Multiple sequence alignment - TraesCS4D01G304700

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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 TraesCS4D01G304700 chr4D 100.000 3319 0 0 1 3319 473163939 473160621 0.000000e+00 6130.0
1 TraesCS4D01G304700 chr4D 96.970 33 1 0 3151 3183 1172873 1172841 4.630000e-04 56.5
2 TraesCS4D01G304700 chr4D 100.000 28 0 0 3157 3184 365321997 365322024 6.000000e-03 52.8
3 TraesCS4D01G304700 chr4B 93.168 3176 93 60 7 3137 595710129 595707033 0.000000e+00 4549.0
4 TraesCS4D01G304700 chr4A 87.107 2420 126 82 124 2458 680048247 680045929 0.000000e+00 2569.0
5 TraesCS4D01G304700 chr4A 86.846 707 35 24 2475 3141 680045871 680045183 0.000000e+00 737.0
6 TraesCS4D01G304700 chr4A 90.503 179 5 6 7 181 680048444 680048274 3.330000e-55 226.0
7 TraesCS4D01G304700 chr1A 97.436 39 1 0 3147 3185 473033796 473033758 2.140000e-07 67.6
8 TraesCS4D01G304700 chr5D 97.297 37 1 0 3147 3183 528829089 528829053 2.760000e-06 63.9
9 TraesCS4D01G304700 chr5D 87.273 55 4 2 3131 3183 270270043 270270096 3.580000e-05 60.2
10 TraesCS4D01G304700 chr5B 97.297 37 1 0 3147 3183 665976742 665976706 2.760000e-06 63.9
11 TraesCS4D01G304700 chr2B 95.122 41 1 1 3147 3186 139935507 139935467 2.760000e-06 63.9
12 TraesCS4D01G304700 chr3A 94.872 39 2 0 3145 3183 454417582 454417544 9.940000e-06 62.1
13 TraesCS4D01G304700 chr3A 100.000 28 0 0 1312 1339 502490497 502490470 6.000000e-03 52.8


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 TraesCS4D01G304700 chr4D 473160621 473163939 3318 True 6130.000000 6130 100.000 1 3319 1 chr4D.!!$R2 3318
1 TraesCS4D01G304700 chr4B 595707033 595710129 3096 True 4549.000000 4549 93.168 7 3137 1 chr4B.!!$R1 3130
2 TraesCS4D01G304700 chr4A 680045183 680048444 3261 True 1177.333333 2569 88.152 7 3141 3 chr4A.!!$R1 3134

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
454 554 0.598158 CGCCTAATTAAGCGCCCGTA 60.598 55.000 14.96 0.0 46.5 4.02 F
480 580 1.138247 GAGAGGGCAATGCAAAGCG 59.862 57.895 7.79 0.0 0.0 4.68 F
2124 2316 0.391130 GTTGACCATGTAGCTGCGGA 60.391 55.000 0.00 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2307 0.102663 TGTACAAACACTCGTCCGCA 59.897 50.0 0.00 0.00 0.00 5.69 R
2198 2398 0.752743 GCCATGGCCTCTACATGCAA 60.753 55.0 27.24 0.00 43.29 4.08 R
3245 3539 0.319727 GATCGAGGATCCTGCTGCAG 60.320 60.0 22.02 22.44 33.37 4.41 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.236146 TGAATCTTGACACACGGGCTAT 59.764 45.455 0.00 0.00 0.00 2.97
182 272 4.469945 CCCAATTCCCTCTACAGTCTACAA 59.530 45.833 0.00 0.00 0.00 2.41
187 277 5.509832 TCCCTCTACAGTCTACAAGTACA 57.490 43.478 0.00 0.00 0.00 2.90
189 279 5.013913 TCCCTCTACAGTCTACAAGTACACT 59.986 44.000 0.00 0.00 0.00 3.55
194 284 8.994429 TCTACAGTCTACAAGTACACTACTAC 57.006 38.462 0.00 0.00 38.26 2.73
206 296 1.208052 CACTACTACACTGGCATGGCT 59.792 52.381 21.08 2.10 0.00 4.75
207 297 1.208052 ACTACTACACTGGCATGGCTG 59.792 52.381 22.17 22.17 0.00 4.85
254 350 5.338219 CCAAAAACCCAGCATGATTAATCCA 60.338 40.000 12.90 1.91 39.69 3.41
454 554 0.598158 CGCCTAATTAAGCGCCCGTA 60.598 55.000 14.96 0.00 46.50 4.02
480 580 1.138247 GAGAGGGCAATGCAAAGCG 59.862 57.895 7.79 0.00 0.00 4.68
481 581 1.303561 AGAGGGCAATGCAAAGCGA 60.304 52.632 7.79 0.00 0.00 4.93
482 582 1.138247 GAGGGCAATGCAAAGCGAG 59.862 57.895 7.79 0.00 0.00 5.03
943 1062 6.633500 CACTTCTGTGGTCTTAAATTTCCA 57.367 37.500 0.00 0.00 40.33 3.53
1043 1166 2.600731 CACTTTACTCCGCTCTGACTG 58.399 52.381 0.00 0.00 0.00 3.51
1044 1167 2.229062 CACTTTACTCCGCTCTGACTGA 59.771 50.000 0.00 0.00 0.00 3.41
1045 1168 2.229302 ACTTTACTCCGCTCTGACTGAC 59.771 50.000 0.00 0.00 0.00 3.51
1046 1169 2.201921 TTACTCCGCTCTGACTGACT 57.798 50.000 0.00 0.00 0.00 3.41
1442 1592 2.034048 GCCTGCTCCTACCTACTGCC 62.034 65.000 0.00 0.00 0.00 4.85
1467 1621 3.224745 ATCGCTCGATCGTCCGTCG 62.225 63.158 22.15 15.90 40.30 5.12
1468 1622 4.939915 CGCTCGATCGTCCGTCGG 62.940 72.222 15.94 4.39 39.45 4.79
1764 1923 4.867599 GGCGATCGTCACGGGGAC 62.868 72.222 16.20 0.00 43.36 4.46
1980 2139 3.559597 GGGACTAAGCTCGCTCCTATAGA 60.560 52.174 0.00 0.00 0.00 1.98
1981 2140 3.687698 GGACTAAGCTCGCTCCTATAGAG 59.312 52.174 0.00 0.00 46.29 2.43
1982 2141 4.563993 GGACTAAGCTCGCTCCTATAGAGA 60.564 50.000 0.00 0.00 46.50 3.10
1983 2142 5.174037 ACTAAGCTCGCTCCTATAGAGAT 57.826 43.478 0.00 0.00 46.50 2.75
1984 2143 5.183228 ACTAAGCTCGCTCCTATAGAGATC 58.817 45.833 0.00 0.00 46.50 2.75
