Multiple sequence alignment - TraesCS1B01G190800

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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 TraesCS1B01G190800 chr1B 100.000 3299 0 0 1 3299 341522287 341525585 0.000000e+00 6093.0
1 TraesCS1B01G190800 chr1B 81.148 122 17 5 3175 3292 61952491 61952372 3.510000e-15 93.5
2 TraesCS1B01G190800 chr1B 90.741 54 4 1 2977 3030 215819154 215819102 1.640000e-08 71.3
3 TraesCS1B01G190800 chr1D 96.589 2990 64 13 1 2973 236274452 236277420 0.000000e+00 4922.0
4 TraesCS1B01G190800 chr1D 78.261 138 25 3 3166 3299 416226939 416227075 2.110000e-12 84.2
5 TraesCS1B01G190800 chr1A 93.408 3019 100 44 1 2973 309742637 309739672 0.000000e+00 4381.0
6 TraesCS1B01G190800 chr1A 88.000 75 8 1 3032 3106 309739601 309739528 1.630000e-13 87.9
7 TraesCS1B01G190800 chr5A 76.259 278 46 13 3034 3299 659246345 659246614 2.670000e-26 130.0
8 TraesCS1B01G190800 chr5A 92.063 63 5 0 3035 3097 224560765 224560827 4.530000e-14 89.8
9 TraesCS1B01G190800 chr5A 92.500 40 2 1 3065 3104 600234357 600234319 4.600000e-04 56.5
10 TraesCS1B01G190800 chr7A 75.269 279 44 15 3035 3299 17706926 17707193 3.480000e-20 110.0
11 TraesCS1B01G190800 chr7A 80.916 131 20 2 3173 3299 715952268 715952397 7.530000e-17 99.0
12 TraesCS1B01G190800 chr7A 91.379 58 4 1 2969 3026 729185158 729185102 9.810000e-11 78.7
13 TraesCS1B01G190800 chr7A 90.909 44 4 0 3061 3104 17395455 17395498 3.560000e-05 60.2
14 TraesCS1B01G190800 chr3B 74.545 275 56 9 3035 3299 584201775 584201505 1.250000e-19 108.0
15 TraesCS1B01G190800 chr7D 74.359 273 57 10 3036 3299 634083989 634083721 1.620000e-18 104.0
16 TraesCS1B01G190800 chr7D 80.435 138 22 2 3166 3299 531198233 531198369 2.090000e-17 100.0
17 TraesCS1B01G190800 chr3D 74.308 253 49 10 3058 3299 306665444 306665197 3.510000e-15 93.5
18 TraesCS1B01G190800 chr3D 90.698 43 4 0 3061 3103 9191122 9191080 1.280000e-04 58.4
19 TraesCS1B01G190800 chr6D 78.986 138 24 3 3166 3299 210138631 210138495 4.530000e-14 89.8
20 TraesCS1B01G190800 chr5B 92.593 54 2 2 2973 3026 317884767 317884716 3.530000e-10 76.8
21 TraesCS1B01G190800 chr5B 92.453 53 2 2 2973 3025 324614873 324614923 1.270000e-09 75.0
22 TraesCS1B01G190800 chr5B 89.286 56 6 0 3038 3093 456501429 456501374 1.640000e-08 71.3
23 TraesCS1B01G190800 chr5D 90.741 54 4 1 2977 3030 472877916 472877864 1.640000e-08 71.3
24 TraesCS1B01G190800 chr5D 92.105 38 3 0 3066 3103 300776929 300776892 2.000000e-03 54.7
25 TraesCS1B01G190800 chr3A 90.741 54 4 1 2977 3030 679310417 679310365 1.640000e-08 71.3
26 TraesCS1B01G190800 chr6A 89.286 56 4 2 2974 3028 500063711 500063765 5.910000e-08 69.4
27 TraesCS1B01G190800 chr6A 94.595 37 2 0 3061 3097 25438867 25438903 1.280000e-04 58.4
28 TraesCS1B01G190800 chr4B 88.136 59 4 3 2974 3030 445020672 445020729 2.120000e-07 67.6
29 TraesCS1B01G190800 chr2A 86.441 59 8 0 2974 3032 729157850 729157792 7.640000e-07 65.8


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 TraesCS1B01G190800 chr1B 341522287 341525585 3298 False 6093.00 6093 100.000 1 3299 1 chr1B.!!$F1 3298
1 TraesCS1B01G190800 chr1D 236274452 236277420 2968 False 4922.00 4922 96.589 1 2973 1 chr1D.!!$F1 2972
2 TraesCS1B01G190800 chr1A 309739528 309742637 3109 True 2234.45 4381 90.704 1 3106 2 chr1A.!!$R1 3105

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
579 587 4.165779 CAACGCCTTCTAATTTCGCAATT 58.834 39.13 0.0 0.0 36.52 2.32 F
1247 1255 0.041839 GCTCACGTTGAACTGCACTG 60.042 55.00 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 1970 0.106918 TGGAAAACGAGGCAACAGGT 60.107 50.0 0.00 0.0 41.41 4.00 R
3229 3297 0.036765 TGTACACGATTGGAGGCCAC 60.037 55.0 5.01 0.0 30.78 5.01 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
317 320 8.655092 TCTTTTTGCGCCTTGAATTTTTATATG 58.345 29.630 4.18 0.00 0.00 1.78
325 328 8.534778 CGCCTTGAATTTTTATATGAGCTTTTC 58.465 33.333 0.00 0.00 0.00 2.29
511 516 7.344612 TCTTTCTGGGTGCACTAAGAATAGATA 59.655 37.037 25.23 14.74 33.15 1.98
579 587 4.165779 CAACGCCTTCTAATTTCGCAATT 58.834 39.130 0.00 0.00 36.52 2.32
585 593 6.325596 GCCTTCTAATTTCGCAATTCTTCTT 58.674 36.000 0.00 0.00 34.29 2.52
983 991 4.275936 GTGGCATATTTCGCTAGGTTTCAT 59.724 41.667 0.00 0.00 0.00 2.57
1196 1204 2.775911 TCTCACATCCCTTTGCTCTG 57.224 50.000 0.00 0.00 0.00 3.35
1197 1205 1.980765 TCTCACATCCCTTTGCTCTGT 59.019 47.619 0.00 0.00 0.00 3.41
1247 1255 0.041839 GCTCACGTTGAACTGCACTG 60.042 55.000 0.00 0.00 0.00 3.66
1382 1390 0.322816 GTCCTGCATTGCTCTTCCCA 60.323 55.000 10.49 0.00 0.00 4.37
1406 1414 6.954852 CACTGTTGTTTTGTTTGCAATTACAG 59.045 34.615 0.00 7.85 36.32 2.74
1658 1666 6.195983 CAGATTGCAGCTCATAATTCGTTTTC 59.804 38.462 0.00 0.00 0.00 2.29
