Multiple sequence alignment - TraesCS6D01G161400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G161400 chr6D 100.000 3969 0 0 1 3969 139931492 139935460 0.000000e+00 7330.0
1 TraesCS6D01G161400 chr6D 97.276 257 7 0 1 257 293105338 293105594 1.690000e-118 436.0
2 TraesCS6D01G161400 chr6D 95.785 261 11 0 1 261 340204448 340204188 4.740000e-114 422.0
3 TraesCS6D01G161400 chr6D 81.481 189 19 8 3522 3695 130209013 130208826 1.490000e-29 141.0
4 TraesCS6D01G161400 chr6D 100.000 48 0 0 2259 2306 139933711 139933758 5.460000e-14 89.8
5 TraesCS6D01G161400 chr6D 100.000 48 0 0 2220 2267 139933750 139933797 5.460000e-14 89.8
6 TraesCS6D01G161400 chr6B 92.411 1265 64 15 410 1669 239734807 239736044 0.000000e+00 1775.0
7 TraesCS6D01G161400 chr6B 94.118 918 25 11 2259 3172 239736632 239737524 0.000000e+00 1369.0
8 TraesCS6D01G161400 chr6B 89.822 619 26 13 1670 2267 239736077 239736679 0.000000e+00 760.0
9 TraesCS6D01G161400 chr6B 90.691 376 26 5 3151 3520 239737537 239737909 3.560000e-135 492.0
10 TraesCS6D01G161400 chr6B 94.048 168 10 0 255 422 239734620 239734787 5.090000e-64 255.0
11 TraesCS6D01G161400 chr6A 86.842 1634 98 52 253 1824 183194135 183195713 0.000000e+00 1718.0
12 TraesCS6D01G161400 chr6A 93.312 613 13 7 2259 2861 183201704 183202298 0.000000e+00 880.0
13 TraesCS6D01G161400 chr6A 93.233 399 15 5 1869 2267 183201365 183201751 9.560000e-161 577.0
14 TraesCS6D01G161400 chr6A 95.192 208 7 2 3029 3235 183202471 183202676 3.820000e-85 326.0
15 TraesCS6D01G161400 chr6A 89.958 239 19 3 3286 3520 183214187 183214424 1.790000e-78 303.0
16 TraesCS6D01G161400 chr6A 77.711 332 45 20 3663 3967 607853312 607853641 4.080000e-40 176.0
17 TraesCS6D01G161400 chr6A 81.538 195 12 11 3522 3693 430923693 430923500 5.350000e-29 139.0
18 TraesCS6D01G161400 chr6A 90.291 103 1 2 2881 2983 183202362 183202455 4.160000e-25 126.0
19 TraesCS6D01G161400 chr2D 98.438 256 4 0 1 256 532005878 532005623 6.050000e-123 451.0
20 TraesCS6D01G161400 chr2D 79.284 391 40 23 3618 3969 177455409 177455021 6.630000e-58 235.0
21 TraesCS6D01G161400 chr2D 77.805 401 47 23 3609 3969 158245501 158245103 4.020000e-50 209.0
22 TraesCS6D01G161400 chr2D 77.179 390 50 22 3522 3873 642303134 642303522 1.460000e-44 191.0
23 TraesCS6D01G161400 chr7D 96.887 257 8 0 1 257 106896081 106896337 7.880000e-117 431.0
24 TraesCS6D01G161400 chr7D 77.165 508 56 22 3522 3969 371256434 371255927 1.430000e-59 241.0
25 TraesCS6D01G161400 chr7D 84.091 220 15 8 3770 3969 30127067 30126848 1.130000e-45 195.0
26 TraesCS6D01G161400 chr3D 96.887 257 8 0 1 257 82121433 82121689 7.880000e-117 431.0
27 TraesCS6D01G161400 chr3D 78.316 392 36 16 3522 3873 412820834 412820452 1.450000e-49 207.0
28 TraesCS6D01G161400 chr3D 76.484 455 44 34 3568 3969 291756189 291755745 5.240000e-44 189.0
29 TraesCS6D01G161400 chr3D 74.950 503 67 28 3514 3964 126392330 126392825 4.080000e-40 176.0
30 TraesCS6D01G161400 chr3D 76.020 392 57 22 3609 3969 105108338 105107953 6.820000e-38 169.0
31 TraesCS6D01G161400 chr3D 81.503 173 15 7 3522 3682 14806330 14806163 4.160000e-25 126.0
32 TraesCS6D01G161400 chr4D 96.498 257 9 0 1 257 346288317 346288573 3.670000e-115 425.0
33 TraesCS6D01G161400 chr4D 96.850 254 7 1 1 253 297898758 297899011 1.320000e-114 424.0
34 TraesCS6D01G161400 chr4D 76.411 496 65 27 3522 3968 29872096 29871604 1.860000e-53 220.0
35 TraesCS6D01G161400 chr4D 76.220 492 64 25 3522 3967 488323486 488323970 1.120000e-50 211.0
36 TraesCS6D01G161400 chr4D 75.000 316 38 25 3568 3872 99187109 99187394 1.510000e-19 108.0
37 TraesCS6D01G161400 chr5D 96.109 257 10 0 1 257 412234553 412234809 1.710000e-113 420.0
38 TraesCS6D01G161400 chr5D 83.651 367 53 6 3609 3969 365681920 365681555 4.910000e-89 339.0
39 TraesCS6D01G161400 chr1D 96.109 257 10 0 1 257 442410793 442410537 1.710000e-113 420.0
40 TraesCS6D01G161400 chr1D 77.904 439 50 22 3568 3968 204796565 204796136 3.090000e-56 230.0
41 TraesCS6D01G161400 chr1D 75.820 488 72 18 3522 3964 69614509 69614023 5.200000e-49 206.0
42 TraesCS6D01G161400 chr1D 88.889 117 8 3 3855 3969 215618603 215618716 5.350000e-29 139.0
43 TraesCS6D01G161400 chr1D 82.828 99 6 1 3519 3606 351509685 351509783 1.180000e-10 78.7
44 TraesCS6D01G161400 chr3A 78.880 393 41 18 3609 3969 375022191 375022573 1.110000e-55 228.0
45 TraesCS6D01G161400 chr3A 83.333 138 17 4 3714 3845 56072814 56072951 5.390000e-24 122.0
46 TraesCS6D01G161400 chr3A 88.235 102 12 0 3568 3669 56388941 56389042 5.390000e-24 122.0
47 TraesCS6D01G161400 chr3A 93.750 48 3 0 3522 3569 32236306 32236353 5.500000e-09 73.1
