Multiple sequence alignment - TraesCS5B01G041000

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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 TraesCS5B01G041000 chr5B 100.000 6481 0 0 1 6481 45361682 45355202 0.000000e+00 11969.0
1 TraesCS5B01G041000 chr5B 87.544 851 85 8 3147 3988 45386628 45385790 0.000000e+00 965.0
2 TraesCS5B01G041000 chr5B 88.179 736 71 8 655 1386 504523056 504523779 0.000000e+00 863.0
3 TraesCS5B01G041000 chr5B 91.762 437 36 0 3971 4407 45357565 45357129 5.560000e-170 608.0
4 TraesCS5B01G041000 chr5B 91.762 437 36 0 4118 4554 45357712 45357276 5.560000e-170 608.0
5 TraesCS5B01G041000 chr5B 91.034 290 26 0 3971 4260 45357418 45357129 6.090000e-105 392.0
6 TraesCS5B01G041000 chr5B 91.034 290 26 0 4265 4554 45357712 45357423 6.090000e-105 392.0
7 TraesCS5B01G041000 chr5B 87.580 314 36 2 2785 3098 45358742 45358432 1.720000e-95 361.0
8 TraesCS5B01G041000 chr5B 87.580 314 36 2 2941 3251 45358898 45358585 1.720000e-95 361.0
9 TraesCS5B01G041000 chr5B 90.253 277 24 3 2552 2826 45246457 45246182 6.180000e-95 359.0
10 TraesCS5B01G041000 chr5B 81.915 282 28 11 2507 2765 45386931 45386650 3.940000e-52 217.0
11 TraesCS5B01G041000 chr5B 83.817 241 17 7 1772 1990 45359654 45359414 6.580000e-50 209.0
12 TraesCS5B01G041000 chr5B 83.817 241 17 7 2029 2269 45359911 45359693 6.580000e-50 209.0
13 TraesCS5B01G041000 chr5B 90.196 153 11 3 2506 2654 45270824 45270672 5.130000e-46 196.0
14 TraesCS5B01G041000 chr5B 79.004 281 36 13 5633 5895 45384026 45383751 3.110000e-38 171.0
15 TraesCS5B01G041000 chr5B 100.000 28 0 0 1883 1910 247653873 247653846 1.200000e-02 52.8
16 TraesCS5B01G041000 chr5D 97.474 3523 67 7 2506 6014 45361108 45357594 0.000000e+00 5993.0
17 TraesCS5B01G041000 chr5D 88.484 851 77 8 3147 3988 45367189 45366351 0.000000e+00 1009.0
18 TraesCS5B01G041000 chr5D 92.945 652 44 2 3 653 66771603 66770953 0.000000e+00 948.0
19 TraesCS5B01G041000 chr5D 92.780 651 47 0 3 653 306787824 306788474 0.000000e+00 942.0
20 TraesCS5B01G041000 chr5D 85.290 707 82 13 2949 3650 45344820 45344131 0.000000e+00 710.0
21 TraesCS5B01G041000 chr5D 93.210 486 17 3 2029 2508 45361625 45361150 0.000000e+00 701.0
22 TraesCS5B01G041000 chr5D 81.853 788 105 22 3319 4090 45263099 45262334 4.270000e-176 628.0
23 TraesCS5B01G041000 chr5D 91.991 437 35 0 3971 4407 45359492 45359056 1.190000e-171 614.0
24 TraesCS5B01G041000 chr5D 91.762 437 36 0 4118 4554 45359639 45359203 5.560000e-170 608.0
25 TraesCS5B01G041000 chr5D 94.226 381 22 0 3412 3792 45373614 45373234 3.370000e-162 582.0
26 TraesCS5B01G041000 chr5D 90.237 379 25 2 1384 1759 45362047 45361678 9.770000e-133 484.0
27 TraesCS5B01G041000 chr5D 90.634 331 24 4 2506 2830 45263437 45263108 3.590000e-117 433.0
28 TraesCS5B01G041000 chr5D 91.034 290 26 0 3971 4260 45359345 45359056 6.090000e-105 392.0
29 TraesCS5B01G041000 chr5D 91.034 290 26 0 4265 4554 45359639 45359350 6.090000e-105 392.0
30 TraesCS5B01G041000 chr5D 88.854 314 32 2 2941 3251 45360825 45360512 3.670000e-102 383.0
31 TraesCS5B01G041000 chr5D 87.821 312 35 2 2787 3098 45360667 45360359 4.780000e-96 363.0
32 TraesCS5B01G041000 chr5D 87.987 308 31 4 3806 4113 45343735 45343434 6.180000e-95 359.0
33 TraesCS5B01G041000 chr5D 85.358 321 36 2 4445 4754 45343543 45343223 8.110000e-84 322.0
34 TraesCS5B01G041000 chr5D 89.015 264 22 1 6218 6481 45356466 45356210 2.920000e-83 320.0
35 TraesCS5B01G041000 chr5D 89.388 245 14 2 1758 1990 45361639 45361395 1.370000e-76 298.0
36 TraesCS5B01G041000 chr5D 82.333 300 41 4 3689 3988 45344131 45343844 3.880000e-62 250.0
37 TraesCS5B01G041000 chr5D 82.119 302 41 8 5303 5593 45365250 45364951 5.020000e-61 246.0
38 TraesCS5B01G041000 chr5D 89.205 176 14 4 2324 2498 45263665 45263494 1.420000e-51 215.0
39 TraesCS5B01G041000 chr5D 84.279 229 23 6 2542 2765 45367431 45367211 1.830000e-50 211.0
40 TraesCS5B01G041000 chr5D 87.234 188 18 2 4160 4341 45366041 45365854 6.580000e-50 209.0
41 TraesCS5B01G041000 chr5D 92.414 145 10 1 2157 2301 150835729 150835586 8.520000e-49 206.0
42 TraesCS5B01G041000 chr5D 90.152 132 13 0 1585 1716 45281560 45281429 8.640000e-39 172.0
43 TraesCS5B01G041000 chr5D 85.271 129 9 3 1630 1757 45264064 45263945 2.450000e-24 124.0
44 TraesCS5B01G041000 chr5D 82.432 148 10 9 1758 1894 45263900 45263758 1.480000e-21 115.0
45 TraesCS5B01G041000 chr5D 92.500 80 6 0 1911 1990 446578511 446578432 1.480000e-21 115.0
46 TraesCS5B01G041000 chr5D 89.231 65 7 0 4277 4341 45373235 45373171 1.500000e-11 82.4
47 TraesCS5B01G041000 chr5D 92.593 54 4 0 5303 5356 45372567 45372514 1.940000e-10 78.7
48 TraesCS5B01G041000 chr5D 100.000 39 0 0 1986 2024 10810383 10810421 9.010000e-09 73.1
49 TraesCS5B01G041000 chr5D 100.000 39 0 0 1986 2024 531664711 531664673 9.010000e-09 73.1
50 TraesCS5B01G041000 chr5D 100.000 29 0 0 5616 5644 45364763 45364735 3.000000e-03 54.7
51 TraesCS5B01G041000 chr5A 96.778 1800 32 14 2029 3804 36321916 36320119 0.000000e+00 2979.0
52 TraesCS5B01G041000 chr5A 92.558 1908 89 13 4118 6014 36319637 36317772 0.000000e+00 2687.0
53 TraesCS5B01G041000 chr5A 96.575 876 25 3 5607 6481 36316861 36315990 0.000000e+00 1447.0
54 TraesCS5B01G041000 chr5A 87.779 851 83 9 3147 3988 36326414 36325576 0.000000e+00 976.0
55 TraesCS5B01G041000 chr5A 89.037 602 66 0 3806 4407 36319802 36319201 0.000000e+00 747.0
56 TraesCS5B01G041000 chr5A 82.570 786 112 15 3319 4090 36254663 36253889 0.000000e+00 669.0
57 TraesCS5B01G041000 chr5A 88.222 433 38 5 2506 2926 36290030 36289599 7.500000e-139 505.0
58 TraesCS5B01G041000 chr5A 91.875 320 19 2 2506 2818 36255078 36254759 2.140000e-119 440.0
59 TraesCS5B01G041000 chr5A 86.582 395 41 6 3806 4194 36325467 36325079 6.010000e-115 425.0
60 TraesCS5B01G041000 chr5A 91.582 297 16 4 1471 1759 36322264 36321969 1.010000e-107 401.0
61 TraesCS5B01G041000 chr5A 90.000 290 29 0 3971 4260 36319490 36319201 6.140000e-100 375.0
62 TraesCS5B01G041000 chr5A 88.217 314 34 2 2941 3251 36321138 36320825 7.940000e-99 372.0
63 TraesCS5B01G041000 chr5A 87.580 314 36 2 2785 3098 36320982 36320672 1.720000e-95 361.0
64 TraesCS5B01G041000 chr5A 87.662 308 32 4 3806 4113 36288287 36287986 2.870000e-93 353.0
65 TraesCS5B01G041000 chr5A 86.047 301 32 2 4445 4736 36288095 36287796 1.360000e-81 315.0
66 TraesCS5B01G041000 chr5A 88.646 229 12 9 1511 1733 36256041 36255821 3.850000e-67 267.0
67 TraesCS5B01G041000 chr5A 82.333 300 41 4 3689 3988 36288683 36288396 3.880000e-62 250.0
68 TraesCS5B01G041000 chr5A 87.234 188 18 2 4160 4341 36325266 36325079 6.580000e-50 209.0
69 TraesCS5B01G041000 chr5A 81.955 266 15 4 1758 1990 36321930 36321665 1.840000e-45 195.0
70 TraesCS5B01G041000 chr5A 83.663 202 21 6 2576 2765 36326637 36326436 5.160000e-41 180.0
71 TraesCS5B01G041000 chr5A 92.793 111 8 0 4445 4555 36325275 36325165 1.870000e-35 161.0
72 TraesCS5B01G041000 chr5A 86.923 130 12 3 5303 5428 36324475 36324347 2.440000e-29 141.0
73 TraesCS5B01G041000 chr5A 93.671 79 5 0 1912 1990 85313551 85313473 1.140000e-22 119.0
74 TraesCS5B01G041000 chr7A 94.009 651 39 0 3 653 591568531 591569181 0.000000e+00 987.0
75 TraesCS5B01G041000 chr7A 86.721 738 76 9 657 1381 591569244 591569972 0.000000e+00 800.0
76 TraesCS5B01G041000 chr7A 86.087 115 9 1 1883 1990 677696245 677696359 4.110000e-22 117.0
77 TraesCS5B01G041000 chr7A 85.000 120 9 3 1885 1995 557557030 557556911 5.310000e-21 113.0
