Multiple sequence alignment - TraesCS5A01G146700

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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 TraesCS5A01G146700 chr5A 100.000 3147 0 0 1 3147 323369658 323372804 0.000000e+00 5812
1 TraesCS5A01G146700 chr5A 84.326 638 87 8 2510 3143 397514000 397513372 2.070000e-171 612
2 TraesCS5A01G146700 chr5D 94.257 2194 96 12 1 2183 232404640 232402466 0.000000e+00 3326
3 TraesCS5A01G146700 chr5D 93.440 686 42 3 2463 3147 541842718 541842035 0.000000e+00 1014
4 TraesCS5A01G146700 chr5B 94.901 1569 56 10 2 1563 272676370 272677921 0.000000e+00 2433
5 TraesCS5A01G146700 chr5B 92.285 674 47 3 2473 3146 511652974 511652306 0.000000e+00 952
6 TraesCS5A01G146700 chr5B 94.369 586 30 1 1598 2183 272677920 272678502 0.000000e+00 896
7 TraesCS5A01G146700 chr6D 95.182 685 33 0 2463 3147 7513417 7514101 0.000000e+00 1083
8 TraesCS5A01G146700 chr6D 88.172 186 20 2 1056 1241 377542240 377542423 1.470000e-53 220
9 TraesCS5A01G146700 chr4B 93.149 686 45 2 2462 3147 66176334 66175651 0.000000e+00 1005
10 TraesCS5A01G146700 chr3D 90.233 645 59 4 2463 3106 171587673 171587032 0.000000e+00 839
11 TraesCS5A01G146700 chr3D 92.149 484 29 5 2464 2944 20701708 20701231 0.000000e+00 675
12 TraesCS5A01G146700 chr7A 86.628 688 42 12 2463 3147 492244897 492244257 0.000000e+00 715
13 TraesCS5A01G146700 chr2D 92.708 480 27 5 2462 2941 41997814 41998285 0.000000e+00 686
14 TraesCS5A01G146700 chr1D 92.340 483 29 5 2462 2944 279085144 279084670 0.000000e+00 680
15 TraesCS5A01G146700 chr6B 88.608 237 24 3 1005 1241 227837925 227837692 5.140000e-73 285
16 TraesCS5A01G146700 chr3B 93.939 99 6 0 246 344 182420298 182420200 1.960000e-32 150


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 TraesCS5A01G146700 chr5A 323369658 323372804 3146 False 5812.0 5812 100.000 1 3147 1 chr5A.!!$F1 3146
1 TraesCS5A01G146700 chr5A 397513372 397514000 628 True 612.0 612 84.326 2510 3143 1 chr5A.!!$R1 633
2 TraesCS5A01G146700 chr5D 232402466 232404640 2174 True 3326.0 3326 94.257 1 2183 1 chr5D.!!$R1 2182
3 TraesCS5A01G146700 chr5D 541842035 541842718 683 True 1014.0 1014 93.440 2463 3147 1 chr5D.!!$R2 684
4 TraesCS5A01G146700 chr5B 272676370 272678502 2132 False 1664.5 2433 94.635 2 2183 2 chr5B.!!$F1 2181
5 TraesCS5A01G146700 chr5B 511652306 511652974 668 True 952.0 952 92.285 2473 3146 1 chr5B.!!$R1 673
6 TraesCS5A01G146700 chr6D 7513417 7514101 684 False 1083.0 1083 95.182 2463 3147 1 chr6D.!!$F1 684
7 TraesCS5A01G146700 chr4B 66175651 66176334 683 True 1005.0 1005 93.149 2462 3147 1 chr4B.!!$R1 685
8 TraesCS5A01G146700 chr3D 171587032 171587673 641 True 839.0 839 90.233 2463 3106 1 chr3D.!!$R2 643
9 TraesCS5A01G146700 chr7A 492244257 492244897 640 True 715.0 715 86.628 2463 3147 1 chr7A.!!$R1 684

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
792 802 0.861185 TTATCGCATGTGCTCGATGC 59.139 50.0 13.95 10.97 44.1 3.91 F
1333 1343 0.178973 TGGTGACGGAGAGAAGGACA 60.179 55.0 0.00 0.00 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1707 0.030638 CCTGCTCAACCAAAACCACG 59.969 55.0 0.0 0.0 0.0 4.94 R
2325 2373 0.099613 CTCTCTCACGCACGCTATGT 59.900 55.0 0.0 0.0 0.0 2.29 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
50 55 6.480981 AGCAAAAAGATGAATTTCCACACTTG 59.519 34.615 0.00 0.00 0.00 3.16
68 75 5.163205 ACACTTGCATACTAGAATATGGGCA 60.163 40.000 0.00 0.00 33.79 5.36
229 238 7.462856 CGAAGTCAATGTACTTAGATTTGGTCG 60.463 40.741 0.00 0.00 39.78 4.79
233 242 6.932400 TCAATGTACTTAGATTTGGTCGTTGT 59.068 34.615 0.00 0.00 0.00 3.32
242 251 1.822506 TTGGTCGTTGTTGTGGTTCA 58.177 45.000 0.00 0.00 0.00 3.18
251 260 4.808364 CGTTGTTGTGGTTCATGGAAAATT 59.192 37.500 0.00 0.00 0.00 1.82
331 340 1.002087 TCGGAAGGAGCAAAGAAGGAC 59.998 52.381 0.00 0.00 0.00 3.85
380 389 8.928270 ACACTACAGAAATAAGTACACTATGC 57.072 34.615 0.00 0.00 0.00 3.14
421 430 2.633657 CACACACGCTTGCAGACC 59.366 61.111 0.00 0.00 0.00 3.85
531 540 1.939974 CACATATGGTGGTGACGAGG 58.060 55.000 7.80 0.00 44.04 4.63
533 542 1.480954 ACATATGGTGGTGACGAGGTC 59.519 52.381 7.80 0.00 0.00 3.85
682 692 3.359654 GTGAACACAAACGACATTGACC 58.640 45.455 0.00 0.00 34.38 4.02
683 693 3.010420 TGAACACAAACGACATTGACCA 58.990 40.909 0.00 0.00 34.38 4.02
684 694 3.629855 TGAACACAAACGACATTGACCAT 59.370 39.130 0.00 0.00 34.38 3.55
685 695 3.624326 ACACAAACGACATTGACCATG 57.376 42.857 0.00 0.00 39.07 3.66
792 802 0.861185 TTATCGCATGTGCTCGATGC 59.139 50.000 13.95 10.97 44.10 3.91
943 953 2.380410 CCGTGGACGCACAGTTAGC 61.380 63.158 0.00 0.00 38.18 3.09
1046 1056 2.743928 GTCCAGGCTTGTCTGCGG 60.744 66.667 0.00 0.00 33.64 5.69
1233 1243 0.946221 CCACGCTGAAGCTTCTTCGT 60.946 55.000 28.09 28.09 39.32 3.85
1260 1270 4.870221 TCATTCTCAAGTTGATGATGCG 57.130 40.909 17.46 3.37 0.00 4.73
