Multiple sequence alignment - TraesCS2A01G406000

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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 TraesCS2A01G406000 chr2A 100.000 3918 0 0 1 3918 661711614 661715531 0.000000e+00 7236
1 TraesCS2A01G406000 chr2B 93.778 3150 132 30 7 3134 609947374 609950481 0.000000e+00 4673
2 TraesCS2A01G406000 chr2B 91.304 506 19 7 3418 3918 609950553 609951038 0.000000e+00 667
3 TraesCS2A01G406000 chr2B 88.811 143 15 1 3145 3286 401145988 401145846 1.450000e-39 174
4 TraesCS2A01G406000 chr2D 94.265 2877 107 26 297 3143 518026243 518029091 0.000000e+00 4346
5 TraesCS2A01G406000 chr2D 92.759 580 14 5 3347 3918 518029168 518029727 0.000000e+00 813
6 TraesCS2A01G406000 chr5D 94.366 142 7 1 3146 3286 294425951 294426092 2.370000e-52 217
7 TraesCS2A01G406000 chr4B 91.549 142 10 2 3146 3286 481491229 481491369 1.110000e-45 195
8 TraesCS2A01G406000 chr4B 90.141 142 11 3 3146 3286 9541732 9541871 8.650000e-42 182
9 TraesCS2A01G406000 chr6B 89.726 146 14 1 3142 3286 3670890 3671035 6.690000e-43 185
10 TraesCS2A01G406000 chr5A 91.241 137 10 2 3146 3281 602969229 602969094 6.690000e-43 185
11 TraesCS2A01G406000 chr1B 89.655 145 15 0 3145 3289 681155569 681155425 6.690000e-43 185
12 TraesCS2A01G406000 chr5B 89.583 144 15 0 3146 3289 657394941 657394798 2.400000e-42 183
13 TraesCS2A01G406000 chr6A 88.966 145 14 2 3146 3289 509274616 509274473 1.120000e-40 178


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 TraesCS2A01G406000 chr2A 661711614 661715531 3917 False 7236.0 7236 100.000 1 3918 1 chr2A.!!$F1 3917
1 TraesCS2A01G406000 chr2B 609947374 609951038 3664 False 2670.0 4673 92.541 7 3918 2 chr2B.!!$F1 3911
2 TraesCS2A01G406000 chr2D 518026243 518029727 3484 False 2579.5 4346 93.512 297 3918 2 chr2D.!!$F1 3621

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
295 302 0.175760 TATCTTGTGTGCGAGGCTCC 59.824 55.0 9.32 2.37 0.0 4.70 F
1825 1862 0.031857 AGATCCTCTTCAGCATCGCG 59.968 55.0 0.00 0.00 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2264 0.169672 CATCCTCAAAGCGGCACAAG 59.830 55.0 1.45 0.00 0.00 3.16 R
3756 3846 0.179048 CCGGGATGTAATCTGCTGCA 60.179 55.0 0.88 0.88 44.71 4.41 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.055458 TGGATCTTTATGTGACTCCGCAA 60.055 43.478 0.00 0.00 36.26 4.85
30 31 3.937814 TCTTTATGTGACTCCGCAATGT 58.062 40.909 0.00 0.00 36.26 2.71
35 36 2.167662 TGTGACTCCGCAATGTCTCTA 58.832 47.619 0.00 0.00 34.57 2.43
48 49 5.449588 GCAATGTCTCTATTGTGTGGATTGG 60.450 44.000 0.00 0.00 39.62 3.16
62 63 1.605712 GGATTGGGTCGACGATCATCC 60.606 57.143 19.91 10.74 33.70 3.51
73 74 1.016627 CGATCATCCATGGCAACGTT 58.983 50.000 6.96 0.00 42.51 3.99
129 130 3.195182 GGTACCTACTTGGGAGAAGTGAC 59.805 52.174 4.06 0.00 41.11 3.67
132 133 2.761208 CCTACTTGGGAGAAGTGACGAT 59.239 50.000 0.00 0.00 0.00 3.73
189 190 7.504926 TCTTTAAAGAGGTGTGTATGGGTAT 57.495 36.000 13.99 0.00 0.00 2.73
192 193 8.612486 TTTAAAGAGGTGTGTATGGGTATCTA 57.388 34.615 0.00 0.00 0.00 1.98
212 213 1.153823 CGTGTGCCGCTTAGCTAGT 60.154 57.895 1.76 0.00 0.00 2.57
223 230 4.898370 CGCTTAGCTAGTGGATTGTTTTC 58.102 43.478 1.76 0.00 0.00 2.29
225 232 4.392138 GCTTAGCTAGTGGATTGTTTTCGT 59.608 41.667 0.00 0.00 0.00 3.85
226 233 5.106673 GCTTAGCTAGTGGATTGTTTTCGTT 60.107 40.000 0.00 0.00 0.00 3.85
230 237 4.084223 GCTAGTGGATTGTTTTCGTTCGAA 60.084 41.667 3.47 3.47 0.00 3.71
236 243 6.197468 GTGGATTGTTTTCGTTCGAATTTTCA 59.803 34.615 0.00 3.91 0.00 2.69
237 244 6.920758 TGGATTGTTTTCGTTCGAATTTTCAT 59.079 30.769 0.00 0.00 0.00 2.57
239 246 7.944649 GGATTGTTTTCGTTCGAATTTTCATTC 59.055 33.333 0.00 10.08 36.20 2.67
252 259 8.600625 TCGAATTTTCATTCATTAACTAGACCG 58.399 33.333 0.00 0.00 39.14 4.79
253 260 8.388103 CGAATTTTCATTCATTAACTAGACCGT 58.612 33.333 0.00 0.00 39.14 4.83
287 294 3.347216 AGTTGTGGGATATCTTGTGTGC 58.653 45.455 2.05 0.00 0.00 4.57
288 295 2.022764 TGTGGGATATCTTGTGTGCG 57.977 50.000 2.05 0.00 0.00 5.34
295 302 0.175760 TATCTTGTGTGCGAGGCTCC 59.824 55.000 9.32 2.37 0.00 4.70
