Multiple sequence alignment - TraesCS4D01G179600

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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 TraesCS4D01G179600 chr4D 100.000 5090 0 0 1 5090 312563161 312568250 0.000000e+00 9400.0
1 TraesCS4D01G179600 chr4D 94.068 118 7 0 4113 4230 494875912 494876029 4.050000e-41 180.0
2 TraesCS4D01G179600 chr4D 90.244 123 12 0 4111 4233 333469591 333469469 1.470000e-35 161.0
3 TraesCS4D01G179600 chr4D 84.459 148 11 6 4780 4921 312583472 312583613 8.890000e-28 135.0
4 TraesCS4D01G179600 chr4D 88.421 95 10 1 3312 3405 101202384 101202478 4.170000e-21 113.0
5 TraesCS4D01G179600 chr4D 100.000 28 0 0 2116 2143 199021268 199021295 9.000000e-03 52.8
6 TraesCS4D01G179600 chr4B 95.238 2289 45 19 1825 4083 389115936 389118190 0.000000e+00 3565.0
7 TraesCS4D01G179600 chr4B 90.294 1906 65 30 1 1829 389113093 389114955 0.000000e+00 2385.0
8 TraesCS4D01G179600 chr4B 92.116 482 19 4 4231 4711 389118194 389118657 0.000000e+00 662.0
9 TraesCS4D01G179600 chr4B 96.364 275 8 1 4714 4986 389118773 389119047 7.770000e-123 451.0
10 TraesCS4D01G179600 chr4B 95.050 101 5 0 4990 5090 389119354 389119454 5.270000e-35 159.0
11 TraesCS4D01G179600 chr4B 92.424 66 5 0 4257 4322 660179337 660179272 1.510000e-15 95.3
12 TraesCS4D01G179600 chr4B 90.909 66 6 0 4257 4322 649651214 649651279 7.020000e-14 89.8
13 TraesCS4D01G179600 chr4B 89.706 68 7 0 4257 4324 491463486 491463553 2.520000e-13 87.9
14 TraesCS4D01G179600 chr4B 86.842 76 10 0 4254 4329 119338582 119338657 9.080000e-13 86.1
15 TraesCS4D01G179600 chr4A 91.508 1519 58 28 803 2275 163918491 163916998 0.000000e+00 2025.0
16 TraesCS4D01G179600 chr4A 92.000 750 40 9 1 747 163919524 163918792 0.000000e+00 1035.0
17 TraesCS4D01G179600 chr4A 93.904 689 27 4 2264 2937 163915329 163914641 0.000000e+00 1026.0
18 TraesCS4D01G179600 chr4A 93.827 567 32 2 3530 4093 163914219 163913653 0.000000e+00 850.0
19 TraesCS4D01G179600 chr4A 82.519 675 43 25 4335 4991 163913630 163913013 1.620000e-144 523.0
20 TraesCS4D01G179600 chr4A 92.453 212 11 4 3013 3223 163914480 163914273 1.070000e-76 298.0
21 TraesCS4D01G179600 chr4A 90.196 102 4 2 4995 5090 163912970 163912869 1.490000e-25 128.0
22 TraesCS4D01G179600 chr4A 86.585 82 7 4 4244 4321 718402746 718402827 2.520000e-13 87.9
23 TraesCS4D01G179600 chr6B 94.531 128 7 0 3203 3330 147680040 147680167 1.120000e-46 198.0
24 TraesCS4D01G179600 chr6B 93.443 122 7 1 4109 4230 248362103 248362223 4.050000e-41 180.0
25 TraesCS4D01G179600 chr6B 89.051 137 14 1 3406 3541 390039467 390039331 8.760000e-38 169.0
26 TraesCS4D01G179600 chr6B 88.158 76 5 4 4257 4331 153239810 153239738 2.520000e-13 87.9
27 TraesCS4D01G179600 chr6B 82.979 94 13 1 4228 4321 435830325 435830235 1.170000e-11 82.4
28 TraesCS4D01G179600 chr6B 86.792 53 6 1 2100 2152 346709892 346709943 1.980000e-04 58.4
29 TraesCS4D01G179600 chr2B 93.233 133 9 0 3199 3331 706301943 706301811 4.020000e-46 196.0
30 TraesCS4D01G179600 chr2B 93.277 119 8 0 4113 4231 412778578 412778696 5.240000e-40 176.0
31 TraesCS4D01G179600 chr2B 88.321 137 15 1 3406 3541 120234193 120234057 4.080000e-36 163.0
32 TraesCS4D01G179600 chr2A 93.798 129 8 0 3202 3330 66802949 66802821 1.450000e-45 195.0
33 TraesCS4D01G179600 chr2A 95.062 81 4 0 3327 3407 74163638 74163718 1.490000e-25 128.0
34 TraesCS4D01G179600 chr1D 93.798 129 8 0 3202 3330 486154366 486154494 1.450000e-45 195.0
35 TraesCS4D01G179600 chr1D 91.367 139 12 0 3192 3330 361881330 361881468 1.870000e-44 191.0
36 TraesCS4D01G179600 chr1D 91.304 138 11 1 3194 3330 88960258 88960395 2.420000e-43 187.0
37 TraesCS4D01G179600 chr1D 93.333 120 8 0 4112 4231 182046802 182046683 1.460000e-40 178.0
38 TraesCS4D01G179600 chr1D 92.562 121 9 0 4111 4231 470925494 470925374 1.880000e-39 174.0
39 TraesCS4D01G179600 chr1D 90.678 118 11 0 4113 4230 28576534 28576651 1.900000e-34 158.0
40 TraesCS4D01G179600 chr1D 97.468 79 2 0 679 757 37213512 37213434 8.890000e-28 135.0
41 TraesCS4D01G179600 chr1D 94.382 89 3 2 679 765 387330273 387330185 8.890000e-28 135.0
42 TraesCS4D01G179600 chr1D 96.296 81 3 0 679 759 342187432 342187352 3.200000e-27 134.0
43 TraesCS4D01G179600 chr1D 95.294 85 1 2 679 760 462054243 462054159 1.150000e-26 132.0
44 TraesCS4D01G179600 chr1D 95.000 80 4 0 3326 3405 163770450 163770371 5.350000e-25 126.0
45 TraesCS4D01G179600 chr1D 84.921 126 17 2 4109 4233 400120020 400119896 5.350000e-25 126.0
46 TraesCS4D01G179600 chr1D 94.048 84 3 1 679 760 462121265 462121182 5.350000e-25 126.0
47 TraesCS4D01G179600 chr1D 93.590 78 5 0 679 756 342229203 342229126 3.220000e-22 117.0
48 TraesCS4D01G179600 chr1D 93.846 65 3 1 4166 4230 359834079 359834142 4.190000e-16 97.1
49 TraesCS4D01G179600 chr1D 90.141 71 7 0 4142 4212 457872441 457872371 5.430000e-15 93.5
50 TraesCS4D01G179600 chr1D 92.188 64 5 0 4258 4321 59131278 59131215 1.950000e-14 91.6
51 TraesCS4D01G179600 chr1D 92.063 63 5 0 4257 4319 377006979 377006917 7.020000e-14 89.8
52 TraesCS4D01G179600 chr1D 90.909 66 6 0 4257 4322 484270520 484270585 7.020000e-14 89.8
53 TraesCS4D01G179600 chr1D 90.769 65 6 0 4257 4321 108103224 108103160 2.520000e-13 87.9
54 TraesCS4D01G179600 chr1D 87.013 77 8 1 4254 4330 73688128 73688202 9.080000e-13 86.1
55 TraesCS4D01G179600 chr1D 94.444 36 2 0 4177 4212 463321813 463321778 7.120000e-04 56.5
56 TraesCS4D01G179600 chr6D 93.750 128 8 0 3203 3330 73498032 73498159 5.200000e-45 193.0
57 TraesCS4D01G179600 chr6D 88.321 137 15 1 3406 3541 426090636 426090500 4.080000e-36 163.0
