Multiple sequence alignment - TraesCS7D01G422800

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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 TraesCS7D01G422800 chr7D 100.000 2815 0 0 1 2815 543550093 543552907 0.000000e+00 5199
1 TraesCS7D01G422800 chr7B 95.141 2264 67 9 1 2250 586630210 586632444 0.000000e+00 3531
2 TraesCS7D01G422800 chr7B 93.077 390 12 6 2437 2815 586632446 586632831 8.810000e-155 556


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 TraesCS7D01G422800 chr7D 543550093 543552907 2814 False 5199.0 5199 100.000 1 2815 1 chr7D.!!$F1 2814
1 TraesCS7D01G422800 chr7B 586630210 586632831 2621 False 2043.5 3531 94.109 1 2815 2 chr7B.!!$F1 2814

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
122 126 0.032952 TTGCTACCCGATGCCGTATC 59.967 55.0 0.00 0.0 0.0 2.24 F
779 791 0.739462 CGAGTTACTCCCGCAATGCA 60.739 55.0 5.91 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 1631 0.734253 CAAGTCTCGTTCCTGCCTCG 60.734 60.0 0.0 0.0 0.0 4.63 R
2356 2371 0.315251 TGTCTGTGAAGTCGCTCTGG 59.685 55.0 0.0 0.0 0.0 3.86 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
59 63 1.254975 GGGTTTCGGTGATTTGGGGG 61.255 60.000 0.00 0.00 0.00 5.40
117 121 2.543777 TCTAATTGCTACCCGATGCC 57.456 50.000 0.00 0.00 0.00 4.40
122 126 0.032952 TTGCTACCCGATGCCGTATC 59.967 55.000 0.00 0.00 0.00 2.24
156 160 6.983307 TGAACACCAATTTAACTTGAACCATG 59.017 34.615 7.10 0.00 0.00 3.66
243 247 6.216569 TGCAATTAGGATAAGACGAGATCAC 58.783 40.000 0.00 0.00 0.00 3.06
284 288 9.178758 GGTCATTAACCTGAAAGATCATTAACT 57.821 33.333 0.00 0.00 45.45 2.24
298 302 9.507329 AAGATCATTAACTTAAAACAGAGAGCA 57.493 29.630 0.00 0.00 0.00 4.26
299 303 9.507329 AGATCATTAACTTAAAACAGAGAGCAA 57.493 29.630 0.00 0.00 0.00 3.91
302 306 9.507329 TCATTAACTTAAAACAGAGAGCAATCT 57.493 29.630 0.00 0.00 0.00 2.40
305 309 7.674471 AACTTAAAACAGAGAGCAATCTACC 57.326 36.000 0.00 0.00 0.00 3.18
306 310 7.010339 ACTTAAAACAGAGAGCAATCTACCT 57.990 36.000 0.00 0.00 0.00 3.08
307 311 7.454225 ACTTAAAACAGAGAGCAATCTACCTT 58.546 34.615 0.00 0.00 0.00 3.50
308 312 7.389053 ACTTAAAACAGAGAGCAATCTACCTTG 59.611 37.037 0.00 0.00 0.00 3.61
309 313 5.489792 AAACAGAGAGCAATCTACCTTGA 57.510 39.130 0.00 0.00 0.00 3.02
310 314 5.489792 AACAGAGAGCAATCTACCTTGAA 57.510 39.130 0.00 0.00 0.00 2.69
311 315 5.489792 ACAGAGAGCAATCTACCTTGAAA 57.510 39.130 0.00 0.00 0.00 2.69
352 356 4.216257 ACAGAACCATTGACATGTTAGCAC 59.784 41.667 0.00 0.00 0.00 4.40
355 359 1.401552 CCATTGACATGTTAGCACGGG 59.598 52.381 0.00 0.00 0.00 5.28
361 365 3.055747 TGACATGTTAGCACGGGTGATTA 60.056 43.478 0.00 0.00 0.00 1.75
362 366 3.936453 GACATGTTAGCACGGGTGATTAA 59.064 43.478 0.00 0.00 0.00 1.40
363 367 3.687698 ACATGTTAGCACGGGTGATTAAC 59.312 43.478 2.38 10.37 35.07 2.01
385 389 4.394920 ACAACAACCGAGGCATGTAAATAG 59.605 41.667 0.00 0.00 0.00 1.73
424 428 2.099098 AGAACGTCCCAAACAAAAGCAG 59.901 45.455 0.00 0.00 0.00 4.24
475 479 2.092212 CCCCAGCCATATGTGAAGTTCT 60.092 50.000 4.17 0.00 0.00 3.01
483 487 4.080919 CCATATGTGAAGTTCTGACAGGGA 60.081 45.833 1.81 0.00 0.00 4.20
619 631 1.074566 ACCTGCCTCTCCTTTTCCTTG 59.925 52.381 0.00 0.00 0.00 3.61
656 668 1.607467 ATGGGCAGGGAGTTGTTGC 60.607 57.895 0.00 0.00 37.11 4.17
659 671 1.187567 GGGCAGGGAGTTGTTGCATT 61.188 55.000 0.00 0.00 39.54 3.56
718 730 3.412386 TCTGCCTTTTCTCTTGGCTTAC 58.588 45.455 0.00 0.00 46.23 2.34
779 791 0.739462 CGAGTTACTCCCGCAATGCA 60.739 55.000 5.91 0.00 0.00 3.96
809 821 3.945285 CCTCTGTTGTGTTACTTGTTGGT 59.055 43.478 0.00 0.00 0.00 3.67
871 883 6.660094 AGCGTAGTATTTAATTGTTTTCCCCA 59.340 34.615 0.00 0.00 0.00 4.96
921 933 9.620259 ATTAGTCTTTCCATCTTAGGATGTTTC 57.380 33.333 13.26 0.00 45.66 2.78
1013 1025 4.780021 ACTGAAGGAGATGTCTGTGGTTAT 59.220 41.667 0.00 0.00 0.00 1.89
1047 1059 1.679977 TCCAGAGCATTTGGGCAGC 60.680 57.895 1.93 0.00 36.34 5.25
1108 1120 8.044060 AGTAATGACATCTTACCATGTTGTTG 57.956 34.615 0.00 0.00 37.11 3.33
1121 1133 3.988379 TGTTGTTGAATCAGCCTTCAC 57.012 42.857 0.00 0.00 34.96 3.18
1128 1140 3.282021 TGAATCAGCCTTCACTAATGGC 58.718 45.455 0.00 0.00 46.42 4.40
1135 1147 2.887152 GCCTTCACTAATGGCCTTATGG 59.113 50.000 3.32 0.00 40.71 2.74
