Multiple sequence alignment - TraesCS7D01G149700

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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 TraesCS7D01G149700 chr7D 100.000 3579 0 0 1 3579 98627343 98623765 0.000000e+00 6610
1 TraesCS7D01G149700 chr7D 84.762 210 20 6 2931 3131 98624346 98624140 2.180000e-47 200
2 TraesCS7D01G149700 chr7D 84.762 210 20 6 2998 3204 98624413 98624213 2.180000e-47 200
3 TraesCS7D01G149700 chr7D 83.908 174 22 6 119 289 98634360 98634190 1.030000e-35 161
4 TraesCS7D01G149700 chr7B 90.491 3155 169 60 14 3102 53637218 53634129 0.000000e+00 4043
5 TraesCS7D01G149700 chr7B 84.053 533 45 17 3074 3579 53634297 53633778 8.990000e-131 477
6 TraesCS7D01G149700 chr7A 87.858 3278 177 82 12 3174 100725175 100722004 0.000000e+00 3644
7 TraesCS7D01G149700 chr7A 80.973 473 38 19 3010 3456 100722239 100721793 9.580000e-86 327
8 TraesCS7D01G149700 chr7A 82.005 389 27 25 147 506 100756807 100756433 1.260000e-74 291
9 TraesCS7D01G149700 chr7A 90.598 117 6 4 3085 3200 100722239 100722127 2.230000e-32 150


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 TraesCS7D01G149700 chr7D 98623765 98627343 3578 True 2336.666667 6610 89.841333 1 3579 3 chr7D.!!$R2 3578
1 TraesCS7D01G149700 chr7B 53633778 53637218 3440 True 2260.000000 4043 87.272000 14 3579 2 chr7B.!!$R1 3565
2 TraesCS7D01G149700 chr7A 100721793 100725175 3382 True 1373.666667 3644 86.476333 12 3456 3 chr7A.!!$R2 3444

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
346 355 0.390860 CACTATTCCCTCCCGCAGAG 59.609 60.0 0.0 0.0 42.83 3.35 F
1465 1540 0.460284 CCAACTCTCGCAATACGGCT 60.460 55.0 0.0 0.0 43.89 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1772 0.173481 TCTCGTGCCTGATTTCCGAG 59.827 55.0 0.00 0.0 44.67 4.63 R
3232 3392 0.117340 AGTACCTGGTCCCAGCTCTT 59.883 55.0 0.63 0.0 42.35 2.85 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
25 26 8.624701 TGAGTAATCGCTTTACAGTTATGTAC 57.375 34.615 9.72 0.00 41.62 2.90
28 29 6.903883 AATCGCTTTACAGTTATGTACCAG 57.096 37.500 0.00 0.00 41.62 4.00
30 31 6.513806 TCGCTTTACAGTTATGTACCAGTA 57.486 37.500 0.00 0.00 41.62 2.74
31 32 6.558009 TCGCTTTACAGTTATGTACCAGTAG 58.442 40.000 0.00 0.00 41.62 2.57
32 33 6.151648 TCGCTTTACAGTTATGTACCAGTAGT 59.848 38.462 0.00 0.00 41.62 2.73
33 34 6.471519 CGCTTTACAGTTATGTACCAGTAGTC 59.528 42.308 0.00 0.00 41.62 2.59
34 35 6.755607 GCTTTACAGTTATGTACCAGTAGTCC 59.244 42.308 0.00 0.00 41.62 3.85
41 42 3.812611 TGTACCAGTAGTCCAGTACCA 57.187 47.619 0.00 0.00 35.33 3.25
113 117 4.968259 TGTGTTACAAGTTGATAGCCTGT 58.032 39.130 10.54 0.00 0.00 4.00
144 148 3.170672 TGCCCCTGCACACTGTCT 61.171 61.111 0.00 0.00 44.23 3.41
145 149 2.670934 GCCCCTGCACACTGTCTG 60.671 66.667 0.00 0.00 37.47 3.51
154 158 3.917988 TGCACACTGTCTGTCTAATCTG 58.082 45.455 0.00 0.00 0.00 2.90
161 165 1.204941 GTCTGTCTAATCTGGCCGTGT 59.795 52.381 0.00 0.00 0.00 4.49
162 166 1.899814 TCTGTCTAATCTGGCCGTGTT 59.100 47.619 0.00 0.00 0.00 3.32
163 167 2.002586 CTGTCTAATCTGGCCGTGTTG 58.997 52.381 0.00 0.00 0.00 3.33
214 218 2.125147 TGCGGACATAGTGCCAGC 60.125 61.111 0.00 0.00 0.00 4.85
346 355 0.390860 CACTATTCCCTCCCGCAGAG 59.609 60.000 0.00 0.00 42.83 3.35
370 400 2.802719 CCGAAAATTCCCTTCTTCCCA 58.197 47.619 0.00 0.00 0.00 4.37
428 468 2.666190 GCACGCACTCCTCTGCAA 60.666 61.111 0.00 0.00 36.94 4.08
637 688 3.864921 CCTGCGCTTTCAGTTAAGGTACT 60.865 47.826 9.73 0.00 33.74 2.73
702 757 2.631428 CACGATTAATGGCGCCCG 59.369 61.111 26.77 21.29 0.00 6.13
774 830 3.733443 ATCGGGGCTATTTTTGAATGC 57.267 42.857 0.00 0.00 0.00 3.56
783 839 2.810439 TTTTTGAATGCGTTCTGGGG 57.190 45.000 19.09 0.00 35.33 4.96
856 912 2.486472 ATGCTCTGTTCCTTGTCCTG 57.514 50.000 0.00 0.00 0.00 3.86
1008 1071 2.022129 CTAACGATCGATGGCCCGC 61.022 63.158 24.34 0.00 0.00 6.13
1017 1080 0.600255 CGATGGCCCGCTTAGTTAGG 60.600 60.000 0.00 0.00 0.00 2.69
1026 1089 1.810412 CGCTTAGTTAGGGATGGTGGC 60.810 57.143 0.00 0.00 39.06 5.01
1143 1209 3.457263 TCCATCCGTGCGCTGCTA 61.457 61.111 9.73 0.00 0.00 3.49
1287 1362 4.309950 CCCCGGCGGTATGGTAGC 62.310 72.222 26.32 0.00 0.00 3.58
1326 1401 3.556999 CGAAAGTATCAGGGAGGAGAGA 58.443 50.000 0.00 0.00 0.00 3.10
