Multiple sequence alignment - TraesCS6D01G283200

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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 TraesCS6D01G283200 chr6D 100.000 6061 0 0 1 6061 390170507 390164447 0.000000e+00 11193
1 TraesCS6D01G283200 chr6D 94.748 1447 69 3 2595 4034 469590405 469591851 0.000000e+00 2244
2 TraesCS6D01G283200 chr6D 91.617 1515 116 7 822 2329 414148097 414146587 0.000000e+00 2084
3 TraesCS6D01G283200 chr6D 88.185 1515 170 6 822 2329 54664406 54665918 0.000000e+00 1797
4 TraesCS6D01G283200 chr6D 88.922 1336 125 10 1004 2329 224569364 224570686 0.000000e+00 1626
5 TraesCS6D01G283200 chr6D 89.045 785 60 15 36 817 226769256 226770017 0.000000e+00 950
6 TraesCS6D01G283200 chr6D 92.969 384 23 4 36 417 454505963 454506344 1.910000e-154 556
7 TraesCS6D01G283200 chr6D 85.409 281 19 12 36 315 97223612 97223871 7.740000e-69 272
8 TraesCS6D01G283200 chr6D 92.188 192 15 0 817 1008 224498610 224498801 7.740000e-69 272
9 TraesCS6D01G283200 chr6D 80.000 330 53 13 493 816 97223974 97224296 1.310000e-56 231
10 TraesCS6D01G283200 chr6D 84.685 111 11 6 711 817 97214057 97213949 8.310000e-19 106
11 TraesCS6D01G283200 chr1B 93.857 1514 85 5 823 2329 139118148 139116636 0.000000e+00 2274
12 TraesCS6D01G283200 chr1B 92.773 1522 100 5 817 2329 117376287 117374767 0.000000e+00 2193
13 TraesCS6D01G283200 chr1B 90.138 1521 137 9 817 2327 65743553 65745070 0.000000e+00 1965
14 TraesCS6D01G283200 chr1B 93.076 621 34 4 5449 6061 508694474 508693855 0.000000e+00 900
15 TraesCS6D01G283200 chr1B 81.319 637 102 16 186 813 90271471 90270843 9.070000e-138 501
16 TraesCS6D01G283200 chr3B 92.956 1519 98 3 817 2327 177852088 177850571 0.000000e+00 2204
17 TraesCS6D01G283200 chr5D 93.478 1472 85 7 2570 4034 525598096 525599563 0.000000e+00 2176
18 TraesCS6D01G283200 chr5D 92.298 1519 101 9 817 2327 116031946 116033456 0.000000e+00 2143
19 TraesCS6D01G283200 chr5D 92.585 1470 99 7 2569 4033 486750108 486751572 0.000000e+00 2102
20 TraesCS6D01G283200 chr5D 84.239 552 77 9 273 817 442766288 442765740 4.160000e-146 529
21 TraesCS6D01G283200 chr5D 90.735 313 27 2 36 347 442766569 442766258 3.380000e-112 416
22 TraesCS6D01G283200 chr1A 93.188 1468 91 8 2570 4032 34975758 34977221 0.000000e+00 2148
23 TraesCS6D01G283200 chr1A 90.938 949 82 4 817 1763 147625902 147626848 0.000000e+00 1273
24 TraesCS6D01G283200 chr1A 87.411 699 76 12 36 729 325790766 325790075 0.000000e+00 793
25 TraesCS6D01G283200 chr1A 88.007 542 42 5 1794 2329 147627101 147627625 2.400000e-173 619
26 TraesCS6D01G283200 chr1A 79.727 513 81 18 311 813 582558472 582558971 3.480000e-92 350
27 TraesCS6D01G283200 chr1A 78.101 516 82 19 311 813 434698237 434697740 1.280000e-76 298
28 TraesCS6D01G283200 chr1A 76.739 460 80 19 363 816 582555441 582555003 1.310000e-56 231
29 TraesCS6D01G283200 chr1A 78.400 375 61 17 454 816 491387866 491388232 6.110000e-55 226
30 TraesCS6D01G283200 chr1A 93.662 142 7 2 36 175 582558279 582558420 1.710000e-50 211
31 TraesCS6D01G283200 chr7D 93.120 1468 94 4 2571 4035 466848025 466846562 0.000000e+00 2145
32 TraesCS6D01G283200 chr7D 91.053 1520 125 10 817 2327 453170934 453169417 0.000000e+00 2043
33 TraesCS6D01G283200 chr7D 90.664 1521 130 8 817 2329 91060499 91062015 0.000000e+00 2012
34 TraesCS6D01G283200 chr7D 88.999 1518 156 7 817 2326 556866986 556868500 0.000000e+00 1868
35 TraesCS6D01G283200 chr7D 93.520 787 49 2 36 820 399645153 399645939 0.000000e+00 1170
36 TraesCS6D01G283200 chr7D 80.611 753 94 24 36 781 529430117 529430824 8.940000e-148 534
37 TraesCS6D01G283200 chr7D 80.645 372 63 7 453 817 555139418 555139049 4.630000e-71 279
38 TraesCS6D01G283200 chr5B 93.084 1446 95 4 2593 4034 243413204 243414648 0.000000e+00 2111
39 TraesCS6D01G283200 chr5B 91.524 1522 114 7 820 2329 1411902 1410384 0.000000e+00 2082
40 TraesCS6D01G283200 chr5B 94.695 622 24 4 5448 6061 593560828 593561448 0.000000e+00 957
41 TraesCS6D01G283200 chr5B 93.559 621 29 7 5449 6061 593476841 593477458 0.000000e+00 915
42 TraesCS6D01G283200 chr5B 92.185 627 37 7 5447 6061 514272601 514271975 0.000000e+00 876
43 TraesCS6D01G283200 chr7B 92.464 1473 102 8 2570 4037 742414506 742413038 0.000000e+00 2097
44 TraesCS6D01G283200 chr7B 91.144 1468 121 7 2570 4034 746374731 746376192 0.000000e+00 1982
45 TraesCS6D01G283200 chr7B 92.616 623 36 5 5448 6061 201534992 201535613 0.000000e+00 887
46 TraesCS6D01G283200 chr6A 91.442 1519 118 8 820 2329 408869177 408867662 0.000000e+00 2074
47 TraesCS6D01G283200 chr6A 87.254 1522 172 12 817 2329 267446019 267444511 0.000000e+00 1716
48 TraesCS6D01G283200 chr6A 90.588 1275 69 16 4035 5265 536767436 536766169 0.000000e+00 1642
49 TraesCS6D01G283200 chr6A 94.086 186 11 0 5262 5447 536766089 536765904 3.580000e-72 283
50 TraesCS6D01G283200 chr6A 93.548 186 11 1 5262 5447 536665015 536664831 5.980000e-70 276
51 TraesCS6D01G283200 chr6A 89.140 221 15 7 2329 2549 536767629 536767418 3.600000e-67 267
52 TraesCS6D01G283200 chr6A 93.662 142 7 2 36 175 158948457 158948316 1.710000e-50 211
53 TraesCS6D01G283200 chr4A 91.020 1470 127 4 2569 4034 731090487 731091955 0.000000e+00 1978
54 TraesCS6D01G283200 chr4A 82.685 797 110 21 26 817 642871056 642870283 0.000000e+00 682
55 TraesCS6D01G283200 chr4A 90.359 446 42 1 36 480 656876160 656875715 8.750000e-163 584
56 TraesCS6D01G283200 chr2D 90.119 1518 137 8 819 2329 131525142 131526653 0.000000e+00 1960
