Multiple sequence alignment - TraesCS3A01G299200

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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 TraesCS3A01G299200 chr3A 100.000 7313 0 0 1 7313 533620197 533627509 0.000000e+00 13505.0
1 TraesCS3A01G299200 chr3B 95.624 2971 84 9 3138 6100 543691014 543688082 0.000000e+00 4724.0
2 TraesCS3A01G299200 chr3B 90.894 1197 78 18 6144 7313 543688084 543686892 0.000000e+00 1578.0
3 TraesCS3A01G299200 chr3B 91.835 992 48 14 2073 3056 543691979 543691013 0.000000e+00 1352.0
4 TraesCS3A01G299200 chr3B 85.615 1147 86 38 98 1202 543694042 543692933 0.000000e+00 1131.0
5 TraesCS3A01G299200 chr3B 83.750 320 38 6 1236 1555 543692847 543692542 2.580000e-74 291.0
6 TraesCS3A01G299200 chr3D 95.695 2718 71 10 3138 5847 417215695 417213016 0.000000e+00 4329.0
7 TraesCS3A01G299200 chr3D 88.779 1818 144 32 1255 3056 417217467 417215694 0.000000e+00 2172.0
8 TraesCS3A01G299200 chr3D 93.819 1084 43 12 5846 6912 417212859 417211783 0.000000e+00 1609.0
9 TraesCS3A01G299200 chr3D 87.348 1233 79 33 1 1203 417218762 417217577 0.000000e+00 1341.0
10 TraesCS3A01G299200 chr3D 88.421 285 22 6 6914 7194 417211738 417211461 4.230000e-87 333.0
11 TraesCS3A01G299200 chrUn 100.000 1718 0 0 1 1718 263816199 263817916 0.000000e+00 3173.0
12 TraesCS3A01G299200 chr4B 94.845 97 5 0 3047 3143 178078908 178078812 1.270000e-32 152.0
13 TraesCS3A01G299200 chr4B 90.090 111 9 2 3048 3157 132052026 132052135 7.650000e-30 143.0
14 TraesCS3A01G299200 chr1D 94.000 100 6 0 3047 3146 484555664 484555763 1.270000e-32 152.0
15 TraesCS3A01G299200 chr1D 94.681 94 5 0 3047 3140 6335600 6335507 5.910000e-31 147.0
16 TraesCS3A01G299200 chr5A 94.681 94 5 0 3055 3148 38014705 38014612 5.910000e-31 147.0
17 TraesCS3A01G299200 chr5A 92.000 100 8 0 3043 3142 453762733 453762832 2.750000e-29 141.0
18 TraesCS3A01G299200 chr7B 93.750 96 6 0 3047 3142 611720347 611720252 2.130000e-30 145.0
19 TraesCS3A01G299200 chr7A 92.079 101 8 0 3045 3145 664215813 664215713 7.650000e-30 143.0
20 TraesCS3A01G299200 chr4D 89.189 111 10 2 3048 3157 93608162 93608271 3.560000e-28 137.0
21 TraesCS3A01G299200 chr1B 94.737 38 2 0 7030 7067 675465213 675465176 7.920000e-05 60.2


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 TraesCS3A01G299200 chr3A 533620197 533627509 7312 False 13505.0 13505 100.0000 1 7313 1 chr3A.!!$F1 7312
1 TraesCS3A01G299200 chr3B 543686892 543694042 7150 True 1815.2 4724 89.5436 98 7313 5 chr3B.!!$R1 7215
2 TraesCS3A01G299200 chr3D 417211461 417218762 7301 True 1956.8 4329 90.8124 1 7194 5 chr3D.!!$R1 7193
3 TraesCS3A01G299200 chrUn 263816199 263817916 1717 False 3173.0 3173 100.0000 1 1718 1 chrUn.!!$F1 1717

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
1738 1903 7.042335 GGGGGATTACGATGATTATAACAGAG 58.958 42.308 0.00 0.00 0.00 3.35 F
2174 2430 0.251354 TTGCATGCCTCTGACTCTCC 59.749 55.000 16.68 0.00 0.00 3.71 F
3068 3333 0.324091 TGTTCTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46 F
3070 3335 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00 F
3136 3401 0.837272 ACATTATGGGACGGTGGGAG 59.163 55.000 0.00 0.00 0.00 4.30 F
3966 4236 1.825090 TGACATTCGGCTTGCTGAAT 58.175 45.000 20.23 20.23 35.26 2.57 F
5290 5560 1.307097 GGATCACTTGCTGATGAGCC 58.693 55.000 0.38 3.73 45.57 4.70 F
6101 6534 1.906105 TATCAACTGTCCGGTGCCCC 61.906 60.000 0.00 0.00 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3123 3388 0.409092 TTACTACTCCCACCGTCCCA 59.591 55.000 0.00 0.00 0.00 4.37 R
3789 4059 1.201429 TTTCTCCTCTCCAGGGCCAC 61.201 60.000 6.18 0.00 40.80 5.01 R
3966 4236 1.614317 GGCCTCTTCCTTGCTTGCTAA 60.614 52.381 0.00 0.00 0.00 3.09 R
4463 4733 2.689658 TCACAGGAGAGGGTTTCTGAA 58.310 47.619 0.00 0.00 35.87 3.02 R
5030 5300 3.041946 ACAAGGAAGGAGGCCAGTATAG 58.958 50.000 5.01 0.00 0.00 1.31 R
5700 5974 1.000731 CCGCTTTCCCATTTGCAAAGA 59.999 47.619 18.19 6.77 29.96 2.52 R
6172 6606 0.600782 GTTGGTTCGGTTGCGGACTA 60.601 55.000 0.00 0.00 0.00 2.59 R
7188 7699 0.822532 CCAGCCCTCCTGATTCATGC 60.823 60.000 0.00 0.00 44.64 4.06 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
1738 1903 7.042335 GGGGGATTACGATGATTATAACAGAG 58.958 42.308 0.00 0.00 0.00 3.35