1206 1218 0.765510 ATTTATCCGAGCCTGGGGAC 59.234 55.000 0.00 0.00 34.58 4.46
1225 1237 4.566907 GGGACCTTGCCATACTTCAGTTTA 60.567 45.833 0.00 0.00 0.00 2.01
1237 1249 3.826729 ACTTCAGTTTAATTGTGAGGGCC 59.173 43.478 0.00 0.00 0.00 5.80
1260 1272 5.047802 CCATATGTTTGAACCTCTGCTGTTT 60.048 40.000 1.24 0.00 0.00 2.83
1280 1292 7.015226 TGTTTGCTGAAATATCTACCAATCG 57.985 36.000 0.00 0.00 0.00 3.34
1478 1490 9.301153 GGTTAAAATACATATTTGCTGGAACTG 57.699 33.333 0.00 0.00 36.14 3.16
1541 1553 4.035558 ACTGGTGTTCATATGCTTTATGCG 59.964 41.667 0.00 0.00 46.63 4.73
1598 1610 7.202195 GGACCAATTATTATGGGAGGTAGAGTT 60.202 40.741 0.00 0.00 42.48 3.01
1599 1611 7.518188 ACCAATTATTATGGGAGGTAGAGTTG 58.482 38.462 0.00 0.00 42.48 3.16
1619 1631 2.358322 TTGGAGTCAACAAAGGGTCC 57.642 50.000 0.00 0.00 0.00 4.46
1660 1672 2.104111 CTGTTTCAGTCCTGGGTGTACA 59.896 50.000 0.00 0.00 0.00 2.90
1661 1673 2.158871 TGTTTCAGTCCTGGGTGTACAC 60.159 50.000 18.01 18.01 0.00 2.90
1680 1692 1.492176 ACACCATGCTAGAGGATTGGG 59.508 52.381 0.00 0.00 0.00 4.12
1700 1712 3.244596 GGGCTGTAAGAGTTCCAGACTTT 60.245 47.826 0.00 0.00 39.19 2.66
1706 1718 7.316544 TGTAAGAGTTCCAGACTTTGTTTTC 57.683 36.000 0.00 0.00 39.19 2.29
1800 1815 5.456548 TGAGATGCTTGAAATGCTTGAAA 57.543 34.783 0.00 0.00 37.94 2.69
1801 1816 5.466819 TGAGATGCTTGAAATGCTTGAAAG 58.533 37.500 0.00 0.00 37.94 2.62
1804 1819 2.071540 GCTTGAAATGCTTGAAAGGCC 58.928 47.619 0.00 0.00 33.64 5.19
1807 1822 1.619827 TGAAATGCTTGAAAGGCCTGG 59.380 47.619 5.69 0.00 0.00 4.45
1916 1931 6.375174 TCACTATGTCCAATTCACTCCATTTG 59.625 38.462 0.00 0.00 0.00 2.32
1921 1936 7.353414 TGTCCAATTCACTCCATTTGTTAAA 57.647 32.000 0.00 0.00 0.00 1.52
2005 2020 7.668052 TGCTATATCTAAACAAAAACTGTGGGT 59.332 33.333 0.00 0.00 38.67 4.51
2038 2053 7.992608 TCTCAATTAGTATGTGTGTATGCCAAT 59.007 33.333 0.00 0.00 0.00 3.16
2043 2058 9.706691 ATTAGTATGTGTGTATGCCAATAGTAC 57.293 33.333 0.00 0.00 0.00 2.73
2081 2096 3.305539 GGTCATCACACGTACTGTACCAA 60.306 47.826 12.08 0.00 0.00 3.67
2179 2194 4.509970 TCAGTCACAAACATAACTTCACCG 59.490 41.667 0.00 0.00 0.00 4.94
2263 2278 6.579666 TTAGCATGGATATTTGAATGAGGC 57.420 37.500 0.00 0.00 0.00 4.70
2264 2279 3.830755 AGCATGGATATTTGAATGAGGCC 59.169 43.478 0.00 0.00 0.00 5.19
2265 2280 3.830755 GCATGGATATTTGAATGAGGCCT 59.169 43.478 3.86 3.86 0.00 5.19
2266 2281 4.082354 GCATGGATATTTGAATGAGGCCTC 60.082 45.833 26.78 26.78 0.00 4.70
2267 2282 4.104383 TGGATATTTGAATGAGGCCTCC 57.896 45.455 29.95 15.18 0.00 4.30
2268 2283 3.723681 TGGATATTTGAATGAGGCCTCCT 59.276 43.478 29.95 18.16 36.03 3.69
2269 2284 4.913355 TGGATATTTGAATGAGGCCTCCTA 59.087 41.667 29.95 13.16 31.76 2.94
2270 2285 5.013495 TGGATATTTGAATGAGGCCTCCTAG 59.987 44.000 29.95 0.00 31.76 3.02
2271 2286 5.249393 GGATATTTGAATGAGGCCTCCTAGA 59.751 44.000 29.95 11.93 31.76 2.43
2272 2287 6.069731 GGATATTTGAATGAGGCCTCCTAGAT 60.070 42.308 29.95 13.88 31.76 1.98
2273 2288 5.659849 ATTTGAATGAGGCCTCCTAGATT 57.340 39.130 29.95 21.45 31.76 2.40
2274 2289 4.696479 TTGAATGAGGCCTCCTAGATTC 57.304 45.455 29.95 27.52 35.13 2.52
2275 2290 2.630098 TGAATGAGGCCTCCTAGATTCG 59.370 50.000 29.95 0.00 36.30 3.34
2276 2291 2.685106 ATGAGGCCTCCTAGATTCGA 57.315 50.000 29.95 8.27 31.76 3.71
2277 2292 2.454336 TGAGGCCTCCTAGATTCGAA 57.546 50.000 29.95 0.00 31.76 3.71
2278 2293 2.747177 TGAGGCCTCCTAGATTCGAAA 58.253 47.619 29.95 3.38 31.76 3.46
2279 2294 2.695666 TGAGGCCTCCTAGATTCGAAAG 59.304 50.000 29.95 0.00 31.76 2.62
2280 2295 2.959707 GAGGCCTCCTAGATTCGAAAGA 59.040 50.000 23.19 0.00 31.76 2.52
2281 2296 3.576550 GAGGCCTCCTAGATTCGAAAGAT 59.423 47.826 23.19 0.00 34.63 2.40
2282 2297 4.742012 AGGCCTCCTAGATTCGAAAGATA 58.258 43.478 0.00 0.00 33.05 1.98
2283 2298 5.148502 AGGCCTCCTAGATTCGAAAGATAA 58.851 41.667 0.00 0.00 33.05 1.75
2284 2299 5.245075 AGGCCTCCTAGATTCGAAAGATAAG 59.755 44.000 0.00 0.00 33.05 1.73
2285 2300 5.244178 GGCCTCCTAGATTCGAAAGATAAGA 59.756 44.000 0.00 0.00 41.60 2.10
2286 2301 6.386654 GCCTCCTAGATTCGAAAGATAAGAG 58.613 44.000 0.00 4.83 41.60 2.85
2287 2302 6.207810 GCCTCCTAGATTCGAAAGATAAGAGA 59.792 42.308 0.00 0.00 41.60 3.10
2288 2303 7.590279 CCTCCTAGATTCGAAAGATAAGAGAC 58.410 42.308 0.00 0.00 41.60 3.36
