Multiple sequence alignment - TraesCS2D01G323000

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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 TraesCS2D01G323000 chr2D 100.000 3289 0 0 1 3289 414957462 414954174 0.000000e+00 6074
1 TraesCS2D01G323000 chr2D 88.774 677 44 13 12 677 416390695 416390040 0.000000e+00 800
2 TraesCS2D01G323000 chr2D 90.253 277 20 4 976 1251 414961972 414961702 4.040000e-94 355
3 TraesCS2D01G323000 chr2D 88.506 261 11 6 784 1042 414962214 414961971 6.900000e-77 298
4 TraesCS2D01G323000 chr2A 95.553 2901 89 21 1 2875 581943519 581940633 0.000000e+00 4606
5 TraesCS2D01G323000 chr2A 91.361 463 31 6 792 1251 581962962 581962506 2.790000e-175 625
6 TraesCS2D01G323000 chr2B 94.978 2728 66 29 157 2833 488194090 488191383 0.000000e+00 4213
7 TraesCS2D01G323000 chr2B 85.878 262 19 9 2686 2944 488046117 488045871 2.520000e-66 263
8 TraesCS2D01G323000 chr2B 98.496 133 2 0 1 133 488194213 488194081 5.490000e-58 235
9 TraesCS2D01G323000 chr5A 83.224 459 74 2 973 1428 663306145 663305687 5.080000e-113 418
10 TraesCS2D01G323000 chr4D 83.224 459 74 2 973 1428 483138748 483138290 5.080000e-113 418
11 TraesCS2D01G323000 chr4D 91.450 269 18 5 3024 3289 277433216 277432950 6.710000e-97 364
12 TraesCS2D01G323000 chr4B 83.224 459 74 2 973 1428 613376186 613375728 5.080000e-113 418
13 TraesCS2D01G323000 chr3D 91.353 266 21 2 3026 3289 109742624 109742889 2.410000e-96 363
14 TraesCS2D01G323000 chr3D 90.909 264 20 4 3028 3289 73451725 73451464 5.220000e-93 351
15 TraesCS2D01G323000 chr6D 90.909 264 22 2 3028 3289 19824265 19824528 1.450000e-93 353
16 TraesCS2D01G323000 chr6D 90.530 264 23 2 3028 3289 368068451 368068714 6.750000e-92 348
17 TraesCS2D01G323000 chr7D 90.909 264 21 3 3028 3289 10959655 10959393 5.220000e-93 351
18 TraesCS2D01G323000 chr7D 90.530 264 22 3 3028 3289 47502473 47502211 2.430000e-91 346
19 TraesCS2D01G323000 chr7D 90.262 267 23 2 3025 3289 91555710 91555975 2.430000e-91 346
20 TraesCS2D01G323000 chr1D 90.299 268 23 3 3024 3289 491692371 491692105 6.750000e-92 348


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 TraesCS2D01G323000 chr2D 414954174 414957462 3288 True 6074.0 6074 100.0000 1 3289 1 chr2D.!!$R1 3288
1 TraesCS2D01G323000 chr2D 416390040 416390695 655 True 800.0 800 88.7740 12 677 1 chr2D.!!$R2 665
2 TraesCS2D01G323000 chr2D 414961702 414962214 512 True 326.5 355 89.3795 784 1251 2 chr2D.!!$R3 467
3 TraesCS2D01G323000 chr2A 581940633 581943519 2886 True 4606.0 4606 95.5530 1 2875 1 chr2A.!!$R1 2874
4 TraesCS2D01G323000 chr2B 488191383 488194213 2830 True 2224.0 4213 96.7370 1 2833 2 chr2B.!!$R2 2832

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
904 933 0.242017 GTCACTTCACAGGGCAATGC 59.758 55.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2446 0.107654 GCCACTCCAGGTATGTCCAC 60.108 60.0 0.0 0.0 39.02 4.02 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
212 219 2.039613 TGGTCTGTGCATTGTATGGTCA 59.960 45.455 0.00 0.00 0.00 4.02
260 267 5.463392 CCATATATTCTTGACCACTCACACG 59.537 44.000 0.00 0.00 0.00 4.49
373 384 6.324770 TCTCTAAGTAGTTCATGCCATCATCA 59.675 38.462 0.00 0.00 0.00 3.07
374 385 7.015974 TCTCTAAGTAGTTCATGCCATCATCAT 59.984 37.037 0.00 0.00 0.00 2.45
375 386 7.157347 TCTAAGTAGTTCATGCCATCATCATC 58.843 38.462 0.00 0.00 0.00 2.92
413 429 6.478016 CAGATCGCAATCTCTTATCTTGTGAA 59.522 38.462 2.37 0.00 40.38 3.18
513 529 5.700373 TGTGCTCCCTTAAATTTTGCAATTC 59.300 36.000 0.00 0.00 30.80 2.17
674 700 2.972625 TCAGAACCTGGCAAACGATAG 58.027 47.619 0.00 0.00 35.23 2.08
675 701 2.301870 TCAGAACCTGGCAAACGATAGT 59.698 45.455 0.00 0.00 41.41 2.12
676 702 3.512329 TCAGAACCTGGCAAACGATAGTA 59.488 43.478 0.00 0.00 39.56 1.82
677 703 4.619863 TCAGAACCTGGCAAACGATAGTAC 60.620 45.833 0.00 0.00 39.56 2.73
903 932 1.808945 GAGTCACTTCACAGGGCAATG 59.191 52.381 0.00 0.00 0.00 2.82
904 933 0.242017 GTCACTTCACAGGGCAATGC 59.758 55.000 0.00 0.00 0.00 3.56
1020 1049 0.038618 TGACCTTGACCATGTCGTCG 60.039 55.000 0.00 0.00 34.95 5.12
1269 1360 1.607467 CTTGCCCTTGAGGTTGGGG 60.607 63.158 0.00 0.00 43.53 4.96
1433 1524 0.179023 TTGATGATGCCTGCGCCATA 60.179 50.000 4.18 0.00 0.00 2.74
2305 2411 1.584175 TAACCGTGCGTGACAAACAT 58.416 45.000 0.00 0.00 0.00 2.71
2340 2446 0.523968 CGCAAGCATGGAATGGAACG 60.524 55.000 0.00 0.00 46.86 3.95
2627 2736 5.276584 CGATATGTGGCTTTTCTCTTCTTCG 60.277 44.000 0.00 0.00 0.00 3.79
2646 2755 2.105821 TCGTTCATGTGACCCTTCCTTT 59.894 45.455 0.00 0.00 0.00 3.11
2668 2777 3.006752 TGTCATGTGCCTGATCGCATATA 59.993 43.478 4.88 0.00 38.38 0.86
2669 2778 3.615937 GTCATGTGCCTGATCGCATATAG 59.384 47.826 4.88 1.93 38.38 1.31
2672 2781 4.071961 TGTGCCTGATCGCATATAGTTT 57.928 40.909 0.00 0.00 41.70 2.66
2673 2782 4.058124 TGTGCCTGATCGCATATAGTTTC 58.942 43.478 0.00 0.00 41.70 2.78
2674 2783 3.433615 GTGCCTGATCGCATATAGTTTCC 59.566 47.826 0.00 0.00 41.70 3.13
2679 2788 6.238759 GCCTGATCGCATATAGTTTCCTTTTT 60.239 38.462 0.00 0.00 0.00 1.94
2714 2849 8.686397 TGTGATTATTTGTTGCAATGTACATC 57.314 30.769 9.23 0.00 0.00 3.06
2739 2874 6.441274 CATCCTGTATTGTTGATGTAATGCC 58.559 40.000 0.00 0.00 32.00 4.40
2834 2974 5.231991 GGTGACTCGACAAAGTTAAACGTTA 59.768 40.000 0.00 0.00 0.00 3.18
