Multiple sequence alignment - TraesCS2B01G418700

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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 TraesCS2B01G418700 chr2B 100.000 5744 0 0 1 5744 599998736 600004479 0.000000e+00 10608
1 TraesCS2B01G418700 chr2B 92.941 85 6 0 2961 3045 37108823 37108907 2.170000e-24 124
2 TraesCS2B01G418700 chr2B 89.247 93 10 0 2955 3047 514859356 514859448 3.640000e-22 117
3 TraesCS2B01G418700 chr2D 94.557 2719 72 35 301 2954 510614382 510617089 0.000000e+00 4132
4 TraesCS2B01G418700 chr2D 93.258 1765 82 18 3979 5739 510617953 510619684 0.000000e+00 2566
5 TraesCS2B01G418700 chr2D 93.435 853 38 5 3042 3889 510617096 510617935 0.000000e+00 1249
6 TraesCS2B01G418700 chr2A 93.969 2736 96 30 1 2675 654363598 654366325 0.000000e+00 4074
7 TraesCS2B01G418700 chr2A 92.552 1826 93 29 3935 5741 654367475 654369276 0.000000e+00 2579
8 TraesCS2B01G418700 chr2A 96.584 849 27 2 3042 3889 654366625 654367472 0.000000e+00 1406
9 TraesCS2B01G418700 chr2A 91.930 285 8 8 2681 2962 654366356 654366628 9.030000e-103 385
10 TraesCS2B01G418700 chr6A 87.425 334 40 2 1301 1633 474987120 474986788 3.250000e-102 383
11 TraesCS2B01G418700 chr6A 79.848 263 53 0 2187 2449 474986349 474986087 5.870000e-45 193
12 TraesCS2B01G418700 chr6B 87.126 334 41 2 1301 1633 485301965 485302297 1.510000e-100 377
13 TraesCS2B01G418700 chr6B 91.566 83 7 0 2960 3042 134639849 134639931 1.310000e-21 115
14 TraesCS2B01G418700 chr6D 86.486 333 45 0 1301 1633 335339360 335339028 3.270000e-97 366
15 TraesCS2B01G418700 chr3D 91.765 85 7 0 2961 3045 501713753 501713669 1.010000e-22 119
16 TraesCS2B01G418700 chr1D 91.765 85 7 0 2961 3045 63705203 63705119 1.010000e-22 119
17 TraesCS2B01G418700 chr1D 87.234 94 11 1 2954 3046 154019419 154019326 7.870000e-19 106
18 TraesCS2B01G418700 chr4B 88.542 96 11 0 2950 3045 420202968 420202873 3.640000e-22 117
19 TraesCS2B01G418700 chr4D 89.773 88 9 0 2958 3045 492602239 492602152 4.700000e-21 113
20 TraesCS2B01G418700 chr3B 89.011 91 10 0 2955 3045 729205880 729205970 4.700000e-21 113


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 TraesCS2B01G418700 chr2B 599998736 600004479 5743 False 10608 10608 100.00000 1 5744 1 chr2B.!!$F3 5743
1 TraesCS2B01G418700 chr2D 510614382 510619684 5302 False 2649 4132 93.75000 301 5739 3 chr2D.!!$F1 5438
2 TraesCS2B01G418700 chr2A 654363598 654369276 5678 False 2111 4074 93.75875 1 5741 4 chr2A.!!$F1 5740
3 TraesCS2B01G418700 chr6A 474986087 474987120 1033 True 288 383 83.63650 1301 2449 2 chr6A.!!$R1 1148

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
53 54 0.038343 GCACGAACCAACAATGCCAT 60.038 50.000 0.00 0.0 0.0 4.40 F
288 289 0.108520 TTCCGTCGCACAATCTACCC 60.109 55.000 0.00 0.0 0.0 3.69 F
756 805 0.467384 ACTGCATCAAGATCCCGGAG 59.533 55.000 0.73 0.0 0.0 4.63 F
2160 2259 1.201880 GAGAGTGAACTGTACGGGGAC 59.798 57.143 6.65 0.0 0.0 4.46 F
2885 3011 0.318441 TCCCAATCTCCGATCGATGC 59.682 55.000 18.66 0.0 0.0 3.91 F
2886 3012 0.319728 CCCAATCTCCGATCGATGCT 59.680 55.000 18.66 0.0 0.0 3.79 F
2976 3106 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 1966 0.897863 AGCTGCGGAAGAGACAGAGT 60.898 55.0 0.00 0.0 33.10 3.24 R
2185 2286 1.931007 GCCTTCTTCCTCCCCTGCAT 61.931 60.0 0.00 0.0 0.00 3.96 R
2541 2642 0.828022 TGTTCCTCCTGTTCACGTGT 59.172 50.0 16.51 0.0 0.00 4.49 R
3956 4091 0.320771 ACTGCAACTAGACAAGCCGG 60.321 55.0 0.00 0.0 0.00 6.13 R
4199 4335 0.824759 AGGATACGGTGAACCTGAGC 59.175 55.0 0.00 0.0 46.39 4.26 R
4406 4547 0.958822 ACCGGTGATTTCAGGTTTGC 59.041 50.0 6.12 0.0 32.38 3.68 R
4767 4911 2.823924 TAACTGCAACGACCAAGCTA 57.176 45.0 0.00 0.0 0.00 3.32 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
53 54 0.038343 GCACGAACCAACAATGCCAT 60.038 50.000 0.00 0.00 0.00 4.40
76 77 3.032017 CTGGCATACCGGATCAACTAG 57.968 52.381 9.46 0.00 46.41 2.57
80 81 3.195825 GGCATACCGGATCAACTAGCTAT 59.804 47.826 9.46 0.00 0.00 2.97
119 120 3.316308 AGATTGTTGACCTCACAAGCAAC 59.684 43.478 4.09 0.00 40.62 4.17
120 121 1.388547 TGTTGACCTCACAAGCAACC 58.611 50.000 0.00 0.00 39.75 3.77
127 128 2.091555 ACCTCACAAGCAACCCCTTTAA 60.092 45.455 0.00 0.00 0.00 1.52
129 130 2.955660 CTCACAAGCAACCCCTTTAACA 59.044 45.455 0.00 0.00 0.00 2.41
134 135 5.064579 CACAAGCAACCCCTTTAACAAAAAG 59.935 40.000 0.00 0.00 0.00 2.27
