Multiple sequence alignment - TraesCS5D01G389900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G389900 chr5D 100.000 8765 0 0 1 8765 458876005 458867241 0.000000e+00 16187.0
1 TraesCS5D01G389900 chr5D 87.232 2099 239 22 5894 7980 492610109 492608028 0.000000e+00 2364.0
2 TraesCS5D01G389900 chr5D 92.189 1485 87 18 1944 3403 258349514 258348034 0.000000e+00 2073.0
3 TraesCS5D01G389900 chr5D 91.711 1496 79 23 1944 3401 279257556 279259044 0.000000e+00 2034.0
4 TraesCS5D01G389900 chr5D 90.312 1507 91 23 1944 3402 532663608 532662109 0.000000e+00 1923.0
5 TraesCS5D01G389900 chr5D 90.139 1511 90 39 1943 3403 69115873 69117374 0.000000e+00 1910.0
6 TraesCS5D01G389900 chr5D 91.410 1234 71 14 1944 3144 305741388 305742619 0.000000e+00 1659.0
7 TraesCS5D01G389900 chr5D 93.484 1059 32 11 917 1946 458871163 458870113 0.000000e+00 1539.0
8 TraesCS5D01G389900 chr5D 93.484 1059 32 11 4843 5893 458875089 458874060 0.000000e+00 1539.0
9 TraesCS5D01G389900 chr5D 76.800 1375 268 35 5955 7312 492569433 492568093 0.000000e+00 725.0
10 TraesCS5D01G389900 chr5D 76.415 1378 258 45 5955 7312 238177266 238178596 0.000000e+00 682.0
11 TraesCS5D01G389900 chr5D 80.533 375 66 5 7406 7775 238178650 238179022 1.860000e-71 281.0
12 TraesCS5D01G389900 chr5D 88.514 148 14 1 8618 8765 458898034 458897890 9.040000e-40 176.0
13 TraesCS5D01G389900 chr5D 87.582 153 18 1 5724 5875 506214189 506214341 9.040000e-40 176.0
14 TraesCS5D01G389900 chr5D 86.275 153 19 2 1778 1928 506214189 506214341 1.960000e-36 165.0
15 TraesCS5D01G389900 chr5D 77.667 300 33 23 4869 5141 492612098 492611806 1.520000e-32 152.0
16 TraesCS5D01G389900 chr5D 79.268 246 27 16 975 1199 492612048 492611806 5.480000e-32 150.0
17 TraesCS5D01G389900 chr5D 80.899 178 24 8 1588 1755 492611695 492611518 1.990000e-26 132.0
18 TraesCS5D01G389900 chr5D 79.096 177 16 9 1332 1500 560280979 560280816 1.560000e-17 102.0
19 TraesCS5D01G389900 chr5D 91.045 67 3 2 1717 1780 535865379 535865445 4.360000e-13 87.9
20 TraesCS5D01G389900 chr5D 91.667 60 3 2 1722 1781 535485338 535485395 2.030000e-11 82.4
21 TraesCS5D01G389900 chr5A 96.823 2959 77 6 4827 7778 577932041 577929093 0.000000e+00 4927.0
22 TraesCS5D01G389900 chr5A 87.534 1484 150 31 1944 3403 215549580 215551052 0.000000e+00 1683.0
23 TraesCS5D01G389900 chr5A 93.377 1057 35 11 917 1946 577932025 577930977 0.000000e+00 1531.0
24 TraesCS5D01G389900 chr5A 85.953 1374 163 22 6608 7966 615291643 615293001 0.000000e+00 1441.0
25 TraesCS5D01G389900 chr5A 88.412 1165 102 23 1944 3083 552935382 552934226 0.000000e+00 1373.0
26 TraesCS5D01G389900 chr5A 76.558 1348 271 32 5979 7312 615304998 615306314 0.000000e+00 697.0
27 TraesCS5D01G389900 chr5A 76.333 1369 276 33 5960 7312 316514263 316512927 0.000000e+00 689.0
28 TraesCS5D01G389900 chr5A 86.818 440 57 1 6163 6602 615291094 615291532 2.840000e-134 490.0
29 TraesCS5D01G389900 chr5A 91.003 289 7 7 7782 8052 577928973 577928686 1.070000e-98 372.0
30 TraesCS5D01G389900 chr5A 87.859 313 21 6 8279 8577 577926533 577926224 1.400000e-92 351.0
31 TraesCS5D01G389900 chr5A 89.873 158 11 3 8611 8765 577932741 577932586 1.930000e-46 198.0
32 TraesCS5D01G389900 chr5A 92.593 135 2 4 7925 8052 577928633 577928500 4.180000e-43 187.0
33 TraesCS5D01G389900 chr5A 87.500 152 16 2 5737 5885 691036084 691035933 1.170000e-38 172.0
34 TraesCS5D01G389900 chr5A 84.211 171 15 5 1332 1492 345670727 345670559 1.180000e-33 156.0
35 TraesCS5D01G389900 chr5A 82.418 182 22 3 1332 1504 10831254 10831074 5.480000e-32 150.0
36 TraesCS5D01G389900 chr5A 84.516 155 12 4 5294 5438 345670711 345670559 9.170000e-30 143.0
37 TraesCS5D01G389900 chr5A 83.871 155 13 4 5294 5438 572302599 572302751 4.270000e-28 137.0
38 TraesCS5D01G389900 chr5A 80.800 125 24 0 8197 8321 195121250 195121374 2.010000e-16 99.0
39 TraesCS5D01G389900 chr5A 95.238 42 2 0 8573 8614 577926214 577926173 5.680000e-07 67.6
40 TraesCS5D01G389900 chr5A 100.000 35 0 0 8135 8169 457568362 457568396 2.040000e-06 65.8
41 TraesCS5D01G389900 chr5B 96.773 1921 60 2 5862 7781 562793717 562791798 0.000000e+00 3203.0
42 TraesCS5D01G389900 chr5B 94.236 798 36 5 918 1706 562795001 562794205 0.000000e+00 1210.0
43 TraesCS5D01G389900 chr5B 92.934 835 28 8 4828 5652 562795018 562794205 0.000000e+00 1186.0
44 TraesCS5D01G389900 chr5B 76.462 1368 275 32 5960 7312 267301749 267300414 0.000000e+00 699.0
45 TraesCS5D01G389900 chr5B 76.488 1378 263 38 5955 7312 607866516 607867852 0.000000e+00 693.0
46 TraesCS5D01G389900 chr5B 91.304 276 9 8 7872 8141 562762851 562762585 6.470000e-96 363.0
47 TraesCS5D01G389900 chr5B 83.041 171 17 5 1332 1492 133703201 133703369 2.550000e-30 145.0
48 TraesCS5D01G389900 chr5B 83.226 155 14 4 5294 5438 133703217 133703369 1.990000e-26 132.0
49 TraesCS5D01G389900 chr5B 93.258 89 4 1 7782 7870 562791679 562791593 7.140000e-26 130.0
50 TraesCS5D01G389900 chr5B 84.071 113 12 5 5294 5406 4829189 4829083 4.330000e-18 104.0
51 TraesCS5D01G389900 chr5B 91.803 61 5 0 5663 5723 118961371 118961311 1.570000e-12 86.1
52 TraesCS5D01G389900 chr5B 78.571 126 27 0 8195 8320 178112322 178112197 5.640000e-12 84.2
53 TraesCS5D01G389900 chr5B 90.164 61 6 0 1717 1777 118961371 118961311 7.290000e-11 80.5
54 TraesCS5D01G389900 chr2D 91.896 1493 81 21 1944 3403 275913671 275915156 0.000000e+00 2050.0
55 TraesCS5D01G389900 chr2D 88.212 1493 142 27 1944 3411 603224142 603222659 0.000000e+00 1751.0
56 TraesCS5D01G389900 chr2D 95.974 919 23 3 1 917 431015485 431016391 0.000000e+00 1480.0
57 TraesCS5D01G389900 chr2D 91.814 452 27 5 4386 4828 617904713 617905163 9.660000e-174 621.0
58 TraesCS5D01G389900 chr2D 91.083 157 8 3 764 917 9946974 9947127 3.210000e-49 207.0
59 TraesCS5D01G389900 chr2D 90.123 162 11 4 5724 5883 594538856 594538698 1.150000e-48 206.0
60 TraesCS5D01G389900 chr2D 88.889 162 12 5 1778 1936 594538856 594538698 2.500000e-45 195.0
61 TraesCS5D01G389900 chr2D 77.841 176 33 3 4207 4377 318406960 318406786 4.330000e-18 104.0
62 TraesCS5D01G389900 chr2D 91.525 59 3 1 1436 1492 19941634 19941692 7.290000e-11 80.5
63 TraesCS5D01G389900 chr2D 86.765 68 6 3 5664 5728 469167781 469167714 1.220000e-08 73.1
64 TraesCS5D01G389900 chr3A 91.284 1480 92 19 1951 3401 42111353 42112824 0.000000e+00 1984.0
65 TraesCS5D01G389900 chr3A 91.161 1482 91 20 1951 3401 42151206 42152678 0.000000e+00 1975.0
66 TraesCS5D01G389900 chr3A 85.210 453 63 4 4377 4826 696016264 696015813 6.200000e-126 462.0
67 TraesCS5D01G389900 chr3A 89.865 148 12 3 1783 1928 745072572 745072426 4.180000e-43 187.0
68 TraesCS5D01G389900 chr3A 89.189 148 13 3 1783 1928 744995479 744995333 1.940000e-41 182.0
69 TraesCS5D01G389900 chr3A 90.226 133 12 1 8633 8764 20226472 20226604 1.170000e-38 172.0
70 TraesCS5D01G389900 chr4A 88.618 1476 135 26 1944 3403 177445703 177447161 0.000000e+00 1764.0
71 TraesCS5D01G389900 chr3D 88.326 1499 122 39 1943 3401 187992041 187993526 0.000000e+00 1749.0
72 TraesCS5D01G389900 chr3D 95.509 757 13 3 1 742 547237710 547236960 0.000000e+00 1190.0
73 TraesCS5D01G389900 chr3D 91.868 455 30 6 4384 4834 595077456 595077005 5.780000e-176 628.0
74 TraesCS5D01G389900 chr3D 89.542 153 15 1 5724 5875 120289847 120289999 8.980000e-45 193.0
75 TraesCS5D01G389900 chr3D 87.952 166 11 6 5725 5882 410990665 410990829 4.180000e-43 187.0
76 TraesCS5D01G389900 chr3D 88.235 153 16 2 1778 1928 120289847 120289999 1.940000e-41 182.0
77 TraesCS5D01G389900 chr3D 87.421 159 11 6 5725 5875 610359232 610359389 3.250000e-39 174.0
78 TraesCS5D01G389900 chr3D 86.145 166 13 6 1779 1935 410990665 410990829 4.210000e-38 171.0
79 TraesCS5D01G389900 chr3D 85.535 159 13 6 1779 1928 610359232 610359389 3.280000e-34 158.0
80 TraesCS5D01G389900 chr3D 81.757 148 18 2 5299 5438 4159162 4159016 2.000000e-21 115.0
81 TraesCS5D01G389900 chr3D 78.344 157 21 5 1358 1505 16141082 16141234 1.210000e-13 89.8
82 TraesCS5D01G389900 chr3D 92.063 63 5 0 5666 5728 524219788 524219726 1.210000e-13 89.8
83 TraesCS5D01G389900 chr3D 92.982 57 4 0 1720 1776 524219788 524219732 5.640000e-12 84.2
84 TraesCS5D01G389900 chr3D 93.878 49 3 0 5658 5706 187851381 187851333 3.390000e-09 75.0
85 TraesCS5D01G389900 chr3D 93.878 49 2 1 5659 5706 27936563 27936611 1.220000e-08 73.1
86 TraesCS5D01G389900 chr3D 91.837 49 3 1 1713 1760 27936563 27936611 5.680000e-07 67.6
87 TraesCS5D01G389900 chr3D 91.667 48 4 0 1713 1760 613837997 613838044 5.680000e-07 67.6
