Multiple sequence alignment - TraesCS7D01G378100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G378100 chr7D 100.000 7632 0 0 1 7632 489293847 489301478 0.000000e+00 14094.0
1 TraesCS7D01G378100 chr7D 90.655 2076 145 21 1631 3688 259364287 259366331 0.000000e+00 2713.0
2 TraesCS7D01G378100 chr7D 90.718 2047 167 9 1608 3642 54534797 54536832 0.000000e+00 2706.0
3 TraesCS7D01G378100 chr7D 93.963 1408 63 12 3696 5095 46557413 46558806 0.000000e+00 2109.0
4 TraesCS7D01G378100 chr7D 88.295 1777 162 32 3696 5446 638359312 638361068 0.000000e+00 2087.0
5 TraesCS7D01G378100 chr7D 88.328 1585 129 28 52 1611 46540324 46541877 0.000000e+00 1851.0
6 TraesCS7D01G378100 chr7D 91.455 749 58 5 3696 4441 176143090 176142345 0.000000e+00 1024.0
7 TraesCS7D01G378100 chr7D 83.571 1053 95 42 342 1359 121820307 121821316 0.000000e+00 915.0
8 TraesCS7D01G378100 chr7D 82.425 973 66 46 5457 6356 484068388 484069328 0.000000e+00 752.0
9 TraesCS7D01G378100 chr7D 85.331 709 83 8 1 709 384055203 384055890 0.000000e+00 713.0
10 TraesCS7D01G378100 chr7D 80.545 550 61 19 1384 1893 638356865 638357408 1.550000e-101 381.0
11 TraesCS7D01G378100 chr7D 78.236 703 75 42 926 1606 184203031 184203677 5.590000e-101 379.0
12 TraesCS7D01G378100 chr7D 98.113 53 1 0 2 54 46540249 46540301 8.150000e-15 93.5
13 TraesCS7D01G378100 chr4B 91.600 1988 150 9 1707 3688 92952830 92954806 0.000000e+00 2730.0
14 TraesCS7D01G378100 chr4B 86.090 1596 158 41 52 1608 384286996 384285426 0.000000e+00 1659.0
15 TraesCS7D01G378100 chr4B 88.230 1198 105 24 4147 5323 655485551 655484369 0.000000e+00 1399.0
16 TraesCS7D01G378100 chr4B 77.984 377 32 23 5746 6077 540726452 540726082 1.010000e-43 189.0
17 TraesCS7D01G378100 chr3B 90.218 2065 174 17 1630 3688 133397593 133395551 0.000000e+00 2669.0
18 TraesCS7D01G378100 chr3B 89.275 2070 186 20 1630 3688 119330361 119332405 0.000000e+00 2560.0
19 TraesCS7D01G378100 chr3B 79.666 1618 224 66 955 2501 662808802 662810385 0.000000e+00 1068.0
20 TraesCS7D01G378100 chr3B 90.278 792 72 3 50 840 759088220 759087433 0.000000e+00 1031.0
21 TraesCS7D01G378100 chr3B 90.537 782 67 4 103 881 662807994 662808771 0.000000e+00 1027.0
22 TraesCS7D01G378100 chr3B 81.940 598 86 10 4854 5447 11560732 11561311 3.200000e-133 486.0
23 TraesCS7D01G378100 chr3B 78.112 233 42 8 5221 5449 708607883 708607656 1.030000e-28 139.0
24 TraesCS7D01G378100 chr3B 86.517 89 8 4 1341 1427 759086897 759086983 2.270000e-15 95.3
25 TraesCS7D01G378100 chr1D 89.981 2076 161 23 1631 3688 48897478 48899524 0.000000e+00 2638.0
26 TraesCS7D01G378100 chr1D 91.966 1531 82 17 3919 5446 318152920 318154412 0.000000e+00 2108.0
27 TraesCS7D01G378100 chr1D 93.750 1248 67 6 1582 2821 175813314 175812070 0.000000e+00 1862.0
28 TraesCS7D01G378100 chr1D 92.752 1159 55 11 4307 5447 175788720 175787573 0.000000e+00 1648.0
29 TraesCS7D01G378100 chr1D 90.455 1100 71 11 52 1143 175815077 175814004 0.000000e+00 1419.0
30 TraesCS7D01G378100 chr1D 83.544 1586 164 46 52 1611 426190176 426188662 0.000000e+00 1393.0
31 TraesCS7D01G378100 chr1D 80.656 1463 175 61 972 2359 335018596 335020025 0.000000e+00 1035.0
32 TraesCS7D01G378100 chr1D 88.889 846 71 11 52 891 335017744 335018572 0.000000e+00 1020.0
33 TraesCS7D01G378100 chr1D 98.000 50 1 0 5 54 175815149 175815100 3.790000e-13 87.9
34 TraesCS7D01G378100 chr7B 89.758 2070 178 16 1630 3688 94124215 94122169 0.000000e+00 2617.0
35 TraesCS7D01G378100 chr7B 94.242 1181 58 3 6448 7627 517931734 517932905 0.000000e+00 1796.0
36 TraesCS7D01G378100 chr7B 87.035 1049 116 10 6585 7629 509735152 509736184 0.000000e+00 1166.0
37 TraesCS7D01G378100 chr7B 85.185 945 70 35 5457 6356 509732533 509733452 0.000000e+00 905.0
38 TraesCS7D01G378100 chr7B 91.880 468 23 4 5745 6208 517930922 517931378 2.320000e-179 640.0
39 TraesCS7D01G378100 chr7B 93.865 326 12 2 6123 6448 517931379 517931696 1.150000e-132 484.0
40 TraesCS7D01G378100 chr7B 92.157 51 4 0 5449 5499 517930887 517930837 1.060000e-08 73.1
41 TraesCS7D01G378100 chr4D 89.680 2064 168 25 1634 3688 500545195 500543168 0.000000e+00 2590.0
42 TraesCS7D01G378100 chr4D 91.479 1772 86 25 3688 5448 99353799 99352082 0.000000e+00 2375.0
43 TraesCS7D01G378100 chr4D 83.353 1676 170 54 1 1609 7137652 7136019 0.000000e+00 1448.0
44 TraesCS7D01G378100 chr4D 87.409 1096 91 15 52 1138 29318025 29319082 0.000000e+00 1216.0
45 TraesCS7D01G378100 chr4D 87.585 878 72 16 1 854 309639151 309638287 0.000000e+00 983.0
46 TraesCS7D01G378100 chr4D 87.083 720 73 7 2 709 99357671 99356960 0.000000e+00 797.0
47 TraesCS7D01G378100 chr4D 81.832 655 82 26 974 1609 99356619 99355983 4.080000e-142 516.0
48 TraesCS7D01G378100 chr4D 78.628 379 26 27 5746 6077 437818861 437818491 4.670000e-47 200.0
49 TraesCS7D01G378100 chr2D 89.403 2076 170 25 1631 3688 98910216 98912259 0.000000e+00 2569.0
50 TraesCS7D01G378100 chr2D 90.646 1037 68 15 52 1079 368971721 368970705 0.000000e+00 1351.0
51 TraesCS7D01G378100 chr2D 92.166 651 48 3 3733 4381 66165033 66164384 0.000000e+00 917.0
52 TraesCS7D01G378100 chr2D 92.545 550 39 2 67 615 77600763 77600215 0.000000e+00 787.0
53 TraesCS7D01G378100 chrUn 89.426 1759 148 23 3696 5448 66806584 66804858 0.000000e+00 2183.0