78 TraesCS5B01G041000 chr4D 93.856 651 40 0 3 653 359114565 359115215 0.000000e+00 981.0
79 TraesCS5B01G041000 chr4D 92.780 651 47 0 3 653 13341571 13340921 0.000000e+00 942.0
80 TraesCS5B01G041000 chr4D 84.153 732 92 11 657 1381 399782482 399783196 0.000000e+00 688.0
81 TraesCS5B01G041000 chr4D 91.724 145 11 1 2157 2301 21147732 21147875 3.960000e-47 200.0
82 TraesCS5B01G041000 chr4D 90.345 145 12 2 2157 2301 416761696 416761838 8.580000e-44 189.0
83 TraesCS5B01G041000 chr4D 89.404 151 11 5 2154 2302 463336498 463336351 1.110000e-42 185.0
84 TraesCS5B01G041000 chr4D 91.045 134 11 1 2157 2290 443723448 443723580 5.160000e-41 180.0
85 TraesCS5B01G041000 chr4D 88.966 145 15 1 2157 2301 479687421 479687278 1.860000e-40 178.0
86 TraesCS5B01G041000 chr4D 87.919 149 16 2 2154 2301 64390467 64390614 2.400000e-39 174.0
87 TraesCS5B01G041000 chr4D 87.500 152 15 2 2150 2301 25439789 25439936 8.640000e-39 172.0
88 TraesCS5B01G041000 chr4D 91.250 80 7 0 1911 1990 466331867 466331946 6.870000e-20 110.0
89 TraesCS5B01G041000 chr4D 90.361 83 4 4 1911 1990 97222929 97223010 8.890000e-19 106.0
90 TraesCS5B01G041000 chr4D 95.385 65 3 0 1926 1990 471702597 471702533 3.200000e-18 104.0
91 TraesCS5B01G041000 chr4D 89.873 79 8 0 1912 1990 19456348 19456426 1.150000e-17 102.0
92 TraesCS5B01G041000 chr4D 89.873 79 8 0 1911 1989 117421319 117421241 1.150000e-17 102.0
93 TraesCS5B01G041000 chr4D 89.157 83 5 2 1911 1990 9879266 9879185 4.130000e-17 100.0
94 TraesCS5B01G041000 chr4D 100.000 39 0 0 1986 2024 333915158 333915120 9.010000e-09 73.1
95 TraesCS5B01G041000 chr4D 97.500 40 1 0 1986 2025 180504485 180504446 1.170000e-07 69.4
96 TraesCS5B01G041000 chr4D 97.500 40 1 0 1985 2024 386984748 386984709 1.170000e-07 69.4
97 TraesCS5B01G041000 chr4D 100.000 37 0 0 1986 2022 471702563 471702527 1.170000e-07 69.4
98 TraesCS5B01G041000 chr4D 100.000 37 0 0 1986 2022 504320324 504320360 1.170000e-07 69.4
99 TraesCS5B01G041000 chr4D 97.143 35 1 0 1449 1483 370305355 370305389 7.020000e-05 60.2
100 TraesCS5B01G041000 chr3D 93.241 651 44 0 3 653 528953769 528953119 0.000000e+00 959.0
101 TraesCS5B01G041000 chr3D 93.088 651 45 0 3 653 527521563 527522213 0.000000e+00 953.0
102 TraesCS5B01G041000 chr3D 86.321 753 78 12 657 1392 528953056 528952312 0.000000e+00 797.0
103 TraesCS5B01G041000 chr3D 88.142 565 45 8 657 1207 527522277 527522833 0.000000e+00 652.0
104 TraesCS5B01G041000 chr3D 91.724 145 11 1 2157 2301 598889893 598889750 3.960000e-47 200.0
105 TraesCS5B01G041000 chr7D 92.934 651 46 0 3 653 158938243 158938893 0.000000e+00 948.0
106 TraesCS5B01G041000 chr7D 91.946 149 11 1 2153 2301 508610977 508611124 2.370000e-49 207.0
107 TraesCS5B01G041000 chr2D 92.791 652 45 2 3 653 607090678 607090028 0.000000e+00 942.0
108 TraesCS5B01G041000 chr2D 84.677 744 75 13 655 1385 650493368 650492651 0.000000e+00 706.0
109 TraesCS5B01G041000 chr2D 91.837 147 10 2 2156 2301 524963801 524963656 3.060000e-48 204.0
110 TraesCS5B01G041000 chr2D 87.209 172 14 4 2155 2321 556927095 556926927 8.580000e-44 189.0
111 TraesCS5B01G041000 chr2D 86.607 112 11 2 1911 2022 487594837 487594944 3.170000e-23 121.0
112 TraesCS5B01G041000 chr2D 91.667 84 3 4 1910 1990 265906271 265906353 5.310000e-21 113.0
113 TraesCS5B01G041000 chr2D 100.000 40 0 0 1985 2024 64726961 64727000 2.510000e-09 75.0
114 TraesCS5B01G041000 chr6D 89.160 738 64 9 657 1390 451184767 451184042 0.000000e+00 905.0
115 TraesCS5B01G041000 chr6D 84.704 693 82 12 657 1342 104357034 104356359 0.000000e+00 671.0
116 TraesCS5B01G041000 chr6D 91.216 148 12 1 2154 2301 8790126 8789980 3.960000e-47 200.0
117 TraesCS5B01G041000 chr6D 91.156 147 10 3 2156 2301 335991174 335991030 5.130000e-46 196.0
118 TraesCS5B01G041000 chr6D 91.034 145 11 2 2157 2301 311548365 311548223 1.840000e-45 195.0
119 TraesCS5B01G041000 chr6D 90.476 147 13 1 2155 2301 90134888 90135033 6.630000e-45 193.0
120 TraesCS5B01G041000 chr6D 90.411 146 12 2 2156 2301 431160829 431160686 2.390000e-44 191.0
121 TraesCS5B01G041000 chr6D 91.250 80 7 0 1911 1990 374817257 374817178 6.870000e-20 110.0
122 TraesCS5B01G041000 chr6D 91.250 80 7 0 1911 1990 443774443 443774364 6.870000e-20 110.0
123 TraesCS5B01G041000 chr6D 100.000 39 0 0 1986 2024 141974413 141974451 9.010000e-09 73.1
124 TraesCS5B01G041000 chr6D 95.652 46 1 1 1986 2030 304102846 304102891 9.010000e-09 73.1
125 TraesCS5B01G041000 chr6B 88.769 739 65 11 655 1390 685352101 685351378 0.000000e+00 889.0
126 TraesCS5B01G041000 chr6B 95.556 45 2 0 1980 2024 11464056 11464100 9.010000e-09 73.1
127 TraesCS5B01G041000 chr6B 91.837 49 3 1 1986 2033 630600551 630600503 4.190000e-07 67.6
128 TraesCS5B01G041000 chr7B 87.092 736 72 10 655 1387 395422330 395423045 0.000000e+00 811.0
129 TraesCS5B01G041000 chr7B 95.455 44 2 0 1986 2029 171985254 171985211 3.240000e-08 71.3
130 TraesCS5B01G041000 chr3B 87.270 707 79 5 683 1386 628728307 628727609 0.000000e+00 797.0
131 TraesCS5B01G041000 chr3B 93.103 145 9 1 2157 2301 552226407 552226550 1.830000e-50 211.0
132 TraesCS5B01G041000 chr2B 85.440 364 42 8 1031 1388 84708216 84707858 1.030000e-97 368.0
133 TraesCS5B01G041000 chr2B 85.399 363 43 8 1031 1388 84733965 84733608 1.030000e-97 368.0
134 TraesCS5B01G041000 chr4A 92.667 150 10 1 2152 2301 213025413 213025561 1.420000e-51 215.0
135 TraesCS5B01G041000 chr4A 92.414 145 10 1 2157 2301 450788272 450788415 8.520000e-49 206.0
136 TraesCS5B01G041000 chr4A 92.405 79 6 0 1911 1989 739303873 739303951 5.310000e-21 113.0
137 TraesCS5B01G041000 chr4A 96.875 64 2 0 2552 2615 526608076 526608139 2.470000e-19 108.0
138 TraesCS5B01G041000 chr3A 91.613 155 11 2 2147 2301 726769138 726768986 5.090000e-51 213.0
139 TraesCS5B01G041000 chr3A 92.941 85 6 0 1911 1995 453935286 453935370 2.450000e-24 124.0
140 TraesCS5B01G041000 chrUn 93.007 143 9 1 2159 2301 80232673 80232814 2.370000e-49 207.0
141 TraesCS5B01G041000 chrUn 90.728 151 12 2 2151 2301 81477633 81477781 3.960000e-47 200.0
142 TraesCS5B01G041000 chrUn 86.364 154 19 2 2148 2301 178825306 178825155 4.020000e-37 167.0
143 TraesCS5B01G041000 chrUn 86.364 154 19 2 2148 2301 322399596 322399445 4.020000e-37 167.0
144 TraesCS5B01G041000 chrUn 86.364 154 19 2 2148 2301 322448223 322448374 4.020000e-37 167.0
145 TraesCS5B01G041000 chrUn 86.364 154 19 2 2148 2301 351659174 351659325 4.020000e-37 167.0
146 TraesCS5B01G041000 chrUn 86.577 149 18 2 2154 2301 96473980 96474127 5.200000e-36 163.0
147 TraesCS5B01G041000 chrUn 86.207 145 19 1 2157 2301 141680746 141680889 8.700000e-34 156.0
148 TraesCS5B01G041000 chrUn 86.301 146 17 3 2157 2301 270956469 270956326 8.700000e-34 156.0
149 TraesCS5B01G041000 chrUn 90.000 80 8 0 1911 1990 237024296 237024375 3.200000e-18 104.0
150 TraesCS5B01G041000 chrUn 95.385 65 3 0 1926 1990 347778281 347778217 3.200000e-18 104.0
151 TraesCS5B01G041000 chrUn 95.385 65 3 0 1926 1990 419948737 419948673 3.200000e-18 104.0
152 TraesCS5B01G041000 chrUn 89.157 83 5 4 1911 1990 82170479 82170560 4.130000e-17 100.0
153 TraesCS5B01G041000 chrUn 88.750 80 8 1 1911 1990 60522447 60522369 5.350000e-16 97.1
154 TraesCS5B01G041000 chrUn 88.750 80 8 1 1911 1990 322081980 322082058 5.350000e-16 97.1
155 TraesCS5B01G041000 chrUn 92.308 65 5 0 1926 1990 277307555 277307491 6.920000e-15 93.5
156 TraesCS5B01G041000 chrUn 96.429 56 2 0 1935 1990 397034943 397034998 6.920000e-15 93.5
157 TraesCS5B01G041000 chrUn 87.500 80 10 0 1911 1990 422206139 422206060 6.920000e-15 93.5