2849 2989 4.617253 AACGTTATGAGCTGGCCATATA 57.383 40.909 5.51 0.13 0.00 0.86
2855 2995 6.372659 CGTTATGAGCTGGCCATATAAAGATT 59.627 38.462 5.51 0.00 0.00 2.40
2864 3004 7.809806 GCTGGCCATATAAAGATTGTCAATAAC 59.190 37.037 5.51 0.00 0.00 1.89
2870 3010 4.939509 AAAGATTGTCAATAACGGGTCG 57.060 40.909 0.00 0.00 0.00 4.79
2875 3015 1.067425 TGTCAATAACGGGTCGTCAGG 60.067 52.381 0.00 0.00 39.99 3.86
2876 3016 1.203052 GTCAATAACGGGTCGTCAGGA 59.797 52.381 0.00 0.00 39.99 3.86
2877 3017 1.894466 TCAATAACGGGTCGTCAGGAA 59.106 47.619 0.00 0.00 39.99 3.36
2878 3018 2.094390 TCAATAACGGGTCGTCAGGAAG 60.094 50.000 0.00 0.00 39.99 3.46
2879 3019 0.175073 ATAACGGGTCGTCAGGAAGC 59.825 55.000 0.00 0.00 39.99 3.86
2880 3020 0.896940 TAACGGGTCGTCAGGAAGCT 60.897 55.000 0.00 0.00 39.99 3.74
2881 3021 2.125912 CGGGTCGTCAGGAAGCTG 60.126 66.667 0.00 0.00 0.00 4.24
2882 3022 2.636412 CGGGTCGTCAGGAAGCTGA 61.636 63.158 0.00 0.00 0.00 4.26
2883 3023 1.216710 GGGTCGTCAGGAAGCTGAG 59.783 63.158 0.00 0.00 33.58 3.35
2884 3024 1.216710 GGTCGTCAGGAAGCTGAGG 59.783 63.158 0.00 0.00 39.68 3.86
2885 3025 1.251527 GGTCGTCAGGAAGCTGAGGA 61.252 60.000 0.00 0.00 43.26 3.71
2886 3026 2.268022 TCGTCAGGAAGCTGAGGAC 58.732 57.895 0.00 0.00 41.46 3.85
2887 3027 0.251386 TCGTCAGGAAGCTGAGGACT 60.251 55.000 0.00 0.00 41.46 3.85
2888 3028 0.605589 CGTCAGGAAGCTGAGGACTT 59.394 55.000 0.00 0.00 40.46 3.01
2889 3029 1.403514 CGTCAGGAAGCTGAGGACTTC 60.404 57.143 0.00 0.00 42.30 3.01
2890 3030 1.899142 GTCAGGAAGCTGAGGACTTCT 59.101 52.381 3.76 0.00 42.58 2.85
2891 3031 1.898472 TCAGGAAGCTGAGGACTTCTG 59.102 52.381 3.76 0.00 42.58 3.02
2892 3032 1.898472 CAGGAAGCTGAGGACTTCTGA 59.102 52.381 3.76 0.00 42.58 3.27
2893 3033 2.301296 CAGGAAGCTGAGGACTTCTGAA 59.699 50.000 3.76 0.00 42.58 3.02
2894 3034 3.055240 CAGGAAGCTGAGGACTTCTGAAT 60.055 47.826 3.76 0.00 42.58 2.57
2895 3035 3.197549 AGGAAGCTGAGGACTTCTGAATC 59.802 47.826 3.76 0.00 42.58 2.52
2896 3036 3.055530 GGAAGCTGAGGACTTCTGAATCA 60.056 47.826 3.76 0.00 42.58 2.57
2897 3037 4.383989 GGAAGCTGAGGACTTCTGAATCAT 60.384 45.833 3.76 0.00 42.58 2.45
2898 3038 4.139859 AGCTGAGGACTTCTGAATCATG 57.860 45.455 0.00 0.00 0.00 3.07
2899 3039 3.118334 AGCTGAGGACTTCTGAATCATGG 60.118 47.826 0.00 0.00 0.00 3.66
2900 3040 3.204526 CTGAGGACTTCTGAATCATGGC 58.795 50.000 0.00 0.00 0.00 4.40
2901 3041 2.573009 TGAGGACTTCTGAATCATGGCA 59.427 45.455 0.00 0.00 0.00 4.92
2902 3042 3.204526 GAGGACTTCTGAATCATGGCAG 58.795 50.000 0.00 0.00 0.00 4.85
2903 3043 2.575279 AGGACTTCTGAATCATGGCAGT 59.425 45.455 0.00 0.00 33.90 4.40
2904 3044 3.009916 AGGACTTCTGAATCATGGCAGTT 59.990 43.478 0.00 0.00 33.90 3.16
2905 3045 3.128242 GGACTTCTGAATCATGGCAGTTG 59.872 47.826 0.00 0.00 33.90 3.16
2906 3046 4.005650 GACTTCTGAATCATGGCAGTTGA 58.994 43.478 0.00 0.00 33.90 3.18
2907 3047 4.401022 ACTTCTGAATCATGGCAGTTGAA 58.599 39.130 0.00 1.34 33.90 2.69
2908 3048 4.458295 ACTTCTGAATCATGGCAGTTGAAG 59.542 41.667 0.00 10.45 33.90 3.02
2909 3049 4.025040 TCTGAATCATGGCAGTTGAAGT 57.975 40.909 0.00 0.00 33.90 3.01
2910 3050 5.164620 TCTGAATCATGGCAGTTGAAGTA 57.835 39.130 0.00 0.00 33.90 2.24
2911 3051 5.559770 TCTGAATCATGGCAGTTGAAGTAA 58.440 37.500 0.00 0.00 33.90 2.24
2912 3052 6.003326 TCTGAATCATGGCAGTTGAAGTAAA 58.997 36.000 0.00 0.00 33.90 2.01
2913 3053 6.149973 TCTGAATCATGGCAGTTGAAGTAAAG 59.850 38.462 0.00 0.00 33.90 1.85
2914 3054 4.708726 ATCATGGCAGTTGAAGTAAAGC 57.291 40.909 0.00 0.00 0.00 3.51
2915 3055 2.819608 TCATGGCAGTTGAAGTAAAGCC 59.180 45.455 0.00 0.00 40.37 4.35
2916 3056 2.656947 TGGCAGTTGAAGTAAAGCCT 57.343 45.000 0.00 0.00 40.52 4.58
2917 3057 2.944129 TGGCAGTTGAAGTAAAGCCTT 58.056 42.857 0.00 0.00 40.52 4.35
2918 3058 3.295973 TGGCAGTTGAAGTAAAGCCTTT 58.704 40.909 0.00 0.00 40.52 3.11
2919 3059 3.704061 TGGCAGTTGAAGTAAAGCCTTTT 59.296 39.130 0.00 0.00 40.52 2.27
2920 3060 4.161377 TGGCAGTTGAAGTAAAGCCTTTTT 59.839 37.500 0.00 0.00 40.52 1.94
2921 3061 4.745125 GGCAGTTGAAGTAAAGCCTTTTTC 59.255 41.667 0.00 0.00 38.21 2.29
2922 3062 5.348164 GCAGTTGAAGTAAAGCCTTTTTCA 58.652 37.500 0.00 0.00 0.00 2.69
2923 3063 5.985530 GCAGTTGAAGTAAAGCCTTTTTCAT 59.014 36.000 5.41 0.00 0.00 2.57
2924 3064 6.479990 GCAGTTGAAGTAAAGCCTTTTTCATT 59.520 34.615 5.41 0.00 0.00 2.57
2925 3065 7.306807 GCAGTTGAAGTAAAGCCTTTTTCATTC 60.307 37.037 5.41 3.52 0.00 2.67
2926 3066 6.918022 AGTTGAAGTAAAGCCTTTTTCATTCG 59.082 34.615 5.41 0.00 0.00 3.34
2927 3067 5.219633 TGAAGTAAAGCCTTTTTCATTCGC 58.780 37.500 0.00 0.00 0.00 4.70
2928 3068 4.846779 AGTAAAGCCTTTTTCATTCGCA 57.153 36.364 0.00 0.00 0.00 5.10
2929 3069 5.195001 AGTAAAGCCTTTTTCATTCGCAA 57.805 34.783 0.00 0.00 0.00 4.85
2930 3070 5.596845 AGTAAAGCCTTTTTCATTCGCAAA 58.403 33.333 0.00 0.00 0.00 3.68
2931 3071 6.045955 AGTAAAGCCTTTTTCATTCGCAAAA 58.954 32.000 0.00 0.00 0.00 2.44
2932 3072 5.408204 AAAGCCTTTTTCATTCGCAAAAG 57.592 34.783 0.00 0.00 38.98 2.27
2940 3080 6.976636 TTTTCATTCGCAAAAGGAAAAAGT 57.023 29.167 15.05 0.00 35.30 2.66
2941 3081 8.480643 TTTTTCATTCGCAAAAGGAAAAAGTA 57.519 26.923 20.87 8.00 40.49 2.24
2942 3082 8.480643 TTTTCATTCGCAAAAGGAAAAAGTAA 57.519 26.923 15.05 0.00 35.30 2.24