54 TraesCS7D01G378100 chrUn 81.988 1016 173 8 6606 7616 277362717 277361707 0.000000e+00 854.0
55 TraesCS7D01G378100 chrUn 86.047 86 10 2 1343 1427 66809349 66809433 2.930000e-14 91.6
56 TraesCS7D01G378100 chr5B 89.034 1760 158 20 3696 5448 99860500 99862231 0.000000e+00 2148.0
57 TraesCS7D01G378100 chr5B 77.809 356 47 24 5745 6074 474047940 474047591 2.810000e-44 191.0
58 TraesCS7D01G378100 chr5B 84.270 89 8 6 1342 1427 516294332 516294247 1.770000e-11 82.4
59 TraesCS7D01G378100 chr6B 86.900 1771 193 25 3696 5449 579651725 579649977 0.000000e+00 1949.0
60 TraesCS7D01G378100 chr6B 86.641 1033 129 3 6583 7607 649831118 649832149 0.000000e+00 1134.0
61 TraesCS7D01G378100 chr6B 90.676 740 64 2 103 840 522677863 522677127 0.000000e+00 979.0
62 TraesCS7D01G378100 chr6B 80.659 698 95 26 4761 5446 26883402 26884071 8.840000e-139 505.0
63 TraesCS7D01G378100 chr6B 84.375 384 36 12 892 1265 522677120 522676751 9.420000e-94 355.0
64 TraesCS7D01G378100 chr6B 75.874 286 53 16 5170 5447 216352213 216352490 1.730000e-26 132.0
65 TraesCS7D01G378100 chr3D 86.957 1771 160 49 3698 5449 492677381 492675663 0.000000e+00 1925.0
66 TraesCS7D01G378100 chr3D 85.952 1680 138 45 1 1611 75121120 75122770 0.000000e+00 1705.0
67 TraesCS7D01G378100 chr3D 88.707 1160 85 27 52 1188 542851020 542852156 0.000000e+00 1375.0
68 TraesCS7D01G378100 chr3D 89.269 848 73 11 50 891 104710872 104711707 0.000000e+00 1046.0
69 TraesCS7D01G378100 chr3D 91.236 696 51 6 3688 4381 542986808 542987495 0.000000e+00 939.0
70 TraesCS7D01G378100 chr3D 82.836 134 5 6 1 116 53562366 53562499 3.770000e-18 104.0
71 TraesCS7D01G378100 chr3D 86.517 89 10 2 1340 1427 542984430 542984343 6.300000e-16 97.1
72 TraesCS7D01G378100 chr2B 88.287 905 74 19 254 1149 102402532 102403413 0.000000e+00 1055.0
73 TraesCS7D01G378100 chr6A 86.667 945 118 3 6671 7607 577721968 577722912 0.000000e+00 1040.0
74 TraesCS7D01G378100 chr6A 82.837 973 155 11 6648 7613 64907085 64908052 0.000000e+00 861.0
75 TraesCS7D01G378100 chr6A 81.935 1013 173 8 6606 7613 64678227 64679234 0.000000e+00 848.0
76 TraesCS7D01G378100 chr6D 83.235 1014 161 7 6606 7616 49184164 49183157 0.000000e+00 922.0
77 TraesCS7D01G378100 chr6D 82.463 1015 170 7 6606 7616 50606505 50605495 0.000000e+00 881.0
78 TraesCS7D01G378100 chr6D 83.527 947 148 5 6676 7616 50181140 50180196 0.000000e+00 878.0
79 TraesCS7D01G378100 chr6D 85.672 335 34 10 968 1293 436949662 436949333 2.640000e-89 340.0
80 TraesCS7D01G378100 chr7A 84.113 919 76 34 5457 6325 551539896 551540794 0.000000e+00 824.0
81 TraesCS7D01G378100 chr7A 81.275 1004 177 8 6612 7613 591025611 591024617 0.000000e+00 802.0
82 TraesCS7D01G378100 chr4A 83.298 946 91 27 83 980 587334929 587334003 0.000000e+00 809.0
83 TraesCS7D01G378100 chr4A 82.224 1007 110 36 628 1611 573902296 573901336 0.000000e+00 804.0
84 TraesCS7D01G378100 chr4A 81.685 273 23 14 5826 6077 30286991 30287257 1.300000e-47 202.0
85 TraesCS7D01G378100 chr5D 82.496 657 84 20 972 1611 45494924 45495566 1.450000e-151 547.0
86 TraesCS7D01G378100 chr5D 78.310 355 43 29 5747 6074 394163295 394162948 1.680000e-46 198.0
87 TraesCS7D01G378100 chr5A 78.492 358 44 25 5744 6074 496135206 496134855 3.610000e-48 204.0
88 TraesCS7D01G378100 chr3A 81.884 138 20 5 5314 5449 27099166 27099032 2.250000e-20 111.0
89 TraesCS7D01G378100 chr3A 79.221 154 26 6 5298 5449 27234512 27234363 1.350000e-17 102.0
90 TraesCS7D01G378100 chr3A 81.343 134 7 6 1 116 64809154 64809021 8.150000e-15 93.5


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 TraesCS7D01G378100 chr7D 489293847 489301478 7631 False 14094.000000 14094 100.000000 1 7632 1 chr7D.!!$F8 7631
1 TraesCS7D01G378100 chr7D 259364287 259366331 2044 False 2713.000000 2713 90.655000 1631 3688 1 chr7D.!!$F5 2057
2 TraesCS7D01G378100 chr7D 54534797 54536832 2035 False 2706.000000 2706 90.718000 1608 3642 1 chr7D.!!$F2 2034
3 TraesCS7D01G378100 chr7D 46557413 46558806 1393 False 2109.000000 2109 93.963000 3696 5095 1 chr7D.!!$F1 1399
4 TraesCS7D01G378100 chr7D 638356865 638361068 4203 False 1234.000000 2087 84.420000 1384 5446 2 chr7D.!!$F10 4062
5 TraesCS7D01G378100 chr7D 176142345 176143090 745 True 1024.000000 1024 91.455000 3696 4441 1 chr7D.!!$R1 745
6 TraesCS7D01G378100 chr7D 46540249 46541877 1628 False 972.250000 1851 93.220500 2 1611 2 chr7D.!!$F9 1609
7 TraesCS7D01G378100 chr7D 121820307 121821316 1009 False 915.000000 915 83.571000 342 1359 1 chr7D.!!$F3 1017
8 TraesCS7D01G378100 chr7D 484068388 484069328 940 False 752.000000 752 82.425000 5457 6356 1 chr7D.!!$F7 899
9 TraesCS7D01G378100 chr7D 384055203 384055890 687 False 713.000000 713 85.331000 1 709 1 chr7D.!!$F6 708
10 TraesCS7D01G378100 chr7D 184203031 184203677 646 False 379.000000 379 78.236000 926 1606 1 chr7D.!!$F4 680
11 TraesCS7D01G378100 chr4B 92952830 92954806 1976 False 2730.000000 2730 91.600000 1707 3688 1 chr4B.!!$F1 1981
12 TraesCS7D01G378100 chr4B 384285426 384286996 1570 True 1659.000000 1659 86.090000 52 1608 1 chr4B.!!$R1 1556
13 TraesCS7D01G378100 chr4B 655484369 655485551 1182 True 1399.000000 1399 88.230000 4147 5323 1 chr4B.!!$R3 1176
14 TraesCS7D01G378100 chr3B 133395551 133397593 2042 True 2669.000000 2669 90.218000 1630 3688 1 chr3B.!!$R1 2058