1335 1410 1.289530 AGGGAGGAGAGAAAGGACGAT 59.710 52.381 0.00 0.00 0.00 3.73
1338 1413 2.104170 GAGGAGAGAAAGGACGATGGT 58.896 52.381 0.00 0.00 0.00 3.55
1398 1473 4.077188 GTGAAGGTCGTGCAGCGC 62.077 66.667 0.00 0.00 41.07 5.92
1465 1540 0.460284 CCAACTCTCGCAATACGGCT 60.460 55.000 0.00 0.00 43.89 5.52
1482 1557 1.554392 GCTGCACAGATCGTCTACAG 58.446 55.000 0.81 0.00 0.00 2.74
1488 1563 2.085320 ACAGATCGTCTACAGCTCGTT 58.915 47.619 0.00 0.00 0.00 3.85
1522 1603 5.647225 TGATGATGTTGATGTTGATCGGAAA 59.353 36.000 0.00 0.00 0.00 3.13
1545 1626 3.738982 TGTGAATGATCGTTGGACTTGT 58.261 40.909 4.51 0.00 0.00 3.16
1551 1632 1.806542 GATCGTTGGACTTGTGCATGT 59.193 47.619 0.00 0.00 0.00 3.21
1691 1772 2.520904 GCAGATGGAAGCGCTCGTC 61.521 63.158 12.06 10.57 0.00 4.20
1697 1778 2.178521 GAAGCGCTCGTCTCGGAA 59.821 61.111 12.06 0.00 0.00 4.30
1877 1958 3.577313 GATCGCCGCCAGCTTTCC 61.577 66.667 0.00 0.00 40.39 3.13
2053 2143 1.749634 AGTAGCACGTACTCCATCACC 59.250 52.381 0.00 0.00 37.41 4.02
2054 2144 1.475280 GTAGCACGTACTCCATCACCA 59.525 52.381 0.00 0.00 0.00 4.17
2055 2145 1.195115 AGCACGTACTCCATCACCAT 58.805 50.000 0.00 0.00 0.00 3.55
2079 2169 1.426621 CATGCATGCACGACTCACC 59.573 57.895 25.37 0.00 0.00 4.02
2080 2170 2.102438 ATGCATGCACGACTCACCG 61.102 57.895 25.37 0.00 0.00 4.94
2081 2171 4.152625 GCATGCACGACTCACCGC 62.153 66.667 14.21 0.00 0.00 5.68
2082 2172 2.738139 CATGCACGACTCACCGCA 60.738 61.111 0.00 0.00 39.01 5.69
2083 2173 2.102438 CATGCACGACTCACCGCAT 61.102 57.895 0.00 0.00 45.65 4.73
2084 2174 2.102438 ATGCACGACTCACCGCATG 61.102 57.895 0.00 0.00 43.21 4.06
2085 2175 2.738521 GCACGACTCACCGCATGT 60.739 61.111 0.00 0.00 0.00 3.21
2086 2176 2.730672 GCACGACTCACCGCATGTC 61.731 63.158 0.00 0.00 0.00 3.06
2087 2177 2.094659 CACGACTCACCGCATGTCC 61.095 63.158 0.00 0.00 0.00 4.02
2140 2230 3.067106 CGTCTTCTCTTTTTGGCAGCTA 58.933 45.455 0.00 0.00 0.00 3.32
2168 2258 1.213013 CAGGTGAAGACGACGAGGG 59.787 63.158 0.00 0.00 0.00 4.30
2242 2332 3.181967 CAAGCGAACGCCGAGGAG 61.182 66.667 15.44 0.00 43.17 3.69
2243 2333 4.436998 AAGCGAACGCCGAGGAGG 62.437 66.667 15.44 0.00 43.17 4.30
2245 2335 4.208686 GCGAACGCCGAGGAGGAT 62.209 66.667 8.03 0.00 45.00 3.24
2246 2336 2.842256 GCGAACGCCGAGGAGGATA 61.842 63.158 8.03 0.00 45.00 2.59
2247 2337 1.283181 CGAACGCCGAGGAGGATAG 59.717 63.158 0.00 0.00 45.00 2.08
2582 2690 1.367840 GAGCCGGTCCGATAAGCAT 59.632 57.895 14.39 0.00 0.00 3.79
2593 2701 1.817217 GATAAGCATACGCACGCGCA 61.817 55.000 12.02 0.00 44.19 6.09
2613 2721 0.869880 CACGCGTGTGTCAGTTCTGA 60.870 55.000 30.50 0.00 41.34 3.27
2681 2797 0.324614 CCATGTCAGGGTGTGCAGTA 59.675 55.000 0.00 0.00 0.00 2.74
2694 2811 1.357272 TGCAGTAGGGTTTGTGGGGT 61.357 55.000 0.00 0.00 0.00 4.95
2779 2909 4.615834 TCGGTTTTGGCGCGCAAC 62.616 61.111 34.42 26.72 0.00 4.17
2853 2984 4.602259 CCGGCGTGTGTGGTCTGT 62.602 66.667 6.01 0.00 0.00 3.41
2855 2986 2.972505 GGCGTGTGTGGTCTGTGG 60.973 66.667 0.00 0.00 0.00 4.17
2860 2991 1.865865 GTGTGTGGTCTGTGGTGTAG 58.134 55.000 0.00 0.00 0.00 2.74
2861 2992 0.105964 TGTGTGGTCTGTGGTGTAGC 59.894 55.000 0.00 0.00 0.00 3.58
2862 2993 0.602905 GTGTGGTCTGTGGTGTAGCC 60.603 60.000 0.00 0.00 37.90 3.93
2863 2994 1.374252 GTGGTCTGTGGTGTAGCCG 60.374 63.158 0.00 0.00 41.21 5.52
2864 2995 1.835267 TGGTCTGTGGTGTAGCCGT 60.835 57.895 0.00 0.00 41.21 5.68
2865 2996 1.374252 GGTCTGTGGTGTAGCCGTG 60.374 63.158 0.00 0.00 41.21 4.94
2869 3000 1.897133 TCTGTGGTGTAGCCGTGTAAT 59.103 47.619 0.00 0.00 41.21 1.89
2870 3001 3.090790 TCTGTGGTGTAGCCGTGTAATA 58.909 45.455 0.00 0.00 41.21 0.98
2871 3002 3.510753 TCTGTGGTGTAGCCGTGTAATAA 59.489 43.478 0.00 0.00 41.21 1.40
2874 3005 4.632251 TGTGGTGTAGCCGTGTAATAAATG 59.368 41.667 0.00 0.00 41.21 2.32
2875 3006 4.034742 GTGGTGTAGCCGTGTAATAAATGG 59.965 45.833 0.00 0.00 41.21 3.16
2879 3010 4.567558 TGTAGCCGTGTAATAAATGGTTCG 59.432 41.667 0.00 0.00 0.00 3.95
2887 3018 6.739550 CGTGTAATAAATGGTTCGGAGTTTTC 59.260 38.462 0.00 0.00 0.00 2.29
2889 3020 7.961283 GTGTAATAAATGGTTCGGAGTTTTCTC 59.039 37.037 0.00 0.00 45.49 2.87
2900 3035 1.132643 GAGTTTTCTCTCCGCTCGCTA 59.867 52.381 0.00 0.00 43.12 4.26
2901 3036 1.751924 AGTTTTCTCTCCGCTCGCTAT 59.248 47.619 0.00 0.00 0.00 2.97
