Multiple sequence alignment - TraesCS5B01G316900

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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 TraesCS5B01G316900 chr5B 100.000 3336 0 0 1 3336 499126155 499129490 0.000000e+00 6161
1 TraesCS5B01G316900 chr5D 96.796 2653 63 12 142 2783 414096729 414099370 0.000000e+00 4409
2 TraesCS5B01G316900 chr5D 86.328 512 25 11 2833 3336 414099367 414099841 1.770000e-142 516
3 TraesCS5B01G316900 chr5D 98.667 150 2 0 1 150 414072502 414072651 1.970000e-67 267
4 TraesCS5B01G316900 chr5A 92.685 2119 125 19 635 2743 526587795 526589893 0.000000e+00 3027
5 TraesCS5B01G316900 chr5A 80.835 407 36 19 237 638 526587141 526587510 7.050000e-72 281
6 TraesCS5B01G316900 chr2A 80.822 146 20 5 1083 1222 32769782 32769925 1.270000e-19 108


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 TraesCS5B01G316900 chr5B 499126155 499129490 3335 False 6161.0 6161 100.000 1 3336 1 chr5B.!!$F1 3335
1 TraesCS5B01G316900 chr5D 414096729 414099841 3112 False 2462.5 4409 91.562 142 3336 2 chr5D.!!$F2 3194
2 TraesCS5B01G316900 chr5A 526587141 526589893 2752 False 1654.0 3027 86.760 237 2743 2 chr5A.!!$F1 2506

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
85 86 0.036164 CTGGGGACATGTGACCGAAA 59.964 55.0 1.15 0.0 41.51 3.46 F
94 95 0.109532 TGTGACCGAAATTCTGCCCA 59.890 50.0 0.00 0.0 0.00 5.36 F
1605 1904 0.035458 AGTGCACCAGAACCTGCTAC 59.965 55.0 14.63 0.0 34.29 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1904 1.675310 TGCATCTTGGCAGGTTCGG 60.675 57.895 0.00 0.0 39.25 4.30 R
1790 2089 2.279741 TGTATCGCTTGGTGAGAATGC 58.720 47.619 0.00 0.0 0.00 3.56 R
2785 3092 0.251916 CTTCCTGACCGGTGGCATTA 59.748 55.000 14.63 0.0 0.00 1.90 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
26 27 8.725148 CATCTAAAGATGTGGATATTAGCAACC 58.275 37.037 11.14 0.00 45.10 3.77
27 28 8.034313 TCTAAAGATGTGGATATTAGCAACCT 57.966 34.615 0.00 0.00 0.00 3.50
28 29 6.949352 AAAGATGTGGATATTAGCAACCTG 57.051 37.500 0.00 0.00 0.00 4.00
29 30 4.392940 AGATGTGGATATTAGCAACCTGC 58.607 43.478 0.00 0.00 45.46 4.85
38 39 4.058797 GCAACCTGCAACCGTACT 57.941 55.556 0.00 0.00 44.26 2.73
39 40 3.220447 GCAACCTGCAACCGTACTA 57.780 52.632 0.00 0.00 44.26 1.82
40 41 1.734163 GCAACCTGCAACCGTACTAT 58.266 50.000 0.00 0.00 44.26 2.12
41 42 2.081462 GCAACCTGCAACCGTACTATT 58.919 47.619 0.00 0.00 44.26 1.73
42 43 3.264104 GCAACCTGCAACCGTACTATTA 58.736 45.455 0.00 0.00 44.26 0.98
43 44 3.063045 GCAACCTGCAACCGTACTATTAC 59.937 47.826 0.00 0.00 44.26 1.89
44 45 4.501071 CAACCTGCAACCGTACTATTACT 58.499 43.478 0.00 0.00 0.00 2.24
45 46 4.813750 ACCTGCAACCGTACTATTACTT 57.186 40.909 0.00 0.00 0.00 2.24
46 47 5.156608 ACCTGCAACCGTACTATTACTTT 57.843 39.130 0.00 0.00 0.00 2.66
47 48 5.554070 ACCTGCAACCGTACTATTACTTTT 58.446 37.500 0.00 0.00 0.00 2.27
48 49 6.700352 ACCTGCAACCGTACTATTACTTTTA 58.300 36.000 0.00 0.00 0.00 1.52
49 50 7.160726 ACCTGCAACCGTACTATTACTTTTAA 58.839 34.615 0.00 0.00 0.00 1.52
50 51 7.661027 ACCTGCAACCGTACTATTACTTTTAAA 59.339 33.333 0.00 0.00 0.00 1.52
51 52 8.505625 CCTGCAACCGTACTATTACTTTTAAAA 58.494 33.333 0.00 0.00 0.00 1.52
52 53 9.881529 CTGCAACCGTACTATTACTTTTAAAAA 57.118 29.630 1.66 0.00 0.00 1.94
68 69 9.934190 ACTTTTAAAAATGCAAGCAAAATACTG 57.066 25.926 0.00 0.00 0.00 2.74
69 70 9.384682 CTTTTAAAAATGCAAGCAAAATACTGG 57.615 29.630 0.00 0.00 0.00 4.00
70 71 5.945466 AAAAATGCAAGCAAAATACTGGG 57.055 34.783 0.00 0.00 0.00 4.45
71 72 3.615224 AATGCAAGCAAAATACTGGGG 57.385 42.857 0.00 0.00 0.00 4.96
72 73 2.300956 TGCAAGCAAAATACTGGGGA 57.699 45.000 0.00 0.00 0.00 4.81
73 74 1.892474 TGCAAGCAAAATACTGGGGAC 59.108 47.619 0.00 0.00 0.00 4.46
74 75 1.892474 GCAAGCAAAATACTGGGGACA 59.108 47.619 0.00 0.00 39.59 4.02
75 76 2.497273 GCAAGCAAAATACTGGGGACAT 59.503 45.455 0.00 0.00 41.51 3.06
76 77 3.676873 GCAAGCAAAATACTGGGGACATG 60.677 47.826 0.00 0.00 41.51 3.21
77 78 3.456380 AGCAAAATACTGGGGACATGT 57.544 42.857 0.00 0.00 41.51 3.21
78 79 3.091545 AGCAAAATACTGGGGACATGTG 58.908 45.455 1.15 0.00 41.51 3.21
79 80 3.088532 GCAAAATACTGGGGACATGTGA 58.911 45.455 1.15 0.00 41.51 3.58
80 81 3.119495 GCAAAATACTGGGGACATGTGAC 60.119 47.826 1.15 0.00 41.51 3.67
81 82 3.366052 AAATACTGGGGACATGTGACC 57.634 47.619 1.15 5.69 41.51 4.02
82 83 0.830648 ATACTGGGGACATGTGACCG 59.169 55.000 1.15 4.59 41.51 4.79
83 84 0.251877 TACTGGGGACATGTGACCGA 60.252 55.000 1.15 1.53 41.51 4.69
