Multiple sequence alignment - TraesCS3B01G057600

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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 TraesCS3B01G057600 chr3B 100.000 7580 0 0 1 7580 30006584 29999005 0.000000e+00 13998.0
1 TraesCS3B01G057600 chr3B 100.000 1937 0 0 7911 9847 29998674 29996738 0.000000e+00 3578.0
2 TraesCS3B01G057600 chr3B 93.054 1382 77 10 5658 7026 29479195 29477820 0.000000e+00 2002.0
3 TraesCS3B01G057600 chr3B 97.339 1090 24 3 1796 2881 54566363 54565275 0.000000e+00 1847.0
4 TraesCS3B01G057600 chr3B 96.872 1087 33 1 1797 2882 30245950 30247036 0.000000e+00 1818.0
5 TraesCS3B01G057600 chr3B 94.597 1129 18 4 668 1796 29497154 29496069 0.000000e+00 1707.0
6 TraesCS3B01G057600 chr3B 92.274 1126 62 4 3854 4954 29486860 29485735 0.000000e+00 1574.0
7 TraesCS3B01G057600 chr3B 87.557 1101 73 28 1797 2881 114171496 114170444 0.000000e+00 1216.0
8 TraesCS3B01G057600 chr3B 88.211 950 92 6 8915 9845 29853780 29854728 0.000000e+00 1116.0
9 TraesCS3B01G057600 chr3B 89.266 885 76 5 8980 9845 29734386 29735270 0.000000e+00 1090.0
10 TraesCS3B01G057600 chr3B 98.741 556 6 1 7026 7580 622107677 622107122 0.000000e+00 987.0
11 TraesCS3B01G057600 chr3B 98.783 493 6 0 7911 8403 345412198 345412690 0.000000e+00 878.0
12 TraesCS3B01G057600 chr3B 98.182 495 9 0 7911 8405 51872199 51871705 0.000000e+00 865.0
13 TraesCS3B01G057600 chr3B 92.118 609 31 7 3244 3849 29495454 29494860 0.000000e+00 843.0
14 TraesCS3B01G057600 chr3B 94.518 456 17 4 1 449 29497619 29497165 0.000000e+00 697.0
15 TraesCS3B01G057600 chr3B 97.541 366 7 2 2882 3245 29496077 29495712 8.400000e-175 625.0
16 TraesCS3B01G057600 chr3B 91.116 439 35 3 5227 5661 29483597 29483159 8.520000e-165 592.0
17 TraesCS3B01G057600 chr3B 77.975 958 149 39 626 1565 30498148 30499061 2.420000e-150 544.0
18 TraesCS3B01G057600 chr3B 77.800 982 144 34 605 1563 29774534 29775464 1.130000e-148 538.0
19 TraesCS3B01G057600 chr3B 77.462 985 157 34 605 1565 29776720 29777663 6.770000e-146 529.0
20 TraesCS3B01G057600 chr3B 77.019 1040 162 43 605 1616 30508776 30509766 8.760000e-145 525.0
21 TraesCS3B01G057600 chr3B 76.596 940 147 44 652 1565 30199859 30200751 5.420000e-122 449.0
22 TraesCS3B01G057600 chr3B 79.814 644 89 21 850 1474 24928705 24929326 1.960000e-116 431.0
23 TraesCS3B01G057600 chr3B 96.109 257 10 0 8404 8660 29477833 29477577 4.250000e-113 420.0
24 TraesCS3B01G057600 chr3B 96.203 237 8 1 8683 8918 29477301 29477065 4.310000e-103 387.0
25 TraesCS3B01G057600 chr3B 89.928 278 17 7 4949 5224 29485691 29485423 2.040000e-91 348.0
26 TraesCS3B01G057600 chr3B 80.214 187 32 5 3658 3843 89169836 89169654 1.730000e-27 135.0
27 TraesCS3B01G057600 chr3B 78.924 223 22 9 370 579 29724055 29724265 2.890000e-25 128.0
28 TraesCS3B01G057600 chr3B 78.571 154 24 6 8720 8871 29627996 29628142 1.050000e-14 93.5
29 TraesCS3B01G057600 chr3B 78.571 140 27 2 188 324 30443053 30443192 1.360000e-13 89.8
30 TraesCS3B01G057600 chr3B 77.273 132 29 1 194 324 29724365 29724496 1.060000e-09 76.8
31 TraesCS3B01G057600 chr3D 87.412 1700 160 27 5227 6908 18829065 18830728 0.000000e+00 1905.0
32 TraesCS3B01G057600 chr3D 92.857 1036 43 12 763 1796 18815457 18816463 0.000000e+00 1474.0
33 TraesCS3B01G057600 chr3D 95.166 931 45 0 8915 9845 18845912 18846842 0.000000e+00 1471.0
34 TraesCS3B01G057600 chr3D 89.379 885 75 5 8980 9845 18952556 18953440 0.000000e+00 1096.0
35 TraesCS3B01G057600 chr3D 88.692 902 81 10 8962 9845 18908536 18909434 0.000000e+00 1081.0
36 TraesCS3B01G057600 chr3D 88.798 732 81 1 3854 4585 18817622 18818352 0.000000e+00 896.0
37 TraesCS3B01G057600 chr3D 87.795 762 76 10 3088 3845 18816600 18817348 0.000000e+00 876.0
38 TraesCS3B01G057600 chr3D 81.048 649 87 16 845 1475 17538052 17537422 1.490000e-132 484.0
39 TraesCS3B01G057600 chr3D 79.563 641 95 18 605 1243 18793019 18793625 9.140000e-115 425.0
40 TraesCS3B01G057600 chr3D 93.651 252 11 3 477 728 18815208 18815454 1.210000e-98 372.0
41 TraesCS3B01G057600 chr3D 77.239 681 112 22 851 1511 17670800 17670143 9.400000e-95 359.0
42 TraesCS3B01G057600 chr3D 93.249 237 15 1 8683 8918 18845640 18845876 2.040000e-91 348.0
43 TraesCS3B01G057600 chr3D 84.615 273 24 9 4949 5221 18818724 18818978 1.270000e-63 255.0
44 TraesCS3B01G057600 chr3D 93.519 108 7 0 2963 3070 18816507 18816614 2.850000e-35 161.0
45 TraesCS3B01G057600 chr3D 82.320 181 26 6 3662 3841 600858001 600857826 1.710000e-32 152.0
46 TraesCS3B01G057600 chr3D 80.723 166 29 3 8708 8871 18742077 18742241 1.040000e-24 126.0
47 TraesCS3B01G057600 chr3D 95.652 69 1 2 2882 2948 18816455 18816523 1.050000e-19 110.0
48 TraesCS3B01G057600 chr3D 78.947 152 30 1 8720 8871 18908223 18908372 1.750000e-17 102.0
49 TraesCS3B01G057600 chr3D 91.935 62 4 1 71 131 18794670 18794731 1.760000e-12 86.1
50 TraesCS3B01G057600 chr3D 86.765 68 8 1 3515 3582 554711028 554710962 3.810000e-09 75.0
51 TraesCS3B01G057600 chr3A 90.031 953 70 4 8918 9845 26232936 26233888 0.000000e+00 1210.0
52 TraesCS3B01G057600 chr3A 89.831 885 71 5 8980 9845 26427525 26428409 0.000000e+00 1118.0
53 TraesCS3B01G057600 chr3A 87.261 942 98 11 8923 9845 26205438 26206376 0.000000e+00 1055.0
54 TraesCS3B01G057600 chr3A 90.874 778 69 1 9070 9845 26406247 26407024 0.000000e+00 1042.0
55 TraesCS3B01G057600 chr3A 80.389 668 104 14 850 1508 19275657 19276306 5.350000e-132 483.0
56 TraesCS3B01G057600 chr3A 85.780 436 42 7 8475 8892 26232424 26232857 2.520000e-120 444.0
57 TraesCS3B01G057600 chr3A 73.993 819 157 28 798 1590 26257492 26258280 2.090000e-71 281.0
58 TraesCS3B01G057600 chr3A 81.379 145 26 1 8727 8871 26010041 26009898 6.250000e-22 117.0
59 TraesCS3B01G057600 chr3A 81.690 142 25 1 8731 8871 26205170 26205311 6.250000e-22 117.0
60 TraesCS3B01G057600 chr3A 90.476 63 5 1 67 128 26204124 26204186 2.280000e-11 82.4
61 TraesCS3B01G057600 chr3A 75.000 216 34 9 6245 6457 26231686 26231884 2.280000e-11 82.4
62 TraesCS3B01G057600 chr3A 95.833 48 2 0 6933 6980 749188079 749188032 2.950000e-10 78.7
63 TraesCS3B01G057600 chr3A 93.750 48 3 0 6933 6980 686910695 686910648 1.370000e-08 73.1
64 TraesCS3B01G057600 chr7D 85.267 991 137 7 3854 4839 511063246 511062260 0.000000e+00 1013.0
65 TraesCS3B01G057600 chr7D 84.060 872 133 5 3972 4840 167633259 167632391 0.000000e+00 835.0
66 TraesCS3B01G057600 chr7D 86.176 680 64 19 2219 2881 440004079 440003413 0.000000e+00 708.0