2917 3052 5.768333 TCGCTATTCGATTGATTGCTATG 57.232 39.130 0.00 0.00 43.16 2.23
2918 3053 4.091945 TCGCTATTCGATTGATTGCTATGC 59.908 41.667 0.00 0.00 43.16 3.14
2919 3054 4.329489 GCTATTCGATTGATTGCTATGCG 58.671 43.478 0.00 0.00 0.00 4.73
2921 3056 0.867746 TCGATTGATTGCTATGCGCC 59.132 50.000 4.18 0.00 38.05 6.53
2922 3057 0.110056 CGATTGATTGCTATGCGCCC 60.110 55.000 4.18 0.00 38.05 6.13
2923 3058 1.242076 GATTGATTGCTATGCGCCCT 58.758 50.000 4.18 0.00 38.05 5.19
2924 3059 1.610522 GATTGATTGCTATGCGCCCTT 59.389 47.619 4.18 0.00 38.05 3.95
2925 3060 1.473258 TTGATTGCTATGCGCCCTTT 58.527 45.000 4.18 0.00 38.05 3.11
2926 3061 0.740149 TGATTGCTATGCGCCCTTTG 59.260 50.000 4.18 0.00 38.05 2.77
2927 3062 0.595825 GATTGCTATGCGCCCTTTGC 60.596 55.000 4.18 3.12 38.05 3.68
2928 3063 1.039233 ATTGCTATGCGCCCTTTGCT 61.039 50.000 4.18 0.00 38.05 3.91
2929 3064 1.250154 TTGCTATGCGCCCTTTGCTT 61.250 50.000 4.18 0.00 38.05 3.91
2930 3065 1.250154 TGCTATGCGCCCTTTGCTTT 61.250 50.000 4.18 0.00 38.05 3.51
2931 3066 0.803380 GCTATGCGCCCTTTGCTTTG 60.803 55.000 4.18 0.00 38.05 2.77
2932 3067 0.527565 CTATGCGCCCTTTGCTTTGT 59.472 50.000 4.18 0.00 38.05 2.83
2933 3068 0.965439 TATGCGCCCTTTGCTTTGTT 59.035 45.000 4.18 0.00 38.05 2.83
2934 3069 0.319813 ATGCGCCCTTTGCTTTGTTC 60.320 50.000 4.18 0.00 38.05 3.18
2935 3070 1.363807 GCGCCCTTTGCTTTGTTCT 59.636 52.632 0.00 0.00 38.05 3.01
2936 3071 0.940991 GCGCCCTTTGCTTTGTTCTG 60.941 55.000 0.00 0.00 38.05 3.02
2937 3072 0.385390 CGCCCTTTGCTTTGTTCTGT 59.615 50.000 0.00 0.00 38.05 3.41
2938 3073 1.202405 CGCCCTTTGCTTTGTTCTGTT 60.202 47.619 0.00 0.00 38.05 3.16
2939 3074 2.738321 CGCCCTTTGCTTTGTTCTGTTT 60.738 45.455 0.00 0.00 38.05 2.83
2940 3075 2.866156 GCCCTTTGCTTTGTTCTGTTTC 59.134 45.455 0.00 0.00 36.87 2.78
2941 3076 3.457234 CCCTTTGCTTTGTTCTGTTTCC 58.543 45.455 0.00 0.00 0.00 3.13
2942 3077 3.118811 CCCTTTGCTTTGTTCTGTTTCCA 60.119 43.478 0.00 0.00 0.00 3.53
2943 3078 4.502962 CCTTTGCTTTGTTCTGTTTCCAA 58.497 39.130 0.00 0.00 0.00 3.53
2944 3079 4.934602 CCTTTGCTTTGTTCTGTTTCCAAA 59.065 37.500 0.00 0.00 0.00 3.28
2945 3080 5.585844 CCTTTGCTTTGTTCTGTTTCCAAAT 59.414 36.000 0.00 0.00 0.00 2.32
2946 3081 6.093909 CCTTTGCTTTGTTCTGTTTCCAAATT 59.906 34.615 0.00 0.00 0.00 1.82
2947 3082 6.660887 TTGCTTTGTTCTGTTTCCAAATTC 57.339 33.333 0.00 0.00 0.00 2.17
2948 3083 5.976458 TGCTTTGTTCTGTTTCCAAATTCT 58.024 33.333 0.00 0.00 0.00 2.40
2949 3084 5.811613 TGCTTTGTTCTGTTTCCAAATTCTG 59.188 36.000 0.00 0.00 0.00 3.02
2950 3085 5.277011 GCTTTGTTCTGTTTCCAAATTCTGC 60.277 40.000 0.00 0.00 0.00 4.26
2951 3086 3.963665 TGTTCTGTTTCCAAATTCTGCG 58.036 40.909 0.00 0.00 0.00 5.18
2952 3087 3.629855 TGTTCTGTTTCCAAATTCTGCGA 59.370 39.130 0.00 0.00 0.00 5.10
2953 3088 4.222114 GTTCTGTTTCCAAATTCTGCGAG 58.778 43.478 0.00 0.00 0.00 5.03
2954 3089 2.813754 TCTGTTTCCAAATTCTGCGAGG 59.186 45.455 0.00 0.00 0.00 4.63
2955 3090 1.885887 TGTTTCCAAATTCTGCGAGGG 59.114 47.619 0.00 0.00 0.00 4.30
2956 3091 2.159382 GTTTCCAAATTCTGCGAGGGA 58.841 47.619 0.00 0.00 0.00 4.20
2957 3092 2.556622 GTTTCCAAATTCTGCGAGGGAA 59.443 45.455 0.00 0.00 32.91 3.97
2958 3093 2.577606 TCCAAATTCTGCGAGGGAAA 57.422 45.000 0.00 0.00 0.00 3.13
2959 3094 2.870175 TCCAAATTCTGCGAGGGAAAA 58.130 42.857 0.00 0.00 0.00 2.29
2960 3095 3.226777 TCCAAATTCTGCGAGGGAAAAA 58.773 40.909 0.00 0.00 0.00 1.94
2961 3096 3.005367 TCCAAATTCTGCGAGGGAAAAAC 59.995 43.478 0.00 0.00 0.00 2.43
2962 3097 3.243704 CCAAATTCTGCGAGGGAAAAACA 60.244 43.478 0.00 0.00 0.00 2.83
2963 3098 4.367450 CAAATTCTGCGAGGGAAAAACAA 58.633 39.130 0.00 0.00 0.00 2.83
2964 3099 3.643159 ATTCTGCGAGGGAAAAACAAC 57.357 42.857 0.00 0.00 0.00 3.32
2965 3100 2.341846 TCTGCGAGGGAAAAACAACT 57.658 45.000 0.00 0.00 0.00 3.16
2966 3101 1.946768 TCTGCGAGGGAAAAACAACTG 59.053 47.619 0.00 0.00 0.00 3.16
2967 3102 1.001378 CTGCGAGGGAAAAACAACTGG 60.001 52.381 0.00 0.00 0.00 4.00
2968 3103 0.313987 GCGAGGGAAAAACAACTGGG 59.686 55.000 0.00 0.00 0.00 4.45
2969 3104 1.975660 CGAGGGAAAAACAACTGGGA 58.024 50.000 0.00 0.00 0.00 4.37
2970 3105 1.607148 CGAGGGAAAAACAACTGGGAC 59.393 52.381 0.00 0.00 0.00 4.46
2971 3106 1.961394 GAGGGAAAAACAACTGGGACC 59.039 52.381 0.00 0.00 0.00 4.46
