Multiple sequence alignment - TraesCS1A01G201700

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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 TraesCS1A01G201700 chr1A 100.000 2750 0 0 1 2750 363008214 363005465 0.000000e+00 5079.0
1 TraesCS1A01G201700 chr1A 86.275 102 10 4 1480 1579 495306919 495307018 1.040000e-19 108.0
2 TraesCS1A01G201700 chr1D 95.652 1840 53 14 327 2160 290706883 290705065 0.000000e+00 2929.0
3 TraesCS1A01G201700 chr1D 87.460 311 16 4 13 323 290708966 290708679 1.220000e-88 337.0
4 TraesCS1A01G201700 chr1D 95.522 67 3 0 2227 2293 453567203 453567269 1.040000e-19 108.0
5 TraesCS1A01G201700 chr1D 89.474 76 8 0 2675 2750 290704023 290703948 2.250000e-16 97.1
6 TraesCS1A01G201700 chr1D 84.314 102 12 4 1480 1579 398246679 398246778 2.250000e-16 97.1
7 TraesCS1A01G201700 chr1D 91.935 62 5 0 2300 2361 290704378 290704317 1.360000e-13 87.9
8 TraesCS1A01G201700 chr1B 95.483 1572 37 14 630 2183 391962239 391960684 0.000000e+00 2479.0
9 TraesCS1A01G201700 chr1B 92.687 629 32 4 13 638 391964318 391963701 0.000000e+00 894.0
10 TraesCS1A01G201700 chr1B 86.275 102 10 4 1480 1579 533748208 533748307 1.040000e-19 108.0
11 TraesCS1A01G201700 chr1B 95.455 66 3 0 2227 2292 452310721 452310786 3.750000e-19 106.0
12 TraesCS1A01G201700 chr1B 94.203 69 4 0 2227 2295 684089056 684089124 3.750000e-19 106.0
13 TraesCS1A01G201700 chrUn 95.455 66 3 0 2227 2292 24003508 24003573 3.750000e-19 106.0
14 TraesCS1A01G201700 chr5B 95.385 65 3 0 2230 2294 10429515 10429451 1.350000e-18 104.0
15 TraesCS1A01G201700 chr3B 94.118 68 4 0 2227 2294 697073771 697073838 1.350000e-18 104.0
16 TraesCS1A01G201700 chr3B 91.111 45 4 0 2182 2226 68445610 68445654 8.220000e-06 62.1
17 TraesCS1A01G201700 chr3B 91.111 45 4 0 2182 2226 429973436 429973480 8.220000e-06 62.1
18 TraesCS1A01G201700 chr5D 93.939 66 4 0 2227 2292 413619808 413619873 1.740000e-17 100.0
19 TraesCS1A01G201700 chr5D 97.619 42 1 0 2173 2214 269020622 269020581 3.800000e-09 73.1
20 TraesCS1A01G201700 chr4D 93.939 66 4 0 2227 2292 483174943 483175008 1.740000e-17 100.0
21 TraesCS1A01G201700 chr4B 92.647 68 5 0 2227 2294 171114617 171114550 6.270000e-17 99.0
22 TraesCS1A01G201700 chr7A 90.000 50 4 1 2179 2228 722380714 722380762 2.290000e-06 63.9
23 TraesCS1A01G201700 chr7A 88.235 51 5 1 2165 2214 372015639 372015589 2.960000e-05 60.2
24 TraesCS1A01G201700 chr4A 91.489 47 3 1 2182 2228 684643534 684643489 2.290000e-06 63.9
25 TraesCS1A01G201700 chr4A 89.362 47 4 1 2182 2228 241027470 241027425 1.060000e-04 58.4
26 TraesCS1A01G201700 chr3A 91.111 45 4 0 2182 2226 700697500 700697456 8.220000e-06 62.1
27 TraesCS1A01G201700 chr2A 90.909 44 3 1 2185 2228 746836659 746836617 1.060000e-04 58.4


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 TraesCS1A01G201700 chr1A 363005465 363008214 2749 True 5079.00 5079 100.00000 1 2750 1 chr1A.!!$R1 2749
1 TraesCS1A01G201700 chr1D 290703948 290708966 5018 True 862.75 2929 91.13025 13 2750 4 chr1D.!!$R1 2737
2 TraesCS1A01G201700 chr1B 391960684 391964318 3634 True 1686.50 2479 94.08500 13 2183 2 chr1B.!!$R1 2170

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
209 220 0.101399 GACTCATCGTGATCGCCAGT 59.899 55.0 0.0 0.0 36.96 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 5409 0.179004 TCGCCCACACCAAACAGATT 60.179 50.0 0.0 0.0 0.0 2.4 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
152 153 0.832626 AGTTTTGCTTTGCCTTGCCT 59.167 45.000 0.00 0.00 0.00 4.75
153 154 1.210234 AGTTTTGCTTTGCCTTGCCTT 59.790 42.857 0.00 0.00 0.00 4.35
154 155 1.331447 GTTTTGCTTTGCCTTGCCTTG 59.669 47.619 0.00 0.00 0.00 3.61
155 156 0.814812 TTTGCTTTGCCTTGCCTTGC 60.815 50.000 0.00 0.00 0.00 4.01
156 157 2.357881 GCTTTGCCTTGCCTTGCC 60.358 61.111 0.00 0.00 0.00 4.52
157 158 2.875804 GCTTTGCCTTGCCTTGCCT 61.876 57.895 0.00 0.00 0.00 4.75
158 159 1.750297 CTTTGCCTTGCCTTGCCTT 59.250 52.632 0.00 0.00 0.00 4.35
159 160 0.601841 CTTTGCCTTGCCTTGCCTTG 60.602 55.000 0.00 0.00 0.00 3.61
160 161 1.336632 TTTGCCTTGCCTTGCCTTGT 61.337 50.000 0.00 0.00 0.00 3.16
161 162 1.747325 TTGCCTTGCCTTGCCTTGTC 61.747 55.000 0.00 0.00 0.00 3.18
206 217 0.872021 GTGGACTCATCGTGATCGCC 60.872 60.000 0.00 0.00 36.96 5.54
207 218 1.319614 TGGACTCATCGTGATCGCCA 61.320 55.000 0.00 0.00 36.96 5.69
208 219 0.596083 GGACTCATCGTGATCGCCAG 60.596 60.000 0.00 0.00 36.96 4.85
209 220 0.101399 GACTCATCGTGATCGCCAGT 59.899 55.000 0.00 0.00 36.96 4.00
210 221 1.333931 GACTCATCGTGATCGCCAGTA 59.666 52.381 0.00 0.00 36.96 2.74
211 222 1.335182 ACTCATCGTGATCGCCAGTAG 59.665 52.381 0.00 0.00 36.96 2.57
265 276 2.027625 GCTGGACGGACTTTCGTGG 61.028 63.158 0.00 0.00 43.96 4.94
274 285 0.111398 GACTTTCGTGGCGTTCGTTC 60.111 55.000 0.00 0.00 0.00 3.95
307 318 1.069636 GTTGAGGAACGCTTGCTTCTG 60.070 52.381 0.00 0.00 0.00 3.02
389 2192 0.179124 CTGTTCGAGACTGCTAGGCC 60.179 60.000 0.00 0.00 0.00 5.19
421 2224 1.405526 GCCTCGACTATTGGCAGTTGA 60.406 52.381 7.70 0.00 45.46 3.18
447 2250 1.812708 CGCTGCTCATGATTGGGATCA 60.813 52.381 0.00 0.00 45.81 2.92
472 2275 2.806856 CGCTTGATCGTGGAGCTGC 61.807 63.158 0.00 0.00 34.33 5.25
480 2283 3.376918 GTGGAGCTGCTTTGGCCC 61.377 66.667 6.82 0.00 37.74 5.80
481 2284 3.583380 TGGAGCTGCTTTGGCCCT 61.583 61.111 6.82 0.00 37.74 5.19
482 2285 2.753446 GGAGCTGCTTTGGCCCTC 60.753 66.667 2.53 0.00 37.74 4.30