1676 1684 4.820894 TTTCTTCCCTACAGTCTAAGGC 57.179 45.455 0.00 0.00 0.00 4.35
1763 1771 4.538490 TGTGTACCCATTGGAGAAGGTAAT 59.462 41.667 3.62 0.00 36.64 1.89
1816 1824 3.364964 CGCGATTAAGCAGTGGAAACTTT 60.365 43.478 0.00 0.00 36.85 2.66
1961 1970 0.732538 CACGACAGACTACGCATGCA 60.733 55.000 19.57 0.00 0.00 3.96
2069 2078 2.473378 CTGCTTCAAGTGCGCTCG 59.527 61.111 9.73 0.00 0.00 5.03
2259 2268 2.492090 CCAGAAGCCGTCGAGGAG 59.508 66.667 6.70 0.00 45.00 3.69
2396 2405 1.033746 GCTGCTGCTGCCCATCTTTA 61.034 55.000 19.30 0.00 38.71 1.85
2460 2469 1.518903 GCCTTGGCTATCGCAATCCC 61.519 60.000 4.11 0.00 38.10 3.85
2472 2481 4.594123 TCGCAATCCCGAATTCTGTATA 57.406 40.909 3.52 0.00 33.77 1.47
2493 2503 3.329542 ATTGCCCGTGCCATCGTCT 62.330 57.895 0.00 0.00 36.33 4.18
2530 2540 7.935338 CAGAATTTGCACAAGTTTGTTCTAT 57.065 32.000 0.00 0.00 39.91 1.98
2532 2542 8.905702 CAGAATTTGCACAAGTTTGTTCTATAC 58.094 33.333 0.00 0.00 39.91 1.47
2567 2577 5.296780 GTCTTGCAATTCCAAGGATATTCGA 59.703 40.000 9.24 0.00 41.89 3.71
2737 2792 5.515797 TCGTACATAAATCAGGAGACAGG 57.484 43.478 0.00 0.00 0.00 4.00
2738 2793 4.954202 TCGTACATAAATCAGGAGACAGGT 59.046 41.667 0.00 0.00 0.00 4.00
2878 2933 2.431954 AGCCTCATCAGAATGTTGGG 57.568 50.000 0.00 0.00 36.05 4.12
2977 3033 3.354131 AAAAAGCAAAAGCGGCGAA 57.646 42.105 12.98 0.00 36.08 4.70
2978 3034 0.927537 AAAAAGCAAAAGCGGCGAAC 59.072 45.000 12.98 0.00 36.08 3.95
2979 3035 0.874175 AAAAGCAAAAGCGGCGAACC 60.874 50.000 12.98 0.00 36.08 3.62
2980 3036 2.010582 AAAGCAAAAGCGGCGAACCA 62.011 50.000 12.98 0.00 36.08 3.67
2981 3037 2.010582 AAGCAAAAGCGGCGAACCAA 62.011 50.000 12.98 0.00 36.08 3.67
2982 3038 2.300066 GCAAAAGCGGCGAACCAAC 61.300 57.895 12.98 0.00 34.57 3.77
2984 3040 0.318614 CAAAAGCGGCGAACCAACAT 60.319 50.000 12.98 0.00 34.57 2.71
2985 3041 0.318614 AAAAGCGGCGAACCAACATG 60.319 50.000 12.98 0.00 34.57 3.21
2986 3042 1.452145 AAAGCGGCGAACCAACATGT 61.452 50.000 12.98 0.00 34.57 3.21
2998 3054 3.772096 AACATGTGGTTGGATGGCT 57.228 47.368 0.00 0.00 38.60 4.75
2999 3055 2.897271 AACATGTGGTTGGATGGCTA 57.103 45.000 0.00 0.00 38.60 3.93
3000 3056 2.425143 ACATGTGGTTGGATGGCTAG 57.575 50.000 0.00 0.00 0.00 3.42
3001 3057 1.915489 ACATGTGGTTGGATGGCTAGA 59.085 47.619 0.00 0.00 0.00 2.43
3002 3058 2.092753 ACATGTGGTTGGATGGCTAGAG 60.093 50.000 0.00 0.00 0.00 2.43
3003 3059 0.911769 TGTGGTTGGATGGCTAGAGG 59.088 55.000 0.00 0.00 0.00 3.69
3004 3060 1.204146 GTGGTTGGATGGCTAGAGGA 58.796 55.000 0.00 0.00 0.00 3.71
3006 3062 1.559682 TGGTTGGATGGCTAGAGGAAC 59.440 52.381 0.00 0.00 0.00 3.62
3007 3063 1.559682 GGTTGGATGGCTAGAGGAACA 59.440 52.381 0.00 0.00 0.00 3.18
3008 3064 2.420687 GGTTGGATGGCTAGAGGAACAG 60.421 54.545 0.00 0.00 0.00 3.16
3009 3065 2.237392 GTTGGATGGCTAGAGGAACAGT 59.763 50.000 0.00 0.00 0.00 3.55
3010 3066 1.833630 TGGATGGCTAGAGGAACAGTG 59.166 52.381 0.00 0.00 0.00 3.66
3011 3067 1.139853 GGATGGCTAGAGGAACAGTGG 59.860 57.143 0.00 0.00 0.00 4.00
3012 3068 0.543749 ATGGCTAGAGGAACAGTGGC 59.456 55.000 0.00 0.00 0.00 5.01
3013 3069 0.835971 TGGCTAGAGGAACAGTGGCA 60.836 55.000 0.00 0.00 0.00 4.92
3014 3070 0.543749 GGCTAGAGGAACAGTGGCAT 59.456 55.000 0.00 0.00 0.00 4.40
3015 3071 1.474143 GGCTAGAGGAACAGTGGCATC 60.474 57.143 0.00 0.00 0.00 3.91
3016 3072 1.474143 GCTAGAGGAACAGTGGCATCC 60.474 57.143 0.00 0.00 0.00 3.51
3018 3074 1.450312 GAGGAACAGTGGCATCCCG 60.450 63.158 1.26 0.00 33.55 5.14
3019 3075 1.899437 GAGGAACAGTGGCATCCCGA 61.899 60.000 1.26 0.00 33.55 5.14
3020 3076 1.450312 GGAACAGTGGCATCCCGAG 60.450 63.158 0.00 0.00 0.00 4.63
3027 3083 4.424711 GGCATCCCGAGCCCACAA 62.425 66.667 0.00 0.00 46.50 3.33
3028 3084 2.361104 GCATCCCGAGCCCACAAA 60.361 61.111 0.00 0.00 0.00 2.83
3029 3085 2.409870 GCATCCCGAGCCCACAAAG 61.410 63.158 0.00 0.00 0.00 2.77
3030 3086 1.299648 CATCCCGAGCCCACAAAGA 59.700 57.895 0.00 0.00 0.00 2.52
3067 3135 7.371936 TCAAAAGGTTTAAACATTACATCCGG 58.628 34.615 17.71 0.00 31.98 5.14
3068 3136 6.904463 AAAGGTTTAAACATTACATCCGGT 57.096 33.333 17.71 0.00 31.98 5.28
3072 3140 5.878669 GGTTTAAACATTACATCCGGTCTCT 59.121 40.000 19.57 0.00 0.00 3.10
3074 3142 2.604046 ACATTACATCCGGTCTCTGC 57.396 50.000 0.00 0.00 0.00 4.26
3079 3147 2.604046 ACATCCGGTCTCTGCATAAC 57.396 50.000 0.00 0.00 0.00 1.89
3081 3149 3.296854 ACATCCGGTCTCTGCATAACTA 58.703 45.455 0.00 0.00 0.00 2.24
3106 3174 5.951747 AGATGCATACAACCATAACCAAGTT 59.048 36.000 0.00 0.00 0.00 2.66
3107 3175 5.637006 TGCATACAACCATAACCAAGTTC 57.363 39.130 0.00 0.00 0.00 3.01
3108 3176 5.073428 TGCATACAACCATAACCAAGTTCA 58.927 37.500 0.00 0.00 0.00 3.18
3109 3177 5.536538 TGCATACAACCATAACCAAGTTCAA 59.463 36.000 0.00 0.00 0.00 2.69
