Multiple sequence alignment - TraesCS5A01G150700

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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 TraesCS5A01G150700 chr5A 100.000 4179 0 0 1 4179 328554789 328550611 0.000000e+00 7718.0
1 TraesCS5A01G150700 chr5B 92.645 3372 139 35 149 3476 277251413 277248107 0.000000e+00 4752.0
2 TraesCS5A01G150700 chr5B 87.919 149 9 5 3782 3922 277247544 277247397 2.580000e-37 167.0
3 TraesCS5A01G150700 chr5B 93.548 62 3 1 1968 2028 465592781 465592720 1.600000e-14 91.6
4 TraesCS5A01G150700 chr5D 92.398 3223 124 50 480 3641 244110727 244107565 0.000000e+00 4482.0
5 TraesCS5A01G150700 chr5D 93.701 508 25 3 3672 4179 243999977 243999477 0.000000e+00 754.0
6 TraesCS5A01G150700 chr5D 86.739 460 52 4 3 461 244136473 244136022 1.730000e-138 503.0
7 TraesCS5A01G150700 chr5D 81.900 221 31 8 3475 3691 61793578 61793793 1.190000e-40 178.0
8 TraesCS5A01G150700 chr5D 77.860 271 48 11 3475 3741 387198209 387198471 1.560000e-34 158.0
9 TraesCS5A01G150700 chr5D 93.548 62 3 1 1968 2028 387195979 387195918 1.600000e-14 91.6
10 TraesCS5A01G150700 chr5D 79.775 89 16 2 1967 2054 297985558 297985471 3.490000e-06 63.9
11 TraesCS5A01G150700 chr3B 83.908 261 32 7 3475 3732 572682070 572681817 1.500000e-59 241.0
12 TraesCS5A01G150700 chr3B 84.034 238 28 6 3499 3733 779691594 779691364 1.960000e-53 220.0
13 TraesCS5A01G150700 chr3B 79.070 258 44 7 3475 3729 284380243 284380493 7.190000e-38 169.0
14 TraesCS5A01G150700 chr3D 83.721 258 32 7 3475 3729 10839042 10839292 6.980000e-58 235.0
15 TraesCS5A01G150700 chr3D 90.805 87 8 0 1967 2053 390048696 390048610 2.640000e-22 117.0
16 TraesCS5A01G150700 chr4B 82.422 256 34 7 3475 3728 18716972 18717218 3.270000e-51 213.0
17 TraesCS5A01G150700 chr7A 80.385 260 42 6 3474 3730 650029952 650029699 5.520000e-44 189.0
18 TraesCS5A01G150700 chr4A 91.011 89 8 0 1968 2056 5665894 5665806 2.040000e-23 121.0
19 TraesCS5A01G150700 chr4A 100.000 28 0 0 3765 3792 735837444 735837417 8.000000e-03 52.8
20 TraesCS5A01G150700 chr1D 85.106 94 14 0 1963 2056 315637031 315636938 3.440000e-16 97.1
21 TraesCS5A01G150700 chr3A 86.207 87 12 0 1969 2055 687290521 687290435 1.240000e-15 95.3
22 TraesCS5A01G150700 chr2B 100.000 37 0 0 3938 3974 705335619 705335583 7.500000e-08 69.4
23 TraesCS5A01G150700 chr2B 100.000 31 0 0 3762 3792 233549961 233549931 1.620000e-04 58.4
24 TraesCS5A01G150700 chr7B 89.091 55 4 2 1970 2023 413108293 413108240 2.700000e-07 67.6
25 TraesCS5A01G150700 chrUn 100.000 31 0 0 3762 3792 87233316 87233286 1.620000e-04 58.4
26 TraesCS5A01G150700 chr6B 100.000 31 0 0 3762 3792 459838247 459838277 1.620000e-04 58.4
27 TraesCS5A01G150700 chr2D 100.000 28 0 0 3765 3792 39319649 39319676 8.000000e-03 52.8


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 TraesCS5A01G150700 chr5A 328550611 328554789 4178 True 7718.0 7718 100.000 1 4179 1 chr5A.!!$R1 4178
1 TraesCS5A01G150700 chr5B 277247397 277251413 4016 True 2459.5 4752 90.282 149 3922 2 chr5B.!!$R2 3773
2 TraesCS5A01G150700 chr5D 244107565 244110727 3162 True 4482.0 4482 92.398 480 3641 1 chr5D.!!$R2 3161
3 TraesCS5A01G150700 chr5D 243999477 243999977 500 True 754.0 754 93.701 3672 4179 1 chr5D.!!$R1 507

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
58 59 0.109597 CAAGGTGCAAAGCGATGGTC 60.110 55.0 0.00 0.0 0.00 4.02 F
145 146 0.110678 ACTGTGACAGGAGGAGACGA 59.889 55.0 17.92 0.0 35.51 4.20 F
371 372 0.466189 CACATATTTCGGGCTGGGCT 60.466 55.0 0.00 0.0 0.00 5.19 F
401 402 0.968405 TGGCCAGGCTTTGACATTTC 59.032 50.0 12.43 0.0 0.00 2.17 F
1958 1983 0.179145 CACCGTCGTTAGGCAGGTAG 60.179 60.0 0.00 0.0 33.30 3.18 F
1959 1984 0.322816 ACCGTCGTTAGGCAGGTAGA 60.323 55.0 0.00 0.0 32.76 2.59 F
2779 2856 0.179076 TGCAGATATGGGACGTGCTG 60.179 55.0 7.11 0.0 35.11 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 1212 0.044244 TACAAGGAAGGGGAGGGGAG 59.956 60.0 0.00 0.00 0.00 4.30 R
1204 1213 0.044244 CTACAAGGAAGGGGAGGGGA 59.956 60.0 0.00 0.00 0.00 4.81 R
1323 1336 0.687354 AGGTGTAGTGCAGGTTCCAG 59.313 55.0 0.00 0.00 0.00 3.86 R
2350 2414 1.089481 GCTCATCGTCCATGGCGAAA 61.089 55.0 27.06 19.29 41.84 3.46 R
2779 2856 0.472471 TGACCACCTCCTTGTTGGAC 59.528 55.0 0.00 0.00 40.56 4.02 R
2875 2952 0.801067 CCATCGACGTCGGGAACTTC 60.801 60.0 35.05 0.00 40.29 3.01 R
4075 4683 0.036010 CTCCAAGGACAACATCGGCT 60.036 55.0 0.00 0.00 0.00 5.52 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
20 21 3.942539 CATGCAATGTTGGCAATGATG 57.057 42.857 1.92 4.00 45.60 3.07
