Multiple sequence alignment - TraesCS1B01G305800

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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 TraesCS1B01G305800 chr1B 100.000 2717 0 0 1 2717 529287091 529289807 0.000000e+00 5018.0
1 TraesCS1B01G305800 chr1B 87.871 404 41 6 1120 1519 422563208 422562809 4.100000e-128 468.0
2 TraesCS1B01G305800 chr1B 86.890 328 12 6 1 297 629847630 629847957 3.350000e-89 339.0
3 TraesCS1B01G305800 chr1B 86.544 327 14 5 1 297 259516686 259517012 1.560000e-87 333.0
4 TraesCS1B01G305800 chr1B 85.366 328 17 5 3 300 49251193 49251519 7.310000e-81 311.0
5 TraesCS1B01G305800 chr1B 82.209 326 28 20 1 298 687331042 687331365 1.250000e-63 254.0
6 TraesCS1B01G305800 chr1B 87.560 209 6 5 109 297 165782477 165782269 9.790000e-55 224.0
7 TraesCS1B01G305800 chr1B 83.688 141 12 11 171 300 26466442 26466302 3.670000e-24 122.0
8 TraesCS1B01G305800 chr1B 80.000 135 23 3 165 298 686883755 686883886 2.230000e-16 97.1
9 TraesCS1B01G305800 chr1D 93.901 2443 70 24 297 2717 393751292 393748907 0.000000e+00 3613.0
10 TraesCS1B01G305800 chr1D 86.168 441 55 6 1082 1519 311988761 311988324 3.170000e-129 472.0
11 TraesCS1B01G305800 chr1D 87.087 333 13 7 1 303 206085795 206085463 1.550000e-92 350.0
12 TraesCS1B01G305800 chr1D 86.544 327 14 5 1 297 247837960 247838286 1.560000e-87 333.0
13 TraesCS1B01G305800 chr1D 81.690 142 13 13 155 288 457092973 457093109 3.700000e-19 106.0
14 TraesCS1B01G305800 chr1A 90.020 2445 106 66 351 2717 492045251 492047635 0.000000e+00 3037.0
15 TraesCS1B01G305800 chr1A 86.005 443 52 9 1082 1519 392084974 392084537 1.470000e-127 466.0
16 TraesCS1B01G305800 chr1A 87.227 321 12 4 1 292 98494918 98495238 3.350000e-89 339.0
17 TraesCS1B01G305800 chr1A 86.029 136 10 8 167 298 30812695 30812565 1.310000e-28 137.0
18 TraesCS1B01G305800 chr3B 87.805 410 48 2 1117 1525 598468518 598468110 1.890000e-131 479.0
19 TraesCS1B01G305800 chr3D 87.317 410 50 2 1117 1525 455106863 455106455 4.100000e-128 468.0
20 TraesCS1B01G305800 chr3D 86.544 327 15 4 1 298 288314799 288314473 1.560000e-87 333.0
21 TraesCS1B01G305800 chr3D 82.477 331 30 14 1 303 486913637 486913967 5.770000e-67 265.0
22 TraesCS1B01G305800 chr3D 79.000 300 41 14 19 297 518131497 518131199 4.620000e-43 185.0
23 TraesCS1B01G305800 chr3D 83.708 178 20 9 127 297 104219114 104219289 2.800000e-35 159.0
24 TraesCS1B01G305800 chr3A 86.553 409 53 2 1118 1525 597547649 597547242 1.480000e-122 449.0
25 TraesCS1B01G305800 chr6B 85.750 400 51 6 1120 1516 687525401 687525005 4.180000e-113 418.0
26 TraesCS1B01G305800 chr2B 87.500 328 11 5 1 298 10075689 10076016 4.300000e-93 351.0
27 TraesCS1B01G305800 chr2B 87.195 328 12 13 1 298 568638450 568638777 2.000000e-91 346.0
28 TraesCS1B01G305800 chr2B 86.970 330 12 9 1 300 790914803 790915131 2.590000e-90 342.0
29 TraesCS1B01G305800 chr5A 85.933 327 16 6 1 297 547116236 547116562 3.370000e-84 322.0
30 TraesCS1B01G305800 chr6D 82.979 329 25 20 1 299 135555244 135554917 4.460000e-68 268.0
31 TraesCS1B01G305800 chr4D 83.934 305 20 11 26 301 355879339 355879035 5.770000e-67 265.0
32 TraesCS1B01G305800 chr4D 81.159 138 16 10 168 297 30389359 30389224 4.790000e-18 102.0
33 TraesCS1B01G305800 chr5D 81.902 326 29 15 2 297 330892617 330892292 5.810000e-62 248.0
34 TraesCS1B01G305800 chr7D 86.730 211 8 3 107 297 107798735 107798525 1.640000e-52 217.0
35 TraesCS1B01G305800 chr7A 81.548 168 15 14 140 297 705951884 705951723 1.020000e-24 124.0
36 TraesCS1B01G305800 chr4B 82.432 148 14 11 165 301 366677635 366677781 4.750000e-23 119.0


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 TraesCS1B01G305800 chr1B 529287091 529289807 2716 False 5018 5018 100.000 1 2717 1 chr1B.!!$F3 2716
1 TraesCS1B01G305800 chr1D 393748907 393751292 2385 True 3613 3613 93.901 297 2717 1 chr1D.!!$R3 2420
2 TraesCS1B01G305800 chr1A 492045251 492047635 2384 False 3037 3037 90.020 351 2717 1 chr1A.!!$F2 2366

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
228 229 0.035056 GTTATGCAGAGGCTGGGTGT 60.035 55.0 0.00 0.0 41.91 4.16 F
230 231 0.035152 TATGCAGAGGCTGGGTGTTG 60.035 55.0 0.00 0.0 41.91 3.33 F
660 700 0.179100 CTAGGCGCACATGCACTACT 60.179 55.0 10.83 0.0 42.21 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1694 1792 0.320374 TACTCGGGAGGTGCTTGTTG 59.680 55.0 0.0 0.0 0.0 3.33 R
1695 1793 1.276622 ATACTCGGGAGGTGCTTGTT 58.723 50.0 0.0 0.0 0.0 2.83 R
2357 2468 0.608640 ATGTGGTTGAGGAGGTCGTC 59.391 55.0 0.0 0.0 0.0 4.20 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
19 20 1.478137 GGTCTATGCTACAACGAGCG 58.522 55.000 0.00 0.00 45.99 5.03
20 21 1.478137 GTCTATGCTACAACGAGCGG 58.522 55.000 0.00 0.00 45.99 5.52
21 22 1.065102 GTCTATGCTACAACGAGCGGA 59.935 52.381 0.00 0.00 45.99 5.54
22 23 1.333931 TCTATGCTACAACGAGCGGAG 59.666 52.381 0.00 0.00 45.99 4.63
23 24 0.384309 TATGCTACAACGAGCGGAGG 59.616 55.000 0.00 0.00 45.99 4.30
24 25 1.605058 ATGCTACAACGAGCGGAGGT 61.605 55.000 0.00 0.00 45.99 3.85
35 36 4.003788 CGGAGGTCCAACCGCTGT 62.004 66.667 13.15 0.00 44.90 4.40
