Multiple sequence alignment - TraesCS4B01G215900

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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 TraesCS4B01G215900 chr4B 100.000 5429 0 0 1517 6945 455623004 455617576 0.000000e+00 10026
1 TraesCS4B01G215900 chr4B 100.000 1128 0 0 1 1128 455624520 455623393 0.000000e+00 2084
2 TraesCS4B01G215900 chr4D 96.843 3484 95 10 3076 6548 370536607 370533128 0.000000e+00 5810
3 TraesCS4B01G215900 chr4D 97.889 1374 27 2 1517 2889 370537961 370536589 0.000000e+00 2375
4 TraesCS4B01G215900 chr4D 95.296 574 23 4 527 1098 370538885 370538314 0.000000e+00 907
5 TraesCS4B01G215900 chr4D 90.311 547 25 3 1 542 370539424 370538901 0.000000e+00 691
6 TraesCS4B01G215900 chr4D 97.834 277 5 1 6669 6945 370532741 370532466 1.750000e-130 477
7 TraesCS4B01G215900 chr4D 100.000 191 0 0 2889 3079 478512369 478512179 3.080000e-93 353
8 TraesCS4B01G215900 chr4A 91.446 2338 132 37 4579 6875 93894203 93896513 0.000000e+00 3147
9 TraesCS4B01G215900 chr4A 97.082 1508 40 4 3076 4580 93892429 93893935 0.000000e+00 2538
10 TraesCS4B01G215900 chr4A 90.668 1393 89 28 1517 2889 93891076 93892447 0.000000e+00 1814
11 TraesCS4B01G215900 chr4A 95.858 507 11 5 631 1128 93890519 93891024 0.000000e+00 811
12 TraesCS4B01G215900 chr4A 90.476 546 43 6 111 648 93889935 93890479 0.000000e+00 712
13 TraesCS4B01G215900 chr4A 100.000 188 0 0 2890 3077 20234722 20234535 1.430000e-91 348
14 TraesCS4B01G215900 chr7A 100.000 191 0 0 2886 3076 105168804 105168994 3.080000e-93 353
15 TraesCS4B01G215900 chr1A 98.500 200 2 1 2877 3075 583789330 583789131 1.110000e-92 351
16 TraesCS4B01G215900 chr1A 92.398 171 13 0 1963 2133 209532711 209532881 1.940000e-60 244
17 TraesCS4B01G215900 chr3B 100.000 189 0 0 2889 3077 277752395 277752207 3.990000e-92 350
18 TraesCS4B01G215900 chr6B 100.000 187 0 0 2890 3076 475722868 475722682 5.160000e-91 346
19 TraesCS4B01G215900 chr5B 98.477 197 1 1 2883 3079 214934732 214934926 5.160000e-91 346
20 TraesCS4B01G215900 chr2A 99.474 190 0 1 2889 3077 661716297 661716486 1.850000e-90 344
21 TraesCS4B01G215900 chr1B 94.762 210 7 4 2860 3068 341370063 341370269 2.420000e-84 324
22 TraesCS4B01G215900 chr2B 90.173 173 14 2 1963 2134 486955613 486955783 9.070000e-54 222


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 TraesCS4B01G215900 chr4B 455617576 455624520 6944 True 6055.0 10026 100.0000 1 6945 2 chr4B.!!$R1 6944
1 TraesCS4B01G215900 chr4D 370532466 370539424 6958 True 2052.0 5810 95.6346 1 6945 5 chr4D.!!$R2 6944
2 TraesCS4B01G215900 chr4A 93889935 93896513 6578 False 1804.4 3147 93.1060 111 6875 5 chr4A.!!$F1 6764

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
247 249 0.033503 TGGCTCGAGGATGAGTGGTA 60.034 55.0 15.58 0.0 38.28 3.25 F
546 586 0.310854 GCTTGGTTGTAGGTGTGTGC 59.689 55.0 0.00 0.0 0.00 4.57 F
1854 1985 0.981183 TGCCCCTACCTAAGTGTGTG 59.019 55.0 0.00 0.0 0.00 3.82 F
2903 3038 0.405585 TTTGAGAAGGGGAGCCTTGG 59.594 55.0 0.00 0.0 0.00 3.61 F
2950 3085 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.0 0.00 0.0 0.00 2.69 F
2959 3094 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.0 0.00 0.0 35.79 3.53 F
3006 3141 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.0 0.00 0.0 0.00 4.51 F
4255 4392 0.390124 AGCATGCATTTTATGGCCCG 59.610 50.0 21.98 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 1985 1.216122 CCATCAAGCTAAGCTCGAGC 58.784 55.000 30.01 30.01 38.25 5.03 R
2519 2653 1.695813 TTGAATGCAACGCAAATCCG 58.304 45.000 0.00 0.00 43.62 4.18 R
2920 3055 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85 R
4879 5298 0.687757 AGGAGGGCGCAGATGTAAGA 60.688 55.000 10.83 0.00 0.00 2.10 R
5369 5788 2.906389 GTGATCTATGCTCCCCCACATA 59.094 50.000 0.00 0.00 0.00 2.29 R
5419 5838 6.174720 TGATCTTTCAAGTGTAGGTTGACT 57.825 37.500 0.00 0.00 33.63 3.41 R
5525 5944 5.385198 CTCTGTAGCTCCCTTCTTCTCTAT 58.615 45.833 0.00 0.00 0.00 1.98 R
6491 6950 0.319900 CTGTGTCTTCCGTGGAGGTG 60.320 60.000 0.00 0.00 41.99 4.00 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
52 53 0.329261 TGCAGCTTAGCATTGGTCCT 59.671 50.000 7.07 0.00 40.11 3.85
177 178 0.828022 AACGGTTGAGATATGCGGGA 59.172 50.000 0.00 0.00 0.00 5.14
200 202 1.668151 GGTCCTGTGCAGTTCGGTC 60.668 63.158 0.00 0.00 0.00 4.79