3110 3178 6.092748 GCATACAACCATAACCAAGTTCAAG 58.907 40.000 0.00 0.00 0.00 3.02
3111 3179 6.294508 GCATACAACCATAACCAAGTTCAAGT 60.295 38.462 0.00 0.00 0.00 3.16
3112 3180 7.657336 CATACAACCATAACCAAGTTCAAGTT 58.343 34.615 0.00 0.00 0.00 2.66
3113 3181 6.538945 ACAACCATAACCAAGTTCAAGTTT 57.461 33.333 0.00 0.00 0.00 2.66
3114 3182 6.941857 ACAACCATAACCAAGTTCAAGTTTT 58.058 32.000 0.00 0.00 0.00 2.43
3115 3183 7.390823 ACAACCATAACCAAGTTCAAGTTTTT 58.609 30.769 0.00 0.00 0.00 1.94
3116 3184 8.532819 ACAACCATAACCAAGTTCAAGTTTTTA 58.467 29.630 0.00 0.00 0.00 1.52
3117 3185 9.372369 CAACCATAACCAAGTTCAAGTTTTTAA 57.628 29.630 0.00 0.00 0.00 1.52
3118 3186 9.945904 AACCATAACCAAGTTCAAGTTTTTAAA 57.054 25.926 0.00 0.00 0.00 1.52
3119 3187 9.945904 ACCATAACCAAGTTCAAGTTTTTAAAA 57.054 25.926 0.00 0.00 0.00 1.52
3140 3208 9.810231 TTAAAAACCGATAAAGACGAAATACAC 57.190 29.630 0.00 0.00 0.00 2.90
3141 3209 5.691508 AACCGATAAAGACGAAATACACG 57.308 39.130 0.00 0.00 0.00 4.49
3142 3210 4.737054 ACCGATAAAGACGAAATACACGT 58.263 39.130 0.00 0.00 46.58 4.49
3143 3211 5.879237 ACCGATAAAGACGAAATACACGTA 58.121 37.500 0.00 0.00 43.97 3.57
3144 3212 5.967674 ACCGATAAAGACGAAATACACGTAG 59.032 40.000 0.00 0.00 43.97 3.51
3146 3214 6.139795 CCGATAAAGACGAAATACACGTAGTC 59.860 42.308 0.00 0.00 41.61 2.59
3147 3215 6.684131 CGATAAAGACGAAATACACGTAGTCA 59.316 38.462 0.00 0.00 41.61 3.41
3148 3216 7.375280 CGATAAAGACGAAATACACGTAGTCAT 59.625 37.037 0.00 0.00 41.61 3.06
3149 3217 9.655769 GATAAAGACGAAATACACGTAGTCATA 57.344 33.333 0.00 0.00 41.61 2.15
3151 3219 7.909777 AAGACGAAATACACGTAGTCATATG 57.090 36.000 0.00 0.00 41.61 1.78
3152 3220 6.436261 AGACGAAATACACGTAGTCATATGG 58.564 40.000 2.13 0.00 41.61 2.74
3153 3221 6.261603 AGACGAAATACACGTAGTCATATGGA 59.738 38.462 2.13 0.00 41.61 3.41
3154 3222 6.436261 ACGAAATACACGTAGTCATATGGAG 58.564 40.000 2.13 0.00 41.61 3.86
3155 3223 6.261603 ACGAAATACACGTAGTCATATGGAGA 59.738 38.462 2.13 0.00 41.61 3.71
3156 3224 7.040617 ACGAAATACACGTAGTCATATGGAGAT 60.041 37.037 2.13 0.00 41.61 2.75
3157 3225 7.808381 CGAAATACACGTAGTCATATGGAGATT 59.192 37.037 2.13 0.00 41.61 2.40
3158 3226 8.818141 AAATACACGTAGTCATATGGAGATTG 57.182 34.615 2.13 0.00 41.61 2.67
3159 3227 5.854010 ACACGTAGTCATATGGAGATTGT 57.146 39.130 2.13 0.00 41.61 2.71
3160 3228 6.954487 ACACGTAGTCATATGGAGATTGTA 57.046 37.500 2.13 0.00 41.61 2.41
3161 3229 7.526142 ACACGTAGTCATATGGAGATTGTAT 57.474 36.000 2.13 0.00 41.61 2.29
3162 3230 8.631480 ACACGTAGTCATATGGAGATTGTATA 57.369 34.615 2.13 0.00 41.61 1.47
3163 3231 8.731605 ACACGTAGTCATATGGAGATTGTATAG 58.268 37.037 2.13 0.00 41.61 1.31
3164 3232 8.947115 CACGTAGTCATATGGAGATTGTATAGA 58.053 37.037 2.13 0.00 41.61 1.98
3165 3233 8.948145 ACGTAGTCATATGGAGATTGTATAGAC 58.052 37.037 2.13 0.00 29.74 2.59
3166 3234 8.399425 CGTAGTCATATGGAGATTGTATAGACC 58.601 40.741 2.13 0.00 0.00 3.85
3167 3235 9.469097 GTAGTCATATGGAGATTGTATAGACCT 57.531 37.037 2.13 0.00 0.00 3.85
3177 3245 9.930693 GGAGATTGTATAGACCTAAAACATAGG 57.069 37.037 0.00 0.00 40.49 2.57
3180 3248 9.930693 GATTGTATAGACCTAAAACATAGGAGG 57.069 37.037 8.46 0.00 38.09 4.30
3181 3249 7.850935 TGTATAGACCTAAAACATAGGAGGG 57.149 40.000 8.46 0.00 38.09 4.30
3182 3250 5.827326 ATAGACCTAAAACATAGGAGGGC 57.173 43.478 8.46 0.00 37.37 5.19
3183 3251 3.460825 AGACCTAAAACATAGGAGGGCA 58.539 45.455 8.46 0.00 39.85 5.36
3184 3252 3.850173 AGACCTAAAACATAGGAGGGCAA 59.150 43.478 8.46 0.00 39.85 4.52
3185 3253 4.291249 AGACCTAAAACATAGGAGGGCAAA 59.709 41.667 8.46 0.00 39.85 3.68
3186 3254 5.044105 AGACCTAAAACATAGGAGGGCAAAT 60.044 40.000 8.46 0.00 39.85 2.32
3187 3255 5.201243 ACCTAAAACATAGGAGGGCAAATC 58.799 41.667 8.46 0.00 38.09 2.17
3188 3256 4.584743 CCTAAAACATAGGAGGGCAAATCC 59.415 45.833 0.00 0.00 36.85 3.01
3189 3257 3.756082 AAACATAGGAGGGCAAATCCA 57.244 42.857 5.57 0.00 39.47 3.41
3190 3258 3.756082 AACATAGGAGGGCAAATCCAA 57.244 42.857 5.57 0.00 39.47 3.53
3191 3259 3.756082 ACATAGGAGGGCAAATCCAAA 57.244 42.857 5.57 0.00 39.47 3.28
3192 3260 3.635591 ACATAGGAGGGCAAATCCAAAG 58.364 45.455 5.57 0.00 39.47 2.77
3193 3261 3.269381 ACATAGGAGGGCAAATCCAAAGA 59.731 43.478 5.57 0.00 39.47 2.52
3194 3262 4.078980 ACATAGGAGGGCAAATCCAAAGAT 60.079 41.667 5.57 0.00 39.47 2.40
3195 3263 3.023939 AGGAGGGCAAATCCAAAGATC 57.976 47.619 5.57 0.00 39.47 2.75
3196 3264 2.312741 AGGAGGGCAAATCCAAAGATCA 59.687 45.455 0.00 0.00 39.47 2.92
3197 3265 3.052338 AGGAGGGCAAATCCAAAGATCAT 60.052 43.478 0.00 0.00 39.47 2.45
3198 3266 3.069158 GGAGGGCAAATCCAAAGATCATG 59.931 47.826 0.00 0.00 36.79 3.07
3199 3267 3.703052 GAGGGCAAATCCAAAGATCATGT 59.297 43.478 0.00 0.00 36.21 3.21
3200 3268 4.098894 AGGGCAAATCCAAAGATCATGTT 58.901 39.130 0.00 0.00 36.21 2.71