58 TraesCS4D01G179600 chr6D 89.344 122 13 0 4113 4234 277047922 277047801 2.450000e-33 154.0
59 TraesCS4D01G179600 chr6D 88.235 119 14 0 4112 4230 391684138 391684020 5.310000e-30 143.0
60 TraesCS4D01G179600 chr6D 95.181 83 2 2 679 759 108458534 108458616 4.140000e-26 130.0
61 TraesCS4D01G179600 chr6D 90.909 66 5 1 4257 4322 234467798 234467862 2.520000e-13 87.9
62 TraesCS4D01G179600 chr6D 90.769 65 6 0 4257 4321 363593387 363593323 2.520000e-13 87.9
63 TraesCS4D01G179600 chr6D 90.476 63 6 0 4257 4319 7657121 7657059 3.270000e-12 84.2
64 TraesCS4D01G179600 chr6D 88.406 69 8 0 4254 4322 95896029 95896097 3.270000e-12 84.2
65 TraesCS4D01G179600 chr6D 88.406 69 8 0 4254 4322 403312329 403312397 3.270000e-12 84.2
66 TraesCS4D01G179600 chr6D 89.231 65 7 0 4257 4321 109243583 109243519 1.170000e-11 82.4
67 TraesCS4D01G179600 chr6D 88.235 68 8 0 4254 4321 129707191 129707258 1.170000e-11 82.4
68 TraesCS4D01G179600 chr6D 87.500 72 8 1 4254 4325 161074569 161074639 1.170000e-11 82.4
69 TraesCS4D01G179600 chr6D 88.406 69 7 1 4257 4325 274493889 274493822 1.170000e-11 82.4
70 TraesCS4D01G179600 chr6D 87.500 72 8 1 4254 4325 337553050 337553120 1.170000e-11 82.4
71 TraesCS4D01G179600 chr6D 84.286 70 5 5 2106 2175 84013196 84013133 4.250000e-06 63.9
72 TraesCS4D01G179600 chr6D 90.000 50 4 1 2099 2147 156763608 156763657 4.250000e-06 63.9
73 TraesCS4D01G179600 chr6D 81.707 82 4 1 4113 4194 63716050 63716120 1.980000e-04 58.4
74 TraesCS4D01G179600 chr7B 95.000 120 6 0 4111 4230 143329516 143329397 6.730000e-44 189.0
75 TraesCS4D01G179600 chr7B 89.362 141 10 4 3404 3541 427686158 427686296 6.780000e-39 172.0
76 TraesCS4D01G179600 chr7B 91.176 68 6 0 4257 4324 1321266 1321333 5.430000e-15 93.5
77 TraesCS4D01G179600 chr7B 83.871 93 11 4 4229 4319 547966905 547966815 9.080000e-13 86.1
78 TraesCS4D01G179600 chr7B 87.719 57 5 2 2101 2156 629885789 629885844 1.180000e-06 65.8
79 TraesCS4D01G179600 chr7A 91.852 135 11 0 3196 3330 708915825 708915691 6.730000e-44 189.0
80 TraesCS4D01G179600 chr7A 98.750 80 1 0 679 758 618084944 618084865 5.310000e-30 143.0
81 TraesCS4D01G179600 chr7A 90.110 91 8 1 3315 3405 71137362 71137273 3.220000e-22 117.0
82 TraesCS4D01G179600 chr7A 87.952 83 7 3 2115 2197 320605647 320605568 1.510000e-15 95.3
83 TraesCS4D01G179600 chr7A 86.842 76 7 3 2115 2190 613935432 613935360 1.170000e-11 82.4
84 TraesCS4D01G179600 chr6A 93.548 124 8 0 4113 4236 277889801 277889678 8.700000e-43 185.0
85 TraesCS4D01G179600 chr6A 89.855 138 11 3 3406 3541 284816306 284816442 1.880000e-39 174.0
86 TraesCS4D01G179600 chr6A 90.984 122 9 2 4113 4233 326741916 326741796 4.080000e-36 163.0
87 TraesCS4D01G179600 chr6A 88.889 72 7 1 4254 4325 314968863 314968933 2.520000e-13 87.9
88 TraesCS4D01G179600 chr6A 80.556 108 9 11 2086 2191 235028692 235028789 7.070000e-09 73.1
89 TraesCS4D01G179600 chr6A 100.000 31 0 0 2116 2146 176352527 176352557 1.980000e-04 58.4
90 TraesCS4D01G179600 chr3D 93.443 122 8 0 4110 4231 107670960 107671081 1.130000e-41 182.0
91 TraesCS4D01G179600 chr3D 98.750 80 1 0 679 758 3302238 3302159 5.310000e-30 143.0
92 TraesCS4D01G179600 chr3D 86.585 82 11 0 4257 4338 160615924 160615843 1.950000e-14 91.6
93 TraesCS4D01G179600 chr3D 89.041 73 7 1 4257 4329 254739799 254739870 7.020000e-14 89.8
94 TraesCS4D01G179600 chr3D 97.222 36 1 0 2112 2147 103452738 103452703 1.530000e-05 62.1
95 TraesCS4D01G179600 chr1B 94.118 119 7 0 4113 4231 1821174 1821056 1.130000e-41 182.0
96 TraesCS4D01G179600 chr1B 92.623 122 7 2 4111 4231 334306797 334306677 1.880000e-39 174.0
97 TraesCS4D01G179600 chr1B 93.750 80 5 0 3326 3405 106875711 106875632 2.490000e-23 121.0
98 TraesCS4D01G179600 chr1B 92.424 66 5 0 4257 4322 121581092 121581027 1.510000e-15 95.3
99 TraesCS4D01G179600 chr5D 94.068 118 7 0 4113 4230 2138576 2138693 4.050000e-41 180.0
100 TraesCS4D01G179600 chr5D 91.525 118 10 0 4113 4230 126577598 126577481 4.080000e-36 163.0
101 TraesCS4D01G179600 chr5D 88.489 139 11 4 3406 3541 517961231 517961095 4.080000e-36 163.0
102 TraesCS4D01G179600 chr5D 85.714 140 20 0 2230 2369 158805345 158805484 1.140000e-31 148.0
103 TraesCS4D01G179600 chr5D 98.765 81 1 0 679 759 521846310 521846230 1.480000e-30 145.0
104 TraesCS4D01G179600 chr5D 97.531 81 2 0 679 759 446400804 446400724 6.870000e-29 139.0
105 TraesCS4D01G179600 chr5D 97.500 80 2 0 679 758 517436405 517436484 2.470000e-28 137.0
106 TraesCS4D01G179600 chr5D 100.000 28 0 0 2116 2143 104096090 104096117 9.000000e-03 52.8
107 TraesCS4D01G179600 chr3B 94.068 118 7 0 4113 4230 52425269 52425386 4.050000e-41 180.0
108 TraesCS4D01G179600 chr3B 88.321 137 15 1 3406 3541 480377066 480377202 4.080000e-36 163.0
109 TraesCS4D01G179600 chr3B 87.770 139 14 2 3406 3541 165268228 165268090 5.270000e-35 159.0
110 TraesCS4D01G179600 chr3B 98.750 80 1 0 679 758 479988668 479988589 5.310000e-30 143.0
111 TraesCS4D01G179600 chr3B 98.750 80 1 0 679 758 606655559 606655480 5.310000e-30 143.0
112 TraesCS4D01G179600 chr1A 93.220 118 8 0 4113 4230 6470465 6470348 1.880000e-39 174.0
113 TraesCS4D01G179600 chr1A 91.597 119 10 0 4113 4231 53442798 53442916 1.130000e-36 165.0
114 TraesCS4D01G179600 chr1A 89.076 119 12 1 4113 4230 1204460 1204578 4.110000e-31 147.0
115 TraesCS4D01G179600 chr1A 98.734 79 1 0 679 757 441953946 441953868 1.910000e-29 141.0
116 TraesCS4D01G179600 chr1A 98.734 79 1 0 679 757 553707477 553707399 1.910000e-29 141.0
117 TraesCS4D01G179600 chr1A 97.468 79 2 0 679 757 36561715 36561637 8.890000e-28 135.0
118 TraesCS4D01G179600 chr1A 96.341 82 3 0 679 760 487079961 487079880 8.890000e-28 135.0