67 TraesCS3B01G057600 chr7D 87.261 628 62 11 1797 2422 568064445 568063834 0.000000e+00 701.0
68 TraesCS3B01G057600 chr7D 86.888 633 63 15 2273 2888 28853452 28852823 0.000000e+00 691.0
69 TraesCS3B01G057600 chr7D 88.268 537 46 11 1797 2333 55394401 55394920 2.330000e-175 627.0
70 TraesCS3B01G057600 chr7D 95.652 46 2 0 6935 6980 571008943 571008898 3.810000e-09 75.0
71 TraesCS3B01G057600 chr7D 87.302 63 5 3 6935 6995 167522196 167522257 1.770000e-07 69.4
72 TraesCS3B01G057600 chr6B 83.874 1110 118 41 1797 2888 576820882 576819816 0.000000e+00 1002.0
73 TraesCS3B01G057600 chr6B 93.617 47 3 0 6934 6980 689119197 689119151 4.930000e-08 71.3
74 TraesCS3B01G057600 chr1B 99.099 555 5 0 7026 7580 683131788 683132342 0.000000e+00 998.0
75 TraesCS3B01G057600 chr1B 81.907 1122 124 42 1794 2882 534948551 534949626 0.000000e+00 874.0
76 TraesCS3B01G057600 chr1B 98.580 493 7 0 7911 8403 683132390 683132882 0.000000e+00 872.0
77 TraesCS3B01G057600 chr1B 87.937 630 71 5 1796 2424 95446047 95445422 0.000000e+00 737.0
78 TraesCS3B01G057600 chr1B 86.378 624 67 14 2274 2881 54130181 54130802 0.000000e+00 665.0
79 TraesCS3B01G057600 chr1B 84.341 645 63 25 2274 2881 449735648 449735005 1.830000e-166 597.0
80 TraesCS3B01G057600 chr1B 89.231 65 7 0 3514 3578 28648249 28648313 2.280000e-11 82.4
81 TraesCS3B01G057600 chr1B 86.301 73 9 1 3523 3595 594907594 594907523 2.950000e-10 78.7
82 TraesCS3B01G057600 chr1B 92.308 52 4 0 6929 6980 647880148 647880097 3.810000e-09 75.0
83 TraesCS3B01G057600 chr4A 98.919 555 5 1 7026 7580 473500857 473500304 0.000000e+00 990.0
84 TraesCS3B01G057600 chr4A 95.695 604 20 6 2282 2881 726975291 726975892 0.000000e+00 966.0
85 TraesCS3B01G057600 chr4A 82.369 1106 161 16 3859 4935 615367295 615366195 0.000000e+00 931.0
86 TraesCS3B01G057600 chr4A 96.875 544 17 0 1797 2340 726974888 726975431 0.000000e+00 911.0
87 TraesCS3B01G057600 chr5B 98.741 556 6 1 7026 7580 386660818 386661373 0.000000e+00 987.0
88 TraesCS3B01G057600 chr5B 98.167 491 9 0 7913 8403 386661540 386662030 0.000000e+00 857.0
89 TraesCS3B01G057600 chr1A 98.741 556 6 1 7026 7580 4263746 4263191 0.000000e+00 987.0
90 TraesCS3B01G057600 chr1A 93.617 47 3 0 6934 6980 32549226 32549272 4.930000e-08 71.3
91 TraesCS3B01G057600 chr1A 93.617 47 3 0 6934 6980 356442905 356442859 4.930000e-08 71.3
92 TraesCS3B01G057600 chr1A 93.617 47 3 0 6934 6980 554084279 554084233 4.930000e-08 71.3
93 TraesCS3B01G057600 chr1A 93.617 47 3 0 6934 6980 580146212 580146166 4.930000e-08 71.3
94 TraesCS3B01G057600 chr2A 98.564 557 6 1 7026 7580 753525284 753525840 0.000000e+00 983.0
95 TraesCS3B01G057600 chr2A 98.378 555 5 1 7026 7580 191937370 191936820 0.000000e+00 972.0
96 TraesCS3B01G057600 chr2A 98.207 502 9 0 7911 8412 191936772 191936271 0.000000e+00 878.0
97 TraesCS3B01G057600 chr2A 100.000 28 0 0 3554 3581 2925757 2925784 1.800000e-02 52.8
98 TraesCS3B01G057600 chr6A 98.559 555 8 0 7026 7580 73460193 73459639 0.000000e+00 981.0
99 TraesCS3B01G057600 chr6A 98.390 497 8 0 7911 8407 73459404 73458908 0.000000e+00 874.0
100 TraesCS3B01G057600 chr6A 81.818 440 48 21 2219 2640 382407205 382407630 3.410000e-89 340.0
101 TraesCS3B01G057600 chr6A 93.617 47 3 0 6934 6980 610234314 610234268 4.930000e-08 71.3
102 TraesCS3B01G057600 chr6A 93.617 47 3 0 6934 6980 613273428 613273382 4.930000e-08 71.3
103 TraesCS3B01G057600 chr7B 98.378 555 9 0 7026 7580 671706915 671707469 0.000000e+00 976.0
104 TraesCS3B01G057600 chr7B 80.082 974 181 13 3854 4821 217459847 217458881 0.000000e+00 712.0
105 TraesCS3B01G057600 chr7B 80.383 209 34 6 5459 5662 715567583 715567377 1.710000e-32 152.0
106 TraesCS3B01G057600 chr7B 95.745 47 2 0 6934 6980 342995303 342995257 1.060000e-09 76.8
107 TraesCS3B01G057600 chr7B 95.745 47 2 0 6934 6980 645394414 645394460 1.060000e-09 76.8
108 TraesCS3B01G057600 chr5D 84.600 987 137 10 3866 4840 434718475 434717492 0.000000e+00 966.0
109 TraesCS3B01G057600 chr5D 82.222 1125 135 45 1797 2881 7032125 7033224 0.000000e+00 909.0
110 TraesCS3B01G057600 chr5D 79.017 977 202 3 3866 4840 302376593 302377568 0.000000e+00 665.0
111 TraesCS3B01G057600 chr5D 80.435 184 31 5 3662 3844 293160595 293160774 1.730000e-27 135.0
112 TraesCS3B01G057600 chr4D 83.046 1103 121 43 1797 2882 502546606 502547659 0.000000e+00 941.0
113 TraesCS3B01G057600 chr4D 95.652 46 2 0 6935 6980 360866998 360867043 3.810000e-09 75.0
114 TraesCS3B01G057600 chr4D 95.122 41 2 0 6940 6980 384965735 384965695 2.300000e-06 65.8
115 TraesCS3B01G057600 chrUn 81.598 1114 168 21 3852 4935 21942666 21943772 0.000000e+00 887.0
116 TraesCS3B01G057600 chrUn 85.782 633 69 17 2274 2887 34133669 34134299 0.000000e+00 651.0
117 TraesCS3B01G057600 chrUn 80.263 152 24 4 8720 8871 37328119 37328264 1.050000e-19 110.0
118 TraesCS3B01G057600 chrUn 81.633 98 13 3 6934 7026 95391235 95391332 1.060000e-09 76.8
119 TraesCS3B01G057600 chr2B 98.975 488 5 0 7911 8398 52422457 52421970 0.000000e+00 874.0
120 TraesCS3B01G057600 chr2B 83.969 262 26 11 3513 3771 787140240 787140488 4.600000e-58 237.0
121 TraesCS3B01G057600 chr2B 76.879 346 57 16 3513 3844 29547057 29547393 3.660000e-39 174.0
122 TraesCS3B01G057600 chr2B 80.749 187 27 8 3661 3842 797075555 797075373 4.800000e-28 137.0
123 TraesCS3B01G057600 chr5A 98.174 493 9 0 7911 8403 43260629 43260137 0.000000e+00 861.0
124 TraesCS3B01G057600 chr5A 95.556 45 2 0 6934 6978 547206744 547206700 1.370000e-08 73.1
125 TraesCS3B01G057600 chr4B 97.984 496 8 1 7911 8404 483774876 483775371 0.000000e+00 859.0
126 TraesCS3B01G057600 chr4B 81.564 179 28 4 3667 3843 57172169 57171994 1.030000e-29 143.0
127 TraesCS3B01G057600 chr1D 81.495 1124 133 48 1797 2881 481958011 481956924 0.000000e+00 854.0
128 TraesCS3B01G057600 chr1D 84.875 681 61 19 2219 2882 483047954 483048609 0.000000e+00 649.0
129 TraesCS3B01G057600 chr1D 93.617 47 3 0 6934 6980 20821558 20821512 4.930000e-08 71.3
130 TraesCS3B01G057600 chr6D 85.735 680 60 20 2219 2881 15379610 15378951 0.000000e+00 684.0
131 TraesCS3B01G057600 chr6D 81.421 183 29 5 3662 3843 430012383 430012205 2.870000e-30 145.0
132 TraesCS3B01G057600 chr7A 83.140 344 36 13 3513 3848 271628865 271628536 2.690000e-75 294.0
133 TraesCS3B01G057600 chr7A 83.019 106 17 1 5466 5570 727704144 727704039 2.930000e-15 95.3
134 TraesCS3B01G057600 chr2D 86.957 69 9 0 3514 3582 11251689 11251757 2.950000e-10 78.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G057600 chr3B 29996738 30006584 9846 True 8788.000000 13998 100.000000 1 9847 2 chr3B.!!$R8 9846