483 2286 2.354343 GAGCTGCTTTGGCCCTCT 59.646 61.111 2.53 0.00 37.74 3.69
616 2419 3.244976 CGGTTCCATTTCATTGCAGAAC 58.755 45.455 3.34 3.34 34.31 3.01
674 3947 3.562557 AGCGAAGGCGTTTTCTTTTCTTA 59.437 39.130 0.00 0.00 46.35 2.10
716 3989 2.746362 GTCTCTGAATCTGCACCCAAAG 59.254 50.000 0.00 0.00 0.00 2.77
800 4074 1.184970 ACGTGGGCCTTTTGGGATTG 61.185 55.000 4.53 0.00 40.82 2.67
911 4195 2.912025 CCTGCCAACACCACCACC 60.912 66.667 0.00 0.00 0.00 4.61
958 4242 3.385577 GCCACAACTTTAATTTTGCGGA 58.614 40.909 7.48 0.00 27.92 5.54
962 4246 6.418141 CCACAACTTTAATTTTGCGGAAAAG 58.582 36.000 19.64 8.54 34.53 2.27
964 4248 5.007234 ACAACTTTAATTTTGCGGAAAAGGC 59.993 36.000 19.64 0.00 34.53 4.35
1293 4577 1.170290 GCGGGCATAACCATGGTACC 61.170 60.000 20.12 16.78 42.05 3.34
1680 4964 2.447714 GGAGACCATCCTGGAGGCC 61.448 68.421 2.09 0.00 45.64 5.19
1688 4972 4.899239 CCTGGAGGCCGTCATCGC 62.899 72.222 0.00 0.00 35.54 4.58
1689 4973 4.899239 CTGGAGGCCGTCATCGCC 62.899 72.222 0.00 0.00 35.54 5.54
1764 5048 2.287129 GCCGTAGTAGCAGTAGAAGAGC 60.287 54.545 0.00 0.00 0.00 4.09
1828 5112 2.876219 GCTGCTCCTTTCTGCTGC 59.124 61.111 0.00 0.00 44.21 5.25
1910 5194 8.430801 AGAATAATTAGAGCTGTGATGTGAAC 57.569 34.615 0.00 0.00 0.00 3.18
1967 5251 1.511305 GCTGCTGCTCCAGTACGTA 59.489 57.895 8.53 0.00 35.28 3.57
2124 5409 2.741759 TATGCAGCTCGTGTCTGAAA 57.258 45.000 11.38 2.03 33.54 2.69
2140 5425 3.636300 TCTGAAAATCTGTTTGGTGTGGG 59.364 43.478 0.00 0.00 0.00 4.61
2141 5426 2.102252 TGAAAATCTGTTTGGTGTGGGC 59.898 45.455 0.00 0.00 0.00 5.36
2142 5427 0.673437 AAATCTGTTTGGTGTGGGCG 59.327 50.000 0.00 0.00 0.00 6.13
2144 5429 0.038166 ATCTGTTTGGTGTGGGCGAT 59.962 50.000 0.00 0.00 0.00 4.58
2146 5431 0.673437 CTGTTTGGTGTGGGCGATTT 59.327 50.000 0.00 0.00 0.00 2.17
2169 6107 3.081804 GGTGGAAGTTGTGGAGTAATGG 58.918 50.000 0.00 0.00 0.00 3.16
2183 6121 7.282224 TGTGGAGTAATGGCAGTTATGAAATAC 59.718 37.037 0.00 0.00 0.00 1.89
2185 6123 6.206829 GGAGTAATGGCAGTTATGAAATACCC 59.793 42.308 0.00 0.00 0.00 3.69
2186 6124 6.068670 AGTAATGGCAGTTATGAAATACCCC 58.931 40.000 0.00 0.00 0.00 4.95
2187 6125 3.306472 TGGCAGTTATGAAATACCCCC 57.694 47.619 0.00 0.00 0.00 5.40
2188 6126 2.856231 TGGCAGTTATGAAATACCCCCT 59.144 45.455 0.00 0.00 0.00 4.79
2189 6127 3.117663 TGGCAGTTATGAAATACCCCCTC 60.118 47.826 0.00 0.00 0.00 4.30
2190 6128 3.487372 GCAGTTATGAAATACCCCCTCC 58.513 50.000 0.00 0.00 0.00 4.30
2194 6132 4.970640 AGTTATGAAATACCCCCTCCGTAA 59.029 41.667 0.00 0.00 0.00 3.18
2195 6133 5.429435 AGTTATGAAATACCCCCTCCGTAAA 59.571 40.000 0.00 0.00 0.00 2.01
2196 6134 6.102174 AGTTATGAAATACCCCCTCCGTAAAT 59.898 38.462 0.00 0.00 0.00 1.40
2197 6135 4.866327 TGAAATACCCCCTCCGTAAATT 57.134 40.909 0.00 0.00 0.00 1.82
2198 6136 5.972327 TGAAATACCCCCTCCGTAAATTA 57.028 39.130 0.00 0.00 0.00 1.40
2199 6137 6.324601 TGAAATACCCCCTCCGTAAATTAA 57.675 37.500 0.00 0.00 0.00 1.40
2200 6138 6.913545 TGAAATACCCCCTCCGTAAATTAAT 58.086 36.000 0.00 0.00 0.00 1.40
2201 6139 8.043429 TGAAATACCCCCTCCGTAAATTAATA 57.957 34.615 0.00 0.00 0.00 0.98
2202 6140 8.671409 TGAAATACCCCCTCCGTAAATTAATAT 58.329 33.333 0.00 0.00 0.00 1.28
2206 6144 7.876978 ACCCCCTCCGTAAATTAATATAAGA 57.123 36.000 0.00 0.00 0.00 2.10
2207 6145 7.914859 ACCCCCTCCGTAAATTAATATAAGAG 58.085 38.462 0.00 0.00 0.00 2.85
2208 6146 6.822170 CCCCCTCCGTAAATTAATATAAGAGC 59.178 42.308 0.00 0.00 0.00 4.09
2209 6147 7.391620 CCCCTCCGTAAATTAATATAAGAGCA 58.608 38.462 0.00 0.00 0.00 4.26
2210 6148 8.047310 CCCCTCCGTAAATTAATATAAGAGCAT 58.953 37.037 0.00 0.00 0.00 3.79
2211 6149 9.449719 CCCTCCGTAAATTAATATAAGAGCATT 57.550 33.333 0.00 0.00 0.00 3.56
2286 6224 8.723942 AACACTCTTATATTAGTTTGCAGAGG 57.276 34.615 0.00 0.00 32.21 3.69
2287 6225 7.275920 ACACTCTTATATTAGTTTGCAGAGGG 58.724 38.462 0.00 0.00 36.55 4.30
2288 6226 7.125811 ACACTCTTATATTAGTTTGCAGAGGGA 59.874 37.037 2.59 0.00 34.50 4.20
2289 6227 7.655328 CACTCTTATATTAGTTTGCAGAGGGAG 59.345 40.741 0.00 0.00 32.92 4.30
2290 6228 7.345914 ACTCTTATATTAGTTTGCAGAGGGAGT 59.654 37.037 0.00 0.00 32.21 3.85
2291 6229 8.777578 TCTTATATTAGTTTGCAGAGGGAGTA 57.222 34.615 0.00 0.00 0.00 2.59
2292 6230 8.639761 TCTTATATTAGTTTGCAGAGGGAGTAC 58.360 37.037 0.00 0.00 0.00 2.73
2293 6231 8.548880 TTATATTAGTTTGCAGAGGGAGTACT 57.451 34.615 0.00 0.00 0.00 2.73
2294 6232 5.763876 ATTAGTTTGCAGAGGGAGTACTT 57.236 39.130 0.00 0.00 0.00 2.24
2295 6233 3.686916 AGTTTGCAGAGGGAGTACTTC 57.313 47.619 0.00 0.00 0.00 3.01
2296 6234 2.303311 AGTTTGCAGAGGGAGTACTTCC 59.697 50.000 12.91 12.91 46.00 3.46
2343 6281 4.685165 CGACAATGGCATGAAAATGTTTCA 59.315 37.500 0.00 5.92 0.00 2.69
2344 6282 5.164031 CGACAATGGCATGAAAATGTTTCAG 60.164 40.000 0.00 3.64 0.00 3.02
2347 6285 5.999205 ATGGCATGAAAATGTTTCAGGTA 57.001 34.783 14.60 6.95 33.28 3.08
2361 6299 6.644347 TGTTTCAGGTATGGAGAGAGAAATC 58.356 40.000 0.00 0.00 0.00 2.17
2362 6300 6.213397 TGTTTCAGGTATGGAGAGAGAAATCA 59.787 38.462 0.00 0.00 0.00 2.57
2363 6301 6.874278 TTCAGGTATGGAGAGAGAAATCAA 57.126 37.500 0.00 0.00 0.00 2.57
2365 6303 8.553085 TTCAGGTATGGAGAGAGAAATCAATA 57.447 34.615 0.00 0.00 0.00 1.90
2366 6304 8.553085 TCAGGTATGGAGAGAGAAATCAATAA 57.447 34.615 0.00 0.00 0.00 1.40
2367 6305 9.163894 TCAGGTATGGAGAGAGAAATCAATAAT 57.836 33.333 0.00 0.00 0.00 1.28
2368 6306 9.434420 CAGGTATGGAGAGAGAAATCAATAATC 57.566 37.037 0.00 0.00 0.00 1.75