84 85 1.125093 ACTGGGGACATGTGACCGAA 61.125 55.000 1.15 0.00 41.51 4.30
85 86 0.036164 CTGGGGACATGTGACCGAAA 59.964 55.000 1.15 0.00 41.51 3.46
86 87 0.695924 TGGGGACATGTGACCGAAAT 59.304 50.000 1.15 0.00 33.40 2.17
87 88 1.074727 TGGGGACATGTGACCGAAATT 59.925 47.619 1.15 0.00 33.40 1.82
88 89 1.743394 GGGGACATGTGACCGAAATTC 59.257 52.381 1.15 0.00 0.00 2.17
89 90 2.618045 GGGGACATGTGACCGAAATTCT 60.618 50.000 1.15 0.00 0.00 2.40
90 91 2.420022 GGGACATGTGACCGAAATTCTG 59.580 50.000 1.15 0.00 0.00 3.02
91 92 2.159517 GGACATGTGACCGAAATTCTGC 60.160 50.000 1.15 0.00 0.00 4.26
92 93 1.812571 ACATGTGACCGAAATTCTGCC 59.187 47.619 0.00 0.00 0.00 4.85
93 94 1.133025 CATGTGACCGAAATTCTGCCC 59.867 52.381 0.00 0.00 0.00 5.36
94 95 0.109532 TGTGACCGAAATTCTGCCCA 59.890 50.000 0.00 0.00 0.00 5.36
95 96 0.521735 GTGACCGAAATTCTGCCCAC 59.478 55.000 0.00 0.00 0.00 4.61
96 97 0.109532 TGACCGAAATTCTGCCCACA 59.890 50.000 0.00 0.00 0.00 4.17
97 98 1.243902 GACCGAAATTCTGCCCACAA 58.756 50.000 0.00 0.00 0.00 3.33
98 99 1.200020 GACCGAAATTCTGCCCACAAG 59.800 52.381 0.00 0.00 0.00 3.16
99 100 1.247567 CCGAAATTCTGCCCACAAGT 58.752 50.000 0.00 0.00 0.00 3.16
100 101 1.613437 CCGAAATTCTGCCCACAAGTT 59.387 47.619 0.00 0.00 0.00 2.66
101 102 2.817258 CCGAAATTCTGCCCACAAGTTA 59.183 45.455 0.00 0.00 0.00 2.24
102 103 3.443681 CCGAAATTCTGCCCACAAGTTAT 59.556 43.478 0.00 0.00 0.00 1.89
103 104 4.638421 CCGAAATTCTGCCCACAAGTTATA 59.362 41.667 0.00 0.00 0.00 0.98
104 105 5.448632 CCGAAATTCTGCCCACAAGTTATAC 60.449 44.000 0.00 0.00 0.00 1.47
105 106 5.560966 AAATTCTGCCCACAAGTTATACG 57.439 39.130 0.00 0.00 0.00 3.06
106 107 3.688694 TTCTGCCCACAAGTTATACGT 57.311 42.857 0.00 0.00 0.00 3.57
107 108 4.804868 TTCTGCCCACAAGTTATACGTA 57.195 40.909 0.00 0.00 0.00 3.57
108 109 5.347620 TTCTGCCCACAAGTTATACGTAT 57.652 39.130 13.54 13.54 0.00 3.06
109 110 4.940463 TCTGCCCACAAGTTATACGTATC 58.060 43.478 12.24 0.00 0.00 2.24
110 111 4.647853 TCTGCCCACAAGTTATACGTATCT 59.352 41.667 12.24 0.70 0.00 1.98
111 112 4.689071 TGCCCACAAGTTATACGTATCTG 58.311 43.478 12.24 8.13 0.00 2.90
112 113 3.493503 GCCCACAAGTTATACGTATCTGC 59.506 47.826 12.24 3.72 0.00 4.26
113 114 4.056050 CCCACAAGTTATACGTATCTGCC 58.944 47.826 12.24 0.00 0.00 4.85
114 115 4.442332 CCCACAAGTTATACGTATCTGCCA 60.442 45.833 12.24 0.00 0.00 4.92
115 116 4.745125 CCACAAGTTATACGTATCTGCCAG 59.255 45.833 12.24 2.12 0.00 4.85
116 117 4.209288 CACAAGTTATACGTATCTGCCAGC 59.791 45.833 12.24 0.00 0.00 4.85
117 118 3.662247 AGTTATACGTATCTGCCAGCC 57.338 47.619 12.24 0.00 0.00 4.85
118 119 2.963101 AGTTATACGTATCTGCCAGCCA 59.037 45.455 12.24 0.00 0.00 4.75
119 120 3.578716 AGTTATACGTATCTGCCAGCCAT 59.421 43.478 12.24 0.00 0.00 4.40
120 121 4.040461 AGTTATACGTATCTGCCAGCCATT 59.960 41.667 12.24 0.00 0.00 3.16
121 122 5.245301 AGTTATACGTATCTGCCAGCCATTA 59.755 40.000 12.24 0.00 0.00 1.90
122 123 2.533266 ACGTATCTGCCAGCCATTAG 57.467 50.000 0.00 0.00 0.00 1.73
123 124 1.151668 CGTATCTGCCAGCCATTAGC 58.848 55.000 0.00 0.00 44.25 3.09
135 136 2.301346 GCCATTAGCTGCCAATGTAGT 58.699 47.619 17.30 0.00 38.99 2.73
136 137 2.689983 GCCATTAGCTGCCAATGTAGTT 59.310 45.455 17.30 0.00 38.99 2.24
137 138 3.243201 GCCATTAGCTGCCAATGTAGTTC 60.243 47.826 17.30 1.04 38.99 3.01
138 139 4.202441 CCATTAGCTGCCAATGTAGTTCT 58.798 43.478 17.30 0.00 32.55 3.01
139 140 5.368145 CCATTAGCTGCCAATGTAGTTCTA 58.632 41.667 17.30 0.00 32.55 2.10
140 141 5.237344 CCATTAGCTGCCAATGTAGTTCTAC 59.763 44.000 17.30 3.33 32.55 2.59
141 142 3.981071 AGCTGCCAATGTAGTTCTACA 57.019 42.857 13.85 13.85 0.00 2.74
142 143 3.600388 AGCTGCCAATGTAGTTCTACAC 58.400 45.455 13.78 3.76 32.16 2.90
143 144 3.261897 AGCTGCCAATGTAGTTCTACACT 59.738 43.478 13.78 1.72 39.87 3.55
151 152 3.079578 TGTAGTTCTACACTGGGACTCG 58.920 50.000 8.38 0.00 35.97 4.18
614 617 3.344204 ACCTACTCGGTCCATGCTATGG 61.344 54.545 8.41 8.41 44.93 2.74
632 635 0.537653 GGCCCTGAGGTGACTACTTC 59.462 60.000 0.00 0.00 44.43 3.01
790 1081 1.002087 AGACTGACCTTTGCTTACCGG 59.998 52.381 0.00 0.00 0.00 5.28
1106 1399 7.856145 CAGTTTCTGCCTCTAAACTATGATT 57.144 36.000 0.00 0.00 42.52 2.57
1284 1577 3.395941 CTGGATACCTCCCTTTTATGCCT 59.604 47.826 0.00 0.00 41.29 4.75
1605 1904 0.035458 AGTGCACCAGAACCTGCTAC 59.965 55.000 14.63 0.00 34.29 3.58
1606 1905 0.955919 GTGCACCAGAACCTGCTACC 60.956 60.000 5.22 0.00 34.29 3.18