1333 1343 0.178973 TGGTGACGGAGAGAAGGACA 60.179 55.000 0.00 0.00 0.00 4.02
1444 1458 7.656707 AAAACAGCTAATGGTTTTTATGCTG 57.343 32.000 10.01 10.01 46.96 4.41
1554 1568 4.084287 AGATCATCAACCACACAAAGCAT 58.916 39.130 0.00 0.00 0.00 3.79
1557 1571 2.064434 TCAACCACACAAAGCATCCA 57.936 45.000 0.00 0.00 0.00 3.41
1563 1577 3.091545 CCACACAAAGCATCCAAGGTAT 58.908 45.455 0.00 0.00 0.00 2.73
1565 1579 4.096382 CCACACAAAGCATCCAAGGTATAC 59.904 45.833 0.00 0.00 0.00 1.47
1569 1583 5.415701 CACAAAGCATCCAAGGTATACAAGT 59.584 40.000 5.01 0.00 0.00 3.16
1570 1584 6.597672 CACAAAGCATCCAAGGTATACAAGTA 59.402 38.462 5.01 0.00 0.00 2.24
1571 1585 6.823689 ACAAAGCATCCAAGGTATACAAGTAG 59.176 38.462 5.01 0.00 0.00 2.57
1572 1586 6.808321 AAGCATCCAAGGTATACAAGTAGA 57.192 37.500 5.01 0.00 0.00 2.59
1573 1587 7.380423 AAGCATCCAAGGTATACAAGTAGAT 57.620 36.000 5.01 0.00 0.00 1.98
1574 1588 8.492415 AAGCATCCAAGGTATACAAGTAGATA 57.508 34.615 5.01 0.00 0.00 1.98
1575 1589 8.671987 AGCATCCAAGGTATACAAGTAGATAT 57.328 34.615 5.01 0.00 0.00 1.63
1576 1590 9.769677 AGCATCCAAGGTATACAAGTAGATATA 57.230 33.333 5.01 0.00 0.00 0.86
1577 1591 9.804758 GCATCCAAGGTATACAAGTAGATATAC 57.195 37.037 5.01 0.00 34.72 1.47
1579 1593 8.048534 TCCAAGGTATACAAGTAGATATACGC 57.951 38.462 5.01 0.00 35.82 4.42
1580 1594 7.666804 TCCAAGGTATACAAGTAGATATACGCA 59.333 37.037 5.01 0.00 35.82 5.24
1581 1595 8.467598 CCAAGGTATACAAGTAGATATACGCAT 58.532 37.037 5.01 0.00 35.82 4.73
1593 1607 9.878599 AGTAGATATACGCATAATTTTTGTTGC 57.121 29.630 0.00 0.00 0.00 4.17
1603 1617 8.334016 GCATAATTTTTGTTGCGTATACATCA 57.666 30.769 3.32 0.00 0.00 3.07
1604 1618 8.802856 GCATAATTTTTGTTGCGTATACATCAA 58.197 29.630 3.32 3.76 0.00 2.57
1609 1623 8.667987 TTTTTGTTGCGTATACATCAAAGATC 57.332 30.769 3.32 0.00 39.26 2.75
1616 1664 7.408910 TGCGTATACATCAAAGATCACAAATG 58.591 34.615 3.32 0.00 0.00 2.32
1659 1707 1.602377 GTGGTACAACAACTCACTGGC 59.398 52.381 0.00 0.00 44.16 4.85
1660 1708 0.865769 GGTACAACAACTCACTGGCG 59.134 55.000 0.00 0.00 0.00 5.69
1667 1715 0.738389 CAACTCACTGGCGTGGTTTT 59.262 50.000 9.05 0.00 41.53 2.43
1672 1720 0.527385 CACTGGCGTGGTTTTGGTTG 60.527 55.000 2.23 0.00 37.50 3.77
2027 2075 1.142097 GCGGGAGACTTGGCTACTC 59.858 63.158 0.00 0.00 0.00 2.59
2064 2112 1.069978 TGATCAGCTGTTTGACGTGGA 59.930 47.619 14.67 0.00 0.00 4.02
2095 2143 2.036572 TTGGATTTGGGGACGGCC 59.963 61.111 0.00 0.00 0.00 6.13
2147 2195 4.871933 CAAAAGTTTGGAGGCTGGTAAT 57.128 40.909 0.00 0.00 34.59 1.89
2158 2206 9.487442 TTTGGAGGCTGGTAATAATAAAATTCT 57.513 29.630 0.00 0.00 0.00 2.40
2183 2231 5.097742 TCACGTCCATGGATGAGTTAAAT 57.902 39.130 35.58 12.52 35.30 1.40
2184 2232 6.228616 TCACGTCCATGGATGAGTTAAATA 57.771 37.500 35.58 11.76 35.30 1.40
2185 2233 6.280643 TCACGTCCATGGATGAGTTAAATAG 58.719 40.000 35.58 14.87 35.30 1.73
2186 2234 6.049149 CACGTCCATGGATGAGTTAAATAGT 58.951 40.000 35.58 10.39 35.30 2.12
2187 2235 6.201044 CACGTCCATGGATGAGTTAAATAGTC 59.799 42.308 35.58 9.76 35.30 2.59
2188 2236 5.402568 CGTCCATGGATGAGTTAAATAGTCG 59.597 44.000 27.27 12.17 33.22 4.18
2189 2237 6.513180 GTCCATGGATGAGTTAAATAGTCGA 58.487 40.000 19.62 0.00 0.00 4.20
2190 2238 7.155328 GTCCATGGATGAGTTAAATAGTCGAT 58.845 38.462 19.62 0.00 0.00 3.59
2191 2239 8.304596 GTCCATGGATGAGTTAAATAGTCGATA 58.695 37.037 19.62 0.00 0.00 2.92
2192 2240 8.304596 TCCATGGATGAGTTAAATAGTCGATAC 58.695 37.037 11.44 0.00 0.00 2.24
2193 2241 7.273598 CCATGGATGAGTTAAATAGTCGATACG 59.726 40.741 5.56 0.00 0.00 3.06
2194 2242 7.268199 TGGATGAGTTAAATAGTCGATACGT 57.732 36.000 0.00 0.00 0.00 3.57
2195 2243 7.136772 TGGATGAGTTAAATAGTCGATACGTG 58.863 38.462 0.00 0.00 0.00 4.49
2196 2244 7.012610 TGGATGAGTTAAATAGTCGATACGTGA 59.987 37.037 0.00 0.00 0.00 4.35
2197 2245 7.859377 GGATGAGTTAAATAGTCGATACGTGAA 59.141 37.037 0.00 0.00 0.00 3.18
2198 2246 9.229784 GATGAGTTAAATAGTCGATACGTGAAA 57.770 33.333 0.00 0.00 0.00 2.69
2199 2247 8.969121 TGAGTTAAATAGTCGATACGTGAAAA 57.031 30.769 0.00 0.00 0.00 2.29
2200 2248 8.853345 TGAGTTAAATAGTCGATACGTGAAAAC 58.147 33.333 0.00 0.00 0.00 2.43
2201 2249 8.746922 AGTTAAATAGTCGATACGTGAAAACA 57.253 30.769 0.00 0.00 0.00 2.83
2202 2250 9.362539 AGTTAAATAGTCGATACGTGAAAACAT 57.637 29.630 0.00 0.00 0.00 2.71
2203 2251 9.405083 GTTAAATAGTCGATACGTGAAAACATG 57.595 33.333 0.00 0.00 0.00 3.21
2204 2252 7.591006 AAATAGTCGATACGTGAAAACATGT 57.409 32.000 0.00 0.00 0.00 3.21
2205 2253 7.591006 AATAGTCGATACGTGAAAACATGTT 57.409 32.000 4.92 4.92 0.00 2.71
2206 2254 5.264060 AGTCGATACGTGAAAACATGTTG 57.736 39.130 12.82 1.26 0.00 3.33
2207 2255 4.748102 AGTCGATACGTGAAAACATGTTGT 59.252 37.500 12.82 6.37 0.00 3.32
2208 2256 4.838642 GTCGATACGTGAAAACATGTTGTG 59.161 41.667 12.82 3.25 0.00 3.33
2209 2257 4.508492 TCGATACGTGAAAACATGTTGTGT 59.492 37.500 12.82 8.93 44.84 3.72
2210 2258 5.690857 TCGATACGTGAAAACATGTTGTGTA 59.309 36.000 12.82 10.72 41.14 2.90