2369 6307 8.601546 AGGTATGGAGAGAGAAATCAATAATCC 58.398 37.037 0.00 0.00 0.00 3.01
2370 6308 8.601546 GGTATGGAGAGAGAAATCAATAATCCT 58.398 37.037 0.00 0.00 0.00 3.24
2373 6311 9.612879 ATGGAGAGAGAAATCAATAATCCTAGA 57.387 33.333 0.00 0.00 0.00 2.43
2374 6312 8.865090 TGGAGAGAGAAATCAATAATCCTAGAC 58.135 37.037 0.00 0.00 0.00 2.59
2375 6313 8.026607 GGAGAGAGAAATCAATAATCCTAGACG 58.973 40.741 0.00 0.00 0.00 4.18
2376 6314 8.472007 AGAGAGAAATCAATAATCCTAGACGT 57.528 34.615 0.00 0.00 0.00 4.34
2377 6315 9.575868 AGAGAGAAATCAATAATCCTAGACGTA 57.424 33.333 0.00 0.00 0.00 3.57
2378 6316 9.834628 GAGAGAAATCAATAATCCTAGACGTAG 57.165 37.037 0.00 0.00 0.00 3.51
2379 6317 8.798402 AGAGAAATCAATAATCCTAGACGTAGG 58.202 37.037 0.00 0.00 46.85 3.18
2380 6318 7.897864 AGAAATCAATAATCCTAGACGTAGGG 58.102 38.462 4.54 0.00 45.65 3.53
2381 6319 6.607004 AATCAATAATCCTAGACGTAGGGG 57.393 41.667 4.54 0.00 45.65 4.79
2382 6320 3.830755 TCAATAATCCTAGACGTAGGGGC 59.169 47.826 4.54 0.00 45.65 5.80
2383 6321 2.299326 TAATCCTAGACGTAGGGGCC 57.701 55.000 4.54 0.00 45.65 5.80
2384 6322 0.561680 AATCCTAGACGTAGGGGCCT 59.438 55.000 0.84 0.00 45.65 5.19
2385 6323 0.178958 ATCCTAGACGTAGGGGCCTG 60.179 60.000 0.84 0.00 45.65 4.85
2386 6324 1.076192 CCTAGACGTAGGGGCCTGT 60.076 63.158 0.84 0.00 42.25 4.00
2387 6325 0.686769 CCTAGACGTAGGGGCCTGTT 60.687 60.000 0.84 0.00 42.25 3.16
2388 6326 1.410648 CCTAGACGTAGGGGCCTGTTA 60.411 57.143 0.84 0.00 42.25 2.41
2389 6327 1.680207 CTAGACGTAGGGGCCTGTTAC 59.320 57.143 0.84 3.46 0.00 2.50
2390 6328 0.251922 AGACGTAGGGGCCTGTTACA 60.252 55.000 0.84 0.00 0.00 2.41
2391 6329 0.175073 GACGTAGGGGCCTGTTACAG 59.825 60.000 5.22 5.22 0.00 2.74
2409 6347 8.514330 TGTTACAGGATTGTTACAGAACTTTT 57.486 30.769 0.00 0.00 40.69 2.27
2410 6348 8.617809 TGTTACAGGATTGTTACAGAACTTTTC 58.382 33.333 0.00 0.00 40.69 2.29
2411 6349 8.837389 GTTACAGGATTGTTACAGAACTTTTCT 58.163 33.333 0.00 0.00 36.95 2.52
2412 6350 7.881775 ACAGGATTGTTACAGAACTTTTCTT 57.118 32.000 0.00 0.00 33.55 2.52
2413 6351 8.974060 ACAGGATTGTTACAGAACTTTTCTTA 57.026 30.769 0.00 0.00 33.55 2.10
2414 6352 9.403583 ACAGGATTGTTACAGAACTTTTCTTAA 57.596 29.630 0.00 0.00 33.55 1.85
2424 6362 8.093659 ACAGAACTTTTCTTAAATCTCTCTGC 57.906 34.615 0.00 0.00 38.11 4.26
2425 6363 7.174080 ACAGAACTTTTCTTAAATCTCTCTGCC 59.826 37.037 0.00 0.00 38.11 4.85
2426 6364 6.657117 AGAACTTTTCTTAAATCTCTCTGCCC 59.343 38.462 0.00 0.00 36.36 5.36
2427 6365 5.257262 ACTTTTCTTAAATCTCTCTGCCCC 58.743 41.667 0.00 0.00 0.00 5.80
2428 6366 3.933861 TTCTTAAATCTCTCTGCCCCC 57.066 47.619 0.00 0.00 0.00 5.40
2429 6367 3.136641 TCTTAAATCTCTCTGCCCCCT 57.863 47.619 0.00 0.00 0.00 4.79
2430 6368 4.280789 TCTTAAATCTCTCTGCCCCCTA 57.719 45.455 0.00 0.00 0.00 3.53
2431 6369 4.631234 TCTTAAATCTCTCTGCCCCCTAA 58.369 43.478 0.00 0.00 0.00 2.69
2432 6370 5.227593 TCTTAAATCTCTCTGCCCCCTAAT 58.772 41.667 0.00 0.00 0.00 1.73
2433 6371 5.672194 TCTTAAATCTCTCTGCCCCCTAATT 59.328 40.000 0.00 0.00 0.00 1.40
2434 6372 4.888626 AAATCTCTCTGCCCCCTAATTT 57.111 40.909 0.00 0.00 0.00 1.82
2435 6373 4.445557 AATCTCTCTGCCCCCTAATTTC 57.554 45.455 0.00 0.00 0.00 2.17
2436 6374 2.127708 TCTCTCTGCCCCCTAATTTCC 58.872 52.381 0.00 0.00 0.00 3.13
2437 6375 1.143889 CTCTCTGCCCCCTAATTTCCC 59.856 57.143 0.00 0.00 0.00 3.97
2438 6376 0.926293 CTCTGCCCCCTAATTTCCCA 59.074 55.000 0.00 0.00 0.00 4.37
2439 6377 1.500736 CTCTGCCCCCTAATTTCCCAT 59.499 52.381 0.00 0.00 0.00 4.00
2440 6378 1.499007 TCTGCCCCCTAATTTCCCATC 59.501 52.381 0.00 0.00 0.00 3.51
2441 6379 0.184933 TGCCCCCTAATTTCCCATCG 59.815 55.000 0.00 0.00 0.00 3.84
2442 6380 0.539669 GCCCCCTAATTTCCCATCGG 60.540 60.000 0.00 0.00 0.00 4.18
2443 6381 0.112412 CCCCCTAATTTCCCATCGGG 59.888 60.000 0.00 0.00 46.11 5.14
2444 6382 0.850784 CCCCTAATTTCCCATCGGGT 59.149 55.000 0.00 0.00 44.74 5.28
2445 6383 1.478654 CCCCTAATTTCCCATCGGGTG 60.479 57.143 0.00 0.00 44.74 4.61
2460 6398 4.459089 GTGGCCGGCCTCACTCTC 62.459 72.222 43.34 21.05 36.94 3.20
2463 6401 3.394836 GCCGGCCTCACTCTCCTT 61.395 66.667 18.11 0.00 0.00 3.36
2464 6402 2.896443 CCGGCCTCACTCTCCTTC 59.104 66.667 0.00 0.00 0.00 3.46
2465 6403 2.726351 CCGGCCTCACTCTCCTTCC 61.726 68.421 0.00 0.00 0.00 3.46
2466 6404 1.684049 CGGCCTCACTCTCCTTCCT 60.684 63.158 0.00 0.00 0.00 3.36
2467 6405 1.671901 CGGCCTCACTCTCCTTCCTC 61.672 65.000 0.00 0.00 0.00 3.71
2468 6406 1.334384 GGCCTCACTCTCCTTCCTCC 61.334 65.000 0.00 0.00 0.00 4.30
2469 6407 1.671901 GCCTCACTCTCCTTCCTCCG 61.672 65.000 0.00 0.00 0.00 4.63
2470 6408 0.033991 CCTCACTCTCCTTCCTCCGA 60.034 60.000 0.00 0.00 0.00 4.55
2471 6409 1.617263 CCTCACTCTCCTTCCTCCGAA 60.617 57.143 0.00 0.00 0.00 4.30
2472 6410 2.383855 CTCACTCTCCTTCCTCCGAAT 58.616 52.381 0.00 0.00 0.00 3.34
2473 6411 2.360801 CTCACTCTCCTTCCTCCGAATC 59.639 54.545 0.00 0.00 0.00 2.52
2474 6412 1.410882 CACTCTCCTTCCTCCGAATCC 59.589 57.143 0.00 0.00 0.00 3.01
2475 6413 1.044611 CTCTCCTTCCTCCGAATCCC 58.955 60.000 0.00 0.00 0.00 3.85
2476 6414 0.398664 TCTCCTTCCTCCGAATCCCC 60.399 60.000 0.00 0.00 0.00 4.81
2477 6415 1.384082 TCCTTCCTCCGAATCCCCC 60.384 63.158 0.00 0.00 0.00 5.40
2478 6416 1.384643 CCTTCCTCCGAATCCCCCT 60.385 63.158 0.00 0.00 0.00 4.79
2479 6417 0.988678 CCTTCCTCCGAATCCCCCTT 60.989 60.000 0.00 0.00 0.00 3.95
2480 6418 0.919710 CTTCCTCCGAATCCCCCTTT 59.080 55.000 0.00 0.00 0.00 3.11