1739 1904 7.093465 GGGGGATTACGATGATTATAACAGAGA 60.093 40.741 0.00 0.00 0.00 3.10
1762 1928 5.548706 TGGCATTTGCATAAATCTTTTGC 57.451 34.783 4.74 0.00 44.36 3.68
1767 1933 7.219344 GGCATTTGCATAAATCTTTTGCATTTC 59.781 33.333 4.74 0.00 45.04 2.17
1803 1969 0.823356 AACCGTGCAGATTTGGTGCT 60.823 50.000 0.00 0.00 41.78 4.40
1810 1976 4.090354 CGTGCAGATTTGGTGCTAATTTTG 59.910 41.667 0.00 0.00 41.78 2.44
1823 1989 5.914074 GTGCTAATTTTGGGCAAACATTTTG 59.086 36.000 0.00 0.00 37.73 2.44
1837 2003 6.582672 GCAAACATTTTGTTAGCCTTACTCTC 59.417 38.462 0.91 0.00 40.14 3.20
1847 2013 7.946207 TGTTAGCCTTACTCTCATAGAGAATG 58.054 38.462 10.80 0.00 45.07 2.67
1849 2016 8.802267 GTTAGCCTTACTCTCATAGAGAATGAT 58.198 37.037 10.80 0.94 45.07 2.45
1912 2081 5.965033 ATGTCCACCTTTGTCTCATAGAT 57.035 39.130 0.00 0.00 0.00 1.98
1923 2092 9.689976 CCTTTGTCTCATAGATCTAACTGTATG 57.310 37.037 6.52 0.37 0.00 2.39
1946 2115 8.650143 ATGAACATTGTACCAAAGTTTCCTAT 57.350 30.769 0.00 0.00 0.00 2.57
1948 2117 6.267496 ACATTGTACCAAAGTTTCCTATGC 57.733 37.500 0.00 0.00 0.00 3.14
1949 2118 6.010219 ACATTGTACCAAAGTTTCCTATGCT 58.990 36.000 0.00 0.00 0.00 3.79
1952 2121 5.626142 TGTACCAAAGTTTCCTATGCTCAA 58.374 37.500 0.00 0.00 0.00 3.02
1966 2135 9.716531 TTCCTATGCTCAATATACTTTGATCTG 57.283 33.333 0.00 0.00 35.20 2.90
1972 2141 6.238566 GCTCAATATACTTTGATCTGCTGCAA 60.239 38.462 3.02 0.00 35.20 4.08
1973 2142 7.628769 TCAATATACTTTGATCTGCTGCAAA 57.371 32.000 3.02 0.00 30.82 3.68
1995 2164 1.162698 CTGTGTGGAGGCTGATGTTG 58.837 55.000 0.00 0.00 0.00 3.33
2002 2171 3.256631 GTGGAGGCTGATGTTGTTTCAAT 59.743 43.478 0.00 0.00 0.00 2.57
2003 2172 3.256383 TGGAGGCTGATGTTGTTTCAATG 59.744 43.478 0.00 0.00 0.00 2.82
2007 2176 4.460382 AGGCTGATGTTGTTTCAATGGTAG 59.540 41.667 0.00 0.00 0.00 3.18
2008 2177 4.218417 GGCTGATGTTGTTTCAATGGTAGT 59.782 41.667 0.00 0.00 0.00 2.73
2011 2180 5.136828 TGATGTTGTTTCAATGGTAGTGGT 58.863 37.500 0.00 0.00 0.00 4.16
2020 2189 6.909550 TTCAATGGTAGTGGTTTGCTAATT 57.090 33.333 0.00 0.00 0.00 1.40
2045 2214 5.163652 GGGTTGCTCAATATGTTGTAGGAAC 60.164 44.000 19.69 19.69 39.73 3.62
2046 2215 5.163652 GGTTGCTCAATATGTTGTAGGAACC 60.164 44.000 25.32 25.32 45.03 3.62
2048 2217 5.754782 TGCTCAATATGTTGTAGGAACCAT 58.245 37.500 1.86 0.00 36.69 3.55
2049 2218 6.186957 TGCTCAATATGTTGTAGGAACCATT 58.813 36.000 1.86 0.00 36.69 3.16
2052 2221 8.345565 GCTCAATATGTTGTAGGAACCATTAAG 58.654 37.037 1.86 0.00 36.69 1.85
2053 2222 8.746052 TCAATATGTTGTAGGAACCATTAAGG 57.254 34.615 1.86 0.00 38.85 2.69
2054 2223 7.284489 TCAATATGTTGTAGGAACCATTAAGGC 59.716 37.037 1.86 0.00 37.48 4.35
2056 2225 4.331968 TGTTGTAGGAACCATTAAGGCTG 58.668 43.478 0.00 0.00 43.14 4.85
2057 2226 4.202524 TGTTGTAGGAACCATTAAGGCTGT 60.203 41.667 0.00 0.00 43.14 4.40
2058 2227 4.216411 TGTAGGAACCATTAAGGCTGTC 57.784 45.455 0.00 0.00 43.14 3.51
2060 2229 3.073274 AGGAACCATTAAGGCTGTCAC 57.927 47.619 0.00 0.00 43.14 3.67
2063 2234 3.412386 GAACCATTAAGGCTGTCACAGT 58.588 45.455 6.68 0.00 43.14 3.55
2078 2333 9.646336 GGCTGTCACAGTTAATTTTATAATACG 57.354 33.333 6.68 0.00 33.43 3.06
2091 2346 3.637911 ATAATACGCAAACACTCCCCA 57.362 42.857 0.00 0.00 0.00 4.96
2103 2358 2.089982 ACACTCCCCATCCTGATCCATA 60.090 50.000 0.00 0.00 0.00 2.74
2104 2359 2.304180 CACTCCCCATCCTGATCCATAC 59.696 54.545 0.00 0.00 0.00 2.39
2111 2366 4.141181 CCCATCCTGATCCATACCAAAAGA 60.141 45.833 0.00 0.00 0.00 2.52
2114 2370 4.843728 TCCTGATCCATACCAAAAGACAC 58.156 43.478 0.00 0.00 0.00 3.67
2119 2375 6.068010 TGATCCATACCAAAAGACACTGTTT 58.932 36.000 0.00 0.00 0.00 2.83
2174 2430 0.251354 TTGCATGCCTCTGACTCTCC 59.749 55.000 16.68 0.00 0.00 3.71
2177 2438 1.690893 GCATGCCTCTGACTCTCCATA 59.309 52.381 6.36 0.00 0.00 2.74
2181 2442 3.495331 TGCCTCTGACTCTCCATATCTC 58.505 50.000 0.00 0.00 0.00 2.75
2187 2448 7.362920 GCCTCTGACTCTCCATATCTCTATTTC 60.363 44.444 0.00 0.00 0.00 2.17
2195 2456 5.773575 TCCATATCTCTATTTCGTGCACTC 58.226 41.667 16.19 0.00 0.00 3.51
2243 2504 1.468520 CACAACCTCGGGCTAATGTTG 59.531 52.381 0.48 0.48 41.47 3.33
2424 2685 5.238583 AGGAGTGTGTTGCTAATGTAAGAC 58.761 41.667 0.00 0.00 33.83 3.01
2533 2795 9.927668 AATTCGTCAAAGATGGACATTAAATTT 57.072 25.926 0.00 0.00 34.97 1.82