15 TraesCS7D01G378100 chr3B 119330361 119332405 2044 False 2560.000000 2560 89.275000 1630 3688 1 chr3B.!!$F2 2058
16 TraesCS7D01G378100 chr3B 662807994 662810385 2391 False 1047.500000 1068 85.101500 103 2501 2 chr3B.!!$F4 2398
17 TraesCS7D01G378100 chr3B 759087433 759088220 787 True 1031.000000 1031 90.278000 50 840 1 chr3B.!!$R3 790
18 TraesCS7D01G378100 chr3B 11560732 11561311 579 False 486.000000 486 81.940000 4854 5447 1 chr3B.!!$F1 593
19 TraesCS7D01G378100 chr1D 48897478 48899524 2046 False 2638.000000 2638 89.981000 1631 3688 1 chr1D.!!$F1 2057
20 TraesCS7D01G378100 chr1D 318152920 318154412 1492 False 2108.000000 2108 91.966000 3919 5446 1 chr1D.!!$F2 1527
21 TraesCS7D01G378100 chr1D 175787573 175788720 1147 True 1648.000000 1648 92.752000 4307 5447 1 chr1D.!!$R1 1140
22 TraesCS7D01G378100 chr1D 426188662 426190176 1514 True 1393.000000 1393 83.544000 52 1611 1 chr1D.!!$R2 1559
23 TraesCS7D01G378100 chr1D 175812070 175815149 3079 True 1122.966667 1862 94.068333 5 2821 3 chr1D.!!$R3 2816
24 TraesCS7D01G378100 chr1D 335017744 335020025 2281 False 1027.500000 1035 84.772500 52 2359 2 chr1D.!!$F3 2307
25 TraesCS7D01G378100 chr7B 94122169 94124215 2046 True 2617.000000 2617 89.758000 1630 3688 1 chr7B.!!$R1 2058
26 TraesCS7D01G378100 chr7B 509732533 509736184 3651 False 1035.500000 1166 86.110000 5457 7629 2 chr7B.!!$F1 2172
27 TraesCS7D01G378100 chr7B 517930922 517932905 1983 False 973.333333 1796 93.329000 5745 7627 3 chr7B.!!$F2 1882
28 TraesCS7D01G378100 chr4D 500543168 500545195 2027 True 2590.000000 2590 89.680000 1634 3688 1 chr4D.!!$R4 2054
29 TraesCS7D01G378100 chr4D 7136019 7137652 1633 True 1448.000000 1448 83.353000 1 1609 1 chr4D.!!$R1 1608
30 TraesCS7D01G378100 chr4D 99352082 99357671 5589 True 1229.333333 2375 86.798000 2 5448 3 chr4D.!!$R5 5446
31 TraesCS7D01G378100 chr4D 29318025 29319082 1057 False 1216.000000 1216 87.409000 52 1138 1 chr4D.!!$F1 1086
32 TraesCS7D01G378100 chr4D 309638287 309639151 864 True 983.000000 983 87.585000 1 854 1 chr4D.!!$R2 853
33 TraesCS7D01G378100 chr2D 98910216 98912259 2043 False 2569.000000 2569 89.403000 1631 3688 1 chr2D.!!$F1 2057
34 TraesCS7D01G378100 chr2D 368970705 368971721 1016 True 1351.000000 1351 90.646000 52 1079 1 chr2D.!!$R3 1027
35 TraesCS7D01G378100 chr2D 66164384 66165033 649 True 917.000000 917 92.166000 3733 4381 1 chr2D.!!$R1 648
36 TraesCS7D01G378100 chr2D 77600215 77600763 548 True 787.000000 787 92.545000 67 615 1 chr2D.!!$R2 548
37 TraesCS7D01G378100 chrUn 66804858 66806584 1726 True 2183.000000 2183 89.426000 3696 5448 1 chrUn.!!$R1 1752
38 TraesCS7D01G378100 chrUn 277361707 277362717 1010 True 854.000000 854 81.988000 6606 7616 1 chrUn.!!$R2 1010
39 TraesCS7D01G378100 chr5B 99860500 99862231 1731 False 2148.000000 2148 89.034000 3696 5448 1 chr5B.!!$F1 1752
40 TraesCS7D01G378100 chr6B 579649977 579651725 1748 True 1949.000000 1949 86.900000 3696 5449 1 chr6B.!!$R1 1753
41 TraesCS7D01G378100 chr6B 649831118 649832149 1031 False 1134.000000 1134 86.641000 6583 7607 1 chr6B.!!$F3 1024
42 TraesCS7D01G378100 chr6B 522676751 522677863 1112 True 667.000000 979 87.525500 103 1265 2 chr6B.!!$R2 1162
43 TraesCS7D01G378100 chr6B 26883402 26884071 669 False 505.000000 505 80.659000 4761 5446 1 chr6B.!!$F1 685
44 TraesCS7D01G378100 chr3D 492675663 492677381 1718 True 1925.000000 1925 86.957000 3698 5449 1 chr3D.!!$R1 1751
45 TraesCS7D01G378100 chr3D 75121120 75122770 1650 False 1705.000000 1705 85.952000 1 1611 1 chr3D.!!$F2 1610
46 TraesCS7D01G378100 chr3D 542851020 542852156 1136 False 1375.000000 1375 88.707000 52 1188 1 chr3D.!!$F4 1136
47 TraesCS7D01G378100 chr3D 104710872 104711707 835 False 1046.000000 1046 89.269000 50 891 1 chr3D.!!$F3 841
48 TraesCS7D01G378100 chr3D 542986808 542987495 687 False 939.000000 939 91.236000 3688 4381 1 chr3D.!!$F5 693
49 TraesCS7D01G378100 chr2B 102402532 102403413 881 False 1055.000000 1055 88.287000 254 1149 1 chr2B.!!$F1 895
50 TraesCS7D01G378100 chr6A 577721968 577722912 944 False 1040.000000 1040 86.667000 6671 7607 1 chr6A.!!$F3 936
51 TraesCS7D01G378100 chr6A 64907085 64908052 967 False 861.000000 861 82.837000 6648 7613 1 chr6A.!!$F2 965
52 TraesCS7D01G378100 chr6A 64678227 64679234 1007 False 848.000000 848 81.935000 6606 7613 1 chr6A.!!$F1 1007
53 TraesCS7D01G378100 chr6D 49183157 49184164 1007 True 922.000000 922 83.235000 6606 7616 1 chr6D.!!$R1 1010
54 TraesCS7D01G378100 chr6D 50605495 50606505 1010 True 881.000000 881 82.463000 6606 7616 1 chr6D.!!$R3 1010
55 TraesCS7D01G378100 chr6D 50180196 50181140 944 True 878.000000 878 83.527000 6676 7616 1 chr6D.!!$R2 940
56 TraesCS7D01G378100 chr7A 551539896 551540794 898 False 824.000000 824 84.113000 5457 6325 1 chr7A.!!$F1 868
57 TraesCS7D01G378100 chr7A 591024617 591025611 994 True 802.000000 802 81.275000 6612 7613 1 chr7A.!!$R1 1001
58 TraesCS7D01G378100 chr4A 587334003 587334929 926 True 809.000000 809 83.298000 83 980 1 chr4A.!!$R2 897
59 TraesCS7D01G378100 chr4A 573901336 573902296 960 True 804.000000 804 82.224000 628 1611 1 chr4A.!!$R1 983
60 TraesCS7D01G378100 chr5D 45494924 45495566 642 False 547.000000 547 82.496000 972 1611 1 chr5D.!!$F1 639