57 TraesCS6D01G283200 chr2D 86.404 787 81 15 36 816 22766323 22767089 0.000000e+00 837
58 TraesCS6D01G283200 chr2D 85.769 787 82 16 36 816 128970721 128971483 0.000000e+00 806
59 TraesCS6D01G283200 chr1D 89.934 1520 139 8 817 2329 193685697 193687209 0.000000e+00 1947
60 TraesCS6D01G283200 chr1D 87.723 1515 175 7 822 2329 6829485 6827975 0.000000e+00 1757
61 TraesCS6D01G283200 chr1D 89.567 786 73 8 36 816 259597559 259596778 0.000000e+00 989
62 TraesCS6D01G283200 chr1D 94.373 622 27 3 5448 6061 437503541 437504162 0.000000e+00 948
63 TraesCS6D01G283200 chr1D 93.473 383 23 2 36 417 206978063 206977682 8.820000e-158 568
64 TraesCS6D01G283200 chr1D 81.200 750 86 27 36 776 482330365 482329662 2.470000e-153 553
65 TraesCS6D01G283200 chr1D 91.906 383 29 2 36 417 431965708 431965327 8.940000e-148 534
66 TraesCS6D01G283200 chr1D 94.000 150 9 0 822 971 413859705 413859556 1.700000e-55 228
67 TraesCS6D01G283200 chr1D 78.157 293 57 6 494 783 206987353 206987641 4.830000e-41 180
68 TraesCS6D01G283200 chr1D 77.019 322 55 14 478 795 206977596 206977290 3.760000e-37 167
69 TraesCS6D01G283200 chr3D 87.795 1524 166 12 817 2329 4931165 4932679 0.000000e+00 1766
70 TraesCS6D01G283200 chr3D 94.534 622 26 3 5448 6061 13602864 13602243 0.000000e+00 953
71 TraesCS6D01G283200 chr3D 94.543 623 25 5 5448 6061 561714019 561714641 0.000000e+00 953
72 TraesCS6D01G283200 chr3D 86.241 705 50 23 36 732 79620504 79621169 0.000000e+00 721
73 TraesCS6D01G283200 chr3D 91.906 383 29 2 36 417 453177299 453177680 8.940000e-148 534
74 TraesCS6D01G283200 chr3D 90.601 383 34 2 36 417 482333003 482332622 1.950000e-139 507
75 TraesCS6D01G283200 chr3D 83.702 362 41 11 461 817 575832563 575832911 5.860000e-85 326
76 TraesCS6D01G283200 chr3D 83.681 288 44 3 490 776 575824882 575824597 1.000000e-67 268
77 TraesCS6D01G283200 chr4D 86.939 1516 190 4 821 2329 497316674 497318188 0.000000e+00 1696
78 TraesCS6D01G283200 chr4D 88.595 491 52 3 817 1303 315073460 315072970 1.450000e-165 593
79 TraesCS6D01G283200 chr4D 80.685 321 54 8 496 813 486341540 486341855 6.070000e-60 243
80 TraesCS6D01G283200 chr4D 91.716 169 6 3 36 201 486319817 486319654 1.700000e-55 228
81 TraesCS6D01G283200 chr4D 83.505 194 28 4 1886 2077 466534292 466534483 1.740000e-40 178
82 TraesCS6D01G283200 chr4D 76.558 337 53 17 453 781 486319473 486319155 1.750000e-35 161
83 TraesCS6D01G283200 chr7A 89.708 787 75 4 36 820 109070821 109070039 0.000000e+00 1000
84 TraesCS6D01G283200 chr7A 94.203 621 28 3 5449 6061 29485154 29484534 0.000000e+00 941
85 TraesCS6D01G283200 chr2A 89.567 786 68 7 36 819 13771179 13771952 0.000000e+00 985
86 TraesCS6D01G283200 chr2A 81.679 786 111 19 36 813 100191661 100190901 1.860000e-174 623
87 TraesCS6D01G283200 chr5A 87.802 746 80 10 36 774 437910259 437911000 0.000000e+00 863
88 TraesCS6D01G283200 chr6B 81.242 789 116 20 36 816 661027580 661026816 5.190000e-170 608
89 TraesCS6D01G283200 chr4B 86.704 534 65 2 1802 2329 622624235 622624768 6.770000e-164 588
90 TraesCS6D01G283200 chr4B 91.480 223 18 1 36 257 99075619 99075841 7.630000e-79 305
91 TraesCS6D01G283200 chr4B 85.766 274 31 4 36 307 11454220 11454487 3.580000e-72 283
92 TraesCS6D01G283200 chr4B 82.353 323 43 13 497 812 628600391 628600076 1.000000e-67 268
93 TraesCS6D01G283200 chr4B 81.024 332 55 7 490 816 37874483 37874155 2.170000e-64 257
94 TraesCS6D01G283200 chrUn 80.735 789 120 20 36 816 5465472 5466236 2.430000e-163 586
95 TraesCS6D01G283200 chrUn 76.981 795 108 37 36 817 374887357 374886625 9.530000e-103 385
96 TraesCS6D01G283200 chrUn 80.734 436 42 15 36 468 383112471 383112075 9.870000e-78 302
97 TraesCS6D01G283200 chrUn 79.292 367 64 10 454 813 5449253 5448892 4.690000e-61 246
98 TraesCS6D01G283200 chrUn 85.022 227 12 7 36 252 22360367 22360153 1.710000e-50 211
99 TraesCS6D01G283200 chrUn 92.199 141 10 1 36 175 118924726 118924866 1.330000e-46 198
100 TraesCS6D01G283200 chrUn 76.708 322 65 8 497 813 118914901 118914585 2.900000e-38 171


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 TraesCS6D01G283200 chr6D 390164447 390170507 6060 True 11193.000000 11193 100.000000 1 6061 1 chr6D.!!$R2 6060
1 TraesCS6D01G283200 chr6D 469590405 469591851 1446 False 2244.000000 2244 94.748000 2595 4034 1 chr6D.!!$F6 1439
2 TraesCS6D01G283200 chr6D 414146587 414148097 1510 True 2084.000000 2084 91.617000 822 2329 1 chr6D.!!$R3 1507
3 TraesCS6D01G283200 chr6D 54664406 54665918 1512 False 1797.000000 1797 88.185000 822 2329 1 chr6D.!!$F1 1507
4 TraesCS6D01G283200 chr6D 224569364 224570686 1322 False 1626.000000 1626 88.922000 1004 2329 1 chr6D.!!$F3 1325
5 TraesCS6D01G283200 chr6D 226769256 226770017 761 False 950.000000 950 89.045000 36 817 1 chr6D.!!$F4 781
6 TraesCS6D01G283200 chr6D 97223612 97224296 684 False 251.500000 272 82.704500 36 816 2 chr6D.!!$F7 780
7 TraesCS6D01G283200 chr1B 139116636 139118148 1512 True 2274.000000 2274 93.857000 823 2329 1 chr1B.!!$R3 1506
8 TraesCS6D01G283200 chr1B 117374767 117376287 1520 True 2193.000000 2193 92.773000 817 2329 1 chr1B.!!$R2 1512
9 TraesCS6D01G283200 chr1B 65743553 65745070 1517 False 1965.000000 1965 90.138000 817 2327 1 chr1B.!!$F1 1510
10 TraesCS6D01G283200 chr1B 508693855 508694474 619 True 900.000000 900 93.076000 5449 6061 1 chr1B.!!$R4 612
11 TraesCS6D01G283200 chr1B 90270843 90271471 628 True 501.000000 501 81.319000 186 813 1 chr1B.!!$R1 627