1 TraesCS3B01G057600 chr3B 54565275 54566363 1088 True 1847.000000 1847 97.339000 1796 2881 1 chr3B.!!$R2 1085
2 TraesCS3B01G057600 chr3B 30245950 30247036 1086 False 1818.000000 1818 96.872000 1797 2882 1 chr3B.!!$F6 1085
3 TraesCS3B01G057600 chr3B 114170444 114171496 1052 True 1216.000000 1216 87.557000 1797 2881 1 chr3B.!!$R4 1084
4 TraesCS3B01G057600 chr3B 29853780 29854728 948 False 1116.000000 1116 88.211000 8915 9845 1 chr3B.!!$F4 930
5 TraesCS3B01G057600 chr3B 29734386 29735270 884 False 1090.000000 1090 89.266000 8980 9845 1 chr3B.!!$F3 865
6 TraesCS3B01G057600 chr3B 622107122 622107677 555 True 987.000000 987 98.741000 7026 7580 1 chr3B.!!$R5 554
7 TraesCS3B01G057600 chr3B 29494860 29497619 2759 True 968.000000 1707 94.693500 1 3849 4 chr3B.!!$R7 3848
8 TraesCS3B01G057600 chr3B 29477065 29486860 9795 True 887.166667 2002 93.114000 3854 8918 6 chr3B.!!$R6 5064
9 TraesCS3B01G057600 chr3B 30498148 30499061 913 False 544.000000 544 77.975000 626 1565 1 chr3B.!!$F8 939
10 TraesCS3B01G057600 chr3B 29774534 29777663 3129 False 533.500000 538 77.631000 605 1565 2 chr3B.!!$F12 960
11 TraesCS3B01G057600 chr3B 30508776 30509766 990 False 525.000000 525 77.019000 605 1616 1 chr3B.!!$F9 1011
12 TraesCS3B01G057600 chr3B 30199859 30200751 892 False 449.000000 449 76.596000 652 1565 1 chr3B.!!$F5 913
13 TraesCS3B01G057600 chr3B 24928705 24929326 621 False 431.000000 431 79.814000 850 1474 1 chr3B.!!$F1 624
14 TraesCS3B01G057600 chr3D 18829065 18830728 1663 False 1905.000000 1905 87.412000 5227 6908 1 chr3D.!!$F2 1681
15 TraesCS3B01G057600 chr3D 18952556 18953440 884 False 1096.000000 1096 89.379000 8980 9845 1 chr3D.!!$F3 865
16 TraesCS3B01G057600 chr3D 18845640 18846842 1202 False 909.500000 1471 94.207500 8683 9845 2 chr3D.!!$F6 1162
17 TraesCS3B01G057600 chr3D 18815208 18818978 3770 False 592.000000 1474 90.983857 477 5221 7 chr3D.!!$F5 4744
18 TraesCS3B01G057600 chr3D 18908223 18909434 1211 False 591.500000 1081 83.819500 8720 9845 2 chr3D.!!$F7 1125
19 TraesCS3B01G057600 chr3D 17537422 17538052 630 True 484.000000 484 81.048000 845 1475 1 chr3D.!!$R1 630
20 TraesCS3B01G057600 chr3D 17670143 17670800 657 True 359.000000 359 77.239000 851 1511 1 chr3D.!!$R2 660
21 TraesCS3B01G057600 chr3D 18793019 18794731 1712 False 255.550000 425 85.749000 71 1243 2 chr3D.!!$F4 1172
22 TraesCS3B01G057600 chr3A 26427525 26428409 884 False 1118.000000 1118 89.831000 8980 9845 1 chr3A.!!$F4 865
23 TraesCS3B01G057600 chr3A 26406247 26407024 777 False 1042.000000 1042 90.874000 9070 9845 1 chr3A.!!$F3 775
24 TraesCS3B01G057600 chr3A 26231686 26233888 2202 False 578.800000 1210 83.603667 6245 9845 3 chr3A.!!$F6 3600
25 TraesCS3B01G057600 chr3A 19275657 19276306 649 False 483.000000 483 80.389000 850 1508 1 chr3A.!!$F1 658
26 TraesCS3B01G057600 chr3A 26204124 26206376 2252 False 418.133333 1055 86.475667 67 9845 3 chr3A.!!$F5 9778
27 TraesCS3B01G057600 chr3A 26257492 26258280 788 False 281.000000 281 73.993000 798 1590 1 chr3A.!!$F2 792
28 TraesCS3B01G057600 chr7D 511062260 511063246 986 True 1013.000000 1013 85.267000 3854 4839 1 chr7D.!!$R4 985
29 TraesCS3B01G057600 chr7D 167632391 167633259 868 True 835.000000 835 84.060000 3972 4840 1 chr7D.!!$R2 868
30 TraesCS3B01G057600 chr7D 440003413 440004079 666 True 708.000000 708 86.176000 2219 2881 1 chr7D.!!$R3 662
31 TraesCS3B01G057600 chr7D 568063834 568064445 611 True 701.000000 701 87.261000 1797 2422 1 chr7D.!!$R5 625
32 TraesCS3B01G057600 chr7D 28852823 28853452 629 True 691.000000 691 86.888000 2273 2888 1 chr7D.!!$R1 615
33 TraesCS3B01G057600 chr7D 55394401 55394920 519 False 627.000000 627 88.268000 1797 2333 1 chr7D.!!$F1 536
34 TraesCS3B01G057600 chr6B 576819816 576820882 1066 True 1002.000000 1002 83.874000 1797 2888 1 chr6B.!!$R1 1091
35 TraesCS3B01G057600 chr1B 683131788 683132882 1094 False 935.000000 998 98.839500 7026 8403 2 chr1B.!!$F4 1377
36 TraesCS3B01G057600 chr1B 534948551 534949626 1075 False 874.000000 874 81.907000 1794 2882 1 chr1B.!!$F3 1088
37 TraesCS3B01G057600 chr1B 95445422 95446047 625 True 737.000000 737 87.937000 1796 2424 1 chr1B.!!$R1 628
38 TraesCS3B01G057600 chr1B 54130181 54130802 621 False 665.000000 665 86.378000 2274 2881 1 chr1B.!!$F2 607
39 TraesCS3B01G057600 chr1B 449735005 449735648 643 True 597.000000 597 84.341000 2274 2881 1 chr1B.!!$R2 607
40 TraesCS3B01G057600 chr4A 473500304 473500857 553 True 990.000000 990 98.919000 7026 7580 1 chr4A.!!$R1 554
41 TraesCS3B01G057600 chr4A 726974888 726975892 1004 False 938.500000 966 96.285000 1797 2881 2 chr4A.!!$F1 1084
42 TraesCS3B01G057600 chr4A 615366195 615367295 1100 True 931.000000 931 82.369000 3859 4935 1 chr4A.!!$R2 1076
43 TraesCS3B01G057600 chr5B 386660818 386662030 1212 False 922.000000 987 98.454000 7026 8403 2 chr5B.!!$F1 1377
44 TraesCS3B01G057600 chr1A 4263191 4263746 555 True 987.000000 987 98.741000 7026 7580 1 chr1A.!!$R1 554
45 TraesCS3B01G057600 chr2A 753525284 753525840 556 False 983.000000 983 98.564000 7026 7580 1 chr2A.!!$F2 554
46 TraesCS3B01G057600 chr2A 191936271 191937370 1099 True 925.000000 972 98.292500 7026 8412 2 chr2A.!!$R1 1386
47 TraesCS3B01G057600 chr6A 73458908 73460193 1285 True 927.500000 981 98.474500 7026 8407 2 chr6A.!!$R3 1381
48 TraesCS3B01G057600 chr7B 671706915 671707469 554 False 976.000000 976 98.378000 7026 7580 1 chr7B.!!$F2 554
49 TraesCS3B01G057600 chr7B 217458881 217459847 966 True 712.000000 712 80.082000 3854 4821 1 chr7B.!!$R1 967
50 TraesCS3B01G057600 chr5D 434717492 434718475 983 True 966.000000 966 84.600000 3866 4840 1 chr5D.!!$R1 974
51 TraesCS3B01G057600 chr5D 7032125 7033224 1099 False 909.000000 909 82.222000 1797 2881 1 chr5D.!!$F1 1084
52 TraesCS3B01G057600 chr5D 302376593 302377568 975 False 665.000000 665 79.017000 3866 4840 1 chr5D.!!$F3 974
53 TraesCS3B01G057600 chr4D 502546606 502547659 1053 False 941.000000 941 83.046000 1797 2882 1 chr4D.!!$F2 1085
54 TraesCS3B01G057600 chrUn 21942666 21943772 1106 False 887.000000 887 81.598000 3852 4935 1 chrUn.!!$F1 1083
55 TraesCS3B01G057600 chrUn 34133669 34134299 630 False 651.000000 651 85.782000 2274 2887 1 chrUn.!!$F2 613
56 TraesCS3B01G057600 chr1D 481956924 481958011 1087 True 854.000000 854 81.495000 1797 2881 1 chr1D.!!$R2 1084
57 TraesCS3B01G057600 chr1D 483047954 483048609 655 False 649.000000 649 84.875000 2219 2882 1 chr1D.!!$F1 663