2481 6419 0.623723 TTCCTCCGAATCCCCCTTTG 59.376 55.000 0.00 0.00 0.00 2.77
2482 6420 1.453928 CCTCCGAATCCCCCTTTGC 60.454 63.158 0.00 0.00 0.00 3.68
2483 6421 1.453928 CTCCGAATCCCCCTTTGCC 60.454 63.158 0.00 0.00 0.00 4.52
2484 6422 2.210144 CTCCGAATCCCCCTTTGCCA 62.210 60.000 0.00 0.00 0.00 4.92
2485 6423 1.076044 CCGAATCCCCCTTTGCCAT 60.076 57.895 0.00 0.00 0.00 4.40
2486 6424 1.394266 CCGAATCCCCCTTTGCCATG 61.394 60.000 0.00 0.00 0.00 3.66
2487 6425 0.684153 CGAATCCCCCTTTGCCATGT 60.684 55.000 0.00 0.00 0.00 3.21
2488 6426 1.114627 GAATCCCCCTTTGCCATGTC 58.885 55.000 0.00 0.00 0.00 3.06
2489 6427 0.413037 AATCCCCCTTTGCCATGTCA 59.587 50.000 0.00 0.00 0.00 3.58
2490 6428 0.324645 ATCCCCCTTTGCCATGTCAC 60.325 55.000 0.00 0.00 0.00 3.67
2491 6429 1.984026 CCCCCTTTGCCATGTCACC 60.984 63.158 0.00 0.00 0.00 4.02
2492 6430 2.342650 CCCCTTTGCCATGTCACCG 61.343 63.158 0.00 0.00 0.00 4.94
2493 6431 1.603455 CCCTTTGCCATGTCACCGT 60.603 57.895 0.00 0.00 0.00 4.83
2494 6432 1.580942 CCTTTGCCATGTCACCGTG 59.419 57.895 0.00 0.00 0.00 4.94
2495 6433 1.172180 CCTTTGCCATGTCACCGTGT 61.172 55.000 0.00 0.00 0.00 4.49
2496 6434 1.518325 CTTTGCCATGTCACCGTGTA 58.482 50.000 0.00 0.00 0.00 2.90
2497 6435 1.876799 CTTTGCCATGTCACCGTGTAA 59.123 47.619 0.00 0.00 0.00 2.41
2498 6436 2.192664 TTGCCATGTCACCGTGTAAT 57.807 45.000 0.00 0.00 0.00 1.89
2499 6437 3.336138 TTGCCATGTCACCGTGTAATA 57.664 42.857 0.00 0.00 0.00 0.98
2500 6438 3.336138 TGCCATGTCACCGTGTAATAA 57.664 42.857 0.00 0.00 0.00 1.40
2501 6439 3.879998 TGCCATGTCACCGTGTAATAAT 58.120 40.909 0.00 0.00 0.00 1.28
2502 6440 3.874543 TGCCATGTCACCGTGTAATAATC 59.125 43.478 0.00 0.00 0.00 1.75
2503 6441 3.250040 GCCATGTCACCGTGTAATAATCC 59.750 47.826 0.00 0.00 0.00 3.01
2504 6442 3.813166 CCATGTCACCGTGTAATAATCCC 59.187 47.826 0.00 0.00 0.00 3.85
2505 6443 4.447290 CATGTCACCGTGTAATAATCCCA 58.553 43.478 0.00 0.00 0.00 4.37
2506 6444 4.131649 TGTCACCGTGTAATAATCCCAG 57.868 45.455 0.00 0.00 0.00 4.45
2507 6445 3.516300 TGTCACCGTGTAATAATCCCAGT 59.484 43.478 0.00 0.00 0.00 4.00
2508 6446 4.117685 GTCACCGTGTAATAATCCCAGTC 58.882 47.826 0.00 0.00 0.00 3.51
2509 6447 3.133362 TCACCGTGTAATAATCCCAGTCC 59.867 47.826 0.00 0.00 0.00 3.85
2510 6448 2.101917 ACCGTGTAATAATCCCAGTCCG 59.898 50.000 0.00 0.00 0.00 4.79
2511 6449 2.101917 CCGTGTAATAATCCCAGTCCGT 59.898 50.000 0.00 0.00 0.00 4.69
2512 6450 3.318839 CCGTGTAATAATCCCAGTCCGTA 59.681 47.826 0.00 0.00 0.00 4.02
2513 6451 4.293415 CGTGTAATAATCCCAGTCCGTAC 58.707 47.826 0.00 0.00 0.00 3.67
2514 6452 4.037208 CGTGTAATAATCCCAGTCCGTACT 59.963 45.833 0.00 0.00 35.91 2.73
2515 6453 5.450965 CGTGTAATAATCCCAGTCCGTACTT 60.451 44.000 0.00 0.00 31.97 2.24
2516 6454 5.751990 GTGTAATAATCCCAGTCCGTACTTG 59.248 44.000 0.00 0.00 31.97 3.16
2517 6455 2.973694 TAATCCCAGTCCGTACTTGC 57.026 50.000 0.00 0.00 31.97 4.01
2518 6456 0.252197 AATCCCAGTCCGTACTTGCC 59.748 55.000 0.00 0.00 31.97 4.52
2519 6457 0.617820 ATCCCAGTCCGTACTTGCCT 60.618 55.000 0.00 0.00 31.97 4.75
2520 6458 0.040058 TCCCAGTCCGTACTTGCCTA 59.960 55.000 0.00 0.00 31.97 3.93
2521 6459 1.120530 CCCAGTCCGTACTTGCCTAT 58.879 55.000 0.00 0.00 31.97 2.57
2522 6460 2.091720 TCCCAGTCCGTACTTGCCTATA 60.092 50.000 0.00 0.00 31.97 1.31
2523 6461 2.897969 CCCAGTCCGTACTTGCCTATAT 59.102 50.000 0.00 0.00 31.97 0.86
2524 6462 3.306088 CCCAGTCCGTACTTGCCTATATG 60.306 52.174 0.00 0.00 31.97 1.78
2525 6463 3.321111 CCAGTCCGTACTTGCCTATATGT 59.679 47.826 0.00 0.00 31.97 2.29
2526 6464 4.299155 CAGTCCGTACTTGCCTATATGTG 58.701 47.826 0.00 0.00 31.97 3.21
2527 6465 3.958798 AGTCCGTACTTGCCTATATGTGT 59.041 43.478 0.00 0.00 29.00 3.72
2528 6466 5.009310 CAGTCCGTACTTGCCTATATGTGTA 59.991 44.000 0.00 0.00 31.97 2.90
2529 6467 5.241064 AGTCCGTACTTGCCTATATGTGTAG 59.759 44.000 0.00 0.00 29.00 2.74
2530 6468 4.022589 TCCGTACTTGCCTATATGTGTAGC 60.023 45.833 0.00 0.00 0.00 3.58
2531 6469 4.261867 CCGTACTTGCCTATATGTGTAGCA 60.262 45.833 0.00 0.00 0.00 3.49
2532 6470 5.286438 CGTACTTGCCTATATGTGTAGCAA 58.714 41.667 0.00 0.00 0.00 3.91
2533 6471 5.751509 CGTACTTGCCTATATGTGTAGCAAA 59.248 40.000 0.00 0.00 0.00 3.68
2534 6472 6.074302 CGTACTTGCCTATATGTGTAGCAAAG 60.074 42.308 0.00 0.00 0.00 2.77
2535 6473 4.576463 ACTTGCCTATATGTGTAGCAAAGC 59.424 41.667 0.00 0.00 0.00 3.51
2536 6474 3.476552 TGCCTATATGTGTAGCAAAGCC 58.523 45.455 0.00 0.00 0.00 4.35
2537 6475 2.814336 GCCTATATGTGTAGCAAAGCCC 59.186 50.000 0.00 0.00 0.00 5.19
2538 6476 3.067106 CCTATATGTGTAGCAAAGCCCG 58.933 50.000 0.00 0.00 0.00 6.13
2539 6477 3.244078 CCTATATGTGTAGCAAAGCCCGA 60.244 47.826 0.00 0.00 0.00 5.14
2540 6478 2.309528 TATGTGTAGCAAAGCCCGAG 57.690 50.000 0.00 0.00 0.00 4.63
2541 6479 0.613260 ATGTGTAGCAAAGCCCGAGA 59.387 50.000 0.00 0.00 0.00 4.04
2542 6480 0.037326 TGTGTAGCAAAGCCCGAGAG 60.037 55.000 0.00 0.00 0.00 3.20
2543 6481 0.246635 GTGTAGCAAAGCCCGAGAGA 59.753 55.000 0.00 0.00 0.00 3.10
2544 6482 0.973632 TGTAGCAAAGCCCGAGAGAA 59.026 50.000 0.00 0.00 0.00 2.87
2545 6483 1.346395 TGTAGCAAAGCCCGAGAGAAA 59.654 47.619 0.00 0.00 0.00 2.52
2546 6484 2.027192 TGTAGCAAAGCCCGAGAGAAAT 60.027 45.455 0.00 0.00 0.00 2.17
2547 6485 3.196901 TGTAGCAAAGCCCGAGAGAAATA 59.803 43.478 0.00 0.00 0.00 1.40
2548 6486 2.911484 AGCAAAGCCCGAGAGAAATAG 58.089 47.619 0.00 0.00 0.00 1.73
2549 6487 2.501723 AGCAAAGCCCGAGAGAAATAGA 59.498 45.455 0.00 0.00 0.00 1.98
