Multiple sequence alignment - TraesCS4A01G395700

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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 TraesCS4A01G395700 chr4A 100.000 6137 0 0 1 6137 670846831 670852967 0.000000e+00 11334.0
1 TraesCS4A01G395700 chr4A 87.692 65 6 2 2094 2157 99009751 99009814 2.370000e-09 75.0
2 TraesCS4A01G395700 chr4A 97.561 41 1 0 5791 5831 670852580 670852620 3.070000e-08 71.3
3 TraesCS4A01G395700 chr4A 97.561 41 1 0 5750 5790 670852621 670852661 3.070000e-08 71.3
4 TraesCS4A01G395700 chr7A 94.357 2995 119 19 797 3762 58224402 58227375 0.000000e+00 4549.0
5 TraesCS4A01G395700 chr7A 94.813 964 22 5 4855 5790 58227371 58228334 0.000000e+00 1478.0
6 TraesCS4A01G395700 chr7A 94.012 167 9 1 5972 6137 254417630 254417796 1.020000e-62 252.0
7 TraesCS4A01G395700 chr7A 89.205 176 15 1 5791 5966 58228294 58228465 3.730000e-52 217.0
8 TraesCS4A01G395700 chr7A 81.707 164 21 5 1924 2080 505658351 505658190 1.800000e-25 128.0
9 TraesCS4A01G395700 chr7A 81.065 169 22 5 1921 2080 430660690 430660857 6.460000e-25 126.0
10 TraesCS4A01G395700 chr7D 93.308 2929 133 26 803 3708 54837786 54834898 0.000000e+00 4265.0
11 TraesCS4A01G395700 chr7D 91.990 799 23 16 4981 5771 54834898 54834133 0.000000e+00 1083.0
12 TraesCS4A01G395700 chr7D 88.747 862 68 9 4028 4865 532628997 532629853 0.000000e+00 1027.0
13 TraesCS4A01G395700 chr7D 90.217 92 8 1 2416 2507 6744875 6744965 1.080000e-22 119.0
14 TraesCS4A01G395700 chr5B 91.556 1125 53 12 3759 4857 529535718 529536826 0.000000e+00 1513.0
15 TraesCS4A01G395700 chr5B 88.335 883 60 18 3911 4765 140116059 140116926 0.000000e+00 1020.0
16 TraesCS4A01G395700 chr5B 87.226 274 21 6 3759 4030 680995931 680996192 3.600000e-77 300.0
17 TraesCS4A01G395700 chr5B 86.471 170 6 6 3908 4068 685468407 685468568 2.940000e-38 171.0
18 TraesCS4A01G395700 chr5B 91.398 93 8 0 2422 2514 402737628 402737536 1.800000e-25 128.0
19 TraesCS4A01G395700 chr2B 99.248 798 5 1 1 797 63040995 63040198 0.000000e+00 1439.0
20 TraesCS4A01G395700 chr2B 98.642 810 8 2 1 808 218061905 218062713 0.000000e+00 1432.0
21 TraesCS4A01G395700 chr2B 90.253 1108 62 14 3762 4828 800774992 800776094 0.000000e+00 1406.0
22 TraesCS4A01G395700 chr2B 89.522 983 51 16 3908 4859 430755083 430756044 0.000000e+00 1197.0
23 TraesCS4A01G395700 chr2B 90.778 900 53 7 3986 4858 584844569 584843673 0.000000e+00 1175.0
24 TraesCS4A01G395700 chr2B 91.238 856 53 7 4030 4863 52692192 52691337 0.000000e+00 1146.0
25 TraesCS4A01G395700 chr2B 88.396 991 64 20 3908 4859 200861662 200862640 0.000000e+00 1146.0
26 TraesCS4A01G395700 chr2B 89.698 796 48 14 4000 4763 777131234 777130441 0.000000e+00 985.0
27 TraesCS4A01G395700 chr2B 88.645 273 19 5 3759 4029 611426832 611427094 7.670000e-84 322.0
28 TraesCS4A01G395700 chr2B 88.235 272 23 2 3759 4029 584844911 584844648 3.570000e-82 316.0
29 TraesCS4A01G395700 chr2B 86.667 270 20 7 3762 4029 44027529 44027274 1.010000e-72 285.0
30 TraesCS4A01G395700 chr2B 80.537 149 20 7 5813 5957 110829623 110829766 8.410000e-19 106.0
31 TraesCS4A01G395700 chr2B 98.039 51 0 1 3980 4029 52692336 52692286 3.050000e-13 87.9
32 TraesCS4A01G395700 chr2B 100.000 30 0 0 5644 5673 735930819 735930848 8.590000e-04 56.5
33 TraesCS4A01G395700 chr3B 98.876 801 7 1 1 799 770733415 770734215 0.000000e+00 1428.0
34 TraesCS4A01G395700 chr3B 88.751 889 56 17 3911 4765 632917388 632916510 0.000000e+00 1048.0
35 TraesCS4A01G395700 chr3B 87.546 273 16 8 3762 4031 693651231 693650974 3.600000e-77 300.0
36 TraesCS4A01G395700 chr3B 85.874 269 18 7 3762 4029 30496772 30496523 1.010000e-67 268.0
37 TraesCS4A01G395700 chr6A 98.875 800 7 2 1 798 558028616 558027817 0.000000e+00 1426.0
38 TraesCS4A01G395700 chr6A 78.947 228 24 13 1863 2080 506433319 506433532 3.860000e-27 134.0
39 TraesCS4A01G395700 chr6A 81.212 165 22 8 1924 2080 104047557 104047394 2.320000e-24 124.0
40 TraesCS4A01G395700 chr6A 84.956 113 14 3 2423 2534 428694 428804 1.810000e-20 111.0
41 TraesCS4A01G395700 chr6A 79.518 166 23 7 1924 2080 92196356 92196193 2.340000e-19 108.0
42 TraesCS4A01G395700 chr6A 78.698 169 26 5 1921 2080 164188950 164189117 3.030000e-18 104.0
43 TraesCS4A01G395700 chr6A 100.000 28 0 0 5646 5673 544479237 544479210 1.100000e-02 52.8
44 TraesCS4A01G395700 chr1A 98.637 807 8 2 1 804 343662834 343662028 0.000000e+00 1426.0
45 TraesCS4A01G395700 chr1A 78.632 234 25 9 1857 2080 462949430 462949212 1.390000e-26 132.0
46 TraesCS4A01G395700 chr1A 93.103 87 6 0 2423 2509 12556181 12556267 1.800000e-25 128.0
47 TraesCS4A01G395700 chr1A 80.357 168 24 6 1921 2080 405961569 405961735 1.080000e-22 119.0
48 TraesCS4A01G395700 chr1A 80.368 163 23 3 1927 2080 144636726 144636564 1.400000e-21 115.0
49 TraesCS4A01G395700 chr1A 80.000 165 24 7 1924 2080 144919378 144919215 5.030000e-21 113.0
50 TraesCS4A01G395700 chr6B 98.752 801 8 1 1 799 204560205 204561005 0.000000e+00 1423.0
51 TraesCS4A01G395700 chr6B 98.628 802 9 1 1 800 481037299 481036498 0.000000e+00 1419.0
52 TraesCS4A01G395700 chr6B 93.452 168 9 2 5972 6137 120649026 120648859 1.320000e-61 248.0
53 TraesCS4A01G395700 chr6B 81.301 123 19 1 5827 5949 644907455 644907337 5.060000e-16 97.1
54 TraesCS4A01G395700 chr6B 89.062 64 5 1 2094 2157 24930176 24930237 1.830000e-10 78.7
55 TraesCS4A01G395700 chr2A 98.872 798 8 1 1 797 762991670 762990873 0.000000e+00 1423.0
56 TraesCS4A01G395700 chr2A 94.611 167 8 1 5972 6137 177014462 177014296 2.190000e-64 257.0
57 TraesCS4A01G395700 chr7B 98.750 800 8 1 1 798 649989407 649990206 0.000000e+00 1421.0
58 TraesCS4A01G395700 chr7B 90.504 853 55 11 4035 4863 529148415 529149265 0.000000e+00 1103.0
59 TraesCS4A01G395700 chr7B 88.279 674 54 7 4204 4857 597180452 597181120 0.000000e+00 784.0
60 TraesCS4A01G395700 chr7B 87.273 275 25 3 3756 4029 585912257 585911992 7.730000e-79 305.0
61 TraesCS4A01G395700 chr7B 84.615 273 26 9 3759 4029 240964499 240964241 2.190000e-64 257.0
62 TraesCS4A01G395700 chr7B 93.642 173 10 1 5966 6137 304122988 304123160 2.190000e-64 257.0
63 TraesCS4A01G395700 chr7B 89.000 100 10 1 2411 2510 559531936 559531838 8.350000e-24 122.0
64 TraesCS4A01G395700 chr7B 88.235 102 10 2 2417 2518 740996150 740996249 3.000000e-23 121.0
65 TraesCS4A01G395700 chr7B 88.000 50 2 2 5828 5877 505184228 505184273 8.590000e-04 56.5
66 TraesCS4A01G395700 chr1B 89.447 976 59 17 3911 4855 266932644 266931682 0.000000e+00 1192.0
67 TraesCS4A01G395700 chr1B 89.651 831 47 14 4030 4821 344366203 344367033 0.000000e+00 1022.0
68 TraesCS4A01G395700 chr1B 91.882 271 13 2 3762 4031 344365850 344366112 2.700000e-98 370.0
69 TraesCS4A01G395700 chr1B 83.117 231 24 9 1863 2080 17762742 17762514 4.850000e-46 196.0