2972 3107 1.573857 AGGGAAAAACAACTGGGACCT 59.426 47.619 0.00 0.00 0.00 3.85
2973 3108 2.787035 AGGGAAAAACAACTGGGACCTA 59.213 45.455 0.00 0.00 0.00 3.08
2974 3109 3.154710 GGGAAAAACAACTGGGACCTAG 58.845 50.000 2.75 2.75 0.00 3.02
2975 3110 3.436035 GGGAAAAACAACTGGGACCTAGT 60.436 47.826 4.33 4.33 0.00 2.57
2976 3111 4.212716 GGAAAAACAACTGGGACCTAGTT 58.787 43.478 17.01 17.01 38.84 2.24
2977 3112 4.647853 GGAAAAACAACTGGGACCTAGTTT 59.352 41.667 19.85 6.06 36.29 2.66
2978 3113 5.221185 GGAAAAACAACTGGGACCTAGTTTC 60.221 44.000 19.85 14.11 36.29 2.78
2979 3114 4.513406 AAACAACTGGGACCTAGTTTCA 57.487 40.909 19.85 0.00 36.29 2.69
2980 3115 3.771577 ACAACTGGGACCTAGTTTCAG 57.228 47.619 19.85 11.90 36.29 3.02
2981 3116 3.314693 ACAACTGGGACCTAGTTTCAGA 58.685 45.455 19.85 0.00 36.29 3.27
2982 3117 3.714798 ACAACTGGGACCTAGTTTCAGAA 59.285 43.478 19.85 0.00 36.29 3.02
2983 3118 4.351111 ACAACTGGGACCTAGTTTCAGAAT 59.649 41.667 19.85 0.00 36.29 2.40
2984 3119 5.163088 ACAACTGGGACCTAGTTTCAGAATT 60.163 40.000 19.85 0.00 36.29 2.17
2985 3120 5.167303 ACTGGGACCTAGTTTCAGAATTC 57.833 43.478 4.33 0.00 0.00 2.17
2986 3121 4.184629 CTGGGACCTAGTTTCAGAATTCG 58.815 47.826 0.00 0.00 0.00 3.34
2987 3122 3.055385 TGGGACCTAGTTTCAGAATTCGG 60.055 47.826 0.00 0.00 0.00 4.30
2988 3123 3.055312 GGGACCTAGTTTCAGAATTCGGT 60.055 47.826 5.48 1.51 0.00 4.69
2989 3124 4.182339 GGACCTAGTTTCAGAATTCGGTC 58.818 47.826 13.45 13.45 39.08 4.79
2990 3125 4.081586 GGACCTAGTTTCAGAATTCGGTCT 60.082 45.833 18.38 12.25 39.58 3.85
2991 3126 4.822026 ACCTAGTTTCAGAATTCGGTCTG 58.178 43.478 5.48 5.60 45.44 3.51
3004 3139 1.613925 TCGGTCTGAACTCTGTTCTGG 59.386 52.381 14.23 7.28 0.00 3.86
3029 3168 3.119708 CCAAATTCTGCGAGGGAAAGAAG 60.120 47.826 0.00 0.00 33.67 2.85
3033 3172 1.971357 TCTGCGAGGGAAAGAAGAACT 59.029 47.619 0.00 0.00 0.00 3.01
3040 3179 0.405973 GGAAAGAAGAACTGGGGCCT 59.594 55.000 0.84 0.00 0.00 5.19
3041 3180 1.539157 GAAAGAAGAACTGGGGCCTG 58.461 55.000 0.84 0.00 0.00 4.85
3047 3186 1.152830 GAACTGGGGCCTGGTTTCA 59.847 57.895 0.84 0.00 0.00 2.69
3048 3187 0.895559 GAACTGGGGCCTGGTTTCAG 60.896 60.000 0.84 3.29 40.59 3.02
3049 3188 1.360393 AACTGGGGCCTGGTTTCAGA 61.360 55.000 11.50 0.00 43.49 3.27
3050 3189 1.360393 ACTGGGGCCTGGTTTCAGAA 61.360 55.000 11.50 0.00 43.49 3.02
3051 3190 0.178964 CTGGGGCCTGGTTTCAGAAA 60.179 55.000 0.84 0.00 43.49 2.52
3052 3191 0.486879 TGGGGCCTGGTTTCAGAAAT 59.513 50.000 0.84 0.00 43.49 2.17
3053 3192 1.186200 GGGGCCTGGTTTCAGAAATC 58.814 55.000 0.84 0.00 43.49 2.17
3054 3193 1.549950 GGGGCCTGGTTTCAGAAATCA 60.550 52.381 8.60 8.60 43.49 2.57
3127 3268 1.186200 GGGGCCAGGTTTCTGAATTC 58.814 55.000 4.39 0.00 43.49 2.17
3135 3276 3.433615 CAGGTTTCTGAATTCGGTCTGAC 59.566 47.826 13.95 0.00 43.49 3.51
3178 3319 4.505313 AATTCTGCGAGGGAAAAAGAAC 57.495 40.909 0.00 0.00 30.17 3.01
3183 3324 0.958876 CGAGGGAAAAAGAACCGGGG 60.959 60.000 6.32 0.00 0.00 5.73
3184 3325 0.611062 GAGGGAAAAAGAACCGGGGG 60.611 60.000 6.32 0.00 0.00 5.40
3186 3327 2.280552 GGAAAAAGAACCGGGGGCC 61.281 63.158 6.32 0.00 0.00 5.80
3187 3328 1.532078 GAAAAAGAACCGGGGGCCA 60.532 57.895 6.32 0.00 0.00 5.36
3189 3330 3.523374 AAAAGAACCGGGGGCCAGG 62.523 63.158 14.75 14.75 0.00 4.45
3198 3349 1.388133 GGGGGCCAGGTTTCTGAAT 59.612 57.895 4.39 0.00 43.49 2.57
3206 3357 3.057245 GCCAGGTTTCTGAATTCTGTTCC 60.057 47.826 7.05 10.07 43.49 3.62
3210 3370 4.823989 AGGTTTCTGAATTCTGTTCCTGTG 59.176 41.667 7.05 0.00 0.00 3.66
3221 3381 1.340889 TGTTCCTGTGCCAAATTCTGC 59.659 47.619 0.00 0.00 0.00 4.26
3227 3387 0.960364 GTGCCAAATTCTGCGAGGGA 60.960 55.000 0.00 0.00 0.00 4.20
3231 3391 2.288763 GCCAAATTCTGCGAGGGAAAAA 60.289 45.455 0.00 0.00 0.00 1.94
3276 3439 4.681942 GCGTAGTACATTATCTTGAGCAGG 59.318 45.833 0.38 0.00 0.00 4.85
3336 3499 2.180017 CAGCAGATTGGCGGCAAC 59.820 61.111 27.95 19.53 40.40 4.17
3357 3520 2.539476 GTATTCATTGGGCGGCAAAAG 58.461 47.619 12.47 2.40 0.00 2.27
3359 3522 0.829602 TTCATTGGGCGGCAAAAGGA 60.830 50.000 12.47 9.13 0.00 3.36
3360 3523 0.614415 TCATTGGGCGGCAAAAGGAT 60.614 50.000 12.47 0.00 0.00 3.24
3365 3528 0.459899 GGGCGGCAAAAGGATAAAGG 59.540 55.000 12.47 0.00 0.00 3.11
3390 3556 1.313091 GGGGGCGCTAGAAAAACTGG 61.313 60.000 7.64 0.00 0.00 4.00