12 TraesCS6D01G283200 chr3B 177850571 177852088 1517 True 2204.000000 2204 92.956000 817 2327 1 chr3B.!!$R1 1510
13 TraesCS6D01G283200 chr5D 525598096 525599563 1467 False 2176.000000 2176 93.478000 2570 4034 1 chr5D.!!$F3 1464
14 TraesCS6D01G283200 chr5D 116031946 116033456 1510 False 2143.000000 2143 92.298000 817 2327 1 chr5D.!!$F1 1510
15 TraesCS6D01G283200 chr5D 486750108 486751572 1464 False 2102.000000 2102 92.585000 2569 4033 1 chr5D.!!$F2 1464
16 TraesCS6D01G283200 chr5D 442765740 442766569 829 True 472.500000 529 87.487000 36 817 2 chr5D.!!$R1 781
17 TraesCS6D01G283200 chr1A 34975758 34977221 1463 False 2148.000000 2148 93.188000 2570 4032 1 chr1A.!!$F1 1462
18 TraesCS6D01G283200 chr1A 147625902 147627625 1723 False 946.000000 1273 89.472500 817 2329 2 chr1A.!!$F3 1512
19 TraesCS6D01G283200 chr1A 325790075 325790766 691 True 793.000000 793 87.411000 36 729 1 chr1A.!!$R1 693
20 TraesCS6D01G283200 chr1A 582558279 582558971 692 False 280.500000 350 86.694500 36 813 2 chr1A.!!$F4 777
21 TraesCS6D01G283200 chr7D 466846562 466848025 1463 True 2145.000000 2145 93.120000 2571 4035 1 chr7D.!!$R2 1464
22 TraesCS6D01G283200 chr7D 453169417 453170934 1517 True 2043.000000 2043 91.053000 817 2327 1 chr7D.!!$R1 1510
23 TraesCS6D01G283200 chr7D 91060499 91062015 1516 False 2012.000000 2012 90.664000 817 2329 1 chr7D.!!$F1 1512
24 TraesCS6D01G283200 chr7D 556866986 556868500 1514 False 1868.000000 1868 88.999000 817 2326 1 chr7D.!!$F4 1509
25 TraesCS6D01G283200 chr7D 399645153 399645939 786 False 1170.000000 1170 93.520000 36 820 1 chr7D.!!$F2 784
26 TraesCS6D01G283200 chr7D 529430117 529430824 707 False 534.000000 534 80.611000 36 781 1 chr7D.!!$F3 745
27 TraesCS6D01G283200 chr5B 243413204 243414648 1444 False 2111.000000 2111 93.084000 2593 4034 1 chr5B.!!$F1 1441
28 TraesCS6D01G283200 chr5B 1410384 1411902 1518 True 2082.000000 2082 91.524000 820 2329 1 chr5B.!!$R1 1509
29 TraesCS6D01G283200 chr5B 593560828 593561448 620 False 957.000000 957 94.695000 5448 6061 1 chr5B.!!$F3 613
30 TraesCS6D01G283200 chr5B 593476841 593477458 617 False 915.000000 915 93.559000 5449 6061 1 chr5B.!!$F2 612
31 TraesCS6D01G283200 chr5B 514271975 514272601 626 True 876.000000 876 92.185000 5447 6061 1 chr5B.!!$R2 614
32 TraesCS6D01G283200 chr7B 742413038 742414506 1468 True 2097.000000 2097 92.464000 2570 4037 1 chr7B.!!$R1 1467
33 TraesCS6D01G283200 chr7B 746374731 746376192 1461 False 1982.000000 1982 91.144000 2570 4034 1 chr7B.!!$F2 1464
34 TraesCS6D01G283200 chr7B 201534992 201535613 621 False 887.000000 887 92.616000 5448 6061 1 chr7B.!!$F1 613
35 TraesCS6D01G283200 chr6A 408867662 408869177 1515 True 2074.000000 2074 91.442000 820 2329 1 chr6A.!!$R3 1509
36 TraesCS6D01G283200 chr6A 267444511 267446019 1508 True 1716.000000 1716 87.254000 817 2329 1 chr6A.!!$R2 1512
37 TraesCS6D01G283200 chr6A 536765904 536767629 1725 True 730.666667 1642 91.271333 2329 5447 3 chr6A.!!$R5 3118
38 TraesCS6D01G283200 chr4A 731090487 731091955 1468 False 1978.000000 1978 91.020000 2569 4034 1 chr4A.!!$F1 1465
39 TraesCS6D01G283200 chr4A 642870283 642871056 773 True 682.000000 682 82.685000 26 817 1 chr4A.!!$R1 791
40 TraesCS6D01G283200 chr2D 131525142 131526653 1511 False 1960.000000 1960 90.119000 819 2329 1 chr2D.!!$F3 1510
41 TraesCS6D01G283200 chr2D 22766323 22767089 766 False 837.000000 837 86.404000 36 816 1 chr2D.!!$F1 780
42 TraesCS6D01G283200 chr2D 128970721 128971483 762 False 806.000000 806 85.769000 36 816 1 chr2D.!!$F2 780
43 TraesCS6D01G283200 chr1D 193685697 193687209 1512 False 1947.000000 1947 89.934000 817 2329 1 chr1D.!!$F1 1512
44 TraesCS6D01G283200 chr1D 6827975 6829485 1510 True 1757.000000 1757 87.723000 822 2329 1 chr1D.!!$R1 1507
45 TraesCS6D01G283200 chr1D 259596778 259597559 781 True 989.000000 989 89.567000 36 816 1 chr1D.!!$R2 780
46 TraesCS6D01G283200 chr1D 437503541 437504162 621 False 948.000000 948 94.373000 5448 6061 1 chr1D.!!$F3 613
47 TraesCS6D01G283200 chr1D 482329662 482330365 703 True 553.000000 553 81.200000 36 776 1 chr1D.!!$R5 740
48 TraesCS6D01G283200 chr1D 206977290 206978063 773 True 367.500000 568 85.246000 36 795 2 chr1D.!!$R6 759
49 TraesCS6D01G283200 chr3D 4931165 4932679 1514 False 1766.000000 1766 87.795000 817 2329 1 chr3D.!!$F1 1512
50 TraesCS6D01G283200 chr3D 13602243 13602864 621 True 953.000000 953 94.534000 5448 6061 1 chr3D.!!$R1 613
51 TraesCS6D01G283200 chr3D 561714019 561714641 622 False 953.000000 953 94.543000 5448 6061 1 chr3D.!!$F4 613
52 TraesCS6D01G283200 chr3D 79620504 79621169 665 False 721.000000 721 86.241000 36 732 1 chr3D.!!$F2 696
53 TraesCS6D01G283200 chr4D 497316674 497318188 1514 False 1696.000000 1696 86.939000 821 2329 1 chr4D.!!$F3 1508
54 TraesCS6D01G283200 chr7A 109070039 109070821 782 True 1000.000000 1000 89.708000 36 820 1 chr7A.!!$R2 784
55 TraesCS6D01G283200 chr7A 29484534 29485154 620 True 941.000000 941 94.203000 5449 6061 1 chr7A.!!$R1 612
56 TraesCS6D01G283200 chr2A 13771179 13771952 773 False 985.000000 985 89.567000 36 819 1 chr2A.!!$F1 783
57 TraesCS6D01G283200 chr2A 100190901 100191661 760 True 623.000000 623 81.679000 36 813 1 chr2A.!!$R1 777
58 TraesCS6D01G283200 chr5A 437910259 437911000 741 False 863.000000 863 87.802000 36 774 1 chr5A.!!$F1 738
59 TraesCS6D01G283200 chr6B 661026816 661027580 764 True 608.000000 608 81.242000 36 816 1 chr6B.!!$R1 780
60 TraesCS6D01G283200 chr4B 622624235 622624768 533 False 588.000000 588 86.704000 1802 2329 1 chr4B.!!$F3 527