2550 6488 2.609916 GCAAAGCCCGAGAGAAATAGAC 59.390 50.000 0.00 0.00 0.00 2.59
2556 6494 3.181489 GCCCGAGAGAAATAGACGAAAGA 60.181 47.826 0.00 0.00 0.00 2.52
2566 6504 7.837863 AGAAATAGACGAAAGATGTGGAGTAA 58.162 34.615 0.00 0.00 0.00 2.24
2572 6510 3.879295 CGAAAGATGTGGAGTAATGGCAT 59.121 43.478 0.00 0.00 0.00 4.40
2592 6530 8.158169 TGGCATGTATGAATATCAAACTTCTC 57.842 34.615 0.00 0.00 0.00 2.87
2614 6552 4.456911 TCGTACGGAGAAACATGTAGAAGT 59.543 41.667 16.52 0.00 0.00 3.01
2615 6553 5.048504 TCGTACGGAGAAACATGTAGAAGTT 60.049 40.000 16.52 0.00 0.00 2.66
2623 6561 7.206981 AGAAACATGTAGAAGTTGACAATGG 57.793 36.000 0.00 0.00 0.00 3.16
2630 6568 4.778534 AGAAGTTGACAATGGCATGAAG 57.221 40.909 0.00 0.00 0.00 3.02
2644 6582 4.344679 TGGCATGAAGATCTTTTTGGTGTT 59.655 37.500 9.87 0.00 0.00 3.32
2670 6608 3.193691 AGAGACATAGGTGGAAGTTGTCG 59.806 47.826 0.00 0.00 41.15 4.35
2673 6611 2.271800 CATAGGTGGAAGTTGTCGAGC 58.728 52.381 0.00 0.00 33.03 5.03
2681 6785 2.096218 GGAAGTTGTCGAGCAATGACAC 60.096 50.000 5.34 2.65 45.42 3.67
2716 6820 7.325660 TCAAACTTCTGATATGGAGAAATGC 57.674 36.000 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 2.876645 CACGCTTCGAGTCGCCTC 60.877 66.667 7.92 0.00 0.00 4.70
131 132 1.599071 GGCAAGGCAAAGCAAAACTTC 59.401 47.619 0.00 0.00 37.75 3.01
152 153 2.362077 GGAGAAAAGCAAGACAAGGCAA 59.638 45.455 0.00 0.00 0.00 4.52
153 154 1.956477 GGAGAAAAGCAAGACAAGGCA 59.044 47.619 0.00 0.00 0.00 4.75
154 155 1.270826 GGGAGAAAAGCAAGACAAGGC 59.729 52.381 0.00 0.00 0.00 4.35
155 156 1.537202 CGGGAGAAAAGCAAGACAAGG 59.463 52.381 0.00 0.00 0.00 3.61
156 157 1.537202 CCGGGAGAAAAGCAAGACAAG 59.463 52.381 0.00 0.00 0.00 3.16
157 158 1.604604 CCGGGAGAAAAGCAAGACAA 58.395 50.000 0.00 0.00 0.00 3.18
158 159 0.250727 CCCGGGAGAAAAGCAAGACA 60.251 55.000 18.48 0.00 0.00 3.41
159 160 0.960861 CCCCGGGAGAAAAGCAAGAC 60.961 60.000 26.32 0.00 0.00 3.01
160 161 1.378762 CCCCGGGAGAAAAGCAAGA 59.621 57.895 26.32 0.00 0.00 3.02
161 162 2.343426 GCCCCGGGAGAAAAGCAAG 61.343 63.158 26.32 0.94 0.00 4.01
206 217 4.496010 CCCTCGTCAAGATTCGTACTACTG 60.496 50.000 0.00 0.00 0.00 2.74
207 218 3.626670 CCCTCGTCAAGATTCGTACTACT 59.373 47.826 0.00 0.00 0.00 2.57
208 219 3.243002 CCCCTCGTCAAGATTCGTACTAC 60.243 52.174 0.00 0.00 0.00 2.73
209 220 2.947652 CCCCTCGTCAAGATTCGTACTA 59.052 50.000 0.00 0.00 0.00 1.82
210 221 1.749634 CCCCTCGTCAAGATTCGTACT 59.250 52.381 0.00 0.00 0.00 2.73
211 222 1.747355 TCCCCTCGTCAAGATTCGTAC 59.253 52.381 0.00 0.00 0.00 3.67
265 276 1.734359 CTAGCAGCTCGAACGAACGC 61.734 60.000 0.00 0.00 0.00 4.84
274 285 0.459237 CCTCAACCACTAGCAGCTCG 60.459 60.000 0.00 0.00 0.00 5.03
307 318 1.677637 CCCGCCACTCCTACTCCTTC 61.678 65.000 0.00 0.00 0.00 3.46
389 2192 1.740585 AGTCGAGGCGCTATAGCTATG 59.259 52.381 21.98 8.34 39.32 2.23
406 2209 2.615912 GGATGCTCAACTGCCAATAGTC 59.384 50.000 0.00 0.00 0.00 2.59
447 2250 2.420022 CTCCACGATCAAGCGGAAAAAT 59.580 45.455 0.00 0.00 35.12 1.82
472 2275 0.875059 GTCAACGAAGAGGGCCAAAG 59.125 55.000 6.18 0.00 0.00 2.77
480 2283 1.738099 CCGGCAGGTCAACGAAGAG 60.738 63.158 0.00 0.00 0.00 2.85
481 2284 2.342279 CCGGCAGGTCAACGAAGA 59.658 61.111 0.00 0.00 0.00 2.87
548 2351 6.526566 TCTAAAGAAAGAAGTTTCGCTGTC 57.473 37.500 0.00 0.00 45.90 3.51
574 2377 0.689623 GGAGGCGATCCCTGATTGAT 59.310 55.000 7.41 0.00 46.60 2.57
575 2378 2.136791 GGAGGCGATCCCTGATTGA 58.863 57.895 7.41 0.00 46.60 2.57
576 2379 4.787871 GGAGGCGATCCCTGATTG 57.212 61.111 7.41 0.00 46.60 2.67
616 2419 1.575244 AGATGGATGATGCGTGTTCG 58.425 50.000 0.00 0.00 40.37 3.95
674 3947 5.308237 AGACATTTCCTCCGGAGCTTTATAT 59.692 40.000 26.87 7.93 31.21 0.86
697 3970 2.787994 ACTTTGGGTGCAGATTCAGAG 58.212 47.619 0.00 0.00 0.00 3.35
800 4074 0.248539 GTATCGTCGACCAGCTGGAC 60.249 60.000 39.19 30.88 38.94 4.02
958 4242 0.408309 GTAGTTGGAGGGGGCCTTTT 59.592 55.000 0.84 0.00 31.76 2.27
962 4246 3.793888 CGGTAGTTGGAGGGGGCC 61.794 72.222 0.00 0.00 0.00 5.80
964 4248 3.793888 GCCGGTAGTTGGAGGGGG 61.794 72.222 1.90 0.00 0.00 5.40
1104 4388 0.658368 CGAGGATGACGACGACATCT 59.342 55.000 29.65 19.84 42.33 2.90
1293 4577 2.847901 CCTGTCGTCGTAGTAGTTGTG 58.152 52.381 0.00 0.00 0.00 3.33
1680 4964 2.024871 GACGAGGAGGCGATGACG 59.975 66.667 0.00 0.00 42.93 4.35
1688 4972 3.862402 CCGACGACGACGAGGAGG 61.862 72.222 20.63 7.41 42.66 4.30
1689 4973 4.517703 GCCGACGACGACGAGGAG 62.518 72.222 20.63 5.41 42.66 3.69
1764 5048 4.838152 CGCCAGGGGACATGACGG 62.838 72.222 0.00 0.00 0.00 4.79
1828 5112 4.393155 TACTGCAGCGTGGGCCAG 62.393 66.667 15.27 1.95 41.24 4.85
1882 5166 6.426328 CACATCACAGCTCTAATTATTCTCCC 59.574 42.308 0.00 0.00 0.00 4.30
1910 5194 2.213499 AGGTTGCAGAAAAGAGTCACG 58.787 47.619 0.00 0.00 0.00 4.35
1952 5236 0.744874 TCCATACGTACTGGAGCAGC 59.255 55.000 17.50 0.00 37.87 5.25
1967 5251 1.640149 TGTCATGTTCCCCACATCCAT 59.360 47.619 0.00 0.00 43.17 3.41
2124 5409 0.179004 TCGCCCACACCAAACAGATT 60.179 50.000 0.00 0.00 0.00 2.40
2140 5425 0.958822 ACAACTTCCACCCAAATCGC 59.041 50.000 0.00 0.00 0.00 4.58
2141 5426 1.269448 CCACAACTTCCACCCAAATCG 59.731 52.381 0.00 0.00 0.00 3.34
2142 5427 2.558359 CTCCACAACTTCCACCCAAATC 59.442 50.000 0.00 0.00 0.00 2.17
2144 5429 1.286553 ACTCCACAACTTCCACCCAAA 59.713 47.619 0.00 0.00 0.00 3.28
2146 5431 1.809133 TACTCCACAACTTCCACCCA 58.191 50.000 0.00 0.00 0.00 4.51