2943 3083 8.480643 TTTCATTCGCAAAAGGAAAAAGTAAA 57.519 26.923 6.27 0.00 0.00 2.01
2944 3084 7.692908 TCATTCGCAAAAGGAAAAAGTAAAG 57.307 32.000 0.00 0.00 0.00 1.85
2945 3085 5.959652 TTCGCAAAAGGAAAAAGTAAAGC 57.040 34.783 0.00 0.00 0.00 3.51
2946 3086 4.364860 TCGCAAAAGGAAAAAGTAAAGCC 58.635 39.130 0.00 0.00 0.00 4.35
2947 3087 4.098807 TCGCAAAAGGAAAAAGTAAAGCCT 59.901 37.500 0.00 0.00 0.00 4.58
2948 3088 4.808895 CGCAAAAGGAAAAAGTAAAGCCTT 59.191 37.500 0.00 0.00 40.49 4.35
2953 3093 7.843490 AAAGGAAAAAGTAAAGCCTTTTCAC 57.157 32.000 0.00 0.00 44.20 3.18
2954 3094 5.914033 AGGAAAAAGTAAAGCCTTTTCACC 58.086 37.500 0.00 0.00 42.32 4.02
2955 3095 5.661312 AGGAAAAAGTAAAGCCTTTTCACCT 59.339 36.000 0.00 13.92 42.32 4.00
2956 3096 6.156256 AGGAAAAAGTAAAGCCTTTTCACCTT 59.844 34.615 0.00 0.00 42.32 3.50
2957 3097 6.821665 GGAAAAAGTAAAGCCTTTTCACCTTT 59.178 34.615 0.00 0.00 42.32 3.11
2958 3098 7.011109 GGAAAAAGTAAAGCCTTTTCACCTTTC 59.989 37.037 0.00 1.82 42.32 2.62
2959 3099 5.531122 AAGTAAAGCCTTTTCACCTTTCC 57.469 39.130 0.00 0.00 31.78 3.13
2960 3100 4.804597 AGTAAAGCCTTTTCACCTTTCCT 58.195 39.130 0.00 0.00 31.78 3.36
2961 3101 5.208890 AGTAAAGCCTTTTCACCTTTCCTT 58.791 37.500 0.00 0.00 31.78 3.36
2962 3102 4.406648 AAAGCCTTTTCACCTTTCCTTG 57.593 40.909 0.00 0.00 0.00 3.61
2963 3103 1.688735 AGCCTTTTCACCTTTCCTTGC 59.311 47.619 0.00 0.00 0.00 4.01
2964 3104 1.270305 GCCTTTTCACCTTTCCTTGCC 60.270 52.381 0.00 0.00 0.00 4.52
2965 3105 1.344438 CCTTTTCACCTTTCCTTGCCC 59.656 52.381 0.00 0.00 0.00 5.36
2966 3106 1.344438 CTTTTCACCTTTCCTTGCCCC 59.656 52.381 0.00 0.00 0.00 5.80
2967 3107 0.560688 TTTCACCTTTCCTTGCCCCT 59.439 50.000 0.00 0.00 0.00 4.79
2968 3108 0.178964 TTCACCTTTCCTTGCCCCTG 60.179 55.000 0.00 0.00 0.00 4.45
2969 3109 1.153756 CACCTTTCCTTGCCCCTGT 59.846 57.895 0.00 0.00 0.00 4.00
2970 3110 0.469892 CACCTTTCCTTGCCCCTGTT 60.470 55.000 0.00 0.00 0.00 3.16
2971 3111 0.178961 ACCTTTCCTTGCCCCTGTTC 60.179 55.000 0.00 0.00 0.00 3.18
2972 3112 0.113190 CCTTTCCTTGCCCCTGTTCT 59.887 55.000 0.00 0.00 0.00 3.01
2973 3113 1.539157 CTTTCCTTGCCCCTGTTCTC 58.461 55.000 0.00 0.00 0.00 2.87
2974 3114 1.074566 CTTTCCTTGCCCCTGTTCTCT 59.925 52.381 0.00 0.00 0.00 3.10
2975 3115 0.401738 TTCCTTGCCCCTGTTCTCTG 59.598 55.000 0.00 0.00 0.00 3.35
2976 3116 1.001641 CCTTGCCCCTGTTCTCTGG 60.002 63.158 0.00 0.00 0.00 3.86
2977 3117 1.676967 CTTGCCCCTGTTCTCTGGC 60.677 63.158 0.00 0.00 44.27 4.85
2979 3119 4.785453 GCCCCTGTTCTCTGGCGG 62.785 72.222 0.00 0.00 33.59 6.13
2980 3120 3.003173 CCCCTGTTCTCTGGCGGA 61.003 66.667 0.00 0.00 0.00 5.54
2981 3121 2.581354 CCCTGTTCTCTGGCGGAG 59.419 66.667 17.47 17.47 43.12 4.63
2985 3125 0.389166 CTGTTCTCTGGCGGAGACAC 60.389 60.000 25.28 23.00 34.89 3.67
2986 3126 1.444553 GTTCTCTGGCGGAGACACG 60.445 63.158 25.28 0.00 34.89 4.49
2987 3127 1.602605 TTCTCTGGCGGAGACACGA 60.603 57.895 25.28 8.45 34.89 4.35
2988 3128 1.587043 TTCTCTGGCGGAGACACGAG 61.587 60.000 25.28 0.00 34.89 4.18
2989 3129 3.057547 CTCTGGCGGAGACACGAGG 62.058 68.421 18.74 0.00 34.89 4.63
2990 3130 4.135153 CTGGCGGAGACACGAGGG 62.135 72.222 0.00 0.00 34.89 4.30
2993 3133 4.803426 GCGGAGACACGAGGGCTG 62.803 72.222 0.00 0.00 35.47 4.85
2994 3134 4.135153 CGGAGACACGAGGGCTGG 62.135 72.222 0.00 0.00 35.47 4.85
2995 3135 4.459089 GGAGACACGAGGGCTGGC 62.459 72.222 0.00 0.00 0.00 4.85
2996 3136 4.803426 GAGACACGAGGGCTGGCG 62.803 72.222 0.00 0.00 0.00 5.69
3012 3152 4.749310 CGCCGGCACTGCTCTCTT 62.749 66.667 28.98 0.00 36.07 2.85
3013 3153 2.817396 GCCGGCACTGCTCTCTTC 60.817 66.667 24.80 0.00 35.10 2.87
3014 3154 2.659016 CCGGCACTGCTCTCTTCA 59.341 61.111 0.00 0.00 0.00 3.02
3015 3155 1.447489 CCGGCACTGCTCTCTTCAG 60.447 63.158 0.00 0.00 37.56 3.02
3016 3156 2.099431 CGGCACTGCTCTCTTCAGC 61.099 63.158 0.00 0.00 40.13 4.26
3017 3157 1.296068 GGCACTGCTCTCTTCAGCT 59.704 57.895 0.00 0.00 40.39 4.24
3018 3158 0.740516 GGCACTGCTCTCTTCAGCTC 60.741 60.000 0.00 0.00 40.39 4.09
3019 3159 0.247185 GCACTGCTCTCTTCAGCTCT 59.753 55.000 0.00 0.00 40.39 4.09
3020 3160 1.999048 CACTGCTCTCTTCAGCTCTG 58.001 55.000 0.00 0.00 40.39 3.35
3021 3161 0.247185 ACTGCTCTCTTCAGCTCTGC 59.753 55.000 0.00 0.00 40.39 4.26
3022 3162 0.533491 CTGCTCTCTTCAGCTCTGCT 59.467 55.000 0.00 0.00 40.39 4.24
3023 3163 0.975135 TGCTCTCTTCAGCTCTGCTT 59.025 50.000 0.00 0.00 40.39 3.91
3024 3164 1.347050 TGCTCTCTTCAGCTCTGCTTT 59.653 47.619 0.00 0.00 40.39 3.51
3025 3165 2.224475 TGCTCTCTTCAGCTCTGCTTTT 60.224 45.455 0.00 0.00 40.39 2.27
3026 3166 2.813172 GCTCTCTTCAGCTCTGCTTTTT 59.187 45.455 0.00 0.00 36.40 1.94
3027 3167 3.999663 GCTCTCTTCAGCTCTGCTTTTTA 59.000 43.478 0.00 0.00 36.40 1.52
3028 3168 4.093261 GCTCTCTTCAGCTCTGCTTTTTAG 59.907 45.833 0.00 0.00 36.40 1.85
3029 3169 5.474578 TCTCTTCAGCTCTGCTTTTTAGA 57.525 39.130 0.00 0.00 36.40 2.10
3030 3170 5.477510 TCTCTTCAGCTCTGCTTTTTAGAG 58.522 41.667 0.00 0.00 43.54 2.43
3046 3186 3.143675 GAGCATCTTCAGCCGTTGA 57.856 52.632 0.00 0.00 0.00 3.18
3047 3187 0.723981 GAGCATCTTCAGCCGTTGAC 59.276 55.000 0.00 0.00 34.94 3.18
3048 3188 0.322975 AGCATCTTCAGCCGTTGACT 59.677 50.000 0.00 0.00 34.94 3.41
3049 3189 0.723981 GCATCTTCAGCCGTTGACTC 59.276 55.000 0.00 0.00 34.94 3.36