247 249 0.033503 TGGCTCGAGGATGAGTGGTA 60.034 55.000 15.58 0.00 38.28 3.25
257 259 2.877168 GGATGAGTGGTAGTACGTCGAT 59.123 50.000 0.00 0.00 0.00 3.59
279 281 1.070134 TGGCGTCATGGGTTCTATAGC 59.930 52.381 0.00 0.00 0.00 2.97
286 288 4.811557 GTCATGGGTTCTATAGCTCACAAC 59.188 45.833 0.00 0.00 0.00 3.32
418 424 1.950472 CACGTGACCAAAATCGCTTC 58.050 50.000 10.90 0.00 0.00 3.86
438 444 1.378762 GGCACTAGGGCTTGTGGAA 59.621 57.895 18.29 0.00 36.94 3.53
460 466 1.229428 CTGCTTTCTTCACCTTCGCA 58.771 50.000 0.00 0.00 0.00 5.10
465 471 1.338107 TTCTTCACCTTCGCAGGAGA 58.662 50.000 8.52 1.79 44.19 3.71
546 586 0.310854 GCTTGGTTGTAGGTGTGTGC 59.689 55.000 0.00 0.00 0.00 4.57
671 768 7.655236 TCTTGATGCAAATTTACAAACATGG 57.345 32.000 0.00 0.00 0.00 3.66
771 869 1.899437 GCCCTTCATGTGGACGAGGA 61.899 60.000 8.66 0.00 0.00 3.71
885 988 1.641123 AATCCGAAAATCGCCGCGTT 61.641 50.000 13.39 0.68 38.82 4.84
938 1041 2.282462 CACCCCCACCTTCAGCAC 60.282 66.667 0.00 0.00 0.00 4.40
1107 1212 2.546778 GCCGAATTCGTCAAGTCCATA 58.453 47.619 25.10 0.00 37.74 2.74
1791 1922 6.977502 GCAGCATAGTGTCGATATATCAATCT 59.022 38.462 13.11 7.49 0.00 2.40
1854 1985 0.981183 TGCCCCTACCTAAGTGTGTG 59.019 55.000 0.00 0.00 0.00 3.82
1857 1988 1.207329 CCCCTACCTAAGTGTGTGCTC 59.793 57.143 0.00 0.00 0.00 4.26
1874 2005 1.216122 CTCGAGCTTAGCTTGATGGC 58.784 55.000 22.82 1.52 46.42 4.40
2096 2230 6.479660 TCAAAAACTGATCAATGCCTTTGTTC 59.520 34.615 0.00 0.07 36.65 3.18
2101 2235 5.537674 ACTGATCAATGCCTTTGTTCTTCTT 59.462 36.000 0.00 0.00 35.79 2.52
2152 2286 4.447616 CCCCCTATCAGTGAATTAATGCCA 60.448 45.833 0.00 0.00 0.00 4.92
2184 2318 7.557719 ACTTGTGGGAATAATGGTTCTTCTATG 59.442 37.037 0.00 0.00 0.00 2.23
2291 2425 7.060633 GCAGGTTTTCATGTAAACAATACGAAG 59.939 37.037 23.89 9.24 39.27 3.79
2506 2640 7.395617 TGTTGCCCTGTTAATACAACTACATA 58.604 34.615 0.00 0.00 40.88 2.29
2528 2662 1.502231 CAGAGGGATACGGATTTGCG 58.498 55.000 0.00 0.00 37.60 4.85
2721 2855 8.014517 TGTGATTTCTTTTTCTTGTTTTGTTGC 58.985 29.630 0.00 0.00 0.00 4.17
2893 3028 9.565090 TCATAGTGGAATATCATTTTGAGAAGG 57.435 33.333 0.00 0.00 0.00 3.46
2894 3029 8.790718 CATAGTGGAATATCATTTTGAGAAGGG 58.209 37.037 0.00 0.00 0.00 3.95
2895 3030 6.131961 AGTGGAATATCATTTTGAGAAGGGG 58.868 40.000 0.00 0.00 0.00 4.79
2896 3031 6.068853 AGTGGAATATCATTTTGAGAAGGGGA 60.069 38.462 0.00 0.00 0.00 4.81
2897 3032 6.264067 GTGGAATATCATTTTGAGAAGGGGAG 59.736 42.308 0.00 0.00 0.00 4.30
2898 3033 5.242615 GGAATATCATTTTGAGAAGGGGAGC 59.757 44.000 0.00 0.00 0.00 4.70
2899 3034 2.514458 TCATTTTGAGAAGGGGAGCC 57.486 50.000 0.00 0.00 0.00 4.70
2900 3035 1.995542 TCATTTTGAGAAGGGGAGCCT 59.004 47.619 0.00 0.00 0.00 4.58
2901 3036 2.379907 TCATTTTGAGAAGGGGAGCCTT 59.620 45.455 0.00 0.00 0.00 4.35
2902 3037 2.292828 TTTTGAGAAGGGGAGCCTTG 57.707 50.000 0.00 0.00 0.00 3.61
2903 3038 0.405585 TTTGAGAAGGGGAGCCTTGG 59.594 55.000 0.00 0.00 0.00 3.61
2904 3039 2.142292 TTGAGAAGGGGAGCCTTGGC 62.142 60.000 2.97 2.97 0.00 4.52
2905 3040 3.689002 GAGAAGGGGAGCCTTGGCG 62.689 68.421 5.95 0.00 0.00 5.69
2913 3048 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
2914 3049 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
2915 3050 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
2916 3051 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
2917 3052 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2918 3053 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
2919 3054 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2924 3059 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2925 3060 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
2926 3061 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2927 3062 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2928 3063 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2929 3064 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2930 3065 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2931 3066 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2932 3067 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2933 3068 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2934 3069 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2935 3070 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2936 3071 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2937 3072 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2938 3073 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2948 3083 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2949 3084 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