158 TraesCS5B01G041000 chrUn 87.500 80 10 0 1911 1990 422315520 422315441 6.920000e-15 93.5
159 TraesCS5B01G041000 chrUn 86.486 74 6 2 1951 2024 58767430 58767499 1.940000e-10 78.7
160 TraesCS5B01G041000 chrUn 95.455 44 2 0 1986 2029 29994440 29994483 3.240000e-08 71.3
161 TraesCS5B01G041000 chrUn 97.436 39 1 0 1986 2024 26794615 26794653 4.190000e-07 67.6
162 TraesCS5B01G041000 chrUn 97.436 39 1 0 1986 2024 31873185 31873147 4.190000e-07 67.6
163 TraesCS5B01G041000 chrUn 97.436 39 1 0 1986 2024 80232753 80232791 4.190000e-07 67.6
164 TraesCS5B01G041000 chrUn 97.436 39 1 0 1986 2024 91372035 91371997 4.190000e-07 67.6
165 TraesCS5B01G041000 chrUn 97.436 39 1 0 1986 2024 95498903 95498865 4.190000e-07 67.6
166 TraesCS5B01G041000 chrUn 97.436 39 1 0 1986 2024 116287238 116287276 4.190000e-07 67.6
167 TraesCS5B01G041000 chrUn 97.436 39 1 0 1986 2024 143992525 143992487 4.190000e-07 67.6
168 TraesCS5B01G041000 chrUn 93.333 45 3 0 1980 2024 422263052 422263096 4.190000e-07 67.6
169 TraesCS5B01G041000 chr1D 92.414 145 10 1 2157 2301 103408879 103408736 8.520000e-49 206.0
170 TraesCS5B01G041000 chr1D 89.655 145 13 2 2157 2301 387944782 387944924 3.990000e-42 183.0
171 TraesCS5B01G041000 chr1D 88.966 145 15 1 2157 2301 481404272 481404415 1.860000e-40 178.0
172 TraesCS5B01G041000 chr1D 87.662 154 16 3 2149 2301 155961666 155961817 6.680000e-40 176.0
173 TraesCS5B01G041000 chr1D 92.500 80 6 0 1911 1990 279722315 279722394 1.480000e-21 115.0
174 TraesCS5B01G041000 chr1D 91.566 83 3 4 1911 1990 166409400 166409319 1.910000e-20 111.0
175 TraesCS5B01G041000 chr1D 84.615 117 10 3 1885 1994 296367435 296367320 6.870000e-20 110.0
176 TraesCS5B01G041000 chr1D 91.250 80 6 1 1912 1990 483054982 483054903 2.470000e-19 108.0
177 TraesCS5B01G041000 chr1D 90.361 83 4 4 1911 1990 331539298 331539379 8.890000e-19 106.0
178 TraesCS5B01G041000 chr1D 97.500 40 1 0 1985 2024 341513444 341513483 1.170000e-07 69.4
179 TraesCS5B01G041000 chr1D 97.436 39 1 0 1986 2024 55178009 55177971 4.190000e-07 67.6
180 TraesCS5B01G041000 chr1D 93.333 45 3 0 1980 2024 150544978 150545022 4.190000e-07 67.6
181 TraesCS5B01G041000 chr1D 95.238 42 2 0 1988 2029 421222620 421222579 4.190000e-07 67.6
182 TraesCS5B01G041000 chr6A 90.000 90 3 6 1911 1997 306727826 306727740 1.910000e-20 111.0
183 TraesCS5B01G041000 chr6A 100.000 39 0 0 1986 2024 326119880 326119842 9.010000e-09 73.1
184 TraesCS5B01G041000 chr4B 83.486 109 16 2 1884 1990 654597633 654597525 4.130000e-17 100.0
185 TraesCS5B01G041000 chr4B 100.000 39 0 0 1986 2024 617405448 617405486 9.010000e-09 73.1
186 TraesCS5B01G041000 chr1A 82.759 116 10 6 1884 1990 96294499 96294385 1.920000e-15 95.3


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G041000 chr5B 45355202 45361682 6480 True 11969.000000 11969 100.000000 1 6481 1 chr5B.!!$R3 6480
1 TraesCS5B01G041000 chr5B 504523056 504523779 723 False 863.000000 863 88.179000 655 1386 1 chr5B.!!$F1 731
2 TraesCS5B01G041000 chr5B 45383751 45386931 3180 True 451.000000 965 82.821000 2507 5895 3 chr5B.!!$R6 3388
3 TraesCS5B01G041000 chr5B 45357129 45359911 2782 True 392.500000 608 88.548250 1772 4554 8 chr5B.!!$R5 2782
4 TraesCS5B01G041000 chr5D 66770953 66771603 650 True 948.000000 948 92.945000 3 653 1 chr5D.!!$R2 650
5 TraesCS5B01G041000 chr5D 306787824 306788474 650 False 942.000000 942 92.780000 3 653 1 chr5D.!!$F2 650
6 TraesCS5B01G041000 chr5D 45356210 45367431 11221 True 767.356250 5993 90.246000 1384 6481 16 chr5D.!!$R8 5097
7 TraesCS5B01G041000 chr5D 45343223 45344820 1597 True 410.250000 710 85.242000 2949 4754 4 chr5D.!!$R7 1805
8 TraesCS5B01G041000 chr5D 45262334 45264064 1730 True 303.000000 628 85.879000 1630 4090 5 chr5D.!!$R6 2460
9 TraesCS5B01G041000 chr5D 45372514 45373614 1100 True 247.700000 582 92.016667 3412 5356 3 chr5D.!!$R9 1944
10 TraesCS5B01G041000 chr5A 36315990 36326637 10647 True 777.066667 2979 89.283733 1471 6481 15 chr5A.!!$R4 5010
11 TraesCS5B01G041000 chr5A 36253889 36256041 2152 True 458.666667 669 87.697000 1511 4090 3 chr5A.!!$R2 2579
12 TraesCS5B01G041000 chr5A 36287796 36290030 2234 True 355.750000 505 86.066000 2506 4736 4 chr5A.!!$R3 2230
13 TraesCS5B01G041000 chr7A 591568531 591569972 1441 False 893.500000 987 90.365000 3 1381 2 chr7A.!!$F2 1378
14 TraesCS5B01G041000 chr4D 359114565 359115215 650 False 981.000000 981 93.856000 3 653 1 chr4D.!!$F6 650
15 TraesCS5B01G041000 chr4D 13340921 13341571 650 True 942.000000 942 92.780000 3 653 1 chr4D.!!$R2 650
16 TraesCS5B01G041000 chr4D 399782482 399783196 714 False 688.000000 688 84.153000 657 1381 1 chr4D.!!$F8 724
17 TraesCS5B01G041000 chr3D 528952312 528953769 1457 True 878.000000 959 89.781000 3 1392 2 chr3D.!!$R2 1389
18 TraesCS5B01G041000 chr3D 527521563 527522833 1270 False 802.500000 953 90.615000 3 1207 2 chr3D.!!$F1 1204
19 TraesCS5B01G041000 chr7D 158938243 158938893 650 False 948.000000 948 92.934000 3 653 1 chr7D.!!$F1 650
20 TraesCS5B01G041000 chr2D 607090028 607090678 650 True 942.000000 942 92.791000 3 653 1 chr2D.!!$R3 650
21 TraesCS5B01G041000 chr2D 650492651 650493368 717 True 706.000000 706 84.677000 655 1385 1 chr2D.!!$R4 730
22 TraesCS5B01G041000 chr6D 451184042 451184767 725 True 905.000000 905 89.160000 657 1390 1 chr6D.!!$R8 733
23 TraesCS5B01G041000 chr6D 104356359 104357034 675 True 671.000000 671 84.704000 657 1342 1 chr6D.!!$R2 685
24 TraesCS5B01G041000 chr6B 685351378 685352101 723 True 889.000000 889 88.769000 655 1390 1 chr6B.!!$R2 735
25 TraesCS5B01G041000 chr7B 395422330 395423045 715 False 811.000000 811 87.092000 655 1387 1 chr7B.!!$F1 732
26 TraesCS5B01G041000 chr3B 628727609 628728307 698 True 797.000000 797 87.270000 683 1386 1 chr3B.!!$R1 703

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
626 627 0.236449 CGGGGTGTTCGCAAAGTAAC 59.764 55.0 0.00 0.00 0.00 2.50 F
928 994 0.524414 GTGGTCCATAAACGTTGCCC 59.476 55.0 0.00 0.00 0.00 5.36 F
1455 1559 0.043053 CGAGCGTTTGTGCGGATATG 60.043 55.0 0.00 0.00 40.67 1.78 F
1825 6506 0.107703 CGTCATTAGGCAGGCCTTCA 60.108 55.0 19.37 6.24 45.70 3.02 F
1834 6515 0.255890 GCAGGCCTTCAATCCTACCA 59.744 55.0 0.00 0.00 0.00 3.25 F
2052 6733 0.826715 TCATAGCAGAGCAGTCCCAC 59.173 55.0 0.00 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 1540 0.043053 CATATCCGCACAAACGCTCG 60.043 55.000 0.0 0.0 0.00 5.03 R
2036 6717 0.251787 TCAGTGGGACTGCTCTGCTA 60.252 55.000 0.0 0.0 45.54 3.49 R
4991 11736 6.708054 CCAGATGTATTCCTTACACTTCATCC 59.292 42.308 0.0 0.0 43.46 3.51 R
5147 11895 2.027745 ACCATCATTCAGACTTCGCACT 60.028 45.455 0.0 0.0 0.00 4.40 R
5255 12010 4.495019 CGAAATCACCAACACGTCTTTCAA 60.495 41.667 0.0 0.0 0.00 2.69 R
5580 12354 4.072131 TGAGCATCAGTGGGTAACTTTTC 58.928 43.478 0.0 0.0 42.56 2.29 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
247 248 3.567164 GCATACAATCTATGCTGGCAAGT 59.433 43.478 0.00 0.00 44.93 3.16
248 249 4.556104 GCATACAATCTATGCTGGCAAGTG 60.556 45.833 0.00 0.00 44.93 3.16
304 305 0.595588 ATCTCTCTGTATCAGCGGCG 59.404 55.000 0.51 0.51 0.00 6.46
361 362 0.605319 CCACGGCCTTGCAGAAACTA 60.605 55.000 3.07 0.00 0.00 2.24
465 466 2.779755 ATGGTCGTGGTGCATTTCTA 57.220 45.000 0.00 0.00 0.00 2.10
500 501 2.681064 GCTTGGCAAGGGCATCCA 60.681 61.111 27.25 0.00 43.71 3.41
581 582 1.161843 CCTTGCCATACGAAAACGGT 58.838 50.000 0.00 0.00 0.00 4.83
626 627 0.236449 CGGGGTGTTCGCAAAGTAAC 59.764 55.000 0.00 0.00 0.00 2.50