61 TraesCS6D01G283200 chrUn 5465472 5466236 764 False 586.000000 586 80.735000 36 816 1 chrUn.!!$F1 780
62 TraesCS6D01G283200 chrUn 374886625 374887357 732 True 385.000000 385 76.981000 36 817 1 chrUn.!!$R4 781

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
328 392 0.388520 CGATTCTCACAGTGCCGTCA 60.389 55.000 0.0 0.0 0.00 4.35 F
1268 1411 1.070445 GGAGATGTCATCTGGGCTCTG 59.930 57.143 20.2 0.0 40.38 3.35 F
2529 2926 0.105778 GAGTGCAGGAGGTGGCTATC 59.894 60.000 0.0 0.0 0.00 2.08 F
2550 2947 0.036010 CGAATGTGGTCCTCTGCCTT 60.036 55.000 0.0 0.0 0.00 4.35 F
4144 4557 0.032130 TCTCAGCGACGCACTTTCTT 59.968 50.000 23.7 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 1534 0.102300 GGAGTTGTTTTGGCAGCGTT 59.898 50.0 0.00 0.00 0.00 4.84 R
2531 2928 0.036010 AAGGCAGAGGACCACATTCG 60.036 55.0 0.00 0.00 0.00 3.34 R
3601 4011 0.107993 CTCCTGCACGTGTCCATCAT 60.108 55.0 18.38 0.00 0.00 2.45 R
4297 4742 0.254178 ACATCATGGACTGGACTGCC 59.746 55.0 0.00 0.00 0.00 4.85 R
5641 6185 0.248907 TAGATGTTAGGCGCTGCGAC 60.249 55.0 28.07 25.36 33.59 5.19 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
114 118 1.270518 CGATTTCGAGGATGGCTGGAT 60.271 52.381 0.00 0.00 43.02 3.41
146 150 4.202264 CGGTGTCTCCTTTTATAGGCTCAT 60.202 45.833 0.00 0.00 44.37 2.90
148 152 6.295349 CGGTGTCTCCTTTTATAGGCTCATAT 60.295 42.308 0.00 0.00 44.37 1.78
161 165 5.057843 AGGCTCATATGACAAATGATGGT 57.942 39.130 0.00 0.00 33.08 3.55
220 224 6.318900 GGAAATTTTAGGATCCCTGTAGTGTG 59.681 42.308 8.55 0.00 34.61 3.82
221 225 6.636454 AATTTTAGGATCCCTGTAGTGTGA 57.364 37.500 8.55 0.00 34.61 3.58
328 392 0.388520 CGATTCTCACAGTGCCGTCA 60.389 55.000 0.00 0.00 0.00 4.35
412 479 1.543208 GCATCAGCGTCCATATTCCCA 60.543 52.381 0.00 0.00 0.00 4.37
427 494 2.819595 CCACGCGTGGGAATCAGG 60.820 66.667 43.64 21.08 46.81 3.86
783 922 1.271325 GGGGGTCCTTTTTGGCAAATG 60.271 52.381 14.29 9.69 35.26 2.32
1268 1411 1.070445 GGAGATGTCATCTGGGCTCTG 59.930 57.143 20.20 0.00 40.38 3.35
1388 1534 3.160585 CCAGTTCTGGCCACCTCA 58.839 61.111 0.00 0.00 0.00 3.86
1565 1712 3.884774 AGCACCAAGGTTCGCCCA 61.885 61.111 0.00 0.00 38.27 5.36
1607 1757 2.497273 GGGCCATTTTAGCACAGTGATT 59.503 45.455 4.39 0.00 32.41 2.57
1701 1852 0.537371 AGAAACCCGGTTGCTCCAAG 60.537 55.000 4.76 0.00 35.57 3.61
1991 2376 3.375699 ACCCGATCAACATTAGGAGAGT 58.624 45.455 0.00 0.00 0.00 3.24
2071 2457 3.826157 TGCACCTCTCCACCTTATTTTTG 59.174 43.478 0.00 0.00 0.00 2.44
2311 2708 1.270732 CCCTGGAGCTCATGCATACTC 60.271 57.143 17.19 6.94 42.74 2.59
2343 2740 3.493129 CGAATCGTGAGTTGTTTCTCCAA 59.507 43.478 0.00 0.00 33.93 3.53
2347 2744 2.549754 CGTGAGTTGTTTCTCCAAGCAT 59.450 45.455 0.00 0.00 33.93 3.79
2384 2781 2.029110 TCAACTCTGTGCACATCGATCA 60.029 45.455 22.00 0.45 0.00 2.92
2386 2783 3.257469 ACTCTGTGCACATCGATCAAT 57.743 42.857 22.00 0.00 0.00 2.57
2388 2785 3.620374 ACTCTGTGCACATCGATCAATTC 59.380 43.478 22.00 0.00 0.00 2.17
2389 2786 3.865446 TCTGTGCACATCGATCAATTCT 58.135 40.909 22.00 0.00 0.00 2.40
2390 2787 3.867493 TCTGTGCACATCGATCAATTCTC 59.133 43.478 22.00 0.00 0.00 2.87
2392 2789 3.201290 GTGCACATCGATCAATTCTCCT 58.799 45.455 13.17 0.00 0.00 3.69
2396 2793 3.041211 ACATCGATCAATTCTCCTCCCA 58.959 45.455 0.00 0.00 0.00 4.37
2397 2794 3.181461 ACATCGATCAATTCTCCTCCCAC 60.181 47.826 0.00 0.00 0.00 4.61
2398 2795 2.466846 TCGATCAATTCTCCTCCCACA 58.533 47.619 0.00 0.00 0.00 4.17
2399 2796 2.168521 TCGATCAATTCTCCTCCCACAC 59.831 50.000 0.00 0.00 0.00 3.82
2400 2797 2.555199 GATCAATTCTCCTCCCACACG 58.445 52.381 0.00 0.00 0.00 4.49
2401 2798 0.613260 TCAATTCTCCTCCCACACGG 59.387 55.000 0.00 0.00 0.00 4.94
2402 2799 1.026718 CAATTCTCCTCCCACACGGC 61.027 60.000 0.00 0.00 0.00 5.68
2403 2800 2.198304 AATTCTCCTCCCACACGGCC 62.198 60.000 0.00 0.00 0.00 6.13
2406 2803 1.762460 CTCCTCCCACACGGCCTAT 60.762 63.158 0.00 0.00 0.00 2.57
2407 2804 0.469331 CTCCTCCCACACGGCCTATA 60.469 60.000 0.00 0.00 0.00 1.31
2408 2805 0.190069 TCCTCCCACACGGCCTATAT 59.810 55.000 0.00 0.00 0.00 0.86
2409 2806 1.430075 TCCTCCCACACGGCCTATATA 59.570 52.381 0.00 0.00 0.00 0.86
2410 2807 2.158279 TCCTCCCACACGGCCTATATAA 60.158 50.000 0.00 0.00 0.00 0.98
2411 2808 2.838202 CCTCCCACACGGCCTATATAAT 59.162 50.000 0.00 0.00 0.00 1.28
2412 2809 3.263425 CCTCCCACACGGCCTATATAATT 59.737 47.826 0.00 0.00 0.00 1.40
2413 2810 4.504858 CTCCCACACGGCCTATATAATTC 58.495 47.826 0.00 0.00 0.00 2.17
2416 2813 5.186409 TCCCACACGGCCTATATAATTCTAC 59.814 44.000 0.00 0.00 0.00 2.59
2422 2819 7.014905 ACACGGCCTATATAATTCTACTGACAA 59.985 37.037 0.00 0.00 0.00 3.18
2451 2848 7.388224 TGTTGTTTGTTAATCGATAGCCTGTAA 59.612 33.333 0.00 0.00 0.00 2.41
2476 2873 2.736531 GCAAAGGGCAAGTGGGTG 59.263 61.111 0.00 0.00 43.97 4.61
2527 2924 2.351244 CGAGTGCAGGAGGTGGCTA 61.351 63.158 0.00 0.00 0.00 3.93
2528 2925 1.680522 CGAGTGCAGGAGGTGGCTAT 61.681 60.000 0.00 0.00 0.00 2.97
2529 2926 0.105778 GAGTGCAGGAGGTGGCTATC 59.894 60.000 0.00 0.00 0.00 2.08
2530 2927 0.618680 AGTGCAGGAGGTGGCTATCA 60.619 55.000 0.00 0.00 0.00 2.15
2531 2928 0.462759 GTGCAGGAGGTGGCTATCAC 60.463 60.000 0.00 0.00 45.34 3.06
2532 2929 1.227380 GCAGGAGGTGGCTATCACG 60.227 63.158 0.00 0.00 46.96 4.35
2533 2930 1.676678 GCAGGAGGTGGCTATCACGA 61.677 60.000 0.00 0.00 46.96 4.35
2534 2931 0.824109 CAGGAGGTGGCTATCACGAA 59.176 55.000 0.00 0.00 46.96 3.85
2535 2932 1.414181 CAGGAGGTGGCTATCACGAAT 59.586 52.381 0.00 0.00 46.96 3.34
