Multiple sequence alignment - TraesCS5D01G312900

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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 TraesCS5D01G312900 chr5D 100.000 3813 0 0 1 3813 408484188 408480376 0.000000e+00 7042.0
1 TraesCS5D01G312900 chr5D 87.097 186 21 2 5 190 504000824 504000642 1.390000e-49 207.0
2 TraesCS5D01G312900 chr5D 76.241 282 52 11 1434 1700 408482557 408482276 6.640000e-28 135.0
3 TraesCS5D01G312900 chr5D 76.241 282 52 11 1632 1913 408482755 408482489 6.640000e-28 135.0
4 TraesCS5D01G312900 chr5D 78.771 179 26 8 2770 2938 80187874 80188050 4.030000e-20 110.0
5 TraesCS5D01G312900 chr5D 78.736 174 25 9 2776 2938 9128303 9128475 5.210000e-19 106.0
6 TraesCS5D01G312900 chr5B 90.994 3631 248 32 213 3813 490053198 490049617 0.000000e+00 4820.0
7 TraesCS5D01G312900 chr5B 98.052 154 3 0 2947 3100 567240455 567240302 6.280000e-68 268.0
8 TraesCS5D01G312900 chr5B 83.513 279 39 6 2374 2647 678906036 678906312 1.760000e-63 254.0
9 TraesCS5D01G312900 chr5B 96.503 143 5 0 2958 3100 567295821 567295963 1.770000e-58 237.0
10 TraesCS5D01G312900 chr5B 88.360 189 21 1 2 190 275345972 275345785 3.830000e-55 226.0
11 TraesCS5D01G312900 chr5B 76.042 288 49 12 1431 1700 490051802 490051517 8.590000e-27 132.0
12 TraesCS5D01G312900 chr5A 92.538 2975 166 29 197 3147 514409009 514406067 0.000000e+00 4213.0
13 TraesCS5D01G312900 chr5A 90.247 687 39 7 3144 3813 514405458 514404783 0.000000e+00 872.0
14 TraesCS5D01G312900 chr5A 77.544 285 43 11 1434 1700 514407576 514407295 6.600000e-33 152.0
15 TraesCS5D01G312900 chr5A 80.503 159 21 9 2776 2925 625734792 625734635 3.110000e-21 113.0
16 TraesCS5D01G312900 chrUn 96.809 188 6 0 3103 3290 86517426 86517239 7.950000e-82 315.0
17 TraesCS5D01G312900 chrUn 96.809 188 6 0 3103 3290 206784944 206784757 7.950000e-82 315.0
18 TraesCS5D01G312900 chrUn 96.809 188 6 0 3103 3290 345388354 345388541 7.950000e-82 315.0
19 TraesCS5D01G312900 chr7D 96.809 188 6 0 3103 3290 203486285 203486098 7.950000e-82 315.0
20 TraesCS5D01G312900 chr7D 96.809 188 6 0 3103 3290 381906262 381906075 7.950000e-82 315.0
21 TraesCS5D01G312900 chr7D 88.830 188 17 2 2 189 472897617 472897800 1.070000e-55 228.0
22 TraesCS5D01G312900 chr7A 96.809 188 6 0 3103 3290 60265599 60265412 7.950000e-82 315.0
23 TraesCS5D01G312900 chr7A 84.644 267 40 1 2377 2642 260027184 260026918 8.120000e-67 265.0
24 TraesCS5D01G312900 chr7A 80.625 160 20 9 2776 2925 486923695 486923537 3.110000e-21 113.0
25 TraesCS5D01G312900 chr6D 96.809 188 6 0 3103 3290 124503820 124503633 7.950000e-82 315.0
26 TraesCS5D01G312900 chr6D 83.150 273 42 3 2377 2646 109274276 109274005 2.940000e-61 246.0
27 TraesCS5D01G312900 chr6D 80.172 116 16 6 2774 2882 427634014 427633899 3.160000e-11 80.5
28 TraesCS5D01G312900 chr4D 96.809 188 6 0 3103 3290 123321771 123321584 7.950000e-82 315.0
29 TraesCS5D01G312900 chr2B 97.516 161 4 0 2940 3100 391174738 391174578 3.750000e-70 276.0
30 TraesCS5D01G312900 chr3A 91.579 190 15 1 2 191 508378523 508378335 1.050000e-65 261.0
31 TraesCS5D01G312900 chr3A 88.398 181 20 1 2 182 7204055 7203876 2.310000e-52 217.0
32 TraesCS5D01G312900 chr2A 84.015 269 40 2 2377 2642 628728207 628727939 4.890000e-64 255.0
33 TraesCS5D01G312900 chr2A 83.643 269 41 2 2377 2642 409644255 409643987 2.270000e-62 250.0
34 TraesCS5D01G312900 chr2A 93.125 160 11 0 2940 3099 25257640 25257799 6.370000e-58 235.0
35 TraesCS5D01G312900 chr2A 93.125 160 11 0 2940 3099 25324101 25324260 6.370000e-58 235.0
36 TraesCS5D01G312900 chr2A 92.500 160 12 0 2940 3099 25306908 25307067 2.960000e-56 230.0
37 TraesCS5D01G312900 chr2A 93.431 137 9 0 2963 3099 25195321 25195457 1.800000e-48 204.0
38 TraesCS5D01G312900 chr6A 83.516 273 42 2 2373 2642 46549127 46548855 6.320000e-63 252.0
39 TraesCS5D01G312900 chr6A 78.736 174 24 11 2775 2937 592444232 592444061 1.870000e-18 104.0
40 TraesCS5D01G312900 chr1D 83.516 273 42 2 2374 2643 14667395 14667667 6.320000e-63 252.0
41 TraesCS5D01G312900 chr1D 89.474 190 18 1 2 191 96699272 96699085 4.920000e-59 239.0
42 TraesCS5D01G312900 chr1D 87.895 190 23 0 2 191 113599646 113599457 1.380000e-54 224.0
43 TraesCS5D01G312900 chr1B 88.421 190 21 1 2 191 156689437 156689625 1.070000e-55 228.0
44 TraesCS5D01G312900 chr3B 87.245 196 24 1 1 196 761366672 761366478 4.960000e-54 222.0
45 TraesCS5D01G312900 chr2D 81.507 146 20 5 2785 2925 344444363 344444220 3.110000e-21 113.0


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 TraesCS5D01G312900 chr5D 408480376 408484188 3812 True 2437.333333 7042 84.160667 1 3813 3 chr5D.!!$R2 3812