3529 3702 1.419387 CCTCAACTCCCTCCCATGATC 59.581 57.143 0.00 0.00 0.00 2.92
3530 3703 2.406559 CTCAACTCCCTCCCATGATCT 58.593 52.381 0.00 0.00 0.00 2.75
3556 3729 1.451449 TTTCCCTTTCAGTGGCCCTA 58.549 50.000 0.00 0.00 0.00 3.53
3557 3730 0.991920 TTCCCTTTCAGTGGCCCTAG 59.008 55.000 0.00 0.00 0.00 3.02
3558 3731 1.077429 CCCTTTCAGTGGCCCTAGC 60.077 63.158 0.00 0.00 38.76 3.42
3559 3732 1.566298 CCCTTTCAGTGGCCCTAGCT 61.566 60.000 0.00 0.00 39.73 3.32
3560 3733 0.107459 CCTTTCAGTGGCCCTAGCTC 60.107 60.000 0.00 0.00 39.73 4.09
3561 3734 0.615331 CTTTCAGTGGCCCTAGCTCA 59.385 55.000 0.00 0.00 39.73 4.26
3563 3736 0.545309 TTCAGTGGCCCTAGCTCAGT 60.545 55.000 0.00 0.00 39.73 3.41
3568 3745 2.513435 GCCCTAGCTCAGTGCAGC 60.513 66.667 0.00 6.49 45.94 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.703621 GGTACATAACTGTAAAGCGATTACTCA 59.296 37.037 14.03 0.54 43.60 3.41
1 2 7.703621 TGGTACATAACTGTAAAGCGATTACTC 59.296 37.037 14.03 0.00 43.60 2.59
2 3 7.549839 TGGTACATAACTGTAAAGCGATTACT 58.450 34.615 14.03 0.95 43.60 2.24
3 4 7.490402 ACTGGTACATAACTGTAAAGCGATTAC 59.510 37.037 8.09 8.09 39.51 1.89
4 5 7.549839 ACTGGTACATAACTGTAAAGCGATTA 58.450 34.615 0.00 0.00 39.51 1.75
5 6 6.403878 ACTGGTACATAACTGTAAAGCGATT 58.596 36.000 0.00 0.00 39.51 3.34
6 7 5.974108 ACTGGTACATAACTGTAAAGCGAT 58.026 37.500 0.00 0.00 39.51 4.58
7 8 5.395682 ACTGGTACATAACTGTAAAGCGA 57.604 39.130 0.00 0.00 39.51 4.93
8 9 6.327934 ACTACTGGTACATAACTGTAAAGCG 58.672 40.000 0.00 0.00 39.51 4.68
9 10 6.755607 GGACTACTGGTACATAACTGTAAAGC 59.244 42.308 0.00 0.00 39.51 3.51
10 11 7.833786 TGGACTACTGGTACATAACTGTAAAG 58.166 38.462 0.00 0.00 39.51 1.85
25 26 1.831106 TGCATGGTACTGGACTACTGG 59.169 52.381 0.00 0.00 0.00 4.00
28 29 3.722147 CTCATGCATGGTACTGGACTAC 58.278 50.000 25.97 0.00 0.00 2.73
30 31 1.134280 GCTCATGCATGGTACTGGACT 60.134 52.381 25.97 0.00 39.41 3.85
31 32 1.303309 GCTCATGCATGGTACTGGAC 58.697 55.000 25.97 4.01 39.41 4.02
32 33 0.911053 TGCTCATGCATGGTACTGGA 59.089 50.000 25.97 10.08 45.31 3.86
33 34 3.482147 TGCTCATGCATGGTACTGG 57.518 52.632 25.97 10.61 45.31 4.00
60 61 6.361748 GCTTTGTGTAAGATGCAAAGAAGAAG 59.638 38.462 17.11 0.00 46.98 2.85
88 89 4.396166 AGGCTATCAACTTGTAACACATGC 59.604 41.667 0.00 0.00 0.00 4.06
113 117 2.415608 GGGCACCGATCAGAGACGA 61.416 63.158 0.00 0.00 40.86 4.20
137 141 2.736719 CGGCCAGATTAGACAGACAGTG 60.737 54.545 2.24 0.00 0.00 3.66
138 142 1.478510 CGGCCAGATTAGACAGACAGT 59.521 52.381 2.24 0.00 0.00 3.55
139 143 1.478510 ACGGCCAGATTAGACAGACAG 59.521 52.381 2.24 0.00 0.00 3.51
140 144 1.204704 CACGGCCAGATTAGACAGACA 59.795 52.381 2.24 0.00 0.00 3.41
141 145 1.204941 ACACGGCCAGATTAGACAGAC 59.795 52.381 2.24 0.00 0.00 3.51
144 148 1.621317 TCAACACGGCCAGATTAGACA 59.379 47.619 2.24 0.00 0.00 3.41
145 149 2.380084 TCAACACGGCCAGATTAGAC 57.620 50.000 2.24 0.00 0.00 2.59
154 158 1.745489 GGACCAGATCAACACGGCC 60.745 63.158 0.00 0.00 0.00 6.13
161 165 0.459899 CATCCGACGGACCAGATCAA 59.540 55.000 21.02 0.00 32.98 2.57
162 166 2.016393 GCATCCGACGGACCAGATCA 62.016 60.000 21.02 0.00 32.98 2.92
163 167 1.300233 GCATCCGACGGACCAGATC 60.300 63.158 21.02 0.99 32.98 2.75
214 218 1.153086 CGGAGGAGCATTTCTGGGG 60.153 63.158 0.00 0.00 0.00 4.96
346 355 2.130272 AGAAGGGAATTTTCGGCCTC 57.870 50.000 0.00 0.00 0.00 4.70
370 400 2.356793 GCGTGACAGCAGCTGAGT 60.357 61.111 29.70 15.28 35.18 3.41
774 830 0.593128 CAAGCTGAAACCCCAGAACG 59.407 55.000 0.00 0.00 36.29 3.95
783 839 4.326766 TGCGCGGCAAGCTGAAAC 62.327 61.111 8.83 0.00 45.59 2.78
829 885 4.141620 ACAAGGAACAGAGCATATCCGAAT 60.142 41.667 0.00 0.00 37.05 3.34
830 886 3.197766 ACAAGGAACAGAGCATATCCGAA 59.802 43.478 0.00 0.00 37.05 4.30
831 887 2.766263 ACAAGGAACAGAGCATATCCGA 59.234 45.455 0.00 0.00 37.05 4.55
832 888 3.126831 GACAAGGAACAGAGCATATCCG 58.873 50.000 0.00 0.00 37.05 4.18
833 889 3.135530 AGGACAAGGAACAGAGCATATCC 59.864 47.826 0.00 0.00 0.00 2.59
834 890 4.125703 CAGGACAAGGAACAGAGCATATC 58.874 47.826 0.00 0.00 0.00 1.63
835 891 3.118112 CCAGGACAAGGAACAGAGCATAT 60.118 47.826 0.00 0.00 0.00 1.78
856 912 1.405121 CCGGTATTTATAGGAGGCGCC 60.405 57.143 21.89 21.89 0.00 6.53
1008 1071 1.202651 CGGCCACCATCCCTAACTAAG 60.203 57.143 2.24 0.00 0.00 2.18