319 326 6.368213 CCTTCCACGTAGTTTTCATACAAAC 58.632 40.000 0.00 0.00 41.61 2.93
327 334 7.702772 ACGTAGTTTTCATACAAACATTTTGCA 59.297 29.630 0.00 0.00 37.78 4.08
425 432 2.092212 CCCTCCATATTTGCACCTCAGT 60.092 50.000 0.00 0.00 0.00 3.41
446 453 0.826256 TAGTCACTCCACCAGCGTGT 60.826 55.000 0.00 0.00 38.41 4.49
490 497 2.654085 CGACGATGCGCACGGTAT 60.654 61.111 27.28 8.62 34.93 2.73
657 664 5.499139 AGTGCCAACATTAATTATGACCG 57.501 39.130 0.00 0.00 37.69 4.79
716 723 3.254654 CGTGTATGGCTGCGACCG 61.255 66.667 0.00 0.00 0.00 4.79
720 727 3.845259 TATGGCTGCGACCGGTCC 61.845 66.667 28.52 20.60 0.00 4.46
745 752 0.530744 TCACCAGCCACACTATCGAC 59.469 55.000 0.00 0.00 0.00 4.20
748 755 1.878522 CAGCCACACTATCGACCGC 60.879 63.158 0.00 0.00 0.00 5.68
843 856 2.051345 CGCTGGCGTGACAAAACC 60.051 61.111 6.83 0.00 34.35 3.27
855 868 3.083293 TGACAAAACCCCGCCTATAAAC 58.917 45.455 0.00 0.00 0.00 2.01
856 869 2.424601 GACAAAACCCCGCCTATAAACC 59.575 50.000 0.00 0.00 0.00 3.27
857 870 2.042026 ACAAAACCCCGCCTATAAACCT 59.958 45.455 0.00 0.00 0.00 3.50
858 871 3.266513 ACAAAACCCCGCCTATAAACCTA 59.733 43.478 0.00 0.00 0.00 3.08
889 903 3.056313 GCCTTGCCGGAATCAGCAC 62.056 63.158 5.05 0.00 39.10 4.40
902 916 4.021925 AGCACCCAACCGAGCTCC 62.022 66.667 8.47 0.00 30.05 4.70
904 918 3.322466 CACCCAACCGAGCTCCCT 61.322 66.667 8.47 0.00 0.00 4.20
905 919 2.529389 ACCCAACCGAGCTCCCTT 60.529 61.111 8.47 0.00 0.00 3.95
906 920 2.045926 CCCAACCGAGCTCCCTTG 60.046 66.667 8.47 9.40 0.00 3.61
907 921 2.747855 CCAACCGAGCTCCCTTGC 60.748 66.667 8.47 0.00 0.00 4.01
908 922 2.032528 CAACCGAGCTCCCTTGCA 59.967 61.111 8.47 0.00 34.99 4.08
909 923 2.032681 AACCGAGCTCCCTTGCAC 59.967 61.111 8.47 0.00 34.99 4.57
918 932 1.461268 TCCCTTGCACACCTCCTCA 60.461 57.895 0.00 0.00 0.00 3.86
1351 1371 7.723172 GGTACCTTCTAAGCTACTCCACTTATA 59.277 40.741 4.06 0.00 0.00 0.98
1352 1372 9.299465 GTACCTTCTAAGCTACTCCACTTATAT 57.701 37.037 0.00 0.00 0.00 0.86
1353 1373 8.785184 ACCTTCTAAGCTACTCCACTTATATT 57.215 34.615 0.00 0.00 0.00 1.28
1354 1374 8.862085 ACCTTCTAAGCTACTCCACTTATATTC 58.138 37.037 0.00 0.00 0.00 1.75
1355 1375 8.861086 CCTTCTAAGCTACTCCACTTATATTCA 58.139 37.037 0.00 0.00 0.00 2.57
1400 1435 7.237173 AGTACACGACTACACGTTACTTAATC 58.763 38.462 0.00 0.00 44.76 1.75
1608 1643 3.849145 GCGCGCTTATTATCTCAGACTAG 59.151 47.826 26.67 0.00 0.00 2.57
1676 1711 2.375766 CGCTGTCTTCCACGCTCAC 61.376 63.158 0.00 0.00 0.00 3.51
1703 1740 3.721706 CCTGCCTCGGCCTTCCTT 61.722 66.667 0.00 0.00 41.09 3.36
1723 1760 3.036429 AACAGGCGAGAGATGGGGC 62.036 63.158 0.00 0.00 0.00 5.80
1825 1862 0.031857 AGATCCTCTTCAGCATCGCG 59.968 55.000 0.00 0.00 0.00 5.87
1999 2036 3.282021 CATGATCTGGGTCATTTCCGTT 58.718 45.455 0.00 0.00 36.72 4.44
2142 2179 3.953712 TGTGCTCGAGATTCAGGTAAA 57.046 42.857 18.75 0.00 0.00 2.01
2148 2185 4.505922 GCTCGAGATTCAGGTAAATGTCAG 59.494 45.833 18.75 0.00 30.42 3.51
2149 2186 5.655488 CTCGAGATTCAGGTAAATGTCAGT 58.345 41.667 6.58 0.00 30.42 3.41
2152 2189 5.394663 CGAGATTCAGGTAAATGTCAGTCCT 60.395 44.000 0.00 0.00 30.42 3.85
2169 2206 4.224818 CAGTCCTGGAAAAGAGATTCTCCT 59.775 45.833 10.09 0.00 0.00 3.69
2170 2207 4.469586 AGTCCTGGAAAAGAGATTCTCCTC 59.530 45.833 10.09 5.03 0.00 3.71
2171 2208 3.777522 TCCTGGAAAAGAGATTCTCCTCC 59.222 47.826 10.09 13.33 33.76 4.30
2172 2209 3.118075 CCTGGAAAAGAGATTCTCCTCCC 60.118 52.174 17.89 12.02 33.76 4.30
2173 2210 3.521126 CTGGAAAAGAGATTCTCCTCCCA 59.479 47.826 17.89 14.78 33.76 4.37
2174 2211 4.114597 TGGAAAAGAGATTCTCCTCCCAT 58.885 43.478 17.89 0.00 33.76 4.00
2206 2249 2.434336 TGCATGTTAGCCTCGTTATCCT 59.566 45.455 0.00 0.00 0.00 3.24
2218 2261 3.186909 TCGTTATCCTTTGCTCATGTCG 58.813 45.455 0.00 0.00 0.00 4.35
2221 2264 2.029838 ATCCTTTGCTCATGTCGTCC 57.970 50.000 0.00 0.00 0.00 4.79
2222 2265 0.976641 TCCTTTGCTCATGTCGTCCT 59.023 50.000 0.00 0.00 0.00 3.85
2237 2280 1.600636 TCCTTGTGCCGCTTTGAGG 60.601 57.895 0.00 0.00 0.00 3.86
2239 2282 0.962356 CCTTGTGCCGCTTTGAGGAT 60.962 55.000 0.00 0.00 0.00 3.24