70 TraesCS4A01G395700 chr1B 91.304 92 8 0 2421 2512 29409023 29408932 6.460000e-25 126.0
71 TraesCS4A01G395700 chr1B 90.625 96 6 2 2416 2511 662552690 662552782 2.320000e-24 124.0
72 TraesCS4A01G395700 chr1B 97.059 34 1 0 5644 5677 593924360 593924327 2.390000e-04 58.4
73 TraesCS4A01G395700 chr1B 96.970 33 0 1 5646 5678 645367003 645367034 3.000000e-03 54.7
74 TraesCS4A01G395700 chr4B 88.345 961 66 18 3921 4859 5485126 5486062 0.000000e+00 1112.0
75 TraesCS4A01G395700 chr4B 87.700 1000 55 24 3908 4857 671059349 671060330 0.000000e+00 1103.0
76 TraesCS4A01G395700 chr4B 86.122 980 75 22 3911 4859 473860704 473859755 0.000000e+00 1000.0
77 TraesCS4A01G395700 chr4B 93.182 88 6 0 2422 2509 277407991 277407904 4.990000e-26 130.0
78 TraesCS4A01G395700 chr4B 85.897 78 8 2 2081 2158 651511665 651511591 5.100000e-11 80.5
79 TraesCS4A01G395700 chr4B 94.444 36 0 2 5827 5861 240690515 240690481 3.000000e-03 54.7
80 TraesCS4A01G395700 chr4D 88.324 865 65 16 4025 4859 12301249 12300391 0.000000e+00 1005.0
81 TraesCS4A01G395700 chr4D 90.526 95 9 0 2416 2510 19394957 19395051 6.460000e-25 126.0
82 TraesCS4A01G395700 chr4D 91.765 85 7 0 2423 2507 483109750 483109666 1.080000e-22 119.0
83 TraesCS4A01G395700 chr4D 90.698 86 8 0 2421 2506 7830327 7830242 1.400000e-21 115.0
84 TraesCS4A01G395700 chr4D 88.172 93 10 1 2417 2509 498045181 498045272 6.500000e-20 110.0
85 TraesCS4A01G395700 chr4D 86.458 96 12 1 2422 2517 502406374 502406280 3.030000e-18 104.0
86 TraesCS4A01G395700 chr4D 85.870 92 13 0 5864 5955 151935886 151935795 1.410000e-16 99.0
87 TraesCS4A01G395700 chr4D 100.000 33 0 0 2126 2158 499285766 499285734 1.850000e-05 62.1
88 TraesCS4A01G395700 chr4D 100.000 32 0 0 2126 2157 365838453 365838422 6.640000e-05 60.2
89 TraesCS4A01G395700 chr4D 100.000 32 0 0 2126 2157 394190387 394190356 6.640000e-05 60.2
90 TraesCS4A01G395700 chr6D 94.012 167 9 1 5972 6137 85800000 85800166 1.020000e-62 252.0
91 TraesCS4A01G395700 chr6D 92.593 81 5 1 2427 2507 140086860 140086939 1.400000e-21 115.0
92 TraesCS4A01G395700 chr6D 88.889 90 10 0 2421 2510 32646913 32646824 1.810000e-20 111.0
93 TraesCS4A01G395700 chr6D 89.535 86 9 0 2424 2509 174592674 174592589 6.500000e-20 110.0
94 TraesCS4A01G395700 chr6D 86.667 90 12 0 2421 2510 321773562 321773473 3.910000e-17 100.0
95 TraesCS4A01G395700 chr6D 86.207 87 12 0 2421 2507 26757950 26757864 1.820000e-15 95.3
96 TraesCS4A01G395700 chr6D 84.946 93 14 0 2419 2511 29232382 29232290 1.820000e-15 95.3
97 TraesCS4A01G395700 chr6D 90.323 62 6 0 2094 2155 13290787 13290848 1.420000e-11 82.4
98 TraesCS4A01G395700 chr6D 100.000 28 0 0 5646 5673 44137828 44137801 1.100000e-02 52.8
99 TraesCS4A01G395700 chr5D 93.064 173 11 1 5966 6137 188340187 188340359 1.020000e-62 252.0
100 TraesCS4A01G395700 chr5D 93.413 167 10 1 5972 6137 152758228 152758062 4.750000e-61 246.0
101 TraesCS4A01G395700 chr5D 93.333 90 6 0 2420 2509 310705353 310705264 3.860000e-27 134.0
102 TraesCS4A01G395700 chr5D 89.412 85 9 0 5864 5948 345193258 345193342 2.340000e-19 108.0
103 TraesCS4A01G395700 chr5D 86.364 66 7 2 2094 2158 464070885 464070949 3.070000e-08 71.3
104 TraesCS4A01G395700 chr5D 84.848 66 6 4 2094 2159 50037456 50037517 5.140000e-06 63.9
105 TraesCS4A01G395700 chr5D 83.582 67 8 3 2094 2159 49761866 49761930 6.640000e-05 60.2
106 TraesCS4A01G395700 chr5D 83.582 67 8 3 2094 2159 50198558 50198622 6.640000e-05 60.2
107 TraesCS4A01G395700 chr5A 93.529 170 10 1 5969 6137 366234816 366234985 1.020000e-62 252.0
108 TraesCS4A01G395700 chr5A 81.871 171 17 8 1921 2080 194809402 194809569 1.390000e-26 132.0
109 TraesCS4A01G395700 chr5A 81.325 166 21 6 1924 2080 318086635 318086471 6.460000e-25 126.0
110 TraesCS4A01G395700 chr5A 81.437 167 20 7 1924 2080 606133636 606133471 6.460000e-25 126.0
111 TraesCS4A01G395700 chr5A 81.212 165 21 6 1924 2080 598506197 598506035 2.320000e-24 124.0
112 TraesCS4A01G395700 chr5A 83.594 128 15 5 5823 5949 649857797 649857675 1.400000e-21 115.0
113 TraesCS4A01G395700 chr5A 87.692 65 5 3 2094 2157 410857572 410857510 8.530000e-09 73.1
114 TraesCS4A01G395700 chr3A 93.064 173 11 1 5966 6137 308688534 308688706 1.020000e-62 252.0
115 TraesCS4A01G395700 chr3A 89.394 66 7 0 2094 2159 491189447 491189512 3.940000e-12 84.2
116 TraesCS4A01G395700 chr2D 82.251 231 25 8 1863 2080 445402670 445402443 1.050000e-42 185.0
117 TraesCS4A01G395700 chr2D 87.755 98 8 4 2414 2510 643842860 643842766 1.810000e-20 111.0
118 TraesCS4A01G395700 chr2D 88.235 85 10 0 5864 5948 602636361 602636445 1.090000e-17 102.0
119 TraesCS4A01G395700 chr2D 88.406 69 6 2 2094 2161 425742590 425742657 1.420000e-11 82.4
120 TraesCS4A01G395700 chr2D 91.379 58 5 0 2103 2160 35800042 35800099 5.100000e-11 80.5
121 TraesCS4A01G395700 chrUn 91.954 87 7 0 2421 2507 377893913 377893827 8.350000e-24 122.0
122 TraesCS4A01G395700 chrUn 90.000 90 9 0 2421 2510 101630798 101630887 3.890000e-22 117.0
123 TraesCS4A01G395700 chrUn 80.000 120 20 3 5826 5945 65114982 65115097 1.100000e-12 86.1
124 TraesCS4A01G395700 chrUn 88.710 62 7 0 2446 2507 73917566 73917627 6.600000e-10 76.8
125 TraesCS4A01G395700 chrUn 90.385 52 4 1 2457 2508 153391892 153391842 3.970000e-07 67.6
126 TraesCS4A01G395700 chrUn 93.182 44 3 0 2116 2159 313622388 313622431 1.430000e-06 65.8
127 TraesCS4A01G395700 chrUn 97.297 37 1 0 2473 2509 289154500 289154536 5.140000e-06 63.9
128 TraesCS4A01G395700 chrUn 97.297 37 1 0 2473 2509 350900301 350900265 5.140000e-06 63.9
129 TraesCS4A01G395700 chrUn 92.857 42 3 0 2467 2508 75091693 75091652 1.850000e-05 62.1
130 TraesCS4A01G395700 chrUn 100.000 32 0 0 2126 2157 32098222 32098253 6.640000e-05 60.2
131 TraesCS4A01G395700 chrUn 96.970 33 1 0 2475 2507 37844517 37844549 8.590000e-04 56.5
132 TraesCS4A01G395700 chrUn 96.875 32 1 0 2422 2453 61798967 61798998 3.000000e-03 54.7
133 TraesCS4A01G395700 chrUn 96.875 32 1 0 2422 2453 61823809 61823840 3.000000e-03 54.7
134 TraesCS4A01G395700 chrUn 96.875 32 1 0 2126 2157 295853753 295853722 3.000000e-03 54.7
135 TraesCS4A01G395700 chrUn 100.000 28 0 0 2483 2510 137673766 137673793 1.100000e-02 52.8
136 TraesCS4A01G395700 chr1D 89.796 98 6 4 2423 2519 307349155 307349249 8.350000e-24 122.0
137 TraesCS4A01G395700 chr1D 91.111 90 5 3 2419 2507 307349242 307349155 1.080000e-22 119.0
138 TraesCS4A01G395700 chr1D 88.660 97 7 3 2422 2518 84711175 84711267 1.400000e-21 115.0
139 TraesCS4A01G395700 chr1D 90.625 64 6 0 2094 2157 279101397 279101460 1.100000e-12 86.1
140 TraesCS4A01G395700 chr1D 87.879 66 7 1 2094 2159 468830155 468830219 6.600000e-10 76.8
141 TraesCS4A01G395700 chr1D 94.872 39 2 0 2119 2157 106843115 106843153 1.850000e-05 62.1
142 TraesCS4A01G395700 chr1D 83.077 65 10 1 2094 2158 302696443 302696506 2.390000e-04 58.4