2289 2304 7.229707 CCTCCTAGATTCGAAAGATAAGAGACA 59.770 40.741 0.00 0.00 41.60 3.41
2290 2305 8.521170 TCCTAGATTCGAAAGATAAGAGACAA 57.479 34.615 0.00 0.00 41.60 3.18
2291 2306 8.407064 TCCTAGATTCGAAAGATAAGAGACAAC 58.593 37.037 0.00 0.00 41.60 3.32
2292 2307 8.191446 CCTAGATTCGAAAGATAAGAGACAACA 58.809 37.037 0.00 0.00 41.60 3.33
2293 2308 9.574458 CTAGATTCGAAAGATAAGAGACAACAA 57.426 33.333 0.00 0.00 41.60 2.83
2297 2312 7.757097 TCGAAAGATAAGAGACAACAATAGC 57.243 36.000 0.00 0.00 33.31 2.97
2298 2313 7.548097 TCGAAAGATAAGAGACAACAATAGCT 58.452 34.615 0.00 0.00 33.31 3.32
2299 2314 8.683615 TCGAAAGATAAGAGACAACAATAGCTA 58.316 33.333 0.00 0.00 33.31 3.32
2300 2315 9.302345 CGAAAGATAAGAGACAACAATAGCTAA 57.698 33.333 0.00 0.00 0.00 3.09
2302 2317 8.655651 AAGATAAGAGACAACAATAGCTAAGC 57.344 34.615 0.00 0.00 0.00 3.09
2303 2318 8.017418 AGATAAGAGACAACAATAGCTAAGCT 57.983 34.615 0.00 0.00 43.41 3.74
2304 2319 9.137459 AGATAAGAGACAACAATAGCTAAGCTA 57.863 33.333 0.00 0.00 45.55 3.32
2305 2320 9.751542 GATAAGAGACAACAATAGCTAAGCTAA 57.248 33.333 0.00 0.00 44.62 3.09
2306 2321 9.757227 ATAAGAGACAACAATAGCTAAGCTAAG 57.243 33.333 0.00 0.00 44.62 2.18
2307 2322 7.411486 AGAGACAACAATAGCTAAGCTAAGA 57.589 36.000 0.00 0.00 44.62 2.10
2308 2323 8.017418 AGAGACAACAATAGCTAAGCTAAGAT 57.983 34.615 0.00 0.00 44.62 2.40
2309 2324 7.925483 AGAGACAACAATAGCTAAGCTAAGATG 59.075 37.037 0.00 0.00 44.62 2.90
2310 2325 7.786030 AGACAACAATAGCTAAGCTAAGATGA 58.214 34.615 0.00 0.00 44.62 2.92
2311 2326 8.260818 AGACAACAATAGCTAAGCTAAGATGAA 58.739 33.333 0.00 0.00 44.62 2.57
2312 2327 8.792830 ACAACAATAGCTAAGCTAAGATGAAA 57.207 30.769 0.00 0.00 44.62 2.69
2313 2328 8.669243 ACAACAATAGCTAAGCTAAGATGAAAC 58.331 33.333 0.00 0.00 44.62 2.78
2314 2329 8.887717 CAACAATAGCTAAGCTAAGATGAAACT 58.112 33.333 0.00 0.00 44.62 2.66
2315 2330 9.454859 AACAATAGCTAAGCTAAGATGAAACTT 57.545 29.630 0.00 0.00 44.62 2.66
2320 2335 8.710835 AGCTAAGCTAAGATGAAACTTAGTTC 57.289 34.615 14.17 0.00 46.21 3.01
2321 2336 7.489757 AGCTAAGCTAAGATGAAACTTAGTTCG 59.510 37.037 14.17 7.04 46.21 3.95
2322 2337 6.410243 AAGCTAAGATGAAACTTAGTTCGC 57.590 37.500 14.17 0.00 46.21 4.70
2323 2338 4.870991 AGCTAAGATGAAACTTAGTTCGCC 59.129 41.667 14.17 0.00 46.21 5.54
2324 2339 4.870991 GCTAAGATGAAACTTAGTTCGCCT 59.129 41.667 14.17 0.00 46.21 5.52
2325 2340 5.220491 GCTAAGATGAAACTTAGTTCGCCTG 60.220 44.000 14.17 0.00 46.21 4.85
2326 2341 4.537135 AGATGAAACTTAGTTCGCCTGA 57.463 40.909 0.00 0.00 0.00 3.86
2327 2342 4.894784 AGATGAAACTTAGTTCGCCTGAA 58.105 39.130 0.00 0.00 0.00 3.02
2328 2343 5.305585 AGATGAAACTTAGTTCGCCTGAAA 58.694 37.500 0.00 0.00 35.46 2.69
2329 2344 5.409826 AGATGAAACTTAGTTCGCCTGAAAG 59.590 40.000 0.00 0.00 35.46 2.62
2330 2345 4.699637 TGAAACTTAGTTCGCCTGAAAGA 58.300 39.130 0.00 0.00 35.46 2.52
2331 2346 5.305585 TGAAACTTAGTTCGCCTGAAAGAT 58.694 37.500 0.00 0.00 35.46 2.40
2332 2347 5.763204 TGAAACTTAGTTCGCCTGAAAGATT 59.237 36.000 0.00 0.00 35.46 2.40
2333 2348 6.932400 TGAAACTTAGTTCGCCTGAAAGATTA 59.068 34.615 0.00 0.00 35.46 1.75
2334 2349 6.969828 AACTTAGTTCGCCTGAAAGATTAG 57.030 37.500 0.00 0.00 35.46 1.73
2335 2350 6.282199 ACTTAGTTCGCCTGAAAGATTAGA 57.718 37.500 0.00 0.00 35.46 2.10
2336 2351 6.879400 ACTTAGTTCGCCTGAAAGATTAGAT 58.121 36.000 0.00 0.00 35.46 1.98
2337 2352 8.008513 ACTTAGTTCGCCTGAAAGATTAGATA 57.991 34.615 0.00 0.00 35.46 1.98
2338 2353 8.475639 ACTTAGTTCGCCTGAAAGATTAGATAA 58.524 33.333 0.00 0.00 35.46 1.75
2339 2354 9.482627 CTTAGTTCGCCTGAAAGATTAGATAAT 57.517 33.333 0.00 0.00 35.46 1.28
2340 2355 9.832445 TTAGTTCGCCTGAAAGATTAGATAATT 57.168 29.630 0.00 0.00 35.46 1.40
2341 2356 8.147642 AGTTCGCCTGAAAGATTAGATAATTG 57.852 34.615 0.00 0.00 35.46 2.32
2342 2357 7.770897 AGTTCGCCTGAAAGATTAGATAATTGT 59.229 33.333 0.00 0.00 35.46 2.71
2343 2358 7.482654 TCGCCTGAAAGATTAGATAATTGTG 57.517 36.000 0.00 0.00 34.07 3.33
2344 2359 7.272244 TCGCCTGAAAGATTAGATAATTGTGA 58.728 34.615 0.00 0.00 34.07 3.58
2345 2360 7.768582 TCGCCTGAAAGATTAGATAATTGTGAA 59.231 33.333 0.00 0.00 34.07 3.18
2346 2361 8.562892 CGCCTGAAAGATTAGATAATTGTGAAT 58.437 33.333 0.00 0.00 34.07 2.57
2363 2378 9.520204 AATTGTGAATAATAATTTTCCAGAGCG 57.480 29.630 0.00 0.00 0.00 5.03