1790 2089 2.032204 GCTGATCTATTTGCAGCCGAAG 60.032 50.000 0.00 0.00 46.94 3.79
1804 2103 0.449388 CCGAAGCATTCTCACCAAGC 59.551 55.000 0.00 0.00 44.75 4.01
1814 2113 0.824109 CTCACCAAGCGATACAGGGA 59.176 55.000 0.00 0.00 0.00 4.20
1817 2116 0.541863 ACCAAGCGATACAGGGAAGG 59.458 55.000 0.00 0.00 0.00 3.46
2045 2344 5.314923 TCTTCTGCAAATTCATGTTAGCC 57.685 39.130 0.00 0.00 0.00 3.93
2049 2348 4.082625 TCTGCAAATTCATGTTAGCCTGTG 60.083 41.667 0.00 0.00 0.00 3.66
2128 2427 7.833682 TCCATGGACATGACAGTGTTTTATATT 59.166 33.333 11.44 0.00 41.20 1.28
2132 2431 8.855110 TGGACATGACAGTGTTTTATATTTTGT 58.145 29.630 0.00 0.00 31.16 2.83
2203 2502 7.724305 TCTTGATAACAAACAGTCACTAACC 57.276 36.000 0.00 0.00 35.49 2.85
2212 2511 4.258702 ACAGTCACTAACCTGTCATCAC 57.741 45.455 0.00 0.00 0.00 3.06
2247 2546 4.381411 GTCATCTGTGGGAATAAGTAGGC 58.619 47.826 0.00 0.00 0.00 3.93
2292 2591 1.624479 ATCCACCCAGAGCAGCTCAG 61.624 60.000 24.64 16.42 32.06 3.35
2300 2599 1.005630 GAGCAGCTCAGTGGACGTT 60.006 57.895 18.17 0.00 0.00 3.99
2332 2631 2.435586 CCTCCTCTGCTTGGTGCG 60.436 66.667 0.00 0.00 46.63 5.34
2512 2814 9.067986 TCAAGGTTTCTTAAGATTTTCTTCCTC 57.932 33.333 5.89 0.00 37.89 3.71
2516 2818 4.514401 TCTTAAGATTTTCTTCCTCGGGC 58.486 43.478 0.00 0.00 37.89 6.13
2671 2973 6.498304 AGAAACTGTGCATTGTTTAGACTTG 58.502 36.000 16.37 0.00 36.64 3.16
2701 3003 5.505654 GGCAACACATTGGGATAATAGAACG 60.506 44.000 0.00 0.00 36.23 3.95
2721 3023 2.713976 CGTCTGAACACGTGAATTTTGC 59.286 45.455 25.01 0.00 34.95 3.68
2735 3037 4.022068 TGAATTTTGCCAGCTTCAGTAAGG 60.022 41.667 0.00 0.00 32.98 2.69
2736 3038 2.656947 TTTGCCAGCTTCAGTAAGGT 57.343 45.000 0.00 0.00 44.16 3.50
2760 3067 7.065923 GGTGAATGGTAGCTTTAAGTAGAAAGG 59.934 40.741 0.00 0.00 36.99 3.11
2768 3075 7.856145 AGCTTTAAGTAGAAAGGATGATGTG 57.144 36.000 0.00 0.00 36.99 3.21
2779 3086 4.630644 AGGATGATGTGAGTTTGAGTGT 57.369 40.909 0.00 0.00 0.00 3.55
2780 3087 4.573900 AGGATGATGTGAGTTTGAGTGTC 58.426 43.478 0.00 0.00 0.00 3.67
2781 3088 4.040829 AGGATGATGTGAGTTTGAGTGTCA 59.959 41.667 0.00 0.00 0.00 3.58
2782 3089 4.940046 GGATGATGTGAGTTTGAGTGTCAT 59.060 41.667 0.00 0.00 0.00 3.06
2783 3090 5.413833 GGATGATGTGAGTTTGAGTGTCATT 59.586 40.000 0.00 0.00 0.00 2.57
2784 3091 6.072286 GGATGATGTGAGTTTGAGTGTCATTT 60.072 38.462 0.00 0.00 0.00 2.32
2785 3092 6.698008 TGATGTGAGTTTGAGTGTCATTTT 57.302 33.333 0.00 0.00 0.00 1.82
2786 3093 7.800155 TGATGTGAGTTTGAGTGTCATTTTA 57.200 32.000 0.00 0.00 0.00 1.52
2787 3094 8.219546 TGATGTGAGTTTGAGTGTCATTTTAA 57.780 30.769 0.00 0.00 0.00 1.52
2788 3095 8.849168 TGATGTGAGTTTGAGTGTCATTTTAAT 58.151 29.630 0.00 0.00 0.00 1.40
2789 3096 9.121517 GATGTGAGTTTGAGTGTCATTTTAATG 57.878 33.333 0.00 0.00 37.75 1.90
2790 3097 6.917477 TGTGAGTTTGAGTGTCATTTTAATGC 59.083 34.615 0.00 0.00 36.36 3.56
2791 3098 6.363357 GTGAGTTTGAGTGTCATTTTAATGCC 59.637 38.462 0.00 0.00 36.36 4.40
2792 3099 6.040278 TGAGTTTGAGTGTCATTTTAATGCCA 59.960 34.615 0.00 0.00 36.36 4.92
2793 3100 6.215845 AGTTTGAGTGTCATTTTAATGCCAC 58.784 36.000 8.21 8.21 43.50 5.01
2794 3101 4.782019 TGAGTGTCATTTTAATGCCACC 57.218 40.909 11.69 5.87 44.04 4.61
2795 3102 3.190327 TGAGTGTCATTTTAATGCCACCG 59.810 43.478 11.69 0.00 44.04 4.94
2796 3103 2.491693 AGTGTCATTTTAATGCCACCGG 59.508 45.455 11.69 0.00 44.04 5.28
2797 3104 2.230266 GTGTCATTTTAATGCCACCGGT 59.770 45.455 0.00 0.00 38.85 5.28
2798 3105 2.490115 TGTCATTTTAATGCCACCGGTC 59.510 45.455 2.59 0.00 36.36 4.79
2799 3106 2.490115 GTCATTTTAATGCCACCGGTCA 59.510 45.455 2.59 0.00 36.36 4.02
2800 3107 2.752354 TCATTTTAATGCCACCGGTCAG 59.248 45.455 2.59 0.00 36.36 3.51
2801 3108 4.433183 TCATTTTAATGCCACCGGTCAGG 61.433 47.826 2.59 5.05 40.12 3.86
2802 3109 0.693622 TTTAATGCCACCGGTCAGGA 59.306 50.000 15.00 6.48 45.00 3.86
2803 3110 0.693622 TTAATGCCACCGGTCAGGAA 59.306 50.000 15.00 4.45 45.00 3.36
2804 3111 0.251916 TAATGCCACCGGTCAGGAAG 59.748 55.000 15.00 0.00 45.00 3.46
2805 3112 1.488705 AATGCCACCGGTCAGGAAGA 61.489 55.000 15.00 0.00 45.00 2.87
2806 3113 1.274703 ATGCCACCGGTCAGGAAGAT 61.275 55.000 15.00 0.66 45.00 2.40
2807 3114 1.450312 GCCACCGGTCAGGAAGATG 60.450 63.158 15.00 0.00 45.00 2.90
2808 3115 1.899437 GCCACCGGTCAGGAAGATGA 61.899 60.000 15.00 0.00 45.00 2.92
2809 3116 0.833287 CCACCGGTCAGGAAGATGAT 59.167 55.000 2.59 0.00 45.00 2.45
2810 3117 1.473965 CCACCGGTCAGGAAGATGATG 60.474 57.143 2.59 0.00 45.00 3.07
2811 3118 1.208052 CACCGGTCAGGAAGATGATGT 59.792 52.381 2.59 0.00 45.00 3.06