627 628 1.310904 GGGGTGTTCGCAAAGTAACA 58.689 50.000 0.00 0.00 33.35 2.41
686 747 1.142097 TCGTGAACGACCAGTGCAA 59.858 52.632 0.50 0.00 40.82 4.08
705 766 3.256631 GCAACCACCACAAGATCTTCATT 59.743 43.478 4.57 0.00 0.00 2.57
746 807 5.496556 TCGATGAATAAATGAAGTGGTGGT 58.503 37.500 0.00 0.00 0.00 4.16
924 990 1.293267 CGCCGTGGTCCATAAACGTT 61.293 55.000 0.00 0.00 35.59 3.99
928 994 0.524414 GTGGTCCATAAACGTTGCCC 59.476 55.000 0.00 0.00 0.00 5.36
1013 1079 3.248602 CCATAACTCCTATGAAAGCACGC 59.751 47.826 0.00 0.00 40.02 5.34
1051 1117 1.138883 GCCATGTCGAGACGTGCTA 59.861 57.895 17.43 0.00 44.71 3.49
1089 1158 3.071206 GAGCAGTGAGGAGGCGGA 61.071 66.667 0.00 0.00 0.00 5.54
1202 1294 2.738521 CAAGGGTGTGCGTCGAGG 60.739 66.667 0.00 0.00 0.00 4.63
1258 1350 1.069978 CACAAGTTTGGGCCGGAAATT 59.930 47.619 5.05 0.00 0.00 1.82
1319 1423 4.424566 GCATGTTGGGCCACGCTG 62.425 66.667 5.23 4.73 0.00 5.18
1344 1448 4.081862 TCGTCTGTTCTATCCCAAACGAAT 60.082 41.667 0.00 0.00 35.26 3.34
1392 1496 3.263425 GGTGGAGTTGGTCTAAGGATTGA 59.737 47.826 0.00 0.00 0.00 2.57
1393 1497 4.263331 GGTGGAGTTGGTCTAAGGATTGAA 60.263 45.833 0.00 0.00 0.00 2.69
1394 1498 5.313712 GTGGAGTTGGTCTAAGGATTGAAA 58.686 41.667 0.00 0.00 0.00 2.69
1395 1499 5.946377 GTGGAGTTGGTCTAAGGATTGAAAT 59.054 40.000 0.00 0.00 0.00 2.17
1396 1500 7.110155 GTGGAGTTGGTCTAAGGATTGAAATA 58.890 38.462 0.00 0.00 0.00 1.40
1398 1502 7.775093 TGGAGTTGGTCTAAGGATTGAAATATG 59.225 37.037 0.00 0.00 0.00 1.78
1400 1504 8.738645 AGTTGGTCTAAGGATTGAAATATGAC 57.261 34.615 0.00 0.00 0.00 3.06
1402 1506 8.616076 GTTGGTCTAAGGATTGAAATATGACAG 58.384 37.037 0.00 0.00 0.00 3.51
1403 1507 8.089625 TGGTCTAAGGATTGAAATATGACAGA 57.910 34.615 0.00 0.00 0.00 3.41
1404 1508 7.987458 TGGTCTAAGGATTGAAATATGACAGAC 59.013 37.037 0.00 0.00 0.00 3.51
1405 1509 8.207545 GGTCTAAGGATTGAAATATGACAGACT 58.792 37.037 0.00 0.00 0.00 3.24
1407 1511 8.981659 TCTAAGGATTGAAATATGACAGACTCA 58.018 33.333 0.00 0.00 0.00 3.41
1409 1513 8.868522 AAGGATTGAAATATGACAGACTCAAA 57.131 30.769 1.73 0.00 30.60 2.69
1410 1514 9.471702 AAGGATTGAAATATGACAGACTCAAAT 57.528 29.630 1.73 0.00 30.60 2.32
1411 1515 8.900781 AGGATTGAAATATGACAGACTCAAATG 58.099 33.333 1.73 0.00 30.60 2.32
1412 1516 7.646922 GGATTGAAATATGACAGACTCAAATGC 59.353 37.037 1.73 0.00 30.60 3.56
1413 1517 7.451501 TTGAAATATGACAGACTCAAATGCA 57.548 32.000 0.00 0.00 30.60 3.96
1414 1518 7.080353 TGAAATATGACAGACTCAAATGCAG 57.920 36.000 0.00 0.00 30.60 4.41
1416 1520 6.674694 AATATGACAGACTCAAATGCAGAC 57.325 37.500 0.00 0.00 30.60 3.51
1417 1521 3.758755 TGACAGACTCAAATGCAGACT 57.241 42.857 0.00 0.00 0.00 3.24
1418 1522 4.077300 TGACAGACTCAAATGCAGACTT 57.923 40.909 0.00 0.00 0.00 3.01
1419 1523 5.213891 TGACAGACTCAAATGCAGACTTA 57.786 39.130 0.00 0.00 0.00 2.24
1421 1525 6.233434 TGACAGACTCAAATGCAGACTTAAT 58.767 36.000 0.00 0.00 0.00 1.40
1422 1526 6.712095 TGACAGACTCAAATGCAGACTTAATT 59.288 34.615 0.00 0.00 0.00 1.40
1431 1535 2.483877 TGCAGACTTAATTTGAGGCGTG 59.516 45.455 0.00 0.00 0.00 5.34
1433 1537 3.424962 GCAGACTTAATTTGAGGCGTGAC 60.425 47.826 0.00 0.00 0.00 3.67
1434 1538 3.125316 CAGACTTAATTTGAGGCGTGACC 59.875 47.826 0.00 0.00 39.61 4.02
1435 1539 2.073816 ACTTAATTTGAGGCGTGACCG 58.926 47.619 0.00 0.00 46.52 4.79
1445 1549 4.409588 CGTGACCGCGAGCGTTTG 62.410 66.667 8.23 3.80 37.81 2.93
1448 1552 4.719616 GACCGCGAGCGTTTGTGC 62.720 66.667 8.23 0.00 37.81 4.57
1452 1556 3.788766 GCGAGCGTTTGTGCGGAT 61.789 61.111 0.00 0.00 40.67 4.18
1453 1557 2.449525 GCGAGCGTTTGTGCGGATA 61.450 57.895 0.00 0.00 40.67 2.59
1454 1558 1.762222 GCGAGCGTTTGTGCGGATAT 61.762 55.000 0.00 0.00 40.67 1.63
1455 1559 0.043053 CGAGCGTTTGTGCGGATATG 60.043 55.000 0.00 0.00 40.67 1.78
1456 1560 0.316196 GAGCGTTTGTGCGGATATGC 60.316 55.000 0.00 0.00 40.67 3.14
1457 1561 1.024046 AGCGTTTGTGCGGATATGCA 61.024 50.000 0.00 0.00 43.95 3.96
1469 1573 2.365582 GGATATGCAAAGTCCGGTTGT 58.634 47.619 0.00 0.00 0.00 3.32
1470 1574 3.537580 GGATATGCAAAGTCCGGTTGTA 58.462 45.455 0.00 0.00 0.00 2.41
1471 1575 3.560068 GGATATGCAAAGTCCGGTTGTAG 59.440 47.826 0.00 0.00 0.00 2.74
1472 1576 2.851263 ATGCAAAGTCCGGTTGTAGA 57.149 45.000 0.00 0.00 0.00 2.59
1473 1577 2.851263 TGCAAAGTCCGGTTGTAGAT 57.149 45.000 0.00 0.00 0.00 1.98
1478 5801 1.853963 AGTCCGGTTGTAGATGCTCT 58.146 50.000 0.00 0.00 0.00 4.09
1496 5819 7.715249 AGATGCTCTAACAGTGTTCTTGTTTAA 59.285 33.333 12.82 0.00 0.00 1.52
1630 5965 2.177531 GCTGCTGCACAACCATCG 59.822 61.111 11.11 0.00 39.41 3.84
1631 5966 2.177531 CTGCTGCACAACCATCGC 59.822 61.111 0.00 0.00 0.00 4.58
1632 5967 3.332493 CTGCTGCACAACCATCGCC 62.332 63.158 0.00 0.00 0.00 5.54
1633 5968 4.465512 GCTGCACAACCATCGCCG 62.466 66.667 0.00 0.00 0.00 6.46
1634 5969 4.465512 CTGCACAACCATCGCCGC 62.466 66.667 0.00 0.00 0.00 6.53
1676 6019 0.471780 TCTCCCTTGTCCTGCTCACA 60.472 55.000 0.00 0.00 0.00 3.58
1717 6060 1.924731 TCTCACCGTGGATCTCACTT 58.075 50.000 11.12 0.00 43.94 3.16
1805 6486 2.526873 AGTCCCACTGAACCGCCT 60.527 61.111 0.00 0.00 0.00 5.52
1806 6487 2.047179 GTCCCACTGAACCGCCTC 60.047 66.667 0.00 0.00 0.00 4.70
1807 6488 3.691342 TCCCACTGAACCGCCTCG 61.691 66.667 0.00 0.00 0.00 4.63
1808 6489 4.003788 CCCACTGAACCGCCTCGT 62.004 66.667 0.00 0.00 0.00 4.18
1809 6490 2.432628 CCACTGAACCGCCTCGTC 60.433 66.667 0.00 0.00 0.00 4.20
1810 6491 2.338620 CACTGAACCGCCTCGTCA 59.661 61.111 0.00 0.00 0.00 4.35
1811 6492 1.079819 CACTGAACCGCCTCGTCAT 60.080 57.895 0.00 0.00 0.00 3.06
1812 6493 0.670546 CACTGAACCGCCTCGTCATT 60.671 55.000 0.00 0.00 0.00 2.57
1813 6494 0.892755 ACTGAACCGCCTCGTCATTA 59.107 50.000 0.00 0.00 0.00 1.90
1814 6495 1.135083 ACTGAACCGCCTCGTCATTAG 60.135 52.381 0.00 0.00 0.00 1.73
1815 6496 0.174845 TGAACCGCCTCGTCATTAGG 59.825 55.000 0.00 0.00 37.17 2.69
1820 6501 4.445699 CCTCGTCATTAGGCAGGC 57.554 61.111 0.00 0.00 0.00 4.85
1821 6502 1.227674 CCTCGTCATTAGGCAGGCC 60.228 63.158 0.97 0.97 0.00 5.19
1823 6504 0.179000 CTCGTCATTAGGCAGGCCTT 59.821 55.000 19.37 0.00 45.70 4.35
1824 6505 0.178068 TCGTCATTAGGCAGGCCTTC 59.822 55.000 19.37 0.00 45.70 3.46
1825 6506 0.107703 CGTCATTAGGCAGGCCTTCA 60.108 55.000 19.37 6.24 45.70 3.02
1826 6507 1.678728 CGTCATTAGGCAGGCCTTCAA 60.679 52.381 19.37 8.10 45.70 2.69
1827 6508 2.659428 GTCATTAGGCAGGCCTTCAAT 58.341 47.619 19.37 10.20 45.70 2.57
1828 6509 2.620585 GTCATTAGGCAGGCCTTCAATC 59.379 50.000 19.37 3.70 45.70 2.67
1829 6510 1.959282 CATTAGGCAGGCCTTCAATCC 59.041 52.381 19.37 0.00 45.70 3.01
1830 6511 1.298953 TTAGGCAGGCCTTCAATCCT 58.701 50.000 19.37 7.52 45.70 3.24
1831 6512 2.190398 TAGGCAGGCCTTCAATCCTA 57.810 50.000 19.37 6.46 45.70 2.94
1832 6513 0.548510 AGGCAGGCCTTCAATCCTAC 59.451 55.000 0.00 0.00 45.70 3.18
1833 6514 0.466372 GGCAGGCCTTCAATCCTACC 60.466 60.000 0.00 0.00 0.00 3.18
1834 6515 0.255890 GCAGGCCTTCAATCCTACCA 59.744 55.000 0.00 0.00 0.00 3.25
1835 6516 1.133668 GCAGGCCTTCAATCCTACCAT 60.134 52.381 0.00 0.00 0.00 3.55
1836 6517 2.579873 CAGGCCTTCAATCCTACCATG 58.420 52.381 0.00 0.00 0.00 3.66
1837 6518 2.092212 CAGGCCTTCAATCCTACCATGT 60.092 50.000 0.00 0.00 0.00 3.21
1838 6519 2.092212 AGGCCTTCAATCCTACCATGTG 60.092 50.000 0.00 0.00 0.00 3.21
1839 6520 2.357154 GGCCTTCAATCCTACCATGTGT 60.357 50.000 0.00 0.00 0.00 3.72
1840 6521 3.356290 GCCTTCAATCCTACCATGTGTT 58.644 45.455 0.00 0.00 0.00 3.32
1841 6522 3.763897 GCCTTCAATCCTACCATGTGTTT 59.236 43.478 0.00 0.00 0.00 2.83
1842 6523 4.947388 GCCTTCAATCCTACCATGTGTTTA 59.053 41.667 0.00 0.00 0.00 2.01
