Multiple sequence alignment - TraesCS3B01G409400

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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 TraesCS3B01G409400 chr3B 100.000 3254 0 0 1 3254 644922212 644918959 0.000000e+00 6010.0
1 TraesCS3B01G409400 chr3D 92.600 2527 123 29 1 2504 482609137 482606652 0.000000e+00 3572.0
2 TraesCS3B01G409400 chr3D 86.224 617 78 7 2500 3115 482606527 482605917 0.000000e+00 662.0
3 TraesCS3B01G409400 chr3A 92.851 2266 106 21 378 2613 625556614 625554375 0.000000e+00 3236.0
4 TraesCS3B01G409400 chr3A 86.089 381 28 11 7 377 625562117 625561752 1.420000e-103 387.0
5 TraesCS3B01G409400 chr3A 81.267 363 65 3 2714 3075 625540923 625540563 1.140000e-74 291.0
6 TraesCS3B01G409400 chr1D 92.241 116 9 0 1802 1917 436069978 436070093 7.220000e-37 165.0
7 TraesCS3B01G409400 chr1D 92.035 113 9 0 1805 1917 32736552 32736440 3.360000e-35 159.0
8 TraesCS3B01G409400 chr7D 92.035 113 9 0 1805 1917 527011279 527011391 3.360000e-35 159.0
9 TraesCS3B01G409400 chr7D 86.792 53 7 0 3003 3055 218180259 218180311 3.510000e-05 60.2
10 TraesCS3B01G409400 chr2D 91.379 116 10 0 1802 1917 562843914 562844029 3.360000e-35 159.0
11 TraesCS3B01G409400 chr1B 89.474 114 12 0 1805 1918 52240261 52240148 9.410000e-31 145.0
12 TraesCS3B01G409400 chr7B 89.286 112 12 0 1807 1918 677704195 677704306 1.220000e-29 141.0
13 TraesCS3B01G409400 chr4A 95.238 42 2 0 2070 2111 114092809 114092850 2.100000e-07 67.6


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 TraesCS3B01G409400 chr3B 644918959 644922212 3253 True 6010 6010 100.000 1 3254 1 chr3B.!!$R1 3253
1 TraesCS3B01G409400 chr3D 482605917 482609137 3220 True 2117 3572 89.412 1 3115 2 chr3D.!!$R1 3114
2 TraesCS3B01G409400 chr3A 625554375 625556614 2239 True 3236 3236 92.851 378 2613 1 chr3A.!!$R2 2235

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
613 634 0.101939 CGAGGGCCTAGTCCGTAAAC 59.898 60.0 5.73 0.0 29.39 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 2387 0.54995 CAGTGCCCTCCAGATCCAAT 59.45 55.0 0.0 0.0 0.0 3.16 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
73 74 4.154347 CGAGCCTCCCCACTCTGC 62.154 72.222 0.00 0.00 0.00 4.26
77 78 2.988839 GCCTCCCCACTCTGCCAAT 61.989 63.158 0.00 0.00 0.00 3.16
78 79 1.225704 CCTCCCCACTCTGCCAATC 59.774 63.158 0.00 0.00 0.00 2.67
80 81 0.107312 CTCCCCACTCTGCCAATCTG 60.107 60.000 0.00 0.00 0.00 2.90
87 88 1.030457 CTCTGCCAATCTGCCAATCC 58.970 55.000 0.00 0.00 0.00 3.01
94 95 0.178981 AATCTGCCAATCCCATCCCG 60.179 55.000 0.00 0.00 0.00 5.14
104 105 2.275089 CCATCCCGTCCCATGCAA 59.725 61.111 0.00 0.00 0.00 4.08
107 108 3.721370 ATCCCGTCCCATGCAAGCC 62.721 63.158 0.00 0.00 0.00 4.35
115 116 1.914764 CCATGCAAGCCCCCTTTGT 60.915 57.895 0.00 0.00 0.00 2.83
154 155 4.974645 TGTAGACATTTCAGGAACCACT 57.025 40.909 0.00 0.00 0.00 4.00
155 156 6.428083 TTGTAGACATTTCAGGAACCACTA 57.572 37.500 0.00 0.00 0.00 2.74
156 157 6.037786 TGTAGACATTTCAGGAACCACTAG 57.962 41.667 0.00 0.00 0.00 2.57
157 158 4.559862 AGACATTTCAGGAACCACTAGG 57.440 45.455 0.00 0.00 42.21 3.02
158 159 3.264450 AGACATTTCAGGAACCACTAGGG 59.736 47.826 0.00 0.00 44.81 3.53
159 160 2.308866 ACATTTCAGGAACCACTAGGGG 59.691 50.000 10.33 10.33 42.91 4.79
160 161 2.127651 TTTCAGGAACCACTAGGGGT 57.872 50.000 12.16 12.16 45.04 4.95
185 191 1.434555 CGCAACATTGGAACTACCGA 58.565 50.000 0.00 0.00 42.61 4.69
251 261 1.038130 ACGGATGGAACTCTCTCGGG 61.038 60.000 0.00 0.00 0.00 5.14
254 264 0.397254 GATGGAACTCTCTCGGGGGA 60.397 60.000 0.00 0.00 0.00 4.81
255 265 0.266152 ATGGAACTCTCTCGGGGGAT 59.734 55.000 0.00 0.00 0.00 3.85
277 287 1.080569 CACCAAGCAAATCGGTGGC 60.081 57.895 0.00 0.00 45.32 5.01
278 288 1.530419 ACCAAGCAAATCGGTGGCA 60.530 52.632 0.00 0.00 0.00 4.92
303 313 4.383649 GTCAAACGTTAAGATCGTGCTACA 59.616 41.667 0.00 0.00 41.38 2.74
304 314 4.619760 TCAAACGTTAAGATCGTGCTACAG 59.380 41.667 0.00 0.00 41.38 2.74
305 315 2.527100 ACGTTAAGATCGTGCTACAGC 58.473 47.619 0.00 0.00 40.07 4.40
306 316 1.852895 CGTTAAGATCGTGCTACAGCC 59.147 52.381 0.00 0.00 41.18 4.85
307 317 2.734175 CGTTAAGATCGTGCTACAGCCA 60.734 50.000 0.00 0.00 41.18 4.75
338 348 1.208052 GTAGGACTGGATCAGCTTGCA 59.792 52.381 0.00 0.00 34.37 4.08
341 351 1.681166 GGACTGGATCAGCTTGCACAT 60.681 52.381 0.00 0.00 34.37 3.21
372 382 0.179145 GTCAAAGCTAGCTCGCGGTA 60.179 55.000 19.65 0.00 34.40 4.02
376 386 1.030488 AAGCTAGCTCGCGGTAGTGA 61.030 55.000 19.65 0.00 41.97 3.41
422 433 2.426738 GAGCTGCCATCTATCTATCGCT 59.573 50.000 0.00 0.00 0.00 4.93
476 496 2.347490 GTGAAGGCCGGAGAAGCA 59.653 61.111 5.05 0.00 0.00 3.91
481 501 2.360475 GGCCGGAGAAGCAAAGCT 60.360 61.111 5.05 0.00 42.56 3.74
540 560 2.039879 ACGCCCCAGAAAGTCAACTATT 59.960 45.455 0.00 0.00 0.00 1.73