58 TraesCS3B01G057600 chr6D 15378951 15379610 659 True 684.000000 684 85.735000 2219 2881 1 chr6D.!!$R1 662

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
243 247 0.034670 ATCCCTTGAGCTTGAGCCAC 60.035 55.000 0.00 0.00 43.38 5.01 F
1171 3662 0.106519 CCCGAGGCTTCCATTTCCAT 60.107 55.000 0.00 0.00 0.00 3.41 F
2537 5162 1.375396 CCACGCCGTTCCTGATTGA 60.375 57.895 0.00 0.00 0.00 2.57 F
3217 5856 0.865769 ATTGGCAAGTCGACGACAAC 59.134 50.000 28.31 16.71 34.60 3.32 F
4608 7791 0.548031 ACCTCATCACATTGCCGGAT 59.452 50.000 5.05 0.00 0.00 4.18 F
5096 8357 0.036732 TCATGCTCCTTCGCCACTTT 59.963 50.000 0.00 0.00 0.00 2.66 F
5100 8361 0.389426 GCTCCTTCGCCACTTTACGA 60.389 55.000 0.00 0.00 36.32 3.43 F
6152 15215 0.392193 GCTATGCTCTGCCACACTGT 60.392 55.000 0.00 0.00 0.00 3.55 F
7538 16685 0.983378 GGTATCTGCCCCCTCTGTGT 60.983 60.000 0.00 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 3779 0.750911 GTGTCCCGGTCGTAGATCCT 60.751 60.000 0.00 0.0 40.67 3.24 R
3052 5690 1.005662 CGCGATGTGATGTTACTGCTG 60.006 52.381 0.00 0.0 0.00 4.41 R
4512 7691 0.030369 CGGGTTAGGGATCGAGAACG 59.970 60.000 0.00 0.0 41.26 3.95 R
5093 8354 0.037605 ACGCAGTCCCCTTCGTAAAG 60.038 55.000 0.00 0.0 38.79 1.85 R
6458 15531 0.178891 AGGCCAAGGTCAGAAGAGGA 60.179 55.000 5.01 0.0 0.00 3.71 R
6681 15815 0.391528 CACTGGCATCATCGACACCA 60.392 55.000 0.00 0.0 0.00 4.17 R
7017 16160 0.397816 CTGGACGAGGGAGGGAAGAT 60.398 60.000 0.00 0.0 0.00 2.40 R
8031 17178 1.067212 GGGATACGCTCGATCACAAGT 59.933 52.381 0.00 0.0 37.60 3.16 R
9379 19302 1.423921 ACTCATCCCCGTTTCCTTTGT 59.576 47.619 0.00 0.0 0.00 2.83 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
46 49 4.201812 CCATGGTGCTGTCAACGTATTTAG 60.202 45.833 2.57 0.00 30.83 1.85
55 58 6.237595 GCTGTCAACGTATTTAGTTCTGCTAG 60.238 42.308 0.00 0.00 0.00 3.42
110 114 4.583871 ACATTTGGATGTTGACTCTCTCC 58.416 43.478 0.00 0.00 43.92 3.71
169 173 7.763528 CACCATGCTCTTCATAATATCTAGTCC 59.236 40.741 0.00 0.00 33.19 3.85
223 227 4.396166 CCTTTGTCTCCGTGCTTCAATATT 59.604 41.667 0.00 0.00 0.00 1.28
243 247 0.034670 ATCCCTTGAGCTTGAGCCAC 60.035 55.000 0.00 0.00 43.38 5.01
304 312 2.124901 CGCATCCCCGGTTGCTAA 60.125 61.111 16.31 0.00 38.33 3.09
308 316 0.455815 CATCCCCGGTTGCTAAAAGC 59.544 55.000 0.00 0.00 42.82 3.51
316 324 1.271926 GGTTGCTAAAAGCCCTCCTCA 60.272 52.381 0.00 0.00 41.51 3.86
330 338 1.374252 CCTCACCGTCCTGGAAACG 60.374 63.158 0.00 0.00 42.00 3.60
336 344 1.569493 CGTCCTGGAAACGTGCTTG 59.431 57.895 0.00 0.00 35.47 4.01
351 359 0.449388 GCTTGATGCTACTGTGCCAC 59.551 55.000 0.00 0.00 38.95 5.01
388 396 3.741344 GGCAACCTGCGTACATCTAATAG 59.259 47.826 0.00 0.00 46.21 1.73
389 397 4.500887 GGCAACCTGCGTACATCTAATAGA 60.501 45.833 0.00 0.00 46.21 1.98
393 401 3.572682 CCTGCGTACATCTAATAGACCCA 59.427 47.826 0.00 0.00 0.00 4.51
397 405 5.813672 TGCGTACATCTAATAGACCCAAAAC 59.186 40.000 0.00 0.00 0.00 2.43
414 422 4.387256 CCAAAACGAACAGTGCTTCAAAAA 59.613 37.500 0.00 0.00 0.00 1.94
423 431 4.454504 ACAGTGCTTCAAAAATAGTACGGG 59.545 41.667 0.00 0.00 33.02 5.28
449 457 1.416049 CGACAATGACAACGCTCCG 59.584 57.895 0.00 0.00 0.00 4.63
450 458 1.282248 CGACAATGACAACGCTCCGT 61.282 55.000 0.00 0.00 43.97 4.69
451 459 0.163788 GACAATGACAACGCTCCGTG 59.836 55.000 0.00 0.00 39.99 4.94
452 460 1.154413 CAATGACAACGCTCCGTGC 60.154 57.895 0.00 0.00 39.99 5.34
453 461 2.325082 AATGACAACGCTCCGTGCC 61.325 57.895 0.00 0.00 39.99 5.01
454 462 2.731691 AATGACAACGCTCCGTGCCT 62.732 55.000 0.00 0.00 39.99 4.75
455 463 3.112709 GACAACGCTCCGTGCCTC 61.113 66.667 0.00 0.00 39.99 4.70
456 464 4.681978 ACAACGCTCCGTGCCTCC 62.682 66.667 0.00 0.00 39.99 4.30
457 465 4.680237 CAACGCTCCGTGCCTCCA 62.680 66.667 0.00 0.00 39.99 3.86
460 468 3.449227 CGCTCCGTGCCTCCAGTA 61.449 66.667 0.00 0.00 38.78 2.74
461 469 2.978824 GCTCCGTGCCTCCAGTAA 59.021 61.111 0.00 0.00 35.15 2.24
462 470 1.522569 GCTCCGTGCCTCCAGTAAT 59.477 57.895 0.00 0.00 35.15 1.89
463 471 0.811616 GCTCCGTGCCTCCAGTAATG 60.812 60.000 0.00 0.00 35.15 1.90
464 472 0.811616 CTCCGTGCCTCCAGTAATGC 60.812 60.000 0.00 0.00 0.00 3.56
465 473 1.078497 CCGTGCCTCCAGTAATGCA 60.078 57.895 0.00 0.00 0.00 3.96
466 474 0.676466 CCGTGCCTCCAGTAATGCAA 60.676 55.000 0.00 0.00 35.16 4.08
467 475 1.382522 CGTGCCTCCAGTAATGCAAT 58.617 50.000 0.00 0.00 35.16 3.56
468 476 1.745087 CGTGCCTCCAGTAATGCAATT 59.255 47.619 0.00 0.00 41.28 2.32
469 477 2.223340 CGTGCCTCCAGTAATGCAATTC 60.223 50.000 0.00 0.00 37.87 2.17
470 478 2.099756 GTGCCTCCAGTAATGCAATTCC 59.900 50.000 0.00 0.00 37.87 3.01
471 479 2.025037 TGCCTCCAGTAATGCAATTCCT 60.025 45.455 0.00 0.00 37.87 3.36
472 480 3.026694 GCCTCCAGTAATGCAATTCCTT 58.973 45.455 0.00 0.00 37.87 3.36
473 481 3.181483 GCCTCCAGTAATGCAATTCCTTG 60.181 47.826 0.00 0.00 37.87 3.61
496 504 6.980593 TGCTCTAAACATAACAGTGCATTTT 58.019 32.000 0.00 0.00 34.79 1.82
503 511 5.964758 ACATAACAGTGCATTTTATGGTGG 58.035 37.500 20.33 5.03 37.47 4.61
524 532 3.119955 GGGAACGTTCCTGATAAAACTGC 60.120 47.826 38.59 18.90 46.72 4.40
534 542 4.876107 CCTGATAAAACTGCGGAACATACT 59.124 41.667 0.00 0.00 0.00 2.12
544 552 2.151202 CGGAACATACTGCACCAACTT 58.849 47.619 0.00 0.00 0.00 2.66
548 556 5.583061 CGGAACATACTGCACCAACTTAATA 59.417 40.000 0.00 0.00 0.00 0.98
574 582 5.817296 TGGATCGAGACATTTGGATGTTAAG 59.183 40.000 0.00 0.00 46.27 1.85
639 649 3.627395 TGGAGAAGTAAATGCGTCCAT 57.373 42.857 0.00 0.00 0.00 3.41
1054 1314 0.107945 CTACAGTGCCAGCTCCTTCC 60.108 60.000 0.00 0.00 0.00 3.46
1168 3659 3.514417 GCCCGAGGCTTCCATTTC 58.486 61.111 7.58 0.00 46.69 2.17
1169 3660 2.121538 GCCCGAGGCTTCCATTTCC 61.122 63.158 7.58 0.00 46.69 3.13
1170 3661 1.302949 CCCGAGGCTTCCATTTCCA 59.697 57.895 0.00 0.00 0.00 3.53
1171 3662 0.106519 CCCGAGGCTTCCATTTCCAT 60.107 55.000 0.00 0.00 0.00 3.41
1279 3779 1.820906 ATCTACGCGTACCTCGGCA 60.821 57.895 16.41 0.00 40.26 5.69
1643 4171 6.815089 AGACCAACTAGACATGATCTGATTC 58.185 40.000 0.00 0.00 38.49 2.52
2537 5162 1.375396 CCACGCCGTTCCTGATTGA 60.375 57.895 0.00 0.00 0.00 2.57
2585 5212 6.818142 CCCGATTGCTTTTTCCAGAAAATATT 59.182 34.615 6.40 0.00 39.69 1.28
2937 5574 4.195225 ACTTAGTAGCTCCAGAACAAGC 57.805 45.455 0.00 0.00 38.84 4.01
3052 5690 1.512926 ATGCACTCGGTCAAACAGTC 58.487 50.000 0.00 0.00 0.00 3.51
3073 5711 0.999406 GCAGTAACATCACATCGCGT 59.001 50.000 5.77 0.00 0.00 6.01
3074 5712 1.393539 GCAGTAACATCACATCGCGTT 59.606 47.619 5.77 0.00 0.00 4.84
3076 5714 3.659735 CAGTAACATCACATCGCGTTTC 58.340 45.455 5.77 0.00 0.00 2.78