2054 2218 3.742327 CGTCTCATGGTGCACCTTGATAT 60.742 47.826 39.50 23.37 45.45 1.63
2055 2219 4.501400 CGTCTCATGGTGCACCTTGATATA 60.501 45.833 39.50 28.85 45.45 0.86
2107 2292 6.643770 CCACAAGTAATGTTGTACTCTACGTT 59.356 38.462 0.00 0.78 41.46 3.99
2108 2293 7.358931 CCACAAGTAATGTTGTACTCTACGTTG 60.359 40.741 0.00 0.00 41.46 4.10
2109 2294 7.380333 CACAAGTAATGTTGTACTCTACGTTGA 59.620 37.037 0.00 0.00 41.46 3.18
2119 2307 3.090037 ACTCTACGTTGACCATGTAGCT 58.910 45.455 0.00 0.00 42.73 3.32
2124 2316 0.391130 GTTGACCATGTAGCTGCGGA 60.391 55.000 0.00 0.00 0.00 5.54
2127 2319 2.279502 GACCATGTAGCTGCGGACGA 62.280 60.000 0.00 0.00 0.00 4.20
2130 2322 1.139734 ATGTAGCTGCGGACGAGTG 59.860 57.895 0.00 0.00 0.00 3.51
2131 2323 1.595993 ATGTAGCTGCGGACGAGTGT 61.596 55.000 0.00 0.00 0.00 3.55
2132 2324 1.080705 GTAGCTGCGGACGAGTGTT 60.081 57.895 0.00 0.00 0.00 3.32
2133 2325 0.666577 GTAGCTGCGGACGAGTGTTT 60.667 55.000 0.00 0.00 0.00 2.83
2161 2361 8.692110 ACATGTGCAAGTAATAAACAATGATG 57.308 30.769 0.00 0.00 0.00 3.07
2192 2392 7.815398 AAATATCGTTGTTCACATGTACGTA 57.185 32.000 15.54 9.30 34.15 3.57
2195 2395 3.976306 TCGTTGTTCACATGTACGTACTG 59.024 43.478 25.12 20.96 34.15 2.74
2196 2396 3.732219 CGTTGTTCACATGTACGTACTGT 59.268 43.478 25.12 21.53 0.00 3.55
2197 2397 4.911033 CGTTGTTCACATGTACGTACTGTA 59.089 41.667 25.12 6.98 0.00 2.74
2198 2398 5.570206 CGTTGTTCACATGTACGTACTGTAT 59.430 40.000 25.12 9.07 35.02 2.29
2200 2400 6.937886 TGTTCACATGTACGTACTGTATTG 57.062 37.500 25.12 16.16 35.02 1.90
2201 2401 5.346551 TGTTCACATGTACGTACTGTATTGC 59.653 40.000 25.12 15.73 35.02 3.56
2202 2402 5.061920 TCACATGTACGTACTGTATTGCA 57.938 39.130 25.12 4.06 35.02 4.08
2203 2403 5.656480 TCACATGTACGTACTGTATTGCAT 58.344 37.500 25.12 6.28 35.02 3.96
2205 2405 5.290885 CACATGTACGTACTGTATTGCATGT 59.709 40.000 25.12 19.28 43.51 3.21
2206 2406 6.474102 CACATGTACGTACTGTATTGCATGTA 59.526 38.462 25.12 1.79 42.10 2.29
2208 2408 6.439675 TGTACGTACTGTATTGCATGTAGA 57.560 37.500 25.12 0.00 35.02 2.59
2209 2409 6.492254 TGTACGTACTGTATTGCATGTAGAG 58.508 40.000 25.12 0.00 35.02 2.43
2213 2413 2.505407 ACTGTATTGCATGTAGAGGCCA 59.495 45.455 5.01 0.00 0.00 5.36
2215 2415 3.479489 TGTATTGCATGTAGAGGCCATG 58.521 45.455 5.01 0.00 42.06 3.66
2228 2428 3.072476 CCATGGCCGGCTATAGCT 58.928 61.111 26.15 0.20 41.70 3.32
2229 2429 2.286826 CCATGGCCGGCTATAGCTA 58.713 57.895 26.15 0.00 41.70 3.32
2230 2430 0.833287 CCATGGCCGGCTATAGCTAT 59.167 55.000 26.15 11.77 41.70 2.97
2231 2431 1.210478 CCATGGCCGGCTATAGCTATT 59.790 52.381 26.15 0.00 41.70 1.73
2232 2432 2.434336 CCATGGCCGGCTATAGCTATTA 59.566 50.000 26.15 7.97 41.70 0.98
2233 2433 3.458189 CATGGCCGGCTATAGCTATTAC 58.542 50.000 26.15 4.32 41.70 1.89
2234 2434 1.475280 TGGCCGGCTATAGCTATTACG 59.525 52.381 28.56 17.15 41.70 3.18
2235 2435 1.202382 GGCCGGCTATAGCTATTACGG 60.202 57.143 28.56 25.88 41.55 4.02
2241 2441 5.105997 CCGGCTATAGCTATTACGGTAAACT 60.106 44.000 23.53 5.81 41.70 2.66
2276 2476 5.624159 CAGTGATCATGGGGCTAATCTAAA 58.376 41.667 0.00 0.00 0.00 1.85
2281 2481 7.066766 GTGATCATGGGGCTAATCTAAATGATC 59.933 40.741 13.28 13.28 44.59 2.92
2282 2482 5.491070 TCATGGGGCTAATCTAAATGATCG 58.509 41.667 0.00 0.00 33.57 3.69
2284 2484 3.650942 TGGGGCTAATCTAAATGATCGGT 59.349 43.478 0.00 0.00 33.57 4.69
2286 2486 3.437049 GGGCTAATCTAAATGATCGGTGC 59.563 47.826 0.00 0.00 33.57 5.01
2290 2495 2.988010 TCTAAATGATCGGTGCTGCT 57.012 45.000 0.00 0.00 0.00 4.24
2307 2512 5.690409 GTGCTGCTATGAATTGAATGAATGG 59.310 40.000 0.00 0.00 0.00 3.16
2351 2563 6.863645 AGTGCGTATATAAATGTAGTCTGCAG 59.136 38.462 7.63 7.63 0.00 4.41
2382 2594 0.179059 TGTCACTTGTCCGTGCATGT 60.179 50.000 4.96 0.00 34.92 3.21
2383 2595 1.069358 TGTCACTTGTCCGTGCATGTA 59.931 47.619 4.96 0.00 34.92 2.29
2384 2596 2.289382 TGTCACTTGTCCGTGCATGTAT 60.289 45.455 4.96 0.00 34.92 2.29
2385 2597 3.056465 TGTCACTTGTCCGTGCATGTATA 60.056 43.478 4.96 0.00 34.92 1.47
2421 2634 4.141756 ACCATGCAATGTTTGAAAGTTGGA 60.142 37.500 0.00 3.33 44.81 3.53
2458 2671 6.358030 GCGCAGAAATTTATGTTGCTATAGTG 59.642 38.462 18.62 0.00 32.80 2.74
2459 2672 7.630026 CGCAGAAATTTATGTTGCTATAGTGA 58.370 34.615 13.94 0.00 32.80 3.41
2461 2674 9.604626 GCAGAAATTTATGTTGCTATAGTGATC 57.395 33.333 13.94 0.00 0.00 2.92
2487 2742 1.943693 GCGCGCACACACACATTTT 60.944 52.632 29.10 0.00 0.00 1.82
2551 2806 1.803366 GCACCCCGGAGATACGTAGG 61.803 65.000 0.73 0.00 0.00 3.18