587 607 7.812690 ATTACGGACCTAATTTGGAAATACC 57.187 36.000 13.16 6.81 39.54 2.73
605 626 1.296715 CACAAAGCGAGGGCCTAGT 59.703 57.895 15.41 0.00 41.24 2.57
606 627 0.741221 CACAAAGCGAGGGCCTAGTC 60.741 60.000 15.41 7.64 41.24 2.59
613 634 0.101939 CGAGGGCCTAGTCCGTAAAC 59.898 60.000 5.73 0.00 29.39 2.01
615 636 1.520120 GGGCCTAGTCCGTAAACGC 60.520 63.158 0.84 0.00 38.18 4.84
616 637 1.216178 GGCCTAGTCCGTAAACGCA 59.784 57.895 0.00 0.00 38.18 5.24
634 655 3.760035 GCTCCGCTCTGACCCGAA 61.760 66.667 0.00 0.00 0.00 4.30
672 693 1.005805 ACAAAGGGCAGCCATGTGATA 59.994 47.619 23.52 0.00 0.00 2.15
673 694 1.406539 CAAAGGGCAGCCATGTGATAC 59.593 52.381 11.15 0.00 0.00 2.24
674 695 0.921896 AAGGGCAGCCATGTGATACT 59.078 50.000 15.19 0.00 0.00 2.12
675 696 0.182061 AGGGCAGCCATGTGATACTG 59.818 55.000 15.19 0.00 0.00 2.74
676 697 0.107017 GGGCAGCCATGTGATACTGT 60.107 55.000 15.19 0.00 32.65 3.55
677 698 1.140852 GGGCAGCCATGTGATACTGTA 59.859 52.381 15.19 0.00 32.65 2.74
748 776 2.670934 AACAGCTGCCTCCGCAAG 60.671 61.111 15.27 0.00 46.66 4.01
847 875 4.081642 AGCACGAATAAACTAGAGCTCCAA 60.082 41.667 10.93 0.00 0.00 3.53
964 993 2.765150 GTCCGGACGCGTTTAACG 59.235 61.111 20.85 13.57 45.88 3.18
989 1019 0.669077 CGGCCGAGCTACTAATCAGT 59.331 55.000 24.07 0.00 38.91 3.41
995 1025 2.358267 CGAGCTACTAATCAGTTCCGGT 59.642 50.000 0.00 0.00 36.14 5.28
1013 1046 0.682209 GTGAAGATGGCAGCCATGGT 60.682 55.000 32.58 18.53 45.26 3.55
1059 1092 0.251653 TGCCGTCCTACTTCCTCTGT 60.252 55.000 0.00 0.00 0.00 3.41
1071 1104 0.816018 TCCTCTGTCCGATCTCGCTC 60.816 60.000 0.00 0.00 38.18 5.03
2055 2088 4.357947 GTGCTGAGGTCCGTCGCA 62.358 66.667 0.00 0.00 0.00 5.10
2266 2299 2.002586 CTTCGTGACGATCAATGCCTT 58.997 47.619 9.08 0.00 35.23 4.35
2464 2500 6.317663 TGATCCCATTTCTTTCATCAGAGA 57.682 37.500 0.00 0.00 0.00 3.10
2465 2501 6.907961 TGATCCCATTTCTTTCATCAGAGAT 58.092 36.000 0.00 0.00 0.00 2.75
2466 2502 8.037723 TGATCCCATTTCTTTCATCAGAGATA 57.962 34.615 0.00 0.00 0.00 1.98
2467 2503 8.496916 TGATCCCATTTCTTTCATCAGAGATAA 58.503 33.333 0.00 0.00 0.00 1.75
2615 2790 3.314553 ACGAACACTCACCTTATGAACG 58.685 45.455 0.00 0.00 36.69 3.95
2616 2791 3.243636 ACGAACACTCACCTTATGAACGT 60.244 43.478 0.00 0.00 36.69 3.99
2617 2792 4.022935 ACGAACACTCACCTTATGAACGTA 60.023 41.667 0.00 0.00 36.69 3.57
2618 2793 4.919168 CGAACACTCACCTTATGAACGTAA 59.081 41.667 0.00 0.00 36.69 3.18
2619 2794 5.060569 CGAACACTCACCTTATGAACGTAAG 59.939 44.000 0.00 6.77 36.69 2.34
2622 2797 6.157211 ACACTCACCTTATGAACGTAAGAAG 58.843 40.000 13.35 10.31 36.69 2.85
2653 2828 3.118261 TGCCCTGATAAGCACCTCTAAAG 60.118 47.826 0.00 0.00 33.08 1.85
2660 2835 7.113658 TGATAAGCACCTCTAAAGGACTAAG 57.886 40.000 0.00 0.00 46.67 2.18
2662 2837 3.173965 AGCACCTCTAAAGGACTAAGCA 58.826 45.455 0.00 0.00 46.67 3.91
2664 2839 3.195825 GCACCTCTAAAGGACTAAGCAGA 59.804 47.826 0.00 0.00 46.67 4.26
2665 2840 4.749976 CACCTCTAAAGGACTAAGCAGAC 58.250 47.826 0.00 0.00 46.67 3.51
2666 2841 3.770388 ACCTCTAAAGGACTAAGCAGACC 59.230 47.826 0.00 0.00 46.67 3.85
2669 2844 5.148651 TCTAAAGGACTAAGCAGACCAAC 57.851 43.478 0.00 0.00 38.88 3.77
2679 2854 2.787994 AGCAGACCAACCTTGAGATTG 58.212 47.619 0.00 0.00 0.00 2.67
2701 2876 3.740115 ACGAACTTAACACATGAGCCTT 58.260 40.909 0.00 0.00 0.00 4.35
2707 2882 5.238583 ACTTAACACATGAGCCTTGTAGTC 58.761 41.667 0.00 0.00 0.00 2.59
2708 2883 3.769739 AACACATGAGCCTTGTAGTCA 57.230 42.857 0.00 0.00 0.00 3.41
2726 2901 1.343465 TCAACGAGAACCTTGTCTCCC 59.657 52.381 0.00 0.00 40.93 4.30
2729 2904 0.247736 CGAGAACCTTGTCTCCCTGG 59.752 60.000 0.00 0.00 40.93 4.45
2806 2981 3.758554 GCCAAGTCTAGATTTTGAAGCCA 59.241 43.478 17.01 0.00 0.00 4.75
2819 2994 0.038166 GAAGCCAGGTGGATTGACCA 59.962 55.000 3.76 0.00 44.94 4.02
2833 3008 4.763793 GGATTGACCATATGATTGTCAGGG 59.236 45.833 3.65 0.00 39.89 4.45
2839 3014 4.008330 CCATATGATTGTCAGGGCATCTC 58.992 47.826 3.65 0.00 0.00 2.75
2843 3018 2.019984 GATTGTCAGGGCATCTCCAAC 58.980 52.381 0.00 0.00 36.21 3.77
2845 3020 2.109126 GTCAGGGCATCTCCAACGC 61.109 63.158 0.00 0.00 36.21 4.84
2859 3034 0.885596 CAACGCCGTCCCCTAAAACA 60.886 55.000 0.00 0.00 0.00 2.83
2860 3035 0.037160 AACGCCGTCCCCTAAAACAT 59.963 50.000 0.00 0.00 0.00 2.71
2866 3041 3.267483 CCGTCCCCTAAAACATACACAG 58.733 50.000 0.00 0.00 0.00 3.66
2872 3047 7.201848 CGTCCCCTAAAACATACACAGTATCTA 60.202 40.741 0.00 0.00 0.00 1.98
2877 3052 9.197694 CCTAAAACATACACAGTATCTATCAGC 57.802 37.037 0.00 0.00 0.00 4.26
2884 3059 3.565902 CACAGTATCTATCAGCGGACTCA 59.434 47.826 0.00 0.00 0.00 3.41
2886 3061 4.830046 ACAGTATCTATCAGCGGACTCATT 59.170 41.667 0.00 0.00 0.00 2.57
2887 3062 5.303078 ACAGTATCTATCAGCGGACTCATTT 59.697 40.000 0.00 0.00 0.00 2.32
2888 3063 5.632764 CAGTATCTATCAGCGGACTCATTTG 59.367 44.000 0.00 0.00 0.00 2.32
