814 34.615 2.29 0.00 0.00 1.73
1469 1523 4.927425 GGAGCGCCGTAATATATTTTCTGA 59.073 41.667 2.29 0.00 0.00 3.27
1471 1525 4.890088 TGGAGCGCCGTAATATATTTTCT 58.110 39.130 2.29 0.00 36.79 2.52
1473 1527 4.328983 CGATGGAGCGCCGTAATATATTTT 59.671 41.667 2.29 0.00 36.79 1.82
1477 1538 1.814394 ACGATGGAGCGCCGTAATATA 59.186 47.619 2.29 0.00 36.79 0.86
1541 1610 8.030106 CCAGATATCTCCTCGTTAAGATTTACC 58.970 40.741 1.03 0.00 34.21 2.85
1565 1675 3.264964 GTCTGACATTTTACCCCTACCCA 59.735 47.826 2.24 0.00 0.00 4.51
1569 1679 4.460948 GTCGTCTGACATTTTACCCCTA 57.539 45.455 8.73 0.00 44.82 3.53
1645 1755 5.346522 GTTCGTCAGATTTTACGGTCCTAT 58.653 41.667 0.00 0.00 39.52 2.57
1707 1817 7.903431 GCCAACTTCATATAACTAAACTTGTCG 59.097 37.037 0.00 0.00 0.00 4.35
1724 1834 2.037901 TGCCTCAAATTGCCAACTTCA 58.962 42.857 0.00 0.00 0.00 3.02
1726 1836 3.557228 TTTGCCTCAAATTGCCAACTT 57.443 38.095 0.00 0.00 0.00 2.66
1814 1969 2.733218 CGGCGAACGTCAGCTGAA 60.733 61.111 20.19 0.00 42.01 3.02
1815 1970 4.717629 CCGGCGAACGTCAGCTGA 62.718 66.667 13.74 13.74 42.01 4.26
1821 1976 1.283736 AATGATAACCGGCGAACGTC 58.716 50.000 9.30 1.63 42.24 4.34
1868 2023 4.742274 CGGTGACCGTGAGAAACA 57.258 55.556 17.28 0.00 42.73 2.83
1886 2041 5.985911 AGAAGTTGGTAGTTAACACACACT 58.014 37.500 8.61 6.93 0.00 3.55
1897 2052 5.216665 TGAGGGGTATAGAAGTTGGTAGT 57.783 43.478 0.00 0.00 0.00 2.73
1912 2067 3.591527 TCATTATGGTTCTGTTGAGGGGT 59.408 43.478 0.00 0.00 0.00 4.95
1959 2114 7.825331 TTCAACACCATATTAGGTTCAAACA 57.175 32.000 0.00 0.00 40.77 2.83
2014 2169 8.846607 GCAAATTGGTAATCGTAGTTACTTTTG 58.153 33.333 0.00 15.68 35.31 2.44
2022 2177 7.859325 ATAACTGCAAATTGGTAATCGTAGT 57.141 32.000 0.00 0.00 0.00 2.73
2026 2181 6.632834 GCACTATAACTGCAAATTGGTAATCG 59.367 38.462 0.00 0.00 34.56 3.34
2055 2210 2.439156 GCGAGGAGGCTTGGCATT 60.439 61.111 0.00 0.00 0.00 3.56
2094 2249 4.492160 TGCTCTAGCGAACGCCCG 62.492 66.667 15.44 7.22 45.83 6.13
2095 2250 2.583593 CTGCTCTAGCGAACGCCC 60.584 66.667 15.44 0.88 45.83 6.13
2096 2251 2.583593 CCTGCTCTAGCGAACGCC 60.584 66.667 15.44 0.79 45.83 5.68
2097 2252 2.583593 CCCTGCTCTAGCGAACGC 60.584 66.667 11.31 11.31 45.83 4.84
2098 2253 1.064946 CTCCCTGCTCTAGCGAACG 59.935 63.158 0.00 0.00 45.83 3.95
2099 2254 1.227118 GCTCCCTGCTCTAGCGAAC 60.227 63.158 0.00 0.00 45.83 3.95
2100 2255 2.427245 GGCTCCCTGCTCTAGCGAA 61.427 63.158 0.00 0.00 45.83 4.70
2101 2256 2.835431 GGCTCCCTGCTCTAGCGA 60.835 66.667 0.00 0.00 45.83 4.93
2102 2257 3.150335 TGGCTCCCTGCTCTAGCG 61.150 66.667 0.00 0.00 45.83 4.26
2103 2258 2.503546 GTGGCTCCCTGCTCTAGC 59.496 66.667 0.00 0.00 42.39 3.42
2104 2259 1.382420 AGGTGGCTCCCTGCTCTAG 60.382 63.158 1.14 0.00 42.39 2.43
2105 2260 1.687146 CAGGTGGCTCCCTGCTCTA 60.687 63.158 10.20 0.00 45.19 2.43
2106 2261 3.007920 CAGGTGGCTCCCTGCTCT 61.008 66.667 10.20 0.00 45.19 4.09
2117 2272 4.704833 CGGTGTGGGAGCAGGTGG 62.705 72.222 0.00 0.00 0.00 4.61
2118 2273 4.704833 CCGGTGTGGGAGCAGGTG 62.705 72.222 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.