1 TraesCS5D01G312900 chr5B 490049617 490053198 3581 True 2476.000000 4820 83.518000 213 3813 2 chr5B.!!$R3 3600
2 TraesCS5D01G312900 chr5A 514404783 514409009 4226 True 1745.666667 4213 86.776333 197 3813 3 chr5A.!!$R2 3616

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
451 453 0.178975 TTCTCCCCGGCAAAACACAT 60.179 50.0 0.0 0.0 0.00 3.21 F
1347 1378 0.041047 TTCACGTACCACGACGACTG 60.041 55.0 0.0 0.0 46.05 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 1879 0.246635 ATACAAGCGAGCGTGGTCTT 59.753 50.0 14.76 0.00 0.00 3.01 R
3219 3873 0.248743 TTCATCATCGTCGGTACCGC 60.249 55.0 29.64 21.84 39.59 5.68 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
36 37 9.313118 AGTTAATTGCAAGTTTACTTTTGAAGG 57.687 29.630 4.05 0.00 33.11 3.46
37 38 9.093970 GTTAATTGCAAGTTTACTTTTGAAGGT 57.906 29.630 4.05 0.00 33.11 3.50
38 39 7.770801 AATTGCAAGTTTACTTTTGAAGGTC 57.229 32.000 4.94 0.00 33.11 3.85
39 40 4.915704 TGCAAGTTTACTTTTGAAGGTCG 58.084 39.130 0.00 0.00 33.11 4.79
40 41 4.396790 TGCAAGTTTACTTTTGAAGGTCGT 59.603 37.500 0.00 0.00 33.11 4.34
41 42 4.733405 GCAAGTTTACTTTTGAAGGTCGTG 59.267 41.667 0.00 0.00 33.11 4.35
42 43 4.547406 AGTTTACTTTTGAAGGTCGTGC 57.453 40.909 0.00 0.00 0.00 5.34
43 44 3.942748 AGTTTACTTTTGAAGGTCGTGCA 59.057 39.130 0.00 0.00 0.00 4.57
44 45 4.578928 AGTTTACTTTTGAAGGTCGTGCAT 59.421 37.500 0.00 0.00 0.00 3.96
45 46 4.742438 TTACTTTTGAAGGTCGTGCATC 57.258 40.909 0.00 0.00 0.00 3.91
46 47 2.571212 ACTTTTGAAGGTCGTGCATCA 58.429 42.857 0.00 0.00 0.00 3.07
47 48 2.948979 ACTTTTGAAGGTCGTGCATCAA 59.051 40.909 0.00 0.00 0.00 2.57
48 49 3.380004 ACTTTTGAAGGTCGTGCATCAAA 59.620 39.130 6.77 6.77 39.33 2.69
49 50 4.037923 ACTTTTGAAGGTCGTGCATCAAAT 59.962 37.500 10.74 0.00 40.36 2.32
50 51 5.240623 ACTTTTGAAGGTCGTGCATCAAATA 59.759 36.000 10.74 3.59 40.36 1.40
51 52 4.678509 TTGAAGGTCGTGCATCAAATAC 57.321 40.909 0.00 0.00 0.00 1.89
52 53 3.006940 TGAAGGTCGTGCATCAAATACC 58.993 45.455 0.00 0.00 0.00 2.73
53 54 1.651987 AGGTCGTGCATCAAATACCG 58.348 50.000 0.00 0.00 32.18 4.02
54 55 1.206132 AGGTCGTGCATCAAATACCGA 59.794 47.619 0.00 0.00 32.18 4.69
55 56 2.158957 AGGTCGTGCATCAAATACCGAT 60.159 45.455 0.00 0.00 32.18 4.18
56 57 2.032894 GGTCGTGCATCAAATACCGATG 60.033 50.000 0.00 0.00 42.62 3.84
64 65 5.791367 CATCAAATACCGATGCAGATAGG 57.209 43.478 0.00 0.00 34.32 2.57
65 66 4.955811 TCAAATACCGATGCAGATAGGT 57.044 40.909 9.57 9.57 40.44 3.08
66 67 5.290493 TCAAATACCGATGCAGATAGGTT 57.710 39.130 9.85 0.00 38.45 3.50
67 68 6.413783 TCAAATACCGATGCAGATAGGTTA 57.586 37.500 9.85 0.00 38.45 2.85
68 69 6.455647 TCAAATACCGATGCAGATAGGTTAG 58.544 40.000 9.85 0.94 38.45 2.34
69 70 2.821991 ACCGATGCAGATAGGTTAGC 57.178 50.000 0.00 0.00 34.06 3.09
70 71 2.320781 ACCGATGCAGATAGGTTAGCT 58.679 47.619 0.00 0.00 34.06 3.32
71 72 3.497332 ACCGATGCAGATAGGTTAGCTA 58.503 45.455 0.00 0.00 34.06 3.32
72 73 3.895656 ACCGATGCAGATAGGTTAGCTAA 59.104 43.478 0.86 0.86 34.06 3.09
73 74 4.021894 ACCGATGCAGATAGGTTAGCTAAG 60.022 45.833 6.38 0.00 34.06 2.18
74 75 4.021894 CCGATGCAGATAGGTTAGCTAAGT 60.022 45.833 6.38 0.00 0.00 2.24
75 76 5.509840 CCGATGCAGATAGGTTAGCTAAGTT 60.510 44.000 6.38 0.54 0.00 2.66
76 77 5.986135 CGATGCAGATAGGTTAGCTAAGTTT 59.014 40.000 6.38 0.00 0.00 2.66
77 78 6.480320 CGATGCAGATAGGTTAGCTAAGTTTT 59.520 38.462 6.38 0.00 0.00 2.43
78 79 7.306866 CGATGCAGATAGGTTAGCTAAGTTTTC 60.307 40.741 6.38 3.35 0.00 2.29
79 80 6.707290 TGCAGATAGGTTAGCTAAGTTTTCA 58.293 36.000 6.38 0.00 0.00 2.69
80 81 7.165485 TGCAGATAGGTTAGCTAAGTTTTCAA 58.835 34.615 6.38 0.00 0.00 2.69
81 82 7.663905 TGCAGATAGGTTAGCTAAGTTTTCAAA 59.336 33.333 6.38 0.00 0.00 2.69
82 83 7.963465 GCAGATAGGTTAGCTAAGTTTTCAAAC 59.037 37.037 6.38 0.00 39.17 2.93
83 84 8.999431 CAGATAGGTTAGCTAAGTTTTCAAACA 58.001 33.333 6.38 0.00 41.30 2.83
84 85 9.000486 AGATAGGTTAGCTAAGTTTTCAAACAC 58.000 33.333 6.38 0.00 41.30 3.32
85 86 8.919777 ATAGGTTAGCTAAGTTTTCAAACACT 57.080 30.769 6.38 0.00 41.30 3.55
86 87 7.260558 AGGTTAGCTAAGTTTTCAAACACTC 57.739 36.000 6.38 0.00 41.30 3.51
87 88 7.054751 AGGTTAGCTAAGTTTTCAAACACTCT 58.945 34.615 6.38 0.11 41.30 3.24
88 89 7.556635 AGGTTAGCTAAGTTTTCAAACACTCTT 59.443 33.333 6.38 0.00 41.30 2.85
89 90 7.644157 GGTTAGCTAAGTTTTCAAACACTCTTG 59.356 37.037 6.38 0.00 41.30 3.02
90 91 8.395633 GTTAGCTAAGTTTTCAAACACTCTTGA 58.604 33.333 6.38 0.00 41.30 3.02
91 92 7.573968 AGCTAAGTTTTCAAACACTCTTGAT 57.426 32.000 5.26 0.00 41.30 2.57
92 93 8.677148 AGCTAAGTTTTCAAACACTCTTGATA 57.323 30.769 5.26 0.00 41.30 2.15
93 94 9.120538 AGCTAAGTTTTCAAACACTCTTGATAA 57.879 29.630 5.26 0.00 41.30 1.75