2891 3066 1.091771 ATCAGCGGACTCATTTGCGG 61.092 55.000 0.00 0.00 0.00 5.69
2892 3067 1.741401 CAGCGGACTCATTTGCGGA 60.741 57.895 0.00 0.00 0.00 5.54
2894 3069 2.032634 GCGGACTCATTTGCGGACA 61.033 57.895 0.00 0.00 0.00 4.02
2916 3091 1.068741 GGATACGAAAGCCGGTCATCT 59.931 52.381 1.90 0.00 43.93 2.90
2918 3093 3.566523 GATACGAAAGCCGGTCATCTAG 58.433 50.000 1.90 0.00 43.93 2.43
2939 3114 1.719709 GCATTCCCTAAACGTCCGC 59.280 57.895 0.00 0.00 0.00 5.54
2941 3116 1.093496 CATTCCCTAAACGTCCGCCC 61.093 60.000 0.00 0.00 0.00 6.13
2942 3117 1.555477 ATTCCCTAAACGTCCGCCCA 61.555 55.000 0.00 0.00 0.00 5.36
2943 3118 1.766625 TTCCCTAAACGTCCGCCCAA 61.767 55.000 0.00 0.00 0.00 4.12
2960 3135 2.500098 CCCAAGTCCGACCTCTTTCATA 59.500 50.000 0.00 0.00 0.00 2.15
2961 3136 3.134804 CCCAAGTCCGACCTCTTTCATAT 59.865 47.826 0.00 0.00 0.00 1.78
2963 3138 3.992260 AGTCCGACCTCTTTCATATCG 57.008 47.619 0.00 0.00 0.00 2.92
2976 3151 7.125536 TCTTTCATATCGAATGCATAGCAAG 57.874 36.000 0.00 0.00 43.62 4.01
2992 3167 7.148035 TGCATAGCAAGATGAGCAAATTAAAGA 60.148 33.333 0.00 0.00 34.76 2.52
2998 3173 4.333926 AGATGAGCAAATTAAAGAGCGGTC 59.666 41.667 6.48 6.48 0.00 4.79
3044 3219 3.853355 AAAGAGGTGCATCTCCATAGG 57.147 47.619 23.46 0.00 34.46 2.57
3057 3232 3.118408 TCTCCATAGGTTTTACATGCGCT 60.118 43.478 9.73 0.00 0.00 5.92
3068 3243 4.495911 TTACATGCGCTTGATCACAAAA 57.504 36.364 27.85 8.56 35.49 2.44
3069 3244 3.367992 ACATGCGCTTGATCACAAAAA 57.632 38.095 27.85 0.00 35.49 1.94
3070 3245 3.311106 ACATGCGCTTGATCACAAAAAG 58.689 40.909 27.85 0.00 35.49 2.27
3073 3248 3.371168 TGCGCTTGATCACAAAAAGTTC 58.629 40.909 9.73 0.00 35.49 3.01
3077 3252 4.261155 CGCTTGATCACAAAAAGTTCCAGA 60.261 41.667 0.00 0.00 35.49 3.86
3078 3253 4.978580 GCTTGATCACAAAAAGTTCCAGAC 59.021 41.667 0.00 0.00 35.49 3.51
3080 3255 3.888930 TGATCACAAAAAGTTCCAGACCC 59.111 43.478 0.00 0.00 0.00 4.46
3083 3258 3.118334 TCACAAAAAGTTCCAGACCCGTA 60.118 43.478 0.00 0.00 0.00 4.02
3095 3270 0.735287 GACCCGTAGTCCAGCGAAAC 60.735 60.000 0.00 0.00 39.84 2.78
3096 3271 1.290955 CCCGTAGTCCAGCGAAACA 59.709 57.895 0.00 0.00 0.00 2.83
3097 3272 0.320073 CCCGTAGTCCAGCGAAACAA 60.320 55.000 0.00 0.00 0.00 2.83
3098 3273 0.788391 CCGTAGTCCAGCGAAACAAC 59.212 55.000 0.00 0.00 0.00 3.32
3099 3274 1.493772 CGTAGTCCAGCGAAACAACA 58.506 50.000 0.00 0.00 0.00 3.33
3103 3278 3.354089 AGTCCAGCGAAACAACAATTG 57.646 42.857 3.24 3.24 0.00 2.32
3116 3291 2.307496 ACAATTGTTGCCATCCCAGA 57.693 45.000 4.92 0.00 0.00 3.86
3117 3292 1.895131 ACAATTGTTGCCATCCCAGAC 59.105 47.619 4.92 0.00 0.00 3.51
3118 3293 1.894466 CAATTGTTGCCATCCCAGACA 59.106 47.619 0.00 0.00 0.00 3.41
3119 3294 1.843368 ATTGTTGCCATCCCAGACAG 58.157 50.000 0.00 0.00 0.00 3.51
3120 3295 0.251297 TTGTTGCCATCCCAGACAGG 60.251 55.000 0.00 0.00 37.03 4.00
3123 3298 2.124403 GCCATCCCAGACAGGCTG 60.124 66.667 14.16 14.16 43.70 4.85
3124 3299 2.124403 CCATCCCAGACAGGCTGC 60.124 66.667 15.89 7.65 43.50 5.25
3125 3300 2.124403 CATCCCAGACAGGCTGCC 60.124 66.667 15.89 11.65 43.50 4.85
3126 3301 3.415087 ATCCCAGACAGGCTGCCC 61.415 66.667 16.57 6.92 43.50 5.36
3142 3317 4.803426 CCGTGCCTCCTCGCTCAC 62.803 72.222 0.00 0.00 0.00 3.51
3143 3318 3.753434 CGTGCCTCCTCGCTCACT 61.753 66.667 0.00 0.00 0.00 3.41
3144 3319 2.659610 GTGCCTCCTCGCTCACTT 59.340 61.111 0.00 0.00 0.00 3.16
3145 3320 1.004440 GTGCCTCCTCGCTCACTTT 60.004 57.895 0.00 0.00 0.00 2.66
3146 3321 1.004560 TGCCTCCTCGCTCACTTTG 60.005 57.895 0.00 0.00 0.00 2.77
3147 3322 2.394563 GCCTCCTCGCTCACTTTGC 61.395 63.158 0.00 0.00 0.00 3.68
3154 3329 3.922175 GCTCACTTTGCGGCAAAC 58.078 55.556 23.23 10.29 0.00 2.93
3155 3330 1.360192 GCTCACTTTGCGGCAAACT 59.640 52.632 23.23 12.40 0.00 2.66
3156 3331 0.661483 GCTCACTTTGCGGCAAACTC 60.661 55.000 23.23 7.73 0.00 3.01
3157 3332 0.040067 CTCACTTTGCGGCAAACTCC 60.040 55.000 23.23 0.00 0.00 3.85
3158 3333 0.465460 TCACTTTGCGGCAAACTCCT 60.465 50.000 23.23 4.47 0.00 3.69
3159 3334 0.040067 CACTTTGCGGCAAACTCCTC 60.040 55.000 23.23 0.00 0.00 3.71
3160 3335 1.172812 ACTTTGCGGCAAACTCCTCC 61.173 55.000 23.23 0.00 0.00 4.30
3161 3336 1.152860 TTTGCGGCAAACTCCTCCA 60.153 52.632 23.23 0.00 0.00 3.86
3162 3337 1.452145 TTTGCGGCAAACTCCTCCAC 61.452 55.000 23.23 0.00 0.00 4.02
3163 3338 2.281484 GCGGCAAACTCCTCCACA 60.281 61.111 0.00 0.00 0.00 4.17
3164 3339 1.675641 GCGGCAAACTCCTCCACAT 60.676 57.895 0.00 0.00 0.00 3.21
3165 3340 1.648467 GCGGCAAACTCCTCCACATC 61.648 60.000 0.00 0.00 0.00 3.06
3166 3341 0.321564 CGGCAAACTCCTCCACATCA 60.322 55.000 0.00 0.00 0.00 3.07
3167 3342 1.679944 CGGCAAACTCCTCCACATCAT 60.680 52.381 0.00 0.00 0.00 2.45
3168 3343 2.019984 GGCAAACTCCTCCACATCATC 58.980 52.381 0.00 0.00 0.00 2.92