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
324 357 0.038166 TGGCTCTTTCCTCCGCATTT 59.962 50.0 0.00 0.00 0.00 2.32 F
505 540 0.309922 TACATCGTCGAAGATCCGCC 59.690 55.0 11.10 0.00 40.67 6.13 F
1290 1651 0.323725 TAGTTCTCGGCGGTAGGGTT 60.324 55.0 7.21 0.00 0.00 4.11 F
2503 3173 0.176680 CTCTGTTCATGAGGGGTCCG 59.823 60.0 0.00 0.00 0.00 4.79 F
2604 3274 0.250234 GCATCTGCTGGTGTCCACTA 59.750 55.0 5.69 0.00 38.21 2.74 F
2649 3319 0.464036 ATGCCATCGTCGTACCACAT 59.536 50.0 0.00 0.00 0.00 3.21 F
3690 4370 0.326143 TGGCATACTGCTCCACCCTA 60.326 55.0 0.00 0.00 44.28 3.53 F
3728 4558 0.389948 GAGCGGTAGGGCCATAATCG 60.390 60.0 6.18 11.06 36.97 3.34 F
5613 7055 0.035056 GCCCCAGCTTGCTTCTCTTA 60.035 55.0 0.00 0.00 35.50 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1666 0.033504 TTCCTCGTCACAGAACTGCC 59.966 55.000 1.46 0.00 0.00 4.85 R
2484 3154 0.176680 CGGACCCCTCATGAACAGAG 59.823 60.000 0.00 0.00 0.00 3.35 R
3273 3944 0.107654 GAAGATGGTCTGAACCCGGG 60.108 60.000 22.25 22.25 45.83 5.73 R
3688 4368 1.067821 GAGGGTCGTGCTCTTCCATAG 59.932 57.143 0.00 0.00 0.00 2.23 R
3689 4369 1.112113 GAGGGTCGTGCTCTTCCATA 58.888 55.000 0.00 0.00 0.00 2.74 R
3728 4558 1.522569 CCCTCGAGGATTGGGTGAC 59.477 63.158 33.39 0.00 38.24 3.67 R
5613 7055 0.326618 ACGGGGAGAATGAGGTGGAT 60.327 55.000 0.00 0.00 0.00 3.41 R
5644 7098 1.009675 CACGCACTTGACACTTGCC 60.010 57.895 2.56 0.00 32.31 4.52 R
7197 10708 0.685097 TCAGTGGTGCCTCCTGTTAC 59.315 55.000 0.00 0.00 37.07 2.50 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
34 35 5.438761 AGCAAACTTGTCCACATAGTTTC 57.561 39.130 12.91 9.99 36.27 2.78
78 104 1.989430 ACAAACGGTGCAACAAGTTG 58.011 45.000 0.98 8.53 38.78 3.16
178 210 2.668632 GATCCACCGGTTCTGGCA 59.331 61.111 2.97 0.00 0.00 4.92
324 357 0.038166 TGGCTCTTTCCTCCGCATTT 59.962 50.000 0.00 0.00 0.00 2.32
395 429 1.447314 GCTTGGCAGCTTCAATGGC 60.447 57.895 0.00 0.00 43.51 4.40
432 466 1.967066 CGGGAGATAGTTGGATCTGCT 59.033 52.381 5.14 0.00 42.31 4.24
505 540 0.309922 TACATCGTCGAAGATCCGCC 59.690 55.000 11.10 0.00 40.67 6.13
681 740 2.925563 CACGGTTCCGTACCTAAACATC 59.074 50.000 16.51 0.00 45.40 3.06
889 1193 7.618137 TCATCATGATTCATCACGAAGGATAT 58.382 34.615 5.16 0.00 40.03 1.63
945 1284 8.588472 CACCTACATCATATCAACTAGGATTCA 58.412 37.037 0.00 0.00 28.51 2.57
1064 1406 4.866508 TCGAAGGAGCTTACTTTTCTCA 57.133 40.909 6.13 0.00 0.00 3.27
1069 1411 6.487689 AAGGAGCTTACTTTTCTCATTTCG 57.512 37.500 0.00 0.00 27.94 3.46
1103 1447 2.817258 TCCGCAAAATCCGTGAAGAAAT 59.183 40.909 0.00 0.00 0.00 2.17
1183 1539 2.124996 CTGGGTGGGGGAGAAGGA 59.875 66.667 0.00 0.00 0.00 3.36
1189 1548 2.125225 GGGGGAGAAGGAGGTGGT 59.875 66.667 0.00 0.00 0.00 4.16
1192 1552 1.002011 GGGAGAAGGAGGTGGTTGC 60.002 63.158 0.00 0.00 0.00 4.17
1261 1622 2.586792 GCAGTAGGGCCAGACAGG 59.413 66.667 6.18 1.17 41.84 4.00
1290 1651 0.323725 TAGTTCTCGGCGGTAGGGTT 60.324 55.000 7.21 0.00 0.00 4.11
1297 1658 3.773404 GCGGTAGGGTTGGCGGTA 61.773 66.667 0.00 0.00 0.00 4.02
1299 1660 2.905681 GGTAGGGTTGGCGGTAGG 59.094 66.667 0.00 0.00 0.00 3.18
1328 1689 0.716108 GTTCTGTGACGAGGAATGCG 59.284 55.000 0.00 0.00 0.00 4.73
1332 1693 1.132640 GTGACGAGGAATGCGCAAC 59.867 57.895 17.11 12.13 0.00 4.17
1335 1696 3.864686 CGAGGAATGCGCAACCCG 61.865 66.667 25.93 23.67 40.75 5.28
1397 1974 2.254508 GTAGGGACCTACCGCCATAAT 58.745 52.381 16.05 0.00 42.11 1.28
1411 1988 0.396435 CATAATGCCTGGCGGTAGGA 59.604 55.000 14.98 0.00 40.42 2.94
1503 2085 3.744003 ATAGGGTGCGGCGGTAGGA 62.744 63.158 9.78 0.00 0.00 2.94
1567 2151 4.704540 CCATAGTACATTTTTGCACCTCCA 59.295 41.667 0.00 0.00 0.00 3.86
1588 2172 7.031226 TCCAAACTTCTCTTGTCTTCAATTG 57.969 36.000 0.00 0.00 32.82 2.32
1616 2200 6.554419 TGCACATAACAATTCAATAGCTCAC 58.446 36.000 0.00 0.00 0.00 3.51
1622 2232 6.422776 AACAATTCAATAGCTCACGGTAAG 57.577 37.500 0.00 0.00 0.00 2.34
1672 2295 2.070783 GCAAGCACACATCCAAAATGG 58.929 47.619 0.00 0.00 39.43 3.16
1678 2301 3.492309 GCACACATCCAAAATGGTTCACA 60.492 43.478 0.00 0.00 39.03 3.58
1681 2304 5.583854 CACACATCCAAAATGGTTCACAAAA 59.416 36.000 0.00 0.00 39.03 2.44
1770 2406 5.240623 TGAAATGTTTCTAGTTCAACGGCAT 59.759 36.000 6.99 0.00 38.02 4.40
1792 2428 0.882042 CACGGCAGCAACTTCAGTCT 60.882 55.000 0.00 0.00 0.00 3.24
1894 2530 1.613255 GCTTTCTGAAACGGGGATGGA 60.613 52.381 0.00 0.00 0.00 3.41
1897 2533 0.902531 TCTGAAACGGGGATGGACTC 59.097 55.000 0.00 0.00 0.00 3.36
1917 2553 2.239654 TCTTCCAATCCTTCTTCGGCAT 59.760 45.455 0.00 0.00 0.00 4.40
1942 2578 0.468226 TCTTCTCACGCTGGGTTGTT 59.532 50.000 0.00 0.00 0.00 2.83
1950 2586 0.738389 CGCTGGGTTGTTTGAGTTGT 59.262 50.000 0.00 0.00 0.00 3.32
1987 2623 1.202663 TCATCGTACTCCTCCTCCTCG 60.203 57.143 0.00 0.00 0.00 4.63
1990 2626 0.733729 CGTACTCCTCCTCCTCGTTG 59.266 60.000 0.00 0.00 0.00 4.10
2031 2667 5.175127 GTCCTCTTCTCCATGTTCTTCTTC 58.825 45.833 0.00 0.00 0.00 2.87
2032 2668 5.046663 GTCCTCTTCTCCATGTTCTTCTTCT 60.047 44.000 0.00 0.00 0.00 2.85
2033 2669 5.545723 TCCTCTTCTCCATGTTCTTCTTCTT 59.454 40.000 0.00 0.00 0.00 2.52
2164 2833 1.888512 GCAGGAGCAAAAACATCCTCA 59.111 47.619 0.00 0.00 41.60 3.86
2176 2845 2.688507 ACATCCTCAGTGTTTGTAGCG 58.311 47.619 0.00 0.00 0.00 4.26
2233 2902 4.820897 TGACGTACTTCTGCAATGAGAAT 58.179 39.130 0.68 0.00 31.51 2.40