2364 2379 7.857734 TGTGAATAATAATTTTCCAGAGCGA 57.142 32.000 0.00 0.00 0.00 4.93
2365 2380 7.693952 TGTGAATAATAATTTTCCAGAGCGAC 58.306 34.615 0.00 0.00 0.00 5.19
2366 2381 7.552687 TGTGAATAATAATTTTCCAGAGCGACT 59.447 33.333 0.00 0.00 0.00 4.18
2367 2382 8.398665 GTGAATAATAATTTTCCAGAGCGACTT 58.601 33.333 0.00 0.00 0.00 3.01
2368 2383 8.612619 TGAATAATAATTTTCCAGAGCGACTTC 58.387 33.333 0.00 0.00 0.00 3.01
2369 2384 8.506168 AATAATAATTTTCCAGAGCGACTTCA 57.494 30.769 0.00 0.00 0.00 3.02
2370 2385 5.803020 ATAATTTTCCAGAGCGACTTCAC 57.197 39.130 0.00 0.00 0.00 3.18
2371 2386 2.613026 TTTTCCAGAGCGACTTCACA 57.387 45.000 0.00 0.00 0.00 3.58
2372 2387 2.154854 TTTCCAGAGCGACTTCACAG 57.845 50.000 0.00 0.00 0.00 3.66
2373 2388 1.328279 TTCCAGAGCGACTTCACAGA 58.672 50.000 0.00 0.00 0.00 3.41
2374 2389 0.598562 TCCAGAGCGACTTCACAGAC 59.401 55.000 0.00 0.00 0.00 3.51
2375 2390 0.315251 CCAGAGCGACTTCACAGACA 59.685 55.000 0.00 0.00 0.00 3.41
2376 2391 1.269778 CCAGAGCGACTTCACAGACAA 60.270 52.381 0.00 0.00 0.00 3.18
2377 2392 1.789464 CAGAGCGACTTCACAGACAAC 59.211 52.381 0.00 0.00 0.00 3.32
2378 2393 1.409064 AGAGCGACTTCACAGACAACA 59.591 47.619 0.00 0.00 0.00 3.33
2379 2394 2.159099 AGAGCGACTTCACAGACAACAA 60.159 45.455 0.00 0.00 0.00 2.83
2380 2395 1.933853 AGCGACTTCACAGACAACAAC 59.066 47.619 0.00 0.00 0.00 3.32
2381 2396 1.933853 GCGACTTCACAGACAACAACT 59.066 47.619 0.00 0.00 0.00 3.16
2382 2397 2.285834 GCGACTTCACAGACAACAACTG 60.286 50.000 0.00 0.00 40.68 3.16
2383 2398 2.285220 CGACTTCACAGACAACAACTGG 59.715 50.000 0.00 0.00 39.38 4.00
2384 2399 2.017049 ACTTCACAGACAACAACTGGC 58.983 47.619 0.00 0.00 39.38 4.85
2385 2400 2.016318 CTTCACAGACAACAACTGGCA 58.984 47.619 0.00 0.00 39.38 4.92
2386 2401 2.121291 TCACAGACAACAACTGGCAA 57.879 45.000 0.00 0.00 39.38 4.52
2387 2402 2.016318 TCACAGACAACAACTGGCAAG 58.984 47.619 0.00 0.00 39.38 4.01
2388 2403 2.016318 CACAGACAACAACTGGCAAGA 58.984 47.619 0.00 0.00 39.38 3.02
2389 2404 2.620115 CACAGACAACAACTGGCAAGAT 59.380 45.455 0.00 0.00 39.38 2.40
2390 2405 3.814842 CACAGACAACAACTGGCAAGATA 59.185 43.478 0.00 0.00 39.38 1.98
2391 2406 4.275689 CACAGACAACAACTGGCAAGATAA 59.724 41.667 0.00 0.00 39.38 1.75
2392 2407 4.516698 ACAGACAACAACTGGCAAGATAAG 59.483 41.667 0.00 0.00 39.38 1.73
2393 2408 4.756642 CAGACAACAACTGGCAAGATAAGA 59.243 41.667 0.00 0.00 34.24 2.10
2394 2409 5.413833 CAGACAACAACTGGCAAGATAAGAT 59.586 40.000 0.00 0.00 34.24 2.40
2395 2410 6.006449 AGACAACAACTGGCAAGATAAGATT 58.994 36.000 0.00 0.00 34.24 2.40
2396 2411 6.491403 AGACAACAACTGGCAAGATAAGATTT 59.509 34.615 0.00 0.00 34.24 2.17
2397 2412 6.449698 ACAACAACTGGCAAGATAAGATTTG 58.550 36.000 0.00 0.00 0.00 2.32
2398 2413 6.265196 ACAACAACTGGCAAGATAAGATTTGA 59.735 34.615 0.00 0.00 0.00 2.69
2399 2414 6.259550 ACAACTGGCAAGATAAGATTTGAC 57.740 37.500 0.00 0.00 32.85 3.18
2400 2415 5.106555 ACAACTGGCAAGATAAGATTTGACG 60.107 40.000 0.00 0.00 35.02 4.35
2401 2416 4.579869 ACTGGCAAGATAAGATTTGACGT 58.420 39.130 0.00 0.00 35.02 4.34
2402 2417 5.730550 ACTGGCAAGATAAGATTTGACGTA 58.269 37.500 0.00 0.00 35.02 3.57
2403 2418 6.170506 ACTGGCAAGATAAGATTTGACGTAA 58.829 36.000 0.00 0.00 35.02 3.18
2404 2419 6.823689 ACTGGCAAGATAAGATTTGACGTAAT 59.176 34.615 0.00 0.00 35.02 1.89
2405 2420 7.985184 ACTGGCAAGATAAGATTTGACGTAATA 59.015 33.333 0.00 0.00 35.02 0.98
2406 2421 8.902540 TGGCAAGATAAGATTTGACGTAATAT 57.097 30.769 0.00 0.00 35.02 1.28
2407 2422 8.988934 TGGCAAGATAAGATTTGACGTAATATC 58.011 33.333 0.00 0.00 35.02 1.63
2408 2423 8.988934 GGCAAGATAAGATTTGACGTAATATCA 58.011 33.333 6.18 0.00 0.00 2.15
2409 2424 9.798885 GCAAGATAAGATTTGACGTAATATCAC 57.201 33.333 6.18 0.00 0.00 3.06
2412 2427 9.698309 AGATAAGATTTGACGTAATATCACTGG 57.302 33.333 6.18 0.00 0.00 4.00
2413 2428 8.833231 ATAAGATTTGACGTAATATCACTGGG 57.167 34.615 6.18 0.00 0.00 4.45
2414 2429 6.479972 AGATTTGACGTAATATCACTGGGA 57.520 37.500 6.18 0.00 0.00 4.37
2415 2430 7.067496 AGATTTGACGTAATATCACTGGGAT 57.933 36.000 6.18 0.00 40.14 3.85
2416 2431 7.509546 AGATTTGACGTAATATCACTGGGATT 58.490 34.615 0.00 0.00 37.44 3.01
2417 2432 7.993183 AGATTTGACGTAATATCACTGGGATTT 59.007 33.333 0.00 0.00 37.44 2.17
2418 2433 7.931578 TTTGACGTAATATCACTGGGATTTT 57.068 32.000 0.00 0.00 37.44 1.82