2536 2933 1.414181 AGGAGGTGGCTATCACGAATG 59.586 52.381 0.00 0.00 46.96 2.67
2537 2934 1.139058 GGAGGTGGCTATCACGAATGT 59.861 52.381 0.00 0.00 46.96 2.71
2538 2935 2.205074 GAGGTGGCTATCACGAATGTG 58.795 52.381 0.00 0.00 46.96 3.21
2539 2936 1.134401 AGGTGGCTATCACGAATGTGG 60.134 52.381 0.00 0.00 46.96 4.17
2540 2937 1.406887 GGTGGCTATCACGAATGTGGT 60.407 52.381 0.00 0.00 46.96 4.16
2541 2938 1.933853 GTGGCTATCACGAATGTGGTC 59.066 52.381 0.00 0.00 46.42 4.02
2542 2939 1.134521 TGGCTATCACGAATGTGGTCC 60.135 52.381 0.00 0.00 46.42 4.46
2543 2940 1.139058 GGCTATCACGAATGTGGTCCT 59.861 52.381 0.00 0.00 46.42 3.85
2544 2941 2.474816 GCTATCACGAATGTGGTCCTC 58.525 52.381 0.00 0.00 46.42 3.71
2545 2942 2.101582 GCTATCACGAATGTGGTCCTCT 59.898 50.000 0.00 0.00 46.42 3.69
2546 2943 2.680312 ATCACGAATGTGGTCCTCTG 57.320 50.000 0.00 0.00 46.42 3.35
2547 2944 0.037326 TCACGAATGTGGTCCTCTGC 60.037 55.000 0.00 0.00 46.42 4.26
2548 2945 1.021390 CACGAATGTGGTCCTCTGCC 61.021 60.000 0.00 0.00 42.59 4.85
2549 2946 1.194781 ACGAATGTGGTCCTCTGCCT 61.195 55.000 0.00 0.00 0.00 4.75
2550 2947 0.036010 CGAATGTGGTCCTCTGCCTT 60.036 55.000 0.00 0.00 0.00 4.35
2551 2948 1.207089 CGAATGTGGTCCTCTGCCTTA 59.793 52.381 0.00 0.00 0.00 2.69
2552 2949 2.633488 GAATGTGGTCCTCTGCCTTAC 58.367 52.381 0.00 0.00 0.00 2.34
2553 2950 0.912486 ATGTGGTCCTCTGCCTTACC 59.088 55.000 0.00 0.00 0.00 2.85
2554 2951 1.218316 GTGGTCCTCTGCCTTACCG 59.782 63.158 0.00 0.00 34.60 4.02
2555 2952 1.987855 TGGTCCTCTGCCTTACCGG 60.988 63.158 0.00 0.00 34.60 5.28
2556 2953 2.732619 GGTCCTCTGCCTTACCGGG 61.733 68.421 6.32 0.00 0.00 5.73
2557 2954 2.365105 TCCTCTGCCTTACCGGGG 60.365 66.667 6.32 0.00 0.00 5.73
2558 2955 2.687566 CCTCTGCCTTACCGGGGT 60.688 66.667 6.32 0.00 0.00 4.95
2559 2956 1.382146 CCTCTGCCTTACCGGGGTA 60.382 63.158 6.32 0.00 0.00 3.69
2560 2957 0.979187 CCTCTGCCTTACCGGGGTAA 60.979 60.000 6.32 9.78 38.14 2.85
2561 2958 0.906775 CTCTGCCTTACCGGGGTAAA 59.093 55.000 6.32 0.00 39.69 2.01
2562 2959 0.906775 TCTGCCTTACCGGGGTAAAG 59.093 55.000 6.32 6.79 39.69 1.85
2563 2960 0.616891 CTGCCTTACCGGGGTAAAGT 59.383 55.000 6.32 0.00 39.69 2.66
2564 2961 1.832998 CTGCCTTACCGGGGTAAAGTA 59.167 52.381 6.32 4.62 39.69 2.24
2565 2962 1.832998 TGCCTTACCGGGGTAAAGTAG 59.167 52.381 6.32 0.33 39.69 2.57
2566 2963 2.110578 GCCTTACCGGGGTAAAGTAGA 58.889 52.381 6.32 0.00 39.69 2.59
2567 2964 2.501316 GCCTTACCGGGGTAAAGTAGAA 59.499 50.000 6.32 0.00 39.69 2.10
2914 3316 1.370437 CTGGCCAGATCAGGATCCG 59.630 63.158 29.88 1.36 38.58 4.18
3108 3512 2.751688 GTTTGGCGAGGTGGGGTA 59.248 61.111 0.00 0.00 0.00 3.69
3260 3664 1.269569 CGAGACAGTGCACAGGTTGTA 60.270 52.381 21.04 0.00 0.00 2.41
3398 3807 0.616395 CCCAAACCCACCCAATACCC 60.616 60.000 0.00 0.00 0.00 3.69
3440 3850 1.592669 GATCGGATGACGGTGGCAG 60.593 63.158 0.00 0.00 44.45 4.85
3601 4011 0.950555 GCTTGGCGTCAGATGTGTGA 60.951 55.000 0.00 0.00 0.00 3.58
3672 4082 2.190578 GCAGCTAGACCGGGCAAT 59.809 61.111 11.69 0.00 0.00 3.56
3742 4152 2.735772 CGGCCTCATACCCAGCAGT 61.736 63.158 0.00 0.00 0.00 4.40
3847 4260 0.250252 TGGCTGCGATGTCTGTTTGA 60.250 50.000 0.00 0.00 0.00 2.69
3916 4329 2.390938 CGACAGTTGTTGCTTAGACGA 58.609 47.619 0.00 0.00 0.00 4.20
3920 4333 4.569943 ACAGTTGTTGCTTAGACGATGAT 58.430 39.130 0.00 0.00 0.00 2.45
3985 4398 6.648879 ATAATTAATAAAGTGGCCGCATGT 57.351 33.333 20.59 5.30 0.00 3.21
3992 4405 2.203001 TGGCCGCATGTATCACCG 60.203 61.111 0.00 0.00 0.00 4.94
4008 4421 3.531207 CGAGATGCAGAGGCCGGA 61.531 66.667 5.05 0.00 40.13 5.14
4093 4506 3.736482 CTCGTACGAGAGCCACCGC 62.736 68.421 36.12 0.00 44.53 5.68
4123 4536 4.148825 GACTGCGACAGGCCCGAT 62.149 66.667 0.00 0.00 42.61 4.18
4131 4544 1.078143 ACAGGCCCGATTTCTCAGC 60.078 57.895 0.00 0.00 0.00 4.26
4133 4546 2.186903 GGCCCGATTTCTCAGCGA 59.813 61.111 0.00 0.00 0.00 4.93
4135 4548 2.517450 GCCCGATTTCTCAGCGACG 61.517 63.158 0.00 0.00 0.00 5.12
4136 4549 2.517450 CCCGATTTCTCAGCGACGC 61.517 63.158 13.03 13.03 0.00 5.19
4144 4557 0.032130 TCTCAGCGACGCACTTTCTT 59.968 50.000 23.70 0.00 0.00 2.52
4148 4561 1.003972 CAGCGACGCACTTTCTTCAAA 60.004 47.619 23.70 0.00 0.00 2.69
4158 4571 2.876550 ACTTTCTTCAAAGGTACGTGCC 59.123 45.455 15.72 15.72 43.12 5.01
4182 4605 3.685550 CGCCCCTCTCCAATAGATTTTGT 60.686 47.826 0.00 0.00 32.41 2.83
4184 4607 4.464947 CCCCTCTCCAATAGATTTTGTCC 58.535 47.826 0.00 0.00 32.41 4.02
4186 4609 4.079787 CCCTCTCCAATAGATTTTGTCCCA 60.080 45.833 0.00 0.00 32.41 4.37
4188 4611 5.591877 CCTCTCCAATAGATTTTGTCCCAAG 59.408 44.000 0.00 0.00 32.41 3.61
4203 4626 1.512310 CAAGGACTCGTCGCTCGTC 60.512 63.158 0.00 0.00 40.80 4.20
4204 4627 2.688794 AAGGACTCGTCGCTCGTCC 61.689 63.158 15.84 15.84 45.88 4.79
4205 4628 3.126225 GGACTCGTCGCTCGTCCT 61.126 66.667 16.15 0.00 42.99 3.85
4206 4629 2.400402 GACTCGTCGCTCGTCCTC 59.600 66.667 0.00 0.00 40.80 3.71
4207 4630 2.358369 ACTCGTCGCTCGTCCTCA 60.358 61.111 0.00 0.00 40.80 3.86
4208 4631 1.909141 GACTCGTCGCTCGTCCTCAA 61.909 60.000 0.00 0.00 40.80 3.02
4209 4632 1.226156 CTCGTCGCTCGTCCTCAAG 60.226 63.158 0.00 0.00 40.80 3.02
4210 4633 1.913451 CTCGTCGCTCGTCCTCAAGT 61.913 60.000 0.00 0.00 40.80 3.16
4211 4634 1.081376 CGTCGCTCGTCCTCAAGTT 60.081 57.895 0.00 0.00 34.52 2.66
4225 4670 6.509039 CGTCCTCAAGTTGTAAGTTGTAACAC 60.509 42.308 10.90 4.96 39.69 3.32
4297 4742 2.587194 CGATTCGCTGGGCAGAGG 60.587 66.667 0.00 0.00 0.00 3.69
4385 4831 1.407979 GGAGATACGGCCTCGAAAAGA 59.592 52.381 0.00 0.00 40.11 2.52
4439 4885 0.460284 CCGATTCCCAGAGACCAACG 60.460 60.000 0.00 0.00 0.00 4.10