94 95 9.899226 GCTAAGTTTTCAAACACTCTTGATAAT 57.101 29.630 5.26 0.00 41.30 1.28
97 98 7.661040 AGTTTTCAAACACTCTTGATAATGGG 58.339 34.615 5.26 0.00 41.30 4.00
98 99 5.643379 TTCAAACACTCTTGATAATGGGC 57.357 39.130 0.00 0.00 35.31 5.36
99 100 3.689161 TCAAACACTCTTGATAATGGGCG 59.311 43.478 0.00 0.00 30.31 6.13
100 101 3.627395 AACACTCTTGATAATGGGCGA 57.373 42.857 0.00 0.00 0.00 5.54
101 102 2.906354 ACACTCTTGATAATGGGCGAC 58.094 47.619 0.00 0.00 0.00 5.19
102 103 2.236146 ACACTCTTGATAATGGGCGACA 59.764 45.455 0.00 0.00 0.00 4.35
103 104 2.609459 CACTCTTGATAATGGGCGACAC 59.391 50.000 0.00 0.00 0.00 3.67
104 105 2.213499 CTCTTGATAATGGGCGACACC 58.787 52.381 0.00 0.00 37.93 4.16
105 106 1.837439 TCTTGATAATGGGCGACACCT 59.163 47.619 0.00 0.00 39.10 4.00
106 107 2.238646 TCTTGATAATGGGCGACACCTT 59.761 45.455 0.00 0.00 39.10 3.50
107 108 2.799126 TGATAATGGGCGACACCTTT 57.201 45.000 0.00 0.00 39.10 3.11
108 109 2.364632 TGATAATGGGCGACACCTTTG 58.635 47.619 0.00 0.00 39.10 2.77
109 110 1.676006 GATAATGGGCGACACCTTTGG 59.324 52.381 0.00 0.00 39.10 3.28
110 111 0.963355 TAATGGGCGACACCTTTGGC 60.963 55.000 0.00 0.00 39.10 4.52
111 112 2.713531 AATGGGCGACACCTTTGGCT 62.714 55.000 0.00 0.00 39.10 4.75
112 113 3.365265 GGGCGACACCTTTGGCTG 61.365 66.667 0.00 0.00 39.10 4.85
113 114 2.281484 GGCGACACCTTTGGCTGA 60.281 61.111 0.00 0.00 34.51 4.26
114 115 1.675641 GGCGACACCTTTGGCTGAT 60.676 57.895 0.00 0.00 34.51 2.90
115 116 1.648467 GGCGACACCTTTGGCTGATC 61.648 60.000 0.00 0.00 34.51 2.92
116 117 1.648467 GCGACACCTTTGGCTGATCC 61.648 60.000 0.00 0.00 0.00 3.36
117 118 0.321564 CGACACCTTTGGCTGATCCA 60.322 55.000 0.00 0.00 44.85 3.41
118 119 1.679944 CGACACCTTTGGCTGATCCAT 60.680 52.381 0.00 0.00 46.04 3.41
119 120 2.450476 GACACCTTTGGCTGATCCATT 58.550 47.619 0.00 0.00 46.04 3.16
120 121 2.424956 GACACCTTTGGCTGATCCATTC 59.575 50.000 0.00 0.00 46.04 2.67
121 122 1.753073 CACCTTTGGCTGATCCATTCC 59.247 52.381 0.00 0.00 46.04 3.01
122 123 1.342374 ACCTTTGGCTGATCCATTCCC 60.342 52.381 0.00 0.00 46.04 3.97
123 124 1.342275 CCTTTGGCTGATCCATTCCCA 60.342 52.381 0.00 0.00 46.04 4.37
124 125 2.674420 CTTTGGCTGATCCATTCCCAT 58.326 47.619 0.00 0.00 46.04 4.00
125 126 2.076207 TTGGCTGATCCATTCCCATG 57.924 50.000 0.00 0.00 46.04 3.66
126 127 1.224436 TGGCTGATCCATTCCCATGA 58.776 50.000 0.00 0.00 40.72 3.07
127 128 1.784593 TGGCTGATCCATTCCCATGAT 59.215 47.619 0.00 0.00 40.72 2.45
128 129 2.224942 TGGCTGATCCATTCCCATGATC 60.225 50.000 0.00 0.00 40.72 2.92
129 130 2.444421 GCTGATCCATTCCCATGATCC 58.556 52.381 0.00 0.00 31.07 3.36
130 131 2.041350 GCTGATCCATTCCCATGATCCT 59.959 50.000 0.00 0.00 31.07 3.24
131 132 3.499926 GCTGATCCATTCCCATGATCCTT 60.500 47.826 0.00 0.00 31.07 3.36
132 133 4.737578 CTGATCCATTCCCATGATCCTTT 58.262 43.478 0.00 0.00 31.07 3.11
133 134 5.145564 CTGATCCATTCCCATGATCCTTTT 58.854 41.667 0.00 0.00 31.07 2.27
134 135 5.531198 TGATCCATTCCCATGATCCTTTTT 58.469 37.500 0.00 0.00 31.07 1.94
135 136 5.364446 TGATCCATTCCCATGATCCTTTTTG 59.636 40.000 0.00 0.00 31.07 2.44
136 137 4.686891 TCCATTCCCATGATCCTTTTTGT 58.313 39.130 0.00 0.00 31.07 2.83
137 138 5.836705 TCCATTCCCATGATCCTTTTTGTA 58.163 37.500 0.00 0.00 31.07 2.41
138 139 6.442961 TCCATTCCCATGATCCTTTTTGTAT 58.557 36.000 0.00 0.00 31.07 2.29
139 140 6.324512 TCCATTCCCATGATCCTTTTTGTATG 59.675 38.462 0.00 0.00 31.07 2.39
140 141 5.596836 TTCCCATGATCCTTTTTGTATGC 57.403 39.130 0.00 0.00 0.00 3.14
141 142 3.960102 TCCCATGATCCTTTTTGTATGCC 59.040 43.478 0.00 0.00 0.00 4.40
142 143 3.705579 CCCATGATCCTTTTTGTATGCCA 59.294 43.478 0.00 0.00 0.00 4.92
143 144 4.441913 CCCATGATCCTTTTTGTATGCCAC 60.442 45.833 0.00 0.00 0.00 5.01
144 145 4.403432 CCATGATCCTTTTTGTATGCCACT 59.597 41.667 0.00 0.00 0.00 4.00
145 146 5.105228 CCATGATCCTTTTTGTATGCCACTT 60.105 40.000 0.00 0.00 0.00 3.16
146 147 5.643379 TGATCCTTTTTGTATGCCACTTC 57.357 39.130 0.00 0.00 0.00 3.01
147 148 5.076182 TGATCCTTTTTGTATGCCACTTCA 58.924 37.500 0.00 0.00 0.00 3.02
148 149 5.538053 TGATCCTTTTTGTATGCCACTTCAA 59.462 36.000 0.00 0.00 0.00 2.69
149 150 5.452078 TCCTTTTTGTATGCCACTTCAAG 57.548 39.130 0.00 0.00 0.00 3.02
150 151 4.892934 TCCTTTTTGTATGCCACTTCAAGT 59.107 37.500 0.00 0.00 0.00 3.16
151 152 4.984161 CCTTTTTGTATGCCACTTCAAGTG 59.016 41.667 10.91 10.91 45.53 3.16
166 167 8.722480 CACTTCAAGTGGTCTATGATCAATAA 57.278 34.615 9.96 0.00 42.35 1.40
167 168 9.166173 CACTTCAAGTGGTCTATGATCAATAAA 57.834 33.333 9.96 0.00 42.35 1.40
168 169 9.388506 ACTTCAAGTGGTCTATGATCAATAAAG 57.611 33.333 0.00 0.00 0.00 1.85
169 170 7.792374 TCAAGTGGTCTATGATCAATAAAGC 57.208 36.000 0.00 0.00 0.00 3.51