88 TraesCS5D01G389900 chr3D 97.222 36 1 0 5407 5442 582027060 582027025 2.640000e-05 62.1
89 TraesCS5D01G389900 chr6D 98.255 917 14 1 1 917 60326913 60325999 0.000000e+00 1604.0
90 TraesCS5D01G389900 chr6D 96.187 918 15 7 1 917 1927455 1928353 0.000000e+00 1483.0
91 TraesCS5D01G389900 chr6D 87.975 158 11 3 5726 5875 211672604 211672761 6.990000e-41 180.0
92 TraesCS5D01G389900 chr6D 80.870 230 18 6 5666 5882 145462671 145462455 3.280000e-34 158.0
93 TraesCS5D01G389900 chr6D 85.030 167 11 7 5726 5880 178849199 178849363 3.280000e-34 158.0
94 TraesCS5D01G389900 chr6D 85.185 162 11 7 5726 5875 21051971 21052131 4.240000e-33 154.0
95 TraesCS5D01G389900 chr6D 93.137 102 7 0 5723 5824 8807037 8807138 5.480000e-32 150.0
96 TraesCS5D01G389900 chr6D 92.157 102 8 0 5723 5824 141446539 141446438 2.550000e-30 145.0
97 TraesCS5D01G389900 chr6D 82.659 173 20 3 1332 1495 470110505 470110676 2.550000e-30 145.0
98 TraesCS5D01G389900 chr6D 90.826 109 7 3 1779 1884 312249503 312249611 9.170000e-30 143.0
99 TraesCS5D01G389900 chr6D 82.941 170 11 8 1778 1930 161556341 161556509 4.270000e-28 137.0
100 TraesCS5D01G389900 chr6D 83.117 154 18 2 5294 5439 148056371 148056218 5.520000e-27 134.0
101 TraesCS5D01G389900 chr6D 83.871 155 6 7 1791 1928 120034050 120034202 7.140000e-26 130.0
102 TraesCS5D01G389900 chr6D 83.824 136 20 2 5726 5861 351111664 351111797 2.570000e-25 128.0
103 TraesCS5D01G389900 chr6D 86.842 114 7 3 1779 1884 58504162 58504049 4.300000e-23 121.0
104 TraesCS5D01G389900 chr6D 80.986 142 23 4 1352 1492 27459943 27459805 9.300000e-20 110.0
105 TraesCS5D01G389900 chr6D 94.366 71 3 1 5664 5733 86643302 86643232 3.350000e-19 108.0
106 TraesCS5D01G389900 chr6D 78.453 181 27 7 1334 1504 451017826 451017648 3.350000e-19 108.0
107 TraesCS5D01G389900 chr6D 93.750 64 4 0 1718 1781 86643302 86643239 7.240000e-16 97.1
108 TraesCS5D01G389900 chr6D 94.643 56 3 0 1873 1928 289353114 289353059 4.360000e-13 87.9
109 TraesCS5D01G389900 chr6D 94.737 57 2 1 1873 1928 373362776 373362720 4.360000e-13 87.9
110 TraesCS5D01G389900 chr6D 77.439 164 24 9 1779 1929 90112237 90112400 1.570000e-12 86.1
111 TraesCS5D01G389900 chr6D 93.103 58 4 0 1873 1930 145462569 145462626 1.570000e-12 86.1
112 TraesCS5D01G389900 chr6D 91.803 61 4 1 1828 1887 437232792 437232852 5.640000e-12 84.2
113 TraesCS5D01G389900 chr6D 92.857 56 4 0 5820 5875 289353114 289353059 2.030000e-11 82.4
114 TraesCS5D01G389900 chr6D 91.667 60 4 1 1873 1931 361524580 361524521 2.030000e-11 82.4
115 TraesCS5D01G389900 chr6D 92.982 57 3 1 5820 5875 373362776 373362720 2.030000e-11 82.4
116 TraesCS5D01G389900 chr6D 83.696 92 5 4 1417 1500 126879027 126878938 2.620000e-10 78.7
117 TraesCS5D01G389900 chr6D 87.324 71 1 1 1434 1496 354357777 354357707 3.390000e-09 75.0
118 TraesCS5D01G389900 chr6D 81.443 97 10 4 5351 5439 445025630 445025534 1.220000e-08 73.1
119 TraesCS5D01G389900 chr6D 95.455 44 2 0 5663 5706 26757861 26757904 4.390000e-08 71.3
120 TraesCS5D01G389900 chr6D 97.561 41 1 0 5666 5706 115051871 115051911 4.390000e-08 71.3
121 TraesCS5D01G389900 chr6D 97.436 39 1 0 1832 1870 125607232 125607194 5.680000e-07 67.6
122 TraesCS5D01G389900 chr6D 93.182 44 3 0 1717 1760 26757861 26757904 2.040000e-06 65.8
123 TraesCS5D01G389900 chr6D 93.182 44 3 0 5663 5706 400060100 400060143 2.040000e-06 65.8
124 TraesCS5D01G389900 chr6D 93.182 44 2 1 1713 1755 29231673 29231716 7.350000e-06 63.9
125 TraesCS5D01G389900 chr6D 95.122 41 1 1 1461 1501 318075973 318075934 7.350000e-06 63.9
126 TraesCS5D01G389900 chr6D 88.000 50 6 0 5657 5706 2784320 2784271 9.500000e-05 60.2
127 TraesCS5D01G389900 chr6D 90.909 44 4 0 1717 1760 400060100 400060143 9.500000e-05 60.2
128 TraesCS5D01G389900 chr6D 97.059 34 1 0 1712 1745 8804332 8804365 3.420000e-04 58.4
129 TraesCS5D01G389900 chr6D 97.059 34 1 0 5658 5691 8804332 8804365 3.420000e-04 58.4
130 TraesCS5D01G389900 chr6D 97.143 35 0 1 5659 5692 29231673 29231707 3.420000e-04 58.4
131 TraesCS5D01G389900 chr6D 100.000 31 0 0 1783 1813 39318413 39318383 3.420000e-04 58.4
132 TraesCS5D01G389900 chr6D 86.000 50 7 0 1711 1760 2784320 2784271 4.000000e-03 54.7
133 TraesCS5D01G389900 chr1D 96.292 917 17 6 1 917 70141388 70142287 0.000000e+00 1489.0
134 TraesCS5D01G389900 chr1D 89.325 459 40 4 4384 4833 94057109 94056651 1.280000e-157 568.0
135 TraesCS5D01G389900 chr1D 90.453 419 21 12 1944 2350 5416893 5417304 1.300000e-147 534.0
136 TraesCS5D01G389900 chr1D 87.117 163 9 6 5725 5875 463381904 463382066 3.250000e-39 174.0
137 TraesCS5D01G389900 chr1D 86.420 162 10 3 5726 5875 332997336 332997175 5.440000e-37 167.0
138 TraesCS5D01G389900 chr1D 86.275 153 19 2 5725 5875 81372417 81372569 1.960000e-36 165.0
139 TraesCS5D01G389900 chr1D 86.275 153 18 3 1779 1928 81372417 81372569 7.040000e-36 163.0
140 TraesCS5D01G389900 chr1D 85.000 160 18 5 5722 5876 165201215 165201373 3.280000e-34 158.0
141 TraesCS5D01G389900 chr1D 84.118 170 20 6 1334 1497 338694173 338694005 3.280000e-34 158.0
142 TraesCS5D01G389900 chr1D 86.164 159 6 6 1783 1928 451226897 451226742 3.280000e-34 158.0
143 TraesCS5D01G389900 chr1D 86.614 127 15 2 5719 5844 323952254 323952129 1.190000e-28 139.0
144 TraesCS5D01G389900 chr1D 83.333 162 14 3 5726 5875 137636015 137636175 4.270000e-28 137.0
145 TraesCS5D01G389900 chr1D 81.111 180 22 5 1332 1501 487869824 487869647 5.520000e-27 134.0
146 TraesCS5D01G389900 chr1D 80.663 181 26 2 1332 1504 468861624 468861445 1.990000e-26 132.0
147 TraesCS5D01G389900 chr1D 81.928 166 18 2 5726 5879 466120174 466120009 7.140000e-26 130.0
148 TraesCS5D01G389900 chr1D 80.435 184 22 9 1332 1506 107614850 107614672 2.570000e-25 128.0
149 TraesCS5D01G389900 chr1D 81.481 162 16 3 1780 1928 137636015 137636175 4.300000e-23 121.0
150 TraesCS5D01G389900 chr1D 88.235 102 9 3 1779 1878 32710920 32711020 1.550000e-22 119.0
151 TraesCS5D01G389900 chr1D 80.982 163 18 7 1783 1932 466120171 466120009 5.560000e-22 117.0
152 TraesCS5D01G389900 chr1D 80.625 160 22 2 1778 1928 398223591 398223750 2.000000e-21 115.0
153 TraesCS5D01G389900 chr1D 83.962 106 12 4 1778 1878 405521892 405521997 7.240000e-16 97.1
154 TraesCS5D01G389900 chr1D 78.313 166 22 7 1777 1928 298744106 298743941 2.610000e-15 95.3
155 TraesCS5D01G389900 chr1D 82.203 118 8 4 1825 1930 451032930 451033046 1.210000e-13 89.8
156 TraesCS5D01G389900 chr1D 80.702 114 19 3 5295 5406 237334438 237334326 1.570000e-12 86.1
157 TraesCS5D01G389900 chr1D 92.982 57 4 0 1873 1929 20974297 20974353 5.640000e-12 84.2
158 TraesCS5D01G389900 chr1D 91.667 60 4 1 1873 1931 286391175 286391234 2.030000e-11 82.4
159 TraesCS5D01G389900 chr1D 89.394 66 5 2 5663 5727 317590249 317590313 2.030000e-11 82.4
160 TraesCS5D01G389900 chr1D 97.826 46 1 0 4156 4201 126610033 126609988 7.290000e-11 80.5
161 TraesCS5D01G389900 chr1D 93.878 49 1 2 1714 1760 24026174 24026126 1.220000e-08 73.1
162 TraesCS5D01G389900 chr1D 93.878 49 2 1 5658 5706 59868035 59867988 1.220000e-08 73.1
163 TraesCS5D01G389900 chr1D 92.308 52 3 1 1709 1760 347215401 347215351 1.220000e-08 73.1
164 TraesCS5D01G389900 chr1D 95.455 44 2 0 5663 5706 356862307 356862350 4.390000e-08 71.3
165 TraesCS5D01G389900 chr1D 100.000 37 0 0 1723 1759 480361292 480361328 1.580000e-07 69.4
166 TraesCS5D01G389900 chr1D 91.837 49 3 1 1712 1760 59868035 59867988 5.680000e-07 67.6
167 TraesCS5D01G389900 chr1D 90.385 52 3 2 5655 5705 307349145 307349195 5.680000e-07 67.6
168 TraesCS5D01G389900 chr1D 90.385 52 4 1 5655 5706 347215401 347215351 5.680000e-07 67.6
169 TraesCS5D01G389900 chr1D 88.462 52 4 2 1709 1759 307349145 307349195 2.640000e-05 62.1
170 TraesCS5D01G389900 chr7D 94.680 921 30 5 1 917 120720916 120721821 0.000000e+00 1411.0
171 TraesCS5D01G389900 chr7D 92.232 914 31 13 1 881 175776549 175775643 0.000000e+00 1258.0
172 TraesCS5D01G389900 chr7D 85.393 89 7 6 5650 5733 185137980 185138067 4.360000e-13 87.9
173 TraesCS5D01G389900 chr7D 100.000 45 0 0 5662 5706 448338304 448338260 5.640000e-12 84.2
174 TraesCS5D01G389900 chr7D 90.196 51 2 3 1461 1508 428034888 428034838 7.350000e-06 63.9
175 TraesCS5D01G389900 chr4D 91.895 950 35 15 1 917 20319203 20318263 0.000000e+00 1290.0
176 TraesCS5D01G389900 chr4D 91.158 950 37 15 1 917 143338999 143339934 0.000000e+00 1245.0
177 TraesCS5D01G389900 chr4D 90.921 782 29 14 169 917 440263213 440262441 0.000000e+00 1013.0