1843 6524 5.594317 GCCTTCAATCCTACCATGTGTTTAT 59.406 40.000 0.00 0.00 0.00 1.40
1844 6525 6.238759 GCCTTCAATCCTACCATGTGTTTATC 60.239 42.308 0.00 0.00 0.00 1.75
1845 6526 6.828273 CCTTCAATCCTACCATGTGTTTATCA 59.172 38.462 0.00 0.00 0.00 2.15
1846 6527 7.012704 CCTTCAATCCTACCATGTGTTTATCAG 59.987 40.741 0.00 0.00 0.00 2.90
1847 6528 6.957631 TCAATCCTACCATGTGTTTATCAGT 58.042 36.000 0.00 0.00 0.00 3.41
1848 6529 7.047891 TCAATCCTACCATGTGTTTATCAGTC 58.952 38.462 0.00 0.00 0.00 3.51
1849 6530 6.560003 ATCCTACCATGTGTTTATCAGTCA 57.440 37.500 0.00 0.00 0.00 3.41
1850 6531 5.730550 TCCTACCATGTGTTTATCAGTCAC 58.269 41.667 0.00 0.00 0.00 3.67
1851 6532 5.247337 TCCTACCATGTGTTTATCAGTCACA 59.753 40.000 0.00 0.00 44.29 3.58
1853 6534 6.599244 CCTACCATGTGTTTATCAGTCACATT 59.401 38.462 7.19 0.00 46.26 2.71
1854 6535 6.899393 ACCATGTGTTTATCAGTCACATTT 57.101 33.333 7.19 0.00 46.26 2.32
1855 6536 6.913170 ACCATGTGTTTATCAGTCACATTTC 58.087 36.000 7.19 0.00 46.26 2.17
1856 6537 6.716628 ACCATGTGTTTATCAGTCACATTTCT 59.283 34.615 7.19 0.00 46.26 2.52
1857 6538 7.231317 ACCATGTGTTTATCAGTCACATTTCTT 59.769 33.333 7.19 0.00 46.26 2.52
1858 6539 7.752239 CCATGTGTTTATCAGTCACATTTCTTC 59.248 37.037 7.19 0.00 46.26 2.87
1859 6540 8.509690 CATGTGTTTATCAGTCACATTTCTTCT 58.490 33.333 7.19 0.00 46.26 2.85
1860 6541 8.450578 TGTGTTTATCAGTCACATTTCTTCTT 57.549 30.769 0.00 0.00 37.20 2.52
1861 6542 8.559536 TGTGTTTATCAGTCACATTTCTTCTTC 58.440 33.333 0.00 0.00 37.20 2.87
1862 6543 8.778358 GTGTTTATCAGTCACATTTCTTCTTCT 58.222 33.333 0.00 0.00 33.04 2.85
1863 6544 9.342308 TGTTTATCAGTCACATTTCTTCTTCTT 57.658 29.630 0.00 0.00 0.00 2.52
1864 6545 9.818796 GTTTATCAGTCACATTTCTTCTTCTTC 57.181 33.333 0.00 0.00 0.00 2.87
1865 6546 9.784531 TTTATCAGTCACATTTCTTCTTCTTCT 57.215 29.630 0.00 0.00 0.00 2.85
1866 6547 9.784531 TTATCAGTCACATTTCTTCTTCTTCTT 57.215 29.630 0.00 0.00 0.00 2.52
1868 6549 9.956640 ATCAGTCACATTTCTTCTTCTTCTTAT 57.043 29.630 0.00 0.00 0.00 1.73
1869 6550 9.429359 TCAGTCACATTTCTTCTTCTTCTTATC 57.571 33.333 0.00 0.00 0.00 1.75
1870 6551 8.663911 CAGTCACATTTCTTCTTCTTCTTATCC 58.336 37.037 0.00 0.00 0.00 2.59
1871 6552 8.378565 AGTCACATTTCTTCTTCTTCTTATCCA 58.621 33.333 0.00 0.00 0.00 3.41
1872 6553 9.171877 GTCACATTTCTTCTTCTTCTTATCCAT 57.828 33.333 0.00 0.00 0.00 3.41
1894 6575 9.392506 TCCATATCTTATCAAATACTCCTTCCA 57.607 33.333 0.00 0.00 0.00 3.53
1930 6611 7.818997 AAGTGAGATATCAATACGGACTACA 57.181 36.000 5.32 0.00 0.00 2.74
1931 6612 7.818997 AGTGAGATATCAATACGGACTACAA 57.181 36.000 5.32 0.00 0.00 2.41
1932 6613 8.234136 AGTGAGATATCAATACGGACTACAAA 57.766 34.615 5.32 0.00 0.00 2.83
1933 6614 8.136165 AGTGAGATATCAATACGGACTACAAAC 58.864 37.037 5.32 0.00 0.00 2.93
1934 6615 7.113124 GTGAGATATCAATACGGACTACAAACG 59.887 40.741 5.32 0.00 0.00 3.60
1935 6616 6.444633 AGATATCAATACGGACTACAAACGG 58.555 40.000 5.32 0.00 0.00 4.44
1936 6617 4.724074 ATCAATACGGACTACAAACGGA 57.276 40.909 0.00 0.00 0.00 4.69
1937 6618 4.724074 TCAATACGGACTACAAACGGAT 57.276 40.909 0.00 0.00 31.40 4.18
1938 6619 4.426416 TCAATACGGACTACAAACGGATG 58.574 43.478 0.00 0.00 30.41 3.51
1939 6620 4.082081 TCAATACGGACTACAAACGGATGT 60.082 41.667 0.96 0.96 37.32 3.06
1940 6621 5.125257 TCAATACGGACTACAAACGGATGTA 59.875 40.000 3.08 3.08 34.75 2.29
1941 6622 5.779529 ATACGGACTACAAACGGATGTAT 57.220 39.130 3.45 0.00 35.37 2.29
1942 6623 6.882610 ATACGGACTACAAACGGATGTATA 57.117 37.500 3.45 0.00 35.37 1.47
1943 6624 5.779529 ACGGACTACAAACGGATGTATAT 57.220 39.130 3.45 0.00 35.37 0.86
1944 6625 6.882610 ACGGACTACAAACGGATGTATATA 57.117 37.500 3.45 0.00 35.37 0.86
1945 6626 7.458409 ACGGACTACAAACGGATGTATATAT 57.542 36.000 3.45 0.00 35.37 0.86
1946 6627 8.565896 ACGGACTACAAACGGATGTATATATA 57.434 34.615 3.45 0.00 35.37 0.86
1947 6628 8.454106 ACGGACTACAAACGGATGTATATATAC 58.546 37.037 14.86 14.86 35.37 1.47
1948 6629 8.453320 CGGACTACAAACGGATGTATATATACA 58.547 37.037 24.22 24.22 46.21 2.29
1979 6660 9.944376 TTAGAGTGTAGATTTACTCATTTTGCT 57.056 29.630 7.09 0.00 44.41 3.91
1980 6661 8.854614 AGAGTGTAGATTTACTCATTTTGCTT 57.145 30.769 7.09 0.00 44.41 3.91
1981 6662 8.940952 AGAGTGTAGATTTACTCATTTTGCTTC 58.059 33.333 7.09 0.00 44.41 3.86
1982 6663 7.743104 AGTGTAGATTTACTCATTTTGCTTCG 58.257 34.615 0.00 0.00 0.00 3.79
1983 6664 7.387948 AGTGTAGATTTACTCATTTTGCTTCGT 59.612 33.333 0.00 0.00 0.00 3.85
1984 6665 8.653338 GTGTAGATTTACTCATTTTGCTTCGTA 58.347 33.333 0.00 0.00 0.00 3.43
1985 6666 9.378551 TGTAGATTTACTCATTTTGCTTCGTAT 57.621 29.630 0.00 0.00 0.00 3.06
1986 6667 9.638300 GTAGATTTACTCATTTTGCTTCGTATG 57.362 33.333 0.00 0.00 0.00 2.39
1987 6668 8.268850 AGATTTACTCATTTTGCTTCGTATGT 57.731 30.769 0.00 0.00 0.00 2.29
1988 6669 9.378551 AGATTTACTCATTTTGCTTCGTATGTA 57.621 29.630 0.00 0.00 0.00 2.29
1989 6670 9.638300 GATTTACTCATTTTGCTTCGTATGTAG 57.362 33.333 0.00 0.00 0.00 2.74
1990 6671 8.766000 TTTACTCATTTTGCTTCGTATGTAGA 57.234 30.769 0.00 0.00 0.00 2.59
1991 6672 8.942338 TTACTCATTTTGCTTCGTATGTAGAT 57.058 30.769 0.00 0.00 0.00 1.98
1992 6673 7.849804 ACTCATTTTGCTTCGTATGTAGATT 57.150 32.000 0.00 0.00 0.00 2.40
1993 6674 8.268850 ACTCATTTTGCTTCGTATGTAGATTT 57.731 30.769 0.00 0.00 0.00 2.17
1994 6675 9.378551 ACTCATTTTGCTTCGTATGTAGATTTA 57.621 29.630 0.00 0.00 0.00 1.40
1995 6676 9.638300 CTCATTTTGCTTCGTATGTAGATTTAC 57.362 33.333 0.00 0.00 0.00 2.01
1996 6677 9.378551 TCATTTTGCTTCGTATGTAGATTTACT 57.621 29.630 0.00 0.00 0.00 2.24
1997 6678 9.638300 CATTTTGCTTCGTATGTAGATTTACTC 57.362 33.333 0.00 0.00 0.00 2.59
1998 6679 8.766000 TTTTGCTTCGTATGTAGATTTACTCA 57.234 30.769 0.00 0.00 0.00 3.41
1999 6680 8.942338 TTTGCTTCGTATGTAGATTTACTCAT 57.058 30.769 0.00 0.00 0.00 2.90
2000 6681 8.942338 TTGCTTCGTATGTAGATTTACTCATT 57.058 30.769 0.00 0.00 0.00 2.57
2001 6682 8.942338 TGCTTCGTATGTAGATTTACTCATTT 57.058 30.769 0.00 0.00 0.00 2.32
2002 6683 9.378551 TGCTTCGTATGTAGATTTACTCATTTT 57.621 29.630 0.00 0.00 0.00 1.82
2003 6684 9.638300 GCTTCGTATGTAGATTTACTCATTTTG 57.362 33.333 0.00 0.00 0.00 2.44
2004 6685 9.638300 CTTCGTATGTAGATTTACTCATTTTGC 57.362 33.333 0.00 0.00 0.00 3.68
2005 6686 8.942338 TCGTATGTAGATTTACTCATTTTGCT 57.058 30.769 0.00 0.00 0.00 3.91
2006 6687 9.031360 TCGTATGTAGATTTACTCATTTTGCTC 57.969 33.333 0.00 0.00 0.00 4.26
2007 6688 8.276325 CGTATGTAGATTTACTCATTTTGCTCC 58.724 37.037 0.00 0.00 0.00 4.70
2008 6689 6.662414 TGTAGATTTACTCATTTTGCTCCG 57.338 37.500 0.00 0.00 0.00 4.63
2009 6690 6.170506 TGTAGATTTACTCATTTTGCTCCGT 58.829 36.000 0.00 0.00 0.00 4.69
2010 6691 7.324935 TGTAGATTTACTCATTTTGCTCCGTA 58.675 34.615 0.00 0.00 0.00 4.02
2011 6692 7.985184 TGTAGATTTACTCATTTTGCTCCGTAT 59.015 33.333 0.00 0.00 0.00 3.06
2012 6693 7.251704 AGATTTACTCATTTTGCTCCGTATG 57.748 36.000 0.00 0.00 0.00 2.39
2013 6694 6.823689 AGATTTACTCATTTTGCTCCGTATGT 59.176 34.615 0.00 0.00 0.00 2.29
2014 6695 7.985184 AGATTTACTCATTTTGCTCCGTATGTA 59.015 33.333 0.00 0.00 0.00 2.29
2015 6696 7.534085 TTTACTCATTTTGCTCCGTATGTAG 57.466 36.000 0.00 0.00 0.00 2.74
2016 6697 5.086104 ACTCATTTTGCTCCGTATGTAGT 57.914 39.130 0.00 0.00 0.00 2.73
2017 6698 5.109903 ACTCATTTTGCTCCGTATGTAGTC 58.890 41.667 0.00 0.00 0.00 2.59
2018 6699 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
2019 6700 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
2020 6701 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
2021 6702 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