170 171 7.568349 TCAAGTGGTCTATGATCAATAAAGCT 58.432 34.615 0.00 0.00 0.00 3.74
171 172 8.049117 TCAAGTGGTCTATGATCAATAAAGCTT 58.951 33.333 0.00 0.00 0.00 3.74
172 173 9.330063 CAAGTGGTCTATGATCAATAAAGCTTA 57.670 33.333 0.00 0.00 0.00 3.09
173 174 9.553064 AAGTGGTCTATGATCAATAAAGCTTAG 57.447 33.333 0.00 0.00 0.00 2.18
174 175 8.709308 AGTGGTCTATGATCAATAAAGCTTAGT 58.291 33.333 0.00 0.00 0.00 2.24
175 176 9.331282 GTGGTCTATGATCAATAAAGCTTAGTT 57.669 33.333 0.00 0.00 0.00 2.24
211 212 5.979288 AACGAGTCTACTTGTAGAATGGT 57.021 39.130 16.11 16.11 39.59 3.55
237 239 6.442952 TGACCGTGGTTAATTCAAAAGATTG 58.557 36.000 0.00 0.00 37.92 2.67
255 257 5.349809 AGATTGCTTCTTACCGCTAGTAAC 58.650 41.667 0.00 0.00 35.98 2.50
270 272 5.661458 GCTAGTAACAAGTATCTTGAGCCA 58.339 41.667 15.04 0.00 0.00 4.75
289 291 2.422597 CAACCGTGCTAATTGAGTCCA 58.577 47.619 0.00 0.00 0.00 4.02
451 453 0.178975 TTCTCCCCGGCAAAACACAT 60.179 50.000 0.00 0.00 0.00 3.21
462 464 3.042887 GCAAAACACATTCCAGTTCGTC 58.957 45.455 0.00 0.00 0.00 4.20
470 472 1.740332 TTCCAGTTCGTCACCGCTGA 61.740 55.000 0.00 0.00 0.00 4.26
471 473 1.734477 CCAGTTCGTCACCGCTGAG 60.734 63.158 0.00 0.00 0.00 3.35
479 481 2.553602 TCGTCACCGCTGAGTAAGTAAA 59.446 45.455 0.00 0.00 0.00 2.01
480 482 2.915463 CGTCACCGCTGAGTAAGTAAAG 59.085 50.000 0.00 0.00 0.00 1.85
481 483 3.365666 CGTCACCGCTGAGTAAGTAAAGA 60.366 47.826 0.00 0.00 0.00 2.52
482 484 4.167268 GTCACCGCTGAGTAAGTAAAGAG 58.833 47.826 0.00 0.00 0.00 2.85
483 485 3.192844 TCACCGCTGAGTAAGTAAAGAGG 59.807 47.826 0.00 0.00 35.89 3.69
484 486 3.192844 CACCGCTGAGTAAGTAAAGAGGA 59.807 47.826 0.00 0.00 34.15 3.71
485 487 3.830755 ACCGCTGAGTAAGTAAAGAGGAA 59.169 43.478 0.00 0.00 34.15 3.36
486 488 4.282703 ACCGCTGAGTAAGTAAAGAGGAAA 59.717 41.667 0.00 0.00 34.15 3.13
487 489 4.865365 CCGCTGAGTAAGTAAAGAGGAAAG 59.135 45.833 0.00 0.00 31.90 2.62
488 490 5.471257 CGCTGAGTAAGTAAAGAGGAAAGT 58.529 41.667 0.00 0.00 0.00 2.66
489 491 6.349944 CCGCTGAGTAAGTAAAGAGGAAAGTA 60.350 42.308 0.00 0.00 31.90 2.24
490 492 7.088905 CGCTGAGTAAGTAAAGAGGAAAGTAA 58.911 38.462 0.00 0.00 0.00 2.24
491 493 7.597743 CGCTGAGTAAGTAAAGAGGAAAGTAAA 59.402 37.037 0.00 0.00 0.00 2.01
539 541 2.532235 CATGCATGGTTGTATGTGTGC 58.468 47.619 19.40 0.00 40.06 4.57
563 565 6.676456 GCCATTGATGTATGTCTGTGTTTCTC 60.676 42.308 0.00 0.00 0.00 2.87
569 571 3.584406 ATGTCTGTGTTTCTCTCTCCG 57.416 47.619 0.00 0.00 0.00 4.63
858 880 5.390251 GCCATAGATTAGTGCATGTTGATCG 60.390 44.000 0.00 0.00 0.00 3.69
861 883 4.375272 AGATTAGTGCATGTTGATCGAGG 58.625 43.478 0.00 0.00 0.00 4.63
866 888 1.137675 TGCATGTTGATCGAGGAGGAG 59.862 52.381 0.00 0.00 0.00 3.69
935 957 3.450457 AGTTAACTCTGGCTGGAGATCAG 59.550 47.826 1.12 0.00 46.03 2.90
1050 1078 3.144506 CAGCCTGAGAGAAGCAAGAAAA 58.855 45.455 0.00 0.00 0.00 2.29
1053 1084 5.413833 CAGCCTGAGAGAAGCAAGAAAATAA 59.586 40.000 0.00 0.00 0.00 1.40
1073 1104 2.031163 ACCACACTCTTGCTCGCC 59.969 61.111 0.00 0.00 0.00 5.54
1161 1192 1.074319 GTGTACGCGGCGATCAAGAA 61.074 55.000 30.94 4.04 0.00 2.52
1327 1358 4.003788 CCACCCGACGAGCTTGGT 62.004 66.667 5.79 0.00 0.00 3.67
1331 1362 1.301401 CCCGACGAGCTTGGTTTCA 60.301 57.895 5.79 0.00 0.00 2.69
1337 1368 0.788391 CGAGCTTGGTTTCACGTACC 59.212 55.000 0.00 0.00 36.17 3.34
1341 1372 1.855513 CTTGGTTTCACGTACCACGA 58.144 50.000 8.20 0.00 46.05 4.35
1346 1377 0.662619 TTTCACGTACCACGACGACT 59.337 50.000 0.00 0.00 46.05 4.18
1347 1378 0.041047 TTCACGTACCACGACGACTG 60.041 55.000 0.00 0.00 46.05 3.51
1348 1379 2.078914 CACGTACCACGACGACTGC 61.079 63.158 0.00 0.00 46.05 4.40
1349 1380 2.868331 CGTACCACGACGACTGCG 60.868 66.667 0.00 0.00 46.05 5.18
1350 1381 3.170585 GTACCACGACGACTGCGC 61.171 66.667 0.00 0.00 42.48 6.09
1351 1382 3.359523 TACCACGACGACTGCGCT 61.360 61.111 9.73 0.00 42.48 5.92
1352 1383 3.318539 TACCACGACGACTGCGCTC 62.319 63.158 9.73 0.00 42.48 5.03
1380 1411 2.766400 CGCCACCGGAGAGTCTCTC 61.766 68.421 20.00 20.00 42.66 3.20
1404 1435 1.617947 AAGCTTTCCTCGGCGGATCT 61.618 55.000 7.21 0.00 42.70 2.75
1415 1446 2.252855 CGGATCTCTACGAGCGCC 59.747 66.667 2.29 0.00 0.00 6.53
1418 1449 1.284408 GATCTCTACGAGCGCCTGG 59.716 63.158 2.29 0.00 0.00 4.45
1421 1452 3.417275 CTCTACGAGCGCCTGGTGG 62.417 68.421 2.29 1.41 0.00 4.61
1814 1848 2.746277 CCAGCCGAAAAGACCCCG 60.746 66.667 0.00 0.00 0.00 5.73
1862 1896 1.956170 CAAGACCACGCTCGCTTGT 60.956 57.895 0.00 0.00 34.54 3.16
1864 1898 0.246635 AAGACCACGCTCGCTTGTAT 59.753 50.000 0.00 0.00 0.00 2.29
2112 2146 0.040067 GCCTTGTTGCTTTCTGTCGG 60.040 55.000 0.00 0.00 0.00 4.79
2315 2349 6.936900 TGGTTCACAAAAGAAAATGGTTGAAA 59.063 30.769 0.00 0.00 0.00 2.69