3169 3344 2.019984 GCAAACTCCTCCACATCATCC 58.980 52.381 0.00 0.00 0.00 3.51
3170 3345 2.618816 GCAAACTCCTCCACATCATCCA 60.619 50.000 0.00 0.00 0.00 3.41
3171 3346 3.894759 CAAACTCCTCCACATCATCCAT 58.105 45.455 0.00 0.00 0.00 3.41
3172 3347 3.853355 AACTCCTCCACATCATCCATC 57.147 47.619 0.00 0.00 0.00 3.51
3173 3348 3.057626 ACTCCTCCACATCATCCATCT 57.942 47.619 0.00 0.00 0.00 2.90
3174 3349 2.971330 ACTCCTCCACATCATCCATCTC 59.029 50.000 0.00 0.00 0.00 2.75
3175 3350 2.302445 CTCCTCCACATCATCCATCTCC 59.698 54.545 0.00 0.00 0.00 3.71
3176 3351 2.090324 TCCTCCACATCATCCATCTCCT 60.090 50.000 0.00 0.00 0.00 3.69
3177 3352 2.302445 CCTCCACATCATCCATCTCCTC 59.698 54.545 0.00 0.00 0.00 3.71
3178 3353 2.970640 CTCCACATCATCCATCTCCTCA 59.029 50.000 0.00 0.00 0.00 3.86
3179 3354 2.702478 TCCACATCATCCATCTCCTCAC 59.298 50.000 0.00 0.00 0.00 3.51
3180 3355 2.224475 CCACATCATCCATCTCCTCACC 60.224 54.545 0.00 0.00 0.00 4.02
3181 3356 2.436911 CACATCATCCATCTCCTCACCA 59.563 50.000 0.00 0.00 0.00 4.17
3182 3357 3.072622 CACATCATCCATCTCCTCACCAT 59.927 47.826 0.00 0.00 0.00 3.55
3183 3358 3.720526 ACATCATCCATCTCCTCACCATT 59.279 43.478 0.00 0.00 0.00 3.16
3184 3359 4.167502 ACATCATCCATCTCCTCACCATTT 59.832 41.667 0.00 0.00 0.00 2.32
3185 3360 4.160642 TCATCCATCTCCTCACCATTTG 57.839 45.455 0.00 0.00 0.00 2.32
3186 3361 2.425143 TCCATCTCCTCACCATTTGC 57.575 50.000 0.00 0.00 0.00 3.68
3187 3362 1.064463 TCCATCTCCTCACCATTTGCC 60.064 52.381 0.00 0.00 0.00 4.52
3188 3363 1.064166 CCATCTCCTCACCATTTGCCT 60.064 52.381 0.00 0.00 0.00 4.75
3189 3364 2.295885 CATCTCCTCACCATTTGCCTC 58.704 52.381 0.00 0.00 0.00 4.70
3190 3365 0.620556 TCTCCTCACCATTTGCCTCC 59.379 55.000 0.00 0.00 0.00 4.30
3191 3366 0.329261 CTCCTCACCATTTGCCTCCA 59.671 55.000 0.00 0.00 0.00 3.86
3192 3367 1.002069 TCCTCACCATTTGCCTCCAT 58.998 50.000 0.00 0.00 0.00 3.41
3193 3368 1.064463 TCCTCACCATTTGCCTCCATC 60.064 52.381 0.00 0.00 0.00 3.51
3194 3369 1.064166 CCTCACCATTTGCCTCCATCT 60.064 52.381 0.00 0.00 0.00 2.90
3195 3370 2.295885 CTCACCATTTGCCTCCATCTC 58.704 52.381 0.00 0.00 0.00 2.75
3196 3371 1.019673 CACCATTTGCCTCCATCTCG 58.980 55.000 0.00 0.00 0.00 4.04
3197 3372 0.107017 ACCATTTGCCTCCATCTCGG 60.107 55.000 0.00 0.00 0.00 4.63
3198 3373 1.450531 CCATTTGCCTCCATCTCGGC 61.451 60.000 0.00 0.00 46.46 5.54
3199 3374 1.152881 ATTTGCCTCCATCTCGGCC 60.153 57.895 0.00 0.00 45.71 6.13
3200 3375 2.947938 ATTTGCCTCCATCTCGGCCG 62.948 60.000 22.12 22.12 45.71 6.13
3204 3379 4.161295 CTCCATCTCGGCCGCCAA 62.161 66.667 23.51 8.52 33.14 4.52
3205 3380 3.466791 CTCCATCTCGGCCGCCAAT 62.467 63.158 23.51 10.76 33.14 3.16
3206 3381 3.282157 CCATCTCGGCCGCCAATG 61.282 66.667 23.51 21.64 0.00 2.82
3207 3382 3.957535 CATCTCGGCCGCCAATGC 61.958 66.667 23.51 0.00 0.00 3.56
3208 3383 4.181010 ATCTCGGCCGCCAATGCT 62.181 61.111 23.51 0.00 34.43 3.79
3209 3384 3.704231 ATCTCGGCCGCCAATGCTT 62.704 57.895 23.51 0.00 34.43 3.91
3210 3385 3.880846 CTCGGCCGCCAATGCTTC 61.881 66.667 23.51 0.00 34.43 3.86
3211 3386 4.713735 TCGGCCGCCAATGCTTCA 62.714 61.111 23.51 0.00 34.43 3.02
3212 3387 3.746889 CGGCCGCCAATGCTTCAA 61.747 61.111 14.67 0.00 34.43 2.69
3213 3388 2.125952 GGCCGCCAATGCTTCAAC 60.126 61.111 3.91 0.00 34.43 3.18
3214 3389 2.650196 GCCGCCAATGCTTCAACA 59.350 55.556 0.00 0.00 34.43 3.33
3215 3390 1.216178 GCCGCCAATGCTTCAACAT 59.784 52.632 0.00 0.00 34.43 2.71
3216 3391 0.803380 GCCGCCAATGCTTCAACATC 60.803 55.000 0.00 0.00 34.43 3.06
3217 3392 0.179129 CCGCCAATGCTTCAACATCC 60.179 55.000 0.00 0.00 34.43 3.51
3218 3393 0.527113 CGCCAATGCTTCAACATCCA 59.473 50.000 0.00 0.00 34.43 3.41
3219 3394 1.067706 CGCCAATGCTTCAACATCCAA 60.068 47.619 0.00 0.00 34.43 3.53
3220 3395 2.609984 CGCCAATGCTTCAACATCCAAA 60.610 45.455 0.00 0.00 34.43 3.28
3221 3396 3.602483 GCCAATGCTTCAACATCCAAAT 58.398 40.909 0.00 0.00 33.53 2.32
3222 3397 4.677514 CGCCAATGCTTCAACATCCAAATA 60.678 41.667 0.00 0.00 34.43 1.40
3223 3398 5.177326 GCCAATGCTTCAACATCCAAATAA 58.823 37.500 0.00 0.00 33.53 1.40
3224 3399 5.292589 GCCAATGCTTCAACATCCAAATAAG 59.707 40.000 0.00 0.00 33.53 1.73
3225 3400 5.813672 CCAATGCTTCAACATCCAAATAAGG 59.186 40.000 0.00 0.00 0.00 2.69
3226 3401 6.351202 CCAATGCTTCAACATCCAAATAAGGA 60.351 38.462 0.00 0.00 43.01 3.36
3227 3402 5.643379 TGCTTCAACATCCAAATAAGGAC 57.357 39.130 0.00 0.00 41.30 3.85
3228 3403 4.155826 TGCTTCAACATCCAAATAAGGACG 59.844 41.667 0.00 0.00 41.30 4.79
3229 3404 4.438744 GCTTCAACATCCAAATAAGGACGG 60.439 45.833 0.00 0.00 41.30 4.79
3230 3405 4.295141 TCAACATCCAAATAAGGACGGT 57.705 40.909 0.00 0.00 41.30 4.83
3231 3406 4.006989 TCAACATCCAAATAAGGACGGTG 58.993 43.478 0.00 0.00 39.83 4.94
3232 3407 3.713826 ACATCCAAATAAGGACGGTGT 57.286 42.857 0.00 0.00 41.30 4.16