2211 2259 6.200475 TCGATACGTGAAAACATGTTGTGTAA 59.800 34.615 12.82 0.00 41.14 2.41
2212 2260 6.515002 CGATACGTGAAAACATGTTGTGTAAG 59.485 38.462 12.82 5.37 41.14 2.34
2213 2261 4.347813 ACGTGAAAACATGTTGTGTAAGC 58.652 39.130 12.82 0.00 41.14 3.09
2214 2262 4.142578 ACGTGAAAACATGTTGTGTAAGCA 60.143 37.500 12.82 0.00 41.14 3.91
2215 2263 4.975502 CGTGAAAACATGTTGTGTAAGCAT 59.024 37.500 12.82 0.00 41.14 3.79
2216 2264 5.115472 CGTGAAAACATGTTGTGTAAGCATC 59.885 40.000 12.82 1.15 41.14 3.91
2217 2265 6.208644 GTGAAAACATGTTGTGTAAGCATCT 58.791 36.000 12.82 0.00 41.14 2.90
2218 2266 6.697019 GTGAAAACATGTTGTGTAAGCATCTT 59.303 34.615 12.82 0.00 41.14 2.40
2219 2267 7.222611 GTGAAAACATGTTGTGTAAGCATCTTT 59.777 33.333 12.82 0.00 41.14 2.52
2220 2268 8.409371 TGAAAACATGTTGTGTAAGCATCTTTA 58.591 29.630 12.82 0.00 41.14 1.85
2221 2269 9.410556 GAAAACATGTTGTGTAAGCATCTTTAT 57.589 29.630 12.82 0.00 41.14 1.40
2222 2270 9.762933 AAAACATGTTGTGTAAGCATCTTTATT 57.237 25.926 12.82 0.00 41.14 1.40
2223 2271 9.762933 AAACATGTTGTGTAAGCATCTTTATTT 57.237 25.926 12.82 0.00 41.14 1.40
2224 2272 9.762933 AACATGTTGTGTAAGCATCTTTATTTT 57.237 25.926 11.07 0.00 41.14 1.82
2225 2273 9.195411 ACATGTTGTGTAAGCATCTTTATTTTG 57.805 29.630 0.00 0.00 39.91 2.44
2226 2274 9.195411 CATGTTGTGTAAGCATCTTTATTTTGT 57.805 29.630 0.00 0.00 0.00 2.83
2241 2289 9.511272 TCTTTATTTTGTAAAAGTACTCTCCCC 57.489 33.333 0.00 0.00 34.88 4.81
2242 2290 7.910441 TTATTTTGTAAAAGTACTCTCCCCG 57.090 36.000 0.00 0.00 0.00 5.73
2243 2291 4.961438 TTTGTAAAAGTACTCTCCCCGT 57.039 40.909 0.00 0.00 0.00 5.28
2244 2292 4.961438 TTGTAAAAGTACTCTCCCCGTT 57.039 40.909 0.00 0.00 0.00 4.44
2245 2293 4.961438 TGTAAAAGTACTCTCCCCGTTT 57.039 40.909 0.00 0.00 0.00 3.60
2246 2294 6.418057 TTGTAAAAGTACTCTCCCCGTTTA 57.582 37.500 0.00 0.00 0.00 2.01
2247 2295 5.783111 TGTAAAAGTACTCTCCCCGTTTAC 58.217 41.667 13.53 13.53 32.95 2.01
2248 2296 4.961438 AAAAGTACTCTCCCCGTTTACA 57.039 40.909 0.00 0.00 0.00 2.41
2249 2297 4.961438 AAAGTACTCTCCCCGTTTACAA 57.039 40.909 0.00 0.00 0.00 2.41
2250 2298 4.961438 AAGTACTCTCCCCGTTTACAAA 57.039 40.909 0.00 0.00 0.00 2.83
2251 2299 4.263018 AGTACTCTCCCCGTTTACAAAC 57.737 45.455 0.00 0.00 35.59 2.93
2252 2300 3.642848 AGTACTCTCCCCGTTTACAAACA 59.357 43.478 5.74 0.00 38.81 2.83
2253 2301 3.782656 ACTCTCCCCGTTTACAAACAT 57.217 42.857 5.74 0.00 38.81 2.71
2254 2302 4.895668 ACTCTCCCCGTTTACAAACATA 57.104 40.909 5.74 0.00 38.81 2.29
2255 2303 5.231702 ACTCTCCCCGTTTACAAACATAA 57.768 39.130 5.74 0.00 38.81 1.90
2256 2304 5.243207 ACTCTCCCCGTTTACAAACATAAG 58.757 41.667 5.74 0.00 38.81 1.73
2257 2305 5.012354 ACTCTCCCCGTTTACAAACATAAGA 59.988 40.000 5.74 2.24 38.81 2.10
2258 2306 6.057321 TCTCCCCGTTTACAAACATAAGAT 57.943 37.500 5.74 0.00 38.81 2.40
2259 2307 7.093201 ACTCTCCCCGTTTACAAACATAAGATA 60.093 37.037 5.74 0.00 38.81 1.98
2260 2308 7.798071 TCTCCCCGTTTACAAACATAAGATAT 58.202 34.615 5.74 0.00 38.81 1.63
2261 2309 8.269317 TCTCCCCGTTTACAAACATAAGATATT 58.731 33.333 5.74 0.00 38.81 1.28
2262 2310 8.810990 TCCCCGTTTACAAACATAAGATATTT 57.189 30.769 5.74 0.00 38.81 1.40
2263 2311 9.245481 TCCCCGTTTACAAACATAAGATATTTT 57.755 29.630 5.74 0.00 38.81 1.82
2264 2312 9.296400 CCCCGTTTACAAACATAAGATATTTTG 57.704 33.333 5.74 0.00 38.81 2.44
2265 2313 9.296400 CCCGTTTACAAACATAAGATATTTTGG 57.704 33.333 5.74 0.00 38.81 3.28
2303 2351 8.783093 TGGATTATCAAAATTGCTATTCCTACG 58.217 33.333 14.25 0.00 33.65 3.51
2304 2352 8.237267 GGATTATCAAAATTGCTATTCCTACGG 58.763 37.037 9.21 0.00 31.56 4.02
2305 2353 8.918202 ATTATCAAAATTGCTATTCCTACGGA 57.082 30.769 0.00 0.00 0.00 4.69
2306 2354 8.918202 TTATCAAAATTGCTATTCCTACGGAT 57.082 30.769 0.00 0.00 0.00 4.18
2308 2356 8.918202 ATCAAAATTGCTATTCCTACGGATAA 57.082 30.769 0.00 0.00 0.00 1.75
2309 2357 8.149973 TCAAAATTGCTATTCCTACGGATAAC 57.850 34.615 0.00 0.00 0.00 1.89
2310 2358 7.990886 TCAAAATTGCTATTCCTACGGATAACT 59.009 33.333 0.00 0.00 0.00 2.24
2311 2359 8.621286 CAAAATTGCTATTCCTACGGATAACTT 58.379 33.333 0.00 0.00 0.00 2.66
2312 2360 7.964604 AATTGCTATTCCTACGGATAACTTC 57.035 36.000 0.00 0.00 0.00 3.01
2313 2361 6.726490 TTGCTATTCCTACGGATAACTTCT 57.274 37.500 0.00 0.00 0.00 2.85
2314 2362 7.828508 TTGCTATTCCTACGGATAACTTCTA 57.171 36.000 0.00 0.00 0.00 2.10
2315 2363 7.211966 TGCTATTCCTACGGATAACTTCTAC 57.788 40.000 0.00 0.00 0.00 2.59
2316 2364 6.072838 TGCTATTCCTACGGATAACTTCTACG 60.073 42.308 0.00 0.00 0.00 3.51
2317 2365 6.148480 GCTATTCCTACGGATAACTTCTACGA 59.852 42.308 0.00 0.00 0.00 3.43
2318 2366 6.949352 ATTCCTACGGATAACTTCTACGAA 57.051 37.500 0.00 0.00 0.00 3.85
2319 2367 6.757897 TTCCTACGGATAACTTCTACGAAA 57.242 37.500 0.00 0.00 0.00 3.46
2320 2368 6.757897 TCCTACGGATAACTTCTACGAAAA 57.242 37.500 0.00 0.00 0.00 2.29
2321 2369 6.555315 TCCTACGGATAACTTCTACGAAAAC 58.445 40.000 0.00 0.00 0.00 2.43
