Multiple sequence alignment - TraesCS6A01G150900

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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 TraesCS6A01G150900 chr6A 100.000 3625 0 0 1 3625 134950475 134946851 0.000000e+00 6695
1 TraesCS6A01G150900 chr6A 93.077 260 12 4 2935 3193 79971847 79971593 3.420000e-100 375
2 TraesCS6A01G150900 chr6D 91.917 2994 133 50 1 2937 110445725 110442784 0.000000e+00 4087
3 TraesCS6A01G150900 chr6D 90.949 453 33 6 3176 3625 110442786 110442339 1.440000e-168 603
4 TraesCS6A01G150900 chr6B 90.323 2821 122 61 4 2746 198987292 198984545 0.000000e+00 3557
5 TraesCS6A01G150900 chr6B 91.244 434 26 7 3200 3625 198983547 198983118 6.750000e-162 580
6 TraesCS6A01G150900 chr3B 96.266 241 8 1 2939 3178 742449919 742450159 9.430000e-106 394
7 TraesCS6A01G150900 chr2B 94.862 253 11 2 2939 3190 13745790 13745539 9.430000e-106 394
8 TraesCS6A01G150900 chr2B 87.234 188 17 6 2116 2298 530307294 530307479 1.320000e-49 207
9 TraesCS6A01G150900 chr2A 95.528 246 10 1 2935 3179 84977525 84977770 3.390000e-105 392
10 TraesCS6A01G150900 chr2A 89.091 165 13 5 2135 2296 594581072 594581234 2.210000e-47 200
11 TraesCS6A01G150900 chr1A 95.142 247 11 1 2936 3181 119951928 119951682 4.390000e-104 388
12 TraesCS6A01G150900 chr1A 95.473 243 10 1 2939 3180 150903052 150902810 1.580000e-103 387
13 TraesCS6A01G150900 chr1B 94.779 249 12 1 2939 3186 575885353 575885105 1.580000e-103 387
14 TraesCS6A01G150900 chr1D 92.776 263 15 4 2936 3195 16232237 16231976 9.500000e-101 377
15 TraesCS6A01G150900 chr3A 90.217 276 22 5 2905 3178 597327073 597327345 4.450000e-94 355
16 TraesCS6A01G150900 chr2D 87.234 188 17 7 2116 2298 450235629 450235814 1.320000e-49 207
17 TraesCS6A01G150900 chr7D 90.196 153 13 2 2129 2280 594729870 594729719 7.940000e-47 198
18 TraesCS6A01G150900 chr7A 87.500 176 17 3 2129 2300 686937954 686938128 7.940000e-47 198
19 TraesCS6A01G150900 chr7B 89.542 153 14 2 2129 2280 667070583 667070432 3.690000e-45 193


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 TraesCS6A01G150900 chr6A 134946851 134950475 3624 True 6695.0 6695 100.0000 1 3625 1 chr6A.!!$R2 3624
1 TraesCS6A01G150900 chr6D 110442339 110445725 3386 True 2345.0 4087 91.4330 1 3625 2 chr6D.!!$R1 3624
2 TraesCS6A01G150900 chr6B 198983118 198987292 4174 True 2068.5 3557 90.7835 4 3625 2 chr6B.!!$R1 3621

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
706 747 0.161870 GAAGCAGTTGTCGCGTCTTC 59.838 55.0 5.77 5.39 35.36 2.87 F
707 748 0.249489 AAGCAGTTGTCGCGTCTTCT 60.249 50.0 5.77 0.34 0.00 2.85 F
1807 1865 0.172578 TTACCCTCGCGTCATCTGTG 59.827 55.0 5.77 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 1827 0.252927 AGGTTCTTGGAGGAGAGGGG 60.253 60.0 0.00 0.0 0.00 4.79 R
2555 2662 1.523501 CGTGCGTGCATGTTGATTAC 58.476 50.0 7.93 0.0 0.00 1.89 R
3020 3135 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.0 0.00 0.0 34.43 6.53 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
95 100 1.708027 GAACGATCGTGAAAGGCGG 59.292 57.895 23.51 0.00 0.00 6.13
119 124 1.202348 GGCTTTTCTGACATTTCGGGG 59.798 52.381 0.00 0.00 0.00 5.73
120 125 1.202348 GCTTTTCTGACATTTCGGGGG 59.798 52.381 0.00 0.00 0.00 5.40
281 286 1.105759 CCCCAGCCTGCATAAAGCTC 61.106 60.000 0.00 0.00 45.94 4.09
304 309 1.946768 CTTTGTCGCTTCCACCTTTGA 59.053 47.619 0.00 0.00 0.00 2.69
321 326 2.583024 TGAGACATTGGCCATGTGAA 57.417 45.000 21.63 0.82 46.96 3.18
324 329 0.174162 GACATTGGCCATGTGAAGCC 59.826 55.000 21.63 3.93 46.96 4.35
326 331 4.095959 GACATTGGCCATGTGAAGCCTC 62.096 54.545 21.63 7.72 46.96 4.70
328 333 4.751431 GGCCATGTGAAGCCTCTT 57.249 55.556 0.00 0.00 46.14 2.85
329 334 2.187073 GGCCATGTGAAGCCTCTTG 58.813 57.895 0.00 0.00 46.14 3.02
330 335 1.509923 GCCATGTGAAGCCTCTTGC 59.490 57.895 0.00 0.00 41.71 4.01
345 368 2.919859 CTCTTGCGTGATATCTATGCGG 59.080 50.000 3.98 5.43 32.80 5.69
354 377 5.061435 CGTGATATCTATGCGGATTTCACAG 59.939 44.000 22.99 16.73 45.76 3.66
378 401 3.467374 TTTTCCACATCAAGTTTGGGC 57.533 42.857 0.00 0.00 0.00 5.36
384 407 1.342174 ACATCAAGTTTGGGCTGCTTG 59.658 47.619 0.00 0.00 40.47 4.01
449 472 3.181451 ACATGATGGTGGTAGTGCTATGG 60.181 47.826 0.00 0.00 0.00 2.74
520 543 6.399639 AGAGCAACTTCTAGGCTATCTTAC 57.600 41.667 0.00 0.00 38.15 2.34
593 616 6.202379 GGAGAATTAATTAGCACTAACCGACC 59.798 42.308 0.00 0.00 0.00 4.79
642 665 2.931386 CGATCGCCGCTTTGATCC 59.069 61.111 0.26 0.00 38.17 3.36
645 668 1.552348 GATCGCCGCTTTGATCCTCG 61.552 60.000 0.00 0.00 35.95 4.63
646 669 2.298158 ATCGCCGCTTTGATCCTCGT 62.298 55.000 0.00 0.00 0.00 4.18
648 671 1.635663 CGCCGCTTTGATCCTCGTTT 61.636 55.000 0.00 0.00 0.00 3.60