2022 6703 5.801531 TTTGCTCCGTATGTAGTCCATAT 57.198 39.130 0.00 0.00 38.29 1.78
2023 6704 5.801531 TTGCTCCGTATGTAGTCCATATT 57.198 39.130 0.00 0.00 38.29 1.28
2024 6705 5.801531 TGCTCCGTATGTAGTCCATATTT 57.198 39.130 0.00 0.00 38.29 1.40
2025 6706 6.169557 TGCTCCGTATGTAGTCCATATTTT 57.830 37.500 0.00 0.00 38.29 1.82
2026 6707 7.292713 TGCTCCGTATGTAGTCCATATTTTA 57.707 36.000 0.00 0.00 38.29 1.52
2027 6708 7.375834 TGCTCCGTATGTAGTCCATATTTTAG 58.624 38.462 0.00 0.00 38.29 1.85
2028 6709 7.231925 TGCTCCGTATGTAGTCCATATTTTAGA 59.768 37.037 0.00 0.00 38.29 2.10
2029 6710 7.755822 GCTCCGTATGTAGTCCATATTTTAGAG 59.244 40.741 0.00 0.00 38.29 2.43
2030 6711 8.929260 TCCGTATGTAGTCCATATTTTAGAGA 57.071 34.615 0.00 0.00 38.29 3.10
2031 6712 9.011095 TCCGTATGTAGTCCATATTTTAGAGAG 57.989 37.037 0.00 0.00 38.29 3.20
2032 6713 8.794553 CCGTATGTAGTCCATATTTTAGAGAGT 58.205 37.037 0.00 0.00 38.29 3.24
2040 6721 8.928448 AGTCCATATTTTAGAGAGTTCATAGCA 58.072 33.333 0.00 0.00 0.00 3.49
2041 6722 9.202273 GTCCATATTTTAGAGAGTTCATAGCAG 57.798 37.037 0.00 0.00 0.00 4.24
2042 6723 9.147732 TCCATATTTTAGAGAGTTCATAGCAGA 57.852 33.333 0.00 0.00 0.00 4.26
2043 6724 9.421806 CCATATTTTAGAGAGTTCATAGCAGAG 57.578 37.037 0.00 0.00 0.00 3.35
2044 6725 8.924691 CATATTTTAGAGAGTTCATAGCAGAGC 58.075 37.037 0.00 0.00 0.00 4.09
2045 6726 5.921962 TTTAGAGAGTTCATAGCAGAGCA 57.078 39.130 0.00 0.00 0.00 4.26
2046 6727 5.512753 TTAGAGAGTTCATAGCAGAGCAG 57.487 43.478 0.00 0.00 0.00 4.24
2047 6728 3.364549 AGAGAGTTCATAGCAGAGCAGT 58.635 45.455 0.00 0.00 0.00 4.40
2048 6729 3.381272 AGAGAGTTCATAGCAGAGCAGTC 59.619 47.826 0.00 0.00 0.00 3.51
2049 6730 2.430332 AGAGTTCATAGCAGAGCAGTCC 59.570 50.000 0.00 0.00 0.00 3.85
2050 6731 1.484240 AGTTCATAGCAGAGCAGTCCC 59.516 52.381 0.00 0.00 0.00 4.46
2051 6732 1.208052 GTTCATAGCAGAGCAGTCCCA 59.792 52.381 0.00 0.00 0.00 4.37
2052 6733 0.826715 TCATAGCAGAGCAGTCCCAC 59.173 55.000 0.00 0.00 0.00 4.61
2053 6734 0.829333 CATAGCAGAGCAGTCCCACT 59.171 55.000 0.00 0.00 0.00 4.00
4564 11274 2.007547 GCCCTCAGAAGCGTTAAGACC 61.008 57.143 0.00 0.00 0.00 3.85
5085 11833 7.736893 ACATCTGAGTTAGTACTGGAAAGTTT 58.263 34.615 5.39 0.00 33.84 2.66
5118 11866 5.278463 CCATGAGTTGGTACTGGAAAAGTTG 60.278 44.000 0.00 0.00 40.99 3.16
5135 11883 6.859420 AAAGTTGTGGAACCATTTAAATGC 57.141 33.333 20.67 9.14 35.08 3.56
5147 11895 7.230849 ACCATTTAAATGCTGAGTTCATCAA 57.769 32.000 20.67 0.00 33.84 2.57
5151 11899 3.844577 AATGCTGAGTTCATCAAGTGC 57.155 42.857 0.00 0.00 37.52 4.40
5168 11916 2.027745 AGTGCGAAGTCTGAATGATGGT 60.028 45.455 0.00 0.00 0.00 3.55
5175 11923 5.063944 CGAAGTCTGAATGATGGTAAGTTGG 59.936 44.000 0.00 0.00 0.00 3.77
5183 11931 6.599244 TGAATGATGGTAAGTTGGCTTCTTAG 59.401 38.462 3.13 0.00 36.22 2.18
5184 11932 4.843728 TGATGGTAAGTTGGCTTCTTAGG 58.156 43.478 3.13 0.00 36.22 2.69
5373 12146 7.173390 ACAAACTTAGGCAGATGAAGTCTTAAC 59.827 37.037 0.00 0.00 34.00 2.01
5431 12204 8.461222 TCTGCATTAACTAATGACCTTCATTTG 58.539 33.333 12.61 7.58 44.03 2.32
5580 12354 7.630242 TTTGAATAATGACTTGGCTAAGAGG 57.370 36.000 17.63 0.00 37.36 3.69
5590 12364 5.314529 ACTTGGCTAAGAGGAAAAGTTACC 58.685 41.667 17.63 0.00 37.36 2.85
5596 12370 5.512576 GCTAAGAGGAAAAGTTACCCACTGA 60.513 44.000 0.00 0.00 35.12 3.41
5931 13097 5.897377 ATTGTGGCTGTTACCTTGTAATC 57.103 39.130 0.00 0.00 0.00 1.75
5932 13098 4.634012 TGTGGCTGTTACCTTGTAATCT 57.366 40.909 0.00 0.00 0.00 2.40
5933 13099 5.748670 TGTGGCTGTTACCTTGTAATCTA 57.251 39.130 0.00 0.00 0.00 1.98
5934 13100 5.484715 TGTGGCTGTTACCTTGTAATCTAC 58.515 41.667 0.00 0.00 0.00 2.59
6058 14545 2.010145 AATGTTCGACACTGATCCGG 57.990 50.000 0.00 0.00 0.00 5.14
6069 14556 4.163427 ACACTGATCCGGATCTATGGATT 58.837 43.478 37.39 20.01 44.92 3.01
6074 14561 1.021390 CCGGATCTATGGATTGCGGC 61.021 60.000 0.00 0.00 31.46 6.53
6148 14635 7.041721 TCAACATAAGTTCGTTAGAGCATCAT 58.958 34.615 0.00 0.00 34.15 2.45
6265 14752 3.674997 TCTGAACTTATGGACCAGTTGC 58.325 45.455 0.00 0.00 33.22 4.17
6271 14758 1.496444 TATGGACCAGTTGCCAGCCA 61.496 55.000 0.00 0.00 37.64 4.75
6363 14850 2.285827 TTGTTGTTGTTCAAAGGCCG 57.714 45.000 0.00 0.00 37.81 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.763793 CCACCTGTCAACTTTGAGATCAAT 59.236 41.667 0.00 0.00 37.98 2.57
110 111 4.321750 GCAGGATCTTTGGATATGGCATTG 60.322 45.833 4.78 0.00 31.46 2.82
142 143 4.631377 GTGTGCACTGTCATATTAGAAGCA 59.369 41.667 19.41 0.00 0.00 3.91
304 305 1.807142 GAGTACTTGAGGCAGCCAAAC 59.193 52.381 15.80 5.24 0.00 2.93
361 362 4.040339 TCCACATGTCTGTTGTCACTGTAT 59.960 41.667 0.00 0.00 31.62 2.29
465 466 5.096443 CAAGCTTGGATTCTCCTCTTACT 57.904 43.478 19.14 0.00 37.46 2.24
500 501 2.501723 ACCCATACTTCGAGTGCAAGAT 59.498 45.455 0.00 0.00 0.00 2.40
581 582 4.214986 TCAAGCCAGATAAATTCCGTCA 57.785 40.909 0.00 0.00 0.00 4.35
626 627 2.280660 CGCCCTGCTCTATGCCTG 60.281 66.667 0.00 0.00 42.00 4.85
627 628 2.765807 ACGCCCTGCTCTATGCCT 60.766 61.111 0.00 0.00 42.00 4.75
653 654 0.160813 CACGACCACATTGAACGACG 59.839 55.000 0.00 0.00 0.00 5.12
686 747 5.440610 GGATAATGAAGATCTTGTGGTGGT 58.559 41.667 14.00 0.00 0.00 4.16
928 994 1.299165 CAGAAGGGATACGACCGCG 60.299 63.158 0.00 0.00 44.79 6.46
1051 1117 3.556306 CCCGGCCGTCCATACCAT 61.556 66.667 26.12 0.00 0.00 3.55
1089 1158 1.141881 CGCCGGCACTATTCTCTGT 59.858 57.895 28.98 0.00 0.00 3.41
1148 1237 0.251653 TCGGGGTCACTAGCAGTTCT 60.252 55.000 0.00 0.00 0.00 3.01
1202 1294 2.813908 GGACATCGTGTGGACGGC 60.814 66.667 0.00 0.00 46.11 5.68
1258 1350 3.546417 CGAATTTCGTCCGTTTTTGACCA 60.546 43.478 10.61 0.00 34.72 4.02
1319 1423 3.367025 CGTTTGGGATAGAACAGACGAAC 59.633 47.826 2.16 0.00 44.76 3.95
1344 1448 1.705002 CCCCATCTTATCCGGGTGCA 61.705 60.000 0.00 0.00 38.40 4.57
1381 1485 8.981659 TGAGTCTGTCATATTTCAATCCTTAGA 58.018 33.333 0.00 0.00 0.00 2.10
1392 1496 6.883217 AGTCTGCATTTGAGTCTGTCATATTT 59.117 34.615 0.00 0.00 34.17 1.40
1393 1497 6.413052 AGTCTGCATTTGAGTCTGTCATATT 58.587 36.000 0.00 0.00 34.17 1.28
1394 1498 5.987098 AGTCTGCATTTGAGTCTGTCATAT 58.013 37.500 0.00 0.00 34.17 1.78
1395 1499 5.411831 AGTCTGCATTTGAGTCTGTCATA 57.588 39.130 0.00 0.00 34.17 2.15
1396 1500 4.283363 AGTCTGCATTTGAGTCTGTCAT 57.717 40.909 0.00 0.00 34.17 3.06
1398 1502 6.734104 ATTAAGTCTGCATTTGAGTCTGTC 57.266 37.500 0.00 0.00 0.00 3.51
1400 1504 7.587629 TCAAATTAAGTCTGCATTTGAGTCTG 58.412 34.615 12.61 0.00 40.41 3.51
1405 1509 5.619757 CGCCTCAAATTAAGTCTGCATTTGA 60.620 40.000 14.64 14.64 42.13 2.69
1407 1511 4.218417 ACGCCTCAAATTAAGTCTGCATTT 59.782 37.500 0.00 0.00 0.00 2.32
1409 1513 3.127548 CACGCCTCAAATTAAGTCTGCAT 59.872 43.478 0.00 0.00 0.00 3.96
1410 1514 2.483877 CACGCCTCAAATTAAGTCTGCA 59.516 45.455 0.00 0.00 0.00 4.41
1411 1515 2.742053 TCACGCCTCAAATTAAGTCTGC 59.258 45.455 0.00 0.00 0.00 4.26
1412 1516 3.125316 GGTCACGCCTCAAATTAAGTCTG 59.875 47.826 0.00 0.00 0.00 3.51
1413 1517 3.335579 GGTCACGCCTCAAATTAAGTCT 58.664 45.455 0.00 0.00 0.00 3.24
1414 1518 2.093783 CGGTCACGCCTCAAATTAAGTC 59.906 50.000 0.00 0.00 34.25 3.01
1416 1520 2.806288 CGGTCACGCCTCAAATTAAG 57.194 50.000 0.00 0.00 34.25 1.85
1431 1535 4.719616 GCACAAACGCTCGCGGTC 62.720 66.667 16.18 0.00 44.69 4.79
1435 1539 1.762222 ATATCCGCACAAACGCTCGC 61.762 55.000 0.00 0.00 0.00 5.03
1436 1540 0.043053 CATATCCGCACAAACGCTCG 60.043 55.000 0.00 0.00 0.00 5.03
1437 1541 0.316196 GCATATCCGCACAAACGCTC 60.316 55.000 0.00 0.00 0.00 5.03
1439 1543 0.179176 TTGCATATCCGCACAAACGC 60.179 50.000 0.00 0.00 42.87 4.84
1440 1544 2.176369 CTTTGCATATCCGCACAAACG 58.824 47.619 0.00 0.00 42.87 3.60