2322 2370 6.375455 TCCTACGGATAACTTCTACGAAAACT 59.625 38.462 0.00 0.00 0.00 2.66
2323 2371 7.031975 CCTACGGATAACTTCTACGAAAACTT 58.968 38.462 0.00 0.00 0.00 2.66
2324 2372 7.543520 CCTACGGATAACTTCTACGAAAACTTT 59.456 37.037 0.00 0.00 0.00 2.66
2325 2373 9.559958 CTACGGATAACTTCTACGAAAACTTTA 57.440 33.333 0.00 0.00 0.00 1.85
2326 2374 8.232497 ACGGATAACTTCTACGAAAACTTTAC 57.768 34.615 0.00 0.00 0.00 2.01
2327 2375 7.867403 ACGGATAACTTCTACGAAAACTTTACA 59.133 33.333 0.00 0.00 0.00 2.41
2328 2376 8.866956 CGGATAACTTCTACGAAAACTTTACAT 58.133 33.333 0.00 0.00 0.00 2.29
2332 2380 7.274442 ACTTCTACGAAAACTTTACATAGCG 57.726 36.000 0.00 0.00 0.00 4.26
2333 2381 6.865205 ACTTCTACGAAAACTTTACATAGCGT 59.135 34.615 0.00 0.00 34.86 5.07
2334 2382 6.621737 TCTACGAAAACTTTACATAGCGTG 57.378 37.500 0.00 0.00 32.62 5.34
2335 2383 4.061570 ACGAAAACTTTACATAGCGTGC 57.938 40.909 0.00 0.00 0.00 5.34
2336 2384 3.081445 CGAAAACTTTACATAGCGTGCG 58.919 45.455 0.00 0.00 0.00 5.34
2337 2385 3.422603 CGAAAACTTTACATAGCGTGCGT 60.423 43.478 0.00 0.00 0.00 5.24
2338 2386 3.449322 AAACTTTACATAGCGTGCGTG 57.551 42.857 0.00 0.00 0.00 5.34
2339 2387 2.357327 ACTTTACATAGCGTGCGTGA 57.643 45.000 7.17 0.00 0.00 4.35
2340 2388 2.259618 ACTTTACATAGCGTGCGTGAG 58.740 47.619 7.17 0.00 0.00 3.51
2341 2389 2.094906 ACTTTACATAGCGTGCGTGAGA 60.095 45.455 7.17 0.00 0.00 3.27
2342 2390 2.188837 TTACATAGCGTGCGTGAGAG 57.811 50.000 7.17 0.00 0.00 3.20
2343 2391 1.375551 TACATAGCGTGCGTGAGAGA 58.624 50.000 7.17 0.00 0.00 3.10
2344 2392 0.099613 ACATAGCGTGCGTGAGAGAG 59.900 55.000 7.17 0.00 0.00 3.20
2345 2393 0.593518 CATAGCGTGCGTGAGAGAGG 60.594 60.000 0.00 0.00 0.00 3.69
2346 2394 2.343163 ATAGCGTGCGTGAGAGAGGC 62.343 60.000 0.00 0.00 35.92 4.70
2347 2395 4.724602 GCGTGCGTGAGAGAGGCA 62.725 66.667 0.00 0.00 43.15 4.75
2348 2396 2.505777 CGTGCGTGAGAGAGGCAG 60.506 66.667 0.00 0.00 45.88 4.85
2349 2397 2.653702 GTGCGTGAGAGAGGCAGT 59.346 61.111 0.00 0.00 45.88 4.40
2350 2398 1.883732 GTGCGTGAGAGAGGCAGTA 59.116 57.895 0.00 0.00 45.88 2.74
2351 2399 0.243907 GTGCGTGAGAGAGGCAGTAA 59.756 55.000 0.00 0.00 45.88 2.24
2352 2400 0.243907 TGCGTGAGAGAGGCAGTAAC 59.756 55.000 0.00 0.00 40.53 2.50
2353 2401 0.458716 GCGTGAGAGAGGCAGTAACC 60.459 60.000 0.00 0.00 35.42 2.85
2354 2402 0.179161 CGTGAGAGAGGCAGTAACCG 60.179 60.000 0.00 0.00 33.69 4.44
2355 2403 0.889306 GTGAGAGAGGCAGTAACCGT 59.111 55.000 0.00 0.00 33.69 4.83
2356 2404 1.272769 GTGAGAGAGGCAGTAACCGTT 59.727 52.381 0.00 0.00 33.69 4.44
2357 2405 2.490903 GTGAGAGAGGCAGTAACCGTTA 59.509 50.000 0.00 0.00 33.69 3.18
2358 2406 3.130693 GTGAGAGAGGCAGTAACCGTTAT 59.869 47.826 0.00 0.00 33.69 1.89
2359 2407 3.130516 TGAGAGAGGCAGTAACCGTTATG 59.869 47.826 0.00 0.00 33.69 1.90
2360 2408 3.362706 AGAGAGGCAGTAACCGTTATGA 58.637 45.455 0.00 0.00 33.69 2.15
2361 2409 3.381908 AGAGAGGCAGTAACCGTTATGAG 59.618 47.826 0.00 0.00 33.69 2.90
2362 2410 3.362706 AGAGGCAGTAACCGTTATGAGA 58.637 45.455 0.00 0.00 33.69 3.27
2363 2411 3.767673 AGAGGCAGTAACCGTTATGAGAA 59.232 43.478 0.00 0.00 33.69 2.87
2364 2412 4.222145 AGAGGCAGTAACCGTTATGAGAAA 59.778 41.667 0.00 0.00 33.69 2.52
2365 2413 4.901868 AGGCAGTAACCGTTATGAGAAAA 58.098 39.130 0.00 0.00 33.69 2.29
2366 2414 5.310451 AGGCAGTAACCGTTATGAGAAAAA 58.690 37.500 0.00 0.00 33.69 1.94
2384 2432 4.882842 AAAAACAAGGGAATAACGGCAT 57.117 36.364 0.00 0.00 0.00 4.40
2385 2433 4.450082 AAAACAAGGGAATAACGGCATC 57.550 40.909 0.00 0.00 0.00 3.91
2386 2434 1.663695 ACAAGGGAATAACGGCATCG 58.336 50.000 0.00 0.00 43.02 3.84
2387 2435 0.944386 CAAGGGAATAACGGCATCGG 59.056 55.000 0.00 0.00 41.39 4.18
2388 2436 0.834612 AAGGGAATAACGGCATCGGA 59.165 50.000 0.00 0.00 41.39 4.55
2389 2437 1.056660 AGGGAATAACGGCATCGGAT 58.943 50.000 0.00 0.00 41.39 4.18
2390 2438 1.420138 AGGGAATAACGGCATCGGATT 59.580 47.619 0.00 0.00 41.39 3.01
2391 2439 2.158667 AGGGAATAACGGCATCGGATTT 60.159 45.455 0.00 0.00 41.39 2.17
2392 2440 2.621526 GGGAATAACGGCATCGGATTTT 59.378 45.455 0.00 0.00 41.39 1.82
2393 2441 3.067601 GGGAATAACGGCATCGGATTTTT 59.932 43.478 0.00 0.00 41.39 1.94
2394 2442 4.041723 GGAATAACGGCATCGGATTTTTG 58.958 43.478 0.00 0.00 41.39 2.44
2395 2443 3.708563 ATAACGGCATCGGATTTTTGG 57.291 42.857 0.00 0.00 41.39 3.28
2396 2444 0.108851 AACGGCATCGGATTTTTGGC 60.109 50.000 0.00 0.00 41.39 4.52
2397 2445 0.965363 ACGGCATCGGATTTTTGGCT 60.965 50.000 2.12 0.00 41.39 4.75
2398 2446 0.248621 CGGCATCGGATTTTTGGCTC 60.249 55.000 2.12 0.00 34.08 4.70
2399 2447 1.106285 GGCATCGGATTTTTGGCTCT 58.894 50.000 0.00 0.00 33.51 4.09
2400 2448 1.202336 GGCATCGGATTTTTGGCTCTG 60.202 52.381 0.00 0.00 33.51 3.35
2401 2449 1.202336 GCATCGGATTTTTGGCTCTGG 60.202 52.381 0.00 0.00 0.00 3.86
2402 2450 2.368439 CATCGGATTTTTGGCTCTGGA 58.632 47.619 0.00 0.00 0.00 3.86
