Multiple sequence alignment - TraesCS3D01G178800

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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 TraesCS3D01G178800 chr3D 100.000 2897 0 0 1 2897 160697398 160700294 0.000000e+00 5350
1 TraesCS3D01G178800 chr3D 90.441 136 13 0 2253 2388 326701545 326701410 2.290000e-41 180
2 TraesCS3D01G178800 chr3B 90.936 2052 137 20 2 2042 237331065 237333078 0.000000e+00 2713
3 TraesCS3D01G178800 chr3B 88.934 244 20 6 2651 2890 237333688 237333928 7.850000e-76 294
4 TraesCS3D01G178800 chr3B 85.091 275 23 9 2389 2646 237333285 237333558 6.160000e-67 265
5 TraesCS3D01G178800 chr3A 94.363 1561 77 7 485 2042 187247306 187248858 0.000000e+00 2385
6 TraesCS3D01G178800 chr3A 93.592 515 12 5 2389 2897 187249113 187249612 0.000000e+00 749
7 TraesCS3D01G178800 chr3A 91.304 207 9 5 2040 2240 187248919 187249122 1.020000e-69 274
8 TraesCS3D01G178800 chr1D 92.143 140 9 2 2253 2392 112751269 112751406 2.280000e-46 196
9 TraesCS3D01G178800 chr6D 91.156 147 8 4 2253 2398 386225850 386225992 8.190000e-46 195
10 TraesCS3D01G178800 chr2D 91.429 140 10 2 2253 2392 79336261 79336124 1.060000e-44 191
11 TraesCS3D01G178800 chr4D 90.345 145 13 1 2253 2397 17255468 17255611 3.810000e-44 189
12 TraesCS3D01G178800 chr7A 91.241 137 10 2 2253 2389 221965293 221965427 4.930000e-43 185
13 TraesCS3D01G178800 chr7D 89.583 144 14 1 2253 2395 88371772 88371629 6.380000e-42 182
14 TraesCS3D01G178800 chr6B 88.971 136 13 2 2253 2388 629461423 629461556 1.790000e-37 167
15 TraesCS3D01G178800 chr2A 88.722 133 15 0 2255 2387 516282471 516282339 2.310000e-36 163


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 TraesCS3D01G178800 chr3D 160697398 160700294 2896 False 5350.000000 5350 100.000000 1 2897 1 chr3D.!!$F1 2896
1 TraesCS3D01G178800 chr3B 237331065 237333928 2863 False 1090.666667 2713 88.320333 2 2890 3 chr3B.!!$F1 2888
2 TraesCS3D01G178800 chr3A 187247306 187249612 2306 False 1136.000000 2385 93.086333 485 2897 3 chr3A.!!$F1 2412

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
883 891 0.388907 CCCCGCCGTTACATATACCG 60.389 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2292 2386 0.319211 AGATCGTCACAAAACGGCGA 60.319 50.0 16.62 0.0 42.8 5.54 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
46 47 1.133167 TCTCCTCAAGGTCAGGTGTGA 60.133 52.381 0.00 0.00 36.34 3.58
54 55 0.610687 GGTCAGGTGTGAAGGGAGAG 59.389 60.000 0.00 0.00 33.27 3.20
67 68 1.226311 GGGAGAGGGGGACAATTCAT 58.774 55.000 0.00 0.00 0.00 2.57
68 69 1.133668 GGGAGAGGGGGACAATTCATG 60.134 57.143 0.00 0.00 0.00 3.07
77 78 4.164221 GGGGGACAATTCATGACTTCTCTA 59.836 45.833 0.00 0.00 0.00 2.43
85 88 9.778741 ACAATTCATGACTTCTCTAGTTTTACA 57.221 29.630 0.00 0.00 37.17 2.41
95 98 8.361889 ACTTCTCTAGTTTTACAAGAGAGTTCC 58.638 37.037 1.96 0.00 44.77 3.62
115 118 9.936759 GAGTTCCCCTATTCTAGATTAAGATTG 57.063 37.037 0.00 0.00 0.00 2.67
118 121 9.447279 TTCCCCTATTCTAGATTAAGATTGACA 57.553 33.333 0.00 0.00 0.00 3.58
119 122 9.094578 TCCCCTATTCTAGATTAAGATTGACAG 57.905 37.037 0.00 0.00 0.00 3.51
131 134 5.712152 AAGATTGACAGGGTTGAATGAAC 57.288 39.130 0.00 0.00 0.00 3.18
147 150 9.944663 GTTGAATGAACTAATCAACTAACACAA 57.055 29.630 9.86 0.00 45.86 3.33
186 189 8.800972 CATAATCCAATAAATTATGCATCGTGC 58.199 33.333 0.19 3.44 45.29 5.34
212 215 3.367321 ACTCTAGGGTTGCTAAGAGGTC 58.633 50.000 0.00 0.00 0.00 3.85
216 219 1.840635 AGGGTTGCTAAGAGGTCCATC 59.159 52.381 0.00 0.00 0.00 3.51
217 220 1.559682 GGGTTGCTAAGAGGTCCATCA 59.440 52.381 0.00 0.00 0.00 3.07
249 252 4.809496 AGCGAGGCCATGCAAGGG 62.809 66.667 19.81 6.76 43.76 3.95
260 263 4.994756 GCAAGGGTGGTGGGTGGG 62.995 72.222 0.00 0.00 0.00 4.61
261 264 3.507713 CAAGGGTGGTGGGTGGGT 61.508 66.667 0.00 0.00 0.00 4.51
262 265 3.507713 AAGGGTGGTGGGTGGGTG 61.508 66.667 0.00 0.00 0.00 4.61
269 272 3.884774 GTGGGTGGGTGCAGGACA 61.885 66.667 0.00 0.00 0.00 4.02
272 275 2.436646 GGTGGGTGCAGGACATCG 60.437 66.667 0.00 0.00 0.00 3.84