3233 3408 3.343617 ACATCCAAATAAGGACGGTGTG 58.656 45.455 0.00 0.00 41.30 3.82
3234 3409 1.816074 TCCAAATAAGGACGGTGTGC 58.184 50.000 0.00 0.00 31.23 4.57
3235 3410 1.072489 TCCAAATAAGGACGGTGTGCA 59.928 47.619 0.00 0.00 31.23 4.57
3236 3411 2.091541 CCAAATAAGGACGGTGTGCAT 58.908 47.619 0.00 0.00 0.00 3.96
3237 3412 2.159393 CCAAATAAGGACGGTGTGCATG 60.159 50.000 0.00 0.00 0.00 4.06
3238 3413 2.746904 CAAATAAGGACGGTGTGCATGA 59.253 45.455 0.00 0.00 0.00 3.07
3239 3414 3.281727 AATAAGGACGGTGTGCATGAT 57.718 42.857 0.00 0.00 0.00 2.45
3240 3415 2.309528 TAAGGACGGTGTGCATGATC 57.690 50.000 0.00 0.00 0.00 2.92
3241 3416 0.324614 AAGGACGGTGTGCATGATCA 59.675 50.000 0.00 0.00 0.00 2.92
3242 3417 0.543277 AGGACGGTGTGCATGATCAT 59.457 50.000 1.18 1.18 0.00 2.45
3243 3418 0.659427 GGACGGTGTGCATGATCATG 59.341 55.000 28.04 28.04 41.60 3.07
3244 3419 0.659427 GACGGTGTGCATGATCATGG 59.341 55.000 31.62 18.64 39.16 3.66
3245 3420 1.357690 CGGTGTGCATGATCATGGC 59.642 57.895 31.62 24.16 39.16 4.40
3246 3421 1.737816 GGTGTGCATGATCATGGCC 59.262 57.895 31.62 19.07 39.16 5.36
3247 3422 1.737816 GTGTGCATGATCATGGCCC 59.262 57.895 31.62 18.44 39.16 5.80
3248 3423 0.754217 GTGTGCATGATCATGGCCCT 60.754 55.000 31.62 0.00 39.16 5.19
3249 3424 0.466739 TGTGCATGATCATGGCCCTC 60.467 55.000 31.62 17.79 39.16 4.30
3250 3425 0.466739 GTGCATGATCATGGCCCTCA 60.467 55.000 31.62 19.89 39.16 3.86
3251 3426 0.481128 TGCATGATCATGGCCCTCAT 59.519 50.000 31.62 0.43 39.16 2.90
3252 3427 1.133294 TGCATGATCATGGCCCTCATT 60.133 47.619 31.62 0.00 39.16 2.57
3253 3428 1.272490 GCATGATCATGGCCCTCATTG 59.728 52.381 31.62 9.24 39.16 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.335145 GGATGGGATTGGCAGATTGG 58.665 55.000 0.00 0.00 0.00 3.16
77 78 1.983119 GACGGGATGGGATTGGCAGA 61.983 60.000 0.00 0.00 0.00 4.26
78 79 1.526917 GACGGGATGGGATTGGCAG 60.527 63.158 0.00 0.00 0.00 4.85
80 81 2.203351 GGACGGGATGGGATTGGC 60.203 66.667 0.00 0.00 0.00 4.52
87 88 1.825191 CTTGCATGGGACGGGATGG 60.825 63.158 0.00 0.00 0.00 3.51
94 95 3.607084 AAGGGGGCTTGCATGGGAC 62.607 63.158 1.34 0.00 0.00 4.46
104 105 3.875390 CTTTGCACAAAGGGGGCT 58.125 55.556 14.08 0.00 42.96 5.19
115 116 3.150903 AAGCTCAGGCCCCTTTGCA 62.151 57.895 0.00 0.00 39.73 4.08
125 126 3.937706 CCTGAAATGTCTACAAGCTCAGG 59.062 47.826 17.22 17.22 40.44 3.86
154 155 2.296073 ATGTTGCGGAAAAACCCCTA 57.704 45.000 0.00 0.00 34.64 3.53
155 156 1.069978 CAATGTTGCGGAAAAACCCCT 59.930 47.619 0.00 0.00 34.64 4.79
156 157 1.507562 CAATGTTGCGGAAAAACCCC 58.492 50.000 0.00 0.00 34.64 4.95
157 158 1.069358 TCCAATGTTGCGGAAAAACCC 59.931 47.619 0.00 0.00 34.64 4.11
158 159 2.517650 TCCAATGTTGCGGAAAAACC 57.482 45.000 0.00 0.00 0.00 3.27
159 160 3.453424 AGTTCCAATGTTGCGGAAAAAC 58.547 40.909 0.00 0.00 42.80 2.43
160 161 3.810310 AGTTCCAATGTTGCGGAAAAA 57.190 38.095 0.00 0.00 42.80 1.94
161 162 3.004944 GGTAGTTCCAATGTTGCGGAAAA 59.995 43.478 0.00 0.00 42.80 2.29
162 163 2.554893 GGTAGTTCCAATGTTGCGGAAA 59.445 45.455 0.00 0.00 42.80 3.13
163 164 2.156098 GGTAGTTCCAATGTTGCGGAA 58.844 47.619 0.00 0.00 38.99 4.30
164 165 1.816074 GGTAGTTCCAATGTTGCGGA 58.184 50.000 0.00 0.00 35.97 5.54
165 166 0.446222 CGGTAGTTCCAATGTTGCGG 59.554 55.000 0.00 0.00 35.57 5.69
166 167 1.434555 TCGGTAGTTCCAATGTTGCG 58.565 50.000 0.00 0.00 35.57 4.85
171 177 4.939052 ACTCCTATCGGTAGTTCCAATG 57.061 45.455 1.27 0.00 35.57 2.82
196 202 1.137086 GAACTCCTATCGGCAGCTCAA 59.863 52.381 0.00 0.00 0.00 3.02
222 228 5.617252 AGAGTTCCATCCGTAGTTCAAAAA 58.383 37.500 0.00 0.00 0.00 1.94
223 229 5.011738 AGAGAGTTCCATCCGTAGTTCAAAA 59.988 40.000 0.00 0.00 0.00 2.44
224 230 4.527038 AGAGAGTTCCATCCGTAGTTCAAA 59.473 41.667 0.00 0.00 0.00 2.69
225 231 4.087182 AGAGAGTTCCATCCGTAGTTCAA 58.913 43.478 0.00 0.00 0.00 2.69
226 232 3.695060 GAGAGAGTTCCATCCGTAGTTCA 59.305 47.826 0.00 0.00 0.00 3.18
227 233 3.242804 CGAGAGAGTTCCATCCGTAGTTC 60.243 52.174 0.00 0.00 0.00 3.01
228 234 2.683867 CGAGAGAGTTCCATCCGTAGTT 59.316 50.000 0.00 0.00 0.00 2.24
229 235 2.290464 CGAGAGAGTTCCATCCGTAGT 58.710 52.381 0.00 0.00 0.00 2.73
230 236 1.604755 CCGAGAGAGTTCCATCCGTAG 59.395 57.143 0.00 0.00 0.00 3.51
267 277 1.068610 CGTTTGACATGCCACCGATTT 60.069 47.619 0.00 0.00 0.00 2.17
277 287 4.081761 GCACGATCTTAACGTTTGACATG 58.918 43.478 5.91 6.40 42.07 3.21
278 288 3.994392 AGCACGATCTTAACGTTTGACAT 59.006 39.130 5.91 0.00 42.07 3.06
306 316 1.153549 GTCCTACCGAGCTGGCTTG 60.154 63.158 0.00 3.00 43.94 4.01
307 317 1.305381 AGTCCTACCGAGCTGGCTT 60.305 57.895 0.00 0.00 43.94 4.35
338 348 0.608130 TTGACTCGCTAGGTGCATGT 59.392 50.000 0.00 0.00 43.06 3.21
341 351 0.670546 GCTTTGACTCGCTAGGTGCA 60.671 55.000 0.00 0.00 43.06 4.57
348 358 0.179150 CGAGCTAGCTTTGACTCGCT 60.179 55.000 20.42 0.00 44.56 4.93