2252 2295 2.538512 TGAGGATGAATGGCGATGAG 57.461 50.000 0.00 0.00 0.00 2.90
2272 2315 2.365617 AGGAAAAGTCGCTGAGAGTGAA 59.634 45.455 0.00 0.00 36.37 3.18
2273 2316 2.734079 GGAAAAGTCGCTGAGAGTGAAG 59.266 50.000 0.00 0.00 36.37 3.02
2274 2317 1.789506 AAAGTCGCTGAGAGTGAAGC 58.210 50.000 0.00 0.00 36.37 3.86
2275 2318 0.676184 AAGTCGCTGAGAGTGAAGCA 59.324 50.000 0.00 0.00 39.47 3.91
2276 2319 0.894141 AGTCGCTGAGAGTGAAGCAT 59.106 50.000 0.00 0.00 39.47 3.79
2278 2321 0.174389 TCGCTGAGAGTGAAGCATCC 59.826 55.000 0.00 0.00 39.47 3.51
2317 2360 3.470567 CCGTCGACGCTGAAGCAC 61.471 66.667 31.73 0.00 42.21 4.40
2368 2411 1.513586 GTTCGCCTACCTCGTCGTG 60.514 63.158 0.00 0.00 0.00 4.35
2371 2414 4.849329 GCCTACCTCGTCGTGGCG 62.849 72.222 13.13 4.96 33.96 5.69
2437 2480 0.042131 ACCAGATACCTCCCAACGGA 59.958 55.000 0.00 0.00 36.45 4.69
2488 2531 4.309950 GACGTGTCCCGGCTGGTT 62.310 66.667 11.58 0.00 43.06 3.67
2548 2591 0.866061 CCACGTTCCAGATCTACGCG 60.866 60.000 14.83 3.53 38.77 6.01
2692 2735 2.581354 CCCTTCCTGTCGGAGCTG 59.419 66.667 0.00 0.00 41.25 4.24
2758 2801 3.057548 TGCTTCATGTGGCTGGCG 61.058 61.111 12.19 0.00 0.00 5.69
2920 2963 1.566018 CCGCCGAGTTCCAGTGAAAC 61.566 60.000 0.00 0.00 30.79 2.78
3000 3047 4.295141 TCCACCAACGGAAGACATATTT 57.705 40.909 0.00 0.00 29.93 1.40
3041 3088 7.336427 TGGCTTGTTTTTCATTTTGTTTCTGAT 59.664 29.630 0.00 0.00 0.00 2.90
3042 3089 7.641020 GGCTTGTTTTTCATTTTGTTTCTGATG 59.359 33.333 0.00 0.00 0.00 3.07
3045 3092 9.650539 TTGTTTTTCATTTTGTTTCTGATGAGA 57.349 25.926 0.00 0.00 30.92 3.27
3148 3201 7.493743 CAGATCAGCTGTTCTATATGCTTTT 57.506 36.000 23.55 0.00 39.85 2.27
3149 3202 7.928103 CAGATCAGCTGTTCTATATGCTTTTT 58.072 34.615 23.55 0.00 39.85 1.94
3171 3224 7.915293 TTTTTCATGGTAATACGTGTCTCAT 57.085 32.000 0.00 0.00 0.00 2.90
3172 3225 7.915293 TTTTCATGGTAATACGTGTCTCATT 57.085 32.000 0.00 0.00 0.00 2.57
3173 3226 7.915293 TTTCATGGTAATACGTGTCTCATTT 57.085 32.000 0.00 0.00 0.00 2.32
3174 3227 9.438228 TTTTCATGGTAATACGTGTCTCATTTA 57.562 29.630 0.00 0.00 0.00 1.40
3175 3228 9.607988 TTTCATGGTAATACGTGTCTCATTTAT 57.392 29.630 0.00 0.00 0.00 1.40
3187 3240 9.095065 ACGTGTCTCATTTATAACATAAGGTTC 57.905 33.333 0.00 0.00 40.96 3.62
3188 3241 9.093970 CGTGTCTCATTTATAACATAAGGTTCA 57.906 33.333 0.00 0.00 40.96 3.18
3199 3252 8.904099 ATAACATAAGGTTCATAGTACAAGCC 57.096 34.615 0.00 0.00 40.96 4.35
3200 3253 6.308015 ACATAAGGTTCATAGTACAAGCCA 57.692 37.500 0.00 0.00 0.00 4.75
3201 3254 6.113411 ACATAAGGTTCATAGTACAAGCCAC 58.887 40.000 0.00 0.00 0.00 5.01
3202 3255 3.247006 AGGTTCATAGTACAAGCCACG 57.753 47.619 0.00 0.00 0.00 4.94
3203 3256 2.565834 AGGTTCATAGTACAAGCCACGT 59.434 45.455 0.00 0.00 0.00 4.49
3204 3257 3.765511 AGGTTCATAGTACAAGCCACGTA 59.234 43.478 0.00 0.00 0.00 3.57
3205 3258 3.861689 GGTTCATAGTACAAGCCACGTAC 59.138 47.826 0.00 0.00 39.64 3.67
3206 3259 4.487948 GTTCATAGTACAAGCCACGTACA 58.512 43.478 9.73 0.00 41.40 2.90
3207 3260 4.994907 TCATAGTACAAGCCACGTACAT 57.005 40.909 9.73 1.12 41.40 2.29
3208 3261 6.267817 GTTCATAGTACAAGCCACGTACATA 58.732 40.000 9.73 2.10 41.40 2.29
3209 3262 5.824429 TCATAGTACAAGCCACGTACATAC 58.176 41.667 9.73 0.00 41.40 2.39
3210 3263 3.515330 AGTACAAGCCACGTACATACC 57.485 47.619 9.73 0.00 41.40 2.73
3211 3264 2.159338 AGTACAAGCCACGTACATACCG 60.159 50.000 9.73 0.00 41.40 4.02
3212 3265 0.889994 ACAAGCCACGTACATACCGA 59.110 50.000 0.00 0.00 0.00 4.69
3213 3266 1.479323 ACAAGCCACGTACATACCGAT 59.521 47.619 0.00 0.00 0.00 4.18
3214 3267 2.124903 CAAGCCACGTACATACCGATC 58.875 52.381 0.00 0.00 0.00 3.69
3215 3268 1.688772 AGCCACGTACATACCGATCT 58.311 50.000 0.00 0.00 0.00 2.75
3216 3269 1.337071 AGCCACGTACATACCGATCTG 59.663 52.381 0.00 0.00 0.00 2.90
3217 3270 1.602165 GCCACGTACATACCGATCTGG 60.602 57.143 0.00 2.55 46.41 3.86
3218 3271 1.602165 CCACGTACATACCGATCTGGC 60.602 57.143 0.00 0.00 43.94 4.85
3219 3272 1.066454 CACGTACATACCGATCTGGCA 59.934 52.381 0.00 0.00 43.94 4.92
3220 3273 1.752498 ACGTACATACCGATCTGGCAA 59.248 47.619 0.00 0.00 43.94 4.52
3221 3274 2.166870 ACGTACATACCGATCTGGCAAA 59.833 45.455 0.00 0.00 43.94 3.68