282 285 1.074926 AGGACATCGGCCTGGATCT 60.075 57.895 0.00 0.00 33.59 2.75
287 290 2.569354 ATCGGCCTGGATCTCTCGC 61.569 63.158 0.00 0.00 0.00 5.03
288 291 2.992817 ATCGGCCTGGATCTCTCGCT 62.993 60.000 0.00 0.00 0.00 4.93
292 295 1.739049 CCTGGATCTCTCGCTGGTC 59.261 63.158 0.00 0.00 0.00 4.02
328 331 4.593864 GCCCTCCGCGGTCATCTC 62.594 72.222 27.15 7.07 0.00 2.75
330 333 1.528542 CCCTCCGCGGTCATCTCTA 60.529 63.158 27.15 1.04 0.00 2.43
378 384 1.132453 GACTCGATCGTGTGGTCATGA 59.868 52.381 25.85 0.00 42.71 3.07
381 387 1.401905 TCGATCGTGTGGTCATGAGAG 59.598 52.381 15.94 0.00 41.96 3.20
418 424 5.300034 TGTTTTTCATGCTCTGCCTATATGG 59.700 40.000 0.00 0.00 39.35 2.74
448 454 0.603707 TTTTGCGAGGCAGGAGTCAG 60.604 55.000 0.00 0.00 40.61 3.51
453 459 1.217779 GAGGCAGGAGTCAGTGCTC 59.782 63.158 14.44 6.14 39.76 4.26
460 466 1.375268 GAGTCAGTGCTCAGTGGCC 60.375 63.158 0.00 0.00 37.07 5.36
464 470 4.694233 AGTGCTCAGTGGCCTGCG 62.694 66.667 3.32 0.00 38.66 5.18
475 481 1.037030 TGGCCTGCGGATTTGGAATC 61.037 55.000 3.32 0.00 0.00 2.52
507 513 5.163385 CCACCCACATATTGATTCTTTGCAT 60.163 40.000 0.00 0.00 0.00 3.96
545 551 0.598419 GGCTCTTGTTGCAAAGCACC 60.598 55.000 19.56 7.97 38.71 5.01
551 557 3.283684 TTGCAAAGCACCCGTCGG 61.284 61.111 3.60 3.60 38.71 4.79
564 570 1.448922 CCGTCGGGCAAACCTTTGAA 61.449 55.000 2.34 0.00 40.55 2.69
589 595 4.800784 CAACATGACTCATGATGCAAACA 58.199 39.130 23.30 0.00 43.81 2.83
608 615 4.305539 ACATCCAATCAGAACATGACCA 57.694 40.909 0.00 0.00 41.91 4.02
623 630 4.253685 CATGACCAATGTCGTAAACCTCT 58.746 43.478 0.00 0.00 44.86 3.69
631 638 2.288213 TGTCGTAAACCTCTGAGCACAG 60.288 50.000 4.57 4.57 44.66 3.66
650 657 2.427812 CAGCATGACCCATGTTGCATAA 59.572 45.455 10.05 0.00 43.58 1.90
665 672 3.457234 TGCATAACTCGTTAGCTGGATG 58.543 45.455 0.00 0.00 0.00 3.51
667 674 4.202253 TGCATAACTCGTTAGCTGGATGAT 60.202 41.667 0.00 0.00 0.00 2.45
671 678 3.296854 ACTCGTTAGCTGGATGATACCA 58.703 45.455 0.00 0.00 38.33 3.25
684 692 4.216257 GGATGATACCAAGCGCAACATAAT 59.784 41.667 11.47 0.00 0.00 1.28
689 697 6.931840 TGATACCAAGCGCAACATAATATGTA 59.068 34.615 11.47 0.00 44.07 2.29
706 714 4.870123 ATGTATTGCAAACCTTCAAGCA 57.130 36.364 1.71 0.00 34.79 3.91
741 749 1.269517 GCCTCATCAGGATCTCACGAC 60.270 57.143 0.00 0.00 43.65 4.34
789 797 5.023920 CGATCATTTCAAAACATCAGTCGG 58.976 41.667 0.00 0.00 0.00 4.79
804 812 4.564116 CGGCCGACGCGTAGGATT 62.564 66.667 37.82 2.85 35.02 3.01
805 813 2.202837 GGCCGACGCGTAGGATTT 60.203 61.111 37.82 1.96 35.02 2.17
848 856 3.133365 AAAGCCCCACGAAGCCACT 62.133 57.895 0.00 0.00 0.00 4.00
878 886 1.449956 GCAACCCCGCCGTTACATA 60.450 57.895 0.00 0.00 0.00 2.29
879 887 0.816421 GCAACCCCGCCGTTACATAT 60.816 55.000 0.00 0.00 0.00 1.78
880 888 1.540797 GCAACCCCGCCGTTACATATA 60.541 52.381 0.00 0.00 0.00 0.86
881 889 2.137523 CAACCCCGCCGTTACATATAC 58.862 52.381 0.00 0.00 0.00 1.47
882 890 0.681175 ACCCCGCCGTTACATATACC 59.319 55.000 0.00 0.00 0.00 2.73
883 891 0.388907 CCCCGCCGTTACATATACCG 60.389 60.000 0.00 0.00 0.00 4.02
884 892 0.388907 CCCGCCGTTACATATACCGG 60.389 60.000 0.00 0.00 43.22 5.28
919 927 2.775856 GCTCCACGATCGCTCCTCA 61.776 63.158 16.60 0.00 0.00 3.86
922 930 2.278206 CACGATCGCTCCTCACCG 60.278 66.667 16.60 0.00 0.00 4.94
923 931 2.750637 ACGATCGCTCCTCACCGT 60.751 61.111 16.60 0.00 0.00 4.83
1515 1523 1.078918 CTCCTTGGCATCAGCGTCA 60.079 57.895 0.00 0.00 43.41 4.35
1516 1524 0.674581 CTCCTTGGCATCAGCGTCAA 60.675 55.000 0.00 0.00 43.41 3.18
1517 1525 0.955428 TCCTTGGCATCAGCGTCAAC 60.955 55.000 0.00 0.00 43.41 3.18
1521 1529 2.027073 GGCATCAGCGTCAACGTCA 61.027 57.895 4.29 0.00 43.41 4.35
1824 1838 3.712907 TACCGGCAAGGCCTGGTC 61.713 66.667 15.50 9.01 46.52 4.02
1842 1856 2.515523 CTTGGATGCCTCGGCCTG 60.516 66.667 0.00 0.00 41.09 4.85
2029 2044 7.750458 CGCAAATACAGTATGATTTTGTTCAGT 59.250 33.333 0.00 0.00 40.71 3.41
2042 2057 2.688507 TGTTCAGTCGGCTCAATCTTC 58.311 47.619 0.00 0.00 0.00 2.87
2043 2058 2.300152 TGTTCAGTCGGCTCAATCTTCT 59.700 45.455 0.00 0.00 0.00 2.85