351 361 1.142778 CCGCGAGCTAGCTTTGACTC 61.143 60.000 20.42 3.84 34.40 3.36
372 382 2.495084 GCCTCGACTTTTCCTTTCACT 58.505 47.619 0.00 0.00 0.00 3.41
376 386 1.235281 GCGGCCTCGACTTTTCCTTT 61.235 55.000 0.00 0.00 39.00 3.11
476 496 2.026729 GCTGGGTTTCTCCTCTAGCTTT 60.027 50.000 0.00 0.00 35.98 3.51
481 501 2.748388 GGTAGCTGGGTTTCTCCTCTA 58.252 52.381 0.00 0.00 36.25 2.43
540 560 8.421249 AATTACTCCTCCATTTGACATTTTGA 57.579 30.769 0.00 0.00 0.00 2.69
587 607 0.741221 GACTAGGCCCTCGCTTTGTG 60.741 60.000 0.00 0.00 30.58 3.33
605 626 2.126228 CGGAGCTGCGTTTACGGA 60.126 61.111 20.53 0.00 40.23 4.69
634 655 2.922950 TTTACTGGTCGCTCGCGGT 61.923 57.895 6.13 3.97 40.25 5.68
672 693 3.691118 GGTGTTCACATGCATCATACAGT 59.309 43.478 0.00 0.00 0.00 3.55
673 694 3.690628 TGGTGTTCACATGCATCATACAG 59.309 43.478 0.00 0.00 0.00 2.74
674 695 3.439825 GTGGTGTTCACATGCATCATACA 59.560 43.478 0.00 0.00 45.39 2.29
675 696 4.019919 GTGGTGTTCACATGCATCATAC 57.980 45.455 0.00 0.00 45.39 2.39
714 739 3.630312 GCTGTTGCCTCCGGATTATTTAA 59.370 43.478 3.57 0.00 0.00 1.52
715 740 3.118038 AGCTGTTGCCTCCGGATTATTTA 60.118 43.478 3.57 0.00 40.80 1.40
827 855 5.662674 AGTTGGAGCTCTAGTTTATTCGT 57.337 39.130 14.64 0.00 0.00 3.85
959 988 4.666397 TCGGCCGCAGCACGTTAA 62.666 61.111 23.51 0.00 42.56 2.01
967 996 0.664767 GATTAGTAGCTCGGCCGCAG 60.665 60.000 23.51 19.56 0.00 5.18
979 1008 5.163447 CCATCTTCACCGGAACTGATTAGTA 60.163 44.000 9.46 0.00 35.69 1.82
989 1019 1.377202 GCTGCCATCTTCACCGGAA 60.377 57.895 9.46 0.00 0.00 4.30
995 1025 0.681887 CACCATGGCTGCCATCTTCA 60.682 55.000 30.49 3.56 43.15 3.02
2151 2184 0.799393 GCGCCTTCTCTTTGGTCTTC 59.201 55.000 0.00 0.00 0.00 2.87
2349 2384 2.043526 AGTGCCCTCCAGATCCAATTTT 59.956 45.455 0.00 0.00 0.00 1.82
2350 2385 1.642762 AGTGCCCTCCAGATCCAATTT 59.357 47.619 0.00 0.00 0.00 1.82
2352 2387 0.549950 CAGTGCCCTCCAGATCCAAT 59.450 55.000 0.00 0.00 0.00 3.16
2360 2396 2.847234 ACGAACCAGTGCCCTCCA 60.847 61.111 0.00 0.00 0.00 3.86
2422 2458 6.295575 GGGATCATCCTCCACAGAATAAGTAG 60.296 46.154 2.93 0.00 36.57 2.57
2433 2469 3.872459 AGAAATGGGATCATCCTCCAC 57.128 47.619 2.93 0.00 36.57 4.02
2464 2500 7.554835 AGCATGAAACATGGCAAAATCATTTAT 59.445 29.630 12.56 0.00 0.00 1.40
2465 2501 6.879993 AGCATGAAACATGGCAAAATCATTTA 59.120 30.769 12.56 0.00 0.00 1.40
2466 2502 5.708230 AGCATGAAACATGGCAAAATCATTT 59.292 32.000 12.56 0.00 0.00 2.32
2467 2503 5.250200 AGCATGAAACATGGCAAAATCATT 58.750 33.333 12.56 0.00 0.00 2.57
2636 2811 6.407074 GCTTAGTCCTTTAGAGGTGCTTATCA 60.407 42.308 0.00 0.00 43.97 2.15
2640 2815 3.583086 TGCTTAGTCCTTTAGAGGTGCTT 59.417 43.478 0.00 0.00 43.97 3.91
2653 2828 2.038557 TCAAGGTTGGTCTGCTTAGTCC 59.961 50.000 0.00 0.00 0.00 3.85
2660 2835 2.485814 GTCAATCTCAAGGTTGGTCTGC 59.514 50.000 3.30 0.00 0.00 4.26
2662 2837 2.632996 TCGTCAATCTCAAGGTTGGTCT 59.367 45.455 3.30 0.00 0.00 3.85
2664 2839 3.139077 GTTCGTCAATCTCAAGGTTGGT 58.861 45.455 3.30 0.00 0.00 3.67
2665 2840 3.403038 AGTTCGTCAATCTCAAGGTTGG 58.597 45.455 3.30 0.00 0.00 3.77
2666 2841 6.018262 TGTTAAGTTCGTCAATCTCAAGGTTG 60.018 38.462 0.00 0.00 0.00 3.77
2669 2844 5.465390 TGTGTTAAGTTCGTCAATCTCAAGG 59.535 40.000 0.00 0.00 0.00 3.61
2679 2854 3.326747 AGGCTCATGTGTTAAGTTCGTC 58.673 45.455 0.00 0.00 0.00 4.20
2701 2876 3.635373 AGACAAGGTTCTCGTTGACTACA 59.365 43.478 7.47 0.00 40.40 2.74
2707 2882 1.344763 AGGGAGACAAGGTTCTCGTTG 59.655 52.381 0.00 0.00 42.74 4.10
2708 2883 1.344763 CAGGGAGACAAGGTTCTCGTT 59.655 52.381 0.00 0.00 42.74 3.85
2766 2941 6.162777 ACTTGGCATGCGTATTTGTATTTTT 58.837 32.000 12.44 0.00 0.00 1.94
2777 2952 3.819564 AATCTAGACTTGGCATGCGTA 57.180 42.857 12.44 0.00 0.00 4.42
2780 2955 4.970662 TCAAAATCTAGACTTGGCATGC 57.029 40.909 9.90 9.90 0.00 4.06
2819 2994 3.654321 TGGAGATGCCCTGACAATCATAT 59.346 43.478 0.00 0.00 34.97 1.78
2833 3008 3.195698 GGACGGCGTTGGAGATGC 61.196 66.667 16.19 0.00 39.65 3.91
2839 3014 1.302671 TTTTAGGGGACGGCGTTGG 60.303 57.895 16.19 0.00 0.00 3.77
2843 3018 1.292992 GTATGTTTTAGGGGACGGCG 58.707 55.000 4.80 4.80 0.00 6.46
2845 3020 3.267483 CTGTGTATGTTTTAGGGGACGG 58.733 50.000 0.00 0.00 0.00 4.79
2859 3034 5.317808 AGTCCGCTGATAGATACTGTGTAT 58.682 41.667 0.00 0.00 0.00 2.29
2860 3035 4.715713 AGTCCGCTGATAGATACTGTGTA 58.284 43.478 0.00 0.00 0.00 2.90
2866 3041 4.387256 GCAAATGAGTCCGCTGATAGATAC 59.613 45.833 0.00 0.00 0.00 2.24
2872 3047 1.091771 CCGCAAATGAGTCCGCTGAT 61.092 55.000 0.00 0.00 0.00 2.90
2877 3052 1.787847 GTGTCCGCAAATGAGTCCG 59.212 57.895 0.00 0.00 0.00 4.79
2884 3059 0.173935 TCGTATCCGTGTCCGCAAAT 59.826 50.000 0.00 0.00 35.01 2.32
2886 3061 0.038435 TTTCGTATCCGTGTCCGCAA 60.038 50.000 0.00 0.00 35.01 4.85
2887 3062 0.457166 CTTTCGTATCCGTGTCCGCA 60.457 55.000 0.00 0.00 35.01 5.69