3222 3275 3.191669 CGTACATACCGATCTGGCAAAA 58.808 45.455 3.85 0.00 43.94 2.44
3223 3276 3.000925 CGTACATACCGATCTGGCAAAAC 59.999 47.826 3.85 0.00 43.94 2.43
3224 3277 3.350219 ACATACCGATCTGGCAAAACT 57.650 42.857 3.85 0.00 43.94 2.66
3225 3278 3.009723 ACATACCGATCTGGCAAAACTG 58.990 45.455 3.85 0.00 43.94 3.16
3226 3279 3.270027 CATACCGATCTGGCAAAACTGA 58.730 45.455 3.85 0.00 43.94 3.41
3227 3280 2.270352 ACCGATCTGGCAAAACTGAA 57.730 45.000 3.85 0.00 43.94 3.02
3228 3281 1.880027 ACCGATCTGGCAAAACTGAAC 59.120 47.619 3.85 0.00 43.94 3.18
3229 3282 1.879380 CCGATCTGGCAAAACTGAACA 59.121 47.619 0.00 0.00 0.00 3.18
3230 3283 2.293122 CCGATCTGGCAAAACTGAACAA 59.707 45.455 0.00 0.00 0.00 2.83
3231 3284 3.243367 CCGATCTGGCAAAACTGAACAAA 60.243 43.478 0.00 0.00 0.00 2.83
3232 3285 4.549458 CGATCTGGCAAAACTGAACAAAT 58.451 39.130 0.00 0.00 0.00 2.32
3233 3286 5.335583 CCGATCTGGCAAAACTGAACAAATA 60.336 40.000 0.00 0.00 0.00 1.40
3234 3287 6.148948 CGATCTGGCAAAACTGAACAAATAA 58.851 36.000 0.00 0.00 0.00 1.40
3235 3288 6.088085 CGATCTGGCAAAACTGAACAAATAAC 59.912 38.462 0.00 0.00 0.00 1.89
3236 3289 6.214191 TCTGGCAAAACTGAACAAATAACA 57.786 33.333 0.00 0.00 0.00 2.41
3237 3290 6.272318 TCTGGCAAAACTGAACAAATAACAG 58.728 36.000 0.00 0.00 37.62 3.16
3238 3291 6.096141 TCTGGCAAAACTGAACAAATAACAGA 59.904 34.615 0.00 0.00 35.85 3.41
3239 3292 6.634805 TGGCAAAACTGAACAAATAACAGAA 58.365 32.000 0.00 0.00 35.85 3.02
3240 3293 6.533367 TGGCAAAACTGAACAAATAACAGAAC 59.467 34.615 0.00 0.00 35.85 3.01
3241 3294 6.291585 GGCAAAACTGAACAAATAACAGAACG 60.292 38.462 0.00 0.00 35.85 3.95
3242 3295 6.627274 CAAAACTGAACAAATAACAGAACGC 58.373 36.000 0.00 0.00 35.85 4.84
3243 3296 5.751243 AACTGAACAAATAACAGAACGCT 57.249 34.783 0.00 0.00 35.85 5.07
3244 3297 6.854496 AACTGAACAAATAACAGAACGCTA 57.146 33.333 0.00 0.00 35.85 4.26
3245 3298 6.467723 ACTGAACAAATAACAGAACGCTAG 57.532 37.500 0.00 0.00 35.85 3.42
3246 3299 5.107065 ACTGAACAAATAACAGAACGCTAGC 60.107 40.000 4.06 4.06 35.85 3.42
3247 3300 4.153475 TGAACAAATAACAGAACGCTAGCC 59.847 41.667 9.66 0.00 0.00 3.93
3248 3301 3.939066 ACAAATAACAGAACGCTAGCCT 58.061 40.909 9.66 0.00 0.00 4.58
3249 3302 4.324267 ACAAATAACAGAACGCTAGCCTT 58.676 39.130 9.66 3.52 0.00 4.35
3250 3303 4.760204 ACAAATAACAGAACGCTAGCCTTT 59.240 37.500 9.66 2.10 0.00 3.11
3251 3304 5.935789 ACAAATAACAGAACGCTAGCCTTTA 59.064 36.000 9.66 3.56 0.00 1.85
3252 3305 6.598064 ACAAATAACAGAACGCTAGCCTTTAT 59.402 34.615 9.66 0.00 0.00 1.40
3253 3306 7.767198 ACAAATAACAGAACGCTAGCCTTTATA 59.233 33.333 9.66 0.00 0.00 0.98
3254 3307 7.710766 AATAACAGAACGCTAGCCTTTATAC 57.289 36.000 9.66 0.00 0.00 1.47
3255 3308 4.730949 ACAGAACGCTAGCCTTTATACA 57.269 40.909 9.66 0.00 0.00 2.29
3256 3309 5.080969 ACAGAACGCTAGCCTTTATACAA 57.919 39.130 9.66 0.00 0.00 2.41
3257 3310 5.484715 ACAGAACGCTAGCCTTTATACAAA 58.515 37.500 9.66 0.00 0.00 2.83
3258 3311 5.581085 ACAGAACGCTAGCCTTTATACAAAG 59.419 40.000 9.66 0.00 40.80 2.77
3272 3325 8.574196 CTTTATACAAAGGAACAACAACCAAG 57.426 34.615 0.00 0.00 37.99 3.61
3273 3326 7.883391 TTATACAAAGGAACAACAACCAAGA 57.117 32.000 0.00 0.00 0.00 3.02
3274 3327 6.783708 ATACAAAGGAACAACAACCAAGAA 57.216 33.333 0.00 0.00 0.00 2.52
3275 3328 5.072040 ACAAAGGAACAACAACCAAGAAG 57.928 39.130 0.00 0.00 0.00 2.85
3276 3329 4.526650 ACAAAGGAACAACAACCAAGAAGT 59.473 37.500 0.00 0.00 0.00 3.01
3277 3330 5.712917 ACAAAGGAACAACAACCAAGAAGTA 59.287 36.000 0.00 0.00 0.00 2.24
3278 3331 6.209788 ACAAAGGAACAACAACCAAGAAGTAA 59.790 34.615 0.00 0.00 0.00 2.24
3279 3332 6.844097 AAGGAACAACAACCAAGAAGTAAA 57.156 33.333 0.00 0.00 0.00 2.01
3280 3333 6.844097 AGGAACAACAACCAAGAAGTAAAA 57.156 33.333 0.00 0.00 0.00 1.52
3281 3334 7.418337 AGGAACAACAACCAAGAAGTAAAAT 57.582 32.000 0.00 0.00 0.00 1.82
3282 3335 7.847096 AGGAACAACAACCAAGAAGTAAAATT 58.153 30.769 0.00 0.00 0.00 1.82
3283 3336 8.973182 AGGAACAACAACCAAGAAGTAAAATTA 58.027 29.630 0.00 0.00 0.00 1.40
3284 3337 9.027129 GGAACAACAACCAAGAAGTAAAATTAC 57.973 33.333 0.00 0.00 0.00 1.89