2812 3119 1.482593 ACCGGTCAGGAAGATGATGTC 59.517 52.381 0.00 0.00 45.00 3.06
2813 3120 1.202580 CCGGTCAGGAAGATGATGTCC 60.203 57.143 0.00 0.00 45.00 4.02
2814 3121 1.202580 CGGTCAGGAAGATGATGTCCC 60.203 57.143 0.00 0.00 34.13 4.46
2815 3122 1.839994 GGTCAGGAAGATGATGTCCCA 59.160 52.381 0.00 0.00 34.13 4.37
2816 3123 2.441001 GGTCAGGAAGATGATGTCCCAT 59.559 50.000 0.00 0.00 34.13 4.00
2817 3124 3.648067 GGTCAGGAAGATGATGTCCCATA 59.352 47.826 0.00 0.00 34.13 2.74
2818 3125 4.262808 GGTCAGGAAGATGATGTCCCATAG 60.263 50.000 0.00 0.00 34.13 2.23
2819 3126 3.906218 TCAGGAAGATGATGTCCCATAGG 59.094 47.826 0.00 0.00 34.13 2.57
2820 3127 3.906218 CAGGAAGATGATGTCCCATAGGA 59.094 47.826 0.00 0.00 41.08 2.94
2821 3128 4.349048 CAGGAAGATGATGTCCCATAGGAA 59.651 45.833 0.00 0.00 46.38 3.36
2822 3129 4.349342 AGGAAGATGATGTCCCATAGGAAC 59.651 45.833 0.00 0.00 46.38 3.62
2823 3130 4.103153 GGAAGATGATGTCCCATAGGAACA 59.897 45.833 0.00 0.00 46.38 3.18
2824 3131 4.970860 AGATGATGTCCCATAGGAACAG 57.029 45.455 0.00 0.00 46.38 3.16
2825 3132 4.560739 AGATGATGTCCCATAGGAACAGA 58.439 43.478 0.00 0.00 46.38 3.41
2826 3133 4.592351 AGATGATGTCCCATAGGAACAGAG 59.408 45.833 0.00 0.00 46.38 3.35
2827 3134 3.724478 TGATGTCCCATAGGAACAGAGT 58.276 45.455 0.00 0.00 46.38 3.24
2828 3135 4.878968 TGATGTCCCATAGGAACAGAGTA 58.121 43.478 0.00 0.00 46.38 2.59
2829 3136 4.649674 TGATGTCCCATAGGAACAGAGTAC 59.350 45.833 0.00 0.00 46.38 2.73
2830 3137 4.332683 TGTCCCATAGGAACAGAGTACT 57.667 45.455 0.00 0.00 46.38 2.73
2831 3138 4.684724 TGTCCCATAGGAACAGAGTACTT 58.315 43.478 0.00 0.00 46.38 2.24
2853 3160 7.215789 ACTTTCATCATTCTGCGATCTCTTAT 58.784 34.615 0.00 0.00 0.00 1.73
2854 3161 7.714377 ACTTTCATCATTCTGCGATCTCTTATT 59.286 33.333 0.00 0.00 0.00 1.40
2921 3228 0.336737 ACTCCTGGGGACTACTCCTG 59.663 60.000 0.00 0.00 37.59 3.86
2974 3281 9.733219 CTAAACTACTAATAGTAACACAGAGGC 57.267 37.037 1.48 0.00 41.00 4.70
2975 3282 7.713734 AACTACTAATAGTAACACAGAGGCA 57.286 36.000 1.48 0.00 41.00 4.75
2976 3283 7.899648 ACTACTAATAGTAACACAGAGGCAT 57.100 36.000 1.48 0.00 40.02 4.40
2977 3284 8.307582 ACTACTAATAGTAACACAGAGGCATT 57.692 34.615 1.48 0.00 40.02 3.56
2978 3285 8.414778 ACTACTAATAGTAACACAGAGGCATTC 58.585 37.037 1.48 0.00 40.02 2.67
2979 3286 6.583562 ACTAATAGTAACACAGAGGCATTCC 58.416 40.000 0.00 0.00 0.00 3.01
2980 3287 2.789409 AGTAACACAGAGGCATTCCC 57.211 50.000 0.00 0.00 0.00 3.97
3009 3316 1.138247 CATGCCGCCAAGCTTTCTC 59.862 57.895 0.00 0.00 0.00 2.87
3020 3327 1.023513 AGCTTTCTCGAGCACATGGC 61.024 55.000 7.81 6.09 45.12 4.40
3074 3389 4.719369 GCGAGCCCAACGACGAGT 62.719 66.667 0.00 0.00 0.00 4.18
3078 3393 2.505557 GCCCAACGACGAGTACGG 60.506 66.667 0.00 0.00 44.46 4.02
3090 3405 0.651031 GAGTACGGGCTGAAAATCGC 59.349 55.000 0.00 0.00 0.00 4.58
3100 3415 2.222908 GCTGAAAATCGCTAGCAGACAC 60.223 50.000 16.45 1.89 36.24 3.67
3101 3416 2.995939 CTGAAAATCGCTAGCAGACACA 59.004 45.455 16.45 6.45 0.00 3.72
3107 3422 0.786581 CGCTAGCAGACACACAACTG 59.213 55.000 16.45 0.00 37.22 3.16
3109 3424 2.693069 GCTAGCAGACACACAACTGAT 58.307 47.619 10.63 0.00 36.38 2.90
3115 3430 3.430218 GCAGACACACAACTGATACAGTC 59.570 47.826 4.88 0.00 44.62 3.51
3119 3434 1.275291 ACACAACTGATACAGTCGGGG 59.725 52.381 4.88 4.89 44.62 5.73
3120 3435 0.902531 ACAACTGATACAGTCGGGGG 59.097 55.000 4.88 0.00 44.62 5.40
3121 3436 0.462047 CAACTGATACAGTCGGGGGC 60.462 60.000 4.88 0.00 44.62 5.80
3122 3437 0.907704 AACTGATACAGTCGGGGGCA 60.908 55.000 4.88 0.00 44.62 5.36
3123 3438 1.330655 ACTGATACAGTCGGGGGCAG 61.331 60.000 0.00 0.00 41.21 4.85
3124 3439 2.109181 GATACAGTCGGGGGCAGC 59.891 66.667 0.00 0.00 0.00 5.25
3125 3440 3.462199 GATACAGTCGGGGGCAGCC 62.462 68.421 1.26 1.26 0.00 4.85
3149 3464 0.393077 ATGGGCTGGTACTACGATGC 59.607 55.000 0.00 0.00 0.00 3.91
3194 3509 2.483876 CTCCTGGCCATACAATACACG 58.516 52.381 5.51 0.00 0.00 4.49
3198 3513 2.272678 TGGCCATACAATACACGAACG 58.727 47.619 0.00 0.00 0.00 3.95
3205 3520 3.637998 ACAATACACGAACGTCTCTGT 57.362 42.857 0.00 0.00 0.00 3.41
3211 3526 1.534163 CACGAACGTCTCTGTGGTCTA 59.466 52.381 0.00 0.00 0.00 2.59
3274 3589 5.706833 TGTACAGATTTGATTGTGTGCAGAT 59.293 36.000 0.00 0.00 31.64 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.664079 AGGTTGCTAATATCCACATCTTTAGAT 58.336 33.333 0.00 0.00 34.56 1.98
2 3 7.933577 CAGGTTGCTAATATCCACATCTTTAGA 59.066 37.037 0.00 0.00 0.00 2.10