3201 3269 4.081309 AGGGCAAATCCAAAGATCATGTTG 60.081 41.667 0.00 0.00 36.21 3.33
3202 3270 4.322953 GGGCAAATCCAAAGATCATGTTGT 60.323 41.667 0.00 0.00 36.21 3.32
3203 3271 4.866486 GGCAAATCCAAAGATCATGTTGTC 59.134 41.667 0.00 0.00 34.01 3.18
3204 3272 5.472148 GCAAATCCAAAGATCATGTTGTCA 58.528 37.500 0.00 0.00 0.00 3.58
3205 3273 6.103997 GCAAATCCAAAGATCATGTTGTCAT 58.896 36.000 0.00 0.00 34.21 3.06
3206 3274 6.255020 GCAAATCCAAAGATCATGTTGTCATC 59.745 38.462 0.00 0.00 31.15 2.92
3207 3275 6.461110 AATCCAAAGATCATGTTGTCATCC 57.539 37.500 0.00 0.00 31.15 3.51
3208 3276 4.920999 TCCAAAGATCATGTTGTCATCCA 58.079 39.130 0.00 0.00 31.15 3.41
3209 3277 5.512298 TCCAAAGATCATGTTGTCATCCAT 58.488 37.500 0.00 0.00 31.15 3.41
3210 3278 5.358725 TCCAAAGATCATGTTGTCATCCATG 59.641 40.000 0.00 6.65 39.82 3.66
3211 3279 5.451381 CCAAAGATCATGTTGTCATCCATGG 60.451 44.000 4.97 4.97 39.12 3.66
3212 3280 4.515028 AGATCATGTTGTCATCCATGGT 57.485 40.909 12.58 6.01 39.12 3.55
3213 3281 5.635278 AGATCATGTTGTCATCCATGGTA 57.365 39.130 12.58 0.00 39.12 3.25
3214 3282 5.371526 AGATCATGTTGTCATCCATGGTAC 58.628 41.667 12.58 9.46 39.12 3.34
3215 3283 4.566426 TCATGTTGTCATCCATGGTACA 57.434 40.909 12.58 11.98 39.12 2.90
3216 3284 4.916183 TCATGTTGTCATCCATGGTACAA 58.084 39.130 19.34 19.34 39.12 2.41
3217 3285 5.320277 TCATGTTGTCATCCATGGTACAAA 58.680 37.500 22.68 16.22 39.12 2.83
3218 3286 5.951148 TCATGTTGTCATCCATGGTACAAAT 59.049 36.000 22.68 17.18 39.12 2.32
3219 3287 6.037726 CATGTTGTCATCCATGGTACAAATG 58.962 40.000 22.68 21.43 34.85 2.32
3220 3288 6.350361 CATGTTGTCATCCATGGTACAAATGT 60.350 38.462 22.68 13.54 34.85 2.71
3221 3289 8.103094 CATGTTGTCATCCATGGTACAAATGTC 61.103 40.741 22.68 13.25 34.85 3.06
3227 3295 3.543884 TGGTACAAATGTCCCTCGC 57.456 52.632 0.00 0.00 31.92 5.03
3228 3296 0.035820 TGGTACAAATGTCCCTCGCC 60.036 55.000 0.00 0.00 31.92 5.54
3229 3297 1.087771 GGTACAAATGTCCCTCGCCG 61.088 60.000 0.00 0.00 0.00 6.46
3230 3298 0.390735 GTACAAATGTCCCTCGCCGT 60.391 55.000 0.00 0.00 0.00 5.68
3231 3299 0.390603 TACAAATGTCCCTCGCCGTG 60.391 55.000 0.00 0.00 0.00 4.94
3232 3300 2.046314 AAATGTCCCTCGCCGTGG 60.046 61.111 0.00 0.00 0.00 4.94
3233 3301 4.778143 AATGTCCCTCGCCGTGGC 62.778 66.667 0.00 0.00 37.85 5.01
3240 3308 4.473520 CTCGCCGTGGCCTCCAAT 62.474 66.667 3.32 0.00 34.18 3.16
3241 3309 4.467084 TCGCCGTGGCCTCCAATC 62.467 66.667 3.32 0.00 34.18 2.67
3243 3311 4.778143 GCCGTGGCCTCCAATCGT 62.778 66.667 3.32 0.00 34.18 3.73
3244 3312 2.819595 CCGTGGCCTCCAATCGTG 60.820 66.667 3.32 0.00 34.18 4.35
3245 3313 2.047274 CGTGGCCTCCAATCGTGT 60.047 61.111 3.32 0.00 34.18 4.49
3246 3314 1.216977 CGTGGCCTCCAATCGTGTA 59.783 57.895 3.32 0.00 34.18 2.90
3247 3315 1.082117 CGTGGCCTCCAATCGTGTAC 61.082 60.000 3.32 0.00 34.18 2.90
3248 3316 0.036765 GTGGCCTCCAATCGTGTACA 60.037 55.000 3.32 0.00 34.18 2.90
3249 3317 0.036765 TGGCCTCCAATCGTGTACAC 60.037 55.000 16.32 16.32 0.00 2.90
3250 3318 0.036765 GGCCTCCAATCGTGTACACA 60.037 55.000 24.98 12.85 0.00 3.72
3251 3319 1.076332 GCCTCCAATCGTGTACACAC 58.924 55.000 24.98 2.41 43.15 3.82
3252 3320 1.722011 CCTCCAATCGTGTACACACC 58.278 55.000 24.98 0.00 43.66 4.16
3253 3321 1.275291 CCTCCAATCGTGTACACACCT 59.725 52.381 24.98 6.48 43.66 4.00
3254 3322 2.607187 CTCCAATCGTGTACACACCTC 58.393 52.381 24.98 0.00 43.66 3.85
3255 3323 2.231478 CTCCAATCGTGTACACACCTCT 59.769 50.000 24.98 2.32 43.66 3.69
3256 3324 2.029380 TCCAATCGTGTACACACCTCTG 60.029 50.000 24.98 13.48 43.66 3.35
3257 3325 2.288825 CCAATCGTGTACACACCTCTGT 60.289 50.000 24.98 0.63 43.66 3.41
3258 3326 3.057104 CCAATCGTGTACACACCTCTGTA 60.057 47.826 24.98 1.02 43.66 2.74
3259 3327 4.552355 CAATCGTGTACACACCTCTGTAA 58.448 43.478 24.98 0.07 43.66 2.41
3260 3328 4.859304 ATCGTGTACACACCTCTGTAAA 57.141 40.909 24.98 0.00 43.66 2.01
3261 3329 4.652421 TCGTGTACACACCTCTGTAAAA 57.348 40.909 24.98 0.00 43.66 1.52
3262 3330 4.362279 TCGTGTACACACCTCTGTAAAAC 58.638 43.478 24.98 0.00 43.66 2.43
3263 3331 3.492011 CGTGTACACACCTCTGTAAAACC 59.508 47.826 24.98 0.00 43.66 3.27
3264 3332 3.492011 GTGTACACACCTCTGTAAAACCG 59.508 47.826 21.14 0.00 40.85 4.44
3265 3333 3.384146 TGTACACACCTCTGTAAAACCGA 59.616 43.478 0.00 0.00 0.00 4.69
3266 3334 3.764237 ACACACCTCTGTAAAACCGAT 57.236 42.857 0.00 0.00 0.00 4.18
3267 3335 3.660865 ACACACCTCTGTAAAACCGATC 58.339 45.455 0.00 0.00 0.00 3.69
3268 3336 3.323979 ACACACCTCTGTAAAACCGATCT 59.676 43.478 0.00 0.00 0.00 2.75
3269 3337 4.202326 ACACACCTCTGTAAAACCGATCTT 60.202 41.667 0.00 0.00 0.00 2.40
3270 3338 4.152402 CACACCTCTGTAAAACCGATCTTG 59.848 45.833 0.00 0.00 0.00 3.02
3271 3339 4.039973 ACACCTCTGTAAAACCGATCTTGA 59.960 41.667 0.00 0.00 0.00 3.02