3285 3338 9.575783 GAACAACAACCAAGAAGTAAAATTACA 57.424 29.630 6.13 0.00 36.12 2.41
3348 3405 7.798596 AAACCTTAAGATCAGCTGATATGTG 57.201 36.000 28.78 17.61 34.37 3.21
3399 3477 8.963725 TGACAACCGAGGACGAAATATATATAT 58.036 33.333 0.00 0.00 42.66 0.86
3443 3521 7.063898 ACAAACAATCATCAGATACAGAACGAG 59.936 37.037 0.00 0.00 33.08 4.18
3617 3695 4.149511 TCTAATGGCATCGTTTGATCCA 57.850 40.909 0.00 0.00 36.72 3.41
3641 3719 7.172875 CCAGATGCATTCTATAGGAGACAAAAG 59.827 40.741 0.00 0.00 32.31 2.27
3681 3767 3.501828 TGTACAACATCAATGAGCCACAC 59.498 43.478 0.00 0.00 0.00 3.82
3688 3774 3.165058 TCAATGAGCCACACGTATCTC 57.835 47.619 0.00 0.00 0.00 2.75
3691 3777 4.584743 TCAATGAGCCACACGTATCTCTAT 59.415 41.667 0.00 0.00 0.00 1.98
3756 3846 2.490217 CGCGTACTAGCAGCACCT 59.510 61.111 0.00 0.00 36.85 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.454678 GAGTCACATAAAGATCCATGCCA 58.545 43.478 0.00 0.00 0.00 4.92
1 2 3.817647 GGAGTCACATAAAGATCCATGCC 59.182 47.826 0.00 0.00 0.00 4.40
2 3 3.496130 CGGAGTCACATAAAGATCCATGC 59.504 47.826 0.00 0.00 0.00 4.06
3 4 3.496130 GCGGAGTCACATAAAGATCCATG 59.504 47.826 0.00 0.00 0.00 3.66
4 5 3.134623 TGCGGAGTCACATAAAGATCCAT 59.865 43.478 0.00 0.00 0.00 3.41
5 6 2.499693 TGCGGAGTCACATAAAGATCCA 59.500 45.455 0.00 0.00 0.00 3.41
13 14 2.760650 AGAGACATTGCGGAGTCACATA 59.239 45.455 0.00 0.00 37.23 2.29
27 28 4.228210 ACCCAATCCACACAATAGAGACAT 59.772 41.667 0.00 0.00 0.00 3.06
30 31 3.118775 CGACCCAATCCACACAATAGAGA 60.119 47.826 0.00 0.00 0.00 3.10
35 36 1.821216 GTCGACCCAATCCACACAAT 58.179 50.000 3.51 0.00 0.00 2.71
48 49 0.946221 GCCATGGATGATCGTCGACC 60.946 60.000 18.40 0.00 0.00 4.79
62 63 1.497278 CGTCTCCAACGTTGCCATG 59.503 57.895 22.93 9.27 46.42 3.66
73 74 1.669115 GCTCAAGCAAGCGTCTCCA 60.669 57.895 0.00 0.00 41.59 3.86
102 103 3.798515 TCTCCCAAGTAGGTACCATTGT 58.201 45.455 15.94 0.00 34.66 2.71
129 130 0.798159 CCACACATGTGTCACCATCG 59.202 55.000 28.38 14.98 42.83 3.84
132 133 2.637382 AGATACCACACATGTGTCACCA 59.363 45.455 28.38 14.04 42.83 4.17
182 183 1.202486 CGGCACACGTTAGATACCCAT 60.202 52.381 0.00 0.00 37.93 4.00
189 190 0.734942 GCTAAGCGGCACACGTTAGA 60.735 55.000 1.45 0.00 46.52 2.10
192 193 0.736325 CTAGCTAAGCGGCACACGTT 60.736 55.000 1.45 0.00 46.52 3.99
212 213 6.266323 TGAAAATTCGAACGAAAACAATCCA 58.734 32.000 13.34 3.96 37.69 3.41
223 230 9.967245 TCTAGTTAATGAATGAAAATTCGAACG 57.033 29.630 0.00 0.00 33.42 3.95
226 233 8.600625 CGGTCTAGTTAATGAATGAAAATTCGA 58.399 33.333 0.00 0.00 33.42 3.71
257 264 7.616935 ACAAGATATCCCACAACTCATGAAAAT 59.383 33.333 0.00 0.00 0.00 1.82
263 270 5.188434 CACACAAGATATCCCACAACTCAT 58.812 41.667 0.00 0.00 0.00 2.90
287 294 2.005960 CTACGTGGAAGGGAGCCTCG 62.006 65.000 0.00 0.00 45.11 4.63
288 295 0.971447 ACTACGTGGAAGGGAGCCTC 60.971 60.000 5.70 0.00 35.64 4.70
295 302 6.017770 TGTTTGTATGAAAACTACGTGGAAGG 60.018 38.462 5.70 0.00 40.11 3.46
425 432 0.251209 ACGCTGGTGGAGTGACTAGA 60.251 55.000 0.00 0.00 35.96 2.43
446 453 2.186076 CGTTTTTAGGTGCAACGCAAA 58.814 42.857 0.00 0.00 41.47 3.68
490 497 5.408299 GCATATATGGACGTTTATGCAGACA 59.592 40.000 14.51 0.00 43.96 3.41
528 535 8.586570 TTAATTTGTTTGTGCAAGGTTAGATG 57.413 30.769 0.00 0.00 0.00 2.90
657 664 2.279502 TACGGTCTCGAGTGCATGCC 62.280 60.000 16.68 6.65 40.11 4.40
700 707 2.890474 CCGGTCGCAGCCATACAC 60.890 66.667 0.00 0.00 0.00 2.90
825 838 2.725815 GTTTTGTCACGCCAGCGC 60.726 61.111 12.72 0.00 44.19 5.92
826 839 2.051345 GGTTTTGTCACGCCAGCG 60.051 61.111 11.05 11.05 46.03 5.18
827 840 2.335011 GGGTTTTGTCACGCCAGC 59.665 61.111 0.00 0.00 0.00 4.85
828 841 3.039134 GGGGTTTTGTCACGCCAG 58.961 61.111 2.23 0.00 46.70 4.85
843 856 0.319405 CCGGTAGGTTTATAGGCGGG 59.681 60.000 0.00 0.00 0.00 6.13
889 903 2.045926 CAAGGGAGCTCGGTTGGG 60.046 66.667 15.63 0.00 0.00 4.12
902 916 0.886490 GTGTGAGGAGGTGTGCAAGG 60.886 60.000 0.00 0.00 0.00 3.61
903 917 0.179048 TGTGTGAGGAGGTGTGCAAG 60.179 55.000 0.00 0.00 0.00 4.01
904 918 0.254462 TTGTGTGAGGAGGTGTGCAA 59.746 50.000 0.00 0.00 0.00 4.08