3 4 7.308229 GCAGGTTGCTAATATCCACATCTTTAG 60.308 40.741 0.00 0.00 40.96 1.85
4 5 6.486657 GCAGGTTGCTAATATCCACATCTTTA 59.513 38.462 0.00 0.00 40.96 1.85
5 6 5.300286 GCAGGTTGCTAATATCCACATCTTT 59.700 40.000 0.00 0.00 40.96 2.52
6 7 4.823989 GCAGGTTGCTAATATCCACATCTT 59.176 41.667 0.00 0.00 40.96 2.40
7 8 4.141413 TGCAGGTTGCTAATATCCACATCT 60.141 41.667 2.48 0.00 45.31 2.90
8 9 4.136796 TGCAGGTTGCTAATATCCACATC 58.863 43.478 2.48 0.00 45.31 3.06
9 10 4.169059 TGCAGGTTGCTAATATCCACAT 57.831 40.909 2.48 0.00 45.31 3.21
10 11 3.643199 TGCAGGTTGCTAATATCCACA 57.357 42.857 2.48 0.00 45.31 4.17
11 12 3.066760 GGTTGCAGGTTGCTAATATCCAC 59.933 47.826 2.48 0.00 45.31 4.02
12 13 3.287222 GGTTGCAGGTTGCTAATATCCA 58.713 45.455 2.48 0.00 45.31 3.41
13 14 2.290641 CGGTTGCAGGTTGCTAATATCC 59.709 50.000 2.48 0.00 45.31 2.59
14 15 2.943033 ACGGTTGCAGGTTGCTAATATC 59.057 45.455 2.48 0.00 45.31 1.63
15 16 2.999331 ACGGTTGCAGGTTGCTAATAT 58.001 42.857 2.48 0.00 45.31 1.28
16 17 2.483014 ACGGTTGCAGGTTGCTAATA 57.517 45.000 2.48 0.00 45.31 0.98
17 18 2.081462 GTACGGTTGCAGGTTGCTAAT 58.919 47.619 2.48 0.00 45.31 1.73
18 19 1.071071 AGTACGGTTGCAGGTTGCTAA 59.929 47.619 2.48 0.00 45.31 3.09
19 20 0.682852 AGTACGGTTGCAGGTTGCTA 59.317 50.000 2.48 0.00 45.31 3.49
20 21 0.682852 TAGTACGGTTGCAGGTTGCT 59.317 50.000 2.48 0.00 45.31 3.91
21 22 1.734163 ATAGTACGGTTGCAGGTTGC 58.266 50.000 0.00 0.00 45.29 4.17
22 23 4.501071 AGTAATAGTACGGTTGCAGGTTG 58.499 43.478 0.00 0.00 35.20 3.77
23 24 4.813750 AGTAATAGTACGGTTGCAGGTT 57.186 40.909 0.00 0.00 35.20 3.50
24 25 4.813750 AAGTAATAGTACGGTTGCAGGT 57.186 40.909 0.00 0.00 35.20 4.00
25 26 7.599630 TTAAAAGTAATAGTACGGTTGCAGG 57.400 36.000 0.00 0.00 35.20 4.85
26 27 9.881529 TTTTTAAAAGTAATAGTACGGTTGCAG 57.118 29.630 0.14 0.00 35.20 4.41
42 43 9.934190 CAGTATTTTGCTTGCATTTTTAAAAGT 57.066 25.926 0.14 0.00 0.00 2.66
43 44 9.384682 CCAGTATTTTGCTTGCATTTTTAAAAG 57.615 29.630 0.14 0.00 0.00 2.27
44 45 8.348507 CCCAGTATTTTGCTTGCATTTTTAAAA 58.651 29.630 0.00 0.00 0.00 1.52
45 46 7.040823 CCCCAGTATTTTGCTTGCATTTTTAAA 60.041 33.333 0.00 0.00 0.00 1.52
46 47 6.429385 CCCCAGTATTTTGCTTGCATTTTTAA 59.571 34.615 0.00 0.00 0.00 1.52
47 48 5.936956 CCCCAGTATTTTGCTTGCATTTTTA 59.063 36.000 0.00 0.00 0.00 1.52
48 49 4.761227 CCCCAGTATTTTGCTTGCATTTTT 59.239 37.500 0.00 0.00 0.00 1.94
49 50 4.041444 TCCCCAGTATTTTGCTTGCATTTT 59.959 37.500 0.00 0.00 0.00 1.82
50 51 3.582208 TCCCCAGTATTTTGCTTGCATTT 59.418 39.130 0.00 0.00 0.00 2.32
51 52 3.055891 GTCCCCAGTATTTTGCTTGCATT 60.056 43.478 0.00 0.00 0.00 3.56
52 53 2.497273 GTCCCCAGTATTTTGCTTGCAT 59.503 45.455 0.00 0.00 0.00 3.96
53 54 1.892474 GTCCCCAGTATTTTGCTTGCA 59.108 47.619 0.00 0.00 0.00 4.08
54 55 1.892474 TGTCCCCAGTATTTTGCTTGC 59.108 47.619 0.00 0.00 0.00 4.01
55 56 3.511146 ACATGTCCCCAGTATTTTGCTTG 59.489 43.478 0.00 0.00 0.00 4.01
56 57 3.511146 CACATGTCCCCAGTATTTTGCTT 59.489 43.478 0.00 0.00 0.00 3.91
57 58 3.091545 CACATGTCCCCAGTATTTTGCT 58.908 45.455 0.00 0.00 0.00 3.91
58 59 3.088532 TCACATGTCCCCAGTATTTTGC 58.911 45.455 0.00 0.00 0.00 3.68
59 60 3.443681 GGTCACATGTCCCCAGTATTTTG 59.556 47.826 0.00 0.00 0.00 2.44
60 61 3.697166 GGTCACATGTCCCCAGTATTTT 58.303 45.455 0.00 0.00 0.00 1.82
61 62 2.355716 CGGTCACATGTCCCCAGTATTT 60.356 50.000 0.00 0.00 0.00 1.40
62 63 1.209504 CGGTCACATGTCCCCAGTATT 59.790 52.381 0.00 0.00 0.00 1.89
63 64 0.830648 CGGTCACATGTCCCCAGTAT 59.169 55.000 0.00 0.00 0.00 2.12
64 65 0.251877 TCGGTCACATGTCCCCAGTA 60.252 55.000 0.00 0.00 0.00 2.74
65 66 1.125093 TTCGGTCACATGTCCCCAGT 61.125 55.000 0.00 0.00 0.00 4.00
66 67 0.036164 TTTCGGTCACATGTCCCCAG 59.964 55.000 0.00 0.00 0.00 4.45
67 68 0.695924 ATTTCGGTCACATGTCCCCA 59.304 50.000 0.00 0.00 0.00 4.96
68 69 1.743394 GAATTTCGGTCACATGTCCCC 59.257 52.381 0.00 0.00 0.00 4.81
69 70 2.420022 CAGAATTTCGGTCACATGTCCC 59.580 50.000 0.00 0.00 0.00 4.46
70 71 2.159517 GCAGAATTTCGGTCACATGTCC 60.160 50.000 0.00 0.00 0.00 4.02
71 72 2.159517 GGCAGAATTTCGGTCACATGTC 60.160 50.000 0.00 0.00 0.00 3.06
72 73 1.812571 GGCAGAATTTCGGTCACATGT 59.187 47.619 0.00 0.00 0.00 3.21
73 74 1.133025 GGGCAGAATTTCGGTCACATG 59.867 52.381 3.63 0.00 0.00 3.21
74 75 1.271871 TGGGCAGAATTTCGGTCACAT 60.272 47.619 3.63 0.00 0.00 3.21
75 76 0.109532 TGGGCAGAATTTCGGTCACA 59.890 50.000 3.63 0.00 0.00 3.58
76 77 0.521735 GTGGGCAGAATTTCGGTCAC 59.478 55.000 3.63 6.48 0.00 3.67