1326 1401 1.675641 GGCAGCACCATCGTCCTTT 60.676 57.895 0.00 0.00 38.86 3.11
1375 1450 2.358737 CACGACCTTCACCCTGGC 60.359 66.667 0.00 0.00 0.00 4.85
1460 1535 1.313091 TAGACGATCTGTGCAGCCGT 61.313 55.000 15.17 15.17 39.04 5.68
1465 1540 1.133216 GAGCTGTAGACGATCTGTGCA 59.867 52.381 0.00 0.00 0.00 4.57
1482 1557 3.052745 TCATCATCTAATCGCAACGAGC 58.947 45.455 0.00 0.00 39.91 5.03
1488 1563 5.993441 ACATCAACATCATCATCTAATCGCA 59.007 36.000 0.00 0.00 0.00 5.10
1522 1603 4.761739 ACAAGTCCAACGATCATTCACAAT 59.238 37.500 0.00 0.00 0.00 2.71
1551 1632 0.839946 GGCTTCTTCCTCCCTGCATA 59.160 55.000 0.00 0.00 0.00 3.14
1682 1763 1.226717 GATTTCCGAGACGAGCGCT 60.227 57.895 11.27 11.27 0.00 5.92
1691 1772 0.173481 TCTCGTGCCTGATTTCCGAG 59.827 55.000 0.00 0.00 44.67 4.63
1718 1799 2.694760 GCCGCCTTGCTTCTCCTTG 61.695 63.158 0.00 0.00 0.00 3.61
2022 2112 3.099267 ACGTGCTACTCAAGATATGCC 57.901 47.619 0.00 0.00 0.00 4.40
2072 2162 3.188786 GCGGACATGCGGTGAGTC 61.189 66.667 0.00 0.00 0.00 3.36
2073 2163 3.315142 ATGCGGACATGCGGTGAGT 62.315 57.895 0.00 0.00 37.81 3.41
2075 2165 2.511373 GATGCGGACATGCGGTGA 60.511 61.111 0.00 0.00 36.35 4.02
2077 2167 4.856801 GGGATGCGGACATGCGGT 62.857 66.667 0.00 0.00 45.01 5.68
2229 2319 1.283181 CTATCCTCCTCGGCGTTCG 59.717 63.158 6.85 0.00 40.90 3.95
2239 2329 1.202952 TCTTCCTCCTCGCTATCCTCC 60.203 57.143 0.00 0.00 0.00 4.30
2240 2330 2.159382 CTCTTCCTCCTCGCTATCCTC 58.841 57.143 0.00 0.00 0.00 3.71
2241 2331 1.203001 CCTCTTCCTCCTCGCTATCCT 60.203 57.143 0.00 0.00 0.00 3.24
2242 2332 1.202952 TCCTCTTCCTCCTCGCTATCC 60.203 57.143 0.00 0.00 0.00 2.59
2243 2333 2.279935 TCCTCTTCCTCCTCGCTATC 57.720 55.000 0.00 0.00 0.00 2.08
2244 2334 2.109128 TGATCCTCTTCCTCCTCGCTAT 59.891 50.000 0.00 0.00 0.00 2.97
2245 2335 1.495148 TGATCCTCTTCCTCCTCGCTA 59.505 52.381 0.00 0.00 0.00 4.26
2246 2336 0.260230 TGATCCTCTTCCTCCTCGCT 59.740 55.000 0.00 0.00 0.00 4.93
2247 2337 0.673437 CTGATCCTCTTCCTCCTCGC 59.327 60.000 0.00 0.00 0.00 5.03
2569 2677 1.137513 GTGCGTATGCTTATCGGACC 58.862 55.000 8.69 0.00 43.34 4.46
2681 2797 1.386772 TCTCCACCCCACAAACCCT 60.387 57.895 0.00 0.00 0.00 4.34
2694 2811 1.077357 GCGAGACCTCTCCTCTCCA 60.077 63.158 0.00 0.00 39.79 3.86
2853 2984 4.193090 CCATTTATTACACGGCTACACCA 58.807 43.478 0.00 0.00 39.03 4.17
2855 2986 5.501252 CGAACCATTTATTACACGGCTACAC 60.501 44.000 0.00 0.00 0.00 2.90
2860 2991 2.937799 TCCGAACCATTTATTACACGGC 59.062 45.455 0.00 0.00 39.13 5.68
2861 2992 4.186159 ACTCCGAACCATTTATTACACGG 58.814 43.478 0.00 0.00 40.36 4.94
2862 2993 5.789710 AACTCCGAACCATTTATTACACG 57.210 39.130 0.00 0.00 0.00 4.49
2863 2994 7.813645 AGAAAACTCCGAACCATTTATTACAC 58.186 34.615 0.00 0.00 0.00 2.90
2864 2995 7.881232 AGAGAAAACTCCGAACCATTTATTACA 59.119 33.333 0.00 0.00 0.00 2.41
2865 2996 8.265165 AGAGAAAACTCCGAACCATTTATTAC 57.735 34.615 0.00 0.00 0.00 1.89
2869 3000 5.243207 GGAGAGAAAACTCCGAACCATTTA 58.757 41.667 0.00 0.00 45.30 1.40
2870 3001 4.072839 GGAGAGAAAACTCCGAACCATTT 58.927 43.478 0.00 0.00 45.30 2.32
2871 3002 3.676093 GGAGAGAAAACTCCGAACCATT 58.324 45.455 0.00 0.00 45.30 3.16
2887 3018 1.942552 TCGAATAGCGAGCGGAGAG 59.057 57.895 0.00 0.00 45.59 3.20
2896 3027 4.329489 GCATAGCAATCAATCGAATAGCG 58.671 43.478 0.00 0.00 42.69 4.26
2919 3054 2.602257 AACAGAACAAAGCAAAGGGC 57.398 45.000 0.00 0.00 45.30 5.19
2921 3056 4.122143 TGGAAACAGAACAAAGCAAAGG 57.878 40.909 0.00 0.00 35.01 3.11
2922 3057 6.667007 ATTTGGAAACAGAACAAAGCAAAG 57.333 33.333 0.00 0.00 44.54 2.77
2923 3058 6.878389 AGAATTTGGAAACAGAACAAAGCAAA 59.122 30.769 0.00 0.00 44.54 3.68
2924 3059 6.313411 CAGAATTTGGAAACAGAACAAAGCAA 59.687 34.615 0.00 0.00 44.54 3.91
2925 3060 5.811613 CAGAATTTGGAAACAGAACAAAGCA 59.188 36.000 0.00 0.00 44.54 3.91
2926 3061 5.277011 GCAGAATTTGGAAACAGAACAAAGC 60.277 40.000 0.00 0.00 44.54 3.51
2927 3062 5.051508 CGCAGAATTTGGAAACAGAACAAAG 60.052 40.000 0.00 0.00 44.54 2.77
2928 3063 4.803088 CGCAGAATTTGGAAACAGAACAAA 59.197 37.500 0.00 0.00 44.54 2.83
2929 3064 4.097135 TCGCAGAATTTGGAAACAGAACAA 59.903 37.500 0.00 0.00 44.54 2.83
2930 3065 3.629855 TCGCAGAATTTGGAAACAGAACA 59.370 39.130 0.00 0.00 44.54 3.18