2888 3063 1.749609 GCTTTCGTATCCGTGTCCGC 61.750 60.000 0.00 0.00 35.01 5.54
2891 3066 1.143969 CCGGCTTTCGTATCCGTGTC 61.144 60.000 0.00 0.00 41.46 3.67
2892 3067 1.153706 CCGGCTTTCGTATCCGTGT 60.154 57.895 0.00 0.00 41.46 4.49
2894 3069 1.140375 GACCGGCTTTCGTATCCGT 59.860 57.895 0.00 0.00 41.46 4.69
2902 3077 0.876342 CGGCTAGATGACCGGCTTTC 60.876 60.000 0.00 0.00 45.74 2.62
2903 3078 1.144057 CGGCTAGATGACCGGCTTT 59.856 57.895 0.00 0.00 45.74 3.51
2904 3079 2.815308 CGGCTAGATGACCGGCTT 59.185 61.111 0.00 0.00 45.74 4.35
2909 3084 0.603975 GGGAATGCGGCTAGATGACC 60.604 60.000 0.00 0.00 0.00 4.02
2911 3086 2.009681 TAGGGAATGCGGCTAGATGA 57.990 50.000 0.00 0.00 0.00 2.92
2916 3091 0.538118 ACGTTTAGGGAATGCGGCTA 59.462 50.000 0.00 0.00 0.00 3.93
2918 3093 1.712018 GGACGTTTAGGGAATGCGGC 61.712 60.000 0.00 0.00 0.00 6.53
2939 3114 0.685097 TGAAAGAGGTCGGACTTGGG 59.315 55.000 8.23 0.00 0.00 4.12
2941 3116 4.045104 CGATATGAAAGAGGTCGGACTTG 58.955 47.826 8.23 0.00 0.00 3.16
2942 3117 3.952323 TCGATATGAAAGAGGTCGGACTT 59.048 43.478 8.23 0.00 33.46 3.01
2943 3118 3.552875 TCGATATGAAAGAGGTCGGACT 58.447 45.455 8.23 0.00 33.46 3.85
2960 3135 3.436015 GCTCATCTTGCTATGCATTCGAT 59.564 43.478 3.54 0.00 38.76 3.59
2961 3136 2.804527 GCTCATCTTGCTATGCATTCGA 59.195 45.455 3.54 0.00 38.76 3.71
2963 3138 4.563337 TTGCTCATCTTGCTATGCATTC 57.437 40.909 3.54 0.00 38.76 2.67
2976 3151 4.333926 AGACCGCTCTTTAATTTGCTCATC 59.666 41.667 0.00 0.00 0.00 2.92
2992 3167 1.521681 GGCGCTATGAAAGACCGCT 60.522 57.895 7.64 0.00 43.70 5.52
2998 3173 0.861837 GTGATCGGGCGCTATGAAAG 59.138 55.000 7.64 0.00 0.00 2.62
3044 3219 3.820689 TGTGATCAAGCGCATGTAAAAC 58.179 40.909 11.47 6.84 0.00 2.43
3057 3232 4.340950 GGGTCTGGAACTTTTTGTGATCAA 59.659 41.667 0.00 0.00 0.00 2.57
3068 3243 1.264295 GGACTACGGGTCTGGAACTT 58.736 55.000 9.90 0.00 43.97 2.66
3069 3244 0.113776 TGGACTACGGGTCTGGAACT 59.886 55.000 9.90 0.00 43.97 3.01
3070 3245 0.531200 CTGGACTACGGGTCTGGAAC 59.469 60.000 9.90 0.00 43.97 3.62
3073 3248 2.893398 GCTGGACTACGGGTCTGG 59.107 66.667 9.90 5.45 43.97 3.86
3077 3252 1.291272 GTTTCGCTGGACTACGGGT 59.709 57.895 0.00 0.00 0.00 5.28
3078 3253 0.320073 TTGTTTCGCTGGACTACGGG 60.320 55.000 0.00 0.00 0.00 5.28
3080 3255 1.493772 TGTTGTTTCGCTGGACTACG 58.506 50.000 0.00 0.00 0.00 3.51
3083 3258 2.687935 ACAATTGTTGTTTCGCTGGACT 59.312 40.909 4.92 0.00 42.22 3.85
3103 3278 2.048603 GCCTGTCTGGGATGGCAAC 61.049 63.158 0.00 0.00 44.34 4.17
3108 3283 2.124403 GGCAGCCTGTCTGGGATG 60.124 66.667 3.29 0.00 44.66 3.51
3109 3284 3.415087 GGGCAGCCTGTCTGGGAT 61.415 66.667 12.43 0.00 43.06 3.85
3125 3300 4.803426 GTGAGCGAGGAGGCACGG 62.803 72.222 0.00 0.00 34.64 4.94
3126 3301 2.771763 AAAGTGAGCGAGGAGGCACG 62.772 60.000 0.00 0.00 36.43 5.34
3127 3302 1.004440 AAAGTGAGCGAGGAGGCAC 60.004 57.895 0.00 0.00 34.64 5.01
3128 3303 1.004560 CAAAGTGAGCGAGGAGGCA 60.005 57.895 0.00 0.00 34.64 4.75
3129 3304 2.394563 GCAAAGTGAGCGAGGAGGC 61.395 63.158 0.00 0.00 0.00 4.70
3130 3305 3.882025 GCAAAGTGAGCGAGGAGG 58.118 61.111 0.00 0.00 0.00 4.30
3137 3312 0.661483 GAGTTTGCCGCAAAGTGAGC 60.661 55.000 27.01 12.13 37.16 4.26
3138 3313 0.040067 GGAGTTTGCCGCAAAGTGAG 60.040 55.000 27.01 0.00 37.16 3.51
3139 3314 0.465460 AGGAGTTTGCCGCAAAGTGA 60.465 50.000 27.01 0.88 37.16 3.41
3140 3315 0.040067 GAGGAGTTTGCCGCAAAGTG 60.040 55.000 27.01 0.00 37.16 3.16
3141 3316 1.172812 GGAGGAGTTTGCCGCAAAGT 61.173 55.000 23.22 23.22 39.36 2.66
3142 3317 1.172180 TGGAGGAGTTTGCCGCAAAG 61.172 55.000 18.80 0.00 33.82 2.77
3143 3318 1.152860 TGGAGGAGTTTGCCGCAAA 60.153 52.632 14.60 14.60 0.00 3.68
3144 3319 1.896660 GTGGAGGAGTTTGCCGCAA 60.897 57.895 0.38 0.38 32.58 4.85
3145 3320 2.281484 GTGGAGGAGTTTGCCGCA 60.281 61.111 0.00 0.00 32.58 5.69
3146 3321 1.648467 GATGTGGAGGAGTTTGCCGC 61.648 60.000 0.00 0.00 0.00 6.53
3147 3322 0.321564 TGATGTGGAGGAGTTTGCCG 60.322 55.000 0.00 0.00 0.00 5.69
3148 3323 2.019984 GATGATGTGGAGGAGTTTGCC 58.980 52.381 0.00 0.00 0.00 4.52
3149 3324 2.019984 GGATGATGTGGAGGAGTTTGC 58.980 52.381 0.00 0.00 0.00 3.68
3150 3325 3.354948 TGGATGATGTGGAGGAGTTTG 57.645 47.619 0.00 0.00 0.00 2.93
3151 3326 3.784763 AGATGGATGATGTGGAGGAGTTT 59.215 43.478 0.00 0.00 0.00 2.66
3152 3327 3.390639 GAGATGGATGATGTGGAGGAGTT 59.609 47.826 0.00 0.00 0.00 3.01
3153 3328 2.971330 GAGATGGATGATGTGGAGGAGT 59.029 50.000 0.00 0.00 0.00 3.85
3154 3329 2.302445 GGAGATGGATGATGTGGAGGAG 59.698 54.545 0.00 0.00 0.00 3.69
3155 3330 2.090324 AGGAGATGGATGATGTGGAGGA 60.090 50.000 0.00 0.00 0.00 3.71
3156 3331 2.302445 GAGGAGATGGATGATGTGGAGG 59.698 54.545 0.00 0.00 0.00 4.30
3157 3332 2.970640 TGAGGAGATGGATGATGTGGAG 59.029 50.000 0.00 0.00 0.00 3.86