183 184 2.680352 ACTCCACGACGCCTCCAT 60.680 61.111 0.00 0.00 0.00 3.41
196 197 2.547855 CGCCTCCATCGAAATCACCATA 60.548 50.000 0.00 0.00 0.00 2.74
221 222 2.629051 CTCTTTGGTTAACCGCCCTAG 58.371 52.381 19.65 11.45 39.43 3.02
232 233 2.660064 CGCCCTAGGGTGCAAGAGT 61.660 63.158 28.16 0.00 39.06 3.24
235 236 1.950954 GCCCTAGGGTGCAAGAGTTTC 60.951 57.143 28.96 3.73 37.65 2.78
256 257 1.169661 TGTCACCCCGCAACAATCAC 61.170 55.000 0.00 0.00 0.00 3.06
262 263 2.046285 CCGCAACAATCACCCCTCC 61.046 63.158 0.00 0.00 0.00 4.30
288 289 0.108520 TTCCGTCGCACAATCTACCC 60.109 55.000 0.00 0.00 0.00 3.69
289 290 1.216977 CCGTCGCACAATCTACCCA 59.783 57.895 0.00 0.00 0.00 4.51
362 363 1.743321 GCCCGGAGATGAGAGGACAG 61.743 65.000 0.73 0.00 0.00 3.51
396 397 1.925455 CAAGGGAGGAGAAGCCCCA 60.925 63.158 0.00 0.00 45.89 4.96
441 442 1.529796 GTCCCCAATGGTGGCGATA 59.470 57.895 0.00 0.00 44.46 2.92
588 610 7.540745 GCATGACATGTCTTAAAATTAAACGGT 59.459 33.333 25.55 0.00 0.00 4.83
589 611 8.849490 CATGACATGTCTTAAAATTAAACGGTG 58.151 33.333 25.55 0.28 0.00 4.94
613 661 6.013639 TGACATCTCATATCATCCTTGCTCAT 60.014 38.462 0.00 0.00 0.00 2.90
620 668 8.142485 TCATATCATCCTTGCTCATGAGATAA 57.858 34.615 27.04 17.75 30.80 1.75
750 799 4.517285 TGGTCCTAAACTGCATCAAGATC 58.483 43.478 0.00 0.00 0.00 2.75
754 803 1.755179 AAACTGCATCAAGATCCCGG 58.245 50.000 0.00 0.00 0.00 5.73
756 805 0.467384 ACTGCATCAAGATCCCGGAG 59.533 55.000 0.73 0.00 0.00 4.63
768 817 4.489737 AGATCCCGGAGTTGGACAATATA 58.510 43.478 0.73 0.00 33.94 0.86
810 859 9.646336 GGCTCATACGTAAATTACAAACAATAG 57.354 33.333 0.00 0.00 0.00 1.73
938 987 2.028476 TCATACTCCTCACAAACCCACG 60.028 50.000 0.00 0.00 0.00 4.94
1084 1133 7.341445 AGAATATATAGCACGATCTTCCTCC 57.659 40.000 0.00 0.00 0.00 4.30
1906 1966 1.347050 CCACACATTTCATTTGCCCCA 59.653 47.619 0.00 0.00 0.00 4.96
2160 2259 1.201880 GAGAGTGAACTGTACGGGGAC 59.798 57.143 6.65 0.00 0.00 4.46
2541 2642 0.598562 GCAGACACTGACGGAGAGAA 59.401 55.000 2.81 0.00 32.44 2.87
2675 2776 2.369860 CTGGATTGATGCACCCTAGCTA 59.630 50.000 0.00 0.00 34.99 3.32
2676 2777 2.369860 TGGATTGATGCACCCTAGCTAG 59.630 50.000 14.20 14.20 34.99 3.42
2677 2778 2.421619 GATTGATGCACCCTAGCTAGC 58.578 52.381 15.74 6.62 34.99 3.42
2678 2779 1.500474 TTGATGCACCCTAGCTAGCT 58.500 50.000 23.12 23.12 34.99 3.32
2774 2900 0.823356 AAACGAGTGGCCAGTTGCAT 60.823 50.000 25.50 13.43 43.89 3.96
2880 3006 1.486726 ACCAAGTCCCAATCTCCGATC 59.513 52.381 0.00 0.00 0.00 3.69
2881 3007 1.539065 CCAAGTCCCAATCTCCGATCG 60.539 57.143 8.51 8.51 0.00 3.69
2883 3009 2.002505 AGTCCCAATCTCCGATCGAT 57.997 50.000 18.66 0.00 0.00 3.59
2884 3010 1.615883 AGTCCCAATCTCCGATCGATG 59.384 52.381 18.66 8.84 0.00 3.84
2885 3011 0.318441 TCCCAATCTCCGATCGATGC 59.682 55.000 18.66 0.00 0.00 3.91
2886 3012 0.319728 CCCAATCTCCGATCGATGCT 59.680 55.000 18.66 0.00 0.00 3.79
2887 3013 1.546029 CCCAATCTCCGATCGATGCTA 59.454 52.381 18.66 0.00 0.00 3.49
2954 3082 5.606348 ACAAGCCTGTTTAATTTCACCAA 57.394 34.783 0.00 0.00 28.57 3.67
2958 3088 5.983540 AGCCTGTTTAATTTCACCAAACAA 58.016 33.333 5.29 0.00 40.54 2.83
2959 3089 6.048509 AGCCTGTTTAATTTCACCAAACAAG 58.951 36.000 5.29 1.48 40.54 3.16
2960 3090 5.815222 GCCTGTTTAATTTCACCAAACAAGT 59.185 36.000 5.29 0.00 40.54 3.16
2961 3091 6.981559 GCCTGTTTAATTTCACCAAACAAGTA 59.018 34.615 5.29 0.00 40.54 2.24
2962 3092 7.042992 GCCTGTTTAATTTCACCAAACAAGTAC 60.043 37.037 5.29 0.00 40.54 2.73
2963 3093 8.194769 CCTGTTTAATTTCACCAAACAAGTACT 58.805 33.333 5.29 0.00 40.54 2.73
2964 3094 9.233232 CTGTTTAATTTCACCAAACAAGTACTC 57.767 33.333 0.00 0.00 40.54 2.59
2965 3095 8.192110 TGTTTAATTTCACCAAACAAGTACTCC 58.808 33.333 0.00 0.00 38.76 3.85
2966 3096 5.784578 AATTTCACCAAACAAGTACTCCC 57.215 39.130 0.00 0.00 0.00 4.30
2967 3097 4.513406 TTTCACCAAACAAGTACTCCCT 57.487 40.909 0.00 0.00 0.00 4.20
2968 3098 3.764237 TCACCAAACAAGTACTCCCTC 57.236 47.619 0.00 0.00 0.00 4.30
2969 3099 2.370849 TCACCAAACAAGTACTCCCTCC 59.629 50.000 0.00 0.00 0.00 4.30
2970 3100 1.346722 ACCAAACAAGTACTCCCTCCG 59.653 52.381 0.00 0.00 0.00 4.63
2971 3101 1.346722 CCAAACAAGTACTCCCTCCGT 59.653 52.381 0.00 0.00 0.00 4.69
2972 3102 2.612221 CCAAACAAGTACTCCCTCCGTC 60.612 54.545 0.00 0.00 0.00 4.79
2973 3103 1.264295 AACAAGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