2577 2839 5.358298 TGTGATACCTCGAGTTATCATCG 57.642 43.478 28.51 7.60 41.50 3.84
2593 2855 2.101415 TCATCGACATCATGGTCTCCAC 59.899 50.000 0.00 0.00 35.80 4.02
2610 2872 8.328758 TGGTCTCCACTGAATGATTATTTTACT 58.671 33.333 0.00 0.00 0.00 2.24
2663 2925 6.951643 ACGTTAAGTTTATGTTCCACTTCAC 58.048 36.000 0.00 0.00 32.88 3.18
2744 3009 0.744414 ATATGCGTGCGGAAACAGCT 60.744 50.000 0.00 0.00 35.28 4.24
2819 3084 7.370383 TGGATACTGCTCAAAAGAAATTTGAC 58.630 34.615 0.00 0.00 44.77 3.18
2924 3189 3.654414 AGACATGGAAGAACGTGAAGAC 58.346 45.455 0.00 0.00 0.00 3.01
3013 3278 6.490040 GCTGGCCTTTCTAACCAATATCAATA 59.510 38.462 3.32 0.00 31.81 1.90
3014 3279 7.177392 GCTGGCCTTTCTAACCAATATCAATAT 59.823 37.037 3.32 0.00 31.81 1.28
3015 3280 9.739276 CTGGCCTTTCTAACCAATATCAATATA 57.261 33.333 3.32 0.00 31.81 0.86
3045 3310 7.657761 GTCTCTCAGTATATAAATTGGGGTGTG 59.342 40.741 0.00 0.00 0.00 3.82
3056 3321 6.584185 AAATTGGGGTGTGTTATGTTCTAC 57.416 37.500 0.00 0.00 0.00 2.59
3057 3322 4.986054 TTGGGGTGTGTTATGTTCTACT 57.014 40.909 0.00 0.00 0.00 2.57
3058 3323 4.546829 TGGGGTGTGTTATGTTCTACTC 57.453 45.455 0.00 0.00 0.00 2.59
3059 3324 3.262405 TGGGGTGTGTTATGTTCTACTCC 59.738 47.826 0.00 0.00 0.00 3.85
3060 3325 3.370209 GGGGTGTGTTATGTTCTACTCCC 60.370 52.174 0.00 0.00 42.99 4.30
3061 3326 3.518303 GGGTGTGTTATGTTCTACTCCCT 59.482 47.826 0.00 0.00 41.40 4.20
3062 3327 4.382793 GGGTGTGTTATGTTCTACTCCCTC 60.383 50.000 0.00 0.00 41.40 4.30
3063 3328 4.382793 GGTGTGTTATGTTCTACTCCCTCC 60.383 50.000 0.00 0.00 0.00 4.30
3064 3329 3.446161 TGTGTTATGTTCTACTCCCTCCG 59.554 47.826 0.00 0.00 0.00 4.63
3065 3330 3.446516 GTGTTATGTTCTACTCCCTCCGT 59.553 47.826 0.00 0.00 0.00 4.69
3066 3331 3.698040 TGTTATGTTCTACTCCCTCCGTC 59.302 47.826 0.00 0.00 0.00 4.79
3067 3332 1.777941 ATGTTCTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
3068 3333 0.324091 TGTTCTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
3069 3334 0.324091 GTTCTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
3070 3335 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
3071 3336 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
3072 3337 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
3073 3338 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
3074 3339 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3075 3340 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3076 3341 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3077 3342 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3078 3343 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3079 3344 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3080 3345 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3082 3347 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
3083 3348 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
3084 3349 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
3085 3350 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
3086 3351 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
3130 3395 6.693315 AAAACATCTTACATTATGGGACGG 57.307 37.500 0.00 0.00 0.00 4.79
3131 3396 5.367945 AACATCTTACATTATGGGACGGT 57.632 39.130 0.00 0.00 0.00 4.83
3132 3397 4.703897 ACATCTTACATTATGGGACGGTG 58.296 43.478 0.00 0.00 0.00 4.94
3133 3398 3.830744 TCTTACATTATGGGACGGTGG 57.169 47.619 0.00 0.00 0.00 4.61
3134 3399 2.436542 TCTTACATTATGGGACGGTGGG 59.563 50.000 0.00 0.00 0.00 4.61
3135 3400 2.177811 TACATTATGGGACGGTGGGA 57.822 50.000 0.00 0.00 0.00 4.37
3136 3401 0.837272 ACATTATGGGACGGTGGGAG 59.163 55.000 0.00 0.00 0.00 4.30
3137 3402 0.837272 CATTATGGGACGGTGGGAGT 59.163 55.000 0.00 0.00 0.00 3.85
3138 3403 2.043992 CATTATGGGACGGTGGGAGTA 58.956 52.381 0.00 0.00 0.00 2.59
3156 3421 7.985184 GTGGGAGTAGTAAATTGTGATGTATGA 59.015 37.037 0.00 0.00 0.00 2.15
3171 3436 7.445096 TGTGATGTATGATGTATGTCCATTTCC 59.555 37.037 0.00 0.00 0.00 3.13
3314 3584 1.999648 TGCATGAAAAGGAGCAGGTT 58.000 45.000 0.00 0.00 32.48 3.50
3432 3702 3.902881 AGGTGATTCTCGAAGCTGAAT 57.097 42.857 0.00 0.00 34.40 2.57
3438 3708 3.616956 TTCTCGAAGCTGAATGGATGT 57.383 42.857 0.00 0.00 0.00 3.06
3519 3789 9.895138 GGGAGGAAGTATGTATTGTTTTTACTA 57.105 33.333 0.00 0.00 0.00 1.82