4591 5037 2.672996 GTGCTCAACACCGGCCAT 60.673 61.111 0.00 0.00 44.02 4.40
4594 5040 1.750399 GCTCAACACCGGCCATCAT 60.750 57.895 0.00 0.00 0.00 2.45
4597 5043 0.964860 TCAACACCGGCCATCATTGG 60.965 55.000 0.00 0.00 46.66 3.16
4615 5061 2.930950 TGGAACAAGGTGAAGTTCAGG 58.069 47.619 5.62 0.00 44.46 3.86
4629 5075 1.125093 TTCAGGAGGAACCGCTGGAA 61.125 55.000 1.50 0.00 44.74 3.53
4672 5129 3.473647 CCTCAGCCATGCGAGGGA 61.474 66.667 13.58 0.00 41.72 4.20
4774 5231 3.115892 GCCGGTGCATTTCGTCGA 61.116 61.111 1.90 0.00 37.47 4.20
4863 5320 1.218230 GGATCGCTCGAATGACCTGC 61.218 60.000 0.00 0.00 0.00 4.85
4897 5354 0.318120 GTGAACGGGACTCGGGTTAA 59.682 55.000 0.00 0.00 44.45 2.01
4908 5365 2.317040 CTCGGGTTAAGCTCCTGGATA 58.683 52.381 4.41 0.00 32.62 2.59
4912 5369 3.306364 CGGGTTAAGCTCCTGGATATCAG 60.306 52.174 4.83 0.47 43.00 2.90
4916 5373 1.375268 GCTCCTGGATATCAGCGCC 60.375 63.158 2.29 0.00 42.05 6.53
4982 5439 4.072839 CCAAAGTTCAGAGGGAGGTTTAC 58.927 47.826 0.00 0.00 0.00 2.01
5008 5465 2.676471 GCATTGGTGCCTTCCGGT 60.676 61.111 0.00 0.00 45.76 5.28
5009 5466 2.275380 GCATTGGTGCCTTCCGGTT 61.275 57.895 0.00 0.00 45.76 4.44
5010 5467 1.883021 CATTGGTGCCTTCCGGTTC 59.117 57.895 0.00 0.00 0.00 3.62
5011 5468 1.304134 ATTGGTGCCTTCCGGTTCC 60.304 57.895 0.00 0.00 0.00 3.62
5012 5469 3.835790 TTGGTGCCTTCCGGTTCCG 62.836 63.158 0.00 4.08 0.00 4.30
5050 5507 2.297033 GGAATGAGCTCCTTTTTGCACA 59.703 45.455 12.15 0.00 34.65 4.57
5085 5542 7.465173 ACTGTAGATATGATGTATACGCTTCG 58.535 38.462 0.00 0.00 0.00 3.79
5207 5664 1.269517 GGCTAGCGATGAGGAGTCTTG 60.270 57.143 9.00 0.00 0.00 3.02
5214 5671 2.028112 CGATGAGGAGTCTTGGACCAAA 60.028 50.000 8.59 0.00 32.18 3.28
5218 5675 1.421646 AGGAGTCTTGGACCAAAGTGG 59.578 52.381 8.59 0.00 45.02 4.00
5234 5691 4.640771 AAGTGGACTGGAGATTAAGCAA 57.359 40.909 0.00 0.00 0.00 3.91
5235 5692 3.944087 AGTGGACTGGAGATTAAGCAAC 58.056 45.455 0.00 0.00 0.00 4.17
5245 5702 1.824230 GATTAAGCAACCATGGCACCA 59.176 47.619 13.04 0.00 0.00 4.17
5247 5704 1.473258 TAAGCAACCATGGCACCATC 58.527 50.000 13.04 0.00 33.90 3.51
5253 5710 2.438975 CATGGCACCATCGCAGGT 60.439 61.111 0.00 0.00 44.48 4.00
5254 5711 2.124570 ATGGCACCATCGCAGGTC 60.125 61.111 0.00 0.00 40.77 3.85
5402 5942 3.745799 TCAAGGTTTAGGCAATGAACGA 58.254 40.909 0.00 0.00 0.00 3.85
5416 5956 1.529438 TGAACGACCTTCGACAATTGC 59.471 47.619 5.05 0.00 43.74 3.56
5417 5957 1.529438 GAACGACCTTCGACAATTGCA 59.471 47.619 5.05 0.00 43.74 4.08
5429 5969 5.277825 TCGACAATTGCATCGTTTCTTTTT 58.722 33.333 15.52 0.00 39.38 1.94
5430 5970 5.398122 TCGACAATTGCATCGTTTCTTTTTC 59.602 36.000 15.52 0.00 39.38 2.29
5436 5976 8.967218 CAATTGCATCGTTTCTTTTTCTTTCTA 58.033 29.630 0.00 0.00 0.00 2.10
5502 6043 0.306840 CATCTGGACGATGCATGCAC 59.693 55.000 25.37 15.77 42.75 4.57
5548 6089 7.653767 AAAGTCCTTACAAAGAGATACAACG 57.346 36.000 0.00 0.00 0.00 4.10
5641 6185 0.249322 CGGGCCTAATACCACAGACG 60.249 60.000 0.84 0.00 0.00 4.18
5777 6327 5.798132 TCTTCAGAACTGTACTGATGCATT 58.202 37.500 0.00 0.00 42.68 3.56
5906 6459 0.112218 ATGCTGCCAAGTACCACCAA 59.888 50.000 0.00 0.00 0.00 3.67
5924 6477 1.670811 CAACCGACACAGCTTGAAGTT 59.329 47.619 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.472361 GGATCGATGTAGTTAAATGTAGCTTTA 57.528 33.333 0.54 0.00 0.00 1.85
14 15 7.169308 CGGATCGATGTAGTTAAATGTAGCTTT 59.831 37.037 0.54 0.00 0.00 3.51
15 16 6.641314 CGGATCGATGTAGTTAAATGTAGCTT 59.359 38.462 0.54 0.00 0.00 3.74
16 17 6.016527 TCGGATCGATGTAGTTAAATGTAGCT 60.017 38.462 0.54 0.00 0.00 3.32
17 18 6.147581 TCGGATCGATGTAGTTAAATGTAGC 58.852 40.000 0.54 0.00 0.00 3.58
18 19 6.305877 GCTCGGATCGATGTAGTTAAATGTAG 59.694 42.308 0.54 0.00 34.61 2.74
19 20 6.147581 GCTCGGATCGATGTAGTTAAATGTA 58.852 40.000 0.54 0.00 34.61 2.29
20 21 4.982916 GCTCGGATCGATGTAGTTAAATGT 59.017 41.667 0.54 0.00 34.61 2.71
21 22 4.982295 TGCTCGGATCGATGTAGTTAAATG 59.018 41.667 0.54 0.00 34.61 2.32
22 23 5.196341 TGCTCGGATCGATGTAGTTAAAT 57.804 39.130 0.54 0.00 34.61 1.40
23 24 4.642445 TGCTCGGATCGATGTAGTTAAA 57.358 40.909 0.54 0.00 34.61 1.52
24 25 4.499188 CCTTGCTCGGATCGATGTAGTTAA 60.499 45.833 0.54 0.00 34.61 2.01
25 26 3.004419 CCTTGCTCGGATCGATGTAGTTA 59.996 47.826 0.54 0.00 34.61 2.24
26 27 2.223829 CCTTGCTCGGATCGATGTAGTT 60.224 50.000 0.54 0.00 34.61 2.24
27 28 1.338337 CCTTGCTCGGATCGATGTAGT 59.662 52.381 0.54 0.00 34.61 2.73
28 29 1.932604 GCCTTGCTCGGATCGATGTAG 60.933 57.143 0.54 0.00 34.61 2.74
29 30 0.032130 GCCTTGCTCGGATCGATGTA 59.968 55.000 0.54 0.00 34.61 2.29
30 31 1.227380 GCCTTGCTCGGATCGATGT 60.227 57.895 0.54 0.00 34.61 3.06
31 32 0.811219 TTGCCTTGCTCGGATCGATG 60.811 55.000 0.54 0.00 34.61 3.84
32 33 0.107703 TTTGCCTTGCTCGGATCGAT 60.108 50.000 0.00 0.00 34.61 3.59
33 34 1.019278 GTTTGCCTTGCTCGGATCGA 61.019 55.000 0.00 0.00 0.00 3.59
34 35 1.021390 AGTTTGCCTTGCTCGGATCG 61.021 55.000 0.00 0.00 0.00 3.69
148 152 7.315142 GCTTATTTTCTCACCATCATTTGTCA 58.685 34.615 0.00 0.00 0.00 3.58
161 165 3.122948 GTCTGTTCGCGCTTATTTTCTCA 59.877 43.478 5.56 0.00 0.00 3.27
328 392 0.250901 ACTTTTGCCTCAGCGGATGT 60.251 50.000 0.00 0.00 44.31 3.06
412 479 4.778143 GCCCTGATTCCCACGCGT 62.778 66.667 5.58 5.58 0.00 6.01
760 899 1.089123 TGCCAAAAAGGACCCCCTAT 58.911 50.000 0.00 0.00 43.48 2.57
796 935 5.390613 CGTGAACGAATTGCTAAAAAGGAT 58.609 37.500 0.00 0.00 43.02 3.24
1066 1207 3.065095 GCTTCTATGAAAGCTTGCTCAGG 59.935 47.826 5.89 2.37 46.51 3.86