143 TraesCS4A01G395700 chr1D 82.353 68 8 2 2094 2158 493932325 493932391 8.590000e-04 56.5
144 TraesCS4A01G395700 chr3D 91.765 85 7 0 2423 2507 459212412 459212496 1.080000e-22 119.0
145 TraesCS4A01G395700 chr3D 89.247 93 8 2 2417 2509 467487456 467487366 1.400000e-21 115.0
146 TraesCS4A01G395700 chr3D 82.540 126 16 4 5827 5951 976151 976031 8.410000e-19 106.0
147 TraesCS4A01G395700 chr3D 89.062 64 7 0 2095 2158 45931395 45931332 5.100000e-11 80.5
148 TraesCS4A01G395700 chr3D 85.938 64 5 3 2094 2157 250931552 250931493 1.430000e-06 65.8
149 TraesCS4A01G395700 chr3D 91.892 37 3 0 5637 5673 164321030 164321066 1.100000e-02 52.8
150 TraesCS4A01G395700 chr3D 100.000 28 0 0 5644 5671 238498743 238498716 1.100000e-02 52.8
151 TraesCS4A01G395700 chr3D 100.000 28 0 0 5646 5673 554963721 554963748 1.100000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G395700 chr4A 670846831 670852967 6136 False 3825.533333 11334 98.374000 1 6137 3 chr4A.!!$F2 6136
1 TraesCS4A01G395700 chr7A 58224402 58228465 4063 False 2081.333333 4549 92.791667 797 5966 3 chr7A.!!$F3 5169
2 TraesCS4A01G395700 chr7D 54834133 54837786 3653 True 2674.000000 4265 92.649000 803 5771 2 chr7D.!!$R1 4968
3 TraesCS4A01G395700 chr7D 532628997 532629853 856 False 1027.000000 1027 88.747000 4028 4865 1 chr7D.!!$F2 837
4 TraesCS4A01G395700 chr5B 529535718 529536826 1108 False 1513.000000 1513 91.556000 3759 4857 1 chr5B.!!$F2 1098
5 TraesCS4A01G395700 chr5B 140116059 140116926 867 False 1020.000000 1020 88.335000 3911 4765 1 chr5B.!!$F1 854
6 TraesCS4A01G395700 chr2B 63040198 63040995 797 True 1439.000000 1439 99.248000 1 797 1 chr2B.!!$R2 796
7 TraesCS4A01G395700 chr2B 218061905 218062713 808 False 1432.000000 1432 98.642000 1 808 1 chr2B.!!$F3 807
8 TraesCS4A01G395700 chr2B 800774992 800776094 1102 False 1406.000000 1406 90.253000 3762 4828 1 chr2B.!!$F7 1066
9 TraesCS4A01G395700 chr2B 430755083 430756044 961 False 1197.000000 1197 89.522000 3908 4859 1 chr2B.!!$F4 951
10 TraesCS4A01G395700 chr2B 200861662 200862640 978 False 1146.000000 1146 88.396000 3908 4859 1 chr2B.!!$F2 951
11 TraesCS4A01G395700 chr2B 777130441 777131234 793 True 985.000000 985 89.698000 4000 4763 1 chr2B.!!$R3 763
12 TraesCS4A01G395700 chr2B 584843673 584844911 1238 True 745.500000 1175 89.506500 3759 4858 2 chr2B.!!$R5 1099
13 TraesCS4A01G395700 chr2B 52691337 52692336 999 True 616.950000 1146 94.638500 3980 4863 2 chr2B.!!$R4 883
14 TraesCS4A01G395700 chr3B 770733415 770734215 800 False 1428.000000 1428 98.876000 1 799 1 chr3B.!!$F1 798
15 TraesCS4A01G395700 chr3B 632916510 632917388 878 True 1048.000000 1048 88.751000 3911 4765 1 chr3B.!!$R2 854
16 TraesCS4A01G395700 chr6A 558027817 558028616 799 True 1426.000000 1426 98.875000 1 798 1 chr6A.!!$R4 797
17 TraesCS4A01G395700 chr1A 343662028 343662834 806 True 1426.000000 1426 98.637000 1 804 1 chr1A.!!$R3 803
18 TraesCS4A01G395700 chr6B 204560205 204561005 800 False 1423.000000 1423 98.752000 1 799 1 chr6B.!!$F2 798
19 TraesCS4A01G395700 chr6B 481036498 481037299 801 True 1419.000000 1419 98.628000 1 800 1 chr6B.!!$R2 799
20 TraesCS4A01G395700 chr2A 762990873 762991670 797 True 1423.000000 1423 98.872000 1 797 1 chr2A.!!$R2 796
21 TraesCS4A01G395700 chr7B 649989407 649990206 799 False 1421.000000 1421 98.750000 1 798 1 chr7B.!!$F5 797
22 TraesCS4A01G395700 chr7B 529148415 529149265 850 False 1103.000000 1103 90.504000 4035 4863 1 chr7B.!!$F3 828
23 TraesCS4A01G395700 chr7B 597180452 597181120 668 False 784.000000 784 88.279000 4204 4857 1 chr7B.!!$F4 653
24 TraesCS4A01G395700 chr1B 266931682 266932644 962 True 1192.000000 1192 89.447000 3911 4855 1 chr1B.!!$R3 944
25 TraesCS4A01G395700 chr1B 344365850 344367033 1183 False 696.000000 1022 90.766500 3762 4821 2 chr1B.!!$F3 1059
26 TraesCS4A01G395700 chr4B 5485126 5486062 936 False 1112.000000 1112 88.345000 3921 4859 1 chr4B.!!$F1 938
27 TraesCS4A01G395700 chr4B 671059349 671060330 981 False 1103.000000 1103 87.700000 3908 4857 1 chr4B.!!$F2 949
28 TraesCS4A01G395700 chr4B 473859755 473860704 949 True 1000.000000 1000 86.122000 3911 4859 1 chr4B.!!$R3 948
29 TraesCS4A01G395700 chr4D 12300391 12301249 858 True 1005.000000 1005 88.324000 4025 4859 1 chr4D.!!$R2 834

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
927 943 0.180406 CCACAGGATAAACCCCTCCG 59.820 60.000 0.0 0.00 40.05 4.63 F
1729 1750 0.113190 TGAGCTGACTCCTGACTGGA 59.887 55.000 0.0 0.64 42.74 3.86 F
2355 2392 1.069358 CGAATCCCTCTAACCTCAGCC 59.931 57.143 0.0 0.00 0.00 4.85 F
2370 2408 1.136305 TCAGCCGTTCGATTTAGGAGG 59.864 52.381 0.0 0.00 0.00 4.30 F
2397 2438 1.604185 GCTAGGATTGCTCTAGGTGCG 60.604 57.143 0.0 0.00 35.85 5.34 F
4656 4913 0.324275 GGGAGAGCAGTGGAGAGAGT 60.324 60.000 0.0 0.00 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1906 0.036765 TCGGAACCACACCATACTGC 60.037 55.000 0.00 0.0 0.00 4.40 R
3695 3747 1.139654 TGCTGACATGCTCCTCCATAC 59.860 52.381 0.00 0.0 0.00 2.39 R
4086 4303 1.095807 GGTTCCTTGACGCCTATGCC 61.096 60.000 0.00 0.0 0.00 4.40 R
4656 4913 1.390383 CCATCTGCCGCTCTCTCTCA 61.390 60.000 0.00 0.0 0.00 3.27 R
4790 5068 4.752142 GCTTTTTAGCGCGCGCCA 62.752 61.111 46.98 35.8 43.17 5.69 R
6064 6373 0.040603 GAAGCTTGCTATCCATGCGC 60.041 55.000 2.10 0.0 46.14 6.09 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
812 820 8.718734 GTTCTTCTAGTATTGTTAGGGTTTGTG 58.281 37.037 0.00 0.00 0.00 3.33
839 847 2.592308 GGTCCACCTCTCCATGGC 59.408 66.667 6.96 0.00 35.81 4.40
840 848 2.592308 GTCCACCTCTCCATGGCC 59.408 66.667 6.96 0.00 35.81 5.36
841 849 2.692368 TCCACCTCTCCATGGCCC 60.692 66.667 6.96 0.00 35.81 5.80
842 850 3.813724 CCACCTCTCCATGGCCCC 61.814 72.222 6.96 0.00 0.00 5.80
843 851 3.016971 CACCTCTCCATGGCCCCA 61.017 66.667 6.96 0.00 0.00 4.96
844 852 2.204291 ACCTCTCCATGGCCCCAA 60.204 61.111 6.96 0.00 0.00 4.12
845 853 2.311854 ACCTCTCCATGGCCCCAAG 61.312 63.158 6.96 0.00 0.00 3.61
846 854 2.123982 CTCTCCATGGCCCCAAGC 60.124 66.667 6.96 0.00 42.60 4.01
927 943 0.180406 CCACAGGATAAACCCCTCCG 59.820 60.000 0.00 0.00 40.05 4.63
1239 1259 3.155167 GAGAGGGATCCGCCGGTT 61.155 66.667 1.63 0.00 37.63 4.44
1242 1262 4.798682 AGGGATCCGCCGGTTCCT 62.799 66.667 27.53 18.04 40.44 3.36
1245 1265 4.547367 GATCCGCCGGTTCCTGGG 62.547 72.222 1.63 0.00 0.00 4.45
1393 1413 1.020861 TATGCTGCCGTGCTCTGTTG 61.021 55.000 0.00 0.00 0.00 3.33
1398 1418 0.814457 TGCCGTGCTCTGTTGTTTTT 59.186 45.000 0.00 0.00 0.00 1.94
1403 1423 3.497118 CGTGCTCTGTTGTTTTTGTTCA 58.503 40.909 0.00 0.00 0.00 3.18
1406 1426 5.636837 GTGCTCTGTTGTTTTTGTTCAGTA 58.363 37.500 0.00 0.00 0.00 2.74
1420 1440 5.703978 TGTTCAGTATTGATGGGTGTTTG 57.296 39.130 0.00 0.00 32.27 2.93
1534 1554 1.086634 GGACTCGCAAGCAGGTGATC 61.087 60.000 0.00 0.00 37.18 2.92