178 TraesCS5D01G389900 chr4D 90.261 421 26 9 1944 2350 101035161 101035580 3.600000e-148 536.0
179 TraesCS5D01G389900 chr4D 86.928 153 16 3 5726 5875 116279756 116279907 1.510000e-37 169.0
180 TraesCS5D01G389900 chr4D 86.928 153 16 4 5726 5875 365080884 365080733 1.510000e-37 169.0
181 TraesCS5D01G389900 chr4D 92.857 112 8 0 4098 4209 100342193 100342304 7.040000e-36 163.0
182 TraesCS5D01G389900 chr4D 86.093 151 21 0 5726 5876 441487999 441488149 7.040000e-36 163.0
183 TraesCS5D01G389900 chr4D 85.987 157 16 4 5725 5875 499555660 499555816 7.040000e-36 163.0
184 TraesCS5D01G389900 chr4D 86.301 146 19 1 1785 1929 441488004 441488149 3.280000e-34 158.0
185 TraesCS5D01G389900 chr4D 85.906 149 18 3 1783 1928 365080881 365080733 1.180000e-33 156.0
186 TraesCS5D01G389900 chr4D 91.667 108 7 2 1779 1884 29833247 29833140 1.970000e-31 148.0
187 TraesCS5D01G389900 chr4D 84.416 154 20 3 5726 5875 63251482 63251329 1.970000e-31 148.0
188 TraesCS5D01G389900 chr4D 83.436 163 13 6 1780 1928 1232596 1232758 1.190000e-28 139.0
189 TraesCS5D01G389900 chr4D 83.444 151 20 4 1783 1928 63251479 63251329 1.530000e-27 135.0
190 TraesCS5D01G389900 chr4D 88.991 109 9 3 1779 1884 43905539 43905431 1.990000e-26 132.0
191 TraesCS5D01G389900 chr4D 85.556 90 13 0 8238 8327 173928958 173928869 2.610000e-15 95.3
192 TraesCS5D01G389900 chr4D 96.078 51 2 0 4207 4257 100342342 100342392 5.640000e-12 84.2
193 TraesCS5D01G389900 chr4D 91.228 57 1 2 5675 5727 487652273 487652217 3.390000e-09 75.0
194 TraesCS5D01G389900 chr6A 91.377 951 40 16 1 917 588565490 588566432 0.000000e+00 1264.0
195 TraesCS5D01G389900 chr6A 84.211 171 15 5 1332 1492 603917563 603917731 1.180000e-33 156.0
196 TraesCS5D01G389900 chr6A 84.516 155 12 4 5294 5438 603917579 603917731 9.170000e-30 143.0
197 TraesCS5D01G389900 chr6A 81.977 172 16 8 1332 1492 436392941 436393108 1.990000e-26 132.0
198 TraesCS5D01G389900 chr6A 82.468 154 16 3 5294 5438 436392957 436393108 3.320000e-24 124.0
199 TraesCS5D01G389900 chr6A 81.699 153 17 4 5294 5438 479039885 479040034 5.560000e-22 117.0
200 TraesCS5D01G389900 chr6A 94.203 69 3 1 5666 5733 104308553 104308485 4.330000e-18 104.0
201 TraesCS5D01G389900 chr6A 79.355 155 19 9 5294 5438 503763027 503763178 7.240000e-16 97.1
202 TraesCS5D01G389900 chr6A 93.548 62 4 0 1720 1781 104308553 104308492 9.370000e-15 93.5
203 TraesCS5D01G389900 chr6A 92.857 56 1 3 1706 1759 504139692 504139638 2.620000e-10 78.7
204 TraesCS5D01G389900 chr7A 90.737 950 51 15 1 917 82116158 82115213 0.000000e+00 1232.0
205 TraesCS5D01G389900 chr7A 87.805 287 33 2 4535 4820 63501147 63501432 1.410000e-87 335.0
206 TraesCS5D01G389900 chr7A 84.118 170 15 5 1332 1491 579481359 579481192 4.240000e-33 154.0
207 TraesCS5D01G389900 chr7A 83.626 171 16 8 1332 1492 49621111 49620943 5.480000e-32 150.0
208 TraesCS5D01G389900 chr7A 82.447 188 18 8 1335 1510 732094532 732094348 5.480000e-32 150.0
209 TraesCS5D01G389900 chr7A 84.416 154 12 4 5294 5437 579481343 579481192 3.300000e-29 141.0
210 TraesCS5D01G389900 chr7A 83.871 155 13 7 5294 5438 49621095 49620943 4.270000e-28 137.0
211 TraesCS5D01G389900 chr7A 92.188 64 5 0 5666 5729 567475365 567475428 3.370000e-14 91.6
212 TraesCS5D01G389900 chr7A 90.323 62 6 0 1720 1781 567475365 567475426 2.030000e-11 82.4
213 TraesCS5D01G389900 chr2A 89.043 721 41 17 1944 2629 581425668 581424951 0.000000e+00 859.0
214 TraesCS5D01G389900 chr2A 96.774 62 1 1 5666 5727 523862851 523862791 1.560000e-17 102.0
215 TraesCS5D01G389900 chr2A 95.000 40 2 0 4207 4246 595401513 595401474 7.350000e-06 63.9
216 TraesCS5D01G389900 chr3B 88.450 658 70 5 3403 4058 470596666 470597319 0.000000e+00 789.0
217 TraesCS5D01G389900 chr3B 87.762 621 72 4 3559 4176 450386440 450387059 0.000000e+00 723.0
218 TraesCS5D01G389900 chr3B 82.819 454 74 4 4377 4827 743516790 743516338 3.810000e-108 403.0
219 TraesCS5D01G389900 chr3B 87.417 151 19 0 5726 5876 733603232 733603082 3.250000e-39 174.0
220 TraesCS5D01G389900 chr3B 79.845 129 26 0 8198 8326 243924620 243924492 2.610000e-15 95.3
221 TraesCS5D01G389900 chrUn 88.608 158 11 3 5726 5876 50639394 50639551 1.500000e-42 185.0
222 TraesCS5D01G389900 chrUn 87.037 162 15 4 5726 5881 31873106 31873267 2.510000e-40 178.0
223 TraesCS5D01G389900 chrUn 86.709 158 13 3 5726 5877 96130986 96131141 1.510000e-37 169.0
224 TraesCS5D01G389900 chrUn 83.146 178 20 3 1332 1500 30689253 30689429 4.240000e-33 154.0
225 TraesCS5D01G389900 chrUn 84.568 162 13 5 5726 5875 141680907 141680746 5.480000e-32 150.0
226 TraesCS5D01G389900 chrUn 84.242 165 10 9 5726 5875 12184741 12184904 7.090000e-31 147.0
227 TraesCS5D01G389900 chrUn 85.430 151 10 2 5737 5875 27078525 27078675 7.090000e-31 147.0
228 TraesCS5D01G389900 chrUn 83.636 165 15 6 5726 5878 127140184 127140020 2.550000e-30 145.0
229 TraesCS5D01G389900 chrUn 92.157 102 7 1 5724 5824 87983402 87983301 9.170000e-30 143.0
230 TraesCS5D01G389900 chrUn 81.768 181 21 5 1336 1505 318851406 318851227 3.300000e-29 141.0
231 TraesCS5D01G389900 chrUn 83.436 163 14 5 1779 1928 96464810 96464972 1.190000e-28 139.0
232 TraesCS5D01G389900 chrUn 83.133 166 13 4 5725 5875 105244587 105244422 4.270000e-28 137.0
233 TraesCS5D01G389900 chrUn 82.840 169 12 4 5725 5877 272972167 272972334 1.530000e-27 135.0
234 TraesCS5D01G389900 chrUn 82.840 169 12 4 5725 5877 347397387 347397220 1.530000e-27 135.0
235 TraesCS5D01G389900 chrUn 81.818 176 17 7 1779 1941 86671478 86671305 5.520000e-27 134.0
236 TraesCS5D01G389900 chrUn 82.424 165 17 4 5723 5875 323779499 323779663 5.520000e-27 134.0
237 TraesCS5D01G389900 chrUn 81.875 160 17 4 5731 5878 86734180 86734339 3.320000e-24 124.0
238 TraesCS5D01G389900 chrUn 81.143 175 16 7 5726 5883 250801055 250800881 3.320000e-24 124.0
239 TraesCS5D01G389900 chrUn 81.143 175 16 7 5726 5883 258351103 258351277 3.320000e-24 124.0
240 TraesCS5D01G389900 chrUn 81.548 168 15 7 1779 1930 272972167 272972334 3.320000e-24 124.0
241 TraesCS5D01G389900 chrUn 81.548 168 15 7 1779 1930 347397387 347397220 3.320000e-24 124.0
242 TraesCS5D01G389900 chrUn 81.143 175 16 7 5726 5883 366086322 366086148 3.320000e-24 124.0
243 TraesCS5D01G389900 chrUn 80.814 172 15 8 1783 1936 250801052 250800881 1.550000e-22 119.0
244 TraesCS5D01G389900 chrUn 80.571 175 16 8 1780 1936 258351103 258351277 1.550000e-22 119.0
245 TraesCS5D01G389900 chrUn 80.814 172 15 8 1783 1936 366086319 366086148 1.550000e-22 119.0
246 TraesCS5D01G389900 chrUn 79.670 182 22 8 1332 1502 32482611 32482788 5.560000e-22 117.0
247 TraesCS5D01G389900 chrUn 79.006 181 25 5 1332 1503 13838155 13837979 2.590000e-20 111.0
248 TraesCS5D01G389900 chrUn 80.625 160 18 5 1785 1931 86734180 86734339 2.590000e-20 111.0
249 TraesCS5D01G389900 chrUn 79.213 178 24 5 5726 5891 94224159 94223983 2.590000e-20 111.0
250 TraesCS5D01G389900 chrUn 79.870 154 22 2 1351 1495 71546747 71546594 4.330000e-18 104.0
251 TraesCS5D01G389900 chrUn 79.870 154 22 2 1351 1495 268022327 268022174 4.330000e-18 104.0
252 TraesCS5D01G389900 chrUn 79.006 181 13 13 1332 1504 474962498 474962335 5.600000e-17 100.0
253 TraesCS5D01G389900 chrUn 78.395 162 28 5 1332 1490 24663244 24663401 2.010000e-16 99.0
254 TraesCS5D01G389900 chrUn 77.714 175 24 9 5726 5886 34149879 34149706 9.370000e-15 93.5
255 TraesCS5D01G389900 chrUn 77.714 175 24 9 5726 5886 282034185 282034012 9.370000e-15 93.5
256 TraesCS5D01G389900 chrUn 77.011 174 29 4 1332 1496 74039621 74039450 1.210000e-13 89.8
257 TraesCS5D01G389900 chrUn 92.857 56 4 0 1873 1928 115041222 115041277 2.030000e-11 82.4
258 TraesCS5D01G389900 chrUn 76.471 170 27 11 5725 5882 266284218 266284050 7.290000e-11 80.5
259 TraesCS5D01G389900 chrUn 76.471 170 27 11 5725 5882 266293145 266292977 7.290000e-11 80.5
260 TraesCS5D01G389900 chrUn 76.829 164 25 11 5725 5876 274834869 274835031 7.290000e-11 80.5
261 TraesCS5D01G389900 chrUn 91.379 58 3 2 1873 1929 29988156 29988100 2.620000e-10 78.7
262 TraesCS5D01G389900 chrUn 90.000 60 6 0 1873 1932 31220551 31220492 2.620000e-10 78.7
263 TraesCS5D01G389900 chrUn 92.727 55 2 2 1875 1928 269561435 269561488 2.620000e-10 78.7
264 TraesCS5D01G389900 chrUn 91.071 56 5 0 5820 5875 115041222 115041277 9.440000e-10 76.8
265 TraesCS5D01G389900 chrUn 93.878 49 3 0 5658 5706 104889329 104889281 3.390000e-09 75.0
266 TraesCS5D01G389900 chrUn 95.349 43 2 0 5664 5706 103121686 103121728 1.580000e-07 69.4