36 37 2.430367 GGAGGTCCAACCGCTGTT 59.570 61.111 0.00 0.00 44.90 3.16
37 38 1.671379 GGAGGTCCAACCGCTGTTC 60.671 63.158 0.00 0.00 44.90 3.18
38 39 1.070786 GAGGTCCAACCGCTGTTCA 59.929 57.895 0.00 0.00 44.90 3.18
39 40 0.534203 GAGGTCCAACCGCTGTTCAA 60.534 55.000 0.00 0.00 44.90 2.69
40 41 0.535102 AGGTCCAACCGCTGTTCAAG 60.535 55.000 0.00 0.00 44.90 3.02
41 42 1.515521 GGTCCAACCGCTGTTCAAGG 61.516 60.000 0.00 0.00 30.42 3.61
42 43 0.534203 GTCCAACCGCTGTTCAAGGA 60.534 55.000 0.00 0.00 30.42 3.36
43 44 0.250295 TCCAACCGCTGTTCAAGGAG 60.250 55.000 0.00 0.00 30.42 3.69
44 45 1.237285 CCAACCGCTGTTCAAGGAGG 61.237 60.000 0.00 0.00 30.42 4.30
45 46 0.535102 CAACCGCTGTTCAAGGAGGT 60.535 55.000 0.00 0.00 37.23 3.85
46 47 0.535102 AACCGCTGTTCAAGGAGGTG 60.535 55.000 0.00 0.00 35.89 4.00
47 48 1.071471 CCGCTGTTCAAGGAGGTGT 59.929 57.895 0.00 0.00 0.00 4.16
48 49 1.230635 CCGCTGTTCAAGGAGGTGTG 61.231 60.000 0.00 0.00 0.00 3.82
49 50 0.532862 CGCTGTTCAAGGAGGTGTGT 60.533 55.000 0.00 0.00 0.00 3.72
50 51 1.270094 CGCTGTTCAAGGAGGTGTGTA 60.270 52.381 0.00 0.00 0.00 2.90
51 52 2.143925 GCTGTTCAAGGAGGTGTGTAC 58.856 52.381 0.00 0.00 0.00 2.90
52 53 2.404215 CTGTTCAAGGAGGTGTGTACG 58.596 52.381 0.00 0.00 0.00 3.67
53 54 1.145803 GTTCAAGGAGGTGTGTACGC 58.854 55.000 0.00 0.00 0.00 4.42
54 55 0.319211 TTCAAGGAGGTGTGTACGCG 60.319 55.000 3.53 3.53 0.00 6.01
55 56 1.736645 CAAGGAGGTGTGTACGCGG 60.737 63.158 12.47 0.00 0.00 6.46
56 57 2.205152 AAGGAGGTGTGTACGCGGT 61.205 57.895 12.47 0.00 0.00 5.68
57 58 1.751349 AAGGAGGTGTGTACGCGGTT 61.751 55.000 12.47 0.00 0.00 4.44
58 59 2.025418 GGAGGTGTGTACGCGGTTG 61.025 63.158 12.47 0.00 0.00 3.77
59 60 2.025418 GAGGTGTGTACGCGGTTGG 61.025 63.158 12.47 0.00 0.00 3.77
60 61 2.029369 GGTGTGTACGCGGTTGGA 59.971 61.111 12.47 0.00 0.00 3.53
61 62 2.025418 GGTGTGTACGCGGTTGGAG 61.025 63.158 12.47 0.00 0.00 3.86
62 63 2.356553 TGTGTACGCGGTTGGAGC 60.357 61.111 12.47 0.00 0.00 4.70
63 64 2.356553 GTGTACGCGGTTGGAGCA 60.357 61.111 12.47 0.00 34.19 4.26
64 65 2.048597 TGTACGCGGTTGGAGCAG 60.049 61.111 12.47 0.00 34.19 4.24
65 66 2.813908 GTACGCGGTTGGAGCAGG 60.814 66.667 12.47 0.00 34.19 4.85
66 67 3.307906 TACGCGGTTGGAGCAGGT 61.308 61.111 12.47 0.00 34.19 4.00
67 68 2.874664 TACGCGGTTGGAGCAGGTT 61.875 57.895 12.47 0.00 34.19 3.50
68 69 3.726517 CGCGGTTGGAGCAGGTTG 61.727 66.667 0.00 0.00 34.19 3.77
69 70 4.043200 GCGGTTGGAGCAGGTTGC 62.043 66.667 0.00 0.00 45.46 4.17
79 80 3.633361 GCAGGTTGCTACAGAGGTT 57.367 52.632 0.00 0.00 40.96 3.50
80 81 1.897560 GCAGGTTGCTACAGAGGTTT 58.102 50.000 0.00 0.00 40.96 3.27
81 82 2.230660 GCAGGTTGCTACAGAGGTTTT 58.769 47.619 0.00 0.00 40.96 2.43
82 83 2.623416 GCAGGTTGCTACAGAGGTTTTT 59.377 45.455 0.00 0.00 40.96 1.94
83 84 3.818773 GCAGGTTGCTACAGAGGTTTTTA 59.181 43.478 0.00 0.00 40.96 1.52
84 85 4.320275 GCAGGTTGCTACAGAGGTTTTTAC 60.320 45.833 0.00 0.00 40.96 2.01
85 86 4.215613 CAGGTTGCTACAGAGGTTTTTACC 59.784 45.833 0.00 0.00 0.00 2.85
86 87 3.504906 GGTTGCTACAGAGGTTTTTACCC 59.495 47.826 0.00 0.00 0.00 3.69
87 88 4.139038 GTTGCTACAGAGGTTTTTACCCA 58.861 43.478 0.00 0.00 0.00 4.51
88 89 4.440826 TGCTACAGAGGTTTTTACCCAA 57.559 40.909 0.00 0.00 0.00 4.12
89 90 4.139038 TGCTACAGAGGTTTTTACCCAAC 58.861 43.478 0.00 0.00 0.00 3.77
90 91 4.139038 GCTACAGAGGTTTTTACCCAACA 58.861 43.478 0.00 0.00 0.00 3.33
91 92 4.765339 GCTACAGAGGTTTTTACCCAACAT 59.235 41.667 0.00 0.00 0.00 2.71
92 93 5.335661 GCTACAGAGGTTTTTACCCAACATG 60.336 44.000 0.00 0.00 0.00 3.21
93 94 3.895041 ACAGAGGTTTTTACCCAACATGG 59.105 43.478 0.00 0.00 37.25 3.66
102 103 2.601067 CCAACATGGGTGGCAGCA 60.601 61.111 19.48 5.16 32.67 4.41
103 104 1.985662 CCAACATGGGTGGCAGCAT 60.986 57.895 19.48 7.36 32.67 3.79
104 105 0.683828 CCAACATGGGTGGCAGCATA 60.684 55.000 19.48 7.19 32.67 3.14
105 106 1.184431 CAACATGGGTGGCAGCATAA 58.816 50.000 19.48 3.65 0.00 1.90
106 107 1.549620 CAACATGGGTGGCAGCATAAA 59.450 47.619 19.48 0.97 0.00 1.40
107 108 2.163810 ACATGGGTGGCAGCATAAAT 57.836 45.000 19.48 3.44 0.00 1.40
108 109 2.034124 ACATGGGTGGCAGCATAAATC 58.966 47.619 19.48 0.00 0.00 2.17
109 110 1.342174 CATGGGTGGCAGCATAAATCC 59.658 52.381 19.48 0.00 0.00 3.01
110 111 0.334335 TGGGTGGCAGCATAAATCCA 59.666 50.000 19.48 2.11 0.00 3.41
111 112 1.063038 TGGGTGGCAGCATAAATCCAT 60.063 47.619 19.48 0.00 0.00 3.41
112 113 1.615392 GGGTGGCAGCATAAATCCATC 59.385 52.381 19.48 0.00 0.00 3.51
113 114 2.590821 GGTGGCAGCATAAATCCATCT 58.409 47.619 12.58 0.00 0.00 2.90
114 115 2.555757 GGTGGCAGCATAAATCCATCTC 59.444 50.000 12.58 0.00 0.00 2.75
115 116 3.216800 GTGGCAGCATAAATCCATCTCA 58.783 45.455 0.00 0.00 0.00 3.27
116 117 3.004106 GTGGCAGCATAAATCCATCTCAC 59.996 47.826 0.00 0.00 0.00 3.51
117 118 2.555757 GGCAGCATAAATCCATCTCACC 59.444 50.000 0.00 0.00 0.00 4.02
118 119 3.484407 GCAGCATAAATCCATCTCACCT 58.516 45.455 0.00 0.00 0.00 4.00
119 120 3.887716 GCAGCATAAATCCATCTCACCTT 59.112 43.478 0.00 0.00 0.00 3.50
120 121 4.340381 GCAGCATAAATCCATCTCACCTTT 59.660 41.667 0.00 0.00 0.00 3.11
121 122 5.506982 GCAGCATAAATCCATCTCACCTTTC 60.507 44.000 0.00 0.00 0.00 2.62