649 672 1.365699 GCCGCTTTGATCCTCGTTTA 58.634 50.000 0.00 0.00 0.00 2.01
652 675 3.000727 CCGCTTTGATCCTCGTTTAAGT 58.999 45.455 0.00 0.00 0.00 2.24
661 701 1.003233 CCTCGTTTAAGTCCAAGCCCT 59.997 52.381 0.00 0.00 0.00 5.19
705 746 1.548973 CGAAGCAGTTGTCGCGTCTT 61.549 55.000 5.77 0.00 35.97 3.01
706 747 0.161870 GAAGCAGTTGTCGCGTCTTC 59.838 55.000 5.77 5.39 35.36 2.87
707 748 0.249489 AAGCAGTTGTCGCGTCTTCT 60.249 50.000 5.77 0.34 0.00 2.85
723 764 4.362476 CTTTGCCTTGCCGCCACC 62.362 66.667 0.00 0.00 0.00 4.61
880 921 3.703127 GTCACCGTCCCTGTCCCC 61.703 72.222 0.00 0.00 0.00 4.81
927 968 3.155167 GGATTCCCTCCCGCGAGT 61.155 66.667 8.23 0.00 38.19 4.18
929 970 3.153270 GATTCCCTCCCGCGAGTCC 62.153 68.421 8.23 0.00 33.93 3.85
1078 1124 2.908940 GTTGCTGCTGGTGGTGCT 60.909 61.111 0.00 0.00 0.00 4.40
1079 1125 2.908428 TTGCTGCTGGTGGTGCTG 60.908 61.111 0.00 0.00 0.00 4.41
1080 1126 3.719646 TTGCTGCTGGTGGTGCTGT 62.720 57.895 0.00 0.00 0.00 4.40
1081 1127 3.667282 GCTGCTGGTGGTGCTGTG 61.667 66.667 0.00 0.00 0.00 3.66
1082 1128 2.981909 CTGCTGGTGGTGCTGTGG 60.982 66.667 0.00 0.00 0.00 4.17
1083 1129 3.779850 CTGCTGGTGGTGCTGTGGT 62.780 63.158 0.00 0.00 0.00 4.16
1084 1130 2.395988 CTGCTGGTGGTGCTGTGGTA 62.396 60.000 0.00 0.00 0.00 3.25
1085 1131 1.672356 GCTGGTGGTGCTGTGGTAG 60.672 63.158 0.00 0.00 0.00 3.18
1100 1146 0.756903 GGTAGTGTGGTGTGAGGTGT 59.243 55.000 0.00 0.00 0.00 4.16
1452 1498 3.478274 GAGGGGCAGGAGCAGGAG 61.478 72.222 0.00 0.00 44.61 3.69
1483 1529 4.063967 TGATGTCGTTCGGCGGCT 62.064 61.111 7.21 0.00 46.81 5.52
1500 1546 2.749044 TCGGTCGACGGGGAGAAG 60.749 66.667 21.27 0.85 44.45 2.85
1501 1547 4.493747 CGGTCGACGGGGAGAAGC 62.494 72.222 14.86 0.00 39.42 3.86
1507 1553 2.604686 ACGGGGAGAAGCAGCAGA 60.605 61.111 0.00 0.00 0.00 4.26
1807 1865 0.172578 TTACCCTCGCGTCATCTGTG 59.827 55.000 5.77 0.00 0.00 3.66
1812 1870 1.205485 CTCGCGTCATCTGTGCTAGC 61.205 60.000 8.10 8.10 0.00 3.42
1978 2041 0.889186 CCACACCAAGCCACAGTACC 60.889 60.000 0.00 0.00 0.00 3.34
1984 2047 1.076332 CAAGCCACAGTACCGTAAGC 58.924 55.000 0.00 0.00 0.00 3.09
2026 2095 5.080068 GCTAACTGTTTTGTATCAACGAGC 58.920 41.667 0.00 0.00 0.00 5.03
2054 2123 5.700832 TGTAATTGATCACTGGTCTTGTGAC 59.299 40.000 0.00 0.00 45.57 3.67
2061 2130 4.439057 TCACTGGTCTTGTGACTAAACAC 58.561 43.478 0.00 0.00 42.54 3.32
2062 2131 4.081365 TCACTGGTCTTGTGACTAAACACA 60.081 41.667 0.00 0.00 46.86 3.72
2406 2502 3.343617 TGATTTCGTGTCCATTTCCTCC 58.656 45.455 0.00 0.00 0.00 4.30
2446 2542 2.303175 TGCCTAATTAAATCCGGCACC 58.697 47.619 10.47 0.00 45.08 5.01
2448 2544 1.265905 CCTAATTAAATCCGGCACCGC 59.734 52.381 2.83 0.00 38.24 5.68
2540 2647 2.895865 CTGGCTGATCGCTGGCTG 60.896 66.667 8.94 4.87 38.95 4.85
2555 2662 1.407618 TGGCTGGCGTGTAGTATACTG 59.592 52.381 15.90 0.00 43.54 2.74
2558 2668 3.067180 GGCTGGCGTGTAGTATACTGTAA 59.933 47.826 15.90 0.00 43.54 2.41
2561 2671 5.506815 GCTGGCGTGTAGTATACTGTAATCA 60.507 44.000 15.90 6.16 43.54 2.57
2565 2675 6.921857 GGCGTGTAGTATACTGTAATCAACAT 59.078 38.462 15.90 0.00 43.54 2.71
2650 2764 4.608269 AGTCTACTACCCTGTACCCTTTC 58.392 47.826 0.00 0.00 0.00 2.62
2651 2765 3.703556 GTCTACTACCCTGTACCCTTTCC 59.296 52.174 0.00 0.00 0.00 3.13
2668 2782 1.527844 CCCTGGGCTAGCTTGATGC 60.528 63.158 15.72 0.00 43.29 3.91
2827 2941 7.136119 GGACGTCATCTTCAAGATACTAAGAG 58.864 42.308 18.91 0.00 32.12 2.85
2828 2942 7.012515 GGACGTCATCTTCAAGATACTAAGAGA 59.987 40.741 18.91 0.00 32.12 3.10
2837 2951 4.904253 AGATACTAAGAGACTTGTCGCC 57.096 45.455 1.08 0.00 0.00 5.54
2892 3006 5.856156 TCAAGCATTGGTCAAATGACAAAT 58.144 33.333 14.93 12.33 46.64 2.32
2918 3033 9.208022 TGAGATCGGCATAAAAATAGAATACAG 57.792 33.333 0.00 0.00 0.00 2.74
2919 3034 9.424319 GAGATCGGCATAAAAATAGAATACAGA 57.576 33.333 0.00 0.00 0.00 3.41
2951 3066 9.886132 TTCTAAAAGGTAGTACTCCATTCATTC 57.114 33.333 0.00 0.00 0.00 2.67
2952 3067 8.483758 TCTAAAAGGTAGTACTCCATTCATTCC 58.516 37.037 0.00 0.00 0.00 3.01
2953 3068 6.636454 AAAGGTAGTACTCCATTCATTCCA 57.364 37.500 0.00 0.00 0.00 3.53
2954 3069 5.615925 AGGTAGTACTCCATTCATTCCAC 57.384 43.478 0.00 0.00 0.00 4.02
2955 3070 5.030147 AGGTAGTACTCCATTCATTCCACA 58.970 41.667 0.00 0.00 0.00 4.17
2956 3071 5.487488 AGGTAGTACTCCATTCATTCCACAA 59.513 40.000 0.00 0.00 0.00 3.33
2957 3072 6.158695 AGGTAGTACTCCATTCATTCCACAAT 59.841 38.462 0.00 0.00 0.00 2.71
2958 3073 6.260936 GGTAGTACTCCATTCATTCCACAATG 59.739 42.308 0.00 0.00 40.91 2.82
2959 3074 5.819991 AGTACTCCATTCATTCCACAATGT 58.180 37.500 0.00 0.00 40.47 2.71
2960 3075 6.957631 AGTACTCCATTCATTCCACAATGTA 58.042 36.000 0.00 0.00 40.47 2.29