2169 6107 3.487372 GGAGGGGGTATTTCATAACTGC 58.513 50.000 0.00 0.00 0.00 4.40
2183 6121 6.822170 GCTCTTATATTAATTTACGGAGGGGG 59.178 42.308 0.00 0.00 0.00 5.40
2185 6123 9.449719 AATGCTCTTATATTAATTTACGGAGGG 57.550 33.333 0.00 0.00 0.00 4.30
2260 6198 9.167311 CCTCTGCAAACTAATATAAGAGTGTTT 57.833 33.333 0.00 0.00 0.00 2.83
2261 6199 7.770897 CCCTCTGCAAACTAATATAAGAGTGTT 59.229 37.037 0.00 0.00 0.00 3.32
2262 6200 7.125811 TCCCTCTGCAAACTAATATAAGAGTGT 59.874 37.037 0.00 0.00 0.00 3.55
2263 6201 7.500992 TCCCTCTGCAAACTAATATAAGAGTG 58.499 38.462 0.00 0.00 0.00 3.51
2264 6202 7.345914 ACTCCCTCTGCAAACTAATATAAGAGT 59.654 37.037 0.00 0.00 0.00 3.24
2265 6203 7.731054 ACTCCCTCTGCAAACTAATATAAGAG 58.269 38.462 0.00 0.00 0.00 2.85
2266 6204 7.676683 ACTCCCTCTGCAAACTAATATAAGA 57.323 36.000 0.00 0.00 0.00 2.10
2267 6205 8.643324 AGTACTCCCTCTGCAAACTAATATAAG 58.357 37.037 0.00 0.00 0.00 1.73
2268 6206 8.548880 AGTACTCCCTCTGCAAACTAATATAA 57.451 34.615 0.00 0.00 0.00 0.98
2269 6207 8.548880 AAGTACTCCCTCTGCAAACTAATATA 57.451 34.615 0.00 0.00 0.00 0.86
2270 6208 7.419172 GGAAGTACTCCCTCTGCAAACTAATAT 60.419 40.741 0.00 0.00 38.44 1.28
2271 6209 6.127140 GGAAGTACTCCCTCTGCAAACTAATA 60.127 42.308 0.00 0.00 38.44 0.98
2272 6210 5.338463 GGAAGTACTCCCTCTGCAAACTAAT 60.338 44.000 0.00 0.00 38.44 1.73
2273 6211 4.020485 GGAAGTACTCCCTCTGCAAACTAA 60.020 45.833 0.00 0.00 38.44 2.24
2274 6212 3.514309 GGAAGTACTCCCTCTGCAAACTA 59.486 47.826 0.00 0.00 38.44 2.24
2275 6213 2.303311 GGAAGTACTCCCTCTGCAAACT 59.697 50.000 0.00 0.00 38.44 2.66
2276 6214 2.038557 TGGAAGTACTCCCTCTGCAAAC 59.961 50.000 0.00 0.00 44.69 2.93
2277 6215 2.334977 TGGAAGTACTCCCTCTGCAAA 58.665 47.619 0.00 0.00 44.69 3.68
2278 6216 2.024176 TGGAAGTACTCCCTCTGCAA 57.976 50.000 0.00 0.00 44.69 4.08
2279 6217 2.024176 TTGGAAGTACTCCCTCTGCA 57.976 50.000 0.00 0.00 44.69 4.41
2280 6218 4.345257 TCATATTGGAAGTACTCCCTCTGC 59.655 45.833 0.00 0.00 44.69 4.26
2281 6219 6.325028 TCTTCATATTGGAAGTACTCCCTCTG 59.675 42.308 0.00 0.00 44.69 3.35
2282 6220 6.444704 TCTTCATATTGGAAGTACTCCCTCT 58.555 40.000 0.00 0.00 44.69 3.69
2283 6221 6.732896 TCTTCATATTGGAAGTACTCCCTC 57.267 41.667 0.00 0.00 44.69 4.30
2284 6222 7.510675 TTTCTTCATATTGGAAGTACTCCCT 57.489 36.000 0.00 0.00 44.69 4.20
2300 6238 9.823647 ATTGTCGACTTCTACATATTTCTTCAT 57.176 29.630 17.92 0.00 0.00 2.57
2301 6239 9.087424 CATTGTCGACTTCTACATATTTCTTCA 57.913 33.333 17.92 0.00 0.00 3.02
2302 6240 8.543774 CCATTGTCGACTTCTACATATTTCTTC 58.456 37.037 17.92 0.00 0.00 2.87
2303 6241 7.011482 GCCATTGTCGACTTCTACATATTTCTT 59.989 37.037 17.92 0.00 0.00 2.52
2309 6247 4.729227 TGCCATTGTCGACTTCTACATA 57.271 40.909 17.92 0.00 0.00 2.29
2343 6281 8.601546 GGATTATTGATTTCTCTCTCCATACCT 58.398 37.037 0.00 0.00 0.00 3.08
2344 6282 8.601546 AGGATTATTGATTTCTCTCTCCATACC 58.398 37.037 0.00 0.00 0.00 2.73
2347 6285 9.612879 TCTAGGATTATTGATTTCTCTCTCCAT 57.387 33.333 0.00 0.00 0.00 3.41
2361 6299 3.056035 GGCCCCTACGTCTAGGATTATTG 60.056 52.174 5.92 0.00 42.34 1.90
2362 6300 3.171528 GGCCCCTACGTCTAGGATTATT 58.828 50.000 5.92 0.00 42.34 1.40
2363 6301 2.382649 AGGCCCCTACGTCTAGGATTAT 59.617 50.000 5.92 0.00 42.34 1.28
2365 6303 0.561680 AGGCCCCTACGTCTAGGATT 59.438 55.000 5.92 0.00 42.34 3.01
2366 6304 0.178958 CAGGCCCCTACGTCTAGGAT 60.179 60.000 5.92 0.00 42.34 3.24
2367 6305 1.229359 CAGGCCCCTACGTCTAGGA 59.771 63.158 5.92 0.00 42.34 2.94
2368 6306 0.686769 AACAGGCCCCTACGTCTAGG 60.687 60.000 0.00 0.00 39.67 3.02
2369 6307 1.680207 GTAACAGGCCCCTACGTCTAG 59.320 57.143 0.00 0.00 0.00 2.43
2370 6308 1.005805 TGTAACAGGCCCCTACGTCTA 59.994 52.381 0.00 0.00 0.00 2.59
2371 6309 0.251922 TGTAACAGGCCCCTACGTCT 60.252 55.000 0.00 0.00 0.00 4.18
2372 6310 0.175073 CTGTAACAGGCCCCTACGTC 59.825 60.000 0.00 0.00 0.00 4.34
2373 6311 1.262640 CCTGTAACAGGCCCCTACGT 61.263 60.000 0.00 0.00 45.13 3.57
2374 6312 1.520666 CCTGTAACAGGCCCCTACG 59.479 63.158 0.00 0.00 45.13 3.51
2380 6318 8.003046 GTTCTGTAACAATCCTGTAACAGGCC 62.003 46.154 0.00 0.00 41.96 5.19
2381 6319 5.106673 GTTCTGTAACAATCCTGTAACAGGC 60.107 44.000 0.00 0.00 41.96 4.85
2382 6320 6.231211 AGTTCTGTAACAATCCTGTAACAGG 58.769 40.000 0.00 0.00 44.16 4.00
2383 6321 7.730364 AAGTTCTGTAACAATCCTGTAACAG 57.270 36.000 0.00 0.00 38.12 3.16
2384 6322 8.514330 AAAAGTTCTGTAACAATCCTGTAACA 57.486 30.769 0.00 0.00 38.12 2.41
2385 6323 8.837389 AGAAAAGTTCTGTAACAATCCTGTAAC 58.163 33.333 0.00 0.00 38.91 2.50
2386 6324 8.974060 AGAAAAGTTCTGTAACAATCCTGTAA 57.026 30.769 0.00 0.00 38.91 2.41
2387 6325 8.974060 AAGAAAAGTTCTGTAACAATCCTGTA 57.026 30.769 0.00 0.00 40.59 2.74
2388 6326 7.881775 AAGAAAAGTTCTGTAACAATCCTGT 57.118 32.000 0.00 0.00 40.59 4.00
2398 6336 9.209175 GCAGAGAGATTTAAGAAAAGTTCTGTA 57.791 33.333 0.00 0.00 40.59 2.74
2399 6337 7.174080 GGCAGAGAGATTTAAGAAAAGTTCTGT 59.826 37.037 0.00 0.00 40.59 3.41
2400 6338 7.361628 GGGCAGAGAGATTTAAGAAAAGTTCTG 60.362 40.741 0.00 0.00 40.59 3.02
2401 6339 6.657117 GGGCAGAGAGATTTAAGAAAAGTTCT 59.343 38.462 0.00 0.00 43.15 3.01
2402 6340 6.127869 GGGGCAGAGAGATTTAAGAAAAGTTC 60.128 42.308 0.00 0.00 0.00 3.01
2403 6341 5.712446 GGGGCAGAGAGATTTAAGAAAAGTT 59.288 40.000 0.00 0.00 0.00 2.66
2404 6342 5.257262 GGGGCAGAGAGATTTAAGAAAAGT 58.743 41.667 0.00 0.00 0.00 2.66
2405 6343 4.642437 GGGGGCAGAGAGATTTAAGAAAAG 59.358 45.833 0.00 0.00 0.00 2.27