122 123 4.818546 AGCATAAATCCATCTCACCTTTCG 59.181 41.667 0.00 0.00 0.00 3.46
123 124 4.816385 GCATAAATCCATCTCACCTTTCGA 59.184 41.667 0.00 0.00 0.00 3.71
124 125 5.277538 GCATAAATCCATCTCACCTTTCGAC 60.278 44.000 0.00 0.00 0.00 4.20
125 126 3.981071 AATCCATCTCACCTTTCGACA 57.019 42.857 0.00 0.00 0.00 4.35
126 127 4.494091 AATCCATCTCACCTTTCGACAT 57.506 40.909 0.00 0.00 0.00 3.06
127 128 5.614324 AATCCATCTCACCTTTCGACATA 57.386 39.130 0.00 0.00 0.00 2.29
128 129 4.655762 TCCATCTCACCTTTCGACATAG 57.344 45.455 0.00 0.00 0.00 2.23
129 130 3.384789 TCCATCTCACCTTTCGACATAGG 59.615 47.826 6.00 6.00 37.56 2.57
130 131 2.961526 TCTCACCTTTCGACATAGGC 57.038 50.000 7.21 0.00 34.79 3.93
131 132 2.176045 TCTCACCTTTCGACATAGGCA 58.824 47.619 7.21 0.00 34.79 4.75
132 133 2.094182 TCTCACCTTTCGACATAGGCAC 60.094 50.000 7.21 0.00 34.79 5.01
133 134 1.621317 TCACCTTTCGACATAGGCACA 59.379 47.619 7.21 0.00 34.79 4.57
134 135 2.037902 TCACCTTTCGACATAGGCACAA 59.962 45.455 7.21 0.00 34.79 3.33
135 136 3.009723 CACCTTTCGACATAGGCACAAT 58.990 45.455 7.21 0.00 34.79 2.71
136 137 3.009723 ACCTTTCGACATAGGCACAATG 58.990 45.455 7.21 0.00 34.79 2.82
137 138 3.009723 CCTTTCGACATAGGCACAATGT 58.990 45.455 0.49 0.49 40.23 2.71
138 139 3.063997 CCTTTCGACATAGGCACAATGTC 59.936 47.826 14.19 14.19 46.36 3.06
141 142 2.024176 GACATAGGCACAATGTCGGT 57.976 50.000 10.53 0.00 42.63 4.69
142 143 1.933853 GACATAGGCACAATGTCGGTC 59.066 52.381 10.53 0.00 42.63 4.79
143 144 1.555075 ACATAGGCACAATGTCGGTCT 59.445 47.619 0.00 0.00 32.02 3.85
144 145 2.027192 ACATAGGCACAATGTCGGTCTT 60.027 45.455 0.00 0.00 32.02 3.01
145 146 2.851263 TAGGCACAATGTCGGTCTTT 57.149 45.000 0.00 0.00 0.00 2.52
146 147 2.851263 AGGCACAATGTCGGTCTTTA 57.149 45.000 0.00 0.00 0.00 1.85
147 148 2.699954 AGGCACAATGTCGGTCTTTAG 58.300 47.619 0.00 0.00 0.00 1.85
148 149 1.737793 GGCACAATGTCGGTCTTTAGG 59.262 52.381 0.00 0.00 0.00 2.69
149 150 2.614481 GGCACAATGTCGGTCTTTAGGA 60.614 50.000 0.00 0.00 0.00 2.94
150 151 2.415512 GCACAATGTCGGTCTTTAGGAC 59.584 50.000 0.00 0.00 43.79 3.85
151 152 3.864921 GCACAATGTCGGTCTTTAGGACT 60.865 47.826 0.00 0.00 43.97 3.85
152 153 3.927142 CACAATGTCGGTCTTTAGGACTC 59.073 47.826 0.00 0.00 43.97 3.36
153 154 3.833070 ACAATGTCGGTCTTTAGGACTCT 59.167 43.478 0.00 0.00 43.97 3.24
154 155 5.014858 ACAATGTCGGTCTTTAGGACTCTA 58.985 41.667 0.00 0.00 43.97 2.43
155 156 5.105837 ACAATGTCGGTCTTTAGGACTCTAC 60.106 44.000 0.00 0.00 43.97 2.59
156 157 4.298103 TGTCGGTCTTTAGGACTCTACT 57.702 45.455 0.00 0.00 43.97 2.57
157 158 5.426689 TGTCGGTCTTTAGGACTCTACTA 57.573 43.478 0.00 0.00 43.97 1.82
158 159 5.999044 TGTCGGTCTTTAGGACTCTACTAT 58.001 41.667 0.00 0.00 43.97 2.12
159 160 6.421485 TGTCGGTCTTTAGGACTCTACTATT 58.579 40.000 0.00 0.00 43.97 1.73
160 161 6.318144 TGTCGGTCTTTAGGACTCTACTATTG 59.682 42.308 0.00 0.00 43.97 1.90
161 162 5.298777 TCGGTCTTTAGGACTCTACTATTGC 59.701 44.000 0.00 0.00 43.97 3.56
162 163 5.507650 CGGTCTTTAGGACTCTACTATTGCC 60.508 48.000 0.00 0.00 43.97 4.52
163 164 5.507650 GGTCTTTAGGACTCTACTATTGCCG 60.508 48.000 0.00 0.00 43.97 5.69
164 165 5.298777 GTCTTTAGGACTCTACTATTGCCGA 59.701 44.000 0.00 0.00 41.46 5.54
165 166 6.016108 GTCTTTAGGACTCTACTATTGCCGAT 60.016 42.308 0.00 0.00 41.46 4.18
166 167 6.550108 TCTTTAGGACTCTACTATTGCCGATT 59.450 38.462 0.00 0.00 0.00 3.34
167 168 6.726490 TTAGGACTCTACTATTGCCGATTT 57.274 37.500 0.00 0.00 0.00 2.17
168 169 4.950050 AGGACTCTACTATTGCCGATTTG 58.050 43.478 0.00 0.00 0.00 2.32
169 170 4.406003 AGGACTCTACTATTGCCGATTTGT 59.594 41.667 0.00 0.00 0.00 2.83
170 171 4.745620 GGACTCTACTATTGCCGATTTGTC 59.254 45.833 0.00 0.00 0.00 3.18
171 172 4.360563 ACTCTACTATTGCCGATTTGTCG 58.639 43.478 0.00 0.00 0.00 4.35
184 185 5.942325 CGATTTGTCGGTTTTTGTTTTCT 57.058 34.783 0.00 0.00 0.00 2.52
185 186 6.325849 CGATTTGTCGGTTTTTGTTTTCTT 57.674 33.333 0.00 0.00 0.00 2.52
186 187 6.399626 CGATTTGTCGGTTTTTGTTTTCTTC 58.600 36.000 0.00 0.00 0.00 2.87
187 188 6.252655 CGATTTGTCGGTTTTTGTTTTCTTCT 59.747 34.615 0.00 0.00 0.00 2.85
188 189 6.698359 TTTGTCGGTTTTTGTTTTCTTCTG 57.302 33.333 0.00 0.00 0.00 3.02
189 190 4.739195 TGTCGGTTTTTGTTTTCTTCTGG 58.261 39.130 0.00 0.00 0.00 3.86
190 191 4.218852 TGTCGGTTTTTGTTTTCTTCTGGT 59.781 37.500 0.00 0.00 0.00 4.00
191 192 5.165676 GTCGGTTTTTGTTTTCTTCTGGTT 58.834 37.500 0.00 0.00 0.00 3.67
192 193 5.287752 GTCGGTTTTTGTTTTCTTCTGGTTC 59.712 40.000 0.00 0.00 0.00 3.62
193 194 4.264380 CGGTTTTTGTTTTCTTCTGGTTCG 59.736 41.667 0.00 0.00 0.00 3.95
194 195 4.565166 GGTTTTTGTTTTCTTCTGGTTCGG 59.435 41.667 0.00 0.00 0.00 4.30
195 196 3.430333 TTTGTTTTCTTCTGGTTCGGC 57.570 42.857 0.00 0.00 0.00 5.54
196 197 2.341846 TGTTTTCTTCTGGTTCGGCT 57.658 45.000 0.00 0.00 0.00 5.52
197 198 1.946768 TGTTTTCTTCTGGTTCGGCTG 59.053 47.619 0.00 0.00 0.00 4.85
198 199 1.947456 GTTTTCTTCTGGTTCGGCTGT 59.053 47.619 0.00 0.00 0.00 4.40
199 200 1.593196 TTTCTTCTGGTTCGGCTGTG 58.407 50.000 0.00 0.00 0.00 3.66
200 201 0.468226 TTCTTCTGGTTCGGCTGTGT 59.532 50.000 0.00 0.00 0.00 3.72