21 22 2.388310 TGCAATGTTGGCAATGATGG 57.612 45.000 1.92 0.00 38.54 3.51
22 23 1.900486 TGCAATGTTGGCAATGATGGA 59.100 42.857 1.92 1.08 38.54 3.41
23 24 2.502130 TGCAATGTTGGCAATGATGGAT 59.498 40.909 1.92 0.00 38.54 3.41
24 25 2.869801 GCAATGTTGGCAATGATGGATG 59.130 45.455 1.92 0.00 0.00 3.51
25 26 2.869801 CAATGTTGGCAATGATGGATGC 59.130 45.455 1.92 0.00 41.82 3.91
26 27 1.855295 TGTTGGCAATGATGGATGCT 58.145 45.000 1.92 0.00 42.20 3.79
27 28 3.015675 TGTTGGCAATGATGGATGCTA 57.984 42.857 1.92 0.00 42.20 3.49
28 29 2.689471 TGTTGGCAATGATGGATGCTAC 59.311 45.455 1.92 0.00 42.20 3.58
29 30 1.596603 TGGCAATGATGGATGCTACG 58.403 50.000 0.00 0.00 42.20 3.51
30 31 1.140652 TGGCAATGATGGATGCTACGA 59.859 47.619 0.00 0.00 42.20 3.43
31 32 2.221169 GGCAATGATGGATGCTACGAA 58.779 47.619 0.00 0.00 42.20 3.85
32 33 2.031682 GGCAATGATGGATGCTACGAAC 60.032 50.000 0.00 0.00 42.20 3.95
33 34 2.874701 GCAATGATGGATGCTACGAACT 59.125 45.455 0.00 0.00 39.46 3.01
34 35 3.303593 GCAATGATGGATGCTACGAACTG 60.304 47.826 0.00 0.00 39.46 3.16
35 36 2.602257 TGATGGATGCTACGAACTGG 57.398 50.000 0.00 0.00 0.00 4.00
36 37 1.221414 GATGGATGCTACGAACTGGC 58.779 55.000 0.00 0.00 0.00 4.85
37 38 0.833287 ATGGATGCTACGAACTGGCT 59.167 50.000 0.00 0.00 0.00 4.75
38 39 1.480789 TGGATGCTACGAACTGGCTA 58.519 50.000 0.00 0.00 0.00 3.93
39 40 1.136305 TGGATGCTACGAACTGGCTAC 59.864 52.381 0.00 0.00 0.00 3.58
40 41 1.136305 GGATGCTACGAACTGGCTACA 59.864 52.381 0.00 0.00 0.00 2.74
41 42 2.418197 GGATGCTACGAACTGGCTACAA 60.418 50.000 0.00 0.00 0.00 2.41
42 43 2.363788 TGCTACGAACTGGCTACAAG 57.636 50.000 0.00 0.00 0.00 3.16
43 44 1.067142 TGCTACGAACTGGCTACAAGG 60.067 52.381 0.00 0.00 0.00 3.61
44 45 1.067071 GCTACGAACTGGCTACAAGGT 60.067 52.381 0.00 0.00 0.00 3.50
45 46 2.607187 CTACGAACTGGCTACAAGGTG 58.393 52.381 0.00 0.00 0.00 4.00
46 47 0.602905 ACGAACTGGCTACAAGGTGC 60.603 55.000 0.00 0.00 0.00 5.01
47 48 0.602638 CGAACTGGCTACAAGGTGCA 60.603 55.000 0.00 0.00 0.00 4.57
48 49 1.604604 GAACTGGCTACAAGGTGCAA 58.395 50.000 0.00 0.00 0.00 4.08
49 50 1.953686 GAACTGGCTACAAGGTGCAAA 59.046 47.619 0.00 0.00 0.00 3.68
50 51 1.609208 ACTGGCTACAAGGTGCAAAG 58.391 50.000 0.00 0.00 0.00 2.77
51 52 0.242017 CTGGCTACAAGGTGCAAAGC 59.758 55.000 0.00 0.00 0.00 3.51
52 53 1.210155 GGCTACAAGGTGCAAAGCG 59.790 57.895 0.00 0.00 33.96 4.68
53 54 1.234615 GGCTACAAGGTGCAAAGCGA 61.235 55.000 0.00 0.00 33.96 4.93
54 55 0.804989 GCTACAAGGTGCAAAGCGAT 59.195 50.000 0.00 0.00 0.00 4.58
55 56 1.466360 GCTACAAGGTGCAAAGCGATG 60.466 52.381 0.00 0.00 0.00 3.84
56 57 1.131126 CTACAAGGTGCAAAGCGATGG 59.869 52.381 0.00 0.00 0.00 3.51
57 58 0.823356 ACAAGGTGCAAAGCGATGGT 60.823 50.000 0.00 0.00 0.00 3.55
58 59 0.109597 CAAGGTGCAAAGCGATGGTC 60.110 55.000 0.00 0.00 0.00 4.02
59 60 0.537143 AAGGTGCAAAGCGATGGTCA 60.537 50.000 0.00 0.00 0.00 4.02
60 61 0.537143 AGGTGCAAAGCGATGGTCAA 60.537 50.000 0.00 0.00 0.00 3.18
61 62 0.387239 GGTGCAAAGCGATGGTCAAC 60.387 55.000 0.00 0.00 0.00 3.18
62 63 0.725784 GTGCAAAGCGATGGTCAACG 60.726 55.000 0.00 0.00 0.00 4.10
68 69 2.809174 CGATGGTCAACGCTGCGA 60.809 61.111 30.47 4.98 0.00 5.10
69 70 2.778679 GATGGTCAACGCTGCGAC 59.221 61.111 30.47 16.32 0.00 5.19
70 71 3.071459 GATGGTCAACGCTGCGACG 62.071 63.158 30.47 18.27 39.50 5.12
71 72 3.567478 ATGGTCAACGCTGCGACGA 62.567 57.895 30.47 20.30 36.70 4.20
72 73 2.809601 GGTCAACGCTGCGACGAT 60.810 61.111 30.47 8.77 36.70 3.73
73 74 2.391821 GTCAACGCTGCGACGATG 59.608 61.111 30.47 19.74 37.20 3.84
74 75 2.809174 TCAACGCTGCGACGATGG 60.809 61.111 30.47 3.40 36.59 3.51
75 76 3.112075 CAACGCTGCGACGATGGT 61.112 61.111 30.47 0.16 32.81 3.55
76 77 3.112075 AACGCTGCGACGATGGTG 61.112 61.111 30.47 0.00 36.70 4.17
95 96 3.277602 CGGCTGCCTGCTAGCATG 61.278 66.667 19.72 17.08 43.09 4.06
96 97 2.905880 GGCTGCCTGCTAGCATGG 60.906 66.667 19.72 21.12 43.09 3.66
97 98 2.191375 GCTGCCTGCTAGCATGGA 59.809 61.111 27.37 21.28 43.09 3.41
98 99 2.185494 GCTGCCTGCTAGCATGGAC 61.185 63.158 27.37 20.40 43.09 4.02
99 100 1.886313 CTGCCTGCTAGCATGGACG 60.886 63.158 27.37 13.88 43.09 4.79
100 101 2.187946 GCCTGCTAGCATGGACGT 59.812 61.111 27.37 0.00 0.00 4.34
101 102 2.176273 GCCTGCTAGCATGGACGTG 61.176 63.158 27.37 12.63 0.00 4.49
102 103 1.219124 CCTGCTAGCATGGACGTGT 59.781 57.895 19.72 0.00 0.00 4.49
103 104 0.459899 CCTGCTAGCATGGACGTGTA 59.540 55.000 19.72 0.00 0.00 2.90
104 105 1.560923 CTGCTAGCATGGACGTGTAC 58.439 55.000 19.72 0.00 0.00 2.90
105 106 1.135139 CTGCTAGCATGGACGTGTACT 59.865 52.381 19.72 0.00 0.00 2.73
106 107 1.548719 TGCTAGCATGGACGTGTACTT 59.451 47.619 14.93 0.00 0.00 2.24