2406 6344 4.292306 AGGGGGCAGAGAGATTTAAGAAAA 59.708 41.667 0.00 0.00 0.00 2.29
2407 6345 3.852578 AGGGGGCAGAGAGATTTAAGAAA 59.147 43.478 0.00 0.00 0.00 2.52
2408 6346 3.464828 AGGGGGCAGAGAGATTTAAGAA 58.535 45.455 0.00 0.00 0.00 2.52
2409 6347 3.136641 AGGGGGCAGAGAGATTTAAGA 57.863 47.619 0.00 0.00 0.00 2.10
2410 6348 5.574970 ATTAGGGGGCAGAGAGATTTAAG 57.425 43.478 0.00 0.00 0.00 1.85
2411 6349 5.994416 AATTAGGGGGCAGAGAGATTTAA 57.006 39.130 0.00 0.00 0.00 1.52
2412 6350 5.163088 GGAAATTAGGGGGCAGAGAGATTTA 60.163 44.000 0.00 0.00 0.00 1.40
2413 6351 4.386873 GGAAATTAGGGGGCAGAGAGATTT 60.387 45.833 0.00 0.00 0.00 2.17
2414 6352 3.139211 GGAAATTAGGGGGCAGAGAGATT 59.861 47.826 0.00 0.00 0.00 2.40
2415 6353 2.713708 GGAAATTAGGGGGCAGAGAGAT 59.286 50.000 0.00 0.00 0.00 2.75
2416 6354 2.127708 GGAAATTAGGGGGCAGAGAGA 58.872 52.381 0.00 0.00 0.00 3.10
2417 6355 1.143889 GGGAAATTAGGGGGCAGAGAG 59.856 57.143 0.00 0.00 0.00 3.20
2418 6356 1.222567 GGGAAATTAGGGGGCAGAGA 58.777 55.000 0.00 0.00 0.00 3.10
2419 6357 0.926293 TGGGAAATTAGGGGGCAGAG 59.074 55.000 0.00 0.00 0.00 3.35
2420 6358 1.499007 GATGGGAAATTAGGGGGCAGA 59.501 52.381 0.00 0.00 0.00 4.26
2421 6359 1.819305 CGATGGGAAATTAGGGGGCAG 60.819 57.143 0.00 0.00 0.00 4.85
2422 6360 0.184933 CGATGGGAAATTAGGGGGCA 59.815 55.000 0.00 0.00 0.00 5.36
2423 6361 0.539669 CCGATGGGAAATTAGGGGGC 60.540 60.000 0.00 0.00 34.06 5.80
2424 6362 3.745723 CCGATGGGAAATTAGGGGG 57.254 57.895 0.00 0.00 34.06 5.40
2443 6381 4.459089 GAGAGTGAGGCCGGCCAC 62.459 72.222 45.13 39.20 38.92 5.01
2446 6384 3.378399 GAAGGAGAGTGAGGCCGGC 62.378 68.421 21.18 21.18 0.00 6.13
2447 6385 2.726351 GGAAGGAGAGTGAGGCCGG 61.726 68.421 0.00 0.00 0.00 6.13
2448 6386 1.671901 GAGGAAGGAGAGTGAGGCCG 61.672 65.000 0.00 0.00 0.00 6.13
2449 6387 1.334384 GGAGGAAGGAGAGTGAGGCC 61.334 65.000 0.00 0.00 0.00 5.19
2450 6388 1.671901 CGGAGGAAGGAGAGTGAGGC 61.672 65.000 0.00 0.00 0.00 4.70
2451 6389 0.033991 TCGGAGGAAGGAGAGTGAGG 60.034 60.000 0.00 0.00 0.00 3.86
2452 6390 1.840737 TTCGGAGGAAGGAGAGTGAG 58.159 55.000 0.00 0.00 0.00 3.51
2453 6391 2.379972 GATTCGGAGGAAGGAGAGTGA 58.620 52.381 0.00 0.00 35.19 3.41
2454 6392 1.410882 GGATTCGGAGGAAGGAGAGTG 59.589 57.143 0.00 0.00 35.19 3.51
2455 6393 1.689892 GGGATTCGGAGGAAGGAGAGT 60.690 57.143 0.00 0.00 35.19 3.24
2456 6394 1.044611 GGGATTCGGAGGAAGGAGAG 58.955 60.000 0.00 0.00 35.19 3.20
2457 6395 0.398664 GGGGATTCGGAGGAAGGAGA 60.399 60.000 0.00 0.00 35.19 3.71
2458 6396 1.411651 GGGGGATTCGGAGGAAGGAG 61.412 65.000 0.00 0.00 35.19 3.69
2459 6397 1.384082 GGGGGATTCGGAGGAAGGA 60.384 63.158 0.00 0.00 35.19 3.36
2460 6398 0.988678 AAGGGGGATTCGGAGGAAGG 60.989 60.000 0.00 0.00 35.19 3.46
2461 6399 0.919710 AAAGGGGGATTCGGAGGAAG 59.080 55.000 0.00 0.00 35.19 3.46
2462 6400 0.623723 CAAAGGGGGATTCGGAGGAA 59.376 55.000 0.00 0.00 36.41 3.36
2463 6401 1.921869 GCAAAGGGGGATTCGGAGGA 61.922 60.000 0.00 0.00 0.00 3.71
2464 6402 1.453928 GCAAAGGGGGATTCGGAGG 60.454 63.158 0.00 0.00 0.00 4.30
2465 6403 1.453928 GGCAAAGGGGGATTCGGAG 60.454 63.158 0.00 0.00 0.00 4.63
2466 6404 1.580066 ATGGCAAAGGGGGATTCGGA 61.580 55.000 0.00 0.00 0.00 4.55
2467 6405 1.076044 ATGGCAAAGGGGGATTCGG 60.076 57.895 0.00 0.00 0.00 4.30
2468 6406 0.684153 ACATGGCAAAGGGGGATTCG 60.684 55.000 0.00 0.00 0.00 3.34
2469 6407 1.114627 GACATGGCAAAGGGGGATTC 58.885 55.000 0.00 0.00 0.00 2.52
2470 6408 0.413037 TGACATGGCAAAGGGGGATT 59.587 50.000 0.00 0.00 0.00 3.01
2471 6409 0.324645 GTGACATGGCAAAGGGGGAT 60.325 55.000 0.58 0.00 0.00 3.85
2472 6410 1.076549 GTGACATGGCAAAGGGGGA 59.923 57.895 0.58 0.00 0.00 4.81
2473 6411 1.984026 GGTGACATGGCAAAGGGGG 60.984 63.158 0.58 0.00 0.00 5.40
2474 6412 2.342650 CGGTGACATGGCAAAGGGG 61.343 63.158 0.58 0.00 0.00 4.79
2475 6413 1.603455 ACGGTGACATGGCAAAGGG 60.603 57.895 0.58 0.00 0.00 3.95
2476 6414 1.172180 ACACGGTGACATGGCAAAGG 61.172 55.000 16.29 0.00 0.00 3.11
2477 6415 1.518325 TACACGGTGACATGGCAAAG 58.482 50.000 16.29 2.23 0.00 2.77
2478 6416 1.968704 TTACACGGTGACATGGCAAA 58.031 45.000 16.29 0.00 0.00 3.68
2479 6417 2.192664 ATTACACGGTGACATGGCAA 57.807 45.000 16.29 0.00 0.00 4.52
2480 6418 3.336138 TTATTACACGGTGACATGGCA 57.664 42.857 16.29 0.00 0.00 4.92
2481 6419 3.250040 GGATTATTACACGGTGACATGGC 59.750 47.826 16.29 0.00 0.00 4.40
2482 6420 3.813166 GGGATTATTACACGGTGACATGG 59.187 47.826 16.29 0.00 0.00 3.66
2483 6421 4.447290 TGGGATTATTACACGGTGACATG 58.553 43.478 16.29 0.00 0.00 3.21
2484 6422 4.163458 ACTGGGATTATTACACGGTGACAT 59.837 41.667 16.29 8.43 0.00 3.06
2485 6423 3.516300 ACTGGGATTATTACACGGTGACA 59.484 43.478 16.29 0.48 0.00 3.58
2486 6424 4.117685 GACTGGGATTATTACACGGTGAC 58.882 47.826 16.29 0.00 29.81 3.67
2487 6425 3.133362 GGACTGGGATTATTACACGGTGA 59.867 47.826 16.29 0.00 29.81 4.02
2488 6426 3.463944 GGACTGGGATTATTACACGGTG 58.536 50.000 6.58 6.58 29.81 4.94
2489 6427 2.101917 CGGACTGGGATTATTACACGGT 59.898 50.000 0.00 0.00 32.56 4.83
2490 6428 2.101917 ACGGACTGGGATTATTACACGG 59.898 50.000 0.00 0.00 0.00 4.94
2491 6429 3.447918 ACGGACTGGGATTATTACACG 57.552 47.619 0.00 0.00 0.00 4.49
2492 6430 5.526506 AGTACGGACTGGGATTATTACAC 57.473 43.478 0.00 0.00 33.41 2.90
2493 6431 5.682990 GCAAGTACGGACTGGGATTATTACA 60.683 44.000 0.00 0.00 35.52 2.41
2494 6432 4.748600 GCAAGTACGGACTGGGATTATTAC 59.251 45.833 0.00 0.00 35.52 1.89
2495 6433 4.202284 GGCAAGTACGGACTGGGATTATTA 60.202 45.833 0.00 0.00 35.52 0.98