119 TraesCS4D01G179600 chr1A 95.122 82 4 0 679 760 553982921 553982840 4.140000e-26 130.0
120 TraesCS4D01G179600 chr1A 90.769 65 6 0 4257 4321 7331852 7331788 2.520000e-13 87.9
121 TraesCS4D01G179600 chr1A 89.706 68 7 0 4257 4324 512476989 512476922 2.520000e-13 87.9
122 TraesCS4D01G179600 chr7D 92.437 119 9 0 4112 4230 31949793 31949675 2.440000e-38 171.0
123 TraesCS4D01G179600 chr7D 95.402 87 2 2 675 759 535550317 535550403 2.470000e-28 137.0
124 TraesCS4D01G179600 chr7D 97.500 80 2 0 679 758 599503416 599503495 2.470000e-28 137.0
125 TraesCS4D01G179600 chr7D 90.909 66 6 0 4257 4322 32642248 32642313 7.020000e-14 89.8
126 TraesCS4D01G179600 chr7D 88.732 71 8 0 4252 4322 392820365 392820295 2.520000e-13 87.9
127 TraesCS4D01G179600 chr7D 92.105 38 3 0 2116 2153 484836147 484836184 3.000000e-03 54.7
128 TraesCS4D01G179600 chr5A 86.331 139 19 0 2230 2368 208747398 208747536 8.830000e-33 152.0
129 TraesCS4D01G179600 chr5A 92.157 102 6 2 659 760 650138210 650138111 5.310000e-30 143.0
130 TraesCS4D01G179600 chr5A 90.278 72 6 1 4254 4324 35825134 35825205 5.430000e-15 93.5
131 TraesCS4D01G179600 chr5A 86.905 84 7 3 4243 4322 667110266 667110183 1.950000e-14 91.6
132 TraesCS4D01G179600 chr5B 95.604 91 3 1 669 758 658145790 658145700 1.480000e-30 145.0
133 TraesCS4D01G179600 chr5B 85.455 110 11 4 3312 3417 469493592 469493484 5.390000e-20 110.0
134 TraesCS4D01G179600 chr5B 84.615 104 12 3 4226 4326 89636061 89636163 3.240000e-17 100.0
135 TraesCS4D01G179600 chr5B 89.855 69 6 1 4257 4325 675951394 675951327 2.520000e-13 87.9
136 TraesCS4D01G179600 chr5B 88.136 59 4 3 2117 2175 496814998 496815053 3.290000e-07 67.6
137 TraesCS4D01G179600 chr3A 98.734 79 1 0 679 757 38279391 38279313 1.910000e-29 141.0
138 TraesCS4D01G179600 chr3A 88.235 85 7 3 2106 2190 466004555 466004636 1.170000e-16 99.0
139 TraesCS4D01G179600 chr2D 93.827 81 5 0 3327 3407 74980843 74980923 6.920000e-24 122.0
140 TraesCS4D01G179600 chr2D 93.750 80 5 0 3326 3405 23166735 23166656 2.490000e-23 121.0
141 TraesCS4D01G179600 chr2D 87.838 74 8 1 4257 4330 559209864 559209792 9.080000e-13 86.1
142 TraesCS4D01G179600 chr2D 81.188 101 16 3 4227 4325 48860565 48860664 1.520000e-10 78.7
143 TraesCS4D01G179600 chr2D 90.741 54 4 1 2106 2159 543828052 543828000 2.540000e-08 71.3
144 TraesCS4D01G179600 chr2D 85.714 63 6 3 2097 2158 194673918 194673858 4.250000e-06 63.9
145 TraesCS4D01G179600 chrUn 90.769 65 6 0 4257 4321 32053032 32052968 2.520000e-13 87.9
146 TraesCS4D01G179600 chrUn 88.406 69 7 1 4257 4325 102887862 102887795 1.170000e-11 82.4
147 TraesCS4D01G179600 chrUn 92.727 55 4 0 4268 4322 31616833 31616779 4.220000e-11 80.5
148 TraesCS4D01G179600 chrUn 87.143 70 7 2 4254 4322 27078821 27078889 1.520000e-10 78.7
149 TraesCS4D01G179600 chrUn 84.337 83 9 3 4243 4321 402791635 402791553 1.520000e-10 78.7
150 TraesCS4D01G179600 chrUn 86.957 69 8 1 4257 4325 19647221 19647154 5.460000e-10 76.8
151 TraesCS4D01G179600 chrUn 86.111 72 9 1 4254 4325 24072659 24072729 5.460000e-10 76.8
152 TraesCS4D01G179600 chrUn 87.692 65 8 0 4257 4321 30405359 30405295 5.460000e-10 76.8
153 TraesCS4D01G179600 chrUn 86.111 72 9 1 4254 4325 30636742 30636812 5.460000e-10 76.8
154 TraesCS4D01G179600 chrUn 86.765 68 9 0 4254 4321 64149761 64149828 5.460000e-10 76.8
155 TraesCS4D01G179600 chrUn 87.692 65 8 0 4257 4321 66416473 66416409 5.460000e-10 76.8
156 TraesCS4D01G179600 chrUn 86.957 69 8 1 4257 4325 103216874 103216807 5.460000e-10 76.8
157 TraesCS4D01G179600 chrUn 86.111 72 9 1 4254 4325 104559241 104559311 5.460000e-10 76.8
158 TraesCS4D01G179600 chrUn 86.667 75 2 7 2101 2175 336947083 336947017 5.460000e-10 76.8
159 TraesCS4D01G179600 chrUn 81.000 100 8 2 4113 4212 255034324 255034412 9.140000e-08 69.4
160 TraesCS4D01G179600 chrUn 100.000 30 0 0 4112 4141 277590764 277590793 7.120000e-04 56.5
161 TraesCS4D01G179600 chrUn 79.775 89 7 2 4113 4201 86295738 86295661 3.000000e-03 54.7


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 TraesCS4D01G179600 chr4D 312563161 312568250 5089 False 9400.000000 9400 100.000000 1 5090 1 chr4D.!!$F3 5089
1 TraesCS4D01G179600 chr4B 389113093 389119454 6361 False 1444.400000 3565 93.812400 1 5090 5 chr4B.!!$F4 5089
2 TraesCS4D01G179600 chr4A 163912869 163919524 6655 True 840.714286 2025 90.915286 1 5090 7 chr4A.!!$R1 5089

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
753 773 0.036306 AAGTCCCGGCGACAGAATTT 59.964 50.000 20.68 7.1 44.66 1.82 F
993 1307 0.389948 TTTCTCGCTCGCTTCCTTCC 60.390 55.000 0.00 0.0 0.00 3.46 F
1333 1666 1.258445 CCTCCTACAACCCGCTCACT 61.258 60.000 0.00 0.0 0.00 3.41 F
2546 5608 1.945394 GGAGTGATGCTCATGCGATTT 59.055 47.619 0.00 0.0 45.88 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 5315 3.202818 TCATGCCTTTCACCAGTGGATAT 59.797 43.478 18.40 0.00 0.00 1.63 R
2322 5362 3.484407 AGCAAGATCTCAAGTTGTTGCT 58.516 40.909 19.45 19.45 44.36 3.91 R
2828 5890 5.079406 CGAAGTTATGCACATGTGTTGTAC 58.921 41.667 26.01 18.14 36.57 2.90 R
4201 7375 0.237498 CGTCCGAAAAAGCTTGACCC 59.763 55.000 0.00 0.00 0.00 4.46 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
139 140 4.445453 TGAGATTCAGACATTTGGATCCG 58.555 43.478 7.39 0.00 34.19 4.18
223 224 6.743575 AGGTATGCTACATTGACTTGTTTC 57.256 37.500 0.00 0.00 0.00 2.78
225 226 4.685169 ATGCTACATTGACTTGTTTCCG 57.315 40.909 0.00 0.00 0.00 4.30
228 229 3.364964 GCTACATTGACTTGTTTCCGGTG 60.365 47.826 0.00 0.00 0.00 4.94
244 245 1.001815 CGGTGACCGCAAACTGAATTT 60.002 47.619 12.53 0.00 41.17 1.82