3050 3190 1.363744 CATCTTCAGCCGTTGACTCC 58.636 55.000 0.00 0.00 34.94 3.85
3051 3191 0.250513 ATCTTCAGCCGTTGACTCCC 59.749 55.000 0.00 0.00 34.94 4.30
3052 3192 1.376037 CTTCAGCCGTTGACTCCCC 60.376 63.158 0.00 0.00 34.94 4.81
3053 3193 2.111999 CTTCAGCCGTTGACTCCCCA 62.112 60.000 0.00 0.00 34.94 4.96
3054 3194 2.046892 CAGCCGTTGACTCCCCAG 60.047 66.667 0.00 0.00 0.00 4.45
3055 3195 3.322466 AGCCGTTGACTCCCCAGG 61.322 66.667 0.00 0.00 0.00 4.45
3056 3196 3.319198 GCCGTTGACTCCCCAGGA 61.319 66.667 0.00 0.00 0.00 3.86
3057 3197 2.663196 CCGTTGACTCCCCAGGAC 59.337 66.667 0.00 0.00 0.00 3.85
3058 3198 2.261671 CGTTGACTCCCCAGGACG 59.738 66.667 0.00 0.00 0.00 4.79
3059 3199 2.047179 GTTGACTCCCCAGGACGC 60.047 66.667 0.00 0.00 0.00 5.19
3060 3200 2.525629 TTGACTCCCCAGGACGCA 60.526 61.111 0.00 0.00 0.00 5.24
3061 3201 1.918293 TTGACTCCCCAGGACGCAT 60.918 57.895 0.00 0.00 0.00 4.73
3062 3202 0.616395 TTGACTCCCCAGGACGCATA 60.616 55.000 0.00 0.00 0.00 3.14
3063 3203 0.616395 TGACTCCCCAGGACGCATAA 60.616 55.000 0.00 0.00 0.00 1.90
3064 3204 0.539986 GACTCCCCAGGACGCATAAA 59.460 55.000 0.00 0.00 0.00 1.40
3065 3205 0.988832 ACTCCCCAGGACGCATAAAA 59.011 50.000 0.00 0.00 0.00 1.52
3066 3206 1.353022 ACTCCCCAGGACGCATAAAAA 59.647 47.619 0.00 0.00 0.00 1.94
3067 3207 2.025321 ACTCCCCAGGACGCATAAAAAT 60.025 45.455 0.00 0.00 0.00 1.82
3068 3208 2.618709 CTCCCCAGGACGCATAAAAATC 59.381 50.000 0.00 0.00 0.00 2.17
3069 3209 1.333619 CCCCAGGACGCATAAAAATCG 59.666 52.381 0.00 0.00 0.00 3.34
3070 3210 1.268539 CCCAGGACGCATAAAAATCGC 60.269 52.381 0.00 0.00 0.00 4.58
3071 3211 1.268539 CCAGGACGCATAAAAATCGCC 60.269 52.381 0.00 0.00 0.00 5.54
3072 3212 1.021968 AGGACGCATAAAAATCGCCC 58.978 50.000 0.00 0.00 0.00 6.13
3073 3213 0.030235 GGACGCATAAAAATCGCCCC 59.970 55.000 0.00 0.00 0.00 5.80
3074 3214 1.021968 GACGCATAAAAATCGCCCCT 58.978 50.000 0.00 0.00 0.00 4.79
3075 3215 0.738389 ACGCATAAAAATCGCCCCTG 59.262 50.000 0.00 0.00 0.00 4.45
3076 3216 0.030638 CGCATAAAAATCGCCCCTGG 59.969 55.000 0.00 0.00 0.00 4.45
3077 3217 0.389025 GCATAAAAATCGCCCCTGGG 59.611 55.000 5.50 5.50 38.57 4.45
3094 3234 4.884257 GGCGAGCCGGCGATACAA 62.884 66.667 23.20 0.00 43.33 2.41
3095 3235 2.661866 GCGAGCCGGCGATACAAT 60.662 61.111 23.20 0.00 0.00 2.71
3096 3236 2.658707 GCGAGCCGGCGATACAATC 61.659 63.158 23.20 10.39 0.00 2.67
3105 3245 4.750460 GATACAATCGGCGCTGGA 57.250 55.556 17.88 10.44 0.00 3.86
3106 3246 2.522060 GATACAATCGGCGCTGGAG 58.478 57.895 17.88 9.11 0.00 3.86
3107 3247 0.946221 GATACAATCGGCGCTGGAGG 60.946 60.000 17.88 8.36 0.00 4.30
3108 3248 2.996168 ATACAATCGGCGCTGGAGGC 62.996 60.000 17.88 0.00 37.64 4.70
3117 3257 3.712907 GCTGGAGGCGGTTGGGTA 61.713 66.667 0.00 0.00 0.00 3.69
3118 3258 3.043999 GCTGGAGGCGGTTGGGTAT 62.044 63.158 0.00 0.00 0.00 2.73
3119 3259 1.146263 CTGGAGGCGGTTGGGTATC 59.854 63.158 0.00 0.00 0.00 2.24
3120 3260 2.325393 CTGGAGGCGGTTGGGTATCC 62.325 65.000 0.00 0.00 0.00 2.59
3121 3261 2.372074 GGAGGCGGTTGGGTATCCA 61.372 63.158 0.00 0.00 42.25 3.41
3131 3271 2.202974 GGTATCCAACCGTCGCCC 60.203 66.667 0.00 0.00 38.88 6.13
3132 3272 2.202974 GTATCCAACCGTCGCCCC 60.203 66.667 0.00 0.00 0.00 5.80
3133 3273 3.472726 TATCCAACCGTCGCCCCC 61.473 66.667 0.00 0.00 0.00 5.40
3146 3286 3.250847 CCCCCAGGCACCGATATT 58.749 61.111 0.00 0.00 0.00 1.28
3147 3287 1.228245 CCCCCAGGCACCGATATTG 60.228 63.158 0.00 0.00 0.00 1.90
3148 3288 1.898574 CCCCAGGCACCGATATTGC 60.899 63.158 0.00 0.00 39.41 3.56
3156 3296 3.715628 GCACCGATATTGCCTCATTTT 57.284 42.857 0.00 0.00 33.58 1.82
3157 3297 4.045636 GCACCGATATTGCCTCATTTTT 57.954 40.909 0.00 0.00 33.58 1.94
3158 3298 4.044426 GCACCGATATTGCCTCATTTTTC 58.956 43.478 0.00 0.00 33.58 2.29
3159 3299 4.282068 CACCGATATTGCCTCATTTTTCG 58.718 43.478 0.00 0.00 0.00 3.46
3160 3300 3.315191 ACCGATATTGCCTCATTTTTCGG 59.685 43.478 6.49 6.49 42.01 4.30
3161 3301 3.300009 CGATATTGCCTCATTTTTCGGC 58.700 45.455 0.00 0.00 44.02 5.54
3162 3302 3.642705 GATATTGCCTCATTTTTCGGCC 58.357 45.455 0.00 0.00 43.12 6.13
3163 3303 0.536724 ATTGCCTCATTTTTCGGCCC 59.463 50.000 0.00 0.00 43.12 5.80
3164 3304 0.829602 TTGCCTCATTTTTCGGCCCA 60.830 50.000 0.00 0.00 43.12 5.36
3165 3305 1.215382 GCCTCATTTTTCGGCCCAC 59.785 57.895 0.00 0.00 37.86 4.61
3166 3306 1.250840 GCCTCATTTTTCGGCCCACT 61.251 55.000 0.00 0.00 37.86 4.00
3167 3307 1.256812 CCTCATTTTTCGGCCCACTT 58.743 50.000 0.00 0.00 0.00 3.16
3168 3308 1.618343 CCTCATTTTTCGGCCCACTTT 59.382 47.619 0.00 0.00 0.00 2.66
3169 3309 2.352715 CCTCATTTTTCGGCCCACTTTC 60.353 50.000 0.00 0.00 0.00 2.62
3170 3310 1.268352 TCATTTTTCGGCCCACTTTCG 59.732 47.619 0.00 0.00 0.00 3.46
3171 3311 0.601057 ATTTTTCGGCCCACTTTCGG 59.399 50.000 0.00 0.00 0.00 4.30
3172 3312 2.077821 TTTTTCGGCCCACTTTCGGC 62.078 55.000 0.00 0.00 46.29 5.54
3177 3317 4.211986 GCCCACTTTCGGCGAATA 57.788 55.556 24.33 13.02 36.47 1.75
3178 3318 2.473457 GCCCACTTTCGGCGAATAA 58.527 52.632 24.33 8.61 36.47 1.40
3179 3319 0.806241 GCCCACTTTCGGCGAATAAA 59.194 50.000 24.33 7.81 36.47 1.40
3180 3320 1.202143 GCCCACTTTCGGCGAATAAAG 60.202 52.381 24.33 19.59 36.47 1.85
3181 3321 1.400494 CCCACTTTCGGCGAATAAAGG 59.600 52.381 24.33 20.51 37.09 3.11