107 108 1.927174 GCTAGCATGGACGTGTACTTG 59.073 52.381 10.63 0.00 0.00 3.16
108 109 2.674177 GCTAGCATGGACGTGTACTTGT 60.674 50.000 10.63 0.00 0.00 3.16
109 110 1.795768 AGCATGGACGTGTACTTGTG 58.204 50.000 0.00 0.00 0.00 3.33
110 111 0.165944 GCATGGACGTGTACTTGTGC 59.834 55.000 0.00 0.00 0.00 4.57
111 112 1.507562 CATGGACGTGTACTTGTGCA 58.492 50.000 12.86 12.86 40.75 4.57
112 113 1.870402 CATGGACGTGTACTTGTGCAA 59.130 47.619 14.06 1.93 39.89 4.08
113 114 1.577468 TGGACGTGTACTTGTGCAAG 58.423 50.000 10.09 10.09 43.79 4.01
123 124 1.418373 CTTGTGCAAGTCGACGATCA 58.582 50.000 10.46 6.25 33.87 2.92
124 125 1.792367 CTTGTGCAAGTCGACGATCAA 59.208 47.619 10.46 11.19 33.87 2.57
125 126 1.136690 TGTGCAAGTCGACGATCAAC 58.863 50.000 10.46 7.15 0.00 3.18
126 127 1.136690 GTGCAAGTCGACGATCAACA 58.863 50.000 10.46 1.38 0.00 3.33
127 128 1.136611 GTGCAAGTCGACGATCAACAC 60.137 52.381 10.46 10.16 0.00 3.32
128 129 1.269569 TGCAAGTCGACGATCAACACT 60.270 47.619 10.46 0.00 0.00 3.55
129 130 1.125021 GCAAGTCGACGATCAACACTG 59.875 52.381 10.46 0.00 0.00 3.66
130 131 2.394708 CAAGTCGACGATCAACACTGT 58.605 47.619 10.46 0.00 0.00 3.55
131 132 2.051879 AGTCGACGATCAACACTGTG 57.948 50.000 10.46 6.19 0.00 3.66
132 133 1.607148 AGTCGACGATCAACACTGTGA 59.393 47.619 15.86 0.00 0.00 3.58
133 134 1.714460 GTCGACGATCAACACTGTGAC 59.286 52.381 15.86 0.00 0.00 3.67
134 135 1.335496 TCGACGATCAACACTGTGACA 59.665 47.619 15.86 0.00 0.00 3.58
135 136 1.716050 CGACGATCAACACTGTGACAG 59.284 52.381 15.86 11.70 37.52 3.51
136 137 2.061773 GACGATCAACACTGTGACAGG 58.938 52.381 17.92 8.42 35.51 4.00
137 138 1.686587 ACGATCAACACTGTGACAGGA 59.313 47.619 17.92 4.62 35.51 3.86
138 139 2.288457 ACGATCAACACTGTGACAGGAG 60.288 50.000 17.92 11.35 35.51 3.69
139 140 2.693069 GATCAACACTGTGACAGGAGG 58.307 52.381 17.92 8.46 35.51 4.30
140 141 1.788229 TCAACACTGTGACAGGAGGA 58.212 50.000 17.92 6.02 35.51 3.71
141 142 1.688735 TCAACACTGTGACAGGAGGAG 59.311 52.381 17.92 6.29 35.51 3.69
142 143 1.688735 CAACACTGTGACAGGAGGAGA 59.311 52.381 17.92 0.00 35.51 3.71
143 144 1.333177 ACACTGTGACAGGAGGAGAC 58.667 55.000 17.92 0.00 35.51 3.36
144 145 0.242286 CACTGTGACAGGAGGAGACG 59.758 60.000 17.92 0.00 35.51 4.18
145 146 0.110678 ACTGTGACAGGAGGAGACGA 59.889 55.000 17.92 0.00 35.51 4.20
146 147 1.248486 CTGTGACAGGAGGAGACGAA 58.752 55.000 4.28 0.00 0.00 3.85
147 148 1.821753 CTGTGACAGGAGGAGACGAAT 59.178 52.381 4.28 0.00 0.00 3.34
148 149 3.017442 CTGTGACAGGAGGAGACGAATA 58.983 50.000 4.28 0.00 0.00 1.75
149 150 3.427573 TGTGACAGGAGGAGACGAATAA 58.572 45.455 0.00 0.00 0.00 1.40
150 151 3.444034 TGTGACAGGAGGAGACGAATAAG 59.556 47.826 0.00 0.00 0.00 1.73
151 152 3.024547 TGACAGGAGGAGACGAATAAGG 58.975 50.000 0.00 0.00 0.00 2.69
152 153 2.362717 GACAGGAGGAGACGAATAAGGG 59.637 54.545 0.00 0.00 0.00 3.95
153 154 2.292323 ACAGGAGGAGACGAATAAGGGT 60.292 50.000 0.00 0.00 0.00 4.34
154 155 2.101582 CAGGAGGAGACGAATAAGGGTG 59.898 54.545 0.00 0.00 0.00 4.61
155 156 2.108970 GGAGGAGACGAATAAGGGTGT 58.891 52.381 0.00 0.00 0.00 4.16
156 157 2.500504 GGAGGAGACGAATAAGGGTGTT 59.499 50.000 0.00 0.00 0.00 3.32
157 158 3.055312 GGAGGAGACGAATAAGGGTGTTT 60.055 47.826 0.00 0.00 0.00 2.83
158 159 4.182339 GAGGAGACGAATAAGGGTGTTTC 58.818 47.826 0.00 0.00 0.00 2.78
213 214 1.705186 AGGGTCACACACTGCCTTATT 59.295 47.619 0.00 0.00 25.25 1.40
217 218 3.058224 GGTCACACACTGCCTTATTGAAC 60.058 47.826 0.00 0.00 0.00 3.18
237 238 1.583054 GGCTGTAGAGGCGGTTTATG 58.417 55.000 0.00 0.00 34.60 1.90
245 246 1.467342 GAGGCGGTTTATGTTTTCGCT 59.533 47.619 0.00 0.00 44.88 4.93
256 257 7.096312 GGTTTATGTTTTCGCTACTATAGTCGG 60.096 40.741 9.12 5.10 0.00 4.79
262 263 1.662309 CGCTACTATAGTCGGTTGGCG 60.662 57.143 9.12 12.38 33.43 5.69
264 265 1.335810 CTACTATAGTCGGTTGGCGCA 59.664 52.381 9.12 0.00 0.00 6.09
266 267 1.958579 ACTATAGTCGGTTGGCGCATA 59.041 47.619 10.83 0.00 0.00 3.14
267 268 2.030185 ACTATAGTCGGTTGGCGCATAG 60.030 50.000 10.83 6.90 0.00 2.23
291 292 2.294074 TGGCCATACTTAATCGCCAAC 58.706 47.619 0.00 0.00 46.28 3.77
296 297 4.275936 GCCATACTTAATCGCCAACTGATT 59.724 41.667 0.00 0.00 39.32 2.57
307 308 1.335810 CCAACTGATTCATGCCGGATG 59.664 52.381 5.05 6.59 0.00 3.51
308 309 2.019249 CAACTGATTCATGCCGGATGT 58.981 47.619 5.05 0.00 33.29 3.06
365 366 5.650543 AGACATTTTTCACATATTTCGGGC 58.349 37.500 0.00 0.00 0.00 6.13
371 372 0.466189 CACATATTTCGGGCTGGGCT 60.466 55.000 0.00 0.00 0.00 5.19
374 375 2.357593 ATATTTCGGGCTGGGCTGGG 62.358 60.000 3.21 0.00 0.00 4.45
401 402 0.968405 TGGCCAGGCTTTGACATTTC 59.032 50.000 12.43 0.00 0.00 2.17