48 TraesCS6D01G161400 chr2B 76.040 505 59 32 3522 3967 121546355 121546856 5.200000e-49 206.0
49 TraesCS6D01G161400 chr2B 75.800 500 68 20 3519 3969 439422511 439422016 1.870000e-48 204.0
50 TraesCS6D01G161400 chr2B 75.915 328 46 21 3568 3868 376121008 376121329 1.920000e-28 137.0
51 TraesCS6D01G161400 chr2A 83.028 218 30 4 3662 3872 160043301 160043518 1.460000e-44 191.0
52 TraesCS6D01G161400 chr2A 84.034 119 15 4 3568 3682 758051667 758051785 1.170000e-20 111.0
53 TraesCS6D01G161400 chr1B 80.150 267 31 10 3725 3969 308578605 308578871 3.150000e-41 180.0
54 TraesCS6D01G161400 chr3B 74.157 445 63 32 3568 3967 384725090 384724653 1.920000e-28 137.0
55 TraesCS6D01G161400 chr1A 84.821 112 15 2 3573 3682 516373582 516373693 1.170000e-20 111.0
56 TraesCS6D01G161400 chr7B 78.378 185 16 4 3522 3682 564169993 564170177 9.080000e-17 99.0


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 TraesCS6D01G161400 chr6D 139931492 139935460 3968 False 2503.20 7330 100.000 1 3969 3 chr6D.!!$F2 3968
1 TraesCS6D01G161400 chr6B 239734620 239737909 3289 False 930.20 1775 92.218 255 3520 5 chr6B.!!$F1 3265
2 TraesCS6D01G161400 chr6A 183194135 183195713 1578 False 1718.00 1718 86.842 253 1824 1 chr6A.!!$F1 1571
3 TraesCS6D01G161400 chr6A 183201365 183202676 1311 False 477.25 880 93.007 1869 3235 4 chr6A.!!$F4 1366
4 TraesCS6D01G161400 chr7D 371255927 371256434 507 True 241.00 241 77.165 3522 3969 1 chr7D.!!$R2 447
5 TraesCS6D01G161400 chr2B 121546355 121546856 501 False 206.00 206 76.040 3522 3967 1 chr2B.!!$F1 445

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
920 958 0.106918 GAGGGGAGCGAGAGAGAGAA 60.107 60.0 0.0 0.0 0.0 2.87 F
1391 1458 0.323178 GGGCATGATATGGAGGGCTG 60.323 60.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2671 2809 0.103390 TCTCGAACTGCACCGTGAAA 59.897 50.0 1.65 0.0 0.00 2.69 R
2994 3181 0.179048 CAGCAGCCATTATGGTCGGA 60.179 55.0 13.28 0.0 40.46 4.55 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
34 35 2.202797 CGTCTAGGCGCTGCACAT 60.203 61.111 2.68 0.00 0.00 3.21
35 36 1.811266 CGTCTAGGCGCTGCACATT 60.811 57.895 2.68 0.00 0.00 2.71
36 37 1.756375 CGTCTAGGCGCTGCACATTC 61.756 60.000 2.68 0.00 0.00 2.67
37 38 1.153369 TCTAGGCGCTGCACATTCC 60.153 57.895 7.64 0.00 0.00 3.01
38 39 1.450134 CTAGGCGCTGCACATTCCA 60.450 57.895 7.64 0.00 0.00 3.53
39 40 0.816825 CTAGGCGCTGCACATTCCAT 60.817 55.000 7.64 0.00 0.00 3.41
40 41 1.096967 TAGGCGCTGCACATTCCATG 61.097 55.000 7.64 0.00 0.00 3.66
41 42 2.703798 GGCGCTGCACATTCCATGT 61.704 57.895 7.64 0.00 46.22 3.21
48 49 3.277133 ACATTCCATGTGTGGCGC 58.723 55.556 0.00 0.00 45.63 6.53
49 50 2.342650 ACATTCCATGTGTGGCGCC 61.343 57.895 22.73 22.73 45.63 6.53
50 51 2.048023 CATTCCATGTGTGGCGCCT 61.048 57.895 29.70 2.88 45.63 5.52
51 52 0.747644 CATTCCATGTGTGGCGCCTA 60.748 55.000 29.70 14.39 45.63 3.93
52 53 0.464373 ATTCCATGTGTGGCGCCTAG 60.464 55.000 29.70 10.46 45.63 3.02
53 54 3.680620 TCCATGTGTGGCGCCTAGC 62.681 63.158 29.70 17.93 45.63 3.42
65 66 4.277593 CCTAGCTCGGAGGCGCTG 62.278 72.222 7.64 0.00 36.29 5.18
66 67 4.940593 CTAGCTCGGAGGCGCTGC 62.941 72.222 7.64 0.00 36.29 5.25
107 108 3.941188 CTGCCACGGTGGACAGGT 61.941 66.667 30.65 0.00 40.96 4.00
108 109 4.248842 TGCCACGGTGGACAGGTG 62.249 66.667 30.65 2.56 40.96 4.00
109 110 4.250305 GCCACGGTGGACAGGTGT 62.250 66.667 30.65 0.00 40.96 4.16
110 111 2.280797 CCACGGTGGACAGGTGTG 60.281 66.667 22.77 0.00 40.96 3.82
111 112 2.972505 CACGGTGGACAGGTGTGC 60.973 66.667 0.00 0.00 36.87 4.57
112 113 3.475494 ACGGTGGACAGGTGTGCA 61.475 61.111 0.00 0.00 44.12 4.57
140 141 2.184322 GCTAGGCGCTGCACAGTA 59.816 61.111 7.64 0.00 35.14 2.74
141 142 2.167861 GCTAGGCGCTGCACAGTAC 61.168 63.158 7.64 0.00 35.14 2.73
142 143 1.874019 CTAGGCGCTGCACAGTACG 60.874 63.158 7.64 0.00 0.00 3.67
143 144 3.350909 TAGGCGCTGCACAGTACGG 62.351 63.158 7.64 0.00 0.00 4.02
145 146 3.777925 GCGCTGCACAGTACGGTG 61.778 66.667 20.22 20.22 41.72 4.94
146 147 2.355837 CGCTGCACAGTACGGTGT 60.356 61.111 24.06 5.01 40.89 4.16
148 149 2.317609 GCTGCACAGTACGGTGTGG 61.318 63.158 24.06 17.89 46.73 4.17
149 150 2.280524 TGCACAGTACGGTGTGGC 60.281 61.111 24.06 12.81 46.73 5.01
150 151 3.411351 GCACAGTACGGTGTGGCG 61.411 66.667 24.06 2.41 46.73 5.69
151 152 3.411351 CACAGTACGGTGTGGCGC 61.411 66.667 16.88 0.00 43.56 6.53
152 153 4.675029 ACAGTACGGTGTGGCGCC 62.675 66.667 22.73 22.73 0.00 6.53
174 175 4.627801 TGGCGGGCGCTACACAAA 62.628 61.111 7.64 0.00 41.60 2.83
175 176 3.358707 GGCGGGCGCTACACAAAA 61.359 61.111 7.64 0.00 41.60 2.44
176 177 2.640421 GCGGGCGCTACACAAAAA 59.360 55.556 7.64 0.00 38.26 1.94