261 262 6.072286 ACTGAATTTGATGCGAGAATTGTTCT 60.072 34.615 0.00 0.00 44.21 3.01
267 268 5.478407 TGATGCGAGAATTGTTCTGTCTTA 58.522 37.500 0.00 0.00 40.87 2.10
296 297 4.021102 AGCTGTAGTGGTGCTTGTAAAT 57.979 40.909 0.00 0.00 32.61 1.40
337 338 5.671082 GCTTTGTCTTGAACTTTTGTTTGGC 60.671 40.000 0.00 0.00 43.66 4.52
606 607 2.484770 GGCCGTGTGTGGATGTATACAT 60.485 50.000 18.31 18.31 39.70 2.29
607 608 3.202906 GCCGTGTGTGGATGTATACATT 58.797 45.455 19.19 3.85 36.57 2.71
608 609 4.373527 GCCGTGTGTGGATGTATACATTA 58.626 43.478 19.19 9.34 36.57 1.90
610 611 5.277154 GCCGTGTGTGGATGTATACATTAAC 60.277 44.000 19.19 18.63 36.57 2.01
641 644 6.980397 GGTTAAAGGGCAAGTGATTATGATTG 59.020 38.462 0.00 0.00 0.00 2.67
747 767 2.029964 GTTCAAGTCCCGGCGACA 59.970 61.111 20.68 0.00 44.66 4.35
748 768 2.027625 GTTCAAGTCCCGGCGACAG 61.028 63.158 20.68 14.18 44.66 3.51
749 769 2.204461 TTCAAGTCCCGGCGACAGA 61.204 57.895 20.68 15.76 44.66 3.41
750 770 1.750341 TTCAAGTCCCGGCGACAGAA 61.750 55.000 20.68 19.27 44.66 3.02
751 771 1.079127 CAAGTCCCGGCGACAGAAT 60.079 57.895 20.68 0.00 44.66 2.40
752 772 0.673644 CAAGTCCCGGCGACAGAATT 60.674 55.000 20.68 4.86 44.66 2.17
753 773 0.036306 AAGTCCCGGCGACAGAATTT 59.964 50.000 20.68 7.10 44.66 1.82
754 774 0.036306 AGTCCCGGCGACAGAATTTT 59.964 50.000 20.68 0.82 44.66 1.82
755 775 0.879090 GTCCCGGCGACAGAATTTTT 59.121 50.000 9.30 0.00 41.54 1.94
771 791 4.589046 TTTTTGGAGGCGGCTTCA 57.411 50.000 17.45 17.45 0.00 3.02
772 792 3.050089 TTTTTGGAGGCGGCTTCAT 57.950 47.368 22.21 0.00 0.00 2.57
773 793 2.208132 TTTTTGGAGGCGGCTTCATA 57.792 45.000 22.21 14.03 0.00 2.15
774 794 1.459450 TTTTGGAGGCGGCTTCATAC 58.541 50.000 22.21 3.07 0.00 2.39
906 1218 1.499007 AGGTTTCCTCTTTCCTTGGCA 59.501 47.619 0.00 0.00 0.00 4.92
907 1219 1.889170 GGTTTCCTCTTTCCTTGGCAG 59.111 52.381 0.00 0.00 0.00 4.85
969 1281 6.361768 AACCCGCTCCCAATTTTAAAATTA 57.638 33.333 22.44 9.48 36.52 1.40
986 1298 4.946784 AATTACAAATTTCTCGCTCGCT 57.053 36.364 0.00 0.00 0.00 4.93
993 1307 0.389948 TTTCTCGCTCGCTTCCTTCC 60.390 55.000 0.00 0.00 0.00 3.46
1016 1330 2.812619 CCCGGCAGGAGGAGAATCC 61.813 68.421 3.68 0.00 45.86 3.01
1045 1365 3.673484 CCACCAAAGCACCGGCAG 61.673 66.667 0.00 0.00 44.61 4.85
1046 1366 3.673484 CACCAAAGCACCGGCAGG 61.673 66.667 0.00 0.00 44.61 4.85
1049 1369 4.047059 CAAAGCACCGGCAGGCAG 62.047 66.667 14.75 0.00 44.61 4.85
1333 1666 1.258445 CCTCCTACAACCCGCTCACT 61.258 60.000 0.00 0.00 0.00 3.41
1448 1781 6.651086 TCTGTCTCGTCCTTTTATCTCTCTA 58.349 40.000 0.00 0.00 0.00 2.43
1450 1783 8.430431 TCTGTCTCGTCCTTTTATCTCTCTATA 58.570 37.037 0.00 0.00 0.00 1.31
1494 1862 5.799213 AGACTTGAGAGGAACATTTACCTG 58.201 41.667 0.00 0.00 36.57 4.00
1591 1965 7.623999 AGTATCTCATAACCAATCCATGAGT 57.376 36.000 9.84 2.46 43.94 3.41
1607 1981 5.935206 TCCATGAGTTATTTTCGTTGCTACA 59.065 36.000 0.00 0.00 0.00 2.74
1943 3302 9.270640 CAAGTAGATGATTTTCTAGAGATTGGG 57.729 37.037 0.00 0.00 0.00 4.12
2373 5413 6.558488 AATATCTCCAGGCCTGAAGATATC 57.442 41.667 39.40 0.00 39.41 1.63
2409 5449 5.509498 TCATACTTTTGGAGGGGAAAGATG 58.491 41.667 3.14 3.56 36.58 2.90
2410 5450 3.903530 ACTTTTGGAGGGGAAAGATGT 57.096 42.857 3.14 0.00 36.58 3.06
2546 5608 1.945394 GGAGTGATGCTCATGCGATTT 59.055 47.619 0.00 0.00 45.88 2.17
2856 5918 4.267690 ACACATGTGCATAACTTCGATACG 59.732 41.667 25.68 0.00 0.00 3.06
2863 5925 6.856426 TGTGCATAACTTCGATACGAATCTAG 59.144 38.462 7.03 0.00 44.85 2.43
3270 6433 7.537596 AGTCAACCATTTGAATATTTGACCA 57.462 32.000 17.49 0.00 43.52 4.02
3271 6434 7.961351 AGTCAACCATTTGAATATTTGACCAA 58.039 30.769 17.49 0.00 43.52 3.67
3272 6435 8.090214 AGTCAACCATTTGAATATTTGACCAAG 58.910 33.333 17.49 0.00 43.52 3.61
3273 6436 8.087750 GTCAACCATTTGAATATTTGACCAAGA 58.912 33.333 13.53 0.00 43.52 3.02
3274 6437 8.814931 TCAACCATTTGAATATTTGACCAAGAT 58.185 29.630 0.00 0.00 38.87 2.40
3275 6438 9.439500 CAACCATTTGAATATTTGACCAAGATT 57.561 29.630 0.00 0.00 34.24 2.40
3354 6517 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
3355 6518 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
3356 6519 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
3357 6520 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
3360 6523 8.066000 CCGTCCCATAATATAAGAACGTTTTTC 58.934 37.037 7.42 0.00 0.00 2.29
3494 6661 3.880490 ACGGTCAAACTTGCACTCATTTA 59.120 39.130 0.00 0.00 0.00 1.40
3499 6666 6.417930 GGTCAAACTTGCACTCATTTAACTTC 59.582 38.462 0.00 0.00 0.00 3.01
3867 7035 6.207614 ACAAAAAGGAATAGACTTCAGGAAGC 59.792 38.462 8.89 2.76 41.99 3.86
3985 7156 8.396272 TCCTTCAAGTATTCCTTCAAAGAAAG 57.604 34.615 0.00 0.00 29.94 2.62
3986 7157 8.217799 TCCTTCAAGTATTCCTTCAAAGAAAGA 58.782 33.333 0.00 0.00 29.94 2.52
4093 7267 5.717078 AAAATGTTCATCTGTCAGCATGT 57.283 34.783 0.00 0.00 37.40 3.21
4094 7268 5.717078 AAATGTTCATCTGTCAGCATGTT 57.283 34.783 0.00 0.00 37.40 2.71
4095 7269 4.696899 ATGTTCATCTGTCAGCATGTTG 57.303 40.909 2.65 2.65 37.40 3.33
4096 7270 3.742385 TGTTCATCTGTCAGCATGTTGA 58.258 40.909 8.32 8.32 37.40 3.18
4098 7272 4.214758 TGTTCATCTGTCAGCATGTTGAAG 59.785 41.667 14.30 13.08 37.40 3.02
4099 7273 2.745821 TCATCTGTCAGCATGTTGAAGC 59.254 45.455 14.30 3.58 37.40 3.86
4100 7274 1.527034 TCTGTCAGCATGTTGAAGCC 58.473 50.000 14.30 2.84 37.40 4.35
4102 7276 1.467734 CTGTCAGCATGTTGAAGCCTC 59.532 52.381 14.30 2.10 37.40 4.70
4103 7277 0.807496 GTCAGCATGTTGAAGCCTCC 59.193 55.000 14.30 0.00 37.40 4.30
4104 7278 0.694771 TCAGCATGTTGAAGCCTCCT 59.305 50.000 10.10 0.00 37.40 3.69
4105 7279 1.074405 TCAGCATGTTGAAGCCTCCTT 59.926 47.619 10.10 0.00 37.40 3.36