2115 2205 3.243636 TGTGTTTCGTGTTACTCTCTCCC 60.244 47.826 0.00 0.00 0.00 4.30
2124 2214 4.409247 GTGTTACTCTCTCCCACCCATATT 59.591 45.833 0.00 0.00 0.00 1.28
2125 2215 5.036916 TGTTACTCTCTCCCACCCATATTT 58.963 41.667 0.00 0.00 0.00 1.40
2202 2292 2.744202 ACTCCATCTGTCGAAATGCAAC 59.256 45.455 0.00 0.00 0.00 4.17
2240 2334 9.606631 TTGTTATAAAGGCTTTGACAAACAATT 57.393 25.926 22.32 0.00 38.36 2.32
2242 2336 8.424731 GTTATAAAGGCTTTGACAAACAATTCG 58.575 33.333 22.32 0.00 38.36 3.34
2243 2337 4.647424 AAGGCTTTGACAAACAATTCGA 57.353 36.364 0.00 0.00 38.36 3.71
2244 2338 4.647424 AGGCTTTGACAAACAATTCGAA 57.353 36.364 0.00 0.00 38.36 3.71
2246 2340 5.600696 AGGCTTTGACAAACAATTCGAAAT 58.399 33.333 0.00 0.00 38.36 2.17
2247 2341 5.463061 AGGCTTTGACAAACAATTCGAAATG 59.537 36.000 11.66 11.66 38.36 2.32
2249 2343 5.276773 GCTTTGACAAACAATTCGAAATGCA 60.277 36.000 13.10 0.06 38.36 3.96
2250 2344 6.653273 TTTGACAAACAATTCGAAATGCAA 57.347 29.167 13.10 6.18 38.36 4.08
2251 2345 5.633996 TGACAAACAATTCGAAATGCAAC 57.366 34.783 13.10 2.17 0.00 4.17
2252 2346 4.205996 TGACAAACAATTCGAAATGCAACG 59.794 37.500 13.10 0.00 0.00 4.10
2253 2347 4.109050 ACAAACAATTCGAAATGCAACGT 58.891 34.783 13.10 3.16 0.00 3.99
2254 2348 4.026968 ACAAACAATTCGAAATGCAACGTG 60.027 37.500 13.10 6.83 0.00 4.49
2255 2349 3.617540 ACAATTCGAAATGCAACGTGA 57.382 38.095 13.10 0.00 0.00 4.35
2256 2350 3.554524 ACAATTCGAAATGCAACGTGAG 58.445 40.909 13.10 0.00 0.00 3.51
2270 2364 2.444421 ACGTGAGTAGTCCACTTAGGG 58.556 52.381 0.00 0.00 46.88 3.53
2271 2365 2.224967 ACGTGAGTAGTCCACTTAGGGT 60.225 50.000 0.00 0.00 46.88 4.34
2272 2366 2.163815 CGTGAGTAGTCCACTTAGGGTG 59.836 54.545 0.00 0.00 44.96 4.61
2273 2367 3.163467 GTGAGTAGTCCACTTAGGGTGT 58.837 50.000 0.00 0.00 43.94 4.16
2274 2368 3.577415 GTGAGTAGTCCACTTAGGGTGTT 59.423 47.826 0.00 0.00 43.94 3.32
2275 2369 3.576982 TGAGTAGTCCACTTAGGGTGTTG 59.423 47.826 0.00 0.00 43.94 3.33
2276 2370 2.904434 AGTAGTCCACTTAGGGTGTTGG 59.096 50.000 0.00 0.00 43.94 3.77
2277 2371 2.112279 AGTCCACTTAGGGTGTTGGA 57.888 50.000 0.00 0.00 43.94 3.53
2278 2372 1.978580 AGTCCACTTAGGGTGTTGGAG 59.021 52.381 0.00 0.00 43.94 3.86
2279 2373 1.697982 GTCCACTTAGGGTGTTGGAGT 59.302 52.381 0.00 0.00 43.94 3.85
2280 2374 1.697432 TCCACTTAGGGTGTTGGAGTG 59.303 52.381 0.00 0.00 43.94 3.51
2281 2375 2.185004 CACTTAGGGTGTTGGAGTGG 57.815 55.000 0.00 0.00 40.79 4.00
2282 2376 1.420138 CACTTAGGGTGTTGGAGTGGT 59.580 52.381 0.00 0.00 40.79 4.16
2283 2377 2.132686 ACTTAGGGTGTTGGAGTGGTT 58.867 47.619 0.00 0.00 0.00 3.67
2284 2378 2.158667 ACTTAGGGTGTTGGAGTGGTTG 60.159 50.000 0.00 0.00 0.00 3.77
2285 2379 0.768622 TAGGGTGTTGGAGTGGTTGG 59.231 55.000 0.00 0.00 0.00 3.77
2286 2380 1.530655 GGGTGTTGGAGTGGTTGGG 60.531 63.158 0.00 0.00 0.00 4.12
2287 2381 1.229076 GGTGTTGGAGTGGTTGGGT 59.771 57.895 0.00 0.00 0.00 4.51
2288 2382 1.106944 GGTGTTGGAGTGGTTGGGTG 61.107 60.000 0.00 0.00 0.00 4.61
2289 2383 1.106944 GTGTTGGAGTGGTTGGGTGG 61.107 60.000 0.00 0.00 0.00 4.61
2290 2384 1.530655 GTTGGAGTGGTTGGGTGGG 60.531 63.158 0.00 0.00 0.00 4.61
2291 2385 1.698116 TTGGAGTGGTTGGGTGGGA 60.698 57.895 0.00 0.00 0.00 4.37
2292 2386 1.071314 TTGGAGTGGTTGGGTGGGAT 61.071 55.000 0.00 0.00 0.00 3.85
2293 2387 1.303282 GGAGTGGTTGGGTGGGATC 59.697 63.158 0.00 0.00 0.00 3.36
2294 2388 1.078426 GAGTGGTTGGGTGGGATCG 60.078 63.158 0.00 0.00 0.00 3.69
2295 2389 2.750237 GTGGTTGGGTGGGATCGC 60.750 66.667 2.14 2.14 0.00 4.58
2296 2390 4.041762 TGGTTGGGTGGGATCGCC 62.042 66.667 7.38 0.12 42.66 5.54
2298 2392 4.404098 GTTGGGTGGGATCGCCGT 62.404 66.667 7.38 0.00 44.27 5.68
2299 2393 3.642503 TTGGGTGGGATCGCCGTT 61.643 61.111 7.38 0.00 44.27 4.44
2300 2394 3.198953 TTGGGTGGGATCGCCGTTT 62.199 57.895 7.38 0.00 44.27 3.60
2301 2395 2.360726 GGGTGGGATCGCCGTTTT 60.361 61.111 7.38 0.00 44.27 2.43
2302 2396 2.696759 GGGTGGGATCGCCGTTTTG 61.697 63.158 7.38 0.00 44.27 2.44
2303 2397 1.969589 GGTGGGATCGCCGTTTTGT 60.970 57.895 7.38 0.00 33.43 2.83