2974 3104 0.614134 ACAAGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
2975 3105 0.613853 CAAGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
2976 3106 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2977 3107 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2978 3108 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2979 3109 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2980 3110 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2981 3111 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2982 3112 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2983 3113 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2984 3114 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2985 3115 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2986 3116 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
2987 3117 6.269194 TCCCTCCGTCCCATAATATAAGAAT 58.731 40.000 0.00 0.00 0.00 2.40
2988 3118 6.156256 TCCCTCCGTCCCATAATATAAGAATG 59.844 42.308 0.00 0.00 0.00 2.67
2989 3119 6.070194 CCCTCCGTCCCATAATATAAGAATGT 60.070 42.308 0.00 0.00 0.00 2.71
2990 3120 7.394816 CCTCCGTCCCATAATATAAGAATGTT 58.605 38.462 0.00 0.00 0.00 2.71
2991 3121 7.883311 CCTCCGTCCCATAATATAAGAATGTTT 59.117 37.037 0.00 0.00 0.00 2.83
2992 3122 9.284968 CTCCGTCCCATAATATAAGAATGTTTT 57.715 33.333 0.00 0.00 0.00 2.43
2993 3123 9.635404 TCCGTCCCATAATATAAGAATGTTTTT 57.365 29.630 0.00 0.00 0.00 1.94
2994 3124 9.893305 CCGTCCCATAATATAAGAATGTTTTTC 57.107 33.333 0.00 0.00 0.00 2.29
3006 3136 7.832503 AAGAATGTTTTTCAAACTGACCAAG 57.167 32.000 1.33 0.00 0.00 3.61
3007 3137 5.812127 AGAATGTTTTTCAAACTGACCAAGC 59.188 36.000 1.33 0.00 0.00 4.01
3008 3138 4.799564 TGTTTTTCAAACTGACCAAGCT 57.200 36.364 1.33 0.00 0.00 3.74
3009 3139 5.146010 TGTTTTTCAAACTGACCAAGCTT 57.854 34.783 0.00 0.00 0.00 3.74
3010 3140 4.928615 TGTTTTTCAAACTGACCAAGCTTG 59.071 37.500 19.93 19.93 33.93 4.01
3011 3141 5.167845 GTTTTTCAAACTGACCAAGCTTGA 58.832 37.500 28.05 7.10 38.84 3.02
3012 3142 5.398603 TTTTCAAACTGACCAAGCTTGAA 57.601 34.783 28.05 11.66 45.08 2.69
3014 3144 5.398603 TTCAAACTGACCAAGCTTGAAAA 57.601 34.783 28.05 10.95 44.25 2.29
3015 3145 5.398603 TCAAACTGACCAAGCTTGAAAAA 57.601 34.783 28.05 9.19 37.90 1.94
3016 3146 5.976458 TCAAACTGACCAAGCTTGAAAAAT 58.024 33.333 28.05 7.31 37.90 1.82
3017 3147 5.811613 TCAAACTGACCAAGCTTGAAAAATG 59.188 36.000 28.05 15.87 37.90 2.32
3018 3148 5.596836 AACTGACCAAGCTTGAAAAATGA 57.403 34.783 28.05 3.41 0.00 2.57
3019 3149 5.796424 ACTGACCAAGCTTGAAAAATGAT 57.204 34.783 28.05 2.55 0.00 2.45
3020 3150 5.776744 ACTGACCAAGCTTGAAAAATGATC 58.223 37.500 28.05 11.30 0.00 2.92
3021 3151 5.537674 ACTGACCAAGCTTGAAAAATGATCT 59.462 36.000 28.05 0.00 0.00 2.75
3022 3152 6.041296 ACTGACCAAGCTTGAAAAATGATCTT 59.959 34.615 28.05 0.00 0.00 2.40
3023 3153 7.231317 ACTGACCAAGCTTGAAAAATGATCTTA 59.769 33.333 28.05 0.00 0.00 2.10
3024 3154 8.125978 TGACCAAGCTTGAAAAATGATCTTAT 57.874 30.769 28.05 0.00 0.00 1.73
3025 3155 9.241919 TGACCAAGCTTGAAAAATGATCTTATA 57.758 29.630 28.05 0.00 0.00 0.98
3160 3291 3.576118 AGGTGATAATGGAGATCGTCAGG 59.424 47.826 0.00 0.00 0.00 3.86
3258 3389 4.021229 TGCATGGCATCTCTTCTTTTCAT 58.979 39.130 0.00 0.00 31.71 2.57
3337 3468 1.080772 CTTCGTCGCAGGCTACACA 60.081 57.895 0.00 0.00 0.00 3.72
3482 3613 5.028549 TCTCTCAGAAACCATAGCATTCC 57.971 43.478 0.00 0.00 0.00 3.01
3498 3629 1.604604 TTCCGCTTCTTTCCAGTTGG 58.395 50.000 0.00 0.00 0.00 3.77
3555 3686 5.763204 TCAGTTTGTTCCTGTCCTATTGTTC 59.237 40.000 0.00 0.00 0.00 3.18
3557 3688 4.610605 TTGTTCCTGTCCTATTGTTCGA 57.389 40.909 0.00 0.00 0.00 3.71
3563 3694 4.649674 TCCTGTCCTATTGTTCGAAGCTAT 59.350 41.667 0.00 0.00 0.00 2.97
3889 4024 5.636965 GCAGTACATTGCCTATGTCTATGAG 59.363 44.000 4.97 0.00 44.15 2.90
3890 4025 6.739843 GCAGTACATTGCCTATGTCTATGAGT 60.740 42.308 4.97 0.00 44.15 3.41
3891 4026 6.644181 CAGTACATTGCCTATGTCTATGAGTG 59.356 42.308 4.97 0.00 44.15 3.51
3892 4027 5.876651 ACATTGCCTATGTCTATGAGTGA 57.123 39.130 0.00 0.00 44.15 3.41
3893 4028 5.851720 ACATTGCCTATGTCTATGAGTGAG 58.148 41.667 0.00 0.00 44.15 3.51
3894 4029 4.327982 TTGCCTATGTCTATGAGTGAGC 57.672 45.455 0.00 0.00 0.00 4.26
3895 4030 2.630098 TGCCTATGTCTATGAGTGAGCC 59.370 50.000 0.00 0.00 0.00 4.70