2323 2357 7.832503 AAAGAAAATGGTTGAAAAGTGACTG 57.167 32.000 0.00 0.00 0.00 3.51
2328 2362 2.025793 TGGTTGAAAAGTGACTGGGACA 60.026 45.455 0.00 0.00 0.00 4.02
2331 2365 1.226746 GAAAAGTGACTGGGACACCG 58.773 55.000 0.00 0.00 40.75 4.94
2384 2419 5.343249 ACGTGTTTACTAACCGTGATATCC 58.657 41.667 0.00 0.00 38.67 2.59
2412 2447 6.012858 AGTCCATCAGGGTTTAAGTGTTGATA 60.013 38.462 0.00 0.00 38.11 2.15
2417 2452 4.092968 CAGGGTTTAAGTGTTGATACTCGC 59.907 45.833 0.00 0.00 0.00 5.03
2501 2536 2.124983 ACTACGAGGCGCCTACGA 60.125 61.111 37.37 25.26 43.93 3.43
2533 2568 6.366061 CGTAAAATCTCAAGATGATATGCCGA 59.634 38.462 0.00 0.00 34.49 5.54
2542 2577 3.505680 AGATGATATGCCGACTCAGTCTC 59.494 47.826 2.61 0.00 0.00 3.36
2576 2611 0.037326 ATGAGTAGGGTGTGTGTGCG 60.037 55.000 0.00 0.00 0.00 5.34
2577 2612 2.027625 GAGTAGGGTGTGTGTGCGC 61.028 63.158 0.00 0.00 0.00 6.09
2578 2613 3.411351 GTAGGGTGTGTGTGCGCG 61.411 66.667 0.00 0.00 0.00 6.86
2588 2623 2.256174 GTGTGTGCGCGTTAATAGAGA 58.744 47.619 8.43 0.00 0.00 3.10
2603 2638 7.411264 CGTTAATAGAGATGAGTGTATGCATGC 60.411 40.741 11.82 11.82 0.00 4.06
2615 2650 6.775088 AGTGTATGCATGCATATATAAACGC 58.225 36.000 36.01 29.89 40.49 4.84
2618 2653 8.387354 GTGTATGCATGCATATATAAACGCTTA 58.613 33.333 36.01 14.24 40.49 3.09
2847 2889 3.247006 ACAATGAGTACACATCCGACC 57.753 47.619 6.24 0.00 0.00 4.79
2853 2895 1.819288 AGTACACATCCGACCTCTGTG 59.181 52.381 0.00 0.00 44.51 3.66
3054 3096 4.128925 TCATCATCTTCAAAGTCTCCCG 57.871 45.455 0.00 0.00 0.00 5.14
3055 3097 3.769300 TCATCATCTTCAAAGTCTCCCGA 59.231 43.478 0.00 0.00 0.00 5.14
3213 3867 8.665685 GTCAACAAGATTCTAAACGAATACCAT 58.334 33.333 0.00 0.00 42.31 3.55
3219 3873 8.888579 AGATTCTAAACGAATACCATAAGTGG 57.111 34.615 0.00 0.00 45.49 4.00
3248 3902 3.917380 CGACGATGATGAAGAGATAAGGC 59.083 47.826 0.00 0.00 0.00 4.35
3402 4064 1.380650 GTCGCTCCTCCTCCTCCTT 60.381 63.158 0.00 0.00 0.00 3.36
3454 4119 1.032794 CGTAGATGGGCAGCACTCTA 58.967 55.000 0.00 0.00 0.00 2.43
3519 4184 2.741985 TGTGTTGGCCTCGATGCG 60.742 61.111 3.32 0.00 0.00 4.73
3589 4254 1.979155 CTCGTGCTCAGACTCCCCA 60.979 63.158 0.00 0.00 0.00 4.96
3618 4296 0.389166 CGTGTCAGTCTCCTTGAGGC 60.389 60.000 0.00 0.00 34.04 4.70
3654 4332 2.064014 GTGCTCGTACTTAACCACCAC 58.936 52.381 0.00 0.00 0.00 4.16
3724 4402 1.005037 ATCGTGCTCTGTGGCGAAA 60.005 52.632 0.00 0.00 36.92 3.46
3795 4473 4.069232 CGAGAAGGCAGCCCGACA 62.069 66.667 8.22 0.00 35.76 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.313118 CCTTCAAAAGTAAACTTGCAATTAACT 57.687 29.630 0.00 0.00 36.12 2.24
11 12 9.093970 ACCTTCAAAAGTAAACTTGCAATTAAC 57.906 29.630 0.00 0.00 36.12 2.01
12 13 9.308318 GACCTTCAAAAGTAAACTTGCAATTAA 57.692 29.630 0.00 0.00 36.12 1.40
13 14 7.646130 CGACCTTCAAAAGTAAACTTGCAATTA 59.354 33.333 0.00 0.00 36.12 1.40
14 15 6.475402 CGACCTTCAAAAGTAAACTTGCAATT 59.525 34.615 0.00 0.00 36.12 2.32
15 16 5.977129 CGACCTTCAAAAGTAAACTTGCAAT 59.023 36.000 0.00 0.00 36.12 3.56
16 17 5.106078 ACGACCTTCAAAAGTAAACTTGCAA 60.106 36.000 0.00 0.00 36.12 4.08
17 18 4.396790 ACGACCTTCAAAAGTAAACTTGCA 59.603 37.500 0.00 0.00 36.12 4.08
18 19 4.733405 CACGACCTTCAAAAGTAAACTTGC 59.267 41.667 0.00 0.00 36.12 4.01
19 20 4.733405 GCACGACCTTCAAAAGTAAACTTG 59.267 41.667 0.00 0.00 36.12 3.16
20 21 4.396790 TGCACGACCTTCAAAAGTAAACTT 59.603 37.500 0.00 0.00 37.91 2.66
21 22 3.942748 TGCACGACCTTCAAAAGTAAACT 59.057 39.130 0.00 0.00 0.00 2.66
22 23 4.281525 TGCACGACCTTCAAAAGTAAAC 57.718 40.909 0.00 0.00 0.00 2.01
23 24 4.576873 TGATGCACGACCTTCAAAAGTAAA 59.423 37.500 0.00 0.00 0.00 2.01
24 25 4.130857 TGATGCACGACCTTCAAAAGTAA 58.869 39.130 0.00 0.00 0.00 2.24
25 26 3.734463 TGATGCACGACCTTCAAAAGTA 58.266 40.909 0.00 0.00 0.00 2.24
26 27 2.571212 TGATGCACGACCTTCAAAAGT 58.429 42.857 0.00 0.00 0.00 2.66
27 28 3.624326 TTGATGCACGACCTTCAAAAG 57.376 42.857 0.00 0.00 0.00 2.27
28 29 4.582701 ATTTGATGCACGACCTTCAAAA 57.417 36.364 13.26 0.72 40.18 2.44
29 30 4.083003 GGTATTTGATGCACGACCTTCAAA 60.083 41.667 12.01 12.01 40.68 2.69
30 31 3.438781 GGTATTTGATGCACGACCTTCAA 59.561 43.478 0.00 0.00 0.00 2.69
31 32 3.006940 GGTATTTGATGCACGACCTTCA 58.993 45.455 0.00 0.00 0.00 3.02
32 33 2.030457 CGGTATTTGATGCACGACCTTC 59.970 50.000 0.00 0.00 0.00 3.46
33 34 2.006888 CGGTATTTGATGCACGACCTT 58.993 47.619 0.00 0.00 0.00 3.50
34 35 1.206132 TCGGTATTTGATGCACGACCT 59.794 47.619 0.00 0.00 0.00 3.85
35 36 1.647346 TCGGTATTTGATGCACGACC 58.353 50.000 0.00 0.00 0.00 4.79
36 37 3.238903 CATCGGTATTTGATGCACGAC 57.761 47.619 0.00 0.00 37.07 4.34
42 43 5.240891 ACCTATCTGCATCGGTATTTGATG 58.759 41.667 0.00 0.00 44.77 3.07