2585 2840 3.366273 GCAGACGAATTTTCCATGCAAGA 60.366 43.478 0.00 0.00 32.58 3.02
2631 2891 4.316022 GTCTACACGACGACGACG 57.684 61.111 17.60 17.60 42.66 5.12
2632 2892 1.775344 GTCTACACGACGACGACGA 59.225 57.895 25.15 3.20 42.66 4.20
2633 2893 0.515315 GTCTACACGACGACGACGAC 60.515 60.000 25.15 7.02 42.66 4.34
2634 2894 1.225583 CTACACGACGACGACGACC 60.226 63.158 25.15 4.43 42.66 4.79
2635 2895 2.554365 CTACACGACGACGACGACCC 62.554 65.000 25.15 1.92 42.66 4.46
2636 2896 4.016629 CACGACGACGACGACCCA 62.017 66.667 25.15 0.00 42.66 4.51
2637 2897 3.720193 ACGACGACGACGACCCAG 61.720 66.667 25.15 2.87 42.66 4.45
2639 2899 3.735029 GACGACGACGACCCAGCT 61.735 66.667 15.32 0.00 42.66 4.24
2640 2900 3.264866 GACGACGACGACCCAGCTT 62.265 63.158 15.32 0.00 42.66 3.74
2641 2901 2.504244 CGACGACGACCCAGCTTC 60.504 66.667 0.00 0.00 42.66 3.86
2655 2915 0.390472 AGCTTCGCTTCACTAGTGGC 60.390 55.000 22.48 17.07 33.89 5.01
2684 2954 1.399714 CCGCCTGGACTACACAGATA 58.600 55.000 0.00 0.00 38.20 1.98
3085 3367 4.901197 TCCACATTAACTTCCTACTGCA 57.099 40.909 0.00 0.00 0.00 4.41
3121 3415 7.707104 AGATCATTTTTGTTCGTCTGTTTTCT 58.293 30.769 0.00 0.00 0.00 2.52
3124 3418 7.186804 TCATTTTTGTTCGTCTGTTTTCTCTC 58.813 34.615 0.00 0.00 0.00 3.20
3142 3436 6.783708 TCTCTCAAGAAAATCTACCTCTCC 57.216 41.667 0.00 0.00 0.00 3.71
3143 3437 6.498538 TCTCTCAAGAAAATCTACCTCTCCT 58.501 40.000 0.00 0.00 0.00 3.69
3144 3438 6.957020 TCTCTCAAGAAAATCTACCTCTCCTT 59.043 38.462 0.00 0.00 0.00 3.36
3145 3439 6.940739 TCTCAAGAAAATCTACCTCTCCTTG 58.059 40.000 0.00 0.00 33.20 3.61
3146 3440 5.491982 TCAAGAAAATCTACCTCTCCTTGC 58.508 41.667 0.00 0.00 32.30 4.01
3147 3441 5.249393 TCAAGAAAATCTACCTCTCCTTGCT 59.751 40.000 0.00 0.00 32.30 3.91
3148 3442 6.440647 TCAAGAAAATCTACCTCTCCTTGCTA 59.559 38.462 0.00 0.00 32.30 3.49
3149 3443 6.875972 AGAAAATCTACCTCTCCTTGCTAA 57.124 37.500 0.00 0.00 0.00 3.09
3150 3444 7.259088 AGAAAATCTACCTCTCCTTGCTAAA 57.741 36.000 0.00 0.00 0.00 1.85
3151 3445 7.334858 AGAAAATCTACCTCTCCTTGCTAAAG 58.665 38.462 0.00 0.00 0.00 1.85
3152 3446 4.681074 ATCTACCTCTCCTTGCTAAAGC 57.319 45.455 0.00 0.00 42.50 3.51
3153 3447 3.714144 TCTACCTCTCCTTGCTAAAGCT 58.286 45.455 3.26 0.00 42.66 3.74
3154 3448 2.777832 ACCTCTCCTTGCTAAAGCTG 57.222 50.000 3.26 0.00 42.66 4.24
3155 3449 1.339535 ACCTCTCCTTGCTAAAGCTGC 60.340 52.381 3.26 0.00 42.66 5.25
3156 3450 1.339438 CCTCTCCTTGCTAAAGCTGCA 60.339 52.381 1.02 0.00 42.66 4.41
3157 3451 2.430465 CTCTCCTTGCTAAAGCTGCAA 58.570 47.619 9.35 9.35 46.48 4.08
3158 3452 2.154462 TCTCCTTGCTAAAGCTGCAAC 58.846 47.619 5.88 0.00 44.24 4.17
3159 3453 1.881973 CTCCTTGCTAAAGCTGCAACA 59.118 47.619 5.88 0.00 44.24 3.33
3160 3454 2.294233 CTCCTTGCTAAAGCTGCAACAA 59.706 45.455 5.88 0.00 44.24 2.83
3161 3455 2.294233 TCCTTGCTAAAGCTGCAACAAG 59.706 45.455 5.88 8.85 44.24 3.16
3162 3456 2.035066 CCTTGCTAAAGCTGCAACAAGT 59.965 45.455 5.88 0.00 44.24 3.16
3163 3457 3.253188 CCTTGCTAAAGCTGCAACAAGTA 59.747 43.478 5.88 0.00 44.24 2.24
3164 3458 4.261572 CCTTGCTAAAGCTGCAACAAGTAA 60.262 41.667 5.88 0.00 44.24 2.24
3165 3459 5.452078 TTGCTAAAGCTGCAACAAGTAAT 57.548 34.783 5.88 0.00 44.24 1.89
3166 3460 6.349280 CCTTGCTAAAGCTGCAACAAGTAATA 60.349 38.462 5.88 0.00 44.24 0.98
3167 3461 6.757897 TGCTAAAGCTGCAACAAGTAATAT 57.242 33.333 1.02 0.00 42.66 1.28
3168 3462 6.554419 TGCTAAAGCTGCAACAAGTAATATG 58.446 36.000 1.02 0.00 42.66 1.78
3169 3463 5.973565 GCTAAAGCTGCAACAAGTAATATGG 59.026 40.000 1.02 0.00 38.21 2.74
3170 3464 6.183360 GCTAAAGCTGCAACAAGTAATATGGA 60.183 38.462 1.02 0.00 38.21 3.41
3171 3465 6.780457 AAAGCTGCAACAAGTAATATGGAT 57.220 33.333 1.02 0.00 0.00 3.41
3172 3466 6.382869 AAGCTGCAACAAGTAATATGGATC 57.617 37.500 1.02 0.00 0.00 3.36
3173 3467 4.512944 AGCTGCAACAAGTAATATGGATCG 59.487 41.667 1.02 0.00 0.00 3.69
3174 3468 4.319766 GCTGCAACAAGTAATATGGATCGG 60.320 45.833 0.00 0.00 0.00 4.18
3175 3469 5.029807 TGCAACAAGTAATATGGATCGGA 57.970 39.130 0.00 0.00 0.00 4.55
3176 3470 5.056480 TGCAACAAGTAATATGGATCGGAG 58.944 41.667 0.00 0.00 0.00 4.63
3177 3471 4.452455 GCAACAAGTAATATGGATCGGAGG 59.548 45.833 0.00 0.00 0.00 4.30
3178 3472 5.741964 GCAACAAGTAATATGGATCGGAGGA 60.742 44.000 0.00 0.00 0.00 3.71
3179 3473 6.288294 CAACAAGTAATATGGATCGGAGGAA 58.712 40.000 0.00 0.00 0.00 3.36
3180 3474 6.102897 ACAAGTAATATGGATCGGAGGAAG 57.897 41.667 0.00 0.00 0.00 3.46