201 202 0.249868 TCTTCTGGTTCGGCTGTGTG 60.250 55.000 0.00 0.00 0.00 3.82
202 203 1.845809 CTTCTGGTTCGGCTGTGTGC 61.846 60.000 0.00 0.00 41.94 4.57
203 204 2.591429 CTGGTTCGGCTGTGTGCA 60.591 61.111 0.00 0.00 45.15 4.57
204 205 1.968017 CTGGTTCGGCTGTGTGCAT 60.968 57.895 0.00 0.00 45.15 3.96
205 206 1.915614 CTGGTTCGGCTGTGTGCATC 61.916 60.000 0.00 0.00 45.15 3.91
206 207 1.672356 GGTTCGGCTGTGTGCATCT 60.672 57.895 0.00 0.00 45.15 2.90
207 208 1.237285 GGTTCGGCTGTGTGCATCTT 61.237 55.000 0.00 0.00 45.15 2.40
208 209 1.438651 GTTCGGCTGTGTGCATCTTA 58.561 50.000 0.00 0.00 45.15 2.10
209 210 1.394917 GTTCGGCTGTGTGCATCTTAG 59.605 52.381 0.00 0.00 45.15 2.18
210 211 0.608130 TCGGCTGTGTGCATCTTAGT 59.392 50.000 0.00 0.00 45.15 2.24
211 212 1.001974 TCGGCTGTGTGCATCTTAGTT 59.998 47.619 0.00 0.00 45.15 2.24
212 213 2.232696 TCGGCTGTGTGCATCTTAGTTA 59.767 45.455 0.00 0.00 45.15 2.24
213 214 3.118775 TCGGCTGTGTGCATCTTAGTTAT 60.119 43.478 0.00 0.00 45.15 1.89
214 215 3.001634 CGGCTGTGTGCATCTTAGTTATG 59.998 47.826 0.00 0.00 45.15 1.90
224 225 3.827008 TCTTAGTTATGCAGAGGCTGG 57.173 47.619 0.00 0.00 41.91 4.85
225 226 2.435805 TCTTAGTTATGCAGAGGCTGGG 59.564 50.000 0.00 0.00 41.91 4.45
226 227 1.879575 TAGTTATGCAGAGGCTGGGT 58.120 50.000 0.00 0.00 41.91 4.51
227 228 0.254178 AGTTATGCAGAGGCTGGGTG 59.746 55.000 0.00 0.00 41.91 4.61
228 229 0.035056 GTTATGCAGAGGCTGGGTGT 60.035 55.000 0.00 0.00 41.91 4.16
229 230 0.698238 TTATGCAGAGGCTGGGTGTT 59.302 50.000 0.00 0.00 41.91 3.32
230 231 0.035152 TATGCAGAGGCTGGGTGTTG 60.035 55.000 0.00 0.00 41.91 3.33
231 232 3.368571 GCAGAGGCTGGGTGTTGC 61.369 66.667 0.00 0.00 36.96 4.17
232 233 2.433446 CAGAGGCTGGGTGTTGCT 59.567 61.111 0.00 0.00 0.00 3.91
233 234 1.673665 CAGAGGCTGGGTGTTGCTC 60.674 63.158 0.00 0.00 0.00 4.26
234 235 2.149383 AGAGGCTGGGTGTTGCTCA 61.149 57.895 0.00 0.00 0.00 4.26
235 236 1.001641 GAGGCTGGGTGTTGCTCAT 60.002 57.895 0.00 0.00 0.00 2.90
236 237 0.253044 GAGGCTGGGTGTTGCTCATA 59.747 55.000 0.00 0.00 0.00 2.15
237 238 0.698238 AGGCTGGGTGTTGCTCATAA 59.302 50.000 0.00 0.00 0.00 1.90
238 239 1.285962 AGGCTGGGTGTTGCTCATAAT 59.714 47.619 0.00 0.00 0.00 1.28
239 240 1.406539 GGCTGGGTGTTGCTCATAATG 59.593 52.381 0.00 0.00 0.00 1.90
240 241 1.202336 GCTGGGTGTTGCTCATAATGC 60.202 52.381 0.00 0.00 0.00 3.56
241 242 2.372264 CTGGGTGTTGCTCATAATGCT 58.628 47.619 0.00 0.00 0.00 3.79
242 243 2.756760 CTGGGTGTTGCTCATAATGCTT 59.243 45.455 0.00 0.00 0.00 3.91
243 244 3.164268 TGGGTGTTGCTCATAATGCTTT 58.836 40.909 0.00 0.00 0.00 3.51
244 245 3.056678 TGGGTGTTGCTCATAATGCTTTG 60.057 43.478 0.00 0.00 0.00 2.77
245 246 3.056607 GGGTGTTGCTCATAATGCTTTGT 60.057 43.478 0.00 0.00 0.00 2.83
246 247 4.157656 GGGTGTTGCTCATAATGCTTTGTA 59.842 41.667 0.00 0.00 0.00 2.41
247 248 5.163519 GGGTGTTGCTCATAATGCTTTGTAT 60.164 40.000 0.00 0.00 0.00 2.29
248 249 5.973565 GGTGTTGCTCATAATGCTTTGTATC 59.026 40.000 0.00 0.00 0.00 2.24
249 250 5.973565 GTGTTGCTCATAATGCTTTGTATCC 59.026 40.000 0.00 0.00 0.00 2.59
250 251 5.651576 TGTTGCTCATAATGCTTTGTATCCA 59.348 36.000 0.00 0.00 0.00 3.41
251 252 5.756195 TGCTCATAATGCTTTGTATCCAC 57.244 39.130 0.00 0.00 0.00 4.02
252 253 5.439721 TGCTCATAATGCTTTGTATCCACT 58.560 37.500 0.00 0.00 0.00 4.00
253 254 5.887598 TGCTCATAATGCTTTGTATCCACTT 59.112 36.000 0.00 0.00 0.00 3.16
254 255 6.183360 TGCTCATAATGCTTTGTATCCACTTG 60.183 38.462 0.00 0.00 0.00 3.16
255 256 6.038603 GCTCATAATGCTTTGTATCCACTTGA 59.961 38.462 0.00 0.00 0.00 3.02
256 257 7.255381 GCTCATAATGCTTTGTATCCACTTGAT 60.255 37.037 0.00 0.00 37.49 2.57
257 258 7.933396 TCATAATGCTTTGTATCCACTTGATG 58.067 34.615 0.00 0.00 34.76 3.07
258 259 4.644103 ATGCTTTGTATCCACTTGATGC 57.356 40.909 0.00 0.00 36.68 3.91
259 260 3.689347 TGCTTTGTATCCACTTGATGCT 58.311 40.909 0.00 0.00 37.04 3.79
260 261 4.081406 TGCTTTGTATCCACTTGATGCTT 58.919 39.130 0.00 0.00 37.04 3.91
261 262 4.156556 TGCTTTGTATCCACTTGATGCTTC 59.843 41.667 0.00 0.00 37.04 3.86
262 263 4.156556 GCTTTGTATCCACTTGATGCTTCA 59.843 41.667 0.00 0.00 37.04 3.02
263 264 5.163581 GCTTTGTATCCACTTGATGCTTCAT 60.164 40.000 2.75 0.00 37.04 2.57
264 265 6.626623 GCTTTGTATCCACTTGATGCTTCATT 60.627 38.462 2.75 0.00 37.04 2.57
265 266 6.839124 TTGTATCCACTTGATGCTTCATTT 57.161 33.333 2.75 0.00 37.04 2.32
266 267 6.839124 TGTATCCACTTGATGCTTCATTTT 57.161 33.333 2.75 0.00 37.04 1.82
267 268 6.623486 TGTATCCACTTGATGCTTCATTTTG 58.377 36.000 2.75 1.64 37.04 2.44
268 269 5.988310 ATCCACTTGATGCTTCATTTTGA 57.012 34.783 2.75 0.00 30.54 2.69
269 270 5.381174 TCCACTTGATGCTTCATTTTGAG 57.619 39.130 2.75 0.28 0.00 3.02
270 271 4.828939 TCCACTTGATGCTTCATTTTGAGT 59.171 37.500 2.75 0.90 0.00 3.41
271 272 5.302568 TCCACTTGATGCTTCATTTTGAGTT 59.697 36.000 2.75 0.00 0.00 3.01
272 273 6.489700 TCCACTTGATGCTTCATTTTGAGTTA 59.510 34.615 2.75 0.00 0.00 2.24
273 274 7.014134 TCCACTTGATGCTTCATTTTGAGTTAA 59.986 33.333 2.75 0.00 0.00 2.01
274 275 7.816031 CCACTTGATGCTTCATTTTGAGTTAAT 59.184 33.333 2.75 0.00 0.00 1.40
275 276 9.844790 CACTTGATGCTTCATTTTGAGTTAATA 57.155 29.630 2.75 0.00 0.00 0.98