77 78 0.109532 TGTGGGCAGAATTTCGGTCA 59.890 50.000 3.63 0.00 0.00 4.02
78 79 1.200020 CTTGTGGGCAGAATTTCGGTC 59.800 52.381 0.00 0.00 0.00 4.79
79 80 1.247567 CTTGTGGGCAGAATTTCGGT 58.752 50.000 0.00 0.00 0.00 4.69
80 81 1.247567 ACTTGTGGGCAGAATTTCGG 58.752 50.000 0.00 0.00 0.00 4.30
81 82 4.701956 ATAACTTGTGGGCAGAATTTCG 57.298 40.909 0.00 0.00 0.00 3.46
82 83 5.123344 ACGTATAACTTGTGGGCAGAATTTC 59.877 40.000 0.00 0.00 0.00 2.17
83 84 5.007682 ACGTATAACTTGTGGGCAGAATTT 58.992 37.500 0.00 0.00 0.00 1.82
84 85 4.585879 ACGTATAACTTGTGGGCAGAATT 58.414 39.130 0.00 0.00 0.00 2.17
85 86 4.216411 ACGTATAACTTGTGGGCAGAAT 57.784 40.909 0.00 0.00 0.00 2.40
86 87 3.688694 ACGTATAACTTGTGGGCAGAA 57.311 42.857 0.00 0.00 0.00 3.02
87 88 4.647853 AGATACGTATAACTTGTGGGCAGA 59.352 41.667 8.34 0.00 0.00 4.26
88 89 4.745125 CAGATACGTATAACTTGTGGGCAG 59.255 45.833 8.34 0.00 0.00 4.85
89 90 4.689071 CAGATACGTATAACTTGTGGGCA 58.311 43.478 8.34 0.00 0.00 5.36
90 91 3.493503 GCAGATACGTATAACTTGTGGGC 59.506 47.826 8.34 0.00 0.00 5.36
91 92 4.056050 GGCAGATACGTATAACTTGTGGG 58.944 47.826 8.34 0.00 0.00 4.61
92 93 4.689071 TGGCAGATACGTATAACTTGTGG 58.311 43.478 8.34 0.00 0.00 4.17
93 94 4.209288 GCTGGCAGATACGTATAACTTGTG 59.791 45.833 20.86 0.00 0.00 3.33
94 95 4.369182 GCTGGCAGATACGTATAACTTGT 58.631 43.478 20.86 0.00 0.00 3.16
95 96 3.741344 GGCTGGCAGATACGTATAACTTG 59.259 47.826 20.86 6.31 0.00 3.16
96 97 3.386726 TGGCTGGCAGATACGTATAACTT 59.613 43.478 20.86 0.00 0.00 2.66
97 98 2.963101 TGGCTGGCAGATACGTATAACT 59.037 45.455 20.86 0.00 0.00 2.24
98 99 3.380479 TGGCTGGCAGATACGTATAAC 57.620 47.619 20.86 0.75 0.00 1.89
99 100 4.617253 AATGGCTGGCAGATACGTATAA 57.383 40.909 20.86 0.00 0.00 0.98
100 101 4.381612 GCTAATGGCTGGCAGATACGTATA 60.382 45.833 20.86 0.47 38.06 1.47
101 102 3.617531 GCTAATGGCTGGCAGATACGTAT 60.618 47.826 20.86 8.05 38.06 3.06
102 103 2.288825 GCTAATGGCTGGCAGATACGTA 60.289 50.000 20.86 0.00 38.06 3.57
103 104 1.541233 GCTAATGGCTGGCAGATACGT 60.541 52.381 20.86 5.92 38.06 3.57
104 105 1.151668 GCTAATGGCTGGCAGATACG 58.848 55.000 20.86 1.64 38.06 3.06
115 116 8.160621 GTAGAACTACATTGGCAGCTAATGGC 62.161 46.154 29.10 15.63 43.63 4.40
116 117 4.202441 AGAACTACATTGGCAGCTAATGG 58.798 43.478 29.10 17.74 39.30 3.16
117 118 5.817296 TGTAGAACTACATTGGCAGCTAATG 59.183 40.000 25.56 25.56 40.77 1.90
118 119 5.817816 GTGTAGAACTACATTGGCAGCTAAT 59.182 40.000 16.03 0.00 46.36 1.73
119 120 5.046591 AGTGTAGAACTACATTGGCAGCTAA 60.047 40.000 16.03 0.00 46.36 3.09
120 121 4.466370 AGTGTAGAACTACATTGGCAGCTA 59.534 41.667 16.03 0.00 46.36 3.32
121 122 3.261897 AGTGTAGAACTACATTGGCAGCT 59.738 43.478 16.03 5.80 46.36 4.24
122 123 3.372206 CAGTGTAGAACTACATTGGCAGC 59.628 47.826 21.49 8.27 46.36 5.25
127 128 5.407407 AGTCCCAGTGTAGAACTACATTG 57.593 43.478 21.96 21.96 46.36 2.82
128 129 4.158025 CGAGTCCCAGTGTAGAACTACATT 59.842 45.833 16.03 10.32 46.36 2.71
129 130 3.695060 CGAGTCCCAGTGTAGAACTACAT 59.305 47.826 16.03 5.02 46.36 2.29
130 131 3.079578 CGAGTCCCAGTGTAGAACTACA 58.920 50.000 10.14 10.14 43.14 2.74
131 132 2.159407 GCGAGTCCCAGTGTAGAACTAC 60.159 54.545 5.18 5.18 36.83 2.73
132 133 2.089980 GCGAGTCCCAGTGTAGAACTA 58.910 52.381 0.00 0.00 36.83 2.24
133 134 0.889306 GCGAGTCCCAGTGTAGAACT 59.111 55.000 0.00 0.00 40.93 3.01
134 135 0.889306 AGCGAGTCCCAGTGTAGAAC 59.111 55.000 0.00 0.00 0.00 3.01
135 136 2.089980 GTAGCGAGTCCCAGTGTAGAA 58.910 52.381 0.00 0.00 0.00 2.10
136 137 1.281287 AGTAGCGAGTCCCAGTGTAGA 59.719 52.381 0.00 0.00 0.00 2.59
137 138 1.752683 AGTAGCGAGTCCCAGTGTAG 58.247 55.000 0.00 0.00 0.00 2.74
138 139 1.816835 CAAGTAGCGAGTCCCAGTGTA 59.183 52.381 0.00 0.00 0.00 2.90
139 140 0.603569 CAAGTAGCGAGTCCCAGTGT 59.396 55.000 0.00 0.00 0.00 3.55
140 141 0.603569 ACAAGTAGCGAGTCCCAGTG 59.396 55.000 0.00 0.00 0.00 3.66
141 142 0.889306 GACAAGTAGCGAGTCCCAGT 59.111 55.000 0.00 0.00 0.00 4.00
142 143 1.178276 AGACAAGTAGCGAGTCCCAG 58.822 55.000 0.00 0.00 32.82 4.45
143 144 2.502142 TAGACAAGTAGCGAGTCCCA 57.498 50.000 0.00 0.00 32.82 4.37
151 152 5.176590 GCATTAGAGTGCATAGACAAGTAGC 59.823 44.000 0.00 0.00 44.43 3.58
614 617 0.173708 CGAAGTAGTCACCTCAGGGC 59.826 60.000 0.00 0.00 35.63 5.19
632 635 5.220662 CCTGGTATCATGCAAACTTCTAACG 60.221 44.000 0.00 0.00 0.00 3.18
790 1081 1.004440 GACACCTGTGGCACTCTCC 60.004 63.158 19.83 0.00 38.82 3.71
991 1282 3.051727 ACCTTTAGGGCCATCTCTCTAGT 60.052 47.826 6.18 0.00 40.27 2.57