2950 3085 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
2951 3086 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
2952 3087 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
2953 3088 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
2954 3089 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
2955 3090 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
2956 3091 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
2957 3092 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
2958 3093 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
2959 3094 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
2960 3095 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
2961 3096 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
2962 3097 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
2973 3108 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
2974 3109 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
2975 3110 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
2976 3111 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
2977 3112 2.560105 GGAAACAGCCTCTTGCAGAAAT 59.440 45.455 0.00 0.00 44.83 2.17
2978 3113 3.572584 GAAACAGCCTCTTGCAGAAATG 58.427 45.455 0.00 0.00 44.83 2.32
2979 3114 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
2980 3115 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
2981 3116 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
2982 3117 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
2983 3118 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
2984 3119 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
2985 3120 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
2986 3121 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
2987 3122 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
2988 3123 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
2989 3124 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
2990 3125 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
2991 3126 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
2992 3127 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2993 3128 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2994 3129 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2995 3130 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2996 3131 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2997 3132 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
2998 3133 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
2999 3134 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
3000 3135 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
3001 3136 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
3002 3137 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
3003 3138 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
3004 3139 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
3005 3140 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
3006 3141 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
3007 3142 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
3008 3143 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
3009 3144 2.351726 GCTGCGTACAATAGACCCAAAG 59.648 50.000 0.00 0.00 0.00 2.77
3010 3145 3.596214 CTGCGTACAATAGACCCAAAGT 58.404 45.455 0.00 0.00 0.00 2.66
3011 3146 3.331150 TGCGTACAATAGACCCAAAGTG 58.669 45.455 0.00 0.00 0.00 3.16
3012 3147 2.676342 GCGTACAATAGACCCAAAGTGG 59.324 50.000 0.00 0.00 37.25 4.00
3013 3148 3.867216 GCGTACAATAGACCCAAAGTGGT 60.867 47.826 0.00 0.00 42.79 4.16
3018 3153 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
3019 3154 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
3020 3155 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
3021 3156 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