905 919 0.179048 CTTGTGTGAGGAGGTGTGCA 60.179 55.000 0.00 0.00 0.00 4.57
906 920 0.886490 CCTTGTGTGAGGAGGTGTGC 60.886 60.000 0.00 0.00 39.25 4.57
907 921 0.469917 ACCTTGTGTGAGGAGGTGTG 59.530 55.000 0.00 0.00 42.04 3.82
908 922 0.759346 GACCTTGTGTGAGGAGGTGT 59.241 55.000 0.00 0.00 43.59 4.16
909 923 1.051812 AGACCTTGTGTGAGGAGGTG 58.948 55.000 0.00 0.00 43.59 4.00
918 932 0.766674 TAGGTGCCCAGACCTTGTGT 60.767 55.000 0.00 0.00 44.53 3.72
950 964 3.773860 AGTATGCGCTAGCTAGCTATG 57.226 47.619 36.02 24.64 46.85 2.23
964 978 1.612463 CCCTCCGGTGTAGTAGTATGC 59.388 57.143 0.00 0.00 0.00 3.14
1351 1371 9.388506 ACTTTATGTTCATCTCTCGATTTGAAT 57.611 29.630 0.00 0.00 0.00 2.57
1352 1372 8.777865 ACTTTATGTTCATCTCTCGATTTGAA 57.222 30.769 0.00 0.00 0.00 2.69
1353 1373 9.302345 GTACTTTATGTTCATCTCTCGATTTGA 57.698 33.333 0.00 0.00 0.00 2.69
1354 1374 9.087424 TGTACTTTATGTTCATCTCTCGATTTG 57.913 33.333 0.00 0.00 0.00 2.32
1355 1375 9.088512 GTGTACTTTATGTTCATCTCTCGATTT 57.911 33.333 0.00 0.00 0.00 2.17
1374 1394 5.424121 AAGTAACGTGTAGTCGTGTACTT 57.576 39.130 14.32 14.32 43.38 2.24
1415 1450 0.818040 ACGTCCTGCAAGAACCCAAC 60.818 55.000 0.00 0.00 34.07 3.77
1649 1684 2.808543 GTGGAAGACAGCGATTGAAAGT 59.191 45.455 0.00 0.00 0.00 2.66
1655 1690 0.737715 GAGCGTGGAAGACAGCGATT 60.738 55.000 0.00 0.00 34.34 3.34
1687 1724 2.124942 GAAGGAAGGCCGAGGCAG 60.125 66.667 16.65 0.00 44.11 4.85
1703 1740 1.617018 CCCCATCTCTCGCCTGTTGA 61.617 60.000 0.00 0.00 0.00 3.18
1723 1760 1.153005 GAGCAGGGCCAGGATCTTG 60.153 63.158 6.18 0.00 0.00 3.02
2086 2123 4.633596 GCGAACGCGATGATGCCG 62.634 66.667 15.93 0.63 40.82 5.69
2142 2179 5.250313 AGAATCTCTTTTCCAGGACTGACAT 59.750 40.000 0.00 0.00 0.00 3.06
2148 2185 4.383661 GGAGGAGAATCTCTTTTCCAGGAC 60.384 50.000 10.38 0.00 34.39 3.85
2149 2186 3.777522 GGAGGAGAATCTCTTTTCCAGGA 59.222 47.826 10.38 0.00 34.39 3.86
2152 2189 3.531059 TGGGAGGAGAATCTCTTTTCCA 58.469 45.455 21.24 16.99 34.39 3.53
2169 2206 1.367346 TGCACTACTTGGGAATGGGA 58.633 50.000 0.00 0.00 0.00 4.37
2170 2207 2.026641 CATGCACTACTTGGGAATGGG 58.973 52.381 0.00 0.00 0.00 4.00
2171 2208 2.726821 ACATGCACTACTTGGGAATGG 58.273 47.619 0.00 0.00 0.00 3.16
2172 2209 4.201950 GCTAACATGCACTACTTGGGAATG 60.202 45.833 0.00 0.00 0.00 2.67
2173 2210 3.947834 GCTAACATGCACTACTTGGGAAT 59.052 43.478 0.00 0.00 0.00 3.01
2174 2211 3.343617 GCTAACATGCACTACTTGGGAA 58.656 45.455 0.00 0.00 0.00 3.97
2206 2249 1.872952 CACAAGGACGACATGAGCAAA 59.127 47.619 0.00 0.00 0.00 3.68
2218 2261 1.576421 CTCAAAGCGGCACAAGGAC 59.424 57.895 1.45 0.00 0.00 3.85
2221 2264 0.169672 CATCCTCAAAGCGGCACAAG 59.830 55.000 1.45 0.00 0.00 3.16
2222 2265 0.250684 TCATCCTCAAAGCGGCACAA 60.251 50.000 1.45 0.00 0.00 3.33
2237 2280 3.629398 ACTTTTCCTCATCGCCATTCATC 59.371 43.478 0.00 0.00 0.00 2.92
2239 2282 3.009723 GACTTTTCCTCATCGCCATTCA 58.990 45.455 0.00 0.00 0.00 2.57
2252 2295 2.440539 TCACTCTCAGCGACTTTTCC 57.559 50.000 0.00 0.00 0.00 3.13
2272 2315 1.340795 CCCTGCAAAGAGAAGGATGCT 60.341 52.381 0.00 0.00 39.49 3.79
2273 2316 1.101331 CCCTGCAAAGAGAAGGATGC 58.899 55.000 0.00 0.00 39.22 3.91
2274 2317 1.101331 GCCCTGCAAAGAGAAGGATG 58.899 55.000 0.00 0.00 32.43 3.51
2275 2318 0.700564 TGCCCTGCAAAGAGAAGGAT 59.299 50.000 0.00 0.00 34.76 3.24
2276 2319 0.250901 GTGCCCTGCAAAGAGAAGGA 60.251 55.000 0.00 0.00 41.47 3.36
2278 2321 1.321474 TTGTGCCCTGCAAAGAGAAG 58.679 50.000 0.00 0.00 41.47 2.85
2317 2360 1.746615 CATGGGCACGTGAGAAGGG 60.747 63.158 22.23 0.00 35.58 3.95
2371 2414 2.760385 ACGGGGTAGAGGCAGAGC 60.760 66.667 0.00 0.00 0.00 4.09
2488 2531 2.125326 CAGGGTGGCGAGACCGATA 61.125 63.158 0.00 0.00 43.94 2.92
2758 2801 1.072159 CCTCCCGGGCTTCATGATC 59.928 63.158 18.49 0.00 0.00 2.92
2884 2927 1.576421 GGGCTTGAAGAACTGCACG 59.424 57.895 0.00 0.00 0.00 5.34
3000 3047 4.525996 ACAAGCCAGCATTACATCACATA 58.474 39.130 0.00 0.00 0.00 2.29
3147 3200 7.915293 ATGAGACACGTATTACCATGAAAAA 57.085 32.000 0.00 0.00 0.00 1.94
3148 3201 7.915293 AATGAGACACGTATTACCATGAAAA 57.085 32.000 0.00 0.00 0.00 2.29