1268 1411 1.685148 GGATGGGGATGTTCTTCTGC 58.315 55.000 0.00 0.00 0.00 4.26
1383 1529 1.034838 TGTTTTGGCAGCGTTGAGGT 61.035 50.000 2.38 0.00 0.00 3.85
1388 1534 0.102300 GGAGTTGTTTTGGCAGCGTT 59.898 50.000 0.00 0.00 0.00 4.84
1607 1757 3.289407 TTTGTGTTGTGGATGTCTGGA 57.711 42.857 0.00 0.00 0.00 3.86
1748 1908 1.308783 CCCCTGCTTTTCTCTTCGGC 61.309 60.000 0.00 0.00 0.00 5.54
1930 2315 2.596923 TGCATTGCGGACCTTGCA 60.597 55.556 3.84 4.57 42.41 4.08
1991 2376 6.489603 TCATTAGGTGGGCTTCAGATAAAAA 58.510 36.000 0.00 0.00 0.00 1.94
2071 2457 1.807573 CGACTTCCTTGCCGAGCTC 60.808 63.158 2.73 2.73 0.00 4.09
2165 2555 2.290577 GGGAGTTCTTCCTGAGCATGTT 60.291 50.000 0.00 0.00 45.98 2.71
2311 2708 0.389817 TCACGATTCGCCAGGACTTG 60.390 55.000 5.86 0.00 0.00 3.16
2343 2740 2.496899 AACCGTGAAATCTCCATGCT 57.503 45.000 0.00 0.00 0.00 3.79
2347 2744 3.813166 GAGTTGAAACCGTGAAATCTCCA 59.187 43.478 0.00 0.00 0.00 3.86
2384 2781 1.299976 GCCGTGTGGGAGGAGAATT 59.700 57.895 0.00 0.00 38.47 2.17
2386 2783 2.449967 TAGGCCGTGTGGGAGGAGAA 62.450 60.000 0.00 0.00 38.47 2.87
2388 2785 0.469331 TATAGGCCGTGTGGGAGGAG 60.469 60.000 0.00 0.00 38.47 3.69
2389 2786 0.190069 ATATAGGCCGTGTGGGAGGA 59.810 55.000 0.00 0.00 38.47 3.71
2390 2787 1.933021 TATATAGGCCGTGTGGGAGG 58.067 55.000 0.00 0.00 38.47 4.30
2392 2789 4.164981 AGAATTATATAGGCCGTGTGGGA 58.835 43.478 0.00 0.00 38.47 4.37
2396 2793 6.492429 TGTCAGTAGAATTATATAGGCCGTGT 59.508 38.462 0.00 0.00 0.00 4.49
2397 2794 6.920817 TGTCAGTAGAATTATATAGGCCGTG 58.079 40.000 0.00 0.00 0.00 4.94
2398 2795 7.534723 TTGTCAGTAGAATTATATAGGCCGT 57.465 36.000 0.00 0.00 0.00 5.68
2399 2796 8.088981 ACTTTGTCAGTAGAATTATATAGGCCG 58.911 37.037 0.00 0.00 31.97 6.13
2400 2797 9.209175 CACTTTGTCAGTAGAATTATATAGGCC 57.791 37.037 0.00 0.00 32.76 5.19
2401 2798 9.765795 ACACTTTGTCAGTAGAATTATATAGGC 57.234 33.333 0.00 0.00 32.76 3.93
2407 2804 9.950680 CAAACAACACTTTGTCAGTAGAATTAT 57.049 29.630 0.00 0.00 45.69 1.28
2408 2805 8.952278 ACAAACAACACTTTGTCAGTAGAATTA 58.048 29.630 0.00 0.00 45.69 1.40
2409 2806 7.826690 ACAAACAACACTTTGTCAGTAGAATT 58.173 30.769 0.00 0.00 45.69 2.17
2410 2807 7.391148 ACAAACAACACTTTGTCAGTAGAAT 57.609 32.000 0.00 0.00 45.69 2.40
2411 2808 6.811253 ACAAACAACACTTTGTCAGTAGAA 57.189 33.333 0.00 0.00 45.69 2.10
2412 2809 6.811253 AACAAACAACACTTTGTCAGTAGA 57.189 33.333 0.00 0.00 45.69 2.59
2413 2810 9.221775 GATTAACAAACAACACTTTGTCAGTAG 57.778 33.333 0.00 0.00 45.69 2.57
2416 2813 6.964370 TCGATTAACAAACAACACTTTGTCAG 59.036 34.615 0.00 0.00 45.69 3.51
2422 2819 6.430000 AGGCTATCGATTAACAAACAACACTT 59.570 34.615 1.71 0.00 0.00 3.16
2434 2831 7.384115 GCATAGTTGTTACAGGCTATCGATTAA 59.616 37.037 1.71 0.00 0.00 1.40
2439 2836 4.368315 TGCATAGTTGTTACAGGCTATCG 58.632 43.478 8.00 6.44 0.00 2.92
2519 2916 1.134401 CCACATTCGTGATAGCCACCT 60.134 52.381 0.00 0.00 46.80 4.00
2521 2918 1.933853 GACCACATTCGTGATAGCCAC 59.066 52.381 0.00 0.00 46.80 5.01
2527 2924 1.406069 GCAGAGGACCACATTCGTGAT 60.406 52.381 0.00 0.00 46.80 3.06
2528 2925 0.037326 GCAGAGGACCACATTCGTGA 60.037 55.000 0.00 0.00 46.80 4.35
2529 2926 1.021390 GGCAGAGGACCACATTCGTG 61.021 60.000 0.00 0.00 43.21 4.35
2530 2927 1.194781 AGGCAGAGGACCACATTCGT 61.195 55.000 0.00 0.00 0.00 3.85
2531 2928 0.036010 AAGGCAGAGGACCACATTCG 60.036 55.000 0.00 0.00 0.00 3.34
2532 2929 2.633488 GTAAGGCAGAGGACCACATTC 58.367 52.381 0.00 0.00 0.00 2.67
2533 2930 1.282157 GGTAAGGCAGAGGACCACATT 59.718 52.381 0.00 0.00 31.89 2.71
2534 2931 0.912486 GGTAAGGCAGAGGACCACAT 59.088 55.000 0.00 0.00 31.89 3.21
2535 2932 1.541310 CGGTAAGGCAGAGGACCACA 61.541 60.000 0.00 0.00 31.89 4.17
2536 2933 1.218316 CGGTAAGGCAGAGGACCAC 59.782 63.158 0.00 0.00 31.89 4.16
2537 2934 1.987855 CCGGTAAGGCAGAGGACCA 60.988 63.158 0.00 0.00 31.89 4.02
2538 2935 2.732619 CCCGGTAAGGCAGAGGACC 61.733 68.421 0.00 0.00 39.21 4.46
2539 2936 2.732619 CCCCGGTAAGGCAGAGGAC 61.733 68.421 0.00 0.00 39.21 3.85
2540 2937 1.877672 TACCCCGGTAAGGCAGAGGA 61.878 60.000 0.00 0.00 39.21 3.71
2541 2938 0.979187 TTACCCCGGTAAGGCAGAGG 60.979 60.000 0.00 0.00 39.21 3.69
2542 2939 0.906775 TTTACCCCGGTAAGGCAGAG 59.093 55.000 0.00 0.00 40.98 3.35
2543 2940 0.906775 CTTTACCCCGGTAAGGCAGA 59.093 55.000 0.00 0.00 40.98 4.26
2544 2941 0.616891 ACTTTACCCCGGTAAGGCAG 59.383 55.000 13.95 8.46 40.06 4.85
2545 2942 1.832998 CTACTTTACCCCGGTAAGGCA 59.167 52.381 13.95 2.75 40.06 4.75
2546 2943 2.110578 TCTACTTTACCCCGGTAAGGC 58.889 52.381 13.95 0.00 40.06 4.35
2547 2944 3.133542 CCTTCTACTTTACCCCGGTAAGG 59.866 52.174 12.78 12.78 40.98 2.69
2548 2945 3.431346 GCCTTCTACTTTACCCCGGTAAG 60.431 52.174 0.00 0.90 40.98 2.34
2549 2946 2.501316 GCCTTCTACTTTACCCCGGTAA 59.499 50.000 0.00 2.07 38.63 2.85
2550 2947 2.110578 GCCTTCTACTTTACCCCGGTA 58.889 52.381 0.00 0.00 0.00 4.02
2551 2948 0.907486 GCCTTCTACTTTACCCCGGT 59.093 55.000 0.00 0.00 0.00 5.28
2552 2949 0.179702 GGCCTTCTACTTTACCCCGG 59.820 60.000 0.00 0.00 0.00 5.73
2553 2950 0.179702 GGGCCTTCTACTTTACCCCG 59.820 60.000 0.84 0.00 0.00 5.73
2555 2952 0.549950 GGGGGCCTTCTACTTTACCC 59.450 60.000 0.84 0.00 36.56 3.69
2556 2953 0.179702 CGGGGGCCTTCTACTTTACC 59.820 60.000 0.84 0.00 0.00 2.85
2557 2954 0.463295 GCGGGGGCCTTCTACTTTAC 60.463 60.000 0.84 0.00 0.00 2.01
2558 2955 1.909975 GCGGGGGCCTTCTACTTTA 59.090 57.895 0.84 0.00 0.00 1.85
2559 2956 2.675371 GCGGGGGCCTTCTACTTT 59.325 61.111 0.84 0.00 0.00 2.66
2560 2957 3.782443 CGCGGGGGCCTTCTACTT 61.782 66.667 0.84 0.00 0.00 2.24