3272 3340 5.178797 CACCTCTGTAAAACCGATCTTGAT 58.821 41.667 0.00 0.00 0.00 2.57
3273 3341 5.643777 CACCTCTGTAAAACCGATCTTGATT 59.356 40.000 0.00 0.00 0.00 2.57
3274 3342 5.875359 ACCTCTGTAAAACCGATCTTGATTC 59.125 40.000 0.00 0.00 0.00 2.52
3275 3343 6.109359 CCTCTGTAAAACCGATCTTGATTCT 58.891 40.000 0.00 0.00 0.00 2.40
3276 3344 6.256757 CCTCTGTAAAACCGATCTTGATTCTC 59.743 42.308 0.00 0.00 0.00 2.87
3277 3345 6.106673 TCTGTAAAACCGATCTTGATTCTCC 58.893 40.000 0.00 0.00 0.00 3.71
3278 3346 5.800296 TGTAAAACCGATCTTGATTCTCCA 58.200 37.500 0.00 0.00 0.00 3.86
3279 3347 5.642063 TGTAAAACCGATCTTGATTCTCCAC 59.358 40.000 0.00 0.00 0.00 4.02
3280 3348 3.981071 AACCGATCTTGATTCTCCACA 57.019 42.857 0.00 0.00 0.00 4.17
3281 3349 3.252974 ACCGATCTTGATTCTCCACAC 57.747 47.619 0.00 0.00 0.00 3.82
3282 3350 2.196749 CCGATCTTGATTCTCCACACG 58.803 52.381 0.00 0.00 0.00 4.49
3283 3351 2.417379 CCGATCTTGATTCTCCACACGT 60.417 50.000 0.00 0.00 0.00 4.49
3284 3352 3.254060 CGATCTTGATTCTCCACACGTT 58.746 45.455 0.00 0.00 0.00 3.99
3285 3353 3.061295 CGATCTTGATTCTCCACACGTTG 59.939 47.826 0.00 0.00 0.00 4.10
3286 3354 3.469008 TCTTGATTCTCCACACGTTGT 57.531 42.857 0.00 0.00 0.00 3.32
3287 3355 4.594123 TCTTGATTCTCCACACGTTGTA 57.406 40.909 0.00 0.00 0.00 2.41
3288 3356 4.951254 TCTTGATTCTCCACACGTTGTAA 58.049 39.130 0.00 0.00 0.00 2.41
3289 3357 5.361427 TCTTGATTCTCCACACGTTGTAAA 58.639 37.500 0.00 0.00 0.00 2.01
3290 3358 5.465390 TCTTGATTCTCCACACGTTGTAAAG 59.535 40.000 0.00 0.00 0.00 1.85
3291 3359 4.951254 TGATTCTCCACACGTTGTAAAGA 58.049 39.130 0.00 0.00 0.00 2.52
3292 3360 4.748102 TGATTCTCCACACGTTGTAAAGAC 59.252 41.667 0.00 0.00 0.00 3.01
3293 3361 2.734670 TCTCCACACGTTGTAAAGACG 58.265 47.619 0.00 0.00 45.46 4.18
3294 3362 2.358582 TCTCCACACGTTGTAAAGACGA 59.641 45.455 3.48 0.00 42.82 4.20
3295 3363 3.005050 TCTCCACACGTTGTAAAGACGAT 59.995 43.478 3.48 0.00 42.82 3.73
3296 3364 3.311106 TCCACACGTTGTAAAGACGATC 58.689 45.455 3.48 0.00 42.82 3.69
3297 3365 3.054166 CCACACGTTGTAAAGACGATCA 58.946 45.455 3.48 0.00 42.82 2.92
3298 3366 3.678072 CCACACGTTGTAAAGACGATCAT 59.322 43.478 3.48 0.00 42.82 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
196 199 7.175641 AGAGAAATGAAGGTGAAACATTACCAG 59.824 37.037 0.00 0.00 43.10 4.00
325 328 2.036556 AACAAAGAAACGATGCAGCG 57.963 45.000 24.69 24.69 37.29 5.18
511 516 2.159142 GGACGAAGGTGGTCGATGTTAT 60.159 50.000 1.02 0.00 43.86 1.89
547 555 3.678056 AGAAGGCGTTGTTATCTGTCA 57.322 42.857 0.00 0.00 0.00 3.58
579 587 7.400339 ACAATAGTCCAAGACATAGGAAGAAGA 59.600 37.037 0.00 0.00 35.29 2.87
585 593 7.973048 ACTAACAATAGTCCAAGACATAGGA 57.027 36.000 0.00 0.00 37.90 2.94
709 717 1.933853 GGAATAGATGTGCCACGTCAC 59.066 52.381 18.72 7.26 36.61 3.67
784 792 1.561542 GGATTTGGGAGAGGCAGAAGA 59.438 52.381 0.00 0.00 0.00 2.87
983 991 8.442632 GAATGTCATCTTGATATTCTTGGTGA 57.557 34.615 15.53 0.00 45.57 4.02
1196 1204 8.121086 CACATGACATAATTCAGAAGATCACAC 58.879 37.037 0.00 0.00 0.00 3.82
1197 1205 7.201670 GCACATGACATAATTCAGAAGATCACA 60.202 37.037 0.00 0.00 0.00 3.58
1247 1255 4.116238 GGAGTAGCTGCACATCTAGAAAC 58.884 47.826 4.12 0.00 0.00 2.78
1382 1390 6.402011 GCTGTAATTGCAAACAAAACAACAGT 60.402 34.615 1.71 0.00 39.77 3.55
1406 1414 6.674694 AGTACAATGTGATGAGATTTCTGC 57.325 37.500 0.00 0.00 0.00 4.26
1558 1566 5.841957 ATTAAATCAGCAGCAAAGGGTAG 57.158 39.130 0.00 0.00 0.00 3.18
1561 1569 4.335315 TCGTATTAAATCAGCAGCAAAGGG 59.665 41.667 0.00 0.00 0.00 3.95
1658 1666 1.763545 GGGCCTTAGACTGTAGGGAAG 59.236 57.143 0.84 0.00 31.95 3.46
1676 1684 2.094675 CAGAGCCATACTTGTTTGGGG 58.905 52.381 11.17 0.00 33.40 4.96
1816 1824 4.993705 AGTTGAGATTTCCCAGTTACCA 57.006 40.909 0.00 0.00 0.00 3.25
1961 1970 0.106918 TGGAAAACGAGGCAACAGGT 60.107 50.000 0.00 0.00 41.41 4.00
2008 2017 1.815003 CAAGGTCATCTGCCAAGGAAC 59.185 52.381 0.00 0.00 0.00 3.62
2277 2286 0.252421 ATGAGTGCTCCTGGTCCTCA 60.252 55.000 0.00 2.05 36.67 3.86
2396 2405 2.159128 CGTGCCTCTGTGAGATGAGAAT 60.159 50.000 0.00 0.00 32.44 2.40
2460 2469 4.690748 ACGGGCAATGATATACAGAATTCG 59.309 41.667 0.00 0.00 0.00 3.34
2472 2481 2.188829 CGATGGCACGGGCAATGAT 61.189 57.895 13.89 0.00 42.43 2.45
2493 2503 4.944962 CAAATTCTGCTACCATTCACGA 57.055 40.909 0.00 0.00 0.00 4.35
2525 2535 8.306313 TGCAAGACCAAGATAGAAGTATAGAA 57.694 34.615 0.00 0.00 0.00 2.10
2526 2536 7.898014 TGCAAGACCAAGATAGAAGTATAGA 57.102 36.000 0.00 0.00 0.00 1.98
2527 2537 9.553064 AATTGCAAGACCAAGATAGAAGTATAG 57.447 33.333 4.94 0.00 0.00 1.31
2528 2538 9.547753 GAATTGCAAGACCAAGATAGAAGTATA 57.452 33.333 4.94 0.00 0.00 1.47
2529 2539 7.500559 GGAATTGCAAGACCAAGATAGAAGTAT 59.499 37.037 16.51 0.00 0.00 2.12