1535 1555 0.390340 GACTCGCAAGCAGGTGATCA 60.390 55.000 0.00 0.00 37.18 2.92
1645 1665 5.874093 AGAGAAAGGTGTTGAGATTCACAT 58.126 37.500 0.00 0.00 36.43 3.21
1690 1711 0.961019 GTTGGCATGTTGGAAGCTGA 59.039 50.000 0.00 0.00 0.00 4.26
1693 1714 3.084536 TGGCATGTTGGAAGCTGATAA 57.915 42.857 0.00 0.00 0.00 1.75
1697 1718 4.199310 GCATGTTGGAAGCTGATAACCTA 58.801 43.478 0.00 0.00 0.00 3.08
1699 1720 5.049129 GCATGTTGGAAGCTGATAACCTATC 60.049 44.000 0.00 0.00 35.74 2.08
1729 1750 0.113190 TGAGCTGACTCCTGACTGGA 59.887 55.000 0.00 0.64 42.74 3.86
1751 1772 9.280174 CTGGATAGTTTCTTGGTTTGTAAGTTA 57.720 33.333 0.00 0.00 0.00 2.24
1823 1851 6.647895 TGGTTTCTTTGTAAGATCTTCCGTAC 59.352 38.462 12.24 5.16 37.38 3.67
1841 1869 3.180584 CGTACGCTCAGATGCTTTATGTC 59.819 47.826 0.52 0.00 0.00 3.06
1865 1893 5.186942 TGCAGTTACCAAAAACTAGTGTGA 58.813 37.500 0.00 0.00 37.61 3.58
1946 1975 6.421801 AGTTTGAAAAATGAATTCCGAGCAAG 59.578 34.615 2.27 0.00 0.00 4.01
1987 2016 8.868744 TGTACGCGAAATAAAGTTTAGAAATG 57.131 30.769 15.93 0.00 0.00 2.32
2178 2214 3.644738 ACAACTTTAGTTTCTCCTCCCGA 59.355 43.478 0.00 0.00 35.83 5.14
2240 2276 7.523293 TTATTCATCACAACCTGACAATTGT 57.477 32.000 11.78 11.78 39.63 2.71
2242 2278 6.558771 TTCATCACAACCTGACAATTGTAG 57.441 37.500 11.95 9.22 36.92 2.74
2254 2290 2.025981 ACAATTGTAGCATGGCAGAGGA 60.026 45.455 9.97 0.00 0.00 3.71
2262 2298 4.756804 TGGCAGAGGAGGGCATAT 57.243 55.556 0.00 0.00 35.74 1.78
2263 2299 2.148611 TGGCAGAGGAGGGCATATG 58.851 57.895 0.00 0.00 35.74 1.78
2276 2312 5.431765 GAGGGCATATGTCTTCTTTTCTGA 58.568 41.667 11.89 0.00 0.00 3.27
2286 2323 8.830915 ATGTCTTCTTTTCTGAGAGGTAGATA 57.169 34.615 0.00 0.00 0.00 1.98
2348 2385 4.945246 TGTTCATAGCGAATCCCTCTAAC 58.055 43.478 0.00 0.00 35.63 2.34
2354 2391 1.539280 GCGAATCCCTCTAACCTCAGC 60.539 57.143 0.00 0.00 0.00 4.26
2355 2392 1.069358 CGAATCCCTCTAACCTCAGCC 59.931 57.143 0.00 0.00 0.00 4.85
2370 2408 1.136305 TCAGCCGTTCGATTTAGGAGG 59.864 52.381 0.00 0.00 0.00 4.30
2376 2414 2.280628 GTTCGATTTAGGAGGGCAGTG 58.719 52.381 0.00 0.00 0.00 3.66
2397 2438 1.604185 GCTAGGATTGCTCTAGGTGCG 60.604 57.143 0.00 0.00 35.85 5.34
2426 2467 8.630917 CCAACACTGCTACACTATATAGTACTT 58.369 37.037 15.03 5.71 34.13 2.24
2821 2862 7.781056 TGCCAATCCAATTATTTAGAAAGACC 58.219 34.615 0.00 0.00 0.00 3.85
3006 3049 9.820725 TGATCAAGATTATTAATTGCCAAAAGG 57.179 29.630 0.00 0.00 0.00 3.11
3088 3131 9.922305 GCTAGTTAATACAATGCTCTTTTACTG 57.078 33.333 0.00 0.00 0.00 2.74
3151 3194 2.945668 GCATAACTTACCAGGGCTTCAG 59.054 50.000 0.00 0.00 0.00 3.02
3231 3274 8.492748 TGTGTATTTTACTTCTCGAATTGTGAC 58.507 33.333 0.00 0.00 0.00 3.67
3293 3336 2.095969 CGATGAAGGTAAAGTGCGCAAA 60.096 45.455 14.00 0.00 0.00 3.68
3367 3418 3.889538 AGTATGTAGTCGCCATTGCTCTA 59.110 43.478 0.00 0.00 34.43 2.43
3376 3427 3.871006 TCGCCATTGCTCTACTACAAATG 59.129 43.478 0.00 0.00 34.43 2.32
3420 3471 5.297527 TGTTCCCAAATTGATCTGATCATCG 59.702 40.000 20.16 9.44 39.39 3.84
3546 3598 5.207110 ACGCATCATTATTCTGCTAGAGT 57.793 39.130 0.00 0.00 33.75 3.24
3547 3599 5.226396 ACGCATCATTATTCTGCTAGAGTC 58.774 41.667 0.00 0.00 33.75 3.36
3674 3726 5.034852 TGTGTCCTAACATATGACATGGG 57.965 43.478 10.38 6.83 40.75 4.00
3695 3747 2.791158 GCTATTTTCCGCCACGATTGTG 60.791 50.000 6.06 6.06 46.00 3.33
3743 3795 4.644685 ACAAACTGGCAGTAGATGTGTTTT 59.355 37.500 22.37 5.02 31.58 2.43
3881 3935 3.666730 GTGCTAAAATGCAGCGCG 58.333 55.556 0.00 0.00 44.20 6.86
3882 3936 2.202466 TGCTAAAATGCAGCGCGC 60.202 55.556 26.66 26.66 42.13 6.86
3968 4022 2.287909 GCGTACATCTAGGCTTCTCCAG 60.288 54.545 0.00 0.00 37.29 3.86
4086 4303 3.604629 ATGTCCTCCGACGTCTGG 58.395 61.111 14.70 16.06 42.37 3.86
4656 4913 0.324275 GGGAGAGCAGTGGAGAGAGT 60.324 60.000 0.00 0.00 0.00 3.24
4836 5114 1.445582 CGAGGGCGCGTCTTTTAGT 60.446 57.895 11.94 0.00 0.00 2.24
4843 5121 1.420312 GCGTCTTTTAGTGCGCCTC 59.580 57.895 4.18 0.00 43.52 4.70
5211 5493 6.264518 GTGGTGTTCCTTCCAGAAAAGAAATA 59.735 38.462 0.00 0.00 34.16 1.40
5459 5746 4.669866 ATGGATCATGGATACCTGCATT 57.330 40.909 0.00 0.00 29.89 3.56
5591 5878 6.153340 AGTCACATATTCCCAACATTTCTTGG 59.847 38.462 0.00 0.00 40.57 3.61
5725 6034 8.333235 ACCAGTATTTGTAATCCAAGATGGTTA 58.667 33.333 0.00 0.00 39.03 2.85
5775 6084 9.573166 TCTATTTCAGAACAATCTCAAAGGAAA 57.427 29.630 0.00 0.00 28.65 3.13
5776 6085 9.617975 CTATTTCAGAACAATCTCAAAGGAAAC 57.382 33.333 0.00 0.00 28.65 2.78
5777 6086 7.645058 TTTCAGAACAATCTCAAAGGAAACT 57.355 32.000 0.00 0.00 36.26 2.66
5778 6087 7.645058 TTCAGAACAATCTCAAAGGAAACTT 57.355 32.000 0.00 0.00 43.66 2.66
5780 6089 8.746052 TCAGAACAATCTCAAAGGAAACTTTA 57.254 30.769 0.00 0.00 46.36 1.85
5781 6090 9.354673 TCAGAACAATCTCAAAGGAAACTTTAT 57.645 29.630 0.00 0.00 46.36 1.40
5782 6091 9.403110 CAGAACAATCTCAAAGGAAACTTTATG 57.597 33.333 0.00 0.00 46.36 1.90
5813 6122 9.007901 ACTTCTATTTCAGAACAATCTCAAAGG 57.992 33.333 0.00 0.00 38.39 3.11
5814 6123 9.224267 CTTCTATTTCAGAACAATCTCAAAGGA 57.776 33.333 0.00 0.00 38.39 3.36
5815 6124 9.573166 TTCTATTTCAGAACAATCTCAAAGGAA 57.427 29.630 0.00 0.00 38.39 3.36
5837 6146 7.794683 AGGAAACTTTATGATATACTCCCTCCA 59.205 37.037 0.00 0.00 37.44 3.86
5841 6150 8.294954 ACTTTATGATATACTCCCTCCATACG 57.705 38.462 0.00 0.00 0.00 3.06
5842 6151 7.342284 ACTTTATGATATACTCCCTCCATACGG 59.658 40.741 0.00 0.00 0.00 4.02
5848 6157 5.997384 ATACTCCCTCCATACGGAATTAC 57.003 43.478 0.00 0.00 42.21 1.89
5857 6166 5.984725 TCCATACGGAATTACTTGTCACAT 58.015 37.500 0.00 0.00 38.83 3.21
5858 6167 7.114866 TCCATACGGAATTACTTGTCACATA 57.885 36.000 0.00 0.00 38.83 2.29
5859 6168 7.557724 TCCATACGGAATTACTTGTCACATAA 58.442 34.615 0.00 0.00 38.83 1.90
5860 6169 8.041919 TCCATACGGAATTACTTGTCACATAAA 58.958 33.333 0.00 0.00 38.83 1.40
5861 6170 8.836413 CCATACGGAATTACTTGTCACATAAAT 58.164 33.333 0.00 0.00 0.00 1.40
5933 6242 6.509418 TCCATTGCTACAACAAGTTATTCC 57.491 37.500 0.00 0.00 31.96 3.01
5934 6243 5.123186 TCCATTGCTACAACAAGTTATTCCG 59.877 40.000 0.00 0.00 31.96 4.30
5970 6279 0.934496 TTTTTCACCTGCTGACGACG 59.066 50.000 0.00 0.00 0.00 5.12
5971 6280 0.103390 TTTTCACCTGCTGACGACGA 59.897 50.000 0.00 0.00 0.00 4.20
5972 6281 0.596600 TTTCACCTGCTGACGACGAC 60.597 55.000 0.00 0.00 0.00 4.34
5973 6282 1.730451 TTCACCTGCTGACGACGACA 61.730 55.000 0.00 0.00 0.00 4.35
5974 6283 1.299850 CACCTGCTGACGACGACAA 60.300 57.895 0.00 0.00 0.00 3.18
5975 6284 1.299926 ACCTGCTGACGACGACAAC 60.300 57.895 0.00 0.00 0.00 3.32
5976 6285 1.299850 CCTGCTGACGACGACAACA 60.300 57.895 0.00 2.08 0.00 3.33
5977 6286 0.874175 CCTGCTGACGACGACAACAA 60.874 55.000 0.00 0.00 0.00 2.83
5978 6287 0.229753 CTGCTGACGACGACAACAAC 59.770 55.000 0.00 0.00 0.00 3.32
5979 6288 0.458716 TGCTGACGACGACAACAACA 60.459 50.000 0.00 0.00 0.00 3.33
5980 6289 0.648441 GCTGACGACGACAACAACAA 59.352 50.000 0.00 0.00 0.00 2.83