2304 2398 1.209127 GTGGGATCGCCGTTTTGTG 59.791 57.895 7.38 0.00 33.83 3.33
2305 2399 1.071642 TGGGATCGCCGTTTTGTGA 59.928 52.632 7.38 0.00 33.83 3.58
2306 2400 1.231958 TGGGATCGCCGTTTTGTGAC 61.232 55.000 7.38 0.00 33.83 3.67
2307 2401 1.131826 GGATCGCCGTTTTGTGACG 59.868 57.895 0.00 0.00 42.43 4.35
2308 2402 1.286354 GGATCGCCGTTTTGTGACGA 61.286 55.000 0.00 0.00 45.47 4.20
2309 2403 0.719465 GATCGCCGTTTTGTGACGAT 59.281 50.000 0.00 0.00 45.47 3.73
2310 2404 0.719465 ATCGCCGTTTTGTGACGATC 59.281 50.000 0.00 0.00 45.47 3.69
2311 2405 0.319211 TCGCCGTTTTGTGACGATCT 60.319 50.000 0.00 0.00 45.47 2.75
2312 2406 1.068402 TCGCCGTTTTGTGACGATCTA 60.068 47.619 0.00 0.00 45.47 1.98
2313 2407 1.058695 CGCCGTTTTGTGACGATCTAC 59.941 52.381 0.00 0.00 45.47 2.59
2314 2408 1.392510 GCCGTTTTGTGACGATCTACC 59.607 52.381 0.00 0.00 45.47 3.18
2315 2409 2.679450 CCGTTTTGTGACGATCTACCA 58.321 47.619 0.00 0.00 45.47 3.25
2316 2410 3.259064 CCGTTTTGTGACGATCTACCAT 58.741 45.455 0.00 0.00 45.47 3.55
2317 2411 3.062099 CCGTTTTGTGACGATCTACCATG 59.938 47.826 0.00 0.00 45.47 3.66
2318 2412 3.483574 CGTTTTGTGACGATCTACCATGC 60.484 47.826 0.00 0.00 45.47 4.06
2319 2413 3.326836 TTTGTGACGATCTACCATGCA 57.673 42.857 0.00 0.00 0.00 3.96
2320 2414 3.326836 TTGTGACGATCTACCATGCAA 57.673 42.857 0.00 0.00 0.00 4.08
2321 2415 3.326836 TGTGACGATCTACCATGCAAA 57.673 42.857 0.00 0.00 0.00 3.68
2322 2416 3.000041 TGTGACGATCTACCATGCAAAC 59.000 45.455 0.00 0.00 0.00 2.93
2323 2417 3.262420 GTGACGATCTACCATGCAAACT 58.738 45.455 0.00 0.00 0.00 2.66
2324 2418 3.307242 GTGACGATCTACCATGCAAACTC 59.693 47.826 0.00 0.00 0.00 3.01
2325 2419 3.195610 TGACGATCTACCATGCAAACTCT 59.804 43.478 0.00 0.00 0.00 3.24
2326 2420 4.184629 GACGATCTACCATGCAAACTCTT 58.815 43.478 0.00 0.00 0.00 2.85
2327 2421 3.935203 ACGATCTACCATGCAAACTCTTG 59.065 43.478 0.00 0.00 35.49 3.02
2328 2422 3.935203 CGATCTACCATGCAAACTCTTGT 59.065 43.478 0.00 0.00 34.79 3.16
2329 2423 5.109210 CGATCTACCATGCAAACTCTTGTA 58.891 41.667 0.00 0.00 34.79 2.41
2330 2424 5.005779 CGATCTACCATGCAAACTCTTGTAC 59.994 44.000 0.00 0.00 34.79 2.90
2331 2425 5.222079 TCTACCATGCAAACTCTTGTACA 57.778 39.130 0.00 0.00 34.79 2.90
2332 2426 5.804639 TCTACCATGCAAACTCTTGTACAT 58.195 37.500 0.00 0.00 34.79 2.29
2333 2427 6.941857 TCTACCATGCAAACTCTTGTACATA 58.058 36.000 0.00 0.00 34.79 2.29
2334 2428 7.564793 TCTACCATGCAAACTCTTGTACATAT 58.435 34.615 0.00 0.00 34.79 1.78
2335 2429 6.683974 ACCATGCAAACTCTTGTACATATC 57.316 37.500 0.00 0.00 34.79 1.63
2336 2430 6.418101 ACCATGCAAACTCTTGTACATATCT 58.582 36.000 0.00 0.00 34.79 1.98
2337 2431 6.886459 ACCATGCAAACTCTTGTACATATCTT 59.114 34.615 0.00 0.00 34.79 2.40
2338 2432 7.394359 ACCATGCAAACTCTTGTACATATCTTT 59.606 33.333 0.00 0.00 34.79 2.52
2339 2433 7.912250 CCATGCAAACTCTTGTACATATCTTTC 59.088 37.037 0.00 0.00 34.79 2.62
2340 2434 8.671921 CATGCAAACTCTTGTACATATCTTTCT 58.328 33.333 0.00 0.00 34.79 2.52
2341 2435 8.256611 TGCAAACTCTTGTACATATCTTTCTC 57.743 34.615 0.00 0.00 34.79 2.87
2342 2436 8.097038 TGCAAACTCTTGTACATATCTTTCTCT 58.903 33.333 0.00 0.00 34.79 3.10
2343 2437 8.599774 GCAAACTCTTGTACATATCTTTCTCTC 58.400 37.037 0.00 0.00 34.79 3.20
2344 2438 9.868277 CAAACTCTTGTACATATCTTTCTCTCT 57.132 33.333 0.00 0.00 0.00 3.10
2347 2441 9.474313 ACTCTTGTACATATCTTTCTCTCTTCT 57.526 33.333 0.00 0.00 0.00 2.85
2360 2454 9.482175 TCTTTCTCTCTTCTATAAAGCTAAGGT 57.518 33.333 0.00 0.00 0.00 3.50
2363 2457 8.380743 TCTCTCTTCTATAAAGCTAAGGTACG 57.619 38.462 0.00 0.00 0.00 3.67
2364 2458 6.968250 TCTCTTCTATAAAGCTAAGGTACGC 58.032 40.000 0.00 0.00 0.00 4.42
2365 2459 6.544931 TCTCTTCTATAAAGCTAAGGTACGCA 59.455 38.462 0.00 0.00 0.00 5.24
2366 2460 7.230913 TCTCTTCTATAAAGCTAAGGTACGCAT 59.769 37.037 0.00 0.00 0.00 4.73
2367 2461 7.723324 TCTTCTATAAAGCTAAGGTACGCATT 58.277 34.615 0.00 0.00 0.00 3.56
2368 2462 8.202137 TCTTCTATAAAGCTAAGGTACGCATTT 58.798 33.333 0.00 0.00 0.00 2.32
2369 2463 7.709269 TCTATAAAGCTAAGGTACGCATTTG 57.291 36.000 0.00 0.00 0.00 2.32