3181 3475 5.602978 ACAAGTAATATGGATCGGAGGAAGT 59.397 40.000 0.00 0.00 0.00 3.01
3182 3476 6.781014 ACAAGTAATATGGATCGGAGGAAGTA 59.219 38.462 0.00 0.00 0.00 2.24
3183 3477 7.455008 ACAAGTAATATGGATCGGAGGAAGTAT 59.545 37.037 0.00 0.00 0.00 2.12
3184 3478 8.967918 CAAGTAATATGGATCGGAGGAAGTATA 58.032 37.037 0.00 0.00 0.00 1.47
3185 3479 9.543231 AAGTAATATGGATCGGAGGAAGTATAA 57.457 33.333 0.00 0.00 0.00 0.98
3186 3480 8.968969 AGTAATATGGATCGGAGGAAGTATAAC 58.031 37.037 0.00 0.00 0.00 1.89
3187 3481 8.968969 GTAATATGGATCGGAGGAAGTATAACT 58.031 37.037 0.00 0.00 0.00 2.24
3188 3482 5.730296 ATGGATCGGAGGAAGTATAACTG 57.270 43.478 0.00 0.00 0.00 3.16
3189 3483 4.543689 TGGATCGGAGGAAGTATAACTGT 58.456 43.478 0.00 0.00 0.00 3.55
3190 3484 4.960469 TGGATCGGAGGAAGTATAACTGTT 59.040 41.667 0.00 0.00 0.00 3.16
3191 3485 5.424252 TGGATCGGAGGAAGTATAACTGTTT 59.576 40.000 0.00 0.00 0.00 2.83
3192 3486 5.753921 GGATCGGAGGAAGTATAACTGTTTG 59.246 44.000 0.00 0.00 0.00 2.93
3193 3487 4.501071 TCGGAGGAAGTATAACTGTTTGC 58.499 43.478 0.00 0.00 0.00 3.68
3194 3488 3.621715 CGGAGGAAGTATAACTGTTTGCC 59.378 47.826 0.00 0.00 0.00 4.52
3195 3489 3.621715 GGAGGAAGTATAACTGTTTGCCG 59.378 47.826 0.00 0.00 0.00 5.69
3196 3490 3.606687 AGGAAGTATAACTGTTTGCCGG 58.393 45.455 0.00 0.00 0.00 6.13
3197 3491 3.262405 AGGAAGTATAACTGTTTGCCGGA 59.738 43.478 5.05 0.00 0.00 5.14
3198 3492 4.004982 GGAAGTATAACTGTTTGCCGGAA 58.995 43.478 5.05 0.00 0.00 4.30
3199 3493 4.456566 GGAAGTATAACTGTTTGCCGGAAA 59.543 41.667 5.05 0.00 0.00 3.13
3200 3494 5.124936 GGAAGTATAACTGTTTGCCGGAAAT 59.875 40.000 5.05 0.00 0.00 2.17
3201 3495 6.316890 GGAAGTATAACTGTTTGCCGGAAATA 59.683 38.462 5.05 0.40 0.00 1.40
3202 3496 6.673154 AGTATAACTGTTTGCCGGAAATAC 57.327 37.500 5.05 2.81 0.00 1.89
3203 3497 6.174760 AGTATAACTGTTTGCCGGAAATACA 58.825 36.000 5.05 7.83 0.00 2.29
3204 3498 6.826741 AGTATAACTGTTTGCCGGAAATACAT 59.173 34.615 5.05 0.00 0.00 2.29
3205 3499 4.434713 AACTGTTTGCCGGAAATACATC 57.565 40.909 5.05 0.00 0.00 3.06
3206 3500 3.686016 ACTGTTTGCCGGAAATACATCT 58.314 40.909 5.05 0.00 0.00 2.90
3207 3501 4.079253 ACTGTTTGCCGGAAATACATCTT 58.921 39.130 5.05 0.00 0.00 2.40
3208 3502 4.082787 ACTGTTTGCCGGAAATACATCTTG 60.083 41.667 5.05 0.00 0.00 3.02
3209 3503 3.823873 TGTTTGCCGGAAATACATCTTGT 59.176 39.130 5.05 0.00 0.00 3.16
3210 3504 5.004448 TGTTTGCCGGAAATACATCTTGTA 58.996 37.500 5.05 0.00 37.24 2.41
3211 3505 5.123186 TGTTTGCCGGAAATACATCTTGTAG 59.877 40.000 5.05 0.00 36.14 2.74
3212 3506 4.481368 TGCCGGAAATACATCTTGTAGT 57.519 40.909 5.05 0.00 36.14 2.73
3213 3507 4.839121 TGCCGGAAATACATCTTGTAGTT 58.161 39.130 5.05 0.48 42.83 2.24
3214 3508 5.979993 TGCCGGAAATACATCTTGTAGTTA 58.020 37.500 5.05 0.00 40.63 2.24
3215 3509 6.588204 TGCCGGAAATACATCTTGTAGTTAT 58.412 36.000 5.05 0.00 40.63 1.89
3216 3510 7.728148 TGCCGGAAATACATCTTGTAGTTATA 58.272 34.615 5.05 0.00 40.63 0.98
3217 3511 8.205512 TGCCGGAAATACATCTTGTAGTTATAA 58.794 33.333 5.05 0.00 40.63 0.98
3218 3512 9.048446 GCCGGAAATACATCTTGTAGTTATAAA 57.952 33.333 5.05 0.00 40.63 1.40
3233 3527 9.140286 TGTAGTTATAAATAAGCAGATCGATGC 57.860 33.333 0.54 1.83 46.88 3.91
3241 3535 2.618165 CAGATCGATGCTGCATGCT 58.382 52.632 21.53 8.78 43.37 3.79
3242 3536 0.235926 CAGATCGATGCTGCATGCTG 59.764 55.000 21.53 19.80 43.37 4.41
3243 3537 0.179054 AGATCGATGCTGCATGCTGT 60.179 50.000 21.53 6.90 43.37 4.40
3244 3538 0.041224 GATCGATGCTGCATGCTGTG 60.041 55.000 21.53 12.81 43.37 3.66
3261 3555 2.588314 GCTGCAGCAGGATCCTCG 60.588 66.667 33.36 9.05 41.59 4.63
3262 3556 3.086391 GCTGCAGCAGGATCCTCGA 62.086 63.158 33.36 0.00 41.59 4.04
3263 3557 1.747145 CTGCAGCAGGATCCTCGAT 59.253 57.895 12.69 3.52 0.00 3.59
3264 3558 0.319727 CTGCAGCAGGATCCTCGATC 60.320 60.000 12.69 2.41 38.25 3.69
3265 3559 1.372748 GCAGCAGGATCCTCGATCG 60.373 63.158 12.69 9.36 39.72 3.69
3266 3560 1.800283 GCAGCAGGATCCTCGATCGA 61.800 60.000 18.32 18.32 39.72 3.59
3267 3561 0.887247 CAGCAGGATCCTCGATCGAT 59.113 55.000 19.78 3.36 39.72 3.59
3268 3562 0.887247 AGCAGGATCCTCGATCGATG 59.113 55.000 19.78 16.34 39.72 3.84
3269 3563 0.735632 GCAGGATCCTCGATCGATGC 60.736 60.000 19.78 19.71 41.50 3.91
3270 3564 0.600057 CAGGATCCTCGATCGATGCA 59.400 55.000 19.78 5.75 39.72 3.96
3271 3565 0.600557 AGGATCCTCGATCGATGCAC 59.399 55.000 19.78 12.15 39.72 4.57
3272 3566 0.600557 GGATCCTCGATCGATGCACT 59.399 55.000 19.78 4.11 39.72 4.40