267 TraesCS5D01G389900 chrUn 91.837 49 4 0 1712 1760 104889329 104889281 1.580000e-07 69.4
268 TraesCS5D01G389900 chrUn 83.133 83 6 2 1417 1491 401089621 401089703 1.580000e-07 69.4
269 TraesCS5D01G389900 chrUn 91.837 49 2 2 1715 1761 69983134 69983182 5.680000e-07 67.6
270 TraesCS5D01G389900 chrUn 82.353 85 7 3 1418 1494 231619545 231619629 5.680000e-07 67.6
271 TraesCS5D01G389900 chrUn 93.023 43 3 0 1718 1760 103121686 103121728 7.350000e-06 63.9
272 TraesCS5D01G389900 chrUn 94.872 39 2 0 1780 1818 95150203 95150241 2.640000e-05 62.1
273 TraesCS5D01G389900 chrUn 100.000 33 0 0 1461 1493 339023887 339023855 2.640000e-05 62.1
274 TraesCS5D01G389900 chrUn 94.444 36 2 0 1720 1755 259481146 259481111 1.000000e-03 56.5
275 TraesCS5D01G389900 chr2B 86.420 162 16 4 5726 5881 719529477 719529316 1.170000e-38 172.0
276 TraesCS5D01G389900 chr2B 78.531 177 31 4 4207 4377 386499004 386498829 9.300000e-20 110.0
277 TraesCS5D01G389900 chr1B 87.333 150 17 2 5726 5875 352890033 352890180 4.210000e-38 171.0
278 TraesCS5D01G389900 chr1B 84.783 138 16 4 1797 1929 634147184 634147321 5.520000e-27 134.0
279 TraesCS5D01G389900 chr1B 78.235 170 25 8 1332 1499 185076183 185076342 2.010000e-16 99.0
280 TraesCS5D01G389900 chr1B 79.487 156 15 11 5294 5436 94323280 94323431 2.610000e-15 95.3
281 TraesCS5D01G389900 chr1B 90.411 73 6 1 5658 5729 342124814 342124886 2.610000e-15 95.3
282 TraesCS5D01G389900 chr1B 88.732 71 7 1 1712 1781 342124814 342124884 1.570000e-12 86.1
283 TraesCS5D01G389900 chr1B 91.379 58 3 2 1722 1779 510788600 510788655 2.620000e-10 78.7
284 TraesCS5D01G389900 chr1B 77.640 161 15 11 5294 5446 566150707 566150560 2.620000e-10 78.7
285 TraesCS5D01G389900 chr1B 95.745 47 2 0 4155 4201 190880173 190880127 9.440000e-10 76.8
286 TraesCS5D01G389900 chr1B 78.261 115 19 5 5295 5406 369190767 369190878 1.580000e-07 69.4
287 TraesCS5D01G389900 chr1A 84.302 172 14 3 5725 5883 181769426 181769597 1.180000e-33 156.0
288 TraesCS5D01G389900 chr1A 84.810 158 20 3 5726 5883 409855022 409855175 1.180000e-33 156.0
289 TraesCS5D01G389900 chr1A 84.431 167 14 3 5722 5876 216420284 216420118 4.240000e-33 154.0
290 TraesCS5D01G389900 chr1A 82.873 181 19 6 5707 5875 496854498 496854318 1.520000e-32 152.0
291 TraesCS5D01G389900 chr1A 83.626 171 16 5 1332 1492 7949517 7949685 5.480000e-32 150.0
292 TraesCS5D01G389900 chr1A 83.529 170 18 3 1332 1492 539849480 539849312 5.480000e-32 150.0
293 TraesCS5D01G389900 chr1A 84.663 163 10 6 1786 1935 268117181 268117341 1.970000e-31 148.0
294 TraesCS5D01G389900 chr1A 83.529 170 16 5 1332 1491 470997327 470997494 1.970000e-31 148.0
295 TraesCS5D01G389900 chr1A 83.140 172 15 6 1779 1936 181769426 181769597 2.550000e-30 145.0
296 TraesCS5D01G389900 chr1A 84.516 155 12 4 5294 5438 539849464 539849312 9.170000e-30 143.0
297 TraesCS5D01G389900 chr1A 83.871 155 13 4 5294 5438 7949533 7949685 4.270000e-28 137.0
298 TraesCS5D01G389900 chr1A 83.766 154 13 4 5294 5437 470997343 470997494 1.530000e-27 135.0
299 TraesCS5D01G389900 chr1A 81.006 179 24 3 1332 1501 548793336 548793159 5.520000e-27 134.0
300 TraesCS5D01G389900 chr1A 82.278 158 23 4 1780 1936 409855022 409855175 1.990000e-26 132.0
301 TraesCS5D01G389900 chr1A 81.006 179 23 5 1332 1502 521852767 521852592 1.990000e-26 132.0
302 TraesCS5D01G389900 chr1A 78.771 179 24 6 1332 1501 508051046 508050873 3.350000e-19 108.0
303 TraesCS5D01G389900 chr1A 81.290 155 9 6 5294 5440 593410046 593410188 3.350000e-19 108.0
304 TraesCS5D01G389900 chr1A 78.286 175 27 4 1334 1499 533905365 533905193 1.560000e-17 102.0
305 TraesCS5D01G389900 chr1A 79.375 160 19 10 1780 1928 384779034 384779190 5.600000e-17 100.0
306 TraesCS5D01G389900 chr1A 77.326 172 25 8 5725 5883 438342106 438341936 1.210000e-13 89.8
307 TraesCS5D01G389900 chr1A 80.531 113 20 2 5295 5406 308203155 308203266 1.570000e-12 86.1
308 TraesCS5D01G389900 chr1A 90.769 65 4 2 1871 1934 436434777 436434840 1.570000e-12 86.1
309 TraesCS5D01G389900 chr1A 91.837 49 4 0 5666 5714 12367508 12367460 1.580000e-07 69.4
310 TraesCS5D01G389900 chr4B 84.967 153 15 6 1783 1928 28307916 28307765 1.970000e-31 148.0
311 TraesCS5D01G389900 chr4B 95.082 61 2 1 5663 5722 192539498 192539558 2.610000e-15 95.3
312 TraesCS5D01G389900 chr4B 75.581 172 30 12 4218 4380 25555614 25555446 3.390000e-09 75.0
313 TraesCS5D01G389900 chr4B 75.000 172 31 12 4218 4379 25556472 25556303 1.580000e-07 69.4
314 TraesCS5D01G389900 chr6B 96.970 33 1 0 8137 8169 335462921 335462889 1.000000e-03 56.5


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 TraesCS5D01G389900 chr5D 458867241 458876005 8764 True 16187.000000 16187 100.000000 1 8765 1 chr5D.!!$R2 8764
1 TraesCS5D01G389900 chr5D 258348034 258349514 1480 True 2073.000000 2073 92.189000 1944 3403 1 chr5D.!!$R1 1459
2 TraesCS5D01G389900 chr5D 279257556 279259044 1488 False 2034.000000 2034 91.711000 1944 3401 1 chr5D.!!$F2 1457
3 TraesCS5D01G389900 chr5D 532662109 532663608 1499 True 1923.000000 1923 90.312000 1944 3402 1 chr5D.!!$R5 1458
4 TraesCS5D01G389900 chr5D 69115873 69117374 1501 False 1910.000000 1910 90.139000 1943 3403 1 chr5D.!!$F1 1460
5 TraesCS5D01G389900 chr5D 305741388 305742619 1231 False 1659.000000 1659 91.410000 1944 3144 1 chr5D.!!$F3 1200
6 TraesCS5D01G389900 chr5D 458870113 458875089 4976 True 1539.000000 1539 93.484000 917 5893 2 chr5D.!!$R7 4976
7 TraesCS5D01G389900 chr5D 492568093 492569433 1340 True 725.000000 725 76.800000 5955 7312 1 chr5D.!!$R4 1357
8 TraesCS5D01G389900 chr5D 492608028 492612098 4070 True 699.500000 2364 81.266500 975 7980 4 chr5D.!!$R8 7005
9 TraesCS5D01G389900 chr5D 238177266 238179022 1756 False 481.500000 682 78.474000 5955 7775 2 chr5D.!!$F6 1820
10 TraesCS5D01G389900 chr5A 215549580 215551052 1472 False 1683.000000 1683 87.534000 1944 3403 1 chr5A.!!$F2 1459
11 TraesCS5D01G389900 chr5A 552934226 552935382 1156 True 1373.000000 1373 88.412000 1944 3083 1 chr5A.!!$R3 1139
12 TraesCS5D01G389900 chr5A 577926173 577932741 6568 True 1090.514286 4927 92.395143 917 8765 7 chr5A.!!$R6 7848
13 TraesCS5D01G389900 chr5A 615291094 615293001 1907 False 965.500000 1441 86.385500 6163 7966 2 chr5A.!!$F6 1803
14 TraesCS5D01G389900 chr5A 615304998 615306314 1316 False 697.000000 697 76.558000 5979 7312 1 chr5A.!!$F5 1333
15 TraesCS5D01G389900 chr5A 316512927 316514263 1336 True 689.000000 689 76.333000 5960 7312 1 chr5A.!!$R2 1352
16 TraesCS5D01G389900 chr5B 562791593 562795018 3425 True 1432.250000 3203 94.300250 918 7870 4 chr5B.!!$R6 6952
17 TraesCS5D01G389900 chr5B 267300414 267301749 1335 True 699.000000 699 76.462000 5960 7312 1 chr5B.!!$R3 1352
18 TraesCS5D01G389900 chr5B 607866516 607867852 1336 False 693.000000 693 76.488000 5955 7312 1 chr5B.!!$F1 1357
19 TraesCS5D01G389900 chr2D 275913671 275915156 1485 False 2050.000000 2050 91.896000 1944 3403 1 chr2D.!!$F3 1459
20 TraesCS5D01G389900 chr2D 603222659 603224142 1483 True 1751.000000 1751 88.212000 1944 3411 1 chr2D.!!$R3 1467
21 TraesCS5D01G389900 chr2D 431015485 431016391 906 False 1480.000000 1480 95.974000 1 917 1 chr2D.!!$F4 916
22 TraesCS5D01G389900 chr3A 42111353 42112824 1471 False 1984.000000 1984 91.284000 1951 3401 1 chr3A.!!$F2 1450
23 TraesCS5D01G389900 chr3A 42151206 42152678 1472 False 1975.000000 1975 91.161000 1951 3401 1 chr3A.!!$F3 1450
24 TraesCS5D01G389900 chr4A 177445703 177447161 1458 False 1764.000000 1764 88.618000 1944 3403 1 chr4A.!!$F1 1459
25 TraesCS5D01G389900 chr3D 187992041 187993526 1485 False 1749.000000 1749 88.326000 1943 3401 1 chr3D.!!$F2 1458
26 TraesCS5D01G389900 chr3D 547236960 547237710 750 True 1190.000000 1190 95.509000 1 742 1 chr3D.!!$R3 741
27 TraesCS5D01G389900 chr6D 60325999 60326913 914 True 1604.000000 1604 98.255000 1 917 1 chr6D.!!$R4 916
28 TraesCS5D01G389900 chr6D 1927455 1928353 898 False 1483.000000 1483 96.187000 1 917 1 chr6D.!!$F1 916
29 TraesCS5D01G389900 chr1D 70141388 70142287 899 False 1489.000000 1489 96.292000 1 917 1 chr1D.!!$F4 916
30 TraesCS5D01G389900 chr7D 120720916 120721821 905 False 1411.000000 1411 94.680000 1 917 1 chr7D.!!$F1 916
31 TraesCS5D01G389900 chr7D 175775643 175776549 906 True 1258.000000 1258 92.232000 1 881 1 chr7D.!!$R1 880
32 TraesCS5D01G389900 chr4D 20318263 20319203 940 True 1290.000000 1290 91.895000 1 917 1 chr4D.!!$R1 916
33 TraesCS5D01G389900 chr4D 143338999 143339934 935 False 1245.000000 1245 91.158000 1 917 1 chr4D.!!$F4 916