177 178 1.442017 GCGGGCGCTACACAAAAAG 60.442 57.895 7.64 0.00 38.26 2.27
178 179 1.209127 CGGGCGCTACACAAAAAGG 59.791 57.895 7.64 0.00 0.00 3.11
179 180 1.512156 CGGGCGCTACACAAAAAGGT 61.512 55.000 7.64 0.00 0.00 3.50
180 181 0.240145 GGGCGCTACACAAAAAGGTC 59.760 55.000 7.64 0.00 0.00 3.85
181 182 0.948678 GGCGCTACACAAAAAGGTCA 59.051 50.000 7.64 0.00 0.00 4.02
182 183 1.069227 GGCGCTACACAAAAAGGTCAG 60.069 52.381 7.64 0.00 0.00 3.51
183 184 1.069227 GCGCTACACAAAAAGGTCAGG 60.069 52.381 0.00 0.00 0.00 3.86
184 185 1.535462 CGCTACACAAAAAGGTCAGGG 59.465 52.381 0.00 0.00 0.00 4.45
185 186 1.886542 GCTACACAAAAAGGTCAGGGG 59.113 52.381 0.00 0.00 0.00 4.79
186 187 2.488347 GCTACACAAAAAGGTCAGGGGA 60.488 50.000 0.00 0.00 0.00 4.81
187 188 2.364972 ACACAAAAAGGTCAGGGGAG 57.635 50.000 0.00 0.00 0.00 4.30
188 189 1.569072 ACACAAAAAGGTCAGGGGAGT 59.431 47.619 0.00 0.00 0.00 3.85
189 190 1.956477 CACAAAAAGGTCAGGGGAGTG 59.044 52.381 0.00 0.00 0.00 3.51
190 191 1.850345 ACAAAAAGGTCAGGGGAGTGA 59.150 47.619 0.00 0.00 0.00 3.41
191 192 2.243736 ACAAAAAGGTCAGGGGAGTGAA 59.756 45.455 0.00 0.00 0.00 3.18
192 193 3.295973 CAAAAAGGTCAGGGGAGTGAAA 58.704 45.455 0.00 0.00 0.00 2.69
193 194 3.897505 CAAAAAGGTCAGGGGAGTGAAAT 59.102 43.478 0.00 0.00 0.00 2.17
194 195 5.076873 CAAAAAGGTCAGGGGAGTGAAATA 58.923 41.667 0.00 0.00 0.00 1.40
195 196 4.576330 AAAGGTCAGGGGAGTGAAATAG 57.424 45.455 0.00 0.00 0.00 1.73
196 197 3.207044 AGGTCAGGGGAGTGAAATAGT 57.793 47.619 0.00 0.00 0.00 2.12
197 198 3.532102 AGGTCAGGGGAGTGAAATAGTT 58.468 45.455 0.00 0.00 0.00 2.24
198 199 3.916989 AGGTCAGGGGAGTGAAATAGTTT 59.083 43.478 0.00 0.00 0.00 2.66
199 200 4.019231 AGGTCAGGGGAGTGAAATAGTTTC 60.019 45.833 0.00 0.00 40.08 2.78
200 201 3.933332 GTCAGGGGAGTGAAATAGTTTCG 59.067 47.826 0.00 0.00 42.55 3.46
207 208 3.471495 GTGAAATAGTTTCGCACCCAG 57.529 47.619 10.21 0.00 46.56 4.45
208 209 2.812011 GTGAAATAGTTTCGCACCCAGT 59.188 45.455 10.21 0.00 46.56 4.00
209 210 3.252458 GTGAAATAGTTTCGCACCCAGTT 59.748 43.478 10.21 0.00 46.56 3.16
210 211 3.500680 TGAAATAGTTTCGCACCCAGTTC 59.499 43.478 0.00 0.00 42.55 3.01
211 212 2.851263 ATAGTTTCGCACCCAGTTCA 57.149 45.000 0.00 0.00 0.00 3.18
212 213 2.851263 TAGTTTCGCACCCAGTTCAT 57.149 45.000 0.00 0.00 0.00 2.57
213 214 1.981256 AGTTTCGCACCCAGTTCATT 58.019 45.000 0.00 0.00 0.00 2.57
214 215 1.880027 AGTTTCGCACCCAGTTCATTC 59.120 47.619 0.00 0.00 0.00 2.67
215 216 1.880027 GTTTCGCACCCAGTTCATTCT 59.120 47.619 0.00 0.00 0.00 2.40
216 217 1.522668 TTCGCACCCAGTTCATTCTG 58.477 50.000 0.00 0.00 35.45 3.02
217 218 0.396435 TCGCACCCAGTTCATTCTGT 59.604 50.000 0.00 0.00 34.02 3.41
218 219 0.518636 CGCACCCAGTTCATTCTGTG 59.481 55.000 0.00 0.00 34.02 3.66
219 220 1.877680 CGCACCCAGTTCATTCTGTGA 60.878 52.381 0.00 0.00 34.02 3.58
220 221 2.229792 GCACCCAGTTCATTCTGTGAA 58.770 47.619 0.00 0.00 44.36 3.18
233 234 7.083875 TCATTCTGTGAAATAATTTCGTCCC 57.916 36.000 0.00 0.00 42.55 4.46
234 235 5.539582 TTCTGTGAAATAATTTCGTCCCG 57.460 39.130 0.00 0.00 42.55 5.14
235 236 4.823157 TCTGTGAAATAATTTCGTCCCGA 58.177 39.130 0.00 0.00 42.55 5.14
236 237 4.868171 TCTGTGAAATAATTTCGTCCCGAG 59.132 41.667 0.00 0.00 42.55 4.63
237 238 3.936453 TGTGAAATAATTTCGTCCCGAGG 59.064 43.478 0.00 0.00 42.55 4.63
238 239 3.937079 GTGAAATAATTTCGTCCCGAGGT 59.063 43.478 0.00 0.00 42.55 3.85
239 240 4.033702 GTGAAATAATTTCGTCCCGAGGTC 59.966 45.833 0.00 0.00 42.55 3.85
240 241 3.899052 AATAATTTCGTCCCGAGGTCA 57.101 42.857 0.00 0.00 37.14 4.02
241 242 3.899052 ATAATTTCGTCCCGAGGTCAA 57.101 42.857 0.00 0.00 37.14 3.18
242 243 2.554370 AATTTCGTCCCGAGGTCAAA 57.446 45.000 0.00 0.00 37.14 2.69
243 244 2.554370 ATTTCGTCCCGAGGTCAAAA 57.446 45.000 0.00 0.00 37.14 2.44
244 245 2.554370 TTTCGTCCCGAGGTCAAAAT 57.446 45.000 0.00 0.00 37.14 1.82
245 246 2.554370 TTCGTCCCGAGGTCAAAATT 57.446 45.000 0.00 0.00 37.14 1.82
246 247 1.803334 TCGTCCCGAGGTCAAAATTG 58.197 50.000 0.00 0.00 0.00 2.32
247 248 1.071071 TCGTCCCGAGGTCAAAATTGT 59.929 47.619 0.00 0.00 0.00 2.71
248 249 1.463444 CGTCCCGAGGTCAAAATTGTC 59.537 52.381 0.00 0.00 0.00 3.18
249 250 2.500229 GTCCCGAGGTCAAAATTGTCA 58.500 47.619 0.00 0.00 0.00 3.58
250 251 2.882137 GTCCCGAGGTCAAAATTGTCAA 59.118 45.455 0.00 0.00 0.00 3.18
251 252 3.316868 GTCCCGAGGTCAAAATTGTCAAA 59.683 43.478 0.00 0.00 0.00 2.69
319 323 5.278463 CCAGAACAGATTCGGTTGAAAACAT 60.278 40.000 6.92 0.00 42.59 2.71
323 327 7.785197 AGAACAGATTCGGTTGAAAACATAAGC 60.785 37.037 6.92 0.00 42.59 3.09
341 345 1.555075 AGCCTGTCATACGATGTTGGT 59.445 47.619 0.00 0.00 0.00 3.67
390 394 3.197766 AGGAACAACTCAACAGAGACACA 59.802 43.478 0.00 0.00 33.55 3.72
