Multiple sequence alignment - TraesCS3D01G267100

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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 TraesCS3D01G267100 chr3D 100.000 3702 0 0 1 3702 370617614 370621315 0.000000e+00 6837.0
1 TraesCS3D01G267100 chr3D 81.982 111 12 8 3 109 565160599 565160493 1.830000e-13 87.9
2 TraesCS3D01G267100 chr3D 97.059 34 0 1 3040 3073 370620550 370620582 5.160000e-04 56.5
3 TraesCS3D01G267100 chr3D 97.059 34 0 1 2937 2969 370620653 370620686 5.160000e-04 56.5
4 TraesCS3D01G267100 chr3A 94.804 2444 80 21 559 2971 491521260 491523687 0.000000e+00 3766.0
5 TraesCS3D01G267100 chr3A 85.714 616 48 9 3101 3702 491523958 491524547 6.790000e-172 614.0
6 TraesCS3D01G267100 chr3A 92.623 366 16 2 160 524 491519504 491519859 1.970000e-142 516.0
7 TraesCS3D01G267100 chr3A 100.000 29 0 0 3040 3068 491523652 491523680 2.000000e-03 54.7
8 TraesCS3D01G267100 chr3B 94.633 1565 57 14 264 1805 482001417 482002977 0.000000e+00 2399.0
9 TraesCS3D01G267100 chr3B 97.884 945 15 1 1935 2879 482004342 482005281 0.000000e+00 1629.0
10 TraesCS3D01G267100 chr3B 90.385 468 33 10 3212 3672 482007322 482007784 4.090000e-169 604.0
11 TraesCS3D01G267100 chr3B 97.196 107 2 1 2866 2972 482006809 482006914 2.940000e-41 180.0
12 TraesCS3D01G267100 chr3B 80.137 146 16 7 1805 1944 482003006 482003144 3.040000e-16 97.1
13 TraesCS3D01G267100 chr3B 100.000 39 0 0 186 224 482001368 482001406 5.130000e-09 73.1
14 TraesCS3D01G267100 chr3B 100.000 29 0 0 3040 3068 482006880 482006908 2.000000e-03 54.7
15 TraesCS3D01G267100 chr6D 94.415 376 21 0 1284 1659 159013201 159012826 2.480000e-161 579.0
16 TraesCS3D01G267100 chr7D 92.593 243 11 1 1281 1516 534658963 534658721 3.540000e-90 342.0
17 TraesCS3D01G267100 chr6A 96.341 82 3 0 1534 1615 88123502 88123583 6.450000e-28 135.0
18 TraesCS3D01G267100 chr6A 80.180 111 15 7 3 110 451446776 451446882 3.960000e-10 76.8
19 TraesCS3D01G267100 chr1A 84.127 126 17 3 1058 1181 554887871 554887995 6.490000e-23 119.0
20 TraesCS3D01G267100 chr1D 83.333 126 18 3 1058 1181 463017432 463017556 3.020000e-21 113.0
21 TraesCS3D01G267100 chr1D 96.923 65 2 0 1452 1516 310145770 310145706 3.910000e-20 110.0
22 TraesCS3D01G267100 chr1B 83.898 118 17 2 1058 1174 638013768 638013884 1.090000e-20 111.0
23 TraesCS3D01G267100 chr5B 95.455 66 3 0 1451 1516 474747684 474747619 5.060000e-19 106.0
24 TraesCS3D01G267100 chr2D 83.333 108 14 4 4 109 94347962 94348067 3.040000e-16 97.1
25 TraesCS3D01G267100 chr6B 83.333 90 9 5 23 109 52051747 52051661 1.100000e-10 78.7
26 TraesCS3D01G267100 chr4B 80.357 112 15 7 3 110 144695990 144696098 1.100000e-10 78.7
27 TraesCS3D01G267100 chr4B 80.000 110 16 6 3 109 512775874 512775980 3.960000e-10 76.8
28 TraesCS3D01G267100 chr4B 79.817 109 16 6 3 107 594610799 594610693 1.430000e-09 75.0
29 TraesCS3D01G267100 chr2A 79.817 109 16 6 3 109 179990386 179990490 1.430000e-09 75.0
30 TraesCS3D01G267100 chr4D 78.899 109 20 3 3 109 95340114 95340221 1.840000e-08 71.3


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 TraesCS3D01G267100 chr3D 370617614 370621315 3701 False 2316.666667 6837 98.039333 1 3702 3 chr3D.!!$F1 3701
1 TraesCS3D01G267100 chr3A 491519504 491524547 5043 False 1237.675000 3766 93.285250 160 3702 4 chr3A.!!$F1 3542
2 TraesCS3D01G267100 chr3B 482001368 482007784 6416 False 719.557143 2399 94.319286 186 3672 7 chr3B.!!$F1 3486

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
27 28 0.036671 AAAAACGGGCTCCTAGGACG 60.037 55.0 16.42 16.42 0.0 4.79 F
1227 2627 0.031111 ATCCGGGTGATCTTGAGGGA 60.031 55.0 0.00 0.00 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 2913 0.179056 CTTGACAAGGACGGTGTGGT 60.179 55.0 7.35 0.0 0.00 4.16 R
3203 7715 0.251787 AAAATGGTCACAGGGGAGCC 60.252 55.0 0.00 0.0 34.46 4.70 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
24 25 2.763651 CGAAAAACGGGCTCCTAGG 58.236 57.895 0.82 0.82 38.46 3.02
25 26 0.248289 CGAAAAACGGGCTCCTAGGA 59.752 55.000 11.98 11.98 38.46 2.94
26 27 1.735386 GAAAAACGGGCTCCTAGGAC 58.265 55.000 7.62 5.08 0.00 3.85
27 28 0.036671 AAAAACGGGCTCCTAGGACG 60.037 55.000 16.42 16.42 0.00 4.79
28 29 2.517484 AAAACGGGCTCCTAGGACGC 62.517 60.000 17.60 18.52 0.00 5.19
31 32 2.913060 GGGCTCCTAGGACGCGAT 60.913 66.667 15.93 0.00 0.00 4.58
32 33 2.499827 GGGCTCCTAGGACGCGATT 61.500 63.158 15.93 0.00 0.00 3.34
33 34 1.300233 GGCTCCTAGGACGCGATTG 60.300 63.158 15.93 7.20 0.00 2.67
34 35 1.300233 GCTCCTAGGACGCGATTGG 60.300 63.158 15.93 9.00 0.00 3.16
35 36 1.364171 CTCCTAGGACGCGATTGGG 59.636 63.158 15.93 9.27 0.00 4.12