2961 3076 7.050377 AGTACTCCATTCATTCCACAATGTAG 58.950 38.462 0.00 0.00 40.47 2.74
2962 3077 5.819991 ACTCCATTCATTCCACAATGTAGT 58.180 37.500 0.00 0.00 40.47 2.73
2963 3078 5.649395 ACTCCATTCATTCCACAATGTAGTG 59.351 40.000 0.00 0.00 40.47 2.74
2964 3079 4.398988 TCCATTCATTCCACAATGTAGTGC 59.601 41.667 0.00 0.00 40.47 4.40
2965 3080 4.400251 CCATTCATTCCACAATGTAGTGCT 59.600 41.667 0.00 0.00 40.47 4.40
2966 3081 5.105635 CCATTCATTCCACAATGTAGTGCTT 60.106 40.000 0.00 0.00 40.47 3.91
2967 3082 5.627499 TTCATTCCACAATGTAGTGCTTC 57.373 39.130 0.00 0.00 40.47 3.86
2968 3083 4.009675 TCATTCCACAATGTAGTGCTTCC 58.990 43.478 0.00 0.00 40.47 3.46
2969 3084 3.788227 TTCCACAATGTAGTGCTTCCT 57.212 42.857 0.00 0.00 38.18 3.36
2970 3085 3.334583 TCCACAATGTAGTGCTTCCTC 57.665 47.619 0.00 0.00 38.18 3.71
2971 3086 2.906389 TCCACAATGTAGTGCTTCCTCT 59.094 45.455 0.00 0.00 38.18 3.69
2972 3087 4.093743 TCCACAATGTAGTGCTTCCTCTA 58.906 43.478 0.00 0.00 38.18 2.43
2973 3088 4.716784 TCCACAATGTAGTGCTTCCTCTAT 59.283 41.667 0.00 0.00 38.18 1.98
2974 3089 5.053145 CCACAATGTAGTGCTTCCTCTATC 58.947 45.833 0.00 0.00 38.18 2.08
2975 3090 5.053145 CACAATGTAGTGCTTCCTCTATCC 58.947 45.833 0.00 0.00 32.04 2.59
2976 3091 4.965532 ACAATGTAGTGCTTCCTCTATCCT 59.034 41.667 0.00 0.00 0.00 3.24
2977 3092 5.069781 ACAATGTAGTGCTTCCTCTATCCTC 59.930 44.000 0.00 0.00 0.00 3.71
2978 3093 3.215151 TGTAGTGCTTCCTCTATCCTCG 58.785 50.000 0.00 0.00 0.00 4.63
2979 3094 2.445682 AGTGCTTCCTCTATCCTCGT 57.554 50.000 0.00 0.00 0.00 4.18
2980 3095 2.028130 AGTGCTTCCTCTATCCTCGTG 58.972 52.381 0.00 0.00 0.00 4.35
2981 3096 0.747255 TGCTTCCTCTATCCTCGTGC 59.253 55.000 0.00 0.00 0.00 5.34
2982 3097 1.036707 GCTTCCTCTATCCTCGTGCT 58.963 55.000 0.00 0.00 0.00 4.40
2983 3098 1.410882 GCTTCCTCTATCCTCGTGCTT 59.589 52.381 0.00 0.00 0.00 3.91
2984 3099 2.544903 GCTTCCTCTATCCTCGTGCTTC 60.545 54.545 0.00 0.00 0.00 3.86
2985 3100 2.437085 TCCTCTATCCTCGTGCTTCA 57.563 50.000 0.00 0.00 0.00 3.02
2986 3101 2.735151 TCCTCTATCCTCGTGCTTCAA 58.265 47.619 0.00 0.00 0.00 2.69
2987 3102 2.427453 TCCTCTATCCTCGTGCTTCAAC 59.573 50.000 0.00 0.00 0.00 3.18
2988 3103 2.428890 CCTCTATCCTCGTGCTTCAACT 59.571 50.000 0.00 0.00 0.00 3.16
2989 3104 3.118956 CCTCTATCCTCGTGCTTCAACTT 60.119 47.826 0.00 0.00 0.00 2.66
2990 3105 4.499183 CTCTATCCTCGTGCTTCAACTTT 58.501 43.478 0.00 0.00 0.00 2.66
2991 3106 4.245660 TCTATCCTCGTGCTTCAACTTTG 58.754 43.478 0.00 0.00 0.00 2.77
2992 3107 2.613026 TCCTCGTGCTTCAACTTTGA 57.387 45.000 0.00 0.00 34.92 2.69
2993 3108 2.210116 TCCTCGTGCTTCAACTTTGAC 58.790 47.619 0.00 0.00 36.83 3.18
2994 3109 1.264288 CCTCGTGCTTCAACTTTGACC 59.736 52.381 0.00 0.00 36.83 4.02
2995 3110 0.934496 TCGTGCTTCAACTTTGACCG 59.066 50.000 0.00 0.00 36.83 4.79
2996 3111 0.655733 CGTGCTTCAACTTTGACCGT 59.344 50.000 0.00 0.00 36.83 4.83
2997 3112 1.862201 CGTGCTTCAACTTTGACCGTA 59.138 47.619 0.00 0.00 36.83 4.02
2998 3113 2.285756 CGTGCTTCAACTTTGACCGTAA 59.714 45.455 0.00 0.00 36.83 3.18
2999 3114 3.242478 CGTGCTTCAACTTTGACCGTAAA 60.242 43.478 0.00 0.00 36.83 2.01
3000 3115 4.553938 CGTGCTTCAACTTTGACCGTAAAT 60.554 41.667 0.00 0.00 36.83 1.40
3001 3116 5.278604 GTGCTTCAACTTTGACCGTAAATT 58.721 37.500 0.00 0.00 36.83 1.82
3002 3117 5.746721 GTGCTTCAACTTTGACCGTAAATTT 59.253 36.000 0.00 0.00 36.83 1.82
3003 3118 6.913673 GTGCTTCAACTTTGACCGTAAATTTA 59.086 34.615 0.00 0.00 36.83 1.40
3004 3119 7.432838 GTGCTTCAACTTTGACCGTAAATTTAA 59.567 33.333 0.00 0.00 36.83 1.52
3005 3120 7.432838 TGCTTCAACTTTGACCGTAAATTTAAC 59.567 33.333 0.00 0.00 36.83 2.01
3006 3121 7.646526 GCTTCAACTTTGACCGTAAATTTAACT 59.353 33.333 0.00 0.00 36.83 2.24
3008 3123 9.934190 TTCAACTTTGACCGTAAATTTAACTAC 57.066 29.630 0.00 0.00 36.83 2.73
3009 3124 8.558700 TCAACTTTGACCGTAAATTTAACTACC 58.441 33.333 0.00 0.00 31.01 3.18
3010 3125 8.344098 CAACTTTGACCGTAAATTTAACTACCA 58.656 33.333 0.00 0.00 0.00 3.25
3011 3126 8.449251 ACTTTGACCGTAAATTTAACTACCAA 57.551 30.769 0.00 0.00 0.00 3.67
3012 3127 8.562052 ACTTTGACCGTAAATTTAACTACCAAG 58.438 33.333 0.00 2.45 0.00 3.61
3013 3128 8.674263 TTTGACCGTAAATTTAACTACCAAGA 57.326 30.769 0.00 0.00 0.00 3.02
3014 3129 7.656707 TGACCGTAAATTTAACTACCAAGAC 57.343 36.000 0.00 0.00 0.00 3.01
3015 3130 6.650390 TGACCGTAAATTTAACTACCAAGACC 59.350 38.462 0.00 0.00 0.00 3.85
3016 3131 5.639082 ACCGTAAATTTAACTACCAAGACCG 59.361 40.000 0.00 0.00 0.00 4.79
3017 3132 5.868801 CCGTAAATTTAACTACCAAGACCGA 59.131 40.000 0.00 0.00 0.00 4.69
3018 3133 6.536224 CCGTAAATTTAACTACCAAGACCGAT 59.464 38.462 0.00 0.00 0.00 4.18
3019 3134 7.064966 CCGTAAATTTAACTACCAAGACCGATT 59.935 37.037 0.00 0.00 0.00 3.34