3775 4045 3.190118 CAGGTTGAGATTGAAAGGCTGAC 59.810 47.826 0.00 0.00 0.00 3.51
3789 4059 3.672808 AGGCTGACTCATGAACAAGAAG 58.327 45.455 0.00 0.00 0.00 2.85
3932 4202 2.925306 GCAAGAGTTGGCATTTGCTCAG 60.925 50.000 14.99 7.58 41.89 3.35
3966 4236 1.825090 TGACATTCGGCTTGCTGAAT 58.175 45.000 20.23 20.23 35.26 2.57
4206 4476 7.153985 AGCAGATAGAGATGATTTGCTTACTC 58.846 38.462 0.00 0.00 40.74 2.59
4208 4478 8.303156 GCAGATAGAGATGATTTGCTTACTCTA 58.697 37.037 0.00 0.00 39.90 2.43
4256 4526 4.985538 ACAATCTTAGAGCCCAAAGAACA 58.014 39.130 0.00 0.00 35.47 3.18
4346 4616 6.322201 TGTTTGATGAAAAGAAAGAGGAGCTT 59.678 34.615 0.00 0.00 38.88 3.74
4463 4733 2.481952 GCGTGCTGAGTTCAAGAAGAAT 59.518 45.455 0.00 0.00 38.76 2.40
4984 5254 5.698545 ACAAGCAACTGTCTTTGATAGAGTC 59.301 40.000 0.00 0.00 32.23 3.36
4985 5255 5.736951 AGCAACTGTCTTTGATAGAGTCT 57.263 39.130 0.00 0.00 32.23 3.24
4986 5256 5.477510 AGCAACTGTCTTTGATAGAGTCTG 58.522 41.667 1.86 0.00 32.23 3.51
4987 5257 5.244851 AGCAACTGTCTTTGATAGAGTCTGA 59.755 40.000 1.86 0.00 32.23 3.27
4988 5258 5.928839 GCAACTGTCTTTGATAGAGTCTGAA 59.071 40.000 1.86 0.00 32.23 3.02
4989 5259 6.425114 GCAACTGTCTTTGATAGAGTCTGAAA 59.575 38.462 1.86 0.00 32.23 2.69
4990 5260 7.041780 GCAACTGTCTTTGATAGAGTCTGAAAA 60.042 37.037 1.86 0.11 32.23 2.29
4991 5261 8.494347 CAACTGTCTTTGATAGAGTCTGAAAAG 58.506 37.037 1.86 9.76 32.23 2.27
4992 5262 7.731054 ACTGTCTTTGATAGAGTCTGAAAAGT 58.269 34.615 16.95 7.18 32.23 2.66
4993 5263 7.870445 ACTGTCTTTGATAGAGTCTGAAAAGTC 59.130 37.037 16.95 13.95 32.23 3.01
4994 5264 7.726216 TGTCTTTGATAGAGTCTGAAAAGTCA 58.274 34.615 16.95 15.52 32.23 3.41
4995 5265 8.204160 TGTCTTTGATAGAGTCTGAAAAGTCAA 58.796 33.333 16.95 9.60 32.23 3.18
4996 5266 9.046296 GTCTTTGATAGAGTCTGAAAAGTCAAA 57.954 33.333 16.95 14.12 34.39 2.69
4997 5267 9.265901 TCTTTGATAGAGTCTGAAAAGTCAAAG 57.734 33.333 21.37 21.37 46.15 2.77
4998 5268 8.964476 TTTGATAGAGTCTGAAAAGTCAAAGT 57.036 30.769 1.86 0.00 32.49 2.66
4999 5269 8.594881 TTGATAGAGTCTGAAAAGTCAAAGTC 57.405 34.615 1.86 0.00 31.88 3.01
5000 5270 7.957002 TGATAGAGTCTGAAAAGTCAAAGTCT 58.043 34.615 1.86 0.00 38.02 3.24
5001 5271 8.424918 TGATAGAGTCTGAAAAGTCAAAGTCTT 58.575 33.333 1.86 0.00 36.22 3.01
5002 5272 9.267084 GATAGAGTCTGAAAAGTCAAAGTCTTT 57.733 33.333 1.86 0.00 36.22 2.52
5003 5273 7.313951 AGAGTCTGAAAAGTCAAAGTCTTTG 57.686 36.000 17.73 17.73 31.55 2.77
5004 5274 7.106239 AGAGTCTGAAAAGTCAAAGTCTTTGA 58.894 34.615 21.59 21.59 46.68 2.69
5030 5300 7.489574 AGAGTCTGAAAAGTCAAAGATGAAC 57.510 36.000 0.00 0.00 37.30 3.18
5054 5324 1.774217 TGGCCTCCTTCCTTGTGGT 60.774 57.895 3.32 0.00 34.23 4.16
5059 5329 1.528129 CTCCTTCCTTGTGGTGAAGC 58.472 55.000 0.00 0.00 37.29 3.86
5226 5496 7.275183 TGGTCATGATAATGGTAGACTTCTTG 58.725 38.462 0.00 0.00 0.00 3.02
5290 5560 1.307097 GGATCACTTGCTGATGAGCC 58.693 55.000 0.38 3.73 45.57 4.70
5507 5780 9.862371 ATAGTATCTTTATGCTAATTCCTGTCG 57.138 33.333 0.00 0.00 34.49 4.35
5509 5782 8.085296 AGTATCTTTATGCTAATTCCTGTCGAG 58.915 37.037 0.00 0.00 0.00 4.04
5641 5915 5.363562 TCAGCAAGGATCATGAATACAGT 57.636 39.130 0.00 0.00 0.00 3.55
5700 5974 3.710165 TCAGCTTCATCTGATGATCTGGT 59.290 43.478 29.54 21.59 39.07 4.00
5740 6014 4.972440 GCGGATAATTCAGATTTTGCTGAC 59.028 41.667 0.00 0.00 44.08 3.51
5931 6364 3.838120 TGTGCTGAACGAGATAACTCTG 58.162 45.455 0.00 0.00 40.65 3.35
5964 6397 2.656947 TCCTGCCAGCTTGTTTAACT 57.343 45.000 0.00 0.00 0.00 2.24
5965 6398 2.944129 TCCTGCCAGCTTGTTTAACTT 58.056 42.857 0.00 0.00 0.00 2.66
5966 6399 2.622942 TCCTGCCAGCTTGTTTAACTTG 59.377 45.455 0.00 0.00 0.00 3.16
5993 6426 9.973450 TTGCTGATTGTTTAGCTTACATTTTTA 57.027 25.926 0.00 0.00 40.52 1.52
6038 6471 7.061557 GCTCTTCTTGTTAATTGCTTTAGCTTG 59.938 37.037 0.00 0.00 42.66 4.01
6040 6473 6.083098 TCTTGTTAATTGCTTTAGCTTGCA 57.917 33.333 0.00 0.00 42.66 4.08
6056 6489 8.746922 TTAGCTTGCAAGTTTTGAATCTTATG 57.253 30.769 26.55 0.00 0.00 1.90
6101 6534 1.906105 TATCAACTGTCCGGTGCCCC 61.906 60.000 0.00 0.00 0.00 5.80
6121 6554 7.286775 GTGCCCCTGTATTTTGGATCTTAAATA 59.713 37.037 8.01 8.01 0.00 1.40
6150 6583 2.332654 CGTGCCCTTGTGCCTTACC 61.333 63.158 0.00 0.00 0.00 2.85
6172 6606 5.010617 ACCGTTTTGATGCTTTATCCTTTGT 59.989 36.000 0.00 0.00 34.77 2.83