419 420 2.215942 TCCAGATCAGACTTGTCCGA 57.784 50.000 0.00 0.00 0.00 4.55
589 590 2.357009 CGCAAGGATTTTCATGGAGAGG 59.643 50.000 0.00 0.00 0.00 3.69
846 854 3.815401 CGAGATAAACATCCATTCACCCC 59.185 47.826 0.00 0.00 0.00 4.95
847 855 4.145052 GAGATAAACATCCATTCACCCCC 58.855 47.826 0.00 0.00 0.00 5.40
848 856 3.531397 AGATAAACATCCATTCACCCCCA 59.469 43.478 0.00 0.00 0.00 4.96
849 857 1.937191 AAACATCCATTCACCCCCAC 58.063 50.000 0.00 0.00 0.00 4.61
850 858 1.084018 AACATCCATTCACCCCCACT 58.916 50.000 0.00 0.00 0.00 4.00
882 890 3.756677 CTCGCTCACGCACACACG 61.757 66.667 0.00 0.00 39.84 4.49
1202 1211 2.558795 GGTCAAGCTTTCCTTTCCTTCC 59.441 50.000 0.00 0.00 0.00 3.46
1203 1212 2.558795 GTCAAGCTTTCCTTTCCTTCCC 59.441 50.000 0.00 0.00 0.00 3.97
1204 1213 2.447047 TCAAGCTTTCCTTTCCTTCCCT 59.553 45.455 0.00 0.00 0.00 4.20
1205 1214 2.822561 CAAGCTTTCCTTTCCTTCCCTC 59.177 50.000 0.00 0.00 0.00 4.30
1206 1215 1.356059 AGCTTTCCTTTCCTTCCCTCC 59.644 52.381 0.00 0.00 0.00 4.30
1233 1243 2.420687 CCTTCCTTGTAGCCATGGAGAC 60.421 54.545 18.40 12.78 43.53 3.36
1320 1333 3.340337 AGCTTCGCTCAAACTGAAAAC 57.660 42.857 0.00 0.00 30.62 2.43
1323 1336 3.850010 GCTTCGCTCAAACTGAAAACCTC 60.850 47.826 0.00 0.00 0.00 3.85
1361 1374 5.663106 ACACCTGAGATACTGTAATCACCAT 59.337 40.000 0.00 0.00 0.00 3.55
1362 1375 5.987953 CACCTGAGATACTGTAATCACCATG 59.012 44.000 0.00 0.00 0.00 3.66
1364 1377 4.620982 TGAGATACTGTAATCACCATGCG 58.379 43.478 0.00 0.00 0.00 4.73
1433 1451 6.700352 AGATCTCCTATGTAGTACGTACTCC 58.300 44.000 30.53 20.73 37.73 3.85
1439 1457 6.986817 TCCTATGTAGTACGTACTCCACTTAC 59.013 42.308 30.53 21.40 37.73 2.34
1477 1502 8.942338 TTTATTGCTCACCAGTGTACTAATAG 57.058 34.615 0.00 0.00 0.00 1.73
1518 1543 2.086869 CAACTGAAATCCGTGGCAGAT 58.913 47.619 0.00 0.00 32.86 2.90
1519 1544 3.270027 CAACTGAAATCCGTGGCAGATA 58.730 45.455 0.00 0.00 32.86 1.98
1520 1545 3.185246 ACTGAAATCCGTGGCAGATAG 57.815 47.619 0.00 0.00 32.86 2.08
1530 1555 3.366476 CCGTGGCAGATAGTAGTATCAGC 60.366 52.174 20.99 20.99 43.89 4.26
1958 1983 0.179145 CACCGTCGTTAGGCAGGTAG 60.179 60.000 0.00 0.00 33.30 3.18
1959 1984 0.322816 ACCGTCGTTAGGCAGGTAGA 60.323 55.000 0.00 0.00 32.76 2.59
1960 1985 1.030457 CCGTCGTTAGGCAGGTAGAT 58.970 55.000 0.00 0.00 0.00 1.98
1961 1986 2.224606 CCGTCGTTAGGCAGGTAGATA 58.775 52.381 0.00 0.00 0.00 1.98
1962 1987 2.225963 CCGTCGTTAGGCAGGTAGATAG 59.774 54.545 0.00 0.00 0.00 2.08
2049 2087 1.444212 CCAGTTTGCATTTCGGCCG 60.444 57.895 22.12 22.12 0.00 6.13
2152 2216 4.664864 CGCGCGCTGTTCTTTGCA 62.665 61.111 30.48 0.00 0.00 4.08
2334 2398 1.219980 TGAGGCTGAGAGGATCCTGAT 59.780 52.381 22.02 7.50 33.66 2.90
2335 2399 1.895131 GAGGCTGAGAGGATCCTGATC 59.105 57.143 22.02 17.24 33.66 2.92
2350 2414 2.091994 CCTGATCTGCAAGGGGAGAATT 60.092 50.000 0.00 0.00 45.12 2.17
2497 2561 3.427773 CCGAAGTGTACTACAGGAAGCTC 60.428 52.174 0.00 0.00 0.00 4.09
2524 2588 2.777832 AGGATGACTTCTTGGTGCTC 57.222 50.000 0.00 0.00 0.00 4.26
2559 2623 5.183331 GGGTAACAAGAGTGGATTTCTTTCC 59.817 44.000 0.00 0.00 32.75 3.13
2587 2651 5.779241 TTCCCTCTAGTTTCATGTCCATT 57.221 39.130 0.00 0.00 0.00 3.16
2588 2652 6.884472 TTCCCTCTAGTTTCATGTCCATTA 57.116 37.500 0.00 0.00 0.00 1.90
2589 2653 6.485830 TCCCTCTAGTTTCATGTCCATTAG 57.514 41.667 0.00 0.00 0.00 1.73
2603 2667 7.498900 TCATGTCCATTAGTACATTCCAATCAC 59.501 37.037 0.00 0.00 34.12 3.06
2634 2698 9.237846 CAACTTCCTTCAATTAAGAACAGTTTC 57.762 33.333 0.00 0.00 37.38 2.78
2635 2699 8.753497 ACTTCCTTCAATTAAGAACAGTTTCT 57.247 30.769 0.00 0.00 44.53 2.52
2636 2700 8.624776 ACTTCCTTCAATTAAGAACAGTTTCTG 58.375 33.333 0.00 0.00 41.56 3.02
2779 2856 0.179076 TGCAGATATGGGACGTGCTG 60.179 55.000 7.11 0.00 35.11 4.41
2950 3027 2.097036 CCAGCAGCCATTTCATCTGAA 58.903 47.619 0.00 0.00 0.00 3.02
2955 3032 3.181489 GCAGCCATTTCATCTGAAGAAGG 60.181 47.826 0.00 0.00 35.21 3.46
2977 3054 4.379243 ACGACCAAGCCGCCTCAG 62.379 66.667 0.00 0.00 0.00 3.35
2978 3055 4.069232 CGACCAAGCCGCCTCAGA 62.069 66.667 0.00 0.00 0.00 3.27
3001 3078 2.028484 GTGCTGTCGTTCACCGGA 59.972 61.111 9.46 0.00 37.11 5.14
3171 3248 1.672881 CGACCAAGAATCATCCAAGGC 59.327 52.381 0.00 0.00 0.00 4.35
3212 3289 2.561858 TGCTCATGCATTGCCAAACTTA 59.438 40.909 16.08 0.00 45.31 2.24
3292 3369 1.081892 CGCATTCAGGGTGTTGAGAG 58.918 55.000 0.00 0.00 0.00 3.20
3428 3509 2.147436 TGAATTGGCGCCAGTTTTTC 57.853 45.000 34.06 28.59 0.00 2.29
3457 3538 5.124457 CCGAATGATTTGAAGATGGTTGACT 59.876 40.000 0.00 0.00 0.00 3.41
3485 3566 1.075525 CCCATGGTACTCCCTCCGA 60.076 63.158 11.73 0.00 0.00 4.55