3020 3135 7.901377 CGTAAATTTAACTACCAAGACCGATTG 59.099 37.037 0.00 0.00 0.00 2.67
3021 3136 5.813080 ATTTAACTACCAAGACCGATTGC 57.187 39.130 0.00 0.00 0.00 3.56
3022 3137 1.722011 AACTACCAAGACCGATTGCG 58.278 50.000 0.00 0.00 37.24 4.85
3046 3161 4.920376 CGGGAGCAAAAATTATACCAGTG 58.080 43.478 0.00 0.00 0.00 3.66
3047 3162 4.638421 CGGGAGCAAAAATTATACCAGTGA 59.362 41.667 0.00 0.00 0.00 3.41
3048 3163 5.124776 CGGGAGCAAAAATTATACCAGTGAA 59.875 40.000 0.00 0.00 0.00 3.18
3049 3164 6.183360 CGGGAGCAAAAATTATACCAGTGAAT 60.183 38.462 0.00 0.00 0.00 2.57
3050 3165 7.555965 GGGAGCAAAAATTATACCAGTGAATT 58.444 34.615 0.00 0.00 0.00 2.17
3051 3166 7.706607 GGGAGCAAAAATTATACCAGTGAATTC 59.293 37.037 0.00 0.00 0.00 2.17
3052 3167 7.432252 GGAGCAAAAATTATACCAGTGAATTCG 59.568 37.037 0.04 0.00 0.00 3.34
3053 3168 7.826690 AGCAAAAATTATACCAGTGAATTCGT 58.173 30.769 0.04 0.00 0.00 3.85
3054 3169 8.952278 AGCAAAAATTATACCAGTGAATTCGTA 58.048 29.630 0.04 0.00 0.00 3.43
3055 3170 9.730420 GCAAAAATTATACCAGTGAATTCGTAT 57.270 29.630 0.04 5.16 0.00 3.06
3059 3174 9.537192 AAATTATACCAGTGAATTCGTATTCGA 57.463 29.630 9.79 0.00 42.55 3.71
3098 3213 2.112297 TTTTTCTCCCGCCGCAGT 59.888 55.556 0.00 0.00 0.00 4.40
3099 3214 1.527380 TTTTTCTCCCGCCGCAGTT 60.527 52.632 0.00 0.00 0.00 3.16
3100 3215 1.791103 TTTTTCTCCCGCCGCAGTTG 61.791 55.000 0.00 0.00 0.00 3.16
3101 3216 4.697756 TTCTCCCGCCGCAGTTGG 62.698 66.667 0.00 0.00 0.00 3.77
3106 3221 3.726517 CCGCCGCAGTTGGTCTTG 61.727 66.667 0.00 0.00 0.00 3.02
3107 3222 2.972505 CGCCGCAGTTGGTCTTGT 60.973 61.111 0.00 0.00 0.00 3.16
3108 3223 2.542907 CGCCGCAGTTGGTCTTGTT 61.543 57.895 0.00 0.00 0.00 2.83
3109 3224 1.225376 CGCCGCAGTTGGTCTTGTTA 61.225 55.000 0.00 0.00 0.00 2.41
3110 3225 0.517316 GCCGCAGTTGGTCTTGTTAG 59.483 55.000 0.00 0.00 0.00 2.34
3111 3226 1.878953 CCGCAGTTGGTCTTGTTAGT 58.121 50.000 0.00 0.00 0.00 2.24
3112 3227 2.218603 CCGCAGTTGGTCTTGTTAGTT 58.781 47.619 0.00 0.00 0.00 2.24
3113 3228 3.395639 CCGCAGTTGGTCTTGTTAGTTA 58.604 45.455 0.00 0.00 0.00 2.24
3114 3229 3.810941 CCGCAGTTGGTCTTGTTAGTTAA 59.189 43.478 0.00 0.00 0.00 2.01
3115 3230 4.273969 CCGCAGTTGGTCTTGTTAGTTAAA 59.726 41.667 0.00 0.00 0.00 1.52
3116 3231 5.048991 CCGCAGTTGGTCTTGTTAGTTAAAT 60.049 40.000 0.00 0.00 0.00 1.40
3117 3232 6.435428 CGCAGTTGGTCTTGTTAGTTAAATT 58.565 36.000 0.00 0.00 0.00 1.82
3118 3233 6.915843 CGCAGTTGGTCTTGTTAGTTAAATTT 59.084 34.615 0.00 0.00 0.00 1.82
3119 3234 8.071368 CGCAGTTGGTCTTGTTAGTTAAATTTA 58.929 33.333 0.00 0.00 0.00 1.40
3120 3235 9.908152 GCAGTTGGTCTTGTTAGTTAAATTTAT 57.092 29.630 0.00 0.00 0.00 1.40
3125 3240 9.575868 TGGTCTTGTTAGTTAAATTTATGGTCA 57.424 29.630 0.00 0.00 0.00 4.02
3140 3255 2.928416 GTCAAAGTTGGACCTCGGG 58.072 57.895 0.00 0.00 0.00 5.14
3141 3256 0.395312 GTCAAAGTTGGACCTCGGGA 59.605 55.000 0.00 0.00 0.00 5.14
3142 3257 1.133363 TCAAAGTTGGACCTCGGGAA 58.867 50.000 0.00 0.00 0.00 3.97
3143 3258 1.071699 TCAAAGTTGGACCTCGGGAAG 59.928 52.381 0.00 0.00 0.00 3.46
3144 3259 0.250770 AAAGTTGGACCTCGGGAAGC 60.251 55.000 0.00 0.00 0.00 3.86
3145 3260 2.434359 GTTGGACCTCGGGAAGCG 60.434 66.667 0.00 0.00 0.00 4.68
3146 3261 4.388499 TTGGACCTCGGGAAGCGC 62.388 66.667 0.00 0.00 0.00 5.92
3164 3279 2.570169 CGCGGACGCAATATATTTTGG 58.430 47.619 17.35 1.75 42.06 3.28
3165 3280 2.222213 CGCGGACGCAATATATTTTGGA 59.778 45.455 17.35 0.00 42.06 3.53
3166 3281 3.303461 CGCGGACGCAATATATTTTGGAA 60.303 43.478 17.35 0.00 42.06 3.53
3167 3282 4.612712 CGCGGACGCAATATATTTTGGAAT 60.613 41.667 17.35 0.00 42.06 3.01
3168 3283 4.616802 GCGGACGCAATATATTTTGGAATG 59.383 41.667 12.31 0.00 41.49 2.67
3169 3284 5.153513 CGGACGCAATATATTTTGGAATGG 58.846 41.667 7.83 0.00 0.00 3.16
3170 3285 5.049060 CGGACGCAATATATTTTGGAATGGA 60.049 40.000 7.83 0.00 0.00 3.41
3171 3286 6.381801 GGACGCAATATATTTTGGAATGGAG 58.618 40.000 7.83 0.00 0.00 3.86
3172 3287 6.331369 ACGCAATATATTTTGGAATGGAGG 57.669 37.500 7.83 0.00 0.00 4.30
3173 3288 5.243730 ACGCAATATATTTTGGAATGGAGGG 59.756 40.000 7.83 0.00 0.00 4.30
3174 3289 5.476599 CGCAATATATTTTGGAATGGAGGGA 59.523 40.000 7.83 0.00 0.00 4.20
3188 3303 7.570982 TGGAATGGAGGGAGTATGAGTTAAATA 59.429 37.037 0.00 0.00 0.00 1.40
3296 4264 8.514594 TGTTTCAATAGGTTGCAATAGAAGAAG 58.485 33.333 0.59 0.00 35.26 2.85
3346 4318 5.524281 TGCATTGTGTTTAGTACGTGAAGAA 59.476 36.000 0.00 0.00 0.00 2.52
3390 4362 9.645128 ATCAATATCATGGTGTAAGGAATTGAA 57.355 29.630 2.96 0.00 35.26 2.69
3443 4416 5.001232 TGAGTTTGCTAACCAGGTGTTATC 58.999 41.667 7.43 0.00 38.71 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 86 1.521681 CCCTCCGCCTTTCACGATC 60.522 63.158 0.00 0.00 0.00 3.69