3273 3567 1.000283 GGATCCTCGATCGATGCACTT 60.000 52.381 19.78 0.56 39.72 3.16
3274 3568 2.229062 GGATCCTCGATCGATGCACTTA 59.771 50.000 19.78 0.00 39.72 2.24
3275 3569 2.776312 TCCTCGATCGATGCACTTAC 57.224 50.000 19.78 0.00 0.00 2.34
3276 3570 2.298610 TCCTCGATCGATGCACTTACT 58.701 47.619 19.78 0.00 0.00 2.24
3277 3571 2.033424 TCCTCGATCGATGCACTTACTG 59.967 50.000 19.78 2.37 0.00 2.74
3278 3572 2.223595 CCTCGATCGATGCACTTACTGT 60.224 50.000 19.78 0.00 0.00 3.55
3279 3573 3.039405 CTCGATCGATGCACTTACTGTC 58.961 50.000 19.78 0.00 0.00 3.51
3280 3574 1.775770 CGATCGATGCACTTACTGTCG 59.224 52.381 10.26 0.00 0.00 4.35
3281 3575 2.791503 CGATCGATGCACTTACTGTCGT 60.792 50.000 10.26 0.00 34.24 4.34
3282 3576 1.977188 TCGATGCACTTACTGTCGTG 58.023 50.000 3.80 5.96 34.24 4.35
3283 3577 0.992072 CGATGCACTTACTGTCGTGG 59.008 55.000 10.78 0.00 0.00 4.94
3284 3578 1.668919 CGATGCACTTACTGTCGTGGT 60.669 52.381 10.78 0.00 0.00 4.16
3285 3579 1.726791 GATGCACTTACTGTCGTGGTG 59.273 52.381 10.78 5.54 34.01 4.17
3286 3580 0.747852 TGCACTTACTGTCGTGGTGA 59.252 50.000 10.78 0.00 33.26 4.02
3287 3581 1.343142 TGCACTTACTGTCGTGGTGAT 59.657 47.619 10.78 0.00 33.26 3.06
3288 3582 2.224185 TGCACTTACTGTCGTGGTGATT 60.224 45.455 10.78 0.00 33.26 2.57
3289 3583 2.806244 GCACTTACTGTCGTGGTGATTT 59.194 45.455 10.78 0.00 33.26 2.17
3290 3584 3.250040 GCACTTACTGTCGTGGTGATTTT 59.750 43.478 10.78 0.00 33.26 1.82
3291 3585 4.772434 CACTTACTGTCGTGGTGATTTTG 58.228 43.478 3.10 0.00 33.26 2.44
3292 3586 3.813166 ACTTACTGTCGTGGTGATTTTGG 59.187 43.478 0.00 0.00 0.00 3.28
3293 3587 2.341846 ACTGTCGTGGTGATTTTGGT 57.658 45.000 0.00 0.00 0.00 3.67
3294 3588 1.946768 ACTGTCGTGGTGATTTTGGTG 59.053 47.619 0.00 0.00 0.00 4.17
3295 3589 0.665835 TGTCGTGGTGATTTTGGTGC 59.334 50.000 0.00 0.00 0.00 5.01
3296 3590 0.665835 GTCGTGGTGATTTTGGTGCA 59.334 50.000 0.00 0.00 0.00 4.57
3297 3591 1.066303 GTCGTGGTGATTTTGGTGCAA 59.934 47.619 0.00 0.00 0.00 4.08
3298 3592 1.336440 TCGTGGTGATTTTGGTGCAAG 59.664 47.619 0.00 0.00 0.00 4.01
3299 3593 1.066908 CGTGGTGATTTTGGTGCAAGT 59.933 47.619 0.00 0.00 0.00 3.16
3300 3594 2.472816 GTGGTGATTTTGGTGCAAGTG 58.527 47.619 0.00 0.00 0.00 3.16
3301 3595 1.202510 TGGTGATTTTGGTGCAAGTGC 60.203 47.619 0.00 0.00 42.50 4.40
3302 3596 1.130955 GTGATTTTGGTGCAAGTGCG 58.869 50.000 0.00 0.00 45.83 5.34
3303 3597 1.028130 TGATTTTGGTGCAAGTGCGA 58.972 45.000 0.00 0.00 45.83 5.10
3304 3598 1.406898 TGATTTTGGTGCAAGTGCGAA 59.593 42.857 0.00 0.00 45.83 4.70
3305 3599 2.159184 TGATTTTGGTGCAAGTGCGAAA 60.159 40.909 0.00 0.00 45.83 3.46
3306 3600 1.919918 TTTTGGTGCAAGTGCGAAAG 58.080 45.000 0.00 0.00 45.83 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.202758 AGCCCGTGTGTCAAGATTCAA 60.203 47.619 0.00 0.00 0.00 2.69
1 2 0.396435 AGCCCGTGTGTCAAGATTCA 59.604 50.000 0.00 0.00 0.00 2.57
2 3 2.380084 TAGCCCGTGTGTCAAGATTC 57.620 50.000 0.00 0.00 0.00 2.52
3 4 4.161565 TCTTATAGCCCGTGTGTCAAGATT 59.838 41.667 0.00 0.00 0.00 2.40
4 5 3.704566 TCTTATAGCCCGTGTGTCAAGAT 59.295 43.478 0.00 0.00 0.00 2.40
5 6 3.093814 TCTTATAGCCCGTGTGTCAAGA 58.906 45.455 0.00 0.00 0.00 3.02
182 272 3.447586 CCATGCCAGTGTAGTAGTGTACT 59.552 47.826 0.00 0.00 42.68 2.73
187 277 1.208052 CAGCCATGCCAGTGTAGTAGT 59.792 52.381 0.00 0.00 0.00 2.73
189 279 1.066215 CACAGCCATGCCAGTGTAGTA 60.066 52.381 0.00 0.00 32.83 1.82
254 350 5.674569 GCATTCATTAGCGCGAAATGGATAT 60.675 40.000 27.28 18.89 31.96 1.63
454 554 1.762460 ATTGCCCTCTCGGACGGAT 60.762 57.895 0.00 0.00 0.00 4.18
480 580 4.331992 GCTGTCCGGATTAAAAACCTACTC 59.668 45.833 7.81 0.00 0.00 2.59
481 581 4.259356 GCTGTCCGGATTAAAAACCTACT 58.741 43.478 7.81 0.00 0.00 2.57
482 582 3.063045 CGCTGTCCGGATTAAAAACCTAC 59.937 47.826 7.81 0.00 0.00 3.18
523 623 1.002544 GGGCATTAATCCTCCCTCTCG 59.997 57.143 8.88 0.00 35.87 4.04
529 631 2.800250 CCATCAGGGCATTAATCCTCC 58.200 52.381 0.00 0.00 0.00 4.30
595 697 2.202743 ATCACATGCCCGTCGTCG 60.203 61.111 0.00 0.00 0.00 5.12
645 747 0.675208 TGCAACCGTCCGTATGCATT 60.675 50.000 3.54 0.00 43.32 3.56
646 748 1.078778 TGCAACCGTCCGTATGCAT 60.079 52.632 3.79 3.79 43.32 3.96
930 1049 3.024547 GAGGGGGCTGGAAATTTAAGAC 58.975 50.000 4.86 1.79 0.00 3.01
943 1062 3.693572 AGAGCTCAGGAGGGGGCT 61.694 66.667 17.77 0.00 37.77 5.19
1078 1201 7.920151 CGATCCTTCCAAAGCTATATCTATCAG 59.080 40.741 0.00 0.00 0.00 2.90
1164 1292 1.134075 CGCTAGCTGCACTTGCTTG 59.866 57.895 13.93 4.03 43.93 4.01