394 398 6.404734 GGAACAACTCAACAGAGACACAATTT 60.405 38.462 0.00 0.00 33.55 1.82
397 401 8.225603 ACAACTCAACAGAGACACAATTTTAT 57.774 30.769 0.00 0.00 33.55 1.40
440 476 5.995565 AGTAAATGGCGTATGGCTAGATA 57.004 39.130 10.19 0.00 42.94 1.98
446 482 3.244387 TGGCGTATGGCTAGATAATTGCA 60.244 43.478 10.19 0.00 42.94 4.08
537 575 4.518970 GGATTCATTTAAGAAGCGGCCATA 59.481 41.667 2.24 0.00 34.87 2.74
627 665 1.856265 GAGCTGTTCCTTTGGCACCG 61.856 60.000 0.00 0.00 0.00 4.94
649 687 1.528129 CTCCTTGCTTTCCAGTGTCC 58.472 55.000 0.00 0.00 0.00 4.02
662 700 2.244769 CCAGTGTCCCCCTCCATAAAAT 59.755 50.000 0.00 0.00 0.00 1.82
820 858 7.405292 TCTGAAACTCCAATCATAAGAACCAT 58.595 34.615 0.00 0.00 0.00 3.55
856 894 4.479993 CCTGCCTGCCTCCCTTCG 62.480 72.222 0.00 0.00 0.00 3.79
920 958 0.106918 GAGGGGAGCGAGAGAGAGAA 60.107 60.000 0.00 0.00 0.00 2.87
940 979 3.797559 AAAAGAGTGGGGAGGAGAAAG 57.202 47.619 0.00 0.00 0.00 2.62
944 983 0.988063 AGTGGGGAGGAGAAAGAAGC 59.012 55.000 0.00 0.00 0.00 3.86
979 1020 2.270923 TCTTTGATCAGTTCATCGCCG 58.729 47.619 0.00 0.00 33.34 6.46
1013 1069 5.680619 TCATTTCTTAATGGCCGTGAGTAT 58.319 37.500 0.00 0.00 41.23 2.12
1020 1079 7.173032 TCTTAATGGCCGTGAGTATCTATCTA 58.827 38.462 0.00 0.00 34.92 1.98
1021 1080 7.834681 TCTTAATGGCCGTGAGTATCTATCTAT 59.165 37.037 0.00 0.00 34.92 1.98
1022 1081 6.458232 AATGGCCGTGAGTATCTATCTATC 57.542 41.667 0.00 0.00 34.92 2.08
1023 1082 5.180810 TGGCCGTGAGTATCTATCTATCT 57.819 43.478 0.00 0.00 34.92 1.98
1069 1128 3.244284 TGTGGTTACCGATGCTTTACTGT 60.244 43.478 0.00 0.00 0.00 3.55
1073 1132 4.802563 GGTTACCGATGCTTTACTGTCTAC 59.197 45.833 0.00 0.00 0.00 2.59
1074 1133 5.393896 GGTTACCGATGCTTTACTGTCTACT 60.394 44.000 0.00 0.00 0.00 2.57
1075 1134 4.373348 ACCGATGCTTTACTGTCTACTC 57.627 45.455 0.00 0.00 0.00 2.59
1094 1153 1.556451 TCCTACTCAGTGCATGCATGT 59.444 47.619 25.64 20.66 0.00 3.21
1096 1155 3.389002 TCCTACTCAGTGCATGCATGTAT 59.611 43.478 25.64 15.76 0.00 2.29
1119 1178 3.246226 GCATGTATGATTCCGACACTGTC 59.754 47.826 0.00 0.00 0.00 3.51
1134 1193 1.769098 CTGTCATGGCCGCTTGATCG 61.769 60.000 0.00 0.00 0.00 3.69
1148 1207 4.201391 CGCTTGATCGTGTATTTGTTTTGC 60.201 41.667 0.00 0.00 0.00 3.68
1164 1223 9.689976 ATTTGTTTTGCTTTTATAATTTTGGCC 57.310 25.926 0.00 0.00 0.00 5.36
1202 1261 7.264221 GTTTGCATAATGGGTTGTGATCAATA 58.736 34.615 0.00 0.00 35.92 1.90
1204 1263 5.535783 TGCATAATGGGTTGTGATCAATAGG 59.464 40.000 0.00 0.00 35.92 2.57
1206 1265 3.600448 ATGGGTTGTGATCAATAGGGG 57.400 47.619 0.00 0.00 35.92 4.79
1228 1288 6.073003 GGGGAGTAGTATGTATGTACACGTAC 60.073 46.154 0.00 2.66 39.30 3.67
1355 1422 2.688794 GCAGCAGCAGACAAGGAGC 61.689 63.158 0.00 0.00 41.58 4.70
1391 1458 0.323178 GGGCATGATATGGAGGGCTG 60.323 60.000 0.00 0.00 0.00 4.85
1619 1692 0.822532 TACCCGCTAGCTAGCTGTCC 60.823 60.000 36.02 13.62 46.85 4.02
1632 1705 1.145738 AGCTGTCCTTGGGTTTGACAT 59.854 47.619 0.00 0.00 38.26 3.06
1633 1706 2.375174 AGCTGTCCTTGGGTTTGACATA 59.625 45.455 0.00 0.00 38.26 2.29
1634 1707 2.488153 GCTGTCCTTGGGTTTGACATAC 59.512 50.000 0.00 0.00 38.26 2.39
1635 1708 2.742053 CTGTCCTTGGGTTTGACATACG 59.258 50.000 0.00 0.00 38.26 3.06
1636 1709 2.081462 GTCCTTGGGTTTGACATACGG 58.919 52.381 0.00 0.00 0.00 4.02
1637 1710 1.979308 TCCTTGGGTTTGACATACGGA 59.021 47.619 0.00 0.00 0.00 4.69
1638 1711 2.027561 TCCTTGGGTTTGACATACGGAG 60.028 50.000 0.00 0.00 0.00 4.63
1763 1872 1.643832 CTCATCTTTAAGCGCCGCC 59.356 57.895 4.98 0.00 0.00 6.13
1827 1943 8.684520 TGAATTTTTAACCAACGAGGAAAGTAA 58.315 29.630 5.70 0.00 41.22 2.24
2975 3162 3.680786 TCAGACAGTGACGGGGCG 61.681 66.667 0.00 0.00 0.00 6.13
2994 3181 4.705023 GGGCGGCTGGTTGATAATATTAAT 59.295 41.667 9.56 0.00 0.00 1.40
3024 3211 1.624336 TGGCTGCTGCTTTTGATCTT 58.376 45.000 15.64 0.00 39.59 2.40
3067 3254 5.393896 GGAACCCTGTAGTGTACACAGTATC 60.394 48.000 27.06 13.10 41.52 2.24
3102 3289 8.800972 TCATTCGTTGTTCGTTATGAGTAATAC 58.199 33.333 0.00 0.00 37.07 1.89
3164 3352 6.219302 GCACTTGGCGTATACGTATTTTAT 57.781 37.500 25.04 4.27 42.22 1.40
3229 3447 3.953712 TGAGACTTCCAAATGCGTAGA 57.046 42.857 0.00 0.00 0.00 2.59
3260 3481 8.529911 GCACGTGTTACTAGAACTAATGTAATC 58.470 37.037 18.38 0.00 0.00 1.75
3263 3484 9.234384 CGTGTTACTAGAACTAATGTAATCTGG 57.766 37.037 0.00 0.00 0.00 3.86
3282 3503 1.787155 GGTGCGTATGAGTGCGATAAG 59.213 52.381 0.00 0.00 35.29 1.73
3284 3505 1.269569 TGCGTATGAGTGCGATAAGGG 60.270 52.381 0.00 0.00 35.29 3.95
3295 3516 4.396166 AGTGCGATAAGGGATGAACAAAAG 59.604 41.667 0.00 0.00 0.00 2.27
3297 3518 3.489229 GCGATAAGGGATGAACAAAAGGC 60.489 47.826 0.00 0.00 0.00 4.35
3302 3523 1.273327 GGGATGAACAAAAGGCTGTGG 59.727 52.381 0.00 0.00 0.00 4.17