464 475 5.268387 TGGAATAGCAAACCATGTTACCAT 58.732 37.500 0.00 0.00 0.00 3.55
514 538 4.415150 CCCAGCCGACACCTGCAT 62.415 66.667 0.00 0.00 0.00 3.96
520 544 1.639298 GCCGACACCTGCATCTGTTC 61.639 60.000 0.00 0.00 0.00 3.18
526 550 0.320771 ACCTGCATCTGTTCGACACC 60.321 55.000 0.00 0.00 0.00 4.16
530 554 1.781555 CATCTGTTCGACACCGCAC 59.218 57.895 0.00 0.00 35.37 5.34
531 555 0.943835 CATCTGTTCGACACCGCACA 60.944 55.000 0.00 0.00 39.43 4.57
554 579 2.108514 CAACGCTGCCACATCCGAT 61.109 57.895 0.00 0.00 0.00 4.18
563 588 1.018752 CCACATCCGATGCACACGAA 61.019 55.000 15.15 0.00 0.00 3.85
589 614 2.732468 CATCTCGATCGGCCGCTG 60.732 66.667 23.51 12.80 0.00 5.18
590 615 3.983494 ATCTCGATCGGCCGCTGG 61.983 66.667 23.51 13.45 0.00 4.85
644 677 1.353022 AGCCTCTACTCCGATCCCTAG 59.647 57.143 0.00 0.00 0.00 3.02
660 700 0.179100 CTAGGCGCACATGCACTACT 60.179 55.000 10.83 0.00 42.21 2.57
661 701 1.067060 CTAGGCGCACATGCACTACTA 59.933 52.381 10.83 0.00 42.21 1.82
662 702 0.460284 AGGCGCACATGCACTACTAC 60.460 55.000 10.83 0.00 42.21 2.73
827 881 2.286294 GCTATCACCTTCAAGCATCACG 59.714 50.000 0.00 0.00 35.05 4.35
863 917 0.321671 TCACTTCACTAGCACCCAGC 59.678 55.000 0.00 0.00 46.19 4.85
1602 1700 4.003788 CCTGGACGCGGTGAAGGT 62.004 66.667 12.47 0.00 0.00 3.50
1858 1956 6.037500 TCTCTTGCCATTTGATTTCACTATCG 59.962 38.462 0.00 0.00 0.00 2.92
1881 1979 7.422399 TCGTTCTCCCTTTTCTTGTTTAATTG 58.578 34.615 0.00 0.00 0.00 2.32
2014 2119 3.825014 AGCTGAACAATTGATCAGTGCTT 59.175 39.130 33.26 20.23 43.97 3.91
2044 2151 2.040145 TCTTGCTCATGTCCCAATGTCA 59.960 45.455 0.00 0.00 0.00 3.58
2157 2264 6.724694 TTTCTTTTGATTACCATGCATTGC 57.275 33.333 0.00 0.46 0.00 3.56
2165 2272 4.970662 TTACCATGCATTGCTTTCTCTC 57.029 40.909 10.49 0.00 0.00 3.20
2166 2273 3.083122 ACCATGCATTGCTTTCTCTCT 57.917 42.857 10.49 0.00 0.00 3.10
2167 2274 4.226427 ACCATGCATTGCTTTCTCTCTA 57.774 40.909 10.49 0.00 0.00 2.43
2168 2275 4.789807 ACCATGCATTGCTTTCTCTCTAT 58.210 39.130 10.49 0.00 0.00 1.98
2169 2276 4.579340 ACCATGCATTGCTTTCTCTCTATG 59.421 41.667 10.49 1.87 0.00 2.23
2170 2277 4.537965 CATGCATTGCTTTCTCTCTATGC 58.462 43.478 10.49 0.00 40.24 3.14
2226 2337 3.434641 GTGAGACGCTGTACTGTGTACTA 59.565 47.826 17.56 5.64 0.00 1.82
2357 2468 0.530650 CACATACAGTAGCCCAGCGG 60.531 60.000 0.00 0.00 0.00 5.52
2383 2494 3.333680 ACCTCCTCAACCACATTACCATT 59.666 43.478 0.00 0.00 0.00 3.16
2410 2521 4.202070 CGAATCCCTTTCCAGAGAGAGTAC 60.202 50.000 0.00 0.00 0.00 2.73
2413 2524 5.118729 TCCCTTTCCAGAGAGAGTACTAG 57.881 47.826 0.00 0.00 0.00 2.57
2414 2525 4.540906 TCCCTTTCCAGAGAGAGTACTAGT 59.459 45.833 0.00 0.00 0.00 2.57
2415 2526 5.730207 TCCCTTTCCAGAGAGAGTACTAGTA 59.270 44.000 0.00 0.00 0.00 1.82
2521 2635 6.688073 AATCTGATCTATAATTGGGACCGT 57.312 37.500 0.00 0.00 0.00 4.83
2585 2699 2.805099 CTGAACTGAACTCAAGGCAGAC 59.195 50.000 0.00 0.00 33.94 3.51
2653 2767 3.103091 GCGGCCGGGGAGTAATCTT 62.103 63.158 29.38 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.478137 CGCTCGTTGTAGCATAGACC 58.522 55.000 0.00 0.00 42.91 3.85
1 2 1.065102 TCCGCTCGTTGTAGCATAGAC 59.935 52.381 0.00 0.00 42.91 2.59
3 4 1.600663 CCTCCGCTCGTTGTAGCATAG 60.601 57.143 0.00 0.00 42.91 2.23
4 5 0.384309 CCTCCGCTCGTTGTAGCATA 59.616 55.000 0.00 0.00 42.91 3.14
5 6 1.141881 CCTCCGCTCGTTGTAGCAT 59.858 57.895 0.00 0.00 42.91 3.79
6 7 2.209064 GACCTCCGCTCGTTGTAGCA 62.209 60.000 0.00 0.00 42.91 3.49
7 8 1.516603 GACCTCCGCTCGTTGTAGC 60.517 63.158 0.00 0.00 39.21 3.58
8 9 1.139095 GGACCTCCGCTCGTTGTAG 59.861 63.158 0.00 0.00 0.00 2.74
9 10 1.180456 TTGGACCTCCGCTCGTTGTA 61.180 55.000 0.00 0.00 39.43 2.41
10 11 2.504274 TTGGACCTCCGCTCGTTGT 61.504 57.895 0.00 0.00 39.43 3.32
11 12 2.027625 GTTGGACCTCCGCTCGTTG 61.028 63.158 0.00 0.00 39.43 4.10
12 13 2.342648 GTTGGACCTCCGCTCGTT 59.657 61.111 0.00 0.00 39.43 3.85
13 14 3.692406 GGTTGGACCTCCGCTCGT 61.692 66.667 0.00 0.00 39.43 4.18
14 15 4.796231 CGGTTGGACCTCCGCTCG 62.796 72.222 13.79 0.00 40.28 5.03
19 20 1.671379 GAACAGCGGTTGGACCTCC 60.671 63.158 7.05 0.00 37.36 4.30
20 21 0.534203 TTGAACAGCGGTTGGACCTC 60.534 55.000 7.05 0.00 37.36 3.85
21 22 0.535102 CTTGAACAGCGGTTGGACCT 60.535 55.000 7.05 0.00 37.36 3.85
22 23 1.515521 CCTTGAACAGCGGTTGGACC 61.516 60.000 7.05 0.00 37.36 4.46
23 24 0.534203 TCCTTGAACAGCGGTTGGAC 60.534 55.000 7.05 0.00 37.36 4.02
24 25 0.250295 CTCCTTGAACAGCGGTTGGA 60.250 55.000 7.05 7.02 37.36 3.53
25 26 1.237285 CCTCCTTGAACAGCGGTTGG 61.237 60.000 7.05 2.40 37.36 3.77
26 27 0.535102 ACCTCCTTGAACAGCGGTTG 60.535 55.000 7.05 0.00 37.36 3.77
27 28 0.535102 CACCTCCTTGAACAGCGGTT 60.535 55.000 0.50 0.50 40.76 4.44
28 29 1.071471 CACCTCCTTGAACAGCGGT 59.929 57.895 0.00 0.00 0.00 5.68
29 30 1.071471 ACACCTCCTTGAACAGCGG 59.929 57.895 0.00 0.00 0.00 5.52
30 31 0.532862 ACACACCTCCTTGAACAGCG 60.533 55.000 0.00 0.00 0.00 5.18
31 32 2.143925 GTACACACCTCCTTGAACAGC 58.856 52.381 0.00 0.00 0.00 4.40
32 33 2.404215 CGTACACACCTCCTTGAACAG 58.596 52.381 0.00 0.00 0.00 3.16
33 34 1.539496 GCGTACACACCTCCTTGAACA 60.539 52.381 0.00 0.00 0.00 3.18