1101 1394 6.735556 ACCAGGGACTTGAATCTTAAATCAT 58.264 36.000 0.00 0.00 34.60 2.45
1106 1399 4.019321 CAGGACCAGGGACTTGAATCTTAA 60.019 45.833 0.00 0.00 34.60 1.85
1605 1904 1.675310 TGCATCTTGGCAGGTTCGG 60.675 57.895 0.00 0.00 39.25 4.30
1606 1905 3.985877 TGCATCTTGGCAGGTTCG 58.014 55.556 0.00 0.00 39.25 3.95
1790 2089 2.279741 TGTATCGCTTGGTGAGAATGC 58.720 47.619 0.00 0.00 0.00 3.56
1804 2103 2.359531 GTGACTCTCCTTCCCTGTATCG 59.640 54.545 0.00 0.00 0.00 2.92
1814 2113 2.896685 CAGTCTTCTGGTGACTCTCCTT 59.103 50.000 0.00 0.00 42.21 3.36
1817 2116 2.887783 TGACAGTCTTCTGGTGACTCTC 59.112 50.000 1.31 0.00 45.14 3.20
2013 2312 6.913170 TGAATTTGCAGAAGAACTAATGTCC 58.087 36.000 0.00 0.00 0.00 4.02
2015 2314 7.889469 ACATGAATTTGCAGAAGAACTAATGT 58.111 30.769 0.00 0.00 0.00 2.71
2045 2344 2.771089 ACAGGCAGTGTAACATCACAG 58.229 47.619 0.00 0.00 41.43 3.66
2049 2348 5.350640 GGTAAGTAACAGGCAGTGTAACATC 59.649 44.000 0.00 0.00 39.03 3.06
2159 2458 5.559148 AGATAGGCTAAGCTGCATAAAGT 57.441 39.130 1.02 0.00 32.92 2.66
2212 2511 4.132336 CACAGATGACCAATACCATCAGG 58.868 47.826 0.00 0.00 41.07 3.86
2247 2546 0.745845 CCCCAGCATCTTCTTCACGG 60.746 60.000 0.00 0.00 0.00 4.94
2292 2591 1.732259 CCTCTGCATTACAACGTCCAC 59.268 52.381 0.00 0.00 0.00 4.02
2300 2599 2.551270 AGGAGGTTCCTCTGCATTACA 58.449 47.619 16.95 0.00 45.66 2.41
2332 2631 0.669625 AAACTTGTCCGCGAGCCTAC 60.670 55.000 8.23 0.00 0.00 3.18
2512 2814 7.712204 ATTTTATTATAAATACTGGGGCCCG 57.288 36.000 19.83 15.38 0.00 6.13
2701 3003 3.042887 GGCAAAATTCACGTGTTCAGAC 58.957 45.455 16.51 0.49 0.00 3.51
2721 3023 3.012518 CCATTCACCTTACTGAAGCTGG 58.987 50.000 0.00 0.00 33.65 4.85
2735 3037 7.822822 TCCTTTCTACTTAAAGCTACCATTCAC 59.177 37.037 0.00 0.00 35.53 3.18
2736 3038 7.913789 TCCTTTCTACTTAAAGCTACCATTCA 58.086 34.615 0.00 0.00 35.53 2.57
2737 3039 8.831550 CATCCTTTCTACTTAAAGCTACCATTC 58.168 37.037 0.00 0.00 35.53 2.67
2738 3040 8.548877 TCATCCTTTCTACTTAAAGCTACCATT 58.451 33.333 0.00 0.00 35.53 3.16
2760 3067 6.492007 AATGACACTCAAACTCACATCATC 57.508 37.500 0.00 0.00 0.00 2.92
2768 3075 6.934561 GGCATTAAAATGACACTCAAACTC 57.065 37.500 6.87 0.00 44.04 3.01
2779 3086 2.752354 CTGACCGGTGGCATTAAAATGA 59.248 45.455 14.63 0.00 38.70 2.57
2780 3087 2.159254 CCTGACCGGTGGCATTAAAATG 60.159 50.000 14.63 0.00 39.40 2.32
2781 3088 2.099405 CCTGACCGGTGGCATTAAAAT 58.901 47.619 14.63 0.00 0.00 1.82
2782 3089 1.074084 TCCTGACCGGTGGCATTAAAA 59.926 47.619 14.63 0.00 0.00 1.52
2783 3090 0.693622 TCCTGACCGGTGGCATTAAA 59.306 50.000 14.63 0.00 0.00 1.52
2784 3091 0.693622 TTCCTGACCGGTGGCATTAA 59.306 50.000 14.63 0.00 0.00 1.40
2785 3092 0.251916 CTTCCTGACCGGTGGCATTA 59.748 55.000 14.63 0.00 0.00 1.90
2786 3093 1.002134 CTTCCTGACCGGTGGCATT 60.002 57.895 14.63 0.00 0.00 3.56
2787 3094 1.274703 ATCTTCCTGACCGGTGGCAT 61.275 55.000 14.63 0.00 0.00 4.40
2788 3095 1.918293 ATCTTCCTGACCGGTGGCA 60.918 57.895 14.63 3.10 0.00 4.92
2789 3096 1.450312 CATCTTCCTGACCGGTGGC 60.450 63.158 14.63 0.00 0.00 5.01
2790 3097 0.833287 ATCATCTTCCTGACCGGTGG 59.167 55.000 14.63 8.62 0.00 4.61
2791 3098 1.208052 ACATCATCTTCCTGACCGGTG 59.792 52.381 14.63 0.00 0.00 4.94
2792 3099 1.482593 GACATCATCTTCCTGACCGGT 59.517 52.381 6.92 6.92 0.00 5.28
2793 3100 1.202580 GGACATCATCTTCCTGACCGG 60.203 57.143 0.00 0.00 0.00 5.28
2794 3101 1.202580 GGGACATCATCTTCCTGACCG 60.203 57.143 0.00 0.00 31.90 4.79
2795 3102 1.839994 TGGGACATCATCTTCCTGACC 59.160 52.381 0.00 0.00 31.90 4.02
2810 3117 5.187186 TGAAAGTACTCTGTTCCTATGGGAC 59.813 44.000 0.00 0.00 42.05 4.46
2811 3118 5.338632 TGAAAGTACTCTGTTCCTATGGGA 58.661 41.667 0.00 0.00 40.36 4.37
2812 3119 5.677319 TGAAAGTACTCTGTTCCTATGGG 57.323 43.478 0.00 0.00 0.00 4.00
2813 3120 6.878317 TGATGAAAGTACTCTGTTCCTATGG 58.122 40.000 0.00 0.00 0.00 2.74
2814 3121 8.954950 AATGATGAAAGTACTCTGTTCCTATG 57.045 34.615 0.00 0.00 0.00 2.23
2815 3122 8.986991 AGAATGATGAAAGTACTCTGTTCCTAT 58.013 33.333 0.00 0.00 0.00 2.57
2816 3123 8.253810 CAGAATGATGAAAGTACTCTGTTCCTA 58.746 37.037 0.00 0.00 39.69 2.94
2817 3124 7.102346 CAGAATGATGAAAGTACTCTGTTCCT 58.898 38.462 0.00 0.00 39.69 3.36
2818 3125 6.183360 GCAGAATGATGAAAGTACTCTGTTCC 60.183 42.308 0.00 0.00 39.69 3.62
2819 3126 6.454848 CGCAGAATGATGAAAGTACTCTGTTC 60.455 42.308 0.00 0.00 39.69 3.18
2820 3127 5.349817 CGCAGAATGATGAAAGTACTCTGTT 59.650 40.000 0.00 0.00 39.69 3.16