36 37 1.380785 TCCTAGGACGCGATTGGGT 60.381 57.895 15.93 1.53 45.02 4.51
47 48 3.918102 GATTGGGTCGATTTTCGCC 57.082 52.632 0.00 0.00 40.21 5.54
52 53 1.641677 GGTCGATTTTCGCCCATCG 59.358 57.895 0.00 4.20 37.90 3.84
53 54 0.808453 GGTCGATTTTCGCCCATCGA 60.808 55.000 8.11 8.11 46.95 3.59
61 62 3.770625 TCGCCCATCGATGCTAAAA 57.229 47.368 20.25 0.97 43.16 1.52
62 63 2.031258 TCGCCCATCGATGCTAAAAA 57.969 45.000 20.25 0.00 43.16 1.94
63 64 2.571212 TCGCCCATCGATGCTAAAAAT 58.429 42.857 20.25 0.00 43.16 1.82
64 65 2.548057 TCGCCCATCGATGCTAAAAATC 59.452 45.455 20.25 1.48 43.16 2.17
65 66 2.290367 CGCCCATCGATGCTAAAAATCA 59.710 45.455 20.25 0.00 41.67 2.57
66 67 3.058016 CGCCCATCGATGCTAAAAATCAT 60.058 43.478 20.25 0.00 41.67 2.45
67 68 4.479619 GCCCATCGATGCTAAAAATCATC 58.520 43.478 20.25 0.00 36.60 2.92
68 69 4.217118 GCCCATCGATGCTAAAAATCATCT 59.783 41.667 20.25 0.00 37.52 2.90
69 70 5.696822 CCCATCGATGCTAAAAATCATCTG 58.303 41.667 20.25 0.94 37.52 2.90
70 71 5.335426 CCCATCGATGCTAAAAATCATCTGG 60.335 44.000 20.25 6.53 37.52 3.86
71 72 5.335426 CCATCGATGCTAAAAATCATCTGGG 60.335 44.000 20.25 0.00 37.52 4.45
72 73 4.136796 TCGATGCTAAAAATCATCTGGGG 58.863 43.478 0.00 0.00 37.52 4.96
73 74 4.136796 CGATGCTAAAAATCATCTGGGGA 58.863 43.478 0.00 0.00 37.52 4.81
74 75 4.214971 CGATGCTAAAAATCATCTGGGGAG 59.785 45.833 0.00 0.00 37.52 4.30
75 76 3.902218 TGCTAAAAATCATCTGGGGAGG 58.098 45.455 0.00 0.00 0.00 4.30
76 77 3.225940 GCTAAAAATCATCTGGGGAGGG 58.774 50.000 0.00 0.00 0.00 4.30
77 78 3.117512 GCTAAAAATCATCTGGGGAGGGA 60.118 47.826 0.00 0.00 0.00 4.20
78 79 3.388552 AAAAATCATCTGGGGAGGGAC 57.611 47.619 0.00 0.00 0.00 4.46
79 80 0.839946 AAATCATCTGGGGAGGGACG 59.160 55.000 0.00 0.00 0.00 4.79
80 81 0.326618 AATCATCTGGGGAGGGACGT 60.327 55.000 0.00 0.00 0.00 4.34
81 82 1.050988 ATCATCTGGGGAGGGACGTG 61.051 60.000 0.00 0.00 0.00 4.49
82 83 1.990060 CATCTGGGGAGGGACGTGT 60.990 63.158 0.00 0.00 0.00 4.49
83 84 1.229529 ATCTGGGGAGGGACGTGTT 60.230 57.895 0.00 0.00 0.00 3.32
84 85 1.553690 ATCTGGGGAGGGACGTGTTG 61.554 60.000 0.00 0.00 0.00 3.33
85 86 3.246112 TGGGGAGGGACGTGTTGG 61.246 66.667 0.00 0.00 0.00 3.77
86 87 4.029809 GGGGAGGGACGTGTTGGG 62.030 72.222 0.00 0.00 0.00 4.12
87 88 4.029809 GGGAGGGACGTGTTGGGG 62.030 72.222 0.00 0.00 0.00 4.96
88 89 4.029809 GGAGGGACGTGTTGGGGG 62.030 72.222 0.00 0.00 0.00 5.40
89 90 4.717313 GAGGGACGTGTTGGGGGC 62.717 72.222 0.00 0.00 0.00 5.80
102 103 4.899239 GGGGCGCGACTGGAGATG 62.899 72.222 13.91 0.00 0.00 2.90
104 105 4.521062 GGCGCGACTGGAGATGCT 62.521 66.667 12.10 0.00 0.00 3.79
105 106 2.959071 GCGCGACTGGAGATGCTC 60.959 66.667 12.10 0.00 0.00 4.26
106 107 2.804167 CGCGACTGGAGATGCTCT 59.196 61.111 0.00 0.00 0.00 4.09
107 108 1.140589 CGCGACTGGAGATGCTCTT 59.859 57.895 0.00 0.00 0.00 2.85
108 109 0.382158 CGCGACTGGAGATGCTCTTA 59.618 55.000 0.00 0.00 0.00 2.10
109 110 1.202302 CGCGACTGGAGATGCTCTTAA 60.202 52.381 0.00 0.00 0.00 1.85
110 111 2.197577 GCGACTGGAGATGCTCTTAAC 58.802 52.381 0.00 0.00 0.00 2.01
111 112 2.455032 CGACTGGAGATGCTCTTAACG 58.545 52.381 0.00 0.00 0.00 3.18
112 113 2.197577 GACTGGAGATGCTCTTAACGC 58.802 52.381 0.00 0.00 0.00 4.84
113 114 1.827969 ACTGGAGATGCTCTTAACGCT 59.172 47.619 0.00 0.00 0.00 5.07
114 115 2.159170 ACTGGAGATGCTCTTAACGCTC 60.159 50.000 0.00 0.00 0.00 5.03
115 116 2.100584 CTGGAGATGCTCTTAACGCTCT 59.899 50.000 0.00 0.00 0.00 4.09
116 117 2.099921 TGGAGATGCTCTTAACGCTCTC 59.900 50.000 0.00 0.00 34.18 3.20
117 118 2.544903 GGAGATGCTCTTAACGCTCTCC 60.545 54.545 16.11 16.11 40.78 3.71
118 119 1.066303 AGATGCTCTTAACGCTCTCCG 59.934 52.381 0.00 0.00 44.21 4.63
127 128 2.049156 CGCTCTCCGTGCAACTCA 60.049 61.111 0.00 0.00 31.75 3.41
128 129 2.375766 CGCTCTCCGTGCAACTCAC 61.376 63.158 0.00 0.00 42.23 3.51
129 130 2.029844 GCTCTCCGTGCAACTCACC 61.030 63.158 0.00 0.00 42.69 4.02
130 131 1.374758 CTCTCCGTGCAACTCACCC 60.375 63.158 0.00 0.00 42.69 4.61
131 132 1.821061 CTCTCCGTGCAACTCACCCT 61.821 60.000 0.00 0.00 42.69 4.34
132 133 0.541063 TCTCCGTGCAACTCACCCTA 60.541 55.000 0.00 0.00 42.69 3.53
133 134 0.108615 CTCCGTGCAACTCACCCTAG 60.109 60.000 0.00 0.00 42.69 3.02
134 135 1.741770 CCGTGCAACTCACCCTAGC 60.742 63.158 0.00 0.00 42.69 3.42
135 136 1.293498 CGTGCAACTCACCCTAGCT 59.707 57.895 0.00 0.00 42.69 3.32
136 137 0.737715 CGTGCAACTCACCCTAGCTC 60.738 60.000 0.00 0.00 42.69 4.09
137 138 0.321671 GTGCAACTCACCCTAGCTCA 59.678 55.000 0.00 0.00 39.79 4.26
138 139 0.321671 TGCAACTCACCCTAGCTCAC 59.678 55.000 0.00 0.00 0.00 3.51