82 87 2.584608 CCCTCCGCCTTTCACGAT 59.415 61.111 0.00 0.00 0.00 3.73
86 91 2.366153 AAAAGCCCCTCCGCCTTTCA 62.366 55.000 0.00 0.00 0.00 2.69
93 98 0.035056 ATGTCAGAAAAGCCCCTCCG 60.035 55.000 0.00 0.00 0.00 4.63
95 100 2.162408 CGAAATGTCAGAAAAGCCCCTC 59.838 50.000 0.00 0.00 0.00 4.30
119 124 0.459489 TTTCCGGCTTAATGCATGCC 59.541 50.000 16.68 14.96 45.15 4.40
120 125 1.536709 CCTTTCCGGCTTAATGCATGC 60.537 52.381 11.82 11.82 45.15 4.06
133 138 1.519455 CAGCTCGCCTACCTTTCCG 60.519 63.158 0.00 0.00 0.00 4.30
244 249 3.411351 CGGTTTGACGCTGTCCCG 61.411 66.667 6.30 7.90 31.26 5.14
281 286 1.813513 AGGTGGAAGCGACAAAGATG 58.186 50.000 0.00 0.00 40.95 2.90
321 326 3.616076 GCATAGATATCACGCAAGAGGCT 60.616 47.826 5.32 0.00 41.67 4.58
324 329 2.919859 CCGCATAGATATCACGCAAGAG 59.080 50.000 5.32 0.00 43.62 2.85
328 333 3.592898 AATCCGCATAGATATCACGCA 57.407 42.857 5.32 0.00 0.00 5.24
329 334 3.926527 TGAAATCCGCATAGATATCACGC 59.073 43.478 5.32 3.37 0.00 5.34
330 335 4.923281 TGTGAAATCCGCATAGATATCACG 59.077 41.667 5.32 3.23 0.00 4.35
332 337 6.101650 ACTGTGAAATCCGCATAGATATCA 57.898 37.500 5.32 0.00 34.34 2.15
333 338 7.426929 AAACTGTGAAATCCGCATAGATATC 57.573 36.000 0.00 0.00 34.34 1.63
334 339 7.807977 AAAACTGTGAAATCCGCATAGATAT 57.192 32.000 0.00 0.00 34.34 1.63
337 360 5.957842 AAAAACTGTGAAATCCGCATAGA 57.042 34.783 0.00 0.00 34.34 1.98
362 385 0.037975 GCAGCCCAAACTTGATGTGG 60.038 55.000 0.00 0.00 0.00 4.17
363 386 0.963962 AGCAGCCCAAACTTGATGTG 59.036 50.000 0.00 0.00 0.00 3.21
364 387 1.342174 CAAGCAGCCCAAACTTGATGT 59.658 47.619 0.00 0.00 42.71 3.06
378 401 5.039333 GCTGTGGAATTATTAAGCAAGCAG 58.961 41.667 0.00 0.00 0.00 4.24
384 407 5.220931 CCAGACAGCTGTGGAATTATTAAGC 60.221 44.000 27.27 4.52 40.63 3.09
547 570 5.316167 TCCGCCTATCGTCTTAGGTTTATA 58.684 41.667 9.49 0.00 40.83 0.98
548 571 4.147321 TCCGCCTATCGTCTTAGGTTTAT 58.853 43.478 9.49 0.00 40.83 1.40
549 572 3.554934 TCCGCCTATCGTCTTAGGTTTA 58.445 45.455 9.49 0.00 40.83 2.01
550 573 2.361438 CTCCGCCTATCGTCTTAGGTTT 59.639 50.000 9.49 0.00 40.83 3.27
572 595 6.646267 TCAGGTCGGTTAGTGCTAATTAATT 58.354 36.000 5.89 5.89 0.00 1.40
593 616 5.851720 AGCATAATGACACTGGTCTATCAG 58.148 41.667 0.00 0.00 44.61 2.90
642 665 2.474410 AGGGCTTGGACTTAAACGAG 57.526 50.000 0.00 0.00 0.00 4.18
645 668 4.079253 TCATCAAGGGCTTGGACTTAAAC 58.921 43.478 0.00 0.00 40.78 2.01
646 669 4.079253 GTCATCAAGGGCTTGGACTTAAA 58.921 43.478 0.00 0.00 40.78 1.52
648 671 2.642311 TGTCATCAAGGGCTTGGACTTA 59.358 45.455 0.00 0.00 40.78 2.24
649 672 1.425066 TGTCATCAAGGGCTTGGACTT 59.575 47.619 0.00 0.00 40.78 3.01
652 675 4.314522 TTTATGTCATCAAGGGCTTGGA 57.685 40.909 0.00 0.00 40.78 3.53
661 701 6.448207 TGCCGATCATTTTTATGTCATCAA 57.552 33.333 0.00 0.00 0.00 2.57
692 732 0.582005 GCAAAGAAGACGCGACAACT 59.418 50.000 15.93 7.46 0.00 3.16
932 973 1.226128 GCAAATCTGGCGTCGCTTC 60.226 57.895 18.11 1.39 0.00 3.86
933 974 2.690778 GGCAAATCTGGCGTCGCTT 61.691 57.895 18.11 0.00 38.51 4.68
934 975 3.127533 GGCAAATCTGGCGTCGCT 61.128 61.111 18.11 0.00 38.51 4.93
1078 1124 0.756294 CCTCACACCACACTACCACA 59.244 55.000 0.00 0.00 0.00 4.17
1079 1125 0.756903 ACCTCACACCACACTACCAC 59.243 55.000 0.00 0.00 0.00 4.16
1080 1126 0.756294 CACCTCACACCACACTACCA 59.244 55.000 0.00 0.00 0.00 3.25
1081 1127 0.756903 ACACCTCACACCACACTACC 59.243 55.000 0.00 0.00 0.00 3.18
1082 1128 1.411246 TCACACCTCACACCACACTAC 59.589 52.381 0.00 0.00 0.00 2.73
1083 1129 1.783071 TCACACCTCACACCACACTA 58.217 50.000 0.00 0.00 0.00 2.74
1084 1130 1.131638 ATCACACCTCACACCACACT 58.868 50.000 0.00 0.00 0.00 3.55
1085 1131 1.229428 CATCACACCTCACACCACAC 58.771 55.000 0.00 0.00 0.00 3.82
1100 1146 4.119363 GCCCCTGCAGCTCCATCA 62.119 66.667 8.66 0.00 37.47 3.07
1143 1189 4.742201 CACGACCCGCACCTCCTG 62.742 72.222 0.00 0.00 0.00 3.86
1452 1498 1.349627 CATCACGAACGCATCCTGC 59.650 57.895 0.00 0.00 40.69 4.85
1453 1499 0.647410 GACATCACGAACGCATCCTG 59.353 55.000 0.00 0.00 0.00 3.86
1454 1500 0.802222 CGACATCACGAACGCATCCT 60.802 55.000 0.00 0.00 35.09 3.24
1483 1529 2.749044 CTTCTCCCCGTCGACCGA 60.749 66.667 10.58 2.19 39.56 4.69
1700 1755 2.595463 ACGGGTTGGAGACGACGA 60.595 61.111 0.00 0.00 46.42 4.20
1769 1827 0.252927 AGGTTCTTGGAGGAGAGGGG 60.253 60.000 0.00 0.00 0.00 4.79
1770 1828 1.662686 AAGGTTCTTGGAGGAGAGGG 58.337 55.000 0.00 0.00 0.00 4.30
1774 1832 2.502130 GAGGGTAAGGTTCTTGGAGGAG 59.498 54.545 0.00 0.00 0.00 3.69
1807 1865 7.778470 ATAAATATTAGGAAGATGCGCTAGC 57.222 36.000 9.73 4.06 45.41 3.42
1812 1870 6.375455 AGGCCAATAAATATTAGGAAGATGCG 59.625 38.462 5.01 0.00 0.00 4.73
1816 1879 7.821566 TGGAAGGCCAATAAATATTAGGAAGA 58.178 34.615 5.01 0.00 42.49 2.87