3022 3157 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
3023 3158 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
3024 3159 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
3025 3160 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
3026 3161 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
3027 3162 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
3028 3163 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
3029 3164 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
3030 3165 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
3031 3166 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
3032 3167 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
3033 3168 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
3034 3169 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
3035 3170 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
3036 3171 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
3037 3172 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
3058 3193 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
3059 3194 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
3060 3195 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
3061 3196 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
3062 3197 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
3063 3198 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
3064 3199 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
3065 3200 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
3066 3201 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
3071 3206 2.203684 CACTGGGGCTGCCCTTTT 60.204 61.111 34.99 17.53 44.66 2.27
3072 3207 1.838396 CACTGGGGCTGCCCTTTTT 60.838 57.895 34.99 15.74 44.66 1.94
3102 3237 8.400947 AGTGGAATATCATTTTGAATGTTCGAG 58.599 33.333 1.09 0.00 0.00 4.04
3118 3253 4.180057 GTTCGAGAAGCAATCTGTCATCT 58.820 43.478 0.00 0.00 38.96 2.90
3122 3257 6.577103 TCGAGAAGCAATCTGTCATCTTTAT 58.423 36.000 0.00 0.00 38.96 1.40
3156 3291 7.921041 ATATCTGGACTTTAGGAGTGATGAA 57.079 36.000 0.00 0.00 39.19 2.57
3189 3324 8.489676 TTGCATAATGGTATTTTGATATGGGT 57.510 30.769 0.00 0.00 0.00 4.51
3282 3417 6.240894 AGCACTCTCAAAATCTCAATAACCA 58.759 36.000 0.00 0.00 0.00 3.67
3413 3548 4.154737 TGATGTCATACTTTCTTGCAGCAC 59.845 41.667 0.00 0.00 0.00 4.40
3424 3560 2.878406 TCTTGCAGCACTGAAGTTTACC 59.122 45.455 0.00 0.00 0.00 2.85
3677 3813 1.003696 GTTCTGTGCTTCTAGGGCCTT 59.996 52.381 13.45 0.00 0.00 4.35
3879 4015 6.561294 ACCTCCCTATTTTCTCAAAATTCCA 58.439 36.000 0.00 0.00 41.16 3.53
3905 4041 1.136363 CGGATGTTGTGTTACTGCACG 60.136 52.381 0.00 0.00 41.94 5.34
4121 4257 6.296145 CCTTCTCAGGGAGAGTAGTCAAAATT 60.296 42.308 0.00 0.00 44.98 1.82
4255 4392 0.390124 AGCATGCATTTTATGGCCCG 59.610 50.000 21.98 0.00 0.00 6.13
4722 5130 4.446371 ACATGCTTCTTCAGTATAGGTGC 58.554 43.478 0.00 0.00 0.00 5.01
4723 5131 4.080919 ACATGCTTCTTCAGTATAGGTGCA 60.081 41.667 0.00 0.00 0.00 4.57
4724 5132 3.861840 TGCTTCTTCAGTATAGGTGCAC 58.138 45.455 8.80 8.80 0.00 4.57
4725 5133 3.515502 TGCTTCTTCAGTATAGGTGCACT 59.484 43.478 17.98 5.41 0.00 4.40
4726 5134 3.868077 GCTTCTTCAGTATAGGTGCACTG 59.132 47.826 17.98 5.96 42.88 3.66
4727 5135 4.621747 GCTTCTTCAGTATAGGTGCACTGT 60.622 45.833 17.98 7.16 42.28 3.55
4728 5136 4.456280 TCTTCAGTATAGGTGCACTGTG 57.544 45.455 17.98 2.76 42.28 3.66
4729 5137 3.832490 TCTTCAGTATAGGTGCACTGTGT 59.168 43.478 17.98 5.55 42.28 3.72
4730 5138 3.592898 TCAGTATAGGTGCACTGTGTG 57.407 47.619 17.98 7.39 42.28 3.82
4731 5139 2.233676 TCAGTATAGGTGCACTGTGTGG 59.766 50.000 17.98 1.81 42.28 4.17
4879 5298 7.676947 TGCTTGTATTGAACCTACTAGACTTT 58.323 34.615 0.00 0.00 0.00 2.66
4938 5357 8.229253 AGGTTTCATTCGGTAACTTTAAAACT 57.771 30.769 0.00 0.00 0.00 2.66
5138 5557 1.596477 CAGGCTAATCCTCCGCAGC 60.596 63.158 0.00 0.00 45.52 5.25
5369 5788 4.290722 ACCAGGAGAATCAGACCAATCTTT 59.709 41.667 0.00 0.00 36.25 2.52
5419 5838 6.148811 CACTAAAAGCTAGTGGAAATTCCGAA 59.851 38.462 7.60 0.00 40.17 4.30
5525 5944 3.056536 GCGGGTGCAATCTATCTCTGATA 60.057 47.826 0.00 0.00 42.15 2.15
5727 6146 0.512952 CCTGAAACGCCTCTTGTTCG 59.487 55.000 0.00 0.00 0.00 3.95
5902 6321 0.877071 AACAAGCTGCTGTTGATCCG 59.123 50.000 1.35 0.00 38.12 4.18