139 140 0.321671 GCAACTCACCCTAGCTCACA 59.678 55.000 0.00 0.00 0.00 3.58
140 141 1.941668 GCAACTCACCCTAGCTCACAC 60.942 57.143 0.00 0.00 0.00 3.82
141 142 0.977395 AACTCACCCTAGCTCACACC 59.023 55.000 0.00 0.00 0.00 4.16
142 143 1.251527 ACTCACCCTAGCTCACACCG 61.252 60.000 0.00 0.00 0.00 4.94
143 144 0.965866 CTCACCCTAGCTCACACCGA 60.966 60.000 0.00 0.00 0.00 4.69
144 145 1.215647 CACCCTAGCTCACACCGAC 59.784 63.158 0.00 0.00 0.00 4.79
145 146 1.228769 ACCCTAGCTCACACCGACA 60.229 57.895 0.00 0.00 0.00 4.35
146 147 1.251527 ACCCTAGCTCACACCGACAG 61.252 60.000 0.00 0.00 0.00 3.51
147 148 0.965866 CCCTAGCTCACACCGACAGA 60.966 60.000 0.00 0.00 0.00 3.41
148 149 0.453793 CCTAGCTCACACCGACAGAG 59.546 60.000 0.00 0.00 0.00 3.35
149 150 1.454201 CTAGCTCACACCGACAGAGA 58.546 55.000 0.00 0.00 0.00 3.10
150 151 1.813178 CTAGCTCACACCGACAGAGAA 59.187 52.381 0.00 0.00 0.00 2.87
151 152 0.600557 AGCTCACACCGACAGAGAAG 59.399 55.000 0.00 0.00 0.00 2.85
152 153 0.389166 GCTCACACCGACAGAGAAGG 60.389 60.000 0.00 0.00 0.00 3.46
153 154 0.389166 CTCACACCGACAGAGAAGGC 60.389 60.000 0.00 0.00 0.00 4.35
154 155 1.112916 TCACACCGACAGAGAAGGCA 61.113 55.000 0.00 0.00 0.00 4.75
155 156 0.036952 CACACCGACAGAGAAGGCAT 60.037 55.000 0.00 0.00 0.00 4.40
156 157 0.247736 ACACCGACAGAGAAGGCATC 59.752 55.000 0.00 0.00 0.00 3.91
157 158 0.460987 CACCGACAGAGAAGGCATCC 60.461 60.000 0.00 0.00 0.00 3.51
158 159 0.904865 ACCGACAGAGAAGGCATCCA 60.905 55.000 0.00 0.00 0.00 3.41
174 175 0.179111 TCCATCGCGCTCTAACCTTG 60.179 55.000 5.56 0.00 0.00 3.61
226 227 1.893808 AGTTGGTGCTGCTCAACGG 60.894 57.895 22.93 0.00 45.47 4.44
248 249 3.755378 GCATCACCATATCAGATCCAACC 59.245 47.826 0.00 0.00 0.00 3.77
353 354 3.152341 AGGCTCAAGAAAACCATCAGTG 58.848 45.455 0.00 0.00 0.00 3.66
375 376 8.875803 CAGTGTGTCTACTTGTTTTTGTACTTA 58.124 33.333 0.00 0.00 0.00 2.24
460 463 2.410730 GTGCTTGCACGTATACGAAGTT 59.589 45.455 30.77 6.27 37.78 2.66
461 464 2.410392 TGCTTGCACGTATACGAAGTTG 59.590 45.455 30.77 18.93 37.78 3.16
538 1884 6.084326 ACACAATAATTCCGCAAAAACTCT 57.916 33.333 0.00 0.00 0.00 3.24
557 1903 9.760077 AAAACTCTTACGAGAAAATCTCTTACA 57.240 29.630 2.78 0.00 41.26 2.41
806 2176 7.307160 CGGCGAAGAATATCTTAAGCATACAAA 60.307 37.037 0.00 0.00 40.01 2.83
861 2238 1.134580 CACCACCACTAGAGCCATCAG 60.135 57.143 0.00 0.00 0.00 2.90
877 2254 2.275134 TCAGCACATCAAAGAGGCAA 57.725 45.000 0.00 0.00 0.00 4.52
878 2255 2.799017 TCAGCACATCAAAGAGGCAAT 58.201 42.857 0.00 0.00 0.00 3.56
922 2299 2.420372 GCTTGGCTTTCCAGCTAGTAAC 59.580 50.000 0.00 0.00 46.44 2.50
931 2308 3.165875 TCCAGCTAGTAACTCAGCTTGT 58.834 45.455 0.00 0.00 45.80 3.16
970 2352 1.414181 CAGGTGATACAGATCGGCCTT 59.586 52.381 0.00 0.00 37.74 4.35
1227 2627 0.031111 ATCCGGGTGATCTTGAGGGA 60.031 55.000 0.00 0.00 0.00 4.20
1268 2672 0.179108 CCTCTCACCGAACCGATTCC 60.179 60.000 0.00 0.00 0.00 3.01
1801 3206 9.817365 GATTAATGCACATCTCATTACATGTAC 57.183 33.333 4.68 0.00 36.47 2.90
1802 3207 8.962884 TTAATGCACATCTCATTACATGTACT 57.037 30.769 4.68 0.00 36.47 2.73
1803 3208 6.856135 ATGCACATCTCATTACATGTACTG 57.144 37.500 15.22 15.22 31.78 2.74
1805 3210 6.872920 TGCACATCTCATTACATGTACTGTA 58.127 36.000 19.26 11.48 39.39 2.74
1806 3211 7.500141 TGCACATCTCATTACATGTACTGTAT 58.500 34.615 19.26 12.87 40.02 2.29
1807 3212 7.439056 TGCACATCTCATTACATGTACTGTATG 59.561 37.037 23.56 23.56 40.02 2.39
1808 3213 7.439356 GCACATCTCATTACATGTACTGTATGT 59.561 37.037 24.33 24.33 40.02 2.29
1809 3214 9.317936 CACATCTCATTACATGTACTGTATGTT 57.682 33.333 25.81 16.96 40.02 2.71
1906 3342 2.726760 GTGACAGTTCAGTGTGATCGAC 59.273 50.000 0.00 0.00 30.10 4.20
2215 4863 1.218316 GTCGGCTTCATCCTCGGTT 59.782 57.895 0.00 0.00 0.00 4.44
2220 4868 0.678048 GCTTCATCCTCGGTTTGGCT 60.678 55.000 0.00 0.00 0.00 4.75
2259 4907 1.204704 TCACTGTACGGCAAGATCCAG 59.795 52.381 0.23 0.00 0.00 3.86
2323 4971 2.116238 TGCTTGGTATCCTCCAGGTAC 58.884 52.381 0.00 0.00 38.80 3.34
2324 4972 2.292918 TGCTTGGTATCCTCCAGGTACT 60.293 50.000 0.00 0.00 38.80 2.73
2703 5355 1.205820 CTGCGACGACGTACTGACA 59.794 57.895 9.33 0.00 41.98 3.58
2764 5416 7.039313 AGGCCCTATTATTTTCATTCGTTTC 57.961 36.000 0.00 0.00 0.00 2.78
2965 7161 4.273318 CTTGTTCAGCTAATTTAGGGGCT 58.727 43.478 5.61 0.00 35.23 5.19
2966 7162 5.437060 CTTGTTCAGCTAATTTAGGGGCTA 58.563 41.667 5.61 0.00 33.43 3.93
2967 7163 5.646692 TGTTCAGCTAATTTAGGGGCTAT 57.353 39.130 5.61 0.00 33.43 2.97
2970 7166 6.546034 TGTTCAGCTAATTTAGGGGCTATTTC 59.454 38.462 5.61 0.00 33.43 2.17
2971 7167 6.515512 TCAGCTAATTTAGGGGCTATTTCT 57.484 37.500 5.61 0.00 33.43 2.52