3217 5856 0.865769 ATTGGCAAGTCGACGACAAC 59.134 50.000 28.31 16.71 34.60 3.32
3222 5861 2.182825 GCAAGTCGACGACAACGATAT 58.817 47.619 28.31 4.29 41.62 1.63
3347 6246 7.337689 TCCAATTATTGAGATGGTTTCACTCAG 59.662 37.037 6.50 0.00 40.82 3.35
3465 6365 1.000827 CGCTCGATAGACTCAATGCCT 60.001 52.381 0.00 0.00 42.67 4.75
3483 6384 2.158564 GCCTTGATCAATGGAGATGGGA 60.159 50.000 21.24 0.00 0.00 4.37
3628 6531 6.039829 GGAACAAAGTCTGAGGTTCAAATCTT 59.960 38.462 0.00 0.00 40.97 2.40
3632 6535 5.489792 AGTCTGAGGTTCAAATCTTGCTA 57.510 39.130 0.00 0.00 0.00 3.49
3693 6597 1.154205 CCGGCGAAGATAGCAACAGG 61.154 60.000 9.30 0.00 36.08 4.00
3755 6659 6.777580 ACATCCAAAACAGTTGAAGATAACCT 59.222 34.615 0.00 0.00 0.00 3.50
3798 6702 1.686587 GCACCCAGTAACCAAAAGCTT 59.313 47.619 0.00 0.00 0.00 3.74
3801 6705 3.253432 CACCCAGTAACCAAAAGCTTCTC 59.747 47.826 0.00 0.00 0.00 2.87
3823 6727 2.949451 AGTCCGCATGAGTGAGTAAG 57.051 50.000 0.00 0.00 0.00 2.34
3834 6738 4.412843 TGAGTGAGTAAGGACCACATACA 58.587 43.478 0.00 0.00 32.33 2.29
3849 6753 4.865925 CCACATACAAATCCAAGCAATGTG 59.134 41.667 0.00 0.00 41.35 3.21
3857 7026 5.789643 AATCCAAGCAATGTGTACAAACT 57.210 34.783 0.00 0.00 0.00 2.66
3874 7043 5.551760 CAAACTACATTTGGAGCTACCTG 57.448 43.478 0.00 0.00 43.52 4.00
3884 7053 2.258748 GAGCTACCTGCCCACCTTCC 62.259 65.000 0.00 0.00 44.23 3.46
3956 7125 7.817418 ACATGAAGACTTTAAACCTAAGCAA 57.183 32.000 0.00 0.00 0.00 3.91
3989 7158 7.681259 TCTTTCAGATATGAAGGGATCTTGA 57.319 36.000 11.72 0.00 32.52 3.02
3998 7167 5.191727 TGAAGGGATCTTGAAATTAGCCA 57.808 39.130 0.00 0.00 32.52 4.75
4053 7222 5.409826 CACTGAAAAACTCCCAGTCATAGAC 59.590 44.000 0.00 0.00 38.93 2.59
4100 7273 4.389374 TGGTCAGAGAGTTGAATTTCCAC 58.611 43.478 0.00 0.00 0.00 4.02
4139 7312 2.218603 CAGCCACTAGTTCCAACGTTT 58.781 47.619 0.00 0.00 0.00 3.60
4273 7449 2.288025 GGCGTCTCCCCTAACCACA 61.288 63.158 0.00 0.00 0.00 4.17
4282 7458 1.406887 CCCCTAACCACACATCTTCCG 60.407 57.143 0.00 0.00 0.00 4.30
4371 7548 4.968259 TCATCAACCCTTTCGAGAAAAGA 58.032 39.130 0.00 0.00 46.18 2.52
4434 7613 6.855763 TTGGAGGTACTTATTCCGTAGAAA 57.144 37.500 0.00 0.00 41.55 2.52
4512 7691 8.966069 AGGAGGCATTTATTCTTAACTTCTAC 57.034 34.615 0.00 0.00 0.00 2.59
4557 7736 4.479158 AGGTCTTTGGGTCTGCAAATAAA 58.521 39.130 0.00 0.00 0.00 1.40
4566 7745 5.043248 GGGTCTGCAAATAAAATTCCATCG 58.957 41.667 0.00 0.00 0.00 3.84
4608 7791 0.548031 ACCTCATCACATTGCCGGAT 59.452 50.000 5.05 0.00 0.00 4.18
4647 7830 7.988904 AGAAGTCTAATCTTTTTCGTATCCG 57.011 36.000 0.00 0.00 0.00 4.18
4840 8026 6.514705 GTGAATCGGGATCACTAGGTAACTAC 60.515 46.154 0.00 0.00 45.65 2.73
4841 8027 8.603416 GTGAATCGGGATCACTAGGTAACTACT 61.603 44.444 0.00 0.00 45.65 2.57
4870 8080 3.537580 TGTTTATATGCGTCTTGGTCCC 58.462 45.455 0.00 0.00 0.00 4.46
4882 8092 0.772124 TTGGTCCCCTTTGGCTCTCT 60.772 55.000 0.00 0.00 0.00 3.10
4977 8236 1.576421 CTCTTGTTGCGTTGCCTCC 59.424 57.895 0.00 0.00 0.00 4.30
5017 8276 2.615447 CCATCAACCACAATCATCCTCG 59.385 50.000 0.00 0.00 0.00 4.63
5091 8352 2.899339 GCCTCATGCTCCTTCGCC 60.899 66.667 0.00 0.00 36.87 5.54
5093 8354 1.817099 CCTCATGCTCCTTCGCCAC 60.817 63.158 0.00 0.00 0.00 5.01
5094 8355 1.220206 CTCATGCTCCTTCGCCACT 59.780 57.895 0.00 0.00 0.00 4.00
5095 8356 0.392193 CTCATGCTCCTTCGCCACTT 60.392 55.000 0.00 0.00 0.00 3.16
5096 8357 0.036732 TCATGCTCCTTCGCCACTTT 59.963 50.000 0.00 0.00 0.00 2.66
5097 8358 1.277842 TCATGCTCCTTCGCCACTTTA 59.722 47.619 0.00 0.00 0.00 1.85
5098 8359 1.398390 CATGCTCCTTCGCCACTTTAC 59.602 52.381 0.00 0.00 0.00 2.01
5099 8360 0.669318 TGCTCCTTCGCCACTTTACG 60.669 55.000 0.00 0.00 0.00 3.18
5100 8361 0.389426 GCTCCTTCGCCACTTTACGA 60.389 55.000 0.00 0.00 36.32 3.43
5101 8362 1.938016 GCTCCTTCGCCACTTTACGAA 60.938 52.381 0.00 0.00 45.27 3.85
5254 10338 1.916651 TCGTTTTCGTTTTCGTCGACA 59.083 42.857 17.16 0.00 44.46 4.35
5301 10385 4.406173 CCTCGTCGTGTCAGCGCT 62.406 66.667 2.64 2.64 0.00 5.92
5342 10426 2.488355 GCGCCGTGTGCTCTAGTA 59.512 61.111 0.00 0.00 38.05 1.82
5374 10458 4.006989 TCATCCACCGTATTTGGTTGAAG 58.993 43.478 0.59 0.00 41.38 3.02
5394 10478 4.314440 GCTGCCTCGTGGTGGACA 62.314 66.667 5.26 0.00 35.27 4.02
5406 10490 1.282738 TGGTGGACACATGCAGATGAT 59.717 47.619 6.97 0.00 33.36 2.45
5436 10521 2.474816 GCTGCGTAAGAATAGGACCTG 58.525 52.381 3.53 0.00 43.02 4.00
5456 10541 1.578583 GATAAGCGCAACCCGTGTAT 58.421 50.000 11.47 0.00 39.71 2.29
5460 10545 2.030401 GCGCAACCCGTGTATCACA 61.030 57.895 0.30 0.00 39.71 3.58
5476 10561 2.653726 TCACAAACACATGGCAACTCT 58.346 42.857 0.00 0.00 37.61 3.24
5487 10572 6.183360 ACACATGGCAACTCTAAACGTTTTTA 60.183 34.615 20.19 6.83 37.61 1.52
5488 10573 6.861055 CACATGGCAACTCTAAACGTTTTTAT 59.139 34.615 20.19 0.00 37.61 1.40
5494 10579 6.199342 GCAACTCTAAACGTTTTTATGGCAAA 59.801 34.615 20.19 0.00 0.00 3.68
5503 10588 7.631915 ACGTTTTTATGGCAAATTTAGTGAC 57.368 32.000 0.00 0.00 0.00 3.67
5504 10589 7.203910 ACGTTTTTATGGCAAATTTAGTGACA 58.796 30.769 0.00 0.00 38.70 3.58
5506 10591 8.707839 CGTTTTTATGGCAAATTTAGTGACATT 58.292 29.630 2.34 0.00 42.23 2.71
5513 10598 6.096705 TGGCAAATTTAGTGACATTAGGATGG 59.903 38.462 0.00 0.00 37.60 3.51
5558 10644 6.822676 TGGCAACTTTCTTTTTGAATGACAAT 59.177 30.769 0.00 0.00 36.37 2.71
5600 10688 6.827586 TTTTACTTCCTTTCGTATGGCAAT 57.172 33.333 0.00 0.00 0.00 3.56
5634 10724 5.505173 AATGTTAGGATTGGATTGCTTCG 57.495 39.130 0.00 0.00 0.00 3.79
5811 14870 3.245519 GCAGTAGGTAAGTAAAGATGCGC 59.754 47.826 0.00 0.00 0.00 6.09
5871 14930 3.411517 CAACCGGGCCCTGAGGAT 61.412 66.667 21.63 5.58 33.47 3.24
5902 14961 1.152030 TGAGCTCCCACTCCCACTT 60.152 57.895 12.15 0.00 35.72 3.16
5922 14981 0.676184 GCTGGTGAGTCTGAGTGTCA 59.324 55.000 0.00 0.00 0.00 3.58
5947 15006 6.361433 TGGTGATCTCCACTTCAGTTAAAAA 58.639 36.000 12.50 0.00 45.03 1.94
5949 15008 6.072452 GGTGATCTCCACTTCAGTTAAAAAGG 60.072 42.308 8.97 0.00 45.03 3.11
5952 15011 6.248569 TCTCCACTTCAGTTAAAAAGGTCT 57.751 37.500 0.00 0.00 0.00 3.85
6001 15062 4.063689 CTCCTTCTCAATTCCCATCATCG 58.936 47.826 0.00 0.00 0.00 3.84
6024 15085 1.605971 GACCGTTCACCTCCCTCTCC 61.606 65.000 0.00 0.00 0.00 3.71
6032 15093 3.775654 CTCCCTCTCCGCGCCTTT 61.776 66.667 0.00 0.00 0.00 3.11
6077 15139 4.885907 GCATCTCTTCAATCTTCCATTCCA 59.114 41.667 0.00 0.00 0.00 3.53
6094 15156 6.828273 TCCATTCCATTGTAACAAGATCGAAT 59.172 34.615 0.00 0.00 0.00 3.34
6109 15171 5.067954 AGATCGAATGATGCATCCATTTCA 58.932 37.500 23.67 6.03 34.67 2.69