5942 6361 9.902684 AGACACTAAAAGATGAATCATCAGATT 57.097 29.630 23.41 16.43 46.85 2.40
5958 6377 1.688735 AGATTAGCCAGAGCATGCGTA 59.311 47.619 13.01 0.00 43.56 4.42
5980 6399 2.349755 GCCGGTCTGGTTAAGCCA 59.650 61.111 1.90 0.00 46.95 4.75
6030 6470 4.250464 TGCAGTTCGTTCTTATACCAAGG 58.750 43.478 0.00 0.00 0.00 3.61
6115 6557 1.818060 GCCACAATTGTACATGCTGGA 59.182 47.619 11.53 0.00 0.00 3.86
6134 6577 7.564793 TGCTGGAAACTAGAAAGCAGATATTA 58.435 34.615 0.00 0.00 38.88 0.98
6143 6586 9.160412 ACTAGAAAGCAGATATTAGGTACCAAT 57.840 33.333 15.94 13.70 0.00 3.16
6145 6588 8.034313 AGAAAGCAGATATTAGGTACCAATGA 57.966 34.615 15.94 0.00 0.00 2.57
6296 6739 5.717119 ACTAGAATTTCCATAAGGGCAGT 57.283 39.130 0.00 0.00 36.21 4.40
6365 6808 3.266510 TCTTAATCAGCGCATCCAGTT 57.733 42.857 11.47 0.00 0.00 3.16
6366 6809 2.938451 TCTTAATCAGCGCATCCAGTTG 59.062 45.455 11.47 0.00 0.00 3.16
6374 6817 2.035961 AGCGCATCCAGTTGTATCGTAT 59.964 45.455 11.47 0.00 0.00 3.06
6395 6838 3.480133 CCCGGGGTGATGACCTCC 61.480 72.222 14.71 0.00 40.08 4.30
6407 6850 3.447586 TGATGACCTCCTTTACTTCCGAG 59.552 47.826 0.00 0.00 0.00 4.63
6424 6881 2.548920 CCGAGGAGAACTATTGCCATCC 60.549 54.545 0.00 0.00 0.00 3.51
6477 6936 1.872388 TTGTTCGATTCAGTTGCGGA 58.128 45.000 0.00 0.00 0.00 5.54
6478 6937 2.093306 TGTTCGATTCAGTTGCGGAT 57.907 45.000 0.00 0.00 0.00 4.18
6491 6950 1.388547 TGCGGATTATGAACCCAAGC 58.611 50.000 0.00 0.00 0.00 4.01
6587 7046 9.692749 TTATTGAGTAGTTTAGTGTGTCTTGAG 57.307 33.333 0.00 0.00 0.00 3.02
6588 7047 6.710597 TGAGTAGTTTAGTGTGTCTTGAGT 57.289 37.500 0.00 0.00 0.00 3.41
6589 7048 7.812690 TGAGTAGTTTAGTGTGTCTTGAGTA 57.187 36.000 0.00 0.00 0.00 2.59
6591 7050 8.689061 TGAGTAGTTTAGTGTGTCTTGAGTAAA 58.311 33.333 0.00 0.00 0.00 2.01
6636 7095 5.241662 AGAGCCATTGTCTTCAGTAACTTC 58.758 41.667 0.00 0.00 0.00 3.01
6656 7115 1.305219 GCGGGCTTCACTGCACATTA 61.305 55.000 0.00 0.00 42.32 1.90
6781 7598 7.288852 TGTTTTCCCCATGAATTTCTTTAGTGA 59.711 33.333 0.00 0.00 31.67 3.41
6926 7743 7.712797 TCACCACAGATTTAAAGACCTTTTTC 58.287 34.615 0.00 0.00 34.23 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.227943 GCTGCTCAAGGTCACCACA 60.228 57.895 0.00 0.00 0.00 4.17
80 81 2.126580 CAACCGAGTCGACGACCC 60.127 66.667 23.76 12.14 32.18 4.46
148 149 0.738389 CTCAACCGTTGCACCACTTT 59.262 50.000 6.37 0.00 0.00 2.66
151 152 1.803334 TATCTCAACCGTTGCACCAC 58.197 50.000 6.37 0.00 0.00 4.16
177 178 0.250901 GAACTGCACAGGACCACCAT 60.251 55.000 2.21 0.00 38.94 3.55
200 202 2.514592 ATGATCCAGTTGCCCGCG 60.515 61.111 0.00 0.00 0.00 6.46
247 249 1.302366 TGACGCCATATCGACGTACT 58.698 50.000 0.00 0.00 40.69 2.73
257 259 3.056107 GCTATAGAACCCATGACGCCATA 60.056 47.826 3.21 0.00 0.00 2.74
279 281 6.346919 CCAATTTCTAGTCACTTCGTTGTGAG 60.347 42.308 12.04 3.73 46.09 3.51
286 288 4.389077 GTCACCCAATTTCTAGTCACTTCG 59.611 45.833 0.00 0.00 0.00 3.79
418 424 1.377725 CCACAAGCCCTAGTGCCAG 60.378 63.158 0.00 0.00 34.48 4.85
438 444 1.230324 GAAGGTGAAGAAAGCAGCGT 58.770 50.000 0.00 0.00 38.68 5.07
700 798 7.012327 TCGAGGGCATGTAAAGAATTTATCAAG 59.988 37.037 0.00 0.00 43.30 3.02
706 804 5.253330 TCTTCGAGGGCATGTAAAGAATTT 58.747 37.500 0.00 0.00 43.42 1.82
752 850 1.450312 CCTCGTCCACATGAAGGGC 60.450 63.158 0.00 1.00 0.00 5.19
771 869 1.609208 ATGCTTCGTTTGTCTGCCTT 58.391 45.000 0.00 0.00 0.00 4.35
1584 1689 8.134202 TGACTCATCTAACTGATTGAACCTAA 57.866 34.615 0.00 0.00 32.05 2.69
1791 1922 4.935352 AGAAAGCTTTGTTACATTGCCA 57.065 36.364 18.30 0.00 0.00 4.92
1854 1985 1.216122 CCATCAAGCTAAGCTCGAGC 58.784 55.000 30.01 30.01 38.25 5.03
1857 1988 2.131183 GTAGCCATCAAGCTAAGCTCG 58.869 52.381 0.00 0.00 46.52 5.03
2096 2230 6.317140 TCTTGTTAGCAGCATATGGAAAGAAG 59.683 38.462 4.56 2.58 0.00 2.85
2101 2235 5.102953 AGTCTTGTTAGCAGCATATGGAA 57.897 39.130 4.56 0.00 0.00 3.53
2152 2286 5.332743 ACCATTATTCCCACAAGTTCATGT 58.667 37.500 0.00 0.00 0.00 3.21
2184 2318 4.864247 CCCACAGTATATTTTTGCTTGCAC 59.136 41.667 0.00 0.00 0.00 4.57
2519 2653 1.695813 TTGAATGCAACGCAAATCCG 58.304 45.000 0.00 0.00 43.62 4.18
2525 2659 2.593346 AAGGTTTTGAATGCAACGCA 57.407 40.000 0.00 0.00 44.86 5.24
2528 2662 7.945033 TGAAGATAAAGGTTTTGAATGCAAC 57.055 32.000 0.00 0.00 32.79 4.17
2879 3014 2.584498 AGGCTCCCCTTCTCAAAATGAT 59.416 45.455 0.00 0.00 38.74 2.45