2403 2451 2.577606 TCGGATTTTTGGCTCTGGAA 57.422 45.000 0.00 0.00 0.00 3.53
2404 2452 2.870175 TCGGATTTTTGGCTCTGGAAA 58.130 42.857 0.00 0.00 0.00 3.13
2405 2453 2.556622 TCGGATTTTTGGCTCTGGAAAC 59.443 45.455 0.00 0.00 0.00 2.78
2406 2454 2.295909 CGGATTTTTGGCTCTGGAAACA 59.704 45.455 0.00 0.00 39.59 2.83
2407 2455 3.056607 CGGATTTTTGGCTCTGGAAACAT 60.057 43.478 0.00 0.00 41.51 2.71
2408 2456 4.157656 CGGATTTTTGGCTCTGGAAACATA 59.842 41.667 0.00 0.00 41.51 2.29
2409 2457 5.163519 CGGATTTTTGGCTCTGGAAACATAT 60.164 40.000 0.00 0.00 41.51 1.78
2410 2458 6.039270 CGGATTTTTGGCTCTGGAAACATATA 59.961 38.462 0.00 0.00 41.51 0.86
2411 2459 7.203218 GGATTTTTGGCTCTGGAAACATATAC 58.797 38.462 0.00 0.00 41.51 1.47
2412 2460 7.068716 GGATTTTTGGCTCTGGAAACATATACT 59.931 37.037 0.00 0.00 41.51 2.12
2413 2461 7.391148 TTTTTGGCTCTGGAAACATATACTC 57.609 36.000 0.00 0.00 41.51 2.59
2414 2462 5.957771 TTGGCTCTGGAAACATATACTCT 57.042 39.130 0.00 0.00 41.51 3.24
2415 2463 5.537300 TGGCTCTGGAAACATATACTCTC 57.463 43.478 0.00 0.00 41.51 3.20
2416 2464 4.038042 TGGCTCTGGAAACATATACTCTCG 59.962 45.833 0.00 0.00 41.51 4.04
2417 2465 4.551388 GCTCTGGAAACATATACTCTCGG 58.449 47.826 0.00 0.00 41.51 4.63
2418 2466 4.278669 GCTCTGGAAACATATACTCTCGGA 59.721 45.833 0.00 0.00 41.51 4.55
2419 2467 5.047660 GCTCTGGAAACATATACTCTCGGAT 60.048 44.000 0.00 0.00 41.51 4.18
2420 2468 6.151312 GCTCTGGAAACATATACTCTCGGATA 59.849 42.308 0.00 0.00 41.51 2.59
2421 2469 7.309255 GCTCTGGAAACATATACTCTCGGATAA 60.309 40.741 0.00 0.00 41.51 1.75
2422 2470 7.883217 TCTGGAAACATATACTCTCGGATAAC 58.117 38.462 0.00 0.00 41.51 1.89
2423 2471 7.504574 TCTGGAAACATATACTCTCGGATAACA 59.495 37.037 0.00 0.00 41.51 2.41
2424 2472 7.658261 TGGAAACATATACTCTCGGATAACAG 58.342 38.462 0.00 0.00 33.40 3.16
2425 2473 7.287005 TGGAAACATATACTCTCGGATAACAGT 59.713 37.037 0.00 0.00 33.40 3.55
2426 2474 8.790718 GGAAACATATACTCTCGGATAACAGTA 58.209 37.037 0.00 0.00 0.00 2.74
2435 2483 8.842358 ACTCTCGGATAACAGTAAAAATCAAA 57.158 30.769 0.00 0.00 0.00 2.69
2436 2484 9.280174 ACTCTCGGATAACAGTAAAAATCAAAA 57.720 29.630 0.00 0.00 0.00 2.44
2484 2532 3.760035 GCGTCGCTCTTCAGGGGA 61.760 66.667 10.68 0.00 33.28 4.81
2538 2589 2.040043 CCCCTCATGCTCCCTCCT 60.040 66.667 0.00 0.00 0.00 3.69
2769 2820 1.006519 CCCTCCTCTCTGTCTTCCTCA 59.993 57.143 0.00 0.00 0.00 3.86
2832 2883 1.012841 CTTTTCTGCTCGGATCTGGC 58.987 55.000 0.62 4.93 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 55 6.824305 AATTGTGCCCATATTCTAGTATGC 57.176 37.500 0.00 0.00 32.03 3.14
229 238 5.584251 ACAATTTTCCATGAACCACAACAAC 59.416 36.000 0.00 0.00 0.00 3.32
233 242 4.701765 CCACAATTTTCCATGAACCACAA 58.298 39.130 0.00 0.00 0.00 3.33
242 251 5.065235 CCTTCTTTTGCCACAATTTTCCAT 58.935 37.500 0.00 0.00 0.00 3.41
251 260 1.398958 GGCCACCTTCTTTTGCCACA 61.399 55.000 0.00 0.00 41.76 4.17
331 340 8.710551 TGTACTGTAATTAACACGTTTACATGG 58.289 33.333 9.54 3.52 35.82 3.66
380 389 2.124011 AATTGGAATAGCGCGCATTG 57.876 45.000 35.10 0.00 0.00 2.82
421 430 5.863935 TCGTTTTCATCCATATATGAGCTCG 59.136 40.000 14.54 7.70 37.20 5.03
531 540 1.394917 GCAATCTCATGTCACCACGAC 59.605 52.381 0.00 0.00 45.61 4.34
533 542 0.729116 GGCAATCTCATGTCACCACG 59.271 55.000 0.00 0.00 0.00 4.94
592 602 7.652105 TCCATCGTGCTCAAGAGTTAATTATAC 59.348 37.037 0.00 0.00 0.00 1.47
682 692 4.315803 TCATCTCTATGAGTGCATGCATG 58.684 43.478 25.64 22.70 37.20 4.06
683 693 4.618920 TCATCTCTATGAGTGCATGCAT 57.381 40.909 25.64 12.95 37.20 3.96
684 694 4.411256 TTCATCTCTATGAGTGCATGCA 57.589 40.909 18.46 18.46 42.97 3.96
685 695 5.469084 TGATTTCATCTCTATGAGTGCATGC 59.531 40.000 11.82 11.82 42.97 4.06
792 802 2.520536 GGGTCAGGGGATGGATCGG 61.521 68.421 0.00 0.00 0.00 4.18
943 953 5.008514 TCGATCTCAGAGTCAGATTAAGCAG 59.991 44.000 0.00 0.00 30.30 4.24
1233 1243 6.212888 TCATCAACTTGAGAATGATCGAGA 57.787 37.500 0.00 0.00 0.00 4.04
1314 1324 0.178973 TGTCCTTCTCTCCGTCACCA 60.179 55.000 0.00 0.00 0.00 4.17
1333 1343 2.680913 GCTTGGCATTGTCGTCGCT 61.681 57.895 0.00 0.00 0.00 4.93
1444 1458 0.747255 TCGGCTAATCTCCTGCTCAC 59.253 55.000 0.00 0.00 0.00 3.51
1554 1568 7.666804 TGCGTATATCTACTTGTATACCTTGGA 59.333 37.037 0.00 0.00 32.63 3.53
1578 1592 8.334016 TGATGTATACGCAACAAAAATTATGC 57.666 30.769 0.00 0.00 35.49 3.14
1582 1596 9.638239 ATCTTTGATGTATACGCAACAAAAATT 57.362 25.926 9.66 1.49 39.45 1.82
1583 1597 9.289303 GATCTTTGATGTATACGCAACAAAAAT 57.711 29.630 9.66 6.49 39.45 1.82
1584 1598 8.293157 TGATCTTTGATGTATACGCAACAAAAA 58.707 29.630 9.66 2.78 39.45 1.94
1585 1599 7.748683 GTGATCTTTGATGTATACGCAACAAAA 59.251 33.333 9.66 6.14 39.45 2.44
1586 1600 7.095017 TGTGATCTTTGATGTATACGCAACAAA 60.095 33.333 9.66 11.22 38.30 2.83
1587 1601 6.370166 TGTGATCTTTGATGTATACGCAACAA 59.630 34.615 9.66 5.48 30.98 2.83
1588 1602 5.872070 TGTGATCTTTGATGTATACGCAACA 59.128 36.000 9.66 3.52 0.00 3.33