43 44 5.489792 ACCTATCTGCATCGGTATTTGAT 57.510 39.130 0.00 0.00 0.00 2.57
44 45 4.955811 ACCTATCTGCATCGGTATTTGA 57.044 40.909 0.00 0.00 0.00 2.69
45 46 5.120830 GCTAACCTATCTGCATCGGTATTTG 59.879 44.000 0.00 0.00 27.78 2.32
46 47 5.012148 AGCTAACCTATCTGCATCGGTATTT 59.988 40.000 0.00 0.00 27.78 1.40
47 48 4.528596 AGCTAACCTATCTGCATCGGTATT 59.471 41.667 0.00 0.00 27.78 1.89
48 49 4.090090 AGCTAACCTATCTGCATCGGTAT 58.910 43.478 0.00 0.00 27.78 2.73
49 50 3.497332 AGCTAACCTATCTGCATCGGTA 58.503 45.455 0.00 0.00 27.78 4.02
50 51 2.320781 AGCTAACCTATCTGCATCGGT 58.679 47.619 0.00 0.00 28.99 4.69
51 52 4.021894 ACTTAGCTAACCTATCTGCATCGG 60.022 45.833 0.86 0.00 0.00 4.18
52 53 5.127693 ACTTAGCTAACCTATCTGCATCG 57.872 43.478 0.86 0.00 0.00 3.84
53 54 7.495934 TGAAAACTTAGCTAACCTATCTGCATC 59.504 37.037 0.86 0.00 0.00 3.91
54 55 7.338710 TGAAAACTTAGCTAACCTATCTGCAT 58.661 34.615 0.86 0.00 0.00 3.96
55 56 6.707290 TGAAAACTTAGCTAACCTATCTGCA 58.293 36.000 0.86 0.00 0.00 4.41
56 57 7.611213 TTGAAAACTTAGCTAACCTATCTGC 57.389 36.000 0.86 0.00 0.00 4.26
57 58 8.999431 TGTTTGAAAACTTAGCTAACCTATCTG 58.001 33.333 0.86 0.00 39.59 2.90
58 59 9.000486 GTGTTTGAAAACTTAGCTAACCTATCT 58.000 33.333 0.86 0.00 39.59 1.98
59 60 9.000486 AGTGTTTGAAAACTTAGCTAACCTATC 58.000 33.333 0.86 0.34 39.59 2.08
60 61 8.919777 AGTGTTTGAAAACTTAGCTAACCTAT 57.080 30.769 0.86 0.00 39.59 2.57
61 62 8.208903 AGAGTGTTTGAAAACTTAGCTAACCTA 58.791 33.333 0.86 0.00 39.59 3.08
62 63 7.054751 AGAGTGTTTGAAAACTTAGCTAACCT 58.945 34.615 0.86 0.00 39.59 3.50
63 64 7.260558 AGAGTGTTTGAAAACTTAGCTAACC 57.739 36.000 0.86 0.00 39.59 2.85
64 65 8.395633 TCAAGAGTGTTTGAAAACTTAGCTAAC 58.604 33.333 0.86 0.00 39.59 2.34
65 66 8.500753 TCAAGAGTGTTTGAAAACTTAGCTAA 57.499 30.769 5.94 5.94 39.59 3.09
66 67 8.677148 ATCAAGAGTGTTTGAAAACTTAGCTA 57.323 30.769 7.39 0.00 40.21 3.32
67 68 7.573968 ATCAAGAGTGTTTGAAAACTTAGCT 57.426 32.000 7.39 0.00 40.21 3.32
68 69 9.899226 ATTATCAAGAGTGTTTGAAAACTTAGC 57.101 29.630 7.39 0.00 40.21 3.09
71 72 8.143835 CCCATTATCAAGAGTGTTTGAAAACTT 58.856 33.333 7.39 0.00 40.21 2.66
72 73 7.661040 CCCATTATCAAGAGTGTTTGAAAACT 58.339 34.615 7.39 0.00 40.21 2.66
73 74 6.366061 GCCCATTATCAAGAGTGTTTGAAAAC 59.634 38.462 0.00 0.00 40.21 2.43
74 75 6.454795 GCCCATTATCAAGAGTGTTTGAAAA 58.545 36.000 0.00 0.00 40.21 2.29
75 76 5.335583 CGCCCATTATCAAGAGTGTTTGAAA 60.336 40.000 0.00 0.00 40.21 2.69
76 77 4.155826 CGCCCATTATCAAGAGTGTTTGAA 59.844 41.667 0.00 0.00 40.21 2.69
77 78 3.689161 CGCCCATTATCAAGAGTGTTTGA 59.311 43.478 0.00 0.00 41.00 2.69
78 79 3.689161 TCGCCCATTATCAAGAGTGTTTG 59.311 43.478 0.00 0.00 0.00 2.93
79 80 3.689649 GTCGCCCATTATCAAGAGTGTTT 59.310 43.478 0.00 0.00 0.00 2.83
80 81 3.270877 GTCGCCCATTATCAAGAGTGTT 58.729 45.455 0.00 0.00 0.00 3.32
81 82 2.236146 TGTCGCCCATTATCAAGAGTGT 59.764 45.455 0.00 0.00 0.00 3.55
82 83 2.609459 GTGTCGCCCATTATCAAGAGTG 59.391 50.000 0.00 0.00 0.00 3.51
83 84 2.420129 GGTGTCGCCCATTATCAAGAGT 60.420 50.000 0.00 0.00 0.00 3.24
84 85 2.158900 AGGTGTCGCCCATTATCAAGAG 60.159 50.000 0.00 0.00 38.26 2.85
85 86 1.837439 AGGTGTCGCCCATTATCAAGA 59.163 47.619 0.00 0.00 38.26 3.02
86 87 2.332063 AGGTGTCGCCCATTATCAAG 57.668 50.000 0.00 0.00 38.26 3.02
87 88 2.752354 CAAAGGTGTCGCCCATTATCAA 59.248 45.455 0.00 0.00 38.26 2.57
88 89 2.364632 CAAAGGTGTCGCCCATTATCA 58.635 47.619 0.00 0.00 38.26 2.15
89 90 1.676006 CCAAAGGTGTCGCCCATTATC 59.324 52.381 0.00 0.00 38.26 1.75
90 91 1.762708 CCAAAGGTGTCGCCCATTAT 58.237 50.000 0.00 0.00 38.26 1.28
91 92 0.963355 GCCAAAGGTGTCGCCCATTA 60.963 55.000 0.00 0.00 38.26 1.90
92 93 2.275380 GCCAAAGGTGTCGCCCATT 61.275 57.895 0.00 0.00 38.26 3.16
93 94 2.676471 GCCAAAGGTGTCGCCCAT 60.676 61.111 0.00 0.00 38.26 4.00
94 95 3.884774 AGCCAAAGGTGTCGCCCA 61.885 61.111 0.00 0.00 38.26 5.36
95 96 3.365265 CAGCCAAAGGTGTCGCCC 61.365 66.667 0.00 0.00 38.26 6.13
96 97 1.648467 GATCAGCCAAAGGTGTCGCC 61.648 60.000 0.00 0.00 42.30 5.54
97 98 1.648467 GGATCAGCCAAAGGTGTCGC 61.648 60.000 0.00 0.00 42.30 5.19
98 99 0.321564 TGGATCAGCCAAAGGTGTCG 60.322 55.000 0.00 0.00 45.87 4.35
99 100 3.650647 TGGATCAGCCAAAGGTGTC 57.349 52.632 0.00 0.00 45.87 3.67
108 109 2.444421 GATCATGGGAATGGATCAGCC 58.556 52.381 0.00 0.00 37.85 4.85
109 110 2.041350 AGGATCATGGGAATGGATCAGC 59.959 50.000 0.00 0.00 39.30 4.26
110 111 4.383931 AAGGATCATGGGAATGGATCAG 57.616 45.455 0.00 0.00 39.30 2.90
111 112 4.819702 AAAGGATCATGGGAATGGATCA 57.180 40.909 0.00 0.00 39.30 2.92
112 113 5.364735 ACAAAAAGGATCATGGGAATGGATC 59.635 40.000 0.00 0.00 37.34 3.36
113 114 5.282946 ACAAAAAGGATCATGGGAATGGAT 58.717 37.500 0.00 0.00 0.00 3.41