2496 6434 3.433173 GGCAAGTACGGACTGGGATTATT 60.433 47.826 0.00 0.00 35.52 1.40
2497 6435 2.104281 GGCAAGTACGGACTGGGATTAT 59.896 50.000 0.00 0.00 35.52 1.28
2498 6436 1.483415 GGCAAGTACGGACTGGGATTA 59.517 52.381 0.00 0.00 35.52 1.75
2499 6437 0.252197 GGCAAGTACGGACTGGGATT 59.748 55.000 0.00 0.00 35.52 3.01
2500 6438 0.617820 AGGCAAGTACGGACTGGGAT 60.618 55.000 0.00 0.00 35.52 3.85
2501 6439 0.040058 TAGGCAAGTACGGACTGGGA 59.960 55.000 0.00 0.00 35.52 4.37
2502 6440 1.120530 ATAGGCAAGTACGGACTGGG 58.879 55.000 0.00 0.00 35.52 4.45
2503 6441 3.321111 ACATATAGGCAAGTACGGACTGG 59.679 47.826 0.00 0.00 35.52 4.00
2504 6442 4.202121 ACACATATAGGCAAGTACGGACTG 60.202 45.833 0.00 0.00 35.52 3.51
2505 6443 3.958798 ACACATATAGGCAAGTACGGACT 59.041 43.478 0.00 0.00 37.59 3.85
2506 6444 4.317671 ACACATATAGGCAAGTACGGAC 57.682 45.455 0.00 0.00 0.00 4.79
2507 6445 4.022589 GCTACACATATAGGCAAGTACGGA 60.023 45.833 0.00 0.00 0.00 4.69
2508 6446 4.235360 GCTACACATATAGGCAAGTACGG 58.765 47.826 0.00 0.00 0.00 4.02
2509 6447 4.866921 TGCTACACATATAGGCAAGTACG 58.133 43.478 0.00 0.00 0.00 3.67
2510 6448 6.292919 GCTTTGCTACACATATAGGCAAGTAC 60.293 42.308 0.00 0.00 42.48 2.73
2511 6449 5.758296 GCTTTGCTACACATATAGGCAAGTA 59.242 40.000 0.00 0.00 42.48 2.24
2512 6450 4.576463 GCTTTGCTACACATATAGGCAAGT 59.424 41.667 0.00 0.00 42.48 3.16
2513 6451 4.023707 GGCTTTGCTACACATATAGGCAAG 60.024 45.833 0.00 0.00 42.48 4.01
2514 6452 3.882888 GGCTTTGCTACACATATAGGCAA 59.117 43.478 0.00 0.00 40.43 4.52
2515 6453 3.476552 GGCTTTGCTACACATATAGGCA 58.523 45.455 0.00 0.00 31.52 4.75
2516 6454 2.814336 GGGCTTTGCTACACATATAGGC 59.186 50.000 0.00 0.00 0.00 3.93
2517 6455 3.067106 CGGGCTTTGCTACACATATAGG 58.933 50.000 0.00 0.00 0.00 2.57
2518 6456 3.990092 TCGGGCTTTGCTACACATATAG 58.010 45.455 0.00 0.00 0.00 1.31
2519 6457 3.639561 TCTCGGGCTTTGCTACACATATA 59.360 43.478 0.00 0.00 0.00 0.86
2520 6458 2.434336 TCTCGGGCTTTGCTACACATAT 59.566 45.455 0.00 0.00 0.00 1.78
2521 6459 1.828595 TCTCGGGCTTTGCTACACATA 59.171 47.619 0.00 0.00 0.00 2.29
2522 6460 0.613260 TCTCGGGCTTTGCTACACAT 59.387 50.000 0.00 0.00 0.00 3.21
2523 6461 0.037326 CTCTCGGGCTTTGCTACACA 60.037 55.000 0.00 0.00 0.00 3.72
2524 6462 0.246635 TCTCTCGGGCTTTGCTACAC 59.753 55.000 0.00 0.00 0.00 2.90
2525 6463 0.973632 TTCTCTCGGGCTTTGCTACA 59.026 50.000 0.00 0.00 0.00 2.74
2526 6464 2.094762 TTTCTCTCGGGCTTTGCTAC 57.905 50.000 0.00 0.00 0.00 3.58
2527 6465 3.704566 TCTATTTCTCTCGGGCTTTGCTA 59.295 43.478 0.00 0.00 0.00 3.49
2528 6466 2.501723 TCTATTTCTCTCGGGCTTTGCT 59.498 45.455 0.00 0.00 0.00 3.91
2529 6467 2.609916 GTCTATTTCTCTCGGGCTTTGC 59.390 50.000 0.00 0.00 0.00 3.68
2530 6468 2.860735 CGTCTATTTCTCTCGGGCTTTG 59.139 50.000 0.00 0.00 0.00 2.77
2531 6469 2.758979 TCGTCTATTTCTCTCGGGCTTT 59.241 45.455 0.00 0.00 0.00 3.51
2532 6470 2.376109 TCGTCTATTTCTCTCGGGCTT 58.624 47.619 0.00 0.00 0.00 4.35
2533 6471 2.054232 TCGTCTATTTCTCTCGGGCT 57.946 50.000 0.00 0.00 0.00 5.19
2534 6472 2.865343 TTCGTCTATTTCTCTCGGGC 57.135 50.000 0.00 0.00 0.00 6.13
2535 6473 4.634184 TCTTTCGTCTATTTCTCTCGGG 57.366 45.455 0.00 0.00 0.00 5.14
2536 6474 5.457148 CACATCTTTCGTCTATTTCTCTCGG 59.543 44.000 0.00 0.00 0.00 4.63
2537 6475 5.457148 CCACATCTTTCGTCTATTTCTCTCG 59.543 44.000 0.00 0.00 0.00 4.04
2538 6476 6.565234 TCCACATCTTTCGTCTATTTCTCTC 58.435 40.000 0.00 0.00 0.00 3.20
2539 6477 6.153680 ACTCCACATCTTTCGTCTATTTCTCT 59.846 38.462 0.00 0.00 0.00 3.10
2540 6478 6.334202 ACTCCACATCTTTCGTCTATTTCTC 58.666 40.000 0.00 0.00 0.00 2.87
2541 6479 6.287589 ACTCCACATCTTTCGTCTATTTCT 57.712 37.500 0.00 0.00 0.00 2.52
2542 6480 8.543774 CATTACTCCACATCTTTCGTCTATTTC 58.456 37.037 0.00 0.00 0.00 2.17
2543 6481 7.495934 CCATTACTCCACATCTTTCGTCTATTT 59.504 37.037 0.00 0.00 0.00 1.40
2544 6482 6.986817 CCATTACTCCACATCTTTCGTCTATT 59.013 38.462 0.00 0.00 0.00 1.73
2545 6483 6.516718 CCATTACTCCACATCTTTCGTCTAT 58.483 40.000 0.00 0.00 0.00 1.98
2546 6484 5.681437 GCCATTACTCCACATCTTTCGTCTA 60.681 44.000 0.00 0.00 0.00 2.59
2547 6485 4.759782 CCATTACTCCACATCTTTCGTCT 58.240 43.478 0.00 0.00 0.00 4.18
2548 6486 3.309954 GCCATTACTCCACATCTTTCGTC 59.690 47.826 0.00 0.00 0.00 4.20
2549 6487 3.270877 GCCATTACTCCACATCTTTCGT 58.729 45.455 0.00 0.00 0.00 3.85
2550 6488 3.270027 TGCCATTACTCCACATCTTTCG 58.730 45.455 0.00 0.00 0.00 3.46
2556 6494 5.308976 TCATACATGCCATTACTCCACAT 57.691 39.130 0.00 0.00 0.00 3.21
2566 6504 8.701908 AGAAGTTTGATATTCATACATGCCAT 57.298 30.769 0.00 0.00 31.96 4.40
2572 6510 7.646526 CCGTACGAGAAGTTTGATATTCATACA 59.353 37.037 18.76 0.00 31.96 2.29
2592 6530 4.730657 ACTTCTACATGTTTCTCCGTACG 58.269 43.478 8.69 8.69 0.00 3.67
2614 6552 5.988310 AAAGATCTTCATGCCATTGTCAA 57.012 34.783 8.78 0.00 0.00 3.18
2615 6553 5.988310 AAAAGATCTTCATGCCATTGTCA 57.012 34.783 8.78 0.00 0.00 3.58
2623 6561 5.531634 TCAACACCAAAAAGATCTTCATGC 58.468 37.500 8.78 0.00 0.00 4.06
2630 6568 5.760253 TGTCTCTCTCAACACCAAAAAGATC 59.240 40.000 0.00 0.00 0.00 2.75
2644 6582 4.323569 ACTTCCACCTATGTCTCTCTCA 57.676 45.455 0.00 0.00 0.00 3.27
2670 6608 7.177498 TGATATTTCATACGTGTCATTGCTC 57.823 36.000 0.00 0.00 0.00 4.26
2673 6611 9.773328 AAGTTTGATATTTCATACGTGTCATTG 57.227 29.630 0.00 0.00 38.42 2.82


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

AutoCloner maintained by Alex Coulton.