3321 3542 2.828520 TGGTTGTTCTTTGTTTGGAGCA 59.171 40.909 0.00 0.00 0.00 4.26
3329 3550 5.843673 TCTTTGTTTGGAGCATTACACAA 57.156 34.783 0.00 0.00 0.00 3.33
3336 3557 6.451393 GTTTGGAGCATTACACAAACCATAA 58.549 36.000 7.65 0.00 44.04 1.90
3340 3561 8.354711 TGGAGCATTACACAAACCATAATAAA 57.645 30.769 0.00 0.00 0.00 1.40
3377 3598 7.712264 TTGCCATTAGTTCTTTCATTGTTTG 57.288 32.000 0.00 0.00 0.00 2.93
3391 3612 6.900568 TCATTGTTTGCTTAAGTGGTTTTG 57.099 33.333 4.02 0.00 0.00 2.44
3422 3643 6.939163 ACAAATATCAGCTGAAGTGAGTTCTT 59.061 34.615 22.50 2.10 35.99 2.52
3427 3648 4.993584 TCAGCTGAAGTGAGTTCTTTCATC 59.006 41.667 15.67 0.00 35.99 2.92
3478 3699 8.712285 ATTCATCCAAAATACTTGCTGAAATG 57.288 30.769 0.00 0.00 0.00 2.32
3492 3716 6.915544 TGCTGAAATGAGTATCTTCATGTC 57.084 37.500 0.00 0.29 40.67 3.06
3497 3721 8.272545 TGAAATGAGTATCTTCATGTCCAAAG 57.727 34.615 4.26 0.00 39.90 2.77
3511 3735 3.953612 TGTCCAAAGACTTGCTGAAATGT 59.046 39.130 0.00 0.00 43.91 2.71
3520 3744 6.268566 AGACTTGCTGAAATGTGTTCTTTTC 58.731 36.000 0.00 0.00 37.85 2.29
3536 3760 1.827315 TTTCGAGCAACTCCAACGCG 61.827 55.000 3.53 3.53 0.00 6.01
3554 3778 2.574929 CCGACCCATTTCGTCCGA 59.425 61.111 0.00 0.00 37.29 4.55
3556 3780 1.214589 CGACCCATTTCGTCCGAGT 59.785 57.895 0.00 0.00 34.16 4.18
3632 3878 3.323286 TTGCCGACCCATTCCCGA 61.323 61.111 0.00 0.00 0.00 5.14
3696 3953 1.150992 GCGCCTACTCCTCCTCCTA 59.849 63.158 0.00 0.00 0.00 2.94
3697 3954 0.251430 GCGCCTACTCCTCCTCCTAT 60.251 60.000 0.00 0.00 0.00 2.57
3702 3959 1.706305 CTACTCCTCCTCCTATCCCGT 59.294 57.143 0.00 0.00 0.00 5.28
3720 3977 0.589223 GTCAATCGGTGGCAAAACGA 59.411 50.000 11.64 11.64 41.20 3.85
3737 3994 1.144093 ACGACCAACATTTCCCTCCAA 59.856 47.619 0.00 0.00 0.00 3.53
3755 4014 1.275010 CAATTTCCCAAAACCTCCCGG 59.725 52.381 0.00 0.00 0.00 5.73
3761 4020 3.324108 AAAACCTCCCGGCCGCTA 61.324 61.111 22.85 8.78 0.00 4.26
3762 4021 2.676265 AAAACCTCCCGGCCGCTAT 61.676 57.895 22.85 0.00 0.00 2.97
3763 4022 1.339644 AAAACCTCCCGGCCGCTATA 61.340 55.000 22.85 2.89 0.00 1.31
3786 4050 4.492160 GCTCGCCATGGACGACGA 62.492 66.667 22.05 16.81 35.35 4.20
3792 4056 2.404186 CCATGGACGACGACCTCGA 61.404 63.158 16.98 0.00 46.14 4.04
3795 4061 1.030488 ATGGACGACGACCTCGATGT 61.030 55.000 16.98 0.00 46.14 3.06
3822 4088 2.756283 CCTCGTCTCCCTCGCCTT 60.756 66.667 0.00 0.00 0.00 4.35
3836 4102 4.410400 CCTTGTCCGGCCTCACCC 62.410 72.222 0.00 0.00 33.26 4.61
3884 4171 0.321653 GCCGCCCAAGAAGAAGAAGA 60.322 55.000 0.00 0.00 0.00 2.87
3888 4175 1.815613 GCCCAAGAAGAAGAAGAAGCC 59.184 52.381 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.756375 GAATGTGCAGCGCCTAGACG 61.756 60.000 2.29 0.00 0.00 4.18
18 19 1.432270 GGAATGTGCAGCGCCTAGAC 61.432 60.000 2.29 0.00 0.00 2.59
19 20 1.153369 GGAATGTGCAGCGCCTAGA 60.153 57.895 2.29 0.00 0.00 2.43
20 21 0.816825 ATGGAATGTGCAGCGCCTAG 60.817 55.000 2.29 0.00 0.00 3.02
21 22 1.096967 CATGGAATGTGCAGCGCCTA 61.097 55.000 2.29 0.00 40.20 3.93
22 23 2.044650 ATGGAATGTGCAGCGCCT 60.045 55.556 2.29 0.00 0.00 5.52
23 24 2.103538 CATGGAATGTGCAGCGCC 59.896 61.111 2.29 0.00 40.20 6.53
37 38 2.124983 AGCTAGGCGCCACACATG 60.125 61.111 31.54 12.28 40.39 3.21
38 39 2.187946 GAGCTAGGCGCCACACAT 59.812 61.111 31.54 10.27 40.39 3.21
39 40 4.435436 CGAGCTAGGCGCCACACA 62.435 66.667 31.54 9.67 40.39 3.72
42 43 4.577246 CTCCGAGCTAGGCGCCAC 62.577 72.222 31.54 17.93 40.39 5.01
48 49 4.277593 CAGCGCCTCCGAGCTAGG 62.278 72.222 6.52 6.52 44.07 3.02
49 50 4.940593 GCAGCGCCTCCGAGCTAG 62.941 72.222 2.29 0.00 44.07 3.42
90 91 3.941188 ACCTGTCCACCGTGGCAG 61.941 66.667 24.16 24.16 39.63 4.85
91 92 4.248842 CACCTGTCCACCGTGGCA 62.249 66.667 13.19 12.68 37.47 4.92
92 93 4.250305 ACACCTGTCCACCGTGGC 62.250 66.667 13.19 8.69 37.47 5.01
93 94 2.280797 CACACCTGTCCACCGTGG 60.281 66.667 11.73 11.73 39.43 4.94
94 95 2.972505 GCACACCTGTCCACCGTG 60.973 66.667 0.00 0.00 0.00 4.94
95 96 3.037686 TTGCACACCTGTCCACCGT 62.038 57.895 0.00 0.00 0.00 4.83
96 97 2.203139 TTGCACACCTGTCCACCG 60.203 61.111 0.00 0.00 0.00 4.94
97 98 2.542907 CGTTGCACACCTGTCCACC 61.543 63.158 0.00 0.00 0.00 4.61
98 99 3.022287 CGTTGCACACCTGTCCAC 58.978 61.111 0.00 0.00 0.00 4.02
99 100 2.899838 GCGTTGCACACCTGTCCA 60.900 61.111 0.00 0.00 0.00 4.02
100 101 3.660111 GGCGTTGCACACCTGTCC 61.660 66.667 0.00 0.00 0.00 4.02
101 102 4.012895 CGGCGTTGCACACCTGTC 62.013 66.667 0.00 0.00 0.00 3.51
124 125 1.874019 CGTACTGTGCAGCGCCTAG 60.874 63.158 2.29 0.00 0.00 3.02
125 126 2.180769 CGTACTGTGCAGCGCCTA 59.819 61.111 2.29 0.00 0.00 3.93
126 127 4.742201 CCGTACTGTGCAGCGCCT 62.742 66.667 2.29 0.00 0.00 5.52