6233 6667 5.179533 CAGGGATGAGCATGATGAAGATAG 58.820 45.833 0.00 0.00 0.00 2.08
6337 6772 2.595238 CAGCTTCCCCGGTAGTATAGT 58.405 52.381 0.00 0.00 0.00 2.12
6456 6895 2.159170 GCTTGTTGGTTTTGTGTGCCTA 60.159 45.455 0.00 0.00 0.00 3.93
6580 7020 5.050837 GCTTGTGGTTTGTGTCAAATTGATC 60.051 40.000 0.00 0.00 0.00 2.92
6732 7177 5.382618 AGAAATTTGTGGCTTGTCTGATC 57.617 39.130 0.00 0.00 0.00 2.92
6755 7208 0.944386 GCTGCTGTGGTTTCTTCGAA 59.056 50.000 0.00 0.00 0.00 3.71
6771 7224 2.123897 AACACCCGGTTGCTGCTT 60.124 55.556 0.00 0.00 38.60 3.91
6793 7246 2.414824 GGTGTTGTTTCGACTGTTGCAA 60.415 45.455 0.00 0.00 0.00 4.08
6884 7347 5.297029 CACGTCAGGTCAGATGTTAGAGATA 59.703 44.000 0.00 0.00 35.65 1.98
6995 7502 4.853924 ACGCAAATCATCAAAGGTTTCT 57.146 36.364 0.00 0.00 0.00 2.52
6996 7503 4.549458 ACGCAAATCATCAAAGGTTTCTG 58.451 39.130 0.00 0.00 0.00 3.02
6997 7504 4.037923 ACGCAAATCATCAAAGGTTTCTGT 59.962 37.500 0.00 0.00 0.00 3.41
6998 7505 4.383649 CGCAAATCATCAAAGGTTTCTGTG 59.616 41.667 0.00 0.00 0.00 3.66
6999 7506 5.531634 GCAAATCATCAAAGGTTTCTGTGA 58.468 37.500 0.00 0.00 41.15 3.58
7002 7509 7.172019 GCAAATCATCAAAGGTTTCTGTGATTT 59.828 33.333 0.00 0.00 43.56 2.17
7003 7510 8.706035 CAAATCATCAAAGGTTTCTGTGATTTC 58.294 33.333 7.28 0.00 43.56 2.17
7014 7521 8.897752 AGGTTTCTGTGATTTCATATCTTTAGC 58.102 33.333 0.00 0.00 0.00 3.09
7015 7522 8.677300 GGTTTCTGTGATTTCATATCTTTAGCA 58.323 33.333 0.00 0.00 0.00 3.49
7072 7579 5.880054 ACTTGTCGCTGCTTTAATACAAT 57.120 34.783 0.00 0.00 0.00 2.71
7180 7691 6.580041 CGTGAAAAAGAAGTGGAAAGATGATG 59.420 38.462 0.00 0.00 0.00 3.07
7188 7699 4.691175 AGTGGAAAGATGATGATGAGACG 58.309 43.478 0.00 0.00 0.00 4.18
7198 7709 4.056050 TGATGATGAGACGCATGAATCAG 58.944 43.478 0.00 0.00 37.34 2.90
7204 7715 1.153086 ACGCATGAATCAGGAGGGC 60.153 57.895 0.00 0.00 0.00 5.19
7205 7716 1.147824 CGCATGAATCAGGAGGGCT 59.852 57.895 0.00 0.00 0.00 5.19
7229 7741 0.036164 GGTGGCACTACACATGACCA 59.964 55.000 18.45 0.00 43.08 4.02
7252 7764 3.803082 GCGCGCATCTCCTTTGCA 61.803 61.111 29.10 0.00 40.14 4.08
7254 7766 1.430632 CGCGCATCTCCTTTGCATT 59.569 52.632 8.75 0.00 40.14 3.56
7274 7786 5.126061 GCATTCCTGCTTAAATCTTTCCTGA 59.874 40.000 0.00 0.00 45.32 3.86
7303 7815 7.309744 CCTTTTTATTTGCTCTCCCACATGTTA 60.310 37.037 0.00 0.00 0.00 2.41
7304 7816 7.531857 TTTTATTTGCTCTCCCACATGTTAA 57.468 32.000 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1724 1889 7.231925 TGCAAATGCCATCTCTGTTATAATCAT 59.768 33.333 2.46 0.00 41.18 2.45
1731 1896 6.772360 TTTATGCAAATGCCATCTCTGTTA 57.228 33.333 2.46 0.00 41.18 2.41
1734 1899 6.085555 AGATTTATGCAAATGCCATCTCTG 57.914 37.500 2.46 0.00 41.18 3.35
1738 1903 6.183360 TGCAAAAGATTTATGCAAATGCCATC 60.183 34.615 2.46 0.24 46.23 3.51
1739 1904 5.648526 TGCAAAAGATTTATGCAAATGCCAT 59.351 32.000 2.46 0.00 46.23 4.40
1762 1928 3.127376 TCGATGCTGACACCAATGAAATG 59.873 43.478 0.00 0.00 0.00 2.32
1767 1933 1.131126 GGTTCGATGCTGACACCAATG 59.869 52.381 0.00 0.00 0.00 2.82
1823 1989 8.172352 TCATTCTCTATGAGAGTAAGGCTAAC 57.828 38.462 3.52 0.00 42.83 2.34
1837 2003 9.565090 TCCAAATAACCTGAATCATTCTCTATG 57.435 33.333 0.00 0.00 35.45 2.23
1849 2016 9.540538 TCCTTTGATTAATCCAAATAACCTGAA 57.459 29.630 12.90 0.00 33.62 3.02
1880 2047 9.614792 GAGACAAAGGTGGACATTAGTATAATT 57.385 33.333 0.00 0.00 0.00 1.40
1889 2056 5.762179 TCTATGAGACAAAGGTGGACATT 57.238 39.130 0.00 0.00 0.00 2.71
1891 2058 5.026121 AGATCTATGAGACAAAGGTGGACA 58.974 41.667 0.00 0.00 0.00 4.02
1923 2092 6.806739 GCATAGGAAACTTTGGTACAATGTTC 59.193 38.462 11.88 0.00 43.89 3.18
1946 2115 5.237996 GCAGCAGATCAAAGTATATTGAGCA 59.762 40.000 7.86 0.00 45.65 4.26
1948 2117 6.856135 TGCAGCAGATCAAAGTATATTGAG 57.144 37.500 0.00 0.00 42.21 3.02
1949 2118 7.553760 TCTTTGCAGCAGATCAAAGTATATTGA 59.446 33.333 12.56 0.00 45.53 2.57
1952 2121 7.012138 CAGTCTTTGCAGCAGATCAAAGTATAT 59.988 37.037 12.56 0.00 45.53 0.86
1961 2130 2.095869 CACACAGTCTTTGCAGCAGATC 60.096 50.000 0.00 0.00 0.00 2.75
1966 2135 0.590195 CTCCACACAGTCTTTGCAGC 59.410 55.000 0.00 0.00 0.00 5.25
1972 2141 1.002888 CATCAGCCTCCACACAGTCTT 59.997 52.381 0.00 0.00 0.00 3.01
1973 2142 0.612229 CATCAGCCTCCACACAGTCT 59.388 55.000 0.00 0.00 0.00 3.24
1974 2143 0.322975 ACATCAGCCTCCACACAGTC 59.677 55.000 0.00 0.00 0.00 3.51