1978 2041 3.913163 GCTAATCTAGTTAGGCGCTTACG 59.087 47.826 7.64 0.00 40.17 3.18
1984 2047 6.149807 AGTTAGCTAGCTAATCTAGTTAGGCG 59.850 42.308 33.67 0.00 45.22 5.52
2015 2078 6.344572 TCAATTACATGTGCTCGTTGATAC 57.655 37.500 9.11 0.00 0.00 2.24
2026 2095 6.149973 ACAAGACCAGTGATCAATTACATGTG 59.850 38.462 9.11 0.00 0.00 3.21
2054 2123 1.893801 ACCGAGGAGACCTGTGTTTAG 59.106 52.381 0.00 0.00 31.76 1.85
2386 2482 2.351726 CGGAGGAAATGGACACGAAATC 59.648 50.000 0.00 0.00 0.00 2.17
2517 2624 2.202797 GCGATCAGCCAGCTCGAA 60.203 61.111 4.21 0.00 38.07 3.71
2540 2647 6.267817 TGTTGATTACAGTATACTACACGCC 58.732 40.000 4.74 0.00 31.68 5.68
2542 2649 7.434013 TGCATGTTGATTACAGTATACTACACG 59.566 37.037 4.74 0.00 40.83 4.49
2555 2662 1.523501 CGTGCGTGCATGTTGATTAC 58.476 50.000 7.93 0.00 0.00 1.89
2558 2668 2.176546 GCGTGCGTGCATGTTGAT 59.823 55.556 14.92 0.00 35.52 2.57
2650 2764 1.527844 GCATCAAGCTAGCCCAGGG 60.528 63.158 12.13 0.00 41.15 4.45
2651 2765 1.527844 GGCATCAAGCTAGCCCAGG 60.528 63.158 12.13 0.00 44.79 4.45
2668 2782 3.299503 ACATTGCCCTAGCCTAATTTGG 58.700 45.455 1.04 1.04 38.69 3.28
2827 2941 3.246619 CAACTTAGAGAGGCGACAAGTC 58.753 50.000 0.00 0.00 0.00 3.01
2828 2942 2.628657 ACAACTTAGAGAGGCGACAAGT 59.371 45.455 0.00 0.00 0.00 3.16
2837 2951 5.899120 TGCTACTGGTACAACTTAGAGAG 57.101 43.478 0.00 0.00 38.70 3.20
2888 3002 9.903682 ATTCTATTTTTATGCCGATCTCATTTG 57.096 29.630 3.21 0.00 0.00 2.32
2891 3005 9.725019 TGTATTCTATTTTTATGCCGATCTCAT 57.275 29.630 0.00 0.00 0.00 2.90
2892 3006 9.208022 CTGTATTCTATTTTTATGCCGATCTCA 57.792 33.333 0.00 0.00 0.00 3.27
2893 3007 9.424319 TCTGTATTCTATTTTTATGCCGATCTC 57.576 33.333 0.00 0.00 0.00 2.75
2894 3008 9.778741 TTCTGTATTCTATTTTTATGCCGATCT 57.221 29.630 0.00 0.00 0.00 2.75
2934 3049 6.823689 ACATTGTGGAATGAATGGAGTACTAC 59.176 38.462 0.00 0.00 41.49 2.73
2935 3050 6.957631 ACATTGTGGAATGAATGGAGTACTA 58.042 36.000 0.00 0.00 41.49 1.82
2936 3051 5.819991 ACATTGTGGAATGAATGGAGTACT 58.180 37.500 0.00 0.00 41.49 2.73
2937 3052 7.251704 CTACATTGTGGAATGAATGGAGTAC 57.748 40.000 0.00 0.00 41.49 2.73
2939 3054 5.819991 ACTACATTGTGGAATGAATGGAGT 58.180 37.500 7.20 0.00 45.22 3.85
2940 3055 5.449588 GCACTACATTGTGGAATGAATGGAG 60.450 44.000 7.20 0.00 43.55 3.86
2941 3056 4.398988 GCACTACATTGTGGAATGAATGGA 59.601 41.667 7.20 0.00 41.49 3.41
2942 3057 4.400251 AGCACTACATTGTGGAATGAATGG 59.600 41.667 7.20 0.00 41.49 3.16
2943 3058 5.571784 AGCACTACATTGTGGAATGAATG 57.428 39.130 7.20 0.00 41.49 2.67
2944 3059 5.126061 GGAAGCACTACATTGTGGAATGAAT 59.874 40.000 7.20 0.00 41.49 2.57
2945 3060 4.458989 GGAAGCACTACATTGTGGAATGAA 59.541 41.667 7.20 0.00 41.49 2.57
2946 3061 4.009675 GGAAGCACTACATTGTGGAATGA 58.990 43.478 7.20 0.00 41.49 2.57
2947 3062 4.012374 AGGAAGCACTACATTGTGGAATG 58.988 43.478 7.20 0.00 44.11 2.67
2948 3063 4.018960 AGAGGAAGCACTACATTGTGGAAT 60.019 41.667 7.20 0.00 38.31 3.01
2949 3064 3.327757 AGAGGAAGCACTACATTGTGGAA 59.672 43.478 7.20 0.00 38.31 3.53
2950 3065 2.906389 AGAGGAAGCACTACATTGTGGA 59.094 45.455 7.20 0.00 38.31 4.02
2951 3066 3.340814 AGAGGAAGCACTACATTGTGG 57.659 47.619 0.00 0.00 38.31 4.17
2952 3067 5.053145 GGATAGAGGAAGCACTACATTGTG 58.947 45.833 0.00 0.00 40.62 3.33
2953 3068 4.965532 AGGATAGAGGAAGCACTACATTGT 59.034 41.667 0.00 0.00 0.00 2.71
2954 3069 5.537188 GAGGATAGAGGAAGCACTACATTG 58.463 45.833 0.00 0.00 0.00 2.82
2955 3070 4.279671 CGAGGATAGAGGAAGCACTACATT 59.720 45.833 0.00 0.00 0.00 2.71
2956 3071 3.823873 CGAGGATAGAGGAAGCACTACAT 59.176 47.826 0.00 0.00 0.00 2.29
2957 3072 3.215151 CGAGGATAGAGGAAGCACTACA 58.785 50.000 0.00 0.00 0.00 2.74
2958 3073 3.003897 CACGAGGATAGAGGAAGCACTAC 59.996 52.174 0.00 0.00 0.00 2.73
2959 3074 3.215151 CACGAGGATAGAGGAAGCACTA 58.785 50.000 0.00 0.00 0.00 2.74
2960 3075 2.028130 CACGAGGATAGAGGAAGCACT 58.972 52.381 0.00 0.00 0.00 4.40
2961 3076 1.537135 GCACGAGGATAGAGGAAGCAC 60.537 57.143 0.00 0.00 0.00 4.40
2962 3077 0.747255 GCACGAGGATAGAGGAAGCA 59.253 55.000 0.00 0.00 0.00 3.91
2963 3078 1.036707 AGCACGAGGATAGAGGAAGC 58.963 55.000 0.00 0.00 0.00 3.86
2964 3079 2.690497 TGAAGCACGAGGATAGAGGAAG 59.310 50.000 0.00 0.00 0.00 3.46
2965 3080 2.735151 TGAAGCACGAGGATAGAGGAA 58.265 47.619 0.00 0.00 0.00 3.36
2966 3081 2.427453 GTTGAAGCACGAGGATAGAGGA 59.573 50.000 0.00 0.00 0.00 3.71
2967 3082 2.428890 AGTTGAAGCACGAGGATAGAGG 59.571 50.000 0.00 0.00 0.00 3.69
2968 3083 3.791973 AGTTGAAGCACGAGGATAGAG 57.208 47.619 0.00 0.00 0.00 2.43
2969 3084 4.021456 TCAAAGTTGAAGCACGAGGATAGA 60.021 41.667 0.00 0.00 33.55 1.98
2970 3085 4.092091 GTCAAAGTTGAAGCACGAGGATAG 59.908 45.833 0.00 0.00 39.21 2.08