3158 3333 2.702478 GTGAGGAGATGGATGATGTGGA 59.298 50.000 0.00 0.00 0.00 4.02
3159 3334 2.224475 GGTGAGGAGATGGATGATGTGG 60.224 54.545 0.00 0.00 0.00 4.17
3160 3335 2.436911 TGGTGAGGAGATGGATGATGTG 59.563 50.000 0.00 0.00 0.00 3.21
3161 3336 2.767972 TGGTGAGGAGATGGATGATGT 58.232 47.619 0.00 0.00 0.00 3.06
3162 3337 4.368565 AATGGTGAGGAGATGGATGATG 57.631 45.455 0.00 0.00 0.00 3.07
3163 3338 4.726583 CAAATGGTGAGGAGATGGATGAT 58.273 43.478 0.00 0.00 0.00 2.45
3164 3339 3.686405 GCAAATGGTGAGGAGATGGATGA 60.686 47.826 0.00 0.00 0.00 2.92
3165 3340 2.621998 GCAAATGGTGAGGAGATGGATG 59.378 50.000 0.00 0.00 0.00 3.51
3166 3341 2.423947 GGCAAATGGTGAGGAGATGGAT 60.424 50.000 0.00 0.00 0.00 3.41
3167 3342 1.064463 GGCAAATGGTGAGGAGATGGA 60.064 52.381 0.00 0.00 0.00 3.41
3168 3343 1.064166 AGGCAAATGGTGAGGAGATGG 60.064 52.381 0.00 0.00 0.00 3.51
3169 3344 2.295885 GAGGCAAATGGTGAGGAGATG 58.704 52.381 0.00 0.00 0.00 2.90
3170 3345 1.213926 GGAGGCAAATGGTGAGGAGAT 59.786 52.381 0.00 0.00 0.00 2.75
3171 3346 0.620556 GGAGGCAAATGGTGAGGAGA 59.379 55.000 0.00 0.00 0.00 3.71
3172 3347 0.329261 TGGAGGCAAATGGTGAGGAG 59.671 55.000 0.00 0.00 0.00 3.69
3173 3348 1.002069 ATGGAGGCAAATGGTGAGGA 58.998 50.000 0.00 0.00 0.00 3.71
3174 3349 1.064166 AGATGGAGGCAAATGGTGAGG 60.064 52.381 0.00 0.00 0.00 3.86
3175 3350 2.295885 GAGATGGAGGCAAATGGTGAG 58.704 52.381 0.00 0.00 0.00 3.51
3176 3351 1.407299 CGAGATGGAGGCAAATGGTGA 60.407 52.381 0.00 0.00 0.00 4.02
3177 3352 1.019673 CGAGATGGAGGCAAATGGTG 58.980 55.000 0.00 0.00 0.00 4.17
3178 3353 0.107017 CCGAGATGGAGGCAAATGGT 60.107 55.000 0.00 0.00 42.00 3.55
3179 3354 2.711711 CCGAGATGGAGGCAAATGG 58.288 57.895 0.00 0.00 42.00 3.16
3187 3362 3.466791 ATTGGCGGCCGAGATGGAG 62.467 63.158 33.48 0.00 42.00 3.86
3188 3363 3.479203 ATTGGCGGCCGAGATGGA 61.479 61.111 33.48 8.01 42.00 3.41
3189 3364 3.282157 CATTGGCGGCCGAGATGG 61.282 66.667 33.48 11.07 42.50 3.51
3190 3365 3.957535 GCATTGGCGGCCGAGATG 61.958 66.667 33.48 26.98 0.00 2.90
3200 3375 2.747396 TTGGATGTTGAAGCATTGGC 57.253 45.000 0.00 0.00 41.61 4.52
3201 3376 5.813672 CCTTATTTGGATGTTGAAGCATTGG 59.186 40.000 0.00 0.00 0.00 3.16
3202 3377 6.532657 GTCCTTATTTGGATGTTGAAGCATTG 59.467 38.462 0.00 0.00 38.52 2.82
3203 3378 6.625740 CGTCCTTATTTGGATGTTGAAGCATT 60.626 38.462 0.00 0.00 38.52 3.56
3204 3379 5.163622 CGTCCTTATTTGGATGTTGAAGCAT 60.164 40.000 0.00 0.00 38.52 3.79
3205 3380 4.155826 CGTCCTTATTTGGATGTTGAAGCA 59.844 41.667 0.00 0.00 38.52 3.91
3206 3381 4.438744 CCGTCCTTATTTGGATGTTGAAGC 60.439 45.833 0.00 0.00 40.56 3.86
3207 3382 4.700213 ACCGTCCTTATTTGGATGTTGAAG 59.300 41.667 0.00 0.00 40.56 3.02
3208 3383 4.457603 CACCGTCCTTATTTGGATGTTGAA 59.542 41.667 0.00 0.00 37.62 2.69
3209 3384 4.006989 CACCGTCCTTATTTGGATGTTGA 58.993 43.478 0.00 0.00 37.62 3.18
3210 3385 3.756434 ACACCGTCCTTATTTGGATGTTG 59.244 43.478 0.00 0.00 40.15 3.33
3211 3386 3.756434 CACACCGTCCTTATTTGGATGTT 59.244 43.478 0.00 0.00 40.56 2.71
3212 3387 3.343617 CACACCGTCCTTATTTGGATGT 58.656 45.455 0.00 0.00 40.56 3.06
3213 3388 2.097466 GCACACCGTCCTTATTTGGATG 59.903 50.000 0.00 0.00 41.53 3.51
3214 3389 2.290641 TGCACACCGTCCTTATTTGGAT 60.291 45.455 0.00 0.00 38.52 3.41
3215 3390 1.072489 TGCACACCGTCCTTATTTGGA 59.928 47.619 0.00 0.00 0.00 3.53
3216 3391 1.529226 TGCACACCGTCCTTATTTGG 58.471 50.000 0.00 0.00 0.00 3.28
3217 3392 2.746904 TCATGCACACCGTCCTTATTTG 59.253 45.455 0.00 0.00 0.00 2.32
3218 3393 3.066291 TCATGCACACCGTCCTTATTT 57.934 42.857 0.00 0.00 0.00 1.40
3219 3394 2.779755 TCATGCACACCGTCCTTATT 57.220 45.000 0.00 0.00 0.00 1.40
3220 3395 2.170397 TGATCATGCACACCGTCCTTAT 59.830 45.455 0.00 0.00 0.00 1.73
3221 3396 1.552792 TGATCATGCACACCGTCCTTA 59.447 47.619 0.00 0.00 0.00 2.69
3222 3397 0.324614 TGATCATGCACACCGTCCTT 59.675 50.000 0.00 0.00 0.00 3.36
3223 3398 0.543277 ATGATCATGCACACCGTCCT 59.457 50.000 7.59 0.00 0.00 3.85
3224 3399 0.659427 CATGATCATGCACACCGTCC 59.341 55.000 22.20 0.00 31.39 4.79
3225 3400 0.659427 CCATGATCATGCACACCGTC 59.341 55.000 27.24 0.00 37.49 4.79
3226 3401 1.378882 GCCATGATCATGCACACCGT 61.379 55.000 27.24 0.00 37.49 4.83
3227 3402 1.357690 GCCATGATCATGCACACCG 59.642 57.895 27.24 14.94 37.49 4.94
3228 3403 1.737816 GGCCATGATCATGCACACC 59.262 57.895 27.24 20.42 37.49 4.16
3229 3404 0.754217 AGGGCCATGATCATGCACAC 60.754 55.000 27.24 21.76 37.49 3.82
3230 3405 0.466739 GAGGGCCATGATCATGCACA 60.467 55.000 27.24 0.00 37.49 4.57
3231 3406 0.466739 TGAGGGCCATGATCATGCAC 60.467 55.000 27.24 22.58 37.49 4.57
3232 3407 0.481128 ATGAGGGCCATGATCATGCA 59.519 50.000 27.24 19.68 37.49 3.96
3233 3408 1.272490 CAATGAGGGCCATGATCATGC 59.728 52.381 27.24 21.48 37.49 4.06


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

AutoCloner maintained by Alex Coulton.