2370 2464 5.751243 ATAAAGCTAAGGTACGCATTTGG 57.249 39.130 0.00 0.00 0.00 3.28
2371 2465 1.379527 AGCTAAGGTACGCATTTGGC 58.620 50.000 0.00 0.00 39.90 4.52
2383 2477 3.552604 GCATTTGGCGTACTCTTGAAA 57.447 42.857 0.00 0.00 0.00 2.69
2384 2478 3.896122 GCATTTGGCGTACTCTTGAAAA 58.104 40.909 0.00 0.00 0.00 2.29
2385 2479 4.295051 GCATTTGGCGTACTCTTGAAAAA 58.705 39.130 0.00 0.00 0.00 1.94
2406 2500 6.421377 AAAAAGACAAACAATCCTGCAAAC 57.579 33.333 0.00 0.00 0.00 2.93
2407 2501 4.734398 AAGACAAACAATCCTGCAAACA 57.266 36.364 0.00 0.00 0.00 2.83
2416 2511 6.362210 ACAATCCTGCAAACAAAAACAATC 57.638 33.333 0.00 0.00 0.00 2.67
2564 2673 7.081976 ACGAACTAAAATGCACCTTACATTTC 58.918 34.615 0.00 0.00 44.76 2.17
2641 2756 2.240493 ATCTAAAGCGCGCCTTACAT 57.760 45.000 30.33 16.00 32.20 2.29
2646 2761 0.109781 AAGCGCGCCTTACATTTGTG 60.110 50.000 30.33 0.00 30.18 3.33
2770 3011 3.060674 CGATGCTATCTTTTCTCTGTGCG 60.061 47.826 0.00 0.00 0.00 5.34
2882 3125 7.346471 TCTTCTAAATCCCTATTGTCCCTTTG 58.654 38.462 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.912487 TTTCTAGCCCCATCACCGGT 60.912 55.000 0.00 0.00 0.00 5.28
4 5 3.496675 GGGTTTCTAGCCCCATCAC 57.503 57.895 6.99 0.00 40.88 3.06
46 47 1.299939 GAATTGTCCCCCTCTCCCTT 58.700 55.000 0.00 0.00 0.00 3.95
54 55 3.054065 AGAGAAGTCATGAATTGTCCCCC 60.054 47.826 24.25 5.80 30.34 5.40
77 78 6.954352 ATAGGGGAACTCTCTTGTAAAACT 57.046 37.500 0.00 0.00 0.00 2.66
85 88 9.374711 CTTAATCTAGAATAGGGGAACTCTCTT 57.625 37.037 0.00 0.00 39.78 2.85
95 98 8.317679 CCCTGTCAATCTTAATCTAGAATAGGG 58.682 40.741 0.00 0.00 39.78 3.53
115 118 6.431234 AGTTGATTAGTTCATTCAACCCTGTC 59.569 38.462 10.47 0.00 46.58 3.51
118 121 7.942341 TGTTAGTTGATTAGTTCATTCAACCCT 59.058 33.333 10.47 0.00 46.58 4.34
119 122 8.021396 GTGTTAGTTGATTAGTTCATTCAACCC 58.979 37.037 10.47 2.22 46.58 4.11
160 163 8.800972 GCACGATGCATAATTTATTGGATTATG 58.199 33.333 0.00 10.83 44.26 1.90
161 164 8.915871 GCACGATGCATAATTTATTGGATTAT 57.084 30.769 0.00 0.00 44.26 1.28
182 185 2.351726 GCAACCCTAGAGTAAATGCACG 59.648 50.000 0.00 0.00 32.80 5.34
186 189 6.127026 ACCTCTTAGCAACCCTAGAGTAAATG 60.127 42.308 0.00 0.00 0.00 2.32
192 195 2.696187 GGACCTCTTAGCAACCCTAGAG 59.304 54.545 0.00 0.00 0.00 2.43
221 224 1.227645 GCCTCGCTGACCATGCATA 60.228 57.895 0.00 0.00 0.00 3.14
234 237 3.136123 CACCCTTGCATGGCCTCG 61.136 66.667 13.15 2.34 0.00 4.63
249 252 4.974721 CCTGCACCCACCCACCAC 62.975 72.222 0.00 0.00 0.00 4.16
260 263 2.821366 CAGGCCGATGTCCTGCAC 60.821 66.667 0.00 0.00 43.88 4.57
269 272 2.569354 GCGAGAGATCCAGGCCGAT 61.569 63.158 0.00 0.00 0.00 4.18
272 275 2.420890 CAGCGAGAGATCCAGGCC 59.579 66.667 0.00 0.00 0.00 5.19
302 305 2.589159 GCGGAGGGCGAGGAATTC 60.589 66.667 0.00 0.00 0.00 2.17
321 324 3.582164 AGGTGAATCCCCTAGAGATGAC 58.418 50.000 0.00 0.00 36.75 3.06
330 333 1.497161 CCGAACTAGGTGAATCCCCT 58.503 55.000 0.00 0.00 36.75 4.79
347 353 2.389866 GATCGAGTCGCTACCACCCG 62.390 65.000 7.92 0.00 0.00 5.28
367 373 1.274728 AGTGCTCTCTCATGACCACAC 59.725 52.381 0.00 0.00 0.00 3.82
388 394 1.001378 AGAGCATGAAAAACACGCACC 60.001 47.619 0.00 0.00 40.37 5.01
395 401 5.766222 CCATATAGGCAGAGCATGAAAAAC 58.234 41.667 0.00 0.00 0.00 2.43
434 440 2.125753 GCACTGACTCCTGCCTCG 60.126 66.667 0.00 0.00 0.00 4.63
439 445 0.037512 CCACTGAGCACTGACTCCTG 60.038 60.000 0.00 0.00 35.72 3.86
440 446 1.825281 GCCACTGAGCACTGACTCCT 61.825 60.000 0.00 0.00 35.72 3.69
460 466 2.797087 GCACATGATTCCAAATCCGCAG 60.797 50.000 0.00 0.00 0.00 5.18
464 470 1.536709 GGCGCACATGATTCCAAATCC 60.537 52.381 10.83 0.00 0.00 3.01
507 513 0.676466 CATGTTGCGCTTGGGAGGTA 60.676 55.000 9.73 0.00 0.00 3.08
545 551 1.448922 TTCAAAGGTTTGCCCGACGG 61.449 55.000 6.99 6.99 38.05 4.79
551 557 0.927537 GTTGCGTTCAAAGGTTTGCC 59.072 50.000 0.00 0.00 38.05 4.52
557 563 2.290367 TGAGTCATGTTGCGTTCAAAGG 59.710 45.455 0.00 0.00 33.37 3.11
588 594 5.126545 ACATTGGTCATGTTCTGATTGGATG 59.873 40.000 0.00 0.00 44.40 3.51
589 595 5.266788 ACATTGGTCATGTTCTGATTGGAT 58.733 37.500 0.00 0.00 44.40 3.41