2530 2540 6.823689 GGAATTGCAAGACCAAGATAGAAGTA 59.176 38.462 16.51 0.00 0.00 2.24
2531 2541 5.649831 GGAATTGCAAGACCAAGATAGAAGT 59.350 40.000 16.51 0.00 0.00 3.01
2532 2542 5.649395 TGGAATTGCAAGACCAAGATAGAAG 59.351 40.000 20.24 0.00 0.00 2.85
2567 2577 0.553612 ATGCTTCCCTCCCCCTCTTT 60.554 55.000 0.00 0.00 0.00 2.52
2737 2792 3.035942 GCTGTTTCGTTGTCAATCACAC 58.964 45.455 0.00 0.00 33.41 3.82
2738 2793 2.032799 GGCTGTTTCGTTGTCAATCACA 59.967 45.455 0.00 0.00 0.00 3.58
2821 2876 2.093890 CCAGCAATAGCATCCACACAA 58.906 47.619 0.00 0.00 45.49 3.33
2980 3036 2.308570 TCTAGCCATCCAACCACATGTT 59.691 45.455 0.00 0.00 37.80 2.71
2981 3037 1.915489 TCTAGCCATCCAACCACATGT 59.085 47.619 0.00 0.00 0.00 3.21
2982 3038 2.569059 CTCTAGCCATCCAACCACATG 58.431 52.381 0.00 0.00 0.00 3.21
2984 3040 0.911769 CCTCTAGCCATCCAACCACA 59.088 55.000 0.00 0.00 0.00 4.17
2985 3041 1.204146 TCCTCTAGCCATCCAACCAC 58.796 55.000 0.00 0.00 0.00 4.16
2986 3042 1.559682 GTTCCTCTAGCCATCCAACCA 59.440 52.381 0.00 0.00 0.00 3.67
2988 3044 2.237392 ACTGTTCCTCTAGCCATCCAAC 59.763 50.000 0.00 0.00 0.00 3.77
2989 3045 2.237143 CACTGTTCCTCTAGCCATCCAA 59.763 50.000 0.00 0.00 0.00 3.53
2990 3046 1.833630 CACTGTTCCTCTAGCCATCCA 59.166 52.381 0.00 0.00 0.00 3.41
2991 3047 1.139853 CCACTGTTCCTCTAGCCATCC 59.860 57.143 0.00 0.00 0.00 3.51
2992 3048 1.474143 GCCACTGTTCCTCTAGCCATC 60.474 57.143 0.00 0.00 0.00 3.51
2993 3049 0.543749 GCCACTGTTCCTCTAGCCAT 59.456 55.000 0.00 0.00 0.00 4.40
2995 3051 0.543749 ATGCCACTGTTCCTCTAGCC 59.456 55.000 0.00 0.00 0.00 3.93
2996 3052 1.474143 GGATGCCACTGTTCCTCTAGC 60.474 57.143 0.00 0.00 0.00 3.42
2997 3053 1.139853 GGGATGCCACTGTTCCTCTAG 59.860 57.143 0.00 0.00 0.00 2.43
2998 3054 1.204146 GGGATGCCACTGTTCCTCTA 58.796 55.000 0.00 0.00 0.00 2.43
2999 3055 1.903877 CGGGATGCCACTGTTCCTCT 61.904 60.000 3.39 0.00 0.00 3.69
3000 3056 1.450312 CGGGATGCCACTGTTCCTC 60.450 63.158 3.39 0.00 0.00 3.71
3001 3057 1.903877 CTCGGGATGCCACTGTTCCT 61.904 60.000 3.39 0.00 0.00 3.36
3002 3058 1.450312 CTCGGGATGCCACTGTTCC 60.450 63.158 3.39 0.00 0.00 3.62
3003 3059 2.109126 GCTCGGGATGCCACTGTTC 61.109 63.158 3.39 0.00 0.00 3.18
3004 3060 2.045926 GCTCGGGATGCCACTGTT 60.046 61.111 3.39 0.00 0.00 3.16
3011 3067 2.361104 TTTGTGGGCTCGGGATGC 60.361 61.111 0.00 0.00 0.00 3.91
3012 3068 0.107017 ATCTTTGTGGGCTCGGGATG 60.107 55.000 0.00 0.00 0.00 3.51
3013 3069 0.107017 CATCTTTGTGGGCTCGGGAT 60.107 55.000 0.00 0.00 0.00 3.85
3014 3070 1.299648 CATCTTTGTGGGCTCGGGA 59.700 57.895 0.00 0.00 0.00 5.14
3015 3071 0.609131 AACATCTTTGTGGGCTCGGG 60.609 55.000 0.00 0.00 35.83 5.14
3016 3072 1.247567 AAACATCTTTGTGGGCTCGG 58.752 50.000 0.00 0.00 35.83 4.63
3018 3074 7.094377 TGAGTAATAAAACATCTTTGTGGGCTC 60.094 37.037 0.00 0.00 35.83 4.70
3019 3075 6.719370 TGAGTAATAAAACATCTTTGTGGGCT 59.281 34.615 0.00 0.00 35.83 5.19
3020 3076 6.919721 TGAGTAATAAAACATCTTTGTGGGC 58.080 36.000 0.00 0.00 35.83 5.36
3061 3129 2.898729 AGTTATGCAGAGACCGGATG 57.101 50.000 9.46 1.98 0.00 3.51
3062 3130 4.215908 TCTTAGTTATGCAGAGACCGGAT 58.784 43.478 9.46 0.00 0.00 4.18
3063 3131 3.628008 TCTTAGTTATGCAGAGACCGGA 58.372 45.455 9.46 0.00 0.00 5.14
3079 3147 7.283127 ACTTGGTTATGGTTGTATGCATCTTAG 59.717 37.037 0.19 0.00 0.00 2.18
3081 3149 5.951747 ACTTGGTTATGGTTGTATGCATCTT 59.048 36.000 0.19 0.00 0.00 2.40
3089 3157 7.648039 AAACTTGAACTTGGTTATGGTTGTA 57.352 32.000 0.00 0.00 0.00 2.41
3106 3174 9.224058 CGTCTTTATCGGTTTTTAAAAACTTGA 57.776 29.630 32.06 28.95 45.70 3.02
3107 3175 9.224058 TCGTCTTTATCGGTTTTTAAAAACTTG 57.776 29.630 32.06 26.04 45.70 3.16
3108 3176 9.786105 TTCGTCTTTATCGGTTTTTAAAAACTT 57.214 25.926 32.06 22.58 45.70 2.66
3109 3177 9.786105 TTTCGTCTTTATCGGTTTTTAAAAACT 57.214 25.926 32.06 20.62 45.70 2.66
3114 3182 9.810231 GTGTATTTCGTCTTTATCGGTTTTTAA 57.190 29.630 0.00 0.00 0.00 1.52
3115 3183 8.161610 CGTGTATTTCGTCTTTATCGGTTTTTA 58.838 33.333 0.00 0.00 0.00 1.52
3116 3184 7.011189 CGTGTATTTCGTCTTTATCGGTTTTT 58.989 34.615 0.00 0.00 0.00 1.94
3117 3185 6.146021 ACGTGTATTTCGTCTTTATCGGTTTT 59.854 34.615 0.00 0.00 36.85 2.43
3118 3186 5.634859 ACGTGTATTTCGTCTTTATCGGTTT 59.365 36.000 0.00 0.00 36.85 3.27
3119 3187 5.163513 ACGTGTATTTCGTCTTTATCGGTT 58.836 37.500 0.00 0.00 36.85 4.44
3120 3188 4.737054 ACGTGTATTTCGTCTTTATCGGT 58.263 39.130 0.00 0.00 36.85 4.69
3121 3189 5.967674 ACTACGTGTATTTCGTCTTTATCGG 59.032 40.000 0.00 0.00 41.72 4.18
3122 3190 6.684131 TGACTACGTGTATTTCGTCTTTATCG 59.316 38.462 0.00 0.00 41.72 2.92
3123 3191 7.959718 TGACTACGTGTATTTCGTCTTTATC 57.040 36.000 0.00 0.00 41.72 1.75
3125 3193 9.442033 CATATGACTACGTGTATTTCGTCTTTA 57.558 33.333 0.00 0.00 41.72 1.85