3550 3631 7.145323 CCTTACAAAGTTTGACCCAGTTTATG 58.855 38.462 22.23 4.12 0.00 1.90
3618 3699 7.640630 GTGAAGTACGTCTTGTGATGTATCTAG 59.359 40.741 10.21 0.00 43.85 2.43
3752 3833 4.902448 AGAAAGAGTGTGAACTACTCCCTT 59.098 41.667 0.00 0.00 44.35 3.95
3810 4411 2.856222 AGAAGTGAAAGGGCTTGACAG 58.144 47.619 0.00 0.00 0.00 3.51
3860 4468 2.159310 CGCTCTTGAGAAGATCGAAGGT 60.159 50.000 4.03 0.00 46.76 3.50
3862 4470 3.119316 GCTCTTGAGAAGATCGAAGGTCA 60.119 47.826 1.30 0.00 36.82 4.02
3890 4498 4.225340 CGCGGTCCTCTCGAGTCG 62.225 72.222 13.13 6.09 0.00 4.18
3933 4541 3.974535 TGGCATGCTAATGACACCA 57.025 47.368 18.92 0.00 44.96 4.17
3948 4556 3.279434 GACACCACTCCACAAACTTTCT 58.721 45.455 0.00 0.00 0.00 2.52
3974 4582 1.078848 CCTGTGAGGCCGAGAAAGG 60.079 63.158 0.00 0.00 0.00 3.11
3981 4589 1.896660 GGCCGAGAAAGGTGCACAA 60.897 57.895 20.43 0.00 0.00 3.33
4000 4608 4.036027 CACAACTCTATTGACATGGATGGC 59.964 45.833 0.00 0.00 35.98 4.40
4026 4634 1.000607 CCAGTTGAGCATGGCATATGC 60.001 52.381 19.79 19.79 44.85 3.14
4042 4650 1.123077 ATGCCTTCTCTGCGTCCATA 58.877 50.000 0.00 0.00 0.00 2.74
4075 4683 1.376543 GAGATGACGTGACCGAGGTA 58.623 55.000 0.00 0.00 37.88 3.08
4093 4701 1.066430 GTAGCCGATGTTGTCCTTGGA 60.066 52.381 0.00 0.00 0.00 3.53
4126 4734 4.075682 TGGACATTTTGGCGTAAAGATGA 58.924 39.130 8.88 0.00 0.00 2.92
4134 4742 7.555639 TTTTGGCGTAAAGATGATTTTAACG 57.444 32.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.611751 CCATCATTGCCAACATTGCATG 59.388 45.455 0.00 0.00 38.76 4.06
2 3 1.900486 TCCATCATTGCCAACATTGCA 59.100 42.857 0.00 0.00 36.84 4.08
3 4 2.676632 TCCATCATTGCCAACATTGC 57.323 45.000 0.00 0.00 0.00 3.56
4 5 2.869801 GCATCCATCATTGCCAACATTG 59.130 45.455 0.00 0.00 32.66 2.82
5 6 2.769663 AGCATCCATCATTGCCAACATT 59.230 40.909 0.00 0.00 39.72 2.71
6 7 2.394632 AGCATCCATCATTGCCAACAT 58.605 42.857 0.00 0.00 39.72 2.71
7 8 1.855295 AGCATCCATCATTGCCAACA 58.145 45.000 0.00 0.00 39.72 3.33
8 9 2.287188 CGTAGCATCCATCATTGCCAAC 60.287 50.000 0.00 0.00 39.72 3.77
10 11 1.140652 TCGTAGCATCCATCATTGCCA 59.859 47.619 0.00 0.00 39.72 4.92
11 12 1.882912 TCGTAGCATCCATCATTGCC 58.117 50.000 0.00 0.00 39.72 4.52
12 13 2.874701 AGTTCGTAGCATCCATCATTGC 59.125 45.455 0.00 0.00 39.17 3.56
13 14 3.249320 CCAGTTCGTAGCATCCATCATTG 59.751 47.826 0.00 0.00 0.00 2.82
14 15 3.470709 CCAGTTCGTAGCATCCATCATT 58.529 45.455 0.00 0.00 0.00 2.57
15 16 2.808202 GCCAGTTCGTAGCATCCATCAT 60.808 50.000 0.00 0.00 0.00 2.45
16 17 1.473257 GCCAGTTCGTAGCATCCATCA 60.473 52.381 0.00 0.00 0.00 3.07
17 18 1.202580 AGCCAGTTCGTAGCATCCATC 60.203 52.381 0.00 0.00 0.00 3.51
18 19 0.833287 AGCCAGTTCGTAGCATCCAT 59.167 50.000 0.00 0.00 0.00 3.41
19 20 1.136305 GTAGCCAGTTCGTAGCATCCA 59.864 52.381 0.00 0.00 0.00 3.41
20 21 1.136305 TGTAGCCAGTTCGTAGCATCC 59.864 52.381 0.00 0.00 0.00 3.51
21 22 2.579207 TGTAGCCAGTTCGTAGCATC 57.421 50.000 0.00 0.00 0.00 3.91
22 23 2.418746 CCTTGTAGCCAGTTCGTAGCAT 60.419 50.000 0.00 0.00 0.00 3.79
23 24 1.067142 CCTTGTAGCCAGTTCGTAGCA 60.067 52.381 0.00 0.00 0.00 3.49
24 25 1.067071 ACCTTGTAGCCAGTTCGTAGC 60.067 52.381 0.00 0.00 0.00 3.58
25 26 2.607187 CACCTTGTAGCCAGTTCGTAG 58.393 52.381 0.00 0.00 0.00 3.51
26 27 1.337447 GCACCTTGTAGCCAGTTCGTA 60.337 52.381 0.00 0.00 0.00 3.43
27 28 0.602905 GCACCTTGTAGCCAGTTCGT 60.603 55.000 0.00 0.00 0.00 3.85
28 29 0.602638 TGCACCTTGTAGCCAGTTCG 60.603 55.000 0.00 0.00 0.00 3.95
29 30 1.604604 TTGCACCTTGTAGCCAGTTC 58.395 50.000 0.00 0.00 0.00 3.01
30 31 1.956477 CTTTGCACCTTGTAGCCAGTT 59.044 47.619 0.00 0.00 0.00 3.16
31 32 1.609208 CTTTGCACCTTGTAGCCAGT 58.391 50.000 0.00 0.00 0.00 4.00
32 33 0.242017 GCTTTGCACCTTGTAGCCAG 59.758 55.000 0.00 0.00 0.00 4.85
33 34 1.514678 CGCTTTGCACCTTGTAGCCA 61.515 55.000 0.00 0.00 0.00 4.75
34 35 1.210155 CGCTTTGCACCTTGTAGCC 59.790 57.895 0.00 0.00 0.00 3.93
35 36 0.804989 ATCGCTTTGCACCTTGTAGC 59.195 50.000 0.00 0.00 0.00 3.58
36 37 1.131126 CCATCGCTTTGCACCTTGTAG 59.869 52.381 0.00 0.00 0.00 2.74
37 38 1.164411 CCATCGCTTTGCACCTTGTA 58.836 50.000 0.00 0.00 0.00 2.41
38 39 0.823356 ACCATCGCTTTGCACCTTGT 60.823 50.000 0.00 0.00 0.00 3.16
39 40 0.109597 GACCATCGCTTTGCACCTTG 60.110 55.000 0.00 0.00 0.00 3.61
40 41 0.537143 TGACCATCGCTTTGCACCTT 60.537 50.000 0.00 0.00 0.00 3.50
41 42 0.537143 TTGACCATCGCTTTGCACCT 60.537 50.000 0.00 0.00 0.00 4.00
42 43 0.387239 GTTGACCATCGCTTTGCACC 60.387 55.000 0.00 0.00 0.00 5.01
43 44 0.725784 CGTTGACCATCGCTTTGCAC 60.726 55.000 0.00 0.00 0.00 4.57
44 45 1.573932 CGTTGACCATCGCTTTGCA 59.426 52.632 0.00 0.00 0.00 4.08
45 46 4.440214 CGTTGACCATCGCTTTGC 57.560 55.556 0.00 0.00 0.00 3.68