2419 2434 7.931578 TTGACGTAATATCACTGGGATTTTT 57.068 32.000 0.00 0.00 37.44 1.94
2466 2481 6.025749 TGAGTTTGTGAGTTCATAGTCGAT 57.974 37.500 0.00 0.00 0.00 3.59
2574 2600 4.589216 TTTGTCAATTCTGAAGCCTTGG 57.411 40.909 0.00 0.00 31.88 3.61
2580 2606 5.047802 GTCAATTCTGAAGCCTTGGATGAAA 60.048 40.000 0.00 0.00 31.88 2.69
2599 2625 6.985188 TGAAATATCAGTTACTTGGAGTGC 57.015 37.500 0.00 0.00 0.00 4.40
2611 2637 4.655963 ACTTGGAGTGCATGTTTGATACT 58.344 39.130 0.00 0.00 0.00 2.12
2612 2638 5.804639 ACTTGGAGTGCATGTTTGATACTA 58.195 37.500 0.00 0.00 0.00 1.82
2613 2639 5.643777 ACTTGGAGTGCATGTTTGATACTAC 59.356 40.000 0.00 0.00 0.00 2.73
2628 2654 3.764810 CTACGCTGCTGGAGCCTCG 62.765 68.421 15.74 4.33 46.01 4.63
2659 2685 5.095490 GTGAAAGATGGTTTATTGCTTCCG 58.905 41.667 0.00 0.00 0.00 4.30
2686 2712 3.824414 AAGCCGTCGTTTATTTTGGAG 57.176 42.857 0.00 0.00 0.00 3.86
2698 2724 6.565999 CGTTTATTTTGGAGGTTGTCTGAGTC 60.566 42.308 0.00 0.00 0.00 3.36
2718 2744 7.327975 TGAGTCCGATGTGTAATTTGTATCTT 58.672 34.615 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 121 4.426416 TGGTGTTCAATAAGGACGATACG 58.574 43.478 0.00 0.00 0.00 3.06
122 126 7.590279 AGTTAAATTGGTGTTCAATAAGGACG 58.410 34.615 0.00 0.00 44.68 4.79
132 136 7.206687 TCATGGTTCAAGTTAAATTGGTGTTC 58.793 34.615 15.06 3.06 0.00 3.18
156 160 7.478520 AGCTACGGTTAATGTGATAATGTTC 57.521 36.000 0.00 0.00 0.00 3.18
284 288 7.450074 TCAAGGTAGATTGCTCTCTGTTTTAA 58.550 34.615 0.00 0.00 32.66 1.52
286 290 5.869579 TCAAGGTAGATTGCTCTCTGTTTT 58.130 37.500 0.00 0.00 32.66 2.43
287 291 5.489792 TCAAGGTAGATTGCTCTCTGTTT 57.510 39.130 0.00 0.00 32.66 2.83
291 295 5.884792 CCATTTTCAAGGTAGATTGCTCTCT 59.115 40.000 0.00 0.00 32.66 3.10
292 296 5.882557 TCCATTTTCAAGGTAGATTGCTCTC 59.117 40.000 0.00 0.00 32.66 3.20
293 297 5.819991 TCCATTTTCAAGGTAGATTGCTCT 58.180 37.500 0.00 0.00 35.39 4.09
294 298 6.705863 ATCCATTTTCAAGGTAGATTGCTC 57.294 37.500 0.00 0.00 0.00 4.26
295 299 8.773033 ATTATCCATTTTCAAGGTAGATTGCT 57.227 30.769 0.00 0.00 0.00 3.91
332 336 3.426159 CCGTGCTAACATGTCAATGGTTC 60.426 47.826 0.00 0.00 38.19 3.62
352 356 2.144730 TCGGTTGTTGTTAATCACCCG 58.855 47.619 7.51 7.51 35.63 5.28
355 359 2.550606 TGCCTCGGTTGTTGTTAATCAC 59.449 45.455 0.00 0.00 0.00 3.06
361 365 2.264005 TACATGCCTCGGTTGTTGTT 57.736 45.000 0.00 0.00 0.00 2.83
362 366 2.264005 TTACATGCCTCGGTTGTTGT 57.736 45.000 0.00 0.00 0.00 3.32
363 367 3.848272 ATTTACATGCCTCGGTTGTTG 57.152 42.857 0.00 0.00 0.00 3.33
385 389 6.744112 ACGTTCTAATCTGAGATCAAGATCC 58.256 40.000 10.41 0.06 38.58 3.36
424 428 0.464554 GGGCAGCAAGGGACATCTAC 60.465 60.000 0.00 0.00 0.00 2.59
475 479 0.397941 CTGTTGCCTCTTCCCTGTCA 59.602 55.000 0.00 0.00 0.00 3.58
483 487 2.069165 GACCCCCACTGTTGCCTCTT 62.069 60.000 0.00 0.00 0.00 2.85
515 527 1.443407 CCATCCTAGGACAGTGCCG 59.557 63.158 15.42 0.00 0.00 5.69
526 538 0.043485 TACCACCACTGGCCATCCTA 59.957 55.000 5.51 0.00 42.08 2.94
606 618 5.395324 CGCCTAGTAATCAAGGAAAAGGAGA 60.395 44.000 0.00 0.00 0.00 3.71
619 631 0.750850 TGTCCCAGCGCCTAGTAATC 59.249 55.000 2.29 0.00 0.00 1.75
779 791 0.767375 ACACAACAGAGGAGGCATGT 59.233 50.000 0.00 0.00 0.00 3.21
921 933 6.258068 GGAAATAAAGGTTGTCAGATAGGACG 59.742 42.308 0.00 0.00 40.72 4.79
1013 1025 1.302192 GGACTGCCGCCTTGTAACA 60.302 57.895 0.00 0.00 0.00 2.41
1047 1059 3.361443 GCAGTAAGCAACGAAACCG 57.639 52.632 0.00 0.00 44.79 4.44
1108 1120 3.978718 GCCATTAGTGAAGGCTGATTC 57.021 47.619 0.00 0.00 44.92 2.52
1121 1133 4.081322 ACCGTAACCATAAGGCCATTAG 57.919 45.455 5.01 0.00 39.06 1.73
1128 1140 6.482308 CAGGAAAGATAACCGTAACCATAAGG 59.518 42.308 0.00 0.00 42.21 2.69
1135 1147 3.937079 CCACCAGGAAAGATAACCGTAAC 59.063 47.826 0.00 0.00 36.89 2.50
1206 1218 6.808212 CACAATTAAACTGAAGTATGGCAAGG 59.192 38.462 0.00 0.00 0.00 3.61
1212 1224 6.404734 GGCCCTCACAATTAAACTGAAGTATG 60.405 42.308 0.00 0.00 0.00 2.39
1225 1237 4.352009 TCAAACATATGGCCCTCACAATT 58.648 39.130 7.80 0.00 0.00 2.32
1237 1249 5.633830 AACAGCAGAGGTTCAAACATATG 57.366 39.130 0.00 0.00 35.29 1.78
1260 1272 5.912892 TCACGATTGGTAGATATTTCAGCA 58.087 37.500 0.00 0.00 0.00 4.41
1280 1292 5.576447 AACCGTCCATGGAAATAAATCAC 57.424 39.130 18.20 0.00 0.00 3.06