2821 3128 4.867047 CGCAGAATGATGAAAGTACTCTGT 59.133 41.667 0.00 0.00 39.69 3.41
2822 3129 5.105063 TCGCAGAATGATGAAAGTACTCTG 58.895 41.667 0.00 0.00 39.69 3.35
2823 3130 5.330455 TCGCAGAATGATGAAAGTACTCT 57.670 39.130 0.00 0.00 39.69 3.24
2824 3131 5.982516 AGATCGCAGAATGATGAAAGTACTC 59.017 40.000 0.00 0.00 43.58 2.59
2825 3132 5.911752 AGATCGCAGAATGATGAAAGTACT 58.088 37.500 0.00 0.00 43.58 2.73
2826 3133 5.982516 AGAGATCGCAGAATGATGAAAGTAC 59.017 40.000 0.00 0.00 43.58 2.73
2827 3134 6.154203 AGAGATCGCAGAATGATGAAAGTA 57.846 37.500 0.00 0.00 43.58 2.24
2828 3135 5.021033 AGAGATCGCAGAATGATGAAAGT 57.979 39.130 0.00 0.00 43.58 2.66
2829 3136 5.987777 AAGAGATCGCAGAATGATGAAAG 57.012 39.130 0.00 0.00 43.58 2.62
2830 3137 9.716531 ATAATAAGAGATCGCAGAATGATGAAA 57.283 29.630 0.00 0.00 43.58 2.69
2831 3138 9.363763 GATAATAAGAGATCGCAGAATGATGAA 57.636 33.333 0.00 0.00 43.58 2.57
2878 3185 1.531423 ACTCGTGTCGCTCTTCCTAA 58.469 50.000 0.00 0.00 0.00 2.69
2921 3228 1.141053 CCCATGCCTTGGTACTACTCC 59.859 57.143 2.44 0.00 44.83 3.85
2959 3266 4.040755 AGGGAATGCCTCTGTGTTACTAT 58.959 43.478 0.00 0.00 0.00 2.12
2960 3267 3.450904 AGGGAATGCCTCTGTGTTACTA 58.549 45.455 0.00 0.00 0.00 1.82
2961 3268 2.237392 GAGGGAATGCCTCTGTGTTACT 59.763 50.000 13.89 0.00 0.00 2.24
2962 3269 2.633488 GAGGGAATGCCTCTGTGTTAC 58.367 52.381 13.89 0.00 0.00 2.50
2963 3270 1.559682 GGAGGGAATGCCTCTGTGTTA 59.440 52.381 20.14 0.00 34.95 2.41
2964 3271 0.329596 GGAGGGAATGCCTCTGTGTT 59.670 55.000 20.14 0.00 34.95 3.32
2965 3272 0.548682 AGGAGGGAATGCCTCTGTGT 60.549 55.000 20.14 0.61 34.95 3.72
2966 3273 0.622665 AAGGAGGGAATGCCTCTGTG 59.377 55.000 20.14 0.00 34.95 3.66
2967 3274 1.376649 AAAGGAGGGAATGCCTCTGT 58.623 50.000 20.14 5.62 34.95 3.41
2968 3275 2.158696 CCTAAAGGAGGGAATGCCTCTG 60.159 54.545 20.14 6.14 42.39 3.35
2969 3276 2.131023 CCTAAAGGAGGGAATGCCTCT 58.869 52.381 20.14 3.54 42.39 3.69
2970 3277 1.477740 GCCTAAAGGAGGGAATGCCTC 60.478 57.143 12.76 12.76 46.81 4.70
2971 3278 0.553333 GCCTAAAGGAGGGAATGCCT 59.447 55.000 0.00 0.00 46.81 4.75
2972 3279 0.468214 GGCCTAAAGGAGGGAATGCC 60.468 60.000 0.00 0.00 46.81 4.40
2973 3280 0.258774 TGGCCTAAAGGAGGGAATGC 59.741 55.000 3.32 0.00 46.81 3.56
2974 3281 2.590821 CATGGCCTAAAGGAGGGAATG 58.409 52.381 3.32 0.00 46.81 2.67
2975 3282 1.133356 GCATGGCCTAAAGGAGGGAAT 60.133 52.381 3.32 0.00 46.81 3.01
2976 3283 0.258774 GCATGGCCTAAAGGAGGGAA 59.741 55.000 3.32 0.00 46.81 3.97
2977 3284 1.645402 GGCATGGCCTAAAGGAGGGA 61.645 60.000 8.35 0.00 46.81 4.20
2978 3285 1.152673 GGCATGGCCTAAAGGAGGG 60.153 63.158 8.35 0.00 46.81 4.30
3038 3345 4.374702 GTTGCGTGGTGCTCTGCG 62.375 66.667 0.00 0.00 46.63 5.18
3064 3372 1.800315 CAGCCCGTACTCGTCGTTG 60.800 63.158 0.00 0.00 35.01 4.10
3065 3373 1.518056 TTCAGCCCGTACTCGTCGTT 61.518 55.000 0.00 0.00 35.01 3.85
3074 3389 1.805120 GCTAGCGATTTTCAGCCCGTA 60.805 52.381 0.00 0.00 0.00 4.02
3078 3393 1.328986 GTCTGCTAGCGATTTTCAGCC 59.671 52.381 10.77 0.00 32.97 4.85
3090 3405 4.809673 TGTATCAGTTGTGTGTCTGCTAG 58.190 43.478 0.00 0.00 0.00 3.42
3100 3415 1.405526 CCCCCGACTGTATCAGTTGTG 60.406 57.143 13.78 4.96 45.44 3.33
3101 3416 0.902531 CCCCCGACTGTATCAGTTGT 59.097 55.000 13.78 0.00 45.44 3.32
3107 3422 2.109181 GCTGCCCCCGACTGTATC 59.891 66.667 0.00 0.00 0.00 2.24
3123 3438 3.556306 TACCAGCCCATAGCCGGC 61.556 66.667 21.89 21.89 43.57 6.13
3124 3439 0.830444 TAGTACCAGCCCATAGCCGG 60.830 60.000 0.00 0.00 45.45 6.13
3125 3440 0.317479 GTAGTACCAGCCCATAGCCG 59.683 60.000 0.00 0.00 45.47 5.52
3126 3441 0.317479 CGTAGTACCAGCCCATAGCC 59.683 60.000 0.00 0.00 45.47 3.93
3127 3442 1.325355 TCGTAGTACCAGCCCATAGC 58.675 55.000 0.00 0.00 44.25 2.97
3149 3464 0.723414 CTACGGTTGCATGCTCTGTG 59.277 55.000 26.21 17.07 0.00 3.66
3174 3489 2.102420 TCGTGTATTGTATGGCCAGGAG 59.898 50.000 13.05 0.00 0.00 3.69
3180 3495 3.184541 AGACGTTCGTGTATTGTATGGC 58.815 45.455 1.74 0.00 0.00 4.40
3194 3509 2.164624 AGCATAGACCACAGAGACGTTC 59.835 50.000 0.00 0.00 0.00 3.95
3198 3513 4.464069 AAAGAGCATAGACCACAGAGAC 57.536 45.455 0.00 0.00 0.00 3.36
3205 3520 3.388024 AGGCGATAAAAGAGCATAGACCA 59.612 43.478 0.00 0.00 0.00 4.02
3211 3526 3.347216 ACACAAGGCGATAAAAGAGCAT 58.653 40.909 0.00 0.00 0.00 3.79
3290 3605 3.575256 ACATGATCCTGCAAAGCAAAAGA 59.425 39.130 0.00 0.00 38.41 2.52


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

AutoCloner maintained by Alex Coulton.