2247 2916 7.088272 TGCAATGAGAATGAAACAATGAGAAG 58.912 34.615 0.00 0.00 0.00 2.85
2322 2991 2.143925 CTTCACCGTTTCCCTCAACTC 58.856 52.381 0.00 0.00 0.00 3.01
2347 3016 2.192443 CTAGCTCGAGTCCCGGGA 59.808 66.667 22.63 22.63 42.61 5.14
2396 3065 4.405116 AAAATGCTTTTGTTCAGCTCCA 57.595 36.364 0.00 0.00 38.19 3.86
2403 3072 4.440663 GCTTTTGTTCAGCTCCAAAGACTT 60.441 41.667 2.67 0.00 34.15 3.01
2431 3100 7.757097 AGTAATAAAATGAGTCAGTAGCACG 57.243 36.000 0.00 0.00 0.00 5.34
2450 3120 4.676196 GCACGAAAGCTGATTTCATCCAAT 60.676 41.667 17.37 0.00 46.50 3.16
2503 3173 0.176680 CTCTGTTCATGAGGGGTCCG 59.823 60.000 0.00 0.00 0.00 4.79
2506 3176 1.762957 CTGTTCATGAGGGGTCCGTAT 59.237 52.381 0.00 0.00 0.00 3.06
2518 3188 2.121948 GGTCCGTATTCCCTAAACCCT 58.878 52.381 0.00 0.00 0.00 4.34
2521 3191 1.069668 CCGTATTCCCTAAACCCTCCG 59.930 57.143 0.00 0.00 0.00 4.63
2540 3210 1.802136 CGTGAAGCTCTCTGATGCTCC 60.802 57.143 5.91 0.00 38.75 4.70
2564 3234 2.457598 TGTAGGCTTCATTCTCGGAGT 58.542 47.619 4.69 0.00 0.00 3.85
2592 3262 0.674895 AACAGGTCTTCGGCATCTGC 60.675 55.000 0.00 0.00 41.14 4.26
2595 3265 1.817099 GGTCTTCGGCATCTGCTGG 60.817 63.158 10.93 0.00 46.99 4.85
2596 3266 1.078848 GTCTTCGGCATCTGCTGGT 60.079 57.895 10.93 0.00 46.99 4.00
2604 3274 0.250234 GCATCTGCTGGTGTCCACTA 59.750 55.000 5.69 0.00 38.21 2.74
2649 3319 0.464036 ATGCCATCGTCGTACCACAT 59.536 50.000 0.00 0.00 0.00 3.21
2723 3394 1.200020 GCCTTTCCACTCGTTCCATTG 59.800 52.381 0.00 0.00 0.00 2.82
2734 3405 3.331150 TCGTTCCATTGCTTCACGTATT 58.669 40.909 0.00 0.00 32.65 1.89
2737 3408 4.377943 CGTTCCATTGCTTCACGTATTTCA 60.378 41.667 0.00 0.00 0.00 2.69
2772 3443 5.188434 TCCCAATCTGTGATTGACTGATTC 58.812 41.667 18.46 0.00 45.32 2.52
2777 3448 7.414208 CCAATCTGTGATTGACTGATTCTTCTG 60.414 40.741 18.46 0.00 45.32 3.02
2866 3537 6.479660 TCAAAACAAGAACTTGGAATCAATGC 59.520 34.615 17.05 0.00 44.45 3.56
2956 3627 1.268352 TGTGTTGCGCCTTACCAAATC 59.732 47.619 4.18 0.00 0.00 2.17
3013 3684 3.290710 ACATAGACACAAATCATGGGCC 58.709 45.455 0.00 0.00 35.04 5.80
3093 3764 5.106118 CCACTCTCGATCATCATTATACGGT 60.106 44.000 0.00 0.00 0.00 4.83
3181 3852 9.110502 GAAATGTAGTTCTTATACCTGGAAAGG 57.889 37.037 0.00 0.00 0.00 3.11
3188 3859 0.541863 ATACCTGGAAAGGCGTGAGG 59.458 55.000 0.00 0.00 0.00 3.86
3244 3915 0.828022 TTGGATTCGCCCGTGTAGAT 59.172 50.000 0.00 0.00 34.97 1.98
3429 4109 1.228894 ACTTCCGCTCTCTGGGTCA 60.229 57.895 0.00 0.00 0.00 4.02
3456 4136 7.201410 CGTCGTCAAGCTACAAAACAAGTATAT 60.201 37.037 0.00 0.00 0.00 0.86
3487 4167 6.086222 AGATGTTAAAATGTAAAGCAGCACG 58.914 36.000 0.00 0.00 0.00 5.34
3630 4310 1.985116 AGAGTTCCCGGAGCAGTCC 60.985 63.158 0.73 0.00 39.88 3.85
3631 4311 2.203788 AGTTCCCGGAGCAGTCCA 60.204 61.111 0.73 0.00 44.18 4.02
3660 4340 3.033659 ACCTCCGTGAGAAGATACCAT 57.966 47.619 2.84 0.00 0.00 3.55
3668 4348 5.071370 CGTGAGAAGATACCATAGGTAGGT 58.929 45.833 2.07 0.00 41.83 3.08
3688 4368 1.153086 CTGGCATACTGCTCCACCC 60.153 63.158 0.00 0.00 44.28 4.61
3689 4369 1.616327 TGGCATACTGCTCCACCCT 60.616 57.895 0.00 0.00 44.28 4.34
3690 4370 0.326143 TGGCATACTGCTCCACCCTA 60.326 55.000 0.00 0.00 44.28 3.53
3691 4371 1.059913 GGCATACTGCTCCACCCTAT 58.940 55.000 0.00 0.00 44.28 2.57
3728 4558 0.389948 GAGCGGTAGGGCCATAATCG 60.390 60.000 6.18 11.06 36.97 3.34
3731 4561 0.677288 CGGTAGGGCCATAATCGTCA 59.323 55.000 6.18 0.00 36.97 4.35
3792 4622 0.464036 TGGAAGTTGTGCGTCTCTGT 59.536 50.000 0.00 0.00 0.00 3.41
3816 4646 2.332654 ACCGGTTGATCAAAGCCGC 61.333 57.895 24.77 7.96 42.54 6.53
3865 4695 0.391228 TACGCTTGAACTGCAGGACA 59.609 50.000 19.93 14.44 0.00 4.02
3895 4725 3.306902 TCGGGCTCTCCTGAAGAAT 57.693 52.632 0.00 0.00 44.57 2.40
3902 4732 0.391661 TCTCCTGAAGAATGGTGCGC 60.392 55.000 0.00 0.00 0.00 6.09
4024 4854 9.325198 CATGGACATAATAGTTAGCAACTTGTA 57.675 33.333 6.82 2.06 42.81 2.41
4084 4915 4.728772 ACCACTCCATTCTCAATGAAACA 58.271 39.130 0.00 0.00 41.46 2.83
4091 4922 2.542020 TCTCAATGAAACAGGCACGA 57.458 45.000 0.00 0.00 0.00 4.35
4113 4944 1.124477 GACGCTTGTCGAACTTAGTGC 59.876 52.381 0.00 0.00 41.67 4.40
4271 5108 4.418013 TGCATAACAAAGGTTCATCACG 57.582 40.909 0.00 0.00 38.45 4.35
4434 5331 4.116961 GACCATGGTTCAAATGCATCATG 58.883 43.478 20.85 13.98 33.78 3.07
4467 5369 5.452078 TTTCTCCAACAACATCCAACATC 57.548 39.130 0.00 0.00 0.00 3.06
4468 5370 3.420893 TCTCCAACAACATCCAACATCC 58.579 45.455 0.00 0.00 0.00 3.51
4469 5371 3.156293 CTCCAACAACATCCAACATCCA 58.844 45.455 0.00 0.00 0.00 3.41
4470 5372 3.570540 TCCAACAACATCCAACATCCAA 58.429 40.909 0.00 0.00 0.00 3.53
4471 5373 3.320541 TCCAACAACATCCAACATCCAAC 59.679 43.478 0.00 0.00 0.00 3.77
4472 5374 3.069300 CCAACAACATCCAACATCCAACA 59.931 43.478 0.00 0.00 0.00 3.33
4473 5375 4.262549 CCAACAACATCCAACATCCAACAT 60.263 41.667 0.00 0.00 0.00 2.71
4697 5605 5.894807 AGTTCAACATTTGTTCTCCAACTG 58.105 37.500 0.00 0.00 39.08 3.16
4904 5820 8.981659 CCTAAATCAATCCTAGGGTTCAAATTT 58.018 33.333 3.59 13.01 0.00 1.82
5032 5950 3.233980 CGGGGCCATCTCGATCCA 61.234 66.667 4.39 0.00 0.00 3.41
5279 6248 3.134879 CGGAGGCCATTACCGCTA 58.865 61.111 5.01 0.00 40.19 4.26
5406 6613 2.619931 TCAAACAGGGGTCAGATCTCA 58.380 47.619 0.00 0.00 0.00 3.27
5528 6934 4.697352 CCCATTCCCATTCTCGCTATAAAG 59.303 45.833 0.00 0.00 0.00 1.85
5553 6975 1.529244 GGAGGCCCCATTCCATTCG 60.529 63.158 0.00 0.00 33.55 3.34