1390 1402 7.169645 TCAGCAAATGCACAAAAAGTAAGATTC 59.830 33.333 8.28 0.00 45.16 2.52
1446 1458 7.491048 CAGCAAATATGTATTTTAACCACCACC 59.509 37.037 0.00 0.00 33.88 4.61
1478 1490 4.946784 ACCGCTGAGATACAAACAAATC 57.053 40.909 0.00 0.00 0.00 2.17
1617 1629 2.035155 TCTCGTTCCTGCCTCGGA 59.965 61.111 0.00 0.00 0.00 4.55
1619 1631 0.734253 CAAGTCTCGTTCCTGCCTCG 60.734 60.000 0.00 0.00 0.00 4.63
1660 1672 1.492176 CCCAATCCTCTAGCATGGTGT 59.508 52.381 7.89 0.00 0.00 4.16
1661 1673 1.816961 GCCCAATCCTCTAGCATGGTG 60.817 57.143 7.89 0.00 0.00 4.17
1680 1692 4.381411 ACAAAGTCTGGAACTCTTACAGC 58.619 43.478 0.00 0.00 37.17 4.40
1700 1712 5.365403 AGACAGTGAAAACAACGAAAACA 57.635 34.783 0.00 0.00 0.00 2.83
1706 1718 4.688879 TGCCTATAGACAGTGAAAACAACG 59.311 41.667 0.00 0.00 0.00 4.10
1800 1815 7.952368 AGATTGATTATTTTAATAGCCAGGCCT 59.048 33.333 8.22 0.00 0.00 5.19
1801 1816 8.127150 AGATTGATTATTTTAATAGCCAGGCC 57.873 34.615 8.22 0.00 0.00 5.19
1804 1819 9.970395 TGCAAGATTGATTATTTTAATAGCCAG 57.030 29.630 0.00 0.00 0.00 4.85
1921 1936 7.043565 GGACACAATTGGATATGCAAGAAAAT 58.956 34.615 15.23 1.18 0.00 1.82
2005 2020 7.555965 ACACACATACTAATTGAGATAGCACA 58.444 34.615 0.00 0.00 0.00 4.57
2043 2058 9.185192 GTGTGATGACCTAAGAAAAGAAATTTG 57.815 33.333 0.00 0.00 0.00 2.32
2060 2075 3.564235 TGGTACAGTACGTGTGATGAC 57.436 47.619 0.00 0.00 40.69 3.06
2081 2096 8.773033 ATAATTCCTTCCAAAGCATACAAGAT 57.227 30.769 0.00 0.00 0.00 2.40
2179 2194 5.537300 TCTACAGGTAGGATTGAATGAGC 57.463 43.478 6.62 0.00 34.06 4.26
2250 2265 6.519043 CGAATCTAGGAGGCCTCATTCAAATA 60.519 42.308 33.29 10.14 34.91 1.40
2251 2266 5.629125 GAATCTAGGAGGCCTCATTCAAAT 58.371 41.667 33.29 15.51 35.13 2.32
2252 2267 4.443457 CGAATCTAGGAGGCCTCATTCAAA 60.443 45.833 33.29 11.32 34.91 2.69
2253 2268 3.070159 CGAATCTAGGAGGCCTCATTCAA 59.930 47.826 33.29 15.84 34.91 2.69
2254 2269 2.630098 CGAATCTAGGAGGCCTCATTCA 59.370 50.000 33.29 17.02 34.91 2.57
2255 2270 2.894126 TCGAATCTAGGAGGCCTCATTC 59.106 50.000 33.29 27.86 34.61 2.67
2256 2271 2.964209 TCGAATCTAGGAGGCCTCATT 58.036 47.619 33.29 23.23 34.61 2.57
2257 2272 2.685106 TCGAATCTAGGAGGCCTCAT 57.315 50.000 33.29 29.46 34.61 2.90
2258 2273 2.454336 TTCGAATCTAGGAGGCCTCA 57.546 50.000 33.29 14.25 34.61 3.86
2259 2274 2.959707 TCTTTCGAATCTAGGAGGCCTC 59.040 50.000 25.59 25.59 34.61 4.70
2260 2275 3.033659 TCTTTCGAATCTAGGAGGCCT 57.966 47.619 3.86 3.86 37.71 5.19
2261 2276 5.244178 TCTTATCTTTCGAATCTAGGAGGCC 59.756 44.000 0.00 0.00 0.00 5.19
2262 2277 6.207810 TCTCTTATCTTTCGAATCTAGGAGGC 59.792 42.308 0.00 0.00 0.00 4.70
2263 2278 7.229707 TGTCTCTTATCTTTCGAATCTAGGAGG 59.770 40.741 0.00 0.00 0.00 4.30
2264 2279 8.160521 TGTCTCTTATCTTTCGAATCTAGGAG 57.839 38.462 0.00 6.79 0.00 3.69
2265 2280 8.407064 GTTGTCTCTTATCTTTCGAATCTAGGA 58.593 37.037 0.00 0.00 0.00 2.94
2266 2281 8.191446 TGTTGTCTCTTATCTTTCGAATCTAGG 58.809 37.037 0.00 0.00 0.00 3.02
2267 2282 9.574458 TTGTTGTCTCTTATCTTTCGAATCTAG 57.426 33.333 0.00 0.00 0.00 2.43
2271 2286 8.821894 GCTATTGTTGTCTCTTATCTTTCGAAT 58.178 33.333 0.00 0.00 0.00 3.34
2272 2287 8.035394 AGCTATTGTTGTCTCTTATCTTTCGAA 58.965 33.333 0.00 0.00 0.00 3.71
2273 2288 7.548097 AGCTATTGTTGTCTCTTATCTTTCGA 58.452 34.615 0.00 0.00 0.00 3.71
2274 2289 7.763172 AGCTATTGTTGTCTCTTATCTTTCG 57.237 36.000 0.00 0.00 0.00 3.46
2276 2291 9.103861 GCTTAGCTATTGTTGTCTCTTATCTTT 57.896 33.333 0.00 0.00 0.00 2.52
2277 2292 8.482128 AGCTTAGCTATTGTTGTCTCTTATCTT 58.518 33.333 4.30 0.00 36.99 2.40
2278 2293 8.017418 AGCTTAGCTATTGTTGTCTCTTATCT 57.983 34.615 4.30 0.00 36.99 1.98
2279 2294 9.751542 TTAGCTTAGCTATTGTTGTCTCTTATC 57.248 33.333 15.16 0.00 41.01 1.75
2280 2295 9.757227 CTTAGCTTAGCTATTGTTGTCTCTTAT 57.243 33.333 15.16 0.00 41.01 1.73
2281 2296 8.967918 TCTTAGCTTAGCTATTGTTGTCTCTTA 58.032 33.333 15.16 0.00 41.01 2.10
2282 2297 7.841956 TCTTAGCTTAGCTATTGTTGTCTCTT 58.158 34.615 15.16 0.00 41.01 2.85
2283 2298 7.411486 TCTTAGCTTAGCTATTGTTGTCTCT 57.589 36.000 15.16 0.00 41.01 3.10
2284 2299 7.923344 TCATCTTAGCTTAGCTATTGTTGTCTC 59.077 37.037 15.16 0.00 41.01 3.36
2285 2300 7.786030 TCATCTTAGCTTAGCTATTGTTGTCT 58.214 34.615 15.16 0.00 41.01 3.41