34 35 1.145803 GCGTACACACCTCCTTGAAC 58.854 55.000 0.00 0.00 0.00 3.18
35 36 0.319211 CGCGTACACACCTCCTTGAA 60.319 55.000 0.00 0.00 0.00 2.69
36 37 1.287815 CGCGTACACACCTCCTTGA 59.712 57.895 0.00 0.00 0.00 3.02
37 38 1.736645 CCGCGTACACACCTCCTTG 60.737 63.158 4.92 0.00 0.00 3.61
38 39 1.751349 AACCGCGTACACACCTCCTT 61.751 55.000 4.92 0.00 0.00 3.36
39 40 2.205152 AACCGCGTACACACCTCCT 61.205 57.895 4.92 0.00 0.00 3.69
40 41 2.025418 CAACCGCGTACACACCTCC 61.025 63.158 4.92 0.00 0.00 4.30
41 42 2.025418 CCAACCGCGTACACACCTC 61.025 63.158 4.92 0.00 0.00 3.85
42 43 2.029964 CCAACCGCGTACACACCT 59.970 61.111 4.92 0.00 0.00 4.00
43 44 2.025418 CTCCAACCGCGTACACACC 61.025 63.158 4.92 0.00 0.00 4.16
44 45 2.664436 GCTCCAACCGCGTACACAC 61.664 63.158 4.92 0.00 0.00 3.82
45 46 2.356553 GCTCCAACCGCGTACACA 60.357 61.111 4.92 0.00 0.00 3.72
46 47 2.356553 TGCTCCAACCGCGTACAC 60.357 61.111 4.92 0.00 0.00 2.90
47 48 2.048597 CTGCTCCAACCGCGTACA 60.049 61.111 4.92 0.00 0.00 2.90
48 49 2.813908 CCTGCTCCAACCGCGTAC 60.814 66.667 4.92 0.00 0.00 3.67
49 50 2.874664 AACCTGCTCCAACCGCGTA 61.875 57.895 4.92 0.00 0.00 4.42
50 51 4.250305 AACCTGCTCCAACCGCGT 62.250 61.111 4.92 0.00 0.00 6.01
51 52 3.726517 CAACCTGCTCCAACCGCG 61.727 66.667 0.00 0.00 0.00 6.46
52 53 4.043200 GCAACCTGCTCCAACCGC 62.043 66.667 0.00 0.00 40.96 5.68
61 62 1.897560 AAACCTCTGTAGCAACCTGC 58.102 50.000 0.00 0.00 45.46 4.85
62 63 4.215613 GGTAAAAACCTCTGTAGCAACCTG 59.784 45.833 0.00 0.00 0.00 4.00
63 64 4.395625 GGTAAAAACCTCTGTAGCAACCT 58.604 43.478 0.00 0.00 0.00 3.50
64 65 3.504906 GGGTAAAAACCTCTGTAGCAACC 59.495 47.826 0.00 0.00 0.00 3.77
65 66 4.139038 TGGGTAAAAACCTCTGTAGCAAC 58.861 43.478 0.00 0.00 0.00 4.17
66 67 4.440826 TGGGTAAAAACCTCTGTAGCAA 57.559 40.909 0.00 0.00 0.00 3.91
67 68 4.139038 GTTGGGTAAAAACCTCTGTAGCA 58.861 43.478 0.00 0.00 0.00 3.49
68 69 4.139038 TGTTGGGTAAAAACCTCTGTAGC 58.861 43.478 0.00 0.00 0.00 3.58
69 70 5.183140 CCATGTTGGGTAAAAACCTCTGTAG 59.817 44.000 0.00 0.00 32.67 2.74
70 71 5.074115 CCATGTTGGGTAAAAACCTCTGTA 58.926 41.667 0.00 0.00 32.67 2.74
71 72 3.895041 CCATGTTGGGTAAAAACCTCTGT 59.105 43.478 0.00 0.00 32.67 3.41
72 73 4.519540 CCATGTTGGGTAAAAACCTCTG 57.480 45.455 0.00 0.00 32.67 3.35
85 86 0.683828 TATGCTGCCACCCATGTTGG 60.684 55.000 6.28 6.28 37.25 3.77
86 87 1.184431 TTATGCTGCCACCCATGTTG 58.816 50.000 0.00 0.00 0.00 3.33
87 88 1.935799 TTTATGCTGCCACCCATGTT 58.064 45.000 0.00 0.00 0.00 2.71
88 89 2.034124 GATTTATGCTGCCACCCATGT 58.966 47.619 0.00 0.00 0.00 3.21
89 90 1.342174 GGATTTATGCTGCCACCCATG 59.658 52.381 0.00 0.00 0.00 3.66
90 91 1.063038 TGGATTTATGCTGCCACCCAT 60.063 47.619 0.00 0.00 0.00 4.00
91 92 0.334335 TGGATTTATGCTGCCACCCA 59.666 50.000 0.00 0.00 0.00 4.51
92 93 1.615392 GATGGATTTATGCTGCCACCC 59.385 52.381 0.00 0.00 32.42 4.61
93 94 2.555757 GAGATGGATTTATGCTGCCACC 59.444 50.000 0.00 0.00 32.42 4.61
94 95 3.004106 GTGAGATGGATTTATGCTGCCAC 59.996 47.826 0.00 0.00 32.42 5.01
95 96 3.216800 GTGAGATGGATTTATGCTGCCA 58.783 45.455 0.00 0.00 34.45 4.92
96 97 2.555757 GGTGAGATGGATTTATGCTGCC 59.444 50.000 0.00 0.00 0.00 4.85
97 98 3.484407 AGGTGAGATGGATTTATGCTGC 58.516 45.455 0.00 0.00 0.00 5.25
98 99 5.277683 CGAAAGGTGAGATGGATTTATGCTG 60.278 44.000 0.00 0.00 0.00 4.41
99 100 4.818546 CGAAAGGTGAGATGGATTTATGCT 59.181 41.667 0.00 0.00 0.00 3.79
100 101 4.816385 TCGAAAGGTGAGATGGATTTATGC 59.184 41.667 0.00 0.00 0.00 3.14
101 102 5.817296 TGTCGAAAGGTGAGATGGATTTATG 59.183 40.000 0.00 0.00 0.00 1.90
102 103 5.989477 TGTCGAAAGGTGAGATGGATTTAT 58.011 37.500 0.00 0.00 0.00 1.40
103 104 5.414789 TGTCGAAAGGTGAGATGGATTTA 57.585 39.130 0.00 0.00 0.00 1.40
104 105 4.286297 TGTCGAAAGGTGAGATGGATTT 57.714 40.909 0.00 0.00 0.00 2.17
105 106 3.981071 TGTCGAAAGGTGAGATGGATT 57.019 42.857 0.00 0.00 0.00 3.01
106 107 4.039730 CCTATGTCGAAAGGTGAGATGGAT 59.960 45.833 0.00 0.00 0.00 3.41
107 108 3.384789 CCTATGTCGAAAGGTGAGATGGA 59.615 47.826 0.00 0.00 0.00 3.41
108 109 3.722147 CCTATGTCGAAAGGTGAGATGG 58.278 50.000 0.00 0.00 0.00 3.51
109 110 3.126831 GCCTATGTCGAAAGGTGAGATG 58.873 50.000 10.48 0.00 35.16 2.90
110 111 2.766263 TGCCTATGTCGAAAGGTGAGAT 59.234 45.455 10.48 0.00 35.16 2.75
111 112 2.094182 GTGCCTATGTCGAAAGGTGAGA 60.094 50.000 10.48 0.00 35.16 3.27
112 113 2.271800 GTGCCTATGTCGAAAGGTGAG 58.728 52.381 10.48 0.00 35.16 3.51
113 114 1.621317 TGTGCCTATGTCGAAAGGTGA 59.379 47.619 10.48 0.00 35.16 4.02
114 115 2.093306 TGTGCCTATGTCGAAAGGTG 57.907 50.000 10.48 0.00 35.16 4.00
115 116 2.851263 TTGTGCCTATGTCGAAAGGT 57.149 45.000 10.48 0.00 35.16 3.50
116 117 3.009723 ACATTGTGCCTATGTCGAAAGG 58.990 45.455 5.55 5.55 30.65 3.11
117 118 4.264543 GACATTGTGCCTATGTCGAAAG 57.735 45.455 11.59 0.00 41.56 2.62
122 123 1.933853 GACCGACATTGTGCCTATGTC 59.066 52.381 14.86 14.86 45.30 3.06
123 124 1.555075 AGACCGACATTGTGCCTATGT 59.445 47.619 0.00 2.89 38.86 2.29
124 125 2.315925 AGACCGACATTGTGCCTATG 57.684 50.000 0.00 0.00 0.00 2.23
125 126 3.350219 AAAGACCGACATTGTGCCTAT 57.650 42.857 0.00 0.00 0.00 2.57
126 127 2.851263 AAAGACCGACATTGTGCCTA 57.149 45.000 0.00 0.00 0.00 3.93