51 52 2.809174 TCGCAGCGTTGACCATCG 60.809 61.111 15.93 0.00 0.00 3.84
52 53 2.778679 GTCGCAGCGTTGACCATC 59.221 61.111 15.93 0.00 0.00 3.51
53 54 2.835701 ATCGTCGCAGCGTTGACCAT 62.836 55.000 15.93 0.00 0.00 3.55
54 55 3.567478 ATCGTCGCAGCGTTGACCA 62.567 57.895 15.93 0.00 0.00 4.02
55 56 2.809601 ATCGTCGCAGCGTTGACC 60.810 61.111 15.93 0.00 0.00 4.02
56 57 2.391821 CATCGTCGCAGCGTTGAC 59.608 61.111 15.93 4.74 34.58 3.18
57 58 2.809174 CCATCGTCGCAGCGTTGA 60.809 61.111 15.93 14.10 34.58 3.18
58 59 3.112075 ACCATCGTCGCAGCGTTG 61.112 61.111 15.93 8.71 0.00 4.10
59 60 3.112075 CACCATCGTCGCAGCGTT 61.112 61.111 15.93 0.00 0.00 4.84
80 81 2.185494 GTCCATGCTAGCAGGCAGC 61.185 63.158 23.57 11.42 45.75 5.25
81 82 1.886313 CGTCCATGCTAGCAGGCAG 60.886 63.158 23.57 11.33 45.75 4.85
82 83 2.187685 CGTCCATGCTAGCAGGCA 59.812 61.111 23.57 6.33 46.63 4.75
83 84 2.176273 CACGTCCATGCTAGCAGGC 61.176 63.158 23.57 11.11 0.00 4.85
84 85 0.459899 TACACGTCCATGCTAGCAGG 59.540 55.000 23.89 23.00 0.00 4.85
85 86 1.135139 AGTACACGTCCATGCTAGCAG 59.865 52.381 23.89 14.42 0.00 4.24
86 87 1.182667 AGTACACGTCCATGCTAGCA 58.817 50.000 21.85 21.85 0.00 3.49
87 88 1.927174 CAAGTACACGTCCATGCTAGC 59.073 52.381 8.10 8.10 0.00 3.42
88 89 2.923655 CACAAGTACACGTCCATGCTAG 59.076 50.000 0.00 0.00 0.00 3.42
89 90 2.929161 GCACAAGTACACGTCCATGCTA 60.929 50.000 0.00 0.00 0.00 3.49
90 91 1.795768 CACAAGTACACGTCCATGCT 58.204 50.000 0.00 0.00 0.00 3.79
91 92 0.165944 GCACAAGTACACGTCCATGC 59.834 55.000 0.00 0.00 0.00 4.06
92 93 1.507562 TGCACAAGTACACGTCCATG 58.492 50.000 0.00 0.00 0.00 3.66
93 94 2.143122 CTTGCACAAGTACACGTCCAT 58.857 47.619 2.12 0.00 33.87 3.41
94 95 1.577468 CTTGCACAAGTACACGTCCA 58.423 50.000 2.12 0.00 33.87 4.02
104 105 1.418373 TGATCGTCGACTTGCACAAG 58.582 50.000 14.70 8.82 43.79 3.16
105 106 1.525197 GTTGATCGTCGACTTGCACAA 59.475 47.619 14.70 9.65 0.00 3.33
106 107 1.136690 GTTGATCGTCGACTTGCACA 58.863 50.000 14.70 4.06 0.00 4.57
107 108 1.136611 GTGTTGATCGTCGACTTGCAC 60.137 52.381 14.70 9.79 32.00 4.57
108 109 1.136690 GTGTTGATCGTCGACTTGCA 58.863 50.000 14.70 5.52 32.00 4.08
109 110 1.125021 CAGTGTTGATCGTCGACTTGC 59.875 52.381 14.70 2.77 32.00 4.01
110 111 2.153817 CACAGTGTTGATCGTCGACTTG 59.846 50.000 14.70 0.00 32.00 3.16
111 112 2.034179 TCACAGTGTTGATCGTCGACTT 59.966 45.455 14.70 0.13 32.00 3.01
112 113 1.607148 TCACAGTGTTGATCGTCGACT 59.393 47.619 14.70 0.00 32.00 4.18
113 114 1.714460 GTCACAGTGTTGATCGTCGAC 59.286 52.381 5.18 5.18 0.00 4.20
114 115 1.335496 TGTCACAGTGTTGATCGTCGA 59.665 47.619 0.00 0.00 0.00 4.20
115 116 1.716050 CTGTCACAGTGTTGATCGTCG 59.284 52.381 0.00 0.00 0.00 5.12
116 117 2.061773 CCTGTCACAGTGTTGATCGTC 58.938 52.381 3.56 0.00 0.00 4.20
117 118 1.686587 TCCTGTCACAGTGTTGATCGT 59.313 47.619 3.56 0.00 0.00 3.73
118 119 2.332104 CTCCTGTCACAGTGTTGATCG 58.668 52.381 3.56 0.00 0.00 3.69
119 120 2.300152 TCCTCCTGTCACAGTGTTGATC 59.700 50.000 3.56 0.00 0.00 2.92
120 121 2.301296 CTCCTCCTGTCACAGTGTTGAT 59.699 50.000 3.56 0.00 0.00 2.57
121 122 1.688735 CTCCTCCTGTCACAGTGTTGA 59.311 52.381 3.56 0.00 0.00 3.18
122 123 1.688735 TCTCCTCCTGTCACAGTGTTG 59.311 52.381 3.56 0.00 0.00 3.33
123 124 1.689273 GTCTCCTCCTGTCACAGTGTT 59.311 52.381 3.56 0.00 0.00 3.32
124 125 1.333177 GTCTCCTCCTGTCACAGTGT 58.667 55.000 3.56 0.00 0.00 3.55
125 126 0.242286 CGTCTCCTCCTGTCACAGTG 59.758 60.000 3.56 0.00 0.00 3.66
126 127 0.110678 TCGTCTCCTCCTGTCACAGT 59.889 55.000 3.56 0.00 0.00 3.55
127 128 1.248486 TTCGTCTCCTCCTGTCACAG 58.752 55.000 0.00 0.00 0.00 3.66
128 129 1.924731 ATTCGTCTCCTCCTGTCACA 58.075 50.000 0.00 0.00 0.00 3.58
129 130 3.181485 CCTTATTCGTCTCCTCCTGTCAC 60.181 52.174 0.00 0.00 0.00 3.67
130 131 3.024547 CCTTATTCGTCTCCTCCTGTCA 58.975 50.000 0.00 0.00 0.00 3.58
131 132 2.362717 CCCTTATTCGTCTCCTCCTGTC 59.637 54.545 0.00 0.00 0.00 3.51
132 133 2.292323 ACCCTTATTCGTCTCCTCCTGT 60.292 50.000 0.00 0.00 0.00 4.00
133 134 2.101582 CACCCTTATTCGTCTCCTCCTG 59.898 54.545 0.00 0.00 0.00 3.86
134 135 2.292323 ACACCCTTATTCGTCTCCTCCT 60.292 50.000 0.00 0.00 0.00 3.69
135 136 2.108970 ACACCCTTATTCGTCTCCTCC 58.891 52.381 0.00 0.00 0.00 4.30
136 137 3.889520 AACACCCTTATTCGTCTCCTC 57.110 47.619 0.00 0.00 0.00 3.71
137 138 3.838903 AGAAACACCCTTATTCGTCTCCT 59.161 43.478 0.00 0.00 0.00 3.69
138 139 4.203654 AGAAACACCCTTATTCGTCTCC 57.796 45.455 0.00 0.00 0.00 3.71
139 140 4.995487 ACAAGAAACACCCTTATTCGTCTC 59.005 41.667 0.00 0.00 0.00 3.36
140 141 4.755123 CACAAGAAACACCCTTATTCGTCT 59.245 41.667 0.00 0.00 0.00 4.18