2931 3066 4.222114 CTCGCAGAATTTGGAAACAGAAC 58.778 43.478 0.00 0.00 37.79 3.01
2932 3067 3.253188 CCTCGCAGAATTTGGAAACAGAA 59.747 43.478 0.00 0.00 37.79 3.02
2933 3068 2.813754 CCTCGCAGAATTTGGAAACAGA 59.186 45.455 0.00 0.00 37.79 3.41
2934 3069 2.095059 CCCTCGCAGAATTTGGAAACAG 60.095 50.000 0.00 0.00 37.79 3.16
2935 3070 1.885887 CCCTCGCAGAATTTGGAAACA 59.114 47.619 0.00 0.00 34.09 2.83
2936 3071 2.159382 TCCCTCGCAGAATTTGGAAAC 58.841 47.619 0.00 0.00 34.09 2.78
2937 3072 2.577606 TCCCTCGCAGAATTTGGAAA 57.422 45.000 0.00 0.00 34.09 3.13
2938 3073 2.577606 TTCCCTCGCAGAATTTGGAA 57.422 45.000 0.00 0.00 34.09 3.53
2939 3074 2.577606 TTTCCCTCGCAGAATTTGGA 57.422 45.000 0.00 0.00 34.09 3.53
2940 3075 3.243704 TGTTTTTCCCTCGCAGAATTTGG 60.244 43.478 0.00 0.00 34.09 3.28
2941 3076 3.976169 TGTTTTTCCCTCGCAGAATTTG 58.024 40.909 0.00 0.00 34.09 2.32
2942 3077 4.099419 AGTTGTTTTTCCCTCGCAGAATTT 59.901 37.500 0.00 0.00 34.09 1.82
2943 3078 3.636764 AGTTGTTTTTCCCTCGCAGAATT 59.363 39.130 0.00 0.00 34.09 2.17
2944 3079 3.004734 CAGTTGTTTTTCCCTCGCAGAAT 59.995 43.478 0.00 0.00 34.09 2.40
2945 3080 2.357637 CAGTTGTTTTTCCCTCGCAGAA 59.642 45.455 0.00 0.00 34.09 3.02
2946 3081 1.946768 CAGTTGTTTTTCCCTCGCAGA 59.053 47.619 0.00 0.00 0.00 4.26
2947 3082 1.001378 CCAGTTGTTTTTCCCTCGCAG 60.001 52.381 0.00 0.00 0.00 5.18
2948 3083 1.028905 CCAGTTGTTTTTCCCTCGCA 58.971 50.000 0.00 0.00 0.00 5.10
2949 3084 0.313987 CCCAGTTGTTTTTCCCTCGC 59.686 55.000 0.00 0.00 0.00 5.03
2950 3085 1.607148 GTCCCAGTTGTTTTTCCCTCG 59.393 52.381 0.00 0.00 0.00 4.63
2951 3086 1.961394 GGTCCCAGTTGTTTTTCCCTC 59.039 52.381 0.00 0.00 0.00 4.30
2952 3087 1.573857 AGGTCCCAGTTGTTTTTCCCT 59.426 47.619 0.00 0.00 0.00 4.20
2953 3088 2.082140 AGGTCCCAGTTGTTTTTCCC 57.918 50.000 0.00 0.00 0.00 3.97
2954 3089 3.828921 ACTAGGTCCCAGTTGTTTTTCC 58.171 45.455 0.00 0.00 0.00 3.13
2955 3090 5.358725 TGAAACTAGGTCCCAGTTGTTTTTC 59.641 40.000 3.23 0.00 36.38 2.29
2956 3091 5.265989 TGAAACTAGGTCCCAGTTGTTTTT 58.734 37.500 3.23 0.00 36.38 1.94
2957 3092 4.862371 TGAAACTAGGTCCCAGTTGTTTT 58.138 39.130 3.23 0.00 36.38 2.43
2958 3093 4.165372 TCTGAAACTAGGTCCCAGTTGTTT 59.835 41.667 3.23 0.00 36.38 2.83
2959 3094 3.714798 TCTGAAACTAGGTCCCAGTTGTT 59.285 43.478 3.23 0.00 36.38 2.83
2960 3095 3.314693 TCTGAAACTAGGTCCCAGTTGT 58.685 45.455 3.23 0.00 36.38 3.32
2961 3096 4.351874 TTCTGAAACTAGGTCCCAGTTG 57.648 45.455 3.23 0.00 36.38 3.16
2962 3097 5.561679 GAATTCTGAAACTAGGTCCCAGTT 58.438 41.667 9.21 0.00 37.85 3.16
2963 3098 4.322801 CGAATTCTGAAACTAGGTCCCAGT 60.323 45.833 3.52 0.00 0.00 4.00
2964 3099 4.184629 CGAATTCTGAAACTAGGTCCCAG 58.815 47.826 3.52 4.28 0.00 4.45
2965 3100 3.055385 CCGAATTCTGAAACTAGGTCCCA 60.055 47.826 3.52 0.00 0.00 4.37
2966 3101 3.055312 ACCGAATTCTGAAACTAGGTCCC 60.055 47.826 3.66 0.00 0.00 4.46
2967 3102 4.081586 AGACCGAATTCTGAAACTAGGTCC 60.082 45.833 22.31 12.22 45.70 4.46
2968 3103 4.865365 CAGACCGAATTCTGAAACTAGGTC 59.135 45.833 20.24 20.24 45.19 3.85
2969 3104 4.822026 CAGACCGAATTCTGAAACTAGGT 58.178 43.478 3.66 9.03 45.19 3.08
2980 3115 4.387256 CAGAACAGAGTTCAGACCGAATTC 59.613 45.833 11.92 0.00 39.91 2.17
2981 3116 4.310769 CAGAACAGAGTTCAGACCGAATT 58.689 43.478 11.92 0.00 35.63 2.17
2982 3117 3.306364 CCAGAACAGAGTTCAGACCGAAT 60.306 47.826 11.92 0.00 35.63 3.34
2983 3118 2.035961 CCAGAACAGAGTTCAGACCGAA 59.964 50.000 11.92 0.00 0.00 4.30
2984 3119 1.613925 CCAGAACAGAGTTCAGACCGA 59.386 52.381 11.92 0.00 0.00 4.69
2985 3120 1.341531 ACCAGAACAGAGTTCAGACCG 59.658 52.381 11.92 0.00 0.00 4.79
2986 3121 3.394719 GAACCAGAACAGAGTTCAGACC 58.605 50.000 11.92 0.00 39.71 3.85
2987 3122 3.181465 TGGAACCAGAACAGAGTTCAGAC 60.181 47.826 11.92 4.10 41.32 3.51
2988 3123 3.038280 TGGAACCAGAACAGAGTTCAGA 58.962 45.455 11.92 0.00 41.32 3.27
2989 3124 3.475566 TGGAACCAGAACAGAGTTCAG 57.524 47.619 11.92 4.26 41.32 3.02
2990 3125 3.924114 TTGGAACCAGAACAGAGTTCA 57.076 42.857 11.92 0.00 41.32 3.18
2991 3126 5.532779 AGAATTTGGAACCAGAACAGAGTTC 59.467 40.000 1.77 1.77 39.31 3.01
2992 3127 5.300286 CAGAATTTGGAACCAGAACAGAGTT 59.700 40.000 0.00 0.00 0.00 3.01
2993 3128 4.823989 CAGAATTTGGAACCAGAACAGAGT 59.176 41.667 0.00 0.00 0.00 3.24