34 TraesCS5D01G389900 chr4D 440262441 440263213 772 True 1013.000000 1013 90.921000 169 917 1 chr4D.!!$R5 748
35 TraesCS5D01G389900 chr6A 588565490 588566432 942 False 1264.000000 1264 91.377000 1 917 1 chr6A.!!$F3 916
36 TraesCS5D01G389900 chr7A 82115213 82116158 945 True 1232.000000 1232 90.737000 1 917 1 chr7A.!!$R1 916
37 TraesCS5D01G389900 chr2A 581424951 581425668 717 True 859.000000 859 89.043000 1944 2629 1 chr2A.!!$R2 685
38 TraesCS5D01G389900 chr3B 470596666 470597319 653 False 789.000000 789 88.450000 3403 4058 1 chr3B.!!$F2 655
39 TraesCS5D01G389900 chr3B 450386440 450387059 619 False 723.000000 723 87.762000 3559 4176 1 chr3B.!!$F1 617

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
142 158 0.906775 TCTGCATCATCAGACCTGCA 59.093 50.000 0.00 3.95 37.41 4.41 F
921 975 2.045561 TGGAAAGAAGCGTTTGACCA 57.954 45.000 0.00 0.00 0.00 4.02 F
6071 7687 3.059472 CTAGACGCGCGCACAACAG 62.059 63.158 32.58 16.12 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
5911 7527 5.163854 CGTTATGGTCAGTGAATTCCAAGTC 60.164 44.000 5.15 0.0 33.55 3.01 R
6557 8176 2.224606 CCGCACATTCTGGCATCTATT 58.775 47.619 0.00 0.0 0.00 1.73 R
8692 12622 0.109342 CCTGGGTGAAGCTGACAAGT 59.891 55.000 0.00 0.0 0.00 3.16 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
142 158 0.906775 TCTGCATCATCAGACCTGCA 59.093 50.000 0.00 3.95 37.41 4.41
356 374 2.882777 AGTTGCGAGCGCGAGATG 60.883 61.111 15.92 0.00 45.51 2.90
441 460 3.561725 GCCTCTCCCAAAAATAGATGTCG 59.438 47.826 0.00 0.00 0.00 4.35
758 808 2.164338 GAAAGGGGAAATGTTGCGGTA 58.836 47.619 0.00 0.00 0.00 4.02
823 877 3.800863 GTCCTCAGCTCGCGTCGA 61.801 66.667 5.77 2.20 0.00 4.20
917 971 2.857748 GTTGGTTGGAAAGAAGCGTTTG 59.142 45.455 0.00 0.00 0.00 2.93
918 972 2.370349 TGGTTGGAAAGAAGCGTTTGA 58.630 42.857 0.00 0.00 0.00 2.69
919 973 2.098443 TGGTTGGAAAGAAGCGTTTGAC 59.902 45.455 0.00 0.00 0.00 3.18
920 974 2.543031 GGTTGGAAAGAAGCGTTTGACC 60.543 50.000 0.00 0.00 0.00 4.02
921 975 2.045561 TGGAAAGAAGCGTTTGACCA 57.954 45.000 0.00 0.00 0.00 4.02
5935 7551 4.695455 ACTTGGAATTCACTGACCATAACG 59.305 41.667 7.93 0.00 32.31 3.18
6071 7687 3.059472 CTAGACGCGCGCACAACAG 62.059 63.158 32.58 16.12 0.00 3.16
6259 7875 5.478332 TCTGACTGACATCTGTGACAAGTAT 59.522 40.000 0.00 0.00 30.00 2.12
6737 8462 1.941999 GCTGGTGGATTTGAGGCTGC 61.942 60.000 0.00 0.00 0.00 5.25
6743 8468 1.450531 GGATTTGAGGCTGCGGGATG 61.451 60.000 0.00 0.00 0.00 3.51
6766 8491 1.603172 CCGTATAGCCGAGCTCCTTTG 60.603 57.143 8.47 0.00 40.44 2.77
6977 8702 5.335426 GCATATACTGGTGAGCATGATTTGG 60.335 44.000 0.00 0.00 0.00 3.28
7151 8878 6.767902 ACATAAGGTGGTGCTAAATATCACTG 59.232 38.462 0.00 0.00 33.91 3.66
7424 9151 8.465201 GCAAATATCCTGAACTCTGAAAATCTT 58.535 33.333 0.00 0.00 0.00 2.40
7425 9152 9.784680 CAAATATCCTGAACTCTGAAAATCTTG 57.215 33.333 0.00 0.00 0.00 3.02
7740 9473 2.440980 GATGGCACTGGCTTCCCC 60.441 66.667 3.97 0.00 40.87 4.81
7756 9489 4.511826 GCTTCCCCGTTCATAAGATAGTTG 59.488 45.833 0.00 0.00 0.00 3.16
7949 10002 1.133915 TGTTTAGATGATTCCGGGGCC 60.134 52.381 0.00 0.00 0.00 5.80
7950 10003 1.143073 GTTTAGATGATTCCGGGGCCT 59.857 52.381 0.84 0.00 0.00 5.19
7991 10044 6.662414 TTCGGCAGAAAATAGTGTTAGATG 57.338 37.500 0.00 0.00 32.65 2.90
8169 12071 4.443266 GGTCAAGAGAGCGCCGCT 62.443 66.667 13.40 13.40 43.88 5.52
8170 12072 2.433318 GTCAAGAGAGCGCCGCTT 60.433 61.111 15.07 6.41 39.88 4.68
8171 12073 2.029844 GTCAAGAGAGCGCCGCTTT 61.030 57.895 15.07 7.73 39.88 3.51
8173 12075 2.435059 AAGAGAGCGCCGCTTTCC 60.435 61.111 23.92 11.47 40.09 3.13
8174 12076 4.803426 AGAGAGCGCCGCTTTCCG 62.803 66.667 23.92 0.00 40.09 4.30
8187 12089 2.923643 GCTTTCCGCGTTTAAATGTCA 58.076 42.857 4.92 0.00 0.00 3.58
8188 12090 2.655001 GCTTTCCGCGTTTAAATGTCAC 59.345 45.455 4.92 0.00 0.00 3.67
8189 12091 2.973419 TTCCGCGTTTAAATGTCACC 57.027 45.000 4.92 0.00 0.00 4.02
8190 12092 1.880271 TCCGCGTTTAAATGTCACCA 58.120 45.000 4.92 0.00 0.00 4.17
8191 12093 2.428491 TCCGCGTTTAAATGTCACCAT 58.572 42.857 4.92 0.00 0.00 3.55
8192 12094 2.160615 TCCGCGTTTAAATGTCACCATG 59.839 45.455 4.92 0.00 0.00 3.66
8193 12095 2.160615 CCGCGTTTAAATGTCACCATGA 59.839 45.455 4.92 0.00 0.00 3.07
8195 12097 3.498082 GCGTTTAAATGTCACCATGACC 58.502 45.455 9.12 0.00 46.40 4.02
8196 12098 3.742786 CGTTTAAATGTCACCATGACCG 58.257 45.455 6.51 0.00 46.40 4.79
8197 12099 3.187637 CGTTTAAATGTCACCATGACCGT 59.812 43.478 6.51 0.00 46.40 4.83
8198 12100 4.668177 CGTTTAAATGTCACCATGACCGTC 60.668 45.833 6.51 0.00 46.40 4.79
8199 12101 1.821216 AAATGTCACCATGACCGTCC 58.179 50.000 6.51 0.00 46.40 4.79
8200 12102 0.391130 AATGTCACCATGACCGTCCG 60.391 55.000 6.51 0.00 46.40 4.79
8201 12103 1.541310 ATGTCACCATGACCGTCCGT 61.541 55.000 6.51 0.00 46.40 4.69
8202 12104 1.445582 GTCACCATGACCGTCCGTC 60.446 63.158 0.00 0.00 41.37 4.79
8203 12105 1.605451 TCACCATGACCGTCCGTCT 60.605 57.895 0.00 0.00 42.49 4.18
8204 12106 1.446099 CACCATGACCGTCCGTCTG 60.446 63.158 0.00 0.00 42.49 3.51
8205 12107 2.509336 CCATGACCGTCCGTCTGC 60.509 66.667 0.00 0.00 42.49 4.26
8206 12108 2.509336 CATGACCGTCCGTCTGCC 60.509 66.667 0.00 0.00 42.49 4.85
8207 12109 2.994995 ATGACCGTCCGTCTGCCA 60.995 61.111 0.00 0.00 42.49 4.92
8208 12110 2.359169 ATGACCGTCCGTCTGCCAT 61.359 57.895 0.00 0.00 42.49 4.40
8209 12111 2.202756 GACCGTCCGTCTGCCATC 60.203 66.667 0.00 0.00 38.57 3.51
8210 12112 3.718210 GACCGTCCGTCTGCCATCC 62.718 68.421 0.00 0.00 38.57 3.51
8211 12113 3.770040 CCGTCCGTCTGCCATCCA 61.770 66.667 0.00 0.00 0.00 3.41
8212 12114 2.501128 CGTCCGTCTGCCATCCAT 59.499 61.111 0.00 0.00 0.00 3.41
8213 12115 1.739667 CGTCCGTCTGCCATCCATA 59.260 57.895 0.00 0.00 0.00 2.74
8214 12116 0.318441 CGTCCGTCTGCCATCCATAT 59.682 55.000 0.00 0.00 0.00 1.78
8215 12117 1.270305 CGTCCGTCTGCCATCCATATT 60.270 52.381 0.00 0.00 0.00 1.28
8216 12118 2.029380 CGTCCGTCTGCCATCCATATTA 60.029 50.000 0.00 0.00 0.00 0.98
8217 12119 3.554129 CGTCCGTCTGCCATCCATATTAA 60.554 47.826 0.00 0.00 0.00 1.40
8218 12120 4.579869 GTCCGTCTGCCATCCATATTAAT 58.420 43.478 0.00 0.00 0.00 1.40
8219 12121 4.393062 GTCCGTCTGCCATCCATATTAATG 59.607 45.833 0.00 0.00 0.00 1.90
8220 12122 4.285775 TCCGTCTGCCATCCATATTAATGA 59.714 41.667 0.00 0.00 34.84 2.57
8221 12123 4.393062 CCGTCTGCCATCCATATTAATGAC 59.607 45.833 0.00 0.00 34.84 3.06
8222 12124 4.996758 CGTCTGCCATCCATATTAATGACA 59.003 41.667 0.00 0.00 34.84 3.58
8223 12125 5.106948 CGTCTGCCATCCATATTAATGACAC 60.107 44.000 0.00 0.00 34.84 3.67
8224 12126 5.764686 GTCTGCCATCCATATTAATGACACA 59.235 40.000 0.00 0.00 34.84 3.72
8225 12127 6.432162 GTCTGCCATCCATATTAATGACACAT 59.568 38.462 0.00 0.00 34.84 3.21
8226 12128 6.431852 TCTGCCATCCATATTAATGACACATG 59.568 38.462 0.00 0.00 34.84 3.21
8227 12129 6.305411 TGCCATCCATATTAATGACACATGA 58.695 36.000 0.00 0.00 34.84 3.07
8228 12130 6.949463 TGCCATCCATATTAATGACACATGAT 59.051 34.615 0.00 0.00 34.84 2.45
8229 12131 7.452189 TGCCATCCATATTAATGACACATGATT 59.548 33.333 0.00 0.00 34.84 2.57
8230 12132 7.758076 GCCATCCATATTAATGACACATGATTG 59.242 37.037 0.00 0.00 34.84 2.67
8231 12133 8.248253 CCATCCATATTAATGACACATGATTGG 58.752 37.037 0.00 1.23 34.84 3.16
8232 12134 8.799367 CATCCATATTAATGACACATGATTGGT 58.201 33.333 0.00 0.00 34.84 3.67
8234 12136 9.859152 TCCATATTAATGACACATGATTGGTAA 57.141 29.630 0.00 0.00 34.84 2.85
8238 12140 5.801350 AATGACACATGATTGGTAAGTCG 57.199 39.130 0.00 0.00 0.00 4.18
8239 12141 3.595173 TGACACATGATTGGTAAGTCGG 58.405 45.455 0.00 0.00 0.00 4.79
8240 12142 3.007506 TGACACATGATTGGTAAGTCGGT 59.992 43.478 0.00 0.00 0.00 4.69
8241 12143 4.000988 GACACATGATTGGTAAGTCGGTT 58.999 43.478 0.00 0.00 0.00 4.44
8242 12144 5.155278 ACACATGATTGGTAAGTCGGTTA 57.845 39.130 0.00 0.00 0.00 2.85
8243 12145 4.933400 ACACATGATTGGTAAGTCGGTTAC 59.067 41.667 0.00 1.22 40.48 2.50
8244 12146 5.175859 CACATGATTGGTAAGTCGGTTACT 58.824 41.667 0.00 0.00 40.93 2.24
8245 12147 5.291128 CACATGATTGGTAAGTCGGTTACTC 59.709 44.000 0.00 1.17 40.93 2.59
8246 12148 4.460948 TGATTGGTAAGTCGGTTACTCC 57.539 45.455 8.05 0.00 40.93 3.85
8247 12149 3.833650 TGATTGGTAAGTCGGTTACTCCA 59.166 43.478 8.05 0.00 40.93 3.86
8248 12150 3.947910 TTGGTAAGTCGGTTACTCCAG 57.052 47.619 8.05 0.00 40.93 3.86
8249 12151 1.547372 TGGTAAGTCGGTTACTCCAGC 59.453 52.381 8.05 0.00 40.93 4.85
8250 12152 1.468736 GGTAAGTCGGTTACTCCAGCG 60.469 57.143 8.05 0.00 40.93 5.18
8251 12153 0.171903 TAAGTCGGTTACTCCAGCGC 59.828 55.000 0.00 0.00 37.50 5.92
8252 12154 2.502692 AAGTCGGTTACTCCAGCGCC 62.503 60.000 2.29 0.00 37.50 6.53