3149 3202 7.915293 AAATGAGACACGTATTACCATGAAA 57.085 32.000 0.00 0.00 0.00 2.69
3161 3214 9.095065 GAACCTTATGTTATAAATGAGACACGT 57.905 33.333 0.00 0.00 37.29 4.49
3162 3215 9.093970 TGAACCTTATGTTATAAATGAGACACG 57.906 33.333 0.00 0.00 37.29 4.49
3173 3226 9.991906 GGCTTGTACTATGAACCTTATGTTATA 57.008 33.333 0.00 0.00 37.29 0.98
3174 3227 8.491134 TGGCTTGTACTATGAACCTTATGTTAT 58.509 33.333 0.00 0.00 37.29 1.89
3175 3228 7.767198 GTGGCTTGTACTATGAACCTTATGTTA 59.233 37.037 0.00 0.00 37.29 2.41
3176 3229 6.598064 GTGGCTTGTACTATGAACCTTATGTT 59.402 38.462 0.00 0.00 40.81 2.71
3177 3230 6.113411 GTGGCTTGTACTATGAACCTTATGT 58.887 40.000 0.00 0.00 0.00 2.29
3178 3231 5.234329 CGTGGCTTGTACTATGAACCTTATG 59.766 44.000 0.00 0.00 0.00 1.90
3179 3232 5.105064 ACGTGGCTTGTACTATGAACCTTAT 60.105 40.000 0.00 0.00 0.00 1.73
3180 3233 4.221262 ACGTGGCTTGTACTATGAACCTTA 59.779 41.667 0.00 0.00 0.00 2.69
3181 3234 3.007614 ACGTGGCTTGTACTATGAACCTT 59.992 43.478 0.00 0.00 0.00 3.50
3182 3235 2.565834 ACGTGGCTTGTACTATGAACCT 59.434 45.455 0.00 0.00 0.00 3.50
3183 3236 2.968675 ACGTGGCTTGTACTATGAACC 58.031 47.619 0.00 0.00 0.00 3.62
3184 3237 4.487948 TGTACGTGGCTTGTACTATGAAC 58.512 43.478 16.75 0.00 42.09 3.18
3185 3238 4.787260 TGTACGTGGCTTGTACTATGAA 57.213 40.909 16.75 0.00 42.09 2.57
3186 3239 4.994907 ATGTACGTGGCTTGTACTATGA 57.005 40.909 16.75 2.28 42.09 2.15
3187 3240 4.980434 GGTATGTACGTGGCTTGTACTATG 59.020 45.833 16.75 0.00 42.09 2.23
3188 3241 4.261322 CGGTATGTACGTGGCTTGTACTAT 60.261 45.833 16.75 12.18 42.09 2.12
3189 3242 3.065233 CGGTATGTACGTGGCTTGTACTA 59.935 47.826 16.75 7.49 42.09 1.82
3190 3243 2.159338 CGGTATGTACGTGGCTTGTACT 60.159 50.000 16.75 8.31 42.09 2.73
3191 3244 2.159393 TCGGTATGTACGTGGCTTGTAC 60.159 50.000 0.00 11.33 41.97 2.90
3192 3245 2.090760 TCGGTATGTACGTGGCTTGTA 58.909 47.619 0.00 0.00 0.00 2.41
3193 3246 0.889994 TCGGTATGTACGTGGCTTGT 59.110 50.000 0.00 0.00 0.00 3.16
3194 3247 2.124903 GATCGGTATGTACGTGGCTTG 58.875 52.381 0.00 0.00 0.00 4.01
3195 3248 2.029623 AGATCGGTATGTACGTGGCTT 58.970 47.619 0.00 0.00 0.00 4.35
3196 3249 1.337071 CAGATCGGTATGTACGTGGCT 59.663 52.381 0.00 0.00 0.00 4.75
3197 3250 1.602165 CCAGATCGGTATGTACGTGGC 60.602 57.143 0.00 0.00 0.00 5.01
3198 3251 1.602165 GCCAGATCGGTATGTACGTGG 60.602 57.143 0.00 0.00 36.97 4.94
3199 3252 1.066454 TGCCAGATCGGTATGTACGTG 59.934 52.381 0.00 0.00 36.97 4.49
3200 3253 1.395635 TGCCAGATCGGTATGTACGT 58.604 50.000 0.00 0.00 36.97 3.57
3201 3254 2.502213 TTGCCAGATCGGTATGTACG 57.498 50.000 5.66 0.00 36.97 3.67
3202 3255 4.034048 CAGTTTTGCCAGATCGGTATGTAC 59.966 45.833 5.66 0.00 36.97 2.90
3203 3256 4.081365 TCAGTTTTGCCAGATCGGTATGTA 60.081 41.667 5.66 0.00 36.97 2.29
3204 3257 3.009723 CAGTTTTGCCAGATCGGTATGT 58.990 45.455 5.66 0.00 36.97 2.29
3205 3258 3.270027 TCAGTTTTGCCAGATCGGTATG 58.730 45.455 5.66 0.00 36.97 2.39
3206 3259 3.627395 TCAGTTTTGCCAGATCGGTAT 57.373 42.857 5.66 0.00 36.97 2.73
3207 3260 3.071479 GTTCAGTTTTGCCAGATCGGTA 58.929 45.455 5.66 0.00 36.97 4.02
3208 3261 1.880027 GTTCAGTTTTGCCAGATCGGT 59.120 47.619 5.66 0.00 36.97 4.69
3209 3262 1.879380 TGTTCAGTTTTGCCAGATCGG 59.121 47.619 0.00 0.00 38.11 4.18
3210 3263 3.624326 TTGTTCAGTTTTGCCAGATCG 57.376 42.857 0.00 0.00 0.00 3.69
3211 3264 6.922957 TGTTATTTGTTCAGTTTTGCCAGATC 59.077 34.615 0.00 0.00 0.00 2.75
3212 3265 6.815089 TGTTATTTGTTCAGTTTTGCCAGAT 58.185 32.000 0.00 0.00 0.00 2.90
3213 3266 6.096141 TCTGTTATTTGTTCAGTTTTGCCAGA 59.904 34.615 0.00 0.00 0.00 3.86
3214 3267 6.272318 TCTGTTATTTGTTCAGTTTTGCCAG 58.728 36.000 0.00 0.00 0.00 4.85
3215 3268 6.214191 TCTGTTATTTGTTCAGTTTTGCCA 57.786 33.333 0.00 0.00 0.00 4.92
3216 3269 6.291585 CGTTCTGTTATTTGTTCAGTTTTGCC 60.292 38.462 0.00 0.00 0.00 4.52
3217 3270 6.627274 CGTTCTGTTATTTGTTCAGTTTTGC 58.373 36.000 0.00 0.00 0.00 3.68
3218 3271 6.472163 AGCGTTCTGTTATTTGTTCAGTTTTG 59.528 34.615 0.00 0.00 0.00 2.44
3219 3272 6.560711 AGCGTTCTGTTATTTGTTCAGTTTT 58.439 32.000 0.00 0.00 0.00 2.43
3220 3273 6.131544 AGCGTTCTGTTATTTGTTCAGTTT 57.868 33.333 0.00 0.00 0.00 2.66