141 142 4.612939 GCACAAGAAACACCCTTATTCGTC 60.613 45.833 0.00 0.00 0.00 4.20
142 143 3.252458 GCACAAGAAACACCCTTATTCGT 59.748 43.478 0.00 0.00 0.00 3.85
143 144 3.252215 TGCACAAGAAACACCCTTATTCG 59.748 43.478 0.00 0.00 0.00 3.34
144 145 4.846779 TGCACAAGAAACACCCTTATTC 57.153 40.909 0.00 0.00 0.00 1.75
145 146 4.501400 GCTTGCACAAGAAACACCCTTATT 60.501 41.667 14.44 0.00 40.79 1.40
146 147 3.005791 GCTTGCACAAGAAACACCCTTAT 59.994 43.478 14.44 0.00 40.79 1.73
147 148 2.360801 GCTTGCACAAGAAACACCCTTA 59.639 45.455 14.44 0.00 40.79 2.69
148 149 1.136891 GCTTGCACAAGAAACACCCTT 59.863 47.619 14.44 0.00 40.79 3.95
149 150 0.746659 GCTTGCACAAGAAACACCCT 59.253 50.000 14.44 0.00 40.79 4.34
150 151 0.746659 AGCTTGCACAAGAAACACCC 59.253 50.000 14.44 0.00 40.79 4.61
151 152 2.357637 TGTAGCTTGCACAAGAAACACC 59.642 45.455 14.44 0.00 40.79 4.16
152 153 3.691049 TGTAGCTTGCACAAGAAACAC 57.309 42.857 14.44 6.01 40.79 3.32
175 176 1.532090 CCTCTGATCGTCTTCCGTTCG 60.532 57.143 0.00 0.00 37.96 3.95
213 214 2.571757 CGCCTCTACAGCCGTTCA 59.428 61.111 0.00 0.00 0.00 3.18
217 218 0.104304 ATAAACCGCCTCTACAGCCG 59.896 55.000 0.00 0.00 0.00 5.52
237 238 4.501921 CCAACCGACTATAGTAGCGAAAAC 59.498 45.833 13.85 0.00 0.00 2.43
245 246 1.391577 TGCGCCAACCGACTATAGTA 58.608 50.000 5.09 0.00 40.02 1.82
256 257 2.793946 CCAGTGCTATGCGCCAAC 59.206 61.111 4.18 0.00 40.23 3.77
262 263 1.972872 AAGTATGGCCAGTGCTATGC 58.027 50.000 13.05 0.00 39.28 3.14
264 265 4.569943 CGATTAAGTATGGCCAGTGCTAT 58.430 43.478 13.05 0.00 42.00 2.97
266 267 2.838736 CGATTAAGTATGGCCAGTGCT 58.161 47.619 13.05 6.09 37.74 4.40
267 268 1.264288 GCGATTAAGTATGGCCAGTGC 59.736 52.381 13.05 3.45 32.34 4.40
291 292 1.600957 GTCACATCCGGCATGAATCAG 59.399 52.381 17.37 5.40 36.21 2.90
296 297 2.511373 GCGTCACATCCGGCATGA 60.511 61.111 17.37 8.98 36.21 3.07
401 402 1.470632 GCTCGGACAAGTCTGATCTGG 60.471 57.143 11.83 2.53 43.40 3.86
419 420 3.139770 AGGCCTGATGATAATTCTTGGCT 59.860 43.478 3.11 0.00 39.12 4.75
825 832 4.145052 GGGGGTGAATGGATGTTTATCTC 58.855 47.826 0.00 0.00 33.68 2.75
846 854 1.427419 CGAGCGAGAGAGTGAGTGG 59.573 63.158 0.00 0.00 0.00 4.00
847 855 1.226267 GCGAGCGAGAGAGTGAGTG 60.226 63.158 0.00 0.00 0.00 3.51
848 856 1.366111 GAGCGAGCGAGAGAGTGAGT 61.366 60.000 0.00 0.00 0.00 3.41
849 857 1.351707 GAGCGAGCGAGAGAGTGAG 59.648 63.158 0.00 0.00 0.00 3.51
850 858 2.456948 CGAGCGAGCGAGAGAGTGA 61.457 63.158 0.00 0.00 0.00 3.41
970 978 0.462759 AAATCTCGGCAGCAGCTACC 60.463 55.000 0.76 0.76 41.70 3.18
971 979 0.654683 CAAATCTCGGCAGCAGCTAC 59.345 55.000 0.00 0.00 41.70 3.58
993 1002 3.282157 CAGATCCCCATTGCCGCG 61.282 66.667 0.00 0.00 0.00 6.46
1202 1211 2.003548 CAAGGAAGGGGAGGGGAGG 61.004 68.421 0.00 0.00 0.00 4.30
1203 1212 0.044244 TACAAGGAAGGGGAGGGGAG 59.956 60.000 0.00 0.00 0.00 4.30
1204 1213 0.044244 CTACAAGGAAGGGGAGGGGA 59.956 60.000 0.00 0.00 0.00 4.81
1205 1214 1.636769 GCTACAAGGAAGGGGAGGGG 61.637 65.000 0.00 0.00 0.00 4.79
1206 1215 1.636769 GGCTACAAGGAAGGGGAGGG 61.637 65.000 0.00 0.00 0.00 4.30
1233 1243 5.585390 ACTTGCAGTGAAGAAAAGAACATG 58.415 37.500 0.00 0.00 0.00 3.21
1320 1333 0.976641 TGTAGTGCAGGTTCCAGAGG 59.023 55.000 0.00 0.00 0.00 3.69
1323 1336 0.687354 AGGTGTAGTGCAGGTTCCAG 59.313 55.000 0.00 0.00 0.00 3.86
1439 1457 7.443272 TGGTGAGCAATAAATATGTCATGAGAG 59.557 37.037 0.00 0.00 0.00 3.20
1518 1543 3.764434 GCTAGGCCATGCTGATACTACTA 59.236 47.826 5.01 0.00 0.00 1.82
1519 1544 2.564947 GCTAGGCCATGCTGATACTACT 59.435 50.000 5.01 0.00 0.00 2.57
1520 1545 2.564947 AGCTAGGCCATGCTGATACTAC 59.435 50.000 19.58 0.00 38.21 2.73
1530 1555 2.855209 AATCTAGCAGCTAGGCCATG 57.145 50.000 26.28 3.83 35.03 3.66
1591 1616 2.419297 GGCGAAGTCCTGATCATCTTGT 60.419 50.000 11.02 0.00 0.00 3.16
1732 1757 4.436998 GGGGCGTCGTCCTCAGTG 62.437 72.222 16.83 0.00 0.00 3.66
1814 1839 2.811317 CTGGTTCTCGTCGCTGGC 60.811 66.667 0.00 0.00 0.00 4.85
1826 1851 2.345244 CGAGGACAGCAGCTGGTT 59.655 61.111 26.38 11.08 35.51 3.67
2295 2359 2.160205 CACCTACGACAAGTCCAGAGA 58.840 52.381 0.00 0.00 0.00 3.10
2296 2360 2.160205 TCACCTACGACAAGTCCAGAG 58.840 52.381 0.00 0.00 0.00 3.35
2334 2398 2.436417 CGAAAATTCTCCCCTTGCAGA 58.564 47.619 0.00 0.00 0.00 4.26
2335 2399 1.135286 GCGAAAATTCTCCCCTTGCAG 60.135 52.381 0.00 0.00 0.00 4.41
2350 2414 1.089481 GCTCATCGTCCATGGCGAAA 61.089 55.000 27.06 19.29 41.84 3.46
2497 2561 5.180868 CACCAAGAAGTCATCCTTTTCAGAG 59.819 44.000 0.00 0.00 32.03 3.35
2524 2588 0.322098 TTGTTACCCCATCAGTGGCG 60.322 55.000 0.00 0.00 44.62 5.69
2559 2623 5.186198 ACATGAAACTAGAGGGAAAATCCG 58.814 41.667 0.00 0.00 37.43 4.18