127 128 2.615493 CCTAAAGACCGACATTGTGCCT 60.615 50.000 0.00 0.00 0.00 4.75
128 129 1.737793 CCTAAAGACCGACATTGTGCC 59.262 52.381 0.00 0.00 0.00 5.01
129 130 2.415512 GTCCTAAAGACCGACATTGTGC 59.584 50.000 0.00 0.00 39.84 4.57
140 141 5.298777 TCGGCAATAGTAGAGTCCTAAAGAC 59.701 44.000 0.00 0.00 46.71 3.01
141 142 5.443283 TCGGCAATAGTAGAGTCCTAAAGA 58.557 41.667 0.00 0.00 0.00 2.52
142 143 5.769484 TCGGCAATAGTAGAGTCCTAAAG 57.231 43.478 0.00 0.00 0.00 1.85
143 144 6.726490 AATCGGCAATAGTAGAGTCCTAAA 57.274 37.500 0.00 0.00 0.00 1.85
144 145 6.097839 ACAAATCGGCAATAGTAGAGTCCTAA 59.902 38.462 0.00 0.00 0.00 2.69
145 146 5.597182 ACAAATCGGCAATAGTAGAGTCCTA 59.403 40.000 0.00 0.00 0.00 2.94
146 147 4.406003 ACAAATCGGCAATAGTAGAGTCCT 59.594 41.667 0.00 0.00 0.00 3.85
147 148 4.694339 ACAAATCGGCAATAGTAGAGTCC 58.306 43.478 0.00 0.00 0.00 3.85
148 149 4.441415 CGACAAATCGGCAATAGTAGAGTC 59.559 45.833 0.00 0.00 44.99 3.36
149 150 4.360563 CGACAAATCGGCAATAGTAGAGT 58.639 43.478 0.00 0.00 44.99 3.24
150 151 4.956034 CGACAAATCGGCAATAGTAGAG 57.044 45.455 0.00 0.00 44.99 2.43
163 164 7.391016 CAGAAGAAAACAAAAACCGACAAATC 58.609 34.615 0.00 0.00 0.00 2.17
164 165 6.312672 CCAGAAGAAAACAAAAACCGACAAAT 59.687 34.615 0.00 0.00 0.00 2.32
165 166 5.635700 CCAGAAGAAAACAAAAACCGACAAA 59.364 36.000 0.00 0.00 0.00 2.83
166 167 5.164954 CCAGAAGAAAACAAAAACCGACAA 58.835 37.500 0.00 0.00 0.00 3.18
167 168 4.218852 ACCAGAAGAAAACAAAAACCGACA 59.781 37.500 0.00 0.00 0.00 4.35
168 169 4.740268 ACCAGAAGAAAACAAAAACCGAC 58.260 39.130 0.00 0.00 0.00 4.79
169 170 5.394224 AACCAGAAGAAAACAAAAACCGA 57.606 34.783 0.00 0.00 0.00 4.69
170 171 4.264380 CGAACCAGAAGAAAACAAAAACCG 59.736 41.667 0.00 0.00 0.00 4.44
171 172 4.565166 CCGAACCAGAAGAAAACAAAAACC 59.435 41.667 0.00 0.00 0.00 3.27
172 173 4.032445 GCCGAACCAGAAGAAAACAAAAAC 59.968 41.667 0.00 0.00 0.00 2.43
173 174 4.081917 AGCCGAACCAGAAGAAAACAAAAA 60.082 37.500 0.00 0.00 0.00 1.94
174 175 3.445805 AGCCGAACCAGAAGAAAACAAAA 59.554 39.130 0.00 0.00 0.00 2.44
175 176 3.020984 AGCCGAACCAGAAGAAAACAAA 58.979 40.909 0.00 0.00 0.00 2.83
176 177 2.357637 CAGCCGAACCAGAAGAAAACAA 59.642 45.455 0.00 0.00 0.00 2.83
177 178 1.946768 CAGCCGAACCAGAAGAAAACA 59.053 47.619 0.00 0.00 0.00 2.83
178 179 1.947456 ACAGCCGAACCAGAAGAAAAC 59.053 47.619 0.00 0.00 0.00 2.43
179 180 1.946768 CACAGCCGAACCAGAAGAAAA 59.053 47.619 0.00 0.00 0.00 2.29
180 181 1.134220 ACACAGCCGAACCAGAAGAAA 60.134 47.619 0.00 0.00 0.00 2.52
181 182 0.468226 ACACAGCCGAACCAGAAGAA 59.532 50.000 0.00 0.00 0.00 2.52
182 183 0.249868 CACACAGCCGAACCAGAAGA 60.250 55.000 0.00 0.00 0.00 2.87
183 184 1.845809 GCACACAGCCGAACCAGAAG 61.846 60.000 0.00 0.00 37.23 2.85
184 185 1.891919 GCACACAGCCGAACCAGAA 60.892 57.895 0.00 0.00 37.23 3.02
185 186 2.280797 GCACACAGCCGAACCAGA 60.281 61.111 0.00 0.00 37.23 3.86
186 187 1.915614 GATGCACACAGCCGAACCAG 61.916 60.000 0.00 0.00 44.83 4.00
187 188 1.965930 GATGCACACAGCCGAACCA 60.966 57.895 0.00 0.00 44.83 3.67
188 189 1.237285 AAGATGCACACAGCCGAACC 61.237 55.000 0.00 0.00 44.83 3.62
189 190 1.394917 CTAAGATGCACACAGCCGAAC 59.605 52.381 0.00 0.00 44.83 3.95
190 191 1.001974 ACTAAGATGCACACAGCCGAA 59.998 47.619 0.00 0.00 44.83 4.30
191 192 0.608130 ACTAAGATGCACACAGCCGA 59.392 50.000 0.00 0.00 44.83 5.54
192 193 1.442769 AACTAAGATGCACACAGCCG 58.557 50.000 0.00 0.00 44.83 5.52
193 194 4.542662 CATAACTAAGATGCACACAGCC 57.457 45.455 0.00 0.00 44.83 4.85
202 203 4.063689 CCAGCCTCTGCATAACTAAGATG 58.936 47.826 0.00 0.00 41.13 2.90
203 204 3.072184 CCCAGCCTCTGCATAACTAAGAT 59.928 47.826 0.00 0.00 41.13 2.40
204 205 2.435805 CCCAGCCTCTGCATAACTAAGA 59.564 50.000 0.00 0.00 41.13 2.10
205 206 2.171448 ACCCAGCCTCTGCATAACTAAG 59.829 50.000 0.00 0.00 41.13 2.18
206 207 2.092968 CACCCAGCCTCTGCATAACTAA 60.093 50.000 0.00 0.00 41.13 2.24
207 208 1.486310 CACCCAGCCTCTGCATAACTA 59.514 52.381 0.00 0.00 41.13 2.24
208 209 0.254178 CACCCAGCCTCTGCATAACT 59.746 55.000 0.00 0.00 41.13 2.24
209 210 0.035056 ACACCCAGCCTCTGCATAAC 60.035 55.000 0.00 0.00 41.13 1.89
210 211 0.698238 AACACCCAGCCTCTGCATAA 59.302 50.000 0.00 0.00 41.13 1.90
211 212 0.035152 CAACACCCAGCCTCTGCATA 60.035 55.000 0.00 0.00 41.13 3.14
212 213 1.303888 CAACACCCAGCCTCTGCAT 60.304 57.895 0.00 0.00 41.13 3.96
213 214 2.113774 CAACACCCAGCCTCTGCA 59.886 61.111 0.00 0.00 41.13 4.41
214 215 3.368571 GCAACACCCAGCCTCTGC 61.369 66.667 0.00 0.00 37.95 4.26
215 216 1.673665 GAGCAACACCCAGCCTCTG 60.674 63.158 0.00 0.00 0.00 3.35
216 217 1.495579 ATGAGCAACACCCAGCCTCT 61.496 55.000 0.00 0.00 0.00 3.69
217 218 0.253044 TATGAGCAACACCCAGCCTC 59.747 55.000 0.00 0.00 0.00 4.70
218 219 0.698238 TTATGAGCAACACCCAGCCT 59.302 50.000 0.00 0.00 0.00 4.58
219 220 1.406539 CATTATGAGCAACACCCAGCC 59.593 52.381 0.00 0.00 0.00 4.85
220 221 1.202336 GCATTATGAGCAACACCCAGC 60.202 52.381 0.00 0.00 0.00 4.85
221 222 2.372264 AGCATTATGAGCAACACCCAG 58.628 47.619 0.00 0.00 0.00 4.45
222 223 2.512692 AGCATTATGAGCAACACCCA 57.487 45.000 0.00 0.00 0.00 4.51