1975 2144 0.767375 AACATCAGCCTCCACACAGT 59.233 50.000 0.00 0.00 0.00 3.55
1995 2164 4.584327 AGCAAACCACTACCATTGAAAC 57.416 40.909 0.00 0.00 0.00 2.78
2002 2171 3.181427 ACCCAATTAGCAAACCACTACCA 60.181 43.478 0.00 0.00 0.00 3.25
2003 2172 3.427573 ACCCAATTAGCAAACCACTACC 58.572 45.455 0.00 0.00 0.00 3.18
2007 2176 2.037121 AGCAACCCAATTAGCAAACCAC 59.963 45.455 0.00 0.00 0.00 4.16
2008 2177 2.298729 GAGCAACCCAATTAGCAAACCA 59.701 45.455 0.00 0.00 0.00 3.67
2011 2180 4.888326 ATTGAGCAACCCAATTAGCAAA 57.112 36.364 0.00 0.00 30.72 3.68
2020 2189 4.018870 TCCTACAACATATTGAGCAACCCA 60.019 41.667 0.00 0.00 39.30 4.51
2045 2214 6.515272 AATTAACTGTGACAGCCTTAATGG 57.485 37.500 13.37 0.00 34.37 3.16
2052 2221 9.646336 CGTATTATAAAATTAACTGTGACAGCC 57.354 33.333 13.37 0.00 34.37 4.85
2053 2222 9.155053 GCGTATTATAAAATTAACTGTGACAGC 57.845 33.333 13.37 0.00 34.37 4.40
2078 2333 0.038166 TCAGGATGGGGAGTGTTTGC 59.962 55.000 0.00 0.00 36.16 3.68
2084 2339 2.625639 GTATGGATCAGGATGGGGAGT 58.374 52.381 0.00 0.00 36.16 3.85
2085 2340 1.912043 GGTATGGATCAGGATGGGGAG 59.088 57.143 0.00 0.00 36.16 4.30
2086 2341 1.225431 TGGTATGGATCAGGATGGGGA 59.775 52.381 0.00 0.00 36.16 4.81
2091 2346 5.192522 AGTGTCTTTTGGTATGGATCAGGAT 59.807 40.000 0.00 0.00 0.00 3.24
2103 2358 7.883311 AGCATATACTAAACAGTGTCTTTTGGT 59.117 33.333 0.00 0.00 32.01 3.67
2104 2359 8.177663 CAGCATATACTAAACAGTGTCTTTTGG 58.822 37.037 0.00 0.00 0.00 3.28
2111 2366 6.761714 GGCTTACAGCATATACTAAACAGTGT 59.238 38.462 0.00 0.00 44.75 3.55
2114 2370 7.495934 AGTTGGCTTACAGCATATACTAAACAG 59.504 37.037 0.00 0.00 44.75 3.16
2119 2375 8.801882 AAAAAGTTGGCTTACAGCATATACTA 57.198 30.769 0.00 0.00 44.75 1.82
2142 2398 2.559440 GCATGCAACAGTTCCCAAAAA 58.441 42.857 14.21 0.00 0.00 1.94
2143 2399 1.202627 GGCATGCAACAGTTCCCAAAA 60.203 47.619 21.36 0.00 0.00 2.44
2149 2405 1.198637 GTCAGAGGCATGCAACAGTTC 59.801 52.381 21.36 6.72 0.00 3.01
2156 2412 0.906282 TGGAGAGTCAGAGGCATGCA 60.906 55.000 21.36 0.00 0.00 3.96
2157 2413 0.469070 ATGGAGAGTCAGAGGCATGC 59.531 55.000 9.90 9.90 0.00 4.06
2161 2417 3.766545 AGAGATATGGAGAGTCAGAGGC 58.233 50.000 0.00 0.00 0.00 4.70
2174 2430 7.649370 AATGAGTGCACGAAATAGAGATATG 57.351 36.000 12.01 0.00 0.00 1.78
2177 2438 5.295292 CCAAATGAGTGCACGAAATAGAGAT 59.705 40.000 12.01 0.00 0.00 2.75
2181 2442 3.127548 AGCCAAATGAGTGCACGAAATAG 59.872 43.478 12.01 1.79 0.00 1.73
2187 2448 1.129251 CTACAGCCAAATGAGTGCACG 59.871 52.381 12.01 0.00 0.00 5.34
2195 2456 7.068103 TGGTAATCATAAACCTACAGCCAAATG 59.932 37.037 0.00 0.00 36.67 2.32
2243 2504 1.886542 ACCAATTCCTTTCGCTCCAAC 59.113 47.619 0.00 0.00 0.00 3.77
2325 2586 0.394080 GCAGATTGCTGGGAAGCTCT 60.394 55.000 0.00 0.00 42.53 4.09
2560 2822 5.061179 TGATGTCGATGATAACTCGAGGTA 58.939 41.667 13.61 13.61 45.00 3.08
2565 2827 4.550422 ACCATGATGTCGATGATAACTCG 58.450 43.478 0.00 0.00 37.47 4.18
2577 2839 3.616956 TTCAGTGGAGACCATGATGTC 57.383 47.619 0.00 0.00 35.28 3.06
2612 2874 9.905713 AGAAGTCTAATGTTGGCATAAGAATAA 57.094 29.630 0.00 0.00 34.39 1.40
2663 2925 4.063689 CAGAGGCAGGTTAAGCAGATATG 58.936 47.826 7.52 0.00 0.00 1.78
2773 3038 4.576053 CCATCATTTCAAGTGCTTCGGATA 59.424 41.667 0.00 0.00 0.00 2.59
2775 3040 2.749076 CCATCATTTCAAGTGCTTCGGA 59.251 45.455 0.00 0.00 0.00 4.55
2777 3042 4.627611 ATCCATCATTTCAAGTGCTTCG 57.372 40.909 0.00 0.00 0.00 3.79
2819 3084 1.639280 GAAGCTTCTCTTCTGCCTCG 58.361 55.000 19.44 0.00 45.99 4.63
2924 3189 1.689273 AGGCGGTATCTTCTAAGCTGG 59.311 52.381 0.00 0.00 0.00 4.85
3016 3281 9.845214 ACCCCAATTTATATACTGAGAGACTAT 57.155 33.333 0.00 0.00 0.00 2.12
3045 3310 3.067883 GGACGGAGGGAGTAGAACATAAC 59.932 52.174 0.00 0.00 0.00 1.89
3056 3321 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3057 3322 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3058 3323 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3059 3324 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
3060 3325 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
3061 3326 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
3106 3371 6.661805 ACCGTCCCATAATGTAAGATGTTTTT 59.338 34.615 0.00 0.00 0.00 1.94
3107 3372 6.094881 CACCGTCCCATAATGTAAGATGTTTT 59.905 38.462 0.00 0.00 0.00 2.43