5981 6290 1.591394 GCTGACGACGACAACAACAAC 60.591 52.381 0.00 0.00 0.00 3.32
5982 6291 1.656594 CTGACGACGACAACAACAACA 59.343 47.619 0.00 0.00 0.00 3.33
5983 6292 2.067013 TGACGACGACAACAACAACAA 58.933 42.857 0.00 0.00 0.00 2.83
5984 6293 2.159814 TGACGACGACAACAACAACAAC 60.160 45.455 0.00 0.00 0.00 3.32
5985 6294 1.799403 ACGACGACAACAACAACAACA 59.201 42.857 0.00 0.00 0.00 3.33
5986 6295 2.223611 ACGACGACAACAACAACAACAA 59.776 40.909 0.00 0.00 0.00 2.83
5987 6296 2.586378 CGACGACAACAACAACAACAAC 59.414 45.455 0.00 0.00 0.00 3.32
5988 6297 3.556513 GACGACAACAACAACAACAACA 58.443 40.909 0.00 0.00 0.00 3.33
5989 6298 3.966154 ACGACAACAACAACAACAACAA 58.034 36.364 0.00 0.00 0.00 2.83
5990 6299 4.360563 ACGACAACAACAACAACAACAAA 58.639 34.783 0.00 0.00 0.00 2.83
5991 6300 4.442733 ACGACAACAACAACAACAACAAAG 59.557 37.500 0.00 0.00 0.00 2.77
5992 6301 4.662891 CGACAACAACAACAACAACAAAGC 60.663 41.667 0.00 0.00 0.00 3.51
5993 6302 3.496507 ACAACAACAACAACAACAAAGCC 59.503 39.130 0.00 0.00 0.00 4.35
5994 6303 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
5995 6304 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
5996 6305 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
5997 6306 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
5998 6307 5.407084 ACAACAACAACAACAAAGCCTTTAC 59.593 36.000 0.00 0.00 0.00 2.01
5999 6308 4.500127 ACAACAACAACAAAGCCTTTACC 58.500 39.130 0.00 0.00 0.00 2.85
6000 6309 3.812156 ACAACAACAAAGCCTTTACCC 57.188 42.857 0.00 0.00 0.00 3.69
6001 6310 2.432874 ACAACAACAAAGCCTTTACCCC 59.567 45.455 0.00 0.00 0.00 4.95
6002 6311 2.432510 CAACAACAAAGCCTTTACCCCA 59.567 45.455 0.00 0.00 0.00 4.96
6003 6312 2.753247 ACAACAAAGCCTTTACCCCAA 58.247 42.857 0.00 0.00 0.00 4.12
6004 6313 3.108376 ACAACAAAGCCTTTACCCCAAA 58.892 40.909 0.00 0.00 0.00 3.28
6005 6314 3.118555 ACAACAAAGCCTTTACCCCAAAC 60.119 43.478 0.00 0.00 0.00 2.93
6006 6315 2.753247 ACAAAGCCTTTACCCCAAACA 58.247 42.857 0.00 0.00 0.00 2.83
6007 6316 3.108376 ACAAAGCCTTTACCCCAAACAA 58.892 40.909 0.00 0.00 0.00 2.83
6008 6317 3.133901 ACAAAGCCTTTACCCCAAACAAG 59.866 43.478 0.00 0.00 0.00 3.16
6009 6318 2.767644 AGCCTTTACCCCAAACAAGT 57.232 45.000 0.00 0.00 0.00 3.16
6010 6319 3.040655 AGCCTTTACCCCAAACAAGTT 57.959 42.857 0.00 0.00 0.00 2.66
6011 6320 2.698274 AGCCTTTACCCCAAACAAGTTG 59.302 45.455 0.00 0.00 36.94 3.16
6020 6329 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
6021 6330 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
6022 6331 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
6023 6332 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
6024 6333 2.188817 ACAAGTTGGGGTAGGCTAGAG 58.811 52.381 7.96 0.00 0.00 2.43
6025 6334 2.188817 CAAGTTGGGGTAGGCTAGAGT 58.811 52.381 0.00 0.00 0.00 3.24
6026 6335 2.572104 CAAGTTGGGGTAGGCTAGAGTT 59.428 50.000 0.00 0.00 0.00 3.01
6027 6336 2.188817 AGTTGGGGTAGGCTAGAGTTG 58.811 52.381 0.00 0.00 0.00 3.16
6028 6337 2.185387 GTTGGGGTAGGCTAGAGTTGA 58.815 52.381 0.00 0.00 0.00 3.18
6029 6338 2.570302 GTTGGGGTAGGCTAGAGTTGAA 59.430 50.000 0.00 0.00 0.00 2.69
6030 6339 2.910544 TGGGGTAGGCTAGAGTTGAAA 58.089 47.619 0.00 0.00 0.00 2.69
6031 6340 2.570302 TGGGGTAGGCTAGAGTTGAAAC 59.430 50.000 0.00 0.00 0.00 2.78
6032 6341 2.093075 GGGGTAGGCTAGAGTTGAAACC 60.093 54.545 0.00 0.00 0.00 3.27
6033 6342 2.093075 GGGTAGGCTAGAGTTGAAACCC 60.093 54.545 0.00 0.00 38.66 4.11
6034 6343 2.570302 GGTAGGCTAGAGTTGAAACCCA 59.430 50.000 0.00 0.00 0.00 4.51
6035 6344 3.200165 GGTAGGCTAGAGTTGAAACCCAT 59.800 47.826 0.00 0.00 0.00 4.00
6036 6345 4.407945 GGTAGGCTAGAGTTGAAACCCATA 59.592 45.833 0.00 0.00 0.00 2.74
6037 6346 5.104652 GGTAGGCTAGAGTTGAAACCCATAA 60.105 44.000 0.00 0.00 0.00 1.90
6038 6347 5.104259 AGGCTAGAGTTGAAACCCATAAG 57.896 43.478 0.00 0.00 0.00 1.73
6039 6348 4.783227 AGGCTAGAGTTGAAACCCATAAGA 59.217 41.667 0.00 0.00 0.00 2.10
6040 6349 5.430089 AGGCTAGAGTTGAAACCCATAAGAT 59.570 40.000 0.00 0.00 0.00 2.40
6041 6350 5.760743 GGCTAGAGTTGAAACCCATAAGATC 59.239 44.000 0.00 0.00 0.00 2.75
6042 6351 6.408662 GGCTAGAGTTGAAACCCATAAGATCT 60.409 42.308 0.00 0.00 0.00 2.75
6043 6352 6.704050 GCTAGAGTTGAAACCCATAAGATCTC 59.296 42.308 0.00 0.00 0.00 2.75
6044 6353 6.627087 AGAGTTGAAACCCATAAGATCTCA 57.373 37.500 0.00 0.00 0.00 3.27
6045 6354 6.410540 AGAGTTGAAACCCATAAGATCTCAC 58.589 40.000 0.00 0.00 0.00 3.51
6046 6355 5.178797 AGTTGAAACCCATAAGATCTCACG 58.821 41.667 0.00 0.00 0.00 4.35
6047 6356 5.046591 AGTTGAAACCCATAAGATCTCACGA 60.047 40.000 0.00 0.00 0.00 4.35
6048 6357 4.755411 TGAAACCCATAAGATCTCACGAC 58.245 43.478 0.00 0.00 0.00 4.34
6049 6358 3.821421 AACCCATAAGATCTCACGACC 57.179 47.619 0.00 0.00 0.00 4.79
6050 6359 2.747177 ACCCATAAGATCTCACGACCA 58.253 47.619 0.00 0.00 0.00 4.02
6051 6360 3.104512 ACCCATAAGATCTCACGACCAA 58.895 45.455 0.00 0.00 0.00 3.67
6052 6361 3.118738 ACCCATAAGATCTCACGACCAAC 60.119 47.826 0.00 0.00 0.00 3.77
6053 6362 3.133003 CCCATAAGATCTCACGACCAACT 59.867 47.826 0.00 0.00 0.00 3.16
6054 6363 4.363999 CCATAAGATCTCACGACCAACTC 58.636 47.826 0.00 0.00 0.00 3.01
6055 6364 4.142160 CCATAAGATCTCACGACCAACTCA 60.142 45.833 0.00 0.00 0.00 3.41
6056 6365 5.452496 CCATAAGATCTCACGACCAACTCAT 60.452 44.000 0.00 0.00 0.00 2.90
6057 6366 3.516981 AGATCTCACGACCAACTCATG 57.483 47.619 0.00 0.00 0.00 3.07
6065 6374 3.915575 CCAACTCATGGCTCTGGC 58.084 61.111 0.00 0.00 43.80 4.85
6066 6375 2.110967 CCAACTCATGGCTCTGGCG 61.111 63.158 0.00 0.00 43.80 5.69
6067 6376 2.437359 AACTCATGGCTCTGGCGC 60.437 61.111 0.00 0.00 39.81 6.53
6068 6377 3.258228 AACTCATGGCTCTGGCGCA 62.258 57.895 10.83 0.00 39.81 6.09
6069 6378 2.203167 CTCATGGCTCTGGCGCAT 60.203 61.111 10.83 0.00 39.81 4.73
6070 6379 2.515290 TCATGGCTCTGGCGCATG 60.515 61.111 10.83 1.97 42.70 4.06
6071 6380 3.592814 CATGGCTCTGGCGCATGG 61.593 66.667 10.83 0.00 40.29 3.66
6072 6381 3.800833 ATGGCTCTGGCGCATGGA 61.801 61.111 10.83 2.59 39.81 3.41
6073 6382 3.129362 ATGGCTCTGGCGCATGGAT 62.129 57.895 10.83 0.00 39.81 3.41
6074 6383 1.771783 ATGGCTCTGGCGCATGGATA 61.772 55.000 10.83 0.00 39.81 2.59
6075 6384 1.670406 GGCTCTGGCGCATGGATAG 60.670 63.158 10.83 0.00 39.81 2.08
6076 6385 2.323580 GCTCTGGCGCATGGATAGC 61.324 63.158 10.83 5.15 0.00 2.97
6077 6386 1.070275 CTCTGGCGCATGGATAGCA 59.930 57.895 10.83 0.00 0.00 3.49
6078 6387 0.533531 CTCTGGCGCATGGATAGCAA 60.534 55.000 10.83 0.00 0.00 3.91
6079 6388 0.533531 TCTGGCGCATGGATAGCAAG 60.534 55.000 10.83 0.00 33.40 4.01
6080 6389 2.126417 CTGGCGCATGGATAGCAAGC 62.126 60.000 10.83 0.00 0.00 4.01
6081 6390 1.895707 GGCGCATGGATAGCAAGCT 60.896 57.895 10.83 0.00 0.00 3.74
6082 6391 1.450531 GGCGCATGGATAGCAAGCTT 61.451 55.000 10.83 0.00 0.00 3.74
6083 6392 0.040603 GCGCATGGATAGCAAGCTTC 60.041 55.000 0.30 0.00 0.00 3.86