1441 1545 3.171277 GACTTTGCATATCCGCACAAAC 58.829 45.455 0.00 0.00 42.87 2.93
1442 1546 2.163412 GGACTTTGCATATCCGCACAAA 59.837 45.455 0.00 0.00 42.87 2.83
1443 1547 1.742831 GGACTTTGCATATCCGCACAA 59.257 47.619 0.00 0.00 42.87 3.33
1444 1548 1.378531 GGACTTTGCATATCCGCACA 58.621 50.000 0.00 0.00 42.87 4.57
1450 1554 4.439057 TCTACAACCGGACTTTGCATATC 58.561 43.478 9.46 0.00 0.00 1.63
1452 1556 3.965379 TCTACAACCGGACTTTGCATA 57.035 42.857 9.46 0.00 0.00 3.14
1453 1557 2.851263 TCTACAACCGGACTTTGCAT 57.149 45.000 9.46 0.00 0.00 3.96
1454 1558 2.422597 CATCTACAACCGGACTTTGCA 58.577 47.619 9.46 0.00 0.00 4.08
1455 1559 1.130561 GCATCTACAACCGGACTTTGC 59.869 52.381 9.46 4.00 0.00 3.68
1456 1560 2.673368 GAGCATCTACAACCGGACTTTG 59.327 50.000 9.46 4.81 0.00 2.77
1457 1561 2.973945 GAGCATCTACAACCGGACTTT 58.026 47.619 9.46 0.00 0.00 2.66
1458 1562 2.674796 GAGCATCTACAACCGGACTT 57.325 50.000 9.46 0.00 0.00 3.01
1471 1575 5.931441 AACAAGAACACTGTTAGAGCATC 57.069 39.130 0.00 0.00 0.00 3.91
1472 1576 7.255139 GGTTAAACAAGAACACTGTTAGAGCAT 60.255 37.037 0.00 0.00 0.00 3.79
1473 1577 6.037830 GGTTAAACAAGAACACTGTTAGAGCA 59.962 38.462 0.00 0.00 0.00 4.26
1478 5801 7.612633 AGGAAAGGTTAAACAAGAACACTGTTA 59.387 33.333 0.00 0.00 0.00 2.41
1496 5819 2.511637 GGATGAGGGATTGAGGAAAGGT 59.488 50.000 0.00 0.00 0.00 3.50
1717 6060 4.977739 AGGGGATTGGATCAACAGAAGATA 59.022 41.667 0.00 0.00 0.00 1.98
1797 6478 2.973420 CCTAATGACGAGGCGGTTC 58.027 57.895 0.00 0.00 0.00 3.62
1803 6484 1.227674 GGCCTGCCTAATGACGAGG 60.228 63.158 0.00 0.00 37.12 4.63
1804 6485 1.826024 AGGCCTGCCTAATGACGAG 59.174 57.895 9.42 0.00 46.14 4.18
1805 6486 4.050313 AGGCCTGCCTAATGACGA 57.950 55.556 9.42 0.00 46.14 4.20
1814 6495 3.102090 GTAGGATTGAAGGCCTGCC 57.898 57.895 5.69 1.34 35.73 4.85
1815 6496 0.255890 TGGTAGGATTGAAGGCCTGC 59.744 55.000 5.69 4.07 35.73 4.85
1816 6497 2.092212 ACATGGTAGGATTGAAGGCCTG 60.092 50.000 5.69 0.00 35.73 4.85
1817 6498 2.092212 CACATGGTAGGATTGAAGGCCT 60.092 50.000 0.00 0.00 38.31 5.19
1818 6499 2.301346 CACATGGTAGGATTGAAGGCC 58.699 52.381 0.00 0.00 0.00 5.19
1819 6500 3.004752 ACACATGGTAGGATTGAAGGC 57.995 47.619 0.00 0.00 0.00 4.35
1820 6501 6.828273 TGATAAACACATGGTAGGATTGAAGG 59.172 38.462 0.00 0.00 0.00 3.46
1821 6502 7.554118 ACTGATAAACACATGGTAGGATTGAAG 59.446 37.037 0.00 0.00 0.00 3.02
1822 6503 7.402054 ACTGATAAACACATGGTAGGATTGAA 58.598 34.615 0.00 0.00 0.00 2.69
1823 6504 6.957631 ACTGATAAACACATGGTAGGATTGA 58.042 36.000 0.00 0.00 0.00 2.57
1824 6505 6.823182 TGACTGATAAACACATGGTAGGATTG 59.177 38.462 0.00 0.00 0.00 2.67
1825 6506 6.823689 GTGACTGATAAACACATGGTAGGATT 59.176 38.462 0.00 0.00 35.06 3.01
1826 6507 6.070251 TGTGACTGATAAACACATGGTAGGAT 60.070 38.462 0.00 0.00 39.17 3.24
1827 6508 5.247337 TGTGACTGATAAACACATGGTAGGA 59.753 40.000 0.00 0.00 39.17 2.94
1828 6509 5.487433 TGTGACTGATAAACACATGGTAGG 58.513 41.667 0.00 0.00 39.17 3.18
1835 6516 8.450578 AAGAAGAAATGTGACTGATAAACACA 57.549 30.769 0.00 0.00 46.04 3.72
1836 6517 8.778358 AGAAGAAGAAATGTGACTGATAAACAC 58.222 33.333 0.00 0.00 35.45 3.32
1837 6518 8.908786 AGAAGAAGAAATGTGACTGATAAACA 57.091 30.769 0.00 0.00 0.00 2.83
1838 6519 9.818796 GAAGAAGAAGAAATGTGACTGATAAAC 57.181 33.333 0.00 0.00 0.00 2.01
1839 6520 9.784531 AGAAGAAGAAGAAATGTGACTGATAAA 57.215 29.630 0.00 0.00 0.00 1.40
1840 6521 9.784531 AAGAAGAAGAAGAAATGTGACTGATAA 57.215 29.630 0.00 0.00 0.00 1.75
1842 6523 9.956640 ATAAGAAGAAGAAGAAATGTGACTGAT 57.043 29.630 0.00 0.00 0.00 2.90
1843 6524 9.429359 GATAAGAAGAAGAAGAAATGTGACTGA 57.571 33.333 0.00 0.00 0.00 3.41
1844 6525 8.663911 GGATAAGAAGAAGAAGAAATGTGACTG 58.336 37.037 0.00 0.00 0.00 3.51
1845 6526 8.378565 TGGATAAGAAGAAGAAGAAATGTGACT 58.621 33.333 0.00 0.00 0.00 3.41
1846 6527 8.553459 TGGATAAGAAGAAGAAGAAATGTGAC 57.447 34.615 0.00 0.00 0.00 3.67
1868 6549 9.392506 TGGAAGGAGTATTTGATAAGATATGGA 57.607 33.333 0.00 0.00 0.00 3.41
1904 6585 9.516546 TGTAGTCCGTATTGATATCTCACTTAT 57.483 33.333 3.98 0.00 0.00 1.73
1905 6586 8.913487 TGTAGTCCGTATTGATATCTCACTTA 57.087 34.615 3.98 0.00 0.00 2.24
1906 6587 7.818997 TGTAGTCCGTATTGATATCTCACTT 57.181 36.000 3.98 0.00 0.00 3.16
1907 6588 7.818997 TTGTAGTCCGTATTGATATCTCACT 57.181 36.000 3.98 0.00 0.00 3.41
1908 6589 7.113124 CGTTTGTAGTCCGTATTGATATCTCAC 59.887 40.741 3.98 0.00 0.00 3.51
1909 6590 7.136772 CGTTTGTAGTCCGTATTGATATCTCA 58.863 38.462 3.98 0.00 0.00 3.27
1910 6591 6.581542 CCGTTTGTAGTCCGTATTGATATCTC 59.418 42.308 3.98 0.00 0.00 2.75
1911 6592 6.263842 TCCGTTTGTAGTCCGTATTGATATCT 59.736 38.462 3.98 0.00 0.00 1.98
1912 6593 6.441274 TCCGTTTGTAGTCCGTATTGATATC 58.559 40.000 0.00 0.00 0.00 1.63
1913 6594 6.395426 TCCGTTTGTAGTCCGTATTGATAT 57.605 37.500 0.00 0.00 0.00 1.63
1914 6595 5.833406 TCCGTTTGTAGTCCGTATTGATA 57.167 39.130 0.00 0.00 0.00 2.15
1915 6596 4.724074 TCCGTTTGTAGTCCGTATTGAT 57.276 40.909 0.00 0.00 0.00 2.57
1916 6597 4.082081 ACATCCGTTTGTAGTCCGTATTGA 60.082 41.667 0.00 0.00 0.00 2.57
1917 6598 4.178540 ACATCCGTTTGTAGTCCGTATTG 58.821 43.478 0.00 0.00 0.00 1.90
1918 6599 4.460948 ACATCCGTTTGTAGTCCGTATT 57.539 40.909 0.00 0.00 0.00 1.89
1919 6600 5.779529 ATACATCCGTTTGTAGTCCGTAT 57.220 39.130 1.87 0.00 35.65 3.06
1920 6601 6.882610 ATATACATCCGTTTGTAGTCCGTA 57.117 37.500 1.87 0.00 35.65 4.02
1921 6602 5.779529 ATATACATCCGTTTGTAGTCCGT 57.220 39.130 1.87 0.00 35.65 4.69
1922 6603 8.453320 TGTATATATACATCCGTTTGTAGTCCG 58.547 37.037 19.51 0.00 38.28 4.79
1953 6634 9.944376 AGCAAAATGAGTAAATCTACACTCTAA 57.056 29.630 3.65 0.00 41.46 2.10
1954 6635 9.944376 AAGCAAAATGAGTAAATCTACACTCTA 57.056 29.630 3.65 0.00 41.46 2.43
1955 6636 8.854614 AAGCAAAATGAGTAAATCTACACTCT 57.145 30.769 3.65 0.00 41.46 3.24
1956 6637 7.900352 CGAAGCAAAATGAGTAAATCTACACTC 59.100 37.037 0.00 0.00 41.31 3.51
1957 6638 7.387948 ACGAAGCAAAATGAGTAAATCTACACT 59.612 33.333 0.00 0.00 0.00 3.55
1958 6639 7.519002 ACGAAGCAAAATGAGTAAATCTACAC 58.481 34.615 0.00 0.00 0.00 2.90
1959 6640 7.667043 ACGAAGCAAAATGAGTAAATCTACA 57.333 32.000 0.00 0.00 0.00 2.74
1960 6641 9.638300 CATACGAAGCAAAATGAGTAAATCTAC 57.362 33.333 0.00 0.00 0.00 2.59
1961 6642 9.378551 ACATACGAAGCAAAATGAGTAAATCTA 57.621 29.630 0.00 0.00 0.00 1.98
1962 6643 8.268850 ACATACGAAGCAAAATGAGTAAATCT 57.731 30.769 0.00 0.00 0.00 2.40
1963 6644 9.638300 CTACATACGAAGCAAAATGAGTAAATC 57.362 33.333 0.00 0.00 0.00 2.17
1964 6645 9.378551 TCTACATACGAAGCAAAATGAGTAAAT 57.621 29.630 0.00 0.00 0.00 1.40
1965 6646 8.766000 TCTACATACGAAGCAAAATGAGTAAA 57.234 30.769 0.00 0.00 0.00 2.01
1966 6647 8.942338 ATCTACATACGAAGCAAAATGAGTAA 57.058 30.769 0.00 0.00 0.00 2.24
1967 6648 8.942338 AATCTACATACGAAGCAAAATGAGTA 57.058 30.769 0.00 0.00 0.00 2.59
1968 6649 7.849804 AATCTACATACGAAGCAAAATGAGT 57.150 32.000 0.00 0.00 0.00 3.41
1969 6650 9.638300 GTAAATCTACATACGAAGCAAAATGAG 57.362 33.333 0.00 0.00 0.00 2.90
1970 6651 9.378551 AGTAAATCTACATACGAAGCAAAATGA 57.621 29.630 0.00 0.00 0.00 2.57
1971 6652 9.638300 GAGTAAATCTACATACGAAGCAAAATG 57.362 33.333 0.00 0.00 0.00 2.32
1972 6653 9.378551 TGAGTAAATCTACATACGAAGCAAAAT 57.621 29.630 0.00 0.00 0.00 1.82
1973 6654 8.766000 TGAGTAAATCTACATACGAAGCAAAA 57.234 30.769 0.00 0.00 0.00 2.44
1974 6655 8.942338 ATGAGTAAATCTACATACGAAGCAAA 57.058 30.769 0.00 0.00 0.00 3.68
1975 6656 8.942338 AATGAGTAAATCTACATACGAAGCAA 57.058 30.769 0.00 0.00 0.00 3.91
1976 6657 8.942338 AAATGAGTAAATCTACATACGAAGCA 57.058 30.769 0.00 0.00 0.00 3.91