5559 6981 2.316108 GCCCCATTCCATTCGGTTTAT 58.684 47.619 0.00 0.00 0.00 1.40
5561 6983 3.561143 CCCCATTCCATTCGGTTTATCA 58.439 45.455 0.00 0.00 0.00 2.15
5562 6984 4.151883 CCCCATTCCATTCGGTTTATCAT 58.848 43.478 0.00 0.00 0.00 2.45
5564 6986 5.183140 CCCCATTCCATTCGGTTTATCATAC 59.817 44.000 0.00 0.00 0.00 2.39
5565 6987 5.767665 CCCATTCCATTCGGTTTATCATACA 59.232 40.000 0.00 0.00 0.00 2.29
5569 6991 6.918892 TCCATTCGGTTTATCATACAACTG 57.081 37.500 0.00 0.00 0.00 3.16
5578 7003 7.469594 CGGTTTATCATACAACTGCTCCTACTA 60.470 40.741 0.00 0.00 0.00 1.82
5582 7010 1.196012 ACAACTGCTCCTACTAGCCC 58.804 55.000 0.00 0.00 42.05 5.19
5585 7013 1.234529 CTGCTCCTACTAGCCCCCT 59.765 63.158 0.00 0.00 42.05 4.79
5588 7016 1.228613 CTCCTACTAGCCCCCTCCG 60.229 68.421 0.00 0.00 0.00 4.63
5613 7055 0.035056 GCCCCAGCTTGCTTCTCTTA 60.035 55.000 0.00 0.00 35.50 2.10
5627 7081 5.163364 TGCTTCTCTTATCCACCTCATTCTC 60.163 44.000 0.00 0.00 0.00 2.87
5674 7147 0.108585 AGTGCGTGTGAACCAGGAAT 59.891 50.000 0.00 0.00 0.00 3.01
5679 7152 2.698803 CGTGTGAACCAGGAATCATCA 58.301 47.619 0.00 0.00 0.00 3.07
5680 7153 2.674852 CGTGTGAACCAGGAATCATCAG 59.325 50.000 0.00 0.00 0.00 2.90
5694 7167 5.510349 GGAATCATCAGACAAGGATCGATCA 60.510 44.000 25.93 4.02 0.00 2.92
5695 7168 5.541953 ATCATCAGACAAGGATCGATCAA 57.458 39.130 25.93 2.24 0.00 2.57
5696 7184 5.541953 TCATCAGACAAGGATCGATCAAT 57.458 39.130 25.93 11.81 0.00 2.57
6153 7646 4.174762 GTTCTCCTCAGTATGGTTCGAAC 58.825 47.826 20.14 20.14 36.16 3.95
6198 7768 3.173953 TGGTTGGATGATGCCTTTCTT 57.826 42.857 0.00 0.00 0.00 2.52
6222 7792 2.856760 AGAGGAGCCTGTGGATAGAA 57.143 50.000 0.00 0.00 0.00 2.10
6293 7872 2.833943 TGCATGCTCCTTCTCAACTAGA 59.166 45.455 20.33 0.00 0.00 2.43
6319 7898 2.661866 GATTGATCGGCCGGTCGG 60.662 66.667 31.88 10.38 38.57 4.79
6374 7989 5.867174 GCTATTTATTTCCACCGCAAAGTTT 59.133 36.000 0.00 0.00 0.00 2.66
6379 7994 3.907894 TTCCACCGCAAAGTTTGTATC 57.092 42.857 16.70 0.00 0.00 2.24
6387 8002 4.082245 CCGCAAAGTTTGTATCCCAAGATT 60.082 41.667 16.70 0.00 33.75 2.40
6468 8129 2.364002 TCTGGGGCTTTTTGTTTACAGC 59.636 45.455 0.00 0.00 0.00 4.40
6484 8145 7.715657 TGTTTACAGCAGAAATGAAACAATCT 58.284 30.769 0.00 0.00 34.74 2.40
6507 8168 9.998106 ATCTATTATAGTGCAAAATAGTCGGTT 57.002 29.630 14.25 1.31 35.58 4.44
6537 8198 7.173562 ACGAACGTGATAGCTAGAGAGATTAAT 59.826 37.037 0.00 0.00 0.00 1.40
6538 8199 8.018520 CGAACGTGATAGCTAGAGAGATTAATT 58.981 37.037 0.00 0.00 0.00 1.40
6644 9721 2.279935 TCACCAATTAAACAGCCGGT 57.720 45.000 1.90 0.00 0.00 5.28
6922 10370 8.912285 TCCTAATCTCCCATAGTCTTATTCCTA 58.088 37.037 0.00 0.00 0.00 2.94
6932 10441 9.717942 CCATAGTCTTATTCCTAAAAGATGGAG 57.282 37.037 0.00 0.00 33.86 3.86
7197 10708 4.031089 CGAAATCGATAGCATCATTCTCCG 59.969 45.833 0.00 0.00 43.02 4.63
7233 10744 4.557205 CACTGAGTTGTAGGTGTTACTCC 58.443 47.826 0.00 0.00 36.94 3.85
7235 10746 3.489355 TGAGTTGTAGGTGTTACTCCGA 58.511 45.455 0.00 0.00 36.94 4.55
7245 10759 1.076332 GTTACTCCGAACAAGCGCAT 58.924 50.000 11.47 0.00 0.00 4.73
7347 10861 4.150359 GGAAATGAGAGCCATGGATGATT 58.850 43.478 18.40 4.23 35.24 2.57
7412 10926 1.756538 CCAAAAGTGTTGCTTCCCTGT 59.243 47.619 0.00 0.00 36.17 4.00
7629 11775 2.814097 GCTTTGGGTTCCTGAACTGCTA 60.814 50.000 9.68 0.00 40.94 3.49
7630 11776 3.690460 CTTTGGGTTCCTGAACTGCTAT 58.310 45.455 9.68 0.00 40.94 2.97
7631 11777 3.806949 TTGGGTTCCTGAACTGCTATT 57.193 42.857 9.68 0.00 40.94 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.736740 GCTTTGTGTTAGTTGGGGTTGTG 60.737 47.826 0.00 0.00 0.00 3.33
78 104 4.626172 CCCGCTCTCTAAACTTGTCTTAAC 59.374 45.833 0.00 0.00 0.00 2.01
324 357 4.202264 GGCCGGAGAATCTATTTCAAGAGA 60.202 45.833 5.05 0.00 36.75 3.10
432 466 3.773667 AGAGAGTGATTGCAGAGATGGAA 59.226 43.478 0.00 0.00 0.00 3.53
505 540 4.106925 GTGGCAGGAGAGGGCTGG 62.107 72.222 0.00 0.00 0.00 4.85
584 619 3.377253 ACATGTACGAGTCCTTCCCTA 57.623 47.619 0.00 0.00 0.00 3.53
585 620 2.233305 ACATGTACGAGTCCTTCCCT 57.767 50.000 0.00 0.00 0.00 4.20
726 961 5.094387 ACCATATGATGAACCCTAGGTAGG 58.906 45.833 8.29 0.00 43.25 3.18
727 962 5.780282 TGACCATATGATGAACCCTAGGTAG 59.220 44.000 8.29 0.00 33.12 3.18
728 963 5.722290 TGACCATATGATGAACCCTAGGTA 58.278 41.667 8.29 0.00 33.12 3.08
856 1140 6.293081 CGTGATGAATCATGATGAACCCTAAC 60.293 42.308 9.46 0.64 44.59 2.34
889 1193 8.585881 GCATCTAGATAATACAAGTTAGGTGGA 58.414 37.037 4.54 0.00 0.00 4.02
956 1295 8.108551 TCATGTTCATGTTCATGTTCATGTTA 57.891 30.769 27.39 18.45 41.22 2.41
1039 1379 4.223032 AGAAAAGTAAGCTCCTTCGATCCA 59.777 41.667 0.00 0.00 0.00 3.41
1064 1406 0.035458 GATCGAGATGGCCCCGAAAT 59.965 55.000 0.00 0.00 35.87 2.17
1069 1411 4.688966 GCGGATCGAGATGGCCCC 62.689 72.222 0.00 0.00 0.00 5.80
1103 1447 2.916355 CCCCCTCCGATCTTCTTCA 58.084 57.895 0.00 0.00 0.00 3.02
1204 1564 4.145365 GGTTTGGGCATTTATAAACCCC 57.855 45.455 21.14 21.14 43.82 4.95
1253 1614 1.478510 CTACAGTGGTAGCCTGTCTGG 59.521 57.143 16.13 7.54 42.03 3.86
1254 1615 2.949451 CTACAGTGGTAGCCTGTCTG 57.051 55.000 16.13 9.56 42.03 3.51
1269 1630 1.033746 CCCTACCGCCGAGAACTACA 61.034 60.000 0.00 0.00 0.00 2.74
1270 1631 1.034292 ACCCTACCGCCGAGAACTAC 61.034 60.000 0.00 0.00 0.00 2.73
1274 1635 2.652095 CCAACCCTACCGCCGAGAA 61.652 63.158 0.00 0.00 0.00 2.87