223 224 3.056607 ACAAAGCATTATGAGCAACACCC 60.057 43.478 0.00 0.00 0.00 4.61
224 225 4.178545 ACAAAGCATTATGAGCAACACC 57.821 40.909 0.00 0.00 0.00 4.16
225 226 5.973565 GGATACAAAGCATTATGAGCAACAC 59.026 40.000 0.00 0.00 0.00 3.32
226 227 6.135290 GGATACAAAGCATTATGAGCAACA 57.865 37.500 0.00 0.00 0.00 3.33
236 237 8.927695 TGAAGCATCAAGTGGATACAAAGCATT 61.928 37.037 0.00 0.00 40.19 3.56
237 238 7.527446 TGAAGCATCAAGTGGATACAAAGCAT 61.527 38.462 0.00 0.00 40.19 3.79
238 239 6.266533 TGAAGCATCAAGTGGATACAAAGCA 61.267 40.000 0.00 0.00 40.19 3.91
239 240 4.156556 TGAAGCATCAAGTGGATACAAAGC 59.843 41.667 0.00 0.00 40.19 3.51
240 241 5.885230 TGAAGCATCAAGTGGATACAAAG 57.115 39.130 0.00 0.00 40.19 2.77
241 242 6.839124 AATGAAGCATCAAGTGGATACAAA 57.161 33.333 0.00 0.00 44.72 2.83
242 243 6.839124 AAATGAAGCATCAAGTGGATACAA 57.161 33.333 0.00 0.00 44.72 2.41
243 244 6.433716 TCAAAATGAAGCATCAAGTGGATACA 59.566 34.615 0.00 0.00 41.97 2.29
244 245 6.855836 TCAAAATGAAGCATCAAGTGGATAC 58.144 36.000 0.00 0.00 39.49 2.24
245 246 6.660521 ACTCAAAATGAAGCATCAAGTGGATA 59.339 34.615 0.00 0.00 39.49 2.59
246 247 5.479375 ACTCAAAATGAAGCATCAAGTGGAT 59.521 36.000 0.00 0.00 39.49 3.41
247 248 4.828939 ACTCAAAATGAAGCATCAAGTGGA 59.171 37.500 0.00 0.00 39.49 4.02
248 249 5.130292 ACTCAAAATGAAGCATCAAGTGG 57.870 39.130 0.00 0.00 39.49 4.00
249 250 8.752766 ATTAACTCAAAATGAAGCATCAAGTG 57.247 30.769 0.00 0.00 39.49 3.16
292 293 3.395941 AGTGTGACAGGGAGATCCTTTTT 59.604 43.478 0.00 0.00 45.47 1.94
293 294 2.982488 AGTGTGACAGGGAGATCCTTTT 59.018 45.455 0.00 0.00 45.47 2.27
294 295 2.625639 AGTGTGACAGGGAGATCCTTT 58.374 47.619 0.00 0.00 45.47 3.11
295 296 2.334006 AGTGTGACAGGGAGATCCTT 57.666 50.000 0.00 0.00 45.47 3.36
314 315 1.965643 AGCATTTTTGGAGCTGCTGAA 59.034 42.857 7.01 0.00 43.02 3.02
396 402 9.173021 TGAAACAGTTATCAGACTCTTTTTCAA 57.827 29.630 0.00 0.00 32.50 2.69
397 403 8.731275 TGAAACAGTTATCAGACTCTTTTTCA 57.269 30.769 0.00 0.00 32.73 2.69
398 404 8.286097 CCTGAAACAGTTATCAGACTCTTTTTC 58.714 37.037 19.21 0.00 44.64 2.29
510 534 2.027073 GCGGTGTCGAACAGATGCA 61.027 57.895 0.00 0.00 39.00 3.96
513 537 4.261888 GTGCGGTGTCGAACAGAT 57.738 55.556 0.00 0.00 44.14 2.90
520 544 1.885388 TTGAGGTTGTGCGGTGTCG 60.885 57.895 0.00 0.00 39.81 4.35
526 550 2.249309 CAGCGTTGAGGTTGTGCG 59.751 61.111 0.00 0.00 0.00 5.34
530 554 1.518056 ATGTGGCAGCGTTGAGGTTG 61.518 55.000 2.38 0.00 0.00 3.77
531 555 1.228245 ATGTGGCAGCGTTGAGGTT 60.228 52.632 2.38 0.00 0.00 3.50
554 579 3.410516 CGGCATCGTTCGTGTGCA 61.411 61.111 19.39 0.00 40.53 4.57
563 588 1.372251 GATCGAGATGCGGCATCGT 60.372 57.895 30.88 21.48 44.67 3.73
660 700 3.183754 CGCGTATGGATGAACAGTTGTA 58.816 45.455 0.00 0.00 0.00 2.41
661 701 1.999735 CGCGTATGGATGAACAGTTGT 59.000 47.619 0.00 0.00 0.00 3.32
662 702 1.267532 GCGCGTATGGATGAACAGTTG 60.268 52.381 8.43 0.00 0.00 3.16
1434 1532 2.758327 AGGTAGATCCGCACGGCA 60.758 61.111 3.66 0.00 41.99 5.69
1587 1685 4.308458 CCACCTTCACCGCGTCCA 62.308 66.667 4.92 0.00 0.00 4.02
1590 1688 2.915659 TCTCCACCTTCACCGCGT 60.916 61.111 4.92 0.00 0.00 6.01
1596 1694 1.202806 CCACTTTGCTCTCCACCTTCA 60.203 52.381 0.00 0.00 0.00 3.02
1602 1700 1.601759 GCTGCCACTTTGCTCTCCA 60.602 57.895 0.00 0.00 0.00 3.86
1694 1792 0.320374 TACTCGGGAGGTGCTTGTTG 59.680 55.000 0.00 0.00 0.00 3.33
1695 1793 1.276622 ATACTCGGGAGGTGCTTGTT 58.723 50.000 0.00 0.00 0.00 2.83
1696 1794 2.032620 CTATACTCGGGAGGTGCTTGT 58.967 52.381 0.00 0.00 0.00 3.16
1858 1956 8.942338 AACAATTAAACAAGAAAAGGGAGAAC 57.058 30.769 0.00 0.00 0.00 3.01
1881 1979 5.171147 TCATAAGGACTCGATCGAGAAAC 57.829 43.478 42.97 31.17 44.53 2.78
1988 2093 2.353889 CTGATCAATTGTTCAGCTCCCG 59.646 50.000 25.84 9.30 35.76 5.14
2014 2119 3.431346 GGACATGAGCAAGACATCAGCTA 60.431 47.826 0.00 0.00 39.02 3.32
2024 2131 2.163010 GTGACATTGGGACATGAGCAAG 59.837 50.000 0.00 0.00 39.30 4.01
2044 2151 4.042311 TGTCACCACAAAGGGTATGTATGT 59.958 41.667 0.00 0.00 43.89 2.29
2057 2164 4.072839 TGCGGTTAATTATGTCACCACAA 58.927 39.130 5.20 0.00 35.64 3.33
2058 2165 3.676093 TGCGGTTAATTATGTCACCACA 58.324 40.909 5.20 0.00 36.78 4.17
2157 2264 6.202570 GCCAAGAACTATGCATAGAGAGAAAG 59.797 42.308 34.86 19.47 34.50 2.62
2165 2272 5.565592 TGTTTGCCAAGAACTATGCATAG 57.434 39.130 28.38 28.38 33.08 2.23
2166 2273 6.528537 AATGTTTGCCAAGAACTATGCATA 57.471 33.333 6.20 6.20 33.08 3.14
2167 2274 5.410355 AATGTTTGCCAAGAACTATGCAT 57.590 34.783 3.79 3.79 33.08 3.96
2168 2275 4.870123 AATGTTTGCCAAGAACTATGCA 57.130 36.364 0.00 0.00 0.00 3.96
2169 2276 4.389687 CCAAATGTTTGCCAAGAACTATGC 59.610 41.667 0.00 0.00 36.86 3.14
2170 2277 5.634859 GTCCAAATGTTTGCCAAGAACTATG 59.365 40.000 0.00 0.00 36.86 2.23
2226 2337 4.202182 ACTTGAAGTGAAAATGCATGTGCT 60.202 37.500 0.00 0.00 42.66 4.40
2357 2468 0.608640 ATGTGGTTGAGGAGGTCGTC 59.391 55.000 0.00 0.00 0.00 4.20
2383 2494 5.208890 TCTCTCTGGAAAGGGATTCGATTA 58.791 41.667 0.00 0.00 39.05 1.75
2694 2812 0.835543 AGAGAGAGCAACAGTGGGCT 60.836 55.000 10.89 10.89 44.48 5.19


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

AutoCloner maintained by Alex Coulton.