2880 3015 1.995542 AGGCTCCCCTTCTCAAAATGA 59.004 47.619 0.00 0.00 38.74 2.57
2881 3016 2.521547 AGGCTCCCCTTCTCAAAATG 57.478 50.000 0.00 0.00 38.74 2.32
2895 3030 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
2896 3031 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
2897 3032 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
2898 3033 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
2899 3034 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2900 3035 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
2901 3036 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
2902 3037 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
2906 3041 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2907 3042 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2908 3043 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2909 3044 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2910 3045 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2911 3046 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2912 3047 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2913 3048 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2914 3049 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2915 3050 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2916 3051 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2917 3052 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2918 3053 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2919 3054 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2920 3055 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2921 3056 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2932 3067 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
2933 3068 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
2934 3069 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
2935 3070 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
2936 3071 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
2937 3072 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
2938 3073 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
2939 3074 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
2940 3075 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
2941 3076 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2942 3077 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
2943 3078 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2944 3079 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2945 3080 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2946 3081 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2947 3082 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2948 3083 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2949 3084 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2950 3085 1.072965 CAAGAGGCTGTTTCCAGGACT 59.927 52.381 0.00 0.00 39.22 3.85
2951 3086 1.528129 CAAGAGGCTGTTTCCAGGAC 58.472 55.000 0.00 0.00 39.22 3.85
2952 3087 0.250901 GCAAGAGGCTGTTTCCAGGA 60.251 55.000 0.00 0.00 39.22 3.86
2953 3088 0.538057 TGCAAGAGGCTGTTTCCAGG 60.538 55.000 0.00 0.00 45.15 4.45
2954 3089 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
2955 3090 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
2956 3091 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
2966 3101 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
2967 3102 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
2968 3103 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
2969 3104 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
2970 3105 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
2971 3106 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2972 3107 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2973 3108 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2974 3109 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2975 3110 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2976 3111 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2977 3112 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2978 3113 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
2979 3114 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