2971 3086 3.994392 GTCAAAGTTGAAGCACGAGGATA 59.006 43.478 0.00 0.00 39.21 2.59
2972 3087 2.808543 GTCAAAGTTGAAGCACGAGGAT 59.191 45.455 0.00 0.00 39.21 3.24
2973 3088 2.210116 GTCAAAGTTGAAGCACGAGGA 58.790 47.619 0.00 0.00 39.21 3.71
2974 3089 1.264288 GGTCAAAGTTGAAGCACGAGG 59.736 52.381 0.00 0.00 39.21 4.63
2975 3090 1.070577 CGGTCAAAGTTGAAGCACGAG 60.071 52.381 0.00 0.00 39.21 4.18
2976 3091 0.934496 CGGTCAAAGTTGAAGCACGA 59.066 50.000 0.00 0.00 39.21 4.35
2977 3092 0.655733 ACGGTCAAAGTTGAAGCACG 59.344 50.000 0.00 2.00 39.21 5.34
2978 3093 3.955771 TTACGGTCAAAGTTGAAGCAC 57.044 42.857 0.00 0.00 39.21 4.40
2979 3094 5.508200 AATTTACGGTCAAAGTTGAAGCA 57.492 34.783 0.00 0.00 39.21 3.91
2980 3095 7.646526 AGTTAAATTTACGGTCAAAGTTGAAGC 59.353 33.333 0.00 0.00 39.21 3.86
2982 3097 9.934190 GTAGTTAAATTTACGGTCAAAGTTGAA 57.066 29.630 0.00 0.00 39.21 2.69
2983 3098 8.558700 GGTAGTTAAATTTACGGTCAAAGTTGA 58.441 33.333 0.00 0.00 34.20 3.18
2984 3099 8.344098 TGGTAGTTAAATTTACGGTCAAAGTTG 58.656 33.333 0.00 0.00 29.44 3.16
2985 3100 8.449251 TGGTAGTTAAATTTACGGTCAAAGTT 57.551 30.769 0.00 0.00 31.36 2.66
2986 3101 8.449251 TTGGTAGTTAAATTTACGGTCAAAGT 57.551 30.769 0.00 0.00 0.00 2.66
2987 3102 8.776470 TCTTGGTAGTTAAATTTACGGTCAAAG 58.224 33.333 0.00 0.00 0.00 2.77
2988 3103 8.558700 GTCTTGGTAGTTAAATTTACGGTCAAA 58.441 33.333 0.00 0.00 0.00 2.69
2989 3104 7.173047 GGTCTTGGTAGTTAAATTTACGGTCAA 59.827 37.037 0.00 0.00 0.00 3.18
2990 3105 6.650390 GGTCTTGGTAGTTAAATTTACGGTCA 59.350 38.462 0.00 0.00 0.00 4.02
2991 3106 6.183360 CGGTCTTGGTAGTTAAATTTACGGTC 60.183 42.308 0.00 0.00 0.00 4.79
2992 3107 5.639082 CGGTCTTGGTAGTTAAATTTACGGT 59.361 40.000 0.00 0.00 0.00 4.83
2993 3108 5.868801 TCGGTCTTGGTAGTTAAATTTACGG 59.131 40.000 0.00 0.00 0.00 4.02
2994 3109 6.949578 TCGGTCTTGGTAGTTAAATTTACG 57.050 37.500 0.00 0.00 0.00 3.18
2995 3110 7.695201 GCAATCGGTCTTGGTAGTTAAATTTAC 59.305 37.037 0.00 0.00 0.00 2.01
2996 3111 7.413219 CGCAATCGGTCTTGGTAGTTAAATTTA 60.413 37.037 0.00 0.00 0.00 1.40
2997 3112 6.617879 GCAATCGGTCTTGGTAGTTAAATTT 58.382 36.000 0.00 0.00 0.00 1.82
2998 3113 5.163794 CGCAATCGGTCTTGGTAGTTAAATT 60.164 40.000 0.00 0.00 0.00 1.82
2999 3114 4.331717 CGCAATCGGTCTTGGTAGTTAAAT 59.668 41.667 0.00 0.00 0.00 1.40
3000 3115 3.680937 CGCAATCGGTCTTGGTAGTTAAA 59.319 43.478 0.00 0.00 0.00 1.52
3001 3116 3.255725 CGCAATCGGTCTTGGTAGTTAA 58.744 45.455 0.00 0.00 0.00 2.01
3002 3117 2.883574 CGCAATCGGTCTTGGTAGTTA 58.116 47.619 0.00 0.00 0.00 2.24
3003 3118 1.722011 CGCAATCGGTCTTGGTAGTT 58.278 50.000 0.00 0.00 0.00 2.24
3004 3119 3.436001 CGCAATCGGTCTTGGTAGT 57.564 52.632 0.00 0.00 0.00 2.73
3016 3131 2.485188 TTTTTGCTCCCGCCGCAATC 62.485 55.000 5.33 0.00 45.67 2.67
3017 3132 1.887344 ATTTTTGCTCCCGCCGCAAT 61.887 50.000 5.33 0.00 45.67 3.56
3018 3133 2.093537 AATTTTTGCTCCCGCCGCAA 62.094 50.000 0.00 0.00 44.83 4.85
3019 3134 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
3020 3135 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
3021 3136 2.287368 GGTATAATTTTTGCTCCCGCCG 60.287 50.000 0.00 0.00 34.43 6.46
3022 3137 2.691011 TGGTATAATTTTTGCTCCCGCC 59.309 45.455 0.00 0.00 34.43 6.13
3023 3138 3.380320 ACTGGTATAATTTTTGCTCCCGC 59.620 43.478 0.00 0.00 0.00 6.13
3024 3139 4.638421 TCACTGGTATAATTTTTGCTCCCG 59.362 41.667 0.00 0.00 0.00 5.14
3025 3140 6.524101 TTCACTGGTATAATTTTTGCTCCC 57.476 37.500 0.00 0.00 0.00 4.30
3026 3141 7.432252 CGAATTCACTGGTATAATTTTTGCTCC 59.568 37.037 6.22 0.00 0.00 4.70
3027 3142 7.968405 ACGAATTCACTGGTATAATTTTTGCTC 59.032 33.333 6.22 0.00 0.00 4.26
3028 3143 7.826690 ACGAATTCACTGGTATAATTTTTGCT 58.173 30.769 6.22 0.00 0.00 3.91
3029 3144 9.730420 ATACGAATTCACTGGTATAATTTTTGC 57.270 29.630 6.22 0.00 0.00 3.68
3033 3148 9.537192 TCGAATACGAATTCACTGGTATAATTT 57.463 29.630 6.22 0.00 45.74 1.82
3081 3196 1.527380 AACTGCGGCGGGAGAAAAA 60.527 52.632 19.55 0.00 35.29 1.94
3082 3197 2.112297 AACTGCGGCGGGAGAAAA 59.888 55.556 19.55 0.00 35.29 2.29
3083 3198 2.668212 CAACTGCGGCGGGAGAAA 60.668 61.111 19.55 0.00 35.29 2.52
3084 3199 4.697756 CCAACTGCGGCGGGAGAA 62.698 66.667 19.55 0.00 35.29 2.87
3089 3204 3.726517 CAAGACCAACTGCGGCGG 61.727 66.667 9.78 7.39 0.00 6.13
3090 3205 1.225376 TAACAAGACCAACTGCGGCG 61.225 55.000 0.51 0.51 0.00 6.46
3091 3206 0.517316 CTAACAAGACCAACTGCGGC 59.483 55.000 0.00 0.00 0.00 6.53
3092 3207 1.878953 ACTAACAAGACCAACTGCGG 58.121 50.000 0.00 0.00 0.00 5.69
3093 3208 5.412526 TTTAACTAACAAGACCAACTGCG 57.587 39.130 0.00 0.00 0.00 5.18
3094 3209 9.908152 ATAAATTTAACTAACAAGACCAACTGC 57.092 29.630 1.21 0.00 0.00 4.40
3099 3214 9.575868 TGACCATAAATTTAACTAACAAGACCA 57.424 29.630 1.21 0.00 0.00 4.02