2286 2301 8.425577 TTCATCTTAGCTTAGCTATTGTTGTC 57.574 34.615 15.16 0.00 41.01 3.18
2287 2302 8.669243 GTTTCATCTTAGCTTAGCTATTGTTGT 58.331 33.333 15.16 0.00 41.01 3.32
2288 2303 8.887717 AGTTTCATCTTAGCTTAGCTATTGTTG 58.112 33.333 15.16 14.49 41.01 3.33
2289 2304 9.454859 AAGTTTCATCTTAGCTTAGCTATTGTT 57.545 29.630 15.16 4.06 41.01 2.83
2294 2309 9.804758 GAACTAAGTTTCATCTTAGCTTAGCTA 57.195 33.333 10.21 10.21 46.13 3.32
2295 2310 7.489757 CGAACTAAGTTTCATCTTAGCTTAGCT 59.510 37.037 12.67 12.67 46.13 3.32
2296 2311 7.614026 CGAACTAAGTTTCATCTTAGCTTAGC 58.386 38.462 11.73 0.00 46.13 3.09
2297 2312 7.254151 GGCGAACTAAGTTTCATCTTAGCTTAG 60.254 40.741 11.73 0.00 46.13 2.18
2298 2313 6.534079 GGCGAACTAAGTTTCATCTTAGCTTA 59.466 38.462 11.73 0.00 46.13 3.09
2299 2314 5.351740 GGCGAACTAAGTTTCATCTTAGCTT 59.648 40.000 11.73 7.01 46.13 3.74
2300 2315 4.870991 GGCGAACTAAGTTTCATCTTAGCT 59.129 41.667 11.73 0.00 46.13 3.32
2301 2316 4.870991 AGGCGAACTAAGTTTCATCTTAGC 59.129 41.667 11.73 1.73 46.13 3.09
2302 2317 6.100004 TCAGGCGAACTAAGTTTCATCTTAG 58.900 40.000 10.63 10.63 47.00 2.18
2303 2318 6.032956 TCAGGCGAACTAAGTTTCATCTTA 57.967 37.500 0.00 0.00 0.00 2.10
2304 2319 4.894784 TCAGGCGAACTAAGTTTCATCTT 58.105 39.130 0.00 0.00 0.00 2.40
2305 2320 4.537135 TCAGGCGAACTAAGTTTCATCT 57.463 40.909 0.00 0.00 0.00 2.90
2306 2321 5.408604 TCTTTCAGGCGAACTAAGTTTCATC 59.591 40.000 0.00 0.00 0.00 2.92
2307 2322 5.305585 TCTTTCAGGCGAACTAAGTTTCAT 58.694 37.500 0.00 0.00 0.00 2.57
2308 2323 4.699637 TCTTTCAGGCGAACTAAGTTTCA 58.300 39.130 0.00 0.00 0.00 2.69
2309 2324 5.864628 ATCTTTCAGGCGAACTAAGTTTC 57.135 39.130 0.00 0.00 0.00 2.78
2310 2325 7.159372 TCTAATCTTTCAGGCGAACTAAGTTT 58.841 34.615 0.00 0.00 0.00 2.66
2311 2326 6.698380 TCTAATCTTTCAGGCGAACTAAGTT 58.302 36.000 0.00 0.00 0.00 2.66
2312 2327 6.282199 TCTAATCTTTCAGGCGAACTAAGT 57.718 37.500 0.00 0.00 0.00 2.24
2313 2328 8.873215 TTATCTAATCTTTCAGGCGAACTAAG 57.127 34.615 0.00 0.00 0.00 2.18
2314 2329 9.832445 AATTATCTAATCTTTCAGGCGAACTAA 57.168 29.630 0.00 0.00 0.00 2.24
2315 2330 9.261180 CAATTATCTAATCTTTCAGGCGAACTA 57.739 33.333 0.00 0.00 0.00 2.24
2316 2331 7.770897 ACAATTATCTAATCTTTCAGGCGAACT 59.229 33.333 0.00 0.00 0.00 3.01
2317 2332 7.852945 CACAATTATCTAATCTTTCAGGCGAAC 59.147 37.037 0.00 0.00 0.00 3.95
2318 2333 7.768582 TCACAATTATCTAATCTTTCAGGCGAA 59.231 33.333 0.00 0.00 0.00 4.70
2319 2334 7.272244 TCACAATTATCTAATCTTTCAGGCGA 58.728 34.615 0.00 0.00 0.00 5.54
2320 2335 7.482654 TCACAATTATCTAATCTTTCAGGCG 57.517 36.000 0.00 0.00 0.00 5.52
2337 2352 9.520204 CGCTCTGGAAAATTATTATTCACAATT 57.480 29.630 0.00 0.00 0.00 2.32
2338 2353 8.902806 TCGCTCTGGAAAATTATTATTCACAAT 58.097 29.630 0.00 0.00 0.00 2.71
2339 2354 8.181573 GTCGCTCTGGAAAATTATTATTCACAA 58.818 33.333 0.00 0.00 0.00 3.33
2340 2355 7.552687 AGTCGCTCTGGAAAATTATTATTCACA 59.447 33.333 0.00 0.00 0.00 3.58
2341 2356 7.920738 AGTCGCTCTGGAAAATTATTATTCAC 58.079 34.615 0.00 0.00 0.00 3.18
2342 2357 8.506168 AAGTCGCTCTGGAAAATTATTATTCA 57.494 30.769 0.00 0.00 0.00 2.57
2343 2358 8.612619 TGAAGTCGCTCTGGAAAATTATTATTC 58.387 33.333 0.00 0.00 0.00 1.75
2344 2359 8.398665 GTGAAGTCGCTCTGGAAAATTATTATT 58.601 33.333 0.00 0.00 0.00 1.40
2345 2360 7.552687 TGTGAAGTCGCTCTGGAAAATTATTAT 59.447 33.333 0.00 0.00 0.00 1.28
2346 2361 6.876789 TGTGAAGTCGCTCTGGAAAATTATTA 59.123 34.615 0.00 0.00 0.00 0.98
2347 2362 5.705441 TGTGAAGTCGCTCTGGAAAATTATT 59.295 36.000 0.00 0.00 0.00 1.40
2348 2363 5.245531 TGTGAAGTCGCTCTGGAAAATTAT 58.754 37.500 0.00 0.00 0.00 1.28
2349 2364 4.637276 TGTGAAGTCGCTCTGGAAAATTA 58.363 39.130 0.00 0.00 0.00 1.40
2350 2365 3.476552 TGTGAAGTCGCTCTGGAAAATT 58.523 40.909 0.00 0.00 0.00 1.82
2351 2366 3.070018 CTGTGAAGTCGCTCTGGAAAAT 58.930 45.455 0.00 0.00 0.00 1.82
2352 2367 2.102420 TCTGTGAAGTCGCTCTGGAAAA 59.898 45.455 0.00 0.00 0.00 2.29
2353 2368 1.686587 TCTGTGAAGTCGCTCTGGAAA 59.313 47.619 0.00 0.00 0.00 3.13
2354 2369 1.000163 GTCTGTGAAGTCGCTCTGGAA 60.000 52.381 0.00 0.00 0.00 3.53
2355 2370 0.598562 GTCTGTGAAGTCGCTCTGGA 59.401 55.000 0.00 0.00 0.00 3.86
2356 2371 0.315251 TGTCTGTGAAGTCGCTCTGG 59.685 55.000 0.00 0.00 0.00 3.86
2357 2372 1.789464 GTTGTCTGTGAAGTCGCTCTG 59.211 52.381 0.00 0.00 0.00 3.35