595 601 3.401033 ACGACATTGGTCATGTTCTGA 57.599 42.857 0.00 0.00 46.96 3.27
598 605 4.454504 AGGTTTACGACATTGGTCATGTTC 59.545 41.667 0.00 0.00 46.96 3.18
608 615 3.244078 TGTGCTCAGAGGTTTACGACATT 60.244 43.478 0.00 0.00 0.00 2.71
613 620 1.071605 GCTGTGCTCAGAGGTTTACG 58.928 55.000 19.61 0.00 43.76 3.18
623 630 0.678684 CATGGGTCATGCTGTGCTCA 60.679 55.000 0.00 0.00 35.02 4.26
631 638 2.428171 AGTTATGCAACATGGGTCATGC 59.572 45.455 7.70 0.26 44.80 4.06
650 657 3.296854 TGGTATCATCCAGCTAACGAGT 58.703 45.455 0.00 0.00 33.19 4.18
665 672 6.241207 ACATATTATGTTGCGCTTGGTATC 57.759 37.500 9.73 0.00 41.63 2.24
667 674 7.580600 CAATACATATTATGTTGCGCTTGGTA 58.419 34.615 14.23 0.00 41.63 3.25
671 678 6.070897 TGCAATACATATTATGTTGCGCTT 57.929 33.333 20.48 6.02 45.39 4.68
684 692 5.973899 TGCTTGAAGGTTTGCAATACATA 57.026 34.783 0.00 0.00 32.12 2.29
689 697 5.212532 TGTTATGCTTGAAGGTTTGCAAT 57.787 34.783 0.00 0.00 38.96 3.56
706 714 5.754782 TGATGAGGCTTGTAACCATGTTAT 58.245 37.500 0.00 0.00 0.00 1.89
741 749 2.658593 CGCTAGCCGTTGGATCCG 60.659 66.667 9.66 0.00 0.00 4.18
789 797 1.280066 TTTAAATCCTACGCGTCGGC 58.720 50.000 23.98 0.00 0.00 5.54
795 803 4.216902 ACCACCTGTTTTTAAATCCTACGC 59.783 41.667 0.00 0.00 0.00 4.42
796 804 5.952526 ACCACCTGTTTTTAAATCCTACG 57.047 39.130 0.00 0.00 0.00 3.51
804 812 7.778853 TGGTCAAGTATAACCACCTGTTTTTAA 59.221 33.333 0.00 0.00 40.60 1.52
805 813 7.288560 TGGTCAAGTATAACCACCTGTTTTTA 58.711 34.615 0.00 0.00 40.60 1.52
848 856 0.535553 GGGGTTGCGTGTCTTGGTAA 60.536 55.000 0.00 0.00 0.00 2.85
901 909 2.026879 GAGGAGCGATCGTGGAGC 59.973 66.667 17.81 0.00 0.00 4.70
919 927 1.867615 CGAGACGAGACTGAACGGT 59.132 57.895 0.00 0.00 0.00 4.83
922 930 1.512310 CGGCGAGACGAGACTGAAC 60.512 63.158 0.00 0.00 35.47 3.18
923 931 2.687805 CCGGCGAGACGAGACTGAA 61.688 63.158 9.30 0.00 35.47 3.02
1134 1142 1.682451 GGATGTAGTGCACGGGGCTA 61.682 60.000 12.01 0.00 45.15 3.93
1184 1192 3.528370 CGGAGGGAGCGTAGTGGG 61.528 72.222 0.00 0.00 0.00 4.61
1279 1287 2.439156 GGAGCTCATGGTGGTGGC 60.439 66.667 17.19 0.00 0.00 5.01
1515 1523 0.336737 AGGAGGAGGAGGATGACGTT 59.663 55.000 0.00 0.00 0.00 3.99
1516 1524 0.106419 GAGGAGGAGGAGGATGACGT 60.106 60.000 0.00 0.00 0.00 4.34
1517 1525 0.184933 AGAGGAGGAGGAGGATGACG 59.815 60.000 0.00 0.00 0.00 4.35
1521 1529 1.503347 GAGGAAGAGGAGGAGGAGGAT 59.497 57.143 0.00 0.00 0.00 3.24
1824 1838 3.801997 AGGCCGAGGCATCCAAGG 61.802 66.667 16.65 0.00 44.11 3.61
2029 2044 4.020573 TCCTTACAAAGAAGATTGAGCCGA 60.021 41.667 0.00 0.00 34.38 5.54
2042 2057 9.678941 GGACAAAGAAGTTTATTCCTTACAAAG 57.321 33.333 0.00 0.00 29.58 2.77
2043 2058 9.416284 AGGACAAAGAAGTTTATTCCTTACAAA 57.584 29.630 0.00 0.00 35.27 2.83
2202 2292 8.406172 AGCCTTTATAACAAATAAAATGCACG 57.594 30.769 0.00 0.00 0.00 5.34
2240 2334 2.984471 GACTACTCACGTTGCATTTCGA 59.016 45.455 12.09 0.00 0.00 3.71
2242 2336 3.064207 TGGACTACTCACGTTGCATTTC 58.936 45.455 0.00 0.00 0.00 2.17
2243 2337 2.806244 GTGGACTACTCACGTTGCATTT 59.194 45.455 0.00 0.00 0.00 2.32
2244 2338 2.037251 AGTGGACTACTCACGTTGCATT 59.963 45.455 0.00 0.00 39.86 3.56
2246 2340 1.037493 AGTGGACTACTCACGTTGCA 58.963 50.000 0.00 0.00 39.86 4.08
2247 2341 2.150397 AAGTGGACTACTCACGTTGC 57.850 50.000 0.00 0.00 39.18 4.17
2249 2343 2.824341 CCCTAAGTGGACTACTCACGTT 59.176 50.000 0.00 0.00 39.18 3.99
2250 2344 2.224967 ACCCTAAGTGGACTACTCACGT 60.225 50.000 0.00 0.00 39.18 4.49
2251 2345 2.163815 CACCCTAAGTGGACTACTCACG 59.836 54.545 0.00 0.00 43.26 4.35
2252 2346 3.870633 CACCCTAAGTGGACTACTCAC 57.129 52.381 0.00 0.00 43.26 3.51
2263 2357 1.815757 ACCACTCCAACACCCTAAGT 58.184 50.000 0.00 0.00 0.00 2.24
2264 2358 2.504367 CAACCACTCCAACACCCTAAG 58.496 52.381 0.00 0.00 0.00 2.18
2265 2359 1.144093 CCAACCACTCCAACACCCTAA 59.856 52.381 0.00 0.00 0.00 2.69
2266 2360 0.768622 CCAACCACTCCAACACCCTA 59.231 55.000 0.00 0.00 0.00 3.53
2267 2361 1.536676 CCAACCACTCCAACACCCT 59.463 57.895 0.00 0.00 0.00 4.34
2268 2362 1.530655 CCCAACCACTCCAACACCC 60.531 63.158 0.00 0.00 0.00 4.61