3109 3224 8.364894 GGTCCAACTTTGACCATAAATTTAACT 58.635 33.333 1.21 0.00 38.76 2.24
3110 3225 8.364894 AGGTCCAACTTTGACCATAAATTTAAC 58.635 33.333 13.24 0.00 41.22 2.01
3111 3226 8.485578 AGGTCCAACTTTGACCATAAATTTAA 57.514 30.769 13.24 0.00 41.22 1.52
3112 3227 7.094549 CGAGGTCCAACTTTGACCATAAATTTA 60.095 37.037 13.24 0.00 41.22 1.40
3113 3228 6.294508 CGAGGTCCAACTTTGACCATAAATTT 60.295 38.462 13.24 0.00 41.22 1.82
3114 3229 5.183140 CGAGGTCCAACTTTGACCATAAATT 59.817 40.000 13.24 0.00 41.22 1.82
3115 3230 4.700213 CGAGGTCCAACTTTGACCATAAAT 59.300 41.667 13.24 0.00 41.22 1.40
3116 3231 4.069304 CGAGGTCCAACTTTGACCATAAA 58.931 43.478 13.24 0.00 41.22 1.40
3117 3232 3.558321 CCGAGGTCCAACTTTGACCATAA 60.558 47.826 13.24 0.00 41.22 1.90
3118 3233 2.027561 CCGAGGTCCAACTTTGACCATA 60.028 50.000 13.24 0.00 41.22 2.74
3119 3234 1.271379 CCGAGGTCCAACTTTGACCAT 60.271 52.381 13.24 0.72 41.22 3.55
3120 3235 0.107831 CCGAGGTCCAACTTTGACCA 59.892 55.000 13.24 0.00 41.22 4.02
3121 3236 0.605589 CCCGAGGTCCAACTTTGACC 60.606 60.000 4.16 4.16 39.18 4.02
3122 3237 0.395312 TCCCGAGGTCCAACTTTGAC 59.605 55.000 0.00 0.00 0.00 3.18
3123 3238 1.071699 CTTCCCGAGGTCCAACTTTGA 59.928 52.381 0.00 0.00 0.00 2.69
3124 3239 1.523758 CTTCCCGAGGTCCAACTTTG 58.476 55.000 0.00 0.00 0.00 2.77
3125 3240 0.250770 GCTTCCCGAGGTCCAACTTT 60.251 55.000 0.00 0.00 0.00 2.66
3126 3241 1.375326 GCTTCCCGAGGTCCAACTT 59.625 57.895 0.00 0.00 0.00 2.66
3127 3242 2.943978 CGCTTCCCGAGGTCCAACT 61.944 63.158 0.00 0.00 40.02 3.16
3128 3243 2.434359 CGCTTCCCGAGGTCCAAC 60.434 66.667 0.00 0.00 40.02 3.77
3129 3244 4.388499 GCGCTTCCCGAGGTCCAA 62.388 66.667 0.00 0.00 40.02 3.53
3144 3259 2.222213 TCCAAAATATATTGCGTCCGCG 59.778 45.455 7.22 0.00 45.51 6.46
3145 3260 3.889196 TCCAAAATATATTGCGTCCGC 57.111 42.857 4.42 4.42 42.35 5.54
3146 3261 5.049060 TCCATTCCAAAATATATTGCGTCCG 60.049 40.000 0.00 0.00 0.00 4.79
3147 3262 6.325919 TCCATTCCAAAATATATTGCGTCC 57.674 37.500 0.00 0.00 0.00 4.79
3148 3263 6.381801 CCTCCATTCCAAAATATATTGCGTC 58.618 40.000 0.00 0.00 0.00 5.19
3149 3264 5.243730 CCCTCCATTCCAAAATATATTGCGT 59.756 40.000 0.00 0.00 0.00 5.24
3150 3265 5.476599 TCCCTCCATTCCAAAATATATTGCG 59.523 40.000 0.00 0.00 0.00 4.85
3151 3266 6.494835 ACTCCCTCCATTCCAAAATATATTGC 59.505 38.462 0.00 0.00 0.00 3.56
3152 3267 9.759473 ATACTCCCTCCATTCCAAAATATATTG 57.241 33.333 0.00 0.00 0.00 1.90
3153 3268 9.759473 CATACTCCCTCCATTCCAAAATATATT 57.241 33.333 0.00 0.00 0.00 1.28
3154 3269 9.127560 TCATACTCCCTCCATTCCAAAATATAT 57.872 33.333 0.00 0.00 0.00 0.86
3155 3270 8.518720 TCATACTCCCTCCATTCCAAAATATA 57.481 34.615 0.00 0.00 0.00 0.86
3156 3271 7.074237 ACTCATACTCCCTCCATTCCAAAATAT 59.926 37.037 0.00 0.00 0.00 1.28
3157 3272 6.389869 ACTCATACTCCCTCCATTCCAAAATA 59.610 38.462 0.00 0.00 0.00 1.40
3158 3273 5.194537 ACTCATACTCCCTCCATTCCAAAAT 59.805 40.000 0.00 0.00 0.00 1.82
3159 3274 4.540099 ACTCATACTCCCTCCATTCCAAAA 59.460 41.667 0.00 0.00 0.00 2.44
3160 3275 4.111577 ACTCATACTCCCTCCATTCCAAA 58.888 43.478 0.00 0.00 0.00 3.28
3161 3276 3.736094 ACTCATACTCCCTCCATTCCAA 58.264 45.455 0.00 0.00 0.00 3.53
3162 3277 3.421394 ACTCATACTCCCTCCATTCCA 57.579 47.619 0.00 0.00 0.00 3.53
3163 3278 5.888982 TTAACTCATACTCCCTCCATTCC 57.111 43.478 0.00 0.00 0.00 3.01
3164 3279 8.871125 TCTATTTAACTCATACTCCCTCCATTC 58.129 37.037 0.00 0.00 0.00 2.67
3165 3280 8.798975 TCTATTTAACTCATACTCCCTCCATT 57.201 34.615 0.00 0.00 0.00 3.16
3166 3281 8.798975 TTCTATTTAACTCATACTCCCTCCAT 57.201 34.615 0.00 0.00 0.00 3.41
3167 3282 8.483758 GTTTCTATTTAACTCATACTCCCTCCA 58.516 37.037 0.00 0.00 0.00 3.86
3168 3283 8.483758 TGTTTCTATTTAACTCATACTCCCTCC 58.516 37.037 0.00 0.00 0.00 4.30
3169 3284 9.315525 GTGTTTCTATTTAACTCATACTCCCTC 57.684 37.037 0.00 0.00 0.00 4.30
3170 3285 8.822805 TGTGTTTCTATTTAACTCATACTCCCT 58.177 33.333 0.00 0.00 0.00 4.20
3171 3286 9.614792 ATGTGTTTCTATTTAACTCATACTCCC 57.385 33.333 0.00 0.00 37.72 4.30
3204 4170 7.450074 ACATGACCACAATAAAGTCTCACTTA 58.550 34.615 0.00 0.00 37.47 2.24
3214 4180 5.268118 TGCAACAACATGACCACAATAAA 57.732 34.783 0.00 0.00 0.00 1.40
3262 4230 5.301551 TGCAACCTATTGAAACACAGAATGT 59.698 36.000 0.00 0.00 45.31 2.71
3275 4243 7.856145 AGACTTCTTCTATTGCAACCTATTG 57.144 36.000 0.00 0.00 33.79 1.90
3296 4264 5.008118 GGCTGCTTTCCAGTCATAATTAGAC 59.992 44.000 0.00 6.86 45.59 2.59
3346 4318 6.989155 ATTGATATCAATTGTGGGATTGCT 57.011 33.333 22.65 0.00 43.48 3.91
3443 4416 2.562298 TCAAGGCCATTTGCAGGTTTAG 59.438 45.455 5.01 0.00 43.89 1.85


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

AutoCloner maintained by Alex Coulton.