2972 7168 6.911308 TCAGCTAATTTAGGGGCTATTTCTT 58.089 36.000 5.61 0.00 33.43 2.52
2973 7169 6.772716 TCAGCTAATTTAGGGGCTATTTCTTG 59.227 38.462 5.61 0.00 33.43 3.02
2974 7170 6.547510 CAGCTAATTTAGGGGCTATTTCTTGT 59.452 38.462 5.61 0.00 33.43 3.16
2976 7172 7.285629 AGCTAATTTAGGGGCTATTTCTTGTTC 59.714 37.037 5.61 0.00 32.94 3.18
2990 7490 9.231297 CTATTTCTTGTTCCCTTGTCTATTTCA 57.769 33.333 0.00 0.00 0.00 2.69
2991 7491 7.889873 TTTCTTGTTCCCTTGTCTATTTCAA 57.110 32.000 0.00 0.00 0.00 2.69
2992 7492 7.889873 TTCTTGTTCCCTTGTCTATTTCAAA 57.110 32.000 0.00 0.00 0.00 2.69
2993 7493 7.889873 TCTTGTTCCCTTGTCTATTTCAAAA 57.110 32.000 0.00 0.00 0.00 2.44
2994 7494 8.299990 TCTTGTTCCCTTGTCTATTTCAAAAA 57.700 30.769 0.00 0.00 0.00 1.94
2995 7495 8.923270 TCTTGTTCCCTTGTCTATTTCAAAAAT 58.077 29.630 0.00 0.00 0.00 1.82
2996 7496 8.885494 TTGTTCCCTTGTCTATTTCAAAAATG 57.115 30.769 0.00 0.00 0.00 2.32
2997 7497 6.928492 TGTTCCCTTGTCTATTTCAAAAATGC 59.072 34.615 0.00 0.00 0.00 3.56
2998 7498 6.916360 TCCCTTGTCTATTTCAAAAATGCT 57.084 33.333 0.00 0.00 0.00 3.79
2999 7499 6.924111 TCCCTTGTCTATTTCAAAAATGCTC 58.076 36.000 0.00 0.00 0.00 4.26
3000 7500 6.071391 TCCCTTGTCTATTTCAAAAATGCTCC 60.071 38.462 0.00 0.00 0.00 4.70
3001 7501 6.101997 CCTTGTCTATTTCAAAAATGCTCCC 58.898 40.000 0.00 0.00 0.00 4.30
3002 7502 5.659440 TGTCTATTTCAAAAATGCTCCCC 57.341 39.130 0.00 0.00 0.00 4.81
3003 7503 5.332743 TGTCTATTTCAAAAATGCTCCCCT 58.667 37.500 0.00 0.00 0.00 4.79
3004 7504 5.185635 TGTCTATTTCAAAAATGCTCCCCTG 59.814 40.000 0.00 0.00 0.00 4.45
3005 7505 2.837532 TTTCAAAAATGCTCCCCTGC 57.162 45.000 0.00 0.00 0.00 4.85
3006 7506 0.602562 TTCAAAAATGCTCCCCTGCG 59.397 50.000 0.00 0.00 35.36 5.18
3007 7507 0.251121 TCAAAAATGCTCCCCTGCGA 60.251 50.000 0.00 0.00 35.36 5.10
3008 7508 0.819582 CAAAAATGCTCCCCTGCGAT 59.180 50.000 0.00 0.00 35.36 4.58
3009 7509 1.205417 CAAAAATGCTCCCCTGCGATT 59.795 47.619 0.00 0.00 35.36 3.34
3010 7510 1.106285 AAAATGCTCCCCTGCGATTC 58.894 50.000 0.00 0.00 35.36 2.52
3011 7511 0.257039 AAATGCTCCCCTGCGATTCT 59.743 50.000 0.00 0.00 35.36 2.40
3012 7512 1.131638 AATGCTCCCCTGCGATTCTA 58.868 50.000 0.00 0.00 35.36 2.10
3013 7513 1.131638 ATGCTCCCCTGCGATTCTAA 58.868 50.000 0.00 0.00 35.36 2.10
3014 7514 0.908910 TGCTCCCCTGCGATTCTAAA 59.091 50.000 0.00 0.00 35.36 1.85
3015 7515 1.280710 TGCTCCCCTGCGATTCTAAAA 59.719 47.619 0.00 0.00 35.36 1.52
3016 7516 2.290641 TGCTCCCCTGCGATTCTAAAAA 60.291 45.455 0.00 0.00 35.36 1.94
3055 7555 7.147976 ACATTTGTCTATTTTCCTTGTTCAGC 58.852 34.615 0.00 0.00 0.00 4.26
3056 7556 6.959639 TTTGTCTATTTTCCTTGTTCAGCT 57.040 33.333 0.00 0.00 0.00 4.24
3057 7557 8.514594 CATTTGTCTATTTTCCTTGTTCAGCTA 58.485 33.333 0.00 0.00 0.00 3.32
3058 7558 8.458573 TTTGTCTATTTTCCTTGTTCAGCTAA 57.541 30.769 0.00 0.00 0.00 3.09
3059 7559 8.635765 TTGTCTATTTTCCTTGTTCAGCTAAT 57.364 30.769 0.00 0.00 0.00 1.73
3060 7560 8.635765 TGTCTATTTTCCTTGTTCAGCTAATT 57.364 30.769 0.00 0.00 0.00 1.40
3061 7561 9.077885 TGTCTATTTTCCTTGTTCAGCTAATTT 57.922 29.630 0.00 0.00 0.00 1.82
3065 7565 6.834168 TTTCCTTGTTCAGCTAATTTAGGG 57.166 37.500 5.61 0.00 0.00 3.53
3066 7566 4.855340 TCCTTGTTCAGCTAATTTAGGGG 58.145 43.478 5.61 0.00 0.00 4.79
3067 7567 3.381590 CCTTGTTCAGCTAATTTAGGGGC 59.618 47.826 5.61 0.00 0.00 5.80
3068 7568 4.273318 CTTGTTCAGCTAATTTAGGGGCT 58.727 43.478 5.61 0.00 35.23 5.19
3069 7569 4.316025 TGTTCAGCTAATTTAGGGGCTT 57.684 40.909 5.61 0.00 32.30 4.35
3070 7570 5.444744 TGTTCAGCTAATTTAGGGGCTTA 57.555 39.130 5.61 0.00 32.30 3.09
3071 7571 6.013554 TGTTCAGCTAATTTAGGGGCTTAT 57.986 37.500 5.61 0.00 32.30 1.73
3072 7572 6.431722 TGTTCAGCTAATTTAGGGGCTTATT 58.568 36.000 5.61 0.00 32.30 1.40
3073 7573 6.546034 TGTTCAGCTAATTTAGGGGCTTATTC 59.454 38.462 5.61 0.00 32.30 1.75
3074 7574 5.631119 TCAGCTAATTTAGGGGCTTATTCC 58.369 41.667 5.61 0.00 32.30 3.01
3075 7575 5.133660 TCAGCTAATTTAGGGGCTTATTCCA 59.866 40.000 5.61 0.00 32.30 3.53
3076 7576 5.833131 CAGCTAATTTAGGGGCTTATTCCAA 59.167 40.000 5.61 0.00 32.30 3.53
3077 7577 6.323739 CAGCTAATTTAGGGGCTTATTCCAAA 59.676 38.462 5.61 0.00 32.30 3.28
3078 7578 6.900743 AGCTAATTTAGGGGCTTATTCCAAAA 59.099 34.615 5.61 0.00 0.00 2.44
3079 7579 7.401782 AGCTAATTTAGGGGCTTATTCCAAAAA 59.598 33.333 5.61 0.00 0.00 1.94
3102 7602 9.764363 AAAAACTCTCTTGTTCATTATTTTCCC 57.236 29.630 0.00 0.00 0.00 3.97
3103 7603 8.712228 AAACTCTCTTGTTCATTATTTTCCCT 57.288 30.769 0.00 0.00 0.00 4.20
3104 7604 8.712228 AACTCTCTTGTTCATTATTTTCCCTT 57.288 30.769 0.00 0.00 0.00 3.95
3105 7605 8.115490 ACTCTCTTGTTCATTATTTTCCCTTG 57.885 34.615 0.00 0.00 0.00 3.61