3108 3373 5.588648 CACCGTCCCATAATGTAAGATGTTT 59.411 40.000 0.00 0.00 0.00 2.83
3109 3374 5.123227 CACCGTCCCATAATGTAAGATGTT 58.877 41.667 0.00 0.00 0.00 2.71
3110 3375 4.444306 CCACCGTCCCATAATGTAAGATGT 60.444 45.833 0.00 0.00 0.00 3.06
3111 3376 4.065088 CCACCGTCCCATAATGTAAGATG 58.935 47.826 0.00 0.00 0.00 2.90
3112 3377 3.072476 CCCACCGTCCCATAATGTAAGAT 59.928 47.826 0.00 0.00 0.00 2.40
3113 3378 2.436542 CCCACCGTCCCATAATGTAAGA 59.563 50.000 0.00 0.00 0.00 2.10
3114 3379 2.436542 TCCCACCGTCCCATAATGTAAG 59.563 50.000 0.00 0.00 0.00 2.34
3115 3380 2.436542 CTCCCACCGTCCCATAATGTAA 59.563 50.000 0.00 0.00 0.00 2.41
3116 3381 2.043992 CTCCCACCGTCCCATAATGTA 58.956 52.381 0.00 0.00 0.00 2.29
3117 3382 0.837272 CTCCCACCGTCCCATAATGT 59.163 55.000 0.00 0.00 0.00 2.71
3118 3383 0.837272 ACTCCCACCGTCCCATAATG 59.163 55.000 0.00 0.00 0.00 1.90
3119 3384 2.326428 CTACTCCCACCGTCCCATAAT 58.674 52.381 0.00 0.00 0.00 1.28
3120 3385 1.007479 ACTACTCCCACCGTCCCATAA 59.993 52.381 0.00 0.00 0.00 1.90
3121 3386 0.632835 ACTACTCCCACCGTCCCATA 59.367 55.000 0.00 0.00 0.00 2.74
3122 3387 0.632835 TACTACTCCCACCGTCCCAT 59.367 55.000 0.00 0.00 0.00 4.00
3123 3388 0.409092 TTACTACTCCCACCGTCCCA 59.591 55.000 0.00 0.00 0.00 4.37
3124 3389 1.560505 TTTACTACTCCCACCGTCCC 58.439 55.000 0.00 0.00 0.00 4.46
3125 3390 3.055602 ACAATTTACTACTCCCACCGTCC 60.056 47.826 0.00 0.00 0.00 4.79
3126 3391 3.930848 CACAATTTACTACTCCCACCGTC 59.069 47.826 0.00 0.00 0.00 4.79
3127 3392 3.579586 TCACAATTTACTACTCCCACCGT 59.420 43.478 0.00 0.00 0.00 4.83
3128 3393 4.196626 TCACAATTTACTACTCCCACCG 57.803 45.455 0.00 0.00 0.00 4.94
3129 3394 5.497474 ACATCACAATTTACTACTCCCACC 58.503 41.667 0.00 0.00 0.00 4.61
3130 3395 7.985184 TCATACATCACAATTTACTACTCCCAC 59.015 37.037 0.00 0.00 0.00 4.61
3131 3396 8.084985 TCATACATCACAATTTACTACTCCCA 57.915 34.615 0.00 0.00 0.00 4.37
3132 3397 8.993121 CATCATACATCACAATTTACTACTCCC 58.007 37.037 0.00 0.00 0.00 4.30
3133 3398 9.547753 ACATCATACATCACAATTTACTACTCC 57.452 33.333 0.00 0.00 0.00 3.85
3156 3421 7.449395 CACCATATTCAGGAAATGGACATACAT 59.551 37.037 20.26 0.00 42.36 2.29
3171 3436 2.158564 AGATGCCCACCACCATATTCAG 60.159 50.000 0.00 0.00 0.00 3.02
3269 3539 9.559958 AACATTTTCTTCATATCATTCAACGAC 57.440 29.630 0.00 0.00 0.00 4.34
3438 3708 7.173907 CAGCTTGTTTTTCTCTTCCATTAGAGA 59.826 37.037 0.00 0.00 46.74 3.10
3519 3789 9.855021 ATAAATAAAGCTGCTAACAAAACGATT 57.145 25.926 0.90 0.00 0.00 3.34
3671 3941 4.237018 TGTAAACTGGAGAAACCTACCCT 58.763 43.478 0.00 0.00 39.86 4.34
3775 4045 1.815003 GGGCCACTTCTTGTTCATGAG 59.185 52.381 4.39 0.00 0.00 2.90
3789 4059 1.201429 TTTCTCCTCTCCAGGGCCAC 61.201 60.000 6.18 0.00 40.80 5.01
3932 4202 4.615912 CGAATGTCAACATTTTGGTCCCTC 60.616 45.833 9.59 0.00 45.72 4.30
3966 4236 1.614317 GGCCTCTTCCTTGCTTGCTAA 60.614 52.381 0.00 0.00 0.00 3.09
4346 4616 6.372659 CAGTAATTCTAGCAGCTTCCTTTTGA 59.627 38.462 0.00 0.00 0.00 2.69
4361 4631 6.761099 ACTCTTCGCTCTTCAGTAATTCTA 57.239 37.500 0.00 0.00 0.00 2.10
4463 4733 2.689658 TCACAGGAGAGGGTTTCTGAA 58.310 47.619 0.00 0.00 35.87 3.02
4501 4771 3.506844 TGCATGTTCTTGCTGCATCTTAA 59.493 39.130 1.84 0.00 40.75 1.85
4620 4890 5.067674 CCCTTAAATCAGCATCGATTTCCAA 59.932 40.000 10.82 3.09 43.02 3.53
4685 4955 5.796935 CACCTTTTGAGAATTTATGTGCTCG 59.203 40.000 0.00 0.00 0.00 5.03
4993 5263 9.050601 ACTTTTCAGACTCTATCAAAGACTTTG 57.949 33.333 19.93 19.93 41.96 2.77
4994 5264 9.267084 GACTTTTCAGACTCTATCAAAGACTTT 57.733 33.333 0.00 0.00 0.00 2.66
4995 5265 8.424918 TGACTTTTCAGACTCTATCAAAGACTT 58.575 33.333 9.35 0.00 0.00 3.01
4996 5266 7.957002 TGACTTTTCAGACTCTATCAAAGACT 58.043 34.615 9.35 0.00 0.00 3.24
4997 5267 8.594881 TTGACTTTTCAGACTCTATCAAAGAC 57.405 34.615 9.35 5.62 31.71 3.01
4999 5269 9.265901 TCTTTGACTTTTCAGACTCTATCAAAG 57.734 33.333 14.31 14.31 46.76 2.77
5000 5270 9.784531 ATCTTTGACTTTTCAGACTCTATCAAA 57.215 29.630 0.00 0.00 34.58 2.69
5001 5271 9.212641 CATCTTTGACTTTTCAGACTCTATCAA 57.787 33.333 0.00 0.00 31.71 2.57
5002 5272 8.588472 TCATCTTTGACTTTTCAGACTCTATCA 58.412 33.333 0.00 0.00 31.71 2.15
5003 5273 8.994429 TCATCTTTGACTTTTCAGACTCTATC 57.006 34.615 0.00 0.00 31.71 2.08
5004 5274 9.213799 GTTCATCTTTGACTTTTCAGACTCTAT 57.786 33.333 0.00 0.00 31.71 1.98