2562 2959 4.525949 GACGCGGGGGCCTTCTAC 62.526 72.222 12.47 0.00 0.00 2.59
2863 3265 2.651361 CACCCTCTTCACGTCGCT 59.349 61.111 0.00 0.00 0.00 4.93
3219 3623 2.042831 CGCCTTCAAAGCCCCAGAG 61.043 63.158 0.00 0.00 0.00 3.35
3260 3664 0.328258 CGTCCCAAGAAATCCACCCT 59.672 55.000 0.00 0.00 0.00 4.34
3289 3694 3.457610 ACGACCGAAGACCAAGTTTTA 57.542 42.857 0.00 0.00 0.00 1.52
3398 3807 1.004979 TGATTTAGTGTTTCCCCCGGG 59.995 52.381 15.80 15.80 0.00 5.73
3410 3820 5.043903 CGTCATCCGATCAACTGATTTAGT 58.956 41.667 0.00 0.00 39.36 2.24
3440 3850 0.611714 AGGGGGTAACGACACATGAC 59.388 55.000 0.00 0.00 37.60 3.06
3601 4011 0.107993 CTCCTGCACGTGTCCATCAT 60.108 55.000 18.38 0.00 0.00 2.45
3672 4082 2.807967 GAGTTGTACTGCTGCATCAACA 59.192 45.455 28.65 20.07 40.19 3.33
3847 4260 3.449018 CGCTGATAGTCTGGGCCTAATAT 59.551 47.826 4.53 1.83 0.00 1.28
3985 4398 0.676184 GCCTCTGCATCTCGGTGATA 59.324 55.000 0.00 0.00 37.47 2.15
3992 4405 2.420890 CTCCGGCCTCTGCATCTC 59.579 66.667 0.00 0.00 40.13 2.75
4093 4506 3.506096 CAGTCATGCGGCTGCCAG 61.506 66.667 20.29 12.51 41.78 4.85
4114 4527 2.176273 CGCTGAGAAATCGGGCCTG 61.176 63.158 4.71 4.71 0.00 4.85
4116 4529 2.174319 GTCGCTGAGAAATCGGGCC 61.174 63.158 0.00 0.00 0.00 5.80
4123 4536 0.859232 GAAAGTGCGTCGCTGAGAAA 59.141 50.000 19.50 0.00 0.00 2.52
4131 4544 1.597663 ACCTTTGAAGAAAGTGCGTCG 59.402 47.619 0.00 0.00 37.47 5.12
4133 4546 2.542595 CGTACCTTTGAAGAAAGTGCGT 59.457 45.455 0.00 0.00 37.47 5.24
4135 4548 3.848554 GCACGTACCTTTGAAGAAAGTGC 60.849 47.826 15.26 15.26 38.66 4.40
4136 4549 3.303791 GGCACGTACCTTTGAAGAAAGTG 60.304 47.826 0.00 1.22 37.47 3.16
4158 4571 1.821061 ATCTATTGGAGAGGGGCGCG 61.821 60.000 0.00 0.00 37.70 6.86
4182 4605 2.282958 AGCGACGAGTCCTTGGGA 60.283 61.111 0.00 0.00 0.00 4.37
4184 4607 2.202492 CGAGCGACGAGTCCTTGG 60.202 66.667 0.00 0.00 45.77 3.61
4186 4609 2.868920 GACGAGCGACGAGTCCTT 59.131 61.111 12.62 0.00 45.77 3.36
4198 4621 4.369182 ACAACTTACAACTTGAGGACGAG 58.631 43.478 0.00 0.00 0.00 4.18
4203 4626 6.671614 TGTGTTACAACTTACAACTTGAGG 57.328 37.500 0.00 0.00 0.00 3.86
4204 4627 7.011950 TGGATGTGTTACAACTTACAACTTGAG 59.988 37.037 0.00 0.00 0.00 3.02
4205 4628 6.824196 TGGATGTGTTACAACTTACAACTTGA 59.176 34.615 0.00 0.00 0.00 3.02
4206 4629 7.022055 TGGATGTGTTACAACTTACAACTTG 57.978 36.000 0.00 0.00 0.00 3.16
4207 4630 7.255451 CCATGGATGTGTTACAACTTACAACTT 60.255 37.037 5.56 0.00 0.00 2.66
4208 4631 6.206634 CCATGGATGTGTTACAACTTACAACT 59.793 38.462 5.56 0.00 0.00 3.16
4209 4632 6.378582 CCATGGATGTGTTACAACTTACAAC 58.621 40.000 5.56 0.00 0.00 3.32
4210 4633 5.048364 GCCATGGATGTGTTACAACTTACAA 60.048 40.000 18.40 0.00 0.00 2.41
4211 4634 4.457603 GCCATGGATGTGTTACAACTTACA 59.542 41.667 18.40 0.00 0.00 2.41
4245 4690 3.260380 AGAGTTCTGTTCCTCATCCTGTG 59.740 47.826 0.00 0.00 0.00 3.66
4297 4742 0.254178 ACATCATGGACTGGACTGCC 59.746 55.000 0.00 0.00 0.00 4.85
4423 4869 1.299976 GGCGTTGGTCTCTGGGAAT 59.700 57.895 0.00 0.00 0.00 3.01
4439 4885 1.139853 CCAGTAGAAGAGGATGGTGGC 59.860 57.143 0.00 0.00 0.00 5.01
4591 5037 4.531854 TGAACTTCACCTTGTTCCAATGA 58.468 39.130 0.00 0.00 41.10 2.57
4594 5040 3.053991 TCCTGAACTTCACCTTGTTCCAA 60.054 43.478 0.00 0.00 41.10 3.53
4597 5043 3.142174 CCTCCTGAACTTCACCTTGTTC 58.858 50.000 0.00 0.00 41.87 3.18
4613 5059 2.960688 GCTTCCAGCGGTTCCTCCT 61.961 63.158 0.00 0.00 0.00 3.69
4649 5095 3.512516 GCATGGCTGAGGTTCGCC 61.513 66.667 0.00 0.00 46.46 5.54
4672 5129 3.557903 ATGCTGTGGAGCTTGGCGT 62.558 57.895 0.00 0.00 46.39 5.68
4728 5185 0.250295 CTCAGGAAAACGCTCACCCA 60.250 55.000 0.00 0.00 0.00 4.51
4897 5354 1.670590 GCGCTGATATCCAGGAGCT 59.329 57.895 0.00 0.00 43.13 4.09
4949 5406 4.072131 TCTGAACTTTGGTGCTATGGTTC 58.928 43.478 0.00 0.00 35.20 3.62
5012 5469 1.909700 TCCACGTATCCGGTATACCC 58.090 55.000 16.47 0.70 37.73 3.69
5013 5470 3.507233 TCATTCCACGTATCCGGTATACC 59.493 47.826 12.27 12.27 37.73 2.73
5014 5471 4.730657 CTCATTCCACGTATCCGGTATAC 58.269 47.826 0.00 7.61 38.78 1.47
5015 5472 3.192001 GCTCATTCCACGTATCCGGTATA 59.808 47.826 0.00 0.00 38.78 1.47
5050 5507 8.187913 ACATCATATCTACAGTTACTGCATCT 57.812 34.615 12.80 0.00 34.37 2.90
5085 5542 7.312899 CCCTACACAAAAAGATCACATTTACC 58.687 38.462 0.00 0.00 0.00 2.85
5137 5594 6.667848 ACAGACCATCGTATATATGGGATTGA 59.332 38.462 17.04 0.00 46.89 2.57
5207 5664 1.056660 TCTCCAGTCCACTTTGGTCC 58.943 55.000 0.00 0.00 39.03 4.46
5214 5671 3.307762 GGTTGCTTAATCTCCAGTCCACT 60.308 47.826 0.00 0.00 0.00 4.00
5218 5675 3.629398 CCATGGTTGCTTAATCTCCAGTC 59.371 47.826 2.57 0.00 0.00 3.51
5234 5691 2.438975 CTGCGATGGTGCCATGGT 60.439 61.111 14.67 0.00 36.70 3.55
5235 5692 3.214123 CCTGCGATGGTGCCATGG 61.214 66.667 7.63 7.63 36.70 3.66
5253 5710 2.125713 CCGGCTATGTGTGCACGA 60.126 61.111 13.13 0.93 0.00 4.35
5254 5711 2.032634 AACCGGCTATGTGTGCACG 61.033 57.895 13.13 0.00 0.00 5.34
5319 5859 9.093970 TGAATAGTTACTTCACATGGTATTTCG 57.906 33.333 0.00 0.00 0.00 3.46
5402 5942 1.808411 ACGATGCAATTGTCGAAGGT 58.192 45.000 21.19 4.75 35.57 3.50
5548 6089 0.320697 ACGGTGGCTTCAGACTTACC 59.679 55.000 0.00 0.00 0.00 2.85
5641 6185 0.248907 TAGATGTTAGGCGCTGCGAC 60.249 55.000 28.07 25.36 33.59 5.19
5777 6327 1.848652 AGCTAGACCGAGCAAGGTTA 58.151 50.000 4.58 0.15 46.09 2.85
5906 6459 1.139058 AGAACTTCAAGCTGTGTCGGT 59.861 47.619 0.00 0.00 0.00 4.69
5924 6477 1.402852 CGCACGACAGATCTTCCAAGA 60.403 52.381 0.00 0.00 39.78 3.02


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

AutoCloner maintained by Alex Coulton.