3106 7606 7.725844 ACTCTCTTGTTCATTATTTTCCCTTGT 59.274 33.333 0.00 0.00 0.00 3.16
3107 7607 8.110860 TCTCTTGTTCATTATTTTCCCTTGTC 57.889 34.615 0.00 0.00 0.00 3.18
3108 7608 7.944554 TCTCTTGTTCATTATTTTCCCTTGTCT 59.055 33.333 0.00 0.00 0.00 3.41
3109 7609 8.110860 TCTTGTTCATTATTTTCCCTTGTCTC 57.889 34.615 0.00 0.00 0.00 3.36
3110 7610 7.944554 TCTTGTTCATTATTTTCCCTTGTCTCT 59.055 33.333 0.00 0.00 0.00 3.10
3111 7611 8.477419 TTGTTCATTATTTTCCCTTGTCTCTT 57.523 30.769 0.00 0.00 0.00 2.85
3112 7612 8.477419 TGTTCATTATTTTCCCTTGTCTCTTT 57.523 30.769 0.00 0.00 0.00 2.52
3113 7613 8.576442 TGTTCATTATTTTCCCTTGTCTCTTTC 58.424 33.333 0.00 0.00 0.00 2.62
3114 7614 8.797438 GTTCATTATTTTCCCTTGTCTCTTTCT 58.203 33.333 0.00 0.00 0.00 2.52
3115 7615 8.940397 TCATTATTTTCCCTTGTCTCTTTCTT 57.060 30.769 0.00 0.00 0.00 2.52
3116 7616 8.796475 TCATTATTTTCCCTTGTCTCTTTCTTG 58.204 33.333 0.00 0.00 0.00 3.02
3274 7817 4.619336 GCAAACTTTTCTCAAAACACGTGA 59.381 37.500 25.01 0.00 0.00 4.35
3275 7818 5.117897 GCAAACTTTTCTCAAAACACGTGAA 59.882 36.000 25.01 0.19 0.00 3.18
3276 7819 6.513317 CAAACTTTTCTCAAAACACGTGAAC 58.487 36.000 25.01 0.00 0.00 3.18
3277 7820 5.622770 ACTTTTCTCAAAACACGTGAACT 57.377 34.783 25.01 2.85 0.00 3.01
3278 7821 6.009115 ACTTTTCTCAAAACACGTGAACTT 57.991 33.333 25.01 9.46 0.00 2.66
3279 7822 6.443792 ACTTTTCTCAAAACACGTGAACTTT 58.556 32.000 25.01 14.93 0.00 2.66
3280 7823 6.921307 ACTTTTCTCAAAACACGTGAACTTTT 59.079 30.769 25.01 15.56 0.00 2.27
3281 7824 7.436970 ACTTTTCTCAAAACACGTGAACTTTTT 59.563 29.630 25.01 15.18 0.00 1.94
3411 7954 5.308825 ACTCCTTCTCAAATTCGTGAATGT 58.691 37.500 0.00 0.00 0.00 2.71
3689 8236 8.716909 CAAACCCGCAATAAAATTGATAAACTT 58.283 29.630 3.86 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.674084 GGAGCCCGTTTTTCGTCGG 61.674 63.158 0.00 0.00 45.42 4.79
3 4 0.388907 TAGGAGCCCGTTTTTCGTCG 60.389 55.000 0.00 0.00 37.94 5.12
4 5 1.356938 CTAGGAGCCCGTTTTTCGTC 58.643 55.000 0.00 0.00 37.94 4.20
5 6 0.036671 CCTAGGAGCCCGTTTTTCGT 60.037 55.000 1.05 0.00 37.94 3.85
6 7 0.248289 TCCTAGGAGCCCGTTTTTCG 59.752 55.000 7.62 0.00 39.52 3.46
7 8 1.735386 GTCCTAGGAGCCCGTTTTTC 58.265 55.000 13.15 0.00 0.00 2.29
8 9 0.036671 CGTCCTAGGAGCCCGTTTTT 60.037 55.000 13.15 0.00 0.00 1.94
9 10 1.595357 CGTCCTAGGAGCCCGTTTT 59.405 57.895 13.15 0.00 0.00 2.43
10 11 3.015312 GCGTCCTAGGAGCCCGTTT 62.015 63.158 13.15 0.00 0.00 3.60
11 12 3.459063 GCGTCCTAGGAGCCCGTT 61.459 66.667 13.15 0.00 0.00 4.44
14 15 2.499827 AATCGCGTCCTAGGAGCCC 61.500 63.158 13.15 0.00 0.00 5.19
15 16 1.300233 CAATCGCGTCCTAGGAGCC 60.300 63.158 13.15 5.06 0.00 4.70
16 17 1.300233 CCAATCGCGTCCTAGGAGC 60.300 63.158 13.15 16.41 0.00 4.70
17 18 1.364171 CCCAATCGCGTCCTAGGAG 59.636 63.158 13.15 7.79 0.00 3.69
18 19 1.380785 ACCCAATCGCGTCCTAGGA 60.381 57.895 7.62 7.62 0.00 2.94
19 20 1.067582 GACCCAATCGCGTCCTAGG 59.932 63.158 5.77 0.82 0.00 3.02
20 21 1.299165 CGACCCAATCGCGTCCTAG 60.299 63.158 5.77 0.00 45.52 3.02
21 22 2.802792 CGACCCAATCGCGTCCTA 59.197 61.111 5.77 0.00 45.52 2.94
29 30 3.918102 GGCGAAAATCGACCCAATC 57.082 52.632 3.61 0.00 43.36 2.67
44 45 2.290367 TGATTTTTAGCATCGATGGGCG 59.710 45.455 26.00 1.57 42.69 6.13
45 46 3.988379 TGATTTTTAGCATCGATGGGC 57.012 42.857 26.00 13.34 0.00 5.36
46 47 5.335426 CCAGATGATTTTTAGCATCGATGGG 60.335 44.000 26.00 9.94 44.23 4.00
47 48 5.335426 CCCAGATGATTTTTAGCATCGATGG 60.335 44.000 26.00 8.82 44.23 3.51
48 49 5.335426 CCCCAGATGATTTTTAGCATCGATG 60.335 44.000 21.27 21.27 44.23 3.84
49 50 4.763793 CCCCAGATGATTTTTAGCATCGAT 59.236 41.667 0.00 0.00 44.23 3.59
50 51 4.136796 CCCCAGATGATTTTTAGCATCGA 58.863 43.478 0.00 0.00 44.23 3.59
51 52 4.136796 TCCCCAGATGATTTTTAGCATCG 58.863 43.478 0.00 0.00 44.23 3.84
52 53 4.522022 CCTCCCCAGATGATTTTTAGCATC 59.478 45.833 0.00 0.00 40.85 3.91
53 54 4.477249 CCTCCCCAGATGATTTTTAGCAT 58.523 43.478 0.00 0.00 0.00 3.79
54 55 3.373001 CCCTCCCCAGATGATTTTTAGCA 60.373 47.826 0.00 0.00 0.00 3.49
55 56 3.117512 TCCCTCCCCAGATGATTTTTAGC 60.118 47.826 0.00 0.00 0.00 3.09
56 57 4.464947 GTCCCTCCCCAGATGATTTTTAG 58.535 47.826 0.00 0.00 0.00 1.85
57 58 3.118038 CGTCCCTCCCCAGATGATTTTTA 60.118 47.826 0.00 0.00 0.00 1.52
58 59 2.357154 CGTCCCTCCCCAGATGATTTTT 60.357 50.000 0.00 0.00 0.00 1.94
59 60 1.212935 CGTCCCTCCCCAGATGATTTT 59.787 52.381 0.00 0.00 0.00 1.82
60 61 0.839946 CGTCCCTCCCCAGATGATTT 59.160 55.000 0.00 0.00 0.00 2.17
61 62 0.326618 ACGTCCCTCCCCAGATGATT 60.327 55.000 0.00 0.00 0.00 2.57
62 63 1.050988 CACGTCCCTCCCCAGATGAT 61.051 60.000 0.00 0.00 0.00 2.45