114 115 4.686891 ACAAAAAGGATCATGGGAATGGA 58.313 39.130 0.00 0.00 0.00 3.41
115 116 6.518493 CATACAAAAAGGATCATGGGAATGG 58.482 40.000 0.00 0.00 0.00 3.16
116 117 5.987347 GCATACAAAAAGGATCATGGGAATG 59.013 40.000 0.00 0.00 0.00 2.67
117 118 5.070847 GGCATACAAAAAGGATCATGGGAAT 59.929 40.000 0.00 0.00 0.00 3.01
118 119 4.405358 GGCATACAAAAAGGATCATGGGAA 59.595 41.667 0.00 0.00 0.00 3.97
119 120 3.960102 GGCATACAAAAAGGATCATGGGA 59.040 43.478 0.00 0.00 0.00 4.37
120 121 3.705579 TGGCATACAAAAAGGATCATGGG 59.294 43.478 0.00 0.00 0.00 4.00
121 122 4.403432 AGTGGCATACAAAAAGGATCATGG 59.597 41.667 0.00 0.00 0.00 3.66
122 123 5.587388 AGTGGCATACAAAAAGGATCATG 57.413 39.130 0.00 0.00 0.00 3.07
123 124 5.716228 TGAAGTGGCATACAAAAAGGATCAT 59.284 36.000 0.00 0.00 0.00 2.45
124 125 5.076182 TGAAGTGGCATACAAAAAGGATCA 58.924 37.500 0.00 0.00 0.00 2.92
125 126 5.643379 TGAAGTGGCATACAAAAAGGATC 57.357 39.130 0.00 0.00 0.00 3.36
126 127 5.539955 ACTTGAAGTGGCATACAAAAAGGAT 59.460 36.000 0.00 0.00 0.00 3.24
127 128 4.892934 ACTTGAAGTGGCATACAAAAAGGA 59.107 37.500 0.00 0.00 0.00 3.36
128 129 4.984161 CACTTGAAGTGGCATACAAAAAGG 59.016 41.667 17.27 0.00 42.35 3.11
141 142 8.722480 TTATTGATCATAGACCACTTGAAGTG 57.278 34.615 18.04 18.04 45.53 3.16
142 143 9.388506 CTTTATTGATCATAGACCACTTGAAGT 57.611 33.333 0.00 0.00 0.00 3.01
143 144 8.341173 GCTTTATTGATCATAGACCACTTGAAG 58.659 37.037 0.00 0.00 0.00 3.02
144 145 8.049117 AGCTTTATTGATCATAGACCACTTGAA 58.951 33.333 0.00 0.00 0.00 2.69
145 146 7.568349 AGCTTTATTGATCATAGACCACTTGA 58.432 34.615 0.00 0.00 0.00 3.02
146 147 7.798596 AGCTTTATTGATCATAGACCACTTG 57.201 36.000 0.00 0.00 0.00 3.16
147 148 9.553064 CTAAGCTTTATTGATCATAGACCACTT 57.447 33.333 3.20 0.00 0.00 3.16
148 149 8.709308 ACTAAGCTTTATTGATCATAGACCACT 58.291 33.333 3.20 0.00 0.00 4.00
149 150 8.894768 ACTAAGCTTTATTGATCATAGACCAC 57.105 34.615 3.20 0.00 0.00 4.16
186 187 7.215085 ACCATTCTACAAGTAGACTCGTTTTT 58.785 34.615 9.34 0.00 41.48 1.94
187 188 6.756221 ACCATTCTACAAGTAGACTCGTTTT 58.244 36.000 9.34 0.00 41.48 2.43
188 189 6.342338 ACCATTCTACAAGTAGACTCGTTT 57.658 37.500 9.34 0.00 41.48 3.60
189 190 5.979288 ACCATTCTACAAGTAGACTCGTT 57.021 39.130 9.34 0.00 41.48 3.85
190 191 6.827251 TCATACCATTCTACAAGTAGACTCGT 59.173 38.462 9.34 6.32 41.48 4.18
191 192 7.133513 GTCATACCATTCTACAAGTAGACTCG 58.866 42.308 9.34 0.76 41.48 4.18
192 193 7.427214 GGTCATACCATTCTACAAGTAGACTC 58.573 42.308 9.34 0.00 38.83 3.36
193 194 6.039493 CGGTCATACCATTCTACAAGTAGACT 59.961 42.308 9.34 2.11 38.88 3.24
194 195 6.183360 ACGGTCATACCATTCTACAAGTAGAC 60.183 42.308 9.34 0.00 38.88 2.59
195 196 5.889853 ACGGTCATACCATTCTACAAGTAGA 59.110 40.000 5.86 5.86 38.47 2.59
211 212 7.931578 ATCTTTTGAATTAACCACGGTCATA 57.068 32.000 0.00 0.00 0.00 2.15
255 257 2.416547 CACGGTTGGCTCAAGATACTTG 59.583 50.000 5.29 5.29 0.00 3.16
270 272 2.301870 TCTGGACTCAATTAGCACGGTT 59.698 45.455 0.00 0.00 0.00 4.44
382 384 1.278127 TGGATCTCGTTGTTCCCTTCC 59.722 52.381 0.00 0.00 34.43 3.46
388 390 0.442699 GCCGTTGGATCTCGTTGTTC 59.557 55.000 0.00 0.00 0.00 3.18
422 424 1.078143 CGGGGAGAAGAAGCCAAGG 60.078 63.158 0.00 0.00 0.00 3.61
462 464 3.192844 TCCTCTTTACTTACTCAGCGGTG 59.807 47.826 8.67 8.67 0.00 4.94
470 472 9.473640 CGTTCTTTACTTTCCTCTTTACTTACT 57.526 33.333 0.00 0.00 0.00 2.24
471 473 8.706936 CCGTTCTTTACTTTCCTCTTTACTTAC 58.293 37.037 0.00 0.00 0.00 2.34
479 481 4.950205 TCACCGTTCTTTACTTTCCTCT 57.050 40.909 0.00 0.00 0.00 3.69
480 482 5.996669 TTTCACCGTTCTTTACTTTCCTC 57.003 39.130 0.00 0.00 0.00 3.71
481 483 7.447594 TCTATTTCACCGTTCTTTACTTTCCT 58.552 34.615 0.00 0.00 0.00 3.36
482 484 7.601508 TCTCTATTTCACCGTTCTTTACTTTCC 59.398 37.037 0.00 0.00 0.00 3.13
483 485 8.530269 TCTCTATTTCACCGTTCTTTACTTTC 57.470 34.615 0.00 0.00 0.00 2.62
484 486 8.365647 TCTCTCTATTTCACCGTTCTTTACTTT 58.634 33.333 0.00 0.00 0.00 2.66
485 487 7.813627 GTCTCTCTATTTCACCGTTCTTTACTT 59.186 37.037 0.00 0.00 0.00 2.24
486 488 7.039923 TGTCTCTCTATTTCACCGTTCTTTACT 60.040 37.037 0.00 0.00 0.00 2.24
487 489 7.088905 TGTCTCTCTATTTCACCGTTCTTTAC 58.911 38.462 0.00 0.00 0.00 2.01
488 490 7.223260 TGTCTCTCTATTTCACCGTTCTTTA 57.777 36.000 0.00 0.00 0.00 1.85
489 491 6.097915 TGTCTCTCTATTTCACCGTTCTTT 57.902 37.500 0.00 0.00 0.00 2.52
490 492 5.723672 TGTCTCTCTATTTCACCGTTCTT 57.276 39.130 0.00 0.00 0.00 2.52
491 493 5.723672 TTGTCTCTCTATTTCACCGTTCT 57.276 39.130 0.00 0.00 0.00 3.01
539 541 6.596888 AGAGAAACACAGACATACATCAATGG 59.403 38.462 0.00 0.00 0.00 3.16
602 612 3.446968 ACCATACACTAACAGGTAGCCA 58.553 45.455 0.00 0.00 32.45 4.75
866 888 5.468540 AATTTTCAACTGGTTAAGGAGGC 57.531 39.130 0.00 0.00 0.00 4.70