3896 4031 2.028567 GCCTATGTCTATGAGTGAGCCC 60.029 54.545 0.00 0.00 0.00 5.19
3897 4032 3.234353 CCTATGTCTATGAGTGAGCCCA 58.766 50.000 0.00 0.00 0.00 5.36
3898 4033 3.837146 CCTATGTCTATGAGTGAGCCCAT 59.163 47.826 0.00 0.00 0.00 4.00
3899 4034 3.766068 ATGTCTATGAGTGAGCCCATG 57.234 47.619 0.00 0.00 0.00 3.66
3900 4035 2.750814 TGTCTATGAGTGAGCCCATGA 58.249 47.619 0.00 0.00 0.00 3.07
3901 4036 3.106827 TGTCTATGAGTGAGCCCATGAA 58.893 45.455 0.00 0.00 0.00 2.57
3902 4037 3.118629 TGTCTATGAGTGAGCCCATGAAC 60.119 47.826 0.00 0.00 0.00 3.18
3903 4038 3.106827 TCTATGAGTGAGCCCATGAACA 58.893 45.455 0.00 0.00 0.00 3.18
3904 4039 2.885135 ATGAGTGAGCCCATGAACAA 57.115 45.000 0.00 0.00 0.00 2.83
3905 4040 2.655090 TGAGTGAGCCCATGAACAAA 57.345 45.000 0.00 0.00 0.00 2.83
3906 4041 2.942804 TGAGTGAGCCCATGAACAAAA 58.057 42.857 0.00 0.00 0.00 2.44
3907 4042 3.295093 TGAGTGAGCCCATGAACAAAAA 58.705 40.909 0.00 0.00 0.00 1.94
3908 4043 3.318839 TGAGTGAGCCCATGAACAAAAAG 59.681 43.478 0.00 0.00 0.00 2.27
3909 4044 3.299503 AGTGAGCCCATGAACAAAAAGT 58.700 40.909 0.00 0.00 0.00 2.66
3910 4045 4.469657 AGTGAGCCCATGAACAAAAAGTA 58.530 39.130 0.00 0.00 0.00 2.24
3911 4046 4.892934 AGTGAGCCCATGAACAAAAAGTAA 59.107 37.500 0.00 0.00 0.00 2.24
3912 4047 5.539955 AGTGAGCCCATGAACAAAAAGTAAT 59.460 36.000 0.00 0.00 0.00 1.89
3913 4048 5.634859 GTGAGCCCATGAACAAAAAGTAATG 59.365 40.000 0.00 0.00 0.00 1.90
3914 4049 5.538053 TGAGCCCATGAACAAAAAGTAATGA 59.462 36.000 0.00 0.00 29.98 2.57
3915 4050 6.029346 AGCCCATGAACAAAAAGTAATGAG 57.971 37.500 0.00 0.00 29.98 2.90
3916 4051 5.774690 AGCCCATGAACAAAAAGTAATGAGA 59.225 36.000 0.00 0.00 29.98 3.27
3917 4052 6.267471 AGCCCATGAACAAAAAGTAATGAGAA 59.733 34.615 0.00 0.00 29.98 2.87
3918 4053 7.038799 AGCCCATGAACAAAAAGTAATGAGAAT 60.039 33.333 0.00 0.00 29.98 2.40
3919 4054 7.276438 GCCCATGAACAAAAAGTAATGAGAATC 59.724 37.037 0.00 0.00 29.98 2.52
3932 4067 3.883830 TGAGAATCAGCCTCTTCTGTC 57.116 47.619 0.00 0.00 42.56 3.51
3933 4068 3.439154 TGAGAATCAGCCTCTTCTGTCT 58.561 45.455 0.00 0.00 42.56 3.41
3937 4072 5.022787 AGAATCAGCCTCTTCTGTCTAAGT 58.977 41.667 0.00 0.00 35.63 2.24
3942 4077 6.116806 TCAGCCTCTTCTGTCTAAGTAGTAG 58.883 44.000 0.00 0.00 35.63 2.57
3946 4081 7.670559 AGCCTCTTCTGTCTAAGTAGTAGAAAA 59.329 37.037 0.00 0.00 40.63 2.29
4014 4149 7.901029 TCTGGCCATTGTTTATTTTCATGTTA 58.099 30.769 5.51 0.00 0.00 2.41
4051 4186 8.417106 GTTCTAGACTGACAATATCTCAATCCA 58.583 37.037 0.00 0.00 0.00 3.41
4055 4190 8.489676 AGACTGACAATATCTCAATCCAGTAT 57.510 34.615 0.00 0.00 34.25 2.12
4059 4194 9.416794 CTGACAATATCTCAATCCAGTATGTAC 57.583 37.037 0.00 0.00 0.00 2.90
4061 4196 9.197694 GACAATATCTCAATCCAGTATGTACAC 57.802 37.037 0.00 0.00 0.00 2.90
4104 4239 3.824443 ACCATTTTCCCAGTAAAAGGACG 59.176 43.478 0.00 0.00 33.19 4.79
4107 4242 4.376225 TTTTCCCAGTAAAAGGACGGAT 57.624 40.909 0.00 0.00 0.00 4.18
4142 4278 6.980397 ACAAAGTACAAGGCAAAATCTTCAAG 59.020 34.615 0.00 0.00 0.00 3.02
4185 4321 5.877491 TCTAGGACATGTATCTACGGATGT 58.123 41.667 0.00 0.00 33.71 3.06
4211 4347 1.166531 AAGTTGCGCTCAGGTTCACC 61.167 55.000 9.73 0.00 0.00 4.02
4272 4408 6.019479 GTCGAGTAAATAAGATTCTGTGGCAG 60.019 42.308 0.00 0.00 0.00 4.85
4337 4474 6.678245 GCGCACTGCAAAAATAAATAAATCAC 59.322 34.615 0.30 0.00 45.45 3.06
4397 4538 4.216257 CACGGATTCTGATTTGGTCTTTGT 59.784 41.667 0.00 0.00 0.00 2.83
4401 4542 6.385033 GGATTCTGATTTGGTCTTTGTTGAG 58.615 40.000 0.00 0.00 0.00 3.02
4406 4547 1.691196 TTGGTCTTTGTTGAGCAGGG 58.309 50.000 0.00 0.00 43.85 4.45
4521 4662 3.243805 TGGCAACATTCATTCACAACCTG 60.244 43.478 0.00 0.00 46.17 4.00
4554 4695 4.157246 ACAGGTAAAATTTTGTCCCCTCC 58.843 43.478 13.76 4.90 0.00 4.30
4629 4771 4.560108 GCTGTGAACAGGCAAAATCTGAAT 60.560 41.667 12.20 0.00 43.94 2.57
4674 4818 0.974383 GGAAGACGGTCAAAGGAGGA 59.026 55.000 11.27 0.00 0.00 3.71
4689 4833 2.108970 GGAGGAAACATAGTCCGGACT 58.891 52.381 37.59 37.59 45.02 3.85
4728 4872 2.923121 GATGGCTTTGACATCCAGCTA 58.077 47.619 2.15 0.00 41.86 3.32
4776 4920 6.291648 TGATGATATCTGGATAGCTTGGTC 57.708 41.667 3.98 0.00 31.42 4.02
4944 5088 4.509616 GGGTTTTTGTACTTTTGGCTGTT 58.490 39.130 0.00 0.00 0.00 3.16
5055 5199 2.791004 GTGCATGAAACTGTTCTTGTGC 59.209 45.455 0.00 10.98 39.78 4.57
5075 5219 1.379576 GCCATGCCTGAAAGCTCCT 60.380 57.895 0.00 0.00 0.00 3.69