3182 3322 1.400494 CCACTTTCGGCGAATAAAGGG 59.600 52.381 24.33 18.34 37.09 3.95
3183 3323 1.092348 ACTTTCGGCGAATAAAGGGC 58.908 50.000 24.33 0.00 37.09 5.19
3184 3324 0.380733 CTTTCGGCGAATAAAGGGCC 59.619 55.000 24.33 0.00 43.42 5.80
3185 3325 1.033202 TTTCGGCGAATAAAGGGCCC 61.033 55.000 24.33 16.46 43.99 5.80
3186 3326 2.124487 CGGCGAATAAAGGGCCCA 60.124 61.111 27.56 2.74 43.99 5.36
3187 3327 1.528309 CGGCGAATAAAGGGCCCAT 60.528 57.895 27.56 10.06 43.99 4.00
3188 3328 0.250553 CGGCGAATAAAGGGCCCATA 60.251 55.000 27.56 17.50 43.99 2.74
3189 3329 1.613255 CGGCGAATAAAGGGCCCATAT 60.613 52.381 27.56 19.09 43.99 1.78
3190 3330 1.818674 GGCGAATAAAGGGCCCATATG 59.181 52.381 27.56 11.89 41.01 1.78
3191 3331 1.818674 GCGAATAAAGGGCCCATATGG 59.181 52.381 27.56 15.41 37.09 2.74
3220 3360 2.590575 CCCATATTCGGCGCGGTT 60.591 61.111 15.06 6.63 0.00 4.44
3221 3361 2.604174 CCCATATTCGGCGCGGTTC 61.604 63.158 15.06 0.00 0.00 3.62
3222 3362 2.544359 CATATTCGGCGCGGTTCG 59.456 61.111 15.06 6.13 42.12 3.95
3223 3363 2.105528 ATATTCGGCGCGGTTCGT 59.894 55.556 15.06 2.64 41.07 3.85
3224 3364 1.947642 ATATTCGGCGCGGTTCGTC 60.948 57.895 15.06 0.00 41.07 4.20
3231 3371 3.759828 CGCGGTTCGTCGTGGTTC 61.760 66.667 0.00 0.00 37.05 3.62
3232 3372 3.759828 GCGGTTCGTCGTGGTTCG 61.760 66.667 0.00 0.00 41.41 3.95
3233 3373 3.101428 CGGTTCGTCGTGGTTCGG 61.101 66.667 0.00 0.00 40.32 4.30
3234 3374 3.408851 GGTTCGTCGTGGTTCGGC 61.409 66.667 0.00 0.00 41.11 5.54
3239 3379 2.659244 GTCGTGGTTCGGCGTTCA 60.659 61.111 6.85 0.79 40.32 3.18
3240 3380 2.106534 TCGTGGTTCGGCGTTCAA 59.893 55.556 6.85 0.00 40.32 2.69
3241 3381 1.301087 TCGTGGTTCGGCGTTCAAT 60.301 52.632 6.85 0.00 40.32 2.57
3242 3382 0.881159 TCGTGGTTCGGCGTTCAATT 60.881 50.000 6.85 0.00 40.32 2.32
3243 3383 0.791422 CGTGGTTCGGCGTTCAATTA 59.209 50.000 6.85 0.00 35.71 1.40
3244 3384 1.395608 CGTGGTTCGGCGTTCAATTAT 59.604 47.619 6.85 0.00 35.71 1.28
3245 3385 2.536130 CGTGGTTCGGCGTTCAATTATC 60.536 50.000 6.85 0.00 35.71 1.75
3246 3386 2.417239 GTGGTTCGGCGTTCAATTATCA 59.583 45.455 6.85 0.00 0.00 2.15
3247 3387 3.075148 TGGTTCGGCGTTCAATTATCAA 58.925 40.909 6.85 0.00 0.00 2.57
3248 3388 3.120130 TGGTTCGGCGTTCAATTATCAAC 60.120 43.478 6.85 0.00 0.00 3.18
3249 3389 3.120130 GGTTCGGCGTTCAATTATCAACA 60.120 43.478 6.85 0.00 0.00 3.33
3250 3390 4.438200 GGTTCGGCGTTCAATTATCAACAT 60.438 41.667 6.85 0.00 0.00 2.71
3251 3391 5.220700 GGTTCGGCGTTCAATTATCAACATA 60.221 40.000 6.85 0.00 0.00 2.29
3252 3392 6.252281 GTTCGGCGTTCAATTATCAACATAA 58.748 36.000 6.85 0.00 0.00 1.90
3253 3393 6.424176 TCGGCGTTCAATTATCAACATAAA 57.576 33.333 6.85 0.00 0.00 1.40
3254 3394 7.022055 TCGGCGTTCAATTATCAACATAAAT 57.978 32.000 6.85 0.00 0.00 1.40
3255 3395 8.144155 TCGGCGTTCAATTATCAACATAAATA 57.856 30.769 6.85 0.00 0.00 1.40
3256 3396 8.779303 TCGGCGTTCAATTATCAACATAAATAT 58.221 29.630 6.85 0.00 0.00 1.28
3257 3397 9.393249 CGGCGTTCAATTATCAACATAAATATT 57.607 29.630 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
212 219 7.951806 TGGAAATCATGAGGGATAAATATTGCT 59.048 33.333 0.09 0.00 0.00 3.91
260 267 1.246056 TGCTTGGTGCCAATCAGAGC 61.246 55.000 3.91 4.66 42.00 4.09
373 384 1.689273 GATCTGCGAACCTAGGTGGAT 59.311 52.381 17.14 13.58 39.71 3.41
374 385 1.112113 GATCTGCGAACCTAGGTGGA 58.888 55.000 17.14 4.00 39.71 4.02
375 386 0.249073 CGATCTGCGAACCTAGGTGG 60.249 60.000 17.14 12.06 44.57 4.61
413 429 9.685276 TTATCAGAGTTATCCACACAAATTGAT 57.315 29.630 0.00 0.00 0.00 2.57
674 700 7.044901 CGCTGTGCATCTGTAATATATACGTAC 60.045 40.741 0.00 0.00 0.00 3.67
675 701 6.964934 CGCTGTGCATCTGTAATATATACGTA 59.035 38.462 0.00 0.00 0.00 3.57
676 702 5.800438 CGCTGTGCATCTGTAATATATACGT 59.200 40.000 0.00 0.00 0.00 3.57
677 703 5.800438 ACGCTGTGCATCTGTAATATATACG 59.200 40.000 0.00 0.00 0.00 3.06
1020 1049 2.487532 GCTCAGCATGGTCATGGGC 61.488 63.158 12.23 0.00 39.16 5.36
1073 1163 1.154263 CTCGTGTCCGTCGACTTCC 60.154 63.158 14.70 1.12 39.94 3.46
1368 1459 4.753662 ACCGGCGACCAGAGGCTA 62.754 66.667 9.30 0.00 0.00 3.93
1476 1567 2.099405 CCCTCTGTCTCTCAAGTCTCC 58.901 57.143 0.00 0.00 0.00 3.71
2305 2411 1.334160 TGCGTCCTACAGTTCTTCCA 58.666 50.000 0.00 0.00 0.00 3.53
2340 2446 0.107654 GCCACTCCAGGTATGTCCAC 60.108 60.000 0.00 0.00 39.02 4.02
2368 2477 3.785859 TCGCCCATGCTCTCCACC 61.786 66.667 0.00 0.00 34.43 4.61
2627 2736 3.222603 ACAAAGGAAGGGTCACATGAAC 58.777 45.455 0.00 0.00 0.00 3.18
2646 2755 1.296068 TGCGATCAGGCACATGACA 59.704 52.632 0.00 0.00 38.17 3.58
2682 2791 9.932699 CATTGCAACAAATAATCACAAAAGAAA 57.067 25.926 0.00 0.00 0.00 2.52
2714 2849 6.441274 GCATTACATCAACAATACAGGATGG 58.559 40.000 0.00 0.00 43.62 3.51
2739 2874 1.354040 GCAGAATATCCATCGAGCGG 58.646 55.000 0.00 0.00 0.00 5.52
2834 2974 5.638133 ACAATCTTTATATGGCCAGCTCAT 58.362 37.500 13.05 4.32 0.00 2.90
2849 2989 4.320870 ACGACCCGTTATTGACAATCTTT 58.679 39.130 3.36 0.00 36.35 2.52
2855 2995 1.067425 CCTGACGACCCGTTATTGACA 60.067 52.381 0.00 0.00 41.37 3.58
2864 3004 2.125912 CAGCTTCCTGACGACCCG 60.126 66.667 0.00 0.00 41.77 5.28
2870 3010 1.899142 AGAAGTCCTCAGCTTCCTGAC 59.101 52.381 0.00 0.00 42.98 3.51
2875 3015 4.199432 TGATTCAGAAGTCCTCAGCTTC 57.801 45.455 0.00 0.00 41.78 3.86