8253 12155 2.992689 TCGGTTACTCCAGCGCCA 60.993 61.111 2.29 0.00 37.58 5.69
8254 12156 2.813908 CGGTTACTCCAGCGCCAC 60.814 66.667 2.29 0.00 35.57 5.01
8255 12157 2.436115 GGTTACTCCAGCGCCACC 60.436 66.667 2.29 0.00 35.97 4.61
8256 12158 2.436115 GTTACTCCAGCGCCACCC 60.436 66.667 2.29 0.00 0.00 4.61
8257 12159 4.077184 TTACTCCAGCGCCACCCG 62.077 66.667 2.29 0.00 40.75 5.28
8269 12171 3.760035 CACCCGTCCGTCCCTCTG 61.760 72.222 0.00 0.00 0.00 3.35
8270 12172 4.296729 ACCCGTCCGTCCCTCTGT 62.297 66.667 0.00 0.00 0.00 3.41
8271 12173 3.450115 CCCGTCCGTCCCTCTGTC 61.450 72.222 0.00 0.00 0.00 3.51
8272 12174 3.812019 CCGTCCGTCCCTCTGTCG 61.812 72.222 0.00 0.00 0.00 4.35
8273 12175 4.477975 CGTCCGTCCCTCTGTCGC 62.478 72.222 0.00 0.00 0.00 5.19
8274 12176 4.131088 GTCCGTCCCTCTGTCGCC 62.131 72.222 0.00 0.00 0.00 5.54
8275 12177 4.361971 TCCGTCCCTCTGTCGCCT 62.362 66.667 0.00 0.00 0.00 5.52
8276 12178 2.439701 CCGTCCCTCTGTCGCCTA 60.440 66.667 0.00 0.00 0.00 3.93
8277 12179 1.828660 CCGTCCCTCTGTCGCCTAT 60.829 63.158 0.00 0.00 0.00 2.57
8281 12183 1.000283 GTCCCTCTGTCGCCTATCATG 60.000 57.143 0.00 0.00 0.00 3.07
8301 12203 2.910319 TGGCTATATAAACGGATGCCCT 59.090 45.455 0.00 0.00 38.23 5.19
8311 12213 1.762522 CGGATGCCCTGGTCATAGCT 61.763 60.000 0.00 0.00 0.00 3.32
8313 12215 0.888285 GATGCCCTGGTCATAGCTGC 60.888 60.000 0.00 0.00 0.00 5.25
8323 12225 0.390492 TCATAGCTGCAGTCATCCGG 59.610 55.000 16.64 0.00 0.00 5.14
8335 12237 0.032515 TCATCCGGCTCCTACCAAGA 60.033 55.000 0.00 0.00 0.00 3.02
8344 12246 3.518303 GGCTCCTACCAAGAAAGTAAGGA 59.482 47.826 0.00 0.00 0.00 3.36
8351 12253 4.822026 ACCAAGAAAGTAAGGAGACATCG 58.178 43.478 0.00 0.00 0.00 3.84
8368 12270 0.818445 TCGAGATCCCTGTAGTCCGC 60.818 60.000 0.00 0.00 0.00 5.54
8373 12275 0.260816 ATCCCTGTAGTCCGCTGGTA 59.739 55.000 0.00 0.00 0.00 3.25
8375 12277 0.683504 CCCTGTAGTCCGCTGGTAGT 60.684 60.000 0.00 0.00 0.00 2.73
8400 12302 4.569719 AATGGAGTAACTTACCACCAGG 57.430 45.455 15.84 0.00 38.40 4.45
8411 12313 0.550147 ACCACCAGGGGAAGCTACAT 60.550 55.000 0.00 0.00 42.91 2.29
8418 12320 0.919710 GGGGAAGCTACATGGGAAGT 59.080 55.000 0.00 0.00 0.00 3.01
8482 12384 3.866651 AGGACAGGTTTGATCTTGATCG 58.133 45.455 6.19 0.00 0.00 3.69
8507 12409 3.245122 GGGAGTTATCAGGACCCAACAAA 60.245 47.826 0.00 0.00 40.20 2.83
8508 12410 4.569865 GGGAGTTATCAGGACCCAACAAAT 60.570 45.833 0.00 0.00 40.20 2.32
8510 12412 5.125578 GGAGTTATCAGGACCCAACAAATTC 59.874 44.000 0.00 0.00 0.00 2.17
8511 12413 5.640147 AGTTATCAGGACCCAACAAATTCA 58.360 37.500 0.00 0.00 0.00 2.57
8512 12414 5.711976 AGTTATCAGGACCCAACAAATTCAG 59.288 40.000 0.00 0.00 0.00 3.02
8513 12415 3.593442 TCAGGACCCAACAAATTCAGT 57.407 42.857 0.00 0.00 0.00 3.41
8515 12417 5.055265 TCAGGACCCAACAAATTCAGTTA 57.945 39.130 0.00 0.00 0.00 2.24
8516 12418 5.450453 TCAGGACCCAACAAATTCAGTTAA 58.550 37.500 0.00 0.00 0.00 2.01
8517 12419 5.300792 TCAGGACCCAACAAATTCAGTTAAC 59.699 40.000 0.00 0.00 0.00 2.01
8604 12534 0.245813 ACCTTCCTTCGTACCGCTTC 59.754 55.000 0.00 0.00 0.00 3.86
8606 12536 1.411493 CTTCCTTCGTACCGCTTCGC 61.411 60.000 0.00 0.00 0.00 4.70
8623 12553 5.855235 GCTTCGCGAGTTAAATAAAAGACT 58.145 37.500 9.59 0.00 0.00 3.24
8624 12554 5.952634 GCTTCGCGAGTTAAATAAAAGACTC 59.047 40.000 9.59 0.00 36.14 3.36
8625 12555 6.399204 TTCGCGAGTTAAATAAAAGACTCC 57.601 37.500 9.59 0.00 36.12 3.85
8626 12556 5.472148 TCGCGAGTTAAATAAAAGACTCCA 58.528 37.500 3.71 0.00 36.12 3.86
8627 12557 5.927689 TCGCGAGTTAAATAAAAGACTCCAA 59.072 36.000 3.71 0.00 36.12 3.53
8628 12558 6.424509 TCGCGAGTTAAATAAAAGACTCCAAA 59.575 34.615 3.71 0.00 36.12 3.28
8629 12559 7.041916 TCGCGAGTTAAATAAAAGACTCCAAAA 60.042 33.333 3.71 0.00 36.12 2.44
8630 12560 7.749126 CGCGAGTTAAATAAAAGACTCCAAAAT 59.251 33.333 0.00 0.00 36.12 1.82
8631 12561 8.850452 GCGAGTTAAATAAAAGACTCCAAAATG 58.150 33.333 0.00 0.00 36.12 2.32
8638 12568 9.883142 AAATAAAAGACTCCAAAATGACACAAA 57.117 25.926 0.00 0.00 0.00 2.83
8641 12571 8.424274 AAAAGACTCCAAAATGACACAAATTC 57.576 30.769 0.00 0.00 0.00 2.17
8642 12572 6.713762 AGACTCCAAAATGACACAAATTCA 57.286 33.333 0.00 0.00 0.00 2.57
8643 12573 6.742109 AGACTCCAAAATGACACAAATTCAG 58.258 36.000 0.00 0.00 0.00 3.02
8644 12574 5.291971 ACTCCAAAATGACACAAATTCAGC 58.708 37.500 0.00 0.00 0.00 4.26
8645 12575 5.069516 ACTCCAAAATGACACAAATTCAGCT 59.930 36.000 0.00 0.00 0.00 4.24
8646 12576 6.265196 ACTCCAAAATGACACAAATTCAGCTA 59.735 34.615 0.00 0.00 0.00 3.32
8647 12577 6.680810 TCCAAAATGACACAAATTCAGCTAG 58.319 36.000 0.00 0.00 0.00 3.42
8648 12578 6.489700 TCCAAAATGACACAAATTCAGCTAGA 59.510 34.615 0.00 0.00 0.00 2.43
8649 12579 6.583806 CCAAAATGACACAAATTCAGCTAGAC 59.416 38.462 0.00 0.00 0.00 2.59
8650 12580 7.365741 CAAAATGACACAAATTCAGCTAGACT 58.634 34.615 0.00 0.00 0.00 3.24
8664 12594 6.389830 CAGCTAGACTGTTCAGATACATCT 57.610 41.667 6.83 1.67 41.86 2.90
8665 12595 7.503521 CAGCTAGACTGTTCAGATACATCTA 57.496 40.000 6.83 2.68 41.86 1.98
8666 12596 7.935520 CAGCTAGACTGTTCAGATACATCTAA 58.064 38.462 6.83 0.00 41.86 2.10
8667 12597 8.409371 CAGCTAGACTGTTCAGATACATCTAAA 58.591 37.037 6.83 0.00 41.86 1.85
8668 12598 8.972127 AGCTAGACTGTTCAGATACATCTAAAA 58.028 33.333 6.83 0.00 34.85 1.52
8669 12599 9.243637 GCTAGACTGTTCAGATACATCTAAAAG 57.756 37.037 6.83 0.00 34.85 2.27
8707 12637 5.948992 AAAGAATACTTGTCAGCTTCACC 57.051 39.130 0.00 0.00 36.39 4.02
8708 12638 3.944087 AGAATACTTGTCAGCTTCACCC 58.056 45.455 0.00 0.00 0.00 4.61
8709 12639 3.327757 AGAATACTTGTCAGCTTCACCCA 59.672 43.478 0.00 0.00 0.00 4.51
8710 12640 2.839486 TACTTGTCAGCTTCACCCAG 57.161 50.000 0.00 0.00 0.00 4.45
8711 12641 0.109342 ACTTGTCAGCTTCACCCAGG 59.891 55.000 0.00 0.00 0.00 4.45
8712 12642 1.228245 TTGTCAGCTTCACCCAGGC 60.228 57.895 0.00 0.00 0.00 4.85
8713 12643 1.993701 TTGTCAGCTTCACCCAGGCA 61.994 55.000 0.00 0.00 0.00 4.75
8714 12644 1.001641 GTCAGCTTCACCCAGGCAT 60.002 57.895 0.00 0.00 0.00 4.40
8715 12645 1.028868 GTCAGCTTCACCCAGGCATC 61.029 60.000 0.00 0.00 0.00 3.91
8716 12646 2.110967 CAGCTTCACCCAGGCATCG 61.111 63.158 0.00 0.00 0.00 3.84
8717 12647 2.268920 GCTTCACCCAGGCATCGA 59.731 61.111 0.00 0.00 0.00 3.59
8718 12648 1.377202 GCTTCACCCAGGCATCGAA 60.377 57.895 0.00 0.00 0.00 3.71
8719 12649 0.960364 GCTTCACCCAGGCATCGAAA 60.960 55.000 0.00 0.00 0.00 3.46
8720 12650 0.804989 CTTCACCCAGGCATCGAAAC 59.195 55.000 0.00 0.00 0.00 2.78
8721 12651 0.953471 TTCACCCAGGCATCGAAACG 60.953 55.000 0.00 0.00 0.00 3.60
8722 12652 1.375396 CACCCAGGCATCGAAACGA 60.375 57.895 0.00 0.00 41.13 3.85
8724 12654 0.828022 ACCCAGGCATCGAAACGATA 59.172 50.000 6.34 0.00 45.19 2.92
8725 12655 1.416401 ACCCAGGCATCGAAACGATAT 59.584 47.619 6.34 0.00 45.19 1.63
8726 12656 1.800586 CCCAGGCATCGAAACGATATG 59.199 52.381 6.34 6.34 45.19 1.78
8727 12657 2.483876 CCAGGCATCGAAACGATATGT 58.516 47.619 6.34 0.00 45.19 2.29
8728 12658 3.554129 CCCAGGCATCGAAACGATATGTA 60.554 47.826 6.34 0.00 45.19 2.29
8729 12659 4.245660 CCAGGCATCGAAACGATATGTAT 58.754 43.478 6.34 0.00 45.19 2.29
8730 12660 4.327357 CCAGGCATCGAAACGATATGTATC 59.673 45.833 6.34 0.00 45.19 2.24
8731 12661 4.327357 CAGGCATCGAAACGATATGTATCC 59.673 45.833 6.34 2.76 45.19 2.59
8732 12662 4.021456 AGGCATCGAAACGATATGTATCCA 60.021 41.667 6.34 0.00 45.19 3.41
8733 12663 4.688879 GGCATCGAAACGATATGTATCCAA 59.311 41.667 6.34 0.00 45.19 3.53
8734 12664 5.389516 GGCATCGAAACGATATGTATCCAAC 60.390 44.000 6.34 0.00 45.19 3.77
8735 12665 5.405571 GCATCGAAACGATATGTATCCAACT 59.594 40.000 6.34 0.00 45.19 3.16
8736 12666 6.584942 GCATCGAAACGATATGTATCCAACTA 59.415 38.462 6.34 0.00 45.19 2.24
8737 12667 7.275779 GCATCGAAACGATATGTATCCAACTAT 59.724 37.037 6.34 0.00 45.19 2.12
8738 12668 8.799091 CATCGAAACGATATGTATCCAACTATC 58.201 37.037 6.34 0.00 45.19 2.08
8739 12669 8.107399 TCGAAACGATATGTATCCAACTATCT 57.893 34.615 0.00 0.00 0.00 1.98
8740 12670 9.223099 TCGAAACGATATGTATCCAACTATCTA 57.777 33.333 0.00 0.00 0.00 1.98
8741 12671 9.836076 CGAAACGATATGTATCCAACTATCTAA 57.164 33.333 0.00 0.00 0.00 2.10
8745 12675 8.244802 ACGATATGTATCCAACTATCTAAGTGC 58.755 37.037 0.00 0.00 38.88 4.40
8746 12676 8.462811 CGATATGTATCCAACTATCTAAGTGCT 58.537 37.037 0.00 0.00 38.88 4.40
8747 12677 9.796120 GATATGTATCCAACTATCTAAGTGCTC 57.204 37.037 0.00 0.00 38.88 4.26
8748 12678 6.406692 TGTATCCAACTATCTAAGTGCTCC 57.593 41.667 0.00 0.00 38.88 4.70
8749 12679 5.897250 TGTATCCAACTATCTAAGTGCTCCA 59.103 40.000 0.00 0.00 38.88 3.86