1589 1603 6.344572 TGTGATCTTTGATGTATACGCAAC 57.655 37.500 9.66 1.43 0.00 4.17
1590 1604 6.976636 TTGTGATCTTTGATGTATACGCAA 57.023 33.333 6.83 6.83 0.00 4.85
1591 1605 6.976636 TTTGTGATCTTTGATGTATACGCA 57.023 33.333 0.00 0.00 0.00 5.24
1592 1606 6.852853 CCATTTGTGATCTTTGATGTATACGC 59.147 38.462 0.00 0.00 0.00 4.42
1593 1607 8.141835 TCCATTTGTGATCTTTGATGTATACG 57.858 34.615 0.00 0.00 0.00 3.06
1596 1610 9.811995 CATTTCCATTTGTGATCTTTGATGTAT 57.188 29.630 0.00 0.00 0.00 2.29
1597 1611 7.760794 GCATTTCCATTTGTGATCTTTGATGTA 59.239 33.333 0.00 0.00 0.00 2.29
1598 1612 6.592607 GCATTTCCATTTGTGATCTTTGATGT 59.407 34.615 0.00 0.00 0.00 3.06
1599 1613 6.592220 TGCATTTCCATTTGTGATCTTTGATG 59.408 34.615 0.00 0.00 0.00 3.07
1600 1614 6.703319 TGCATTTCCATTTGTGATCTTTGAT 58.297 32.000 0.00 0.00 0.00 2.57
1601 1615 6.099159 TGCATTTCCATTTGTGATCTTTGA 57.901 33.333 0.00 0.00 0.00 2.69
1602 1616 6.788684 TTGCATTTCCATTTGTGATCTTTG 57.211 33.333 0.00 0.00 0.00 2.77
1603 1617 7.804843 TTTTGCATTTCCATTTGTGATCTTT 57.195 28.000 0.00 0.00 0.00 2.52
1604 1618 7.716123 TCTTTTTGCATTTCCATTTGTGATCTT 59.284 29.630 0.00 0.00 0.00 2.40
1609 1623 8.016801 GGTATTCTTTTTGCATTTCCATTTGTG 58.983 33.333 0.00 0.00 0.00 3.33
1616 1664 6.089417 CACGAAGGTATTCTTTTTGCATTTCC 59.911 38.462 0.00 0.00 35.50 3.13
1659 1707 0.030638 CCTGCTCAACCAAAACCACG 59.969 55.000 0.00 0.00 0.00 4.94
1660 1708 1.338020 CTCCTGCTCAACCAAAACCAC 59.662 52.381 0.00 0.00 0.00 4.16
1667 1715 3.236047 TGTAGTAACTCCTGCTCAACCA 58.764 45.455 0.00 0.00 0.00 3.67
1672 1720 4.093556 GTGCATTTGTAGTAACTCCTGCTC 59.906 45.833 0.00 0.00 0.00 4.26
1973 2021 2.995872 AACTGCTCTCGAGGGACGC 61.996 63.158 18.81 12.70 42.26 5.19
1974 2022 1.153939 CAACTGCTCTCGAGGGACG 60.154 63.158 18.81 8.19 44.09 4.79
1975 2023 1.446966 GCAACTGCTCTCGAGGGAC 60.447 63.158 18.81 8.21 38.21 4.46
2002 2050 1.811266 CAAGTCTCCCGCCATGTCG 60.811 63.158 0.00 0.00 0.00 4.35
2027 2075 3.452264 TGATCATACTGGTTCACCTCTGG 59.548 47.826 0.00 0.00 36.82 3.86
2064 2112 1.161843 ATCCAACGGCGAAAACGAAT 58.838 45.000 16.62 0.00 34.93 3.34
2095 2143 2.202797 CTCACATCCGTCGCCCAG 60.203 66.667 0.00 0.00 0.00 4.45
2103 2151 3.274586 CATGCCCGCTCACATCCG 61.275 66.667 0.00 0.00 0.00 4.18
2147 2195 7.990314 TCCATGGACGTGATCAGAATTTTATTA 59.010 33.333 11.44 0.00 0.00 0.98
2158 2206 2.110578 ACTCATCCATGGACGTGATCA 58.889 47.619 18.99 0.00 0.00 2.92
2168 2216 7.808381 ACGTATCGACTATTTAACTCATCCATG 59.192 37.037 0.00 0.00 0.00 3.66
2183 2231 5.921976 ACAACATGTTTTCACGTATCGACTA 59.078 36.000 8.77 0.00 0.00 2.59
2184 2232 4.748102 ACAACATGTTTTCACGTATCGACT 59.252 37.500 8.77 0.00 0.00 4.18
2185 2233 4.838642 CACAACATGTTTTCACGTATCGAC 59.161 41.667 8.77 0.00 0.00 4.20
2186 2234 4.508492 ACACAACATGTTTTCACGTATCGA 59.492 37.500 8.77 0.00 38.98 3.59
2187 2235 4.768145 ACACAACATGTTTTCACGTATCG 58.232 39.130 8.77 0.00 38.98 2.92
2188 2236 6.302313 GCTTACACAACATGTTTTCACGTATC 59.698 38.462 8.77 0.00 43.19 2.24
2189 2237 6.140110 GCTTACACAACATGTTTTCACGTAT 58.860 36.000 8.77 0.00 43.19 3.06
2190 2238 5.064834 TGCTTACACAACATGTTTTCACGTA 59.935 36.000 8.77 3.59 43.19 3.57
2191 2239 4.142578 TGCTTACACAACATGTTTTCACGT 60.143 37.500 8.77 0.00 43.19 4.49
2192 2240 4.346970 TGCTTACACAACATGTTTTCACG 58.653 39.130 8.77 0.00 43.19 4.35
2193 2241 6.208644 AGATGCTTACACAACATGTTTTCAC 58.791 36.000 8.77 0.00 43.19 3.18
2194 2242 6.389830 AGATGCTTACACAACATGTTTTCA 57.610 33.333 8.77 0.00 43.19 2.69
2195 2243 7.698836 AAAGATGCTTACACAACATGTTTTC 57.301 32.000 8.77 0.00 43.19 2.29
2196 2244 9.762933 AATAAAGATGCTTACACAACATGTTTT 57.237 25.926 8.77 0.00 43.19 2.43
2197 2245 9.762933 AAATAAAGATGCTTACACAACATGTTT 57.237 25.926 8.77 0.00 43.19 2.83
2198 2246 9.762933 AAAATAAAGATGCTTACACAACATGTT 57.237 25.926 4.92 4.92 43.19 2.71
2199 2247 9.195411 CAAAATAAAGATGCTTACACAACATGT 57.805 29.630 0.00 0.00 46.06 3.21
2200 2248 9.195411 ACAAAATAAAGATGCTTACACAACATG 57.805 29.630 0.00 0.00 0.00 3.21
2215 2263 9.511272 GGGGAGAGTACTTTTACAAAATAAAGA 57.489 33.333 0.00 0.00 35.75 2.52
2216 2264 8.448615 CGGGGAGAGTACTTTTACAAAATAAAG 58.551 37.037 0.00 0.00 37.38 1.85
2217 2265 7.938490 ACGGGGAGAGTACTTTTACAAAATAAA 59.062 33.333 0.00 0.00 0.00 1.40
2218 2266 7.452562 ACGGGGAGAGTACTTTTACAAAATAA 58.547 34.615 0.00 0.00 0.00 1.40
2219 2267 7.008021 ACGGGGAGAGTACTTTTACAAAATA 57.992 36.000 0.00 0.00 0.00 1.40
2220 2268 5.872963 ACGGGGAGAGTACTTTTACAAAAT 58.127 37.500 0.00 0.00 0.00 1.82
2221 2269 5.294734 ACGGGGAGAGTACTTTTACAAAA 57.705 39.130 0.00 0.00 0.00 2.44
2222 2270 4.961438 ACGGGGAGAGTACTTTTACAAA 57.039 40.909 0.00 0.00 0.00 2.83
2223 2271 4.961438 AACGGGGAGAGTACTTTTACAA 57.039 40.909 0.00 0.00 0.00 2.41
2224 2272 4.961438 AAACGGGGAGAGTACTTTTACA 57.039 40.909 0.00 0.00 0.00 2.41
2225 2273 5.783111 TGTAAACGGGGAGAGTACTTTTAC 58.217 41.667 13.53 13.53 30.97 2.01