6084 6393 0.590195 CGCATGGATAGCAAGCTTCC 59.410 55.000 0.00 7.95 0.00 3.46
6085 6394 1.683943 GCATGGATAGCAAGCTTCCA 58.316 50.000 20.33 20.33 43.37 3.53
6086 6395 1.336125 GCATGGATAGCAAGCTTCCAC 59.664 52.381 20.41 10.72 42.09 4.02
6087 6396 1.600957 CATGGATAGCAAGCTTCCACG 59.399 52.381 20.41 13.24 42.09 4.94
6088 6397 0.744414 TGGATAGCAAGCTTCCACGC 60.744 55.000 16.61 0.00 34.65 5.34
6089 6398 0.744414 GGATAGCAAGCTTCCACGCA 60.744 55.000 8.96 0.00 0.00 5.24
6090 6399 1.303309 GATAGCAAGCTTCCACGCAT 58.697 50.000 8.96 1.45 0.00 4.73
6091 6400 1.672881 GATAGCAAGCTTCCACGCATT 59.327 47.619 8.96 0.00 0.00 3.56
6092 6401 1.086696 TAGCAAGCTTCCACGCATTC 58.913 50.000 8.96 0.00 0.00 2.67
6093 6402 1.153958 GCAAGCTTCCACGCATTCC 60.154 57.895 0.00 0.00 0.00 3.01
6094 6403 1.589716 GCAAGCTTCCACGCATTCCT 61.590 55.000 0.00 0.00 0.00 3.36
6095 6404 1.737838 CAAGCTTCCACGCATTCCTA 58.262 50.000 0.00 0.00 0.00 2.94
6096 6405 2.292267 CAAGCTTCCACGCATTCCTAT 58.708 47.619 0.00 0.00 0.00 2.57
6097 6406 2.246719 AGCTTCCACGCATTCCTATC 57.753 50.000 0.00 0.00 0.00 2.08
6098 6407 1.202698 AGCTTCCACGCATTCCTATCC 60.203 52.381 0.00 0.00 0.00 2.59
6099 6408 1.475034 GCTTCCACGCATTCCTATCCA 60.475 52.381 0.00 0.00 0.00 3.41
6100 6409 2.811873 GCTTCCACGCATTCCTATCCAT 60.812 50.000 0.00 0.00 0.00 3.41
6101 6410 3.557054 GCTTCCACGCATTCCTATCCATA 60.557 47.826 0.00 0.00 0.00 2.74
6102 6411 4.641396 CTTCCACGCATTCCTATCCATAA 58.359 43.478 0.00 0.00 0.00 1.90
6103 6412 4.002906 TCCACGCATTCCTATCCATAAC 57.997 45.455 0.00 0.00 0.00 1.89
6104 6413 3.646162 TCCACGCATTCCTATCCATAACT 59.354 43.478 0.00 0.00 0.00 2.24
6105 6414 4.836175 TCCACGCATTCCTATCCATAACTA 59.164 41.667 0.00 0.00 0.00 2.24
6106 6415 5.047306 TCCACGCATTCCTATCCATAACTAG 60.047 44.000 0.00 0.00 0.00 2.57
6107 6416 5.279506 CCACGCATTCCTATCCATAACTAGT 60.280 44.000 0.00 0.00 0.00 2.57
6108 6417 6.223852 CACGCATTCCTATCCATAACTAGTT 58.776 40.000 13.68 13.68 0.00 2.24
6109 6418 6.366332 CACGCATTCCTATCCATAACTAGTTC 59.634 42.308 12.39 0.00 0.00 3.01
6110 6419 6.267928 ACGCATTCCTATCCATAACTAGTTCT 59.732 38.462 12.39 0.00 0.00 3.01
6111 6420 7.155328 CGCATTCCTATCCATAACTAGTTCTT 58.845 38.462 12.39 0.00 0.00 2.52
6112 6421 7.657761 CGCATTCCTATCCATAACTAGTTCTTT 59.342 37.037 12.39 0.00 0.00 2.52
6113 6422 8.778358 GCATTCCTATCCATAACTAGTTCTTTG 58.222 37.037 12.39 8.57 0.00 2.77
6114 6423 9.277783 CATTCCTATCCATAACTAGTTCTTTGG 57.722 37.037 12.39 16.76 0.00 3.28
6115 6424 7.989947 TCCTATCCATAACTAGTTCTTTGGT 57.010 36.000 22.05 15.54 0.00 3.67
6116 6425 7.792032 TCCTATCCATAACTAGTTCTTTGGTG 58.208 38.462 22.05 16.06 0.00 4.17
6117 6426 7.622081 TCCTATCCATAACTAGTTCTTTGGTGA 59.378 37.037 22.05 15.24 0.00 4.02
6118 6427 8.432805 CCTATCCATAACTAGTTCTTTGGTGAT 58.567 37.037 22.05 15.54 0.00 3.06
6121 6430 8.375493 TCCATAACTAGTTCTTTGGTGATACT 57.625 34.615 22.05 0.00 0.00 2.12
6122 6431 8.475639 TCCATAACTAGTTCTTTGGTGATACTC 58.524 37.037 22.05 0.00 0.00 2.59
6123 6432 7.711339 CCATAACTAGTTCTTTGGTGATACTCC 59.289 40.741 12.39 0.00 0.00 3.85
6124 6433 6.681729 AACTAGTTCTTTGGTGATACTCCA 57.318 37.500 1.12 0.00 0.00 3.86
6125 6434 6.681729 ACTAGTTCTTTGGTGATACTCCAA 57.318 37.500 0.00 0.00 42.29 3.53
6126 6435 7.259088 ACTAGTTCTTTGGTGATACTCCAAT 57.741 36.000 6.20 0.00 43.25 3.16
6127 6436 7.331791 ACTAGTTCTTTGGTGATACTCCAATC 58.668 38.462 6.20 0.00 43.25 2.67
6128 6437 5.501156 AGTTCTTTGGTGATACTCCAATCC 58.499 41.667 6.20 0.00 43.25 3.01
6129 6438 5.251700 AGTTCTTTGGTGATACTCCAATCCT 59.748 40.000 6.20 0.00 43.25 3.24
6130 6439 5.779241 TCTTTGGTGATACTCCAATCCTT 57.221 39.130 6.20 0.00 43.25 3.36
6131 6440 5.745227 TCTTTGGTGATACTCCAATCCTTC 58.255 41.667 6.20 0.00 43.25 3.46
6132 6441 5.250543 TCTTTGGTGATACTCCAATCCTTCA 59.749 40.000 6.20 0.00 43.25 3.02
6133 6442 5.512942 TTGGTGATACTCCAATCCTTCAA 57.487 39.130 0.00 0.00 39.62 2.69
6134 6443 5.102953 TGGTGATACTCCAATCCTTCAAG 57.897 43.478 0.00 0.00 31.50 3.02
6135 6444 4.536090 TGGTGATACTCCAATCCTTCAAGT 59.464 41.667 0.00 0.00 31.50 3.16
6136 6445 5.119694 GGTGATACTCCAATCCTTCAAGTC 58.880 45.833 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
306 309 9.051679 TCCAAATACCATACTCAATTGAATACG 57.948 33.333 9.88 0.00 0.00 3.06
779 787 3.696051 ACAATACTAGAAGAACGCCCGTA 59.304 43.478 0.00 0.00 0.00 4.02
839 847 2.283894 GTCTTTGGGGGCTTGGGG 60.284 66.667 0.00 0.00 0.00 4.96
840 848 2.499303 ATCGTCTTTGGGGGCTTGGG 62.499 60.000 0.00 0.00 0.00 4.12
841 849 0.254747 TATCGTCTTTGGGGGCTTGG 59.745 55.000 0.00 0.00 0.00 3.61
842 850 1.743394 GTTATCGTCTTTGGGGGCTTG 59.257 52.381 0.00 0.00 0.00 4.01
843 851 1.677820 CGTTATCGTCTTTGGGGGCTT 60.678 52.381 0.00 0.00 0.00 4.35
844 852 0.107848 CGTTATCGTCTTTGGGGGCT 60.108 55.000 0.00 0.00 0.00 5.19
845 853 2.390427 CGTTATCGTCTTTGGGGGC 58.610 57.895 0.00 0.00 0.00 5.80
927 943 4.324991 ACGGGGCTGTTTCGTCCC 62.325 66.667 0.00 0.00 45.64 4.46
975 995 4.321515 AACGGGTAGGGGACGGGT 62.322 66.667 0.00 0.00 0.00 5.28
985 1005 2.101835 GCATTTCGCCGAACGGGTA 61.102 57.895 15.01 0.00 43.89 3.69
1072 1092 3.420482 GATGGAGTGGGGGTGGGG 61.420 72.222 0.00 0.00 0.00 4.96
1078 1098 4.181010 CAGGGCGATGGAGTGGGG 62.181 72.222 0.00 0.00 0.00 4.96
1393 1413 6.512297 ACACCCATCAATACTGAACAAAAAC 58.488 36.000 0.00 0.00 34.49 2.43
1398 1418 4.522405 CCAAACACCCATCAATACTGAACA 59.478 41.667 0.00 0.00 34.49 3.18
1403 1423 3.756434 CGAACCAAACACCCATCAATACT 59.244 43.478 0.00 0.00 0.00 2.12
1406 1426 2.870175 TCGAACCAAACACCCATCAAT 58.130 42.857 0.00 0.00 0.00 2.57
1420 1440 1.128692 CCAGACTGCGAATTTCGAACC 59.871 52.381 22.25 5.55 43.74 3.62
1501 1521 1.067060 CGAGTCCAATCATACTGCCGA 59.933 52.381 0.00 0.00 0.00 5.54
1534 1554 3.094572 ACAAGGCAGAGGAAAATCCATG 58.905 45.455 0.00 0.00 39.61 3.66
1535 1555 3.359950 GACAAGGCAGAGGAAAATCCAT 58.640 45.455 0.00 0.00 39.61 3.41
1690 1711 5.244626 GCTCAAAATGGCATGGATAGGTTAT 59.755 40.000 0.00 0.00 0.00 1.89
1693 1714 2.961062 GCTCAAAATGGCATGGATAGGT 59.039 45.455 0.00 0.00 0.00 3.08
1697 1718 2.429610 GTCAGCTCAAAATGGCATGGAT 59.570 45.455 0.00 0.00 0.00 3.41
1699 1720 1.822990 AGTCAGCTCAAAATGGCATGG 59.177 47.619 0.00 0.00 0.00 3.66
1823 1851 2.033065 GCAGACATAAAGCATCTGAGCG 60.033 50.000 4.70 0.00 42.07 5.03
1841 1869 5.295787 TCACACTAGTTTTTGGTAACTGCAG 59.704 40.000 13.48 13.48 38.72 4.41
1865 1893 3.198068 CCATACTGCTAAGACGTGCATT 58.802 45.455 0.00 0.00 38.59 3.56
1878 1906 0.036765 TCGGAACCACACCATACTGC 60.037 55.000 0.00 0.00 0.00 4.40
1922 1951 6.420604 TCTTGCTCGGAATTCATTTTTCAAAC 59.579 34.615 7.93 0.00 0.00 2.93
1946 1975 8.981370 TTCGCGTACATCAACAATATAAATTC 57.019 30.769 5.77 0.00 0.00 2.17
1974 2003 9.908152 GTGCCAATTAGTACATTTCTAAACTTT 57.092 29.630 0.00 0.00 32.32 2.66
1987 2016 6.150474 AGTGGTTGTATTGTGCCAATTAGTAC 59.850 38.462 5.85 0.00 32.26 2.73
2044 2073 2.234414 GGGTTCCACCACGTACATCTTA 59.766 50.000 0.00 0.00 41.02 2.10