3126 3194 7.434307 CCATATGACTACGTGTATTTCGTCTTT 59.566 37.037 3.65 0.00 41.72 2.52
3127 3195 6.916387 CCATATGACTACGTGTATTTCGTCTT 59.084 38.462 3.65 0.00 41.72 3.01
3128 3196 6.261603 TCCATATGACTACGTGTATTTCGTCT 59.738 38.462 3.65 0.00 41.72 4.18
3129 3197 6.432936 TCCATATGACTACGTGTATTTCGTC 58.567 40.000 3.65 0.00 41.72 4.20
3130 3198 6.261603 TCTCCATATGACTACGTGTATTTCGT 59.738 38.462 3.65 0.00 43.86 3.85
3131 3199 6.665465 TCTCCATATGACTACGTGTATTTCG 58.335 40.000 3.65 0.00 0.00 3.46
3132 3200 8.916654 CAATCTCCATATGACTACGTGTATTTC 58.083 37.037 3.65 0.00 0.00 2.17
3133 3201 8.421784 ACAATCTCCATATGACTACGTGTATTT 58.578 33.333 3.65 0.00 0.00 1.40
3134 3202 7.952671 ACAATCTCCATATGACTACGTGTATT 58.047 34.615 3.65 0.00 0.00 1.89
3135 3203 7.526142 ACAATCTCCATATGACTACGTGTAT 57.474 36.000 3.65 0.00 0.00 2.29
3136 3204 6.954487 ACAATCTCCATATGACTACGTGTA 57.046 37.500 3.65 0.00 0.00 2.90
3137 3205 5.854010 ACAATCTCCATATGACTACGTGT 57.146 39.130 3.65 0.00 0.00 4.49
3138 3206 8.947115 TCTATACAATCTCCATATGACTACGTG 58.053 37.037 3.65 0.00 0.00 4.49
3139 3207 8.948145 GTCTATACAATCTCCATATGACTACGT 58.052 37.037 3.65 0.00 0.00 3.57
3140 3208 8.399425 GGTCTATACAATCTCCATATGACTACG 58.601 40.741 3.65 0.00 0.00 3.51
3141 3209 9.469097 AGGTCTATACAATCTCCATATGACTAC 57.531 37.037 3.65 0.00 0.00 2.73
3151 3219 9.930693 CCTATGTTTTAGGTCTATACAATCTCC 57.069 37.037 0.00 0.00 0.00 3.71
3154 3222 9.930693 CCTCCTATGTTTTAGGTCTATACAATC 57.069 37.037 0.00 0.00 36.16 2.67
3155 3223 8.881262 CCCTCCTATGTTTTAGGTCTATACAAT 58.119 37.037 0.00 0.00 36.16 2.71
3156 3224 7.202066 GCCCTCCTATGTTTTAGGTCTATACAA 60.202 40.741 0.00 0.00 36.16 2.41
3157 3225 6.269307 GCCCTCCTATGTTTTAGGTCTATACA 59.731 42.308 0.00 0.00 36.16 2.29
3158 3226 6.269307 TGCCCTCCTATGTTTTAGGTCTATAC 59.731 42.308 0.00 0.00 36.16 1.47
3159 3227 6.387127 TGCCCTCCTATGTTTTAGGTCTATA 58.613 40.000 0.00 0.00 36.16 1.31
3160 3228 5.224441 TGCCCTCCTATGTTTTAGGTCTAT 58.776 41.667 0.00 0.00 36.16 1.98
3161 3229 4.627015 TGCCCTCCTATGTTTTAGGTCTA 58.373 43.478 0.00 0.00 36.16 2.59
3162 3230 3.460825 TGCCCTCCTATGTTTTAGGTCT 58.539 45.455 0.00 0.00 36.16 3.85
3163 3231 3.926058 TGCCCTCCTATGTTTTAGGTC 57.074 47.619 0.00 0.00 36.16 3.85
3164 3232 4.668138 TTTGCCCTCCTATGTTTTAGGT 57.332 40.909 0.00 0.00 36.16 3.08
3165 3233 4.584743 GGATTTGCCCTCCTATGTTTTAGG 59.415 45.833 0.00 0.00 36.06 2.69
3166 3234 5.200483 TGGATTTGCCCTCCTATGTTTTAG 58.800 41.667 0.00 0.00 34.97 1.85
3167 3235 5.199982 TGGATTTGCCCTCCTATGTTTTA 57.800 39.130 0.00 0.00 34.97 1.52
3168 3236 4.059773 TGGATTTGCCCTCCTATGTTTT 57.940 40.909 0.00 0.00 34.97 2.43
3169 3237 3.756082 TGGATTTGCCCTCCTATGTTT 57.244 42.857 0.00 0.00 34.97 2.83
3170 3238 3.756082 TTGGATTTGCCCTCCTATGTT 57.244 42.857 0.00 0.00 34.97 2.71
3171 3239 3.269381 TCTTTGGATTTGCCCTCCTATGT 59.731 43.478 0.00 0.00 34.97 2.29
3172 3240 3.902218 TCTTTGGATTTGCCCTCCTATG 58.098 45.455 0.00 0.00 34.97 2.23
3173 3241 4.168675 TGATCTTTGGATTTGCCCTCCTAT 59.831 41.667 0.00 0.00 34.97 2.57
3174 3242 3.527253 TGATCTTTGGATTTGCCCTCCTA 59.473 43.478 0.00 0.00 34.97 2.94
3175 3243 2.312741 TGATCTTTGGATTTGCCCTCCT 59.687 45.455 0.00 0.00 34.97 3.69
3176 3244 2.738743 TGATCTTTGGATTTGCCCTCC 58.261 47.619 0.00 0.00 34.97 4.30
3177 3245 3.703052 ACATGATCTTTGGATTTGCCCTC 59.297 43.478 0.00 0.00 34.97 4.30
3178 3246 3.716431 ACATGATCTTTGGATTTGCCCT 58.284 40.909 0.00 0.00 34.97 5.19
3179 3247 4.186159 CAACATGATCTTTGGATTTGCCC 58.814 43.478 0.00 0.00 34.97 5.36
3180 3248 4.824289 ACAACATGATCTTTGGATTTGCC 58.176 39.130 0.00 0.00 31.46 4.52
3181 3249 5.472148 TGACAACATGATCTTTGGATTTGC 58.528 37.500 0.00 0.00 31.46 3.68
3182 3250 6.755141 GGATGACAACATGATCTTTGGATTTG 59.245 38.462 0.00 0.00 36.82 2.32
3183 3251 6.438108 TGGATGACAACATGATCTTTGGATTT 59.562 34.615 0.00 0.00 36.82 2.17
3184 3252 5.953548 TGGATGACAACATGATCTTTGGATT 59.046 36.000 0.00 0.00 36.82 3.01
3185 3253 5.512298 TGGATGACAACATGATCTTTGGAT 58.488 37.500 0.00 0.00 36.82 3.41
3186 3254 4.920999 TGGATGACAACATGATCTTTGGA 58.079 39.130 0.00 0.00 36.82 3.53
3187 3255 5.451381 CCATGGATGACAACATGATCTTTGG 60.451 44.000 19.43 0.00 45.55 3.28
3188 3256 5.126545 ACCATGGATGACAACATGATCTTTG 59.873 40.000 21.47 0.00 45.55 2.77
3189 3257 5.266788 ACCATGGATGACAACATGATCTTT 58.733 37.500 21.47 0.00 45.55 2.52
3190 3258 4.863548 ACCATGGATGACAACATGATCTT 58.136 39.130 21.47 0.00 45.55 2.40
3191 3259 4.515028 ACCATGGATGACAACATGATCT 57.485 40.909 21.47 4.66 45.55 2.75
3192 3260 5.125356 TGTACCATGGATGACAACATGATC 58.875 41.667 21.47 11.93 45.55 2.92
3193 3261 5.114764 TGTACCATGGATGACAACATGAT 57.885 39.130 21.47 9.45 45.55 2.45
3194 3262 4.566426 TGTACCATGGATGACAACATGA 57.434 40.909 21.47 3.88 45.55 3.07