1977 6658 9.638300 CAAAATGAGTAAATCTACATACGAAGC 57.362 33.333 0.00 0.00 0.00 3.86
1978 6659 9.638300 GCAAAATGAGTAAATCTACATACGAAG 57.362 33.333 0.00 0.00 0.00 3.79
1979 6660 9.378551 AGCAAAATGAGTAAATCTACATACGAA 57.621 29.630 0.00 0.00 0.00 3.85
1980 6661 8.942338 AGCAAAATGAGTAAATCTACATACGA 57.058 30.769 0.00 0.00 0.00 3.43
1981 6662 8.276325 GGAGCAAAATGAGTAAATCTACATACG 58.724 37.037 0.00 0.00 0.00 3.06
1982 6663 8.276325 CGGAGCAAAATGAGTAAATCTACATAC 58.724 37.037 0.00 0.00 0.00 2.39
1983 6664 7.985184 ACGGAGCAAAATGAGTAAATCTACATA 59.015 33.333 0.00 0.00 0.00 2.29
1984 6665 6.823689 ACGGAGCAAAATGAGTAAATCTACAT 59.176 34.615 0.00 0.00 0.00 2.29
1985 6666 6.170506 ACGGAGCAAAATGAGTAAATCTACA 58.829 36.000 0.00 0.00 0.00 2.74
1986 6667 6.663944 ACGGAGCAAAATGAGTAAATCTAC 57.336 37.500 0.00 0.00 0.00 2.59
1987 6668 7.985184 ACATACGGAGCAAAATGAGTAAATCTA 59.015 33.333 0.00 0.00 0.00 1.98
1988 6669 6.823689 ACATACGGAGCAAAATGAGTAAATCT 59.176 34.615 0.00 0.00 0.00 2.40
1989 6670 7.016361 ACATACGGAGCAAAATGAGTAAATC 57.984 36.000 0.00 0.00 0.00 2.17
1990 6671 7.769044 ACTACATACGGAGCAAAATGAGTAAAT 59.231 33.333 0.00 0.00 0.00 1.40
1991 6672 7.101054 ACTACATACGGAGCAAAATGAGTAAA 58.899 34.615 0.00 0.00 0.00 2.01
1992 6673 6.636705 ACTACATACGGAGCAAAATGAGTAA 58.363 36.000 0.00 0.00 0.00 2.24
1993 6674 6.216801 ACTACATACGGAGCAAAATGAGTA 57.783 37.500 0.00 0.00 0.00 2.59
1994 6675 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1995 6676 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
1996 6677 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
1997 6678 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
1998 6679 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
1999 6680 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
2000 6681 5.801531 ATATGGACTACATACGGAGCAAA 57.198 39.130 0.00 0.00 44.41 3.68
2001 6682 5.801531 AATATGGACTACATACGGAGCAA 57.198 39.130 0.00 0.00 44.41 3.91
2002 6683 5.801531 AAATATGGACTACATACGGAGCA 57.198 39.130 0.00 0.00 44.41 4.26
2003 6684 7.600065 TCTAAAATATGGACTACATACGGAGC 58.400 38.462 0.00 0.00 44.41 4.70
2004 6685 9.011095 TCTCTAAAATATGGACTACATACGGAG 57.989 37.037 0.00 0.00 44.41 4.63
2005 6686 8.929260 TCTCTAAAATATGGACTACATACGGA 57.071 34.615 0.00 0.00 44.41 4.69
2006 6687 8.794553 ACTCTCTAAAATATGGACTACATACGG 58.205 37.037 0.00 0.00 44.41 4.02
2014 6695 8.928448 TGCTATGAACTCTCTAAAATATGGACT 58.072 33.333 0.00 0.00 0.00 3.85
2015 6696 9.202273 CTGCTATGAACTCTCTAAAATATGGAC 57.798 37.037 0.00 0.00 0.00 4.02
2016 6697 9.147732 TCTGCTATGAACTCTCTAAAATATGGA 57.852 33.333 0.00 0.00 0.00 3.41
2017 6698 9.421806 CTCTGCTATGAACTCTCTAAAATATGG 57.578 37.037 0.00 0.00 0.00 2.74
2018 6699 8.924691 GCTCTGCTATGAACTCTCTAAAATATG 58.075 37.037 0.00 0.00 0.00 1.78
2019 6700 8.646004 TGCTCTGCTATGAACTCTCTAAAATAT 58.354 33.333 0.00 0.00 0.00 1.28
2020 6701 8.011844 TGCTCTGCTATGAACTCTCTAAAATA 57.988 34.615 0.00 0.00 0.00 1.40
2021 6702 6.882656 TGCTCTGCTATGAACTCTCTAAAAT 58.117 36.000 0.00 0.00 0.00 1.82
2022 6703 6.071108 ACTGCTCTGCTATGAACTCTCTAAAA 60.071 38.462 0.00 0.00 0.00 1.52
2023 6704 5.420421 ACTGCTCTGCTATGAACTCTCTAAA 59.580 40.000 0.00 0.00 0.00 1.85
2024 6705 4.952957 ACTGCTCTGCTATGAACTCTCTAA 59.047 41.667 0.00 0.00 0.00 2.10
2025 6706 4.531854 ACTGCTCTGCTATGAACTCTCTA 58.468 43.478 0.00 0.00 0.00 2.43
2026 6707 3.364549 ACTGCTCTGCTATGAACTCTCT 58.635 45.455 0.00 0.00 0.00 3.10
2027 6708 3.490761 GGACTGCTCTGCTATGAACTCTC 60.491 52.174 0.00 0.00 0.00 3.20
2028 6709 2.430332 GGACTGCTCTGCTATGAACTCT 59.570 50.000 0.00 0.00 0.00 3.24
2029 6710 2.482839 GGGACTGCTCTGCTATGAACTC 60.483 54.545 0.00 0.00 0.00 3.01
2030 6711 1.484240 GGGACTGCTCTGCTATGAACT 59.516 52.381 0.00 0.00 0.00 3.01
2031 6712 1.208052 TGGGACTGCTCTGCTATGAAC 59.792 52.381 0.00 0.00 0.00 3.18
2032 6713 1.208052 GTGGGACTGCTCTGCTATGAA 59.792 52.381 0.00 0.00 0.00 2.57
2033 6714 0.826715 GTGGGACTGCTCTGCTATGA 59.173 55.000 0.00 0.00 0.00 2.15
2034 6715 0.829333 AGTGGGACTGCTCTGCTATG 59.171 55.000 0.00 0.00 0.00 2.23
2035 6716 0.829333 CAGTGGGACTGCTCTGCTAT 59.171 55.000 0.00 0.00 39.62 2.97
2036 6717 0.251787 TCAGTGGGACTGCTCTGCTA 60.252 55.000 0.00 0.00 45.54 3.49
2037 6718 1.123861 TTCAGTGGGACTGCTCTGCT 61.124 55.000 0.00 0.00 45.54 4.24
2038 6719 0.952984 GTTCAGTGGGACTGCTCTGC 60.953 60.000 0.00 0.00 45.54 4.26
2039 6720 0.321122 GGTTCAGTGGGACTGCTCTG 60.321 60.000 0.00 0.00 45.54 3.35
2040 6721 1.484444 GGGTTCAGTGGGACTGCTCT 61.484 60.000 0.00 0.00 45.54 4.09
2041 6722 1.003233 GGGTTCAGTGGGACTGCTC 60.003 63.158 0.00 0.00 45.54 4.26
2042 6723 1.462238 AGGGTTCAGTGGGACTGCT 60.462 57.895 0.00 0.00 45.54 4.24
2043 6724 1.003233 GAGGGTTCAGTGGGACTGC 60.003 63.158 0.00 0.00 45.54 4.40
2045 6726 1.700186 GAAAGAGGGTTCAGTGGGACT 59.300 52.381 0.00 0.00 0.00 3.85
2046 6727 1.700186 AGAAAGAGGGTTCAGTGGGAC 59.300 52.381 0.00 0.00 0.00 4.46
2047 6728 2.118403 AGAAAGAGGGTTCAGTGGGA 57.882 50.000 0.00 0.00 0.00 4.37
2048 6729 2.373502 AGAAGAAAGAGGGTTCAGTGGG 59.626 50.000 0.00 0.00 0.00 4.61
2049 6730 3.406764 CAGAAGAAAGAGGGTTCAGTGG 58.593 50.000 0.00 0.00 0.00 4.00
2050 6731 2.810852 GCAGAAGAAAGAGGGTTCAGTG 59.189 50.000 0.00 0.00 0.00 3.66
2051 6732 2.224646 GGCAGAAGAAAGAGGGTTCAGT 60.225 50.000 0.00 0.00 0.00 3.41
2052 6733 2.039613 AGGCAGAAGAAAGAGGGTTCAG 59.960 50.000 0.00 0.00 0.00 3.02
2053 6734 2.057922 AGGCAGAAGAAAGAGGGTTCA 58.942 47.619 0.00 0.00 0.00 3.18
4991 11736 6.708054 CCAGATGTATTCCTTACACTTCATCC 59.292 42.308 0.00 0.00 43.46 3.51
5112 11860 6.482973 CAGCATTTAAATGGTTCCACAACTTT 59.517 34.615 26.13 0.00 44.02 2.66
5118 11866 5.391312 ACTCAGCATTTAAATGGTTCCAC 57.609 39.130 26.13 10.75 44.02 4.02
5135 11883 3.062763 ACTTCGCACTTGATGAACTCAG 58.937 45.455 0.00 0.00 34.68 3.35
5147 11895 2.027745 ACCATCATTCAGACTTCGCACT 60.028 45.455 0.00 0.00 0.00 4.40
5151 11899 5.063944 CCAACTTACCATCATTCAGACTTCG 59.936 44.000 0.00 0.00 0.00 3.79
5168 11916 5.818678 TCTTGTCCTAAGAAGCCAACTTA 57.181 39.130 0.00 0.00 35.82 2.24
5255 12010 4.495019 CGAAATCACCAACACGTCTTTCAA 60.495 41.667 0.00 0.00 0.00 2.69
5270 12025 7.241376 CAGGGTTACAACTATTTCGAAATCAC 58.759 38.462 25.89 10.88 0.00 3.06
5431 12204 9.374838 ATTCATTTGAAAGAATGTAATTCCAGC 57.625 29.630 0.00 0.00 44.02 4.85
5580 12354 4.072131 TGAGCATCAGTGGGTAACTTTTC 58.928 43.478 0.00 0.00 42.56 2.29
5596 12370 2.547430 CGAGCATCCATGTACTGAGCAT 60.547 50.000 0.00 0.00 0.00 3.79
5644 12793 8.967664 ACAAATTAACCGCAATATAACTAGGA 57.032 30.769 0.00 0.00 0.00 2.94
5958 13124 4.277476 TGTTCAAACACACTCCATCCTTT 58.723 39.130 0.00 0.00 33.17 3.11
5959 13125 3.897239 TGTTCAAACACACTCCATCCTT 58.103 40.909 0.00 0.00 33.17 3.36
6058 14545 0.801251 GCTGCCGCAATCCATAGATC 59.199 55.000 0.00 0.00 35.78 2.75
6069 14556 4.075854 TACATCACCGCTGCCGCA 62.076 61.111 0.00 0.00 35.30 5.69
6074 14561 0.095245 CGCAAACTACATCACCGCTG 59.905 55.000 0.00 0.00 0.00 5.18
6106 14593 0.473755 TGAACAGAGGAAAGCCAGCA 59.526 50.000 0.00 0.00 36.29 4.41
6117 14604 7.410942 GCTCTAACGAACTTATGTTGAACAGAG 60.411 40.741 3.74 7.02 36.39 3.35
6201 14688 3.066064 CGACAGATCCAGTCTACTGAAGG 59.934 52.174 11.69 0.00 46.59 3.46
6265 14752 1.424302 AGGATCAGGATCATTGGCTGG 59.576 52.381 11.12 0.00 39.54 4.85
6271 14758 6.012771 TGAAGCATATCAGGATCAGGATCATT 60.013 38.462 11.12 0.00 39.54 2.57
6363 14850 2.890109 CGCAGCATCTGAATCGGCC 61.890 63.158 0.00 0.00 32.44 6.13


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

AutoCloner maintained by Alex Coulton.