128 129 3.777925 CACCGTACTGTGCAGCGC 61.778 66.667 0.00 0.00 0.00 5.92
129 130 2.355837 ACACCGTACTGTGCAGCG 60.356 61.111 16.36 0.00 39.93 5.18
130 131 2.317609 CCACACCGTACTGTGCAGC 61.318 63.158 16.36 0.00 40.33 5.25
131 132 2.317609 GCCACACCGTACTGTGCAG 61.318 63.158 16.36 9.56 40.33 4.41
132 133 2.280524 GCCACACCGTACTGTGCA 60.281 61.111 16.36 0.00 40.33 4.57
133 134 3.411351 CGCCACACCGTACTGTGC 61.411 66.667 16.36 8.04 40.33 4.57
134 135 3.411351 GCGCCACACCGTACTGTG 61.411 66.667 15.04 15.04 41.19 3.66
135 136 4.675029 GGCGCCACACCGTACTGT 62.675 66.667 24.80 0.00 0.00 3.55
157 158 4.627801 TTTGTGTAGCGCCCGCCA 62.628 61.111 2.29 0.00 43.17 5.69
158 159 2.796245 CTTTTTGTGTAGCGCCCGCC 62.796 60.000 2.29 0.00 43.17 6.13
159 160 1.442017 CTTTTTGTGTAGCGCCCGC 60.442 57.895 2.29 4.20 42.33 6.13
160 161 1.209127 CCTTTTTGTGTAGCGCCCG 59.791 57.895 2.29 0.00 0.00 6.13
161 162 0.240145 GACCTTTTTGTGTAGCGCCC 59.760 55.000 2.29 0.00 0.00 6.13
162 163 0.948678 TGACCTTTTTGTGTAGCGCC 59.051 50.000 2.29 0.00 0.00 6.53
163 164 1.069227 CCTGACCTTTTTGTGTAGCGC 60.069 52.381 0.00 0.00 0.00 5.92
164 165 1.535462 CCCTGACCTTTTTGTGTAGCG 59.465 52.381 0.00 0.00 0.00 4.26
165 166 1.886542 CCCCTGACCTTTTTGTGTAGC 59.113 52.381 0.00 0.00 0.00 3.58
166 167 3.181443 ACTCCCCTGACCTTTTTGTGTAG 60.181 47.826 0.00 0.00 0.00 2.74
167 168 2.781174 ACTCCCCTGACCTTTTTGTGTA 59.219 45.455 0.00 0.00 0.00 2.90
168 169 1.569072 ACTCCCCTGACCTTTTTGTGT 59.431 47.619 0.00 0.00 0.00 3.72
169 170 1.956477 CACTCCCCTGACCTTTTTGTG 59.044 52.381 0.00 0.00 0.00 3.33
170 171 1.850345 TCACTCCCCTGACCTTTTTGT 59.150 47.619 0.00 0.00 0.00 2.83
171 172 2.656947 TCACTCCCCTGACCTTTTTG 57.343 50.000 0.00 0.00 0.00 2.44
172 173 3.680777 TTTCACTCCCCTGACCTTTTT 57.319 42.857 0.00 0.00 0.00 1.94
173 174 3.903530 ATTTCACTCCCCTGACCTTTT 57.096 42.857 0.00 0.00 0.00 2.27
174 175 3.916989 ACTATTTCACTCCCCTGACCTTT 59.083 43.478 0.00 0.00 0.00 3.11
175 176 3.532102 ACTATTTCACTCCCCTGACCTT 58.468 45.455 0.00 0.00 0.00 3.50
176 177 3.207044 ACTATTTCACTCCCCTGACCT 57.793 47.619 0.00 0.00 0.00 3.85
177 178 4.262617 GAAACTATTTCACTCCCCTGACC 58.737 47.826 0.00 0.00 39.45 4.02
178 179 3.933332 CGAAACTATTTCACTCCCCTGAC 59.067 47.826 2.50 0.00 39.63 3.51
179 180 3.618997 GCGAAACTATTTCACTCCCCTGA 60.619 47.826 2.50 0.00 39.63 3.86
180 181 2.678336 GCGAAACTATTTCACTCCCCTG 59.322 50.000 2.50 0.00 39.63 4.45
181 182 2.304761 TGCGAAACTATTTCACTCCCCT 59.695 45.455 2.50 0.00 39.63 4.79
182 183 2.418976 GTGCGAAACTATTTCACTCCCC 59.581 50.000 2.50 0.00 39.63 4.81
183 184 2.418976 GGTGCGAAACTATTTCACTCCC 59.581 50.000 2.50 0.00 39.63 4.30
184 185 2.418976 GGGTGCGAAACTATTTCACTCC 59.581 50.000 2.50 2.81 39.63 3.85
185 186 3.071479 TGGGTGCGAAACTATTTCACTC 58.929 45.455 2.50 0.00 39.63 3.51
186 187 3.074412 CTGGGTGCGAAACTATTTCACT 58.926 45.455 2.50 0.00 39.63 3.41
187 188 2.812011 ACTGGGTGCGAAACTATTTCAC 59.188 45.455 2.50 0.00 39.63 3.18
188 189 3.134574 ACTGGGTGCGAAACTATTTCA 57.865 42.857 2.50 0.00 39.63 2.69
189 190 3.500680 TGAACTGGGTGCGAAACTATTTC 59.499 43.478 0.00 0.00 36.32 2.17
190 191 3.482436 TGAACTGGGTGCGAAACTATTT 58.518 40.909 0.00 0.00 0.00 1.40
191 192 3.134574 TGAACTGGGTGCGAAACTATT 57.865 42.857 0.00 0.00 0.00 1.73
192 193 2.851263 TGAACTGGGTGCGAAACTAT 57.149 45.000 0.00 0.00 0.00 2.12
193 194 2.851263 ATGAACTGGGTGCGAAACTA 57.149 45.000 0.00 0.00 0.00 2.24
194 195 1.880027 GAATGAACTGGGTGCGAAACT 59.120 47.619 0.00 0.00 0.00 2.66
195 196 1.880027 AGAATGAACTGGGTGCGAAAC 59.120 47.619 0.00 0.00 0.00 2.78
196 197 1.879380 CAGAATGAACTGGGTGCGAAA 59.121 47.619 0.00 0.00 39.69 3.46
197 198 1.202758 ACAGAATGAACTGGGTGCGAA 60.203 47.619 0.00 0.00 39.69 4.70
198 199 0.396435 ACAGAATGAACTGGGTGCGA 59.604 50.000 0.00 0.00 39.69 5.10
199 200 0.518636 CACAGAATGAACTGGGTGCG 59.481 55.000 0.00 0.00 39.69 5.34
200 201 1.896220 TCACAGAATGAACTGGGTGC 58.104 50.000 0.00 0.00 41.49 5.01
208 209 7.535139 GGGACGAAATTATTTCACAGAATGAA 58.465 34.615 16.57 0.00 45.92 2.57
209 210 7.083875 GGGACGAAATTATTTCACAGAATGA 57.916 36.000 16.57 0.00 37.72 2.57
229 230 2.500229 TGACAATTTTGACCTCGGGAC 58.500 47.619 0.00 0.00 0.00 4.46
230 231 2.940994 TGACAATTTTGACCTCGGGA 57.059 45.000 0.00 0.00 0.00 5.14
231 232 3.317993 ACTTTGACAATTTTGACCTCGGG 59.682 43.478 0.00 0.00 0.00 5.14
232 233 4.568152 ACTTTGACAATTTTGACCTCGG 57.432 40.909 0.00 0.00 0.00 4.63
233 234 4.207019 GCAACTTTGACAATTTTGACCTCG 59.793 41.667 11.61 0.00 0.00 4.63
234 235 5.232838 CAGCAACTTTGACAATTTTGACCTC 59.767 40.000 11.61 0.00 0.00 3.85
235 236 5.111293 CAGCAACTTTGACAATTTTGACCT 58.889 37.500 11.61 0.84 0.00 3.85