63 64 1.685765 CACGTCCCTCCCCAGATGA 60.686 63.158 0.00 0.00 0.00 2.92
64 65 1.553690 AACACGTCCCTCCCCAGATG 61.554 60.000 0.00 0.00 0.00 2.90
65 66 1.229529 AACACGTCCCTCCCCAGAT 60.230 57.895 0.00 0.00 0.00 2.90
66 67 2.203182 AACACGTCCCTCCCCAGA 59.797 61.111 0.00 0.00 0.00 3.86
67 68 2.347490 CAACACGTCCCTCCCCAG 59.653 66.667 0.00 0.00 0.00 4.45
68 69 3.246112 CCAACACGTCCCTCCCCA 61.246 66.667 0.00 0.00 0.00 4.96
69 70 4.029809 CCCAACACGTCCCTCCCC 62.030 72.222 0.00 0.00 0.00 4.81
70 71 4.029809 CCCCAACACGTCCCTCCC 62.030 72.222 0.00 0.00 0.00 4.30
71 72 4.029809 CCCCCAACACGTCCCTCC 62.030 72.222 0.00 0.00 0.00 4.30
72 73 4.717313 GCCCCCAACACGTCCCTC 62.717 72.222 0.00 0.00 0.00 4.30
85 86 4.899239 CATCTCCAGTCGCGCCCC 62.899 72.222 0.00 0.00 0.00 5.80
87 88 4.521062 AGCATCTCCAGTCGCGCC 62.521 66.667 0.00 0.00 0.00 6.53
88 89 2.959071 GAGCATCTCCAGTCGCGC 60.959 66.667 0.00 0.00 0.00 6.86
99 100 1.202313 ACGGAGAGCGTTAAGAGCATC 60.202 52.381 5.76 3.52 37.01 3.91
100 101 0.818296 ACGGAGAGCGTTAAGAGCAT 59.182 50.000 5.76 0.00 37.01 3.79
101 102 0.109272 CACGGAGAGCGTTAAGAGCA 60.109 55.000 5.76 0.00 37.01 4.26
102 103 1.414527 GCACGGAGAGCGTTAAGAGC 61.415 60.000 0.00 0.00 32.66 4.09
103 104 2.654939 GCACGGAGAGCGTTAAGAG 58.345 57.895 0.00 0.00 32.66 2.85
104 105 4.883026 GCACGGAGAGCGTTAAGA 57.117 55.556 0.00 0.00 32.66 2.10
111 112 3.555428 GTGAGTTGCACGGAGAGC 58.445 61.111 0.00 0.00 46.44 4.09
118 119 0.321671 TGAGCTAGGGTGAGTTGCAC 59.678 55.000 0.00 0.00 46.98 4.57
119 120 0.321671 GTGAGCTAGGGTGAGTTGCA 59.678 55.000 0.00 0.00 0.00 4.08
120 121 0.321671 TGTGAGCTAGGGTGAGTTGC 59.678 55.000 0.00 0.00 0.00 4.17
121 122 1.338200 GGTGTGAGCTAGGGTGAGTTG 60.338 57.143 0.00 0.00 0.00 3.16
122 123 0.977395 GGTGTGAGCTAGGGTGAGTT 59.023 55.000 0.00 0.00 0.00 3.01
123 124 1.251527 CGGTGTGAGCTAGGGTGAGT 61.252 60.000 0.00 0.00 0.00 3.41
124 125 0.965866 TCGGTGTGAGCTAGGGTGAG 60.966 60.000 0.00 0.00 0.00 3.51
125 126 1.076014 TCGGTGTGAGCTAGGGTGA 59.924 57.895 0.00 0.00 0.00 4.02
126 127 1.215647 GTCGGTGTGAGCTAGGGTG 59.784 63.158 0.00 0.00 0.00 4.61
127 128 1.228769 TGTCGGTGTGAGCTAGGGT 60.229 57.895 0.00 0.00 0.00 4.34
128 129 0.965866 TCTGTCGGTGTGAGCTAGGG 60.966 60.000 0.00 0.00 0.00 3.53
129 130 0.453793 CTCTGTCGGTGTGAGCTAGG 59.546 60.000 0.00 0.00 0.00 3.02
130 131 1.454201 TCTCTGTCGGTGTGAGCTAG 58.546 55.000 0.00 0.00 0.00 3.42
131 132 1.813178 CTTCTCTGTCGGTGTGAGCTA 59.187 52.381 0.00 0.00 0.00 3.32
132 133 0.600557 CTTCTCTGTCGGTGTGAGCT 59.399 55.000 0.00 0.00 0.00 4.09
133 134 0.389166 CCTTCTCTGTCGGTGTGAGC 60.389 60.000 0.00 0.00 0.00 4.26
134 135 0.389166 GCCTTCTCTGTCGGTGTGAG 60.389 60.000 0.00 0.00 0.00 3.51
135 136 1.112916 TGCCTTCTCTGTCGGTGTGA 61.113 55.000 0.00 0.00 0.00 3.58
136 137 0.036952 ATGCCTTCTCTGTCGGTGTG 60.037 55.000 0.00 0.00 0.00 3.82
137 138 0.247736 GATGCCTTCTCTGTCGGTGT 59.752 55.000 0.00 0.00 0.00 4.16
138 139 0.460987 GGATGCCTTCTCTGTCGGTG 60.461 60.000 0.00 0.00 0.00 4.94
139 140 0.904865 TGGATGCCTTCTCTGTCGGT 60.905 55.000 0.00 0.00 0.00 4.69
140 141 0.467384 ATGGATGCCTTCTCTGTCGG 59.533 55.000 0.00 0.00 0.00 4.79
141 142 1.863267 GATGGATGCCTTCTCTGTCG 58.137 55.000 0.00 0.00 0.00 4.35
142 143 1.863267 CGATGGATGCCTTCTCTGTC 58.137 55.000 0.00 0.00 0.00 3.51
143 144 0.179062 GCGATGGATGCCTTCTCTGT 60.179 55.000 0.00 0.00 0.00 3.41
144 145 1.220169 CGCGATGGATGCCTTCTCTG 61.220 60.000 0.00 0.00 0.00 3.35
145 146 1.068753 CGCGATGGATGCCTTCTCT 59.931 57.895 0.00 0.00 0.00 3.10
146 147 2.602322 GCGCGATGGATGCCTTCTC 61.602 63.158 12.10 0.00 0.00 2.87
147 148 2.590007 GCGCGATGGATGCCTTCT 60.590 61.111 12.10 0.00 0.00 2.85
148 149 2.590007 AGCGCGATGGATGCCTTC 60.590 61.111 12.10 0.00 0.00 3.46
149 150 1.748329 TAGAGCGCGATGGATGCCTT 61.748 55.000 12.10 0.00 0.00 4.35
150 151 1.748329 TTAGAGCGCGATGGATGCCT 61.748 55.000 12.10 0.00 0.00 4.75
151 152 1.300931 TTAGAGCGCGATGGATGCC 60.301 57.895 12.10 0.00 0.00 4.40
152 153 1.560860 GGTTAGAGCGCGATGGATGC 61.561 60.000 12.10 0.00 0.00 3.91
153 154 0.032678 AGGTTAGAGCGCGATGGATG 59.967 55.000 12.10 0.00 0.00 3.51
154 155 0.753262 AAGGTTAGAGCGCGATGGAT 59.247 50.000 12.10 0.00 0.00 3.41
155 156 0.179111 CAAGGTTAGAGCGCGATGGA 60.179 55.000 12.10 0.00 0.00 3.41
156 157 1.766143 GCAAGGTTAGAGCGCGATGG 61.766 60.000 12.10 0.00 0.00 3.51
157 158 1.638467 GCAAGGTTAGAGCGCGATG 59.362 57.895 12.10 0.00 0.00 3.84
158 159 4.110493 GCAAGGTTAGAGCGCGAT 57.890 55.556 12.10 1.23 0.00 4.58
226 227 3.755378 GGTTGGATCTGATATGGTGATGC 59.245 47.826 0.00 0.00 0.00 3.91
248 249 0.667993 ACACCATCCAACAAACGCTG 59.332 50.000 0.00 0.00 0.00 5.18