4106 7280 2.305635 TCAGCATGTTGAAGCCTCCTTA 59.694 45.455 10.10 0.00 37.40 2.69
4107 7281 3.084039 CAGCATGTTGAAGCCTCCTTAA 58.916 45.455 2.97 0.00 0.00 1.85
4108 7282 3.698040 CAGCATGTTGAAGCCTCCTTAAT 59.302 43.478 2.97 0.00 0.00 1.40
4109 7283 3.698040 AGCATGTTGAAGCCTCCTTAATG 59.302 43.478 0.00 0.00 0.00 1.90
4110 7284 3.445096 GCATGTTGAAGCCTCCTTAATGT 59.555 43.478 0.00 0.00 0.00 2.71
4111 7285 4.676196 GCATGTTGAAGCCTCCTTAATGTG 60.676 45.833 0.00 0.00 0.00 3.21
4112 7286 4.098914 TGTTGAAGCCTCCTTAATGTGT 57.901 40.909 0.00 0.00 0.00 3.72
4113 7287 5.235850 TGTTGAAGCCTCCTTAATGTGTA 57.764 39.130 0.00 0.00 0.00 2.90
4114 7288 5.001232 TGTTGAAGCCTCCTTAATGTGTAC 58.999 41.667 0.00 0.00 0.00 2.90
4115 7289 5.221843 TGTTGAAGCCTCCTTAATGTGTACT 60.222 40.000 0.00 0.00 0.00 2.73
4116 7290 5.086104 TGAAGCCTCCTTAATGTGTACTC 57.914 43.478 0.00 0.00 0.00 2.59
4117 7291 4.081087 TGAAGCCTCCTTAATGTGTACTCC 60.081 45.833 0.00 0.00 0.00 3.85
4118 7292 2.772515 AGCCTCCTTAATGTGTACTCCC 59.227 50.000 0.00 0.00 0.00 4.30
4119 7293 2.772515 GCCTCCTTAATGTGTACTCCCT 59.227 50.000 0.00 0.00 0.00 4.20
4120 7294 3.181464 GCCTCCTTAATGTGTACTCCCTC 60.181 52.174 0.00 0.00 0.00 4.30
4121 7295 3.388350 CCTCCTTAATGTGTACTCCCTCC 59.612 52.174 0.00 0.00 0.00 4.30
4122 7296 3.028850 TCCTTAATGTGTACTCCCTCCG 58.971 50.000 0.00 0.00 0.00 4.63
4123 7297 2.764572 CCTTAATGTGTACTCCCTCCGT 59.235 50.000 0.00 0.00 0.00 4.69
4124 7298 3.181478 CCTTAATGTGTACTCCCTCCGTC 60.181 52.174 0.00 0.00 0.00 4.79
4125 7299 1.192428 AATGTGTACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
4126 7300 1.035932 ATGTGTACTCCCTCCGTCCG 61.036 60.000 0.00 0.00 0.00 4.79
4127 7301 2.044650 TGTACTCCCTCCGTCCGG 60.045 66.667 0.00 0.00 0.00 5.14
4128 7302 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
4129 7303 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
4130 7304 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
4131 7305 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
4132 7306 1.218316 CTCCCTCCGTCCGGAAAAG 59.782 63.158 5.23 3.59 44.66 2.27
4133 7307 2.436115 CCCTCCGTCCGGAAAAGC 60.436 66.667 5.23 0.00 44.66 3.51
4134 7308 2.663196 CCTCCGTCCGGAAAAGCT 59.337 61.111 5.23 0.00 44.66 3.74
4135 7309 1.003718 CCTCCGTCCGGAAAAGCTT 60.004 57.895 5.23 0.00 44.66 3.74
4136 7310 1.298859 CCTCCGTCCGGAAAAGCTTG 61.299 60.000 5.23 0.00 44.66 4.01
4137 7311 0.602905 CTCCGTCCGGAAAAGCTTGT 60.603 55.000 5.23 0.00 44.66 3.16
4138 7312 0.601841 TCCGTCCGGAAAAGCTTGTC 60.602 55.000 5.23 8.23 42.05 3.18
4139 7313 1.574702 CCGTCCGGAAAAGCTTGTCC 61.575 60.000 24.00 24.00 37.50 4.02
4140 7314 1.574702 CGTCCGGAAAAGCTTGTCCC 61.575 60.000 26.94 13.97 0.00 4.46
4141 7315 0.536460 GTCCGGAAAAGCTTGTCCCA 60.536 55.000 26.94 13.18 0.00 4.37
4142 7316 0.183971 TCCGGAAAAGCTTGTCCCAA 59.816 50.000 26.94 14.20 0.00 4.12
4143 7317 0.598065 CCGGAAAAGCTTGTCCCAAG 59.402 55.000 26.94 14.69 0.00 3.61
4144 7318 0.039165 CGGAAAAGCTTGTCCCAAGC 60.039 55.000 26.94 18.69 43.31 4.01
4150 7324 3.027419 GCTTGTCCCAAGCTTGTCT 57.973 52.632 24.35 0.00 40.01 3.41
4151 7325 1.322442 GCTTGTCCCAAGCTTGTCTT 58.678 50.000 24.35 0.00 40.01 3.01
4152 7326 1.683385 GCTTGTCCCAAGCTTGTCTTT 59.317 47.619 24.35 0.00 40.01 2.52
4153 7327 2.287849 GCTTGTCCCAAGCTTGTCTTTC 60.288 50.000 24.35 10.65 40.01 2.62
4154 7328 2.727123 TGTCCCAAGCTTGTCTTTCA 57.273 45.000 24.35 12.85 31.27 2.69
4155 7329 3.011566 TGTCCCAAGCTTGTCTTTCAA 57.988 42.857 24.35 1.41 31.27 2.69
4156 7330 3.360867 TGTCCCAAGCTTGTCTTTCAAA 58.639 40.909 24.35 0.00 35.48 2.69
4157 7331 3.960102 TGTCCCAAGCTTGTCTTTCAAAT 59.040 39.130 24.35 0.00 35.48 2.32
4158 7332 4.202141 TGTCCCAAGCTTGTCTTTCAAATG 60.202 41.667 24.35 5.47 35.48 2.32
4159 7333 3.321682 TCCCAAGCTTGTCTTTCAAATGG 59.678 43.478 24.35 14.01 35.48 3.16
4160 7334 3.321682 CCCAAGCTTGTCTTTCAAATGGA 59.678 43.478 24.35 0.00 36.92 3.41
4161 7335 4.020839 CCCAAGCTTGTCTTTCAAATGGAT 60.021 41.667 24.35 0.00 36.92 3.41
4162 7336 4.927425 CCAAGCTTGTCTTTCAAATGGATG 59.073 41.667 24.35 0.00 36.92 3.51
4163 7337 5.510179 CCAAGCTTGTCTTTCAAATGGATGT 60.510 40.000 24.35 0.00 36.92 3.06
4164 7338 5.130292 AGCTTGTCTTTCAAATGGATGTG 57.870 39.130 0.00 0.00 35.48 3.21
4165 7339 4.586001 AGCTTGTCTTTCAAATGGATGTGT 59.414 37.500 0.00 0.00 35.48 3.72
4166 7340 4.919754 GCTTGTCTTTCAAATGGATGTGTC 59.080 41.667 0.00 0.00 35.48 3.67
4167 7341 5.278660 GCTTGTCTTTCAAATGGATGTGTCT 60.279 40.000 0.00 0.00 35.48 3.41
4168 7342 6.072508 GCTTGTCTTTCAAATGGATGTGTCTA 60.073 38.462 0.00 0.00 35.48 2.59
4169 7343 7.439157 TTGTCTTTCAAATGGATGTGTCTAG 57.561 36.000 0.00 0.00 32.64 2.43
4170 7344 5.412594 TGTCTTTCAAATGGATGTGTCTAGC 59.587 40.000 0.00 0.00 0.00 3.42
4171 7345 5.412594 GTCTTTCAAATGGATGTGTCTAGCA 59.587 40.000 0.00 0.00 0.00 3.49
4194 7368 4.130118 CCAAGTTGGTGCTAGATACATCC 58.870 47.826 14.21 0.00 31.35 3.51
4195 7369 4.384098 CCAAGTTGGTGCTAGATACATCCA 60.384 45.833 14.21 0.00 31.35 3.41
4196 7370 5.371526 CAAGTTGGTGCTAGATACATCCAT 58.628 41.667 0.00 0.00 0.00 3.41
4197 7371 5.636903 AGTTGGTGCTAGATACATCCATT 57.363 39.130 0.00 0.00 0.00 3.16
4198 7372 6.006275 AGTTGGTGCTAGATACATCCATTT 57.994 37.500 0.00 0.00 0.00 2.32
4199 7373 5.824624 AGTTGGTGCTAGATACATCCATTTG 59.175 40.000 0.00 0.00 0.00 2.32
4200 7374 5.628797 TGGTGCTAGATACATCCATTTGA 57.371 39.130 0.00 0.00 0.00 2.69
4201 7375 5.614308 TGGTGCTAGATACATCCATTTGAG 58.386 41.667 0.00 0.00 0.00 3.02
4202 7376 4.999950 GGTGCTAGATACATCCATTTGAGG 59.000 45.833 0.00 0.00 0.00 3.86
4203 7377 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
4204 7378 4.660303 TGCTAGATACATCCATTTGAGGGT 59.340 41.667 0.00 0.00 0.00 4.34