5186 5332 2.819154 CCGATGTGTCGCATGGCA 60.819 61.111 2.97 0.00 46.32 4.92
5187 5333 2.705220 CGATGTGTCGCATGGCAG 59.295 61.111 2.97 0.00 41.49 4.85
5188 5334 2.102438 CGATGTGTCGCATGGCAGT 61.102 57.895 2.97 0.00 41.49 4.40
5217 5363 9.023962 TGAGAGCCACACTTAATAATTGAAAAT 57.976 29.630 0.00 0.00 0.00 1.82
5239 5385 5.698741 TCCAGGAATTCTCTGCAGATTTA 57.301 39.130 18.63 5.94 0.00 1.40
5243 5389 7.031975 CCAGGAATTCTCTGCAGATTTAAAAC 58.968 38.462 18.63 5.61 0.00 2.43
5244 5390 7.094032 CCAGGAATTCTCTGCAGATTTAAAACT 60.094 37.037 18.63 7.86 0.00 2.66
5245 5391 8.950210 CAGGAATTCTCTGCAGATTTAAAACTA 58.050 33.333 18.63 0.00 0.00 2.24
5246 5392 9.520515 AGGAATTCTCTGCAGATTTAAAACTAA 57.479 29.630 18.63 1.54 0.00 2.24
5252 5398 9.912634 TCTCTGCAGATTTAAAACTAAAATTGG 57.087 29.630 18.63 0.00 0.00 3.16
5253 5399 9.696917 CTCTGCAGATTTAAAACTAAAATTGGT 57.303 29.630 18.63 0.00 0.00 3.67
5299 5446 2.167662 TGTTACCTGACAGAGCGATCA 58.832 47.619 2.38 0.00 0.00 2.92
5300 5447 2.164422 TGTTACCTGACAGAGCGATCAG 59.836 50.000 2.38 0.00 41.75 2.90
5366 5513 4.213564 ACTTGATCTCTGAATGACACCC 57.786 45.455 0.00 0.00 0.00 4.61
5384 5531 3.068165 CACCCTTTCCAACTCAAAACCTC 59.932 47.826 0.00 0.00 0.00 3.85
5422 5569 2.980233 GCGCTTTGCTGTCCCTGT 60.980 61.111 0.00 0.00 41.73 4.00
5475 5622 1.593750 GAGGCGCAGATAGCACAGG 60.594 63.158 10.83 0.00 46.13 4.00
5505 5653 5.560722 TTAAAACTGATGGTGTCCAGAGA 57.439 39.130 0.00 0.00 36.75 3.10
5507 5655 0.891373 ACTGATGGTGTCCAGAGACG 59.109 55.000 0.00 0.00 46.74 4.18
5511 5659 2.290705 TGATGGTGTCCAGAGACGTCTA 60.291 50.000 20.09 0.00 46.74 2.59
5566 5714 1.202818 AGGGAAGCTTTCTGTGGACAC 60.203 52.381 4.35 0.00 0.00 3.67
5717 5870 1.241315 GGGTACGCAACAGGCAACAT 61.241 55.000 4.83 0.00 45.17 2.71
5724 5877 2.397549 GCAACAGGCAACATTGAACTC 58.602 47.619 0.00 0.00 43.97 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.484236 CATTGTTGGTTCGTGCATTGTAT 58.516 39.130 0.00 0.00 0.00 2.29
53 54 3.239449 AGTTGATCCGGTATGCCAGATA 58.761 45.455 0.00 0.00 32.28 1.98
80 81 6.313519 ACAATCTAACCTTCAGGCTATGAA 57.686 37.500 5.08 5.08 45.79 2.57
89 90 5.163248 TGTGAGGTCAACAATCTAACCTTCA 60.163 40.000 0.00 0.00 42.15 3.02
119 120 3.389656 TGCCTTCCTTTTTGTTAAAGGGG 59.610 43.478 14.45 10.48 45.26 4.79
120 121 4.141824 TGTGCCTTCCTTTTTGTTAAAGGG 60.142 41.667 14.45 3.58 45.26 3.95
127 128 2.483538 GCATGTGTGCCTTCCTTTTTGT 60.484 45.455 0.00 0.00 45.76 2.83
129 130 2.531522 GCATGTGTGCCTTCCTTTTT 57.468 45.000 0.00 0.00 45.76 1.94
153 154 2.364002 TCGTGGAGTGACTCATGAACAA 59.636 45.455 15.33 0.00 31.08 2.83
183 184 6.318648 CCAAAGAGGAATTATGGTGATTTCGA 59.681 38.462 0.00 0.00 41.22 3.71
196 197 2.823747 GGCGGTTAACCAAAGAGGAATT 59.176 45.455 24.14 0.00 41.22 2.17
221 222 0.586802 GACACGAAACTCTTGCACCC 59.413 55.000 0.00 0.00 0.00 4.61
256 257 1.807495 GACGGAATCTAGCGGAGGGG 61.807 65.000 0.00 0.00 0.00 4.79
262 263 0.800683 TTGTGCGACGGAATCTAGCG 60.801 55.000 0.00 0.00 0.00 4.26
396 397 1.158007 AGTTTTCTCCCCATGGTGGT 58.842 50.000 11.73 0.00 35.17 4.16
441 442 1.067516 GCCTGTTGTTGTTGCACATCT 59.932 47.619 0.00 0.00 0.00 2.90
539 540 7.035612 TGCTCTCTTCTTTCCTTTTTGAAAAC 58.964 34.615 0.00 0.00 34.06 2.43
588 610 5.306160 TGAGCAAGGATGATATGAGATGTCA 59.694 40.000 0.00 0.00 37.02 3.58
589 611 5.791666 TGAGCAAGGATGATATGAGATGTC 58.208 41.667 0.00 0.00 0.00 3.06
613 661 7.087007 CCTTCATTCTCGATTCGATTATCTCA 58.913 38.462 9.54 0.00 34.61 3.27
620 668 3.384789 TGACCCTTCATTCTCGATTCGAT 59.615 43.478 9.54 0.00 34.61 3.59
750 799 4.127171 CACTTATATTGTCCAACTCCGGG 58.873 47.826 0.00 0.00 0.00 5.73
754 803 8.948631 TTCATCTCACTTATATTGTCCAACTC 57.051 34.615 0.00 0.00 0.00 3.01
756 805 9.994432 CTTTTCATCTCACTTATATTGTCCAAC 57.006 33.333 0.00 0.00 0.00 3.77
768 817 2.376518 TGAGCCCCTTTTCATCTCACTT 59.623 45.455 0.00 0.00 0.00 3.16
810 859 1.741528 CAAATTGCATTTGCCCCCTC 58.258 50.000 0.00 0.00 42.57 4.30
854 903 1.909700 TCACCATCTTTGAAGGCACC 58.090 50.000 0.00 0.00 0.00 5.01
1215 1264 4.531351 TCGCCGATGATGGGGATA 57.469 55.556 0.00 0.00 45.08 2.59
1906 1966 0.897863 AGCTGCGGAAGAGACAGAGT 60.898 55.000 0.00 0.00 33.10 3.24
2185 2286 1.931007 GCCTTCTTCCTCCCCTGCAT 61.931 60.000 0.00 0.00 0.00 3.96
2322 2423 3.665675 GAGGTCCAGCGCGATGGTT 62.666 63.158 39.10 26.58 41.43 3.67