1275 1636 3.072468 CCAACCCTACCGCCGAGA 61.072 66.667 0.00 0.00 0.00 4.04
1295 1656 2.436115 GAACTGCCCGCACCCTAC 60.436 66.667 0.00 0.00 0.00 3.18
1296 1657 2.606519 AGAACTGCCCGCACCCTA 60.607 61.111 0.00 0.00 0.00 3.53
1297 1658 4.335647 CAGAACTGCCCGCACCCT 62.336 66.667 0.00 0.00 0.00 4.34
1299 1660 3.357079 CACAGAACTGCCCGCACC 61.357 66.667 1.46 0.00 0.00 5.01
1303 1664 1.734477 CTCGTCACAGAACTGCCCG 60.734 63.158 1.46 2.54 0.00 6.13
1304 1665 1.374758 CCTCGTCACAGAACTGCCC 60.375 63.158 1.46 0.00 0.00 5.36
1305 1666 0.033504 TTCCTCGTCACAGAACTGCC 59.966 55.000 1.46 0.00 0.00 4.85
1307 1668 1.728971 GCATTCCTCGTCACAGAACTG 59.271 52.381 0.00 0.00 0.00 3.16
1338 1699 2.461110 GGATGTGCAACGCTACCGG 61.461 63.158 0.00 0.00 42.39 5.28
1345 1922 2.461110 GGCGGTAGGATGTGCAACG 61.461 63.158 0.00 0.00 42.39 4.10
1397 1974 2.687200 ACATCCTACCGCCAGGCA 60.687 61.111 13.30 0.00 42.76 4.75
1411 1988 0.251165 AAAGCGGTAGGGTTGCACAT 60.251 50.000 0.00 0.00 36.26 3.21
1475 2057 1.827394 GCACCCTATGGCGGTAAGA 59.173 57.895 0.00 0.00 33.59 2.10
1503 2085 4.202524 ACACATGGTGGTAGGTTTGTACAT 60.203 41.667 0.00 0.00 37.94 2.29
1567 2151 9.143631 CAAAACAATTGAAGACAAGAGAAGTTT 57.856 29.630 13.59 0.00 39.46 2.66
1588 2172 8.243289 AGCTATTGAATTGTTATGTGCAAAAC 57.757 30.769 0.00 0.00 0.00 2.43
1606 2190 4.051922 GACCATCTTACCGTGAGCTATTG 58.948 47.826 0.00 0.00 0.00 1.90
1616 2200 4.730949 TCTTAGTTGGACCATCTTACCG 57.269 45.455 10.34 0.00 0.00 4.02
1647 2268 1.097232 TGGATGTGTGCTTGCTATGC 58.903 50.000 0.00 0.00 0.00 3.14
1770 2406 1.153269 TGAAGTTGCTGCCGTGTCA 60.153 52.632 0.00 0.00 0.00 3.58
1852 2488 1.711206 GTCCTACTCACCGCAAGAAC 58.289 55.000 0.00 0.00 43.02 3.01
1894 2530 2.355209 GCCGAAGAAGGATTGGAAGAGT 60.355 50.000 0.00 0.00 0.00 3.24
1897 2533 2.113860 TGCCGAAGAAGGATTGGAAG 57.886 50.000 0.00 0.00 0.00 3.46
1917 2553 1.757118 CCCAGCGTGAGAAGAGGAATA 59.243 52.381 0.00 0.00 0.00 1.75
1942 2578 0.834612 ACGGACCTCCAACAACTCAA 59.165 50.000 0.00 0.00 35.14 3.02
1950 2586 0.896479 TGATGACGACGGACCTCCAA 60.896 55.000 0.00 0.00 35.14 3.53
1987 2623 2.159170 CGATGAGGAGGAAGAGGACAAC 60.159 54.545 0.00 0.00 0.00 3.32
1990 2626 1.679153 GACGATGAGGAGGAAGAGGAC 59.321 57.143 0.00 0.00 0.00 3.85
2031 2667 1.110518 GGGCGAGGAGGGAGTAGAAG 61.111 65.000 0.00 0.00 0.00 2.85
2032 2668 1.076192 GGGCGAGGAGGGAGTAGAA 60.076 63.158 0.00 0.00 0.00 2.10
2033 2669 1.997256 GAGGGCGAGGAGGGAGTAGA 61.997 65.000 0.00 0.00 0.00 2.59
2131 2797 0.949588 CTCCTGCAGCGATGCATAGG 60.950 60.000 30.41 26.57 44.47 2.57
2164 2833 0.464735 TTGGGTGCGCTACAAACACT 60.465 50.000 9.73 0.00 34.70 3.55
2233 2902 7.660112 ACATTGCATAACTTCTCATTGTTTCA 58.340 30.769 0.00 0.00 0.00 2.69
2247 2916 4.091424 GCAGAAGTTCGACATTGCATAAC 58.909 43.478 8.68 0.00 0.00 1.89
2250 2919 2.153645 TGCAGAAGTTCGACATTGCAT 58.846 42.857 11.49 0.00 36.71 3.96
2322 2991 1.062880 GGACTCGAGCTAGTGAGAACG 59.937 57.143 13.61 0.00 36.11 3.95
2347 3016 4.559704 GCCTCTGATGCGCTTAGTACTATT 60.560 45.833 9.73 0.00 0.00 1.73
2403 3072 9.719355 TGCTACTGACTCATTTTATTACTTTGA 57.281 29.630 0.00 0.00 0.00 2.69
2450 3120 6.258287 TGTTTTTATCTCTTTTCAACCGACGA 59.742 34.615 0.00 0.00 0.00 4.20
2484 3154 0.176680 CGGACCCCTCATGAACAGAG 59.823 60.000 0.00 0.00 0.00 3.35
2486 3156 1.191535 TACGGACCCCTCATGAACAG 58.808 55.000 0.00 0.00 0.00 3.16
2503 3173 2.767960 TCACGGAGGGTTTAGGGAATAC 59.232 50.000 0.00 0.00 0.00 1.89
2506 3176 1.626825 CTTCACGGAGGGTTTAGGGAA 59.373 52.381 0.00 0.00 0.00 3.97
2518 3188 0.174389 GCATCAGAGAGCTTCACGGA 59.826 55.000 0.00 0.00 0.00 4.69
2521 3191 1.473080 GGGAGCATCAGAGAGCTTCAC 60.473 57.143 7.95 0.81 42.04 3.18
2540 3210 1.927174 CGAGAATGAAGCCTACAACGG 59.073 52.381 0.00 0.00 0.00 4.44
2592 3262 2.990479 GGCCCTAGTGGACACCAG 59.010 66.667 0.00 0.00 44.36 4.00
2604 3274 3.386237 GTCTGCGTCTGAGGCCCT 61.386 66.667 18.51 0.00 0.00 5.19
2649 3319 2.552743 GGACGATACGAGGATCACATGA 59.447 50.000 0.00 0.00 33.17 3.07
2703 3374 1.200020 CAATGGAACGAGTGGAAAGGC 59.800 52.381 0.00 0.00 0.00 4.35
2734 3405 3.050089 GGGAAGCCCAACATGTGAA 57.950 52.632 0.00 0.00 44.65 3.18
2772 3443 1.096386 GCAGGATGAGCAGGCAGAAG 61.096 60.000 0.00 0.00 39.69 2.85
2777 3448 1.734137 CATTGCAGGATGAGCAGGC 59.266 57.895 0.00 0.00 43.75 4.85
2866 3537 1.445582 GAGTACCACAAGCCGTCCG 60.446 63.158 0.00 0.00 0.00 4.79
2921 3592 4.116585 ACACACCACCAACCGGCA 62.117 61.111 0.00 0.00 34.57 5.69
2927 3598 3.057547 GCGCAACACACACCACCAA 62.058 57.895 0.30 0.00 0.00 3.67
2968 3639 3.591073 GGAGTACCACTTGCCACAGCA 62.591 57.143 0.00 0.00 41.09 4.41
2992 3663 3.290710 GGCCCATGATTTGTGTCTATGT 58.709 45.455 0.00 0.00 0.00 2.29
3013 3684 3.664025 TTCTCTGGCGGTGCATCGG 62.664 63.158 22.81 4.42 0.00 4.18
3093 3764 2.806434 TGGTACTAGGTTACTTGGCGA 58.194 47.619 0.00 0.00 0.00 5.54
3181 3852 2.437359 AGCTTGATGCCCTCACGC 60.437 61.111 6.72 6.72 46.62 5.34
3271 3942 4.096003 ATGGTCTGAACCCGGGCG 62.096 66.667 24.08 6.90 45.83 6.13
3273 3944 0.107654 GAAGATGGTCTGAACCCGGG 60.108 60.000 22.25 22.25 45.83 5.73
3274 3945 0.460284 CGAAGATGGTCTGAACCCGG 60.460 60.000 0.00 0.00 45.83 5.73
3282 3953 2.480416 GCGAAGATGACGAAGATGGTCT 60.480 50.000 0.00 0.00 35.45 3.85
3285 3965 1.212616 GGCGAAGATGACGAAGATGG 58.787 55.000 0.00 0.00 0.00 3.51