1427 1570 2.417936 GCGGCAGTAGGTAGGAGC 59.582 66.667 0.00 0.00 0.00 4.70
1467 1621 8.446273 CAAGCATATTATAAGTAGACATGCACC 58.554 37.037 6.44 0.00 39.72 5.01
1468 1622 8.993121 ACAAGCATATTATAAGTAGACATGCAC 58.007 33.333 6.44 0.00 39.72 4.57
1519 1673 3.345808 CCCCGACTGCACAACACG 61.346 66.667 0.00 0.00 0.00 4.49
1782 1941 3.244580 ATCTCCATGCCGCCGGAT 61.245 61.111 7.68 0.00 0.00 4.18
2054 2218 2.902705 AACAGTCCTCGTTGCACTTA 57.097 45.000 0.00 0.00 0.00 2.24
2055 2219 2.159014 TGTAACAGTCCTCGTTGCACTT 60.159 45.455 0.00 0.00 34.61 3.16
2107 2292 1.218047 GTCCGCAGCTACATGGTCA 59.782 57.895 0.00 0.00 0.00 4.02
2108 2293 1.878522 CGTCCGCAGCTACATGGTC 60.879 63.158 0.00 0.00 0.00 4.02
2109 2294 2.184322 CGTCCGCAGCTACATGGT 59.816 61.111 0.00 0.00 0.00 3.55
2119 2307 0.102663 TGTACAAACACTCGTCCGCA 59.897 50.000 0.00 0.00 0.00 5.69
2124 2316 2.556257 TGCACATGTACAAACACTCGT 58.444 42.857 0.00 0.00 38.78 4.18
2127 2319 6.633500 ATTACTTGCACATGTACAAACACT 57.367 33.333 12.47 0.00 38.78 3.55
2130 2322 8.789881 TGTTTATTACTTGCACATGTACAAAC 57.210 30.769 12.47 6.74 33.09 2.93
2131 2323 9.973450 ATTGTTTATTACTTGCACATGTACAAA 57.027 25.926 12.47 0.00 0.00 2.83
2132 2324 9.404348 CATTGTTTATTACTTGCACATGTACAA 57.596 29.630 11.00 11.00 0.00 2.41
2133 2325 8.787852 TCATTGTTTATTACTTGCACATGTACA 58.212 29.630 0.00 0.00 0.00 2.90
2161 2361 8.662141 ACATGTGAACAACGATATTTAGTTACC 58.338 33.333 0.00 0.00 0.00 2.85
2192 2392 2.505407 TGGCCTCTACATGCAATACAGT 59.495 45.455 3.32 0.00 0.00 3.55
2195 2395 2.816087 CCATGGCCTCTACATGCAATAC 59.184 50.000 3.32 0.00 43.29 1.89
2196 2396 2.815215 GCCATGGCCTCTACATGCAATA 60.815 50.000 27.24 0.00 43.29 1.90
2197 2397 1.991121 CCATGGCCTCTACATGCAAT 58.009 50.000 3.32 0.00 43.29 3.56
2198 2398 0.752743 GCCATGGCCTCTACATGCAA 60.753 55.000 27.24 0.00 43.29 4.08
2200 2400 3.755434 GCCATGGCCTCTACATGC 58.245 61.111 27.24 0.00 43.29 4.06
2213 2413 2.100916 CGTAATAGCTATAGCCGGCCAT 59.899 50.000 26.15 19.34 43.38 4.40
2215 2415 1.202382 CCGTAATAGCTATAGCCGGCC 60.202 57.143 26.15 7.28 43.38 6.13
2218 2418 5.947443 AGTTTACCGTAATAGCTATAGCCG 58.053 41.667 21.17 15.91 43.38 5.52
2220 2420 7.541437 CCTCAAGTTTACCGTAATAGCTATAGC 59.459 40.741 17.33 17.33 42.49 2.97
2221 2421 8.790718 TCCTCAAGTTTACCGTAATAGCTATAG 58.209 37.037 6.68 1.90 0.00 1.31
2222 2422 8.696043 TCCTCAAGTTTACCGTAATAGCTATA 57.304 34.615 6.68 0.00 0.00 1.31
2223 2423 7.287235 ACTCCTCAAGTTTACCGTAATAGCTAT 59.713 37.037 0.00 0.00 33.03 2.97
2224 2424 6.604795 ACTCCTCAAGTTTACCGTAATAGCTA 59.395 38.462 0.00 0.00 33.03 3.32
2225 2425 5.421374 ACTCCTCAAGTTTACCGTAATAGCT 59.579 40.000 0.00 0.00 33.03 3.32
2226 2426 5.658468 ACTCCTCAAGTTTACCGTAATAGC 58.342 41.667 0.00 0.00 33.03 2.97
2227 2427 6.534079 CCAACTCCTCAAGTTTACCGTAATAG 59.466 42.308 0.00 0.00 46.26 1.73
2228 2428 6.400568 CCAACTCCTCAAGTTTACCGTAATA 58.599 40.000 0.00 0.00 46.26 0.98
2229 2429 5.243207 CCAACTCCTCAAGTTTACCGTAAT 58.757 41.667 0.00 0.00 46.26 1.89
2230 2430 4.634199 CCAACTCCTCAAGTTTACCGTAA 58.366 43.478 0.00 0.00 46.26 3.18
2231 2431 3.555586 GCCAACTCCTCAAGTTTACCGTA 60.556 47.826 0.00 0.00 46.26 4.02
2232 2432 2.809299 GCCAACTCCTCAAGTTTACCGT 60.809 50.000 0.00 0.00 46.26 4.83
2233 2433 1.804748 GCCAACTCCTCAAGTTTACCG 59.195 52.381 0.00 0.00 46.26 4.02
2234 2434 2.814336 CTGCCAACTCCTCAAGTTTACC 59.186 50.000 0.00 0.00 46.26 2.85
2235 2435 3.251004 CACTGCCAACTCCTCAAGTTTAC 59.749 47.826 0.00 0.00 46.26 2.01
2241 2441 1.699083 TGATCACTGCCAACTCCTCAA 59.301 47.619 0.00 0.00 0.00 3.02
2276 2476 2.916702 TTCATAGCAGCACCGATCAT 57.083 45.000 0.00 0.00 0.00 2.45
2281 2481 3.313249 TCATTCAATTCATAGCAGCACCG 59.687 43.478 0.00 0.00 0.00 4.94
2282 2482 4.906065 TCATTCAATTCATAGCAGCACC 57.094 40.909 0.00 0.00 0.00 5.01
2284 2484 5.595133 TCCATTCATTCAATTCATAGCAGCA 59.405 36.000 0.00 0.00 0.00 4.41
2286 2486 7.808381 GTCATCCATTCATTCAATTCATAGCAG 59.192 37.037 0.00 0.00 0.00 4.24
2290 2495 7.806409 ACGTCATCCATTCATTCAATTCATA 57.194 32.000 0.00 0.00 0.00 2.15
2307 2512 8.670804 ACGCACTTAATTATATCTACGTCATC 57.329 34.615 0.00 0.00 0.00 2.92
2351 2563 3.403038 ACAAGTGACACATACCAGAAGC 58.597 45.455 8.59 0.00 0.00 3.86
2382 2594 4.018597 TGCATGGTGATGGTGGCATATATA 60.019 41.667 0.00 0.00 0.00 0.86
2383 2595 3.245336 TGCATGGTGATGGTGGCATATAT 60.245 43.478 0.00 0.00 0.00 0.86
2384 2596 2.107901 TGCATGGTGATGGTGGCATATA 59.892 45.455 0.00 0.00 0.00 0.86
2385 2597 1.133419 TGCATGGTGATGGTGGCATAT 60.133 47.619 0.00 0.00 0.00 1.78