6113 15175 5.068067 TCGAATGATGCATCCATTTCATGTT 59.932 36.000 23.67 4.98 34.67 2.71
6152 15215 0.392193 GCTATGCTCTGCCACACTGT 60.392 55.000 0.00 0.00 0.00 3.55
6202 15265 1.647213 CTAAACACCACATCGTCGTCG 59.353 52.381 0.00 0.00 38.55 5.12
6206 15269 2.019951 ACCACATCGTCGTCGTTGC 61.020 57.895 12.00 0.00 39.47 4.17
6423 15496 1.534175 GGTCGCCAACTACGATCTCTG 60.534 57.143 0.00 0.00 42.26 3.35
6458 15531 5.011431 TGTGACATCAAGATCTGAGTGAACT 59.989 40.000 0.00 0.00 37.52 3.01
6463 15590 4.671831 TCAAGATCTGAGTGAACTCCTCT 58.328 43.478 7.96 5.08 42.20 3.69
6651 15780 1.395045 CCGCCAGAGAGTATGAGCCA 61.395 60.000 0.00 0.00 0.00 4.75
6681 15815 1.973281 CGGTGGCAAGGAACTGCAT 60.973 57.895 0.00 0.00 40.86 3.96
6838 15977 6.402118 GCCGTATTAACACCGACTACGATATA 60.402 42.308 4.55 0.00 42.66 0.86
6908 16051 5.581874 TCACACGTATCATAGTCGTTACTCA 59.418 40.000 0.00 0.00 37.15 3.41
6981 16124 3.341823 CCCCTCTTTTCACATGAGAGTG 58.658 50.000 0.00 0.00 40.85 3.51
7009 16152 8.806146 AGCTGTTGATTTCATAAATTAGTGGTT 58.194 29.630 0.00 0.00 0.00 3.67
7045 16188 3.151022 CTCGTCCAGCTCCTCCCC 61.151 72.222 0.00 0.00 0.00 4.81
7538 16685 0.983378 GGTATCTGCCCCCTCTGTGT 60.983 60.000 0.00 0.00 0.00 3.72
7954 17101 2.422276 ATTTGCTGAACTCCAAACGC 57.578 45.000 0.00 0.00 34.18 4.84
8031 17178 6.647895 GGACTCTTTGGACTGTTCGTAATAAA 59.352 38.462 0.00 0.00 0.00 1.40
8048 17195 6.141844 CGTAATAAACTTGTGATCGAGCGTAT 59.858 38.462 0.00 0.00 0.00 3.06
8169 17316 1.299392 CATCGCCGATCTTCGCTCA 60.299 57.895 0.00 0.00 38.82 4.26
8412 17559 9.419297 GAAAGCCTTTTTCGGTAATTAAATCTT 57.581 29.630 0.00 0.00 0.00 2.40
8413 17560 8.981724 AAGCCTTTTTCGGTAATTAAATCTTC 57.018 30.769 0.00 0.00 0.00 2.87
8414 17561 7.544622 AGCCTTTTTCGGTAATTAAATCTTCC 58.455 34.615 0.00 0.00 0.00 3.46
8415 17562 6.755141 GCCTTTTTCGGTAATTAAATCTTCCC 59.245 38.462 0.00 0.00 0.00 3.97
8416 17563 7.363530 GCCTTTTTCGGTAATTAAATCTTCCCT 60.364 37.037 0.00 0.00 0.00 4.20
8431 17578 3.135167 TCTTCCCTTTTTACCTCACACGT 59.865 43.478 0.00 0.00 0.00 4.49
8450 17597 3.150767 CGTAAAATTTGGGGGTCAGTGA 58.849 45.455 0.00 0.00 0.00 3.41
8470 17617 7.942341 TCAGTGAGACCATGTTAAAATTTACCT 59.058 33.333 0.00 0.00 0.00 3.08
8510 17657 5.987953 TCATGCATCTAACTGCTAATGACTC 59.012 40.000 0.00 0.00 42.75 3.36
8535 17682 5.770162 CCTCTGTCCCAAAATAACTGAAGTT 59.230 40.000 0.71 0.71 41.73 2.66
8676 18053 2.097466 ACAACGGACACTTGCAGAAAAG 59.903 45.455 0.00 0.00 0.00 2.27
8678 18055 2.213499 ACGGACACTTGCAGAAAAGAG 58.787 47.619 0.00 0.00 0.00 2.85
8679 18056 1.532868 CGGACACTTGCAGAAAAGAGG 59.467 52.381 0.00 0.00 0.00 3.69
8950 18661 5.659048 GCTCTAAGCTTGTGCGTAATAAT 57.341 39.130 9.86 0.00 45.42 1.28
9061 18773 8.507249 GCCTGGAAATCATTATGACTGTATTAC 58.493 37.037 0.00 0.00 0.00 1.89
9094 18832 3.899980 TCCATCTCAGGTATGACATCAGG 59.100 47.826 0.00 0.00 0.00 3.86
9099 18837 4.141158 TCTCAGGTATGACATCAGGAGCTA 60.141 45.833 0.00 0.00 0.00 3.32
9116 18854 4.068599 GAGCTACAACCTTTCTCTTTGCT 58.931 43.478 0.00 0.00 0.00 3.91
9143 18881 9.996554 TGTCTTTATGTGTTGATATGGTATAGG 57.003 33.333 0.00 0.00 0.00 2.57
9152 18890 6.043938 TGTTGATATGGTATAGGAAGGGGAAC 59.956 42.308 0.00 0.00 0.00 3.62
9246 19169 2.024176 TGGATCGCTAGCTCCAAAAC 57.976 50.000 20.35 2.63 39.48 2.43
9257 19180 5.175856 GCTAGCTCCAAAACGATACATGTAG 59.824 44.000 11.91 1.09 0.00 2.74
9260 19183 5.351465 AGCTCCAAAACGATACATGTAGTTG 59.649 40.000 11.91 9.56 0.00 3.16
9281 19204 7.210873 AGTTGGAGATAATGAAGATAACGTCC 58.789 38.462 0.00 0.00 0.00 4.79
9283 19206 8.358148 GTTGGAGATAATGAAGATAACGTCCTA 58.642 37.037 0.00 0.00 0.00 2.94
9353 19276 6.780901 AGGAAGACTATATGATGGTCGTCTA 58.219 40.000 14.85 0.00 44.35 2.59
9379 19302 4.761227 TGCTGTGAAATTCTTGCATGACTA 59.239 37.500 1.02 0.00 0.00 2.59
9585 19508 3.916035 TGGGAGAGGCTATATGCGATAT 58.084 45.455 0.00 0.00 44.05 1.63
9761 19684 0.595095 GCAAGCTTTCAGTGACTGGG 59.405 55.000 13.33 4.91 31.51 4.45
9845 19768 9.118236 GTTTCAACAAAGTCAGATGTTTATAGC 57.882 33.333 0.00 0.00 37.66 2.97
9846 19769 8.621532 TTCAACAAAGTCAGATGTTTATAGCT 57.378 30.769 0.00 0.00 37.66 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 49 7.374272 TGATGCAATACTATCTCTAGCAGAAC 58.626 38.462 0.00 0.00 33.62 3.01
110 114 4.935808 GTGTTTACTTCTCCATACCCACTG 59.064 45.833 0.00 0.00 0.00 3.66
176 180 4.588951 AGAACATAGTATGATCCCGCAAGA 59.411 41.667 17.13 0.00 33.93 3.02
223 227 1.210478 GTGGCTCAAGCTCAAGGGATA 59.790 52.381 1.46 0.00 41.70 2.59
304 312 2.593956 GGACGGTGAGGAGGGCTTT 61.594 63.158 0.00 0.00 0.00 3.51
308 316 3.077556 CCAGGACGGTGAGGAGGG 61.078 72.222 0.00 0.00 0.00 4.30
316 324 2.280592 GCACGTTTCCAGGACGGT 60.281 61.111 5.72 0.00 44.34 4.83
330 338 4.323515 GTGGCACAGTAGCATCAAGCAC 62.324 54.545 13.86 0.00 44.14 4.40
336 344 2.802667 CGCGTGGCACAGTAGCATC 61.803 63.158 19.09 0.00 41.80 3.91
388 396 1.021968 AGCACTGTTCGTTTTGGGTC 58.978 50.000 0.00 0.00 0.00 4.46
389 397 1.404035 GAAGCACTGTTCGTTTTGGGT 59.596 47.619 0.00 0.00 0.00 4.51
393 401 7.033185 ACTATTTTTGAAGCACTGTTCGTTTT 58.967 30.769 0.00 0.00 0.00 2.43
397 405 5.783654 CGTACTATTTTTGAAGCACTGTTCG 59.216 40.000 0.00 0.00 0.00 3.95
414 422 2.092968 TGTCGGTACAGTCCCGTACTAT 60.093 50.000 4.25 0.00 45.63 2.12
423 431 2.407361 CGTTGTCATTGTCGGTACAGTC 59.593 50.000 0.00 0.00 36.83 3.51
449 457 2.099756 GGAATTGCATTACTGGAGGCAC 59.900 50.000 0.00 0.00 35.74 5.01
450 458 2.025037 AGGAATTGCATTACTGGAGGCA 60.025 45.455 0.00 0.00 30.53 4.75
451 459 2.659428 AGGAATTGCATTACTGGAGGC 58.341 47.619 0.00 0.00 30.53 4.70
452 460 3.181483 GCAAGGAATTGCATTACTGGAGG 60.181 47.826 8.03 0.00 46.60 4.30
453 461 4.037858 GCAAGGAATTGCATTACTGGAG 57.962 45.455 8.03 0.00 46.60 3.86
464 472 7.752239 CACTGTTATGTTTAGAGCAAGGAATTG 59.248 37.037 0.00 0.00 0.00 2.32
465 473 7.575720 GCACTGTTATGTTTAGAGCAAGGAATT 60.576 37.037 0.00 0.00 0.00 2.17
466 474 6.127897 GCACTGTTATGTTTAGAGCAAGGAAT 60.128 38.462 0.00 0.00 0.00 3.01
467 475 5.181245 GCACTGTTATGTTTAGAGCAAGGAA 59.819 40.000 0.00 0.00 0.00 3.36
468 476 4.695455 GCACTGTTATGTTTAGAGCAAGGA 59.305 41.667 0.00 0.00 0.00 3.36
469 477 4.455533 TGCACTGTTATGTTTAGAGCAAGG 59.544 41.667 0.00 0.00 35.61 3.61
470 478 5.611796 TGCACTGTTATGTTTAGAGCAAG 57.388 39.130 0.00 0.00 35.61 4.01
471 479 6.573664 AATGCACTGTTATGTTTAGAGCAA 57.426 33.333 0.00 0.00 40.42 3.91
472 480 6.573664 AAATGCACTGTTATGTTTAGAGCA 57.426 33.333 0.00 0.00 41.07 4.26
473 481 9.013490 CATAAAATGCACTGTTATGTTTAGAGC 57.987 33.333 13.80 0.00 32.80 4.09
474 482 9.507280 CCATAAAATGCACTGTTATGTTTAGAG 57.493 33.333 17.83 5.05 34.71 2.43