2178 2214 1.153086 GCCGATGCCAGAGATGGTT 60.153 57.895 0.00 0.00 0.00 3.67
2240 2276 2.446848 GCCCTCCTCTGCCATGCTA 61.447 63.158 0.00 0.00 0.00 3.49
2242 2278 2.060567 TATGCCCTCCTCTGCCATGC 62.061 60.000 0.00 0.00 0.00 4.06
2254 2290 5.190528 TCTCAGAAAAGAAGACATATGCCCT 59.809 40.000 1.58 0.00 0.00 5.19
2262 2298 7.148222 CGTATCTACCTCTCAGAAAAGAAGACA 60.148 40.741 0.00 0.00 0.00 3.41
2263 2299 7.066043 TCGTATCTACCTCTCAGAAAAGAAGAC 59.934 40.741 0.00 0.00 0.00 3.01
2276 2312 4.141228 TCTGGAACCATCGTATCTACCTCT 60.141 45.833 0.00 0.00 0.00 3.69
2348 2385 1.136305 TCCTAAATCGAACGGCTGAGG 59.864 52.381 0.00 0.00 0.00 3.86
2354 2391 0.177141 TGCCCTCCTAAATCGAACGG 59.823 55.000 0.00 0.00 0.00 4.44
2355 2392 1.134788 ACTGCCCTCCTAAATCGAACG 60.135 52.381 0.00 0.00 0.00 3.95
2370 2408 0.817229 GAGCAATCCTAGCCACTGCC 60.817 60.000 0.00 0.00 38.69 4.85
2376 2414 1.270571 GCACCTAGAGCAATCCTAGCC 60.271 57.143 0.00 0.00 33.91 3.93
2397 2438 7.887381 ACTATATAGTGTAGCAGTGTTGGATC 58.113 38.462 14.71 0.00 34.72 3.36
3006 3049 4.553330 TGGTATCCTGAACAAAGTCTCC 57.447 45.455 0.00 0.00 0.00 3.71
3020 3063 6.374333 ACAGACATGTTAACACAATGGTATCC 59.626 38.462 11.22 0.00 35.63 2.59
3105 3148 9.822185 GCTACAGATAATGAATTTTGGGAAAAT 57.178 29.630 0.00 0.00 42.62 1.82
3293 3336 3.883489 GTGTTGGCTCAACCTTTAGAACT 59.117 43.478 13.35 0.00 42.96 3.01
3376 3427 6.018343 GGAACATAGATTCAGAAGCAAGTAGC 60.018 42.308 0.31 0.00 46.19 3.58
3420 3471 5.808540 GGTTTTGAACACCTACAAGGAAAAC 59.191 40.000 0.00 5.83 37.67 2.43
3455 3507 6.484288 AGGGATGTAAATGTTCTCATCAACA 58.516 36.000 0.00 0.00 40.54 3.33
3674 3726 1.400494 ACAATCGTGGCGGAAAATAGC 59.600 47.619 0.00 0.00 0.00 2.97
3695 3747 1.139654 TGCTGACATGCTCCTCCATAC 59.860 52.381 0.00 0.00 0.00 2.39
3743 3795 7.561722 AGATGCTCTTAGATCTAGTTGTTACCA 59.438 37.037 2.02 0.00 0.00 3.25
3865 3917 2.202466 GCGCGCTGCATTTTAGCA 60.202 55.556 26.67 0.00 45.45 3.49
4086 4303 1.095807 GGTTCCTTGACGCCTATGCC 61.096 60.000 0.00 0.00 0.00 4.40
4656 4913 1.390383 CCATCTGCCGCTCTCTCTCA 61.390 60.000 0.00 0.00 0.00 3.27
4790 5068 4.752142 GCTTTTTAGCGCGCGCCA 62.752 61.111 46.98 35.80 43.17 5.69
4836 5114 2.124983 GCATCTCCAAGAGGCGCA 60.125 61.111 10.83 0.00 42.34 6.09
4976 5258 6.207417 CAGACATTATGAAGGAACAGGTTTGT 59.793 38.462 0.00 0.00 39.87 2.83
5010 5292 7.974675 GCGGTATGATGTACTGCAAATATAAT 58.025 34.615 12.72 0.00 46.18 1.28
5211 5493 0.333312 TCCAAACACCACCACCAAGT 59.667 50.000 0.00 0.00 0.00 3.16
5459 5746 3.893813 GGGTTTAGAGCTTCGGGTATCTA 59.106 47.826 0.00 0.00 0.00 1.98
5547 5834 5.972382 GTGACTCGAGTTTCAGTATATGACC 59.028 44.000 21.08 1.74 37.77 4.02
5591 5878 5.112686 CACAGAGCTTACTCAATAAGGACC 58.887 45.833 0.00 0.00 46.09 4.46
5666 5973 6.079763 CGAGGATCACAAACAAACAATGTAG 58.920 40.000 0.00 0.00 36.59 2.74
5671 5978 3.942115 TCACGAGGATCACAAACAAACAA 59.058 39.130 0.00 0.00 33.17 2.83
5673 5980 4.279659 GTTCACGAGGATCACAAACAAAC 58.720 43.478 0.00 0.00 33.17 2.93
5787 6096 9.007901 CCTTTGAGATTGTTCTGAAATAGAAGT 57.992 33.333 0.00 0.00 45.71 3.01
5788 6097 9.224267 TCCTTTGAGATTGTTCTGAAATAGAAG 57.776 33.333 0.00 0.00 45.71 2.85
5789 6098 9.573166 TTCCTTTGAGATTGTTCTGAAATAGAA 57.427 29.630 0.00 0.00 43.01 2.10
5790 6099 9.573166 TTTCCTTTGAGATTGTTCTGAAATAGA 57.427 29.630 0.00 0.00 35.05 1.98
5791 6100 9.617975 GTTTCCTTTGAGATTGTTCTGAAATAG 57.382 33.333 0.00 0.00 35.05 1.73
5792 6101 9.354673 AGTTTCCTTTGAGATTGTTCTGAAATA 57.645 29.630 0.00 0.00 35.05 1.40
5793 6102 8.242729 AGTTTCCTTTGAGATTGTTCTGAAAT 57.757 30.769 0.00 0.00 35.05 2.17
5812 6121 7.974504 TGGAGGGAGTATATCATAAAGTTTCC 58.025 38.462 0.00 0.00 0.00 3.13
5815 6124 8.750298 CGTATGGAGGGAGTATATCATAAAGTT 58.250 37.037 0.00 0.00 0.00 2.66
5835 6144 7.780008 TTATGTGACAAGTAATTCCGTATGG 57.220 36.000 0.00 0.00 0.00 2.74
5920 6229 2.671396 CTCCGTCCGGAATAACTTGTTG 59.329 50.000 5.23 0.00 44.66 3.33
5921 6230 2.354403 CCTCCGTCCGGAATAACTTGTT 60.354 50.000 5.23 0.00 44.66 2.83
5933 6242 1.400737 AAATCTACTCCCTCCGTCCG 58.599 55.000 0.00 0.00 0.00 4.79
5934 6243 3.908643 AAAAATCTACTCCCTCCGTCC 57.091 47.619 0.00 0.00 0.00 4.79
5966 6275 2.512289 TGTTGTTGTTGTTGTCGTCG 57.488 45.000 0.00 0.00 0.00 5.12
5967 6276 3.556513 TGTTGTTGTTGTTGTTGTCGTC 58.443 40.909 0.00 0.00 0.00 4.20
5968 6277 3.627732 TGTTGTTGTTGTTGTTGTCGT 57.372 38.095 0.00 0.00 0.00 4.34
5969 6278 4.662891 GCTTTGTTGTTGTTGTTGTTGTCG 60.663 41.667 0.00 0.00 0.00 4.35
5970 6279 4.376920 GGCTTTGTTGTTGTTGTTGTTGTC 60.377 41.667 0.00 0.00 0.00 3.18
5971 6280 3.496507 GGCTTTGTTGTTGTTGTTGTTGT 59.503 39.130 0.00 0.00 0.00 3.32
5972 6281 3.745458 AGGCTTTGTTGTTGTTGTTGTTG 59.255 39.130 0.00 0.00 0.00 3.33
5973 6282 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
5974 6283 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
5975 6284 5.163903 GGTAAAGGCTTTGTTGTTGTTGTTG 60.164 40.000 22.32 0.00 0.00 3.33
5976 6285 4.932799 GGTAAAGGCTTTGTTGTTGTTGTT 59.067 37.500 22.32 0.00 0.00 2.83
5977 6286 4.500127 GGTAAAGGCTTTGTTGTTGTTGT 58.500 39.130 22.32 0.00 0.00 3.32
5978 6287 3.868661 GGGTAAAGGCTTTGTTGTTGTTG 59.131 43.478 22.32 0.00 0.00 3.33
5979 6288 3.118555 GGGGTAAAGGCTTTGTTGTTGTT 60.119 43.478 22.32 0.00 0.00 2.83
5980 6289 2.432874 GGGGTAAAGGCTTTGTTGTTGT 59.567 45.455 22.32 0.00 0.00 3.32
5981 6290 2.432510 TGGGGTAAAGGCTTTGTTGTTG 59.567 45.455 22.32 0.00 0.00 3.33
5982 6291 2.753247 TGGGGTAAAGGCTTTGTTGTT 58.247 42.857 22.32 0.00 0.00 2.83
5983 6292 2.463047 TGGGGTAAAGGCTTTGTTGT 57.537 45.000 22.32 0.00 0.00 3.32
5984 6293 3.118592 TGTTTGGGGTAAAGGCTTTGTTG 60.119 43.478 22.32 0.00 0.00 3.33
5985 6294 3.108376 TGTTTGGGGTAAAGGCTTTGTT 58.892 40.909 22.32 0.00 0.00 2.83
5986 6295 2.753247 TGTTTGGGGTAAAGGCTTTGT 58.247 42.857 22.32 0.00 0.00 2.83
5987 6296 3.133901 ACTTGTTTGGGGTAAAGGCTTTG 59.866 43.478 22.32 3.56 0.00 2.77
5988 6297 3.380393 ACTTGTTTGGGGTAAAGGCTTT 58.620 40.909 17.76 17.76 0.00 3.51
5989 6298 3.040655 ACTTGTTTGGGGTAAAGGCTT 57.959 42.857 0.00 0.00 0.00 4.35
5990 6299 2.698274 CAACTTGTTTGGGGTAAAGGCT 59.302 45.455 0.00 0.00 0.00 4.58
5991 6300 3.106242 CAACTTGTTTGGGGTAAAGGC 57.894 47.619 0.00 0.00 0.00 4.35
6001 6310 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
6002 6311 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
6003 6312 2.572104 CTCTAGCCTACCCCAACTTGTT 59.428 50.000 0.00 0.00 0.00 2.83
6004 6313 2.188817 CTCTAGCCTACCCCAACTTGT 58.811 52.381 0.00 0.00 0.00 3.16
6005 6314 2.188817 ACTCTAGCCTACCCCAACTTG 58.811 52.381 0.00 0.00 0.00 3.16
6006 6315 2.572104 CAACTCTAGCCTACCCCAACTT 59.428 50.000 0.00 0.00 0.00 2.66
6007 6316 2.188817 CAACTCTAGCCTACCCCAACT 58.811 52.381 0.00 0.00 0.00 3.16
6008 6317 2.185387 TCAACTCTAGCCTACCCCAAC 58.815 52.381 0.00 0.00 0.00 3.77
6009 6318 2.634639 TCAACTCTAGCCTACCCCAA 57.365 50.000 0.00 0.00 0.00 4.12