4205 7379 5.221722 TGCTAGATACATCCATTTGAGGGTC 60.222 44.000 0.00 0.00 0.00 4.46
4206 7380 5.221722 GCTAGATACATCCATTTGAGGGTCA 60.222 44.000 0.00 0.00 0.00 4.02
4207 7381 5.715439 AGATACATCCATTTGAGGGTCAA 57.285 39.130 0.00 0.00 34.03 3.18
4208 7382 5.688807 AGATACATCCATTTGAGGGTCAAG 58.311 41.667 0.00 0.00 37.70 3.02
4209 7383 2.450476 ACATCCATTTGAGGGTCAAGC 58.550 47.619 0.00 0.00 37.70 4.01
4210 7384 2.042162 ACATCCATTTGAGGGTCAAGCT 59.958 45.455 0.00 0.00 37.70 3.74
4211 7385 2.978156 TCCATTTGAGGGTCAAGCTT 57.022 45.000 0.00 0.00 37.70 3.74
4212 7386 3.243359 TCCATTTGAGGGTCAAGCTTT 57.757 42.857 0.00 0.00 37.70 3.51
4213 7387 3.575805 TCCATTTGAGGGTCAAGCTTTT 58.424 40.909 0.00 0.00 37.70 2.27
4214 7388 3.966665 TCCATTTGAGGGTCAAGCTTTTT 59.033 39.130 0.00 0.00 37.70 1.94
4215 7389 4.039124 TCCATTTGAGGGTCAAGCTTTTTC 59.961 41.667 0.00 0.00 37.70 2.29
4216 7390 3.708563 TTTGAGGGTCAAGCTTTTTCG 57.291 42.857 0.00 0.00 37.70 3.46
4217 7391 1.604604 TGAGGGTCAAGCTTTTTCGG 58.395 50.000 0.00 0.00 0.00 4.30
4218 7392 1.142060 TGAGGGTCAAGCTTTTTCGGA 59.858 47.619 0.00 0.00 0.00 4.55
4219 7393 1.535896 GAGGGTCAAGCTTTTTCGGAC 59.464 52.381 0.00 0.10 0.00 4.79
4220 7394 0.237498 GGGTCAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
4221 7395 0.237498 GGTCAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
4222 7396 1.223187 GTCAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
4223 7397 1.194772 GTCAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
4224 7398 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
4225 7399 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
4226 7400 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
4227 7401 1.019805 GCTTTTTCGGACGGAGGGAG 61.020 60.000 0.00 0.00 0.00 4.30
4228 7402 0.320697 CTTTTTCGGACGGAGGGAGT 59.679 55.000 0.00 0.00 0.00 3.85
4229 7403 1.547372 CTTTTTCGGACGGAGGGAGTA 59.453 52.381 0.00 0.00 0.00 2.59
4307 7481 6.973474 AGACAAATCTAAGACGAGTAATTCGG 59.027 38.462 0.00 0.00 43.11 4.30
4321 7495 2.353610 TTCGGGGCGAAGGGAGTAC 61.354 63.158 0.00 0.00 41.05 2.73
4322 7496 4.203076 CGGGGCGAAGGGAGTACG 62.203 72.222 0.00 0.00 0.00 3.67
4415 7590 5.695851 ATTGTGATCAAGACTGTTGAACC 57.304 39.130 0.00 0.00 36.97 3.62
4428 7603 2.174639 TGTTGAACCCATCACCTGTCTT 59.825 45.455 0.00 0.00 37.92 3.01
4461 7636 7.068103 ACTGACAATTGACATTTTGTGTTCCTA 59.932 33.333 13.59 0.00 42.36 2.94
4556 7731 8.097662 CCTCTAGTTTCTAGAAAACCAATCAGT 58.902 37.037 19.30 1.15 31.33 3.41
4557 7732 9.495572 CTCTAGTTTCTAGAAAACCAATCAGTT 57.504 33.333 19.30 0.03 31.33 3.16
4558 7733 9.847224 TCTAGTTTCTAGAAAACCAATCAGTTT 57.153 29.630 19.30 0.00 41.67 2.66
4588 7763 5.479306 AGAATATCGTTGGCAATATACGCT 58.521 37.500 1.92 0.00 35.40 5.07
4590 7765 1.577468 TCGTTGGCAATATACGCTGG 58.423 50.000 1.92 0.00 35.40 4.85
4591 7766 0.586319 CGTTGGCAATATACGCTGGG 59.414 55.000 1.92 0.00 0.00 4.45
4593 7768 1.873591 GTTGGCAATATACGCTGGGAG 59.126 52.381 1.92 0.00 0.00 4.30
4594 7769 1.128200 TGGCAATATACGCTGGGAGT 58.872 50.000 0.00 0.00 0.00 3.85
4596 7771 2.701423 TGGCAATATACGCTGGGAGTTA 59.299 45.455 0.00 0.00 0.00 2.24
4597 7772 3.064931 GGCAATATACGCTGGGAGTTAC 58.935 50.000 0.00 0.00 0.00 2.50
4986 8295 9.820725 CTTTGAATTATTTCATGCTTTATCCCA 57.179 29.630 1.11 0.00 41.38 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.515272 TTTCATCAGCTCAGTTTAATTCCC 57.485 37.500 0.00 0.00 0.00 3.97
139 140 5.958955 ACCAGATGTAAGTACCGTCTTTAC 58.041 41.667 0.00 0.00 0.00 2.01
225 226 2.034053 TCAAATTCAGTTTGCGGTCACC 59.966 45.455 0.00 0.00 45.45 4.02
228 229 2.663119 GCATCAAATTCAGTTTGCGGTC 59.337 45.455 0.00 0.00 45.45 4.79
244 245 3.930336 AGACAGAACAATTCTCGCATCA 58.070 40.909 0.00 0.00 38.11 3.07
246 247 5.724328 TCTAAGACAGAACAATTCTCGCAT 58.276 37.500 0.00 0.00 38.11 4.73
247 248 5.134202 TCTAAGACAGAACAATTCTCGCA 57.866 39.130 0.00 0.00 38.11 5.10
248 249 6.654793 AATCTAAGACAGAACAATTCTCGC 57.345 37.500 0.00 0.00 38.11 5.03
261 262 7.067129 CACCACTACAGCTACTAATCTAAGACA 59.933 40.741 0.00 0.00 0.00 3.41
267 268 4.282496 AGCACCACTACAGCTACTAATCT 58.718 43.478 0.00 0.00 36.73 2.40
296 297 8.830201 AGACAAAGCATTATAAACATTGCAAA 57.170 26.923 1.71 0.00 37.56 3.68
314 315 5.407995 TGCCAAACAAAAGTTCAAGACAAAG 59.592 36.000 0.00 0.00 0.00 2.77
337 338 1.727511 CCGGCACCACCTATTGCATG 61.728 60.000 0.00 0.00 40.75 4.06
543 544 7.747155 AATCCAAATTCATGTTTTGCATTGA 57.253 28.000 14.48 9.18 35.19 2.57
606 607 1.881324 GCCCTTTAACCTGCGTGTTAA 59.119 47.619 6.54 6.54 38.55 2.01
607 608 1.202782 TGCCCTTTAACCTGCGTGTTA 60.203 47.619 0.00 0.00 0.00 2.41
608 609 0.466555 TGCCCTTTAACCTGCGTGTT 60.467 50.000 0.00 0.00 0.00 3.32
610 611 0.240945 CTTGCCCTTTAACCTGCGTG 59.759 55.000 0.00 0.00 0.00 5.34
641 644 5.593010 AGCTTTAGTCTGAACCATATCGAC 58.407 41.667 0.00 0.00 0.00 4.20
754 774 1.816224 GTATGAAGCCGCCTCCAAAAA 59.184 47.619 0.00 0.00 0.00 1.94
755 775 1.459450 GTATGAAGCCGCCTCCAAAA 58.541 50.000 0.00 0.00 0.00 2.44
756 776 0.393808 GGTATGAAGCCGCCTCCAAA 60.394 55.000 0.00 0.00 0.00 3.28
757 777 1.223487 GGTATGAAGCCGCCTCCAA 59.777 57.895 0.00 0.00 0.00 3.53
758 778 2.908015 GGTATGAAGCCGCCTCCA 59.092 61.111 0.00 0.00 0.00 3.86
759 779 2.280186 CGGTATGAAGCCGCCTCC 60.280 66.667 0.00 0.00 42.82 4.30
765 785 1.271102 TGCCAAAAACGGTATGAAGCC 59.729 47.619 0.00 0.00 0.00 4.35
766 786 2.715737 TGCCAAAAACGGTATGAAGC 57.284 45.000 0.00 0.00 0.00 3.86
767 787 4.497473 TCTTGCCAAAAACGGTATGAAG 57.503 40.909 0.00 0.00 0.00 3.02
768 788 5.461032 AATCTTGCCAAAAACGGTATGAA 57.539 34.783 0.00 0.00 30.51 2.57
769 789 5.461032 AAATCTTGCCAAAAACGGTATGA 57.539 34.783 0.00 0.00 31.11 2.15