475 483 9.019656 ACCATAAAATGCACTGTTATGTTTAGA 57.980 29.630 17.83 0.00 34.71 2.10
524 532 1.808411 AGTTGGTGCAGTATGTTCCG 58.192 50.000 0.00 0.00 39.31 4.30
534 542 5.432645 TCGATCCATTATTAAGTTGGTGCA 58.567 37.500 0.00 0.00 0.00 4.57
544 552 8.156820 ACATCCAAATGTCTCGATCCATTATTA 58.843 33.333 9.36 1.12 42.59 0.98
548 556 4.785301 ACATCCAAATGTCTCGATCCATT 58.215 39.130 4.37 4.37 42.59 3.16
591 599 9.485206 ACACGCTAGAGAGACTTAATTTAAAAA 57.515 29.630 0.00 0.00 0.00 1.94
603 611 3.468770 TCTCCATACACGCTAGAGAGAC 58.531 50.000 0.00 0.00 0.00 3.36
613 621 3.863424 ACGCATTTACTTCTCCATACACG 59.137 43.478 0.00 0.00 0.00 4.49
639 649 3.500680 GCCAACGACTTTGAATGGTTCTA 59.499 43.478 0.00 0.00 37.39 2.10
1054 1314 3.661944 AGAATCTGCTGTGAGACACAAG 58.338 45.455 6.08 2.38 44.08 3.16
1169 3660 1.369091 GAAGCACAGGGCCACGTATG 61.369 60.000 6.18 0.00 46.50 2.39
1170 3661 1.078426 GAAGCACAGGGCCACGTAT 60.078 57.895 6.18 0.00 46.50 3.06
1171 3662 2.345991 GAAGCACAGGGCCACGTA 59.654 61.111 6.18 0.00 46.50 3.57
1279 3779 0.750911 GTGTCCCGGTCGTAGATCCT 60.751 60.000 0.00 0.00 40.67 3.24
1863 4393 2.167693 CCCGACTTGGTAGTTATCAGCA 59.832 50.000 0.00 0.00 33.84 4.41
2113 4646 2.203938 ACGGATGGTGGAGGTGGT 60.204 61.111 0.00 0.00 0.00 4.16
2537 5162 5.012046 GGTCCCTGATGTTTTCTGGAAAAAT 59.988 40.000 9.65 6.62 44.21 1.82
2585 5212 2.891191 AAAAAGCAATCGGGTCCCTA 57.109 45.000 6.29 0.00 0.00 3.53
2952 5589 3.743899 GCATTTGCTTGTTTCCCTCCAAA 60.744 43.478 0.00 0.00 38.21 3.28
2955 5592 1.344114 TGCATTTGCTTGTTTCCCTCC 59.656 47.619 3.94 0.00 42.66 4.30
3052 5690 1.005662 CGCGATGTGATGTTACTGCTG 60.006 52.381 0.00 0.00 0.00 4.41
3073 5711 5.649557 CATGTGACTGACAACAAAAGGAAA 58.350 37.500 0.00 0.00 38.36 3.13
3074 5712 4.439974 GCATGTGACTGACAACAAAAGGAA 60.440 41.667 0.00 0.00 38.36 3.36
3076 5714 3.374745 GCATGTGACTGACAACAAAAGG 58.625 45.455 0.00 0.00 38.36 3.11
3217 5856 7.919690 TCATTAAGGAGTTGCTCAAAATATCG 58.080 34.615 0.00 0.00 31.08 2.92
3222 5861 9.162764 GTACTATCATTAAGGAGTTGCTCAAAA 57.837 33.333 0.00 0.00 31.08 2.44
3317 6216 8.133627 GTGAAACCATCTCAATAATTGGATCAG 58.866 37.037 0.00 0.00 33.02 2.90
3347 6246 8.937634 TTACGAATCTATCCTTAAACCAACTC 57.062 34.615 0.00 0.00 0.00 3.01
3590 6493 9.513906 TCAGACTTTGTTCCACATATTATTTGA 57.486 29.630 0.00 0.00 0.00 2.69
3591 6494 9.778993 CTCAGACTTTGTTCCACATATTATTTG 57.221 33.333 0.00 0.00 0.00 2.32
3592 6495 8.960591 CCTCAGACTTTGTTCCACATATTATTT 58.039 33.333 0.00 0.00 0.00 1.40
3593 6496 8.109634 ACCTCAGACTTTGTTCCACATATTATT 58.890 33.333 0.00 0.00 0.00 1.40
3594 6497 7.633789 ACCTCAGACTTTGTTCCACATATTAT 58.366 34.615 0.00 0.00 0.00 1.28
3595 6498 7.016153 ACCTCAGACTTTGTTCCACATATTA 57.984 36.000 0.00 0.00 0.00 0.98
3596 6499 5.880901 ACCTCAGACTTTGTTCCACATATT 58.119 37.500 0.00 0.00 0.00 1.28
3597 6500 5.505181 ACCTCAGACTTTGTTCCACATAT 57.495 39.130 0.00 0.00 0.00 1.78
3598 6501 4.974645 ACCTCAGACTTTGTTCCACATA 57.025 40.909 0.00 0.00 0.00 2.29
3599 6502 3.864789 ACCTCAGACTTTGTTCCACAT 57.135 42.857 0.00 0.00 0.00 3.21
3602 6505 3.924114 TGAACCTCAGACTTTGTTCCA 57.076 42.857 0.00 0.00 37.01 3.53
3710 6614 6.095720 GGATGTCGAGCTAATAATAGGCTAGT 59.904 42.308 0.00 0.00 36.37 2.57
3801 6705 2.879002 ACTCACTCATGCGGACTATG 57.121 50.000 0.00 0.00 0.00 2.23
3823 6727 3.088532 TGCTTGGATTTGTATGTGGTCC 58.911 45.455 0.00 0.00 0.00 4.46
3834 6738 6.160576 AGTTTGTACACATTGCTTGGATTT 57.839 33.333 0.00 0.00 0.00 2.17
3849 6753 6.092259 CAGGTAGCTCCAAATGTAGTTTGTAC 59.908 42.308 0.00 0.00 44.58 2.90
3857 7026 1.211949 GGGCAGGTAGCTCCAAATGTA 59.788 52.381 11.05 0.00 44.79 2.29
3874 7043 2.003937 TTGGTTAAAGGAAGGTGGGC 57.996 50.000 0.00 0.00 0.00 5.36
3947 7116 9.131791 TCTGAAAGATTAAAGTTTTGCTTAGGT 57.868 29.630 0.00 0.00 38.67 3.08
3989 7158 9.034800 TGGATTTAATTGACTCTTGGCTAATTT 57.965 29.630 0.00 0.00 0.00 1.82
4139 7312 0.104777 CAGGGGATCTCTGATGGGGA 60.105 60.000 9.89 0.00 34.36 4.81
4273 7449 4.200874 ACGACTAGATTCTCGGAAGATGT 58.799 43.478 0.00 0.00 40.84 3.06
4282 7458 6.470556 GGTAACGGTAAAACGACTAGATTCTC 59.529 42.308 0.00 0.00 37.61 2.87
4345 7522 2.233922 TCTCGAAAGGGTTGATGAGGAC 59.766 50.000 0.00 0.00 0.00 3.85
4371 7548 1.333177 CCGCTAGGCCTAATGACTCT 58.667 55.000 14.85 0.00 0.00 3.24
4434 7613 2.777692 ACCGAGGGTACATGGATTCAAT 59.222 45.455 0.00 0.00 32.11 2.57
4512 7691 0.030369 CGGGTTAGGGATCGAGAACG 59.970 60.000 0.00 0.00 41.26 3.95
4557 7736 7.467267 CGAAATACAGATTGGTTCGATGGAATT 60.467 37.037 0.00 0.00 34.05 2.17
4566 7745 7.333672 AGGTTAAGACGAAATACAGATTGGTTC 59.666 37.037 0.00 0.00 0.00 3.62
4647 7830 7.713942 TCCTAACTTTCTTTGAAGTACTGGTTC 59.286 37.037 0.00 0.00 38.86 3.62
4840 8026 6.408858 AGACGCATATAAACAACAGTTCAG 57.591 37.500 0.00 0.00 0.00 3.02
4841 8027 6.348132 CCAAGACGCATATAAACAACAGTTCA 60.348 38.462 0.00 0.00 0.00 3.18
4870 8080 1.537202 CGGTTTTGAGAGAGCCAAAGG 59.463 52.381 0.00 0.00 35.29 3.11
4996 8255 2.615447 CGAGGATGATTGTGGTTGATGG 59.385 50.000 0.00 0.00 0.00 3.51
5017 8276 2.358737 CAGGGACGTTGTGAGGGC 60.359 66.667 0.00 0.00 0.00 5.19
5075 8336 1.817099 GTGGCGAAGGAGCATGAGG 60.817 63.158 0.00 0.00 39.27 3.86
5080 8341 0.669318 CGTAAAGTGGCGAAGGAGCA 60.669 55.000 0.00 0.00 39.27 4.26
5082 8343 2.074547 TTCGTAAAGTGGCGAAGGAG 57.925 50.000 0.00 0.00 41.36 3.69
5086 8347 0.320946 CCCCTTCGTAAAGTGGCGAA 60.321 55.000 0.00 0.00 43.55 4.70
5087 8348 1.186917 TCCCCTTCGTAAAGTGGCGA 61.187 55.000 0.00 0.00 30.66 5.54
5088 8349 1.017701 GTCCCCTTCGTAAAGTGGCG 61.018 60.000 0.00 0.00 30.66 5.69
5091 8352 1.439679 GCAGTCCCCTTCGTAAAGTG 58.560 55.000 0.00 0.00 0.00 3.16
5093 8354 0.037605 ACGCAGTCCCCTTCGTAAAG 60.038 55.000 0.00 0.00 38.79 1.85
5094 8355 0.320073 CACGCAGTCCCCTTCGTAAA 60.320 55.000 0.00 0.00 41.61 2.01
5095 8356 1.290955 CACGCAGTCCCCTTCGTAA 59.709 57.895 0.00 0.00 41.61 3.18
5096 8357 1.466025 AACACGCAGTCCCCTTCGTA 61.466 55.000 0.00 0.00 41.61 3.43
5097 8358 2.710724 GAACACGCAGTCCCCTTCGT 62.711 60.000 0.00 0.00 41.61 3.85
5098 8359 2.027625 GAACACGCAGTCCCCTTCG 61.028 63.158 0.00 0.00 41.61 3.79
5099 8360 0.670854 GAGAACACGCAGTCCCCTTC 60.671 60.000 0.00 0.00 41.61 3.46
5100 8361 1.371558 GAGAACACGCAGTCCCCTT 59.628 57.895 0.00 0.00 41.61 3.95
5101 8362 1.194781 ATGAGAACACGCAGTCCCCT 61.195 55.000 0.00 0.00 41.61 4.79
5102 8363 0.321653 AATGAGAACACGCAGTCCCC 60.322 55.000 0.00 0.00 41.61 4.81
5103 8364 1.523758 AAATGAGAACACGCAGTCCC 58.476 50.000 0.00 0.00 41.61 4.46
5224 8485 3.684103 AACGAAAACGAAGCATCACAA 57.316 38.095 0.00 0.00 0.00 3.33