5005 5275 8.424918 AGTTCATCTTTGACTTTTCAGACTCTA 58.575 33.333 0.00 0.00 31.71 2.43
5006 5276 7.278875 AGTTCATCTTTGACTTTTCAGACTCT 58.721 34.615 0.00 0.00 31.71 3.24
5007 5277 7.489574 AGTTCATCTTTGACTTTTCAGACTC 57.510 36.000 0.00 0.00 31.71 3.36
5030 5300 3.041946 ACAAGGAAGGAGGCCAGTATAG 58.958 50.000 5.01 0.00 0.00 1.31
5054 5324 7.851228 TCTTAGGAGTTGAATTATGAGCTTCA 58.149 34.615 0.00 0.00 0.00 3.02
5260 5530 4.157105 CAGCAAGTGATCCATTGATGTCAA 59.843 41.667 14.00 0.00 37.87 3.18
5290 5560 2.435586 CTCCAGCTTGGTCGCCTG 60.436 66.667 0.00 0.00 39.03 4.85
5641 5915 3.589735 TCAGGTTCTGTGGCCCTTTATTA 59.410 43.478 0.00 0.00 32.61 0.98
5700 5974 1.000731 CCGCTTTCCCATTTGCAAAGA 59.999 47.619 18.19 6.77 29.96 2.52
5894 6326 7.323656 CGTTCAGCACAAAATTAGGTAAAGAAG 59.676 37.037 0.00 0.00 0.00 2.85
5911 6343 3.854809 GTCAGAGTTATCTCGTTCAGCAC 59.145 47.826 0.00 0.00 44.65 4.40
5931 6364 1.414550 GGCAGGATAGACTTGGAGGTC 59.585 57.143 0.00 0.00 36.56 3.85
5964 6397 6.384258 TGTAAGCTAAACAATCAGCAACAA 57.616 33.333 0.00 0.00 40.36 2.83
5965 6398 6.573664 ATGTAAGCTAAACAATCAGCAACA 57.426 33.333 5.97 0.00 40.36 3.33
5966 6399 7.873739 AAATGTAAGCTAAACAATCAGCAAC 57.126 32.000 5.97 0.00 40.36 4.17
5993 6426 9.532494 AGAAGAGCAGTGTGATATATAAGATCT 57.468 33.333 0.00 0.00 0.00 2.75
6018 6451 6.768029 TTGCAAGCTAAAGCAATTAACAAG 57.232 33.333 14.79 0.00 44.98 3.16
6121 6554 1.903877 AAGGGCACGCTAGCAGTGAT 61.904 55.000 30.55 18.40 41.83 3.06
6129 6562 1.832719 TAAGGCACAAGGGCACGCTA 61.833 55.000 0.00 0.00 46.44 4.26
6150 6583 7.305474 ACTACAAAGGATAAAGCATCAAAACG 58.695 34.615 0.00 0.00 35.11 3.60
6172 6606 0.600782 GTTGGTTCGGTTGCGGACTA 60.601 55.000 0.00 0.00 0.00 2.59
6233 6667 4.377839 TCCTCTTCATCTTCGTCATCAC 57.622 45.455 0.00 0.00 0.00 3.06
6337 6772 2.690497 GCCTACAGTCAGCTCTGTATGA 59.310 50.000 16.87 0.91 45.74 2.15
6456 6895 0.962356 CCAAAACCTCCGCTGCTCAT 60.962 55.000 0.00 0.00 0.00 2.90
6580 7020 2.267961 GCTGTTCCTACACCCCCG 59.732 66.667 0.00 0.00 0.00 5.73
6732 7177 0.877071 AAGAAACCACAGCAGCATCG 59.123 50.000 0.00 0.00 0.00 3.84
6755 7208 2.906897 CAAGCAGCAACCGGGTGT 60.907 61.111 23.08 4.89 46.68 4.16
6771 7224 1.131504 GCAACAGTCGAAACAACACCA 59.868 47.619 0.00 0.00 0.00 4.17
6793 7246 3.816580 TTGCGATGCAATGCAATGT 57.183 42.105 20.94 0.00 45.45 2.71
6847 7300 1.358759 GACGTGGCCCTGTTTGTTG 59.641 57.895 0.00 0.00 0.00 3.33
6848 7301 1.077357 TGACGTGGCCCTGTTTGTT 60.077 52.632 0.00 0.00 0.00 2.83
6995 7502 7.049754 TGCTCTGCTAAAGATATGAAATCACA 58.950 34.615 0.00 0.00 33.29 3.58
6996 7503 7.488187 TGCTCTGCTAAAGATATGAAATCAC 57.512 36.000 0.00 0.00 33.29 3.06
6997 7504 8.687292 AATGCTCTGCTAAAGATATGAAATCA 57.313 30.769 0.00 0.00 33.29 2.57
6998 7505 9.962783 AAAATGCTCTGCTAAAGATATGAAATC 57.037 29.630 0.00 0.00 33.29 2.17
7002 7509 8.743085 AGAAAAATGCTCTGCTAAAGATATGA 57.257 30.769 0.00 0.00 33.29 2.15
7003 7510 9.448294 GAAGAAAAATGCTCTGCTAAAGATATG 57.552 33.333 0.00 0.00 33.29 1.78
7013 7520 6.907741 AGAAAGTAGAAGAAAAATGCTCTGC 58.092 36.000 0.00 0.00 0.00 4.26
7014 7521 7.743838 CGAAGAAAGTAGAAGAAAAATGCTCTG 59.256 37.037 0.00 0.00 0.00 3.35
7015 7522 7.657761 TCGAAGAAAGTAGAAGAAAAATGCTCT 59.342 33.333 0.00 0.00 0.00 4.09
7072 7579 7.484324 GCTTTTTAGCTCAAAAATGCAACAAAA 59.516 29.630 19.79 3.75 43.42 2.44
7086 7593 7.336931 CCCTAAATCTAACTGCTTTTTAGCTCA 59.663 37.037 0.00 0.00 35.49 4.26
7110 7617 1.135721 CATCTGCTTTTTAGCCAGCCC 59.864 52.381 0.00 0.00 34.91 5.19
7164 7675 5.233902 CGTCTCATCATCATCTTTCCACTTC 59.766 44.000 0.00 0.00 0.00 3.01
7180 7691 3.058450 CTCCTGATTCATGCGTCTCATC 58.942 50.000 0.00 0.00 31.79 2.92
7188 7699 0.822532 CCAGCCCTCCTGATTCATGC 60.823 60.000 0.00 0.00 44.64 4.06
7204 7715 1.302511 GTGTAGTGCCACCCACCAG 60.303 63.158 4.37 0.00 45.83 4.00
7205 7716 1.422977 ATGTGTAGTGCCACCCACCA 61.423 55.000 11.40 3.01 45.83 4.17
7252 7764 6.488715 AGTCAGGAAAGATTTAAGCAGGAAT 58.511 36.000 0.00 0.00 0.00 3.01
7254 7766 5.491982 GAGTCAGGAAAGATTTAAGCAGGA 58.508 41.667 0.00 0.00 0.00 3.86
7268 7780 6.306987 AGAGCAAATAAAAAGGAGTCAGGAA 58.693 36.000 0.00 0.00 0.00 3.36
7274 7786 4.767409 GTGGGAGAGCAAATAAAAAGGAGT 59.233 41.667 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.