2980 3115 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
2981 3116 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
2982 3117 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
2983 3118 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
2984 3119 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
2985 3120 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
2986 3121 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
2987 3122 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
2988 3123 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
2989 3124 3.370978 CACTTTGGGTCTATTGTACGCAG 59.629 47.826 0.00 0.00 40.36 5.18
2990 3125 3.331150 CACTTTGGGTCTATTGTACGCA 58.669 45.455 0.00 0.00 37.94 5.24
2991 3126 2.676342 CCACTTTGGGTCTATTGTACGC 59.324 50.000 0.00 0.00 32.67 4.42
2992 3127 3.934068 ACCACTTTGGGTCTATTGTACG 58.066 45.455 0.00 0.00 43.37 3.67
3002 3137 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
3003 3138 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
3004 3139 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
3005 3140 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
3006 3141 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
3007 3142 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
3008 3143 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
3009 3144 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
3010 3145 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
3011 3146 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
3012 3147 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
3013 3148 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
3014 3149 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
3015 3150 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
3016 3151 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
3017 3152 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
3018 3153 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
3019 3154 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
3020 3155 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
3032 3167 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
3035 3170 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3036 3171 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3037 3172 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3038 3173 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3040 3175 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
3041 3176 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
3042 3177 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
3043 3178 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
3044 3179 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
3045 3180 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
3046 3181 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
3047 3182 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
3048 3183 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
3075 3210 9.389755 TCGAACATTCAAAATGATATTCCACTA 57.610 29.630 6.67 0.00 0.00 2.74
3076 3211 8.279970 TCGAACATTCAAAATGATATTCCACT 57.720 30.769 6.67 0.00 0.00 4.00
3077 3212 8.397906 TCTCGAACATTCAAAATGATATTCCAC 58.602 33.333 6.67 0.00 0.00 4.02
3078 3213 8.504812 TCTCGAACATTCAAAATGATATTCCA 57.495 30.769 6.67 0.00 0.00 3.53
3079 3214 9.443283 CTTCTCGAACATTCAAAATGATATTCC 57.557 33.333 6.67 0.00 0.00 3.01
3080 3215 8.951969 GCTTCTCGAACATTCAAAATGATATTC 58.048 33.333 6.67 0.41 0.00 1.75
3081 3216 8.461222 TGCTTCTCGAACATTCAAAATGATATT 58.539 29.630 6.67 0.00 0.00 1.28
3082 3217 7.988737 TGCTTCTCGAACATTCAAAATGATAT 58.011 30.769 6.67 0.00 0.00 1.63
3083 3218 7.376435 TGCTTCTCGAACATTCAAAATGATA 57.624 32.000 6.67 0.00 0.00 2.15
3180 3315 9.253832 AGAATAAAACATTTCACACCCATATCA 57.746 29.630 0.00 0.00 0.00 2.15
3189 3324 7.432869 CCTGTCCAAGAATAAAACATTTCACA 58.567 34.615 0.00 0.00 0.00 3.58
3282 3417 5.741962 ATCTATATGTCAGACATGCAGCT 57.258 39.130 24.15 10.57 39.53 4.24
3387 3522 6.151691 GCTGCAAGAAAGTATGACATCAAAA 58.848 36.000 0.00 0.00 34.07 2.44
3413 3548 8.553459 AATCACATGACTAAGGTAAACTTCAG 57.447 34.615 0.00 0.00 40.64 3.02