2358 2373 1.409064 TGTTGTCTGTGAAGTCGCTCT 59.591 47.619 0.00 0.00 0.00 4.09
2359 2374 1.852942 TGTTGTCTGTGAAGTCGCTC 58.147 50.000 0.00 0.00 0.00 5.03
2360 2375 1.933853 GTTGTTGTCTGTGAAGTCGCT 59.066 47.619 0.00 0.00 0.00 4.93
2361 2376 1.933853 AGTTGTTGTCTGTGAAGTCGC 59.066 47.619 0.00 0.00 0.00 5.19
2362 2377 2.285220 CCAGTTGTTGTCTGTGAAGTCG 59.715 50.000 0.00 0.00 0.00 4.18
2363 2378 2.032178 GCCAGTTGTTGTCTGTGAAGTC 59.968 50.000 0.00 0.00 0.00 3.01
2364 2379 2.017049 GCCAGTTGTTGTCTGTGAAGT 58.983 47.619 0.00 0.00 0.00 3.01
2365 2380 2.016318 TGCCAGTTGTTGTCTGTGAAG 58.984 47.619 0.00 0.00 0.00 3.02
2366 2381 2.121291 TGCCAGTTGTTGTCTGTGAA 57.879 45.000 0.00 0.00 0.00 3.18
2367 2382 2.016318 CTTGCCAGTTGTTGTCTGTGA 58.984 47.619 0.00 0.00 0.00 3.58
2368 2383 2.016318 TCTTGCCAGTTGTTGTCTGTG 58.984 47.619 0.00 0.00 0.00 3.66
2369 2384 2.418368 TCTTGCCAGTTGTTGTCTGT 57.582 45.000 0.00 0.00 0.00 3.41
2370 2385 4.756642 TCTTATCTTGCCAGTTGTTGTCTG 59.243 41.667 0.00 0.00 0.00 3.51
2371 2386 4.973168 TCTTATCTTGCCAGTTGTTGTCT 58.027 39.130 0.00 0.00 0.00 3.41
2372 2387 5.886960 ATCTTATCTTGCCAGTTGTTGTC 57.113 39.130 0.00 0.00 0.00 3.18
2373 2388 6.265196 TCAAATCTTATCTTGCCAGTTGTTGT 59.735 34.615 0.00 0.00 0.00 3.32
2374 2389 6.583806 GTCAAATCTTATCTTGCCAGTTGTTG 59.416 38.462 0.00 0.00 0.00 3.33
2375 2390 6.568462 CGTCAAATCTTATCTTGCCAGTTGTT 60.568 38.462 0.00 0.00 0.00 2.83
2376 2391 5.106555 CGTCAAATCTTATCTTGCCAGTTGT 60.107 40.000 0.00 0.00 0.00 3.32
2377 2392 5.106555 ACGTCAAATCTTATCTTGCCAGTTG 60.107 40.000 0.00 0.00 0.00 3.16
2378 2393 5.003804 ACGTCAAATCTTATCTTGCCAGTT 58.996 37.500 0.00 0.00 0.00 3.16
2379 2394 4.579869 ACGTCAAATCTTATCTTGCCAGT 58.420 39.130 0.00 0.00 0.00 4.00
2380 2395 6.662414 TTACGTCAAATCTTATCTTGCCAG 57.338 37.500 0.00 0.00 0.00 4.85
2381 2396 8.902540 ATATTACGTCAAATCTTATCTTGCCA 57.097 30.769 0.00 0.00 0.00 4.92
2382 2397 8.988934 TGATATTACGTCAAATCTTATCTTGCC 58.011 33.333 0.00 0.00 0.00 4.52
2383 2398 9.798885 GTGATATTACGTCAAATCTTATCTTGC 57.201 33.333 0.00 0.00 0.00 4.01
2386 2401 9.698309 CCAGTGATATTACGTCAAATCTTATCT 57.302 33.333 0.00 0.00 0.00 1.98
2387 2402 8.926710 CCCAGTGATATTACGTCAAATCTTATC 58.073 37.037 0.00 0.00 0.00 1.75
2388 2403 8.647796 TCCCAGTGATATTACGTCAAATCTTAT 58.352 33.333 0.00 0.00 0.00 1.73
2389 2404 8.014070 TCCCAGTGATATTACGTCAAATCTTA 57.986 34.615 0.00 0.00 0.00 2.10
2390 2405 6.884832 TCCCAGTGATATTACGTCAAATCTT 58.115 36.000 0.00 0.00 0.00 2.40
2391 2406 6.479972 TCCCAGTGATATTACGTCAAATCT 57.520 37.500 0.00 0.00 0.00 2.40
2392 2407 7.730364 AATCCCAGTGATATTACGTCAAATC 57.270 36.000 0.00 0.00 31.83 2.17
2393 2408 8.519799 AAAATCCCAGTGATATTACGTCAAAT 57.480 30.769 0.00 0.00 31.83 2.32
2394 2409 7.931578 AAAATCCCAGTGATATTACGTCAAA 57.068 32.000 0.00 0.00 31.83 2.69
2395 2410 7.931578 AAAAATCCCAGTGATATTACGTCAA 57.068 32.000 0.00 0.00 31.83 3.18
2429 2444 9.071276 ACTCACAAACTCAATTATCTGACAATT 57.929 29.630 0.00 0.00 0.00 2.32
2430 2445 8.627208 ACTCACAAACTCAATTATCTGACAAT 57.373 30.769 0.00 0.00 0.00 2.71
2431 2446 8.450578 AACTCACAAACTCAATTATCTGACAA 57.549 30.769 0.00 0.00 0.00 3.18
2432 2447 7.714813 TGAACTCACAAACTCAATTATCTGACA 59.285 33.333 0.00 0.00 0.00 3.58
2433 2448 8.087982 TGAACTCACAAACTCAATTATCTGAC 57.912 34.615 0.00 0.00 0.00 3.51
2434 2449 8.853077 ATGAACTCACAAACTCAATTATCTGA 57.147 30.769 0.00 0.00 0.00 3.27
2466 2481 2.946329 ACACCACAAACATAAAGTGCGA 59.054 40.909 0.00 0.00 32.09 5.10
2513 2528 7.700322 ACACATGATAAGAGTAATACAAGCG 57.300 36.000 0.00 0.00 0.00 4.68
2555 2581 3.507162 TCCAAGGCTTCAGAATTGACA 57.493 42.857 0.00 0.00 31.71 3.58
2573 2599 7.254932 GCACTCCAAGTAACTGATATTTCATCC 60.255 40.741 0.00 0.00 0.00 3.51
2574 2600 7.280876 TGCACTCCAAGTAACTGATATTTCATC 59.719 37.037 0.00 0.00 0.00 2.92
2580 2606 5.994250 ACATGCACTCCAAGTAACTGATAT 58.006 37.500 0.00 0.00 0.00 1.63
2599 2625 3.001634 CCAGCAGCGTAGTATCAAACATG 59.998 47.826 0.00 0.00 0.00 3.21
2628 2654 0.698818 ACCATCTTTCACTCCACCCC 59.301 55.000 0.00 0.00 0.00 4.95
2659 2685 6.466730 CCAAAATAAACGACGGCTTAATGTAC 59.533 38.462 0.00 0.00 0.00 2.90
2686 2712 1.000955 ACACATCGGACTCAGACAACC 59.999 52.381 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.