460 463 7.336931 GGCTCTTATCTTATTGACTGGAAAACA 59.663 37.037 0.00 0.00 0.00 2.83
461 464 7.201741 GGGCTCTTATCTTATTGACTGGAAAAC 60.202 40.741 0.00 0.00 0.00 2.43
484 488 1.202627 TGGTCTTGCAAACAAATGGGC 60.203 47.619 0.00 0.00 34.74 5.36
508 512 3.493129 TGCGGAATTATTGTGTATCTCGC 59.507 43.478 0.00 0.00 39.84 5.03
806 2176 2.661866 GACGGACGCAGCTTGTGT 60.662 61.111 2.60 2.60 44.78 3.72
861 2238 1.820519 TCCATTGCCTCTTTGATGTGC 59.179 47.619 0.00 0.00 0.00 4.57
922 2299 0.242825 TAACCGGACGACAAGCTGAG 59.757 55.000 9.46 0.00 0.00 3.35
931 2308 2.345760 GGAGCCAGTAACCGGACGA 61.346 63.158 9.46 0.00 0.00 4.20
970 2352 3.636313 GATCCACCGACGCCGTGAA 62.636 63.158 0.00 0.00 0.00 3.18
1268 2672 1.429825 CGTACTGGAGGAGACAGCG 59.570 63.158 0.00 0.00 39.55 5.18
1509 2913 0.179056 CTTGACAAGGACGGTGTGGT 60.179 55.000 7.35 0.00 0.00 4.16
1761 3166 4.463515 CATTAATCATGCACGAGGTGAG 57.536 45.455 0.00 0.00 35.23 3.51
1801 3206 6.441274 AGCAACAGTTTCATCAAACATACAG 58.559 36.000 0.00 0.00 43.98 2.74
1802 3207 6.389830 AGCAACAGTTTCATCAAACATACA 57.610 33.333 0.00 0.00 43.98 2.29
1803 3208 6.917477 TGAAGCAACAGTTTCATCAAACATAC 59.083 34.615 0.00 0.00 43.98 2.39
1805 3210 5.904941 TGAAGCAACAGTTTCATCAAACAT 58.095 33.333 0.00 0.00 43.98 2.71
1806 3211 5.321959 TGAAGCAACAGTTTCATCAAACA 57.678 34.783 0.00 0.00 43.98 2.83
1807 3212 5.878261 CTGAAGCAACAGTTTCATCAAAC 57.122 39.130 0.00 0.00 42.14 2.93
1955 4598 4.526262 ACTGCACTAATGGTTAAAATGCCA 59.474 37.500 0.00 0.00 39.33 4.92
2215 4863 4.892965 AGCCACAACGCCAGCCAA 62.893 61.111 0.00 0.00 0.00 4.52
2220 4868 1.836999 ATACTCCAGCCACAACGCCA 61.837 55.000 0.00 0.00 0.00 5.69
2259 4907 1.945394 CTATGTGCTGGAACATCTGCC 59.055 52.381 0.00 0.00 41.09 4.85
2687 5339 0.633733 CATTGTCAGTACGTCGTCGC 59.366 55.000 0.00 0.00 41.18 5.19
2703 5355 4.373156 ACAAGAACCCTAGTCAAGCATT 57.627 40.909 0.00 0.00 0.00 3.56
2764 5416 5.695851 ACAACAACAGCATAAGAAGAAGG 57.304 39.130 0.00 0.00 0.00 3.46
2965 7161 9.581289 TTGAAATAGACAAGGGAACAAGAAATA 57.419 29.630 0.00 0.00 0.00 1.40
2966 7162 8.477419 TTGAAATAGACAAGGGAACAAGAAAT 57.523 30.769 0.00 0.00 0.00 2.17
2967 7163 7.889873 TTGAAATAGACAAGGGAACAAGAAA 57.110 32.000 0.00 0.00 0.00 2.52
2970 7166 8.981647 CATTTTTGAAATAGACAAGGGAACAAG 58.018 33.333 0.00 0.00 0.00 3.16
2971 7167 7.440856 GCATTTTTGAAATAGACAAGGGAACAA 59.559 33.333 0.00 0.00 0.00 2.83
2972 7168 6.928492 GCATTTTTGAAATAGACAAGGGAACA 59.072 34.615 0.00 0.00 0.00 3.18
2973 7169 7.154656 AGCATTTTTGAAATAGACAAGGGAAC 58.845 34.615 0.00 0.00 0.00 3.62
2974 7170 7.301868 AGCATTTTTGAAATAGACAAGGGAA 57.698 32.000 0.00 0.00 0.00 3.97
2976 7172 6.101997 GGAGCATTTTTGAAATAGACAAGGG 58.898 40.000 0.00 0.00 0.00 3.95
2990 7490 1.478105 GAATCGCAGGGGAGCATTTTT 59.522 47.619 0.00 0.00 0.00 1.94
2991 7491 1.106285 GAATCGCAGGGGAGCATTTT 58.894 50.000 0.00 0.00 0.00 1.82
2992 7492 0.257039 AGAATCGCAGGGGAGCATTT 59.743 50.000 0.00 0.00 0.00 2.32
2993 7493 1.131638 TAGAATCGCAGGGGAGCATT 58.868 50.000 0.00 0.00 0.00 3.56
2994 7494 1.131638 TTAGAATCGCAGGGGAGCAT 58.868 50.000 0.00 0.00 0.00 3.79
2995 7495 0.908910 TTTAGAATCGCAGGGGAGCA 59.091 50.000 0.00 0.00 0.00 4.26
2996 7496 2.038387 TTTTAGAATCGCAGGGGAGC 57.962 50.000 0.00 0.00 0.00 4.70
3029 7529 8.296713 GCTGAACAAGGAAAATAGACAAATGTA 58.703 33.333 0.00 0.00 0.00 2.29
3030 7530 7.014615 AGCTGAACAAGGAAAATAGACAAATGT 59.985 33.333 0.00 0.00 0.00 2.71
3031 7531 7.373493 AGCTGAACAAGGAAAATAGACAAATG 58.627 34.615 0.00 0.00 0.00 2.32
3032 7532 7.530426 AGCTGAACAAGGAAAATAGACAAAT 57.470 32.000 0.00 0.00 0.00 2.32
3033 7533 6.959639 AGCTGAACAAGGAAAATAGACAAA 57.040 33.333 0.00 0.00 0.00 2.83
3034 7534 8.635765 ATTAGCTGAACAAGGAAAATAGACAA 57.364 30.769 0.00 0.00 0.00 3.18
3035 7535 8.635765 AATTAGCTGAACAAGGAAAATAGACA 57.364 30.769 0.00 0.00 0.00 3.41
3039 7539 8.966868 CCCTAAATTAGCTGAACAAGGAAAATA 58.033 33.333 0.00 0.00 0.00 1.40
3040 7540 7.093333 CCCCTAAATTAGCTGAACAAGGAAAAT 60.093 37.037 0.00 0.00 0.00 1.82
3041 7541 6.210584 CCCCTAAATTAGCTGAACAAGGAAAA 59.789 38.462 0.00 0.00 0.00 2.29
3042 7542 5.714806 CCCCTAAATTAGCTGAACAAGGAAA 59.285 40.000 0.00 0.00 0.00 3.13
3043 7543 5.261216 CCCCTAAATTAGCTGAACAAGGAA 58.739 41.667 0.00 0.00 0.00 3.36
3044 7544 4.855340 CCCCTAAATTAGCTGAACAAGGA 58.145 43.478 0.00 0.00 0.00 3.36
3045 7545 3.381590 GCCCCTAAATTAGCTGAACAAGG 59.618 47.826 0.00 0.00 0.00 3.61
3046 7546 4.273318 AGCCCCTAAATTAGCTGAACAAG 58.727 43.478 0.00 0.00 33.41 3.16
3047 7547 4.316025 AGCCCCTAAATTAGCTGAACAA 57.684 40.909 0.00 0.00 33.41 2.83
3048 7548 4.316025 AAGCCCCTAAATTAGCTGAACA 57.684 40.909 0.00 0.00 35.30 3.18