236 237 4.869861 ACAGCAACTTTGACAATTTTGACC 59.130 37.500 11.61 0.00 0.00 4.02
237 238 6.407475 AACAGCAACTTTGACAATTTTGAC 57.593 33.333 11.61 5.22 0.00 3.18
238 239 8.196771 AGATAACAGCAACTTTGACAATTTTGA 58.803 29.630 11.61 0.00 0.00 2.69
239 240 8.356533 AGATAACAGCAACTTTGACAATTTTG 57.643 30.769 5.34 5.34 0.00 2.44
240 241 9.463443 GTAGATAACAGCAACTTTGACAATTTT 57.537 29.630 0.00 0.00 0.00 1.82
241 242 8.629158 TGTAGATAACAGCAACTTTGACAATTT 58.371 29.630 0.00 0.00 33.01 1.82
242 243 8.165239 TGTAGATAACAGCAACTTTGACAATT 57.835 30.769 0.00 0.00 33.01 2.32
243 244 7.744087 TGTAGATAACAGCAACTTTGACAAT 57.256 32.000 0.00 0.00 33.01 2.71
319 323 3.196901 ACCAACATCGTATGACAGGCTTA 59.803 43.478 0.00 0.00 0.00 3.09
323 327 2.095853 GCAACCAACATCGTATGACAGG 59.904 50.000 2.48 0.00 0.00 4.00
406 410 9.217223 CATACGCCATTTACTTTGTTATTGTAC 57.783 33.333 0.00 0.00 0.00 2.90
440 476 4.463070 AGGCAGGAAAACAAATTGCAATT 58.537 34.783 18.99 18.99 36.53 2.32
446 482 3.454082 TGGTCAAGGCAGGAAAACAAATT 59.546 39.130 0.00 0.00 0.00 1.82
537 575 4.868116 ACGGTGGTTGTTGCGGCT 62.868 61.111 0.00 0.00 0.00 5.52
627 665 1.202818 ACACTGGAAAGCAAGGAGGAC 60.203 52.381 0.00 0.00 0.00 3.85
649 687 1.410153 GCTGTGCATTTTATGGAGGGG 59.590 52.381 0.00 0.00 0.00 4.79
662 700 0.669619 CAGTTGGAATGTGCTGTGCA 59.330 50.000 0.00 0.00 35.60 4.57
820 858 3.797353 GCGATGGAAGGGGCAGGA 61.797 66.667 0.00 0.00 0.00 3.86
856 894 2.123033 GGAGGAGAGAGGGAGCCC 60.123 72.222 0.00 0.00 0.00 5.19
920 958 3.327439 TCTTTCTCCTCCCCACTCTTTT 58.673 45.455 0.00 0.00 0.00 2.27
940 979 1.663135 GAGAACCTCTTGCGATGCTTC 59.337 52.381 0.00 0.00 0.00 3.86
962 1003 0.461870 CCCGGCGATGAACTGATCAA 60.462 55.000 9.30 0.00 42.54 2.57
979 1020 6.395629 CCATTAAGAAATGATGATGATGCCC 58.604 40.000 0.00 0.00 44.50 5.36
1013 1069 9.999660 AGATGTAAACGTAGTGAGATAGATAGA 57.000 33.333 0.00 0.00 45.00 1.98
1020 1079 4.341520 GGGGAGATGTAAACGTAGTGAGAT 59.658 45.833 0.00 0.00 45.00 2.75
1021 1080 3.698040 GGGGAGATGTAAACGTAGTGAGA 59.302 47.826 0.00 0.00 45.00 3.27
1022 1081 3.700038 AGGGGAGATGTAAACGTAGTGAG 59.300 47.826 0.00 0.00 45.00 3.51
1023 1082 3.705051 AGGGGAGATGTAAACGTAGTGA 58.295 45.455 0.00 0.00 45.00 3.41
1069 1128 2.690497 GCATGCACTGAGTAGGAGTAGA 59.310 50.000 14.21 0.00 0.00 2.59
1073 1132 2.210961 CATGCATGCACTGAGTAGGAG 58.789 52.381 25.37 0.00 0.00 3.69
1074 1133 1.556451 ACATGCATGCACTGAGTAGGA 59.444 47.619 25.37 0.00 0.00 2.94
1075 1134 2.034104 ACATGCATGCACTGAGTAGG 57.966 50.000 25.37 1.71 0.00 3.18
1094 1153 4.990426 CAGTGTCGGAATCATACATGCATA 59.010 41.667 0.00 0.00 0.00 3.14
1096 1155 3.197265 CAGTGTCGGAATCATACATGCA 58.803 45.455 0.00 0.00 0.00 3.96
1102 1161 3.741075 GCCATGACAGTGTCGGAATCATA 60.741 47.826 18.17 0.00 34.95 2.15
1103 1162 2.910199 CCATGACAGTGTCGGAATCAT 58.090 47.619 18.17 3.04 34.95 2.45
1105 1164 1.009829 GCCATGACAGTGTCGGAATC 58.990 55.000 18.17 3.11 34.95 2.52
1106 1165 0.392998 GGCCATGACAGTGTCGGAAT 60.393 55.000 18.17 3.84 34.95 3.01
1107 1166 1.003839 GGCCATGACAGTGTCGGAA 60.004 57.895 18.17 1.35 34.95 4.30
1108 1167 2.662596 GGCCATGACAGTGTCGGA 59.337 61.111 18.17 2.12 34.95 4.55
1109 1168 2.815211 CGGCCATGACAGTGTCGG 60.815 66.667 18.17 14.69 34.95 4.79
1119 1178 0.809636 TACACGATCAAGCGGCCATG 60.810 55.000 2.24 0.00 35.12 3.66
1148 1207 7.499895 AGCAATCATGGGCCAAAATTATAAAAG 59.500 33.333 11.89 1.83 0.00 2.27
1164 1223 0.388778 TGCAAACGCAGCAATCATGG 60.389 50.000 0.00 0.00 39.39 3.66
1190 1249 5.615925 ACTACTCCCCTATTGATCACAAC 57.384 43.478 0.00 0.00 38.90 3.32
1202 1261 5.068636 CGTGTACATACATACTACTCCCCT 58.931 45.833 0.00 0.00 38.63 4.79
1204 1263 6.346919 CGTACGTGTACATACATACTACTCCC 60.347 46.154 7.22 0.00 38.63 4.30
1206 1265 6.584954 CCGTACGTGTACATACATACTACTC 58.415 44.000 15.21 0.00 38.63 2.59
1228 1288 0.462937 TGGTCAATTCCATACGGCCG 60.463 55.000 26.86 26.86 31.96 6.13
1259 1323 2.039480 CCCCATGATCCATCATCGTTCT 59.961 50.000 0.00 0.00 45.23 3.01
1307 1371 1.408702 ACCATGTGTTGCCAACTTGAC 59.591 47.619 9.30 0.00 0.00 3.18
1355 1422 1.467678 CCCAGATCCGTGAGCCCTAG 61.468 65.000 0.00 0.00 0.00 3.02
1391 1458 3.534056 GAGCATGCCATGTGCCCC 61.534 66.667 15.66 0.00 43.50 5.80
1619 1692 3.053831 ACTCCGTATGTCAAACCCAAG 57.946 47.619 0.00 0.00 0.00 3.61
1678 1783 2.944409 AAGGCCAACCAACGTACGCA 62.944 55.000 16.72 0.00 39.06 5.24
1763 1872 9.020731 ACCTTAATAAGTTCCAGGTTGTAATTG 57.979 33.333 0.00 0.00 33.89 2.32
1882 2002 5.704888 CACCACGCCAAAATCTTAATAACA 58.295 37.500 0.00 0.00 0.00 2.41
1916 2036 4.740822 CACCGGCCCTTTCCCCTG 62.741 72.222 0.00 0.00 0.00 4.45
2269 2401 4.735132 TAGTGCTGCGCCGGTGAC 62.735 66.667 21.76 10.95 0.00 3.67