770 790 4.625311 GGAAATCTTGCCAAAAACGGTATG 59.375 41.667 0.00 0.00 0.00 2.39
771 791 4.526650 AGGAAATCTTGCCAAAAACGGTAT 59.473 37.500 0.00 0.00 0.00 2.73
772 792 3.892588 AGGAAATCTTGCCAAAAACGGTA 59.107 39.130 0.00 0.00 0.00 4.02
773 793 2.698274 AGGAAATCTTGCCAAAAACGGT 59.302 40.909 0.00 0.00 0.00 4.83
774 794 3.385193 AGGAAATCTTGCCAAAAACGG 57.615 42.857 0.00 0.00 0.00 4.44
896 1208 0.884704 GAGCACGACTGCCAAGGAAA 60.885 55.000 0.00 0.00 45.53 3.13
906 1218 3.649277 GATGGCCACGAGCACGACT 62.649 63.158 8.16 0.00 46.50 4.18
907 1219 3.188786 GATGGCCACGAGCACGAC 61.189 66.667 8.16 0.00 46.50 4.34
969 1281 1.464997 GGAAGCGAGCGAGAAATTTGT 59.535 47.619 0.00 0.00 0.00 2.83
986 1298 0.837272 CTGCCGGGATTAGGAAGGAA 59.163 55.000 2.18 0.00 30.48 3.36
993 1307 0.470080 TCTCCTCCTGCCGGGATTAG 60.470 60.000 2.18 0.00 44.15 1.73
1032 1352 4.047059 CTGCCTGCCGGTGCTTTG 62.047 66.667 1.90 0.00 38.71 2.77
1591 1965 6.978343 AGCATAGTGTAGCAACGAAAATAA 57.022 33.333 0.00 0.00 0.00 1.40
1607 1981 4.551702 TGTGTGTTGATGGTAGCATAGT 57.448 40.909 7.54 0.00 0.00 2.12
1691 2067 3.341823 GTGTCATGTTCAGATTCTGGCT 58.658 45.455 13.59 0.00 31.51 4.75
1943 3302 5.699915 ACACATGATATATGCTGTCTCTTGC 59.300 40.000 0.00 0.00 0.00 4.01
2275 5315 3.202818 TCATGCCTTTCACCAGTGGATAT 59.797 43.478 18.40 0.00 0.00 1.63
2322 5362 3.484407 AGCAAGATCTCAAGTTGTTGCT 58.516 40.909 19.45 19.45 44.36 3.91
2373 5413 7.885297 TCCAAAAGTATGAAACATCTCCAAAG 58.115 34.615 0.00 0.00 0.00 2.77
2409 5449 7.115947 CAGATCAGCCAAAGAGAAAAATGAAAC 59.884 37.037 0.00 0.00 0.00 2.78
2410 5450 7.149973 CAGATCAGCCAAAGAGAAAAATGAAA 58.850 34.615 0.00 0.00 0.00 2.69
2828 5890 5.079406 CGAAGTTATGCACATGTGTTGTAC 58.921 41.667 26.01 18.14 36.57 2.90
3279 6442 9.274065 GGAATTGCGGATATCGTTATTTTATTC 57.726 33.333 0.00 0.00 41.72 1.75
3280 6443 9.010029 AGGAATTGCGGATATCGTTATTTTATT 57.990 29.630 0.00 0.00 41.72 1.40
3281 6444 8.561738 AGGAATTGCGGATATCGTTATTTTAT 57.438 30.769 0.00 0.00 41.72 1.40
3282 6445 7.972832 AGGAATTGCGGATATCGTTATTTTA 57.027 32.000 0.00 0.00 41.72 1.52
3389 6552 8.985805 CATAAAAAGTACTCCGTCCCATAATAC 58.014 37.037 0.00 0.00 0.00 1.89
3464 6631 6.977213 AGTGCAAGTTTGACCGTATTTTAAT 58.023 32.000 0.00 0.00 0.00 1.40
3474 6641 5.831997 AGTTAAATGAGTGCAAGTTTGACC 58.168 37.500 0.00 0.00 0.00 4.02
3985 7156 6.208599 TCCCACAATAACAATGTTCCTTCTTC 59.791 38.462 0.22 0.00 0.00 2.87
3986 7157 6.074648 TCCCACAATAACAATGTTCCTTCTT 58.925 36.000 0.22 0.00 0.00 2.52
4093 7267 5.488341 GAGTACACATTAAGGAGGCTTCAA 58.512 41.667 0.00 0.00 0.00 2.69
4094 7268 4.081087 GGAGTACACATTAAGGAGGCTTCA 60.081 45.833 0.00 0.00 0.00 3.02
4095 7269 4.443621 GGAGTACACATTAAGGAGGCTTC 58.556 47.826 0.00 0.00 0.00 3.86
4096 7270 3.200165 GGGAGTACACATTAAGGAGGCTT 59.800 47.826 0.00 0.00 0.00 4.35
4098 7272 2.772515 AGGGAGTACACATTAAGGAGGC 59.227 50.000 0.00 0.00 0.00 4.70
4099 7273 3.388350 GGAGGGAGTACACATTAAGGAGG 59.612 52.174 0.00 0.00 0.00 4.30
4100 7274 3.068307 CGGAGGGAGTACACATTAAGGAG 59.932 52.174 0.00 0.00 0.00 3.69
4102 7276 2.764572 ACGGAGGGAGTACACATTAAGG 59.235 50.000 0.00 0.00 0.00 2.69
4103 7277 3.181478 GGACGGAGGGAGTACACATTAAG 60.181 52.174 0.00 0.00 0.00 1.85
4104 7278 2.762327 GGACGGAGGGAGTACACATTAA 59.238 50.000 0.00 0.00 0.00 1.40
4105 7279 2.381911 GGACGGAGGGAGTACACATTA 58.618 52.381 0.00 0.00 0.00 1.90
4106 7280 1.192428 GGACGGAGGGAGTACACATT 58.808 55.000 0.00 0.00 0.00 2.71
4107 7281 1.035932 CGGACGGAGGGAGTACACAT 61.036 60.000 0.00 0.00 0.00 3.21
4108 7282 1.676635 CGGACGGAGGGAGTACACA 60.677 63.158 0.00 0.00 0.00 3.72
4109 7283 2.413142 CCGGACGGAGGGAGTACAC 61.413 68.421 4.40 0.00 37.50 2.90
4110 7284 2.044650 CCGGACGGAGGGAGTACA 60.045 66.667 4.40 0.00 37.50 2.90
4111 7285 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
4112 7286 0.251742 TTTTCCGGACGGAGGGAGTA 60.252 55.000 13.64 0.00 46.06 2.59
4113 7287 1.534717 TTTTCCGGACGGAGGGAGT 60.535 57.895 13.64 0.00 46.06 3.85
4114 7288 1.218316 CTTTTCCGGACGGAGGGAG 59.782 63.158 13.64 9.15 46.06 4.30
4115 7289 2.951101 GCTTTTCCGGACGGAGGGA 61.951 63.158 13.64 1.83 46.06 4.20
4116 7290 2.436115 GCTTTTCCGGACGGAGGG 60.436 66.667 13.64 8.97 46.06 4.30
4117 7291 1.003718 AAGCTTTTCCGGACGGAGG 60.004 57.895 13.64 9.30 46.06 4.30
4118 7292 0.602905 ACAAGCTTTTCCGGACGGAG 60.603 55.000 13.64 3.27 46.06 4.63
4119 7293 0.601841 GACAAGCTTTTCCGGACGGA 60.602 55.000 1.83 9.76 43.52 4.69
4120 7294 1.574702 GGACAAGCTTTTCCGGACGG 61.575 60.000 15.65 3.96 0.00 4.79
4121 7295 1.574702 GGGACAAGCTTTTCCGGACG 61.575 60.000 22.30 0.00 32.00 4.79
4122 7296 0.536460 TGGGACAAGCTTTTCCGGAC 60.536 55.000 22.30 11.43 31.92 4.79
4123 7297 1.840598 TGGGACAAGCTTTTCCGGA 59.159 52.632 22.30 10.91 31.92 5.14
4124 7298 4.492604 TGGGACAAGCTTTTCCGG 57.507 55.556 22.30 0.00 31.92 5.14
4132 7306 6.232513 TTGAAAGACAAGCTTGGGACAAGC 62.233 45.833 29.18 22.54 43.31 4.01
4133 7307 3.381272 TTGAAAGACAAGCTTGGGACAAG 59.619 43.478 29.18 3.71 37.48 3.16
4134 7308 3.360867 TTGAAAGACAAGCTTGGGACAA 58.639 40.909 29.18 21.59 37.48 3.18
4135 7309 2.727123 TGAAAGACAAGCTTGGGACA 57.273 45.000 29.18 17.71 36.80 4.02
4136 7310 4.301628 CATTTGAAAGACAAGCTTGGGAC 58.698 43.478 29.18 19.11 39.77 4.46
4137 7311 3.321682 CCATTTGAAAGACAAGCTTGGGA 59.678 43.478 29.18 7.03 39.77 4.37
4138 7312 3.321682 TCCATTTGAAAGACAAGCTTGGG 59.678 43.478 29.18 16.37 39.77 4.12
4139 7313 4.589216 TCCATTTGAAAGACAAGCTTGG 57.411 40.909 29.18 12.28 39.77 3.61
4140 7314 5.404366 CACATCCATTTGAAAGACAAGCTTG 59.596 40.000 24.84 24.84 39.77 4.01
4141 7315 5.069516 ACACATCCATTTGAAAGACAAGCTT 59.930 36.000 0.00 0.00 39.77 3.74