2587 2651 3.449377 TGGAGCGTGATTGGAATGTACTA 59.551 43.478 0.00 0.00 0.00 1.82
2588 2652 2.236146 TGGAGCGTGATTGGAATGTACT 59.764 45.455 0.00 0.00 0.00 2.73
2589 2653 2.627945 TGGAGCGTGATTGGAATGTAC 58.372 47.619 0.00 0.00 0.00 2.90
2603 2667 4.695455 TCTTAATTGAAGGAAGTTGGAGCG 59.305 41.667 0.00 0.00 35.67 5.03
2634 2698 3.599343 TCAGTTGCAATAGTACCAGCAG 58.401 45.455 0.59 0.00 38.35 4.24
2635 2699 3.694043 TCAGTTGCAATAGTACCAGCA 57.306 42.857 0.59 0.00 34.79 4.41
2636 2700 5.567138 ATTTCAGTTGCAATAGTACCAGC 57.433 39.130 0.59 0.00 0.00 4.85
2693 2757 5.588246 TCAGTTAACAGTTGCTTGATGTCAA 59.412 36.000 8.61 0.00 0.00 3.18
2779 2856 0.472471 TGACCACCTCCTTGTTGGAC 59.528 55.000 0.00 0.00 40.56 4.02
2875 2952 0.801067 CCATCGACGTCGGGAACTTC 60.801 60.000 35.05 0.00 40.29 3.01
2950 3027 1.302033 CTTGGTCGTGCTGCCTTCT 60.302 57.895 0.00 0.00 0.00 2.85
3001 3078 0.890996 CCAGAGCCTTGCGGAAACTT 60.891 55.000 0.00 0.00 0.00 2.66
3171 3248 4.750598 AGCATGAATCGATCAGTCAATCAG 59.249 41.667 0.00 0.00 42.53 2.90
3248 3325 2.159282 ACACGGCGTATGAAACTAGGAG 60.159 50.000 14.22 0.00 0.00 3.69
3249 3326 1.820519 ACACGGCGTATGAAACTAGGA 59.179 47.619 14.22 0.00 0.00 2.94
3250 3327 2.288961 ACACGGCGTATGAAACTAGG 57.711 50.000 14.22 0.00 0.00 3.02
3251 3328 3.060363 GTGAACACGGCGTATGAAACTAG 59.940 47.826 14.22 0.00 0.00 2.57
3252 3329 2.988493 GTGAACACGGCGTATGAAACTA 59.012 45.455 14.22 0.00 0.00 2.24
3253 3330 1.796459 GTGAACACGGCGTATGAAACT 59.204 47.619 14.22 0.00 0.00 2.66
3288 3365 4.332819 CCAACCGAATTAATGTCCACTCTC 59.667 45.833 0.00 0.00 0.00 3.20
3292 3369 2.490115 TGCCAACCGAATTAATGTCCAC 59.510 45.455 0.00 0.00 0.00 4.02
3428 3509 5.126061 ACCATCTTCAAATCATTCGGAAAGG 59.874 40.000 0.00 0.00 0.00 3.11
3470 3551 2.759355 TGAAATCGGAGGGAGTACCAT 58.241 47.619 0.00 0.00 43.89 3.55
3583 3664 6.859508 CACAAGACGTACTTCACTATTGTACA 59.140 38.462 1.85 0.00 37.11 2.90
3597 3678 5.530171 TCCCTAGATACATCACAAGACGTAC 59.470 44.000 0.00 0.00 0.00 3.67
3600 3681 5.713792 ATCCCTAGATACATCACAAGACG 57.286 43.478 0.00 0.00 0.00 4.18
3645 3726 9.995003 TTGACCAAATTTGTAAAAGAAGCATAT 57.005 25.926 16.73 0.00 0.00 1.78
3646 3727 9.823647 TTTGACCAAATTTGTAAAAGAAGCATA 57.176 25.926 16.73 0.00 0.00 3.14
3647 3728 8.729805 TTTGACCAAATTTGTAAAAGAAGCAT 57.270 26.923 16.73 0.00 0.00 3.79
3648 3729 8.553459 TTTTGACCAAATTTGTAAAAGAAGCA 57.447 26.923 16.73 1.33 0.00 3.91
3668 3749 9.284594 CGAGAAGTCAAACTTTACAAATTTTGA 57.715 29.630 15.81 13.20 41.90 2.69
3669 3750 9.284594 TCGAGAAGTCAAACTTTACAAATTTTG 57.715 29.630 7.59 7.59 38.80 2.44
3670 3751 9.849166 TTCGAGAAGTCAAACTTTACAAATTTT 57.151 25.926 0.00 0.00 38.80 1.82
3703 3784 9.394767 TGTTTCACAATGTAGTGCATATAGAAT 57.605 29.630 0.00 0.00 39.35 2.40
3704 3785 8.785329 TGTTTCACAATGTAGTGCATATAGAA 57.215 30.769 0.00 0.00 39.35 2.10
3705 3786 8.257306 TCTGTTTCACAATGTAGTGCATATAGA 58.743 33.333 0.00 0.00 39.35 1.98
3706 3787 8.424274 TCTGTTTCACAATGTAGTGCATATAG 57.576 34.615 0.00 0.00 39.35 1.31
3707 3788 8.785329 TTCTGTTTCACAATGTAGTGCATATA 57.215 30.769 0.00 0.00 39.35 0.86
3717 3798 5.647658 TCACACTCTTTCTGTTTCACAATGT 59.352 36.000 0.00 0.00 0.00 2.71
3725 3806 6.049790 GGAGTAGTTCACACTCTTTCTGTTT 58.950 40.000 2.81 0.00 41.78 2.83
3732 3813 4.221041 GCTAAGGGAGTAGTTCACACTCTT 59.779 45.833 2.81 0.00 41.00 2.85
3752 3833 3.819564 ATGTAAGACATTGAGCCGCTA 57.180 42.857 0.00 0.00 34.67 4.26
3890 4498 4.024048 TGGCAAATCTCTTGACGAAGAAAC 60.024 41.667 0.00 0.00 37.77 2.78
3924 4532 3.297134 AGTTTGTGGAGTGGTGTCATT 57.703 42.857 0.00 0.00 0.00 2.57
3930 4538 3.366052 ACAGAAAGTTTGTGGAGTGGT 57.634 42.857 16.33 0.00 0.00 4.16
3974 4582 4.002982 TCCATGTCAATAGAGTTGTGCAC 58.997 43.478 10.75 10.75 0.00 4.57
3981 4589 2.435805 ACGCCATCCATGTCAATAGAGT 59.564 45.455 0.00 0.00 0.00 3.24
4000 4608 1.210931 CATGCTCAACTGGCCAACG 59.789 57.895 7.01 0.00 0.00 4.10
4026 4634 0.596083 CGCTATGGACGCAGAGAAGG 60.596 60.000 0.00 0.00 0.00 3.46
4035 4643 1.585521 GACGGTGTCGCTATGGACG 60.586 63.158 0.00 0.00 39.83 4.79
4061 4669 2.488820 GGCTACCTCGGTCACGTC 59.511 66.667 0.00 0.00 41.85 4.34
4067 4675 1.255667 ACAACATCGGCTACCTCGGT 61.256 55.000 0.00 0.00 0.00 4.69
4075 4683 0.036010 CTCCAAGGACAACATCGGCT 60.036 55.000 0.00 0.00 0.00 5.52
4093 4701 4.680440 GCCAAAATGTCCAAGTGTTGTTCT 60.680 41.667 0.00 0.00 0.00 3.01
4126 4734 4.624452 GTGTTCGAGCTACTCCGTTAAAAT 59.376 41.667 0.00 0.00 0.00 1.82
4134 4742 1.516603 GCGGTGTTCGAGCTACTCC 60.517 63.158 0.00 0.00 42.43 3.85


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

AutoCloner maintained by Alex Coulton.