2876 3016 4.515361 CATGATTCAGAAGTCCTCAGCTT 58.485 43.478 0.00 0.00 0.00 3.74
2877 3017 3.118334 CCATGATTCAGAAGTCCTCAGCT 60.118 47.826 0.00 0.00 0.00 4.24
2878 3018 3.204526 CCATGATTCAGAAGTCCTCAGC 58.795 50.000 0.00 0.00 0.00 4.26
2879 3019 3.204526 GCCATGATTCAGAAGTCCTCAG 58.795 50.000 0.00 0.00 0.00 3.35
2880 3020 2.573009 TGCCATGATTCAGAAGTCCTCA 59.427 45.455 0.00 0.00 0.00 3.86
2881 3021 3.204526 CTGCCATGATTCAGAAGTCCTC 58.795 50.000 0.00 0.00 32.26 3.71
2882 3022 2.575279 ACTGCCATGATTCAGAAGTCCT 59.425 45.455 13.86 0.00 34.57 3.85
2883 3023 2.996631 ACTGCCATGATTCAGAAGTCC 58.003 47.619 13.86 0.00 34.57 3.85
2884 3024 4.005650 TCAACTGCCATGATTCAGAAGTC 58.994 43.478 13.86 0.00 34.57 3.01
2885 3025 4.025040 TCAACTGCCATGATTCAGAAGT 57.975 40.909 13.86 0.00 34.57 3.01
2886 3026 4.458295 ACTTCAACTGCCATGATTCAGAAG 59.542 41.667 13.86 11.96 34.57 2.85
2887 3027 4.401022 ACTTCAACTGCCATGATTCAGAA 58.599 39.130 13.86 0.00 34.57 3.02
2888 3028 4.025040 ACTTCAACTGCCATGATTCAGA 57.975 40.909 13.86 0.00 34.57 3.27
2889 3029 5.885230 TTACTTCAACTGCCATGATTCAG 57.115 39.130 0.00 1.01 36.45 3.02
2890 3030 5.335897 GCTTTACTTCAACTGCCATGATTCA 60.336 40.000 0.00 0.00 0.00 2.57
2891 3031 5.098211 GCTTTACTTCAACTGCCATGATTC 58.902 41.667 0.00 0.00 0.00 2.52
2892 3032 4.082026 GGCTTTACTTCAACTGCCATGATT 60.082 41.667 0.00 0.00 36.51 2.57
2893 3033 3.445096 GGCTTTACTTCAACTGCCATGAT 59.555 43.478 0.00 0.00 36.51 2.45
2894 3034 2.819608 GGCTTTACTTCAACTGCCATGA 59.180 45.455 0.00 0.00 36.51 3.07
2895 3035 2.821969 AGGCTTTACTTCAACTGCCATG 59.178 45.455 0.00 0.00 38.06 3.66
2896 3036 3.160679 AGGCTTTACTTCAACTGCCAT 57.839 42.857 0.00 0.00 38.06 4.40
2897 3037 2.656947 AGGCTTTACTTCAACTGCCA 57.343 45.000 0.00 0.00 38.06 4.92
2898 3038 4.322080 AAAAGGCTTTACTTCAACTGCC 57.678 40.909 13.77 0.00 36.66 4.85
2899 3039 5.348164 TGAAAAAGGCTTTACTTCAACTGC 58.652 37.500 19.58 0.83 0.00 4.40
2900 3040 7.096477 CGAATGAAAAAGGCTTTACTTCAACTG 60.096 37.037 23.52 15.06 0.00 3.16
2901 3041 6.918022 CGAATGAAAAAGGCTTTACTTCAACT 59.082 34.615 23.52 16.46 0.00 3.16
2902 3042 6.345803 GCGAATGAAAAAGGCTTTACTTCAAC 60.346 38.462 23.52 19.40 0.00 3.18
2903 3043 5.689961 GCGAATGAAAAAGGCTTTACTTCAA 59.310 36.000 23.52 12.25 0.00 2.69
2904 3044 5.219633 GCGAATGAAAAAGGCTTTACTTCA 58.780 37.500 22.50 22.50 0.00 3.02
2905 3045 5.219633 TGCGAATGAAAAAGGCTTTACTTC 58.780 37.500 13.77 14.28 0.00 3.01
2906 3046 5.195001 TGCGAATGAAAAAGGCTTTACTT 57.805 34.783 13.77 4.65 0.00 2.24
2907 3047 4.846779 TGCGAATGAAAAAGGCTTTACT 57.153 36.364 13.77 3.41 0.00 2.24
2908 3048 5.898630 TTTGCGAATGAAAAAGGCTTTAC 57.101 34.783 13.77 11.03 0.00 2.01
2909 3049 6.523676 CTTTTGCGAATGAAAAAGGCTTTA 57.476 33.333 13.77 0.00 44.07 1.85
2910 3050 5.408204 CTTTTGCGAATGAAAAAGGCTTT 57.592 34.783 6.68 6.68 44.07 3.51
2915 3055 7.463544 ACTTTTTCCTTTTGCGAATGAAAAAG 58.536 30.769 32.93 32.93 46.36 2.27
2916 3056 7.371126 ACTTTTTCCTTTTGCGAATGAAAAA 57.629 28.000 22.96 22.96 31.67 1.94
2917 3057 6.976636 ACTTTTTCCTTTTGCGAATGAAAA 57.023 29.167 15.50 15.50 0.00 2.29
2918 3058 8.480643 TTTACTTTTTCCTTTTGCGAATGAAA 57.519 26.923 7.48 7.48 0.00 2.69
2919 3059 7.254286 GCTTTACTTTTTCCTTTTGCGAATGAA 60.254 33.333 1.13 0.00 0.00 2.57
2920 3060 6.200097 GCTTTACTTTTTCCTTTTGCGAATGA 59.800 34.615 1.13 0.00 0.00 2.57
2921 3061 6.354858 GCTTTACTTTTTCCTTTTGCGAATG 58.645 36.000 0.00 0.00 0.00 2.67
2922 3062 5.465390 GGCTTTACTTTTTCCTTTTGCGAAT 59.535 36.000 0.00 0.00 0.00 3.34
2923 3063 4.806775 GGCTTTACTTTTTCCTTTTGCGAA 59.193 37.500 0.00 0.00 0.00 4.70
2924 3064 4.098807 AGGCTTTACTTTTTCCTTTTGCGA 59.901 37.500 0.00 0.00 0.00 5.10
2925 3065 4.368315 AGGCTTTACTTTTTCCTTTTGCG 58.632 39.130 0.00 0.00 0.00 4.85
2926 3066 6.677781 AAAGGCTTTACTTTTTCCTTTTGC 57.322 33.333 11.52 0.00 42.58 3.68
2936 3076 5.661312 AGGAAAGGTGAAAAGGCTTTACTTT 59.339 36.000 21.30 21.30 42.17 2.66
2937 3077 5.208890 AGGAAAGGTGAAAAGGCTTTACTT 58.791 37.500 13.77 12.09 0.00 2.24
2938 3078 4.804597 AGGAAAGGTGAAAAGGCTTTACT 58.195 39.130 13.77 6.74 0.00 2.24
2939 3079 5.289595 CAAGGAAAGGTGAAAAGGCTTTAC 58.710 41.667 13.77 8.61 0.00 2.01
2940 3080 4.202212 GCAAGGAAAGGTGAAAAGGCTTTA 60.202 41.667 13.77 0.00 0.00 1.85
2941 3081 3.432186 GCAAGGAAAGGTGAAAAGGCTTT 60.432 43.478 6.68 6.68 0.00 3.51
2942 3082 2.103094 GCAAGGAAAGGTGAAAAGGCTT 59.897 45.455 0.00 0.00 0.00 4.35
2943 3083 1.688735 GCAAGGAAAGGTGAAAAGGCT 59.311 47.619 0.00 0.00 0.00 4.58
2944 3084 1.270305 GGCAAGGAAAGGTGAAAAGGC 60.270 52.381 0.00 0.00 0.00 4.35
2945 3085 1.344438 GGGCAAGGAAAGGTGAAAAGG 59.656 52.381 0.00 0.00 0.00 3.11
2946 3086 1.344438 GGGGCAAGGAAAGGTGAAAAG 59.656 52.381 0.00 0.00 0.00 2.27
2947 3087 1.062505 AGGGGCAAGGAAAGGTGAAAA 60.063 47.619 0.00 0.00 0.00 2.29
2948 3088 0.560688 AGGGGCAAGGAAAGGTGAAA 59.439 50.000 0.00 0.00 0.00 2.69
2949 3089 0.178964 CAGGGGCAAGGAAAGGTGAA 60.179 55.000 0.00 0.00 0.00 3.18
2950 3090 1.360393 ACAGGGGCAAGGAAAGGTGA 61.360 55.000 0.00 0.00 0.00 4.02
2951 3091 0.469892 AACAGGGGCAAGGAAAGGTG 60.470 55.000 0.00 0.00 0.00 4.00
2952 3092 0.178961 GAACAGGGGCAAGGAAAGGT 60.179 55.000 0.00 0.00 0.00 3.50
2953 3093 0.113190 AGAACAGGGGCAAGGAAAGG 59.887 55.000 0.00 0.00 0.00 3.11