2391 2604 2.997303 CAAACATTGCATGGTGATGGTG 59.003 45.455 0.00 0.00 33.60 4.17
2421 2634 1.106351 TTCTGCGCACCAACAACCAT 61.106 50.000 5.66 0.00 0.00 3.55
2487 2742 6.020121 CGTACTGTTTCGTCTTGAAAGAAAGA 60.020 38.462 0.00 0.00 46.85 2.52
2551 2806 2.580470 CGTCTGCGATCGATGCACC 61.580 63.158 21.57 0.00 41.33 5.01
2826 3096 5.413309 TTCAAACCAATCTCCTCTCTCTC 57.587 43.478 0.00 0.00 0.00 3.20
2827 3097 5.743117 CATTCAAACCAATCTCCTCTCTCT 58.257 41.667 0.00 0.00 0.00 3.10
3085 3367 9.079833 CGAACAAAAATGATCTAAAATCTGCAT 57.920 29.630 0.00 0.00 0.00 3.96
3121 3415 6.575254 GCAAGGAGAGGTAGATTTTCTTGAGA 60.575 42.308 0.00 0.00 34.14 3.27
3124 3418 5.495640 AGCAAGGAGAGGTAGATTTTCTTG 58.504 41.667 0.00 0.00 35.03 3.02
3138 3432 2.566833 TTGCAGCTTTAGCAAGGAGA 57.433 45.000 5.88 0.00 46.13 3.71
3144 3438 6.404623 CCATATTACTTGTTGCAGCTTTAGCA 60.405 38.462 1.17 0.00 45.16 3.49
3145 3439 5.973565 CCATATTACTTGTTGCAGCTTTAGC 59.026 40.000 1.17 0.00 42.49 3.09
3146 3440 7.320443 TCCATATTACTTGTTGCAGCTTTAG 57.680 36.000 1.17 0.00 0.00 1.85
3147 3441 7.254761 CGATCCATATTACTTGTTGCAGCTTTA 60.255 37.037 1.17 0.00 0.00 1.85
3148 3442 6.458751 CGATCCATATTACTTGTTGCAGCTTT 60.459 38.462 1.17 0.00 0.00 3.51
3149 3443 5.008019 CGATCCATATTACTTGTTGCAGCTT 59.992 40.000 1.17 0.00 0.00 3.74
3150 3444 4.512944 CGATCCATATTACTTGTTGCAGCT 59.487 41.667 1.17 0.00 0.00 4.24
3151 3445 4.319766 CCGATCCATATTACTTGTTGCAGC 60.320 45.833 0.00 0.00 0.00 5.25
3152 3446 5.056480 TCCGATCCATATTACTTGTTGCAG 58.944 41.667 0.00 0.00 0.00 4.41
3153 3447 5.029807 TCCGATCCATATTACTTGTTGCA 57.970 39.130 0.00 0.00 0.00 4.08
3154 3448 4.452455 CCTCCGATCCATATTACTTGTTGC 59.548 45.833 0.00 0.00 0.00 4.17
3155 3449 5.853936 TCCTCCGATCCATATTACTTGTTG 58.146 41.667 0.00 0.00 0.00 3.33
3156 3450 6.099845 ACTTCCTCCGATCCATATTACTTGTT 59.900 38.462 0.00 0.00 0.00 2.83
3157 3451 5.602978 ACTTCCTCCGATCCATATTACTTGT 59.397 40.000 0.00 0.00 0.00 3.16
3158 3452 6.102897 ACTTCCTCCGATCCATATTACTTG 57.897 41.667 0.00 0.00 0.00 3.16
3159 3453 9.543231 TTATACTTCCTCCGATCCATATTACTT 57.457 33.333 0.00 0.00 0.00 2.24
3160 3454 8.968969 GTTATACTTCCTCCGATCCATATTACT 58.031 37.037 0.00 0.00 0.00 2.24
3161 3455 8.968969 AGTTATACTTCCTCCGATCCATATTAC 58.031 37.037 0.00 0.00 0.00 1.89
3162 3456 8.967918 CAGTTATACTTCCTCCGATCCATATTA 58.032 37.037 0.00 0.00 0.00 0.98
3163 3457 7.455008 ACAGTTATACTTCCTCCGATCCATATT 59.545 37.037 0.00 0.00 0.00 1.28
3164 3458 6.954684 ACAGTTATACTTCCTCCGATCCATAT 59.045 38.462 0.00 0.00 0.00 1.78
3165 3459 6.312529 ACAGTTATACTTCCTCCGATCCATA 58.687 40.000 0.00 0.00 0.00 2.74
3166 3460 5.148502 ACAGTTATACTTCCTCCGATCCAT 58.851 41.667 0.00 0.00 0.00 3.41
3167 3461 4.543689 ACAGTTATACTTCCTCCGATCCA 58.456 43.478 0.00 0.00 0.00 3.41
3168 3462 5.532664 AACAGTTATACTTCCTCCGATCC 57.467 43.478 0.00 0.00 0.00 3.36
3169 3463 5.234543 GCAAACAGTTATACTTCCTCCGATC 59.765 44.000 0.00 0.00 0.00 3.69
3170 3464 5.116882 GCAAACAGTTATACTTCCTCCGAT 58.883 41.667 0.00 0.00 0.00 4.18
3171 3465 4.501071 GCAAACAGTTATACTTCCTCCGA 58.499 43.478 0.00 0.00 0.00 4.55
3172 3466 3.621715 GGCAAACAGTTATACTTCCTCCG 59.378 47.826 0.00 0.00 0.00 4.63
3173 3467 3.621715 CGGCAAACAGTTATACTTCCTCC 59.378 47.826 0.00 0.00 0.00 4.30
3174 3468 3.621715 CCGGCAAACAGTTATACTTCCTC 59.378 47.826 0.00 0.00 0.00 3.71
3175 3469 3.262405 TCCGGCAAACAGTTATACTTCCT 59.738 43.478 0.00 0.00 0.00 3.36
3176 3470 3.602483 TCCGGCAAACAGTTATACTTCC 58.398 45.455 0.00 0.00 0.00 3.46
3177 3471 5.616488 TTTCCGGCAAACAGTTATACTTC 57.384 39.130 0.00 0.00 0.00 3.01
3178 3472 6.655848 TGTATTTCCGGCAAACAGTTATACTT 59.344 34.615 0.00 0.00 0.00 2.24
3179 3473 6.174760 TGTATTTCCGGCAAACAGTTATACT 58.825 36.000 0.00 0.00 0.00 2.12
3180 3474 6.425577 TGTATTTCCGGCAAACAGTTATAC 57.574 37.500 0.00 0.00 0.00 1.47
3181 3475 7.051623 AGATGTATTTCCGGCAAACAGTTATA 58.948 34.615 0.00 0.00 0.00 0.98
3182 3476 5.885912 AGATGTATTTCCGGCAAACAGTTAT 59.114 36.000 0.00 0.00 0.00 1.89
3183 3477 5.250200 AGATGTATTTCCGGCAAACAGTTA 58.750 37.500 0.00 0.00 0.00 2.24
3184 3478 4.079253 AGATGTATTTCCGGCAAACAGTT 58.921 39.130 0.00 0.00 0.00 3.16
3185 3479 3.686016 AGATGTATTTCCGGCAAACAGT 58.314 40.909 0.00 0.00 0.00 3.55
3186 3480 4.082787 ACAAGATGTATTTCCGGCAAACAG 60.083 41.667 0.00 0.00 0.00 3.16
3187 3481 3.823873 ACAAGATGTATTTCCGGCAAACA 59.176 39.130 0.00 0.13 0.00 2.83
3188 3482 4.434713 ACAAGATGTATTTCCGGCAAAC 57.565 40.909 0.00 0.00 0.00 2.93