935 957 2.882137 CAGAGGAGGAGATTAGACCGTC 59.118 54.545 0.00 0.00 0.00 4.79
1050 1078 2.867109 AGCAAGAGTGTGGTGCTTAT 57.133 45.000 0.00 0.00 46.25 1.73
1161 1192 2.672307 ACGACGACCTCCGCTTCT 60.672 61.111 0.00 0.00 43.32 2.85
1312 1343 1.301479 GAAACCAAGCTCGTCGGGT 60.301 57.895 0.00 0.00 34.43 5.28
1324 1355 0.594540 CGTCGTGGTACGTGAAACCA 60.595 55.000 4.53 4.53 44.75 3.67
1327 1358 0.662619 AGTCGTCGTGGTACGTGAAA 59.337 50.000 0.00 0.00 43.14 2.69
1331 1362 2.253452 GCAGTCGTCGTGGTACGT 59.747 61.111 0.00 0.00 43.14 3.57
1361 1392 3.063084 GAGACTCTCCGGTGGCGT 61.063 66.667 0.00 0.00 0.00 5.68
1369 1400 1.725066 CTTCCGCGAGAGACTCTCC 59.275 63.158 23.78 16.12 40.34 3.71
1404 1435 3.449227 CCACCAGGCGCTCGTAGA 61.449 66.667 7.64 0.00 0.00 2.59
1521 1552 2.434884 AGCCTCCGTCGCATTGTG 60.435 61.111 0.00 0.00 0.00 3.33
1617 1651 3.878519 CCCGTCCTCTCGTCTCGC 61.879 72.222 0.00 0.00 0.00 5.03
1759 1793 1.536943 GCGAGAGACCCTCCAGTTGT 61.537 60.000 0.00 0.00 38.71 3.32
1845 1879 0.246635 ATACAAGCGAGCGTGGTCTT 59.753 50.000 14.76 0.00 0.00 3.01
1849 1883 2.813179 GCCATACAAGCGAGCGTGG 61.813 63.158 14.76 8.50 0.00 4.94
1871 1905 1.255882 CAGCTCTGAGACTGGTGACT 58.744 55.000 9.28 0.00 0.00 3.41
2071 2105 3.248446 TTAGGCGCCACTGACCCAC 62.248 63.158 31.54 0.00 0.00 4.61
2286 2320 6.829849 ACCATTTTCTTTTGTGAACCATCAT 58.170 32.000 0.00 0.00 38.01 2.45
2294 2328 7.875041 TCACTTTTCAACCATTTTCTTTTGTGA 59.125 29.630 0.00 0.00 0.00 3.58
2315 2349 0.470456 TACCGGTGTCCCAGTCACTT 60.470 55.000 19.93 0.00 36.25 3.16
2323 2357 2.288640 CCGATTCTTATACCGGTGTCCC 60.289 54.545 19.93 0.00 37.40 4.46
2328 2362 3.155501 CTCCTCCGATTCTTATACCGGT 58.844 50.000 13.98 13.98 42.34 5.28
2331 2365 4.759183 ACGTACTCCTCCGATTCTTATACC 59.241 45.833 0.00 0.00 0.00 2.73
2333 2367 7.498900 TGTTTACGTACTCCTCCGATTCTTATA 59.501 37.037 0.00 0.00 0.00 0.98
2375 2410 1.970640 TGATGGACTGGGGATATCACG 59.029 52.381 4.83 0.00 0.00 4.35
2457 2492 5.072329 ACGGAGACATCTTATCCCATTGAAT 59.928 40.000 0.00 0.00 0.00 2.57
2465 2500 2.879646 AGTCGACGGAGACATCTTATCC 59.120 50.000 10.46 0.00 43.24 2.59
2501 2536 8.954950 ATCATCTTGAGATTTTACGAAGTCAT 57.045 30.769 0.00 0.00 35.39 3.06
2533 2568 0.322997 CCACCTCCGAGAGACTGAGT 60.323 60.000 0.00 0.00 0.00 3.41
2542 2577 2.311463 ACTCATATGACCACCTCCGAG 58.689 52.381 0.00 0.00 0.00 4.63
2576 2611 5.920840 TGCATACACTCATCTCTATTAACGC 59.079 40.000 0.00 0.00 0.00 4.84
2577 2612 7.411264 GCATGCATACACTCATCTCTATTAACG 60.411 40.741 14.21 0.00 0.00 3.18
2578 2613 7.386025 TGCATGCATACACTCATCTCTATTAAC 59.614 37.037 18.46 0.00 0.00 2.01
2588 2623 8.606602 CGTTTATATATGCATGCATACACTCAT 58.393 33.333 36.22 24.69 41.09 2.90
2618 2653 7.307573 GCCTTTTATTTAACACAGTACAGACGT 60.308 37.037 0.00 0.00 0.00 4.34
2695 2737 9.745880 CTCGCGTATAATATTAGGTCCATATTT 57.254 33.333 5.77 0.00 30.85 1.40
2696 2738 7.866393 GCTCGCGTATAATATTAGGTCCATATT 59.134 37.037 5.77 0.00 32.62 1.28
2697 2739 7.013942 TGCTCGCGTATAATATTAGGTCCATAT 59.986 37.037 5.77 0.00 0.00 1.78
2781 2823 9.589461 TTTAAGTCAATAAAATCCACCCTTGTA 57.411 29.630 0.00 0.00 0.00 2.41
2847 2889 4.177026 GTGTGCATCCTAACTACACAGAG 58.823 47.826 0.00 0.00 41.54 3.35
2853 2895 2.280628 GGCTGTGTGCATCCTAACTAC 58.719 52.381 0.00 0.00 45.15 2.73
2927 2969 2.434428 CACAAGAGAAAGGCAGAGCAT 58.566 47.619 0.00 0.00 0.00 3.79
3054 3096 7.734924 TTCTTCCATGTTATGATGCTACATC 57.265 36.000 0.55 0.55 30.45 3.06
3055 3097 7.013655 GGTTTCTTCCATGTTATGATGCTACAT 59.986 37.037 0.00 0.00 32.98 2.29
3213 3867 1.031571 ATCGTCGGTACCGCCACTTA 61.032 55.000 29.64 13.76 39.59 2.24
3219 3873 0.248743 TTCATCATCGTCGGTACCGC 60.249 55.000 29.64 21.84 39.59 5.68
3223 3877 5.181433 CCTTATCTCTTCATCATCGTCGGTA 59.819 44.000 0.00 0.00 0.00 4.02
3225 3879 4.480541 CCTTATCTCTTCATCATCGTCGG 58.519 47.826 0.00 0.00 0.00 4.79
3402 4064 4.196778 TTTGGCAGGGTGCGACCA 62.197 61.111 7.49 0.00 46.21 4.02
3454 4119 1.258445 CCAAGGTCTACCAGCGGACT 61.258 60.000 1.26 0.00 38.89 3.85
3498 4163 2.879233 ATCGAGGCCAACACACCGT 61.879 57.895 5.01 0.00 0.00 4.83
3589 4254 2.357517 CTGACACGAAGGGCGCTT 60.358 61.111 16.91 16.91 46.04 4.68
3618 4296 2.124236 ACGTAGAGGAGGAGGCCG 60.124 66.667 0.00 0.00 0.00 6.13
3642 4320 2.031465 CGCCGGTGGTGGTTAAGT 59.969 61.111 7.26 0.00 0.00 2.24
3724 4402 3.677648 CCGAACTGGGACGTCCGT 61.678 66.667 27.68 18.21 38.76 4.69
3777 4455 4.070552 GTCGGGCTGCCTTCTCGT 62.071 66.667 19.68 0.00 0.00 4.18
3790 4468 0.803768 CCGAGATCTGCAACTGTCGG 60.804 60.000 16.18 16.18 40.86 4.79
3795 4473 2.185350 CGGCCGAGATCTGCAACT 59.815 61.111 24.07 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.