2954 3094 1.074566 AGAGAACAGGGGCAAGGAAAG 59.925 52.381 0.00 0.00 0.00 2.62
2955 3095 1.149101 AGAGAACAGGGGCAAGGAAA 58.851 50.000 0.00 0.00 0.00 3.13
2956 3096 0.401738 CAGAGAACAGGGGCAAGGAA 59.598 55.000 0.00 0.00 0.00 3.36
2957 3097 1.492133 CCAGAGAACAGGGGCAAGGA 61.492 60.000 0.00 0.00 0.00 3.36
2958 3098 1.001641 CCAGAGAACAGGGGCAAGG 60.002 63.158 0.00 0.00 0.00 3.61
2959 3099 1.676967 GCCAGAGAACAGGGGCAAG 60.677 63.158 0.00 0.00 45.70 4.01
2960 3100 2.436109 GCCAGAGAACAGGGGCAA 59.564 61.111 0.00 0.00 45.70 4.52
2961 3101 4.020617 CGCCAGAGAACAGGGGCA 62.021 66.667 0.00 0.00 46.75 5.36
2962 3102 4.785453 CCGCCAGAGAACAGGGGC 62.785 72.222 0.00 0.00 42.98 5.80
2963 3103 3.003173 TCCGCCAGAGAACAGGGG 61.003 66.667 0.00 0.00 35.87 4.79
2964 3104 2.581354 CTCCGCCAGAGAACAGGG 59.419 66.667 0.00 0.00 46.50 4.45
2971 3111 2.487428 CTCGTGTCTCCGCCAGAG 59.513 66.667 0.00 0.00 44.75 3.35
2972 3112 3.062466 CCTCGTGTCTCCGCCAGA 61.062 66.667 0.00 0.00 0.00 3.86
2973 3113 4.135153 CCCTCGTGTCTCCGCCAG 62.135 72.222 0.00 0.00 0.00 4.85
2976 3116 4.803426 CAGCCCTCGTGTCTCCGC 62.803 72.222 0.00 0.00 0.00 5.54
2977 3117 4.135153 CCAGCCCTCGTGTCTCCG 62.135 72.222 0.00 0.00 0.00 4.63
2978 3118 4.459089 GCCAGCCCTCGTGTCTCC 62.459 72.222 0.00 0.00 0.00 3.71
2979 3119 4.803426 CGCCAGCCCTCGTGTCTC 62.803 72.222 0.00 0.00 0.00 3.36
2995 3135 4.749310 AAGAGAGCAGTGCCGGCG 62.749 66.667 23.90 8.96 36.08 6.46
2996 3136 2.817396 GAAGAGAGCAGTGCCGGC 60.817 66.667 22.73 22.73 0.00 6.13
2997 3137 1.447489 CTGAAGAGAGCAGTGCCGG 60.447 63.158 12.58 0.00 0.00 6.13
2998 3138 2.099431 GCTGAAGAGAGCAGTGCCG 61.099 63.158 12.58 0.00 38.95 5.69
2999 3139 0.740516 GAGCTGAAGAGAGCAGTGCC 60.741 60.000 12.58 3.25 41.83 5.01
3000 3140 0.247185 AGAGCTGAAGAGAGCAGTGC 59.753 55.000 7.13 7.13 41.83 4.40
3001 3141 1.999048 CAGAGCTGAAGAGAGCAGTG 58.001 55.000 0.00 0.00 41.83 3.66
3002 3142 0.247185 GCAGAGCTGAAGAGAGCAGT 59.753 55.000 0.85 0.00 41.83 4.40
3003 3143 0.533491 AGCAGAGCTGAAGAGAGCAG 59.467 55.000 0.85 0.00 41.83 4.24
3004 3144 0.975135 AAGCAGAGCTGAAGAGAGCA 59.025 50.000 0.85 0.00 41.83 4.26
3005 3145 2.097680 AAAGCAGAGCTGAAGAGAGC 57.902 50.000 0.85 0.00 39.62 4.09
3006 3146 5.477510 TCTAAAAAGCAGAGCTGAAGAGAG 58.522 41.667 0.85 0.00 39.62 3.20
3007 3147 5.474578 TCTAAAAAGCAGAGCTGAAGAGA 57.525 39.130 0.85 0.00 39.62 3.10
3008 3148 5.783100 CTCTAAAAAGCAGAGCTGAAGAG 57.217 43.478 0.85 0.00 39.62 2.85
3020 3160 3.486542 CGGCTGAAGATGCTCTAAAAAGC 60.487 47.826 0.00 0.00 42.82 3.51
3021 3161 3.686726 ACGGCTGAAGATGCTCTAAAAAG 59.313 43.478 0.00 0.00 0.00 2.27
3022 3162 3.674997 ACGGCTGAAGATGCTCTAAAAA 58.325 40.909 0.00 0.00 0.00 1.94
3023 3163 3.334583 ACGGCTGAAGATGCTCTAAAA 57.665 42.857 0.00 0.00 0.00 1.52
3024 3164 3.002791 CAACGGCTGAAGATGCTCTAAA 58.997 45.455 0.00 0.00 0.00 1.85
3025 3165 2.233676 TCAACGGCTGAAGATGCTCTAA 59.766 45.455 0.00 0.00 0.00 2.10
3026 3166 1.824852 TCAACGGCTGAAGATGCTCTA 59.175 47.619 0.00 0.00 0.00 2.43
3027 3167 0.610174 TCAACGGCTGAAGATGCTCT 59.390 50.000 0.00 0.00 0.00 4.09
3028 3168 0.723981 GTCAACGGCTGAAGATGCTC 59.276 55.000 0.00 0.00 35.22 4.26
3029 3169 0.322975 AGTCAACGGCTGAAGATGCT 59.677 50.000 0.00 0.00 35.22 3.79
3030 3170 0.723981 GAGTCAACGGCTGAAGATGC 59.276 55.000 0.00 0.00 35.22 3.91
3031 3171 1.363744 GGAGTCAACGGCTGAAGATG 58.636 55.000 0.00 0.00 35.22 2.90
3032 3172 0.250513 GGGAGTCAACGGCTGAAGAT 59.749 55.000 0.00 0.00 35.22 2.40
3033 3173 1.671742 GGGAGTCAACGGCTGAAGA 59.328 57.895 0.00 0.00 35.22 2.87
3034 3174 1.376037 GGGGAGTCAACGGCTGAAG 60.376 63.158 0.00 0.00 35.22 3.02
3035 3175 2.111999 CTGGGGAGTCAACGGCTGAA 62.112 60.000 0.00 0.00 35.22 3.02
3036 3176 2.525629 TGGGGAGTCAACGGCTGA 60.526 61.111 0.00 0.00 0.00 4.26
3037 3177 2.046892 CTGGGGAGTCAACGGCTG 60.047 66.667 0.00 0.00 0.00 4.85
3038 3178 3.322466 CCTGGGGAGTCAACGGCT 61.322 66.667 0.00 0.00 0.00 5.52
3039 3179 3.319198 TCCTGGGGAGTCAACGGC 61.319 66.667 0.00 0.00 0.00 5.68
3040 3180 2.663196 GTCCTGGGGAGTCAACGG 59.337 66.667 0.00 0.00 29.39 4.44
3041 3181 2.261671 CGTCCTGGGGAGTCAACG 59.738 66.667 0.00 0.00 29.39 4.10
3042 3182 2.047179 GCGTCCTGGGGAGTCAAC 60.047 66.667 0.00 0.00 29.39 3.18
3043 3183 0.616395 TATGCGTCCTGGGGAGTCAA 60.616 55.000 0.00 0.00 29.39 3.18
3044 3184 0.616395 TTATGCGTCCTGGGGAGTCA 60.616 55.000 0.00 0.00 29.39 3.41
3045 3185 0.539986 TTTATGCGTCCTGGGGAGTC 59.460 55.000 0.00 0.00 29.39 3.36
3046 3186 0.988832 TTTTATGCGTCCTGGGGAGT 59.011 50.000 0.00 0.00 29.39 3.85
3047 3187 2.122783 TTTTTATGCGTCCTGGGGAG 57.877 50.000 0.00 0.00 29.39 4.30
3048 3188 2.650322 GATTTTTATGCGTCCTGGGGA 58.350 47.619 0.00 0.00 0.00 4.81
3049 3189 1.333619 CGATTTTTATGCGTCCTGGGG 59.666 52.381 0.00 0.00 0.00 4.96
3050 3190 1.268539 GCGATTTTTATGCGTCCTGGG 60.269 52.381 0.00 0.00 0.00 4.45
3051 3191 1.268539 GGCGATTTTTATGCGTCCTGG 60.269 52.381 0.00 0.00 0.00 4.45
3052 3192 1.268539 GGGCGATTTTTATGCGTCCTG 60.269 52.381 0.00 0.00 45.64 3.86
3053 3193 1.021968 GGGCGATTTTTATGCGTCCT 58.978 50.000 0.00 0.00 45.64 3.85
3054 3194 3.544615 GGGCGATTTTTATGCGTCC 57.455 52.632 0.00 0.00 42.93 4.79
3055 3195 1.021968 AGGGGCGATTTTTATGCGTC 58.978 50.000 0.00 0.00 0.00 5.19
3056 3196 0.738389 CAGGGGCGATTTTTATGCGT 59.262 50.000 0.00 0.00 0.00 5.24