2391 2492 3.633094 GAGCAGCTTGACGCCGAGA 62.633 63.158 0.00 0.00 40.39 4.04
2541 2642 0.828022 TGTTCCTCCTGTTCACGTGT 59.172 50.000 16.51 0.00 0.00 4.49
2774 2900 7.552687 CCCAAGATTCTTGTGCTACTAATAACA 59.447 37.037 21.75 0.00 0.00 2.41
2954 3082 1.264295 GGACGGAGGGAGTACTTGTT 58.736 55.000 0.00 0.00 0.00 2.83
2958 3088 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.00 0.00 0.00 2.73
2959 3089 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2960 3090 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2961 3091 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2962 3092 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2963 3093 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2964 3094 6.070194 ACATTCTTATATTATGGGACGGAGGG 60.070 42.308 0.00 0.00 0.00 4.30
2965 3095 6.947464 ACATTCTTATATTATGGGACGGAGG 58.053 40.000 0.00 0.00 0.00 4.30
2966 3096 8.848474 AAACATTCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
2967 3097 9.635404 AAAAACATTCTTATATTATGGGACGGA 57.365 29.630 0.00 0.00 0.00 4.69
2968 3098 9.893305 GAAAAACATTCTTATATTATGGGACGG 57.107 33.333 0.00 0.00 0.00 4.79
2980 3110 9.533253 CTTGGTCAGTTTGAAAAACATTCTTAT 57.467 29.630 5.72 0.00 0.00 1.73
2981 3111 7.491048 GCTTGGTCAGTTTGAAAAACATTCTTA 59.509 33.333 5.72 0.00 0.00 2.10
2982 3112 6.313658 GCTTGGTCAGTTTGAAAAACATTCTT 59.686 34.615 5.72 0.00 0.00 2.52
2983 3113 5.812127 GCTTGGTCAGTTTGAAAAACATTCT 59.188 36.000 5.72 0.00 0.00 2.40
2984 3114 5.812127 AGCTTGGTCAGTTTGAAAAACATTC 59.188 36.000 5.72 0.00 0.00 2.67
2985 3115 5.733676 AGCTTGGTCAGTTTGAAAAACATT 58.266 33.333 5.72 0.00 0.00 2.71
2986 3116 5.343307 AGCTTGGTCAGTTTGAAAAACAT 57.657 34.783 5.72 0.00 0.00 2.71
2987 3117 4.799564 AGCTTGGTCAGTTTGAAAAACA 57.200 36.364 5.72 0.00 0.00 2.83
2988 3118 5.167845 TCAAGCTTGGTCAGTTTGAAAAAC 58.832 37.500 25.73 0.00 46.50 2.43
2989 3119 5.398603 TCAAGCTTGGTCAGTTTGAAAAA 57.601 34.783 25.73 0.00 46.50 1.94
2994 3124 5.811613 TCATTTTTCAAGCTTGGTCAGTTTG 59.188 36.000 25.73 14.37 43.40 2.93
2995 3125 5.976458 TCATTTTTCAAGCTTGGTCAGTTT 58.024 33.333 25.73 3.34 0.00 2.66
2996 3126 5.596836 TCATTTTTCAAGCTTGGTCAGTT 57.403 34.783 25.73 4.91 0.00 3.16
2997 3127 5.537674 AGATCATTTTTCAAGCTTGGTCAGT 59.462 36.000 25.73 7.58 0.00 3.41
2998 3128 6.022163 AGATCATTTTTCAAGCTTGGTCAG 57.978 37.500 25.73 11.48 0.00 3.51
2999 3129 6.409524 AAGATCATTTTTCAAGCTTGGTCA 57.590 33.333 25.73 8.13 0.00 4.02
3012 3142 9.759473 CCCTGTCCCATAATATAAGATCATTTT 57.241 33.333 0.00 0.00 0.00 1.82
3013 3143 8.339247 CCCCTGTCCCATAATATAAGATCATTT 58.661 37.037 0.00 0.00 0.00 2.32
3014 3144 7.091811 CCCCCTGTCCCATAATATAAGATCATT 60.092 40.741 0.00 0.00 0.00 2.57
3015 3145 6.391055 CCCCCTGTCCCATAATATAAGATCAT 59.609 42.308 0.00 0.00 0.00 2.45
3016 3146 5.731187 CCCCCTGTCCCATAATATAAGATCA 59.269 44.000 0.00 0.00 0.00 2.92
3017 3147 5.970640 TCCCCCTGTCCCATAATATAAGATC 59.029 44.000 0.00 0.00 0.00 2.75
3018 3148 5.939437 TCCCCCTGTCCCATAATATAAGAT 58.061 41.667 0.00 0.00 0.00 2.40
3019 3149 5.162648 ACTCCCCCTGTCCCATAATATAAGA 60.163 44.000 0.00 0.00 0.00 2.10
3020 3150 5.101529 ACTCCCCCTGTCCCATAATATAAG 58.898 45.833 0.00 0.00 0.00 1.73
3021 3151 5.114743 ACTCCCCCTGTCCCATAATATAA 57.885 43.478 0.00 0.00 0.00 0.98
3022 3152 4.796185 ACTCCCCCTGTCCCATAATATA 57.204 45.455 0.00 0.00 0.00 0.86
3023 3153 3.674358 ACTCCCCCTGTCCCATAATAT 57.326 47.619 0.00 0.00 0.00 1.28
3024 3154 4.579850 TTACTCCCCCTGTCCCATAATA 57.420 45.455 0.00 0.00 0.00 0.98
3025 3155 3.448277 TTACTCCCCCTGTCCCATAAT 57.552 47.619 0.00 0.00 0.00 1.28
3026 3156 2.974285 TTACTCCCCCTGTCCCATAA 57.026 50.000 0.00 0.00 0.00 1.90
3027 3157 4.499472 CTTATTACTCCCCCTGTCCCATA 58.501 47.826 0.00 0.00 0.00 2.74
3028 3158 3.327439 CTTATTACTCCCCCTGTCCCAT 58.673 50.000 0.00 0.00 0.00 4.00
3029 3159 2.631268 CCTTATTACTCCCCCTGTCCCA 60.631 54.545 0.00 0.00 0.00 4.37
3030 3160 2.055579 CCTTATTACTCCCCCTGTCCC 58.944 57.143 0.00 0.00 0.00 4.46
3031 3161 2.772930 ACCTTATTACTCCCCCTGTCC 58.227 52.381 0.00 0.00 0.00 4.02
3032 3162 4.812653 TCTACCTTATTACTCCCCCTGTC 58.187 47.826 0.00 0.00 0.00 3.51
3033 3163 4.913154 TCTACCTTATTACTCCCCCTGT 57.087 45.455 0.00 0.00 0.00 4.00
3034 3164 6.354938 GTTTTCTACCTTATTACTCCCCCTG 58.645 44.000 0.00 0.00 0.00 4.45
3035 3165 5.431073 GGTTTTCTACCTTATTACTCCCCCT 59.569 44.000 0.00 0.00 44.10 4.79