8750 12680 5.957771 ATCCAACTATCTAAGTGCTCCAA 57.042 39.130 0.00 0.00 38.88 3.53
8751 12681 5.755409 TCCAACTATCTAAGTGCTCCAAA 57.245 39.130 0.00 0.00 38.88 3.28
8752 12682 6.313519 TCCAACTATCTAAGTGCTCCAAAT 57.686 37.500 0.00 0.00 38.88 2.32
8753 12683 6.349300 TCCAACTATCTAAGTGCTCCAAATC 58.651 40.000 0.00 0.00 38.88 2.17
8754 12684 5.235186 CCAACTATCTAAGTGCTCCAAATCG 59.765 44.000 0.00 0.00 38.88 3.34
8755 12685 4.372656 ACTATCTAAGTGCTCCAAATCGC 58.627 43.478 0.00 0.00 36.93 4.58
8756 12686 1.640428 TCTAAGTGCTCCAAATCGCG 58.360 50.000 0.00 0.00 0.00 5.87
8757 12687 1.203758 TCTAAGTGCTCCAAATCGCGA 59.796 47.619 13.09 13.09 0.00 5.87
8758 12688 1.999735 CTAAGTGCTCCAAATCGCGAA 59.000 47.619 15.24 0.00 0.00 4.70
8759 12689 1.234821 AAGTGCTCCAAATCGCGAAA 58.765 45.000 15.24 0.00 0.00 3.46
8760 12690 1.453155 AGTGCTCCAAATCGCGAAAT 58.547 45.000 15.24 1.44 0.00 2.17
8761 12691 2.627945 AGTGCTCCAAATCGCGAAATA 58.372 42.857 15.24 0.00 0.00 1.40
8762 12692 3.006940 AGTGCTCCAAATCGCGAAATAA 58.993 40.909 15.24 0.00 0.00 1.40
8763 12693 3.438781 AGTGCTCCAAATCGCGAAATAAA 59.561 39.130 15.24 0.00 0.00 1.40
8764 12694 3.542310 GTGCTCCAAATCGCGAAATAAAC 59.458 43.478 15.24 0.65 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 158 4.383850 TGCTGCTGTTTTTATGTGTGTT 57.616 36.364 0.00 0.00 0.00 3.32
250 266 0.679321 TGGCATGTGTGTGTGTGTGT 60.679 50.000 0.00 0.00 0.00 3.72
356 374 1.742768 CCCATACACTCTCTCCGGC 59.257 63.158 0.00 0.00 0.00 6.13
823 877 3.900892 CGGACCCGATGTAGCGCT 61.901 66.667 17.26 17.26 42.83 5.92
832 886 2.515523 GAGATCCGACGGACCCGA 60.516 66.667 21.02 0.00 42.83 5.14
917 971 4.595538 TGCGTGTCGTGGGTGGTC 62.596 66.667 0.00 0.00 0.00 4.02
918 972 3.683966 TTTGCGTGTCGTGGGTGGT 62.684 57.895 0.00 0.00 0.00 4.16
919 973 2.897846 TTTGCGTGTCGTGGGTGG 60.898 61.111 0.00 0.00 0.00 4.61
920 974 1.983196 TTGTTTGCGTGTCGTGGGTG 61.983 55.000 0.00 0.00 0.00 4.61
921 975 1.098712 ATTGTTTGCGTGTCGTGGGT 61.099 50.000 0.00 0.00 0.00 4.51
5911 7527 5.163854 CGTTATGGTCAGTGAATTCCAAGTC 60.164 44.000 5.15 0.00 33.55 3.01
5912 7528 4.695455 CGTTATGGTCAGTGAATTCCAAGT 59.305 41.667 5.15 0.00 33.55 3.16
5935 7551 6.808829 TCATTTCCATGTGAAAGAATATGGC 58.191 36.000 12.76 0.00 45.74 4.40
6071 7687 5.106277 GCTTTGAAAGGATAGTGGTGGTTAC 60.106 44.000 7.09 0.00 0.00 2.50
6259 7875 5.700832 GTCTTTGATGGCATTATACCGATCA 59.299 40.000 0.00 0.00 0.00 2.92
6557 8176 2.224606 CCGCACATTCTGGCATCTATT 58.775 47.619 0.00 0.00 0.00 1.73
6743 8468 1.580437 GAGCTCGGCTATACGGACC 59.420 63.158 0.00 0.00 39.88 4.46
6766 8491 4.742438 TGAGTTAGGAAAATTGACGTGC 57.258 40.909 0.00 0.00 0.00 5.34
7151 8878 4.063998 TCCACATCTGCAGACATGATAC 57.936 45.455 20.97 0.00 0.00 2.24
7355 9082 4.396790 ACCGAAAAGCTAAGTGTTTTGACA 59.603 37.500 0.00 0.00 0.00 3.58
7366 9093 9.974980 AGAAATATTTCAAAACCGAAAAGCTAA 57.025 25.926 26.02 0.00 38.33 3.09
7369 9096 7.009440 GCAGAAATATTTCAAAACCGAAAAGC 58.991 34.615 26.02 10.64 38.33 3.51
7424 9151 5.534278 TCCAAGTTATTGTCAAACTGCATCA 59.466 36.000 0.00 0.00 37.26 3.07
7425 9152 6.012658 TCCAAGTTATTGTCAAACTGCATC 57.987 37.500 0.00 0.00 37.26 3.91
7624 9357 1.760086 CCTGCTCCTCGTCCTCCAT 60.760 63.158 0.00 0.00 0.00 3.41
7699 9432 0.605589 AGTTCTTCGAGCACCTCCAG 59.394 55.000 0.00 0.00 0.00 3.86
7740 9473 6.253727 GTCACTCCACAACTATCTTATGAACG 59.746 42.308 0.00 0.00 0.00 3.95
7756 9489 9.832445 TCCTATAATTATCAAAAGTCACTCCAC 57.168 33.333 0.00 0.00 0.00 4.02
7780 9632 1.358759 CACCGGCACAACAAACTCC 59.641 57.895 0.00 0.00 0.00 3.85
7803 9655 3.517612 AGCCTTGTGGTCTAGTAAAGGA 58.482 45.455 3.98 0.00 39.88 3.36
7949 10002 3.671433 CGAATGAAGCCACACCATGAAAG 60.671 47.826 0.00 0.00 0.00 2.62
7950 10003 2.228582 CGAATGAAGCCACACCATGAAA 59.771 45.455 0.00 0.00 0.00 2.69
7991 10044 9.722056 CCATATTACTTGTCTTAGATTTGTTGC 57.278 33.333 0.00 0.00 0.00 4.17
8086 11907 8.844244 GCAGTGAACAATATCAAGGATTCTTAT 58.156 33.333 0.00 0.00 0.00 1.73
8087 11908 8.049117 AGCAGTGAACAATATCAAGGATTCTTA 58.951 33.333 0.00 0.00 0.00 2.10
8088 11909 6.888632 AGCAGTGAACAATATCAAGGATTCTT 59.111 34.615 0.00 0.00 0.00 2.52
8089 11910 6.421485 AGCAGTGAACAATATCAAGGATTCT 58.579 36.000 0.00 0.00 0.00 2.40
8090 11911 6.690194 AGCAGTGAACAATATCAAGGATTC 57.310 37.500 0.00 0.00 0.00 2.52
8091 11912 7.341805 AGTAGCAGTGAACAATATCAAGGATT 58.658 34.615 0.00 0.00 0.00 3.01
8111 11932 2.000447 GTTCATGGTCCACGAAGTAGC 59.000 52.381 0.00 0.00 41.61 3.58
8146 12048 2.811317 GCTCTCTTGACCGGCGTG 60.811 66.667 6.01 0.00 0.00 5.34
8147 12049 4.421479 CGCTCTCTTGACCGGCGT 62.421 66.667 6.01 0.00 40.78 5.68
8154 12056 1.738099 GAAAGCGGCGCTCTCTTGA 60.738 57.895 36.44 0.00 38.25 3.02
8169 12071 2.617308 TGGTGACATTTAAACGCGGAAA 59.383 40.909 12.47 8.37 33.40 3.13
8170 12072 2.219458 TGGTGACATTTAAACGCGGAA 58.781 42.857 12.47 0.00 33.40 4.30
8171 12073 1.880271 TGGTGACATTTAAACGCGGA 58.120 45.000 12.47 0.00 33.40 5.54
8184 12086 1.445582 GACGGACGGTCATGGTGAC 60.446 63.158 10.76 1.54 46.23 3.67
8185 12087 2.967397 GACGGACGGTCATGGTGA 59.033 61.111 10.76 0.00 45.36 4.02
8192 12094 2.202756 GATGGCAGACGGACGGTC 60.203 66.667 5.05 5.05 46.45 4.79
8193 12095 3.771160 GGATGGCAGACGGACGGT 61.771 66.667 0.00 0.00 0.00 4.83
8194 12096 1.744320 TATGGATGGCAGACGGACGG 61.744 60.000 0.00 0.00 0.00 4.79
8195 12097 0.318441 ATATGGATGGCAGACGGACG 59.682 55.000 0.00 0.00 0.00 4.79
8196 12098 2.550830 AATATGGATGGCAGACGGAC 57.449 50.000 0.00 0.00 0.00 4.79
8197 12099 4.285775 TCATTAATATGGATGGCAGACGGA 59.714 41.667 0.00 0.00 32.40 4.69
8198 12100 4.393062 GTCATTAATATGGATGGCAGACGG 59.607 45.833 0.00 0.00 32.40 4.79
8199 12101 4.996758 TGTCATTAATATGGATGGCAGACG 59.003 41.667 0.00 0.00 33.31 4.18
8200 12102 5.764686 TGTGTCATTAATATGGATGGCAGAC 59.235 40.000 6.21 0.00 38.43 3.51
8201 12103 5.939447 TGTGTCATTAATATGGATGGCAGA 58.061 37.500 6.21 3.36 38.43 4.26
8202 12104 6.431852 TCATGTGTCATTAATATGGATGGCAG 59.568 38.462 6.21 0.00 38.43 4.85
8203 12105 6.305411 TCATGTGTCATTAATATGGATGGCA 58.695 36.000 0.00 0.00 35.67 4.92
8204 12106 6.822667 TCATGTGTCATTAATATGGATGGC 57.177 37.500 0.00 0.00 32.40 4.40
8205 12107 8.248253 CCAATCATGTGTCATTAATATGGATGG 58.752 37.037 0.00 0.00 32.40 3.51
8206 12108 8.799367 ACCAATCATGTGTCATTAATATGGATG 58.201 33.333 0.00 0.00 32.40 3.51
8207 12109 8.945195 ACCAATCATGTGTCATTAATATGGAT 57.055 30.769 0.00 0.00 32.40 3.41
8208 12110 9.859152 TTACCAATCATGTGTCATTAATATGGA 57.141 29.630 0.00 0.00 32.40 3.41
8212 12114 9.040939 CGACTTACCAATCATGTGTCATTAATA 57.959 33.333 0.00 0.00 0.00 0.98
8213 12115 7.012327 CCGACTTACCAATCATGTGTCATTAAT 59.988 37.037 0.00 0.00 0.00 1.40
8214 12116 6.315144 CCGACTTACCAATCATGTGTCATTAA 59.685 38.462 0.00 0.00 0.00 1.40
8215 12117 5.815222 CCGACTTACCAATCATGTGTCATTA 59.185 40.000 0.00 0.00 0.00 1.90
8216 12118 4.635765 CCGACTTACCAATCATGTGTCATT 59.364 41.667 0.00 0.00 0.00 2.57
8217 12119 4.191544 CCGACTTACCAATCATGTGTCAT 58.808 43.478 0.00 0.00 0.00 3.06
8218 12120 3.007506 ACCGACTTACCAATCATGTGTCA 59.992 43.478 0.00 0.00 0.00 3.58
8219 12121 3.596214 ACCGACTTACCAATCATGTGTC 58.404 45.455 0.00 0.00 0.00 3.67
8220 12122 3.695830 ACCGACTTACCAATCATGTGT 57.304 42.857 0.00 0.00 0.00 3.72
8221 12123 5.175859 AGTAACCGACTTACCAATCATGTG 58.824 41.667 0.00 0.00 36.13 3.21
8222 12124 5.416271 AGTAACCGACTTACCAATCATGT 57.584 39.130 0.00 0.00 36.13 3.21
8223 12125 4.809426 GGAGTAACCGACTTACCAATCATG 59.191 45.833 0.00 0.00 39.06 3.07
8224 12126 4.468510 TGGAGTAACCGACTTACCAATCAT 59.531 41.667 0.00 0.00 39.06 2.45
8225 12127 3.833650 TGGAGTAACCGACTTACCAATCA 59.166 43.478 0.00 0.00 39.06 2.57
8226 12128 4.430908 CTGGAGTAACCGACTTACCAATC 58.569 47.826 0.00 0.00 39.06 2.67
8227 12129 3.369157 GCTGGAGTAACCGACTTACCAAT 60.369 47.826 0.00 0.00 39.06 3.16
8228 12130 2.028748 GCTGGAGTAACCGACTTACCAA 60.029 50.000 0.00 0.00 39.06 3.67
8229 12131 1.547372 GCTGGAGTAACCGACTTACCA 59.453 52.381 0.00 0.00 39.06 3.25
8230 12132 1.468736 CGCTGGAGTAACCGACTTACC 60.469 57.143 0.00 0.00 39.06 2.85
8231 12133 1.905449 CGCTGGAGTAACCGACTTAC 58.095 55.000 0.00 0.00 39.06 2.34
8232 12134 0.171903 GCGCTGGAGTAACCGACTTA 59.828 55.000 0.00 0.00 39.06 2.24
8233 12135 1.080025 GCGCTGGAGTAACCGACTT 60.080 57.895 0.00 0.00 39.06 3.01
8234 12136 2.572284 GCGCTGGAGTAACCGACT 59.428 61.111 0.00 0.00 42.90 4.18
8235 12137 2.508663 GGCGCTGGAGTAACCGAC 60.509 66.667 7.64 0.00 42.61 4.79
8236 12138 2.992689 TGGCGCTGGAGTAACCGA 60.993 61.111 7.64 0.00 42.61 4.69
8237 12139 2.813908 GTGGCGCTGGAGTAACCG 60.814 66.667 7.64 0.00 42.61 4.44