2994 3129 4.320788 GCAGAATTTGGAACCAGAACAGAG 60.321 45.833 0.00 0.00 0.00 3.35
2995 3130 3.569701 GCAGAATTTGGAACCAGAACAGA 59.430 43.478 0.00 0.00 0.00 3.41
2996 3131 3.610114 CGCAGAATTTGGAACCAGAACAG 60.610 47.826 0.00 0.00 0.00 3.16
2997 3132 2.293122 CGCAGAATTTGGAACCAGAACA 59.707 45.455 0.00 0.00 0.00 3.18
3004 3139 1.821216 TCCCTCGCAGAATTTGGAAC 58.179 50.000 0.00 0.00 34.09 3.62
3029 3168 0.895559 CTGAAACCAGGCCCCAGTTC 60.896 60.000 0.00 0.00 0.00 3.01
3033 3172 0.486879 ATTTCTGAAACCAGGCCCCA 59.513 50.000 4.73 0.00 32.62 4.96
3040 3179 6.550854 AGACCAAATTCTGATTTCTGAAACCA 59.449 34.615 4.73 0.29 37.36 3.67
3041 3180 6.865205 CAGACCAAATTCTGATTTCTGAAACC 59.135 38.462 4.73 0.00 45.19 3.27
3053 3192 5.762218 AGAACAGAGTTCAGACCAAATTCTG 59.238 40.000 11.92 6.78 42.75 3.02
3054 3193 5.762218 CAGAACAGAGTTCAGACCAAATTCT 59.238 40.000 11.92 0.00 0.00 2.40
3060 3199 4.262635 GGAATCAGAACAGAGTTCAGACCA 60.263 45.833 11.92 0.00 0.00 4.02
3068 3207 5.182760 GCAGAATTTGGAATCAGAACAGAGT 59.817 40.000 0.00 0.00 0.00 3.24
3074 3213 3.691118 CCTCGCAGAATTTGGAATCAGAA 59.309 43.478 0.00 0.00 34.09 3.02
3127 3268 0.389391 ACACAACAGAGGTCAGACCG 59.611 55.000 14.32 2.62 44.90 4.79
3135 3276 3.743521 TGGAATCAGAACACAACAGAGG 58.256 45.455 0.00 0.00 0.00 3.69
3178 3319 4.740822 CAGAAACCTGGCCCCCGG 62.741 72.222 0.00 0.00 0.00 5.73
3183 3324 2.519013 ACAGAATTCAGAAACCTGGCC 58.481 47.619 8.44 0.00 32.62 5.36
3184 3325 3.057245 GGAACAGAATTCAGAAACCTGGC 60.057 47.826 8.44 9.33 32.62 4.85
3186 3327 4.823989 ACAGGAACAGAATTCAGAAACCTG 59.176 41.667 24.47 24.47 45.07 4.00
3187 3328 4.823989 CACAGGAACAGAATTCAGAAACCT 59.176 41.667 8.44 8.44 0.00 3.50
3189 3330 4.540824 GCACAGGAACAGAATTCAGAAAC 58.459 43.478 8.44 0.00 0.00 2.78
3198 3349 3.318839 CAGAATTTGGCACAGGAACAGAA 59.681 43.478 0.00 0.00 42.39 3.02
3206 3357 0.169672 CCTCGCAGAATTTGGCACAG 59.830 55.000 0.00 0.00 35.52 3.66
3210 3370 0.887933 TTTCCCTCGCAGAATTTGGC 59.112 50.000 0.00 0.00 34.09 4.52
3231 3391 0.984995 GTACCTGGTCCCAGCTCTTT 59.015 55.000 0.63 0.00 42.35 2.52
3232 3392 0.117340 AGTACCTGGTCCCAGCTCTT 59.883 55.000 0.63 0.00 42.35 2.85
3233 3393 1.008403 TAGTACCTGGTCCCAGCTCT 58.992 55.000 0.63 7.80 42.35 4.09
3235 3395 0.688087 GCTAGTACCTGGTCCCAGCT 60.688 60.000 0.63 2.87 42.35 4.24
3236 3396 1.823976 GCTAGTACCTGGTCCCAGC 59.176 63.158 0.63 6.67 42.35 4.85
3237 3397 0.683504 ACGCTAGTACCTGGTCCCAG 60.684 60.000 0.63 6.35 43.26 4.45
3238 3398 0.625316 TACGCTAGTACCTGGTCCCA 59.375 55.000 0.63 0.00 0.00 4.37
3276 3439 1.275291 TCCACCAGAATCGGACAGTTC 59.725 52.381 0.00 0.00 0.00 3.01
3292 3455 1.182667 GCACCCCCAGTAAATTCCAC 58.817 55.000 0.00 0.00 0.00 4.02
3318 3481 3.751246 TTGCCGCCAATCTGCTGC 61.751 61.111 0.00 0.00 41.25 5.25
3326 3489 1.135546 CAATGAATACGTTGCCGCCAA 60.136 47.619 0.00 0.00 36.44 4.52
3327 3490 0.449786 CAATGAATACGTTGCCGCCA 59.550 50.000 0.00 0.00 36.44 5.69
3328 3491 0.248458 CCAATGAATACGTTGCCGCC 60.248 55.000 0.00 0.00 40.48 6.13
3329 3492 0.248458 CCCAATGAATACGTTGCCGC 60.248 55.000 0.00 0.00 40.48 6.53
3330 3493 0.248458 GCCCAATGAATACGTTGCCG 60.248 55.000 0.00 0.00 40.48 5.69
3331 3494 0.248458 CGCCCAATGAATACGTTGCC 60.248 55.000 0.00 0.00 40.48 4.52
3332 3495 0.248458 CCGCCCAATGAATACGTTGC 60.248 55.000 0.00 0.00 40.48 4.17
3333 3496 0.248458 GCCGCCCAATGAATACGTTG 60.248 55.000 0.00 0.00 41.21 4.10
3334 3497 0.678366 TGCCGCCCAATGAATACGTT 60.678 50.000 0.00 0.00 0.00 3.99
3335 3498 0.678366 TTGCCGCCCAATGAATACGT 60.678 50.000 0.00 0.00 0.00 3.57
3336 3499 0.453793 TTTGCCGCCCAATGAATACG 59.546 50.000 0.00 0.00 32.49 3.06
3337 3500 2.539476 CTTTTGCCGCCCAATGAATAC 58.461 47.619 0.00 0.00 32.49 1.89
3338 3501 1.480137 CCTTTTGCCGCCCAATGAATA 59.520 47.619 0.00 0.00 32.49 1.75
3357 3520 2.110420 CCCCCGTCGCCTTTATCC 59.890 66.667 0.00 0.00 0.00 2.59
3378 3543 2.095364 CAGCAGCTGCCAGTTTTTCTAG 60.095 50.000 34.39 6.74 43.38 2.43
3529 3702 2.887152 CACTGAAAGGGAAAACTCCCAG 59.113 50.000 12.69 3.69 43.23 4.45
3530 3703 2.424234 CCACTGAAAGGGAAAACTCCCA 60.424 50.000 12.69 0.00 43.23 4.37
3541 3714 0.107459 GAGCTAGGGCCACTGAAAGG 60.107 60.000 6.18 0.00 37.47 3.11


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

AutoCloner maintained by Alex Coulton.