3036 3166 5.398353 GGGTTTTCTACCTTATTACTCCCCC 60.398 48.000 0.00 0.00 46.86 5.40
3037 3167 5.398353 GGGGTTTTCTACCTTATTACTCCCC 60.398 48.000 0.00 0.00 46.86 4.81
3038 3168 5.398353 GGGGGTTTTCTACCTTATTACTCCC 60.398 48.000 0.00 0.00 46.86 4.30
3039 3169 5.192321 TGGGGGTTTTCTACCTTATTACTCC 59.808 44.000 0.00 0.00 46.86 3.85
3040 3170 6.157471 TCTGGGGGTTTTCTACCTTATTACTC 59.843 42.308 0.00 0.00 46.86 2.59
3092 3222 2.160417 GGCGTCAGTTCAGAAATTCAGG 59.840 50.000 0.00 0.00 0.00 3.86
3160 3291 4.166011 GGCACGATGTTGGCGAGC 62.166 66.667 0.00 0.00 43.04 5.03
3337 3468 2.833151 TACCCCATCCCGCTGGAACT 62.833 60.000 0.00 0.00 45.98 3.01
3482 3613 1.593196 TCACCAACTGGAAAGAAGCG 58.407 50.000 1.86 0.00 38.94 4.68
3498 3629 0.392998 ATGACCTGAACGGCCATCAC 60.393 55.000 2.24 0.00 28.48 3.06
3555 3686 6.594937 CCTACTTCCTAGGTACTATAGCTTCG 59.405 46.154 9.08 0.00 41.70 3.79
3557 3688 7.257126 CCTCCTACTTCCTAGGTACTATAGCTT 60.257 44.444 9.08 0.00 41.70 3.74
3563 3694 3.986134 CCCCTCCTACTTCCTAGGTACTA 59.014 52.174 9.08 0.00 42.79 1.82
3724 3856 1.938585 TTGGTCTCGGGATCAGAACT 58.061 50.000 0.00 0.00 33.73 3.01
3873 4008 3.070159 GGCTCACTCATAGACATAGGCAA 59.930 47.826 0.00 0.00 0.00 4.52
3889 4024 3.733443 ACTTTTTGTTCATGGGCTCAC 57.267 42.857 0.00 0.00 0.00 3.51
3890 4025 5.538053 TCATTACTTTTTGTTCATGGGCTCA 59.462 36.000 0.00 0.00 0.00 4.26
3891 4026 6.024552 TCATTACTTTTTGTTCATGGGCTC 57.975 37.500 0.00 0.00 0.00 4.70
3892 4027 5.774690 TCTCATTACTTTTTGTTCATGGGCT 59.225 36.000 0.00 0.00 0.00 5.19
3893 4028 6.024552 TCTCATTACTTTTTGTTCATGGGC 57.975 37.500 0.00 0.00 0.00 5.36
3894 4029 8.306038 TGATTCTCATTACTTTTTGTTCATGGG 58.694 33.333 0.00 0.00 0.00 4.00
3895 4030 9.350357 CTGATTCTCATTACTTTTTGTTCATGG 57.650 33.333 0.00 0.00 0.00 3.66
3896 4031 8.857216 GCTGATTCTCATTACTTTTTGTTCATG 58.143 33.333 0.00 0.00 0.00 3.07
3897 4032 8.031277 GGCTGATTCTCATTACTTTTTGTTCAT 58.969 33.333 0.00 0.00 0.00 2.57
3898 4033 7.231317 AGGCTGATTCTCATTACTTTTTGTTCA 59.769 33.333 0.00 0.00 0.00 3.18
3899 4034 7.597386 AGGCTGATTCTCATTACTTTTTGTTC 58.403 34.615 0.00 0.00 0.00 3.18
3900 4035 7.449704 AGAGGCTGATTCTCATTACTTTTTGTT 59.550 33.333 0.00 0.00 33.92 2.83
3901 4036 6.944862 AGAGGCTGATTCTCATTACTTTTTGT 59.055 34.615 0.00 0.00 33.92 2.83
3902 4037 7.388460 AGAGGCTGATTCTCATTACTTTTTG 57.612 36.000 0.00 0.00 33.92 2.44
3903 4038 7.887495 AGAAGAGGCTGATTCTCATTACTTTTT 59.113 33.333 0.00 0.00 29.80 1.94
3904 4039 7.336427 CAGAAGAGGCTGATTCTCATTACTTTT 59.664 37.037 8.27 0.00 38.14 2.27
3905 4040 6.822676 CAGAAGAGGCTGATTCTCATTACTTT 59.177 38.462 8.27 0.00 38.14 2.66
3906 4041 6.070309 ACAGAAGAGGCTGATTCTCATTACTT 60.070 38.462 8.27 0.00 39.20 2.24
3907 4042 5.424895 ACAGAAGAGGCTGATTCTCATTACT 59.575 40.000 8.27 0.00 39.20 2.24
3908 4043 5.669477 ACAGAAGAGGCTGATTCTCATTAC 58.331 41.667 8.27 0.00 39.20 1.89
3909 4044 5.660417 AGACAGAAGAGGCTGATTCTCATTA 59.340 40.000 8.27 0.00 39.20 1.90
3910 4045 4.470664 AGACAGAAGAGGCTGATTCTCATT 59.529 41.667 8.27 0.00 39.20 2.57
3911 4046 4.032310 AGACAGAAGAGGCTGATTCTCAT 58.968 43.478 8.27 1.66 39.20 2.90
3912 4047 3.439154 AGACAGAAGAGGCTGATTCTCA 58.561 45.455 8.27 0.00 39.20 3.27
3913 4048 5.127031 ACTTAGACAGAAGAGGCTGATTCTC 59.873 44.000 8.27 0.97 39.20 2.87
3914 4049 5.022787 ACTTAGACAGAAGAGGCTGATTCT 58.977 41.667 0.00 0.00 39.20 2.40
3915 4050 5.337578 ACTTAGACAGAAGAGGCTGATTC 57.662 43.478 0.00 0.00 39.20 2.52
3916 4051 5.955355 ACTACTTAGACAGAAGAGGCTGATT 59.045 40.000 0.00 0.00 39.20 2.57
3917 4052 5.515106 ACTACTTAGACAGAAGAGGCTGAT 58.485 41.667 0.00 0.00 39.20 2.90
3918 4053 4.924625 ACTACTTAGACAGAAGAGGCTGA 58.075 43.478 0.00 0.00 39.20 4.26
3919 4054 6.116806 TCTACTACTTAGACAGAAGAGGCTG 58.883 44.000 0.00 0.00 41.63 4.85
3920 4055 6.316280 TCTACTACTTAGACAGAAGAGGCT 57.684 41.667 0.00 0.00 31.28 4.58
3921 4056 7.393841 TTTCTACTACTTAGACAGAAGAGGC 57.606 40.000 0.00 0.00 36.48 4.70
3946 4081 5.985911 ACTAGACAAGCCGGTGTATAATTT 58.014 37.500 1.90 0.00 0.00 1.82
3948 4083 5.357257 CAACTAGACAAGCCGGTGTATAAT 58.643 41.667 1.90 0.00 0.00 1.28
3949 4084 4.751060 CAACTAGACAAGCCGGTGTATAA 58.249 43.478 1.90 0.00 0.00 0.98
3952 4087 1.337447 GCAACTAGACAAGCCGGTGTA 60.337 52.381 1.90 0.00 0.00 2.90
3956 4091 0.320771 ACTGCAACTAGACAAGCCGG 60.321 55.000 0.00 0.00 0.00 6.13