3424 3560 9.973450 ACTGCTAGTATTAATCACATGACTAAG 57.027 33.333 0.00 0.00 0.00 2.18
3641 3777 4.505191 CACAGAACAAGAAATGCCAACAAG 59.495 41.667 0.00 0.00 0.00 3.16
3648 3784 4.234530 AGAAGCACAGAACAAGAAATGC 57.765 40.909 0.00 0.00 0.00 3.56
3677 3813 7.161404 ACAGCTTTGTCATAACATACTTCTCA 58.839 34.615 0.00 0.00 34.73 3.27
3879 4015 3.876914 CAGTAACACAACATCCGGCATAT 59.123 43.478 0.00 0.00 0.00 1.78
4255 4392 3.243737 TGGTGACCATGTATATGACGAGC 60.244 47.826 0.00 0.00 36.36 5.03
4552 4690 7.976734 AGTACTGCTAACAATAGACACTTCATC 59.023 37.037 0.00 0.00 0.00 2.92
4616 5024 2.791560 CGAAGTTGAGCCATGTCTATCG 59.208 50.000 0.00 0.00 0.00 2.92
4618 5026 4.679373 ATCGAAGTTGAGCCATGTCTAT 57.321 40.909 0.00 0.00 0.00 1.98
4722 5130 1.597742 ACAAAGCTAGCCACACAGTG 58.402 50.000 12.13 0.00 0.00 3.66
4723 5131 2.348411 AACAAAGCTAGCCACACAGT 57.652 45.000 12.13 0.00 0.00 3.55
4724 5132 5.182001 AGAAATAACAAAGCTAGCCACACAG 59.818 40.000 12.13 0.00 0.00 3.66
4725 5133 5.070001 AGAAATAACAAAGCTAGCCACACA 58.930 37.500 12.13 0.00 0.00 3.72
4726 5134 5.412904 AGAGAAATAACAAAGCTAGCCACAC 59.587 40.000 12.13 0.00 0.00 3.82
4727 5135 5.560724 AGAGAAATAACAAAGCTAGCCACA 58.439 37.500 12.13 0.00 0.00 4.17
4728 5136 6.502136 AAGAGAAATAACAAAGCTAGCCAC 57.498 37.500 12.13 0.00 0.00 5.01
4729 5137 6.490040 ACAAAGAGAAATAACAAAGCTAGCCA 59.510 34.615 12.13 0.00 0.00 4.75
4730 5138 6.914259 ACAAAGAGAAATAACAAAGCTAGCC 58.086 36.000 12.13 0.00 0.00 3.93
4731 5139 9.331106 GTTACAAAGAGAAATAACAAAGCTAGC 57.669 33.333 6.62 6.62 0.00 3.42
4879 5298 0.687757 AGGAGGGCGCAGATGTAAGA 60.688 55.000 10.83 0.00 0.00 2.10
5369 5788 2.906389 GTGATCTATGCTCCCCCACATA 59.094 50.000 0.00 0.00 0.00 2.29
5419 5838 6.174720 TGATCTTTCAAGTGTAGGTTGACT 57.825 37.500 0.00 0.00 33.63 3.41
5525 5944 5.385198 CTCTGTAGCTCCCTTCTTCTCTAT 58.615 45.833 0.00 0.00 0.00 1.98
5727 6146 2.050077 GTGCGGTTTGCTTGCTCC 60.050 61.111 0.00 0.00 46.63 4.70
5902 6321 3.951775 AGTGTCTTCTGATCACCACTC 57.048 47.619 0.00 0.00 33.21 3.51
5942 6361 0.530650 GCTTACGCATGCTCTGGCTA 60.531 55.000 17.13 0.00 36.28 3.93
5958 6377 0.321653 CTTAACCAGACCGGCAGCTT 60.322 55.000 0.00 0.00 39.03 3.74
5980 6399 3.187227 CAGCGCTTTCACTGTATTTCACT 59.813 43.478 7.50 0.00 0.00 3.41
6030 6470 2.281276 CGCGGCCCCTTATAACCC 60.281 66.667 0.00 0.00 0.00 4.11
6034 6474 2.035237 CTGTTCCGCGGCCCCTTATA 62.035 60.000 23.51 0.00 0.00 0.98
6115 6557 8.989131 TGGTACCTAATATCTGCTTTCTAGTTT 58.011 33.333 14.36 0.00 0.00 2.66
6134 6577 6.493166 TGAATTTCCATCTTCATTGGTACCT 58.507 36.000 14.36 0.00 35.64 3.08
6143 6586 5.947566 TCAGCAGAATGAATTTCCATCTTCA 59.052 36.000 0.00 0.00 39.69 3.02
6145 6588 6.627508 GCTTCAGCAGAATGAATTTCCATCTT 60.628 38.462 0.00 0.00 39.69 2.40
6296 6739 7.497595 ACTCTGAATATTGGCACGAATACTAA 58.502 34.615 0.00 0.00 0.00 2.24
6365 6808 1.183030 CCCCGGGCTGATACGATACA 61.183 60.000 17.73 0.00 0.00 2.29
6366 6809 1.183676 ACCCCGGGCTGATACGATAC 61.184 60.000 17.73 0.00 0.00 2.24
6374 6817 3.399181 GTCATCACCCCGGGCTGA 61.399 66.667 20.82 20.82 0.00 4.26
6395 6838 5.520649 GCAATAGTTCTCCTCGGAAGTAAAG 59.479 44.000 0.00 0.00 35.56 1.85
6407 6850 4.429854 AAGAGGATGGCAATAGTTCTCC 57.570 45.455 0.00 0.00 0.00 3.71
6477 6936 2.311542 TGGAGGTGCTTGGGTTCATAAT 59.688 45.455 0.00 0.00 0.00 1.28
6478 6937 1.707989 TGGAGGTGCTTGGGTTCATAA 59.292 47.619 0.00 0.00 0.00 1.90
6491 6950 0.319900 CTGTGTCTTCCGTGGAGGTG 60.320 60.000 0.00 0.00 41.99 4.00
6561 7020 9.692749 CTCAAGACACACTAAACTACTCAATAA 57.307 33.333 0.00 0.00 0.00 1.40
6606 7065 3.262420 GAAGACAATGGCTCTTCGCTAA 58.738 45.455 0.00 0.00 35.57 3.09
6607 7066 2.233676 TGAAGACAATGGCTCTTCGCTA 59.766 45.455 8.98 0.00 44.58 4.26
6610 7069 2.693069 ACTGAAGACAATGGCTCTTCG 58.307 47.619 8.98 6.96 44.58 3.79
6616 7075 3.424962 GCGAAGTTACTGAAGACAATGGC 60.425 47.826 0.00 0.00 0.00 4.40
6627 7086 0.669318 TGAAGCCCGCGAAGTTACTG 60.669 55.000 8.23 0.00 0.00 2.74
6629 7088 0.669625 AGTGAAGCCCGCGAAGTTAC 60.670 55.000 8.23 0.00 0.00 2.50
6656 7115 7.338703 TCCTGATAGTAATCGACACAACTACTT 59.661 37.037 0.00 0.00 34.60 2.24
6709 7524 3.560453 CCGGAAACCTTTTGTAGATCCCA 60.560 47.826 0.00 0.00 0.00 4.37
6781 7598 1.194781 AATGAGGACTGGCAGGACGT 61.195 55.000 20.34 13.50 0.00 4.34


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

AutoCloner maintained by Alex Coulton.