3189 3483 5.250200 ACTACAAGATGTATTTCCGGCAAA 58.750 37.500 0.00 0.00 31.66 3.68
3190 3484 4.839121 ACTACAAGATGTATTTCCGGCAA 58.161 39.130 0.00 0.00 31.66 4.52
3191 3485 4.481368 ACTACAAGATGTATTTCCGGCA 57.519 40.909 0.00 0.00 31.66 5.69
3192 3486 8.597662 TTATAACTACAAGATGTATTTCCGGC 57.402 34.615 0.00 0.00 31.66 6.13
3207 3501 9.140286 GCATCGATCTGCTTATTTATAACTACA 57.860 33.333 3.74 0.00 39.12 2.74
3244 3538 2.380433 ATCGAGGATCCTGCTGCAGC 62.380 60.000 31.89 31.89 42.50 5.25
3245 3539 0.319727 GATCGAGGATCCTGCTGCAG 60.320 60.000 22.02 22.44 33.37 4.41
3246 3540 1.744639 GATCGAGGATCCTGCTGCA 59.255 57.895 22.02 0.88 33.37 4.41
3247 3541 1.372748 CGATCGAGGATCCTGCTGC 60.373 63.158 22.02 3.13 35.83 5.25
3248 3542 0.887247 ATCGATCGAGGATCCTGCTG 59.113 55.000 22.02 9.03 35.83 4.41
3249 3543 0.887247 CATCGATCGAGGATCCTGCT 59.113 55.000 24.50 2.55 35.83 4.24
3250 3544 0.735632 GCATCGATCGAGGATCCTGC 60.736 60.000 31.78 25.21 37.20 4.85
3251 3545 0.600057 TGCATCGATCGAGGATCCTG 59.400 55.000 31.78 20.01 35.83 3.86
3252 3546 0.600557 GTGCATCGATCGAGGATCCT 59.399 55.000 31.78 16.13 35.83 3.24
3253 3547 0.600557 AGTGCATCGATCGAGGATCC 59.399 55.000 31.78 17.65 35.83 3.36
3254 3548 2.430546 AAGTGCATCGATCGAGGATC 57.569 50.000 31.78 21.61 35.88 3.36
3255 3549 2.887783 AGTAAGTGCATCGATCGAGGAT 59.112 45.455 31.78 16.39 0.00 3.24
3256 3550 2.033424 CAGTAAGTGCATCGATCGAGGA 59.967 50.000 31.78 17.56 0.00 3.71
3257 3551 2.223595 ACAGTAAGTGCATCGATCGAGG 60.224 50.000 24.45 24.45 0.00 4.63
3258 3552 3.039405 GACAGTAAGTGCATCGATCGAG 58.961 50.000 23.84 15.68 0.00 4.04
3259 3553 2.538939 CGACAGTAAGTGCATCGATCGA 60.539 50.000 21.86 21.86 34.77 3.59
3260 3554 1.775770 CGACAGTAAGTGCATCGATCG 59.224 52.381 9.36 9.36 34.77 3.69
3261 3555 2.531912 CACGACAGTAAGTGCATCGATC 59.468 50.000 10.33 0.00 36.64 3.69
3262 3556 2.530177 CACGACAGTAAGTGCATCGAT 58.470 47.619 10.33 0.00 36.64 3.59
3263 3557 1.402325 CCACGACAGTAAGTGCATCGA 60.402 52.381 10.33 0.00 37.07 3.59
3264 3558 0.992072 CCACGACAGTAAGTGCATCG 59.008 55.000 2.27 2.27 37.07 3.84
3265 3559 1.726791 CACCACGACAGTAAGTGCATC 59.273 52.381 0.00 0.00 37.07 3.91
3266 3560 1.343142 TCACCACGACAGTAAGTGCAT 59.657 47.619 0.00 0.00 37.07 3.96
3267 3561 0.747852 TCACCACGACAGTAAGTGCA 59.252 50.000 0.00 0.00 37.07 4.57
3268 3562 2.080286 ATCACCACGACAGTAAGTGC 57.920 50.000 0.00 0.00 37.07 4.40
3269 3563 4.319477 CCAAAATCACCACGACAGTAAGTG 60.319 45.833 0.00 2.43 36.01 3.16
3270 3564 3.813166 CCAAAATCACCACGACAGTAAGT 59.187 43.478 0.00 0.00 0.00 2.24
3271 3565 3.813166 ACCAAAATCACCACGACAGTAAG 59.187 43.478 0.00 0.00 0.00 2.34
3272 3566 3.562141 CACCAAAATCACCACGACAGTAA 59.438 43.478 0.00 0.00 0.00 2.24
3273 3567 3.135225 CACCAAAATCACCACGACAGTA 58.865 45.455 0.00 0.00 0.00 2.74
3274 3568 1.946768 CACCAAAATCACCACGACAGT 59.053 47.619 0.00 0.00 0.00 3.55
3275 3569 1.334960 GCACCAAAATCACCACGACAG 60.335 52.381 0.00 0.00 0.00 3.51
3276 3570 0.665835 GCACCAAAATCACCACGACA 59.334 50.000 0.00 0.00 0.00 4.35
3277 3571 0.665835 TGCACCAAAATCACCACGAC 59.334 50.000 0.00 0.00 0.00 4.34
3278 3572 1.336440 CTTGCACCAAAATCACCACGA 59.664 47.619 0.00 0.00 0.00 4.35
3279 3573 1.066908 ACTTGCACCAAAATCACCACG 59.933 47.619 0.00 0.00 0.00 4.94
3280 3574 2.472816 CACTTGCACCAAAATCACCAC 58.527 47.619 0.00 0.00 0.00 4.16
3281 3575 1.202510 GCACTTGCACCAAAATCACCA 60.203 47.619 0.00 0.00 41.59 4.17
3282 3576 1.501169 GCACTTGCACCAAAATCACC 58.499 50.000 0.00 0.00 41.59 4.02
3283 3577 1.130955 CGCACTTGCACCAAAATCAC 58.869 50.000 1.48 0.00 42.21 3.06
3284 3578 1.028130 TCGCACTTGCACCAAAATCA 58.972 45.000 1.48 0.00 42.21 2.57
3285 3579 2.132740 TTCGCACTTGCACCAAAATC 57.867 45.000 1.48 0.00 42.21 2.17
3286 3580 2.472816 CTTTCGCACTTGCACCAAAAT 58.527 42.857 1.48 0.00 42.21 1.82
3287 3581 1.919918 CTTTCGCACTTGCACCAAAA 58.080 45.000 1.48 0.00 42.21 2.44
3288 3582 0.527385 GCTTTCGCACTTGCACCAAA 60.527 50.000 1.48 0.00 42.21 3.28
3289 3583 1.065600 GCTTTCGCACTTGCACCAA 59.934 52.632 1.48 0.00 42.21 3.67
3290 3584 2.117779 TGCTTTCGCACTTGCACCA 61.118 52.632 1.48 0.00 42.25 4.17
3291 3585 2.721231 TGCTTTCGCACTTGCACC 59.279 55.556 1.48 0.00 42.25 5.01
3299 3593 0.886043 ATGTGAGCTGTGCTTTCGCA 60.886 50.000 0.00 0.00 45.60 5.10
3300 3594 1.871772 ATGTGAGCTGTGCTTTCGC 59.128 52.632 0.00 0.00 39.88 4.70


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

AutoCloner maintained by Alex Coulton.