4142 7316 4.586001 ACACATCCATTTGAAAGACAAGCT 59.414 37.500 0.00 0.00 39.77 3.74
4143 7317 4.874970 ACACATCCATTTGAAAGACAAGC 58.125 39.130 0.00 0.00 39.77 4.01
4144 7318 6.323203 AGACACATCCATTTGAAAGACAAG 57.677 37.500 0.00 0.00 39.77 3.16
4145 7319 6.072508 GCTAGACACATCCATTTGAAAGACAA 60.073 38.462 0.00 0.00 36.65 3.18
4146 7320 5.412594 GCTAGACACATCCATTTGAAAGACA 59.587 40.000 0.00 0.00 0.00 3.41
4147 7321 5.412594 TGCTAGACACATCCATTTGAAAGAC 59.587 40.000 0.00 0.00 0.00 3.01
4148 7322 5.559770 TGCTAGACACATCCATTTGAAAGA 58.440 37.500 0.00 0.00 0.00 2.52
4149 7323 5.885230 TGCTAGACACATCCATTTGAAAG 57.115 39.130 0.00 0.00 0.00 2.62
4172 7346 4.130118 GGATGTATCTAGCACCAACTTGG 58.870 47.826 6.24 6.24 45.02 3.61
4173 7347 4.769688 TGGATGTATCTAGCACCAACTTG 58.230 43.478 0.00 0.00 0.00 3.16
4174 7348 5.636903 ATGGATGTATCTAGCACCAACTT 57.363 39.130 0.00 0.00 0.00 2.66
4175 7349 5.636903 AATGGATGTATCTAGCACCAACT 57.363 39.130 0.00 0.00 0.00 3.16
4176 7350 5.822519 TCAAATGGATGTATCTAGCACCAAC 59.177 40.000 0.00 0.00 0.00 3.77
4177 7351 6.000246 TCAAATGGATGTATCTAGCACCAA 58.000 37.500 0.00 0.00 0.00 3.67
4178 7352 5.455183 CCTCAAATGGATGTATCTAGCACCA 60.455 44.000 0.00 0.00 0.00 4.17
4179 7353 4.999950 CCTCAAATGGATGTATCTAGCACC 59.000 45.833 0.00 0.00 0.00 5.01
4180 7354 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
4181 7355 4.660303 ACCCTCAAATGGATGTATCTAGCA 59.340 41.667 0.00 0.00 0.00 3.49
4182 7356 5.221722 TGACCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 0.00 3.42
4183 7357 6.425210 TGACCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 0.00 2.43
4184 7358 6.688922 GCTTGACCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.73 1.98
4185 7359 5.688807 CTTGACCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.73 1.98
4186 7360 4.276926 GCTTGACCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.73 2.24
4187 7361 4.079558 AGCTTGACCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.73 2.29
4188 7362 3.266772 AGCTTGACCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.73 2.29
4189 7363 2.042162 AGCTTGACCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.73 3.06
4190 7364 2.731572 AGCTTGACCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.73 3.51
4191 7365 3.463048 AAGCTTGACCCTCAAATGGAT 57.537 42.857 0.00 0.00 35.73 3.41
4192 7366 2.978156 AAGCTTGACCCTCAAATGGA 57.022 45.000 0.00 0.00 35.73 3.41
4193 7367 4.309933 GAAAAAGCTTGACCCTCAAATGG 58.690 43.478 0.00 0.00 35.73 3.16
4194 7368 3.983344 CGAAAAAGCTTGACCCTCAAATG 59.017 43.478 0.00 0.00 35.73 2.32
4195 7369 3.005791 CCGAAAAAGCTTGACCCTCAAAT 59.994 43.478 0.00 0.00 35.73 2.32
4196 7370 2.360801 CCGAAAAAGCTTGACCCTCAAA 59.639 45.455 0.00 0.00 35.73 2.69
4197 7371 1.953686 CCGAAAAAGCTTGACCCTCAA 59.046 47.619 0.00 0.00 34.79 3.02
4198 7372 1.142060 TCCGAAAAAGCTTGACCCTCA 59.858 47.619 0.00 0.00 0.00 3.86
4199 7373 1.535896 GTCCGAAAAAGCTTGACCCTC 59.464 52.381 0.00 0.00 0.00 4.30
4200 7374 1.605753 GTCCGAAAAAGCTTGACCCT 58.394 50.000 0.00 0.00 0.00 4.34
4201 7375 0.237498 CGTCCGAAAAAGCTTGACCC 59.763 55.000 0.00 0.00 0.00 4.46
4202 7376 0.237498 CCGTCCGAAAAAGCTTGACC 59.763 55.000 0.00 0.00 0.00 4.02
4203 7377 1.194772 CTCCGTCCGAAAAAGCTTGAC 59.805 52.381 0.00 1.34 0.00 3.18
4204 7378 1.508632 CTCCGTCCGAAAAAGCTTGA 58.491 50.000 0.00 0.00 0.00 3.02
4205 7379 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
4206 7380 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
4207 7381 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
4208 7382 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
4209 7383 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
4210 7384 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
4211 7385 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
4212 7386 1.856629 AATACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
4213 7387 2.301346 GTAATACTCCCTCCGTCCGAA 58.699 52.381 0.00 0.00 0.00 4.30
4214 7388 1.477558 GGTAATACTCCCTCCGTCCGA 60.478 57.143 0.00 0.00 0.00 4.55
4215 7389 0.957362 GGTAATACTCCCTCCGTCCG 59.043 60.000 0.00 0.00 0.00 4.79
4216 7390 2.237643 GAGGTAATACTCCCTCCGTCC 58.762 57.143 0.00 0.00 41.22 4.79
4225 7399 7.270779 AGTAATTTGGAACGGAGGTAATACTC 58.729 38.462 0.00 0.00 36.76 2.59
4226 7400 7.191593 AGTAATTTGGAACGGAGGTAATACT 57.808 36.000 0.00 0.00 0.00 2.12
4227 7401 7.550196 TCAAGTAATTTGGAACGGAGGTAATAC 59.450 37.037 0.00 0.00 37.39 1.89
4228 7402 7.550196 GTCAAGTAATTTGGAACGGAGGTAATA 59.450 37.037 0.00 0.00 37.39 0.98
4229 7403 6.373495 GTCAAGTAATTTGGAACGGAGGTAAT 59.627 38.462 0.00 0.00 37.39 1.89
4240 7414 9.796120 CAACACTAAAAAGTCAAGTAATTTGGA 57.204 29.630 0.00 0.00 37.39 3.53
4305 7479 4.203076 CGTACTCCCTTCGCCCCG 62.203 72.222 0.00 0.00 0.00 5.73
4307 7481 0.321034 AAAACGTACTCCCTTCGCCC 60.321 55.000 0.00 0.00 0.00 6.13
4397 7572 3.855255 TGGGTTCAACAGTCTTGATCA 57.145 42.857 0.00 0.00 0.00 2.92
4415 7590 1.162698 CAGTGCAAGACAGGTGATGG 58.837 55.000 0.00 0.00 0.00 3.51
4428 7603 2.916640 TGTCAATTGTCAGTCAGTGCA 58.083 42.857 5.13 0.00 0.00 4.57
4461 7636 4.397420 TGCAGGACACACTGATAAATTGT 58.603 39.130 0.00 0.00 40.97 2.71
4561 7736 8.388103 GCGTATATTGCCAACGATATTCTAAAT 58.612 33.333 0.00 0.00 38.89 1.40
4588 7763 8.026396 GGAGTATTAACTTATGGTAACTCCCA 57.974 38.462 11.18 0.00 43.83 4.37
4926 8232 0.822944 TGGATGTGTGTGGGCACTTG 60.823 55.000 0.00 0.00 45.44 3.16
5013 8630 7.923461 TGGATATGGATTATTCAACCCGAATA 58.077 34.615 0.00 0.00 42.76 1.75


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

AutoCloner maintained by Alex Coulton.