5225 8486 3.684103 AAACGAAAACGAAGCATCACA 57.316 38.095 0.00 0.00 0.00 3.58
5254 10338 3.859414 GCCGCTGGCTCTCAGGAT 61.859 66.667 11.61 0.00 46.69 3.24
5273 10357 4.373116 GACGAGGAGGCCAACGCA 62.373 66.667 5.01 0.00 36.38 5.24
5301 10385 2.994995 ACCATGGTCGAGTCGCCA 60.995 61.111 24.26 24.26 37.42 5.69
5342 10426 7.416213 CCAAATACGGTGGATGATTTTATGTGT 60.416 37.037 0.00 0.00 38.54 3.72
5374 10458 4.767255 CCACCACGAGGCAGCCTC 62.767 72.222 29.53 29.53 46.44 4.70
5394 10478 2.357952 GTGCATGACATCATCTGCATGT 59.642 45.455 12.07 0.00 40.89 3.21
5406 10490 1.625759 CTTACGCAGCGTGCATGACA 61.626 55.000 30.67 5.33 45.36 3.58
5436 10521 0.460635 TACACGGGTTGCGCTTATCC 60.461 55.000 9.73 5.56 0.00 2.59
5456 10541 2.653726 AGAGTTGCCATGTGTTTGTGA 58.346 42.857 0.00 0.00 0.00 3.58
5460 10545 3.630312 ACGTTTAGAGTTGCCATGTGTTT 59.370 39.130 0.00 0.00 0.00 2.83
5476 10561 9.745880 TCACTAAATTTGCCATAAAAACGTTTA 57.254 25.926 15.03 0.00 33.76 2.01
5487 10572 7.201938 CCATCCTAATGTCACTAAATTTGCCAT 60.202 37.037 0.00 0.00 0.00 4.40
5488 10573 6.096705 CCATCCTAATGTCACTAAATTTGCCA 59.903 38.462 0.00 0.00 0.00 4.92
5494 10579 6.426587 AGTTGCCATCCTAATGTCACTAAAT 58.573 36.000 0.00 0.00 0.00 1.40
5503 10588 7.546358 TGACAAATAAAGTTGCCATCCTAATG 58.454 34.615 0.00 0.00 31.29 1.90
5504 10589 7.716799 TGACAAATAAAGTTGCCATCCTAAT 57.283 32.000 0.00 0.00 31.29 1.73
5506 10591 6.350110 GCTTGACAAATAAAGTTGCCATCCTA 60.350 38.462 0.00 0.00 31.29 2.94
5513 10598 4.143052 GCCATGCTTGACAAATAAAGTTGC 60.143 41.667 0.22 0.00 31.29 4.17
5610 10700 5.973565 CGAAGCAATCCAATCCTAACATTTC 59.026 40.000 0.00 0.00 0.00 2.17
5617 10707 2.288666 GCACGAAGCAATCCAATCCTA 58.711 47.619 0.00 0.00 44.79 2.94
5902 14961 0.676184 GACACTCAGACTCACCAGCA 59.324 55.000 0.00 0.00 0.00 4.41
5949 15008 3.004944 AGAAGAAGAACACGAGGTCAGAC 59.995 47.826 0.00 0.00 0.00 3.51
5952 15011 2.956333 TGAGAAGAAGAACACGAGGTCA 59.044 45.455 0.00 0.00 0.00 4.02
5957 15016 3.452755 TTGCTGAGAAGAAGAACACGA 57.547 42.857 0.00 0.00 0.00 4.35
6001 15062 1.186267 AGGGAGGTGAACGGTCTGAC 61.186 60.000 0.33 0.00 0.00 3.51
6046 15107 5.091261 AGATTGAAGAGATGCTAACGGTT 57.909 39.130 0.00 0.00 0.00 4.44
6077 15139 6.682423 TGCATCATTCGATCTTGTTACAAT 57.318 33.333 0.00 0.00 0.00 2.71
6109 15171 3.628646 GAGGTGGCTGCGGGAACAT 62.629 63.158 0.00 0.00 0.00 2.71
6128 15190 3.275338 GGCAGAGCATAGCACGGC 61.275 66.667 3.36 3.36 39.12 5.68
6136 15199 1.521450 GCAACAGTGTGGCAGAGCAT 61.521 55.000 18.12 0.00 31.84 3.79
6163 15226 3.391382 GCGTGGGTGGCTAGGACT 61.391 66.667 0.00 0.00 0.00 3.85
6202 15265 2.954753 CTTGCAGGACGACCGCAAC 61.955 63.158 23.23 6.78 44.09 4.17
6206 15269 4.680237 TGGCTTGCAGGACGACCG 62.680 66.667 0.00 0.00 41.83 4.79
6237 15305 3.441101 AGCCAGAACAGGTACATCACTA 58.559 45.455 0.00 0.00 0.00 2.74
6364 15432 4.550669 TGTAGGAGATGTCCATGATCTGT 58.449 43.478 12.14 0.00 46.80 3.41
6423 15496 4.961511 TGTCACAGGTGCCGTCGC 62.962 66.667 0.00 0.00 0.00 5.19
6458 15531 0.178891 AGGCCAAGGTCAGAAGAGGA 60.179 55.000 5.01 0.00 0.00 3.71
6463 15590 0.823356 GTGCAAGGCCAAGGTCAGAA 60.823 55.000 5.01 0.00 0.00 3.02
6681 15815 0.391528 CACTGGCATCATCGACACCA 60.392 55.000 0.00 0.00 0.00 4.17
6807 15946 3.864583 GTCGGTGTTAATACGGCAATGTA 59.135 43.478 5.22 0.00 31.66 2.29
6838 15977 3.121030 GCGCAGTGCCACTCGAAT 61.121 61.111 17.01 0.00 37.76 3.34
6908 16051 6.369890 CCGCTTGCTACAAATCACTATGATAT 59.630 38.462 0.00 0.00 35.76 1.63
6947 16090 1.102938 AGAGGGGGTAAGAGGGAGTT 58.897 55.000 0.00 0.00 0.00 3.01
6981 16124 9.294030 CCACTAATTTATGAAATCAACAGCTTC 57.706 33.333 0.00 0.00 0.00 3.86
7009 16152 4.473559 ACGAGGGAGGGAAGATTTAATCAA 59.526 41.667 7.74 0.00 0.00 2.57
7017 16160 0.397816 CTGGACGAGGGAGGGAAGAT 60.398 60.000 0.00 0.00 0.00 2.40
7412 16559 2.494918 GGAGACGGACGGACCATG 59.505 66.667 0.00 0.00 38.90 3.66
8031 17178 1.067212 GGGATACGCTCGATCACAAGT 59.933 52.381 0.00 0.00 37.60 3.16
8048 17195 1.748122 GTAGCACGACGGAGAGGGA 60.748 63.158 0.00 0.00 0.00 4.20
8412 17559 4.686191 TTACGTGTGAGGTAAAAAGGGA 57.314 40.909 0.00 0.00 0.00 4.20
8413 17560 5.754543 TTTTACGTGTGAGGTAAAAAGGG 57.245 39.130 0.00 0.00 42.09 3.95
8414 17561 7.168469 CCAAATTTTACGTGTGAGGTAAAAAGG 59.832 37.037 14.73 13.17 45.47 3.11
8415 17562 7.168469 CCCAAATTTTACGTGTGAGGTAAAAAG 59.832 37.037 14.73 9.76 45.47 2.27
8416 17563 6.979238 CCCAAATTTTACGTGTGAGGTAAAAA 59.021 34.615 14.73 0.00 45.47 1.94
8431 17578 4.403734 GTCTCACTGACCCCCAAATTTTA 58.596 43.478 0.00 0.00 39.69 1.52
8484 17631 5.757320 GTCATTAGCAGTTAGATGCATGACT 59.243 40.000 2.46 2.21 46.14 3.41
8510 17657 4.301072 TCAGTTATTTTGGGACAGAGGG 57.699 45.455 0.00 0.00 42.39 4.30
8676 18053 3.676646 GCATTGCAACATTCAAGTTCCTC 59.323 43.478 0.00 0.00 0.00 3.71
8678 18055 3.656559 AGCATTGCAACATTCAAGTTCC 58.343 40.909 11.91 0.00 0.00 3.62
8679 18056 4.553323 AGAGCATTGCAACATTCAAGTTC 58.447 39.130 11.91 0.00 0.00 3.01
8862 18473 6.476378 AGCTACTGGTATATAAATGGCCAAG 58.524 40.000 10.96 0.00 0.00 3.61
8912 18583 7.692908 GCTTAGAGCTACTTGTTTCAGATAG 57.307 40.000 0.00 0.00 38.45 2.08
8950 18661 4.223556 TGCCATAAATTTACCGGTCTCA 57.776 40.909 12.40 0.00 0.00 3.27
9061 18773 8.262933 TCATACCTGAGATGGAAGCATATATTG 58.737 37.037 0.00 0.00 0.00 1.90
9064 18800 6.725834 TGTCATACCTGAGATGGAAGCATATA 59.274 38.462 0.00 0.00 30.18 0.86
9094 18832 4.068599 AGCAAAGAGAAAGGTTGTAGCTC 58.931 43.478 0.00 0.00 0.00 4.09
9143 18881 5.510430 AGAAACCATAATCTGTTCCCCTTC 58.490 41.667 0.00 0.00 0.00 3.46
9152 18890 6.886459 TCTTGGAAAGGAGAAACCATAATCTG 59.114 38.462 0.00 0.00 46.24 2.90
9246 19169 9.133627 CTTCATTATCTCCAACTACATGTATCG 57.866 37.037 5.91 0.00 0.00 2.92
9257 19180 7.210873 AGGACGTTATCTTCATTATCTCCAAC 58.789 38.462 0.00 0.00 0.00 3.77
9260 19183 8.740906 TGATAGGACGTTATCTTCATTATCTCC 58.259 37.037 8.36 0.00 32.44 3.71
9281 19204 7.705325 CCTTTTCCAAGCTGATCATTTTGATAG 59.295 37.037 16.67 9.81 37.20 2.08
9283 19206 6.211986 TCCTTTTCCAAGCTGATCATTTTGAT 59.788 34.615 16.67 0.00 40.34 2.57
9353 19276 4.038282 TCATGCAAGAATTTCACAGCAACT 59.962 37.500 12.30 0.00 35.45 3.16
9379 19302 1.423921 ACTCATCCCCGTTTCCTTTGT 59.576 47.619 0.00 0.00 0.00 2.83
9585 19508 1.934589 CCACGAGCAATACCGATTGA 58.065 50.000 1.88 0.00 44.59 2.57
9593 19516 0.464036 ATTCGAGGCCACGAGCAATA 59.536 50.000 24.17 10.74 46.50 1.90
9761 19684 6.238484 CGATGAATCCAATTGTTCCTCTAACC 60.238 42.308 4.43 0.00 37.27 2.85


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

AutoCloner maintained by Alex Coulton.