3195 3263 5.641783 TTTGTACCATGGATGACAACATG 57.358 39.130 21.47 13.65 43.07 3.21
3196 3264 5.716228 ACATTTGTACCATGGATGACAACAT 59.284 36.000 21.47 15.95 39.67 2.71
3197 3265 5.076182 ACATTTGTACCATGGATGACAACA 58.924 37.500 21.47 14.68 31.78 3.33
3198 3266 5.393027 GGACATTTGTACCATGGATGACAAC 60.393 44.000 21.47 12.26 31.78 3.32
3199 3267 4.704540 GGACATTTGTACCATGGATGACAA 59.295 41.667 21.47 20.77 0.00 3.18
3200 3268 4.269183 GGACATTTGTACCATGGATGACA 58.731 43.478 21.47 16.10 0.00 3.58
3201 3269 4.900635 GGACATTTGTACCATGGATGAC 57.099 45.455 21.47 13.59 0.00 3.06
3211 3279 0.390735 ACGGCGAGGGACATTTGTAC 60.391 55.000 16.62 0.00 0.00 2.90
3212 3280 0.390603 CACGGCGAGGGACATTTGTA 60.391 55.000 16.62 0.00 0.00 2.41
3213 3281 1.671054 CACGGCGAGGGACATTTGT 60.671 57.895 16.62 0.00 0.00 2.83
3214 3282 2.398554 CCACGGCGAGGGACATTTG 61.399 63.158 16.62 0.00 0.00 2.32
3215 3283 2.046314 CCACGGCGAGGGACATTT 60.046 61.111 16.62 0.00 0.00 2.32
3216 3284 4.778143 GCCACGGCGAGGGACATT 62.778 66.667 24.39 0.00 0.00 2.71
3223 3291 4.473520 ATTGGAGGCCACGGCGAG 62.474 66.667 16.62 5.31 43.06 5.03
3224 3292 4.467084 GATTGGAGGCCACGGCGA 62.467 66.667 16.62 0.00 43.06 5.54
3226 3294 4.778143 ACGATTGGAGGCCACGGC 62.778 66.667 5.01 0.00 41.06 5.68
3227 3295 2.233605 TACACGATTGGAGGCCACGG 62.234 60.000 5.01 0.00 30.78 4.94
3228 3296 1.082117 GTACACGATTGGAGGCCACG 61.082 60.000 5.01 3.18 30.78 4.94
3229 3297 0.036765 TGTACACGATTGGAGGCCAC 60.037 55.000 5.01 0.00 30.78 5.01
3230 3298 0.036765 GTGTACACGATTGGAGGCCA 60.037 55.000 10.84 0.00 0.00 5.36
3231 3299 0.036765 TGTGTACACGATTGGAGGCC 60.037 55.000 20.61 0.00 0.00 5.19
3232 3300 1.076332 GTGTGTACACGATTGGAGGC 58.924 55.000 20.61 0.00 37.10 4.70
3242 3310 3.492011 CGGTTTTACAGAGGTGTGTACAC 59.508 47.826 19.36 19.36 45.72 2.90
3243 3311 3.384146 TCGGTTTTACAGAGGTGTGTACA 59.616 43.478 0.00 0.00 37.52 2.90
3244 3312 3.981211 TCGGTTTTACAGAGGTGTGTAC 58.019 45.455 0.00 0.00 37.52 2.90
3245 3313 4.525487 AGATCGGTTTTACAGAGGTGTGTA 59.475 41.667 0.00 0.00 37.52 2.90
3246 3314 3.323979 AGATCGGTTTTACAGAGGTGTGT 59.676 43.478 0.00 0.00 37.52 3.72
3247 3315 3.926616 AGATCGGTTTTACAGAGGTGTG 58.073 45.455 0.00 0.00 37.52 3.82
3248 3316 4.039973 TCAAGATCGGTTTTACAGAGGTGT 59.960 41.667 0.00 0.00 41.06 4.16
3249 3317 4.566004 TCAAGATCGGTTTTACAGAGGTG 58.434 43.478 0.00 0.00 0.00 4.00
3250 3318 4.884668 TCAAGATCGGTTTTACAGAGGT 57.115 40.909 0.00 0.00 0.00 3.85
3251 3319 6.109359 AGAATCAAGATCGGTTTTACAGAGG 58.891 40.000 0.00 0.00 0.00 3.69
3252 3320 6.256757 GGAGAATCAAGATCGGTTTTACAGAG 59.743 42.308 0.00 0.00 36.25 3.35
3253 3321 6.106673 GGAGAATCAAGATCGGTTTTACAGA 58.893 40.000 0.00 0.00 36.25 3.41
3254 3322 5.874810 TGGAGAATCAAGATCGGTTTTACAG 59.125 40.000 0.00 0.00 36.25 2.74
3255 3323 5.642063 GTGGAGAATCAAGATCGGTTTTACA 59.358 40.000 0.00 0.00 36.25 2.41
3256 3324 5.642063 TGTGGAGAATCAAGATCGGTTTTAC 59.358 40.000 0.00 0.00 36.25 2.01
3257 3325 5.642063 GTGTGGAGAATCAAGATCGGTTTTA 59.358 40.000 0.00 0.00 36.25 1.52
3258 3326 4.455877 GTGTGGAGAATCAAGATCGGTTTT 59.544 41.667 0.00 0.00 36.25 2.43
3259 3327 4.003648 GTGTGGAGAATCAAGATCGGTTT 58.996 43.478 0.00 0.00 36.25 3.27
3260 3328 3.600388 GTGTGGAGAATCAAGATCGGTT 58.400 45.455 0.00 0.00 36.25 4.44
3261 3329 2.417379 CGTGTGGAGAATCAAGATCGGT 60.417 50.000 0.00 0.00 36.25 4.69
3262 3330 2.196749 CGTGTGGAGAATCAAGATCGG 58.803 52.381 0.00 0.00 36.25 4.18
3263 3331 2.881074 ACGTGTGGAGAATCAAGATCG 58.119 47.619 0.00 0.00 36.25 3.69
3264 3332 3.997021 ACAACGTGTGGAGAATCAAGATC 59.003 43.478 0.00 0.00 36.25 2.75
3265 3333 4.008074 ACAACGTGTGGAGAATCAAGAT 57.992 40.909 0.00 0.00 36.25 2.40
3266 3334 3.469008 ACAACGTGTGGAGAATCAAGA 57.531 42.857 0.00 0.00 36.25 3.02
3267 3335 5.465390 TCTTTACAACGTGTGGAGAATCAAG 59.535 40.000 0.00 0.00 36.25 3.02
3268 3336 5.235616 GTCTTTACAACGTGTGGAGAATCAA 59.764 40.000 0.00 0.00 36.25 2.57
3269 3337 4.748102 GTCTTTACAACGTGTGGAGAATCA 59.252 41.667 0.00 0.00 36.25 2.57
3270 3338 4.143389 CGTCTTTACAACGTGTGGAGAATC 60.143 45.833 0.00 0.00 35.47 2.52
3271 3339 3.739300 CGTCTTTACAACGTGTGGAGAAT 59.261 43.478 0.00 0.00 35.47 2.40
3272 3340 3.117794 CGTCTTTACAACGTGTGGAGAA 58.882 45.455 0.00 0.00 35.47 2.87
3273 3341 2.358582 TCGTCTTTACAACGTGTGGAGA 59.641 45.455 0.00 0.00 40.86 3.71
3274 3342 2.734670 TCGTCTTTACAACGTGTGGAG 58.265 47.619 0.00 0.00 40.86 3.86
3275 3343 2.867287 TCGTCTTTACAACGTGTGGA 57.133 45.000 0.00 0.00 40.86 4.02
3276 3344 3.054166 TGATCGTCTTTACAACGTGTGG 58.946 45.455 0.00 0.00 40.86 4.17
3277 3345 4.903638 ATGATCGTCTTTACAACGTGTG 57.096 40.909 0.00 0.00 40.86 3.82


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

AutoCloner maintained by Alex Coulton.