2269 2363 1.106944 CACCCAACCACTCCAACACC 61.107 60.000 0.00 0.00 0.00 4.16
2270 2364 1.106944 CCACCCAACCACTCCAACAC 61.107 60.000 0.00 0.00 0.00 3.32
2271 2365 1.228793 CCACCCAACCACTCCAACA 59.771 57.895 0.00 0.00 0.00 3.33
2272 2366 1.530655 CCCACCCAACCACTCCAAC 60.531 63.158 0.00 0.00 0.00 3.77
2273 2367 1.071314 ATCCCACCCAACCACTCCAA 61.071 55.000 0.00 0.00 0.00 3.53
2274 2368 1.465188 ATCCCACCCAACCACTCCA 60.465 57.895 0.00 0.00 0.00 3.86
2275 2369 1.303282 GATCCCACCCAACCACTCC 59.697 63.158 0.00 0.00 0.00 3.85
2276 2370 1.078426 CGATCCCACCCAACCACTC 60.078 63.158 0.00 0.00 0.00 3.51
2277 2371 3.077907 CGATCCCACCCAACCACT 58.922 61.111 0.00 0.00 0.00 4.00
2278 2372 2.750237 GCGATCCCACCCAACCAC 60.750 66.667 0.00 0.00 0.00 4.16
2279 2373 4.041762 GGCGATCCCACCCAACCA 62.042 66.667 0.00 0.00 0.00 3.67
2281 2375 3.912745 AACGGCGATCCCACCCAAC 62.913 63.158 16.62 0.00 0.00 3.77
2282 2376 2.700407 AAAACGGCGATCCCACCCAA 62.700 55.000 16.62 0.00 0.00 4.12
2283 2377 3.198953 AAAACGGCGATCCCACCCA 62.199 57.895 16.62 0.00 0.00 4.51
2284 2378 2.360726 AAAACGGCGATCCCACCC 60.361 61.111 16.62 0.00 0.00 4.61
2285 2379 1.969589 ACAAAACGGCGATCCCACC 60.970 57.895 16.62 0.00 0.00 4.61
2286 2380 1.209127 CACAAAACGGCGATCCCAC 59.791 57.895 16.62 0.00 0.00 4.61
2287 2381 1.071642 TCACAAAACGGCGATCCCA 59.928 52.632 16.62 0.00 0.00 4.37
2288 2382 1.500396 GTCACAAAACGGCGATCCC 59.500 57.895 16.62 0.00 0.00 3.85
2289 2383 1.131826 CGTCACAAAACGGCGATCC 59.868 57.895 16.62 0.00 38.96 3.36
2290 2384 0.719465 ATCGTCACAAAACGGCGATC 59.281 50.000 16.62 0.00 42.80 3.69
2291 2385 0.719465 GATCGTCACAAAACGGCGAT 59.281 50.000 16.62 0.00 43.65 4.58
2292 2386 0.319211 AGATCGTCACAAAACGGCGA 60.319 50.000 16.62 0.00 42.80 5.54
2293 2387 1.058695 GTAGATCGTCACAAAACGGCG 59.941 52.381 4.80 4.80 42.80 6.46
2294 2388 1.392510 GGTAGATCGTCACAAAACGGC 59.607 52.381 0.00 0.00 42.80 5.68
2295 2389 2.679450 TGGTAGATCGTCACAAAACGG 58.321 47.619 0.00 0.00 42.80 4.44
2296 2390 3.483574 GCATGGTAGATCGTCACAAAACG 60.484 47.826 0.00 0.00 43.92 3.60
2297 2391 3.435327 TGCATGGTAGATCGTCACAAAAC 59.565 43.478 0.00 0.00 0.00 2.43
2298 2392 3.669536 TGCATGGTAGATCGTCACAAAA 58.330 40.909 0.00 0.00 0.00 2.44
2299 2393 3.326836 TGCATGGTAGATCGTCACAAA 57.673 42.857 0.00 0.00 0.00 2.83
2300 2394 3.326836 TTGCATGGTAGATCGTCACAA 57.673 42.857 0.00 0.00 0.00 3.33
2301 2395 3.000041 GTTTGCATGGTAGATCGTCACA 59.000 45.455 0.00 0.00 0.00 3.58
2302 2396 3.262420 AGTTTGCATGGTAGATCGTCAC 58.738 45.455 0.00 0.00 0.00 3.67
2303 2397 3.195610 AGAGTTTGCATGGTAGATCGTCA 59.804 43.478 0.00 0.00 0.00 4.35
2304 2398 3.786635 AGAGTTTGCATGGTAGATCGTC 58.213 45.455 0.00 0.00 0.00 4.20
2305 2399 3.895232 AGAGTTTGCATGGTAGATCGT 57.105 42.857 0.00 0.00 0.00 3.73
2306 2400 3.935203 ACAAGAGTTTGCATGGTAGATCG 59.065 43.478 0.00 0.00 37.85 3.69
2307 2401 5.874810 TGTACAAGAGTTTGCATGGTAGATC 59.125 40.000 0.00 0.00 37.85 2.75
2308 2402 5.804639 TGTACAAGAGTTTGCATGGTAGAT 58.195 37.500 0.00 0.00 37.85 1.98
2309 2403 5.222079 TGTACAAGAGTTTGCATGGTAGA 57.778 39.130 0.00 0.00 37.85 2.59
2310 2404 7.712639 AGATATGTACAAGAGTTTGCATGGTAG 59.287 37.037 0.00 0.00 37.85 3.18
2311 2405 7.564793 AGATATGTACAAGAGTTTGCATGGTA 58.435 34.615 0.00 0.00 37.85 3.25
2312 2406 6.418101 AGATATGTACAAGAGTTTGCATGGT 58.582 36.000 0.00 0.00 37.85 3.55
2313 2407 6.932356 AGATATGTACAAGAGTTTGCATGG 57.068 37.500 0.00 0.00 37.85 3.66
2314 2408 8.671921 AGAAAGATATGTACAAGAGTTTGCATG 58.328 33.333 0.00 0.00 37.85 4.06
2315 2409 8.798859 AGAAAGATATGTACAAGAGTTTGCAT 57.201 30.769 0.00 0.00 37.85 3.96
2316 2410 8.097038 AGAGAAAGATATGTACAAGAGTTTGCA 58.903 33.333 0.00 0.00 37.85 4.08
2317 2411 8.485976 AGAGAAAGATATGTACAAGAGTTTGC 57.514 34.615 0.00 0.00 37.85 3.68
2318 2412 9.868277 AGAGAGAAAGATATGTACAAGAGTTTG 57.132 33.333 0.00 0.00 40.24 2.93
2321 2415 9.474313 AGAAGAGAGAAAGATATGTACAAGAGT 57.526 33.333 0.00 0.00 0.00 3.24
2334 2428 9.482175 ACCTTAGCTTTATAGAAGAGAGAAAGA 57.518 33.333 0.00 0.00 30.29 2.52