6010 6319 2.570302 GTTTCAACTCTAGCCTACCCCA 59.430 50.000 0.00 0.00 0.00 4.96
6011 6320 2.093075 GGTTTCAACTCTAGCCTACCCC 60.093 54.545 0.00 0.00 0.00 4.95
6012 6321 2.093075 GGGTTTCAACTCTAGCCTACCC 60.093 54.545 0.00 0.00 37.41 3.69
6013 6322 2.570302 TGGGTTTCAACTCTAGCCTACC 59.430 50.000 0.00 0.00 0.00 3.18
6014 6323 3.975168 TGGGTTTCAACTCTAGCCTAC 57.025 47.619 0.00 0.00 0.00 3.18
6015 6324 5.962031 TCTTATGGGTTTCAACTCTAGCCTA 59.038 40.000 0.00 0.00 0.00 3.93
6016 6325 4.783227 TCTTATGGGTTTCAACTCTAGCCT 59.217 41.667 0.00 0.00 0.00 4.58
6017 6326 5.099042 TCTTATGGGTTTCAACTCTAGCC 57.901 43.478 0.00 0.00 0.00 3.93
6018 6327 6.587273 AGATCTTATGGGTTTCAACTCTAGC 58.413 40.000 0.00 0.00 0.00 3.42
6019 6328 7.708752 GTGAGATCTTATGGGTTTCAACTCTAG 59.291 40.741 0.00 0.00 0.00 2.43
6020 6329 7.556844 GTGAGATCTTATGGGTTTCAACTCTA 58.443 38.462 0.00 0.00 0.00 2.43
6021 6330 6.410540 GTGAGATCTTATGGGTTTCAACTCT 58.589 40.000 0.00 0.00 0.00 3.24
6022 6331 5.292101 CGTGAGATCTTATGGGTTTCAACTC 59.708 44.000 0.00 0.00 0.00 3.01
6023 6332 5.046591 TCGTGAGATCTTATGGGTTTCAACT 60.047 40.000 6.85 0.00 33.31 3.16
6024 6333 5.063564 GTCGTGAGATCTTATGGGTTTCAAC 59.936 44.000 6.85 0.00 45.19 3.18
6025 6334 5.175859 GTCGTGAGATCTTATGGGTTTCAA 58.824 41.667 6.85 0.00 45.19 2.69
6026 6335 4.382685 GGTCGTGAGATCTTATGGGTTTCA 60.383 45.833 6.85 0.00 45.19 2.69
6027 6336 4.120589 GGTCGTGAGATCTTATGGGTTTC 58.879 47.826 6.85 0.00 45.19 2.78
6028 6337 3.517901 TGGTCGTGAGATCTTATGGGTTT 59.482 43.478 6.85 0.00 43.23 3.27
6029 6338 3.104512 TGGTCGTGAGATCTTATGGGTT 58.895 45.455 6.85 0.00 43.23 4.11
6030 6339 2.747177 TGGTCGTGAGATCTTATGGGT 58.253 47.619 6.85 0.00 43.23 4.51
6031 6340 3.133003 AGTTGGTCGTGAGATCTTATGGG 59.867 47.826 6.85 0.00 43.23 4.00
6032 6341 4.142160 TGAGTTGGTCGTGAGATCTTATGG 60.142 45.833 6.85 0.00 43.23 2.74
6033 6342 4.998788 TGAGTTGGTCGTGAGATCTTATG 58.001 43.478 0.00 0.00 43.23 1.90
6034 6343 5.452496 CCATGAGTTGGTCGTGAGATCTTAT 60.452 44.000 0.00 0.00 44.07 1.73
6035 6344 4.142160 CCATGAGTTGGTCGTGAGATCTTA 60.142 45.833 0.00 0.00 44.07 2.10
6036 6345 3.368843 CCATGAGTTGGTCGTGAGATCTT 60.369 47.826 0.00 0.00 44.07 2.40
6037 6346 2.167281 CCATGAGTTGGTCGTGAGATCT 59.833 50.000 0.00 0.00 44.07 2.75
6038 6347 2.544685 CCATGAGTTGGTCGTGAGATC 58.455 52.381 0.00 0.00 44.07 2.75
6039 6348 2.680312 CCATGAGTTGGTCGTGAGAT 57.320 50.000 0.00 0.00 44.07 2.75
6049 6358 2.758089 GCGCCAGAGCCATGAGTTG 61.758 63.158 0.00 0.00 34.57 3.16
6050 6359 2.437359 GCGCCAGAGCCATGAGTT 60.437 61.111 0.00 0.00 34.57 3.01
6051 6360 3.040206 ATGCGCCAGAGCCATGAGT 62.040 57.895 4.18 0.00 36.02 3.41
6052 6361 2.203167 ATGCGCCAGAGCCATGAG 60.203 61.111 4.18 0.00 36.02 2.90
6053 6362 2.515290 CATGCGCCAGAGCCATGA 60.515 61.111 4.18 0.00 44.14 3.07
6054 6363 3.592814 CCATGCGCCAGAGCCATG 61.593 66.667 4.18 0.00 42.54 3.66
6055 6364 1.771783 TATCCATGCGCCAGAGCCAT 61.772 55.000 4.18 0.00 36.02 4.40
6056 6365 2.387476 CTATCCATGCGCCAGAGCCA 62.387 60.000 4.18 0.00 36.02 4.75
6057 6366 1.670406 CTATCCATGCGCCAGAGCC 60.670 63.158 4.18 0.00 36.02 4.70
6058 6367 2.323580 GCTATCCATGCGCCAGAGC 61.324 63.158 4.18 0.23 37.71 4.09
6059 6368 0.533531 TTGCTATCCATGCGCCAGAG 60.534 55.000 4.18 0.00 0.00 3.35
6060 6369 0.533531 CTTGCTATCCATGCGCCAGA 60.534 55.000 4.18 0.00 0.00 3.86
6061 6370 1.947013 CTTGCTATCCATGCGCCAG 59.053 57.895 4.18 0.00 0.00 4.85
6062 6371 2.188829 GCTTGCTATCCATGCGCCA 61.189 57.895 4.18 0.00 35.30 5.69
6063 6372 1.450531 AAGCTTGCTATCCATGCGCC 61.451 55.000 4.18 0.00 46.14 6.53
6064 6373 0.040603 GAAGCTTGCTATCCATGCGC 60.041 55.000 2.10 0.00 46.14 6.09
6065 6374 0.590195 GGAAGCTTGCTATCCATGCG 59.410 55.000 11.19 0.00 46.14 4.73
6066 6375 1.336125 GTGGAAGCTTGCTATCCATGC 59.664 52.381 19.34 11.21 44.55 4.06
6067 6376 1.600957 CGTGGAAGCTTGCTATCCATG 59.399 52.381 19.34 20.51 44.55 3.66
6068 6377 1.959042 CGTGGAAGCTTGCTATCCAT 58.041 50.000 19.34 0.00 44.55 3.41
6069 6378 0.744414 GCGTGGAAGCTTGCTATCCA 60.744 55.000 19.34 9.80 40.84 3.41
6070 6379 0.744414 TGCGTGGAAGCTTGCTATCC 60.744 55.000 19.34 6.99 38.13 2.59
6071 6380 1.303309 ATGCGTGGAAGCTTGCTATC 58.697 50.000 19.34 8.59 38.13 2.08
6072 6381 1.672881 GAATGCGTGGAAGCTTGCTAT 59.327 47.619 19.34 5.76 38.13 2.97
6073 6382 1.086696 GAATGCGTGGAAGCTTGCTA 58.913 50.000 19.34 2.82 38.13 3.49
6074 6383 1.589716 GGAATGCGTGGAAGCTTGCT 61.590 55.000 19.34 0.00 38.13 3.91
6075 6384 1.153958 GGAATGCGTGGAAGCTTGC 60.154 57.895 11.58 11.58 38.13 4.01
6076 6385 1.737838 TAGGAATGCGTGGAAGCTTG 58.262 50.000 2.10 0.00 38.13 4.01
6077 6386 2.565841 GATAGGAATGCGTGGAAGCTT 58.434 47.619 0.00 0.00 38.13 3.74
6078 6387 1.202698 GGATAGGAATGCGTGGAAGCT 60.203 52.381 0.00 0.00 38.13 3.74
6079 6388 1.230324 GGATAGGAATGCGTGGAAGC 58.770 55.000 0.00 0.00 37.71 3.86
6080 6389 2.620251 TGGATAGGAATGCGTGGAAG 57.380 50.000 0.00 0.00 0.00 3.46
6081 6390 4.102524 AGTTATGGATAGGAATGCGTGGAA 59.897 41.667 0.00 0.00 0.00 3.53
6082 6391 3.646162 AGTTATGGATAGGAATGCGTGGA 59.354 43.478 0.00 0.00 0.00 4.02
6083 6392 4.008074 AGTTATGGATAGGAATGCGTGG 57.992 45.455 0.00 0.00 0.00 4.94
6084 6393 5.784177 ACTAGTTATGGATAGGAATGCGTG 58.216 41.667 0.00 0.00 0.00 5.34
6085 6394 6.267928 AGAACTAGTTATGGATAGGAATGCGT 59.732 38.462 8.42 0.00 0.00 5.24
6086 6395 6.692486 AGAACTAGTTATGGATAGGAATGCG 58.308 40.000 8.42 0.00 0.00 4.73
6087 6396 8.778358 CAAAGAACTAGTTATGGATAGGAATGC 58.222 37.037 8.42 0.00 0.00 3.56
6088 6397 9.277783 CCAAAGAACTAGTTATGGATAGGAATG 57.722 37.037 21.61 3.77 0.00 2.67
6089 6398 9.004231 ACCAAAGAACTAGTTATGGATAGGAAT 57.996 33.333 28.20 11.24 0.00 3.01
6090 6399 8.265055 CACCAAAGAACTAGTTATGGATAGGAA 58.735 37.037 28.20 0.00 0.00 3.36
6091 6400 7.622081 TCACCAAAGAACTAGTTATGGATAGGA 59.378 37.037 28.20 19.71 0.00 2.94
6092 6401 7.792032 TCACCAAAGAACTAGTTATGGATAGG 58.208 38.462 28.20 17.43 0.00 2.57
6095 6404 8.993424 AGTATCACCAAAGAACTAGTTATGGAT 58.007 33.333 28.20 19.15 0.00 3.41
6096 6405 8.375493 AGTATCACCAAAGAACTAGTTATGGA 57.625 34.615 28.20 15.26 0.00 3.41
6097 6406 7.711339 GGAGTATCACCAAAGAACTAGTTATGG 59.289 40.741 23.26 23.26 36.25 2.74
6098 6407 8.258007 TGGAGTATCACCAAAGAACTAGTTATG 58.742 37.037 8.42 8.17 36.25 1.90
6099 6408 8.375493 TGGAGTATCACCAAAGAACTAGTTAT 57.625 34.615 8.42 1.58 36.25 1.89
6100 6409 7.786046 TGGAGTATCACCAAAGAACTAGTTA 57.214 36.000 8.42 0.00 36.25 2.24
6101 6410 6.681729 TGGAGTATCACCAAAGAACTAGTT 57.318 37.500 8.13 8.13 36.25 2.24
6102 6411 6.681729 TTGGAGTATCACCAAAGAACTAGT 57.318 37.500 0.00 0.00 43.22 2.57
6112 6421 4.536090 ACTTGAAGGATTGGAGTATCACCA 59.464 41.667 0.00 0.00 36.25 4.17
6113 6422 5.104259 ACTTGAAGGATTGGAGTATCACC 57.896 43.478 0.00 0.00 36.25 4.02


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

AutoCloner maintained by Alex Coulton.