3221 3274 5.751243 AGCGTTCTGTTATTTGTTCAGTT 57.249 34.783 0.00 0.00 0.00 3.16
3222 3275 5.107065 GCTAGCGTTCTGTTATTTGTTCAGT 60.107 40.000 0.00 0.00 0.00 3.41
3223 3276 5.316770 GCTAGCGTTCTGTTATTTGTTCAG 58.683 41.667 0.00 0.00 0.00 3.02
3224 3277 4.153475 GGCTAGCGTTCTGTTATTTGTTCA 59.847 41.667 9.00 0.00 0.00 3.18
3225 3278 4.392138 AGGCTAGCGTTCTGTTATTTGTTC 59.608 41.667 9.00 0.00 0.00 3.18
3226 3279 4.324267 AGGCTAGCGTTCTGTTATTTGTT 58.676 39.130 9.00 0.00 0.00 2.83
3227 3280 3.939066 AGGCTAGCGTTCTGTTATTTGT 58.061 40.909 9.00 0.00 0.00 2.83
3228 3281 4.946784 AAGGCTAGCGTTCTGTTATTTG 57.053 40.909 16.67 0.00 0.00 2.32
3229 3282 7.767198 TGTATAAAGGCTAGCGTTCTGTTATTT 59.233 33.333 21.95 7.43 0.00 1.40
3230 3283 7.270047 TGTATAAAGGCTAGCGTTCTGTTATT 58.730 34.615 21.95 8.12 0.00 1.40
3231 3284 6.812998 TGTATAAAGGCTAGCGTTCTGTTAT 58.187 36.000 21.95 17.06 0.00 1.89
3232 3285 6.211587 TGTATAAAGGCTAGCGTTCTGTTA 57.788 37.500 21.95 11.63 0.00 2.41
3233 3286 5.080969 TGTATAAAGGCTAGCGTTCTGTT 57.919 39.130 21.95 9.83 0.00 3.16
3234 3287 4.730949 TGTATAAAGGCTAGCGTTCTGT 57.269 40.909 21.95 13.35 0.00 3.41
3235 3288 6.037423 CTTTGTATAAAGGCTAGCGTTCTG 57.963 41.667 21.95 4.32 39.67 3.02
3247 3300 8.410141 TCTTGGTTGTTGTTCCTTTGTATAAAG 58.590 33.333 5.04 5.04 42.34 1.85
3248 3301 8.294954 TCTTGGTTGTTGTTCCTTTGTATAAA 57.705 30.769 0.00 0.00 0.00 1.40
3249 3302 7.883391 TCTTGGTTGTTGTTCCTTTGTATAA 57.117 32.000 0.00 0.00 0.00 0.98
3250 3303 7.558444 ACTTCTTGGTTGTTGTTCCTTTGTATA 59.442 33.333 0.00 0.00 0.00 1.47
3251 3304 6.379988 ACTTCTTGGTTGTTGTTCCTTTGTAT 59.620 34.615 0.00 0.00 0.00 2.29
3252 3305 5.712917 ACTTCTTGGTTGTTGTTCCTTTGTA 59.287 36.000 0.00 0.00 0.00 2.41
3253 3306 4.526650 ACTTCTTGGTTGTTGTTCCTTTGT 59.473 37.500 0.00 0.00 0.00 2.83
3254 3307 5.072040 ACTTCTTGGTTGTTGTTCCTTTG 57.928 39.130 0.00 0.00 0.00 2.77
3255 3308 6.844097 TTACTTCTTGGTTGTTGTTCCTTT 57.156 33.333 0.00 0.00 0.00 3.11
3256 3309 6.844097 TTTACTTCTTGGTTGTTGTTCCTT 57.156 33.333 0.00 0.00 0.00 3.36
3257 3310 6.844097 TTTTACTTCTTGGTTGTTGTTCCT 57.156 33.333 0.00 0.00 0.00 3.36
3258 3311 9.027129 GTAATTTTACTTCTTGGTTGTTGTTCC 57.973 33.333 0.00 0.00 0.00 3.62
3259 3312 9.575783 TGTAATTTTACTTCTTGGTTGTTGTTC 57.424 29.630 2.45 0.00 34.77 3.18
3348 3405 9.722056 CATGCTTTATTTCTTGTAGTCATTACC 57.278 33.333 0.00 0.00 0.00 2.85
3362 3440 4.394920 TCCTCGGTTGTCATGCTTTATTTC 59.605 41.667 0.00 0.00 0.00 2.17
3403 3481 9.528018 GATGATTGTTTGTTCCTTTTGTTCTTA 57.472 29.630 0.00 0.00 0.00 2.10
3404 3482 8.040132 TGATGATTGTTTGTTCCTTTTGTTCTT 58.960 29.630 0.00 0.00 0.00 2.52
3405 3483 7.555087 TGATGATTGTTTGTTCCTTTTGTTCT 58.445 30.769 0.00 0.00 0.00 3.01
3406 3484 7.706179 TCTGATGATTGTTTGTTCCTTTTGTTC 59.294 33.333 0.00 0.00 0.00 3.18
3407 3485 7.555087 TCTGATGATTGTTTGTTCCTTTTGTT 58.445 30.769 0.00 0.00 0.00 2.83
3408 3486 7.111247 TCTGATGATTGTTTGTTCCTTTTGT 57.889 32.000 0.00 0.00 0.00 2.83
3409 3487 9.132521 GTATCTGATGATTGTTTGTTCCTTTTG 57.867 33.333 0.00 0.00 34.32 2.44
3410 3488 8.859090 TGTATCTGATGATTGTTTGTTCCTTTT 58.141 29.630 0.00 0.00 34.32 2.27
3411 3489 8.408043 TGTATCTGATGATTGTTTGTTCCTTT 57.592 30.769 0.00 0.00 34.32 3.11
3412 3490 7.884877 TCTGTATCTGATGATTGTTTGTTCCTT 59.115 33.333 0.00 0.00 34.32 3.36
3413 3491 7.397221 TCTGTATCTGATGATTGTTTGTTCCT 58.603 34.615 0.00 0.00 34.32 3.36
3414 3492 7.615582 TCTGTATCTGATGATTGTTTGTTCC 57.384 36.000 0.00 0.00 34.32 3.62
3415 3493 7.689812 CGTTCTGTATCTGATGATTGTTTGTTC 59.310 37.037 0.00 0.00 34.32 3.18
3416 3494 7.387673 TCGTTCTGTATCTGATGATTGTTTGTT 59.612 33.333 0.00 0.00 34.32 2.83
3443 3521 2.405892 ATGCACAACTGAAAACTCGC 57.594 45.000 0.00 0.00 0.00 5.03
3617 3695 7.222872 CCTTTTGTCTCCTATAGAATGCATCT 58.777 38.462 0.00 1.57 42.48 2.90
3641 3719 6.479972 TGTACAGCATATATATAGGCACCC 57.520 41.667 26.28 13.91 42.06 4.61
3756 3846 0.179048 CCGGGATGTAATCTGCTGCA 60.179 55.000 0.88 0.88 44.71 4.41


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

AutoCloner maintained by Alex Coulton.