8238 12140 2.436115 GGTGGCGCTGGAGTAACC 60.436 66.667 7.64 0.35 39.54 2.85
8239 12141 2.436115 GGGTGGCGCTGGAGTAAC 60.436 66.667 7.64 0.00 0.00 2.50
8240 12142 4.077184 CGGGTGGCGCTGGAGTAA 62.077 66.667 7.64 0.00 0.00 2.24
8252 12154 3.760035 CAGAGGGACGGACGGGTG 61.760 72.222 0.00 0.00 0.00 4.61
8253 12155 4.296729 ACAGAGGGACGGACGGGT 62.297 66.667 0.00 0.00 0.00 5.28
8254 12156 3.450115 GACAGAGGGACGGACGGG 61.450 72.222 0.00 0.00 0.00 5.28
8255 12157 3.812019 CGACAGAGGGACGGACGG 61.812 72.222 0.00 0.00 0.00 4.79
8256 12158 4.477975 GCGACAGAGGGACGGACG 62.478 72.222 0.00 0.00 35.59 4.79
8257 12159 4.131088 GGCGACAGAGGGACGGAC 62.131 72.222 0.00 0.00 0.00 4.79
8258 12160 2.280404 ATAGGCGACAGAGGGACGGA 62.280 60.000 0.00 0.00 0.00 4.69
8259 12161 1.797211 GATAGGCGACAGAGGGACGG 61.797 65.000 0.00 0.00 0.00 4.79
8260 12162 1.101635 TGATAGGCGACAGAGGGACG 61.102 60.000 0.00 0.00 0.00 4.79
8261 12163 1.000283 CATGATAGGCGACAGAGGGAC 60.000 57.143 0.00 0.00 0.00 4.46
8262 12164 1.332195 CATGATAGGCGACAGAGGGA 58.668 55.000 0.00 0.00 0.00 4.20
8263 12165 0.319728 CCATGATAGGCGACAGAGGG 59.680 60.000 0.00 0.00 0.00 4.30
8264 12166 0.320247 GCCATGATAGGCGACAGAGG 60.320 60.000 0.00 0.00 46.12 3.69
8265 12167 3.207677 GCCATGATAGGCGACAGAG 57.792 57.895 0.00 0.00 46.12 3.35
8273 12175 6.425114 GCATCCGTTTATATAGCCATGATAGG 59.575 42.308 0.00 0.00 0.00 2.57
8274 12176 6.425114 GGCATCCGTTTATATAGCCATGATAG 59.575 42.308 0.00 0.00 40.29 2.08
8275 12177 6.288294 GGCATCCGTTTATATAGCCATGATA 58.712 40.000 0.00 0.00 40.29 2.15
8276 12178 5.126067 GGCATCCGTTTATATAGCCATGAT 58.874 41.667 0.00 0.00 40.29 2.45
8277 12179 4.513442 GGCATCCGTTTATATAGCCATGA 58.487 43.478 0.00 0.00 40.29 3.07
8281 12183 3.270877 CAGGGCATCCGTTTATATAGCC 58.729 50.000 0.00 0.00 39.86 3.93
8293 12195 0.250640 CAGCTATGACCAGGGCATCC 60.251 60.000 12.64 4.19 0.00 3.51
8295 12197 1.150081 GCAGCTATGACCAGGGCAT 59.850 57.895 14.03 14.03 0.00 4.40
8301 12203 1.139654 GGATGACTGCAGCTATGACCA 59.860 52.381 15.27 1.02 0.00 4.02
8311 12213 1.381191 TAGGAGCCGGATGACTGCA 60.381 57.895 5.05 0.00 0.00 4.41
8313 12215 1.043116 TGGTAGGAGCCGGATGACTG 61.043 60.000 5.05 0.00 0.00 3.51
8323 12225 4.466726 TCTCCTTACTTTCTTGGTAGGAGC 59.533 45.833 10.37 0.00 36.16 4.70
8335 12237 4.342665 GGGATCTCGATGTCTCCTTACTTT 59.657 45.833 0.00 0.00 0.00 2.66
8344 12246 3.482436 GACTACAGGGATCTCGATGTCT 58.518 50.000 0.00 0.00 0.00 3.41
8351 12253 0.671251 CAGCGGACTACAGGGATCTC 59.329 60.000 0.00 0.00 0.00 2.75
8368 12270 7.333672 GGTAAGTTACTCCATTTGAACTACCAG 59.666 40.741 12.65 0.00 31.96 4.00
8373 12275 6.002082 GGTGGTAAGTTACTCCATTTGAACT 58.998 40.000 12.65 0.00 33.60 3.01
8375 12277 5.942961 TGGTGGTAAGTTACTCCATTTGAA 58.057 37.500 19.06 4.07 33.68 2.69
8400 12302 1.473434 CGACTTCCCATGTAGCTTCCC 60.473 57.143 0.00 0.00 0.00 3.97
8411 12313 2.198827 ATGAATGTTGCGACTTCCCA 57.801 45.000 5.50 2.05 0.00 4.37
8418 12320 7.381139 GGAAAACTTTCTAAATGAATGTTGCGA 59.619 33.333 9.36 0.00 45.93 5.10
8548 12464 1.517475 GTCTTCCCGCGCTCTTCTC 60.517 63.158 5.56 0.00 0.00 2.87
8549 12465 1.536943 AAGTCTTCCCGCGCTCTTCT 61.537 55.000 5.56 0.00 0.00 2.85
8550 12466 1.079317 GAAGTCTTCCCGCGCTCTTC 61.079 60.000 5.56 4.19 0.00 2.87
8604 12534 5.773239 TGGAGTCTTTTATTTAACTCGCG 57.227 39.130 0.00 0.00 39.20 5.87
8615 12545 9.528018 GAATTTGTGTCATTTTGGAGTCTTTTA 57.472 29.630 0.00 0.00 0.00 1.52
8616 12546 8.040132 TGAATTTGTGTCATTTTGGAGTCTTTT 58.960 29.630 0.00 0.00 0.00 2.27
8617 12547 7.555087 TGAATTTGTGTCATTTTGGAGTCTTT 58.445 30.769 0.00 0.00 0.00 2.52
8618 12548 7.111247 TGAATTTGTGTCATTTTGGAGTCTT 57.889 32.000 0.00 0.00 0.00 3.01
8619 12549 6.713762 TGAATTTGTGTCATTTTGGAGTCT 57.286 33.333 0.00 0.00 0.00 3.24
8620 12550 5.403466 GCTGAATTTGTGTCATTTTGGAGTC 59.597 40.000 0.00 0.00 0.00 3.36
8621 12551 5.069516 AGCTGAATTTGTGTCATTTTGGAGT 59.930 36.000 0.00 0.00 0.00 3.85
8622 12552 5.535333 AGCTGAATTTGTGTCATTTTGGAG 58.465 37.500 0.00 0.00 0.00 3.86
8623 12553 5.534207 AGCTGAATTTGTGTCATTTTGGA 57.466 34.783 0.00 0.00 0.00 3.53
8624 12554 6.583806 GTCTAGCTGAATTTGTGTCATTTTGG 59.416 38.462 0.00 0.00 0.00 3.28
8625 12555 7.365741 AGTCTAGCTGAATTTGTGTCATTTTG 58.634 34.615 0.00 0.00 0.00 2.44
8626 12556 7.516198 AGTCTAGCTGAATTTGTGTCATTTT 57.484 32.000 0.00 0.00 0.00 1.82
8638 12568 7.287466 AGATGTATCTGAACAGTCTAGCTGAAT 59.713 37.037 17.52 8.36 40.65 2.57
8639 12569 6.605194 AGATGTATCTGAACAGTCTAGCTGAA 59.395 38.462 17.52 5.49 40.65 3.02
8640 12570 6.125719 AGATGTATCTGAACAGTCTAGCTGA 58.874 40.000 17.52 0.00 40.65 4.26
8641 12571 6.389830 AGATGTATCTGAACAGTCTAGCTG 57.610 41.667 11.23 11.23 42.37 4.24
8642 12572 8.526667 TTTAGATGTATCTGAACAGTCTAGCT 57.473 34.615 4.67 0.00 37.76 3.32
8643 12573 9.243637 CTTTTAGATGTATCTGAACAGTCTAGC 57.756 37.037 4.67 0.00 37.76 3.42
8683 12613 6.239036 GGGTGAAGCTGACAAGTATTCTTTTT 60.239 38.462 0.00 0.00 0.00 1.94
8684 12614 5.241728 GGGTGAAGCTGACAAGTATTCTTTT 59.758 40.000 0.00 0.00 0.00 2.27
8685 12615 4.762251 GGGTGAAGCTGACAAGTATTCTTT 59.238 41.667 0.00 0.00 0.00 2.52
8686 12616 4.202461 TGGGTGAAGCTGACAAGTATTCTT 60.202 41.667 0.00 0.00 0.00 2.52
8687 12617 3.327757 TGGGTGAAGCTGACAAGTATTCT 59.672 43.478 0.00 0.00 0.00 2.40
8688 12618 3.674997 TGGGTGAAGCTGACAAGTATTC 58.325 45.455 0.00 0.00 0.00 1.75
8689 12619 3.560025 CCTGGGTGAAGCTGACAAGTATT 60.560 47.826 0.00 0.00 0.00 1.89
8690 12620 2.026822 CCTGGGTGAAGCTGACAAGTAT 60.027 50.000 0.00 0.00 0.00 2.12
8691 12621 1.347707 CCTGGGTGAAGCTGACAAGTA 59.652 52.381 0.00 0.00 0.00 2.24
8692 12622 0.109342 CCTGGGTGAAGCTGACAAGT 59.891 55.000 0.00 0.00 0.00 3.16
8693 12623 1.239968 GCCTGGGTGAAGCTGACAAG 61.240 60.000 0.00 0.00 0.00 3.16
8694 12624 1.228245 GCCTGGGTGAAGCTGACAA 60.228 57.895 0.00 0.00 0.00 3.18
8695 12625 1.782201 ATGCCTGGGTGAAGCTGACA 61.782 55.000 0.00 0.00 0.00 3.58
8696 12626 1.001641 ATGCCTGGGTGAAGCTGAC 60.002 57.895 0.00 0.00 0.00 3.51
8697 12627 1.300963 GATGCCTGGGTGAAGCTGA 59.699 57.895 0.00 0.00 0.00 4.26
8698 12628 2.110967 CGATGCCTGGGTGAAGCTG 61.111 63.158 0.00 0.00 0.00 4.24
8699 12629 1.841302 TTCGATGCCTGGGTGAAGCT 61.841 55.000 0.00 0.00 0.00 3.74
8700 12630 0.960364 TTTCGATGCCTGGGTGAAGC 60.960 55.000 0.00 0.00 0.00 3.86
8701 12631 0.804989 GTTTCGATGCCTGGGTGAAG 59.195 55.000 0.00 0.00 0.00 3.02
8702 12632 0.953471 CGTTTCGATGCCTGGGTGAA 60.953 55.000 0.00 0.00 0.00 3.18
8703 12633 1.375396 CGTTTCGATGCCTGGGTGA 60.375 57.895 0.00 0.00 0.00 4.02
8704 12634 0.744414 ATCGTTTCGATGCCTGGGTG 60.744 55.000 3.85 0.00 45.24 4.61
8705 12635 0.828022 TATCGTTTCGATGCCTGGGT 59.172 50.000 13.70 0.00 46.43 4.51
8706 12636 1.800586 CATATCGTTTCGATGCCTGGG 59.199 52.381 13.70 0.00 46.43 4.45
8707 12637 2.483876 ACATATCGTTTCGATGCCTGG 58.516 47.619 13.70 0.00 46.43 4.45
8708 12638 4.327357 GGATACATATCGTTTCGATGCCTG 59.673 45.833 13.70 10.65 46.43 4.85
8709 12639 4.021456 TGGATACATATCGTTTCGATGCCT 60.021 41.667 13.70 0.36 44.67 4.75
8710 12640 4.242475 TGGATACATATCGTTTCGATGCC 58.758 43.478 13.70 6.86 44.67 4.40
8726 12656 6.406692 TGGAGCACTTAGATAGTTGGATAC 57.593 41.667 0.00 0.00 33.85 2.24
8727 12657 7.432148 TTTGGAGCACTTAGATAGTTGGATA 57.568 36.000 0.00 0.00 33.85 2.59
8728 12658 5.957771 TTGGAGCACTTAGATAGTTGGAT 57.042 39.130 0.00 0.00 33.85 3.41
8729 12659 5.755409 TTTGGAGCACTTAGATAGTTGGA 57.245 39.130 0.00 0.00 33.85 3.53
8730 12660 5.235186 CGATTTGGAGCACTTAGATAGTTGG 59.765 44.000 0.00 0.00 33.85 3.77
8731 12661 5.277058 GCGATTTGGAGCACTTAGATAGTTG 60.277 44.000 0.00 0.00 33.85 3.16
8732 12662 4.811557 GCGATTTGGAGCACTTAGATAGTT 59.188 41.667 0.00 0.00 33.85 2.24
8733 12663 4.372656 GCGATTTGGAGCACTTAGATAGT 58.627 43.478 0.00 0.00 37.68 2.12
8734 12664 3.426859 CGCGATTTGGAGCACTTAGATAG 59.573 47.826 0.00 0.00 0.00 2.08
8735 12665 3.067601 TCGCGATTTGGAGCACTTAGATA 59.932 43.478 3.71 0.00 0.00 1.98
8736 12666 2.159099 TCGCGATTTGGAGCACTTAGAT 60.159 45.455 3.71 0.00 0.00 1.98
8737 12667 1.203758 TCGCGATTTGGAGCACTTAGA 59.796 47.619 3.71 0.00 0.00 2.10
8738 12668 1.640428 TCGCGATTTGGAGCACTTAG 58.360 50.000 3.71 0.00 0.00 2.18
8739 12669 2.087501 TTCGCGATTTGGAGCACTTA 57.912 45.000 10.88 0.00 0.00 2.24
8740 12670 1.234821 TTTCGCGATTTGGAGCACTT 58.765 45.000 10.88 0.00 0.00 3.16
8741 12671 1.453155 ATTTCGCGATTTGGAGCACT 58.547 45.000 10.88 0.00 0.00 4.40
8742 12672 3.398954 TTATTTCGCGATTTGGAGCAC 57.601 42.857 10.88 0.00 0.00 4.40
8743 12673 3.753842 GTTTATTTCGCGATTTGGAGCA 58.246 40.909 10.88 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.