3429 4109 2.542597 TGTTTTGTAGCTTGACGACGT 58.457 42.857 0.00 0.00 0.00 4.34
3469 4149 2.224549 ACGCGTGCTGCTTTACATTTTA 59.775 40.909 12.93 0.00 43.27 1.52
3475 4155 1.635663 ATGGACGCGTGCTGCTTTAC 61.636 55.000 30.67 6.27 43.27 2.01
3487 4167 6.470235 CACTTTCTTTCAAATATCATGGACGC 59.530 38.462 0.00 0.00 0.00 5.19
3630 4310 2.557056 TCTCACGGAGGTAGTGTTTCTG 59.443 50.000 1.76 0.00 40.28 3.02
3631 4311 2.872732 TCTCACGGAGGTAGTGTTTCT 58.127 47.619 1.76 0.00 40.28 2.52
3688 4368 1.067821 GAGGGTCGTGCTCTTCCATAG 59.932 57.143 0.00 0.00 0.00 2.23
3689 4369 1.112113 GAGGGTCGTGCTCTTCCATA 58.888 55.000 0.00 0.00 0.00 2.74
3690 4370 1.901085 GAGGGTCGTGCTCTTCCAT 59.099 57.895 0.00 0.00 0.00 3.41
3691 4371 2.636412 CGAGGGTCGTGCTCTTCCA 61.636 63.158 0.00 0.00 34.72 3.53
3694 4374 3.279183 CTCGAGGGTCGTGCTCTT 58.721 61.111 3.91 0.00 41.35 2.85
3728 4558 1.522569 CCCTCGAGGATTGGGTGAC 59.477 63.158 33.39 0.00 38.24 3.67
3792 4622 2.398840 TTTGATCAACCGGTGGCGGA 62.399 55.000 8.52 4.16 0.00 5.54
3816 4646 3.102107 CTCGTCCACTCGGCTCTCG 62.102 68.421 0.00 0.00 40.90 4.04
3902 4732 1.989966 ATGGAGTACGACGAGCGGTG 61.990 60.000 0.00 0.00 46.49 4.94
4084 4915 1.738099 GACAAGCGTCATCGTGCCT 60.738 57.895 0.00 0.00 42.13 4.75
4091 4922 2.987149 CACTAAGTTCGACAAGCGTCAT 59.013 45.455 0.00 0.00 42.74 3.06
4167 4998 7.326454 TGCTTATGCCTATGTTTATGCAAAAA 58.674 30.769 0.00 0.00 38.71 1.94
4168 4999 6.871844 TGCTTATGCCTATGTTTATGCAAAA 58.128 32.000 0.00 0.00 38.71 2.44
4169 5000 6.462552 TGCTTATGCCTATGTTTATGCAAA 57.537 33.333 0.00 0.00 38.71 3.68
4467 5369 9.483916 AAAACAATATGATATGATGCATGTTGG 57.516 29.630 2.46 6.26 43.51 3.77
4674 5581 5.894807 CAGTTGGAGAACAAATGTTGAACT 58.105 37.500 3.05 4.19 46.84 3.01
4697 5605 5.541845 TGCTATGATGCAAGTAGTGGATAC 58.458 41.667 0.00 0.00 38.62 2.24
4904 5820 9.429109 ACTCCCCTTTTTGAACTAGATTAAAAA 57.571 29.630 12.69 12.69 29.90 1.94
4908 5824 7.324388 TCACTCCCCTTTTTGAACTAGATTA 57.676 36.000 0.00 0.00 0.00 1.75
5070 5989 2.586425 CCTCTCTCATCTCCTCCACTC 58.414 57.143 0.00 0.00 0.00 3.51
5279 6248 4.081807 GGTAGGAAACTTATCCACGTCAGT 60.082 45.833 0.00 0.00 42.27 3.41
5553 6975 6.583562 AGTAGGAGCAGTTGTATGATAAACC 58.416 40.000 0.00 0.00 0.00 3.27
5559 6981 3.637229 GGCTAGTAGGAGCAGTTGTATGA 59.363 47.826 0.00 0.00 44.76 2.15
5561 6983 2.966516 GGGCTAGTAGGAGCAGTTGTAT 59.033 50.000 0.00 0.00 44.76 2.29
5562 6984 2.385803 GGGCTAGTAGGAGCAGTTGTA 58.614 52.381 0.00 0.00 44.76 2.41
5564 6986 0.466124 GGGGCTAGTAGGAGCAGTTG 59.534 60.000 0.00 0.00 44.76 3.16
5565 6987 0.691413 GGGGGCTAGTAGGAGCAGTT 60.691 60.000 0.00 0.00 44.76 3.16
5569 6991 1.534476 GGAGGGGGCTAGTAGGAGC 60.534 68.421 0.00 0.00 42.05 4.70
5605 7043 5.221621 GGGAGAATGAGGTGGATAAGAGAAG 60.222 48.000 0.00 0.00 0.00 2.85
5607 7049 4.227197 GGGAGAATGAGGTGGATAAGAGA 58.773 47.826 0.00 0.00 0.00 3.10
5608 7050 3.326297 GGGGAGAATGAGGTGGATAAGAG 59.674 52.174 0.00 0.00 0.00 2.85
5613 7055 0.326618 ACGGGGAGAATGAGGTGGAT 60.327 55.000 0.00 0.00 0.00 3.41
5644 7098 1.009675 CACGCACTTGACACTTGCC 60.010 57.895 2.56 0.00 32.31 4.52
5674 7147 5.163374 ACATTGATCGATCCTTGTCTGATGA 60.163 40.000 22.31 0.00 0.00 2.92
5679 7152 4.895889 TCCTACATTGATCGATCCTTGTCT 59.104 41.667 25.02 11.25 0.00 3.41
5680 7153 5.201713 TCCTACATTGATCGATCCTTGTC 57.798 43.478 25.02 4.34 0.00 3.18
6153 7646 2.333014 GAAGTCAGCTCCACTTCGAAG 58.667 52.381 23.43 23.43 40.23 3.79
6198 7768 0.115152 TCCACAGGCTCCTCTTCTGA 59.885 55.000 0.00 0.00 33.19 3.27
6222 7792 2.679716 GAGTTGAGGCCCAGGCAT 59.320 61.111 11.50 2.35 44.11 4.40
6293 7872 3.393800 CGGCCGATCAATCAATCTACTT 58.606 45.455 24.07 0.00 0.00 2.24
6319 7898 4.101942 TCACGAAACAAAACACAAGCATC 58.898 39.130 0.00 0.00 0.00 3.91
6374 7989 5.216622 ACCTGCTACTAATCTTGGGATACA 58.783 41.667 0.00 0.00 39.74 2.29
6379 7994 3.181461 CCAGACCTGCTACTAATCTTGGG 60.181 52.174 0.00 0.00 0.00 4.12
6387 8002 1.281287 ACGAGACCAGACCTGCTACTA 59.719 52.381 0.00 0.00 0.00 1.82
6484 8145 7.922278 ACGAACCGACTATTTTGCACTATAATA 59.078 33.333 0.00 0.00 0.00 0.98
6537 8198 9.473007 TCCATAAGATGTTTGGTCATTTGATAA 57.527 29.630 4.52 0.00 0.00 1.75
6538 8199 8.902806 GTCCATAAGATGTTTGGTCATTTGATA 58.097 33.333 4.52 0.00 0.00 2.15
6539 8200 7.415541 CGTCCATAAGATGTTTGGTCATTTGAT 60.416 37.037 4.52 0.00 0.00 2.57
6540 8201 6.128035 CGTCCATAAGATGTTTGGTCATTTGA 60.128 38.462 4.52 0.00 0.00 2.69
6541 8202 6.029607 CGTCCATAAGATGTTTGGTCATTTG 58.970 40.000 4.52 0.00 0.00 2.32
6542 8203 5.125417 CCGTCCATAAGATGTTTGGTCATTT 59.875 40.000 4.52 0.00 0.00 2.32
6545 8206 3.605634 CCGTCCATAAGATGTTTGGTCA 58.394 45.455 4.52 0.00 0.00 4.02
6644 9721 7.520937 GCGTTTGATCACTTTTTCCCTTTAGTA 60.521 37.037 0.00 0.00 0.00 1.82
6922 10370 8.358582 ACTCTGAAATATTTGCTCCATCTTTT 57.641 30.769 5.17 0.00 0.00 2.27
6926 10374 9.060347 TCATTACTCTGAAATATTTGCTCCATC 57.940 33.333 5.17 0.00 0.00 3.51
7197 10708 0.685097 TCAGTGGTGCCTCCTGTTAC 59.315 55.000 0.00 0.00 37.07 2.50
7233 10744 1.328680 AGCTGAATATGCGCTTGTTCG 59.671 47.619 21.86 18.00 35.28 3.95
7235 10746 1.672881 GGAGCTGAATATGCGCTTGTT 59.327 47.619 9.73 7.03 33.47 2.83
7412 10926 9.929180 GCTCCTGTTATGAATATGTACTATGAA 57.071 33.333 0.00 0.00 0.00 2.57
7582 11102 0.823356 GCCAAGCACAGGACAGGAAA 60.823 55.000 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.