2337 2431 8.838365 CGTACCTTAGCTTTATAGAAGAGAGAA 58.162 37.037 0.00 0.00 0.00 2.87
2338 2432 7.041235 GCGTACCTTAGCTTTATAGAAGAGAGA 60.041 40.741 0.00 0.00 0.00 3.10
2339 2433 7.079475 GCGTACCTTAGCTTTATAGAAGAGAG 58.921 42.308 0.00 0.00 0.00 3.20
2340 2434 6.544931 TGCGTACCTTAGCTTTATAGAAGAGA 59.455 38.462 0.00 0.00 0.00 3.10
2341 2435 6.736123 TGCGTACCTTAGCTTTATAGAAGAG 58.264 40.000 0.00 0.00 0.00 2.85
2342 2436 6.704289 TGCGTACCTTAGCTTTATAGAAGA 57.296 37.500 0.00 0.00 0.00 2.87
2343 2437 7.948278 AATGCGTACCTTAGCTTTATAGAAG 57.052 36.000 0.00 0.00 0.00 2.85
2344 2438 7.225931 CCAAATGCGTACCTTAGCTTTATAGAA 59.774 37.037 0.00 0.00 31.78 2.10
2345 2439 6.704493 CCAAATGCGTACCTTAGCTTTATAGA 59.296 38.462 0.00 0.00 31.78 1.98
2346 2440 6.565999 GCCAAATGCGTACCTTAGCTTTATAG 60.566 42.308 0.00 0.00 31.78 1.31
2347 2441 5.237779 GCCAAATGCGTACCTTAGCTTTATA 59.762 40.000 0.00 0.00 31.78 0.98
2348 2442 4.036380 GCCAAATGCGTACCTTAGCTTTAT 59.964 41.667 0.00 0.00 31.78 1.40
2349 2443 3.375922 GCCAAATGCGTACCTTAGCTTTA 59.624 43.478 0.00 0.00 31.78 1.85
2350 2444 2.163613 GCCAAATGCGTACCTTAGCTTT 59.836 45.455 0.00 0.00 33.11 3.51
2351 2445 1.743394 GCCAAATGCGTACCTTAGCTT 59.257 47.619 0.00 0.00 0.00 3.74
2352 2446 1.379527 GCCAAATGCGTACCTTAGCT 58.620 50.000 0.00 0.00 0.00 3.32
2353 2447 3.918102 GCCAAATGCGTACCTTAGC 57.082 52.632 0.00 0.00 0.00 3.09
2363 2457 3.552604 TTTCAAGAGTACGCCAAATGC 57.447 42.857 0.00 0.00 0.00 3.56
2383 2477 5.936956 TGTTTGCAGGATTGTTTGTCTTTTT 59.063 32.000 0.00 0.00 0.00 1.94
2384 2478 5.486526 TGTTTGCAGGATTGTTTGTCTTTT 58.513 33.333 0.00 0.00 0.00 2.27
2385 2479 5.083533 TGTTTGCAGGATTGTTTGTCTTT 57.916 34.783 0.00 0.00 0.00 2.52
2386 2480 4.734398 TGTTTGCAGGATTGTTTGTCTT 57.266 36.364 0.00 0.00 0.00 3.01
2387 2481 4.734398 TTGTTTGCAGGATTGTTTGTCT 57.266 36.364 0.00 0.00 0.00 3.41
2388 2482 5.793026 TTTTGTTTGCAGGATTGTTTGTC 57.207 34.783 0.00 0.00 0.00 3.18
2389 2483 5.471456 TGTTTTTGTTTGCAGGATTGTTTGT 59.529 32.000 0.00 0.00 0.00 2.83
2390 2484 5.936054 TGTTTTTGTTTGCAGGATTGTTTG 58.064 33.333 0.00 0.00 0.00 2.93
2391 2485 6.566197 TTGTTTTTGTTTGCAGGATTGTTT 57.434 29.167 0.00 0.00 0.00 2.83
2392 2486 6.373774 TGATTGTTTTTGTTTGCAGGATTGTT 59.626 30.769 0.00 0.00 0.00 2.83
2393 2487 5.879223 TGATTGTTTTTGTTTGCAGGATTGT 59.121 32.000 0.00 0.00 0.00 2.71
2394 2488 6.037391 AGTGATTGTTTTTGTTTGCAGGATTG 59.963 34.615 0.00 0.00 0.00 2.67
2395 2489 6.037391 CAGTGATTGTTTTTGTTTGCAGGATT 59.963 34.615 0.00 0.00 0.00 3.01
2396 2490 5.524646 CAGTGATTGTTTTTGTTTGCAGGAT 59.475 36.000 0.00 0.00 0.00 3.24
2397 2491 4.869297 CAGTGATTGTTTTTGTTTGCAGGA 59.131 37.500 0.00 0.00 0.00 3.86
2398 2492 4.034279 CCAGTGATTGTTTTTGTTTGCAGG 59.966 41.667 0.00 0.00 0.00 4.85
2399 2493 4.869297 TCCAGTGATTGTTTTTGTTTGCAG 59.131 37.500 0.00 0.00 0.00 4.41
2400 2494 4.825422 TCCAGTGATTGTTTTTGTTTGCA 58.175 34.783 0.00 0.00 0.00 4.08
2401 2495 5.523188 TGATCCAGTGATTGTTTTTGTTTGC 59.477 36.000 0.00 0.00 0.00 3.68
2402 2496 7.536895 TTGATCCAGTGATTGTTTTTGTTTG 57.463 32.000 0.00 0.00 0.00 2.93
2403 2497 9.260002 GTATTGATCCAGTGATTGTTTTTGTTT 57.740 29.630 0.00 0.00 0.00 2.83
2404 2498 8.641541 AGTATTGATCCAGTGATTGTTTTTGTT 58.358 29.630 0.00 0.00 0.00 2.83
2405 2499 8.084073 CAGTATTGATCCAGTGATTGTTTTTGT 58.916 33.333 0.00 0.00 0.00 2.83
2406 2500 7.062605 GCAGTATTGATCCAGTGATTGTTTTTG 59.937 37.037 0.00 0.00 0.00 2.44
2407 2501 7.092716 GCAGTATTGATCCAGTGATTGTTTTT 58.907 34.615 0.00 0.00 0.00 1.94
2416 2511 5.121105 TGAGATTGCAGTATTGATCCAGTG 58.879 41.667 0.00 0.00 0.00 3.66
2564 2673 7.386851 TGACCTCAGTAACTTCCTTCTAATTG 58.613 38.462 0.00 0.00 0.00 2.32
2601 2713 9.684702 TTAGATATGTAACCCCCTTCTTCTATT 57.315 33.333 0.00 0.00 0.00 1.73
2614 2726 2.157085 GGCGCGCTTTAGATATGTAACC 59.843 50.000 32.29 3.82 0.00 2.85
2688 2929 6.472016 TGAATTATGCCACTTGTCACTTCTA 58.528 36.000 0.00 0.00 0.00 2.10
2770 3011 3.055094 ACAAGTACAGTCCCCATCATGAC 60.055 47.826 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.