2270 2402 4.735132 GTAGTGCTGCGCCGGTGA 62.735 66.667 21.76 2.83 0.00 4.02
2432 2564 4.765449 CTGCTGCTGCGGCTGGTA 62.765 66.667 31.19 12.57 43.34 3.25
2671 2809 0.103390 TCTCGAACTGCACCGTGAAA 59.897 50.000 1.65 0.00 0.00 2.69
2800 2938 2.816777 AGGATTTCTTGGGCTTCCTC 57.183 50.000 0.00 0.00 31.06 3.71
2846 2984 2.017783 GCGTCGGCGTCAAACTGTA 61.018 57.895 12.58 0.00 40.81 2.74
2868 3010 3.834610 CGGTGAACAGGAAGTAGTAGTG 58.165 50.000 0.00 0.00 0.00 2.74
2869 3011 2.230750 GCGGTGAACAGGAAGTAGTAGT 59.769 50.000 0.00 0.00 0.00 2.73
2870 3012 2.230508 TGCGGTGAACAGGAAGTAGTAG 59.769 50.000 0.00 0.00 0.00 2.57
2919 3106 1.455786 CGTAGACCTGCACAAAACGAG 59.544 52.381 0.00 0.00 0.00 4.18
2921 3108 0.511221 CCGTAGACCTGCACAAAACG 59.489 55.000 0.00 0.00 0.00 3.60
2975 3162 6.093633 GGTCGGATTAATATTATCAACCAGCC 59.906 42.308 0.00 0.00 0.00 4.85
2994 3181 0.179048 CAGCAGCCATTATGGTCGGA 60.179 55.000 13.28 0.00 40.46 4.55
3004 3191 1.848652 AGATCAAAAGCAGCAGCCAT 58.151 45.000 0.00 0.00 43.56 4.40
3005 3192 1.624336 AAGATCAAAAGCAGCAGCCA 58.376 45.000 0.00 0.00 43.56 4.75
3024 3211 8.787818 AGGGTTCCTTCCAGAAAAACATATATA 58.212 33.333 7.31 0.00 0.00 0.86
3067 3254 5.204833 ACGAACAACGAATGAACAAATGAG 58.795 37.500 0.00 0.00 45.77 2.90
3164 3352 3.581755 GATACACAGAGTTTGGCACGTA 58.418 45.455 0.00 0.00 0.00 3.57
3260 3481 0.528466 ATCGCACTCATACGCACCAG 60.528 55.000 0.00 0.00 0.00 4.00
3263 3484 1.787155 CCTTATCGCACTCATACGCAC 59.213 52.381 0.00 0.00 0.00 5.34
3282 3503 1.273327 CCACAGCCTTTTGTTCATCCC 59.727 52.381 0.00 0.00 0.00 3.85
3284 3505 3.181476 ACAACCACAGCCTTTTGTTCATC 60.181 43.478 0.00 0.00 0.00 2.92
3295 3516 2.929398 CAAACAAAGAACAACCACAGCC 59.071 45.455 0.00 0.00 0.00 4.85
3297 3518 4.423732 CTCCAAACAAAGAACAACCACAG 58.576 43.478 0.00 0.00 0.00 3.66
3302 3523 6.019881 GTGTAATGCTCCAAACAAAGAACAAC 60.020 38.462 0.00 0.00 0.00 3.32
3321 3542 8.976353 TGGATGCTTTATTATGGTTTGTGTAAT 58.024 29.630 0.00 0.00 0.00 1.89
3336 3557 9.715121 CTAATGGCAATAAAATGGATGCTTTAT 57.285 29.630 0.00 0.00 38.79 1.40
3340 3561 6.736110 ACTAATGGCAATAAAATGGATGCT 57.264 33.333 0.00 0.00 38.79 3.79
3373 3594 7.921745 TGTTATACCAAAACCACTTAAGCAAAC 59.078 33.333 1.29 0.00 0.00 2.93
3391 3612 8.662781 TCACTTCAGCTGATATTTGTTATACC 57.337 34.615 19.04 0.00 0.00 2.73
3406 3627 3.993081 CGATGAAAGAACTCACTTCAGCT 59.007 43.478 7.68 0.00 0.00 4.24
3446 3667 8.227507 AGCAAGTATTTTGGATGAATATACCCT 58.772 33.333 0.00 0.00 0.00 4.34
3453 3674 8.533657 TCATTTCAGCAAGTATTTTGGATGAAT 58.466 29.630 0.00 0.00 0.00 2.57
3478 3699 6.183360 GCAAGTCTTTGGACATGAAGATACTC 60.183 42.308 0.00 0.00 41.87 2.59
3487 3708 4.572985 TTTCAGCAAGTCTTTGGACATG 57.427 40.909 0.00 0.00 44.36 3.21
3492 3716 4.311816 ACACATTTCAGCAAGTCTTTGG 57.688 40.909 0.00 0.00 34.79 3.28
3497 3721 5.172053 CGAAAAGAACACATTTCAGCAAGTC 59.828 40.000 0.00 0.00 35.72 3.01
3511 3735 2.912771 TGGAGTTGCTCGAAAAGAACA 58.087 42.857 0.00 0.00 0.00 3.18
3520 3744 4.430423 GCGCGTTGGAGTTGCTCG 62.430 66.667 8.43 0.00 0.00 5.03
3615 3861 3.323286 TCGGGAATGGGTCGGCAA 61.323 61.111 0.00 0.00 0.00 4.52
3643 3889 1.226379 CGCCGACACAAATGATGCC 60.226 57.895 0.00 0.00 0.00 4.40
3646 3892 2.749865 CCGCGCCGACACAAATGAT 61.750 57.895 0.00 0.00 0.00 2.45
3648 3894 3.418913 TCCGCGCCGACACAAATG 61.419 61.111 0.00 0.00 0.00 2.32
3683 3940 1.704070 GACGGGATAGGAGGAGGAGTA 59.296 57.143 0.00 0.00 0.00 2.59
3687 3944 1.896465 GATTGACGGGATAGGAGGAGG 59.104 57.143 0.00 0.00 0.00 4.30
3702 3959 0.589223 GTCGTTTTGCCACCGATTGA 59.411 50.000 0.00 0.00 32.68 2.57
3720 3977 3.582647 GGAAATTGGAGGGAAATGTTGGT 59.417 43.478 0.00 0.00 0.00 3.67
3724 3981 3.558608 TGGGAAATTGGAGGGAAATGT 57.441 42.857 0.00 0.00 0.00 2.71
3760 4019 1.284715 CATGGCGAGCGACCGTATA 59.715 57.895 0.00 0.00 0.00 1.47
3761 4020 2.027605 CATGGCGAGCGACCGTAT 59.972 61.111 0.00 0.00 0.00 3.06
3762 4021 4.201679 CCATGGCGAGCGACCGTA 62.202 66.667 0.00 0.00 0.00 4.02
3767 4031 4.492160 GTCGTCCATGGCGAGCGA 62.492 66.667 25.06 19.24 39.14 4.93
3809 4075 2.579738 GGACAAGGCGAGGGAGAC 59.420 66.667 0.00 0.00 0.00 3.36
3810 4076 3.068691 CGGACAAGGCGAGGGAGA 61.069 66.667 0.00 0.00 0.00 3.71
3907 4194 1.118965 TCCTCTTGGCCGACTTCACA 61.119 55.000 0.00 0.00 0.00 3.58
3909 4196 0.321671 CTTCCTCTTGGCCGACTTCA 59.678 55.000 0.00 0.00 0.00 3.02
3911 4198 1.679898 CCTTCCTCTTGGCCGACTT 59.320 57.895 0.00 0.00 0.00 3.01
3919 4206 2.586792 CTCCGGCCCTTCCTCTTG 59.413 66.667 0.00 0.00 0.00 3.02
3943 4230 1.284982 CTTCGTCCCTTGCGTCTGTG 61.285 60.000 0.00 0.00 0.00 3.66
3944 4231 1.006102 CTTCGTCCCTTGCGTCTGT 60.006 57.895 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.