2226 2274 6.418057 TTGTAAACGGGGAGAGTACTTTTA 57.582 37.500 0.00 0.00 0.00 1.52
2227 2275 4.961438 TGTAAACGGGGAGAGTACTTTT 57.039 40.909 0.00 0.00 0.00 2.27
2228 2276 4.961438 TTGTAAACGGGGAGAGTACTTT 57.039 40.909 0.00 0.00 0.00 2.66
2229 2277 4.101430 TGTTTGTAAACGGGGAGAGTACTT 59.899 41.667 0.00 0.00 41.74 2.24
2230 2278 3.642848 TGTTTGTAAACGGGGAGAGTACT 59.357 43.478 0.00 0.00 41.74 2.73
2231 2279 3.993920 TGTTTGTAAACGGGGAGAGTAC 58.006 45.455 3.35 0.00 41.74 2.73
2232 2280 4.895668 ATGTTTGTAAACGGGGAGAGTA 57.104 40.909 3.35 0.00 41.74 2.59
2233 2281 3.782656 ATGTTTGTAAACGGGGAGAGT 57.217 42.857 3.35 0.00 41.74 3.24
2234 2282 5.484715 TCTTATGTTTGTAAACGGGGAGAG 58.515 41.667 3.35 0.00 41.74 3.20
2235 2283 5.486735 TCTTATGTTTGTAAACGGGGAGA 57.513 39.130 3.35 2.17 41.74 3.71
2236 2284 8.446599 AATATCTTATGTTTGTAAACGGGGAG 57.553 34.615 3.35 0.19 41.74 4.30
2237 2285 8.810990 AAATATCTTATGTTTGTAAACGGGGA 57.189 30.769 3.35 0.61 41.74 4.81
2238 2286 9.296400 CAAAATATCTTATGTTTGTAAACGGGG 57.704 33.333 3.35 0.00 41.74 5.73
2239 2287 9.296400 CCAAAATATCTTATGTTTGTAAACGGG 57.704 33.333 3.35 0.00 41.74 5.28
2277 2325 8.783093 CGTAGGAATAGCAATTTTGATAATCCA 58.217 33.333 19.46 7.60 46.44 3.41
2299 2347 8.458212 AAAGTTTTCGTAGAAGTTATCCGTAG 57.542 34.615 0.00 0.00 45.90 3.51
2300 2348 9.341899 GTAAAGTTTTCGTAGAAGTTATCCGTA 57.658 33.333 0.00 0.00 45.90 4.02
2301 2349 7.867403 TGTAAAGTTTTCGTAGAAGTTATCCGT 59.133 33.333 0.00 0.00 45.90 4.69
2302 2350 8.231304 TGTAAAGTTTTCGTAGAAGTTATCCG 57.769 34.615 0.00 0.00 45.90 4.18
2306 2354 8.853345 CGCTATGTAAAGTTTTCGTAGAAGTTA 58.147 33.333 19.89 0.00 45.90 2.24
2307 2355 7.383300 ACGCTATGTAAAGTTTTCGTAGAAGTT 59.617 33.333 19.89 3.58 45.90 2.66
2308 2356 6.865205 ACGCTATGTAAAGTTTTCGTAGAAGT 59.135 34.615 19.89 15.93 45.90 3.01
2309 2357 7.164858 CACGCTATGTAAAGTTTTCGTAGAAG 58.835 38.462 19.89 15.48 45.90 2.85
2310 2358 6.400303 GCACGCTATGTAAAGTTTTCGTAGAA 60.400 38.462 19.89 0.00 45.90 2.10
2311 2359 5.061311 GCACGCTATGTAAAGTTTTCGTAGA 59.939 40.000 19.89 0.00 0.00 2.59
2312 2360 5.245850 GCACGCTATGTAAAGTTTTCGTAG 58.754 41.667 14.11 14.11 0.00 3.51
2313 2361 4.201513 CGCACGCTATGTAAAGTTTTCGTA 60.202 41.667 0.00 0.00 0.00 3.43
2314 2362 3.422603 CGCACGCTATGTAAAGTTTTCGT 60.423 43.478 0.00 0.00 0.00 3.85
2315 2363 3.081445 CGCACGCTATGTAAAGTTTTCG 58.919 45.455 0.00 0.00 0.00 3.46
2316 2364 3.838550 CACGCACGCTATGTAAAGTTTTC 59.161 43.478 0.00 0.00 0.00 2.29
2317 2365 3.495377 TCACGCACGCTATGTAAAGTTTT 59.505 39.130 0.00 0.00 0.00 2.43
2318 2366 3.061322 TCACGCACGCTATGTAAAGTTT 58.939 40.909 0.00 0.00 0.00 2.66
2319 2367 2.666508 CTCACGCACGCTATGTAAAGTT 59.333 45.455 0.00 0.00 0.00 2.66
2320 2368 2.094906 TCTCACGCACGCTATGTAAAGT 60.095 45.455 0.00 0.00 0.00 2.66
2321 2369 2.526077 TCTCACGCACGCTATGTAAAG 58.474 47.619 0.00 0.00 0.00 1.85
2322 2370 2.162809 TCTCTCACGCACGCTATGTAAA 59.837 45.455 0.00 0.00 0.00 2.01
2323 2371 1.741145 TCTCTCACGCACGCTATGTAA 59.259 47.619 0.00 0.00 0.00 2.41
2324 2372 1.330829 CTCTCTCACGCACGCTATGTA 59.669 52.381 0.00 0.00 0.00 2.29
2325 2373 0.099613 CTCTCTCACGCACGCTATGT 59.900 55.000 0.00 0.00 0.00 2.29
2326 2374 0.593518 CCTCTCTCACGCACGCTATG 60.594 60.000 0.00 0.00 0.00 2.23
2327 2375 1.730487 CCTCTCTCACGCACGCTAT 59.270 57.895 0.00 0.00 0.00 2.97
2328 2376 3.052620 GCCTCTCTCACGCACGCTA 62.053 63.158 0.00 0.00 0.00 4.26
2329 2377 4.427661 GCCTCTCTCACGCACGCT 62.428 66.667 0.00 0.00 0.00 5.07
2330 2378 4.724602 TGCCTCTCTCACGCACGC 62.725 66.667 0.00 0.00 0.00 5.34
2331 2379 1.923227 TACTGCCTCTCTCACGCACG 61.923 60.000 0.00 0.00 0.00 5.34
2332 2380 0.243907 TTACTGCCTCTCTCACGCAC 59.756 55.000 0.00 0.00 0.00 5.34
2333 2381 0.243907 GTTACTGCCTCTCTCACGCA 59.756 55.000 0.00 0.00 0.00 5.24
2334 2382 0.458716 GGTTACTGCCTCTCTCACGC 60.459 60.000 0.00 0.00 0.00 5.34
2335 2383 0.179161 CGGTTACTGCCTCTCTCACG 60.179 60.000 0.00 0.00 0.00 4.35
2336 2384 0.889306 ACGGTTACTGCCTCTCTCAC 59.111 55.000 0.00 0.00 0.00 3.51
2337 2385 1.629043 AACGGTTACTGCCTCTCTCA 58.371 50.000 0.00 0.00 0.00 3.27
2338 2386 3.380637 TCATAACGGTTACTGCCTCTCTC 59.619 47.826 2.10 0.00 0.00 3.20
2339 2387 3.362706 TCATAACGGTTACTGCCTCTCT 58.637 45.455 2.10 0.00 0.00 3.10
2340 2388 3.380637 TCTCATAACGGTTACTGCCTCTC 59.619 47.826 2.10 0.00 0.00 3.20
2341 2389 3.362706 TCTCATAACGGTTACTGCCTCT 58.637 45.455 2.10 0.00 0.00 3.69
2342 2390 3.795623 TCTCATAACGGTTACTGCCTC 57.204 47.619 2.10 0.00 0.00 4.70
2343 2391 4.546829 TTTCTCATAACGGTTACTGCCT 57.453 40.909 2.10 0.00 0.00 4.75
2344 2392 5.616488 TTTTTCTCATAACGGTTACTGCC 57.384 39.130 2.10 0.00 0.00 4.85
2363 2411 4.617298 CGATGCCGTTATTCCCTTGTTTTT 60.617 41.667 0.00 0.00 0.00 1.94
2364 2412 3.119637 CGATGCCGTTATTCCCTTGTTTT 60.120 43.478 0.00 0.00 0.00 2.43
2365 2413 2.422127 CGATGCCGTTATTCCCTTGTTT 59.578 45.455 0.00 0.00 0.00 2.83