3958 4093 2.742589 GGTTACTGCAACTAGACAAGCC 59.257 50.000 0.00 0.00 37.30 4.35
3959 4094 3.186613 GTGGTTACTGCAACTAGACAAGC 59.813 47.826 0.00 0.00 37.30 4.01
3960 4095 4.377021 TGTGGTTACTGCAACTAGACAAG 58.623 43.478 0.00 0.00 37.30 3.16
3961 4096 4.409718 TGTGGTTACTGCAACTAGACAA 57.590 40.909 0.00 0.00 37.30 3.18
4014 4149 1.437547 AGTCTAGAACCCTGAACCCCT 59.562 52.381 0.00 0.00 0.00 4.79
4051 4186 5.724328 CACATGAGGTTCTGTGTACATACT 58.276 41.667 0.00 0.00 38.33 2.12
4055 4190 2.549992 GGCACATGAGGTTCTGTGTACA 60.550 50.000 0.00 0.00 43.66 2.90
4059 4194 3.327600 TGGCACATGAGGTTCTGTG 57.672 52.632 0.00 0.00 44.40 3.66
4104 4239 9.516314 GCCTTGTACTTTGTTATATTTCAATCC 57.484 33.333 0.00 0.00 0.00 3.01
4185 4321 0.950555 CTGAGCGCAACTTGCTACCA 60.951 55.000 11.47 5.64 44.18 3.25
4199 4335 0.824759 AGGATACGGTGAACCTGAGC 59.175 55.000 0.00 0.00 46.39 4.26
4211 4347 2.152016 TCGATCACCTAGCAGGATACG 58.848 52.381 8.91 8.48 46.39 3.06
4272 4408 3.126514 CACATCTCACACAATCTTGGAGC 59.873 47.826 0.00 0.00 0.00 4.70
4369 4510 4.141287 ACCAAATCAGAATCCGTGTTTCA 58.859 39.130 0.00 0.00 0.00 2.69
4406 4547 0.958822 ACCGGTGATTTCAGGTTTGC 59.041 50.000 6.12 0.00 32.38 3.68
4518 4659 7.619964 ATTTTACCTGTATTTCGTAACCAGG 57.380 36.000 16.19 16.19 46.48 4.45
4521 4662 9.681692 ACAAAATTTTACCTGTATTTCGTAACC 57.318 29.630 2.44 0.00 0.00 2.85
4629 4771 9.591792 CATCTGAACATGAGAAAGATACAGTTA 57.408 33.333 0.00 0.00 0.00 2.24
4728 4872 5.600669 AAAAGGGTCAGTTCTTAGGGAAT 57.399 39.130 0.00 0.00 36.24 3.01
4753 4897 5.105595 CGACCAAGCTATCCAGATATCATCA 60.106 44.000 5.32 0.00 0.00 3.07
4767 4911 2.823924 TAACTGCAACGACCAAGCTA 57.176 45.000 0.00 0.00 0.00 3.32
4770 4914 3.181505 TGTGTTTAACTGCAACGACCAAG 60.182 43.478 0.00 0.00 0.00 3.61
4776 4920 5.034152 ACAATCTTGTGTTTAACTGCAACG 58.966 37.500 0.00 0.00 40.49 4.10
4800 4944 3.360249 AATATGATCTTTTGCAGGCGC 57.640 42.857 0.00 0.00 39.24 6.53
4801 4945 5.916883 CCTAAAATATGATCTTTTGCAGGCG 59.083 40.000 0.00 0.00 0.00 5.52
4924 5068 5.346551 ACGAAACAGCCAAAAGTACAAAAAC 59.653 36.000 0.00 0.00 0.00 2.43
4944 5088 4.452825 TGACTAACCACATGGAAAACGAA 58.547 39.130 4.53 0.00 38.94 3.85
5055 5199 1.664321 GGAGCTTTCAGGCATGGCTG 61.664 60.000 36.58 36.58 33.13 4.85
5068 5212 1.419387 AGCTGAGAACAACAGGAGCTT 59.581 47.619 0.00 0.00 36.09 3.74
5075 5219 3.623060 GTCTGAACAAGCTGAGAACAACA 59.377 43.478 0.00 0.00 0.00 3.33
5186 5332 3.838244 TTAAGTGTGGCTCTCAACACT 57.162 42.857 2.71 2.71 44.25 3.55
5187 5333 6.743575 ATTATTAAGTGTGGCTCTCAACAC 57.256 37.500 0.00 0.00 38.08 3.32
5188 5334 6.939730 TCAATTATTAAGTGTGGCTCTCAACA 59.060 34.615 4.01 0.00 0.00 3.33
5217 5363 4.581309 AAATCTGCAGAGAATTCCTGGA 57.419 40.909 22.96 16.84 32.51 3.86
5239 5385 6.983890 GTCCATGACACACCAATTTTAGTTTT 59.016 34.615 0.00 0.00 32.09 2.43
5243 5389 5.703978 TGTCCATGACACACCAATTTTAG 57.296 39.130 0.00 0.00 37.67 1.85
5244 5390 5.506483 CGTTGTCCATGACACACCAATTTTA 60.506 40.000 0.00 0.00 42.60 1.52
5245 5391 4.692228 GTTGTCCATGACACACCAATTTT 58.308 39.130 0.00 0.00 42.60 1.82
5246 5392 3.243367 CGTTGTCCATGACACACCAATTT 60.243 43.478 0.00 0.00 42.60 1.82
5249 5395 1.304254 CGTTGTCCATGACACACCAA 58.696 50.000 0.00 0.00 42.60 3.67
5251 5397 1.234615 CCCGTTGTCCATGACACACC 61.235 60.000 0.00 0.00 42.60 4.16
5252 5398 0.250124 TCCCGTTGTCCATGACACAC 60.250 55.000 0.00 0.00 42.60 3.82
5253 5399 0.470341 TTCCCGTTGTCCATGACACA 59.530 50.000 0.00 0.00 42.60 3.72
5295 5442 4.593864 GGCGACCCGAGGCTGATC 62.594 72.222 0.00 0.00 0.00 2.92
5299 5446 4.162690 GAATGGCGACCCGAGGCT 62.163 66.667 0.00 0.00 35.01 4.58
5366 5513 5.109210 GTTTGGAGGTTTTGAGTTGGAAAG 58.891 41.667 0.00 0.00 0.00 2.62
5384 5531 2.294233 CAGAGGACACCAACATGTTTGG 59.706 50.000 19.38 19.38 44.91 3.28
5422 5569 4.054671 CAAAGACGGGCAAAATTTAAGCA 58.945 39.130 14.99 0.00 0.00 3.91
5505 5653 2.901249 AGCACGCCATTATTTAGACGT 58.099 42.857 0.00 0.00 0.00 4.34
5507 5655 5.277345 CCAACTAGCACGCCATTATTTAGAC 60.277 44.000 0.00 0.00 0.00 2.59
5511 5659 2.687935 CCCAACTAGCACGCCATTATTT 59.312 45.455 0.00 0.00 0.00 1.40
5566 5714 2.107141 GAGATCTTGTCCCCGGCG 59.893 66.667 0.00 0.00 0.00 6.46
5717 5870 4.354155 CGCCAACGGAGAGTTCAA 57.646 55.556 0.00 0.00 42.02 2.69


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

AutoCloner maintained by Alex Coulton.