3049 7549 6.016192 GGAATAAGCCCCTAAATTAGCTGAAC 60.016 42.308 0.00 0.00 35.30 3.18
3050 7550 6.068670 GGAATAAGCCCCTAAATTAGCTGAA 58.931 40.000 0.00 0.00 35.30 3.02
3051 7551 5.133660 TGGAATAAGCCCCTAAATTAGCTGA 59.866 40.000 0.00 0.00 35.30 4.26
3052 7552 5.385198 TGGAATAAGCCCCTAAATTAGCTG 58.615 41.667 0.00 0.00 35.30 4.24
3053 7553 5.663158 TGGAATAAGCCCCTAAATTAGCT 57.337 39.130 0.00 0.00 37.10 3.32
3054 7554 6.724893 TTTGGAATAAGCCCCTAAATTAGC 57.275 37.500 0.00 0.00 0.00 3.09
3076 7576 9.764363 GGGAAAATAATGAACAAGAGAGTTTTT 57.236 29.630 0.00 0.00 0.00 1.94
3077 7577 9.147732 AGGGAAAATAATGAACAAGAGAGTTTT 57.852 29.630 0.00 0.00 0.00 2.43
3078 7578 8.712228 AGGGAAAATAATGAACAAGAGAGTTT 57.288 30.769 0.00 0.00 0.00 2.66
3079 7579 8.579863 CAAGGGAAAATAATGAACAAGAGAGTT 58.420 33.333 0.00 0.00 0.00 3.01
3080 7580 7.725844 ACAAGGGAAAATAATGAACAAGAGAGT 59.274 33.333 0.00 0.00 0.00 3.24
3081 7581 8.115490 ACAAGGGAAAATAATGAACAAGAGAG 57.885 34.615 0.00 0.00 0.00 3.20
3082 7582 7.944554 AGACAAGGGAAAATAATGAACAAGAGA 59.055 33.333 0.00 0.00 0.00 3.10
3083 7583 8.115490 AGACAAGGGAAAATAATGAACAAGAG 57.885 34.615 0.00 0.00 0.00 2.85
3084 7584 7.944554 AGAGACAAGGGAAAATAATGAACAAGA 59.055 33.333 0.00 0.00 0.00 3.02
3085 7585 8.115490 AGAGACAAGGGAAAATAATGAACAAG 57.885 34.615 0.00 0.00 0.00 3.16
3086 7586 8.477419 AAGAGACAAGGGAAAATAATGAACAA 57.523 30.769 0.00 0.00 0.00 2.83
3087 7587 8.477419 AAAGAGACAAGGGAAAATAATGAACA 57.523 30.769 0.00 0.00 0.00 3.18
3088 7588 8.797438 AGAAAGAGACAAGGGAAAATAATGAAC 58.203 33.333 0.00 0.00 0.00 3.18
3089 7589 8.940397 AGAAAGAGACAAGGGAAAATAATGAA 57.060 30.769 0.00 0.00 0.00 2.57
3090 7590 8.796475 CAAGAAAGAGACAAGGGAAAATAATGA 58.204 33.333 0.00 0.00 0.00 2.57
3091 7591 8.579863 ACAAGAAAGAGACAAGGGAAAATAATG 58.420 33.333 0.00 0.00 0.00 1.90
3092 7592 8.712228 ACAAGAAAGAGACAAGGGAAAATAAT 57.288 30.769 0.00 0.00 0.00 1.28
3093 7593 8.413229 CAACAAGAAAGAGACAAGGGAAAATAA 58.587 33.333 0.00 0.00 0.00 1.40
3094 7594 7.559897 ACAACAAGAAAGAGACAAGGGAAAATA 59.440 33.333 0.00 0.00 0.00 1.40
3095 7595 6.381133 ACAACAAGAAAGAGACAAGGGAAAAT 59.619 34.615 0.00 0.00 0.00 1.82
3096 7596 5.714806 ACAACAAGAAAGAGACAAGGGAAAA 59.285 36.000 0.00 0.00 0.00 2.29
3097 7597 5.261216 ACAACAAGAAAGAGACAAGGGAAA 58.739 37.500 0.00 0.00 0.00 3.13
3098 7598 4.855340 ACAACAAGAAAGAGACAAGGGAA 58.145 39.130 0.00 0.00 0.00 3.97
3099 7599 4.503714 ACAACAAGAAAGAGACAAGGGA 57.496 40.909 0.00 0.00 0.00 4.20
3100 7600 4.399303 ACAACAACAAGAAAGAGACAAGGG 59.601 41.667 0.00 0.00 0.00 3.95
3101 7601 5.567138 ACAACAACAAGAAAGAGACAAGG 57.433 39.130 0.00 0.00 0.00 3.61
3102 7602 6.306356 CACAACAACAACAAGAAAGAGACAAG 59.694 38.462 0.00 0.00 0.00 3.16
3103 7603 6.148948 CACAACAACAACAAGAAAGAGACAA 58.851 36.000 0.00 0.00 0.00 3.18
3104 7604 5.698832 CACAACAACAACAAGAAAGAGACA 58.301 37.500 0.00 0.00 0.00 3.41
3105 7605 4.558860 GCACAACAACAACAAGAAAGAGAC 59.441 41.667 0.00 0.00 0.00 3.36
3106 7606 4.671508 CGCACAACAACAACAAGAAAGAGA 60.672 41.667 0.00 0.00 0.00 3.10
3107 7607 3.543494 CGCACAACAACAACAAGAAAGAG 59.457 43.478 0.00 0.00 0.00 2.85
3108 7608 3.057876 ACGCACAACAACAACAAGAAAGA 60.058 39.130 0.00 0.00 0.00 2.52
3109 7609 3.241701 ACGCACAACAACAACAAGAAAG 58.758 40.909 0.00 0.00 0.00 2.62
3110 7610 3.238441 GACGCACAACAACAACAAGAAA 58.762 40.909 0.00 0.00 0.00 2.52
3111 7611 2.226674 TGACGCACAACAACAACAAGAA 59.773 40.909 0.00 0.00 0.00 2.52
3112 7612 1.807142 TGACGCACAACAACAACAAGA 59.193 42.857 0.00 0.00 0.00 3.02
3113 7613 2.254918 TGACGCACAACAACAACAAG 57.745 45.000 0.00 0.00 0.00 3.16
3114 7614 2.706555 TTGACGCACAACAACAACAA 57.293 40.000 0.00 0.00 33.18 2.83
3115 7615 2.706555 TTTGACGCACAACAACAACA 57.293 40.000 0.00 0.00 38.29 3.33
3116 7616 2.920490 ACATTTGACGCACAACAACAAC 59.080 40.909 0.00 0.00 38.29 3.32
3198 7710 0.469144 GGTCACAGGGGAGCCAAAAA 60.469 55.000 0.00 0.00 0.00 1.94
3199 7711 1.152830 GGTCACAGGGGAGCCAAAA 59.847 57.895 0.00 0.00 0.00 2.44
3203 7715 0.251787 AAAATGGTCACAGGGGAGCC 60.252 55.000 0.00 0.00 34.46 4.70
3204 7716 1.632589 AAAAATGGTCACAGGGGAGC 58.367 50.000 0.00 0.00 35.89 4.70
3379 7922 6.564873 CGAATTTGAGAAGGAGTTCACTGAAC 60.565 42.308 13.25 13.25 42.25 3.18
3655 8202 9.242477 CAATTTTATTGCGGGTTTGAAATTTTT 57.758 25.926 0.00 0.00 0.00 1.94
3657 8204 8.159344 TCAATTTTATTGCGGGTTTGAAATTT 57.841 26.923 0.00 0.00 0.00 1.82
3658 8205 7.736447 TCAATTTTATTGCGGGTTTGAAATT 57.264 28.000 0.00 0.00 0.00 1.82
3659 8206 7.920160 ATCAATTTTATTGCGGGTTTGAAAT 57.080 28.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.