3057 3197 0.030638 CCAGGGGCGATTTTTATGCG 59.969 55.000 0.00 0.00 0.00 4.73
3058 3198 0.389025 CCCAGGGGCGATTTTTATGC 59.611 55.000 0.00 0.00 0.00 3.14
3059 3199 1.039856 CCCCAGGGGCGATTTTTATG 58.960 55.000 13.35 0.00 35.35 1.90
3060 3200 3.531821 CCCCAGGGGCGATTTTTAT 57.468 52.632 13.35 0.00 35.35 1.40
3077 3217 4.884257 TTGTATCGCCGGCTCGCC 62.884 66.667 26.68 10.48 0.00 5.54
3078 3218 2.658707 GATTGTATCGCCGGCTCGC 61.659 63.158 26.68 12.33 0.00 5.03
3079 3219 2.365068 CGATTGTATCGCCGGCTCG 61.365 63.158 26.68 20.74 46.55 5.03
3080 3220 3.538841 CGATTGTATCGCCGGCTC 58.461 61.111 26.68 12.39 46.55 4.70
3088 3228 0.946221 CCTCCAGCGCCGATTGTATC 60.946 60.000 2.29 0.00 0.00 2.24
3089 3229 1.069765 CCTCCAGCGCCGATTGTAT 59.930 57.895 2.29 0.00 0.00 2.29
3090 3230 2.499205 CCTCCAGCGCCGATTGTA 59.501 61.111 2.29 0.00 0.00 2.41
3100 3240 2.942648 GATACCCAACCGCCTCCAGC 62.943 65.000 0.00 0.00 38.52 4.85
3101 3241 1.146263 GATACCCAACCGCCTCCAG 59.854 63.158 0.00 0.00 0.00 3.86
3102 3242 2.372074 GGATACCCAACCGCCTCCA 61.372 63.158 0.00 0.00 0.00 3.86
3103 3243 1.917336 TTGGATACCCAACCGCCTCC 61.917 60.000 0.00 0.00 46.94 4.30
3104 3244 1.605453 TTGGATACCCAACCGCCTC 59.395 57.895 0.00 0.00 46.94 4.70
3105 3245 3.829224 TTGGATACCCAACCGCCT 58.171 55.556 0.00 0.00 46.94 5.52
3112 3252 2.580276 GCGACGGTTGGATACCCA 59.420 61.111 0.00 0.00 44.70 4.51
3113 3253 2.202974 GGCGACGGTTGGATACCC 60.203 66.667 0.00 0.00 44.70 3.69
3114 3254 2.202974 GGGCGACGGTTGGATACC 60.203 66.667 0.00 0.00 44.03 2.73
3115 3255 2.202974 GGGGCGACGGTTGGATAC 60.203 66.667 0.00 0.00 0.00 2.24
3116 3256 3.472726 GGGGGCGACGGTTGGATA 61.473 66.667 0.00 0.00 0.00 2.59
3129 3269 1.228245 CAATATCGGTGCCTGGGGG 60.228 63.158 0.00 0.00 0.00 5.40
3130 3270 1.898574 GCAATATCGGTGCCTGGGG 60.899 63.158 0.00 0.00 35.91 4.96
3131 3271 3.749981 GCAATATCGGTGCCTGGG 58.250 61.111 0.00 0.00 35.91 4.45
3136 3276 3.715628 AAAATGAGGCAATATCGGTGC 57.284 42.857 0.00 0.00 41.45 5.01
3137 3277 4.282068 CGAAAAATGAGGCAATATCGGTG 58.718 43.478 0.00 0.00 0.00 4.94
3138 3278 3.315191 CCGAAAAATGAGGCAATATCGGT 59.685 43.478 0.00 0.00 42.58 4.69
3139 3279 3.888934 CCGAAAAATGAGGCAATATCGG 58.111 45.455 0.00 0.00 42.01 4.18
3148 3288 1.256812 AAGTGGGCCGAAAAATGAGG 58.743 50.000 0.00 0.00 0.00 3.86
3149 3289 2.668279 CGAAAGTGGGCCGAAAAATGAG 60.668 50.000 0.00 0.00 0.00 2.90
3150 3290 1.268352 CGAAAGTGGGCCGAAAAATGA 59.732 47.619 0.00 0.00 0.00 2.57
3151 3291 1.668628 CCGAAAGTGGGCCGAAAAATG 60.669 52.381 0.00 0.00 0.00 2.32
3152 3292 0.601057 CCGAAAGTGGGCCGAAAAAT 59.399 50.000 0.00 0.00 0.00 1.82
3153 3293 2.034607 CCGAAAGTGGGCCGAAAAA 58.965 52.632 0.00 0.00 0.00 1.94
3154 3294 2.557372 GCCGAAAGTGGGCCGAAAA 61.557 57.895 0.00 0.00 44.97 2.29
3155 3295 2.981350 GCCGAAAGTGGGCCGAAA 60.981 61.111 0.00 0.00 44.97 3.46
3161 3301 1.400494 CCTTTATTCGCCGAAAGTGGG 59.600 52.381 2.60 0.78 31.89 4.61
3162 3302 1.400494 CCCTTTATTCGCCGAAAGTGG 59.600 52.381 2.60 4.21 31.89 4.00
3163 3303 1.202143 GCCCTTTATTCGCCGAAAGTG 60.202 52.381 2.60 0.00 31.89 3.16
3164 3304 1.092348 GCCCTTTATTCGCCGAAAGT 58.908 50.000 2.60 0.00 31.89 2.66
3165 3305 0.380733 GGCCCTTTATTCGCCGAAAG 59.619 55.000 2.60 0.00 31.92 2.62
3166 3306 1.033202 GGGCCCTTTATTCGCCGAAA 61.033 55.000 17.04 0.00 43.99 3.46
3167 3307 1.452470 GGGCCCTTTATTCGCCGAA 60.452 57.895 17.04 0.33 43.99 4.30
3168 3308 1.990160 ATGGGCCCTTTATTCGCCGA 61.990 55.000 25.70 0.00 43.99 5.54
3169 3309 0.250553 TATGGGCCCTTTATTCGCCG 60.251 55.000 25.70 0.00 43.99 6.46
3170 3310 1.818674 CATATGGGCCCTTTATTCGCC 59.181 52.381 25.70 0.00 42.23 5.54
3171 3311 1.818674 CCATATGGGCCCTTTATTCGC 59.181 52.381 25.70 0.00 0.00 4.70
3184 3324 2.292267 GGCATATTCTCGCCCATATGG 58.708 52.381 15.41 15.41 42.82 2.74
3203 3343 2.590575 AACCGCGCCGAATATGGG 60.591 61.111 0.00 0.00 0.00 4.00
3204 3344 2.935955 GAACCGCGCCGAATATGG 59.064 61.111 0.00 0.00 0.00 2.74
3205 3345 2.142418 GACGAACCGCGCCGAATATG 62.142 60.000 17.85 0.00 46.04 1.78
3206 3346 1.947642 GACGAACCGCGCCGAATAT 60.948 57.895 17.85 0.00 46.04 1.28
3207 3347 2.580326 GACGAACCGCGCCGAATA 60.580 61.111 17.85 0.00 46.04 1.75
3215 3355 3.759828 CGAACCACGACGAACCGC 61.760 66.667 0.00 0.00 45.77 5.68
3216 3356 3.101428 CCGAACCACGACGAACCG 61.101 66.667 0.00 0.00 45.77 4.44
3217 3357 3.408851 GCCGAACCACGACGAACC 61.409 66.667 0.00 0.00 45.77 3.62
3222 3362 1.562575 ATTGAACGCCGAACCACGAC 61.563 55.000 0.00 0.00 45.77 4.34
3223 3363 0.881159 AATTGAACGCCGAACCACGA 60.881 50.000 0.00 0.00 45.77 4.35
3224 3364 0.791422 TAATTGAACGCCGAACCACG 59.209 50.000 0.00 0.00 42.18 4.94
3225 3365 2.417239 TGATAATTGAACGCCGAACCAC 59.583 45.455 0.00 0.00 0.00 4.16
3226 3366 2.701107 TGATAATTGAACGCCGAACCA 58.299 42.857 0.00 0.00 0.00 3.67
3227 3367 3.120130 TGTTGATAATTGAACGCCGAACC 60.120 43.478 0.00 0.00 0.00 3.62
3228 3368 4.073169 TGTTGATAATTGAACGCCGAAC 57.927 40.909 0.00 0.00 0.00 3.95
3229 3369 4.955925 ATGTTGATAATTGAACGCCGAA 57.044 36.364 0.00 0.00 0.00 4.30
3230 3370 6.424176 TTTATGTTGATAATTGAACGCCGA 57.576 33.333 0.00 0.00 0.00 5.54
3231 3371 8.948853 ATATTTATGTTGATAATTGAACGCCG 57.051 30.769 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.