2366 2414 2.014128 CGATGCCGTTATTCCCTTGTT 58.986 47.619 0.00 0.00 0.00 2.83
2367 2415 1.663695 CGATGCCGTTATTCCCTTGT 58.336 50.000 0.00 0.00 0.00 3.16
2368 2416 0.944386 CCGATGCCGTTATTCCCTTG 59.056 55.000 0.00 0.00 0.00 3.61
2369 2417 0.834612 TCCGATGCCGTTATTCCCTT 59.165 50.000 0.00 0.00 0.00 3.95
2370 2418 1.056660 ATCCGATGCCGTTATTCCCT 58.943 50.000 0.00 0.00 0.00 4.20
2371 2419 1.892209 AATCCGATGCCGTTATTCCC 58.108 50.000 0.00 0.00 0.00 3.97
2372 2420 3.982576 AAAATCCGATGCCGTTATTCC 57.017 42.857 0.00 0.00 0.00 3.01
2373 2421 4.041723 CCAAAAATCCGATGCCGTTATTC 58.958 43.478 0.00 0.00 0.00 1.75
2374 2422 3.736740 GCCAAAAATCCGATGCCGTTATT 60.737 43.478 0.00 0.00 0.00 1.40
2375 2423 2.223711 GCCAAAAATCCGATGCCGTTAT 60.224 45.455 0.00 0.00 0.00 1.89
2376 2424 1.133407 GCCAAAAATCCGATGCCGTTA 59.867 47.619 0.00 0.00 0.00 3.18
2377 2425 0.108851 GCCAAAAATCCGATGCCGTT 60.109 50.000 0.00 0.00 0.00 4.44
2378 2426 0.965363 AGCCAAAAATCCGATGCCGT 60.965 50.000 0.00 0.00 0.00 5.68
2379 2427 0.248621 GAGCCAAAAATCCGATGCCG 60.249 55.000 0.00 0.00 0.00 5.69
2380 2428 1.106285 AGAGCCAAAAATCCGATGCC 58.894 50.000 0.00 0.00 0.00 4.40
2381 2429 1.202336 CCAGAGCCAAAAATCCGATGC 60.202 52.381 0.00 0.00 0.00 3.91
2382 2430 2.368439 TCCAGAGCCAAAAATCCGATG 58.632 47.619 0.00 0.00 0.00 3.84
2383 2431 2.806945 TCCAGAGCCAAAAATCCGAT 57.193 45.000 0.00 0.00 0.00 4.18
2384 2432 2.556622 GTTTCCAGAGCCAAAAATCCGA 59.443 45.455 0.00 0.00 0.00 4.55
2385 2433 2.295909 TGTTTCCAGAGCCAAAAATCCG 59.704 45.455 0.00 0.00 0.00 4.18
2386 2434 4.541973 ATGTTTCCAGAGCCAAAAATCC 57.458 40.909 0.00 0.00 0.00 3.01
2387 2435 8.000780 AGTATATGTTTCCAGAGCCAAAAATC 57.999 34.615 0.00 0.00 0.00 2.17
2388 2436 7.836183 AGAGTATATGTTTCCAGAGCCAAAAAT 59.164 33.333 0.00 0.00 0.00 1.82
2389 2437 7.175104 AGAGTATATGTTTCCAGAGCCAAAAA 58.825 34.615 0.00 0.00 0.00 1.94
2390 2438 6.721318 AGAGTATATGTTTCCAGAGCCAAAA 58.279 36.000 0.00 0.00 0.00 2.44
2391 2439 6.313519 AGAGTATATGTTTCCAGAGCCAAA 57.686 37.500 0.00 0.00 0.00 3.28
2392 2440 5.451937 CGAGAGTATATGTTTCCAGAGCCAA 60.452 44.000 0.00 0.00 0.00 4.52
2393 2441 4.038042 CGAGAGTATATGTTTCCAGAGCCA 59.962 45.833 0.00 0.00 0.00 4.75
2394 2442 4.551388 CGAGAGTATATGTTTCCAGAGCC 58.449 47.826 0.00 0.00 0.00 4.70
2395 2443 4.278669 TCCGAGAGTATATGTTTCCAGAGC 59.721 45.833 0.00 0.00 0.00 4.09
2396 2444 6.582677 ATCCGAGAGTATATGTTTCCAGAG 57.417 41.667 0.00 0.00 0.00 3.35
2397 2445 7.504574 TGTTATCCGAGAGTATATGTTTCCAGA 59.495 37.037 0.00 0.00 0.00 3.86
2398 2446 7.658261 TGTTATCCGAGAGTATATGTTTCCAG 58.342 38.462 0.00 0.00 0.00 3.86
2399 2447 7.287005 ACTGTTATCCGAGAGTATATGTTTCCA 59.713 37.037 0.00 0.00 0.00 3.53
2400 2448 7.659186 ACTGTTATCCGAGAGTATATGTTTCC 58.341 38.462 0.00 0.00 0.00 3.13
2409 2457 9.932207 TTTGATTTTTACTGTTATCCGAGAGTA 57.068 29.630 0.00 0.00 0.00 2.59
2410 2458 8.842358 TTTGATTTTTACTGTTATCCGAGAGT 57.158 30.769 0.00 0.00 0.00 3.24
2436 2484 9.228949 GCTTCCTGATTATGATCAAACATCTAT 57.771 33.333 0.00 0.00 41.55 1.98
2437 2485 8.212995 TGCTTCCTGATTATGATCAAACATCTA 58.787 33.333 0.00 0.00 41.55 1.98
2438 2486 7.013083 GTGCTTCCTGATTATGATCAAACATCT 59.987 37.037 0.00 0.00 41.55 2.90
2439 2487 7.137426 GTGCTTCCTGATTATGATCAAACATC 58.863 38.462 0.00 2.39 41.55 3.06
2440 2488 6.040166 GGTGCTTCCTGATTATGATCAAACAT 59.960 38.462 0.00 0.00 41.55 2.71
2441 2489 5.357878 GGTGCTTCCTGATTATGATCAAACA 59.642 40.000 0.00 0.00 41.55 2.83
2442 2490 5.221126 GGGTGCTTCCTGATTATGATCAAAC 60.221 44.000 0.00 0.00 41.55 2.93
2443 2491 4.889409 GGGTGCTTCCTGATTATGATCAAA 59.111 41.667 0.00 0.00 41.55 2.69
2444 2492 4.464008 GGGTGCTTCCTGATTATGATCAA 58.536 43.478 0.00 0.00 41.55 2.57
2445 2493 3.494924 CGGGTGCTTCCTGATTATGATCA 60.495 47.826 0.00 0.00 45.09 2.92
2446 2494 3.070018 CGGGTGCTTCCTGATTATGATC 58.930 50.000 1.90 0.00 45.09 2.92
2447 2495 2.811873 GCGGGTGCTTCCTGATTATGAT 60.812 50.000 10.68 0.00 45.09 2.45
2448 2496 1.475034 GCGGGTGCTTCCTGATTATGA 60.475 52.381 10.68 0.00 45.09 2.15
2449 2497 0.947244 GCGGGTGCTTCCTGATTATG 59.053 55.000 10.68 0.00 45.09 1.90
2450 2498 0.532862 CGCGGGTGCTTCCTGATTAT 60.533 55.000 0.00 0.00 45.09 1.28
2451 2499 1.153449 CGCGGGTGCTTCCTGATTA 60.153 57.895 0.00 0.00 45.09 1.75
2452 2500 2.436646 CGCGGGTGCTTCCTGATT 60.437 61.111 0.00 0.00 45.09 2.57
2453 2501 3.665675 GACGCGGGTGCTTCCTGAT 62.666 63.158 10.96 0.00 45.09 2.90
2454 2502 4.373116 GACGCGGGTGCTTCCTGA 62.373 66.667 10.96 0.00 45.09 3.86
2484 2532 4.753662 TAGGTCACCCGAGCCGCT 62.754 66.667 0.00 0.00 40.69 5.52
2527 2578 2.123077 CGAGGGAGGAGGGAGCAT 60.123 66.667 0.00 0.00 0.00 3.79
2597 2648 1.822371 GAGACGAGAGAGAAAAGGCCT 59.178 52.381 0.00 0.00 0.00 5.19
2810 2861 0.908198 AGATCCGAGCAGAAAAGCCT 59.092 50.000 0.00 0.00 34.23 4.58
2989 3042 0.751643 GCACCTCACCAAACACCAGT 60.752 55.000 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.